#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
ACKR2	1238	broad.mit.edu	37	3	42906480	42906480	+	Silent	SNP	G	G	T			TCGA-DJ-A4V2-01A-11D-A257-08	TCGA-DJ-A4V2-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5c5ac429-f523-4c6c-b4d6-0de91d50a945	47627937-0a98-41cf-ac54-096a2900b4ae	g.chr3:42906480G>T	ENST00000422265.1	+	3	661	c.486G>T	c.(484-486)ctG>ctT	p.L162L	ACKR2_ENST00000442925.1_Silent_p.L162L|RP11-141M3.5_ENST00000471537.1_RNA|KRBOX1_ENST00000426937.1_Intron|CYP8B1_ENST00000437102.1_Intron|ACKR2_ENST00000273145.2_Silent_p.L162L	NM_001296.4	NP_001287.2	O00590	ACKR2_HUMAN	atypical chemokine receptor 2	162					chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|inflammatory response (GO:0006954)|multicellular organismal development (GO:0007275)|neutrophil activation (GO:0042119)|receptor-mediated endocytosis (GO:0006898)	actin filament (GO:0005884)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	C-C chemokine receptor activity (GO:0016493)|C-X-C chemokine receptor activity (GO:0016494)|chemokine receptor activity (GO:0004950)|scavenger receptor activity (GO:0005044)										CCAAGAGCCTGCTCCTTGCTA	0.537																																						uc003cme.3																			0				NS(1)|endometrium(1)|kidney(1)|large_intestine(10)|lung(10)|skin(2)|urinary_tract(1)	26						c.(484-486)ctG>ctT		Homo sapiens chemokine binding protein 2 (CCBP2), mRNA.							74.0	77.0	76.0					3																	42906480		2203	4300	6503	SO:0001819	synonymous_variant	1238				chemotaxis|immune response|multicellular organismal development	integral to plasma membrane	C-X-C chemokine receptor activity	g.chr3:42906480G>T	U94888	CCDS2706.1	3p21.3	2013-07-17	2013-07-16	2013-07-16	ENSG00000144648	ENSG00000144648		"""GPCR / Class A : Chemokine receptors : Atypical"""	1565	protein-coding gene	gene with protein product		602648	"""chemokine binding protein 2"""	CMKBR9, CCBP2		9364936, 9405404, 16148	Standard	NM_001296		Approved	CCR10, D6, CCR9	uc003cme.3	O00590	OTTHUMG00000133040	ENST00000422265.1:c.486G>T	3.37:g.42906480G>T			Somatic				CCBP2_uc003cmf.3_Silent_p.L162L|CCBP2_uc003cmg.3_Intron|CCBP2_uc021wwm.1_Silent_p.L162L	p.L162L	NM_001296	NP_001287	WXS	Illumina GAIIx	Phase_I	O00590	CCBP2_HUMAN		KIRC - Kidney renal clear cell carcinoma(284;0.241)	2	664	+			162					B2R8Y8|O00537|Q53YA1|Q86UN9|Q96A02	Silent	SNP	ENST00000422265.1	37	c.486G>T	CCDS2706.1																																																																																				0.537	ACKR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256645.2	NM_001296		30	73	0	0	0	1	0	30	73				
CLTCL1	8218	broad.mit.edu	37	22	19222058	19222058	+	Missense_Mutation	SNP	C	C	T			TCGA-DJ-A4V2-01A-11D-A257-08	TCGA-DJ-A4V2-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5c5ac429-f523-4c6c-b4d6-0de91d50a945	47627937-0a98-41cf-ac54-096a2900b4ae	g.chr22:19222058C>T	ENST00000263200.10	-	7	1213	c.1141G>A	c.(1141-1143)Gcc>Acc	p.A381T	CLTCL1_ENST00000353891.5_Missense_Mutation_p.A381T|CLTCL1_ENST00000427926.1_Missense_Mutation_p.A381T	NM_007098.3	NP_009029.3	P53675	CLH2_HUMAN	clathrin, heavy chain-like 1	381	Globular terminal domain.				anatomical structure morphogenesis (GO:0009653)|intracellular protein transport (GO:0006886)|mitotic nuclear division (GO:0007067)|positive regulation of glucose import (GO:0046326)|receptor-mediated endocytosis (GO:0006898)|signal transduction (GO:0007165)	clathrin coat of coated pit (GO:0030132)|clathrin coat of trans-Golgi network vesicle (GO:0030130)|clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|coated vesicle (GO:0030135)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|spindle (GO:0005819)|trans-Golgi network (GO:0005802)	signal transducer activity (GO:0004871)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(3)|cervix(2)|endometrium(9)|kidney(3)|large_intestine(11)|lung(9)|ovary(5)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49	Colorectal(54;0.0993)					GCAACTTTGGCGGCTTCAGCA	0.453			T	?	ALCL																																	uc021wle.1				Dom	yes		22	22q11.21	8218	T	"""clathrin, heavy polypeptide-like 1"""			L	?		ALCL		0				breast(2)|central_nervous_system(3)|cervix(2)|endometrium(9)|kidney(3)|large_intestine(11)|lung(9)|ovary(5)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49						c.(1141-1143)Gcc>Acc		Homo sapiens clathrin, heavy chain-like 1 (CLTCL1), transcript variant 1, mRNA.							44.0	44.0	44.0					22																	19222058		1893	4120	6013	SO:0001583	missense	8218				anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis	clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network	protein binding|signal transducer activity|structural molecule activity	g.chr22:19222058C>T		CCDS46662.1, CCDS54497.1, CCDS46662.2, CCDS54497.2	22q11.2	2008-06-10	2006-09-29		ENSG00000070371	ENSG00000070371			2093	protein-coding gene	gene with protein product		601273	"""clathrin, heavy polypeptide-like 1"""	CLTCL		8844170, 15133132	Standard	NM_007098		Approved	CLTD, CLH22, CHC22	uc021wle.1	P53675	OTTHUMG00000150109	ENST00000263200.10:c.1141G>A	22.37:g.19222058C>T	ENSP00000445677:p.Ala381Thr		Somatic				CLTCL1_uc021wld.1_Missense_Mutation_p.A381T|CLTCL1_uc021wlc.1_Missense_Mutation_p.A381T|CLTCL1_uc021wlf.1_Missense_Mutation_p.A381T|CLTCL1_uc011agw.1_Missense_Mutation_p.A381T	p.A381T	NM_007098	NP_009029	WXS	Illumina GAIIx	Phase_I	P53675	CLH2_HUMAN			6	1216	-	Colorectal(54;0.0993)		381			Globular terminal domain.		B7Z7U5|Q14017|Q15808|Q15809	Missense_Mutation	SNP	ENST00000263200.10	37	c.1141G>A	CCDS46662.1	.	.	.	.	.	.	.	.	.	.	C	20.3	3.973458	0.74246	.	.	ENSG00000070371	ENST00000353891;ENST00000263200;ENST00000427926	T;T;T	0.57907	0.37;0.37;0.37	3.29	3.29	0.37713	Armadillo-type fold (1);	0.079527	0.49305	D	0.000154	T	0.69396	0.3106	M	0.93197	3.39	0.80722	D	1	P;B	0.40970	0.734;0.233	P;B	0.46076	0.503;0.234	T	0.80306	-0.1438	10	0.66056	D	0.02	-9.9549	15.0953	0.72229	0.0:1.0:0.0:0.0	.	381;381	P53675-2;P53675	.;CLH2_HUMAN	T	381	ENSP00000439662:A381T;ENSP00000445677:A381T;ENSP00000441158:A381T	ENSP00000445677:A381T	A	-	1	0	CLTCL1	17602058	0.999000	0.42202	1.000000	0.80357	0.860000	0.49131	4.094000	0.57721	1.847000	0.53656	0.460000	0.39030	GCC		0.453	CLTCL1-001	KNOWN	non_canonical_genome_sequence_error|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316397.5	NM_007098		3	31	0	0	0	1	0	3	31				
GPR179	440435	broad.mit.edu	37	17	36486995	36486995	+	Silent	SNP	G	G	A			TCGA-DJ-A4V2-01A-11D-A257-08	TCGA-DJ-A4V2-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5c5ac429-f523-4c6c-b4d6-0de91d50a945	47627937-0a98-41cf-ac54-096a2900b4ae	g.chr17:36486995G>A	ENST00000342292.4	-	11	2477	c.2457C>T	c.(2455-2457)agC>agT	p.S819S	GPR179_ENST00000584976.1_5'Flank	NM_001004334.2	NP_001004334.2	Q6PRD1	GP179_HUMAN	G protein-coupled receptor 179	819					visual perception (GO:0007601)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(4)|cervix(2)|endometrium(9)|kidney(3)|large_intestine(16)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	60	Breast(7;2.97e-12)	Breast(25;0.0101)|Ovarian(249;0.15)				GGTTGTGGGCGCTGGCTGACC	0.652																																						uc002hpz.3																			0				breast(4)|cervix(2)|endometrium(9)|kidney(3)|large_intestine(16)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	60						c.(2455-2457)agC>agT		Homo sapiens G protein-coupled receptor 179 (GPR179), mRNA.							10.0	12.0	11.0					17																	36486995		1908	4091	5999	SO:0001819	synonymous_variant	440435					integral to membrane|plasma membrane	G-protein coupled receptor activity	g.chr17:36486995G>A		CCDS42308.1	17q21.1	2014-05-06	2006-02-16	2006-02-16	ENSG00000188888	ENSG00000277399		"""GPCR / Class C : Orphans"""	31371	protein-coding gene	gene with protein product		614515	"""GPR158-like 1"", ""GPR179"""	GPR158L1			Standard	NM_001004334		Approved	CSNB1E	uc002hpz.3	Q6PRD1	OTTHUMG00000188545	ENST00000342292.4:c.2457C>T	17.37:g.36486995G>A			Somatic					p.S819S	NM_001004334	NP_001004334	WXS	Illumina GAIIx	Phase_I	Q6PRD1	GP179_HUMAN			10	2478	-	Breast(7;2.97e-12)	Breast(25;0.0101)|Ovarian(249;0.15)	819						Silent	SNP	ENST00000342292.4	37	c.2457C>T	CCDS42308.1																																																																																				0.652	GPR179-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255329.2			5	5	0	0	0	1	0	5	5				
TDO2	6999	broad.mit.edu	37	4	156825198	156825198	+	Missense_Mutation	SNP	G	G	T			TCGA-DJ-A4V2-01A-11D-A257-08	TCGA-DJ-A4V2-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5c5ac429-f523-4c6c-b4d6-0de91d50a945	47627937-0a98-41cf-ac54-096a2900b4ae	g.chr4:156825198G>T	ENST00000536354.2	+	2	128	c.64G>T	c.(64-66)Ggc>Tgc	p.G22C		NM_005651.3	NP_005642.1			tryptophan 2,3-dioxygenase											breast(3)|endometrium(1)|large_intestine(4)|lung(7)|prostate(1)|skin(1)|urinary_tract(1)	18	all_hematologic(180;0.24)	Renal(120;0.0854)		KIRC - Kidney renal clear cell carcinoma(143;0.0455)|Kidney(143;0.0568)|COAD - Colon adenocarcinoma(41;0.141)		CCCCGTAGAAGGCAGCGAAGA	0.388																																					Colon(57;928 1036 2595 6946 26094)	uc003ipf.1																			0				breast(3)|endometrium(1)|large_intestine(4)|lung(7)|prostate(1)|skin(1)|urinary_tract(1)	18						c.(64-66)Ggc>Tgc		Homo sapiens tryptophan 2,3-dioxygenase (TDO2), mRNA.	L-Tryptophan(DB00150)						85.0	86.0	86.0					4																	156825198		2203	4300	6503	SO:0001583	missense	6999				tryptophan catabolic process to kynurenine	cytosol	tryptophan 2,3-dioxygenase activity	g.chr4:156825198G>T		CCDS34086.1	4q31-q32	2008-02-05				ENSG00000151790	1.13.11.11		11708	protein-coding gene	gene with protein product		191070					Standard	NM_005651		Approved	TDO, TPH2	uc003ipf.2	P48775		ENST00000536354.2:c.64G>T	4.37:g.156825198G>T	ENSP00000444788:p.Gly22Cys		Somatic					p.G22C	NM_005651	NP_005642	WXS	Illumina GAIIx	Phase_I	P48775	T23O_HUMAN		KIRC - Kidney renal clear cell carcinoma(143;0.0455)|Kidney(143;0.0568)|COAD - Colon adenocarcinoma(41;0.141)	1	128	+	all_hematologic(180;0.24)	Renal(120;0.0854)	22						Missense_Mutation	SNP	ENST00000536354.2	37	c.64G>T	CCDS34086.1	.	.	.	.	.	.	.	.	.	.	G	14.00	2.404254	0.42613	.	.	ENSG00000151790	ENST00000536354	.	.	.	5.59	3.85	0.44370	.	0.430807	0.28349	N	0.015666	T	0.37919	0.1021	L	0.46157	1.445	0.33113	D	0.540753	P	0.40660	0.726	B	0.32980	0.156	T	0.53746	-0.8395	9	0.56958	D	0.05	-1.0563	12.4964	0.55931	0.1376:0.0:0.8624:0.0	.	22	P48775	T23O_HUMAN	C	22	.	ENSP00000281525:G22C	G	+	1	0	TDO2	157044648	1.000000	0.71417	0.028000	0.17463	0.678000	0.39670	4.823000	0.62694	0.714000	0.32081	0.650000	0.86243	GGC		0.388	TDO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366209.3	NM_005651		20	36	0	0	0	1	0	20	36				
GJD2	57369	broad.mit.edu	37	15	35045227	35045227	+	Nonsense_Mutation	SNP	G	G	A			TCGA-DJ-A4V2-01A-11D-A257-08	TCGA-DJ-A4V2-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5c5ac429-f523-4c6c-b4d6-0de91d50a945	47627937-0a98-41cf-ac54-096a2900b4ae	g.chr15:35045227G>A	ENST00000290374.4	-	2	894	c.418C>T	c.(418-420)Cga>Tga	p.R140*	RP11-814P5.1_ENST00000558707.1_RNA|RP11-814P5.1_ENST00000503496.1_RNA	NM_020660.2	NP_065711.1	Q9UKL4	CXD2_HUMAN	gap junction protein, delta 2, 36kDa	140					action potential (GO:0001508)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|visual perception (GO:0007601)	connexon complex (GO:0005922)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	gap junction channel activity (GO:0005243)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(10)|ovary(1)|pancreas(1)|urinary_tract(1)	19		all_lung(180;9.67e-07)		all cancers(64;2.75e-18)|GBM - Glioblastoma multiforme(113;1.9e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0156)		TTATCTTCTCGTTTGCCCCCA	0.532																																						uc001zis.1																			0				endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(10)|ovary(1)|pancreas(1)|urinary_tract(1)	19						c.(418-420)Cga>Tga		Homo sapiens gap junction protein, delta 2, 36kDa (GJD2), mRNA.							130.0	135.0	133.0					15																	35045227		2201	4298	6499	SO:0001587	stop_gained	57369				synaptic transmission	connexon complex|integral to membrane	gap junction channel activity	g.chr15:35045227G>A	AB037509	CCDS10040.1	15q13.1	2008-02-04	2007-11-06	2007-11-06	ENSG00000159248	ENSG00000159248		"""Ion channels / Gap junction proteins (connexins)"""	19154	protein-coding gene	gene with protein product	"""connexin 36"""	607058	"""gap junction protein, alpha 9, 36kDa"""	GJA9		10462698	Standard	NM_020660		Approved	CX36	uc001zis.2	Q9UKL4	OTTHUMG00000129674	ENST00000290374.4:c.418C>T	15.37:g.35045227G>A	ENSP00000290374:p.Arg140*		Somatic				AK092087_uc001zit.1_5'Flank	p.R140*	NM_020660	NP_065711	WXS	Illumina GAIIx	Phase_I	Q9UKL4	CXD2_HUMAN		all cancers(64;2.75e-18)|GBM - Glioblastoma multiforme(113;1.9e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0156)	1	418	-		all_lung(180;9.67e-07)	140					Q2M241|Q9P2R0	Nonsense_Mutation	SNP	ENST00000290374.4	37	c.418C>T	CCDS10040.1	.	.	.	.	.	.	.	.	.	.	G	39	7.644941	0.98409	.	.	ENSG00000159248	ENST00000290374	.	.	.	5.44	3.48	0.39840	.	1.388510	0.04567	N	0.392577	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.10377	T	0.69	.	12.2373	0.54522	0.0:0.0:0.6906:0.3094	.	.	.	.	X	140	.	ENSP00000290374:R140X	R	-	1	2	GJD2	32832519	1.000000	0.71417	0.977000	0.42913	0.994000	0.84299	2.424000	0.44714	0.778000	0.33520	0.650000	0.86243	CGA		0.532	GJD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251875.2			40	132	0	0	0	1	0	40	132				
BRAF	673	broad.mit.edu	37	7	140453136	140453136	+	Missense_Mutation	SNP	A	A	T	rs121913377|rs113488022|rs121913227|rs397516897		TCGA-DJ-A4V2-01A-11D-A257-08	TCGA-DJ-A4V2-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5c5ac429-f523-4c6c-b4d6-0de91d50a945	47627937-0a98-41cf-ac54-096a2900b4ae	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		26	43	0	0	0	1	0	26	43				
CDH9	1007	broad.mit.edu	37	5	26903745	26903745	+	Splice_Site	SNP	C	C	T			TCGA-DJ-A4V2-01A-11D-A257-08	TCGA-DJ-A4V2-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5c5ac429-f523-4c6c-b4d6-0de91d50a945	47627937-0a98-41cf-ac54-096a2900b4ae	g.chr5:26903745C>T	ENST00000231021.4	-	6	1172		c.e6+1			NM_016279.3	NP_057363.3	Q9ULB4	CADH9_HUMAN	cadherin 9, type 2 (T1-cadherin)						adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(25)|lung(80)|ovary(5)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	137						TGAAAAGAAACCTGTTTGACA	0.383																																					Melanoma(8;187 585 15745 40864 52829)	uc010iug.3																			0				breast(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(25)|lung(80)|ovary(5)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	137						c.(1000-1002)Gtt>Att		Homo sapiens cadherin 9, type 2 (T1-cadherin) (CDH9), mRNA.							202.0	187.0	192.0					5																	26903745		2203	4300	6503	SO:0001630	splice_region_variant	1007				adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding	g.chr5:26903745C>T	AB035302	CCDS3893.1	5p14	2010-01-26			ENSG00000113100	ENSG00000113100		"""Cadherins / Major cadherins"""	1768	protein-coding gene	gene with protein product		609974				2059658	Standard	NM_016279		Approved		uc003jgs.1	Q9ULB4	OTTHUMG00000090671	ENST00000231021.4:c.999+1G>A	5.37:g.26903745C>T			Somatic				CDH9_uc003jgs.1_Splice_Site_p.Q333_splice	p.V334I	NM_016279	NP_057363	WXS	Illumina GAIIx	Phase_I	Q9ULB4	CADH9_HUMAN			5	1169	-			0			Cadherin 3.		Q3B7I5	Missense_Mutation	SNP	ENST00000231021.4	37	c.1000G>A	CCDS3893.1	.	.	.	.	.	.	.	.	.	.	C	27.2	4.808678	0.90707	.	.	ENSG00000113100	ENST00000231021	.	.	.	5.74	5.74	0.90152	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.906	0.92462	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	CDH9	26939502	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	7.747000	0.85070	2.881000	0.98747	0.650000	0.86243	.		0.383	CDH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207352.1	NM_016279	Intron	7	183	0	0	0	1	0	7	183				
ATR	545	broad.mit.edu	37	3	142266707	142266707	+	Nonsense_Mutation	SNP	G	G	A			TCGA-DJ-A4V2-01A-11D-A257-08	TCGA-DJ-A4V2-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5c5ac429-f523-4c6c-b4d6-0de91d50a945	47627937-0a98-41cf-ac54-096a2900b4ae	g.chr3:142266707G>A	ENST00000350721.4	-	16	3338	c.3217C>T	c.(3217-3219)Caa>Taa	p.Q1073*	ATR_ENST00000383101.3_Nonsense_Mutation_p.Q1009*	NM_001184.3	NP_001175.2	Q13535	ATR_HUMAN	ATR serine/threonine kinase	1073					cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|cellular response to UV (GO:0034644)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|multicellular organismal development (GO:0007275)|negative regulation of DNA replication (GO:0008156)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|protein autophosphorylation (GO:0046777)|regulation of protein binding (GO:0043393)|replicative senescence (GO:0090399)|response to drug (GO:0042493)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)|PML body (GO:0016605)|XY body (GO:0001741)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|MutLalpha complex binding (GO:0032405)|MutSalpha complex binding (GO:0032407)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(10)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(20)|liver(2)|lung(45)|ovary(3)|skin(10)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(4)	122						TGCAATCCTTGGAAATCTTGT	0.348								Other conserved DNA damage response genes																														uc003eux.4																			0				NS(1)|breast(10)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(20)|liver(2)|lung(45)|ovary(3)|skin(10)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(4)	122						c.(3217-3219)Caa>Taa	Other conserved DNA damage response genes	Homo sapiens ataxia telangiectasia and Rad3 related (ATR), mRNA.							92.0	94.0	94.0					3																	142266707		2203	4300	6503	SO:0001587	stop_gained	545				DNA damage checkpoint|DNA repair|DNA replication|cell cycle|cellular response to UV|cellular response to gamma radiation|multicellular organismal development|negative regulation of DNA replication|peptidyl-serine phosphorylation|positive regulation of DNA damage response, signal transduction by p53 class mediator|protein autophosphorylation|replicative senescence	PML body	ATP binding|DNA binding|MutLalpha complex binding|MutSalpha complex binding|protein serine/threonine kinase activity	g.chr3:142266707G>A	U76308	CCDS3124.1	3q23	2014-06-17	2014-06-17		ENSG00000175054	ENSG00000175054			882	protein-coding gene	gene with protein product	"""MEC1, mitosis entry checkpoint 1, homolog (S. cerevisiae)"""	601215	"""ataxia telangiectasia and Rad3 related"""			8978690, 8610130	Standard	NM_001184		Approved	FRP1, SCKL, SCKL1, MEC1	uc003eux.4	Q13535	OTTHUMG00000159234	ENST00000350721.4:c.3217C>T	3.37:g.142266707G>A	ENSP00000343741:p.Gln1073*		Somatic					p.Q1073*	NM_001184	NP_001175	WXS	Illumina GAIIx	Phase_I	Q13535	ATR_HUMAN			15	3339	-			1073					Q59HB2|Q7KYL3|Q93051|Q9BXK4	Nonsense_Mutation	SNP	ENST00000350721.4	37	c.3217C>T	CCDS3124.1	.	.	.	.	.	.	.	.	.	.	G	42	9.686941	0.99238	.	.	ENSG00000175054	ENST00000350721;ENST00000383101	.	.	.	5.89	5.89	0.94794	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-15.533	20.2566	0.98424	0.0:0.0:1.0:0.0	.	.	.	.	X	1073;1009	.	ENSP00000343741:Q1073X	Q	-	1	0	ATR	143749397	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	8.010000	0.88615	2.793000	0.96121	0.561000	0.74099	CAA		0.348	ATR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353995.2	NM_001184		16	32	0	0	0	1	0	16	32				
CEP164	22897	broad.mit.edu	37	11	117280645	117280645	+	Missense_Mutation	SNP	G	G	A	rs200520898		TCGA-DJ-A4V2-01A-11D-A257-08	TCGA-DJ-A4V2-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5c5ac429-f523-4c6c-b4d6-0de91d50a945	47627937-0a98-41cf-ac54-096a2900b4ae	g.chr11:117280645G>A	ENST00000278935.3	+	30	4207	c.4060G>A	c.(4060-4062)Gac>Aac	p.D1354N	CEP164_ENST00000533706.1_3'UTR	NM_001271933.1|NM_014956.4	NP_001258862.1|NP_055771.4	Q9UPV0	CE164_HUMAN	centrosomal protein 164kDa	1354					cilium assembly (GO:0042384)|DNA repair (GO:0006281)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary transition fiber (GO:0097539)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|nucleus (GO:0005634)				breast(3)|central_nervous_system(1)|kidney(7)|large_intestine(12)|lung(18)|ovary(3)|prostate(3)	47	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;4e-05)|Epithelial(105;0.0008)		AACGGTGGACGACTTCCTGTT	0.587																																						uc001prc.3																			0				breast(3)|central_nervous_system(1)|kidney(7)|large_intestine(12)|lung(18)|ovary(3)|prostate(3)	47						c.(4060-4062)Gac>Aac		Homo sapiens centrosomal protein 164kDa (CEP164), mRNA.		G	ASN/ASP	1,4401	2.1+/-5.4	0,1,2200	60.0	62.0	61.0		4060	3.3	1.0	11		61	4,8588	3.0+/-9.4	0,4,4292	yes	missense	CEP164	NM_014956.4	23	0,5,6492	AA,AG,GG		0.0466,0.0227,0.0385	probably-damaging	1354/1461	117280645	5,12989	2201	4296	6497	SO:0001583	missense	22897				DNA repair|G2/M transition of mitotic cell cycle|cell division|mitosis	centriole|cytosol|nucleus		g.chr11:117280645G>A	AB028975	CCDS31683.1	11q23.3	2014-02-20			ENSG00000110274	ENSG00000110274			29182	protein-coding gene	gene with protein product		614848				10470851, 14654843	Standard	NM_014956		Approved	KIAA1052, NPHP15	uc001prc.3	Q9UPV0	OTTHUMG00000167070	ENST00000278935.3:c.4060G>A	11.37:g.117280645G>A	ENSP00000278935:p.Asp1354Asn		Somatic				CEP164_uc001prb.3_Missense_Mutation_p.D1349N|CEP164_uc001prf.3_Non-coding_Transcript|CEP164_uc009yzp.1_Non-coding_Transcript|CEP164_uc001prg.1_Missense_Mutation_p.D779N	p.D1354N	NM_014956	NP_055771	WXS	Illumina GAIIx	Phase_I	Q9UPV0	CE164_HUMAN		BRCA - Breast invasive adenocarcinoma(274;4e-05)|Epithelial(105;0.0008)	29	4207	+	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)	1354					Q6PKH9|Q7Z2X9|Q9NVS0|Q9UFJ6	Missense_Mutation	SNP	ENST00000278935.3	37	c.4060G>A	CCDS31683.1	.	.	.	.	.	.	.	.	.	.	G	14.66	2.602001	0.46423	2.27E-4	4.66E-4	ENSG00000110274	ENST00000278935	T	0.28255	1.62	4.4	3.35	0.38373	.	0.259238	0.27535	N	0.018926	T	0.19287	0.0463	L	0.50333	1.59	0.26284	N	0.978237	B;B	0.32350	0.366;0.366	B;B	0.17722	0.019;0.019	T	0.12889	-1.0530	10	0.39692	T	0.17	-11.3448	2.7669	0.05322	0.2339:0.2934:0.4727:0.0	.	1354;1349	Q9UPV0;Q9UPV0-2	CE164_HUMAN;.	N	1354	ENSP00000278935:D1354N	ENSP00000278935:D1354N	D	+	1	0	CEP164	116785855	0.980000	0.34600	0.989000	0.46669	0.615000	0.37417	2.265000	0.43311	2.006000	0.58801	0.561000	0.74099	GAC		0.587	CEP164-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392893.1	NM_014956		25	61	0	0	0	1	0	25	61				
CD74	972	broad.mit.edu	37	5	149784320	149784321	+	Frame_Shift_Del	DEL	CT	CT	-			TCGA-DJ-A4V2-01A-11D-A257-08	TCGA-DJ-A4V2-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5c5ac429-f523-4c6c-b4d6-0de91d50a945	47627937-0a98-41cf-ac54-096a2900b4ae	g.chr5:149784320_149784321delCT	ENST00000009530.7	-	6	548_549	c.547_548delAG	c.(547-549)agcfs	p.S183fs	CD74_ENST00000377795.3_Intron|CD74_ENST00000353334.6_Frame_Shift_Del_p.S183fs|CD74_ENST00000524315.1_Intron			P04233	HG2A_HUMAN	CD74 molecule, major histocompatibility complex, class II invariant chain	183					activation of MAPK activity (GO:0000187)|antigen processing and presentation of endogenous antigen (GO:0019883)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell proliferation (GO:0008283)|chaperone mediated protein folding requiring cofactor (GO:0051085)|defense response (GO:0006952)|immunoglobulin mediated immune response (GO:0016064)|intracellular protein transport (GO:0006886)|macrophage migration inhibitory factor signaling pathway (GO:0035691)|negative regulation of apoptotic process (GO:0043066)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:1902166)|negative regulation of mature B cell apoptotic process (GO:0002906)|negative regulation of peptide secretion (GO:0002792)|negative regulation of T cell differentiation (GO:0045581)|negative thymic T cell selection (GO:0045060)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of chemokine (C-X-C motif) ligand 2 production (GO:2000343)|positive regulation of cytokine-mediated signaling pathway (GO:0001961)|positive regulation of dendritic cell antigen processing and presentation (GO:0002606)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of macrophage cytokine production (GO:0060907)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of T cell differentiation (GO:0045582)|positive regulation of type 2 immune response (GO:0002830)|positive thymic T cell selection (GO:0045059)|prostaglandin biosynthetic process (GO:0001516)|protein complex assembly (GO:0006461)|regulation of macrophage activation (GO:0043030)|signal transduction (GO:0007165)|T cell selection (GO:0045058)	cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|ER to Golgi transport vesicle membrane (GO:0012507)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|lysosomal lumen (GO:0043202)|lysosomal membrane (GO:0005765)|macrophage migration inhibitory factor receptor complex (GO:0035692)|membrane (GO:0016020)|MHC class II protein complex (GO:0042613)|multivesicular body (GO:0005771)|NOS2-CD74 complex (GO:0035693)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)|vacuole (GO:0005773)	beta-amyloid binding (GO:0001540)|cytokine binding (GO:0019955)|cytokine receptor activity (GO:0004896)|identical protein binding (GO:0042802)|macrophage migration inhibitory factor binding (GO:0035718)|MHC class II protein binding (GO:0042289)|MHC class II protein binding, via antigen binding groove (GO:0042658)|MHC class II protein complex binding (GO:0023026)|protein binding involved in protein folding (GO:0044183)			breast(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(1)	5		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			GTGCATCCAGCTCTCAAAGACC	0.559			T	ROS1	NSCLC																																	uc003lsc.3				Dom	yes		5	5q32	972	T	"""CD74 molecule, major histocompatibility complex, class II invariant chain"""			E	ROS1		NSCLC		0				breast(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(1)	5						c.(547-549)agcfs		Homo sapiens CD74 molecule, major histocompatibility complex, class II invariant chain (CD74), transcript variant 1, mRNA.																																				SO:0001589	frameshift_variant	972				antigen processing and presentation of endogenous antigen|cell proliferation|immunoglobulin mediated immune response|intracellular protein transport|negative regulation of DNA damage response, signal transduction by p53 class mediator|negative regulation of apoptosis|negative regulation of peptide secretion|positive regulation of B cell proliferation|positive regulation of ERK1 and ERK2 cascade|positive regulation of chemokine (C-X-C motif) ligand 2 production|positive regulation of cytokine-mediated signaling pathway|positive regulation of fibroblast proliferation|positive regulation of macrophage cytokine production|positive regulation of neutrophil chemotaxis|positive regulation of peptidyl-tyrosine phosphorylation|prostaglandin biosynthetic process|protein complex assembly|regulation of macrophage activation	Golgi apparatus|endoplasmic reticulum membrane|integral to membrane|lysosome|receptor complex	MHC class II protein binding|beta-amyloid binding|cytokine receptor activity|identical protein binding	g.chr5:149784320_149784321delCT		CCDS34276.1, CCDS47308.1, CCDS47309.1	5q32	2012-09-20	2006-03-28		ENSG00000019582	ENSG00000019582		"""CD molecules"""	1697	protein-coding gene	gene with protein product	"""HLA-DR-gamma"", ""Ia-associated invariant chain"", ""gamma chain of class II antigens"", ""MHC HLA-DR gamma chain"""	142790	"""CD74 antigen (invariant polypeptide of major histocompatibility complex, class II antigen-associated)"""	DHLAG		6324166, 3001652	Standard	NM_004355		Approved		uc003lsc.3	P04233	OTTHUMG00000163559	ENST00000009530.7:c.547_548delAG	5.37:g.149784322_149784323delCT	ENSP00000009530:p.Ser183fs		Somatic				CD74_uc003lsd.3_Frame_Shift_Del_p.S183fs|CD74_uc003lse.3_Intron	p.S183fs	NM_001025159	NP_001020330	WXS	Illumina GAIIx	Phase_I	P04233	HG2A_HUMAN	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		5	734_735	-		all_hematologic(541;0.224)	183					A8K7R1|B4DNE8|D3DQG3|D3DQG4|Q14597|Q29832|Q5U0J8|Q8SNA0|Q8WLP6	Frame_Shift_Del	DEL	ENST00000009530.7	37	c.547_548delAG	CCDS47309.1																																																																																				0.559	CD74-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374178.1	NM_004355		2	4						2	4	---	---	---	---
CPD	1362	broad.mit.edu	37	17	28706683	28706683	+	Frame_Shift_Del	DEL	C	C	-	rs530282755		TCGA-DJ-A4V2-01A-11D-A257-08	TCGA-DJ-A4V2-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5c5ac429-f523-4c6c-b4d6-0de91d50a945	47627937-0a98-41cf-ac54-096a2900b4ae	g.chr17:28706683delC	ENST00000225719.4	+	1	761	c.685delC	c.(685-687)cccfs	p.P230fs	CPD_ENST00000543464.2_5'Flank	NM_001304.4	NP_001295.2	O75976	CBPD_HUMAN	carboxypeptidase D	230	Carboxypeptidase-like 1.					extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	metallocarboxypeptidase activity (GO:0004181)|serine-type carboxypeptidase activity (GO:0004185)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(9)|liver(1)|lung(13)|skin(5)|stomach(1)|urinary_tract(1)	36						CACCGGCGAACCCCCCGCCCT	0.701																																						uc002hfb.2																			0				central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(9)|liver(1)|lung(13)|skin(5)|stomach(1)|urinary_tract(1)	36						c.(685-687)cccfs		Homo sapiens carboxypeptidase D (CPD), transcript variant 1, mRNA.																																				SO:0001589	frameshift_variant	1362				proteolysis	integral to membrane	metallocarboxypeptidase activity|serine-type carboxypeptidase activity|zinc ion binding	g.chr17:28706683delC	U65090	CCDS11257.1, CCDS56025.1	17q11.2	2012-02-10			ENSG00000108582	ENSG00000108582	3.4.17.22		2301	protein-coding gene	gene with protein product	"""metallocarboxypeptidase D"""	603102				9628828, 9355738	Standard	NM_001304		Approved	GP180	uc002hfb.2	O75976	OTTHUMG00000132797	ENST00000225719.4:c.685delC	17.37:g.28706683delC	ENSP00000225719:p.Pro230fs		Somatic				CPD_uc010wbo.2_5'Flank|CPD_uc010wbp.2_5'Flank	p.P229fs	NM_001304	NP_001295	WXS	Illumina GAIIx	Phase_I	O75976	CBPD_HUMAN			0	742	+			229			Carboxypeptidase-like 1.		B7Z7T9|B7ZAU4|F5GZH6|O15377|Q86SH9|Q86XE6	Frame_Shift_Del	DEL	ENST00000225719.4	37	c.685delC	CCDS11257.1																																																																																				0.701	CPD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256214.3	NM_001304		3	5						3	5	---	---	---	---
