#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
KIAA1211	57482	broad.mit.edu	37	4	57182522	57182522	+	Missense_Mutation	SNP	G	G	A			TCGA-DJ-A3UK-01A-11D-A22D-08	TCGA-DJ-A3UK-10A-01D-A22D-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b796fc76-16ca-4659-a0a1-8b6f58ae6493	e5f80f02-e798-4861-bd03-6933647e5d7d	g.chr4:57182522G>A	ENST00000504228.1	+	6	2959	c.2854G>A	c.(2854-2856)Gca>Aca	p.A952T	KIAA1211_ENST00000541073.1_Missense_Mutation_p.A945T|KIAA1211_ENST00000264229.6_Missense_Mutation_p.A952T			Q6ZU35	K1211_HUMAN	KIAA1211	952	Pro-rich.									endometrium(7)|large_intestine(10)|lung(39)|ovary(2)|prostate(3)|skin(3)|stomach(1)	65	Glioma(25;0.08)|all_neural(26;0.101)					CGACAAGGCAGCAAACAAAAT	0.632																																						uc003hbk.2																			0				endometrium(7)|large_intestine(10)|lung(39)|ovary(2)|prostate(3)|skin(3)|stomach(1)	65						c.(2854-2856)Gca>Aca		Homo sapiens KIAA1211 (KIAA1211), mRNA.							46.0	56.0	53.0					4																	57182522		2084	4210	6294	SO:0001583	missense	57482							g.chr4:57182522G>A	AB033037	CCDS43230.1	4q12	2012-08-03			ENSG00000109265	ENSG00000109265			29219	protein-coding gene	gene with protein product						10574462, 11230166	Standard	NM_020722		Approved		uc003hbk.2	Q6ZU35	OTTHUMG00000160749	ENST00000504228.1:c.2854G>A	4.37:g.57182522G>A	ENSP00000423366:p.Ala952Thr		Somatic				KIAA1211_uc010iha.2_Missense_Mutation_p.A945T|KIAA1211_uc011bzz.1_Missense_Mutation_p.A862T|KIAA1211_uc003hbm.1_Missense_Mutation_p.A838T	p.A952T	NM_020722	NP_065773	WXS	Illumina GAIIx	Phase_I	Q6ZU35	K1211_HUMAN			7	3245	+	Glioma(25;0.08)|all_neural(26;0.101)		952			Pro-rich.		Q9NTE2|Q9NTP8|Q9ULK9	Missense_Mutation	SNP	ENST00000504228.1	37	c.2854G>A	CCDS43230.1	.	.	.	.	.	.	.	.	.	.	G	9.111	1.006633	0.19199	.	.	ENSG00000109265	ENST00000264229;ENST00000504228;ENST00000541073	T;T;T	0.12774	2.66;2.66;2.65	4.74	3.9	0.45041	.	.	.	.	.	T	0.16128	0.0388	L	0.54323	1.7	0.09310	N	1	B;B;B	0.19073	0.033;0.013;0.013	B;B;B	0.15484	0.013;0.013;0.013	T	0.11131	-1.0600	9	0.45353	T	0.12	-7.1922	13.2293	0.59933	0.0771:0.0:0.9229:0.0	.	945;945;952	B7ZVZ4;F5H1N7;Q6ZU35	.;.;K1211_HUMAN	T	952;952;945	ENSP00000264229:A952T;ENSP00000423366:A952T;ENSP00000444006:A945T	ENSP00000264229:A952T	A	+	1	0	KIAA1211	56877279	0.159000	0.22864	0.035000	0.18076	0.203000	0.24098	2.569000	0.45973	1.215000	0.43411	-0.448000	0.05591	GCA		0.632	KIAA1211-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362097.2	NM_020722		3	63	0	0	0	1	0	3	63				
USP32P3	347716	broad.mit.edu	37	17	20320065	20320065	+	RNA	SNP	G	G	A			TCGA-DJ-A3UK-01A-11D-A22D-08	TCGA-DJ-A3UK-10A-01D-A22D-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b796fc76-16ca-4659-a0a1-8b6f58ae6493	e5f80f02-e798-4861-bd03-6933647e5d7d	g.chr17:20320065G>A	ENST00000583574.2	+	0	333									ubiquitin specific peptidase 32 pseudogene 3																		GGAACTGGGAGGACTGCACTA	0.547																																						uc002gwx.3																			0													Homo sapiens, clone IMAGE:4938453, mRNA.																																						0							g.chr17:20320065G>A			17p11.2	2013-02-15			ENSG00000189423	ENSG00000189423			43576	pseudogene	pseudogene							Standard	NG_002719		Approved				OTTHUMG00000179809		17.37:g.20320065G>A			Somatic								WXS	Illumina GAIIx	Phase_I					0		+									RNA	SNP	ENST00000583574.2	37	c.644G>A																																																																																					0.547	USP32P3-003	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000467714.1	NG_002719		3	46	0	0	0	1	0	3	46				
CHRNE	1145	broad.mit.edu	37	17	4805305	4805305	+	Missense_Mutation	SNP	G	G	A	rs121909512		TCGA-DJ-A3UK-01A-11D-A22D-08	TCGA-DJ-A3UK-10A-01D-A22D-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b796fc76-16ca-4659-a0a1-8b6f58ae6493	e5f80f02-e798-4861-bd03-6933647e5d7d	g.chr17:4805305G>A	ENST00000293780.4	-	5	432	c.422C>T	c.(421-423)cCg>cTg	p.P141L	C17orf107_ENST00000381365.3_3'UTR|CHRNE_ENST00000575637.1_5'UTR	NM_000080.3	NP_000071.1	Q04844	ACHE_HUMAN	cholinergic receptor, nicotinic, epsilon (muscle)	141			P -> L (in FCCMS; marked decrease in rate of AChR channel opening; reduction in frequency of open channel state and resistance to desensitization by ACh). {ECO:0000269|PubMed:8755487}.		cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|muscle contraction (GO:0006936)|regulation of membrane potential (GO:0042391)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, cholinergic (GO:0007271)|transport (GO:0006810)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|cation transmembrane transporter activity (GO:0008324)			central_nervous_system(1)|cervix(1)|kidney(1)|large_intestine(5)|lung(3)|prostate(1)	12					Galantamine(DB00674)	GTAGATGGCCGGAGGCAGCCA	0.617																																						uc002fzk.1																			0				central_nervous_system(1)|cervix(1)|kidney(1)|large_intestine(5)|lung(3)|prostate(1)	12	GRCh37	CM960299	CHRNE	M	rs121909512	c.(421-423)cCg>cTg		Homo sapiens cholinergic receptor, nicotinic, epsilon (CHRNE), mRNA.							56.0	52.0	54.0					17																	4805305		2203	4300	6503	SO:0001583	missense	1145				muscle contraction|synaptic transmission, cholinergic	cell junction|nicotinic acetylcholine-gated receptor-channel complex|postsynaptic membrane	acetylcholine receptor activity|nicotinic acetylcholine-activated cation-selective channel activity	g.chr17:4805305G>A	X66403	CCDS11058.1	17p13.2	2012-02-11	2012-02-07		ENSG00000108556	ENSG00000108556		"""Cholinergic receptors"", ""Ligand-gated ion channels / Acetylcholine receptors, nicotinic"""	1966	protein-coding gene	gene with protein product	"""acetylcholine receptor, nicotinic, epsilon (muscle)"""	100725	"""cholinergic receptor, nicotinic, epsilon"""			7688301	Standard	NM_000080		Approved	ACHRE	uc002fzk.1	Q04844	OTTHUMG00000090778	ENST00000293780.4:c.422C>T	17.37:g.4805305G>A	ENSP00000293780:p.Pro141Leu		Somatic				C17orf107_uc002fzl.3_3'UTR	p.P141L	NM_000080	NP_000071	WXS	Illumina GAIIx	Phase_I	Q04844	ACHE_HUMAN			4	433	-			141		P -> L (in FCCMS; marked decrease in rate of AChR channel opening; reduction in frequency of open channel state and resistance to desensitization by ACh).			D3DTK6	Missense_Mutation	SNP	ENST00000293780.4	37	c.422C>T	CCDS11058.1	.	.	.	.	.	.	.	.	.	.	G	28.3	4.906638	0.92107	.	.	ENSG00000108556	ENST00000293780	D	0.81821	-1.54	4.78	4.78	0.61160	Neurotransmitter-gated ion-channel ligand-binding (3);	0.000000	0.85682	D	0.000000	D	0.92743	0.7693	H	0.95950	3.745	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.94760	0.7935	10	0.87932	D	0	.	15.3477	0.74355	0.0:0.0:1.0:0.0	.	141	Q04844	ACHE_HUMAN	L	141	ENSP00000293780:P141L	ENSP00000293780:P141L	P	-	2	0	CHRNE	4746084	1.000000	0.71417	0.979000	0.43373	0.678000	0.39670	9.585000	0.98223	2.500000	0.84329	0.561000	0.74099	CCG		0.617	CHRNE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207560.3			3	102	0	0	0	1	0	3	102				
TBC1D16	125058	broad.mit.edu	37	17	77926572	77926572	+	Silent	SNP	G	G	A			TCGA-DJ-A3UK-01A-11D-A22D-08	TCGA-DJ-A3UK-10A-01D-A22D-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b796fc76-16ca-4659-a0a1-8b6f58ae6493	e5f80f02-e798-4861-bd03-6933647e5d7d	g.chr17:77926572G>A	ENST00000310924.2	-	4	940	c.825C>T	c.(823-825)aaC>aaT	p.N275N	TBC1D16_ENST00000570373.1_5'Flank|TBC1D16_ENST00000576768.1_5'Flank|TBC1D16_ENST00000572862.1_5'Flank|TBC1D16_ENST00000340848.7_5'Flank	NM_001271844.1|NM_001271845.1|NM_019020.2	NP_001258773.1|NP_001258774.1|NP_061893.2	Q8TBP0	TBC16_HUMAN	TBC1 domain family, member 16	275							Rab GTPase activator activity (GO:0005097)			NS(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(13)|ovary(1)|prostate(3)	28	all_neural(118;0.167)		OV - Ovarian serous cystadenocarcinoma(97;0.00739)|BRCA - Breast invasive adenocarcinoma(99;0.0819)			GCAGGAGGCCGTTGCTGTCCG	0.682																																					Ovarian(14;397 562 4850 31922 49378)	uc002jxj.3																			0				NS(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(13)|ovary(1)|prostate(3)	28						c.(823-825)aaC>aaT		Homo sapiens TBC1 domain family, member 16 (TBC1D16), mRNA.							24.0	28.0	27.0					17																	77926572		2200	4298	6498	SO:0001819	synonymous_variant	125058					intracellular	Rab GTPase activator activity	g.chr17:77926572G>A	AL157485	CCDS11766.1, CCDS62351.1, CCDS62352.1, CCDS62353.1	17q25.3	2013-07-10				ENSG00000167291			28356	protein-coding gene	gene with protein product						23019362	Standard	NM_019020		Approved	MGC25062, FLJ20748	uc002jxj.4	Q8TBP0		ENST00000310924.2:c.825C>T	17.37:g.77926572G>A			Somatic				TBC1D16_uc002jxh.3_5'Flank|TBC1D16_uc002jxi.3_5'Flank|TBC1D16_uc002jxk.1_5'Flank	p.N275N	NM_019020	NP_061893	WXS	Illumina GAIIx	Phase_I	Q8TBP0	TBC16_HUMAN	OV - Ovarian serous cystadenocarcinoma(97;0.00739)|BRCA - Breast invasive adenocarcinoma(99;0.0819)		3	941	-	all_neural(118;0.167)		275					B9A6L7|I3L1E0|I3L4U2|Q8N3Z4|Q96DH7	Silent	SNP	ENST00000310924.2	37	c.825C>T	CCDS11766.1																																																																																				0.682	TBC1D16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437145.1	NM_019020		4	102	0	0	0	1	0	4	102				
ATP6V1A	523	broad.mit.edu	37	3	113505224	113505224	+	Missense_Mutation	SNP	T	T	C			TCGA-DJ-A3UK-01A-11D-A22D-08	TCGA-DJ-A3UK-10A-01D-A22D-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b796fc76-16ca-4659-a0a1-8b6f58ae6493	e5f80f02-e798-4861-bd03-6933647e5d7d	g.chr3:113505224T>C	ENST00000273398.3	+	6	818	c.710T>C	c.(709-711)cTt>cCt	p.L237P	ATP6V1A_ENST00000538620.1_Missense_Mutation_p.L204P	NM_001690.3	NP_001681.2	P38606	VATA_HUMAN	ATPase, H+ transporting, lysosomal 70kDa, V1 subunit A	237					ATP hydrolysis coupled proton transport (GO:0015991)|cellular iron ion homeostasis (GO:0006879)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|microvillus (GO:0005902)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|proton-transporting two-sector ATPase complex (GO:0016469)|proton-transporting V-type ATPase, V1 domain (GO:0033180)	ATP binding (GO:0005524)|proton-transporting ATPase activity, rotational mechanism (GO:0046961)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(17)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34					Alendronate(DB00630)|Etidronic acid(DB01077)|Tiludronate(DB01133)	CTTGATGCCCTTTTTCCGTAA	0.423																																						uc003eao.3																			0				breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(17)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						c.(709-711)cTt>cCt		Homo sapiens ATPase, H+ transporting, lysosomal 70kDa, V1 subunit A (ATP6V1A), mRNA.							219.0	201.0	207.0					3																	113505224		2203	4300	6503	SO:0001583	missense	523				ATP hydrolysis coupled proton transport|cellular iron ion homeostasis|insulin receptor signaling pathway|transferrin transport	cytosol|integral to plasma membrane|proton-transporting V-type ATPase, V1 domain	ATP binding|hydrogen ion transporting ATP synthase activity, rotational mechanism|proton-transporting ATPase activity, rotational mechanism	g.chr3:113505224T>C	L09235	CCDS2976.1	3q13.31	2010-04-21	2002-08-29	2003-04-25	ENSG00000114573	ENSG00000114573	3.6.3.14	"""ATPases / V-type"""	851	protein-coding gene	gene with protein product		607027	"""ATPase, H+ transporting, lysosomal (vacuolar proton pump), alpha polypeptide, 70kD, isoform 1"""	VPP2, ATP6A1, ATP6V1A1		8463241	Standard	NM_001690		Approved	Vma1, VA68	uc003eao.3	P38606	OTTHUMG00000159295	ENST00000273398.3:c.710T>C	3.37:g.113505224T>C	ENSP00000273398:p.Leu237Pro		Somatic				ATP6V1A_uc011bik.2_Missense_Mutation_p.L204P	p.L237P	NM_001690	NP_001681	WXS	Illumina GAIIx	Phase_I	P38606	VATA_HUMAN			5	818	+			237					B2RBR8|B7Z1R5|D3DN75|Q53YD9|Q96DY6|Q9UHY3	Missense_Mutation	SNP	ENST00000273398.3	37	c.710T>C	CCDS2976.1	.	.	.	.	.	.	.	.	.	.	T	20.3	3.972517	0.74246	.	.	ENSG00000114573	ENST00000273398;ENST00000538620	D;D	0.84223	-1.82;-1.82	5.33	4.17	0.49024	ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.94062	0.8097	H	0.96208	3.785	0.80722	D	1	D	0.71674	0.998	D	0.73708	0.981	D	0.94260	0.7501	10	0.87932	D	0	-16.1423	10.9912	0.47551	0.0:0.0737:0.0:0.9263	.	237	P38606	VATA_HUMAN	P	237;204	ENSP00000273398:L237P;ENSP00000439874:L204P	ENSP00000273398:L237P	L	+	2	0	ATP6V1A	114987914	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	7.484000	0.81180	0.873000	0.35799	-0.353000	0.07706	CTT		0.423	ATP6V1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354457.1	NM_001690		4	255	0	0	0	1	0	4	255				
SCPEP1	59342	broad.mit.edu	37	17	55058499	55058499	+	Missense_Mutation	SNP	G	G	A			TCGA-DJ-A3UK-01A-11D-A22D-08	TCGA-DJ-A3UK-10A-01D-A22D-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b796fc76-16ca-4659-a0a1-8b6f58ae6493	e5f80f02-e798-4861-bd03-6933647e5d7d	g.chr17:55058499G>A	ENST00000262288.3	+	2	188	c.133G>A	c.(133-135)Gtc>Atc	p.V45I	RP5-1107A17.4_ENST00000572877.1_RNA|SCPEP1_ENST00000571898.1_3'UTR	NM_021626.2	NP_067639.1	Q9HB40	RISC_HUMAN	serine carboxypeptidase 1	45					negative regulation of blood pressure (GO:0045776)|positive regulation of vasodilation (GO:0045909)|retinoic acid metabolic process (GO:0042573)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	serine-type carboxypeptidase activity (GO:0004185)			endometrium(3)|kidney(1)|large_intestine(3)|lung(5)|skin(2)	14	Breast(9;2.86e-08)					TTATGTGACGGTCCGCAAGGA	0.493																																						uc002iuv.4																			0				endometrium(3)|kidney(1)|large_intestine(3)|lung(5)|skin(2)	14						c.(133-135)Gtc>Atc		Homo sapiens serine carboxypeptidase 1 (SCPEP1), mRNA.							144.0	117.0	126.0					17																	55058499		2203	4300	6503	SO:0001583	missense	59342				proteolysis	extracellular region	serine-type carboxypeptidase activity	g.chr17:55058499G>A	AF282618	CCDS11593.1	17q22	2012-09-20			ENSG00000121064	ENSG00000121064			29507	protein-coding gene	gene with protein product	"""retinoid inducible serine carboxypeptidase"""					11447226, 12975309	Standard	NM_021626		Approved	RISC	uc002iuv.4	Q9HB40	OTTHUMG00000178129	ENST00000262288.3:c.133G>A	17.37:g.55058499G>A	ENSP00000262288:p.Val45Ile		Somatic				SCPEP1_uc010dcl.3_Non-coding_Transcript|SCPEP1_uc010wnk.2_5'UTR	p.V45I	NM_021626	NP_067639	WXS	Illumina GAIIx	Phase_I	Q9HB40	RISC_HUMAN			1	186	+	Breast(9;2.86e-08)		45					Q96A94|Q9H3F0	Missense_Mutation	SNP	ENST00000262288.3	37	c.133G>A	CCDS11593.1	.	.	.	.	.	.	.	.	.	.	G	16.89	3.247593	0.59103	.	.	ENSG00000121064	ENST00000262288	T	0.54479	0.57	5.84	4.87	0.63330	.	0.057623	0.64402	N	0.000001	T	0.70124	0.3188	M	0.80422	2.495	0.53688	D	0.999978	D	0.64830	0.994	P	0.62298	0.9	T	0.73642	-0.3918	10	0.52906	T	0.07	-19.048	12.9923	0.58627	0.0741:0.0:0.9259:0.0	.	45	Q9HB40	RISC_HUMAN	I	45	ENSP00000262288:V45I	ENSP00000262288:V45I	V	+	1	0	SCPEP1	52413498	1.000000	0.71417	0.719000	0.30619	0.032000	0.12392	5.084000	0.64462	1.468000	0.48064	0.655000	0.94253	GTC		0.493	SCPEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440622.1	NM_021626		3	67	0	0	0	1	0	3	67				
MUC16	94025	broad.mit.edu	37	19	9090831	9090831	+	Silent	SNP	A	A	G			TCGA-DJ-A3UK-01A-11D-A22D-08	TCGA-DJ-A3UK-10A-01D-A22D-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b796fc76-16ca-4659-a0a1-8b6f58ae6493	e5f80f02-e798-4861-bd03-6933647e5d7d	g.chr19:9090831A>G	ENST00000397910.4	-	1	1187	c.984T>C	c.(982-984)ccT>ccC	p.P328P		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	328	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						TCATGGAAAAAGGGATAGCTG	0.522																																						uc002mkp.3																			0				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						c.(982-984)ccT>ccC		Homo sapiens mucin 16, cell surface associated (MUC16), mRNA.							96.0	95.0	96.0					19																	9090831		2041	4195	6236	SO:0001819	synonymous_variant	94025				cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding	g.chr19:9090831A>G	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.984T>C	19.37:g.9090831A>G			Somatic					p.P328P	NM_024690	NP_078966	WXS	Illumina GAIIx	Phase_I	Q8WXI7	MUC16_HUMAN			0	1188	-			328			Thr-rich.		Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	37	c.984T>C	CCDS54212.1																																																																																				0.522	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		4	92	0	0	0	1	0	4	92				
BRE	9577	broad.mit.edu	37	2	28152748	28152748	+	Missense_Mutation	SNP	A	A	T			TCGA-DJ-A3UK-01A-11D-A22D-08	TCGA-DJ-A3UK-10A-01D-A22D-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b796fc76-16ca-4659-a0a1-8b6f58ae6493	e5f80f02-e798-4861-bd03-6933647e5d7d	g.chr2:28152748A>T	ENST00000342045.2	+	4	319	c.178A>T	c.(178-180)Ata>Tta	p.I60L	BRE_ENST00000603461.1_3'UTR|BRE_ENST00000379632.2_Missense_Mutation_p.I60L|BRE_ENST00000344773.2_Missense_Mutation_p.I60L|BRE_ENST00000379624.1_Missense_Mutation_p.I60L|BRE_ENST00000361704.2_Missense_Mutation_p.I60L	NM_199194.2	NP_954664.1			brain and reproductive organ-expressed (TNFRSF1A modulator)											NS(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(11)|prostate(2)|skin(2)	23	Acute lymphoblastic leukemia(172;0.155)					TAAACTGCACATACCATATGC	0.343																																						uc002rls.3																			0				NS(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(11)|prostate(2)|skin(2)	23						c.(178-180)Ata>Tta		Homo sapiens brain and reproductive organ-expressed (TNFRSF1A modulator) (BRE), transcript variant 1, mRNA.							92.0	88.0	89.0					2																	28152748		2203	4300	6503	SO:0001583	missense	9577				G2/M transition DNA damage checkpoint|apoptosis|chromatin modification|double-strand break repair|positive regulation of DNA repair|positive regulation of anti-apoptosis|response to ionizing radiation|signal transduction	BRCA1-A complex|BRISC complex|cytoplasm|nuclear ubiquitin ligase complex	peroxisome targeting sequence binding|polyubiquitin binding|tumor necrosis factor receptor binding	g.chr2:28152748A>T	AF015767	CCDS1763.1, CCDS1764.1, CCDS1765.1	2p23	2008-02-05			ENSG00000158019	ENSG00000158019			1106	protein-coding gene	gene with protein product	"""BRCA1/BRCA2-containing complex, subunit 4"""	610497				9737713, 7826398	Standard	NM_004899		Approved	BRCC45, BRCC4	uc002rls.3	Q9NXR7	OTTHUMG00000097831	ENST00000342045.2:c.178A>T	2.37:g.28152748A>T	ENSP00000339371:p.Ile60Leu		Somatic				BRE_uc002rlp.1_Missense_Mutation_p.I60L|BRE_uc002rlq.3_Missense_Mutation_p.I60L|BRE_uc002rlr.3_Missense_Mutation_p.I60L|BRE_uc002rlt.3_Missense_Mutation_p.I60L|BRE_uc002rlu.3_Missense_Mutation_p.I60L|BRE_uc002rlv.3_5'UTR	p.I60L	NM_004899	NP_004890	WXS	Illumina GAIIx	Phase_I	Q9NXR7	BRE_HUMAN			2	430	+	Acute lymphoblastic leukemia(172;0.155)		60			UEV-like 1.			Missense_Mutation	SNP	ENST00000342045.2	37	c.178A>T	CCDS1763.1	.	.	.	.	.	.	.	.	.	.	A	22.9	4.352849	0.82132	.	.	ENSG00000158019	ENST00000436924;ENST00000344773;ENST00000379624;ENST00000342045;ENST00000379632;ENST00000361704;ENST00000379629	T	0.51574	0.7	5.04	5.04	0.67666	.	0.000000	0.85682	D	0.000000	T	0.56321	0.1977	L	0.48642	1.525	0.58432	D	0.999991	P;B;B;P	0.38863	0.65;0.241;0.202;0.65	P;B;B;P	0.54140	0.743;0.117;0.071;0.658	T	0.55179	-0.8181	10	0.41790	T	0.15	-17.2749	12.5917	0.56447	1.0:0.0:0.0:0.0	.	60;60;60;60	Q9NXR7-1;Q9NXR7;Q9NXR7-4;Q9NXR7-3	.;BRE_HUMAN;.;.	L	60	ENSP00000368950:I60L	ENSP00000339371:I60L	I	+	1	0	BRE	28006252	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	7.169000	0.77578	2.017000	0.59298	0.533000	0.62120	ATA		0.343	BRE-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215114.1			3	81	0	0	0	1	0	3	81				
ABI3BP	25890	broad.mit.edu	37	3	100473513	100473513	+	Missense_Mutation	SNP	T	T	G			TCGA-DJ-A3UK-01A-11D-A22D-08	TCGA-DJ-A3UK-10A-01D-A22D-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b796fc76-16ca-4659-a0a1-8b6f58ae6493	e5f80f02-e798-4861-bd03-6933647e5d7d	g.chr3:100473513T>G	ENST00000284322.5	-	31	2849	c.2740A>C	c.(2740-2742)Aaa>Caa	p.K914Q	ABI3BP_ENST00000383691.4_Missense_Mutation_p.K868Q|ABI3BP_ENST00000471714.1_Missense_Mutation_p.K1616Q	NM_015429.3	NP_056244.2	Q7Z7G0	TARSH_HUMAN	ABI family, member 3 (NESH) binding protein	914	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				extracellular matrix organization (GO:0030198)|positive regulation of cell-substrate adhesion (GO:0010811)	extracellular space (GO:0005615)|interstitial matrix (GO:0005614)	heparin binding (GO:0008201)			central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(18)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	50						AGCGGGTTTTTGGGTTTCACC	0.413																																						uc003dun.3																			0				central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(18)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	50						c.(2740-2742)Aaa>Caa		Homo sapiens ABI family, member 3 (NESH) binding protein (ABI3BP), mRNA.							81.0	73.0	75.0					3																	100473513		1844	4094	5938	SO:0001583	missense	25890					extracellular space		g.chr3:100473513T>G	AB056106	CCDS46880.1	3q12.2	2013-02-11	2008-09-12		ENSG00000154175	ENSG00000154175		"""Fibronectin type III domain containing"""	17265	protein-coding gene	gene with protein product	"""target of Nesh-SH3"""	606279				11501947	Standard	NM_015429		Approved	NESHBP, DKFZP586L2024, TARSH	uc003dun.3	Q7Z7G0	OTTHUMG00000159094	ENST00000284322.5:c.2740A>C	3.37:g.100473513T>G	ENSP00000284322:p.Lys914Gln		Somatic				ABI3BP_uc003duj.3_Missense_Mutation_p.K494Q|ABI3BP_uc003duk.3_Missense_Mutation_p.K623Q|ABI3BP_uc003dul.3_Missense_Mutation_p.K744Q|ABI3BP_uc011bhd.2_Missense_Mutation_p.K868Q|ABI3BP_uc003dum.3_Missense_Mutation_p.K325Q	p.K914Q	NM_015429	NP_056244	WXS	Illumina GAIIx	Phase_I	Q7Z7G0	TARSH_HUMAN			30	2825	-			914			Fibronectin type-III 2.		B3KSL4|Q6ZW20|Q6ZW22|Q9C082|Q9UFI6	Missense_Mutation	SNP	ENST00000284322.5	37	c.2740A>C	CCDS46880.1	.	.	.	.	.	.	.	.	.	.	T	18.96	3.733795	0.69189	.	.	ENSG00000154175	ENST00000471714;ENST00000284322;ENST00000383692;ENST00000429331;ENST00000383691	T;T;T	0.56275	0.47;0.47;0.47	5.68	5.68	0.88126	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.207410	0.49916	D	0.000128	T	0.67468	0.2896	M	0.76328	2.33	0.46798	D	0.999207	P;B;D;D	0.61697	0.873;0.058;0.99;0.973	P;B;P;P	0.56751	0.663;0.139;0.805;0.787	T	0.67979	-0.5530	10	0.37606	T	0.19	-13.8888	15.9179	0.79535	0.0:0.0:0.0:1.0	.	868;914;1616;623	B4DSV9;Q7Z7G0;D3YTG3;D3YTD6	.;TARSH_HUMAN;.;.	Q	1616;914;623;325;868	ENSP00000420524:K1616Q;ENSP00000284322:K914Q;ENSP00000373189:K868Q	ENSP00000284322:K914Q	K	-	1	0	ABI3BP	101956203	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	5.738000	0.68613	2.157000	0.67596	0.455000	0.32223	AAA		0.413	ABI3BP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000353260.1			2	11	0	0	0	1	0	2	11				
FOXP3	50943	broad.mit.edu	37	X	49113414	49113414	+	Silent	SNP	G	G	A			TCGA-DJ-A3UK-01A-11D-A22D-08	TCGA-DJ-A3UK-10A-01D-A22D-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b796fc76-16ca-4659-a0a1-8b6f58ae6493	e5f80f02-e798-4861-bd03-6933647e5d7d	g.chrX:49113414G>A	ENST00000376207.4	-	5	697	c.510C>T	c.(508-510)acC>acT	p.T170T	FOXP3_ENST00000455775.2_Silent_p.T170T|FOXP3_ENST00000376197.1_Silent_p.T120T|FOXP3_ENST00000557224.1_Silent_p.T135T|FOXP3_ENST00000518685.1_Silent_p.T135T|FOXP3_ENST00000376199.2_Silent_p.T135T	NM_014009.3	NP_054728.2	Q9BZS1	FOXP3_HUMAN	forkhead box P3	170					B cell homeostasis (GO:0001782)|CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation (GO:0002361)|chromatin remodeling (GO:0006338)|cytokine production (GO:0001816)|myeloid cell homeostasis (GO:0002262)|negative regulation of activated T cell proliferation (GO:0046007)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chronic inflammatory response (GO:0002677)|negative regulation of CREB transcription factor activity (GO:0032792)|negative regulation of cytokine biosynthetic process (GO:0042036)|negative regulation of cytokine secretion (GO:0050710)|negative regulation of histone acetylation (GO:0035067)|negative regulation of histone deacetylation (GO:0031064)|negative regulation of immune response (GO:0050777)|negative regulation of interferon-gamma biosynthetic process (GO:0045077)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-10 production (GO:0032693)|negative regulation of interleukin-2 biosynthetic process (GO:0045085)|negative regulation of interleukin-2 production (GO:0032703)|negative regulation of interleukin-4 production (GO:0032713)|negative regulation of interleukin-5 production (GO:0032714)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of isotype switching to IgE isotypes (GO:0048294)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of T cell cytokine production (GO:0002725)|negative regulation of T cell proliferation (GO:0042130)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of tumor necrosis factor production (GO:0032720)|positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation (GO:0032831)|positive regulation of histone acetylation (GO:0035066)|positive regulation of immature T cell proliferation in thymus (GO:0033092)|positive regulation of interleukin-4 production (GO:0032753)|positive regulation of peripheral T cell tolerance induction (GO:0002851)|positive regulation of T cell anergy (GO:0002669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta1 production (GO:0032914)|regulation of isotype switching to IgG isotypes (GO:0048302)|regulation of transcription, DNA-templated (GO:0006355)|response to virus (GO:0009615)|T cell activation (GO:0042110)|T cell homeostasis (GO:0043029)|T cell mediated immunity (GO:0002456)|T cell receptor signaling pathway (GO:0050852)|tolerance induction to self antigen (GO:0002513)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|protein complex (GO:0043234)	histone acetyltransferase binding (GO:0035035)|histone deacetylase binding (GO:0042826)|metal ion binding (GO:0046872)|NF-kappaB binding (GO:0051059)|NFAT protein binding (GO:0051525)|protein homodimerization activity (GO:0042803)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(5)|ovary(1)	10	Ovarian(276;0.236)					GATTTGGGAAGGTGCAGAGCA	0.652																																					GBM(182;1432 2112 16160 23073 31774)	uc011mnb.2																			0				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(5)|ovary(1)	10						c.(508-510)acC>acT		Homo sapiens forkhead box P3 (FOXP3), transcript variant 1, mRNA.							62.0	42.0	49.0					X																	49113414		2203	4300	6503	SO:0001819	synonymous_variant	50943				B cell homeostasis|T cell homeostasis|T cell receptor signaling pathway|cerebellum development|chromatin remodeling|embryo development|myeloid cell homeostasis|negative regulation of CREB transcription factor activity|negative regulation of NF-kappaB transcription factor activity|negative regulation of T cell cytokine production|negative regulation of activated T cell proliferation|negative regulation of chronic inflammatory response|negative regulation of cytokine secretion|negative regulation of histone acetylation|negative regulation of histone deacetylation|negative regulation of interferon-gamma biosynthetic process|negative regulation of interferon-gamma production|negative regulation of interleukin-10 production|negative regulation of interleukin-2 biosynthetic process|negative regulation of interleukin-2 production|negative regulation of interleukin-4 production|negative regulation of interleukin-5 production|negative regulation of interleukin-6 production|negative regulation of isotype switching to IgE isotypes|negative regulation of tumor necrosis factor production|pattern specification process|positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation|positive regulation of T cell anergy|positive regulation of histone acetylation|positive regulation of immature T cell proliferation in thymus|positive regulation of peripheral T cell tolerance induction|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transforming growth factor-beta1 production|post-embryonic development|regulation of isotype switching to IgG isotypes|response to virus|tolerance induction to self antigen	cytoplasm|nucleus|transcription factor complex	DNA bending activity|NF-kappaB binding|NFAT protein binding|chromatin binding|double-stranded DNA binding|histone acetyltransferase binding|histone deacetylase binding|promoter binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription corepressor activity|zinc ion binding	g.chrX:49113414G>A		CCDS14323.1, CCDS48109.1	Xp11.23	2014-09-17		2002-09-20	ENSG00000049768	ENSG00000049768		"""Forkhead boxes"""	6106	protein-coding gene	gene with protein product		300292	"""immune dysregulation, polyendocrinopathy, enteropathy, X-linked"""	IPEX		10677306, 11138001	Standard	NM_014009		Approved	JM2, XPID, AIID, PIDX, DIETER, SCURFIN	uc004dnf.4	Q9BZS1	OTTHUMG00000024135	ENST00000376207.4:c.510C>T	X.37:g.49113414G>A			Somatic				FOXP3_uc011mnc.2_Silent_p.T170T|FOXP3_uc004dnf.4_Silent_p.T170T|FOXP3_uc004dne.4_Silent_p.T135T|FOXP3_uc022bwa.1_Silent_p.T120T	p.T170T	NM_014009	NP_054728	WXS	Illumina GAIIx	Phase_I	Q9BZS1	FOXP3_HUMAN			3	532	-	Ovarian(276;0.236)		170					A5HJT1|B7ZLG0|B9UN80|O60827|Q14DD8|Q4ZH51	Silent	SNP	ENST00000376207.4	37	c.510C>T	CCDS14323.1																																																																																				0.652	FOXP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060814.1	NM_014009		3	91	0	0	0	1	0	3	91				
PHACTR1	221692	broad.mit.edu	37	6	13283734	13283734	+	Silent	SNP	C	C	T	rs376680831		TCGA-DJ-A3UK-01A-11D-A22D-08	TCGA-DJ-A3UK-10A-01D-A22D-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b796fc76-16ca-4659-a0a1-8b6f58ae6493	e5f80f02-e798-4861-bd03-6933647e5d7d	g.chr6:13283734C>T	ENST00000379335.3	+	3	387	c.282C>T	c.(280-282)gaC>gaT	p.D94D	RP1-257A7.4_ENST00000606150.1_RNA|PHACTR1_ENST00000332995.7_Silent_p.D530D|RP1-257A7.4_ENST00000399446.2_RNA|PHACTR1_ENST00000457702.2_Silent_p.D385D|PHACTR1_ENST00000379329.1_Silent_p.D94D			Q9C0D0	PHAR1_HUMAN	phosphatase and actin regulator 1	530					actin cytoskeleton reorganization (GO:0031532)|actomyosin structure organization (GO:0031032)|cell motility (GO:0048870)|stress fiber assembly (GO:0043149)	cell junction (GO:0030054)|cytosol (GO:0005829)|nucleus (GO:0005634)|synapse (GO:0045202)	actin binding (GO:0003779)|protein phosphatase inhibitor activity (GO:0004864)			breast(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|ovary(1)|skin(2)|upper_aerodigestive_tract(3)	26	Breast(50;0.0427)|Ovarian(93;0.12)	all_hematologic(90;0.122)|Lung SC(78;0.195)	Epithelial(50;0.146)|BRCA - Breast invasive adenocarcinoma(129;0.239)			AGGTGGCTGACGCTCAGGACT	0.597																																						uc003nah.2																			0				breast(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|ovary(1)|skin(2)|upper_aerodigestive_tract(3)	26						c.(1588-1590)gaC>gaT		Homo sapiens phosphatase and actin regulator 1 (PHACTR1), transcript variant 1, mRNA.		C	,,	0,4168		0,0,2084	105.0	119.0	114.0		1590,,1590	-2.4	0.9	6		114	1,8415		0,1,4207	no	coding-synonymous,intron,coding-synonymous	PHACTR1,LOC100130357	NM_001242648.1,NM_001242698.1,NM_030948.2	,,	0,1,6291	TT,TC,CC		0.0119,0.0,0.0079	,,	530/581,,530/581	13283734	1,12583	2084	4208	6292	SO:0001819	synonymous_variant	221692					cell junction|cytoplasm|synapse	actin binding|protein phosphatase inhibitor activity	g.chr6:13283734C>T	AB051520	CCDS75401.1	6p23	2013-01-24	2004-05-20	2004-05-21	ENSG00000112137	ENSG00000112137		"""Phosphatase and actin regulators"""	20990	protein-coding gene	gene with protein product		608723	"""RPEL repeat containing 1"""	RPEL1		11214970, 15107502	Standard	NM_030948		Approved	KIAA1733, dJ257A7.2	uc010jpc.3	Q9C0D0	OTTHUMG00000014270	ENST00000379335.3:c.282C>T	6.37:g.13283734C>T			Somatic				PHACTR1_uc010jpc.3_Silent_p.D530D|TBC1D7_uc003naj.3_Intron|TBC1D7_uc011dis.2_Intron|LOC100130357_uc003nak.1_Intron	p.D530D	NM_030948	NP_112210	WXS	Illumina GAIIx	Phase_I	Q9C0D0	PHAR1_HUMAN	Epithelial(50;0.146)|BRCA - Breast invasive adenocarcinoma(129;0.239)		12	1963	+	Breast(50;0.0427)|Ovarian(93;0.12)	all_hematologic(90;0.122)|Lung SC(78;0.195)	530					A8K1V2|Q3MJ93|Q5JSJ2	Silent	SNP	ENST00000379335.3	37	c.1590C>T		.	.	.	.	.	.	.	.	.	.	C	10.70	1.423086	0.25639	0.0	1.19E-4	ENSG00000112137	ENST00000415087	.	.	.	5.9	-2.39	0.06602	.	.	.	.	.	T	0.49423	0.1556	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.56050	-0.8043	4	.	.	.	-20.7442	12.7679	0.57403	0.0:0.5098:0.0:0.4902	.	.	.	.	M	365	.	.	T	+	2	0	PHACTR1	13391713	0.000000	0.05858	0.857000	0.33713	0.994000	0.84299	-1.970000	0.01504	-0.426000	0.07360	0.655000	0.94253	ACG		0.597	PHACTR1-003	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000039878.1	XM_166420		9	210	0	0	0	1	0	9	210				
LDB2	9079	broad.mit.edu	37	4	16900067	16900067	+	Silent	SNP	G	G	A			TCGA-DJ-A3UK-01A-11D-A22D-08	TCGA-DJ-A3UK-10A-01D-A22D-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b796fc76-16ca-4659-a0a1-8b6f58ae6493	e5f80f02-e798-4861-bd03-6933647e5d7d	g.chr4:16900067G>A	ENST00000304523.5	-	1	365	c.42C>T	c.(40-42)ttC>ttT	p.F14F	LDB2_ENST00000515064.1_Silent_p.F14F|LDB2_ENST00000441778.2_Silent_p.F14F|LDB2_ENST00000502640.1_Silent_p.F14F	NM_001290.3	NP_001281.1	O43679	LDB2_HUMAN	LIM domain binding 2	14					epithelial structure maintenance (GO:0010669)|hair follicle development (GO:0001942)|positive regulation of cellular component biogenesis (GO:0044089)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|somatic stem cell maintenance (GO:0035019)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	LIM domain binding (GO:0030274)|transcription cofactor activity (GO:0003712)			breast(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(23)|urinary_tract(1)	33						AAAATGGGCCGAAAGGAGAAG	0.458																																						uc003goz.3																			0				breast(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(23)|urinary_tract(1)	33						c.(40-42)ttC>ttT		Homo sapiens LIM domain binding 2 (LDB2), transcript variant 1, mRNA.							196.0	173.0	181.0					4																	16900067		2203	4300	6503	SO:0001819	synonymous_variant	9079						LIM domain binding|transcription cofactor activity	g.chr4:16900067G>A	AF068651	CCDS3420.1, CCDS47031.1	4p16	2008-08-01			ENSG00000169744	ENSG00000169744			6533	protein-coding gene	gene with protein product		603450				9853615, 9880598, 10861853	Standard	NM_001290		Approved	CLIM1, LDB1	uc003goz.3	O43679	OTTHUMG00000048212	ENST00000304523.5:c.42C>T	4.37:g.16900067G>A			Somatic				LDB2_uc003gpa.3_Silent_p.F14F|LDB2_uc011bxh.2_Silent_p.F14F|LDB2_uc003gpb.3_Silent_p.F14F|LDB2_uc010iee.3_Silent_p.F14F	p.F14F	NM_001290	NP_001281	WXS	Illumina GAIIx	Phase_I	O43679	LDB2_HUMAN			0	358	-			14					O60619|O75480	Silent	SNP	ENST00000304523.5	37	c.42C>T	CCDS3420.1																																																																																				0.458	LDB2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250321.2			3	79	0	0	0	1	0	3	79				
GAS2L2	246176	broad.mit.edu	37	17	34074068	34074068	+	Missense_Mutation	SNP	G	G	A	rs199814494		TCGA-DJ-A3UK-01A-11D-A22D-08	TCGA-DJ-A3UK-10A-01D-A22D-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b796fc76-16ca-4659-a0a1-8b6f58ae6493	e5f80f02-e798-4861-bd03-6933647e5d7d	g.chr17:34074068G>A	ENST00000254466.6	-	5	1079	c.1052C>T	c.(1051-1053)aCg>aTg	p.T351M	GAS2L2_ENST00000587565.1_Missense_Mutation_p.T335M	NM_139285.3	NP_644814.1	Q8NHY3	GA2L2_HUMAN	growth arrest-specific 2 like 2	351					cell cycle arrest (GO:0007050)|microtubule bundle formation (GO:0001578)|negative regulation of microtubule depolymerization (GO:0007026)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	actin filament binding (GO:0051015)|cytoskeletal adaptor activity (GO:0008093)|microtubule binding (GO:0008017)			central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	35		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		GGAGGCCCCCGTCCCTGCTCC	0.612																																						uc002hjv.2																			0				central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	35						c.(1051-1053)aCg>aTg		Homo sapiens growth arrest-specific 2 like 2 (GAS2L2), mRNA.							36.0	40.0	39.0					17																	34074068		2202	4300	6502	SO:0001583	missense	246176				cell cycle arrest	cytoplasm|cytoskeleton		g.chr17:34074068G>A	AF508784	CCDS11298.1	17q21	2014-05-06			ENSG00000132139	ENSG00000270765			24846	protein-coding gene	gene with protein product		611398				12584248	Standard	NM_139285		Approved	GAR17	uc002hjv.2	Q8NHY3	OTTHUMG00000188386	ENST00000254466.6:c.1052C>T	17.37:g.34074068G>A	ENSP00000254466:p.Thr351Met		Somatic					p.T351M	NM_139285	NP_644814	WXS	Illumina GAIIx	Phase_I	Q8NHY3	GA2L2_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)	4	1080	-		Ovarian(249;0.17)	351					Q8NHY4	Missense_Mutation	SNP	ENST00000254466.6	37	c.1052C>T	CCDS11298.1	.	.	.	.	.	.	.	.	.	.	G	8.108	0.778080	0.16120	.	.	ENSG00000132139	ENST00000254466	T	0.18502	2.21	4.8	2.69	0.31865	.	1.269660	0.05621	N	0.579895	T	0.13970	0.0338	L	0.29908	0.895	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.29274	-1.0017	10	0.42905	T	0.14	0.788	6.6506	0.22959	0.3146:0.0:0.6854:0.0	.	351	Q8NHY3	GA2L2_HUMAN	M	351	ENSP00000254466:T351M	ENSP00000254466:T351M	T	-	2	0	GAS2L2	31098181	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.405000	0.21015	0.667000	0.31107	-0.221000	0.12465	ACG		0.612	GAS2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256497.1	NM_139285		10	96	0	0	0	1	0	10	96				
NAA11	84779	broad.mit.edu	37	4	80246702	80246702	+	Silent	SNP	G	G	A			TCGA-DJ-A3UK-01A-11D-A22D-08	TCGA-DJ-A3UK-10A-01D-A22D-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b796fc76-16ca-4659-a0a1-8b6f58ae6493	e5f80f02-e798-4861-bd03-6933647e5d7d	g.chr4:80246702G>A	ENST00000286794.4	-	1	502	c.330C>T	c.(328-330)caC>caT	p.H110H	NAA11_ENST00000513733.1_5'Flank	NM_032693.2	NP_116082.1	Q9BSU3	NAA11_HUMAN	N(alpha)-acetyltransferase 11, NatA catalytic subunit	110	N-acetyltransferase. {ECO:0000255|PROSITE-ProRule:PRU00532}.				N-terminal protein amino acid acetylation (GO:0006474)	NatA complex (GO:0031415)|nucleus (GO:0005634)	peptide alpha-N-acetyltransferase activity (GO:0004596)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(4)|lung(9)|ovary(1)|pancreas(1)|skin(2)	23						TCTTCCTGACGTGCAGAGACA	0.522																																						uc003hlt.4																			0				NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(4)|lung(9)|ovary(1)|pancreas(1)|skin(2)	23						c.(328-330)caC>caT		Homo sapiens N(alpha)-acetyltransferase 11, NatA catalytic subunit (NAA11), mRNA.							58.0	62.0	61.0					4																	80246702		2093	4241	6334	SO:0001819	synonymous_variant	84779					cytoplasm|nucleus	peptide alpha-N-acetyltransferase activity|protein binding	g.chr4:80246702G>A		CCDS47084.1	4q21.23	2010-05-07	2010-01-14	2010-01-14		ENSG00000156269	2.3.1.88	"""N(alpha)-acetyltransferase subunits"""	28125	protein-coding gene	gene with protein product			"""ARD1 homolog B (S. cerevisiae)"""	ARD1B		16638120, 19660095	Standard	NM_032693		Approved	ARD2, hARD2	uc003hlt.4	Q9BSU3		ENST00000286794.4:c.330C>T	4.37:g.80246702G>A			Somatic				NAA11_uc021xpl.1_Silent_p.H110H	p.H110H	NM_032693	NP_116082	WXS	Illumina GAIIx	Phase_I	Q9BSU3	NAA11_HUMAN			0	470	-			110			N-acetyltransferase.		Q66K19|Q6P479	Silent	SNP	ENST00000286794.4	37	c.330C>T	CCDS47084.1																																																																																				0.522	NAA11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362922.1			17	46	0	0	0	1	0	17	46				
SHMT1	6470	broad.mit.edu	37	17	18232139	18232139	+	Silent	SNP	C	C	T			TCGA-DJ-A3UK-01A-11D-A22D-08	TCGA-DJ-A3UK-10A-01D-A22D-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b796fc76-16ca-4659-a0a1-8b6f58ae6493	e5f80f02-e798-4861-bd03-6933647e5d7d	g.chr17:18232139C>T	ENST00000316694.3	-	12	1511	c.1377G>A	c.(1375-1377)gcG>gcA	p.A459A	SHMT1_ENST00000539052.1_Silent_p.A321A|RP1-178F10.3_ENST00000577764.1_lincRNA|SHMT1_ENST00000354098.3_Silent_p.A420A|SHMT1_ENST00000352886.6_Silent_p.A379A	NM_004169.3	NP_004160.3	P34896	GLYC_HUMAN	serine hydroxymethyltransferase 1 (soluble)	459					carnitine biosynthetic process (GO:0045329)|cellular nitrogen compound metabolic process (GO:0034641)|folic acid metabolic process (GO:0046655)|glycine biosynthetic process from serine (GO:0019264)|L-serine catabolic process (GO:0006565)|protein homotetramerization (GO:0051289)|protein tetramerization (GO:0051262)|purine nucleobase biosynthetic process (GO:0009113)|small molecule metabolic process (GO:0044281)|tetrahydrofolate interconversion (GO:0035999)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	amino acid binding (GO:0016597)|glycine hydroxymethyltransferase activity (GO:0004372)|L-allo-threonine aldolase activity (GO:0008732)|protein homodimerization activity (GO:0042803)|pyridoxal phosphate binding (GO:0030170)			breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(5)|ovary(1)	13					Glycine(DB00145)|Mimosine(DB01055)|Tetrahydrofolic acid(DB00116)	CCTGCACGGCCGCCTGGTACT	0.612																																						uc002gta.3																			0				breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(5)|ovary(1)	13						c.(1375-1377)gcG>gcA		Homo sapiens serine hydroxymethyltransferase 1 (soluble) (SHMT1), nuclear gene encoding mitochondrial protein, transcript variant 1, mRNA.	Glycine(DB00145)|Mimosine(DB01055)|Pyridoxal Phosphate(DB00114)|Tetrahydrofolic acid(DB00116)						35.0	34.0	34.0					17																	18232139		2203	4300	6503	SO:0001819	synonymous_variant	6470				L-serine catabolic process|carnitine biosynthetic process|folic acid metabolic process|one-carbon metabolic process|purine base biosynthetic process	cytosol|nucleus	glycine hydroxymethyltransferase activity|protein homodimerization activity|pyridoxal phosphate binding	g.chr17:18232139C>T		CCDS11196.1, CCDS11197.1, CCDS62112.1	17p11.2	2010-04-23			ENSG00000176974	ENSG00000176974	2.1.2.1		10850	protein-coding gene	gene with protein product	"""cytoplasmic serine hydroxymethyltransferase"", ""14 kDa protein"""	182144				8505317	Standard	NM_004169		Approved	CSHMT, SHMT, MGC15229, MGC24556	uc002gta.3	P34896	OTTHUMG00000059094	ENST00000316694.3:c.1377G>A	17.37:g.18232139C>T			Somatic				SHMT1_uc002gsz.3_Silent_p.A234A|SHMT1_uc002gtb.3_Silent_p.A420A|SHMT1_uc010vxt.2_Silent_p.A321A	p.A459A	NM_004169	NP_004160	WXS	Illumina GAIIx	Phase_I	P34896	GLYC_HUMAN			11	1567	-			459					B4DPM9|D3DXD0|Q96HY0|Q9UMD1|Q9UMD2	Silent	SNP	ENST00000316694.3	37	c.1377G>A	CCDS11196.1																																																																																				0.612	SHMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130831.2	NM_004169		3	43	0	0	0	1	0	3	43				
FXYD4	53828	broad.mit.edu	37	10	43869919	43869919	+	Splice_Site	SNP	C	C	G			TCGA-DJ-A3UK-01A-11D-A22D-08	TCGA-DJ-A3UK-10A-01D-A22D-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b796fc76-16ca-4659-a0a1-8b6f58ae6493	e5f80f02-e798-4861-bd03-6933647e5d7d	g.chr10:43869919C>G	ENST00000476166.1	+	4	373	c.39C>G	c.(37-39)ggC>ggG	p.G13G	FXYD4_ENST00000480834.1_3'UTR	NM_173160.2	NP_775183.1	P59646	FXYD4_HUMAN	FXYD domain containing ion transport regulator 4	13					ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ion channel activity (GO:0005216)			NS(1)|large_intestine(1)|lung(3)	5						CCCACACAGGCCTGACTGCCT	0.587																																					GBM(173;880 2047 13035 42390 49655)	uc001jaq.1																			0				NS(1)|large_intestine(1)|lung(3)	5						c.e4-1		Homo sapiens FXYD domain containing ion transport regulator 4 (FXYD4), transcript variant 2, mRNA.							141.0	136.0	138.0					10																	43869919		2203	4300	6503	SO:0001630	splice_region_variant	53828					integral to membrane		g.chr10:43869919C>G		CCDS7203.1	10q11.21	2008-02-01	2002-01-14		ENSG00000150201	ENSG00000150201			4028	protein-coding gene	gene with protein product			"""FXYD domain-containing ion transport regulator 4"""			10950925, 12763854	Standard	NM_001184963		Approved	CHIF	uc001jaq.1	P59646	OTTHUMG00000018027	ENST00000476166.1:c.38-1C>G	10.37:g.43869919C>G			Somatic					p.G13_splice	NM_001184963	NP_001171892	WXS	Illumina GAIIx	Phase_I	P59646	FXYD4_HUMAN			4	370	+			13					Q6UWZ1|Q7Z4M5	Splice_Site	SNP	ENST00000476166.1	37	c.38_splice	CCDS7203.1																																																																																				0.587	FXYD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047698.2	NM_173160	Silent	95	164	0	0	0	1	0	95	164				
TLL2	7093	broad.mit.edu	37	10	98188429	98188429	+	Silent	SNP	C	C	A	rs141217387		TCGA-DJ-A3UK-01A-11D-A22D-08	TCGA-DJ-A3UK-10A-01D-A22D-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b796fc76-16ca-4659-a0a1-8b6f58ae6493	e5f80f02-e798-4861-bd03-6933647e5d7d	g.chr10:98188429C>A	ENST00000357947.3	-	5	822	c.597G>T	c.(595-597)acG>acT	p.T199T	TLL2_ENST00000469598.1_5'UTR	NM_012465.3	NP_036597.1	Q9Y6L7	TLL2_HUMAN	tolloid-like 2	199	Metalloprotease. {ECO:0000250}.				cell differentiation (GO:0030154)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)	extracellular region (GO:0005576)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(15)|lung(22)|ovary(1)|pancreas(1)|prostate(1)|skin(3)	58		Colorectal(252;0.0846)		Epithelial(162;1.51e-07)|all cancers(201;7.59e-06)		TTTCCTCATCCGTCCTTTCTA	0.498																																						uc001kml.2																			0				NS(1)|breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(15)|lung(22)|ovary(1)|pancreas(1)|prostate(1)|skin(3)	58						c.(595-597)acG>acT		Homo sapiens tolloid-like 2 (TLL2), mRNA.							138.0	114.0	122.0					10																	98188429		2203	4300	6503	SO:0001819	synonymous_variant	7093				cell differentiation|multicellular organismal development|proteolysis	extracellular region	calcium ion binding|metalloendopeptidase activity|zinc ion binding	g.chr10:98188429C>A	AF059516	CCDS7449.1	10q23-q24	2008-07-29			ENSG00000095587	ENSG00000095587			11844	protein-coding gene	gene with protein product		606743				10516436	Standard	NM_012465		Approved		uc001kml.2	Q9Y6L7	OTTHUMG00000018833	ENST00000357947.3:c.597G>T	10.37:g.98188429C>A			Somatic				TLL2_uc009xvf.2_Silent_p.T147T	p.T199T	NM_012465	NP_036597	WXS	Illumina GAIIx	Phase_I	Q9Y6L7	TLL2_HUMAN		Epithelial(162;1.51e-07)|all cancers(201;7.59e-06)	4	838	-		Colorectal(252;0.0846)	199			Metalloprotease (By similarity).		A6NDK0|Q2M1H1|Q6PJN5|Q9UQ00	Silent	SNP	ENST00000357947.3	37	c.597G>T	CCDS7449.1																																																																																				0.498	TLL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049608.1			3	86	0	0	0	1	0	3	86				
ADAMDEC1	27299	broad.mit.edu	37	8	24254877	24254877	+	Missense_Mutation	SNP	G	G	A			TCGA-DJ-A3UK-01A-11D-A22D-08	TCGA-DJ-A3UK-10A-01D-A22D-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b796fc76-16ca-4659-a0a1-8b6f58ae6493	e5f80f02-e798-4861-bd03-6933647e5d7d	g.chr8:24254877G>A	ENST00000256412.4	+	6	755	c.535G>A	c.(535-537)Gaa>Aaa	p.E179K	ADAMDEC1_ENST00000522298.1_Missense_Mutation_p.E100K|RP11-624C23.1_ENST00000523578.1_RNA|RP11-624C23.1_ENST00000519689.1_RNA|ADAMDEC1_ENST00000538205.1_Missense_Mutation_p.E100K	NM_014479.3	NP_055294.1	O15204	ADEC1_HUMAN	ADAM-like, decysin 1	179					immune response (GO:0006955)|negative regulation of cell adhesion (GO:0007162)	extracellular region (GO:0005576)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|large_intestine(4)|skin(2)|stomach(1)	9		Prostate(55;0.0181)		Colorectal(74;0.016)|COAD - Colon adenocarcinoma(73;0.0646)|BRCA - Breast invasive adenocarcinoma(99;0.168)		TAACCAGGAGGAACAAGACCC	0.458																																					Ovarian(147;687 1849 3699 25981 31337)	uc003xdz.2																			0				NS(1)|breast(1)|large_intestine(4)|skin(2)|stomach(1)	9						c.(535-537)Gaa>Aaa		Homo sapiens ADAM-like, decysin 1 (ADAMDEC1), transcript variant 1, mRNA.							221.0	213.0	216.0					8																	24254877		2203	4300	6503	SO:0001583	missense	27299				integrin-mediated signaling pathway|negative regulation of cell adhesion|proteolysis	extracellular region|integral to membrane	integrin binding|metalloendopeptidase activity|zinc ion binding	g.chr8:24254877G>A	Y13323	CCDS6044.1, CCDS55212.1	8p12	2008-08-07			ENSG00000134028	ENSG00000134028			16299	protein-coding gene	gene with protein product		606393				9271581, 12037602	Standard	NM_001145271		Approved	M12.219	uc003xdz.2	O15204	OTTHUMG00000097858	ENST00000256412.4:c.535G>A	8.37:g.24254877G>A	ENSP00000256412:p.Glu179Lys		Somatic				ADAMDEC1_uc010lub.2_Missense_Mutation_p.E100K|ADAMDEC1_uc011lab.1_Missense_Mutation_p.E100K	p.E179K	NM_014479	NP_001138744	WXS	Illumina GAIIx	Phase_I	O15204	ADEC1_HUMAN		Colorectal(74;0.016)|COAD - Colon adenocarcinoma(73;0.0646)|BRCA - Breast invasive adenocarcinoma(99;0.168)	5	755	+		Prostate(55;0.0181)	179					B7ZAK5	Missense_Mutation	SNP	ENST00000256412.4	37	c.535G>A	CCDS6044.1	.	.	.	.	.	.	.	.	.	.	G	12.29	1.893755	0.33442	.	.	ENSG00000134028	ENST00000256412;ENST00000538205;ENST00000522298	T;T;T	0.02656	4.21;4.22;4.22	5.53	4.65	0.58169	.	0.312065	0.27595	N	0.018665	T	0.02012	0.0063	N	0.08118	0	0.09310	N	1	B	0.33379	0.41	B	0.37267	0.245	T	0.50162	-0.8860	10	0.11182	T	0.66	-14.8166	12.4375	0.55608	0.0:0.1684:0.8316:0.0	.	179	O15204	ADEC1_HUMAN	K	179;100;100	ENSP00000256412:E179K;ENSP00000442592:E100K;ENSP00000428993:E100K	ENSP00000256412:E179K	E	+	1	0	ADAMDEC1	24310822	0.761000	0.28439	0.016000	0.15963	0.033000	0.12548	3.368000	0.52357	1.325000	0.45301	0.557000	0.71058	GAA		0.458	ADAMDEC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215149.2	NM_014479		6	286	0	0	0	1	0	6	286				
ANGPT4	51378	broad.mit.edu	37	20	853717	853717	+	Silent	SNP	G	G	A			TCGA-DJ-A3UK-01A-11D-A22D-08	TCGA-DJ-A3UK-10A-01D-A22D-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b796fc76-16ca-4659-a0a1-8b6f58ae6493	e5f80f02-e798-4861-bd03-6933647e5d7d	g.chr20:853717G>A	ENST00000381922.3	-	9	1500	c.1398C>T	c.(1396-1398)taC>taT	p.Y466Y	ANGPT4_ENST00000546022.1_3'UTR	NM_015985.2	NP_057069.1	Q9Y264	ANGP4_HUMAN	angiopoietin 4	466	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cellular response to hypoxia (GO:0071456)|leukocyte migration (GO:0050900)|negative regulation of angiogenesis (GO:0016525)|negative regulation of apoptotic process (GO:0043066)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	receptor tyrosine kinase binding (GO:0030971)|transmembrane receptor protein tyrosine kinase activator activity (GO:0030297)			breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(12)|ovary(2)|prostate(1)	27						GAGCGTGGTAGTAGACGCCGT	0.612																																					Pancreas(181;481 2077 3259 31286 49856)	uc002wei.3																			0				breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(12)|ovary(2)|prostate(1)	27						c.(1396-1398)taC>taT		Homo sapiens angiopoietin 4 (ANGPT4), mRNA.							104.0	92.0	96.0					20																	853717		2203	4300	6503	SO:0001819	synonymous_variant	51378				anti-apoptosis|blood coagulation|cellular response to hypoxia|leukocyte migration|negative regulation of angiogenesis|negative regulation of blood vessel endothelial cell migration|positive regulation of angiogenesis|positive regulation of blood vessel endothelial cell migration|positive regulation of peptidyl-tyrosine phosphorylation|signal transduction	extracellular space	receptor tyrosine kinase binding|transmembrane receptor protein tyrosine kinase activator activity	g.chr20:853717G>A	AF074332	CCDS13009.1	20p13	2013-02-06			ENSG00000101280	ENSG00000101280		"""Fibrinogen C domain containing"""	487	protein-coding gene	gene with protein product		603705				10051567, 10218486	Standard	NM_015985		Approved		uc002wei.3	Q9Y264	OTTHUMG00000031652	ENST00000381922.3:c.1398C>T	20.37:g.853717G>A			Somatic				ANGPT4_uc010zpn.2_3'UTR	p.Y466Y	NM_015985	NP_057069	WXS	Illumina GAIIx	Phase_I	Q9Y264	ANGP4_HUMAN			8	1501	-			466			Fibrinogen C-terminal.		B4E3J9|Q5TFF4|Q9H4Z4	Silent	SNP	ENST00000381922.3	37	c.1398C>T	CCDS13009.1																																																																																				0.612	ANGPT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077493.1	NM_015985		3	66	0	0	0	1	0	3	66				
BRAF	673	broad.mit.edu	37	7	140453136	140453136	+	Missense_Mutation	SNP	A	A	T	rs121913377|rs113488022|rs121913227|rs397516897		TCGA-DJ-A3UK-01A-11D-A22D-08	TCGA-DJ-A3UK-10A-01D-A22D-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b796fc76-16ca-4659-a0a1-8b6f58ae6493	e5f80f02-e798-4861-bd03-6933647e5d7d	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		41	49	0	0	0	1	0	41	49				
HCAR1	27198	broad.mit.edu	37	12	123214145	123214145	+	Missense_Mutation	SNP	G	G	A			TCGA-DJ-A3UK-01A-11D-A22D-08	TCGA-DJ-A3UK-10A-01D-A22D-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b796fc76-16ca-4659-a0a1-8b6f58ae6493	e5f80f02-e798-4861-bd03-6933647e5d7d	g.chr12:123214145G>A	ENST00000436083.2	-	1	1245	c.742C>T	c.(742-744)Ccc>Tcc	p.P248S	HCAR1_ENST00000356987.2_Missense_Mutation_p.P248S|HCAR1_ENST00000432564.1_Missense_Mutation_p.P248S			Q9BXC0	HCAR1_HUMAN	hydroxycarboxylic acid receptor 1	248					response to estradiol (GO:0032355)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|breast(3)|endometrium(1)|kidney(1)|lung(1)|ovary(1)|pancreas(1)|skin(1)	10						GCACTCGAGGGCACCGTCCAG	0.537																																						uc001ucz.3																			0				NS(1)|breast(3)|endometrium(1)|kidney(1)|lung(1)|ovary(1)|pancreas(1)|skin(1)	10						c.(742-744)Ccc>Tcc		Homo sapiens hydroxycarboxylic acid receptor 1 (HCAR1), mRNA.							71.0	67.0	69.0					12																	123214145		2203	4300	6503	SO:0001583	missense	27198				response to estradiol stimulus	integral to membrane|plasma membrane	G-protein coupled receptor activity	g.chr12:123214145G>A	AF411110	CCDS9236.1	12q24.31	2012-08-08	2011-05-30	2011-05-30	ENSG00000196917	ENSG00000196917		"""GPCR / Class A : Hydroxy-carboxylic acid receptors"""	4532	protein-coding gene	gene with protein product	"""lactate receptor 1"""	606923	"""G protein-coupled receptor 104"", ""G protein-coupled receptor 81"""	GPR104, GPR81		11574155, 19047060, 18952058, 21454438	Standard	NM_032554		Approved	HCA1, FKSG80, TA-GPCR, LACR1	uc001ucz.3	Q9BXC0		ENST00000436083.2:c.742C>T	12.37:g.123214145G>A	ENSP00000409980:p.Pro248Ser		Somatic				HCAR1_uc001ucw.1_Non-coding_Transcript	p.P248S	NM_032554	NP_115943	WXS	Illumina GAIIx	Phase_I	Q9BXC0	HCAR1_HUMAN			0	985	-			248					B2R9X4|Q3Y5J3|Q4VBN1|Q6NXU5	Missense_Mutation	SNP	ENST00000436083.2	37	c.742C>T	CCDS9236.1	.	.	.	.	.	.	.	.	.	.	G	0.822	-0.748250	0.03065	.	.	ENSG00000196917	ENST00000356987;ENST00000432564;ENST00000436083	T;T;T	0.70749	-0.51;-0.51;-0.51	5.51	2.72	0.32119	GPCR, rhodopsin-like superfamily (1);	0.212673	0.33670	N	0.004667	T	0.52613	0.1745	L	0.42245	1.32	0.22342	N	0.999188	B	0.14012	0.009	B	0.14023	0.01	T	0.31503	-0.9941	10	0.08179	T	0.78	-9.2199	4.2561	0.10717	0.2541:0.0:0.5865:0.1594	.	248	Q9BXC0	HCAR1_HUMAN	S	248	ENSP00000349478:P248S;ENSP00000389255:P248S;ENSP00000409980:P248S	ENSP00000349478:P248S	P	-	1	0	HCAR1	121780098	0.346000	0.24844	0.942000	0.38095	0.150000	0.21749	0.011000	0.13264	0.301000	0.22738	-0.136000	0.14681	CCC		0.537	HCAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401415.1			4	76	0	0	0	1	0	4	76				
LAMA2	3908	broad.mit.edu	37	6	129649469	129649469	+	Missense_Mutation	SNP	G	G	A			TCGA-DJ-A3UK-01A-11D-A22D-08	TCGA-DJ-A3UK-10A-01D-A22D-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b796fc76-16ca-4659-a0a1-8b6f58ae6493	e5f80f02-e798-4861-bd03-6933647e5d7d	g.chr6:129649469G>A	ENST00000421865.2	+	29	4272	c.4223G>A	c.(4222-4224)cGc>cAc	p.R1408H		NM_000426.3|NM_001079823.1	NP_000417|NP_001073291.1	P24043	LAMA2_HUMAN	laminin, alpha 2	1408	Laminin EGF-like 14; second part. {ECO:0000255|PROSITE-ProRule:PRU00460}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|myelination in peripheral nervous system (GO:0022011)|positive regulation of synaptic transmission, cholinergic (GO:0032224)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|sarcolemma (GO:0042383)	structural molecule activity (GO:0005198)	p.R1408H(1)		NS(2)|biliary_tract(2)|breast(10)|central_nervous_system(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(35)|lung(84)|ovary(10)|prostate(4)|skin(9)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(2)	194				OV - Ovarian serous cystadenocarcinoma(136;0.178)|all cancers(137;0.245)		CCAGGTGGCCGCACCCCTGGA	0.502																																						uc021zfb.1																			1	Substitution - Missense(1)	p.R1408H(2)	endometrium(1)	NS(2)|biliary_tract(2)|breast(10)|central_nervous_system(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(35)|lung(84)|ovary(10)|prostate(4)|skin(9)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(2)	194						c.(4222-4224)cGc>cAc		Homo sapiens laminin, alpha 2 (LAMA2), transcript variant 1, mRNA.							128.0	112.0	117.0					6																	129649469		2203	4300	6503	SO:0001583	missense	3908				cell adhesion|muscle organ development|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	laminin-1 complex	receptor binding|structural molecule activity	g.chr6:129649469G>A	Z26653	CCDS5138.1	6q22-q23	2014-09-17	2008-08-01		ENSG00000196569	ENSG00000196569		"""Laminins"""	6482	protein-coding gene	gene with protein product	"""merosin"", ""congenital muscular dystrophy"""	156225		LAMM		2185464, 8294519	Standard	NM_000426		Approved		uc003qbn.3	P24043	OTTHUMG00000015545	ENST00000421865.2:c.4223G>A	6.37:g.129649469G>A	ENSP00000400365:p.Arg1408His		Somatic				LAMA2_uc003qbn.3_Missense_Mutation_p.R1408H|LAMA2_uc003qbo.3_Missense_Mutation_p.R1408H	p.R1408H	NM_000426	NP_000417	WXS	Illumina GAIIx	Phase_I	P24043	LAMA2_HUMAN		OV - Ovarian serous cystadenocarcinoma(136;0.178)|all cancers(137;0.245)	28	4328	+			1408			Laminin EGF-like 14; second part.		Q14736|Q5VUM2|Q93022	Missense_Mutation	SNP	ENST00000421865.2	37	c.4223G>A	CCDS5138.1	.	.	.	.	.	.	.	.	.	.	G	11.21	1.572298	0.28092	.	.	ENSG00000196569	ENST00000358023;ENST00000354729;ENST00000421865	T	0.34275	1.37	5.15	-1.18	0.09617	.	0.687206	0.14601	N	0.309637	T	0.07773	0.0195	N	0.19112	0.55	0.09310	N	1	B;B	0.19073	0.026;0.033	B;B	0.19391	0.007;0.025	T	0.32561	-0.9902	10	0.54805	T	0.06	.	5.9866	0.19438	0.2666:0.2318:0.5016:0.0	.	1408;1408	A6NF00;P24043	.;LAMA2_HUMAN	H	1408	ENSP00000400365:R1408H	ENSP00000346769:R1408H	R	+	2	0	LAMA2	129691162	0.000000	0.05858	0.054000	0.19295	0.465000	0.32709	-0.324000	0.07986	-0.063000	0.13065	0.467000	0.42956	CGC		0.502	LAMA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042180.1			5	131	0	0	0	1	0	5	131				
B3GNT6	192134	broad.mit.edu	37	11	76751195	76751195	+	Silent	SNP	G	G	A			TCGA-DJ-A3UK-01A-11D-A22D-08	TCGA-DJ-A3UK-10A-01D-A22D-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b796fc76-16ca-4659-a0a1-8b6f58ae6493	e5f80f02-e798-4861-bd03-6933647e5d7d	g.chr11:76751195G>A	ENST00000533140.1	+	2	738	c.600G>A	c.(598-600)aaG>aaA	p.K200K	B3GNT6_ENST00000421061.1_Silent_p.K111K|B3GNT6_ENST00000354301.5_Silent_p.K200K			O43505	B3GN1_HUMAN	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 6 (core 3 synthase)	0					axon guidance (GO:0007411)|carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|poly-N-acetyllactosamine biosynthetic process (GO:0030311)|protein glycosylation (GO:0006486)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)	N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase activity (GO:0008532)			central_nervous_system(1)|kidney(2)|lung(4)|prostate(1)	8						TCACGCTCAAGCACCTGCACT	0.697																																						uc021qnp.1																			0				central_nervous_system(1)|kidney(2)|lung(4)|prostate(1)	8						c.(598-600)aaG>aaA		Homo sapiens UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 6 (core 3 synthase) (B3GNT6), mRNA.							44.0	48.0	46.0					11																	76751195		2195	4284	6479	SO:0001819	synonymous_variant	192134				O-glycan processing, core 3	Golgi membrane|integral to membrane	beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,3-N-acetylglucosaminyltransferase activity|galactosyltransferase activity	g.chr11:76751195G>A	AB073740	CCDS53681.1	11q13.4	2013-02-19			ENSG00000198488	ENSG00000198488		"""Beta 3-glycosyltransferases"""	24141	protein-coding gene	gene with protein product		615315				11821425	Standard	NM_138706		Approved	B3Gn-T6	uc021qnp.1	Q6ZMB0		ENST00000533140.1:c.600G>A	11.37:g.76751195G>A			Somatic				B3GNT6_uc021qnq.1_Silent_p.K200K	p.K200K	NM_138706	NP_619651	WXS	Illumina GAIIx	Phase_I	Q6ZMB0	B3GN6_HUMAN			1	688	+			200					Q4TTN0	Silent	SNP	ENST00000533140.1	37	c.600G>A	CCDS53681.1																																																																																				0.697	B3GNT6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000382740.2	NM_138706		78	88	0	0	0	1	0	78	88				
