#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_ACHILLES_Lineage_Results_Top_Genes	i_Annotation_Transcript	i_CCLE_ONCOMAP_overlapping_mutations	i_CCLE_ONCOMAP_total_mutations_in_gene	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Mutation_Type	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Other_Diseases	i_CGC_Tissue Type	i_CGC_Translocation_Partner	i_CGC_Tumor_Types_Germline	i_CGC_Tumor_Types_Somatic	i_COSMIC_fusion_genes	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_mutations	i_COSMIC_overlapping_primary_sites	i_COSMIC_tissue_types_affected	i_COSMIC_total_alterations_in_gene	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Codon_Change	i_DNARepairGenes_Role	i_Description	i_DrugBank	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_FamilialCancerDatabase_Syndromes	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_GO_Biological_Process	i_GO_Cellular_Component	i_GO_Molecular_Function	i_Genome_Change	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_MUTSIG_Published_Results	i_OREGANNO_ID	i_OREGANNO_Values	i_ORegAnno_bin	i_Other_Transcripts	i_Protein_Change	i_Refseq_mRNA_Id	i_Refseq_prot_Id	i_SwissProt_acc_Id	i_SwissProt_entry_Id	i_TCGAscape_Amplification_Peaks	i_TCGAscape_Deletion_Peaks	i_Transcript_Exon	i_Transcript_Position	i_Transcript_Strand	i_Tumorscape_Amplification_Peaks	i_Tumorscape_Deletion_Peaks	i_UniProt_AApos	i_UniProt_Experimental_Info	i_UniProt_Natural_Variations	i_UniProt_Region	i_UniProt_Site	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_cDNA_Change	i_ccds_id	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_type	i_havana_transcript	i_refseq_mrna_id	i_secondary_variant_classification	i_t_alt_count_full	i_t_ref_count_full	isArtifactMode	oxoGCut	pox	pox_cutoff	qox	t_alt_count	t_ref_count	validation_alt_allele	validation_method	validation_status	validation_tumor_sample
FRG1B	284802	broad.mit.edu	37	20	29625955	29625955	+	Nonsense_Mutation	SNP	A	A	T			TCGA-EL-A4JW-01A-11D-A257-08	TCGA-EL-A4JW-11A-12D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8f3ed41c-8506-4db3-b856-ca823d511258	9b411822-8132-4319-a3a5-0600a50a1c7d	g.chr20:29625955A>T	ENST00000278882.3	+	5	579	c.199A>T	c.(199-201)Aga>Tga	p.R67*	FRG1B_ENST00000358464.4_Nonsense_Mutation_p.R67*|FRG1B_ENST00000439954.2_Nonsense_Mutation_p.R72*			Q9BZ01	FRG1B_HUMAN	FSHD region gene 1 family, member B	67										endometrium(10)|kidney(21)|lung(3)|pancreas(1)|prostate(9)|urinary_tract(9)	53						AATTGGACCAAGAGAACAATG	0.338																																						ENST00000278882.3																			0				endometrium(10)|kidney(21)|lung(3)|pancreas(1)|prostate(9)|urinary_tract(9)	53						c.(199-201)Aga>Tga																																						SO:0001587	stop_gained	0							g.chr20:29625955A>T			20q11.1	2013-03-18	2007-10-11	2007-10-11	ENSG00000149531	ENSG00000149531			15792	other	unknown			"""chromosome 20 open reading frame 80"""	C20orf80			Standard	NR_003579		Approved	bA348I14.2	uc010ztl.1	Q9BZ01	OTTHUMG00000032157	ENST00000278882.3:c.199A>T	20.37:g.29625955A>T	ENSP00000278882:p.Arg67*					FRG1B_ENST00000358464.4_Nonsense_Mutation_p.R67*|FRG1B_ENST00000439954.2_Nonsense_Mutation_p.R72*	p.R67*							5	579	+								C4AME5	Nonsense_Mutation	SNP	ENST00000278882.3	37	c.199A>T		.	.	.	.	.	.	.	.	.	.	a	29.6	5.022161	0.93462	.	.	ENSG00000149531	ENST00000278882;ENST00000439954;ENST00000358464	.	.	.	1.68	1.68	0.24146	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.20519	T	0.43	.	7.3757	0.26827	1.0:0.0:0.0:0.0	.	.	.	.	X	67;72;67	.	ENSP00000278882:R67X	R	+	1	2	FRG1B	28239616	1.000000	0.71417	1.000000	0.80357	0.120000	0.20174	3.670000	0.54569	1.028000	0.39785	0.155000	0.16302	AGA		0.338	FRG1B-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000078494.2	NR_003579		6	79	0	0	0	1	0	6	79				
KIAA1257	57501	broad.mit.edu	37	3	128706481	128706481	+	Silent	SNP	G	G	A			TCGA-EL-A4JW-01A-11D-A257-08	TCGA-EL-A4JW-11A-12D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8f3ed41c-8506-4db3-b856-ca823d511258	9b411822-8132-4319-a3a5-0600a50a1c7d	g.chr3:128706481G>A	ENST00000265068.5	-	4	812	c.645C>T	c.(643-645)gaC>gaT	p.D215D	KIAA1257_ENST00000515659.1_Silent_p.D103D|KIAA1257_ENST00000511438.1_Silent_p.D215D|KIAA1257_ENST00000510149.1_5'UTR	NM_020741.2	NP_065792.1	Q9ULG3	K1257_HUMAN	KIAA1257	215										breast(1)|endometrium(2)|large_intestine(3)|lung(6)|skin(2)	14						AAGCTCCCACGTCGTCTGTGA	0.428																																						ENST00000265068.5																			0				breast(1)|endometrium(2)|large_intestine(3)|lung(6)|skin(2)	14						c.(643-645)gaC>gaT		KIAA1257							128.0	125.0	126.0					3																	128706481		1844	4081	5925	SO:0001819	synonymous_variant	57501							g.chr3:128706481G>A	AB033083	CCDS46905.1	3q21.3	2011-11-07			ENSG00000114656	ENSG00000114656			29231	protein-coding gene	gene with protein product						10574462	Standard	NM_020741		Approved		uc003elj.4	Q9ULG3	OTTHUMG00000159946	ENST00000265068.5:c.645C>T	3.37:g.128706481G>A						KIAA1257_ENST00000515659.1_Silent_p.D103D|KIAA1257_ENST00000510149.1_5'UTR|KIAA1257_ENST00000511438.1_Silent_p.D215D	p.D215D	NM_020741.2	NP_065792.1	Q9ULG3	K1257_HUMAN			4	812	-			215					Q8IXY7|Q8N5T4	Silent	SNP	ENST00000265068.5	37	c.645C>T	CCDS46905.1																																																																																				0.428	KIAA1257-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000358430.1	NM_020741		5	64	0	0	0	1	0	5	64				
CHEK2	11200	broad.mit.edu	37	22	29091841	29091841	+	Silent	SNP	G	G	A	rs146546850	byFrequency	TCGA-EL-A4JW-01A-11D-A257-08	TCGA-EL-A4JW-11A-12D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8f3ed41c-8506-4db3-b856-ca823d511258	9b411822-8132-4319-a3a5-0600a50a1c7d	g.chr22:29091841G>A	ENST00000405598.1	-	12	1307	c.1116C>T	c.(1114-1116)tcC>tcT	p.S372S	CHEK2_ENST00000382565.1_Intron|CHEK2_ENST00000544772.1_Silent_p.S151S|CHEK2_ENST00000403642.1_Silent_p.S281S|CHEK2_ENST00000382566.1_3'UTR|CHEK2_ENST00000328354.6_Silent_p.S372S|CHEK2_ENST00000382580.2_Silent_p.S415S|CHEK2_ENST00000402731.1_Silent_p.S343S|CHEK2_ENST00000404276.1_Silent_p.S372S|CHEK2_ENST00000464581.1_5'Flank|CHEK2_ENST00000382578.1_Silent_p.S281S|CHEK2_ENST00000348295.3_Silent_p.S343S			O96017	CHK2_HUMAN	checkpoint kinase 2	372	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.|T-loop/activation segment.				cellular protein catabolic process (GO:0044257)|cellular response to DNA damage stimulus (GO:0006974)|DNA damage checkpoint (GO:0000077)|DNA damage induced protein phosphorylation (GO:0006975)|double-strand break repair (GO:0006302)|G2/M transition of mitotic cell cycle (GO:0000086)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|positive regulation of transcription, DNA-templated (GO:0045893)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|protein stabilization (GO:0050821)|regulation of protein catabolic process (GO:0042176)|regulation of transcription, DNA-templated (GO:0006355)|replicative senescence (GO:0090399)|response to gamma radiation (GO:0010332)|signal transduction in response to DNA damage (GO:0042770)|signal transduction involved in intra-S DNA damage checkpoint (GO:0072428)|spindle assembly involved in mitosis (GO:0090307)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)|PML body (GO:0016605)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|ubiquitin protein ligase binding (GO:0031625)	p.S372S(8)		central_nervous_system(17)|endometrium(2)|kidney(11)|large_intestine(2)|lung(11)|ovary(1)|prostate(4)|stomach(2)	50						CCAAAATCTTGGAGTGCCCAA	0.413			F			breast		Direct reversal of damage;Other conserved DNA damage response genes																														ENST00000544772.1			yes	Rec		familial breast cancer	22	22q12.1	11200	F	CHK2 checkpoint homolog (S. pombe)			E		breast			8	Substitution - coding silent(8)	p.S372S(8)	kidney(4)|prostate(2)|endometrium(1)|central_nervous_system(1)	central_nervous_system(17)|endometrium(2)|kidney(11)|large_intestine(2)|lung(11)|ovary(1)|prostate(4)|stomach(2)	50						c.(451-453)tcC>tcT	Direct reversal of damage;Other conserved DNA damage response genes	checkpoint kinase 2							43.0	44.0	44.0					22																	29091841		2203	4300	6503	SO:0001819	synonymous_variant	11200				cell cycle|DNA damage checkpoint|DNA damage response, signal transduction resulting in induction of apoptosis|replicative senescence	PML body	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity	g.chr22:29091841G>A	AF086904	CCDS13843.1, CCDS13844.1, CCDS33629.1	22q12.1	2014-09-17	2011-11-11	2001-09-27	ENSG00000183765	ENSG00000183765			16627	protein-coding gene	gene with protein product		604373	"""CHK2 (checkpoint, S.pombe) homolog"", ""CHK2 checkpoint homolog (S. pombe)"""	RAD53		9836640, 10097108	Standard	NM_001257387		Approved	CDS1, CHK2, HuCds1, PP1425, bA444G7	uc003adt.1	O96017	OTTHUMG00000151023	ENST00000405598.1:c.1116C>T	22.37:g.29091841G>A						CHEK2_ENST00000382578.1_Silent_p.S281S|CHEK2_ENST00000328354.6_Silent_p.S372S|CHEK2_ENST00000404276.1_Silent_p.S372S|CHEK2_ENST00000402731.1_Silent_p.S343S|CHEK2_ENST00000348295.3_Silent_p.S343S|CHEK2_ENST00000405598.1_Silent_p.S372S|CHEK2_ENST00000382566.1_3'UTR|CHEK2_ENST00000403642.1_Silent_p.S281S|CHEK2_ENST00000382580.2_Silent_p.S415S|CHEK2_ENST00000382565.1_Intron	p.S151S	NM_001257387.1	NP_001244316.1	O96017	CHK2_HUMAN			12	1889	-			372			FHA.		A8K3Y9|B7ZBF3|B7ZBF4|B7ZBF5|Q6QA03|Q6QA04|Q6QA05|Q6QA06|Q6QA07|Q6QA08|Q6QA10|Q6QA11|Q6QA12|Q6QA13|Q9HBS5|Q9HCQ8|Q9UGF0|Q9UGF1	Silent	SNP	ENST00000405598.1	37	c.453C>T	CCDS13843.1	.	.	.	.	.	.	.	.	.	.	G	5.792	0.330417	0.10956	.	.	ENSG00000183765	ENST00000434810	.	.	.	5.89	-2.11	0.07187	.	.	.	.	.	T	0.42154	0.1190	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.33854	-0.9852	4	.	.	.	-7.6356	3.2532	0.06822	0.327:0.1103:0.4613:0.1014	.	.	.	.	L	116	.	.	P	-	2	0	CHEK2	27421841	0.997000	0.39634	0.996000	0.52242	0.470000	0.32858	0.318000	0.19504	-0.075000	0.12798	-0.907000	0.02831	CCA		0.413	CHEK2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000321150.1	NM_001005735		5	54	0	0	0	1	0	5	54				
PRRC2C	23215	broad.mit.edu	37	1	171509227	171509227	+	Silent	SNP	A	A	G			TCGA-EL-A4JW-01A-11D-A257-08	TCGA-EL-A4JW-11A-12D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8f3ed41c-8506-4db3-b856-ca823d511258	9b411822-8132-4319-a3a5-0600a50a1c7d	g.chr1:171509227A>G	ENST00000338920.4	+	16	2853	c.2616A>G	c.(2614-2616)caA>caG	p.Q872Q	PRRC2C_ENST00000392078.3_Silent_p.Q874Q|PRRC2C_ENST00000426496.2_Silent_p.Q872Q|PRRC2C_ENST00000367742.3_Silent_p.Q874Q	NM_015172.3	NP_055987.2	Q9Y520	PRC2C_HUMAN	proline-rich coiled-coil 2C	872					hematopoietic progenitor cell differentiation (GO:0002244)	membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)										CACAAGTACAAAAGTTTTTAA	0.398																																						ENST00000367742.3																			0											c.(2620-2622)caA>caG		proline-rich coiled-coil 2C							141.0	144.0	143.0					1																	171509227		2203	4300	6503	SO:0001819	synonymous_variant	23215						protein C-terminus binding	g.chr1:171509227A>G	AL096857	CCDS1296.2	1q24.3	2012-07-18	2010-12-09	2010-12-09	ENSG00000117523	ENSG00000117523			24903	protein-coding gene	gene with protein product			"""BAT2 domain containing 1"", ""HLA-B associated transcript 2-like 2"""	BAT2D1, BAT2L2		10470851, 12443540	Standard	NM_015172		Approved	KIAA1096, XTP2	uc010pmg.2	Q9Y520	OTTHUMG00000034665	ENST00000338920.4:c.2616A>G	1.37:g.171509227A>G						PRRC2C_ENST00000338920.4_Silent_p.Q872Q|PRRC2C_ENST00000392078.3_Silent_p.Q874Q|PRRC2C_ENST00000426496.2_Silent_p.Q872Q	p.Q874Q			Q9Y520	PRC2C_HUMAN			16	2864	+			872					Q05DM8|Q49A39|Q6PD54|Q9H2N2|Q9HA05|Q9NSM8|Q9NXL3|Q9UF29|Q9UPQ6	Silent	SNP	ENST00000338920.4	37	c.2622A>G	CCDS1296.2																																																																																				0.398	PRRC2C-010	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000314826.4	NM_015172		38	71	0	0	0	1	0	38	71				
LOC101927079	101927079	broad.mit.edu	37	15	22332432	22332432	+	RNA	SNP	C	C	T	rs376977769		TCGA-EL-A4JW-01A-11D-A257-08	TCGA-EL-A4JW-11A-12D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8f3ed41c-8506-4db3-b856-ca823d511258	9b411822-8132-4319-a3a5-0600a50a1c7d	g.chr15:22332432C>T	ENST00000558896.1	+	0	239																											AAGATTCTAACGTGACAGAAC	0.343																																						ENST00000558896.1																			0																																																			0							g.chr15:22332432C>T																													15.37:g.22332432C>T														0	239	+									RNA	SNP	ENST00000558896.1	37																																																																																						0.343	RP11-69H14.6-001	KNOWN	basic	sense_overlapping	sense_overlapping	OTTHUMT00000417625.1			5	73	0	0	0	1	0	5	73				
FAM120B	84498	broad.mit.edu	37	6	170627281	170627281	+	Missense_Mutation	SNP	C	C	T			TCGA-EL-A4JW-01A-11D-A257-08	TCGA-EL-A4JW-11A-12D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8f3ed41c-8506-4db3-b856-ca823d511258	9b411822-8132-4319-a3a5-0600a50a1c7d	g.chr6:170627281C>T	ENST00000476287.1	+	2	911	c.803C>T	c.(802-804)tCa>tTa	p.S268L	FAM120B_ENST00000537664.1_Missense_Mutation_p.S291L|FAM120B_ENST00000540480.1_Missense_Mutation_p.S280L|FAM120B_ENST00000252510.9_Intron	NM_032448.1	NP_115824.1	Q96EK7	F120B_HUMAN	family with sequence similarity 120B	268					cell differentiation (GO:0030154)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(11)|liver(1)|lung(15)|ovary(1)|prostate(2)|skin(2)	44		Breast(66;0.000338)|Esophageal squamous(34;0.241)		OV - Ovarian serous cystadenocarcinoma(33;3.94e-22)|BRCA - Breast invasive adenocarcinoma(81;6.47e-06)|GBM - Glioblastoma multiforme(31;0.0899)		TTAGCTGTGTCAGACCATATA	0.353																																						ENST00000476287.1																			0				endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(11)|liver(1)|lung(15)|ovary(1)|prostate(2)|skin(2)	44						c.(802-804)tCa>tTa		family with sequence similarity 120B							73.0	80.0	78.0					6																	170627281		2202	4300	6502	SO:0001583	missense	84498				cell differentiation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	protein binding	g.chr6:170627281C>T	AB058741	CCDS5314.1, CCDS75555.1	6q27	2011-04-13	2006-07-04	2006-07-04	ENSG00000112584	ENSG00000112584			21109	protein-coding gene	gene with protein product	"""PPARgamma constitutive coactivator 1"", ""constitutive coactivator of PPAR-gamma"""	612266	"""KIAA1838"""	KIAA1838		14585507	Standard	NM_032448		Approved	PGCC1, CCPG	uc003qxp.3	Q96EK7	OTTHUMG00000016080	ENST00000476287.1:c.803C>T	6.37:g.170627281C>T	ENSP00000417970:p.Ser268Leu					FAM120B_ENST00000540480.1_Missense_Mutation_p.S280L|FAM120B_ENST00000537664.1_Missense_Mutation_p.S291L|FAM120B_ENST00000252510.9_Intron	p.S268L	NM_032448.1	NP_115824.1	Q96EK7	F120B_HUMAN		OV - Ovarian serous cystadenocarcinoma(33;3.94e-22)|BRCA - Breast invasive adenocarcinoma(81;6.47e-06)|GBM - Glioblastoma multiforme(31;0.0899)	2	911	+		Breast(66;0.000338)|Esophageal squamous(34;0.241)	268					B4DL34|Q86V68|Q96JI9	Missense_Mutation	SNP	ENST00000476287.1	37	c.803C>T	CCDS5314.1	.	.	.	.	.	.	.	.	.	.	C	17.76	3.467965	0.63625	.	.	ENSG00000112584	ENST00000540480;ENST00000537664;ENST00000476287	T;T;T	0.10099	2.92;2.91;2.93	5.36	5.36	0.76844	.	0.251545	0.38005	N	0.001850	T	0.09202	0.0227	L	0.47716	1.5	0.80722	D	1	P;P	0.43826	0.818;0.818	B;B	0.43082	0.318;0.407	T	0.06481	-1.0824	10	0.44086	T	0.13	-15.9785	19.4494	0.94861	0.0:1.0:0.0:0.0	.	268;268	Q96EK7;F2Z2E1	F120B_HUMAN;.	L	280;291;268	ENSP00000444125:S280L;ENSP00000440125:S291L;ENSP00000417970:S268L	ENSP00000436640:S268L	S	+	2	0	FAM120B	170469206	1.000000	0.71417	0.947000	0.38551	0.957000	0.61999	5.487000	0.66863	2.645000	0.89757	0.650000	0.86243	TCA		0.353	FAM120B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000043259.2	NM_032448		8	76	0	0	0	1	0	8	76				
POM121L9P	29774	broad.mit.edu	37	22	24659734	24659734	+	RNA	SNP	T	T	C			TCGA-EL-A4JW-01A-11D-A257-08	TCGA-EL-A4JW-11A-12D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8f3ed41c-8506-4db3-b856-ca823d511258	9b411822-8132-4319-a3a5-0600a50a1c7d	g.chr22:24659734T>C	ENST00000414583.2	+	0	3259					NR_003714.1				POM121 transmembrane nucleoporin-like 9, pseudogene																		CTCTCTCCTGTGGGAGGGGGG	0.632																																						ENST00000414583.2																			0																																																			0							g.chr22:24659734T>C	AL040062, AL117401		22q11.22	2012-03-13	2012-03-13		ENSG00000128262	ENSG00000128262			30080	pseudogene	pseudogene			"""POM121 membrane glycoprotein-like 9, pseudogene"""				Standard	NR_003714		Approved				OTTHUMG00000150763		22.37:g.24659734T>C								NR_003714.1						0	3259	+									RNA	SNP	ENST00000414583.2	37																																																																																						0.632	POM121L9P-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000319991.1	NM_014549		3	15	0	0	0	1	0	3	15				
GOT2	2806	broad.mit.edu	37	16	58750077	58750077	+	Missense_Mutation	SNP	C	C	A			TCGA-EL-A4JW-01A-11D-A257-08	TCGA-EL-A4JW-11A-12D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8f3ed41c-8506-4db3-b856-ca823d511258	9b411822-8132-4319-a3a5-0600a50a1c7d	g.chr16:58750077C>A	ENST00000245206.5	-	8	988	c.860G>T	c.(859-861)cGt>cTt	p.R287L	GOT2_ENST00000564400.1_5'UTR|GOT2_ENST00000434819.2_Missense_Mutation_p.R244L	NM_002080.2	NP_002071.2	P00505	AATM_HUMAN	glutamic-oxaloacetic transaminase 2, mitochondrial	287					2-oxoglutarate metabolic process (GO:0006103)|4-hydroxyproline catabolic process (GO:0019470)|aspartate biosynthetic process (GO:0006532)|aspartate catabolic process (GO:0006533)|aspartate metabolic process (GO:0006531)|carbohydrate metabolic process (GO:0005975)|cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|fatty acid transport (GO:0015908)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|glutamate catabolic process to 2-oxoglutarate (GO:0019551)|glutamate catabolic process to aspartate (GO:0019550)|glutamate metabolic process (GO:0006536)|oxaloacetate metabolic process (GO:0006107)|response to ethanol (GO:0045471)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	kynurenine-oxoglutarate transaminase activity (GO:0016212)|L-aspartate:2-oxoglutarate aminotransferase activity (GO:0004069)|L-phenylalanine:2-oxoglutarate aminotransferase activity (GO:0080130)|poly(A) RNA binding (GO:0044822)|pyridoxal phosphate binding (GO:0030170)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(2)|lung(8)|prostate(2)|skin(1)	22					L-Aspartic Acid(DB00128)	GGCTCCTACACGCTCACCTGA	0.428																																						ENST00000245206.5																			0				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(2)|lung(8)|prostate(2)|skin(1)	22						c.(859-861)cGt>cTt		glutamic-oxaloacetic transaminase 2, mitochondrial	L-Aspartic Acid(DB00128)|L-Glutamic Acid(DB00142)|Pyridoxal Phosphate(DB00114)						125.0	114.0	117.0					16																	58750077		2198	4300	6498	SO:0001583	missense	2806				aspartate catabolic process|fatty acid transport|gluconeogenesis|response to ethanol	mitochondrial matrix|plasma membrane	L-aspartate:2-oxoglutarate aminotransferase activity|protein binding|pyridoxal phosphate binding	g.chr16:58750077C>A		CCDS10801.1, CCDS67045.1	16q21	2013-05-29	2013-05-29		ENSG00000125166	ENSG00000125166	2.6.1.1		4433	protein-coding gene	gene with protein product	"""kynurenine aminotransferase IV"", ""aspartate aminotransferase 2"", ""aspartate transaminase 2"""	138150	"""glutamic-oxaloacetic transaminase 2, mitochondrial (aspartate aminotransferase 2)"""			17442055	Standard	NM_002080		Approved	mitAAT, KATIV, KAT4	uc002eof.1	P00505	OTTHUMG00000133769	ENST00000245206.5:c.860G>T	16.37:g.58750077C>A	ENSP00000245206:p.Arg287Leu					GOT2_ENST00000564400.1_5'UTR|GOT2_ENST00000434819.2_Missense_Mutation_p.R244L	p.R287L	NM_002080.2	NP_002071.2	P00505	AATM_HUMAN			8	988	-			287					B4DJA6|E7ERW2|Q53FL3|Q9BWA3	Missense_Mutation	SNP	ENST00000245206.5	37	c.860G>T	CCDS10801.1	.	.	.	.	.	.	.	.	.	.	C	33	5.237324	0.95240	.	.	ENSG00000125166	ENST00000245206;ENST00000434819	D;D	0.98249	-4.82;-4.82	5.32	5.32	0.75619	Aminotransferase, class I/classII (1);Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.000000	0.85682	D	0.000000	D	0.99369	0.9778	H	0.97023	3.925	0.80722	D	1	D;D	0.89917	0.998;1.0	D;D	0.91635	0.995;0.999	D	0.98595	1.0656	9	.	.	.	4.689	18.3515	0.90339	0.0:1.0:0.0:0.0	.	244;287	E7ERW2;P00505	.;AATM_HUMAN	L	287;244	ENSP00000245206:R287L;ENSP00000394100:R244L	.	R	-	2	0	GOT2	57307578	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	7.471000	0.80985	2.662000	0.90505	0.591000	0.81541	CGT		0.428	GOT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258289.3			20	46	1	0	4.96729e-08	1	5.48115e-08	20	46				
PARG	8505	broad.mit.edu	37	10	51093329	51093329	+	Missense_Mutation	SNP	C	C	T			TCGA-EL-A4JW-01A-11D-A257-08	TCGA-EL-A4JW-11A-12D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8f3ed41c-8506-4db3-b856-ca823d511258	9b411822-8132-4319-a3a5-0600a50a1c7d	g.chr10:51093329C>T	ENST00000402038.3	-	4	294	c.295G>A	c.(295-297)Gca>Aca	p.A99T		NM_003631.2	NP_003622.2	Q86W56	PARG_HUMAN	poly (ADP-ribose) glycohydrolase	584	A-domain.				carbohydrate metabolic process (GO:0005975)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	poly(ADP-ribose) glycohydrolase activity (GO:0004649)	p.A584T(1)		endometrium(5)|kidney(2)|lung(1)|ovary(2)	10				Epithelial(53;0.213)		TGAGCTTCTGCTTCTTCAAGT	0.318																																						ENST00000402038.3																			1	Substitution - Missense(1)	p.A584T(1)	kidney(1)	endometrium(5)|kidney(2)|lung(1)|ovary(2)	10						c.(295-297)Gca>Aca		poly (ADP-ribose) glycohydrolase							235.0	183.0	198.0					10																	51093329		692	1589	2281	SO:0001583	missense	8505				carbohydrate metabolic process	nucleus	poly(ADP-ribose) glycohydrolase activity	g.chr10:51093329C>T	AF005043	CCDS73130.1	10q11.23	2012-04-20			ENSG00000227345	ENSG00000227345	3.2.1.143		8605	protein-coding gene	gene with protein product		603501				9115250, 10449915	Standard	NM_003631		Approved		uc001jif.3	Q86W56	OTTHUMG00000018201	ENST00000402038.3:c.295G>A	10.37:g.51093329C>T	ENSP00000384408:p.Ala99Thr						p.A99T	NM_003631.2	NP_003622.2	Q86W56	PARG_HUMAN		Epithelial(53;0.213)	4	294	-			584					A5YBK3|B2RC24|B4DIU5|B4DYR4|I6RUV3|Q6E4P6|Q6E4P7|Q7Z742|Q9Y4W7	Missense_Mutation	SNP	ENST00000402038.3	37	c.295G>A		.	.	.	.	.	.	.	.	.	.	C	12.89	2.073258	0.36566	.	.	ENSG00000227345	ENST00000402038	.	.	.	3.88	2.96	0.34315	.	.	.	.	.	T	0.46678	0.1405	M	0.61703	1.905	.	.	.	B;B;P;P;P;B	0.41947	0.002;0.003;0.574;0.766;0.766;0.006	B;B;B;B;B;B	0.38616	0.006;0.006;0.191;0.179;0.277;0.01	T	0.56631	-0.7947	7	0.18710	T	0.47	-4.0352	11.9338	0.52862	0.0:0.9123:0.0:0.0877	.	502;584;135;99;124;584	Q86W56-2;Q86W56;A5YBK3;Q5SQP4;B4DX76;Q0MQR4	.;PARG_HUMAN;.;.;.;.	T	99	.	ENSP00000384408:A99T	A	-	1	0	PARG	50763335	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	1.907000	0.39897	0.952000	0.37798	0.407000	0.27541	GCA		0.318	PARG-001	KNOWN	mRNA_start_NF|cds_start_NF|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000048011.2	NM_003631		6	43	0	0	0	1	0	6	43				
LIN7C	55327	broad.mit.edu	37	11	27528432	27528432	+	5'Flank	SNP	C	C	T			TCGA-EL-A4JW-01A-11D-A257-08	TCGA-EL-A4JW-11A-12D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8f3ed41c-8506-4db3-b856-ca823d511258	9b411822-8132-4319-a3a5-0600a50a1c7d	g.chr11:27528432C>T	ENST00000278193.2	-	0	0				BDNF-AS_ENST00000502161.2_RNA|BDNF-AS_ENST00000501176.2_RNA|BDNF-AS_ENST00000499568.2_RNA|BDNF-AS_ENST00000499008.3_RNA|BDNF-AS_ENST00000530686.1_RNA|BDNF-AS_ENST00000532965.1_RNA|LIN7C_ENST00000524596.1_5'Flank|BDNF-AS_ENST00000500662.2_RNA	NM_018362.3	NP_060832.1	Q9NUP9	LIN7C_HUMAN	lin-7 homolog C (C. elegans)						exocytosis (GO:0006887)|morphogenesis of an epithelial sheet (GO:0002011)|neurotransmitter secretion (GO:0007269)|protein transport (GO:0015031)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|MPP7-DLG1-LIN7 complex (GO:0097025)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|tight junction (GO:0005923)	cytoskeletal protein binding (GO:0008092)|L27 domain binding (GO:0097016)|protein domain specific binding (GO:0019904)			endometrium(2)|lung(2)|upper_aerodigestive_tract(1)	5						GAGTGTGTCGCCGCGGCCATC	0.657																																						ENST00000499008.3																			0																																																	SO:0001631	upstream_gene_variant	0							g.chr11:27528432C>T	AK002077	CCDS7864.1	11p14	2008-07-18				ENSG00000148943			17789	protein-coding gene	gene with protein product	"""LIN-7 protein 3"""	612332				10341223	Standard	NM_018362		Approved	MALS-3, Lin7c, LIN-7C, LIN-7-C, VELI3, FLJ11215	uc001mrl.3	Q9NUP9			11.37:g.27528432C>T	Exception_encountered					BDNF-AS_ENST00000501176.2_RNA|BDNF-AS_ENST00000502161.2_RNA|BDNF-AS_ENST00000532965.1_RNA|BDNF-AS_ENST00000500662.2_RNA|BDNF-AS_ENST00000499568.2_RNA|BDNF-AS_ENST00000530686.1_RNA		NR_002832.2						0	34	+									RNA	SNP	ENST00000278193.2	37		CCDS7864.1																																																																																				0.657	LIN7C-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388311.2	NM_018362		5	11	0	0	0	1	0	5	11				
SLC6A8	6535	broad.mit.edu	37	X	152957468	152957468	+	Missense_Mutation	SNP	C	C	A			TCGA-EL-A4JW-01A-11D-A257-08	TCGA-EL-A4JW-11A-12D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8f3ed41c-8506-4db3-b856-ca823d511258	9b411822-8132-4319-a3a5-0600a50a1c7d	g.chrX:152957468C>A	ENST00000253122.5	+	4	1159	c.683C>A	c.(682-684)cCa>cAa	p.P228Q	SLC6A8_ENST00000430077.2_Missense_Mutation_p.P113Q	NM_001142805.1|NM_005629.3	NP_001136277.1|NP_005620.1	P48029	SC6A8_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 8	228					cellular nitrogen compound metabolic process (GO:0034641)|creatine metabolic process (GO:0006600)|creatine transmembrane transport (GO:1902598)|creatine transport (GO:0015881)|muscle contraction (GO:0006936)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	creatine transmembrane transporter activity (GO:0005308)|creatine:sodium symporter activity (GO:0005309)|neurotransmitter:sodium symporter activity (GO:0005328)			breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(5)|pancreas(1)|upper_aerodigestive_tract(1)	13	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)				Creatine(DB00148)	CTGGAGGTGCCAGGGGCCCTC	0.612																																						ENST00000253122.5																			0				breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(5)|pancreas(1)|upper_aerodigestive_tract(1)	13						c.(682-684)cCa>cAa		solute carrier family 6 (neurotransmitter transporter), member 8	Creatine(DB00148)						31.0	22.0	26.0					X																	152957468		2197	4283	6480	SO:0001583	missense	6535				creatine metabolic process|muscle contraction	integral to plasma membrane	creatine:sodium symporter activity|neurotransmitter:sodium symporter activity	g.chrX:152957468C>A		CCDS14726.1, CCDS48190.1	Xq28	2013-07-19	2013-07-19		ENSG00000130821	ENSG00000130821		"""Solute carriers"""	11055	protein-coding gene	gene with protein product	"""creatine transporter"""	300036	"""solute carrier family 6 (neurotransmitter transporter, creatine), member 8"""			7774949	Standard	NM_001142805		Approved	CRTR, CT1	uc004fib.3	P48029	OTTHUMG00000024208	ENST00000253122.5:c.683C>A	X.37:g.152957468C>A	ENSP00000253122:p.Pro228Gln					SLC6A8_ENST00000430077.2_Missense_Mutation_p.P113Q	p.P228Q	NM_001142805.1|NM_005629.3	NP_001136277.1|NP_005620.1	P48029	SC6A8_HUMAN			4	1159	+	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)		228					B2KY47|B4DIA3|E9PFC0|Q13032|Q66I36	Missense_Mutation	SNP	ENST00000253122.5	37	c.683C>A	CCDS14726.1	.	.	.	.	.	.	.	.	.	.	c	15.61	2.885353	0.51908	.	.	ENSG00000130821	ENST00000253122;ENST00000430077	T;T	0.75938	-0.98;-0.98	4.09	4.09	0.47781	.	.	.	.	.	T	0.68851	0.3046	L	0.58810	1.83	0.36146	D	0.847109	B;P;B	0.35139	0.129;0.486;0.131	B;B;B	0.36030	0.091;0.216;0.091	T	0.75510	-0.3292	9	0.54805	T	0.06	.	8.4116	0.32646	0.0:0.8861:0.0:0.1139	.	228;247;228	D3DWV2;Q59EV7;P48029	.;.;SC6A8_HUMAN	Q	228;113	ENSP00000253122:P228Q;ENSP00000403041:P113Q	ENSP00000253122:P228Q	P	+	2	0	SLC6A8	152610662	0.003000	0.15002	0.990000	0.47175	0.982000	0.71751	0.986000	0.29590	1.878000	0.54408	0.529000	0.55759	CCA		0.612	SLC6A8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061003.1			11	15	1	0	5.50884e-06	1	5.87609e-06	11	15				
LRRC37A5P	652972	broad.mit.edu	37	9	114371493	114371493	+	RNA	SNP	C	C	T	rs12351897	byFrequency	TCGA-EL-A4JW-01A-11D-A257-08	TCGA-EL-A4JW-11A-12D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8f3ed41c-8506-4db3-b856-ca823d511258	9b411822-8132-4319-a3a5-0600a50a1c7d	g.chr9:114371493C>T	ENST00000374304.1	-	0	306							Q49AS3	L37A5_HUMAN	leucine rich repeat containing 37, member A5, pseudogene																		CTTCTCACATCGTTGTTGGGG	0.502													C|||	1845	0.368411	0.4448	0.5	5008	,	,		23453	0.4474		0.2266	False		,,,				2504	0.2362					ENST00000374304.1																			0																																																			0							g.chr9:114371493C>T	BC031236		9q31.3	2012-10-16	2012-03-07	2012-03-07	ENSG00000204173	ENSG00000204173			23369	pseudogene	pseudogene			"""chromosome 9 open reading frame 29"""	C9orf29			Standard	NR_034087		Approved		uc022bly.1	Q49AS3	OTTHUMG00000020494		9.37:g.114371493C>T														0	306	-								Q5JVP0	RNA	SNP	ENST00000374304.1	37			773	0.35393772893772896	194	0.3943089430894309	169	0.46685082872928174	227	0.3968531468531469	183	0.24142480211081793	c	0.736	-0.778241	0.02929	.	.	ENSG00000204173	ENST00000374306;ENST00000536054	.	.	.	0.822	-0.181	0.13291	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.22996	N	0.998455	.	.	.	.	.	.	T	0.47420	-0.9119	4	0.14252	T	0.57	.	3.5499	0.07843	0.0:0.7029:0.0:0.2971	rs12351897;rs58946173	.	.	.	N	39;31	.	ENSP00000363425:D39N	D	-	1	0	C9orf29	113411314	0.002000	0.14202	0.006000	0.13384	0.002000	0.02628	0.617000	0.24359	-0.064000	0.13043	-0.844000	0.03045	GAT		0.502	LRRC37A5P-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000053655.2	NR_034087		9	83	0	0	0	1	0	9	83				
CYP4F8	11283	broad.mit.edu	37	19	15729056	15729056	+	RNA	SNP	C	C	G	rs714772	byFrequency	TCGA-EL-A4JW-01A-11D-A257-08	TCGA-EL-A4JW-11A-12D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8f3ed41c-8506-4db3-b856-ca823d511258	9b411822-8132-4319-a3a5-0600a50a1c7d	g.chr19:15729056C>G	ENST00000441682.2	+	0	407							P98187	CP4F8_HUMAN	cytochrome P450, family 4, subfamily F, polypeptide 8						icosanoid metabolic process (GO:0006690)|prostaglandin metabolic process (GO:0006693)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	alkane 1-monooxygenase activity (GO:0018685)|aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(14)|skin(1)	26						TACTCAGCCCCTTCCTTCCTG	0.537													.|||	1603	0.320088	0.3472	0.4164	5008	,	,		20826	0.4643		0.1938	False		,,,				2504	0.1963					ENST00000441682.2																			0				breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(14)|skin(1)	26								cytochrome P450, family 4, subfamily F, polypeptide 8																																						11283				prostaglandin metabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	alkane 1-monooxygenase activity|aromatase activity|electron carrier activity|heme binding|oxygen binding|protein binding	g.chr19:15729056C>G	AF133298	CCDS74303.1	19p13.12	2013-11-11	2003-01-14		ENSG00000186526	ENSG00000186526		"""Cytochrome P450s"""	2648	protein-coding gene	gene with protein product		611545	"""cytochrome P450, subfamily IVF, polypeptide 8"""			10405341	Standard	NM_007253		Approved		uc002nbi.3	P98187	OTTHUMG00000182386		19.37:g.15729056C>G										P98187	CP4F8_HUMAN			0	407	+									RNA	SNP	ENST00000441682.2	37																																																																																						0.537	CYP4F8-201	KNOWN	basic	processed_transcript	processed_transcript		NM_007253		4	29	0	0	0	1	0	4	29				
DOCK3	1795	broad.mit.edu	37	3	51418794	51418794	+	Missense_Mutation	SNP	A	A	C			TCGA-EL-A4JW-01A-11D-A257-08	TCGA-EL-A4JW-11A-12D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8f3ed41c-8506-4db3-b856-ca823d511258	9b411822-8132-4319-a3a5-0600a50a1c7d	g.chr3:51418794A>C	ENST00000266037.9	+	53	5920	c.5897A>C	c.(5896-5898)gAc>gCc	p.D1966A		NM_004947.4	NP_004938.1	Q8IZD9	DOCK3_HUMAN	dedicator of cytokinesis 3	1966					small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	guanyl-nucleotide exchange factor activity (GO:0005085)			breast(2)|cervix(1)|endometrium(10)|kidney(4)|lung(22)|prostate(5)|urinary_tract(1)	45				BRCA - Breast invasive adenocarcinoma(193;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00449)|Kidney(197;0.00518)		ATCCCTCAGGACCCCATGGAC	0.677																																						ENST00000266037.9																			0				breast(2)|cervix(1)|endometrium(10)|kidney(4)|lung(22)|prostate(5)|urinary_tract(1)	45						c.(5896-5898)gAc>gCc		dedicator of cytokinesis 3							46.0	54.0	51.0					3																	51418794		2130	4233	6363	SO:0001583	missense	1795					cytoplasm	GTP binding|GTPase binding|guanyl-nucleotide exchange factor activity|SH3 domain binding	g.chr3:51418794A>C	AB002297	CCDS46835.1	3p21	2008-02-01			ENSG00000088538	ENSG00000088538			2989	protein-coding gene	gene with protein product		603123	"""dedicator of cyto-kinesis 3"""			9205841	Standard	NM_004947		Approved	KIAA0299, MOCA, PBP	uc011bds.2	Q8IZD9	OTTHUMG00000156892	ENST00000266037.9:c.5897A>C	3.37:g.51418794A>C	ENSP00000266037:p.Asp1966Ala						p.D1966A	NM_004947.4	NP_004938.1	Q8IZD9	DOCK3_HUMAN		BRCA - Breast invasive adenocarcinoma(193;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00449)|Kidney(197;0.00518)	53	5920	+			1966					O15017	Missense_Mutation	SNP	ENST00000266037.9	37	c.5897A>C	CCDS46835.1	.	.	.	.	.	.	.	.	.	.	A	12.79	2.042618	0.35989	.	.	ENSG00000088538	ENST00000266037	T	0.04654	3.58	6.17	6.17	0.99709	.	0.107759	0.64402	D	0.000009	T	0.05273	0.0140	L	0.36672	1.1	0.40513	D	0.980752	B	0.22003	0.063	B	0.22386	0.039	T	0.35151	-0.9800	10	0.08599	T	0.76	.	15.3933	0.74767	1.0:0.0:0.0:0.0	.	1966	Q8IZD9	DOCK3_HUMAN	A	1966	ENSP00000266037:D1966A	ENSP00000266037:D1966A	D	+	2	0	DOCK3	51393834	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	4.732000	0.62029	2.371000	0.80710	0.533000	0.62120	GAC		0.677	DOCK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346478.5	NM_004947		9	32	0	0	0	1	0	9	32				
RRN3P2	653390	broad.mit.edu	37	16	29110458	29110458	+	RNA	SNP	T	T	C	rs561841139		TCGA-EL-A4JW-01A-11D-A257-08	TCGA-EL-A4JW-11A-12D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8f3ed41c-8506-4db3-b856-ca823d511258	9b411822-8132-4319-a3a5-0600a50a1c7d	g.chr16:29110458T>C	ENST00000564580.1	+	0	1131							A6NIE6	RN3P2_HUMAN	RNA polymerase I transcription factor homolog (S. cerevisiae) pseudogene 2									p.W375R(25)									GAATTTTGAGTGGATAGTGAT	0.328																																						ENST00000564580.1																			25	Substitution - Missense(25)	p.W375R(25)	endometrium(19)|kidney(4)|prostate(2)																																																0							g.chr16:29110458T>C			16p11.2	2011-12-02			ENSG00000103472	ENSG00000103472			37619	pseudogene	pseudogene							Standard	NR_003369		Approved		uc002dsf.4	A6NIE6			16.37:g.29110458T>C														0	1131	+									RNA	SNP	ENST00000564580.1	37			.	.	.	.	.	.	.	.	.	.	N	5.632	0.301362	0.10678	.	.	ENSG00000103472	ENST00000427965	.	.	.	1.93	1.93	0.25924	.	0.000000	0.64402	N	0.000001	T	0.11239	0.0274	.	.	.	.	.	.	.	.	.	.	.	.	T	0.29701	-1.0003	5	0.02654	T	1	.	2.7527	0.05285	0.2724:0.5536:0.0:0.174	.	.	.	.	R	375	.	ENSP00000398611:W375R	W	+	1	0	AC009093.1	29017959	1.000000	0.71417	0.564000	0.28396	0.423000	0.31445	3.439000	0.52878	0.163000	0.19507	-1.160000	0.01791	TGG		0.328	RRN3P2-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000433243.1	NR_003369		5	49	0	0	0	1	0	5	49				
UQCRC1	7384	broad.mit.edu	37	3	48638425	48638425	+	Missense_Mutation	SNP	T	T	C			TCGA-EL-A4JW-01A-11D-A257-08	TCGA-EL-A4JW-11A-12D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8f3ed41c-8506-4db3-b856-ca823d511258	9b411822-8132-4319-a3a5-0600a50a1c7d	g.chr3:48638425T>C	ENST00000203407.5	-	8	1365	c.949A>G	c.(949-951)Act>Gct	p.T317A		NM_003365.2	NP_003356.2	P31930	QCR1_HUMAN	ubiquinol-cytochrome c reductase core protein I	317					aerobic respiration (GO:0009060)|cellular metabolic process (GO:0044237)|hydrogen ion transmembrane transport (GO:1902600)|mitochondrial electron transport, ubiquinol to cytochrome c (GO:0006122)|oxidation-reduction process (GO:0055114)|oxidative phosphorylation (GO:0006119)|respiratory electron transport chain (GO:0022904)|response to activity (GO:0014823)|response to alkaloid (GO:0043279)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain (GO:0005746)|mitochondrial respiratory chain complex III (GO:0005750)|mitochondrion (GO:0005739)	metal ion binding (GO:0046872)|ubiquinol-cytochrome-c reductase activity (GO:0008121)			breast(1)|endometrium(2)|large_intestine(2)|lung(2)|ovary(2)|pancreas(1)|prostate(4)|skin(1)|urinary_tract(1)	16				BRCA - Breast invasive adenocarcinoma(193;0.000293)|KIRC - Kidney renal clear cell carcinoma(197;0.00551)|Kidney(197;0.00621)		CCACCATAAGTGCAGTCATAG	0.622																																					NSCLC(81;1112 1427 27031 32409 45529)	ENST00000203407.5																			0				breast(1)|endometrium(2)|large_intestine(2)|lung(2)|ovary(2)|pancreas(1)|prostate(4)|skin(1)|urinary_tract(1)	16						c.(949-951)Act>Gct		ubiquinol-cytochrome c reductase core protein I	Atovaquone(DB01117)						52.0	47.0	48.0					3																	48638425		2203	4300	6503	SO:0001583	missense	7384				aerobic respiration|proteolysis		metalloendopeptidase activity|ubiquinol-cytochrome-c reductase activity|zinc ion binding	g.chr3:48638425T>C	BC009586	CCDS2774.1	3p21	2011-07-04			ENSG00000010256	ENSG00000010256	1.10.2.2	"""Mitochondrial respiratory chain complex / Complex III"""	12585	protein-coding gene	gene with protein product		191328				8407948	Standard	NM_003365		Approved	D3S3191, QCR1, UQCR1	uc003cub.1	P31930	OTTHUMG00000133539	ENST00000203407.5:c.949A>G	3.37:g.48638425T>C	ENSP00000203407:p.Thr317Ala						p.T317A	NM_003365.2	NP_003356.2	P31930	QCR1_HUMAN		BRCA - Breast invasive adenocarcinoma(193;0.000293)|KIRC - Kidney renal clear cell carcinoma(197;0.00551)|Kidney(197;0.00621)	8	1365	-			317					B2R7R8|Q96DD2	Missense_Mutation	SNP	ENST00000203407.5	37	c.949A>G	CCDS2774.1	.	.	.	.	.	.	.	.	.	.	T	13.80	2.345514	0.41498	.	.	ENSG00000010256	ENST00000203407	T	0.10763	2.84	5.72	5.72	0.89469	Peptidase M16, C-terminal (1);Peptidase M16, core (1);Metalloenzyme, LuxS/M16 peptidase-like, metal-binding (1);	0.000000	0.85682	D	0.000000	T	0.24967	0.0606	L	0.42744	1.35	0.58432	D	0.999997	B;D	0.69078	0.035;0.997	B;D	0.80764	0.057;0.994	T	0.01440	-1.1354	10	0.25106	T	0.35	-26.1093	15.9994	0.80280	0.0:0.0:0.0:1.0	.	202;317	B4DUL5;P31930	.;QCR1_HUMAN	A	317	ENSP00000203407:T317A	ENSP00000203407:T317A	T	-	1	0	UQCRC1	48613429	1.000000	0.71417	0.999000	0.59377	0.971000	0.66376	4.094000	0.57721	2.187000	0.69744	0.459000	0.35465	ACT		0.622	UQCRC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257517.1	NM_003365		14	26	0	0	0	1	0	14	26				
BRAF	673	broad.mit.edu	37	7	140453136	140453136	+	Missense_Mutation	SNP	A	A	T	rs121913377|rs113488022|rs121913227|rs397516897		TCGA-EL-A4JW-01A-11D-A257-08	TCGA-EL-A4JW-11A-12D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8f3ed41c-8506-4db3-b856-ca823d511258	9b411822-8132-4319-a3a5-0600a50a1c7d	g.chr7:140453136A>T	ENST00000288602.6	-	15	1859	c.1799T>A	c.(1798-1800)gTg>gAg	p.V600E		NM_004333.4	NP_004324.2	P15056	BRAF_HUMAN	B-Raf proto-oncogene, serine/threonine kinase	600	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		V -> D (in a melanoma cell line; requires 2 nucleotide substitutions). {ECO:0000269|PubMed:12068308}.|V -> E (in CRC; also found in sarcoma, metastatic melanoma, ovarian serous carcinoma, pilocytic astrocytoma; somatic mutation; most common mutation; constitutive and elevated kinase activity; efficiently induces cell transformation; suppression of mutation in melanoma causes growth arrest and promotes apoptosis; loss of regulation by PMRT5). {ECO:0000269|PubMed:12068308, ECO:0000269|PubMed:12198537, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:23263490, ECO:0000269|PubMed:24455489}.		activation of MAPKK activity (GO:0000186)|CD4-positive, alpha-beta T cell differentiation (GO:0043367)|cellular response to calcium ion (GO:0071277)|cellular response to drug (GO:0035690)|fibroblast growth factor receptor signaling pathway (GO:0008543)|long-term synaptic potentiation (GO:0060291)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of fibroblast migration (GO:0010764)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of synaptic vesicle exocytosis (GO:2000301)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of gene expression (GO:0010628)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive T cell selection (GO:0043368)|protein heterooligomerization (GO:0051291)|protein phosphorylation (GO:0006468)|regulation of cell proliferation (GO:0042127)|response to cAMP (GO:0051591)|response to epidermal growth factor (GO:0070849)|response to peptide hormone (GO:0043434)|small GTPase mediated signal transduction (GO:0007264)|somatic stem cell maintenance (GO:0035019)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	cell body (GO:0044297)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.V600E(15453)|p.V600K(252)|p.V600R(44)|p.V600D(16)|p.V600A(12)|p.V600_K601>E(12)|p.V600G(11)|p.T599_R603>I(2)|p.V600Q(2)|p.V600_S605>EK(1)|p.V600_S605>DV(1)|p.V600_S605>D(1)|p.T599_V600insDFGLAT(1)	SLC45A3/BRAF(2)|AGTRAP/BRAF(2)|FAM131B_ENST00000443739/BRAF(7)|AKAP9_ENST00000356239/BRAF(10)|KIAA1549/BRAF(703)|FCHSD1/BRAF(2)	NS(588)|adrenal_gland(3)|autonomic_ganglia(3)|biliary_tract(29)|bone(7)|breast(21)|central_nervous_system(99)|cervix(6)|endometrium(33)|eye(72)|gastrointestinal_tract_(site_indeterminate)(2)|genital_tract(4)|haematopoietic_and_lymphoid_tissue(436)|kidney(3)|large_intestine(6953)|liver(17)|lung(192)|oesophagus(4)|ovary(275)|pancreas(15)|pituitary(1)|prostate(25)|salivary_gland(1)|skin(6285)|small_intestine(12)|soft_tissue(40)|stomach(11)|testis(7)|thyroid(12220)|upper_aerodigestive_tract(13)|urinary_tract(3)	27380	Melanoma(164;0.00956)				Dabrafenib(DB08912)|Regorafenib(DB08896)|Sorafenib(DB00398)|Vemurafenib(DB08881)	TCGAGATTTCACTGTAGCTAG	0.368	V600D(K029AX_SKIN)|V600D(WM115_SKIN)|V600D(WM2664_SKIN)|V600E(8505C_THYROID)|V600E(A101D_SKIN)|V600E(A2058_SKIN)|V600E(A375_SKIN)|V600E(A673_BONE)|V600E(AM38_CENTRAL_NERVOUS_SYSTEM)|V600E(BCPAP_THYROID)|V600E(BHT101_THYROID)|V600E(BT474_BREAST)|V600E(C32_SKIN)|V600E(CL34_LARGE_INTESTINE)|V600E(COLO205_LARGE_INTESTINE)|V600E(COLO679_SKIN)|V600E(COLO741_SKIN)|V600E(COLO783_SKIN)|V600E(COLO800_SKIN)|V600E(COLO818_SKIN)|V600E(COLO829_SKIN)|V600E(COLO849_SKIN)|V600E(DBTRG05MG_CENTRAL_NERVOUS_SYSTEM)|V600E(DU4475_BREAST)|V600E(ES2_OVARY)|V600E(G361_SKIN)|V600E(GCT_SOFT_TISSUE)|V600E(HS294T_SKIN)|V600E(HS695T_SKIN)|V600E(HS939T_SKIN)|V600E(IGR1_SKIN)|V600E(IGR37_SKIN)|V600E(IGR39_SKIN)|V600E(K029AX_SKIN)|V600E(KG1C_CENTRAL_NERVOUS_SYSTEM)|V600E(LOXIMVI_SKIN)|V600E(MALME3M_SKIN)|V600E(MELHO_SKIN)|V600E(OUMS23_LARGE_INTESTINE)|V600E(RKO_LARGE_INTESTINE)|V600E(RPMI7951_SKIN)|V600E(RVH421_SKIN)|V600E(SH4_SKIN)|V600E(SIGM5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|V600E(SKHEP1_LIVER)|V600E(SKMEL24_SKIN)|V600E(SKMEL28_SKIN)|V600E(SKMEL5_SKIN)|V600E(SW1417_LARGE_INTESTINE)|V600E(UACC257_SKIN)|V600E(UACC62_SKIN)|V600E(WM793_SKIN)|V600E(WM88_SKIN)|V600E(WM983B_SKIN)	61	"""Mis, T, O"""	"""AKAP9, KIAA1549"""	"""melanoma, colorectal, papillary thyroid, borderline ov, Non small-cell lung cancer (NSCLC), cholangiocarcinoma, pilocytic astrocytoma"""		Cardio-facio-cutaneous syndrome		Cardiofaciocutaneous syndrome																												Colon(40;35 892 2973 5743 27438)	ENST00000288602.6	V600D(K029AX_SKIN)|V600D(WM115_SKIN)|V600D(WM2664_SKIN)|V600E(8505C_THYROID)|V600E(A101D_SKIN)|V600E(A2058_SKIN)|V600E(A375_SKIN)|V600E(A673_BONE)|V600E(AM38_CENTRAL_NERVOUS_SYSTEM)|V600E(BCPAP_THYROID)|V600E(BHT101_THYROID)|V600E(BT474_BREAST)|V600E(C32_SKIN)|V600E(CL34_LARGE_INTESTINE)|V600E(COLO205_LARGE_INTESTINE)|V600E(COLO679_SKIN)|V600E(COLO741_SKIN)|V600E(COLO783_SKIN)|V600E(COLO800_SKIN)|V600E(COLO818_SKIN)|V600E(COLO829_SKIN)|V600E(COLO849_SKIN)|V600E(DBTRG05MG_CENTRAL_NERVOUS_SYSTEM)|V600E(DU4475_BREAST)|V600E(ES2_OVARY)|V600E(G361_SKIN)|V600E(GCT_SOFT_TISSUE)|V600E(HS294T_SKIN)|V600E(HS695T_SKIN)|V600E(HS939T_SKIN)|V600E(IGR1_SKIN)|V600E(IGR37_SKIN)|V600E(IGR39_SKIN)|V600E(K029AX_SKIN)|V600E(KG1C_CENTRAL_NERVOUS_SYSTEM)|V600E(LOXIMVI_SKIN)|V600E(MALME3M_SKIN)|V600E(MELHO_SKIN)|V600E(OUMS23_LARGE_INTESTINE)|V600E(RKO_LARGE_INTESTINE)|V600E(RPMI7951_SKIN)|V600E(RVH421_SKIN)|V600E(SH4_SKIN)|V600E(SIGM5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|V600E(SKHEP1_LIVER)|V600E(SKMEL24_SKIN)|V600E(SKMEL28_SKIN)|V600E(SKMEL5_SKIN)|V600E(SW1417_LARGE_INTESTINE)|V600E(UACC257_SKIN)|V600E(UACC62_SKIN)|V600E(WM793_SKIN)|V600E(WM88_SKIN)|V600E(WM983B_SKIN)	61		Dom	yes		7	7q34	673	"""Mis, T, O"""	v-raf murine sarcoma viral oncogene homolog B1	yes	Cardio-facio-cutaneous syndrome	E	"""AKAP9, KIAA1549"""		"""melanoma, colorectal, papillary thyroid, borderline ov, Non small-cell lung cancer (NSCLC), cholangiocarcinoma, pilocytic astrocytoma"""	SLC45A3/BRAF(2)|AGTRAP/BRAF(2)|FAM131B_ENST00000443739/BRAF(7)|AKAP9_ENST00000356239/BRAF(10)|KIAA1549/BRAF(703)|FCHSD1/BRAF(2)	15808	Substitution - Missense(15790)|Complex - deletion inframe(17)|Insertion - In frame(1)	p.V600E(15453)|p.V600K(252)|p.V600R(44)|p.V600D(16)|p.V600A(12)|p.V600_K601>E(12)|p.V600G(11)|p.T599_R603>I(2)|p.V600Q(2)|p.V600_S605>EK(1)|p.V600_S605>DV(1)|p.V600_S605>D(1)|p.T599_V600insDFGLAT(1)	thyroid(7476)|skin(3822)|large_intestine(3288)|NS(360)|haematopoietic_and_lymphoid_tissue(336)|ovary(211)|lung(58)|eye(57)|central_nervous_system(53)|soft_tissue(30)|biliary_tract(18)|liver(17)|prostate(13)|breast(10)|upper_aerodigestive_tract(9)|endometrium(8)|pancreas(8)|testis(7)|small_intestine(7)|genital_tract(4)|stomach(4)|bone(3)|autonomic_ganglia(2)|oesophagus(2)|urinary_tract(2)|adrenal_gland(2)|pituitary(1)	NS(588)|adrenal_gland(3)|autonomic_ganglia(3)|biliary_tract(29)|bone(7)|breast(21)|central_nervous_system(99)|cervix(6)|endometrium(33)|eye(72)|gastrointestinal_tract_(site_indeterminate)(2)|genital_tract(4)|haematopoietic_and_lymphoid_tissue(436)|kidney(3)|large_intestine(6953)|liver(17)|lung(192)|oesophagus(4)|ovary(275)|pancreas(15)|pituitary(1)|prostate(25)|salivary_gland(1)|skin(6285)|small_intestine(12)|soft_tissue(40)|stomach(11)|testis(7)|thyroid(12220)|upper_aerodigestive_tract(13)|urinary_tract(3)	27380						c.(1798-1800)gTg>gAg		v-raf murine sarcoma viral oncogene homolog B	Sorafenib(DB00398)						112.0	104.0	107.0					7																	140453136		2203	4300	6503	SO:0001583	missense	673	Cardiofaciocutaneous syndrome	Familial Cancer Database	CFC, CFCS	activation of MAPKK activity|anti-apoptosis|nerve growth factor receptor signaling pathway|organ morphogenesis|positive regulation of peptidyl-serine phosphorylation|small GTPase mediated signal transduction|synaptic transmission	cytosol|nucleus|plasma membrane	ATP binding|metal ion binding	g.chr7:140453136A>T	M95712	CCDS5863.1	7q34	2014-09-17	2014-06-26		ENSG00000157764	ENSG00000157764			1097	protein-coding gene	gene with protein product		164757	"""v-raf murine sarcoma viral oncogene homolog B"""			2284096, 1565476	Standard	NM_004333		Approved	BRAF1	uc003vwc.4	P15056	OTTHUMG00000157457	ENST00000288602.6:c.1799T>A	7.37:g.140453136A>T	ENSP00000288602:p.Val600Glu						p.V600E	NM_004333.4	NP_004324.2	P15056	BRAF_HUMAN			15	1859	-	Melanoma(164;0.00956)		600		V -> D (in a melanoma cell line; requires 2 nucleotide substitutions).|V -> E (in sarcoma, colorectal adenocarcinoma, metastatic melanoma, ovarian serous carcinoma, pilocytic astrocytoma; somatic mutation; most common mutation; constitutive and elevated kinase activity; efficiently induces cell transformation; suppression of mutation in melanoma causes growth arrest and promotes apoptosis).	Protein kinase.		A4D1T4|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q13878|Q3MIN6|Q9UDP8|Q9Y6T3	Missense_Mutation	SNP	ENST00000288602.6	37	c.1799T>A	CCDS5863.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	24.0|24.0	4.486113|4.486113	0.84854|0.84854	.|.	.|.	ENSG00000157764|ENSG00000157764	ENST00000288602|ENST00000496384	D|.	0.81739|.	-1.53|.	5.65|5.65	5.65|5.65	0.86999|0.86999	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|.	0.61565|.	0.2357|.	L|L	0.42245|0.42245	1.32|1.32	0.80722|0.80722	D|D	1|1	D|.	0.55385|.	0.971|.	D|.	0.66351|.	0.943|.	T|.	0.58160|.	-0.7685|.	10|.	0.87932|.	D|.	0|.	.|.	15.9326|15.9326	0.79675|0.79675	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	600|.	P15056|.	BRAF_HUMAN|.	E|R	600|208	ENSP00000288602:V600E|.	ENSP00000288602:V600E|.	V|X	-|-	2|1	0|0	BRAF|BRAF	140099605|140099605	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	9.197000|9.197000	0.94985|0.94985	2.169000|2.169000	0.68431|0.68431	0.529000|0.529000	0.55759|0.55759	GTG|TGA		0.368	BRAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348886.1	NM_004333		13	48	0	0	0	1	0	13	48				
CELF5	60680	broad.mit.edu	37	19	3281319	3281319	+	Missense_Mutation	SNP	C	C	G			TCGA-EL-A4JW-01A-11D-A257-08	TCGA-EL-A4JW-11A-12D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8f3ed41c-8506-4db3-b856-ca823d511258	9b411822-8132-4319-a3a5-0600a50a1c7d	g.chr19:3281319C>G	ENST00000292672.2	+	6	763	c.726C>G	c.(724-726)agC>agG	p.S242R	CELF5_ENST00000541430.2_Missense_Mutation_p.S242R	NM_021938.3	NP_068757.2	Q8N6W0	CELF5_HUMAN	CUGBP, Elav-like family member 5	242					mRNA processing (GO:0006397)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			kidney(1)|large_intestine(2)|lung(7)|ovary(2)|skin(1)	13						TGCCCTTCAGCCCCTACAGTG	0.642																																						ENST00000541430.2																			0				kidney(1)|large_intestine(2)|lung(7)|ovary(2)|skin(1)	13						c.(724-726)agC>agG		CUGBP, Elav-like family member 5							98.0	87.0	90.0					19																	3281319		2203	4300	6503	SO:0001583	missense	60680				mRNA processing	cytoplasm|nucleus	nucleotide binding|RNA binding	g.chr19:3281319C>G	AF248649	CCDS12106.1, CCDS54197.1	19p13	2013-02-12	2010-02-19	2010-02-19		ENSG00000161082		"""RNA binding motif (RRM) containing"""	14058	protein-coding gene	gene with protein product		612680	"""Bruno (Drosophila) -like 5, RNA binding protein"", ""bruno-like 5, RNA binding protein (Drosophila)"""	BRUNOL5		10893231	Standard	NM_001172673		Approved		uc002lxm.3	Q8N6W0		ENST00000292672.2:c.726C>G	19.37:g.3281319C>G	ENSP00000292672:p.Ser242Arg					CELF5_ENST00000292672.2_Missense_Mutation_p.S242R	p.S242R	NM_001172673.1	NP_001166144.1	Q8N6W0	CELF5_HUMAN			6	762	+			242					D6W614|O75253|Q59GP2|Q86VW6|Q9BZC0|Q9NR86	Missense_Mutation	SNP	ENST00000292672.2	37	c.726C>G	CCDS12106.1	.	.	.	.	.	.	.	.	.	.	C	17.65	3.442570	0.63067	.	.	ENSG00000161082	ENST00000292672;ENST00000541430;ENST00000334293	T;T;T	0.28255	2.35;1.77;1.62	3.46	2.39	0.29439	.	0.153984	0.56097	D	0.000023	T	0.43389	0.1245	L	0.59436	1.845	0.39926	D	0.97422	P;D;B	0.71674	0.725;0.998;0.006	B;D;B	0.66847	0.391;0.947;0.005	T	0.42949	-0.9421	10	0.72032	D	0.01	-6.7708	6.3239	0.21232	0.0:0.762:0.0:0.2379	.	128;242;242	B4DFI3;Q8N6W0-2;Q8N6W0	.;.;CELF5_HUMAN	R	242;242;128	ENSP00000292672:S242R;ENSP00000443498:S242R;ENSP00000335182:S128R	ENSP00000292672:S242R	S	+	3	2	CELF5	3232319	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	1.603000	0.36794	1.655000	0.50712	0.313000	0.20887	AGC		0.642	CELF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452574.1	NM_021938		14	71	0	0	0	1	0	14	71				
RPL18A	6142	broad.mit.edu	37	19	17973820	17973820	+	Missense_Mutation	SNP	C	C	T			TCGA-EL-A4JW-01A-11D-A257-08	TCGA-EL-A4JW-11A-12D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8f3ed41c-8506-4db3-b856-ca823d511258	9b411822-8132-4319-a3a5-0600a50a1c7d	g.chr19:17973820C>T	ENST00000222247.5	+	4	503	c.422C>T	c.(421-423)gCt>gTt	p.A141V	RPL18A_ENST00000600147.1_Splice_Site|SNORA68_ENST00000384437.1_RNA|RPL18A_ENST00000599870.1_Missense_Mutation_p.A112V|RPL18A_ENST00000599898.1_Missense_Mutation_p.A102V	NM_000980.3	NP_000971.1	Q02543	RL18A_HUMAN	ribosomal protein L18a	141					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			NS(1)|endometrium(1)|kidney(1)|large_intestine(1)|upper_aerodigestive_tract(1)	5						CGCCGGCCGGCTGTCAAGCAG	0.677																																						ENST00000599870.1																			0				NS(1)|endometrium(1)|kidney(1)|large_intestine(1)|upper_aerodigestive_tract(1)	5						c.(334-336)gCt>gTt		ribosomal protein L18a							20.0	23.0	22.0					19																	17973820		2202	4299	6501	SO:0001583	missense	6142				endocrine pancreas development|translational elongation|translational termination|viral transcription	cytosolic large ribosomal subunit	protein binding|RNA binding|structural constituent of ribosome	g.chr19:17973820C>T	AB007175	CCDS12367.1	19p13.11	2011-04-06			ENSG00000105640	ENSG00000105640		"""L ribosomal proteins"""	10311	protein-coding gene	gene with protein product	"""60S ribosomal protein L18a"", ""ribosomal protein L18a-like protein"""	604178				9582194	Standard	NM_000980		Approved	L18A	uc002nhp.3	Q02543		ENST00000222247.5:c.422C>T	19.37:g.17973820C>T	ENSP00000222247:p.Ala141Val					RPL18A_ENST00000600147.1_Splice_Site|RPL18A_ENST00000599898.1_Missense_Mutation_p.A102V|RPL18A_ENST00000222247.5_Missense_Mutation_p.A141V	p.A112V			Q02543	RL18A_HUMAN			3	934	+			141						Missense_Mutation	SNP	ENST00000222247.5	37	c.335C>T	CCDS12367.1	.	.	.	.	.	.	.	.	.	.	C	8.734	0.917319	0.17982	.	.	ENSG00000105640	ENST00000222247	.	.	.	4.71	4.71	0.59529	.	0.055575	0.64402	D	0.000001	T	0.60090	0.2242	M	0.64997	1.995	0.80722	D	1	B	0.17268	0.021	B	0.22601	0.04	T	0.57027	-0.7881	8	.	.	.	.	15.5239	0.75887	0.0:1.0:0.0:0.0	.	141	Q02543	RL18A_HUMAN	V	141	.	.	A	+	2	0	RPL18A	17834820	1.000000	0.71417	0.265000	0.24526	0.175000	0.22909	7.688000	0.84153	2.337000	0.79520	0.460000	0.39030	GCT		0.677	RPL18A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466679.1	NM_000980		15	21	0	0	0	1	0	15	21				
GPR149	344758	broad.mit.edu	37	3	154138835	154138835	+	Frame_Shift_Del	DEL	G	G	-			TCGA-EL-A4JW-01A-11D-A257-08	TCGA-EL-A4JW-11A-12D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8f3ed41c-8506-4db3-b856-ca823d511258	9b411822-8132-4319-a3a5-0600a50a1c7d	g.chr3:154138835delG	ENST00000389740.2	-	3	1715	c.1616delC	c.(1615-1617)cctfs	p.P539fs		NM_001038705.1	NP_001033794.1	Q86SP6	GP149_HUMAN	G protein-coupled receptor 149	539					antral ovarian follicle growth (GO:0001547)|estrous cycle phase (GO:0060206)|negative regulation of ovulation (GO:0060280)|preantral ovarian follicle growth (GO:0001546)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			autonomic_ganglia(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(22)|ovary(7)|prostate(1)|skin(1)|urinary_tract(2)	47			LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.173)			TACCTGACGAGGGGTTCTTTC	0.368																																						ENST00000389740.2																			0				autonomic_ganglia(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(22)|ovary(7)|prostate(1)|skin(1)|urinary_tract(2)	47						c.(1615-1617)ctfs		G protein-coupled receptor 149							56.0	50.0	52.0					3																	154138835		1828	4079	5907	SO:0001589	frameshift_variant	344758					integral to membrane|plasma membrane	G-protein coupled receptor activity	g.chr3:154138835delG	AY255534	CCDS43162.1	3q25.2	2012-08-21			ENSG00000174948	ENSG00000174948		"""GPCR / Class A : Orphans"""	23627	protein-coding gene	gene with protein product						12679517	Standard	NM_001038705		Approved	PGR10, IEDA	uc003faa.3	Q86SP6	OTTHUMG00000159131	ENST00000389740.2:c.1616delC	3.37:g.154138835delG	ENSP00000374390:p.Pro539fs						p.P539fs	NM_001038705.1	NP_001033794.1	Q86SP6	GP149_HUMAN	LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.173)		3	1715	-			539						Frame_Shift_Del	DEL	ENST00000389740.2	37	c.1616delC	CCDS43162.1																																																																																				0.368	GPR149-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353430.1	XM_293580		16	16						16	16	---	---	---	---
SNHG14	104472715	broad.mit.edu	37	15	25299376	25299376	+	RNA	DEL	A	A	-	rs537538276		TCGA-EL-A4JW-01A-11D-A257-08	TCGA-EL-A4JW-11A-12D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8f3ed41c-8506-4db3-b856-ca823d511258	9b411822-8132-4319-a3a5-0600a50a1c7d	g.chr15:25299376delA	ENST00000549804.2	+	0	98				SNHG14_ENST00000547292.1_RNA|SNORD116-2_ENST00000384274.1_RNA|SNORD116-1_ENST00000384335.1_RNA|SNORD116-3_ENST00000384287.1_RNA|RP11-701H24.10_ENST00000552781.1_RNA					small nucleolar RNA host gene 14 (non-protein coding)																		ATGAGTCCCCAAAAAAAACAT	0.493																																						ENST00000549804.2																			0																				195.0	183.0	187.0					15																	25299376		876	1991	2867			0							g.chr15:25299376delA			15q11.2	2014-01-17	2011-08-22	2011-08-22	ENSG00000224078	ENSG00000224078		"""Long non-coding RNAs"""	37462	non-coding RNA	RNA, long non-coding	"""non-protein coding RNA 214"""		"""UBE3A antisense RNA 1 (non-protein coding)"""	UBE3A-AS1		23771028	Standard			Approved	NCRNA00214, UBE3A-AS			OTTHUMG00000056661		15.37:g.25299376delA						SNORD116-2_ENST00000384274.1_RNA|SNHG14_ENST00000547292.1_RNA								0	98	+									RNA	DEL	ENST00000549804.2	37																																																																																						0.493	SNHG14-012	KNOWN	non_canonical_other|basic	antisense	processed_transcript	OTTHUMT00000408278.2			8	160						8	160	---	---	---	---
CTC-513N18.6	0	broad.mit.edu	37	19	20634038	20634039	+	lincRNA	DEL	TG	TG	-	rs144024329		TCGA-EL-A4JW-01A-11D-A257-08	TCGA-EL-A4JW-11A-12D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8f3ed41c-8506-4db3-b856-ca823d511258	9b411822-8132-4319-a3a5-0600a50a1c7d	g.chr19:20634038_20634039delTG	ENST00000598131.1	+	0	160																											TTAGTAAAAATGTGTGTGTGTG	0.401																																						ENST00000598131.1																			0																																																			0							g.chr19:20634038_20634039delTG																													19.37:g.20634048_20634049delTG														0	160	+									RNA	DEL	ENST00000598131.1	37																																																																																						0.401	CTC-513N18.6-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000463072.1			8	34						8	34	---	---	---	---
