#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_Mutation_Status	i_OREGANNO_ID	i_OREGANNO_Values	i_ORegAnno_bin	i_Other_Transcripts	i_Protein_Change	i_Refseq_mRNA_Id	i_Refseq_prot_Id	i_Sequence_Source	i_Sequencer	i_Sequencing_Phase	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
HTR3B	9177	broad.mit.edu	37	11	113815463	113815463	+	Missense_Mutation	SNP	G	G	A			TCGA-KS-A4I5-01A-11D-A257-08	TCGA-KS-A4I5-11A-11D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af67f563-1ff5-4bde-98d3-2a8423cf3dc3	e2e7d21f-54cf-4016-9a52-93ece18ee0d6	g.chr11:113815463G>A	ENST00000260191.2	+	8	1333	c.1076G>A	c.(1075-1077)cGt>cAt	p.R359H	HTR3B_ENST00000537778.1_Missense_Mutation_p.R348H	NM_006028.4	NP_006019.1	O95264	5HT3B_HUMAN	5-hydroxytryptamine (serotonin) receptor 3B, ionotropic	359					cation transmembrane transport (GO:0098655)|ion transmembrane transport (GO:0034220)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	ion channel activity (GO:0005216)|serotonin receptor activity (GO:0004993)|serotonin-activated cation-selective channel activity (GO:0005232)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(11)	20		all_cancers(61;6.81e-18)|all_epithelial(67;6.67e-11)|all_hematologic(158;4.67e-05)|Melanoma(852;0.000316)|Acute lymphoblastic leukemia(157;0.000976)|Breast(348;0.0101)|Prostate(24;0.0154)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;3.04e-06)|Epithelial(105;1.98e-05)|all cancers(92;0.000201)|OV - Ovarian serous cystadenocarcinoma(223;0.151)	Ergoloid mesylate(DB01049)	AGGGCCCAACGTGCTGTGGTA	0.532																																						uc001pok.3																			0				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(11)	20						c.(1075-1077)cGt>cAt		Homo sapiens 5-hydroxytryptamine (serotonin) receptor 3B (HTR3B), mRNA.							156.0	129.0	138.0					11																	113815463		2201	4296	6497	SO:0001583	missense	9177				synaptic transmission	integral to plasma membrane|postsynaptic membrane	serotonin receptor activity|serotonin-activated cation-selective channel activity	g.chr11:113815463G>A	AF080582	CCDS8364.1	11q23.1	2012-05-22	2012-02-03		ENSG00000149305	ENSG00000149305		"""5-HT (serotonin) receptors"", ""Ligand-gated ion channels / 5-HT (serotonin) receptors, ionotropic"""	5298	protein-coding gene	gene with protein product		604654	"""5-hydroxytryptamine (serotonin) receptor 3B"""			9950429, 10521471	Standard	NM_006028		Approved	5-HT3B	uc001pok.3	O95264	OTTHUMG00000168210	ENST00000260191.2:c.1076G>A	11.37:g.113815463G>A	ENSP00000260191:p.Arg359His		Somatic				HTR3B_uc001pol.3_Missense_Mutation_p.R348H	p.R359H	NM_006028	NP_006019	WXS	Illumina GAIIx	Phase_I	O95264	5HT3B_HUMAN		BRCA - Breast invasive adenocarcinoma(274;3.04e-06)|Epithelial(105;1.98e-05)|all cancers(92;0.000201)|OV - Ovarian serous cystadenocarcinoma(223;0.151)	7	1214	+		all_cancers(61;6.81e-18)|all_epithelial(67;6.67e-11)|all_hematologic(158;4.67e-05)|Melanoma(852;0.000316)|Acute lymphoblastic leukemia(157;0.000976)|Breast(348;0.0101)|Prostate(24;0.0154)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)	359					B0YJ23|Q0VJC3	Missense_Mutation	SNP	ENST00000260191.2	37	c.1076G>A	CCDS8364.1	.	.	.	.	.	.	.	.	.	.	G	11.44	1.638656	0.29157	.	.	ENSG00000149305	ENST00000260191;ENST00000537778	T;T	0.22539	1.95;1.95	5.11	-5.21	0.02815	Neurotransmitter-gated ion-channel transmembrane domain (1);	1.885990	0.01948	N	0.042405	T	0.08846	0.0219	N	0.08118	0	0.09310	N	1	B;B	0.06786	0.001;0.0	B;B	0.04013	0.001;0.0	T	0.16837	-1.0389	10	0.36615	T	0.2	4.6974	1.3729	0.02214	0.3098:0.358:0.148:0.1841	.	348;359	O95264-2;O95264	.;5HT3B_HUMAN	H	359;348	ENSP00000260191:R359H;ENSP00000443118:R348H	ENSP00000260191:R359H	R	+	2	0	HTR3B	113320673	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.468000	0.02350	-0.815000	0.04346	-0.345000	0.07892	CGT		0.532	HTR3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398842.1	NM_006028		29	44	0	0	0	1	0	29	44				
DLC1	10395	broad.mit.edu	37	8	13251080	13251080	+	Silent	SNP	T	T	G			TCGA-KS-A4I5-01A-11D-A257-08	TCGA-KS-A4I5-11A-11D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af67f563-1ff5-4bde-98d3-2a8423cf3dc3	e2e7d21f-54cf-4016-9a52-93ece18ee0d6	g.chr8:13251080T>G	ENST00000276297.4	-	4	1705	c.1296A>C	c.(1294-1296)ggA>ggC	p.G432G	DLC1_ENST00000316609.5_Silent_p.G432G|DLC1_ENST00000511869.1_Silent_p.G432G	NM_182643.2	NP_872584.2	Q96QB1	RHG07_HUMAN	DLC1 Rho GTPase activating protein	432					actin cytoskeleton organization (GO:0030036)|activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|focal adhesion assembly (GO:0048041)|forebrain development (GO:0030900)|heart morphogenesis (GO:0003007)|hindbrain morphogenesis (GO:0021575)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of Rho protein signal transduction (GO:0035024)|negative regulation of stress fiber assembly (GO:0051497)|neural tube closure (GO:0001843)|positive regulation of execution phase of apoptosis (GO:1900119)|positive regulation of protein dephosphorylation (GO:0035307)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	lipid binding (GO:0008289)|Rho GTPase activator activity (GO:0005100)|SH2 domain binding (GO:0042169)			NS(2)|breast(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(39)|lung(32)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	110						TGGGTTTGGTTCCAGAATTGG	0.413																																						uc003wwm.2																			0				NS(2)|breast(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(39)|lung(32)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	110						c.(1294-1296)ggA>ggC		Homo sapiens deleted in liver cancer 1 (DLC1), transcript variant 1, mRNA.							134.0	133.0	133.0					8																	13251080		2203	4300	6503	SO:0001819	synonymous_variant	10395				actin cytoskeleton organization|activation of caspase activity|focal adhesion assembly|forebrain development|heart morphogenesis|hindbrain morphogenesis|induction of apoptosis|negative regulation of Rho protein signal transduction|negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of stress fiber assembly|neural tube closure|positive regulation of protein dephosphorylation|regulation of cell shape|small GTPase mediated signal transduction	caveola|cytosol|focal adhesion|nucleus	Rho GTPase activator activity|SH2 domain binding	g.chr8:13251080T>G	AF035119	CCDS5989.1, CCDS5990.1, CCDS5991.1, CCDS5991.2, CCDS55201.1	8p22	2014-06-20	2014-06-20		ENSG00000164741	ENSG00000164741		"""Rho GTPase activating proteins"", ""StAR-related lipid transfer (START) domain containing"""	2897	protein-coding gene	gene with protein product	"""StAR-related lipid transfer (START) domain containing 12"""	604258	"""deleted in liver cancer 1"""			9605766, 11214970	Standard	NM_182643		Approved	HP, ARHGAP7, STARD12, DLC-1, p122-RhoGAP	uc003wwm.2	Q96QB1	OTTHUMG00000090825	ENST00000276297.4:c.1296A>C	8.37:g.13251080T>G			Somatic				DLC1_uc003wwn.3_Silent_p.G432G|DLC1_uc011kxy.2_Silent_p.G432G	p.G432G	NM_182643	NP_872584	WXS	Illumina GAIIx	Phase_I	Q96QB1	RHG07_HUMAN			3	1740	-			432					B4DR10|B8PTI0|E9PDZ8|E9PF76|E9PGY9|O14868|O43199|Q7Z5R8|Q86UC6|Q9C0E0|Q9H7A2	Silent	SNP	ENST00000276297.4	37	c.1296A>C	CCDS5989.1																																																																																				0.413	DLC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207632.2	NM_182643, NM_006094		47	49	0	0	0	1	0	47	49				
BDH1	622	broad.mit.edu	37	3	197239158	197239158	+	Missense_Mutation	SNP	C	C	A			TCGA-KS-A4I5-01A-11D-A257-08	TCGA-KS-A4I5-11A-11D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af67f563-1ff5-4bde-98d3-2a8423cf3dc3	e2e7d21f-54cf-4016-9a52-93ece18ee0d6	g.chr3:197239158C>A	ENST00000392378.2	-	7	950	c.640G>T	c.(640-642)Ggg>Tgg	p.G214W	BDH1_ENST00000441275.1_Missense_Mutation_p.G127W|BDH1_ENST00000392379.1_Missense_Mutation_p.G214W|BDH1_ENST00000358186.2_Missense_Mutation_p.G214W	NM_004051.4	NP_004042.1	Q02338	BDH_HUMAN	3-hydroxybutyrate dehydrogenase, type 1	214					adipose tissue development (GO:0060612)|brain development (GO:0007420)|cellular ketone body metabolic process (GO:0046950)|cellular lipid metabolic process (GO:0044255)|ketone body biosynthetic process (GO:0046951)|ketone body catabolic process (GO:0046952)|liver development (GO:0001889)|response to cadmium ion (GO:0046686)|response to corticosterone (GO:0051412)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to growth hormone (GO:0060416)|response to insulin (GO:0032868)|response to nutrient (GO:0007584)|response to starvation (GO:0042594)|response to toxic substance (GO:0009636)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	3-hydroxybutyrate dehydrogenase activity (GO:0003858)|phospholipid binding (GO:0005543)			endometrium(2)|large_intestine(1)|lung(6)|ovary(1)|skin(1)	11	all_cancers(143;3.35e-10)|Ovarian(172;0.0418)|Breast(254;0.0437)	Lung NSC(153;0.118)	Epithelial(36;3.52e-24)|all cancers(36;1.79e-22)|OV - Ovarian serous cystadenocarcinoma(49;2.32e-19)|LUSC - Lung squamous cell carcinoma(58;1.02e-06)|Lung(62;1.34e-06)	GBM - Glioblastoma multiforme(93;0.0977)		GCCTCTACCCCGAACTTGGTG	0.632																																						uc003fxr.3																			0		p.F213L(1)		endometrium(2)|large_intestine(1)|lung(6)|ovary(1)|skin(1)	11						c.(640-642)Ggg>Tgg		Homo sapiens 3-hydroxybutyrate dehydrogenase, type 1 (BDH1), nuclear gene encoding mitochondrial protein, transcript variant 3, mRNA.	NADH(DB00157)						43.0	44.0	43.0					3																	197239158		2203	4300	6503	SO:0001583	missense	622				cellular lipid metabolic process|ketone body biosynthetic process|ketone body catabolic process	mitochondrial matrix	3-hydroxybutyrate dehydrogenase activity	g.chr3:197239158C>A	M93107	CCDS3328.1	3q29	2011-09-14	2005-11-15	2005-11-15	ENSG00000161267	ENSG00000161267	1.1.1.30	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"""	1027	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 9C, member 1"""	603063	"""3-hydroxybutyrate dehydrogenase (heart, mitochondrial)"""	BDH		1639787, 19027726	Standard	XM_005269352		Approved	SDR9C1	uc003fxs.3	Q02338	OTTHUMG00000155478	ENST00000392378.2:c.640G>T	3.37:g.197239158C>A	ENSP00000376183:p.Gly214Trp		Somatic				BDH1_uc003fxs.3_Missense_Mutation_p.G214W|BDH1_uc003fxu.3_Missense_Mutation_p.G214W	p.G214W	NM_203314	NP_976060	WXS	Illumina GAIIx	Phase_I	Q02338	BDH_HUMAN	Epithelial(36;3.52e-24)|all cancers(36;1.79e-22)|OV - Ovarian serous cystadenocarcinoma(49;2.32e-19)|LUSC - Lung squamous cell carcinoma(58;1.02e-06)|Lung(62;1.34e-06)	GBM - Glioblastoma multiforme(93;0.0977)	7	1042	-	all_cancers(143;3.35e-10)|Ovarian(172;0.0418)|Breast(254;0.0437)	Lung NSC(153;0.118)	214					D3DXC0|Q96ET1|Q9BRZ4	Missense_Mutation	SNP	ENST00000392378.2	37	c.640G>T	CCDS3328.1	.	.	.	.	.	.	.	.	.	.	C	21.2	4.115886	0.77323	.	.	ENSG00000161267	ENST00000392378;ENST00000358186;ENST00000392379;ENST00000441275;ENST00000446746	D;D;D;D;D	0.94184	-3.37;-3.37;-3.37;-3.37;-3.37	5.3	5.3	0.74995	Short-chain dehydrogenase/reductase, conserved site (1);NAD(P)-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.96694	0.8921	M	0.81239	2.535	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97089	0.9789	10	0.87932	D	0	.	16.8338	0.85951	0.0:1.0:0.0:0.0	.	214	Q02338	BDH_HUMAN	W	214;214;214;127;127	ENSP00000376183:G214W;ENSP00000350914:G214W;ENSP00000376184:G214W;ENSP00000411014:G127W;ENSP00000387648:G127W	ENSP00000350914:G214W	G	-	1	0	BDH1	198723555	1.000000	0.71417	0.957000	0.39632	0.414000	0.31173	7.711000	0.84669	2.634000	0.89283	0.655000	0.94253	GGG		0.632	BDH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340267.1	NM_004051		20	36	0	0	0	1	0	20	36				
PCDHGA3	56112	broad.mit.edu	37	5	140725487	140725487	+	Silent	SNP	G	G	A			TCGA-KS-A4I5-01A-11D-A257-08	TCGA-KS-A4I5-11A-11D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af67f563-1ff5-4bde-98d3-2a8423cf3dc3	e2e7d21f-54cf-4016-9a52-93ece18ee0d6	g.chr5:140725487G>A	ENST00000253812.6	+	1	1887	c.1887G>A	c.(1885-1887)gcG>gcA	p.A629A	PCDHGA2_ENST00000394576.2_Intron|PCDHGA1_ENST00000517417.1_Intron	NM_018916.3|NM_032011.1	NP_061739.2|NP_114400.1	Q9Y5H0	PCDG3_HUMAN	protocadherin gamma subfamily A, 3	629	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.A629A(1)		breast(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGCGCACGGCGCGAGCCCTGC	0.701																																						uc003ljm.2																			1	Substitution - coding silent(1)	p.A629A(1)	lung(1)	breast(2)|central_nervous_system(2)|endometrium(6)|kidney(4)|large_intestine(4)|lung(10)|ovary(4)|prostate(1)|urinary_tract(2)	35						c.(1885-1887)gcG>gcA		Homo sapiens protocadherin gamma subfamily A, 3 (PCDHGA3), transcript variant 1, mRNA.							9.0	14.0	13.0					5																	140725487		1964	3983	5947	SO:0001819	synonymous_variant	56097				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding	g.chr5:140725487G>A	AF152510	CCDS47290.1, CCDS75329.1	5q31	2010-01-26			ENSG00000254245	ENSG00000254245		"""Cadherins / Protocadherins : Clustered"""	8701	other	protocadherin		606290				10380929	Standard	NM_032011		Approved	PCDH-GAMMA-A3		Q9Y5H0	OTTHUMG00000163680	ENST00000253812.6:c.1887G>A	5.37:g.140725487G>A			Somatic				PCDHGC5_uc003lji.2_Intron|PCDHGC5_uc003ljk.2_Intron|PCDHGC5_uc011dap.2_Silent_p.A629A	p.A629A	NM_018916	NP_061739	WXS	Illumina GAIIx	Phase_I	Q9Y5F6	PCDGM_HUMAN	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		0	1887	+			631			Cadherin 6.		Q9Y5D4	Silent	SNP	ENST00000253812.6	37	c.1887G>A	CCDS47290.1																																																																																				0.701	PCDHGA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377017.1	NM_018916		33	67	0	0	0	1	0	33	67				
FAM124B	79843	broad.mit.edu	37	2	225266211	225266211	+	Missense_Mutation	SNP	G	G	A	rs181816086		TCGA-KS-A4I5-01A-11D-A257-08	TCGA-KS-A4I5-11A-11D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af67f563-1ff5-4bde-98d3-2a8423cf3dc3	e2e7d21f-54cf-4016-9a52-93ece18ee0d6	g.chr2:225266211G>A	ENST00000409685.3	-	1	540	c.275C>T	c.(274-276)tCg>tTg	p.S92L	FAM124B_ENST00000243806.2_Missense_Mutation_p.S92L|FAM124B_ENST00000389874.3_Missense_Mutation_p.S92L	NM_001122779.1	NP_001116251.1	Q9H5Z6	F124B_HUMAN	family with sequence similarity 124B	92										endometrium(2)|large_intestine(2)|lung(7)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)	16		Renal(207;0.0112)|all_lung(227;0.0126)|Lung NSC(271;0.0161)|all_hematologic(139;0.138)		Epithelial(121;4.4e-10)|all cancers(144;2.02e-07)|Lung(261;0.00766)|LUSC - Lung squamous cell carcinoma(224;0.00825)		CTGCCATGGCGAATGCTGGAG	0.582													G|||	1	0.000199681	0.0	0.0014	5008	,	,		18416	0.0		0.0	False		,,,				2504	0.0					uc002vnx.3																			0				endometrium(2)|large_intestine(2)|lung(7)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)	16						c.(274-276)tCg>tTg		Homo sapiens family with sequence similarity 124B (FAM124B), transcript variant 1, mRNA.							60.0	56.0	57.0					2																	225266211		2203	4300	6503	SO:0001583	missense	79843						protein binding	g.chr2:225266211G>A	AK075126	CCDS2461.1, CCDS46527.1	2q36.2	2008-02-05			ENSG00000124019	ENSG00000124019			26224	protein-coding gene	gene with protein product						12477932	Standard	NM_001122779		Approved	FLJ22746	uc002vnx.3	Q9H5Z6	OTTHUMG00000133168	ENST00000409685.3:c.275C>T	2.37:g.225266211G>A	ENSP00000386895:p.Ser92Leu		Somatic				FAM124B_uc002vnw.3_Missense_Mutation_p.S92L	p.S92L	NM_001122779	NP_001116251	WXS	Illumina GAIIx	Phase_I	Q9H5Z6	F124B_HUMAN		Epithelial(121;4.4e-10)|all cancers(144;2.02e-07)|Lung(261;0.00766)|LUSC - Lung squamous cell carcinoma(224;0.00825)	0	501	-		Renal(207;0.0112)|all_lung(227;0.0126)|Lung NSC(271;0.0161)|all_hematologic(139;0.138)	92					A6NNC7|Q8NBZ4|Q8TAV7	Missense_Mutation	SNP	ENST00000409685.3	37	c.275C>T	CCDS46527.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	G	14.33	2.502052	0.44455	.	.	ENSG00000124019	ENST00000389874;ENST00000409685;ENST00000243806	T;T;T	0.44881	0.91;0.91;0.91	5.69	4.81	0.61882	.	0.273838	0.41938	D	0.000784	T	0.27798	0.0684	N	0.22421	0.69	0.25126	N	0.990606	P;P	0.47106	0.89;0.89	B;B	0.34418	0.182;0.088	T	0.15780	-1.0425	10	0.72032	D	0.01	-1.9118	15.3105	0.74028	0.0:0.1794:0.8206:0.0	.	92;92	Q9H5Z6;Q9H5Z6-2	F124B_HUMAN;.	L	92	ENSP00000374524:S92L;ENSP00000386895:S92L;ENSP00000243806:S92L	ENSP00000243806:S92L	S	-	2	0	FAM124B	224974455	1.000000	0.71417	0.152000	0.22495	0.155000	0.21991	7.377000	0.79668	1.399000	0.46721	0.655000	0.94253	TCG		0.582	FAM124B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330873.1	NM_024785		13	36	0	0	0	1	0	13	36				
BRAF	673	broad.mit.edu	37	7	140453136	140453136	+	Missense_Mutation	SNP	A	A	T	rs121913377|rs113488022|rs121913227|rs397516897		TCGA-KS-A4I5-01A-11D-A257-08	TCGA-KS-A4I5-11A-11D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af67f563-1ff5-4bde-98d3-2a8423cf3dc3	e2e7d21f-54cf-4016-9a52-93ece18ee0d6	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)	uc003vwc.4	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(41204)|p.V600K(615)|p.V600?(377)|p.V600R(99)|p.V600D(40)|p.V600_K601>E(30)|p.V600L(28)|p.V600A(24)|p.V600G(22)|p.V600M(22)|p.A598_T599insV(7)|p.T599_V600insT(7)|p.T599I(5)|p.V600Q(4)|p.T599_R603>I(4)|p.T599_V600insTT(3)|p.T599_V600insDFGLAT(2)|p.T599_V600>IAL(2)|p.V600_S605>EK(2)|p.T599T(2)|p.V600_S605>DV(2)|p.V600_S605>D(2)|p.V600_W604del(1)|p.V600V(1)|p.T599_V600insV(1)|p.V600>DLAT(1)|p.D594_T599del(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		Homo sapiens v-raf murine sarcoma viral oncogene homolog B1 (BRAF), mRNA.	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		Somatic					p.V600E	NM_004333	NP_004324	WXS	Illumina GAIIx	Phase_I	P15056	BRAF_HUMAN			14	1860	-	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		21	40	0	0	0	1	0	21	40				
C17orf59	54785	broad.mit.edu	37	17	8093098	8093098	+	Missense_Mutation	SNP	A	A	C			TCGA-KS-A4I5-01A-11D-A257-08	TCGA-KS-A4I5-11A-11D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af67f563-1ff5-4bde-98d3-2a8423cf3dc3	e2e7d21f-54cf-4016-9a52-93ece18ee0d6	g.chr17:8093098A>C	ENST00000389017.4	-	1	466	c.361T>G	c.(361-363)Tcc>Gcc	p.S121A	MIR3676_ENST00000579470.1_RNA	NM_017622.2	NP_060092.2	Q96GS4	CQ059_HUMAN	chromosome 17 open reading frame 59	121										large_intestine(2)|lung(3)|urinary_tract(1)	6						CTCCCGGAGGAGGGCTTGCCC	0.731																																						uc010vut.2																			0				large_intestine(2)|lung(3)|urinary_tract(1)	6						c.(361-363)Tcc>Gcc		Homo sapiens chromosome 17 open reading frame 59 (C17orf59), mRNA.							8.0	9.0	9.0					17																	8093098		1795	3741	5536	SO:0001583	missense	54785							g.chr17:8093098A>C	BC018880	CCDS11133.2	17p13.1	2005-12-16			ENSG00000196544	ENSG00000196544			25939	protein-coding gene	gene with protein product						12477932	Standard	NM_017622		Approved	FLJ20014	uc010vut.2	Q96GS4	OTTHUMG00000153930	ENST00000389017.4:c.361T>G	17.37:g.8093098A>C	ENSP00000373669:p.Ser121Ala		Somatic					p.S121A	NM_017622	NP_060092	WXS	Illumina GAIIx	Phase_I	Q96GS4	CQ059_HUMAN			0	467	-			121					Q53HS4|Q9NXW8	Missense_Mutation	SNP	ENST00000389017.4	37	c.361T>G	CCDS11133.2	.	.	.	.	.	.	.	.	.	.	C	0.007	-1.936579	0.00484	.	.	ENSG00000196544	ENST00000389017	.	.	.	5.41	2.08	0.27032	.	0.784045	0.10974	N	0.613490	T	0.12860	0.0312	N	0.03608	-0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.32851	-0.9891	9	0.02654	T	1	0.816	6.24	0.20785	0.4977:0.4141:0.0:0.0882	.	121	Q96GS4	CQ059_HUMAN	A	121	.	ENSP00000373669:S121A	S	-	1	0	C17orf59	8033823	0.000000	0.05858	0.000000	0.03702	0.090000	0.18270	0.279000	0.18771	0.247000	0.21414	-0.217000	0.12591	TCC		0.731	C17orf59-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333072.1	NM_017622		6	12	0	0	0	1	0	6	12				
MED9	55090	broad.mit.edu	37	17	17380300	17380300	+	5'UTR	SNP	G	G	A	rs528515567		TCGA-KS-A4I5-01A-11D-A257-08	TCGA-KS-A4I5-11A-11D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af67f563-1ff5-4bde-98d3-2a8423cf3dc3	e2e7d21f-54cf-4016-9a52-93ece18ee0d6	g.chr17:17380300G>A	ENST00000268711.3	+	0	1				MED9_ENST00000580462.1_5'Flank	NM_018019.2	NP_060489.1	Q9NWA0	MED9_HUMAN	mediator complex subunit 9							mediator complex (GO:0016592)	RNA polymerase II transcription cofactor activity (GO:0001104)			cervix(1)|endometrium(1)|large_intestine(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	7						GTGGTGACGTGTAGAGTGCGC	0.711													G|||	1	0.000199681	0.0008	0.0	5008	,	,		9622	0.0		0.0	False		,,,				2504	0.0					uc002grh.1																			0				cervix(1)|endometrium(1)|large_intestine(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	7						c.e1-1		Homo sapiens mediator complex subunit 9 (MED9), mRNA.																																				SO:0001623	5_prime_UTR_variant	55090				regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent		protein binding	g.chr17:17380300G>A	BC000647	CCDS11184.1	17p11.2	2007-07-30	2007-07-30		ENSG00000141026	ENSG00000141026			25487	protein-coding gene	gene with protein product		609878	"""mediator of RNA polymerase II transcription, subunit 9 homolog (S. cerevisiae)"""			11997338	Standard	NM_018019		Approved	FLJ10193, MED25	uc002grh.1	Q9NWA0	OTTHUMG00000059293	ENST00000268711.3:c.-56G>A	17.37:g.17380300G>A			Somatic						NM_018019	NP_060489	WXS	Illumina GAIIx	Phase_I	Q9NWA0	MED9_HUMAN			1	1	+									Splice_Site	SNP	ENST00000268711.3	37	c.-55_splice	CCDS11184.1																																																																																				0.711	MED9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131669.2	NM_018019		6	34	0	0	0	1	0	6	34				
SPTA1	6708	broad.mit.edu	37	1	158583518	158583518	+	Missense_Mutation	SNP	G	G	T			TCGA-KS-A4I5-01A-11D-A257-08	TCGA-KS-A4I5-11A-11D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af67f563-1ff5-4bde-98d3-2a8423cf3dc3	e2e7d21f-54cf-4016-9a52-93ece18ee0d6	g.chr1:158583518G>T	ENST00000368147.4	-	50	7162	c.6982C>A	c.(6982-6984)Cca>Aca	p.P2328T	SPTA1_ENST00000485680.1_5'Flank	NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	2328	EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.				actin filament capping (GO:0051693)|actin filament organization (GO:0007015)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|lymphocyte homeostasis (GO:0002260)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of protein binding (GO:0032092)|positive regulation of T cell proliferation (GO:0042102)|regulation of cell shape (GO:0008360)	actin cytoskeleton (GO:0015629)|cuticular plate (GO:0032437)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)			NS(3)|breast(7)|cervix(1)|endometrium(22)|kidney(9)|large_intestine(29)|liver(2)|lung(183)|ovary(5)|prostate(18)|skin(11)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(6)	307	all_hematologic(112;0.0378)					TACCTCCCTGGATCCACAGCA	0.493																																						uc001fst.1																			0				NS(3)|breast(7)|cervix(1)|endometrium(22)|kidney(9)|large_intestine(29)|liver(2)|lung(183)|ovary(5)|prostate(18)|skin(11)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(6)	307						c.(6982-6984)Cca>Aca		Homo sapiens spectrin, alpha, erythrocytic 1 (elliptocytosis 2) (SPTA1), mRNA.							69.0	68.0	69.0					1																	158583518		1945	4133	6078	SO:0001583	missense	6708				actin filament capping|actin filament organization|axon guidance|regulation of cell shape	cytosol|intrinsic to internal side of plasma membrane|spectrin|spectrin-associated cytoskeleton	actin filament binding|calcium ion binding|structural constituent of cytoskeleton	g.chr1:158583518G>T	M61877	CCDS41423.1	1q21	2014-06-23	2014-06-23		ENSG00000163554	ENSG00000163554		"""EF-hand domain containing"""	11272	protein-coding gene	gene with protein product	"""elliptocytosis 2"""	182860	"""spectrin, alpha, erythrocytic 1 (elliptocytosis 2)"""				Standard	NM_003126		Approved	EL2	uc001fst.1	P02549	OTTHUMG00000019636	ENST00000368147.4:c.6982C>A	1.37:g.158583518G>T	ENSP00000357129:p.Pro2328Thr		Somatic					p.P2328T	NM_003126	NP_003117	WXS	Illumina GAIIx	Phase_I	P02549	SPTA1_HUMAN			49	7181	-	all_hematologic(112;0.0378)		2328			EF-hand 2.		Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Missense_Mutation	SNP	ENST00000368147.4	37	c.6982C>A	CCDS41423.1	.	.	.	.	.	.	.	.	.	.	G	19.84	3.901793	0.72754	.	.	ENSG00000163554	ENST00000368148;ENST00000368147	T;T	0.20463	2.07;2.07	5.1	5.1	0.69264	EF-hand-like domain (1);	0.000000	0.31989	N	0.006760	T	0.40719	0.1128	M	0.76170	2.325	0.58432	D	0.999997	D	0.89917	1.0	D	0.79108	0.992	T	0.30387	-0.9980	10	0.72032	D	0.01	.	17.2641	0.87081	0.0:0.0:1.0:0.0	.	2328	P02549	SPTA1_HUMAN	T	2328;2325	ENSP00000357130:P2328T;ENSP00000357129:P2325T	ENSP00000357129:P2325T	P	-	1	0	SPTA1	156850142	1.000000	0.71417	0.639000	0.29394	0.608000	0.37181	8.730000	0.91510	2.661000	0.90470	0.650000	0.86243	CCA		0.493	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126		14	34	0	0	0	1	0	14	34				
FAT3	120114	broad.mit.edu	37	11	92568204	92568204	+	Missense_Mutation	SNP	G	G	C			TCGA-KS-A4I5-01A-11D-A257-08	TCGA-KS-A4I5-11A-11D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af67f563-1ff5-4bde-98d3-2a8423cf3dc3	e2e7d21f-54cf-4016-9a52-93ece18ee0d6	g.chr11:92568204G>C	ENST00000298047.6	+	14	10057	c.10040G>C	c.(10039-10041)aGt>aCt	p.S3347T	FAT3_ENST00000525166.1_Missense_Mutation_p.S3197T|FAT3_ENST00000409404.2_Missense_Mutation_p.S3347T			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	3347	Cadherin 31. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(10)|kidney(4)|large_intestine(11)|liver(2)|lung(37)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	85		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)				GACGTCTACAGTGCGGTTATC	0.517										TCGA Ovarian(4;0.039)																												uc001pdj.4																			0				NS(1)|breast(2)|endometrium(10)|kidney(4)|large_intestine(11)|liver(2)|lung(37)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	85						c.(10039-10041)aGt>aCt		Homo sapiens FAT tumor suppressor homolog 3 (Drosophila) (FAT3), mRNA.							53.0	54.0	54.0					11																	92568204		1952	4155	6107	SO:0001583	missense	120114				homophilic cell adhesion|multicellular organismal development	integral to membrane|plasma membrane	calcium ion binding	g.chr11:92568204G>C	AB076400		11q14.3	2013-05-31	2013-05-31		ENSG00000165323	ENSG00000165323		"""Cadherins / Cadherin-related"""	23112	protein-coding gene	gene with protein product	"""cadherin-related family member 10"""	612483	"""FAT tumor suppressor homolog 3 (Drosophila)"""			11811999	Standard	NM_001008781		Approved	KIAA1989, CDHF15, CDHR10	uc001pdj.4	Q8TDW7	OTTHUMG00000154468	ENST00000298047.6:c.10040G>C	11.37:g.92568204G>C	ENSP00000298047:p.Ser3347Thr	TCGA Ovarian(4;0.039)	Somatic					p.S3347T	NM_001008781	NP_001008781	WXS	Illumina GAIIx	Phase_I	Q8TDW7	FAT3_HUMAN			13	10057	+		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)	3347			Cadherin 31.		B5MDB0|Q96AU6	Missense_Mutation	SNP	ENST00000298047.6	37	c.10040G>C		.	.	.	.	.	.	.	.	.	.	G	7.110	0.575858	0.13623	.	.	ENSG00000165323	ENST00000298047;ENST00000409404;ENST00000525166	T;T;T	0.02525	4.26;4.26;4.26	5.46	5.46	0.80206	.	.	.	.	.	T	0.02888	0.0086	N	0.20328	0.56	0.80722	D	1	B	0.22800	0.075	B	0.22386	0.039	T	0.54576	-0.8273	9	0.10636	T	0.68	.	19.3231	0.94250	0.0:0.0:1.0:0.0	.	3347	Q8TDW7-3	.	T	3347;3347;3197	ENSP00000298047:S3347T;ENSP00000387040:S3347T;ENSP00000432586:S3197T	ENSP00000298047:S3347T	S	+	2	0	FAT3	92207852	1.000000	0.71417	0.953000	0.39169	0.291000	0.27294	5.258000	0.65479	2.539000	0.85634	0.655000	0.94253	AGT		0.517	FAT3-201	KNOWN	basic	protein_coding	protein_coding		NM_001008781		7	10	0	0	0	1	0	7	10				
RREB1	6239	broad.mit.edu	37	6	7231362	7231362	+	Silent	SNP	C	C	T			TCGA-KS-A4I5-01A-11D-A257-08	TCGA-KS-A4I5-11A-11D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af67f563-1ff5-4bde-98d3-2a8423cf3dc3	e2e7d21f-54cf-4016-9a52-93ece18ee0d6	g.chr6:7231362C>T	ENST00000349384.6	+	10	3344	c.3030C>T	c.(3028-3030)ggC>ggT	p.G1010G	RREB1_ENST00000379938.2_Silent_p.G1010G|RREB1_ENST00000379933.3_Silent_p.G1010G|RREB1_ENST00000334984.6_Silent_p.G1010G	NM_001003698.3	NP_001003698.1	Q92766	RREB1_HUMAN	ras responsive element binding protein 1	1010	Pro-rich.				multicellular organismal development (GO:0007275)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|Ras protein signal transduction (GO:0007265)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear body (GO:0016604)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(5)|lung(18)|ovary(5)|pancreas(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	58	Ovarian(93;0.0398)	all_hematologic(90;0.0384)|Prostate(151;0.191)				CCCTGCAGGGCCCTGTTCAGC	0.667																																						uc003mxb.3																			0				breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(5)|lung(18)|ovary(5)|pancreas(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	58						c.(3028-3030)ggC>ggT		Homo sapiens ras responsive element binding protein 1 (RREB1), transcript variant 1, mRNA.							18.0	22.0	20.0					6																	7231362		2190	4266	6456	SO:0001819	synonymous_variant	6239				Ras protein signal transduction|multicellular organismal development|positive regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	cytoplasm|nuclear speck	DNA binding|zinc ion binding	g.chr6:7231362C>T	U26914	CCDS34335.1, CCDS34336.1, CCDS54963.1	6p25	2013-01-08			ENSG00000124782	ENSG00000124782		"""Zinc fingers, C2H2-type"""	10449	protein-coding gene	gene with protein product	"""hindsight homolog (drosophila)"""	602209				9367691, 18394891	Standard	NM_001003698		Approved	HNT	uc003mxb.3	Q92766	OTTHUMG00000014201	ENST00000349384.6:c.3030C>T	6.37:g.7231362C>T			Somatic				RREB1_uc021yky.1_Silent_p.G1010G|RREB1_uc003mxc.3_Silent_p.G1010G|RREB1_uc010jnx.3_Silent_p.G1010G|RREB1_uc021ykz.1_Silent_p.G1010G|RREB1_uc021yla.1_Intron	p.G1010G	NM_001003699	NP_001003699	WXS	Illumina GAIIx	Phase_I	Q92766	RREB1_HUMAN			9	3522	+	Ovarian(93;0.0398)	all_hematologic(90;0.0384)|Prostate(151;0.191)	1010			Pro-rich.		A2RRF5|E2GM80|E2GM81|O75567|O75568|Q5VYB2|Q6BEP5|Q6BEP6|Q6BEP8|Q86SU2|Q9Y474	Silent	SNP	ENST00000349384.6	37	c.3030C>T	CCDS34336.1																																																																																				0.667	RREB1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000352985.1			5	40	0	0	0	1	0	5	40				
COL22A1	169044	broad.mit.edu	37	8	139668161	139668161	+	Silent	SNP	C	C	T			TCGA-KS-A4I5-01A-11D-A257-08	TCGA-KS-A4I5-11A-11D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af67f563-1ff5-4bde-98d3-2a8423cf3dc3	e2e7d21f-54cf-4016-9a52-93ece18ee0d6	g.chr8:139668161C>T	ENST00000303045.6	-	45	3758	c.3312G>A	c.(3310-3312)ggG>ggA	p.G1104G	COL22A1_ENST00000435777.1_Silent_p.G1084G|COL22A1_ENST00000341807.4_5'UTR	NM_152888.1	NP_690848.1	Q8NFW1	COMA1_HUMAN	collagen, type XXII, alpha 1	1104	Gly-rich.|Pro-rich.				extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(14)|large_intestine(29)|lung(107)|ovary(13)|pancreas(1)|prostate(3)|skin(12)|upper_aerodigestive_tract(15)|urinary_tract(4)	211	all_epithelial(106;1.55e-12)|Lung NSC(106;1.67e-05)|all_lung(105;3.39e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0517)			GATTTATGTCCCCTGGAGACA	0.388										HNSCC(7;0.00092)																												uc003yvd.3																			0				breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(14)|large_intestine(29)|lung(107)|ovary(13)|pancreas(1)|prostate(3)|skin(12)|upper_aerodigestive_tract(15)|urinary_tract(4)	211						c.(3310-3312)ggG>ggA		Homo sapiens collagen, type XXII, alpha 1 (COL22A1), mRNA.							203.0	206.0	205.0					8																	139668161		2203	4300	6503	SO:0001819	synonymous_variant	169044				cell adhesion	collagen|cytoplasm	structural molecule activity	g.chr8:139668161C>T	AF406780	CCDS6376.1	8q24.3	2013-01-16			ENSG00000169436	ENSG00000169436		"""Collagens"""	22989	protein-coding gene	gene with protein product		610026					Standard	NM_152888		Approved		uc003yvd.3	Q8NFW1	OTTHUMG00000150035	ENST00000303045.6:c.3312G>A	8.37:g.139668161C>T		HNSCC(7;0.00092)	Somatic				COL22A1_uc011ljo.2_Silent_p.G384G	p.G1104G	NM_152888	NP_690848	WXS	Illumina GAIIx	Phase_I	Q8NFW1	COMA1_HUMAN	BRCA - Breast invasive adenocarcinoma(115;0.0517)		44	3759	-	all_epithelial(106;1.55e-12)|Lung NSC(106;1.67e-05)|all_lung(105;3.39e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		1104			Gly-rich.|Pro-rich.		B7ZMH0|C9K0G4|Q8IVT9	Silent	SNP	ENST00000303045.6	37	c.3312G>A	CCDS6376.1																																																																																				0.388	COL22A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000315905.2	XM_291257		7	131	0	0	0	1	0	7	131				
PSMA4	5685	broad.mit.edu	37	15	78837982	78837982	+	Missense_Mutation	SNP	G	G	A			TCGA-KS-A4I5-01A-11D-A257-08	TCGA-KS-A4I5-11A-11D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af67f563-1ff5-4bde-98d3-2a8423cf3dc3	e2e7d21f-54cf-4016-9a52-93ece18ee0d6	g.chr15:78837982G>A	ENST00000044462.7	+	7	533	c.383G>A	c.(382-384)cGt>cAt	p.R128H	PSMA4_ENST00000559082.1_Missense_Mutation_p.R128H|PSMA4_ENST00000558341.1_Intron|PSMA4_ENST00000560217.1_Missense_Mutation_p.R97H|PSMA4_ENST00000558281.1_Missense_Mutation_p.R128H|PSMA4_ENST00000413382.2_Missense_Mutation_p.R57H|PSMA4_ENST00000557929.1_3'UTR|PSMA4_ENST00000558094.1_Missense_Mutation_p.R40H	NM_002789.4	NP_002780.1	P25789	PSA4_HUMAN	proteasome (prosome, macropain) subunit, alpha type, 4	128					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome complex (GO:0000502)|proteasome core complex (GO:0005839)|proteasome core complex, alpha-subunit complex (GO:0019773)	threonine-type endopeptidase activity (GO:0004298)			kidney(2)|large_intestine(2)|lung(2)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	9						AAAGGAAAACGTCCCTTTGGT	0.408																																						uc002bdu.4																			0				kidney(2)|large_intestine(2)|lung(2)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	9						c.(382-384)cGt>cAt		Homo sapiens proteasome (prosome, macropain) subunit, alpha type, 4 (PSMA4), transcript variant 1, mRNA.							200.0	198.0	199.0					15																	78837982		2196	4293	6489	SO:0001583	missense	5685				DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle|anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|interspecies interaction between organisms|mRNA metabolic process|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|viral reproduction	cytoplasm|nucleus|proteasome core complex, alpha-subunit complex	identical protein binding|threonine-type endopeptidase activity	g.chr15:78837982G>A	BC005361	CCDS10303.1, CCDS45319.1	15q24.1	2004-01-19			ENSG00000041357	ENSG00000041357		"""Proteasome (prosome, macropain) subunits"""	9533	protein-coding gene	gene with protein product		176846				2025653	Standard	NM_002789		Approved	HC9, HsT17706	uc010blf.3	P25789	OTTHUMG00000143859	ENST00000044462.7:c.383G>A	15.37:g.78837982G>A	ENSP00000044462:p.Arg128His		Somatic				PSMA4_uc010blf.3_Missense_Mutation_p.R128H|PSMA4_uc002bdv.4_Missense_Mutation_p.R57H|PSMA4_uc002bdw.4_Missense_Mutation_p.R104H|PSMA4_uc002bdx.4_Missense_Mutation_p.R57H	p.R128H	NM_002789	NP_001096138	WXS	Illumina GAIIx	Phase_I	P25789	PSA4_HUMAN			6	541	+			128					D3DW86|Q53XP2|Q567Q5|Q8TBD1	Missense_Mutation	SNP	ENST00000044462.7	37	c.383G>A	CCDS10303.1	.	.	.	.	.	.	.	.	.	.	G	32	5.182317	0.94885	.	.	ENSG00000041357	ENST00000413382;ENST00000044462	T;T	0.29655	1.56;1.56	6.08	5.17	0.71159	.	0.044138	0.85682	D	0.000000	T	0.72645	0.3486	H	0.99026	4.405	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.85025	0.0914	10	0.87932	D	0	-10.1268	15.4166	0.74974	0.0663:0.0:0.9337:0.0	.	128	P25789	PSA4_HUMAN	H	57;128	ENSP00000402118:R57H;ENSP00000044462:R128H	ENSP00000044462:R128H	R	+	2	0	PSMA4	76625037	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	9.575000	0.98187	1.586000	0.49944	0.591000	0.81541	CGT		0.408	PSMA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000290107.5	NM_002789		46	62	0	0	0	1	0	46	62				
MUC6	4588	broad.mit.edu	37	11	1030583	1030583	+	Frame_Shift_Del	DEL	G	G	-	rs369364495	byFrequency	TCGA-KS-A4I5-01A-11D-A257-08	TCGA-KS-A4I5-11A-11D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af67f563-1ff5-4bde-98d3-2a8423cf3dc3	e2e7d21f-54cf-4016-9a52-93ece18ee0d6	g.chr11:1030583delG	ENST00000421673.2	-	7	932	c.882delC	c.(880-882)cccfs	p.P294fs		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	294					cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)	extracellular matrix structural constituent (GO:0005201)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(8)|kidney(10)|large_intestine(6)|lung(43)|ovary(4)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	80		all_cancers(49;3.3e-08)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		all cancers(45;1.24e-24)|BRCA - Breast invasive adenocarcinoma(625;0.00031)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		AGCACAGGCCGGGGCTCCGCC	0.706																																						uc001lsw.2																			0				breast(1)|central_nervous_system(1)|cervix(2)|endometrium(8)|kidney(10)|large_intestine(6)|lung(43)|ovary(4)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	80						c.(880-882)cccfs		Homo sapiens mucin 6, oligomeric mucus/gel-forming (MUC6), mRNA.							3.0	4.0	4.0					11																	1030583		1614	3675	5289	SO:0001589	frameshift_variant	4588				maintenance of gastrointestinal epithelium	extracellular region	extracellular matrix structural constituent	g.chr11:1030583delG	U97698, AY312160	CCDS44513.1	11p15.5	2008-02-05	2006-03-14		ENSG00000184956	ENSG00000184956		"""Mucins"""	7517	protein-coding gene	gene with protein product		158374	"""mucin 6, gastric"""			7680650	Standard	NM_005961		Approved		uc001lsw.2	Q6W4X9	OTTHUMG00000165140	ENST00000421673.2:c.882delC	11.37:g.1030583delG	ENSP00000406861:p.Pro294fs		Somatic					p.P294fs	NM_005961	NP_005952	WXS	Illumina GAIIx	Phase_I	Q6W4X9	MUC6_HUMAN		all cancers(45;1.24e-24)|BRCA - Breast invasive adenocarcinoma(625;0.00031)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	6	933	-		all_cancers(49;3.3e-08)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)	294					O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	Frame_Shift_Del	DEL	ENST00000421673.2	37	c.882delC	CCDS44513.1																																																																																				0.706	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382120.2	XM_290540		2	4						2	4	---	---	---	---
