#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_Annotation_Transcript	i_CCLE_ONCOMAP_overlapping_mutations	i_CCLE_ONCOMAP_total_mutations_in_gene	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_Mutation_Type	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Other_Diseases	i_CGC_Tissue Type	i_CGC_Translocation_Partner	i_CGC_Tumor_Types_Germline	i_CGC_Tumor_Types_Somatic	i_COSMIC_fusion_genes	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_mutations	i_COSMIC_overlapping_primary_sites	i_COSMIC_tissue_types_affected	i_COSMIC_total_alterations_in_gene	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Codon_Change	i_DNARepairGenes_Role	i_Description	i_DrugBank	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_FamilialCancerDatabase_Syndromes	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_GO_Biological_Process	i_GO_Cellular_Component	i_GO_Molecular_Function	i_Genome_Change	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_MUTSIG_Published_Results	i_OREGANNO_ID	i_OREGANNO_Values	i_ORegAnno_bin	i_Other_Transcripts	i_Protein_Change	i_Refseq_mRNA_Id	i_Refseq_prot_Id	i_SwissProt_acc_Id	i_SwissProt_entry_Id	i_TCGAscape_Amplification_Peaks	i_TCGAscape_Deletion_Peaks	i_Transcript_Exon	i_Transcript_Position	i_Transcript_Strand	i_Tumorscape_Amplification_Peaks	i_Tumorscape_Deletion_Peaks	i_UniProt_AApos	i_UniProt_Experimental_Info	i_UniProt_Natural_Variations	i_UniProt_Region	i_UniProt_Site	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_cDNA_Change	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_refseq_mrna_id	i_secondary_variant_classification	i_t_alt_count_full	i_t_ref_count_full	isArtifactMode	oxoGCut	pox	pox_cutoff	qox	t_alt_count	t_ref_count	validation_alt_allele	validation_method	validation_status	validation_tumor_sample
MYO15A	51168	broad.mit.edu	37	17	18077153	18077153	+	Missense_Mutation	SNP	C	C	T	rs371592889		TCGA-EL-A3ZQ-01A-11D-A23M-08	TCGA-EL-A3ZQ-11A-11D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4694460d-de2a-4b9e-9391-dc57816752bf	a51fd081-0952-40bf-8412-b293d88100dc	g.chr17:18077153C>T	ENST00000205890.5	+	65	10747	c.10409C>T	c.(10408-10410)aCg>aTg	p.T3470M	RP11-258F1.1_ENST00000583062.1_RNA|RP11-258F1.1_ENST00000577847.1_RNA|MYO15A_ENST00000451725.2_Intron|MYO15A_ENST00000418233.3_Missense_Mutation_p.T734M	NM_016239.3	NP_057323.3	Q9UKN7	MYO15_HUMAN	myosin XVA	3470	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.|Tail.				inner ear morphogenesis (GO:0042472)|locomotory behavior (GO:0007626)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|stereocilium (GO:0032420)	ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(5)|central_nervous_system(2)|endometrium(17)|kidney(3)|large_intestine(16)|lung(27)|ovary(3)|pancreas(1)|prostate(6)|skin(13)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	99	all_neural(463;0.228)					CAGCGGCCCACGGCCAACTCC	0.662																																						ENST00000205890.5																			0				breast(5)|central_nervous_system(2)|endometrium(17)|kidney(3)|large_intestine(16)|lung(27)|ovary(3)|pancreas(1)|prostate(6)|skin(13)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	99						c.(10408-10410)aCg>aTg		myosin XVA		C	MET/THR	1,3907		0,1,1953	40.0	43.0	42.0		10409	5.0	0.9	17		42	0,8272		0,0,4136	no	missense	MYO15A	NM_016239.3	81	0,1,6089	TT,TC,CC		0.0,0.0256,0.0082	probably-damaging	3470/3531	18077153	1,12179	1954	4136	6090	SO:0001583	missense	51168				sensory perception of sound	cytoplasm|myosin complex|stereocilium	actin binding|ATP binding|calmodulin binding|motor activity	g.chr17:18077153C>T	AF144094	CCDS42271.1	17p11.2	2011-09-27			ENSG00000091536	ENSG00000091536		"""Myosins / Myosin superfamily : Class XV"""	7594	protein-coding gene	gene with protein product		602666		DFNB3, MYO15		9603736	Standard	NM_016239		Approved		uc021trl.1	Q9UKN7	OTTHUMG00000059390	ENST00000205890.5:c.10409C>T	17.37:g.18077153C>T	ENSP00000205890:p.Thr3470Met					RP11-258F1.1_ENST00000577847.1_RNA|MYO15A_ENST00000451725.2_Intron|MYO15A_ENST00000418233.3_Missense_Mutation_p.T734M	p.T3470M	NM_016239.3	NP_057323.3	Q9UKN7	MYO15_HUMAN			65	10747	+	all_neural(463;0.228)		3470			FERM.|Tail.		B4DFC7	Missense_Mutation	SNP	ENST00000205890.5	37	c.10409C>T	CCDS42271.1	.	.	.	.	.	.	.	.	.	.	C	15.71	2.914501	0.52546	2.56E-4	0.0	ENSG00000091536	ENST00000205890	D	0.88431	-2.38	5.95	4.98	0.66077	FERM domain (1);	.	.	.	.	D	0.92047	0.7480	L	0.56769	1.78	0.80722	D	1	P;D	0.89917	0.507;1.0	B;P	0.61800	0.114;0.894	D	0.92201	0.5768	9	0.52906	T	0.07	.	14.701	0.69157	0.0:0.9299:0.0:0.0701	.	734;3470	B4DFC7;Q9UKN7	.;MYO15_HUMAN	M	3470	ENSP00000205890:T3470M	ENSP00000205890:T3470M	T	+	2	0	MYO15A	18017878	1.000000	0.71417	0.915000	0.36163	0.995000	0.86356	5.858000	0.69532	1.516000	0.48900	0.655000	0.94253	ACG		0.662	MYO15A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132048.1	NM_016239		6	78	0	0	0	1	0	6	78				
CROCCP2	84809	broad.mit.edu	37	1	16956467	16956467	+	lincRNA	SNP	A	A	T	rs1762950	byFrequency	TCGA-EL-A3ZQ-01A-11D-A23M-08	TCGA-EL-A3ZQ-11A-11D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4694460d-de2a-4b9e-9391-dc57816752bf	a51fd081-0952-40bf-8412-b293d88100dc	g.chr1:16956467A>T	ENST00000412962.1	-	0	294							Q86T23	CROL1_HUMAN	ciliary rootlet coiled-coil, rootletin pseudogene 2						centrosome organization (GO:0051297)	ciliary rootlet (GO:0035253)											gcaattttttaaatttttagt	0.567													.|||	2275	0.454273	0.4803	0.4207	5008	,	,		61852	0.504		0.4364	False		,,,				2504	0.41					ENST00000412962.1																			0																																																			0							g.chr1:16956467A>T	AK090414		1p36.13	2010-07-08	2010-07-08	2010-07-08	ENSG00000215908	ENSG00000215908			28170	pseudogene	pseudogene			"""ciliary rootlet coiled-coil, rootletin-like 1"""	CROCCL1		12477932	Standard	NR_026752		Approved	MGC12760	uc001azf.3	Q86T23	OTTHUMG00000037884		1.37:g.16956467A>T														0	294	-								Q8NF65|Q96FR5|Q9BRE8	RNA	SNP	ENST00000412962.1	37																																																																																						0.567	CROCCP2-003	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000092784.1	NR_026752.1		5	22	0	0	0	1	0	5	22				
UGGT2	55757	broad.mit.edu	37	13	96705526	96705526	+	Missense_Mutation	SNP	A	A	T			TCGA-EL-A3ZQ-01A-11D-A23M-08	TCGA-EL-A3ZQ-11A-11D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4694460d-de2a-4b9e-9391-dc57816752bf	a51fd081-0952-40bf-8412-b293d88100dc	g.chr13:96705526A>T	ENST00000376747.3	-	1	111	c.41T>A	c.(40-42)cTa>cAa	p.L14Q	UGGT2_ENST00000397618.3_Missense_Mutation_p.L14Q|UGGT2_ENST00000376712.4_Missense_Mutation_p.L14Q|UGGT2_ENST00000376714.3_Missense_Mutation_p.L14Q	NM_020121.3	NP_064506.3	Q9NYU1	UGGG2_HUMAN	UDP-glucose glycoprotein glucosyltransferase 2	14					cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)|UDP-glucosylation (GO:0097359)	endoplasmic reticulum lumen (GO:0005788)	UDP-glucose:glycoprotein glucosyltransferase activity (GO:0003980)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(17)|lung(20)|ovary(3)|pancreas(1)|prostate(4)|urinary_tract(2)	60						TGTGGAGCCTAGTAGCAGCCG	0.687																																						ENST00000376747.3																			0				NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(17)|lung(20)|ovary(3)|pancreas(1)|prostate(4)|urinary_tract(2)	60						c.(40-42)cTa>cAa		UDP-glucose glycoprotein glucosyltransferase 2							9.0	9.0	9.0					13																	96705526		2149	4198	6347	SO:0001583	missense	55757				post-translational protein modification|protein folding|protein N-linked glycosylation via asparagine	endoplasmic reticulum lumen|ER-Golgi intermediate compartment	UDP-glucose:glycoprotein glucosyltransferase activity	g.chr13:96705526A>T	AF227906	CCDS9480.1	13q32.1	2009-07-23	2009-07-23	2009-07-23	ENSG00000102595	ENSG00000102595			15664	protein-coding gene	gene with protein product	"""UDP-glucose:glycoprotein glucosyltransferase 2"""	605898	"""UDP-glucose ceramide glucosyltransferase-like 2"""	UGCGL2		10694380	Standard	NM_020121		Approved	FLJ11485, HUGT2, FLJ10873, MGC150689, MGC87276, MGC117360	uc001vmt.3	Q9NYU1	OTTHUMG00000017230	ENST00000376747.3:c.41T>A	13.37:g.96705526A>T	ENSP00000365938:p.Leu14Gln					UGGT2_ENST00000397618.3_Missense_Mutation_p.L14Q|UGGT2_ENST00000376714.3_Missense_Mutation_p.L14Q|UGGT2_ENST00000376712.4_Missense_Mutation_p.L14Q	p.L14Q	NM_020121.3	NP_064506.3	Q9NYU1	UGGG2_HUMAN			1	111	-			14					A6NKL4|Q08AD0|Q5JQR8|Q8N5K0|Q9UFC4	Missense_Mutation	SNP	ENST00000376747.3	37	c.41T>A	CCDS9480.1	.	.	.	.	.	.	.	.	.	.	A	20.5	3.993327	0.74703	.	.	ENSG00000102595	ENST00000376747;ENST00000376722;ENST00000376714;ENST00000397618;ENST00000376712	T;T	0.36699	2.89;1.24	4.08	4.08	0.47627	.	0.549730	0.17455	N	0.173655	T	0.57227	0.2039	M	0.76574	2.34	0.26092	N	0.980948	D;D;B	0.76494	0.999;0.999;0.272	D;D;B	0.85130	0.997;0.997;0.042	T	0.49000	-0.8984	10	0.87932	D	0	-7.1028	9.6163	0.39694	1.0:0.0:0.0:0.0	.	14;14;14	Q2TAA6;E7EMU6;Q9NYU1	.;.;UGGG2_HUMAN	Q	14	ENSP00000365938:L14Q;ENSP00000380743:L14Q	ENSP00000365902:L14Q	L	-	2	0	UGGT2	95503527	0.473000	0.25878	0.179000	0.23059	0.004000	0.04260	1.814000	0.38972	1.841000	0.53522	0.379000	0.24179	CTA		0.687	UGGT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045507.1	NM_020121		5	11	0	0	0	1	0	5	11				
CLCNKB	1188	broad.mit.edu	37	1	16378296	16378296	+	Silent	SNP	A	A	C	rs199755248		TCGA-EL-A3ZQ-01A-11D-A23M-08	TCGA-EL-A3ZQ-11A-11D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4694460d-de2a-4b9e-9391-dc57816752bf	a51fd081-0952-40bf-8412-b293d88100dc	g.chr1:16378296A>C	ENST00000375679.4	+	14	1500	c.1389A>C	c.(1387-1389)ccA>ccC	p.P463P	CLCNKB_ENST00000375667.3_Silent_p.P294P	NM_000085.4	NP_000076.2	P51801	CLCKB_HUMAN	chloride channel, voltage-sensitive Kb	463					excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|regulation of anion transport (GO:0044070)|transmembrane transport (GO:0055085)|transport (GO:0006810)	chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	adenyl nucleotide binding (GO:0030554)|metal ion binding (GO:0046872)|voltage-gated chloride channel activity (GO:0005247)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(2)|prostate(1)|skin(6)|stomach(2)|urinary_tract(1)	21		Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Colorectal(212;8.04e-08)|COAD - Colon adenocarcinoma(227;5.46e-06)|BRCA - Breast invasive adenocarcinoma(304;9.02e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.00655)|READ - Rectum adenocarcinoma(331;0.0649)		CCATCATGCCAGGGGGGTATG	0.622													C|||	1	0.000199681	0.0	0.0	5008	,	,		18264	0.001		0.0	False		,,,				2504	0.0					ENST00000375679.4																			0				breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(2)|prostate(1)|skin(6)|stomach(2)|urinary_tract(1)	21	GRCh37	CD004305	CLCNKB	D		c.(1387-1389)ccA>ccC		chloride channel, voltage-sensitive Kb							66.0	66.0	66.0					1																	16378296		2203	4300	6503	SO:0001819	synonymous_variant	1188							g.chr1:16378296A>C	AK098217	CCDS168.1, CCDS57974.1	1p36	2012-09-26	2012-02-23		ENSG00000184908	ENSG00000184908		"""Ion channels / Chloride channels : Voltage-sensitive"""	2027	protein-coding gene	gene with protein product		602023	"""chloride channel Kb"""				Standard	NM_000085		Approved	hClC-Kb		P51801	OTTHUMG00000009530	ENST00000375679.4:c.1389A>C	1.37:g.16378296A>C						CLCNKB_ENST00000375667.3_Silent_p.P294P	p.P463P	NM_000085.4	NP_000076.2				UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Colorectal(212;8.04e-08)|COAD - Colon adenocarcinoma(227;5.46e-06)|BRCA - Breast invasive adenocarcinoma(304;9.02e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.00655)|READ - Rectum adenocarcinoma(331;0.0649)	14	1500	+		Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)						B3KUY3|Q5T5Q7|Q5T5Q8	Silent	SNP	ENST00000375679.4	37	c.1389A>C	CCDS168.1																																																																																				0.622	CLCNKB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026331.1	NM_000085		6	96	0	0	0	1	0	6	96				
USP6	9098	broad.mit.edu	37	17	5042837	5042837	+	Missense_Mutation	SNP	C	C	T	rs61745111	byFrequency	TCGA-EL-A3ZQ-01A-11D-A23M-08	TCGA-EL-A3ZQ-11A-11D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4694460d-de2a-4b9e-9391-dc57816752bf	a51fd081-0952-40bf-8412-b293d88100dc	g.chr17:5042837C>T	ENST00000574788.1	+	22	3596	c.1366C>T	c.(1366-1368)Cgg>Tgg	p.R456W	USP6_ENST00000332776.4_Missense_Mutation_p.R456W|USP6_ENST00000304328.5_Missense_Mutation_p.R139W|USP6_ENST00000250066.6_Missense_Mutation_p.R456W			P35125	UBP6_HUMAN	ubiquitin specific peptidase 6	456					cellular protein modification process (GO:0006464)|protein deubiquitination (GO:0016579)|regulation of vesicle-mediated transport (GO:0060627)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	calmodulin binding (GO:0005516)|cysteine-type endopeptidase activity (GO:0004197)|nucleic acid binding (GO:0003676)|Rab GTPase activator activity (GO:0005097)|ubiquitin-specific protease activity (GO:0004843)	p.R456W(1)		breast(2)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(4)|lung(15)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	34						GTCAATGCCCCGGCTCCCAAC	0.612			T	"""COL1A1, CDH11, ZNF9, OMD"""	aneurysmal bone cysts								C|||	509	0.101637	0.1982	0.0375	5008	,	,		18531	0.0784		0.1153	False		,,,				2504	0.0266					ENST00000574788.1				Dom	yes		17	17p13	9098	T	ubiquitin specific peptidase 6 (Tre-2 oncogene)			M	"""COL1A1, CDH11, ZNF9, OMD"""		aneurysmal bone cysts		1	Substitution - Missense(1)	p.R456W(1)	lung(1)	breast(2)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(4)|lung(15)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	34						c.(1366-1368)Cgg>Tgg		ubiquitin specific peptidase 6 (Tre-2 oncogene)		C	TRP/ARG	710,3696	291.3+/-281.4	62,586,1555	51.0	59.0	56.0		1366	-0.5	0.0	17	dbSNP_129	56	951,7649	208.3+/-249.8	52,847,3401	yes	missense	USP6	NM_004505.2	101	114,1433,4956	TT,TC,CC		11.0581,16.1144,12.771	benign	456/1407	5042837	1661,11345	2203	4300	6503	SO:0001583	missense	9098				protein deubiquitination|regulation of vesicle-mediated transport|ubiquitin-dependent protein catabolic process	lysosome|plasma membrane|recycling endosome	calmodulin binding|cysteine-type endopeptidase activity|nucleic acid binding|protein binding|Rab GTPase activator activity|ubiquitin thiolesterase activity|ubiquitin-specific protease activity	g.chr17:5042837C>T	X63547	CCDS11069.2	17p13	2014-06-12	2014-06-12		ENSG00000129204	ENSG00000129204	3.4.19.12	"""Ubiquitin-specific peptidases"""	12629	protein-coding gene	gene with protein product	"""ubiquitin carboxyl-terminal hydrolase 6"", ""TBC1D3 and USP32 fusion"", ""Tre-2 oncogene"""	604334	"""ubiquitin specific protease 6 (Tre-2 oncogene)"", ""TRE oncogene, Smith Magenis syndrome chromosome region"", ""ubiquitin specific peptidase 6 (Tre-2 oncogene)"""	HRP1, TRESMCR		12838346, 1349106	Standard	NM_004505		Approved	Tre-2, TRE17, Tre2	uc002gav.1	P35125	OTTHUMG00000099449	ENST00000574788.1:c.1366C>T	17.37:g.5042837C>T	ENSP00000460380:p.Arg456Trp					USP6_ENST00000250066.6_Missense_Mutation_p.R456W|USP6_ENST00000304328.5_Missense_Mutation_p.R139W|USP6_ENST00000332776.4_Missense_Mutation_p.R456W	p.R456W			P35125	UBP6_HUMAN			22	3596	+			456					Q15634|Q86WP6|Q8IWT4	Missense_Mutation	SNP	ENST00000574788.1	37	c.1366C>T	CCDS11069.2	250	0.11446886446886446	97	0.19715447154471544	16	0.04419889502762431	52	0.09090909090909091	85	0.11213720316622691	C	1.018	-0.685710	0.03328	0.161144	0.110581	ENSG00000129204	ENST00000332776;ENST00000250066;ENST00000304328	T;T;T	0.25749	2.19;2.68;1.78	0.266	-0.532	0.11890	.	0.290613	0.37012	N	0.002286	T	0.00012	0.0000	N	0.24115	0.695	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.38373	-0.9664	8	0.87932	D	0	.	.	.	.	rs61745111	139;456	P35125-2;P35125	.;UBP6_HUMAN	W	456;456;139	ENSP00000328010:R456W;ENSP00000250066:R456W;ENSP00000305473:R139W	ENSP00000250066:R456W	R	+	1	2	USP6	4983561	0.025000	0.19082	0.000000	0.03702	0.000000	0.00434	-1.254000	0.02874	-2.211000	0.00737	-2.287000	0.00268	CGG		0.612	USP6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438990.1	NM_004505		5	72	0	0	0	1	0	5	72				
DNAJC12	56521	broad.mit.edu	37	10	69556970	69556970	+	Splice_Site	SNP	T	T	C			TCGA-EL-A3ZQ-01A-11D-A23M-08	TCGA-EL-A3ZQ-11A-11D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4694460d-de2a-4b9e-9391-dc57816752bf	a51fd081-0952-40bf-8412-b293d88100dc	g.chr10:69556970T>C	ENST00000225171.2	-	5	655		c.e5-2		DNAJC12_ENST00000483798.2_Splice_Site	NM_021800.2	NP_068572.1	Q9UKB3	DJC12_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 12											breast(2)|kidney(2)|large_intestine(1)|lung(6)|upper_aerodigestive_tract(1)	12						CTGCAAAACCTTTAAAGGAAA	0.378																																						ENST00000225171.2																			0				breast(2)|kidney(2)|large_intestine(1)|lung(6)|upper_aerodigestive_tract(1)	12						c.e5-2		DnaJ (Hsp40) homolog, subfamily C, member 12							52.0	50.0	51.0					10																	69556970		2203	4300	6503	SO:0001630	splice_region_variant	56521				protein folding		heat shock protein binding|unfolded protein binding	g.chr10:69556970T>C	AF176012	CCDS7271.1, CCDS7272.1	10q21.3	2011-09-02			ENSG00000108176	ENSG00000108176		"""Heat shock proteins / DNAJ (HSP40)"""	28908	protein-coding gene	gene with protein product	"""J domain protein 1"""	606060				10760603	Standard	NM_021800		Approved	JDP1	uc001jnb.3	Q9UKB3	OTTHUMG00000018339	ENST00000225171.2:c.503-2A>G	10.37:g.69556970T>C						DNAJC12_ENST00000483798.2_Splice_Site		NM_021800.2	NP_068572.1	Q9UKB3	DJC12_HUMAN			5	655	-								Q5JVQ1|Q9UKB2	Splice_Site	SNP	ENST00000225171.2	37		CCDS7271.1	.	.	.	.	.	.	.	.	.	.	T	9.862	1.196580	0.22037	.	.	ENSG00000108176	ENST00000225171	.	.	.	5.49	3.06	0.35304	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	0.999999	.	.	.	.	.	.	.	.	.	.	.	.	.	.	7.1003	0.25333	0.1469:0.0:0.1539:0.6992	.	.	.	.	.	-1	.	.	.	-	.	.	DNAJC12	69226976	0.887000	0.30362	0.001000	0.08648	0.020000	0.10135	2.209000	0.42806	0.418000	0.25898	0.533000	0.62120	.		0.378	DNAJC12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048291.1	NM_021800	Intron	9	12	0	0	0	1	0	9	12				
DAXX	1616	broad.mit.edu	37	6	33287900	33287900	+	Silent	SNP	C	C	T			TCGA-EL-A3ZQ-01A-11D-A23M-08	TCGA-EL-A3ZQ-11A-11D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4694460d-de2a-4b9e-9391-dc57816752bf	a51fd081-0952-40bf-8412-b293d88100dc	g.chr6:33287900C>T	ENST00000374542.5	-	5	1557	c.1353G>A	c.(1351-1353)gaG>gaA	p.E451E	DAXX_ENST00000477162.1_5'UTR|DAXX_ENST00000266000.6_Silent_p.E451E|DAXX_ENST00000414083.2_Silent_p.E376E|ZBTB22_ENST00000418724.1_5'Flank|ZBTB22_ENST00000431845.2_5'Flank	NM_001141969.1|NM_001141970.1|NM_001350.4	NP_001135441.1|NP_001135442.1|NP_001341.1	Q9UER7	DAXX_HUMAN	death-domain associated protein	451	Asp/Glu-rich (acidic).|Necessary for interaction with USP7.				activation of JUN kinase activity (GO:0007257)|androgen receptor signaling pathway (GO:0030521)|apoptotic process (GO:0006915)|chromatin remodeling (GO:0006338)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|mitotic cytokinesis (GO:0000281)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of neuron death (GO:1901216)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein phosphorylation (GO:0001934)|regulation of protein ubiquitination (GO:0031396)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|heterochromatin (GO:0000792)|nucleus (GO:0005634)|PML body (GO:0016605)|SWI/SNF superfamily-type complex (GO:0070603)	androgen receptor binding (GO:0050681)|enzyme binding (GO:0019899)|heat shock protein binding (GO:0031072)|histone binding (GO:0042393)|p53 binding (GO:0002039)|protein homodimerization activity (GO:0042803)|protein kinase activator activity (GO:0030295)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|receptor signaling protein activity (GO:0005057)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)	p.E451E(2)		breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(2)|lung(7)|ovary(3)|pancreas(18)|prostate(3)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	55						cttcttcttcctcctcctcct	0.557			"""Mis, F, N"""		Pancreatic neuroendocrine tumors. Paediatric GBM																																	ENST00000374542.5				Rec	yes		6	6p21.3	1616	"""Mis, F, N"""	death-domain associated protein			E			Pancreatic neuroendocrine tumors. Paediatric GBM		2	Substitution - coding silent(2)	p.E451E(2)	prostate(1)|kidney(1)	breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(2)|lung(7)|ovary(3)|pancreas(18)|prostate(3)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	55						c.(1351-1353)gaG>gaA		death-domain associated protein							127.0	100.0	109.0					6																	33287900		2203	4300	6503	SO:0001819	synonymous_variant	1616				activation of JUN kinase activity|androgen receptor signaling pathway|apoptosis|induction of apoptosis via death domain receptors|interspecies interaction between organisms|negative regulation of transcription, DNA-dependent|regulation of protein ubiquitination|transcription, DNA-dependent	chromosome, centromeric region|cytosol|nucleolus|PML body	androgen receptor binding|heat shock protein binding|p53 binding|protein homodimerization activity|protein N-terminus binding|receptor signaling protein activity|transcription factor binding|ubiquitin protein ligase binding	g.chr6:33287900C>T	AF006041	CCDS4776.1, CCDS59008.1	6p21.3	2008-08-29	2008-08-29			ENSG00000204209			2681	protein-coding gene	gene with protein product		603186	"""death-associated protein 6"""			9407001, 9215629	Standard	NM_001141970		Approved	DAP6	uc011dre.2	Q9UER7		ENST00000374542.5:c.1353G>A	6.37:g.33287900C>T						DAXX_ENST00000477162.1_5'UTR|DAXX_ENST00000266000.6_Silent_p.E451E|DAXX_ENST00000414083.2_Silent_p.E376E	p.E451E	NM_001141969.1|NM_001141970.1|NM_001350.4	NP_001135441.1|NP_001135442.1|NP_001341.1	Q9UER7	DAXX_HUMAN			5	1557	-			451			Asp/Glu-rich (acidic).|Necessary for interaction with USP7.		B4E1I3|F5H082|O14747|O15141|O15208|Q5STK9|Q9BWI3	Silent	SNP	ENST00000374542.5	37	c.1353G>A	CCDS4776.1																																																																																				0.557	DAXX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076403.1			4	44	0	0	0	1	0	4	44				
USH1G	124590	broad.mit.edu	37	17	72916218	72916218	+	Missense_Mutation	SNP	C	C	T			TCGA-EL-A3ZQ-01A-11D-A23M-08	TCGA-EL-A3ZQ-11A-11D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4694460d-de2a-4b9e-9391-dc57816752bf	a51fd081-0952-40bf-8412-b293d88100dc	g.chr17:72916218C>T	ENST00000319642.1	-	2	895	c.713G>A	c.(712-714)cGc>cAc	p.R238H		NM_001282489.1|NM_173477.2	NP_001269418.1|NP_775748.2	Q495M9	USH1G_HUMAN	Usher syndrome 1G (autosomal recessive)	238					equilibrioception (GO:0050957)|inner ear morphogenesis (GO:0042472)|inner ear receptor cell differentiation (GO:0060113)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	spectrin binding (GO:0030507)		HN1/USH1G(2)	endometrium(1)|kidney(1)|large_intestine(4)|lung(4)|prostate(1)|skin(3)	14	all_lung(278;0.172)|Lung NSC(278;0.207)					GGCGCTCTTGCGCCCATCCTC	0.687																																						ENST00000319642.1																		HN1/USH1G(2)	0				endometrium(1)|kidney(1)|large_intestine(4)|lung(4)|prostate(1)|skin(3)	14						c.(712-714)cGc>cAc		Usher syndrome 1G (autosomal recessive)							38.0	43.0	42.0					17																	72916218		2198	4279	6477	SO:0001583	missense	124590				equilibrioception|photoreceptor cell maintenance|sensory perception of sound	actin cytoskeleton		g.chr17:72916218C>T	AK091243	CCDS32725.1	17q25.1	2013-01-10			ENSG00000182040	ENSG00000182040		"""Sterile alpha motif (SAM) domain containing"", ""Ankyrin repeat domain containing"""	16356	protein-coding gene	gene with protein product		607696				12588794	Standard	NM_001282489		Approved	Sans, FLJ33924, ANKS4A	uc002jme.1	Q495M9	OTTHUMG00000178864	ENST00000319642.1:c.713G>A	17.37:g.72916218C>T	ENSP00000320076:p.Arg238His						p.R238H	NM_173477.2	NP_775748.2	Q495M9	USH1G_HUMAN			2	895	-	all_lung(278;0.172)|Lung NSC(278;0.207)		238					Q8N251	Missense_Mutation	SNP	ENST00000319642.1	37	c.713G>A	CCDS32725.1	.	.	.	.	.	.	.	.	.	.	C	23.9	4.472612	0.84640	.	.	ENSG00000182040	ENST00000319642	T	0.74209	-0.82	3.68	3.68	0.42216	.	0.000000	0.85682	D	0.000000	D	0.83547	0.5278	M	0.61703	1.905	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	D	0.85180	0.1003	10	0.52906	T	0.07	-25.7575	15.9969	0.80256	0.0:1.0:0.0:0.0	.	238	Q495M9	USH1G_HUMAN	H	238	ENSP00000320076:R238H	ENSP00000320076:R238H	R	-	2	0	USH1G	70427813	1.000000	0.71417	1.000000	0.80357	0.781000	0.44180	7.604000	0.82830	2.075000	0.62263	0.485000	0.47835	CGC		0.687	USH1G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443676.1	NM_173477		7	104	0	0	0	1	0	7	104				
U2AF2	11338	broad.mit.edu	37	19	56171880	56171880	+	Splice_Site	SNP	A	A	C			TCGA-EL-A3ZQ-01A-11D-A23M-08	TCGA-EL-A3ZQ-11A-11D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4694460d-de2a-4b9e-9391-dc57816752bf	a51fd081-0952-40bf-8412-b293d88100dc	g.chr19:56171880A>C	ENST00000308924.4	+	4	270		c.e4-1		U2AF2_ENST00000590551.1_5'Flank|CTD-2537I9.12_ENST00000585940.1_RNA|CTD-2537I9.12_ENST00000589456.1_RNA|U2AF2_ENST00000450554.2_Splice_Site			P26368	U2AF2_HUMAN	U2 small nuclear RNA auxiliary factor 2						gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	enzyme binding (GO:0019899)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.?(2)		biliary_tract(1)|central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)|urinary_tract(2)	21		Colorectal(82;0.00244)|Ovarian(87;0.133)	BRCA - Breast invasive adenocarcinoma(297;0.18)	GBM - Glioblastoma multiforme(193;0.107)		CACCTCCCCCAGTCGTTCCCC	0.637																																						ENST00000450554.2																			2	Unknown(2)	p.?(2)	prostate(1)|central_nervous_system(1)	biliary_tract(1)|central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)|urinary_tract(2)	21						c.e4-1		U2 small nuclear RNA auxiliary factor 2							28.0	26.0	27.0					19																	56171880		2203	4300	6503	SO:0001630	splice_region_variant	11338				mRNA 3'-end processing|mRNA export from nucleus|termination of RNA polymerase II transcription	nucleoplasm|spliceosomal complex	enzyme binding|nucleotide binding|RNA binding	g.chr19:56171880A>C	BC008740	CCDS12933.1, CCDS46197.1	19q13.43	2014-09-17	2006-04-11			ENSG00000063244		"""RNA binding motif (RRM) containing"""	23156	protein-coding gene	gene with protein product	"""U2 small nuclear ribonucleoprotein auxiliary factor (65kD)"", ""splicing factor U2AF 65 kD subunit"", ""U2 snRNP auxiliary factor large subunit"""	191318	"""U2 (RNU2) small nuclear RNA auxiliary factor 2"""			1538748	Standard	XM_006722994		Approved	U2AF65	uc002qlu.3	P26368		ENST00000308924.4:c.231-1A>C	19.37:g.56171880A>C						U2AF2_ENST00000308924.4_Splice_Site		NM_001012478.1|NM_007279.2	NP_001012496.1|NP_009210.1	P26368	U2AF2_HUMAN	BRCA - Breast invasive adenocarcinoma(297;0.18)	GBM - Glioblastoma multiforme(193;0.107)	4	1189	+		Colorectal(82;0.00244)|Ovarian(87;0.133)						Q96HC5	Splice_Site	SNP	ENST00000308924.4	37		CCDS12933.1	.	.	.	.	.	.	.	.	.	.	-	17.96	3.515229	0.64634	.	.	ENSG00000063244	ENST00000308924;ENST00000450554	.	.	.	3.61	3.61	0.41365	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.1346	0.42699	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	U2AF2	60863692	1.000000	0.71417	0.999000	0.59377	0.994000	0.84299	8.427000	0.90275	1.646000	0.50622	0.387000	0.25754	.		0.637	U2AF2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000453599.1	NM_007279	Intron	4	11	0	0	0	1	0	4	11				
NTNG1	22854	broad.mit.edu	37	1	107867092	107867092	+	Silent	SNP	A	A	C			TCGA-EL-A3ZQ-01A-11D-A23M-08	TCGA-EL-A3ZQ-11A-11D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4694460d-de2a-4b9e-9391-dc57816752bf	a51fd081-0952-40bf-8412-b293d88100dc	g.chr1:107867092A>C	ENST00000370068.1	+	3	1281	c.435A>C	c.(433-435)acA>acC	p.T145T	NTNG1_ENST00000370072.3_Silent_p.T145T|NTNG1_ENST00000370071.2_Silent_p.T145T|NTNG1_ENST00000370065.1_Silent_p.T145T|NTNG1_ENST00000370074.4_Silent_p.T145T|NTNG1_ENST00000477948.1_3'UTR|NTNG1_ENST00000370073.2_Silent_p.T145T|NTNG1_ENST00000370067.1_Silent_p.T145T|NTNG1_ENST00000370070.2_Silent_p.T145T|NTNG1_ENST00000542803.1_Silent_p.T145T|NTNG1_ENST00000370061.3_Silent_p.T145T|NTNG1_ENST00000370066.1_Silent_p.T145T			Q9Y2I2	NTNG1_HUMAN	netrin G1	145	Laminin N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00466}.				axonogenesis (GO:0007409)	anchored component of plasma membrane (GO:0046658)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(8)|liver(1)|lung(15)|ovary(2)|prostate(2)|skin(3)|soft_tissue(1)|urinary_tract(1)	37		all_epithelial(167;1.39e-05)|all_lung(203;0.000115)|Lung NSC(277;0.000238)|Breast(1374;0.243)		Lung(183;0.0946)|BRCA - Breast invasive adenocarcinoma(282;0.237)|Epithelial(280;0.245)		TTGAGCTAACAGACAACATAG	0.463																																						ENST00000370067.1																			0				NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(8)|liver(1)|lung(15)|ovary(2)|prostate(2)|skin(3)|soft_tissue(1)|urinary_tract(1)	37						c.(433-435)acA>acC		netrin G1							101.0	105.0	103.0					1																	107867092		2203	4299	6502	SO:0001819	synonymous_variant	22854				axonogenesis	anchored to plasma membrane	protein binding	g.chr1:107867092A>C	AB023193	CCDS30785.1, CCDS44179.1, CCDS44180.1	1p13.2-p13.1	2013-03-01			ENSG00000162631	ENSG00000162631		"""Netrins"""	23319	protein-coding gene	gene with protein product	"""netrin G1f"", ""Netrin-G1"""	608818				10964959	Standard	NM_001113226		Approved	KIAA0976, Lmnt1	uc001dvh.4	Q9Y2I2	OTTHUMG00000010965	ENST00000370068.1:c.435A>C	1.37:g.107867092A>C						NTNG1_ENST00000370061.3_Silent_p.T145T|NTNG1_ENST00000370065.1_Silent_p.T145T|NTNG1_ENST00000370070.2_Silent_p.T145T|NTNG1_ENST00000370071.2_Silent_p.T145T|NTNG1_ENST00000477948.1_3'UTR|NTNG1_ENST00000370066.1_Silent_p.T145T|NTNG1_ENST00000370072.3_Silent_p.T145T|NTNG1_ENST00000370074.4_Silent_p.T145T|NTNG1_ENST00000542803.1_Silent_p.T145T|NTNG1_ENST00000370068.1_Silent_p.T145T|NTNG1_ENST00000370073.2_Silent_p.T145T	p.T145T			Q9Y2I2	NTNG1_HUMAN		Lung(183;0.0946)|BRCA - Breast invasive adenocarcinoma(282;0.237)|Epithelial(280;0.245)	3	1062	+		all_epithelial(167;1.39e-05)|all_lung(203;0.000115)|Lung NSC(277;0.000238)|Breast(1374;0.243)	145			Laminin N-terminal.		Q5VU86|Q5VU87|Q5VU89|Q5VU90|Q5VU91|Q7Z2Y3|Q8N633	Silent	SNP	ENST00000370068.1	37	c.435A>C	CCDS44180.1																																																																																				0.463	NTNG1-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000030340.1	NM_014917		29	51	0	0	0	1	0	29	51				
SMCR8	140775	broad.mit.edu	37	17	18219366	18219366	+	Missense_Mutation	SNP	A	A	G			TCGA-EL-A3ZQ-01A-11D-A23M-08	TCGA-EL-A3ZQ-11A-11D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4694460d-de2a-4b9e-9391-dc57816752bf	a51fd081-0952-40bf-8412-b293d88100dc	g.chr17:18219366A>G	ENST00000406438.3	+	1	743	c.263A>G	c.(262-264)aAt>aGt	p.N88S	TOP3A_ENST00000582230.1_5'Flank|TOP3A_ENST00000321105.5_5'Flank|TOP3A_ENST00000542570.1_5'Flank	NM_144775.2	NP_658988.2	Q8TEV9	SMCR8_HUMAN	Smith-Magenis syndrome chromosome region, candidate 8	88						nucleus (GO:0005634)		p.N88S(1)		breast(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(1)|lung(7)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	21						TTTGATCTCAATTACTTCTCC	0.507																																						ENST00000406438.3																			1	Substitution - Missense(1)	p.N88S(1)	kidney(1)	breast(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(1)|lung(7)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	21						c.(262-264)aAt>aGt		Smith-Magenis syndrome chromosome region, candidate 8							204.0	186.0	192.0					17																	18219366		2203	4300	6503	SO:0001583	missense	140775							g.chr17:18219366A>G	AF467440	CCDS11195.2	17p11.2	2014-06-12			ENSG00000176994	ENSG00000176994			17921	protein-coding gene	gene with protein product						11997338, 23248642	Standard	NM_144775		Approved	FLJ34716	uc002gsy.4	Q8TEV9	OTTHUMG00000059394	ENST00000406438.3:c.263A>G	17.37:g.18219366A>G	ENSP00000385025:p.Asn88Ser						p.N88S	NM_144775.2	NP_658988.2	Q8TEV9	SMCR8_HUMAN			1	743	+			88					A5PKZ5|Q3ZCN0|Q6PJL3	Missense_Mutation	SNP	ENST00000406438.3	37	c.263A>G	CCDS11195.2	.	.	.	.	.	.	.	.	.	.	A	18.77	3.695730	0.68386	.	.	ENSG00000176994	ENST00000406438	T	0.29655	1.56	5.81	5.81	0.92471	.	0.000000	0.85682	D	0.000000	T	0.52058	0.1711	L	0.54323	1.7	0.58432	D	0.999999	D	0.89917	1.0	D	0.87578	0.998	T	0.51156	-0.8741	10	0.56958	D	0.05	-16.7337	16.1605	0.81700	1.0:0.0:0.0:0.0	.	88	Q8TEV9	SMCR8_HUMAN	S	88	ENSP00000385025:N88S	ENSP00000385025:N88S	N	+	2	0	SMCR8	18160091	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.829000	0.92055	2.220000	0.72140	0.533000	0.62120	AAT		0.507	SMCR8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132065.2	NM_144775		69	111	0	0	0	1	0	69	111				
DIP2C	22982	broad.mit.edu	37	10	459978	459978	+	Missense_Mutation	SNP	C	C	G			TCGA-EL-A3ZQ-01A-11D-A23M-08	TCGA-EL-A3ZQ-11A-11D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4694460d-de2a-4b9e-9391-dc57816752bf	a51fd081-0952-40bf-8412-b293d88100dc	g.chr10:459978C>G	ENST00000280886.6	-	8	1019	c.932G>C	c.(931-933)gGc>gCc	p.G311A	DIP2C_ENST00000381496.3_Missense_Mutation_p.G204A	NM_014974.2	NP_055789.1	Q9Y2E4	DIP2C_HUMAN	DIP2 disco-interacting protein 2 homolog C (Drosophila)	311						nucleus (GO:0005634)	catalytic activity (GO:0003824)			breast(8)|endometrium(6)|kidney(10)|large_intestine(13)|lung(26)|ovary(3)|prostate(6)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(4)	81		all_cancers(4;0.00336)|all_lung(4;0.00732)|Lung NSC(4;0.00785)|all_epithelial(10;0.0159)|Colorectal(49;0.235)	OV - Ovarian serous cystadenocarcinoma(33;0.136)	Epithelial(11;0.0123)|all cancers(11;0.0467)|Lung(33;0.0864)|OV - Ovarian serous cystadenocarcinoma(14;0.106)		CGTGACCACGCCCAGCTGCTC	0.627																																						ENST00000280886.6																			0				breast(8)|endometrium(6)|kidney(10)|large_intestine(13)|lung(26)|ovary(3)|prostate(6)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(4)	81						c.(931-933)gGc>gCc		DIP2 disco-interacting protein 2 homolog C (Drosophila)							49.0	52.0	51.0					10																	459978		2203	4299	6502	SO:0001583	missense	22982					nucleus	catalytic activity|transcription factor binding	g.chr10:459978C>G	BC035216	CCDS7054.1	10p15.3	2006-01-13	2006-01-13	2006-01-13	ENSG00000151240	ENSG00000151240			29150	protein-coding gene	gene with protein product		611380	"""KIAA0934"""	KIAA0934			Standard	NM_014974		Approved		uc001ifp.3	Q9Y2E4	OTTHUMG00000017532	ENST00000280886.6:c.932G>C	10.37:g.459978C>G	ENSP00000280886:p.Gly311Ala					DIP2C_ENST00000381496.3_Missense_Mutation_p.G204A	p.G311A	NM_014974.2	NP_055789.1	Q9Y2E4	DIP2C_HUMAN	OV - Ovarian serous cystadenocarcinoma(33;0.136)	Epithelial(11;0.0123)|all cancers(11;0.0467)|Lung(33;0.0864)|OV - Ovarian serous cystadenocarcinoma(14;0.106)	8	1019	-		all_cancers(4;0.00336)|all_lung(4;0.00732)|Lung NSC(4;0.00785)|all_epithelial(10;0.0159)|Colorectal(49;0.235)	311					B4DPI5|Q5SS78	Missense_Mutation	SNP	ENST00000280886.6	37	c.932G>C	CCDS7054.1	.	.	.	.	.	.	.	.	.	.	C	12.54	1.969294	0.34754	.	.	ENSG00000151240	ENST00000280886;ENST00000381496	T;T	0.45668	0.89;0.89	5.22	5.22	0.72569	.	0.000000	0.85682	D	0.000000	T	0.40546	0.1121	L	0.58428	1.81	0.80722	D	1	B;B	0.17038	0.02;0.0	B;B	0.16722	0.016;0.001	T	0.37291	-0.9712	10	0.08599	T	0.76	-26.2516	18.7949	0.91990	0.0:1.0:0.0:0.0	.	204;311	E7EPU2;Q9Y2E4	.;DIP2C_HUMAN	A	311;204	ENSP00000280886:G311A;ENSP00000370907:G204A	ENSP00000280886:G311A	G	-	2	0	DIP2C	449978	1.000000	0.71417	0.948000	0.38648	0.303000	0.27691	7.776000	0.85560	2.427000	0.82271	0.655000	0.94253	GGC		0.627	DIP2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046389.1	NM_014974		27	76	0	0	0	1	0	27	76				
BRAF	673	broad.mit.edu	37	7	140453136	140453136	+	Missense_Mutation	SNP	A	A	T	rs121913377|rs113488022|rs121913227|rs397516897		TCGA-EL-A3ZQ-01A-11D-A23M-08	TCGA-EL-A3ZQ-11A-11D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4694460d-de2a-4b9e-9391-dc57816752bf	a51fd081-0952-40bf-8412-b293d88100dc	g.chr7:140453136A>T	ENST00000288602.6	-	15	1859	c.1799T>A	c.(1798-1800)gTg>gAg	p.V600E		NM_004333.4	NP_004324.2	P15056	BRAF_HUMAN	B-Raf proto-oncogene, serine/threonine kinase	600	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		V -> D (in a melanoma cell line; requires 2 nucleotide substitutions). {ECO:0000269|PubMed:12068308}.|V -> E (in CRC; also found in sarcoma, metastatic melanoma, ovarian serous carcinoma, pilocytic astrocytoma; somatic mutation; most common mutation; constitutive and elevated kinase activity; efficiently induces cell transformation; suppression of mutation in melanoma causes growth arrest and promotes apoptosis; loss of regulation by PMRT5). {ECO:0000269|PubMed:12068308, ECO:0000269|PubMed:12198537, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:23263490, ECO:0000269|PubMed:24455489}.		activation of MAPKK activity (GO:0000186)|CD4-positive, alpha-beta T cell differentiation (GO:0043367)|cellular response to calcium ion (GO:0071277)|cellular response to drug (GO:0035690)|fibroblast growth factor receptor signaling pathway (GO:0008543)|long-term synaptic potentiation (GO:0060291)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of fibroblast migration (GO:0010764)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of synaptic vesicle exocytosis (GO:2000301)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of gene expression (GO:0010628)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive T cell selection (GO:0043368)|protein heterooligomerization (GO:0051291)|protein phosphorylation (GO:0006468)|regulation of cell proliferation (GO:0042127)|response to cAMP (GO:0051591)|response to epidermal growth factor (GO:0070849)|response to peptide hormone (GO:0043434)|small GTPase mediated signal transduction (GO:0007264)|somatic stem cell maintenance (GO:0035019)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	cell body (GO:0044297)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.V600E(15453)|p.V600K(252)|p.V600R(44)|p.V600D(16)|p.V600A(12)|p.V600_K601>E(12)|p.V600G(11)|p.T599_R603>I(2)|p.V600Q(2)|p.V600_S605>EK(1)|p.V600_S605>DV(1)|p.V600_S605>D(1)|p.T599_V600insDFGLAT(1)	SLC45A3/BRAF(2)|AGTRAP/BRAF(2)|FAM131B_ENST00000443739/BRAF(7)|AKAP9_ENST00000356239/BRAF(10)|KIAA1549/BRAF(703)|FCHSD1/BRAF(2)	NS(588)|adrenal_gland(3)|autonomic_ganglia(3)|biliary_tract(29)|bone(7)|breast(21)|central_nervous_system(99)|cervix(6)|endometrium(33)|eye(72)|gastrointestinal_tract_(site_indeterminate)(2)|genital_tract(4)|haematopoietic_and_lymphoid_tissue(436)|kidney(3)|large_intestine(6953)|liver(17)|lung(192)|oesophagus(4)|ovary(275)|pancreas(15)|pituitary(1)|prostate(25)|salivary_gland(1)|skin(6285)|small_intestine(12)|soft_tissue(40)|stomach(11)|testis(7)|thyroid(12220)|upper_aerodigestive_tract(13)|urinary_tract(3)	27380	Melanoma(164;0.00956)				Dabrafenib(DB08912)|Regorafenib(DB08896)|Sorafenib(DB00398)|Vemurafenib(DB08881)	TCGAGATTTCACTGTAGCTAG	0.368	V600D(K029AX_SKIN)|V600D(WM115_SKIN)|V600D(WM2664_SKIN)|V600E(8505C_THYROID)|V600E(A101D_SKIN)|V600E(A2058_SKIN)|V600E(A375_SKIN)|V600E(A673_BONE)|V600E(AM38_CENTRAL_NERVOUS_SYSTEM)|V600E(BCPAP_THYROID)|V600E(BHT101_THYROID)|V600E(BT474_BREAST)|V600E(C32_SKIN)|V600E(CL34_LARGE_INTESTINE)|V600E(COLO205_LARGE_INTESTINE)|V600E(COLO679_SKIN)|V600E(COLO741_SKIN)|V600E(COLO783_SKIN)|V600E(COLO800_SKIN)|V600E(COLO818_SKIN)|V600E(COLO829_SKIN)|V600E(COLO849_SKIN)|V600E(DBTRG05MG_CENTRAL_NERVOUS_SYSTEM)|V600E(DU4475_BREAST)|V600E(ES2_OVARY)|V600E(G361_SKIN)|V600E(GCT_SOFT_TISSUE)|V600E(HS294T_SKIN)|V600E(HS695T_SKIN)|V600E(HS939T_SKIN)|V600E(IGR1_SKIN)|V600E(IGR37_SKIN)|V600E(IGR39_SKIN)|V600E(K029AX_SKIN)|V600E(KG1C_CENTRAL_NERVOUS_SYSTEM)|V600E(LOXIMVI_SKIN)|V600E(MALME3M_SKIN)|V600E(MELHO_SKIN)|V600E(OUMS23_LARGE_INTESTINE)|V600E(RKO_LARGE_INTESTINE)|V600E(RPMI7951_SKIN)|V600E(RVH421_SKIN)|V600E(SH4_SKIN)|V600E(SIGM5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|V600E(SKHEP1_LIVER)|V600E(SKMEL24_SKIN)|V600E(SKMEL28_SKIN)|V600E(SKMEL5_SKIN)|V600E(SW1417_LARGE_INTESTINE)|V600E(UACC257_SKIN)|V600E(UACC62_SKIN)|V600E(WM793_SKIN)|V600E(WM88_SKIN)|V600E(WM983B_SKIN)	61	"""Mis, T, O"""	"""AKAP9, KIAA1549"""	"""melanoma, colorectal, papillary thyroid, borderline ov, Non small-cell lung cancer (NSCLC), cholangiocarcinoma, pilocytic astrocytoma"""		Cardio-facio-cutaneous syndrome		Cardiofaciocutaneous syndrome																												Colon(40;35 892 2973 5743 27438)	ENST00000288602.6	V600D(K029AX_SKIN)|V600D(WM115_SKIN)|V600D(WM2664_SKIN)|V600E(8505C_THYROID)|V600E(A101D_SKIN)|V600E(A2058_SKIN)|V600E(A375_SKIN)|V600E(A673_BONE)|V600E(AM38_CENTRAL_NERVOUS_SYSTEM)|V600E(BCPAP_THYROID)|V600E(BHT101_THYROID)|V600E(BT474_BREAST)|V600E(C32_SKIN)|V600E(CL34_LARGE_INTESTINE)|V600E(COLO205_LARGE_INTESTINE)|V600E(COLO679_SKIN)|V600E(COLO741_SKIN)|V600E(COLO783_SKIN)|V600E(COLO800_SKIN)|V600E(COLO818_SKIN)|V600E(COLO829_SKIN)|V600E(COLO849_SKIN)|V600E(DBTRG05MG_CENTRAL_NERVOUS_SYSTEM)|V600E(DU4475_BREAST)|V600E(ES2_OVARY)|V600E(G361_SKIN)|V600E(GCT_SOFT_TISSUE)|V600E(HS294T_SKIN)|V600E(HS695T_SKIN)|V600E(HS939T_SKIN)|V600E(IGR1_SKIN)|V600E(IGR37_SKIN)|V600E(IGR39_SKIN)|V600E(K029AX_SKIN)|V600E(KG1C_CENTRAL_NERVOUS_SYSTEM)|V600E(LOXIMVI_SKIN)|V600E(MALME3M_SKIN)|V600E(MELHO_SKIN)|V600E(OUMS23_LARGE_INTESTINE)|V600E(RKO_LARGE_INTESTINE)|V600E(RPMI7951_SKIN)|V600E(RVH421_SKIN)|V600E(SH4_SKIN)|V600E(SIGM5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|V600E(SKHEP1_LIVER)|V600E(SKMEL24_SKIN)|V600E(SKMEL28_SKIN)|V600E(SKMEL5_SKIN)|V600E(SW1417_LARGE_INTESTINE)|V600E(UACC257_SKIN)|V600E(UACC62_SKIN)|V600E(WM793_SKIN)|V600E(WM88_SKIN)|V600E(WM983B_SKIN)	61		Dom	yes		7	7q34	673	"""Mis, T, O"""	v-raf murine sarcoma viral oncogene homolog B1	yes	Cardio-facio-cutaneous syndrome	E	"""AKAP9, KIAA1549"""		"""melanoma, colorectal, papillary thyroid, borderline ov, Non small-cell lung cancer (NSCLC), cholangiocarcinoma, pilocytic astrocytoma"""	SLC45A3/BRAF(2)|AGTRAP/BRAF(2)|FAM131B_ENST00000443739/BRAF(7)|AKAP9_ENST00000356239/BRAF(10)|KIAA1549/BRAF(703)|FCHSD1/BRAF(2)	15808	Substitution - Missense(15790)|Complex - deletion inframe(17)|Insertion - In frame(1)	p.V600E(15453)|p.V600K(252)|p.V600R(44)|p.V600D(16)|p.V600A(12)|p.V600_K601>E(12)|p.V600G(11)|p.T599_R603>I(2)|p.V600Q(2)|p.V600_S605>EK(1)|p.V600_S605>DV(1)|p.V600_S605>D(1)|p.T599_V600insDFGLAT(1)	thyroid(7476)|skin(3822)|large_intestine(3288)|NS(360)|haematopoietic_and_lymphoid_tissue(336)|ovary(211)|lung(58)|eye(57)|central_nervous_system(53)|soft_tissue(30)|biliary_tract(18)|liver(17)|prostate(13)|breast(10)|upper_aerodigestive_tract(9)|endometrium(8)|pancreas(8)|testis(7)|small_intestine(7)|genital_tract(4)|stomach(4)|bone(3)|autonomic_ganglia(2)|oesophagus(2)|urinary_tract(2)|adrenal_gland(2)|pituitary(1)	NS(588)|adrenal_gland(3)|autonomic_ganglia(3)|biliary_tract(29)|bone(7)|breast(21)|central_nervous_system(99)|cervix(6)|endometrium(33)|eye(72)|gastrointestinal_tract_(site_indeterminate)(2)|genital_tract(4)|haematopoietic_and_lymphoid_tissue(436)|kidney(3)|large_intestine(6953)|liver(17)|lung(192)|oesophagus(4)|ovary(275)|pancreas(15)|pituitary(1)|prostate(25)|salivary_gland(1)|skin(6285)|small_intestine(12)|soft_tissue(40)|stomach(11)|testis(7)|thyroid(12220)|upper_aerodigestive_tract(13)|urinary_tract(3)	27380						c.(1798-1800)gTg>gAg		v-raf murine sarcoma viral oncogene homolog B	Sorafenib(DB00398)						112.0	104.0	107.0					7																	140453136		2203	4300	6503	SO:0001583	missense	673	Cardiofaciocutaneous syndrome	Familial Cancer Database	CFC, CFCS	activation of MAPKK activity|anti-apoptosis|nerve growth factor receptor signaling pathway|organ morphogenesis|positive regulation of peptidyl-serine phosphorylation|small GTPase mediated signal transduction|synaptic transmission	cytosol|nucleus|plasma membrane	ATP binding|metal ion binding	g.chr7:140453136A>T	M95712	CCDS5863.1	7q34	2014-09-17	2014-06-26		ENSG00000157764	ENSG00000157764			1097	protein-coding gene	gene with protein product		164757	"""v-raf murine sarcoma viral oncogene homolog B"""			2284096, 1565476	Standard	NM_004333		Approved	BRAF1	uc003vwc.4	P15056	OTTHUMG00000157457	ENST00000288602.6:c.1799T>A	7.37:g.140453136A>T	ENSP00000288602:p.Val600Glu						p.V600E	NM_004333.4	NP_004324.2	P15056	BRAF_HUMAN			15	1859	-	Melanoma(164;0.00956)		600		V -> D (in a melanoma cell line; requires 2 nucleotide substitutions).|V -> E (in sarcoma, colorectal adenocarcinoma, metastatic melanoma, ovarian serous carcinoma, pilocytic astrocytoma; somatic mutation; most common mutation; constitutive and elevated kinase activity; efficiently induces cell transformation; suppression of mutation in melanoma causes growth arrest and promotes apoptosis).	Protein kinase.		A4D1T4|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q13878|Q3MIN6|Q9UDP8|Q9Y6T3	Missense_Mutation	SNP	ENST00000288602.6	37	c.1799T>A	CCDS5863.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	24.0|24.0	4.486113|4.486113	0.84854|0.84854	.|.	.|.	ENSG00000157764|ENSG00000157764	ENST00000288602|ENST00000496384	D|.	0.81739|.	-1.53|.	5.65|5.65	5.65|5.65	0.86999|0.86999	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|.	0.61565|.	0.2357|.	L|L	0.42245|0.42245	1.32|1.32	0.80722|0.80722	D|D	1|1	D|.	0.55385|.	0.971|.	D|.	0.66351|.	0.943|.	T|.	0.58160|.	-0.7685|.	10|.	0.87932|.	D|.	0|.	.|.	15.9326|15.9326	0.79675|0.79675	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	600|.	P15056|.	BRAF_HUMAN|.	E|R	600|208	ENSP00000288602:V600E|.	ENSP00000288602:V600E|.	V|X	-|-	2|1	0|0	BRAF|BRAF	140099605|140099605	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	9.197000|9.197000	0.94985|0.94985	2.169000|2.169000	0.68431|0.68431	0.529000|0.529000	0.55759|0.55759	GTG|TGA		0.368	BRAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348886.1	NM_004333		17	28	0	0	0	1	0	17	28				
FOLH1	2346	broad.mit.edu	37	11	49208318	49208318	+	Missense_Mutation	SNP	C	C	T			TCGA-EL-A3ZQ-01A-11D-A23M-08	TCGA-EL-A3ZQ-11A-11D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4694460d-de2a-4b9e-9391-dc57816752bf	a51fd081-0952-40bf-8412-b293d88100dc	g.chr11:49208318C>T	ENST00000256999.2	-	5	777	c.517G>A	c.(517-519)Gat>Aat	p.D173N	FOLH1_ENST00000343844.4_5'UTR|FOLH1_ENST00000533034.1_Missense_Mutation_p.D158N|FOLH1_ENST00000340334.7_Missense_Mutation_p.D158N|FOLH1_ENST00000356696.3_Missense_Mutation_p.D173N	NM_004476.1	NP_004467.1	Q04609	FOLH1_HUMAN	folate hydrolase (prostate-specific membrane antigen) 1	173					folic acid-containing compound metabolic process (GO:0006760)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	carboxypeptidase activity (GO:0004180)|dipeptidase activity (GO:0016805)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|peptidase activity (GO:0008233)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(7)|lung(34)|ovary(1)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	60					Capromab(DB00089)	TACACTAGATCGCCCTGTTGA	0.393																																						ENST00000340334.7																			0				NS(2)|breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(7)|lung(34)|ovary(1)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	60						c.(472-474)Gat>Aat		folate hydrolase (prostate-specific membrane antigen) 1	Capromab(DB00089)|L-Glutamic Acid(DB00142)						90.0	89.0	89.0					11																	49208318		2201	4298	6499	SO:0001583	missense	2346				proteolysis	cytoplasm|integral to plasma membrane|membrane fraction|nucleus	carboxypeptidase activity|dipeptidase activity|metal ion binding|metallopeptidase activity	g.chr11:49208318C>T	M99487	CCDS7946.1, CCDS31493.1, CCDS53626.1, CCDS53627.1, CCDS53628.1	11p11.2	2011-07-22			ENSG00000086205	ENSG00000086205	3.4.17.21		3788	protein-coding gene	gene with protein product	"""glutamate carboxylase II"", ""glutamate carboxypeptidase II"""	600934		FOLH		9838072	Standard	NM_001193472		Approved	PSM, PSMA, NAALAD1, NAALAdase, GCP2, GCPII	uc001ngy.3	Q04609	OTTHUMG00000166625	ENST00000256999.2:c.517G>A	11.37:g.49208318C>T	ENSP00000256999:p.Asp173Asn					FOLH1_ENST00000533034.1_Missense_Mutation_p.D158N|FOLH1_ENST00000256999.2_Missense_Mutation_p.D173N|FOLH1_ENST00000343844.4_5'UTR|FOLH1_ENST00000356696.3_Missense_Mutation_p.D173N	p.D158N	NM_001193471.1|NM_001193472.1	NP_001180400.1|NP_001180401.1	Q04609	FOLH1_HUMAN			6	840	-			173					A4UU12|A9CB79|B7Z312|B7Z343|D3DQS5|E9PDX8|O43748|Q16305|Q541A4|Q8TAY3|Q9NP15|Q9NYE2|Q9P1P8	Missense_Mutation	SNP	ENST00000256999.2	37	c.472G>A	CCDS7946.1	.	.	.	.	.	.	.	.	.	.	C	13.96	2.392086	0.42410	.	.	ENSG00000086205	ENST00000256999;ENST00000356696;ENST00000340334;ENST00000533034;ENST00000389724	T;T;T;T	0.06768	3.26;3.26;3.26;3.26	3.05	3.05	0.35203	Protease-associated domain, PA (1);	0.236753	0.29266	N	0.012650	T	0.09555	0.0235	L	0.52266	1.64	0.80722	D	1	B;B;B;B	0.25169	0.119;0.04;0.06;0.002	B;B;B;B	0.25759	0.063;0.021;0.039;0.003	T	0.11494	-1.0585	10	0.46703	T	0.11	.	11.9601	0.53003	0.0:1.0:0.0:0.0	.	158;158;173;173	Q04609-9;Q04609-7;Q04609-8;Q04609	.;.;.;FOLH1_HUMAN	N	173;173;158;158;173	ENSP00000256999:D173N;ENSP00000349129:D173N;ENSP00000344131:D158N;ENSP00000431463:D158N	ENSP00000256999:D173N	D	-	1	0	FOLH1	49164894	1.000000	0.71417	0.990000	0.47175	0.636000	0.38137	6.933000	0.75874	1.746000	0.51805	0.430000	0.28490	GAT		0.393	FOLH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390896.1	NM_004476		14	32	0	0	0	1	0	14	32				
ACSS3	79611	broad.mit.edu	37	12	81503376	81503376	+	Missense_Mutation	SNP	G	G	A	rs368706037		TCGA-EL-A3ZQ-01A-11D-A23M-08	TCGA-EL-A3ZQ-11A-11D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4694460d-de2a-4b9e-9391-dc57816752bf	a51fd081-0952-40bf-8412-b293d88100dc	g.chr12:81503376G>A	ENST00000548058.1	+	2	1259	c.349G>A	c.(349-351)Gtt>Att	p.V117I	RP11-543H12.1_ENST00000547123.1_RNA|ACSS3_ENST00000261206.3_Missense_Mutation_p.V116I			Q9H6R3	ACSS3_HUMAN	acyl-CoA synthetase short-chain family member 3	117						mitochondrion (GO:0005739)	acetate-CoA ligase activity (GO:0003987)|ATP binding (GO:0005524)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(5)|kidney(2)|large_intestine(7)|liver(3)|lung(20)|ovary(1)|skin(4)|upper_aerodigestive_tract(2)	51						TTACAATGCCGTTGATCGTCA	0.323																																						ENST00000548058.1																			0				NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(5)|kidney(2)|large_intestine(7)|liver(3)|lung(20)|ovary(1)|skin(4)|upper_aerodigestive_tract(2)	51						c.(349-351)Gtt>Att		acyl-CoA synthetase short-chain family member 3		G	ILE/VAL	1,4405	2.1+/-5.4	0,1,2202	108.0	106.0	107.0		349	0.4	1.0	12		107	0,8598		0,0,4299	no	missense	ACSS3	NM_024560.2	29	0,1,6501	AA,AG,GG		0.0,0.0227,0.0077	benign	117/687	81503376	1,13003	2203	4299	6502	SO:0001583	missense	79611					mitochondrion	acetate-CoA ligase activity|ATP binding	g.chr12:81503376G>A		CCDS9022.1	12q21.31	2014-08-08			ENSG00000111058	ENSG00000111058		"""Acyl-CoA synthetase family"""	24723	protein-coding gene	gene with protein product		614356				17762044	Standard	NM_024560		Approved	FLJ21963	uc001szl.1	Q9H6R3	OTTHUMG00000170179	ENST00000548058.1:c.349G>A	12.37:g.81503376G>A	ENSP00000449535:p.Val117Ile					ACSS3_ENST00000261206.3_Missense_Mutation_p.V116I|RP11-543H12.1_ENST00000547123.1_RNA	p.V117I			Q9H6R3	ACSS3_HUMAN			2	1259	+			117					Q8NC66	Missense_Mutation	SNP	ENST00000548058.1	37	c.349G>A	CCDS9022.1	.	.	.	.	.	.	.	.	.	.	G	11.49	1.655604	0.29425	2.27E-4	0.0	ENSG00000111058	ENST00000549175;ENST00000548058;ENST00000261206	T;T;T	0.47528	0.84;2.9;2.9	6.07	0.424	0.16468	Acyl-CoA synthase, domain of unknown function DUF3448 (1);	0.161948	0.53938	N	0.000060	T	0.27798	0.0684	N	0.21097	0.63	0.80722	D	1	B	0.11235	0.004	B	0.14578	0.011	T	0.03545	-1.1026	10	0.33940	T	0.23	-7.6977	6.4092	0.21682	0.4976:0.1319:0.3705:0.0	.	117	Q9H6R3	ACSS3_HUMAN	I	9;117;116	ENSP00000447748:V9I;ENSP00000449535:V117I;ENSP00000261206:V116I	ENSP00000261206:V116I	V	+	1	0	ACSS3	80027507	0.991000	0.36638	0.976000	0.42696	0.870000	0.49936	0.255000	0.18333	-0.119000	0.11830	-1.052000	0.02337	GTT		0.323	ACSS3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000407794.1	NM_024560		3	26	0	0	0	1	0	3	26				
MED15P9	285103	broad.mit.edu	37	2	130893080	130893081	+	RNA	INS	-	-	A			TCGA-EL-A3ZQ-01A-11D-A23M-08	TCGA-EL-A3ZQ-11A-11D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4694460d-de2a-4b9e-9391-dc57816752bf	a51fd081-0952-40bf-8412-b293d88100dc	g.chr2:130893080_130893081insA	ENST00000427638.1	+	0	541_542					NR_033903.1				mediator complex subunit 15 pseudogene 9																		gactccatctcaaaaaaaaaaa	0.564																																						ENST00000427638.1																			0																																																			0							g.chr2:130893080_130893081insA	BC036597		2q21.1	2014-05-06	2013-08-13	2013-08-13	ENSG00000223760	ENSG00000223760			44130	pseudogene	pseudogene			"""CCDC74B antisense RNA 1 (non-protein coding)"", ""CCDC74B antisense RNA 1"""	CCDC74B-AS1			Standard	NR_033903		Approved		uc021voa.1				2.37:g.130893091_130893091dupA								NR_033903.1						0	541_542	+									RNA	INS	ENST00000427638.1	37																																																																																						0.564	MED15P9-002	KNOWN	basic|exp_conf	processed_transcript	pseudogene	OTTHUMT00000470767.1	NR_033903		2	4						2	4	---	---	---	---
PCDHGB4	8641	broad.mit.edu	37	5	140767492	140767497	+	In_Frame_Del	DEL	TGCCAG	TGCCAG	-	rs145222727|rs370380135	byFrequency	TCGA-EL-A3ZQ-01A-11D-A23M-08	TCGA-EL-A3ZQ-11A-11D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4694460d-de2a-4b9e-9391-dc57816752bf	a51fd081-0952-40bf-8412-b293d88100dc	g.chr5:140767492_140767497delTGCCAG	ENST00000519479.1	+	1	41_46	c.41_46delTGCCAG	c.(40-48)ctgccagtg>ctg	p.PV15del	PCDHGA2_ENST00000394576.2_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGB1_ENST00000523390.1_Intron	NM_003736.2|NM_018925.2|NM_032098.1	NP_003727.1|NP_061748.1|NP_115269.1	Q9UN71	PCDGG_HUMAN	protocadherin gamma subfamily B, 4	15					calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.P15_V16delPV(1)		endometrium(9)|kidney(3)|large_intestine(4)|lung(14)|ovary(1)|prostate(1)|stomach(3)|urinary_tract(2)	37			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCTGAGAGGCTGCCAGTGCTCTTTCT	0.617											OREG0016859	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)		166	0.033147	0.0045	0.0476	5008	,	,		16199	0.0		0.0944	False		,,,				2504	0.0327					ENST00000519479.1																			1	Deletion - In frame(1)	p.P15_V16delPV(1)	prostate(1)	endometrium(9)|kidney(3)|large_intestine(4)|lung(14)|ovary(1)|prostate(1)|stomach(3)|urinary_tract(2)	37						c.(40-48)ctg>c					,,,,,,,,,,,	50,3074		6,38,1518					,,,,,,,,,,,	3.7	0.9		dbSNP_134	6	518,6570		64,390,3090	no	coding,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,coding	PCDHGB4,PCDHGB3,PCDHGB2,PCDHGB1,PCDHGA7,PCDHGA6,PCDHGA5,PCDHGA4,PCDHGA3,PCDHGA2,PCDHGA1	NM_032098.1,NM_018924.2,NM_018923.2,NM_018922.2,NM_018920.2,NM_018919.2,NM_018918.2,NM_018917.2,NM_018916.3,NM_018915.2,NM_018912.2,NM_003736.2	,,,,,,,,,,,	70,428,4608	A1A1,A1R,RR		7.3081,1.6005,5.5621	,,,,,,,,,,,	,,,,,,,,,,,		568,9644				SO:0001651	inframe_deletion	0							g.chr5:140767492_140767497delTGCCAG	AF152520	CCDS54928.1, CCDS75337.1	5q31	2010-01-26				ENSG00000253953		"""Cadherins / Protocadherins : Clustered"""	8711	other	protocadherin	"""fibroblast cadherin FIB2"", ""cadherin 20"""	603058				10380929	Standard	NM_003736		Approved	FIB2, CDH20, PCDH-GAMMA-B4		Q9UN71		ENST00000519479.1:c.41_46delTGCCAG	5.37:g.140767492_140767497delTGCCAG	ENSP00000428288:p.Pro15_Val16del		OREG0016859	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	1658	PCDHGA6_ENST00000517434.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA5_ENST00000518069.1_Intron	p.LPV14del	NM_003736.2|NM_018925.2|NM_032098.1	NP_003727.1|NP_061748.1|NP_115269.1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		1	41_46	+								O15099|Q2M267|Q9UN64	In_Frame_Del	DEL	ENST00000519479.1	37	c.41_46delTGCCAG	CCDS54928.1																																																																																				0.617	PCDHGB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374745.1	NM_003736		2	4						2	4	---	---	---	---
TG	7038	broad.mit.edu	37	8	133895206	133895207	+	Frame_Shift_Ins	INS	-	-	G			TCGA-EL-A3ZQ-01A-11D-A23M-08	TCGA-EL-A3ZQ-11A-11D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4694460d-de2a-4b9e-9391-dc57816752bf	a51fd081-0952-40bf-8412-b293d88100dc	g.chr8:133895206_133895207insG	ENST00000220616.4	+	8	1077_1078	c.1037_1038insG	c.(1036-1041)atgcatfs	p.H347fs	TG_ENST00000377869.1_Frame_Shift_Ins_p.H347fs	NM_003235.4	NP_003226.4	P01266	THYG_HUMAN	thyroglobulin	347	Thyroglobulin type-1 4. {ECO:0000255|PROSITE-ProRule:PRU00500}.				hormone biosynthetic process (GO:0042446)|iodide transport (GO:0015705)|regulation of myelination (GO:0031641)|signal transduction (GO:0007165)|thyroid gland development (GO:0030878)|thyroid hormone generation (GO:0006590)	extracellular region (GO:0005576)|extracellular space (GO:0005615)				NS(1)|breast(11)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(34)|liver(2)|lung(59)|ovary(9)|pancreas(2)|prostate(6)|skin(7)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(8)	168	Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)	Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0559)|Breast(495;0.0735)	BRCA - Breast invasive adenocarcinoma(115;0.000701)	KIRC - Kidney renal clear cell carcinoma(542;0.0546)		GGGAAGGAAATGCATGGAACCC	0.614																																						ENST00000220616.4																			0				NS(1)|breast(11)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(34)|liver(2)|lung(59)|ovary(9)|pancreas(2)|prostate(6)|skin(7)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(8)	168						c.(1036-1038)acafs		thyroglobulin																																				SO:0001589	frameshift_variant	7038				hormone biosynthetic process|signal transduction|thyroid gland development|thyroid hormone generation	extracellular space	hormone activity	g.chr8:133895206_133895207insG	AU141420	CCDS34944.1	8q24	2012-10-02			ENSG00000042832	ENSG00000042832			11764	protein-coding gene	gene with protein product		188450					Standard	NM_003235		Approved	TGN, AITD3	uc003ytw.3	P01266	OTTHUMG00000164649	ENST00000220616.4:c.1038dupG	8.37:g.133895207_133895207dupG	ENSP00000220616:p.His347fs					TG_ENST00000377869.1_Frame_Shift_Ins_p.T346fs	p.T346fs	NM_003235.4	NP_003226.4	P01266	THYG_HUMAN	BRCA - Breast invasive adenocarcinoma(115;0.000701)	KIRC - Kidney renal clear cell carcinoma(542;0.0546)	8	1077_1078	+	Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)	Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0559)|Breast(495;0.0735)	346			Thyroglobulin type-1 4.		O15274|O43899|Q15593|Q15948|Q9NYR1|Q9NYR2|Q9UMZ0|Q9UNY3	Frame_Shift_Ins	INS	ENST00000220616.4	37	c.1037_1038insG	CCDS34944.1																																																																																				0.614	TG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379606.1	NM_003235		20	26						20	26	---	---	---	---
ZFHX3	463	broad.mit.edu	37	16	72991713	72991715	+	In_Frame_Del	DEL	CCA	CCA	-	rs4788682	byFrequency	TCGA-EL-A3ZQ-01A-11D-A23M-08	TCGA-EL-A3ZQ-11A-11D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4694460d-de2a-4b9e-9391-dc57816752bf	a51fd081-0952-40bf-8412-b293d88100dc	g.chr16:72991713_72991715delCCA	ENST00000268489.5	-	2	3002_3004	c.2330_2332delTGG	c.(2329-2334)gtggct>gct	p.V777del	ZFHX3_ENST00000397992.5_Intron	NM_006885.3	NP_008816.3	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3	777	Poly-Ala.		V -> A (in dbSNP:rs4788682). {ECO:0000269|PubMed:7592926}.		brain development (GO:0007420)|cell cycle arrest (GO:0007050)|muscle organ development (GO:0007517)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of myoblast differentiation (GO:0045663)|regulation of neuron differentiation (GO:0045664)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	enzyme binding (GO:0019899)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)	p.V777V(1)		NS(3)|breast(7)|cervix(2)|endometrium(18)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(22)|liver(1)|lung(46)|ovary(5)|pancreas(1)|prostate(15)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(11)	153		Ovarian(137;0.13)				gccgccgcagccaccgccgccgc	0.635																																						ENST00000268489.5																			1	Substitution - coding silent(1)	p.V777V(1)	lung(1)	NS(3)|breast(7)|cervix(2)|endometrium(18)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(22)|liver(1)|lung(46)|ovary(5)|pancreas(1)|prostate(15)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(11)	153						c.(2329-2334)gct>g		zinc finger homeobox 3			,	1706,1886		582,542,672					,	5.5	0.1			17	4240,2792		1606,1028,882	no	coding,intron	ZFHX3	NM_006885.3,NM_001164766.1	,	2188,1570,1554	A1A1,A1R,RR		39.7042,47.4944,44.0324	,	,		5946,4678				SO:0001651	inframe_deletion	463				muscle organ development|negative regulation of myoblast differentiation|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription, DNA-dependent|positive regulation of myoblast differentiation	transcription factor complex	enzyme binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|transcription regulatory region DNA binding|zinc ion binding	g.chr16:72991713_72991715delCCA	D10250	CCDS10908.1, CCDS54035.1	16q22.3	2012-03-09	2007-08-09	2007-08-09	ENSG00000140836	ENSG00000140836		"""Zinc fingers, C2H2-type"", ""Homeoboxes / ZF class"""	777	protein-coding gene	gene with protein product		104155	"""AT-binding transcription factor 1"""	ATBF1		1719379, 7592926	Standard	NM_006885		Approved	ZNF927	uc002fck.3	Q15911	OTTHUMG00000137599	ENST00000268489.5:c.2330_2332delTGG	16.37:g.72991713_72991715delCCA	ENSP00000268489:p.Val777del					ZFHX3_ENST00000397992.5_Intron	p.VA777del	NM_006885.3	NP_008816.3	Q15911	ZFHX3_HUMAN			2	3002_3004	-		Ovarian(137;0.13)	777		V -> A (in dbSNP:rs4788682).	Poly-Ala.		D3DWS8|O15101|Q13719	In_Frame_Del	DEL	ENST00000268489.5	37	c.2330_2332delTGG	CCDS10908.1																																																																																				0.635	ZFHX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269008.1	NM_006885		7	216						7	216	---	---	---	---
DDX52	11056	broad.mit.edu	37	17	36003614	36003614	+	5'Flank	DEL	T	T	-	rs59697282		TCGA-EL-A3ZQ-01A-11D-A23M-08	TCGA-EL-A3ZQ-11A-11D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4694460d-de2a-4b9e-9391-dc57816752bf	a51fd081-0952-40bf-8412-b293d88100dc	g.chr17:36003614delT	ENST00000349699.2	-	0	0				DDX52_ENST00000394367.3_5'Flank|RP11-697E22.2_ENST00000586163.1_RNA|RP11-697E22.2_ENST00000586950.1_RNA	NM_007010.3	NP_008941.2	Q9Y2R4	DDX52_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 52							membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)			biliary_tract(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(5)|ovary(1)|skin(3)	17		Breast(25;0.00637)|Ovarian(249;0.15)				ATTAtttatcttttttttttt	0.507																																						ENST00000586163.1																			0																																																	SO:0001631	upstream_gene_variant	0							g.chr17:36003614delT	AF077033	CCDS11323.1	17q21.1	2014-05-06			ENSG00000141141	ENSG00000278053		"""DEAD-boxes"""	20038	protein-coding gene	gene with protein product		612500				11124703	Standard	XM_006721650		Approved	ROK1	uc002hoi.2	Q9Y2R4	OTTHUMG00000188475		17.37:g.36003614delT	Exception_encountered					RP11-697E22.2_ENST00000586950.1_RNA								0	590	+								Q86YG1|Q8N213|Q9NVE0|Q9Y482	RNA	DEL	ENST00000349699.2	37		CCDS11323.1																																																																																				0.507	DDX52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256795.1	NM_152300		2	4						2	4	---	---	---	---
SF3A1	10291	broad.mit.edu	37	22	30742328	30742330	+	In_Frame_Del	DEL	CTG	CTG	-	rs141985009	byFrequency	TCGA-EL-A3ZQ-01A-11D-A23M-08	TCGA-EL-A3ZQ-11A-11D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4694460d-de2a-4b9e-9391-dc57816752bf	a51fd081-0952-40bf-8412-b293d88100dc	g.chr22:30742328_30742330delCTG	ENST00000215793.8	-	3	518_520	c.364_366delCAG	c.(364-366)cagdel	p.Q122del	SF3A1_ENST00000439242.1_Intron	NM_005877.4	NP_005868.1	Q15459	SF3A1_HUMAN	splicing factor 3a, subunit 1, 120kDa	122	Poly-Gln.				gene expression (GO:0010467)|mRNA 3'-splice site recognition (GO:0000389)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U2-type spliceosomal complex (GO:0005684)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(9)|ovary(4)|pancreas(1)|prostate(1)|urinary_tract(1)	29						GCTGGGTGGTCTGCTGCTGCTGC	0.606																																						ENST00000215793.7																			0				endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(9)|ovary(4)|pancreas(1)|prostate(1)|urinary_tract(1)	29						c.(364-366)del		splicing factor 3a, subunit 1, 120kDa																																				SO:0001651	inframe_deletion	10291				nuclear mRNA 3'-splice site recognition	catalytic step 2 spliceosome|nucleoplasm|U2-type spliceosomal complex	protein binding|RNA binding	g.chr22:30742328_30742330delCTG	X85237	CCDS13875.1	22q12.2	2014-09-17	2002-08-29		ENSG00000099995	ENSG00000099995			10765	protein-coding gene	gene with protein product		605595	"""splicing factor 3a, subunit 1, 120kD"""			7489498	Standard	NM_005877		Approved	SF3a120, SAP114, PRPF21, Prp21	uc003ahl.3	Q15459	OTTHUMG00000151005	ENST00000215793.8:c.364_366delCAG	22.37:g.30742337_30742339delCTG	ENSP00000215793:p.Gln122del					SF3A1_ENST00000439242.1_Intron	p.Q122del	NM_005877.4	NP_005868.1	Q15459	SF3A1_HUMAN			3	518_520	-			122			Poly-Gln.		E9PAW1	In_Frame_Del	DEL	ENST00000215793.8	37	c.364_366delCAG	CCDS13875.1																																																																																				0.606	SF3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320916.2	NM_005877		8	122						8	122	---	---	---	---
