#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_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_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	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_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	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_ORegAnno_bin	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	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	t_alt_count	t_ref_count
CYP2C19	1557	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	10	96602618	96602618	+	Missense_Mutation	SNP	G	G	A	rs138142612		TCGA-HT-7677-01A-11D-2253-08	TCGA-HT-7677-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a4bfd9a-4a16-41c9-91cb-97351c76ab0e	d27dc741-a306-47c4-a333-155ac43c9484	g.chr10:96602618G>A	ENST00000371321.3	+	7	1068	c.986G>A	c.(985-987)cGt>cAt	p.R329H	CYP2C19_ENST00000464755.1_3'UTR	NM_000769.1	NP_000760	P33261	CP2CJ_HUMAN	cytochrome P450, family 2, subfamily C, polypeptide 19	329			R -> H (in allele CYP2C19*18). {ECO:0000269|PubMed:16141610}.		arachidonic acid metabolic process (GO:0019369)|drug metabolic process (GO:0017144)|epoxygenase P450 pathway (GO:0019373)|exogenous drug catabolic process (GO:0042738)|heterocycle metabolic process (GO:0046483)|monoterpenoid metabolic process (GO:0016098)|omega-hydroxylase P450 pathway (GO:0097267)|oxidation-reduction process (GO:0055114)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|intracellular membrane-bounded organelle (GO:0043231)	(R)-limonene 6-monooxygenase activity (GO:0052741)|(S)-limonene 6-monooxygenase activity (GO:0018675)|(S)-limonene 7-monooxygenase activity (GO:0018676)|enzyme binding (GO:0019899)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity (GO:0016491)|oxygen binding (GO:0019825)|steroid hydroxylase activity (GO:0008395)			central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(5)|lung(17)|ovary(4)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	43		Colorectal(252;0.09)		all cancers(201;6.02e-07)|KIRC - Kidney renal clear cell carcinoma(50;0.0672)|Kidney(138;0.0838)	Acenocoumarol(DB01418)|Acetylsalicylic acid(DB00945)|Adinazolam(DB00546)|Almotriptan(DB00918)|Aminoglutethimide(DB00357)|Aminophenazone(DB01424)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amoxicillin(DB01060)|Amprenavir(DB00701)|Antipyrine(DB01435)|Apixaban(DB06605)|Aprepitant(DB00673)|Arformoterol(DB01274)|Artemether(DB06697)|Atomoxetine(DB00289)|Atorvastatin(DB01076)|Axitinib(DB06626)|Azelastine(DB00972)|Benzatropine(DB00245)|Bicalutamide(DB01128)|Bifonazole(DB04794)|Bortezomib(DB00188)|Bromazepam(DB01558)|Brompheniramine(DB00835)|Bupivacaine(DB00297)|Buprenorphine(DB00921)|Carbamazepine(DB00564)|Carbinoxamine(DB00748)|Carisoprodol(DB00395)|Chloramphenicol(DB00446)|Chlorpropamide(DB00672)|Cholecalciferol(DB00169)|Cilostazol(DB01166)|Cimetidine(DB00501)|Cisapride(DB00604)|Citalopram(DB00215)|Clarithromycin(DB01211)|Clevidipine(DB04920)|Clobazam(DB00349)|Clomipramine(DB01242)|Clopidogrel(DB00758)|Clotiazepam(DB01559)|Clotrimazole(DB00257)|Clozapine(DB00363)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dapsone(DB00250)|Delavirdine(DB00705)|Desipramine(DB01151)|Desloratadine(DB00967)|Dexamethasone(DB01234)|Dexfenfluramine(DB01191)|Dextromethorphan(DB00514)|Diazepam(DB00829)|Diclofenac(DB00586)|Diltiazem(DB00343)|Dimethyl sulfoxide(DB01093)|Diphenhydramine(DB01075)|Dopamine(DB00988)|Doxazosin(DB00590)|Doxepin(DB01142)|Dronabinol(DB00470)|Efavirenz(DB00625)|Eletriptan(DB00216)|Enfuvirtide(DB00109)|Enzalutamide(DB08899)|Escitalopram(DB01175)|Esomeprazole(DB00736)|Estradiol(DB00783)|Ethanol(DB00898)|Ethotoin(DB00754)|Etoricoxib(DB01628)|Etravirine(DB06414)|Famotidine(DB00927)|Felbamate(DB00949)|Fluconazole(DB00196)|Flunitrazepam(DB01544)|Fluoxetine(DB00472)|Flutamide(DB00499)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Formoterol(DB00983)|Fosphenytoin(DB01320)|Gefitinib(DB00317)|Gemfibrozil(DB01241)|Gliclazide(DB01120)|Glucosamine(DB01296)|Glyburide(DB01016)|Guanfacine(DB01018)|Haloperidol(DB00502)|Hexobarbital(DB01355)|Ibuprofen(DB01050)|Ifosfamide(DB01181)|Imatinib(DB00619)|Imipramine(DB00458)|Indinavir(DB00224)|Indomethacin(DB00328)|Isoniazid(DB00951)|Ketobemidone(DB06738)|Ketoconazole(DB01026)|Lansoprazole(DB00448)|Lapatinib(DB01259)|Levomilnacipran(DB08918)|Lopinavir(DB01601)|Loratadine(DB00455)|Lorcaserin(DB04871)|Losartan(DB00678)|Lovastatin(DB00227)|LULICONAZOLE(DB08933)|Lumiracoxib(DB01283)|MACITENTAN(DB08932)|Melatonin(DB01065)|Memantine(DB01043)|Meprobamate(DB00371)|Methadone(DB00333)|Methazolamide(DB00703)|Methimazole(DB00763)|Methsuximide(DB05246)|Methylphenobarbital(DB00849)|Metoprolol(DB00264)|Miconazole(DB01110)|Moclobemide(DB01171)|Modafinil(DB00745)|Nelfinavir(DB00220)|Nicardipine(DB00622)|Nicotine(DB00184)|Nilutamide(DB00665)|Nilvadipine(DB06712)|Norethindrone(DB00717)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Omeprazole(DB00338)|Ospemifene(DB04938)|Oxcarbazepine(DB00776)|Oxiconazole(DB00239)|Pantoprazole(DB00213)|Pegvisomant(DB00082)|Pentamidine(DB00738)|Pentobarbital(DB00312)|Perphenazine(DB00850)|Pethidine(DB00454)|Phenelzine(DB00780)|Phenobarbital(DB01174)|Phensuximide(DB00832)|Phenytoin(DB00252)|Pimozide(DB01100)|Pioglitazone(DB01132)|Pipotiazine(DB01621)|Podofilox(DB01179)|Prasugrel(DB06209)|Praziquantel(DB01058)|Prednisone(DB00635)|Primidone(DB00794)|Probenecid(DB01032)|Progesterone(DB00396)|Proguanil(DB01131)|Promazine(DB00420)|Propofol(DB00818)|Propranolol(DB00571)|Quazepam(DB01589)|Quetiapine(DB01224)|Quinine(DB00468)|Rabeprazole(DB01129)|Ramelteon(DB00980)|Ranitidine(DB00863)|Regorafenib(DB08896)|Rifampicin(DB01045)|Rilpivirine(DB08864)|Ritonavir(DB00503)|Rosiglitazone(DB00412)|Rosuvastatin(DB01098)|Saquinavir(DB01232)|Selegiline(DB01037)|Sertraline(DB01104)|Sildenafil(DB00203)|Simvastatin(DB00641)|Sitaxentan(DB06268)|Sorafenib(DB00398)|Sulfanilamide(DB00259)|Tamoxifen(DB00675)|Tapentadol(DB06204)|Telmisartan(DB00966)|Temazepam(DB00231)|Teniposide(DB00444)|Terbinafine(DB00857)|Testosterone(DB00624)|Thalidomide(DB01041)|Thioridazine(DB00679)|Ticlopidine(DB00208)|Timolol(DB00373)|Tioconazole(DB01007)|Tipranavir(DB00932)|Tofacitinib(DB08895)|Tolbutamide(DB01124)|Tolterodine(DB01036)|Topiramate(DB00273)|Torasemide(DB00214)|Trabectedin(DB05109)|Tranylcypromine(DB00752)|Trimethadione(DB00347)|Trimipramine(DB00726)|Troleandomycin(DB01361)|Valproic Acid(DB00313)|Venlafaxine(DB00285)|Verapamil(DB00661)|Vismodegib(DB08828)|Voriconazole(DB00582)|Warfarin(DB00682)|Zafirlukast(DB00549)|Zidovudine(DB00495)|Zolpidem(DB00425)|Zonisamide(DB00909)	GAGATTGAACGTGTCGTTGGC	0.498																																																0								G	HIS/ARG	0,4406		0,0,2203	162.0	144.0	150.0		986	1.4	0.0	10	dbSNP_134	150	2,8598	2.2+/-6.3	0,2,4298	no	missense	CYP2C19	NM_000769.1	29	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	benign	329/491	96602618	2,13004	2203	4300	6503	SO:0001583	missense	1557			M61854	CCDS7436.1	10q24	2007-12-14	2003-01-14		ENSG00000165841	ENSG00000165841		"""Cytochrome P450s"""	2621	protein-coding gene	gene with protein product		124020	"""cytochrome P450, subfamily IIC (mephenytoin 4-hydroxylase), polypeptide 19"""	CYP2C		2009263, 8530044	Standard	NM_000769		Approved	P450IIC19, CPCJ	uc010qnz.2	P33261	OTTHUMG00000018799	ENST00000371321.3:c.986G>A	10.37:g.96602618G>A	ENSP00000360372:p.Arg329His		P33259|Q8WZB1|Q8WZB2|Q9UCD4	Missense_Mutation	SNP	ENST00000371321.3	37	CCDS7436.1	.	.	.	.	.	.	.	.	.	.	G	1.069	-0.670567	0.03403	0.0	2.33E-4	ENSG00000165841	ENST00000371321	T	0.69926	-0.44	3.37	1.37	0.22104	.	0.923473	0.09030	U	0.858958	T	0.62307	0.2417	M	0.70595	2.14	0.09310	N	1	B	0.22480	0.07	B	0.12837	0.008	T	0.49698	-0.8912	10	0.33940	T	0.23	.	7.8143	0.29249	0.2267:0.0:0.7733:0.0	.	329	P33261	CP2CJ_HUMAN	H	329	ENSP00000360372:R329H	ENSP00000360372:R329H	R	+	2	0	CYP2C19	96592608	0.000000	0.05858	0.014000	0.15608	0.055000	0.15305	-4.079000	0.00299	0.061000	0.16311	-0.362000	0.07510	CGT		0.498	CYP2C19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049490.1	NM_000769		22	172	22	172
OR52B6	340980	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	11	5603034	5603034	+	Missense_Mutation	SNP	G	G	A			TCGA-HT-7677-01A-11D-2253-08	TCGA-HT-7677-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a4bfd9a-4a16-41c9-91cb-97351c76ab0e	d27dc741-a306-47c4-a333-155ac43c9484	g.chr11:5603034G>A	ENST00000345043.2	+	1	928	c.928G>A	c.(928-930)Gtt>Att	p.V310I	HBG2_ENST00000380259.2_Intron|AC015691.13_ENST00000394793.2_RNA	NM_001005162.2	NP_001005162.2	Q8NGF0	O52B6_HUMAN	olfactory receptor, family 52, subfamily B, member 6	310						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|kidney(2)|lung(7)|ovary(1)|prostate(1)	12		Medulloblastoma(188;0.00225)|Breast(177;0.0204)|all_neural(188;0.0212)		Epithelial(150;3.56e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		GCTCAATCCCGTTATTTATGG	0.443																																																0													204.0	186.0	192.0					11																	5603034		1927	4131	6058	SO:0001583	missense	340980			AB065858	CCDS41611.1	11p15.4	2012-08-09			ENSG00000187747	ENSG00000187747		"""GPCR / Class A : Olfactory receptors"""	15211	protein-coding gene	gene with protein product							Standard	NM_001005162		Approved		uc010qzi.2	Q8NGF0	OTTHUMG00000066906	ENST00000345043.2:c.928G>A	11.37:g.5603034G>A	ENSP00000341581:p.Val310Ile		Q6IFI7	Missense_Mutation	SNP	ENST00000345043.2	37	CCDS41611.1	.	.	.	.	.	.	.	.	.	.	G	0.003	-2.426543	0.00186	.	.	ENSG00000187747	ENST00000345043	T	0.32753	1.44	4.8	-3.3	0.05003	GPCR, rhodopsin-like superfamily (1);	0.193648	0.24571	N	0.037392	T	0.07954	0.0199	N	0.02842	-0.48	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.35325	-0.9793	10	0.02654	T	1	.	7.2378	0.26079	0.3837:0.1407:0.4757:0.0	.	310	Q8NGF0	O52B6_HUMAN	I	310	ENSP00000341581:V310I	ENSP00000341581:V310I	V	+	1	0	OR52B6	5559610	0.000000	0.05858	0.029000	0.17559	0.152000	0.21847	-0.941000	0.03925	-0.476000	0.06842	-1.076000	0.02234	GTT		0.443	OR52B6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143397.1	NM_001005162		74	98	74	98
LTBR	4055	hgsc.bcm.edu;broad.mit.edu	37	12	6499942	6499942	+	Missense_Mutation	SNP	G	G	A			TCGA-HT-7677-01A-11D-2253-08	TCGA-HT-7677-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a4bfd9a-4a16-41c9-91cb-97351c76ab0e	d27dc741-a306-47c4-a333-155ac43c9484	g.chr12:6499942G>A	ENST00000228918.4	+	10	1473	c.1147G>A	c.(1147-1149)Gaa>Aaa	p.E383K	LTBR_ENST00000541102.1_Missense_Mutation_p.E240K|LTBR_ENST00000539925.1_Missense_Mutation_p.E364K	NM_002342.2	NP_002333.1	P36941	TNR3_HUMAN	lymphotoxin beta receptor (TNFR superfamily, member 3)	383					apoptotic process (GO:0006915)|cellular response to mechanical stimulus (GO:0071260)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of JNK cascade (GO:0046330)|signal transduction (GO:0007165)|viral process (GO:0016032)	integral component of membrane (GO:0016021)	identical protein binding (GO:0042802)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|cervix(1)|kidney(2)|large_intestine(4)|lung(4)|ovary(1)|prostate(2)	15						AGCTACCCCCGAACCTCCATA	0.612																																																0													75.0	81.0	79.0					12																	6499942		2203	4300	6503	SO:0001583	missense	4055			L04270	CCDS8544.1, CCDS59233.1	12p13	2013-05-22				ENSG00000111321		"""Tumor necrosis factor receptor superfamily"""	6718	protein-coding gene	gene with protein product		600979		D12S370		8171323, 8486360	Standard	NM_002342		Approved	TNFCR, TNFR-RP, TNFR2-RP, TNF-R-III, TNFRSF3	uc001qny.2	P36941		ENST00000228918.4:c.1147G>A	12.37:g.6499942G>A	ENSP00000228918:p.Glu383Lys		B7Z1D2|D3DUR2|F5GXE7	Missense_Mutation	SNP	ENST00000228918.4	37	CCDS8544.1	.	.	.	.	.	.	.	.	.	.	G	11.89	1.773613	0.31411	.	.	ENSG00000111321	ENST00000539925;ENST00000228918;ENST00000540343;ENST00000541102	T;T;T	0.37752	1.18;1.18;1.18	4.49	4.49	0.54785	.	1.998500	0.02320	N	0.072874	T	0.33294	0.0858	L	0.32530	0.975	0.21290	N	0.999736	P;P;P	0.41748	0.761;0.649;0.567	B;B;B	0.35182	0.197;0.097;0.086	T	0.43393	-0.9394	10	0.87932	D	0	-6.1771	12.5421	0.56177	0.0:0.0:1.0:0.0	.	364;364;383	F5GXE7;B7Z1D2;P36941	.;.;TNR3_HUMAN	K	364;383;276;240	ENSP00000440875:E364K;ENSP00000228918:E383K;ENSP00000438605:E240K	ENSP00000228918:E383K	E	+	1	0	LTBR	6370203	0.966000	0.33281	0.823000	0.32752	0.026000	0.11368	4.503000	0.60407	2.333000	0.79357	0.555000	0.69702	GAA		0.612	LTBR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399422.1			7	154	7	154
KRT75	9119	hgsc.bcm.edu;broad.mit.edu	37	12	52822506	52822506	+	Missense_Mutation	SNP	C	C	T	rs140579691	byFrequency	TCGA-HT-7677-01A-11D-2253-08	TCGA-HT-7677-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a4bfd9a-4a16-41c9-91cb-97351c76ab0e	d27dc741-a306-47c4-a333-155ac43c9484	g.chr12:52822506C>T	ENST00000252245.5	-	6	1277	c.1057G>A	c.(1057-1059)Gca>Aca	p.A353T	RP11-1020M18.10_ENST00000548135.1_RNA	NM_004693.2	NP_004684.2	O95678	K2C75_HUMAN	keratin 75	353	Coil 2.|Rod.				hematopoietic progenitor cell differentiation (GO:0002244)	extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(13)|lung(10)|prostate(1)|skin(1)	28				BRCA - Breast invasive adenocarcinoma(357;0.192)		TGTCTGCCTGCGGTGACCTGC	0.547													C|||	6	0.00119808	0.0045	0.0	5008	,	,		20297	0.0		0.0	False		,,,				2504	0.0															0								C	THR/ALA	9,4397	15.5+/-35.6	0,9,2194	153.0	127.0	136.0		1057	5.4	0.1	12	dbSNP_134	136	0,8600		0,0,4300	yes	missense	KRT75	NM_004693.2	58	0,9,6494	TT,TC,CC		0.0,0.2043,0.0692	probably-damaging	353/552	52822506	9,12997	2203	4300	6503	SO:0001583	missense	9119			Y19212	CCDS8827.1	12q13.13	2013-06-25			ENSG00000170454	ENSG00000170454		"""-"", ""Intermediate filaments type II, keratins (basic)"""	24431	protein-coding gene	gene with protein product		609025				9856802, 10692104, 16831889	Standard	NM_004693		Approved	K6HF	uc001saj.2	O95678	OTTHUMG00000169592	ENST00000252245.5:c.1057G>A	12.37:g.52822506C>T	ENSP00000252245:p.Ala353Thr		B4DQU4|Q9NSA9	Missense_Mutation	SNP	ENST00000252245.5	37	CCDS8827.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	21.2	4.116244	0.77323	0.002043	0.0	ENSG00000170454	ENST00000252245	T	0.78924	-1.22	5.42	5.42	0.78866	Prefoldin (1);Filament (1);	0.000000	0.53938	D	0.000053	D	0.90909	0.7143	M	0.93241	3.395	0.49915	D	0.999838	D	0.89917	1.0	D	0.85130	0.997	D	0.92980	0.6405	10	0.87932	D	0	.	15.5774	0.76404	0.1382:0.8618:0.0:0.0	.	353	O95678	K2C75_HUMAN	T	353	ENSP00000252245:A353T	ENSP00000252245:A353T	A	-	1	0	KRT75	51108773	0.999000	0.42202	0.111000	0.21465	0.376000	0.30014	4.092000	0.57707	2.544000	0.85801	0.561000	0.74099	GCA		0.547	KRT75-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404968.1	NM_004693		10	137	10	137
HVCN1	84329	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	12	111099098	111099098	+	Silent	SNP	G	G	C			TCGA-HT-7677-01A-11D-2253-08	TCGA-HT-7677-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a4bfd9a-4a16-41c9-91cb-97351c76ab0e	d27dc741-a306-47c4-a333-155ac43c9484	g.chr12:111099098G>C	ENST00000356742.5	-	3	930	c.177C>G	c.(175-177)ccC>ccG	p.P59P	HVCN1_ENST00000439744.2_Silent_p.P39P|HVCN1_ENST00000242607.8_Silent_p.P59P|HVCN1_ENST00000548312.1_Silent_p.P59P			Q96D96	HVCN1_HUMAN	hydrogen voltage-gated channel 1	59					cellular response to pH (GO:0071467)|cellular response to zinc ion (GO:0071294)|multicellular organism reproduction (GO:0032504)|proton transport (GO:0015992)|response to pH (GO:0009268)|response to zinc ion (GO:0010043)|single fertilization (GO:0007338)|sperm-egg recognition (GO:0035036)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	voltage-gated cation channel activity (GO:0022843)|voltage-gated proton channel activity (GO:0030171)			NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|lung(6)|prostate(1)|skin(1)	19						AGACTGGTGTGGGTGGTGGCT	0.622																																																0													63.0	65.0	64.0					12																	111099098		2203	4300	6503	SO:0001819	synonymous_variant	84329			BC007277	CCDS31900.1, CCDS58278.1	12q24.11	2011-12-09	2006-03-24	2006-03-24	ENSG00000122986	ENSG00000122986		"""Voltage-gated ion channels / Hydrogen voltage-gated channel"""	28240	protein-coding gene	gene with protein product	"""voltage sensor domain-only protein"""	611227				20961760, 16556803, 18356202, 22020278	Standard	NM_032369		Approved	MGC15619, Hv1, VSOP	uc001trs.2	Q96D96		ENST00000356742.5:c.177C>G	12.37:g.111099098G>C			A8MQ37|B4DEB3|F8WCH5|Q6UW11|Q96IS5	Silent	SNP	ENST00000356742.5	37	CCDS31900.1																																																																																				0.622	HVCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404653.1	NM_032369		24	80	24	80
HCAR1	27198	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	12	123214713	123214713	+	Silent	SNP	G	G	A			TCGA-HT-7677-01A-11D-2253-08	TCGA-HT-7677-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a4bfd9a-4a16-41c9-91cb-97351c76ab0e	d27dc741-a306-47c4-a333-155ac43c9484	g.chr12:123214713G>A	ENST00000436083.2	-	1	677	c.174C>T	c.(172-174)gcC>gcT	p.A58A	HCAR1_ENST00000356987.2_Silent_p.A58A|HCAR1_ENST00000432564.1_Silent_p.A58A			Q9BXC0	HCAR1_HUMAN	hydroxycarboxylic acid receptor 1	58					response to estradiol (GO:0032355)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|breast(3)|endometrium(1)|kidney(1)|lung(1)|ovary(1)|pancreas(1)|skin(1)	10						AATCAGCCACGGCCAAATTGA	0.542																																																0													94.0	87.0	89.0					12																	123214713		2203	4300	6503	SO:0001819	synonymous_variant	27198			AF411110	CCDS9236.1	12q24.31	2012-08-08	2011-05-30	2011-05-30	ENSG00000196917	ENSG00000196917		"""GPCR / Class A : Hydroxy-carboxylic acid receptors"""	4532	protein-coding gene	gene with protein product	"""lactate receptor 1"""	606923	"""G protein-coupled receptor 104"", ""G protein-coupled receptor 81"""	GPR104, GPR81		11574155, 19047060, 18952058, 21454438	Standard	NM_032554		Approved	HCA1, FKSG80, TA-GPCR, LACR1	uc001ucz.3	Q9BXC0		ENST00000436083.2:c.174C>T	12.37:g.123214713G>A			B2R9X4|Q3Y5J3|Q4VBN1|Q6NXU5	Silent	SNP	ENST00000436083.2	37	CCDS9236.1																																																																																				0.542	HCAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401415.1			21	36	21	36
PTPN9	5780	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	15	75761319	75761319	+	Missense_Mutation	SNP	A	A	C			TCGA-HT-7677-01A-11D-2253-08	TCGA-HT-7677-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a4bfd9a-4a16-41c9-91cb-97351c76ab0e	d27dc741-a306-47c4-a333-155ac43c9484	g.chr15:75761319A>C	ENST00000306726.2	-	13	2085	c.1573T>G	c.(1573-1575)Ttc>Gtc	p.F525V		NM_002833.2	NP_002824.1	P43378	PTN9_HUMAN	protein tyrosine phosphatase, non-receptor type 9	525	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)	non-membrane spanning protein tyrosine phosphatase activity (GO:0004726)|protein tyrosine phosphatase activity (GO:0004725)			central_nervous_system(1)|endometrium(4)|large_intestine(4)|lung(9)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						AGTGAGCAGAAGGTACCTGAA	0.512																																																0													63.0	52.0	56.0					15																	75761319		2197	4294	6491	SO:0001583	missense	5780				CCDS10280.1	15q23	2011-06-09			ENSG00000169410	ENSG00000169410		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"""	9661	protein-coding gene	gene with protein product		600768				1557404	Standard	NM_002833		Approved	MEG2	uc002bal.3	P43378	OTTHUMG00000142838	ENST00000306726.2:c.1573T>G	15.37:g.75761319A>C	ENSP00000303554:p.Phe525Val		Q53XR9	Missense_Mutation	SNP	ENST00000306726.2	37	CCDS10280.1	.	.	.	.	.	.	.	.	.	.	A	15.41	2.825623	0.50739	.	.	ENSG00000169410	ENST00000306726;ENST00000544966	T	0.17528	2.27	6.17	6.17	0.99709	Protein-tyrosine phosphatase, receptor/non-receptor type (4);Protein-tyrosine/Dual-specificity phosphatase (1);	0.046595	0.85682	D	0.000000	T	0.41465	0.1160	M	0.74467	2.265	0.58432	D	0.999999	D	0.61080	0.989	D	0.75484	0.986	T	0.32079	-0.9920	10	0.87932	D	0	.	11.8444	0.52376	0.9307:0.0:0.0693:0.0	.	525	P43378	PTN9_HUMAN	V	525;515	ENSP00000303554:F525V	ENSP00000303554:F525V	F	-	1	0	PTPN9	73548372	1.000000	0.71417	1.000000	0.80357	0.359000	0.29487	4.717000	0.61923	2.371000	0.80710	0.533000	0.62120	TTC		0.512	PTPN9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286474.1			17	25	17	25
IL17C	27189	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	16	88705399	88705399	+	Missense_Mutation	SNP	G	G	A			TCGA-HT-7677-01A-11D-2253-08	TCGA-HT-7677-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a4bfd9a-4a16-41c9-91cb-97351c76ab0e	d27dc741-a306-47c4-a333-155ac43c9484	g.chr16:88705399G>A	ENST00000244241.4	+	2	66	c.17G>A	c.(16-18)gGc>gAc	p.G6D		NM_013278.3	NP_037410.1	Q9P0M4	IL17C_HUMAN	interleukin 17C	6					cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|inflammatory response (GO:0006954)|neutrophil differentiation (GO:0030223)|positive regulation of cytokine production involved in inflammatory response (GO:1900017)	extracellular space (GO:0005615)	cytokine activity (GO:0005125)			large_intestine(1)|lung(1)	2				BRCA - Breast invasive adenocarcinoma(80;0.0477)		CTCCTCCCCGGCCTCCTGTTT	0.642																																																0													83.0	95.0	91.0					16																	88705399		1985	4160	6145	SO:0001583	missense	27189			AF152099	CCDS42217.1	16q24	2011-07-14			ENSG00000124391	ENSG00000124391		"""Interleukins and interleukin receptors"""	5983	protein-coding gene	gene with protein product		604628				10639155	Standard	NM_013278		Approved	IL-17C, CX2, IL-21, MGC126884, MGC138401	uc002fla.3	Q9P0M4		ENST00000244241.4:c.17G>A	16.37:g.88705399G>A	ENSP00000244241:p.Gly6Asp		Q3MIG8|Q9HC75	Missense_Mutation	SNP	ENST00000244241.4	37	CCDS42217.1	.	.	.	.	.	.	.	.	.	.	G	12.15	1.852181	0.32699	.	.	ENSG00000124391	ENST00000244241	T	0.49139	0.79	4.37	2.36	0.29203	.	1.308000	0.05185	N	0.502128	T	0.34861	0.0912	N	0.19112	0.55	0.09310	N	1	B	0.13594	0.008	B	0.12156	0.007	T	0.32955	-0.9887	10	0.87932	D	0	-6.0654	6.6338	0.22872	0.0956:0.0:0.7289:0.1755	.	6	Q9P0M4	IL17C_HUMAN	D	6	ENSP00000244241:G6D	ENSP00000244241:G6D	G	+	2	0	IL17C	87232900	0.055000	0.20627	0.229000	0.23960	0.558000	0.35554	0.364000	0.20325	0.395000	0.25257	0.555000	0.69702	GGC		0.642	IL17C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422575.1	NM_013278		58	257	58	257
DSC2	1824	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	18	28650804	28650804	+	Missense_Mutation	SNP	G	G	A	rs180863872	byFrequency	TCGA-HT-7677-01A-11D-2253-08	TCGA-HT-7677-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a4bfd9a-4a16-41c9-91cb-97351c76ab0e	d27dc741-a306-47c4-a333-155ac43c9484	g.chr18:28650804G>A	ENST00000280904.6	-	14	2581	c.2138C>T	c.(2137-2139)aCg>aTg	p.T713M	DSC2_ENST00000251081.6_Missense_Mutation_p.T713M|snoU13_ENST00000459603.1_RNA	NM_024422.3	NP_077740.1	Q02487	DSC2_HUMAN	desmocollin 2	713					bundle of His cell to Purkinje myocyte communication (GO:0086069)|cardiac muscle cell-cardiac muscle cell adhesion (GO:0086042)|cell adhesion (GO:0007155)|cellular response to starvation (GO:0009267)|homophilic cell adhesion (GO:0007156)|regulation of heart rate by cardiac conduction (GO:0086091)|ventricular cardiac muscle cell action potential (GO:0086005)	cell-cell adherens junction (GO:0005913)|cytoplasmic vesicle (GO:0031410)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intercalated disc (GO:0014704)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(2)|kidney(1)|large_intestine(2)|lung(12)|ovary(2)|prostate(1)|skin(1)	21			OV - Ovarian serous cystadenocarcinoma(10;0.0241)			ACAGACCAGCGTAAACAGGAT	0.363													G|||	2	0.000399361	0.0	0.0029	5008	,	,		15032	0.0		0.0	False		,,,				2504	0.0															0													87.0	88.0	88.0					18																	28650804		2203	4300	6503	SO:0001583	missense	1824			X56807	CCDS11892.1, CCDS11893.1	18q12.1	2014-09-17			ENSG00000134755	ENSG00000134755		"""Cadherins / Major cadherins"""	3036	protein-coding gene	gene with protein product		125645		DSC3		7774948	Standard	NM_024422		Approved	CDHF2	uc002kwl.4	Q02487	OTTHUMG00000131981	ENST00000280904.6:c.2138C>T	18.37:g.28650804G>A	ENSP00000280904:p.Thr713Met			Missense_Mutation	SNP	ENST00000280904.6	37	CCDS11892.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	G	18.30	3.593497	0.66219	.	.	ENSG00000134755	ENST00000251081;ENST00000280904;ENST00000438199;ENST00000399347	T;T	0.58940	0.34;0.3	6.08	6.08	0.98989	.	0.000000	0.33327	N	0.005033	T	0.77032	0.4071	M	0.75615	2.305	0.47819	D	0.999529	D;D	0.89917	0.999;1.0	P;D	0.67900	0.902;0.954	T	0.75889	-0.3158	10	0.54805	T	0.06	.	20.6721	0.99693	0.0:0.0:1.0:0.0	.	713;713	Q02487;Q02487-2	DSC2_HUMAN;.	M	713;713;479;726	ENSP00000251081:T713M;ENSP00000280904:T713M	ENSP00000251081:T713M	T	-	2	0	DSC2	26904802	1.000000	0.71417	0.981000	0.43875	0.394000	0.30568	6.206000	0.72154	2.894000	0.99253	0.591000	0.81541	ACG		0.363	DSC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254943.1	NM_004949		16	67	16	67
MIDN	90007	hgsc.bcm.edu;broad.mit.edu	37	19	1255053	1255053	+	Silent	SNP	C	C	T			TCGA-HT-7677-01A-11D-2253-08	TCGA-HT-7677-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a4bfd9a-4a16-41c9-91cb-97351c76ab0e	d27dc741-a306-47c4-a333-155ac43c9484	g.chr19:1255053C>T	ENST00000591446.2	+	5	1258	c.849C>T	c.(847-849)acC>acT	p.T283T	MIDN_ENST00000300952.2_Silent_p.T283T			Q504T8	MIDN_HUMAN	midnolin	283						cytosol (GO:0005829)|nucleolus (GO:0005730)				NS(1)|endometrium(3)|kidney(1)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)	13		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;7.93e-06)|all_lung(49;1.25e-05)|Breast(49;0.000172)|Hepatocellular(1079;0.137)		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)		TCTCAGGGACCTTCTCTGGTA	0.617																																																0													63.0	65.0	65.0					19																	1255053		2203	4299	6502	SO:0001819	synonymous_variant	90007			AC004221	CCDS32864.1	19p13.3	2013-09-20			ENSG00000167470	ENSG00000167470			16298	protein-coding gene	gene with protein product		606700				10974535	Standard	XM_005259671		Approved		uc002lrp.3	Q504T8	OTTHUMG00000180144	ENST00000591446.2:c.849C>T	19.37:g.1255053C>T			Q96BW8	Silent	SNP	ENST00000591446.2	37	CCDS32864.1																																																																																				0.617	MIDN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449965.2			6	106	6	106
FCHO1	23149	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	19	17886277	17886277	+	Missense_Mutation	SNP	G	G	A			TCGA-HT-7677-01A-11D-2253-08	TCGA-HT-7677-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a4bfd9a-4a16-41c9-91cb-97351c76ab0e	d27dc741-a306-47c4-a333-155ac43c9484	g.chr19:17886277G>A	ENST00000596536.1	+	15	1241	c.958G>A	c.(958-960)Gtg>Atg	p.V320M	FCHO1_ENST00000597512.1_Missense_Mutation_p.V327M|FCHO1_ENST00000594202.1_Missense_Mutation_p.V320M|FCHO1_ENST00000252771.7_Missense_Mutation_p.V320M|FCHO1_ENST00000596951.1_Missense_Mutation_p.V320M|FCHO1_ENST00000600676.1_Missense_Mutation_p.V320M|FCHO1_ENST00000595033.1_Missense_Mutation_p.V270M|FCHO1_ENST00000539407.1_Missense_Mutation_p.V320M|FCHO1_ENST00000389133.4_Missense_Mutation_p.V320M	NM_015122.2	NP_055937.1	O14526	FCHO1_HUMAN	FCH domain only 1	320	Mediates interaction with the adaptor protein complex AP-2.				clathrin coat assembly (GO:0048268)|clathrin-mediated endocytosis (GO:0072583)	coated pit (GO:0005905)|plasma membrane (GO:0005886)	AP-2 adaptor complex binding (GO:0035612)			NS(2)|breast(1)|large_intestine(6)|liver(1)|lung(12)	22						ATGTCCAGAGGTGGATGAAGA	0.597											OREG0025349	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				0													94.0	93.0	93.0					19																	17886277		2203	4300	6503	SO:0001583	missense	23149			AB006628	CCDS32955.1, CCDS59365.1, CCDS59366.1	19p13.12	2008-02-05				ENSG00000130475			29002	protein-coding gene	gene with protein product		613437				12477932	Standard	NM_001161357		Approved	KIAA0290	uc002nhg.3	O14526		ENST00000596536.1:c.958G>A	19.37:g.17886277G>A	ENSP00000470731:p.Val320Met	721	A6NHE6|A8K5U5|B4E120|Q05C93|Q8IW22	Missense_Mutation	SNP	ENST00000596536.1	37	CCDS32955.1	.	.	.	.	.	.	.	.	.	.	G	16.16	3.045672	0.55110	.	.	ENSG00000130475	ENST00000252771;ENST00000389133;ENST00000539407	T;T;T	0.49720	0.77;0.77;0.77	4.23	4.23	0.50019	.	0.780481	0.11151	N	0.594146	T	0.66607	0.2806	M	0.69358	2.11	0.58432	D	0.999999	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.76575	0.972;0.972;0.988	T	0.60469	-0.7257	10	0.33940	T	0.23	-19.8383	14.4506	0.67382	0.0:0.0:1.0:0.0	.	270;320;320	B4E120;O14526;O14526-2	.;FCHO1_HUMAN;.	M	320	ENSP00000252771:V320M;ENSP00000373785:V320M;ENSP00000437978:V320M	ENSP00000252771:V320M	V	+	1	0	FCHO1	17747277	1.000000	0.71417	1.000000	0.80357	0.342000	0.28953	8.304000	0.89958	2.075000	0.62263	0.491000	0.48974	GTG		0.597	FCHO1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466946.2	NM_015122		25	243	25	243
CIC	23152	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	19	42799051	42799051	+	Missense_Mutation	SNP	G	G	T			TCGA-HT-7677-01A-11D-2253-08	TCGA-HT-7677-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a4bfd9a-4a16-41c9-91cb-97351c76ab0e	d27dc741-a306-47c4-a333-155ac43c9484	g.chr19:42799051G>T	ENST00000575354.2	+	20	4575	c.4535G>T	c.(4534-4536)cGt>cTt	p.R1512L	CIC_ENST00000160740.3_Missense_Mutation_p.R1510L|CIC_ENST00000572681.2_Missense_Mutation_p.R2418L	NM_015125.3	NP_055940.3	Q96RK0	CIC_HUMAN	capicua transcriptional repressor	1512					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			autonomic_ganglia(1)|breast(5)|central_nervous_system(32)|endometrium(10)|kidney(2)|large_intestine(7)|lung(9)|ovary(7)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	82		Prostate(69;0.00682)				TTGAAGATCCGTGAGGTGCGC	0.627			"""Mis, F, S"""		oligodendroglioma																																		Rec	yes		19	19q13.2	23152	capicua homolog		O	0													51.0	51.0	51.0					19																	42799051		2203	4300	6503	SO:0001583	missense	23152			AB002304	CCDS12601.1	19q13.2	2013-03-15	2013-03-15		ENSG00000079432	ENSG00000079432			14214	protein-coding gene	gene with protein product		612082	"""capicua (Drosophila) homolog"", ""capicua homolog (Drosophila)"""			12393275, 15981098	Standard	NM_015125		Approved	KIAA0306	uc002otf.1	Q96RK0		ENST00000575354.2:c.4535G>T	19.37:g.42799051G>T	ENSP00000458663:p.Arg1512Leu		Q7LGI1|Q9UEG5|Q9Y6T1	Missense_Mutation	SNP	ENST00000575354.2	37	CCDS12601.1	.	.	.	.	.	.	.	.	.	.	G	24.1	4.488509	0.84854	.	.	ENSG00000079432	ENST00000160740	.	.	.	4.49	4.49	0.54785	.	.	.	.	.	T	0.64875	0.2638	L	0.29908	0.895	0.48901	D	0.999725	D	0.65815	0.995	D	0.70227	0.968	T	0.68712	-0.5336	8	0.87932	D	0	-6.0224	15.0527	0.71888	0.0:0.0:1.0:0.0	.	1512	Q96RK0	CIC_HUMAN	L	1512	.	ENSP00000160740:R1512L	R	+	2	0	CIC	47490891	1.000000	0.71417	0.993000	0.49108	0.974000	0.67602	8.215000	0.89762	2.513000	0.84729	0.491000	0.48974	CGT		0.627	CIC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000438532.2			64	28	64	28
CA11	770	hgsc.bcm.edu;broad.mit.edu	37	19	49143394	49143394	+	Silent	SNP	G	G	A			TCGA-HT-7677-01A-11D-2253-08	TCGA-HT-7677-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a4bfd9a-4a16-41c9-91cb-97351c76ab0e	d27dc741-a306-47c4-a333-155ac43c9484	g.chr19:49143394G>A	ENST00000084798.4	-	4	1108	c.429C>T	c.(427-429)gcC>gcT	p.A143A	SEC1P_ENST00000430145.2_RNA|DBP_ENST00000222122.5_5'Flank|DBP_ENST00000601104.1_5'Flank	NM_001217.3	NP_001208.2	O75493	CAH11_HUMAN	carbonic anhydrase XI	143						basolateral plasma membrane (GO:0016323)|extracellular region (GO:0005576)				breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(8)	14		all_epithelial(76;2.38e-06)|all_lung(116;4.89e-06)|Lung NSC(112;9.34e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000103)|all cancers(93;0.000119)|GBM - Glioblastoma multiforme(486;0.00634)|Epithelial(262;0.016)	Zonisamide(DB00909)	GTTCCGAGCCGGCTCCGTCGC	0.607																																																0													86.0	78.0	80.0					19																	49143394		2203	4300	6503	SO:0001819	synonymous_variant	770			AF067662	CCDS12729.1	19q13.3	2012-07-02			ENSG00000063180	ENSG00000063180		"""Carbonic anhydrases"""	1370	protein-coding gene	gene with protein product	"""CA-RP XI"", ""carbonic anhydrase-related protein XI"", ""carbonic anhydrase-related protein 2"""	604644				9878252	Standard	XR_243956		Approved	CARP2, CARPX1	uc002pjz.1	O75493		ENST00000084798.4:c.429C>T	19.37:g.49143394G>A			O60596|Q6FHI1|Q9UEC4	Silent	SNP	ENST00000084798.4	37	CCDS12729.1																																																																																				0.607	CA11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466172.1	NM_001217		6	94	6	94
ITLN1	55600	hgsc.bcm.edu;ucsc.edu	37	1	160851055	160851055	+	Silent	SNP	G	G	A	rs61734482	byFrequency	TCGA-HT-7677-01A-11D-2253-08	TCGA-HT-7677-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a4bfd9a-4a16-41c9-91cb-97351c76ab0e	d27dc741-a306-47c4-a333-155ac43c9484	g.chr1:160851055G>A	ENST00000326245.3	-	5	568	c.453C>T	c.(451-453)caC>caT	p.H151H	ITLN1_ENST00000487531.1_5'UTR	NM_017625.2	NP_060095.2	Q8WWA0	ITLN1_HUMAN	intelectin 1 (galactofuranose binding)	151	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				positive regulation of glucose import (GO:0046326)|positive regulation of protein phosphorylation (GO:0001934)|response to nematode (GO:0009624)	anchored component of membrane (GO:0031225)|brush border membrane (GO:0031526)|extracellular vesicular exosome (GO:0070062)|membrane raft (GO:0045121)|receptor complex (GO:0043235)	carbohydrate binding (GO:0030246)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(1)|lung(6)|ovary(2)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)	21	all_cancers(52;2.99e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00737)			TATTGGGCACGTGCCAGATGC	0.587													G|||	71	0.0141773	0.0507	0.0029	5008	,	,		20706	0.001		0.001	False		,,,				2504	0.0															0								G		170,4236	113.3+/-151.4	5,160,2038	162.0	133.0	143.0		453	-7.6	0.8	1	dbSNP_129	143	0,8600		0,0,4300	no	coding-synonymous	ITLN1	NM_017625.2		5,160,6338	AA,AG,GG		0.0,3.8584,1.3071		151/314	160851055	170,12836	2203	4300	6503	SO:0001819	synonymous_variant	55600			AB036706	CCDS1211.1	1q21.3	2008-02-05			ENSG00000179914	ENSG00000179914			18259	protein-coding gene	gene with protein product		609873				11313366, 11181563	Standard	NM_017625		Approved	ITLN, FLJ20022, LFR, HL-1, hIntL	uc001fxc.3	Q8WWA0	OTTHUMG00000028604	ENST00000326245.3:c.453C>T	1.37:g.160851055G>A			Q5IWS4|Q5VYI4|Q6YDJ3|Q9NP67	Silent	SNP	ENST00000326245.3	37	CCDS1211.1																																																																																				0.587	ITLN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071462.1	NM_017625		36	242	36	242
F5	2153	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	1	169524423	169524423	+	Missense_Mutation	SNP	T	T	C	rs370875907		TCGA-HT-7677-01A-11D-2253-08	TCGA-HT-7677-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a4bfd9a-4a16-41c9-91cb-97351c76ab0e	d27dc741-a306-47c4-a333-155ac43c9484	g.chr1:169524423T>C	ENST00000367797.3	-	7	1316	c.1115A>G	c.(1114-1116)gAc>gGc	p.D372G	F5_ENST00000367796.3_Missense_Mutation_p.D372G|F5_ENST00000546081.1_Missense_Mutation_p.D235G	NM_000130.4	NP_000121	P12259	FA5_HUMAN	coagulation factor V (proaccelerin, labile factor)	372	F5/8 type A 2.|Plastocyanin-like 3.				blood circulation (GO:0008015)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)|vesicle (GO:0031982)	copper ion binding (GO:0005507)			NS(1)|breast(4)|central_nervous_system(4)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(24)|lung(55)|ovary(3)|prostate(4)|skin(5)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(1)	128	all_hematologic(923;0.208)				ART-123(DB05777)|Drotrecogin alfa(DB00055)	AACTCACTTGTCCATATTCGC	0.468																																																0													207.0	191.0	196.0					1																	169524423		2203	4300	6503	SO:0001583	missense	2153			M14335	CCDS1281.1	1q23	2012-10-02			ENSG00000198734	ENSG00000198734			3542	protein-coding gene	gene with protein product		612309					Standard	NM_000130		Approved		uc001ggg.1	P12259	OTTHUMG00000034595	ENST00000367797.3:c.1115A>G	1.37:g.169524423T>C	ENSP00000356771:p.Asp372Gly		A8K6E8|Q14285|Q2EHR5|Q5R346|Q5R347|Q6UPU6|Q8WWQ6	Missense_Mutation	SNP	ENST00000367797.3	37	CCDS1281.1	.	.	.	.	.	.	.	.	.	.	T	25.8	4.676602	0.88445	.	.	ENSG00000198734	ENST00000367797;ENST00000367796;ENST00000546081	D;D;D	0.99089	-5.41;-5.41;-5.41	5.78	5.78	0.91487	Cupredoxin (2);	0.048257	0.85682	D	0.000000	D	0.98905	0.9629	M	0.75447	2.3	0.46774	D	0.999193	D	0.76494	0.999	P	0.58820	0.846	D	0.99601	1.0978	9	0.72032	D	0.01	.	16.109	0.81247	0.0:0.0:0.0:1.0	.	372	P12259	FA5_HUMAN	G	372;372;235	ENSP00000356771:D372G;ENSP00000356770:D372G;ENSP00000439664:D235G	ENSP00000356770:D372G	D	-	2	0	F5	167791047	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	6.954000	0.76001	2.210000	0.71456	0.528000	0.53228	GAC		0.468	F5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083712.1	NM_000130		35	232	35	232
CFHR3	10878	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	1	196749062	196749062	+	Missense_Mutation	SNP	C	C	T	rs574536456		TCGA-HT-7677-01A-11D-2253-08	TCGA-HT-7677-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a4bfd9a-4a16-41c9-91cb-97351c76ab0e	d27dc741-a306-47c4-a333-155ac43c9484	g.chr1:196749062C>T	ENST00000367425.4	+	3	481	c.389C>T	c.(388-390)aCg>aTg	p.T130M	CFHR3_ENST00000471440.2_Missense_Mutation_p.T130M|CFHR3_ENST00000391985.3_Missense_Mutation_p.T130M	NM_021023.5	NP_066303.2	Q02985	FHR3_HUMAN	complement factor H-related 3	130	Sushi 2. {ECO:0000255|PROSITE- ProRule:PRU00302}.					blood microparticle (GO:0072562)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)		p.T130M(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(4)|lung(6)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	18						GTTACATGTACGGAGAAAGGC	0.473													-|||	1	0.000199681	0.0	0.0	5008	,	,		11779	0.0		0.0	False		,,,				2504	0.001															1	Substitution - Missense(1)	urinary_tract(1)											85.0	84.0	85.0					1																	196749062		1904	4137	6041	SO:0001583	missense	10878			X68679	CCDS30958.1, CCDS53453.1	1q32	2014-09-17		2006-02-28	ENSG00000116785	ENSG00000116785		"""Complement system"""	16980	protein-coding gene	gene with protein product	"""complement factor H related 3"""	605336		CFHL3		8428964, 10380701	Standard	NM_021023		Approved	FHR-3, HLF4, FHR3, DOWN16	uc001gtl.3	Q02985	OTTHUMG00000035929	ENST00000367425.4:c.389C>T	1.37:g.196749062C>T	ENSP00000356395:p.Thr130Met		B4DPR0|Q9UJ16	Missense_Mutation	SNP	ENST00000367425.4	37	CCDS30958.1	.	.	.	.	.	.	.	.	.	.	.	11.47	1.648809	0.29336	.	.	ENSG00000116785	ENST00000367425;ENST00000471440;ENST00000391985;ENST00000542253	T;T;T	0.65916	-0.18;-0.18;-0.18	3.67	2.74	0.32292	Complement control module (2);Sushi/SCR/CCP (3);	.	.	.	.	T	0.69486	0.3116	M	0.79343	2.45	0.09310	N	1	P;D;P	0.60575	0.875;0.988;0.943	P;P;B	0.54889	0.598;0.763;0.258	T	0.57365	-0.7824	9	0.31617	T	0.26	.	7.6977	0.28604	0.0:0.8732:0.0:0.1268	.	130;130;130	B4DPR0;Q02985;Q6NSD3	.;FHR3_HUMAN;.	M	130	ENSP00000356395:T130M;ENSP00000436258:T130M;ENSP00000375845:T130M	ENSP00000356395:T130M	T	+	2	0	CFHR3	195015685	0.132000	0.22450	0.037000	0.18230	0.005000	0.04900	1.146000	0.31589	0.653000	0.30826	0.398000	0.26397	ACG		0.473	CFHR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087505.2	NM_021023		41	79	41	79
MRAP	56246	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	21	33684248	33684248	+	Missense_Mutation	SNP	G	G	A			TCGA-HT-7677-01A-11D-2253-08	TCGA-HT-7677-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a4bfd9a-4a16-41c9-91cb-97351c76ab0e	d27dc741-a306-47c4-a333-155ac43c9484	g.chr21:33684248G>A	ENST00000399784.2	+	5	647	c.460G>A	c.(460-462)Gtc>Atc	p.V154I	MRAP_ENST00000303645.5_Missense_Mutation_p.V154I|MRAP_ENST00000497833.1_3'UTR|MRAP_ENST00000399786.3_Intron|MRAP_ENST00000339944.4_Intron|URB1_ENST00000382751.3_3'UTR	NM_178817.3	NP_848932.1	Q8TCY5	MRAP_HUMAN	melanocortin 2 receptor accessory protein	154					brown fat cell differentiation (GO:0050873)|positive regulation of cAMP biosynthetic process (GO:0030819)|protein localization to cell surface (GO:0034394)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	corticotropin hormone receptor binding (GO:0031780)|type 1 melanocortin receptor binding (GO:0070996)|type 3 melanocortin receptor binding (GO:0031781)|type 4 melanocortin receptor binding (GO:0031782)|type 5 melanocortin receptor binding (GO:0031783)			endometrium(1)|large_intestine(2)|lung(3)	6						GGGTCCCCTCGTCAGGAGCAA	0.602																																																0													47.0	46.0	46.0					21																	33684248		2203	4299	6502	SO:0001583	missense	56246			AF454915	CCDS13612.1, CCDS13613.1	21q22.1	2005-10-30	2005-02-01	2005-02-07	ENSG00000170262	ENSG00000170262			1304	protein-coding gene	gene with protein product		609196	"""chromosome 21 open reading frame 61"""	C21orf61		12036298, 15654338	Standard	NM_178817		Approved	B27, FALP	uc002ypj.3	Q8TCY5	OTTHUMG00000085309	ENST00000399784.2:c.460G>A	21.37:g.33684248G>A	ENSP00000382684:p.Val154Ile		Q5EBR3|Q8TDB7|Q8WXC1|Q8WXC2	Missense_Mutation	SNP	ENST00000399784.2	37	CCDS13613.1	.	.	.	.	.	.	.	.	.	.	G	8.511	0.866617	0.17250	.	.	ENSG00000170262	ENST00000399784;ENST00000303645	D;D	0.88046	-2.33;-2.33	4.36	-8.72	0.00845	.	.	.	.	.	T	0.72326	0.3446	N	0.22421	0.69	0.09310	N	1	B	0.09022	0.002	B	0.06405	0.002	T	0.55685	-0.8102	9	0.24483	T	0.36	-17.1272	8.494	0.33117	0.6007:0.2113:0.188:0.0	.	154	Q8TCY5	MRAP_HUMAN	I	154	ENSP00000382684:V154I;ENSP00000306697:V154I	ENSP00000306697:V154I	V	+	1	0	MRAP	32606119	0.000000	0.05858	0.000000	0.03702	0.013000	0.08279	-1.107000	0.03316	-2.113000	0.00833	-0.736000	0.03550	GTC		0.602	MRAP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000193092.1	NM_178817		35	57	35	57
SPTBN1	6711	hgsc.bcm.edu;broad.mit.edu	37	2	54859857	54859857	+	Missense_Mutation	SNP	A	A	G			TCGA-HT-7677-01A-11D-2253-08	TCGA-HT-7677-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a4bfd9a-4a16-41c9-91cb-97351c76ab0e	d27dc741-a306-47c4-a333-155ac43c9484	g.chr2:54859857A>G	ENST00000356805.4	+	17	4000	c.3719A>G	c.(3718-3720)aAc>aGc	p.N1240S	SPTBN1_ENST00000333896.5_Missense_Mutation_p.N1227S	NM_003128.2	NP_003119.2	Q01082	SPTB2_HUMAN	spectrin, beta, non-erythrocytic 1	1240					actin filament capping (GO:0051693)|axon guidance (GO:0007411)|Golgi to plasma membrane protein transport (GO:0043001)|membrane assembly (GO:0071709)|mitotic cytokinesis (GO:0000281)|plasma membrane organization (GO:0007009)|protein targeting to plasma membrane (GO:0072661)	axolemma (GO:0030673)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|protein complex (GO:0043234)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin binding (GO:0003779)|ankyrin binding (GO:0030506)|phospholipid binding (GO:0005543)|poly(A) RNA binding (GO:0044822)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|breast(8)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(11)|lung(27)|ovary(4)|prostate(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	82			Lung(47;0.24)			AGCGATGGGAACATCAACTCA	0.507																																																0													124.0	109.0	114.0					2																	54859857		2203	4300	6503	SO:0001583	missense	6711				CCDS33198.1, CCDS33199.1	2p21	2013-01-10			ENSG00000115306	ENSG00000115306		"""Pleckstrin homology (PH) domain containing"""	11275	protein-coding gene	gene with protein product		182790					Standard	NM_003128		Approved		uc002rxu.3	Q01082	OTTHUMG00000133746	ENST00000356805.4:c.3719A>G	2.37:g.54859857A>G	ENSP00000349259:p.Asn1240Ser		B2RP63|O60837|Q16057|Q53R99|Q59ER3|Q8IX99	Missense_Mutation	SNP	ENST00000356805.4	37	CCDS33198.1	.	.	.	.	.	.	.	.	.	.	A	32	5.169245	0.94768	.	.	ENSG00000115306	ENST00000356805;ENST00000333896	T;T	0.32023	1.47;1.47	5.46	5.46	0.80206	.	0.000000	0.85682	D	0.000000	T	0.53997	0.1831	M	0.85945	2.785	0.58432	D	0.999993	P;P	0.46220	0.756;0.874	P;P	0.53760	0.461;0.734	T	0.61792	-0.6990	10	0.72032	D	0.01	.	15.5486	0.76129	1.0:0.0:0.0:0.0	.	1227;1240	Q01082-3;Q01082	.;SPTB2_HUMAN	S	1240;1227	ENSP00000349259:N1240S;ENSP00000334156:N1227S	ENSP00000334156:N1227S	N	+	2	0	SPTBN1	54713361	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.463000	0.80869	2.081000	0.62600	0.533000	0.62120	AAC		0.507	SPTBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258115.3			3	58	3	58
SCN3A	6328	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	165948831	165948831	+	Silent	SNP	G	G	C			TCGA-HT-7677-01A-11D-2253-08	TCGA-HT-7677-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a4bfd9a-4a16-41c9-91cb-97351c76ab0e	d27dc741-a306-47c4-a333-155ac43c9484	g.chr2:165948831G>C	ENST00000360093.3	-	27	5231	c.4740C>G	c.(4738-4740)ctC>ctG	p.L1580L	SCN3A_ENST00000283254.7_Silent_p.L1580L|SCN3A_ENST00000465043.1_5'UTR|AC013463.2_ENST00000431341.1_RNA|SCN3A_ENST00000409101.3_Silent_p.L1531L|SCN3A_ENST00000540861.1_Silent_p.L63L	NM_001081677.1	NP_001075146.1	Q9NY46	SCN3A_HUMAN	sodium channel, voltage-gated, type III, alpha subunit	1580					membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			NS(1)|breast(7)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(19)|liver(2)|lung(47)|ovary(6)|prostate(3)|skin(10)|upper_aerodigestive_tract(4)|urinary_tract(3)	120					Lacosamide(DB06218)|Valproic Acid(DB00313)|Zonisamide(DB00909)	AGTAGTGTCTGAGGGAGACGA	0.438																																																0													141.0	123.0	129.0					2																	165948831		2203	4300	6503	SO:0001819	synonymous_variant	6328			AF035685	CCDS33312.1, CCDS46440.1	2q24	2012-02-26	2007-01-23		ENSG00000153253	ENSG00000153253		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10590	protein-coding gene	gene with protein product		182391	"""sodium channel, voltage-gated, type III, alpha polypeptide"""			9589372, 16382098	Standard	NM_001081676		Approved	Nav1.3	uc002ucx.3	Q9NY46	OTTHUMG00000044171	ENST00000360093.3:c.4740C>G	2.37:g.165948831G>C			Q16142|Q53SX0|Q9BZB3|Q9C006|Q9NYK2|Q9P2J1|Q9UPD1|Q9Y6P4	Silent	SNP	ENST00000360093.3	37																																																																																					0.438	SCN3A-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_006922		40	62	40	62
IDH1	3417	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	209113112	209113112	+	Missense_Mutation	SNP	C	C	T	rs121913500		TCGA-HT-7677-01A-11D-2253-08	TCGA-HT-7677-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a4bfd9a-4a16-41c9-91cb-97351c76ab0e	d27dc741-a306-47c4-a333-155ac43c9484	g.chr2:209113112C>T	ENST00000415913.1	-	4	776	c.395G>A	c.(394-396)cGt>cAt	p.R132H	IDH1_ENST00000345146.2_Missense_Mutation_p.R132H|IDH1_ENST00000446179.1_Missense_Mutation_p.R132H	NM_001282387.1	NP_001269316.1	O75874	IDHC_HUMAN	isocitrate dehydrogenase 1 (NADP+), soluble	132			R -> C (in colorectal cancer and glioma samples; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha- ketoglutarate but instead alpha- ketoglutarate is converted to R(-)-2- hydroxyglutarate). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:19117336}.|R -> G (in a glioma sample; glioblastoma multiforme; somatic mutation). {ECO:0000269|PubMed:19117336}.|R -> H (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:18772396}.|R -> L (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:19117336}.|R -> S (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:18772396}.		2-oxoglutarate metabolic process (GO:0006103)|cellular lipid metabolic process (GO:0044255)|female gonad development (GO:0008585)|glutathione metabolic process (GO:0006749)|glyoxylate cycle (GO:0006097)|isocitrate metabolic process (GO:0006102)|NADPH regeneration (GO:0006740)|response to oxidative stress (GO:0006979)|response to steroid hormone (GO:0048545)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	isocitrate dehydrogenase (NADP+) activity (GO:0004450)|magnesium ion binding (GO:0000287)|NAD binding (GO:0051287)|NADP binding (GO:0050661)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)	p.R132H(2774)|p.R132L(59)|p.R132V(1)|p.G131_R132>VL(1)		NS(1)|autonomic_ganglia(2)|biliary_tract(24)|bone(237)|central_nervous_system(3764)|endometrium(3)|haematopoietic_and_lymphoid_tissue(794)|kidney(2)|large_intestine(7)|lung(7)|prostate(6)|skin(5)|soft_tissue(12)|thyroid(22)|urinary_tract(1)	4887				Epithelial(149;0.0322)|LUSC - Lung squamous cell carcinoma(261;0.0711)|Lung(261;0.136)		ATAAGCATGACGACCTATGAT	0.393			Mis		gliobastoma																																Pancreas(158;264 1958 3300 35450 36047)		Dom	yes		2	2q33.3	3417	"""isocitrate dehydrogenase 1 (NADP+), soluble"""		O	2835	Substitution - Missense(2834)|Complex - compound substitution(1)	central_nervous_system(2579)|haematopoietic_and_lymphoid_tissue(205)|bone(43)|prostate(4)|biliary_tract(2)|urinary_tract(1)|skin(1)											79.0	73.0	75.0					2																	209113112		2203	4300	6503	SO:0001583	missense	3417				CCDS2381.1	2q34	2014-09-17			ENSG00000138413	ENSG00000138413	1.1.1.42		5382	protein-coding gene	gene with protein product		147700					Standard	NM_005896		Approved		uc002vcu.3	O75874	OTTHUMG00000132943	ENST00000415913.1:c.395G>A	2.37:g.209113112C>T	ENSP00000390265:p.Arg132His		Q567U4|Q6FHQ6|Q7Z3V0|Q93090|Q9NTJ9|Q9UKW8	Missense_Mutation	SNP	ENST00000415913.1	37	CCDS2381.1	.	.	.	.	.	.	.	.	.	.	C	25.6	4.657324	0.88154	.	.	ENSG00000138413	ENST00000345146;ENST00000446179;ENST00000415913;ENST00000415282	D;D;D;D	0.86956	-2.19;-2.19;-2.19;-2.19	5.57	4.69	0.59074	Isopropylmalate dehydrogenase-like domain (2);	0.000000	0.85682	D	0.000000	D	0.93145	0.7817	H	0.99379	4.54	0.80722	D	1	B	0.25486	0.127	B	0.25405	0.06	D	0.92324	0.5868	10	0.87932	D	0	-20.0399	14.3783	0.66895	0.0:0.9288:0.0:0.0712	.	132	O75874	IDHC_HUMAN	H	132	ENSP00000260985:R132H;ENSP00000410513:R132H;ENSP00000390265:R132H;ENSP00000391075:R132H	ENSP00000260985:R132H	R	-	2	0	IDH1	208821357	1.000000	0.71417	0.997000	0.53966	0.992000	0.81027	6.088000	0.71371	1.356000	0.45884	0.555000	0.69702	CGT		0.393	IDH1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336672.1			37	53	37	53
FGD5	152273	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	3	14862573	14862573	+	Silent	SNP	G	G	A	rs371257394		TCGA-HT-7677-01A-11D-2253-08	TCGA-HT-7677-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a4bfd9a-4a16-41c9-91cb-97351c76ab0e	d27dc741-a306-47c4-a333-155ac43c9484	g.chr3:14862573G>A	ENST00000285046.5	+	1	2105	c.1995G>A	c.(1993-1995)acG>acA	p.T665T	FGD5_ENST00000543601.1_Silent_p.T424T	NM_152536.3	NP_689749.3	Q6ZNL6	FGD5_HUMAN	FYVE, RhoGEF and PH domain containing 5	665					actin cytoskeleton organization (GO:0030036)|cytoskeleton organization (GO:0007010)|filopodium assembly (GO:0046847)|positive regulation of GTPase activity (GO:0043547)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|small GTPase binding (GO:0031267)			NS(2)|breast(2)|endometrium(3)|kidney(5)|large_intestine(10)|lung(25)|ovary(3)|pancreas(1)|prostate(2)|urinary_tract(1)	54						AGAAGAAGACGGAGAACAAAT	0.512													G|||	1	0.000199681	0.0008	0.0	5008	,	,		19923	0.0		0.0	False		,,,				2504	0.0															0								G		4,3964		0,4,1980	80.0	80.0	80.0		1995	-10.6	0.0	3		80	0,8342		0,0,4171	no	coding-synonymous	FGD5	NM_152536.3		0,4,6151	AA,AG,GG		0.0,0.1008,0.0325		665/1463	14862573	4,12306	1984	4171	6155	SO:0001819	synonymous_variant	152273			AK097276	CCDS46767.1	3p25.1	2013-01-10			ENSG00000154783	ENSG00000154783		"""Zinc fingers, FYVE domain containing"", ""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	19117	protein-coding gene	gene with protein product		614788					Standard	NM_152536		Approved	ZFYVE23, FLJ39957, FLJ00274	uc003bzc.3	Q6ZNL6	OTTHUMG00000155556	ENST00000285046.5:c.1995G>A	3.37:g.14862573G>A			B3KVQ3|Q6MZY1|Q7Z303|Q8IYP3|Q8N861|Q8N8G4	Silent	SNP	ENST00000285046.5	37	CCDS46767.1																																																																																				0.512	FGD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340628.1	NM_152536		34	40	34	40
XIRP1	165904	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	3	39227360	39227360	+	Missense_Mutation	SNP	G	G	A	rs371572701		TCGA-HT-7677-01A-11D-2253-08	TCGA-HT-7677-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a4bfd9a-4a16-41c9-91cb-97351c76ab0e	d27dc741-a306-47c4-a333-155ac43c9484	g.chr3:39227360G>A	ENST00000340369.3	-	2	3805	c.3577C>T	c.(3577-3579)Cgg>Tgg	p.R1193W	XIRP1_ENST00000396251.1_Intron|XIRP1_ENST00000421646.1_Intron	NM_194293.2	NP_919269.2	Q702N8	XIRP1_HUMAN	xin actin-binding repeat containing 1	1193					cardiac muscle cell development (GO:0055013)|negative regulation of cell proliferation (GO:0008285)|regulation of membrane potential (GO:0042391)|sarcomere organization (GO:0045214)	fascia adherens (GO:0005916)	poly(A) RNA binding (GO:0044822)	p.R1193W(1)		breast(4)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(14)|lung(22)|ovary(4)|pancreas(1)|prostate(2)|skin(6)	71				KIRC - Kidney renal clear cell carcinoma(284;0.0517)|Kidney(284;0.065)		GGCTCCTCCCGCCCTGGCCCA	0.677																																																1	Substitution - Missense(1)	endometrium(1)						G	,TRP/ARG	0,4402		0,0,2201	21.0	25.0	24.0		,3577	-0.5	0.0	3		24	1,8599		0,1,4299	no	intron,missense	XIRP1	NM_001198621.1,NM_194293.2	,101	0,1,6500	AA,AG,GG		0.0116,0.0,0.0077	,benign	,1193/1844	39227360	1,13001	2201	4300	6501	SO:0001583	missense	165904			AW755250	CCDS2683.1, CCDS56245.1	3p21.33	2008-02-05	2007-06-27	2007-06-27	ENSG00000168334	ENSG00000168334			14301	protein-coding gene	gene with protein product		609777	"""cardiomyopathy associated 1"""	CMYA1		12203715, 15454575	Standard	NM_001198621		Approved	DKFZp451D042, Xin	uc003cjk.2	Q702N8	OTTHUMG00000131297	ENST00000340369.3:c.3577C>T	3.37:g.39227360G>A	ENSP00000343140:p.Arg1193Trp		A0JP25|A4QPE2|Q68DF2|Q6ZTR3|Q702N9|Q8IVN7|Q8N1N3|Q8N904|Q8TCG7	Missense_Mutation	SNP	ENST00000340369.3	37	CCDS2683.1	.	.	.	.	.	.	.	.	.	.	G	9.595	1.127172	0.20959	0.0	1.16E-4	ENSG00000168334	ENST00000340369	T	0.03745	3.82	4.57	-0.46	0.12175	.	0.830318	0.10387	N	0.680851	T	0.01835	0.0058	N	0.03608	-0.345	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.46638	-0.9177	10	0.40728	T	0.16	.	7.4287	0.27115	0.518:0.0:0.482:0.0	.	1193	Q702N8	XIRP1_HUMAN	W	1193	ENSP00000343140:R1193W	ENSP00000343140:R1193W	R	-	1	2	XIRP1	39202364	0.000000	0.05858	0.000000	0.03702	0.937000	0.57800	-0.345000	0.07770	-0.208000	0.10171	0.561000	0.74099	CGG		0.677	XIRP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254065.1	XM_093522		6	47	6	47
DDX39B	7919	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	6	31506618	31506618	+	Silent	SNP	C	C	T			TCGA-HT-7677-01A-11D-2253-08	TCGA-HT-7677-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a4bfd9a-4a16-41c9-91cb-97351c76ab0e	d27dc741-a306-47c4-a333-155ac43c9484	g.chr6:31506618C>T	ENST00000396172.1	-	4	984	c.354G>A	c.(352-354)gtG>gtA	p.V118V	DDX39B_ENST00000449074.2_3'UTR|SNORD117_ENST00000364915.1_RNA|DDX39B_ENST00000415382.2_Intron|SNORD84_ENST00000584275.1_RNA|DDX39B_ENST00000453105.2_Silent_p.V71V|ATP6V1G2-DDX39B_ENST00000376185.1_3'UTR|DDX39B_ENST00000376177.2_Silent_p.V118V|DDX39B_ENST00000458640.1_Silent_p.V118V|DDX39B_ENST00000417556.2_Silent_p.V133V	NM_004640.6	NP_004631.1	Q13838	DX39B_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 39B	118	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				ATP catabolic process (GO:0006200)|mRNA export from nucleus (GO:0006406)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of DNA damage checkpoint (GO:2000002)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|RNA secondary structure unwinding (GO:0010501)|RNA splicing (GO:0008380)|spliceosomal complex assembly (GO:0000245)|viral mRNA export from host cell nucleus (GO:0046784)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|transcription export complex (GO:0000346)	ATP binding (GO:0005524)|ATP-dependent protein binding (GO:0043008)|ATP-dependent RNA helicase activity (GO:0004004)|poly(A) RNA binding (GO:0044822)|RNA-dependent ATPase activity (GO:0008186)|U4 snRNA binding (GO:0030621)|U6 snRNA binding (GO:0017070)			NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	19						TGTGACACATCACCAGTACAG	0.453																																																0													139.0	132.0	134.0					6																	31506618		2203	4300	6503	SO:0001819	synonymous_variant	7919			Z37166	CCDS4697.1	6p21.33	2011-02-09	2011-02-08	2011-02-08	ENSG00000198563	ENSG00000198563		"""DEAD-boxes"""	13917	protein-coding gene	gene with protein product	"""U2AF65-associated protein 56"""	142560	"""HLA-B associated transcript 1"""	BAT1		7601445, 2813433	Standard	NM_004640		Approved	D6S81E, UAP56	uc003ntu.3	Q13838	OTTHUMG00000031165	ENST00000396172.1:c.354G>A	6.37:g.31506618C>T			B0S8C0|O43496|Q0EFA1|Q2L6F9|Q53GL9|Q5RJ64|Q5RJ66|Q5ST94|Q5STB4|Q5STB5|Q5STB7|Q5STB8|Q5STU4|Q5STU5|Q5STU6|Q5STU8|Q71V76	Silent	SNP	ENST00000396172.1	37	CCDS4697.1																																																																																				0.453	DDX39B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259083.1	NM_004640		11	87	11	87
RARS2	57038	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	6	88229954	88229954	+	Missense_Mutation	SNP	C	C	A			TCGA-HT-7677-01A-11D-2253-08	TCGA-HT-7677-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a4bfd9a-4a16-41c9-91cb-97351c76ab0e	d27dc741-a306-47c4-a333-155ac43c9484	g.chr6:88229954C>A	ENST00000369536.5	-	13	1101	c.1056G>T	c.(1054-1056)aaG>aaT	p.K352N	RARS2_ENST00000497828.1_5'Flank	NM_020320.3	NP_064716.2	Q5T160	SYRM_HUMAN	arginyl-tRNA synthetase 2, mitochondrial	352					arginyl-tRNA aminoacylation (GO:0006420)|gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)	mitochondrial matrix (GO:0005759)	arginine-tRNA ligase activity (GO:0004814)|ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(7)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	22		all_cancers(76;3.93e-06)|Acute lymphoblastic leukemia(125;3.55e-10)|Prostate(29;3.51e-09)|all_hematologic(105;3.29e-06)|all_epithelial(107;0.00575)		BRCA - Breast invasive adenocarcinoma(108;0.0456)		GCTGAAAATGCTTTTTTTGTC	0.328																																																0													200.0	191.0	194.0					6																	88229954		2203	4300	6503	SO:0001583	missense	57038			AK093934	CCDS5011.1	6q16.1	2011-07-01	2007-09-27	2007-02-23	ENSG00000146282	ENSG00000146282	6.1.1.19	"""Aminoacyl tRNA synthetases / Class I"""	21406	protein-coding gene	gene with protein product	"""arginine tRNA ligase 2, mitochondrial (putative)"""	611524	"""arginyl-tRNA synthetase-like"""	RARSL		17847012	Standard	NM_020320		Approved	MGC14993, MGC23778, PRO1992, dJ382I10.6, DALRD2	uc003pme.3	Q5T160	OTTHUMG00000015178	ENST00000369536.5:c.1056G>T	6.37:g.88229954C>A	ENSP00000358549:p.Lys352Asn		B2RDT7|Q96FU5|Q9H8K8	Missense_Mutation	SNP	ENST00000369536.5	37	CCDS5011.1	.	.	.	.	.	.	.	.	.	.	C	6.342	0.431134	0.12045	.	.	ENSG00000146282	ENST00000369536	T	0.62364	0.03	5.76	-2.17	0.07059	Arginyl-tRNA synthetase, class Ia, core (1);Rossmann-like alpha/beta/alpha sandwich fold (1);	0.591382	0.19919	N	0.103138	T	0.07818	0.0196	N	0.01096	-1.015	0.19300	N	0.99997	B	0.02656	0.0	B	0.04013	0.001	T	0.42616	-0.9441	10	0.15066	T	0.55	.	5.2895	0.15719	0.3361:0.2206:0.0:0.4434	.	352	Q5T160	SYRM_HUMAN	N	352	ENSP00000358549:K352N	ENSP00000358549:K352N	K	-	3	2	RARS2	88286673	0.001000	0.12720	0.986000	0.45419	0.960000	0.62799	-0.113000	0.10774	-0.105000	0.12132	-0.977000	0.02584	AAG		0.328	RARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041448.1	NM_020320		26	157	26	157
FHL5	9457	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	6	97053913	97053913	+	Missense_Mutation	SNP	A	A	G			TCGA-HT-7677-01A-11D-2253-08	TCGA-HT-7677-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a4bfd9a-4a16-41c9-91cb-97351c76ab0e	d27dc741-a306-47c4-a333-155ac43c9484	g.chr6:97053913A>G	ENST00000326771.2	+	5	850	c.470A>G	c.(469-471)aAg>aGg	p.K157R	FHL5_ENST00000541107.1_Missense_Mutation_p.K157R	NM_020482.4	NP_065228.4	Q5TD97	FHL5_HUMAN	four and a half LIM domains 5	157	LIM zinc-binding 2. {ECO:0000255|PROSITE- ProRule:PRU00125}.				positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(4)|lung(17)|ovary(2)|urinary_tract(1)	27		all_cancers(76;1.57e-07)|Acute lymphoblastic leukemia(125;4.93e-10)|all_hematologic(75;3.55e-07)|all_epithelial(107;0.00266)|Colorectal(196;0.0341)|Lung NSC(302;0.204)		BRCA - Breast invasive adenocarcinoma(108;0.0948)		TGTTTTGAGAAGGAGTTTGCT	0.383																																																0													111.0	100.0	103.0					6																	97053913		2203	4300	6503	SO:0001583	missense	9457			AF278541	CCDS5035.1	6q16.1-q16.3	2008-02-05			ENSG00000112214	ENSG00000112214			17371	protein-coding gene	gene with protein product		605126					Standard	NM_020482		Approved	FLJ33049, ACT, dJ393D12.2	uc003pot.2	Q5TD97	OTTHUMG00000015239	ENST00000326771.2:c.470A>G	6.37:g.97053913A>G	ENSP00000326022:p.Lys157Arg		B2RBD1|E1P526|Q5TD98|Q8WW21|Q9NQU2	Missense_Mutation	SNP	ENST00000326771.2	37	CCDS5035.1	.	.	.	.	.	.	.	.	.	.	A	14.25	2.480284	0.44044	.	.	ENSG00000112214	ENST00000541107;ENST00000326771;ENST00000450218	D;D;D	0.87491	-2.26;-2.26;-2.26	6.06	2.3	0.28687	Zinc finger, LIM-type (3);	0.000000	0.47455	D	0.000225	T	0.67822	0.2934	L	0.31804	0.96	0.49299	D	0.999771	B	0.21381	0.055	B	0.30646	0.118	T	0.63125	-0.6707	10	0.44086	T	0.13	.	6.8993	0.24273	0.7634:0.0:0.1247:0.1119	.	157	Q5TD97	FHL5_HUMAN	R	157	ENSP00000442357:K157R;ENSP00000326022:K157R;ENSP00000396390:K157R	ENSP00000326022:K157R	K	+	2	0	FHL5	97160634	1.000000	0.71417	1.000000	0.80357	0.614000	0.37383	5.289000	0.65656	0.516000	0.28340	0.528000	0.53228	AAG		0.383	FHL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041559.1	NM_020482		10	68	10	68
EYA4	2070	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	6	133783471	133783471	+	Splice_Site	SNP	A	A	T			TCGA-HT-7677-01A-11D-2253-08	TCGA-HT-7677-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a4bfd9a-4a16-41c9-91cb-97351c76ab0e	d27dc741-a306-47c4-a333-155ac43c9484	g.chr6:133783471A>T	ENST00000367895.5	+	8	901		c.e8-1		EYA4_ENST00000452339.2_Splice_Site|EYA4_ENST00000431403.2_Splice_Site|EYA4_ENST00000355167.3_Splice_Site|EYA4_ENST00000355286.6_Splice_Site|EYA4_ENST00000430974.2_Splice_Site|EYA4_ENST00000531901.1_Splice_Site|EYA4_ENST00000525849.1_Splice_Site	NM_004100.4	NP_004091.3	O95677	EYA4_HUMAN	EYA transcriptional coactivator and phosphatase 4						anatomical structure morphogenesis (GO:0009653)|chromatin modification (GO:0016568)|DNA repair (GO:0006281)|inner ear development (GO:0048839)|middle ear morphogenesis (GO:0042474)|regulation of transcription, DNA-templated (GO:0006355)|sensory perception of sound (GO:0007605)|transcription, DNA-templated (GO:0006351)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|protein tyrosine phosphatase activity (GO:0004725)			breast(1)|central_nervous_system(3)|endometrium(5)|kidney(2)|large_intestine(11)|lung(25)|skin(1)	48	Colorectal(23;0.221)			GBM - Glioblastoma multiforme(68;0.00457)|OV - Ovarian serous cystadenocarcinoma(155;0.0152)		TCTGATATTTAGGCCCTATCC	0.438																																					Melanoma(57;398 1237 3528 4702 7415)											0													184.0	174.0	178.0					6																	133783471		2203	4300	6503	SO:0001630	splice_region_variant	2070			Y17114	CCDS5165.1, CCDS5166.1, CCDS43506.1, CCDS75521.1, CCDS75523.1	6q23	2014-09-17	2014-06-19		ENSG00000112319	ENSG00000112319		"""Protein tyrosine phosphatases / Asp-based PTPs"""	3522	protein-coding gene	gene with protein product		603550	"""eyes absent (Drosophila) homolog 4"", ""eyes absent homolog 4 (Drosophila)"""	DFNA10, CMD1J		9887327, 11159937	Standard	NM_004100		Approved		uc003qed.4	O95677	OTTHUMG00000015602	ENST00000367895.5:c.438-1A>T	6.37:g.133783471A>T			B7Z7F7|O95464|O95679|Q8IW39|Q9NTR7	Splice_Site	SNP	ENST00000367895.5	37	CCDS5165.1	.	.	.	.	.	.	.	.	.	.	A	21.7	4.188616	0.78789	.	.	ENSG00000112319	ENST00000452339;ENST00000430974;ENST00000367895;ENST00000355167;ENST00000355286;ENST00000531901;ENST00000525849;ENST00000431403	.	.	.	5.96	5.96	0.96718	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.4447	0.83919	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	EYA4	133825164	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.962000	0.93254	2.284000	0.76573	0.528000	0.53228	.		0.438	EYA4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000042282.2	NM_004100	Intron	32	222	32	222
NPSR1	387129	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	7	34724169	34724169	+	Silent	SNP	G	G	A			TCGA-HT-7677-01A-11D-2253-08	TCGA-HT-7677-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a4bfd9a-4a16-41c9-91cb-97351c76ab0e	d27dc741-a306-47c4-a333-155ac43c9484	g.chr7:34724169G>A	ENST00000360581.1	+	2	281	c.153G>A	c.(151-153)gaG>gaA	p.E51E	NPSR1_ENST00000465305.1_Silent_p.E51E|NPSR1_ENST00000381553.3_Silent_p.E51E|NPSR1-AS1_ENST00000419766.1_RNA|NPSR1_ENST00000381542.1_Silent_p.E51E|NPSR1_ENST00000359791.1_Silent_p.E51E|NPSR1_ENST00000381539.3_Silent_p.E51E|NPSR1_ENST00000531252.1_Silent_p.E51E	NM_207172.1	NP_997055.1	Q6W5P4	NPSR1_HUMAN	neuropeptide S receptor 1	51						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	neuropeptide receptor activity (GO:0008188)|vasopressin receptor activity (GO:0005000)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(5)|lung(14)|pancreas(1)|skin(7)	31					Halothane(DB01159)	TGCAGACTGAGCAATTGATAA	0.433																																																0													183.0	177.0	179.0					7																	34724169		2203	4300	6503	SO:0001819	synonymous_variant	387129			AY255536	CCDS5443.1, CCDS5444.1, CCDS75579.1, CCDS75580.1, CCDS75581.1	7p14.3	2012-08-08	2006-05-10	2006-05-10	ENSG00000187258	ENSG00000187258		"""GPCR / Class A : Neuropeptide receptors : S"""	23631	protein-coding gene	gene with protein product		608595	"""G protein-coupled receptor 154"""	GPR154		12679517, 15073379	Standard	NM_207173		Approved	PGR14, GPRA	uc003tei.1	Q6W5P4	OTTHUMG00000099383	ENST00000360581.1:c.153G>A	7.37:g.34724169G>A			A2RTZ4|Q2XP58|Q56H76|Q56H77|Q56H78|Q6JSL4|Q6JSL5|Q6JSL6|Q6JSL7|Q6JSL8|Q6W5P3|Q6ZMB8	Silent	SNP	ENST00000360581.1	37	CCDS5444.1																																																																																				0.433	NPSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216837.1	NM_207173		39	70	39	70
PSD3	23362	hgsc.bcm.edu;broad.mit.edu	37	8	18393449	18393449	+	Missense_Mutation	SNP	T	T	C			TCGA-HT-7677-01A-11D-2253-08	TCGA-HT-7677-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a4bfd9a-4a16-41c9-91cb-97351c76ab0e	d27dc741-a306-47c4-a333-155ac43c9484	g.chr8:18393449T>C	ENST00000327040.8	-	16	3050	c.2948A>G	c.(2947-2949)tAt>tGt	p.Y983C	PSD3_ENST00000286485.8_Missense_Mutation_p.Y449C|PSD3_ENST00000523619.1_Missense_Mutation_p.Y918C|PSD3_ENST00000440756.2_Missense_Mutation_p.Y985C|PSD3_ENST00000428502.2_Missense_Mutation_p.Y312C	NM_015310.3	NP_056125.3	Q9NYI0	PSD3_HUMAN	pleckstrin and Sec7 domain containing 3	984					neuron differentiation (GO:0030182)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)	cell junction (GO:0030054)|postsynaptic membrane (GO:0045211)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(8)|ovary(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20				Colorectal(111;0.0281)|READ - Rectum adenocarcinoma(644;0.183)		AATGCTGACATACATTTCATA	0.488																																																0													98.0	86.0	90.0					8																	18393449		2203	4300	6503	SO:0001583	missense	23362			AF243495	CCDS34854.1, CCDS43720.1	8p21.3	2013-01-10			ENSG00000156011	ENSG00000156011		"""Pleckstrin homology (PH) domain containing"""	19093	protein-coding gene	gene with protein product		614440					Standard	NM_206909		Approved	KIAA0942, HCA67, EFA6R, DKFZp761K1423	uc003wza.3	Q9NYI0	OTTHUMG00000163711	ENST00000327040.8:c.2948A>G	8.37:g.18393449T>C	ENSP00000324127:p.Tyr983Cys		A6NFQ4|E9KL50|Q6B003|Q9Y2F1	Missense_Mutation	SNP	ENST00000327040.8	37	CCDS43720.1	.	.	.	.	.	.	.	.	.	.	T	14.41	2.526913	0.44969	.	.	ENSG00000156011	ENST00000327040;ENST00000440756;ENST00000381690;ENST00000286485;ENST00000428502;ENST00000523619	T;T;T;T	0.47177	1.55;1.54;0.85;1.54	5.8	5.8	0.92144	.	0.000000	0.41823	U	0.000801	T	0.70919	0.3279	M	0.83774	2.66	0.58432	D	0.999999	D;D;D;D	0.89917	1.0;1.0;1.0;0.999	D;D;D;D	0.91635	0.999;0.999;0.999;0.954	T	0.75772	-0.3200	10	0.87932	D	0	.	14.0873	0.64964	0.0:0.0:0.0:1.0	.	983;984;449;312	E9KL50;Q9NYI0;Q9NYI0-3;B4DKF8	.;PSD3_HUMAN;.;.	C	983;985;205;449;312;918	ENSP00000324127:Y983C;ENSP00000401704:Y985C;ENSP00000286485:Y449C;ENSP00000430640:Y918C	ENSP00000286485:Y449C	Y	-	2	0	PSD3	18437729	1.000000	0.71417	0.041000	0.18516	0.321000	0.28281	6.367000	0.73099	2.205000	0.71048	0.533000	0.62120	TAT		0.488	PSD3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000374867.1	NM_015310		4	100	4	100
NUGGC	389643	hgsc.bcm.edu;broad.mit.edu	37	8	27891083	27891083	+	Silent	SNP	G	G	T			TCGA-HT-7677-01A-11D-2253-08	TCGA-HT-7677-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a4bfd9a-4a16-41c9-91cb-97351c76ab0e	d27dc741-a306-47c4-a333-155ac43c9484	g.chr8:27891083G>T	ENST00000413272.2	-	14	1885	c.1743C>A	c.(1741-1743)atC>atA	p.I581I	NUGGC_ENST00000341513.6_Silent_p.I581I	NM_001010906.1	NP_001010906.1	Q68CJ6	SLIP_HUMAN	nuclear GTPase, germinal center associated	581					cellular response to DNA damage stimulus (GO:0006974)|somatic hypermutation of immunoglobulin genes (GO:0016446)	nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)										AAACAGGGTCGATCTGGTCAT	0.453																																																0													80.0	73.0	76.0					8																	27891083		1893	4110	6003	SO:0001819	synonymous_variant	389643			AB075870	CCDS47833.1	8p21.1	2012-06-07	2012-06-07	2012-06-07	ENSG00000189233	ENSG00000189233			33550	protein-coding gene	gene with protein product	"""speckled-like pattern in the germinal center"""		"""chromosome 8 open reading frame 80"""	C8orf80		19734146	Standard	NM_001010906		Approved	HMFN0672, SLIP-GC	uc003xgm.4	Q68CJ6	OTTHUMG00000155970	ENST00000413272.2:c.1743C>A	8.37:g.27891083G>T			Q6ZP73	Silent	SNP	ENST00000413272.2	37	CCDS47833.1																																																																																				0.453	NUGGC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000342494.1	NM_001010906		4	43	4	43
DMRTA1	63951	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	9	22451627	22451627	+	Missense_Mutation	SNP	C	C	T			TCGA-HT-7677-01A-11D-2253-08	TCGA-HT-7677-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a4bfd9a-4a16-41c9-91cb-97351c76ab0e	d27dc741-a306-47c4-a333-155ac43c9484	g.chr9:22451627C>T	ENST00000325870.2	+	2	1457	c.1232C>T	c.(1231-1233)cCt>cTt	p.P411L		NM_022160.2	NP_071443.2	Q5VZB9	DMRTA_HUMAN	DMRT-like family A1	411					male mating behavior (GO:0060179)|ovarian follicle development (GO:0001541)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|kidney(1)|large_intestine(3)|lung(6)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	15		all_cancers(5;4.09e-243)|Acute lymphoblastic leukemia(3;8.25e-150)|all_hematologic(3;4.25e-147)|Esophageal squamous(3;2.32e-09)|Renal(3;1.71e-07)|Breast(3;2.07e-06)|Hepatocellular(5;0.00563)		GBM - Glioblastoma multiforme(1;5.12e-278)|Lung(24;8.2e-52)|LUSC - Lung squamous cell carcinoma(38;1.46e-37)|OV - Ovarian serous cystadenocarcinoma(39;0.0517)		GCTTTCTCTCCTCTTCAAACT	0.408																																																0													114.0	120.0	118.0					9																	22451627		2203	4300	6503	SO:0001583	missense	63951			AJ290954	CCDS6514.1	9p21.3	2008-05-15			ENSG00000176399	ENSG00000176399			13826	protein-coding gene	gene with protein product		614803					Standard	NM_022160		Approved		uc003zpp.1	Q5VZB9	OTTHUMG00000019693	ENST00000325870.2:c.1232C>T	9.37:g.22451627C>T	ENSP00000319651:p.Pro411Leu		A1L481|Q8N8Y9|Q9H4B9	Missense_Mutation	SNP	ENST00000325870.2	37	CCDS6514.1	.	.	.	.	.	.	.	.	.	.	C	26.6	4.752197	0.89753	.	.	ENSG00000176399	ENST00000325870	T	0.62105	0.05	5.92	5.92	0.95590	.	0.000000	0.85682	D	0.000000	T	0.81950	0.4931	M	0.82823	2.61	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.83492	0.0070	10	0.87932	D	0	-20.0783	19.0887	0.93217	0.0:1.0:0.0:0.0	.	411	Q5VZB9	DMRTA_HUMAN	L	411	ENSP00000319651:P411L	ENSP00000319651:P411L	P	+	2	0	DMRTA1	22441627	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	6.560000	0.73950	2.801000	0.96364	0.650000	0.86243	CCT		0.408	DMRTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051935.2			29	84	29	84
SOX17	64321	broad.mit.edu;ucsc.edu	37	8	55372386	55372386	+	Missense_Mutation	SNP	A	A	G			TCGA-HT-7677-01A-11D-2253-08	TCGA-HT-7677-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a4bfd9a-4a16-41c9-91cb-97351c76ab0e	d27dc741-a306-47c4-a333-155ac43c9484	g.chr8:55372386A>G	ENST00000297316.4	+	2	1280	c.1076A>G	c.(1075-1077)gAc>gGc	p.D359G		NM_022454.3	NP_071899.1	Q9H6I2	SOX17_HUMAN	SRY (sex determining region Y)-box 17	359	Sox C-terminal. {ECO:0000255|PROSITE- ProRule:PRU00849}.				angiogenesis (GO:0001525)|canonical Wnt signaling pathway (GO:0060070)|cardiac cell fate determination (GO:0060913)|cardiogenic plate morphogenesis (GO:0003142)|cell migration involved in gastrulation (GO:0042074)|common bile duct development (GO:0061009)|embryonic foregut morphogenesis (GO:0048617)|embryonic heart tube development (GO:0035050)|embryonic heart tube morphogenesis (GO:0003143)|endocardial cell differentiation (GO:0060956)|endocardium formation (GO:0060214)|endoderm formation (GO:0001706)|endodermal cell fate determination (GO:0007493)|endodermal digestive tract morphogenesis (GO:0061031)|gall bladder development (GO:0061010)|heart formation (GO:0060914)|heart looping (GO:0001947)|inner cell mass cellular morphogenesis (GO:0001828)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell growth (GO:0030308)|negative regulation of mesodermal cell fate specification (GO:0042662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of Wnt signaling pathway involved in heart development (GO:0003308)|outflow tract morphogenesis (GO:0003151)|positive regulation of cell differentiation (GO:0045597)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of skeletal muscle tissue development (GO:0048643)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein destabilization (GO:0031648)|protein stabilization (GO:0050821)|regulation of cardiac cell fate specification (GO:2000043)|regulation of embryonic development (GO:0045995)|regulation of stem cell division (GO:2000035)|regulation of stem cell proliferation (GO:0072091)|regulation of transcription from RNA polymerase II promoter involved in definitive endodermal cell fate specification (GO:0060807)|regulation of transcription, DNA-templated (GO:0006355)|renal system development (GO:0072001)|rostrocaudal neural tube patterning (GO:0021903)|signal transduction involved in regulation of gene expression (GO:0023019)|spermatogenesis (GO:0007283)|stem cell fate specification (GO:0048866)|vasculogenesis (GO:0001570)	nuclear transcription factor complex (GO:0044798)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	beta-catenin binding (GO:0008013)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			endometrium(6)|kidney(1)|large_intestine(3)|lung(7)|prostate(1)	18		Lung NSC(129;0.109)|all_epithelial(80;0.176)|all_lung(136;0.181)	OV - Ovarian serous cystadenocarcinoma(7;1.9e-07)|Epithelial(17;1.7e-05)|all cancers(17;0.000159)			GGGGAGGTGGACCGCACGGAA	0.692																																																0													31.0	37.0	35.0					8																	55372386		2202	4300	6502	SO:0001583	missense	64321			AB073988	CCDS6159.1	8q11.23	2014-09-04			ENSG00000164736	ENSG00000164736		"""SRY (sex determining region Y)-boxes"""	18122	protein-coding gene	gene with protein product		610928				11786926	Standard	NM_022454		Approved		uc003xsb.4	Q9H6I2	OTTHUMG00000164377	ENST00000297316.4:c.1076A>G	8.37:g.55372386A>G	ENSP00000297316:p.Asp359Gly			Missense_Mutation	SNP	ENST00000297316.4	37	CCDS6159.1	.	.	.	.	.	.	.	.	.	.	A	17.89	3.499828	0.64298	.	.	ENSG00000164736	ENST00000297316	D	0.91124	-2.79	5.09	3.88	0.44766	.	0.058457	0.64402	D	0.000004	D	0.88142	0.6357	M	0.71871	2.18	0.53688	D	0.999975	B	0.23442	0.085	B	0.26094	0.066	D	0.86395	0.1738	10	0.72032	D	0.01	.	6.6186	0.22790	0.7868:0.0:0.0758:0.1374	.	359	Q9H6I2	SOX17_HUMAN	G	359	ENSP00000297316:D359G	ENSP00000297316:D359G	D	+	2	0	SOX17	55534939	1.000000	0.71417	1.000000	0.80357	0.933000	0.57130	7.250000	0.78287	1.925000	0.55765	0.374000	0.22700	GAC		0.692	SOX17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378526.2			14	41	14	41
TRAF7	84231	broad.mit.edu;ucsc.edu	37	16	2223509	2223509	+	Missense_Mutation	SNP	T	T	C			TCGA-HT-7677-01A-11D-2253-08	TCGA-HT-7677-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a4bfd9a-4a16-41c9-91cb-97351c76ab0e	d27dc741-a306-47c4-a333-155ac43c9484	g.chr16:2223509T>C	ENST00000326181.6	+	11	1172	c.1040T>C	c.(1039-1041)cTc>cCc	p.L347P		NM_032271.2	NP_115647.2	Q6Q0C0	TRAF7_HUMAN	TNF receptor-associated factor 7, E3 ubiquitin protein ligase	347					activation of MAPKKK activity (GO:0000185)|apoptotic process (GO:0006915)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of MAPK cascade (GO:0043410)|protein ubiquitination (GO:0016567)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasmic vesicle (GO:0031410)|ubiquitin ligase complex (GO:0000151)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)|pancreas(1)|prostate(2)|skin(1)	23						CAGAGCAAGCTCAGCGAGGAC	0.682																																																0													47.0	44.0	45.0					16																	2223509		2197	4300	6497	SO:0001583	missense	84231			AL136921	CCDS10461.1	16p13.3	2013-01-10	2012-02-23	2004-06-04	ENSG00000131653	ENSG00000131653		"""RING-type (C3HC4) zinc fingers"", ""WD repeat domain containing"""	20456	protein-coding gene	gene with protein product		606692	"""ring finger and WD repeat domain 1"", ""TNF receptor-associated factor 7"""	RFWD1		11230166, 15001576	Standard	NM_032271		Approved	RNF119, DKFZp586I021, MGC7807	uc002cow.3	Q6Q0C0	OTTHUMG00000128826	ENST00000326181.6:c.1040T>C	16.37:g.2223509T>C	ENSP00000318944:p.Leu347Pro		Q9H073	Missense_Mutation	SNP	ENST00000326181.6	37	CCDS10461.1	.	.	.	.	.	.	.	.	.	.	T	17.29	3.351122	0.61183	.	.	ENSG00000131653	ENST00000326181	T	0.54866	0.55	4.6	4.6	0.57074	.	0.000000	0.64402	D	0.000001	T	0.51278	0.1665	L	0.29908	0.895	0.80722	D	1	P	0.45396	0.857	P	0.50791	0.65	T	0.55964	-0.8057	10	0.66056	D	0.02	-26.712	12.9549	0.58421	0.0:0.0:0.0:1.0	.	347	Q6Q0C0	TRAF7_HUMAN	P	347	ENSP00000318944:L347P	ENSP00000318944:L347P	L	+	2	0	TRAF7	2163510	1.000000	0.71417	0.982000	0.44146	0.214000	0.24535	7.386000	0.79775	1.914000	0.55421	0.459000	0.35465	CTC		0.682	TRAF7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250762.1	NM_032271		40	66	40	66
LPCAT3	10162	broad.mit.edu;ucsc.edu	37	12	7083747	7083747	+	IGR	SNP	C	C	T			TCGA-HT-7677-01A-11D-2253-08	TCGA-HT-7677-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a4bfd9a-4a16-41c9-91cb-97351c76ab0e	d27dc741-a306-47c4-a333-155ac43c9484	g.chr12:7083747C>T	ENST00000261407.4	-	0	2268				EMG1_ENST00000261406.6_Nonsense_Mutation_p.R101*|LPCAT3_ENST00000535021.1_5'Flank|EMG1_ENST00000546220.1_3'UTR	NM_005768.5	NP_005759.4	Q6P1A2	MBOA5_HUMAN	lysophosphatidylcholine acyltransferase 3						glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid metabolic process (GO:0006644)|regulation of plasma lipoprotein particle levels (GO:0097006)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	1-acylglycerophosphocholine O-acyltransferase activity (GO:0047184)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(2)|lung(4)|ovary(1)|skin(2)	17						TCCCCTGAACCGAGCTGGCTT	0.493																																																0													41.0	40.0	40.0					12																	7083747		1917	4119	6036	SO:0001628	intergenic_variant	10436			U72515	CCDS8572.1	12p13.31	2010-05-12	2008-06-24	2008-06-24	ENSG00000111684	ENSG00000111684			30244	protein-coding gene	gene with protein product		611950	"""O-acyltransferase (membrane bound) domain containing 5"", ""membrane bound O-acyltransferase domain containing 5"""	OACT5, MBOAT5		8723724, 9074930, 18195019	Standard	NM_005768		Approved	C3F, nessy	uc001qsi.3	Q6P1A2	OTTHUMG00000168970		12.37:g.7083747C>T			B2RDH0|B7Z3N3|Q7KZS1|Q92980|Q9BW40	RNA	SNP	ENST00000261407.4	37	CCDS8572.1																																																																																				0.493	LPCAT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401812.1	NM_005768		16	34	16	34
FUBP1	8880	broad.mit.edu;hgsc.bcm.edu	37	1	78430643	78430643	+	Frame_Shift_Del	DEL	C	C	-			TCGA-HT-7677-01A-11D-2253-08	TCGA-HT-7677-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a4bfd9a-4a16-41c9-91cb-97351c76ab0e	d27dc741-a306-47c4-a333-155ac43c9484	g.chr1:78430643delC	ENST00000370768.2	-	9	728	c.647delG	c.(646-648)ggafs	p.G216fs	FUBP1_ENST00000370767.1_Frame_Shift_Del_p.G216fs|FUBP1_ENST00000436586.2_Frame_Shift_Del_p.G237fs	NM_003902.3	NP_003893.2	Q96AE4	FUBP1_HUMAN	far upstream element (FUSE) binding protein 1	216	KH 2. {ECO:0000255|PROSITE- ProRule:PRU00117}.				positive regulation of gene expression (GO:0010628)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded DNA binding (GO:0003697)			central_nervous_system(7)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(1)|upper_aerodigestive_tract(3)	17						CATTTTAACTCCAGCCCGTTC	0.363			"""F, N"""		oligodendroglioma																																		Rec	yes		1	1p13.1	8880	far upstream element (FUSE) binding protein 1		O	0													76.0	84.0	81.0					1																	78430643		2203	4300	6503	SO:0001589	frameshift_variant	8880			U05040	CCDS683.1	1p31.1	2008-02-05			ENSG00000162613	ENSG00000162613			4004	protein-coding gene	gene with protein product		603444		FUBP		8125259	Standard	XM_005271309		Approved	FBP	uc001dii.3	Q96AE4	OTTHUMG00000040799	ENST00000370768.2:c.647delG	1.37:g.78430643delC	ENSP00000359804:p.Gly216fs		Q12828	Frame_Shift_Del	DEL	ENST00000370768.2	37	CCDS683.1																																																																																				0.363	FUBP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098030.3	NM_003902		44	33	44	33
TRIP12	9320	broad.mit.edu;hgsc.bcm.edu	37	2	230638967	230638968	+	Frame_Shift_Del	DEL	CT	CT	-			TCGA-HT-7677-01A-11D-2253-08	TCGA-HT-7677-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a4bfd9a-4a16-41c9-91cb-97351c76ab0e	d27dc741-a306-47c4-a333-155ac43c9484	g.chr2:230638967_230638968delCT	ENST00000283943.5	-	37	5492_5493	c.5314_5315delAG	c.(5314-5316)agtfs	p.S1772fs	TRIP12_ENST00000389045.3_Frame_Shift_Del_p.S1502fs|TRIP12_ENST00000389044.4_Frame_Shift_Del_p.S1820fs	NM_001284214.1|NM_004238.1	NP_001271143.1|NP_004229.1	Q14669	TRIPC_HUMAN	thyroid hormone receptor interactor 12	1772					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|embryo development (GO:0009790)|negative regulation of double-strand break repair (GO:2000780)|negative regulation of histone H2A K63-linked ubiquitination (GO:1901315)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligase activity (GO:0016874)|thyroid hormone receptor binding (GO:0046966)|ubiquitin-protein transferase activity (GO:0004842)			breast(2)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(19)|lung(32)|ovary(5)|prostate(4)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	87		Renal(207;0.025)|all_hematologic(139;0.122)|all_lung(227;0.126)|Acute lymphoblastic leukemia(138;0.164)		Epithelial(121;4.76e-13)|all cancers(144;4.34e-10)|LUSC - Lung squamous cell carcinoma(224;0.00864)|Lung(119;0.0116)		ATACTGTAGACTCTCTTTGGTC	0.361																																																0																																										SO:0001589	frameshift_variant	9320			L40383	CCDS33391.1, CCDS63145.1, CCDS63146.1	2q36.3	2008-05-27			ENSG00000153827	ENSG00000153827			12306	protein-coding gene	gene with protein product		604506				7776974	Standard	XM_005246961		Approved	KIAA0045	uc002vpw.1	Q14669	OTTHUMG00000153623	ENST00000283943.5:c.5314_5315delAG	2.37:g.230638971_230638972delCT	ENSP00000283943:p.Ser1772fs		D4HL82|Q14CA3|Q14CF1|Q15644|Q53R87|Q53TE7	Frame_Shift_Del	DEL	ENST00000283943.5	37	CCDS33391.1																																																																																				0.361	TRIP12-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000331861.3	NM_004238		44	64	44	64
ARID1B	57492	broad.mit.edu;hgsc.bcm.edu	37	6	157469999	157469999	+	Frame_Shift_Del	DEL	G	G	-			TCGA-HT-7677-01A-11D-2253-08	TCGA-HT-7677-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a4bfd9a-4a16-41c9-91cb-97351c76ab0e	d27dc741-a306-47c4-a333-155ac43c9484	g.chr6:157469999delG	ENST00000350026.5	+	8	2755	c.2754delG	c.(2752-2754)atgfs	p.M918fs	ARID1B_ENST00000367148.1_Frame_Shift_Del_p.M918fs|ARID1B_ENST00000346085.5_Frame_Shift_Del_p.M931fs|ARID1B_ENST00000275248.4_Frame_Shift_Del_p.M860fs|ARID1B_ENST00000478761.2_3'UTR	NM_017519.2	NP_059989.2	Q8NFD5	ARI1B_HUMAN	AT rich interactive domain 1B (SWI1-like)	918					chromatin-mediated maintenance of transcription (GO:0048096)|nervous system development (GO:0007399)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)			NS(2)|breast(5)|central_nervous_system(4)|endometrium(12)|kidney(4)|large_intestine(11)|lung(30)|ovary(3)|pancreas(1)|prostate(4)|skin(2)|urinary_tract(3)	81		Breast(66;0.000162)|Ovarian(120;0.0265)		OV - Ovarian serous cystadenocarcinoma(65;3.19e-17)|BRCA - Breast invasive adenocarcinoma(81;1.01e-05)		GGCCAGGAATGGGGCCGCCAA	0.587																																																0													42.0	43.0	43.0					6																	157469999		2203	4293	6496	SO:0001589	frameshift_variant	57492			AF521671	CCDS5251.1, CCDS5251.2, CCDS55072.1	6q25.3	2014-09-17			ENSG00000049618	ENSG00000049618		"""-"""	18040	protein-coding gene	gene with protein product		614556					Standard	NM_017519		Approved	KIAA1235, ELD/OSA1, p250R, BAF250b, DAN15, 6A3-5	uc003qqo.3	Q8NFD5	OTTHUMG00000015890	ENST00000350026.5:c.2754delG	6.37:g.157469999delG	ENSP00000055163:p.Met918fs		Q5JRD1|Q5VYC4|Q8IZY8|Q8TEV0|Q8TF02|Q99491|Q9ULI5	Frame_Shift_Del	DEL	ENST00000350026.5	37	CCDS5251.2																																																																																				0.587	ARID1B-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000372723.1	NM_020732		31	62	31	62
OR7A17	26333	broad.mit.edu;hgsc.bcm.edu	37	19	14991283	14991284	+	Frame_Shift_Del	DEL	TT	TT	-			TCGA-HT-7677-01A-11D-2253-08	TCGA-HT-7677-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a4bfd9a-4a16-41c9-91cb-97351c76ab0e	d27dc741-a306-47c4-a333-155ac43c9484	g.chr19:14991283_14991284delTT	ENST00000327462.2	-	1	980_981	c.884_885delAA	c.(883-885)aaafs	p.K295fs		NM_030901.1	NP_112163.1	O14581	OR7AH_HUMAN	olfactory receptor, family 7, subfamily A, member 17	295						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|cervix(1)|large_intestine(2)|lung(6)|prostate(1)|skin(1)	12	Ovarian(108;0.203)					TCTTTATGTCTTTATTCCTCAG	0.436																																																0																																										SO:0001589	frameshift_variant	26333			X64993	CCDS12319.1	19p13.12	2012-08-09				ENSG00000185385		"""GPCR / Class A : Olfactory receptors"""	8363	protein-coding gene	gene with protein product						1370859	Standard	NM_030901		Approved	HTPCRX19	uc010xob.2	O14581		ENST00000327462.2:c.884_885delAA	19.37:g.14991283_14991284delTT	ENSP00000328144:p.Lys295fs		Q6IFQ6|Q96R98	Frame_Shift_Del	DEL	ENST00000327462.2	37	CCDS12319.1																																																																																				0.436	OR7A17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466523.1	NM_030901		20	86	20	86
