#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
TPRG1L	127262	hgsc.bcm.edu	37	1	3544177	3544177	+	Missense_Mutation	SNP	C	C	A			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr1:3544177C>A	ENST00000378344.2	+	4	655	c.584C>A	c.(583-585)cCg>cAg	p.P195Q	TPRG1L_ENST00000344579.5_Missense_Mutation_p.P136Q|RP11-46F15.2_ENST00000435049.1_RNA	NM_182752.3	NP_877429.2	Q5T0D9	TPRGL_HUMAN	tumor protein p63 regulated 1-like	195						cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)|synaptic vesicle (GO:0008021)				endometrium(2)|kidney(2)|large_intestine(1)|lung(2)|prostate(1)	8	all_cancers(77;0.0119)|all_epithelial(69;0.00481)|Ovarian(185;0.0634)|Lung NSC(156;0.162)|all_lung(157;0.172)	all_epithelial(116;7.37e-22)|all_lung(118;8.23e-09)|Lung NSC(185;3.55e-06)|Breast(487;0.000659)|Renal(390;0.00121)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Lung SC(97;0.0262)|Ovarian(437;0.0308)|Medulloblastoma(700;0.211)		Epithelial(90;3.41e-38)|OV - Ovarian serous cystadenocarcinoma(86;3.83e-22)|GBM - Glioblastoma multiforme(42;4.77e-14)|Colorectal(212;1.12e-05)|COAD - Colon adenocarcinoma(227;5.61e-05)|Kidney(185;0.000351)|BRCA - Breast invasive adenocarcinoma(365;0.000688)|KIRC - Kidney renal clear cell carcinoma(229;0.00553)|STAD - Stomach adenocarcinoma(132;0.00645)|Lung(427;0.201)		ACAGAACACCCGATGGCTGGC	0.537																																					p.P195Q		Atlas-SNP	.											.	TPRG1L	24	.	0			c.C584A						PASS	.						144.0	145.0	145.0					1																	3544177		2203	4300	6503	SO:0001583	missense	127262	exon4			AACACCCGATGGC	BC019034	CCDS47.1	1p36.32	2008-02-05	2008-01-16	2008-01-16	ENSG00000158109	ENSG00000158109			27007	protein-coding gene	gene with protein product		611460	"""family with sequence similarity 79, member A"""	FAM79A		12477932	Standard	NM_182752		Approved	RP11-46F15.3, FLJ21811	uc001akm.3	Q5T0D9	OTTHUMG00000000609	ENST00000378344.2:c.584C>A	chr1.hg19:g.3544177C>A	ENSP00000367595:p.Pro195Gln	289.0	0.0	.		255.0	12.0	.	NM_182752	A8K1K4|Q8WV04	Missense_Mutation	SNP	ENST00000378344.2	hg19	CCDS47.1	.	.	.	.	.	.	.	.	.	.	C	22.8	4.343531	0.82022	.	.	ENSG00000158109	ENST00000378344;ENST00000456805;ENST00000344579	.	.	.	4.93	4.93	0.64822	.	0.000000	0.85682	D	0.000000	D	0.83248	0.5213	M	0.83223	2.63	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.86311	0.1686	9	0.87932	D	0	-0.7616	17.1228	0.86706	0.0:1.0:0.0:0.0	.	136;195	Q5T0D9-2;Q5T0D9	.;TPRGL_HUMAN	Q	195;152;136	.	ENSP00000339714:P136Q	P	+	2	0	TPRG1L	3534037	1.000000	0.71417	0.980000	0.43619	0.972000	0.66771	5.803000	0.69129	2.282000	0.76494	0.563000	0.77884	CCG	.	.	.	none		0.537	TPRG1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001466.1	NM_182752	
CC2D1B	200014	hgsc.bcm.edu	37	1	52819228	52819228	+	Missense_Mutation	SNP	G	G	C			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr1:52819228G>C	ENST00000371586.2	-	24	2678	c.2540C>G	c.(2539-2541)aCt>aGt	p.T847S	CC2D1B_ENST00000460261.1_5'UTR|RP11-155O18.6_ENST00000606527.1_RNA|CC2D1B_ENST00000284376.3_Missense_Mutation_p.T841S	NM_032449.2	NP_115825.1	Q5T0F9	C2D1B_HUMAN	coiled-coil and C2 domain containing 1B	847						nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)			breast(1)|large_intestine(6)|lung(13)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	27						CCAGTTCTCAGTGACCATCTG	0.592																																					p.T847S		Atlas-SNP	.											.	CC2D1B	73	.	0			c.C2540G						PASS	.						48.0	46.0	47.0					1																	52819228		2203	4300	6503	SO:0001583	missense	200014	exon24			TTCTCAGTGACCA	AB058739	CCDS30714.1	1p32.3	2008-02-05			ENSG00000154222	ENSG00000154222			29386	protein-coding gene	gene with protein product						11347906	Standard	NM_032449		Approved	KIAA1836	uc001ctq.2	Q5T0F9	OTTHUMG00000008102	ENST00000371586.2:c.2540C>G	chr1.hg19:g.52819228G>C	ENSP00000360642:p.Thr847Ser	48.0	0.0	.		46.0	22.0	.	NM_032449	Q49AE8|Q5T0F8|Q5T0G0|Q6ZNQ1|Q96AP3|Q96I04|Q96JJ1	Missense_Mutation	SNP	ENST00000371586.2	hg19	CCDS30714.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	16.43|16.43	3.121445|3.121445	0.56613|0.56613	.|.	.|.	ENSG00000154222|ENSG00000154222	ENST00000450942|ENST00000371586;ENST00000284376	.|T;T	.|0.21543	.|2.0;2.0	4.97|4.97	4.06|4.06	0.47325|0.47325	.|.	.|0.215167	.|0.44483	.|D	.|0.000459	T|T	0.27524|0.27524	0.0676|0.0676	L|L	0.53249|0.53249	1.67|1.67	0.80722|0.80722	D|D	1|1	.|P;P	.|0.43477	.|0.808;0.757	.|P;B	.|0.46026	.|0.501;0.327	T|T	0.03051|0.03051	-1.1078|-1.1078	5|10	.|0.48119	.|T	.|0.1	-6.0069|-6.0069	13.5782|13.5782	0.61888|0.61888	0.0745:0.0:0.9255:0.0|0.0745:0.0:0.9255:0.0	.|.	.|841;847	.|Q5T0F9-2;Q5T0F9	.|.;C2D1B_HUMAN	V|S	761|847;841	.|ENSP00000360642:T847S;ENSP00000284376:T841S	.|ENSP00000284376:T841S	L|T	-|-	1|2	2|0	CC2D1B|CC2D1B	52591816|52591816	1.000000|1.000000	0.71417|0.71417	0.830000|0.830000	0.32933|0.32933	0.821000|0.821000	0.46438|0.46438	6.187000|6.187000	0.72039|0.72039	1.323000|1.323000	0.45263|0.45263	0.561000|0.561000	0.74099|0.74099	CTG|ACT	.	.	.	none		0.592	CC2D1B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000022189.1	NM_032449	
DPYD	1806	hgsc.bcm.edu	37	1	98058809	98058809	+	Nonsense_Mutation	SNP	T	T	A			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr1:98058809T>A	ENST00000370192.3	-	10	1193	c.1093A>T	c.(1093-1095)Aaa>Taa	p.K365*		NM_000110.3	NP_000101	Q12882	DPYD_HUMAN	dihydropyrimidine dehydrogenase	365					beta-alanine biosynthetic process (GO:0019483)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase catabolic process (GO:0006145)|pyrimidine nucleobase catabolic process (GO:0006208)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside catabolic process (GO:0046135)|small molecule metabolic process (GO:0044281)|thymidine catabolic process (GO:0006214)|thymine catabolic process (GO:0006210)|UMP biosynthetic process (GO:0006222)|uracil catabolic process (GO:0006212)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	4 iron, 4 sulfur cluster binding (GO:0051539)|dihydroorotate dehydrogenase activity (GO:0004152)|dihydropyrimidine dehydrogenase (NADP+) activity (GO:0017113)|flavin adenine dinucleotide binding (GO:0050660)|metal ion binding (GO:0046872)|NADP binding (GO:0050661)|protein homodimerization activity (GO:0042803)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(18)|lung(30)|ovary(4)|prostate(6)|skin(7)|upper_aerodigestive_tract(1)	83		all_epithelial(167;0.000185)|all_lung(203;0.00318)|Lung NSC(277;0.00994)		Colorectal(170;0.0165)|Epithelial(280;0.0526)|all cancers(265;0.104)|READ - Rectum adenocarcinoma(84;0.171)|Lung(183;0.216)	Capecitabine(DB01101)|Flavin adenine dinucleotide(DB03147)|Fluorouracil(DB00544)	ACAAAGCCTTTTCTGAAGACG	0.448																																					p.K365X		Atlas-SNP	.											.	DPYD	219	.	0			c.A1093T						PASS	.						119.0	116.0	117.0					1																	98058809		2203	4300	6503	SO:0001587	stop_gained	1806	exon10			AGCCTTTTCTGAA	U20938	CCDS30777.1, CCDS53346.1	1p22	2014-09-17			ENSG00000188641	ENSG00000188641	1.3.1.2		3012	protein-coding gene	gene with protein product		612779				7713523	Standard	NM_000110		Approved	DPD	uc001drv.3	Q12882	OTTHUMG00000039683	ENST00000370192.3:c.1093A>T	chr1.hg19:g.98058809T>A	ENSP00000359211:p.Lys365*	116.0	0.0	.		140.0	53.0	.	NM_000110	A2RRQ2|A2RRQ3|A8K5A2|A8MWG9|B1AN21|E9PFN1|Q16694|Q16761|Q32NB0|Q96HL6|Q96TH1	Nonsense_Mutation	SNP	ENST00000370192.3	hg19	CCDS30777.1	.	.	.	.	.	.	.	.	.	.	T	39	7.840231	0.98519	.	.	ENSG00000188641	ENST00000370192	.	.	.	6.17	6.17	0.99709	.	0.048348	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-20.3061	15.3933	0.74767	0.0:0.0:0.0:1.0	.	.	.	.	X	365	.	ENSP00000359211:K365X	K	-	1	0	DPYD	97831397	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.664000	0.68045	2.371000	0.80710	0.533000	0.62120	AAA	.	.	.	none		0.448	DPYD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095698.3	NM_000110	
RHBG	57127	hgsc.bcm.edu	37	1	156347130	156347130	+	Missense_Mutation	SNP	G	G	C			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr1:156347130G>C	ENST00000368249.1	+	2	264	c.226G>C	c.(226-228)Ggc>Cgc	p.G76R	RHBG_ENST00000537040.1_Intron|RHBG_ENST00000255013.3_Missense_Mutation_p.G7R|RHBG_ENST00000451864.2_Missense_Mutation_p.G7R|RHBG_ENST00000400992.2_Missense_Mutation_p.G7R|RHBG_ENST00000368246.2_Missense_Mutation_p.G76R	NM_001256396.1|NM_020407.4	NP_001243325.1|NP_065140.3	Q9H310	RHBG_HUMAN	Rh family, B glycoprotein (gene/pseudogene)	76			G -> D (in dbSNP:rs2245623). {ECO:0000269|PubMed:14702039, ECO:0000269|Ref.5}.		ammonium transmembrane transport (GO:0072488)|ammonium transport (GO:0015696)|transepithelial ammonium transport (GO:0070634)|transmembrane transport (GO:0055085)	anchored component of plasma membrane (GO:0046658)|basolateral plasma membrane (GO:0016323)|cytoplasmic vesicle (GO:0031410)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|spectrin-associated cytoskeleton (GO:0014731)	ammonium transmembrane transporter activity (GO:0008519)|ankyrin binding (GO:0030506)			endometrium(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(3)|skin(2)|stomach(1)|urinary_tract(1)	22	Hepatocellular(266;0.158)					CGTGGGCTTTGGCTTCCTCAT	0.637																																					p.G76R		Atlas-SNP	.											.	RHBG	133	.	0			c.G226C						PASS	.						142.0	144.0	143.0					1																	156347130		2203	4300	6503	SO:0001583	missense	57127	exon2			GGCTTTGGCTTCC	AF193807		1q22	2013-05-22	2009-01-22		ENSG00000132677	ENSG00000132677		"""Solute carriers"""	14572	protein-coding gene	gene with protein product		607079	"""Rhesus blood group, B glycoprotein"""			10852913	Standard	NM_020407		Approved	SLC42A2	uc010pho.3	Q9H310	OTTHUMG00000024057	ENST00000368249.1:c.226G>C	chr1.hg19:g.156347130G>C	ENSP00000357232:p.Gly76Arg	207.0	0.0	.		147.0	47.0	.	NM_020407	A8K475|Q5SZW4|Q5SZW6|Q5SZW7|Q6P193|Q6YJI2|Q6YJI3	Missense_Mutation	SNP	ENST00000368249.1	hg19		.	.	.	.	.	.	.	.	.	.	G	29.7	5.031766	0.93575	.	.	ENSG00000132677	ENST00000368249;ENST00000368246;ENST00000400992;ENST00000255013;ENST00000451864	D;D;D;D;D	0.81579	-1.51;-1.51;-1.51;-1.51;-1.51	4.86	4.86	0.63082	Ammonium transporter AmtB-like (3);	0.000000	0.85682	D	0.000000	D	0.91744	0.7389	H	0.94582	3.555	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.93736	0.7046	10	0.87932	D	0	-6.6399	16.7188	0.85405	0.0:0.0:1.0:0.0	.	76;7;113	Q9H310;Q9H310-3;Q5SZW5	RHBG_HUMAN;.;.	R	76;76;7;7;7	ENSP00000357232:G76R;ENSP00000357229:G76R;ENSP00000383777:G7R;ENSP00000255013:G7R;ENSP00000389836:G7R	ENSP00000255013:G7R	G	+	1	0	RHBG	154613754	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	6.365000	0.73090	2.512000	0.84698	0.561000	0.74099	GGC	.	.	.	none		0.637	RHBG-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000060589.2	NM_001256395	
ADAM17	6868	hgsc.bcm.edu	37	2	9645412	9645412	+	Missense_Mutation	SNP	T	T	G			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr2:9645412T>G	ENST00000310823.3	-	12	1609	c.1427A>C	c.(1426-1428)aAa>aCa	p.K476T	RP11-400L8.2_ENST00000480764.1_RNA|RP11-400L8.2_ENST00000472619.1_RNA	NM_003183.4	NP_003174.3	P78536	ADA17_HUMAN	ADAM metallopeptidase domain 17	476	Disintegrin. {ECO:0000255|PROSITE- ProRule:PRU00068}.				apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|B cell differentiation (GO:0030183)|cell adhesion (GO:0007155)|cell adhesion mediated by integrin (GO:0033627)|cell motility (GO:0048870)|collagen catabolic process (GO:0030574)|epidermal growth factor receptor signaling pathway (GO:0007173)|epidermal growth factor-activated receptor transactivation by G-protein coupled receptor signaling pathway (GO:0035625)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|germinal center formation (GO:0002467)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|membrane protein ectodomain proteolysis (GO:0006509)|membrane protein intracellular domain proteolysis (GO:0031293)|negative regulation of interleukin-8 production (GO:0032717)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neurotrophin TRK receptor signaling pathway (GO:0048011)|neutrophil mediated immunity (GO:0002446)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|PMA-inducible membrane protein ectodomain proteolysis (GO:0051088)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cellular component movement (GO:0051272)|positive regulation of chemokine production (GO:0032722)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of leukocyte chemotaxis (GO:0002690)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of T cell chemotaxis (GO:0010820)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|proteolysis (GO:0006508)|regulation of mast cell apoptotic process (GO:0033025)|response to drug (GO:0042493)|response to high density lipoprotein particle (GO:0055099)|response to hypoxia (GO:0001666)|response to lipopolysaccharide (GO:0032496)|spleen development (GO:0048536)|T cell differentiation in thymus (GO:0033077)|wound healing, spreading of epidermal cells (GO:0035313)	actin cytoskeleton (GO:0015629)|apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	integrin binding (GO:0005178)|interleukin-6 receptor binding (GO:0005138)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|Notch binding (GO:0005112)|PDZ domain binding (GO:0030165)|zinc ion binding (GO:0008270)			breast(1)|cervix(4)|endometrium(2)|kidney(2)|large_intestine(7)|lung(8)|ovary(1)|prostate(2)|skin(1)	28	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.225)		CCCACAAACTTTATTGCTGCG	0.438																																					p.K476T		Atlas-SNP	.											.	ADAM17	61	.	0			c.A1427C						PASS	.						178.0	155.0	163.0					2																	9645412		2203	4300	6503	SO:0001583	missense	6868	exon12			CAAACTTTATTGC	U69611	CCDS1665.1	2p25	2010-08-05	2008-07-31		ENSG00000151694	ENSG00000151694		"""ADAM metallopeptidase domain containing"", ""CD molecules"""	195	protein-coding gene	gene with protein product		603639	"""tumor necrosis factor, alpha, converting enzyme"""	TACE		9034190, 9574564	Standard	NM_003183		Approved	cSVP, CD156B	uc002qzu.3	P78536	OTTHUMG00000090425	ENST00000310823.3:c.1427A>C	chr2.hg19:g.9645412T>G	ENSP00000309968:p.Lys476Thr	120.0	0.0	.		154.0	72.0	.	NM_003183	O60226	Missense_Mutation	SNP	ENST00000310823.3	hg19	CCDS1665.1	.	.	.	.	.	.	.	.	.	.	T	12.83	2.056207	0.36277	.	.	ENSG00000151694	ENST00000310823	T	0.21191	2.02	5.66	3.33	0.38152	Blood coagulation inhibitor, Disintegrin (1);	0.226724	0.51477	D	0.000087	T	0.18718	0.0449	L	0.46670	1.46	0.80722	D	1	B;B	0.10296	0.003;0.003	B;B	0.12156	0.007;0.007	T	0.03325	-1.1048	10	0.48119	T	0.1	.	9.5244	0.39156	0.0:0.1409:0.0:0.8591	.	476;476	B2RNB2;P78536	.;ADA17_HUMAN	T	476	ENSP00000309968:K476T	ENSP00000309968:K476T	K	-	2	0	ADAM17	9562863	1.000000	0.71417	0.994000	0.49952	0.915000	0.54546	3.947000	0.56652	0.444000	0.26612	0.460000	0.39030	AAA	.	.	.	none		0.438	ADAM17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206857.1		
APOB	338	hgsc.bcm.edu	37	2	21260848	21260848	+	Silent	SNP	G	G	A			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr2:21260848G>A	ENST00000233242.1	-	5	646	c.519C>T	c.(517-519)gcC>gcT	p.A173A	APOB_ENST00000399256.4_Silent_p.A173A	NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	173	Vitellogenin. {ECO:0000255|PROSITE- ProRule:PRU00557}.				artery morphogenesis (GO:0048844)|blood coagulation (GO:0007596)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to tumor necrosis factor (GO:0071356)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle remodeling (GO:0034374)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol biosynthetic process (GO:0045540)|response to carbohydrate (GO:0009743)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to virus (GO:0009615)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|triglyceride catabolic process (GO:0019433)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	actin cytoskeleton (GO:0015629)|chylomicron (GO:0042627)|chylomicron remnant (GO:0034360)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome lumen (GO:0031904)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate-density lipoprotein particle (GO:0034363)|intracellular membrane-bounded organelle (GO:0043231)|low-density lipoprotein particle (GO:0034362)|mature chylomicron (GO:0034359)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|lipase binding (GO:0035473)|low-density lipoprotein particle receptor binding (GO:0050750)|phospholipid binding (GO:0005543)			NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					ACACTTGCTTGGCTTCTTCTG	0.458																																					p.A173A		Atlas-SNP	.											.	APOB	761	.	0			c.C519T						PASS	.						128.0	129.0	129.0					2																	21260848		2203	4300	6503	SO:0001819	synonymous_variant	338	exon5			TTGCTTGGCTTCT	M14162	CCDS1703.1	2p24-p23	2013-05-29	2013-05-29		ENSG00000084674	ENSG00000084674		"""Apolipoproteins"""	603	protein-coding gene	gene with protein product		107730	"""apolipoprotein B (including Ag(x) antigen)"""				Standard	NM_000384		Approved		uc002red.3	P04114	OTTHUMG00000090785	ENST00000233242.1:c.519C>T	chr2.hg19:g.21260848G>A		140.0	0.0	.		173.0	94.0	.	NM_000384	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Silent	SNP	ENST00000233242.1	hg19	CCDS1703.1																																																																																			.	.	.	none		0.458	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1		
ATAD2B	54454	hgsc.bcm.edu	37	2	24051776	24051776	+	Missense_Mutation	SNP	C	C	A			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr2:24051776C>A	ENST00000238789.5	-	15	2105	c.1762G>T	c.(1762-1764)Gac>Tac	p.D588Y	ATAD2B_ENST00000474583.1_5'UTR	NM_001242338.1|NM_017552.2	NP_001229267.1|NP_060022.1	Q9ULI0	ATD2B_HUMAN	ATPase family, AAA domain containing 2B	588						nucleus (GO:0005634)	ATP binding (GO:0005524)|lysine-acetylated histone binding (GO:0070577)			central_nervous_system(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GGATTCCAGTCCCTGGTATGG	0.333																																					p.D588Y		Atlas-SNP	.											.	ATAD2B	110	.	0			c.G1762T						PASS	.						121.0	114.0	116.0					2																	24051776		1842	4090	5932	SO:0001583	missense	54454	exon15			TCCAGTCCCTGGT	AB033066	CCDS46227.1	2p24.1-p23.3	2010-04-21		2007-02-08	ENSG00000119778	ENSG00000119778		"""ATPases / AAA-type"""	29230	protein-coding gene	gene with protein product		615347					Standard	XM_005264372		Approved	KIAA1240	uc002rek.4	Q9ULI0	OTTHUMG00000151902	ENST00000238789.5:c.1762G>T	chr2.hg19:g.24051776C>A	ENSP00000238789:p.Asp588Tyr	97.0	0.0	.		138.0	59.0	.	NM_001242338	B9ZVQ5|Q6ZNA6|Q8N9E7	Missense_Mutation	SNP	ENST00000238789.5	hg19	CCDS46227.1	.	.	.	.	.	.	.	.	.	.	C	15.81	2.944509	0.53079	.	.	ENSG00000119778	ENST00000238789;ENST00000458510	D;D	0.94931	-3.56;-1.77	4.7	4.7	0.59300	.	.	.	.	.	D	0.95023	0.8389	L	0.60957	1.885	0.49299	D	0.999776	D	0.54047	0.964	P	0.53912	0.737	D	0.95210	0.8324	9	0.72032	D	0.01	.	14.2998	0.66339	0.1494:0.8506:0.0:0.0	.	588	Q9ULI0	ATD2B_HUMAN	Y	588;26	ENSP00000238789:D588Y;ENSP00000392764:D26Y	ENSP00000238789:D588Y	D	-	1	0	ATAD2B	23905280	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	3.884000	0.56175	2.551000	0.86045	0.650000	0.86243	GAC	.	.	.	none		0.333	ATAD2B-001	KNOWN	mRNA_end_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324333.1	NM_017552	
AGBL5	60509	hgsc.bcm.edu	37	2	27291539	27291539	+	Missense_Mutation	SNP	A	A	G			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr2:27291539A>G	ENST00000360131.4	+	13	2441	c.2282A>G	c.(2281-2283)gAg>gGg	p.E761G		NM_021831.5	NP_068603.4	Q8NDL9	CBPC5_HUMAN	ATP/GTP binding protein-like 5	761					protein branching point deglutamylation (GO:0035611)|protein deglutamylation (GO:0035608)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	metallocarboxypeptidase activity (GO:0004181)|tubulin binding (GO:0015631)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|large_intestine(5)|lung(8)|ovary(3)|pancreas(1)|prostate(2)|skin(1)	28	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GACAAACCAGAGGCTGTCATG	0.512																																					p.E761G		Atlas-SNP	.											.	AGBL5	126	.	0			c.A2282G						PASS	.						84.0	85.0	85.0					2																	27291539		2203	4300	6503	SO:0001583	missense	60509	exon13			AACCAGAGGCTGT	BC007415	CCDS1732.3, CCDS42665.1	2p23.3	2014-06-23			ENSG00000084693	ENSG00000084693			26147	protein-coding gene	gene with protein product	"""cytosolic carboxypeptidase 5"""	615900				24022482	Standard	NM_001035507		Approved	FLJ21839, CCP5	uc002rie.3	Q8NDL9	OTTHUMG00000128406	ENST00000360131.4:c.2282A>G	chr2.hg19:g.27291539A>G	ENSP00000353249:p.Glu761Gly	117.0	0.0	.		180.0	52.0	.	NM_021831	A2VDI7|B7WPG9|B7Z7I7|D6W548|Q53SW0|Q53SZ0|Q96IK8|Q9H6V0|Q9H8P8	Missense_Mutation	SNP	ENST00000360131.4	hg19	CCDS1732.3	.	.	.	.	.	.	.	.	.	.	A	10.83	1.459849	0.26248	.	.	ENSG00000084693	ENST00000360131	T	0.17370	2.28	5.61	4.46	0.54185	.	0.426245	0.25285	N	0.031768	T	0.10723	0.0262	N	0.19112	0.55	0.32634	N	0.521593	B	0.13145	0.007	B	0.09377	0.004	T	0.03641	-1.1017	10	0.87932	D	0	-0.026	7.4869	0.27439	0.9054:0.0:0.0946:0.0	.	761	Q8NDL9	CBPC5_HUMAN	G	761	ENSP00000353249:E761G	ENSP00000353249:E761G	E	+	2	0	AGBL5	27145043	1.000000	0.71417	1.000000	0.80357	0.237000	0.25408	2.781000	0.47750	2.123000	0.65237	0.459000	0.35465	GAG	.	.	.	none		0.512	AGBL5-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000309033.1	NM_021831	
SLC4A5	57835	hgsc.bcm.edu	37	2	74458396	74458396	+	Missense_Mutation	SNP	C	C	A			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr2:74458396C>A	ENST00000423644.1	-	24	3032	c.2635G>T	c.(2635-2637)Ggg>Tgg	p.G879W	SLC4A5_ENST00000394019.2_Silent_p.T938T|RP11-287D1.3_ENST00000451608.2_3'UTR|SLC4A5_ENST00000377632.1_Silent_p.T938T|SLC4A5_ENST00000346834.4_Silent_p.T938T|SLC4A5_ENST00000483195.1_5'UTR|SLC4A5_ENST00000357822.5_Silent_p.T938T|SLC4A5_ENST00000359484.4_Silent_p.T836T|SLC4A5_ENST00000377634.4_Silent_p.T938T|SLC4A5_ENST00000358683.4_Silent_p.T836T					solute carrier family 4 (sodium bicarbonate cotransporter), member 5											breast(5)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(12)|lung(13)|ovary(5)|pancreas(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	48						CAGAGATTCCCGTCAGGATGA	0.562																																					p.T938T		Atlas-SNP	.											.	SLC4A5	215	.	0			c.G2814T						PASS	.						179.0	146.0	157.0					2																	74458396		2203	4300	6503	SO:0001583	missense	57835	exon20			GATTCCCGTCAGG	AF243499	CCDS1936.1, CCDS1937.1	2p13.1	2013-07-19	2013-07-19		ENSG00000188687	ENSG00000188687		"""Solute carriers"""	18168	protein-coding gene	gene with protein product		606757	"""solute carrier family 4, sodium bicarbonate cotransporter, member 5"""			10978526, 11087115	Standard	NM_133478		Approved	NBC4	uc002sko.1	Q9BY07	OTTHUMG00000090263	ENST00000423644.1:c.2635G>T	chr2.hg19:g.74458396C>A	ENSP00000395804:p.Gly879Trp	97.0	0.0	.		137.0	11.0	.	NM_021196		Silent	SNP	ENST00000423644.1	hg19		.	.	.	.	.	.	.	.	.	.	C	5.936	0.356646	0.11239	.	.	ENSG00000188687	ENST00000423644;ENST00000425249	T;T	0.74315	-0.83;-0.47	4.47	-8.36	0.00980	.	.	.	.	.	T	0.52996	0.1769	.	.	.	0.19575	N	0.999969	B	0.11235	0.004	B	0.09377	0.004	T	0.41070	-0.9529	8	0.59425	D	0.04	.	1.6798	0.02830	0.3015:0.1537:0.0994:0.4453	.	841	E7EQT3	.	W	879;841	ENSP00000395804:G879W;ENSP00000405678:G841W	ENSP00000395804:G879W	G	-	1	0	SLC4A5	74311904	0.000000	0.05858	0.373000	0.26003	0.924000	0.55760	-4.346000	0.00249	-2.458000	0.00538	-2.805000	0.00112	GGG	.	.	.	none		0.562	SLC4A5-204	KNOWN	basic	protein_coding	protein_coding			
SEMA4F	10505	hgsc.bcm.edu	37	2	74906851	74906851	+	Silent	SNP	C	C	A	rs367999393		TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr2:74906851C>A	ENST00000357877.2	+	14	1977	c.1828C>A	c.(1828-1830)Cgg>Agg	p.R610R	SEMA4F_ENST00000339773.5_Silent_p.R455R|SEMA4F_ENST00000473350.1_3'UTR	NM_004263.3	NP_004254.2	O95754	SEM4F_HUMAN	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4F	610	Ig-like C2-type.				axon guidance (GO:0007411)|cell-cell signaling (GO:0007267)|negative regulation of axon extension (GO:0030517)|nervous system development (GO:0007399)|retinal ganglion cell axon guidance (GO:0031290)	endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	receptor activity (GO:0004872)			biliary_tract(1)|breast(2)|endometrium(8)|kidney(3)|large_intestine(9)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(2)	45						ACTCACCCCCCGGCGGGATGG	0.627																																					p.R610R		Atlas-SNP	.											.	SEMA4F	89	.	0			c.C1828A						PASS	.						73.0	72.0	73.0					2																	74906851		2203	4300	6503	SO:0001819	synonymous_variant	10505	exon14			ACCCCCCGGCGGG	AF038652	CCDS1955.1, CCDS62942.1, CCDS74529.1	2p13.1	2008-05-21			ENSG00000135622	ENSG00000135622		"""Semaphorins"""	10734	protein-coding gene	gene with protein product	"""m-Sema M"""	603706		SEMAM		10051670	Standard	NM_004263		Approved	SEMAW	uc002sna.2	O95754	OTTHUMG00000129952	ENST00000357877.2:c.1828C>A	chr2.hg19:g.74906851C>A		149.0	0.0	.		143.0	10.0	.	NM_004263	Q542Y7|Q9NS35	Silent	SNP	ENST00000357877.2	hg19	CCDS1955.1																																																																																			.	.	.	alt		0.627	SEMA4F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252214.2	NM_004263	
SNRNP200	23020	hgsc.bcm.edu	37	2	96953697	96953697	+	Missense_Mutation	SNP	C	C	A	rs397514574		TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr2:96953697C>A	ENST00000323853.5	-	25	3346	c.3269G>T	c.(3268-3270)cGg>cTg	p.R1090L	SNRNP200_ENST00000349783.5_Intron	NM_014014.4	NP_054733.2	O75643	U520_HUMAN	small nuclear ribonucleoprotein 200kDa (U5)	1090	SEC63 1.		R -> L (in RP33). {ECO:0000269|PubMed:19710410}.		ATP catabolic process (GO:0006200)|cis assembly of pre-catalytic spliceosome (GO:0000354)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|osteoblast differentiation (GO:0001649)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U5 snRNP (GO:0005682)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|ATP-dependent RNA helicase activity (GO:0004004)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)			breast(3)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(18)|lung(37)|ovary(7)|prostate(4)|skin(5)|stomach(1)|urinary_tract(1)	90						TCGCATCAACCGGCCAGCCGA	0.502																																					p.R1090L		Atlas-SNP	.											.	SNRNP200	195	.	0			c.G3269T						PASS	.						126.0	111.0	116.0					2																	96953697		2203	4300	6503	SO:0001583	missense	23020	exon25			ATCAACCGGCCAG	AL831994	CCDS2020.1	2q11.2	2013-05-13	2008-10-29	2008-10-29	ENSG00000144028	ENSG00000144028			30859	protein-coding gene	gene with protein product	"""U5 snRNP specific protein, 200 KD"""	601664	"""activating signal cointegrator 1 complex subunit 3-like 1"", ""retinitis pigmentosa 33 (autosomal dominant)"""	ASCC3L1, RP33		9872452, 8670905, 9774689, 9539711, 16612614, 19878916	Standard	NM_014014		Approved	U5-200KD, HELIC2, KIAA0788, BRR2	uc002svu.3	O75643	OTTHUMG00000130455	ENST00000323853.5:c.3269G>T	chr2.hg19:g.96953697C>A	ENSP00000317123:p.Arg1090Leu	170.0	0.0	.		191.0	9.0	.	NM_014014	O94884|Q6NZY0|Q6PX59|Q8NBE6|Q96IF2|Q9H7S0	Missense_Mutation	SNP	ENST00000323853.5	hg19	CCDS2020.1	.	.	.	.	.	.	.	.	.	.	C	29.6	5.016736	0.93404	.	.	ENSG00000144028	ENST00000323853;ENST00000540328	T	0.70869	-0.52	5.3	5.3	0.74995	Sec63 domain (3);	0.000000	0.85682	D	0.000000	D	0.89473	0.6725	H	0.95850	3.73	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.92387	0.5918	10	0.87932	D	0	-19.469	17.8872	0.88861	0.0:1.0:0.0:0.0	.	1090	O75643	U520_HUMAN	L	1090;765	ENSP00000317123:R1090L	ENSP00000317123:R1090L	R	-	2	0	SNRNP200	96317424	1.000000	0.71417	0.999000	0.59377	0.790000	0.44656	7.570000	0.82390	2.755000	0.94549	0.561000	0.74099	CGG	.	.	.	none		0.502	SNRNP200-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252846.2	NM_014014	
NEB	4703	hgsc.bcm.edu	37	2	152522655	152522655	+	Silent	SNP	G	G	T	rs142074817	byFrequency	TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr2:152522655G>T	ENST00000172853.10	-	41	5127	c.4980C>A	c.(4978-4980)ccC>ccA	p.P1660P	NEB_ENST00000604864.1_Silent_p.P1660P|NEB_ENST00000397345.3_Silent_p.P1660P|NEB_ENST00000427231.2_Silent_p.P1660P|NEB_ENST00000603639.1_Silent_p.P1660P|NEB_ENST00000409198.1_Silent_p.P1660P			P20929	NEBU_HUMAN	nebulin	1660					muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|regulation of actin filament length (GO:0030832)|somatic muscle development (GO:0007525)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Z disc (GO:0030018)	structural constituent of muscle (GO:0008307)			NS(5)|autonomic_ganglia(3)|breast(9)|central_nervous_system(5)|cervix(3)|endometrium(35)|kidney(16)|large_intestine(77)|liver(1)|lung(99)|ovary(9)|pancreas(3)|prostate(13)|skin(7)|stomach(8)|upper_aerodigestive_tract(6)|urinary_tract(2)	301				BRCA - Breast invasive adenocarcinoma(221;0.219)		TCAAGGCATCGGGCAGGAGAG	0.488																																					p.P1660P		Atlas-SNP	.											.	NEB	1697	.	0			c.C4980A						PASS	.						268.0	262.0	264.0					2																	152522655		2077	4215	6292	SO:0001819	synonymous_variant	4703	exon41			GGCATCGGGCAGG	X83957	CCDS46424.1, CCDS54407.1, CCDS54408.1, CCDS74588.1	2q22	2014-09-17			ENSG00000183091	ENSG00000183091			7720	protein-coding gene	gene with protein product	"""nemaline myopathy type 2"""	161650		NEM2		10051637, 9359044	Standard	NM_001164507		Approved	NEB177D	uc010fnx.3	P20929	OTTHUMG00000153784	ENST00000172853.10:c.4980C>A	chr2.hg19:g.152522655G>T		227.0	0.0	.		248.0	10.0	.	NM_004543	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Silent	SNP	ENST00000172853.10	hg19																																																																																				.	G|0.998;A|0.002	.	alt		0.488	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543	
FRZB	2487	hgsc.bcm.edu	37	2	183699593	183699593	+	Silent	SNP	G	G	T			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr2:183699593G>T	ENST00000295113.4	-	6	1570	c.961C>A	c.(961-963)Cgg>Agg	p.R321R		NM_001463.3	NP_001454.2	Q92765	SFRP3_HUMAN	frizzled-related protein	321					brain development (GO:0007420)|cochlea morphogenesis (GO:0090103)|convergent extension involved in organogenesis (GO:0060029)|epithelium development (GO:0060429)|gonad development (GO:0008406)|mammary gland involution (GO:0060056)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cartilage development (GO:0061037)|negative regulation of cell development (GO:0010721)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of hepatocyte differentiation (GO:0070367)|negative regulation of Wnt signaling pathway (GO:0030178)|neural crest cell differentiation (GO:0014033)|positive regulation of apoptotic process (GO:0043065)|positive regulation of fat cell differentiation (GO:0045600)|skeletal system development (GO:0001501)|somite development (GO:0061053)|vasculature development (GO:0001944)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|membrane (GO:0016020)	PDZ domain binding (GO:0030165)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(12)|ovary(2)|prostate(1)|skin(1)	21			OV - Ovarian serous cystadenocarcinoma(117;0.109)|Epithelial(96;0.231)			CGTGCTTGCCGGGGGTTCGAG	0.443																																					p.R321R		Atlas-SNP	.											.	FRZB	42	.	0			c.C961A						PASS	.						125.0	120.0	122.0					2																	183699593		2203	4300	6503	SO:0001819	synonymous_variant	2487	exon6			CTTGCCGGGGGTT	U24163	CCDS2286.1	2q32.1	2013-09-19			ENSG00000162998	ENSG00000162998		"""Secreted frizzled-related proteins"""	3959	protein-coding gene	gene with protein product		605083				8824257, 9118218	Standard	NM_001463		Approved	FRZB-PEN, FRZB1, SRFP3, FRP-3, SFRP3, FRE, FRITZ, FRZB-1, FZRB, hFIZ	uc002upa.2	Q92765	OTTHUMG00000132597	ENST00000295113.4:c.961C>A	chr2.hg19:g.183699593G>T		93.0	0.0	.		156.0	9.0	.	NM_001463	O00181|Q99686	Silent	SNP	ENST00000295113.4	hg19	CCDS2286.1																																																																																			.	.	.	none		0.443	FRZB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255808.1	NM_001463	
FAM171B	165215	hgsc.bcm.edu	37	2	187627072	187627072	+	Missense_Mutation	SNP	C	C	A			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr2:187627072C>A	ENST00000304698.5	+	8	2206	c.2003C>A	c.(2002-2004)cCg>cAg	p.P668Q		NM_177454.3	NP_803237.3	Q6P995	F171B_HUMAN	family with sequence similarity 171, member B	668						integral component of membrane (GO:0016021)	DNA binding (GO:0003677)			NS(1)|breast(6)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(10)|lung(22)|ovary(6)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	54						AAGCCCTCCCCGCATCCCAGA	0.483																																					p.P668Q		Atlas-SNP	.											FAM171B,NS,carcinoma,0,2	FAM171B	146	.	0			c.C2003A						PASS	.						77.0	86.0	83.0					2																	187627072		2203	4300	6503	SO:0001583	missense	165215	exon8			CCTCCCCGCATCC	AF361495	CCDS33347.1	2q32.2	2008-06-16	2008-06-16	2008-06-16	ENSG00000144369	ENSG00000144369			29412	protein-coding gene	gene with protein product			"""KIAA1946"""	KIAA1946		11853319	Standard	NM_177454		Approved	FLJ34104	uc002ups.3	Q6P995	OTTHUMG00000154278	ENST00000304698.5:c.2003C>A	chr2.hg19:g.187627072C>A	ENSP00000304108:p.Pro668Gln	166.0	0.0	.		212.0	11.0	.	NM_177454	Q53SK3|Q8N1Y4|Q8N3K1|Q8N970|Q8NB81|Q8TF55|Q8WYR8	Missense_Mutation	SNP	ENST00000304698.5	hg19	CCDS33347.1	.	.	.	.	.	.	.	.	.	.	C	12.44	1.938791	0.34189	.	.	ENSG00000144369	ENST00000304698	T	0.37235	1.21	6.02	6.02	0.97574	.	0.110302	0.64402	D	0.000005	T	0.39963	0.1098	L	0.47016	1.485	0.37615	D	0.92108	P;P	0.36027	0.533;0.533	B;B	0.37091	0.241;0.241	T	0.41698	-0.9494	10	0.87932	D	0	-16.1339	20.547	0.99278	0.0:1.0:0.0:0.0	.	668;669	Q6P995;A8K122	F171B_HUMAN;.	Q	668	ENSP00000304108:P668Q	ENSP00000304108:P668Q	P	+	2	0	FAM171B	187335317	0.987000	0.35691	0.821000	0.32701	0.569000	0.35902	4.610000	0.61155	2.850000	0.98022	0.650000	0.86243	CCG	.	.	.	none		0.483	FAM171B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334679.1	NM_177454	
UNC80	285175	hgsc.bcm.edu	37	2	210640757	210640757	+	Silent	SNP	C	C	A	rs538956139		TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr2:210640757C>A	ENST00000439458.1	+	3	366	c.286C>A	c.(286-288)Cga>Aga	p.R96R	UNC80_ENST00000478701.1_3'UTR|UNC80_ENST00000272845.6_Silent_p.R96R	NM_032504.1	NP_115893.1	Q8N2C7	UNC80_HUMAN	unc-80 homolog (C. elegans)	96					ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(9)|ovary(1)|prostate(1)	20						GCTTTCAAACCGAAACAAGCT	0.473																																					p.R96R		Atlas-SNP	.											.	UNC80	280	.	0			c.C286A						PASS	.						151.0	134.0	139.0					2																	210640757		2203	4300	6503	SO:0001819	synonymous_variant	285175	exon3			TCAAACCGAAACA	AK090815	CCDS2387.1, CCDS46504.1, CCDS2387.2	2q35	2009-08-17	2009-08-17	2009-08-17	ENSG00000144406	ENSG00000144406			26582	protein-coding gene	gene with protein product		612636	"""chromosome 2 open reading frame 21"""	C2orf21		19092807	Standard	NM_032504		Approved	FLJ33496, KIAA1843, UNC-80	uc010zjc.1	Q8N2C7	OTTHUMG00000132963	ENST00000439458.1:c.286C>A	chr2.hg19:g.210640757C>A		197.0	0.0	.		245.0	10.0	.	NM_182587	B2RN50|B4DQY9|B4DZB3|C4IXS8|C9J1U3|Q96JI4|Q96SS0	Silent	SNP	ENST00000439458.1	hg19	CCDS46504.1																																																																																			.	.	.	none		0.473	UNC80-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_182587	
TNS1	7145	hgsc.bcm.edu	37	2	218713795	218713795	+	Missense_Mutation	SNP	G	G	A	rs200862766		TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr2:218713795G>A	ENST00000171887.4	-	17	1522	c.1070C>T	c.(1069-1071)aCg>aTg	p.T357M	TNS1_ENST00000419504.1_Missense_Mutation_p.T357M|TNS1_ENST00000430930.1_Missense_Mutation_p.T357M|TNS1_ENST00000480665.1_5'UTR	NM_022648.4	NP_072174.3	Q9HBL0	TENS1_HUMAN	tensin 1	357					cell-substrate junction assembly (GO:0007044)|fibroblast migration (GO:0010761)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)	poly(A) RNA binding (GO:0044822)			breast(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(23)|liver(1)|lung(24)|ovary(3)|pancreas(1)|prostate(3)|skin(5)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	79		Renal(207;0.0483)|Lung NSC(271;0.213)		Epithelial(149;4.43e-06)|all cancers(144;0.000653)|LUSC - Lung squamous cell carcinoma(224;0.0091)|Lung(261;0.013)		TGGCCCCTGCGTGTGTCCCAC	0.577																																					p.T357M		Atlas-SNP	.											.	TNS1	251	.	0			c.C1070T						PASS	.	G	MET/THR	0,4406		0,0,2203	89.0	89.0	89.0		1070	4.3	1.0	2		89	2,8598	2.2+/-6.3	0,2,4298	no	missense	TNS1	NM_022648.4	81	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	benign	357/1736	218713795	2,13004	2203	4300	6503	SO:0001583	missense	7145	exon17			CCCTGCGTGTGTC	AB209238	CCDS2407.1	2q35-q36	2014-06-13	2005-05-13	2005-05-13	ENSG00000079308	ENSG00000079308		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"", ""SH2 domain containing"""	11973	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 155"""	600076	"""tensin"", ""matrix-remodelling associated 6"""	TNS, MXRA6			Standard	NM_022648		Approved	DKFZp586K0617, PPP1R155	uc002vgt.2	Q9HBL0	OTTHUMG00000133056	ENST00000171887.4:c.1070C>T	chr2.hg19:g.218713795G>A	ENSP00000171887:p.Thr357Met	189.0	0.0	.		198.0	38.0	.	NM_022648	Q4ZG71|Q6IPI5	Missense_Mutation	SNP	ENST00000171887.4	hg19	CCDS2407.1	.	.	.	.	.	.	.	.	.	.	G	17.74	3.464168	0.63513	0.0	2.33E-4	ENSG00000079308	ENST00000171887;ENST00000419504;ENST00000430930;ENST00000446903;ENST00000413554	D;D;D;D;D	0.96334	-3.5;-3.49;-3.51;-3.83;-3.98	5.22	4.34	0.51931	.	0.767219	0.12422	N	0.470300	D	0.95255	0.8461	M	0.83603	2.65	0.80722	D	1	P;B;B;P;P	0.43519	0.809;0.423;0.345;0.704;0.704	B;B;B;B;B	0.32090	0.14;0.053;0.05;0.09;0.09	D	0.94356	0.7583	10	0.66056	D	0.02	.	14.202	0.65710	0.0727:0.0:0.9273:0.0	.	357;411;357;357;357	B2RU35;A1L0S7;Q9HBL0;E9PGF5;E9PF55	.;.;TENS1_HUMAN;.;.	M	357;357;357;482;425	ENSP00000171887:T357M;ENSP00000408724:T357M;ENSP00000406016:T357M;ENSP00000405460:T482M;ENSP00000400383:T425M	ENSP00000171887:T357M	T	-	2	0	TNS1	218422040	1.000000	0.71417	0.991000	0.47740	0.969000	0.65631	7.726000	0.84824	1.404000	0.46819	0.655000	0.94253	ACG	.	G|0.999;A|0.001	0.001	weak		0.577	TNS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256672.2	NM_022648	
UGT1A5	54579	hgsc.bcm.edu	37	2	234622277	234622277	+	Missense_Mutation	SNP	A	A	G			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr2:234622277A>G	ENST00000373414.3	+	1	640	c.640A>G	c.(640-642)Atg>Gtg	p.M214V	UGT1A6_ENST00000480628.1_Intron|UGT1A6_ENST00000373424.1_Intron|UGT1A1_ENST00000609637.1_Intron|UGT1A1_ENST00000373450.4_Intron|UGT1A10_ENST00000344644.5_Intron|UGT1A1_ENST00000608381.1_Missense_Mutation_p.M214V|UGT1A10_ENST00000373445.1_Intron|UGT1A9_ENST00000354728.4_Intron|UGT1A6_ENST00000406651.1_Intron|UGT1A7_ENST00000373426.3_Intron|UGT1A6_ENST00000305139.6_Intron			P35504	UD15_HUMAN	UDP glucuronosyltransferase 1 family, polypeptide A5	214						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	glucuronosyltransferase activity (GO:0015020)			cervix(1)|endometrium(3)|large_intestine(4)|lung(9)|ovary(1)|skin(3)|urinary_tract(1)	22		Breast(86;0.000765)|all_lung(227;0.00267)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0328)|Lung NSC(271;0.0457)|Lung SC(224;0.128)		Epithelial(121;4.51e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000523)|Lung(119;0.00271)|LUSC - Lung squamous cell carcinoma(224;0.00645)		GGTCAAGAACATGCTCTACCC	0.483																																					p.M214V		Atlas-SNP	.											UGT1A5,NS,carcinoma,0,1	UGT1A5	66	.	0			c.A640G						PASS	.						209.0	197.0	201.0					2																	234622277		2203	4300	6503	SO:0001583	missense	54579	exon1			AAGAACATGCTCT	M84129	CCDS33404.1	2q37	2010-03-05	2005-07-20		ENSG00000240224	ENSG00000240224		"""UDP glucuronosyltransferases"""	12537	other	complex locus constituent		606430	"""UDP glycosyltransferase 1 family, polypeptide A5"""			9295054, 1339448	Standard	NM_019078		Approved	UGT1E		P35504	OTTHUMG00000059120	ENST00000373414.3:c.640A>G	chr2.hg19:g.234622277A>G	ENSP00000362513:p.Met214Val	352.0	1.0	.		368.0	195.0	.	NM_019078	B8K294	Missense_Mutation	SNP	ENST00000373414.3	hg19	CCDS33404.1	.	.	.	.	.	.	.	.	.	.	A	9.408	1.079672	0.20309	.	.	ENSG00000240224	ENST00000373414	T	0.61040	0.14	4.77	-0.524	0.11920	.	0.585446	0.20090	N	0.099480	T	0.34221	0.0890	N	0.25201	0.72	0.26978	N	0.965428	B;B	0.13594	0.008;0.008	B;B	0.23150	0.044;0.044	T	0.12604	-1.0541	10	0.45353	T	0.12	.	1.3681	0.02205	0.4274:0.2431:0.2117:0.1179	.	214;214	Q5DSZ9;P35504	.;UD15_HUMAN	V	214	ENSP00000362513:M214V	ENSP00000362513:M214V	M	+	1	0	UGT1A5	234287016	0.000000	0.05858	0.992000	0.48379	0.655000	0.38815	-0.882000	0.04174	-0.055000	0.13244	0.459000	0.35465	ATG	.	.	.	none		0.483	UGT1A5-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000130985.1	NM_019078	
D2HGDH	728294	hgsc.bcm.edu	37	2	242695394	242695394	+	Missense_Mutation	SNP	C	C	A			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr2:242695394C>A	ENST00000321264.4	+	9	1480	c.1271C>A	c.(1270-1272)cCg>cAg	p.P424Q	AC114730.7_ENST00000417267.1_RNA|D2HGDH_ENST00000403782.1_Missense_Mutation_p.P290Q|D2HGDH_ENST00000486953.1_3'UTR	NM_152783.3	NP_689996.4	Q8N465	D2HDH_HUMAN	D-2-hydroxyglutarate dehydrogenase	424					2-oxoglutarate metabolic process (GO:0006103)|cellular metabolic process (GO:0044237)|cellular protein metabolic process (GO:0044267)|response to cobalt ion (GO:0032025)|response to manganese ion (GO:0010042)|response to zinc ion (GO:0010043)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	(R)-2-hydroxyglutarate dehydrogenase activity (GO:0051990)|flavin adenine dinucleotide binding (GO:0050660)|UDP-N-acetylmuramate dehydrogenase activity (GO:0008762)			breast(1)|endometrium(3)|lung(10)|skin(1)|urinary_tract(1)	16		all_cancers(19;1.09e-40)|all_epithelial(40;2.03e-18)|Breast(86;1.53e-05)|all_lung(227;0.00338)|Renal(207;0.00502)|Ovarian(221;0.00716)|Lung NSC(271;0.012)|Esophageal squamous(248;0.129)|Melanoma(123;0.144)|all_hematologic(139;0.158)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;4.59e-33)|all cancers(36;9.89e-31)|OV - Ovarian serous cystadenocarcinoma(60;7.89e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.63e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0833)		CGCCTCGGCCCGCACGCCAAG	0.706																																					p.P424Q		Atlas-SNP	.											D2HGDH,NS,malignant_melanoma,0,1	D2HGDH	39	.	0			c.C1271A						PASS	.						66.0	56.0	59.0					2																	242695394		2203	4296	6499	SO:0001583	missense	728294	exon9			TCGGCCCGCACGC	AK091725	CCDS33426.1, CCDS74684.1	2p25.3	2010-05-11			ENSG00000180902	ENSG00000180902	1.1.99.-		28358	protein-coding gene	gene with protein product		609186				15070399, 15609246	Standard	NM_152783		Approved	MGC25181, D2HGD, FLJ42195	uc002wce.1	Q8N465	OTTHUMG00000151474	ENST00000321264.4:c.1271C>A	chr2.hg19:g.242695394C>A	ENSP00000315351:p.Pro424Gln	107.0	0.0	.		132.0	7.0	.	NM_152783	B4E3L6|E7ENP2|Q6IQ24|Q8N5Q8	Missense_Mutation	SNP	ENST00000321264.4	hg19	CCDS33426.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	7.370|7.370	0.626555|0.626555	0.14257|0.14257	.|.	.|.	ENSG00000180902|ENSG00000180902	ENST00000321264;ENST00000403782;ENST00000542211|ENST00000445308	D;D|.	0.83075|.	-1.68;-1.68|.	5.31|5.31	2.19|2.19	0.27852|0.27852	FAD-linked oxidase-like, C-terminal (1);FAD-linked oxidase, C-terminal (1);|.	0.575624|.	0.18171|.	N|.	0.149454|.	T|T	0.18045|0.18045	0.0433|0.0433	N|N	0.13098|0.13098	0.295|0.295	0.09310|0.09310	N|N	1|1	B|.	0.10296|.	0.003|.	B|.	0.19666|.	0.026|.	T|T	0.20273|0.20273	-1.0280|-1.0280	10|5	0.22706|.	T|.	0.39|.	-15.5113|-15.5113	3.1273|3.1273	0.06412|0.06412	0.1851:0.541:0.1039:0.17|0.1851:0.541:0.1039:0.17	.|.	424|.	Q8N465|.	D2HDH_HUMAN|.	Q|S	424;290;44|223	ENSP00000315351:P424Q;ENSP00000384723:P290Q|.	ENSP00000315351:P424Q|.	P|R	+|+	2|1	0|0	D2HGDH|D2HGDH	242344067|242344067	0.000000|0.000000	0.05858|0.05858	0.001000|0.001000	0.08648|0.08648	0.021000|0.021000	0.10359|0.10359	-0.148000|-0.148000	0.10219|0.10219	0.618000|0.618000	0.30179|0.30179	0.467000|0.467000	0.42956|0.42956	CCG|CGC	.	.	.	none		0.706	D2HGDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322794.2	NM_152783	
SYNPR	132204	hgsc.bcm.edu	37	3	63466530	63466530	+	Missense_Mutation	SNP	C	C	T			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr3:63466530C>T	ENST00000295894.5	+	2	416	c.47C>T	c.(46-48)gCa>gTa	p.A16V	SYNPR_ENST00000465156.1_Missense_Mutation_p.A16V|SYNPR_ENST00000460711.1_Missense_Mutation_p.A27V|SYNPR_ENST00000479198.1_Missense_Mutation_p.A16V|SYNPR_ENST00000478300.1_Missense_Mutation_p.A36V|SYNPR_ENST00000478744.1_3'UTR|SYNPR-AS1_ENST00000488201.1_RNA	NM_144642.4	NP_653243.1	Q8TBG9	SYNPR_HUMAN	synaptoporin	16	MARVEL. {ECO:0000255|PROSITE- ProRule:PRU00581}.					cell junction (GO:0030054)|integral component of synaptic vesicle membrane (GO:0030285)|neuron projection (GO:0043005)	transporter activity (GO:0005215)			NS(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(3)	8				BRCA - Breast invasive adenocarcinoma(55;0.000918)|KIRC - Kidney renal clear cell carcinoma(15;0.0658)|Kidney(15;0.0904)		TTTGCATTTGCAACATGCGGT	0.433																																					p.A36V	NSCLC(29;1052 1116 20025 32519)	Atlas-SNP	.											.	SYNPR	38	.	0			c.C107T						PASS	.						160.0	161.0	160.0					3																	63466530		1945	4146	6091	SO:0001583	missense	132204	exon3			CATTTGCAACATG	AF411860	CCDS46859.1, CCDS46860.1	3p14.3	2011-07-28			ENSG00000163630	ENSG00000163630			16507	protein-coding gene	gene with protein product						8034131, 12974474	Standard	NM_144642		Approved	MGC26651, SPO	uc003dlp.3	Q8TBG9	OTTHUMG00000158699	ENST00000295894.5:c.47C>T	chr3.hg19:g.63466530C>T	ENSP00000295894:p.Ala16Val	280.0	1.0	.		239.0	94.0	.	NM_001130003	B2R675|G5E9W4	Missense_Mutation	SNP	ENST00000295894.5	hg19	CCDS46860.1	.	.	.	.	.	.	.	.	.	.	C	23.4	4.408930	0.83340	.	.	ENSG00000163630	ENST00000478300;ENST00000295894;ENST00000479198;ENST00000460711;ENST00000465156	T;T;T;T;T	0.76186	-1.0;-1.0;-1.0;-1.0;-1.0	5.38	5.38	0.77491	Marvel (1);MARVEL-like domain (1);	0.105267	0.64402	D	0.000004	D	0.87597	0.6217	M	0.90870	3.155	0.80722	D	1	D;D;D	0.60160	0.979;0.979;0.987	P;P;P	0.58013	0.831;0.831;0.74	D	0.90454	0.4441	10	0.87932	D	0	-3.3962	18.124	0.89580	0.0:1.0:0.0:0.0	.	27;16;36	B3KVD8;Q8TBG9;G5E9W4	.;SYNPR_HUMAN;.	V	36;16;16;27;16	ENSP00000418994:A36V;ENSP00000295894:A16V;ENSP00000418929:A16V;ENSP00000418701:A27V;ENSP00000418123:A16V	ENSP00000295894:A16V	A	+	2	0	SYNPR	63441570	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.487000	0.81328	2.523000	0.85059	0.650000	0.86243	GCA	.	.	.	none		0.433	SYNPR-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000351787.1		
P2RY1	5028	hgsc.bcm.edu	37	3	152553966	152553966	+	Missense_Mutation	SNP	A	A	G			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr3:152553966A>G	ENST00000305097.3	+	1	1231	c.395A>G	c.(394-396)cAt>cGt	p.H132R		NM_002563.3	NP_002554.1	P47900	P2RY1_HUMAN	purinergic receptor P2Y, G-protein coupled, 1	132					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|aging (GO:0007568)|blood coagulation (GO:0007596)|brain development (GO:0007420)|cell surface receptor signaling pathway (GO:0007166)|eating behavior (GO:0042755)|G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of binding (GO:0051100)|negative regulation of norepinephrine secretion (GO:0010700)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|platelet activation (GO:0030168)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of hormone secretion (GO:0046887)|positive regulation of inositol trisphosphate biosynthetic process (GO:0032962)|positive regulation of ion transport (GO:0043270)|positive regulation of penile erection (GO:0060406)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein localization to plasma membrane (GO:0072659)|regulation of receptor activity (GO:0010469)|regulation of vasodilation (GO:0042312)|relaxation of muscle (GO:0090075)|response to growth factor (GO:0070848)|response to mechanical stimulus (GO:0009612)|sensory perception of pain (GO:0019233)|signal transduction involved in regulation of gene expression (GO:0023019)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cell body (GO:0044297)|cell surface (GO:0009986)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	ADP binding (GO:0043531)|ADP-activated nucleotide receptor activity (GO:0045032)|ATP binding (GO:0005524)|ATP-activated nucleotide receptor activity (GO:0045031)|G-protein coupled purinergic nucleotide receptor activity (GO:0045028)|receptor activity (GO:0004872)|scaffold protein binding (GO:0097110)			breast(1)|endometrium(1)|large_intestine(7)|lung(11)|ovary(1)|prostate(2)	23			LUSC - Lung squamous cell carcinoma(72;0.0628)|Lung(72;0.11)			TTCATCTTTCATGTGAACCTC	0.507																																					p.H132R		Atlas-SNP	.											.	P2RY1	49	.	0			c.A395G						PASS	.						79.0	76.0	77.0					3																	152553966		2203	4300	6503	SO:0001583	missense	5028	exon1			TCTTTCATGTGAA	U42029	CCDS3169.1	3q25.2	2012-08-08			ENSG00000169860	ENSG00000169860		"""Purinergic receptors"", ""GPCR / Class A : Purinergic receptors, P2Y"""	8539	protein-coding gene	gene with protein product		601167				8579591	Standard	NM_002563		Approved	P2Y1	uc003ezq.3	P47900	OTTHUMG00000159694	ENST00000305097.3:c.395A>G	chr3.hg19:g.152553966A>G	ENSP00000304767:p.His132Arg	85.0	0.0	.		100.0	34.0	.	NM_002563		Missense_Mutation	SNP	ENST00000305097.3	hg19	CCDS3169.1	.	.	.	.	.	.	.	.	.	.	A	20.6	4.019475	0.75275	.	.	ENSG00000169860	ENST00000305097	T	0.71698	-0.59	5.76	5.76	0.90799	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	D	0.82944	0.5147	M	0.79475	2.455	0.80722	D	1	D	0.58268	0.982	D	0.62955	0.909	D	0.85045	0.0925	10	0.66056	D	0.02	.	15.2728	0.73717	1.0:0.0:0.0:0.0	.	132	P47900	P2RY1_HUMAN	R	132	ENSP00000304767:H132R	ENSP00000304767:H132R	H	+	2	0	P2RY1	154036656	1.000000	0.71417	0.987000	0.45799	0.981000	0.71138	9.210000	0.95106	2.186000	0.69663	0.533000	0.62120	CAT	.	.	.	none		0.507	P2RY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356943.1	NM_002563	
SH3TC1	54436	hgsc.bcm.edu	37	4	8230107	8230107	+	Silent	SNP	C	C	T			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr4:8230107C>T	ENST00000245105.3	+	12	2753	c.2686C>T	c.(2686-2688)Ctg>Ttg	p.L896L	SH3TC1_ENST00000539824.1_Silent_p.L820L	NM_018986.3	NP_061859	Q8TE82	S3TC1_HUMAN	SH3 domain and tetratricopeptide repeats 1	896										NS(1)|breast(3)|endometrium(4)|kidney(4)|large_intestine(6)|lung(10)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	33						GGCTCGGGACCTGGGCCAGCA	0.692																																					p.L896L	NSCLC(145;2298 2623 35616 37297)	Atlas-SNP	.											.	SH3TC1	105	.	0			c.C2686T						PASS	.						37.0	43.0	41.0					4																	8230107		2203	4299	6502	SO:0001819	synonymous_variant	54436	exon12			CGGGACCTGGGCC	AK074093	CCDS3399.1	4p16.1	2013-01-11			ENSG00000125089	ENSG00000125089		"""Tetratricopeptide (TTC) repeat domain containing"""	26009	protein-coding gene	gene with protein product							Standard	NM_018986		Approved	FLJ20356	uc003gkv.4	Q8TE82	OTTHUMG00000160934	ENST00000245105.3:c.2686C>T	chr4.hg19:g.8230107C>T		102.0	0.0	.		116.0	57.0	.	NM_018986	Q4W5G5	Silent	SNP	ENST00000245105.3	hg19	CCDS3399.1																																																																																			.	.	.	none		0.692	SH3TC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206991.2	NM_018986	
ACOX3	8310	hgsc.bcm.edu	37	4	8368755	8368755	+	Missense_Mutation	SNP	C	C	A			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr4:8368755C>A	ENST00000356406.5	-	18	2113	c.2036G>T	c.(2035-2037)cGg>cTg	p.R679L	ACOX3_ENST00000503233.1_Missense_Mutation_p.R679L|ACOX3_ENST00000413009.2_3'UTR|ACOX3_ENST00000515797.1_5'UTR	NM_003501.2	NP_003492.2	O15254	ACOX3_HUMAN	acyl-CoA oxidase 3, pristanoyl	679					cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|small molecule metabolic process (GO:0044281)	membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	acyl-CoA dehydrogenase activity (GO:0003995)|flavin adenine dinucleotide binding (GO:0050660)|pristanoyl-CoA oxidase activity (GO:0016402)|receptor binding (GO:0005102)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(9)|lung(17)|prostate(1)|skin(3)|stomach(1)	42						CCAGGATGCCCGCTCCAACAC	0.483																																					p.R679L		Atlas-SNP	.											.	ACOX3	70	.	0			c.G2036T						PASS	.						105.0	97.0	99.0					4																	8368755		2203	4300	6503	SO:0001583	missense	8310	exon18			GATGCCCGCTCCA	Y11411	CCDS3401.1, CCDS47017.1	4p15.3	2010-04-30	2010-04-30		ENSG00000087008	ENSG00000087008	1.3.3.6		121	protein-coding gene	gene with protein product		603402	"""acyl-Coenzyme A oxidase 3, pristanoyl"""			9271077	Standard	NM_003501		Approved		uc003glc.4	O15254	OTTHUMG00000090509	ENST00000356406.5:c.2036G>T	chr4.hg19:g.8368755C>A	ENSP00000348775:p.Arg679Leu	93.0	0.0	.		128.0	8.0	.	NM_003501	Q96AJ8	Missense_Mutation	SNP	ENST00000356406.5	hg19	CCDS3401.1	.	.	.	.	.	.	.	.	.	.	C	24.5	4.543529	0.86022	.	.	ENSG00000087008	ENST00000356406;ENST00000503233	T;T	0.49720	0.77;0.77	5.16	5.16	0.70880	Acyl-CoA oxidase, C-terminal (1);Acyl-CoA dehydrogenase/oxidase C-terminal (1);	0.000000	0.64402	D	0.000002	T	0.74801	0.3764	M	0.91972	3.26	0.58432	D	0.99999	D	0.89917	1.0	D	0.97110	1.0	T	0.79313	-0.1855	10	0.46703	T	0.11	-25.9722	16.1529	0.81634	0.0:1.0:0.0:0.0	.	679	O15254	ACOX3_HUMAN	L	679	ENSP00000348775:R679L;ENSP00000421625:R679L	ENSP00000348775:R679L	R	-	2	0	ACOX3	8419655	0.997000	0.39634	0.064000	0.19789	0.008000	0.06430	5.682000	0.68182	2.411000	0.81874	0.655000	0.94253	CGG	.	.	.	none		0.483	ACOX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206997.4		
LAP3	51056	hgsc.bcm.edu	37	4	17586652	17586653	+	Missense_Mutation	DNP	AC	AC	GA			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	A|C	A|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr4:17586652_17586653AC>GA	ENST00000226299.4	+	6	871_872	c.597_598AC>GA	c.(595-600)gcACgc>gcGAgc	p.R200S	AC006160.5_ENST00000511010.1_RNA|LAP3_ENST00000606142.1_Missense_Mutation_p.R169S	NM_015907.2	NP_056991.2	P28838	AMPL_HUMAN	leucine aminopeptidase 3	200					proteolysis (GO:0006508)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|trans-Golgi network (GO:0005802)	aminopeptidase activity (GO:0004177)|manganese ion binding (GO:0030145)|metalloexopeptidase activity (GO:0008235)			endometrium(4)|kidney(1)|large_intestine(4)|lung(10)|urinary_tract(1)	20						AGAACTTGGCACGCCAATTGAT	0.475																																					p.A199A|p.R200S		Atlas-SNP	.											.|LAP3,NS,carcinoma,0,1	LAP3	50	.	0			c.A597G|c.C598A						PASS	.																																			SO:0001583	missense	51056	exon6			CTTGGCACGCCAA|TTGGCACGCCAAT	AF061738	CCDS3422.1	4p15.33	2012-07-25	2003-09-12		ENSG00000002549	ENSG00000002549	3.4.11.1		18449	protein-coding gene	gene with protein product		170250	"""peptidase S"""	PEPS		6350155, 689684	Standard	NM_015907		Approved	LAPEP, LAP	uc003gph.1	P28838	OTTHUMG00000048214	Exception_encountered	chr4.hg19:g.17586652_17586653delinsGA	ENSP00000226299:p.Arg200Ser	66.0|69.0	0.0|1.0	.		89.0|91.0	23.0|24.0	.	NM_015907	B3KMQ3|Q6IAM6|Q6P0L6|Q9UQE3	Silent|Missense_Mutation	SNP	ENST00000226299.4	hg19	CCDS3422.1																																																																																			.	.	.	none		0.475	LAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250365.1		
CCDC110	256309	hgsc.bcm.edu	37	4	186382305	186382305	+	Silent	SNP	C	C	A	rs141194686	byFrequency	TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr4:186382305C>A	ENST00000307588.3	-	5	321	c.246G>T	c.(244-246)tcG>tcT	p.S82S	CCDC110_ENST00000393540.3_Intron|CCDC110_ENST00000507501.1_5'UTR|CCDC110_ENST00000510617.1_Silent_p.S82S	NM_152775.3	NP_689988.1	Q8TBZ0	CC110_HUMAN	coiled-coil domain containing 110	82						nucleus (GO:0005634)		p.S82S(1)		NS(1)|breast(1)|central_nervous_system(2)|endometrium(6)|kidney(3)|large_intestine(8)|lung(9)	30		all_lung(41;1.3e-11)|Lung NSC(41;2.25e-11)|Melanoma(20;7.86e-05)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|Prostate(90;0.0283)|Colorectal(36;0.0381)|all_hematologic(60;0.0749)		OV - Ovarian serous cystadenocarcinoma(60;1.13e-10)|BRCA - Breast invasive adenocarcinoma(30;8.01e-05)|GBM - Glioblastoma multiforme(59;0.00014)|STAD - Stomach adenocarcinoma(60;0.000777)|LUSC - Lung squamous cell carcinoma(40;0.00921)|COAD - Colon adenocarcinoma(29;0.0105)|READ - Rectum adenocarcinoma(43;0.164)		CACTGATTTCCGACTGTACCT	0.289																																					p.S82S		Atlas-SNP	.											CCDC110,rectum,carcinoma,0,1	CCDC110	78	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G246T						PASS	.						90.0	89.0	89.0					4																	186382305		2203	4296	6499	SO:0001819	synonymous_variant	256309	exon5			GATTTCCGACTGT	AB080722	CCDS3843.1, CCDS47170.1	4q35.1	2010-12-24			ENSG00000168491	ENSG00000168491			28504	protein-coding gene	gene with protein product	"""cancer/testis antigen 52"""	609488				18160854	Standard	NM_152775		Approved	KM-HN-1, MGC33607, CT52	uc003ixu.4	Q8TBZ0	OTTHUMG00000160415	ENST00000307588.3:c.246G>T	chr4.hg19:g.186382305C>A		97.0	1.0	.		171.0	8.0	.	NM_152775	Q86YI9|Q8N7W0	Silent	SNP	ENST00000307588.3	hg19	CCDS3843.1																																																																																			.	C|0.999;T|0.001	.	alt		0.289	CCDC110-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000360519.2	NM_152775	
WDR70	55100	hgsc.bcm.edu	37	5	37381726	37381726	+	Silent	SNP	C	C	T			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr5:37381726C>T	ENST00000265107.4	+	3	270	c.114C>T	c.(112-114)gaC>gaT	p.D38D	WDR70_ENST00000504564.1_Silent_p.D38D	NM_018034.2	NP_060504.1	Q9NW82	WDR70_HUMAN	WD repeat domain 70	38							enzyme binding (GO:0019899)			central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(5)|lung(18)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	37	all_lung(31;0.000285)		COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			GCACATTTGACTTGGAAGCAA	0.378																																					p.D38D		Atlas-SNP	.											.	WDR70	76	.	0			c.C114T						PASS	.						119.0	127.0	124.0					5																	37381726		2203	4300	6503	SO:0001819	synonymous_variant	55100	exon3			ATTTGACTTGGAA	BC009648	CCDS34147.1	5p13.2	2013-01-09			ENSG00000082068	ENSG00000082068		"""WD repeat domain containing"""	25495	protein-coding gene	gene with protein product						12477932	Standard	NM_018034		Approved	FLJ10233	uc003jkv.3	Q9NW82	OTTHUMG00000162263	ENST00000265107.4:c.114C>T	chr5.hg19:g.37381726C>T		166.0	0.0	.		220.0	71.0	.	NM_018034	Q9H053	Silent	SNP	ENST00000265107.4	hg19	CCDS34147.1																																																																																			.	.	.	none		0.378	WDR70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368294.1	NM_018034	
SLCO4C1	353189	hgsc.bcm.edu	37	5	101599479	101599479	+	Missense_Mutation	SNP	C	C	A			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr5:101599479C>A	ENST00000310954.6	-	4	1094	c.808G>T	c.(808-810)Ggt>Tgt	p.G270C		NM_180991.4	NP_851322.3			solute carrier organic anion transporter family, member 4C1											breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(16)|ovary(1)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(5)	50		all_cancers(142;1.86e-08)|all_epithelial(76;5.24e-12)|Prostate(80;0.00124)|Colorectal(57;0.00332)|Ovarian(225;0.024)|Lung NSC(167;0.0402)|all_lung(232;0.0486)		Epithelial(69;4.07e-14)|COAD - Colon adenocarcinoma(37;0.00986)		ATAGCATAACCGGTTCCTAGA	0.378																																					p.G270C		Atlas-SNP	.											.	SLCO4C1	113	.	0			c.G808T						PASS	.						129.0	121.0	123.0					5																	101599479		2203	4300	6503	SO:0001583	missense	353189	exon4			CATAACCGGTTCC	AY273896	CCDS34205.1	5q21	2013-05-22	2003-11-25		ENSG00000173930	ENSG00000173930		"""Solute carriers"""	23612	protein-coding gene	gene with protein product		609013					Standard	NM_180991		Approved	SLC21A20, OATP4C1, OATPX, OATP-H	uc003knm.3	Q6ZQN7	OTTHUMG00000162757	ENST00000310954.6:c.808G>T	chr5.hg19:g.101599479C>A	ENSP00000309741:p.Gly270Cys	131.0	0.0	.		137.0	9.0	.	NM_180991		Missense_Mutation	SNP	ENST00000310954.6	hg19	CCDS34205.1	.	.	.	.	.	.	.	.	.	.	C	14.68	2.607691	0.46527	.	.	ENSG00000173930	ENST00000310954	T	0.80824	-1.42	5.24	5.24	0.73138	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.085636	0.49916	D	0.000129	D	0.85283	0.5661	M	0.66506	2.035	0.38375	D	0.944971	P	0.34546	0.456	P	0.45946	0.498	D	0.85158	0.0990	10	0.39692	T	0.17	.	19.1822	0.93628	0.0:1.0:0.0:0.0	.	270	Q6ZQN7	SO4C1_HUMAN	C	270	ENSP00000309741:G270C	ENSP00000309741:G270C	G	-	1	0	SLCO4C1	101627378	1.000000	0.71417	1.000000	0.80357	0.021000	0.10359	5.387000	0.66243	2.598000	0.87819	0.650000	0.86243	GGT	.	.	.	none		0.378	SLCO4C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370332.1	NM_180991	
PSD2	84249	hgsc.bcm.edu	37	5	139216448	139216448	+	Missense_Mutation	SNP	G	G	T			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr5:139216448G>T	ENST00000274710.3	+	10	1661	c.1456G>T	c.(1456-1458)Ggg>Tgg	p.G486W		NM_032289.2	NP_115665.1	Q9BQI7	PSD2_HUMAN	pleckstrin and Sec7 domain containing 2	486					neuron differentiation (GO:0030182)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|phospholipid binding (GO:0005543)			breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(10)|liver(2)|lung(15)|ovary(1)|prostate(2)	38			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGACAAGTTCGGGACAGGCAC	0.602																																					p.G486W		Atlas-SNP	.											.	PSD2	88	.	0			c.G1456T						PASS	.						164.0	148.0	154.0					5																	139216448		2203	4300	6503	SO:0001583	missense	84249	exon10			AAGTTCGGGACAG	AL136559	CCDS4216.1	5q31.3	2013-01-10			ENSG00000146005	ENSG00000146005		"""Pleckstrin homology (PH) domain containing"""	19092	protein-coding gene	gene with protein product							Standard	NM_032289		Approved	DKFZp761B0514	uc003leu.1	Q9BQI7	OTTHUMG00000129240	ENST00000274710.3:c.1456G>T	chr5.hg19:g.139216448G>T	ENSP00000274710:p.Gly486Trp	152.0	0.0	.		108.0	8.0	.	NM_032289	D3DQD3|Q8N3J8	Missense_Mutation	SNP	ENST00000274710.3	hg19	CCDS4216.1	.	.	.	.	.	.	.	.	.	.	G	23.9	4.470024	0.84533	.	.	ENSG00000146005	ENST00000274710	T	0.13307	2.6	5.37	5.37	0.77165	.	0.053535	0.85682	D	0.000000	T	0.30262	0.0759	L	0.53249	1.67	0.58432	D	0.999998	D	0.67145	0.996	P	0.59288	0.855	T	0.01030	-1.1475	10	0.87932	D	0	.	17.2612	0.87070	0.0:0.0:1.0:0.0	.	486	Q9BQI7	PSD2_HUMAN	W	486	ENSP00000274710:G486W	ENSP00000274710:G486W	G	+	1	0	PSD2	139196632	1.000000	0.71417	1.000000	0.80357	0.936000	0.57629	7.214000	0.77958	2.524000	0.85096	0.555000	0.69702	GGG	.	.	.	none		0.602	PSD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251339.1	NM_032289	
APBB3	10307	hgsc.bcm.edu	37	5	139938231	139938231	+	Missense_Mutation	SNP	C	C	A			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr5:139938231C>A	ENST00000357560.4	-	13	1843	c.1400G>T	c.(1399-1401)cGg>cTg	p.R467L	SRA1_ENST00000336283.6_5'Flank|SRA1_ENST00000520427.1_5'Flank|APBB3_ENST00000356738.2_Missense_Mutation_p.R472L|APBB3_ENST00000508496.2_Missense_Mutation_p.R244L|APBB3_ENST00000358580.5_3'UTR|APBB3_ENST00000354402.5_Missense_Mutation_p.R474L|APBB3_ENST00000412920.3_Missense_Mutation_p.R465L	NM_006051.3|NM_133173.2	NP_006042.3|NP_573419.2	O95704	APBB3_HUMAN	amyloid beta (A4) precursor protein-binding, family B, member 3	467						actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(2)|prostate(1)	11			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GAAGACACCCCGCTTTCGAGG	0.607																																					p.R474L		Atlas-SNP	.											APBB3,NS,carcinoma,0,1	APBB3	34	.	0			c.G1421T						PASS	.						76.0	84.0	81.0					5																	139938231		2203	4300	6503	SO:0001583	missense	10307	exon12			ACACCCCGCTTTC	AB018247	CCDS4227.1, CCDS4228.1, CCDS4229.1, CCDS47279.1	5q31	2008-02-05			ENSG00000113108	ENSG00000113108			20708	protein-coding gene	gene with protein product		602711				9407065	Standard	NM_133172		Approved	FE65L2	uc003lgd.1	O95704	OTTHUMG00000129504	ENST00000357560.4:c.1400G>T	chr5.hg19:g.139938231C>A	ENSP00000350171:p.Arg467Leu	163.0	0.0	.		132.0	8.0	.	NM_006051	B3KQN9|Q08AG4|Q96Q18|Q9BYD4|Q9NYX6|Q9NYX7|Q9NYX8	Missense_Mutation	SNP	ENST00000357560.4	hg19	CCDS4229.1	.	.	.	.	.	.	.	.	.	.	C	22.6	4.308074	0.81247	.	.	ENSG00000113108	ENST00000356738;ENST00000354402;ENST00000357560;ENST00000508496;ENST00000412920	T;T;T;T;T	0.51574	1.74;1.73;1.74;0.7;1.74	5.03	5.03	0.67393	.	0.151653	0.37906	N	0.001888	T	0.55065	0.1897	L	0.27053	0.805	0.80722	D	1	D;D	0.76494	0.995;0.999	P;D	0.83275	0.878;0.996	T	0.52132	-0.8616	9	.	.	.	-17.5903	15.2742	0.73728	0.0:1.0:0.0:0.0	.	465;472	O95704-2;O95704-3	.;.	L	472;474;467;244;465	ENSP00000349177:R472L;ENSP00000346378:R474L;ENSP00000350171:R467L;ENSP00000444013:R244L;ENSP00000402591:R465L	.	R	-	2	0	APBB3	139918415	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	3.647000	0.54403	2.350000	0.79820	0.455000	0.32223	CGG	.	.	.	none		0.607	APBB3-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251677.2	NM_006051	
MDGA1	266727	hgsc.bcm.edu	37	6	37622577	37622577	+	Splice_Site	SNP	C	C	A			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr6:37622577C>A	ENST00000434837.3	-	5	1889	c.711G>T	c.(709-711)acG>acT	p.T237T	MDGA1_ENST00000505425.1_Splice_Site_p.T237T|MDGA1_ENST00000297153.7_Splice_Site_p.T237T	NM_153487.3	NP_705691.1	Q8NFP4	MDGA1_HUMAN	MAM domain containing glycosylphosphatidylinositol anchor 1	237					brain development (GO:0007420)|cerebral cortex radially oriented cell migration (GO:0021799)|neuron migration (GO:0001764)|spinal cord association neuron differentiation (GO:0021527)	anchored component of plasma membrane (GO:0046658)|extracellular space (GO:0005615)		p.T237T(1)		central_nervous_system(2)|endometrium(6)|kidney(3)|large_intestine(12)|lung(11)|prostate(1)|skin(2)|urinary_tract(1)	38						TGCCTGTACCCGTGGTGTTGG	0.602																																					p.T237T		Atlas-SNP	.											MDGA1,NS,carcinoma,0,2	MDGA1	104	.	1	Substitution - coding silent(1)	lung(1)	c.G711T						PASS	.						214.0	225.0	222.0					6																	37622577		2169	4258	6427	SO:0001630	splice_region_variant	266727	exon5			TGTACCCGTGGTG	AF478693	CCDS47417.1	6p21	2013-01-29			ENSG00000112139	ENSG00000112139		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	19267	protein-coding gene	gene with protein product		609626				15922729, 15019943	Standard	NM_153487		Approved	GPIM, MAMDC3	uc003onu.1	Q8NFP4	OTTHUMG00000014626	ENST00000434837.3:c.712+1G>T	chr6.hg19:g.37622577C>A		282.0	2.0	.		263.0	12.0	.	NM_153487	A6NHG0|Q8NBE3	Silent	SNP	ENST00000434837.3	hg19	CCDS47417.1																																																																																			.	.	.	none		0.602	MDGA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040419.3		Silent
TULP4	56995	hgsc.bcm.edu	37	6	158873218	158873218	+	Silent	SNP	C	C	A			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr6:158873218C>A	ENST00000367097.3	+	5	2134	c.777C>A	c.(775-777)acC>acA	p.T259T	TULP4_ENST00000367094.2_Silent_p.T259T	NM_020245.4	NP_064630.2	Q9NRJ4	TULP4_HUMAN	tubby like protein 4	259					intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)|regulation of transcription, DNA-templated (GO:0006355)|response to nutrient (GO:0007584)	cytoplasm (GO:0005737)	sequence-specific DNA binding transcription factor activity (GO:0003700)	p.T259T(1)		endometrium(7)|kidney(2)|large_intestine(15)|lung(17)|ovary(1)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	49		Breast(66;0.000781)|Ovarian(120;0.0308)|Lung SC(201;0.164)|Prostate(117;0.171)		OV - Ovarian serous cystadenocarcinoma(65;1.64e-18)|BRCA - Breast invasive adenocarcinoma(81;2.67e-05)		CTCTGCTCACCGTCAGCTTCA	0.537																																					p.T259T		Atlas-SNP	.											.	TULP4	137	.	1	Substitution - coding silent(1)	lung(1)	c.C777A						PASS	.						185.0	148.0	161.0					6																	158873218		2203	4300	6503	SO:0001819	synonymous_variant	56995	exon5			GCTCACCGTCAGC		CCDS34561.1, CCDS34562.1	6q25-q26	2013-01-10			ENSG00000130338	ENSG00000130338		"""WD repeat domain containing"""	15530	protein-coding gene	gene with protein product						11595174	Standard	NM_020245		Approved	TUSP, KIAA1397	uc003qrf.3	Q9NRJ4	OTTHUMG00000015910	ENST00000367097.3:c.777C>A	chr6.hg19:g.158873218C>A		169.0	0.0	.		153.0	7.0	.	NM_020245	Q5T3M2|Q5T3M3|Q9HD22|Q9P2F0	Silent	SNP	ENST00000367097.3	hg19	CCDS34561.1																																																																																			.	.	.	none		0.537	TULP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042869.1	NM_020245	
SLC13A1	6561	hgsc.bcm.edu	37	7	122765636	122765636	+	Silent	SNP	A	A	G			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr7:122765636A>G	ENST00000194130.2	-	11	1266	c.1227T>C	c.(1225-1227)ccT>ccC	p.P409P	SLC13A1_ENST00000539873.1_3'UTR	NM_022444.3	NP_071889.2	Q9BZW2	S13A1_HUMAN	solute carrier family 13 (sodium/sulfate symporter), member 1	409					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sodium:sulfate symporter activity (GO:0015382)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|lung(20)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	45					Succinic acid(DB00139)	TTTCTCCTGTAGGTGTAGTTT	0.368																																					p.P409P		Atlas-SNP	.											.	SLC13A1	110	.	0			c.T1227C						PASS	.						123.0	129.0	127.0					7																	122765636		2203	4300	6503	SO:0001819	synonymous_variant	6561	exon11			TCCTGTAGGTGTA		CCDS5786.1	7q31.32	2013-07-18	2013-07-18		ENSG00000081800	ENSG00000081800		"""Solute carriers"""	10916	protein-coding gene	gene with protein product		606193	"""solute carrier family 13 (sodium/sulphate symporters), member 1"""			11161786	Standard	NM_022444		Approved	NaSi-1, NAS1	uc003vkm.3	Q9BZW2	OTTHUMG00000157087	ENST00000194130.2:c.1227T>C	chr7.hg19:g.122765636A>G		192.0	0.0	.		384.0	147.0	.	NM_022444	Q9H5Z0	Silent	SNP	ENST00000194130.2	hg19	CCDS5786.1																																																																																			.	.	.	none		0.368	SLC13A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347404.1	NM_022444	
AKR1B15	441282	hgsc.bcm.edu	37	7	134260255	134260255	+	Missense_Mutation	SNP	G	G	T			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr7:134260255G>T	ENST00000457545.2	+	7	857	c.597G>T	c.(595-597)ttG>ttT	p.L199F	AKR1B15_ENST00000423958.1_Missense_Mutation_p.L171F	NM_001080538.2	NP_001074007.2	C9JRZ8	AK1BF_HUMAN	aldo-keto reductase family 1, member B15	199							oxidoreductase activity (GO:0016491)			endometrium(1)|kidney(3)|large_intestine(2)|lung(10)|ovary(1)|urinary_tract(1)	18						AGAGGCTCTTGAACAAACCTG	0.463																																					p.L199F		Atlas-SNP	.											.	AKR1B15	105	.	0			c.G597T						PASS	.						71.0	77.0	75.0					7																	134260255		2203	4300	6503	SO:0001583	missense	441282	exon7			GCTCTTGAACAAA		CCDS47715.1, CCDS47715.2	7q33	2009-09-09			ENSG00000227471	ENSG00000227471		"""Aldo-keto reductases"""	37281	protein-coding gene	gene with protein product							Standard	NM_001080538		Approved		uc011kpr.2	C9JRZ8	OTTHUMG00000155376	ENST00000457545.2:c.597G>T	chr7.hg19:g.134260255G>T	ENSP00000389289:p.Leu199Phe	164.0	0.0	.		265.0	97.0	.	NM_001080538	C9J3V2	Missense_Mutation	SNP	ENST00000457545.2	hg19	CCDS47715.2	.	.	.	.	.	.	.	.	.	.	G	14.27	2.484711	0.44147	.	.	ENSG00000227471	ENST00000457545;ENST00000423958	T;T	0.21031	2.03;2.03	3.82	0.986	0.19784	NADP-dependent oxidoreductase domain (3);	.	.	.	.	T	0.42832	0.1220	M	0.80508	2.5	0.47308	D	0.999386	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.23619	-1.0183	9	0.87932	D	0	.	7.683	0.28524	0.2865:0.0:0.7135:0.0	.	171;199	C9JRZ8-2;C9JRZ8	.;AK1BF_HUMAN	F	199;171	ENSP00000389289:L199F;ENSP00000397009:L171F	ENSP00000397009:L171F	L	+	3	2	AKR1B15	133910795	0.998000	0.40836	0.832000	0.32986	0.573000	0.36030	0.344000	0.19962	-0.004000	0.14419	0.543000	0.68304	TTG	.	.	.	none		0.463	AKR1B15-001	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000339726.2		
BMP1	649	hgsc.bcm.edu	37	8	22058658	22058658	+	Intron	SNP	G	G	T			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr8:22058658G>T	ENST00000306385.5	+	16	2777				BMP1_ENST00000354870.5_Intron|BMP1_ENST00000306349.8_Missense_Mutation_p.R712L	NM_006129.4	NP_006120.1	P13497	BMP1_HUMAN	bone morphogenetic protein 1						cartilage condensation (GO:0001502)|cell differentiation (GO:0030154)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|lipoprotein metabolic process (GO:0042157)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|positive regulation of cartilage development (GO:0061036)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|membrane-bounded vesicle (GO:0031988)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|peptidase activity (GO:0008233)|zinc ion binding (GO:0008270)	p.R712L(1)		breast(1)|endometrium(7)|kidney(2)|large_intestine(7)|lung(7)|ovary(2)|prostate(1)|skin(3)	30				Colorectal(74;0.00229)|COAD - Colon adenocarcinoma(73;0.0661)|READ - Rectum adenocarcinoma(644;0.11)		CAGCCCCCTCGGGGACGCCCC	0.627																																					p.R712L		Atlas-SNP	.											BMP1_ENST00000306349,NS,carcinoma,0,1	BMP1	131	.	1	Substitution - Missense(1)	lung(1)	c.G2135T						PASS	.						67.0	81.0	76.0					8																	22058658		2203	4300	6503	SO:0001627	intron_variant	649	exon16			CCCCTCGGGGACG		CCDS6026.1, CCDS34856.1	8p21	2013-02-06	2004-08-09		ENSG00000168487	ENSG00000168487	3.4.24.19	"""Bone morphogenetic proteins"""	1067	protein-coding gene	gene with protein product	"""procollagen C-endopeptidase"""	112264	"""procollagen C-endopeptidase"""	PCOLC		2004778	Standard	NM_006129		Approved		uc003xbg.3	P13497	OTTHUMG00000097761	ENST00000306385.5:c.2108-658G>T	chr8.hg19:g.22058658G>T		221.0	2.0	.		165.0	7.0	.	NM_001199	A8K6F5|B2RN46|D3DSR0|Q13292|Q13872|Q14874|Q99421|Q99422|Q99423|Q9UL38	Missense_Mutation	SNP	ENST00000306385.5	hg19	CCDS6026.1	.	.	.	.	.	.	.	.	.	.	G	18.14	3.557340	0.65425	.	.	ENSG00000168487	ENST00000306349	T	0.61627	0.09	4.16	4.16	0.48862	.	.	.	.	.	T	0.38321	0.1036	N	0.08118	0	0.80722	D	1	P;P	0.37612	0.602;0.458	B;B	0.37780	0.258;0.192	T	0.46331	-0.9199	9	0.62326	D	0.03	.	11.9617	0.53011	0.0:0.0:1.0:0.0	.	785;712	Q59F71;P13497-2	.;.	L	712	ENSP00000306121:R712L	ENSP00000306121:R712L	R	+	2	0	BMP1	22114603	0.999000	0.42202	1.000000	0.80357	0.990000	0.78478	3.757000	0.55212	1.854000	0.53819	0.407000	0.27541	CGG	.	.	.	none		0.627	BMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214995.2	NM_006132	
OXR1	55074	hgsc.bcm.edu	37	8	107718929	107718929	+	Silent	SNP	T	T	C			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr8:107718929T>C	ENST00000442977.2	+	8	1282	c.1183T>C	c.(1183-1185)Tta>Cta	p.L395L	OXR1_ENST00000312046.6_Silent_p.L387L|OXR1_ENST00000445937.1_Silent_p.L394L|OXR1_ENST00000452423.2_5'UTR|OXR1_ENST00000531443.1_Silent_p.L394L|OXR1_ENST00000517566.2_Silent_p.L394L|OXR1_ENST00000497705.1_Silent_p.L327L	NM_001198532.1	NP_001185461.1	Q8N573	OXR1_HUMAN	oxidation resistance 1	395					adult walking behavior (GO:0007628)|cellular response to hydroperoxide (GO:0071447)|negative regulation of neuron apoptotic process (GO:0043524)|response to oxidative stress (GO:0006979)	mitochondrion (GO:0005739)|nucleolus (GO:0005730)	oxidoreductase activity (GO:0016491)			NS(2)|breast(2)|endometrium(2)|large_intestine(9)|lung(10)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	31			OV - Ovarian serous cystadenocarcinoma(57;1.81e-09)			TCCTGGTCACTTAAGATCTGA	0.368																																					p.L395L		Atlas-SNP	.											.	OXR1	190	.	0			c.T1183C						PASS	.						86.0	89.0	88.0					8																	107718929		2203	4300	6503	SO:0001819	synonymous_variant	55074	exon8			GGTCACTTAAGAT	AF309387	CCDS6304.2, CCDS47909.1, CCDS56547.1, CCDS56548.1, CCDS56549.1, CCDS56550.1	8q23	2013-03-14			ENSG00000164830	ENSG00000164830			15822	protein-coding gene	gene with protein product	"""TBC/LysM-associated domain containing 3"""	605609				11114193	Standard	NM_181354		Approved	TLDC3	uc011lht.2	Q8N573	OTTHUMG00000167682	ENST00000442977.2:c.1183T>C	chr8.hg19:g.107718929T>C		63.0	0.0	.		71.0	19.0	.	NM_001198532	A6NK11|A8KA34|B3KXL1|B7Z402|B7Z8N5|D3HIS6|Q3LIB5|Q6ZVK9|Q8N8V0|Q9H266|Q9NWC7	Silent	SNP	ENST00000442977.2	hg19	CCDS56548.1																																																																																			.	.	.	none		0.368	OXR1-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_181354	
COL22A1	169044	hgsc.bcm.edu	37	8	139737673	139737673	+	Missense_Mutation	SNP	C	C	T			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr8:139737673C>T	ENST00000303045.6	-	24	2596	c.2150G>A	c.(2149-2151)gGa>gAa	p.G717E	COL22A1_ENST00000435777.1_Missense_Mutation_p.G717E	NM_152888.1	NP_690848.1	Q8NFW1	COMA1_HUMAN	collagen, type XXII, alpha 1	717	Collagen-like 5.|Gly-rich.|Pro-rich.				extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(14)|large_intestine(29)|lung(107)|ovary(13)|pancreas(1)|prostate(3)|skin(12)|upper_aerodigestive_tract(15)|urinary_tract(4)	211	all_epithelial(106;1.55e-12)|Lung NSC(106;1.67e-05)|all_lung(105;3.39e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0517)			ACCAGGGGGTCCTGGAGGGCC	0.582										HNSCC(7;0.00092)																											p.G717E		Atlas-SNP	.											COL22A1,NS,carcinoma,0,1	COL22A1	390	.	0			c.G2150A						PASS	.						50.0	57.0	55.0					8																	139737673		2203	4300	6503	SO:0001583	missense	169044	exon24			GGGGGTCCTGGAG	AF406780	CCDS6376.1	8q24.3	2013-01-16			ENSG00000169436	ENSG00000169436		"""Collagens"""	22989	protein-coding gene	gene with protein product		610026					Standard	NM_152888		Approved		uc003yvd.3	Q8NFW1	OTTHUMG00000150035	ENST00000303045.6:c.2150G>A	chr8.hg19:g.139737673C>T	ENSP00000303153:p.Gly717Glu	131.0	0.0	.		127.0	44.0	.	NM_152888	B7ZMH0|C9K0G4|Q8IVT9	Missense_Mutation	SNP	ENST00000303045.6	hg19	CCDS6376.1	.	.	.	.	.	.	.	.	.	.	C	16.16	3.043885	0.55110	.	.	ENSG00000169436	ENST00000303045;ENST00000435777;ENST00000545577	D;D	0.99353	-5.77;-5.14	4.8	4.8	0.61643	.	0.000000	0.49305	D	0.000157	D	0.99722	0.9892	H	0.99719	4.725	0.52099	D	0.999949	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.96966	0.9705	10	0.87932	D	0	.	14.0818	0.64929	0.0:1.0:0.0:0.0	.	717;717	Q8NFW1-2;Q8NFW1	.;COMA1_HUMAN	E	717;717;430	ENSP00000303153:G717E;ENSP00000387655:G717E	ENSP00000303153:G717E	G	-	2	0	COL22A1	139806855	1.000000	0.71417	1.000000	0.80357	0.892000	0.51952	3.436000	0.52856	2.567000	0.86603	0.655000	0.94253	GGA	.	.	.	none		0.582	COL22A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000315905.2	XM_291257	
KIAA0020	9933	hgsc.bcm.edu	37	9	2811557	2811557	+	Missense_Mutation	SNP	C	C	A	rs2270889	byFrequency	TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr9:2811557C>A	ENST00000397885.2	-	15	1645	c.1439G>T	c.(1438-1440)cGg>cTg	p.R480L		NM_014878.4	NP_055693.4	Q15397	K0020_HUMAN	KIAA0020	480	PUM-HD. {ECO:0000255|PROSITE- ProRule:PRU00318}.		R -> Q (in dbSNP:rs2270889).			endoplasmic reticulum (GO:0005783)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(4)|ovary(1)	21				GBM - Glioblastoma multiforme(50;0.0319)		TAGGAGCTCCCGTCTGCGGAC	0.438																																					p.R480L		Atlas-SNP	.											.	KIAA0020	56	.	0			c.G1439T						PASS	.						99.0	97.0	98.0					9																	2811557		2203	4300	6503	SO:0001583	missense	9933	exon15			AGCTCCCGTCTGC	AL832239	CCDS6448.2	9p24.2	2012-11-29			ENSG00000080608	ENSG00000080608			29676	protein-coding gene	gene with protein product	"""penguin homolog (Drosophila)"", ""minor histocompatibility antigen HA-8"""	609960				7584026, 7584028, 21266351	Standard	NM_014878		Approved	XTP5, PEN, PUF6, hPUF-A, HA-8	uc003zhp.1	Q15397	OTTHUMG00000019450	ENST00000397885.2:c.1439G>T	chr9.hg19:g.2811557C>A	ENSP00000380982:p.Arg480Leu	150.0	0.0	.		140.0	7.0	.	NM_014878	A8K804|Q547G7|Q5SZY9|Q6IB47|Q96B27|Q96L78|Q96L79|Q96L80	Missense_Mutation	SNP	ENST00000397885.2	hg19	CCDS6448.2	.	.	.	.	.	.	.	.	.	.	C	17.99	3.523165	0.64747	.	.	ENSG00000080608	ENST00000397885	T	0.45668	0.89	5.97	4.9	0.64082	CPL (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.246724	0.42420	D	0.000701	T	0.37404	0.1002	L	0.48642	1.525	0.09310	N	1	B;P	0.38582	0.322;0.638	B;B	0.40741	0.258;0.339	T	0.29518	-1.0009	10	0.36615	T	0.2	-23.6222	10.0978	0.42486	0.0:0.8152:0.0:0.1848	.	340;480	B2RDG4;Q15397	.;K0020_HUMAN	L	480	ENSP00000380982:R480L	ENSP00000380982:R480L	R	-	2	0	KIAA0020	2801557	0.006000	0.16342	0.339000	0.25562	0.986000	0.74619	0.406000	0.21032	2.836000	0.97738	0.655000	0.94253	CGG	.	C|0.996;T|0.004	.	alt		0.438	KIAA0020-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051529.3	NM_014878	
ADD3	120	hgsc.bcm.edu	37	10	111860443	111860443	+	Missense_Mutation	SNP	C	C	G			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr10:111860443C>G	ENST00000356080.4	+	2	399	c.32C>G	c.(31-33)aCc>aGc	p.T11S	ADD3_ENST00000497125.1_3'UTR|ADD3_ENST00000360162.3_Missense_Mutation_p.T11S|ADD3_ENST00000277900.8_Missense_Mutation_p.T11S	NM_016824.3	NP_058432.1	Q9UEY8	ADDG_HUMAN	adducin 3 (gamma)	11						cell cortex (GO:0005938)|cell-cell junction (GO:0005911)|condensed nuclear chromosome (GO:0000794)|cytoskeleton (GO:0005856)|membrane (GO:0016020)|plasma membrane (GO:0005886)	structural constituent of cytoskeleton (GO:0005200)			central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(9)|ovary(2)|pancreas(1)|prostate(1)|skin(3)	29		Breast(234;0.052)|Lung NSC(174;0.223)		Epithelial(162;4.15e-05)|all cancers(201;0.000587)|BRCA - Breast invasive adenocarcinoma(275;0.0742)		GGCGTGATTACCACTCCTCCT	0.418																																					p.T11S		Atlas-SNP	.											.	ADD3	89	.	0			c.C32G						PASS	.						84.0	70.0	74.0					10																	111860443		2203	4300	6503	SO:0001583	missense	120	exon2			TGATTACCACTCC	U37122	CCDS7561.1, CCDS7562.1	10q25.2	2005-11-08			ENSG00000148700	ENSG00000148700			245	protein-coding gene	gene with protein product		601568		ADDL		8893809	Standard	XM_005269529		Approved		uc001kyv.3	Q9UEY8	OTTHUMG00000019032	ENST00000356080.4:c.32C>G	chr10.hg19:g.111860443C>G	ENSP00000348381:p.Thr11Ser	77.0	0.0	.		72.0	28.0	.	NM_001121	D3DRA8|O43243|Q5VU09|Q92773|Q9UEY7	Missense_Mutation	SNP	ENST00000356080.4	hg19	CCDS7561.1	.	.	.	.	.	.	.	.	.	.	C	21.5	4.165457	0.78339	.	.	ENSG00000148700	ENST00000360162;ENST00000356080;ENST00000277900	T;T;T	0.30714	1.52;1.52;1.52	6.06	6.06	0.98353	.	0.000000	0.85682	D	0.000000	T	0.47377	0.1442	M	0.76838	2.35	0.80722	D	1	P;B	0.51653	0.947;0.383	P;B	0.48400	0.576;0.155	T	0.32107	-0.9919	10	0.30078	T	0.28	-16.68	20.6397	0.99537	0.0:1.0:0.0:0.0	.	11;11	Q9UEY8;Q9UEY8-2	ADDG_HUMAN;.	S	11	ENSP00000353286:T11S;ENSP00000348381:T11S;ENSP00000277900:T11S	ENSP00000277900:T11S	T	+	2	0	ADD3	111850433	1.000000	0.71417	0.988000	0.46212	0.954000	0.61252	7.481000	0.81124	2.880000	0.98712	0.650000	0.86243	ACC	.	.	.	none		0.418	ADD3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050289.1	NM_019903	
MRVI1	10335	hgsc.bcm.edu	37	11	10647666	10647666	+	Silent	SNP	C	C	G			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr11:10647666C>G	ENST00000436272.1	-	8	1212	c.1134G>C	c.(1132-1134)cgG>cgC	p.R378R	MRVI1_ENST00000547195.1_Silent_p.R314R|MRVI1_ENST00000534266.2_Silent_p.R90R|MRVI1_ENST00000424001.1_Silent_p.R90R|MRVI1_ENST00000423302.2_Silent_p.R405R|MRVI1_ENST00000527509.2_Silent_p.R314R|MRVI1_ENST00000531107.1_Silent_p.R397R|MRVI1_ENST00000558540.1_Silent_p.R90R|MRVI1_ENST00000552103.1_Silent_p.R314R|MRVI1_ENST00000545852.1_Silent_p.R90R|MRVI1_ENST00000421747.1_Silent_p.R396R|MRVI1_ENST00000541483.1_Intron			Q9Y6F6	MRVI1_HUMAN	murine retrovirus integration site 1 homolog	378					blood coagulation (GO:0007596)|cGMP-mediated signaling (GO:0019934)|relaxation of vascular smooth muscle (GO:0060087)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|platelet dense tubular network membrane (GO:0031095)|sarcoplasmic reticulum (GO:0016529)				central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(4)|ovary(2)|prostate(2)	22				all cancers(16;2.68e-07)|Epithelial(150;3.04e-07)|BRCA - Breast invasive adenocarcinoma(625;0.0723)		CTTTCTGCAGCCGGGGGCCAG	0.647																																					p.R405R		Atlas-SNP	.											.	MRVI1	113	.	0			c.G1215C						PASS	.						16.0	18.0	18.0					11																	10647666		1874	4079	5953	SO:0001819	synonymous_variant	10335	exon9			CTGCAGCCGGGGG	AF081249	CCDS44538.1, CCDS44539.1, CCDS44540.1, CCDS44538.2, CCDS55745.1, CCDS55746.1	11p15.4	2014-09-11			ENSG00000072952	ENSG00000072952			7237	protein-coding gene	gene with protein product	"""inositol 1,4,5-triphosphate-associated cGMP kinase substrate"", ""IP3R-associated cGMP kinase substrate"""	604673				10321731	Standard	NM_001098579		Approved	JAW1L, IRAG	uc010rcb.1	Q9Y6F6	OTTHUMG00000165773	ENST00000436272.1:c.1134G>C	chr11.hg19:g.10647666C>G		42.0	0.0	.		30.0	11.0	.	NM_130385	B7Z3T4|B7Z6I2|B7Z9A3|E9PQY6|F5H6A1|J3KQZ7|Q17S00|Q9UNY1	Silent	SNP	ENST00000436272.1	hg19																																																																																				.	.	.	none		0.647	MRVI1-203	KNOWN	basic	protein_coding	protein_coding		NM_001098579	
HPS5	11234	hgsc.bcm.edu	37	11	18309441	18309441	+	Splice_Site	SNP	G	G	A			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr11:18309441G>A	ENST00000349215.3	-	17	2837	c.2560C>T	c.(2560-2562)Cgg>Tgg	p.R854W	HPS5_ENST00000537258.1_5'Flank|HPS5_ENST00000396253.3_Splice_Site_p.R740W|HPS5_ENST00000352460.3_5'UTR|HPS5_ENST00000438420.2_Splice_Site_p.R740W	NM_181507.1	NP_852608.1	Q9UPZ3	HPS5_HUMAN	Hermansky-Pudlak syndrome 5	854					blood coagulation (GO:0007596)|organelle organization (GO:0006996)|pigmentation (GO:0043473)	BLOC-2 complex (GO:0031084)				breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(17)|ovary(1)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	30						ACAACTTACCGGGTAGCATAA	0.363									Hermansky-Pudlak syndrome																												p.R854W		Atlas-SNP	.											.	HPS5	70	.	0			c.C2560T						PASS	.						140.0	122.0	129.0					11																	18309441		2199	4293	6492	SO:0001630	splice_region_variant	11234	exon17	Familial Cancer Database	HPS, HPS1-8	CTTACCGGGTAGC	AB023234	CCDS7836.1, CCDS7837.1	11p14	2014-06-18			ENSG00000110756	ENSG00000110756			17022	protein-coding gene	gene with protein product		607521				10231032, 10094488	Standard	NM_181507		Approved		uc001mod.1	Q9UPZ3	OTTHUMG00000166612	ENST00000349215.3:c.2561+1C>T	chr11.hg19:g.18309441G>A		53.0	0.0	.		53.0	24.0	.	NM_181507	A8K6J8|A8K8S1|D3DQX9|D3DQY0|O95942|Q8N4U0	Missense_Mutation	SNP	ENST00000349215.3	hg19	CCDS7836.1	.	.	.	.	.	.	.	.	.	.	G	14.03	2.415187	0.42817	.	.	ENSG00000110756	ENST00000396253;ENST00000438420;ENST00000349215;ENST00000544218	D;D;D;D	0.88046	-2.33;-2.33;-2.33;-2.33	5.36	-0.639	0.11497	.	0.091394	0.85682	D	0.000000	D	0.90017	0.6883	M	0.66939	2.045	0.48830	D	0.999711	D	0.76494	0.999	D	0.65443	0.935	D	0.88319	0.2961	10	0.87932	D	0	.	10.3165	0.43740	0.0768:0.0:0.2154:0.7078	.	854	Q9UPZ3	HPS5_HUMAN	W	740;740;854;40	ENSP00000379552:R740W;ENSP00000399590:R740W;ENSP00000265967:R854W;ENSP00000441781:R40W	ENSP00000265967:R854W	R	-	1	2	HPS5	18266017	0.959000	0.32827	0.725000	0.30721	0.174000	0.22865	1.548000	0.36201	-0.008000	0.14320	-0.475000	0.04921	CGG	.	.	.	none		0.363	HPS5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390808.1	NM_181507	Missense_Mutation
OR5M8	219484	hgsc.bcm.edu	37	11	56258788	56258788	+	Missense_Mutation	SNP	C	C	A	rs574852072	byFrequency	TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr11:56258788C>A	ENST00000327216.2	-	1	83	c.59G>T	c.(58-60)cGg>cTg	p.R20L		NM_001005282.1	NP_001005282.1	Q8NGP6	OR5M8_HUMAN	olfactory receptor, family 5, subfamily M, member 8	20						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(22)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	37	Esophageal squamous(21;0.00352)					TTGTAATTCCCGGCGACTGGT	0.483																																					p.R20L		Atlas-SNP	.											OR5M8,caecum,carcinoma,0,1	OR5M8	74	.	0			c.G59T						PASS	.						80.0	85.0	83.0					11																	56258788		2201	4296	6497	SO:0001583	missense	219484	exon1			AATTCCCGGCGAC	AB065744	CCDS31533.1	11q11	2012-08-09			ENSG00000181371	ENSG00000181371		"""GPCR / Class A : Olfactory receptors"""	14846	protein-coding gene	gene with protein product							Standard	NM_001005282		Approved		uc001nix.1	Q8NGP6	OTTHUMG00000166877	ENST00000327216.2:c.59G>T	chr11.hg19:g.56258788C>A	ENSP00000323354:p.Arg20Leu	134.0	1.0	.		131.0	7.0	.	NM_001005282	B2RNM5|Q6IEW3|Q96RB8	Missense_Mutation	SNP	ENST00000327216.2	hg19	CCDS31533.1	.	.	.	.	.	.	.	.	.	.	C	9.468	1.094793	0.20471	.	.	ENSG00000181371	ENST00000327216	T	0.00421	7.46	4.13	-7.18	0.01505	.	1.292630	0.06259	N	0.693636	T	0.00178	0.0005	N	0.05280	-0.08	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.39683	-0.9602	10	0.51188	T	0.08	0.1659	3.5083	0.07699	0.209:0.2522:0.4222:0.1166	.	20	Q8NGP6	OR5M8_HUMAN	L	20	ENSP00000323354:R20L	ENSP00000323354:R20L	R	-	2	0	OR5M8	56015364	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-4.691000	0.00198	-1.486000	0.01851	-1.292000	0.01352	CGG	.	.	.	none		0.483	OR5M8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391641.1	NM_001005282	
NPAT	4863	hgsc.bcm.edu	37	11	108032024	108032024	+	Silent	SNP	A	A	G			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr11:108032024A>G	ENST00000278612.8	-	17	3894	c.3789T>C	c.(3787-3789)agT>agC	p.S1263S		NM_002519.2	NP_002510.2	Q14207	NPAT_HUMAN	nuclear protein, ataxia-telangiectasia locus	1263					positive regulation of transcription, DNA-templated (GO:0045893)|regulation of gene expression (GO:0010468)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|transcription, DNA-templated (GO:0006351)	Cajal body (GO:0015030)|cytoplasm (GO:0005737)|Gemini of coiled bodies (GO:0097504)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein C-terminus binding (GO:0008022)|protein N-terminus binding (GO:0047485)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(21)|ovary(2)|prostate(2)|skin(5)	46		all_cancers(61;2.31e-10)|all_epithelial(67;1.11e-06)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		BRCA - Breast invasive adenocarcinoma(274;1.05e-05)|Epithelial(105;3.01e-05)|all cancers(92;0.000816)|Colorectal(284;0.116)		CAGGTAAATCACTACTATCAG	0.443																																					p.S1263S		Atlas-SNP	.											.	NPAT	124	.	0			c.T3789C						PASS	.						107.0	105.0	106.0					11																	108032024		1852	4092	5944	SO:0001819	synonymous_variant	4863	exon17			TAAATCACTACTA	X97186	CCDS41710.1	11q22-q23	2008-02-01			ENSG00000149308	ENSG00000149308			7896	protein-coding gene	gene with protein product		601448				9205109	Standard	NM_002519		Approved	E14	uc001pjz.4	Q14207	OTTHUMG00000166385	ENST00000278612.8:c.3789T>C	chr11.hg19:g.108032024A>G		164.0	0.0	.		132.0	54.0	.	NM_002519	A8K1V5|A8K6M2|Q13632|Q14967|Q16580|Q86W55|Q8IWE9	Silent	SNP	ENST00000278612.8	hg19	CCDS41710.1	.	.	.	.	.	.	.	.	.	.	A	0.009	-1.813585	0.00600	.	.	ENSG00000149308	ENST00000527296	.	.	.	3.92	-3.71	0.04424	.	.	.	.	.	T	0.35970	0.0950	.	.	.	0.44275	D	0.997137	.	.	.	.	.	.	T	0.37197	-0.9716	4	.	.	.	-0.1192	0.4805	0.00547	0.1833:0.2475:0.2586:0.3106	.	.	.	.	A	262	.	.	V	-	2	0	NPAT	107537234	0.001000	0.12720	0.012000	0.15200	0.023000	0.10783	-0.273000	0.08548	-0.420000	0.07427	-0.256000	0.11100	GTG	.	.	.	none		0.443	NPAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389506.2	NM_002519	
IGSF9B	22997	hgsc.bcm.edu	37	11	133790126	133790126	+	Missense_Mutation	SNP	C	C	A			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr11:133790126C>A	ENST00000321016.8	-	18	3724	c.3494G>T	c.(3493-3495)gGc>gTc	p.G1165V	IGSF9B_ENST00000533871.2_Missense_Mutation_p.G1165V			Q9UPX0	TUTLB_HUMAN	immunoglobulin superfamily, member 9B	1165	Pro-rich.				homophilic cell adhesion (GO:0007156)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)	dendrite (GO:0030425)|inhibitory synapse (GO:0060077)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)				breast(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(18)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	44	all_hematologic(175;0.127)	all_cancers(12;1.58e-21)|all_epithelial(12;5.17e-16)|all_lung(97;1.6e-05)|Lung NSC(97;3.86e-05)|Breast(109;0.000126)|Medulloblastoma(222;0.0245)|all_neural(223;0.0505)|Esophageal squamous(93;0.0559)		Epithelial(10;7.19e-10)|BRCA - Breast invasive adenocarcinoma(10;9.69e-09)|all cancers(11;1.23e-08)|OV - Ovarian serous cystadenocarcinoma(99;0.00328)|Lung(977;0.221)		GGTGTCCAGGCCAAATGTGCT	0.692																																					p.G1165V		Atlas-SNP	.											.	IGSF9B	290	.	0			c.G3494T						PASS	.						30.0	34.0	33.0					11																	133790126		1905	4106	6011	SO:0001583	missense	22997	exon18			TCCAGGCCAAATG	AK097578	CCDS61010.1	11q25	2013-02-11	2005-10-12	2005-11-20				"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	32326	protein-coding gene	gene with protein product		613773					Standard	NM_001277285		Approved	KIAA1030	uc031qfh.1	Q9UPX0		ENST00000321016.8:c.3494G>T	chr11.hg19:g.133790126C>A	ENSP00000317980:p.Gly1165Val	108.0	0.0	.		99.0	39.0	.	NM_014987	G5EA26	Missense_Mutation	SNP	ENST00000321016.8	hg19		.	.	.	.	.	.	.	.	.	.	C	15.82	2.946783	0.53186	.	.	ENSG00000080854	ENST00000321016;ENST00000533871	T;T	0.65364	0.18;-0.15	5.08	5.08	0.68730	.	0.000000	0.45606	D	0.000349	T	0.50205	0.1602	N	0.19112	0.55	0.58432	D	0.999991	P	0.35774	0.519	B	0.34418	0.182	T	0.57225	-0.7848	10	0.62326	D	0.03	.	18.0591	0.89371	0.0:1.0:0.0:0.0	.	1165	Q9UPX0	TUTLB_HUMAN	V	1165;1007	ENSP00000317980:G1165V;ENSP00000436552:G1007V	ENSP00000317980:G1165V	G	-	2	0	IGSF9B	133295336	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.261000	0.65496	2.358000	0.79984	0.455000	0.32223	GGC	.	.	.	none		0.692	IGSF9B-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		XM_290502	
IGSF9B	22997	hgsc.bcm.edu	37	11	133794760	133794760	+	Missense_Mutation	SNP	C	C	T			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr11:133794760C>T	ENST00000321016.8	-	15	2304	c.2074G>A	c.(2074-2076)Gat>Aat	p.D692N	IGSF9B_ENST00000533871.2_Missense_Mutation_p.D692N			Q9UPX0	TUTLB_HUMAN	immunoglobulin superfamily, member 9B	692	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				homophilic cell adhesion (GO:0007156)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)	dendrite (GO:0030425)|inhibitory synapse (GO:0060077)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)				breast(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(18)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	44	all_hematologic(175;0.127)	all_cancers(12;1.58e-21)|all_epithelial(12;5.17e-16)|all_lung(97;1.6e-05)|Lung NSC(97;3.86e-05)|Breast(109;0.000126)|Medulloblastoma(222;0.0245)|all_neural(223;0.0505)|Esophageal squamous(93;0.0559)		Epithelial(10;7.19e-10)|BRCA - Breast invasive adenocarcinoma(10;9.69e-09)|all cancers(11;1.23e-08)|OV - Ovarian serous cystadenocarcinoma(99;0.00328)|Lung(977;0.221)		CTGATCAGATCCTGCATGACG	0.587																																					p.D692N		Atlas-SNP	.											.	IGSF9B	290	.	0			c.G2074A						PASS	.						114.0	123.0	120.0					11																	133794760		2090	4217	6307	SO:0001583	missense	22997	exon15			TCAGATCCTGCAT	AK097578	CCDS61010.1	11q25	2013-02-11	2005-10-12	2005-11-20				"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	32326	protein-coding gene	gene with protein product		613773					Standard	NM_001277285		Approved	KIAA1030	uc031qfh.1	Q9UPX0		ENST00000321016.8:c.2074G>A	chr11.hg19:g.133794760C>T	ENSP00000317980:p.Asp692Asn	239.0	0.0	.		174.0	55.0	.	NM_014987	G5EA26	Missense_Mutation	SNP	ENST00000321016.8	hg19		.	.	.	.	.	.	.	.	.	.	C	34	5.382681	0.95967	.	.	ENSG00000080854	ENST00000321016;ENST00000533871;ENST00000527648	T;T;T	0.56941	0.43;0.43;0.43	5.02	5.02	0.67125	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.41500	D	0.000871	T	0.64505	0.2604	L	0.46157	1.445	0.53005	D	0.999967	P	0.42518	0.782	P	0.56278	0.795	T	0.62353	-0.6872	10	0.42905	T	0.14	.	18.7177	0.91682	0.0:1.0:0.0:0.0	.	692	Q9UPX0	TUTLB_HUMAN	N	692;534;692	ENSP00000317980:D692N;ENSP00000436552:D534N;ENSP00000436576:D692N	ENSP00000317980:D692N	D	-	1	0	IGSF9B	133299970	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.637000	0.83313	2.493000	0.84123	0.655000	0.94253	GAT	.	.	.	none		0.587	IGSF9B-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		XM_290502	
NACA	4666	hgsc.bcm.edu	37	12	57114205	57114205	+	Missense_Mutation	SNP	G	G	A			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr12:57114205G>A	ENST00000454682.1	-	3	1390	c.1109C>T	c.(1108-1110)aCt>aTt	p.T370I	NACA_ENST00000548563.1_Intron|NACA_ENST00000550952.1_Missense_Mutation_p.T370I|NACA_ENST00000551793.1_Intron|NACA_ENST00000546392.1_Intron|NACA_ENST00000356769.3_Intron|NACA_ENST00000552540.1_Intron|NACA_ENST00000393891.4_Intron	NM_001113203.2	NP_001106674.2	E9PAV3	NACAM_HUMAN	nascent polypeptide-associated complex alpha subunit	370	Pro-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(1)|ovary(2)|upper_aerodigestive_tract(1)	10						GGCAGCCACAGTAGCAGGAAC	0.488			T	BCL6	NHL																																p.T370I		Atlas-SNP	.		Dom	yes		12	12q23-q24.1	4666	nascent-polypeptide-associated complex alpha polypeptide		L	NACA_ENST00000550952,NS,carcinoma,0,2	NACA	131	.	0			c.C1109T						PASS	.						60.0	55.0	56.0					12																	57114205		1568	3582	5150	SO:0001583	missense	4666	exon3			GCCACAGTAGCAG	X80909	CCDS31837.1, CCDS44925.1, CCDS44925.2	12q23-q24.1	2008-09-05	2007-04-20		ENSG00000196531	ENSG00000196531			7629	protein-coding gene	gene with protein product		601234	"""nascent-polypeptide-associated complex alpha polypeptide"""			8047162	Standard	NM_001113202		Approved	NACA1	uc001sma.2	E9PAV3		ENST00000454682.1:c.1109C>T	chr12.hg19:g.57114205G>A	ENSP00000403817:p.Thr370Ile	42.0	0.0	.		46.0	27.0	.	NM_001113203		Missense_Mutation	SNP	ENST00000454682.1	hg19		.	.	.	.	.	.	.	.	.	.	G	14.65	2.598833	0.46318	.	.	ENSG00000196531	ENST00000454682;ENST00000550952	T;T	0.47869	0.83;0.9	3.29	3.29	0.37713	.	.	.	.	.	T	0.23171	0.0560	N	0.08118	0	0.09310	N	1	P;B	0.38978	0.652;0.358	B;B	0.30943	0.122;0.117	T	0.03750	-1.1007	9	0.26408	T	0.33	.	10.4563	0.44553	0.0:0.0:1.0:0.0	.	370;370	E9PAV3;F8VU71	.;.	I	370	ENSP00000403817:T370I;ENSP00000448035:T370I	ENSP00000403817:T370I	T	-	2	0	NACA	55400472	0.001000	0.12720	0.018000	0.16275	0.537000	0.34900	0.083000	0.14871	1.569000	0.49696	0.306000	0.20318	ACT	.	.	.	none		0.488	NACA-201	KNOWN	basic	protein_coding	protein_coding		NM_005594	
MBD6	114785	hgsc.bcm.edu	37	12	57918527	57918527	+	Silent	SNP	C	C	A			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr12:57918527C>A	ENST00000355673.3	+	4	494	c.138C>A	c.(136-138)tcC>tcA	p.S46S	MBD6_ENST00000431731.2_Silent_p.S46S|MBD6_ENST00000549231.1_3'UTR	NM_052897.3	NP_443129.3	Q96DN6	MBD6_HUMAN	methyl-CpG binding domain protein 6	46	MBD. {ECO:0000255|PROSITE- ProRule:PRU00338}.					chromocenter (GO:0010369)|nucleus (GO:0005634)	chromatin binding (GO:0003682)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(8)|lung(8)|ovary(1)|urinary_tract(1)	31						AGCTGTCTTCCTTGGAGCAAA	0.572																																					p.S46S		Atlas-SNP	.											.	MBD6	99	.	0			c.C138A						PASS	.						83.0	76.0	78.0					12																	57918527		2203	4300	6503	SO:0001819	synonymous_variant	114785	exon4			GTCTTCCTTGGAG	AB067474	CCDS8944.1	12q13.2	2008-02-05				ENSG00000166987			20445	protein-coding gene	gene with protein product						12529184	Standard	NM_052897		Approved	KIAA1887	uc001soj.1	Q96DN6		ENST00000355673.3:c.138C>A	chr12.hg19:g.57918527C>A		106.0	0.0	.		132.0	45.0	.	NM_052897	Q8N3M0|Q8NA81|Q96Q00	Silent	SNP	ENST00000355673.3	hg19	CCDS8944.1																																																																																			.	.	.	none		0.572	MBD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407250.1		
CCDC70	83446	hgsc.bcm.edu	37	13	52439890	52439890	+	Missense_Mutation	SNP	C	C	A	rs17076052	byFrequency	TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr13:52439890C>A	ENST00000242819.4	+	2	672	c.376C>A	c.(376-378)Cgc>Agc	p.R126S		NM_031290.2	NP_112580.2	Q6NSX1	CCD70_HUMAN	coiled-coil domain containing 70	126			R -> C (in dbSNP:rs17076052).			extracellular region (GO:0005576)|plasma membrane (GO:0005886)				breast(1)|large_intestine(4)|lung(7)|skin(2)|urinary_tract(1)	15		Breast(56;0.000207)|Lung NSC(96;0.00145)|Prostate(109;0.0107)|Hepatocellular(98;0.065)|all_neural(104;0.19)		GBM - Glioblastoma multiforme(99;2.4e-08)		GAAAAAGTACCGCACTTTCTG	0.468																																					p.R126S		Atlas-SNP	.											.	CCDC70	31	.	0			c.C376A						PASS	.						111.0	125.0	120.0					13																	52439890		2203	4300	6503	SO:0001583	missense	83446	exon2			AAGTACCGCACTT		CCDS9431.1	13q14.3	2006-02-07			ENSG00000123171	ENSG00000123171			25303	protein-coding gene	gene with protein product						11230166	Standard	NM_031290		Approved	DKFZP434K1172, FLJ25853	uc001vfu.4	Q6NSX1	OTTHUMG00000016950	ENST00000242819.4:c.376C>A	chr13.hg19:g.52439890C>A	ENSP00000242819:p.Arg126Ser	236.0	0.0	.		286.0	14.0	.	NM_031290	Q8N7A8|Q9H097	Missense_Mutation	SNP	ENST00000242819.4	hg19	CCDS9431.1	.	.	.	.	.	.	.	.	.	.	C	4.364	0.067073	0.08388	.	.	ENSG00000123171	ENST00000242819	T	0.21543	2.0	5.93	-0.542	0.11854	.	0.271361	0.25723	N	0.028737	T	0.18087	0.0434	M	0.65975	2.015	0.80722	P	0.0	P	0.35844	0.524	B	0.28465	0.09	T	0.16482	-1.0401	9	0.33940	T	0.23	-18.1723	11.3004	0.49302	0.6742:0.2599:0.0:0.0659	.	126	Q6NSX1	CCD70_HUMAN	S	126	ENSP00000242819:R126S	ENSP00000242819:R126S	R	+	1	0	CCDC70	51337891	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.113000	0.10774	-0.486000	0.06744	-2.156000	0.00330	CGC	.	C|0.927;T|0.073	.	alt		0.468	CCDC70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045033.2	NM_031290	
UBR1	197131	hgsc.bcm.edu	37	15	43299382	43299382	+	Missense_Mutation	SNP	C	C	T			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr15:43299382C>T	ENST00000290650.4	-	30	3388	c.3310G>A	c.(3310-3312)Gaa>Aaa	p.E1104K	UBR1_ENST00000382177.2_3'UTR|UBR1_ENST00000568782.1_5'UTR	NM_174916.2	NP_777576.1	Q8IWV7	UBR1_HUMAN	ubiquitin protein ligase E3 component n-recognin 1	1104					cellular response to leucine (GO:0071233)|negative regulation of TOR signaling (GO:0032007)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|proteasome complex (GO:0000502)|ubiquitin ligase complex (GO:0000151)	leucine binding (GO:0070728)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(2)|endometrium(2)|kidney(7)|large_intestine(12)|lung(25)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	58		all_cancers(109;4.32e-15)|all_epithelial(112;4.05e-13)|Lung NSC(122;1.75e-08)|all_lung(180;2e-07)|Melanoma(134;0.0179)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;4.08e-07)|COAD - Colon adenocarcinoma(120;0.185)|Colorectal(105;0.214)		ACCTCCTGTTCTTCTTGGCAA	0.473																																					p.E1104K		Atlas-SNP	.											.	UBR1	124	.	0			c.G3310A						PASS	.						128.0	115.0	119.0					15																	43299382		2203	4299	6502	SO:0001583	missense	197131	exon30			CCTGTTCTTCTTG		CCDS10091.1	15q13	2008-06-23			ENSG00000159459	ENSG00000159459		"""Ubiquitin protein ligase E3 component n-recognins"""	16808	protein-coding gene	gene with protein product		605981				9653112	Standard	NM_174916		Approved		uc001zqq.3	Q8IWV7	OTTHUMG00000130702	ENST00000290650.4:c.3310G>A	chr15.hg19:g.43299382C>T	ENSP00000290650:p.Glu1104Lys	121.0	0.0	.		137.0	49.0	.	NM_174916	O60708|O75492|Q14D45|Q68DN9|Q8IWY6|Q96JY4	Missense_Mutation	SNP	ENST00000290650.4	hg19	CCDS10091.1	.	.	.	.	.	.	.	.	.	.	C	34	5.388214	0.95988	.	.	ENSG00000159459	ENST00000290650	T	0.55760	0.5	4.99	4.99	0.66335	Zinc finger, RING/FYVE/PHD-type (1);	0.050391	0.85682	D	0.000000	T	0.71829	0.3386	M	0.71206	2.165	0.80722	D	1	D	0.76494	0.999	D	0.80764	0.994	T	0.71066	-0.4700	10	0.40728	T	0.16	-8.6741	18.4574	0.90725	0.0:1.0:0.0:0.0	.	1104	Q8IWV7	UBR1_HUMAN	K	1104	ENSP00000290650:E1104K	ENSP00000290650:E1104K	E	-	1	0	UBR1	41086674	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	7.320000	0.79064	2.593000	0.87608	0.655000	0.94253	GAA	.	.	.	none		0.473	UBR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253202.1	NM_174916	
PKD1	5310	hgsc.bcm.edu	37	16	2155892	2155892	+	Silent	SNP	A	A	G			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr16:2155892A>G	ENST00000262304.4	-	20	8045	c.7837T>C	c.(7837-7839)Ttg>Ctg	p.L2613L	PKD1_ENST00000423118.1_Silent_p.L2613L|PKD1_ENST00000561991.1_5'UTR	NM_001009944.2	NP_001009944	P98161	PKD1_HUMAN	polycystic kidney disease 1 (autosomal dominant)	2613	REJ. {ECO:0000255|PROSITE- ProRule:PRU00511}.		Missing (in PKD1; unknown pathological significance). {ECO:0000269|PubMed:11571556}.		anatomical structure morphogenesis (GO:0009653)|branching morphogenesis of an epithelial tube (GO:0048754)|calcium ion transmembrane transport (GO:0070588)|calcium-independent cell-matrix adhesion (GO:0007161)|cartilage condensation (GO:0001502)|cartilage development (GO:0051216)|cation transmembrane transport (GO:0098655)|cell cycle arrest (GO:0007050)|cell-matrix adhesion (GO:0007160)|cytoplasmic sequestering of transcription factor (GO:0042994)|detection of mechanical stimulus (GO:0050982)|digestive tract development (GO:0048565)|embryonic placenta development (GO:0001892)|genitalia development (GO:0048806)|heart development (GO:0007507)|homophilic cell adhesion (GO:0007156)|in utero embryonic development (GO:0001701)|JAK-STAT cascade (GO:0007259)|kidney development (GO:0001822)|liver development (GO:0001889)|lung epithelium development (GO:0060428)|mesonephric duct development (GO:0072177)|mesonephric tubule development (GO:0072164)|metanephric ascending thin limb development (GO:0072218)|metanephric collecting duct development (GO:0072205)|metanephric distal tubule morphogenesis (GO:0072287)|metanephric proximal tubule development (GO:0072237)|neural tube development (GO:0021915)|neuropeptide signaling pathway (GO:0007218)|nitrogen compound metabolic process (GO:0006807)|peptidyl-serine phosphorylation (GO:0018105)|placenta blood vessel development (GO:0060674)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of protein binding (GO:0032092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein export from nucleus (GO:0006611)|regulation of mitotic spindle organization (GO:0060236)|regulation of proteasomal protein catabolic process (GO:0061136)|response to fluid shear stress (GO:0034405)|skin development (GO:0043588)|spinal cord development (GO:0021510)	basolateral plasma membrane (GO:0016323)|cilium (GO:0005929)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lateral plasma membrane (GO:0016328)|motile primary cilium (GO:0031512)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|polycystin complex (GO:0002133)	calcium channel activity (GO:0005262)|carbohydrate binding (GO:0030246)|cation channel activity (GO:0005261)|ion channel binding (GO:0044325)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)	p.L2613L(1)		breast(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|kidney(6)|lung(34)|prostate(4)|skin(10)|upper_aerodigestive_tract(3)|urinary_tract(3)	72						ACCAGGGCCAACGAGTACTCG	0.657																																					p.L2613L		Atlas-SNP	.											PKD1,NS,carcinoma,0,1	PKD1	184	.	1	Substitution - coding silent(1)	lung(1)	c.T7837C						PASS	.						46.0	45.0	45.0					16																	2155892		1400	2465	3865	SO:0001819	synonymous_variant	5310	exon20			GGGCCAACGAGTA	L33243	CCDS32369.1, CCDS45385.1	16p13.3	2014-01-28			ENSG00000008710	ENSG00000008710		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	9008	protein-coding gene	gene with protein product	"""polycystin 1"", ""transient receptor potential cation channel, subfamily P, member 1"""	601313					Standard	NM_001009944		Approved	PBP, Pc-1, TRPP1	uc002cos.1	P98161	OTTHUMG00000155795	ENST00000262304.4:c.7837T>C	chr16.hg19:g.2155892A>G		44.0	0.0	.		36.0	4.0	.	NM_000296	Q15140|Q15141	Silent	SNP	ENST00000262304.4	hg19	CCDS32369.1																																																																																			.	.	.	none		0.657	PKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341688.1		
ZFHX3	463	hgsc.bcm.edu	37	16	72992635	72992635	+	Silent	SNP	T	T	C			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr16:72992635T>C	ENST00000268489.5	-	2	2082	c.1410A>G	c.(1408-1410)gaA>gaG	p.E470E	ZFHX3_ENST00000397992.5_Intron	NM_006885.3	NP_008816.3	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3	470	Poly-Glu.				brain development (GO:0007420)|cell cycle arrest (GO:0007050)|muscle organ development (GO:0007517)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of myoblast differentiation (GO:0045663)|regulation of neuron differentiation (GO:0045664)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	enzyme binding (GO:0019899)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			NS(3)|breast(7)|cervix(2)|endometrium(18)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(22)|liver(1)|lung(46)|ovary(5)|pancreas(1)|prostate(15)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(11)	153		Ovarian(137;0.13)				cctccgcctcttcctcctcct	0.587																																					p.E470E		Atlas-SNP	.											.	ZFHX3	404	.	0			c.A1410G						PASS	.						38.0	42.0	40.0					16																	72992635		2198	4300	6498	SO:0001819	synonymous_variant	463	exon2			CGCCTCTTCCTCC	D10250	CCDS10908.1, CCDS54035.1	16q22.3	2012-03-09	2007-08-09	2007-08-09	ENSG00000140836	ENSG00000140836		"""Zinc fingers, C2H2-type"", ""Homeoboxes / ZF class"""	777	protein-coding gene	gene with protein product		104155	"""AT-binding transcription factor 1"""	ATBF1		1719379, 7592926	Standard	NM_006885		Approved	ZNF927	uc002fck.3	Q15911	OTTHUMG00000137599	ENST00000268489.5:c.1410A>G	chr16.hg19:g.72992635T>C		61.0	0.0	.		36.0	4.0	.	NM_006885	D3DWS8|O15101|Q13719	Silent	SNP	ENST00000268489.5	hg19	CCDS10908.1																																																																																			.	.	.	none		0.587	ZFHX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269008.1	NM_006885	
ZFHX3	463	hgsc.bcm.edu	37	16	72992638	72992638	+	Silent	SNP	C	C	T			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr16:72992638C>T	ENST00000268489.5	-	2	2079	c.1407G>A	c.(1405-1407)gaG>gaA	p.E469E	ZFHX3_ENST00000397992.5_Intron	NM_006885.3	NP_008816.3	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3	469	Poly-Glu.				brain development (GO:0007420)|cell cycle arrest (GO:0007050)|muscle organ development (GO:0007517)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of myoblast differentiation (GO:0045663)|regulation of neuron differentiation (GO:0045664)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	enzyme binding (GO:0019899)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			NS(3)|breast(7)|cervix(2)|endometrium(18)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(22)|liver(1)|lung(46)|ovary(5)|pancreas(1)|prostate(15)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(11)	153		Ovarian(137;0.13)				ccgcctcttcctcctcctctt	0.587																																					p.E469E		Atlas-SNP	.											.	ZFHX3	404	.	0			c.G1407A						PASS	.						38.0	41.0	40.0					16																	72992638		2198	4300	6498	SO:0001819	synonymous_variant	463	exon2			CTCTTCCTCCTCC	D10250	CCDS10908.1, CCDS54035.1	16q22.3	2012-03-09	2007-08-09	2007-08-09	ENSG00000140836	ENSG00000140836		"""Zinc fingers, C2H2-type"", ""Homeoboxes / ZF class"""	777	protein-coding gene	gene with protein product		104155	"""AT-binding transcription factor 1"""	ATBF1		1719379, 7592926	Standard	NM_006885		Approved	ZNF927	uc002fck.3	Q15911	OTTHUMG00000137599	ENST00000268489.5:c.1407G>A	chr16.hg19:g.72992638C>T		59.0	0.0	.		38.0	9.0	.	NM_006885	D3DWS8|O15101|Q13719	Silent	SNP	ENST00000268489.5	hg19	CCDS10908.1																																																																																			.	.	.	none		0.587	ZFHX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269008.1	NM_006885	
METTL16	79066	hgsc.bcm.edu	37	17	2323643	2323643	+	Missense_Mutation	SNP	C	C	A	rs201182820		TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr17:2323643C>A	ENST00000263092.6	-	10	1437	c.1310G>T	c.(1309-1311)cGg>cTg	p.R437L	METTL16_ENST00000571669.2_5'UTR|METTL16_ENST00000538844.1_Missense_Mutation_p.R219L	NM_024086.3	NP_076991.3	Q86W50	MET16_HUMAN	methyltransferase like 16	437							methyltransferase activity (GO:0008168)|poly(A) RNA binding (GO:0044822)			kidney(2)|large_intestine(9)|lung(4)|ovary(2)|skin(1)|urinary_tract(1)	19						CTCGCCTTCCCGCAGAGCAGG	0.647																																					p.R437L		Atlas-SNP	.											.	METTL16	75	.	0			c.G1310T						PASS	.						54.0	61.0	59.0					17																	2323643		1828	4070	5898	SO:0001583	missense	79066	exon10			CCTTCCCGCAGAG	AK027410	CCDS42232.1	17p13.3	2011-03-02	2011-03-02	2011-03-02	ENSG00000127804	ENSG00000127804			28484	protein-coding gene	gene with protein product			"""methyltransferase 10 domain containing"""	METT10D		18021804	Standard	NM_024086		Approved	MGC3329	uc002fut.3	Q86W50		ENST00000263092.6:c.1310G>T	chr17.hg19:g.2323643C>A	ENSP00000263092:p.Arg437Leu	197.0	0.0	.		247.0	10.0	.	NM_024086	D3DTI8|Q86TE5|Q96T16|Q9BVG7	Missense_Mutation	SNP	ENST00000263092.6	hg19	CCDS42232.1	.	.	.	.	.	.	.	.	.	.	C	0.028	-1.357504	0.01245	.	.	ENSG00000127804	ENST00000263092;ENST00000537138;ENST00000538844	T;T	0.42131	1.0;0.98	4.96	-9.91	0.00458	.	1.656050	0.03445	N	0.209819	T	0.17152	0.0412	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.10800	-1.0614	10	0.20046	T	0.44	.	5.2765	0.15653	0.0792:0.3013:0.4229:0.1966	.	437	Q86W50	MET16_HUMAN	L	437;117;219	ENSP00000263092:R437L;ENSP00000443633:R219L	ENSP00000263092:R437L	R	-	2	0	METTL16	2270393	0.000000	0.05858	0.000000	0.03702	0.060000	0.15804	-2.154000	0.01285	-3.074000	0.00252	0.511000	0.50034	CGG	.	C|0.999;T|0.001	.	alt		0.647	METTL16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437653.2	NM_024086	
RAP1GAP2	23108	hgsc.bcm.edu	37	17	2898695	2898695	+	Silent	SNP	C	C	A			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr17:2898695C>A	ENST00000254695.8	+	13	1069	c.979C>A	c.(979-981)Cgg>Agg	p.R327R	RAP1GAP2_ENST00000542807.1_Silent_p.R327R|RAP1GAP2_ENST00000366401.4_Silent_p.R312R|RAP1GAP2_ENST00000540393.2_Silent_p.R308R	NM_015085.4	NP_055900.4	Q684P5	RPGP2_HUMAN	RAP1 GTPase activating protein 2	327	Rap-GAP. {ECO:0000255|PROSITE- ProRule:PRU00165}.				negative regulation of neuron projection development (GO:0010977)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|neuron projection (GO:0043005)|nuclear membrane (GO:0031965)	Rap GTPase activator activity (GO:0046582)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)	11						CACAACATTCCGGGACAGGGA	0.562																																					p.R327R		Atlas-SNP	.											.	RAP1GAP2	90	.	0			c.C979A						PASS	.						128.0	134.0	132.0					17																	2898695		2192	4300	6492	SO:0001819	synonymous_variant	23108	exon13			ACATTCCGGGACA	AB028962	CCDS45573.1, CCDS45574.1	17p13.3	2009-09-14	2009-09-14	2009-09-14		ENSG00000132359			29176	protein-coding gene	gene with protein product			"""GTPase activating RANGAP domain-like 4"", ""GTPase activating Rap/RanGAP domain-like 4"""	GARNL4		15632203	Standard	NM_015085		Approved	KIAA1039	uc010ckd.3	Q684P5		ENST00000254695.8:c.979C>A	chr17.hg19:g.2898695C>A		285.0	0.0	.		314.0	13.0	.	NM_015085	B2RTY5|Q684P4|Q6AI00|Q6ZVF0|Q9UPW2	Silent	SNP	ENST00000254695.8	hg19	CCDS45573.1																																																																																			.	.	.	none		0.562	RAP1GAP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000438208.2		
MPRIP	23164	hgsc.bcm.edu	37	17	17030034	17030034	+	Missense_Mutation	SNP	G	G	A			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr17:17030034G>A	ENST00000341712.4	+	4	286	c.286G>A	c.(286-288)Ggc>Agc	p.G96S	MPRIP_ENST00000395804.3_Missense_Mutation_p.G96S|MPRIP_ENST00000395811.5_Missense_Mutation_p.G96S|MPRIP_ENST00000444976.1_Missense_Mutation_p.G96S			Q6WCQ1	MPRIP_HUMAN	myosin phosphatase Rho interacting protein	96	Interaction with F-actin. {ECO:0000250}.|PH 1. {ECO:0000255|PROSITE- ProRule:PRU00145}.					actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)				biliary_tract(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(9)|ovary(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	31						CCTTCCTCAGGGCACCATCAA	0.602																																					p.G96S		Atlas-SNP	.											.	MPRIP	87	.	0			c.G286A						PASS	.						80.0	73.0	75.0					17																	17030034		2203	4300	6503	SO:0001583	missense	23164	exon4			CCTCAGGGCACCA	BC014102	CCDS32578.1, CCDS42268.1	17p11.2	2013-01-10			ENSG00000133030	ENSG00000133030		"""Pleckstrin homology (PH) domain containing"""	30321	protein-coding gene	gene with protein product	"""Rho interacting protein 3"""	612935				10048485	Standard	NM_201274		Approved	RHOIP3, M-RIP, p116Rip	uc002gqy.2	Q6WCQ1	OTTHUMG00000059276	ENST00000341712.4:c.286G>A	chr17.hg19:g.17030034G>A	ENSP00000342379:p.Gly96Ser	96.0	0.0	.		127.0	36.0	.	NM_015134	Q3KQZ5|Q5FB94|Q6DHW2|Q7Z5Y2|Q8N390|Q96G40	Missense_Mutation	SNP	ENST00000341712.4	hg19	CCDS32578.1	.	.	.	.	.	.	.	.	.	.	G	33	5.203730	0.95033	.	.	ENSG00000133030	ENST00000444976;ENST00000395811;ENST00000395804;ENST00000341712	D;D;D;D	0.95518	-3.73;-3.73;-3.73;-3.73	5.59	5.59	0.84812	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	.	.	.	.	D	0.97826	0.9286	M	0.80982	2.52	0.80722	D	1	D;D	0.89917	1.0;0.996	D;D	0.91635	0.999;0.993	D	0.98164	1.0448	9	0.66056	D	0.02	.	19.5944	0.95530	0.0:0.0:1.0:0.0	.	96;96	Q6WCQ1-2;Q6WCQ1	.;MPRIP_HUMAN	S	96	ENSP00000400189:G96S;ENSP00000379156:G96S;ENSP00000379149:G96S;ENSP00000342379:G96S	ENSP00000342379:G96S	G	+	1	0	MPRIP	16970759	1.000000	0.71417	0.993000	0.49108	0.756000	0.42949	9.414000	0.97362	2.642000	0.89623	0.561000	0.74099	GGC	.	.	.	none		0.602	MPRIP-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000131587.1	NM_015134	
PHF12	57649	hgsc.bcm.edu	37	17	27251080	27251080	+	Missense_Mutation	SNP	T	T	A			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr17:27251080T>A	ENST00000332830.4	-	4	1372	c.562A>T	c.(562-564)Att>Ttt	p.I188F	RP11-20B24.5_ENST00000582631.1_RNA|RP11-20B24.5_ENST00000580782.1_RNA|PHF12_ENST00000582655.1_5'UTR|PHF12_ENST00000577226.1_Missense_Mutation_p.I188F|PHF12_ENST00000268756.3_Missense_Mutation_p.I188F	NM_001033561.1	NP_001028733.1			PHD finger protein 12											breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(8)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	30	all_cancers(5;1.95e-14)|all_epithelial(6;5e-18)|Lung NSC(42;0.01)		Epithelial(11;1.64e-05)|all cancers(11;7.47e-05)|BRCA - Breast invasive adenocarcinoma(11;9.79e-05)			TCCACGTCAATGATGTCTTCG	0.602																																					p.I188F		Atlas-SNP	.											.	PHF12	69	.	0			c.A562T						PASS	.						83.0	65.0	71.0					17																	27251080		2203	4300	6503	SO:0001583	missense	57649	exon4			CGTCAATGATGTC	AB040956	CCDS11247.1, CCDS32598.1	17q11.2	2013-01-28			ENSG00000109118	ENSG00000109118		"""Zinc fingers, PHD-type"""	20816	protein-coding gene	gene with protein product						11390640	Standard	XM_005258015		Approved	PF1, KIAA1523	uc002hdg.1	Q96QT6	OTTHUMG00000132676	ENST00000332830.4:c.562A>T	chr17.hg19:g.27251080T>A	ENSP00000329933:p.Ile188Phe	63.0	0.0	.		89.0	51.0	.	NM_020889		Missense_Mutation	SNP	ENST00000332830.4	hg19	CCDS32598.1	.	.	.	.	.	.	.	.	.	.	T	15.88	2.962952	0.53507	.	.	ENSG00000109118	ENST00000332830;ENST00000378879;ENST00000268756	D;D;D	0.94793	-3.48;-3.52;-3.52	5.8	4.72	0.59763	.	0.213282	0.49305	D	0.000141	D	0.93527	0.7934	L	0.44542	1.39	0.46260	D	0.998956	D;D;B;D	0.57899	0.968;0.981;0.437;0.968	P;P;B;P	0.54026	0.474;0.74;0.068;0.474	D	0.91577	0.5276	10	0.36615	T	0.2	-19.0128	10.4673	0.44616	0.0:0.0766:0.0:0.9234	.	170;188;188;188	B4DFE2;Q96QT6-2;Q2TAK2;Q96QT6	.;.;.;PHF12_HUMAN	F	188	ENSP00000329933:I188F;ENSP00000368157:I188F;ENSP00000268756:I188F	ENSP00000268756:I188F	I	-	1	0	PHF12	24275206	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	2.241000	0.43097	1.031000	0.39867	0.533000	0.62120	ATT	.	.	.	none		0.602	PHF12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255941.1	NM_020889	
GJC1	10052	hgsc.bcm.edu	37	17	42882624	42882624	+	Missense_Mutation	SNP	C	C	G			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr17:42882624C>G	ENST00000426548.1	-	3	831	c.562G>C	c.(562-564)Gag>Cag	p.E188Q	GJC1_ENST00000592524.1_Missense_Mutation_p.E188Q|GJC1_ENST00000330514.4_Missense_Mutation_p.E188Q|GJC1_ENST00000590758.1_Missense_Mutation_p.E188Q	NM_001080383.1|NM_005497.3	NP_001073852.1|NP_005488.2	P36383	CXG1_HUMAN	gap junction protein, gamma 1, 45kDa	188					atrial cardiac muscle cell action potential (GO:0086014)|cardiac muscle tissue development (GO:0048738)|cell development (GO:0048468)|cell-cell junction assembly (GO:0007043)|gap junction assembly (GO:0016264)|membrane organization (GO:0061024)|muscle contraction (GO:0006936)|synaptic transmission (GO:0007268)|transport (GO:0006810)|vasculogenesis (GO:0001570)|visual perception (GO:0007601)	connexon complex (GO:0005922)|endoplasmic reticulum membrane (GO:0005789)|gap junction (GO:0005921)|integral component of membrane (GO:0016021)|intercalated disc (GO:0014704)|plasma membrane (GO:0005886)	gap junction channel activity (GO:0005243)|ion channel activity (GO:0005216)			NS(1)|kidney(1)|large_intestine(5)|liver(1)|lung(10)|prostate(1)	19		Prostate(33;0.0959)				AAACCCACCTCAAACACGGTC	0.493																																					p.E188Q		Atlas-SNP	.											.	GJC1	45	.	0			c.G562C						PASS	.						188.0	173.0	178.0					17																	42882624		2203	4300	6503	SO:0001583	missense	10052	exon3			CCACCTCAAACAC	U03493	CCDS11487.1	17q21.31	2008-02-04	2007-11-06	2007-11-06		ENSG00000182963		"""Ion channels / Gap junction proteins (connexins)"""	4280	protein-coding gene	gene with protein product	"""connexin 45"""	608655	"""gap junction protein, alpha 7, 45kDa"""	GJA7		7966354	Standard	NM_005497		Approved	CX45	uc002ihl.3	P36383		ENST00000426548.1:c.562G>C	chr17.hg19:g.42882624C>G	ENSP00000411528:p.Glu188Gln	219.0	0.0	.		358.0	131.0	.	NM_005497	B3KW68|Q4VAY0	Missense_Mutation	SNP	ENST00000426548.1	hg19	CCDS11487.1	.	.	.	.	.	.	.	.	.	.	C	21.8	4.201522	0.79015	.	.	ENSG00000182963	ENST00000426548;ENST00000330514	D;D	0.97850	-4.57;-4.57	5.52	5.52	0.82312	Gap junction protein, cysteine-rich domain (1);	0.000000	0.85682	D	0.000000	D	0.99306	0.9757	H	0.98218	4.175	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98674	1.0689	10	0.87932	D	0	.	18.419	0.90582	0.0:1.0:0.0:0.0	.	188	P36383	CXG1_HUMAN	Q	188	ENSP00000411528:E188Q;ENSP00000333193:E188Q	ENSP00000333193:E188Q	E	-	1	0	GJC1	40238150	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	7.805000	0.86005	2.581000	0.87130	0.514000	0.50259	GAG	.	.	.	none		0.493	GJC1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448661.1	NM_005497	
SAMD14	201191	hgsc.bcm.edu	37	17	48190273	48190273	+	Missense_Mutation	SNP	T	T	G			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr17:48190273T>G	ENST00000330175.4	-	10	1555	c.1238A>C	c.(1237-1239)gAg>gCg	p.E413A	SAMD14_ENST00000503131.1_Missense_Mutation_p.E441A	NM_001257359.1	NP_001244288.1	Q8IZD0	SAM14_HUMAN	sterile alpha motif domain containing 14	413										breast(1)|endometrium(1)|kidney(4)|large_intestine(4)|lung(3)|prostate(1)|urinary_tract(1)	15						CTTCTTGGCCTCCTGCTCTCG	0.697																																					p.E441A		Atlas-SNP	.											.	SAMD14	36	.	0			c.A1322C						PASS	.						40.0	43.0	42.0					17																	48190273		2203	4300	6503	SO:0001583	missense	201191	exon11			TTGGCCTCCTGCT		CCDS11560.1, CCDS58562.1	17q21.33	2013-01-10				ENSG00000167100		"""Sterile alpha motif (SAM) domain containing"""	27312	protein-coding gene	gene with protein product						8619474	Standard	NM_174920		Approved	FLJ36890	uc002iqg.4	Q8IZD0		ENST00000330175.4:c.1238A>C	chr17.hg19:g.48190273T>G	ENSP00000329144:p.Glu413Ala	102.0	0.0	.		133.0	51.0	.	NM_174920	A5D8V1|Q8N2X0	Missense_Mutation	SNP	ENST00000330175.4	hg19	CCDS58562.1	.	.	.	.	.	.	.	.	.	.	T	16.48	3.134428	0.56828	.	.	ENSG00000167100	ENST00000330175;ENST00000285206;ENST00000503131	.	.	.	5.11	4.02	0.46733	.	0.370723	0.24490	N	0.038069	T	0.47544	0.1451	L	0.27053	0.805	0.27885	N	0.939546	D;B	0.63880	0.993;0.137	D;B	0.68192	0.956;0.046	T	0.37911	-0.9685	9	0.59425	D	0.04	-11.4398	10.0803	0.42386	0.0:0.0:0.1686:0.8313	.	413;441	Q8IZD0;Q8IZD0-2	SAM14_HUMAN;.	A	413;425;441	.	ENSP00000285206:E425A	E	-	2	0	SAMD14	45545272	0.996000	0.38824	1.000000	0.80357	0.862000	0.49288	2.701000	0.47094	0.773000	0.33404	0.379000	0.24179	GAG	.	.	.	none		0.697	SAMD14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366661.1	NM_174920	
CACNA1G	8913	hgsc.bcm.edu	37	17	48669448	48669448	+	Missense_Mutation	SNP	G	G	A			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr17:48669448G>A	ENST00000359106.5	+	13	2905	c.2905G>A	c.(2905-2907)Gcg>Acg	p.A969T	CACNA1G_ENST00000502264.1_Missense_Mutation_p.A969T|CACNA1G_ENST00000514079.1_Missense_Mutation_p.A969T|CACNA1G_ENST00000507609.1_Missense_Mutation_p.A969T|CACNA1G_ENST00000513689.2_Missense_Mutation_p.A969T|CACNA1G_ENST00000507336.1_Missense_Mutation_p.A969T|CACNA1G_ENST00000510115.1_Missense_Mutation_p.A969T|CACNA1G_ENST00000507896.1_Missense_Mutation_p.A969T|CACNA1G_ENST00000510366.1_Missense_Mutation_p.A969T|CACNA1G_ENST00000416767.4_Missense_Mutation_p.A969T|CACNA1G_ENST00000505165.1_Missense_Mutation_p.A969T|CACNA1G_ENST00000354983.4_Missense_Mutation_p.A969T|CACNA1G_ENST00000514717.1_Missense_Mutation_p.A969T|CACNA1G_ENST00000515411.1_Missense_Mutation_p.A969T|CACNA1G_ENST00000514181.1_Missense_Mutation_p.A969T|CACNA1G_ENST00000512389.1_Missense_Mutation_p.A969T|CACNA1G_ENST00000442258.2_Missense_Mutation_p.A969T|CACNA1G_ENST00000429973.2_Missense_Mutation_p.A969T|CACNA1G_ENST00000513964.1_Missense_Mutation_p.A969T|CACNA1G_ENST00000507510.2_Missense_Mutation_p.A969T|CACNA1G_ENST00000360761.4_Missense_Mutation_p.A969T|CACNA1G_ENST00000503485.1_Missense_Mutation_p.A969T|CACNA1G_ENST00000515765.1_Missense_Mutation_p.A969T|CACNA1G_ENST00000515165.1_Missense_Mutation_p.A969T|CACNA1G_ENST00000358244.5_Missense_Mutation_p.A969T|CACNA1G_ENST00000352832.5_Missense_Mutation_p.A969T	NM_018896.4	NP_061496.2	O43497	CAC1G_HUMAN	calcium channel, voltage-dependent, T type, alpha 1G subunit	969					axon guidance (GO:0007411)|calcium ion import (GO:0070509)|membrane depolarization during action potential (GO:0086010)|positive regulation of calcium ion-dependent exocytosis (GO:0045956)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of heart rate (GO:0002027)|regulation of membrane potential (GO:0042391)|response to nickel cation (GO:0010045)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	low voltage-gated calcium channel activity (GO:0008332)|scaffold protein binding (GO:0097110)			breast(5)|cervix(1)|endometrium(13)|kidney(5)|lung(23)	47	Breast(11;6.7e-17)		BRCA - Breast invasive adenocarcinoma(22;7.52e-09)		Cinnarizine(DB00568)|Ethosuximide(DB00593)|Flunarizine(DB04841)|Methsuximide(DB05246)|Spironolactone(DB00421)|Trimethadione(DB00347)|Verapamil(DB00661)|Zonisamide(DB00909)	GGGCTTCCAGGCGGAGGTAAC	0.582																																					p.A969T		Atlas-SNP	.											.	CACNA1G	659	.	0			c.G2905A						PASS	.						50.0	55.0	53.0					17																	48669448		2071	4210	6281	SO:0001583	missense	8913	exon13			TTCCAGGCGGAGG	AC004590	CCDS45730.1, CCDS45731.1, CCDS45732.1, CCDS45733.1, CCDS45734.1, CCDS45735.1, CCDS45736.1, CCDS45737.1, CCDS54142.1, CCDS54143.1, CCDS54144.1, CCDS54145.1, CCDS54146.1, CCDS58565.1, CCDS58566.1, CCDS58567.1, CCDS58568.1, CCDS58569.1, CCDS58570.1, CCDS58571.1, CCDS58572.1, CCDS58573.1, CCDS58574.1, CCDS58575.1, CCDS58576.1	17q22	2012-03-07	2007-02-16		ENSG00000006283	ENSG00000006283		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1394	protein-coding gene	gene with protein product		604065				9495342, 16382099	Standard	NM_001256334		Approved	Cav3.1, NBR13	uc002irk.2	O43497	OTTHUMG00000162180	ENST00000359106.5:c.2905G>A	chr17.hg19:g.48669448G>A	ENSP00000352011:p.Ala969Thr	59.0	0.0	.		96.0	40.0	.	NM_001256360	D6RA64|E7EPR0|O43498|O94770|Q19QY8|Q19QY9|Q19QZ0|Q19QZ1|Q19QZ2|Q19QZ3|Q19QZ4|Q19QZ5|Q19QZ6|Q19QZ7|Q19QZ8|Q19QZ9|Q19R00|Q19R01|Q19R02|Q19R03|Q19R04|Q19R05|Q19R06|Q19R07|Q19R08|Q19R09|Q19R10|Q19R11|Q19R12|Q19R13|Q19R15|Q19R16|Q19R17|Q19R18|Q2TAC4|Q9NYU4|Q9NYU5|Q9NYU6|Q9NYU7|Q9NYU8|Q9NYU9|Q9NYV0|Q9NYV1|Q9UHN9|Q9UHP0|Q9ULU6|Q9UNG7|Q9Y5T2|Q9Y5T3	Missense_Mutation	SNP	ENST00000359106.5	hg19	CCDS45730.1	.	.	.	.	.	.	.	.	.	.	g	14.26	2.482345	0.44147	.	.	ENSG00000006283	ENST00000360761;ENST00000352832;ENST00000416767;ENST00000354983;ENST00000442258;ENST00000502264;ENST00000512389;ENST00000513964;ENST00000514717;ENST00000510366;ENST00000503485;ENST00000507510;ENST00000507336;ENST00000513689;ENST00000507609;ENST00000510115;ENST00000515165;ENST00000514181;ENST00000515765;ENST00000514079;ENST00000358244;ENST00000359106;ENST00000429973;ENST00000515411;ENST00000505165;ENST00000507896	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.97186	-4.13;-4.12;-4.28;-4.08;-4.13;-4.12;-4.16;-4.26;-4.22;-4.24;-4.25;-4.11;-4.12;-4.2;-4.12;-4.07;-4.16;-4.12;-4.12;-4.16;-4.12;-4.12;-4.16;-4.11;-4.16;-4.17	5.08	1.63	0.23807	.	0.106565	0.64402	N	0.000006	D	0.88142	0.6357	N	0.02916	-0.46	0.33790	D	0.625335	B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B	0.22080	0.064;0.0;0.0;0.0;0.0;0.001;0.001;0.0;0.001;0.019;0.0;0.001;0.002;0.0;0.001;0.001;0.007;0.0;0.0;0.001;0.001;0.002;0.0;0.001;0.001;0.013	B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B	0.25987	0.017;0.005;0.001;0.005;0.001;0.006;0.004;0.001;0.004;0.013;0.001;0.017;0.02;0.001;0.004;0.007;0.029;0.005;0.001;0.008;0.003;0.007;0.001;0.007;0.001;0.065	T	0.82715	-0.0320	10	0.23891	T	0.37	.	5.465	0.16637	0.6206:0.0:0.3794:0.0	.	969;969;969;969;969;969;969;969;969;969;969;969;969;969;969;969;969;969;969;969;969;969;969;969;969;969	Q19QZ5;Q19QZ1;Q19QZ4;Q19R07;Q19QY8;Q19R10;Q19QZ6;Q19QZ3;Q19R06;Q19R00;Q19R04;O43497-10;Q19QZ9;Q19QZ7;Q19R08;Q19QZ8;Q19R03;O43497-4;Q19R02;Q19R12;Q19R17;Q19R11;Q2TAC4;O43497;Q19R13;O43497-11	.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;CAC1G_HUMAN;.;.	T	969	ENSP00000353990:A969T;ENSP00000339302:A969T;ENSP00000392390:A969T;ENSP00000347078:A969T;ENSP00000409759:A969T;ENSP00000425522:A969T;ENSP00000426261:A969T;ENSP00000425451:A969T;ENSP00000422407:A969T;ENSP00000426814:A969T;ENSP00000427238:A969T;ENSP00000423112:A969T;ENSP00000420918:A969T;ENSP00000426172:A969T;ENSP00000423045:A969T;ENSP00000427173:A969T;ENSP00000426098:A969T;ENSP00000425698:A969T;ENSP00000426232:A969T;ENSP00000423317:A969T;ENSP00000350979:A969T;ENSP00000352011:A969T;ENSP00000414388:A969T;ENSP00000423155:A969T;ENSP00000422268:A969T;ENSP00000421518:A969T	ENSP00000339302:A969T	A	+	1	0	CACNA1G	46024447	1.000000	0.71417	0.982000	0.44146	0.980000	0.70556	2.660000	0.46749	0.553000	0.29044	0.462000	0.41574	GCG	.	.	.	none		0.582	CACNA1G-013	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367895.1	NM_018896	
TNRC6C	57690	hgsc.bcm.edu	37	17	76045567	76045567	+	Missense_Mutation	SNP	G	G	T	rs143335497	byFrequency	TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr17:76045567G>T	ENST00000588061.1	+	5	1151	c.424G>T	c.(424-426)Ggg>Tgg	p.G142W	TNRC6C_ENST00000301624.4_Missense_Mutation_p.G142W|TNRC6C_ENST00000335749.4_Missense_Mutation_p.G142W|TNRC6C_ENST00000588847.1_Missense_Mutation_p.G142W|TNRC6C_ENST00000544502.1_Missense_Mutation_p.G142W|TNRC6C_ENST00000541771.1_Missense_Mutation_p.G142W			Q9HCJ0	TNR6C_HUMAN	trinucleotide repeat containing 6C	142	Sufficient for interaction with argonaute family proteins.				embryonic hemopoiesis (GO:0035162)|endoderm formation (GO:0001706)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|innate immune response (GO:0045087)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|regulation of gene silencing by miRNA (GO:0060964)	cytosol (GO:0005829)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(9)|lung(16)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	40			BRCA - Breast invasive adenocarcinoma(99;0.00269)|Lung(188;0.0973)			CAACCAGAACGGGAACCCAAC	0.517																																					p.G142W		Atlas-SNP	.											.	TNRC6C	173	.	0			c.G424T						PASS	.						59.0	61.0	60.0					17																	76045567		2002	4187	6189	SO:0001583	missense	57690	exon4			CAGAACGGGAACC	AL834429	CCDS45798.1, CCDS45799.1	17q25.3	2012-10-04			ENSG00000078687	ENSG00000078687		"""Trinucleotide (CAG) repeat containing"""	29318	protein-coding gene	gene with protein product		610741					Standard	NM_018996		Approved	KIAA1582, FLJ20015	uc002juf.2	Q9HCJ0	OTTHUMG00000132642	ENST00000588061.1:c.424G>T	chr17.hg19:g.76045567G>T	ENSP00000468647:p.Gly142Trp	108.0	0.0	.		151.0	9.0	.	NM_018996	G3XAB8|Q86UE5|Q8N3D8|Q96MU9	Missense_Mutation	SNP	ENST00000588061.1	hg19	CCDS45798.1	.	.	.	.	.	.	.	.	.	.	G	15.97	2.988405	0.53934	.	.	ENSG00000078687	ENST00000455761;ENST00000395801;ENST00000335749;ENST00000301624;ENST00000541771;ENST00000544502	T;T;T;T	0.15603	2.41;2.42;2.42;2.41	5.36	5.36	0.76844	.	0.166883	0.52532	D	0.000071	T	0.39358	0.1075	L	0.50333	1.59	0.58432	D	0.999997	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.997	T	0.06481	-1.0824	10	0.72032	D	0.01	-11.4286	19.277	0.94036	0.0:0.0:1.0:0.0	.	142;142;142	G3XAB8;Q9HCJ0-2;Q9HCJ0	.;.;TNR6C_HUMAN	W	142	ENSP00000336783:G142W;ENSP00000301624:G142W;ENSP00000440310:G142W;ENSP00000442421:G142W	ENSP00000301624:G142W	G	+	1	0	TNRC6C	73557162	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	4.622000	0.61240	2.782000	0.95742	0.655000	0.94253	GGG	.	G|0.999;A|0.001	.	alt		0.517	TNRC6C-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000395947.1	NM_018996	
TBC1D16	125058	hgsc.bcm.edu	37	17	77922704	77922704	+	Missense_Mutation	SNP	C	C	A	rs181752232	byFrequency	TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr17:77922704C>A	ENST00000310924.2	-	8	1623	c.1508G>T	c.(1507-1509)cGg>cTg	p.R503L	TBC1D16_ENST00000576768.1_Missense_Mutation_p.R128L|TBC1D16_ENST00000572862.1_Missense_Mutation_p.R141L|TBC1D16_ENST00000570373.1_Missense_Mutation_p.R142L|TBC1D16_ENST00000340848.7_Missense_Mutation_p.R141L	NM_001271844.1|NM_001271845.1|NM_019020.2	NP_001258773.1|NP_001258774.1|NP_061893.2	Q8TBP0	TBC16_HUMAN	TBC1 domain family, member 16	503	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.						Rab GTPase activator activity (GO:0005097)			NS(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(13)|ovary(1)|prostate(3)	28	all_neural(118;0.167)		OV - Ovarian serous cystadenocarcinoma(97;0.00739)|BRCA - Breast invasive adenocarcinoma(99;0.0819)			GTCTTCCCCCCGGAAGAACTG	0.572																																					p.R503L	Ovarian(14;397 562 4850 31922 49378)	Atlas-SNP	.											.	TBC1D16	48	.	0			c.G1508T						PASS	.						222.0	178.0	193.0					17																	77922704		2203	4300	6503	SO:0001583	missense	125058	exon8			TCCCCCCGGAAGA	AL157485	CCDS11766.1, CCDS62351.1, CCDS62352.1, CCDS62353.1	17q25.3	2013-07-10				ENSG00000167291			28356	protein-coding gene	gene with protein product						23019362	Standard	NM_019020		Approved	MGC25062, FLJ20748	uc002jxj.4	Q8TBP0		ENST00000310924.2:c.1508G>T	chr17.hg19:g.77922704C>A	ENSP00000309794:p.Arg503Leu	140.0	0.0	.		219.0	11.0	.	NM_019020	B9A6L7|I3L1E0|I3L4U2|Q8N3Z4|Q96DH7	Missense_Mutation	SNP	ENST00000310924.2	hg19	CCDS11766.1	.	.	.	.	.	.	.	.	.	.	C	16.56	3.158742	0.57368	.	.	ENSG00000167291	ENST00000340848;ENST00000310924	T;T	0.10477	2.87;2.87	5.18	5.18	0.71444	Rab-GAP/TBC domain (4);	0.132210	0.50627	D	0.000114	T	0.20292	0.0488	L	0.59436	1.845	0.80722	D	1	P;B;B;B	0.38048	0.616;0.327;0.327;0.327	P;B;B;B	0.45138	0.471;0.258;0.258;0.299	T	0.00964	-1.1498	10	0.34782	T	0.22	-12.5599	18.692	0.91586	0.0:1.0:0.0:0.0	.	163;503;503;141	Q96DH7;Q8TBP0;B9A6L7;Q8N3Z4	.;TBC16_HUMAN;.;.	L	141;503	ENSP00000341517:R141L;ENSP00000309794:R503L	ENSP00000309794:R503L	R	-	2	0	TBC1D16	75537299	1.000000	0.71417	0.953000	0.39169	0.915000	0.54546	4.631000	0.61304	2.392000	0.81423	0.655000	0.94253	CGG	.	C|0.999;G|0.001	.	alt		0.572	TBC1D16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437145.1	NM_019020	
DYM	54808	hgsc.bcm.edu	37	18	46645145	46645145	+	Missense_Mutation	SNP	G	G	A			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr18:46645145G>A	ENST00000269445.6	-	15	2172	c.1715C>T	c.(1714-1716)tCa>tTa	p.S572L	RP11-15F12.3_ENST00000585251.1_RNA|DYM_ENST00000442713.2_Missense_Mutation_p.S382L	NM_017653.3	NP_060123.3	Q7RTS9	DYM_HUMAN	dymeclin	572					bone development (GO:0060348)|Golgi organization (GO:0007030)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)	enzyme binding (GO:0019899)			NS(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(6)|skin(1)|upper_aerodigestive_tract(1)	18						ATCCTGAAATGAAGGATGAGT	0.353																																					p.S572L		Atlas-SNP	.											.	DYM	52	.	0			c.C1715T						PASS	.						136.0	120.0	126.0					18																	46645145		2203	4300	6503	SO:0001583	missense	54808	exon15			TGAAATGAAGGAT	AK000078	CCDS11937.1	18q21.1	2008-03-12			ENSG00000141627	ENSG00000141627			21317	protein-coding gene	gene with protein product		607461					Standard	NM_017653		Approved	FLJ20071, DMC, SMC	uc002ldi.1	Q7RTS9	OTTHUMG00000132659	ENST00000269445.6:c.1715C>T	chr18.hg19:g.46645145G>A	ENSP00000269445:p.Ser572Leu	63.0	0.0	.		70.0	22.0	.	NM_017653	A8K5I8|B2RCF9|B4DKI7|Q3ZTS8|Q6P2P5|Q8N2M0|Q9BVE9|Q9NPU7	Missense_Mutation	SNP	ENST00000269445.6	hg19	CCDS11937.1	.	.	.	.	.	.	.	.	.	.	G	31	5.094436	0.94149	.	.	ENSG00000141627	ENST00000442713;ENST00000269445	D;D	0.81908	-1.55;-1.55	5.51	5.51	0.81932	.	0.000000	0.85682	D	0.000000	D	0.86981	0.6064	L	0.48362	1.52	0.80722	D	1	P;D;P	0.56287	0.879;0.975;0.481	B;P;B	0.56648	0.399;0.803;0.22	D	0.87691	0.2554	10	0.66056	D	0.02	-11.3305	19.412	0.94677	0.0:0.0:1.0:0.0	.	382;394;572	Q7RTS9-2;Q9NXS9;Q7RTS9	.;.;DYM_HUMAN	L	382;572	ENSP00000395942:S382L;ENSP00000269445:S572L	ENSP00000269445:S572L	S	-	2	0	DYM	44899143	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.827000	0.99397	2.601000	0.87937	0.650000	0.86243	TCA	.	.	.	none		0.353	DYM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255912.3	NM_017653	
SSBP4	170463	hgsc.bcm.edu	37	19	18538728	18538728	+	Missense_Mutation	SNP	G	G	A			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr19:18538728G>A	ENST00000270061.7	+	4	509	c.215G>A	c.(214-216)tGc>tAc	p.C72Y	SSBP4_ENST00000348495.6_Missense_Mutation_p.C72Y|SSBP4_ENST00000598159.2_3'UTR	NM_032627.4	NP_116016.1	Q9BWG4	SSBP4_HUMAN	single stranded DNA binding protein 4	72						nucleus (GO:0005634)	single-stranded DNA binding (GO:0003697)			endometrium(2)|kidney(1)|skin(1)	4						GACCTGTACTGCGCGGCGCCT	0.667																																					p.C72Y		Atlas-SNP	.											.	SSBP4	19	.	0			c.G215A						PASS	.						77.0	70.0	72.0					19																	18538728		2203	4300	6503	SO:0001583	missense	170463	exon4			TGTACTGCGCGGC		CCDS12378.1, CCDS32960.1	19p13.1	2008-02-05				ENSG00000130511			15676	protein-coding gene	gene with protein product		607391				12079286	Standard	NM_032627		Approved		uc002niy.3	Q9BWG4		ENST00000270061.7:c.215G>A	chr19.hg19:g.18538728G>A	ENSP00000270061:p.Cys72Tyr	163.0	0.0	.		107.0	40.0	.	NM_001009998	Q9BWW5	Missense_Mutation	SNP	ENST00000270061.7	hg19	CCDS12378.1	.	.	.	.	.	.	.	.	.	.	G	13.61	2.288142	0.40494	.	.	ENSG00000130511	ENST00000270061;ENST00000348495	.	.	.	3.7	3.7	0.42460	.	0.000000	0.85682	U	0.000000	T	0.58921	0.2156	L	0.57536	1.79	0.58432	D	0.999999	B;B	0.25048	0.048;0.117	B;B	0.27715	0.077;0.082	T	0.64193	-0.6465	9	0.72032	D	0.01	-16.1844	12.9926	0.58627	0.0:0.0:1.0:0.0	.	72;72	Q9BWW5;Q9BWG4	.;SSBP4_HUMAN	Y	72	.	ENSP00000270061:C72Y	C	+	2	0	SSBP4	18399728	1.000000	0.71417	0.932000	0.37286	0.036000	0.12997	8.730000	0.91510	1.883000	0.54544	0.561000	0.74099	TGC	.	.	.	none		0.667	SSBP4-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000466348.3	NM_032627	
SLC25A42	284439	hgsc.bcm.edu	37	19	19218750	19218750	+	Missense_Mutation	SNP	G	G	T			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr19:19218750G>T	ENST00000318596.7	+	7	696	c.545G>T	c.(544-546)gGg>gTg	p.G182V	SLC25A42_ENST00000600275.1_3'UTR	NM_178526.4	NP_848621.2	Q86VD7	S2542_HUMAN	solute carrier family 25, member 42	182					ADP transport (GO:0015866)|AMP transport (GO:0080121)|ATP transport (GO:0015867)|coenzyme A transmembrane transport (GO:0035349)|metabolic process (GO:0008152)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	adenosine-diphosphatase activity (GO:0043262)|ADP transmembrane transporter activity (GO:0015217)|AMP transmembrane transporter activity (GO:0080122)|ATP transmembrane transporter activity (GO:0005347)|coenzyme A transmembrane transporter activity (GO:0015228)			cervix(1)|large_intestine(2)|lung(3)	6			OV - Ovarian serous cystadenocarcinoma(5;5.4e-06)|Epithelial(12;0.000497)			AGAGAAGAGGGGCTGAAGACT	0.572																																					p.G182V		Atlas-SNP	.											.	SLC25A42	18	.	0			c.G545T						PASS	.						119.0	105.0	110.0					19																	19218750		2203	4300	6503	SO:0001583	missense	284439	exon7			AAGAGGGGCTGAA		CCDS32966.1	19p13.11	2013-05-22			ENSG00000181035	ENSG00000181035		"""Solute carriers"""	28380	protein-coding gene	gene with protein product		610823				16949250, 19429682	Standard	NM_178526		Approved	MGC26694	uc002nlf.3	Q86VD7		ENST00000318596.7:c.545G>T	chr19.hg19:g.19218750G>T	ENSP00000326693:p.Gly182Val	139.0	0.0	.		134.0	51.0	.	NM_178526	D2T2J5|O14553|O43378	Missense_Mutation	SNP	ENST00000318596.7	hg19	CCDS32966.1	.	.	.	.	.	.	.	.	.	.	G	23.6	4.441353	0.83993	.	.	ENSG00000181035	ENST00000318596	D	0.95238	-3.65	5.26	5.26	0.73747	Mitochondrial carrier domain (2);	0.000000	0.85682	D	0.000000	D	0.98701	0.9564	H	0.99435	4.565	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.99686	1.1000	10	0.87932	D	0	-10.1963	17.8525	0.88751	0.0:0.0:1.0:0.0	.	182	Q86VD7	S2542_HUMAN	V	182	ENSP00000326693:G182V	ENSP00000326693:G182V	G	+	2	0	SLC25A42	19079750	1.000000	0.71417	0.987000	0.45799	0.753000	0.42808	8.259000	0.89855	2.449000	0.82847	0.491000	0.48974	GGG	.	.	.	none		0.572	SLC25A42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465931.1	NM_178526	
ZNF254	9534	hgsc.bcm.edu	37	19	24310237	24310237	+	Nonsense_Mutation	SNP	A	A	T			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr19:24310237A>T	ENST00000357002.4	+	4	1550	c.1435A>T	c.(1435-1437)Aga>Tga	p.R479*	ZNF254_ENST00000342944.6_Nonsense_Mutation_p.R394*	NM_001278661.1|NM_001278662.1|NM_001278664.1|NM_001278677.1|NM_001278678.1|NM_203282.2	NP_001265590.1|NP_001265591.1|NP_001265593.1|NP_001265606.1|NP_001265607.1|NP_975011.3	O75437	ZN254_HUMAN	zinc finger protein 254	479					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)						all_cancers(12;0.086)|all_lung(12;0.00528)|Lung NSC(12;0.00731)|all_epithelial(12;0.0186)				AACCCTAACTAGACATAAGAG	0.388																																					p.R479X		Atlas-SNP	.											.	ZNF254	88	.	0			c.A1435T						PASS	.						62.0	62.0	62.0					19																	24310237		2203	4299	6502	SO:0001587	stop_gained	9534	exon4			CTAACTAGACATA	AF054180	CCDS32983.1, CCDS62622.1, CCDS62623.1, CCDS74323.1, CCDS74324.1	19p13	2013-01-08				ENSG00000213096		"""Zinc fingers, C2H2-type"", ""-"""	13047	protein-coding gene	gene with protein product		604768	"""zinc finger protein 539"""	ZNF91L, ZNF539		9653160	Standard	NM_001278661		Approved	HD-ZNF1, BMZF-5	uc002nru.3	O75437		ENST00000357002.4:c.1435A>T	chr19.hg19:g.24310237A>T	ENSP00000349494:p.Arg479*	107.0	0.0	.		74.0	21.0	.	NM_203282	A4QPC0|Q86XL7	Nonsense_Mutation	SNP	ENST00000357002.4	hg19	CCDS32983.1	.	.	.	.	.	.	.	.	.	.	A	35	5.491375	0.96339	.	.	ENSG00000213096	ENST00000342944;ENST00000357002	.	.	.	1.07	-2.07	0.07276	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.12430	T	0.62	.	3.7155	0.08437	0.6048:0.3952:0.0:0.0	.	.	.	.	X	394;479	.	ENSP00000445527:R394X	R	+	1	2	ZNF254	24102077	0.000000	0.05858	0.040000	0.18447	0.918000	0.54935	-0.462000	0.06704	-0.565000	0.06061	0.248000	0.18094	AGA	.	.	.	none		0.388	ZNF254-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466453.1	NM_004876	
SPINT2	10653	hgsc.bcm.edu	37	19	38774304	38774304	+	Silent	SNP	G	G	T			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr19:38774304G>T	ENST00000301244.7	+	2	579	c.144G>T	c.(142-144)cgG>cgT	p.R48R	SPINT2_ENST00000587090.1_5'UTR|SPINT2_ENST00000454580.3_Intron	NM_021102.3	NP_066925.1	O43291	SPIT2_HUMAN	serine peptidase inhibitor, Kunitz type, 2	48	BPTI/Kunitz inhibitor 1. {ECO:0000255|PROSITE-ProRule:PRU00031}.	Reactive bond. {ECO:0000250}.			cellular component movement (GO:0006928)|negative regulation of endopeptidase activity (GO:0010951)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)			large_intestine(2)|lung(1)|ovary(1)	4	all_cancers(60;6.83e-07)		Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292)			GCAGATGCCGGGCCTCCATGC	0.562																																					p.R48R		Atlas-SNP	.											.	SPINT2	17	.	0			c.G144T						PASS	.						170.0	144.0	153.0					19																	38774304		2203	4300	6503	SO:0001819	synonymous_variant	10653	exon2			ATGCCGGGCCTCC	U78095	CCDS12510.1, CCDS54261.1	19q13.2	2010-05-12	2005-08-17		ENSG00000167642	ENSG00000167642			11247	protein-coding gene	gene with protein product	"""placental bikunin"""	605124	"""serine protease inhibitor, Kunitz type, 2"""			9115294, 9346890	Standard	NM_021102		Approved	Kop, HAI-2	uc002ohr.2	O43291		ENST00000301244.7:c.144G>T	chr19.hg19:g.38774304G>T		211.0	0.0	.		208.0	55.0	.	NM_021102	A8K667|B4DLU1|O00271|O14895|Q5TZQ3|Q969E0	Silent	SNP	ENST00000301244.7	hg19	CCDS12510.1																																																																																			.	.	.	none		0.562	SPINT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458151.2		
ZNF471	57573	hgsc.bcm.edu	37	19	57037032	57037032	+	Silent	SNP	A	A	G			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr19:57037032A>G	ENST00000308031.5	+	5	1729	c.1596A>G	c.(1594-1596)caA>caG	p.Q532Q	ZNF471_ENST00000593197.1_Intron|ZNF471_ENST00000591537.1_3'UTR	NM_020813.2	NP_065864.2	Q9BX82	ZN471_HUMAN	zinc finger protein 471	532					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|liver(2)|lung(8)|ovary(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	36		Colorectal(82;5.46e-05)|Ovarian(87;0.0822)|Renal(1328;0.157)		GBM - Glioblastoma multiforme(193;0.0307)		ACCTTGCCCAACATCAGAAAA	0.398																																					p.Q532Q	Colon(65;957 1402 6678 10163)|Esophageal Squamous(159;2295 2541 15408 21211)	Atlas-SNP	.											.	ZNF471	99	.	0			c.A1596G						PASS	.						105.0	111.0	109.0					19																	57037032		2203	4300	6503	SO:0001819	synonymous_variant	57573	exon5			TGCCCAACATCAG	AB037817	CCDS12945.1	19q13.43	2013-01-08				ENSG00000196263		"""Zinc fingers, C2H2-type"", ""-"""	23226	protein-coding gene	gene with protein product						10718198	Standard	NM_020813		Approved	KIAA1396, Z1971	uc002qnh.3	Q9BX82		ENST00000308031.5:c.1596A>G	chr19.hg19:g.57037032A>G		152.0	0.0	.		121.0	40.0	.	NM_020813	B4DF32|O75260|Q08AD6|Q08AD7|Q8N3V1|Q9P2F1	Silent	SNP	ENST00000308031.5	hg19	CCDS12945.1																																																																																			.	.	.	none		0.398	ZNF471-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458405.1	NM_020813	
BPIFA2	140683	hgsc.bcm.edu	37	20	31761923	31761923	+	Missense_Mutation	SNP	C	C	T			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr20:31761923C>T	ENST00000253362.2	+	4	487	c.341C>T	c.(340-342)gCt>gTt	p.A114V	BPIFA2_ENST00000354932.5_Missense_Mutation_p.A114V			Q96DR5	BPIA2_HUMAN	BPI fold containing family A, member 2	114						extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	lipopolysaccharide binding (GO:0001530)										GATGTCAAAGCTGAACCGATC	0.507																																					p.A114V		Atlas-SNP	.											.	.	.	.	0			c.C341T						PASS	.						192.0	132.0	152.0					20																	31761923		2203	4300	6503	SO:0001583	missense	140683	exon4			TCAAAGCTGAACC	AF432917	CCDS13214.1	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000131050	ENSG00000131050		"""BPI fold containing"""	16203	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 70"""	C20orf70		11971875	Standard	NM_080574		Approved	bA49G10.1, SPLUNC2, PSP	uc002wyo.1	Q96DR5	OTTHUMG00000032244	ENST00000253362.2:c.341C>T	chr20.hg19:g.31761923C>T	ENSP00000253362:p.Ala114Val	119.0	0.0	.		136.0	38.0	.	NM_080574	Q9BQQ0	Missense_Mutation	SNP	ENST00000253362.2	hg19	CCDS13214.1	.	.	.	.	.	.	.	.	.	.	C	1.293	-0.607118	0.03717	.	.	ENSG00000131050	ENST00000253362;ENST00000354932	T;T	0.04758	3.56;3.56	4.11	-1.34	0.09143	.	1.919610	0.02314	N	0.072384	T	0.03520	0.0101	N	0.20685	0.6	0.09310	N	1	P	0.39862	0.692	B	0.42692	0.395	T	0.35276	-0.9795	10	0.02654	T	1	-22.3913	3.4184	0.07384	0.1782:0.4121:0.0:0.4097	.	114	Q96DR5	BPIA2_HUMAN	V	114	ENSP00000253362:A114V;ENSP00000347012:A114V	ENSP00000253362:A114V	A	+	2	0	BPIFA2	31225584	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-1.978000	0.01494	-0.194000	0.10399	0.561000	0.74099	GCT	.	.	.	none		0.507	BPIFA2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257117.1	NM_080574	
GNAS	2778	hgsc.bcm.edu	37	20	57415512	57415512	+	Silent	SNP	C	C	A			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr20:57415512C>A	ENST00000313949.7	+	1	740	c.351C>A	c.(349-351)tcC>tcA	p.S117S	GNAS-AS1_ENST00000424094.2_RNA|GNAS-AS1_ENST00000598163.1_RNA|GNAS_ENST00000371098.2_Silent_p.S117S|GNAS-AS1_ENST00000443966.1_RNA|GNAS_ENST00000371075.3_Silent_p.S117S			P63092	GNAS2_HUMAN	GNAS complex locus	0					activation of adenylate cyclase activity (GO:0007190)|adenylate cyclase-activating adrenergic receptor signaling pathway (GO:0071880)|adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|blood coagulation (GO:0007596)|bone development (GO:0060348)|cAMP biosynthetic process (GO:0006171)|cellular response to catecholamine stimulus (GO:0071870)|cellular response to glucagon stimulus (GO:0071377)|cellular response to prostaglandin E stimulus (GO:0071380)|cognition (GO:0050890)|developmental growth (GO:0048589)|energy reserve metabolic process (GO:0006112)|hair follicle placode formation (GO:0060789)|intracellular transport (GO:0046907)|platelet aggregation (GO:0070527)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of Ras GTPase activity (GO:0032320)|regulation of insulin secretion (GO:0050796)|sensory perception of smell (GO:0007608)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|intrinsic component of membrane (GO:0031224)|membrane (GO:0016020)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)	adenylate cyclase activity (GO:0004016)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)			adrenal_gland(12)|autonomic_ganglia(1)|biliary_tract(5)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(37)|liver(9)|lung(9)|ovary(16)|pancreas(56)|parathyroid(5)|pituitary(228)|prostate(2)|small_intestine(1)|stomach(1)|testis(2)|thyroid(35)|upper_aerodigestive_tract(3)|urinary_tract(1)	441	all_lung(29;0.0104)		BRCA - Breast invasive adenocarcinoma(13;2.19e-08)|Colorectal(105;0.109)			AGACCGAGTCCGAAATCGAGT	0.642			Mis		pituitary adenoma		"""McCune-Albright syndrome; pseudohypoparathyroidism, type IA"""			TSP Lung(22;0.16)																											p.S117S	Colon(117;935 1597 6045 8307 46442)	Atlas-SNP	.		Dom	yes		20	20q13.2	2778	"""guanine nucleotide binding protein (G protein), alpha stimulating activity polypeptide 1"""	yes	E	.	GNAS	867	.	0			c.C351A						PASS	.						101.0	94.0	96.0					20																	57415512		2203	4300	6503	SO:0001819	synonymous_variant	2778	exon1			CGAGTCCGAAATC	M21142	CCDS13471.1, CCDS13472.1, CCDS42892.1, CCDS46622.1, CCDS46623.1, CCDS46624.1	20q13.2-q13.3	2010-03-01	2001-12-19	2001-12-20	ENSG00000087460	ENSG00000087460			4392	protein-coding gene	gene with protein product	"""secretogranin VI"""	139320	"""guanine nucleotide binding protein (G protein), alpha stimulating activity polypeptide 1"""	GNAS1			Standard	NM_000516		Approved	NESP55, NESP, GNASXL, GPSA, SCG6	uc002xzw.3	O95467	OTTHUMG00000033069	ENST00000313949.7:c.351C>A	chr20.hg19:g.57415512C>A		142.0	0.0	.		133.0	7.0	.	NM_016592	A6NI00|E1P5G5|P04895|Q12927|Q14433|Q32P26|Q5JWD2|Q5JWD4|Q5JWD5|Q6NR75|Q6NXS0|Q8TBC0|Q96H70	Silent	SNP	ENST00000313949.7	hg19	CCDS13471.1																																																																																			.	.	.	none		0.642	GNAS-002	KNOWN	NMD_exception|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080418.7	NM_000516	
MX1	4599	hgsc.bcm.edu	37	21	42807881	42807881	+	Missense_Mutation	SNP	G	G	A	rs150271063		TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr21:42807881G>A	ENST00000398600.2	+	8	1248	c.223G>A	c.(223-225)Gtc>Atc	p.V75I	MX1_ENST00000398598.3_Missense_Mutation_p.V75I|MX1_ENST00000455164.2_Missense_Mutation_p.V75I|MX1_ENST00000288383.6_Missense_Mutation_p.V75I	NM_001144925.1	NP_001138397.1	P20591	MX1_HUMAN	MX dynamin-like GTPase 1	75	Dynamin-type G.|GTPase domain (Globular).				apoptotic process (GO:0006915)|cytokine-mediated signaling pathway (GO:0019221)|defense response (GO:0006952)|defense response to virus (GO:0051607)|innate immune response (GO:0045087)|negative regulation of viral genome replication (GO:0045071)|response to type I interferon (GO:0034340)|response to virus (GO:0009615)|signal transduction (GO:0007165)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(9)|lung(5)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	27		Prostate(19;3.18e-07)|all_epithelial(19;0.0277)				AGCCATCGCCGTCATCGGGGA	0.607																																					p.V75I		Atlas-SNP	.											.	MX1	58	.	0			c.G223A						PASS	.	G	ILE/VAL,ILE/VAL,ILE/VAL	1,4405	2.1+/-5.4	0,1,2202	81.0	80.0	80.0		223,223,223	4.5	1.0	21	dbSNP_134	80	5,8595	4.3+/-15.6	0,5,4295	no	missense,missense,missense	MX1	NM_001144925.1,NM_001178046.1,NM_002462.3	29,29,29	0,6,6497	AA,AG,GG		0.0581,0.0227,0.0461	probably-damaging,probably-damaging,probably-damaging	75/663,75/663,75/663	42807881	6,13000	2203	4300	6503	SO:0001583	missense	4599	exon8			ATCGCCGTCATCG		CCDS13673.1, CCDS74796.1	21q22.3	2014-07-15	2014-07-15		ENSG00000157601	ENSG00000157601			7532	protein-coding gene	gene with protein product	"""interferon-inducible protein p78"""	147150	"""myxovirus (influenza) resistance 1, homolog of murine (interferon-inducible protein p78)"", ""myxovirus (influenza virus) resistance 1, interferon-inducible protein p78 (mouse)"""			17570575	Standard	XM_005260979		Approved	IFI-78K, MxA	uc010goq.3	P20591	OTTHUMG00000086755	ENST00000398600.2:c.223G>A	chr21.hg19:g.42807881G>A	ENSP00000381601:p.Val75Ile	132.0	0.0	.		101.0	40.0	.	NM_001144925	B2RDA5|B3KU10|C9IYV7|C9J8D6|C9JN19|C9JN88|C9JUL1|C9JZS6|D3DSI8|Q86YP5|Q96CI3	Missense_Mutation	SNP	ENST00000398600.2	hg19	CCDS13673.1	.	.	.	.	.	.	.	.	.	.	G	32	5.146034	0.94603	2.27E-4	5.81E-4	ENSG00000157601	ENST00000398600;ENST00000398598;ENST00000455164;ENST00000424365;ENST00000417963;ENST00000441677;ENST00000288383	D;D;D;D;D;D	0.98192	-4.78;-4.78;-4.78;-3.97;-3.97;-3.22	4.48	4.48	0.54585	Dynamin, GTPase domain (2);	0.000000	0.85682	D	0.000000	D	0.98957	0.9645	M	0.91459	3.21	0.80722	D	1	D	0.63046	0.992	P	0.60236	0.871	D	0.99501	1.0953	10	0.87932	D	0	-65.9432	16.5923	0.84769	0.0:0.0:1.0:0.0	.	75	P20591	MX1_HUMAN	I	75	ENSP00000381601:V75I;ENSP00000381599:V75I;ENSP00000410523:V75I;ENSP00000400923:V75I;ENSP00000402215:V75I;ENSP00000288383:V75I	ENSP00000288383:V75I	V	+	1	0	MX1	41729751	1.000000	0.71417	0.959000	0.39883	0.933000	0.57130	8.419000	0.90253	2.445000	0.82738	0.561000	0.74099	GTC	.	G|1.000;A|0.000	0.000	weak		0.607	MX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195161.2		
UBR3	130507	hgsc.bcm.edu	37	2	170843280	170843281	+	Frame_Shift_Ins	INS	-	-	T			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr2:170843280_170843281insT	ENST00000272793.5	+	25	3810_3811	c.3760_3761insT	c.(3760-3762)gttfs	p.V1254fs	UBR3_ENST00000418381.1_Frame_Shift_Ins_p.V1254fs|UBR3_ENST00000392631.1_Frame_Shift_Ins_p.V75fs			Q6ZT12	UBR3_HUMAN	ubiquitin protein ligase E3 component n-recognin 3 (putative)	1254					embryo development (GO:0009790)|in utero embryonic development (GO:0001701)|olfactory behavior (GO:0042048)|sensory perception of smell (GO:0007608)|suckling behavior (GO:0001967)|ubiquitin-dependent protein catabolic process (GO:0006511)	integral component of membrane (GO:0016021)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(9)|liver(1)|lung(8)|ovary(1)|prostate(3)|stomach(1)	33						TACTGGATTAGTTGTACTGTTA	0.396																																					p.V1254fs		Atlas-INDEL	.											.	UBR3	182	.	0			c.3760_3761insT						PASS	.																																			SO:0001589	frameshift_variant	130507	exon25			.	AL834144	CCDS2238.2	2q31.1	2008-06-23	2008-06-23	2007-11-29	ENSG00000144357	ENSG00000144357		"""Ubiquitin protein ligase E3 component n-recognins"""	30467	protein-coding gene	gene with protein product		613831	"""zinc finger protein 650"""	ZNF650		17462990	Standard	NM_172070		Approved	KIAA2024, DKFZp434P117, FLJ37422	uc010zdi.2	Q6ZT12	OTTHUMG00000132229	ENST00000272793.5:c.3762dupT	chr2.hg19:g.170843282_170843282dupT	ENSP00000272793:p.Val1254fs	85.0	0.0	0		136.0	32.0	0.235294	NM_172070	B4DZR7|Q2KHN5|Q6ZR55|Q6ZSC2|Q8IVE7|Q8ND96	Frame_Shift_Ins	INS	ENST00000272793.5	hg19																																																																																				.	.	.	none		0.396	UBR3-001	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000255290.2	NM_172070	
TPD52	7163	hgsc.bcm.edu	37	8	80963849	80963851	+	In_Frame_Del	DEL	GAT	GAT	-			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	GAT	GAT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr8:80963849_80963851delGAT	ENST00000379097.3	-	4	779_781	c.417_419delATC	c.(415-420)acatct>act	p.S140del	TPD52_ENST00000379096.5_In_Frame_Del_p.S100del|TPD52_ENST00000520527.1_In_Frame_Del_p.S140del|TPD52_ENST00000517427.1_In_Frame_Del_p.S140del|TPD52_ENST00000537855.1_In_Frame_Del_p.S140del|TPD52_ENST00000519303.2_5'UTR|TPD52_ENST00000518937.1_In_Frame_Del_p.S100del|TPD52_ENST00000523395.1_5'Flank|TPD52_ENST00000448733.2_In_Frame_Del_p.S140del	NM_001025252.1	NP_001020423.1	P55327	TPD52_HUMAN	tumor protein D52	140					anatomical structure morphogenesis (GO:0009653)|B cell differentiation (GO:0030183)|positive regulation of cell proliferation (GO:0008284)|secretion (GO:0046903)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|perinuclear region of cytoplasm (GO:0048471)	calcium ion binding (GO:0005509)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			endometrium(1)|large_intestine(2)|lung(3)|ovary(1)|prostate(1)	8	all_epithelial(4;1.13e-09)|Lung NSC(7;9.71e-07)|all_lung(9;3.75e-06)	Lung NSC(129;3.55e-06)|all_lung(136;1.53e-05)|Acute lymphoblastic leukemia(644;0.158)	BRCA - Breast invasive adenocarcinoma(6;0.00181)|Epithelial(68;0.0149)|all cancers(69;0.0612)			TAAGGTTTCAGATGTCTTCTTGT	0.404																																					p.140_140del		Atlas-INDEL	.											.	TPD52	40	.	0			c.418_420del						PASS	.																																			SO:0001651	inframe_deletion	7163	exon4			.	U18914	CCDS34912.1, CCDS47879.1, CCDS55249.1, CCDS75757.1, CCDS75758.1, CCDS75759.1	8q21.13	2014-06-24			ENSG00000076554	ENSG00000076554			12005	protein-coding gene	gene with protein product		604068				7796418	Standard	NM_001287144		Approved	D52, hD52, N8L	uc003ybr.1	P55327	OTTHUMG00000164565	ENST00000379097.3:c.417_419delATC	chr8.hg19:g.80963849_80963851delGAT	ENSP00000368391:p.Ser140del	74.0	0.0	0		75.0	26.0	0.346667	NM_001025252	B7Z414|C9J502|D0UFD1|D0UFD2|D0UFD3|D0UFD4|D0UFD5|E5RKB4|Q13056|Q53EK8|Q6FGP3|Q6FGS3|Q86YZ2|Q9UCX8	In_Frame_Del	DEL	ENST00000379097.3	hg19	CCDS34912.1																																																																																			.	.	.	none		0.404	TPD52-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000379539.2	NM_005079	
ITSN2	50618	hgsc.bcm.edu	37	2	24509153	24509155	+	In_Frame_Del	DEL	TTC	TTC	-	rs201163358		TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	TTC	TTC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr2:24509153_24509155delTTC	ENST00000355123.4	-	16	2232_2234	c.1789_1791delGAA	c.(1789-1791)gaadel	p.E597del	ITSN2_ENST00000361999.3_In_Frame_Del_p.E597del|ITSN2_ENST00000406921.3_In_Frame_Del_p.E597del	NM_006277.2	NP_006268.2	Q9NZM3	ITSN2_HUMAN	intersectin 2	597					endocytosis (GO:0006897)|positive regulation of signal transduction (GO:0009967)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|SH3/SH2 adaptor activity (GO:0005070)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(8)|large_intestine(11)|liver(3)|lung(28)|ovary(2)|stomach(1)	61	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CATCTAACTGTTCTTTAAGTCTT	0.286																																					p.597_598del		Atlas-INDEL	.											.	ITSN2	224	.	0			c.1790_1792del						PASS	.																																			SO:0001651	inframe_deletion	50618	exon16			.	AB033082	CCDS1710.2, CCDS1711.2, CCDS46230.1	2p23.3	2013-09-19	2002-10-30		ENSG00000198399	ENSG00000198399		"""Rho guanine nucleotide exchange factors"", ""EF-hand domain containing"""	6184	protein-coding gene	gene with protein product	"""SH3 domain protein 1B"", ""SH3P18-like WASP associated protein"""	604464	"""SH3 domain protein 1B"""	SH3D1B		10922467, 11748279	Standard	NM_006277		Approved	KIAA1256, SWAP, SH3P18, SWA, PRO2015	uc002rfe.2	Q9NZM3	OTTHUMG00000090818	ENST00000355123.4:c.1789_1791delGAA	chr2.hg19:g.24509153_24509155delTTC	ENSP00000347244:p.Glu597del	67.0	0.0	0		120.0	24.0	0.2	NM_006277	O95062|Q15812|Q9HAK4|Q9NXE6|Q9NYG0|Q9NZM2|Q9ULG4	In_Frame_Del	DEL	ENST00000355123.4	hg19	CCDS1710.2																																																																																			.	.	.	none		0.286	ITSN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207620.2	NM_006277	
TOPBP1	11073	hgsc.bcm.edu	37	3	133329894	133329895	+	Frame_Shift_Ins	INS	-	-	CT			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr3:133329894_133329895insCT	ENST00000260810.5	-	25	4257_4258	c.4126_4127insAG	c.(4126-4128)agafs	p.R1376fs		NM_007027.3	NP_008958.2	Q92547	TOPB1_HUMAN	topoisomerase (DNA) II binding protein 1	1376					cellular response to DNA damage stimulus (GO:0006974)|DNA metabolic process (GO:0006259)|DNA repair (GO:0006281)|response to ionizing radiation (GO:0010212)	chromosome (GO:0005694)|condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|male germ cell nucleus (GO:0001673)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|protein C-terminus binding (GO:0008022)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(5)|lung(14)|ovary(2)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)	40						TTTTCTCCATCTCATTGCTGCA	0.356								Other conserved DNA damage response genes																													p.R1376fs	Ovarian(21;193 658 4424 15423 17362)	Atlas-INDEL	.											.	TOPBP1	218	.	0			c.4127_4128insAG						PASS	.																																			SO:0001589	frameshift_variant	11073	exon25			.	AB019397	CCDS46919.1	3q22.1	2004-06-21			ENSG00000163781	ENSG00000163781			17008	protein-coding gene	gene with protein product		607760				9461304, 9039502	Standard	NM_007027		Approved	KIAA0259, TOP2BP1	uc003eps.3	Q92547	OTTHUMG00000159773	ENST00000260810.5:c.4126_4127insAG	chr3.hg19:g.133329894_133329895insCT	ENSP00000260810:p.Arg1376fs	230.0	0.0	0		249.0	88.0	0.353414	NM_007027	B7Z7W8|Q7LGC1|Q9UEB9	Frame_Shift_Ins	INS	ENST00000260810.5	hg19	CCDS46919.1																																																																																			.	.	.	none		0.356	TOPBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357254.1	NM_007027	
USHBP1	83878	hgsc.bcm.edu	37	19	17370111	17370111	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr19:17370111delC	ENST00000252597.3	-	7	1206	c.1033delG	c.(1033-1035)gccfs	p.A345fs	USHBP1_ENST00000431146.2_Frame_Shift_Del_p.A281fs	NM_031941.3	NP_114147.2			Usher syndrome 1C binding protein 1											breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(10)|liver(1)|lung(12)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	44						TACTGCAAGGCCAGATGCAAT	0.602																																					p.A345fs		Atlas-INDEL	.											.	USHBP1	85	.	0			c.1034delC						PASS	.						53.0	49.0	50.0					19																	17370111		2203	4300	6503	SO:0001589	frameshift_variant	83878	exon7			.	AK096028	CCDS12353.1	19p13.11	2013-06-10			ENSG00000130307	ENSG00000130307			24058	protein-coding gene	gene with protein product		611810				11311560	Standard	XM_005260093		Approved	MCC2, AIEBP, FLJ38709	uc002nfs.1	Q8N6Y0	OTTHUMG00000182730	ENST00000252597.3:c.1033delG	chr19.hg19:g.17370111delC	ENSP00000252597:p.Ala345fs	50.0	0.0	0		41.0	12.0	0.292683	NM_031941		Frame_Shift_Del	DEL	ENST00000252597.3	hg19	CCDS12353.1																																																																																			.	.	.	none		0.602	USHBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463328.1	NM_031941	
MYCN	4613	hgsc.bcm.edu	37	2	16082320	16082321	+	Frame_Shift_Ins	INS	-	-	G			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr2:16082320_16082321insG	ENST00000281043.3	+	2	431_432	c.134_135insG	c.(133-138)ccggggfs	p.PG45fs	MYCNOS_ENST00000453400.1_RNA|MYCNOS_ENST00000448719.1_RNA|MYCNOS_ENST00000420452.1_RNA|MYCNOS_ENST00000419083.1_RNA|MYCNOS_ENST00000439180.1_RNA	NM_005378.4	NP_005369.2	P04198	MYCN_HUMAN	v-myc avian myelocytomatosis viral oncogene neuroblastoma derived homolog	45					branching morphogenesis of an epithelial tube (GO:0048754)|cartilage condensation (GO:0001502)|embryonic digit morphogenesis (GO:0042733)|embryonic skeletal system morphogenesis (GO:0048704)|lung development (GO:0030324)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|positive regulation of cell death (GO:0010942)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	chromatin (GO:0000785)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|autonomic_ganglia(1)|breast(1)|central_nervous_system(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	31	all_cancers(1;1.35e-08)|all_neural(1;2.92e-24)|Lung SC(1;3.26e-07)|Medulloblastoma(1;6.9e-06)|all_lung(1;1.26e-05)|Glioma(3;0.135)|Acute lymphoblastic leukemia(172;0.155)|all_epithelial(1;0.169)|all_hematologic(175;0.197)		GBM - Glioblastoma multiforme(3;0.000332)			TCGACCCCCCCGGGGGAGGACA	0.644			A		neuroblastoma																																p.P45fs		Atlas-INDEL	.		Dom	yes		2	2p24.1	4613	"""v-myc myelocytomatosis viral related oncogene, neuroblastoma derived (avian)"""		O	.	MYCN	63	.	0			c.134_135insG	GRCh37	CI084293	MYCN	I		PASS	.																																			SO:0001589	frameshift_variant	4613	exon2			.	BC002712	CCDS1687.1	2p24.3	2013-08-14	2013-07-09		ENSG00000134323	ENSG00000134323		"""Basic helix-loop-helix proteins"""	7559	protein-coding gene	gene with protein product		164840		NMYC			Standard	XM_006711886		Approved	bHLHe37, N-myc, MYCNOT	uc002rci.3	P04198	OTTHUMG00000039579	ENST00000281043.3:c.139dupG	chr2.hg19:g.16082325_16082325dupG	ENSP00000281043:p.Pro45fs	47.0	0.0	0		49.0	23.0	0.469388	NM_005378	Q53XS5|Q6LDT9	Frame_Shift_Ins	INS	ENST00000281043.3	hg19	CCDS1687.1																																																																																			.	.	.	none		0.644	MYCN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095469.2	NM_005378	
NDUFS1	4719	hgsc.bcm.edu	37	2	207006722	207006724	+	In_Frame_Del	DEL	AGA	AGA	-			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	AGA	AGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr2:207006722_207006724delAGA	ENST00000233190.6	-	12	1469_1471	c.1203_1205delTCT	c.(1201-1206)cttctg>ctg	p.401_402LL>L	NDUFS1_ENST00000455934.2_In_Frame_Del_p.415_416LL>L|NDUFS1_ENST00000449699.1_In_Frame_Del_p.401_402LL>L|NDUFS1_ENST00000432169.1_In_Frame_Del_p.290_291LL>L|NDUFS1_ENST00000423725.1_In_Frame_Del_p.344_345LL>L|NDUFS1_ENST00000457011.1_In_Frame_Del_p.285_286LL>L|NDUFS1_ENST00000440274.1_In_Frame_Del_p.365_366LL>L	NM_005006.6	NP_004997.4	P28331	NDUS1_HUMAN	NADH dehydrogenase (ubiquinone) Fe-S protein 1, 75kDa (NADH-coenzyme Q reductase)	401					apoptotic mitochondrial changes (GO:0008637)|ATP metabolic process (GO:0046034)|cellular metabolic process (GO:0044237)|cellular respiration (GO:0045333)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|reactive oxygen species metabolic process (GO:0072593)|regulation of mitochondrial membrane potential (GO:0051881)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrial respiratory chain complex I (GO:0005747)	2 iron, 2 sulfur cluster binding (GO:0051537)|4 iron, 4 sulfur cluster binding (GO:0051539)|electron carrier activity (GO:0009055)|metal ion binding (GO:0046872)|NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(7)|lung(15)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						TGTACCAACCAGAAGAACAACAT	0.325																																					p.416_416del		Atlas-INDEL	.											.	NDUFS1	82	.	0			c.1246_1248del						PASS	.																																			SO:0001651	inframe_deletion	4719	exon12			.		CCDS2366.1, CCDS56162.1, CCDS56163.1, CCDS56164.1, CCDS56165.1	2q33-q34	2011-07-04	2002-08-29		ENSG00000023228	ENSG00000023228	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7707	protein-coding gene	gene with protein product	"""complex I 75kDa subunit"", ""NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial"""	157655	"""NADH dehydrogenase (ubiquinone) Fe-S protein 1 (75kD) (NADH-coenzyme Q reductase)"""			1935949	Standard	NM_005006		Approved	CI-75k	uc010ziq.2	P28331	OTTHUMG00000132892	ENST00000233190.6:c.1203_1205delTCT	chr2.hg19:g.207006725_207006727delAGA	ENSP00000233190:p.Leu402del	101.0	0.0	0		138.0	21.0	0.152174	NM_001199984	B4DIN9|B4DJA0|B4DPG1|B4DUC1|E7ENF3|Q53TR8|Q8N1C4|Q8TCC9	In_Frame_Del	DEL	ENST00000233190.6	hg19	CCDS2366.1																																																																																			.	.	.	none		0.325	NDUFS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256391.4	NM_005006	
