#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_ACHILLES_Lineage_Results_Top_Genes	i_BAM_File	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_Mutation_Status	i_ORegAnno_bin	i_Sequence_Source	i_Sequencer	i_Sequencing_Phase	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_match_norm_validation_allele1	i_refseq_mrna_id	i_secondary_variant_classification
ABCB1	5243	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	7	87183102	87183102	+	Missense_Mutation	SNP	T	T	C			TCGA-BP-5184-01A-01D-1429-08	TCGA-BP-5184-11A-01D-1429-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ddebed14-f47f-46e6-ac39-c74ed3363211	5d1f5125-65c2-4c47-843d-da1c531fdb04	g.chr7:87183102T>C	ENST00000265724.3	-	10	1391	c.974A>G	c.(973-975)gAa>gGa	p.E325G	ABCB1_ENST00000543898.1_Missense_Mutation_p.E261G	NM_000927.4	NP_000918.2	P08183	MDR1_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 1	325	ABC transmembrane type-1 1. {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.E325G(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)	AATAGAATATTCCCCTGAGAG	0.398																																																	1	Substitution - Missense(1)	kidney(1)											117.0	110.0	112.0					7																	87183102		2203	4300	6503	SO:0001583	missense	5243			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.974A>G	7.37:g.87183102T>C	ENSP00000265724:p.Glu325Gly	Somatic		WXS	Illumina HiSeq	Phase_I	A8K294|B5AK60|Q12755|Q14812	Missense_Mutation	SNP	ENST00000265724.3	37	CCDS5608.1	.	.	.	.	.	.	.	.	.	.	T	11.87	1.769017	0.31320	.	.	ENSG00000085563	ENST00000543174;ENST00000265724;ENST00000543898	T;T	0.79247	-1.25;-1.25	5.3	5.3	0.74995	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	0.169280	0.52532	D	0.000063	T	0.68220	0.2977	L	0.31371	0.925	0.44966	D	0.997988	B;B	0.14805	0.006;0.011	B;B	0.26094	0.016;0.066	T	0.64774	-0.6328	10	0.42905	T	0.14	-17.4675	11.5283	0.50593	0.0:0.0:0.1496:0.8504	.	261;325	B5AK60;P08183	.;MDR1_HUMAN	G	106;325;261	ENSP00000265724:E325G;ENSP00000444095:E261G	ENSP00000265724:E325G	E	-	2	0	ABCB1	87021038	0.954000	0.32549	0.782000	0.31804	0.267000	0.26476	4.974000	0.63771	2.129000	0.65627	0.528000	0.53228	GAA		0.398	ABCB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335444.2		NM_000927	
ALPK2	115701	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	18	56205081	56205081	+	Missense_Mutation	SNP	C	C	T			TCGA-BP-5184-01A-01D-1429-08	TCGA-BP-5184-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ddebed14-f47f-46e6-ac39-c74ed3363211	5d1f5125-65c2-4c47-843d-da1c531fdb04	g.chr18:56205081C>T	ENST00000361673.3	-	5	2551	c.2338G>A	c.(2338-2340)Gaa>Aaa	p.E780K	RP11-1151B14.4_ENST00000591360.1_RNA	NM_052947.3	NP_443179.3	Q86TB3	ALPK2_HUMAN	alpha-kinase 2	780						nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.E780K(1)|p.E146K(1)		NS(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(33)|ovary(7)|prostate(1)|skin(10)|upper_aerodigestive_tract(2)	84						TCTGTGGGTTCAGGGGAAGCA	0.537																																																	2	Substitution - Missense(2)	kidney(2)											155.0	140.0	145.0					18																	56205081		2203	4300	6503	SO:0001583	missense	115701			AY044450	CCDS11966.2	18q21.31	2013-01-11			ENSG00000198796	ENSG00000198796		"""Immunoglobulin superfamily / I-set domain containing"""	20565	protein-coding gene	gene with protein product	"""heart alpha-kinase"""					10021370	Standard	NM_052947		Approved	HAK	uc002lhj.4	Q86TB3	OTTHUMG00000132755	ENST00000361673.3:c.2338G>A	18.37:g.56205081C>T	ENSP00000354991:p.Glu780Lys	Somatic		WXS	Illumina HiSeq	Phase_I	Q6ZUX0|Q8NAT5|Q96L95	Missense_Mutation	SNP	ENST00000361673.3	37	CCDS11966.2	.	.	.	.	.	.	.	.	.	.	C	17.98	3.521097	0.64747	.	.	ENSG00000198796	ENST00000361673	T	0.47177	0.85	5.57	3.74	0.42951	.	1.540450	0.04021	N	0.299793	T	0.56441	0.1985	L	0.52573	1.65	0.09310	N	1	P;P	0.46912	0.886;0.728	P;B	0.48425	0.577;0.321	T	0.49380	-0.8946	10	0.72032	D	0.01	-0.617	12.4279	0.55557	0.0:0.6619:0.3381:0.0	.	780;780	Q86TB3-2;Q86TB3	.;ALPK2_HUMAN	K	780	ENSP00000354991:E780K	ENSP00000354991:E780K	E	-	1	0	ALPK2	54356061	0.026000	0.19158	0.003000	0.11579	0.016000	0.09150	1.316000	0.33620	0.680000	0.31366	0.591000	0.81541	GAA		0.537	ALPK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256126.1		NM_052947	
VPS51	738	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	64875906	64875906	+	Silent	SNP	C	C	A			TCGA-BP-5184-01A-01D-1429-08	TCGA-BP-5184-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ddebed14-f47f-46e6-ac39-c74ed3363211	5d1f5125-65c2-4c47-843d-da1c531fdb04	g.chr11:64875906C>A	ENST00000279281.3	+	5	1055	c.963C>A	c.(961-963)gcC>gcA	p.A321A	AP003068.9_ENST00000528887.1_RNA|VPS51_ENST00000527646.1_3'UTR	NM_013265.2	NP_037397.2	Q9UID3	VPS51_HUMAN	vacuolar protein sorting 51 homolog (S. cerevisiae)	321					autophagy (GO:0006914)|lipid transport (GO:0006869)|protein transport (GO:0015031)|retrograde transport, endosome to Golgi (GO:0042147)	GARP complex (GO:0000938)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)		p.A321A(1)									TGGCGGCGGCCTACCAGGAGC	0.706																																																	1	Substitution - coding silent(1)	kidney(1)											16.0	21.0	20.0					11																	64875906		2193	4290	6483	SO:0001819	synonymous_variant	0			AF024631	CCDS8093.1	11q13.1	2012-07-19	2012-07-19	2012-07-19	ENSG00000149823	ENSG00000149823			1172	protein-coding gene	gene with protein product	"""fat-free homolog (zebrafish)"""	615738	"""chromosome 11 open reading frame 3"", ""chromosome 11 open reading frame 2"""	C11orf3, C11orf2		9286704, 20685960	Standard	NM_013265		Approved	ANG2, ANG3, FFR	uc001ocr.2	Q9UID3	OTTHUMG00000165600	ENST00000279281.3:c.963C>A	11.37:g.64875906C>A		Somatic		WXS	Illumina HiSeq	Phase_I	Q6PJV5|Q7L8A6|Q8WZ35|Q96DF4|Q96GR3	Silent	SNP	ENST00000279281.3	37	CCDS8093.1																																																																																				0.706	VPS51-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385217.1		NM_013265	
CACHD1	57685	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	65117974	65117974	+	Silent	SNP	T	T	C			TCGA-BP-5184-01A-01D-1429-08	TCGA-BP-5184-11A-01D-1429-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ddebed14-f47f-46e6-ac39-c74ed3363211	5d1f5125-65c2-4c47-843d-da1c531fdb04	g.chr1:65117974T>C	ENST00000371073.2	+	10	1521	c.1521T>C	c.(1519-1521)acT>acC	p.T507T	CACHD1_ENST00000290039.5_Silent_p.T456T|CACHD1_ENST00000495994.1_3'UTR			Q5VU97	CAHD1_HUMAN	cache domain containing 1	507	Cache 1.				calcium ion transport (GO:0006816)	integral component of membrane (GO:0016021)		p.T456T(1)		breast(4)|endometrium(3)|kidney(3)|large_intestine(20)|lung(14)|ovary(2)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	55						CTTCCTATACTTTTCTCATAG	0.343																																																	1	Substitution - coding silent(1)	kidney(1)											174.0	148.0	157.0					1																	65117974		2203	4300	6503	SO:0001819	synonymous_variant	57685			AB046793	CCDS628.2	1p31.3	2008-02-05	2005-10-11	2005-10-11	ENSG00000158966	ENSG00000158966			29314	protein-coding gene	gene with protein product			"""von Willebrand factor type A and cache domain containing 1"""	VWCD1		10997877	Standard	NM_020925		Approved	KIAA1573	uc001dbo.1	Q5VU97	OTTHUMG00000009030	ENST00000371073.2:c.1521T>C	1.37:g.65117974T>C		Somatic		WXS	Illumina HiSeq	Phase_I	Q49AE9|Q658T4|Q7Z3P2|Q9H7W4|Q9H9W3|Q9HCJ9	Silent	SNP	ENST00000371073.2	37																																																																																					0.343	CACHD1-201	KNOWN	basic	protein_coding	protein_coding			NM_020925	
CDK5RAP1	51654	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	20	31946924	31946924	+	Silent	SNP	G	G	A			TCGA-BP-5184-01A-01D-1429-08	TCGA-BP-5184-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ddebed14-f47f-46e6-ac39-c74ed3363211	5d1f5125-65c2-4c47-843d-da1c531fdb04	g.chr20:31946924G>A	ENST00000357886.4	-	15	1884	c.1731C>T	c.(1729-1731)acC>acT	p.T577T	CDK5RAP1_ENST00000339269.5_Silent_p.T486T|CDK5RAP1_ENST00000346416.2_Silent_p.T563T|CDK5RAP1_ENST00000473997.1_Silent_p.T473T			Q96SZ6	CK5P1_HUMAN	CDK5 regulatory subunit associated protein 1	577	CDK5R1-binding.|TRAM.				brain development (GO:0007420)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|regulation of neuron differentiation (GO:0045664)|tRNA modification (GO:0006400)	cytoplasm (GO:0005737)	4 iron, 4 sulfur cluster binding (GO:0051539)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)|transferase activity (GO:0016740)	p.T563T(1)		endometrium(2)|kidney(2)|large_intestine(3)|lung(12)|ovary(3)|skin(3)|urinary_tract(1)	26						AACTGGCTGAGGTGATCTGAA	0.502																																																	1	Substitution - coding silent(1)	kidney(1)											107.0	98.0	101.0					20																	31946924		2203	4300	6503	SO:0001819	synonymous_variant	51654			AF152097	CCDS13219.1, CCDS63255.1	20q11.21	2012-09-20	2002-07-22	2002-07-26	ENSG00000101391	ENSG00000101391			15880	protein-coding gene	gene with protein product		608200	"""chromosome 20 open reading frame 34"""	C20orf34		10721722, 11882646, 15329498	Standard	NM_016408		Approved	CGI-05, HSPC167, C42	uc002wyy.4	Q96SZ6	OTTHUMG00000032256	ENST00000357886.4:c.1731C>T	20.37:g.31946924G>A		Somatic		WXS	Illumina HiSeq	Phase_I	A8K7R0|Q5QP46|Q5QP47|Q5QP48|Q675N4|Q675N5|Q9BVG6|Q9BWZ5|Q9H859|Q9NZZ9|Q9Y3F0	Silent	SNP	ENST00000357886.4	37		.	.	.	.	.	.	.	.	.	.	G	0.193	-1.051828	0.01981	.	.	ENSG00000101391	ENST00000427097	.	.	.	5.2	-3.18	0.05186	.	.	.	.	.	T	0.36248	0.0960	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.33343	-0.9872	4	.	.	.	-10.4828	0.2082	0.00153	0.2949:0.2423:0.2332:0.2295	.	.	.	.	L	232	.	.	P	-	2	0	CDK5RAP1	31410585	0.907000	0.30839	0.701000	0.30321	0.038000	0.13279	-0.253000	0.08794	-0.629000	0.05575	-0.882000	0.02950	CCT		0.502	CDK5RAP1-011	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000078697.1		NM_016408	
CHRNA1	1134	hgsc.bcm.edu;ucsc.edu	37	2	175614765	175614767	+	In_Frame_Del	DEL	AAC	AAC	-			TCGA-BP-5184-01A-01D-1429-08	TCGA-BP-5184-11A-01D-1429-08	AAC	AAC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ddebed14-f47f-46e6-ac39-c74ed3363211	5d1f5125-65c2-4c47-843d-da1c531fdb04	g.chr2:175614765_175614767delAAC	ENST00000261007.5	-	8	1050_1052	c.984_986delGTT	c.(982-987)gtgttc>gtc	p.F329del	CHRNA1_ENST00000409219.1_In_Frame_Del_p.F304del|CHRNA1_ENST00000348749.5_In_Frame_Del_p.F304del|AC018890.6_ENST00000442996.1_RNA|CHRNA1_ENST00000409542.1_In_Frame_Del_p.F222del	NM_001039523.2	NP_001034612.1	P02708	ACHA_HUMAN	cholinergic receptor, nicotinic, alpha 1 (muscle)	329					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|ion transmembrane transport (GO:0034220)|muscle cell cellular homeostasis (GO:0046716)|musculoskeletal movement (GO:0050881)|neuromuscular junction development (GO:0007528)|neuromuscular process (GO:0050905)|neuromuscular synaptic transmission (GO:0007274)|neuron cellular homeostasis (GO:0070050)|neuronal action potential (GO:0019228)|regulation of membrane potential (GO:0042391)|signal transduction (GO:0007165)|skeletal muscle contraction (GO:0003009)|skeletal muscle tissue growth (GO:0048630)|synaptic transmission (GO:0007268)|transport (GO:0006810)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|cell surface (GO:0009986)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|ion channel activity (GO:0005216)			breast(3)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(15)|ovary(3)|prostate(3)|skin(4)	37					Galantamine(DB00674)	GGCAATGACGAACACCATGGTGA	0.532																																																	0																																										SO:0001651	inframe_deletion	1134			Y00762	CCDS2261.1, CCDS33331.1	2q31.1	2012-02-11	2006-02-01		ENSG00000138435	ENSG00000138435		"""Cholinergic receptors"", ""Ligand-gated ion channels / Acetylcholine receptors, nicotinic"""	1955	protein-coding gene	gene with protein product	"""acetylcholine receptor, nicotinic, alpha 1 (muscle)"""	100690	"""cholinergic receptor, nicotinic, alpha polypeptide 1 (muscle)"""	CHRNA			Standard	NM_001039523		Approved		uc002uje.2	P02708	OTTHUMG00000132357	ENST00000261007.5:c.984_986delGTT	2.37:g.175614765_175614767delAAC	ENSP00000261007:p.Phe329del	Somatic		WXS	Illumina HiSeq	Phase_I	B4DRV6|D3DPE8	In_Frame_Del	DEL	ENST00000261007.5	37	CCDS33331.1																																																																																				0.532	CHRNA1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000334116.1			
CSPP1	79848	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	8	68007701	68007701	+	Missense_Mutation	SNP	A	A	T			TCGA-BP-5184-01A-01D-1429-08	TCGA-BP-5184-11A-01D-1429-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ddebed14-f47f-46e6-ac39-c74ed3363211	5d1f5125-65c2-4c47-843d-da1c531fdb04	g.chr8:68007701A>T	ENST00000262210.5	+	6	715	c.684A>T	c.(682-684)caA>caT	p.Q228H	CSPP1_ENST00000412460.1_5'UTR	NM_024790.6	NP_079066.5	Q1MSJ5	CSPP1_HUMAN	centrosome and spindle pole associated protein 1	263					positive regulation of cell division (GO:0051781)|positive regulation of cytokinesis (GO:0032467)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|spindle (GO:0005819)|spindle pole (GO:0000922)		p.Q228H(1)		NS(1)|breast(3)|endometrium(4)|kidney(3)|large_intestine(11)|lung(17)|ovary(5)|prostate(3)|skin(1)|urinary_tract(1)	49	Breast(64;0.214)	Lung NSC(129;0.0908)|all_lung(136;0.152)	Epithelial(68;0.00145)|OV - Ovarian serous cystadenocarcinoma(28;0.00589)|all cancers(69;0.0069)|BRCA - Breast invasive adenocarcinoma(89;0.153)			GATACCGACAACTAGATGATG	0.378																																																	1	Substitution - Missense(1)	kidney(1)											103.0	95.0	98.0					8																	68007701		1828	4086	5914	SO:0001583	missense	79848			AJ583433	CCDS43744.1	8q13.2	2014-02-24			ENSG00000104218	ENSG00000104218			26193	protein-coding gene	gene with protein product		611654				15580290, 24360807	Standard	NM_024790		Approved	FLJ22490, CSPP, JBTS21	uc003xxj.3	Q1MSJ5	OTTHUMG00000164564	ENST00000262210.5:c.684A>T	8.37:g.68007701A>T	ENSP00000262210:p.Gln228His	Somatic		WXS	Illumina HiSeq	Phase_I	A6ND63|Q70F00|Q8TBC1	Missense_Mutation	SNP	ENST00000262210.5	37	CCDS43744.1	.	.	.	.	.	.	.	.	.	.	A	17.91	3.504393	0.64410	.	.	ENSG00000104218	ENST00000262210;ENST00000389042	T	0.76839	-1.05	5.95	3.61	0.41365	.	0.355647	0.14779	U	0.298919	T	0.75510	0.3859	L	0.46157	1.445	0.80722	D	1	P;P;P	0.42993	0.797;0.755;0.755	P;P;P	0.47470	0.548;0.465;0.465	T	0.71083	-0.4695	10	0.56958	D	0.05	-7.9518	8.1105	0.30911	0.6864:0.0:0.3136:0.0	.	228;263;263	Q1MSJ5-1;Q1MSJ5;F8W7C3	.;CSPP1_HUMAN;.	H	228;263	ENSP00000262210:Q228H	ENSP00000262210:Q228H	Q	+	3	2	CSPP1	68170255	0.990000	0.36364	0.992000	0.48379	0.973000	0.67179	2.142000	0.42177	0.524000	0.28502	0.528000	0.53228	CAA		0.378	CSPP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379254.1		NM_024790	
EBAG9	9166	broad.mit.edu;ucsc.edu	37	8	110567065	110567065	+	Silent	SNP	G	G	A			TCGA-BP-5184-01A-01D-1429-08	TCGA-BP-5184-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ddebed14-f47f-46e6-ac39-c74ed3363211	5d1f5125-65c2-4c47-843d-da1c531fdb04	g.chr8:110567065G>A	ENST00000337573.5	+	4	570	c.270G>A	c.(268-270)ctG>ctA	p.L90L	EBAG9_ENST00000529502.1_3'UTR|EBAG9_ENST00000531677.1_Silent_p.L90L|EBAG9_ENST00000395785.2_Silent_p.L90L	NM_001278938.1|NM_004215.3	NP_001265867.1|NP_004206.1	O00559	RCAS1_HUMAN	estrogen receptor binding site associated, antigen, 9	90					regulation of cell growth (GO:0001558)	focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|secretory granule (GO:0030141)	peptidase activator activity involved in apoptotic process (GO:0016505)	p.L90L(1)		cervix(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(2)	10			OV - Ovarian serous cystadenocarcinoma(57;1.39e-14)			TGGAACAACTGGAACCTGACT	0.383																																																	1	Substitution - coding silent(1)	kidney(1)											142.0	128.0	133.0					8																	110567065		2203	4300	6503	SO:0001819	synonymous_variant	9166			AB007619	CCDS6313.1	8q23	2013-03-07			ENSG00000147654	ENSG00000147654			3123	protein-coding gene	gene with protein product		605772					Standard	NM_004215		Approved	EB9, RCAS1	uc003ynf.3	O00559	OTTHUMG00000165346	ENST00000337573.5:c.270G>A	8.37:g.110567065G>A		Somatic		WXS	Illumina GAIIx	Phase_I	A8K3N6|Q5Y8C7|Q6IB20|Q9BS76	Silent	SNP	ENST00000337573.5	37	CCDS6313.1																																																																																				0.383	EBAG9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383536.1		NM_004215	
ELOVL1	64834	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	43829743	43829743	+	Silent	SNP	C	C	T			TCGA-BP-5184-01A-01D-1429-08	TCGA-BP-5184-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ddebed14-f47f-46e6-ac39-c74ed3363211	5d1f5125-65c2-4c47-843d-da1c531fdb04	g.chr1:43829743C>T	ENST00000372458.3	-	8	801	c.684G>A	c.(682-684)caG>caA	p.Q228Q	ELOVL1_ENST00000470769.1_5'UTR|ELOVL1_ENST00000413844.2_Silent_p.Q201Q	NM_001256399.1|NM_001256402.1|NM_022821.3	NP_001243328.1|NP_001243331.1|NP_073732.1	Q9BW60	ELOV1_HUMAN	ELOVL fatty acid elongase 1	228					cellular lipid metabolic process (GO:0044255)|fatty acid elongation, monounsaturated fatty acid (GO:0034625)|fatty acid elongation, saturated fatty acid (GO:0019367)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|triglyceride biosynthetic process (GO:0019432)|very long-chain fatty acid biosynthetic process (GO:0042761)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|membrane (GO:0016020)	fatty acid elongase activity (GO:0009922)	p.Q228Q(1)		endometrium(1)|kidney(1)|large_intestine(1)|prostate(1)	4	all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				TGACTGGGTACTGGTAGTTAC	0.473																																																	1	Substitution - coding silent(1)	kidney(1)											118.0	102.0	108.0					1																	43829743		2203	4300	6503	SO:0001819	synonymous_variant	64834			AK001653	CCDS485.1, CCDS57987.1	1p34	2011-05-25	2011-05-25		ENSG00000066322	ENSG00000066322			14418	protein-coding gene	gene with protein product		611813	"""elongation of very long chain fatty acids (FEN1/Elo2, SUR4/Elo3, yeast)-like 1"""				Standard	NM_022821		Approved	Ssc1	uc031pmf.1	Q9BW60	OTTHUMG00000007422	ENST00000372458.3:c.684G>A	1.37:g.43829743C>T		Somatic		WXS	Illumina HiSeq	Phase_I	B4DP24|Q53HT2|Q5JUY3|Q8WXU3|Q9NVD9|Q9Y396	Silent	SNP	ENST00000372458.3	37	CCDS485.1																																																																																				0.473	ELOVL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019496.1		NM_022821	
FDXACB1	91893	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	111749783	111749783	+	Missense_Mutation	SNP	T	T	C			TCGA-BP-5184-01A-01D-1429-08	TCGA-BP-5184-11A-01D-1429-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ddebed14-f47f-46e6-ac39-c74ed3363211	5d1f5125-65c2-4c47-843d-da1c531fdb04	g.chr11:111749783T>C	ENST00000260257.4	-	1	121	c.74A>G	c.(73-75)gAt>gGt	p.D25G	ALG9_ENST00000524880.1_Missense_Mutation_p.D25G|FDXACB1_ENST00000542429.1_5'UTR|C11orf1_ENST00000529270.1_5'Flank|C11orf1_ENST00000530214.1_5'Flank|ALG9_ENST00000527377.1_5'Flank|C11orf1_ENST00000528125.1_Intron|C11orf1_ENST00000260276.3_5'Flank	NM_138378.2	NP_612387.1	Q9BRP7	FDXA1_HUMAN	ferredoxin-fold anticodon binding domain containing 1	25					phenylalanyl-tRNA aminoacylation (GO:0006432)|tRNA processing (GO:0008033)		ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|phenylalanine-tRNA ligase activity (GO:0004826)|tRNA binding (GO:0000049)	p.D25G(4)		endometrium(1)|kidney(3)|large_intestine(2)|lung(9)|ovary(1)|upper_aerodigestive_tract(3)	19						AGTGCTCTGATCCAGGGTTTC	0.667											OREG0021330	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																					4	Substitution - Missense(4)	kidney(4)											29.0	39.0	36.0					11																	111749783		1988	4178	6166	SO:0001583	missense	91893				CCDS44729.1	11q23.1	2011-04-15			ENSG00000255561	ENSG00000255561			25110	protein-coding gene	gene with protein product	"""hypothetical protein BC006136"""						Standard	NR_038364		Approved	LOC91893, hCG_2033039	uc001pmc.4	Q9BRP7	OTTHUMG00000166795	ENST00000260257.4:c.74A>G	11.37:g.111749783T>C	ENSP00000260257:p.Asp25Gly	Somatic	1437	WXS	Illumina HiSeq	Phase_I	A0PJW7|B4DUU2	Missense_Mutation	SNP	ENST00000260257.4	37	CCDS44729.1	.	.	.	.	.	.	.	.	.	.	T	13.80	2.345140	0.41498	.	.	ENSG00000086848;ENSG00000255561	ENST00000428306;ENST00000260257	T	0.27557	1.66	6.17	1.29	0.21616	Domain of unknown function DUF2431 (1);	0.531773	0.22239	N	0.062716	T	0.09291	0.0229	N	0.02665	-0.54	0.58432	D	0.999996	B	0.10296	0.003	B	0.08055	0.003	T	0.12426	-1.0548	10	0.19590	T	0.45	.	3.7088	0.08411	0.1574:0.2491:0.0:0.5934	.	25	Q9BRP7	FDXA1_HUMAN	G	25	ENSP00000260257:D25G	ENSP00000387627:D25G	D	-	2	0	FDXACB1;ALG9	111254993	0.008000	0.16893	0.366000	0.25914	0.040000	0.13550	0.676000	0.25247	0.520000	0.28426	0.533000	0.62120	GAT		0.667	FDXACB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391497.1		NM_138378	
FGF13	2258	broad.mit.edu;ucsc.edu	37	X	137715047	137715047	+	Silent	SNP	G	G	A	rs371293414		TCGA-BP-5184-01A-01D-1429-08	TCGA-BP-5184-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ddebed14-f47f-46e6-ac39-c74ed3363211	5d1f5125-65c2-4c47-843d-da1c531fdb04	g.chrX:137715047G>A	ENST00000315930.6	-	5	1363	c.702C>T	c.(700-702)aaC>aaT	p.N234N	FGF13_ENST00000541469.1_Silent_p.N188N|FGF13_ENST00000305414.4_Silent_p.N181N|FGF13_ENST00000370603.3_Silent_p.N244N|FGF13_ENST00000441825.2_Silent_p.N215N	NM_004114.3	NP_004105.1	Q92913	FGF13_HUMAN	fibroblast growth factor 13	234					cell-cell signaling (GO:0007267)|cerebral cortex cell migration (GO:0021795)|establishment of neuroblast polarity (GO:0045200)|hippocampus development (GO:0021766)|learning (GO:0007612)|MAPK cascade (GO:0000165)|memory (GO:0007613)|microtubule polymerization (GO:0046785)|negative regulation of collateral sprouting (GO:0048671)|negative regulation of microtubule depolymerization (GO:0007026)|nervous system development (GO:0007399)|neuron migration (GO:0001764)|positive regulation of protein kinase activity (GO:0045860)|protein localization to plasma membrane (GO:0072659)|signal transduction (GO:0007165)	axon (GO:0030424)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular region (GO:0005576)|filopodium (GO:0030175)|growth cone (GO:0030426)|intercalated disc (GO:0014704)|microtubule (GO:0005874)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	beta-tubulin binding (GO:0048487)|growth factor activity (GO:0008083)|ion channel binding (GO:0044325)|microtubule binding (GO:0008017)|protein kinase activator activity (GO:0030295)|sodium channel regulator activity (GO:0017080)	p.N244N(1)|p.N234N(1)|p.N181N(1)		breast(2)|endometrium(3)|kidney(2)|large_intestine(5)|lung(10)|ovary(1)|prostate(1)	24	Acute lymphoblastic leukemia(192;0.000127)					ATTTGCCTCCGTTCAGCACGC	0.527																																																	3	Substitution - coding silent(3)	kidney(3)						G	,,,,,	0,3835		0,0,0,1632,571	230.0	177.0	195.0		564,732,645,645,702,543	-8.9	0.6	X		195	2,6726		0,1,1,2427,1871	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	FGF13	NM_001139498.1,NM_001139500.1,NM_001139501.1,NM_001139502.1,NM_004114.3,NM_033642.2	,,,,,	0,1,1,4059,2442	AA,AG,A,GG,G		0.0297,0.0,0.0189	,,,,,	188/200,244/256,215/227,215/227,234/246,181/193	137715047	2,10561	2203	4300	6503	SO:0001819	synonymous_variant	2258			BC034340	CCDS14664.1, CCDS14665.1, CCDS55511.1	Xq26.3	2008-02-05			ENSG00000129682	ENSG00000129682			3670	protein-coding gene	gene with protein product	"""fibroblast growth factor homologous factor 2"""	300070				8790420	Standard	NM_033642		Approved	FHF2, FGF2	uc011mwj.2	Q92913	OTTHUMG00000022532	ENST00000315930.6:c.702C>T	X.37:g.137715047G>A		Somatic		WXS	Illumina GAIIx	Phase_I	B1AK18|B7Z4M7|B7Z8N0|D3DWH4|O95830|Q9NZH9|Q9NZI0	Silent	SNP	ENST00000315930.6	37	CCDS14665.1																																																																																				0.527	FGF13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058534.2		NM_004114	
HBB	3043	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	5247899	5247899	+	Missense_Mutation	SNP	C	C	A	rs33916541		TCGA-BP-5184-01A-01D-1429-08	TCGA-BP-5184-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ddebed14-f47f-46e6-ac39-c74ed3363211	5d1f5125-65c2-4c47-843d-da1c531fdb04	g.chr11:5247899C>A	ENST00000335295.4	-	2	272	c.223G>T	c.(223-225)Ggc>Tgc	p.G75C	CoTC_ribozyme_ENST00000408104.1_RNA	NM_000518.4	NP_000509.1	P68871	HBB_HUMAN	hemoglobin, beta	75			G -> R (in Aalborg; unstable).|G -> V (in Bushwick; unstable).		bicarbonate transport (GO:0015701)|blood coagulation (GO:0007596)|hydrogen peroxide catabolic process (GO:0042744)|nitric oxide transport (GO:0030185)|oxidation-reduction process (GO:0055114)|oxygen transport (GO:0015671)|platelet aggregation (GO:0070527)|positive regulation of cell death (GO:0010942)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|protein heterooligomerization (GO:0051291)|regulation of blood pressure (GO:0008217)|regulation of blood vessel size (GO:0050880)|renal absorption (GO:0070293)|response to hydrogen peroxide (GO:0042542)|small molecule metabolic process (GO:0044281)	blood microparticle (GO:0072562)|cytosol (GO:0005829)|endocytic vesicle lumen (GO:0071682)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|haptoglobin-hemoglobin complex (GO:0031838)|hemoglobin complex (GO:0005833)	heme binding (GO:0020037)|hemoglobin binding (GO:0030492)|iron ion binding (GO:0005506)|oxygen binding (GO:0019825)|oxygen transporter activity (GO:0005344)	p.G75C(1)		central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(7)|skin(1)	15		Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212)		Epithelial(150;2.76e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)	Iron Dextran(DB00893)	TGAGCCAGGCCATCACTAAAG	0.537									Sickle Cell Trait																																								1	Substitution - Missense(1)	kidney(1)											160.0	136.0	144.0					11																	5247899		2201	4298	6499	SO:0001583	missense	3043	Familial Cancer Database		J00173	CCDS7753.1	11p15.5	2014-05-19			ENSG00000244734	ENSG00000244734			4827	protein-coding gene	gene with protein product		141900				2649166	Standard	NM_000518		Approved	CD113t-C, HBD, beta-globin	uc001mae.1	P68871	OTTHUMG00000066678	ENST00000335295.4:c.223G>T	11.37:g.5247899C>A	ENSP00000333994:p.Gly75Cys	Somatic		WXS	Illumina HiSeq	Phase_I	A4GX73|B2ZUE0|P02023|Q13852|Q14481|Q14510|Q45KT0|Q549N7|Q6FI08|Q6R7N2|Q8IZI1|Q9BX96|Q9UCD6|Q9UCP8|Q9UCP9	Missense_Mutation	SNP	ENST00000335295.4	37	CCDS7753.1	.	.	.	.	.	.	.	.	.	.	c	16.13	3.036793	0.54896	.	.	ENSG00000244734	ENST00000335295;ENST00000380315	D;D	0.92911	-3.13;-3.13	5.1	5.1	0.69264	Globin-like (1);Globin, structural domain (1);	.	.	.	.	D	0.94324	0.8176	L	0.45352	1.415	0.49299	D	0.999776	D	0.76494	0.999	D	0.81914	0.995	D	0.94657	0.7844	9	0.87932	D	0	-13.8604	17.6123	0.88058	0.0:1.0:0.0:0.0	.	75	P68871	HBB_HUMAN	C	75	ENSP00000333994:G75C;ENSP00000369671:G75C	ENSP00000333994:G75C	G	-	1	0	HBB	5204475	1.000000	0.71417	0.199000	0.23439	0.047000	0.14425	6.988000	0.76212	2.812000	0.96745	0.555000	0.69702	GGC		0.537	HBB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142977.2		NM_000518	
GRIA4	2893	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	105842733	105842733	+	Missense_Mutation	SNP	G	G	A			TCGA-BP-5184-01A-01D-1429-08	TCGA-BP-5184-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ddebed14-f47f-46e6-ac39-c74ed3363211	5d1f5125-65c2-4c47-843d-da1c531fdb04	g.chr11:105842733G>A	ENST00000530497.1	+	14	2387	c.2387G>A	c.(2386-2388)gGa>gAa	p.G796E	GRIA4_ENST00000525187.1_Intron|GRIA4_ENST00000393127.2_Intron|RNU6-277P_ENST00000516272.1_RNA|GRIA4_ENST00000282499.5_Missense_Mutation_p.G796E|GRIA4_ENST00000533094.1_Intron			P48058	GRIA4_HUMAN	glutamate receptor, ionotropic, AMPA 4	796					glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|vesicle (GO:0031982)	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:0004971)|extracellular-glutamate-gated ion channel activity (GO:0005234)|ionotropic glutamate receptor activity (GO:0004970)	p.G796E(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(24)|liver(2)|lung(25)|ovary(4)|pancreas(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(6)	82		Melanoma(852;0.000902)|Acute lymphoblastic leukemia(157;0.000994)|all_hematologic(158;0.0017)|Breast(348;0.0323)		BRCA - Breast invasive adenocarcinoma(274;0.000147)|Epithelial(105;0.0291)|all cancers(92;0.0899)		GGTGAATGTGGACCCAAGGAC	0.468																																																	1	Substitution - Missense(1)	kidney(1)											112.0	111.0	112.0					11																	105842733		2201	4299	6500	SO:0001583	missense	2893			U16129	CCDS8333.1, CCDS41706.1, CCDS41707.1	11q22	2012-08-29	2012-02-03		ENSG00000152578	ENSG00000152578		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4574	protein-coding gene	gene with protein product		138246	"""glutamate receptor, ionotrophic, AMPA 4"""	GLUR4			Standard	NM_001077244		Approved	GluA4, GLURD	uc001pix.2	P48058	OTTHUMG00000166236	ENST00000530497.1:c.2387G>A	11.37:g.105842733G>A	ENSP00000435775:p.Gly796Glu	Somatic		WXS	Illumina HiSeq	Phase_I	Q86XE8	Missense_Mutation	SNP	ENST00000530497.1	37	CCDS8333.1	.	.	.	.	.	.	.	.	.	.	G	28.1	4.886680	0.91814	.	.	ENSG00000152578	ENST00000282499;ENST00000530497	T;T	0.50548	0.74;0.74	5.55	5.55	0.83447	Ionotropic glutamate receptor (1);	0.000000	0.64402	D	0.000007	T	0.51143	0.1657	N	0.20610	0.595	0.80722	D	1	P	0.51240	0.943	P	0.55391	0.775	T	0.53641	-0.8410	10	0.54805	T	0.06	.	19.5116	0.95144	0.0:0.0:1.0:0.0	.	796	P48058	GRIA4_HUMAN	E	796	ENSP00000282499:G796E;ENSP00000435775:G796E	ENSP00000282499:G796E	G	+	2	0	GRIA4	105347943	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.835000	0.99442	2.619000	0.88677	0.655000	0.94253	GGA		0.468	GRIA4-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000388593.1			
HERC5	51191	broad.mit.edu;hgsc.bcm.edu	37	4	89425491	89425491	+	Silent	SNP	C	C	T			TCGA-BP-5184-01A-01D-1429-08	TCGA-BP-5184-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ddebed14-f47f-46e6-ac39-c74ed3363211	5d1f5125-65c2-4c47-843d-da1c531fdb04	g.chr4:89425491C>T	ENST00000264350.3	+	21	2844	c.2691C>T	c.(2689-2691)atC>atT	p.I897I	HERC5_ENST00000508159.1_Silent_p.I535I	NM_016323.3	NP_057407.2	Q9UII4	HERC5_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase 5	897	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|innate immune response (GO:0045087)|ISG15-protein conjugation (GO:0032020)|negative regulation of type I interferon production (GO:0032480)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of defense response to virus (GO:0050688)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ISG15 ligase activity (GO:0042296)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)	p.I897I(1)		NS(2)|breast(3)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(11)|liver(2)|lung(17)|ovary(4)|prostate(1)|skin(4)	53		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000209)		AAGACATTATCAAATTATTCC	0.328																																					Esophageal Squamous(39;887 1012 34045 50514)												1	Substitution - coding silent(1)	kidney(1)											81.0	83.0	82.0					4																	89425491		2203	4299	6502	SO:0001819	synonymous_variant	51191			AB027289	CCDS3630.1	4q22.1-q23	2012-02-23	2012-02-23		ENSG00000138646	ENSG00000138646			24368	protein-coding gene	gene with protein product		608242	"""hect domain and RLD 5"""			10581175	Standard	NM_016323		Approved	CEB1	uc003hrt.4	Q9UII4	OTTHUMG00000130953	ENST00000264350.3:c.2691C>T	4.37:g.89425491C>T		Somatic		WXS	Illumina HiSeq	Phase_I	B2RTQ1|Q69G20	Silent	SNP	ENST00000264350.3	37	CCDS3630.1																																																																																				0.328	HERC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253554.2		NM_016323	
KCNH7	90134	broad.mit.edu;hgsc.bcm.edu	37	2	163253263	163253263	+	Missense_Mutation	SNP	T	T	G			TCGA-BP-5184-01A-01D-1429-08	TCGA-BP-5184-11A-01D-1429-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ddebed14-f47f-46e6-ac39-c74ed3363211	5d1f5125-65c2-4c47-843d-da1c531fdb04	g.chr2:163253263T>G	ENST00000332142.5	-	11	2699	c.2600A>C	c.(2599-2601)cAt>cCt	p.H867P		NM_033272.3	NP_150375.2	Q9NS40	KCNH7_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 7	867					circadian rhythm (GO:0007623)|potassium ion transmembrane transport (GO:0071805)|protein heterooligomerization (GO:0051291)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	inward rectifier potassium channel activity (GO:0005242)|signal transducer activity (GO:0004871)|voltage-gated potassium channel activity (GO:0005249)	p.H867P(1)		NS(1)|biliary_tract(1)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(22)|lung(53)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(3)	108					Doxazosin(DB00590)|Ibutilide(DB00308)|Miconazole(DB01110)|Prazosin(DB00457)|Terazosin(DB01162)	TGCGCTCTCATGCCTTAGGTT	0.338																																					GBM(196;1492 2208 17507 24132 45496)												1	Substitution - Missense(1)	kidney(1)											67.0	64.0	65.0					2																	163253263		2202	4298	6500	SO:0001583	missense	90134			AF032897	CCDS2219.1, CCDS2220.1	2q24.3	2012-07-05			ENSG00000184611	ENSG00000184611		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	18863	protein-coding gene	gene with protein product		608169				16382104	Standard	NM_173162		Approved	Kv11.3, HERG3, erg3	uc002uch.2	Q9NS40	OTTHUMG00000132069	ENST00000332142.5:c.2600A>C	2.37:g.163253263T>G	ENSP00000331727:p.His867Pro	Somatic		WXS	Illumina HiSeq	Phase_I	Q53QU4|Q53TB7|Q53TP9|Q8IV15	Missense_Mutation	SNP	ENST00000332142.5	37	CCDS2219.1	.	.	.	.	.	.	.	.	.	.	T	16.03	3.006737	0.54361	.	.	ENSG00000184611	ENST00000332142	D	0.98567	-5.0	5.43	5.43	0.79202	RmlC-like jelly roll fold (1);	0.048232	0.85682	D	0.000000	D	0.94598	0.8259	N	0.08118	0	0.80722	D	1	B	0.20671	0.047	B	0.26614	0.071	D	0.92052	0.5649	10	0.62326	D	0.03	.	15.481	0.75528	0.0:0.0:0.0:1.0	.	867	Q9NS40	KCNH7_HUMAN	P	867	ENSP00000331727:H867P	ENSP00000331727:H867P	H	-	2	0	KCNH7	162961509	1.000000	0.71417	0.968000	0.41197	0.964000	0.63967	6.276000	0.72601	2.070000	0.61991	0.477000	0.44152	CAT		0.338	KCNH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255093.1		NM_033272	
KCNN4	3783	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	19	44273604	44273604	+	Missense_Mutation	SNP	C	C	T			TCGA-BP-5184-01A-01D-1429-08	TCGA-BP-5184-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ddebed14-f47f-46e6-ac39-c74ed3363211	5d1f5125-65c2-4c47-843d-da1c531fdb04	g.chr19:44273604C>T	ENST00000262888.3	-	6	1434	c.1039G>A	c.(1039-1041)Gcc>Acc	p.A347T		NM_002250.2	NP_002241.1	O15554	KCNN4_HUMAN	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 4	347	Calmodulin-binding.				calcium ion transport (GO:0006816)|cell volume homeostasis (GO:0006884)|defense response (GO:0006952)|immune system process (GO:0002376)|phospholipid translocation (GO:0045332)|positive regulation of protein secretion (GO:0050714)|positive regulation of T cell receptor signaling pathway (GO:0050862)|potassium ion export (GO:0071435)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|saliva secretion (GO:0046541)|stabilization of membrane potential (GO:0030322)|synaptic transmission (GO:0007268)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|membrane raft (GO:0045121)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	calcium-activated potassium channel activity (GO:0015269)|calmodulin binding (GO:0005516)|Intermediate conductance calcium-activated potassium channel activity (GO:0022894)|protein phosphatase binding (GO:0019903)	p.A347T(1)		biliary_tract(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	15		Prostate(69;0.0352)			Clotrimazole(DB00257)|Enflurane(DB00228)|Halothane(DB01159)|Miconazole(DB01110)|Procaine(DB00721)|Quinine(DB00468)	GCGTTGATGGCGGCCAGCAGC	0.587																																																	1	Substitution - Missense(1)	kidney(1)											73.0	67.0	69.0					19																	44273604		2203	4300	6503	SO:0001583	missense	3783			AF022797	CCDS12630.1	19q13.2	2012-07-05				ENSG00000104783		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, calcium-activated"""	6293	protein-coding gene	gene with protein product		602754				9380751, 9407042, 16382103	Standard	NM_002250		Approved	KCa3.1, hSK4, hKCa4, hIKCa1	uc002oxl.3	O15554		ENST00000262888.3:c.1039G>A	19.37:g.44273604C>T	ENSP00000262888:p.Ala347Thr	Somatic		WXS	Illumina HiSeq	Phase_I	Q53XR4	Missense_Mutation	SNP	ENST00000262888.3	37	CCDS12630.1	.	.	.	.	.	.	.	.	.	.	C	34	5.394349	0.96009	.	.	ENSG00000104783	ENST00000262888;ENST00000407385	D	0.99886	-7.52	5.23	5.23	0.72850	Calmodulin-binding domain (2);	0.113604	0.64402	D	0.000015	D	0.99880	0.9943	M	0.83774	2.66	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.96218	0.9158	10	0.87932	D	0	-17.5868	16.6654	0.85252	0.0:1.0:0.0:0.0	.	347	O15554	KCNN4_HUMAN	T	347;215	ENSP00000262888:A347T	ENSP00000262888:A347T	A	-	1	0	KCNN4	48965444	0.999000	0.42202	0.992000	0.48379	0.969000	0.65631	4.254000	0.58798	2.612000	0.88384	0.655000	0.94253	GCC		0.587	KCNN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463598.1		NM_002250	
NCAPD3	23310	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	134062791	134062791	+	Missense_Mutation	SNP	C	C	T			TCGA-BP-5184-01A-01D-1429-08	TCGA-BP-5184-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ddebed14-f47f-46e6-ac39-c74ed3363211	5d1f5125-65c2-4c47-843d-da1c531fdb04	g.chr11:134062791C>T	ENST00000534548.2	-	16	1902	c.1838G>A	c.(1837-1839)tGc>tAc	p.C613Y		NM_015261.2	NP_056076.1	P42695	CNDD3_HUMAN	non-SMC condensin II complex, subunit D3	613					mitotic cell cycle (GO:0000278)|mitotic chromosome condensation (GO:0007076)	germinal vesicle (GO:0042585)|membrane (GO:0016020)|nuclear condensin complex (GO:0000799)|nuclear pericentric heterochromatin (GO:0031618)|nucleoplasm (GO:0005654)	methylated histone binding (GO:0035064)	p.C613Y(1)		NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(10)|kidney(5)|large_intestine(9)|liver(1)|lung(28)|ovary(3)|prostate(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	71	all_hematologic(175;0.127)	all_cancers(12;1.68e-21)|all_epithelial(12;5.86e-16)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000182)|Medulloblastoma(222;0.0245)|all_neural(223;0.0505)|Esophageal squamous(93;0.0559)		Epithelial(10;8.74e-10)|BRCA - Breast invasive adenocarcinoma(10;1e-08)|all cancers(11;1.46e-08)|OV - Ovarian serous cystadenocarcinoma(99;0.00345)|Lung(977;0.227)		GATCTGCACGCATCTAGGCTG	0.498																																																	1	Substitution - Missense(1)	kidney(1)											56.0	56.0	56.0					11																	134062791		2201	4297	6498	SO:0001583	missense	23310			AK124878	CCDS31723.1	11q25	2008-02-04			ENSG00000151503	ENSG00000151503			28952	protein-coding gene	gene with protein product		609276				7584044, 8619474, 14532007	Standard	NM_015261		Approved	hCAP-D3, CAP-D3, hHCP-6, KIAA0056, FLJ42888, hcp-6	uc001qhd.1	P42695	OTTHUMG00000167172	ENST00000534548.2:c.1838G>A	11.37:g.134062791C>T	ENSP00000433681:p.Cys613Tyr	Somatic		WXS	Illumina HiSeq	Phase_I	A6NFS2|Q4KMQ9	Missense_Mutation	SNP	ENST00000534548.2	37	CCDS31723.1	.	.	.	.	.	.	.	.	.	.	C	3.306	-0.141787	0.06669	.	.	ENSG00000151503	ENST00000534548	T	0.65549	-0.16	5.37	3.5	0.40072	Armadillo-like helical (1);Armadillo-type fold (1);	0.390189	0.32935	N	0.005465	T	0.45276	0.1334	L	0.47716	1.5	0.54753	D	0.999987	B	0.06786	0.001	B	0.04013	0.001	T	0.30060	-0.9991	10	0.02654	T	1	-4.4051	6.4937	0.22130	0.0:0.6555:0.1486:0.1958	.	613	P42695	CNDD3_HUMAN	Y	613	ENSP00000433681:C613Y	ENSP00000431612:C613Y	C	-	2	0	NCAPD3	133568001	0.855000	0.29742	0.167000	0.22817	0.053000	0.15095	2.072000	0.41510	0.752000	0.32923	-0.226000	0.12346	TGC		0.498	NCAPD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393575.2		NM_015261	
NRG2	9542	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	5	139232130	139232130	+	Silent	SNP	G	G	A			TCGA-BP-5184-01A-01D-1429-08	TCGA-BP-5184-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ddebed14-f47f-46e6-ac39-c74ed3363211	5d1f5125-65c2-4c47-843d-da1c531fdb04	g.chr5:139232130G>A	ENST00000361474.1	-	8	1655	c.1431C>T	c.(1429-1431)aaC>aaT	p.N477N	NRG2_ENST00000545385.1_Silent_p.N479N|NRG2_ENST00000358522.3_Silent_p.N479N|NRG2_ENST00000541337.1_Silent_p.N411N|NRG2_ENST00000394770.1_3'UTR|NRG2_ENST00000289409.4_Silent_p.N471N|CTB-35F21.4_ENST00000504413.1_RNA|NRG2_ENST00000289422.7_Silent_p.N485N|NRG2_ENST00000340391.3_Silent_p.N274N	NM_004883.2	NP_004874.1	O14511	NRG2_HUMAN	neuregulin 2	477					embryo development (GO:0009790)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)	p.N477N(1)		breast(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(5)|ovary(1)|pancreas(2)|prostate(1)|skin(1)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(1)	25			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGGCTGGCACGTTCTTGGAAA	0.527																																																	1	Substitution - coding silent(1)	kidney(1)											174.0	156.0	162.0					5																	139232130		2203	4300	6503	SO:0001819	synonymous_variant	9542				CCDS4217.1, CCDS54910.1	5q23-q33	2013-01-11			ENSG00000158458	ENSG00000158458		"""Immunoglobulin superfamily / I-set domain containing"""	7998	protein-coding gene	gene with protein product	"""neural- and thymus-derived activator for ErbB kinases"", ""divergent of neuregulin-1"""	603818				9168114, 9168115	Standard	NM_004883		Approved	Don-1, NTAK, HRG2	uc003lev.2	O14511	OTTHUMG00000129241	ENST00000361474.1:c.1431C>T	5.37:g.139232130G>A		Somatic		WXS	Illumina HiSeq	Phase_I		Silent	SNP	ENST00000361474.1	37	CCDS4217.1																																																																																				0.527	NRG2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251340.1		NM_013982	
OLFM2	93145	hgsc.bcm.edu;ucsc.edu	37	19	9968474	9968475	+	Frame_Shift_Ins	INS	-	-	AT			TCGA-BP-5184-01A-01D-1429-08	TCGA-BP-5184-11A-01D-1429-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ddebed14-f47f-46e6-ac39-c74ed3363211	5d1f5125-65c2-4c47-843d-da1c531fdb04	g.chr19:9968474_9968475insAT	ENST00000264833.4	-	3	461_462	c.276_277insAT	c.(274-279)tatgtafs	p.V93fs	OLFM2_ENST00000590841.1_Frame_Shift_Ins_p.V15fs	NM_058164.2	NP_477512.1	O95897	NOE2_HUMAN	olfactomedin 2	93					protein secretion (GO:0009306)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|extracellular region (GO:0005576)|synapse (GO:0045202)				breast(1)|cervix(1)|endometrium(3)|large_intestine(8)|lung(9)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)	31						ATGCCGCGTACATACTGGAGGT	0.619																																																	0																																										SO:0001589	frameshift_variant	93145			AF131839	CCDS12221.1	19p13.2	2008-07-03				ENSG00000105088			17189	protein-coding gene	gene with protein product	"""noelin 2"""						Standard	NM_058164		Approved	OlfC, NOE2	uc002mmp.3	O95897		ENST00000264833.4:c.275_276dupAT	19.37:g.9968475_9968476dupAT	ENSP00000264833:p.Val93fs	Somatic		WXS	Illumina HiSeq	Phase_I	Q6IMJ3|Q96FC2	Frame_Shift_Ins	INS	ENST00000264833.4	37	CCDS12221.1																																																																																				0.619	OLFM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451119.1			
PBRM1	55193	hgsc.bcm.edu;ucsc.edu	37	3	52613123	52613123	+	Frame_Shift_Del	DEL	A	A	-			TCGA-BP-5184-01A-01D-1429-08	TCGA-BP-5184-11A-01D-1429-08	A	A	A	-	A	A	Unknown	Valid	Somatic	Phase_I	WXS	PGM			Illumina GAIIx	ddebed14-f47f-46e6-ac39-c74ed3363211	5d1f5125-65c2-4c47-843d-da1c531fdb04	g.chr3:52613123delA	ENST00000296302.7	-	21	3481	c.3480delT	c.(3478-3480)gttfs	p.V1160fs	PBRM1_ENST00000409057.1_Frame_Shift_Del_p.V1160fs|PBRM1_ENST00000410007.1_Frame_Shift_Del_p.V1135fs|SMIM4_ENST00000476842.1_3'UTR|PBRM1_ENST00000394830.3_Frame_Shift_Del_p.V1135fs|PBRM1_ENST00000356770.4_Frame_Shift_Del_p.V1128fs|PBRM1_ENST00000337303.4_Frame_Shift_Del_p.V1160fs|PBRM1_ENST00000409114.3_Frame_Shift_Del_p.V1175fs|PBRM1_ENST00000409767.1_Frame_Shift_Del_p.V1175fs			Q86U86	PB1_HUMAN	polybromo 1	1160	BAH 2. {ECO:0000255|PROSITE- ProRule:PRU00370}.				chromatin remodeling (GO:0006338)|heart development (GO:0007507)|mitotic nuclear division (GO:0007067)|negative regulation of cell proliferation (GO:0008285)|placenta development (GO:0001890)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	kinetochore (GO:0000776)|nuclear chromosome (GO:0000228)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)	p.G1129fs*57(1)|p.G1161fs*57(1)		breast(5)|endometrium(5)|kidney(301)|liver(1)|lung(22)|pancreas(1)	335				BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)		CACAGTCGCCAACCTTCAGCC	0.473			"""Mis, N, F, S, D, O"""		"""clear cell renal carcinoma, breast"""																																			Rec	yes		3	3p21	55193	polybromo 1		E	2	Deletion - Frameshift(2)	kidney(2)											183.0	152.0	163.0					3																	52613123		2203	4300	6503	SO:0001589	frameshift_variant	55193			BC015323	CCDS43099.1	3p21	2007-03-29			ENSG00000163939	ENSG00000163939			30064	protein-coding gene	gene with protein product		606083				11078522, 11483580	Standard	NM_018313		Approved	BAF180, PB1	uc003der.2	Q86U86	OTTHUMG00000152663	ENST00000296302.7:c.3480delT	3.37:g.52613123delA	ENSP00000296302:p.Val1160fs	Somatic		WXS	Illumina HiSeq	Phase_I	A1L381|A1L382|A4FUJ7|Q1RMD1|Q1RMD2|Q96MS2|Q9H2T3|Q9H2T4|Q9H2T5|Q9H301|Q9H314	Frame_Shift_Del	DEL	ENST00000296302.7	37																																																																																					0.473	PBRM1-008	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000327232.1		NM_018165	
PCF11	51585	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	82877723	82877723	+	Missense_Mutation	SNP	A	A	G			TCGA-BP-5184-01A-01D-1429-08	TCGA-BP-5184-11A-01D-1429-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ddebed14-f47f-46e6-ac39-c74ed3363211	5d1f5125-65c2-4c47-843d-da1c531fdb04	g.chr11:82877723A>G	ENST00000298281.4	+	5	2236	c.1784A>G	c.(1783-1785)aAa>aGa	p.K595R		NM_015885.3	NP_056969.2	O94913	PCF11_HUMAN	PCF11 cleavage and polyadenylation factor subunit	595					gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA cleavage (GO:0006379)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	mRNA cleavage factor complex (GO:0005849)|nucleoplasm (GO:0005654)		p.K595R(1)|p.K694R(1)		cervix(1)|endometrium(3)|kidney(4)|large_intestine(1)|lung(22)|ovary(1)|urinary_tract(1)	33						AAGTCTGCCAAAAGATGGAAA	0.353																																																	2	Substitution - Missense(2)	kidney(2)											73.0	74.0	74.0					11																	82877723		1755	3855	5610	SO:0001583	missense	51585			AB020631	CCDS44689.1	11q13	2013-07-02	2013-07-02		ENSG00000165494	ENSG00000165494			30097	protein-coding gene	gene with protein product		608876	"""PCF11, cleavage and polyadenylation factor II subunit, homolog (S. cerevisiae)"", ""PCF11, cleavage and polyadenylation factor subunit, homolog (S. cerevisiae)"""			11060040	Standard	NM_015885		Approved	KIAA0824	uc001ozx.4	O94913	OTTHUMG00000167031	ENST00000298281.4:c.1784A>G	11.37:g.82877723A>G	ENSP00000298281:p.Lys595Arg	Somatic		WXS	Illumina HiSeq	Phase_I	A6H8W7|O43671|Q6P0X8	Missense_Mutation	SNP	ENST00000298281.4	37	CCDS44689.1	.	.	.	.	.	.	.	.	.	.	A	22.2	4.254154	0.80135	.	.	ENSG00000165494	ENST00000298281;ENST00000530660;ENST00000530304	T;T;T	0.52526	1.63;0.69;0.66	6.07	6.07	0.98685	.	0.000000	0.64402	D	0.000005	T	0.58293	0.2112	L	0.32530	0.975	0.45087	D	0.998109	D;D	0.69078	0.997;0.996	D;P	0.75020	0.985;0.874	T	0.54801	-0.8239	9	.	.	.	.	16.6406	0.85098	1.0:0.0:0.0:0.0	.	595;595	E9PQ01;O94913	.;PCF11_HUMAN	R	595	ENSP00000298281:K595R;ENSP00000434540:K595R;ENSP00000431567:K595R	.	K	+	2	0	PCF11	82555371	1.000000	0.71417	0.998000	0.56505	0.994000	0.84299	8.431000	0.90285	2.326000	0.78906	0.533000	0.62120	AAA		0.353	PCF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392548.2		NM_015885	
PRKD1	5587	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	14	30066775	30066775	+	Missense_Mutation	SNP	C	C	A			TCGA-BP-5184-01A-01D-1429-08	TCGA-BP-5184-11A-01D-1429-08	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	ddebed14-f47f-46e6-ac39-c74ed3363211	5d1f5125-65c2-4c47-843d-da1c531fdb04	g.chr14:30066775C>A	ENST00000331968.5	-	16	2585	c.2356G>T	c.(2356-2358)Gat>Tat	p.D786Y	PRKD1_ENST00000415220.2_Missense_Mutation_p.D794Y	NM_002742.2	NP_002733.2	Q15139	KPCD1_HUMAN	protein kinase D1	786	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|cellular response to oxidative stress (GO:0034599)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|Golgi organization (GO:0007030)|Golgi vesicle transport (GO:0048193)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|intracellular signal transduction (GO:0035556)|negative regulation of cell death (GO:0060548)|negative regulation of endocytosis (GO:0045806)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of endothelial cell chemotaxis (GO:2001028)|positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway (GO:0038033)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of histone deacetylase activity (GO:1901727)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of neuron projection development (GO:0010976)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein autophosphorylation (GO:0046777)|regulation of integrin-mediated signaling pathway (GO:2001044)|regulation of keratinocyte proliferation (GO:0010837)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	cell cortex (GO:0005938)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)	p.D786Y(2)		NS(1)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(21)|lung(32)|ovary(2)|prostate(1)|skin(4)|urinary_tract(2)	78	Hepatocellular(127;0.0604)		LUAD - Lung adenocarcinoma(48;0.00527)|Lung(238;0.0252)	GBM - Glioblastoma multiforme(265;0.00888)		ATGTCTTCATCTTCATTAAAT	0.413																																																	2	Substitution - Missense(2)	kidney(2)											152.0	142.0	146.0					14																	30066775		2203	4300	6503	SO:0001583	missense	5587				CCDS9637.1	14q11	2013-01-10	2004-10-28	2004-10-30	ENSG00000184304	ENSG00000184304	2.7.11.1	"""Pleckstrin homology (PH) domain containing"""	9407	protein-coding gene	gene with protein product		605435	"""protein kinase C, mu"""	PRKCM		8119958, 10965134	Standard	NM_002742		Approved	PKCM, PKD, PKC-mu	uc001wqh.3	Q15139	OTTHUMG00000140203	ENST00000331968.5:c.2356G>T	14.37:g.30066775C>A	ENSP00000333568:p.Asp786Tyr	Somatic		WXS	Illumina HiSeq	Phase_I	A6NL64|B2RAF6	Missense_Mutation	SNP	ENST00000331968.5	37	CCDS9637.1	.	.	.	.	.	.	.	.	.	.	C	25.2	4.618655	0.87460	.	.	ENSG00000184304	ENST00000331968;ENST00000415220	D;D	0.83673	-1.75;-1.75	5.62	5.62	0.85841	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.91040	0.7181	M	0.77406	2.37	0.80722	D	1	D	0.63046	0.992	D	0.63597	0.916	D	0.91419	0.5157	10	0.87932	D	0	-20.7771	20.0303	0.97534	0.0:1.0:0.0:0.0	.	786	Q15139	KPCD1_HUMAN	Y	786;794	ENSP00000333568:D786Y;ENSP00000390535:D794Y	ENSP00000333568:D786Y	D	-	1	0	PRKD1	29136526	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.776000	0.85560	2.794000	0.96219	0.650000	0.86243	GAT		0.413	PRKD1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000276611.2		NM_002742	
SPEG	10290	hgsc.bcm.edu	37	2	220331989	220331990	+	Frame_Shift_Ins	INS	-	-	G	rs568360621		TCGA-BP-5184-01A-01D-1429-08	TCGA-BP-5184-11A-01D-1429-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ddebed14-f47f-46e6-ac39-c74ed3363211	5d1f5125-65c2-4c47-843d-da1c531fdb04	g.chr2:220331989_220331990insG	ENST00000312358.7	+	10	3107_3108	c.2975_2976insG	c.(2974-2979)gcggggfs	p.AG992fs	SPEG_ENST00000485813.1_3'UTR	NM_005876.4	NP_005867.3	Q15772	SPEG_HUMAN	SPEG complex locus	992	Ig-like 4.				cardiac muscle cell development (GO:0055013)|in utero embryonic development (GO:0001701)|muscle organ development (GO:0007517)|negative regulation of cell proliferation (GO:0008285)|respiratory system development (GO:0060541)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(3)|endometrium(10)|kidney(2)|large_intestine(9)|lung(42)|ovary(5)|pancreas(1)|prostate(8)|skin(1)|stomach(9)|upper_aerodigestive_tract(4)|urinary_tract(4)	100		Renal(207;0.0183)		Epithelial(149;4.5e-10)|all cancers(144;7.93e-08)|Lung(261;0.00639)|LUSC - Lung squamous cell carcinoma(224;0.00829)|READ - Rectum adenocarcinoma(5;0.163)		TGCCTGGTGGCGGGGCCCACTG	0.663																																																	0																																										SO:0001589	frameshift_variant	10290			BC006346	CCDS42824.1, CCDS54432.1	2q35	2013-01-11	2006-04-27	2006-04-27	ENSG00000072195	ENSG00000072195		"""Immunoglobulin superfamily / I-set domain containing"""	16901	protein-coding gene	gene with protein product		615950	"""aortic preferentially expressed gene 1"""	APEG1		8663449, 10973969	Standard	NM_005876		Approved	MGC12676, KIAA1297, SPEGalpha, SPEGbeta, BPEG	uc010fwg.3	Q15772	OTTHUMG00000058925	ENST00000312358.7:c.2979dupG	2.37:g.220331993_220331993dupG	ENSP00000311684:p.Ala992fs	Somatic		WXS	Illumina HiSeq	Phase_I	A8K0G6|A8MRU0|Q27J74|Q695L1|Q6FGA6|Q6ZQW1|Q6ZTL8|Q9P2P9	Frame_Shift_Ins	INS	ENST00000312358.7	37	CCDS42824.1																																																																																				0.663	SPEG-004	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130252.2		NM_005876	
THAP9	79725	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	4	83839957	83839957	+	Missense_Mutation	SNP	T	T	A			TCGA-BP-5184-01A-01D-1429-08	TCGA-BP-5184-11A-01D-1429-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ddebed14-f47f-46e6-ac39-c74ed3363211	5d1f5125-65c2-4c47-843d-da1c531fdb04	g.chr4:83839957T>A	ENST00000302236.5	+	5	2643	c.2592T>A	c.(2590-2592)gaT>gaA	p.D864E	LIN54_ENST00000505905.1_Intron	NM_024672.4	NP_078948.3	Q9H5L6	THAP9_HUMAN	THAP domain containing 9	864					DNA integration (GO:0015074)|DNA recombination (GO:0006310)|transposition, DNA-mediated (GO:0006313)		metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|transferase activity (GO:0016740)|transposase activity (GO:0004803)	p.D864E(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(13)|lung(5)|ovary(2)|pancreas(2)|prostate(1)|upper_aerodigestive_tract(3)	33		Hepatocellular(203;0.114)				AGAGAACTGATATGAAAACTT	0.313																																																	1	Substitution - Missense(1)	kidney(1)											47.0	51.0	50.0					4																	83839957		2201	4297	6498	SO:0001583	missense	79725			AK091412	CCDS3598.1	4q21.3	2013-01-25			ENSG00000168152	ENSG00000168152		"""THAP (C2CH-type zinc finger) domain containing"""	23192	protein-coding gene	gene with protein product		612537				12575992	Standard	NM_024672		Approved	FLJ34093	uc003hnt.2	Q9H5L6	OTTHUMG00000130291	ENST00000302236.5:c.2592T>A	4.37:g.83839957T>A	ENSP00000305533:p.Asp864Glu	Somatic		WXS	Illumina HiSeq	Phase_I	B3KRE2|Q59AC9	Missense_Mutation	SNP	ENST00000302236.5	37	CCDS3598.1	.	.	.	.	.	.	.	.	.	.	T	0.001	-3.158924	0.00028	.	.	ENSG00000168152	ENST00000302236;ENST00000536314	D	0.89681	-2.55	4.19	0.247	0.15521	.	0.829398	0.10130	N	0.712161	T	0.69949	0.3168	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.57376	-0.7822	10	0.05959	T	0.93	-7.6645	3.4652	0.07548	0.617:0.0:0.2098:0.1732	.	864	Q9H5L6	THAP9_HUMAN	E	864	ENSP00000305533:D864E	ENSP00000305533:D864E	D	+	3	2	THAP9	84058981	0.022000	0.18835	0.002000	0.10522	0.007000	0.05969	1.143000	0.31553	0.052000	0.16007	-1.017000	0.02453	GAT		0.313	THAP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252633.1		NM_024672	
TRPV4	59341	broad.mit.edu;hgsc.bcm.edu|hgsc.bcm.edu	37	12	110226511	110226512	+	Missense_Mutation	DNP	GG	GG	AC	rs576390203		TCGA-BP-5184-01A-01D-1429-08	TCGA-BP-5184-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ddebed14-f47f-46e6-ac39-c74ed3363211	5d1f5125-65c2-4c47-843d-da1c531fdb04	g.chr12:110226511_110226512GG>AC	ENST00000418703.2	-	12	1995_1996	c.1901_1902CC>GT	c.(1900-1902)tCC>tGT	p.S634C	TRPV4_ENST00000392719.2_Missense_Mutation_p.S587C|TRPV4_ENST00000537083.1_Missense_Mutation_p.S574C|TRPV4_ENST00000261740.2_Missense_Mutation_p.S634C|TRPV4_ENST00000536838.1_Missense_Mutation_p.S600C|TRPV4_ENST00000346520.2_Missense_Mutation_p.S574C|TRPV4_ENST00000541794.1_Missense_Mutation_p.S587C|TRPV4_ENST00000544971.1_Missense_Mutation_p.S527C	NM_001177431.1	NP_001170902.1	Q9HBA0	TRPV4_HUMAN	transient receptor potential cation channel, subfamily V, member 4	634					actin cytoskeleton reorganization (GO:0031532)|actin filament organization (GO:0007015)|calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cell death (GO:0008219)|cell volume homeostasis (GO:0006884)|cell-cell junction assembly (GO:0007043)|cellular calcium ion homeostasis (GO:0006874)|cellular hypotonic response (GO:0071476)|cellular response to heat (GO:0034605)|cellular response to osmotic stress (GO:0071470)|cortical microtubule organization (GO:0043622)|hyperosmotic salinity response (GO:0042538)|ion transmembrane transport (GO:0034220)|microtubule polymerization (GO:0046785)|negative regulation of neuron projection development (GO:0010977)|osmosensory signaling pathway (GO:0007231)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of microtubule depolymerization (GO:0031117)|regulation of response to osmotic stress (GO:0047484)|response to mechanical stimulus (GO:0009612)|transmembrane transport (GO:0055085)|vasopressin secretion (GO:0030103)	adherens junction (GO:0005912)|cell surface (GO:0009986)|cilium (GO:0005929)|cortical actin cytoskeleton (GO:0030864)|cytoplasmic microtubule (GO:0005881)|cytoplasmic vesicle (GO:0031410)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|alpha-tubulin binding (GO:0043014)|ATP binding (GO:0005524)|beta-tubulin binding (GO:0048487)|calcium channel activity (GO:0005262)|calmodulin binding (GO:0005516)|cation channel activity (GO:0005261)|microtubule binding (GO:0008017)|osmosensor activity (GO:0005034)|protein kinase binding (GO:0019901)|protein kinase C binding (GO:0005080)|SH2 domain binding (GO:0042169)	p.S634C(1)|p.S634S(1)		breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(7)|lung(7)|ovary(3)|prostate(2)|skin(4)|stomach(1)	35						GGTTCAGGAGGGAGACCAGGGC	0.579																																																	2	Substitution - Missense(1)|Substitution - coding silent(1)	kidney(2)																																								SO:0001583	missense	59341			AF263523	CCDS9134.1, CCDS9135.1, CCDS53827.1, CCDS53828.1, CCDS53829.1	12q24.1	2014-09-17				ENSG00000111199		"""Voltage-gated ion channels / Transient receptor potential cation channels"", ""Ankyrin repeat domain containing"""	18083	protein-coding gene	gene with protein product	"""osmosensitive transient receptor potential channel 4"""	605427				11025659, 11081638, 16382100, 20037587	Standard	NM_147204		Approved	OTRPC4, TRP12, VROAC, VRL-2, VR-OAC, CMT2C	uc001tpk.2	Q9HBA0		ENST00000418703.2:c.1901_1902delinsAC	12.37:g.110226511_110226512delinsAC	ENSP00000406191:p.Ser634Cys	Somatic		WXS	Illumina HiSeq	Phase_I	B7ZKQ6|Q17R79|Q2Y122|Q2Y123|Q2Y124|Q86YZ6|Q8NDY7|Q8NG64|Q96Q92|Q96RS7|Q9HBC0	Silent|Missense_Mutation	SNP	ENST00000418703.2	37	CCDS9134.1																																																																																				0.579	TRPV4-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403270.1		NM_021625	
TSNARE1	203062	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	8	143412303	143412303	+	Silent	SNP	G	G	A			TCGA-BP-5184-01A-01D-1429-08	TCGA-BP-5184-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ddebed14-f47f-46e6-ac39-c74ed3363211	5d1f5125-65c2-4c47-843d-da1c531fdb04	g.chr8:143412303G>A	ENST00000307180.3	-	6	969	c.852C>T	c.(850-852)tcC>tcT	p.S284S	TSNARE1_ENST00000519651.1_Silent_p.S65S|TSNARE1_ENST00000524325.1_Silent_p.S284S|TSNARE1_ENST00000520166.1_Silent_p.S284S	NM_145003.3	NP_659440.2	Q96NA8	TSNA1_HUMAN	t-SNARE domain containing 1	284					intracellular protein transport (GO:0006886)|synaptic vesicle exocytosis (GO:0016079)	integral component of membrane (GO:0016021)|SNARE complex (GO:0031201)	SNAP receptor activity (GO:0005484)|SNARE binding (GO:0000149)	p.S284S(1)		breast(1)|endometrium(3)|kidney(4)|large_intestine(1)|lung(6)|ovary(2)|stomach(2)|urinary_tract(1)	20	all_cancers(97;7.39e-11)|all_epithelial(106;8.98e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000332)|Ovarian(258;0.0315)|Acute lymphoblastic leukemia(118;0.155)					GTGTCCCTAAGGACTGAAGGC	0.627																																																	1	Substitution - coding silent(1)	kidney(1)											151.0	116.0	128.0					8																	143412303		2203	4300	6503	SO:0001819	synonymous_variant	203062					8q24.3	2005-08-18							26437	protein-coding gene	gene with protein product						14702039	Standard	XM_005250828		Approved	FLJ31164	uc003ywk.3	Q96NA8		ENST00000307180.3:c.852C>T	8.37:g.143412303G>A		Somatic		WXS	Illumina HiSeq	Phase_I	B7ZLB0|Q14D03	Silent	SNP	ENST00000307180.3	37	CCDS6384.1																																																																																				0.627	TSNARE1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding			NM_145003	
UBE2O	63893	hgsc.bcm.edu	37	17	74387548	74387549	+	Frame_Shift_Ins	INS	-	-	C			TCGA-BP-5184-01A-01D-1429-08	TCGA-BP-5184-11A-01D-1429-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ddebed14-f47f-46e6-ac39-c74ed3363211	5d1f5125-65c2-4c47-843d-da1c531fdb04	g.chr17:74387548_74387549insC	ENST00000319380.7	-	18	3418_3419	c.3354_3355insG	c.(3352-3357)cggcccfs	p.P1119fs		NM_022066.3	NP_071349.3	Q9C0C9	UBE2O_HUMAN	ubiquitin-conjugating enzyme E2O	1119					positive regulation of BMP signaling pathway (GO:0030513)|protein K63-linked ubiquitination (GO:0070534)|protein monoubiquitination (GO:0006513)|retrograde transport, endosome to Golgi (GO:0042147)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(17)|ovary(2)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	36						ACCTCGGGGGGCCGCCGCACCA	0.599																																																	0																																										SO:0001589	frameshift_variant	63893			AB051521	CCDS32742.1	17q25.1	2013-10-09			ENSG00000175931	ENSG00000175931			29554	protein-coding gene	gene with protein product						11311559, 11214970	Standard	NM_022066		Approved	E2-230K	uc002jrm.4	Q9C0C9	OTTHUMG00000180178	ENST00000319380.7:c.3355dupG	17.37:g.74387550_74387550dupC	ENSP00000323687:p.Pro1119fs	Somatic		WXS	Illumina HiSeq	Phase_I	A6NDU5|Q69YP4|Q6PIZ2|Q86UA4|Q8N425|Q8TBN1|Q9BSW1|Q9H6E6|Q9H7E4|Q9H9B2	Frame_Shift_Ins	INS	ENST00000319380.7	37	CCDS32742.1																																																																																				0.599	UBE2O-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450123.1		NM_022066	
UTRN	7402	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	6	145103091	145103091	+	Missense_Mutation	SNP	T	T	A			TCGA-BP-5184-01A-01D-1429-08	TCGA-BP-5184-11A-01D-1429-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ddebed14-f47f-46e6-ac39-c74ed3363211	5d1f5125-65c2-4c47-843d-da1c531fdb04	g.chr6:145103091T>A	ENST00000367545.3	+	60	8666	c.8666T>A	c.(8665-8667)aTt>aAt	p.I2889N	UTRN_ENST00000367526.4_Missense_Mutation_p.I444N	NM_007124.2	NP_009055.2	P46939	UTRO_HUMAN	utrophin	2889	Interaction with SYNM.				aging (GO:0007568)|muscle cell differentiation (GO:0042692)|muscle contraction (GO:0006936)|muscle organ development (GO:0007517)|neuron projection morphogenesis (GO:0048812)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of sodium ion transmembrane transporter activity (GO:2000649)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dystrophin-associated glycoprotein complex (GO:0016010)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane (GO:0016020)|membrane raft (GO:0045121)|myofibril (GO:0030016)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|protein kinase binding (GO:0019901)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)	p.I2889N(1)		NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(1)|cervix(2)|endometrium(21)|kidney(10)|large_intestine(29)|lung(56)|ovary(5)|pancreas(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	148		Ovarian(120;0.218)		OV - Ovarian serous cystadenocarcinoma(155;5.72e-07)|GBM - Glioblastoma multiforme(68;4.9e-05)|Colorectal(48;0.213)		ACAAATGAAATTTTCAAACAG	0.368																																																	1	Substitution - Missense(1)	kidney(1)											99.0	95.0	96.0					6																	145103091		2203	4300	6503	SO:0001583	missense	7402			AK023675	CCDS34547.1	6q24	2008-02-05	2006-12-13		ENSG00000152818	ENSG00000152818			12635	protein-coding gene	gene with protein product		128240	"""utrophin (homologous to dystrophin)"""	DMDL		1426262	Standard	NM_007124		Approved	DRP, DRP1	uc003qkt.3	P46939	OTTHUMG00000015746	ENST00000367545.3:c.8666T>A	6.37:g.145103091T>A	ENSP00000356515:p.Ile2889Asn	Somatic		WXS	Illumina HiSeq	Phase_I	Q5SYY1|Q5SZ57|Q9UJ40	Missense_Mutation	SNP	ENST00000367545.3	37	CCDS34547.1	.	.	.	.	.	.	.	.	.	.	T	16.12	3.032629	0.54790	.	.	ENSG00000152818	ENST00000367545;ENST00000367526	T;T	0.66460	-0.21;-0.21	5.49	5.49	0.81192	EF-hand domain, type 1 (1);EF-hand-like domain (1);	0.289894	0.24409	N	0.038763	T	0.48677	0.1513	L	0.49126	1.545	0.29572	N	0.849855	B	0.13145	0.007	B	0.18871	0.023	T	0.52975	-0.8503	10	0.66056	D	0.02	.	15.5871	0.76491	0.0:0.0:0.0:1.0	.	2889	P46939	UTRO_HUMAN	N	2889;444	ENSP00000356515:I2889N;ENSP00000356496:I444N	ENSP00000356496:I444N	I	+	2	0	UTRN	145144784	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	4.137000	0.58010	2.087000	0.62958	0.455000	0.32223	ATT		0.368	UTRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042551.1			
UNC93A	54346	broad.mit.edu;ucsc.edu	37	6	167721380	167721380	+	Missense_Mutation	SNP	T	T	C			TCGA-BP-5184-01A-01D-1429-08	TCGA-BP-5184-11A-01D-1429-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ddebed14-f47f-46e6-ac39-c74ed3363211	5d1f5125-65c2-4c47-843d-da1c531fdb04	g.chr6:167721380T>C	ENST00000230256.3	+	7	1265	c.1090T>C	c.(1090-1092)Tgg>Cgg	p.W364R	UNC93A_ENST00000366829.2_Missense_Mutation_p.W322R	NM_018974.3	NP_061847.2	Q86WB7	UN93A_HUMAN	unc-93 homolog A (C. elegans)	364						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.W364R(1)		breast(2)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(7)|lung(20)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	40		Breast(66;7.62e-05)|Ovarian(120;0.105)		OV - Ovarian serous cystadenocarcinoma(33;2.22e-20)|BRCA - Breast invasive adenocarcinoma(81;6.17e-07)|GBM - Glioblastoma multiforme(31;0.00492)		AGATGCCGTCTGGCAGACACA	0.607																																																	1	Substitution - Missense(1)	kidney(1)											96.0	72.0	80.0					6																	167721380		2203	4300	6503	SO:0001583	missense	54346			AJ508812	CCDS5300.1, CCDS47515.1	6q27	2014-05-16	2001-11-28		ENSG00000112494	ENSG00000112494			12570	protein-coding gene	gene with protein product		607995	"""unc93 (C.elegans) homolog A"""			12381271	Standard	NM_001143947		Approved	dJ366N23.2, dJ366N23.1	uc003qvq.3	Q86WB7	OTTHUMG00000016021	ENST00000230256.3:c.1090T>C	6.37:g.167721380T>C	ENSP00000230256:p.Trp364Arg	Somatic		WXS	Illumina GAIIx	Phase_I	B3KRP5|Q4QQJ4|Q5JZD6	Missense_Mutation	SNP	ENST00000230256.3	37	CCDS5300.1	.	.	.	.	.	.	.	.	.	.	T	12.90	2.076773	0.36662	.	.	ENSG00000112494	ENST00000230256;ENST00000366829	T;T	0.18016	2.24;2.24	4.56	3.37	0.38596	Major facilitator superfamily domain, general substrate transporter (1);	0.069159	0.64402	D	0.000006	T	0.34803	0.0910	M	0.90198	3.095	0.80722	D	1	D;D	0.89917	1.0;0.998	D;D	0.73380	0.98;0.966	T	0.33574	-0.9863	10	0.66056	D	0.02	-11.5938	9.1931	0.37211	0.0:0.0904:0.0:0.9096	.	322;364	Q4QQJ4;Q86WB7	.;UN93A_HUMAN	R	364;322	ENSP00000230256:W364R;ENSP00000355794:W322R	ENSP00000230256:W364R	W	+	1	0	UNC93A	167641370	1.000000	0.71417	0.817000	0.32601	0.040000	0.13550	5.012000	0.64017	1.692000	0.51112	0.460000	0.39030	TGG		0.607	UNC93A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043125.2		NM_018974	
VHL	7428	hgsc.bcm.edu;ucsc.edu	37	3	10188284	10188287	+	Frame_Shift_Del	DEL	GACG	GACG	-	rs372757722		TCGA-BP-5184-01A-01D-1429-08	TCGA-BP-5184-11A-01D-1429-08	GACG	GACG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ddebed14-f47f-46e6-ac39-c74ed3363211	5d1f5125-65c2-4c47-843d-da1c531fdb04	g.chr3:10188284_10188287delGACG	ENST00000256474.2	+	2	1267_1270	c.427_430delGACG	c.(427-432)gacggafs	p.DG143fs	VHL_ENST00000345392.2_Intron|VHL_ENST00000477538.1_3'UTR	NM_000551.3	NP_000542.1	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor, E3 ubiquitin protein ligase	143	Involved in binding to CCT complex.		D -> E (in VHLD; type II). {ECO:0000269|PubMed:8825918}.		cell morphogenesis (GO:0000902)|cellular response to hypoxia (GO:0071456)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061428)|positive regulation of cell differentiation (GO:0045597)|positive regulation of transcription, DNA-templated (GO:0045893)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|transcription factor binding (GO:0008134)|ubiquitin protein ligase activity (GO:0061630)|ubiquitin-protein transferase activity (GO:0004842)	p.G144fs*14(5)|p.G144*(3)|p.N141fs*16(2)|p.D143E(2)|p.D143fs*16(2)|p.V142fs*30(1)|p.G144R(1)|p.Q145fs*30(1)|p.G144fs*29(1)|p.D143fs*29(1)|p.N141fs*30(1)|p.S139fs*12(1)|p.G144fs*19(1)		adrenal_gland(25)|autonomic_ganglia(3)|central_nervous_system(2)|endometrium(6)|kidney(1662)|large_intestine(14)|lung(6)|pancreas(18)|paratesticular_tissues(1)|pleura(1)|skin(1)|soft_tissue(24)|thyroid(3)|upper_aerodigestive_tract(3)	1769				Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569)		TCTCAATGTTGACGGACAGCCTAT	0.426		1	"""D, Mis, N, F, S"""		"""renal, hemangioma, pheochromocytoma"""	"""renal, hemangioma, pheochromocytoma"""			von Hippel-Lindau disease;Pheochromocytoma (Adrenal), Familial;Chuvash Polycythemia																														yes	Rec	yes	von Hippel-Lindau syndrome	3	3p25	7428	von Hippel-Lindau syndrome gene		"""E, M, O"""	22	Deletion - Frameshift(15)|Substitution - Missense(3)|Substitution - Nonsense(3)|Insertion - Frameshift(1)	kidney(20)|adrenal_gland(1)|endometrium(1)	GRCh37	CD951875|CM982008	VHL	D|M																																				SO:0001589	frameshift_variant	7428	Familial Cancer Database	VHL; ;Erythrocytosis, Familial type 2	L15409	CCDS2597.1, CCDS2598.1	3p25.3	2014-09-17	2012-02-23		ENSG00000134086	ENSG00000134086			12687	protein-coding gene	gene with protein product		608537	"""von Hippel-Lindau syndrome"", ""von Hippel-Lindau tumor suppressor"""			9671762	Standard	NM_000551		Approved	VHL1	uc003bvc.3	P40337	OTTHUMG00000128668	ENST00000256474.2:c.427_430delGACG	3.37:g.10188284_10188287delGACG	ENSP00000256474:p.Asp143fs	Somatic		WXS	Illumina HiSeq	Phase_I	B2RE45|Q13599|Q6PDA9	Frame_Shift_Del	DEL	ENST00000256474.2	37	CCDS2597.1																																																																																				0.426	VHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250559.1		NM_000551	
ZC3H13	23091	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	13	46584527	46584527	+	Silent	SNP	A	A	G	rs374265880		TCGA-BP-5184-01A-01D-1429-08	TCGA-BP-5184-11A-01D-1429-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ddebed14-f47f-46e6-ac39-c74ed3363211	5d1f5125-65c2-4c47-843d-da1c531fdb04	g.chr13:46584527A>G	ENST00000242848.4	-	7	1050	c.702T>C	c.(700-702)gaT>gaC	p.D234D	ZC3H13_ENST00000282007.3_Silent_p.D234D|ZC3H13_ENST00000470308.1_5'UTR			Q5T200	ZC3HD_HUMAN	zinc finger CCCH-type containing 13	234	Ser-rich.						metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)	p.D234D(1)		cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(27)|lung(25)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	79		Lung NSC(96;7.26e-05)|Breast(56;0.000118)|Prostate(109;0.00217)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;4.18e-05)		ATGTCTTCCTATCTTTCTTGC	0.423																																					Esophageal Squamous(187;747 2077 11056 31291 44172)												1	Substitution - coding silent(1)	kidney(1)						A		0,4406		0,0,2203	121.0	113.0	115.0		702	-5.5	0.9	13		115	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	ZC3H13	NM_015070.3		0,1,6502	GG,GA,AA		0.0116,0.0,0.0077		234/1565	46584527	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	23091			AB020660	CCDS9400.1	13q14.11	2012-07-05	2006-05-15	2006-05-15	ENSG00000123200	ENSG00000123200		"""Zinc fingers, CCCH-type domain containing"""	20368	protein-coding gene	gene with protein product			"""KIAA0853"""	KIAA0853		10048485	Standard	XM_005266301		Approved	DKFZp434D1812	uc001vas.1	Q5T200	OTTHUMG00000016863	ENST00000242848.4:c.702T>C	13.37:g.46584527A>G		Somatic		WXS	Illumina HiSeq	Phase_I	A2A323|O94936|Q5T1Z9|Q7Z7J3|Q8NDT6|Q9H0L6	Silent	SNP	ENST00000242848.4	37																																																																																					0.423	ZC3H13-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000044789.1		NM_015070	
GOLGA6L5P	374650	broad.mit.edu	37	15	85056021	85056021	+	RNA	SNP	T	T	C	rs1062001		TCGA-BP-5184-01A-01D-1429-08	TCGA-BP-5184-11A-01D-1429-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ddebed14-f47f-46e6-ac39-c74ed3363211	5d1f5125-65c2-4c47-843d-da1c531fdb04	g.chr15:85056021T>C	ENST00000560239.1	-	0	984				GOLGA6L5_ENST00000414190.2_RNA																							GTAGCTGCTCTACCTTAGATG	0.502																																																	0																																												374650																															15.37:g.85056021T>C		Somatic		WXS	Illumina GAIIx	Phase_I		RNA	SNP	ENST00000560239.1	37																																																																																					0.502	RP11-182J1.12-001	KNOWN	mRNA_end_NF|basic|readthrough_transcript	processed_transcript	processed_transcript	OTTHUMT00000418581.1			
ZNF592	9640	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	15	85326331	85326331	+	Missense_Mutation	SNP	G	G	T			TCGA-BP-5184-01A-01D-1429-08	TCGA-BP-5184-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ddebed14-f47f-46e6-ac39-c74ed3363211	5d1f5125-65c2-4c47-843d-da1c531fdb04	g.chr15:85326331G>T	ENST00000560079.2	+	4	713	c.425G>T	c.(424-426)aGt>aTt	p.S142I	ZNF592_ENST00000299927.3_Missense_Mutation_p.S142I	NM_014630.2	NP_055445.2	Q92610	ZN592_HUMAN	zinc finger protein 592	142					cell death (GO:0008219)|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.S142I(1)		breast(2)|endometrium(2)|kidney(1)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(2)|urinary_tract(1)	40			BRCA - Breast invasive adenocarcinoma(143;0.0587)			AACCAGTTCAGTCCAATCTCC	0.483																																																	1	Substitution - Missense(1)	kidney(1)											112.0	120.0	117.0					15																	85326331		2203	4299	6502	SO:0001583	missense	9640			D86966	CCDS32317.1	15q25.2	2011-03-15				ENSG00000166716		"""Zinc fingers, C2H2-type"""	28986	protein-coding gene	gene with protein product		613624	"""spinocerebellar ataxia, autosomal recessive 5"""	SCAR5		9039502, 12030328, 20531441	Standard	NM_014630		Approved	KIAA0211, CAMOS	uc002bld.3	Q92610		ENST00000560079.2:c.425G>T	15.37:g.85326331G>T	ENSP00000452877:p.Ser142Ile	Somatic		WXS	Illumina HiSeq	Phase_I	Q2M1T2|Q504Y9	Missense_Mutation	SNP	ENST00000560079.2	37	CCDS32317.1	.	.	.	.	.	.	.	.	.	.	G	17.50	3.405752	0.62288	.	.	ENSG00000166716	ENST00000299927	T	0.01252	5.1	6.06	6.06	0.98353	.	0.036447	0.85682	D	0.000000	T	0.06826	0.0174	L	0.52573	1.65	0.54753	D	0.999987	D	0.89917	1.0	D	0.74674	0.984	T	0.04427	-1.0952	10	0.87932	D	0	-13.8171	18.1147	0.89549	0.0:0.0:1.0:0.0	.	142	Q92610	ZN592_HUMAN	I	142	ENSP00000299927:S142I	ENSP00000299927:S142I	S	+	2	0	ZNF592	83127335	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.461000	0.80834	2.882000	0.98803	0.655000	0.94253	AGT		0.483	ZNF592-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418779.2		NM_014630	
HMGB3P1	128872	broad.mit.edu	37	20	33421797	33421797	+	IGR	DEL	T	T	-	rs200631461		TCGA-BP-5184-01A-01D-1429-08	TCGA-BP-5184-11A-01D-1429-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ddebed14-f47f-46e6-ac39-c74ed3363211	5d1f5125-65c2-4c47-843d-da1c531fdb04	g.chr20:33421797delT								NCOA6 (8345 upstream) : GGT7 (10725 downstream)																							TCTCTCTCTCttttttttttt	0.468																																																	0																																										SO:0001628	intergenic_variant	0																															20.37:g.33421797delT		Somatic		WXS	Illumina GAIIx	Phase_I		RNA	DEL		37																																																																																				0	0.468									
PIPSL	266971	broad.mit.edu	37	10	95719506	95719506	+	RNA	SNP	T	T	G			TCGA-BP-5184-01A-01D-1429-08	TCGA-BP-5184-11A-01D-1429-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ddebed14-f47f-46e6-ac39-c74ed3363211	5d1f5125-65c2-4c47-843d-da1c531fdb04	g.chr10:95719506T>G	ENST00000480546.1	-	0	1791					NR_002319.2		A2A3N6	PIPSL_HUMAN	PIP5K1A and PSMD4-like, pseudogene							cytoplasm (GO:0005737)	phosphatidylinositol phosphate kinase activity (GO:0016307)										GTGTCTGGGGTGAGTGTGGTC	0.527																																																	0																																												266971			BC068549		10q23.33	2010-10-27	2010-10-27	2007-07-06	ENSG00000180764	ENSG00000180764		"""Proteasome (prosome, macropain) subunits"""	23733	pseudogene	pseudogene			"""proteasome (prosome, macropain) 26S subunit, non-ATPase, 4, pseudogene 2"", ""phosphatidylinositol-4-phosphate 5-kinase, type I-like 1"", ""PIP5K1A and PSMD4-like"""	PSMD4P2, PIP5K1L1		16344562	Standard	NR_002319		Approved	PIP5K1A-PSMD4, PIP5K1P3	uc009xuj.2	A2A3N6	OTTHUMG00000137480		10.37:g.95719506T>G		Somatic		WXS	Illumina GAIIx	Phase_I	Q6NUK8	Missense_Mutation	SNP	ENST00000480546.1	37																																																																																					0.527	PIPSL-002	PUTATIVE	basic	processed_transcript	pseudogene	OTTHUMT00000351483.1		NR_002319	
PMVK	10654	broad.mit.edu	37	1	154904889	154904889	+	Missense_Mutation	SNP	A	A	T			TCGA-BP-5184-01A-01D-1429-08	TCGA-BP-5184-11A-01D-1429-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ddebed14-f47f-46e6-ac39-c74ed3363211	5d1f5125-65c2-4c47-843d-da1c531fdb04	g.chr1:154904889A>T	ENST00000368467.3	-	2	403	c.98T>A	c.(97-99)cTt>cAt	p.L33H		NM_006556.3	NP_006547.1	Q15126	PMVK_HUMAN	phosphomevalonate kinase	33					cholesterol biosynthetic process (GO:0006695)|isopentenyl diphosphate biosynthetic process, mevalonate pathway (GO:0019287)|response to cholesterol (GO:0070723)|small molecule metabolic process (GO:0044281)|sterol biosynthetic process (GO:0016126)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|peroxisome (GO:0005777)	ATP binding (GO:0005524)|phosphomevalonate kinase activity (GO:0004631)	p.L33H(1)		endometrium(1)|kidney(1)|large_intestine(1)|lung(3)	6	all_epithelial(22;4.9e-30)|all_lung(78;4.1e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)|all_neural(408;0.142)		BRCA - Breast invasive adenocarcinoma(34;0.00034)			ATCAGCTCCAAGTCTGCAGGA	0.542																																																	1	Substitution - Missense(1)	kidney(1)											98.0	88.0	92.0					1																	154904889		2203	4300	6503	SO:0001583	missense	10654			L77213	CCDS1073.1	1q21.3	2012-09-20			ENSG00000163344	ENSG00000163344	2.7.4.2		9141	protein-coding gene	gene with protein product		607622				8663599, 10191291	Standard	NM_006556		Approved	PMK, PMKA, HUMPMKI	uc001ffq.3	Q15126	OTTHUMG00000037415	ENST00000368467.3:c.98T>A	1.37:g.154904889A>T	ENSP00000357452:p.Leu33His	Somatic		WXS	Illumina GAIIx	Phase_I	Q5TZW9	Missense_Mutation	SNP	ENST00000368467.3	37	CCDS1073.1	.	.	.	.	.	.	.	.	.	.	A	22.4	4.284149	0.80803	.	.	ENSG00000163344	ENST00000368467	T	0.60548	0.18	4.59	4.59	0.56863	.	0.000000	0.64402	D	0.000002	T	0.69133	0.3077	M	0.83483	2.645	0.38190	D	0.939885	D	0.89917	1.0	D	0.75020	0.985	T	0.75241	-0.3387	10	0.72032	D	0.01	-16.4749	10.5455	0.45058	1.0:0.0:0.0:0.0	.	33	Q15126	PMVK_HUMAN	H	33	ENSP00000357452:L33H	ENSP00000357452:L33H	L	-	2	0	PMVK	153171513	0.998000	0.40836	0.082000	0.20525	0.784000	0.44337	5.638000	0.67861	2.053000	0.61076	0.459000	0.35465	CTT		0.542	PMVK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091088.1		NM_006556	
LINC01347	731275	broad.mit.edu	37	1	243251423	243251423	+	lincRNA	DEL	A	A	-	rs200578702	byFrequency	TCGA-BP-5184-01A-01D-1429-08	TCGA-BP-5184-11A-01D-1429-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ddebed14-f47f-46e6-ac39-c74ed3363211	5d1f5125-65c2-4c47-843d-da1c531fdb04	g.chr1:243251423delA	ENST00000417964.1	-	0	1346																											actccatctcaaaaaaaaaaa	0.458													|||unknown(NO_COVERAGE)	1468	0.293131	0.3033	0.3098	5008	,	,		13610	0.3333		0.2396	False		,,,				2504	0.2812																0																																												0																															1.37:g.243251423delA		Somatic		WXS	Illumina GAIIx	Phase_I		RNA	DEL	ENST00000417964.1	37																																																																																					0.458	RP11-261C10.3-006	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000096168.1			
