#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
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	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_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	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_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	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_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	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
ZNF436	80818	hgsc.bcm.edu	37	1	23688888	23688888	+	Silent	SNP	C	C	A			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	.						118.0	113.0	114.0					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	
PSMB4	5692	hgsc.bcm.edu	37	1	151372078	151372078	+	Silent	SNP	G	G	A			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	.						56.0	61.0	59.0					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	
RIT1	6016	hgsc.bcm.edu	37	1	155870300	155870300	+	Missense_Mutation	SNP	C	C	A			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	.						243.0	242.0	242.0					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	
SPATA17	128153	hgsc.bcm.edu	37	1	217975148	217975148	+	Nonsense_Mutation	SNP	G	G	T			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	.						50.0	51.0	51.0					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	
OBSCN	84033	hgsc.bcm.edu	37	1	228494234	228494234	+	Missense_Mutation	SNP	G	G	A			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	.						31.0	35.0	34.0					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	
ACTR1B	10120	hgsc.bcm.edu	37	2	98277105	98277105	+	Missense_Mutation	SNP	C	C	A			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	.						87.0	87.0	87.0					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	
MAP4K4	9448	hgsc.bcm.edu	37	2	102493544	102493544	+	Silent	SNP	C	C	A			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	.						180.0	175.0	177.0					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	
UPP2	151531	hgsc.bcm.edu	37	2	158971732	158971732	+	Silent	SNP	A	A	G			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	.						105.0	104.0	104.0					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	
TTN	7273	hgsc.bcm.edu	37	2	179430006	179430006	+	Silent	SNP	G	G	T			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	.						131.0	125.0	127.0					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	
TTN	7273	hgsc.bcm.edu	37	2	179468605	179468605	+	Missense_Mutation	SNP	A	A	G			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	.						65.0	62.0	63.0					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	
RPL37A	6168	hgsc.bcm.edu	37	2	217364692	217364692	+	Silent	SNP	T	T	A			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	.						129.0	125.0	126.0					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	
NBEAL2	23218	hgsc.bcm.edu	37	3	47049869	47049869	+	Missense_Mutation	SNP	G	G	A			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	.						49.0	48.0	48.0					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	
NICN1	84276	hgsc.bcm.edu	37	3	49463424	49463424	+	Silent	SNP	C	C	G			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	.						87.0	65.0	72.0					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	
PCBP4	57060	hgsc.bcm.edu	37	3	51995031	51995031	+	Missense_Mutation	SNP	C	C	A			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	.						127.0	128.0	127.0					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	
POC1A	25886	hgsc.bcm.edu	37	3	52109979	52109979	+	Missense_Mutation	SNP	C	C	A	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	.						136.0	119.0	124.0					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	
SFMBT1	51460	hgsc.bcm.edu	37	3	52988412	52988412	+	Missense_Mutation	SNP	A	A	G			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	.						111.0	116.0	114.0					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	
FAM3D	131177	hgsc.bcm.edu	37	3	58625897	58625897	+	Silent	SNP	C	C	A			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	.						227.0	192.0	204.0					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	
ZBTB11	27107	hgsc.bcm.edu	37	3	101390027	101390027	+	Missense_Mutation	SNP	A	A	G			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	.						73.0	73.0	73.0					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	
ALDH1L1	10840	hgsc.bcm.edu	37	3	125850317	125850317	+	Silent	SNP	C	C	A			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	.						90.0	79.0	83.0					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	
SLCO2A1	6578	hgsc.bcm.edu	37	3	133692538	133692538	+	Silent	SNP	G	G	C	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	.						87.0	73.0	78.0					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	
PSMD2	5708	hgsc.bcm.edu	37	3	184026587	184026587	+	Missense_Mutation	SNP	G	G	T			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	.						110.0	113.0	112.0					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	
ATP13A3	79572	hgsc.bcm.edu	37	3	194146121	194146121	+	Missense_Mutation	SNP	G	G	A			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	.						97.0	90.0	93.0					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	
ZBTB49	166793	hgsc.bcm.edu	37	4	4322599	4322599	+	Silent	SNP	C	C	A			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	.						54.0	51.0	52.0					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	
CCKAR	886	hgsc.bcm.edu	37	4	26483517	26483517	+	Missense_Mutation	SNP	C	C	T			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	.						103.0	95.0	98.0					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		
ANXA3	306	hgsc.bcm.edu	37	4	79516549	79516549	+	Silent	SNP	A	A	G			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	.						184.0	186.0	186.0					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	
PLRG1	5356	hgsc.bcm.edu	37	4	155470082	155470082	+	Silent	SNP	T	T	C			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	.						76.0	71.0	73.0					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	
PCSK1	5122	hgsc.bcm.edu	37	5	95728748	95728748	+	Missense_Mutation	SNP	C	C	T	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	163.0	170.0	168.0		2219,2078,1289	5.1	1.0	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	
CHD1	1105	hgsc.bcm.edu	37	5	98236974	98236974	+	Missense_Mutation	SNP	T	T	C	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	137.0	133.0	134.0		503	5.6	1.0	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	
GTF2H4	2968	hgsc.bcm.edu	37	6	30877829	30877829	+	Silent	SNP	C	C	T			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	.						114.0	130.0	124.0					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	
HLA-DQA2	3118	hgsc.bcm.edu	37	6	32714066	32714066	+	Silent	SNP	C	C	T	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	0.0	5008	,	,		21667	0.0		0.0	False		,,,				2504	0.001				p.C221C		Atlas-SNP	.											.	HLA-DQA2	27	.	0			c.C663T						PASS	.						163.0	160.0	161.0					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	
SYNE1	23345	hgsc.bcm.edu	37	6	152671451	152671451	+	Missense_Mutation	SNP	T	T	C			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	.						102.0	93.0	96.0					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	
ARID1B	57492	hgsc.bcm.edu	37	6	157527600	157527600	+	Silent	SNP	G	G	A			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	.						60.0	61.0	61.0					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	
ABCB1	5243	hgsc.bcm.edu	37	7	87179321	87179321	+	Missense_Mutation	SNP	C	C	A			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	.						147.0	134.0	139.0					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	
ANGPT2	285	hgsc.bcm.edu	37	8	6360731	6360731	+	Missense_Mutation	SNP	G	G	T			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	.						235.0	190.0	205.0					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	
BIN3	55909	hgsc.bcm.edu	37	8	22488017	22488017	+	Silent	SNP	G	G	A			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	.						176.0	176.0	176.0					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		
RAB11FIP1	80223	hgsc.bcm.edu	37	8	37732715	37732715	+	Missense_Mutation	SNP	G	G	T			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	.						260.0	251.0	254.0					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	
PTPRD	5789	hgsc.bcm.edu	37	9	8471073	8471073	+	Missense_Mutation	SNP	T	T	C			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	.						115.0	113.0	114.0					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		
TOPORS	10210	hgsc.bcm.edu	37	9	32541815	32541815	+	Missense_Mutation	SNP	C	C	G	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	.						195.0	186.0	189.0					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	
VCP	7415	hgsc.bcm.edu	37	9	35061057	35061057	+	Silent	SNP	A	A	G			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	.						229.0	212.0	218.0					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	
TMEM2	23670	hgsc.bcm.edu	37	9	74313090	74313090	+	Missense_Mutation	SNP	G	G	T			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	.						155.0	125.0	135.0					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	
SPATA31D1	389763	hgsc.bcm.edu	37	9	84609482	84609482	+	Missense_Mutation	SNP	T	T	C			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	.						28.0	25.0	26.0					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	
PAPPA	5069	hgsc.bcm.edu	37	9	118949550	118949550	+	Missense_Mutation	SNP	G	G	T			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	.						84.0	79.0	81.0					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	
SPTAN1	6709	hgsc.bcm.edu	37	9	131370474	131370474	+	Silent	SNP	C	C	A	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	.						162.0	166.0	165.0					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	
CPEB3	22849	hgsc.bcm.edu	37	10	93812079	93812079	+	Missense_Mutation	SNP	A	A	G			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	.						101.0	86.0	91.0					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	
HARBI1	283254	hgsc.bcm.edu	37	11	46637368	46637368	+	Silent	SNP	C	C	A			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	.						201.0	196.0	198.0					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	
PPP6R3	55291	hgsc.bcm.edu	37	11	68377390	68377390	+	Silent	SNP	T	T	A			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	.						174.0	149.0	157.0					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	
CACNA1C	775	hgsc.bcm.edu	37	12	2566788	2566788	+	Nonsense_Mutation	SNP	G	G	T			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	.						121.0	135.0	131.0					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	
PEX5	5830	hgsc.bcm.edu	37	12	7343122	7343122	+	Splice_Site	SNP	T	T	C			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	.						24.0	27.0	26.0					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
ITPR2	3709	hgsc.bcm.edu	37	12	26749865	26749865	+	Missense_Mutation	SNP	G	G	T			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	.						93.0	94.0	94.0					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	
IPO8	10526	hgsc.bcm.edu	37	12	30790088	30790088	+	Silent	SNP	C	C	G			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	.						133.0	120.0	124.0					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	
FAM60A	58516	hgsc.bcm.edu	37	12	31435663	31435663	+	Missense_Mutation	SNP	A	A	C			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	.						38.0	40.0	39.0					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	
HSP90B1	7184	hgsc.bcm.edu	37	12	104336447	104336447	+	Missense_Mutation	SNP	T	T	C			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	.						116.0	113.0	114.0					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	
MYO1H	283446	hgsc.bcm.edu	37	12	109834250	109834250	+	Missense_Mutation	SNP	C	C	T			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	.						68.0	68.0	68.0					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	
NCOR2	9612	hgsc.bcm.edu	37	12	124848291	124848291	+	Silent	SNP	A	A	G			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	.						39.0	56.0	51.0					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	
EP400	57634	hgsc.bcm.edu	37	12	132522561	132522562	+	Missense_Mutation	DNP	GC	GC	AT			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	
KBTBD6	89890	hgsc.bcm.edu	37	13	41704906	41704906	+	Missense_Mutation	SNP	T	T	C			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	.						179.0	179.0	179.0					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	
NALCN	259232	hgsc.bcm.edu	37	13	101944368	101944368	+	Missense_Mutation	SNP	G	G	T			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	.						317.0	247.0	271.0					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	
SIPA1L1	26037	hgsc.bcm.edu	37	14	72055716	72055716	+	Missense_Mutation	SNP	T	T	C			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	.						59.0	61.0	60.0					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	
THBS1	7057	hgsc.bcm.edu	37	15	39885267	39885267	+	Missense_Mutation	SNP	T	T	C			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	.						78.0	68.0	71.0					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	
ZNF106	64397	hgsc.bcm.edu	37	15	42742117	42742117	+	Missense_Mutation	SNP	C	C	A			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	.						169.0	166.0	167.0					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	
EPB42	2038	hgsc.bcm.edu	37	15	43508525	43508525	+	Missense_Mutation	SNP	C	C	T	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	102.0	90.0	94.0		227,137	-5.0	0.0	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	
HMG20A	10363	hgsc.bcm.edu	37	15	77756662	77756662	+	Missense_Mutation	SNP	A	A	G			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	.						130.0	110.0	117.0					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	
TSC2	7249	hgsc.bcm.edu	37	16	2130345	2130345	+	Missense_Mutation	SNP	G	G	A			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	.						41.0	46.0	45.0					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	
LOC81691	81691	hgsc.bcm.edu	37	16	20851091	20851091	+	Silent	SNP	C	C	T			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	.						288.0	274.0	279.0					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		
CTDNEP1	23399	hgsc.bcm.edu	37	17	7149598	7149598	+	Missense_Mutation	SNP	A	A	G			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	.						117.0	108.0	111.0					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	
NCOR1	9611	hgsc.bcm.edu	37	17	16089949	16089949	+	Nonsense_Mutation	SNP	G	G	C			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	.						91.0	81.0	84.0					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	
SRCIN1	80725	hgsc.bcm.edu	37	17	36708962	36708962	+	Splice_Site	SNP	C	C	G			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	.						54.0	63.0	60.0					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
CASC3	22794	hgsc.bcm.edu	37	17	38319005	38319005	+	Nonsense_Mutation	SNP	G	G	A			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	.						72.0	66.0	68.0					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	
COIL	8161	hgsc.bcm.edu	37	17	55028268	55028268	+	Missense_Mutation	SNP	C	C	A	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	.						94.0	98.0	97.0					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		
MPO	4353	hgsc.bcm.edu	37	17	56348163	56348163	+	Missense_Mutation	SNP	A	A	T			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	.						233.0	180.0	198.0					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		
KCNJ16	3773	hgsc.bcm.edu	37	17	68129132	68129132	+	Silent	SNP	C	C	A	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	.						76.0	82.0	80.0					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	
RAB37	326624	hgsc.bcm.edu	37	17	72736999	72736999	+	Silent	SNP	C	C	A	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	.						101.0	99.0	99.0					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	
PSMD8	5714	hgsc.bcm.edu	37	19	38874011	38874011	+	Missense_Mutation	SNP	A	A	G			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	.						49.0	41.0	43.0					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	
CEACAM6	4680	hgsc.bcm.edu	37	19	42260867	42260867	+	Splice_Site	SNP	C	C	A			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	.						242.0	241.0	241.0					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
ZNF180	7733	hgsc.bcm.edu	37	19	44981073	44981073	+	Missense_Mutation	SNP	G	G	C			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	.						77.0	77.0	77.0					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	
LILRA3	11026	hgsc.bcm.edu	37	19	54803120	54803120	+	Missense_Mutation	SNP	G	G	T			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	.						134.0	113.0	120.0					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		
ZNF324B	388569	hgsc.bcm.edu	37	19	58966903	58966903	+	Missense_Mutation	SNP	T	T	A			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	.						36.0	40.0	39.0					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	
EPB41L1	2036	hgsc.bcm.edu	37	20	34800245	34800245	+	Missense_Mutation	SNP	A	A	G			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	.						88.0	79.0	82.0					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	
SETD4	54093	hgsc.bcm.edu	37	21	37410517	37410517	+	Missense_Mutation	SNP	C	C	G			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	.						179.0	173.0	175.0					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	
CERK	64781	hgsc.bcm.edu	37	22	47108141	47108141	+	Missense_Mutation	SNP	T	T	G			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	.						241.0	179.0	200.0					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	
AMER1	139285	hgsc.bcm.edu	37	X	63411696	63411696	+	Missense_Mutation	SNP	G	G	A			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	.						61.0	50.0	54.0					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	
TMPO	7112	hgsc.bcm.edu	37	12	98941479	98941479	+	Frame_Shift_Del	DEL	A	A	-			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	.						107.0	107.0	107.0					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	
UBR4	23352	hgsc.bcm.edu	37	1	19448476	19448477	+	Frame_Shift_Ins	INS	-	-	A			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	
SCN8A	6334	hgsc.bcm.edu	37	12	52145329	52145329	+	Frame_Shift_Del	DEL	C	C	-			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	.						147.0	140.0	142.0					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	
RRP12	23223	hgsc.bcm.edu	37	10	99120314	99120314	+	Frame_Shift_Del	DEL	G	G	-			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	.						170.0	143.0	152.0					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	
CDK13	8621	hgsc.bcm.edu	37	7	40117701	40117701	+	Frame_Shift_Del	DEL	T	T	-			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	.						152.0	143.0	146.0					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	
