#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
SH3BGR	6450	broad.mit.edu	37	21	40834416	40834416	+	Missense_Mutation	SNP	C	C	T			TCGA-EL-A3CP-01A-11D-A19J-08	TCGA-EL-A3CP-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	064b25ee-8746-499f-96f9-9bbde3961bb8	5aeaaf99-9861-46f1-b614-7cf0ed7f11dd	g.chr21:40834416C>T	ENST00000333634.4	+	2	428	c.350C>T	c.(349-351)cCt>cTt	p.P117L	SH3BGR_ENST00000380637.3_Missense_Mutation_p.P6L|SH3BGR_ENST00000458295.1_Missense_Mutation_p.P6L|SH3BGR_ENST00000380634.1_Missense_Mutation_p.P6L|SH3BGR_ENST00000380631.1_Missense_Mutation_p.P6L	NM_007341.2	NP_031367	P55822	SH3BG_HUMAN	SH3 domain binding glutamate-rich protein	117					positive regulation of signal transduction (GO:0009967)|protein complex assembly (GO:0006461)	cytosol (GO:0005829)	SH3/SH2 adaptor activity (GO:0005070)			NS(1)|breast(1)|kidney(1)|large_intestine(3)|lung(2)	8		all_cancers(19;1.16e-23)|all_epithelial(19;1.22e-20)|Prostate(19;2.55e-06)|Breast(209;0.0133)		STAD - Stomach adenocarcinoma(101;0.00151)		GAGAATGTTCCTGGAGAGAAA	0.418																																						ENST00000333634.4																			0				NS(1)|breast(1)|kidney(1)|large_intestine(3)|lung(2)	8						c.(349-351)cCt>cTt		SH3 domain binding glutamic acid-rich protein							106.0	115.0	112.0					21																	40834416		2203	4300	6503	SO:0001583	missense	6450				protein complex assembly	cytosol	SH3 domain binding|SH3/SH2 adaptor activity	g.chr21:40834416C>T		CCDS13666.1, CCDS33560.1	21q22.3	2014-02-19	2014-02-19		ENSG00000185437	ENSG00000185437			10822	protein-coding gene	gene with protein product	"""21-glutamic acid-rich protein"""	602230	"""SH3 domain binding glutamic acid-rich protein"""			9050928	Standard	NM_007341		Approved	21-GARP	uc002yya.3	P55822	OTTHUMG00000074113	ENST00000333634.4:c.350C>T	21.37:g.40834416C>T	ENSP00000332513:p.Pro117Leu					SH3BGR_ENST00000380634.1_Missense_Mutation_p.P6L|SH3BGR_ENST00000380637.3_Missense_Mutation_p.P6L|SH3BGR_ENST00000380631.1_Missense_Mutation_p.P6L|SH3BGR_ENST00000458295.1_Missense_Mutation_p.P6L	p.P117L	NM_007341.2	NP_031367.1	P55822	SH3BG_HUMAN		STAD - Stomach adenocarcinoma(101;0.00151)	2	428	+		all_cancers(19;1.16e-23)|all_epithelial(19;1.22e-20)|Prostate(19;2.55e-06)|Breast(209;0.0133)	117					A6ND59|D3DSI2|Q9BRB8	Missense_Mutation	SNP	ENST00000333634.4	37	c.350C>T	CCDS13666.1	.	.	.	.	.	.	.	.	.	.	C	28.6	4.932479	0.92458	.	.	ENSG00000185437	ENST00000380637;ENST00000380634;ENST00000458295;ENST00000440288;ENST00000380631;ENST00000333634	T;T;T;T;T	0.77489	0.62;0.62;0.72;0.62;-1.1	4.98	4.98	0.66077	Thioredoxin-like fold (2);	0.000000	0.85682	D	0.000000	D	0.89210	0.6650	M	0.83692	2.655	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.90663	0.4592	10	0.72032	D	0.01	.	18.6519	0.91433	0.0:1.0:0.0:0.0	.	117	P55822	SH3BG_HUMAN	L	6;6;6;6;6;117	ENSP00000370011:P6L;ENSP00000370008:P6L;ENSP00000401572:P6L;ENSP00000370005:P6L;ENSP00000332513:P117L	ENSP00000332513:P117L	P	+	2	0	SH3BGR	39756286	1.000000	0.71417	0.991000	0.47740	0.995000	0.86356	7.319000	0.79040	2.479000	0.83701	0.655000	0.94253	CCT		0.418	SH3BGR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157377.6	NM_007341		4	61	0	0	0	1	0	4	61				
CNKSR1	10256	broad.mit.edu	37	1	26515956	26515956	+	Missense_Mutation	SNP	C	C	T	rs1045105	byFrequency	TCGA-EL-A3CP-01A-11D-A19J-08	TCGA-EL-A3CP-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	064b25ee-8746-499f-96f9-9bbde3961bb8	5aeaaf99-9861-46f1-b614-7cf0ed7f11dd	g.chr1:26515956C>T	ENST00000374253.5	+	21	2119	c.2080C>T	c.(2080-2082)Cac>Tac	p.H694Y	CNKSR1_ENST00000361530.6_Missense_Mutation_p.H687Y|CATSPER4_ENST00000456354.2_5'Flank|CNKSR1_ENST00000531191.1_Missense_Mutation_p.H429Y	NM_006314.2	NP_006305.2	Q969H4	CNKR1_HUMAN	connector enhancer of kinase suppressor of Ras 1	694				H -> N (in Ref. 1; AAC80558). {ECO:0000305}.	Ras protein signal transduction (GO:0007265)|Rho protein signal transduction (GO:0007266)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell cortex (GO:0005938)|cell-cell junction (GO:0005911)|plasma membrane (GO:0005886)	protein binding, bridging (GO:0030674)	p.H687Y(1)		breast(4)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(8)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	28		Colorectal(325;3.46e-05)|all_lung(284;0.000116)|Lung NSC(340;0.000154)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0133)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0298)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;2.72e-26)|Colorectal(126;1.24e-08)|COAD - Colon adenocarcinoma(152;9.31e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00072)|BRCA - Breast invasive adenocarcinoma(304;0.000959)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.00823)|READ - Rectum adenocarcinoma(331;0.0649)		ACAGTCCCCCCACTCCCTGCC	0.637													C|||	88	0.0175719	0.0605	0.0101	5008	,	,		17563	0.0		0.0	False		,,,				2504	0.001				NSCLC(180;1396 2109 28270 30756 34275)	ENST00000531191.1																			1	Substitution - Missense(1)	p.H687Y(1)	kidney(1)	breast(4)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(8)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	28						c.(1285-1287)Cac>Tac		connector enhancer of kinase suppressor of Ras 1							132.0	134.0	133.0					1																	26515956		2203	4300	6503	SO:0001583	missense	10256				Rho protein signal transduction|transmembrane receptor protein tyrosine kinase signaling pathway	cell cortex|cell-cell junction	protein binding, bridging	g.chr1:26515956C>T	AF100153	CCDS276.1, CCDS72732.1	1p35.3	2013-01-10			ENSG00000142675	ENSG00000142675		"""Sterile alpha motif (SAM) domain containing"", ""Pleckstrin homology (PH) domain containing"""	19700	protein-coding gene	gene with protein product		603272				9814705	Standard	NM_006314		Approved	CNK1, KSR, CNK	uc001blm.4	Q969H4	OTTHUMG00000007541	ENST00000374253.5:c.2080C>T	1.37:g.26515956C>T	ENSP00000363371:p.His694Tyr					CNKSR1_ENST00000374253.5_Missense_Mutation_p.H694Y|CNKSR1_ENST00000361530.6_Missense_Mutation_p.H687Y	p.H429Y			Q969H4	CNKR1_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;2.72e-26)|Colorectal(126;1.24e-08)|COAD - Colon adenocarcinoma(152;9.31e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00072)|BRCA - Breast invasive adenocarcinoma(304;0.000959)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.00823)|READ - Rectum adenocarcinoma(331;0.0649)	20	2292	+		Colorectal(325;3.46e-05)|all_lung(284;0.000116)|Lung NSC(340;0.000154)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0133)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0298)	694			PH.		B1AMW9|O95381	Missense_Mutation	SNP	ENST00000374253.5	37	c.1285C>T		.	.	.	.	.	.	.	.	.	.	C	0.015	-1.559943	0.00910	.	.	ENSG00000142675	ENST00000361530;ENST00000374253;ENST00000531191	T;T;T	0.14266	2.53;2.53;2.52	4.66	2.77	0.32553	.	1.288580	0.04684	N	0.412844	T	0.11495	0.0280	L	0.44542	1.39	0.80722	P	0.0	B;B	0.22604	0.044;0.072	B;B	0.19946	0.018;0.027	T	0.40478	-0.9561	9	0.02654	T	1	-0.9495	6.9902	0.24751	0.1255:0.6606:0.1346:0.0793	.	694;687	Q969H4;Q53GM7	CNKR1_HUMAN;.	Y	687;694;429	ENSP00000354609:H687Y;ENSP00000363371:H694Y;ENSP00000431817:H429Y	ENSP00000354609:H687Y	H	+	1	0	CNKSR1	26388543	0.000000	0.05858	0.005000	0.12908	0.007000	0.05969	0.030000	0.13688	0.660000	0.30964	-0.808000	0.03180	CAC		0.637	CNKSR1-007	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000089943.2	NM_006314		4	70	0	0	0	1	0	4	70				
CES1	1066	broad.mit.edu	37	16	55855375	55855375	+	Missense_Mutation	SNP	G	G	T	rs563293177		TCGA-EL-A3CP-01A-11D-A19J-08	TCGA-EL-A3CP-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	064b25ee-8746-499f-96f9-9bbde3961bb8	5aeaaf99-9861-46f1-b614-7cf0ed7f11dd	g.chr16:55855375G>T	ENST00000361503.4	-	5	725	c.595C>A	c.(595-597)Cgc>Agc	p.R199S	CES1_ENST00000566555.1_5'UTR|CES1_ENST00000422046.2_Missense_Mutation_p.R199S|CES1_ENST00000360526.3_Missense_Mutation_p.R200S			P23141	EST1_HUMAN	carboxylesterase 1	199			R -> H (in dbSNP:rs2307243).		epithelial cell differentiation (GO:0030855)|metabolic process (GO:0008152)|response to toxic substance (GO:0009636)	endoplasmic reticulum (GO:0005783)	carboxylic ester hydrolase activity (GO:0052689)|methylumbelliferyl-acetate deacetylase activity (GO:0047374)								all cancers(182;0.13)|Epithelial(162;0.137)	Benzocaine(DB01086)|Capecitabine(DB01101)|Ciclesonide(DB01410)|Clopidogrel(DB00758)|Cyclandelate(DB04838)|Dabigatran etexilate(DB06695)|Indomethacin(DB00328)|Irinotecan(DB00762)|L-Carnitine(DB00583)|Mycophenolate mofetil(DB00688)|Oseltamivir(DB00198)|Probucol(DB01599)|Rufinamide(DB06201)|Tamoxifen(DB00675)|Trandolapril(DB00519)	TGGACCCAGCGCAGGGCAGCC	0.587																																					NSCLC(162;1801 2756 42904 52896)	ENST00000422046.2																			0											c.(595-597)Cgc>Agc		carboxylesterase 1	Aminoglutethimide(DB00357)|Bezafibrate(DB01393)|Cholestyramine(DB01432)|Moexipril(DB00691)						49.0	51.0	50.0					16																	55855375		2198	4300	6498	SO:0001583	missense	1066				response to toxin	endoplasmic reticulum lumen	carboxylesterase activity|methyl indole-3-acetate esterase activity|methyl jasmonate esterase activity|methyl salicylate esterase activity	g.chr16:55855375G>T	BC012418	CCDS32450.1, CCDS45488.1, CCDS45489.1	16q22.2	2010-10-12	2010-10-12		ENSG00000198848	ENSG00000198848	3.1.1.1	"""Carboxylesterases"""	1863	protein-coding gene	gene with protein product	"""human monocyte/macrophage serine esterase 1"""	114835	"""carboxylesterase 1 (monocyte/macrophage serine esterase 1)"""			2070086, 20931200	Standard	XM_005255774		Approved	HMSE, CES2, HMSE1, SES1, CEH, CES1A1, CES1A2	uc002eil.3	P23141		ENST00000361503.4:c.595C>A	16.37:g.55855375G>T	ENSP00000355193:p.Arg199Ser					CES1_ENST00000566555.1_5'UTR|CES1_ENST00000360526.3_Missense_Mutation_p.R200S|CES1_ENST00000361503.4_Missense_Mutation_p.R199S	p.R199S			P23141	EST1_HUMAN		all cancers(182;0.13)|Epithelial(162;0.137)	5	876	-			199		R -> H (in dbSNP:rs2307243).			A6NIM1|A8K3K8|A8K844|E9PAU8|P82127|Q00015|Q13657|Q14062|Q16737|Q16788|Q549X7|Q549X8|Q86UK2|Q96EE8|Q9UC52|Q9UDG8|Q9UK77|Q9ULY2	Missense_Mutation	SNP	ENST00000361503.4	37	c.595C>A	CCDS45488.1	.	.	.	.	.	.	.	.	.	.	.	13.42	2.230494	0.39399	.	.	ENSG00000198848	ENST00000360526;ENST00000361503;ENST00000422046;ENST00000426667	T;T;T	0.70399	-0.48;-0.48;-0.48	4.18	4.18	0.49190	Carboxylesterase, type B (1);	0.736535	0.12828	N	0.435838	T	0.73666	0.3616	M	0.81802	2.56	0.23673	N	0.99714	B;B;B	0.20368	0.024;0.024;0.044	B;B;B	0.23716	0.033;0.033;0.048	T	0.66670	-0.5865	10	0.51188	T	0.08	.	14.0527	0.64747	0.0:0.0:1.0:0.0	.	199;199;200	E9PAU8;P23141;P23141-2	.;EST1_HUMAN;.	S	200;199;199;64	ENSP00000353720:R200S;ENSP00000355193:R199S;ENSP00000390492:R199S	ENSP00000353720:R200S	R	-	1	0	CES1	54412876	0.961000	0.32948	0.578000	0.28575	0.533000	0.34776	5.401000	0.66326	1.906000	0.55180	0.456000	0.33151	CGC		0.587	CES1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000433285.1	NM_001266		3	35	1	0	0.184627	1	0.184627	3	35				
SPATA31D1	389763	broad.mit.edu	37	9	84606454	84606454	+	Missense_Mutation	SNP	A	A	T			TCGA-EL-A3CP-01A-11D-A19J-08	TCGA-EL-A3CP-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	064b25ee-8746-499f-96f9-9bbde3961bb8	5aeaaf99-9861-46f1-b614-7cf0ed7f11dd	g.chr9:84606454A>T	ENST00000344803.2	+	4	1116	c.1069A>T	c.(1069-1071)Acc>Tcc	p.T357S		NM_001001670.2	NP_001001670.1	Q6ZQQ2	S31D1_HUMAN	SPATA31 subfamily D, member 1	357					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											TTCAGAATTCACCTGGTGGCA	0.463																																						ENST00000344803.2																			0											c.(1069-1071)Acc>Tcc		SPATA31 subfamily D, member 1							144.0	131.0	135.0					9																	84606454		1911	4138	6049	SO:0001583	missense	389763							g.chr9:84606454A>T		CCDS47986.1	9q21.32	2012-10-12	2012-10-12	2012-10-12	ENSG00000214929	ENSG00000214929			37283	protein-coding gene	gene with protein product			"""family with sequence similarity 75, member D1"""	FAM75D1			Standard	NM_001001670		Approved	FLJ46321	uc004amn.3	Q6ZQQ2	OTTHUMG00000169122	ENST00000344803.2:c.1069A>T	9.37:g.84606454A>T	ENSP00000341988:p.Thr357Ser						p.T357S	NM_001001670.2	NP_001001670.1					4	1116	+									Missense_Mutation	SNP	ENST00000344803.2	37	c.1069A>T	CCDS47986.1	.	.	.	.	.	.	.	.	.	.	T	0.013	-1.643233	0.00792	.	.	ENSG00000214929	ENST00000344803	T	0.02916	4.11	2.87	-0.897	0.10553	.	0.954226	0.08565	N	0.926948	T	0.00552	0.0018	N	0.00057	-2.36	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.45789	-0.9237	10	0.02654	T	1	0.1707	3.1464	0.06473	0.2025:0.3803:0.0:0.4172	.	357	Q6ZQQ2	F75D1_HUMAN	S	357	ENSP00000341988:T357S	ENSP00000341988:T357S	T	+	1	0	FAM75D1	83796274	0.000000	0.05858	0.000000	0.03702	0.019000	0.09904	0.003000	0.13083	-0.512000	0.06505	-0.262000	0.10625	ACC		0.463	SPATA31D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402325.1	NM_001001670		4	109	0	0	0	1	0	4	109				
HK3	3101	broad.mit.edu	37	5	176314337	176314337	+	Splice_Site	SNP	C	C	T			TCGA-EL-A3CP-01A-11D-A19J-08	TCGA-EL-A3CP-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	064b25ee-8746-499f-96f9-9bbde3961bb8	5aeaaf99-9861-46f1-b614-7cf0ed7f11dd	g.chr5:176314337C>T	ENST00000292432.5	-	12	1693	c.1602G>A	c.(1600-1602)gaG>gaA	p.E534E		NM_002115.2	NP_002106.2	P52790	HXK3_HUMAN	hexokinase 3 (white cell)	534	Catalytic.|Hexokinase type-1 2.				carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|cellular glucose homeostasis (GO:0001678)|glucose 6-phosphate metabolic process (GO:0051156)|glucose transport (GO:0015758)|glycolytic process (GO:0006096)|hexose metabolic process (GO:0019318)|hexose transport (GO:0008645)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|protein complex (GO:0043234)	ATP binding (GO:0005524)|fructokinase activity (GO:0008865)|glucokinase activity (GO:0004340)|hexokinase activity (GO:0004396)|hormone binding (GO:0042562)|mannokinase activity (GO:0019158)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(21)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	47	all_cancers(89;0.000104)|Renal(175;0.000269)|Lung NSC(126;0.00696)|all_lung(126;0.0115)	Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			AATCCCCTCGCTCTGTGGGGG	0.637																																						ENST00000292432.5																			0				breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(21)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	47						c.e12-1		hexokinase 3 (white cell)							68.0	75.0	73.0					5																	176314337		2203	4300	6503	SO:0001630	splice_region_variant	3101				glucose transport|glycolysis|transmembrane transport	cytosol|membrane	ATP binding|glucokinase activity	g.chr5:176314337C>T		CCDS4407.1	5q35.2	2008-02-05			ENSG00000160883	ENSG00000160883	2.7.1.1		4925	protein-coding gene	gene with protein product		142570				8812439	Standard	NM_002115		Approved		uc003mfa.3	P52790	OTTHUMG00000130855	ENST00000292432.5:c.1601-1G>A	5.37:g.176314337C>T							p.E534_splice	NM_002115.2	NP_002106.2	P52790	HXK3_HUMAN	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)		12	1693	-	all_cancers(89;0.000104)|Renal(175;0.000269)|Lung NSC(126;0.00696)|all_lung(126;0.0115)	Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	534			Catalytic.		Q8N1E7	Splice_Site	SNP	ENST00000292432.5	37	c.1600_splice	CCDS4407.1																																																																																				0.637	HK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253428.1		Silent	13	39	0	0	0	1	0	13	39				
DTX1	1840	broad.mit.edu	37	12	113515335	113515335	+	Missense_Mutation	SNP	T	T	G			TCGA-EL-A3CP-01A-11D-A19J-08	TCGA-EL-A3CP-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	064b25ee-8746-499f-96f9-9bbde3961bb8	5aeaaf99-9861-46f1-b614-7cf0ed7f11dd	g.chr12:113515335T>G	ENST00000257600.3	+	2	869	c.366T>G	c.(364-366)gaT>gaG	p.D122E		NM_004416.2	NP_004407.2	Q86Y01	DTX1_HUMAN	deltex 1, E3 ubiquitin ligase	122	WWE 2. {ECO:0000255|PROSITE- ProRule:PRU00248}.				cell surface receptor signaling pathway (GO:0007166)|glial cell differentiation (GO:0010001)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of T cell differentiation (GO:0045581)|Notch signaling pathway (GO:0007219)|protein ubiquitination (GO:0016567)|regulation of Notch signaling pathway (GO:0008593)|regulation of RNA biosynthetic process (GO:2001141)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ligase activity (GO:0016874)|Notch binding (GO:0005112)|transcription coactivator activity (GO:0003713)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(2)|lung(11)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	32						CGGCCTACGATATGGACATCT	0.622																																						ENST00000257600.3																			0				central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(2)|lung(11)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	32						c.(364-366)gaT>gaG		deltex homolog 1 (Drosophila)							102.0	80.0	87.0					12																	113515335		2203	4300	6503	SO:0001583	missense	1840				negative regulation of neuron differentiation|Notch signaling pathway|regulation of Notch signaling pathway|transcription from RNA polymerase II promoter	cytoplasm|nucleus	Notch binding|SH3 domain binding|transcription coactivator activity|ubiquitin protein ligase binding|zinc ion binding	g.chr12:113515335T>G	AF053700	CCDS9164.1	12q24	2014-01-28	2014-01-28			ENSG00000135144			3060	protein-coding gene	gene with protein product		602582	"""deltex homolog 1 (Drosophila)"""			9590294, 12670957	Standard	NM_004416		Approved	hDx-1	uc001tuk.1	Q86Y01	OTTHUMG00000169610	ENST00000257600.3:c.366T>G	12.37:g.113515335T>G	ENSP00000257600:p.Asp122Glu						p.D122E	NM_004416.2	NP_004407.2	Q86Y01	DTX1_HUMAN			2	869	+			122			WWE 2.		O60630|Q9BS04	Missense_Mutation	SNP	ENST00000257600.3	37	c.366T>G	CCDS9164.1	.	.	.	.	.	.	.	.	.	.	T	8.577	0.881366	0.17467	.	.	ENSG00000135144	ENST00000257600	T	0.36157	1.27	3.13	2.21	0.28008	WWE domain (2);WWE domain, subgroup (1);	0.133606	0.47455	D	0.000233	T	0.34513	0.0900	L	0.45352	1.415	0.40375	D	0.979381	D	0.59767	0.986	P	0.55923	0.787	T	0.36407	-0.9749	10	0.08179	T	0.78	-11.4703	6.2807	0.21005	0.0:0.7501:0.0:0.2499	.	122	Q86Y01	DTX1_HUMAN	E	122	ENSP00000257600:D122E	ENSP00000257600:D122E	D	+	3	2	DTX1	111999718	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	3.418000	0.52721	0.496000	0.27904	-0.483000	0.04790	GAT		0.622	DTX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405045.2			5	62	0	0	0	1	0	5	62				
CROCC	9696	broad.mit.edu	37	1	17272075	17272075	+	Missense_Mutation	SNP	G	G	A	rs2781608		TCGA-EL-A3CP-01A-11D-A19J-08	TCGA-EL-A3CP-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	064b25ee-8746-499f-96f9-9bbde3961bb8	5aeaaf99-9861-46f1-b614-7cf0ed7f11dd	g.chr1:17272075G>A	ENST00000375541.5	+	15	2179	c.2110G>A	c.(2110-2112)Gcc>Acc	p.A704T	CROCC_ENST00000467938.1_3'UTR	NM_014675.3	NP_055490.3			ciliary rootlet coiled-coil, rootletin									p.A704T(11)		breast(3)|central_nervous_system(2)|cervix(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(1)|lung(20)|ovary(3)|prostate(9)|skin(3)|urinary_tract(1)	62		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000174)|all_lung(284;0.000234)|Renal(390;0.000518)|Ovarian(437;0.00669)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.63e-06)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.181)		GGCCGAGAAGGCCGAGGTGGC	0.657																																						ENST00000375541.5																			11	Substitution - Missense(11)	p.A704T(11)	kidney(7)|endometrium(1)|prostate(1)|lung(1)|central_nervous_system(1)	breast(3)|central_nervous_system(2)|cervix(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(1)|lung(20)|ovary(3)|prostate(9)|skin(3)|urinary_tract(1)	62						c.(2110-2112)Gcc>Acc		ciliary rootlet coiled-coil, rootletin							20.0	18.0	19.0					1																	17272075		2199	4291	6490	SO:0001583	missense	9696				cell cycle|cell projection organization|centrosome organization|protein localization	actin cytoskeleton|centriole|ciliary rootlet|plasma membrane	kinesin binding|structural molecule activity	g.chr1:17272075G>A	AB007914	CCDS30616.1	1p36.13	2010-06-04	2009-03-04	2009-03-04	ENSG00000058453	ENSG00000058453			21299	protein-coding gene	gene with protein product	"""rootletin, ciliary rootlet protein"""	615776				12427867, 17971504	Standard	XM_006711056		Approved	rootletin, ROLT	uc001azt.2	Q5TZA2	OTTHUMG00000002200	ENST00000375541.5:c.2110G>A	1.37:g.17272075G>A	ENSP00000364691:p.Ala704Thr					CROCC_ENST00000467938.1_3'UTR	p.A704T	NM_014675.3	NP_055490.3	Q5TZA2	CROCC_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.63e-06)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.181)	15	2179	+		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000174)|all_lung(284;0.000234)|Renal(390;0.000518)|Ovarian(437;0.00669)|Myeloproliferative disorder(586;0.0255)	704						Missense_Mutation	SNP	ENST00000375541.5	37	c.2110G>A	CCDS30616.1	202	0.0924908424908425	54	0.10975609756097561	27	0.07458563535911603	41	0.07167832167832168	80	0.10554089709762533	g	7.919	0.738064	0.15574	.	.	ENSG00000058453	ENST00000375541;ENST00000445545	T	0.10668	2.85	5.01	4.1	0.47936	.	.	.	.	.	T	0.00300	0.0009	L	0.47716	1.5	0.30387	N	0.781339	D;P;P	0.57899	0.981;0.952;0.873	P;P;B	0.52554	0.702;0.579;0.439	T	0.02477	-1.1153	9	0.16420	T	0.52	.	13.1749	0.59621	0.0795:0.0:0.9205:0.0	rs2781608;rs3871256;rs3872330	567;7;704	A1L0S8;Q5TZA2-2;Q5TZA2	.;.;CROCC_HUMAN	T	704;585	ENSP00000364691:A704T	ENSP00000364691:A704T	A	+	1	0	CROCC	17144662	0.999000	0.42202	0.970000	0.41538	0.013000	0.08279	2.720000	0.47252	1.448000	0.47680	-0.215000	0.12644	GCC		0.657	CROCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006249.2	NM_014675		3	32	0	0	0	1	0	3	32				
KIAA1109	84162	broad.mit.edu	37	4	123193357	123193357	+	Missense_Mutation	SNP	A	A	G			TCGA-EL-A3CP-01A-11D-A19J-08	TCGA-EL-A3CP-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	064b25ee-8746-499f-96f9-9bbde3961bb8	5aeaaf99-9861-46f1-b614-7cf0ed7f11dd	g.chr4:123193357A>G	ENST00000264501.4	+	48	8616	c.8243A>G	c.(8242-8244)gAg>gGg	p.E2748G	KIAA1109_ENST00000455637.1_Missense_Mutation_p.E2748G|KIAA1109_ENST00000388738.3_Missense_Mutation_p.E2748G			Q2LD37	K1109_HUMAN	KIAA1109	2748					regulation of cell growth (GO:0001558)|regulation of epithelial cell differentiation (GO:0030856)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(7)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(6)|large_intestine(33)|liver(4)|lung(74)|ovary(9)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(6)|urinary_tract(3)	172						GTTGTGTTTGAGAATGAACAA	0.383																																						ENST00000264501.4																			0				breast(7)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(6)|large_intestine(33)|liver(4)|lung(74)|ovary(9)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(6)|urinary_tract(3)	172						c.(8242-8244)gAg>gGg		KIAA1109							93.0	88.0	90.0					4																	123193357		1912	4113	6025	SO:0001583	missense	84162				regulation of cell growth|regulation of epithelial cell differentiation	integral to membrane|nucleus		g.chr4:123193357A>G	AL137384	CCDS43267.1	4q28.1	2012-07-09			ENSG00000138688	ENSG00000138688			26953	protein-coding gene	gene with protein product	"""fragile site-associated"""	611565				16386706	Standard	NM_015312		Approved	FLJ21404, FSA, KIAA1371, Tweek	uc003ieh.3	Q2LD37	OTTHUMG00000150116	ENST00000264501.4:c.8243A>G	4.37:g.123193357A>G	ENSP00000264501:p.Glu2748Gly					KIAA1109_ENST00000455637.1_Missense_Mutation_p.E2748G|KIAA1109_ENST00000388738.3_Missense_Mutation_p.E2748G	p.E2748G			Q2LD37	K1109_HUMAN			48	8616	+			2748					Q4W598|Q5CZA9|Q6ZS70|Q6ZV75|Q86XA5|Q8WVD8|Q9H742|Q9NT48|Q9NTC3|Q9NTI4|Q9P2H6|Q9UPP3	Missense_Mutation	SNP	ENST00000264501.4	37	c.8243A>G	CCDS43267.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	A|A|A	22.5|22.5|22.5	4.302448|4.302448|4.302448	0.81136|0.81136|0.81136	.|.|.	.|.|.	ENSG00000138688|ENSG00000138688|ENSG00000138688	ENST00000264501;ENST00000388738;ENST00000455637|ENST00000446180|ENST00000419325	T;T;T|.|.	0.25749|.|.	2.36;2.36;1.78|.|.	5.87|5.87|5.87	5.87|5.87|5.87	0.94306|0.94306|0.94306	.|.|.	0.000000|.|.	0.85682|.|.	D|.|.	0.000000|.|.	T|T|.	0.60996|0.60996|.	0.2312|0.2312|.	L|L|L	0.40543|0.40543|0.40543	1.245|1.245|1.245	0.53005|0.53005|0.53005	D|D|D	0.999962|0.999962|0.999962	D;D;D|.|.	0.76494|.|.	0.989;0.999;0.998|.|.	D;D;D|.|.	0.78314|.|.	0.979;0.991;0.979|.|.	T|T|.	0.57033|0.57033|.	-0.7880|-0.7880|.	10|5|.	0.72032|.|.	D|.|.	0.01|.|.	.|.|.	16.2774|16.2774|16.2774	0.82651|0.82651|0.82651	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.|.	2748;2747;2748|.|.	Q2LD37-6;Q2LD37-2;Q2LD37|.|.	.;.;K1109_HUMAN|.|.	G|G|W	2748|1321|705	ENSP00000264501:E2748G;ENSP00000373390:E2748G;ENSP00000389925:E2748G|.|.	ENSP00000264501:E2748G|.|.	E|R|X	+|+|+	2|1|3	0|2|0	KIAA1109|KIAA1109|KIAA1109	123412807|123412807|123412807	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.998000|0.998000|0.998000	0.95712|0.95712|0.95712	8.739000|8.739000|8.739000	0.91574|0.91574|0.91574	2.247000|2.247000|2.247000	0.74100|0.74100|0.74100	0.482000|0.482000|0.482000	0.46254|0.46254|0.46254	GAG|AGA|TGA		0.383	KIAA1109-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316415.1	NM_020797		14	48	0	0	0	1	0	14	48				
LOC101927648	101927648	broad.mit.edu	37	1	143403560	143403560	+	lincRNA	SNP	G	G	A			TCGA-EL-A3CP-01A-11D-A19J-08	TCGA-EL-A3CP-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	064b25ee-8746-499f-96f9-9bbde3961bb8	5aeaaf99-9861-46f1-b614-7cf0ed7f11dd	g.chr1:143403560G>A	ENST00000423249.1	-	0	59																											GGATTTCTTTGGCCACTTTGG	0.458																																						ENST00000423249.1																			0																																																			0							g.chr1:143403560G>A																													1.37:g.143403560G>A														0	59	-									RNA	SNP	ENST00000423249.1	37																																																																																						0.458	RP11-435B5.4-002	KNOWN	not_best_in_genome_evidence|basic	lincRNA	lincRNA	OTTHUMT00000037552.1			4	18	0	0	0	1	0	4	18				
TYW1	55253	broad.mit.edu	37	7	66474575	66474575	+	Silent	SNP	C	C	T	rs376806090		TCGA-EL-A3CP-01A-11D-A19J-08	TCGA-EL-A3CP-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	064b25ee-8746-499f-96f9-9bbde3961bb8	5aeaaf99-9861-46f1-b614-7cf0ed7f11dd	g.chr7:66474575C>T	ENST00000359626.5	+	4	443	c.279C>T	c.(277-279)ttC>ttT	p.F93F		NM_018264.2	NP_060734.2	Q9NV66	TYW1_HUMAN	tRNA-yW synthesizing protein 1 homolog (S. cerevisiae)	93	Flavodoxin-like. {ECO:0000255|PROSITE- ProRule:PRU00088}.				tRNA processing (GO:0008033)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	4 iron, 4 sulfur cluster binding (GO:0051539)|FMN binding (GO:0010181)|iron ion binding (GO:0005506)|lyase activity (GO:0016829)|oxidoreductase activity (GO:0016491)			breast(1)|endometrium(8)|kidney(10)|large_intestine(4)|lung(13)|ovary(1)|prostate(2)|skin(3)|stomach(2)|urinary_tract(2)	46		Lung NSC(55;0.0846)|all_lung(88;0.183)				ATTAGGGATTCGCAACAGTTC	0.398																																						ENST00000359626.5																			0				breast(1)|endometrium(8)|kidney(10)|large_intestine(4)|lung(13)|ovary(1)|prostate(2)|skin(3)|stomach(2)|urinary_tract(2)	46						c.(277-279)ttC>ttT		tRNA-yW synthesizing protein 1 homolog (S. cerevisiae)							134.0	119.0	124.0					7																	66474575		2203	4300	6503	SO:0001819	synonymous_variant	55253				tRNA processing		4 iron, 4 sulfur cluster binding|FMN binding|iron ion binding|oxidoreductase activity	g.chr7:66474575C>T	AK001762	CCDS5538.1	7q11.21	2007-11-29	2007-11-29	2007-11-29	ENSG00000198874	ENSG00000198874			25598	protein-coding gene	gene with protein product	"""tRNA-yW synthesizing protein 1 homolog A (S. cerevisiae)"""	611243	"""radical S-adenosyl methionine and flavodoxin domains 1"""	RSAFD1		16162496, 17150819	Standard	NM_018264		Approved	FLJ10900, MGC23001, MGC60291, YPL207W, TYW1A	uc003tvn.4	Q9NV66	OTTHUMG00000129723	ENST00000359626.5:c.279C>T	7.37:g.66474575C>T							p.F93F	NM_018264.2	NP_060734.2	Q9NV66	TYW1_HUMAN			4	443	+		Lung NSC(55;0.0846)|all_lung(88;0.183)	93			Flavodoxin-like.		Q6PJG8|Q75MG8|Q75MN3|Q86V12|Q8IVS7|Q9H9C4	Silent	SNP	ENST00000359626.5	37	c.279C>T	CCDS5538.1																																																																																				0.398	TYW1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251932.2	NM_018264		5	75	0	0	0	1	0	5	75				
GOLGA6L17P	642402	broad.mit.edu	37	15	85053124	85053124	+	RNA	SNP	G	G	T	rs192508624	byFrequency	TCGA-EL-A3CP-01A-11D-A19J-08	TCGA-EL-A3CP-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	064b25ee-8746-499f-96f9-9bbde3961bb8	5aeaaf99-9861-46f1-b614-7cf0ed7f11dd	g.chr15:85053124G>T	ENST00000414190.2	-	0	328					NR_003246.2																						TAAATGTTTTGTTTTTTTTTT	0.353																																						ENST00000414190.2																			0																																																			0							g.chr15:85053124G>T																													15.37:g.85053124G>T								NR_003246.2						0	328	-									RNA	SNP	ENST00000414190.2	37																																																																																						0.353	GOLGA6L5-003	KNOWN	mRNA_end_NF|basic	processed_transcript	pseudogene	OTTHUMT00000418579.1			3	26	1	0	0.115264	1	0.118008	3	26				
KRTAP4-11	653240	broad.mit.edu	37	17	39274291	39274291	+	Missense_Mutation	SNP	T	T	C	rs200214744|rs565505867	byFrequency	TCGA-EL-A3CP-01A-11D-A19J-08	TCGA-EL-A3CP-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	064b25ee-8746-499f-96f9-9bbde3961bb8	5aeaaf99-9861-46f1-b614-7cf0ed7f11dd	g.chr17:39274291T>C	ENST00000391413.2	-	1	315	c.277A>G	c.(277-279)Atg>Gtg	p.M93V		NM_033059.3	NP_149048.2	Q9BYQ6	KR411_HUMAN	keratin associated protein 4-11	93	27 X 5 AA repeats of C-C-[GIKRQVHEL]- [SPTR]-[STVQRMC].					keratin filament (GO:0045095)		p.M93V(4)		endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|lung(8)|prostate(5)|skin(1)	33		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			TGGCAGCACATAGACTGGCAG	0.662																																						ENST00000391413.2																			4	Substitution - Missense(4)	p.M93V(4)	endometrium(3)|kidney(1)	endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|lung(8)|prostate(5)|skin(1)	33						c.(277-279)Atg>Gtg		keratin associated protein 4-11							6.0	10.0	8.0					17																	39274291		651	1556	2207	SO:0001583	missense	653240					keratin filament		g.chr17:39274291T>C	AC025904	CCDS45675.1	17q21.2	2013-06-25			ENSG00000212721	ENSG00000212721		"""Keratin associated proteins"""	18911	protein-coding gene	gene with protein product			"""keratin associated protein 4-14"""	KRTAP4-14			Standard	NM_033059		Approved	KAP4.11, KAP4.14	uc002hvz.3	Q9BYQ6	OTTHUMG00000133586	ENST00000391413.2:c.277A>G	17.37:g.39274291T>C	ENSP00000375232:p.Met93Val						p.M93V	NM_033059.3	NP_149048.2	Q9BYQ6	KR411_HUMAN	STAD - Stomach adenocarcinoma(17;0.000371)		1	315	-		Breast(137;0.000496)	93			27 X 5 AA repeats of C-C-[GIKRQVHEL]- [SPTR]-[STVQRMC].		A0AUY2	Missense_Mutation	SNP	ENST00000391413.2	37	c.277A>G	CCDS45675.1	.	.	.	.	.	.	.	.	.	.	.	0.073	-1.199029	0.01581	.	.	ENSG00000212721	ENST00000391413	T	0.00580	6.43	4.25	-4.9	0.03094	.	.	.	.	.	T	0.00109	0.0003	N	0.00040	-2.49	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.43097	-0.9412	9	0.02654	T	1	.	0.4739	0.00536	0.3479:0.2455:0.1203:0.2863	.	93	Q9BYQ6	KR411_HUMAN	V	93	ENSP00000375232:M93V	ENSP00000375232:M93V	M	-	1	0	KRTAP4-11	36527817	.	.	0.012000	0.15200	0.010000	0.07245	.	.	-1.319000	0.02286	-1.132000	0.01976	ATG		0.662	KRTAP4-11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257690.1			5	47	0	0	0	1	0	5	47				
TDRD6	221400	broad.mit.edu	37	6	46656684	46656684	+	Silent	SNP	G	G	A			TCGA-EL-A3CP-01A-11D-A19J-08	TCGA-EL-A3CP-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	064b25ee-8746-499f-96f9-9bbde3961bb8	5aeaaf99-9861-46f1-b614-7cf0ed7f11dd	g.chr6:46656684G>A	ENST00000316081.6	+	1	819	c.819G>A	c.(817-819)tcG>tcA	p.S273S	RP11-446F17.3_ENST00000434329.2_RNA|RP11-446F17.3_ENST00000571590.1_RNA|TDRD6_ENST00000544460.1_Silent_p.S273S|RP11-446F17.3_ENST00000422284.2_RNA	NM_001010870.2	NP_001010870.1	O60522	TDRD6_HUMAN	tudor domain containing 6	273					germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|P granule (GO:0043186)				NS(1)|breast(9)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(25)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	80			Lung(136;0.192)			GCAGCGTCTCGCAGGAGATCC	0.627																																						ENST00000544460.1																			0				NS(1)|breast(9)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(25)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	80						c.(817-819)tcG>tcA		tudor domain containing 6							31.0	28.0	29.0					6																	46656684		2202	4300	6502	SO:0001819	synonymous_variant	221400				cell differentiation|multicellular organismal development|spermatogenesis	chromatoid body	nucleic acid binding	g.chr6:46656684G>A	AF039442	CCDS34470.1, CCDS55017.1	6p12.3	2013-01-23			ENSG00000180113	ENSG00000180113		"""Tudor domain containing"""	21339	protein-coding gene	gene with protein product	"""cancer/testis antigen 41.2"", ""spermatogenesis associated 36"""	611200				9610721	Standard	NM_001010870		Approved	NY-CO-45, bA446F17.4, CT41.2, SPATA36	uc003oyj.3	O60522	OTTHUMG00000014788	ENST00000316081.6:c.819G>A	6.37:g.46656684G>A						TDRD6_ENST00000316081.6_Silent_p.S273S	p.S273S	NM_001168359.1	NP_001161831.1	O60522	TDRD6_HUMAN	Lung(136;0.192)		1	1073	+			273					B3KWU2|F5H5M3|Q5HYB1|Q5VTS4|Q6ZMX5	Silent	SNP	ENST00000316081.6	37	c.819G>A	CCDS34470.1																																																																																				0.627	TDRD6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040800.1	XM_166443		3	23	0	0	0	1	0	3	23				
FAM86B3P	286042	broad.mit.edu	37	8	8095902	8095902	+	RNA	SNP	T	T	C			TCGA-EL-A3CP-01A-11D-A19J-08	TCGA-EL-A3CP-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	064b25ee-8746-499f-96f9-9bbde3961bb8	5aeaaf99-9861-46f1-b614-7cf0ed7f11dd	g.chr8:8095902T>C	ENST00000310542.3	+	0	0				ALG1L13P_ENST00000523017.1_RNA					family with sequence similarity 86, member B3, pseudogene																		ACACTCCCCCTAGGAGGGATC	0.632																																						ENST00000523017.1																			0																																																			0							g.chr8:8095902T>C			8p23.1	2013-06-10			ENSG00000173295	ENSG00000173295			44371	pseudogene	pseudogene							Standard	NR_024361		Approved		uc011kwt.2		OTTHUMG00000163669		8.37:g.8095902T>C														0	608	-									RNA	SNP	ENST00000310542.3	37																																																																																						0.632	FAM86B3P-005	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000448496.1			3	40	0	0	0	1	0	3	40				
PPAP2C	8612	broad.mit.edu	37	19	281534	281534	+	Missense_Mutation	SNP	A	A	G	rs61738956	byFrequency	TCGA-EL-A3CP-01A-11D-A19J-08	TCGA-EL-A3CP-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	064b25ee-8746-499f-96f9-9bbde3961bb8	5aeaaf99-9861-46f1-b614-7cf0ed7f11dd	g.chr19:281534A>G	ENST00000269812.3	-	6	770	c.721T>C	c.(721-723)Tgc>Cgc	p.C241R	PPAP2C_ENST00000327790.3_Missense_Mutation_p.C262R|PPAP2C_ENST00000434325.2_Missense_Mutation_p.C185R	NM_003712.2|NM_177526.1	NP_003703.1|NP_803545.1	O43688	LPP2_HUMAN	phosphatidic acid phosphatase type 2C	241					dephosphorylation (GO:0016311)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	phosphatidate phosphatase activity (GO:0008195)|phosphoprotein phosphatase activity (GO:0004721)			breast(1)|central_nervous_system(1)|endometrium(1)|lung(1)|skin(1)	5		all_cancers(10;1.13e-36)|all_epithelial(18;1.46e-23)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.1e-06)|all_lung(49;1.55e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GAGATGTAGCAGACCTGGTAG	0.617													.|||	4	0.000798722	0.003	0.0	5008	,	,		16144	0.0		0.0	False		,,,				2504	0.0					ENST00000269812.3																			0				breast(1)|central_nervous_system(1)|endometrium(1)|lung(1)|skin(1)	5						c.(721-723)Tgc>Cgc		phosphatidic acid phosphatase type 2C		G	ARG/CYS,ARG/CYS,ARG/CYS	16,4390		0,16,2187	72.0	64.0	67.0		721,553,784	0.2	0.3	19	dbSNP_129	67	0,8600		0,0,4300	yes	missense,missense,missense	PPAP2C	NM_003712.2,NM_177526.1,NM_177543.1	180,180,180	0,16,6487	GG,GA,AA		0.0,0.3631,0.123	benign,benign,benign	241/289,185/233,262/310	281534	16,12990	2203	4300	6503	SO:0001583	missense	8612				sphingolipid metabolic process	integral to membrane|plasma membrane	phosphatidate phosphatase activity|phosphoprotein phosphatase activity|sphingosine-1-phosphate phosphatase activity	g.chr19:281534A>G	AF035959	CCDS12023.1, CCDS12024.1, CCDS45889.1	19p13	2009-05-27				ENSG00000141934	3.1.3.4		9230	protein-coding gene	gene with protein product		607126				9570154, 9607309	Standard	NM_177543		Approved	PAP-2c, LPP2	uc002loh.3	O43688		ENST00000269812.3:c.721T>C	19.37:g.281534A>G	ENSP00000269812:p.Cys241Arg					PPAP2C_ENST00000434325.2_Missense_Mutation_p.C185R|PPAP2C_ENST00000327790.3_Missense_Mutation_p.C262R	p.C241R	NM_003712.2|NM_177526.1	NP_003703.1|NP_803545.1	O43688	LPP2_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)	6	770	-		all_cancers(10;1.13e-36)|all_epithelial(18;1.46e-23)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.1e-06)|all_lung(49;1.55e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)	241					A6NLV0|E9PAY8	Missense_Mutation	SNP	ENST00000269812.3	37	c.721T>C	CCDS12023.1	.	.	.	.	.	.	.	.	.	.	.	1.421	-0.572972	0.03882	0.003631	0.0	ENSG00000141934	ENST00000269812;ENST00000327790;ENST00000434325	T;T;T	0.73363	-0.74;-0.74;-0.74	5.05	0.224	0.15297	Phosphatidic acid phosphatase/chloroperoxidase, N-terminal (1);	0.335612	0.30168	N	0.010257	T	0.30572	0.0769	N	0.00064	-2.31	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.50423	-0.8830	10	0.44086	T	0.13	-25.9811	9.7739	0.40607	0.3795:0.0:0.6205:0.0	.	241;262	O43688;O43688-2	LPP2_HUMAN;.	R	241;262;185	ENSP00000269812:C241R;ENSP00000329697:C262R;ENSP00000388565:C185R	ENSP00000269812:C241R	C	-	1	0	PPAP2C	232534	0.053000	0.20554	0.260000	0.24451	0.251000	0.25915	1.204000	0.32296	-0.070000	0.12908	-0.349000	0.07799	TGC		0.617	PPAP2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451777.2			3	42	0	0	0	1	0	3	42				
DFNB31	25861	broad.mit.edu	37	9	117166263	117166263	+	Silent	SNP	G	G	T			TCGA-EL-A3CP-01A-11D-A19J-08	TCGA-EL-A3CP-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	064b25ee-8746-499f-96f9-9bbde3961bb8	5aeaaf99-9861-46f1-b614-7cf0ed7f11dd	g.chr9:117166263G>T	ENST00000362057.3	-	10	2499	c.2331C>A	c.(2329-2331)ggC>ggA	p.G777G	DFNB31_ENST00000374059.3_Silent_p.G426G|DFNB31_ENST00000265134.6_Silent_p.G394G	NM_001173425.1|NM_015404.3	NP_001166896.1|NP_056219	Q9P202	WHRN_HUMAN	deafness, autosomal recessive 31	777					inner ear receptor stereocilium organization (GO:0060122)|retina homeostasis (GO:0001895)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	actin filament (GO:0005884)|cilium (GO:0005929)|cytoplasm (GO:0005737)|stereocilia ankle link complex (GO:0002142)|stereocilium (GO:0032420)				central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(9)|liver(1)|lung(14)|ovary(5)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						GCCTTCCTCGGCCTGGGGCGC	0.652																																						ENST00000362057.3																			0				central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(9)|liver(1)|lung(14)|ovary(5)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						c.(2329-2331)ggC>ggA		deafness, autosomal recessive 31							84.0	73.0	77.0					9																	117166263		2203	4300	6503	SO:0001819	synonymous_variant	25861				inner ear receptor stereocilium organization|retina homeostasis|sensory perception of light stimulus|sensory perception of sound	cytoplasm|growth cone|stereocilium		g.chr9:117166263G>T	AK056190	CCDS6806.1, CCDS43870.1	9q32	2013-06-19			ENSG00000095397	ENSG00000095397			16361	protein-coding gene	gene with protein product	"""whirlin"""	607928				12833159, 17171570	Standard	NM_015404		Approved	CIP98, WHRN, USH2D, PDZD7B	uc004biz.4	Q9P202	OTTHUMG00000020539	ENST00000362057.3:c.2331C>A	9.37:g.117166263G>T						DFNB31_ENST00000265134.6_Silent_p.G394G|DFNB31_ENST00000374059.3_Silent_p.G426G	p.G777G	NM_001173425.1|NM_015404.3	NP_001166896.1|NP_056219.3	Q9P202	WHRN_HUMAN			10	2499	-			777					A5PKU1|A5PKZ9|Q5TAU9|Q5TAV0|Q5TAV1|Q5TAV2|Q96MZ9|Q9H9F4|Q9UFZ3	Silent	SNP	ENST00000362057.3	37	c.2331C>A	CCDS6806.1																																																																																				0.652	DFNB31-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053776.2	NM_015404		41	84	1	0	2.58029e-29	1	2.84493e-29	41	84				
OR2T35	403244	broad.mit.edu	37	1	248801588	248801588	+	Splice_Site	SNP	C	C	T	rs180849677	byFrequency	TCGA-EL-A3CP-01A-11D-A19J-08	TCGA-EL-A3CP-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	064b25ee-8746-499f-96f9-9bbde3961bb8	5aeaaf99-9861-46f1-b614-7cf0ed7f11dd	g.chr1:248801588C>T	ENST00000317450.3	-	1	971	c.972G>A	c.(970-972)taG>taA	p.*324*		NM_001001827.1	NP_001001827.1	Q8NGX2	O2T35_HUMAN	olfactory receptor, family 2, subfamily T, member 35	0						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|large_intestine(1)|lung(1)|ovary(1)|prostate(1)|skin(1)	6	all_cancers(71;2.04e-05)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)	all_cancers(173;0.237)	OV - Ovarian serous cystadenocarcinoma(106;0.0265)			GGAGTCCCTGCTAGCCCTTCC	0.552													C|||	77	0.0153754	0.0522	0.0101	5008	,	,		4750	0.0		0.001	False		,,,				2504	0.0					ENST00000317450.3																			0				endometrium(1)|large_intestine(1)|lung(1)|ovary(1)|prostate(1)|skin(1)	6						c.e1+1		olfactory receptor, family 2, subfamily T, member 35							21.0	6.0	12.0					1																	248801588		1903	2671	4574	SO:0001630	splice_region_variant	403244				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity	g.chr1:248801588C>T	BK004475	CCDS31123.1	1q44	2012-08-09			ENSG00000177151	ENSG00000177151		"""GPCR / Class A : Olfactory receptors"""	31257	protein-coding gene	gene with protein product							Standard	NM_001001827		Approved		uc001ies.1	Q8NGX2	OTTHUMG00000040380	ENST00000317450.3:c.969+1G>A	1.37:g.248801588C>T							p.*324_splice	NM_001001827.1	NP_001001827.1	Q8NGX2	O2T35_HUMAN	OV - Ovarian serous cystadenocarcinoma(106;0.0265)		1	971	-	all_cancers(71;2.04e-05)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)	all_cancers(173;0.237)	0					Q6IEY7	Splice_Site	SNP	ENST00000317450.3	37	c.969_splice	CCDS31123.1																																																																																				0.552	OR2T35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097130.1	NM_001001827	Silent	4	58	0	0	0	1	0	4	58				
LAT	27040	broad.mit.edu	37	16	28996725	28996725	+	5'UTR	SNP	G	G	A	rs77760721	byFrequency	TCGA-EL-A3CP-01A-11D-A19J-08	TCGA-EL-A3CP-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	064b25ee-8746-499f-96f9-9bbde3961bb8	5aeaaf99-9861-46f1-b614-7cf0ed7f11dd	g.chr16:28996725G>A	ENST00000360872.5	+	0	65				LAT_ENST00000395461.3_Missense_Mutation_p.R32Q|LAT_ENST00000566177.1_5'Flank|LAT_ENST00000563964.1_3'UTR|RP11-264B17.3_ENST00000569969.1_RNA|LAT_ENST00000395456.2_5'UTR|LAT_ENST00000354453.4_5'Flank|LAT_ENST00000564277.1_5'UTR|LAT_ENST00000454369.2_5'UTR			O43561	LAT_HUMAN	linker for activation of T cells						blood coagulation (GO:0007596)|calcium-mediated signaling (GO:0019722)|Fc-epsilon receptor signaling pathway (GO:0038095)|gene expression (GO:0010467)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|intracellular signal transduction (GO:0035556)|lymphocyte homeostasis (GO:0002260)|mast cell degranulation (GO:0043303)|platelet activation (GO:0030168)|positive regulation of signal transduction (GO:0009967)|Ras protein signal transduction (GO:0007265)|regulation of T cell activation (GO:0050863)|T cell activation (GO:0042110)|T cell receptor signaling pathway (GO:0050852)	cell-cell junction (GO:0005911)|COP9 signalosome (GO:0008180)|immunological synapse (GO:0001772)|integral component of membrane (GO:0016021)|mast cell granule (GO:0042629)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|SH3/SH2 adaptor activity (GO:0005070)			large_intestine(2)|lung(3)|urinary_tract(1)	6		Hepatocellular(780;0.244)				AGCCTGCTCCGAGCTCCCCTG	0.667													G|||	78	0.0155751	0.0567	0.0043	5008	,	,		15377	0.0		0.0	False		,,,				2504	0.0					ENST00000395461.3																			0				large_intestine(2)|lung(3)|urinary_tract(1)	6						c.(94-96)cGa>cAa		linker for activation of T cells		G	,,GLN/ARG,	207,4187	124.5+/-161.8	9,189,1999	46.0	41.0	43.0		,,95,	-0.1	0.0	16	dbSNP_132	43	2,8598	1.2+/-3.3	0,2,4298	yes	utr-5,utr-5,missense,utr-5	LAT	NM_001014987.1,NM_001014988.1,NM_001014989.1,NM_014387.3	,,43,	9,191,6297	AA,AG,GG		0.0233,4.711,1.6084	,,,	,,32/270,	28996725	209,12785	2197	4300	6497	SO:0001623	5_prime_UTR_variant	0				calcium-mediated signaling|integrin-mediated signaling pathway|mast cell degranulation|platelet activation|Ras protein signal transduction|regulation of T cell activation|T cell receptor signaling pathway	immunological synapse|integral to membrane|intracellular|membrane raft	SH3/SH2 adaptor activity	g.chr16:28996725G>A	AF036905	CCDS10647.1, CCDS32425.1, CCDS45455.1, CCDS53999.1	16q13	2011-11-01			ENSG00000213658	ENSG00000213658			18874	protein-coding gene	gene with protein product	"""linker for activation of T cells, transmembrane adaptor"""	602354				9489702	Standard	NM_014387		Approved	LAT1	uc010vdj.2	O43561	OTTHUMG00000131761	ENST00000360872.5:c.-14G>A	16.37:g.28996725G>A						LAT_ENST00000395456.2_5'UTR|RP11-264B17.3_ENST00000569969.1_RNA|LAT_ENST00000454369.2_5'UTR|LAT_ENST00000360872.5_5'UTR|LAT_ENST00000563964.1_3'UTR|LAT_ENST00000564277.1_5'UTR	p.R32Q	NM_001014989.1	NP_001014989.2	O43561	LAT_HUMAN			2	131	+		Hepatocellular(780;0.244)	236					B7WPI0|C7C5T6|G5E9K3|O43919	Missense_Mutation	SNP	ENST00000360872.5	37	c.95G>A	CCDS10647.1	27	0.012362637362637362	26	0.052845528455284556	1	0.0027624309392265192	0	0.0	0	0.0	G	18.88	3.717261	0.68844	0.04711	2.33E-4	ENSG00000213658	ENST00000395461	.	.	.	3.79	-0.0848	0.13689	.	.	.	.	.	T	0.02267	0.0070	N	0.08118	0	0.09310	N	0.999999	B	0.12630	0.006	B	0.04013	0.001	T	0.23440	-1.0188	8	0.20046	T	0.44	0.1718	6.0968	0.20025	0.5364:0.0:0.4636:0.0	.	32	B7WPI0	.	Q	32	.	ENSP00000378845:R32Q	R	+	2	0	LAT	28904226	0.000000	0.05858	0.004000	0.12327	0.486000	0.33341	-2.695000	0.00828	0.006000	0.14734	0.462000	0.41574	CGA		0.667	LAT-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254688.2			3	26	0	0	0	1	0	3	26				
ZNF181	339318	broad.mit.edu	37	19	35232200	35232200	+	Missense_Mutation	SNP	T	T	G	rs143797666	byFrequency	TCGA-EL-A3CP-01A-11D-A19J-08	TCGA-EL-A3CP-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	064b25ee-8746-499f-96f9-9bbde3961bb8	5aeaaf99-9861-46f1-b614-7cf0ed7f11dd	g.chr19:35232200T>G	ENST00000492450.1	+	4	1003	c.914T>G	c.(913-915)gTc>gGc	p.V305G	ZNF181_ENST00000392232.3_Missense_Mutation_p.V349G|ZNF181_ENST00000459757.2_Missense_Mutation_p.V304G			Q2M3W8	ZN181_HUMAN	zinc finger protein 181	305					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.V241G(4)		endometrium(6)|kidney(2)|large_intestine(1)|lung(7)|ovary(2)|prostate(3)|skin(1)	22	all_lung(56;1.13e-07)|Lung NSC(56;1.81e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.138)			TTTAGCCATGTCTCATCACTT	0.413													T|||	3	0.000599042	0.0	0.0	5008	,	,		22105	0.002		0.0	False		,,,				2504	0.001					ENST00000392232.3																			4	Substitution - Missense(4)	p.V241G(4)	lung(2)|endometrium(2)	endometrium(6)|kidney(2)|large_intestine(1)|lung(7)|ovary(2)|prostate(3)|skin(1)	22						c.(1045-1047)gTc>gGc		zinc finger protein 181							91.0	88.0	89.0					19																	35232200		2203	4300	6503	SO:0001583	missense	339318				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding	g.chr19:35232200T>G	BC104759, H54888	CCDS32990.2, CCDS46043.1	19q13.13	2013-01-08	2006-04-27		ENSG00000197841	ENSG00000197841		"""Zinc fingers, C2H2-type"", ""-"""	12971	protein-coding gene	gene with protein product		606741	"""zinc finger protein 181 (HHZ181)"""				Standard	NM_001029997		Approved	HHZ181, MGC44316	uc002nvu.3	Q2M3W8	OTTHUMG00000157508	ENST00000492450.1:c.914T>G	19.37:g.35232200T>G	ENSP00000420727:p.Val305Gly					ZNF181_ENST00000459757.1_Missense_Mutation_p.V304G|ZNF181_ENST00000492450.1_Missense_Mutation_p.V305G	p.V349G			Q2M3W8	ZN181_HUMAN	LUSC - Lung squamous cell carcinoma(66;0.138)		6	1214	+	all_lung(56;1.13e-07)|Lung NSC(56;1.81e-07)|Esophageal squamous(110;0.162)		305					B7ZKX3|Q49A75	Missense_Mutation	SNP	ENST00000492450.1	37	c.1046T>G	CCDS32990.2	.	.	.	.	.	.	.	.	.	.	T	1.102	-0.660828	0.03454	.	.	ENSG00000197841	ENST00000392232;ENST00000425140;ENST00000492450;ENST00000459757	T;T;T	0.38560	2.43;1.13;1.13	2.89	2.89	0.33648	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.16642	0.0400	N	0.10733	0.035	0.09310	N	0.999999	P;B	0.38978	0.652;0.0	B;B	0.30179	0.112;0.001	T	0.04017	-1.0984	9	0.22109	T	0.4	.	5.4169	0.16378	0.2509:0.0:0.0:0.749	.	304;305	B7ZKX3;Q2M3W8	.;ZN181_HUMAN	G	349;304;305;304	ENSP00000376065:V349G;ENSP00000420727:V305G;ENSP00000419435:V304G	ENSP00000376065:V349G	V	+	2	0	ZNF181	39924040	0.000000	0.05858	0.880000	0.34516	0.765000	0.43378	-0.861000	0.04268	1.565000	0.49641	0.402000	0.26972	GTC		0.413	ZNF181-002	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000349005.3	NM_001029997		6	102	0	0	0	1	0	6	102				
ZNF407	55628	broad.mit.edu	37	18	72346448	72346448	+	Missense_Mutation	SNP	T	T	C			TCGA-EL-A3CP-01A-11D-A19J-08	TCGA-EL-A3CP-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	064b25ee-8746-499f-96f9-9bbde3961bb8	5aeaaf99-9861-46f1-b614-7cf0ed7f11dd	g.chr18:72346448T>C	ENST00000299687.5	+	1	3473	c.3473T>C	c.(3472-3474)tTc>tCc	p.F1158S	ZNF407_ENST00000309902.6_Missense_Mutation_p.F1158S|ZNF407_ENST00000582337.1_Missense_Mutation_p.F1158S|ZNF407_ENST00000577538.1_Missense_Mutation_p.F1158S	NM_017757.2	NP_060227.2	Q9C0G0	ZN407_HUMAN	zinc finger protein 407	1158					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(6)|kidney(7)|large_intestine(21)|lung(23)|ovary(4)|prostate(3)|upper_aerodigestive_tract(2)	67		Esophageal squamous(42;0.131)|Prostate(75;0.173)		BRCA - Breast invasive adenocarcinoma(31;0.184)		GAATCTAATTTCAATGAAGAC	0.383																																						ENST00000299687.5																			0				central_nervous_system(1)|endometrium(6)|kidney(7)|large_intestine(21)|lung(23)|ovary(4)|prostate(3)|upper_aerodigestive_tract(2)	67						c.(3472-3474)tTc>tCc		zinc finger protein 407							63.0	65.0	64.0					18																	72346448		1879	4135	6014	SO:0001583	missense	55628				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding	g.chr18:72346448T>C	AB051490	CCDS45885.1, CCDS54191.1, CCDS58634.1	18q23	2013-01-08			ENSG00000215421	ENSG00000215421		"""Zinc fingers, C2H2-type"""	19904	protein-coding gene	gene with protein product		615894				11214970	Standard	NM_017757		Approved	FLJ20307, FLJ13839, KIAA1703	uc002llw.2	Q9C0G0		ENST00000299687.5:c.3473T>C	18.37:g.72346448T>C	ENSP00000299687:p.Phe1158Ser					ZNF407_ENST00000582337.1_Missense_Mutation_p.F1158S|ZNF407_ENST00000577538.1_Missense_Mutation_p.F1158S|ZNF407_ENST00000309902.6_Missense_Mutation_p.F1158S	p.F1158S	NM_017757.2	NP_060227.2	Q9C0G0	ZN407_HUMAN		BRCA - Breast invasive adenocarcinoma(31;0.184)	1	3473	+		Esophageal squamous(42;0.131)|Prostate(75;0.173)	1158					B5MD54|Q96MY0|Q9H8A1|Q9NXD4|Q9NXD7	Missense_Mutation	SNP	ENST00000299687.5	37	c.3473T>C	CCDS45885.1	.	.	.	.	.	.	.	.	.	.	T	9.998	1.232794	0.22626	.	.	ENSG00000215421	ENST00000299687;ENST00000309902	T;T	0.08984	3.03;3.47	5.86	4.71	0.59529	.	0.527164	0.19270	N	0.118421	T	0.03136	0.0092	N	0.08118	0	0.09310	N	1	B;P;B	0.37276	0.435;0.589;0.255	B;B;B	0.27500	0.08;0.058;0.026	T	0.44034	-0.9354	10	0.45353	T	0.12	.	2.2165	0.03961	0.1908:0.081:0.1334:0.5948	.	1158;1158;1158	Q9C0G0-3;Q9C0G0-2;Q9C0G0	.;.;ZN407_HUMAN	S	1158	ENSP00000299687:F1158S;ENSP00000310359:F1158S	ENSP00000299687:F1158S	F	+	2	0	ZNF407	70475436	0.020000	0.18652	0.135000	0.22099	0.737000	0.42083	2.225000	0.42954	-0.173000	0.10761	0.655000	0.94253	TTC		0.383	ZNF407-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444903.1	NM_017757		21	82	0	0	0	1	0	21	82				
IGSF3	3321	broad.mit.edu	37	1	117150895	117150895	+	Silent	SNP	C	C	T	rs61730485		TCGA-EL-A3CP-01A-11D-A19J-08	TCGA-EL-A3CP-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	064b25ee-8746-499f-96f9-9bbde3961bb8	5aeaaf99-9861-46f1-b614-7cf0ed7f11dd	g.chr1:117150895C>T	ENST00000369486.3	-	5	1656	c.891G>A	c.(889-891)ccG>ccA	p.P297P	IGSF3_ENST00000318837.6_Silent_p.P297P|IGSF3_ENST00000369483.1_Silent_p.P297P	NM_001007237.1	NP_001007238.1	O75054	IGSF3_HUMAN	immunoglobulin superfamily, member 3	297	Ig-like C2-type 3.				lacrimal gland development (GO:0032808)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)				NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(31)|ovary(4)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	62	Lung SC(450;0.225)	all_cancers(81;1.24e-06)|all_epithelial(167;4.85e-07)|all_lung(203;1.66e-06)|Lung NSC(69;1.11e-05)		Lung(183;0.0142)|Colorectal(144;0.0929)|LUSC - Lung squamous cell carcinoma(189;0.108)|COAD - Colon adenocarcinoma(174;0.139)|all cancers(265;0.159)|Epithelial(280;0.166)		TGAACTCCACCGGCTCGCCCA	0.542																																						ENST00000369486.3																			0				NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(31)|ovary(4)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	62						c.(889-891)ccG>ccA		immunoglobulin superfamily, member 3							13.0	15.0	14.0					1																	117150895		2109	4190	6299	SO:0001819	synonymous_variant	3321					integral to membrane		g.chr1:117150895C>T	AF031174	CCDS30813.1, CCDS30814.1	1p13	2013-01-29			ENSG00000143061	ENSG00000143061		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5950	protein-coding gene	gene with protein product		603491				9790749	Standard	NM_001007237		Approved	V8, EWI-3, MGC117164	uc031pnr.1	O75054	OTTHUMG00000022751	ENST00000369486.3:c.891G>A	1.37:g.117150895C>T						IGSF3_ENST00000369483.1_Silent_p.P297P|IGSF3_ENST00000318837.6_Silent_p.P297P	p.P297P	NM_001007237.1	NP_001007238.1	O75054	IGSF3_HUMAN		Lung(183;0.0142)|Colorectal(144;0.0929)|LUSC - Lung squamous cell carcinoma(189;0.108)|COAD - Colon adenocarcinoma(174;0.139)|all cancers(265;0.159)|Epithelial(280;0.166)	5	1656	-	Lung SC(450;0.225)	all_cancers(81;1.24e-06)|all_epithelial(167;4.85e-07)|all_lung(203;1.66e-06)|Lung NSC(69;1.11e-05)	297			Ig-like C2-type 3.		A6NJZ6|A6NMC7	Silent	SNP	ENST00000369486.3	37	c.891G>A	CCDS30813.1																																																																																				0.542	IGSF3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000059040.1	NM_001542		3	33	0	0	0	1	0	3	33				
FYCO1	79443	broad.mit.edu	37	3	46009289	46009289	+	Missense_Mutation	SNP	G	G	A	rs141828619		TCGA-EL-A3CP-01A-11D-A19J-08	TCGA-EL-A3CP-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	064b25ee-8746-499f-96f9-9bbde3961bb8	5aeaaf99-9861-46f1-b614-7cf0ed7f11dd	g.chr3:46009289G>A	ENST00000296137.2	-	8	1742	c.1537C>T	c.(1537-1539)Cgg>Tgg	p.R513W	FYCO1_ENST00000535325.1_Missense_Mutation_p.R513W	NM_024513.3	NP_078789.2	Q9BQS8	FYCO1_HUMAN	FYVE and coiled-coil domain containing 1	513					plus-end-directed vesicle transport along microtubule (GO:0072383)	autophagic vacuole (GO:0005776)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)	metal ion binding (GO:0046872)			NS(4)|breast(3)|central_nervous_system(1)|endometrium(11)|kidney(2)|large_intestine(9)|lung(17)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	54				BRCA - Breast invasive adenocarcinoma(193;0.00147)|KIRC - Kidney renal clear cell carcinoma(197;0.0272)|Kidney(197;0.0323)		TGCAGCTGCCGGGTCAGAGAC	0.582																																						ENST00000296137.2																			0				NS(4)|breast(3)|central_nervous_system(1)|endometrium(11)|kidney(2)|large_intestine(9)|lung(17)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	54						c.(1537-1539)Cgg>Tgg		FYVE and coiled-coil domain containing 1		G	TRP/ARG	3,4403	6.2+/-15.9	0,3,2200	91.0	95.0	94.0		1537	-2.0	0.1	3	dbSNP_134	94	0,8600		0,0,4300	yes	missense	FYCO1	NM_024513.2	101	0,3,6500	AA,AG,GG		0.0,0.0681,0.0231	benign	513/1479	46009289	3,13003	2203	4300	6503	SO:0001583	missense	79443				transport	integral to membrane	metal ion binding|protein binding	g.chr3:46009289G>A	AJ292348	CCDS2734.1	3p21.3	2008-02-05			ENSG00000163820	ENSG00000163820		"""Zinc fingers, FYVE domain containing"""	14673	protein-coding gene	gene with protein product		607182				11896456	Standard	NM_024513		Approved	FLJ13335, ZFYVE7	uc003cpb.5	Q9BQS8	OTTHUMG00000133447	ENST00000296137.2:c.1537C>T	3.37:g.46009289G>A	ENSP00000296137:p.Arg513Trp					FYCO1_ENST00000535325.1_Missense_Mutation_p.R513W	p.R513W	NM_024513.3	NP_078789.2	Q9BQS8	FYCO1_HUMAN		BRCA - Breast invasive adenocarcinoma(193;0.00147)|KIRC - Kidney renal clear cell carcinoma(197;0.0272)|Kidney(197;0.0323)	8	1742	-			513					B7ZKT7|Q3MJE6|Q86T41|Q86TB1|Q8TEF9|Q96IV5|Q9H8P9	Missense_Mutation	SNP	ENST00000296137.2	37	c.1537C>T	CCDS2734.1	.	.	.	.	.	.	.	.	.	.	G	10.46	1.356931	0.24598	6.81E-4	0.0	ENSG00000163820	ENST00000296137;ENST00000535325	T;T	0.21361	2.01;2.02	5.33	-1.97	0.07503	.	0.524023	0.20597	N	0.089237	T	0.10380	0.0254	L	0.31294	0.92	0.09310	N	0.999999	B;B	0.20052	0.041;0.041	B;B	0.10450	0.004;0.005	T	0.14868	-1.0457	10	0.54805	T	0.06	-24.1064	1.3055	0.02087	0.1672:0.3404:0.2196:0.2728	.	513;513	B7ZKT7;Q9BQS8	.;FYCO1_HUMAN	W	513	ENSP00000296137:R513W;ENSP00000441178:R513W	ENSP00000296137:R513W	R	-	1	2	FYCO1	45984293	0.007000	0.16637	0.099000	0.21106	0.976000	0.68499	0.358000	0.20216	-0.034000	0.13713	0.655000	0.94253	CGG		0.582	FYCO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257320.2	NM_024513		5	142	0	0	0	1	0	5	142				
BRAF	673	broad.mit.edu	37	7	140453136	140453136	+	Missense_Mutation	SNP	A	A	T	rs121913377|rs113488022|rs121913227|rs397516897		TCGA-EL-A3CP-01A-11D-A19J-08	TCGA-EL-A3CP-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	064b25ee-8746-499f-96f9-9bbde3961bb8	5aeaaf99-9861-46f1-b614-7cf0ed7f11dd	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		35	57	0	0	0	1	0	35	57				
AGAP6	414189	broad.mit.edu	37	10	51768543	51768543	+	Missense_Mutation	SNP	T	T	C	rs368970869		TCGA-EL-A3CP-01A-11D-A19J-08	TCGA-EL-A3CP-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	064b25ee-8746-499f-96f9-9bbde3961bb8	5aeaaf99-9861-46f1-b614-7cf0ed7f11dd	g.chr10:51768543T>C	ENST00000374056.4	+	7	987	c.589T>C	c.(589-591)Tcg>Ccg	p.S197P	AGAP6_ENST00000412531.3_Missense_Mutation_p.S220P			Q5VW22	AGAP6_HUMAN	ArfGAP with GTPase domain, ankyrin repeat and PH domain 6	197					regulation of ARF GTPase activity (GO:0032312)		ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)	p.S220P(3)		NS(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|liver(1)|lung(8)|prostate(3)|skin(1)|stomach(2)	29						CTCCATTCCATCGACTCCCAG	0.532																																						ENST00000374056.4																			3	Substitution - Missense(3)	p.S220P(3)	endometrium(2)|NS(1)	NS(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|liver(1)|lung(8)|prostate(3)|skin(1)|stomach(2)	29						c.(589-591)Tcg>Ccg		ArfGAP with GTPase domain, ankyrin repeat and PH domain 6																																				SO:0001583	missense	414189				regulation of ARF GTPase activity		ARF GTPase activator activity|zinc ion binding	g.chr10:51768543T>C		CCDS44397.1	10q11.23	2013-01-10	2008-09-22	2008-09-22	ENSG00000204149	ENSG00000204149		"""ADP-ribosylation factor GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"", ""Ankyrin repeat domain containing"""	23466	protein-coding gene	gene with protein product			"""centaurin, gamma-like family, member 3"""	CTGLF3			Standard	NM_001077665		Approved	bA324H6.1	uc001jix.4	Q5VW22	OTTHUMG00000018220	ENST00000374056.4:c.589T>C	10.37:g.51768543T>C	ENSP00000363168:p.Ser197Pro					AGAP6_ENST00000412531.3_Missense_Mutation_p.S220P	p.S197P			C9IYN2	C9IYN2_HUMAN			7	987	+			220						Missense_Mutation	SNP	ENST00000374056.4	37	c.589T>C		.	.	.	.	.	.	.	.	.	.	.	7.332	0.619129	0.14129	.	.	ENSG00000204149	ENST00000374056;ENST00000412531	T	0.56776	0.44	0.0465	0.0465	0.14256	.	0.149774	0.46145	D	0.000318	T	0.42314	0.1197	M	0.65498	2.005	0.37828	D	0.92861	B	0.14012	0.009	B	0.13407	0.009	T	0.20140	-1.0284	10	0.31617	T	0.26	.	4.565	0.12180	0.0:6.0E-4:0.0:0.9994	.	220	C9IYN2	.	P	220;197	ENSP00000400972:S197P	ENSP00000363168:S220P	S	+	1	0	AGAP6	51438549	1.000000	0.71417	0.059000	0.19551	0.060000	0.15804	3.691000	0.54720	0.115000	0.18071	0.113000	0.15668	TCG		0.532	AGAP6-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_001077665		5	128	0	0	0	1	0	5	128				
GCC2	9648	broad.mit.edu	37	2	109087883	109087884	+	Frame_Shift_Ins	INS	-	-	A			TCGA-EL-A3CP-01A-11D-A19J-08	TCGA-EL-A3CP-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	064b25ee-8746-499f-96f9-9bbde3961bb8	5aeaaf99-9861-46f1-b614-7cf0ed7f11dd	g.chr2:109087883_109087884insA	ENST00000309863.6	+	6	2812_2813	c.2098_2099insA	c.(2098-2100)gaafs	p.E700fs		NM_181453.3	NP_852118	Q8IWJ2	GCC2_HUMAN	GRIP and coiled-coil domain containing 2	700					Golgi ribbon formation (GO:0090161)|late endosome to Golgi transport (GO:0034499)|microtubule anchoring (GO:0034453)|microtubule organizing center organization (GO:0031023)|protein localization to Golgi apparatus (GO:0034067)|protein targeting to Golgi (GO:0000042)|protein targeting to lysosome (GO:0006622)|recycling endosome to Golgi transport (GO:0071955)|regulation of protein exit from endoplasmic reticulum (GO:0070861)|retrograde transport, endosome to Golgi (GO:0042147)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)|trans-Golgi network (GO:0005802)	identical protein binding (GO:0042802)			breast(8)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(10)|lung(19)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	54						ACTCAGTTCAGAAAAAAAACAG	0.307																																						ENST00000309863.6																			0				breast(8)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(10)|lung(19)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	54						c.(2098-2100)aaafs		GRIP and coiled-coil domain containing 2																																				SO:0001589	frameshift_variant	9648				Golgi ribbon formation|late endosome to Golgi transport|microtubule anchoring|microtubule organizing center organization|protein localization in Golgi apparatus|protein targeting to lysosome|recycling endosome to Golgi transport|regulation of protein exit from endoplasmic reticulum	membrane|trans-Golgi network	identical protein binding	g.chr2:109087883_109087884insA	BC020645	CCDS33268.1	2q12.3	2008-02-05	2004-03-05		ENSG00000135968	ENSG00000135968			23218	protein-coding gene	gene with protein product		612711	"""GRIP and coiled-coil domain-containing 2"""			12446665	Standard	NM_181453		Approved	GCC185, KIAA0336	uc002tec.3	Q8IWJ2	OTTHUMG00000153214	ENST00000309863.6:c.2106dupA	2.37:g.109087891_109087891dupA	ENSP00000307939:p.Glu700fs						p.K700fs	NM_181453.3	NP_852118.1	Q8IWJ2	GCC2_HUMAN			6	2812_2813	+			700					A6H8X8|O15045|Q4ZG46|Q8TDH3|Q9H2G8	Frame_Shift_Ins	INS	ENST00000309863.6	37	c.2098_2099insA	CCDS33268.1																																																																																				0.307	GCC2-014	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358516.3	NM_014635		8	295						8	295	---	---	---	---
LINC00969	440993	broad.mit.edu	37	3	195400814	195400815	+	lincRNA	INS	-	-	TT	rs371598334		TCGA-EL-A3CP-01A-11D-A19J-08	TCGA-EL-A3CP-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	064b25ee-8746-499f-96f9-9bbde3961bb8	5aeaaf99-9861-46f1-b614-7cf0ed7f11dd	g.chr3:195400814_195400815insTT	ENST00000445430.1	+	0	1410_1411									long intergenic non-protein coding RNA 969																		ACCTGGTTGTCTGGTCAGGCAT	0.574																																						ENST00000445430.1																			0																																																			0							g.chr3:195400814_195400815insTT	AK128346		3q29	2013-06-07			ENSG00000242086	ENSG00000242086		"""Long non-coding RNAs"""	48729	non-coding RNA	RNA, long non-coding							Standard	XR_427455		Approved				OTTHUMG00000155834		3.37:g.195400814_195400815insTT														0	1410_1411	+									RNA	INS	ENST00000445430.1	37																																																																																						0.574	LINC00969-038	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000341951.1			8	40						8	40	---	---	---	---
MSH3	4437	broad.mit.edu	37	5	79950742	79950750	+	In_Frame_Del	DEL	CCCCCAGCT	CCCCCAGCT	-	rs144629981|rs3045983|rs557874766|rs1047489	byFrequency	TCGA-EL-A3CP-01A-11D-A19J-08	TCGA-EL-A3CP-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	064b25ee-8746-499f-96f9-9bbde3961bb8	5aeaaf99-9861-46f1-b614-7cf0ed7f11dd	g.chr5:79950742_79950750delCCCCCAGCT	ENST00000265081.6	+	1	276_284	c.196_204delCCCCCAGCT	c.(196-204)cccccagctdel	p.PPA66del	DHFR_ENST00000505337.1_5'Flank|DHFR_ENST00000504396.1_5'Flank|DHFR_ENST00000511032.1_5'Flank|DHFR_ENST00000513048.1_5'Flank|DHFR_ENST00000439211.2_5'UTR	NM_002439.4	NP_002430.3	P20585	MSH3_HUMAN	mutS homolog 3	66					ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)|maintenance of DNA repeat elements (GO:0043570)|meiotic mismatch repair (GO:0000710)|mismatch repair (GO:0006298)|negative regulation of DNA recombination (GO:0045910)|positive regulation of helicase activity (GO:0051096)|reciprocal meiotic recombination (GO:0007131)|somatic recombination of immunoglobulin gene segments (GO:0016447)	membrane (GO:0016020)|MutSbeta complex (GO:0032302)|nuclear chromosome (GO:0000228)|nucleus (GO:0005634)	ATP binding (GO:0005524)|centromeric DNA binding (GO:0019237)|damaged DNA binding (GO:0003684)|DNA-dependent ATPase activity (GO:0008094)|double-strand/single-strand DNA junction binding (GO:0000406)|enzyme binding (GO:0019899)|heteroduplex DNA loop binding (GO:0000404)|Y-form DNA binding (GO:0000403)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(12)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	29		Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244)		OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33)		gCCCCCAGCGCCCCCAGCTCCCGCCTTCC	0.732								Mismatch excision repair (MMR)						1174	0.234425	0.2874	0.2061	5008	,	,		7173	0.0565		0.2535	False		,,,				2504	0.3466				Melanoma(88;1010 1399 13793 26548 36275)	ENST00000265081.6																			0				NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(12)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	29						c.(196-204)del	Mismatch excision repair (MMR)	mutS homolog 3			,	1105,2179		342,421,879					,	4.0	1.0		dbSNP_102	4	1941,4615		567,807,1904	no	coding,utr-5	DHFR,MSH3	NM_002439.3,NM_000791.3	,	909,1228,2783	A1A1,A1R,RR		29.6065,33.648,30.9553	,	,		3046,6794				SO:0001651	inframe_deletion	4437				maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments	MutSbeta complex|nuclear chromosome	ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding	g.chr5:79950742_79950750delCCCCCAGCT	U61981	CCDS34195.1	5q11-q12	2013-09-12	2013-09-12		ENSG00000113318	ENSG00000113318			7326	protein-coding gene	gene with protein product	"""Divergent upstream protein"", ""Mismatch repair protein 1"""	600887	"""mutS (E. coli) homolog 3"", ""mutS homolog 3 (E. coli)"""				Standard	NM_002439		Approved	DUP, MRP1	uc003kgz.4	P20585	OTTHUMG00000162540	ENST00000265081.6:c.196_204delCCCCCAGCT	5.37:g.79950742_79950750delCCCCCAGCT	ENSP00000265081:p.Pro66_Ala68del					DHFR_ENST00000439211.2_5'UTR	p.PPA66del	NM_002439.4	NP_002430.3	P20585	MSH3_HUMAN		OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33)	1	276_284	+		Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244)	66					A1L480|A1L482|A6NMM6|Q6PJT5|Q86UQ6|Q92867	In_Frame_Del	DEL	ENST00000265081.6	37	c.196_204delCCCCCAGCT	CCDS34195.1																																																																																				0.732	MSH3-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369471.1	NM_002439		6	4						6	4	---	---	---	---
CCNT1	904	broad.mit.edu	37	12	49087434	49087436	+	In_Frame_Del	DEL	ATG	ATG	-	rs371197465		TCGA-EL-A3CP-01A-11D-A19J-08	TCGA-EL-A3CP-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	064b25ee-8746-499f-96f9-9bbde3961bb8	5aeaaf99-9861-46f1-b614-7cf0ed7f11dd	g.chr12:49087434_49087436delATG	ENST00000261900.3	-	9	1783_1785	c.1561_1563delCAT	c.(1561-1563)catdel	p.H521del		NM_001240.3	NP_001231.2	O60563	CCNT1_HUMAN	cyclin T1	521	His-rich.				cell cycle (GO:0007049)|cell division (GO:0051301)|gene expression (GO:0010467)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral transcription (GO:0050434)|protein phosphorylation (GO:0006468)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|positive transcription elongation factor complex b (GO:0008024)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|snRNA binding (GO:0017069)|transcription regulatory region DNA binding (GO:0044212)			breast(3)|endometrium(1)|kidney(1)|large_intestine(4)|lung(13)|ovary(3)|skin(2)	27						AGTGGTGATTATGATGATGATGA	0.443																																						ENST00000261900.3																			0				breast(3)|endometrium(1)|kidney(1)|large_intestine(4)|lung(13)|ovary(3)|skin(2)	27						c.(1561-1563)del		cyclin T1				12,4250		0,12,2119						4.8	1.0			307	3,8241		1,1,4120	no	coding	CCNT1	NM_001240.2		1,13,6239	A1A1,A1R,RR		0.0364,0.2816,0.1199				15,12491				SO:0001651	inframe_deletion	904				cell cycle|cell division|interspecies interaction between organisms|positive regulation of viral transcription|protein phosphorylation|regulation of cyclin-dependent protein kinase activity|regulation of transcription, DNA-dependent|transcription elongation from RNA polymerase II promoter|viral reproduction	nucleoplasm	DNA binding|protein kinase binding	g.chr12:49087434_49087436delATG	AF048730	CCDS8766.1, CCDS61109.1	12q13.11	2010-11-15			ENSG00000129315	ENSG00000129315			1599	protein-coding gene	gene with protein product		143055	"""human immunodeficiency virus type 1 (HIV-1) expression (elevated) 1"""	HIVE1		9491887, 9499409	Standard	NM_001240		Approved	CCNT, CYCT1	uc001rsd.4	O60563	OTTHUMG00000170393	ENST00000261900.3:c.1561_1563delCAT	12.37:g.49087443_49087445delATG	ENSP00000261900:p.His521del						p.H521del	NM_001240.3	NP_001231.2	O60563	CCNT1_HUMAN			9	1783_1785	-			521			His-rich.		A9XU13|E7EX76|O60581	In_Frame_Del	DEL	ENST00000261900.3	37	c.1561_1563delCAT	CCDS8766.1																																																																																				0.443	CCNT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408853.1	NM_001240		8	437						8	437	---	---	---	---
TPTE2P1	646405	broad.mit.edu	37	13	25527490	25527491	+	RNA	INS	-	-	AAAAAG	rs375560921|rs201773491	byFrequency	TCGA-EL-A3CP-01A-11D-A19J-08	TCGA-EL-A3CP-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	064b25ee-8746-499f-96f9-9bbde3961bb8	5aeaaf99-9861-46f1-b614-7cf0ed7f11dd	g.chr13:25527490_25527491insAAAAAG	ENST00000429698.1	-	0	282							Q5T6R2	TPT2L_HUMAN	transmembrane phosphoinositide 3-phosphatase and tensin homolog 2 pseudogene 1																		AGGAAGGTTCTAAAAAAAATTT	0.252														9	0.00179712	0.0008	0.0014	5008	,	,		20326	0.004		0.003	False		,,,				2504	0.0					ENST00000429698.1																			0																																																			0							g.chr13:25527490_25527491insAAAAAG			13q12.12-q12.13	2012-10-03			ENSG00000253771	ENSG00000253771			35196	pseudogene	pseudogene							Standard	NR_026730		Approved		uc010tdh.2	Q5T6R2	OTTHUMG00000016596		13.37:g.25527490_25527491insAAAAAG														0	282	-								B3KST4|B4DMH9	RNA	INS	ENST00000429698.1	37																																																																																						0.252	TPTE2P1-003	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000044206.1			4	8						4	8	---	---	---	---
RP11-252A24.2	0	broad.mit.edu	37	16	74372915	74372915	+	RNA	DEL	T	T	-	rs397827801|rs11353924|rs532713769|rs398078750		TCGA-EL-A3CP-01A-11D-A19J-08	TCGA-EL-A3CP-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	064b25ee-8746-499f-96f9-9bbde3961bb8	5aeaaf99-9861-46f1-b614-7cf0ed7f11dd	g.chr16:74372915delT	ENST00000429810.2	-	0	1404																											ACGTAGtttgttttttttttt	0.438																																						ENST00000429810.2																			0																																																			0							g.chr16:74372915delT																													16.37:g.74372915delT														0	1404	-									RNA	DEL	ENST00000429810.2	37																																																																																						0.438	RP11-252A24.2-003	KNOWN	basic	retained_intron	pseudogene	OTTHUMT00000434683.1			3	4						3	4	---	---	---	---
SHANK1	50944	broad.mit.edu	37	19	51171632	51171634	+	In_Frame_Del	DEL	GCC	GCC	-			TCGA-EL-A3CP-01A-11D-A19J-08	TCGA-EL-A3CP-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	064b25ee-8746-499f-96f9-9bbde3961bb8	5aeaaf99-9861-46f1-b614-7cf0ed7f11dd	g.chr19:51171632_51171634delGCC	ENST00000293441.1	-	22	3601_3603	c.3583_3585delGGC	c.(3583-3585)ggcdel	p.G1195del	SHANK1_ENST00000391813.1_In_Frame_Del_p.G582del|SHANK1_ENST00000359082.3_In_Frame_Del_p.G1186del|SHANK1_ENST00000391814.1_In_Frame_Del_p.G1203del|SYT3_ENST00000544769.1_5'UTR	NM_016148.2	NP_057232.2	Q9Y566	SHAN1_HUMAN	SH3 and multiple ankyrin repeat domains 1	1195	Poly-Gly.				adult behavior (GO:0030534)|associative learning (GO:0008306)|cytoskeletal anchoring at plasma membrane (GO:0007016)|dendritic spine morphogenesis (GO:0060997)|determination of affect (GO:0050894)|habituation (GO:0046959)|long-term memory (GO:0007616)|negative regulation of actin filament bundle assembly (GO:0032232)|neuromuscular process controlling balance (GO:0050885)|olfactory behavior (GO:0042048)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|protein complex assembly (GO:0006461)|protein localization to synapse (GO:0035418)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|righting reflex (GO:0060013)|social behavior (GO:0035176)|synapse maturation (GO:0060074)|vocalization behavior (GO:0071625)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|excitatory synapse (GO:0060076)|intracellular (GO:0005622)|membrane (GO:0016020)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuron projection (GO:0043005)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	ankyrin repeat binding (GO:0071532)|GKAP/Homer scaffold activity (GO:0030160)|identical protein binding (GO:0042802)|ionotropic glutamate receptor binding (GO:0035255)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)|scaffold protein binding (GO:0097110)|SH3 domain binding (GO:0017124)|somatostatin receptor binding (GO:0031877)			breast(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(15)|liver(1)|lung(21)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)	64		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00493)|GBM - Glioblastoma multiforme(134;0.0199)		tgggcgaggAGCCGCCGCCGCCG	0.808																																						ENST00000293441.1																			0				breast(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(15)|liver(1)|lung(21)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)	64						c.(3583-3585)del		SH3 and multiple ankyrin repeat domains 1				27,1311		6,15,648						0.9	0.7			4	98,3172		20,58,1557	no	coding	SHANK1	NM_016148.2		26,73,2205	A1A1,A1R,RR		2.9969,2.0179,2.7127				125,4483				SO:0001651	inframe_deletion	50944				cytoskeletal anchoring at plasma membrane	cell junction|cytoplasm|dendrite|membrane fraction|postsynaptic density|postsynaptic membrane	ionotropic glutamate receptor binding	g.chr19:51171632_51171634delGCC	AF163302	CCDS12799.1	19q13.3	2013-01-10			ENSG00000161681	ENSG00000161681		"""Sterile alpha motif (SAM) domain containing"", ""Ankyrin repeat domain containing"""	15474	protein-coding gene	gene with protein product	"""somatostatin receptor-interacting protein"""	604999				10551867	Standard	NM_016148		Approved	SSTRIP, SPANK-1, synamon	uc002psx.1	Q9Y566	OTTHUMG00000137380	ENST00000293441.1:c.3583_3585delGGC	19.37:g.51171641_51171643delGCC	ENSP00000293441:p.Gly1195del					SYT3_ENST00000544769.1_5'UTR|SHANK1_ENST00000359082.3_In_Frame_Del_p.G1186del|SHANK1_ENST00000391814.1_In_Frame_Del_p.G1203del|SHANK1_ENST00000391813.1_In_Frame_Del_p.G582del	p.G1195del	NM_016148.2	NP_057232.2	Q9Y566	SHAN1_HUMAN		OV - Ovarian serous cystadenocarcinoma(262;0.00493)|GBM - Glioblastoma multiforme(134;0.0199)	22	3601_3603	-		all_neural(266;0.057)	1195			Poly-Gly.		A8MXP5|B7WNY6|Q9NYW9	In_Frame_Del	DEL	ENST00000293441.1	37	c.3583_3585delGGC	CCDS12799.1																																																																																				0.808	SHANK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268071.1	NM_016148		2	4						2	4	---	---	---	---
