#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
CDHR1	92211	broad.mit.edu	37	10	85972907	85972907	+	Missense_Mutation	SNP	G	G	C	rs144856473		TCGA-EL-A3T8-01A-21D-A22D-08	TCGA-EL-A3T8-11A-11D-A22D-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	47a0cb63-dd19-49fe-983d-a2e786795355	e475f95d-8efb-4df4-9682-9608c5081ea7	g.chr10:85972907G>C	ENST00000372117.3	+	16	1946	c.1843G>C	c.(1843-1845)Gag>Cag	p.E615Q	CDHR1_ENST00000332904.3_Missense_Mutation_p.E615Q|CDHR1_ENST00000440770.2_Missense_Mutation_p.E319Q	NM_033100.2	NP_149091.1	Q96JP9	CDHR1_HUMAN	cadherin-related family member 1	615	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cellular process (GO:0009987)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)	integral component of plasma membrane (GO:0005887)|photoreceptor outer segment membrane (GO:0042622)	calcium ion binding (GO:0005509)	p.E615K(1)		breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(21)|ovary(1)|prostate(1)|skin(1)	36						CACCCATGCAGAGCCCGCCAA	0.572																																						uc001kcv.3																			1	Substitution - Missense(1)	p.E615K(2)	lung(1)	breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(21)|ovary(1)|prostate(1)|skin(1)	36						c.(1843-1845)Gag>Cag		Homo sapiens cadherin-related family member 1 (CDHR1), transcript variant 1, mRNA.							121.0	107.0	112.0					10																	85972907		2203	4300	6503	SO:0001583	missense	92211				homophilic cell adhesion		calcium ion binding|receptor activity	g.chr10:85972907G>C	AB053448	CCDS7372.1, CCDS53548.1	10q23.1	2014-01-28	2010-01-25	2010-01-25	ENSG00000148600	ENSG00000148600		"""Cadherins / Cadherin-related"""	14550	protein-coding gene	gene with protein product		609502	"""protocadherin 21"""	PCDH21		11597768	Standard	NM_001171971		Approved	KIAA1775, CORD15, RP65	uc001kcv.3	Q96JP9	OTTHUMG00000018634	ENST00000372117.3:c.1843G>C	10.37:g.85972907G>C	ENSP00000361189:p.Glu615Gln		Somatic				CDHR1_uc001kcw.3_Missense_Mutation_p.E615Q|CDHR1_uc009xst.3_Missense_Mutation_p.E319Q|CDHR1_uc001kcx.3_5'UTR	p.E615Q	NM_033100	NP_149091	WXS	Illumina GAIIx	Phase_I	Q96JP9	CDHR1_HUMAN			15	1948	+			615			Cadherin 6.		Q69YZ8|Q8IXY5	Missense_Mutation	SNP	ENST00000372117.3	37	c.1843G>C	CCDS7372.1	.	.	.	.	.	.	.	.	.	.	G	21.7	4.184239	0.78677	.	.	ENSG00000148600	ENST00000332904;ENST00000372117;ENST00000440770	T;T;T	0.54071	0.59;0.59;0.59	5.93	5.93	0.95920	Cadherin (4);Cadherin-like (1);	0.199139	0.52532	D	0.000071	T	0.56877	0.2015	N	0.17764	0.52	0.52501	D	0.999955	D;P;D	0.62365	0.991;0.82;0.99	P;P;D	0.63033	0.898;0.628;0.91	T	0.52449	-0.8574	10	0.30078	T	0.28	-28.6022	17.8347	0.88692	0.0:0.0:1.0:0.0	.	319;615;615	E7EN47;Q96JP9-2;Q96JP9	.;.;CDHR1_HUMAN	Q	615;615;319	ENSP00000331063:E615Q;ENSP00000361189:E615Q;ENSP00000415980:E319Q	ENSP00000331063:E615Q	E	+	1	0	CDHR1	85962887	1.000000	0.71417	0.980000	0.43619	0.588000	0.36517	9.326000	0.96389	2.814000	0.96858	0.655000	0.94253	GAG		0.572	CDHR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049111.1	NM_033100		7	128	0	0	0	1	0	7	128				
OR10G2	26534	broad.mit.edu	37	14	22102364	22102364	+	Missense_Mutation	SNP	G	G	A	rs375960315		TCGA-EL-A3T8-01A-21D-A22D-08	TCGA-EL-A3T8-11A-11D-A22D-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	47a0cb63-dd19-49fe-983d-a2e786795355	e475f95d-8efb-4df4-9682-9608c5081ea7	g.chr14:22102364G>A	ENST00000542433.1	-	1	732	c.635C>T	c.(634-636)gCc>gTc	p.A212V		NM_001005466.1	NP_001005466.1	Q8NGC3	O10G2_HUMAN	olfactory receptor, family 10, subfamily G, member 2	212						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(12)|prostate(1)|skin(2)|stomach(2)	22	all_cancers(95;0.00113)	Acute lymphoblastic leukemia(2;0.0279)		GBM - Glioblastoma multiforme(265;0.0142)		GCAACTGGCGGCCACTACCCT	0.532																																						uc010tmc.2																			0				cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(12)|prostate(1)|skin(2)|stomach(2)	22						c.(634-636)gCc>gTc		Homo sapiens olfactory receptor, family 10, subfamily G, member 2 (OR10G2), mRNA.							61.0	67.0	65.0					14																	22102364		2198	4294	6492	SO:0001583	missense	26534				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity	g.chr14:22102364G>A		CCDS32047.1	14q11.2	2013-09-24			ENSG00000255582	ENSG00000255582		"""GPCR / Class A : Olfactory receptors"""	8170	protein-coding gene	gene with protein product						8188290	Standard	NM_001005466		Approved		uc010tmc.2	Q8NGC3	OTTHUMG00000168890	ENST00000542433.1:c.635C>T	14.37:g.22102364G>A	ENSP00000445383:p.Ala212Val		Somatic					p.A212V	NM_001005466	NP_001005466	WXS	Illumina GAIIx	Phase_I	Q8NGC3	O10G2_HUMAN		GBM - Glioblastoma multiforme(265;0.0142)	0	635	-	all_cancers(95;0.00113)	Acute lymphoblastic leukemia(2;0.0279)	212					B2RPD0	Missense_Mutation	SNP	ENST00000542433.1	37	c.635C>T	CCDS32047.1	.	.	.	.	.	.	.	.	.	.	G	5.308	0.242235	0.10077	.	.	ENSG00000255582	ENST00000542433	T	0.35605	1.3	3.92	2.98	0.34508	GPCR, rhodopsin-like superfamily (1);	0.294724	0.24039	N	0.042115	T	0.20901	0.0503	N	0.11427	0.14	0.26746	N	0.970308	B	0.16396	0.017	B	0.21708	0.036	T	0.20405	-1.0276	10	0.56958	D	0.05	-5.3532	10.7849	0.46398	0.0:0.1949:0.8051:0.0	.	212	Q8NGC3	O10G2_HUMAN	V	212	ENSP00000445383:A212V	ENSP00000445383:A212V	A	-	2	0	OR10G2	21172204	0.000000	0.05858	0.964000	0.40570	0.147000	0.21601	0.163000	0.16520	0.795000	0.33922	0.557000	0.71058	GCC		0.532	OR10G2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401525.1			3	112	0	0	0	1	0	3	112				
FAM117B	150864	broad.mit.edu	37	2	203590986	203590986	+	Missense_Mutation	SNP	G	G	T			TCGA-EL-A3T8-01A-21D-A22D-08	TCGA-EL-A3T8-11A-11D-A22D-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	47a0cb63-dd19-49fe-983d-a2e786795355	e475f95d-8efb-4df4-9682-9608c5081ea7	g.chr2:203590986G>T	ENST00000392238.2	+	4	860	c.860G>T	c.(859-861)cGc>cTc	p.R287L	FAM117B_ENST00000303116.6_Missense_Mutation_p.R43L			Q6P1L5	F117B_HUMAN	family with sequence similarity 117, member B	287										breast(3)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(4)|lung(5)|ovary(1)	17						GCAAAATTACGCCAGCAGTTG	0.393																																						uc010zhx.2																			0		p.K286*(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(4)|lung(5)|ovary(1)	17						c.(859-861)cGc>cTc		Homo sapiens family with sequence similarity 117, member B (FAM117B), mRNA.							126.0	121.0	123.0					2																	203590986		2203	4300	6503	SO:0001583	missense	150864							g.chr2:203590986G>T	AB053315	CCDS33362.1, CCDS33362.2	2q33	2008-08-18	2008-08-18	2008-08-18	ENSG00000138439	ENSG00000138439			14440	protein-coding gene	gene with protein product			"""amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 13"""	ALS2CR13		11586298	Standard	NM_173511		Approved	FLJ38771	uc010zhx.2	Q6P1L5	OTTHUMG00000154550	ENST00000392238.2:c.860G>T	2.37:g.203590986G>T	ENSP00000376071:p.Arg287Leu		Somatic					p.R287L	NM_173511	NP_775782	WXS	Illumina GAIIx	Phase_I	Q6P1L5	F117B_HUMAN			3	870	+			287					Q53QZ5|Q585T9|Q8N8W1|Q96Q34	Missense_Mutation	SNP	ENST00000392238.2	37	c.860G>T	CCDS33362.2	.	.	.	.	.	.	.	.	.	.	G	29.8	5.038610	0.93630	.	.	ENSG00000138439	ENST00000303116;ENST00000392238	.	.	.	5.71	5.71	0.89125	.	0.048721	0.85682	D	0.000000	T	0.78604	0.4309	M	0.62723	1.935	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.79271	-0.1872	9	0.72032	D	0.01	-11.0079	19.4656	0.94935	0.0:0.0:1.0:0.0	.	287	Q6P1L5	F117B_HUMAN	L	43;287	.	ENSP00000306299:R43L	R	+	2	0	FAM117B	203299231	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.451000	0.90343	2.691000	0.91804	0.563000	0.77884	CGC		0.393	FAM117B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000335888.3	NM_173511		4	95	0	0	0	1	0	4	95				
QSER1	79832	broad.mit.edu	37	11	32956671	32956671	+	Silent	SNP	G	G	A			TCGA-EL-A3T8-01A-21D-A22D-08	TCGA-EL-A3T8-11A-11D-A22D-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	47a0cb63-dd19-49fe-983d-a2e786795355	e475f95d-8efb-4df4-9682-9608c5081ea7	g.chr11:32956671G>A	ENST00000399302.2	+	4	3815	c.3480G>A	c.(3478-3480)ggG>ggA	p.G1160G	QSER1_ENST00000527788.1_Silent_p.G921G	NM_001076786.1	NP_001070254.1	Q2KHR3	QSER1_HUMAN	glutamine and serine rich 1	1160										breast(5)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(16)|ovary(4)|prostate(1)|skin(5)|stomach(1)|urinary_tract(1)	48	Breast(20;0.158)					TGAAATCCGGGCCCAAGCAGC	0.448																																						uc001mty.3																			0				breast(5)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(16)|ovary(4)|prostate(1)|skin(5)|stomach(1)|urinary_tract(1)	48						c.(3478-3480)ggG>ggA		Homo sapiens glutamine and serine rich 1 (QSER1), mRNA.							80.0	80.0	80.0					11																	32956671		1869	4095	5964	SO:0001819	synonymous_variant	79832							g.chr11:32956671G>A	AL834141	CCDS41631.1	11p13	2014-02-12			ENSG00000060749	ENSG00000060749			26154	protein-coding gene	gene with protein product							Standard	XM_006718323		Approved	FLJ21924	uc001mty.3	Q2KHR3		ENST00000399302.2:c.3480G>A	11.37:g.32956671G>A			Somatic				QSER1_uc001mtz.1_Silent_p.G921G|QSER1_uc001mua.3_Silent_p.G665G	p.G1160G	NM_001076786	NP_001070254	WXS	Illumina GAIIx	Phase_I	Q2KHR3	QSER1_HUMAN			3	3747	+	Breast(20;0.158)		1160					Q6ZU30|Q6ZUR5	Silent	SNP	ENST00000399302.2	37	c.3480G>A	CCDS41631.1	.	.	.	.	.	.	.	.	.	.	G	5.667	0.307716	0.10733	.	.	ENSG00000060749	ENST00000524678	T	0.67865	-0.29	5.46	-1.42	0.08913	.	0.000000	0.64402	D	0.000001	T	0.61299	0.2336	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.57648	-0.7775	7	0.72032	D	0.01	.	1.2095	0.01902	0.3085:0.1078:0.364:0.2197	.	.	.	.	D	181	ENSP00000432136:G181D	ENSP00000432136:G181D	G	+	2	0	QSER1	32913247	0.292000	0.24362	0.998000	0.56505	0.987000	0.75469	-0.337000	0.07852	0.013000	0.14918	0.467000	0.42956	GGC		0.448	QSER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388448.1	NM_024774		3	64	0	0	0	1	0	3	64				
FECH	2235	broad.mit.edu	37	18	55247321	55247321	+	Missense_Mutation	SNP	C	C	T			TCGA-EL-A3T8-01A-21D-A22D-08	TCGA-EL-A3T8-11A-11D-A22D-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	47a0cb63-dd19-49fe-983d-a2e786795355	e475f95d-8efb-4df4-9682-9608c5081ea7	g.chr18:55247321C>T	ENST00000262093.5	-	2	329	c.178G>A	c.(178-180)Gtt>Att	p.V60I	FECH_ENST00000585699.1_Intron|FECH_ENST00000382873.3_Missense_Mutation_p.V60I	NM_000140.3|NM_001012515.2	NP_000131.2|NP_001012533.1	P22830	HEMH_HUMAN	ferrochelatase	60					cellular response to dexamethasone stimulus (GO:0071549)|cholesterol metabolic process (GO:0008203)|detection of UV (GO:0009589)|erythrocyte differentiation (GO:0030218)|generation of precursor metabolites and energy (GO:0006091)|heme biosynthetic process (GO:0006783)|iron ion homeostasis (GO:0055072)|porphyrin-containing compound metabolic process (GO:0006778)|protoporphyrinogen IX metabolic process (GO:0046501)|regulation of eIF2 alpha phosphorylation by heme (GO:0010999)|regulation of gene expression (GO:0010468)|regulation of hemoglobin biosynthetic process (GO:0046984)|response to arsenic-containing substance (GO:0046685)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to insecticide (GO:0017085)|response to lead ion (GO:0010288)|response to light stimulus (GO:0009416)|response to methylmercury (GO:0051597)|response to platinum ion (GO:0070541)|small molecule metabolic process (GO:0044281)|very-low-density lipoprotein particle assembly (GO:0034379)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)	2 iron, 2 sulfur cluster binding (GO:0051537)|ferrochelatase activity (GO:0004325)|ferrous iron binding (GO:0008198)|heme binding (GO:0020037)|iron-responsive element binding (GO:0030350)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(5)|prostate(1)|upper_aerodigestive_tract(1)	15		Colorectal(73;0.227)				TGCGGTTGAACTTGAGGTTTT	0.522																																						uc002lgp.4																			0				central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(5)|prostate(1)|upper_aerodigestive_tract(1)	15						c.(178-180)Gtt>Att		Homo sapiens ferrochelatase (FECH), nuclear gene encoding mitochondrial protein, transcript variant 1, mRNA.							164.0	148.0	153.0					18																	55247321		2203	4300	6503	SO:0001583	missense	2235				generation of precursor metabolites and energy|heme biosynthetic process|protoporphyrinogen IX metabolic process|response to light stimulus	mitochondrial inner membrane|mitochondrial matrix	2 iron, 2 sulfur cluster binding|ferrochelatase activity|ferrous iron binding|protein binding	g.chr18:55247321C>T	D00726	CCDS11964.1, CCDS32836.1	18q21.2-q21.3	2010-05-11	2010-05-11		ENSG00000066926	ENSG00000066926	4.99.1.1		3647	protein-coding gene	gene with protein product	"""protoporphyria"""	612386	"""ferrochelatase (protoporphyria)"""			1838349	Standard	NM_001012515		Approved		uc002lgp.4	P22830	OTTHUMG00000132740	ENST00000262093.5:c.178G>A	18.37:g.55247321C>T	ENSP00000262093:p.Val60Ile		Somatic				FECH_uc002lgq.4_Missense_Mutation_p.V60I|FECH_uc002lgr.4_5'UTR	p.V60I	NM_001012515	NP_001012533	WXS	Illumina GAIIx	Phase_I	P22830	HEMH_HUMAN			1	295	-		Colorectal(73;0.227)	60					A8KA72|Q8IXN1|Q8NAN0	Missense_Mutation	SNP	ENST00000262093.5	37	c.178G>A	CCDS11964.1	.	.	.	.	.	.	.	.	.	.	C	10.60	1.395538	0.25205	.	.	ENSG00000066926	ENST00000262093;ENST00000382873	D;D	0.97665	-4.47;-4.48	5.6	5.6	0.85130	.	0.417679	0.26424	N	0.024454	D	0.93022	0.7779	L	0.27053	0.805	0.21915	N	0.999474	B;B	0.10296	0.0;0.003	B;B	0.11329	0.001;0.006	D	0.83722	0.0193	10	0.36615	T	0.2	-3.1101	10.9244	0.47184	0.0:0.9146:0.0:0.0854	.	60;60	P22830;P22830-2	HEMH_HUMAN;.	I	60	ENSP00000262093:V60I;ENSP00000372326:V60I	ENSP00000262093:V60I	V	-	1	0	FECH	53398319	0.963000	0.33076	0.702000	0.30337	0.115000	0.19883	2.526000	0.45607	2.788000	0.95919	0.650000	0.86243	GTT		0.522	FECH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256098.1			9	142	0	0	0	1	0	9	142				
RBM28	55131	broad.mit.edu	37	7	127963614	127963614	+	Missense_Mutation	SNP	C	C	T	rs553213737	byFrequency	TCGA-EL-A3T8-01A-21D-A22D-08	TCGA-EL-A3T8-11A-11D-A22D-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	47a0cb63-dd19-49fe-983d-a2e786795355	e475f95d-8efb-4df4-9682-9608c5081ea7	g.chr7:127963614C>T	ENST00000223073.2	-	13	1484	c.1370G>A	c.(1369-1371)gGt>gAt	p.G457D	RBM28_ENST00000415472.2_Missense_Mutation_p.G316D|RBM28_ENST00000481788.1_5'Flank	NM_018077.2	NP_060547.2	Q9NW13	RBM28_HUMAN	RNA binding motif protein 28	457					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleolus (GO:0005730)|spliceosomal complex (GO:0005681)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|kidney(7)|large_intestine(3)|lung(8)|ovary(2)	21						AGCACTCACACCCTCTGCAGC	0.458													C|||	3	0.000599042	0.0	0.0	5008	,	,		23021	0.0		0.0	False		,,,				2504	0.0031					uc003vmp.2																			0				breast(1)|kidney(7)|large_intestine(3)|lung(8)|ovary(2)	21						c.(1369-1371)gGt>gAt		Homo sapiens RNA binding motif protein 28 (RBM28), transcript variant 1, mRNA.							219.0	197.0	204.0					7																	127963614		2203	4300	6503	SO:0001583	missense	55131				RNA splicing|mRNA processing	Golgi apparatus|nucleolus|spliceosomal complex	RNA binding|nucleotide binding	g.chr7:127963614C>T	AK001239	CCDS5801.1, CCDS55159.1	7q32.2	2013-02-12			ENSG00000106344	ENSG00000106344		"""RNA binding motif (RRM) containing"""	21863	protein-coding gene	gene with protein product		612074					Standard	NM_018077		Approved	FLJ10377	uc003vmp.2	Q9NW13	OTTHUMG00000157711	ENST00000223073.2:c.1370G>A	7.37:g.127963614C>T	ENSP00000223073:p.Gly457Asp		Somatic				RBM28_uc011koj.1_Missense_Mutation_p.G316D	p.G457D	NM_018077	NP_060547	WXS	Illumina GAIIx	Phase_I	Q9NW13	RBM28_HUMAN			12	1485	-			457					A4D100|B4DU52|E9PDD9|Q53H65|Q96CV3	Missense_Mutation	SNP	ENST00000223073.2	37	c.1370G>A	CCDS5801.1	.	.	.	.	.	.	.	.	.	.	C	26.8	4.776431	0.90195	.	.	ENSG00000106344	ENST00000223073;ENST00000415472	T;T	0.22134	2.9;1.97	5.93	5.93	0.95920	.	0.138154	0.64402	D	0.000003	T	0.45377	0.1339	M	0.63208	1.945	0.80722	D	1	B;D;B	0.89917	0.243;1.0;0.243	B;D;B	0.91635	0.341;0.999;0.168	T	0.06391	-1.0829	10	0.37606	T	0.19	-14.6238	17.8347	0.88692	0.0:1.0:0.0:0.0	.	316;457;316	E9PDD9;Q9NW13;B4DU52	.;RBM28_HUMAN;.	D	457;316	ENSP00000223073:G457D;ENSP00000390517:G316D	ENSP00000223073:G457D	G	-	2	0	RBM28	127750850	1.000000	0.71417	1.000000	0.80357	0.840000	0.47671	6.476000	0.73587	2.814000	0.96858	0.655000	0.94253	GGT		0.458	RBM28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349442.2	NM_018077		6	140	0	0	0	1	0	6	140				
BRAF	673	broad.mit.edu	37	7	140453136	140453136	+	Missense_Mutation	SNP	A	A	T	rs121913377|rs113488022|rs121913227|rs397516897		TCGA-EL-A3T8-01A-21D-A22D-08	TCGA-EL-A3T8-11A-11D-A22D-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	47a0cb63-dd19-49fe-983d-a2e786795355	e475f95d-8efb-4df4-9682-9608c5081ea7	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		31	48	0	0	0	1	0	31	48				
AGPS	8540	broad.mit.edu	37	2	178307134	178307134	+	Splice_Site	SNP	G	G	A			TCGA-EL-A3T8-01A-21D-A22D-08	TCGA-EL-A3T8-11A-11D-A22D-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	47a0cb63-dd19-49fe-983d-a2e786795355	e475f95d-8efb-4df4-9682-9608c5081ea7	g.chr2:178307134G>A	ENST00000264167.4	+	7	855		c.e7-1		AGPS_ENST00000409888.1_Intron	NM_003659.3	NP_003650.1	O00116	ADAS_HUMAN	alkylglycerone phosphate synthase						cellular lipid metabolic process (GO:0044255)|ether lipid biosynthetic process (GO:0008611)|lipid biosynthetic process (GO:0008610)|small molecule metabolic process (GO:0044281)	intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|peroxisomal matrix (GO:0005782)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	alkylglycerone-phosphate synthase activity (GO:0008609)|FAD binding (GO:0071949)|UDP-N-acetylmuramate dehydrogenase activity (GO:0008762)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(8)|lung(12)|ovary(2)|skin(1)	32			OV - Ovarian serous cystadenocarcinoma(117;0.0018)|Epithelial(96;0.00919)|all cancers(119;0.0358)			TATTTTGGCAGGAGGAACAAG	0.333																																						uc002ull.2																			0				breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(8)|lung(12)|ovary(2)|skin(1)	32						c.e7-1		Homo sapiens alkylglycerone phosphate synthase (AGPS), mRNA.							94.0	98.0	96.0					2																	178307134		2203	4300	6503	SO:0001630	splice_region_variant	8540				ether lipid biosynthetic process	peroxisomal matrix|peroxisomal membrane|plasma membrane	alkylglycerone-phosphate synthase activity|flavin adenine dinucleotide binding|oxidoreductase activity	g.chr2:178307134G>A	Y09443	CCDS2275.1	2q	2008-02-05			ENSG00000018510	ENSG00000018510	2.5.1.26		327	protein-coding gene	gene with protein product		603051				9187299, 9553082	Standard	NM_003659		Approved	ADHAPS, ADAS, ALDHPSY, ADPS, ADAP-S	uc002ull.2	O00116	OTTHUMG00000132530	ENST00000264167.4:c.710-1G>A	2.37:g.178307134G>A			Somatic				AGPS_uc010zfb.1_Splice_Site_p.G147_splice	p.G237_splice	NM_003659	NP_003650	WXS	Illumina GAIIx	Phase_I	O00116	ADAS_HUMAN	OV - Ovarian serous cystadenocarcinoma(117;0.0018)|Epithelial(96;0.00919)|all cancers(119;0.0358)		7	757	+			237			FAD-binding PCMH-type.		A5D8U9|Q2TU35	Splice_Site	SNP	ENST00000264167.4	37	c.710_splice	CCDS2275.1	.	.	.	.	.	.	.	.	.	.	G	23.2	4.390334	0.82902	.	.	ENSG00000018510	ENST00000264167;ENST00000536686	.	.	.	5.88	5.88	0.94601	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.8327	0.96642	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	AGPS	178015380	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	8.056000	0.89455	2.779000	0.95612	0.643000	0.83706	.		0.333	AGPS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255730.2		Intron	3	87	0	0	0	1	0	3	87				
MARS	4141	broad.mit.edu	37	12	57892382	57892382	+	Missense_Mutation	SNP	G	G	A			TCGA-EL-A3T8-01A-21D-A22D-08	TCGA-EL-A3T8-11A-11D-A22D-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	47a0cb63-dd19-49fe-983d-a2e786795355	e475f95d-8efb-4df4-9682-9608c5081ea7	g.chr12:57892382G>A	ENST00000262027.5	+	9	1201	c.1067G>A	c.(1066-1068)cGc>cAc	p.R356H	MARS_ENST00000315473.5_Missense_Mutation_p.R122H|MARS_ENST00000447721.2_3'UTR	NM_004990.3	NP_004981.2	P56192	SYMC_HUMAN	methionyl-tRNA synthetase	356					gene expression (GO:0010467)|methionyl-tRNA aminoacylation (GO:0006431)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|methionine-tRNA ligase activity (GO:0004825)|tRNA binding (GO:0000049)			breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(8)|ovary(3)|pancreas(1)|prostate(2)|skin(1)	33			GBM - Glioblastoma multiforme(3;4.27e-41)		L-Methionine(DB00134)	ATTTTTGGTCGCACCACCACT	0.498																																						uc001sog.3																			0				breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(8)|ovary(3)|pancreas(1)|prostate(2)|skin(1)	33						c.(1066-1068)cGc>cAc		Homo sapiens methionyl-tRNA synthetase (MARS), mRNA.	L-Methionine(DB00134)						174.0	151.0	159.0					12																	57892382		2203	4300	6503	SO:0001583	missense	4141				methionyl-tRNA aminoacylation	cytosol	ATP binding|methionine-tRNA ligase activity|protein binding|tRNA binding	g.chr12:57892382G>A	X94754	CCDS8942.1	12q13.3	2014-05-06	2007-02-26		ENSG00000166986	ENSG00000166986	6.1.1.10	"""Aminoacyl tRNA synthetases / Class I"""	6898	protein-coding gene	gene with protein product	"""methionine tRNA ligase 1, cytoplasmic"""	156560				10448063, 24482476	Standard	NM_004990		Approved	MetRS, SPG70	uc001sog.3	P56192	OTTHUMG00000169996	ENST00000262027.5:c.1067G>A	12.37:g.57892382G>A	ENSP00000262027:p.Arg356His		Somatic				MARS_uc001sof.1_Non-coding_Transcript|MARS_uc010srp.1_Missense_Mutation_p.R229H|MARS_uc010srq.1_Missense_Mutation_p.R122H	p.R356H	NM_004990	NP_004981	WXS	Illumina GAIIx	Phase_I	P56192	SYMC_HUMAN	GBM - Glioblastoma multiforme(3;4.27e-41)		8	1221	+			356					B3KVK7|Q14895|Q53H14|Q96A15|Q96BZ0|Q9NSE0	Missense_Mutation	SNP	ENST00000262027.5	37	c.1067G>A	CCDS8942.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	20.2|20.2	3.951278|3.951278	0.73787|0.73787	.|.	.|.	ENSG00000166986|ENSG00000166986	ENST00000552371|ENST00000262027;ENST00000315473	.|T;T	.|0.55588	.|0.99;0.51	4.86|4.86	4.86|4.86	0.63082|0.63082	.|Aminoacyl-tRNA synthetase, class I (M) (1);Rossmann-like alpha/beta/alpha sandwich fold (1);	.|0.050938	.|0.85682	.|D	.|0.000000	T|T	0.78078|0.78078	0.4227|0.4227	M|M	0.90922|0.90922	3.16|3.16	0.80722|0.80722	D|D	1|1	.|D;D;D	.|0.89917	.|1.0;0.998;0.995	.|D;D;D	.|0.70487	.|0.969;0.931;0.968	D|D	0.83958|0.83958	0.0320|0.0320	5|10	.|0.87932	.|D	.|0	-10.8416|-10.8416	17.1304|17.1304	0.86725|0.86725	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|122;229;356	.|A6NC17;B4E0E9;P56192	.|.;.;SYMC_HUMAN	T|H	189|356;122	.|ENSP00000262027:R356H;ENSP00000314653:R122H	.|ENSP00000262027:R356H	A|R	+|+	1|2	0|0	MARS|MARS	56178649|56178649	1.000000|1.000000	0.71417|0.71417	0.987000|0.987000	0.45799|0.45799	0.165000|0.165000	0.22458|0.22458	9.318000|9.318000	0.96334|0.96334	2.433000|2.433000	0.82419|0.82419	0.561000|0.561000	0.74099|0.74099	GCA|CGC		0.498	MARS-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407014.1	NM_004990		3	100	0	0	0	1	0	3	100				
ATP6V1C1	528	broad.mit.edu	37	8	104066176	104066176	+	Missense_Mutation	SNP	G	G	A			TCGA-EL-A3T8-01A-21D-A22D-08	TCGA-EL-A3T8-11A-11D-A22D-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	47a0cb63-dd19-49fe-983d-a2e786795355	e475f95d-8efb-4df4-9682-9608c5081ea7	g.chr8:104066176G>A	ENST00000395862.3	+	7	697	c.538G>A	c.(538-540)Gag>Aag	p.E180K	ATP6V1C1_ENST00000518738.1_Missense_Mutation_p.E180K|ATP6V1C1_ENST00000521514.1_Missense_Mutation_p.E105K|ATP6V1C1_ENST00000518857.1_Missense_Mutation_p.E105K	NM_001695.4	NP_001686.1	P21283	VATC1_HUMAN	ATPase, H+ transporting, lysosomal 42kDa, V1 subunit C1	180					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)|proton transport (GO:0015992)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	apical part of cell (GO:0045177)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)|proton-transporting two-sector ATPase complex (GO:0016469)|proton-transporting V-type ATPase, V1 domain (GO:0033180)	hydrogen-exporting ATPase activity, phosphorylative mechanism (GO:0008553)|proton-transporting ATPase activity, rotational mechanism (GO:0046961)|transporter activity (GO:0005215)			breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(6)|urinary_tract(1)	13	Lung NSC(17;0.000427)|all_lung(17;0.000533)		OV - Ovarian serous cystadenocarcinoma(57;3.57e-05)|STAD - Stomach adenocarcinoma(118;0.133)			TCTTGATTCAGAGTATCTCGT	0.308																																						uc003ykz.4																			0				breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(6)|urinary_tract(1)	13						c.(538-540)Gag>Aag		Homo sapiens ATPase, H+ transporting, lysosomal 42kDa, V1 subunit C1 (ATP6V1C1), mRNA.							161.0	155.0	157.0					8																	104066176		2203	4299	6502	SO:0001583	missense	528				ATP hydrolysis coupled proton transport|cellular iron ion homeostasis|insulin receptor signaling pathway|transferrin transport	cytosol|plasma membrane|proton-transporting V-type ATPase, V1 domain	protein binding|proton-transporting ATPase activity, rotational mechanism	g.chr8:104066176G>A	X69151	CCDS6296.1	8p22.3	2011-05-24	2006-01-13	2002-05-10	ENSG00000155097	ENSG00000155097	3.6.3.14	"""ATPases / V-type"""	856	protein-coding gene	gene with protein product		603097	"""ATPase, H+ transporting, lysosomal (vacuolar proton pump) 42kD"", ""ATPase, H+ transporting, lysosomal 42kDa, V1 subunit C, isoform 1"""	ATP6D, ATP6C		8250920, 14580332	Standard	NM_001695		Approved	VATC, Vma5	uc003ykz.4	P21283	OTTHUMG00000164761	ENST00000395862.3:c.538G>A	8.37:g.104066176G>A	ENSP00000379203:p.Glu180Lys		Somatic				ATP6V1C1_uc010mbz.3_Missense_Mutation_p.E105K|ATP6V1C1_uc003yla.3_Missense_Mutation_p.E180K|ATP6V1C1_uc011lhl.2_Missense_Mutation_p.E105K	p.E180K	NM_001695	NP_001686	WXS	Illumina GAIIx	Phase_I	P21283	VATC1_HUMAN	OV - Ovarian serous cystadenocarcinoma(57;3.57e-05)|STAD - Stomach adenocarcinoma(118;0.133)		6	783	+	Lung NSC(17;0.000427)|all_lung(17;0.000533)		180						Missense_Mutation	SNP	ENST00000395862.3	37	c.538G>A	CCDS6296.1	.	.	.	.	.	.	.	.	.	.	G	36	5.755180	0.96898	.	.	ENSG00000155097	ENST00000518857;ENST00000395862;ENST00000521514;ENST00000518738	T;T;T;T	0.61510	0.1;0.1;0.1;0.1	5.46	5.46	0.80206	.	0.000000	0.85682	D	0.000000	D	0.83649	0.5300	H	0.97340	3.985	0.80722	D	1	D	0.54964	0.969	P	0.59595	0.86	D	0.89556	0.3803	10	0.87932	D	0	.	19.2989	0.94134	0.0:0.0:1.0:0.0	.	180	P21283	VATC1_HUMAN	K	105;180;105;180	ENSP00000428204:E105K;ENSP00000379203:E180K;ENSP00000430129:E105K;ENSP00000430282:E180K	ENSP00000379203:E180K	E	+	1	0	ATP6V1C1	104135352	1.000000	0.71417	0.998000	0.56505	0.998000	0.95712	8.001000	0.88508	2.563000	0.86464	0.655000	0.94253	GAG		0.308	ATP6V1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380101.1	NM_001695		7	82	0	0	0	1	0	7	82				
TDP1	55775	broad.mit.edu	37	14	90430003	90430003	+	Missense_Mutation	SNP	C	C	A			TCGA-EL-A3T8-01A-21D-A22D-08	TCGA-EL-A3T8-11A-11D-A22D-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	47a0cb63-dd19-49fe-983d-a2e786795355	e475f95d-8efb-4df4-9682-9608c5081ea7	g.chr14:90430003C>A	ENST00000335725.4	+	3	795	c.545C>A	c.(544-546)gCc>gAc	p.A182D	TDP1_ENST00000555565.1_Intron|TDP1_ENST00000555880.1_Missense_Mutation_p.A182D|TDP1_ENST00000393454.2_Missense_Mutation_p.A182D|TDP1_ENST00000393452.3_Missense_Mutation_p.A182D|TDP1_ENST00000357382.3_5'UTR	NM_018319.3	NP_060789.2	Q9NUW8	TYDP1_HUMAN	tyrosyl-DNA phosphodiesterase 1	182					cell death (GO:0008219)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|single strand break repair (GO:0000012)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	3'-tyrosyl-DNA phosphodiesterase activity (GO:0017005)|double-stranded DNA binding (GO:0003690)|exonuclease activity (GO:0004527)|single-stranded DNA binding (GO:0003697)			NS(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|ovary(3)|prostate(1)|urinary_tract(1)	25		all_cancers(154;0.185)		COAD - Colon adenocarcinoma(157;0.23)		AACTCTGGAGCCCTCCACATC	0.512								Repair of DNA-protein crosslinks																														uc001xxy.3																			0				NS(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|ovary(3)|prostate(1)|urinary_tract(1)	25						c.(544-546)gCc>gAc	Repair of DNA-protein crosslinks	Homo sapiens tyrosyl-DNA phosphodiesterase 1 (TDP1), transcript variant 1, mRNA.							46.0	47.0	46.0					14																	90430003		2203	4300	6503	SO:0001583	missense	55775				cell death|double-strand break repair|single strand break repair	cytoplasm|nucleus	3'-tyrosyl-DNA phosphodiesterase activity|double-stranded DNA binding|exonuclease activity|protein binding|single-stranded DNA binding	g.chr14:90430003C>A	AF182002	CCDS9888.1	14q32.11	2008-08-11				ENSG00000042088			18884	protein-coding gene	gene with protein product		607198				11839309, 12244316	Standard	XM_005267847		Approved	FLJ11090, SCAN1	uc001xxz.3	Q9NUW8		ENST00000335725.4:c.545C>A	14.37:g.90430003C>A	ENSP00000337353:p.Ala182Asp		Somatic				TDP1_uc010atm.3_Non-coding_Transcript|TDP1_uc001xxz.3_Missense_Mutation_p.A182D|TDP1_uc010atn.3_Missense_Mutation_p.A182D|TDP1_uc001xya.3_5'UTR|TDP1_uc001xyb.3_Non-coding_Transcript	p.A182D	NM_018319	NP_060789	WXS	Illumina GAIIx	Phase_I	Q9NUW8	TYDP1_HUMAN		COAD - Colon adenocarcinoma(157;0.23)	2	844	+		all_cancers(154;0.185)	182					Q2HXX4|Q86TV8|Q96BK7|Q9NZM7|Q9NZM8	Missense_Mutation	SNP	ENST00000335725.4	37	c.545C>A	CCDS9888.1	.	.	.	.	.	.	.	.	.	.	C	23.4	4.414528	0.83449	.	.	ENSG00000042088	ENST00000393452;ENST00000554180;ENST00000393454;ENST00000553617;ENST00000335725;ENST00000555880	T;T;T;T;T;T	0.42900	0.96;0.96;0.96;0.96;0.96;0.96	5.56	4.66	0.58398	.	0.049515	0.85682	D	0.000000	T	0.62405	0.2425	M	0.82323	2.585	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.87578	0.982;0.989;0.998;0.989	T	0.61739	-0.7001	10	0.07644	T	0.81	-6.6798	14.6892	0.69072	0.0:0.9293:0.0:0.0707	.	182;182;182;182	G3V2F4;E7EPD8;G3V4W8;Q9NUW8	.;.;.;TYDP1_HUMAN	D	182;182;182;83;182;182	ENSP00000377098:A182D;ENSP00000450872:A182D;ENSP00000377099:A182D;ENSP00000450708:A83D;ENSP00000337353:A182D;ENSP00000450628:A182D	ENSP00000337353:A182D	A	+	2	0	TDP1	89499756	1.000000	0.71417	1.000000	0.80357	0.839000	0.47603	5.335000	0.65929	2.596000	0.87737	0.561000	0.74099	GCC		0.512	TDP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411239.1	NM_018319		4	48	0	0	0	1	0	4	48				
SFMBT2	57713	broad.mit.edu	37	10	7242431	7242431	+	Silent	SNP	C	C	A			TCGA-EL-A3T8-01A-21D-A22D-08	TCGA-EL-A3T8-11A-11D-A22D-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	47a0cb63-dd19-49fe-983d-a2e786795355	e475f95d-8efb-4df4-9682-9608c5081ea7	g.chr10:7242431C>A	ENST00000361972.4	-	14	1593	c.1503G>T	c.(1501-1503)gtG>gtT	p.V501V	SFMBT2_ENST00000397167.1_Silent_p.V501V	NM_001018039.1	NP_001018049.1	Q5VUG0	SMBT2_HUMAN	Scm-like with four mbt domains 2	501					negative regulation of gene expression (GO:0010629)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	histone binding (GO:0042393)			NS(2)|breast(3)|central_nervous_system(4)|endometrium(7)|kidney(2)|large_intestine(26)|lung(34)|ovary(5)|pancreas(2)|skin(9)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	99						TCTTAACAGGCACTGTGGGCG	0.438																																						uc009xio.2																			0				NS(2)|breast(3)|central_nervous_system(4)|endometrium(7)|kidney(2)|large_intestine(26)|lung(34)|ovary(5)|pancreas(2)|skin(9)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	99						c.(1501-1503)gtG>gtT		Homo sapiens Scm-like with four mbt domains 2 (SFMBT2), transcript variant 2, mRNA.							111.0	111.0	111.0					10																	7242431		2203	4300	6503	SO:0001819	synonymous_variant	57713				regulation of transcription, DNA-dependent	nucleus		g.chr10:7242431C>A	AB046837	CCDS31138.1	10p15.1	2013-01-10	2003-11-14		ENSG00000198879	ENSG00000198879		"""Sterile alpha motif (SAM) domain containing"""	20256	protein-coding gene	gene with protein product		615392	"""Scm-related gene containing four mbt domains 2"""			10997877	Standard	NM_001029880		Approved	KIAA1617	uc009xio.2	Q5VUG0	OTTHUMG00000017630	ENST00000361972.4:c.1503G>T	10.37:g.7242431C>A			Somatic				SFMBT2_uc001ijn.2_Silent_p.V501V|SFMBT2_uc010qay.2_Intron	p.V501V	NM_001018039	NP_001018049	WXS	Illumina GAIIx	Phase_I	Q5VUG0	SMBT2_HUMAN			13	1594	-			501					A7MD09|Q9HCF5	Silent	SNP	ENST00000361972.4	37	c.1503G>T	CCDS31138.1																																																																																				0.438	SFMBT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046673.1	NM_001029880		28	36	0	0	0	1	0	28	36				
ZDBF2	57683	broad.mit.edu	37	2	207169562	207169562	+	Missense_Mutation	SNP	G	G	A			TCGA-EL-A3T8-01A-21D-A22D-08	TCGA-EL-A3T8-11A-11D-A22D-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	47a0cb63-dd19-49fe-983d-a2e786795355	e475f95d-8efb-4df4-9682-9608c5081ea7	g.chr2:207169562G>A	ENST00000374423.3	+	5	696	c.310G>A	c.(310-312)Gaa>Aaa	p.E104K		NM_020923.1	NP_065974.1	Q9HCK1	ZDBF2_HUMAN	zinc finger, DBF-type containing 2	104							nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			endometrium(4)|kidney(5)|large_intestine(28)|lung(50)|ovary(4)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	95						GGATGCTACCGAAGAGAGACC	0.458																																						uc002vbp.2																			0				endometrium(4)|kidney(5)|large_intestine(28)|lung(50)|ovary(4)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	95						c.(310-312)Gaa>Aaa		Homo sapiens zinc finger, DBF-type containing 2 (ZDBF2), mRNA.							84.0	81.0	82.0					2																	207169562		1969	4154	6123	SO:0001583	missense	57683						nucleic acid binding|zinc ion binding	g.chr2:207169562G>A	AB046791	CCDS46501.1, CCDS74637.1	2q33.3	2013-01-10			ENSG00000204186	ENSG00000204186		"""Zinc fingers, DBF-type"""	29313	protein-coding gene	gene with protein product						10997877	Standard	XM_005246711		Approved	FLJ45338, KIAA1571	uc002vbp.2	Q9HCK1	OTTHUMG00000154648	ENST00000374423.3:c.310G>A	2.37:g.207169562G>A	ENSP00000363545:p.Glu104Lys		Somatic					p.E104K	NM_020923	NP_065974	WXS	Illumina GAIIx	Phase_I	Q9HCK1	ZDBF2_HUMAN			4	560	+			104					Q6ZNP7|Q6ZSN8	Missense_Mutation	SNP	ENST00000374423.3	37	c.310G>A	CCDS46501.1	.	.	.	.	.	.	.	.	.	.	G	7.932	0.740941	0.15642	.	.	ENSG00000204186	ENST00000374423	T	0.17370	2.28	4.68	2.72	0.32119	.	1.458410	0.04756	N	0.425444	T	0.06462	0.0166	N	0.14661	0.345	0.09310	N	1	P	0.45240	0.854	B	0.29524	0.103	T	0.11299	-1.0593	10	0.02654	T	1	.	5.1627	0.15070	0.1066:0.0:0.6893:0.204	.	104	Q9HCK1	ZDBF2_HUMAN	K	104	ENSP00000363545:E104K	ENSP00000363545:E104K	E	+	1	0	ZDBF2	206877807	0.023000	0.18921	0.002000	0.10522	0.002000	0.02628	0.663000	0.25053	1.110000	0.41699	0.650000	0.86243	GAA		0.458	ZDBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336458.1	NM_020923		17	30	0	0	0	1	0	17	30				
NOD2	64127	broad.mit.edu	37	16	50759417	50759417	+	Missense_Mutation	SNP	T	T	A			TCGA-EL-A3T8-01A-21D-A22D-08	TCGA-EL-A3T8-11A-11D-A22D-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	47a0cb63-dd19-49fe-983d-a2e786795355	e475f95d-8efb-4df4-9682-9608c5081ea7	g.chr16:50759417T>A	ENST00000300589.2	+	10	3005	c.2900T>A	c.(2899-2901)cTc>cAc	p.L967H		NM_022162.1	NP_071445.1	Q9HC29	NOD2_HUMAN	nucleotide-binding oligomerization domain containing 2	967					activation of MAPK activity (GO:0000187)|activation of MAPK activity involved in innate immune response (GO:0035419)|cellular response to muramyl dipeptide (GO:0071225)|cellular response to peptidoglycan (GO:0071224)|cytokine production involved in immune response (GO:0002367)|defense response (GO:0006952)|defense response to bacterium (GO:0042742)|defense response to Gram-positive bacterium (GO:0050830)|detection of bacterium (GO:0016045)|detection of biotic stimulus (GO:0009595)|detection of muramyl dipeptide (GO:0032498)|immunoglobulin production involved in immunoglobulin mediated immune response (GO:0002381)|innate immune response (GO:0045087)|innate immune response in mucosa (GO:0002227)|intracellular signal transduction (GO:0035556)|JNK cascade (GO:0007254)|macrophage inflammatory protein-1 alpha production (GO:0071608)|maintenance of gastrointestinal epithelium (GO:0030277)|microglial cell activation involved in immune response (GO:0002282)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of inflammatory response to antigenic stimulus (GO:0002862)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of interleukin-18 production (GO:0032701)|negative regulation of interleukin-2 production (GO:0032703)|negative regulation of macrophage apoptotic process (GO:2000110)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of T cell mediated immunity (GO:0002710)|negative regulation of toll-like receptor 2 signaling pathway (GO:0034136)|negative regulation of tumor necrosis factor production (GO:0032720)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing 2 signaling pathway (GO:0070431)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of B cell activation (GO:0050871)|positive regulation of biosynthetic process of antibacterial peptides active against Gram-positive bacteria (GO:0006965)|positive regulation of dendritic cell antigen processing and presentation (GO:0002606)|positive regulation of dendritic cell cytokine production (GO:0002732)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of gamma-delta T cell activation (GO:0046645)|positive regulation of humoral immune response mediated by circulating immunoglobulin (GO:0002925)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-1 beta production (GO:0032731)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-17 production (GO:0032740)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of JNK cascade (GO:0046330)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of oxidoreductase activity (GO:0051353)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phagocytosis (GO:0050766)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of prostaglandin-E synthase activity (GO:2000363)|positive regulation of prostaglandin-endoperoxide synthase activity (GO:0060585)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of stress-activated MAPK cascade (GO:0032874)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of type 2 immune response (GO:0002830)|protein oligomerization (GO:0051259)|regulation of inflammatory response (GO:0050727)|regulation of neutrophil chemotaxis (GO:0090022)|response to exogenous dsRNA (GO:0043330)|response to lipopolysaccharide (GO:0032496)|response to muramyl dipeptide (GO:0032495)|response to nutrient (GO:0007584)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|vesicle (GO:0031982)	ATP binding (GO:0005524)|CARD domain binding (GO:0050700)|enzyme binding (GO:0019899)|muramyl dipeptide binding (GO:0032500)|peptidoglycan binding (GO:0042834)|protein kinase binding (GO:0019901)			cervix(1)|endometrium(5)|kidney(3)|large_intestine(7)|lung(30)|ovary(3)|skin(3)	52		all_cancers(37;0.0156)				GAGAACCATCTCCAGGATGAA	0.413																																						uc002egm.1																			0		p.L967L(2)		cervix(1)|endometrium(5)|kidney(3)|large_intestine(7)|lung(30)|ovary(3)|skin(3)	52						c.(2899-2901)cTc>cAc		Homo sapiens nucleotide-binding oligomerization domain containing 2 (NOD2), mRNA.							95.0	93.0	94.0					16																	50759417		2198	4300	6498	SO:0001583	missense	64127				JNK cascade|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|Toll signaling pathway|activation of MAPK activity involved in innate immune response|cytokine production involved in immune response|detection of bacterium|detection of muramyl dipeptide|negative regulation of macrophage apoptosis|nucleotide-binding oligomerization domain containing 2 signaling pathway|positive regulation of B cell activation|positive regulation of ERK1 and ERK2 cascade|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of JNK cascade|positive regulation of NF-kappaB transcription factor activity|positive regulation of Notch signaling pathway|positive regulation of dendritic cell antigen processing and presentation|positive regulation of epithelial cell proliferation|positive regulation of gamma-delta T cell activation|positive regulation of interleukin-1 beta secretion|positive regulation of interleukin-10 production|positive regulation of interleukin-17 production|positive regulation of interleukin-6 production|positive regulation of nitric-oxide synthase biosynthetic process|positive regulation of phosphatidylinositol 3-kinase activity|positive regulation of prostaglandin-E synthase activity|positive regulation of prostaglandin-endoperoxide synthase activity|positive regulation of stress-activated MAPK cascade|positive regulation of tumor necrosis factor production|positive regulation of type 2 immune response|protein oligomerization|stress-activated MAPK cascade|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cell surface|cytosol|plasma membrane|vesicle	ATP binding|CARD domain binding|muramyl dipeptide binding|protein kinase binding	g.chr16:50759417T>A	AF178930	CCDS10746.1	16q12	2014-09-17	2006-12-08	2006-12-08	ENSG00000167207	ENSG00000167207		"""Nucleotide-binding domain and leucine rich repeat containing"""	5331	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 2"", ""NOD-like receptor C2"", ""NLR family, CARD domain containing 2"""	605956	"""caspase recruitment domain family, member 15"""	IBD1, CARD15		7809109, 8587604	Standard	XM_005256084		Approved	BLAU, CD, PSORAS1, CLR16.3, NLRC2	uc002egm.1	Q9HC29	OTTHUMG00000133171	ENST00000300589.2:c.2900T>A	16.37:g.50759417T>A	ENSP00000300589:p.Leu967His		Somatic				NOD2_uc010vgq.1_Missense_Mutation_p.L12H	p.L967H	NM_022162	NP_071445	WXS	Illumina GAIIx	Phase_I	Q9HC29	NOD2_HUMAN			9	3005	+		all_cancers(37;0.0156)	967					E2JEQ6|Q96RH5|Q96RH6|Q96RH8	Missense_Mutation	SNP	ENST00000300589.2	37	c.2900T>A	CCDS10746.1	.	.	.	.	.	.	.	.	.	.	T	19.91	3.915185	0.73098	.	.	ENSG00000167207	ENST00000526417;ENST00000300589;ENST00000431240	T	0.60672	0.17	5.97	5.97	0.96955	.	0.225081	0.31685	N	0.007221	T	0.79009	0.4374	M	0.91406	3.205	0.29266	N	0.870981	D	0.71674	0.998	D	0.64877	0.93	T	0.79969	-0.1579	10	0.87932	D	0	.	12.8422	0.57809	0.0:0.0:0.0:1.0	.	967	Q9HC29	NOD2_HUMAN	H	940;967;107	ENSP00000300589:L967H	ENSP00000300589:L967H	L	+	2	0	NOD2	49316918	0.793000	0.28825	0.684000	0.30055	0.995000	0.86356	3.578000	0.53892	2.288000	0.76882	0.533000	0.62120	CTC		0.413	NOD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256876.2	NM_022162		3	90	0	0	0	1	0	3	90				
