#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_ORegAnno_bin	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
AHNAK2	113146	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	14	105418731	105418731	+	Frame_Shift_Del	DEL	G	G	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	2cb6b578-8543-4a12-8331-1721ddc47303	1e656287-a1d9-4273-bbd2-c4909d29366d	g.chr14:105418731delG	ENST00000333244.5	-	7	3176	c.3057delC	c.(3055-3057)gccfs	p.A1019fs	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	1019						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)				cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			CATCCACCAAGGCCTTGATGG	0.577																																																	0													188.0	203.0	198.0					14																	105418731		1975	4163	6138	SO:0001589	frameshift_variant	113146			AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"""chromosome 14 open reading frame 78"""	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.3057delC	14.37:g.105418731delG	ENSP00000353114:p.Ala1019fs		Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Frame_Shift_Del	DEL	ENST00000333244.5	37	CCDS45177.1																																																																																				0.577	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1		NM_138420	
ARHGAP5	394	hgsc.bcm.edu	37	14	32561313	32561313	+	Nonsense_Mutation	SNP	C	C	T	rs201986816	byFrequency	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	2cb6b578-8543-4a12-8331-1721ddc47303	1e656287-a1d9-4273-bbd2-c4909d29366d	g.chr14:32561313C>T	ENST00000345122.3	+	2	1753	c.1438C>T	c.(1438-1440)Cga>Tga	p.R480*	ARHGAP5_ENST00000432921.1_Nonsense_Mutation_p.R480*|ARHGAP5_ENST00000396582.2_Intron|ARHGAP5_ENST00000539826.2_Nonsense_Mutation_p.R480*|ARHGAP5_ENST00000556611.1_Nonsense_Mutation_p.R480*|ARHGAP5_ENST00000433497.1_Intron	NM_001030055.1	NP_001025226.1	Q13017	RHG05_HUMAN	Rho GTPase activating protein 5	480	FF 3.				cell adhesion (GO:0007155)|GTP catabolic process (GO:0006184)|mammary gland development (GO:0030879)|positive regulation of cell migration (GO:0030335)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell size (GO:0008361)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|Rho GTPase activator activity (GO:0005100)|SH2 domain binding (GO:0042169)			NS(2)|breast(10)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(10)|lung(12)|ovary(4)|skin(1)|stomach(1)|urinary_tract(4)	55	Hepatocellular(127;0.0604)|Prostate(35;0.15)|Breast(36;0.186)		LUAD - Lung adenocarcinoma(48;0.00192)|Lung(238;0.00714)|BRCA - Breast invasive adenocarcinoma(188;0.0952)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.00566)		TAGGCATCAGCGAGAAATAGT	0.383																																					NSCLC(9;77 350 3443 29227 41353)												0													70.0	72.0	71.0					14																	32561313		2203	4298	6501	SO:0001587	stop_gained	394			U17032	CCDS32062.1, CCDS45095.1	14q12	2010-02-05						"""Rho GTPase activating proteins"""	675	protein-coding gene	gene with protein product		602680	"""growth factor independent 2"""	GFI2		8537347	Standard	XM_005267635		Approved	RhoGAP5, p190-B, p190BRhoGAP	uc001wrn.3	Q13017		ENST00000345122.3:c.1438C>T	14.37:g.32561313C>T	ENSP00000371897:p.Arg480*		A1L375|A1L376|A8KAA1|D3DS89|D3DS90|Q05BE8|Q05BU8|Q59ER0|Q6DHZ3	Nonsense_Mutation	SNP	ENST00000345122.3	37	CCDS32062.1	.	.	.	.	.	.	.	.	.	.	C	39	7.554307	0.98355	.	.	ENSG00000100852	ENST00000556611;ENST00000539826;ENST00000345122;ENST00000432921	.	.	.	6.02	5.11	0.69529	.	0.057780	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.06891	T	0.86	.	14.0719	0.64865	0.3873:0.6127:0.0:0.0	.	.	.	.	X	480	.	ENSP00000371897:R480X	R	+	1	2	ARHGAP5	31631064	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.567000	0.45956	1.483000	0.48342	0.650000	0.86243	CGA		0.383	ARHGAP5-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000409735.1		NM_001030055	
ARHGAP5	394	hgsc.bcm.edu	37	14	32561316	32561316	+	Nonsense_Mutation	SNP	G	G	T	rs200628183	byFrequency	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	2cb6b578-8543-4a12-8331-1721ddc47303	1e656287-a1d9-4273-bbd2-c4909d29366d	g.chr14:32561316G>T	ENST00000345122.3	+	2	1756	c.1441G>T	c.(1441-1443)Gaa>Taa	p.E481*	ARHGAP5_ENST00000432921.1_Nonsense_Mutation_p.E481*|ARHGAP5_ENST00000396582.2_Intron|ARHGAP5_ENST00000539826.2_Nonsense_Mutation_p.E481*|ARHGAP5_ENST00000556611.1_Nonsense_Mutation_p.E481*|ARHGAP5_ENST00000433497.1_Intron	NM_001030055.1	NP_001025226.1	Q13017	RHG05_HUMAN	Rho GTPase activating protein 5	481	FF 3.				cell adhesion (GO:0007155)|GTP catabolic process (GO:0006184)|mammary gland development (GO:0030879)|positive regulation of cell migration (GO:0030335)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell size (GO:0008361)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|Rho GTPase activator activity (GO:0005100)|SH2 domain binding (GO:0042169)			NS(2)|breast(10)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(10)|lung(12)|ovary(4)|skin(1)|stomach(1)|urinary_tract(4)	55	Hepatocellular(127;0.0604)|Prostate(35;0.15)|Breast(36;0.186)		LUAD - Lung adenocarcinoma(48;0.00192)|Lung(238;0.00714)|BRCA - Breast invasive adenocarcinoma(188;0.0952)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.00566)		GCATCAGCGAGAAATAGTTGA	0.373																																					NSCLC(9;77 350 3443 29227 41353)												0													69.0	70.0	70.0					14																	32561316		2203	4297	6500	SO:0001587	stop_gained	394			U17032	CCDS32062.1, CCDS45095.1	14q12	2010-02-05						"""Rho GTPase activating proteins"""	675	protein-coding gene	gene with protein product		602680	"""growth factor independent 2"""	GFI2		8537347	Standard	XM_005267635		Approved	RhoGAP5, p190-B, p190BRhoGAP	uc001wrn.3	Q13017		ENST00000345122.3:c.1441G>T	14.37:g.32561316G>T	ENSP00000371897:p.Glu481*		A1L375|A1L376|A8KAA1|D3DS89|D3DS90|Q05BE8|Q05BU8|Q59ER0|Q6DHZ3	Nonsense_Mutation	SNP	ENST00000345122.3	37	CCDS32062.1	.	.	.	.	.	.	.	.	.	.	G	40	8.091676	0.98648	.	.	ENSG00000100852	ENST00000556611;ENST00000539826;ENST00000345122;ENST00000432921	.	.	.	6.02	6.02	0.97574	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.31617	T	0.26	.	20.547	0.99278	0.0:0.0:1.0:0.0	.	.	.	.	X	481	.	ENSP00000371897:E481X	E	+	1	0	ARHGAP5	31631067	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.869000	0.99810	2.850000	0.98022	0.650000	0.86243	GAA		0.373	ARHGAP5-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000409735.1		NM_001030055	
ARHGAP5	394	hgsc.bcm.edu	37	14	32561340	32561340	+	Missense_Mutation	SNP	G	G	A	rs78337553		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	2cb6b578-8543-4a12-8331-1721ddc47303	1e656287-a1d9-4273-bbd2-c4909d29366d	g.chr14:32561340G>A	ENST00000345122.3	+	2	1780	c.1465G>A	c.(1465-1467)Gag>Aag	p.E489K	ARHGAP5_ENST00000432921.1_Missense_Mutation_p.E489K|ARHGAP5_ENST00000396582.2_Intron|ARHGAP5_ENST00000539826.2_Missense_Mutation_p.E489K|ARHGAP5_ENST00000556611.1_Missense_Mutation_p.E489K|ARHGAP5_ENST00000433497.1_Intron	NM_001030055.1	NP_001025226.1	Q13017	RHG05_HUMAN	Rho GTPase activating protein 5	489	FF 4.				cell adhesion (GO:0007155)|GTP catabolic process (GO:0006184)|mammary gland development (GO:0030879)|positive regulation of cell migration (GO:0030335)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell size (GO:0008361)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|Rho GTPase activator activity (GO:0005100)|SH2 domain binding (GO:0042169)	p.E489K(1)		NS(2)|breast(10)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(10)|lung(12)|ovary(4)|skin(1)|stomach(1)|urinary_tract(4)	55	Hepatocellular(127;0.0604)|Prostate(35;0.15)|Breast(36;0.186)		LUAD - Lung adenocarcinoma(48;0.00192)|Lung(238;0.00714)|BRCA - Breast invasive adenocarcinoma(188;0.0952)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.00566)		AGCCAAAGAAGAGTTTCAAGA	0.343																																					NSCLC(9;77 350 3443 29227 41353)												1	Substitution - Missense(1)	stomach(1)											60.0	61.0	61.0					14																	32561340		2203	4298	6501	SO:0001583	missense	394			U17032	CCDS32062.1, CCDS45095.1	14q12	2010-02-05						"""Rho GTPase activating proteins"""	675	protein-coding gene	gene with protein product		602680	"""growth factor independent 2"""	GFI2		8537347	Standard	XM_005267635		Approved	RhoGAP5, p190-B, p190BRhoGAP	uc001wrn.3	Q13017		ENST00000345122.3:c.1465G>A	14.37:g.32561340G>A	ENSP00000371897:p.Glu489Lys		A1L375|A1L376|A8KAA1|D3DS89|D3DS90|Q05BE8|Q05BU8|Q59ER0|Q6DHZ3	Missense_Mutation	SNP	ENST00000345122.3	37	CCDS32062.1	.	.	.	.	.	.	.	.	.	.	G	19.00	3.741262	0.69304	.	.	ENSG00000100852	ENST00000556611;ENST00000539826;ENST00000345122;ENST00000432921	T;T;T;T	0.32023	1.47;1.47;1.47;1.47	6.02	6.02	0.97574	FF domain (2);	0.044905	0.85682	D	0.000000	T	0.39009	0.1062	N	0.22421	0.69	0.80722	D	1	P;P	0.42296	0.734;0.775	P;P	0.52066	0.562;0.689	T	0.11060	-1.0603	10	0.62326	D	0.03	.	20.547	0.99278	0.0:0.0:1.0:0.0	.	489;489	Q13017-2;Q13017	.;RHG05_HUMAN	K	489	ENSP00000452222:E489K;ENSP00000441692:E489K;ENSP00000371897:E489K;ENSP00000393307:E489K	ENSP00000371897:E489K	E	+	1	0	ARHGAP5	31631091	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.869000	0.99810	2.850000	0.98022	0.650000	0.86243	GAG		0.343	ARHGAP5-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000409735.1		NM_001030055	
ATF6B	1388	hgsc.bcm.edu	37	6	32088654	32088655	+	Frame_Shift_Ins	INS	-	-	G	rs557874697		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	2cb6b578-8543-4a12-8331-1721ddc47303	1e656287-a1d9-4273-bbd2-c4909d29366d	g.chr6:32088654_32088655insG	ENST00000375203.3	-	8	757_758	c.725_726insC	c.(724-726)ccgfs	p.P242fs	ATF6B_ENST00000375201.4_Frame_Shift_Ins_p.P239fs	NM_001136153.1|NM_004381.4	NP_001129625.1|NP_004372.3	Q99941	ATF6B_HUMAN	activating transcription factor 6 beta	242					response to unfolded protein (GO:0006986)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(11)|prostate(2)|skin(1)|urinary_tract(1)	22						GCTGCAGTGGCGGCTTCCGGGT	0.569																																																	0																																										SO:0001589	frameshift_variant	1388				CCDS47408.1, CCDS4737.1	6p21.3	2013-01-10	2008-10-21	2008-10-21	ENSG00000213676	ENSG00000213676		"""basic leucine zipper proteins"""	2349	protein-coding gene	gene with protein product		600984	"""cAMP responsive element binding protein-like 1"""	CREBL1		11256944, 14973138	Standard	NM_004381		Approved	G13	uc003nzn.3	Q99941	OTTHUMG00000031296	ENST00000375203.3:c.726dupC	6.37:g.32088656_32088656dupG	ENSP00000364349:p.Pro242fs		B0UYX6|Q13269|Q14343|Q14345|Q5SSW7|Q99635|Q99637|Q9H3V9|Q9H3W1|Q9NPL0	Frame_Shift_Ins	INS	ENST00000375203.3	37	CCDS4737.1																																																																																				0.569	ATF6B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000076638.2			
BMPR2	659	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	203420922	203420922	+	Missense_Mutation	SNP	A	A	T			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	2cb6b578-8543-4a12-8331-1721ddc47303	1e656287-a1d9-4273-bbd2-c4909d29366d	g.chr2:203420922A>T	ENST00000374580.4	+	12	3073	c.2534A>T	c.(2533-2535)gAa>gTa	p.E845V	BMPR2_ENST00000374574.2_Intron	NM_001204.6	NP_001195.2	Q13873	BMPR2_HUMAN	bone morphogenetic protein receptor, type II (serine/threonine kinase)	845					activin receptor signaling pathway (GO:0032924)|anterior/posterior pattern specification (GO:0009952)|artery development (GO:0060840)|blood vessel remodeling (GO:0001974)|BMP signaling pathway (GO:0030509)|brain development (GO:0007420)|cellular response to starvation (GO:0009267)|chondrocyte development (GO:0002063)|limb development (GO:0060173)|lung alveolus development (GO:0048286)|lymphangiogenesis (GO:0001946)|lymphatic endothelial cell differentiation (GO:0060836)|mesoderm formation (GO:0001707)|negative regulation of cell growth (GO:0030308)|negative regulation of chondrocyte proliferation (GO:1902731)|negative regulation of DNA biosynthetic process (GO:2000279)|negative regulation of systemic arterial blood pressure (GO:0003085)|negative regulation of vasoconstriction (GO:0045906)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of bone mineralization (GO:0030501)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|regulation of cell proliferation (GO:0042127)|regulation of lung blood pressure (GO:0014916)|retina vasculature development in camera-type eye (GO:0061298)|transcription from RNA polymerase II promoter (GO:0006366)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|venous blood vessel development (GO:0060841)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|caveola (GO:0005901)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular space (GO:0005615)|fully spanning plasma membrane (GO:0044214)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	activin receptor activity, type II (GO:0016362)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|transforming growth factor beta-activated receptor activity (GO:0005024)	p.E845V(1)		autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(6)|large_intestine(11)|lung(7)|ovary(4)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(2)	42						AGGGCCCAAGAAATGTTGCAG	0.468																																																	1	Substitution - Missense(1)	kidney(1)											119.0	112.0	114.0					2																	203420922		2203	4300	6503	SO:0001583	missense	659			Z48923	CCDS33361.1	2q33-q34	2014-09-17			ENSG00000204217	ENSG00000204217			1078	protein-coding gene	gene with protein product		600799	"""primary pulmonary hypertension 1"""	PPH1		7791754	Standard	NM_001204		Approved	BRK-3, T-ALK, BMPR3, BMPR-II	uc002uzf.4	Q13873	OTTHUMG00000133617	ENST00000374580.4:c.2534A>T	2.37:g.203420922A>T	ENSP00000363708:p.Glu845Val		Q13161|Q16569|Q4ZG08|Q53SA5|Q585T8	Missense_Mutation	SNP	ENST00000374580.4	37	CCDS33361.1	.	.	.	.	.	.	.	.	.	.	A	13.68	2.309229	0.40895	.	.	ENSG00000204217	ENST00000374580	D	0.90676	-2.71	6.17	6.17	0.99709	.	0.315381	0.39146	N	0.001451	D	0.85120	0.5624	N	0.19112	0.55	0.80722	D	1	B	0.23735	0.09	B	0.20767	0.031	T	0.81831	-0.0752	10	0.72032	D	0.01	.	16.8222	0.85835	1.0:0.0:0.0:0.0	.	845	Q13873	BMPR2_HUMAN	V	845	ENSP00000363708:E845V	ENSP00000363708:E845V	E	+	2	0	BMPR2	203129167	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	3.613000	0.54152	2.371000	0.80710	0.533000	0.62120	GAA		0.468	BMPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257743.1		NM_001204	
BMPR2	659	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	203420924	203420924	+	Missense_Mutation	SNP	A	A	T			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	2cb6b578-8543-4a12-8331-1721ddc47303	1e656287-a1d9-4273-bbd2-c4909d29366d	g.chr2:203420924A>T	ENST00000374580.4	+	12	3075	c.2536A>T	c.(2536-2538)Atg>Ttg	p.M846L	BMPR2_ENST00000374574.2_Intron	NM_001204.6	NP_001195.2	Q13873	BMPR2_HUMAN	bone morphogenetic protein receptor, type II (serine/threonine kinase)	846					activin receptor signaling pathway (GO:0032924)|anterior/posterior pattern specification (GO:0009952)|artery development (GO:0060840)|blood vessel remodeling (GO:0001974)|BMP signaling pathway (GO:0030509)|brain development (GO:0007420)|cellular response to starvation (GO:0009267)|chondrocyte development (GO:0002063)|limb development (GO:0060173)|lung alveolus development (GO:0048286)|lymphangiogenesis (GO:0001946)|lymphatic endothelial cell differentiation (GO:0060836)|mesoderm formation (GO:0001707)|negative regulation of cell growth (GO:0030308)|negative regulation of chondrocyte proliferation (GO:1902731)|negative regulation of DNA biosynthetic process (GO:2000279)|negative regulation of systemic arterial blood pressure (GO:0003085)|negative regulation of vasoconstriction (GO:0045906)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of bone mineralization (GO:0030501)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|regulation of cell proliferation (GO:0042127)|regulation of lung blood pressure (GO:0014916)|retina vasculature development in camera-type eye (GO:0061298)|transcription from RNA polymerase II promoter (GO:0006366)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|venous blood vessel development (GO:0060841)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|caveola (GO:0005901)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular space (GO:0005615)|fully spanning plasma membrane (GO:0044214)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	activin receptor activity, type II (GO:0016362)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|transforming growth factor beta-activated receptor activity (GO:0005024)	p.M846L(1)		autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(6)|large_intestine(11)|lung(7)|ovary(4)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(2)	42						GGCCCAAGAAATGTTGCAGAA	0.468																																																	1	Substitution - Missense(1)	kidney(1)											121.0	113.0	116.0					2																	203420924		2203	4300	6503	SO:0001583	missense	659			Z48923	CCDS33361.1	2q33-q34	2014-09-17			ENSG00000204217	ENSG00000204217			1078	protein-coding gene	gene with protein product		600799	"""primary pulmonary hypertension 1"""	PPH1		7791754	Standard	NM_001204		Approved	BRK-3, T-ALK, BMPR3, BMPR-II	uc002uzf.4	Q13873	OTTHUMG00000133617	ENST00000374580.4:c.2536A>T	2.37:g.203420924A>T	ENSP00000363708:p.Met846Leu		Q13161|Q16569|Q4ZG08|Q53SA5|Q585T8	Missense_Mutation	SNP	ENST00000374580.4	37	CCDS33361.1	.	.	.	.	.	.	.	.	.	.	A	8.545	0.874096	0.17395	.	.	ENSG00000204217	ENST00000374580	D	0.88046	-2.33	6.17	3.67	0.42095	.	0.231983	0.56097	N	0.000022	T	0.72819	0.3508	N	0.08118	0	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.64748	-0.6334	10	0.17832	T	0.49	.	12.9586	0.58444	0.7452:0.2548:0.0:0.0	.	846	Q13873	BMPR2_HUMAN	L	846	ENSP00000363708:M846L	ENSP00000363708:M846L	M	+	1	0	BMPR2	203129169	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	0.922000	0.28734	1.138000	0.42230	0.533000	0.62120	ATG		0.468	BMPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257743.1		NM_001204	
FAM218A	152756	hgsc.bcm.edu;ucsc.edu	37	4	165878425	165878426	+	Frame_Shift_Del	DEL	TC	TC	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10	TC	TC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	2cb6b578-8543-4a12-8331-1721ddc47303	1e656287-a1d9-4273-bbd2-c4909d29366d	g.chr4:165878425_165878426delTC	ENST00000513876.2	+	1	326_327	c.251_252delTC	c.(250-252)ttcfs	p.F84fs	TRIM61_ENST00000329314.5_Intron	NM_153027.1	NP_694572.1	Q96MZ4	F218A_HUMAN	family with sequence similarity 218, member A	84																	CGAATCGTTTTCTCCGCGTGCC	0.594																																																	0																																										SO:0001589	frameshift_variant	0			AK056221	CCDS3807.1	4q32.3	2012-03-01	2012-03-01	2012-03-01	ENSG00000250486	ENSG00000250486			26466	protein-coding gene	gene with protein product			"""chromosome 4 open reading frame 39"""	C4orf39		12477932	Standard	NM_153027		Approved	FLJ31659	uc003iqx.1	Q96MZ4	OTTHUMG00000161252	ENST00000513876.2:c.251_252delTC	4.37:g.165878427_165878428delTC	ENSP00000427428:p.Phe84fs			Frame_Shift_Del	DEL	ENST00000513876.2	37	CCDS3807.1																																																																																				0.594	FAM218A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364308.1		NM_153027	
CTSS	1520	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	150724283	150724283	+	Missense_Mutation	SNP	C	C	G			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	2cb6b578-8543-4a12-8331-1721ddc47303	1e656287-a1d9-4273-bbd2-c4909d29366d	g.chr1:150724283C>G	ENST00000368985.3	-	5	861	c.601G>C	c.(601-603)Gac>Cac	p.D201H	CTSS_ENST00000480760.1_5'UTR|CTSS_ENST00000448301.2_Missense_Mutation_p.D151H	NM_001199739.1|NM_004079.4	NP_001186668.1|NP_004070.3	P25774	CATS_HUMAN	cathepsin S	201					adaptive immune response (GO:0002250)|antigen processing and presentation (GO:0019882)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|basement membrane disassembly (GO:0034769)|cellular response to thyroid hormone stimulus (GO:0097067)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|immune response (GO:0006955)|innate immune response (GO:0045087)|positive regulation of inflammatory response (GO:0050729)|proteolysis (GO:0006508)|proteolysis involved in cellular protein catabolic process (GO:0051603)|toll-like receptor signaling pathway (GO:0002224)	endolysosome lumen (GO:0036021)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)|membrane (GO:0016020)	collagen binding (GO:0005518)|cysteine-type endopeptidase activity (GO:0004197)|fibronectin binding (GO:0001968)|laminin binding (GO:0043236)|proteoglycan binding (GO:0043394)	p.D201H(1)		cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(5)|skin(1)|stomach(1)|urinary_tract(1)	15	all_cancers(9;6.17e-52)|all_epithelial(9;9.7e-43)|all_lung(15;5.74e-35)|Lung NSC(24;2.09e-31)|Breast(34;0.00146)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Melanoma(130;0.128)|Colorectal(459;0.171)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0485)|Epithelial(6;5.02e-21)|all cancers(9;1.28e-20)|OV - Ovarian serous cystadenocarcinoma(6;1.09e-14)|BRCA - Breast invasive adenocarcinoma(12;0.00501)|LUSC - Lung squamous cell carcinoma(543;0.171)			TAGGAAGCGTCTGAGTCGATG	0.473																																																	1	Substitution - Missense(1)	kidney(1)											208.0	177.0	188.0					1																	150724283		2203	4300	6503	SO:0001583	missense	1520			M90696	CCDS968.1, CCDS55634.1	1q21	2008-02-05			ENSG00000163131	ENSG00000163131	3.4.22.27	"""Cathepsins"""	2545	protein-coding gene	gene with protein product		116845				1373132	Standard	NM_001199739		Approved		uc001evn.3	P25774	OTTHUMG00000035010	ENST00000368985.3:c.601G>C	1.37:g.150724283C>G	ENSP00000357981:p.Asp201His		B4DWC9|D3DV05|Q5T5I0|Q6FHS5|Q9BUG3	Missense_Mutation	SNP	ENST00000368985.3	37	CCDS968.1	.	.	.	.	.	.	.	.	.	.	C	20.4	3.983541	0.74474	.	.	ENSG00000163131	ENST00000448301;ENST00000368985	D;T	0.97665	-4.48;1.9	5.34	5.34	0.76211	Peptidase C1A, papain C-terminal (2);	0.533495	0.22034	N	0.065560	D	0.97486	0.9177	L	0.48877	1.53	0.80722	D	1	D;D	0.69078	0.997;0.996	D;D	0.72982	0.979;0.976	D	0.98556	1.0639	10	0.87932	D	0	.	18.0329	0.89290	0.0:1.0:0.0:0.0	.	151;201	B4DWC9;P25774	.;CATS_HUMAN	H	151;201	ENSP00000408414:D151H;ENSP00000357981:D201H	ENSP00000357981:D201H	D	-	1	0	CTSS	148990907	1.000000	0.71417	0.207000	0.23584	0.506000	0.33950	7.776000	0.85560	2.660000	0.90430	0.650000	0.86243	GAC		0.473	CTSS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084737.1		NM_004079	
DIAPH1	1729	hgsc.bcm.edu	37	5	140953563	140953563	+	Silent	SNP	T	T	A	rs374236039|rs3075570		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	2cb6b578-8543-4a12-8331-1721ddc47303	1e656287-a1d9-4273-bbd2-c4909d29366d	g.chr5:140953563T>A	ENST00000398557.4	-	16	1994	c.1854A>T	c.(1852-1854)ccA>ccT	p.P618P	DIAPH1_ENST00000398566.3_Silent_p.P609P|DIAPH1_ENST00000398562.2_Silent_p.P609P|DIAPH1_ENST00000520569.1_Silent_p.P564P|DIAPH1_ENST00000389054.3_Silent_p.P618P|DIAPH1_ENST00000253811.6_Silent_p.P618P|DIAPH1_ENST00000389057.5_Silent_p.P609P|DIAPH1_ENST00000518047.1_Silent_p.P609P	NM_005219.4	NP_005210.3	O60610	DIAP1_HUMAN	diaphanous-related formin 1	618	FH1.				actin filament polymerization (GO:0030041)|cellular response to histamine (GO:0071420)|cytoskeleton organization (GO:0007010)|positive regulation of cell migration (GO:0030335)|protein localization to microtubule (GO:0035372)|regulation of cell shape (GO:0008360)|regulation of microtubule-based process (GO:0032886)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)|mitotic spindle (GO:0072686)|ruffle membrane (GO:0032587)	ion channel binding (GO:0044325)|poly(A) RNA binding (GO:0044822)|receptor binding (GO:0005102)			breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(12)|pancreas(1)|skin(2)|stomach(2)	23			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCAAaggaggtggaggaggag	0.577																																																	0													21.0	21.0	21.0					5																	140953563		1987	4116	6103	SO:0001819	synonymous_variant	1729			BC007411		5q31	2013-05-24	2013-05-24		ENSG00000131504	ENSG00000131504			2876	protein-coding gene	gene with protein product		602121	"""diaphanous (Drosophila, homolog) 1"", ""diaphanous homolog 1 (Drosophila)"""	DFNA1		9360932, 1350680	Standard	NM_005219		Approved	hDIA1, LFHL1	uc003llb.4	O60610	OTTHUMG00000149893	ENST00000398557.4:c.1854A>T	5.37:g.140953563T>A			A6NF18|B7ZKW2|E9PEZ2|Q17RN4|Q59FH8|Q9UC76	Silent	SNP	ENST00000398557.4	37	CCDS43374.1																																																																																				0.577	DIAPH1-203	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding			NM_005219	
EGFL8	80864	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	6	32134517	32134517	+	Silent	SNP	G	G	A			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	2cb6b578-8543-4a12-8331-1721ddc47303	1e656287-a1d9-4273-bbd2-c4909d29366d	g.chr6:32134517G>A	ENST00000395512.1	+	4	369	c.264G>A	c.(262-264)gaG>gaA	p.E88E	EGFL8_ENST00000333845.6_Silent_p.E88E|AGPAT1_ENST00000490711.1_5'Flank|PPT2-EGFL8_ENST00000422437.1_3'UTR			Q99944	EGFL8_HUMAN	EGF-like-domain, multiple 8	88	EMI. {ECO:0000255|PROSITE- ProRule:PRU00384}.					extracellular region (GO:0005576)	calcium ion binding (GO:0005509)	p.E88E(1)		cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(4)|urinary_tract(1)	10						TGAGGCGGGAGGTTCAGCAGA	0.657																																																	1	Substitution - coding silent(1)	kidney(1)											44.0	53.0	50.0					6																	32134517		2203	4300	6503	SO:0001819	synonymous_variant	80864			U89336	CCDS4743.1	6p21	2010-06-25	2003-05-21	2003-05-23	ENSG00000241404	ENSG00000241404			13944	protein-coding gene	gene with protein product		609897	"""chromosome 6 open reading frame 8"""	C6orf8			Standard	NM_030652		Approved	NG3		Q99944	OTTHUMG00000031222	ENST00000395512.1:c.264G>A	6.37:g.32134517G>A			B0S884|G5E9Q0|Q5JP23|Q5SSX3|Q8IV30	Silent	SNP	ENST00000395512.1	37	CCDS4743.1																																																																																				0.657	EGFL8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076463.3		NM_030652	
EPHA10	284656	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	38186483	38186483	+	Missense_Mutation	SNP	C	C	T			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	2cb6b578-8543-4a12-8331-1721ddc47303	1e656287-a1d9-4273-bbd2-c4909d29366d	g.chr1:38186483C>T	ENST00000373048.4	-	12	2179	c.2180G>A	c.(2179-2181)aGc>aAc	p.S727N	EPHA10_ENST00000540011.1_3'UTR|EPHA10_ENST00000330210.7_Missense_Mutation_p.S222N|EPHA10_ENST00000427468.2_Missense_Mutation_p.S727N|EPHA10_ENST00000446149.2_5'UTR	NM_001099439.1	NP_001092909.1	Q5JZY3	EPHAA_HUMAN	EPH receptor A10	727	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				ephrin receptor signaling pathway (GO:0048013)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|transmembrane-ephrin receptor activity (GO:0005005)	p.S728N(1)		NS(2)|breast(4)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(4)|lung(13)|prostate(3)|skin(8)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	50	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				GGCCCCATGGCTCATGTACTC	0.562																																																	1	Substitution - Missense(1)	kidney(1)											71.0	78.0	76.0					1																	38186483		2020	4157	6177	SO:0001583	missense	284656			AK090974	CCDS425.1, CCDS41305.1	1p34.3	2013-02-11			ENSG00000183317	ENSG00000183317		"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	19987	protein-coding gene	gene with protein product		611123				12477932	Standard	NM_001099439		Approved	FLJ16103, FLJ33655	uc009vvi.3	Q5JZY3	OTTHUMG00000004325	ENST00000373048.4:c.2180G>A	1.37:g.38186483C>T	ENSP00000362139:p.Ser727Asn		A4FU89|J3KPB5|Q6NW42	Missense_Mutation	SNP	ENST00000373048.4	37	CCDS41305.1	.	.	.	.	.	.	.	.	.	.	C	13.79	2.342783	0.41498	.	.	ENSG00000183317	ENST00000330210;ENST00000427468;ENST00000373048	T;T;T	0.62639	0.01;0.01;0.01	4.41	2.5	0.30297	Serine-threonine/tyrosine-protein kinase (2);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.190617	0.25971	N	0.027127	T	0.44871	0.1314	N	0.25380	0.74	0.80722	D	1	B	0.02656	0.0	B	0.08055	0.003	T	0.30563	-0.9974	10	0.59425	D	0.04	.	7.105	0.25358	0.0:0.7145:0.0:0.2855	.	727	Q5JZY3	EPHAA_HUMAN	N	222;727;727	ENSP00000330379:S222N;ENSP00000397746:S727N;ENSP00000362139:S727N	ENSP00000330379:S222N	S	-	2	0	EPHA10	37959070	0.996000	0.38824	0.992000	0.48379	0.987000	0.75469	0.554000	0.23407	0.408000	0.25621	0.467000	0.42956	AGC		0.562	EPHA10-003	KNOWN	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000012497.2		NM_173641	
GIPR	2696	broad.mit.edu	37	19	46185190	46185190	+	Silent	SNP	C	C	T			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2cb6b578-8543-4a12-8331-1721ddc47303	1e656287-a1d9-4273-bbd2-c4909d29366d	g.chr19:46185190C>T	ENST00000590918.1	+	14	1497	c.1398C>T	c.(1396-1398)tgC>tgT	p.C466C	GIPR_ENST00000304207.8_Silent_p.C430C|GIPR_ENST00000263281.3_3'UTR	NM_000164.2	NP_000155.1	P48546	GIPR_HUMAN	gastric inhibitory polypeptide receptor	466					activation of adenylate cyclase activity (GO:0007190)|cell surface receptor signaling pathway (GO:0007166)|desensitization of G-protein coupled receptor protein signaling pathway (GO:0002029)|endocrine pancreas development (GO:0031018)|generation of precursor metabolites and energy (GO:0006091)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of insulin secretion (GO:0032024)|response to axon injury (GO:0048678)|response to calcium ion (GO:0051592)|response to fatty acid (GO:0070542)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	gastric inhibitory peptide receptor activity (GO:0016519)|peptide hormone binding (GO:0017046)|transmembrane signaling receptor activity (GO:0004888)	p.C466C(1)		endometrium(1)|kidney(2)|lung(5)|prostate(1)|skin(2)|urinary_tract(1)	12		Ovarian(192;0.051)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0056)|GBM - Glioblastoma multiforme(486;0.0832)|Epithelial(262;0.199)		AAAGTTACTGCTAGGGGGCGG	0.652																																																	1	Substitution - coding silent(1)	kidney(1)											15.0	16.0	16.0					19																	46185190		2148	4179	6327	SO:0001819	synonymous_variant	2696				CCDS12671.1	19q13.2-q13.3	2012-08-10				ENSG00000010310		"""GPCR / Class B : Glucagon receptors"""	4271	protein-coding gene	gene with protein product		137241				7490109	Standard	NM_000164		Approved		uc002pcu.1	P48546		ENST00000590918.1:c.1398C>T	19.37:g.46185190C>T			B7WP14|B7ZKQ0|Q14401|Q16400|Q52M04|Q9UPI1	Silent	SNP	ENST00000590918.1	37	CCDS12671.1																																																																																				0.652	GIPR-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000459640.1			
IGSF3	3321	hgsc.bcm.edu	37	1	117142613	117142613	+	Missense_Mutation	SNP	C	C	T	rs76151115	byFrequency	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	2cb6b578-8543-4a12-8331-1721ddc47303	1e656287-a1d9-4273-bbd2-c4909d29366d	g.chr1:117142613C>T	ENST00000369486.3	-	7	2744	c.1979G>A	c.(1978-1980)cGa>cAa	p.R660Q	IGSF3_ENST00000369483.1_Missense_Mutation_p.R680Q|IGSF3_ENST00000318837.6_Missense_Mutation_p.R680Q	NM_001007237.1	NP_001007238.1	O75054	IGSF3_HUMAN	immunoglobulin superfamily, member 3	660	Ig-like C2-type 5.				lacrimal gland development (GO:0032808)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)				NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(31)|ovary(4)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	62	Lung SC(450;0.225)	all_cancers(81;1.24e-06)|all_epithelial(167;4.85e-07)|all_lung(203;1.66e-06)|Lung NSC(69;1.11e-05)		Lung(183;0.0142)|Colorectal(144;0.0929)|LUSC - Lung squamous cell carcinoma(189;0.108)|COAD - Colon adenocarcinoma(174;0.139)|all cancers(265;0.159)|Epithelial(280;0.166)		CTCCGCCAGTCGCGTCCAGGT	0.612																																																	0													69.0	54.0	59.0					1																	117142613		2203	4300	6503	SO:0001583	missense	3321			AF031174	CCDS30813.1, CCDS30814.1	1p13	2013-01-29			ENSG00000143061	ENSG00000143061		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5950	protein-coding gene	gene with protein product		603491				9790749	Standard	NM_001007237		Approved	V8, EWI-3, MGC117164	uc031pnr.1	O75054	OTTHUMG00000022751	ENST00000369486.3:c.1979G>A	1.37:g.117142613C>T	ENSP00000358498:p.Arg660Gln		A6NJZ6|A6NMC7	Missense_Mutation	SNP	ENST00000369486.3	37	CCDS30813.1	.	.	.	.	.	.	.	.	.	.	C	12.58	1.979753	0.34942	.	.	ENSG00000143061	ENST00000369486;ENST00000369483;ENST00000318837	T;T;T	0.03212	4.01;4.04;4.04	4.56	2.7	0.31948	Immunoglobulin subtype (1);	0.270543	0.31010	N	0.008430	T	0.01353	0.0044	L	0.29908	0.895	0.36040	D	0.840027	D;D;D	0.59767	0.982;0.986;0.986	B;P;P	0.45310	0.345;0.476;0.476	T	0.64071	-0.6493	10	0.22706	T	0.39	-28.9658	8.7768	0.34767	0.0:0.8142:0.0:0.1858	.	680;660;680	O75054-2;O75054;A6NJZ6	.;IGSF3_HUMAN;.	Q	660;680;680	ENSP00000358498:R660Q;ENSP00000358495:R680Q;ENSP00000321184:R680Q	ENSP00000321184:R680Q	R	-	2	0	IGSF3	116944136	0.789000	0.28775	0.602000	0.28890	0.526000	0.34562	2.194000	0.42668	0.550000	0.28991	-0.384000	0.06662	CGA		0.612	IGSF3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000059040.1		NM_001542	
IFI16	3428	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	158988366	158988366	+	Silent	SNP	G	G	A			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	2cb6b578-8543-4a12-8331-1721ddc47303	1e656287-a1d9-4273-bbd2-c4909d29366d	g.chr1:158988366G>A	ENST00000295809.7	+	5	1152	c.897G>A	c.(895-897)aaG>aaA	p.K299K	IFI16_ENST00000430894.2_Silent_p.K247K|IFI16_ENST00000448393.2_Silent_p.K299K|IFI16_ENST00000340979.6_Silent_p.K299K|IFI16_ENST00000368131.4_Silent_p.K299K|IFI16_ENST00000359709.3_Silent_p.K243K|IFI16_ENST00000368132.3_Silent_p.K299K			Q16666	IF16_HUMAN	interferon, gamma-inducible protein 16	299	HIN-200 1. {ECO:0000255|PROSITE- ProRule:PRU00106}.|Interaction with TP53 C-terminus.				activation of cysteine-type endopeptidase activity (GO:0097202)|activation of innate immune response (GO:0002218)|autophagy (GO:0006914)|cell proliferation (GO:0008283)|cellular response to glucose starvation (GO:0042149)|cellular response to ionizing radiation (GO:0071479)|defense response to virus (GO:0051607)|hemopoiesis (GO:0030097)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|monocyte differentiation (GO:0030224)|myeloid cell differentiation (GO:0030099)|negative regulation of cysteine-type endopeptidase activity (GO:2000117)|negative regulation of DNA binding (GO:0043392)|negative regulation of innate immune response (GO:0045824)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of viral genome replication (GO:0045071)|positive regulation of cytokine production (GO:0001819)|positive regulation of interleukin-1 beta production (GO:0032731)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|regulation of autophagy (GO:0010506)|regulation of gene expression, epigenetic (GO:0040029)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nuclear speck (GO:0016607)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	core promoter binding (GO:0001047)|double-stranded DNA binding (GO:0003690)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)|transcription factor binding (GO:0008134)	p.K299K(1)		cervix(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(12)|ovary(1)|prostate(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29	all_hematologic(112;0.0429)					ACAGAGCAAAGGAAACTCTGA	0.348																																																	1	Substitution - coding silent(1)	kidney(1)											71.0	76.0	74.0					1																	158988366		2203	4300	6503	SO:0001819	synonymous_variant	3428			M63838	CCDS1180.3, CCDS58039.1	1q22	2008-02-05			ENSG00000163565	ENSG00000163565			5395	protein-coding gene	gene with protein product		147586				1526658, 7959953	Standard	NM_005531		Approved	IFNGIP1, PYHIN2	uc010pis.2	Q16666	OTTHUMG00000037108	ENST00000295809.7:c.897G>A	1.37:g.158988366G>A			B4DJT8|H3BLV7|Q59GX0|Q5T3W7|Q5T3W8|Q5T3X0|Q5T3X1|Q5T3X2|Q8N9E5|Q8NEQ7|Q96AJ5|Q9UH78	Silent	SNP	ENST00000295809.7	37		.	.	.	.	.	.	.	.	.	.	G	2.715	-0.267917	0.05754	.	.	ENSG00000163565	ENST00000448393	.	.	.	3.09	-6.17	0.02091	.	.	.	.	.	T	0.04815	0.0130	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.27706	-1.0066	4	.	.	.	.	0.933	0.01339	0.289:0.1232:0.3645:0.2232	.	.	.	.	K	120	.	.	R	+	2	0	IFI16	157254990	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-4.396000	0.00241	-1.736000	0.01352	0.555000	0.69702	AGG		0.348	IFI16-013	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000421720.1		NM_005531	
ISL1	3670	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	5	50685635	50685635	+	Missense_Mutation	SNP	G	G	C			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	2cb6b578-8543-4a12-8331-1721ddc47303	1e656287-a1d9-4273-bbd2-c4909d29366d	g.chr5:50685635G>C	ENST00000230658.7	+	4	1219	c.634G>C	c.(634-636)Gag>Cag	p.E212Q	ISL1_ENST00000511384.1_Missense_Mutation_p.E212Q|ISL1_ENST00000505475.2_3'UTR	NM_002202.2	NP_002193.2	P61371	ISL1_HUMAN	ISL LIM homeobox 1	212					atrial septum morphogenesis (GO:0060413)|axon regeneration (GO:0031103)|cardiac cell fate determination (GO:0060913)|cardiac muscle cell myoblast differentiation (GO:0060379)|cardiac right ventricle morphogenesis (GO:0003215)|cellular response to glucocorticoid stimulus (GO:0071385)|endocardial cushion morphogenesis (GO:0003203)|innervation (GO:0060384)|mesenchymal cell differentiation (GO:0048762)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of inflammatory response (GO:0050728)|negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of protein homodimerization activity (GO:0090074)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural crest cell migration (GO:0001755)|neuron fate specification (GO:0048665)|outflow tract morphogenesis (GO:0003151)|outflow tract septum morphogenesis (GO:0003148)|pancreas development (GO:0031016)|peripheral nervous system neuron axonogenesis (GO:0048936)|pharyngeal system development (GO:0060037)|pituitary gland development (GO:0021983)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA binding (GO:0043388)|positive regulation of granulocyte colony-stimulating factor production (GO:0071657)|positive regulation of granulocyte macrophage colony-stimulating factor production (GO:0032725)|positive regulation of insulin secretion (GO:0032024)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-1 alpha production (GO:0032730)|positive regulation of interleukin-1 beta production (GO:0032731)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of macrophage colony-stimulating factor production (GO:1901258)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|retinal ganglion cell axon guidance (GO:0031290)|secondary heart field specification (GO:0003139)|sensory system development (GO:0048880)|spinal cord motor neuron cell fate specification (GO:0021520)|spinal cord motor neuron differentiation (GO:0021522)|trigeminal nerve development (GO:0021559)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|visceral motor neuron differentiation (GO:0021524)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	bHLH transcription factor binding (GO:0043425)|chromatin binding (GO:0003682)|enhancer sequence-specific DNA binding (GO:0001158)|estrogen receptor binding (GO:0030331)|ligand-dependent nuclear receptor binding (GO:0016922)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II transcription coactivator activity (GO:0001105)|zinc ion binding (GO:0008270)	p.E212Q(1)		NS(1)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(11)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	31		Lung NSC(810;0.000845)|Breast(144;0.0411)				GCTCATGAAGGAGCAACTGGT	0.587																																																	1	Substitution - Missense(1)	kidney(1)											67.0	78.0	74.0					5																	50685635		2203	4300	6503	SO:0001583	missense	3670			BC031213	CCDS43314.1	5q11.2	2012-03-09	2007-07-13		ENSG00000016082	ENSG00000016082		"""Homeoboxes / LIM class"""	6132	protein-coding gene	gene with protein product		600366	"""ISL1 transcription factor, LIM/homeodomain, (islet-1)"""			7912209	Standard	NM_002202		Approved	Isl-1, ISLET1	uc003jor.3	P61371	OTTHUMG00000162281	ENST00000230658.7:c.634G>C	5.37:g.50685635G>C	ENSP00000230658:p.Glu212Gln		P20663|P47894	Missense_Mutation	SNP	ENST00000230658.7	37	CCDS43314.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	27.0|27.0	4.790679|4.790679	0.90367|0.90367	.|.	.|.	ENSG00000016082|ENSG00000016082	ENST00000230658;ENST00000503187;ENST00000511384|ENST00000505475	D;D|.	0.96427|.	-4.01;-4.01|.	5.58|5.58	5.58|5.58	0.84498|0.84498	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.72787|0.72787	0.3504|0.3504	L|L	0.52206|0.52206	1.635|1.635	0.80722|0.80722	D|D	1|1	D|.	0.89917|.	1.0|.	D|.	0.79784|.	0.993|.	T|T	0.74460|0.74460	-0.3658|-0.3658	10|6	0.87932|0.87932	D|D	0|0	.|.	19.565|19.565	0.95389|0.95389	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	212|.	P61371|.	ISL1_HUMAN|.	Q|A	212|158	ENSP00000230658:E212Q;ENSP00000422676:E212Q|.	ENSP00000230658:E212Q|ENSP00000421737:G158A	E|G	+|+	1|2	0|0	ISL1|ISL1	50721392|50721392	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.699000|0.699000	0.40488|0.40488	9.743000|9.743000	0.98849|0.98849	2.598000|2.598000	0.87819|0.87819	0.585000|0.585000	0.79938|0.79938	GAG|GGA		0.587	ISL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368413.3		NM_002202	
KIAA1598	57698	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	10	118719667	118719667	+	Missense_Mutation	SNP	C	C	T			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	2cb6b578-8543-4a12-8331-1721ddc47303	1e656287-a1d9-4273-bbd2-c4909d29366d	g.chr10:118719667C>T	ENST00000355371.4	-	4	744	c.247G>A	c.(247-249)Gct>Act	p.A83T	KIAA1598_ENST00000392903.2_Missense_Mutation_p.A83T|KIAA1598_ENST00000497044.1_5'UTR|KIAA1598_ENST00000392901.4_Missense_Mutation_p.A23T|KIAA1598_ENST00000260777.10_Missense_Mutation_p.A83T	NM_001127211.2|NM_001258298.1|NM_001258299.1	NP_001120683.1|NP_001245227.1|NP_001245228.1	A0MZ66	SHOT1_HUMAN	KIAA1598	83					axon guidance (GO:0007411)|regulation of establishment of cell polarity (GO:2000114)|regulation of neuron migration (GO:2001222)	axonal growth cone (GO:0044295)		p.A83T(2)		endometrium(1)|kidney(1)|large_intestine(5)|lung(3)	10				all cancers(201;0.00494)		AAAGCTTCAGCACTTTCTCGA	0.373																																																	2	Substitution - Missense(2)	kidney(2)											86.0	83.0	84.0					10																	118719667		2203	4300	6503	SO:0001583	missense	57698			BC022348	CCDS31293.1, CCDS44482.1, CCDS58097.1, CCDS73207.1, CCDS73208.1	10q26.12	2007-01-30			ENSG00000187164	ENSG00000187164			29319	protein-coding gene	gene with protein product		611171				10997877, 17030985	Standard	NM_001127211		Approved	shootin1, shootin-1	uc009xyw.4	A0MZ66	OTTHUMG00000019114	ENST00000355371.4:c.247G>A	10.37:g.118719667C>T	ENSP00000347532:p.Ala83Thr		A8MYU7|B3KRD3|B3KRH2|B3KTE0|B3KTJ7|B3KTJ8|B4E3U1|B7Z7Z9|Q68DG1|Q6PIM5|Q9HCH4|Q9NUV0	Missense_Mutation	SNP	ENST00000355371.4	37	CCDS44482.1	.	.	.	.	.	.	.	.	.	.	C	35	5.415511	0.96092	.	.	ENSG00000187164	ENST00000392903;ENST00000260777;ENST00000355371;ENST00000392901	D;D;D;D	0.92048	-2.96;-2.96;-2.96;-2.96	5.98	5.98	0.97165	.	0.047237	0.85682	D	0.000000	D	0.95720	0.8608	M	0.75615	2.305	0.53688	D	0.999979	D;D;D	0.89917	1.0;0.994;1.0	D;D;D	0.87578	0.998;0.955;0.998	D	0.92759	0.6222	10	0.16420	T	0.52	-13.2913	20.4561	0.99145	0.0:1.0:0.0:0.0	.	83;83;53	A0MZ66;A0MZ66-2;A0MZ66-6	SHOT1_HUMAN;.;.	T	83;83;83;23	ENSP00000376636:A83T;ENSP00000260777:A83T;ENSP00000347532:A83T;ENSP00000376635:A23T	ENSP00000260777:A83T	A	-	1	0	KIAA1598	118709657	1.000000	0.71417	0.999000	0.59377	0.998000	0.95712	7.058000	0.76676	2.847000	0.97988	0.591000	0.81541	GCT		0.373	KIAA1598-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			NM_018330	
LINC00691	152024	broad.mit.edu	37	3	24138195	24138196	+	lincRNA	INS	-	-	T	rs529392893		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2cb6b578-8543-4a12-8331-1721ddc47303	1e656287-a1d9-4273-bbd2-c4909d29366d	g.chr3:24138195_24138196insT	ENST00000436123.1	-	0	2527_2528									long intergenic non-protein coding RNA 691																		GTTTTTTCCTGTTTTTTTTGAA	0.337																																																	0																																												0					3p24.2	2012-11-13			ENSG00000224074	ENSG00000224074		"""Long non-coding RNAs"""	44514	non-coding RNA	RNA, long non-coding							Standard	NR_026834		Approved		uc003ccv.2		OTTHUMG00000155662		3.37:g.24138203_24138203dupT				RNA	INS	ENST00000436123.1	37																																																																																					0.337	LINC00691-003	KNOWN	mRNA_start_NF|basic	lincRNA	lincRNA	OTTHUMT00000341066.1			
LRP11	84918	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	6	150174142	150174142	+	Missense_Mutation	SNP	C	C	A			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	2cb6b578-8543-4a12-8331-1721ddc47303	1e656287-a1d9-4273-bbd2-c4909d29366d	g.chr6:150174142C>A	ENST00000239367.2	-	2	773	c.768G>T	c.(766-768)atG>atT	p.M256I	LRP11_ENST00000546019.1_Start_Codon_SNP_p.M1I|LRP11_ENST00000367368.2_Missense_Mutation_p.M256I|RP11-350J20.12_ENST00000472053.2_RNA	NM_032832.5	NP_116221.3	Q86VZ4	LRP11_HUMAN	low density lipoprotein receptor-related protein 11	256	PKD. {ECO:0000255|PROSITE- ProRule:PRU00151}.					integral component of membrane (GO:0016021)		p.M256I(1)		cervix(1)|kidney(5)|large_intestine(1)|lung(1)	8		Ovarian(120;0.0907)	BRCA - Breast invasive adenocarcinoma(37;0.193)	OV - Ovarian serous cystadenocarcinoma(155;4.56e-12)|GBM - Glioblastoma multiforme(68;0.225)		GCGTTACCTTCATGTCCACTG	0.527																																																	1	Substitution - Missense(1)	kidney(1)											88.0	79.0	82.0					6																	150174142		2203	4300	6503	SO:0001583	missense	84918			AK027641	CCDS5220.1	6q24.3	2013-02-27			ENSG00000120256	ENSG00000120256		"""Low density lipoprotein receptors"""	16936	protein-coding gene	gene with protein product							Standard	NM_032832		Approved	bA350J20.3, MANSC3	uc003qng.2	Q86VZ4	OTTHUMG00000015801	ENST00000239367.2:c.768G>T	6.37:g.150174142C>A	ENSP00000239367:p.Met256Ile		Q5VYC0|Q96SN6	Missense_Mutation	SNP	ENST00000239367.2	37	CCDS5220.1	.	.	.	.	.	.	.	.	.	.	C	35	5.476251	0.96291	.	.	ENSG00000120256	ENST00000239367;ENST00000546019;ENST00000367368	T;D;T	0.97066	3.57;-4.23;2.86	5.45	5.45	0.79879	PKD/Chitinase domain (1);PKD domain (3);	0.077012	0.85682	D	0.000000	D	0.96056	0.8715	L	0.35644	1.08	0.80722	D	1	D;D	0.65815	0.995;0.984	P;P	0.59115	0.852;0.724	D	0.95362	0.8456	10	0.36615	T	0.2	-14.4133	16.2004	0.82067	0.0:1.0:0.0:0.0	.	256;256	Q5VYB9;Q86VZ4	.;LRP11_HUMAN	I	256;1;256	ENSP00000239367:M256I;ENSP00000440196:M1I;ENSP00000356338:M256I	ENSP00000239367:M256I	M	-	3	0	LRP11	150215835	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	4.146000	0.58072	2.562000	0.86427	0.591000	0.81541	ATG		0.527	LRP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042664.1		NM_032832	
LRRK1	79705	broad.mit.edu;hgsc.bcm.edu	37	15	101606305	101606305	+	Missense_Mutation	SNP	C	C	T			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	2cb6b578-8543-4a12-8331-1721ddc47303	1e656287-a1d9-4273-bbd2-c4909d29366d	g.chr15:101606305C>T	ENST00000388948.3	+	32	6022	c.5663C>T	c.(5662-5664)tCc>tTc	p.S1888F	RP11-505E24.2_ENST00000559857.1_RNA|LRRK1_ENST00000532145.1_3'UTR|LRRK1_ENST00000284395.5_Missense_Mutation_p.S1885F	NM_024652.3	NP_078928.3			leucine-rich repeat kinase 1									p.S1900F(1)|p.S1888F(1)		breast(2)|central_nervous_system(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|lung(25)|ovary(4)|prostate(1)|skin(1)	72	Melanoma(26;0.00505)|Lung NSC(78;0.00793)|all_lung(78;0.0094)		OV - Ovarian serous cystadenocarcinoma(32;0.000932)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)			GGTGCTGCCTCCGACAGGTCT	0.617																																																	2	Substitution - Missense(2)	kidney(2)											98.0	106.0	104.0					15																	101606305		2145	4264	6409	SO:0001583	missense	79705			AB058693	CCDS42086.1	15q26.3	2007-01-29			ENSG00000154237	ENSG00000154237			18608	protein-coding gene	gene with protein product		610986				11347906, 14654223	Standard	XM_005254979		Approved	FLJ23119, KIAA1790, Roco1, RIPK6	uc002bwr.3	Q38SD2	OTTHUMG00000165514	ENST00000388948.3:c.5663C>T	15.37:g.101606305C>T	ENSP00000373600:p.Ser1888Phe			Missense_Mutation	SNP	ENST00000388948.3	37	CCDS42086.1	.	.	.	.	.	.	.	.	.	.	C	12.15	1.852297	0.32699	.	.	ENSG00000154237	ENST00000388948;ENST00000284395;ENST00000529762;ENST00000542170	T;T	0.74632	-0.83;-0.86	5.35	5.35	0.76521	.	0.699658	0.14725	N	0.302133	T	0.69160	0.3080	L	0.60455	1.87	0.09310	N	0.999997	B	0.29805	0.257	B	0.24541	0.054	T	0.64807	-0.6320	10	0.66056	D	0.02	.	10.5967	0.45343	0.0:0.8763:0.0:0.1237	.	1888	Q38SD2	LRRK1_HUMAN	F	1888;1885;579;442	ENSP00000373600:S1888F;ENSP00000284395:S1885F	ENSP00000284395:S1885F	S	+	2	0	LRRK1	99423828	0.004000	0.15560	0.034000	0.17996	0.420000	0.31355	1.842000	0.39250	2.492000	0.84095	0.655000	0.94253	TCC		0.617	LRRK1-003	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384567.2		NM_024652	
DPM1	8813	broad.mit.edu	37	20	49575435	49575435	+	5'Flank	DEL	A	A	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2cb6b578-8543-4a12-8331-1721ddc47303	1e656287-a1d9-4273-bbd2-c4909d29366d	g.chr20:49575435delA	ENST00000371588.5	-	0	0				DPM1_ENST00000371582.4_5'Flank|DPM1_ENST00000371583.5_5'Flank|MOCS3_ENST00000244051.1_Frame_Shift_Del_p.E20fs|DPM1_ENST00000466152.1_5'Flank	NM_003859.1	NP_003850.1	O60762	DPM1_HUMAN	dolichyl-phosphate mannosyltransferase polypeptide 1, catalytic subunit						C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|dolichol metabolic process (GO:0019348)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|GDP-mannose metabolic process (GO:0019673)|GPI anchor biosynthetic process (GO:0006506)|post-translational protein modification (GO:0043687)|protein mannosylation (GO:0035268)|protein N-linked glycosylation via asparagine (GO:0018279)|protein O-linked mannosylation (GO:0035269)	dolichol-phosphate-mannose synthase complex (GO:0033185)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|membrane (GO:0016020)|nucleus (GO:0005634)	alcohol binding (GO:0043178)|dolichyl-phosphate beta-D-mannosyltransferase activity (GO:0004582)|dolichyl-phosphate-mannose-protein mannosyltransferase activity (GO:0004169)|mannose binding (GO:0005537)			endometrium(1)|large_intestine(1)|lung(2)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	7						CAACGTGAGGAGGAATTGAAT	0.597																																																	0													57.0	56.0	56.0					20																	49575435		2191	4276	6467	SO:0001631	upstream_gene_variant	27304			AF007875	CCDS13434.1	20q13.1	2013-02-26			ENSG00000000419	ENSG00000000419	2.4.1.83	"""Glycosyltransferase family 2 domain containing"""	3005	protein-coding gene	gene with protein product	"""DPM synthase complex, catalytic subunit"""	603503				9223280, 9535917	Standard	NM_003859		Approved	MPDS, CDGIE	uc002xvw.1	O60762	OTTHUMG00000032742		20.37:g.49575435delA	Exception_encountered		O15157|Q6IB78|Q96HK0	Frame_Shift_Del	DEL	ENST00000371588.5	37	CCDS13434.1																																																																																				0.597	DPM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079716.1		NM_003859	
MORC2	22880	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	22	31328363	31328363	+	Missense_Mutation	SNP	G	G	C			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	2cb6b578-8543-4a12-8331-1721ddc47303	1e656287-a1d9-4273-bbd2-c4909d29366d	g.chr22:31328363G>C	ENST00000397641.3	-	24	3232	c.2824C>G	c.(2824-2826)Cta>Gta	p.L942V	MORC2_ENST00000215862.4_Missense_Mutation_p.L880V|MORC2-AS1_ENST00000441558.1_RNA			Q9Y6X9	MORC2_HUMAN	MORC family CW-type zinc finger 2	942						cytoplasm (GO:0005737)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)	p.L880V(1)		breast(2)|kidney(2)|large_intestine(5)|lung(4)|ovary(2)|pancreas(1)|skin(4)|upper_aerodigestive_tract(1)	21						AAAGATATTAGCTCATCTGAA	0.463																																																	1	Substitution - Missense(1)	kidney(1)											139.0	127.0	131.0					22																	31328363		2203	4300	6503	SO:0001583	missense	22880			AB020659	CCDS33636.1	22q12.2	2005-06-15	2005-06-15	2005-06-15	ENSG00000133422	ENSG00000133422			23573	protein-coding gene	gene with protein product			"""zinc finger, CW-type with coiled-coil domain 1"", ""zinc finger, CW type with coiled-coil domain 1"""	ZCWCC1		14607086	Standard	XM_005261391		Approved	ZCW3, KIAA0852, AC004542.C22.1	uc003aje.1	Q9Y6X9	OTTHUMG00000151193	ENST00000397641.3:c.2824C>G	22.37:g.31328363G>C	ENSP00000380763:p.Leu942Val		B2RNB1|Q9UF28|Q9Y6V2	Missense_Mutation	SNP	ENST00000397641.3	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	15.08|15.08	2.727783|2.727783	0.48833|0.48833	.|.	.|.	ENSG00000133422|ENSG00000133422	ENST00000445980|ENST00000397641;ENST00000215862	.|T;T	.|0.26373	.|1.75;1.74	5.48|5.48	5.48|5.48	0.80851|0.80851	.|.	.|0.143081	.|0.45606	.|D	.|0.000342	T|T	0.44891|0.44891	0.1315|0.1315	L|L	0.59436|0.59436	1.845|1.845	0.80722|0.80722	D|D	1|1	.|D	.|0.69078	.|0.997	.|D	.|0.78314	.|0.991	T|T	0.31558|0.31558	-0.9939|-0.9939	5|10	.|0.66056	.|D	.|0.02	.|.	10.8587|10.8587	0.46815|0.46815	0.1151:0.0:0.8849:0.0|0.1151:0.0:0.8849:0.0	.|.	.|942	.|Q9Y6X9	.|MORC2_HUMAN	G|V	103|942;880	.|ENSP00000380763:L942V;ENSP00000215862:L880V	.|ENSP00000215862:L880V	A|L	-|-	2|1	0|2	MORC2|MORC2	29658363|29658363	1.000000|1.000000	0.71417|0.71417	0.992000|0.992000	0.48379|0.48379	0.987000|0.987000	0.75469|0.75469	2.658000|2.658000	0.46733|0.46733	2.745000|2.745000	0.94114|0.94114	0.655000|0.655000	0.94253|0.94253	GCT|CTA		0.463	MORC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000321710.2		NM_014941	
MRPL14	64928	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	6	44084332	44084332	+	Missense_Mutation	SNP	C	C	T			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	2cb6b578-8543-4a12-8331-1721ddc47303	1e656287-a1d9-4273-bbd2-c4909d29366d	g.chr6:44084332C>T	ENST00000372014.3	-	2	148	c.17G>A	c.(16-18)gGg>gAg	p.G6E		NM_032111.2	NP_115487.2	Q6P1L8	RM14_HUMAN	mitochondrial ribosomal protein L14	6					translation (GO:0006412)	mitochondrion (GO:0005739)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)	p.G6E(1)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|skin(1)	12	all_cancers(18;1.66e-06)|Lung NSC(15;0.00108)|all_lung(25;0.00278)|Hepatocellular(11;0.00309)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0181)			GCCCCAGAGCCCAGTAAAGAA	0.448																																																	1	Substitution - Missense(1)	kidney(1)											80.0	85.0	83.0					6																	44084332		2203	4300	6503	SO:0001583	missense	64928			AB051339	CCDS34460.1	6p21.3	2012-09-13			ENSG00000180992	ENSG00000180992		"""Mitochondrial ribosomal proteins / large subunits"""	14279	protein-coding gene	gene with protein product		611827					Standard	XM_005249300		Approved	RPML32, MRP-L32	uc003owp.3	Q6P1L8	OTTHUMG00000014756	ENST00000372014.3:c.17G>A	6.37:g.44084332C>T	ENSP00000361084:p.Gly6Glu		B2R575|Q96Q72	Missense_Mutation	SNP	ENST00000372014.3	37	CCDS34460.1	.	.	.	.	.	.	.	.	.	.	C	12.61	1.988935	0.35131	.	.	ENSG00000180992	ENST00000372014	.	.	.	5.03	3.2	0.36748	.	0.366614	0.27375	N	0.019659	T	0.13072	0.0317	L	0.27053	0.805	0.09310	N	1	B	0.23377	0.084	B	0.24155	0.051	T	0.16512	-1.0400	9	0.66056	D	0.02	-0.9524	8.3111	0.32071	0.0:0.7571:0.157:0.0859	.	6	Q6P1L8	RM14_HUMAN	E	6	.	ENSP00000361084:G6E	G	-	2	0	MRPL14	44192310	0.000000	0.05858	0.017000	0.16124	0.888000	0.51559	0.449000	0.21744	0.750000	0.32877	0.655000	0.94253	GGG		0.448	MRPL14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040707.1		NM_032111	
MUC4	4585	hgsc.bcm.edu	37	3	195505960	195505960	+	Missense_Mutation	SNP	G	G	C	rs112020305	byFrequency	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	2cb6b578-8543-4a12-8331-1721ddc47303	1e656287-a1d9-4273-bbd2-c4909d29366d	g.chr3:195505960G>C	ENST00000463781.3	-	2	12950	c.12491C>G	c.(12490-12492)aCc>aGc	p.T4164S	MUC4_ENST00000475231.1_Missense_Mutation_p.T4164S|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.T4164S(2)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GGAAGCGTCGGTGACAGGAAG	0.587													.|||	17	0.00339457	0.0129	0.0	5008	,	,		10875	0.0		0.0	False		,,,				2504	0.0																2	Substitution - Missense(2)	kidney(1)|endometrium(1)											19.0	12.0	14.0					3																	195505960		671	1528	2199	SO:0001583	missense	4585			AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.12491C>G	3.37:g.195505960G>C	ENSP00000417498:p.Thr4164Ser		O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	g	4.985	0.182849	0.09495	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.35789	1.38;1.29	.	.	.	.	.	.	.	.	T	0.19248	0.0462	N	0.19112	0.55	0.09310	N	0.999997	P	0.37985	0.613	B	0.35899	0.213	T	0.14587	-1.0467	7	.	.	.	.	5.8529	0.18704	9.0E-4:0.0:0.9991:0.0	.	4036	E7ESK3	.	S	4164	ENSP00000417498:T4164S;ENSP00000420243:T4164S	.	T	-	2	0	MUC4	196990739	0.002000	0.14202	0.025000	0.17156	0.022000	0.10575	0.413000	0.21148	0.073000	0.16731	0.074000	0.15403	ACC		0.587	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6		NM_018406	
MYH3	4621	hgsc.bcm.edu;ucsc.edu	37	17	10537344	10537344	+	Frame_Shift_Del	DEL	C	C	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	2cb6b578-8543-4a12-8331-1721ddc47303	1e656287-a1d9-4273-bbd2-c4909d29366d	g.chr17:10537344delC	ENST00000583535.1	-	32	4599	c.4512delG	c.(4510-4512)aagfs	p.K1504fs	MYH3_ENST00000226209.7_Frame_Shift_Del_p.K1504fs	NM_002470.3	NP_002461.2	P11055	MYH3_HUMAN	myosin, heavy chain 3, skeletal muscle, embryonic	1504					actin filament-based movement (GO:0030048)|ATP catabolic process (GO:0006200)|embryonic limb morphogenesis (GO:0030326)|face morphogenesis (GO:0060325)|muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|sarcomere organization (GO:0045214)|skeletal muscle contraction (GO:0003009)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|sarcomere (GO:0030017)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(5)|large_intestine(18)|lung(30)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	83						GCTCTAAGTTCTTATTTTCCC	0.478																																																	0													185.0	155.0	165.0					17																	10537344		2203	4300	6503	SO:0001589	frameshift_variant	4621				CCDS11157.1	17p13.1	2013-09-19	2006-09-29		ENSG00000109063	ENSG00000109063		"""Myosins / Myosin superfamily : Class II"""	7573	protein-coding gene	gene with protein product	"""myosin, skeletal, heavy chain, embryonic 1"", ""muscle embryonic myosin heavy chain 3"""	160720	"""myosin, heavy polypeptide 3, skeletal muscle, embryonic"""			2726495	Standard	NM_002470		Approved	MYHC-EMB, MYHSE1, HEMHC, SMHCE	uc002gmq.2	P11055	OTTHUMG00000130367	ENST00000583535.1:c.4512delG	17.37:g.10537344delC	ENSP00000464317:p.Lys1504fs		Q15492	Frame_Shift_Del	DEL	ENST00000583535.1	37	CCDS11157.1																																																																																				0.478	MYH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252734.2		NM_002470	
MYH3	4621	hgsc.bcm.edu;ucsc.edu	37	17	10537346	10537347	+	Frame_Shift_Del	DEL	TA	TA	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10	TA	TA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	2cb6b578-8543-4a12-8331-1721ddc47303	1e656287-a1d9-4273-bbd2-c4909d29366d	g.chr17:10537346_10537347delTA	ENST00000583535.1	-	32	4596_4597	c.4509_4510delTA	c.(4507-4512)aataagfs	p.N1503fs	MYH3_ENST00000226209.7_Frame_Shift_Del_p.N1503fs	NM_002470.3	NP_002461.2	P11055	MYH3_HUMAN	myosin, heavy chain 3, skeletal muscle, embryonic	1503					actin filament-based movement (GO:0030048)|ATP catabolic process (GO:0006200)|embryonic limb morphogenesis (GO:0030326)|face morphogenesis (GO:0060325)|muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|sarcomere organization (GO:0045214)|skeletal muscle contraction (GO:0003009)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|sarcomere (GO:0030017)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(5)|large_intestine(18)|lung(30)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	83						TCTAAGTTCTTATTTTCCCGTT	0.48																																																	0																																										SO:0001589	frameshift_variant	4621				CCDS11157.1	17p13.1	2013-09-19	2006-09-29		ENSG00000109063	ENSG00000109063		"""Myosins / Myosin superfamily : Class II"""	7573	protein-coding gene	gene with protein product	"""myosin, skeletal, heavy chain, embryonic 1"", ""muscle embryonic myosin heavy chain 3"""	160720	"""myosin, heavy polypeptide 3, skeletal muscle, embryonic"""			2726495	Standard	NM_002470		Approved	MYHC-EMB, MYHSE1, HEMHC, SMHCE	uc002gmq.2	P11055	OTTHUMG00000130367	ENST00000583535.1:c.4509_4510delTA	17.37:g.10537346_10537347delTA	ENSP00000464317:p.Asn1503fs		Q15492	Frame_Shift_Del	DEL	ENST00000583535.1	37	CCDS11157.1																																																																																				0.480	MYH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252734.2		NM_002470	
NOTCH3	4854	broad.mit.edu;hgsc.bcm.edu	37	19	15290202	15290202	+	Missense_Mutation	SNP	G	G	C			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	2cb6b578-8543-4a12-8331-1721ddc47303	1e656287-a1d9-4273-bbd2-c4909d29366d	g.chr19:15290202G>C	ENST00000263388.2	-	21	3508	c.3433C>G	c.(3433-3435)Ctc>Gtc	p.L1145V		NM_000435.2	NP_000426.2	Q9UM47	NOTC3_HUMAN	notch 3	1145	EGF-like 29; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				forebrain development (GO:0030900)|gene expression (GO:0010467)|glomerular capillary formation (GO:0072104)|negative regulation of neuron differentiation (GO:0045665)|neuron fate commitment (GO:0048663)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|positive regulation of smooth muscle cell proliferation (GO:0048661)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)	p.L1145V(2)		breast(4)|central_nervous_system(3)|endometrium(10)|kidney(3)|large_intestine(16)|liver(1)|lung(31)|ovary(8)|prostate(3)|skin(7)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	93			OV - Ovarian serous cystadenocarcinoma(3;2.6e-20)|Epithelial(3;1.34e-16)|all cancers(3;5.13e-15)			CAGGAGCAGAGATAGCGGGCC	0.607																																																	2	Substitution - Missense(2)	kidney(2)											85.0	78.0	80.0					19																	15290202		2203	4300	6503	SO:0001583	missense	4854			U97669	CCDS12326.1	19p13.2-p13.1	2013-01-10	2010-06-24			ENSG00000074181		"""Ankyrin repeat domain containing"""	7883	protein-coding gene	gene with protein product		600276	"""Notch (Drosophila) homolog 3"", ""Notch homolog 3 (Drosophila)"""	CADASIL		7835890	Standard	NM_000435		Approved	CASIL	uc002nan.3	Q9UM47		ENST00000263388.2:c.3433C>G	19.37:g.15290202G>C	ENSP00000263388:p.Leu1145Val		Q9UEB3|Q9UPL3|Q9Y6L8	Missense_Mutation	SNP	ENST00000263388.2	37	CCDS12326.1	.	.	.	.	.	.	.	.	.	.	G	11.82	1.753123	0.31046	.	.	ENSG00000074181	ENST00000263388;ENST00000539383	D	0.87179	-2.22	4.3	3.18	0.36537	EGF-like calcium-binding, conserved site (1);EGF (1);EGF-like calcium-binding (1);Epidermal growth factor-like, type 3 (1);	.	.	.	.	T	0.64091	0.2567	N	0.01091	-1.02	0.33501	D	0.589931	B;B	0.21753	0.002;0.06	B;B	0.25987	0.019;0.065	T	0.65537	-0.6144	9	0.20519	T	0.43	.	6.5434	0.22392	0.0:0.1674:0.5104:0.3222	.	1096;1145	Q59FL3;Q9UM47	.;NOTC3_HUMAN	V	1145;1095	ENSP00000263388:L1145V	ENSP00000263388:L1145V	L	-	1	0	NOTCH3	15151202	1.000000	0.71417	1.000000	0.80357	0.778000	0.44026	3.091000	0.50199	1.934000	0.56057	0.561000	0.74099	CTC		0.607	NOTCH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465714.1		NM_000435	
OSBPL1A	114876	hgsc.bcm.edu;ucsc.edu	37	18	21898718	21898721	+	Frame_Shift_Del	DEL	ACCA	ACCA	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10	ACCA	ACCA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	2cb6b578-8543-4a12-8331-1721ddc47303	1e656287-a1d9-4273-bbd2-c4909d29366d	g.chr18:21898718_21898721delACCA	ENST00000319481.3	-	8	884_887	c.678_681delTGGT	c.(676-681)gttggtfs	p.VG226fs	MIR320C2_ENST00000390762.1_RNA	NM_080597.3	NP_542164.2	Q9BXW6	OSBL1_HUMAN	oxysterol binding protein-like 1A	226	Interaction with RAB7A.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cholesterol metabolic process (GO:0008203)|lipid transport (GO:0006869)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|late endosome (GO:0005770)|lysosomal membrane (GO:0005765)|nucleus (GO:0005634)	cholesterol binding (GO:0015485)|phospholipid binding (GO:0005543)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(16)|ovary(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	36	all_cancers(21;0.000396)|all_epithelial(16;4.36e-06)|Lung NSC(20;0.00171)|all_lung(20;0.0055)|Colorectal(14;0.0505)|Ovarian(20;0.17)					GTACCTTATTACCAACAAGAATGT	0.289																																																	0																																										SO:0001589	frameshift_variant	114876			AF392449, AF274714	CCDS11884.1, CCDS11885.1, CCDS56056.1	18q11.2	2014-06-03	2014-06-03	2014-06-03	ENSG00000141447	ENSG00000141447		"""Oxysterol binding proteins"", ""Ankyrin repeat domain containing"""	16398	protein-coding gene	gene with protein product		606730	"""oxysterol binding protein-like 1B"""	OSBPL1B		11279184, 10588946	Standard	NM_080597		Approved	ORP-1, ORP1	uc002kve.3	Q9BXW6	OTTHUMG00000131944	ENST00000319481.3:c.678_681delTGGT	18.37:g.21898718_21898721delACCA	ENSP00000320291:p.Val226fs		B7Z7D3|Q9BZF5|Q9NW87	Frame_Shift_Del	DEL	ENST00000319481.3	37	CCDS11884.1																																																																																				0.289	OSBPL1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254902.1		NM_080597	
PON3	5446	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	7	94993300	94993300	+	Silent	SNP	C	C	A			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	2cb6b578-8543-4a12-8331-1721ddc47303	1e656287-a1d9-4273-bbd2-c4909d29366d	g.chr7:94993300C>A	ENST00000265627.5	-	6	580	c.570G>T	c.(568-570)ctG>ctT	p.L190L	PON3_ENST00000427422.1_Silent_p.L190L|PON1_ENST00000542556.1_Intron|PON3_ENST00000451904.1_Silent_p.L190L	NM_000940.2	NP_000931.1	Q15166	PON3_HUMAN	paraoxonase 3	190					aromatic compound catabolic process (GO:0019439)|carboxylic acid catabolic process (GO:0046395)|coumarin catabolic process (GO:0046226)|phenylacetate catabolic process (GO:0010124)|response to external stimulus (GO:0009605)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)	3,4-dihydrocoumarin hydrolase activity (GO:0018733)|aryldialkylphosphatase activity (GO:0004063)|arylesterase activity (GO:0004064)|dihydrocoumarin hydrolase activity (GO:0047856)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)	p.L190L(1)		breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)|pancreas(1)|prostate(2)|skin(2)	24	all_cancers(62;1.04e-10)|all_epithelial(64;3.67e-09)|Lung NSC(181;0.239)		STAD - Stomach adenocarcinoma(171;0.0151)		Edetic Acid(DB00974)|Lovastatin(DB00227)	CAAAAAATGACAGGAGGGAGT	0.433																																																	1	Substitution - coding silent(1)	kidney(1)											166.0	164.0	165.0					7																	94993300		2203	4300	6503	SO:0001819	synonymous_variant	5446			L48516, AF320003	CCDS5639.1	7q21.3	2014-03-14			ENSG00000105852	ENSG00000105852	3.1.1.2	"""Paraoxonases"""	9206	protein-coding gene	gene with protein product	"""arylesterase 3"""	602720				8661009	Standard	NM_000940		Approved			Q15166	OTTHUMG00000153917	ENST00000265627.5:c.570G>T	7.37:g.94993300C>A			A4D1H8|O75855|O76060|Q6IRU9|Q8IX97|Q9BZH9	Silent	SNP	ENST00000265627.5	37	CCDS5639.1																																																																																				0.433	PON3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333007.1		NM_000940	
PTGS2	5743	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	186643675	186643675	+	Missense_Mutation	SNP	A	A	C			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	2cb6b578-8543-4a12-8331-1721ddc47303	1e656287-a1d9-4273-bbd2-c4909d29366d	g.chr1:186643675A>C	ENST00000367468.5	-	10	1761	c.1625T>G	c.(1624-1626)tTt>tGt	p.F542C	PTGS2_ENST00000490885.2_5'UTR	NM_000963.2	NP_000954.1	P35354	PGH2_HUMAN	prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclooxygenase)	542					anagen (GO:0042640)|angiogenesis (GO:0001525)|arachidonic acid metabolic process (GO:0019369)|bone mineralization (GO:0030282)|brown fat cell differentiation (GO:0050873)|cellular component movement (GO:0006928)|cellular response to ATP (GO:0071318)|cellular response to hypoxia (GO:0071456)|cellular response to mechanical stimulus (GO:0071260)|cellular response to UV (GO:0034644)|cyclooxygenase pathway (GO:0019371)|decidualization (GO:0046697)|embryo implantation (GO:0007566)|inflammatory response (GO:0006954)|learning (GO:0007612)|lipoxygenase pathway (GO:0019372)|maintenance of blood-brain barrier (GO:0035633)|memory (GO:0007613)|negative regulation of calcium ion transport (GO:0051926)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell proliferation (GO:0008285)|negative regulation of smooth muscle contraction (GO:0045986)|negative regulation of synaptic transmission, dopaminergic (GO:0032227)|ovulation (GO:0030728)|positive regulation of apoptotic process (GO:0043065)|positive regulation of brown fat cell differentiation (GO:0090336)|positive regulation of cell migration involved in sprouting angiogenesis (GO:0090050)|positive regulation of fever generation (GO:0031622)|positive regulation of fibroblast growth factor production (GO:0090271)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of platelet-derived growth factor production (GO:0090362)|positive regulation of prostaglandin biosynthetic process (GO:0031394)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of synaptic plasticity (GO:0031915)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of transforming growth factor beta production (GO:0071636)|positive regulation of vasoconstriction (GO:0045907)|positive regulation vascular endothelial growth factor production (GO:0010575)|prostaglandin biosynthetic process (GO:0001516)|prostaglandin metabolic process (GO:0006693)|regulation of blood pressure (GO:0008217)|regulation of inflammatory response (GO:0050727)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to fatty acid (GO:0070542)|response to fructose (GO:0009750)|response to glucocorticoid (GO:0051384)|response to lipopolysaccharide (GO:0032496)|response to lithium ion (GO:0010226)|response to manganese ion (GO:0010042)|response to oxidative stress (GO:0006979)|response to tumor necrosis factor (GO:0034612)|response to vitamin D (GO:0033280)|sensory perception of pain (GO:0019233)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|neuron projection (GO:0043005)|nucleus (GO:0005634)|protein complex (GO:0043234)	arachidonate 15-lipoxygenase activity (GO:0050473)|enzyme binding (GO:0019899)|heme binding (GO:0020037)|lipid binding (GO:0008289)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)|prostaglandin-endoperoxide synthase activity (GO:0004666)	p.F542C(2)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(5)|lung(11)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	27					Acetaminophen(DB00316)|Acetylsalicylic acid(DB00945)|Aldesleukin(DB00041)|Aminosalicylic Acid(DB00233)|Antipyrine(DB01435)|Antrafenine(DB01419)|Balsalazide(DB01014)|Bromfenac(DB00963)|Bumetanide(DB00887)|Carprofen(DB00821)|Celecoxib(DB00482)|Chlorphenesin(DB00856)|Cisplatin(DB00515)|Clodronate(DB00720)|Dapsone(DB00250)|Desmopressin(DB00035)|Diclofenac(DB00586)|Diflunisal(DB00861)|Dihomo-gamma-linolenic acid(DB00154)|Drospirenone(DB01395)|Etanercept(DB00005)|Etodolac(DB00749)|Etoposide(DB00773)|Etoricoxib(DB01628)|Fenoprofen(DB00573)|Flurbiprofen(DB00712)|Ginseng(DB01404)|Ibuprofen(DB01050)|Icosapent(DB00159)|Indomethacin(DB00328)|Ketoprofen(DB01009)|Ketorolac(DB00465)|Lenalidomide(DB00480)|Lornoxicam(DB06725)|Lumiracoxib(DB01283)|Magnesium salicylate(DB01397)|Meclofenamic acid(DB00939)|Mefenamic acid(DB00784)|Meloxicam(DB00814)|Mesalazine(DB00244)|Nabumetone(DB00461)|Naproxen(DB00788)|Nepafenac(DB06802)|Niflumic Acid(DB04552)|Nonoxynol-9(DB06804)|Oxaprozin(DB00991)|Phenylbutazone(DB00812)|Piroxicam(DB00554)|Pomalidomide(DB08910)|Risedronate(DB00884)|Salicylate-sodium(DB01398)|Salicylic acid(DB00936)|Salsalate(DB01399)|Sulfasalazine(DB00795)|Sulindac(DB00605)|Suprofen(DB00870)|Tafluprost(DB08819)|Tenoxicam(DB00469)|Tetrahydrobiopterin(DB00360)|Thalidomide(DB01041)|Tiaprofenic acid(DB01600)|Tolmetin(DB00500)|Triamcinolone(DB00620)|Trisalicylate-choline(DB01401)	GATGATTTGAAAACCCACTTC	0.433																																																	2	Substitution - Missense(2)	kidney(2)											186.0	164.0	172.0					1																	186643675		2203	4300	6503	SO:0001583	missense	5743			D28235	CCDS1371.1	1q25.2-q25.3	2008-02-05			ENSG00000073756	ENSG00000073756	1.14.99.1		9605	protein-coding gene	gene with protein product		600262				1380156	Standard	NM_000963		Approved	COX2	uc001gsb.3	P35354	OTTHUMG00000035473	ENST00000367468.5:c.1625T>G	1.37:g.186643675A>C	ENSP00000356438:p.Phe542Cys		A8K802|Q16876	Missense_Mutation	SNP	ENST00000367468.5	37	CCDS1371.1	.	.	.	.	.	.	.	.	.	.	A	23.1	4.369075	0.82463	.	.	ENSG00000073756	ENST00000367468	T	0.69040	-0.37	5.34	5.34	0.76211	.	0.000000	0.85682	D	0.000000	D	0.86171	0.5869	M	0.93197	3.39	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.89970	0.4093	10	0.87932	D	0	-19.4498	15.3237	0.74144	1.0:0.0:0.0:0.0	.	542	P35354	PGH2_HUMAN	C	542	ENSP00000356438:F542C	ENSP00000356438:F542C	F	-	2	0	PTGS2	184910298	1.000000	0.71417	0.986000	0.45419	0.972000	0.66771	9.103000	0.94232	2.002000	0.58637	0.528000	0.53228	TTT		0.433	PTGS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086157.2		NM_000963	
PTPRN	5798	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	220159737	220159737	+	Missense_Mutation	SNP	C	C	T	rs548633041		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	2cb6b578-8543-4a12-8331-1721ddc47303	1e656287-a1d9-4273-bbd2-c4909d29366d	g.chr2:220159737C>T	ENST00000295718.2	-	19	2875	c.2635G>A	c.(2635-2637)Ggc>Agc	p.G879S	PTPRN_ENST00000423636.2_Missense_Mutation_p.G789S|PTPRN_ENST00000497977.1_5'UTR|MIR153-1_ENST00000384914.1_RNA|PTPRN_ENST00000409251.3_Missense_Mutation_p.G850S	NM_002846.3	NP_002837.1	Q16849	PTPRN_HUMAN	protein tyrosine phosphatase, receptor type, N	879	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				cytokine-mediated signaling pathway (GO:0019221)|peptidyl-tyrosine dephosphorylation (GO:0035335)|response to cAMP (GO:0051591)|response to estrogen (GO:0043627)|response to glucose (GO:0009749)|response to insulin (GO:0032868)|response to reactive oxygen species (GO:0000302)	integral component of plasma membrane (GO:0005887)	spectrin binding (GO:0030507)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)	p.G879S(1)		breast(3)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(28)|ovary(3)|prostate(4)|skin(11)|upper_aerodigestive_tract(1)|urinary_tract(1)	65		Renal(207;0.0474)		Epithelial(149;4.22e-07)|all cancers(144;8.82e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)|STAD - Stomach adenocarcinoma(1183;0.0875)		GCCGGTGTGCCCTCTGCCGGC	0.716													C|||	1	0.000199681	0.0	0.0	5008	,	,		12687	0.0		0.0	False		,,,				2504	0.001																1	Substitution - Missense(1)	kidney(1)											31.0	37.0	35.0					2																	220159737		2199	4298	6497	SO:0001583	missense	5798				CCDS2440.1, CCDS56167.1, CCDS56168.1	2q35-q36.1	2011-06-09			ENSG00000054356	ENSG00000054356		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"""	9676	protein-coding gene	gene with protein product		601773				8024693	Standard	NM_001199763		Approved	IA-2	uc002vkz.3	Q16849	OTTHUMG00000133129	ENST00000295718.2:c.2635G>A	2.37:g.220159737C>T	ENSP00000295718:p.Gly879Ser		B4DK12|F5GZS3|Q08319|Q53QD6|Q6NSL1	Missense_Mutation	SNP	ENST00000295718.2	37	CCDS2440.1	.	.	.	.	.	.	.	.	.	.	C	37	6.578634	0.97680	.	.	ENSG00000054356	ENST00000409251;ENST00000295718;ENST00000539342;ENST00000537666	T;T;T	0.17213	2.29;2.29;2.29	5.18	5.18	0.71444	Protein-tyrosine phosphatase, receptor/non-receptor type (4);	0.000000	0.85682	D	0.000000	T	0.40909	0.1136	L	0.60904	1.88	0.80722	D	1	D;D	0.89917	1.0;0.963	D;D	0.97110	1.0;0.93	T	0.16217	-1.0410	10	0.87932	D	0	.	18.502	0.90886	0.0:1.0:0.0:0.0	.	850;879	Q6NSL1;Q16849	.;PTPRN_HUMAN	S	850;879;850;789	ENSP00000386638:G850S;ENSP00000295718:G879S;ENSP00000444244:G789S	ENSP00000295718:G879S	G	-	1	0	PTPRN	219867981	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.719000	0.61937	2.689000	0.91719	0.637000	0.83480	GGC		0.716	PTPRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256819.2			
Unknown	0	broad.mit.edu	37	8	86786310	86786310	+	IGR	SNP	G	G	T	rs150998281		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2cb6b578-8543-4a12-8331-1721ddc47303	1e656287-a1d9-4273-bbd2-c4909d29366d	g.chr8:86786310G>T								REXO1L10P (27565 upstream) : CTA-392E5.1 (65623 downstream)																							ccttcatttcgttatgtaccc	0.423																																																	0																																										SO:0001628	intergenic_variant	254958																															8.37:g.86786310G>T				RNA	SNP		37																																																																																				0	0.423									
RGMB	285704	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	5	98115300	98115300	+	Silent	SNP	A	A	T			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	2cb6b578-8543-4a12-8331-1721ddc47303	1e656287-a1d9-4273-bbd2-c4909d29366d	g.chr5:98115300A>T	ENST00000513185.1	+	2	589	c.153A>T	c.(151-153)ccA>ccT	p.P51P	RGMB_ENST00000504776.1_3'UTR|RGMB_ENST00000308234.7_Silent_p.P92P			Q6NW40	RGMB_HUMAN	repulsive guidance molecule family member b	51					axon guidance (GO:0007411)|BMP signaling pathway (GO:0030509)|cell adhesion (GO:0007155)|positive regulation of transcription, DNA-templated (GO:0045893)|signal transduction (GO:0007165)	anchored component of plasma membrane (GO:0046658)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)	identical protein binding (GO:0042802)	p.P92P(1)		haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(2)|upper_aerodigestive_tract(1)	10		all_cancers(142;2.76e-08)|all_epithelial(76;2.98e-11)|all_lung(232;0.000485)|Lung NSC(167;0.000693)|Prostate(80;0.000986)|Ovarian(225;0.024)|Colorectal(57;0.117)		COAD - Colon adenocarcinoma(37;0.0587)		GCCAACAGCCAGCCCAATGTC	0.463																																																	1	Substitution - coding silent(1)	kidney(1)											178.0	178.0	178.0					5																	98115300		1995	4157	6152	SO:0001819	synonymous_variant	285704			AK074887	CCDS47251.1	5q21.1	2013-11-06	2013-11-06		ENSG00000174136	ENSG00000174136			26896	protein-coding gene	gene with protein product		612687	"""RGM domain family, member B"""			19324014	Standard	NM_001012761		Approved	FLJ90406, DRAGON	uc003knc.3	Q6NW40	OTTHUMG00000162745	ENST00000513185.1:c.153A>T	5.37:g.98115300A>T			D6R9A0|Q8NC92	Silent	SNP	ENST00000513185.1	37																																																																																					0.463	RGMB-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000370308.1		NM_173670	
SCAF1	58506	hgsc.bcm.edu	37	19	50154291	50154294	+	Frame_Shift_Del	DEL	TGCA	TGCA	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10	TGCA	TGCA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	2cb6b578-8543-4a12-8331-1721ddc47303	1e656287-a1d9-4273-bbd2-c4909d29366d	g.chr19:50154291_50154294delTGCA	ENST00000360565.3	+	7	769_772	c.645_648delTGCA	c.(643-648)cctgcafs	p.PA215fs		NM_021228.2	NP_067051.2	Q9H7N4	SFR19_HUMAN	SR-related CTD-associated factor 1	215	Pro-rich.				mRNA processing (GO:0006397)|RNA splicing (GO:0008380)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	RNA binding (GO:0003723)	p.A219fs*11(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(2)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	20		all_lung(116;1.05e-05)|Lung NSC(112;3.77e-05)|all_neural(266;0.196)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00113)|GBM - Glioblastoma multiforme(134;0.0204)		cACCGCCCCCTGCACCCCCAGCCC	0.691																																																	1	Insertion - Frameshift(1)	central_nervous_system(1)																																								SO:0001589	frameshift_variant	58506			AK024444	CCDS33074.1	19q13.3-q13.4	2011-01-10			ENSG00000126461	ENSG00000126461			30403	protein-coding gene	gene with protein product						11461075	Standard	NM_021228		Approved	SR-A1, FLJ00034	uc002poq.3	Q9H7N4		ENST00000360565.3:c.645_648delTGCA	19.37:g.50154291_50154294delTGCA	ENSP00000353769:p.Pro215fs		Q7Z5V7|Q8WVA1|Q9NR59	Frame_Shift_Del	DEL	ENST00000360565.3	37	CCDS33074.1																																																																																				0.691	SCAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465764.1		NM_021228	
SELL	6402	hgsc.bcm.edu;ucsc.edu	37	1	169665718	169665718	+	Intron	SNP	G	G	A	rs571157995		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	2cb6b578-8543-4a12-8331-1721ddc47303	1e656287-a1d9-4273-bbd2-c4909d29366d	g.chr1:169665718G>A	ENST00000236147.4	-	8	1281				C1orf112_ENST00000498289.1_Intron	NM_000655.4	NP_000646.2	P14151	LYAM1_HUMAN	selectin L						blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|leukocyte migration (GO:0050900)|regulation of immune response (GO:0050776)|response to ATP (GO:0033198)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|glycosphingolipid binding (GO:0043208)|heparin binding (GO:0008201)|protease binding (GO:0002020)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|kidney(2)|large_intestine(3)|lung(5)|urinary_tract(1)	15	all_hematologic(923;0.208)					ATAGAGAAAAGGCATTAGCAA	0.343																																																	0													43.0	41.0	41.0					1																	169665718		1794	4022	5816	SO:0001627	intron_variant	6402			M25280	CCDS53427.1	1q23-q25	2008-07-31	2008-07-31		ENSG00000188404	ENSG00000188404		"""CD molecules"""	10720	protein-coding gene	gene with protein product		153240	"""lymphocyte adhesion molecule 1"""	LYAM1, LNHR		2664786, 1375831	Standard	NR_029467		Approved	LSEL, LAM1, LAM-1, hLHRc, Leu-8, Lyam-1, PLNHR, CD62L	uc001ggk.3	P14151	OTTHUMG00000034809	ENST00000236147.4:c.1121-24C>T	1.37:g.169665718G>A			B2R6Q8|P15023|Q9UJ43	RNA	SNP	ENST00000236147.4	37	CCDS53427.1																																																																																				0.343	SELL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084233.1		NM_000655	
TFDP3	51270	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	X	132351243	132351243	+	Missense_Mutation	SNP	T	T	G			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	2cb6b578-8543-4a12-8331-1721ddc47303	1e656287-a1d9-4273-bbd2-c4909d29366d	g.chrX:132351243T>G	ENST00000310125.4	-	1	1133	c.1045A>C	c.(1045-1047)Aat>Cat	p.N349H		NM_016521.2	NP_057605.3	Q5H9I0	TFDP3_HUMAN	transcription factor Dp family, member 3	349					cellular response to DNA damage stimulus (GO:0006974)|G1/S transition of mitotic cell cycle (GO:0000082)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.N349H(1)|p.N289H(1)		breast(1)|endometrium(2)|kidney(4)|large_intestine(1)|lung(8)|ovary(1)|prostate(2)	19	Acute lymphoblastic leukemia(192;0.000127)					CACGTGCCATTAGACCTGGAA	0.552																																																	2	Substitution - Missense(2)	kidney(2)											101.0	101.0	101.0					X																	132351243		2201	4300	6501	SO:0001583	missense	51270			AF219119	CCDS14636.2	Xq26.2	2009-03-25			ENSG00000183434	ENSG00000183434			24603	protein-coding gene	gene with protein product	"""E2F-like protein"", ""cancer/testis antigen 30"""	300772				12097419	Standard	NM_016521		Approved	HCA661, E2F-like, CT30	uc004exb.1	Q5H9I0	OTTHUMG00000022433	ENST00000310125.4:c.1045A>C	X.37:g.132351243T>G	ENSP00000385461:p.Asn349His		Q6DK49|Q9NZ54	Missense_Mutation	SNP	ENST00000310125.4	37	CCDS14636.2	.	.	.	.	.	.	.	.	.	.	T	11.42	1.634434	0.29068	.	.	ENSG00000183434	ENST00000310125	T	0.25414	1.8	1.03	-0.239	0.13050	.	.	.	.	.	T	0.21468	0.0517	L	0.57536	1.79	0.26596	N	0.973108	B	0.18310	0.027	B	0.14023	0.01	T	0.31475	-0.9942	9	0.66056	D	0.02	.	3.6921	0.08350	0.0:0.3061:0.0:0.6939	.	349	Q5H9I0	TFDP3_HUMAN	H	349	ENSP00000385461:N349H	ENSP00000385461:N349H	N	-	1	0	TFDP3	132178909	0.027000	0.19231	0.009000	0.14445	0.008000	0.06430	0.650000	0.24858	0.245000	0.21373	0.242000	0.17961	AAT		0.552	TFDP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058337.1		NM_016521	
TANGO6	79613	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	16	68953056	68953056	+	Silent	SNP	C	C	A	rs375170838		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	2cb6b578-8543-4a12-8331-1721ddc47303	1e656287-a1d9-4273-bbd2-c4909d29366d	g.chr16:68953056C>A	ENST00000261778.1	+	12	2073	c.2061C>A	c.(2059-2061)acC>acA	p.T687T		NM_024562.1	NP_078838.1	Q9C0B7	TNG6_HUMAN	transport and golgi organization 6 homolog (Drosophila)	687						integral component of membrane (GO:0016021)		p.T687T(1)|p.T216T(1)									CAGAGAGCACCGTGGAATCAC	0.527																																																	2	Substitution - coding silent(2)	kidney(2)											82.0	79.0	80.0					16																	68953056		2132	4237	6369	SO:0001819	synonymous_variant	0				CCDS45516.1	16q22.1	2012-12-13	2012-12-13	2012-12-13	ENSG00000103047	ENSG00000103047			25749	protein-coding gene	gene with protein product			"""transmembrane and coiled-coil domains 7"""	TMCO7		11214970	Standard	NM_024562		Approved	FLJ12688, KIAA1746	uc002ewi.4	Q9C0B7	OTTHUMG00000176743	ENST00000261778.1:c.2061C>A	16.37:g.68953056C>A			Q569F9|Q9H9K1	Silent	SNP	ENST00000261778.1	37	CCDS45516.1																																																																																				0.527	TANGO6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433471.2		XM_928235.2	
TP53BP2	7159	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	223983853	223983853	+	Silent	SNP	T	T	A			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	2cb6b578-8543-4a12-8331-1721ddc47303	1e656287-a1d9-4273-bbd2-c4909d29366d	g.chr1:223983853T>A	ENST00000343537.7	-	13	2679	c.2388A>T	c.(2386-2388)ccA>ccT	p.P796P	TP53BP2_ENST00000498843.1_5'UTR|TP53BP2_ENST00000391879.2_Silent_p.P29P|TP53BP2_ENST00000391878.2_Silent_p.P667P	NM_001031685.2	NP_001026855.2	Q13625	ASPP2_HUMAN	tumor protein p53 binding protein 2	790					cell cycle (GO:0007049)|central nervous system development (GO:0007417)|embryo development ending in birth or egg hatching (GO:0009792)|heart development (GO:0007507)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|negative regulation of cell cycle (GO:0045786)|positive regulation of signal transduction (GO:0009967)|response to ionizing radiation (GO:0010212)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	identical protein binding (GO:0042802)|NF-kappaB binding (GO:0051059)|SH3/SH2 adaptor activity (GO:0005070)	p.P667P(1)|p.P796P(1)		NS(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(9)|ovary(2)|prostate(1)|skin(2)	29				GBM - Glioblastoma multiforme(131;0.0958)		CATGTAAATATGGATTCTGGA	0.512																																																	2	Substitution - coding silent(2)	kidney(2)											118.0	128.0	125.0					1																	223983853		2203	4300	6503	SO:0001819	synonymous_variant	7159			U09582	CCDS1538.1, CCDS44319.1	1q41	2014-06-24	2014-06-24		ENSG00000143514	ENSG00000143514		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Ankyrin repeat domain containing"""	12000	protein-coding gene	gene with protein product		602143	"""tumor protein p53-binding protein, 2"""			8668206, 8016121	Standard	NM_005426		Approved	PPP1R13A, ASPP2, 53BP2	uc010pvb.2	Q13625	OTTHUMG00000037379	ENST00000343537.7:c.2388A>T	1.37:g.223983853T>A			B4DG66|Q12892|Q86X75|Q96KQ3	Silent	SNP	ENST00000343537.7	37	CCDS44319.1																																																																																				0.512	TP53BP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090985.3		NM_001031685, NM_005426	
TRAP1	10131	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	16	3726076	3726076	+	Missense_Mutation	SNP	A	A	G			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	2cb6b578-8543-4a12-8331-1721ddc47303	1e656287-a1d9-4273-bbd2-c4909d29366d	g.chr16:3726076A>G	ENST00000246957.5	-	7	863	c.775T>C	c.(775-777)Tcc>Ccc	p.S259P	TRAP1_ENST00000573872.1_5'UTR|TRAP1_ENST00000538171.1_Missense_Mutation_p.S206P|TRAP1_ENST00000575671.1_Missense_Mutation_p.S50P	NM_016292.2	NP_057376.2	Q12931	TRAP1_HUMAN	TNF receptor-associated protein 1	259					chaperone-mediated protein folding (GO:0061077)|negative regulation of cellular respiration (GO:1901856)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|regulation of reactive oxygen species metabolic process (GO:2000377)|response to stress (GO:0006950)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|tumor necrosis factor receptor binding (GO:0005164)	p.S259P(1)		central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(3)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	19		Ovarian(90;0.0261)				TTGCAGTCGGATTTCAGGTGG	0.577																																																	1	Substitution - Missense(1)	kidney(1)											113.0	109.0	110.0					16																	3726076		2197	4300	6497	SO:0001583	missense	10131			AF154108	CCDS10508.1, CCDS61824.1	16p13.3	2011-09-02			ENSG00000126602	ENSG00000126602		"""Heat shock proteins / HSPC"""	16264	protein-coding gene	gene with protein product		606219				10652318, 7876093	Standard	NM_016292		Approved	HSP75, HSP90L	uc002cvt.4	Q12931	OTTHUMG00000129427	ENST00000246957.5:c.775T>C	16.37:g.3726076A>G	ENSP00000246957:p.Ser259Pro		B4DR68|D3DUC8|F5H897|O43642|O75235|Q9UHL5	Missense_Mutation	SNP	ENST00000246957.5	37	CCDS10508.1	.	.	.	.	.	.	.	.	.	.	A	12.33	1.904399	0.33628	.	.	ENSG00000126602	ENST00000246957;ENST00000538171	T;T	0.76709	-1.04;-1.04	5.32	-3.25	0.05079	Heat shock protein Hsp90, N-terminal (1);ATPase-like, ATP-binding domain (3);	0.712422	0.13777	N	0.363480	T	0.47691	0.1459	N	0.01649	-0.78	0.26210	N	0.979315	B;B	0.02656	0.0;0.0	B;B	0.09377	0.001;0.004	T	0.38222	-0.9671	10	0.66056	D	0.02	-0.7703	9.7626	0.40541	0.232:0.5587:0.2093:0.0	.	206;259	F5H897;Q12931	.;TRAP1_HUMAN	P	259;206	ENSP00000246957:S259P;ENSP00000442070:S206P	ENSP00000246957:S259P	S	-	1	0	TRAP1	3666077	0.894000	0.30519	0.058000	0.19502	0.820000	0.46376	0.335000	0.19806	-0.849000	0.04158	0.460000	0.39030	TCC		0.577	TRAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251586.2		NM_016292	
UBE3C	9690	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	7	156974262	156974262	+	Missense_Mutation	SNP	A	A	G			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	2cb6b578-8543-4a12-8331-1721ddc47303	1e656287-a1d9-4273-bbd2-c4909d29366d	g.chr7:156974262A>G	ENST00000348165.5	+	7	1027	c.667A>G	c.(667-669)Att>Gtt	p.I223V	UBE3C_ENST00000389103.4_Missense_Mutation_p.I180V	NM_014671.2	NP_055486.2	Q15386	UBE3C_HUMAN	ubiquitin protein ligase E3C	223					protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|intracellular (GO:0005622)|nucleus (GO:0005634)|proteasome complex (GO:0000502)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)	p.I223V(1)		central_nervous_system(2)|endometrium(3)|kidney(16)|large_intestine(13)|lung(25)|ovary(2)|prostate(1)|urinary_tract(1)	63		all_hematologic(28;0.0185)|all_epithelial(9;0.0664)	OV - Ovarian serous cystadenocarcinoma(82;0.00448)	UCEC - Uterine corpus endometrioid carcinoma (81;0.19)		TCCATCAAGTATTGAATATTC	0.328																																																	1	Substitution - Missense(1)	kidney(1)											78.0	78.0	78.0					7																	156974262		2203	4300	6503	SO:0001583	missense	9690			AK127280	CCDS34789.1	7q36.3	2004-05-04			ENSG00000009335	ENSG00000009335			16803	protein-coding gene	gene with protein product		614454				7584026, 11278995	Standard	NM_014671		Approved	KIAA0010, KIAA10	uc010lqs.3	Q15386	OTTHUMG00000157239	ENST00000348165.5:c.667A>G	7.37:g.156974262A>G	ENSP00000309198:p.Ile223Val		A4D235|A6NCP3|Q8TC15|Q96CR4|Q9UDU3	Missense_Mutation	SNP	ENST00000348165.5	37	CCDS34789.1	.	.	.	.	.	.	.	.	.	.	A	13.89	2.372225	0.42003	.	.	ENSG00000009335	ENST00000348165;ENST00000389103	T	0.41065	1.01	5.18	4.03	0.46877	.	0.116985	0.64402	N	0.000018	T	0.41558	0.1164	L	0.50333	1.59	0.43787	D	0.99632	B;B;P	0.47910	0.078;0.427;0.902	B;B;P	0.48189	0.012;0.204;0.57	T	0.13072	-1.0523	10	0.20046	T	0.44	.	10.5143	0.44881	0.9243:0.0:0.0757:0.0	.	223;223;180	Q15386;Q15386-2;Q15386-3	UBE3C_HUMAN;.;.	V	223;180	ENSP00000309198:I223V	ENSP00000309198:I223V	I	+	1	0	UBE3C	156667023	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.670000	0.46833	0.827000	0.34685	0.455000	0.32223	ATT		0.328	UBE3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348108.1		NM_014671	
PTP4A2	8073	broad.mit.edu	37	1	32373167	32373167	+	3'UTR	DEL	T	T	-	rs558600453	byFrequency	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2cb6b578-8543-4a12-8331-1721ddc47303	1e656287-a1d9-4273-bbd2-c4909d29366d	g.chr1:32373167delT	ENST00000602725.1	-	0	2207				PTP4A2_ENST00000344035.6_3'UTR|RP11-84A19.4_ENST00000602889.1_lincRNA			Q12974	TP4A2_HUMAN	protein tyrosine phosphatase type IVA, member 2						peptidyl-tyrosine dephosphorylation (GO:0035335)	cytoplasm (GO:0005737)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	prenylated protein tyrosine phosphatase activity (GO:0004727)			kidney(1)|large_intestine(1)|lung(1)|urinary_tract(1)	4		Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0606)|all_neural(195;0.0837)|Breast(348;0.174)				AAACCAGGGATTTTTTTTTTT	0.393													|||unknown(HR)	28	0.00559105	0.0023	0.0058	5008	,	,		20285	0.0		0.003	False		,,,				2504	0.0184																0																																										SO:0001624	3_prime_UTR_variant	0			L48723	CCDS348.1, CCDS53292.1, CCDS59193.1	1p35	2011-06-09			ENSG00000184007	ENSG00000184007		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : PRLs"""	9635	protein-coding gene	gene with protein product		601584		PTP4A		8661118, 9514946	Standard	NM_080391		Approved	HU-PP-1, PTPCAAX2, OV-1, ptp-IV1a, PRL-2	uc001bty.2	Q12974	OTTHUMG00000003801	ENST00000602725.1:c.*1286A>-	1.37:g.32373167delT			A8K9I8|B4DM39|D3DPP0|E9PGJ6|O00649|Q15197|Q15259|Q15260|Q15261|R4GN50	RNA	DEL	ENST00000602725.1	37	CCDS348.1																																																																																				0.393	PTP4A2-019	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000468092.1		NM_080391	
FAM63B	54629	broad.mit.edu	37	15	59153166	59153167	+	3'UTR	INS	-	-	A	rs147767896|rs34605445	byFrequency	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2cb6b578-8543-4a12-8331-1721ddc47303	1e656287-a1d9-4273-bbd2-c4909d29366d	g.chr15:59153166_59153167insA	ENST00000559228.1	+	0	8305_8306				RP11-30K9.5_ENST00000558042.1_RNA			Q8NBR6	FA63B_HUMAN	family with sequence similarity 63, member B											central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(1)|liver(2)|lung(4)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	15						GACAGCTTGTTACAGATTCACA	0.342													A|A|AA|insertion	1432	0.285942	0.0855	0.4135	5008	,	,		18610	0.1091		0.5696	False		,,,				2504	0.3569																0																																										SO:0001624	3_prime_UTR_variant	0			AK075319	CCDS42046.1, CCDS45268.1	15q21.3	2005-08-09							26954	protein-coding gene	gene with protein product						10574461	Standard	NM_001040450		Approved	KIAA1164	uc002afj.3	Q8NBR6		ENST00000559228.1:c.*6358->A	15.37:g.59153167_59153167dupA			B2RTT8|Q9ULQ6	RNA	INS	ENST00000559228.1	37	CCDS42046.1																																																																																				0.342	FAM63B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000416230.1		NM_019092	
SMG1P7	100506060	broad.mit.edu	37	16	70268080	70268081	+	RNA	DNP	TG	TG	CA			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10	T|G	T|G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2cb6b578-8543-4a12-8331-1721ddc47303	1e656287-a1d9-4273-bbd2-c4909d29366d	g.chr16:70268080_70268081TG>CA	ENST00000459379.1	-	0	0																											GTCTTACTGTTGGCTAAAAGGC	0.376																																																	0																																												0																														Exception_encountered	16.37:g.70268080_70268081delinsCA				RNA	SNP	ENST00000459379.1	37																																																																																					0.376	snoU13.216-201	NOVEL	basic	snoRNA	snoRNA				
NPIPB15	440348	broad.mit.edu	37	16	74425826	74425826	+	Missense_Mutation	SNP	G	G	A			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2cb6b578-8543-4a12-8331-1721ddc47303	1e656287-a1d9-4273-bbd2-c4909d29366d	g.chr16:74425826G>A	ENST00000429990.1	+	7	1276	c.1180G>A	c.(1180-1182)Gca>Aca	p.A394T				A6NHN6	NPB15_HUMAN	nuclear pore complex interacting protein family, member B15	394						extracellular region (GO:0005576)		p.A394T(2)|p.A333T(2)									ggaggccgaggcacaacaatt	0.552																																																	4	Substitution - Missense(4)	endometrium(2)|kidney(2)											5.0	7.0	7.0					16																	74425826		1730	3815	5545	SO:0001583	missense	0			BC160029		16q22.3	2013-06-11	2013-06-11	2013-06-11	ENSG00000196436	ENSG00000196436			34409	protein-coding gene	gene with protein product			"""nuclear pore complex interacting protein-like 2"""	NPIPL2			Standard	XM_005256273		Approved	LOC440348	uc010vmt.1	A6NHN6	OTTHUMG00000156916	ENST00000429990.1:c.1180G>A	16.37:g.74425826G>A	ENSP00000411140:p.Ala394Thr		C9J9U8	Missense_Mutation	SNP	ENST00000429990.1	37		.	.	.	.	.	.	.	.	.	.	g	6.091	0.385122	0.11524	.	.	ENSG00000196436	ENST00000504746;ENST00000429990	T	0.47869	0.83	.	.	.	.	.	.	.	.	T	0.22551	0.0544	N	0.08118	0	0.19300	N	0.999978	B	0.06786	0.001	B	0.04013	0.001	T	0.18147	-1.0346	7	0.27082	T	0.32	.	.	.	.	.	333	A6NHN6	NPPL2_HUMAN	T	258;394	ENSP00000411140:A394T	ENSP00000411140:A394T	A	+	1	0	NPIPL2	72983327	.	.	0.000000	0.03702	0.000000	0.00434	.	.	0.000000	0.14550	0.000000	0.15137	GCA		0.552	NPIPB15-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000346597.2		NM_001018059	
NUP210P1	255330	broad.mit.edu	37	3	126385091	126385091	+	RNA	DEL	C	C	-	rs547540000|rs146507124	byFrequency	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2cb6b578-8543-4a12-8331-1721ddc47303	1e656287-a1d9-4273-bbd2-c4909d29366d	g.chr3:126385091delC	ENST00000357061.3	+	0	347					NR_034158.1				nucleoporin 210kDa pseudogene 1																		GGTGCTGCTGCTTGGAGCCGT	0.607													C|C|-|deletion	83	0.0165735	0.0166	0.0144	5008	,	,		18728	0.002		0.0427	False		,,,				2504	0.0061																0																																												0			BC042038		3q21.2	2011-08-16	2011-08-16	2011-08-16	ENSG00000198284	ENSG00000198284			27399	pseudogene	pseudogene			"""chromosome 3 open reading frame 46"""	C3orf46			Standard	NR_034158		Approved		uc003eje.1		OTTHUMG00000159577		3.37:g.126385091delC				Frame_Shift_Del	DEL	ENST00000357061.3	37																																																																																					0.607	NUP210P1-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000356320.1		NR_034158	
USP15	9958	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	12	62790158	62790158	+	Missense_Mutation	SNP	G	G	C			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	2cb6b578-8543-4a12-8331-1721ddc47303	1e656287-a1d9-4273-bbd2-c4909d29366d	g.chr12:62790158G>C	ENST00000280377.5	+	20	2712	c.2654G>C	c.(2653-2655)gGa>gCa	p.G885A	USP15_ENST00000353364.3_Missense_Mutation_p.G856A|USP15_ENST00000393654.3_Missense_Mutation_p.G860A	NM_001252078.1	NP_001239007.1	Q9Y4E8	UBP15_HUMAN	ubiquitin specific peptidase 15	885	USP.				BMP signaling pathway (GO:0030509)|monoubiquitinated protein deubiquitination (GO:0035520)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|protein deubiquitination (GO:0016579)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|identical protein binding (GO:0042802)|SMAD binding (GO:0046332)|transforming growth factor beta receptor binding (GO:0005160)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)	p.G856A(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(8)|lung(15)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	37			GBM - Glioblastoma multiforme(1;0.000276)	GBM - Glioblastoma multiforme(28;0.0622)		AACCACTATGGAGGGATGGGA	0.373																																					Melanoma(181;615 2041 39364 49691 50001)												1	Substitution - Missense(1)	kidney(1)											118.0	108.0	111.0					12																	62790158		2203	4300	6503	SO:0001583	missense	9958			AB011101	CCDS8963.1, CCDS58250.1, CCDS58251.1	12q14	2006-07-18	2005-08-08					"""Ubiquitin-specific peptidases"""	12613	protein-coding gene	gene with protein product		604731	"""ubiquitin specific protease 15"""			12838346	Standard	NM_001252078		Approved	KIAA0529, UNPH4	uc001src.2	Q9Y4E8	OTTHUMG00000170186	ENST00000280377.5:c.2654G>C	12.37:g.62790158G>C	ENSP00000280377:p.Gly885Ala		Q08AL5|Q9H8G9|Q9HCA6|Q9UNP0|Q9Y5B5	Missense_Mutation	SNP	ENST00000280377.5	37	CCDS58251.1	.	.	.	.	.	.	.	.	.	.	G	32	5.132674	0.94517	.	.	ENSG00000135655	ENST00000353364;ENST00000280377;ENST00000393654;ENST00000549415	T;T;D;T	0.84730	0.49;0.49;-1.89;0.49	5.47	5.47	0.80525	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2, conserved site (1);Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.051373	0.85682	D	0.000000	D	0.95118	0.8418	H	0.95745	3.715	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.96048	0.9029	9	.	.	.	-18.354	19.6937	0.96012	0.0:0.0:1.0:0.0	.	885;856	Q9Y4E8;Q9Y4E8-2	UBP15_HUMAN;.	A	856;885;860;87	ENSP00000258123:G856A;ENSP00000280377:G885A;ENSP00000377264:G860A;ENSP00000448372:G87A	.	G	+	2	0	USP15	61076425	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.869000	0.99810	2.720000	0.93068	0.650000	0.86243	GGA		0.373	USP15-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000407831.2		NM_006313	
VCX	26609	hgsc.bcm.edu	37	X	7811830	7811859	+	In_Frame_Del	DEL	GAACCACTGAGTCAGGAGAGCGAGGTGGAA	GAACCACTGAGTCAGGAGAGCGAGGTGGAA	-	rs200761534|rs145031736|rs374291810|rs139413469		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10	GAACCACTGAGTCAGGAGAGCGAGGTGGAA	GAACCACTGAGTCAGGAGAGCGAGGTGGAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	2cb6b578-8543-4a12-8331-1721ddc47303	1e656287-a1d9-4273-bbd2-c4909d29366d	g.chrX:7811830_7811859delGAACCACTGAGTCAGGAGAGCGAGGTGGAA	ENST00000381059.3	+	3	613_642	c.394_423delGAACCACTGAGTCAGGAGAGCGAGGTGGAA	c.(394-423)gaaccactgagtcaggagagcgaggtggaadel	p.EPLSQESEVE132del	VCX_ENST00000341408.4_Splice_Site_p.ENH119del	NM_013452.2	NP_038480.2	Q9H320	VCX1_HUMAN	variable charge, X-linked	132	10 X 10 AA tandem repeats of L-S-Q-E-S- [EQ]-V-E-E-P.|Glu-rich.				chromatin organization (GO:0006325)|ribosome assembly (GO:0042255)|spermatogenesis (GO:0007283)	nucleolus (GO:0005730)|nucleus (GO:0005634)	chromatin binding (GO:0003682)			NS(1)|endometrium(4)|large_intestine(2)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	10		Colorectal(8;0.0136)|Medulloblastoma(8;0.184)				CCAGGTGGAGGAACCACTGAGTCAGGAGAGCGAGGTGGAAGAACCACTGA	0.604																																																	0																																										SO:0001651	inframe_deletion	26609			AF167081	CCDS14128.1	Xp22.31	2008-02-05	2003-09-12		ENSG00000182583	ENSG00000182583			12667	protein-coding gene	gene with protein product		300229	"""variable charge, X chromosome"""			10607842, 10903929	Standard	NM_013452		Approved	VCX1, VCX10R, VCX-10r, VCX-B1	uc004crz.3	Q9H320	OTTHUMG00000028608	ENST00000381059.3:c.394_423delGAACCACTGAGTCAGGAGAGCGAGGTGGAA	X.37:g.7811830_7811859delGAACCACTGAGTCAGGAGAGCGAGGTGGAA	ENSP00000370447:p.Glu132_Glu141del		A0JNS5|Q4V774|Q9P0H3	In_Frame_Del	DEL	ENST00000381059.3	37	CCDS14128.1																																																																																				0.604	VCX-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000071474.1		NM_013452	
VHL	7428	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	10191569	10191569	+	Frame_Shift_Del	DEL	C	C	-	rs5030824		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	2cb6b578-8543-4a12-8331-1721ddc47303	1e656287-a1d9-4273-bbd2-c4909d29366d	g.chr3:10191569delC	ENST00000256474.2	+	3	1402	c.562delC	c.(562-564)ctgfs	p.L188fs	VHL_ENST00000477538.1_3'UTR|VHL_ENST00000345392.2_Frame_Shift_Del_p.L147fs	NM_000551.3	NP_000542.1	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor, E3 ubiquitin protein ligase	188			L -> P (in VHLD; type I-II). {ECO:0000269|PubMed:9829912}.|L -> Q (in VHLD; type I). {ECO:0000269|PubMed:8956040}.|L -> V (in ECYT2, pheochromocytoma and VHLD; type IIA; dbSNP:rs5030824). {ECO:0000269|PubMed:12000816, ECO:0000269|PubMed:12844285}.		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.D187_L188del(2)|p.L188V(1)|p.L188fs*14(1)|p.D187_N193del(1)|p.E186fs*14(1)|p.Y185fs*11(1)|p.D187fs*14(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)		CTACGAAGATCTGGAAGACCA	0.502		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"""	8	Deletion - Frameshift(4)|Deletion - In frame(3)|Substitution - Missense(1)	kidney(8)	GRCh37	CD071417|CM951300	VHL	D|M	rs5030824						77.0	70.0	73.0					3																	10191569		2203	4300	6503	SO:0001589	frameshift_variant	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.562delC	3.37:g.10191569delC	ENSP00000256474:p.Leu188fs		B2RE45|Q13599|Q6PDA9	Frame_Shift_Del	DEL	ENST00000256474.2	37	CCDS2597.1																																																																																				0.502	VHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250559.1		NM_000551	
XIST	7503	broad.mit.edu	37	X	73071846	73071846	+	lincRNA	DEL	A	A	-	rs200290800		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2cb6b578-8543-4a12-8331-1721ddc47303	1e656287-a1d9-4273-bbd2-c4909d29366d	g.chrX:73071846delA	ENST00000429829.1	-	0	742					NR_001564.2				X inactive specific transcript (non-protein coding)																		ATGGGCGATGAAAAAAAAAAA	0.413																																																	0													25.0	25.0	25.0					X																	73071846		876	1990	2866			7503			M97168		Xq13.2	2013-12-18	2013-02-07		ENSG00000229807	ENSG00000229807		"""Long non-coding RNAs"", ""-"""	12810	non-coding RNA	RNA, long non-coding	"""long intergenic non-protein coding RNA 1"""	314670	"""X (inactive)-specific transcript"", ""X (inactive)-specific transcript (non-protein coding)"""	DXS399E		1985261, 2034279	Standard	NR_001564		Approved	NCRNA00001, DXS1089, swd66, LINC00001	uc004ebm.2		OTTHUMG00000021839		X.37:g.73071846delA				RNA	DEL	ENST00000429829.1	37																																																																																					0.413	XIST-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000057239.1		NR_001564	
ZNF653	115950	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	19	11598181	11598181	+	Missense_Mutation	SNP	G	G	A	rs562892839		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	2cb6b578-8543-4a12-8331-1721ddc47303	1e656287-a1d9-4273-bbd2-c4909d29366d	g.chr19:11598181G>A	ENST00000293771.5	-	4	1233	c.1097C>T	c.(1096-1098)aCc>aTc	p.T366I	CTC-398G3.6_ENST00000585656.1_Intron	NM_138783.3	NP_620138.2	Q96CK0	ZN653_HUMAN	zinc finger protein 653	366					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.T366I(1)		endometrium(2)|kidney(3)|large_intestine(2)|lung(8)|prostate(1)|skin(1)	17						CTCTGTCTGGGTGTAGGCTGC	0.647													G|||	1	0.000199681	0.0	0.0	5008	,	,		16047	0.0		0.0	False		,,,				2504	0.001				Pancreas(83;980 1446 4542 6441 43352)												1	Substitution - Missense(1)	kidney(1)											60.0	50.0	53.0					19																	11598181		2203	4300	6503	SO:0001583	missense	115950			AY072704	CCDS12261.1	19p13.2	2013-01-08						"""Zinc fingers, C2H2-type"""	25196	protein-coding gene	gene with protein product		611371				12477932	Standard	NM_138783		Approved	Zip67	uc002mrz.2	Q96CK0		ENST00000293771.5:c.1097C>T	19.37:g.11598181G>A	ENSP00000293771:p.Thr366Ile		Q96AS7	Missense_Mutation	SNP	ENST00000293771.5	37	CCDS12261.1	.	.	.	.	.	.	.	.	.	.	G	16.07	3.020116	0.54576	.	.	ENSG00000161914	ENST00000293771	T	0.11821	2.74	4.26	4.26	0.50523	.	0.196730	0.43919	D	0.000520	T	0.21841	0.0526	N	0.24115	0.695	0.35638	D	0.810763	D	0.71674	0.998	P	0.61874	0.895	T	0.26950	-1.0088	10	0.62326	D	0.03	-37.6417	15.8046	0.78483	0.0:0.0:1.0:0.0	.	366	Q96CK0	ZN653_HUMAN	I	366	ENSP00000293771:T366I	ENSP00000293771:T366I	T	-	2	0	ZNF653	11459181	1.000000	0.71417	1.000000	0.80357	0.803000	0.45373	4.021000	0.57196	2.075000	0.62263	0.462000	0.41574	ACC		0.647	ZNF653-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458836.2		NM_138783	
