#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
CELSR1	9620	broad.mit.edu	37	22	46760065	46760065	+	Missense_Mutation	SNP	C	C	A	rs199624773		TCGA-J8-A3YG-01A-11D-A22Z-08	TCGA-J8-A3YG-10A-01D-A22Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	832df42e-2582-466d-9df2-7869fcf12057	d2dc5691-bdd9-4dd7-8794-69fc54dad1cb	g.chr22:46760065C>A	ENST00000262738.3	-	34	8862	c.8863G>T	c.(8863-8865)Gcc>Tcc	p.A2955S		NM_014246.1	NP_055061.1	Q9NYQ6	CELR1_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 1	2955					anterior/posterior pattern specification (GO:0009952)|apical protein localization (GO:0045176)|central nervous system development (GO:0007417)|establishment of body hair planar orientation (GO:0048105)|establishment of planar polarity (GO:0001736)|establishment of planar polarity of embryonic epithelium (GO:0042249)|G-protein coupled receptor signaling pathway (GO:0007186)|hair follicle development (GO:0001942)|homophilic cell adhesion (GO:0007156)|inner ear morphogenesis (GO:0042472)|lateral sprouting involved in lung morphogenesis (GO:0060490)|locomotory behavior (GO:0007626)|neural tube closure (GO:0001843)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|orthogonal dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060488)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|planar dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060489)|protein localization involved in establishment of planar polarity (GO:0090251)|regulation of actin cytoskeleton organization (GO:0032956)|Rho protein signal transduction (GO:0007266)|wound healing (GO:0042060)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)|protein dimerization activity (GO:0046983)|transmembrane signaling receptor activity (GO:0004888)			breast(8)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(13)|lung(27)|ovary(2)|pancreas(2)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(3)	95		Ovarian(80;0.00142)|Breast(42;0.00296)|all_neural(38;0.0416)|Colorectal(5;0.0766)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00643)|BRCA - Breast invasive adenocarcinoma(115;0.171)		TCACAGTCGGCCAGCTTCTCC	0.662																																						ENST00000262738.3																			0				breast(8)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(13)|lung(27)|ovary(2)|pancreas(2)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(3)	95						c.(8863-8865)Gcc>Tcc		cadherin, EGF LAG seven-pass G-type receptor 1							41.0	47.0	45.0					22																	46760065		2203	4298	6501	SO:0001583	missense	9620				central nervous system development|homophilic cell adhesion|neural tube closure|neuropeptide signaling pathway	integral to plasma membrane	calcium ion binding|G-protein coupled receptor activity|protein dimerization activity	g.chr22:46760065C>A	AF231024	CCDS14076.1	22q13.31	2014-08-08	2013-02-18		ENSG00000075275	ENSG00000075275		"""Cadherins / Major cadherins"", ""-"", ""GPCR / Class B : Orphans"""	1850	protein-coding gene	gene with protein product	"""flamingo homolog 2 (Drosophila)"""	604523	"""cadherin, EGF LAG seven-pass G-type receptor 1, flamingo (Drosophila) homolog"""			9339365	Standard	XM_006724383		Approved	ME2, HFMI2, FMI2, CDHF9	uc003bhw.1	Q9NYQ6	OTTHUMG00000150423	ENST00000262738.3:c.8863G>T	22.37:g.46760065C>A	ENSP00000262738:p.Ala2955Ser						p.A2955S	NM_014246.1	NP_055061.1	Q9NYQ6	CELR1_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (28;0.00643)|BRCA - Breast invasive adenocarcinoma(115;0.171)	34	8862	-		Ovarian(80;0.00142)|Breast(42;0.00296)|all_neural(38;0.0416)|Colorectal(5;0.0766)	2955					O95722|Q5TH47|Q9BWQ5|Q9Y506|Q9Y526	Missense_Mutation	SNP	ENST00000262738.3	37	c.8863G>T	CCDS14076.1	.	.	.	.	.	.	.	.	.	.	C	8.818	0.936855	0.18206	.	.	ENSG00000075275	ENST00000262738	T	0.67171	-0.25	4.85	3.76	0.43208	.	0.448042	0.17288	U	0.179775	T	0.47544	0.1451	L	0.31157	0.91	0.80722	D	1	B	0.25486	0.127	B	0.23852	0.049	T	0.36432	-0.9748	10	0.02654	T	1	.	10.5066	0.44836	0.3874:0.6126:0.0:0.0	.	2955	Q9NYQ6	CELR1_HUMAN	S	2955	ENSP00000262738:A2955S	ENSP00000262738:A2955S	A	-	1	0	CELSR1	45138729	1.000000	0.71417	0.991000	0.47740	0.762000	0.43233	2.118000	0.41949	2.211000	0.71520	0.563000	0.77884	GCC		0.662	CELSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318037.1	NM_014246		15	50	1	0	1.99824e-07	1	1.99824e-07	15	50				
WASH3P	374666	broad.mit.edu	37	15	102515299	102515299	+	RNA	SNP	G	G	A	rs201972834		TCGA-J8-A3YG-01A-11D-A22Z-08	TCGA-J8-A3YG-10A-01D-A22Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	832df42e-2582-466d-9df2-7869fcf12057	d2dc5691-bdd9-4dd7-8794-69fc54dad1cb	g.chr15:102515299G>A	ENST00000557932.1	+	0	1145				DDX11L9_ENST00000562189.1_RNA			C4AMC7	WASH3_HUMAN	WAS protein family homolog 3 pseudogene						Arp2/3 complex-mediated actin nucleation (GO:0034314)|endosomal transport (GO:0016197)|retrograde transport, endosome to Golgi (GO:0042147)	early endosome (GO:0005769)|filopodium (GO:0030175)|lamellipodium (GO:0030027)|membrane (GO:0016020)|recycling endosome (GO:0055037)|WASH complex (GO:0071203)	alpha-tubulin binding (GO:0043014)	p.G374S(10)		central_nervous_system(1)|endometrium(6)|kidney(11)|prostate(5)|stomach(1)|urinary_tract(1)	25						TGGGGGCATCGGCAAGGCCAA	0.652																																						ENST00000557932.1																			10	Substitution - Missense(10)	p.G374S(10)	kidney(7)|prostate(2)|endometrium(1)	central_nervous_system(1)|endometrium(6)|kidney(11)|prostate(5)|stomach(1)|urinary_tract(1)	25																																														0							g.chr15:102515299G>A			15q26.3	2014-03-20	2008-01-16	2008-01-16	ENSG00000185596	ENSG00000185596		"""WAS protein homologs"""	24362	pseudogene	pseudogene			"""family with sequence similarity 39, member D pseudogene"""	FAM39DP		11701968, 18159949	Standard	NR_003659		Approved	FLJ25222	uc002cdi.3	C4AMC7	OTTHUMG00000172275		15.37:g.102515299G>A														0	1145	+									RNA	SNP	ENST00000557932.1	37			.	.	.	.	.	.	.	.	.	.	g	2.376	-0.343229	0.05243	.	.	ENSG00000185596	ENST00000338304;ENST00000398121	.	.	.	1.01	1.01	0.19927	.	0.000000	0.85682	D	0.000000	T	0.41926	0.1180	.	.	.	.	.	.	.	.	.	.	.	.	T	0.51044	-0.8755	4	.	.	.	-23.1056	7.9382	0.29941	0.0:0.0:1.0:0.0	.	.	.	.	S	383;374	.	.	G	+	1	0	WASH3P	100332822	1.000000	0.71417	0.997000	0.53966	0.230000	0.25150	8.205000	0.89743	0.863000	0.35553	0.184000	0.17185	GGC		0.652	WASH3P-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000417608.1	NM_199163		3	27	0	0	0	1	0	3	27				
BRAF	673	broad.mit.edu	37	7	140453136	140453136	+	Missense_Mutation	SNP	A	A	T	rs121913377|rs113488022|rs121913227|rs397516897		TCGA-J8-A3YG-01A-11D-A22Z-08	TCGA-J8-A3YG-10A-01D-A22Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	832df42e-2582-466d-9df2-7869fcf12057	d2dc5691-bdd9-4dd7-8794-69fc54dad1cb	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		10	28	0	0	0	1	0	10	28				
FRG1B	284802	broad.mit.edu	37	20	29625877	29625877	+	Missense_Mutation	SNP	G	G	A	rs7266938	byFrequency	TCGA-J8-A3YG-01A-11D-A22Z-08	TCGA-J8-A3YG-10A-01D-A22Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	832df42e-2582-466d-9df2-7869fcf12057	d2dc5691-bdd9-4dd7-8794-69fc54dad1cb	g.chr20:29625877G>A	ENST00000278882.3	+	5	501	c.121G>A	c.(121-123)Gcc>Acc	p.A41T	FRG1B_ENST00000358464.4_Missense_Mutation_p.A41T|FRG1B_ENST00000439954.2_Missense_Mutation_p.A46T			Q9BZ01	FRG1B_HUMAN	FSHD region gene 1 family, member B	41								p.A41T(2)		endometrium(10)|kidney(21)|lung(3)|pancreas(1)|prostate(9)|urinary_tract(9)	53						GTACAGAATCGCCCTGAAATC	0.358																																						ENST00000278882.3																			2	Substitution - Missense(2)	p.A41T(2)	urinary_tract(2)	endometrium(10)|kidney(21)|lung(3)|pancreas(1)|prostate(9)|urinary_tract(9)	53						c.(121-123)Gcc>Acc																																						SO:0001583	missense	0							g.chr20:29625877G>A			20q11.1	2013-03-18	2007-10-11	2007-10-11	ENSG00000149531	ENSG00000149531			15792	other	unknown			"""chromosome 20 open reading frame 80"""	C20orf80			Standard	NR_003579		Approved	bA348I14.2	uc010ztl.1	Q9BZ01	OTTHUMG00000032157	ENST00000278882.3:c.121G>A	20.37:g.29625877G>A	ENSP00000278882:p.Ala41Thr					FRG1B_ENST00000358464.4_Missense_Mutation_p.A41T|FRG1B_ENST00000439954.2_Missense_Mutation_p.A46T	p.A41T							5	501	+								C4AME5	Missense_Mutation	SNP	ENST00000278882.3	37	c.121G>A		.	.	.	.	.	.	.	.	.	.	g	8.740	0.918766	0.17982	.	.	ENSG00000149531	ENST00000278882;ENST00000439954;ENST00000358464	T	0.62498	0.02	1.68	1.68	0.24146	.	0.000000	0.85682	D	0.000000	T	0.48277	0.1491	.	.	.	0.52099	D	0.999942	B	0.24186	0.099	B	0.27715	0.082	T	0.43956	-0.9359	9	0.33940	T	0.23	.	9.3557	0.38164	0.0:0.0:1.0:0.0	rs7266938;rs7266938	46	F5H5R5	.	T	41;46;41	ENSP00000408863:A46T	ENSP00000278882:A41T	A	+	1	0	FRG1B	28239538	1.000000	0.71417	0.993000	0.49108	0.033000	0.12548	5.232000	0.65332	1.250000	0.43966	0.184000	0.17185	GCC		0.358	FRG1B-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000078494.2	NR_003579		4	34	0	0	0	1	0	4	34				
SWSAP1	126074	broad.mit.edu	37	19	11485510	11485510	+	Missense_Mutation	SNP	G	G	C			TCGA-J8-A3YG-01A-11D-A22Z-08	TCGA-J8-A3YG-10A-01D-A22Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	832df42e-2582-466d-9df2-7869fcf12057	d2dc5691-bdd9-4dd7-8794-69fc54dad1cb	g.chr19:11485510G>C	ENST00000312423.2	+	1	150	c.91G>C	c.(91-93)Ggg>Cgg	p.G31R	CTD-2342J14.6_ENST00000590399.1_RNA	NM_175871.3	NP_787067.2	Q6NVH7	SWAP1_HUMAN	SWIM-type zinc finger 7 associated protein 1	31					ATP catabolic process (GO:0006200)|double-strand break repair via homologous recombination (GO:0000724)|protein stabilization (GO:0050821)	nucleus (GO:0005634)|Shu complex (GO:0097196)	ATPase activity (GO:0016887)|single-stranded DNA binding (GO:0003697)										AGAGGCGGCGGGGGAGGGCCA	0.627																																						ENST00000312423.2																			0											c.(91-93)Ggg>Cgg		SWIM-type zinc finger 7 associated protein 1							50.0	59.0	56.0					19																	11485510		2203	4300	6503	SO:0001583	missense	126074							g.chr19:11485510G>C	AK092438	CCDS12259.1	19p13.2	2011-11-24	2011-11-24	2011-11-24	ENSG00000173928	ENSG00000173928			26638	protein-coding gene	gene with protein product	"""zinc finger, SWIM-type containing 7 associated protein 1"", ""SWS1-associated protein 1"""	614536	"""chromosome 19 open reading frame 39"""	C19orf39		21965664	Standard	NM_175871		Approved	FLJ35119, ZSWIM7AP1, SWS1AP1	uc002mrg.1	Q6NVH7		ENST00000312423.2:c.91G>C	19.37:g.11485510G>C	ENSP00000310008:p.Gly31Arg					CTD-2342J14.6_ENST00000590399.1_RNA	p.G31R	NM_175871.3	NP_787067.2	Q6NVH7	CS039_HUMAN			1	150	+			31					Q8NAM1	Missense_Mutation	SNP	ENST00000312423.2	37	c.91G>C	CCDS12259.1	.	.	.	.	.	.	.	.	.	.	G	24.9	4.582910	0.86748	.	.	ENSG00000173928	ENST00000312423	T	0.77358	-1.09	5.44	3.31	0.37934	.	0.298863	0.26773	N	0.022568	T	0.69061	0.3069	L	0.48877	1.53	0.35125	D	0.767393	B	0.34161	0.439	B	0.39876	0.312	T	0.65446	-0.6166	10	0.05721	T	0.95	-13.8607	10.7253	0.46064	0.1579:0.0:0.8421:0.0	.	31	Q6NVH7	CS039_HUMAN	R	31	ENSP00000310008:G31R	ENSP00000310008:G31R	G	+	1	0	C19orf39	11346510	1.000000	0.71417	0.944000	0.38274	0.967000	0.64934	4.181000	0.58303	0.668000	0.31126	0.561000	0.74099	GGG		0.627	SWSAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458789.1	NM_175871		19	80	0	0	0	1	0	19	80				
DEFB119	245932	broad.mit.edu	37	20	29976940	29976940	+	Intron	SNP	G	G	A			TCGA-J8-A3YG-01A-11D-A22Z-08	TCGA-J8-A3YG-10A-01D-A22Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	832df42e-2582-466d-9df2-7869fcf12057	d2dc5691-bdd9-4dd7-8794-69fc54dad1cb	g.chr20:29976940G>A	ENST00000376321.3	-	1	181				DEFB119_ENST00000376315.2_Missense_Mutation_p.P52L|DEFB119_ENST00000339144.3_Intron|DEFB119_ENST00000492344.1_Intron	NM_153289.3	NP_695021.2	Q8N690	DB119_HUMAN	defensin, beta 119						defense response to bacterium (GO:0042742)	extracellular region (GO:0005576)				large_intestine(2)|lung(1)|prostate(1)	4	all_hematologic(12;0.158)		Colorectal(19;0.00254)|COAD - Colon adenocarcinoma(19;0.0347)			ATAACGACTAGGAACACAGCA	0.448																																						ENST00000376315.2																			0				large_intestine(2)|lung(1)|prostate(1)	4						c.(154-156)cCt>cTt		defensin, beta 119							197.0	170.0	179.0					20																	29976940		2203	4300	6503	SO:0001627	intron_variant	245932				defense response to bacterium	extracellular region		g.chr20:29976940G>A	AA939044	CCDS13178.1, CCDS33455.1	20q11.21	2007-02-19	2003-10-06		ENSG00000180483	ENSG00000180483		"""Defensins, beta"""	18099	protein-coding gene	gene with protein product			"""defensin, beta 120"""	DEFB120		11854508	Standard	NM_153289		Approved	DEFB-19, DEFB-20	uc002wvu.2	Q8N690	OTTHUMG00000032172	ENST00000376321.3:c.61+1285C>T	20.37:g.29976940G>A						DEFB119_ENST00000376321.3_Intron|DEFB119_ENST00000339144.3_Intron|DEFB119_ENST00000492344.1_Intron	p.P52L	NM_001271209.1|NM_153323.4	NP_001258138.1|NP_697018.1	Q8N690	DB119_HUMAN	Colorectal(19;0.00254)|COAD - Colon adenocarcinoma(19;0.0347)		2	154	-	all_hematologic(12;0.158)		58					Q5GRG1|Q5JWP1|Q5TH42|Q8N689	Missense_Mutation	SNP	ENST00000376321.3	37	c.155C>T	CCDS13178.1	.	.	.	.	.	.	.	.	.	.	G	16.21	3.059660	0.55325	.	.	ENSG00000180483	ENST00000376315	T	0.32515	1.45	3.64	-2.67	0.06059	.	1.726480	0.03263	N	0.183560	T	0.21186	0.0510	.	.	.	0.21064	N	0.999796	B	0.19935	0.04	B	0.17098	0.017	T	0.24548	-1.0157	9	0.33141	T	0.24	-0.4087	8.8657	0.35284	0.3207:0.0:0.6793:0.0	.	52	Q8N690-2	.	L	52	ENSP00000365492:P52L	ENSP00000365492:P52L	P	-	2	0	DEFB119	29440601	0.006000	0.16342	0.022000	0.16811	0.981000	0.71138	-0.552000	0.06020	-0.509000	0.06532	-0.253000	0.11424	CCT		0.448	DEFB119-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078514.1	NM_153289		15	55	0	0	0	1	0	15	55				
FCHSD1	89848	broad.mit.edu	37	5	141026744	141026744	+	Silent	SNP	G	G	C			TCGA-J8-A3YG-01A-11D-A22Z-08	TCGA-J8-A3YG-10A-01D-A22Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	832df42e-2582-466d-9df2-7869fcf12057	d2dc5691-bdd9-4dd7-8794-69fc54dad1cb	g.chr5:141026744G>C	ENST00000435817.2	-	10	932	c.882C>G	c.(880-882)tcC>tcG	p.S294S	FCHSD1_ENST00000522126.1_Silent_p.S218S|FCHSD1_ENST00000523856.1_5'UTR|FCHSD1_ENST00000522783.1_Silent_p.S292S	NM_033449.2	NP_258260.1	Q86WN1	FCSD1_HUMAN	FCH and double SH3 domains 1	294									FCHSD1/BRAF(2)	central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(8)|lung(5)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	24			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GTGGGGTGGGGGAAAATACAC	0.502																																						ENST00000435817.2																		FCHSD1/BRAF(2)	0				central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(8)|lung(5)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	24						c.(880-882)tcC>tcG		FCH and double SH3 domains 1							38.0	42.0	41.0					5																	141026744		1900	4119	6019	SO:0001819	synonymous_variant	89848							g.chr5:141026744G>C	AK027281	CCDS47295.1	5q31.3	2008-02-05			ENSG00000197948	ENSG00000197948			25463	protein-coding gene	gene with protein product						11214971, 15067381	Standard	NM_033449		Approved	FLJ00007	uc003llk.3	Q86WN1	OTTHUMG00000163762	ENST00000435817.2:c.882C>G	5.37:g.141026744G>C						FCHSD1_ENST00000522126.1_Silent_p.S218S|FCHSD1_ENST00000522783.1_Silent_p.S292S|FCHSD1_ENST00000523856.1_5'UTR	p.S294S	NM_033449.2	NP_258260.1	Q86WN1	FCSD1_HUMAN	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		10	932	-			294					Q6UX75|Q86Y77|Q9NXX8	Silent	SNP	ENST00000435817.2	37	c.882C>G	CCDS47295.1																																																																																				0.502	FCHSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375282.2	NM_033449		4	3	0	0	0	1	0	4	3				
TUSC5	286753	broad.mit.edu	37	17	1183415	1183415	+	Silent	SNP	C	C	G			TCGA-J8-A3YG-01A-11D-A22Z-08	TCGA-J8-A3YG-10A-01D-A22Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	832df42e-2582-466d-9df2-7869fcf12057	d2dc5691-bdd9-4dd7-8794-69fc54dad1cb	g.chr17:1183415C>G	ENST00000333813.3	+	1	459	c.120C>G	c.(118-120)acC>acG	p.T40T		NM_172367.2	NP_758955.2	Q8IXB3	TUSC5_HUMAN	tumor suppressor candidate 5	40					response to biotic stimulus (GO:0009607)	integral component of membrane (GO:0016021)				endometrium(2)|kidney(2)|large_intestine(3)|lung(2)|prostate(4)|skin(2)	15				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)		ATGACAAGACCCTGAATCTGT	0.612																																						ENST00000333813.3																			0				endometrium(2)|kidney(2)|large_intestine(3)|lung(2)|prostate(4)|skin(2)	15						c.(118-120)acC>acG		tumor suppressor candidate 5							71.0	77.0	75.0					17																	1183415		1964	4145	6109	SO:0001819	synonymous_variant	286753				response to biotic stimulus	integral to membrane		g.chr17:1183415C>G	AB090231	CCDS42225.1	17p13.3	2009-10-16			ENSG00000184811	ENSG00000184811			29592	protein-coding gene	gene with protein product	"""located at seventeen p thirteen point three 1"", ""interferon induced transmembrane protein domain containing 3"""	612211				12660825	Standard	NM_172367		Approved	LOST1, IFITMD3	uc002fsi.1	Q8IXB3	OTTHUMG00000132196	ENST00000333813.3:c.120C>G	17.37:g.1183415C>G							p.T40T	NM_172367.2	NP_758955.2	Q8IXB3	TUSC5_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)	1	459	+			40					A6NMK4	Silent	SNP	ENST00000333813.3	37	c.120C>G	CCDS42225.1																																																																																				0.612	TUSC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255249.1	NM_172367		22	67	0	0	0	1	0	22	67				
SACM1L	22908	broad.mit.edu	37	3	45785079	45785079	+	Missense_Mutation	SNP	T	T	C			TCGA-J8-A3YG-01A-11D-A22Z-08	TCGA-J8-A3YG-10A-01D-A22Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	832df42e-2582-466d-9df2-7869fcf12057	d2dc5691-bdd9-4dd7-8794-69fc54dad1cb	g.chr3:45785079T>C	ENST00000389061.5	+	20	1886	c.1682T>C	c.(1681-1683)aTt>aCt	p.I561T	SACM1L_ENST00000541314.1_Missense_Mutation_p.I500T|RN7SL145P_ENST00000469955.2_RNA|SACM1L_ENST00000418611.1_Missense_Mutation_p.I458T	NM_014016.3	NP_054735.3	Q9NTJ5	SAC1_HUMAN	SAC1 suppressor of actin mutations 1-like (yeast)	561					phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of endoplasmic reticulum membrane (GO:0030176)	phosphatase activity (GO:0016791)|phosphatidylinositol bisphosphate phosphatase activity (GO:0034593)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphatidylinositol-4-phosphate phosphatase activity (GO:0043812)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|stomach(1)	23				BRCA - Breast invasive adenocarcinoma(193;0.0102)|KIRC - Kidney renal clear cell carcinoma(197;0.0234)|Kidney(197;0.0277)		GTTGCAAGCATTGGAACATTT	0.373																																						ENST00000389061.5																			0				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|stomach(1)	23						c.(1681-1683)aTt>aCt		SAC1 suppressor of actin mutations 1-like (yeast)							162.0	160.0	161.0					3																	45785079		2203	4300	6503	SO:0001583	missense	22908					Golgi apparatus		g.chr3:45785079T>C	AB020658	CCDS33745.1	3p21.3	2010-03-11			ENSG00000211456	ENSG00000211456			17059	protein-coding gene	gene with protein product		606569				10048485, 11352561	Standard	NM_014016		Approved	SAC1, KIAA0851	uc003cos.2	Q9NTJ5	OTTHUMG00000156653	ENST00000389061.5:c.1682T>C	3.37:g.45785079T>C	ENSP00000373713:p.Ile561Thr					SACM1L_ENST00000541314.1_Missense_Mutation_p.I500T|SACM1L_ENST00000418611.1_Missense_Mutation_p.I458T	p.I561T	NM_014016.3	NP_054735.3	Q9NTJ5	SAC1_HUMAN		BRCA - Breast invasive adenocarcinoma(193;0.0102)|KIRC - Kidney renal clear cell carcinoma(197;0.0234)|Kidney(197;0.0277)	20	1886	+			561					A8K527|B4DK71|O94935|Q7LA14|Q7LA22|Q96AX7|Q9NQ46|Q9NQ57	Missense_Mutation	SNP	ENST00000389061.5	37	c.1682T>C	CCDS33745.1	.	.	.	.	.	.	.	.	.	.	T	13.82	2.350313	0.41599	.	.	ENSG00000211456	ENST00000418611;ENST00000389061;ENST00000541314	T;T;T	0.45668	0.91;0.9;0.89	5.78	5.78	0.91487	.	0.245967	0.40302	N	0.001131	T	0.34395	0.0896	L	0.31926	0.97	0.40602	D	0.981595	B;B;B	0.10296	0.002;0.003;0.002	B;B;B	0.11329	0.001;0.006;0.004	T	0.10965	-1.0607	10	0.25751	T	0.34	-5.2419	15.7875	0.78319	0.0:0.0:0.0:1.0	.	500;204;561	B4DK71;B3KX17;Q9NTJ5	.;.;SAC1_HUMAN	T	458;561;500	ENSP00000396387:I458T;ENSP00000373713:I561T;ENSP00000443373:I500T	ENSP00000373713:I561T	I	+	2	0	SACM1L	45760083	0.998000	0.40836	1.000000	0.80357	0.997000	0.91878	2.940000	0.49003	2.214000	0.71695	0.528000	0.53228	ATT		0.373	SACM1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345065.2	NM_014016		12	62	0	0	0	1	0	12	62				
PLXND1	23129	broad.mit.edu	37	3	129289655	129289655	+	Missense_Mutation	SNP	C	C	A	rs140631068		TCGA-J8-A3YG-01A-11D-A22Z-08	TCGA-J8-A3YG-10A-01D-A22Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	832df42e-2582-466d-9df2-7869fcf12057	d2dc5691-bdd9-4dd7-8794-69fc54dad1cb	g.chr3:129289655C>A	ENST00000324093.4	-	19	3902	c.3724G>T	c.(3724-3726)Gcg>Tcg	p.A1242S	PLXND1_ENST00000393239.1_Missense_Mutation_p.A1242S	NM_015103.2	NP_055918	Q9Y4D7	PLXD1_HUMAN	plexin D1	1242					angiogenesis (GO:0001525)|axon guidance (GO:0007411)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|endothelial cell migration (GO:0043542)|outflow tract morphogenesis (GO:0003151)|patterning of blood vessels (GO:0001569)|positive regulation of protein binding (GO:0032092)|regulation of angiogenesis (GO:0045765)|regulation of cell migration (GO:0030334)|semaphorin-plexin signaling pathway (GO:0071526)|synapse assembly (GO:0007416)	integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)	protein domain specific binding (GO:0019904)|semaphorin receptor activity (GO:0017154)	p.A1242T(1)	PLXND1/TMCC1(4)	NS(1)|breast(1)|endometrium(4)|kidney(5)|large_intestine(17)|lung(28)|prostate(10)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	72						CCCACGGCCGCGCCCAGGGAC	0.632																																					Ovarian(97;366 1484 3738 22084 39045)	ENST00000393239.1																		PLXND1/TMCC1(4)	1	Substitution - Missense(1)	p.A1242T(1)	large_intestine(1)	NS(1)|breast(1)|endometrium(4)|kidney(5)|large_intestine(17)|lung(28)|prostate(10)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	72						c.(3724-3726)Gcg>Tcg		plexin D1							131.0	142.0	138.0					3																	129289655		2203	4300	6503	SO:0001583	missense	23129				axon guidance	integral to membrane|intracellular|plasma membrane		g.chr3:129289655C>A	AY116661	CCDS33854.1	3q21.3	2007-05-16			ENSG00000004399	ENSG00000004399		"""Plexins"""	9107	protein-coding gene	gene with protein product		604282				12412018	Standard	NM_015103		Approved	KIAA0620	uc003emx.2	Q9Y4D7	OTTHUMG00000159547	ENST00000324093.4:c.3724G>T	3.37:g.129289655C>A	ENSP00000317128:p.Ala1242Ser					PLXND1_ENST00000324093.4_Missense_Mutation_p.A1242S	p.A1242S			Q9Y4D7	PLXD1_HUMAN			19	3902	-			1242					A7E2C6|C9JPZ6|Q6PJS9|Q8IZJ2|Q9BTQ2	Missense_Mutation	SNP	ENST00000324093.4	37	c.3724G>T	CCDS33854.1	.	.	.	.	.	.	.	.	.	.	C	0.186	-1.057488	0.01965	.	.	ENSG00000004399	ENST00000324093;ENST00000393239	T;T	0.33438	1.45;1.41	4.78	-2.45	0.06481	Immunoglobulin-like fold (1);	0.482216	0.20400	N	0.093061	T	0.08670	0.0215	N	0.03324	-0.35	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.36672	-0.9738	10	0.02654	T	1	.	7.4293	0.27118	0.1273:0.1403:0.0:0.7324	.	1242	Q9Y4D7	PLXD1_HUMAN	S	1242	ENSP00000317128:A1242S;ENSP00000376931:A1242S	ENSP00000317128:A1242S	A	-	1	0	PLXND1	130772345	0.999000	0.42202	0.000000	0.03702	0.011000	0.07611	0.585000	0.23879	-0.274000	0.09232	0.491000	0.48974	GCG		0.632	PLXND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356132.4	NM_015103		16	173	1	0	6.72482e-11	1	7.84563e-11	16	173				
HSD17B7P2	158160	broad.mit.edu	37	10	38654432	38654432	+	RNA	SNP	A	A	G	rs2257765		TCGA-J8-A3YG-01A-11D-A22Z-08	TCGA-J8-A3YG-10A-01D-A22Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	832df42e-2582-466d-9df2-7869fcf12057	d2dc5691-bdd9-4dd7-8794-69fc54dad1cb	g.chr10:38654432A>G	ENST00000494540.1	+	0	599					NR_003086.1				hydroxysteroid (17-beta) dehydrogenase 7 pseudogene 2																		TCATCTCGCAATGCAAGGAAA	0.453																																						ENST00000494540.1																			0																																																			0							g.chr10:38654432A>G			10p11.1	2011-06-29			ENSG00000099251	ENSG00000099251			28120	pseudogene	pseudogene						10544267	Standard	NR_003086		Approved	HSD17B7, bA291L22.1	uc010qex.1		OTTHUMG00000017993		10.37:g.38654432A>G								NR_003086.1						0	599	+									RNA	SNP	ENST00000494540.1	37																																																																																						0.453	HSD17B7P2-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000047631.2	NR_003086		3	31	0	0	0	1	0	3	31				
ZNF598	90850	broad.mit.edu	37	16	2049882	2049883	+	In_Frame_Ins	INS	-	-	TCC	rs61746014|rs377495742|rs370831505|rs141374045	byFrequency	TCGA-J8-A3YG-01A-11D-A22Z-08	TCGA-J8-A3YG-10A-01D-A22Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	832df42e-2582-466d-9df2-7869fcf12057	d2dc5691-bdd9-4dd7-8794-69fc54dad1cb	g.chr16:2049882_2049883insTCC	ENST00000563630.1	-	9	1744_1745	c.1502_1503insGGA	c.(1501-1503)gac>gaGGAc	p.500_501insE	ZNF598_ENST00000431526.1_In_Frame_Ins_p.555_556insE|ZNF598_ENST00000562103.1_In_Frame_Ins_p.500_501insE|AC005606.15_ENST00000567515.1_lincRNA			Q86UK7	ZN598_HUMAN	zinc finger protein 598	555							poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.E555_D556insE(1)		NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|lung(7)|skin(1)|urinary_tract(1)	16						CCGGGCCGCCGTCCTCCTCCTC	0.703														518	0.103435	0.0061	0.1801	5008	,	,		13556	0.0387		0.1501	False		,,,				2504	0.1994					ENST00000563630.1																			1	Insertion - In frame(1)	p.E555_D556insE(1)	kidney(1)	NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|lung(7)|skin(1)|urinary_tract(1)	16						c.(1501-1503)ggg>gGGAgg		zinc finger protein 598																																				SO:0001652	inframe_insertion	90850					intracellular	zinc ion binding	g.chr16:2049882_2049883insTCC	BC029270		16p13.3	2008-05-02				ENSG00000167962		"""Zinc fingers, C2H2-type"""	28079	protein-coding gene	gene with protein product							Standard	NM_178167		Approved	FLJ00086	uc002cof.2	Q86UK7		ENST00000563630.1:c.1500_1502dupGGA	16.37:g.2049889_2049891dupTCC	ENSP00000455882:p.Glu500_Glu500dup					ZNF598_ENST00000562103.1_In_Frame_Ins_p.501_502insR|ZNF598_ENST00000431526.1_In_Frame_Ins_p.556_557insR	p.501_502insR			Q86UK7	ZN598_HUMAN			9	1744_1745	-			556					Q8IW49|Q8N3D9|Q96FG3|Q9H7J3	In_Frame_Ins	INS	ENST00000563630.1	37	c.1502_1503insGGA																																																																																					0.703	ZNF598-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000434439.1	NM_178167		5	11						5	11	---	---	---	---
NUDT11	55190	broad.mit.edu	37	X	51239296	51239309	+	Start_Codon_Del	DEL	TCCTCGAGGCAGCC	TCCTCGAGGCAGCC	-	rs78182391		TCGA-J8-A3YG-01A-11D-A22Z-08	TCGA-J8-A3YG-10A-01D-A22Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	832df42e-2582-466d-9df2-7869fcf12057	d2dc5691-bdd9-4dd7-8794-69fc54dad1cb	g.chrX:51239296_51239309delTCCTCGAGGCAGCC	ENST00000375992.3	-	0	139_152					NM_018159.3	NP_060629.2	Q96G61	NUD11_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 11						inositol phosphate metabolic process (GO:0043647)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|intracellular (GO:0005622)	diphosphoinositol-polyphosphate diphosphatase activity (GO:0008486)|inositol diphosphate tetrakisphosphate diphosphatase activity (GO:0052840)|inositol-1,5-bisdiphosphate-2,3,4,6-tetrakisphosphate 1-diphosphatase activity (GO:0052846)|inositol-1,5-bisdiphosphate-2,3,4,6-tetrakisphosphate 5-diphosphatase activity (GO:0052847)|inositol-1-diphosphate-2,3,4,5,6-pentakisphosphate diphosphatase activity (GO:0052843)|inositol-3,5-bisdiphosphate-2,3,4,6-tetrakisphosphate 5-diphosphatase activity (GO:0052848)|inositol-3-diphosphate-1,2,4,5,6-pentakisphosphate diphosphatase activity (GO:0052844)|inositol-5-diphosphate-1,2,3,4,6-pentakisphosphate diphosphatase activity (GO:0052845)|metal ion binding (GO:0046872)	p.?(5)		breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(2)|prostate(1)|upper_aerodigestive_tract(2)	9	Ovarian(276;0.236)					TTGCACTTCATCCTCGAGGCAGCCTCCTCGAGGC	0.692										HNSCC(48;0.14)				2406	0.637351	0.497	0.4928	3775	,	,		5662	0.4464		0.4553	False		,,,				2504	0.5102				GBM(38;198 791 1498 11752 13599)	ENST00000375992.3																			5	Unknown(5)	p.?(5)	upper_aerodigestive_tract(2)|prostate(1)|breast(1)|central_nervous_system(1)	breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(2)|prostate(1)|upper_aerodigestive_tract(2)	9								nudix (nucleoside diphosphate linked moiety X)-type motif 11				1710,202		758,11,183,87,17						3.0	1.0		dbSNP_131	12	3133,173		1220,1,692,66,40	no	frameshift	NUDT11	NM_018159.3		1978,12,875,153,57	A1A1,A1R,A1,RR,R		5.2329,10.5649,7.1867				4843,375				SO:0001582	initiator_codon_variant	0					cytoplasm	diphosphoinositol-polyphosphate diphosphatase activity|metal ion binding	g.chrX:51239296_51239309delTCCTCGAGGCAGCC	AK001490	CCDS43952.1	Xp11.22-p11.1	2014-05-20			ENSG00000196368	ENSG00000196368		"""Nudix motif containing"""	18011	protein-coding gene	gene with protein product						12105228	Standard	NM_018159		Approved	DIPP3b, FLJ10628, hDIPP3beta	uc010njt.3	Q96G61	OTTHUMG00000021531		X.37:g.51239296_51239309delTCCTCGAGGCAGCC		HNSCC(48;0.14)						NM_018159.3	NP_060629.2	Q96G61	NUD11_HUMAN			0	139_152	-	Ovarian(276;0.236)							Q9NVN0	Translation_Start_Site	DEL	ENST00000375992.3	37		CCDS43952.1																																																																																				0.692	NUDT11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056579.1			6	5						6	5	---	---	---	---
