#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_ACHILLES_Lineage_Results_Top_Genes	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_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	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_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	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_Mutation_Status	i_ORegAnno_bin	i_Sequence_Source	i_Sequencer	i_Sequencing_Phase	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_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_match_norm_validation_allele1	i_refseq_mrna_id	i_secondary_variant_classification
ABI1	10006	broad.mit.edu	37	10	27054165	27054165	+	Missense_Mutation	SNP	G	G	T			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3b685193-f1fa-4c1b-949b-bcdb2d1b934c	224a12b0-8203-45e5-a23e-3c913d687bd7	g.chr10:27054165G>T	ENST00000376142.2	-	7	873	c.802C>A	c.(802-804)Cca>Aca	p.P268T	ABI1_ENST00000376140.3_Missense_Mutation_p.P268T|ABI1_ENST00000376160.1_Missense_Mutation_p.P263T|ABI1_ENST00000376138.3_Missense_Mutation_p.P268T|ABI1_ENST00000359188.4_Missense_Mutation_p.P268T|ABI1_ENST00000376137.4_Missense_Mutation_p.P269T|ABI1_ENST00000376139.2_Missense_Mutation_p.P263T|ABI1_ENST00000346832.5_Missense_Mutation_p.P285T|ABI1_ENST00000376166.1_Missense_Mutation_p.P263T|ABI1_ENST00000490841.2_Missense_Mutation_p.P204T|ABI1_ENST00000376170.4_Missense_Mutation_p.P268T|ABI1_ENST00000355394.4_Missense_Mutation_p.P269T|ABI1_ENST00000536334.1_Missense_Mutation_p.P269T|ABI1_ENST00000376134.3_Missense_Mutation_p.P269T	NM_005470.3	NP_005461.2	Q8IZP0	ABI1_HUMAN	abl-interactor 1	268	Pro-rich.				actin polymerization or depolymerization (GO:0008154)|cellular component movement (GO:0006928)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|lamellipodium morphogenesis (GO:0072673)|megakaryocyte development (GO:0035855)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine phosphorylation (GO:0018108)|somitogenesis (GO:0001756)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell junction (GO:0030054)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|intracellular (GO:0005622)|lamellipodium (GO:0030027)|neuron projection (GO:0043005)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|SCAR complex (GO:0031209)	cytoskeletal protein binding (GO:0008092)|protein complex binding (GO:0032403)|protein tyrosine kinase activator activity (GO:0030296)	p.P268T(1)		central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(9)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						ATAGTGGGTGGCGAAGGTGTA	0.363																																																	1	Substitution - Missense(1)	kidney(1)											65.0	62.0	63.0					10																	27054165		2203	4300	6503	SO:0001583	missense	10006			U87166	CCDS7150.1, CCDS31169.1, CCDS31170.1, CCDS31171.1, CCDS53497.1, CCDS53498.1, CCDS53499.1, CCDS53500.1, CCDS53501.1, CCDS73077.1, CCDS73078.1	10p12.1	2009-05-29	2004-03-17	2004-03-19	ENSG00000136754	ENSG00000136754			11320	protein-coding gene	gene with protein product		603050	"""spectrin SH3 domain binding protein 1"""	SSH3BP1		9593709, 9010225	Standard	NM_005470		Approved	E3B1, ABI-1	uc001isx.3	Q8IZP0	OTTHUMG00000017848	ENST00000376142.2:c.802C>A	10.37:g.27054165G>T	ENSP00000365312:p.Pro268Thr	Somatic		WXS	Illumina GAIIx	Phase_I	A9Z1Y6|B3KX62|B4DQ58|H7BXI6|O15147|O76049|O95060|Q5T2R3|Q5T2R4|Q5T2R6|Q5T2R7|Q5T2R9|Q5W070|Q5W072|Q8TB63|Q96S81|Q9NXZ9|Q9NYB8	Missense_Mutation	SNP	ENST00000376142.2	37	CCDS7150.1	.	.	.	.	.	.	.	.	.	.	G	19.68	3.872929	0.72180	.	.	ENSG00000136754	ENST00000376138;ENST00000376170;ENST00000376166;ENST00000376160;ENST00000376142;ENST00000359188;ENST00000376139;ENST00000355394;ENST00000346832;ENST00000376134;ENST00000376137;ENST00000536334;ENST00000490841;ENST00000376140	T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.44482	1.12;1.14;1.11;1.05;1.03;1.03;1.02;1.13;1.1;0.92;1.11;1.08;1.05;1.04	5.7	5.7	0.88788	.	0.276343	0.41938	D	0.000793	T	0.59582	0.2204	L	0.52011	1.625	0.48288	D	0.999622	D;B;P;D;P;P;B;P;P;B;D;P;P	0.69078	0.958;0.016;0.945;0.997;0.658;0.875;0.361;0.813;0.859;0.411;0.958;0.796;0.658	B;B;P;D;B;P;B;P;P;P;P;P;B	0.66979	0.395;0.015;0.468;0.948;0.358;0.69;0.118;0.76;0.479;0.475;0.783;0.691;0.394	T	0.52472	-0.8571	10	0.35671	T	0.21	-8.2215	19.8201	0.96590	0.0:0.0:1.0:0.0	.	268;268;204;263;134;263;293;268;285;268;263;268;268	B6VEX4;B6VEX3;B4DQ58;Q8IZP0-10;B4DKX2;Q5T2R9;Q59G41;Q8IZP0-6;B3KX62;Q8IZP0-3;Q8IZP0-5;Q8IZP0-9;Q8IZP0	.;.;.;.;.;.;.;.;.;.;.;.;ABI1_HUMAN	T	268;268;263;263;268;268;263;269;285;269;269;269;204;268	ENSP00000365308:P268T;ENSP00000365340:P268T;ENSP00000365336:P263T;ENSP00000365330:P263T;ENSP00000365312:P268T;ENSP00000352114:P268T;ENSP00000365309:P263T;ENSP00000347555:P269T;ENSP00000279599:P285T;ENSP00000365304:P269T;ENSP00000365307:P269T;ENSP00000439646:P269T;ENSP00000440101:P204T;ENSP00000365310:P268T	ENSP00000279599:P285T	P	-	1	0	ABI1	27094171	1.000000	0.71417	1.000000	0.80357	0.925000	0.55904	4.840000	0.62817	2.693000	0.91896	0.563000	0.77884	CCA		0.363	ABI1-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000047287.1		NM_005470	
AK2	204	hgsc.bcm.edu;ucsc.edu	37	1	33476404	33476404	+	3'UTR	SNP	T	T	G	rs76230073	byFrequency	TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3b685193-f1fa-4c1b-949b-bcdb2d1b934c	224a12b0-8203-45e5-a23e-3c913d687bd7	g.chr1:33476404T>G	ENST00000373449.2	-	0	766				RP1-117O3.2_ENST00000427524.1_RNA|AK2_ENST00000491241.1_5'UTR|AK2_ENST00000548033.1_3'UTR|AK2_ENST00000467905.1_3'UTR	NM_001199199.1|NM_013411.4	NP_001186128.1|NP_037543.1			adenylate kinase 2											kidney(1)|large_intestine(2)|lung(4)|skin(1)	8		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)				ATGAGCAGTGTTGCAGTCTCG	0.542																																																	0													84.0	78.0	80.0					1																	33476404		2203	4300	6503	SO:0001624	3_prime_UTR_variant	204			U84371	CCDS373.1, CCDS374.1	1p35.1	2014-09-17			ENSG00000004455	ENSG00000004455	2.7.4.3	"""Adenylate kinases"""	362	protein-coding gene	gene with protein product		103020				8843353, 6961883	Standard	NM_013411		Approved		uc001bwp.2	P54819	OTTHUMG00000004131	ENST00000373449.2:c.*26A>C	1.37:g.33476404T>G		Somatic		WXS	Illumina HiSeq	Phase_I		RNA	SNP	ENST00000373449.2	37	CCDS373.1																																																																																				0.542	AK2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011884.1		NM_001625	
AKAP6	9472	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	14	33293956	33293956	+	Nonsense_Mutation	SNP	C	C	T			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	3b685193-f1fa-4c1b-949b-bcdb2d1b934c	224a12b0-8203-45e5-a23e-3c913d687bd7	g.chr14:33293956C>T	ENST00000280979.4	+	13	7107	c.6937C>T	c.(6937-6939)Cga>Tga	p.R2313*	AKAP6_ENST00000557272.1_Intron	NM_004274.4	NP_004265.3	Q13023	AKAP6_HUMAN	A kinase (PRKA) anchor protein 6	2313					action potential (GO:0001508)|cAMP-mediated signaling (GO:0019933)|cellular response to cAMP (GO:0071320)|cellular response to cytokine stimulus (GO:0071345)|negative regulation of cAMP biosynthetic process (GO:0030818)|positive regulation of calcineurin-NFAT signaling cascade (GO:0070886)|positive regulation of cell growth (GO:0030307)|positive regulation of cell growth involved in cardiac muscle cell development (GO:0061051)|positive regulation of delayed rectifier potassium channel activity (GO:1902261)|positive regulation of NFAT protein import into nucleus (GO:0051533)|positive regulation of potassium ion transmembrane transport (GO:1901381)|positive regulation of protein phosphatase type 2B activity (GO:0032514)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|positive regulation of ryanodine-sensitive calcium-release channel activity (GO:0060316)|protein targeting (GO:0006605)|regulation of membrane repolarization (GO:0060306)|regulation of protein kinase A signaling (GO:0010738)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)	calcium channel complex (GO:0034704)|caveola (GO:0005901)|cytoplasm (GO:0005737)|intercalated disc (GO:0014704)|junctional sarcoplasmic reticulum membrane (GO:0014701)|nuclear envelope (GO:0005635)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)	adenylate cyclase binding (GO:0008179)|ion channel binding (GO:0044325)|protein anchor (GO:0043495)|protein complex scaffold (GO:0032947)|protein kinase A binding (GO:0051018)|protein kinase A regulatory subunit binding (GO:0034237)	p.R2313*(1)		NS(2)|breast(10)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(25)|lung(42)|ovary(5)|pancreas(2)|prostate(3)|skin(9)|urinary_tract(2)	122	Breast(36;0.0388)|Prostate(35;0.15)		LUAD - Lung adenocarcinoma(48;0.00107)|Lung(238;0.00677)|STAD - Stomach adenocarcinoma(7;0.116)	GBM - Glioblastoma multiforme(265;0.019)		TCATGAAAAACGACATAGAAA	0.418																																					Melanoma(49;821 1200 7288 13647 42351)												1	Substitution - Nonsense(1)	kidney(1)											65.0	69.0	68.0					14																	33293956		2146	4281	6427	SO:0001587	stop_gained	9472			AB002309	CCDS9644.1	14q12	2008-08-11			ENSG00000151320	ENSG00000151320		"""A-kinase anchor proteins"""	376	protein-coding gene	gene with protein product	"""protein kinase A anchoring protein 6"""	604691				7721854, 9205841	Standard	NM_004274		Approved	KIAA0311, mAKAP, AKAP100, PRKA6, ADAP6	uc001wrq.3	Q13023	OTTHUMG00000140207	ENST00000280979.4:c.6937C>T	14.37:g.33293956C>T	ENSP00000280979:p.Arg2313*	Somatic		WXS	Illumina HiSeq	Phase_I	A7E242|A7E2D4|O15028	Nonsense_Mutation	SNP	ENST00000280979.4	37	CCDS9644.1	.	.	.	.	.	.	.	.	.	.	C	46	12.390023	0.99663	.	.	ENSG00000151320	ENST00000280979	.	.	.	5.45	4.56	0.56223	.	0.549985	0.16265	N	0.222066	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	3.1872	9.2416	0.37500	0.2078:0.6604:0.1318:0.0	.	.	.	.	X	2313	.	ENSP00000280979:R2313X	R	+	1	2	AKAP6	32363707	0.981000	0.34729	0.640000	0.29408	0.702000	0.40608	0.920000	0.28705	1.290000	0.44636	0.467000	0.42956	CGA		0.418	AKAP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276617.2		NM_004274	
AMBRA1	55626	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	46563577	46563577	+	Missense_Mutation	SNP	A	A	G			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3b685193-f1fa-4c1b-949b-bcdb2d1b934c	224a12b0-8203-45e5-a23e-3c913d687bd7	g.chr11:46563577A>G	ENST00000458649.2	-	7	2408	c.1990T>C	c.(1990-1992)Tcc>Ccc	p.S664P	AMBRA1_ENST00000528950.1_Missense_Mutation_p.S664P|AMBRA1_ENST00000298834.3_Missense_Mutation_p.S664P|AMBRA1_ENST00000533727.1_Missense_Mutation_p.S574P|AMBRA1_ENST00000426438.1_Missense_Mutation_p.S664P|AMBRA1_ENST00000314845.3_Missense_Mutation_p.S574P|AMBRA1_ENST00000534300.1_Missense_Mutation_p.S664P			Q9C0C7	AMRA1_HUMAN	autophagy/beclin-1 regulator 1	664					autophagy (GO:0006914)|cell differentiation (GO:0030154)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron apoptotic process (GO:0043524)|neural tube development (GO:0021915)	axoneme (GO:0005930)|cytoplasm (GO:0005737)|phagocytic vesicle (GO:0045335)		p.S664P(1)|p.S574P(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(6)|lung(10)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	39				GBM - Glioblastoma multiforme(35;0.0435)|Lung(87;0.182)		GATCTGCTGGACTGGGTGTAA	0.552																																																	2	Substitution - Missense(2)	kidney(2)											97.0	89.0	92.0					11																	46563577		2201	4299	6500	SO:0001583	missense	55626			AB051523	CCDS31475.1, CCDS58132.1, CCDS73281.1	11p11.2	2013-01-09			ENSG00000110497	ENSG00000110497		"""WD repeat domain containing"", ""DDB1 and CUL4 associated factors"""	25990	protein-coding gene	gene with protein product	"""WD repeat domain 94"", ""DDB1 and CUL4 associated factor 3"""	611359				17622796, 17603510, 17589504	Standard	NM_001267782		Approved	FLJ20294, KIAA1736, WDR94, DCAF3	uc001ncv.3	Q9C0C7	OTTHUMG00000166500	ENST00000458649.2:c.1990T>C	11.37:g.46563577A>G	ENSP00000415327:p.Ser664Pro	Somatic		WXS	Illumina HiSeq	Phase_I	A6XN33|D3DQP8|G3V193|Q86XD6|Q9H8Z0|Q9NXE7	Missense_Mutation	SNP	ENST00000458649.2	37		.	.	.	.	.	.	.	.	.	.	A	8.336	0.827695	0.16749	.	.	ENSG00000110497	ENST00000314845;ENST00000533727;ENST00000534300;ENST00000426438;ENST00000298834;ENST00000314823;ENST00000458649;ENST00000528950	D;T;D;T;D;D;T	0.90504	-2.68;-0.73;-2.68;-0.47;-2.68;-2.68;-0.47	5.79	2.02	0.26589	.	0.213506	0.50627	D	0.000111	T	0.75398	0.3844	N	0.04508	-0.205	0.43617	D	0.995992	B;B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0;0.0	B;B;B;B;B;B	0.06405	0.0;0.002;0.002;0.001;0.001;0.001	T	0.66571	-0.5890	10	0.37606	T	0.19	.	6.3951	0.21609	0.6193:0.2531:0.1276:0.0	.	664;664;664;574;574;574	Q9C0C7;Q9C0C7-3;Q9C0C7-2;G3V193;Q9C0C7-5;Q9C0C7-4	AMRA1_HUMAN;.;.;.;.;.	P	574;574;664;664;664;574;664;664	ENSP00000318313:S574P;ENSP00000433372:S574P;ENSP00000431926:S664P;ENSP00000410899:S664P;ENSP00000298834:S664P;ENSP00000415327:S664P;ENSP00000433945:S664P	ENSP00000298834:S664P	S	-	1	0	AMBRA1	46520153	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	1.298000	0.33412	0.993000	0.38866	0.533000	0.62120	TCC		0.552	AMBRA1-005	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000390103.1		NM_017749	
ANKRD20A1	84210	broad.mit.edu	37	9	67934791	67934794	+	Frame_Shift_Del	DEL	AAAG	AAAG	-	rs375030402|rs550666541	byFrequency	TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08	AAAG	AAAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3b685193-f1fa-4c1b-949b-bcdb2d1b934c	224a12b0-8203-45e5-a23e-3c913d687bd7	g.chr9:67934791_67934794delAAAG	ENST00000377477.2	+	4	673_676	c.561_564delAAAG	c.(559-564)aaaaagfs	p.KK187fs	RNU6-368P_ENST00000391117.1_RNA	NM_032250.3	NP_115626.2	Q5TYW2	A20A1_HUMAN	ankyrin repeat domain 20 family, member A1	187						plasma membrane (GO:0005886)				kidney(1)|large_intestine(4)|lung(5)|urinary_tract(1)	11						TTTTATTGAAAAAGAAAGCAAGTT	0.309														73	0.0145767	0.0	0.0086	5008	,	,		20736	0.003		0.0239	False		,,,				2504	0.0409																0																																										SO:0001589	frameshift_variant	441425			AL136793	CCDS6620.1	9p12	2014-04-16	2005-08-23	2005-08-23	ENSG00000196774	ENSG00000260691		"""Ankyrin repeat domain containing"""	23665	protein-coding gene	gene with protein product			"""ankyrin repeat domain 20A"""	ANKRD20A			Standard	NM_032250		Approved	DKFZp434A171		Q5TYW2	OTTHUMG00000188594	ENST00000377477.2:c.561_564delAAAG	9.37:g.67934795_67934798delAAAG	ENSP00000366697:p.Lys187fs	Somatic		WXS	Illumina GAIIx	Phase_I	Q9H0H6	Frame_Shift_Del	DEL	ENST00000377477.2	37	CCDS6620.1																																																																																				0.309	ANKRD20A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083800.1			
ARFGEF2	10564	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	20	47591319	47591319	+	Missense_Mutation	SNP	A	A	C			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3b685193-f1fa-4c1b-949b-bcdb2d1b934c	224a12b0-8203-45e5-a23e-3c913d687bd7	g.chr20:47591319A>C	ENST00000371917.4	+	13	1682	c.1682A>C	c.(1681-1683)aAg>aCg	p.K561T		NM_006420.2	NP_006411.2	Q9Y6D5	BIG2_HUMAN	ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited)	561					endomembrane system organization (GO:0010256)|endosome organization (GO:0007032)|exocytosis (GO:0006887)|Golgi to plasma membrane transport (GO:0006893)|intracellular signal transduction (GO:0035556)|positive regulation of GTPase activity (GO:0043547)|positive regulation of tumor necrosis factor production (GO:0032760)|protein transport (GO:0015031)|receptor recycling (GO:0001881)|regulation of ARF protein signal transduction (GO:0032012)|vesicle-mediated transport (GO:0016192)	asymmetric synapse (GO:0032279)|axonemal microtubule (GO:0005879)|cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|recycling endosome (GO:0055037)|symmetric synapse (GO:0032280)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|GABA receptor binding (GO:0050811)|guanyl-nucleotide exchange factor activity (GO:0005085)|protein kinase A regulatory subunit binding (GO:0034237)	p.K561T(1)		breast(7)|cervix(2)|endometrium(8)|kidney(4)|large_intestine(11)|lung(19)|ovary(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	63			BRCA - Breast invasive adenocarcinoma(12;0.00148)|Colorectal(8;0.198)			AGCCTGAGGAAGAAAGGCCTG	0.517																																					Esophageal Squamous(176;1738 1974 26285 33069 35354)												1	Substitution - Missense(1)	kidney(1)											92.0	80.0	84.0					20																	47591319		2203	4300	6503	SO:0001583	missense	10564			AF084521	CCDS13411.1	20q13.13	2010-08-20			ENSG00000124198	ENSG00000124198		"""A-kinase anchor proteins"""	15853	protein-coding gene	gene with protein product	"""Brefeldin A-inhibited guanine nucleotide-exchange protein 2"""	605371				10212200	Standard	NM_006420		Approved	BIG2	uc002xtx.4	Q9Y6D5	OTTHUMG00000032687	ENST00000371917.4:c.1682A>C	20.37:g.47591319A>C	ENSP00000360985:p.Lys561Thr	Somatic		WXS	Illumina HiSeq	Phase_I	Q5TFT9|Q9NTS1	Missense_Mutation	SNP	ENST00000371917.4	37	CCDS13411.1	.	.	.	.	.	.	.	.	.	.	A	20.7	4.027477	0.75390	.	.	ENSG00000124198	ENST00000538445;ENST00000371917	T	0.65364	-0.15	5.66	5.66	0.87406	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.56455	0.1986	L	0.45698	1.435	0.80722	D	1	B	0.20780	0.048	B	0.23419	0.046	T	0.51926	-0.8643	10	0.20046	T	0.44	.	15.9017	0.79384	1.0:0.0:0.0:0.0	.	561	Q9Y6D5	BIG2_HUMAN	T	561	ENSP00000360985:K561T	ENSP00000360985:K561T	K	+	2	0	ARFGEF2	47024726	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.310000	0.96267	2.153000	0.67306	0.460000	0.39030	AAG		0.517	ARFGEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079627.1		NM_006420	
ATRX	546	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	X	76855280	76855280	+	Missense_Mutation	SNP	C	C	T			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	3b685193-f1fa-4c1b-949b-bcdb2d1b934c	224a12b0-8203-45e5-a23e-3c913d687bd7	g.chrX:76855280C>T	ENST00000373344.5	-	24	5921	c.5707G>A	c.(5707-5709)Gat>Aat	p.D1903N	ATRX_ENST00000395603.3_Missense_Mutation_p.D1865N|ATRX_ENST00000480283.1_5'UTR	NM_000489.3	NP_000480.3	P46100	ATRX_HUMAN	alpha thalassemia/mental retardation syndrome X-linked	1903					ATP catabolic process (GO:0006200)|cellular response to hydroxyurea (GO:0072711)|chromatin remodeling (GO:0006338)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA duplex unwinding (GO:0032508)|DNA methylation (GO:0006306)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication-independent nucleosome assembly (GO:0006336)|forebrain development (GO:0030900)|negative regulation of telomeric RNA transcription from RNA pol II promoter (GO:1901581)|nucleosome assembly (GO:0006334)|positive regulation of nuclear cell cycle DNA replication (GO:0010571)|positive regulation of telomere maintenance (GO:0032206)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|replication fork processing (GO:0031297)|seminiferous tubule development (GO:0072520)|Sertoli cell development (GO:0060009)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nuclear heterochromatin (GO:0005720)|nucleolus (GO:0005730)|nucleus (GO:0005634)|SWI/SNF superfamily-type complex (GO:0070603)|telomeric heterochromatin (GO:0031933)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|chromo shadow domain binding (GO:0070087)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA translocase activity (GO:0015616)|helicase activity (GO:0004386)|histone binding (GO:0042393)|methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)	p.D1903N(2)|p.?(1)		bone(1)|breast(6)|central_nervous_system(31)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(15)|kidney(14)|large_intestine(1)|liver(1)|lung(40)|ovary(2)|pancreas(13)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	145						CTGTCTTCATCAAAATAACCC	0.294			"""Mis, F, N"""		"""Pancreatic neuroendocrine tumors, paediatric GBM"""		ATR-X (alpha thalassemia/mental retardation) syndrome																																	Rec	yes		X	Xq21.1	546	alpha thalassemia/mental retardation syndrome X-linked	yes	E	3	Substitution - Missense(2)|Unknown(1)	kidney(2)|bone(1)											44.0	42.0	43.0					X																	76855280		2203	4294	6497	SO:0001583	missense	546			U72937	CCDS14434.1, CCDS14435.1	Xq21.1	2014-06-17	2010-06-24		ENSG00000085224	ENSG00000085224			886	protein-coding gene	gene with protein product	"""RAD54 homolog (S. cerevisiae)"""	300032	"""alpha thalassemia/mental retardation syndrome X-linked (RAD54 (S. cerevisiae) homolog)"", ""Juberg-Marsidi syndrome"""	RAD54, JMS		7874112, 1415255, 8503439, 8630485	Standard	NM_000489		Approved	XH2, XNP	uc004ecp.4	P46100	OTTHUMG00000022686	ENST00000373344.5:c.5707G>A	X.37:g.76855280C>T	ENSP00000362441:p.Asp1903Asn	Somatic		WXS	Illumina HiSeq	Phase_I	D3DTE2|P51068|Q15886|Q59FB5|Q59H31|Q5H9A2|Q5JWI4|Q7Z2J1|Q9H0Z1|Q9NTS3	Missense_Mutation	SNP	ENST00000373344.5	37	CCDS14434.1	.	.	.	.	.	.	.	.	.	.	C	19.38	3.816521	0.70912	.	.	ENSG00000085224	ENST00000373344;ENST00000395603	D;D	0.92858	-3.12;-3.12	5.34	5.34	0.76211	.	0.000000	0.85682	U	0.000000	D	0.94032	0.8088	L	0.38175	1.15	0.80722	D	1	D;D	0.89917	1.0;0.988	D;P	0.87578	0.998;0.788	D	0.94275	0.7514	10	0.51188	T	0.08	-12.2217	18.3055	0.90179	0.0:1.0:0.0:0.0	.	1865;1903	P46100-4;P46100	.;ATRX_HUMAN	N	1903;1865	ENSP00000362441:D1903N;ENSP00000378967:D1865N	ENSP00000362441:D1903N	D	-	1	0	ATRX	76741936	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	7.445000	0.80570	2.348000	0.79779	0.594000	0.82650	GAT		0.294	ATRX-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058860.2		NM_000489	
BNC1	646	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	15	83933213	83933213	+	Missense_Mutation	SNP	A	A	G			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3b685193-f1fa-4c1b-949b-bcdb2d1b934c	224a12b0-8203-45e5-a23e-3c913d687bd7	g.chr15:83933213A>G	ENST00000345382.2	-	4	875	c.790T>C	c.(790-792)Tat>Cat	p.Y264H	BNC1_ENST00000569704.1_Missense_Mutation_p.Y257H|RP11-382A20.4_ENST00000565495.1_RNA	NM_001717.3	NP_001708.3	Q01954	BNC1_HUMAN	basonuclin 1	264					chromosome organization (GO:0051276)|epidermis development (GO:0008544)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|regulation of transcription from RNA polymerase I promoter (GO:0006356)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.Y264H(1)		NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(18)|ovary(4)|prostate(2)|skin(4)|urinary_tract(1)	56						TCCAACATATATTGTTCGGGC	0.498																																																	1	Substitution - Missense(1)	kidney(1)											83.0	82.0	82.0					15																	83933213		2203	4300	6503	SO:0001583	missense	646			L03427	CCDS10324.1, CCDS73771.1	15q25.1	2013-05-20	2004-04-30	2004-05-04	ENSG00000169594	ENSG00000169594		"""Zinc fingers, C2H2-type"""	1081	protein-coding gene	gene with protein product		601930	"""basonuclin"""	BNC		1332044	Standard	NM_001717		Approved	HsT19447	uc002bjt.1	Q01954	OTTHUMG00000147362	ENST00000345382.2:c.790T>C	15.37:g.83933213A>G	ENSP00000307041:p.Tyr264His	Somatic		WXS	Illumina HiSeq	Phase_I	Q15840	Missense_Mutation	SNP	ENST00000345382.2	37	CCDS10324.1	.	.	.	.	.	.	.	.	.	.	A	5.301	0.241001	0.10077	.	.	ENSG00000169594	ENST00000345382;ENST00000541809	T	0.03272	3.99	5.23	2.85	0.33270	.	0.630970	0.16849	N	0.197006	T	0.02688	0.0081	L	0.33137	0.985	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.06405	0.002;0.002	T	0.46386	-0.9195	10	0.15499	T	0.54	-9.3412	4.0817	0.09929	0.6411:0.2176:0.1413:0.0	.	257;264	F5GY04;Q01954	.;BNC1_HUMAN	H	264;257	ENSP00000307041:Y264H	ENSP00000307041:Y264H	Y	-	1	0	BNC1	81724217	0.469000	0.25846	0.026000	0.17262	0.965000	0.64279	1.807000	0.38902	0.985000	0.38656	0.533000	0.62120	TAT		0.498	BNC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304006.1		NM_001717	
C1QTNF9	338872	broad.mit.edu;hgsc.bcm.edu	37	13	24893010	24893010	+	Missense_Mutation	SNP	G	G	T			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3b685193-f1fa-4c1b-949b-bcdb2d1b934c	224a12b0-8203-45e5-a23e-3c913d687bd7	g.chr13:24893010G>T	ENST00000382071.2	+	3	306	c.221G>T	c.(220-222)gGa>gTa	p.G74V	C1QTNF9-AS1_ENST00000449656.1_RNA|RP11-307N16.6_ENST00000382141.4_3'UTR|C1QTNF9_ENST00000332018.4_Missense_Mutation_p.G74V			P0C862	C1T9A_HUMAN	C1q and tumor necrosis factor related protein 9	74	Collagen-like 1.					collagen trimer (GO:0005581)|extracellular region (GO:0005576)		p.G74V(1)		endometrium(1)|kidney(2)|lung(6)	9		all_cancers(29;3.55e-20)|all_epithelial(30;4.25e-17)|all_lung(29;1.04e-16)|Lung SC(185;0.0225)|Breast(139;0.052)		all cancers(112;0.00565)|Epithelial(112;0.027)|OV - Ovarian serous cystadenocarcinoma(117;0.115)|Lung(94;0.159)		GGAGAGAAGGGAGAACGAGGT	0.453																																																	1	Substitution - Missense(1)	kidney(1)											156.0	154.0	154.0					13																	24893010		2203	4298	6501	SO:0001583	missense	338872			BC040438	CCDS9306.1	13q12.12	2010-08-18			ENSG00000240654	ENSG00000240654			28732	protein-coding gene	gene with protein product		614285				12975309, 18787108	Standard	NM_178540		Approved	MGC48915, CTRP9, C1QTNF9A, AQL1	uc001upj.3	P0C862	OTTHUMG00000016576	ENST00000382071.2:c.221G>T	13.37:g.24893010G>T	ENSP00000371503:p.Gly74Val	Somatic		WXS	Illumina HiSeq	Phase_I	A2A3T6|Q0VGC5|Q5VX65|Q5VX66|Q8IUU4	Missense_Mutation	SNP	ENST00000382071.2	37	CCDS9306.1	.	.	.	.	.	.	.	.	.	.	g	13.91	2.377102	0.42105	.	.	ENSG00000240654	ENST00000382071;ENST00000332018;ENST00000382066	D;D	0.99637	-6.29;-6.29	3.59	3.59	0.41128	.	0.000000	0.85682	D	0.000000	D	0.99746	0.9899	H	0.96576	3.845	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.96890	0.9652	10	0.87932	D	0	.	14.7045	0.69179	0.0:0.0:1.0:0.0	.	74	P0C862	C1T9A_HUMAN	V	74	ENSP00000371503:G74V;ENSP00000333737:G74V	ENSP00000333737:G74V	G	+	2	0	C1QTNF9	23791010	1.000000	0.71417	1.000000	0.80357	0.167000	0.22549	6.319000	0.72871	1.982000	0.57802	0.603000	0.83216	GGA		0.453	C1QTNF9-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044177.1		NM_178540	
CDH18	1016	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	5	19612594	19612594	+	Missense_Mutation	SNP	C	C	T			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3b685193-f1fa-4c1b-949b-bcdb2d1b934c	224a12b0-8203-45e5-a23e-3c913d687bd7	g.chr5:19612594C>T	ENST00000507958.1	-	8	1750	c.760G>A	c.(760-762)Gtc>Atc	p.V254I	CDH18_ENST00000506372.1_Missense_Mutation_p.V254I|CDH18_ENST00000274170.4_Missense_Mutation_p.V254I|CDH18_ENST00000511273.1_Missense_Mutation_p.V254I|CDH18_ENST00000382275.1_Missense_Mutation_p.V254I|CDH18_ENST00000502796.1_Missense_Mutation_p.V254I			Q13634	CAD18_HUMAN	cadherin 18, type 2	254	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.V254I(2)		breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(24)|lung(76)|ovary(5)|prostate(4)|skin(6)|upper_aerodigestive_tract(1)	138	Lung NSC(1;0.00734)|all_lung(1;0.0197)					GTGATGTTGACTGTTGTAGAT	0.408																																																	2	Substitution - Missense(2)	kidney(2)											211.0	189.0	196.0					5																	19612594		2203	4300	6503	SO:0001583	missense	1016			U59325	CCDS3889.1, CCDS54835.1, CCDS75229.1	5p14.3	2010-01-26			ENSG00000145526	ENSG00000145526		"""Cadherins / Major cadherins"""	1757	protein-coding gene	gene with protein product		603019				9030594, 10191097	Standard	NM_004934		Approved	CDH14, EY-CADHERIN	uc003jgd.3	Q13634	OTTHUMG00000090578	ENST00000507958.1:c.760G>A	5.37:g.19612594C>T	ENSP00000425093:p.Val254Ile	Somatic		WXS	Illumina HiSeq	Phase_I	A8K0I2|B4DHG6|Q8N5Z2	Missense_Mutation	SNP	ENST00000507958.1	37	CCDS3889.1	.	.	.	.	.	.	.	.	.	.	C	14.29	2.490497	0.44249	.	.	ENSG00000145526	ENST00000382275;ENST00000507958;ENST00000542864;ENST00000274170;ENST00000506372;ENST00000502796;ENST00000515257;ENST00000511273	T;T;T;T;T;T;T	0.64260	-0.09;-0.09;-0.09;-0.09;-0.09;-0.09;-0.09	5.95	5.95	0.96441	Cadherin (5);Cadherin-like (1);	0.061088	0.64402	D	0.000002	T	0.56572	0.1994	L	0.53671	1.685	0.41594	D	0.988816	B;B	0.19935	0.04;0.023	B;B	0.23275	0.045;0.045	T	0.50775	-0.8788	9	.	.	.	.	12.2837	0.54779	0.0:0.9225:0.0:0.0775	.	254;254	B4DHG6;Q13634	.;CAD18_HUMAN	I	254;254;254;254;254;254;200;254	ENSP00000371710:V254I;ENSP00000425093:V254I;ENSP00000274170:V254I;ENSP00000424931:V254I;ENSP00000422138:V254I;ENSP00000427383:V200I;ENSP00000425854:V254I	.	V	-	1	0	CDH18	19648351	0.999000	0.42202	0.965000	0.40720	0.474000	0.32979	3.747000	0.55134	2.817000	0.96982	0.563000	0.77884	GTC		0.408	CDH18-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366747.1		NM_004934	
CNKSR1	10256	hgsc.bcm.edu	37	1	26510311	26510311	+	Frame_Shift_Del	DEL	C	C	-	rs201305445	byFrequency	TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3b685193-f1fa-4c1b-949b-bcdb2d1b934c	224a12b0-8203-45e5-a23e-3c913d687bd7	g.chr1:26510311delC	ENST00000374253.5	+	9	905	c.866delC	c.(865-867)accfs	p.T289fs	CNKSR1_ENST00000361530.6_Frame_Shift_Del_p.T282fs|CNKSR1_ENST00000531191.1_Frame_Shift_Del_p.T24fs	NM_006314.2	NP_006305.2	Q969H4	CNKR1_HUMAN	connector enhancer of kinase suppressor of Ras 1	289	Pro-rich.				Ras protein signal transduction (GO:0007265)|Rho protein signal transduction (GO:0007266)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell cortex (GO:0005938)|cell-cell junction (GO:0005911)|plasma membrane (GO:0005886)	protein binding, bridging (GO:0030674)			breast(4)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(8)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	28		Colorectal(325;3.46e-05)|all_lung(284;0.000116)|Lung NSC(340;0.000154)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0133)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0298)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;2.72e-26)|Colorectal(126;1.24e-08)|COAD - Colon adenocarcinoma(152;9.31e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00072)|BRCA - Breast invasive adenocarcinoma(304;0.000959)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.00823)|READ - Rectum adenocarcinoma(331;0.0649)		ATACCGGAGACCCCCCCACAG	0.667														59	0.0117812	0.0008	0.0202	5008	,	,		6575	0.001		0.0348	False		,,,				2504	0.0082				NSCLC(180;1396 2109 28270 30756 34275)												0										5,37,4224		0,0,5,0,37,2091	44.0	46.0	45.0			-0.5	0.0	1		47	1,431,7822		0,0,1,13,405,3708	no	codingComplex	CNKSR1	NM_006314.2		0,0,6,13,442,5799	A1A1,A1A2,A1R,A2A2,A2R,RR		5.2338,0.9845,3.7859			26510311	6,468,12046	2203	4300	6503	SO:0001589	frameshift_variant	10256			AF100153	CCDS276.1, CCDS72732.1	1p35.3	2013-01-10			ENSG00000142675	ENSG00000142675		"""Sterile alpha motif (SAM) domain containing"", ""Pleckstrin homology (PH) domain containing"""	19700	protein-coding gene	gene with protein product		603272				9814705	Standard	NM_006314		Approved	CNK1, KSR, CNK	uc001blm.4	Q969H4	OTTHUMG00000007541	ENST00000374253.5:c.866delC	1.37:g.26510311delC	ENSP00000363371:p.Thr289fs	Somatic		WXS	Illumina HiSeq	Phase_I	B1AMW9|O95381	Frame_Shift_Del	DEL	ENST00000374253.5	37																																																																																					0.667	CNKSR1-007	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000089943.2		NM_006314	
CTSG	1511	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	14	25043508	25043508	+	Silent	SNP	G	G	A			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3b685193-f1fa-4c1b-949b-bcdb2d1b934c	224a12b0-8203-45e5-a23e-3c913d687bd7	g.chr14:25043508G>A	ENST00000216336.2	-	4	573	c.537C>T	c.(535-537)taC>taT	p.Y179Y		NM_001911.2	NP_001902.1	P08311	CATG_HUMAN	cathepsin G	179	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				angiotensin maturation (GO:0002003)|cellular protein metabolic process (GO:0044267)|defense response to fungus (GO:0050832)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|immune response (GO:0006955)|negative regulation of growth of symbiont in host (GO:0044130)|neutrophil mediated killing of gram-positive bacterium (GO:0070946)|positive regulation of immune response (GO:0050778)|proteolysis (GO:0006508)|response to lipopolysaccharide (GO:0032496)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|secretory granule (GO:0030141)	heparin binding (GO:0008201)|peptidase activity (GO:0008233)|serine-type endopeptidase activity (GO:0004252)	p.Y179Y(1)		autonomic_ganglia(1)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(2)|skin(1)|urinary_tract(1)	25				GBM - Glioblastoma multiforme(265;0.0269)		TTCGGGGGTCGTAGGAACCGA	0.627																																																	1	Substitution - coding silent(1)	kidney(1)											91.0	76.0	81.0					14																	25043508		2203	4300	6503	SO:0001819	synonymous_variant	1511			M16117	CCDS9631.1	14q12	2013-02-25			ENSG00000100448	ENSG00000100448		"""Cathepsins"", ""Endogenous ligands"""	2532	protein-coding gene	gene with protein product		116830				2569462	Standard	NM_001911		Approved	CG	uc001wpq.3	P08311	OTTHUMG00000140182	ENST00000216336.2:c.537C>T	14.37:g.25043508G>A		Somatic		WXS	Illumina HiSeq	Phase_I	Q6IBJ6|Q9UCA5|Q9UCU6	Silent	SNP	ENST00000216336.2	37	CCDS9631.1																																																																																				0.627	CTSG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276536.2		NM_001911	
CYC1	1537	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	8	145151520	145151520	+	Silent	SNP	C	C	T			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3b685193-f1fa-4c1b-949b-bcdb2d1b934c	224a12b0-8203-45e5-a23e-3c913d687bd7	g.chr8:145151520C>T	ENST00000318911.4	+	5	718	c.645C>T	c.(643-645)ctC>ctT	p.L215L	SHARPIN_ENST00000533948.1_5'Flank	NM_001916.3	NP_001907	P08574	CY1_HUMAN	cytochrome c-1	215			L -> F (in MC3DN6). {ECO:0000269|PubMed:23910460}.		cellular metabolic process (GO:0044237)|respiratory electron transport chain (GO:0022904)|response to glucagon (GO:0033762)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|respiratory chain (GO:0070469)	electron transporter, transferring electrons from CoQH2-cytochrome c reductase complex and cytochrome c oxidase complex activity (GO:0045155)|heme binding (GO:0020037)|iron ion binding (GO:0005506)	p.L215L(1)		endometrium(1)|kidney(1)|large_intestine(2)|lung(8)|ovary(1)|prostate(2)	15	all_cancers(97;2.87e-11)|all_epithelial(106;2.16e-09)|Lung NSC(106;5.89e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;3.38e-41)|Epithelial(56;8.71e-40)|all cancers(56;3e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			TCTCCCTGCTCACGGGCTACT	0.602											OREG0019052	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																					1	Substitution - coding silent(1)	kidney(1)											99.0	83.0	88.0					8																	145151520		2203	4300	6503	SO:0001819	synonymous_variant	1537			BC001006	CCDS6415.1	8q24	2011-07-04			ENSG00000179091	ENSG00000179091		"""Mitochondrial respiratory chain complex / Complex III"""	2579	protein-coding gene	gene with protein product		123980					Standard	NM_001916		Approved	UQCR4	uc003zaz.4	P08574	OTTHUMG00000165242	ENST00000318911.4:c.645C>T	8.37:g.145151520C>T		Somatic	1692	WXS	Illumina HiSeq	Phase_I	Q5U062|Q6FHS7	Silent	SNP	ENST00000318911.4	37	CCDS6415.1																																																																																				0.602	CYC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382895.1		NM_001916	
CYP46A1	10858	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	14	100191787	100191787	+	Missense_Mutation	SNP	C	C	A			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3b685193-f1fa-4c1b-949b-bcdb2d1b934c	224a12b0-8203-45e5-a23e-3c913d687bd7	g.chr14:100191787C>A	ENST00000261835.3	+	13	1340	c.1236C>A	c.(1234-1236)aaC>aaA	p.N412K	CYP46A1_ENST00000554176.1_Missense_Mutation_p.N249K|CYP46A1_ENST00000423126.2_Missense_Mutation_p.N315K	NM_006668.1	NP_006659.1	Q9Y6A2	CP46A_HUMAN	cytochrome P450, family 46, subfamily A, polypeptide 1	412					bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|cholesterol catabolic process (GO:0006707)|nervous system development (GO:0007399)|small molecule metabolic process (GO:0044281)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	cholesterol 24-hydroxylase activity (GO:0033781)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|steroid hydroxylase activity (GO:0008395)	p.N412K(1)		breast(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(12)|prostate(1)|skin(1)	25		Melanoma(154;0.0866)|all_epithelial(191;0.179)				TGACTTTCAACCCCGATCGCT	0.607																																																	1	Substitution - Missense(1)	kidney(1)											102.0	90.0	94.0					14																	100191787		2203	4300	6503	SO:0001583	missense	10858			AF094480	CCDS9954.1	14q32.2	2013-05-03	2003-02-14	2003-02-28	ENSG00000036530	ENSG00000036530		"""Cytochrome P450s"""	2641	protein-coding gene	gene with protein product		604087	"""cytochrome P450, subfamily 46 (cholesterol 24-hydroxylase)"""	CYP46		10377398	Standard	NM_006668		Approved		uc001ygo.3	Q9Y6A2	OTTHUMG00000171510	ENST00000261835.3:c.1236C>A	14.37:g.100191787C>A	ENSP00000261835:p.Asn412Lys	Somatic		WXS	Illumina HiSeq	Phase_I	B4DHP8|E7EQG9|Q8N2B0	Missense_Mutation	SNP	ENST00000261835.3	37	CCDS9954.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	18.98|18.98	3.738031|3.738031	0.69304|0.69304	.|.	.|.	ENSG00000036530|ENSG00000036530	ENST00000261835;ENST00000423126;ENST00000554176|ENST00000380228	T;T;T|.	0.68624|.	-0.34;-0.27;-0.27|.	4.48|4.48	3.56|3.56	0.40772|0.40772	.|.	0.110477|.	0.64402|.	D|.	0.000014|.	T|T	0.34337|0.34337	0.0894|0.0894	N|N	0.11064|0.11064	0.09|0.09	0.46654|0.46654	D|D	0.999147|0.999147	P;P|.	0.47191|.	0.891;0.757|.	P;P|.	0.52627|.	0.704;0.519|.	T|T	0.09574|0.09574	-1.0668|-1.0668	10|5	0.45353|.	T|.	0.12|.	.|.	9.0371|9.0371	0.36293|0.36293	0.0:0.8891:0.0:0.1109|0.0:0.8891:0.0:0.1109	.|.	249;412|.	Q8N2B0;Q9Y6A2|.	.;CP46A_HUMAN|.	K|T	412;315;249|399	ENSP00000261835:N412K;ENSP00000405779:N315K;ENSP00000450553:N249K|.	ENSP00000261835:N412K|.	N|P	+|+	3|1	2|0	CYP46A1|CYP46A1	99261540|99261540	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.992000|0.992000	0.81027|0.81027	1.337000|1.337000	0.33862|0.33862	2.218000|2.218000	0.71995|0.71995	0.563000|0.563000	0.77884|0.77884	AAC|CCC		0.607	CYP46A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413814.1			
NSG1	27065	broad.mit.edu;hgsc.bcm.edu	37	4	4411393	4411393	+	Missense_Mutation	SNP	G	G	A			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3b685193-f1fa-4c1b-949b-bcdb2d1b934c	224a12b0-8203-45e5-a23e-3c913d687bd7	g.chr4:4411393G>A	ENST00000421177.2	+	8	2331	c.340G>A	c.(340-342)Gat>Aat	p.D114N	NSG1_ENST00000504171.1_Missense_Mutation_p.D75N|NSG1_ENST00000397958.1_Missense_Mutation_p.D114N|NSG1_ENST00000505246.1_Missense_Mutation_p.D114N|NSG1_ENST00000513555.1_Missense_Mutation_p.D114N|NSG1_ENST00000433139.2_Missense_Mutation_p.D114N|NSG1_ENST00000506380.1_Missense_Mutation_p.D114N			P42857	NSG1_HUMAN		114					clathrin coat assembly (GO:0048268)|dopamine receptor signaling pathway (GO:0007212)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)		p.D114N(1)									CGCCTGCCCCGATGGGTTCGT	0.597																																																	1	Substitution - Missense(1)	kidney(1)											136.0	109.0	118.0					4																	4411393		2203	4300	6503	SO:0001583	missense	0																														ENST00000421177.2:c.340G>A	4.37:g.4411393G>A	ENSP00000388823:p.Asp114Asn	Somatic		WXS	Illumina HiSeq	Phase_I	B4DXC5|Q49AQ1	Missense_Mutation	SNP	ENST00000421177.2	37	CCDS3376.1	.	.	.	.	.	.	.	.	.	.	G	17.08	3.298688	0.60195	.	.	ENSG00000168824	ENST00000421177;ENST00000513555;ENST00000505246;ENST00000506380;ENST00000397958;ENST00000433139;ENST00000504171	.	.	.	3.99	3.99	0.46301	.	0.270733	0.35262	N	0.003328	T	0.49915	0.1585	L	0.39245	1.2	0.51767	D	0.99993	P;B	0.35612	0.512;0.107	B;B	0.34038	0.174;0.058	T	0.59974	-0.7353	9	0.87932	D	0	-12.5959	16.2803	0.82673	0.0:0.0:1.0:0.0	.	75;114	B4DXC5;P42857	.;NSG1_HUMAN	N	114;114;114;114;114;114;75	.	ENSP00000381049:D114N	D	+	1	0	AC110814.1	4462294	1.000000	0.71417	0.416000	0.26546	0.741000	0.42261	8.847000	0.92166	2.043000	0.60533	0.561000	0.74099	GAT		0.597	NSG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246799.1			
DHX37	57647	broad.mit.edu	37	12	125465134	125465134	+	Missense_Mutation	SNP	T	T	C			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3b685193-f1fa-4c1b-949b-bcdb2d1b934c	224a12b0-8203-45e5-a23e-3c913d687bd7	g.chr12:125465134T>C	ENST00000308736.2	-	4	738	c.640A>G	c.(640-642)Atg>Gtg	p.M214V	DHX37_ENST00000544745.1_Start_Codon_SNP_p.M1V	NM_032656.3	NP_116045.2	Q8IY37	DHX37_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 37	214							ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)	p.M214V(1)		breast(5)|cervix(1)|endometrium(9)|kidney(5)|large_intestine(11)|liver(1)|lung(27)|ovary(1)|prostate(2)|skin(3)	65	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;8.05e-05)|Epithelial(86;0.000486)|all cancers(50;0.00653)		GGAACAGTCATCCCAGCCGGC	0.692																																																	1	Substitution - Missense(1)	kidney(1)											39.0	41.0	40.0					12																	125465134		2203	4300	6503	SO:0001583	missense	57647			AB040950	CCDS9261.1	12q24.31	2004-03-25	2003-06-13	2003-06-20		ENSG00000150990		"""DEAH-boxes"""	17210	protein-coding gene	gene with protein product			"""DEAD/DEAH box helicase DDX37"""	DDX37		10819331	Standard	NM_032656		Approved	KIAA1517, MGC4322, MGC2695	uc001ugy.3	Q8IY37		ENST00000308736.2:c.640A>G	12.37:g.125465134T>C	ENSP00000311135:p.Met214Val	Somatic		WXS	Illumina GAIIx	Phase_I	Q9BUI7|Q9P211	Missense_Mutation	SNP	ENST00000308736.2	37	CCDS9261.1	.	.	.	.	.	.	.	.	.	.	T	6.602	0.479534	0.12581	.	.	ENSG00000150990	ENST00000308736;ENST00000544745	T;T	0.02787	4.23;4.16	5.05	-0.815	0.10843	.	2.365320	0.01212	N	0.007872	T	0.01800	0.0057	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.43393	-0.9394	10	0.29301	T	0.29	-16.1152	2.3355	0.04246	0.1426:0.0855:0.2939:0.4779	.	214	Q8IY37	DHX37_HUMAN	V	214;1	ENSP00000311135:M214V;ENSP00000439009:M1V	ENSP00000311135:M214V	M	-	1	0	DHX37	124031087	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.554000	0.06006	0.200000	0.20447	0.528000	0.53228	ATG		0.692	DHX37-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			NM_032656	
DST	667	broad.mit.edu;hgsc.bcm.edu	37	6	56472759	56472759	+	Missense_Mutation	SNP	C	C	T			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	PGM			Illumina GAIIx	3b685193-f1fa-4c1b-949b-bcdb2d1b934c	224a12b0-8203-45e5-a23e-3c913d687bd7	g.chr6:56472759C>T	ENST00000361203.3	-	36	6041	c.6034G>A	c.(6034-6036)Gat>Aat	p.D2012N	DST_ENST00000312431.6_Missense_Mutation_p.D2012N|DST_ENST00000244364.6_Intron|DST_ENST00000421834.2_Intron|DST_ENST00000370769.4_Missense_Mutation_p.D2012N|DST_ENST00000370788.2_Intron|DST_ENST00000370754.5_Missense_Mutation_p.D2190N|DST_ENST00000446842.2_Missense_Mutation_p.D1686N			Q03001	DYST_HUMAN	dystonin	2012					axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell motility (GO:0048870)|cytoplasmic microtubule organization (GO:0031122)|cytoskeleton organization (GO:0007010)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|maintenance of cell polarity (GO:0030011)|microtubule cytoskeleton organization (GO:0000226)|regulation of microtubule polymerization or depolymerization (GO:0031110)|response to wounding (GO:0009611)|retrograde axon cargo transport (GO:0008090)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integral component of membrane (GO:0016021)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|neurofilament cytoskeleton (GO:0060053)|nucleus (GO:0005634)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|microtubule plus-end binding (GO:0051010)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)			NS(1)|breast(5)|central_nervous_system(8)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(43)|ovary(7)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	105	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			AAGTCTCCATCGTACAGCAAA	0.393																																																	0													56.0	55.0	55.0					6																	56472759		1930	4127	6057	SO:0001583	missense	667			M22942, M69225	CCDS4959.1, CCDS47443.1, CCDS75474.1	6p12.1	2013-01-10	2004-06-25	2004-07-01	ENSG00000151914	ENSG00000151914		"""EF-hand domain containing"""	1090	protein-coding gene	gene with protein product		113810	"""bullous pemphigoid antigen 1, 230/240kDa"""	BPAG1		2461961, 2276744	Standard	NM_001144770		Approved	BP240, KIAA0728, FLJ21489, FLJ13425, FLJ32235, FLJ30627, CATX-15, BPA, MACF2	uc021zba.2	Q03001	OTTHUMG00000014913	ENST00000361203.3:c.6034G>A	6.37:g.56472759C>T	ENSP00000354508:p.Asp2012Asn	Somatic		WXS	Illumina HiSeq	Phase_I	B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	Intron	SNP	ENST00000361203.3	37		.	.	.	.	.	.	.	.	.	.	C	18.42	3.620645	0.66787	.	.	ENSG00000151914	ENST00000370754;ENST00000370769;ENST00000446842;ENST00000312431;ENST00000361203;ENST00000439203	T;T;T;D;T;T	0.85339	-0.33;-0.36;0.48;-1.97;-0.39;-0.74	5.55	5.55	0.83447	.	0.000000	0.53938	D	0.000044	D	0.91023	0.7176	.	.	.	0.32212	N	0.576451	D	0.89917	1.0	D	0.72075	0.976	D	0.92159	0.5734	8	0.87932	D	0	.	14.8067	0.69962	0.1448:0.8552:0.0:0.0	.	1686	Q03001-9	.	N	2190;2012;1686;2012;2012;1686	ENSP00000359790:D2190N;ENSP00000359805:D2012N;ENSP00000393645:D1686N;ENSP00000307959:D2012N;ENSP00000354508:D2012N;ENSP00000404924:D1686N	ENSP00000307959:D2012N	D	-	1	0	DST	56580718	1.000000	0.71417	0.997000	0.53966	0.986000	0.74619	5.962000	0.70364	2.609000	0.88269	0.563000	0.77884	GAT		0.393	DST-004	NOVEL	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000041021.3		NM_001723	
EDC3	80153	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	15	74925269	74925269	+	Missense_Mutation	SNP	A	A	T			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3b685193-f1fa-4c1b-949b-bcdb2d1b934c	224a12b0-8203-45e5-a23e-3c913d687bd7	g.chr15:74925269A>T	ENST00000315127.4	-	7	1392	c.1211T>A	c.(1210-1212)gTg>gAg	p.V404E	EDC3_ENST00000568176.1_Missense_Mutation_p.V404E|EDC3_ENST00000426797.3_Missense_Mutation_p.V404E	NM_001142444.1|NM_025083.3	NP_001135916.1|NP_079359.2	Q96F86	EDC3_HUMAN	enhancer of mRNA decapping 3	404	YjeF N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00719}.				exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|RNA metabolic process (GO:0016070)	cytosol (GO:0005829)|membrane (GO:0016020)	identical protein binding (GO:0042802)|RNA binding (GO:0003723)	p.V404E(1)		breast(3)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(2)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	16						GACCAGGTCCACAGGGCTAGT	0.602											OREG0023286	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																					1	Substitution - Missense(1)	kidney(1)											61.0	43.0	49.0					15																	74925269		2197	4296	6493	SO:0001583	missense	80153			BC011534	CCDS10267.1	15q24.1	2013-05-02	2013-05-02	2006-07-07	ENSG00000179151	ENSG00000179151			26114	protein-coding gene	gene with protein product		609842	"""yjeF domain containing (E.coli)"", ""LSM16 homolog (EDC3, S. cerevisiae)"", ""enhancer of mRNA decapping 3 homolog (S. cerevisiae)"""	YJDC, LSM16		15225602, 17533573, 22483619	Standard	NM_025083		Approved	FLJ21128, hYjeF_N2-15q23, YJEFN2	uc002aym.3	Q96F86	OTTHUMG00000142815	ENST00000315127.4:c.1211T>A	15.37:g.74925269A>T	ENSP00000320503:p.Val404Glu	Somatic	1156	WXS	Illumina HiSeq	Phase_I	B3KPH0|D3DW61|Q9H797	Missense_Mutation	SNP	ENST00000315127.4	37	CCDS10267.1	.	.	.	.	.	.	.	.	.	.	A	26.3	4.725862	0.89298	.	.	ENSG00000179151	ENST00000315127;ENST00000426797	T;T	0.45668	0.89;0.89	5.6	5.6	0.85130	YjeF-related protein, N-terminal (4);	0.053470	0.85682	D	0.000000	T	0.65354	0.2683	M	0.74881	2.28	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.68496	-0.5393	10	0.59425	D	0.04	-7.0734	15.7774	0.78232	1.0:0.0:0.0:0.0	.	404	Q96F86	EDC3_HUMAN	E	404	ENSP00000320503:V404E;ENSP00000401343:V404E	ENSP00000320503:V404E	V	-	2	0	EDC3	72712322	1.000000	0.71417	0.996000	0.52242	0.998000	0.95712	8.794000	0.91867	2.135000	0.66039	0.459000	0.35465	GTG		0.602	EDC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286399.1		NM_025083	
F11R	50848	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	160969694	160969694	+	Missense_Mutation	SNP	C	C	A	rs553706719		TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3b685193-f1fa-4c1b-949b-bcdb2d1b934c	224a12b0-8203-45e5-a23e-3c913d687bd7	g.chr1:160969694C>A	ENST00000368026.6	-	6	940	c.666G>T	c.(664-666)atG>atT	p.M222I	F11R_ENST00000537746.1_Missense_Mutation_p.M173I|F11R_ENST00000289779.3_3'UTR|F11R_ENST00000472573.1_5'Flank	NM_016946.4	NP_058642.1	Q9Y624	JAM1_HUMAN	F11 receptor	222	Ig-like V-type 2.				blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|epithelial cell differentiation (GO:0030855)|extracellular matrix organization (GO:0030198)|inflammatory response (GO:0006954)|leukocyte migration (GO:0050900)|tight junction assembly (GO:0070830)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	cell junction (GO:0030054)|cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|microtubule cytoskeleton (GO:0015630)|plasma membrane (GO:0005886)|tight junction (GO:0005923)		p.M222I(1)		breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(2)	12	all_cancers(52;6.73e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00207)			CATTTGAAGTCATGGGTGTCC	0.522																																																	1	Substitution - Missense(1)	kidney(1)											92.0	86.0	88.0					1																	160969694		2203	4300	6503	SO:0001583	missense	50848			AF111713	CCDS1213.1	1q21.2-q21.3	2013-01-29	2003-02-07	2003-02-14	ENSG00000158769	ENSG00000158769		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	14685	protein-coding gene	gene with protein product		605721	"""junctional adhesion molecule 1"""	JAM1		10395639, 7646439	Standard	NM_016946		Approved	PAM-1, JCAM, JAM-1, JAM-A, JAMA, CD321	uc009wtt.3	Q9Y624	OTTHUMG00000028602	ENST00000368026.6:c.666G>T	1.37:g.160969694C>A	ENSP00000357005:p.Met222Ile	Somatic		WXS	Illumina HiSeq	Phase_I	B7Z941	Missense_Mutation	SNP	ENST00000368026.6	37	CCDS1213.1	.	.	.	.	.	.	.	.	.	.	C	10.79	1.449640	0.26074	.	.	ENSG00000158769	ENST00000368026;ENST00000335772;ENST00000289779;ENST00000537746;ENST00000436182	T;T;T	0.67345	-0.26;-0.26;-0.26	5.41	2.41	0.29592	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.875727	0.10470	N	0.670825	T	0.31979	0.0814	L	0.34521	1.04	0.09310	N	1	B;B;B;B;B	0.22146	0.065;0.057;0.016;0.016;0.016	B;B;B;B;B	0.23716	0.022;0.048;0.013;0.013;0.013	T	0.26121	-1.0112	10	0.42905	T	0.14	.	5.1023	0.14766	0.1654:0.659:0.0:0.1755	.	226;173;222;222;222	B7Z5W1;B7Z941;Q6FIB4;Q9Y624;D3DVF0	.;.;.;JAM1_HUMAN;.	I	222;222;222;173;226	ENSP00000357005:M222I;ENSP00000440812:M173I;ENSP00000394809:M226I	ENSP00000289779:M222I	M	-	3	0	F11R	159236318	0.006000	0.16342	0.001000	0.08648	0.001000	0.01503	2.130000	0.42064	0.805000	0.34159	0.563000	0.77884	ATG		0.522	F11R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071458.3		NM_016946	
FAM160A2	84067	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	6233079	6233079	+	Missense_Mutation	SNP	G	G	A			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3b685193-f1fa-4c1b-949b-bcdb2d1b934c	224a12b0-8203-45e5-a23e-3c913d687bd7	g.chr11:6233079G>A	ENST00000449352.2	-	12	2839	c.2576C>T	c.(2575-2577)tCc>tTc	p.S859F	FAM160A2_ENST00000529360.1_5'UTR|FAM160A2_ENST00000265978.4_Missense_Mutation_p.S873F			Q8N612	F16A2_HUMAN	family with sequence similarity 160, member A2	859					early endosome to late endosome transport (GO:0045022)|endosome organization (GO:0007032)|endosome to lysosome transport (GO:0008333)|lysosome organization (GO:0007040)|protein transport (GO:0015031)	FHF complex (GO:0070695)		p.S873F(1)		NS(1)|endometrium(3)|kidney(2)|large_intestine(7)|liver(1)|lung(14)|ovary(2)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	42						CTCCCCCAAGGATGGCCTCCG	0.617																																																	1	Substitution - Missense(1)	kidney(1)											92.0	100.0	97.0					11																	6233079		2201	4294	6495	SO:0001583	missense	84067				CCDS7760.1, CCDS44530.1	11p15.4	2008-06-05	2008-06-05	2008-06-05	ENSG00000051009	ENSG00000051009			25378	protein-coding gene	gene with protein product			"""chromosome 11 open reading frame 56"""	C11orf56		11230166, 11214970	Standard	NM_001098794		Approved	FLJ22665, KIAA1759, DKFZP566M1046	uc001mck.4	Q8N612	OTTHUMG00000133379	ENST00000449352.2:c.2576C>T	11.37:g.6233079G>A	ENSP00000416918:p.Ser859Phe	Somatic		WXS	Illumina HiSeq	Phase_I	Q9C0A4|Q9H0N3|Q9H624	Missense_Mutation	SNP	ENST00000449352.2	37	CCDS44530.1	.	.	.	.	.	.	.	.	.	.	G	14.11	2.437489	0.43224	.	.	ENSG00000051009	ENST00000449352;ENST00000265978	T;T	0.10382	2.88;2.88	5.29	5.29	0.74685	.	0.000000	0.85682	D	0.000000	T	0.32224	0.0822	M	0.63843	1.955	0.80722	D	1	D;D	0.76494	0.998;0.999	D;D	0.85130	0.994;0.997	T	0.01557	-1.1325	10	0.66056	D	0.02	-8.0878	17.4915	0.87705	0.0:0.0:1.0:0.0	.	859;873	Q8N612;Q8N612-2	F16A2_HUMAN;.	F	859;873	ENSP00000416918:S859F;ENSP00000265978:S873F	ENSP00000265978:S873F	S	-	2	0	FAM160A2	6189655	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	8.945000	0.92985	2.468000	0.83385	0.650000	0.86243	TCC		0.617	FAM160A2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000383759.1		NM_032127	
FAT3	120114	hgsc.bcm.edu;ucsc.edu	37	11	92257814	92257814	+	Missense_Mutation	SNP	G	G	A			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3b685193-f1fa-4c1b-949b-bcdb2d1b934c	224a12b0-8203-45e5-a23e-3c913d687bd7	g.chr11:92257814G>A	ENST00000298047.6	+	2	3324	c.3307G>A	c.(3307-3309)Gca>Aca	p.A1103T	FAT3_ENST00000409404.2_Missense_Mutation_p.A1103T|FAT3_ENST00000541502.1_Missense_Mutation_p.A1103T|FAT3_ENST00000525166.1_Missense_Mutation_p.A953T			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	1103	Cadherin 10. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.A1103T(2)		NS(1)|breast(2)|endometrium(10)|kidney(4)|large_intestine(11)|liver(2)|lung(37)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	85		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)				CATCACTGCCGCAGACATTCT	0.438										TCGA Ovarian(4;0.039)																																							2	Substitution - Missense(2)	kidney(2)											72.0	68.0	70.0					11																	92257814		1953	4150	6103	SO:0001583	missense	120114			AB076400		11q14.3	2013-05-31	2013-05-31		ENSG00000165323	ENSG00000165323		"""Cadherins / Cadherin-related"""	23112	protein-coding gene	gene with protein product	"""cadherin-related family member 10"""	612483	"""FAT tumor suppressor homolog 3 (Drosophila)"""			11811999	Standard	NM_001008781		Approved	KIAA1989, CDHF15, CDHR10	uc001pdj.4	Q8TDW7	OTTHUMG00000154468	ENST00000298047.6:c.3307G>A	11.37:g.92257814G>A	ENSP00000298047:p.Ala1103Thr	Somatic		WXS	Illumina HiSeq	Phase_I	B5MDB0|Q96AU6	Missense_Mutation	SNP	ENST00000298047.6	37		.	.	.	.	.	.	.	.	.	.	G	13.88	2.369405	0.42003	.	.	ENSG00000165323	ENST00000298047;ENST00000409404;ENST00000541502;ENST00000525166	T;T;T;T	0.48522	4.65;4.65;0.81;4.65	5.68	5.68	0.88126	.	.	.	.	.	T	0.37320	0.0999	L	0.37630	1.12	0.42996	D	0.994509	P	0.35307	0.494	B	0.27796	0.083	T	0.18335	-1.0340	9	0.14656	T	0.56	.	19.7917	0.96461	0.0:0.0:1.0:0.0	.	1103	Q8TDW7-3	.	T	1103;1103;1103;953	ENSP00000298047:A1103T;ENSP00000387040:A1103T;ENSP00000443786:A1103T;ENSP00000432586:A953T	ENSP00000298047:A1103T	A	+	1	0	FAT3	91897462	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.177000	0.58276	2.685000	0.91497	0.650000	0.86243	GCA		0.438	FAT3-201	KNOWN	basic	protein_coding	protein_coding			NM_001008781	
HIVEP3	59269	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	42049239	42049239	+	Silent	SNP	G	G	A	rs199930261		TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3b685193-f1fa-4c1b-949b-bcdb2d1b934c	224a12b0-8203-45e5-a23e-3c913d687bd7	g.chr1:42049239G>A	ENST00000372583.1	-	4	2115	c.1230C>T	c.(1228-1230)aaC>aaT	p.N410N	HIVEP3_ENST00000372584.1_Silent_p.N410N|HIVEP3_ENST00000429157.2_Silent_p.N410N|HIVEP3_ENST00000247584.5_Silent_p.N410N	NM_024503.4	NP_078779.2	Q5T1R4	ZEP3_HUMAN	human immunodeficiency virus type I enhancer binding protein 3	410	No DNA binding activity or transactivation activity, but complete prevention of TRAF-dependent NF-Kappa-B activation; associates with TRAF2 and JUN. {ECO:0000250}.|Ser-rich.				positive regulation of transcription, DNA-templated (GO:0045893)|skeletal muscle cell differentiation (GO:0035914)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.N410N(1)		NS(2)|breast(3)|central_nervous_system(5)|endometrium(13)|kidney(3)|large_intestine(13)|lung(33)|ovary(4)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	85	Ovarian(52;0.00769)|all_hematologic(146;0.109)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0367)				AGGACTTGGCGTTGGTGTTTG	0.602																																																	1	Substitution - coding silent(1)	kidney(1)						G	,	0,4406		0,0,2203	118.0	104.0	109.0		1230,1230	-6.9	0.6	1		109	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	HIVEP3	NM_001127714.2,NM_024503.4	,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,	410/2406,410/2407	42049239	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	59269			AF278765	CCDS463.1, CCDS44124.1	1p34	2013-01-08	2001-11-28		ENSG00000127124	ENSG00000127124		"""Zinc fingers, C2H2-type"""	13561	protein-coding gene	gene with protein product	"""kappabinding protein-1"""	606649	"""human immunodeficiency virus type I enhancer-binding protein 3"""			11161801	Standard	NR_038260		Approved	KRC, KBP1, KBP-1, SHN3, FLJ16752, KIAA1555, ZAS3, Schnurri-3, ZNF40C	uc001cha.4	Q5T1R4	OTTHUMG00000006361	ENST00000372583.1:c.1230C>T	1.37:g.42049239G>A		Somatic		WXS	Illumina HiSeq	Phase_I	A7YY91|Q5T1R5|Q9BZS0|Q9HCL7	Silent	SNP	ENST00000372583.1	37	CCDS463.1																																																																																				0.602	HIVEP3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000016978.1		NM_024503	
KEL	3792	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	7	142649604	142649604	+	Missense_Mutation	SNP	G	G	A			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3b685193-f1fa-4c1b-949b-bcdb2d1b934c	224a12b0-8203-45e5-a23e-3c913d687bd7	g.chr7:142649604G>A	ENST00000355265.2	-	10	1669	c.1195C>T	c.(1195-1197)Cca>Tca	p.P399S	KEL_ENST00000479768.2_5'UTR	NM_000420.2	NP_000411.1	P23276	KELL_HUMAN	Kell blood group, metallo-endopeptidase	399					vasoconstriction (GO:0042310)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)	p.P399S(1)		central_nervous_system(1)|endometrium(3)|kidney(5)|large_intestine(11)|lung(34)|ovary(3)|prostate(2)|skin(1)	60	Melanoma(164;0.059)					ACCATGGGTGGTTGCTCTGTC	0.542																																																	1	Substitution - Missense(1)	kidney(1)											140.0	119.0	126.0					7																	142649604		2203	4300	6503	SO:0001583	missense	3792			BC003135	CCDS34766.1	7q33	2014-07-19	2006-10-10		ENSG00000197993	ENSG00000197993		"""CD molecules"", ""Blood group antigens"""	6308	protein-coding gene	gene with protein product		613883	"""Kell blood group"", ""Kell blood group, metalloendopeptidase"""			1712490, 7683930	Standard	NM_000420		Approved	ECE3, CD238	uc003wcb.3	P23276	OTTHUMG00000157159	ENST00000355265.2:c.1195C>T	7.37:g.142649604G>A	ENSP00000347409:p.Pro399Ser	Somatic		WXS	Illumina HiSeq	Phase_I	B2RBV4|Q96RS8|Q99885	Missense_Mutation	SNP	ENST00000355265.2	37	CCDS34766.1	.	.	.	.	.	.	.	.	.	.	G	11.33	1.607930	0.28623	.	.	ENSG00000197993	ENST00000355265	T	0.73469	-0.75	5.28	3.27	0.37495	Peptidase M13 (1);	0.504521	0.18493	N	0.139593	T	0.57489	0.2057	L	0.35288	1.05	0.19945	N	0.999949	P	0.43788	0.817	B	0.38880	0.284	T	0.50474	-0.8824	10	0.37606	T	0.19	-5.82	4.9231	0.13880	0.1081:0.0:0.6794:0.2124	.	399	P23276	KELL_HUMAN	S	399	ENSP00000347409:P399S	ENSP00000347409:P399S	P	-	1	0	KEL	142359726	0.519000	0.26242	0.355000	0.25773	0.979000	0.70002	2.427000	0.44740	1.403000	0.46800	0.655000	0.94253	CCA		0.542	KEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347671.2		NM_000420	
KCNH2	3757	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	7	150675001	150675001	+	Start_Codon_SNP	SNP	T	T	A	rs199473036		TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3b685193-f1fa-4c1b-949b-bcdb2d1b934c	224a12b0-8203-45e5-a23e-3c913d687bd7	g.chr7:150675001T>A	ENST00000262186.5	-	1	402	c.1A>T	c.(1-3)Atg>Ttg	p.M1L	KCNH2_ENST00000430723.3_Start_Codon_SNP_p.M1L	NM_000238.3	NP_000229.1	Q12809	KCNH2_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 2	1					cardiac muscle contraction (GO:0060048)|cellular response to drug (GO:0035690)|membrane depolarization during action potential (GO:0086010)|membrane repolarization during action potential (GO:0086011)|membrane repolarization during cardiac muscle cell action potential (GO:0086013)|negative regulation of potassium ion export (GO:1902303)|negative regulation of potassium ion transmembrane transport (GO:1901380)|positive regulation of potassium ion transmembrane transport (GO:1901381)|potassium ion export (GO:0071435)|potassium ion homeostasis (GO:0055075)|potassium ion transmembrane transport (GO:0071805)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of heart rate by hormone (GO:0003064)|regulation of membrane potential (GO:0042391)|regulation of membrane repolarization (GO:0060306)|regulation of potassium ion transmembrane transport (GO:1901379)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|synaptic transmission (GO:0007268)|ventricular cardiac muscle cell action potential (GO:0086005)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|identical protein binding (GO:0042802)|inward rectifier potassium channel activity (GO:0005242)|phosphorelay sensor kinase activity (GO:0000155)|protein homodimerization activity (GO:0042803)|ubiquitin protein ligase binding (GO:0031625)|voltage-gated potassium channel activity (GO:0005249)|voltage-gated potassium channel activity involved in ventricular cardiac muscle cell action potential repolarization (GO:1902282)	p.M1L(2)		NS(1)|cervix(1)|endometrium(10)|kidney(1)|large_intestine(5)|lung(14)|ovary(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)	42	all_neural(206;0.219)		OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)	Alfuzosin(DB00346)|Amiodarone(DB01118)|Amsacrine(DB00276)|Astemizole(DB00637)|Carvedilol(DB01136)|Chlorpromazine(DB00477)|Cisapride(DB00604)|Dofetilide(DB00204)|Doxazosin(DB00590)|Doxepin(DB01142)|Dronedarone(DB04855)|Halofantrine(DB01218)|Ibutilide(DB00308)|Imipramine(DB00458)|Miconazole(DB01110)|Pimozide(DB01100)|Prazosin(DB00457)|Propafenone(DB01182)|Quinidine(DB00908)|Sertindole(DB06144)|Sotalol(DB00489)|Terazosin(DB01162)|Thioridazine(DB00679)|Verapamil(DB00661)	CGCACCGGCATCCTGAGCCCA	0.756																																					GBM(137;110 1844 13671 20123 45161)												2	Substitution - Missense(2)	kidney(2)											13.0	14.0	14.0					7																	150675001		2192	4280	6472	SO:0001582	initiator_codon_variant	3757			U04270	CCDS5910.1, CCDS5911.1	7q36.1	2014-09-17			ENSG00000055118	ENSG00000055118		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6251	protein-coding gene	gene with protein product		152427		LQT2		18616963, 7842012, 8159766, 16382104	Standard	NM_000238		Approved	Kv11.1, HERG, erg1	uc003wic.3	Q12809	OTTHUMG00000158341	ENST00000262186.5:c.1A>T	7.37:g.150675001T>A	ENSP00000262186:p.Met1Leu	Somatic		WXS	Illumina HiSeq	Phase_I	A5H1P7|C4PFH9|D3DX04|O75418|O75680|Q708S9|Q9BT72|Q9BUT7|Q9H3P0	Missense_Mutation	SNP	ENST00000262186.5	37	CCDS5910.1	.	.	.	.	.	.	.	.	.	.	T	26.6	4.756705	0.89843	.	.	ENSG00000055118	ENST00000262186;ENST00000430723	D;D	0.99552	-5.7;-6.15	3.32	3.32	0.38043	.	0.581429	0.12697	U	0.446695	D	0.99450	0.9805	.	.	.	0.80722	D	1	P;B	0.43024	0.798;0.425	P;B	0.60236	0.871;0.251	D	0.98528	1.0626	9	0.87932	D	0	.	9.9318	0.41528	0.0:0.0:0.0:1.0	.	1;1	G5E9I0;Q12809	.;KCNH2_HUMAN	L	1	ENSP00000262186:M1L;ENSP00000387657:M1L	ENSP00000262186:M1L	M	-	1	0	KCNH2	150305934	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	5.022000	0.64078	1.281000	0.44480	0.254000	0.18369	ATG		0.756	KCNH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350741.2		NM_000238	Missense_Mutation
KLHL32	114792	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	6	97562309	97562309	+	Missense_Mutation	SNP	G	G	T			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3b685193-f1fa-4c1b-949b-bcdb2d1b934c	224a12b0-8203-45e5-a23e-3c913d687bd7	g.chr6:97562309G>T	ENST00000369261.4	+	7	1641	c.1278G>T	c.(1276-1278)tgG>tgT	p.W426C	KLHL32_ENST00000544166.1_Intron|KLHL32_ENST00000536676.1_Missense_Mutation_p.W390C|KLHL32_ENST00000539200.1_Missense_Mutation_p.W357C	NM_052904.3	NP_443136.2	Q96NJ5	KLH32_HUMAN	kelch-like family member 32	426								p.W426C(1)		breast(2)|endometrium(3)|kidney(4)|large_intestine(9)|lung(13)|ovary(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	38		all_cancers(76;1.19e-06)|Acute lymphoblastic leukemia(125;5.83e-10)|all_hematologic(75;3.67e-07)|all_epithelial(107;0.00778)|Colorectal(196;0.122)		BRCA - Breast invasive adenocarcinoma(108;0.0558)		AGAACAAATGGACTTTTGTTC	0.468																																																	1	Substitution - Missense(1)	kidney(1)											97.0	85.0	89.0					6																	97562309		2203	4300	6503	SO:0001583	missense	114792			AB067487	CCDS5038.1, CCDS69154.1, CCDS69155.1, CCDS75495.1	6q16.3	2013-02-22	2013-02-22	2007-01-09	ENSG00000186231	ENSG00000186231		"""Kelch-like"", ""BTB/POZ domain containing"""	21221	protein-coding gene	gene with protein product			"""BTB and kelch domain containing 5"", ""KIAA1900"", ""kelch-like 32 (Drosophila)"""	BKLHD5, KIAA1900			Standard	NM_052904		Approved		uc010kcm.1	Q96NJ5	OTTHUMG00000015247	ENST00000369261.4:c.1278G>T	6.37:g.97562309G>T	ENSP00000358265:p.Trp426Cys	Somatic		WXS	Illumina HiSeq	Phase_I	B7Z346|B7Z4E2|E1P528|Q5THT0|Q96PY7	Missense_Mutation	SNP	ENST00000369261.4	37	CCDS5038.1	.	.	.	.	.	.	.	.	.	.	G	22.1	4.249610	0.80024	.	.	ENSG00000186231	ENST00000369261;ENST00000536676;ENST00000539200	D;D;D	0.96940	-4.18;-4.18;-4.18	5.65	5.65	0.86999	Kelch-type beta propeller (1);	0.000000	0.85682	D	0.000000	D	0.99118	0.9696	H	0.98487	4.245	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;0.999;1.0;0.999	D	0.99029	1.0820	10	0.87932	D	0	.	19.9142	0.97043	0.0:0.0:1.0:0.0	.	357;390;426;426	B7Z4E2;B7Z346;Q96NJ5;Q6IQ08	.;.;KLH32_HUMAN;.	C	426;390;357	ENSP00000358265:W426C;ENSP00000440382:W390C;ENSP00000441527:W357C	ENSP00000358265:W426C	W	+	3	0	KLHL32	97669030	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	9.229000	0.95273	2.941000	0.99782	0.655000	0.94253	TGG		0.468	KLHL32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041570.1		NM_052904	
LAMP3	27074	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	182871518	182871518	+	Silent	SNP	A	A	G			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3b685193-f1fa-4c1b-949b-bcdb2d1b934c	224a12b0-8203-45e5-a23e-3c913d687bd7	g.chr3:182871518A>G	ENST00000265598.3	-	2	966	c.711T>C	c.(709-711)tgT>tgC	p.C237C	LAMP3_ENST00000466939.1_Silent_p.C213C	NM_014398.3	NP_055213.2	Q9UQV4	LAMP3_HUMAN	lysosomal-associated membrane protein 3	237					cell proliferation (GO:0008283)|immune system process (GO:0002376)	alveolar lamellar body membrane (GO:0097233)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)		p.C237C(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(6)|lung(9)|ovary(2)|prostate(2)	28	all_cancers(143;9.14e-14)|Ovarian(172;0.0355)		all cancers(12;2.91e-44)|Epithelial(37;5.52e-38)|LUSC - Lung squamous cell carcinoma(7;7.12e-25)|Lung(8;6.39e-23)|OV - Ovarian serous cystadenocarcinoma(80;4.16e-21)			CTGCTTTTATACAGAGTCTGC	0.498																																																	1	Substitution - coding silent(1)	kidney(1)											105.0	100.0	102.0					3																	182871518		2203	4300	6503	SO:0001819	synonymous_variant	27074			AB013924	CCDS3242.1	3q26.3-q27	2011-11-24			ENSG00000078081	ENSG00000078081		"""CD molecules"""	14582	protein-coding gene	gene with protein product		605883				9721848	Standard	NM_014398		Approved	LAMP, TSC403, DC-LAMP, DCLAMP, CD208	uc003flh.4	Q9UQV4	OTTHUMG00000158387	ENST00000265598.3:c.711T>C	3.37:g.182871518A>G		Somatic		WXS	Illumina HiSeq	Phase_I	D3DNS4|O94781|Q8NEC8	Silent	SNP	ENST00000265598.3	37	CCDS3242.1																																																																																				0.498	LAMP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350863.1			
MAP1B	4131	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	5	71495395	71495395	+	Silent	SNP	G	G	A			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3b685193-f1fa-4c1b-949b-bcdb2d1b934c	224a12b0-8203-45e5-a23e-3c913d687bd7	g.chr5:71495395G>A	ENST00000296755.7	+	5	6511	c.6213G>A	c.(6211-6213)aaG>aaA	p.K2071K		NM_005909.3	NP_005900.2	P46821	MAP1B_HUMAN	microtubule-associated protein 1B	2071					axon extension (GO:0048675)|cellular process (GO:0009987)|dendrite development (GO:0016358)|establishment of monopolar cell polarity (GO:0061162)|microtubule bundle formation (GO:0001578)|mitochondrion transport along microtubule (GO:0047497)|negative regulation of intracellular transport (GO:0032387)|positive regulation of axon extension (GO:0045773)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|plasma membrane (GO:0005886)|synapse (GO:0045202)	structural molecule activity (GO:0005198)	p.K2071K(1)		NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(42)|liver(1)|lung(28)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	104		Lung NSC(167;0.00202)|Ovarian(174;0.0175)|Prostate(461;0.142)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;7.99e-54)		CAGAAAAGAAGTCCCCCTCAG	0.478																																					Melanoma(17;367 822 11631 31730 47712)												1	Substitution - coding silent(1)	kidney(1)											125.0	134.0	131.0					5																	71495395		2203	4300	6503	SO:0001819	synonymous_variant	4131			L06237	CCDS4012.1	5q13	2014-06-12			ENSG00000131711	ENSG00000131711			6836	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 102"""	157129				1881920	Standard	NM_005909		Approved	MAP5, PPP1R102	uc003kbw.4	P46821	OTTHUMG00000100952	ENST00000296755.7:c.6213G>A	5.37:g.71495395G>A		Somatic		WXS	Illumina HiSeq	Phase_I	A2BDK5	Silent	SNP	ENST00000296755.7	37	CCDS4012.1																																																																																				0.478	MAP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218561.6		NM_005909	
SLC25A51P1	442229	broad.mit.edu	37	6	66498794	66498794	+	IGR	SNP	C	C	T			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3b685193-f1fa-4c1b-949b-bcdb2d1b934c	224a12b0-8203-45e5-a23e-3c913d687bd7	g.chr6:66498794C>T								EYS (81676 upstream) : AC002485.1 (570523 downstream)																							GCCTTCAAGGCACTGAAATGT	0.438																																																	0																																										SO:0001628	intergenic_variant	0																															6.37:g.66498794C>T		Somatic		WXS	Illumina GAIIx	Phase_I		RNA	SNP		37																																																																																				0	0.438									
MFSD6L	162387	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	17	8702126	8702126	+	Missense_Mutation	SNP	C	C	T			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3b685193-f1fa-4c1b-949b-bcdb2d1b934c	224a12b0-8203-45e5-a23e-3c913d687bd7	g.chr17:8702126C>T	ENST00000329805.4	-	1	541	c.313G>A	c.(313-315)Gtg>Atg	p.V105M		NM_152599.3	NP_689812.3	Q8IWD5	MFS6L_HUMAN	major facilitator superfamily domain containing 6-like	105						integral component of membrane (GO:0016021)		p.V105M(1)		central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(1)|lung(7)|skin(4)	17						GGGAAGTGCACCCGATTTTTG	0.617																																																	1	Substitution - Missense(1)	kidney(1)											69.0	75.0	73.0					17																	8702126		2203	4300	6503	SO:0001583	missense	162387			AK093092	CCDS11146.1	17p13.1	2014-05-30			ENSG00000185156	ENSG00000185156			26656	protein-coding gene	gene with protein product							Standard	NM_152599		Approved	FLJ35773	uc002glp.2	Q8IWD5	OTTHUMG00000178584	ENST00000329805.4:c.313G>A	17.37:g.8702126C>T	ENSP00000330051:p.Val105Met	Somatic		WXS	Illumina HiSeq	Phase_I	Q6YL34|Q8NA76	Missense_Mutation	SNP	ENST00000329805.4	37	CCDS11146.1	.	.	.	.	.	.	.	.	.	.	C	8.194	0.796591	0.16327	.	.	ENSG00000185156	ENST00000329805	T	0.54479	0.57	4.17	-0.594	0.11664	.	3.247110	0.01429	N	0.014663	T	0.47469	0.1447	L	0.47716	1.5	0.09310	N	1	B	0.19073	0.033	B	0.21151	0.033	T	0.29610	-1.0006	10	0.39692	T	0.17	-6.324	7.8793	0.29612	0.232:0.6429:0.0:0.1251	.	105	Q8IWD5	MFS6L_HUMAN	M	105	ENSP00000330051:V105M	ENSP00000330051:V105M	V	-	1	0	MFSD6L	8642851	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.051000	0.14141	-0.150000	0.11195	-2.983000	0.00079	GTG		0.617	MFSD6L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442554.1		NM_152599	
MKI67	4288	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	10	129906582	129906582	+	Missense_Mutation	SNP	C	C	A			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3b685193-f1fa-4c1b-949b-bcdb2d1b934c	224a12b0-8203-45e5-a23e-3c913d687bd7	g.chr10:129906582C>A	ENST00000368654.3	-	13	3897	c.3522G>T	c.(3520-3522)atG>atT	p.M1174I	MKI67_ENST00000368653.3_Missense_Mutation_p.M814I	NM_002417.4	NP_002408.3	P46013	KI67_HUMAN	marker of proliferation Ki-67	1174	16 X 122 AA approximate repeats.				cell proliferation (GO:0008283)|cellular response to heat (GO:0034605)|DNA metabolic process (GO:0006259)|hyaluronan metabolic process (GO:0030212)|meiotic nuclear division (GO:0007126)|organ regeneration (GO:0031100)|response to organic cyclic compound (GO:0014070)	chromosome, centromeric region (GO:0000775)|condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)	p.M1174I(1)		NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(30)|lung(64)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|soft_tissue(1)|stomach(10)|upper_aerodigestive_tract(4)|urinary_tract(4)	159		all_epithelial(44;2.12e-05)|all_lung(145;0.00679)|Lung NSC(174;0.00998)|all_neural(114;0.0936)|Colorectal(57;0.14)|Breast(234;0.166)|Melanoma(40;0.203)				TGGGCGTAAGCATGGCTTTCC	0.473																																																	1	Substitution - Missense(1)	kidney(1)											305.0	290.0	295.0					10																	129906582		2203	4300	6503	SO:0001583	missense	4288			X65550	CCDS7659.1, CCDS53588.1	10q26.2	2014-06-12	2013-10-10		ENSG00000148773	ENSG00000148773			7107	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 105"""	176741	"""antigen identified by monoclonal antibody Ki-67"""			2571566, 16206250	Standard	NM_002417		Approved	MIB-, PPP1R105	uc001lke.3	P46013	OTTHUMG00000019255	ENST00000368654.3:c.3522G>T	10.37:g.129906582C>A	ENSP00000357643:p.Met1174Ile	Somatic		WXS	Illumina HiSeq	Phase_I	Q5VWH2	Missense_Mutation	SNP	ENST00000368654.3	37	CCDS7659.1	.	.	.	.	.	.	.	.	.	.	C	6.238	0.412046	0.11812	.	.	ENSG00000148773	ENST00000368654;ENST00000368653;ENST00000537609	T;T	0.02301	4.35;4.35	2.74	-4.75	0.03239	.	2.038790	0.02651	N	0.106475	T	0.02533	0.0077	L	0.48642	1.525	0.09310	N	1	B;B;B	0.30563	0.035;0.098;0.285	B;B;B	0.28916	0.017;0.075;0.096	T	0.38628	-0.9652	10	0.31617	T	0.26	.	4.9083	0.13809	0.1649:0.213:0.0:0.6221	.	1173;814;1174	F5H4V4;P46013-2;P46013	.;.;KI67_HUMAN	I	1174;814;1173	ENSP00000357643:M1174I;ENSP00000357642:M814I	ENSP00000357642:M814I	M	-	3	0	MKI67	129796572	0.006000	0.16342	0.000000	0.03702	0.000000	0.00434	1.464000	0.35288	-1.215000	0.02610	-0.379000	0.06801	ATG		0.473	MKI67-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050999.1		NM_002417	
MKNK2	2872	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	19	2043146	2043146	+	Missense_Mutation	SNP	A	A	T			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3b685193-f1fa-4c1b-949b-bcdb2d1b934c	224a12b0-8203-45e5-a23e-3c913d687bd7	g.chr19:2043146A>T	ENST00000591601.1	-	6	505	c.470T>A	c.(469-471)cTg>cAg	p.L157Q	MKNK2_ENST00000309340.7_Missense_Mutation_p.L157Q|MKNK2_ENST00000591142.1_5'Flank|MKNK2_ENST00000588014.1_5'Flank|MKNK2_ENST00000250896.3_Missense_Mutation_p.L157Q|MKNK2_ENST00000541165.1_Missense_Mutation_p.L26Q|MKNK2_ENST00000591588.1_5'Flank			Q9HBH9	MKNK2_HUMAN	MAP kinase interacting serine/threonine kinase 2	157	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell surface receptor signaling pathway (GO:0007166)|cellular response to arsenic-containing substance (GO:0071243)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|hemopoiesis (GO:0030097)|intracellular signal transduction (GO:0035556)|protein phosphorylation (GO:0006468)|regulation of translation (GO:0006417)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)	p.L157Q(2)		breast(1)|kidney(3)|large_intestine(3)|lung(3)	10		Ovarian(11;2.11e-07)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CTCAAACACCAGGTAGAAGCG	0.632																																																	2	Substitution - Missense(2)	kidney(2)											148.0	149.0	149.0					19																	2043146		2203	4300	6503	SO:0001583	missense	2872			AF125532	CCDS12079.1, CCDS12080.1	19p13.3	2012-12-20			ENSG00000099875	ENSG00000099875			7111	protein-coding gene	gene with protein product	"""Putative map kinase interacting kinase"""	605069	"""G protein-coupled receptor kinase 7"""	GPRK7		11013076	Standard	NM_199054		Approved	MNK2	uc002lus.2	Q9HBH9	OTTHUMG00000180020	ENST00000591601.1:c.470T>A	19.37:g.2043146A>T	ENSP00000467811:p.Leu157Gln	Somatic		WXS	Illumina HiSeq	Phase_I	Q6GPI3|Q9HBH8|Q9UHR0|Q9Y2N6	Missense_Mutation	SNP	ENST00000591601.1	37	CCDS12080.1	.	.	.	.	.	.	.	.	.	.	a	25.2	4.617565	0.87359	.	.	ENSG00000099875	ENST00000309340;ENST00000250896;ENST00000541165	T;T;T	0.55413	0.52;0.52;0.52	4.37	4.37	0.52481	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.64402	D	0.000003	T	0.75759	0.3893	M	0.91717	3.235	0.80722	D	1	D;D	0.65815	0.993;0.995	D;D	0.70935	0.971;0.959	T	0.81324	-0.0984	10	0.87932	D	0	-5.0022	11.8334	0.52309	1.0:0.0:0.0:0.0	.	157;157	Q9HBH9;Q9HBH9-2	MKNK2_HUMAN;.	Q	157;157;26	ENSP00000309485:L157Q;ENSP00000250896:L157Q;ENSP00000438904:L26Q	ENSP00000250896:L157Q	L	-	2	0	MKNK2	1994146	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.226000	0.78060	1.733000	0.51620	0.454000	0.30748	CTG		0.632	MKNK2-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000449312.1		NM_199054	
NAV2	89797	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	19735259	19735259	+	Silent	SNP	C	C	A			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3b685193-f1fa-4c1b-949b-bcdb2d1b934c	224a12b0-8203-45e5-a23e-3c913d687bd7	g.chr11:19735259C>A	ENST00000396087.3	+	1	117	c.18C>A	c.(16-18)gtC>gtA	p.V6V	NAV2_ENST00000396085.1_Silent_p.V6V|RP11-359E10.1_ENST00000603468.1_lincRNA|NAV2_ENST00000360655.4_Intron|NAV2_ENST00000349880.4_Silent_p.V6V	NM_001244963.1	NP_001231892.1	Q8IVL1	NAV2_HUMAN	neuron navigator 2	6					glossopharyngeal nerve development (GO:0021563)|locomotory behavior (GO:0007626)|optic nerve development (GO:0021554)|regulation of systemic arterial blood pressure by baroreceptor feedback (GO:0003025)|sensory perception of smell (GO:0007608)|sensory perception of sound (GO:0007605)|vagus nerve development (GO:0021564)	interstitial matrix (GO:0005614)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|heparin binding (GO:0008201)	p.V6V(1)		NS(1)|breast(2)|central_nervous_system(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(26)|lung(38)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	116						CCATCCTGGTCGCCTCCAAAA	0.716																																																	1	Substitution - coding silent(1)	kidney(1)											23.0	25.0	24.0					11																	19735259		2199	4291	6490	SO:0001819	synonymous_variant	89797			AB037840	CCDS7850.1, CCDS7851.2, CCDS44552.1, CCDS53612.1, CCDS58126.1	11p15.1	2008-07-18			ENSG00000166833	ENSG00000166833	3.6.1.1		15997	protein-coding gene	gene with protein product	"""pore membrane and/or filament interacting like protein 2"", ""retinoic acid inducible gene in neuroblastoma 1"", ""helicase, APC down-regulated 1"""	607026				12079279, 12062803	Standard	NM_145117		Approved	FLJ10633, FLJ11030, HELAD1, KIAA1419, POMFIL2, RAINB1, FLJ23707	uc010rdm.2	Q8IVL1	OTTHUMG00000151837	ENST00000396087.3:c.18C>A	11.37:g.19735259C>A		Somatic		WXS	Illumina HiSeq	Phase_I	A6NEC1|Q8IVK3|Q8IVK4|Q8IVK5|Q8IVK6|Q8IVK7|Q8IVK8|Q8NHC9|Q8NHD0|Q8TDE9|Q8TDF0|Q8TEB3|Q96B30|Q9NUZ6|Q9NVM7|Q9P2C8	Silent	SNP	ENST00000396087.3	37	CCDS58126.1																																																																																				0.716	NAV2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324112.1		NM_145117	
NRG3	10718	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	10	84744979	84744979	+	Missense_Mutation	SNP	G	G	A			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3b685193-f1fa-4c1b-949b-bcdb2d1b934c	224a12b0-8203-45e5-a23e-3c913d687bd7	g.chr10:84744979G>A	ENST00000404547.1	+	10	1781	c.1781G>A	c.(1780-1782)aGg>aAg	p.R594K	NRG3_ENST00000372142.2_Missense_Mutation_p.R373K|NRG3_ENST00000372141.2_Missense_Mutation_p.R570K|NRG3_ENST00000556918.1_Missense_Mutation_p.R400K|NRG3_ENST00000404576.2_Missense_Mutation_p.R374K|NRG3_ENST00000545131.1_Missense_Mutation_p.R220K|NRG3_ENST00000537893.1_Missense_Mutation_p.R220K			P56975	NRG3_HUMAN	neuregulin 3	594					activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|intracellular signal transduction (GO:0035556)|mammary placode formation (GO:0060596)|pattern specification process (GO:0007389)|regulation of cell growth (GO:0001558)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	growth factor activity (GO:0008083)|receptor tyrosine kinase binding (GO:0030971)|transmembrane receptor protein tyrosine kinase activator activity (GO:0030297)	p.R373M(1)|p.R570M(1)|p.R570K(1)|p.R373K(1)		breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(41)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	69				GBM - Glioblastoma multiforme(1;2.5e-18)|all cancers(1;2.85e-09)		TCATCCACAAGGGCCAGTTCT	0.443																																																	4	Substitution - Missense(4)	lung(2)|kidney(2)											129.0	140.0	136.0					10																	84744979		2203	4300	6503	SO:0001583	missense	10718			AK098823	CCDS31233.1, CCDS53547.1	10q22-q23	2003-09-09			ENSG00000185737	ENSG00000185737			7999	protein-coding gene	gene with protein product		605533				9275162	Standard	NM_001010848		Approved		uc001kco.2	P56975	OTTHUMG00000018626	ENST00000404547.1:c.1781G>A	10.37:g.84744979G>A	ENSP00000384796:p.Arg594Lys	Somatic		WXS	Illumina HiSeq	Phase_I	A4D7U1|Q0PEH2|Q5VYH3	Missense_Mutation	SNP	ENST00000404547.1	37	CCDS31233.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.032634	0.75504	.	.	ENSG00000185737	ENST00000372141;ENST00000404547;ENST00000537287;ENST00000372142;ENST00000404576;ENST00000556918;ENST00000545131;ENST00000537893	T;T;T;T;T;T;T	0.54279	1.19;0.97;1.01;0.58;1.16;0.65;0.65	5.95	5.95	0.96441	.	0.000000	0.85682	D	0.000000	T	0.69815	0.3153	L	0.58101	1.795	0.52501	D	0.999958	D;D;D;D	0.69078	0.99;0.997;0.996;0.99	D;D;D;D	0.77557	0.979;0.99;0.987;0.979	T	0.66709	-0.5855	10	0.44086	T	0.13	-10.4837	17.8962	0.88888	0.0:0.0:1.0:0.0	.	569;594;373;570	B9EGV5;P56975;P56975-3;P56975-4	.;NRG3_HUMAN;.;.	K	570;594;569;373;374;400;220;220	ENSP00000361214:R570K;ENSP00000384796:R594K;ENSP00000361215:R373K;ENSP00000385804:R374K;ENSP00000451376:R400K;ENSP00000441201:R220K;ENSP00000440377:R220K	ENSP00000361214:R570K	R	+	2	0	NRG3	84734959	1.000000	0.71417	0.995000	0.50966	0.999000	0.98932	6.668000	0.74457	2.827000	0.97445	0.650000	0.86243	AGG		0.443	NRG3-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000412262.1		XM_166086	
NRXN3	9369	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	14	79434650	79434650	+	Missense_Mutation	SNP	G	G	C			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3b685193-f1fa-4c1b-949b-bcdb2d1b934c	224a12b0-8203-45e5-a23e-3c913d687bd7	g.chr14:79434650G>C	ENST00000554719.1	+	11	2475	c.1984G>C	c.(1984-1986)Gct>Cct	p.A662P	NRXN3_ENST00000335750.5_Missense_Mutation_p.A662P	NM_004796.4	NP_004787.2	Q9HDB5	NRX3B_HUMAN	neurexin 3	0					adult behavior (GO:0030534)|angiogenesis (GO:0001525)|learning (GO:0007612)|neuron cell-cell adhesion (GO:0007158)|neurotransmitter secretion (GO:0007269)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synapse maturation (GO:0090129)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|vocalization behavior (GO:0071625)	integral component of membrane (GO:0016021)	cell adhesion molecule binding (GO:0050839)|neuroligin family protein binding (GO:0097109)	p.A662P(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(23)|lung(40)|ovary(3)|pancreas(2)|prostate(5)|skin(7)|upper_aerodigestive_tract(9)|urinary_tract(1)	104		Renal(4;0.00876)		BRCA - Breast invasive adenocarcinoma(234;0.00544)|Kidney(3;0.029)|KIRC - Kidney renal clear cell carcinoma(182;0.223)		CATCAATGATGCTCTTCATCG	0.512																																																	1	Substitution - Missense(1)	kidney(1)											137.0	115.0	123.0					14																	79434650		2203	4300	6503	SO:0001583	missense	9369			AB018286	CCDS9870.1, CCDS9871.1, CCDS45145.1, CCDS61515.1	14q31	2010-01-19				ENSG00000021645			8010	protein-coding gene	gene with protein product		600567	"""chromosome 14 open reading frame 60"""	C14orf60		11944992, 12379233	Standard	NM_004796		Approved	KIAA0743	uc001xun.4	Q9HDB5		ENST00000554719.1:c.1984G>C	14.37:g.79434650G>C	ENSP00000451648:p.Ala662Pro	Somatic		WXS	Illumina HiSeq	Phase_I	A5PKW8|A8MPU5|B3KPM7|Q6NUR0|Q8IUD8	Missense_Mutation	SNP	ENST00000554719.1	37	CCDS9870.1	.	.	.	.	.	.	.	.	.	.	G	26.4	4.733053	0.89482	.	.	ENSG00000021645	ENST00000330071;ENST00000332068;ENST00000554719;ENST00000335750	T;T	0.80909	-1.43;-1.43	6.17	6.17	0.99709	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (1);	0.000000	0.85682	D	0.000000	D	0.90487	0.7020	.	.	.	0.80722	D	1	D;D	0.89917	1.0;0.995	D;P	0.91635	0.999;0.882	D	0.88843	0.3314	8	.	.	.	.	20.8794	0.99867	0.0:0.0:1.0:0.0	.	1035;662	Q9Y4C0;Q9Y4C0-3	NRX3A_HUMAN;.	P	1035;1024;662;662	ENSP00000451648:A662P;ENSP00000338349:A662P	.	A	+	1	0	NRXN3	78504403	1.000000	0.71417	0.999000	0.59377	0.399000	0.30720	9.869000	0.99810	2.941000	0.99782	0.655000	0.94253	GCT		0.512	NRXN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413787.1		NM_001105250	
OR1G1	8390	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	17	3030489	3030489	+	Silent	SNP	G	G	A			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3b685193-f1fa-4c1b-949b-bcdb2d1b934c	224a12b0-8203-45e5-a23e-3c913d687bd7	g.chr17:3030489G>A	ENST00000328890.2	-	1	386	c.357C>T	c.(355-357)gcC>gcT	p.A119A		NM_003555.1	NP_003546.1	P47890	OR1G1_HUMAN	olfactory receptor, family 1, subfamily G, member 1	119					signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.A119A(1)		kidney(1)|large_intestine(4)|lung(3)|skin(3)	11						AGCAGTCATAGGCCATGACCG	0.488																																					Colon(127;1481 1654 8243 19426 50557)												1	Substitution - coding silent(1)	kidney(1)											84.0	77.0	79.0					17																	3030489		2203	4300	6503	SO:0001819	synonymous_variant	8390			U04689	CCDS11020.1	17p13.3	2012-08-09			ENSG00000183024	ENSG00000183024		"""GPCR / Class A : Olfactory receptors"""	8204	protein-coding gene	gene with protein product				OR1G2		8004088, 9500546	Standard	NM_003555		Approved	OR17-209	uc002fvc.1	P47890	OTTHUMG00000090618	ENST00000328890.2:c.357C>T	17.37:g.3030489G>A		Somatic		WXS	Illumina HiSeq	Phase_I	Q4VBM1|Q6IFL9|Q9UM76	Silent	SNP	ENST00000328890.2	37	CCDS11020.1																																																																																				0.488	OR1G1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207206.2			
P2RX1	5023	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	17	3819428	3819428	+	Missense_Mutation	SNP	A	A	G			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3b685193-f1fa-4c1b-949b-bcdb2d1b934c	224a12b0-8203-45e5-a23e-3c913d687bd7	g.chr17:3819428A>G	ENST00000225538.3	-	1	366	c.92T>C	c.(91-93)gTt>gCt	p.V31A		NM_002558.2	NP_002549.1	P51575	P2RX1_HUMAN	purinergic receptor P2X, ligand-gated ion channel, 1	31					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|ceramide biosynthetic process (GO:0046513)|insemination (GO:0007320)|ion transport (GO:0006811)|neuronal action potential (GO:0019228)|platelet activation (GO:0030168)|positive regulation of ion transport (GO:0043270)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|purinergic nucleotide receptor signaling pathway (GO:0035590)|regulation of blood pressure (GO:0008217)|regulation of calcium ion transport (GO:0051924)|regulation of vascular smooth muscle contraction (GO:0003056)|response to ATP (GO:0033198)|serotonin secretion by platelet (GO:0002554)|signal transduction (GO:0007165)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)|vasoconstriction (GO:0042310)	external side of cell outer membrane (GO:0031240)|integral component of nuclear inner membrane (GO:0005639)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)	ATP binding (GO:0005524)|calcium channel activity (GO:0005262)|cation channel activity (GO:0005261)|drug binding (GO:0008144)|extracellular ATP-gated cation channel activity (GO:0004931)|purinergic nucleotide receptor activity (GO:0001614)|zinc ion binding (GO:0008270)	p.V31A(1)		cervix(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|skin(2)	13				LUAD - Lung adenocarcinoma(2;1.9e-05)|Lung(3;0.0173)		TCGGAAGATAACGCCCACCTT	0.657																																																	1	Substitution - Missense(1)	kidney(1)											110.0	97.0	101.0					17																	3819428		2203	4300	6503	SO:0001583	missense	5023			X83688	CCDS11040.1	17p13.3	2012-01-17				ENSG00000108405		"""Purinergic receptors"", ""Ligand-gated ion channels / Purinergic receptors, ionotropic"""	8533	protein-coding gene	gene with protein product		600845				8834001	Standard	NM_002558		Approved	P2X1	uc002fww.3	P51575		ENST00000225538.3:c.92T>C	17.37:g.3819428A>G	ENSP00000225538:p.Val31Ala	Somatic		WXS	Illumina HiSeq	Phase_I	Q9UK84	Missense_Mutation	SNP	ENST00000225538.3	37	CCDS11040.1	.	.	.	.	.	.	.	.	.	.	A	14.97	2.695140	0.48202	.	.	ENSG00000108405	ENST00000225538	T	0.04970	3.52	4.7	4.7	0.59300	.	0.436617	0.22084	N	0.064850	T	0.07503	0.0189	L	0.38175	1.15	0.30126	N	0.80527	B	0.24483	0.104	B	0.29942	0.109	T	0.06991	-1.0796	10	0.33940	T	0.23	-10.4028	13.3006	0.60324	1.0:0.0:0.0:0.0	.	31	P51575	P2RX1_HUMAN	A	31	ENSP00000225538:V31A	ENSP00000225538:V31A	V	-	2	0	P2RX1	3766177	0.985000	0.35326	0.133000	0.22050	0.438000	0.31896	8.166000	0.89665	1.883000	0.54544	0.402000	0.26972	GTT		0.657	P2RX1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438391.1		NM_002558	
OR4D1	26689	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	17	56233390	56233390	+	Missense_Mutation	SNP	G	G	T			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3b685193-f1fa-4c1b-949b-bcdb2d1b934c	224a12b0-8203-45e5-a23e-3c913d687bd7	g.chr17:56233390G>T	ENST00000268912.5	+	1	897	c.876G>T	c.(874-876)caG>caT	p.Q292H		NM_012374.1	NP_036506.1	Q15615	OR4D1_HUMAN	olfactory receptor, family 4, subfamily D, member 1	292					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.Q292H(1)		kidney(2)|large_intestine(4)|lung(4)|ovary(1)|stomach(1)|urinary_tract(1)	13						TGAGAAACCAGGACATGAAAG	0.463																																																	1	Substitution - Missense(1)	kidney(1)											45.0	46.0	46.0					17																	56233390		2194	4296	6490	SO:0001583	missense	26689			X89670	CCDS42365.1	17q22	2012-08-09			ENSG00000141194	ENSG00000141194		"""GPCR / Class A : Olfactory receptors"""	8293	protein-coding gene	gene with protein product				OR4D3		9119360	Standard	NM_012374		Approved	TPCR16	uc010wno.2	Q15615		ENST00000268912.5:c.876G>T	17.37:g.56233390G>T	ENSP00000365451:p.Gln292His	Somatic		WXS	Illumina HiSeq	Phase_I	B2RN14|Q8NGB1|Q96R76	Missense_Mutation	SNP	ENST00000268912.5	37	CCDS42365.1	.	.	.	.	.	.	.	.	.	.	g	6.975	0.549888	0.13374	.	.	ENSG00000141194	ENST00000268912	T	0.38077	1.16	5.63	3.42	0.39159	.	0.323823	0.27019	N	0.021336	T	0.29945	0.0749	L	0.42686	1.345	0.33598	D	0.601926	B	0.13594	0.008	B	0.12837	0.008	T	0.39099	-0.9630	10	0.52906	T	0.07	-1.6845	10.5517	0.45092	0.1724:0.0:0.8276:0.0	.	292	Q15615	OR4D1_HUMAN	H	292	ENSP00000365451:Q292H	ENSP00000365451:Q292H	Q	+	3	2	OR4D1	53588389	0.066000	0.20996	1.000000	0.80357	0.122000	0.20287	0.048000	0.14078	1.216000	0.43427	0.543000	0.68304	CAG		0.463	OR4D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443364.1			
PBRM1	55193	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	52643360	52643360	+	Nonsense_Mutation	SNP	C	C	A			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	3b685193-f1fa-4c1b-949b-bcdb2d1b934c	224a12b0-8203-45e5-a23e-3c913d687bd7	g.chr3:52643360C>A	ENST00000296302.7	-	16	2537	c.2536G>T	c.(2536-2538)Gaa>Taa	p.E846*	PBRM1_ENST00000410007.1_Nonsense_Mutation_p.E846*|PBRM1_ENST00000409057.1_Nonsense_Mutation_p.E846*|PBRM1_ENST00000409114.3_Nonsense_Mutation_p.E861*|PBRM1_ENST00000409767.1_Nonsense_Mutation_p.E861*|PBRM1_ENST00000356770.4_Nonsense_Mutation_p.E814*|PBRM1_ENST00000337303.4_Nonsense_Mutation_p.E846*|PBRM1_ENST00000394830.3_Nonsense_Mutation_p.E846*			Q86U86	PB1_HUMAN	polybromo 1	846	Bromo 6. {ECO:0000255|PROSITE- ProRule:PRU00035}.				chromatin remodeling (GO:0006338)|heart development (GO:0007507)|mitotic nuclear division (GO:0007067)|negative regulation of cell proliferation (GO:0008285)|placenta development (GO:0001890)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	kinetochore (GO:0000776)|nuclear chromosome (GO:0000228)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)	p.E846*(2)|p.E814*(1)		breast(5)|endometrium(5)|kidney(301)|liver(1)|lung(22)|pancreas(1)	335				BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)		TCCAATACTTCAAACATATGC	0.328			"""Mis, N, F, S, D, O"""		"""clear cell renal carcinoma, breast"""																																			Rec	yes		3	3p21	55193	polybromo 1		E	3	Substitution - Nonsense(3)	kidney(3)											70.0	70.0	70.0					3																	52643360		2203	4300	6503	SO:0001587	stop_gained	55193			BC015323	CCDS43099.1	3p21	2007-03-29			ENSG00000163939	ENSG00000163939			30064	protein-coding gene	gene with protein product		606083				11078522, 11483580	Standard	NM_018313		Approved	BAF180, PB1	uc003der.2	Q86U86	OTTHUMG00000152663	ENST00000296302.7:c.2536G>T	3.37:g.52643360C>A	ENSP00000296302:p.Glu846*	Somatic		WXS	Illumina HiSeq	Phase_I	A1L381|A1L382|A4FUJ7|Q1RMD1|Q1RMD2|Q96MS2|Q9H2T3|Q9H2T4|Q9H2T5|Q9H301|Q9H314	Nonsense_Mutation	SNP	ENST00000296302.7	37		.	.	.	.	.	.	.	.	.	.	C	40	8.481039	0.98829	.	.	ENSG00000163939	ENST00000356770;ENST00000394830;ENST00000296302;ENST00000337303;ENST00000409057;ENST00000410007;ENST00000409114;ENST00000409767;ENST00000423351;ENST00000446103	.	.	.	6.08	6.08	0.98989	.	0.090804	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.08599	T	0.76	.	20.6634	0.99662	0.0:1.0:0.0:0.0	.	.	.	.	X	814;846;846;846;846;846;861;861;846;805	.	ENSP00000296302:E846X	E	-	1	0	PBRM1	52618400	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.792000	0.85828	2.894000	0.99253	0.655000	0.94253	GAA		0.328	PBRM1-008	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000327232.1		NM_018165	
PCNXL2	80003	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	233150461	233150461	+	Nonsense_Mutation	SNP	G	G	T			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3b685193-f1fa-4c1b-949b-bcdb2d1b934c	224a12b0-8203-45e5-a23e-3c913d687bd7	g.chr1:233150461G>T	ENST00000258229.9	-	28	5136	c.4902C>A	c.(4900-4902)tgC>tgA	p.C1634*	PCNXL2_ENST00000344698.2_Nonsense_Mutation_p.C286*	NM_014801.3	NP_055616.3	A6NKB5	PCX2_HUMAN	pecanex-like 2 (Drosophila)	1634						integral component of membrane (GO:0016021)		p.C1634*(1)		NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(7)|large_intestine(19)|lung(30)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	86		all_cancers(173;0.0347)|Prostate(94;0.137)				TCCCCAGGGTGCACAGGGCGA	0.537																																																	1	Substitution - Nonsense(1)	kidney(1)											93.0	92.0	92.0					1																	233150461		1961	4143	6104	SO:0001587	stop_gained	80003			AK055374	CCDS44335.1	1q42.2	2008-02-05	2001-11-28		ENSG00000135749	ENSG00000135749			8736	protein-coding gene	gene with protein product			"""pecanex (Drosophila)-like 2"""			12477932	Standard	NM_014801		Approved	KIAA0435, FLJ11383	uc001hvl.2	A6NKB5	OTTHUMG00000037824	ENST00000258229.9:c.4902C>A	1.37:g.233150461G>T	ENSP00000258229:p.Cys1634*	Somatic		WXS	Illumina HiSeq	Phase_I	O43162|Q5T9Z8|Q5TDF1|Q8TEP4|Q96HP9|Q9HAL8	Nonsense_Mutation	SNP	ENST00000258229.9	37	CCDS44335.1	.	.	.	.	.	.	.	.	.	.	G	46	12.225042	0.99648	.	.	ENSG00000135749	ENST00000344698;ENST00000258229	.	.	.	5.38	-0.834	0.10779	.	0.049191	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	11.2778	0.49176	0.4229:0.0:0.5771:0.0	.	.	.	.	X	286;1634	.	ENSP00000258229:C1634X	C	-	3	2	PCNXL2	231217084	0.946000	0.32159	0.967000	0.41034	0.297000	0.27493	0.015000	0.13355	-0.456000	0.07043	-0.492000	0.04666	TGC		0.537	PCNXL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092480.3		NM_014801	
PCSK1	5122	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	5	95728885	95728885	+	Missense_Mutation	SNP	G	G	C			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3b685193-f1fa-4c1b-949b-bcdb2d1b934c	224a12b0-8203-45e5-a23e-3c913d687bd7	g.chr5:95728885G>C	ENST00000311106.3	-	14	2319	c.2082C>G	c.(2080-2082)aaC>aaG	p.N694K	CTD-2337A12.1_ENST00000502645.2_RNA|PCSK1_ENST00000508626.1_Missense_Mutation_p.N647K|PCSK1_ENST00000513085.1_5'UTR	NM_000439.4|NM_001177876.1	NP_000430.3|NP_001171347.1	P29120	NEC1_HUMAN	proprotein convertase subtilisin/kexin type 1	694					cell-cell signaling (GO:0007267)|cellular protein metabolic process (GO:0044267)|metabolic process (GO:0008152)|peptide biosynthetic process (GO:0043043)|peptide hormone processing (GO:0016486)|proteolysis (GO:0006508)|regulation of insulin secretion (GO:0050796)	extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|secretory granule lumen (GO:0034774)	serine-type endopeptidase activity (GO:0004252)	p.N694K(1)		NS(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(14)|ovary(2)|prostate(3)|skin(3)|urinary_tract(2)	36		all_cancers(142;2.67e-06)|all_epithelial(76;6.92e-09)|all_lung(232;0.00307)|Lung NSC(167;0.00452)|Ovarian(225;0.0112)|Colorectal(57;0.0341)|Breast(839;0.244)		all cancers(79;3.44e-16)	"""""""Insulin(DB00071)|Insulin Regular(DB00030)"""	CATAAGGGATGTTGAGCTTTG	0.458																																																	1	Substitution - Missense(1)	kidney(1)											117.0	124.0	121.0					5																	95728885		2203	4300	6503	SO:0001583	missense	5122				CCDS4081.1, CCDS54881.1	5q15-q21	2008-07-18			ENSG00000175426	ENSG00000175426			8743	protein-coding gene	gene with protein product	"""prohormone convertase 3"", ""prohormone convertase 1"", ""neuroendocrine convertase 1"", ""proprotein convertase 1"""	162150		NEC1		1765368	Standard	NM_000439		Approved	PC1, PC3, SPC3	uc003kls.2	P29120	OTTHUMG00000122089	ENST00000311106.3:c.2082C>G	5.37:g.95728885G>C	ENSP00000308024:p.Asn694Lys	Somatic		WXS	Illumina HiSeq	Phase_I	B7Z8T7|E9PHA1|P78478|Q92532	Missense_Mutation	SNP	ENST00000311106.3	37	CCDS4081.1	.	.	.	.	.	.	.	.	.	.	G	2.553	-0.303528	0.05495	.	.	ENSG00000175426	ENST00000311106;ENST00000508626	T;T	0.63744	0.09;-0.06	5.76	1.67	0.24075	.	0.601698	0.18930	N	0.127246	T	0.24431	0.0592	N	0.01352	-0.895	0.09310	N	0.999996	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.32824	-0.9892	10	0.02654	T	1	-6.2452	7.5542	0.27814	0.3384:0.1199:0.5416:0.0	.	647;694	E9PHA1;P29120	.;NEC1_HUMAN	K	694;647	ENSP00000308024:N694K;ENSP00000421600:N647K	ENSP00000308024:N694K	N	-	3	2	PCSK1	95754641	0.928000	0.31464	0.556000	0.28293	0.793000	0.44817	1.425000	0.34859	0.349000	0.23975	0.655000	0.94253	AAC		0.458	PCSK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242851.1		NM_000439	
PDS5B	23047	hgsc.bcm.edu;ucsc.edu	37	13	33232396	33232396	+	Frame_Shift_Del	DEL	A	A	-			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3b685193-f1fa-4c1b-949b-bcdb2d1b934c	224a12b0-8203-45e5-a23e-3c913d687bd7	g.chr13:33232396delA	ENST00000315596.10	+	4	519	c.333delA	c.(331-333)acafs	p.T111fs		NM_015032.3	NP_055847.1	Q9NTI5	PDS5B_HUMAN	PDS5, regulator of cohesion maintenance, homolog B (S. cerevisiae)	111					cell proliferation (GO:0008283)|mitotic cell cycle (GO:0000278)|mitotic sister chromatid cohesion (GO:0007064)|negative regulation of cell proliferation (GO:0008285)|regulation of cell proliferation (GO:0042127)	chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)			NS(2)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(14)|lung(14)|ovary(5)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)	62		Lung SC(185;0.0367)		all cancers(112;5.55e-06)|Epithelial(112;2.7e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00303)|BRCA - Breast invasive adenocarcinoma(63;0.0204)		TGTTTATAACAAGACAGTTGA	0.299																																																	0													50.0	46.0	47.0					13																	33232396		1786	4052	5838	SO:0001589	frameshift_variant	23047			AB023196	CCDS41878.1	13q12.3	2008-02-05	2007-07-18	2007-07-18	ENSG00000083642	ENSG00000083642			20418	protein-coding gene	gene with protein product		605333	"""androgen-induced proliferation inhibitor"""	APRIN		8812419, 10215036	Standard	NM_015032		Approved	AS3, KIAA0979, FLJ23236, CG008	uc010abf.3	Q9NTI5	OTTHUMG00000016704	ENST00000315596.10:c.333delA	13.37:g.33232396delA	ENSP00000313851:p.Thr111fs	Somatic		WXS	Illumina HiSeq	Phase_I	Q5R3S3|Q5W0K8|Q6NSC3|Q8IXT6|Q9H5N8|Q9Y2I5|Q9Y451	Frame_Shift_Del	DEL	ENST00000315596.10	37	CCDS41878.1																																																																																				0.299	PDS5B-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044428.3		NM_015032	
PLEKHH3	79990	broad.mit.edu	37	17	40820279	40820279	+	Missense_Mutation	SNP	G	G	T			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3b685193-f1fa-4c1b-949b-bcdb2d1b934c	224a12b0-8203-45e5-a23e-3c913d687bd7	g.chr17:40820279G>T	ENST00000591022.1	-	13	2635	c.2248C>A	c.(2248-2250)Ccc>Acc	p.P750T	PLEKHH3_ENST00000456950.2_5'UTR|PLEKHH3_ENST00000412503.1_Missense_Mutation_p.P573T|PLEKHH3_ENST00000293349.6_Missense_Mutation_p.P747T	NM_024927.4	NP_079203	Q7Z736	PKHH3_HUMAN	pleckstrin homology domain containing, family H (with MyTH4 domain) member 3	750	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				signal transduction (GO:0007165)	cytoskeleton (GO:0005856)|extracellular space (GO:0005615)		p.P750T(1)		endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|ovary(1)|prostate(2)|skin(2)	13		Breast(137;0.00116)		BRCA - Breast invasive adenocarcinoma(366;0.14)		TCGGGGGAGGGGTTGGCCAAG	0.627																																																	1	Substitution - Missense(1)	kidney(1)											36.0	42.0	40.0					17																	40820279		2203	4300	6503	SO:0001583	missense	79990			BC052978	CCDS11434.1	17q21.2	2013-01-11				ENSG00000068137		"""Pleckstrin homology (PH) domain containing"""	26105	protein-coding gene	gene with protein product						12477932	Standard	NM_024927		Approved	FLJ21019	uc002iau.3	Q7Z736		ENST00000591022.1:c.2248C>A	17.37:g.40820279G>T	ENSP00000468678:p.Pro750Thr	Somatic		WXS	Illumina GAIIx	Phase_I	C9JQ76|Q59H20|Q96B28|Q9H7D6|Q9NT18	Missense_Mutation	SNP	ENST00000591022.1	37	CCDS11434.1	.	.	.	.	.	.	.	.	.	.	G	16.67	3.188930	0.57909	.	.	ENSG00000068137	ENST00000293349;ENST00000412503	D	0.87179	-2.22	4.61	2.59	0.31030	FERM domain (1);	0.155671	0.30473	N	0.009557	T	0.73273	0.3566	N	0.22421	0.69	0.22737	N	0.998793	B	0.10296	0.003	B	0.06405	0.002	T	0.55347	-0.8155	10	0.21540	T	0.41	-19.6066	5.0908	0.14708	0.1051:0.0:0.6871:0.2078	.	750	Q7Z736	PKHH3_HUMAN	T	750;573	ENSP00000411885:P573T	ENSP00000293349:P750T	P	-	1	0	PLEKHH3	38073805	1.000000	0.71417	0.992000	0.48379	0.998000	0.95712	2.407000	0.44565	1.273000	0.44346	0.555000	0.69702	CCC		0.627	PLEKHH3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000452332.1		NM_024927	
PLXNA4	91584	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	7	132192713	132192713	+	Missense_Mutation	SNP	C	C	T	rs529364377		TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3b685193-f1fa-4c1b-949b-bcdb2d1b934c	224a12b0-8203-45e5-a23e-3c913d687bd7	g.chr7:132192713C>T	ENST00000359827.3	-	2	1702	c.740G>A	c.(739-741)gGt>gAt	p.G247D	PLXNA4_ENST00000423507.2_Missense_Mutation_p.G247D|PLXNA4_ENST00000378539.5_Missense_Mutation_p.G247D|PLXNA4_ENST00000321063.4_Missense_Mutation_p.G247D			Q9HCM2	PLXA4_HUMAN	plexin A4	247	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				anterior commissure morphogenesis (GO:0021960)|axon guidance (GO:0007411)|chemorepulsion of branchiomotor axon (GO:0021793)|facial nerve structural organization (GO:0021612)|glossopharyngeal nerve morphogenesis (GO:0021615)|postganglionic parasympathetic nervous system development (GO:0021784)|regulation of axon extension involved in axon guidance (GO:0048841)|regulation of negative chemotaxis (GO:0050923)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|sympathetic nervous system development (GO:0048485)|trigeminal nerve structural organization (GO:0021637)|vagus nerve morphogenesis (GO:0021644)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)	p.G247D(4)		NS(1)|breast(1)|endometrium(3)|kidney(4)|large_intestine(14)|lung(17)|ovary(1)|prostate(2)|skin(1)|stomach(1)	45						ACTGCTAAAACCATAGACATA	0.483													C|||	1	0.000199681	0.0	0.0	5008	,	,		23320	0.0		0.001	False		,,,				2504	0.0																4	Substitution - Missense(4)	kidney(4)											92.0	85.0	87.0					7																	132192713		2203	4300	6503	SO:0001583	missense	91584			AB046770, AK123428	CCDS5826.1, CCDS43646.1, CCDS43647.1	7q32.3	2007-09-26	2007-09-26	2007-09-26	ENSG00000221866	ENSG00000221866		"""Plexins"""	9102	protein-coding gene	gene with protein product		604280	"""plexin A4, A"", ""plexin A4, B"""	PLXNA4A, PLXNA4B			Standard	NM_181775		Approved	KIAA1550, DKFZp434G0625PRO34003, FAYV2820	uc003vra.4	Q9HCM2	OTTHUMG00000155108	ENST00000359827.3:c.740G>A	7.37:g.132192713C>T	ENSP00000352882:p.Gly247Asp	Somatic		WXS	Illumina HiSeq	Phase_I	A4D1N6|E9PAM2|Q6UWC6|Q6ZW89|Q8N969|Q8ND00|Q8NEN3|Q9NTD4	Missense_Mutation	SNP	ENST00000359827.3	37	CCDS43646.1	.	.	.	.	.	.	.	.	.	.	C	23.2	4.393131	0.83011	.	.	ENSG00000221866	ENST00000321063;ENST00000359827;ENST00000423507;ENST00000378539	T;T;T;T	0.05649	3.41;3.41;3.41;3.41	5.7	5.7	0.88788	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.000000	0.64402	U	0.000004	T	0.34048	0.0884	M	0.89287	3.02	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.998;0.999;0.994	T	0.18304	-1.0341	10	0.87932	D	0	.	19.8377	0.96663	0.0:1.0:0.0:0.0	.	247;247;247	Q9HCM2-2;A4D1N6;Q9HCM2	.;.;PLXA4_HUMAN	D	247	ENSP00000323194:G247D;ENSP00000352882:G247D;ENSP00000392772:G247D;ENSP00000367800:G247D	ENSP00000323194:G247D	G	-	2	0	PLXNA4	131843253	1.000000	0.71417	1.000000	0.80357	0.888000	0.51559	7.818000	0.86416	2.711000	0.92665	0.561000	0.74099	GGT		0.483	PLXNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338422.2		NM_181775	
POLG2	11232	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	17	62481972	62481972	+	Missense_Mutation	SNP	C	C	T	rs563195356		TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3b685193-f1fa-4c1b-949b-bcdb2d1b934c	224a12b0-8203-45e5-a23e-3c913d687bd7	g.chr17:62481972C>T	ENST00000539111.2	-	5	1050	c.983G>A	c.(982-984)cGa>cAa	p.R328Q	POLG2_ENST00000582501.1_5'UTR	NM_007215.3	NP_009146.2	Q9UHN1	DPOG2_HUMAN	polymerase (DNA directed), gamma 2, accessory subunit	328					DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA-dependent DNA replication (GO:0006261)	extracellular vesicular exosome (GO:0070062)|mitochondrial chromosome (GO:0000262)|mitochondrial nucleoid (GO:0042645)	DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)	p.R328Q(1)		central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(1)|lung(4)|skin(2)|stomach(1)|urinary_tract(1)	15	Breast(5;2.15e-14)		BRCA - Breast invasive adenocarcinoma(8;4.97e-11)			CACATTTTTTCGTCCATCTCG	0.423																																					Colon(3;18 21 435 17652 48887)												1	Substitution - Missense(1)	kidney(1)											88.0	81.0	84.0					17																	62481972		2203	4300	6503	SO:0001583	missense	11232			U94703	CCDS32706.1	17q23.3	2012-05-18			ENSG00000256525	ENSG00000256525		"""DNA polymerases"""	9180	protein-coding gene	gene with protein product		604983				9153213	Standard	NM_007215		Approved	MTPOLB, HP55	uc002jei.3	Q9UHN1		ENST00000539111.2:c.983G>A	17.37:g.62481972C>T	ENSP00000442563:p.Arg328Gln	Somatic		WXS	Illumina HiSeq	Phase_I	O00419|Q0IJ81|Q96GW2|Q9UK35|Q9UK94	Missense_Mutation	SNP	ENST00000539111.2	37	CCDS32706.1	.	.	.	.	.	.	.	.	.	.	C	33	5.196957	0.94960	.	.	ENSG00000256525	ENST00000539111	T	0.78595	-1.19	5.94	5.94	0.96194	.	0.061511	0.64402	D	0.000010	D	0.87188	0.6115	M	0.65975	2.015	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.78314	0.991;0.991	T	0.82999	-0.0178	10	0.26408	T	0.33	-20.4195	20.4384	0.99098	0.0:1.0:0.0:0.0	.	328;328	E5KS15;Q9UHN1	.;DPOG2_HUMAN	Q	328	ENSP00000442563:R328Q	ENSP00000442563:R328Q	R	-	2	0	POLG2	59912434	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	6.187000	0.72039	2.831000	0.97527	0.644000	0.83932	CGA		0.423	POLG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443820.1		NM_007215	
PPP2R4	5524	broad.mit.edu;ucsc.edu	37	9	131909727	131909727	+	Missense_Mutation	SNP	C	C	A			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3b685193-f1fa-4c1b-949b-bcdb2d1b934c	224a12b0-8203-45e5-a23e-3c913d687bd7	g.chr9:131909727C>A	ENST00000337738.1	+	11	1328	c.1061C>A	c.(1060-1062)cCt>cAt	p.P354H	PPP2R4_ENST00000423100.1_Missense_Mutation_p.P57H|PPP2R4_ENST00000347048.4_Missense_Mutation_p.P100H|PPP2R4_ENST00000414510.1_Missense_Mutation_p.P57H|PPP2R4_ENST00000358994.4_Missense_Mutation_p.P319H|PPP2R4_ENST00000434095.1_Missense_Mutation_p.P57H|PPP2R4_ENST00000393370.2_Missense_Mutation_p.P319H|PPP2R4_ENST00000432651.1_Missense_Mutation_p.P57H|PPP2R4_ENST00000348141.5_Missense_Mutation_p.P325H|PPP2R4_ENST00000357197.4_Missense_Mutation_p.P290H|PPP2R4_ENST00000435132.1_Missense_Mutation_p.P57H|PPP2R4_ENST00000419582.1_Missense_Mutation_p.P57H|PPP2R4_ENST00000355007.3_Missense_Mutation_p.P277H	NM_178001.2	NP_821068.1	Q15257	PTPA_HUMAN	protein phosphatase 2A activator, regulatory subunit 4	354					ATP catabolic process (GO:0006200)|mitotic spindle organization in nucleus (GO:0030472)|negative regulation of phosphoprotein phosphatase activity (GO:0032515)|negative regulation of protein dephosphorylation (GO:0035308)|positive regulation of apoptotic process (GO:0043065)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|positive regulation of protein dephosphorylation (GO:0035307)|protein folding (GO:0006457)|protein peptidyl-prolyl isomerization (GO:0000413)|regulation of phosphoprotein phosphatase activity (GO:0043666)	calcium channel complex (GO:0034704)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|protein phosphatase type 2A complex (GO:0000159)	ATP binding (GO:0005524)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase type 2A regulator activity (GO:0008601)|protein tyrosine phosphatase activator activity (GO:0008160)|receptor binding (GO:0005102)	p.P354H(1)		breast(3)|endometrium(1)|kidney(1)|lung(3)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	12		Medulloblastoma(224;0.235)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0178)		CCCATCCATCCTGTCACGTCG	0.642																																					Colon(158;2158 2504 4450 20433)												1	Substitution - Missense(1)	kidney(1)											71.0	56.0	61.0					9																	131909727		2203	4300	6503	SO:0001583	missense	5524			X73478	CCDS6920.1, CCDS65156.1, CCDS75917.1	9q34	2010-06-18	2007-01-22		ENSG00000119383	ENSG00000119383		"""Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"""	9308	protein-coding gene	gene with protein product	"""phosphotyrosyl phosphatase activator"", ""PP2A phosphatase activator"""	600756	"""protein phosphatase 2A, regulatory subunit B' (PR 53)"""			8530035	Standard	NM_021131		Approved	PTPA, PR53	uc004bxm.2	Q15257	OTTHUMG00000020774	ENST00000337738.1:c.1061C>A	9.37:g.131909727C>A	ENSP00000337448:p.Pro354His	Somatic		WXS	Illumina GAIIx	Phase_I	A2A347|A9IZU4|B4DXM4|Q15258|Q53GZ3|Q5TZQ2|Q9BUK1|Q9NNZ7|Q9NNZ8|Q9NNZ9	Missense_Mutation	SNP	ENST00000337738.1	37		.	.	.	.	.	.	.	.	.	.	C	37	5.992493	0.97179	.	.	ENSG00000119383	ENST00000358994;ENST00000393370;ENST00000337738;ENST00000348141;ENST00000347048;ENST00000357197;ENST00000355007;ENST00000423100;ENST00000414510;ENST00000419582;ENST00000432651;ENST00000435132;ENST00000434095	T;T;T;T;T;T;T;T;T;T;T;T;T	0.29142	1.58;1.58;1.58;1.58;1.58;1.58;1.58;1.58;1.58;1.58;1.58;1.58;1.58	5.16	5.16	0.70880	.	0.000000	0.85682	D	0.000000	T	0.58409	0.2120	M	0.77616	2.38	0.80722	D	1	D;P;B;B;D	0.89917	1.0;0.77;0.447;0.216;1.0	D;P;B;B;D	0.78314	0.991;0.497;0.063;0.285;0.986	T	0.63470	-0.6630	10	0.72032	D	0.01	.	17.6371	0.88125	0.0:1.0:0.0:0.0	.	290;100;277;354;319	Q15257-3;Q68CR8;Q15257-4;Q15257;Q15257-2	.;.;.;PTPA_HUMAN;.	H	319;319;354;325;100;290;277;57;57;57;57;57;57	ENSP00000351885:P319H;ENSP00000377036:P319H;ENSP00000337448:P354H;ENSP00000335200:P325H;ENSP00000337412:P100H;ENSP00000349726:P290H;ENSP00000347109:P277H;ENSP00000408316:P57H;ENSP00000408726:P57H;ENSP00000394001:P57H;ENSP00000416661:P57H;ENSP00000387726:P57H;ENSP00000411604:P57H	ENSP00000337448:P354H	P	+	2	0	PPP2R4	130949548	1.000000	0.71417	0.058000	0.19502	0.936000	0.57629	7.332000	0.79203	2.400000	0.81607	0.561000	0.74099	CCT		0.642	PPP2R4-201	KNOWN	basic	protein_coding	protein_coding			NM_021131	
RAPGEF4	11069	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	173894949	173894949	+	Silent	SNP	C	C	T			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3b685193-f1fa-4c1b-949b-bcdb2d1b934c	224a12b0-8203-45e5-a23e-3c913d687bd7	g.chr2:173894949C>T	ENST00000397081.3	+	26	2759	c.2616C>T	c.(2614-2616)aaC>aaT	p.N872N	RAPGEF4_ENST00000539331.1_Silent_p.N719N|RAPGEF4_ENST00000264111.6_Silent_p.N871N|RAPGEF4_ENST00000409036.1_Silent_p.N872N|RAPGEF4_ENST00000535187.1_Silent_p.N652N|RAPGEF4_ENST00000538974.1_Silent_p.N701N|RAPGEF4_ENST00000540783.1_Silent_p.N719N|RAPGEF4_ENST00000397087.3_Silent_p.N728N	NM_007023.3	NP_008954.2	Q8WZA2	RPGF4_HUMAN	Rap guanine nucleotide exchange factor (GEF) 4	872	Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00168}.				blood coagulation (GO:0007596)|calcium ion-dependent exocytosis (GO:0017156)|cAMP-mediated signaling (GO:0019933)|energy reserve metabolic process (GO:0006112)|G-protein coupled receptor signaling pathway (GO:0007186)|insulin secretion (GO:0030073)|platelet activation (GO:0030168)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Ras GTPase activity (GO:0032320)|regulation of exocytosis (GO:0017157)|regulation of insulin secretion (GO:0050796)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	cAMP-dependent protein kinase complex (GO:0005952)|cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cAMP binding (GO:0030552)|cAMP-dependent protein kinase regulator activity (GO:0008603)|guanyl-nucleotide exchange factor activity (GO:0005085)|Ras GTPase binding (GO:0017016)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)	p.N872N(1)		breast(1)|central_nervous_system(2)|endometrium(5)|kidney(5)|large_intestine(14)|lung(13)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	47			OV - Ovarian serous cystadenocarcinoma(117;0.194)			GACTAAGTAACGTTGCTGTGA	0.443																																																	1	Substitution - coding silent(1)	kidney(1)											113.0	111.0	112.0					2																	173894949		1916	4137	6053	SO:0001819	synonymous_variant	11069			U78516	CCDS42775.1, CCDS42776.1, CCDS63060.1, CCDS63061.1, CCDS74604.1	2q31-q32	2008-02-05	2004-03-26		ENSG00000091428	ENSG00000091428			16626	protein-coding gene	gene with protein product	"""cAMP-regulated guanine nucleotide exchange factor II"", "" exchange protein directly activated by cAMP 2"""	606058	"""RAP guanine-nucleotide-exchange factor (GEF) 4"""			10777494, 9856955	Standard	NM_007023		Approved	cAMP-GEFII, CGEF2	uc002uhv.4	Q8WZA2	OTTHUMG00000133677	ENST00000397081.3:c.2616C>T	2.37:g.173894949C>T		Somatic		WXS	Illumina HiSeq	Phase_I	B2R7R3|B7Z283|B7Z3T6|B7Z912|O95636|Q8IXK6|Q8TAA4	Silent	SNP	ENST00000397081.3	37	CCDS42775.1																																																																																				0.443	RAPGEF4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257864.2		NM_007023	
RBM45	129831	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	178990777	178990777	+	Silent	SNP	C	C	G			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3b685193-f1fa-4c1b-949b-bcdb2d1b934c	224a12b0-8203-45e5-a23e-3c913d687bd7	g.chr2:178990777C>G	ENST00000286070.5	+	9	1391	c.1299C>G	c.(1297-1299)gcC>gcG	p.A433A		NM_152945.2	NP_694453.2	Q8IUH3	RBM45_HUMAN	RNA binding motif protein 45	435	RRM 3. {ECO:0000255|PROSITE- ProRule:PRU00176}.				cell differentiation (GO:0030154)|nervous system development (GO:0007399)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.A433A(2)		endometrium(3)|kidney(2)|large_intestine(8)|lung(10)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	27			OV - Ovarian serous cystadenocarcinoma(117;0.00854)|Epithelial(96;0.00957)|all cancers(119;0.037)			CCAAGTATGCCGATAGAATAA	0.388																																																	2	Substitution - coding silent(2)	large_intestine(1)|kidney(1)											159.0	144.0	149.0					2																	178990777		2203	4300	6503	SO:0001819	synonymous_variant	129831			AF526533	CCDS33335.1	2q31.2	2013-02-12			ENSG00000155636	ENSG00000155636		"""RNA binding motif (RRM) containing"""	24468	protein-coding gene	gene with protein product	"""developmentally regulated RNA binding protein 1"""	608888				12220514	Standard	XM_005246287		Approved	DRB1, FLJ44612	uc002ulv.3	Q8IUH3	OTTHUMG00000154202	ENST00000286070.5:c.1299C>G	2.37:g.178990777C>G		Somatic		WXS	Illumina HiSeq	Phase_I	Q6NYL0|Q8NFC9	Silent	SNP	ENST00000286070.5	37	CCDS33335.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	9.068|9.068	0.996195|0.996195	0.19043|0.19043	.|.	.|.	ENSG00000155636|ENSG00000155636	ENST00000455903|ENST00000424099	.|.	.|.	.|.	5.74|5.74	-2.19|-2.19	0.07015|0.07015	.|.	.|.	.|.	.|.	.|.	T|T	0.41026|0.41026	0.1141|0.1141	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.27400|0.27400	-1.0075|-1.0075	4|4	.|.	.|.	.|.	-18.3773|-18.3773	2.3916|2.3916	0.04379|0.04379	0.2966:0.2297:0.0646:0.4091|0.2966:0.2297:0.0646:0.4091	.|.	.|.	.|.	.|.	R|G	94|32	.|.	.|.	P|R	+|+	2|1	0|2	RBM45|RBM45	178699023|178699023	0.990000|0.990000	0.36364|0.36364	0.986000|0.986000	0.45419|0.45419	0.947000|0.947000	0.59692|0.59692	0.419000|0.419000	0.21247|0.21247	-0.648000|-0.648000	0.05437|0.05437	-1.072000|-1.072000	0.02254|0.02254	CCG|CGA		0.388	RBM45-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334375.2		NM_152945	
RAPH1	65059	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	204305222	204305222	+	Silent	SNP	T	T	A			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3b685193-f1fa-4c1b-949b-bcdb2d1b934c	224a12b0-8203-45e5-a23e-3c913d687bd7	g.chr2:204305222T>A	ENST00000319170.5	-	14	2990	c.2691A>T	c.(2689-2691)gcA>gcT	p.A897A	RAPH1_ENST00000457812.1_Intron|ABI2_ENST00000295851.5_3'UTR|RAPH1_ENST00000374493.3_Silent_p.A949A	NM_213589.1	NP_998754.1	Q70E73	RAPH1_HUMAN	Ras association (RalGDS/AF-6) and pleckstrin homology domains 1	897					axon extension (GO:0048675)|cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)		p.A897A(1)		breast(5)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(7)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32						TTGCTTTTACTGCAGGAGGGG	0.587																																																	1	Substitution - coding silent(1)	kidney(1)											81.0	98.0	92.0					2																	204305222		2203	4300	6503	SO:0001819	synonymous_variant	65059			AJ584699	CCDS2359.1, CCDS2360.1	2q33	2013-01-10	2003-11-25	2003-11-26	ENSG00000173166	ENSG00000173166		"""Pleckstrin homology (PH) domain containing"""	14436	protein-coding gene	gene with protein product	"""amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 18"""	609035	"""amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 9"""	ALS2CR9, ALS2CR18			Standard	NM_203365		Approved	KIAA1681	uc002vad.3	Q70E73	OTTHUMG00000132876	ENST00000319170.5:c.2691A>T	2.37:g.204305222T>A		Somatic		WXS	Illumina HiSeq	Phase_I	Q96Q37|Q9C0I2	Silent	SNP	ENST00000319170.5	37	CCDS2359.1																																																																																				0.587	RAPH1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256363.2		NM_025252	
SAMD9	54809	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	7	92733297	92733297	+	Missense_Mutation	SNP	A	A	G			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3b685193-f1fa-4c1b-949b-bcdb2d1b934c	224a12b0-8203-45e5-a23e-3c913d687bd7	g.chr7:92733297A>G	ENST00000379958.2	-	3	2383	c.2114T>C	c.(2113-2115)tTt>tCt	p.F705S		NM_001193307.1|NM_017654.3	NP_001180236.1|NP_060124.2	Q5K651	SAMD9_HUMAN	sterile alpha motif domain containing 9	705						cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)		p.F705S(1)		NS(1)|breast(4)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(20)|lung(32)|ovary(4)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	88	all_cancers(62;5.71e-11)|all_epithelial(64;3.25e-10)|Breast(17;0.000675)|Lung NSC(181;0.0969)|all_lung(186;0.125)		STAD - Stomach adenocarcinoma(171;0.000302)			CCTTTTGACAAAAGGTGAAGA	0.353																																																	1	Substitution - Missense(1)	kidney(1)											151.0	151.0	151.0					7																	92733297		2203	4300	6503	SO:0001583	missense	54809			AB095925	CCDS34680.1	7q21.2	2013-01-10	2004-07-15	2004-07-16	ENSG00000205413	ENSG00000205413		"""Sterile alpha motif (SAM) domain containing"""	1348	protein-coding gene	gene with protein product		610456	"""chromosome 7 open reading frame 5"""	C7orf5			Standard	NM_017654		Approved	KIAA2004, FLJ20073	uc003umg.3	Q5K651	OTTHUMG00000155809	ENST00000379958.2:c.2114T>C	7.37:g.92733297A>G	ENSP00000369292:p.Phe705Ser	Somatic		WXS	Illumina HiSeq	Phase_I	A2RU68|Q5K649|Q6P080|Q75N21|Q8IVG6|Q9NXS8	Missense_Mutation	SNP	ENST00000379958.2	37	CCDS34680.1	.	.	.	.	.	.	.	.	.	.	A	17.12	3.307391	0.60305	.	.	ENSG00000205413	ENST00000379958;ENST00000446617	T;T	0.30714	1.52;2.35	4.51	4.51	0.55191	.	0.000000	0.64402	D	0.000001	T	0.55401	0.1918	M	0.78637	2.42	0.41367	D	0.987469	D	0.89917	1.0	D	0.83275	0.996	T	0.62101	-0.6925	10	0.87932	D	0	.	12.7659	0.57391	1.0:0.0:0.0:0.0	.	705	Q5K651	SAMD9_HUMAN	S	705	ENSP00000369292:F705S;ENSP00000414529:F705S	ENSP00000369292:F705S	F	-	2	0	SAMD9	92571233	1.000000	0.71417	0.994000	0.49952	0.866000	0.49608	8.578000	0.90777	1.891000	0.54761	0.496000	0.49642	TTT		0.353	SAMD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341761.1		NM_017654	
SLC6A19	340024	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	5	1217053	1217053	+	Missense_Mutation	SNP	T	T	C			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3b685193-f1fa-4c1b-949b-bcdb2d1b934c	224a12b0-8203-45e5-a23e-3c913d687bd7	g.chr5:1217053T>C	ENST00000304460.10	+	8	1222	c.1166T>C	c.(1165-1167)cTc>cCc	p.L389P		NM_001003841.2	NP_001003841.1	Q695T7	S6A19_HUMAN	solute carrier family 6 (neutral amino acid transporter), member 19	389					amino acid transport (GO:0006865)|ion transport (GO:0006811)|response to nutrient (GO:0007584)|transmembrane transport (GO:0055085)	brush border membrane (GO:0031526)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	neurotransmitter:sodium symporter activity (GO:0005328)|neutral amino acid transmembrane transporter activity (GO:0015175)	p.L389P(1)		breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|lung(25)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	44	all_cancers(3;3.55e-15)|Lung NSC(6;2.89e-14)|all_lung(6;2.2e-13)|all_epithelial(6;3.75e-10)		Epithelial(17;0.000356)|all cancers(22;0.00137)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|Lung(60;0.185)			AACGCCTTCCTCTCAGAGGTA	0.662																																																	1	Substitution - Missense(1)	kidney(1)											104.0	101.0	102.0					5																	1217053		2203	4300	6503	SO:0001583	missense	340024			AK096054	CCDS34130.1	5p15	2013-07-19			ENSG00000174358	ENSG00000174358		"""Solute carriers"""	27960	protein-coding gene	gene with protein product	"""Hartnup disease"""	608893					Standard	NM_001003841		Approved		uc003jbw.4	Q695T7	OTTHUMG00000161636	ENST00000304460.10:c.1166T>C	5.37:g.1217053T>C	ENSP00000305302:p.Leu389Pro	Somatic		WXS	Illumina HiSeq	Phase_I	A8K446	Missense_Mutation	SNP	ENST00000304460.10	37	CCDS34130.1	.	.	.	.	.	.	.	.	.	.	T	21.6	4.179604	0.78564	.	.	ENSG00000174358	ENST00000304460	T	0.75938	-0.98	4.85	4.85	0.62838	.	0.000000	0.85682	D	0.000000	D	0.89608	0.6764	H	0.95437	3.67	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.92284	0.5836	10	0.87932	D	0	.	12.982	0.58570	0.0:0.0:0.0:1.0	.	389	Q695T7	S6A19_HUMAN	P	389	ENSP00000305302:L389P	ENSP00000305302:L389P	L	+	2	0	SLC6A19	1270053	1.000000	0.71417	0.913000	0.36048	0.601000	0.36947	7.064000	0.76721	1.817000	0.53016	0.402000	0.26972	CTC		0.662	SLC6A19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365557.1		XM_291120	
SMARCA5	8467	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	4	144465930	144465930	+	Missense_Mutation	SNP	G	G	A			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3b685193-f1fa-4c1b-949b-bcdb2d1b934c	224a12b0-8203-45e5-a23e-3c913d687bd7	g.chr4:144465930G>A	ENST00000283131.3	+	17	2675	c.2213G>A	c.(2212-2214)aGa>aAa	p.R738K		NM_003601.3	NP_003592.3	O60264	SMCA5_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 5	738					ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|CENP-A containing nucleosome assembly (GO:0034080)|chromatin remodeling (GO:0006338)|chromatin silencing at rDNA (GO:0000183)|DNA-templated transcription, initiation (GO:0006352)|double-strand break repair (GO:0006302)|nucleosome assembly (GO:0006334)|nucleosome positioning (GO:0016584)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	chromatin silencing complex (GO:0005677)|condensed chromosome (GO:0000793)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|NURF complex (GO:0016589)|RSF complex (GO:0031213)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)	p.R738K(1)	EWSR1/SMARCA5(2)	endometrium(2)|kidney(2)|large_intestine(9)|lung(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	21	all_hematologic(180;0.158)					AAACGAGAAAGAAAAGCCAAC	0.393																																																	1	Substitution - Missense(1)	kidney(1)											155.0	147.0	150.0					4																	144465930		2203	4300	6503	SO:0001583	missense	8467			AB010882	CCDS3761.1	4q31.1-q31.2	2011-04-20			ENSG00000153147	ENSG00000153147			11101	protein-coding gene	gene with protein product		603375				9730600	Standard	NM_003601		Approved	hSNF2H, hISWI, ISWI	uc003ijg.3	O60264	OTTHUMG00000161474	ENST00000283131.3:c.2213G>A	4.37:g.144465930G>A	ENSP00000283131:p.Arg738Lys	Somatic		WXS	Illumina HiSeq	Phase_I		Missense_Mutation	SNP	ENST00000283131.3	37	CCDS3761.1	.	.	.	.	.	.	.	.	.	.	G	37	6.051802	0.97236	.	.	ENSG00000153147	ENST00000283131;ENST00000536484;ENST00000535006	D	0.93426	-3.22	5.8	5.8	0.92144	.	0.000000	0.85682	D	0.000000	D	0.96756	0.8941	H	0.95780	3.72	0.80722	D	1	P	0.45768	0.866	P	0.48089	0.566	D	0.97098	0.9795	10	0.56958	D	0.05	-8.0588	20.058	0.97661	0.0:0.0:1.0:0.0	.	738	O60264	SMCA5_HUMAN	K	738;681;681	ENSP00000283131:R738K	ENSP00000283131:R738K	R	+	2	0	SMARCA5	144685380	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.763000	0.98947	2.752000	0.94435	0.655000	0.94253	AGA		0.393	SMARCA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365077.3			
TLR2	7097	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	4	154625344	154625344	+	Missense_Mutation	SNP	C	C	A			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3b685193-f1fa-4c1b-949b-bcdb2d1b934c	224a12b0-8203-45e5-a23e-3c913d687bd7	g.chr4:154625344C>A	ENST00000260010.6	+	1	2693	c.1285C>A	c.(1285-1287)Cct>Act	p.P429T		NM_003264.3	NP_003255.2	O60603	TLR2_HUMAN	toll-like receptor 2	429					apoptotic process (GO:0006915)|cell surface pattern recognition receptor signaling pathway (GO:0002752)|cellular response to bacterial lipopeptide (GO:0071221)|cellular response to diacyl bacterial lipopeptide (GO:0071726)|cellular response to lipoteichoic acid (GO:0071223)|cellular response to peptidoglycan (GO:0071224)|cellular response to triacyl bacterial lipopeptide (GO:0071727)|central nervous system myelin formation (GO:0032289)|chloramphenicol transport (GO:0042892)|defense response to Gram-positive bacterium (GO:0050830)|detection of diacyl bacterial lipopeptide (GO:0042496)|detection of triacyl bacterial lipopeptide (GO:0042495)|I-kappaB phosphorylation (GO:0007252)|immune response (GO:0006955)|induction by symbiont of defense-related host nitric oxide production (GO:0052063)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|leukotriene metabolic process (GO:0006691)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|microglial cell activation involved in immune response (GO:0002282)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|negative regulation of cell proliferation (GO:0008285)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of interleukin-17 production (GO:0032700)|nitric oxide metabolic process (GO:0046209)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of chemokine production (GO:0032722)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-18 production (GO:0032741)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of leukocyte migration (GO:0002687)|positive regulation of macrophage cytokine production (GO:0060907)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of oligodendrocyte differentiation (GO:0048714)|positive regulation of toll-like receptor signaling pathway (GO:0034123)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of Wnt signaling pathway (GO:0030177)|response to fatty acid (GO:0070542)|response to hypoxia (GO:0001666)|response to insulin (GO:0032868)|response to molecule of fungal origin (GO:0002238)|response to progesterone (GO:0032570)|response to toxic substance (GO:0009636)|signal transduction (GO:0007165)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)	cell body (GO:0044297)|cell projection (GO:0042995)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|Toll-like receptor 1-Toll-like receptor 2 protein complex (GO:0035354)|Toll-like receptor 2-Toll-like receptor 6 protein complex (GO:0035355)	diacyl lipopeptide binding (GO:0042498)|lipopolysaccharide receptor activity (GO:0001875)|lipoteichoic acid binding (GO:0070891)|peptidoglycan binding (GO:0042834)|protein heterodimerization activity (GO:0046982)|receptor activity (GO:0004872)|signaling pattern recognition receptor activity (GO:0008329)|transmembrane signaling receptor activity (GO:0004888)|triacyl lipopeptide binding (GO:0042497)	p.P429T(1)		breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(11)|ovary(1)|pancreas(1)|skin(1)|urinary_tract(1)	29	all_hematologic(180;0.093)	Renal(120;0.117)			OspA lipoprotein(DB00045)	TCATTCTATGCCTGAAACTTG	0.373																																																	1	Substitution - Missense(1)	kidney(1)											61.0	64.0	63.0					4																	154625344		2203	4300	6503	SO:0001583	missense	7097			U88878	CCDS3784.1	4q32	2008-02-05				ENSG00000137462		"""CD molecules"""	11848	protein-coding gene	gene with protein product		603028				9435236	Standard	XM_005263193		Approved	TIL4, CD282	uc003inq.3	O60603		ENST00000260010.6:c.1285C>A	4.37:g.154625344C>A	ENSP00000260010:p.Pro429Thr	Somatic		WXS	Illumina HiSeq	Phase_I	B3Y612|D1CS45|D1CS48|D1CS49|O15454|Q8NI00	Missense_Mutation	SNP	ENST00000260010.6	37	CCDS3784.1	.	.	.	.	.	.	.	.	.	.	C	12.71	2.020835	0.35606	.	.	ENSG00000137462	ENST00000260010	T	0.59224	0.28	5.42	3.7	0.42460	.	0.000000	0.85682	D	0.000000	T	0.74030	0.3663	H	0.96970	3.915	0.40488	D	0.980511	P	0.35807	0.522	B	0.43701	0.428	T	0.76796	-0.2827	10	0.87932	D	0	.	9.084	0.36570	0.0:0.7778:0.0:0.2222	.	429	O60603	TLR2_HUMAN	T	429	ENSP00000260010:P429T	ENSP00000260010:P429T	P	+	1	0	TLR2	154844794	1.000000	0.71417	0.961000	0.40146	0.680000	0.39746	2.899000	0.48679	0.671000	0.31185	0.563000	0.77884	CCT		0.373	TLR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365205.1			
TRAPPC2	6399	broad.mit.edu;hgsc.bcm.edu	37	X	13738010	13738010	+	Missense_Mutation	SNP	C	C	T			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3b685193-f1fa-4c1b-949b-bcdb2d1b934c	224a12b0-8203-45e5-a23e-3c913d687bd7	g.chrX:13738010C>T	ENST00000380579.1	-	3	265	c.73G>A	c.(73-75)Gct>Act	p.A25T	TRAPPC2_ENST00000458511.2_Missense_Mutation_p.A59T|TRAPPC2_ENST00000453655.2_Missense_Mutation_p.A25T|TRAPPC2_ENST00000358231.5_Missense_Mutation_p.A25T|TRAPPC2_ENST00000519885.1_Missense_Mutation_p.A25T|TRAPPC2_ENST00000359680.5_Missense_Mutation_p.A25T			P0DI81	TPC2A_HUMAN	trafficking protein particle complex 2	25					ER to Golgi vesicle-mediated transport (GO:0006888)|regulation of transcription, DNA-templated (GO:0006355)|skeletal system development (GO:0001501)|transcription, DNA-templated (GO:0006351)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	ion channel binding (GO:0044325)|transcription factor binding (GO:0008134)	p.A25T(1)		kidney(1)	1						GCCTTCCCAGCTGGCAAAAAC	0.358																																																	1	Substitution - Missense(1)	kidney(1)											48.0	39.0	42.0					X																	13738010		1814	4069	5883	SO:0001583	missense	6399			AF157061	CCDS48082.1, CCDS48083.1, CCDS48083.2	Xp22	2011-10-10	2005-01-26		ENSG00000196459	ENSG00000196459		"""Trafficking protein particle complex"""	23068	protein-coding gene	gene with protein product		300202	"""spondyloepiphyseal dysplasia, late"""	SEDL		14597397	Standard	NM_014563		Approved	TRS20, SEDT, MIP-2A, ZNF547L, hYP38334	uc010nej.2	P0DI81	OTTHUMG00000021157	ENST00000380579.1:c.73G>A	X.37:g.13738010C>T	ENSP00000369953:p.Ala25Thr	Somatic		WXS	Illumina HiSeq	Phase_I	A6NEG0|O14582|Q9HD16	Missense_Mutation	SNP	ENST00000380579.1	37	CCDS48082.1	.	.	.	.	.	.	.	.	.	.	C	8.159	0.789113	0.16258	.	.	ENSG00000196459	ENST00000453655;ENST00000359680;ENST00000380579;ENST00000358231;ENST00000458511;ENST00000519885;ENST00000426522;ENST00000518847	D;D;D;D;D;D;D	0.90385	-2.66;-2.66;-2.66;-2.66;-2.66;-2.66;-2.66	5.33	1.24	0.21308	Longin-like (1);	0.521756	0.21431	N	0.074644	D	0.85026	0.5603	L	0.31752	0.955	0.25125	N	0.990618	B;B	0.17268	0.021;0.008	B;B	0.17098	0.017;0.015	T	0.62515	-0.6838	10	0.15066	T	0.55	-7.0074	20.3441	0.98786	0.0:0.3065:0.6935:0.0	.	59;25	P0DI81-2;P0DI81	.;TPC2A_HUMAN	T	25;25;25;25;59;25;25;25	ENSP00000394629:A25T;ENSP00000352708:A25T;ENSP00000369953:A25T;ENSP00000350966:A25T;ENSP00000392495:A59T;ENSP00000430725:A25T;ENSP00000428900:A25T	ENSP00000350966:A25T	A	-	1	0	TRAPPC2	13647931	0.421000	0.25465	0.994000	0.49952	0.984000	0.73092	-0.289000	0.08365	-0.098000	0.12285	0.594000	0.82650	GCT		0.358	TRAPPC2-002	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055805.2		NM_014563	
DCDC1	341019	broad.mit.edu;ucsc.edu	37	11	31086042	31086042	+	Frame_Shift_Del	DEL	C	C	-			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3b685193-f1fa-4c1b-949b-bcdb2d1b934c	224a12b0-8203-45e5-a23e-3c913d687bd7	g.chr11:31086042delC	ENST00000597505.1	-	18	2564	c.2565delG	c.(2563-2565)gagfs	p.E855fs	DCDC1_ENST00000437348.1_5'UTR			P59894	DCDC1_HUMAN	doublecortin domain containing 1	0					intracellular signal transduction (GO:0035556)					central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(17)|pancreas(2)|prostate(1)|skin(1)|stomach(1)	31	Lung SC(675;0.225)					TAGGATGTTTCTCTTCCAGTT	0.458																																																	0													183.0	176.0	178.0					11																	31086042		1895	4129	6024	SO:0001589	frameshift_variant	0			AY247970	CCDS7872.1	11p14.1	2013-05-22			ENSG00000170959	ENSG00000170959			20625	protein-coding gene	gene with protein product		608062				12820024	Standard	NM_181807		Approved		uc001msv.3	P59894	OTTHUMG00000150144	ENST00000597505.1:c.2565delG	11.37:g.31086042delC	ENSP00000472625:p.Glu855fs	Somatic		WXS	Illumina GAIIx	Phase_I	A6PVL6|B7WNX6|Q6ZU04	Frame_Shift_Del	DEL	ENST00000597505.1	37																																																																																					0.458	DCDC1-010	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000463167.1		NM_181807	
URB2	9816	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	229773890	229773890	+	Missense_Mutation	SNP	C	C	T			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3b685193-f1fa-4c1b-949b-bcdb2d1b934c	224a12b0-8203-45e5-a23e-3c913d687bd7	g.chr1:229773890C>T	ENST00000258243.2	+	4	3666	c.3530C>T	c.(3529-3531)gCa>gTa	p.A1177V		NM_014777.2	NP_055592.2	Q14146	URB2_HUMAN	URB2 ribosome biogenesis 2 homolog (S. cerevisiae)	1177						aggresome (GO:0016235)|nucleolus (GO:0005730)|nucleus (GO:0005634)		p.A1177V(1)		breast(1)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(33)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(6)	73						TCTTTTCAGGCAGCCTTGCAG	0.493																																																	1	Substitution - Missense(1)	kidney(1)											155.0	156.0	156.0					1																	229773890		2203	4300	6503	SO:0001583	missense	9816			D50923	CCDS31052.1	1q42.13	2009-11-06	2008-10-01	2008-10-01	ENSG00000135763	ENSG00000135763			28967	protein-coding gene	gene with protein product	"""nucleolar preribosomal-associated protein 1"""		"""KIAA0133"""	KIAA0133		8590280	Standard	NM_014777		Approved	NPA2, NET10	uc001hts.1	Q14146	OTTHUMG00000039464	ENST00000258243.2:c.3530C>T	1.37:g.229773890C>T	ENSP00000258243:p.Ala1177Val	Somatic		WXS	Illumina HiSeq	Phase_I	Q5VYC9	Missense_Mutation	SNP	ENST00000258243.2	37	CCDS31052.1	.	.	.	.	.	.	.	.	.	.	C	20.1	3.940217	0.73557	.	.	ENSG00000135763	ENST00000258243	T	0.33216	1.42	5.65	3.72	0.42706	.	0.162448	0.56097	D	0.000033	T	0.19167	0.0460	L	0.29908	0.895	0.32110	N	0.589456	P	0.45126	0.851	B	0.37550	0.253	T	0.17440	-1.0369	9	.	.	.	-13.0773	10.0615	0.42277	0.1196:0.7629:0.0:0.1175	.	1177	Q14146	URB2_HUMAN	V	1177	ENSP00000258243:A1177V	.	A	+	2	0	URB2	227840513	0.139000	0.22563	0.989000	0.46669	0.769000	0.43574	0.400000	0.20932	1.515000	0.48885	0.585000	0.79938	GCA		0.493	URB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095232.1		NM_014777	
VHL	7428	broad.mit.edu;ucsc.edu	37	3	10188309	10188309	+	Missense_Mutation	SNP	T	T	C			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3b685193-f1fa-4c1b-949b-bcdb2d1b934c	224a12b0-8203-45e5-a23e-3c913d687bd7	g.chr3:10188309T>C	ENST00000256474.2	+	2	1292	c.452T>C	c.(451-453)aTc>aCc	p.I151T	VHL_ENST00000477538.1_3'UTR|VHL_ENST00000345392.2_Intron	NM_000551.3	NP_000542.1	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor, E3 ubiquitin protein ligase	151	Involved in binding to CCT complex.				cell morphogenesis (GO:0000902)|cellular response to hypoxia (GO:0071456)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061428)|positive regulation of cell differentiation (GO:0045597)|positive regulation of transcription, DNA-templated (GO:0045893)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|transcription factor binding (GO:0008134)|ubiquitin protein ligase activity (GO:0061630)|ubiquitin-protein transferase activity (GO:0004842)	p.I151T(7)|p.I151S(6)|p.I151N(3)|p.I151>?(1)|p.?(1)|p.N150fs*7(1)|p.I151_T152del(1)|p.I151fs*8(1)|p.G144fs*19(1)		adrenal_gland(25)|autonomic_ganglia(3)|central_nervous_system(2)|endometrium(6)|kidney(1662)|large_intestine(14)|lung(6)|pancreas(18)|paratesticular_tissues(1)|pleura(1)|skin(1)|soft_tissue(24)|thyroid(3)|upper_aerodigestive_tract(3)	1769				Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569)		TTTGCCAATATCACACTGCCA	0.398		1	"""D, Mis, N, F, S"""		"""renal, hemangioma, pheochromocytoma"""	"""renal, hemangioma, pheochromocytoma"""			von Hippel-Lindau disease;Pheochromocytoma (Adrenal), Familial;Chuvash Polycythemia																														yes	Rec	yes	von Hippel-Lindau syndrome	3	3p25	7428	von Hippel-Lindau syndrome gene		"""E, M, O"""	22	Substitution - Missense(16)|Deletion - Frameshift(3)|Complex(1)|Deletion - In frame(1)|Unknown(1)	kidney(22)	GRCh37	CM994244	VHL	M							195.0	182.0	187.0					3																	10188309		2203	4300	6503	SO:0001583	missense	7428	Familial Cancer Database	VHL; ;Erythrocytosis, Familial type 2	L15409	CCDS2597.1, CCDS2598.1	3p25.3	2014-09-17	2012-02-23		ENSG00000134086	ENSG00000134086			12687	protein-coding gene	gene with protein product		608537	"""von Hippel-Lindau syndrome"", ""von Hippel-Lindau tumor suppressor"""			9671762	Standard	NM_000551		Approved	VHL1	uc003bvc.3	P40337	OTTHUMG00000128668	ENST00000256474.2:c.452T>C	3.37:g.10188309T>C	ENSP00000256474:p.Ile151Thr	Somatic		WXS	Illumina GAIIx	Phase_I	B2RE45|Q13599|Q6PDA9	Missense_Mutation	SNP	ENST00000256474.2	37	CCDS2597.1	.	.	.	.	.	.	.	.	.	.	T	19.92	3.915471	0.73098	.	.	ENSG00000134086	ENST00000256474;ENST00000450183	D	0.99876	-7.41	4.89	4.89	0.63831	von Hippel-Lindau disease tumor suppressor,  beta domain (1);von Hippel-Lindau disease tumour suppressor, beta/alpha domain (2);	0.000000	0.85682	D	0.000000	D	0.99796	0.9913	M	0.76574	2.34	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.96623	0.9461	10	0.87932	D	0	0.0775	12.7607	0.57363	0.0:0.0:0.0:1.0	.	151	P40337	VHL_HUMAN	T	151;69	ENSP00000256474:I151T	ENSP00000256474:I151T	I	+	2	0	VHL	10163309	1.000000	0.71417	1.000000	0.80357	0.938000	0.57974	5.968000	0.70413	1.966000	0.57179	0.460000	0.39030	ATC		0.398	VHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250559.1		NM_000551	
VPS13C	54832	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	15	62257054	62257055	+	Frame_Shift_Del	DEL	AG	AG	-			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08	AG	AG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3b685193-f1fa-4c1b-949b-bcdb2d1b934c	224a12b0-8203-45e5-a23e-3c913d687bd7	g.chr15:62257054_62257055delAG	ENST00000261517.5	-	31	3130_3131	c.3057_3058delCT	c.(3055-3060)gcctttfs	p.F1020fs	VPS13C_ENST00000249837.3_Frame_Shift_Del_p.F977fs|VPS13C_ENST00000395896.4_Frame_Shift_Del_p.F1020fs|VPS13C_ENST00000395898.3_Frame_Shift_Del_p.F977fs	NM_020821.2	NP_065872.1			vacuolar protein sorting 13 homolog C (S. cerevisiae)											NS(3)|breast(4)|endometrium(4)|kidney(9)|large_intestine(26)|lung(46)|ovary(5)|prostate(6)|skin(6)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	117						AAAGATGAAAAGGCCACCTAAA	0.376																																																	0																																										SO:0001589	frameshift_variant	54832			AJ608770	CCDS10180.1, CCDS32257.1, CCDS45272.1, CCDS58367.1	15q21.3	2009-07-09	2006-04-04		ENSG00000129003	ENSG00000129003			23594	protein-coding gene	gene with protein product		608879	"""vacuolar protein sorting 13C (yeast)"""				Standard	NM_018080		Approved	FLJ20136, FLJ10381, KIAA1421	uc002agz.3	Q709C8	OTTHUMG00000132801	ENST00000261517.5:c.3057_3058delCT	15.37:g.62257054_62257055delAG	ENSP00000261517:p.Phe1020fs	Somatic		WXS	Illumina HiSeq	Phase_I		Frame_Shift_Del	DEL	ENST00000261517.5	37	CCDS32257.1																																																																																				0.376	VPS13C-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000415997.1		NM_017684	
VPS25	84313	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	17	40925522	40925522	+	Missense_Mutation	SNP	A	A	G			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3b685193-f1fa-4c1b-949b-bcdb2d1b934c	224a12b0-8203-45e5-a23e-3c913d687bd7	g.chr17:40925522A>G	ENST00000253794.2	+	1	69	c.29A>G	c.(28-30)cAg>cGg	p.Q10R		NM_032353.2	NP_115729.1	Q9BRG1	VPS25_HUMAN	vacuolar protein sorting 25 homolog (S. cerevisiae)	10					endosomal transport (GO:0016197)|membrane organization (GO:0061024)|protein transport (GO:0015031)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	protein homodimerization activity (GO:0042803)	p.Q10R(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)	5		Breast(137;0.00104)		BRCA - Breast invasive adenocarcinoma(366;0.0745)		TGGCCGTGGCAGTATCGCTTC	0.632																																																	1	Substitution - Missense(1)	kidney(1)											176.0	149.0	158.0					17																	40925522		2203	4300	6503	SO:0001583	missense	84313			AB014763	CCDS11438.1	17q21.31	2014-02-12	2006-04-04		ENSG00000131475	ENSG00000131475			28122	protein-coding gene	gene with protein product		610907	"""vacuolar protein sorting 25 (yeast)"""			15511219	Standard	NM_032353		Approved	MGC10540, EAP20, DERP9	uc002ibi.3	Q9BRG1		ENST00000253794.2:c.29A>G	17.37:g.40925522A>G	ENSP00000253794:p.Gln10Arg	Somatic		WXS	Illumina HiSeq	Phase_I	B2R581	Missense_Mutation	SNP	ENST00000253794.2	37	CCDS11438.1	.	.	.	.	.	.	.	.	.	.	A	29.8	5.032827	0.93575	.	.	ENSG00000131475	ENST00000253794	T	0.42131	0.98	5.04	5.04	0.67666	ESCRT-II complex, Vps25 subunit, N-terminal winged helix (1);	0.000000	0.85682	D	0.000000	T	0.64605	0.2613	M	0.84846	2.72	0.80722	D	1	D	0.69078	0.997	D	0.65443	0.935	T	0.65981	-0.6036	10	0.25106	T	0.35	-16.5249	14.4533	0.67399	1.0:0.0:0.0:0.0	.	10	Q9BRG1	VPS25_HUMAN	R	10	ENSP00000253794:Q10R	ENSP00000253794:Q10R	Q	+	2	0	VPS25	38179048	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.602000	0.90868	1.898000	0.54952	0.459000	0.35465	CAG		0.632	VPS25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452383.1		NM_032353	
WDR48	57599	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	39108073	39108073	+	Silent	SNP	A	A	T			TCGA-CJ-4903-01A-01D-1429-08	TCGA-CJ-4903-11A-01D-1429-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3b685193-f1fa-4c1b-949b-bcdb2d1b934c	224a12b0-8203-45e5-a23e-3c913d687bd7	g.chr3:39108073A>T	ENST00000302313.5	+	4	331	c.303A>T	c.(301-303)gtA>gtT	p.V101V	WDR48_ENST00000544962.1_Intron|WDR48_ENST00000418020.1_De_novo_Start_OutOfFrame|WDR48_ENST00000396258.3_Silent_p.V19V	NM_020839.2	NP_065890.1	Q8TAF3	WDR48_HUMAN	WD repeat domain 48	101					double-strand break repair via homologous recombination (GO:0000724)|embryonic organ development (GO:0048568)|homeostasis of number of cells (GO:0048872)|multicellular organism growth (GO:0035264)|positive regulation of epithelial cell proliferation (GO:0050679)|protein deubiquitination (GO:0016579)|regulation of protein monoubiquitination (GO:1902525)|seminiferous tubule development (GO:0072520)|single fertilization (GO:0007338)|skeletal system morphogenesis (GO:0048705)|skin development (GO:0043588)|spermatogenesis (GO:0007283)|viral process (GO:0016032)	intracellular membrane-bounded organelle (GO:0043231)|lysosome (GO:0005764)|nucleus (GO:0005634)		p.V101V(1)		breast(2)|kidney(1)|large_intestine(2)|lung(4)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	15				KIRC - Kidney renal clear cell carcinoma(284;0.0588)|Kidney(284;0.0738)		CAGTAAAAGTATGGAATGCAC	0.333																																																	1	Substitution - coding silent(1)	kidney(1)											145.0	134.0	138.0					3																	39108073		2203	4300	6503	SO:0001819	synonymous_variant	57599			AF468833	CCDS33738.1	3p21.33	2014-06-16			ENSG00000114742	ENSG00000114742		"""WD repeat domain containing"""	30914	protein-coding gene	gene with protein product		612167				10819331, 12196293, 24482476	Standard	NM_020839		Approved	KIAA1449, P80, SPG60	uc003cit.3	Q8TAF3	OTTHUMG00000155972	ENST00000302313.5:c.303A>T	3.37:g.39108073A>T		Somatic		WXS	Illumina HiSeq	Phase_I	B4DM86|B4DQI2|B4DY84|Q63HJ2|Q658Y1|Q8N3Z1|Q9NSK8|Q9P279	Silent	SNP	ENST00000302313.5	37	CCDS33738.1																																																																																				0.333	WDR48-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342529.1		NM_020839	
