#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_AAChange	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_Codon	i_COSMIC_Gene	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ChromChange	i_Chromosome_hg18	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Drug_Target	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_End_position_hg18	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Exon	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_Start_position_hg18	i_TranscriptID	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
CTRL	1506	hgsc.bcm.edu	37	16	67964671	67964672	+	Frame_Shift_Ins	INS	-	-	A			TCGA-AA-3521-01A-01W-0831-10	TCGA-AA-3521-10A-01W-0831-10	-	-	-	A	-	-	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AA-3521-01A-01W-0831-10	TCGA-AA-3521-10A-01W-0831-10	g.chr16:67964671_67964672insA	ENST00000574481.1	-	4	836_837	c.275_276insT	c.(274-276)cgafs	p.R92fs	CTRL_ENST00000576408.1_5'UTR	NM_001907.2	NP_001898.1	P40313	CTRL_HUMAN	chymotrypsin-like	92	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				digestion (GO:0007586)|proteolysis (GO:0006508)	extracellular space (GO:0005615)	serine-type endopeptidase activity (GO:0004252)	p.S93fs*20(1)		kidney(1)|large_intestine(2)|urinary_tract(1)	4		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.00412)|Epithelial(162;0.018)|all cancers(182;0.118)		CGTTTGATGATCGGTCATACTC	0.639																																					p.R92fs												.	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.276_277insT	16						.																																			66522173	SO:0001589	frameshift_variant	1506	exon4				CCDS10852.1	16q22.1	2008-02-05			ENSG00000141086	ENSG00000141086			2524	protein-coding gene	gene with protein product		118888				8268911	Standard	NM_001907		Approved		uc002euw.3	P40313	OTTHUMG00000137552	ENST00000574481.1:c.275_276insT	16.37:g.67964671_67964672insA	ENSP00000458537:p.Arg92fs		66522172	NM_001907		Frame_Shift_Ins	INS	ENST00000574481.1	37	CCDS10852.1																																																																																				0.639	CTRL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268886.3		
CYP2C9	1559	hgsc.bcm.edu	37	10	96708875	96708876	+	Frame_Shift_Ins	INS	-	-	G			TCGA-AA-3521-01A-01W-0831-10	TCGA-AA-3521-10A-01W-0831-10	-	-	-	G	-	-	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AA-3521-01A-01W-0831-10	TCGA-AA-3521-10A-01W-0831-10	g.chr10:96708875_96708876insG	ENST00000260682.6	+	5	665_666	c.653_654insG	c.(652-657)aattttfs	p.N218fs		NM_000771.3	NP_000762.2	P11712	CP2C9_HUMAN	cytochrome P450, family 2, subfamily C, polypeptide 9	218					arachidonic acid metabolic process (GO:0019369)|cellular amide metabolic process (GO:0043603)|drug catabolic process (GO:0042737)|drug metabolic process (GO:0017144)|epoxygenase P450 pathway (GO:0019373)|exogenous drug catabolic process (GO:0042738)|monocarboxylic acid metabolic process (GO:0032787)|monoterpenoid metabolic process (GO:0016098)|omega-hydroxylase P450 pathway (GO:0097267)|oxidation-reduction process (GO:0055114)|oxidative demethylation (GO:0070989)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|urea metabolic process (GO:0019627)|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)|caffeine oxidase activity (GO:0034875)|drug binding (GO:0008144)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity (GO:0016491)|steroid hydroxylase activity (GO:0008395)	p.N218fs*7(1)		breast(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(9)|ovary(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	34		Colorectal(252;0.0902)		all cancers(201;6.93e-05)	Acenocoumarol(DB01418)|Acetaminophen(DB00316)|Acetylsalicylic acid(DB00945)|Agomelatine(DB06594)|Alosetron(DB00969)|Alprazolam(DB00404)|Aminophenazone(DB01424)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Amodiaquine(DB00613)|Amprenavir(DB00701)|Anastrozole(DB01217)|Antipyrine(DB01435)|Apixaban(DB06605)|Aprepitant(DB00673)|Arformoterol(DB01274)|Artemether(DB06697)|Atazanavir(DB01072)|Atorvastatin(DB01076)|Atovaquone(DB01117)|Azelastine(DB00972)|Bexarotene(DB00307)|Bicalutamide(DB01128)|Bortezomib(DB00188)|Bosentan(DB00559)|Brompheniramine(DB00835)|Buprenorphine(DB00921)|Bupropion(DB01156)|Cabozantinib(DB08875)|Caffeine(DB00201)|Candesartan(DB00796)|Capecitabine(DB01101)|Carbamazepine(DB00564)|Carbinoxamine(DB00748)|Carvedilol(DB01136)|Celecoxib(DB00482)|Chloramphenicol(DB00446)|Chlorpropamide(DB00672)|Cholecalciferol(DB00169)|Cimetidine(DB00501)|Cinnarizine(DB00568)|Cisapride(DB00604)|Cisplatin(DB00515)|Clevidipine(DB04920)|Clopidogrel(DB00758)|Clotrimazole(DB00257)|Clozapine(DB00363)|Cocaine(DB00907)|Colchicine(DB01394)|Cyclizine(DB01176)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dapagliflozin(DB06292)|Dapsone(DB00250)|Delavirdine(DB00705)|Desloratadine(DB00967)|Dexamethasone(DB01234)|Dexfenfluramine(DB01191)|Dextromethorphan(DB00514)|Dextropropoxyphene(DB00647)|Diazepam(DB00829)|Diclofenac(DB00586)|Diclofenamide(DB01144)|Dicoumarol(DB00266)|Diethylstilbestrol(DB00255)|Diltiazem(DB00343)|Diphenhydramine(DB01075)|Disulfiram(DB00822)|Dolasetron(DB00757)|Donepezil(DB00843)|Dopamine(DB00988)|Dorzolamide(DB00869)|Doxepin(DB01142)|Dronabinol(DB00470)|Efavirenz(DB00625)|Eletriptan(DB00216)|Enzalutamide(DB08899)|Epinephrine(DB00668)|Epoprostenol(DB01240)|Eprosartan(DB00876)|Estradiol(DB00783)|Estrone(DB00655)|Estropipate(DB04574)|Eszopiclone(DB00402)|Ethanol(DB00898)|Etodolac(DB00749)|Etoricoxib(DB01628)|Etravirine(DB06414)|Felodipine(DB01023)|Fenofibrate(DB01039)|Flecainide(DB01195)|Fluconazole(DB00196)|Flunarizine(DB04841)|Flunitrazepam(DB01544)|Fluorouracil(DB00544)|Fluoxetine(DB00472)|Flurbiprofen(DB00712)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Formoterol(DB00983)|Fosphenytoin(DB01320)|Gefitinib(DB00317)|Gemfibrozil(DB01241)|Ginkgo biloba(DB01381)|Gliclazide(DB01120)|Glimepiride(DB00222)|Glipizide(DB01067)|Glyburide(DB01016)|Guanfacine(DB01018)|Haloperidol(DB00502)|Halothane(DB01159)|Hexobarbital(DB01355)|Histamine Phosphate(DB00667)|Human Serum Albumin(DB00062)|Hydromorphone(DB00327)|Ibuprofen(DB01050)|Idarubicin(DB01177)|Ifosfamide(DB01181)|Imatinib(DB00619)|Indinavir(DB00224)|Indomethacin(DB00328)|Irbesartan(DB01029)|Isoniazid(DB00951)|Ketamine(DB01221)|Ketobemidone(DB06738)|Ketoconazole(DB01026)|Ketoprofen(DB01009)|Lansoprazole(DB00448)|Leflunomide(DB01097)|Lidocaine(DB00281)|Lopinavir(DB01601)|Loratadine(DB00455)|Lornoxicam(DB06725)|Losartan(DB00678)|Lovastatin(DB00227)|Lumiracoxib(DB01283)|Medroxyprogesterone Acetate(DB00603)|Mefenamic acid(DB00784)|Melatonin(DB01065)|Meloxicam(DB00814)|Mestranol(DB01357)|Methadone(DB00333)|Methazolamide(DB00703)|Methimazole(DB00763)|Methoxyflurane(DB01028)|Metronidazole(DB00916)|Miconazole(DB01110)|Mirtazapine(DB00370)|Moclobemide(DB01171)|Modafinil(DB00745)|Montelukast(DB00471)|Naproxen(DB00788)|Nateglinide(DB00731)|Nelfinavir(DB00220)|Nevirapine(DB00238)|Nicardipine(DB00622)|Niclosamide(DB06803)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilotinib(DB04868)|Nilutamide(DB00665)|Nilvadipine(DB06712)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Omeprazole(DB00338)|Ondansetron(DB00904)|Ospemifene(DB04938)|Oxaprozin(DB00991)|Paclitaxel(DB01229)|Pantoprazole(DB00213)|Paramethadione(DB00617)|Paroxetine(DB00715)|Perphenazine(DB00850)|Phenobarbital(DB01174)|Phenprocoumon(DB00946)|Phentermine(DB00191)|Phenylbutazone(DB00812)|Phenytoin(DB00252)|Pioglitazone(DB01132)|Piroxicam(DB00554)|Pitavastatin(DB08860)|Pranlukast(DB01411)|Prasugrel(DB06209)|Pravastatin(DB00175)|Primidone(DB00794)|Probenecid(DB01032)|Progesterone(DB00396)|Proguanil(DB01131)|Promazine(DB00420)|Promethazine(DB01069)|Propafenone(DB01182)|Propofol(DB00818)|Pyrimethamine(DB00205)|Quazepam(DB01589)|Quinidine(DB00908)|Quinine(DB00468)|Rabeprazole(DB01129)|Regorafenib(DB08896)|Rifampicin(DB01045)|Rifapentine(DB01201)|Ritonavir(DB00503)|Rosiglitazone(DB00412)|Rosuvastatin(DB01098)|Salicylic acid(DB00936)|Saquinavir(DB01232)|Secobarbital(DB00418)|Selegiline(DB01037)|Sertraline(DB01104)|Sildenafil(DB00203)|Simvastatin(DB00641)|Sitaxentan(DB06268)|Sorafenib(DB00398)|Sulfadiazine(DB00359)|Sulfadimethoxine(DB06150)|Sulfamethizole(DB00576)|Sulfamethoxazole(DB01015)|Sulfamoxole(DB08798)|Sulfanilamide(DB00259)|Sulfaphenazole(DB06729)|Sulfapyridine(DB00891)|Sulfinpyrazone(DB01138)|Sulfisoxazole(DB00263)|Suprofen(DB00870)|Tamoxifen(DB00675)|Tapentadol(DB06204)|Temazepam(DB00231)|Teniposide(DB00444)|Tenoxicam(DB00469)|Terbinafine(DB00857)|Testosterone(DB00624)|Thalidomide(DB01041)|Theophylline(DB00277)|Thiamylal(DB01154)|Thioridazine(DB00679)|Ticlopidine(DB00208)|Tioconazole(DB01007)|Tolbutamide(DB01124)|Tolcapone(DB00323)|Tolterodine(DB01036)|Torasemide(DB00214)|Trabectedin(DB05109)|Tranylcypromine(DB00752)|Treprostinil(DB00374)|Tretinoin(DB00755)|Triazolam(DB00897)|Trimethadione(DB00347)|Trimethoprim(DB00440)|Trimipramine(DB00726)|Troleandomycin(DB01361)|Valproic Acid(DB00313)|Valsartan(DB00177)|Venlafaxine(DB00285)|Verapamil(DB00661)|Vismodegib(DB08828)|Voriconazole(DB00582)|Warfarin(DB00682)|Ximelagatran(DB04898)|Zafirlukast(DB00549)|Zalcitabine(DB00943)|Zidovudine(DB00495)|Zileuton(DB00744)|Zolpidem(DB00425)|Zopiclone(DB01198)	ATCTGCAATAATTTTTCTCCTA	0.267																																					p.N218fs	Ovarian(54;1266 1406 16072 35076)											.	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.653_654insG	10						.																																			96698866	SO:0001589	frameshift_variant	1559	exon5			M61855	CCDS7437.1	10q24.1	2007-12-14	2003-01-14		ENSG00000138109	ENSG00000138109		"""Cytochrome P450s"""	2623	protein-coding gene	gene with protein product		601130	"""cytochrome P450, subfamily IIC (mephenytoin 4-hydroxylase), polypeptide 9"""	CYP2C10		2009263, 7841444	Standard	NM_000771		Approved	P450IIC9	uc001kka.4	P11712	OTTHUMG00000018805	Exception_encountered	10.37:g.96708875_96708876insG	ENSP00000260682:p.Asn218fs		96698865	NM_000771	P11713|Q16756|Q16872|Q5VX92|Q6IRV8|Q8WW80	Frame_Shift_Ins	INS	ENST00000260682.6	37	CCDS7437.1																																																																																				0.267	CYP2C9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049501.1	NM_000771	
WBSCR17	64409	hgsc.bcm.edu	37	7	71177028	71177028	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3521-01A-01W-0831-10	TCGA-AA-3521-10A-01W-0831-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	TCGA-AA-3521-01A-01W-0831-10	TCGA-AA-3521-10A-01W-0831-10	g.chr7:71177028C>T	ENST00000333538.5	+	11	2328	c.1694C>T	c.(1693-1695)aCg>aTg	p.T565M	WBSCR17_ENST00000498380.2_3'UTR	NM_022479.1	NP_071924.1	Q6IS24	GLTL3_HUMAN	Williams-Beuren syndrome chromosome region 17	565	Ricin B-type lectin. {ECO:0000255|PROSITE-ProRule:PRU00174}.				protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)	p.T565K(1)|p.T565M(1)		NS(5)|breast(2)|central_nervous_system(1)|endometrium(7)|kidney(7)|large_intestine(22)|lung(45)|ovary(2)|pancreas(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	100		all_cancers(73;0.2)|Lung NSC(55;0.094)|all_lung(88;0.125)				AACAAGGGCACGGGACGCTGC	0.567																																					p.T565M												.	.	2	Substitution - Missense(2)	large_intestine(1)|lung(1)	c.C1694T	7						.						73.0	79.0	77.0					7																	71177028		2203	4300	6503	70814964	SO:0001583	missense	64409	exon11			AF410457	CCDS5540.1	7q11.23	2014-03-13			ENSG00000185274	ENSG00000185274		"""Glycosyltransferase family 2 domain containing"""	16347	protein-coding gene	gene with protein product	"""polypeptide N-acetylgalactosaminyltransferase-like 3"", ""polypeptide GalNAc transferase 3"""	615137				12073013, 15744064, 22787146	Standard	NM_022479		Approved	GALNTL3, GalNAc-T5L	uc003tvy.4	Q6IS24	OTTHUMG00000129783	ENST00000333538.5:c.1694C>T	7.37:g.71177028C>T	ENSP00000329654:p.Thr565Met		70814964	NM_022479	Q8NFV9|Q9NTA8	Missense_Mutation	SNP	ENST00000333538.5	37	CCDS5540.1	.	.	.	.	.	.	.	.	.	.	C	23.8	4.454667	0.84209	.	.	ENSG00000185274	ENST00000333538	T	0.29917	1.55	5.26	5.26	0.73747	Ricin B-related lectin (1);Ricin B lectin (3);	0.000000	0.85682	D	0.000000	T	0.61578	0.2358	M	0.85859	2.78	0.54753	D	0.999986	D	0.89917	1.0	D	0.79784	0.993	T	0.68315	-0.5441	10	0.87932	D	0	.	17.861	0.88781	0.0:1.0:0.0:0.0	.	565	Q6IS24	GLTL3_HUMAN	M	565	ENSP00000329654:T565M	ENSP00000329654:T565M	T	+	2	0	WBSCR17	70814964	0.999000	0.42202	0.998000	0.56505	0.954000	0.61252	4.439000	0.59968	2.456000	0.83038	0.563000	0.77884	ACG		0.567	WBSCR17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252006.1	NM_022479	
ABCB1	5243	hgsc.bcm.edu	37	7	87145948	87145948	+	Silent	SNP	G	G	A			TCGA-AA-3521-01A-01W-0831-10	TCGA-AA-3521-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AA-3521-01A-01W-0831-10	TCGA-AA-3521-10A-01W-0831-10	g.chr7:87145948G>A	ENST00000265724.3	-	25	3378	c.2961C>T	c.(2959-2961)gcC>gcT	p.A987A	ABCB1_ENST00000488737.2_5'UTR|ABCB1_ENST00000543898.1_Silent_p.A923A	NM_000927.4	NP_000918.2	P08183	MDR1_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 1	987	ABC transmembrane type-1 2. {ECO:0000255|PROSITE-ProRule:PRU00441}.				drug transmembrane transport (GO:0006855)|G2/M transition of mitotic cell cycle (GO:0000086)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)|stem cell proliferation (GO:0072089)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)|xenobiotic-transporting ATPase activity (GO:0008559)	p.A987A(1)		NS(1)|breast(6)|central_nervous_system(2)|endometrium(14)|kidney(9)|large_intestine(14)|lung(48)|ovary(4)|prostate(6)|skin(6)|upper_aerodigestive_tract(1)	111	Esophageal squamous(14;0.00164)				Acebutolol(DB01193)|Acetaminophen(DB00316)|Acetylsalicylic acid(DB00945)|Adenosine triphosphate(DB00171)|ado-trastuzumab emtansine(DB05773)|Afatinib(DB08916)|Albendazole(DB00518)|Alfentanil(DB00802)|Alitretinoin(DB00523)|Amantadine(DB00915)|Aminohippurate(DB00345)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Amprenavir(DB00701)|Amsacrine(DB00276)|Apixaban(DB06605)|Arsenic trioxide(DB01169)|Astemizole(DB00637)|Atazanavir(DB01072)|Atenolol(DB00335)|Atorvastatin(DB01076)|Axitinib(DB06626)|Azelastine(DB00972)|Azithromycin(DB00207)|Benzocaine(DB01086)|Bepridil(DB01244)|Betamethasone(DB00443)|Biperiden(DB00810)|Boceprevir(DB08873)|Bosutinib(DB06616)|Brentuximab vedotin(DB08870)|Bromocriptine(DB01200)|Buprenorphine(DB00921)|Buspirone(DB00490)|Cabazitaxel(DB06772)|Caffeine(DB00201)|Canagliflozin(DB08907)|Candesartan(DB00796)|Captopril(DB01197)|Carbamazepine(DB00564)|Carfilzomib(DB08889)|Carvedilol(DB01136)|Caspofungin(DB00520)|Chloroquine(DB00608)|Chlorpromazine(DB00477)|Chlorpropamide(DB00672)|Chlorprothixene(DB01239)|Cilazapril(DB01340)|Cimetidine(DB00501)|Ciprofloxacin(DB00537)|Cisplatin(DB00515)|Citalopram(DB00215)|Clarithromycin(DB01211)|Clobazam(DB00349)|Clofazimine(DB00845)|Clomifene(DB00882)|Clomipramine(DB01242)|Clonidine(DB00575)|Clopidogrel(DB00758)|Clotrimazole(DB00257)|Clozapine(DB00363)|Colchicine(DB01394)|Conjugated Estrogens(DB00286)|Crizotinib(DB08865)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dabigatran etexilate(DB06695)|Dabrafenib(DB08912)|Dactinomycin(DB00970)|Dapagliflozin(DB06292)|Dasatinib(DB01254)|Daunorubicin(DB00694)|Debrisoquin(DB04840)|Desipramine(DB01151)|Desloratadine(DB00967)|Dexamethasone(DB01234)|Dextromethorphan(DB00514)|Diazepam(DB00829)|Diclofenac(DB00586)|Diethylstilbestrol(DB00255)|Digitoxin(DB01396)|Digoxin(DB00390)|Dihydroergotamine(DB00320)|Diltiazem(DB00343)|Dipyridamole(DB00975)|Docetaxel(DB01248)|Domperidone(DB01184)|Doxazosin(DB00590)|Doxepin(DB01142)|Doxorubicin(DB00997)|Dronabinol(DB00470)|Dronedarone(DB04855)|Eletriptan(DB00216)|Enalapril(DB00584)|Enzalutamide(DB08899)|Epinastine(DB00751)|Ergonovine(DB01253)|Ergotamine(DB00696)|Erlotinib(DB00530)|Erythromycin(DB00199)|Estradiol(DB00783)|Estramustine(DB01196)|Estriol(DB04573)|Estrone(DB00655)|Ethinyl Estradiol(DB00977)|Etoposide(DB00773)|Etravirine(DB06414)|Ezetimibe(DB00973)|Felodipine(DB01023)|Fentanyl(DB00813)|Fesoterodine(DB06702)|Fexofenadine(DB00950)|Fidaxomicin(DB08874)|Fluconazole(DB00196)|Fluoxetine(DB00472)|Flupentixol(DB00875)|Fluphenazine(DB00623)|Flurazepam(DB00690)|Fluticasone furoate(DB08906)|Fluvoxamine(DB00176)|Gefitinib(DB00317)|Gemcitabine(DB00441)|Glyburide(DB01016)|Gramicidin D(DB00027)|Haloperidol(DB00502)|Hydrocortisone(DB00741)|Ibuprofen(DB01050)|Imatinib(DB00619)|Imipramine(DB00458)|Indacaterol(DB05039)|Indinavir(DB00224)|Indomethacin(DB00328)|Irinotecan(DB00762)|Itraconazole(DB01167)|Ivacaftor(DB08820)|Ivermectin(DB00602)|Ketamine(DB01221)|Ketazolam(DB01587)|Ketoconazole(DB01026)|Lamivudine(DB00709)|Lamotrigine(DB00555)|Lansoprazole(DB00448)|Lapatinib(DB01259)|Lenalidomide(DB00480)|Levetiracetam(DB01202)|Levofloxacin(DB01137)|Levomilnacipran(DB08918)|Levothyroxine(DB00451)|Lidocaine(DB00281)|Linagliptin(DB08882)|Liothyronine(DB00279)|Liotrix(DB01583)|Lisinopril(DB00722)|Lomitapide(DB08827)|Loperamide(DB00836)|Lopinavir(DB01601)|Loratadine(DB00455)|Losartan(DB00678)|Lovastatin(DB00227)|Mannitol(DB00742)|Maprotiline(DB00934)|Mebendazole(DB00643)|Mefloquine(DB00358)|Megestrol acetate(DB00351)|Meprobamate(DB00371)|Methadone(DB00333)|Methotrexate(DB00563)|Methylprednisolone(DB00959)|Metoprolol(DB00264)|Miconazole(DB01110)|Midazolam(DB00683)|Mifepristone(DB00834)|Mirabegron(DB08893)|Mitomycin(DB00305)|Mitoxantrone(DB01204)|Morphine(DB00295)|Mycophenolate mofetil(DB00688)|Nadolol(DB01203)|Naloxone(DB01183)|Naltrexone(DB00704)|Nefazodone(DB01149)|Nelfinavir(DB00220)|Neostigmine(DB01400)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilotinib(DB04868)|Nisoldipine(DB00401)|Nitrazepam(DB01595)|Nitrendipine(DB01054)|Nizatidine(DB00585)|Norethindrone(DB00717)|Olanzapine(DB00334)|Omeprazole(DB00338)|Paclitaxel(DB01229)|Pantoprazole(DB00213)|Paroxetine(DB00715)|Pazopanib(DB06589)|Perindopril(DB00790)|Phenobarbital(DB01174)|Phenytoin(DB00252)|Pimozide(DB01100)|Pitavastatin(DB08860)|Pomalidomide(DB08910)|Ponatinib(DB08901)|Posaconazole(DB01263)|Pravastatin(DB00175)|Prazosin(DB00457)|Prednisolone(DB00860)|Prednisone(DB00635)|Probenecid(DB01032)|Progesterone(DB00396)|Promethazine(DB01069)|Propafenone(DB01182)|Propranolol(DB00571)|Protriptyline(DB00344)|Quetiapine(DB01224)|Quinacrine(DB01103)|Quinidine(DB00908)|Quinine(DB00468)|Ranitidine(DB00863)|Reboxetine(DB00234)|Regorafenib(DB08896)|Reserpine(DB00206)|Rifampicin(DB01045)|Rilpivirine(DB08864)|Risperidone(DB00734)|Ritonavir(DB00503)|Rivaroxaban(DB06228)|Roxithromycin(DB00778)|Salicylic acid(DB00936)|Saquinavir(DB01232)|Scopolamine(DB00747)|Selegiline(DB01037)|Sertraline(DB01104)|Silodosin(DB06207)|SIMEPREVIR(DB06290)|Simvastatin(DB00641)|Sirolimus(DB00877)|Sitagliptin(DB01261)|SOFOSBUVIR(DB08934)|Sorafenib(DB00398)|Sparfloxacin(DB01208)|Spironolactone(DB00421)|Streptozocin(DB00428)|Sulfinpyrazone(DB01138)|Sumatriptan(DB00669)|Sunitinib(DB01268)|Tacrolimus(DB00864)|Tamoxifen(DB00675)|Telaprevir(DB05521)|Telmisartan(DB00966)|Temsirolimus(DB06287)|Terazosin(DB01162)|Testosterone(DB00624)|Ticagrelor(DB08816)|Timolol(DB00373)|Tolvaptan(DB06212)|Topotecan(DB01030)|Toremifene(DB00539)|Trazodone(DB00656)|Trifluoperazine(DB00831)|Triflupromazine(DB00508)|Trimethoprim(DB00440)|Trimipramine(DB00726)|Troleandomycin(DB01361)|Vecuronium(DB01339)|Venlafaxine(DB00285)|Verapamil(DB00661)|Vinblastine(DB00570)|Vincristine(DB00541)|Vinorelbine(DB00361)|Vismodegib(DB08828)|Voacamine(DB04877)|Zidovudine(DB00495)	CTTGCCCCACGGCCATGGCAC	0.443																																					p.A987A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2961T	7						.						115.0	99.0	104.0					7																	87145948		2203	4300	6503	86983884	SO:0001819	synonymous_variant	5243	exon25			M14758	CCDS5608.1	7q21.12	2012-03-14	2004-05-12		ENSG00000085563	ENSG00000085563		"""CD molecules"", ""ATP binding cassette transporters / subfamily B"""	40	protein-coding gene	gene with protein product	"""multidrug resistance protein 1"""	171050	"""colchicin sensitivity"""	PGY1, MDR1, CLCS		3027054	Standard	NM_000927		Approved	P-gp, CD243, GP170, ABC20	uc003uiz.2	P08183	OTTHUMG00000023393	ENST00000265724.3:c.2961C>T	7.37:g.87145948G>A			86983884	NM_000927	A8K294|B5AK60|Q12755|Q14812	Silent	SNP	ENST00000265724.3	37	CCDS5608.1																																																																																				0.443	ABCB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335444.2	NM_000927	
SAMD9	54809	hgsc.bcm.edu	37	7	92731710	92731710	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3521-01A-01W-0831-10	TCGA-AA-3521-10A-01W-0831-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AA-3521-01A-01W-0831-10	TCGA-AA-3521-10A-01W-0831-10	g.chr7:92731710C>A	ENST00000379958.2	-	3	3970	c.3701G>T	c.(3700-3702)gGa>gTa	p.G1234V		NM_001193307.1|NM_017654.3	NP_001180236.1|NP_060124.2	Q5K651	SAMD9_HUMAN	sterile alpha motif domain containing 9	1234						cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)		p.G1234V(1)		NS(1)|breast(4)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(20)|lung(32)|ovary(4)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	88	all_cancers(62;5.71e-11)|all_epithelial(64;3.25e-10)|Breast(17;0.000675)|Lung NSC(181;0.0969)|all_lung(186;0.125)		STAD - Stomach adenocarcinoma(171;0.000302)			ATCACTACTTCCTGATACAAA	0.294																																					p.G1234V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3701T	7						.						64.0	74.0	70.0					7																	92731710		2202	4296	6498	92569646	SO:0001583	missense	54809	exon2			AB095925	CCDS34680.1	7q21.2	2013-01-10	2004-07-15	2004-07-16	ENSG00000205413	ENSG00000205413		"""Sterile alpha motif (SAM) domain containing"""	1348	protein-coding gene	gene with protein product		610456	"""chromosome 7 open reading frame 5"""	C7orf5			Standard	NM_017654		Approved	KIAA2004, FLJ20073	uc003umg.3	Q5K651	OTTHUMG00000155809	ENST00000379958.2:c.3701G>T	7.37:g.92731710C>A	ENSP00000369292:p.Gly1234Val		92569646	NM_001193307	A2RU68|Q5K649|Q6P080|Q75N21|Q8IVG6|Q9NXS8	Missense_Mutation	SNP	ENST00000379958.2	37	CCDS34680.1	.	.	.	.	.	.	.	.	.	.	C	11.87	1.767490	0.31320	.	.	ENSG00000205413	ENST00000379958;ENST00000446617	T;T	0.24538	1.85;2.64	4.28	4.28	0.50868	.	0.076123	0.50627	D	0.000112	T	0.43433	0.1247	L	0.57536	1.79	0.53005	D	0.999965	D	0.89917	1.0	D	0.74674	0.984	T	0.35001	-0.9806	10	0.72032	D	0.01	.	10.0644	0.42295	0.0:0.9001:0.0:0.0999	.	1234	Q5K651	SAMD9_HUMAN	V	1234	ENSP00000369292:G1234V;ENSP00000414529:G1234V	ENSP00000369292:G1234V	G	-	2	0	SAMD9	92569646	0.628000	0.27138	0.960000	0.40013	0.269000	0.26545	0.908000	0.28545	2.203000	0.70933	0.543000	0.68304	GGA		0.294	SAMD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341761.1	NM_017654	
PDK4	5166	hgsc.bcm.edu	37	7	95224434	95224434	+	Missense_Mutation	SNP	C	C	T	rs147359178		TCGA-AA-3521-01A-01W-0831-10	TCGA-AA-3521-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AA-3521-01A-01W-0831-10	TCGA-AA-3521-10A-01W-0831-10	g.chr7:95224434C>T	ENST00000005178.5	-	2	370	c.173G>A	c.(172-174)cGa>cAa	p.R58Q	AC002451.3_ENST00000416502.1_RNA|AC002451.3_ENST00000432265.1_RNA	NM_002612.3	NP_002603.1	Q16654	PDK4_HUMAN	pyruvate dehydrogenase kinase, isozyme 4	58					cellular metabolic process (GO:0044237)|cellular response to fatty acid (GO:0071398)|cellular response to starvation (GO:0009267)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|insulin receptor signaling pathway (GO:0008286)|negative regulation of anoikis (GO:2000811)|protein phosphorylation (GO:0006468)|pyruvate metabolic process (GO:0006090)|reactive oxygen species metabolic process (GO:0072593)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|regulation of bone resorption (GO:0045124)|regulation of cellular ketone metabolic process (GO:0010565)|regulation of fatty acid biosynthetic process (GO:0042304)|regulation of fatty acid oxidation (GO:0046320)|regulation of glucose metabolic process (GO:0010906)|regulation of pH (GO:0006885)|response to starvation (GO:0042594)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|pyruvate dehydrogenase (acetyl-transferring) kinase activity (GO:0004740)	p.R58Q(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|liver(1)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	15	all_cancers(62;1.06e-10)|all_epithelial(64;1.04e-09)|Lung NSC(181;0.128)|all_lung(186;0.151)		STAD - Stomach adenocarcinoma(171;0.0151)			CAATTCTTGTCGCAAAAATGC	0.343																																					p.R58Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G173A	7						.						94.0	94.0	94.0					7																	95224434		2203	4300	6503	95062370	SO:0001583	missense	5166	exon2			U54617	CCDS5643.1	7q21.3-q22.1	2008-07-18	2005-11-16		ENSG00000004799	ENSG00000004799			8812	protein-coding gene	gene with protein product		602527	"""pyruvate dehydrogenase kinase, isoenzyme 4"""			7499431	Standard	NM_002612		Approved		uc003uoa.3	Q16654	OTTHUMG00000153977	ENST00000005178.5:c.173G>A	7.37:g.95224434C>T	ENSP00000005178:p.Arg58Gln		95062370	NM_002612		Missense_Mutation	SNP	ENST00000005178.5	37	CCDS5643.1	.	.	.	.	.	.	.	.	.	.	C	36	5.789432	0.96945	.	.	ENSG00000004799	ENST00000005178;ENST00000542888	T	0.33438	1.41	5.3	5.3	0.74995	Branched-chain alpha-ketoacid dehydrogenase kinase/Pyruvate dehydrogenase kinase, N-terminal (3);	0.000000	0.85682	D	0.000000	T	0.56485	0.1988	M	0.75777	2.31	0.80722	D	1	D	0.76494	0.999	D	0.67725	0.953	T	0.54649	-0.8262	10	0.42905	T	0.14	.	19.3413	0.94342	0.0:1.0:0.0:0.0	.	58	Q16654	PDK4_HUMAN	Q	58;22	ENSP00000005178:R58Q	ENSP00000005178:R58Q	R	-	2	0	PDK4	95062370	0.970000	0.33590	0.987000	0.45799	0.999000	0.98932	7.818000	0.86416	2.660000	0.90430	0.650000	0.86243	CGA		0.343	PDK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333298.1	NM_002612	
XRCC2	7516	hgsc.bcm.edu	37	7	152346017	152346017	+	Missense_Mutation	SNP	T	T	G			TCGA-AA-3521-01A-01W-0831-10	TCGA-AA-3521-10A-01W-0831-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AA-3521-01A-01W-0831-10	TCGA-AA-3521-10A-01W-0831-10	g.chr7:152346017T>G	ENST00000359321.1	-	3	638	c.553A>C	c.(553-555)Aat>Cat	p.N185H	XRCC2_ENST00000495707.1_5'UTR	NM_005431.1	NP_005422.1	O43543	XRCC2_HUMAN	X-ray repair complementing defective repair in Chinese hamster cells 2	185					centrosome organization (GO:0051297)|DNA repair (GO:0006281)|double-strand break repair via homologous recombination (GO:0000724)|in utero embryonic development (GO:0001701)|meiotic nuclear division (GO:0007126)|mitotic cell cycle (GO:0000278)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of neurogenesis (GO:0050769)|response to gamma radiation (GO:0010332)|response to X-ray (GO:0010165)|strand invasion (GO:0042148)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|Rad51B-Rad51C-Rad51D-XRCC2 complex (GO:0033063)|replication fork (GO:0005657)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)	p.N185H(1)		NS(1)|breast(1)|large_intestine(5)|liver(1)|lung(1)|prostate(2)	11		all_hematologic(28;0.0592)|Prostate(32;0.081)	OV - Ovarian serous cystadenocarcinoma(82;0.0423)	UCEC - Uterine corpus endometrioid carcinoma (81;0.0429)		CGATAGTCATTTACAAGCTTC	0.448								Homologous recombination																													p.N185H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A553C	7						.						117.0	121.0	120.0					7																	152346017		2203	4300	6503	151976950	SO:0001583	missense	7516	exon3			Y08837	CCDS5933.1	7q36	2006-05-04			ENSG00000196584	ENSG00000196584			12829	protein-coding gene	gene with protein product	"""RAD51-like"""	600375				7607692, 10422536	Standard	NM_005431		Approved		uc003wld.3	O43543	OTTHUMG00000151470	ENST00000359321.1:c.553A>C	7.37:g.152346017T>G	ENSP00000352271:p.Asn185His		151976950	NM_005431	B2R925	Missense_Mutation	SNP	ENST00000359321.1	37	CCDS5933.1	.	.	.	.	.	.	.	.	.	.	T	11.16	1.558265	0.27827	.	.	ENSG00000196584	ENST00000359321	T	0.40476	1.03	5.06	1.26	0.21427	DNA recombination/repair protein RecA/RadB, ATP-binding domain (1);DNA recombination and repair protein Rad51, C-terminal (1);	0.557797	0.20958	N	0.082615	T	0.38772	0.1053	L	0.32530	0.975	0.09310	N	1	P	0.45428	0.858	P	0.51355	0.667	T	0.21314	-1.0249	10	0.72032	D	0.01	-3.0437	7.0443	0.25037	0.0:0.0744:0.2816:0.644	.	185	O43543	XRCC2_HUMAN	H	185	ENSP00000352271:N185H	ENSP00000352271:N185H	N	-	1	0	XRCC2	151976950	0.000000	0.05858	0.000000	0.03702	0.218000	0.24690	0.265000	0.18515	-0.024000	0.13941	0.383000	0.25322	AAT		0.448	XRCC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322783.1	NM_005431	
XKR7	343702	hgsc.bcm.edu	37	20	30584665	30584665	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3521-01A-01W-0831-10	TCGA-AA-3521-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AA-3521-01A-01W-0831-10	TCGA-AA-3521-10A-01W-0831-10	g.chr20:30584665G>A	ENST00000562532.2	+	3	1319	c.1145G>A	c.(1144-1146)cGc>cAc	p.R382H		NM_001011718.1	NP_001011718.1	Q5GH72	XKR7_HUMAN	XK, Kell blood group complex subunit-related family, member 7	382						integral component of membrane (GO:0016021)		p.R382H(1)		breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|liver(1)|lung(19)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	34			Colorectal(19;0.00306)|COAD - Colon adenocarcinoma(19;0.0347)			CGCAGCCGCCGCCGCATGACC	0.582																																					p.R382H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1145A	20						.						45.0	39.0	41.0					20																	30584665		2203	4300	6503	30048326	SO:0001583	missense	343702	exon3			AY534245	CCDS33459.1	20q11.21	2014-07-16	2006-01-12		ENSG00000260903	ENSG00000260903			23062	protein-coding gene	gene with protein product			"""X Kell blood group precursor-related family, member 7"", ""chromosome 20 open reading frame 159"""	C20orf159			Standard	NM_001011718		Approved	dJ310O13.4	uc002wxe.3	Q5GH72	OTTHUMG00000032198	ENST00000562532.2:c.1145G>A	20.37:g.30584665G>A	ENSP00000477059:p.Arg382His		30048326	NM_001011718	Q9NUG5	Missense_Mutation	SNP	ENST00000562532.2	37	CCDS33459.1	.	.	.	.	.	.	.	.	.	.	G	4.845	0.157145	0.09236	.	.	ENSG00000101321	ENST00000217299	T	0.63744	-0.06	5.16	3.2	0.36748	.	0.376195	0.30620	N	0.009230	T	0.42177	0.1191	N	0.16656	0.425	0.22127	N	0.999341	B	0.15930	0.015	B	0.12156	0.007	T	0.17992	-1.0351	10	0.15952	T	0.53	.	11.3416	0.49535	0.2394:0.0:0.7606:0.0	.	382	Q5GH72	XKR7_HUMAN	H	382	ENSP00000217299:R382H	ENSP00000217299:R382H	R	+	2	0	XKR7	30048326	0.889000	0.30405	0.998000	0.56505	0.713000	0.41058	0.755000	0.26405	0.207000	0.20607	-1.134000	0.01955	CGC		0.582	XKR7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078597.3	NM_001011718	
SULF2	55959	hgsc.bcm.edu	37	20	46307450	46307450	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3521-01A-01W-0831-10	TCGA-AA-3521-10A-01W-0831-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AA-3521-01A-01W-0831-10	TCGA-AA-3521-10A-01W-0831-10	g.chr20:46307450T>C	ENST00000359930.4	-	8	2014	c.1163A>G	c.(1162-1164)aAg>aGg	p.K388R	SULF2_ENST00000467815.1_Missense_Mutation_p.K388R|SULF2_ENST00000484875.1_Missense_Mutation_p.K388R|CTD-2653D5.1_ENST00000526566.2_RNA|SULF2_ENST00000361612.4_Missense_Mutation_p.K388R	NM_018837.3	NP_061325.1	Q8IWU5	SULF2_HUMAN	sulfatase 2	388					bone development (GO:0060348)|cartilage development (GO:0051216)|chondrocyte development (GO:0002063)|embryonic skeletal system development (GO:0048706)|esophagus smooth muscle contraction (GO:0014846)|glial cell-derived neurotrophic factor receptor signaling pathway (GO:0035860)|glomerular basement membrane development (GO:0032836)|glomerular filtration (GO:0003094)|heparan sulfate proteoglycan metabolic process (GO:0030201)|innervation (GO:0060384)|kidney development (GO:0001822)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|positive regulation of Wnt signaling pathway (GO:0030177)|positive regulation vascular endothelial growth factor production (GO:0010575)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	arylsulfatase activity (GO:0004065)|calcium ion binding (GO:0005509)|N-acetylglucosamine-6-sulfatase activity (GO:0008449)	p.K388R(1)		breast(2)|endometrium(4)|kidney(1)|large_intestine(7)|lung(22)|ovary(4)|pancreas(1)|prostate(5)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	54						GTCCAGCAGCTTGAGGATGGA	0.602																																					p.K388R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1163G	20						.						134.0	125.0	128.0					20																	46307450		2203	4300	6503	45740857	SO:0001583	missense	55959	exon8			AY101176	CCDS13408.1, CCDS13409.1, CCDS13409.2	20q13.12-q13.13	2008-05-14			ENSG00000196562	ENSG00000196562			20392	protein-coding gene	gene with protein product		610013				12368295	Standard	NM_018837		Approved	KIAA1247, HSULF-2, SULF-2	uc002xto.3	Q8IWU5	OTTHUMG00000032675	ENST00000359930.4:c.1163A>G	20.37:g.46307450T>C	ENSP00000353007:p.Lys388Arg		45740857	NM_198596	E1P5U6|Q5JYE1|Q6UX86|Q96SG2|Q9H1H0|Q9UJR3|Q9ULH3	Missense_Mutation	SNP	ENST00000359930.4	37	CCDS13408.1	.	.	.	.	.	.	.	.	.	.	t	18.46	3.629632	0.67015	.	.	ENSG00000196562	ENST00000359930;ENST00000484875;ENST00000361612;ENST00000467815	D;D;D;D	0.96265	-3.96;-3.96;-3.96;-3.96	5.37	5.37	0.77165	Alkaline phosphatase-like, alpha/beta/alpha (1);Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	0.198837	0.51477	D	0.000097	D	0.95645	0.8584	L	0.39245	1.2	0.54753	D	0.999986	P;P	0.48998	0.9;0.918	P;P	0.54856	0.571;0.762	D	0.94179	0.7430	10	0.19147	T	0.46	-20.6722	15.3777	0.74625	0.0:0.0:0.0:1.0	.	388;388	Q8IWU5-2;Q8IWU5	.;SULF2_HUMAN	R	388	ENSP00000353007:K388R;ENSP00000418290:K388R;ENSP00000354662:K388R;ENSP00000418442:K388R	ENSP00000353007:K388R	K	-	2	0	SULF2	45740857	1.000000	0.71417	1.000000	0.80357	0.897000	0.52465	8.037000	0.88933	2.040000	0.60383	0.375000	0.23000	AAG		0.602	SULF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079606.1	NM_018837	
ZNF112	7771	hgsc.bcm.edu	37	19	44833061	44833061	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3521-01A-01W-0831-10	TCGA-AA-3521-10A-01W-0831-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AA-3521-01A-01W-0831-10	TCGA-AA-3521-10A-01W-0831-10	g.chr19:44833061T>C	ENST00000337401.4	-	5	1355	c.1267A>G	c.(1267-1269)Agt>Ggt	p.S423G	ZNF112_ENST00000354340.4_Missense_Mutation_p.S417G|ZNF112_ENST00000536500.1_Missense_Mutation_p.S440G	NM_001083335.1	NP_001076804.1	Q9UJU3	ZN112_HUMAN	zinc finger protein 112	423					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.S417G(1)									CAAATGAAACTCTTTCCATAC	0.363																																					p.S417G												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1249G	19						.						88.0	86.0	87.0					19																	44833061		2202	4300	6502	49524901	SO:0001583	missense	7771	exon4			AF198358		19q13.2	2014-02-06	2012-11-27		ENSG00000062370	ENSG00000062370		"""Zinc fingers, C2H2-type"""	12892	protein-coding gene	gene with protein product		603994	"""zinc finger protein 112 homolog (mouse)"", ""zinc finger protein 228"""	ZFP112, ZNF228			Standard	NM_013380		Approved			Q9UJU3	OTTHUMG00000182357	ENST00000337401.4:c.1267A>G	19.37:g.44833061T>C	ENSP00000337081:p.Ser423Gly		49524901	NM_013380	A4FU53|Q9HCA7	Missense_Mutation	SNP	ENST00000337401.4	37	CCDS54276.1	.	.	.	.	.	.	.	.	.	.	T	0	-2.704747	0.00096	.	.	ENSG00000062370	ENST00000337401;ENST00000412927;ENST00000354340;ENST00000536500;ENST00000253426	T;T;T	0.16457	2.34;2.34;2.34	4.51	-1.13	0.09775	.	.	.	.	.	T	0.05181	0.0138	N	0.02973	-0.45	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.44097	-0.9350	9	0.09843	T	0.71	-0.1003	5.4649	0.16637	0.133:0.4555:0.0:0.4114	.	422;440;423	B4DYT4;F5GWS7;Q9UJU3	.;.;ZF112_HUMAN	G	423;423;417;440;422	ENSP00000337081:S423G;ENSP00000346305:S417G;ENSP00000441990:S440G	ENSP00000253426:S422G	S	-	1	0	ZNF285	49524901	0.000000	0.05858	0.000000	0.03702	0.372000	0.29890	-1.846000	0.01676	-0.071000	0.12886	-0.366000	0.07423	AGT		0.363	ZNF112-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460744.1	NM_013380	
SYNGR4	23546	hgsc.bcm.edu	37	19	48879376	48879376	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3521-01A-01W-0831-10	TCGA-AA-3521-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AA-3521-01A-01W-0831-10	TCGA-AA-3521-10A-01W-0831-10	g.chr19:48879376G>A	ENST00000344846.2	+	5	756	c.506G>A	c.(505-507)cGa>cAa	p.R169Q	SYNGR4_ENST00000601610.1_Silent_p.P145P|SYNGR4_ENST00000595322.1_Silent_p.P73P	NM_012451.3	NP_036583.2	O95473	SNG4_HUMAN	synaptogyrin 4	169	MARVEL. {ECO:0000255|PROSITE- ProRule:PRU00581}.					integral component of membrane (GO:0016021)		p.R169Q(2)		breast(1)|endometrium(2)|large_intestine(4)|lung(2)|skin(1)	10		all_epithelial(76;5.08e-07)|all_lung(116;5.76e-06)|Lung NSC(112;1.18e-05)|Prostate(7;0.0143)|all_neural(266;0.0189)|Ovarian(192;0.0261)|Breast(70;0.203)		OV - Ovarian serous cystadenocarcinoma(262;0.000138)|all cancers(93;0.00017)|Epithelial(262;0.0138)|GBM - Glioblastoma multiforme(486;0.0146)		CAGGACCTCCGAAATGATGCT	0.602																																					p.R169Q												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G506A	19						.						108.0	100.0	103.0					19																	48879376		2203	4300	6503	53571188	SO:0001583	missense	23546	exon5			AJ011733	CCDS12717.1	19q13.3	2008-07-04				ENSG00000105467			11502	protein-coding gene	gene with protein product		608373					Standard	NM_012451		Approved		uc002piz.3	O95473		ENST00000344846.2:c.506G>A	19.37:g.48879376G>A	ENSP00000344041:p.Arg169Gln		53571188	NM_012451	Q3KP58	Missense_Mutation	SNP	ENST00000344846.2	37	CCDS12717.1	.	.	.	.	.	.	.	.	.	.	G	13.57	2.278017	0.40294	.	.	ENSG00000105467	ENST00000344846	T	0.48201	0.82	5.61	-1.81	0.07882	Marvel (1);	0.948152	0.08692	N	0.907770	T	0.33789	0.0875	L	0.39566	1.225	0.09310	N	0.999995	B	0.22480	0.07	B	0.10450	0.005	T	0.26155	-1.0111	10	0.18710	T	0.47	-2.6799	9.3572	0.38173	0.4716:0.0:0.5284:0.0	.	169	O95473	SNG4_HUMAN	Q	169	ENSP00000344041:R169Q	ENSP00000344041:R169Q	R	+	2	0	SYNGR4	53571188	0.058000	0.20735	0.014000	0.15608	0.784000	0.44337	0.192000	0.17096	-0.331000	0.08501	-0.378000	0.06908	CGA		0.602	SYNGR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465704.1		
XKR6	286046	hgsc.bcm.edu	37	8	10755507	10755507	+	Silent	SNP	G	G	A	rs200925376	byFrequency	TCGA-AA-3521-01A-01W-0831-10	TCGA-AA-3521-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AA-3521-01A-01W-0831-10	TCGA-AA-3521-10A-01W-0831-10	g.chr8:10755507G>A	ENST00000416569.2	-	3	1907	c.1881C>T	c.(1879-1881)gaC>gaT	p.D627D	XKR6_ENST00000304437.2_Silent_p.D348D	NM_173683.3	NP_775954.2	Q5GH73	XKR6_HUMAN	XK, Kell blood group complex subunit-related family, member 6	627						integral component of membrane (GO:0016021)		p.D627D(1)		breast(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(8)|ovary(2)|prostate(1)|skin(3)	31				Lung(29;0.0407)|COAD - Colon adenocarcinoma(149;0.0555)		GGAGTGGTCCGTCTCGATATC	0.473																																					p.D627D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1881T	8						.						125.0	116.0	119.0					8																	10755507		2203	4300	6503	10792917	SO:0001819	synonymous_variant	286046	exon3			BC024146	CCDS5978.2	8p23.1	2009-05-27	2006-01-12	2005-07-28	ENSG00000171044	ENSG00000171044			27806	protein-coding gene	gene with protein product			"""chromosome 8 open reading frame 7"", ""chromosome 8 open reading frame 21"", ""X Kell blood group precursor-related family, member 6"", ""chromosome 8 open reading frame 5"""	C8orf7, C8orf21, C8orf5			Standard	NM_173683		Approved		uc003wtk.1	Q5GH73	OTTHUMG00000129351	ENST00000416569.2:c.1881C>T	8.37:g.10755507G>A			10792917	NM_173683	Q8TBA0	Silent	SNP	ENST00000416569.2	37	CCDS5978.2	.	.	.	.	.	.	.	.	.	.	G	2.627	-0.287214	0.05605	.	.	ENSG00000171044	ENST00000382461	.	.	.	4.4	-5.68	0.02436	.	.	.	.	.	T	0.61837	0.2379	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.63152	-0.6701	4	.	.	.	-8.6594	13.7885	0.63123	0.7085:0.0:0.2915:0.0	.	.	.	.	M	404	.	.	T	-	2	0	XKR6	10792917	0.912000	0.30974	0.901000	0.35422	0.997000	0.91878	-0.002000	0.12924	-1.164000	0.02790	0.549000	0.68633	ACG		0.473	XKR6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383958.1	NM_173683	
BAALC	79870	hgsc.bcm.edu	37	8	104225281	104225281	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3521-01A-01W-0831-10	TCGA-AA-3521-10A-01W-0831-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AA-3521-01A-01W-0831-10	TCGA-AA-3521-10A-01W-0831-10	g.chr8:104225281A>G	ENST00000297574.6	+	3	539	c.400A>G	c.(400-402)Acc>Gcc	p.T134A	BAALC_ENST00000438105.2_Intron|RP11-318M2.2_ENST00000499522.2_RNA|BAALC_ENST00000309982.5_Missense_Mutation_p.T99A|RP11-318M2.2_ENST00000523614.2_RNA			Q8WXS3	BAALC_HUMAN	brain and acute leukemia, cytoplasmic	134						cytoplasm (GO:0005737)|membrane (GO:0016020)		p.T99A(1)		kidney(1)|large_intestine(3)|lung(3)	7			OV - Ovarian serous cystadenocarcinoma(57;3.49e-05)|STAD - Stomach adenocarcinoma(118;0.133)			AGGCCCTCTGACCCAGAAACA	0.582																																					p.T99A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A295G	8						.						100.0	95.0	97.0					8																	104225281		2203	4300	6503	104294457	SO:0001583	missense	79870	exon2			AF363578	CCDS6297.1, CCDS47906.1	8q22.3	2008-07-29			ENSG00000164929	ENSG00000164929			14333	protein-coding gene	gene with protein product		606602				11707601	Standard	NM_024812		Approved		uc003yld.3	Q8WXS3	OTTHUMG00000164782	ENST00000297574.6:c.400A>G	8.37:g.104225281A>G	ENSP00000297574:p.Thr134Ala		104294457	NM_024812	Q8WTP6|Q8WXS0|Q8WXS1|Q8WXS2|Q9HA93	Missense_Mutation	SNP	ENST00000297574.6	37		.	.	.	.	.	.	.	.	.	.	A	15.79	2.937844	0.52972	.	.	ENSG00000164929	ENST00000309982;ENST00000297574	T;T	0.44482	0.92;0.95	5.69	2.0	0.26442	.	0.472069	0.21640	N	0.071345	T	0.15305	0.0369	.	.	.	0.80722	D	1	B;B	0.28998	0.02;0.23	B;B	0.19946	0.012;0.027	T	0.12760	-1.0535	9	0.06757	T	0.87	-5.7666	2.408	0.04417	0.6051:0.159:0.0836:0.1522	.	134;99	Q8WXS3;Q8WXS3-2	BAALC_HUMAN;.	A	99;134	ENSP00000312457:T99A;ENSP00000297574:T134A	ENSP00000297574:T134A	T	+	1	0	BAALC	104294457	0.938000	0.31826	0.997000	0.53966	0.998000	0.95712	0.405000	0.21015	0.165000	0.19558	0.533000	0.62120	ACC		0.582	BAALC-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000380257.1		
HRNR	388697	hgsc.bcm.edu	37	1	152195714	152195714	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3521-01A-01W-0831-10	TCGA-AA-3521-10A-01W-0831-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AA-3521-01A-01W-0831-10	TCGA-AA-3521-10A-01W-0831-10	g.chr1:152195714G>T	ENST00000368801.2	-	2	91	c.16C>A	c.(16-18)Caa>Aaa	p.Q6K	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_001009931.1	NP_001009931.1	Q86YZ3	HORN_HUMAN	hornerin	6	S-100-like.				establishment of skin barrier (GO:0061436)|hematopoietic progenitor cell differentiation (GO:0002244)|keratinization (GO:0031424)	cornified envelope (GO:0001533)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)	p.Q6K(1)		autonomic_ganglia(1)|breast(6)|central_nervous_system(2)|cervix(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|liver(1)|lung(84)|ovary(5)|prostate(6)|skin(12)|stomach(9)|upper_aerodigestive_tract(5)|urinary_tract(6)	192	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			ATGACGCCTTGTAGGAGTTTA	0.393																																					p.Q6K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C16A	1						.						121.0	113.0	116.0					1																	152195714		2203	4300	6503	150462338	SO:0001583	missense	388697	exon2			AB104446	CCDS30859.1	1q21.3	2013-01-10			ENSG00000197915	ENSG00000197915		"""EF-hand domain containing"""	20846	protein-coding gene	gene with protein product	"""filaggrin family member 3"""						Standard	NM_001009931		Approved	S100a18, S100A16, FLG3	uc001ezt.2	Q86YZ3	OTTHUMG00000012243	ENST00000368801.2:c.16C>A	1.37:g.152195714G>T	ENSP00000357791:p.Gln6Lys		150462338	NM_001009931	Q5DT20|Q5U1F4	Missense_Mutation	SNP	ENST00000368801.2	37	CCDS30859.1	.	.	.	.	.	.	.	.	.	.	G	6.792	0.515094	0.12944	.	.	ENSG00000197915	ENST00000368801	T	0.07908	3.15	5.29	-2.4	0.06583	S100/CaBP-9k-type, calcium binding, subdomain (1);EF-hand-like domain (1);	.	.	.	.	T	0.01092	0.0036	N	0.10760	0.04	0.09310	N	1	B	0.30634	0.288	B	0.25884	0.064	T	0.46190	-0.9209	9	0.29301	T	0.29	.	8.502	0.33163	0.0:0.3602:0.2425:0.3973	.	6	Q86YZ3	HORN_HUMAN	K	6	ENSP00000357791:Q6K	ENSP00000357791:Q6K	Q	-	1	0	HRNR	150462338	0.000000	0.05858	0.003000	0.11579	0.040000	0.13550	-1.027000	0.03592	-0.177000	0.10690	-0.467000	0.05162	CAA		0.393	HRNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034016.1	XM_373868	
RIT1	6016	hgsc.bcm.edu	37	1	155874539	155874539	+	Missense_Mutation	SNP	A	A	T			TCGA-AA-3521-01A-01W-0831-10	TCGA-AA-3521-10A-01W-0831-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	TCGA-AA-3521-01A-01W-0831-10	TCGA-AA-3521-10A-01W-0831-10	g.chr1:155874539A>T	ENST00000368323.3	-	4	424	c.220T>A	c.(220-222)Ttg>Atg	p.L74M	RIT1_ENST00000539040.1_Missense_Mutation_p.L38M|RIT1_ENST00000368322.3_Missense_Mutation_p.L91M	NM_006912.5	NP_008843.1	Q92963	RIT1_HUMAN	Ras-like without CAAX 1	74					GTP catabolic process (GO:0006184)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Ras protein signal transduction (GO:0007265)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	plasma membrane (GO:0005886)	calmodulin binding (GO:0005516)|GTP binding (GO:0005525)	p.L74M(1)		breast(1)|kidney(1)|large_intestine(3)|lung(12)|skin(1)|urinary_tract(1)	19	Hepatocellular(266;0.133)|all_hematologic(923;0.145)|all_neural(408;0.195)		OV - Ovarian serous cystadenocarcinoma(3;1.79e-05)			GCTGTATCCAAAATGTCCAGA	0.418																																					p.L74M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T220A	1						.						95.0	87.0	90.0					1																	155874539		2203	4300	6503	154141163	SO:0001583	missense	6016	exon4			AF084462	CCDS1123.1, CCDS58037.1, CCDS58036.1	1q21.2	2014-05-09	2002-09-11	2002-09-13	ENSG00000143622	ENSG00000143622			10023	protein-coding gene	gene with protein product	"""Ric-like, expressed in many tissues"", ""GTP-binding protein Roc1"""	609591	"""Ric (Drosophila)-like, expressed in many tissues"""	RIT		8824319, 8918462	Standard	NM_006912		Approved	RIBB, ROC1, MGC125864, MGC125865	uc031pqc.1	Q92963	OTTHUMG00000014104	ENST00000368323.3:c.220T>A	1.37:g.155874539A>T	ENSP00000357306:p.Leu74Met		154141163	NM_006912	B4DQE8|O00646|O00720|Q5VY89|Q5VY90	Missense_Mutation	SNP	ENST00000368323.3	37	CCDS1123.1	.	.	.	.	.	.	.	.	.	.	A	17.08	3.297471	0.60086	.	.	ENSG00000143622	ENST00000368323;ENST00000539040;ENST00000368322	T;T;T	0.80566	-1.39;-1.39;-1.39	4.88	1.3	0.21679	Small GTP-binding protein domain (1);	0.000000	0.56097	D	0.000023	T	0.80204	0.4580	M	0.67569	2.06	0.50632	D	0.999888	D	0.89917	1.0	D	0.97110	1.0	T	0.78682	-0.2109	10	0.87932	D	0	.	4.9232	0.13880	0.5025:0.1598:0.3377:0.0	.	74	Q92963	RIT1_HUMAN	M	74;38;91	ENSP00000357306:L74M;ENSP00000441950:L38M;ENSP00000357305:L91M	ENSP00000357305:L91M	L	-	1	2	RIT1	154141163	0.993000	0.37304	0.998000	0.56505	0.986000	0.74619	0.833000	0.27504	0.065000	0.16485	0.260000	0.18958	TTG		0.418	RIT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039593.1	NM_006912	
METTL13	51603	hgsc.bcm.edu	37	1	171761295	171761295	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3521-01A-01W-0831-10	TCGA-AA-3521-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AA-3521-01A-01W-0831-10	TCGA-AA-3521-10A-01W-0831-10	g.chr1:171761295G>A	ENST00000361735.3	+	6	1879	c.1613G>A	c.(1612-1614)gGc>gAc	p.G538D	METTL13_ENST00000362019.3_Missense_Mutation_p.G452D|METTL13_ENST00000466643.1_3'UTR|METTL13_ENST00000458517.1_Missense_Mutation_p.G537D|METTL13_ENST00000367737.5_Missense_Mutation_p.G382D	NM_015935.4	NP_057019.3	Q8N6R0	MET13_HUMAN	methyltransferase like 13	538							methyltransferase activity (GO:0008168)	p.G538D(1)		breast(3)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(8)|lung(17)|stomach(3)	41						CAGTGGTTTGGCTTCTCCCAG	0.537																																					p.G452D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1355A	1						.						146.0	128.0	134.0					1																	171761295		2203	4300	6503	170027918	SO:0001583	missense	51603	exon6			AF132936	CCDS1299.1, CCDS1300.1, CCDS30936.1	1q24-q25.3	2009-02-23	2009-02-23	2009-02-23	ENSG00000010165	ENSG00000010165			24248	protein-coding gene	gene with protein product			"""KIAA0859"""	KIAA0859		10810093, 10048485	Standard	NM_001007239		Approved	CGI-01	uc001ghz.3	Q8N6R0	OTTHUMG00000034912	ENST00000361735.3:c.1613G>A	1.37:g.171761295G>A	ENSP00000354920:p.Gly538Asp		170027918	NM_014955	A6NFK0|A8K6S5|O94940|Q53EZ6|Q5TGP9|Q5TGQ0|Q8N2P8|Q96J11|Q96SQ0|Q9Y2Z1|Q9Y3M6	Missense_Mutation	SNP	ENST00000361735.3	37	CCDS1299.1	.	.	.	.	.	.	.	.	.	.	G	21.9	4.213971	0.79352	.	.	ENSG00000010165	ENST00000458517;ENST00000362019;ENST00000367737;ENST00000361735;ENST00000367736;ENST00000341850	T;T;T;T;T	0.78003	0.03;0.03;0.03;0.03;-1.14	5.8	4.86	0.63082	.	0.044434	0.85682	D	0.000000	T	0.80555	0.4645	L	0.53729	1.69	0.58432	D	0.999998	D;D;D	0.89917	0.999;0.999;1.0	D;D;D	0.75484	0.986;0.973;0.986	T	0.79147	-0.1923	10	0.29301	T	0.29	-31.8881	16.2636	0.82563	0.0:0.133:0.867:0.0	.	537;382;538	B4E2X3;Q8N6R0-1;Q8N6R0	.;.;MTL13_HUMAN	D	537;452;382;538;238;235	ENSP00000401955:G537D;ENSP00000355393:G452D;ENSP00000356711:G382D;ENSP00000354920:G538D;ENSP00000356710:G238D	ENSP00000341732:G235D	G	+	2	0	METTL13	170027918	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.303000	0.72794	1.398000	0.46701	0.655000	0.94253	GGC		0.537	METTL13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084528.5	NM_014955	
LPHN2	23266	hgsc.bcm.edu	37	1	82409063	82409063	+	Nonsense_Mutation	SNP	G	G	T			TCGA-AA-3521-01A-01W-0831-10	TCGA-AA-3521-10A-01W-0831-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AA-3521-01A-01W-0831-10	TCGA-AA-3521-10A-01W-0831-10	g.chr1:82409063G>T	ENST00000370728.1	+	8	1453	c.808G>T	c.(808-810)Gaa>Taa	p.E270*	LPHN2_ENST00000370727.1_Nonsense_Mutation_p.E270*|LPHN2_ENST00000469377.2_Intron|LPHN2_ENST00000335786.5_Nonsense_Mutation_p.E270*|LPHN2_ENST00000319517.6_Nonsense_Mutation_p.E270*|LPHN2_ENST00000370723.1_Nonsense_Mutation_p.E270*|LPHN2_ENST00000370730.1_Nonsense_Mutation_p.E270*|LPHN2_ENST00000370721.1_Nonsense_Mutation_p.E274*|LPHN2_ENST00000271029.4_Nonsense_Mutation_p.E270*|LPHN2_ENST00000370715.1_Nonsense_Mutation_p.E270*|LPHN2_ENST00000359929.3_Nonsense_Mutation_p.E270*|LPHN2_ENST00000370713.1_Nonsense_Mutation_p.E270*|LPHN2_ENST00000394879.1_Nonsense_Mutation_p.E270*|LPHN2_ENST00000370717.2_Nonsense_Mutation_p.E270*|LPHN2_ENST00000370725.1_Nonsense_Mutation_p.E270*			O95490	LPHN2_HUMAN	latrophilin 2	270	Olfactomedin-like. {ECO:0000255|PROSITE- ProRule:PRU00446}.				G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|G-protein coupled receptor activity (GO:0004930)|latrotoxin receptor activity (GO:0016524)	p.E270*(1)		NS(3)|breast(6)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(18)|liver(2)|lung(37)|ovary(3)|pancreas(1)|prostate(3)|skin(22)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(5)	119				all cancers(265;0.00142)|Epithelial(280;0.00829)|OV - Ovarian serous cystadenocarcinoma(397;0.077)|STAD - Stomach adenocarcinoma(256;0.248)		AGCAGTTGATGAAAATGGTTT	0.418																																					p.E270X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.G808T	1						.						142.0	134.0	137.0					1																	82409063		2203	4300	6503	82181651	SO:0001587	stop_gained	23266	exon5			AJ131581	CCDS689.1, CCDS72811.1	1p31.1	2014-08-08	2003-03-17	2003-05-02	ENSG00000117114	ENSG00000117114		"""-"", ""GPCR / Class B : Orphans"""	18582	protein-coding gene	gene with protein product		607018	"""latrophilin 1"""	LPHH1		10760572	Standard	XR_248786		Approved	KIAA0786, LEC1	uc001diu.3	O95490	OTTHUMG00000009844	ENST00000370728.1:c.808G>T	1.37:g.82409063G>T	ENSP00000359763:p.Glu270*		82181651	NM_012302	A5XEI2|B1ALT8|B1ALT9|B1ALU0|B1ALU2|B1ALU4|B1ALU5|B1ALU6|O94882|Q5VX76|Q9UKY5|Q9UKY6	Nonsense_Mutation	SNP	ENST00000370728.1	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	44|44	10.578521|10.578521	0.99431|0.99431	.|.	.|.	ENSG00000117114|ENSG00000117114	ENST00000370721;ENST00000370728;ENST00000370730;ENST00000370727;ENST00000370725;ENST00000370723;ENST00000359929;ENST00000370715;ENST00000370713;ENST00000319517;ENST00000370717;ENST00000394879;ENST00000271029;ENST00000335786|ENST00000449420	.|.	.|.	.|.	5.52|5.52	5.52|5.52	0.82312|0.82312	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	.|T	.|0.71290	.|0.3322	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.69522	.|-0.5123	.|3	0.87932|.	D|.	0|.	.|.	19.4356|19.4356	0.94792|0.94792	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|.	.|.	.|.	X|I	274;270;270;270;270;270;270;270;270;270;270;270;270;270|137	.|.	ENSP00000271029:E270X|.	E|M	+|+	1|3	0|0	LPHN2|LPHN2	82181651|82181651	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.982000|0.982000	0.71751|0.71751	9.476000|9.476000	0.97823|0.97823	2.591000|2.591000	0.87537|0.87537	0.455000|0.455000	0.32223|0.32223	GAA|ATG		0.418	LPHN2-007	KNOWN	non_canonical_conserved|not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000027188.1	NM_012302	
ARHGAP29	9411	hgsc.bcm.edu	37	1	94650972	94650972	+	Missense_Mutation	SNP	G	G	A	rs561134145		TCGA-AA-3521-01A-01W-0831-10	TCGA-AA-3521-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AA-3521-01A-01W-0831-10	TCGA-AA-3521-10A-01W-0831-10	g.chr1:94650972G>A	ENST00000260526.6	-	17	2028	c.1846C>T	c.(1846-1848)Cgc>Tgc	p.R616C	ARHGAP29_ENST00000482481.1_5'UTR	NM_004815.3	NP_004806.3	Q52LW3	RHG29_HUMAN	Rho GTPase activating protein 29	616					positive regulation of Rho GTPase activity (GO:0032321)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	metal ion binding (GO:0046872)|PDZ domain binding (GO:0030165)|Rho GTPase activator activity (GO:0005100)	p.R616C(1)		NS(1)|breast(5)|endometrium(6)|kidney(2)|large_intestine(9)|lung(19)|ovary(1)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	54		all_lung(203;0.000732)|Lung NSC(277;0.00328)		all cancers(265;0.0187)|Epithelial(280;0.159)		CTCAATTTGCGAAACTTGTGT	0.378													G|||	1	0.000199681	0.0008	0.0	5008	,	,		14586	0.0		0.0	False		,,,				2504	0.0				p.R616C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1846T	1						.						155.0	143.0	147.0					1																	94650972		2203	4300	6503	94423560	SO:0001583	missense	9411	exon17				CCDS748.1	1p22.1	2011-06-29			ENSG00000137962	ENSG00000137962		"""Rho GTPase activating proteins"""	30207	protein-coding gene	gene with protein product		610496				9305890	Standard	NM_004815		Approved	PARG1	uc001dqj.4	Q52LW3	OTTHUMG00000010643	ENST00000260526.6:c.1846C>T	1.37:g.94650972G>A	ENSP00000260526:p.Arg616Cys		94423560	NM_004815	O15463|Q59H86|Q5VYZ0|Q6NVX2|Q8TBI6	Missense_Mutation	SNP	ENST00000260526.6	37	CCDS748.1	.	.	.	.	.	.	.	.	.	.	G	19.91	3.914850	0.72983	.	.	ENSG00000137962	ENST00000260526	D	0.94184	-3.37	5.7	4.8	0.61643	Protein kinase C-like, phorbol ester/diacylglycerol binding (4);	0.000000	0.37136	N	0.002231	D	0.94324	0.8176	M	0.64404	1.975	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.947;1.0	D	0.94909	0.8063	10	0.87932	D	0	-5.8885	10.3173	0.43745	0.0698:0.0:0.7954:0.1348	.	616;616	F8VWZ8;Q52LW3	.;RHG29_HUMAN	C	616	ENSP00000260526:R616C	ENSP00000260526:R616C	R	-	1	0	ARHGAP29	94423560	1.000000	0.71417	0.998000	0.56505	0.997000	0.91878	4.438000	0.59961	1.426000	0.47256	0.655000	0.94253	CGC		0.378	ARHGAP29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029376.2	NM_004815	
LAMB3	3914	hgsc.bcm.edu	37	1	209788663	209788663	+	Missense_Mutation	SNP	G	G	A	rs370023805		TCGA-AA-3521-01A-01W-0831-10	TCGA-AA-3521-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AA-3521-01A-01W-0831-10	TCGA-AA-3521-10A-01W-0831-10	g.chr1:209788663G>A	ENST00000356082.4	-	23	3606	c.3472C>T	c.(3472-3474)Cgt>Tgt	p.R1158C	LAMB3_ENST00000391911.1_Missense_Mutation_p.R1158C|LAMB3_ENST00000367030.3_Missense_Mutation_p.R1158C	NM_000228.2	NP_000219.2	Q13751	LAMB3_HUMAN	laminin, beta 3	1158	Domain I.				brown fat cell differentiation (GO:0050873)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	extracellular region (GO:0005576)|laminin-5 complex (GO:0005610)	structural molecule activity (GO:0005198)	p.R1158C(1)		NS(1)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(11)|lung(13)|ovary(1)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	45				OV - Ovarian serous cystadenocarcinoma(81;0.0519)		ATGTGGTCACGGATCTGCTCC	0.587																																					p.R1158C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C3472T	1						.	G	CYS/ARG,CYS/ARG,CYS/ARG	0,4406		0,0,2203	144.0	115.0	125.0		3472,3472,3472	4.6	1.0	1		125	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense	LAMB3	NM_000228.2,NM_001017402.1,NM_001127641.1	180,180,180	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging	1158/1173,1158/1173,1158/1173	209788663	1,13005	2203	4300	6503	207855286	SO:0001583	missense	3914	exon22			D37766	CCDS1487.1	1q32	2013-03-01	2002-08-29		ENSG00000196878	ENSG00000196878		"""Laminins"""	6490	protein-coding gene	gene with protein product		150310	"""laminin, beta 3 (nicein (125kD), kalinin (140kD), BM600 (125kD))"""	LAMNB1		8088808, 7774918	Standard	NM_001127641		Approved	nicein-125kDa, kalinin-140kDa, BM600-125kDa	uc001hhh.3	Q13751	OTTHUMG00000036360	ENST00000356082.4:c.3472C>T	1.37:g.209788663G>A	ENSP00000348384:p.Arg1158Cys		207855286	NM_001017402	D3DT88|O14947|Q14733|Q9UJK4|Q9UJL1	Missense_Mutation	SNP	ENST00000356082.4	37	CCDS1487.1	.	.	.	.	.	.	.	.	.	.	G	17.28	3.349455	0.61183	0.0	1.16E-4	ENSG00000196878	ENST00000391911;ENST00000356082;ENST00000367030	T;T;T	0.38722	1.12;1.12;1.12	5.56	4.64	0.57946	.	0.079457	0.53938	D	0.000058	T	0.54159	0.1841	L	0.36672	1.1	0.58432	D	0.999994	D	0.89917	1.0	D	0.85130	0.997	T	0.57412	-0.7816	10	0.72032	D	0.01	.	13.7584	0.62950	0.0:0.0:0.8461:0.1539	.	1158	Q13751	LAMB3_HUMAN	C	1158	ENSP00000375778:R1158C;ENSP00000348384:R1158C;ENSP00000355997:R1158C	ENSP00000348384:R1158C	R	-	1	0	LAMB3	207855286	1.000000	0.71417	0.985000	0.45067	0.472000	0.32918	4.747000	0.62141	1.341000	0.45600	0.455000	0.32223	CGT		0.587	LAMB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088525.2	NM_000228	
FIG4	9896	hgsc.bcm.edu	37	6	110081484	110081484	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3521-01A-01W-0831-10	TCGA-AA-3521-10A-01W-0831-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AA-3521-01A-01W-0831-10	TCGA-AA-3521-10A-01W-0831-10	g.chr6:110081484T>C	ENST00000230124.3	+	11	1293	c.1169T>C	c.(1168-1170)cTg>cCg	p.L390P	FIG4_ENST00000441478.2_Missense_Mutation_p.L113P	NM_014845.5	NP_055660.1	Q92562	FIG4_HUMAN	FIG4 phosphoinositide 5-phosphatase	390	SAC. {ECO:0000255|PROSITE- ProRule:PRU00183}.				cell death (GO:0008219)|locomotory behavior (GO:0007626)|myelin assembly (GO:0032288)|negative regulation of myelination (GO:0031642)|neuron development (GO:0048666)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phospholipid metabolic process (GO:0006644)|pigmentation (GO:0043473)|positive regulation of neuron projection development (GO:0010976)|small molecule metabolic process (GO:0044281)|vacuole organization (GO:0007033)	early endosome membrane (GO:0031901)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|late endosome membrane (GO:0031902)	phosphatidylinositol-3,5-bisphosphate 5-phosphatase activity (GO:0043813)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphatidylinositol-4-phosphate phosphatase activity (GO:0043812)	p.L390P(1)		central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)	32		all_cancers(87;8.63e-07)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;0.000124)|all_lung(197;0.0187)|Colorectal(196;0.0492)|Lung SC(18;0.0548)		OV - Ovarian serous cystadenocarcinoma(136;0.0355)|Epithelial(106;0.038)|all cancers(137;0.0425)|BRCA - Breast invasive adenocarcinoma(108;0.079)		GAAAGAATTCTGAGTGAAGAA	0.368																																					p.L390P												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T1169C	6						.						146.0	119.0	128.0					6																	110081484		2203	4300	6503	110188177	SO:0001583	missense	9896	exon11			D87464	CCDS5078.1	6q21	2014-09-17	2014-08-04	2007-07-30	ENSG00000112367	ENSG00000112367			16873	protein-coding gene	gene with protein product		609390	"""KIAA0274"", ""FIG4 homolog (S. cerevisiae)"", ""FIG4 homolog, SAC1 lipid phosphatase domain containing (S. cerevisiae)"""	KIAA0274		9039502, 11274189, 17572665	Standard	NM_014845		Approved	SAC3, hSac3, dJ249I4.1, ALS11, CMT4J	uc003ptt.2	Q92562	OTTHUMG00000015352	ENST00000230124.3:c.1169T>C	6.37:g.110081484T>C	ENSP00000230124:p.Leu390Pro		110188177	NM_014845	Q53H49|Q5TCS6	Missense_Mutation	SNP	ENST00000230124.3	37	CCDS5078.1	.	.	.	.	.	.	.	.	.	.	T	22.2	4.264103	0.80358	.	.	ENSG00000112367	ENST00000441478;ENST00000230124	T;T	0.75260	-0.92;-0.92	5.49	5.49	0.81192	Synaptojanin, N-terminal (2);	0.000000	0.64402	D	0.000003	D	0.89252	0.6662	H	0.96333	3.805	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.92735	0.6203	10	0.87932	D	0	-12.7933	15.5902	0.76521	0.0:0.0:0.0:1.0	.	113;390	F5H8L9;Q92562	.;FIG4_HUMAN	P	113;390	ENSP00000399443:L113P;ENSP00000230124:L390P	ENSP00000230124:L390P	L	+	2	0	FIG4	110188177	1.000000	0.71417	1.000000	0.80357	0.924000	0.55760	5.981000	0.70524	2.081000	0.62600	0.460000	0.39030	CTG		0.368	FIG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041768.1	NM_014845	
SERINC1	57515	hgsc.bcm.edu	37	6	122775300	122775300	+	Silent	SNP	T	T	A			TCGA-AA-3521-01A-01W-0831-10	TCGA-AA-3521-10A-01W-0831-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AA-3521-01A-01W-0831-10	TCGA-AA-3521-10A-01W-0831-10	g.chr6:122775300T>A	ENST00000339697.4	-	4	531	c.447A>T	c.(445-447)acA>acT	p.T149T		NM_020755.2	NP_065806.1	Q9NRX5	SERC1_HUMAN	serine incorporator 1	149					L-serine transport (GO:0015825)|phosphatidylserine metabolic process (GO:0006658)|phospholipid biosynthetic process (GO:0008654)|positive regulation of transferase activity (GO:0051347)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	L-serine transmembrane transporter activity (GO:0015194)	p.T149T(1)		endometrium(2)|kidney(2)|large_intestine(4)|liver(1)|lung(2)|ovary(1)|skin(1)	13				GBM - Glioblastoma multiforme(226;0.126)		TCTTACCAGTTGTAAAAGTTC	0.274																																					p.T149T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A447T	6						.						27.0	28.0	27.0					6																	122775300		2195	4284	6479	122816999	SO:0001819	synonymous_variant	57515	exon4			AF087902	CCDS5125.1	6q22.32	2006-02-09	2005-10-14	2005-10-14	ENSG00000111897	ENSG00000111897			13464	protein-coding gene	gene with protein product		614548	"""tumor differentially expressed 2"""	TDE2		10637174	Standard	NM_020755		Approved	TMS-2, TDE1L, KIAA1253	uc003pyy.1	Q9NRX5	OTTHUMG00000015487	ENST00000339697.4:c.447A>T	6.37:g.122775300T>A			122816999	NM_020755	B3KY69|E1P565|O75655|Q7Z2F5|Q8TAG1|Q9NTH8|Q9ULG7	Silent	SNP	ENST00000339697.4	37	CCDS5125.1																																																																																				0.274	SERINC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042031.2	NM_020755	
PLEKHG1	57480	hgsc.bcm.edu	37	6	151140837	151140837	+	Silent	SNP	T	T	C			TCGA-AA-3521-01A-01W-0831-10	TCGA-AA-3521-10A-01W-0831-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AA-3521-01A-01W-0831-10	TCGA-AA-3521-10A-01W-0831-10	g.chr6:151140837T>C	ENST00000358517.2	+	12	1546	c.1335T>C	c.(1333-1335)agT>agC	p.S445S	PLEKHG1_ENST00000367328.1_Silent_p.S445S			Q9ULL1	PKHG1_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 1	445							Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.S445S(1)		breast(3)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(10)|lung(19)|ovary(5)|prostate(4)|stomach(1)|urinary_tract(3)	53			BRCA - Breast invasive adenocarcinoma(37;0.0923)	OV - Ovarian serous cystadenocarcinoma(155;6.69e-13)		TCTGTTACAGTCCTGAGGGAG	0.443																																					p.S445S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T1335C	6						.						162.0	157.0	159.0					6																	151140837		2203	4300	6503	151182530	SO:0001819	synonymous_variant	57480	exon13			AB033035	CCDS34552.1	6q25.1	2013-01-11			ENSG00000120278	ENSG00000120278		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	20884	protein-coding gene	gene with protein product						10574462	Standard	XM_005267064		Approved	KIAA1209, ARHGEF41	uc003qny.1	Q9ULL1	OTTHUMG00000015824	ENST00000358517.2:c.1335T>C	6.37:g.151140837T>C			151182530	NM_001029884	Q5T1F2	Silent	SNP	ENST00000358517.2	37	CCDS34552.1																																																																																				0.443	PLEKHG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042691.1		
KLHDC3	116138	hgsc.bcm.edu	37	6	42985054	42985054	+	Missense_Mutation	SNP	C	C	T	rs200646992		TCGA-AA-3521-01A-01W-0831-10	TCGA-AA-3521-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AA-3521-01A-01W-0831-10	TCGA-AA-3521-10A-01W-0831-10	g.chr6:42985054C>T	ENST00000326974.4	+	2	319	c.124C>T	c.(124-126)Cgt>Tgt	p.R42C	KLHDC3_ENST00000244670.8_5'UTR|KLHDC3_ENST00000332245.8_Missense_Mutation_p.R42C	NM_057161.3	NP_476502.1	Q9BQ90	KLDC3_HUMAN	kelch domain containing 3	42					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|reciprocal meiotic recombination (GO:0007131)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)	chromatin binding (GO:0003682)	p.R42C(1)		cervix(1)|endometrium(1)|large_intestine(1)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	9			Colorectal(64;0.00237)|all cancers(41;0.0034)|COAD - Colon adenocarcinoma(64;0.00473)|OV - Ovarian serous cystadenocarcinoma(102;0.0539)|KIRC - Kidney renal clear cell carcinoma(15;0.133)|Kidney(15;0.188)			TGAGACACTGCGTCAGATAGA	0.592																																					p.R42C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C124T	6						.						122.0	124.0	123.0					6																	42985054		2203	4300	6503	43093032	SO:0001583	missense	116138	exon2			AB055925	CCDS4880.1	6p21.1	2003-06-12			ENSG00000124702	ENSG00000124702			20704	protein-coding gene	gene with protein product		611248				12444059, 12606021	Standard	NM_057161		Approved	PEAS, hPeas, dJ20C7.3	uc003otl.3	Q9BQ90	OTTHUMG00000014714	ENST00000326974.4:c.124C>T	6.37:g.42985054C>T	ENSP00000313995:p.Arg42Cys		43093032	NM_057161	A8K2W9	Missense_Mutation	SNP	ENST00000326974.4	37	CCDS4880.1	.	.	.	.	.	.	.	.	.	.	C	18.39	3.614099	0.66672	.	.	ENSG00000124702	ENST00000326974;ENST00000432243;ENST00000394096;ENST00000332245	T;T	0.66995	-0.24;2.26	5.05	5.05	0.67936	Kelch-type beta propeller (1);	0.000000	0.85682	D	0.000000	T	0.68348	0.2991	L	0.41236	1.265	0.80722	D	1	B;D;D	0.89917	0.29;1.0;1.0	B;D;D	0.76071	0.133;0.983;0.987	T	0.70487	-0.4858	10	0.52906	T	0.07	.	13.7262	0.62759	0.1541:0.8459:0.0:0.0	.	42;42;42	E7ENU0;E7ERR0;Q9BQ90	.;.;KLDC3_HUMAN	C	42	ENSP00000313995:R42C;ENSP00000331562:R42C	ENSP00000313995:R42C	R	+	1	0	KLHDC3	43093032	1.000000	0.71417	0.997000	0.53966	0.995000	0.86356	4.481000	0.60250	2.509000	0.84616	0.655000	0.94253	CGT		0.592	KLHDC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040570.1	NM_057161	
GPR116	221395	hgsc.bcm.edu	37	6	46851378	46851378	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3521-01A-01W-0831-10	TCGA-AA-3521-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AA-3521-01A-01W-0831-10	TCGA-AA-3521-10A-01W-0831-10	g.chr6:46851378C>T	ENST00000283296.7	-	6	818	c.530G>A	c.(529-531)aGa>aAa	p.R177K	GPR116_ENST00000478711.1_5'Flank|GPR116_ENST00000265417.7_Missense_Mutation_p.R177K|GPR116_ENST00000456426.2_Missense_Mutation_p.R177K|GPR116_ENST00000362015.4_Missense_Mutation_p.R177K	NM_001098518.1	NP_001091988.1	Q8IZF2	GP116_HUMAN	G protein-coupled receptor 116	177	SEA. {ECO:0000255|PROSITE- ProRule:PRU00188}.				energy reserve metabolic process (GO:0006112)|fat cell differentiation (GO:0045444)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|neuropeptide signaling pathway (GO:0007218)|regulation of lipid metabolic process (GO:0019216)|surfactant homeostasis (GO:0043129)	cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.R177K(1)		breast(2)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|lung(21)|ovary(1)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	59			Lung(136;0.192)			TACATTTAGTCTGACTCTCAT	0.408																																					p.R177K	NSCLC(59;410 1274 8751 36715 50546)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G530A	6						.						101.0	94.0	96.0					6																	46851378		2203	4300	6503	46959337	SO:0001583	missense	221395	exon6			AB018301	CCDS4919.1	6p12.3	2014-08-08			ENSG00000069122	ENSG00000069122		"""-"", ""GPCR / Class B : Orphans"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	19030	protein-coding gene	gene with protein product						12435584	Standard	NM_001098518		Approved	DKFZp564O1923, KIAA0758	uc003oyo.3	Q8IZF2	OTTHUMG00000014793	ENST00000283296.7:c.530G>A	6.37:g.46851378C>T	ENSP00000283296:p.Arg177Lys		46959337	NM_001098518	O94858|Q5TF06|Q6RGN2|Q86SP0|Q9Y3Z2	Missense_Mutation	SNP	ENST00000283296.7	37	CCDS4919.1	.	.	.	.	.	.	.	.	.	.	C	2.928	-0.221677	0.06061	.	.	ENSG00000069122	ENST00000452370;ENST00000283296;ENST00000362015;ENST00000456426;ENST00000265417	T;T;T;T	0.32272	1.46;1.46;1.46;1.46	5.71	2.61	0.31194	SEA (2);	0.169179	0.42172	D	0.000759	T	0.04770	0.0129	N	0.05199	-0.095	0.80722	D	1	B;B;B	0.10296	0.003;0.0;0.003	B;B;B	0.13407	0.009;0.005;0.009	T	0.17561	-1.0365	10	0.27082	T	0.32	-21.6711	5.8458	0.18665	0.0:0.6451:0.0:0.3549	.	177;177;177	A8K0D8;Q8IZF2-3;Q8IZF2	.;.;GP116_HUMAN	K	177	ENSP00000283296:R177K;ENSP00000354563:R177K;ENSP00000412866:R177K;ENSP00000265417:R177K	ENSP00000265417:R177K	R	-	2	0	GPR116	46959337	1.000000	0.71417	0.998000	0.56505	0.074000	0.17049	0.422000	0.21296	0.776000	0.33473	-0.794000	0.03295	AGA		0.408	GPR116-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040806.2	NM_015234	
BAI3	577	hgsc.bcm.edu	37	6	69666692	69666692	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-3521-01A-01W-0831-10	TCGA-AA-3521-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AA-3521-01A-01W-0831-10	TCGA-AA-3521-10A-01W-0831-10	g.chr6:69666692C>T	ENST00000370598.1	+	8	2337	c.1516C>T	c.(1516-1518)Cga>Tga	p.R506*		NM_001704.2	NP_001695	O60242	BAI3_HUMAN	brain-specific angiogenesis inhibitor 3	506	TSP type-1 4. {ECO:0000255|PROSITE- ProRule:PRU00210}.				G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of angiogenesis (GO:0016525)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.R506*(2)|p.R506R(1)		NS(2)|breast(4)|central_nervous_system(5)|endometrium(5)|kidney(2)|large_intestine(28)|liver(1)|lung(111)|ovary(10)|pancreas(4)|prostate(7)|skin(22)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	210		all_lung(197;0.212)				CAATGAGCAGCGATGCCCTGG	0.428																																					p.R506X												.	.	3	Substitution - Nonsense(2)|Substitution - coding silent(1)	large_intestine(2)|lung(1)	c.C1516T	6						.						118.0	118.0	118.0					6																	69666692		2203	4300	6503	69723413	SO:0001587	stop_gained	577	exon8			AB005299	CCDS4968.1	6q12	2014-08-08			ENSG00000135298	ENSG00000135298		"""-"", ""GPCR / Class B : Orphans"""	945	protein-coding gene	gene with protein product		602684				9533023	Standard	NM_001704		Approved	KIAA0550	uc003pev.4	O60242	OTTHUMG00000014982	ENST00000370598.1:c.1516C>T	6.37:g.69666692C>T	ENSP00000359630:p.Arg506*		69723413	NM_001704	B7Z1K0|O60297|Q2NKN6|Q5VY37|Q9BX54	Nonsense_Mutation	SNP	ENST00000370598.1	37	CCDS4968.1	.	.	.	.	.	.	.	.	.	.	C	46	12.842583	0.99700	.	.	ENSG00000135298	ENST00000370598	.	.	.	5.19	4.2	0.49525	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	12.9396	0.58335	0.2751:0.7249:0.0:0.0	.	.	.	.	X	506	.	ENSP00000359630:R506X	R	+	1	2	BAI3	69723413	1.000000	0.71417	0.999000	0.59377	0.970000	0.65996	3.080000	0.50112	2.595000	0.87683	0.650000	0.86243	CGA		0.428	BAI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041120.1		
SYNE1	23345	hgsc.bcm.edu	37	6	152464860	152464860	+	Silent	SNP	G	G	T			TCGA-AA-3521-01A-01W-0831-10	TCGA-AA-3521-10A-01W-0831-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AA-3521-01A-01W-0831-10	TCGA-AA-3521-10A-01W-0831-10	g.chr6:152464860G>T	ENST00000367255.5	-	138	25618	c.25017C>A	c.(25015-25017)ggC>ggA	p.G8339G	SYNE1_ENST00000347037.5_5'UTR|SYNE1_ENST00000448038.1_Silent_p.G8291G|SYNE1_ENST00000354674.4_Silent_p.G517G|SYNE1_ENST00000265368.4_Silent_p.G8339G|SYNE1_ENST00000423061.1_Silent_p.G8291G|SYNE1_ENST00000539504.1_Silent_p.G494G|SYNE1_ENST00000341594.5_Silent_p.G7951G|SYNE1_ENST00000356820.4_Silent_p.G2863G	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	8339					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)	p.G8339G(2)		NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		CCAGGGCTTTGCCCAGTTGTC	0.483										HNSCC(10;0.0054)																											p.G2863G												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C8589A	6						.						124.0	122.0	122.0					6																	152464860		2203	4300	6503	152506553	SO:0001819	synonymous_variant	23345	exon53			AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"""myocyte nuclear envelope protein 1"", ""nuclear envelope spectrin repeat-1"""	608441	"""chromosome 6 open reading frame 98"""	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.25017C>A	6.37:g.152464860G>T			152506553	NM_015293	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Silent	SNP	ENST00000367255.5	37	CCDS5236.2																																																																																				0.483	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961	
SLC6A4	6532	hgsc.bcm.edu	37	17	28536249	28536249	+	Silent	SNP	G	G	A	rs150907184		TCGA-AA-3521-01A-01W-0831-10	TCGA-AA-3521-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	TCGA-AA-3521-01A-01W-0831-10	TCGA-AA-3521-10A-01W-0831-10	g.chr17:28536249G>A	ENST00000401766.2	-	11	1973	c.1461C>T	c.(1459-1461)taC>taT	p.Y487Y	RP11-354P11.4_ENST00000581633.1_RNA|SLC6A4_ENST00000261707.3_Silent_p.Y487Y			P31645	SC6A4_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 4	487					brain morphogenesis (GO:0048854)|cellular response to cGMP (GO:0071321)|cellular response to retinoic acid (GO:0071300)|circadian rhythm (GO:0007623)|memory (GO:0007613)|monoamine transport (GO:0015844)|negative regulation of cerebellar granule cell precursor proliferation (GO:0021941)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of organ growth (GO:0046621)|negative regulation of synaptic transmission, dopaminergic (GO:0032227)|positive regulation of cell cycle (GO:0045787)|positive regulation of gene expression (GO:0010628)|protein homooligomerization (GO:0051260)|protein oligomerization (GO:0051259)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to hypoxia (GO:0001666)|response to nutrient (GO:0007584)|response to toxic substance (GO:0009636)|serotonin transport (GO:0006837)|serotonin uptake (GO:0051610)|social behavior (GO:0035176)|sperm ejaculation (GO:0042713)|thalamus development (GO:0021794)|vasoconstriction (GO:0042310)	cytosol (GO:0005829)|endomembrane system (GO:0012505)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)|cocaine binding (GO:0019811)|monoamine transmembrane transporter activity (GO:0008504)|Rab GTPase binding (GO:0017137)|serotonin transmembrane transporter activity (GO:0015222)|serotonin:sodium symporter activity (GO:0005335)	p.Y487Y(1)		breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(8)|ovary(1)|prostate(1)|skin(4)	25					Amitriptyline(DB00321)|Amoxapine(DB00543)|Amphetamine(DB00182)|Atomoxetine(DB00289)|Chlorphenamine(DB01114)|Citalopram(DB00215)|Clomipramine(DB01242)|Cocaine(DB00907)|Desipramine(DB01151)|Desvenlafaxine(DB06700)|Dexfenfluramine(DB01191)|Dexmethylphenidate(DB06701)|Dextromethorphan(DB00514)|Dopamine(DB00988)|Doxepin(DB01142)|Duloxetine(DB00476)|Ephedra(DB01363)|Escitalopram(DB01175)|Fluoxetine(DB00472)|Fluvoxamine(DB00176)|Imipramine(DB00458)|Levomilnacipran(DB08918)|Loxapine(DB00408)|Mazindol(DB00579)|Methamphetamine(DB01577)|Methylphenidate(DB00422)|Mianserin(DB06148)|Milnacipran(DB04896)|Minaprine(DB00805)|Mirtazapine(DB00370)|Nefazodone(DB01149)|Nortriptyline(DB00540)|Paroxetine(DB00715)|Pethidine(DB00454)|Phentermine(DB00191)|Protriptyline(DB00344)|Pseudoephedrine(DB00852)|Sertraline(DB01104)|Sibutramine(DB01105)|Tapentadol(DB06204)|Tramadol(DB00193)|Trazodone(DB00656)|Trimipramine(DB00726)|Venlafaxine(DB00285)|Verapamil(DB00661)|Vilazodone(DB06684)	GCTTCACCACGTAGGCCCCTC	0.617																																					p.Y487Y												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1461T	17						.	G		0,4406		0,0,2203	52.0	49.0	50.0		1461	-2.1	1.0	17	dbSNP_134	50	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	SLC6A4	NM_001045.4		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		487/631	28536249	1,13005	2203	4300	6503	25560375	SO:0001819	synonymous_variant	6532	exon12			L05568	CCDS11256.1	17q11.2	2014-01-30	2013-07-19		ENSG00000108576	ENSG00000108576		"""Solute carriers"""	11050	protein-coding gene	gene with protein product	"""serotonin transporter 1"""	182138	"""solute carrier family 6 (neurotransmitter transporter, serotonin), member 4"", ""5-hydroxytryptamine (serotonin) transporter"", ""obsessive-compulsive disorder 1"""	HTT, OCD1		7681602, 19806148	Standard	NM_001045		Approved	5-HTT, SERT1	uc002hey.5	P31645	OTTHUMG00000132751	ENST00000401766.2:c.1461C>T	17.37:g.28536249G>A			25560375	NM_001045	Q5EE02	Silent	SNP	ENST00000401766.2	37	CCDS11256.1																																																																																				0.617	SLC6A4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256115.3	NM_001045	
ENO3	2027	hgsc.bcm.edu	37	17	4860313	4860313	+	Missense_Mutation	SNP	C	C	T	rs202150244	byFrequency	TCGA-AA-3521-01A-01W-0831-10	TCGA-AA-3521-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AA-3521-01A-01W-0831-10	TCGA-AA-3521-10A-01W-0831-10	g.chr17:4860313C>T	ENST00000323997.6	+	12	1408	c.1276C>T	c.(1276-1278)Cgc>Tgc	p.R426C	ENO3_ENST00000518175.1_Missense_Mutation_p.R426C|ENO3_ENST00000519584.1_Missense_Mutation_p.R383C	NM_001976.4|NM_053013.3	NP_001967.3|NP_443739.3	P13929	ENOB_HUMAN	enolase 3 (beta, muscle)	426					aging (GO:0007568)|carbohydrate metabolic process (GO:0005975)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|response to drug (GO:0042493)|skeletal muscle tissue regeneration (GO:0043403)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|phosphopyruvate hydratase complex (GO:0000015)|plasma membrane (GO:0005886)	magnesium ion binding (GO:0000287)|phosphopyruvate hydratase activity (GO:0004634)	p.R426C(1)		cervix(1)|endometrium(1)|large_intestine(4)|lung(8)|ovary(1)	15						CTTTGCTGGACGCAAGTTCCG	0.552											OREG0024110	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	2	0.000399361	0.0	0.0	5008	,	,		17925	0.0		0.001	False		,,,				2504	0.001				p.R426C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1276T	17						.	C	CYS/ARG,CYS/ARG,CYS/ARG	0,4406		0,0,2203	136.0	135.0	135.0		1147,1276,1276	4.9	1.0	17		135	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense	ENO3	NM_001193503.1,NM_001976.4,NM_053013.3	180,180,180	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign,benign,benign	383/392,426/435,426/435	4860313	1,13005	2203	4300	6503	4801037	SO:0001583	missense	2027	exon12			X16504	CCDS11062.1, CCDS54070.1	17p13.2	2013-09-19	2004-11-22		ENSG00000108515	ENSG00000108515	4.2.1.11		3354	protein-coding gene	gene with protein product		131370	"""enolase 3, (beta, muscle)"""				Standard	NM_001976		Approved		uc002gab.4	P13929	OTTHUMG00000099394	ENST00000323997.6:c.1276C>T	17.37:g.4860313C>T	ENSP00000324105:p.Arg426Cys	622	4801037	NM_053013	B4DUI6|B4DUM6|D3DTL2|E7ENK8|Q96AE2	Missense_Mutation	SNP	ENST00000323997.6	37	CCDS11062.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	22.8	4.337292	0.81911	0.0	1.16E-4	ENSG00000108515	ENST00000323997;ENST00000519584;ENST00000518175	T;T;T	0.53857	0.6;0.6;0.6	5.87	4.9	0.64082	Enolase, C-terminal (1);	0.185960	0.47852	N	0.000210	T	0.63768	0.2539	M	0.78637	2.42	0.53688	D	0.999976	D;P;D	0.59357	0.985;0.952;0.985	P;P;P	0.51895	0.681;0.683;0.681	T	0.69764	-0.5057	10	0.87932	D	0	-19.2406	12.3007	0.54872	0.306:0.694:0.0:0.0	.	426;383;426	P13929;P13929-3;D3DTL2	ENOB_HUMAN;.;.	C	426;383;426	ENSP00000324105:R426C;ENSP00000430636:R383C;ENSP00000431087:R426C	ENSP00000324105:R426C	R	+	1	0	ENO3	4801037	0.005000	0.15991	1.000000	0.80357	0.996000	0.88848	1.935000	0.40173	1.503000	0.48686	0.644000	0.83932	CGC		0.552	ENO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216851.2		
WNK4	65266	hgsc.bcm.edu	37	17	40945636	40945636	+	Silent	SNP	G	G	A			TCGA-AA-3521-01A-01W-0831-10	TCGA-AA-3521-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AA-3521-01A-01W-0831-10	TCGA-AA-3521-10A-01W-0831-10	g.chr17:40945636G>A	ENST00000246914.5	+	12	2205	c.2184G>A	c.(2182-2184)tcG>tcA	p.S728S		NM_032387.4	NP_115763.2	Q96J92	WNK4_HUMAN	WNK lysine deficient protein kinase 4	728					chloride transport (GO:0006821)|distal tubule morphogenesis (GO:0072156)|intracellular signal transduction (GO:0035556)|ion homeostasis (GO:0050801)|ion transport (GO:0006811)|negative regulation of pancreatic juice secretion (GO:0090188)|protein localization (GO:0008104)|protein phosphorylation (GO:0006468)|regulation of cellular process (GO:0050794)|renal sodium ion absorption (GO:0070294)	cytoplasm (GO:0005737)|tight junction (GO:0005923)	ATP binding (GO:0005524)|chloride channel inhibitor activity (GO:0019869)|protein serine/threonine kinase activity (GO:0004674)	p.S728S(1)|p.S716S(1)		NS(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(10)|ovary(3)|prostate(1)|skin(5)|stomach(1)	35		Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.0749)		TTCTGCCTTCGGAGCGAGATG	0.532																																					p.S728S	Esophageal Squamous(6;201 374 4964 23855 42828)											.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.G2184A	17						.						98.0	78.0	85.0					17																	40945636		2203	4300	6503	38199162	SO:0001819	synonymous_variant	65266	exon12			AJ309861	CCDS11439.1	17q21-q22	2005-01-19	2005-01-19	2005-01-19		ENSG00000126562			14544	protein-coding gene	gene with protein product		601844	"""protein kinase, lysine deficient 4"""	PRKWNK4			Standard	NM_032387		Approved		uc002ibj.3	Q96J92		ENST00000246914.5:c.2184G>A	17.37:g.40945636G>A			38199162	NM_032387	B0LPI0|Q8N8X3|Q8N8Z2|Q96DT8|Q9BYS5	Silent	SNP	ENST00000246914.5	37	CCDS11439.1																																																																																				0.532	WNK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452389.1		
NARF	26502	hgsc.bcm.edu	37	17	80430511	80430511	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3521-01A-01W-0831-10	TCGA-AA-3521-10A-01W-0831-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	TCGA-AA-3521-01A-01W-0831-10	TCGA-AA-3521-10A-01W-0831-10	g.chr17:80430511C>T	ENST00000309794.11	+	5	655	c.457C>T	c.(457-459)Cgt>Tgt	p.R153C	NARF_ENST00000581743.1_3'UTR|NARF_ENST00000457415.3_Missense_Mutation_p.R153C|NARF_ENST00000345415.7_Missense_Mutation_p.R105C|NARF_ENST00000412079.2_Intron|NARF_ENST00000390006.4_Missense_Mutation_p.R94C	NM_012336.3|NM_031968.2	NP_036468.1|NP_114174.1	Q9UHQ1	NARF_HUMAN	nuclear prelamin A recognition factor	153						lamin filament (GO:0005638)|nuclear lamina (GO:0005652)|nuclear lumen (GO:0031981)|nucleus (GO:0005634)	lamin binding (GO:0005521)	p.R153C(1)		endometrium(2)|kidney(2)|large_intestine(5)|lung(8)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	24	Breast(20;0.00106)|all_neural(118;0.0804)		OV - Ovarian serous cystadenocarcinoma(97;0.0143)|BRCA - Breast invasive adenocarcinoma(99;0.0369)			AGAATTCGTGCGTCGCTATCG	0.552																																					p.R153C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C457T	17						.						127.0	111.0	116.0					17																	80430511		2203	4300	6503	78023800	SO:0001583	missense	26502	exon5			BC000438	CCDS32777.1, CCDS42403.1, CCDS42404.1	17q25.3	2011-12-19			ENSG00000141562	ENSG00000141562			29916	protein-coding gene	gene with protein product	"""iron-only hydrogenase-like protein 2"""	605349				10514485, 15667261	Standard	NM_031968		Approved	FLJ10067, DKFZp434G0420, IOP2	uc002kfg.4	Q9UHQ1		ENST00000309794.11:c.457C>T	17.37:g.80430511C>T	ENSP00000309899:p.Arg153Cys		78023800	NM_031968	A6NCJ3|B3KPX2|K4DI98|Q96AY9|Q9BWC6	Missense_Mutation	SNP	ENST00000309794.11	37	CCDS32777.1	.	.	.	.	.	.	.	.	.	.	C	16.22	3.060628	0.55432	.	.	ENSG00000141562	ENST00000390006;ENST00000374611;ENST00000309794;ENST00000345415	T;T;T;T	0.44482	0.92;0.92;0.92;0.92	5.64	4.67	0.58626	Iron hydrogenase, large subunit, C-terminal (1);Iron hydrogenase (1);	0.234303	0.45361	D	0.000379	T	0.38878	0.1057	L	0.48362	1.52	0.80722	D	1	B;B;B;B	0.21688	0.015;0.004;0.019;0.059	B;B;B;B	0.24155	0.021;0.012;0.035;0.051	T	0.33701	-0.9858	10	0.72032	D	0.01	-24.6293	13.9702	0.64235	0.0:0.9264:0.0:0.0736	.	153;105;153;153	Q9UHQ1-2;Q9UHQ1-3;E9PH27;Q9UHQ1	.;.;.;NARF_HUMAN	C	94;153;153;105	ENSP00000374656:R94C;ENSP00000363739:R153C;ENSP00000309899:R153C;ENSP00000283996:R105C	ENSP00000309899:R153C	R	+	1	0	NARF	78023800	1.000000	0.71417	0.998000	0.56505	0.989000	0.77384	5.466000	0.66731	2.674000	0.91012	0.651000	0.88453	CGT		0.552	NARF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443573.2	NM_031968	
NRIP1	8204	hgsc.bcm.edu	37	21	16339129	16339129	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3521-01A-01W-0831-10	TCGA-AA-3521-10A-01W-0831-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AA-3521-01A-01W-0831-10	TCGA-AA-3521-10A-01W-0831-10	g.chr21:16339129T>C	ENST00000400202.1	-	3	2097	c.1385A>G	c.(1384-1386)aAc>aGc	p.N462S	NRIP1_ENST00000400199.1_Missense_Mutation_p.N462S|AF127577.10_ENST00000446301.1_RNA|NRIP1_ENST00000318948.4_Missense_Mutation_p.N462S			P48552	NRIP1_HUMAN	nuclear receptor interacting protein 1	462	Repression domain 2.|Required for targeting to small nuclear foci.				androgen receptor signaling pathway (GO:0030521)|lipid storage (GO:0019915)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|ovarian follicle rupture (GO:0001543)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|histone deacetylase complex (GO:0000118)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|estrogen receptor binding (GO:0030331)|glucocorticoid receptor binding (GO:0035259)|nuclear hormone receptor binding (GO:0035257)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)	p.N462S(1)		cervix(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(6)|lung(13)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	39				Epithelial(23;1.19e-05)|all cancers(11;4.64e-05)|COAD - Colon adenocarcinoma(22;0.000232)|Colorectal(24;0.0006)|OV - Ovarian serous cystadenocarcinoma(11;0.00418)|Lung(58;0.199)|LUSC - Lung squamous cell carcinoma(23;0.24)		TTGAGTGAAGTTATCCAGGGA	0.393																																					p.N462S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1385G	21						.						135.0	129.0	131.0					21																	16339129		2203	4299	6502	15261000	SO:0001583	missense	8204	exon4			X84373	CCDS13568.1	21q11.2	2008-07-31			ENSG00000180530	ENSG00000180530			8001	protein-coding gene	gene with protein product	"""receptor interacting protein 140"", ""nuclear factor RIP140"""	602490				7641693, 9521594	Standard	NM_003489		Approved	RIP140	uc002yjx.2	P48552	OTTHUMG00000074323	ENST00000400202.1:c.1385A>G	21.37:g.16339129T>C	ENSP00000383063:p.Asn462Ser		15261000	NM_003489	Q8IWE8	Missense_Mutation	SNP	ENST00000400202.1	37	CCDS13568.1	.	.	.	.	.	.	.	.	.	.	T	15.07	2.725417	0.48833	.	.	ENSG00000180530	ENST00000400199;ENST00000400202;ENST00000318948	T;T;T	0.20598	2.06;2.06;2.06	5.85	4.69	0.59074	.	0.103586	0.64402	D	0.000005	T	0.15478	0.0373	L	0.40543	1.245	0.43250	D	0.995179	P	0.42518	0.782	B	0.34652	0.187	T	0.04041	-1.0982	10	0.30854	T	0.27	-13.1972	12.0721	0.53622	0.0:0.068:0.0:0.932	.	462	P48552	NRIP1_HUMAN	S	462	ENSP00000383060:N462S;ENSP00000383063:N462S;ENSP00000327213:N462S	ENSP00000327213:N462S	N	-	2	0	NRIP1	15261000	1.000000	0.71417	1.000000	0.80357	0.949000	0.60115	4.749000	0.62155	2.236000	0.73375	0.528000	0.53228	AAC		0.393	NRIP1-002	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157926.1	NM_003489	
COLEC12	81035	hgsc.bcm.edu	37	18	347142	347142	+	Silent	SNP	G	G	A	rs199985975		TCGA-AA-3521-01A-01W-0831-10	TCGA-AA-3521-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AA-3521-01A-01W-0831-10	TCGA-AA-3521-10A-01W-0831-10	g.chr18:347142G>A	ENST00000400256.3	-	5	687	c.480C>T	c.(478-480)aaC>aaT	p.N160N		NM_130386.2	NP_569057	Q5KU26	COL12_HUMAN	collectin sub-family member 12	160					carbohydrate mediated signaling (GO:0009756)|defense response (GO:0006952)|innate immune response (GO:0045087)|pattern recognition receptor signaling pathway (GO:0002221)|phagocytosis, recognition (GO:0006910)|protein homooligomerization (GO:0051260)|receptor-mediated endocytosis (GO:0006898)	collagen trimer (GO:0005581)|endocytic vesicle membrane (GO:0030666)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	galactose binding (GO:0005534)|low-density lipoprotein particle binding (GO:0030169)|metal ion binding (GO:0046872)|scavenger receptor activity (GO:0005044)|signaling pattern recognition receptor activity (GO:0008329)	p.N160N(1)		cervix(2)|endometrium(3)|kidney(2)|large_intestine(10)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	46		all_cancers(4;0.0442)|Myeloproliferative disorder(11;0.0426)				TGAGGAAAGAGTTATTCTCCA	0.478																																					p.N160N												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C480T	18						.						130.0	122.0	125.0					18																	347142		2203	4300	6503	337142	SO:0001819	synonymous_variant	81035	exon5			AB038518	CCDS32782.1	18p11.32	2013-09-19			ENSG00000158270	ENSG00000158270		"""Collectins"""	16016	protein-coding gene	gene with protein product		607621				11162630	Standard	NM_130386		Approved	SRCL, CL-P1, SCARA4	uc002kkm.3	Q5KU26	OTTHUMG00000178145	ENST00000400256.3:c.480C>T	18.37:g.347142G>A			337142	NM_130386	Q6P9F2|Q8TCR2|Q8WZA4|Q9BY85|Q9BYH7	Silent	SNP	ENST00000400256.3	37	CCDS32782.1																																																																																				0.478	COLEC12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440746.1		
WDR7	23335	hgsc.bcm.edu	37	18	54424243	54424243	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3521-01A-01W-0831-10	TCGA-AA-3521-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AA-3521-01A-01W-0831-10	TCGA-AA-3521-10A-01W-0831-10	g.chr18:54424243C>T	ENST00000254442.3	+	15	2630	c.2419C>T	c.(2419-2421)Ctt>Ttt	p.L807F	WDR7_ENST00000357574.3_Missense_Mutation_p.L807F|WDR7_ENST00000589935.1_Intron	NM_015285.2	NP_056100.2	Q9Y4E6	WDR7_HUMAN	WD repeat domain 7	807					hematopoietic progenitor cell differentiation (GO:0002244)			p.L807F(1)		NS(1)|breast(5)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(14)|lung(37)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)	78				Lung(128;0.0238)|Colorectal(16;0.0296)		TATGTCCTGCCTTCACGCCTG	0.453																																					p.L807F												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2419T	18						.						158.0	150.0	153.0					18																	54424243		2203	4300	6503	52575241	SO:0001583	missense	23335	exon15			AB011113	CCDS11962.1, CCDS11963.1	18q21.31	2013-01-09			ENSG00000091157	ENSG00000091157		"""WD repeat domain containing"""	13490	protein-coding gene	gene with protein product		613473				10828621	Standard	XM_005266674		Approved	KIAA0541, TRAG	uc002lgk.1	Q9Y4E6	OTTHUMG00000132721	ENST00000254442.3:c.2419C>T	18.37:g.54424243C>T	ENSP00000254442:p.Leu807Phe		52575241	NM_015285	A7E2C8|Q86UX5|Q86VP2|Q96PS7	Missense_Mutation	SNP	ENST00000254442.3	37	CCDS11962.1	.	.	.	.	.	.	.	.	.	.	C	25.5	4.646311	0.87958	.	.	ENSG00000091157	ENST00000254442;ENST00000357574;ENST00000444065;ENST00000398311	D;D	0.83673	-1.75;-1.58	5.83	5.83	0.93111	.	0.000000	0.85682	D	0.000000	D	0.89842	0.6832	L	0.56340	1.77	0.80722	D	1	D;D	0.89917	1.0;0.998	D;D	0.91635	0.999;0.991	D	0.89488	0.3755	10	0.59425	D	0.04	.	19.7075	0.96079	0.0:1.0:0.0:0.0	.	807;807	Q9Y4E6-2;Q9Y4E6	.;WDR7_HUMAN	F	807;807;132;807	ENSP00000254442:L807F;ENSP00000350187:L807F	ENSP00000254442:L807F	L	+	1	0	WDR7	52575241	1.000000	0.71417	0.995000	0.50966	0.989000	0.77384	7.687000	0.84139	2.749000	0.94314	0.655000	0.94253	CTT		0.453	WDR7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256062.1		
DSEL	92126	hgsc.bcm.edu	37	18	65178817	65178817	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3521-01A-01W-0831-10	TCGA-AA-3521-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AA-3521-01A-01W-0831-10	TCGA-AA-3521-10A-01W-0831-10	g.chr18:65178817G>A	ENST00000310045.7	-	2	4532	c.3059C>T	c.(3058-3060)aCg>aTg	p.T1020M	CTD-2541J13.2_ENST00000581951.1_RNA|CTD-2541J13.2_ENST00000583493.1_RNA	NM_032160.2	NP_115536.1	Q8IZU8	DSEL_HUMAN	dermatan sulfate epimerase-like	1010					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	isomerase activity (GO:0016853)|sulfotransferase activity (GO:0008146)	p.T1020M(1)		NS(3)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(25)|lung(23)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	74		Esophageal squamous(42;0.129)				AAGCTTTAACGTCCAGCTTCC	0.423																																					p.T1020M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C3059T	18						.						77.0	82.0	80.0					18																	65178817		2203	4300	6503	63329797	SO:0001583	missense	92126	exon2			AF480435	CCDS11995.1	18q22.1	2007-01-29	2007-01-29	2007-01-29	ENSG00000171451	ENSG00000171451			18144	protein-coding gene	gene with protein product		611125	"""chromosome 18 open reading frame 4"""	C18orf4		16505484	Standard	NM_032160		Approved	NCAG1, FLJ11477	uc002lke.1	Q8IZU8	OTTHUMG00000132804	ENST00000310045.7:c.3059C>T	18.37:g.65178817G>A	ENSP00000310565:p.Thr1020Met		63329797	NM_032160	Q17RH1|Q6P5Z3	Missense_Mutation	SNP	ENST00000310045.7	37	CCDS11995.1	.	.	.	.	.	.	.	.	.	.	G	17.91	3.505111	0.64410	.	.	ENSG00000171451	ENST00000310045;ENST00000397964	T	0.22134	1.97	5.17	5.17	0.71159	Sulfotransferase domain (1);	0.420052	0.22620	U	0.057720	T	0.44265	0.1285	L	0.60455	1.87	0.38428	D	0.94637	D	0.89917	1.0	D	0.67231	0.95	T	0.46105	-0.9215	10	0.72032	D	0.01	-12.3842	18.6816	0.91548	0.0:0.0:1.0:0.0	.	1010	Q8IZU8	DSEL_HUMAN	M	1020;1010	ENSP00000310565:T1020M	ENSP00000310565:T1020M	T	-	2	0	DSEL	63329797	1.000000	0.71417	0.965000	0.40720	0.975000	0.68041	5.452000	0.66638	2.403000	0.81681	0.563000	0.77884	ACG		0.423	DSEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256221.1	NM_032160	
DDX54	79039	hgsc.bcm.edu	37	12	113614668	113614668	+	Silent	SNP	G	G	A	rs143973951	byFrequency	TCGA-AA-3521-01A-01W-0831-10	TCGA-AA-3521-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	TCGA-AA-3521-01A-01W-0831-10	TCGA-AA-3521-10A-01W-0831-10	g.chr12:113614668G>A	ENST00000306014.5	-	7	756	c.729C>T	c.(727-729)taC>taT	p.Y243Y	DDX54_ENST00000314045.7_Silent_p.Y243Y|Y_RNA_ENST00000364338.1_RNA	NM_024072.3	NP_076977.3	Q8TDD1	DDX54_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 54	243	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				ATP catabolic process (GO:0006200)|intracellular estrogen receptor signaling pathway (GO:0030520)|regulation of transcription, DNA-templated (GO:0006355)|RNA metabolic process (GO:0016070)|RNA processing (GO:0006396)|transcription, DNA-templated (GO:0006351)	membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|estrogen receptor binding (GO:0030331)|poly(A) RNA binding (GO:0044822)|receptor binding (GO:0005102)|transcription corepressor activity (GO:0003714)	p.Y243Y(1)		breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	31						CGAACACCACGTATTCCACAC	0.567													G|||	4	0.000798722	0.0	0.0	5008	,	,		19851	0.004		0.0	False		,,,				2504	0.0				p.Y243Y												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C729T	12						.						165.0	136.0	146.0					12																	113614668		2203	4300	6503	112099051	SO:0001819	synonymous_variant	79039	exon7			AF144056	CCDS31907.1, CCDS44984.1	12q24.11	2006-01-30				ENSG00000123064		"""DEAD-boxes"""	20084	protein-coding gene	gene with protein product		611665				12466272	Standard	NM_001111322		Approved	MGC2835, APR-5, DP97	uc001tuq.4	Q8TDD1	OTTHUMG00000169676	ENST00000306014.5:c.729C>T	12.37:g.113614668G>A			112099051	NM_024072	Q86YT8|Q9BRZ1	Silent	SNP	ENST00000306014.5	37	CCDS31907.1																																																																																				0.567	DDX54-002	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405435.1	NM_024072	
CD163L1	283316	hgsc.bcm.edu	37	12	7556228	7556228	+	Silent	SNP	A	A	G			TCGA-AA-3521-01A-01W-0831-10	TCGA-AA-3521-10A-01W-0831-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AA-3521-01A-01W-0831-10	TCGA-AA-3521-10A-01W-0831-10	g.chr12:7556228A>G	ENST00000313599.3	-	6	1368	c.1311T>C	c.(1309-1311)tcT>tcC	p.S437S	CD163L1_ENST00000416109.2_Silent_p.S447S|CD163L1_ENST00000396630.1_Silent_p.S437S			Q9NR16	C163B_HUMAN	CD163 molecule-like 1	437	SRCR 4. {ECO:0000255|PROSITE- ProRule:PRU00196}.					extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	scavenger receptor activity (GO:0005044)	p.S437S(1)		breast(5)|central_nervous_system(3)|endometrium(8)|kidney(3)|large_intestine(18)|lung(37)|ovary(8)|prostate(3)|skin(6)|stomach(1)|urinary_tract(4)	96						TCCCAGTGCAAGATATGCTGT	0.448																																					p.S437S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T1311C	12						.						144.0	134.0	138.0					12																	7556228		2203	4300	6503	7447495	SO:0001819	synonymous_variant	283316	exon6			AF264014	CCDS8577.1, CCDS73434.1	12p13.31	2006-03-28	2006-03-28			ENSG00000177675			30375	protein-coding gene	gene with protein product		606079	"""CD163 antigen-like 1"""			11124526, 11086079	Standard	XM_005253348		Approved	M160, CD163B	uc001qsy.3	Q9NR16		ENST00000313599.3:c.1311T>C	12.37:g.7556228A>G			7447495	NM_174941	B4E0G7|C9JHR7|E7EVK4|Q2M3B7|Q6UWC2	Silent	SNP	ENST00000313599.3	37	CCDS8577.1																																																																																				0.448	CD163L1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399329.1	NM_174941	
KRAS	3845	hgsc.bcm.edu	37	12	25380276	25380276	+	Missense_Mutation	SNP	T	T	A	rs121913240		TCGA-AA-3521-01A-01W-0831-10	TCGA-AA-3521-10A-01W-0831-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AA-3521-01A-01W-0831-10	TCGA-AA-3521-10A-01W-0831-10	g.chr12:25380276T>A	ENST00000256078.4	-	3	245	c.182A>T	c.(181-183)cAa>cTa	p.Q61L	KRAS_ENST00000311936.3_Missense_Mutation_p.Q61L|KRAS_ENST00000557334.1_Intron|AC087239.1_ENST00000594112.1_5'Flank	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	61			Q -> H (in lung carcinoma; dbSNP:rs17851045). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:16533793, ECO:0000269|Ref.7}.|Q -> R (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to glucocorticoid (GO:0051384)|response to mineralocorticoid (GO:0051385)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	focal adhesion (GO:0005925)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GMP binding (GO:0019002)|GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.Q61L(73)|p.Q61R(56)|p.Q61P(12)	UBE2L3/KRAS(2)	NS(6)|adrenal_gland(1)|autonomic_ganglia(3)|biliary_tract(532)|bone(2)|breast(32)|central_nervous_system(14)|cervix(50)|endometrium(411)|eye(4)|gastrointestinal_tract_(site_indeterminate)(7)|genital_tract(1)|haematopoietic_and_lymphoid_tissue(385)|kidney(8)|large_intestine(15267)|liver(29)|lung(3407)|oesophagus(16)|ovary(612)|pancreas(3739)|penis(1)|peritoneum(6)|prostate(96)|salivary_gland(6)|skin(45)|small_intestine(68)|soft_tissue(88)|stomach(207)|testis(17)|thymus(5)|thyroid(159)|upper_aerodigestive_tract(68)|urinary_tract(57)	25349	all_cancers(2;1e-35)|all_epithelial(2;1.97e-38)|all_lung(3;2.1e-23)|Lung NSC(3;1.16e-22)|Acute lymphoblastic leukemia(6;0.00231)|all_hematologic(7;0.00259)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12)		OV - Ovarian serous cystadenocarcinoma(3;1.23e-21)|Epithelial(3;1.31e-20)|all cancers(3;5.45e-18)|STAD - Stomach adenocarcinoma(2;2.68e-05)			GTACTCCTCTTGACCTGCTGT	0.418	Q61L(NCIH650_LUNG)|Q61L(SW948_LARGE_INTESTINE)|Q61R(PANC0213_PANCREAS)	119	Mis		"""pancreatic, colorectal, lung, thyroid, AML, others"""				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)																											p.Q61L	Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)		Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		"""L, E, M, O"""	KRAS,thyroid,NS,Substitution - Missense,0	.	141	Substitution - Missense(141)	large_intestine(63)|lung(27)|thyroid(14)|haematopoietic_and_lymphoid_tissue(9)|pancreas(6)|skin(5)|stomach(3)|cervix(3)|upper_aerodigestive_tract(2)|soft_tissue(1)|central_nervous_system(1)|biliary_tract(1)|endometrium(1)|urinary_tract(1)|gastrointestinal_tract_(site_indeterminate)(1)|breast(1)|prostate(1)|kidney(1)	c.A182T	12						.						109.0	97.0	101.0					12																	25380276		2203	4300	6503	25271543	SO:0001583	missense	3845	exon3	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	BC010502	CCDS8702.1, CCDS8703.1	12p12.1	2014-09-17	2013-07-08	2005-01-24	ENSG00000133703	ENSG00000133703			6407	protein-coding gene	gene with protein product		190070	"""v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog"", ""v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog"""	KRAS2			Standard	NM_004985		Approved	KRAS1	uc001rgp.1	P01116		ENST00000256078.4:c.182A>T	12.37:g.25380276T>A	ENSP00000256078:p.Gln61Leu		25271543	NM_004985	A8K8Z5|B0LPF9|P01118|Q96D10	Missense_Mutation	SNP	ENST00000256078.4	37	CCDS8703.1	.	.	.	.	.	.	.	.	.	.	T	28.1	4.889058	0.91814	.	.	ENSG00000133703	ENST00000311936;ENST00000256078	D;D	0.83992	-1.79;-1.79	5.77	5.77	0.91146	Small GTP-binding protein domain (1);	0.049057	0.85682	D	0.000000	D	0.92097	0.7495	H	0.96333	3.805	0.80722	D	1	D;P	0.58970	0.984;0.812	P;P	0.53689	0.732;0.69	D	0.94295	0.7532	10	0.72032	D	0.01	.	15.5753	0.76373	0.0:0.0:0.0:1.0	.	61;61	P01116-2;P01116	.;RASK_HUMAN	L	61	ENSP00000308495:Q61L;ENSP00000256078:Q61L	ENSP00000256078:Q61L	Q	-	2	0	KRAS	25271543	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.983000	0.88140	2.326000	0.78906	0.533000	0.62120	CAA		0.418	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	NM_033360	
MON2	23041	hgsc.bcm.edu	37	12	62938690	62938690	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3521-01A-01W-0831-10	TCGA-AA-3521-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AA-3521-01A-01W-0831-10	TCGA-AA-3521-10A-01W-0831-10	g.chr12:62938690C>T	ENST00000393632.2	+	21	2870	c.2479C>T	c.(2479-2481)Cca>Tca	p.P827S	MON2_ENST00000552115.1_Missense_Mutation_p.P827S|MON2_ENST00000393630.3_Missense_Mutation_p.P828S|MON2_ENST00000393629.2_Missense_Mutation_p.P827S|MON2_ENST00000546600.1_Missense_Mutation_p.P827S|MON2_ENST00000280379.6_Missense_Mutation_p.P828S|MON2_ENST00000552738.1_Missense_Mutation_p.P804S|RNU6-399P_ENST00000365164.1_RNA	NM_015026.2	NP_055841.2	Q7Z3U7	MON2_HUMAN	MON2 homolog (S. cerevisiae)	827					actin cytoskeleton organization (GO:0030036)|Golgi to endosome transport (GO:0006895)|positive regulation of GTPase activity (GO:0043547)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	extracellular vesicular exosome (GO:0070062)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)	p.P827S(1)		NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(3)|large_intestine(15)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	57			BRCA - Breast invasive adenocarcinoma(9;0.218)	GBM - Glioblastoma multiforme(28;0.128)		CTGCCAGCATCCAAACTCTCG	0.333																																					p.P827S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2479T	12						.						55.0	55.0	55.0					12																	62938690		2202	4300	6502	61224957	SO:0001583	missense	23041	exon21				CCDS31849.1, CCDS61175.1, CCDS61177.1, CCDS61178.1	12q14.1	2014-08-12	2006-04-04		ENSG00000061987	ENSG00000061987			29177	protein-coding gene	gene with protein product			"""MON2 homolog (yeast)"""			16301316, 24285343	Standard	NM_015026		Approved	KIAA1040	uc001sre.3	Q7Z3U7	OTTHUMG00000169992	ENST00000393632.2:c.2479C>T	12.37:g.62938690C>T	ENSP00000377252:p.Pro827Ser		61224957	NM_015026	A5D8U7|A7E2Y0|B9EGP5|F8VWA6|F8W1Z6|Q86TA2|Q8N3I5|Q8NAI0|Q8NHE2|Q9UPW1	Missense_Mutation	SNP	ENST00000393632.2	37	CCDS31849.1	.	.	.	.	.	.	.	.	.	.	C	16.64	3.178938	0.57692	.	.	ENSG00000061987	ENST00000393632;ENST00000393630;ENST00000280379;ENST00000546600;ENST00000552738;ENST00000393629;ENST00000552115	T;T;T;T;T;T;T	0.65732	-0.17;-0.17;-0.17;-0.17;-0.17;-0.17;1.33	5.76	4.87	0.63330	.	0.000000	0.85682	D	0.000000	T	0.64227	0.2579	L	0.31664	0.95	0.80722	D	1	B;P;B;D	0.53151	0.434;0.589;0.216;0.958	B;B;B;P	0.56163	0.178;0.372;0.237;0.793	T	0.62765	-0.6785	9	.	.	.	-9.9247	16.3158	0.82923	0.1331:0.8669:0.0:0.0	.	827;804;827;827	B9EGP5;F8VWA6;F8W1Z6;Q7Z3U7-4	.;.;.;.	S	827;828;828;827;804;827;827	ENSP00000377252:P827S;ENSP00000377250:P828S;ENSP00000280379:P828S;ENSP00000447407:P827S;ENSP00000449215:P804S;ENSP00000377249:P827S;ENSP00000446635:P827S	.	P	+	1	0	MON2	61224957	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	4.946000	0.63576	1.420000	0.47138	0.650000	0.86243	CCA		0.333	MON2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406767.3	NM_015026	
TBX3	6926	hgsc.bcm.edu	37	12	115118889	115118889	+	Nonsense_Mutation	SNP	A	A	T			TCGA-AA-3521-01A-01W-0831-10	TCGA-AA-3521-10A-01W-0831-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AA-3521-01A-01W-0831-10	TCGA-AA-3521-10A-01W-0831-10	g.chr12:115118889A>T	ENST00000257566.3	-	2	841	c.452T>A	c.(451-453)tTa>tAa	p.L151*	TBX3_ENST00000349155.2_Nonsense_Mutation_p.L151*	NM_016569.3	NP_057653.3	O15119	TBX3_HUMAN	T-box 3	151					anterior/posterior axis specification, embryo (GO:0008595)|atrioventricular bundle cell differentiation (GO:0003167)|blood vessel development (GO:0001568)|branching involved in mammary gland duct morphogenesis (GO:0060444)|cardiac muscle cell fate commitment (GO:0060923)|cell aging (GO:0007569)|cellular senescence (GO:0090398)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|female genitalia development (GO:0030540)|follicle-stimulating hormone secretion (GO:0046884)|forelimb morphogenesis (GO:0035136)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|limbic system development (GO:0021761)|luteinizing hormone secretion (GO:0032275)|male genitalia development (GO:0030539)|mammary gland development (GO:0030879)|mammary placode formation (GO:0060596)|mesoderm morphogenesis (GO:0048332)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epithelial cell differentiation (GO:0030857)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|organ morphogenesis (GO:0009887)|outflow tract morphogenesis (GO:0003151)|palate development (GO:0060021)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell proliferation (GO:0008284)|positive regulation of stem cell proliferation (GO:2000648)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|sinoatrial node cell development (GO:0060931)|skeletal system development (GO:0001501)|specification of organ position (GO:0010159)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)|ventricular septum morphogenesis (GO:0060412)	nucleus (GO:0005634)	RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.L151*(1)		breast(5)|endometrium(1)|kidney(1)|large_intestine(6)|lung(21)|ovary(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	47	Medulloblastoma(191;0.163)|all_neural(191;0.178)			BRCA - Breast invasive adenocarcinoma(302;0.0574)		GTCCATCAATAAAATGTATTT	0.383																																					p.L151X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.T452A	12						.						131.0	138.0	136.0					12																	115118889		2203	4300	6503	113603272	SO:0001587	stop_gained	6926	exon2			BC025258	CCDS9175.1, CCDS9176.1	12q24.21	2013-09-05	2008-07-31		ENSG00000135111	ENSG00000135111		"""T-boxes"""	11602	protein-coding gene	gene with protein product		601621	"""ulnar mammary syndrome"""	UMS		8988164	Standard	NM_005996		Approved	TBX3-ISO, XHL	uc001tvt.1	O15119	OTTHUMG00000169586	ENST00000257566.3:c.452T>A	12.37:g.115118889A>T	ENSP00000257566:p.Leu151*		113603272	NM_005996	Q8TB20|Q9UKF8	Nonsense_Mutation	SNP	ENST00000257566.3	37	CCDS9176.1	.	.	.	.	.	.	.	.	.	.	A	46	12.937916	0.99707	.	.	ENSG00000135111	ENST00000349155;ENST00000257566;ENST00000361100	.	.	.	5.75	5.75	0.90469	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.2319	0.73398	1.0:0.0:0.0:0.0	.	.	.	.	X	151	.	ENSP00000257566:L151X	L	-	2	0	TBX3	113603272	1.000000	0.71417	0.977000	0.42913	0.954000	0.61252	8.959000	0.93110	2.197000	0.70478	0.533000	0.62120	TTA		0.383	TBX3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000404947.2	NM_016569, NM_005996	
TGM5	9333	hgsc.bcm.edu	37	15	43545061	43545061	+	Missense_Mutation	SNP	G	G	T	rs74487005		TCGA-AA-3521-01A-01W-0831-10	TCGA-AA-3521-10A-01W-0831-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AA-3521-01A-01W-0831-10	TCGA-AA-3521-10A-01W-0831-10	g.chr15:43545061G>T	ENST00000220420.5	-	6	765	c.758C>A	c.(757-759)gCg>gAg	p.A253E	TGM5_ENST00000349114.4_Missense_Mutation_p.A171E	NM_201631.3	NP_963925.2	O43548	TGM5_HUMAN	transglutaminase 5	253					cellular protein modification process (GO:0006464)|epidermis development (GO:0008544)|peptide cross-linking (GO:0018149)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)	p.A253E(1)		central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(11)|lung(15)|skin(6)|urinary_tract(1)	44		all_cancers(109;1.37e-14)|all_epithelial(112;1.26e-12)|Lung NSC(122;2.46e-08)|all_lung(180;2.75e-07)|Melanoma(134;0.0476)|Colorectal(260;0.216)		GBM - Glioblastoma multiforme(94;4e-07)	L-Glutamine(DB00130)	CGTCCACTCCGCAGGGTTGGC	0.562																																					p.A171E												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C512A	15						.						83.0	73.0	77.0					15																	43545061		2202	4299	6501	41332353	SO:0001583	missense	9333	exon5			AF035960	CCDS32211.1, CCDS32212.1	15q15	2004-07-07				ENSG00000104055		"""Transglutaminases"""	11781	protein-coding gene	gene with protein product		603805				9452468, 11390390	Standard	NM_201631		Approved	TGX	uc001zrd.2	O43548		ENST00000220420.5:c.758C>A	15.37:g.43545061G>T	ENSP00000220420:p.Ala253Glu		41332353	NM_004245	O43549|Q0VF40|Q9UEZ4	Missense_Mutation	SNP	ENST00000220420.5	37	CCDS32212.1	.	.	.	.	.	.	.	.	.	.	G	12.34	1.908033	0.33721	.	.	ENSG00000104055	ENST00000220420;ENST00000349114;ENST00000396996	D;D	0.89196	-2.48;-2.48	4.64	1.7	0.24286	.	0.194845	0.44688	D	0.000440	D	0.82273	0.5001	L	0.27053	0.805	0.09310	N	1	P;P	0.45212	0.853;0.677	B;P	0.45406	0.413;0.479	T	0.73525	-0.3955	10	0.44086	T	0.13	-2.2943	8.8617	0.35261	0.2576:0.0:0.7424:0.0	.	171;253	O43548-2;O43548	.;TGM5_HUMAN	E	253;171;252	ENSP00000220420:A253E;ENSP00000220419:A171E	ENSP00000220420:A253E	A	-	2	0	TGM5	41332353	0.000000	0.05858	0.068000	0.19968	0.315000	0.28087	0.420000	0.21263	0.145000	0.18977	-0.254000	0.11334	GCG		0.562	TGM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432257.1	NM_004245	
TGM7	116179	hgsc.bcm.edu	37	15	43571424	43571424	+	Missense_Mutation	SNP	G	G	A	rs369585501		TCGA-AA-3521-01A-01W-0831-10	TCGA-AA-3521-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AA-3521-01A-01W-0831-10	TCGA-AA-3521-10A-01W-0831-10	g.chr15:43571424G>A	ENST00000452443.2	-	11	1734	c.1730C>T	c.(1729-1731)aCg>aTg	p.T577M		NM_052955.2	NP_443187.1	Q96PF1	TGM7_HUMAN	transglutaminase 7	577					peptide cross-linking (GO:0018149)		metal ion binding (GO:0046872)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)	p.T577M(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(8)|lung(16)|ovary(2)|prostate(4)|skin(1)	39		all_cancers(109;2.12e-14)|all_epithelial(112;1.99e-12)|Lung NSC(122;2.46e-08)|all_lung(180;2.75e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;9.14e-07)	L-Glutamine(DB00130)	CTTTTCGTCCGTTAGCTTGTT	0.527																																					p.T577M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1730T	15						.	G	MET/THR	0,4404		0,0,2202	88.0	75.0	79.0		1730	2.4	0.8	15		79	1,8597	1.2+/-3.3	0,1,4298	no	missense	TGM7	NM_052955.2	81	0,1,6500	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	577/711	43571424	1,13001	2202	4299	6501	41358716	SO:0001583	missense	116179	exon11			AF363393	CCDS32213.1	15q15.2	2004-07-01				ENSG00000159495		"""Transglutaminases"""	30790	protein-coding gene	gene with protein product	"""transglutaminase Z"""	606776				11390390	Standard	NM_052955		Approved	TGMZ	uc001zrf.1	Q96PF1		ENST00000452443.2:c.1730C>T	15.37:g.43571424G>A	ENSP00000389466:p.Thr577Met		41358716	NM_052955		Missense_Mutation	SNP	ENST00000452443.2	37	CCDS32213.1	.	.	.	.	.	.	.	.	.	.	G	16.24	3.065996	0.55539	0.0	1.16E-4	ENSG00000159495	ENST00000452443	T	0.33216	1.42	5.42	2.36	0.29203	Transglutaminase, C-terminal (1);Immunoglobulin-like fold (1);	0.393578	0.26746	N	0.022704	T	0.43523	0.1251	M	0.74647	2.275	0.09310	N	1	D	0.76494	0.999	P	0.60117	0.869	T	0.16217	-1.0410	10	0.46703	T	0.11	-8.078	4.7992	0.13289	0.1956:0.1919:0.6125:0.0	.	577	Q96PF1	TGM7_HUMAN	M	577	ENSP00000389466:T577M	ENSP00000389466:T577M	T	-	2	0	TGM7	41358716	0.998000	0.40836	0.830000	0.32933	0.909000	0.53808	2.101000	0.41787	1.292000	0.44672	0.655000	0.94253	ACG		0.527	TGM7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432489.1	NM_052955	
CYP11A1	1583	hgsc.bcm.edu	37	15	74637399	74637399	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3521-01A-01W-0831-10	TCGA-AA-3521-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AA-3521-01A-01W-0831-10	TCGA-AA-3521-10A-01W-0831-10	g.chr15:74637399C>T	ENST00000268053.6	-	3	765	c.611G>A	c.(610-612)cGc>cAc	p.R204H	CYP11A1_ENST00000419019.2_Missense_Mutation_p.R46H|CYP11A1_ENST00000541301.1_Intron|CYP11A1_ENST00000358632.4_Missense_Mutation_p.R46H	NM_000781.2	NP_000772.2	P05108	CP11A_HUMAN	cytochrome P450, family 11, subfamily A, polypeptide 1	204					biphenyl metabolic process (GO:0018879)|C21-steroid hormone biosynthetic process (GO:0006700)|cellular response to antibiotic (GO:0071236)|cellular response to cadmium ion (GO:0071276)|cellular response to cAMP (GO:0071320)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|cellular response to interleukin-1 (GO:0071347)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to peptide hormone stimulus (GO:0071375)|cellular response to transforming growth factor beta stimulus (GO:0071560)|cellular response to tumor necrosis factor (GO:0071356)|cerebellum development (GO:0021549)|cholesterol metabolic process (GO:0008203)|dibenzo-p-dioxin metabolic process (GO:0018894)|estrogen biosynthetic process (GO:0006703)|fractalkine metabolic process (GO:0050756)|granulosa cell differentiation (GO:0060014)|hippocampus development (GO:0021766)|Leydig cell differentiation (GO:0033327)|maternal process involved in female pregnancy (GO:0060135)|mating behavior (GO:0007617)|phenol-containing compound metabolic process (GO:0018958)|phthalate metabolic process (GO:0018963)|progesterone biosynthetic process (GO:0006701)|response to alkaloid (GO:0043279)|response to corticosterone (GO:0051412)|response to drug (GO:0042493)|response to fungicide (GO:0060992)|response to gamma radiation (GO:0010332)|response to genistein (GO:0033595)|response to hydrogen peroxide (GO:0042542)|response to insecticide (GO:0017085)|response to L-ascorbic acid (GO:0033591)|response to salt stress (GO:0009651)|response to vitamin E (GO:0033197)|Schwann cell differentiation (GO:0014037)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|sterol metabolic process (GO:0016125)|testosterone biosynthetic process (GO:0061370)|vitamin D metabolic process (GO:0042359)|xenobiotic metabolic process (GO:0006805)	mitochondrial crista (GO:0030061)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|perikaryon (GO:0043204)	cholesterol binding (GO:0015485)|cholesterol monooxygenase (side-chain-cleaving) activity (GO:0008386)|heme binding (GO:0020037)|iron ion binding (GO:0005506)	p.R204H(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(3)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	20					Aminoglutethimide(DB00357)|Cholecalciferol(DB00169)|Clomifene(DB00882)|Clotrimazole(DB00257)|Dexamethasone(DB01234)|Digitoxin(DB01396)|Digoxin(DB00390)|Dinoprostone(DB00917)|Glutethimide(DB01437)|Ketoconazole(DB01026)|Omeprazole(DB00338)|Saquinavir(DB01232)|Terbinafine(DB00857)|Testosterone(DB00624)	AAAGGCAAAGCGGAACAGGTC	0.567																																					p.R204H	Esophageal Squamous(87;818 1337 4093 9268 37314)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G611A	15						.						87.0	80.0	82.0					15																	74637399		2197	4296	6493	72424452	SO:0001583	missense	1583	exon3			AK056794	CCDS32291.1, CCDS45303.1	15q23-q24	2010-05-04	2003-01-14	2003-01-17	ENSG00000140459	ENSG00000140459	1.14.15.6	"""Cytochrome P450s"""	2590	protein-coding gene	gene with protein product	"""cholesterol monooxygenase (side-chain-cleaving)"""	118485	"""cytochrome P450, subfamily XIA (cholesterol side chain cleavage)"""	CYP11A			Standard	NM_000781		Approved	P450SCC	uc002axt.2	P05108	OTTHUMG00000150716	ENST00000268053.6:c.611G>A	15.37:g.74637399C>T	ENSP00000268053:p.Arg204His		72424452	NM_000781	A8K8D5|B3KPU8|G3XAD7|Q15081|Q16805|Q8N1A7	Missense_Mutation	SNP	ENST00000268053.6	37	CCDS32291.1	.	.	.	.	.	.	.	.	.	.	C	15.99	2.995020	0.54041	.	.	ENSG00000140459	ENST00000268053;ENST00000358632;ENST00000419019;ENST00000450547	T;T;T	0.69306	-0.39;-0.39;-0.39	4.51	3.59	0.41128	.	0.238158	0.42682	N	0.000663	T	0.51822	0.1697	L	0.43646	1.37	0.80722	D	1	P;B;P	0.37466	0.596;0.205;0.596	B;B;B	0.29077	0.098;0.058;0.066	T	0.48468	-0.9033	10	0.33940	T	0.23	-16.8806	10.5091	0.44851	0.0:0.9076:0.0:0.0924	.	204;174;204	E7EPP8;B4DTE5;P05108	.;.;CP11A_HUMAN	H	204;46;46;116	ENSP00000268053:R204H;ENSP00000351455:R46H;ENSP00000405488:R46H	ENSP00000268053:R204H	R	-	2	0	CYP11A1	72424452	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	2.963000	0.49184	0.884000	0.36064	0.643000	0.83706	CGC		0.567	CYP11A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319737.1		
CHD2	1106	hgsc.bcm.edu	37	15	93521522	93521522	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3521-01A-01W-0831-10	TCGA-AA-3521-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AA-3521-01A-01W-0831-10	TCGA-AA-3521-10A-01W-0831-10	g.chr15:93521522C>T	ENST00000394196.4	+	21	3704	c.2636C>T	c.(2635-2637)gCg>gTg	p.A879V	CHD2_ENST00000557381.1_Missense_Mutation_p.A879V	NM_001271.3	NP_001262.3	O14647	CHD2_HUMAN	chromodomain helicase DNA binding protein 2	879	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				cellular response to DNA damage stimulus (GO:0006974)|chromatin modification (GO:0016568)|DNA duplex unwinding (GO:0032508)|hematopoietic stem cell differentiation (GO:0060218)|muscle organ development (GO:0007517)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|core promoter sequence-specific DNA binding (GO:0001046)|DNA binding (GO:0003677)|histone binding (GO:0042393)|poly(A) RNA binding (GO:0044822)	p.A879V(1)		breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|kidney(2)|large_intestine(10)|lung(17)|ovary(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	47	Lung NSC(78;0.00976)|all_lung(78;0.016)		BRCA - Breast invasive adenocarcinoma(143;0.0282)|OV - Ovarian serous cystadenocarcinoma(32;0.0814)			TTGGCTTCAGCGGACACAGTC	0.498																																					p.A879V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2636T	15						.						120.0	108.0	112.0					15																	93521522		2197	4298	6495	91322526	SO:0001583	missense	1106	exon21			AF006514	CCDS10374.2, CCDS45356.1	15q26	2008-07-18			ENSG00000173575	ENSG00000173575			1917	protein-coding gene	gene with protein product		602119				9326634	Standard	NM_001042572		Approved	FLJ38614, DKFZp547I1315, DKFZp781D1727, DKFZp686E01200	uc002bsp.3	O14647	OTTHUMG00000149845	ENST00000394196.4:c.2636C>T	15.37:g.93521522C>T	ENSP00000377747:p.Ala879Val		91322526	NM_001271	C6G482|Q96IP5	Missense_Mutation	SNP	ENST00000394196.4	37	CCDS10374.2	.	.	.	.	.	.	.	.	.	.	C	36	5.641643	0.96704	.	.	ENSG00000173575	ENST00000394196;ENST00000557381	T;T	0.77098	-1.07;-1.07	5.82	5.82	0.92795	Helicase, C-terminal (3);	0.000000	0.33938	U	0.004420	D	0.93494	0.7924	H	0.98276	4.19	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.997;1.0;0.994	D	0.95405	0.8493	10	0.87932	D	0	-17.6295	20.1001	0.97870	0.0:1.0:0.0:0.0	.	879;879;879	A8K9Y5;O14647;O14647-2	.;CHD2_HUMAN;.	V	879	ENSP00000377747:A879V;ENSP00000451366:A879V	ENSP00000377747:A879V	A	+	2	0	CHD2	91322526	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.792000	0.85828	2.760000	0.94817	0.655000	0.94253	GCG		0.498	CHD2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000313528.3	NM_001271	
PGM2	55276	hgsc.bcm.edu	37	4	37839220	37839220	+	Silent	SNP	G	G	A	rs143672303	byFrequency	TCGA-AA-3521-01A-01W-0831-10	TCGA-AA-3521-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AA-3521-01A-01W-0831-10	TCGA-AA-3521-10A-01W-0831-10	g.chr4:37839220G>A	ENST00000381967.4	+	4	526	c.426G>A	c.(424-426)acG>acA	p.T142T	PGM2_ENST00000544359.1_5'UTR|PGM2_ENST00000537241.1_Intron	NM_018290.3	NP_060760.2	Q96G03	PGM2_HUMAN	phosphoglucomutase 2	142					carbohydrate metabolic process (GO:0005975)|deoxyribose phosphate catabolic process (GO:0046386)|galactose catabolic process (GO:0019388)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|glycogen catabolic process (GO:0005980)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	magnesium ion binding (GO:0000287)|phosphoglucomutase activity (GO:0004614)|phosphopentomutase activity (GO:0008973)	p.T142T(1)		breast(1)|kidney(2)|large_intestine(3)|lung(10)|ovary(2)|urinary_tract(1)	19						CTGATATAACGCCAACCCCCT	0.448																																					p.T142T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G426A	4						.			0,4406		0,0,2203	178.0	161.0	167.0		426	-3.0	1.0	4	dbSNP_134	167	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	PGM2	NM_018290.3		0,2,6501	AA,AG,GG		0.0233,0.0,0.0154		142/613	37839220	2,13004	2203	4300	6503	37515615	SO:0001819	synonymous_variant	55276	exon4			BC010087	CCDS3443.1	4p14	2012-10-02			ENSG00000169299	ENSG00000169299	5.4.2.2		8906	protein-coding gene	gene with protein product	"""phosphopentomutase"""	172000				9549096	Standard	NM_018290		Approved	FLJ10983	uc011byb.1	Q96G03	OTTHUMG00000097813	ENST00000381967.4:c.426G>A	4.37:g.37839220G>A			37515615	NM_018290	B4E0G8|Q53FP5|Q5QTR0|Q9H0P9|Q9NV22	Silent	SNP	ENST00000381967.4	37	CCDS3443.1																																																																																				0.448	PGM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215079.2	NM_018290	
PDHA2	5161	hgsc.bcm.edu	37	4	96761911	96761911	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3521-01A-01W-0831-10	TCGA-AA-3521-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AA-3521-01A-01W-0831-10	TCGA-AA-3521-10A-01W-0831-10	g.chr4:96761911G>A	ENST00000295266.4	+	1	673	c.610G>A	c.(610-612)Gaa>Aaa	p.E204K		NM_005390.4	NP_005381.1	P29803	ODPAT_HUMAN	pyruvate dehydrogenase (lipoamide) alpha 2	204					glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|pyruvate metabolic process (GO:0006090)|tricarboxylic acid cycle (GO:0006099)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	pyruvate dehydrogenase (acetyl-transferring) activity (GO:0004739)	p.E204K(1)		NS(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(23)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	46		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;1.23e-06)		GCAGATAGCCGAAGCTTTCAA	0.458																																					p.E204K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G610A	4						.						56.0	61.0	59.0					4																	96761911		2203	4300	6503	96980934	SO:0001583	missense	5161	exon1				CCDS3644.1	4q22-q23	2009-11-09			ENSG00000163114	ENSG00000163114	1.2.4.1		8807	protein-coding gene	gene with protein product		179061		PDHAL			Standard	NM_005390		Approved		uc003htr.4	P29803	OTTHUMG00000130990	ENST00000295266.4:c.610G>A	4.37:g.96761911G>A	ENSP00000295266:p.Glu204Lys		96980934	NM_005390	B2R9Q3|Q0VDI5|Q4VC02|Q6NXQ1	Missense_Mutation	SNP	ENST00000295266.4	37	CCDS3644.1	.	.	.	.	.	.	.	.	.	.	G	26.5	4.740574	0.89573	.	.	ENSG00000163114	ENST00000295266	D	0.98862	-5.19	4.67	4.67	0.58626	Dehydrogenase, E1 component (1);	0.000000	0.85682	D	0.000000	D	0.99582	0.9849	H	0.99609	4.655	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.97365	0.9972	10	0.87932	D	0	-14.0377	15.4624	0.75369	0.0:0.0:1.0:0.0	.	204	P29803	ODPAT_HUMAN	K	204	ENSP00000295266:E204K	ENSP00000295266:E204K	E	+	1	0	PDHA2	96980934	1.000000	0.71417	0.311000	0.25182	0.975000	0.68041	8.852000	0.92215	2.587000	0.87381	0.467000	0.42956	GAA		0.458	PDHA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253608.1		
GRIPAP1	56850	hgsc.bcm.edu	37	X	48847416	48847416	+	Silent	SNP	C	C	T			TCGA-AA-3521-01A-01W-0831-10	TCGA-AA-3521-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AA-3521-01A-01W-0831-10	TCGA-AA-3521-10A-01W-0831-10	g.chrX:48847416C>T	ENST00000376441.1	-	7	598	c.564G>A	c.(562-564)ccG>ccA	p.P188P	GRIPAP1_ENST00000376444.3_Silent_p.P143P|GRIPAP1_ENST00000376425.3_Silent_p.P188P|GRIPAP1_ENST00000473581.1_5'UTR|GRIPAP1_ENST00000376423.4_Silent_p.P135P	NM_020137.3	NP_064522.3	Q4V328	GRAP1_HUMAN	GRIP1 associated protein 1	188						blood microparticle (GO:0072562)|endosome (GO:0005768)		p.P135P(2)|p.P188P(1)		breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(2)	10						CCTCTGCCAACGGCATGGGGG	0.597																																					p.P188P												.	.	3	Substitution - coding silent(3)	large_intestine(3)	c.G564A	X						.						67.0	63.0	64.0					X																	48847416		2203	4300	6503	48732360	SO:0001819	synonymous_variant	56850	exon7			AB032993	CCDS35248.1	Xp11.23	2008-02-05			ENSG00000068400	ENSG00000068400			18706	protein-coding gene	gene with protein product		300408				10896157	Standard	NM_020137		Approved	GRASP-1, GRASP1, KIAA1167, MPMGp800B12492Q3, DKFZp434P0630	uc004dly.1	Q4V328	OTTHUMG00000033192	ENST00000376441.1:c.564G>A	X.37:g.48847416C>T			48732360	NM_020137	A6NL78|Q3MJ75|Q4V327|Q4V330|Q5HYG1|Q6N046|Q96DH8|Q9NQ43|Q9ULQ3	Silent	SNP	ENST00000376441.1	37	CCDS35248.1																																																																																				0.597	GRIPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080970.2	NM_207672	
AMER1	139285	hgsc.bcm.edu	37	X	63412002	63412002	+	Nonsense_Mutation	SNP	C	C	A			TCGA-AA-3521-01A-01W-0831-10	TCGA-AA-3521-10A-01W-0831-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AA-3521-01A-01W-0831-10	TCGA-AA-3521-10A-01W-0831-10	g.chrX:63412002C>A	ENST00000330258.3	-	2	1437	c.1165G>T	c.(1165-1167)Gaa>Taa	p.E389*	AMER1_ENST00000403336.1_Nonsense_Mutation_p.E389*|AMER1_ENST00000374869.3_Nonsense_Mutation_p.E389*	NM_152424.3	NP_689637.3	Q5JTC6	AMER1_HUMAN	APC membrane recruitment protein 1	389	Glu-rich.				adipose tissue development (GO:0060612)|bone development (GO:0060348)|mesenchymal cell differentiation involved in kidney development (GO:0072161)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|regulation of canonical Wnt signaling pathway (GO:0060828)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)	p.0?(67)|p.E389*(2)									tcctctaattccacctcttct	0.498																																					p.E389X												.	.	69	Whole gene deletion(67)|Substitution - Nonsense(2)	kidney(65)|large_intestine(3)|ovary(1)	c.G1165T	X						.						169.0	164.0	166.0					X																	63412002		2203	4300	6503	63328727	SO:0001587	stop_gained	139285	exon2			AK097146	CCDS14377.2	Xq11.1	2012-12-03	2012-12-03	2012-12-03	ENSG00000184675	ENSG00000184675		"""-"""	26837	protein-coding gene	gene with protein product	"""Wilms Tumor on the X"", ""adenomatous polyposis coli membrane recruitment 1"""	300647	"""family with sequence similarity 123B"""	FAM123B		21304492, 21498506, 20843316	Standard	NM_152424		Approved	RP11-403E24.2, FLJ39827, WTX	uc004dvo.3	Q5JTC6	OTTHUMG00000021703	ENST00000330258.3:c.1165G>T	X.37:g.63412002C>A	ENSP00000329117:p.Glu389*		63328727	NM_152424	A2IB86|Q8N885	Nonsense_Mutation	SNP	ENST00000330258.3	37	CCDS14377.2	.	.	.	.	.	.	.	.	.	.	C	35	5.569746	0.96540	.	.	ENSG00000184675	ENST00000374869;ENST00000330258;ENST00000403336	.	.	.	5.2	4.33	0.51752	.	0.267142	0.38005	N	0.001846	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.12103	T	0.63	-14.8729	13.7592	0.62954	0.0:0.8488:0.1512:0.0	.	.	.	.	X	389	.	ENSP00000329117:E389X	E	-	1	0	FAM123B	63328727	0.988000	0.35896	0.835000	0.33067	0.306000	0.27790	3.647000	0.54403	1.298000	0.44778	0.600000	0.82982	GAA		0.498	AMER1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316584.1	NM_152424	
ATP2B3	492	hgsc.bcm.edu	37	X	152825308	152825308	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3521-01A-01W-0831-10	TCGA-AA-3521-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AA-3521-01A-01W-0831-10	TCGA-AA-3521-10A-01W-0831-10	g.chrX:152825308G>A	ENST00000349466.2	+	17	3073	c.2747G>A	c.(2746-2748)cGc>cAc	p.R916H	ATP2B3_ENST00000370186.1_Missense_Mutation_p.R902H|ATP2B3_ENST00000370181.2_Missense_Mutation_p.R902H|ATP2B3_ENST00000263519.4_Missense_Mutation_p.R916H|ATP2B3_ENST00000393842.1_Missense_Mutation_p.R902H|ATP2B3_ENST00000359149.3_Missense_Mutation_p.R916H|ATP2B3_ENST00000460549.1_3'UTR			Q16720	AT2B3_HUMAN	ATPase, Ca++ transporting, plasma membrane 3	916					blood coagulation (GO:0007596)|cell death (GO:0008219)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)|transport (GO:0006810)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|metal ion binding (GO:0046872)	p.R916H(2)|p.R902H(1)		NS(2)|breast(5)|endometrium(7)|large_intestine(8)|lung(23)|ovary(1)|pancreas(1)|skin(3)	50	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					CCGTACGGCCGCGACAAGCCC	0.597																																					p.R916H												.	.	3	Substitution - Missense(3)	large_intestine(3)	c.G2747A	X						.						87.0	69.0	75.0					X																	152825308		2203	4300	6503	152478502	SO:0001583	missense	492	exon16			U60414	CCDS14722.1, CCDS35440.1	Xq28	2014-07-18			ENSG00000067842	ENSG00000067842	3.6.3.8	"""ATPases / P-type"""	816	protein-coding gene	gene with protein product	"""plasma membrane calcium-transporting ATPase 3"", ""cilia and flagella associated protein 39"""	300014	"""spinocerebellar ataxia, X-linked 1"", ""cerebellar ataxia 2 (X-linked)"""	SCAX1, CLA2		8187550, 22912398	Standard	NM_021949		Approved	PMCA3, CFAP39	uc004fht.1	Q16720	OTTHUMG00000024202	ENST00000349466.2:c.2747G>A	X.37:g.152825308G>A	ENSP00000343886:p.Arg916His		152478502	NM_021949	B7WNR8|B7WNY5|Q12995|Q16858	Missense_Mutation	SNP	ENST00000349466.2	37	CCDS35440.1	.	.	.	.	.	.	.	.	.	.	G	28.1	4.888541	0.91814	.	.	ENSG00000067842	ENST00000370186;ENST00000349466;ENST00000393842;ENST00000359149;ENST00000263519;ENST00000370181	D;D;D;D;D;D	0.96200	-3.94;-3.94;-3.94;-3.94;-3.94;-3.94	5.32	5.32	0.75619	ATPase, P-type cation-transporter, C-terminal (1);ATPase, P-type,  transmembrane domain (1);	0.063219	0.64402	D	0.000005	D	0.98729	0.9573	H	0.98276	4.19	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.80764	0.994;0.99	D	0.99727	1.1011	10	0.72032	D	0.01	-30.5185	16.7389	0.85454	0.0:0.0:1.0:0.0	.	916;916	Q16720;Q16720-2	AT2B3_HUMAN;.	H	902;916;902;916;916;902	ENSP00000359205:R902H;ENSP00000343886:R916H;ENSP00000377425:R902H;ENSP00000352062:R916H;ENSP00000263519:R916H;ENSP00000359200:R902H	ENSP00000263519:R916H	R	+	2	0	ATP2B3	152478502	1.000000	0.71417	0.848000	0.33437	0.725000	0.41563	7.944000	0.87722	2.212000	0.71576	0.529000	0.55759	CGC		0.597	ATP2B3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060957.1	NM_021949	
AGFG1	3267	hgsc.bcm.edu	37	2	228398397	228398397	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3521-01A-01W-0831-10	TCGA-AA-3521-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AA-3521-01A-01W-0831-10	TCGA-AA-3521-10A-01W-0831-10	g.chr2:228398397C>T	ENST00000310078.8	+	7	1207	c.947C>T	c.(946-948)aCg>aTg	p.T316M	AGFG1_ENST00000409171.1_Missense_Mutation_p.T316M|AGFG1_ENST00000409315.1_Missense_Mutation_p.T316M|AGFG1_ENST00000373671.3_Missense_Mutation_p.T276M|AGFG1_ENST00000409979.2_Missense_Mutation_p.T340M	NM_001135188.1|NM_001135189.1|NM_004504.4	NP_001128660.1|NP_001128661.1|NP_004495.2	P52594	AGFG1_HUMAN	ArfGAP with FG repeats 1	316					cell differentiation (GO:0030154)|mRNA export from nucleus (GO:0006406)|multicellular organismal development (GO:0007275)|regulation of ARF GTPase activity (GO:0032312)|spermatogenesis (GO:0007283)	cytoplasmic vesicle (GO:0031410)|intracellular membrane-bounded organelle (GO:0043231)|nuclear pore (GO:0005643)	ARF GTPase activator activity (GO:0008060)|DNA binding (GO:0003677)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)	p.T316M(1)		central_nervous_system(1)|endometrium(1)|large_intestine(5)|liver(2)|lung(2)|ovary(1)|prostate(1)|skin(4)|stomach(1)	18						AAAGTTTCAACGAACAAAGCT	0.403																																					p.T316M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C947T	2						.						90.0	86.0	88.0					2																	228398397		2203	4300	6503	228106641	SO:0001583	missense	3267	exon7				CCDS2467.1, CCDS46533.1, CCDS46534.1, CCDS46535.1	2q36	2009-11-30	2008-09-22	2008-09-22	ENSG00000173744	ENSG00000173744		"""ADP-ribosylation factor GTPase activating proteins"""	5175	protein-coding gene	gene with protein product		600862	"""HIV-1 Rev binding protein"""	HRB		7637788	Standard	NM_004504		Approved	RIP, RAB	uc002vpd.2	P52594	OTTHUMG00000133186	ENST00000310078.8:c.947C>T	2.37:g.228398397C>T	ENSP00000312059:p.Thr316Met		228106641	NM_004504	B3KUL1|E9PHX7|Q15277|Q4VAS0|Q4VAS1|Q4VAS3|Q53QT8|Q53R11	Missense_Mutation	SNP	ENST00000310078.8	37	CCDS2467.1	.	.	.	.	.	.	.	.	.	.	C	14.32	2.501656	0.44455	.	.	ENSG00000173744	ENST00000409979;ENST00000542592;ENST00000310078;ENST00000409315;ENST00000373671;ENST00000409171	T;T;T;T;T	0.25579	1.88;1.89;1.89;1.79;1.89	5.14	5.14	0.70334	.	0.894044	0.09808	N	0.753201	T	0.19366	0.0465	L	0.29908	0.895	0.18873	N	0.999989	B;B;B;B	0.15719	0.013;0.004;0.014;0.002	B;B;B;B	0.12837	0.008;0.007;0.001;0.003	T	0.07139	-1.0788	10	0.44086	T	0.13	.	6.6795	0.23113	0.0:0.7782:0.0:0.2218	.	276;316;340;316	P52594-2;P52594-3;E9PHX7;P52594	.;.;.;AGFG1_HUMAN	M	340;325;316;316;276;316	ENSP00000387282:T340M;ENSP00000312059:T316M;ENSP00000387154:T316M;ENSP00000362775:T276M;ENSP00000387218:T316M	ENSP00000312059:T316M	T	+	2	0	AGFG1	228106641	0.996000	0.38824	0.720000	0.30636	0.989000	0.77384	5.303000	0.65738	2.395000	0.81488	0.655000	0.94253	ACG		0.403	AGFG1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256895.2	NM_004504	
OR13C3	138803	hgsc.bcm.edu	37	9	107298883	107298883	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3521-01A-01W-0831-10	TCGA-AA-3521-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AA-3521-01A-01W-0831-10	TCGA-AA-3521-10A-01W-0831-10	g.chr9:107298883C>T	ENST00000374781.2	-	1	254	c.212G>A	c.(211-213)gGc>gAc	p.G71D		NM_001001961.1	NP_001001961.1	Q8NGS6	O13C3_HUMAN	olfactory receptor, family 13, subfamily C, member 3	71						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.G71D(1)		endometrium(2)|large_intestine(7)|lung(7)|pancreas(1)|prostate(1)|skin(1)	19						AACACCATTGCCAATTAGAAT	0.388																																					p.G71D	GBM(86;1248 1274 14222 15028 46219)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G212A	9						.						125.0	108.0	114.0					9																	107298883		2203	4300	6503	106338704	SO:0001583	missense	138803	exon1				CCDS35089.1	9q31.1	2013-09-24			ENSG00000204246	ENSG00000204246		"""GPCR / Class A : Olfactory receptors"""	14704	protein-coding gene	gene with protein product							Standard	NM_001001961		Approved		uc004bcb.1	Q8NGS6	OTTHUMG00000020406	ENST00000374781.2:c.212G>A	9.37:g.107298883C>T	ENSP00000363913:p.Gly71Asp		106338704	NM_001001961	Q5VVG1|Q6IF52	Missense_Mutation	SNP	ENST00000374781.2	37	CCDS35089.1	.	.	.	.	.	.	.	.	.	.	C	17.26	3.345053	0.61073	.	.	ENSG00000204246	ENST00000374781	T	0.00538	6.71	4.81	4.81	0.61882	GPCR, rhodopsin-like superfamily (1);	0.000000	0.46758	D	0.000274	T	0.03959	0.0111	H	0.95114	3.625	0.32853	D	0.506941	D	0.89917	1.0	D	0.81914	0.995	T	0.01345	-1.1379	10	0.87932	D	0	.	15.7602	0.78073	0.0:1.0:0.0:0.0	.	71	Q8NGS6	O13C3_HUMAN	D	71	ENSP00000363913:G71D	ENSP00000363913:G71D	G	-	2	0	OR13C3	106338704	0.021000	0.18746	1.000000	0.80357	0.845000	0.48019	2.548000	0.45794	2.658000	0.90341	0.655000	0.94253	GGC		0.388	OR13C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053477.2		
PCDH20	64881	hgsc.bcm.edu	37	13	61986611	61986611	+	Nonsense_Mutation	SNP	C	C	A			TCGA-AA-3521-01A-01W-0831-10	TCGA-AA-3521-10A-01W-0831-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AA-3521-01A-01W-0831-10	TCGA-AA-3521-10A-01W-0831-10	g.chr13:61986611C>A	ENST00000409186.1	-	5	3726	c.1621G>T	c.(1621-1623)Gaa>Taa	p.E541*	PCDH20_ENST00000409204.4_Nonsense_Mutation_p.E541*			Q8N6Y1	PCD20_HUMAN	protocadherin 20	541	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)	p.E514*(1)		breast(3)|central_nervous_system(2)|endometrium(3)|kidney(4)|large_intestine(14)|liver(1)|lung(23)|ovary(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	58		Breast(118;0.195)|Prostate(109;0.229)		GBM - Glioblastoma multiforme(99;0.000118)		ATGGTTAGTTCTATTAAGGGT	0.413																																					p.E541X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.G1621T	13						.						152.0	156.0	155.0					13																	61986611		2203	4300	6503	60884612	SO:0001587	stop_gained	64881	exon2			AF169693	CCDS9442.2	13q21	2010-01-26			ENSG00000197991	ENSG00000197991		"""Cadherins / Protocadherins : Non-clustered"""	14257	protein-coding gene	gene with protein product		614449					Standard	NM_022843		Approved	PCDH13, FLJ22218	uc001vid.4	Q8N6Y1	OTTHUMG00000017012	ENST00000409186.1:c.1621G>T	13.37:g.61986611C>A	ENSP00000386653:p.Glu541*		60884612	NM_022843	A8K1K9|B1AQU2|Q8NDN4|Q9NRT9	Nonsense_Mutation	SNP	ENST00000409186.1	37	CCDS9442.2	.	.	.	.	.	.	.	.	.	.	C	39	7.775596	0.98483	.	.	ENSG00000197991	ENST00000409204;ENST00000409186;ENST00000358674	.	.	.	6.06	5.23	0.72850	.	0.000000	0.64402	D	0.000003	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.41790	T	0.15	.	17.014	0.86413	0.1285:0.8715:0.0:0.0	.	.	.	.	X	541;541;287	.	ENSP00000351500:E287X	E	-	1	0	PCDH20	60884612	1.000000	0.71417	1.000000	0.80357	0.910000	0.53928	4.025000	0.57225	1.586000	0.49944	-0.133000	0.14855	GAA		0.413	PCDH20-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333054.2	NM_022843	
SLITRK5	26050	hgsc.bcm.edu	37	13	88327735	88327735	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3521-01A-01W-0831-10	TCGA-AA-3521-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AA-3521-01A-01W-0831-10	TCGA-AA-3521-10A-01W-0831-10	g.chr13:88327735C>T	ENST00000325089.6	+	2	311	c.92C>T	c.(91-93)aCa>aTa	p.T31I	SLITRK5_ENST00000400028.3_Intron	NM_015567.1	NP_056382.1	O94991	SLIK5_HUMAN	SLIT and NTRK-like family, member 5	31					adult behavior (GO:0030534)|axonogenesis (GO:0007409)|cardiovascular system development (GO:0072358)|dendrite morphogenesis (GO:0048813)|grooming behavior (GO:0007625)|response to xenobiotic stimulus (GO:0009410)|skin development (GO:0043588)|striatum development (GO:0021756)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)		p.T31I(1)		breast(1)|central_nervous_system(2)|endometrium(6)|kidney(6)|large_intestine(14)|lung(40)|ovary(2)|pancreas(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(4)	81	all_neural(89;0.101)|Medulloblastoma(90;0.163)					TTTGCTGTAACATCTCTCGTC	0.463																																					p.T31I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C92T	13						.						156.0	133.0	141.0					13																	88327735		2203	4300	6503	87125736	SO:0001583	missense	26050	exon2			AB020725	CCDS9465.1	13q31.1	2004-04-16	2004-01-08		ENSG00000165300	ENSG00000165300			20295	protein-coding gene	gene with protein product		609680	"""leucine rich repeat containing 11"""	LRRC11		10048485, 14557068	Standard	NM_015567		Approved	bA364G4.2, KIAA0918	uc001vln.3	O94991	OTTHUMG00000017167	ENST00000325089.6:c.92C>T	13.37:g.88327735C>T	ENSP00000366283:p.Thr31Ile		87125736	NM_015567	B3KNB8|B4DSH5|Q5VT81	Missense_Mutation	SNP	ENST00000325089.6	37	CCDS9465.1	.	.	.	.	.	.	.	.	.	.	C	12.96	2.094278	0.36952	.	.	ENSG00000165300	ENST00000325089	T	0.59224	0.28	5.94	5.94	0.96194	.	0.220418	0.39274	N	0.001403	T	0.50531	0.1621	L	0.39898	1.24	0.80722	D	1	B	0.12013	0.005	B	0.10450	0.005	T	0.38001	-0.9681	9	.	.	.	-4.7452	17.8571	0.88767	0.0:1.0:0.0:0.0	.	31	O94991	SLIK5_HUMAN	I	31	ENSP00000366283:T31I	.	T	+	2	0	SLITRK5	87125736	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.459000	0.80802	2.826000	0.97356	0.561000	0.74099	ACA		0.463	SLITRK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045416.3		
CRTAC1	55118	hgsc.bcm.edu	37	10	99655008	99655008	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3521-01A-01W-0831-10	TCGA-AA-3521-10A-01W-0831-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AA-3521-01A-01W-0831-10	TCGA-AA-3521-10A-01W-0831-10	g.chr10:99655008C>A	ENST00000370597.3	-	11	1835	c.1480G>T	c.(1480-1482)Ggc>Tgc	p.G494C	CRTAC1_ENST00000370591.2_Missense_Mutation_p.G494C|CRTAC1_ENST00000298819.4_Missense_Mutation_p.G494C	NM_018058.6	NP_060528.3	Q9NQ79	CRAC1_HUMAN	cartilage acidic protein 1	494						extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)	p.G494C(1)		autonomic_ganglia(1)|breast(1)|endometrium(6)|kidney(3)|large_intestine(7)|lung(6)|ovary(6)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(1)	35		Colorectal(252;0.24)		Epithelial(162;2.18e-10)|all cancers(201;3.27e-09)		TCACCCAGGCCAAAGTGTGCC	0.617																																					p.G494C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1480T	10						.						72.0	64.0	67.0					10																	99655008		2203	4300	6503	99644998	SO:0001583	missense	55118	exon11			AJ276171	CCDS31266.1, CCDS55723.1	10q22	2007-12-03			ENSG00000095713	ENSG00000095713			14882	protein-coding gene	gene with protein product		606276				11139377	Standard	NM_018058		Approved	FLJ10320, CEP-68, ASPIC1	uc001kou.2	Q9NQ79	OTTHUMG00000018871	ENST00000370597.3:c.1480G>T	10.37:g.99655008C>A	ENSP00000359629:p.Gly494Cys		99644998	NM_018058	B1ALN4|Q5T4F8|Q8N4H6|Q8TE52|Q9NQ78|Q9NQ80|Q9NW46	Missense_Mutation	SNP	ENST00000370597.3	37	CCDS31266.1	.	.	.	.	.	.	.	.	.	.	C	25.2	4.613209	0.87359	.	.	ENSG00000095713	ENST00000413387;ENST00000370597;ENST00000298819;ENST00000309155;ENST00000370591	T;D;T;D;D	0.92348	-1.25;-3.02;-0.85;-2.65;-2.66	5.06	5.06	0.68205	ASPIC/UnbV (1);	0.000000	0.85682	D	0.000000	D	0.97685	0.9241	H	0.97707	4.06	0.80722	D	1	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.91635	0.998;0.975;0.999	D	0.99406	1.0929	10	0.87932	D	0	-26.1695	18.0162	0.89241	0.0:1.0:0.0:0.0	.	494;494;390	Q9NQ79-2;Q9NQ79;Q5T4F6	.;CRAC1_HUMAN;.	C	390;494;494;486;494	ENSP00000408445:G390C;ENSP00000359629:G494C;ENSP00000298819:G494C;ENSP00000310810:G486C;ENSP00000359623:G494C	ENSP00000298819:G494C	G	-	1	0	CRTAC1	99644998	1.000000	0.71417	1.000000	0.80357	0.860000	0.49131	7.683000	0.84093	2.339000	0.79563	0.462000	0.41574	GGC		0.617	CRTAC1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000049754.1	NM_018058	
APC	324	hgsc.bcm.edu	37	5	112175757	112175757	+	Nonsense_Mutation	SNP	T	T	A			TCGA-AA-3521-01A-01W-0831-10	TCGA-AA-3521-10A-01W-0831-10	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	TCGA-AA-3521-01A-01W-0831-10	TCGA-AA-3521-10A-01W-0831-10	g.chr5:112175757T>A	ENST00000457016.1	+	16	4846	c.4466T>A	c.(4465-4467)tTa>tAa	p.L1489*	APC_ENST00000257430.4_Nonsense_Mutation_p.L1489*|CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000508376.2_Nonsense_Mutation_p.L1489*			P25054	APC_HUMAN	adenomatous polyposis coli	1489	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.L1488fs*18(17)|p.T1487fs*17(10)|p.L1488fs*23(3)|p.L1489fs*18(3)|p.L1489fs*19(2)|p.?(1)|p.K1454fs*3(1)|p.L1488fs*13(1)|p.K1192fs*3(1)|p.T1487fs*23(1)|p.L1488fs*22(1)|p.L1489*(1)|p.H1490fs*24(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		GATACTTTATTACATTTTGCC	0.443		12	"""D, Mis, N, F, S"""		"""colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"""	"""colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"""			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											p.L1471X	NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"""E, M, O"""	.	.	43	Deletion - Frameshift(36)|Insertion - Frameshift(3)|Complex - frameshift(2)|Substitution - Nonsense(1)|Unknown(1)	large_intestine(39)|thyroid(1)|lung(1)|soft_tissue(1)|skin(1)	c.T4412A	5						.						69.0	70.0	70.0					5																	112175757		2202	4300	6502	112203656	SO:0001587	stop_gained	324	exon14	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Armadillo repeat containing"""	583	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 46"""	611731	"""adenomatosis polyposis coli"""			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.4466T>A	5.37:g.112175757T>A	ENSP00000413133:p.Leu1489*		112203656	NM_001127511	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	T	42	9.543472	0.99201	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376	.	.	.	6.16	6.16	0.99307	.	0.140258	0.49916	D	0.000132	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-6.1145	16.8061	0.85666	0.0:0.0:0.0:1.0	.	.	.	.	X	1489	.	.	L	+	2	0	APC	112203656	0.999000	0.42202	0.588000	0.28705	0.934000	0.57294	7.698000	0.84413	2.367000	0.80283	0.528000	0.53228	TTA		0.443	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038	
HDAC3	8841	hgsc.bcm.edu	37	5	141009658	141009658	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3521-01A-01W-0831-10	TCGA-AA-3521-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AA-3521-01A-01W-0831-10	TCGA-AA-3521-10A-01W-0831-10	g.chr5:141009658G>A	ENST00000305264.3	-	4	395	c.316C>T	c.(316-318)Cgt>Tgt	p.R106C		NM_003883.3	NP_003874.2	O15379	HDAC3_HUMAN	histone deacetylase 3	106	Histone deacetylase.				cellular lipid metabolic process (GO:0044255)|chromatin modification (GO:0016568)|circadian regulation of gene expression (GO:0032922)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell cycle (GO:0045786)|negative regulation of JNK cascade (GO:0046329)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|protein deacetylation (GO:0006476)|regulation of mitotic cell cycle (GO:0007346)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|spindle assembly (GO:0051225)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|histone deacetylase complex (GO:0000118)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|chromatin DNA binding (GO:0031490)|cyclin binding (GO:0030332)|enzyme binding (GO:0019899)|histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|protein deacetylase activity (GO:0033558)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)	p.R106C(1)		endometrium(1)|large_intestine(2)|lung(3)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	13			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		Vorinostat(DB02546)	CCTGTGTAACGCGAGCAGAAC	0.572																																					p.R106C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C316T	5						.						134.0	139.0	137.0					5																	141009658		2203	4300	6503	140989842	SO:0001583	missense	8841	exon4			AF059650	CCDS4264.1	5q31.1-q31.2	2008-07-18			ENSG00000171720	ENSG00000171720	3.5.1.98		4854	protein-coding gene	gene with protein product		605166				9501169, 9464271	Standard	NM_003883		Approved	RPD3, HD3, RPD3-2	uc003llf.2	O15379	OTTHUMG00000129629	ENST00000305264.3:c.316C>T	5.37:g.141009658G>A	ENSP00000302967:p.Arg106Cys		140989842	NM_003883	D3DQE1|O43268|Q9UEI5|Q9UEV0	Missense_Mutation	SNP	ENST00000305264.3	37	CCDS4264.1	.	.	.	.	.	.	.	.	.	.	G	20.5	4.002785	0.74932	.	.	ENSG00000171720	ENST00000305264	T	0.70516	-0.49	5.33	5.33	0.75918	Histone deacetylase domain (2);	0.000000	0.85682	D	0.000000	T	0.79149	0.4397	L	0.54908	1.71	0.80722	D	1	D	0.65815	0.995	P	0.57548	0.823	T	0.80569	-0.1324	10	0.72032	D	0.01	-16.3506	18.8002	0.92013	0.0:0.0:1.0:0.0	.	106	O15379	HDAC3_HUMAN	C	106	ENSP00000302967:R106C	ENSP00000302967:R106C	R	-	1	0	HDAC3	140989842	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.090000	0.57693	2.757000	0.94681	0.655000	0.94253	CGT		0.572	HDAC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251824.2	NM_003883	
