#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
STAG3	10734	broad.mit.edu	37	7	99780445	99780445	+	Missense_Mutation	SNP	G	G	A			TCGA-BJ-A45H-01A-12D-A23U-08	TCGA-BJ-A45H-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4bdbc383-8f81-410a-833e-1f039ceabddf	8cb61ce1-4085-4752-9f1e-91d7c1fee6ab	g.chr7:99780445G>A	ENST00000426455.1	+	4	726	c.319G>A	c.(319-321)Gcc>Acc	p.A107T	STAG3_ENST00000394018.2_Missense_Mutation_p.A107T|STAG3_ENST00000317296.5_Missense_Mutation_p.A107T	NM_001282716.1	NP_001269645.1	Q9UJ98	STAG3_HUMAN	stromal antigen 3	107					chromosome segregation (GO:0007059)|synaptonemal complex assembly (GO:0007130)	chromosome, centromeric region (GO:0000775)|extracellular space (GO:0005615)|lateral element (GO:0000800)|male germ cell nucleus (GO:0001673)|meiotic cohesin complex (GO:0030893)|nuclear meiotic cohesin complex (GO:0034991)|nucleolus (GO:0005730)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)|transverse filament (GO:0000802)				breast(1)|central_nervous_system(2)|endometrium(6)|kidney(3)|large_intestine(11)|lung(30)|ovary(5)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	66	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					TGTGAAAGCCGCCAAAAGTGA	0.463																																						ENST00000426455.1																			0				breast(1)|central_nervous_system(2)|endometrium(6)|kidney(3)|large_intestine(11)|lung(30)|ovary(5)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	66						c.(319-321)Gcc>Acc		stromal antigen 3							242.0	238.0	239.0					7																	99780445		2203	4300	6503	SO:0001583	missense	10734				chromosome segregation|synaptonemal complex assembly	chromosome, centromeric region|meiotic cohesin complex|synaptonemal complex	binding	g.chr7:99780445G>A	AJ007798	CCDS34703.1, CCDS64730.1, CCDS75642.1	7q22	2008-02-01			ENSG00000066923	ENSG00000066923			11356	protein-coding gene	gene with protein product		608489				10698974	Standard	XM_005250116		Approved		uc003utx.1	Q9UJ98	OTTHUMG00000155183	ENST00000426455.1:c.319G>A	7.37:g.99780445G>A	ENSP00000400359:p.Ala107Thr					STAG3_ENST00000394018.2_Missense_Mutation_p.A107T|STAG3_ENST00000317296.5_Missense_Mutation_p.A107T	p.A107T			Q9UJ98	STAG3_HUMAN			4	726	+	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)		107					A6H8Z1|B4DZ10|D6W5U8|H7BYK9|Q8NDP3	Missense_Mutation	SNP	ENST00000426455.1	37	c.319G>A	CCDS34703.1	.	.	.	.	.	.	.	.	.	.	G	21.2	4.112214	0.77210	.	.	ENSG00000066923	ENST00000426455;ENST00000394018;ENST00000416412;ENST00000339784;ENST00000317296;ENST00000422690;ENST00000439782	T;T;T	0.28069	1.93;1.63;1.93	5.32	5.32	0.75619	.	0.000000	0.43919	D	0.000512	T	0.52869	0.1761	M	0.68952	2.095	0.42720	D	0.993672	D;B	0.89917	1.0;0.32	D;B	0.64506	0.926;0.056	T	0.54860	-0.8230	10	0.87932	D	0	-15.4632	16.5495	0.84470	0.0:0.0:1.0:0.0	.	107;107	B4DZ10;Q9UJ98	.;STAG3_HUMAN	T	107	ENSP00000400359:A107T;ENSP00000377586:A107T;ENSP00000319318:A107T	ENSP00000319318:A107T	A	+	1	0	STAG3	99618381	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	6.209000	0.72171	2.773000	0.95371	0.585000	0.79938	GCC		0.463	STAG3-004	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000338734.2	NM_012447		5	303	0	0	0	0.000602	0	5	303				
TMEM138	51524	broad.mit.edu	37	11	61136166	61136166	+	Missense_Mutation	SNP	G	G	C			TCGA-BJ-A45H-01A-12D-A23U-08	TCGA-BJ-A45H-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4bdbc383-8f81-410a-833e-1f039ceabddf	8cb61ce1-4085-4752-9f1e-91d7c1fee6ab	g.chr11:61136166G>C	ENST00000278826.6	+	5	1033	c.474G>C	c.(472-474)atG>atC	p.M158I	TMEM138_ENST00000381787.2_Missense_Mutation_p.M100I	NM_016464.4	NP_057548.1	Q9NPI0	TM138_HUMAN	transmembrane protein 138	158					cilium assembly (GO:0042384)	cilium (GO:0005929)|integral component of membrane (GO:0016021)|vacuole (GO:0005773)				central_nervous_system(1)|large_intestine(2)|lung(1)|upper_aerodigestive_tract(1)	5						AGGAGTTCATGCAAGTTCGAA	0.498																																						ENST00000278826.6																			0				central_nervous_system(1)|large_intestine(2)|lung(1)|upper_aerodigestive_tract(1)	5						c.(472-474)atG>atC		transmembrane protein 138							115.0	90.0	99.0					11																	61136166		2203	4299	6502	SO:0001583	missense	51524					integral to membrane		g.chr11:61136166G>C	AF151030	CCDS8005.1	11q12.2	2014-01-28			ENSG00000149483	ENSG00000149483			26944	protein-coding gene	gene with protein product		614459					Standard	NM_016464		Approved	HSPC196, JBTS16	uc001nrl.2	Q9NPI0	OTTHUMG00000168145	ENST00000278826.6:c.474G>C	11.37:g.61136166G>C	ENSP00000278826:p.Met158Ile					TMEM138_ENST00000381787.2_Missense_Mutation_p.M100I	p.M158I	NM_016464.4	NP_057548.1	Q9NPI0	TM138_HUMAN			5	1033	+			158					A6NGA7|B4E044|Q5JPE1	Missense_Mutation	SNP	ENST00000278826.6	37	c.474G>C	CCDS8005.1	.	.	.	.	.	.	.	.	.	.	G	8.300	0.819696	0.16607	.	.	ENSG00000149483	ENST00000278826;ENST00000381787	D;D	0.87491	-2.26;-2.26	5.95	2.8	0.32819	.	0.503070	0.23571	N	0.046756	T	0.64897	0.2640	N	0.02916	-0.46	0.26228	N	0.979059	B	0.06786	0.001	B	0.01281	0.0	T	0.52675	-0.8544	10	0.31617	T	0.26	.	2.3249	0.04220	0.2416:0.1172:0.4898:0.1515	.	158	Q9NPI0	TM138_HUMAN	I	158;100	ENSP00000278826:M158I;ENSP00000371206:M100I	ENSP00000278826:M158I	M	+	3	0	TMEM138	60892742	0.057000	0.20700	0.999000	0.59377	0.993000	0.82548	-0.703000	0.05063	0.810000	0.34279	0.655000	0.94253	ATG		0.498	TMEM138-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398399.2	NM_016464		3	40	0	0	0	0.004672	0	3	40				
TCF7L2	6934	broad.mit.edu	37	10	114903693	114903693	+	Missense_Mutation	SNP	C	C	T			TCGA-BJ-A45H-01A-12D-A23U-08	TCGA-BJ-A45H-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4bdbc383-8f81-410a-833e-1f039ceabddf	8cb61ce1-4085-4752-9f1e-91d7c1fee6ab	g.chr10:114903693C>T	ENST00000355995.4	+	7	1204	c.697C>T	c.(697-699)Cct>Tct	p.P233S	TCF7L2_ENST00000352065.5_Missense_Mutation_p.P210S|TCF7L2_ENST00000536810.1_Missense_Mutation_p.P233S|TCF7L2_ENST00000538897.1_Missense_Mutation_p.P233S|TCF7L2_ENST00000369389.1_5'UTR|TCF7L2_ENST00000545257.1_Missense_Mutation_p.P233S|TCF7L2_ENST00000355717.4_Missense_Mutation_p.P257S|TCF7L2_ENST00000534894.1_Missense_Mutation_p.P233S|TCF7L2_ENST00000542695.1_5'UTR|TCF7L2_ENST00000543371.1_Missense_Mutation_p.P233S|TCF7L2_ENST00000349937.2_Missense_Mutation_p.P233S|TCF7L2_ENST00000369397.4_Missense_Mutation_p.P210S|TCF7L2_ENST00000369395.1_Missense_Mutation_p.P258S			Q9NQB0	TF7L2_HUMAN	transcription factor 7-like 2 (T-cell specific, HMG-box)	233	Mediates interaction with MAD2L2.|Pro-rich.				blood vessel development (GO:0001568)|bone mineralization (GO:0030282)|brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|catenin import into nucleus (GO:0035411)|cell cycle arrest (GO:0007050)|cell proliferation (GO:0008283)|cellular response to starvation (GO:0009267)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic genitalia morphogenesis (GO:0030538)|embryonic hindgut morphogenesis (GO:0048619)|face morphogenesis (GO:0060325)|fat cell differentiation (GO:0045444)|generation of neurons (GO:0048699)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|glycogen metabolic process (GO:0005977)|insulin metabolic process (GO:1901142)|maintenance of DNA repeat elements (GO:0043570)|multicellular organism growth (GO:0035264)|myoblast fate commitment (GO:0048625)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of organ growth (GO:0046621)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of type B pancreatic cell apoptotic process (GO:2000675)|neural tube development (GO:0021915)|odontogenesis of dentin-containing tooth (GO:0042475)|oligodendrocyte development (GO:0014003)|pancreas development (GO:0031016)|pituitary gland development (GO:0021983)|positive regulation of apoptotic process (GO:0043065)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of gluconeogenesis (GO:0045722)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of insulin secretion (GO:0032024)|positive regulation of protein binding (GO:0032092)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of triglyceride biosynthetic process (GO:0010867)|post-embryonic development (GO:0009791)|regulation of hormone metabolic process (GO:0032350)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|regulation of myelination (GO:0031641)|regulation of oligodendrocyte differentiation (GO:0048713)|regulation of skeletal muscle tissue development (GO:0048641)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to glucose (GO:0009749)|secretory granule localization (GO:0032252)|skin development (GO:0043588)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	beta-catenin-TCF7L2 complex (GO:0070369)|cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein-DNA complex (GO:0032993)|transcription factor complex (GO:0005667)	armadillo repeat domain binding (GO:0070016)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|gamma-catenin binding (GO:0045295)|nuclear hormone receptor binding (GO:0035257)|protein kinase binding (GO:0019901)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II repressing transcription factor binding (GO:0001103)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)		VTI1A/TCF7L2(8)	central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(24)|liver(2)|lung(8)|ovary(1)|skin(1)	41		Breast(234;0.058)|Colorectal(252;0.0615)		Epithelial(162;0.00554)|all cancers(201;0.02)		AATCCCACGGCCTCCGCACCC	0.522			T	VTI1A	colorectal																																	ENST00000545257.1				Dom	yes		10	10q25.3	6934	T	transcription factor 7-like 2			E	VTI1A		colorectal	VTI1A/TCF7L2(8)	0				central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(24)|liver(2)|lung(8)|ovary(1)|skin(1)	41						c.(697-699)Cct>Tct		transcription factor 7-like 2 (T-cell specific, HMG-box)							79.0	67.0	71.0					10																	114903693		2203	4300	6503	SO:0001583	missense	6934				anti-apoptosis|blood vessel development|canonical Wnt receptor signaling pathway involved in positive regulation of epithelial to mesenchymal transition|cell cycle arrest|cell proliferation|fat cell differentiation|glucose homeostasis|maintenance of DNA repeat elements|myoblast cell fate commitment|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|pancreas development|positive regulation of heparan sulfate proteoglycan biosynthetic process|positive regulation of insulin secretion|positive regulation of protein binding|positive regulation of protein export from nucleus|positive regulation of protein kinase B signaling cascade|positive regulation of transcription from RNA polymerase II promoter|regulation of hormone metabolic process|regulation of smooth muscle cell proliferation|response to glucose stimulus	beta-catenin-TCF7L2 complex|PML body|protein-DNA complex	armadillo repeat domain binding|beta-catenin binding|gamma-catenin binding|nuclear hormone receptor binding|protein kinase binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription factor binding|transcription regulatory region DNA binding	g.chr10:114903693C>T	X62871	CCDS7576.1, CCDS53578.1, CCDS55729.1, CCDS73196.1, CCDS73197.1, CCDS73198.1	10q25.3	2006-11-24			ENSG00000148737	ENSG00000148737			11641	protein-coding gene	gene with protein product		602228		TCF4		1741298	Standard	NM_001146283		Approved	TCF-4	uc001lae.4	Q9NQB0	OTTHUMG00000019070	ENST00000355995.4:c.697C>T	10.37:g.114903693C>T	ENSP00000348274:p.Pro233Ser					TCF7L2_ENST00000369395.1_Missense_Mutation_p.P258S|TCF7L2_ENST00000352065.5_Missense_Mutation_p.P210S|TCF7L2_ENST00000536810.1_Missense_Mutation_p.P233S|TCF7L2_ENST00000542695.1_5'UTR|TCF7L2_ENST00000543371.1_Missense_Mutation_p.P233S|TCF7L2_ENST00000538897.1_Missense_Mutation_p.P233S|TCF7L2_ENST00000349937.2_Missense_Mutation_p.P233S|TCF7L2_ENST00000355717.4_Missense_Mutation_p.P257S|TCF7L2_ENST00000369389.1_5'UTR|TCF7L2_ENST00000369397.4_Missense_Mutation_p.P210S|TCF7L2_ENST00000534894.1_Missense_Mutation_p.P233S|TCF7L2_ENST00000355995.4_Missense_Mutation_p.P233S	p.P233S			Q9NQB0	TF7L2_HUMAN		Epithelial(162;0.00554)|all cancers(201;0.02)	7	1204	+		Breast(234;0.058)|Colorectal(252;0.0615)	233			Mediates interaction with MAD2L2.|Pro-rich.		B4DRJ8|B9X074|C6ZRJ8|C6ZRK0|E2GH14|E2GH19|E2GH20|E2GH24|E2GH25|E9PFH9|F8W742|F8W7T5|O00185|Q9NQB1|Q9NQB2|Q9NQB3|Q9NQB4|Q9NQB5|Q9NQB6|Q9NQB7|Q9ULC2	Missense_Mutation	SNP	ENST00000355995.4	37	c.697C>T		.	.	.	.	.	.	.	.	.	.	c	23.1	4.369547	0.82463	.	.	ENSG00000148737	ENST00000355995;ENST00000545257;ENST00000543371;ENST00000536810;ENST00000355717;ENST00000538897;ENST00000534894;ENST00000369397;ENST00000349937;ENST00000352065;ENST00000369395	D;D;D;D;D;D;D;D;D	0.99207	-5.0;-5.0;-5.0;-5.01;-5.53;-5.56;-5.54;-5.0;-5.54	5.26	4.35	0.52113	CTNNB1 binding, N-teminal (1);	0.110472	0.64402	D	0.000007	D	0.99202	0.9723	M	0.61703	1.905	0.80722	D	1	B;D;B;P;P;P;D;D;D;B;P;P;B;D;D;D;B;B;P	0.89917	0.071;0.974;0.41;0.869;0.933;0.87;0.994;0.964;0.971;0.051;0.941;0.621;0.447;1.0;0.999;0.971;0.117;0.393;0.629	B;P;B;P;P;P;D;P;P;B;P;P;B;D;D;P;B;B;P	0.87578	0.089;0.88;0.349;0.796;0.796;0.593;0.912;0.79;0.739;0.088;0.855;0.593;0.439;0.993;0.998;0.796;0.343;0.406;0.542	D	0.99406	1.0929	10	0.59425	D	0.04	-9.0972	16.1275	0.81404	0.0:0.866:0.134:0.0	.	90;50;127;233;104;152;210;210;210;176;233;210;210;210;257;210;233;210;210	B4DJZ2;B7Z9Z6;B4DWD5;Q9NQB0;C6ZRK4;C6ZRJ6;C6ZRJ9;F8W742;B4DRJ8;C6ZRK2;B9X074;C6ZRJ8;C6ZRK1;C6ZRJ7;F8W7T5;C6ZRK5;Q9NQB0-7;Q9NQB0-10;Q6FHW4	.;.;.;TF7L2_HUMAN;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.	S	233;233;233;233;257;233;233;210;233;210;258	ENSP00000348274:P233S;ENSP00000440547:P233S;ENSP00000444972:P233S;ENSP00000446238:P233S;ENSP00000347949:P257S;ENSP00000446172:P233S;ENSP00000443626:P233S;ENSP00000358404:P210S;ENSP00000344823:P210S	ENSP00000298692:P233S	P	+	1	0	TCF7L2	114893683	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.028000	0.70889	1.330000	0.45394	0.655000	0.94253	CCT		0.522	TCF7L2-203	KNOWN	basic	protein_coding	protein_coding		NM_030756		15	38	0	0	0	0.004007	0	15	38				
NPAS2	4862	broad.mit.edu	37	2	101554284	101554284	+	Missense_Mutation	SNP	C	C	T			TCGA-BJ-A45H-01A-12D-A23U-08	TCGA-BJ-A45H-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4bdbc383-8f81-410a-833e-1f039ceabddf	8cb61ce1-4085-4752-9f1e-91d7c1fee6ab	g.chr2:101554284C>T	ENST00000335681.5	+	5	628	c.343C>T	c.(343-345)Cct>Tct	p.P115S	NPAS2_ENST00000542504.1_Missense_Mutation_p.P180S|NPAS2_ENST00000486017.1_3'UTR	NM_002518.3	NP_002509.2	Q99743	NPAS2_HUMAN	neuronal PAS domain protein 2	115	PAS 1. {ECO:0000255|PROSITE- ProRule:PRU00140}.				cellular lipid metabolic process (GO:0044255)|cellular response to DNA damage stimulus (GO:0006974)|central nervous system development (GO:0007417)|circadian regulation of gene expression (GO:0032922)|circadian sleep/wake cycle (GO:0042745)|locomotor rhythm (GO:0045475)|negative regulation of cell death (GO:0060548)|positive regulation of DNA repair (GO:0045739)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of response to DNA damage stimulus (GO:2001020)|response to redox state (GO:0051775)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	core promoter binding (GO:0001047)|DNA binding (GO:0003677)|Hsp90 protein binding (GO:0051879)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			cervix(1)|endometrium(3)|large_intestine(7)|lung(9)|ovary(3)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						CAGTATCACGCCTCTCCTTGG	0.453																																						ENST00000335681.5																			0				cervix(1)|endometrium(3)|large_intestine(7)|lung(9)|ovary(3)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						c.(343-345)Cct>Tct		neuronal PAS domain protein 2							248.0	213.0	225.0					2																	101554284		2203	4300	6503	SO:0001583	missense	4862				central nervous system development|positive regulation of transcription from RNA polymerase II promoter|rhythmic process	transcription factor complex	DNA binding|Hsp90 protein binding|sequence-specific DNA binding transcription factor activity|signal transducer activity	g.chr2:101554284C>T	U77970	CCDS2048.1	2q11.2	2013-05-21			ENSG00000170485	ENSG00000170485		"""Basic helix-loop-helix proteins"""	7895	protein-coding gene	gene with protein product		603347				9012850, 9079689	Standard	NM_002518		Approved	MOP4, PASD4, bHLHe9	uc002tap.1	Q99743	OTTHUMG00000130675	ENST00000335681.5:c.343C>T	2.37:g.101554284C>T	ENSP00000338283:p.Pro115Ser					NPAS2_ENST00000542504.1_Missense_Mutation_p.P180S|NPAS2_ENST00000486017.1_3'UTR	p.P115S	NM_002518.3	NP_002509.2	Q99743	NPAS2_HUMAN			5	628	+			115			PAS 1.		Q4ZFV9|Q53SQ3|Q86V96|Q99629	Missense_Mutation	SNP	ENST00000335681.5	37	c.343C>T	CCDS2048.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	7.101|7.101	0.574021|0.574021	0.13623|0.13623	.|.	.|.	ENSG00000170485|ENSG00000170485	ENST00000448812|ENST00000335681;ENST00000542504;ENST00000451740	.|T;T;T	.|0.16196	.|2.36;2.36;2.36	5.93|5.93	5.93|5.93	0.95920|0.95920	.|PAS (3);PAS fold (1);	.|0.058507	.|0.64402	.|D	.|0.000001	T|T	0.07683|0.07683	0.0193|0.0193	N|N	0.02539|0.02539	-0.55|-0.55	0.54753|0.54753	D|D	0.999985|0.999985	.|B;B	.|0.30973	.|0.257;0.302	.|B;B	.|0.36666	.|0.147;0.23	T|T	0.21759|0.21759	-1.0236|-1.0236	5|10	.|0.02654	.|T	.|1	.|.	14.1654|14.1654	0.65473|0.65473	0.0:0.9279:0.0:0.0721|0.0:0.9279:0.0:0.0721	.|.	.|180;115	.|F5H027;Q99743	.|.;NPAS2_HUMAN	V|S	104|115;180;101	.|ENSP00000338283:P115S;ENSP00000438428:P180S;ENSP00000395265:P101S	.|ENSP00000338283:P115S	A|P	+|+	2|1	0|0	NPAS2|NPAS2	100920716|100920716	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	4.248000|4.248000	0.58760|0.58760	2.808000|2.808000	0.96608|0.96608	0.655000|0.655000	0.94253|0.94253	GCC|CCT		0.453	NPAS2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253168.3			14	161	0	0	0	0.002450	0	14	161				
HLA-C	3107	broad.mit.edu	37	6	31239616	31239616	+	Missense_Mutation	SNP	C	C	A	rs1050445	byFrequency	TCGA-BJ-A45H-01A-12D-A23U-08	TCGA-BJ-A45H-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4bdbc383-8f81-410a-833e-1f039ceabddf	8cb61ce1-4085-4752-9f1e-91d7c1fee6ab	g.chr6:31239616C>A	ENST00000376228.5	-	2	117	c.103G>T	c.(103-105)Gcc>Tcc	p.A35S	HLA-C_ENST00000383329.3_Missense_Mutation_p.A35S	NM_002117.5	NP_002108.4	Q95604	1C17_HUMAN	major histocompatibility complex, class I, C	35	Alpha-1.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	peptide antigen binding (GO:0042605)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(4)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	17						CGGGACACGGCGGTGTCGAAA	0.721													c|||	1172	0.234026	0.2428	0.2939	5008	,	,		12672	0.2937		0.1948	False		,,,				2504	0.1585					ENST00000383329.3																			0				central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(4)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	17						c.(103-105)Gcc>Tcc		major histocompatibility complex, class I, C							18.0	18.0	18.0					6																	31239616		1475	2675	4150	SO:0001583	missense	3107				antigen processing and presentation of peptide antigen via MHC class I|interferon-gamma-mediated signaling pathway|interspecies interaction between organisms|regulation of immune response|type I interferon-mediated signaling pathway	integral to membrane|MHC class I protein complex		g.chr6:31239616C>A	M11886	CCDS34393.1	6p21.3	2014-01-30			ENSG00000204525	ENSG00000204525		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4933	protein-coding gene	gene with protein product		142840	"""psoriasis susceptibility 1"""	HLA-JY3, D6S204, PSORS1		3863816, 16642438	Standard	NM_001243042		Approved		uc003nsy.3	P04222	OTTHUMG00000031154	ENST00000376228.5:c.103G>T	6.37:g.31239616C>A	ENSP00000365402:p.Ala35Ser					HLA-C_ENST00000376228.5_Missense_Mutation_p.A35S	p.A35S			Q9TNN7	1C05_HUMAN			2	117	-			35			Alpha-1.		O02864|O02958|Q29643|Q9MY30	Missense_Mutation	SNP	ENST00000376228.5	37	c.103G>T	CCDS34393.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	c|c	6.895|6.895	0.534735|0.534735	0.13188|0.13188	.|.	.|.	ENSG00000204525|ENSG00000204525	ENST00000376228;ENST00000383329;ENST00000396254;ENST00000539307|ENST00000415537	T;T|.	0.00966|.	5.49;5.49|.	2.16|2.16	-2.86|-2.86	0.05717|0.05717	MHC class I, alpha chain, alpha1/alpha2 (1);MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);|.	1.333240|.	0.06305|.	U|.	0.701534|.	T|T	0.15912|0.15912	0.0383|0.0383	L|L	0.48877|0.48877	1.53|1.53	0.80722|0.80722	P|P	0.0|0.0	B;B;B;B|.	0.06786|.	0.001;0.0;0.0;0.0|.	B;B;B;B|.	0.30105|.	0.111;0.069;0.069;0.069|.	T|T	0.23404|0.23404	-1.0189|-1.0189	9|4	0.02654|.	T|.	1|.	.|.	4.1764|4.1764	0.10353|0.10353	0.5673:0.2969:0.0:0.1358|0.5673:0.2969:0.0:0.1358	rs1050445;rs3190759;rs3190813;rs17413569|rs1050445;rs3190759;rs3190813;rs17413569	35;35;35;35|.	A2AEA4;A6H578;A2AEA2;P10321|.	.;.;.;1C07_HUMAN|.	S|L	35;35;35;72|34	ENSP00000365402:A35S;ENSP00000372819:A35S|.	ENSP00000365402:A35S|.	A|R	-|-	1|2	0|0	HLA-C|HLA-C	31347595|31347595	0.000000|0.000000	0.05858|0.05858	0.013000|0.013000	0.15412|0.15412	0.003000|0.003000	0.03518|0.03518	-2.010000|-2.010000	0.01454|0.01454	-0.823000|-0.823000	0.04301|0.04301	-0.680000|-0.680000	0.03767|0.03767	GCC|CGC		0.721	HLA-C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076281.3	NM_002117		4	38	1	0	0.000602214	0.000602	0.00110406	4	38				
CHD7	55636	broad.mit.edu	37	8	61735125	61735125	+	Silent	SNP	C	C	T			TCGA-BJ-A45H-01A-12D-A23U-08	TCGA-BJ-A45H-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4bdbc383-8f81-410a-833e-1f039ceabddf	8cb61ce1-4085-4752-9f1e-91d7c1fee6ab	g.chr8:61735125C>T	ENST00000423902.2	+	12	3500	c.3021C>T	c.(3019-3021)ctC>ctT	p.L1007L	CHD7_ENST00000524602.1_Intron|CHD7_ENST00000525508.1_Silent_p.L1007L	NM_017780.3	NP_060250.2	Q9P2D1	CHD7_HUMAN	chromodomain helicase DNA binding protein 7	1007	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				adult heart development (GO:0007512)|adult walking behavior (GO:0007628)|artery morphogenesis (GO:0048844)|blood circulation (GO:0008015)|central nervous system development (GO:0007417)|chromatin modification (GO:0016568)|cognition (GO:0050890)|cranial nerve development (GO:0021545)|embryonic hindlimb morphogenesis (GO:0035116)|epithelium development (GO:0060429)|face development (GO:0060324)|female genitalia development (GO:0030540)|genitalia development (GO:0048806)|heart morphogenesis (GO:0003007)|in utero embryonic development (GO:0001701)|inner ear morphogenesis (GO:0042472)|limb development (GO:0060173)|nose development (GO:0043584)|olfactory behavior (GO:0042048)|olfactory bulb development (GO:0021772)|olfactory nerve development (GO:0021553)|palate development (GO:0060021)|positive regulation of multicellular organism growth (GO:0040018)|regulation of growth hormone secretion (GO:0060123)|regulation of neurogenesis (GO:0050767)|regulation of transcription, DNA-templated (GO:0006355)|retina development in camera-type eye (GO:0060041)|rRNA processing (GO:0006364)|semicircular canal morphogenesis (GO:0048752)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|T cell differentiation (GO:0030217)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			NS(1)|breast(6)|central_nervous_system(8)|cervix(2)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(16)|lung(49)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|urinary_tract(3)	123		all_cancers(86;0.2)|all_lung(136;0.0402)|Lung NSC(129;0.0459)|all_epithelial(80;0.0477)	BRCA - Breast invasive adenocarcinoma(89;0.143)			TTACATTTCTCTATGAGATAT	0.393																																						ENST00000423902.2																			0				NS(1)|breast(6)|central_nervous_system(8)|cervix(2)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(16)|lung(49)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|urinary_tract(3)	123						c.(3019-3021)ctC>ctT		chromodomain helicase DNA binding protein 7							131.0	129.0	129.0					8																	61735125		1825	4080	5905	SO:0001819	synonymous_variant	55636				central nervous system development|chromatin modification|cognition|cranial nerve development|face development|heart morphogenesis|in utero embryonic development|inner ear morphogenesis|nose development|palate development|regulation of growth hormone secretion|regulation of transcription, DNA-dependent|retina development in camera-type eye|skeletal system development|T cell differentiation|transcription, DNA-dependent	nucleus	ATP binding|chromatin binding|DNA binding|helicase activity	g.chr8:61735125C>T	AB037837	CCDS47865.1	8q12.2	2014-09-17				ENSG00000171316			20626	protein-coding gene	gene with protein product		608892	"""CHARGE association"""	CRG		15300250, 18834967	Standard	NM_017780		Approved	KIAA1416, FLJ20357, FLJ20361	uc003xue.3	Q9P2D1		ENST00000423902.2:c.3021C>T	8.37:g.61735125C>T						CHD7_ENST00000525508.1_Silent_p.L1007L|CHD7_ENST00000524602.1_Intron	p.L1007L	NM_017780.3	NP_060250.2	Q9P2D1	CHD7_HUMAN	BRCA - Breast invasive adenocarcinoma(89;0.143)		12	3500	+		all_cancers(86;0.2)|all_lung(136;0.0402)|Lung NSC(129;0.0459)|all_epithelial(80;0.0477)	1007			Helicase ATP-binding.		D0VBA5|E9PNZ2|Q05DI5|Q2TAN4|Q66K35|Q7Z6C0|Q7Z7Q2|Q9NXA0|Q9NXA3	Silent	SNP	ENST00000423902.2	37	c.3021C>T	CCDS47865.1																																																																																				0.393	CHD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383468.2	XM_098762		18	132	0	0	0	0.001523	0	18	132				
PRPF8	10594	broad.mit.edu	37	17	1564035	1564035	+	Missense_Mutation	SNP	C	C	T			TCGA-BJ-A45H-01A-12D-A23U-08	TCGA-BJ-A45H-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4bdbc383-8f81-410a-833e-1f039ceabddf	8cb61ce1-4085-4752-9f1e-91d7c1fee6ab	g.chr17:1564035C>T	ENST00000572621.1	-	28	4860	c.4595G>A	c.(4594-4596)cGt>cAt	p.R1532H	PRPF8_ENST00000304992.6_Missense_Mutation_p.R1532H			Q6P2Q9	PRP8_HUMAN	pre-mRNA processing factor 8	1532	Linker.				gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|U5 snRNP (GO:0005682)	poly(A) RNA binding (GO:0044822)|U5 snRNA binding (GO:0030623)|U6 snRNA binding (GO:0017070)			NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(13)|lung(24)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(3)	77				UCEC - Uterine corpus endometrioid carcinoma (25;0.0855)		GGTGAATCTACGATTGGGAAT	0.502																																						ENST00000572621.1																			0				NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(13)|lung(24)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(3)	77						c.(4594-4596)cGt>cAt		pre-mRNA processing factor 8							135.0	123.0	127.0					17																	1564035		2203	4300	6503	SO:0001583	missense	10594					catalytic step 2 spliceosome|nuclear speck|U5 snRNP	protein binding|RNA binding	g.chr17:1564035C>T	AB007510	CCDS11010.1	17p13.3	2013-07-16	2013-06-10		ENSG00000174231	ENSG00000174231			17340	protein-coding gene	gene with protein product		607300	"""PRP8 pre-mRNA processing factor 8 homolog (yeast)"", ""PRP8 pre-mRNA processing factor 8 homolog (S. cerevisiae)"""	RP13		11468273, 10411133	Standard	NM_006445		Approved	PRPC8, Prp8, hPrp8, SNRNP220	uc002fte.3	Q6P2Q9	OTTHUMG00000090553	ENST00000572621.1:c.4595G>A	17.37:g.1564035C>T	ENSP00000460348:p.Arg1532His					PRPF8_ENST00000304992.6_Missense_Mutation_p.R1532H	p.R1532H			Q6P2Q9	PRP8_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (25;0.0855)	28	4860	-			1532					O14547|O75965	Missense_Mutation	SNP	ENST00000572621.1	37	c.4595G>A	CCDS11010.1	.	.	.	.	.	.	.	.	.	.	c	30	5.051892	0.93793	.	.	ENSG00000174231	ENST00000304992;ENST00000540177	D	0.84873	-1.91	6.17	6.17	0.99709	Pre-mRNA-processing-splicing factor 8, U6-snRNA-binding (1);	0.000000	0.85682	D	0.000000	D	0.94105	0.8110	M	0.88105	2.93	0.80722	D	1	D	0.89917	1.0	D	0.76575	0.988	D	0.93932	0.7215	10	0.87932	D	0	.	20.8794	0.99867	0.0:1.0:0.0:0.0	.	1532	Q6P2Q9	PRP8_HUMAN	H	1532;59	ENSP00000304350:R1532H	ENSP00000304350:R1532H	R	-	2	0	PRPF8	1510785	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	5.935000	0.70145	2.941000	0.99782	0.655000	0.94253	CGT		0.502	PRPF8-002	NOVEL	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438412.2			5	59	0	0	0	0.000602	0	5	59				
MKI67	4288	broad.mit.edu	37	10	129906562	129906562	+	Missense_Mutation	SNP	C	C	T			TCGA-BJ-A45H-01A-12D-A23U-08	TCGA-BJ-A45H-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4bdbc383-8f81-410a-833e-1f039ceabddf	8cb61ce1-4085-4752-9f1e-91d7c1fee6ab	g.chr10:129906562C>T	ENST00000368654.3	-	13	3917	c.3542G>A	c.(3541-3543)gGa>gAa	p.G1181E	MKI67_ENST00000368653.3_Missense_Mutation_p.G821E	NM_002417.4	NP_002408.3	P46013	KI67_HUMAN	marker of proliferation Ki-67	1181	16 X 122 AA approximate repeats.				cell proliferation (GO:0008283)|cellular response to heat (GO:0034605)|DNA metabolic process (GO:0006259)|hyaluronan metabolic process (GO:0030212)|meiotic nuclear division (GO:0007126)|organ regeneration (GO:0031100)|response to organic cyclic compound (GO:0014070)	chromosome, centromeric region (GO:0000775)|condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)			NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(30)|lung(64)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|soft_tissue(1)|stomach(10)|upper_aerodigestive_tract(4)|urinary_tract(4)	159		all_epithelial(44;2.12e-05)|all_lung(145;0.00679)|Lung NSC(174;0.00998)|all_neural(114;0.0936)|Colorectal(57;0.14)|Breast(234;0.166)|Melanoma(40;0.203)				CTCATCACCTCCTGCTGGTTT	0.468																																						ENST00000368654.3																			0				NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(30)|lung(64)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|soft_tissue(1)|stomach(10)|upper_aerodigestive_tract(4)|urinary_tract(4)	159						c.(3541-3543)gGa>gAa		marker of proliferation Ki-67							267.0	254.0	259.0					10																	129906562		2203	4300	6503	SO:0001583	missense	4288				cell proliferation	nucleolus	ATP binding|protein C-terminus binding	g.chr10:129906562C>T	X65550	CCDS7659.1, CCDS53588.1	10q26.2	2014-06-12	2013-10-10		ENSG00000148773	ENSG00000148773			7107	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 105"""	176741	"""antigen identified by monoclonal antibody Ki-67"""			2571566, 16206250	Standard	NM_002417		Approved	MIB-, PPP1R105	uc001lke.3	P46013	OTTHUMG00000019255	ENST00000368654.3:c.3542G>A	10.37:g.129906562C>T	ENSP00000357643:p.Gly1181Glu					MKI67_ENST00000368653.3_Missense_Mutation_p.G821E	p.G1181E	NM_002417.4	NP_002408.3	P46013	KI67_HUMAN			13	3917	-		all_epithelial(44;2.12e-05)|all_lung(145;0.00679)|Lung NSC(174;0.00998)|all_neural(114;0.0936)|Colorectal(57;0.14)|Breast(234;0.166)|Melanoma(40;0.203)	1181			16 X 122 AA approximate repeats.		Q5VWH2	Missense_Mutation	SNP	ENST00000368654.3	37	c.3542G>A	CCDS7659.1	.	.	.	.	.	.	.	.	.	.	C	0.007	-1.993908	0.00439	.	.	ENSG00000148773	ENST00000368654;ENST00000368653;ENST00000537609	T;T	0.01804	4.63;4.63	2.61	-5.23	0.02798	.	2.090630	0.02647	N	0.105986	T	0.01124	0.0037	N	0.25890	0.77	0.09310	N	1	B;B;B	0.13145	0.001;0.007;0.005	B;B;B	0.15484	0.001;0.013;0.004	T	0.47749	-0.9093	10	0.02654	T	1	.	0.189	0.00132	0.2608:0.1806:0.2667:0.2919	.	1180;821;1181	F5H4V4;P46013-2;P46013	.;.;KI67_HUMAN	E	1181;821;1180	ENSP00000357643:G1181E;ENSP00000357642:G821E	ENSP00000357642:G821E	G	-	2	0	MKI67	129796552	0.522000	0.26266	0.000000	0.03702	0.006000	0.05464	0.185000	0.16958	-2.123000	0.00823	-0.802000	0.03209	GGA		0.468	MKI67-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050999.1	NM_002417		15	261	0	0	0	0.002450	0	15	261				
PPP1R12B	4660	broad.mit.edu	37	1	202531948	202531948	+	Silent	SNP	C	C	T	rs375992469		TCGA-BJ-A45H-01A-12D-A23U-08	TCGA-BJ-A45H-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4bdbc383-8f81-410a-833e-1f039ceabddf	8cb61ce1-4085-4752-9f1e-91d7c1fee6ab	g.chr1:202531948C>T	ENST00000608999.1	+	20	2703	c.2550C>T	c.(2548-2550)taC>taT	p.Y850Y	PPP1R12B_ENST00000391959.3_Silent_p.Y76Y|PPP1R12B_ENST00000336894.4_Silent_p.Y850Y|PPP1R12B_ENST00000367270.4_Silent_p.Y76Y|PPP1R12B_ENST00000290419.5_3'UTR	NM_001197131.1|NM_002481.3	NP_001184060.1|NP_002472.2	O60237	MYPT2_HUMAN	protein phosphatase 1, regulatory subunit 12B	850					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|positive regulation of catalytic activity (GO:0043085)|regulation of muscle contraction (GO:0006937)|signal transduction (GO:0007165)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)	enzyme activator activity (GO:0008047)			central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(7)|lung(17)|ovary(4)|skin(3)|urinary_tract(1)	41			BRCA - Breast invasive adenocarcinoma(75;0.166)			GTGATTCTTACGGTGACCGGG	0.493																																						ENST00000406302.3																			0				central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(7)|lung(17)|ovary(4)|skin(3)|urinary_tract(1)	41						c.(2548-2550)taC>taT		protein phosphatase 1, regulatory subunit 12B							52.0	61.0	58.0					1																	202531948		2203	4300	6503	SO:0001819	synonymous_variant	4660				regulation of muscle contraction|signal transduction	cytoplasm	enzyme activator activity	g.chr1:202531948C>T	AB003062	CCDS1426.1, CCDS44294.1, CCDS44295.1, CCDS53458.1, CCDS53459.1, CCDS73005.1	1q32.1	2013-01-10	2011-10-04	2001-08-10	ENSG00000077157	ENSG00000077157		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Ankyrin repeat domain containing"""	7619	protein-coding gene	gene with protein product	"""myosin phosphatase regulatory subunit"", ""myosin phosphatase, target subunit 2"""	603768	"""protein phosphatase 1, regulatory (inhibitor) subunit 12B"""	MYPT2		9570949	Standard	NM_002481		Approved	MGC87886, MGC131980, PP1bp55	uc001gya.2	O60237	OTTHUMG00000041393	ENST00000608999.1:c.2550C>T	1.37:g.202531948C>T						PPP1R12B_ENST00000336894.4_Silent_p.Y850Y|PPP1R12B_ENST00000367270.4_Silent_p.Y76Y|PPP1R12B_ENST00000391959.3_Silent_p.Y76Y|PPP1R12B_ENST00000290419.5_3'UTR	p.Y850Y	NM_001197131.1|NM_002481.3	NP_001184060.1|NP_002472.2	O60237	MYPT2_HUMAN	BRCA - Breast invasive adenocarcinoma(75;0.166)		20	2703	+			850					A8MYF5|B7ZMN6|Q2TAI8|Q5T506|Q5VUK2|Q8N179|Q9HCB7|Q9HCB8	Silent	SNP	ENST00000608999.1	37	c.2550C>T	CCDS1426.1																																																																																				0.493	PPP1R12B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000099166.3	NM_032105		4	135	0	0	0	0.000248	0	4	135				
TXNL1	9352	broad.mit.edu	37	18	54293600	54293600	+	Nonsense_Mutation	SNP	G	G	A			TCGA-BJ-A45H-01A-12D-A23U-08	TCGA-BJ-A45H-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4bdbc383-8f81-410a-833e-1f039ceabddf	8cb61ce1-4085-4752-9f1e-91d7c1fee6ab	g.chr18:54293600G>A	ENST00000217515.6	-	2	391	c.187C>T	c.(187-189)Cag>Tag	p.Q63*	TXNL1_ENST00000590954.1_Nonsense_Mutation_p.Q63*|TXNL1_ENST00000540155.1_5'UTR	NM_004786.2	NP_004777.1	O43396	TXNL1_HUMAN	thioredoxin-like 1	63	Thioredoxin.				cell redox homeostasis (GO:0045454)|glycerol ether metabolic process (GO:0006662)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|proteasome complex (GO:0000502)	disulfide oxidoreductase activity (GO:0015036)|protein disulfide oxidoreductase activity (GO:0015035)			endometrium(1)|large_intestine(1)|lung(1)|urinary_tract(1)	4				READ - Rectum adenocarcinoma(59;0.193)|Colorectal(16;0.211)		ACCTGACACTGATGTACATCG	0.343																																						ENST00000217515.6																			0				endometrium(1)|large_intestine(1)|lung(1)|urinary_tract(1)	4						c.(187-189)Cag>Tag		thioredoxin-like 1							128.0	134.0	132.0					18																	54293600		2203	4300	6503	SO:0001587	stop_gained	9352				cell redox homeostasis|electron transport chain|glycerol ether metabolic process|transport	cytoplasm	electron carrier activity|protein disulfide oxidoreductase activity	g.chr18:54293600G>A	AF003938	CCDS11961.1	18q21.31	2011-01-17	2004-05-06	2004-05-07	ENSG00000091164	ENSG00000091164			12436	protein-coding gene	gene with protein product	"""thioredoxin-like, 32kD"""	603049	"""thioredoxin-like, 32kDa"""	TXNL		9473519, 9668102	Standard	NM_004786		Approved	Txl, TRP32	uc002lgg.3	O43396	OTTHUMG00000132722	ENST00000217515.6:c.187C>T	18.37:g.54293600G>A	ENSP00000217515:p.Gln63*					TXNL1_ENST00000590954.1_Nonsense_Mutation_p.Q63*|TXNL1_ENST00000540155.1_5'UTR	p.Q63*	NM_004786.2	NP_004777.1	O43396	TXNL1_HUMAN		READ - Rectum adenocarcinoma(59;0.193)|Colorectal(16;0.211)	2	391	-			63			Thioredoxin.			Nonsense_Mutation	SNP	ENST00000217515.6	37	c.187C>T	CCDS11961.1	.	.	.	.	.	.	.	.	.	.	G	37	6.504314	0.97620	.	.	ENSG00000091164	ENST00000217515	.	.	.	5.56	4.68	0.58851	.	0.228496	0.45606	D	0.000347	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.9832	0.80127	0.0:0.1354:0.8646:0.0	.	.	.	.	X	63	.	ENSP00000217515:Q63X	Q	-	1	0	TXNL1	52444598	1.000000	0.71417	1.000000	0.80357	0.831000	0.47069	6.696000	0.74598	1.328000	0.45358	0.655000	0.94253	CAG		0.343	TXNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256064.2			7	114	0	0	0	0.003080	0	7	114				
SIPA1L1	26037	broad.mit.edu	37	14	72117175	72117175	+	Missense_Mutation	SNP	C	C	G			TCGA-BJ-A45H-01A-12D-A23U-08	TCGA-BJ-A45H-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4bdbc383-8f81-410a-833e-1f039ceabddf	8cb61ce1-4085-4752-9f1e-91d7c1fee6ab	g.chr14:72117175C>G	ENST00000555818.1	+	5	2290	c.1942C>G	c.(1942-1944)Cga>Gga	p.R648G	SIPA1L1_ENST00000358550.2_Missense_Mutation_p.R648G|SIPA1L1_ENST00000537413.1_Missense_Mutation_p.R123G|SIPA1L1_ENST00000381232.3_Missense_Mutation_p.R648G	NM_001284247.1|NM_015556.1	NP_001271176.1|NP_056371.1	O43166	SI1L1_HUMAN	signal-induced proliferation-associated 1 like 1	648	Rap-GAP. {ECO:0000255|PROSITE- ProRule:PRU00165}.				actin cytoskeleton reorganization (GO:0031532)|activation of Rap GTPase activity (GO:0032861)|ephrin receptor signaling pathway (GO:0048013)|regulation of axonogenesis (GO:0050770)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of Rap GTPase activity (GO:0032317)|regulation of synaptic plasticity (GO:0048167)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	GTPase activator activity (GO:0005096)			NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(11)|kidney(1)|large_intestine(22)|liver(2)|lung(25)|ovary(3)|prostate(3)|skin(3)|stomach(1)	78				all cancers(60;0.00169)|BRCA - Breast invasive adenocarcinoma(234;0.00912)|OV - Ovarian serous cystadenocarcinoma(108;0.0109)		ATTGGGAGAGCGAGTTCGGCT	0.443																																						ENST00000555818.1																			0				NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(11)|kidney(1)|large_intestine(22)|liver(2)|lung(25)|ovary(3)|prostate(3)|skin(3)|stomach(1)	78						c.(1942-1944)Cga>Gga		signal-induced proliferation-associated 1 like 1							108.0	104.0	106.0					14																	72117175		2203	4300	6503	SO:0001583	missense	26037				actin cytoskeleton reorganization|activation of Rap GTPase activity|regulation of dendritic spine morphogenesis	cell junction|cytoplasm|dendritic spine|postsynaptic density|postsynaptic membrane|synaptosome	GTPase activator activity	g.chr14:72117175C>G	AB007900	CCDS9807.1, CCDS61490.1, CCDS61491.1	14q24.1	2003-12-11				ENSG00000197555			20284	protein-coding gene	gene with protein product						9858596	Standard	XM_005267514		Approved	KIAA0440, E6TP1	uc001xmr.1	O43166		ENST00000555818.1:c.1942C>G	14.37:g.72117175C>G	ENSP00000450832:p.Arg648Gly					SIPA1L1_ENST00000381232.3_Missense_Mutation_p.R648G|SIPA1L1_ENST00000358550.2_Missense_Mutation_p.R648G|SIPA1L1_ENST00000537413.1_Missense_Mutation_p.R123G	p.R648G	NM_015556.1	NP_056371.1	O43166	SI1L1_HUMAN		all cancers(60;0.00169)|BRCA - Breast invasive adenocarcinoma(234;0.00912)|OV - Ovarian serous cystadenocarcinoma(108;0.0109)	5	2290	+			648			Rap-GAP.		J3KP19|O95321|Q9UDU4|Q9UNU4	Missense_Mutation	SNP	ENST00000555818.1	37	c.1942C>G	CCDS9807.1	.	.	.	.	.	.	.	.	.	.	C	19.05	3.751466	0.69533	.	.	ENSG00000197555	ENST00000381232;ENST00000555818;ENST00000358550;ENST00000537413;ENST00000555066	D;D;D;D;D	0.95171	-3.63;-3.63;-3.63;-3.63;-3.63	5.56	4.65	0.58169	Rap/ran-GAP (2);	0.051517	0.85682	D	0.000000	D	0.97810	0.9281	M	0.92738	3.34	0.58432	D	0.999994	D;P;D;D;D	0.76494	0.998;0.88;0.995;0.999;0.997	D;P;D;D;D	0.81914	0.972;0.762;0.949;0.979;0.995	D	0.98903	1.0777	10	0.87932	D	0	-15.1891	15.9431	0.79773	0.1361:0.8639:0.0:0.0	.	123;648;123;648;648	F5GYF8;A6H8W6;B4DYX7;O43166-2;O43166	.;.;.;.;SI1L1_HUMAN	G	648;648;648;123;164	ENSP00000370630:R648G;ENSP00000450832:R648G;ENSP00000351352:R648G;ENSP00000440682:R123G;ENSP00000452450:R164G	ENSP00000351352:R648G	R	+	1	2	SIPA1L1	71186928	1.000000	0.71417	0.919000	0.36401	0.863000	0.49368	2.845000	0.48254	1.435000	0.47434	0.655000	0.94253	CGA		0.443	SIPA1L1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412806.1	NM_015556		8	69	0	0	0	0.003080	0	8	69				
BRAF	673	broad.mit.edu	37	7	140453136	140453136	+	Missense_Mutation	SNP	A	A	T	rs121913377|rs113488022|rs121913227|rs397516897		TCGA-BJ-A45H-01A-12D-A23U-08	TCGA-BJ-A45H-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4bdbc383-8f81-410a-833e-1f039ceabddf	8cb61ce1-4085-4752-9f1e-91d7c1fee6ab	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		14	50	0	0	0	0.002450	0	14	50				
AK9	221264	broad.mit.edu	37	6	109954219	109954219	+	Missense_Mutation	SNP	C	C	T			TCGA-BJ-A45H-01A-12D-A23U-08	TCGA-BJ-A45H-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4bdbc383-8f81-410a-833e-1f039ceabddf	8cb61ce1-4085-4752-9f1e-91d7c1fee6ab	g.chr6:109954219C>T	ENST00000424296.2	-	12	1237	c.1161G>A	c.(1159-1161)atG>atA	p.M387I	AK9_ENST00000341338.6_5'UTR|AK9_ENST00000285397.5_Missense_Mutation_p.M387I|AK9_ENST00000368948.2_Missense_Mutation_p.M387I	NM_001145128.2	NP_001138600.2	Q5TCS8	KAD9_HUMAN	adenylate kinase 9	387					ADP phosphorylation (GO:0006757)|AMP phosphorylation (GO:0006756)|CDP phosphorylation (GO:0061508)|CMP phosphorylation (GO:0061566)|dADP phosphorylation (GO:0006174)|dAMP phosphorylation (GO:0061565)|dCDP phosphorylation (GO:0061570)|dCMP phosphorylation (GO:0061567)|dGDP phosphorylation (GO:0006186)|GDP phosphorylation (GO:0061568)|TDP phosphorylation (GO:0061571)|UDP phosphorylation (GO:0061569)	cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|nucleoside diphosphate kinase activity (GO:0004550)|nucleoside phosphate kinase activity (GO:0050145)										GTGGTCCTGGCATAGGTGGAA	0.373																																						ENST00000424296.2																			0											c.(1159-1161)atG>atA		adenylate kinase 9							139.0	128.0	132.0					6																	109954219		2203	4300	6503	SO:0001583	missense	221264							g.chr6:109954219C>T	AK131244, BC146443, BC087860	CCDS5077.1, CCDS55048.1	6q21	2013-04-29	2013-04-29	2013-04-29			2.7.4.3		33814	protein-coding gene	gene with protein product		615358	"""chromosome 6 open reading frame 224"", ""adenylate kinase domain containing 2"", ""chromosome 6 open reading frame 199"", ""adenylate kinase domain containing 1"""	C6orf224, AKD2, C6orf199, AKD1		23416111	Standard	NM_145025		Approved	FLJ42177, FLJ25791, dJ70A9.1, MGC26954		Q5TCS8		ENST00000424296.2:c.1161G>A	6.37:g.109954219C>T	ENSP00000410186:p.Met387Ile					AK9_ENST00000285397.5_Missense_Mutation_p.M387I|AK9_ENST00000368948.2_Missense_Mutation_p.M387I|AK9_ENST00000341338.6_5'UTR	p.M387I	NM_001145128.2	NP_001138600.2					12	1237	-								A6NL75|B2RDJ0|B6ZDM7|Q3MIS4|Q5I0W8|Q6ZNF1|Q6ZVR7|Q8N7C6|Q8WW00|Q96NF4	Missense_Mutation	SNP	ENST00000424296.2	37	c.1161G>A	CCDS55048.1	.	.	.	.	.	.	.	.	.	.	C	22.1	4.249544	0.80024	.	.	ENSG00000155085	ENST00000424296;ENST00000368948;ENST00000285397	T;T;T	0.64991	-0.13;-0.08;2.69	5.6	5.6	0.85130	.	0.037370	0.85682	D	0.000000	T	0.35508	0.0934	N	0.04768	-0.165	0.80722	D	1	P;B	0.49307	0.922;0.327	P;B	0.45610	0.487;0.394	T	0.32241	-0.9914	9	.	.	.	-18.7395	19.5908	0.95509	0.0:1.0:0.0:0.0	.	387;387	Q5TCS8-2;Q5TCS8	.;AKD1_HUMAN	I	387	ENSP00000410186:M387I;ENSP00000357944:M387I;ENSP00000285397:M387I	.	M	-	3	0	AKD1	110060912	1.000000	0.71417	1.000000	0.80357	0.859000	0.49053	5.412000	0.66392	2.628000	0.89032	0.467000	0.42956	ATG		0.373	AK9-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001145128		14	36	0	0	0	0.004007	0	14	36				
LOC101927209	101927209	broad.mit.edu	37	1	142713977	142713977	+	lincRNA	DEL	T	T	-	rs140223576		TCGA-BJ-A45H-01A-12D-A23U-08	TCGA-BJ-A45H-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4bdbc383-8f81-410a-833e-1f039ceabddf	8cb61ce1-4085-4752-9f1e-91d7c1fee6ab	g.chr1:142713977delT	ENST00000610091.1	-	0	1681																											ATCCATATACTAAAAAGGTTA	0.294																																						ENST00000369381.2																			0																																																			0							g.chr1:142713977delT																													1.37:g.142713977delT														0	628	-									RNA	DEL	ENST00000610091.1	37																																																																																						0.294	RP11-417J8.6-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000037265.2			3	4						3	4	---	---	---	---
