#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
DNAH9	1770	broad.mit.edu	37	17	11757449	11757449	+	Missense_Mutation	SNP	G	G	A			TCGA-DJ-A4UL-01A-11D-A257-08	TCGA-DJ-A4UL-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1f10660a-2465-42ed-a2a9-206fbf06bc3f	008c8709-0bc8-4d3c-8792-abc47b447fac	g.chr17:11757449G>A	ENST00000262442.4	+	50	9705	c.9637G>A	c.(9637-9639)Gtc>Atc	p.V3213I	DNAH9_ENST00000454412.2_Missense_Mutation_p.V3213I	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	3213	Stalk. {ECO:0000250}.				cell projection organization (GO:0030030)|cellular component movement (GO:0006928)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|spermatogenesis (GO:0007283)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(2)|autonomic_ganglia(1)|breast(15)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(6)|kidney(17)|large_intestine(49)|liver(2)|lung(123)|ovary(6)|pancreas(1)|prostate(6)|skin(21)|stomach(2)|upper_aerodigestive_tract(13)|urinary_tract(4)	290		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)		GGCTGCTAAGGTCACCATGGC	0.562																																						ENST00000262442.3																			0				NS(2)|autonomic_ganglia(1)|breast(15)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(6)|kidney(17)|large_intestine(49)|liver(2)|lung(123)|ovary(6)|pancreas(1)|prostate(6)|skin(21)|stomach(2)|upper_aerodigestive_tract(13)|urinary_tract(4)	290						c.(9637-9639)Gtc>Atc		dynein, axonemal, heavy chain 9							92.0	84.0	87.0					17																	11757449		2203	4300	6503	SO:0001583	missense	1770				cell projection organization|cellular component movement|microtubule-based movement|spermatogenesis	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity	g.chr17:11757449G>A	U61740	CCDS11160.1, CCDS11161.1	17p12	2009-05-07	2006-09-04		ENSG00000007174	ENSG00000007174		"""Axonemal dyneins"""	2953	protein-coding gene	gene with protein product		603330	"""dynein, axonemal, heavy polypeptide 17-like"", ""dynein, axonemal, heavy polypeptide 9"""	DNAH17L		8812413, 11247663	Standard	NM_001372		Approved	Dnahc9, KIAA0357, HL20, HL-20, DNAL1, DYH9	uc002gne.3	Q9NYC9	OTTHUMG00000130383	ENST00000262442.4:c.9637G>A	17.37:g.11757449G>A	ENSP00000262442:p.Val3213Ile					DNAH9_ENST00000454412.2_Missense_Mutation_p.V3213I	p.V3213I	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)	50	9705	+		Breast(5;0.0122)|all_epithelial(5;0.131)	3213			Stalk (By similarity).		A2VCQ8|O15064|O95494|Q9NQ28	Missense_Mutation	SNP	ENST00000262442.4	37	c.9637G>A	CCDS11160.1	.	.	.	.	.	.	.	.	.	.	G	6.572	0.473925	0.12521	.	.	ENSG00000007174	ENST00000262442;ENST00000454412;ENST00000413703	T;T	0.75477	-0.94;-0.94	5.49	3.05	0.35203	Dynein heavy chain, coiled coil stalk (1);	0.391329	0.25596	N	0.029596	T	0.46889	0.1416	N	0.10685	0.025	0.80722	D	1	B	0.06786	0.001	B	0.15052	0.012	T	0.38929	-0.9638	10	0.02654	T	1	.	8.3555	0.32327	0.0977:0.0:0.7589:0.1434	.	3213	Q9NYC9	DYH9_HUMAN	I	3213;3213;1795	ENSP00000262442:V3213I;ENSP00000414874:V3213I	ENSP00000262442:V3213I	V	+	1	0	DNAH9	11698174	1.000000	0.71417	0.995000	0.50966	0.989000	0.77384	2.979000	0.49313	0.594000	0.29761	0.650000	0.86243	GTC		0.562	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372		28	54	0	0	0	1	0	28	54				
SNHG14	104472715	broad.mit.edu	37	15	25415809	25415809	+	RNA	SNP	C	C	T	rs2739838	byFrequency	TCGA-DJ-A4UL-01A-11D-A257-08	TCGA-DJ-A4UL-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1f10660a-2465-42ed-a2a9-206fbf06bc3f	008c8709-0bc8-4d3c-8792-abc47b447fac	g.chr15:25415809C>T	ENST00000441592.2	+	0	0				SNHG14_ENST00000553149.1_RNA|SNORD115-1_ENST00000364961.1_RNA|SNORD115-2_ENST00000362842.1_RNA					small nucleolar RNA host gene 14 (non-protein coding)																		CTGCACTGAGCTGTGGTGAGC	0.622													C|||	3566	0.712061	0.2458	0.8127	5008	,	,		15929	0.998		0.7584	False		,,,				2504	0.9284					ENST00000549301.1																			0																																																			0							g.chr15:25415809C>T			15q11.2	2014-01-17	2011-08-22	2011-08-22	ENSG00000224078	ENSG00000224078		"""Long non-coding RNAs"""	37462	non-coding RNA	RNA, long non-coding	"""non-protein coding RNA 214"""		"""UBE3A antisense RNA 1 (non-protein coding)"""	UBE3A-AS1		23771028	Standard			Approved	NCRNA00214, UBE3A-AS			OTTHUMG00000056661		15.37:g.25415809C>T						SNHG14_ENST00000553149.1_RNA								0	323	+									RNA	SNP	ENST00000441592.2	37																																																																																						0.622	SNHG14-009	KNOWN	basic	antisense	processed_transcript	OTTHUMT00000126736.3			6	102	0	0	0	1	0	6	102				
MCCD1	401250	broad.mit.edu	37	6	31496941	31496941	+	Silent	SNP	G	G	A			TCGA-DJ-A4UL-01A-11D-A257-08	TCGA-DJ-A4UL-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1f10660a-2465-42ed-a2a9-206fbf06bc3f	008c8709-0bc8-4d3c-8792-abc47b447fac	g.chr6:31496941G>A	ENST00000376191.2	+	1	448	c.150G>A	c.(148-150)ggG>ggA	p.G50G	DDX39B_ENST00000462421.1_5'Flank	NM_001011700.2	NP_001011700.2	P59942	MCCD1_HUMAN	mitochondrial coiled-coil domain 1	50						mitochondrion (GO:0005739)				skin(1)	1						GAGGAAATGGGAAGATGACGT	0.562																																						ENST00000376191.2																			0				skin(1)	1						c.(148-150)ggG>ggA		mitochondrial coiled-coil domain 1							98.0	87.0	91.0					6																	31496941		1510	2709	4219	SO:0001819	synonymous_variant	401250					mitochondrion		g.chr6:31496941G>A		CCDS34396.1	6p21.3	2003-10-17				ENSG00000204511			20668	protein-coding gene	gene with protein product		609624				14527716	Standard	NM_001011700		Approved		uc003ntp.1	P59942		ENST00000376191.2:c.150G>A	6.37:g.31496941G>A							p.G50G	NM_001011700.2	NP_001011700.2	P59942	MCCD1_HUMAN			1	448	+			50					A2AB29|A2RUP7|B0UZB2|Q7RTY2	Silent	SNP	ENST00000376191.2	37	c.150G>A	CCDS34396.1																																																																																				0.562	MCCD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259099.1			30	39	0	0	0	1	0	30	39				
RP11-478B9.1	0	broad.mit.edu	37	12	45457749	45457749	+	RNA	SNP	G	G	A	rs116849587	byFrequency	TCGA-DJ-A4UL-01A-11D-A257-08	TCGA-DJ-A4UL-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1f10660a-2465-42ed-a2a9-206fbf06bc3f	008c8709-0bc8-4d3c-8792-abc47b447fac	g.chr12:45457749G>A	ENST00000548424.1	+	0	448																											TTGGCCTGGGGCAGTTCACCA	0.458													G|||	266	0.053115	0.0008	0.0403	5008	,	,		21780	0.1954		0.007	False		,,,				2504	0.0337					ENST00000548424.1																			0																																																			0							g.chr12:45457749G>A																													12.37:g.45457749G>A														0	448	+									RNA	SNP	ENST00000548424.1	37																																																																																						0.458	RP11-478B9.1-001	KNOWN	basic	antisense	antisense	OTTHUMT00000404811.1			4	77	0	0	0	1	0	4	77				
OR4A47	403253	broad.mit.edu	37	11	48510460	48510460	+	Missense_Mutation	SNP	G	G	A	rs148277853		TCGA-DJ-A4UL-01A-11D-A257-08	TCGA-DJ-A4UL-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1f10660a-2465-42ed-a2a9-206fbf06bc3f	008c8709-0bc8-4d3c-8792-abc47b447fac	g.chr11:48510460G>A	ENST00000446524.1	+	1	192	c.116G>A	c.(115-117)gGc>gAc	p.G39D		NM_001005512.2	NP_001005512.2	Q6IF82	O4A47_HUMAN	olfactory receptor, family 4, subfamily A, member 47	39						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(2)|endometrium(1)|kidney(1)|large_intestine(2)|lung(18)|ovary(1)|skin(1)|urinary_tract(2)	29						ACCATGGTGGGCAACCTGCTC	0.413																																						ENST00000446524.1																			0				NS(1)|breast(2)|endometrium(1)|kidney(1)|large_intestine(2)|lung(18)|ovary(1)|skin(1)|urinary_tract(2)	29						c.(115-117)gGc>gAc		olfactory receptor, family 4, subfamily A, member 47		G	ASP/GLY	0,4402		0,0,2201	41.0	39.0	40.0		116	4.0	0.5	11	dbSNP_134	40	1,8589		0,1,4294	no	missense	OR4A47	NM_001005512.2	94	0,1,6495	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	39/310	48510460	1,12991	2201	4295	6496	SO:0001583	missense	403253				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity	g.chr11:48510460G>A	BK004380	CCDS31490.1	11p11.2	2012-08-09			ENSG00000237388	ENSG00000237388		"""GPCR / Class A : Olfactory receptors"""	31266	protein-coding gene	gene with protein product							Standard	NM_001005512		Approved		uc010rhx.2	Q6IF82	OTTHUMG00000166581	ENST00000446524.1:c.116G>A	11.37:g.48510460G>A	ENSP00000412752:p.Gly39Asp						p.G39D	NM_001005512.2	NP_001005512.2	Q6IF82	O4A47_HUMAN			1	192	+			39						Missense_Mutation	SNP	ENST00000446524.1	37	c.116G>A	CCDS31490.1	.	.	.	.	.	.	.	.	.	.	N	10.45	1.354311	0.24512	0.0	1.16E-4	ENSG00000237388	ENST00000446524	T	0.04360	3.64	4.91	4.0	0.46444	GPCR, rhodopsin-like superfamily (1);	0.000000	0.53938	D	0.000046	T	0.29652	0.0740	H	0.95470	3.675	0.27622	N	0.948316	D	0.89917	1.0	D	0.97110	1.0	T	0.37842	-0.9688	10	0.87932	D	0	.	11.2318	0.48916	0.091:0.0:0.909:0.0	.	39	Q6IF82	O4A47_HUMAN	D	39	ENSP00000412752:G39D	ENSP00000412752:G39D	G	+	2	0	OR4A47	48467036	0.710000	0.27896	0.543000	0.28128	0.002000	0.02628	1.076000	0.30729	1.051000	0.40369	-0.254000	0.11334	GGC		0.413	OR4A47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390559.1	NM_001005512		22	24	0	0	0	1	0	22	24				
GOLGA3	2802	broad.mit.edu	37	12	133350748	133350748	+	Missense_Mutation	SNP	C	C	G			TCGA-DJ-A4UL-01A-11D-A257-08	TCGA-DJ-A4UL-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1f10660a-2465-42ed-a2a9-206fbf06bc3f	008c8709-0bc8-4d3c-8792-abc47b447fac	g.chr12:133350748C>G	ENST00000450791.2	-	22	4485	c.4302G>C	c.(4300-4302)caG>caC	p.Q1434H	GOLGA3_ENST00000204726.3_Missense_Mutation_p.Q1434H			Q08378	GOGA3_HUMAN	golgin A3	1434					intra-Golgi vesicle-mediated transport (GO:0006891)	cytosol (GO:0005829)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extrinsic component of Golgi membrane (GO:0090498)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi transport complex (GO:0017119)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	transporter activity (GO:0005215)			breast(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(4)|lung(33)|ovary(3)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	64	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0176)|Lung NSC(355;0.204)		OV - Ovarian serous cystadenocarcinoma(86;2.27e-08)|Epithelial(86;3.34e-07)|all cancers(50;9.4e-06)		CGTACTTGAGCTGCTGGAGGC	0.602																																						ENST00000204726.3																			0				breast(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(4)|lung(33)|ovary(3)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	64						c.(4300-4302)caG>caC		golgin A3							60.0	57.0	58.0					12																	133350748		2203	4300	6503	SO:0001583	missense	2802				intra-Golgi vesicle-mediated transport	Golgi cisterna membrane|Golgi transport complex	protein binding|transporter activity	g.chr12:133350748C>G	AF485338	CCDS9281.1, CCDS53846.1	12q24.33	2010-02-12	2010-02-12		ENSG00000090615	ENSG00000090615			4426	protein-coding gene	gene with protein product	"""SY2/SY10 protein"", ""Golgi complex-associated protein of 170 kD"""	602581	"""golgi autoantigen, golgin subfamily a, 3"""			8315394, 15829563	Standard	NM_001172557		Approved	golgin-160, GCP170, MEA-2	uc001ukz.1	Q08378	OTTHUMG00000168023	ENST00000450791.2:c.4302G>C	12.37:g.133350748C>G	ENSP00000410378:p.Gln1434His					GOLGA3_ENST00000450791.2_Missense_Mutation_p.Q1434H	p.Q1434H	NM_005895.3	NP_005886.2	Q08378	GOGA3_HUMAN		OV - Ovarian serous cystadenocarcinoma(86;2.27e-08)|Epithelial(86;3.34e-07)|all cancers(50;9.4e-06)	23	4860	-	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0176)|Lung NSC(355;0.204)	1434					A5PKX6|O43241|Q6P9C7|Q86XW3|Q8TDA9|Q8WZA3	Missense_Mutation	SNP	ENST00000450791.2	37	c.4302G>C	CCDS9281.1	.	.	.	.	.	.	.	.	.	.	C	19.48	3.834819	0.71373	.	.	ENSG00000090615	ENST00000204726;ENST00000450791	T;T	0.26810	1.71;1.71	5.58	0.784	0.18578	.	0.000000	0.85682	D	0.000000	T	0.35364	0.0929	L	0.36672	1.1	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.03413	-1.1039	10	0.72032	D	0.01	.	9.0793	0.36542	0.0:0.4558:0.0:0.5442	.	1434	Q08378	GOGA3_HUMAN	H	1434	ENSP00000204726:Q1434H;ENSP00000410378:Q1434H	ENSP00000204726:Q1434H	Q	-	3	2	GOLGA3	131860821	0.366000	0.25014	0.998000	0.56505	0.991000	0.79684	-0.326000	0.07965	-0.106000	0.12110	0.655000	0.94253	CAG		0.602	GOLGA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397569.2	NM_005895		20	34	0	0	0	1	0	20	34				
LOC101927209	101927209	broad.mit.edu	37	1	142713773	142713773	+	lincRNA	SNP	C	C	G	rs199933143		TCGA-DJ-A4UL-01A-11D-A257-08	TCGA-DJ-A4UL-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1f10660a-2465-42ed-a2a9-206fbf06bc3f	008c8709-0bc8-4d3c-8792-abc47b447fac	g.chr1:142713773C>G	ENST00000610091.1	-	0	1885																											TCTTTTTCCACATTGTCATTT	0.284																																						ENST00000369381.2																			0																																																			0							g.chr1:142713773C>G																													1.37:g.142713773C>G														0	832	-									RNA	SNP	ENST00000610091.1	37																																																																																						0.284	RP11-417J8.6-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000037265.2			5	50	0	0	0	1	0	5	50				
MLLT3	4300	broad.mit.edu	37	9	20414343	20414343	+	Silent	SNP	A	A	G	rs372894655	byFrequency	TCGA-DJ-A4UL-01A-11D-A257-08	TCGA-DJ-A4UL-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1f10660a-2465-42ed-a2a9-206fbf06bc3f	008c8709-0bc8-4d3c-8792-abc47b447fac	g.chr9:20414343A>G	ENST00000380338.4	-	5	787	c.501T>C	c.(499-501)agT>agC	p.S167S	MLLT3_ENST00000429426.2_Silent_p.S164S|MLLT3_ENST00000475957.1_5'UTR|MLLT3_ENST00000355930.6_5'UTR	NM_004529.2	NP_004520.2	P42568	AF9_HUMAN	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 3	167	Poly-Ser.				anterior/posterior pattern specification (GO:0009952)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of Wnt signaling pathway, planar cell polarity pathway (GO:2000096)|regulation of transcription, DNA-templated (GO:0006355)|segment specification (GO:0007379)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)		p.S167S(19)		central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(6)|lung(24)|ovary(1)|prostate(4)|skin(1)|urinary_tract(7)	66				GBM - Glioblastoma multiforme(3;4.35e-105)|Lung(42;3.48e-06)|LUSC - Lung squamous cell carcinoma(42;7.92e-05)		tgctgctgctactgctgctgc	0.532			T	MLL	ALL								A|||	612	0.122204	0.1505	0.1066	5008	,	,		12422	0.0833		0.0716	False		,,,				2504	0.1871					ENST00000380338.4				Dom	yes		9	9p22	4300	T	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 3 (AF9)"""			L	MLL		ALL		19	Substitution - coding silent(19)	p.S167S(19)	lung(8)|kidney(5)|endometrium(3)|central_nervous_system(1)|urinary_tract(1)|prostate(1)	central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(6)|lung(24)|ovary(1)|prostate(4)|skin(1)|urinary_tract(7)	66						c.(499-501)agT>agC		myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 3							8.0	15.0	13.0					9																	20414343		1537	3257	4794	SO:0001819	synonymous_variant	4300				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	protein binding	g.chr9:20414343A>G	L13744	CCDS6494.1	9p22	2008-02-05	2001-11-28		ENSG00000171843	ENSG00000171843			7136	protein-coding gene	gene with protein product		159558	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 3"""			8506309, 8414510	Standard	NM_001286691		Approved	AF-9, AF9, YEATS3	uc003zoe.2	P42568	OTTHUMG00000019650	ENST00000380338.4:c.501T>C	9.37:g.20414343A>G						MLLT3_ENST00000475957.1_5'UTR|MLLT3_ENST00000355930.6_5'UTR|MLLT3_ENST00000429426.2_Silent_p.S164S	p.S167S	NM_004529.2	NP_004520.2	P42568	AF9_HUMAN		GBM - Glioblastoma multiforme(3;4.35e-105)|Lung(42;3.48e-06)|LUSC - Lung squamous cell carcinoma(42;7.92e-05)	5	787	-			167			Poly-Ser.		B1AMQ2|B2R7B3|B7Z755|D3DRJ8|Q8IVB0	Silent	SNP	ENST00000380338.4	37	c.501T>C	CCDS6494.1																																																																																				0.532	MLLT3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051872.1	NM_004529		8	63	0	0	0	1	0	8	63				
TBP	6908	broad.mit.edu	37	6	170871094	170871094	+	Silent	SNP	G	G	A			TCGA-DJ-A4UL-01A-11D-A257-08	TCGA-DJ-A4UL-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1f10660a-2465-42ed-a2a9-206fbf06bc3f	008c8709-0bc8-4d3c-8792-abc47b447fac	g.chr6:170871094G>A	ENST00000392092.2	+	3	549	c.270G>A	c.(268-270)caG>caA	p.Q90Q	TBP_ENST00000230354.6_Silent_p.Q90Q|TBP_ENST00000540980.1_Silent_p.Q70Q	NM_003194.4	NP_003185.1	P20226	TBP_HUMAN	TATA box binding protein	90	Poly-Gln.				cell death (GO:0008219)|gene expression (GO:0010467)|positive regulation of transcription, DNA-templated (GO:0045893)|spermatogenesis (GO:0007283)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription from RNA polymerase III promoter (GO:0006383)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	cytoplasm (GO:0005737)|female pronucleus (GO:0001939)|male pronucleus (GO:0001940)|nuclear euchromatin (GO:0005719)|nucleoplasm (GO:0005654)|transcription factor TFIIA complex (GO:0005672)|transcription factor TFIID complex (GO:0005669)	repressing transcription factor binding (GO:0070491)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(9)|ovary(1)|prostate(4)|urinary_tract(1)	26		Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246)		OV - Ovarian serous cystadenocarcinoma(33;1.07e-22)|BRCA - Breast invasive adenocarcinoma(81;5.01e-06)|GBM - Glioblastoma multiforme(31;0.00591)		agcagcagcagcagcagcagc	0.622																																						ENST00000392092.2																			0				breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(9)|ovary(1)|prostate(4)|urinary_tract(1)	26						c.(268-270)caG>caA		TATA box binding protein							22.0	28.0	26.0					6																	170871094		1899	3721	5620	SO:0001819	synonymous_variant	6908				cell death|interspecies interaction between organisms|transcription elongation from RNA polymerase II promoter|transcription from RNA polymerase III promoter|viral reproduction	transcription factor TFIIA complex|transcription factor TFIID complex	repressing transcription factor binding|transcription regulatory region DNA binding	g.chr6:170871094G>A	M55654	CCDS5315.1, CCDS55077.1	6q27	2014-04-02			ENSG00000112592	ENSG00000112592		"""General transcription factors"""	11588	protein-coding gene	gene with protein product		600075		GTF2D1, SCA17		2194289, 11448935	Standard	NM_003194		Approved	TFIID	uc003qxu.3	P20226	OTTHUMG00000016084	ENST00000392092.2:c.270G>A	6.37:g.170871094G>A						TBP_ENST00000540980.1_Silent_p.Q70Q|TBP_ENST00000230354.6_Silent_p.Q90Q	p.Q90Q	NM_003194.4	NP_003185.1	P20226	TBP_HUMAN		OV - Ovarian serous cystadenocarcinoma(33;1.07e-22)|BRCA - Breast invasive adenocarcinoma(81;5.01e-06)|GBM - Glioblastoma multiforme(31;0.00591)	3	549	+		Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246)	90			Poly-Gln.		B4E3B3|F5H869|Q16845|Q6IBM6|Q9UC02	Silent	SNP	ENST00000392092.2	37	c.270G>A	CCDS5315.1																																																																																				0.622	TBP-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043271.2	NM_003194		4	46	0	0	0	1	0	4	46				
DRD4	1815	broad.mit.edu	37	11	640585	640585	+	Silent	SNP	C	C	T			TCGA-DJ-A4UL-01A-11D-A257-08	TCGA-DJ-A4UL-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1f10660a-2465-42ed-a2a9-206fbf06bc3f	008c8709-0bc8-4d3c-8792-abc47b447fac	g.chr11:640585C>T	ENST00000176183.5	+	4	1254	c.1242C>T	c.(1240-1242)gcC>gcT	p.A414A		NM_000797.3	NP_000788.2	P21917	DRD4_HUMAN	dopamine receptor D4	462					activation of MAPK activity (GO:0000187)|adenylate cyclase-inhibiting dopamine receptor signaling pathway (GO:0007195)|adult locomotory behavior (GO:0008344)|arachidonic acid secretion (GO:0050482)|behavioral fear response (GO:0001662)|behavioral response to cocaine (GO:0048148)|behavioral response to ethanol (GO:0048149)|cellular calcium ion homeostasis (GO:0006874)|circadian rhythm (GO:0007623)|dopamine metabolic process (GO:0042417)|dopamine receptor signaling pathway (GO:0007212)|fear response (GO:0042596)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of cAMP biosynthetic process (GO:0030818)|negative regulation of protein secretion (GO:0050709)|negative regulation of voltage-gated calcium channel activity (GO:1901386)|olfactory learning (GO:0008355)|photoperiodism (GO:0009648)|positive regulation of dopamine uptake involved in synaptic transmission (GO:0051586)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of kinase activity (GO:0033674)|positive regulation of penile erection (GO:0060406)|positive regulation of sodium:proton antiporter activity (GO:0032417)|regulation of calcium-mediated signaling (GO:0050848)|regulation of circadian rhythm (GO:0042752)|regulation of dopamine metabolic process (GO:0042053)|regulation of inhibitory postsynaptic membrane potential (GO:0060080)|regulation of neurotransmitter secretion (GO:0046928)|response to amphetamine (GO:0001975)|response to histamine (GO:0034776)|response to steroid hormone (GO:0048545)|retina development in camera-type eye (GO:0060041)|short-term memory (GO:0007614)|social behavior (GO:0035176)|synaptic transmission, dopaminergic (GO:0001963)	cell cortex (GO:0005938)|dendritic spine (GO:0043197)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|terminal bouton (GO:0043195)|vesicle membrane (GO:0012506)	dopamine binding (GO:0035240)|dopamine neurotransmitter receptor activity (GO:0004952)|dopamine neurotransmitter receptor activity, coupled via Gi/Go (GO:0001591)|drug binding (GO:0008144)|identical protein binding (GO:0042802)|potassium channel regulator activity (GO:0015459)|SH3 domain binding (GO:0017124)			NS(1)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	4		all_cancers(49;1.69e-08)|all_epithelial(84;1.65e-05)|Breast(177;0.000231)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.106)|all_lung(207;0.136)		all cancers(45;4.36e-28)|Epithelial(43;2.59e-27)|OV - Ovarian serous cystadenocarcinoma(40;3.53e-21)|BRCA - Breast invasive adenocarcinoma(625;4.23e-05)|Lung(200;0.0234)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Amoxapine(DB00543)|Apomorphine(DB00714)|Aripiprazole(DB01238)|Asenapine(DB06216)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Chlorpromazine(DB00477)|Clozapine(DB00363)|Dopamine(DB00988)|Iloperidone(DB04946)|L-DOPA(DB01235)|Lisuride(DB00589)|Loxapine(DB00408)|Methotrimeprazine(DB01403)|Olanzapine(DB00334)|Paliperidone(DB01267)|Pergolide(DB01186)|Pramipexole(DB00413)|Promazine(DB00420)|Propiomazine(DB00777)|Quetiapine(DB01224)|Remoxipride(DB00409)|Risperidone(DB00734)|Ropinirole(DB00268)|Rotigotine(DB05271)|Ziprasidone(DB00246)	TCCGCAAGGCCCTGCGTGCCT	0.657																																						ENST00000176183.5																			0				NS(1)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	4						c.(1240-1242)gcC>gcT		dopamine receptor D4	Apomorphine(DB00714)|Clozapine(DB00363)|Olanzapine(DB00334)|Pramipexole(DB00413)|Promazine(DB00420)|Propiomazine(DB00777)|Ropinirole(DB00268)|Thiethylperazine(DB00372)|Ziprasidone(DB00246)						72.0	63.0	66.0					11																	640585		2202	4298	6500	SO:0001819	synonymous_variant	1815				activation of MAPK activity|adult locomotory behavior|arachidonic acid secretion|behavioral fear response|behavioral response to cocaine|behavioral response to ethanol|inhibition of adenylate cyclase activity by dopamine receptor signaling pathway|negative regulation of calcium ion transport via voltage-gated calcium channel activity|negative regulation of cAMP biosynthetic process|negative regulation of protein secretion|positive regulation of sodium:hydrogen antiporter activity|regulation of dopamine metabolic process|regulation of inhibitory postsynaptic membrane potential|response to amphetamine|response to histamine|social behavior	integral to plasma membrane	dopamine D4 receptor activity|drug binding|potassium channel regulator activity|SH3 domain binding	g.chr11:640585C>T	L12398	CCDS7710.1	11p15.5	2012-08-08			ENSG00000069696	ENSG00000069696		"""GPCR / Class A : Dopamine receptors"""	3025	protein-coding gene	gene with protein product		126452					Standard	NM_000797		Approved		uc001lqp.2	P21917	OTTHUMG00000133312	ENST00000176183.5:c.1242C>T	11.37:g.640585C>T							p.A414A	NM_000797.3	NP_000788.2	P21917	DRD4_HUMAN		all cancers(45;4.36e-28)|Epithelial(43;2.59e-27)|OV - Ovarian serous cystadenocarcinoma(40;3.53e-21)|BRCA - Breast invasive adenocarcinoma(625;4.23e-05)|Lung(200;0.0234)|LUSC - Lung squamous cell carcinoma(625;0.0703)	4	1254	+		all_cancers(49;1.69e-08)|all_epithelial(84;1.65e-05)|Breast(177;0.000231)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.106)|all_lung(207;0.136)	462					B0M0J7|Q7Z7Q5|Q8NGM5	Silent	SNP	ENST00000176183.5	37	c.1242C>T	CCDS7710.1																																																																																				0.657	DRD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257109.1	NM_000797		23	36	0	0	0	1	0	23	36				
LOC101927209	101927209	broad.mit.edu	37	1	142713774	142713774	+	lincRNA	SNP	A	A	G	rs201023195		TCGA-DJ-A4UL-01A-11D-A257-08	TCGA-DJ-A4UL-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1f10660a-2465-42ed-a2a9-206fbf06bc3f	008c8709-0bc8-4d3c-8792-abc47b447fac	g.chr1:142713774A>G	ENST00000610091.1	-	0	1884																											CTTTTTCCACATTGTCATTTT	0.284																																						ENST00000369381.2																			0																																																			0							g.chr1:142713774A>G																													1.37:g.142713774A>G														0	831	-									RNA	SNP	ENST00000610091.1	37																																																																																						0.284	RP11-417J8.6-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000037265.2			5	50	0	0	0	1	0	5	50				
BMS1P20	96610	broad.mit.edu	37	22	22661187	22661187	+	RNA	SNP	G	G	A			TCGA-DJ-A4UL-01A-11D-A257-08	TCGA-DJ-A4UL-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1f10660a-2465-42ed-a2a9-206fbf06bc3f	008c8709-0bc8-4d3c-8792-abc47b447fac	g.chr22:22661187G>A	ENST00000426066.1	+	0	279					NR_027293.1				BMS1 pseudogene 20																		CCCCCACCCCGTCATGTACAG	0.413																																						ENST00000426066.1																			0																																																			0							g.chr22:22661187G>A			22q11.22	2013-09-20			ENSG00000236850	ENSG00000236850			49153	pseudogene	pseudogene							Standard	XR_430414		Approved				OTTHUMG00000151046		22.37:g.22661187G>A								NR_027293.1						0	279	+									RNA	SNP	ENST00000426066.1	37																																																																																						0.413	BMS1P20-001	KNOWN	basic|readthrough_transcript	processed_transcript	processed_transcript	OTTHUMT00000473090.1			7	31	0	0	0	1	0	7	31				
POM121L9P	29774	broad.mit.edu	37	22	24659578	24659578	+	RNA	SNP	A	A	G			TCGA-DJ-A4UL-01A-11D-A257-08	TCGA-DJ-A4UL-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1f10660a-2465-42ed-a2a9-206fbf06bc3f	008c8709-0bc8-4d3c-8792-abc47b447fac	g.chr22:24659578A>G	ENST00000414583.2	+	0	3103					NR_003714.1				POM121 transmembrane nucleoporin-like 9, pseudogene																		TGCGCAGGCCAACACTCACTG	0.617																																						ENST00000414583.2																			0																																																			0							g.chr22:24659578A>G	AL040062, AL117401		22q11.22	2012-03-13	2012-03-13		ENSG00000128262	ENSG00000128262			30080	pseudogene	pseudogene			"""POM121 membrane glycoprotein-like 9, pseudogene"""				Standard	NR_003714		Approved				OTTHUMG00000150763		22.37:g.24659578A>G								NR_003714.1						0	3103	+									RNA	SNP	ENST00000414583.2	37																																																																																						0.617	POM121L9P-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000319991.1	NM_014549		4	21	0	0	0	1	0	4	21				
GLIS3	169792	broad.mit.edu	37	9	3937126	3937126	+	Missense_Mutation	SNP	T	T	C			TCGA-DJ-A4UL-01A-11D-A257-08	TCGA-DJ-A4UL-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1f10660a-2465-42ed-a2a9-206fbf06bc3f	008c8709-0bc8-4d3c-8792-abc47b447fac	g.chr9:3937126T>C	ENST00000324333.10	-	4	1502	c.1309A>G	c.(1309-1311)Aca>Gca	p.T437A	GLIS3_ENST00000381971.3_Missense_Mutation_p.T592A|GLIS3_ENST00000461870.1_5'UTR	NM_152629.3	NP_689842.3	Q8NEA6	GLIS3_HUMAN	GLIS family zinc finger 3	437					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription from RNA polymerase II promoter (GO:0006366)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(12)|lung(4)|ovary(2)|prostate(1)|skin(1)	26		Acute lymphoblastic leukemia(2;0.00464)|Breast(48;0.148)		Lung(2;0.00163)|GBM - Glioblastoma multiforme(50;0.00301)|LUSC - Lung squamous cell carcinoma(2;0.0148)		TTCTCGCCTGTGTGGCTCCGC	0.507																																						ENST00000324333.10																			0				NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(12)|lung(4)|ovary(2)|prostate(1)|skin(1)	26						c.(1309-1311)Aca>Gca		GLIS family zinc finger 3							103.0	103.0	103.0					9																	3937126		2203	4300	6503	SO:0001583	missense	169792				negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter		DNA binding|zinc ion binding	g.chr9:3937126T>C	BC033899	CCDS6451.1, CCDS43784.1	9p24.2	2008-05-02	2004-07-16	2004-07-16	ENSG00000107249	ENSG00000107249		"""Zinc fingers, C2H2-type"""	28510	protein-coding gene	gene with protein product		610192	"""zinc finger protein 515"""	ZNF515		14500813	Standard	NM_152629		Approved	MGC33662	uc003zhx.1	Q8NEA6	OTTHUMG00000019463	ENST00000324333.10:c.1309A>G	9.37:g.3937126T>C	ENSP00000325494:p.Thr437Ala					GLIS3_ENST00000461870.1_5'UTR|GLIS3_ENST00000381971.3_Missense_Mutation_p.T592A	p.T437A	NM_152629.3	NP_689842.3	Q8NEA6	GLIS3_HUMAN		Lung(2;0.00163)|GBM - Glioblastoma multiforme(50;0.00301)|LUSC - Lung squamous cell carcinoma(2;0.0148)	4	1502	-		Acute lymphoblastic leukemia(2;0.00464)|Breast(48;0.148)	437					B1AL19|Q1PHK5	Missense_Mutation	SNP	ENST00000324333.10	37	c.1309A>G	CCDS6451.1	.	.	.	.	.	.	.	.	.	.	T	24.0	4.484958	0.84854	.	.	ENSG00000107249	ENST00000324333;ENST00000381971	T;T	0.51574	0.7;0.7	5.94	5.94	0.96194	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.47455	U	0.000228	T	0.66036	0.2749	L	0.58428	1.81	0.80722	D	1	D;D;P;D	0.67145	0.983;0.983;0.711;0.996	D;D;P;D	0.77004	0.933;0.933;0.514;0.989	T	0.68465	-0.5401	10	0.87932	D	0	.	16.0679	0.80897	0.0:0.0:0.0:1.0	.	105;105;592;437	Q1PHK2;Q1PHK3;Q8NEA6-2;Q8NEA6	.;.;.;GLIS3_HUMAN	A	437;592	ENSP00000325494:T437A;ENSP00000371398:T592A	ENSP00000325494:T437A	T	-	1	0	GLIS3	3927126	1.000000	0.71417	0.998000	0.56505	0.993000	0.82548	8.040000	0.89188	2.265000	0.75225	0.482000	0.46254	ACA		0.507	GLIS3-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000051559.1	NM_152629		40	74	0	0	0	1	0	40	74				
ZNRD1-AS1	80862	broad.mit.edu	37	6	29977377	29977377	+	RNA	SNP	C	C	G			TCGA-DJ-A4UL-01A-11D-A257-08	TCGA-DJ-A4UL-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1f10660a-2465-42ed-a2a9-206fbf06bc3f	008c8709-0bc8-4d3c-8792-abc47b447fac	g.chr6:29977377C>G	ENST00000376797.3	-	0	731				ZNRD1-AS1_ENST00000425604.1_RNA|ZNRD1-AS1_ENST00000420251.1_RNA|HLA-J_ENST00000462773.1_RNA|ZNRD1-AS1_ENST00000444051.1_RNA|ZNRD1-AS1_ENST00000448093.1_RNA			Q2KJ03	ZRAS1_HUMAN	ZNRD1 antisense RNA 1																		TTTGTGACTTCAAGAACCCTG	0.458																																						ENST00000376797.3																			0																																																			0							g.chr6:29977377C>G	AF032110		6p21.33	2014-08-14	2012-08-15	2010-11-25	ENSG00000204623	ENSG00000204623		"""Long non-coding RNAs"""	13924	non-coding RNA	RNA, long non-coding		615714	"""chromosome 6 open reading frame 12"", ""non-protein coding RNA 171"", ""ZNRD1 antisense RNA (non-protein coding)"", ""ZNRD1 antisense RNA 1 (non-protein coding)"""	C6orf12, NCRNA00171, ZNRD1AS, ZNRD1-AS		9553157, 11130983, 25110835	Standard	NR_026751		Approved	HTEX4, Em:AB023056.3	uc003rto.3	Q2KJ03	OTTHUMG00000031109		6.37:g.29977377C>G						ZNRD1-AS1_ENST00000425604.1_RNA|HLA-J_ENST00000462773.1_RNA|ZNRD1-AS1_ENST00000420251.1_RNA|ZNRD1-AS1_ENST00000448093.1_RNA								0	731	-									RNA	SNP	ENST00000376797.3	37																																																																																						0.458	ZNRD1-AS1-006	KNOWN	basic|exp_conf	antisense	antisense	OTTHUMT00000253083.1	NR_026751		3	32	0	0	0	1	0	3	32				
TPTE	7179	broad.mit.edu	37	21	11012916	11012916	+	Splice_Site	SNP	C	C	A			TCGA-DJ-A4UL-01A-11D-A257-08	TCGA-DJ-A4UL-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1f10660a-2465-42ed-a2a9-206fbf06bc3f	008c8709-0bc8-4d3c-8792-abc47b447fac	g.chr21:11012916C>A	ENST00000415664.2	-	8	1004		c.e8+1					P56180	TPTE_HUMAN	transmembrane phosphatase with tensin homology						peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	ion channel activity (GO:0005216)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(19)|lung(76)|ovary(2)|prostate(2)|skin(8)|urinary_tract(1)	130			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		TCAAATTTTACCTAGCTTTTT	0.299																																						ENST00000415664.2																			0				NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(19)|lung(76)|ovary(2)|prostate(2)|skin(8)|urinary_tract(1)	130						c.e8+1		transmembrane phosphatase with tensin homology																																				SO:0001630	splice_region_variant	7179				signal transduction	integral to membrane	ion channel activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity	g.chr21:11012916C>A	AF007118	CCDS74771.1, CCDS74772.1, CCDS74773.1	21p11	2011-06-09			ENSG00000166157	ENSG00000274391		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"""	12023	protein-coding gene	gene with protein product	"""PTEN-related tyrosine phosphatase"", ""cancer/testis antigen 44"""	604336				10830953, 14659893	Standard	NM_001290224		Approved	PTEN2, CT44	uc002yip.1	P56180	OTTHUMG00000074127	ENST00000415664.2:c.2332+1G>T	21.37:g.11012916C>A										P56180	TPTE_HUMAN	Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)	8	1004	-								B2RAP7|C9J6D6|C9JKK8|Q6XPS4|Q6XPS5|Q71JA8|Q8NCS8	Splice_Site	SNP	ENST00000415664.2	37																																																																																						0.299	TPTE-006	KNOWN	basic	processed_transcript	protein_coding	OTTHUMT00000340030.1		Intron	10	31	1	0	7.48243e-07	1	7.68466e-07	10	31				
CGRRF1	10668	broad.mit.edu	37	14	54976644	54976644	+	De_novo_Start_InFrame	SNP	G	G	A	rs75987656	byFrequency	TCGA-DJ-A4UL-01A-11D-A257-08	TCGA-DJ-A4UL-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1f10660a-2465-42ed-a2a9-206fbf06bc3f	008c8709-0bc8-4d3c-8792-abc47b447fac	g.chr14:54976644G>A	ENST00000216420.7	+	0	99					NM_006568.2	NP_006559.1	Q99675	CGRF1_HUMAN	cell growth regulator with ring finger domain 1						cell cycle arrest (GO:0007050)|negative regulation of cell proliferation (GO:0008285)|response to stress (GO:0006950)	intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			endometrium(3)|kidney(2)|lung(5)|ovary(2)|stomach(1)	13						gggctccgcggctggagccgg	0.622											OREG0022692	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	242	0.0483227	0.0408	0.0605	5008	,	,		14612	0.0952		0.005	False		,,,				2504	0.046					ENST00000216420.7																			0				endometrium(3)|kidney(2)|lung(5)|ovary(2)|stomach(1)	13								cell growth regulator with ring finger domain 1		G		177,4229	115.4+/-153.4	4,169,2030	48.0	46.0	46.0			3.2	0.0	14	dbSNP_132	46	12,8588	9.8+/-36.6	0,12,4288	no	utr-5	CGRRF1	NM_006568.2		4,181,6318	AA,AG,GG		0.1395,4.0172,1.4532			54976644	189,12817	2203	4300	6503			10668				cell cycle arrest|negative regulation of cell proliferation|response to stress		zinc ion binding	g.chr14:54976644G>A	BC015063	CCDS9719.1	14q22.2	2013-09-20			ENSG00000100532	ENSG00000100532		"""RING-type (C3HC4) zinc fingers"""	15528	protein-coding gene	gene with protein product		606138				8968090	Standard	NM_006568		Approved	CGR19, RNF197	uc001xay.3	Q99675	OTTHUMG00000140308		14.37:g.54976644G>A			OREG0022692	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	1004			NM_006568.2	NP_006559.1	Q99675	CGRF1_HUMAN			0	99	+								Q96BX2	Translation_Start_Site	SNP	ENST00000216420.7	37		CCDS9719.1																																																																																				0.622	CGRRF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276905.2	NM_006568		3	36	0	0	0	1	0	3	36				
BRAF	673	broad.mit.edu	37	7	140453136	140453136	+	Missense_Mutation	SNP	A	A	T	rs121913377|rs113488022|rs121913227|rs397516897		TCGA-DJ-A4UL-01A-11D-A257-08	TCGA-DJ-A4UL-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1f10660a-2465-42ed-a2a9-206fbf06bc3f	008c8709-0bc8-4d3c-8792-abc47b447fac	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		25	47	0	0	0	1	0	25	47				
GIMAP1	170575	broad.mit.edu	37	7	150417467	150417467	+	Silent	SNP	C	C	T			TCGA-DJ-A4UL-01A-11D-A257-08	TCGA-DJ-A4UL-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1f10660a-2465-42ed-a2a9-206fbf06bc3f	008c8709-0bc8-4d3c-8792-abc47b447fac	g.chr7:150417467C>T	ENST00000307194.5	+	3	515	c.375C>T	c.(373-375)acC>acT	p.T125T		NM_130759.3	NP_570115.1	Q8WWP7	GIMA1_HUMAN	GTPase, IMAP family member 1	125	AIG1-type G.				B cell differentiation (GO:0030183)|T cell differentiation (GO:0030217)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	GTP binding (GO:0005525)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(3)|lung(14)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	28			OV - Ovarian serous cystadenocarcinoma(82;0.0145)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		GTCGGTTCACCGCCCAGGACC	0.637																																						ENST00000307194.5																			0				NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(3)|lung(14)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	28						c.(373-375)acC>acT		GTPase, IMAP family member 1							46.0	44.0	45.0					7																	150417467		2203	4300	6503	SO:0001819	synonymous_variant	170575							g.chr7:150417467C>T	AJ306287	CCDS5906.1	7q36.1	2014-04-04			ENSG00000213203	ENSG00000213203		"""GTPases, IMAP"""	23237	protein-coding gene	gene with protein product	"""immune-associated nucleotide-binding protein 2"""	608084				15474311, 18701445	Standard	NM_130759		Approved	HIMAP1, IMAP38, IMAP1, IAN2		Q8WWP7	OTTHUMG00000157489	ENST00000307194.5:c.375C>T	7.37:g.150417467C>T							p.T125T	NM_130759.3	NP_570115.1			OV - Ovarian serous cystadenocarcinoma(82;0.0145)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)	3	515	+								B2RCI3|Q8NAZ0	Silent	SNP	ENST00000307194.5	37	c.375C>T	CCDS5906.1																																																																																				0.637	GIMAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348951.2	NM_130759		20	38	0	0	0	1	0	20	38				
LRRC37A4P	55073	broad.mit.edu	37	17	43587569	43587569	+	RNA	SNP	G	G	C	rs202189074		TCGA-DJ-A4UL-01A-11D-A257-08	TCGA-DJ-A4UL-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1f10660a-2465-42ed-a2a9-206fbf06bc3f	008c8709-0bc8-4d3c-8792-abc47b447fac	g.chr17:43587569G>C	ENST00000579913.1	-	0	1444				RP11-798G7.5_ENST00000253803.2_RNA	NR_002940.2				leucine rich repeat containing 37, member A4, pseudogene																		aactccgtctgaaaagaaaag	0.443																																						ENST00000253803.2																			0																																																			0							g.chr17:43587569G>C	AK000982		17q21.31	2014-04-01	2012-03-07	2012-03-07	ENSG00000214425	ENSG00000214425			25479	pseudogene	pseudogene			"""leucine rich repeat containing 37, member A4 (pseudogene)"""	LRRC37A4			Standard	NR_002940		Approved	FLJ10120	uc031rhd.1		OTTHUMG00000179212		17.37:g.43587569G>C						LRRC37A4P_ENST00000579913.1_RNA								0	267	+									RNA	SNP	ENST00000579913.1	37																																																																																						0.443	LRRC37A4P-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000445300.1	NR_002940		4	38	0	0	0	1	0	4	38				
EVPL	2125	broad.mit.edu	37	17	74011029	74011029	+	Silent	SNP	G	G	C			TCGA-DJ-A4UL-01A-11D-A257-08	TCGA-DJ-A4UL-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1f10660a-2465-42ed-a2a9-206fbf06bc3f	008c8709-0bc8-4d3c-8792-abc47b447fac	g.chr17:74011029G>C	ENST00000301607.3	-	17	2443	c.2190C>G	c.(2188-2190)cgC>cgG	p.R730R	EVPL_ENST00000586740.1_Silent_p.R752R	NM_001988.2	NP_001979.2	Q92817	EVPL_HUMAN	envoplakin	730	Globular 1.				epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)	cell junction (GO:0030054)|cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	protein binding, bridging (GO:0030674)|structural molecule activity (GO:0005198)			breast(4)|central_nervous_system(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(14)|ovary(2)|pancreas(2)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)	54						CGGCGTGGTAGCGGTCGGTGA	0.667																																						ENST00000301607.3																			0				breast(4)|central_nervous_system(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(14)|ovary(2)|pancreas(2)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)	54						c.(2188-2190)cgC>cgG		envoplakin							33.0	35.0	34.0					17																	74011029		2202	4299	6501	SO:0001819	synonymous_variant	2125				keratinization|peptide cross-linking	cornified envelope|cytoplasm|desmosome	protein binding, bridging|structural molecule activity	g.chr17:74011029G>C	U53786	CCDS11737.1	17q25	2008-07-18				ENSG00000167880			3503	protein-coding gene	gene with protein product		601590				8938451, 10409435	Standard	NM_001988		Approved	EVPK	uc002jqi.2	Q92817		ENST00000301607.3:c.2190C>G	17.37:g.74011029G>C						EVPL_ENST00000586740.1_Silent_p.R752R	p.R730R	NM_001988.2	NP_001979.2	Q92817	EVPL_HUMAN			17	2443	-			730			Globular 1.		A0AUV5	Silent	SNP	ENST00000301607.3	37	c.2190C>G	CCDS11737.1																																																																																				0.667	EVPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449483.1	NM_001988		12	21	0	0	0	1	0	12	21				
INTS4L2	644619	broad.mit.edu	37	7	65150816	65150817	+	RNA	INS	-	-	C	rs376935907		TCGA-DJ-A4UL-01A-11D-A257-08	TCGA-DJ-A4UL-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1f10660a-2465-42ed-a2a9-206fbf06bc3f	008c8709-0bc8-4d3c-8792-abc47b447fac	g.chr7:65150816_65150817insC	ENST00000430126.2	+	0	757							Q2T9F4	IN4L2_HUMAN	integrator complex subunit 4-like 2																		TTCATCCCTCACCCCCCCCCCC	0.465																																						ENST00000430126.2																			0																																																			0							g.chr7:65150816_65150817insC	BC111554		7q11.21	2013-03-26			ENSG00000232270	ENSG00000273024			22351	other	unknown							Standard	NR_027392		Approved	MGC133166	uc003tue.2	Q2T9F4	OTTHUMG00000156558		7.37:g.65150827_65150827dupC														0	757	+									RNA	INS	ENST00000430126.2	37																																																																																						0.465	INTS4L2-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000345545.2	NR_027392		4	7						4	7	---	---	---	---
