#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_ACHILLES_Lineage_Results_Top_Genes	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_ORegAnno_bin	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_ccds_id	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_type	i_havana_transcript	i_refseq_mrna_id	i_secondary_variant_classification	i_t_alt_count_full	i_t_ref_count_full	t_alt_count	t_ref_count
MYO3A	53904	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	10	26463288	26463288	+	Missense_Mutation	SNP	G	G	T			TCGA-HT-7688-01A-11D-2253-08	TCGA-HT-7688-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	35602eec-d9a6-4b1f-b4bf-0304d6f0337a	b1e48d0a-6c17-45b0-856c-58b9eba686c8	g.chr10:26463288G>T	ENST00000265944.5	+	30	4261	c.4095G>T	c.(4093-4095)caG>caT	p.Q1365H	MYO3A_ENST00000543632.1_Intron	NM_017433.4	NP_059129.3	Q8NEV4	MYO3A_HUMAN	myosin IIIA	1365	IQ 3. {ECO:0000255|PROSITE- ProRule:PRU00116}.				ATP catabolic process (GO:0006200)|inner ear development (GO:0048839)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of filopodium assembly (GO:0051491)|protein autophosphorylation (GO:0046777)|response to stimulus (GO:0050896)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|filamentous actin (GO:0031941)|filopodium (GO:0030175)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|photoreceptor inner segment (GO:0001917)|stereocilium bundle tip (GO:0032426)	actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|plus-end directed microfilament motor activity (GO:0060002)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(9)|central_nervous_system(3)|endometrium(9)|kidney(10)|large_intestine(28)|liver(1)|lung(46)|ovary(11)|pancreas(1)|prostate(6)|skin(11)|stomach(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	146						GAAGGCAGCAGTTGAGGAAGG	0.438																																																0													147.0	134.0	139.0					10																	26463288		2203	4300	6503	SO:0001583	missense	53904			AF229172	CCDS7148.1	10p11.1	2011-09-27	2004-05-19		ENSG00000095777	ENSG00000095777		"""Myosins / Myosin superfamily : Class III"""	7601	protein-coding gene	gene with protein product		606808	"""deafness, autosomal recessive 30"""	DFNB30		10936054	Standard	NM_017433		Approved		uc001isn.2	Q8NEV4	OTTHUMG00000017837	ENST00000265944.5:c.4095G>T	10.37:g.26463288G>T	ENSP00000265944:p.Gln1365His		Q4G0X2|Q5VZ28|Q8WX17|Q9NYS8	Missense_Mutation	SNP	ENST00000265944.5	37	CCDS7148.1	.	.	.	.	.	.	.	.	.	.	G	15.29	2.790568	0.50102	.	.	ENSG00000095777	ENST00000265944	T	0.78816	-1.21	5.73	-0.0819	0.13701	.	0.265537	0.43579	D	0.000547	T	0.79203	0.4406	L	0.39898	1.24	0.39229	D	0.963647	D	0.67145	0.996	D	0.64877	0.93	T	0.77619	-0.2520	10	0.72032	D	0.01	.	10.6713	0.45760	0.5169:0.0:0.4831:0.0	.	1365	Q8NEV4	MYO3A_HUMAN	H	1365	ENSP00000265944:Q1365H	ENSP00000265944:Q1365H	Q	+	3	2	MYO3A	26503294	0.059000	0.20769	0.023000	0.16930	0.152000	0.21847	-0.176000	0.09811	-0.311000	0.08754	-0.253000	0.11424	CAG		0.438	MYO3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047259.1	NM_017433		21	118	21	118
CYP2C19	1557	hgsc.bcm.edu;broad.mit.edu	37	10	96535297	96535297	+	Splice_Site	SNP	G	G	C	rs77576043		TCGA-HT-7688-01A-11D-2253-08	TCGA-HT-7688-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	35602eec-d9a6-4b1f-b4bf-0304d6f0337a	b1e48d0a-6c17-45b0-856c-58b9eba686c8	g.chr10:96535297G>C	ENST00000371321.3	+	3	563		c.e3+1		CYP2C19_ENST00000464755.1_Splice_Site	NM_000769.1	NP_000760	P33261	CP2CJ_HUMAN	cytochrome P450, family 2, subfamily C, polypeptide 19						arachidonic acid metabolic process (GO:0019369)|drug metabolic process (GO:0017144)|epoxygenase P450 pathway (GO:0019373)|exogenous drug catabolic process (GO:0042738)|heterocycle metabolic process (GO:0046483)|monoterpenoid metabolic process (GO:0016098)|omega-hydroxylase P450 pathway (GO:0097267)|oxidation-reduction process (GO:0055114)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|intracellular membrane-bounded organelle (GO:0043231)	(R)-limonene 6-monooxygenase activity (GO:0052741)|(S)-limonene 6-monooxygenase activity (GO:0018675)|(S)-limonene 7-monooxygenase activity (GO:0018676)|enzyme binding (GO:0019899)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity (GO:0016491)|oxygen binding (GO:0019825)|steroid hydroxylase activity (GO:0008395)			central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(5)|lung(17)|ovary(4)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	43		Colorectal(252;0.09)		all cancers(201;6.02e-07)|KIRC - Kidney renal clear cell carcinoma(50;0.0672)|Kidney(138;0.0838)	Acenocoumarol(DB01418)|Acetylsalicylic acid(DB00945)|Adinazolam(DB00546)|Almotriptan(DB00918)|Aminoglutethimide(DB00357)|Aminophenazone(DB01424)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amoxicillin(DB01060)|Amprenavir(DB00701)|Antipyrine(DB01435)|Apixaban(DB06605)|Aprepitant(DB00673)|Arformoterol(DB01274)|Artemether(DB06697)|Atomoxetine(DB00289)|Atorvastatin(DB01076)|Axitinib(DB06626)|Azelastine(DB00972)|Benzatropine(DB00245)|Bicalutamide(DB01128)|Bifonazole(DB04794)|Bortezomib(DB00188)|Bromazepam(DB01558)|Brompheniramine(DB00835)|Bupivacaine(DB00297)|Buprenorphine(DB00921)|Carbamazepine(DB00564)|Carbinoxamine(DB00748)|Carisoprodol(DB00395)|Chloramphenicol(DB00446)|Chlorpropamide(DB00672)|Cholecalciferol(DB00169)|Cilostazol(DB01166)|Cimetidine(DB00501)|Cisapride(DB00604)|Citalopram(DB00215)|Clarithromycin(DB01211)|Clevidipine(DB04920)|Clobazam(DB00349)|Clomipramine(DB01242)|Clopidogrel(DB00758)|Clotiazepam(DB01559)|Clotrimazole(DB00257)|Clozapine(DB00363)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dapsone(DB00250)|Delavirdine(DB00705)|Desipramine(DB01151)|Desloratadine(DB00967)|Dexamethasone(DB01234)|Dexfenfluramine(DB01191)|Dextromethorphan(DB00514)|Diazepam(DB00829)|Diclofenac(DB00586)|Diltiazem(DB00343)|Dimethyl sulfoxide(DB01093)|Diphenhydramine(DB01075)|Dopamine(DB00988)|Doxazosin(DB00590)|Doxepin(DB01142)|Dronabinol(DB00470)|Efavirenz(DB00625)|Eletriptan(DB00216)|Enfuvirtide(DB00109)|Enzalutamide(DB08899)|Escitalopram(DB01175)|Esomeprazole(DB00736)|Estradiol(DB00783)|Ethanol(DB00898)|Ethotoin(DB00754)|Etoricoxib(DB01628)|Etravirine(DB06414)|Famotidine(DB00927)|Felbamate(DB00949)|Fluconazole(DB00196)|Flunitrazepam(DB01544)|Fluoxetine(DB00472)|Flutamide(DB00499)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Formoterol(DB00983)|Fosphenytoin(DB01320)|Gefitinib(DB00317)|Gemfibrozil(DB01241)|Gliclazide(DB01120)|Glucosamine(DB01296)|Glyburide(DB01016)|Guanfacine(DB01018)|Haloperidol(DB00502)|Hexobarbital(DB01355)|Ibuprofen(DB01050)|Ifosfamide(DB01181)|Imatinib(DB00619)|Imipramine(DB00458)|Indinavir(DB00224)|Indomethacin(DB00328)|Isoniazid(DB00951)|Ketobemidone(DB06738)|Ketoconazole(DB01026)|Lansoprazole(DB00448)|Lapatinib(DB01259)|Levomilnacipran(DB08918)|Lopinavir(DB01601)|Loratadine(DB00455)|Lorcaserin(DB04871)|Losartan(DB00678)|Lovastatin(DB00227)|LULICONAZOLE(DB08933)|Lumiracoxib(DB01283)|MACITENTAN(DB08932)|Melatonin(DB01065)|Memantine(DB01043)|Meprobamate(DB00371)|Methadone(DB00333)|Methazolamide(DB00703)|Methimazole(DB00763)|Methsuximide(DB05246)|Methylphenobarbital(DB00849)|Metoprolol(DB00264)|Miconazole(DB01110)|Moclobemide(DB01171)|Modafinil(DB00745)|Nelfinavir(DB00220)|Nicardipine(DB00622)|Nicotine(DB00184)|Nilutamide(DB00665)|Nilvadipine(DB06712)|Norethindrone(DB00717)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Omeprazole(DB00338)|Ospemifene(DB04938)|Oxcarbazepine(DB00776)|Oxiconazole(DB00239)|Pantoprazole(DB00213)|Pegvisomant(DB00082)|Pentamidine(DB00738)|Pentobarbital(DB00312)|Perphenazine(DB00850)|Pethidine(DB00454)|Phenelzine(DB00780)|Phenobarbital(DB01174)|Phensuximide(DB00832)|Phenytoin(DB00252)|Pimozide(DB01100)|Pioglitazone(DB01132)|Pipotiazine(DB01621)|Podofilox(DB01179)|Prasugrel(DB06209)|Praziquantel(DB01058)|Prednisone(DB00635)|Primidone(DB00794)|Probenecid(DB01032)|Progesterone(DB00396)|Proguanil(DB01131)|Promazine(DB00420)|Propofol(DB00818)|Propranolol(DB00571)|Quazepam(DB01589)|Quetiapine(DB01224)|Quinine(DB00468)|Rabeprazole(DB01129)|Ramelteon(DB00980)|Ranitidine(DB00863)|Regorafenib(DB08896)|Rifampicin(DB01045)|Rilpivirine(DB08864)|Ritonavir(DB00503)|Rosiglitazone(DB00412)|Rosuvastatin(DB01098)|Saquinavir(DB01232)|Selegiline(DB01037)|Sertraline(DB01104)|Sildenafil(DB00203)|Simvastatin(DB00641)|Sitaxentan(DB06268)|Sorafenib(DB00398)|Sulfanilamide(DB00259)|Tamoxifen(DB00675)|Tapentadol(DB06204)|Telmisartan(DB00966)|Temazepam(DB00231)|Teniposide(DB00444)|Terbinafine(DB00857)|Testosterone(DB00624)|Thalidomide(DB01041)|Thioridazine(DB00679)|Ticlopidine(DB00208)|Timolol(DB00373)|Tioconazole(DB01007)|Tipranavir(DB00932)|Tofacitinib(DB08895)|Tolbutamide(DB01124)|Tolterodine(DB01036)|Topiramate(DB00273)|Torasemide(DB00214)|Trabectedin(DB05109)|Tranylcypromine(DB00752)|Trimethadione(DB00347)|Trimipramine(DB00726)|Troleandomycin(DB01361)|Valproic Acid(DB00313)|Venlafaxine(DB00285)|Verapamil(DB00661)|Vismodegib(DB08828)|Voriconazole(DB00582)|Warfarin(DB00682)|Zafirlukast(DB00549)|Zidovudine(DB00495)|Zolpidem(DB00425)|Zonisamide(DB00909)	AAAACCAAGGGTGGGTGAACA	0.498																																																0													161.0	156.0	158.0					10																	96535297		2203	4300	6503	SO:0001630	splice_region_variant	1557			M61854	CCDS7436.1	10q24	2007-12-14	2003-01-14		ENSG00000165841	ENSG00000165841		"""Cytochrome P450s"""	2621	protein-coding gene	gene with protein product		124020	"""cytochrome P450, subfamily IIC (mephenytoin 4-hydroxylase), polypeptide 19"""	CYP2C		2009263, 8530044	Standard	NM_000769		Approved	P450IIC19, CPCJ	uc010qnz.2	P33261	OTTHUMG00000018799	ENST00000371321.3:c.481+1G>C	10.37:g.96535297G>C			P33259|Q8WZB1|Q8WZB2|Q9UCD4	Splice_Site	SNP	ENST00000371321.3	37	CCDS7436.1	.	.	.	.	.	.	.	.	.	.	-	8.181	0.793795	0.16327	.	.	ENSG00000165841	ENST00000371321	.	.	.	3.9	3.9	0.45041	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	9.2773	0.37707	0.0:0.0:0.7845:0.2155	.	.	.	.	.	-1	.	.	.	+	.	.	CYP2C19	96525287	1.000000	0.71417	0.507000	0.27676	0.196000	0.23810	7.725000	0.84808	1.888000	0.54679	0.405000	0.27470	.		0.498	CYP2C19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049490.1	NM_000769	Intron	11	184	11	184
CFAP43	80217	hgsc.bcm.edu;broad.mit.edu	37	10	105990460	105990460	+	Silent	SNP	G	G	A	rs374123628		TCGA-HT-7688-01A-11D-2253-08	TCGA-HT-7688-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	35602eec-d9a6-4b1f-b4bf-0304d6f0337a	b1e48d0a-6c17-45b0-856c-58b9eba686c8	g.chr10:105990460G>A	ENST00000357060.3	-	2	322	c.207C>T	c.(205-207)ggC>ggT	p.G69G	WDR96_ENST00000278064.2_5'UTR|WDR96_ENST00000369720.1_5'UTR|WDR96_ENST00000369719.1_5'UTR|WDR96_ENST00000428666.1_Silent_p.G69G	NM_025145.5	NP_079421.5												p.G69G(2)		NS(1)|breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(14)|lung(21)|ovary(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	72						TTGCCATGACGCCCACAATTC	0.408																																																2	Substitution - coding silent(2)	large_intestine(2)						G		0,4406		0,0,2203	144.0	132.0	136.0		207	1.3	1.0	10		136	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	WDR96	NM_025145.5		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		69/1666	105990460	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	80217																														ENST00000357060.3:c.207C>T	10.37:g.105990460G>A				Silent	SNP	ENST00000357060.3	37	CCDS31281.1																																																																																				0.408	WDR96-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				5	87	5	87
DCHS1	8642	hgsc.bcm.edu;broad.mit.edu	37	11	6645159	6645159	+	Missense_Mutation	SNP	C	C	G			TCGA-HT-7688-01A-11D-2253-08	TCGA-HT-7688-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	35602eec-d9a6-4b1f-b4bf-0304d6f0337a	b1e48d0a-6c17-45b0-856c-58b9eba686c8	g.chr11:6645159C>G	ENST00000299441.3	-	21	8159	c.7748G>C	c.(7747-7749)aGc>aCc	p.S2583T	RP11-732A19.5_ENST00000526456.1_RNA	NM_003737.2	NP_003728.1	Q96JQ0	PCD16_HUMAN	dachsous cadherin-related 1	2583	Cadherin 24. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|calcium-dependent cell-cell adhesion (GO:0016339)|cochlea development (GO:0090102)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|neural tube development (GO:0021915)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|post-anal tail morphogenesis (GO:0036342)	apical part of cell (GO:0045177)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(16)|liver(1)|lung(41)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	103		Medulloblastoma(188;0.00263)|all_neural(188;0.026)		Epithelial(150;6.35e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		CACGACTGAGCTTTGGGGTGG	0.537																																																0													109.0	98.0	102.0					11																	6645159		2201	4296	6497	SO:0001583	missense	8642			AB000895	CCDS7771.1	11p15.4	2013-10-04	2013-10-04	2004-09-03	ENSG00000166341	ENSG00000166341		"""Cadherins / Cadherin-related"""	13681	protein-coding gene	gene with protein product	"""cadherin-related family member 6"""	603057	"""protocadherin 16"", ""dachsous 1 (Drosophila)"""	CDH25, PCDH16		9199196	Standard	XM_005253207		Approved	FIB1, KIAA1773, FLJ11790, CDHR6	uc001mem.1	Q96JQ0	OTTHUMG00000133398	ENST00000299441.3:c.7748G>C	11.37:g.6645159C>G	ENSP00000299441:p.Ser2583Thr		O15098	Missense_Mutation	SNP	ENST00000299441.3	37	CCDS7771.1	.	.	.	.	.	.	.	.	.	.	C	12.14	1.848311	0.32699	.	.	ENSG00000166341	ENST00000299441	T	0.52295	0.67	5.03	5.03	0.67393	Cadherin (4);Cadherin-like (1);	0.000000	0.53938	D	0.000052	T	0.56156	0.1966	N	0.25890	0.77	0.80722	D	1	D	0.76494	0.999	D	0.83275	0.996	T	0.52305	-0.8593	10	0.32370	T	0.25	.	17.1275	0.86718	0.0:1.0:0.0:0.0	.	2583	Q96JQ0	PCD16_HUMAN	T	2583	ENSP00000299441:S2583T	ENSP00000299441:S2583T	S	-	2	0	DCHS1	6601735	1.000000	0.71417	0.987000	0.45799	0.053000	0.15095	5.887000	0.69751	2.626000	0.88956	0.650000	0.86243	AGC		0.537	DCHS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257258.1	NM_003737		10	185	10	185
DCHS1	8642	hgsc.bcm.edu;broad.mit.edu	37	11	6645181	6645181	+	Missense_Mutation	SNP	C	C	G			TCGA-HT-7688-01A-11D-2253-08	TCGA-HT-7688-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	35602eec-d9a6-4b1f-b4bf-0304d6f0337a	b1e48d0a-6c17-45b0-856c-58b9eba686c8	g.chr11:6645181C>G	ENST00000299441.3	-	21	8137	c.7726G>C	c.(7726-7728)Gac>Cac	p.D2576H	RP11-732A19.5_ENST00000526456.1_RNA	NM_003737.2	NP_003728.1	Q96JQ0	PCD16_HUMAN	dachsous cadherin-related 1	2576	Cadherin 24. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|calcium-dependent cell-cell adhesion (GO:0016339)|cochlea development (GO:0090102)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|neural tube development (GO:0021915)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|post-anal tail morphogenesis (GO:0036342)	apical part of cell (GO:0045177)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(16)|liver(1)|lung(41)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	103		Medulloblastoma(188;0.00263)|all_neural(188;0.026)		Epithelial(150;6.35e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TGCCCACGGTCAGCTGCAGCC	0.562																																																0													72.0	68.0	69.0					11																	6645181		2201	4296	6497	SO:0001583	missense	8642			AB000895	CCDS7771.1	11p15.4	2013-10-04	2013-10-04	2004-09-03	ENSG00000166341	ENSG00000166341		"""Cadherins / Cadherin-related"""	13681	protein-coding gene	gene with protein product	"""cadherin-related family member 6"""	603057	"""protocadherin 16"", ""dachsous 1 (Drosophila)"""	CDH25, PCDH16		9199196	Standard	XM_005253207		Approved	FIB1, KIAA1773, FLJ11790, CDHR6	uc001mem.1	Q96JQ0	OTTHUMG00000133398	ENST00000299441.3:c.7726G>C	11.37:g.6645181C>G	ENSP00000299441:p.Asp2576His		O15098	Missense_Mutation	SNP	ENST00000299441.3	37	CCDS7771.1	.	.	.	.	.	.	.	.	.	.	C	11.23	1.578145	0.28180	.	.	ENSG00000166341	ENST00000299441	T	0.68903	-0.36	5.03	4.13	0.48395	Cadherin (4);Cadherin-like (1);	0.000000	0.47852	D	0.000204	D	0.86661	0.5986	H	0.96916	3.905	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	D	0.90164	0.4230	10	0.87932	D	0	.	12.3353	0.55062	0.0:0.9181:0.0:0.0819	.	2576	Q96JQ0	PCD16_HUMAN	H	2576	ENSP00000299441:D2576H	ENSP00000299441:D2576H	D	-	1	0	DCHS1	6601757	1.000000	0.71417	1.000000	0.80357	0.003000	0.03518	7.629000	0.83207	1.363000	0.46019	-0.145000	0.13849	GAC		0.562	DCHS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257258.1	NM_003737		6	119	6	119
RPUSD4	84881	hgsc.bcm.edu;broad.mit.edu	37	11	126075477	126075477	+	Missense_Mutation	SNP	C	C	T	rs143531642		TCGA-HT-7688-01A-11D-2253-08	TCGA-HT-7688-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	35602eec-d9a6-4b1f-b4bf-0304d6f0337a	b1e48d0a-6c17-45b0-856c-58b9eba686c8	g.chr11:126075477C>T	ENST00000298317.4	-	5	735	c.682G>A	c.(682-684)Gat>Aat	p.D228N	RPUSD4_ENST00000533628.1_Intron|RPUSD4_ENST00000534393.1_5'UTR	NM_032795.2	NP_116184.2	Q96CM3	RUSD4_HUMAN	RNA pseudouridylate synthase domain containing 4	228					pseudouridine synthesis (GO:0001522)	mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|pseudouridine synthase activity (GO:0009982)			breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(3)|lung(8)|skin(1)	17	all_hematologic(175;0.145)	Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.0919)|all_lung(97;0.0994)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.13e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0761)		ATTTTCCCATCGTCCATGCGG	0.557																																																0													121.0	109.0	113.0					11																	126075477		2201	4299	6500	SO:0001583	missense	84881			BC014131	CCDS8469.1, CCDS53721.1	11q24.2	2013-02-11			ENSG00000165526	ENSG00000165526		"""RNA pseudouridylate synthase domain containing"""	25898	protein-coding gene	gene with protein product							Standard	NM_032795		Approved	FLJ14494	uc001qde.3	Q96CM3	OTTHUMG00000165815	ENST00000298317.4:c.682G>A	11.37:g.126075477C>T	ENSP00000298317:p.Asp228Asn		E9PML2|Q96K56	Missense_Mutation	SNP	ENST00000298317.4	37	CCDS8469.1	.	.	.	.	.	.	.	.	.	.	C	3.700	-0.061676	0.07317	.	.	ENSG00000165526	ENST00000298317	T	0.14516	2.5	5.72	-0.435	0.12279	Pseudouridine synthase, RsuA and RluB/C/D/E/F (1);Pseudouridine synthase, catalytic domain (1);	0.902722	0.09786	N	0.756001	T	0.12135	0.0295	L	0.48218	1.51	0.23411	N	0.997736	B	0.06786	0.001	B	0.04013	0.001	T	0.35226	-0.9797	10	0.27785	T	0.31	-1.3144	9.4769	0.38878	0.0:0.5043:0.0:0.4957	.	228	Q96CM3	RUSD4_HUMAN	N	228	ENSP00000298317:D228N	ENSP00000298317:D228N	D	-	1	0	RPUSD4	125580687	0.000000	0.05858	0.223000	0.23860	0.107000	0.19398	-0.024000	0.12435	-0.096000	0.12329	-1.004000	0.02495	GAT		0.557	RPUSD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386336.1	NM_032795		9	121	9	121
CUL4A	8451	hgsc.bcm.edu;broad.mit.edu	37	13	113891149	113891149	+	Silent	SNP	T	T	C			TCGA-HT-7688-01A-11D-2253-08	TCGA-HT-7688-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	35602eec-d9a6-4b1f-b4bf-0304d6f0337a	b1e48d0a-6c17-45b0-856c-58b9eba686c8	g.chr13:113891149T>C	ENST00000375440.4	+	9	945	c.861T>C	c.(859-861)atT>atC	p.I287I	CUL4A_ENST00000375441.3_Silent_p.I187I|CUL4A_ENST00000326335.4_Silent_p.I187I|CUL4A_ENST00000451881.1_Silent_p.I187I	NM_001008895.1	NP_001008895.1	Q13619	CUL4A_HUMAN	cullin 4A	287					cell cycle arrest (GO:0007050)|DNA repair (GO:0006281)|G1/S transition of mitotic cell cycle (GO:0000082)|hemopoiesis (GO:0030097)|intrinsic apoptotic signaling pathway (GO:0097193)|negative regulation of cell proliferation (GO:0008285)|negative regulation of granulocyte differentiation (GO:0030853)|positive regulation of cell proliferation (GO:0008284)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567)|regulation of DNA damage checkpoint (GO:2000001)|regulation of nucleotide-excision repair (GO:2000819)|regulation of protein metabolic process (GO:0051246)|somatic stem cell maintenance (GO:0035019)|viral process (GO:0016032)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)|Cul4A-RING E3 ubiquitin ligase complex (GO:0031464)				NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(1)|large_intestine(5)|lung(5)|skin(1)	17	Lung NSC(43;0.0161)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0482)|all_epithelial(44;0.0148)|all_lung(25;0.0271)|Lung NSC(25;0.0977)|Breast(118;0.188)	all cancers(43;0.112)			AACCACTGATTGCTTGTGTGG	0.358																																																0													106.0	106.0	106.0					13																	113891149		2203	4300	6503	SO:0001819	synonymous_variant	8451			U58090	CCDS9533.1, CCDS41908.1, CCDS73604.1	13q34	2011-05-24			ENSG00000139842	ENSG00000139842			2554	protein-coding gene	gene with protein product		603137				8681378	Standard	NM_001008895		Approved		uc021rmv.1	Q13619	OTTHUMG00000017384	ENST00000375440.4:c.861T>C	13.37:g.113891149T>C			A2A2W2|O75834|Q589T6|Q5TC62|Q6UP08|Q9UP17	Silent	SNP	ENST00000375440.4	37	CCDS41908.1																																																																																				0.358	CUL4A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045888.3	NM_003589		4	70	4	70
SUPT16H	11198	hgsc.bcm.edu;broad.mit.edu	37	14	21838616	21838616	+	Missense_Mutation	SNP	A	A	G			TCGA-HT-7688-01A-11D-2253-08	TCGA-HT-7688-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	35602eec-d9a6-4b1f-b4bf-0304d6f0337a	b1e48d0a-6c17-45b0-856c-58b9eba686c8	g.chr14:21838616A>G	ENST00000216297.2	-	4	700	c.362T>C	c.(361-363)aTg>aCg	p.M121T		NM_007192.3	NP_009123.1	Q9Y5B9	SP16H_HUMAN	suppressor of Ty 16 homolog (S. cerevisiae)	121					DNA repair (GO:0006281)|DNA replication (GO:0006260)|gene expression (GO:0010467)|nucleosome disassembly (GO:0006337)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|positive regulation of viral transcription (GO:0050434)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(4)|kidney(1)|large_intestine(9)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	27	all_cancers(95;0.00115)		Epithelial(56;1.62e-06)|all cancers(55;1.49e-05)	GBM - Glioblastoma multiforme(265;0.0159)		GGCTTCAATCATTTTGTCAAA	0.383																																																0													136.0	125.0	129.0					14																	21838616		2202	4300	6502	SO:0001583	missense	11198			AF152961	CCDS9569.1	14q11.1	2008-08-13	2001-11-28		ENSG00000092201	ENSG00000092201			11465	protein-coding gene	gene with protein product	"""facilitates chromatin remodeling 140 kDa subunit"""	605012	"""suppressor of Ty (S.cerevisiae) 16 homolog"""			9489704, 11239457	Standard	NM_007192		Approved	FACT, FACTP140, SPT16/CDC68, FLJ14010, FLJ10857, CDC68	uc001wao.2	Q9Y5B9	OTTHUMG00000029685	ENST00000216297.2:c.362T>C	14.37:g.21838616A>G	ENSP00000216297:p.Met121Thr		Q6GMT8|Q6P2F1|Q6PJM1|Q9NRX0	Missense_Mutation	SNP	ENST00000216297.2	37	CCDS9569.1	.	.	.	.	.	.	.	.	.	.	A	16.65	3.181100	0.57800	.	.	ENSG00000092201	ENST00000216297;ENST00000538230	.	.	.	5.87	5.87	0.94306	.	0.038047	0.85682	D	0.000000	T	0.59945	0.2231	L	0.54323	1.7	0.80722	D	1	B	0.16802	0.019	B	0.18263	0.021	T	0.57653	-0.7774	9	0.56958	D	0.05	-23.2946	15.2599	0.73613	1.0:0.0:0.0:0.0	.	121	Q9Y5B9	SP16H_HUMAN	T	121	.	ENSP00000216297:M121T	M	-	2	0	SUPT16H	20908456	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.778000	0.91785	2.247000	0.74100	0.482000	0.46254	ATG		0.383	SUPT16H-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000074025.2			4	62	4	62
CHD8	57680	hgsc.bcm.edu;broad.mit.edu	37	14	21861840	21861840	+	Silent	SNP	T	T	G			TCGA-HT-7688-01A-11D-2253-08	TCGA-HT-7688-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	35602eec-d9a6-4b1f-b4bf-0304d6f0337a	b1e48d0a-6c17-45b0-856c-58b9eba686c8	g.chr14:21861840T>G	ENST00000557364.1	-	32	6377	c.6114A>C	c.(6112-6114)ccA>ccC	p.P2038P	CHD8_ENST00000555962.1_5'Flank|CHD8_ENST00000430710.3_Silent_p.P1759P|CHD8_ENST00000399982.2_Silent_p.P2038P|SNORD9_ENST00000362566.1_RNA			Q9HCK8	CHD8_HUMAN	chromodomain helicase DNA binding protein 8	2038					ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|canonical Wnt signaling pathway (GO:0060070)|DNA duplex unwinding (GO:0032508)|in utero embryonic development (GO:0001701)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of Wnt signaling pathway (GO:0030178)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	MLL1 complex (GO:0071339)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|beta-catenin binding (GO:0008013)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA-dependent ATPase activity (GO:0008094)|histone binding (GO:0042393)|methylated histone binding (GO:0035064)|p53 binding (GO:0002039)			NS(2)|breast(1)|central_nervous_system(1)|cervix(4)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(8)|lung(33)|ovary(6)|prostate(7)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	85	all_cancers(95;0.00121)		Epithelial(56;2.55e-06)|all cancers(55;1.73e-05)	GBM - Glioblastoma multiforme(265;0.00424)		CATAGTCTTGTGGGGTTGGTC	0.547																																																0													57.0	59.0	58.0					14																	21861840		1999	4169	6168	SO:0001819	synonymous_variant	57680			AB046784	CCDS45081.1, CCDS53885.1	14q11.2	2008-02-05	2004-06-22	2004-06-23		ENSG00000100888			20153	protein-coding gene	gene with protein product		610528	"""helicase with SNF2 domain 1"""	HELSNF1		10997877	Standard	NM_020920		Approved	KIAA1564, DUPLIN	uc001war.2	Q9HCK8		ENST00000557364.1:c.6114A>C	14.37:g.21861840T>G			Q4G0D8|Q68DQ0|Q6DKH9|Q6P440|Q6ZNL7|Q8N3Z9|Q8NCY4|Q8TBR9|Q96F26	Silent	SNP	ENST00000557364.1	37	CCDS53885.1																																																																																				0.547	CHD8-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410436.1	NM_020920		5	60	5	60
TRIM9	114088	hgsc.bcm.edu;broad.mit.edu	37	14	51446210	51446210	+	Silent	SNP	T	T	C			TCGA-HT-7688-01A-11D-2253-08	TCGA-HT-7688-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	35602eec-d9a6-4b1f-b4bf-0304d6f0337a	b1e48d0a-6c17-45b0-856c-58b9eba686c8	g.chr14:51446210T>C	ENST00000298355.3	-	9	3086	c.1965A>G	c.(1963-1965)agA>agG	p.R655R	TRIM9_ENST00000338969.5_Silent_p.R736R	NM_015163.5	NP_055978.4	Q9C026	TRIM9_HUMAN	tripartite motif containing 9	655	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				negative regulation of calcium ion-dependent exocytosis (GO:0045955)|negative regulation of SNARE complex assembly (GO:0035544)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|synaptic vesicle exocytosis (GO:0016079)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dendrite (GO:0030425)|synaptic vesicle (GO:0008021)	ligase activity (GO:0016874)|protein homodimerization activity (GO:0042803)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|endometrium(4)|kidney(2)|large_intestine(7)|liver(1)|lung(11)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	31	all_epithelial(31;0.00418)|Breast(41;0.148)					TCAAGTTTTTTCTATTTAAGT	0.453																																																0													197.0	215.0	209.0					14																	51446210		2203	4300	6503	SO:0001819	synonymous_variant	114088			AF220036	CCDS9703.1, CCDS45105.1	14q21.3	2013-02-11	2011-01-25		ENSG00000100505	ENSG00000100505		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"", ""Fibronectin type III domain containing"""	16288	protein-coding gene	gene with protein product		606555	"""tripartite motif-containing 9"""			11331580, 11524423	Standard	NM_015163		Approved	SPRING, RNF91	uc001wyx.4	Q9C026	OTTHUMG00000140291	ENST00000298355.3:c.1965A>G	14.37:g.51446210T>C			D3DSB7|D3DSB8|Q92557|Q96D24|Q96NI4|Q9C025|Q9C027	Silent	SNP	ENST00000298355.3	37	CCDS9703.1																																																																																				0.453	TRIM9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276874.1	NM_015163		13	222	13	222
GATM	2628	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	15	45658331	45658331	+	Silent	SNP	T	T	C			TCGA-HT-7688-01A-11D-2253-08	TCGA-HT-7688-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	35602eec-d9a6-4b1f-b4bf-0304d6f0337a	b1e48d0a-6c17-45b0-856c-58b9eba686c8	g.chr15:45658331T>C	ENST00000396659.3	-	6	1230	c.891A>G	c.(889-891)aaA>aaG	p.K297K	GATM_ENST00000558336.1_Silent_p.K297K	NM_001482.2	NP_001473.1	P50440	GATM_HUMAN	glycine amidinotransferase (L-arginine:glycine amidinotransferase)	297					cellular nitrogen compound metabolic process (GO:0034641)|creatine biosynthetic process (GO:0006601)|creatine metabolic process (GO:0006600)|embryo development (GO:0009790)|response to mercury ion (GO:0046689)|response to nutrient (GO:0007584)|response to oxidative stress (GO:0006979)|response to peptide hormone (GO:0043434)|small molecule metabolic process (GO:0044281)|tissue regeneration (GO:0042246)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)	glycine amidinotransferase activity (GO:0015068)|hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amidines (GO:0016813)			biliary_tract(1)|breast(1)|endometrium(1)|large_intestine(2)|lung(6)|prostate(2)|skin(1)|urinary_tract(1)	15		all_cancers(109;1.25e-09)|all_epithelial(112;5.56e-08)|Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;4.87e-16)|GBM - Glioblastoma multiforme(94;1.97e-06)	Glycine(DB00145)|L-Ornithine(DB00129)	GATTGGGATCTTTAAAGGAGA	0.428																																																0													173.0	154.0	160.0					15																	45658331		2198	4298	6496	SO:0001819	synonymous_variant	2628			S68805	CCDS10122.1	15q15.1	2007-12-06			ENSG00000171766	ENSG00000171766	2.1.4.1		4175	protein-coding gene	gene with protein product		602360				8313955	Standard	NM_001482		Approved	AGAT	uc001zvc.3	P50440	OTTHUMG00000131427	ENST00000396659.3:c.891A>G	15.37:g.45658331T>C			B4DH99|B4DPI3|Q53EQ4	Silent	SNP	ENST00000396659.3	37	CCDS10122.1																																																																																				0.428	GATM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254220.2	NM_001482		23	68	23	68
SEMA6D	80031	hgsc.bcm.edu;broad.mit.edu	37	15	48052514	48052514	+	Nonsense_Mutation	SNP	T	T	A			TCGA-HT-7688-01A-11D-2253-08	TCGA-HT-7688-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	35602eec-d9a6-4b1f-b4bf-0304d6f0337a	b1e48d0a-6c17-45b0-856c-58b9eba686c8	g.chr15:48052514T>A	ENST00000316364.5	+	3	562	c.123T>A	c.(121-123)taT>taA	p.Y41*	SEMA6D_ENST00000355997.3_Nonsense_Mutation_p.Y41*|SEMA6D_ENST00000354744.4_Nonsense_Mutation_p.Y41*|SEMA6D_ENST00000389433.2_Nonsense_Mutation_p.Y41*|SEMA6D_ENST00000537942.1_Nonsense_Mutation_p.Y41*|SEMA6D_ENST00000389428.3_Nonsense_Mutation_p.Y41*|SEMA6D_ENST00000389432.2_Nonsense_Mutation_p.Y41*|SEMA6D_ENST00000536845.2_Nonsense_Mutation_p.Y41*|SEMA6D_ENST00000558816.1_Nonsense_Mutation_p.Y41*|SEMA6D_ENST00000358066.4_Nonsense_Mutation_p.Y41*|SEMA6D_ENST00000389425.3_Nonsense_Mutation_p.Y41*|SEMA6D_ENST00000558014.1_Nonsense_Mutation_p.Y41*	NM_153618.1	NP_705871.1	Q8NFY4	SEM6D_HUMAN	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D	41	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|negative regulation of smooth muscle cell migration (GO:0014912)|positive regulation of smooth muscle cell migration (GO:0014911)|ventricular system development (GO:0021591)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			biliary_tract(1)|breast(4)|endometrium(4)|kidney(5)|large_intestine(10)|lung(42)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(4)	77		all_lung(180;0.000635)|Myeloproliferative disorder(241;0.116)|Melanoma(134;0.18)		all cancers(107;1.2e-11)|GBM - Glioblastoma multiforme(94;1.2e-06)		CAAGGCAATATCCGGTTTTTA	0.418																																																0													101.0	91.0	94.0					15																	48052514		2198	4297	6495	SO:0001587	stop_gained	80031			AF389430	CCDS32224.1, CCDS32225.1, CCDS32226.1, CCDS32227.1, CCDS32228.1, CCDS32229.1	15q21.1	2006-09-18				ENSG00000137872		"""Semaphorins"""	16770	protein-coding gene	gene with protein product		609295				12110693, 14977921	Standard	NM_020858		Approved	KIAA1479, FLJ11598	uc001zvy.3	Q8NFY4		ENST00000316364.5:c.123T>A	15.37:g.48052514T>A	ENSP00000324857:p.Tyr41*		A6NF10|A6NM95|A6NNK1|A7E2A0|Q8NFY3|Q8NFY5|Q8NFY6|Q8NFY7|Q9P249	Nonsense_Mutation	SNP	ENST00000316364.5	37	CCDS32225.1	.	.	.	.	.	.	.	.	.	.	T	39	7.305995	0.98200	.	.	ENSG00000137872	ENST00000537942;ENST00000536845;ENST00000316364;ENST00000389433;ENST00000389432;ENST00000354744;ENST00000358066;ENST00000389428;ENST00000355997;ENST00000389425	.	.	.	5.76	4.65	0.58169	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	11.2119	0.48804	0.0:0.0711:0.0:0.9289	.	.	.	.	X	41	.	ENSP00000324857:Y41X	Y	+	3	2	SEMA6D	45839806	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.787000	0.55439	2.202000	0.70862	0.533000	0.62120	TAT		0.418	SEMA6D-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416868.1	NM_024966		3	59	3	59
PDE8A	5151	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	15	85619979	85619979	+	Missense_Mutation	SNP	G	G	C			TCGA-HT-7688-01A-11D-2253-08	TCGA-HT-7688-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	35602eec-d9a6-4b1f-b4bf-0304d6f0337a	b1e48d0a-6c17-45b0-856c-58b9eba686c8	g.chr15:85619979G>C	ENST00000310298.4	+	6	759	c.507G>C	c.(505-507)gaG>gaC	p.E169D	PDE8A_ENST00000557957.1_Missense_Mutation_p.E97D|PDE8A_ENST00000339708.5_Missense_Mutation_p.E169D|PDE8A_ENST00000394553.1_Missense_Mutation_p.E169D|PDE8A_ENST00000557819.2_3'UTR			O60658	PDE8A_HUMAN	phosphodiesterase 8A	169					cAMP catabolic process (GO:0006198)|cyclic nucleotide metabolic process (GO:0009187)|phosphorelay signal transduction system (GO:0000160)|regulation of transcription, DNA-templated (GO:0006355)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(8)|ovary(2)|pancreas(1)|prostate(1)|skin(2)	25	Colorectal(223;0.227)		BRCA - Breast invasive adenocarcinoma(143;0.0608)		Caffeine(DB00201)|Ketotifen(DB00920)	ATAGAGAAGAGTTGTCCGTAA	0.294																																																0													206.0	198.0	201.0					15																	85619979		2203	4299	6502	SO:0001583	missense	5151			AF056490	CCDS10336.1, CCDS10337.1, CCDS58397.1	15q25.3	2008-05-14			ENSG00000073417	ENSG00000073417	3.1.4.17	"""Phosphodiesterases"""	8793	protein-coding gene	gene with protein product		602972				9618252	Standard	NM_001243137		Approved	HsT19550	uc002blh.3	O60658	OTTHUMG00000148670	ENST00000310298.4:c.507G>C	15.37:g.85619979G>C	ENSP00000311453:p.Glu169Asp		B3KXE6|H0YMZ7|Q6P9H3|Q969I1|Q96PC9|Q96PD0|Q96PD1|Q96T71|Q9UMB7|Q9UMC3	Missense_Mutation	SNP	ENST00000310298.4	37	CCDS10336.1	.	.	.	.	.	.	.	.	.	.	G	8.558	0.877091	0.17395	.	.	ENSG00000073417	ENST00000310298;ENST00000394553;ENST00000339708	T;T;T	0.42900	0.96;0.96;0.96	4.19	-2.56	0.06268	Signal transduction response regulator, receiver domain (1);	0.253429	0.38111	N	0.001802	T	0.45478	0.1344	L	0.48877	1.53	0.32264	N	0.569725	D;D	0.76494	0.997;0.999	D;D	0.83275	0.961;0.996	T	0.51228	-0.8732	10	0.27082	T	0.32	.	5.7001	0.17877	0.5435:0.1509:0.3056:0.0	.	169;169	O60658-2;O60658	.;PDE8A_HUMAN	D	169	ENSP00000311453:E169D;ENSP00000378056:E169D;ENSP00000340679:E169D	ENSP00000311453:E169D	E	+	3	2	PDE8A	83420983	0.136000	0.22515	0.050000	0.19076	0.338000	0.28826	0.308000	0.19314	-0.351000	0.08249	-0.908000	0.02827	GAG		0.294	PDE8A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000309018.1	NM_002605		14	150	14	150
TP53	7157	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	17	7578394	7578394	+	Missense_Mutation	SNP	T	T	C			TCGA-HT-7688-01A-11D-2253-08	TCGA-HT-7688-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	35602eec-d9a6-4b1f-b4bf-0304d6f0337a	b1e48d0a-6c17-45b0-856c-58b9eba686c8	g.chr17:7578394T>C	ENST00000269305.4	-	5	725	c.536A>G	c.(535-537)cAt>cGt	p.H179R	TP53_ENST00000455263.2_Missense_Mutation_p.H179R|TP53_ENST00000574684.1_5'UTR|TP53_ENST00000420246.2_Missense_Mutation_p.H179R|TP53_ENST00000359597.4_Missense_Mutation_p.H179R|TP53_ENST00000413465.2_Missense_Mutation_p.H179R|TP53_ENST00000445888.2_Missense_Mutation_p.H179R	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	179	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		H -> D (in sporadic cancers; somatic mutation).|H -> L (in sporadic cancers; somatic mutation).|H -> N (in sporadic cancers; somatic mutation).|H -> P (in sporadic cancers; somatic mutation).|H -> Q (in sporadic cancers; somatic mutation).|H -> R (in sporadic cancers; somatic mutation).|H -> Y (in LFS; germline mutation and in sporadic cancers; somatic mutation).|HH -> QS (in a sporadic cancer; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.H179R(108)|p.H179L(43)|p.P177_C182delPHHERC(8)|p.0?(8)|p.H47L(4)|p.H86L(4)|p.C176_R181delCPHHER(3)|p.R174fs*24(3)|p.H179P(3)|p.H178_S183delHHERCS(3)|p.R175_E180delRCPHHE(3)|p.P177fs*3(2)|p.V173fs*59(2)|p.H86R(2)|p.H47R(2)|p.R174fs*1(2)|p.H179fs*68(1)|p.C176fs*65(1)|p.P177_H179delPHH(1)|p.V173fs*23(1)|p.V172_E180delVVRRCPHHE(1)|p.R174_H179delRRCPHH(1)|p.E171_H179delEVVRRCPHH(1)|p.R81fs*24(1)|p.R174_E180>K(1)|p.H46_S51delHHERCS(1)|p.H178fs*6(1)|p.P177_E180delPHHE(1)|p.R42fs*24(1)|p.H85_S90delHHERCS(1)|p.E171fs*1(1)|p.R174fs*3(1)|p.E171fs*61(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	GCAGCGCTCATGGTGGGGGCA	0.642		111	"""Mis, N, F"""		"""breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"""	"""breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"""		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"""L, E, M, O"""	217	Substitution - Missense(166)|Deletion - In frame(24)|Deletion - Frameshift(18)|Whole gene deletion(8)|Complex - deletion inframe(1)	lung(35)|breast(32)|large_intestine(29)|upper_aerodigestive_tract(26)|oesophagus(21)|ovary(21)|central_nervous_system(16)|haematopoietic_and_lymphoid_tissue(8)|urinary_tract(6)|pancreas(6)|liver(5)|bone(4)|biliary_tract(3)|cervix(1)|stomach(1)|endometrium(1)|salivary_gland(1)|skin(1)											47.0	47.0	47.0					17																	7578394		2203	4300	6503	SO:0001583	missense	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"""Li-Fraumeni syndrome"""	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.536A>G	17.37:g.7578394T>C	ENSP00000269305:p.His179Arg		Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	T	26.0	4.694391	0.88830	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944;ENST00000414315	D;D;D;D;D;D;D;D	0.99909	-7.87;-7.87;-7.87;-7.87;-7.87;-7.87;-7.87;-7.87	5.47	5.47	0.80525	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.048592	0.85682	D	0.000000	D	0.99917	0.9961	M	0.92507	3.315	0.80722	D	1	D;D;D;D;D;D;D	0.89917	0.989;1.0;0.985;1.0;0.995;1.0;0.996	D;D;D;D;D;D;D	0.97110	0.929;0.996;0.912;1.0;0.985;0.995;0.937	D	0.95874	0.8893	10	0.87932	D	0	-15.4889	13.8032	0.63214	0.0:0.0:0.0:1.0	.	140;179;179;86;179;179;179	B4E095;P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;.;P53_HUMAN;.;.	R	179;179;179;179;179;179;168;86;47;86;47	ENSP00000410739:H179R;ENSP00000352610:H179R;ENSP00000269305:H179R;ENSP00000398846:H179R;ENSP00000391127:H179R;ENSP00000391478:H179R;ENSP00000425104:H47R;ENSP00000423862:H86R	ENSP00000269305:H179R	H	-	2	0	TP53	7519119	1.000000	0.71417	0.945000	0.38365	0.856000	0.48823	6.263000	0.72521	2.208000	0.71279	0.460000	0.39030	CAT		0.642	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		65	50	65	50
ZNF207	7756	hgsc.bcm.edu;broad.mit.edu	37	17	30696691	30696691	+	Silent	SNP	G	G	A			TCGA-HT-7688-01A-11D-2253-08	TCGA-HT-7688-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	35602eec-d9a6-4b1f-b4bf-0304d6f0337a	b1e48d0a-6c17-45b0-856c-58b9eba686c8	g.chr17:30696691G>A	ENST00000321233.6	+	11	1504	c.1350G>A	c.(1348-1350)ccG>ccA	p.P450P	ZNF207_ENST00000341711.6_Silent_p.P367P|ZNF207_ENST00000342555.6_Silent_p.P469P|ZNF207_ENST00000394673.2_Silent_p.P435P|ZNF207_ENST00000394670.4_Silent_p.P466P|ZNF207_ENST00000577908.1_Silent_p.P466P	NM_003457.3	NP_003448.1	O43670	ZN207_HUMAN	zinc finger protein 207	450					attachment of spindle microtubules to kinetochore (GO:0008608)|mitotic sister chromatid segregation (GO:0000070)|mitotic spindle assembly checkpoint (GO:0007094)|protein stabilization (GO:0050821)|regulation of chromosome segregation (GO:0051983)|regulation of transcription, DNA-templated (GO:0006355)	kinetochore (GO:0000776)|microtubule (GO:0005874)|nucleus (GO:0005634)	DNA binding (GO:0003677)|heparin binding (GO:0008201)|microtubule binding (GO:0008017)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|kidney(2)|lung(3)|urinary_tract(2)	10		Breast(31;0.116)|Ovarian(249;0.182)	BRCA - Breast invasive adenocarcinoma(9;0.239)			GGCAGGGACCGCCAATGGTGC	0.527																																																0													71.0	63.0	66.0					17																	30696691		2203	4300	6503	SO:0001819	synonymous_variant	7756			AF046001	CCDS11271.1, CCDS32614.1, CCDS42294.1	17q11.2	2008-07-10			ENSG00000010244	ENSG00000010244		"""Zinc fingers, C2H2-type"""	12998	protein-coding gene	gene with protein product		603428				9799612	Standard	NM_001098507		Approved		uc002hhj.4	O43670	OTTHUMG00000132810	ENST00000321233.6:c.1350G>A	17.37:g.30696691G>A			A8K6Y6|E1P660|E1P661|E1P662|Q53XS9|Q96HW5|Q9BUQ7	Silent	SNP	ENST00000321233.6	37	CCDS11271.1																																																																																				0.527	ZNF207-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256251.2			7	65	7	65
CCR7	1236	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	17	38715155	38715155	+	Missense_Mutation	SNP	A	A	G			TCGA-HT-7688-01A-11D-2253-08	TCGA-HT-7688-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	35602eec-d9a6-4b1f-b4bf-0304d6f0337a	b1e48d0a-6c17-45b0-856c-58b9eba686c8	g.chr17:38715155A>G	ENST00000246657.2	-	2	112	c.50T>C	c.(49-51)gTc>gCc	p.V17A	CCR7_ENST00000579344.1_Missense_Mutation_p.V11A	NM_001838.3	NP_001829.1	P32248	CCR7_HUMAN	chemokine (C-C motif) receptor 7	17					activation of Rho GTPase activity (GO:0032862)|cellular response to cytokine stimulus (GO:0071345)|chemokine (C-C motif) ligand 19 signaling pathway (GO:0038115)|chemokine (C-C motif) ligand 21 signaling pathway (GO:0038116)|chemokine-mediated signaling pathway (GO:0070098)|dendritic cell chemotaxis (GO:0002407)|establishment of T cell polarity (GO:0001768)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|inflammatory response (GO:0006954)|interleukin-12 secretion (GO:0072610)|lymphocyte migration into lymph node (GO:0097022)|mature dendritic cell differentiation (GO:0097029)|myeloid dendritic cell chemotaxis (GO:0002408)|negative regulation of leukocyte apoptotic process (GO:2000107)|negative thymic T cell selection (GO:0045060)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell motility (GO:2000147)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of dendritic cell antigen processing and presentation (GO:0002606)|positive regulation of dendritic cell chemotaxis (GO:2000510)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of glycoprotein biosynthetic process involved in immunological synapse formation (GO:2000526)|positive regulation of humoral immune response (GO:0002922)|positive regulation of hypersensitivity (GO:0002885)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of immunological synapse formation (GO:2000522)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of JNK cascade (GO:0046330)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of pseudopodium assembly (GO:0031274)|positive regulation of T cell costimulation (GO:2000525)|positive regulation of T cell receptor signaling pathway (GO:0050862)|regulation of dendritic cell dendrite assembly (GO:2000547)|regulation of interferon-gamma production (GO:0032649)|regulation of interleukin-1 beta secretion (GO:0050706)|release of sequestered calcium ion into cytosol (GO:0051209)|response to lipopolysaccharide (GO:0032496)|response to nitric oxide (GO:0071731)|response to prostaglandin E (GO:0034695)|ruffle organization (GO:0031529)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	C-C chemokine receptor activity (GO:0016493)|C-C motif chemokine 19 receptor activity (GO:0038117)|C-C motif chemokine 21 receptor activity (GO:0038121)|chemokine (C-C motif) ligand 19 binding (GO:0035757)|chemokine (C-C motif) ligand 21 binding (GO:0035758)|G-protein coupled receptor activity (GO:0004930)			breast(1)|large_intestine(4)|lung(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	8		Breast(137;0.000496)				CTGGAAAATGACAAGGAGAGC	0.498																																																0													73.0	66.0	69.0					17																	38715155		2203	4300	6503	SO:0001583	missense	1236				CCDS11369.1	17q12-q21.2	2012-08-08			ENSG00000126353	ENSG00000126353		"""GPCR / Class A : Chemokine receptors : C-C motif"", ""CD molecules"""	1608	protein-coding gene	gene with protein product		600242		CMKBR7, EBI1		8383238	Standard	NM_001838		Approved	BLR2, CDw197, CD197	uc002huw.3	P32248	OTTHUMG00000133375	ENST00000246657.2:c.50T>C	17.37:g.38715155A>G	ENSP00000246657:p.Val17Ala			Missense_Mutation	SNP	ENST00000246657.2	37	CCDS11369.1	.	.	.	.	.	.	.	.	.	.	A	9.910	1.209132	0.22205	.	.	ENSG00000126353	ENST00000246657	T	0.61158	0.13	4.9	4.9	0.64082	.	0.583336	0.16150	N	0.227324	T	0.49712	0.1573	L	0.46157	1.445	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.39375	-0.9617	10	0.39692	T	0.17	.	10.8408	0.46715	1.0:0.0:0.0:0.0	.	17	P32248	CCR7_HUMAN	A	17	ENSP00000246657:V17A	ENSP00000246657:V17A	V	-	2	0	CCR7	35968681	0.069000	0.21087	0.063000	0.19743	0.577000	0.36160	4.633000	0.61318	2.053000	0.61076	0.402000	0.26972	GTC		0.498	CCR7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257222.1			7	61	7	61
C17orf47	284083	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	17	56620229	56620229	+	Missense_Mutation	SNP	C	C	T			TCGA-HT-7688-01A-11D-2253-08	TCGA-HT-7688-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	35602eec-d9a6-4b1f-b4bf-0304d6f0337a	b1e48d0a-6c17-45b0-856c-58b9eba686c8	g.chr17:56620229C>T	ENST00000321691.3	-	1	1500	c.1319G>A	c.(1318-1320)aGc>aAc	p.S440N	RP11-112H10.4_ENST00000578022.1_RNA|SEPT4_ENST00000412945.3_5'Flank|SEPT4_ENST00000457347.2_5'Flank|RP11-112H10.4_ENST00000580769.1_RNA|RP11-112H10.4_ENST00000580589.1_RNA	NM_001038704.2	NP_001033793	Q8NEP4	CQ047_HUMAN	chromosome 17 open reading frame 47	440										NS(1)|breast(2)|endometrium(1)|kidney(4)|large_intestine(4)|lung(9)|prostate(1)|skin(1)|urinary_tract(1)	24	Medulloblastoma(34;0.127)|all_neural(34;0.237)					TGTCAGCTGGCTTTGGGGTGT	0.507																																																0													130.0	140.0	136.0					17																	56620229		2203	4300	6503	SO:0001583	missense	0				CCDS32691.1	17q23.2	2012-10-11			ENSG00000181013	ENSG00000181013			26844	protein-coding gene	gene with protein product							Standard	NM_001038704		Approved	FLJ40121	uc002iwq.2	Q8NEP4	OTTHUMG00000179244	ENST00000321691.3:c.1319G>A	17.37:g.56620229C>T	ENSP00000354874:p.Ser440Asn		Q8N821	Missense_Mutation	SNP	ENST00000321691.3	37	CCDS32691.1	.	.	.	.	.	.	.	.	.	.	C	10.78	1.446510	0.25987	.	.	ENSG00000181013	ENST00000321691	T	0.39997	1.05	5.62	3.58	0.41010	.	0.233302	0.38605	N	0.001637	T	0.27027	0.0662	N	0.17082	0.46	0.09310	N	1	P	0.44816	0.844	P	0.44772	0.46	T	0.06427	-1.0827	10	0.25106	T	0.35	-6.6392	6.981	0.24704	0.0:0.7286:0.1763:0.0951	.	440	Q8NEP4	CQ047_HUMAN	N	440	ENSP00000354874:S440N	ENSP00000354874:S440N	S	-	2	0	C17orf47	53975228	0.241000	0.23857	0.209000	0.23619	0.358000	0.29455	1.082000	0.30803	0.677000	0.31305	0.561000	0.74099	AGC		0.507	C17orf47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445443.1	NM_001038704		48	89	48	89
ABCA6	23460	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	17	67080574	67080574	+	Splice_Site	SNP	T	T	C			TCGA-HT-7688-01A-11D-2253-08	TCGA-HT-7688-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	35602eec-d9a6-4b1f-b4bf-0304d6f0337a	b1e48d0a-6c17-45b0-856c-58b9eba686c8	g.chr17:67080574T>C	ENST00000284425.2	-	33	4433	c.4259A>G	c.(4258-4260)aAg>aGg	p.K1420R	ABCA6_ENST00000446604.2_5'UTR	NM_080284.2	NP_525023.2	Q8N139	ABCA6_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 6	1420	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(6)|endometrium(5)|kidney(17)|large_intestine(18)|lung(20)|ovary(3)|prostate(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	82	Breast(10;5.65e-12)					CGCACGTACCTTTCTCGTGAT	0.453																																																0													355.0	306.0	323.0					17																	67080574		2203	4300	6503	SO:0001630	splice_region_variant	23460			U66680	CCDS11683.1	17q21	2012-03-14			ENSG00000154262	ENSG00000154262		"""ATP binding cassette transporters / subfamily A"""	36	protein-coding gene	gene with protein product		612504				8894702	Standard	NM_080284		Approved	EST155051	uc002jhw.1	Q8N139		ENST00000284425.2:c.4260+1A>G	17.37:g.67080574T>C			Q6NSH9|Q8N856|Q8WWZ6	Splice_Site	SNP	ENST00000284425.2	37	CCDS11683.1	.	.	.	.	.	.	.	.	.	.	T	16.24	3.066577	0.55539	.	.	ENSG00000154262	ENST00000284425;ENST00000446604	T	0.06608	3.28	5.7	3.43	0.39272	ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.241301	0.28566	N	0.014891	T	0.11537	0.0281	N	0.25094	0.71	0.80722	D	1	D	0.76494	0.999	D	0.83275	0.996	T	0.06881	-1.0802	10	0.87932	D	0	.	7.1555	0.25635	0.2783:0.0:0.1242:0.5975	.	1420	Q8N139	ABCA6_HUMAN	R	1420;280	ENSP00000284425:K1420R	ENSP00000284425:K1420R	K	-	2	0	ABCA6	64592169	1.000000	0.71417	0.970000	0.41538	0.266000	0.26442	3.973000	0.56845	0.386000	0.24997	0.533000	0.62120	AAG		0.453	ABCA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450463.1	NM_080284	Missense_Mutation	159	387	159	387
SLC26A11	284129	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	17	78199637	78199637	+	Splice_Site	SNP	A	A	G			TCGA-HT-7688-01A-11D-2253-08	TCGA-HT-7688-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	35602eec-d9a6-4b1f-b4bf-0304d6f0337a	b1e48d0a-6c17-45b0-856c-58b9eba686c8	g.chr17:78199637A>G	ENST00000361193.3	+	6	795	c.515A>G	c.(514-516)aAc>aGc	p.N172S	SLC26A11_ENST00000546047.2_Splice_Site_p.N172S|SLC26A11_ENST00000572725.1_Splice_Site_p.N172S|SLC26A11_ENST00000411502.3_Splice_Site_p.N172S	NM_001166347.1|NM_173626.3	NP_001159819.1|NP_775897.3			solute carrier family 26 (anion exchanger), member 11											central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(6)|lung(7)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	28	all_neural(118;0.0538)		OV - Ovarian serous cystadenocarcinoma(97;0.0344)|BRCA - Breast invasive adenocarcinoma(99;0.0908)			TTTGGACAGAACCTGCTGGGA	0.587																																																0													189.0	154.0	166.0					17																	78199637		2203	4300	6503	SO:0001630	splice_region_variant	284129				CCDS11771.2	17q25	2013-07-18	2013-07-18		ENSG00000181045	ENSG00000181045		"""Solute carriers"""	14471	protein-coding gene	gene with protein product		610117	"""solute carrier family 26, member 11"""				Standard	NM_001166347		Approved		uc010dhv.2	Q86WA9	OTTHUMG00000133419	ENST00000361193.3:c.514-1A>G	17.37:g.78199637A>G				Splice_Site	SNP	ENST00000361193.3	37	CCDS11771.2	.	.	.	.	.	.	.	.	.	.	A	10.34	1.323931	0.24080	.	.	ENSG00000181045	ENST00000411502;ENST00000546047;ENST00000361193	D;D;D	0.92752	-3.1;-3.1;-3.1	3.56	3.56	0.40772	Sulphate transporter (1);	0.099482	0.64402	D	0.000003	T	0.82250	0.4996	N	0.16066	0.365	0.49213	D	0.99976	B	0.24132	0.098	B	0.27076	0.076	T	0.74569	-0.3622	10	0.14252	T	0.57	-19.0658	9.0998	0.36662	0.8155:0.1844:0.0:0.0	.	172	Q86WA9	S2611_HUMAN	S	172	ENSP00000403998:N172S;ENSP00000440724:N172S;ENSP00000355384:N172S	ENSP00000355384:N172S	N	+	2	0	SLC26A11	75814232	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	5.604000	0.67626	1.477000	0.48234	0.383000	0.25322	AAC		0.587	SLC26A11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257281.1		Missense_Mutation	26	163	26	163
ASXL3	80816	hgsc.bcm.edu;broad.mit.edu	37	18	31325552	31325552	+	Missense_Mutation	SNP	G	G	C			TCGA-HT-7688-01A-11D-2253-08	TCGA-HT-7688-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	35602eec-d9a6-4b1f-b4bf-0304d6f0337a	b1e48d0a-6c17-45b0-856c-58b9eba686c8	g.chr18:31325552G>C	ENST00000269197.5	+	12	5740	c.5740G>C	c.(5740-5742)Gac>Cac	p.D1914H		NM_030632.1	NP_085135.1	Q9C0F0	ASXL3_HUMAN	additional sex combs like transcriptional regulator 3	1914					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(3)|endometrium(3)|kidney(3)|large_intestine(6)|lung(22)|ovary(2)|pancreas(1)|skin(2)|urinary_tract(1)	43						ATTTCATGTTGACAAGAATGG	0.532																																																0													103.0	106.0	105.0					18																	31325552		1985	4150	6135	SO:0001583	missense	80816			AB051500	CCDS45847.1	18q11	2014-06-17	2014-06-17	2007-02-01		ENSG00000141431			29357	protein-coding gene	gene with protein product		615115	"""KIAA1713"", ""additional sex combs like 3 (Drosophila)"""	KIAA1713		11214970	Standard	NM_030632		Approved		uc010dmg.1	Q9C0F0		ENST00000269197.5:c.5740G>C	18.37:g.31325552G>C	ENSP00000269197:p.Asp1914His		Q6ZMX6|Q96MU3|Q9UFC5	Missense_Mutation	SNP	ENST00000269197.5	37	CCDS45847.1	.	.	.	.	.	.	.	.	.	.	G	15.34	2.803142	0.50315	.	.	ENSG00000141431	ENST00000269197	T	0.19669	2.13	5.59	4.71	0.59529	.	.	.	.	.	T	0.23094	0.0558	N	0.19112	0.55	0.33088	D	0.537568	D	0.61697	0.99	P	0.52031	0.688	T	0.30851	-0.9964	9	0.72032	D	0.01	.	13.5689	0.61834	0.0758:0.0:0.9242:0.0	.	1914	Q9C0F0	ASXL3_HUMAN	H	1914	ENSP00000269197:D1914H	ENSP00000269197:D1914H	D	+	1	0	ASXL3	29579550	1.000000	0.71417	0.856000	0.33681	0.881000	0.50899	5.402000	0.66332	1.323000	0.45263	0.655000	0.94253	GAC		0.532	ASXL3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441865.2			5	116	5	116
MC4R	4160	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	18	58038877	58038877	+	Missense_Mutation	SNP	G	G	A			TCGA-HT-7688-01A-11D-2253-08	TCGA-HT-7688-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	35602eec-d9a6-4b1f-b4bf-0304d6f0337a	b1e48d0a-6c17-45b0-856c-58b9eba686c8	g.chr18:58038877G>A	ENST00000299766.3	-	1	1124	c.706C>T	c.(706-708)Cgc>Tgc	p.R236C		NM_005912.2	NP_005903.2	P32245	MC4R_HUMAN	melanocortin 4 receptor	236					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|diet induced thermogenesis (GO:0002024)|energy reserve metabolic process (GO:0006112)|feeding behavior (GO:0007631)|insulin secretion (GO:0030073)|negative regulation of feeding behavior (GO:2000252)|positive regulation of bone resorption (GO:0045780)|positive regulation of cAMP biosynthetic process (GO:0030819)|regulation of grooming behavior (GO:2000821)|response to insulin (GO:0032868)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	melanocortin receptor activity (GO:0004977)|melanocyte-stimulating hormone receptor activity (GO:0004980)|neuropeptide binding (GO:0042923)|peptide hormone binding (GO:0017046)|ubiquitin protein ligase binding (GO:0031625)			endometrium(2)|kidney(1)|large_intestine(5)|liver(2)|lung(5)|ovary(1)|upper_aerodigestive_tract(1)	17		Colorectal(73;0.0946)				GCACCTTGGCGGATGGCACCA	0.517																																																0													72.0	66.0	68.0					18																	58038877		2203	4300	6503	SO:0001583	missense	4160			AY236539	CCDS11976.1	18q22	2012-08-10			ENSG00000166603	ENSG00000166603		"""GPCR / Class A : Melanocortin receptors"""	6932	protein-coding gene	gene with protein product		155541				7949735, 9763669	Standard	NM_005912		Approved		uc002lie.1	P32245	OTTHUMG00000132766	ENST00000299766.3:c.706C>T	18.37:g.58038877G>A	ENSP00000299766:p.Arg236Cys		B2RAC3|Q16317|Q3MIJ6	Missense_Mutation	SNP	ENST00000299766.3	37	CCDS11976.1	.	.	.	.	.	.	.	.	.	.	G	15.17	2.752621	0.49362	.	.	ENSG00000166603	ENST00000299766	T	0.46451	0.87	5.85	5.85	0.93711	GPCR, rhodopsin-like superfamily (1);	0.165998	0.56097	D	0.000036	T	0.48537	0.1505	M	0.73598	2.24	0.58432	D	0.999999	B	0.25441	0.126	B	0.24848	0.056	T	0.47774	-0.9091	10	0.66056	D	0.02	.	17.6572	0.88181	0.0:0.0:1.0:0.0	.	236	P32245	MC4R_HUMAN	C	236	ENSP00000299766:R236C	ENSP00000299766:R236C	R	-	1	0	MC4R	56189857	1.000000	0.71417	1.000000	0.80357	0.819000	0.46315	6.762000	0.74950	2.773000	0.95371	0.655000	0.94253	CGC		0.517	MC4R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256139.1	NM_005912		11	61	11	61
KRI1	65095	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	19	10671046	10671046	+	Missense_Mutation	SNP	G	G	A			TCGA-HT-7688-01A-11D-2253-08	TCGA-HT-7688-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	35602eec-d9a6-4b1f-b4bf-0304d6f0337a	b1e48d0a-6c17-45b0-856c-58b9eba686c8	g.chr19:10671046G>A	ENST00000312962.6	-	9	779	c.760C>T	c.(760-762)Cgc>Tgc	p.R254C	KRI1_ENST00000537964.1_5'Flank|KRI1_ENST00000361821.5_Missense_Mutation_p.R250C	NM_023008.3	NP_075384.3	Q8N9T8	KRI1_HUMAN	KRI1 homolog (S. cerevisiae)	248	Glu-rich.					nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(11)|ovary(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	26			Epithelial(33;9.2e-06)|all cancers(31;3.9e-05)			tcctcATAGCGTTTGTTGAGG	0.552																																																0													76.0	65.0	69.0					19																	10671046		2203	4300	6503	SO:0001583	missense	65095				CCDS12242.1	19p13.2	2008-02-05			ENSG00000129347	ENSG00000129347			25769	protein-coding gene	gene with protein product						12878157	Standard	NM_023008		Approved	FLJ12949	uc002moy.1	Q8N9T8	OTTHUMG00000150343	ENST00000312962.6:c.760C>T	19.37:g.10671046G>A	ENSP00000320917:p.Arg254Cys		Q2M1R5|Q2M1R7|Q7L5J7|Q96G92|Q9BU50|Q9H6I1|Q9H978	Missense_Mutation	SNP	ENST00000312962.6	37	CCDS12242.1	.	.	.	.	.	.	.	.	.	.	G	24.1	4.492169	0.84962	.	.	ENSG00000129347	ENST00000312962;ENST00000361821;ENST00000541101	T;T	0.09538	3.14;2.97	5.36	3.06	0.35304	.	0.575472	0.17428	N	0.174578	T	0.29588	0.0738	M	0.73962	2.25	0.38175	D	0.939454	D;D	0.89917	1.0;1.0	P;P	0.62184	0.828;0.899	T	0.28618	-1.0038	10	0.54805	T	0.06	-14.9221	14.3394	0.66614	0.0:0.4219:0.578:0.0	.	254;250	Q8N9T8;D3YTE0	KRI1_HUMAN;.	C	254;250;254	ENSP00000320917:R254C;ENSP00000355366:R250C	ENSP00000320917:R254C	R	-	1	0	KRI1	10532046	0.997000	0.39634	1.000000	0.80357	0.993000	0.82548	0.774000	0.26675	1.197000	0.43143	0.563000	0.77884	CGC		0.552	KRI1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317705.1	NM_023008		7	57	7	57
CYP4F22	126410	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	19	15651449	15651449	+	Missense_Mutation	SNP	G	G	A	rs146265982		TCGA-HT-7688-01A-11D-2253-08	TCGA-HT-7688-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	35602eec-d9a6-4b1f-b4bf-0304d6f0337a	b1e48d0a-6c17-45b0-856c-58b9eba686c8	g.chr19:15651449G>A	ENST00000269703.3	+	8	1059	c.860G>A	c.(859-861)cGt>cAt	p.R287H	CYP4F22_ENST00000601005.2_Missense_Mutation_p.R287H	NM_173483.3	NP_775754.2	Q6NT55	CP4FN_HUMAN	cytochrome P450, family 4, subfamily F, polypeptide 22	287						endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen (GO:0016705)			endometrium(6)|large_intestine(9)|lung(16)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|soft_tissue(1)	37						CGGGCACTGCGTCAGCAGGGG	0.632																																																0													52.0	49.0	50.0					19																	15651449		2203	4300	6503	SO:0001583	missense	126410				CCDS12331.1	19p13.12	2013-11-11			ENSG00000171954	ENSG00000171954		"""Cytochrome P450s"""	26820	protein-coding gene	gene with protein product		611495				16436457	Standard	NM_173483		Approved	FLJ39501	uc002nbh.4	Q6NT55	OTTHUMG00000182451	ENST00000269703.3:c.860G>A	19.37:g.15651449G>A	ENSP00000269703:p.Arg287His		Q8N8H4	Missense_Mutation	SNP	ENST00000269703.3	37	CCDS12331.1	.	.	.	.	.	.	.	.	.	.	G	8.074	0.770824	0.15983	.	.	ENSG00000171954	ENST00000269703	T	0.69435	-0.4	5.39	-8.26	0.01021	.	0.837839	0.11097	N	0.600125	T	0.41811	0.1175	N	0.16790	0.44	0.09310	N	1	B	0.06786	0.001	B	0.10450	0.005	T	0.26710	-1.0095	10	0.49607	T	0.09	.	8.7882	0.34835	0.628:0.2224:0.1495:0.0	.	287	Q6NT55	CP4FN_HUMAN	H	287	ENSP00000269703:R287H	ENSP00000269703:R287H	R	+	2	0	CYP4F22	15512449	0.000000	0.05858	0.000000	0.03702	0.077000	0.17291	-1.885000	0.01620	-1.278000	0.02408	-0.476000	0.04901	CGT		0.632	CYP4F22-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461338.2	NM_173483		25	80	25	80
NPHS1	4868	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	19	36340183	36340183	+	Silent	SNP	G	G	A			TCGA-HT-7688-01A-11D-2253-08	TCGA-HT-7688-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	35602eec-d9a6-4b1f-b4bf-0304d6f0337a	b1e48d0a-6c17-45b0-856c-58b9eba686c8	g.chr19:36340183G>A	ENST00000378910.5	-	7	794	c.795C>T	c.(793-795)tgC>tgT	p.C265C	NPHS1_ENST00000591817.1_5'Flank|NPHS1_ENST00000353632.6_Silent_p.C265C	NM_004646.3	NP_004637.1	O60500	NPHN_HUMAN	nephrosis 1, congenital, Finnish type (nephrin)	265	Ig-like C2-type 3.		C -> R (in NPHS1). {ECO:0000269|PubMed:17290294}.		cell adhesion (GO:0007155)|excretion (GO:0007588)|glomerular basement membrane development (GO:0032836)|glomerular visceral epithelial cell development (GO:0072015)|JNK cascade (GO:0007254)|myoblast fusion (GO:0007520)|positive regulation of actin filament polymerization (GO:0030838)|regulation of excretion (GO:0044062)|skeletal muscle tissue development (GO:0007519)	cell projection (GO:0042995)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|slit diaphragm (GO:0036057)	myosin binding (GO:0017022)			NS(2)|breast(1)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(16)|liver(1)|lung(26)|ovary(5)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	74	all_lung(56;7.14e-07)|Lung NSC(56;1.12e-06)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			CTCGGGCCACGCACGGCAGCT	0.657																																																0													28.0	27.0	27.0					19																	36340183		2203	4300	6503	SO:0001819	synonymous_variant	4868				CCDS32996.1	19q12-q13.1	2014-09-17				ENSG00000161270		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	7908	protein-coding gene	gene with protein product		602716				9915943, 9660941	Standard	NM_004646		Approved	CNF, NPHN	uc002oby.3	O60500		ENST00000378910.5:c.795C>T	19.37:g.36340183G>A			A6NDH2|C3RX61	Silent	SNP	ENST00000378910.5	37	CCDS32996.1																																																																																				0.657	NPHS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452553.1			14	31	14	31
SIPA1L3	23094	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	19	38643516	38643516	+	Silent	SNP	T	T	C			TCGA-HT-7688-01A-11D-2253-08	TCGA-HT-7688-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	35602eec-d9a6-4b1f-b4bf-0304d6f0337a	b1e48d0a-6c17-45b0-856c-58b9eba686c8	g.chr19:38643516T>C	ENST00000222345.6	+	13	4079	c.3570T>C	c.(3568-3570)gaT>gaC	p.D1190D		NM_015073.1	NP_055888.1	O60292	SI1L3_HUMAN	signal-induced proliferation-associated 1 like 3	1190					hematopoietic progenitor cell differentiation (GO:0002244)|regulation of small GTPase mediated signal transduction (GO:0051056)	extracellular space (GO:0005615)	GTPase activator activity (GO:0005096)			NS(1)|breast(3)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(22)|ovary(2)|prostate(4)|skin(3)	59			Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292)			TATCTCTTGATCCCCACTTCA	0.617																																																0													155.0	145.0	148.0					19																	38643516		2203	4300	6503	SO:0001819	synonymous_variant	23094			AB011117	CCDS33007.1	19q13.13	2008-02-05			ENSG00000105738	ENSG00000105738			23801	protein-coding gene	gene with protein product							Standard	XM_005258671		Approved	KIAA0545	uc002ohk.3	O60292	OTTHUMG00000073727	ENST00000222345.6:c.3570T>C	19.37:g.38643516T>C			Q2TV87	Silent	SNP	ENST00000222345.6	37	CCDS33007.1																																																																																				0.617	SIPA1L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000156294.2	XM_032278		47	202	47	202
ZNF17	7565	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	19	57932608	57932608	+	Missense_Mutation	SNP	A	A	G			TCGA-HT-7688-01A-11D-2253-08	TCGA-HT-7688-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	35602eec-d9a6-4b1f-b4bf-0304d6f0337a	b1e48d0a-6c17-45b0-856c-58b9eba686c8	g.chr19:57932608A>G	ENST00000601808.1	+	3	1961	c.1748A>G	c.(1747-1749)aAa>aGa	p.K583R	AC004076.7_ENST00000597410.1_Intron|ZNF17_ENST00000307658.7_Missense_Mutation_p.K585R	NM_006959.2	NP_008890.2	P17021	ZNF17_HUMAN	zinc finger protein 17	583					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	16		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0694)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.0234)|GBM - Glioblastoma multiforme(193;0.000426)|Lung(386;0.176)		AGAACTTACAAATGCAGCAAA	0.428																																					Melanoma(149;1637 1853 29914 42869 44988)											0													53.0	54.0	53.0					19																	57932608		2084	4246	6330	SO:0001583	missense	7565			X52341	CCDS42636.1	19q13.43	2013-01-08	2006-05-10			ENSG00000186272		"""Zinc fingers, C2H2-type"", ""-"""	12958	protein-coding gene	gene with protein product			"""zinc finger protein 17 (HPF3, KOX 10)"""			2115127, 2014798	Standard	NM_006959		Approved	HPF3, KOX10, KIAA1947, FLJ40864, FLJ46058, FLJ46615	uc002qoo.1	P17021		ENST00000601808.1:c.1748A>G	19.37:g.57932608A>G	ENSP00000471905:p.Lys583Arg		B3KXU2|B3KY20|Q8N7M1|Q8N893|Q8TF54	Missense_Mutation	SNP	ENST00000601808.1	37	CCDS42636.1	.	.	.	.	.	.	.	.	.	.	A	14.69	2.609717	0.46527	.	.	ENSG00000186272	ENST00000307658	.	.	.	2.35	1.25	0.21368	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.36717	0.0977	L	0.58969	1.84	0.09310	N	1	P;P	0.48694	0.914;0.478	P;B	0.49252	0.604;0.16	T	0.20571	-1.0271	8	0.48119	T	0.1	.	2.6185	0.04910	0.6302:0.0:0.1382:0.2316	.	585;583	P17021-2;P17021	.;ZNF17_HUMAN	R	583	.	ENSP00000302455:K583R	K	+	2	0	ZNF17	62624420	0.000000	0.05858	0.000000	0.03702	0.457000	0.32468	-0.104000	0.10923	0.127000	0.18452	0.383000	0.25322	AAA		0.428	ZNF17-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000466384.1	NM_006959		10	36	10	36
TAS1R2	80834	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	1	19181078	19181078	+	Missense_Mutation	SNP	C	C	T			TCGA-HT-7688-01A-11D-2253-08	TCGA-HT-7688-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	35602eec-d9a6-4b1f-b4bf-0304d6f0337a	b1e48d0a-6c17-45b0-856c-58b9eba686c8	g.chr1:19181078C>T	ENST00000375371.3	-	3	907	c.886G>A	c.(886-888)Gcc>Acc	p.A296T	RP13-279N23.2_ENST00000494072.3_3'UTR	NM_152232.2	NP_689418.2	Q8TE23	TS1R2_HUMAN	taste receptor, type 1, member 2	296					detection of chemical stimulus involved in sensory perception of sweet taste (GO:0001582)|G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of cytokinesis (GO:0032467)|sensory perception of sweet taste (GO:0050916)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	protein heterodimerization activity (GO:0046982)|taste receptor activity (GO:0008527)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(10)|lung(14)|ovary(1)|pancreas(3)|prostate(1)|skin(3)|stomach(1)	45		Colorectal(325;3.46e-05)|all_lung(284;0.000321)|Lung NSC(340;0.000398)|Renal(390;0.000518)|Breast(348;0.000812)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00466)|BRCA - Breast invasive adenocarcinoma(304;3.56e-05)|Kidney(64;0.000177)|KIRC - Kidney renal clear cell carcinoma(64;0.00262)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)	Aspartame(DB00168)	ATCCACACGGCGCCAGTGAAG	0.637																																																0													55.0	53.0	54.0					1																	19181078		2203	4300	6503	SO:0001583	missense	80834				CCDS187.1	1p36.13	2012-08-22	2003-03-07		ENSG00000179002	ENSG00000179002		"""Taste receptors / Type 1"", ""GPCR / Unclassified : Taste receptors"""	14905	protein-coding gene	gene with protein product		606226	"""G protein-coupled receptor 71"""	GPR71			Standard	NM_152232		Approved	T1R2, TR2	uc001bba.1	Q8TE23	OTTHUMG00000002442	ENST00000375371.3:c.886G>A	1.37:g.19181078C>T	ENSP00000364520:p.Ala296Thr		Q5TZ19	Missense_Mutation	SNP	ENST00000375371.3	37	CCDS187.1	.	.	.	.	.	.	.	.	.	.	C	6.826	0.521544	0.13005	.	.	ENSG00000179002	ENST00000375371	D	0.82526	-1.62	4.89	-4.99	0.03010	Extracellular ligand-binding receptor (1);	2.484110	0.01813	N	0.033595	T	0.67050	0.2852	N	0.19112	0.55	0.09310	N	1	B	0.22346	0.068	B	0.17433	0.018	T	0.52548	-0.8561	10	0.29301	T	0.29	.	3.4977	0.07661	0.1074:0.1192:0.1023:0.6712	.	296	Q8TE23	TS1R2_HUMAN	T	296	ENSP00000364520:A296T	ENSP00000364520:A296T	A	-	1	0	TAS1R2	19053665	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	-0.309000	0.08145	-1.054000	0.03214	0.561000	0.74099	GCC		0.637	TAS1R2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000006953.1			15	54	15	54
SNRNP40	9410	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	1	31744294	31744294	+	Missense_Mutation	SNP	T	T	C			TCGA-HT-7688-01A-11D-2253-08	TCGA-HT-7688-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	35602eec-d9a6-4b1f-b4bf-0304d6f0337a	b1e48d0a-6c17-45b0-856c-58b9eba686c8	g.chr1:31744294T>C	ENST00000263694.4	-	6	725	c.707A>G	c.(706-708)gAt>gGt	p.D236G	SNRNP40_ENST00000489853.1_5'UTR|SNRNP40_ENST00000446633.2_Missense_Mutation_p.D236G|SNRNP40_ENST00000373720.3_5'Flank	NM_004814.2	NP_004805.2	Q96DI7	SNR40_HUMAN	small nuclear ribonucleoprotein 40kDa (U5)	236					gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|small nucleolar ribonucleoprotein complex (GO:0005732)|U5 snRNP (GO:0005682)	poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|large_intestine(1)|lung(3)|upper_aerodigestive_tract(1)	7						AGTCACTGAATCTGCATGGCC	0.448																																																0													80.0	81.0	80.0					1																	31744294		2203	4300	6503	SO:0001583	missense	9410			AF090988	CCDS340.1	1p35.2	2013-01-09	2008-10-29	2008-10-29	ENSG00000060688	ENSG00000060688		"""WD repeat domain containing"""	30857	protein-coding gene	gene with protein product		607797	"""WD repeat domain 57 (U5 snRNP specific)"""	WDR57		9774689, 9731529, 10788320	Standard	NM_004814		Approved	PRP8BP, SPF38, PRPF8BP, HPRP8BP	uc009vtt.3	Q96DI7	OTTHUMG00000003790	ENST00000263694.4:c.707A>G	1.37:g.31744294T>C	ENSP00000263694:p.Asp236Gly		B4DQJ1|O75938|O95320	Missense_Mutation	SNP	ENST00000263694.4	37	CCDS340.1	.	.	.	.	.	.	.	.	.	.	T	29.5	5.014257	0.93404	.	.	ENSG00000060688	ENST00000263694;ENST00000446633	T;T	0.58797	0.31;0.31	5.76	5.76	0.90799	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.67487	0.2898	L	0.38953	1.18	0.80722	D	1	D;D	0.71674	0.998;0.995	D;D	0.75484	0.986;0.954	T	0.66256	-0.5969	10	0.38643	T	0.18	.	16.087	0.81065	0.0:0.0:0.0:1.0	.	236;236	B4DQJ1;Q96DI7	.;SNR40_HUMAN	G	236	ENSP00000263694:D236G;ENSP00000406841:D236G	ENSP00000263694:D236G	D	-	2	0	SNRNP40	31516881	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.979000	0.88103	2.202000	0.70862	0.533000	0.62120	GAT		0.448	SNRNP40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010657.1	NM_004814		7	63	7	63
RLF	6018	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	1	40702367	40702367	+	Missense_Mutation	SNP	C	C	G			TCGA-HT-7688-01A-11D-2253-08	TCGA-HT-7688-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	35602eec-d9a6-4b1f-b4bf-0304d6f0337a	b1e48d0a-6c17-45b0-856c-58b9eba686c8	g.chr1:40702367C>G	ENST00000372771.4	+	8	2020	c.1993C>G	c.(1993-1995)Ctg>Gtg	p.L665V		NM_012421.3	NP_036553.2	Q13129	RLF_HUMAN	rearranged L-myc fusion	665					chromosome organization (GO:0051276)|DNA integration (GO:0015074)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(11)|kidney(4)|large_intestine(18)|lung(18)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(4)|urinary_tract(2)	68	Lung NSC(20;4.38e-06)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;5.87e-19)|Epithelial(16;7.02e-16)|all cancers(16;1.69e-14)|Lung(16;0.0427)|LUSC - Lung squamous cell carcinoma(16;0.0461)			AGATTGCCACCTGCAAGACAG	0.418																																																0													121.0	120.0	120.0					1																	40702367		2203	4300	6503	SO:0001583	missense	6018				CCDS448.1	1p32	2010-05-07	2005-08-16		ENSG00000117000	ENSG00000117000		"""Zinc fingers, C2H2-type"""	10025	protein-coding gene	gene with protein product		180610	"""rearranged L-myc fusion sequence"""			1649386	Standard	NM_012421		Approved	ZNF292L, Zn-15L	uc001cfc.4	Q13129	OTTHUMG00000005763	ENST00000372771.4:c.1993C>G	1.37:g.40702367C>G	ENSP00000361857:p.Leu665Val		Q14CQ1|Q9NU60	Missense_Mutation	SNP	ENST00000372771.4	37	CCDS448.1	.	.	.	.	.	.	.	.	.	.	C	10.01	1.234241	0.22626	.	.	ENSG00000117000	ENST00000372771;ENST00000535839	T	0.53423	0.62	6.17	6.17	0.99709	.	0.064498	0.64402	D	0.000006	T	0.53578	0.1805	L	0.32530	0.975	0.54753	D	0.99998	P;D	0.57899	0.508;0.981	B;P	0.53490	0.234;0.727	T	0.40515	-0.9559	10	0.37606	T	0.19	-4.7098	20.8794	0.99867	0.0:1.0:0.0:0.0	.	358;665	F5H2M5;Q13129	.;RLF_HUMAN	V	665;358	ENSP00000361857:L665V	ENSP00000361857:L665V	L	+	1	2	RLF	40474954	0.885000	0.30320	1.000000	0.80357	0.996000	0.88848	0.840000	0.27600	2.941000	0.99782	0.655000	0.94253	CTG		0.418	RLF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000015767.1	NM_012421		51	111	51	111
AGL	178	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	1	100353559	100353559	+	Missense_Mutation	SNP	G	G	A			TCGA-HT-7688-01A-11D-2253-08	TCGA-HT-7688-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	35602eec-d9a6-4b1f-b4bf-0304d6f0337a	b1e48d0a-6c17-45b0-856c-58b9eba686c8	g.chr1:100353559G>A	ENST00000294724.4	+	21	3185	c.2707G>A	c.(2707-2709)Gag>Aag	p.E903K	AGL_ENST00000361915.3_Missense_Mutation_p.E903K|AGL_ENST00000361522.4_Missense_Mutation_p.E886K|AGL_ENST00000370163.3_Missense_Mutation_p.E903K|AGL_ENST00000370165.3_Missense_Mutation_p.E903K|AGL_ENST00000361302.3_Missense_Mutation_p.E887K|AGL_ENST00000370161.2_Missense_Mutation_p.E887K	NM_000028.2	NP_000019.2	P35573	GDE_HUMAN	amylo-alpha-1, 6-glucosidase, 4-alpha-glucanotransferase	903					carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|glycogen catabolic process (GO:0005980)|response to glucocorticoid (GO:0051384)|response to nutrient (GO:0007584)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|inclusion body (GO:0016234)|isoamylase complex (GO:0043033)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)	4-alpha-glucanotransferase activity (GO:0004134)|amylo-alpha-1,6-glucosidase activity (GO:0004135)|glycogen debranching enzyme activity (GO:0004133)|polysaccharide binding (GO:0030247)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(9)|lung(35)|ovary(1)|prostate(4)|skin(3)|urinary_tract(1)	69		all_epithelial(167;2.2e-06)|all_lung(203;0.000295)|Lung NSC(277;0.00131)		Epithelial(280;0.15)|COAD - Colon adenocarcinoma(174;0.151)|Lung(183;0.209)|all cancers(265;0.237)		AACTTTGGCTGAGCTAAATCA	0.373																																																0													95.0	91.0	92.0					1																	100353559		2203	4300	6503	SO:0001583	missense	178			BC078663	CCDS759.1, CCDS760.1, CCDS761.1	1p21	2010-04-27	2010-04-27		ENSG00000162688	ENSG00000162688	2.4.1.25, 3.2.1.33		321	protein-coding gene	gene with protein product	"""glycogen debranching enzyme"", ""glycogen storage disease type III"""	610860	"""amylo-1, 6-glucosidase, 4-alpha-glucanotransferase"""			1505983	Standard	NM_000028		Approved		uc001dsi.1	P35573	OTTHUMG00000010803	ENST00000294724.4:c.2707G>A	1.37:g.100353559G>A	ENSP00000294724:p.Glu903Lys		A6NCX7|A6NEK2|D3DT51|P78354|P78544|Q59H92|Q6AZ90|Q9UF08	Missense_Mutation	SNP	ENST00000294724.4	37	CCDS759.1	.	.	.	.	.	.	.	.	.	.	G	21.3	4.124933	0.77436	.	.	ENSG00000162688	ENST00000361915;ENST00000370165;ENST00000370163;ENST00000294724;ENST00000361302;ENST00000370161;ENST00000361522	T;T;T;T;T;T;T	0.32753	1.44;1.44;1.44;1.44;1.44;1.44;1.44	5.24	5.24	0.73138	.	0.049346	0.85682	D	0.000000	T	0.17704	0.0425	L	0.34521	1.04	0.52099	D	0.999948	B;B;B	0.23249	0.082;0.082;0.049	B;B;B	0.25614	0.062;0.062;0.028	T	0.03306	-1.1050	10	0.54805	T	0.06	.	19.1783	0.93612	0.0:0.0:1.0:0.0	.	886;887;903	P35573-2;P35573-3;P35573	.;.;GDE_HUMAN	K	903;903;903;903;887;887;886	ENSP00000355106:E903K;ENSP00000359184:E903K;ENSP00000359182:E903K;ENSP00000294724:E903K;ENSP00000354971:E887K;ENSP00000359180:E887K;ENSP00000354635:E886K	ENSP00000294724:E903K	E	+	1	0	AGL	100126147	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	8.869000	0.92326	2.595000	0.87683	0.544000	0.68410	GAG		0.373	AGL-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029778.1	NM_000028		6	57	6	57
SYCP1	6847	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	1	115487052	115487052	+	Missense_Mutation	SNP	A	A	G			TCGA-HT-7688-01A-11D-2253-08	TCGA-HT-7688-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	35602eec-d9a6-4b1f-b4bf-0304d6f0337a	b1e48d0a-6c17-45b0-856c-58b9eba686c8	g.chr1:115487052A>G	ENST00000369522.3	+	24	2259	c.2019A>G	c.(2017-2019)atA>atG	p.I673M	SYCP1_ENST00000369518.1_Missense_Mutation_p.I673M	NM_001282541.1|NM_003176.2	NP_001269470.1|NP_003167.2	Q15431	SYCP1_HUMAN	synaptonemal complex protein 1	673					chiasma assembly (GO:0051026)|lateral element assembly (GO:0051878)|meiotic DNA repair synthesis (GO:0000711)|reciprocal meiotic recombination (GO:0007131)|regulation of protein localization (GO:0032880)|sperm chromatin condensation (GO:0035092)|spermatogenesis (GO:0007283)|synaptonemal complex assembly (GO:0007130)	central element (GO:0000801)|male germ cell nucleus (GO:0001673)|transverse filament (GO:0000802)	DNA binding (GO:0003677)		RGS22/SYCP1(2)	NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(17)|lung(20)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	48	Lung SC(450;0.211)	all_cancers(81;8.65e-08)|all_epithelial(167;3.32e-07)|all_lung(203;6.55e-06)|Lung NSC(69;1.11e-05)|Acute lymphoblastic leukemia(138;0.221)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)		ACAAAAAGATATCAGAAGAAA	0.279																																																0													31.0	35.0	34.0					1																	115487052		2201	4281	6482	SO:0001583	missense	6847			D67035	CCDS879.1, CCDS72840.1	1p13-p12	2009-03-12			ENSG00000198765	ENSG00000198765			11487	protein-coding gene	gene with protein product	"""cancer/testis antigen 8"""	602162				9560255	Standard	XM_005271154		Approved	HOM-TES-14, SCP1, CT8	uc001efr.3	Q15431	OTTHUMG00000012057	ENST00000369522.3:c.2019A>G	1.37:g.115487052A>G	ENSP00000358535:p.Ile673Met		O14963|Q5VXJ6	Missense_Mutation	SNP	ENST00000369522.3	37	CCDS879.1	.	.	.	.	.	.	.	.	.	.	A	10.88	1.474237	0.26423	.	.	ENSG00000198765	ENST00000369522;ENST00000536734;ENST00000455987;ENST00000369518	T;T;T	0.56275	0.47;0.47;0.47	4.24	0.369	0.16151	.	0.993065	0.08200	N	0.982476	T	0.23171	0.0560	L	0.54323	1.7	0.20703	N	0.999867	B;B	0.12630	0.006;0.006	B;B	0.19666	0.026;0.026	T	0.33163	-0.9879	10	0.44086	T	0.13	0.0291	4.0177	0.09652	0.6736:0.0:0.1747:0.1517	.	673;673	B7ZLS9;Q15431	.;SYCP1_HUMAN	M	673	ENSP00000358535:I673M;ENSP00000410011:I673M;ENSP00000358531:I673M	ENSP00000358531:I673M	I	+	3	3	SYCP1	115288575	0.002000	0.14202	0.994000	0.49952	0.978000	0.69477	0.166000	0.16583	-0.143000	0.11334	0.533000	0.62120	ATA		0.279	SYCP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033386.1	NM_003176		4	31	4	31
CD1E	913	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	1	158325321	158325321	+	Missense_Mutation	SNP	G	G	A	rs142840776		TCGA-HT-7688-01A-11D-2253-08	TCGA-HT-7688-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	35602eec-d9a6-4b1f-b4bf-0304d6f0337a	b1e48d0a-6c17-45b0-856c-58b9eba686c8	g.chr1:158325321G>A	ENST00000368167.3	+	3	826	c.587G>A	c.(586-588)gGg>gAg	p.G196E	CD1E_ENST00000368161.3_Missense_Mutation_p.G196E|CD1E_ENST00000368165.3_Intron|CD1E_ENST00000434258.1_Missense_Mutation_p.G194E|CD1E_ENST00000368154.1_Intron|CD1E_ENST00000368163.3_Missense_Mutation_p.G196E|CD1E_ENST00000368160.3_Missense_Mutation_p.G196E|CD1E_ENST00000368157.1_Intron|CD1E_ENST00000452291.2_Intron|CD1E_ENST00000444681.2_Missense_Mutation_p.G97E|CD1E_ENST00000368164.3_Intron|CD1E_ENST00000368166.3_Intron|CD1E_ENST00000368155.3_Intron|CD1E_ENST00000368156.1_Intron	NM_030893.3	NP_112155.2	P15812	CD1E_HUMAN	CD1e molecule	196	Ig-like.				antigen processing and presentation (GO:0019882)|immune response (GO:0006955)	endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)	lipid binding (GO:0008289)	p.G196E(1)		breast(2)|endometrium(2)|kidney(1)|large_intestine(6)|lung(27)|pancreas(1)|prostate(4)|skin(4)|stomach(1)|urinary_tract(1)	49	all_hematologic(112;0.0378)					TTTCTAGCGGGGCTCATGGAA	0.473																																																1	Substitution - Missense(1)	skin(1)											45.0	45.0	45.0					1																	158325321		1911	4132	6043	SO:0001583	missense	913			AJ289111	CCDS41417.1, CCDS41418.1, CCDS41419.1, CCDS41420.1, CCDS41421.1, CCDS41422.1, CCDS53387.1, CCDS53388.1, CCDS53389.1, CCDS53390.1, CCDS53384.1, CCDS53385.1, CCDS53386.1	1q23.1	2014-01-14	2006-03-28		ENSG00000158488	ENSG00000158488		"""CD molecules"", ""Immunoglobulin superfamily / C1-set domain containing"""	1638	protein-coding gene	gene with protein product		188411	"""CD1E antigen, e polypeptide"", ""CD1e antigen"""			10948205	Standard	NM_001042585		Approved		uc001fse.3	P15812	OTTHUMG00000017515	ENST00000368167.3:c.587G>A	1.37:g.158325321G>A	ENSP00000357149:p.Gly196Glu		B4DZV3|E7EP01|Q5TDJ9|Q5TDK3|Q5TDK4|Q5TDK5|Q5TDK6|Q5TDK8|Q5TDL1|Q712E4|Q712E5|Q712E6|Q712E7|Q712E8|Q712E9|Q712F0|Q712F1|Q712F2|Q712F3|Q712F4|Q712F5|Q96TD0|Q96TD1|Q9UMM1|Q9Y5M3	Missense_Mutation	SNP	ENST00000368167.3	37	CCDS41417.1	.	.	.	.	.	.	.	.	.	.	G	15.34	2.803525	0.50315	.	.	ENSG00000158488	ENST00000434258;ENST00000444681;ENST00000368167;ENST00000368163;ENST00000368160;ENST00000368161	T;T;T;T;T;T	0.07114	3.22;3.22;3.22;3.22;3.22;3.22	4.53	3.62	0.41486	Immunoglobulin-like (1);MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);	0.300108	0.24262	N	0.040073	T	0.21022	0.0506	M	0.92784	3.345	0.09310	N	1	D;D;P;D;D;D;D	0.89917	0.998;0.985;0.886;0.997;0.979;1.0;0.999	D;P;P;D;P;D;D	0.78314	0.944;0.778;0.79;0.963;0.589;0.991;0.985	T	0.10917	-1.0609	10	0.66056	D	0.02	-7.9638	8.7344	0.34519	0.105:0.0:0.895:0.0	.	97;194;97;196;196;196;196	B4E042;E7ET31;E7EP01;P15812-2;P15812;P15812-3;P15812-4	.;.;.;.;CD1E_HUMAN;.;.	E	194;97;196;196;196;196	ENSP00000401957:G194E;ENSP00000402906:G97E;ENSP00000357149:G196E;ENSP00000357145:G196E;ENSP00000357142:G196E;ENSP00000357143:G196E	ENSP00000357142:G196E	G	+	2	0	CD1E	156591945	0.007000	0.16637	0.004000	0.12327	0.012000	0.07955	1.709000	0.37909	1.264000	0.44198	0.563000	0.77884	GGG		0.473	CD1E-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000046353.3	NM_030893		7	48	7	48
SCYL3	57147	hgsc.bcm.edu;broad.mit.edu	37	1	169823532	169823532	+	Missense_Mutation	SNP	A	A	G			TCGA-HT-7688-01A-11D-2253-08	TCGA-HT-7688-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	35602eec-d9a6-4b1f-b4bf-0304d6f0337a	b1e48d0a-6c17-45b0-856c-58b9eba686c8	g.chr1:169823532A>G	ENST00000367770.1	-	12	2095	c.2048T>C	c.(2047-2049)aTt>aCt	p.I683T	SCYL3_ENST00000367772.4_Missense_Mutation_p.I683T|SCYL3_ENST00000367771.6_Missense_Mutation_p.I629T			Q8IZE3	PACE1_HUMAN	SCY1-like 3 (S. cerevisiae)	683	Interaction with EZR.				cell migration (GO:0016477)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)	ATP binding (GO:0005524)|transferase activity, transferring phosphorus-containing groups (GO:0016772)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(7)|lung(5)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	27	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)					AGAAGGCTTAATTTCTGGGAT	0.393																																																0													135.0	139.0	138.0					1																	169823532		2203	4300	6503	SO:0001583	missense	57147			BC014662	CCDS1286.1, CCDS1287.1	1q24.2	2008-02-05			ENSG00000000457	ENSG00000000457			19285	protein-coding gene	gene with protein product	"""ezrin-binding partner PACE-1"""	608192				12651155	Standard	NM_020423		Approved	PACE-1, PACE1	uc001ggs.3	Q8IZE3	OTTHUMG00000035941	ENST00000367770.1:c.2048T>C	1.37:g.169823532A>G	ENSP00000356744:p.Ile683Thr		A8K8Z2|Q5THA6|Q5THA8|Q8IZN9|Q96C56|Q9UBK6	Missense_Mutation	SNP	ENST00000367770.1	37	CCDS1287.1	.	.	.	.	.	.	.	.	.	.	A	24.2	4.510162	0.85282	.	.	ENSG00000000457	ENST00000367772;ENST00000367771;ENST00000367770	T;T;T	0.60171	0.21;0.21;0.21	5.79	5.79	0.91817	.	0.000000	0.85682	D	0.000000	T	0.69333	0.3099	M	0.66939	2.045	0.58432	D	0.999999	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.996;0.998;0.991	T	0.73953	-0.3820	10	0.87932	D	0	-24.0871	15.7969	0.78420	1.0:0.0:0.0:0.0	.	275;629;683	B4E2Y0;Q8IZE3-2;Q8IZE3	.;.;PACE1_HUMAN	T	683;629;683	ENSP00000356746:I683T;ENSP00000356745:I629T;ENSP00000356744:I683T	ENSP00000356744:I683T	I	-	2	0	SCYL3	168090156	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.919000	0.92770	2.207000	0.71202	0.533000	0.62120	ATT		0.393	SCYL3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087550.4	NM_181093		7	121	7	121
MROH9	80133	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	1	170928725	170928725	+	Missense_Mutation	SNP	T	T	C			TCGA-HT-7688-01A-11D-2253-08	TCGA-HT-7688-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	35602eec-d9a6-4b1f-b4bf-0304d6f0337a	b1e48d0a-6c17-45b0-856c-58b9eba686c8	g.chr1:170928725T>C	ENST00000367758.3	+	5	374	c.275T>C	c.(274-276)aTt>aCt	p.I92T	MROH9_ENST00000367759.4_Missense_Mutation_p.I92T	NM_025063.2	NP_079339.2	Q5TGP6	MROH9_HUMAN	maestro heat-like repeat family member 9	92																	TATGAGTACATTGAGGACATG	0.363																																																0													114.0	107.0	109.0					1																	170928725		1853	4103	5956	SO:0001583	missense	80133			AK027203	CCDS41436.1, CCDS53429.1	1q24.3	2012-12-19	2012-12-19	2012-12-19	ENSG00000117501	ENSG00000117501		"""maestro heat-like repeat containing"""	26287	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 129"""	C1orf129			Standard	NM_025063		Approved	FLJ23550, ARMC11	uc010plz.2	Q5TGP6	OTTHUMG00000041456	ENST00000367758.3:c.275T>C	1.37:g.170928725T>C	ENSP00000356732:p.Ile92Thr		A0PJM0|A0PJM2|F5GWX6|Q9H5D7	Missense_Mutation	SNP	ENST00000367758.3	37	CCDS41436.1	.	.	.	.	.	.	.	.	.	.	T	4.376	0.069386	0.08436	.	.	ENSG00000117501	ENST00000367759;ENST00000367758	T;T	0.13778	4.16;2.56	5.61	-6.53	0.01866	.	2.213880	0.01733	N	0.028996	T	0.01320	0.0043	N	0.03115	-0.41	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.32693	-0.9897	10	0.17832	T	0.49	11.0206	8.0028	0.30308	0.3112:0.4538:0.0:0.235	.	92;92	F5GWX6;Q5TGP6	.;CA129_HUMAN	T	92	ENSP00000356733:I92T;ENSP00000356732:I92T	ENSP00000356732:I92T	I	+	2	0	C1orf129	169195349	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.135000	0.01306	-1.521000	0.01771	-1.027000	0.02421	ATT		0.363	MROH9-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000099327.1	NM_025063		8	55	8	55
OR2M7	391196	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	1	248486965	248486965	+	Missense_Mutation	SNP	C	C	A			TCGA-HT-7688-01A-11D-2253-08	TCGA-HT-7688-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	35602eec-d9a6-4b1f-b4bf-0304d6f0337a	b1e48d0a-6c17-45b0-856c-58b9eba686c8	g.chr1:248486965C>A	ENST00000317965.2	-	1	934	c.906G>T	c.(904-906)atG>atT	p.M302I		NM_001004691.1	NP_001004691.1	Q8NG81	OR2M7_HUMAN	olfactory receptor, family 2, subfamily M, member 7	302						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.M302I(1)		breast(1)|endometrium(6)|large_intestine(3)|lung(29)|skin(3)	42	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			CTAAGATTTTCATTAATGCTC	0.403																																																1	Substitution - Missense(1)	lung(1)											66.0	67.0	67.0					1																	248486965		2203	4300	6503	SO:0001583	missense	391196			BK004486	CCDS31111.1	1q44	2012-08-09			ENSG00000177186	ENSG00000177186		"""GPCR / Class A : Olfactory receptors"""	19594	protein-coding gene	gene with protein product							Standard	NM_001004691		Approved		uc010pzk.2	Q8NG81	OTTHUMG00000040461	ENST00000317965.2:c.906G>T	1.37:g.248486965C>A	ENSP00000324557:p.Met302Ile		B2RNL0|Q6IEX6	Missense_Mutation	SNP	ENST00000317965.2	37	CCDS31111.1	.	.	.	.	.	.	.	.	.	.	C	7.615	0.675690	0.14841	.	.	ENSG00000177186	ENST00000317965	T	0.35973	1.28	1.88	-0.801	0.10893	.	.	.	.	.	T	0.17492	0.0420	N	0.13235	0.315	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.22941	-1.0202	9	0.52906	T	0.07	.	2.7367	0.05242	0.2407:0.4691:0.0:0.2902	.	302	Q8NG81	OR2M7_HUMAN	I	302	ENSP00000324557:M302I	ENSP00000324557:M302I	M	-	3	0	OR2M7	246553588	0.001000	0.12720	0.006000	0.13384	0.008000	0.06430	-0.152000	0.10159	0.732000	0.32470	0.184000	0.17185	ATG		0.403	OR2M7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097357.1	NM_001004691		8	71	8	71
TGM6	343641	hgsc.bcm.edu;broad.mit.edu	37	20	2411182	2411182	+	Missense_Mutation	SNP	T	T	C			TCGA-HT-7688-01A-11D-2253-08	TCGA-HT-7688-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	35602eec-d9a6-4b1f-b4bf-0304d6f0337a	b1e48d0a-6c17-45b0-856c-58b9eba686c8	g.chr20:2411182T>C	ENST00000202625.2	+	11	1830	c.1769T>C	c.(1768-1770)gTc>gCc	p.V590A	TGM6_ENST00000381423.1_Missense_Mutation_p.V590A	NM_198994.2	NP_945345.2	O95932	TGM3L_HUMAN	transglutaminase 6	590					cell death (GO:0008219)|peptide cross-linking (GO:0018149)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)			breast(1)|endometrium(6)|kidney(2)|large_intestine(2)|lung(32)|ovary(4)|prostate(1)|skin(4)	52					L-Glutamine(DB00130)	ATGTGCCTTGTCACCAAAGGA	0.458																																																0													104.0	87.0	93.0					20																	2411182		2203	4300	6503	SO:0001583	missense	343641			AF540970	CCDS13025.1, CCDS58761.1	20p13	2010-12-19	2004-07-05	2004-07-07	ENSG00000166948	ENSG00000166948		"""Transglutaminases"""	16255	protein-coding gene	gene with protein product	"""spinocerebellar ataxia 35"""	613900	"""transglutaminase 3-like"""	TGM3L		11390390, 21106500	Standard	NM_198994		Approved	dJ734P14.3, TGY, SCA35	uc002wfy.1	O95932	OTTHUMG00000031692	ENST00000202625.2:c.1769T>C	20.37:g.2411182T>C	ENSP00000202625:p.Val590Ala		Q5JXU4|Q5JXU5|Q719M2|Q719M3|Q9Y4U8	Missense_Mutation	SNP	ENST00000202625.2	37	CCDS13025.1	.	.	.	.	.	.	.	.	.	.	T	15.98	2.991716	0.54041	.	.	ENSG00000166948	ENST00000202625;ENST00000381423	T;T	0.78246	-1.16;-1.16	5.88	5.88	0.94601	Transglutaminase, C-terminal (2);Immunoglobulin-like fold (1);	0.205007	0.43416	D	0.000577	T	0.75525	0.3861	M	0.66939	2.045	0.31558	N	0.657886	B;B	0.33266	0.404;0.4	B;B	0.33254	0.16;0.103	T	0.79327	-0.1849	10	0.44086	T	0.13	-46.5442	12.6797	0.56914	0.0:0.0:0.0:1.0	.	590;590	O95932-2;O95932	.;TGM3L_HUMAN	A	590	ENSP00000202625:V590A;ENSP00000370831:V590A	ENSP00000202625:V590A	V	+	2	0	TGM6	2359182	0.844000	0.29557	0.999000	0.59377	0.591000	0.36615	2.941000	0.49011	2.242000	0.73789	0.533000	0.62120	GTC		0.458	TGM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077581.2	NM_198994		4	63	4	63
TPX2	22974	hgsc.bcm.edu;broad.mit.edu	37	20	30388772	30388772	+	Splice_Site	SNP	G	G	C			TCGA-HT-7688-01A-11D-2253-08	TCGA-HT-7688-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	35602eec-d9a6-4b1f-b4bf-0304d6f0337a	b1e48d0a-6c17-45b0-856c-58b9eba686c8	g.chr20:30388772G>C	ENST00000300403.6	+	18	2661		c.e18-1		TPX2_ENST00000340513.4_Splice_Site	NM_012112.4	NP_036244.2	Q9ULW0	TPX2_HUMAN	TPX2, microtubule-associated						activation of protein kinase activity (GO:0032147)|apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|mitotic nuclear division (GO:0007067)|regulation of mitotic spindle organization (GO:0060236)	axon hillock (GO:0043203)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)|spindle (GO:0005819)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|protein kinase binding (GO:0019901)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(9)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	28			Epithelial(4;0.000771)|Colorectal(19;0.00306)|all cancers(5;0.004)|COAD - Colon adenocarcinoma(19;0.0347)|OV - Ovarian serous cystadenocarcinoma(3;0.0656)			TTACTTTGCAGGTGCATAAGG	0.398																																																0													177.0	158.0	164.0					20																	30388772		2203	4300	6503	SO:0001630	splice_region_variant	22974			AF098158	CCDS13190.1	20q11.2	2013-07-23	2013-07-23	2003-10-08	ENSG00000088325	ENSG00000088325			1249	protein-coding gene	gene with protein product		605917	"""chromosome 20 open reading frame 1"", ""TPX2, microtubule-associated, homolog (Xenopus laevis)"""	C20orf2, C20orf1		9207457, 10393424	Standard	NM_012112		Approved	p100, DIL-2	uc002wwp.1	Q9ULW0	OTTHUMG00000032190	ENST00000300403.6:c.2134-1G>C	20.37:g.30388772G>C			Q9H1R4|Q9NRA3|Q9UFN9|Q9UL00|Q9Y2M1	Splice_Site	SNP	ENST00000300403.6	37	CCDS13190.1	.	.	.	.	.	.	.	.	.	.	G	18.48	3.632855	0.67015	.	.	ENSG00000088325	ENST00000300403;ENST00000340513	.	.	.	5.22	5.22	0.72569	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.9537	0.89062	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	TPX2	29852433	1.000000	0.71417	1.000000	0.80357	0.738000	0.42128	7.797000	0.85911	2.714000	0.92807	0.561000	0.74099	.		0.398	TPX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078569.2		Intron	10	166	10	166
EIF2AK3	9451	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	88913303	88913303	+	Missense_Mutation	SNP	T	T	C			TCGA-HT-7688-01A-11D-2253-08	TCGA-HT-7688-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	35602eec-d9a6-4b1f-b4bf-0304d6f0337a	b1e48d0a-6c17-45b0-856c-58b9eba686c8	g.chr2:88913303T>C	ENST00000303236.3	-	2	678	c.377A>G	c.(376-378)aAg>aGg	p.K126R	EIF2AK3_ENST00000419748.1_5'UTR	NM_004836.5	NP_004827.4	Q9NZJ5	E2AK3_HUMAN	eukaryotic translation initiation factor 2-alpha kinase 3	126					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of signaling protein activity involved in unfolded protein response (GO:0006987)|bone mineralization (GO:0030282)|calcium-mediated signaling (GO:0019722)|cellular protein metabolic process (GO:0044267)|chondrocyte development (GO:0002063)|endocrine pancreas development (GO:0031018)|endoplasmic reticulum organization (GO:0007029)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER overload response (GO:0006983)|fat cell differentiation (GO:0045444)|insulin secretion (GO:0030073)|insulin-like growth factor receptor signaling pathway (GO:0048009)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|lactation (GO:0007595)|negative regulation of apoptotic process (GO:0043066)|negative regulation of gene expression (GO:0010629)|negative regulation of myelination (GO:0031642)|negative regulation of translation (GO:0017148)|negative regulation of translational initiation in response to stress (GO:0032057)|ossification (GO:0001503)|positive regulation of protein binding (GO:0032092)|positive regulation of signal transduction (GO:0009967)|protein autophosphorylation (GO:0046777)|protein homooligomerization (GO:0051260)|protein phosphorylation (GO:0006468)|regulation of fatty acid metabolic process (GO:0019217)|response to endoplasmic reticulum stress (GO:0034976)|skeletal system development (GO:0001501)|SREBP signaling pathway (GO:0032933)|translation (GO:0006412)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|eukaryotic translation initiation factor 2alpha kinase activity (GO:0004694)|identical protein binding (GO:0042802)|protein kinase activity (GO:0004672)|protein phosphatase binding (GO:0019903)|protein serine/threonine kinase activity (GO:0004674)			ovary(3)	3						ATCCCACTGCTTTTTACCATG	0.353																																					GBM(138;671 1851 16235 39058 45249)											0													123.0	109.0	114.0					2																	88913303		2203	4300	6503	SO:0001583	missense	9451			AF110146	CCDS33241.1	2p12	2008-05-21			ENSG00000172071	ENSG00000172071			3255	protein-coding gene	gene with protein product		604032				10026192, 10575235	Standard	NM_004836		Approved	PEK, PERK	uc002stc.4	Q9NZJ5	OTTHUMG00000155046	ENST00000303236.3:c.377A>G	2.37:g.88913303T>C	ENSP00000307235:p.Lys126Arg		A0AVH1|A0AVH2|B2RCU9|O95846|Q53QY0|Q53SB1	Missense_Mutation	SNP	ENST00000303236.3	37	CCDS33241.1	.	.	.	.	.	.	.	.	.	.	T	17.77	3.471166	0.63625	.	.	ENSG00000172071	ENST00000303236	T	0.30448	1.53	5.38	5.38	0.77491	Quinonprotein alcohol dehydrogenase-like (2);	0.000000	0.85682	D	0.000000	T	0.51601	0.1684	M	0.72118	2.19	0.47862	D	0.999533	D	0.69078	0.997	D	0.75020	0.985	T	0.48399	-0.9039	10	0.14252	T	0.57	-23.781	15.3963	0.74798	0.0:0.0:0.0:1.0	.	126	Q9NZJ5	E2AK3_HUMAN	R	126	ENSP00000307235:K126R	ENSP00000307235:K126R	K	-	2	0	EIF2AK3	88694418	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.597000	0.82733	2.028000	0.59812	0.533000	0.62120	AAG		0.353	EIF2AK3-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000338233.2	NM_004836		10	137	10	137
PTPN4	5775	hgsc.bcm.edu;broad.mit.edu	37	2	120709680	120709680	+	Silent	SNP	A	A	G			TCGA-HT-7688-01A-11D-2253-08	TCGA-HT-7688-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	35602eec-d9a6-4b1f-b4bf-0304d6f0337a	b1e48d0a-6c17-45b0-856c-58b9eba686c8	g.chr2:120709680A>G	ENST00000263708.2	+	19	2559	c.1788A>G	c.(1786-1788)gaA>gaG	p.E596E	PTPN4_ENST00000544261.1_Silent_p.E229E	NM_002830.3	NP_002821.1	P29074	PTN4_HUMAN	protein tyrosine phosphatase, non-receptor type 4 (megakaryocyte)	596					peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytoskeleton (GO:0005856)	non-membrane spanning protein tyrosine phosphatase activity (GO:0004726)			endometrium(3)|kidney(2)|large_intestine(7)|lung(15)|ovary(2)|urinary_tract(1)	30					Alendronate(DB00630)	ATTCTGGGGAACTCATGCTTC	0.403																																																0													168.0	157.0	161.0					2																	120709680		2203	4300	6503	SO:0001819	synonymous_variant	5775				CCDS2129.1	2q14.2	2011-06-09			ENSG00000088179	ENSG00000088179		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"""	9656	protein-coding gene	gene with protein product		176878				1648233	Standard	NM_002830		Approved	PTPMEG	uc002tmf.2	P29074	OTTHUMG00000131436	ENST00000263708.2:c.1788A>G	2.37:g.120709680A>G			B2RBV8|Q9UDA7	Silent	SNP	ENST00000263708.2	37	CCDS2129.1																																																																																				0.403	PTPN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254233.2			7	117	7	117
TTN	7273	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	179463964	179463964	+	Silent	SNP	G	G	A			TCGA-HT-7688-01A-11D-2253-08	TCGA-HT-7688-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	35602eec-d9a6-4b1f-b4bf-0304d6f0337a	b1e48d0a-6c17-45b0-856c-58b9eba686c8	g.chr2:179463964G>A	ENST00000591111.1	-	240	51857	c.51633C>T	c.(51631-51633)ggC>ggT	p.G17211G	TTN_ENST00000342992.6_Silent_p.G16284G|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000589487.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000589234.1_RNA|TTN_ENST00000460472.2_Silent_p.G9787G|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000359218.5_Silent_p.G9912G|TTN-AS1_ENST00000456053.1_RNA|TTN_ENST00000589042.1_Silent_p.G18852G|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000342175.6_Silent_p.G9979G|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000590932.1_RNA			Q8WZ42	TITIN_HUMAN	titin	17211	Fibronectin type-III 24. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CATATTCATGGCCTTCTAGCA	0.428																																																0													206.0	196.0	199.0					2																	179463964		1901	4116	6017	SO:0001819	synonymous_variant	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.51633C>T	2.37:g.179463964G>A			A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	37																																																																																					0.428	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		29	137	29	137
IDH1	3417	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	209113112	209113112	+	Missense_Mutation	SNP	C	C	T	rs121913500		TCGA-HT-7688-01A-11D-2253-08	TCGA-HT-7688-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	35602eec-d9a6-4b1f-b4bf-0304d6f0337a	b1e48d0a-6c17-45b0-856c-58b9eba686c8	g.chr2:209113112C>T	ENST00000415913.1	-	4	776	c.395G>A	c.(394-396)cGt>cAt	p.R132H	IDH1_ENST00000345146.2_Missense_Mutation_p.R132H|IDH1_ENST00000446179.1_Missense_Mutation_p.R132H	NM_001282387.1	NP_001269316.1	O75874	IDHC_HUMAN	isocitrate dehydrogenase 1 (NADP+), soluble	132			R -> C (in colorectal cancer and glioma samples; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha- ketoglutarate but instead alpha- ketoglutarate is converted to R(-)-2- hydroxyglutarate). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:19117336}.|R -> G (in a glioma sample; glioblastoma multiforme; somatic mutation). {ECO:0000269|PubMed:19117336}.|R -> H (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:18772396}.|R -> L (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:19117336}.|R -> S (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:18772396}.		2-oxoglutarate metabolic process (GO:0006103)|cellular lipid metabolic process (GO:0044255)|female gonad development (GO:0008585)|glutathione metabolic process (GO:0006749)|glyoxylate cycle (GO:0006097)|isocitrate metabolic process (GO:0006102)|NADPH regeneration (GO:0006740)|response to oxidative stress (GO:0006979)|response to steroid hormone (GO:0048545)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	isocitrate dehydrogenase (NADP+) activity (GO:0004450)|magnesium ion binding (GO:0000287)|NAD binding (GO:0051287)|NADP binding (GO:0050661)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)	p.R132H(2774)|p.R132L(59)|p.R132V(1)|p.G131_R132>VL(1)		NS(1)|autonomic_ganglia(2)|biliary_tract(24)|bone(237)|central_nervous_system(3764)|endometrium(3)|haematopoietic_and_lymphoid_tissue(794)|kidney(2)|large_intestine(7)|lung(7)|prostate(6)|skin(5)|soft_tissue(12)|thyroid(22)|urinary_tract(1)	4887				Epithelial(149;0.0322)|LUSC - Lung squamous cell carcinoma(261;0.0711)|Lung(261;0.136)		ATAAGCATGACGACCTATGAT	0.393			Mis		gliobastoma																																Pancreas(158;264 1958 3300 35450 36047)		Dom	yes		2	2q33.3	3417	"""isocitrate dehydrogenase 1 (NADP+), soluble"""		O	2835	Substitution - Missense(2834)|Complex - compound substitution(1)	central_nervous_system(2579)|haematopoietic_and_lymphoid_tissue(205)|bone(43)|prostate(4)|biliary_tract(2)|urinary_tract(1)|skin(1)											79.0	73.0	75.0					2																	209113112		2203	4300	6503	SO:0001583	missense	3417				CCDS2381.1	2q34	2014-09-17			ENSG00000138413	ENSG00000138413	1.1.1.42		5382	protein-coding gene	gene with protein product		147700					Standard	NM_005896		Approved		uc002vcu.3	O75874	OTTHUMG00000132943	ENST00000415913.1:c.395G>A	2.37:g.209113112C>T	ENSP00000390265:p.Arg132His		Q567U4|Q6FHQ6|Q7Z3V0|Q93090|Q9NTJ9|Q9UKW8	Missense_Mutation	SNP	ENST00000415913.1	37	CCDS2381.1	.	.	.	.	.	.	.	.	.	.	C	25.6	4.657324	0.88154	.	.	ENSG00000138413	ENST00000345146;ENST00000446179;ENST00000415913;ENST00000415282	D;D;D;D	0.86956	-2.19;-2.19;-2.19;-2.19	5.57	4.69	0.59074	Isopropylmalate dehydrogenase-like domain (2);	0.000000	0.85682	D	0.000000	D	0.93145	0.7817	H	0.99379	4.54	0.80722	D	1	B	0.25486	0.127	B	0.25405	0.06	D	0.92324	0.5868	10	0.87932	D	0	-20.0399	14.3783	0.66895	0.0:0.9288:0.0:0.0712	.	132	O75874	IDHC_HUMAN	H	132	ENSP00000260985:R132H;ENSP00000410513:R132H;ENSP00000390265:R132H;ENSP00000391075:R132H	ENSP00000260985:R132H	R	-	2	0	IDH1	208821357	1.000000	0.71417	0.997000	0.53966	0.992000	0.81027	6.088000	0.71371	1.356000	0.45884	0.555000	0.69702	CGT		0.393	IDH1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336672.1			26	73	26	73
NEK4	6787	hgsc.bcm.edu;broad.mit.edu	37	3	52802575	52802575	+	Missense_Mutation	SNP	G	G	A			TCGA-HT-7688-01A-11D-2253-08	TCGA-HT-7688-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	35602eec-d9a6-4b1f-b4bf-0304d6f0337a	b1e48d0a-6c17-45b0-856c-58b9eba686c8	g.chr3:52802575G>A	ENST00000233027.5	-	2	341	c.139C>T	c.(139-141)Cgg>Tgg	p.R47W	NEK4_ENST00000535191.1_Intron|NEK4_ENST00000383721.4_Missense_Mutation_p.R47W	NM_001193533.1|NM_003157.4	NP_001180462.1|NP_003148.2	P51957	NEK4_HUMAN	NIMA-related kinase 4	47	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				mitotic nuclear division (GO:0007067)|protein phosphorylation (GO:0006468)	nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(9)|lung(10)	26				BRCA - Breast invasive adenocarcinoma(193;7.44e-05)|Kidney(197;0.000711)|KIRC - Kidney renal clear cell carcinoma(197;0.00086)|OV - Ovarian serous cystadenocarcinoma(275;0.0513)		GCAGCTCGCCGCTCTCGGCTA	0.453																																																0													107.0	104.0	105.0					3																	52802575		2203	4300	6503	SO:0001583	missense	6787			L20321	CCDS2863.1, CCDS54593.1	3p21.1	2012-11-15	2012-11-15	2002-05-10	ENSG00000114904	ENSG00000114904	2.7.11.1		11399	protein-coding gene	gene with protein product	"""serine/threonine protein kinase-2"""	601959	"""serine/threonine kinase 2"", ""NIMA (never in mitosis gene a)-related kinase 4"""	STK2		8208544	Standard	NM_001193533		Approved	NRK2, pp12301	uc003dfq.4	P51957	OTTHUMG00000158836	ENST00000233027.5:c.139C>T	3.37:g.52802575G>A	ENSP00000233027:p.Arg47Trp		A5YM70|B2R633|B7Z200|Q6P576	Missense_Mutation	SNP	ENST00000233027.5	37	CCDS2863.1	.	.	.	.	.	.	.	.	.	.	G	12.01	1.809774	0.31961	.	.	ENSG00000114904	ENST00000233027;ENST00000383721	T;T	0.67171	-0.25;-0.25	5.73	4.82	0.62117	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	0.64402	D	0.000003	D	0.82365	0.5021	M	0.82923	2.615	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.85102	0.0958	10	0.87932	D	0	.	13.7533	0.62921	0.0:0.0:0.664:0.336	.	47;47	P51957-2;P51957	.;NEK4_HUMAN	W	47	ENSP00000233027:R47W;ENSP00000373227:R47W	ENSP00000233027:R47W	R	-	1	2	NEK4	52777615	1.000000	0.71417	1.000000	0.80357	0.583000	0.36354	2.970000	0.49240	1.355000	0.45865	0.563000	0.77884	CGG		0.453	NEK4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000352386.2	NM_003157		7	127	7	127
CWH43	80157	hgsc.bcm.edu;broad.mit.edu	37	4	49000535	49000535	+	Missense_Mutation	SNP	C	C	G			TCGA-HT-7688-01A-11D-2253-08	TCGA-HT-7688-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	35602eec-d9a6-4b1f-b4bf-0304d6f0337a	b1e48d0a-6c17-45b0-856c-58b9eba686c8	g.chr4:49000535C>G	ENST00000226432.4	+	6	955	c.772C>G	c.(772-774)Cgt>Ggt	p.R258G	CWH43_ENST00000513409.1_Missense_Mutation_p.R231G	NM_025087.2	NP_079363.2	Q9H720	PG2IP_HUMAN	cell wall biogenesis 43 C-terminal homolog (S. cerevisiae)	258					GPI anchor biosynthetic process (GO:0006506)	integral component of membrane (GO:0016021)				cervix(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(26)|ovary(1)|prostate(1)|skin(4)|urinary_tract(1)	43						TTTGTGGTTTCGTGGTACTGG	0.443																																																0													561.0	430.0	474.0					4																	49000535		2203	4300	6503	SO:0001583	missense	80157				CCDS3486.1, CCDS68697.1	4p12-p11	2010-09-21			ENSG00000109182	ENSG00000109182			26133	protein-coding gene	gene with protein product						17714445, 17761529	Standard	NM_025087		Approved	FLJ21511, CWH43-C	uc003gyv.3	Q9H720	OTTHUMG00000128627	ENST00000226432.4:c.772C>G	4.37:g.49000535C>G	ENSP00000226432:p.Arg258Gly		B2RPD7	Missense_Mutation	SNP	ENST00000226432.4	37	CCDS3486.1	.	.	.	.	.	.	.	.	.	.	C	0.228	-1.023471	0.02061	.	.	ENSG00000109182	ENST00000226432;ENST00000513409	T;T	0.44881	1.48;0.91	4.16	2.42	0.29668	.	0.756295	0.11956	N	0.513270	T	0.18467	0.0443	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.21621	-1.0240	9	.	.	.	.	3.2787	0.06907	0.1837:0.5149:0.0:0.3013	.	258	Q9H720	PG2IP_HUMAN	G	258;231	ENSP00000226432:R258G;ENSP00000422802:R231G	.	R	+	1	0	CWH43	48695292	0.058000	0.20735	0.356000	0.25785	0.008000	0.06430	0.130000	0.15850	0.701000	0.31803	0.591000	0.81541	CGT		0.443	CWH43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250496.2	NM_025087		11	152	11	152
KDR	3791	hgsc.bcm.edu;broad.mit.edu	37	4	55981079	55981079	+	Missense_Mutation	SNP	T	T	C			TCGA-HT-7688-01A-11D-2253-08	TCGA-HT-7688-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	35602eec-d9a6-4b1f-b4bf-0304d6f0337a	b1e48d0a-6c17-45b0-856c-58b9eba686c8	g.chr4:55981079T>C	ENST00000263923.4	-	5	915	c.620A>G	c.(619-621)gAa>gGa	p.E207G		NM_002253.2	NP_002244.1	P35968	VGFR2_HUMAN	kinase insert domain receptor (a type III receptor tyrosine kinase)	207	Ig-like C2-type 2.				angiogenesis (GO:0001525)|branching morphogenesis of an epithelial tube (GO:0048754)|calcium ion homeostasis (GO:0055074)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|cell fate commitment (GO:0045165)|cell maturation (GO:0048469)|cell migration involved in sprouting angiogenesis (GO:0002042)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|embryonic hemopoiesis (GO:0035162)|endothelial cell differentiation (GO:0045446)|endothelium development (GO:0003158)|extracellular matrix organization (GO:0030198)|lung alveolus development (GO:0048286)|lymph vessel development (GO:0001945)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|ovarian follicle development (GO:0001541)|peptidyl-tyrosine autophosphorylation (GO:0038083)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of vasculogenesis (GO:2001214)|protein autophosphorylation (GO:0046777)|regulation of cell shape (GO:0008360)|signal transduction by phosphorylation (GO:0023014)|surfactant homeostasis (GO:0043129)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|vascular endothelial growth factor signaling pathway (GO:0038084)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sorting endosome (GO:0097443)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|Hsp90 protein binding (GO:0051879)|integrin binding (GO:0005178)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor binding (GO:0038085)|vascular endothelial growth factor-activated receptor activity (GO:0005021)			NS(1)|breast(3)|central_nervous_system(4)|endometrium(2)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(16)|lung(71)|ovary(2)|prostate(2)|skin(10)|soft_tissue(4)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	135	all_cancers(7;0.0255)|all_lung(4;0.00175)|Lung NSC(11;0.00384)|all_epithelial(27;0.034)|Glioma(25;0.08)|all_neural(26;0.101)		Epithelial(7;0.189)		Axitinib(DB06626)|Cabozantinib(DB08875)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	CTGGTAACTTTCATCATTAAT	0.373			Mis		"""NSCLC, angiosarcoma"""					TSP Lung(20;0.16)																													Dom	yes		4	4q11-q12	3791	vascular endothelial growth factor receptor 2		E	0													86.0	86.0	86.0					4																	55981079		2203	4300	6503	SO:0001583	missense	3791			AF035121	CCDS3497.1	4q11-q12	2013-01-29			ENSG00000128052	ENSG00000128052	2.7.10.1	"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6307	protein-coding gene	gene with protein product		191306				1417831	Standard	NM_002253		Approved	FLK1, VEGFR, VEGFR2, CD309	uc003has.3	P35968	OTTHUMG00000128734	ENST00000263923.4:c.620A>G	4.37:g.55981079T>C	ENSP00000263923:p.Glu207Gly		A2RRS0|B5A925|C5IFA0|O60723|Q14178	Missense_Mutation	SNP	ENST00000263923.4	37	CCDS3497.1	.	.	.	.	.	.	.	.	.	.	T	26.3	4.721633	0.89298	.	.	ENSG00000128052	ENST00000263923	T	0.04970	3.52	5.9	5.9	0.94986	Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.26159	0.0638	M	0.73598	2.24	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	T	0.00402	-1.1762	10	0.51188	T	0.08	.	16.315	0.82915	0.0:0.0:0.0:1.0	.	207;207	P35968-2;P35968	.;VGFR2_HUMAN	G	207	ENSP00000263923:E207G	ENSP00000263923:E207G	E	-	2	0	KDR	55675836	1.000000	0.71417	0.977000	0.42913	0.930000	0.56654	7.361000	0.79497	2.250000	0.74265	0.533000	0.62120	GAA		0.373	KDR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250645.1			4	58	4	58
DNAH5	1767	hgsc.bcm.edu;broad.mit.edu	37	5	13792273	13792273	+	Missense_Mutation	SNP	T	T	C			TCGA-HT-7688-01A-11D-2253-08	TCGA-HT-7688-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	35602eec-d9a6-4b1f-b4bf-0304d6f0337a	b1e48d0a-6c17-45b0-856c-58b9eba686c8	g.chr5:13792273T>C	ENST00000265104.4	-	50	8382	c.8278A>G	c.(8278-8280)Aga>Gga	p.R2760G		NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	2760	AAA 3. {ECO:0000250}.				cilium movement (GO:0003341)|lateral ventricle development (GO:0021670)|left/right axis specification (GO:0070986)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					ACAGAATCTCTCACTTCTTCT	0.423									Kartagener syndrome																																							0													111.0	107.0	108.0					5																	13792273		2203	4300	6503	SO:0001583	missense	1767	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	AJ132090	CCDS3882.1	5p15.2	2008-07-18	2006-09-04		ENSG00000039139	ENSG00000039139		"""Axonemal dyneins"""	2950	protein-coding gene	gene with protein product	"""dynein heavy chain 5"""	603335	"""dynein, axonemal, heavy polypeptide 5"""			9256245, 11788826	Standard	NM_001369		Approved	Dnahc5, HL1, PCD, CILD3, KTGNR	uc003jfd.2	Q8TE73	OTTHUMG00000090533	ENST00000265104.4:c.8278A>G	5.37:g.13792273T>C	ENSP00000265104:p.Arg2760Gly		Q92860|Q96L74|Q9H5S7|Q9HCG9	Missense_Mutation	SNP	ENST00000265104.4	37	CCDS3882.1	.	.	.	.	.	.	.	.	.	.	T	4.012	-0.000388	0.07819	.	.	ENSG00000039139	ENST00000265104	T	0.35973	1.28	5.51	1.59	0.23543	ATPase, AAA+ type, core (1);	0.479994	0.24587	N	0.037260	T	0.31670	0.0804	M	0.70595	2.14	0.26051	N	0.981476	B	0.02656	0.0	B	0.13407	0.009	T	0.28776	-1.0033	10	0.15499	T	0.54	.	8.3166	0.32104	0.0:0.0686:0.2566:0.6748	.	2760	Q8TE73	DYH5_HUMAN	G	2760	ENSP00000265104:R2760G	ENSP00000265104:R2760G	R	-	1	2	DNAH5	13845273	0.101000	0.21875	0.974000	0.42286	0.200000	0.23975	1.005000	0.29834	0.413000	0.25759	0.533000	0.62120	AGA		0.423	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369		4	70	4	70
PDZD2	23037	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	5	32090257	32090257	+	Missense_Mutation	SNP	C	C	T	rs147353592	byFrequency	TCGA-HT-7688-01A-11D-2253-08	TCGA-HT-7688-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	35602eec-d9a6-4b1f-b4bf-0304d6f0337a	b1e48d0a-6c17-45b0-856c-58b9eba686c8	g.chr5:32090257C>T	ENST00000438447.1	+	20	7091	c.6703C>T	c.(6703-6705)Cgg>Tgg	p.R2235W	PDZD2_ENST00000282493.3_Missense_Mutation_p.R2235W			O15018	PDZD2_HUMAN	PDZ domain containing 2	2235					cell adhesion (GO:0007155)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|nucleus (GO:0005634)		p.R2235W(1)		NS(2)|breast(4)|central_nervous_system(5)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(31)|lung(58)|ovary(6)|prostate(2)|skin(8)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	148						CCATTTTGGACGGGAGGGTCA	0.632																																																1	Substitution - Missense(1)	urinary_tract(1)						C	TRP/ARG	0,4406		0,0,2203	160.0	173.0	168.0		6703	4.2	1.0	5	dbSNP_134	168	3,8597	2.2+/-6.3	0,3,4297	yes	missense	PDZD2	NM_178140.2	101	0,3,6500	TT,TC,CC		0.0349,0.0,0.0231	probably-damaging	2235/2840	32090257	3,13003	2203	4300	6503	SO:0001583	missense	23037			AB002298	CCDS34137.1	5p14.1	2008-02-05	2006-01-24	2006-01-24		ENSG00000133401			18486	protein-coding gene	gene with protein product		610697	"""PDZ domain containing 3"""	PDZK3		9205841	Standard	XM_005248271		Approved	KIAA0300	uc003jhm.3	O15018		ENST00000438447.1:c.6703C>T	5.37:g.32090257C>T	ENSP00000402033:p.Arg2235Trp		Q9BXD4	Missense_Mutation	SNP	ENST00000438447.1	37	CCDS34137.1	.	.	.	.	.	.	.	.	.	.	C	17.44	3.389537	0.61956	0.0	3.49E-4	ENSG00000133401	ENST00000438447;ENST00000382161;ENST00000282493	T;T	0.07327	3.2;3.2	5.04	4.15	0.48705	.	0.300128	0.24339	N	0.039397	T	0.14485	0.0350	L	0.59436	1.845	0.33822	D	0.629156	D	0.76494	0.999	P	0.53689	0.732	T	0.09640	-1.0665	10	0.66056	D	0.02	.	6.0917	0.19999	0.0:0.6412:0.2499:0.1089	.	2235	O15018	PDZD2_HUMAN	W	2235;2036;2235	ENSP00000402033:R2235W;ENSP00000282493:R2235W	ENSP00000282493:R2235W	R	+	1	2	PDZD2	32126014	0.999000	0.42202	0.972000	0.41901	0.597000	0.36814	3.260000	0.51523	2.323000	0.78572	0.561000	0.74099	CGG		0.632	PDZD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366608.1			48	491	48	491
MAP1B	4131	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	5	71493611	71493611	+	Missense_Mutation	SNP	A	A	G			TCGA-HT-7688-01A-11D-2253-08	TCGA-HT-7688-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	35602eec-d9a6-4b1f-b4bf-0304d6f0337a	b1e48d0a-6c17-45b0-856c-58b9eba686c8	g.chr5:71493611A>G	ENST00000296755.7	+	5	4727	c.4429A>G	c.(4429-4431)Aaa>Gaa	p.K1477E		NM_005909.3	NP_005900.2	P46821	MAP1B_HUMAN	microtubule-associated protein 1B	1477					axon extension (GO:0048675)|cellular process (GO:0009987)|dendrite development (GO:0016358)|establishment of monopolar cell polarity (GO:0061162)|microtubule bundle formation (GO:0001578)|mitochondrion transport along microtubule (GO:0047497)|negative regulation of intracellular transport (GO:0032387)|positive regulation of axon extension (GO:0045773)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|plasma membrane (GO:0005886)|synapse (GO:0045202)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(42)|liver(1)|lung(28)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	104		Lung NSC(167;0.00202)|Ovarian(174;0.0175)|Prostate(461;0.142)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;7.99e-54)		CCAAGAAAAGAAAACTGATGA	0.403																																					Melanoma(17;367 822 11631 31730 47712)											0													82.0	81.0	81.0					5																	71493611		2203	4300	6503	SO:0001583	missense	4131			L06237	CCDS4012.1	5q13	2014-06-12			ENSG00000131711	ENSG00000131711			6836	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 102"""	157129				1881920	Standard	NM_005909		Approved	MAP5, PPP1R102	uc003kbw.4	P46821	OTTHUMG00000100952	ENST00000296755.7:c.4429A>G	5.37:g.71493611A>G	ENSP00000296755:p.Lys1477Glu		A2BDK5	Missense_Mutation	SNP	ENST00000296755.7	37	CCDS4012.1	.	.	.	.	.	.	.	.	.	.	A	13.41	2.229618	0.39399	.	.	ENSG00000131711	ENST00000296755	T	0.04119	3.7	5.54	4.4	0.53042	.	0.162190	0.43747	D	0.000540	T	0.03827	0.0108	N	0.24115	0.695	0.33746	D	0.619997	B;B	0.10296	0.003;0.001	B;B	0.08055	0.002;0.003	T	0.11036	-1.0604	10	0.48119	T	0.1	-17.0295	8.2401	0.31654	0.8507:0.0:0.1493:0.0	.	1351;1477	A2BDK6;P46821	.;MAP1B_HUMAN	E	1477	ENSP00000296755:K1477E	ENSP00000296755:K1477E	K	+	1	0	MAP1B	71529367	1.000000	0.71417	0.983000	0.44433	0.884000	0.51177	5.635000	0.67841	2.119000	0.64992	0.454000	0.30748	AAA		0.403	MAP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218561.6	NM_005909		16	36	16	36
LVRN	206338	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	5	115298645	115298645	+	Silent	SNP	C	C	T			TCGA-HT-7688-01A-11D-2253-08	TCGA-HT-7688-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	35602eec-d9a6-4b1f-b4bf-0304d6f0337a	b1e48d0a-6c17-45b0-856c-58b9eba686c8	g.chr5:115298645C>T	ENST00000357872.4	+	1	455	c.331C>T	c.(331-333)Ctg>Ttg	p.L111L	AQPEP_ENST00000395528.2_5'UTR	NM_173800.4	NP_776161.3	Q6Q4G3	AMPQ_HUMAN		111						integral component of membrane (GO:0016021)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)										CGATCTGGAGCTGTGGCCGCA	0.701																																																0													36.0	42.0	40.0					5																	115298645		2200	4296	6496	SO:0001819	synonymous_variant	206338																														ENST00000357872.4:c.331C>T	5.37:g.115298645C>T			A8K6J0|C9JGD2|Q32MR1|Q4G0I9|Q4G0V2|Q86XA3|Q8NBZ2	Silent	SNP	ENST00000357872.4	37	CCDS4124.1																																																																																				0.701	AQPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250852.1			24	97	24	97
FOXQ1	94234	hgsc.bcm.edu;broad.mit.edu	37	6	1313391	1313391	+	Missense_Mutation	SNP	G	G	A			TCGA-HT-7688-01A-11D-2253-08	TCGA-HT-7688-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	35602eec-d9a6-4b1f-b4bf-0304d6f0337a	b1e48d0a-6c17-45b0-856c-58b9eba686c8	g.chr6:1313391G>A	ENST00000296839.2	+	1	717	c.452G>A	c.(451-453)gGc>gAc	p.G151D		NM_033260.3	NP_150285.3	Q9C009	FOXQ1_HUMAN	forkhead box Q1	151					hair follicle morphogenesis (GO:0031069)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			lung(1)|urinary_tract(1)	2	Ovarian(93;0.0733)	Breast(5;0.052)|all_lung(73;0.0713)|all_hematologic(90;0.0895)		OV - Ovarian serous cystadenocarcinoma(45;0.0954)|BRCA - Breast invasive adenocarcinoma(62;0.18)		TACCTCATGGGCAAGTTCCCC	0.652																																																0													37.0	38.0	38.0					6																	1313391		2198	4291	6489	SO:0001583	missense	94234			AF153341	CCDS4471.1	6p25	2008-02-05			ENSG00000164379	ENSG00000164379		"""Forkhead boxes"""	20951	protein-coding gene	gene with protein product		612788				11747606, 12011061	Standard	NM_033260		Approved	HFH1	uc003mtl.4	Q9C009	OTTHUMG00000016160	ENST00000296839.2:c.452G>A	6.37:g.1313391G>A	ENSP00000296839:p.Gly151Asp		Q9NS06	Missense_Mutation	SNP	ENST00000296839.2	37	CCDS4471.1	.	.	.	.	.	.	.	.	.	.	G	4.140	0.024242	0.08006	.	.	ENSG00000164379	ENST00000296839	D	0.95001	-3.58	3.87	0.879	0.19155	Winged helix-turn-helix transcription repressor DNA-binding (1);Transcription factor, fork head (4);	0.290116	0.28821	U	0.014040	T	0.59487	0.2197	N	0.00980	-1.08	0.32136	N	0.586073	P	0.35944	0.529	B	0.38921	0.285	T	0.67461	-0.5665	10	0.02654	T	1	.	5.1247	0.14878	0.1908:0.3273:0.4819:0.0	.	151	Q9C009	FOXQ1_HUMAN	D	151	ENSP00000296839:G151D	ENSP00000296839:G151D	G	+	2	0	FOXQ1	1258391	0.734000	0.28142	0.476000	0.27291	0.445000	0.32107	0.427000	0.21379	-0.151000	0.11176	0.184000	0.17185	GGC		0.652	FOXQ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043410.1	NM_033260		4	78	4	78
TREML2	79865	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	6	41160191	41160191	+	Missense_Mutation	SNP	G	G	A			TCGA-HT-7688-01A-11D-2253-08	TCGA-HT-7688-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	35602eec-d9a6-4b1f-b4bf-0304d6f0337a	b1e48d0a-6c17-45b0-856c-58b9eba686c8	g.chr6:41160191G>A	ENST00000483722.1	-	5	1125	c.940C>T	c.(940-942)Ccc>Tcc	p.P314S		NM_024807.2	NP_079083.2	Q5T2D2	TRML2_HUMAN	triggering receptor expressed on myeloid cells-like 2	314					T cell activation (GO:0042110)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			breast(1)|central_nervous_system(1)|large_intestine(1)|lung(13)|ovary(1)|prostate(1)	18	Ovarian(28;0.0418)|Colorectal(47;0.196)					TCCACATAGGGCTCTGGTCTT	0.587																																																0													114.0	96.0	102.0					6																	41160191		2203	4300	6503	SO:0001583	missense	79865			AK023755	CCDS4853.1, CCDS4853.2	6p21.1	2013-01-11	2004-04-14	2004-04-16	ENSG00000112195	ENSG00000112195		"""Immunoglobulin superfamily / V-set domain containing"""	21092	protein-coding gene	gene with protein product	"""TREM-like transcript 2"""	609715	"""chromosome 6 open reading frame 76"""	C6orf76		12645956	Standard	NM_024807		Approved	FLJ13693, TLT2, dJ238O23.1	uc010jxm.1	Q5T2D2	OTTHUMG00000016349	ENST00000483722.1:c.940C>T	6.37:g.41160191G>A	ENSP00000418767:p.Pro314Ser		Q08AP8|Q08AP9|Q8IWY0|Q9H8E9	Missense_Mutation	SNP	ENST00000483722.1	37	CCDS4853.2	.	.	.	.	.	.	.	.	.	.	G	12.26	1.884539	0.33255	.	.	ENSG00000112195	ENST00000483722	T	0.09163	3.01	4.45	1.53	0.23141	.	1.231110	0.05662	N	0.587196	T	0.03871	0.0109	L	0.56769	1.78	0.24546	N	0.994045	B	0.30584	0.286	B	0.25884	0.064	T	0.43212	-0.9405	10	0.62326	D	0.03	0.0017	4.3394	0.11103	0.2019:0.0:0.6137:0.1844	.	314	Q5T2D2	TRML2_HUMAN	S	314	ENSP00000418767:P314S	ENSP00000418767:P314S	P	-	1	0	TREML2	41268169	0.993000	0.37304	0.074000	0.20217	0.077000	0.17291	0.971000	0.29396	0.165000	0.19558	0.462000	0.41574	CCC		0.587	TREML2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043756.3	NM_024807		7	46	7	46
PRDM1	639	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	6	106553291	106553291	+	Missense_Mutation	SNP	G	G	A			TCGA-HT-7688-01A-11D-2253-08	TCGA-HT-7688-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	35602eec-d9a6-4b1f-b4bf-0304d6f0337a	b1e48d0a-6c17-45b0-856c-58b9eba686c8	g.chr6:106553291G>A	ENST00000369096.4	+	5	1490	c.1256G>A	c.(1255-1257)gGc>gAc	p.G419D	PRDM1_ENST00000369089.3_Missense_Mutation_p.G285D|PRDM1_ENST00000369091.2_Missense_Mutation_p.G383D	NM_001198.3	NP_001189.2	O75626	PRDM1_HUMAN	PR domain containing 1, with ZNF domain	419					cell fate commitment (GO:0045165)|eye photoreceptor cell development (GO:0042462)|germ cell development (GO:0007281)|intestinal epithelial cell development (GO:0060576)|maternal placenta development (GO:0001893)|negative regulation of B cell proliferation (GO:0030889)|negative regulation of lipopolysaccharide-mediated signaling pathway (GO:0031665)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of B cell differentiation (GO:0045579)|positive regulation of gene expression (GO:0010628)|post-embryonic development (GO:0009791)|transcription, DNA-templated (GO:0006351)|trophoblast giant cell differentiation (GO:0060707)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(59)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|skin(5)|urinary_tract(2)	94	Breast(9;0.022)	all_cancers(87;2.2e-31)|all_epithelial(87;2.03e-21)|Acute lymphoblastic leukemia(125;4.99e-11)|all_lung(197;7.55e-09)|all_hematologic(75;5.82e-08)|Lung NSC(302;1.28e-06)|Colorectal(196;0.0112)|Ovarian(999;0.0365)		all cancers(137;1.83e-46)|Epithelial(106;5.59e-35)|OV - Ovarian serous cystadenocarcinoma(136;1.99e-20)|GBM - Glioblastoma multiforme(226;3.72e-11)|BRCA - Breast invasive adenocarcinoma(108;1.38e-05)		CCCCCCTACGGCATGAATTGT	0.587			"""D, N, Mis, F, S"""		DLBCL																																		Rec	yes		6	6q21	639	"""PR domain containing 1, with ZNF domain"""		L	0													75.0	58.0	64.0					6																	106553291		2203	4300	6503	SO:0001583	missense	639				CCDS5054.2, CCDS34505.1	6q21	2013-01-08			ENSG00000057657	ENSG00000057657		"""Zinc fingers, C2H2-type"""	9346	protein-coding gene	gene with protein product		603423		BLIMP1		1851123	Standard	NM_001198		Approved	PRDI-BF1	uc003prd.2	O75626	OTTHUMG00000015299	ENST00000369096.4:c.1256G>A	6.37:g.106553291G>A	ENSP00000358092:p.Gly419Asp		B2REA6|E1P5E0|Q86WM7	Missense_Mutation	SNP	ENST00000369096.4	37	CCDS5054.2	.	.	.	.	.	.	.	.	.	.	G	14.01	2.407857	0.42715	.	.	ENSG00000057657	ENST00000369091;ENST00000369096;ENST00000456278;ENST00000369089	T;T;T	0.07216	3.23;3.21;3.21	5.32	5.32	0.75619	.	0.336949	0.36002	N	0.002858	T	0.04679	0.0127	M	0.63428	1.95	0.37659	D	0.922688	B;B	0.34181	0.236;0.44	B;B	0.30029	0.11;0.075	T	0.27088	-1.0084	10	0.29301	T	0.29	-18.0932	12.8014	0.57588	0.0854:0.0:0.9146:0.0	.	285;419	Q86WM7;O75626	.;PRDM1_HUMAN	D	383;419;383;285	ENSP00000358087:G383D;ENSP00000358092:G419D;ENSP00000358085:G285D	ENSP00000358085:G285D	G	+	2	0	PRDM1	106659984	1.000000	0.71417	0.906000	0.35671	0.966000	0.64601	4.173000	0.58249	2.492000	0.84095	0.655000	0.94253	GGC		0.587	PRDM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041661.3			10	65	10	65
IL6	3569	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	7	22769188	22769188	+	Missense_Mutation	SNP	A	A	T			TCGA-HT-7688-01A-11D-2253-08	TCGA-HT-7688-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	35602eec-d9a6-4b1f-b4bf-0304d6f0337a	b1e48d0a-6c17-45b0-856c-58b9eba686c8	g.chr7:22769188A>T	ENST00000404625.1	+	5	839	c.380A>T	c.(379-381)gAg>gTg	p.E127V	IL6_ENST00000420258.2_Missense_Mutation_p.E181V|IL6_ENST00000407492.1_Missense_Mutation_p.E51V|IL6_ENST00000406575.1_Missense_Mutation_p.E127V|IL6_ENST00000401651.1_Missense_Mutation_p.E51V|IL6_ENST00000401630.3_Missense_Mutation_p.E104V|IL6_ENST00000258743.5_Missense_Mutation_p.E127V|AC073072.5_ENST00000325042.2_RNA			P05231	IL6_HUMAN	interleukin 6	127					acute-phase response (GO:0006953)|aging (GO:0007568)|bone remodeling (GO:0046849)|branching involved in salivary gland morphogenesis (GO:0060445)|cell growth (GO:0016049)|cell redox homeostasis (GO:0045454)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to lipopolysaccharide (GO:0071222)|cytokine-mediated signaling pathway (GO:0019221)|defense response to Gram-negative bacterium (GO:0050829)|defense response to Gram-positive bacterium (GO:0050830)|defense response to protozoan (GO:0042832)|defense response to virus (GO:0051607)|endocrine pancreas development (GO:0031018)|epithelial cell proliferation involved in salivary gland morphogenesis (GO:0060664)|glucagon secretion (GO:0070091)|hepatic immune response (GO:0002384)|humoral immune response (GO:0006959)|inflammatory response (GO:0006954)|interleukin-6-mediated signaling pathway (GO:0070102)|monocyte chemotaxis (GO:0002548)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chemokine biosynthetic process (GO:0045079)|negative regulation of collagen biosynthetic process (GO:0032966)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of cytokine secretion (GO:0050710)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of gluconeogenesis (GO:0045721)|negative regulation of hormone secretion (GO:0046888)|negative regulation of lipid storage (GO:0010888)|negative regulation of muscle organ development (GO:0048635)|negative regulation of neuron death (GO:1901215)|negative regulation of protein kinase activity (GO:0006469)|neuron projection development (GO:0031175)|neutrophil apoptotic process (GO:0001781)|neutrophil mediated immunity (GO:0002446)|platelet activation (GO:0030168)|positive regulation of acute inflammatory response (GO:0002675)|positive regulation of apoptotic process (GO:0043065)|positive regulation of B cell activation (GO:0050871)|positive regulation of cell proliferation (GO:0008284)|positive regulation of chemokine production (GO:0032722)|positive regulation of DNA replication (GO:0045740)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of immunoglobulin secretion (GO:0051024)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of leukocyte chemotaxis (GO:0002690)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein import into nucleus, translocation (GO:0033160)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of STAT protein import into nucleus (GO:2000366)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of T-helper 2 cell differentiation (GO:0045630)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of translation (GO:0045727)|positive regulation of transmission of nerve impulse (GO:0051971)|positive regulation of type B pancreatic cell apoptotic process (GO:2000676)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|regulation of angiogenesis (GO:0045765)|regulation of cell shape (GO:0008360)|regulation of circadian sleep/wake cycle, non-REM sleep (GO:0045188)|regulation of vascular endothelial growth factor production (GO:0010574)|response to amino acid (GO:0043200)|response to antibiotic (GO:0046677)|response to caffeine (GO:0031000)|response to calcium ion (GO:0051592)|response to cold (GO:0009409)|response to drug (GO:0042493)|response to electrical stimulus (GO:0051602)|response to glucocorticoid (GO:0051384)|response to heat (GO:0009408)|response to insulin (GO:0032868)|response to mechanical stimulus (GO:0009612)|response to nutrient levels (GO:0031667)|response to peptidoglycan (GO:0032494)|T-helper 17 cell lineage commitment (GO:0072540)	external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|interleukin-6 receptor complex (GO:0005896)	cytokine activity (GO:0005125)|growth factor activity (GO:0008083)|interleukin-6 receptor binding (GO:0005138)			breast(1)|endometrium(2)|large_intestine(4)|lung(1)	8					Ginseng(DB01404)	GTATACCTAGAGTACCTCCAG	0.458																																					Esophageal Squamous(47;342 1214 13936 33513)											0													154.0	153.0	153.0					7																	22769188		2203	4300	6503	SO:0001583	missense	3569			M18403	CCDS5375.1	7p21-p15	2014-04-04	2014-04-04		ENSG00000136244	ENSG00000136244		"""Interleukins and interleukin receptors"", ""Interferons"""	6018	protein-coding gene	gene with protein product	"""interferon, beta 2"""	147620	"""interleukin 6 (interferon, beta 2)"""	IFNB2		3294161	Standard	NM_000600		Approved	IL-6, BSF2, HGF, HSF	uc003svj.4	P05231	OTTHUMG00000023178	ENST00000404625.1:c.380A>T	7.37:g.22769188A>T	ENSP00000385675:p.Glu127Val		Q9UCU2|Q9UCU3|Q9UCU4	Missense_Mutation	SNP	ENST00000404625.1	37	CCDS5375.1	.	.	.	.	.	.	.	.	.	.	A	16.28	3.077358	0.55753	.	.	ENSG00000136244	ENST00000404625;ENST00000426291;ENST00000401651;ENST00000258743;ENST00000420258;ENST00000407492;ENST00000401630;ENST00000406575	T;T;T;T;T;T;T;T	0.34072	1.38;1.38;1.38;1.38;1.38;1.38;1.38;1.38	5.87	3.49	0.39957	Four-helical cytokine-like, core (1);Four-helical cytokine, core (1);	1.204080	0.05394	N	0.539489	T	0.47451	0.1446	L	0.32530	0.975	0.09310	N	1	D;D;D	0.65815	0.992;0.989;0.995	P;D;D	0.65684	0.845;0.916;0.937	T	0.24333	-1.0163	10	0.72032	D	0.01	-1.1131	6.305	0.21133	0.7591:0.1598:0.0811:0.0	.	181;127;127	B4DNQ5;B5MC14;P05231	.;.;IL6_HUMAN	V	127;127;51;127;181;51;104;127	ENSP00000385675:E127V;ENSP00000405150:E127V;ENSP00000385718:E51V;ENSP00000258743:E127V;ENSP00000405994:E181V;ENSP00000385043:E51V;ENSP00000384928:E104V;ENSP00000385227:E127V	ENSP00000258743:E127V	E	+	2	0	IL6	22735713	0.018000	0.18449	0.000000	0.03702	0.002000	0.02628	3.020000	0.49643	0.556000	0.29098	-0.316000	0.08728	GAG		0.458	IL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250225.2	NM_000600		11	72	11	72
GRB10	2887	hgsc.bcm.edu;broad.mit.edu	37	7	50686969	50686969	+	Silent	SNP	T	T	C			TCGA-HT-7688-01A-11D-2253-08	TCGA-HT-7688-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	35602eec-d9a6-4b1f-b4bf-0304d6f0337a	b1e48d0a-6c17-45b0-856c-58b9eba686c8	g.chr7:50686969T>C	ENST00000401949.1	-	9	1144	c.675A>G	c.(673-675)gaA>gaG	p.E225E	GRB10_ENST00000402578.1_Silent_p.E167E|GRB10_ENST00000407526.1_Silent_p.E167E|GRB10_ENST00000406641.1_Silent_p.E167E|GRB10_ENST00000398810.2_Silent_p.E167E|GRB10_ENST00000402497.1_Silent_p.E167E|GRB10_ENST00000398812.2_Silent_p.E225E|GRB10_ENST00000335866.3_Silent_p.E167E|GRB10_ENST00000403097.1_Silent_p.E219E|GRB10_ENST00000357271.5_Silent_p.E225E|GRB10_ENST00000439599.1_Silent_p.E219E			Q13322	GRB10_HUMAN	growth factor receptor-bound protein 10	225	Ras-associating. {ECO:0000255|PROSITE- ProRule:PRU00166}.				insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|negative regulation of glucose import (GO:0046325)|negative regulation of glycogen biosynthetic process (GO:0045719)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of phosphorylation (GO:0042326)|negative regulation of Wnt signaling pathway (GO:0030178)|positive regulation of phosphorylation (GO:0042327)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|response to insulin (GO:0032868)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	insulin receptor binding (GO:0005158)|SH3/SH2 adaptor activity (GO:0005070)			NS(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(2)|lung(19)|ovary(3)|skin(3)|upper_aerodigestive_tract(2)	41	Glioma(55;0.08)|all_neural(89;0.245)					GCTCATGGTCTTCCAAGCACC	0.443									Russell-Silver syndrome																																							0													89.0	91.0	90.0					7																	50686969		1988	4171	6159	SO:0001819	synonymous_variant	2887	Familial Cancer Database	Silver-Russell Dwarfism, Silver-Russell syndrome, SRS, Russel-Silver Dwarfism		CCDS43582.1, CCDS43583.1, CCDS47586.1	7p12.2	2013-02-14			ENSG00000106070	ENSG00000106070		"""Pleckstrin homology (PH) domain containing"", ""SH2 domain containing"""	4564	protein-coding gene	gene with protein product		601523					Standard	NM_005311		Approved		uc003tpi.2	Q13322	OTTHUMG00000150622	ENST00000401949.1:c.675A>G	7.37:g.50686969T>C			A4D258|A7VJ95|A8K0E6|D3DVM9|O00427|O00701|O75222|Q92606|Q92907|Q92948	Silent	SNP	ENST00000401949.1	37	CCDS43582.1																																																																																				0.443	GRB10-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319157.1			6	123	6	123
INTS9	55756	hgsc.bcm.edu;broad.mit.edu	37	8	28625815	28625815	+	Missense_Mutation	SNP	C	C	G			TCGA-HT-7688-01A-11D-2253-08	TCGA-HT-7688-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	35602eec-d9a6-4b1f-b4bf-0304d6f0337a	b1e48d0a-6c17-45b0-856c-58b9eba686c8	g.chr8:28625815C>G	ENST00000521022.1	-	17	1906	c.1825G>C	c.(1825-1827)Gag>Cag	p.E609Q	INTS9_ENST00000416984.2_Missense_Mutation_p.E588Q|INTS9_ENST00000521777.1_Missense_Mutation_p.E585Q|INTS9_ENST00000397363.4_Missense_Mutation_p.E503Q	NM_018250.3	NP_060720.2	Q9NV88	INT9_HUMAN	integrator complex subunit 9	609					snRNA processing (GO:0016180)	cytoplasm (GO:0005737)|integrator complex (GO:0032039)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(6)|pancreas(2)|prostate(1)|urinary_tract(2)	19		Ovarian(32;0.0439)		KIRC - Kidney renal clear cell carcinoma(542;0.127)|Kidney(114;0.152)		GCTGTGTCCTCCACCTTAATA	0.502																																																0													198.0	190.0	193.0					8																	28625815		2203	4300	6503	SO:0001583	missense	55756			BC025267	CCDS34873.1, CCDS55215.1, CCDS55216.1	8p21.1	2008-02-05			ENSG00000104299	ENSG00000104299			25592	protein-coding gene	gene with protein product		611352				16239144	Standard	NM_001172562		Approved	FLJ10871, CPSF2L, RC-74	uc011lav.2	Q9NV88	OTTHUMG00000164030	ENST00000521022.1:c.1825G>C	8.37:g.28625815C>G	ENSP00000429065:p.Glu609Gln		B7Z560|B7Z6M5|O00224|Q8TB16	Missense_Mutation	SNP	ENST00000521022.1	37	CCDS34873.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	20.7|20.7	4.039865|4.039865	0.75732|0.75732	.|.	.|.	ENSG00000104299|ENSG00000104299	ENST00000521022;ENST00000416984;ENST00000541706;ENST00000521777;ENST00000397363|ENST00000517383	T;T;T;T|.	0.51817|.	0.69;0.7;0.69;0.7|.	5.11|5.11	5.11|5.11	0.69529|0.69529	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.73450|0.73450	0.3588|0.3588	M|M	0.64567|0.64567	1.98|1.98	0.80722|0.80722	D|D	1|1	D;P|.	0.55800|.	0.973;0.656|.	P;B|.	0.49528|.	0.614;0.275|.	T|T	0.72235|0.72235	-0.4352|-0.4352	10|5	0.37606|.	T|.	0.19|.	-19.5542|-19.5542	18.5577|18.5577	0.91090|0.91090	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	588;609|.	B7Z6M5;Q9NV88|.	.;INT9_HUMAN|.	Q|C	609;588;453;585;503|100	ENSP00000429065:E609Q;ENSP00000398208:E588Q;ENSP00000430943:E585Q;ENSP00000380520:E503Q|.	ENSP00000380520:E503Q|.	E|W	-|-	1|3	0|0	INTS9|INTS9	28681734|28681734	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.988000|0.988000	0.76386|0.76386	7.703000|7.703000	0.84585|0.84585	2.366000|2.366000	0.80165|0.80165	0.655000|0.655000	0.94253|0.94253	GAG|TGG		0.502	INTS9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376846.1	NM_018250		11	196	11	196
TG	7038	hgsc.bcm.edu;broad.mit.edu	37	8	133912511	133912511	+	Silent	SNP	G	G	A			TCGA-HT-7688-01A-11D-2253-08	TCGA-HT-7688-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	35602eec-d9a6-4b1f-b4bf-0304d6f0337a	b1e48d0a-6c17-45b0-856c-58b9eba686c8	g.chr8:133912511G>A	ENST00000220616.4	+	15	3400	c.3360G>A	c.(3358-3360)tcG>tcA	p.S1120S	TG_ENST00000377869.1_Silent_p.S1120S	NM_003235.4	NP_003226.4	P01266	THYG_HUMAN	thyroglobulin	1120	Thyroglobulin type-1 9. {ECO:0000255|PROSITE-ProRule:PRU00500}.				hormone biosynthetic process (GO:0042446)|iodide transport (GO:0015705)|regulation of myelination (GO:0031641)|signal transduction (GO:0007165)|thyroid gland development (GO:0030878)|thyroid hormone generation (GO:0006590)	extracellular region (GO:0005576)|extracellular space (GO:0005615)				NS(1)|breast(11)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(34)|liver(2)|lung(59)|ovary(9)|pancreas(2)|prostate(6)|skin(7)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(8)	168	Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)	Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0559)|Breast(495;0.0735)	BRCA - Breast invasive adenocarcinoma(115;0.000701)	KIRC - Kidney renal clear cell carcinoma(542;0.0546)		TGCAGGCATCGGGGGCTGGCA	0.622																																																0													60.0	52.0	54.0					8																	133912511		2203	4300	6503	SO:0001819	synonymous_variant	7038			AU141420	CCDS34944.1	8q24	2012-10-02			ENSG00000042832	ENSG00000042832			11764	protein-coding gene	gene with protein product		188450					Standard	NM_003235		Approved	TGN, AITD3	uc003ytw.3	P01266	OTTHUMG00000164649	ENST00000220616.4:c.3360G>A	8.37:g.133912511G>A			O15274|O43899|Q15593|Q15948|Q9NYR1|Q9NYR2|Q9UMZ0|Q9UNY3	Silent	SNP	ENST00000220616.4	37	CCDS34944.1	.	.	.	.	.	.	.	.	.	.	G	0.120	-1.126999	0.01770	.	.	ENSG00000042832	ENST00000518505	.	.	.	5.55	-11.1	0.00147	.	.	.	.	.	T	0.26122	0.0637	.	.	.	0.18873	N	0.999988	.	.	.	.	.	.	T	0.30592	-0.9973	4	.	.	.	.	10.2821	0.43545	0.5849:0.263:0.1521:0.0	.	.	.	.	Q	87	.	.	R	+	2	0	TG	133981693	0.000000	0.05858	0.000000	0.03702	0.022000	0.10575	-1.924000	0.01565	-3.693000	0.00120	-2.069000	0.00389	CGG		0.622	TG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379606.1	NM_003235		5	58	5	58
RORB	6096	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	9	77257632	77257632	+	Nonsense_Mutation	SNP	C	C	T			TCGA-HT-7688-01A-11D-2253-08	TCGA-HT-7688-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	35602eec-d9a6-4b1f-b4bf-0304d6f0337a	b1e48d0a-6c17-45b0-856c-58b9eba686c8	g.chr9:77257632C>T	ENST00000396204.2	+	4	571	c.571C>T	c.(571-573)Caa>Taa	p.Q191*	RORB_ENST00000376896.3_Nonsense_Mutation_p.Q180*			Q92753	RORB_HUMAN	RAR-related orphan receptor B	191	Hinge. {ECO:0000255}.				amacrine cell differentiation (GO:0035881)|cellular response to retinoic acid (GO:0071300)|eye photoreceptor cell development (GO:0042462)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of circadian rhythm (GO:0042752)|regulation of transcription, DNA-templated (GO:0006355)|retina development in camera-type eye (GO:0060041)|retinal cone cell development (GO:0046549)|retinal rod cell development (GO:0046548)|rhythmic process (GO:0048511)|transcription initiation from RNA polymerase II promoter (GO:0006367)|visual perception (GO:0007601)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			breast(2)|large_intestine(4)|lung(1)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	12					Melatonin(DB01065)	ACAGATAAAGCAAGAACCTAT	0.468																																																0													81.0	76.0	78.0					9																	77257632		2203	4300	6503	SO:0001587	stop_gained	6096			Y08639	CCDS6646.1	9q22	2013-01-16			ENSG00000198963	ENSG00000198963		"""Nuclear hormone receptors"""	10259	protein-coding gene	gene with protein product		601972				7926749	Standard	NM_006914		Approved	RZRB, NR1F2, ROR-BETA	uc004ajh.3	Q92753	OTTHUMG00000020026	ENST00000396204.2:c.571C>T	9.37:g.77257632C>T	ENSP00000379507:p.Gln191*		Q8WX73	Nonsense_Mutation	SNP	ENST00000396204.2	37		.	.	.	.	.	.	.	.	.	.	C	37	6.187082	0.97357	.	.	ENSG00000198963	ENST00000376896;ENST00000396204	.	.	.	5.75	5.75	0.90469	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.10636	T	0.68	.	19.9525	0.97208	0.0:1.0:0.0:0.0	.	.	.	.	X	180;191	.	ENSP00000366093:Q180X	Q	+	1	0	RORB	76447452	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.487000	0.81328	2.719000	0.93026	0.655000	0.94253	CAA		0.468	RORB-201	KNOWN	basic	protein_coding	protein_coding				11	68	11	68
MSL3	10943	hgsc.bcm.edu;ucsc.edu	37	X	11783854	11783854	+	Intron	SNP	T	T	C			TCGA-HT-7688-01A-11D-2253-08	TCGA-HT-7688-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	35602eec-d9a6-4b1f-b4bf-0304d6f0337a	b1e48d0a-6c17-45b0-856c-58b9eba686c8	g.chrX:11783854T>C	ENST00000312196.4	+	9	1276				MSL3_ENST00000337339.2_Missense_Mutation_p.F393L|MSL3_ENST00000361672.2_Intron|MSL3_ENST00000467141.1_Intron|MSL3_ENST00000380693.3_Intron|MSL3_ENST00000398527.2_Intron	NM_078629.3	NP_523353.2	Q8N5Y2	MS3L1_HUMAN	male-specific lethal 3 homolog (Drosophila)						chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|multicellular organismal development (GO:0007275)|transcription from RNA polymerase II promoter (GO:0006366)	MSL complex (GO:0072487)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|methylated histone binding (GO:0035064)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(3)|cervix(1)|kidney(3)|large_intestine(3)|lung(6)|ovary(1)|urinary_tract(1)	19						AAAGAGTAGGTTCATTCTCGG	0.587																																																0													107.0	92.0	97.0					X																	11783854		2203	4300	6503	SO:0001627	intron_variant	10943			AF117065	CCDS14147.1, CCDS14148.1, CCDS14149.1, CCDS55369.1, CCDS65213.1	Xp22.3	2008-10-29	2008-10-29	2008-10-29	ENSG00000005302	ENSG00000005302			7370	protein-coding gene	gene with protein product		300609	"""male-specific lethal-3 (Drosophila)-like 1"", ""male-specific lethal 3-like 1 (Drosophila)"""	MSL3L1		10395802, 10908644	Standard	NM_078628		Approved		uc004cuw.3	Q8N5Y2	OTTHUMG00000021132	ENST00000312196.4:c.1171+6T>C	X.37:g.11783854T>C			A6NCU2|A6NHW8|A8K165|B4DUV8|B7Z227|Q9UG70|Q9Y5Z8	Missense_Mutation	SNP	ENST00000312196.4	37	CCDS14147.1	.	.	.	.	.	.	.	.	.	.	T	6.813	0.519126	0.13005	.	.	ENSG00000005302	ENST00000337339	T	0.05855	3.38	4.32	4.32	0.51571	.	.	.	.	.	T	0.03695	0.0105	N	0.08118	0	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.46638	-0.9177	8	.	.	.	.	13.0401	0.58895	0.0:0.0:0.0:1.0	.	393	A6NHW8	.	L	393	ENSP00000338078:F393L	.	F	+	1	0	MSL3	11693775	0.998000	0.40836	0.915000	0.36163	0.812000	0.45895	2.345000	0.44018	1.515000	0.48885	0.486000	0.48141	TTC		0.587	MSL3-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055757.1	NM_006800		25	136	25	136
FMR1NB	158521	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	X	147084823	147084823	+	Missense_Mutation	SNP	A	A	G			TCGA-HT-7688-01A-11D-2253-08	TCGA-HT-7688-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	35602eec-d9a6-4b1f-b4bf-0304d6f0337a	b1e48d0a-6c17-45b0-856c-58b9eba686c8	g.chrX:147084823A>G	ENST00000370467.3	+	2	454	c.380A>G	c.(379-381)aAt>aGt	p.N127S		NM_152578.2	NP_689791.1	Q8N0W7	FMR1N_HUMAN	fragile X mental retardation 1 neighbor	127	P-type.					integral component of membrane (GO:0016021)|nucleolus (GO:0005730)		p.F130fs*17(1)		breast(2)|cervix(1)|endometrium(3)|large_intestine(7)|lung(10)|ovary(1)|skin(1)	25	Acute lymphoblastic leukemia(192;6.56e-05)					GCTTTGCTGAATTTTTTCTTT	0.373																																																1	Insertion - Frameshift(1)	lung(1)											98.0	89.0	92.0					X																	147084823		2203	4299	6502	SO:0001583	missense	158521				CCDS14683.1	Xq28	2009-03-25			ENSG00000176988	ENSG00000176988			26372	protein-coding gene	gene with protein product	"""cancer/testis antigen 37"""					12601173	Standard	NM_152578		Approved	FLJ25736, NY-SAR-35, CT37	uc004fcm.3	Q8N0W7	OTTHUMG00000022608	ENST00000370467.3:c.380A>G	X.37:g.147084823A>G	ENSP00000359498:p.Asn127Ser		D3DWT3	Missense_Mutation	SNP	ENST00000370467.3	37	CCDS14683.1	.	.	.	.	.	.	.	.	.	.	A	8.613	0.889635	0.17540	.	.	ENSG00000176988	ENST00000370467	T	0.45276	0.9	4.94	-9.88	0.00467	.	2.316320	0.01768	N	0.031027	T	0.19406	0.0466	N	0.08118	0	0.09310	N	1	B	0.16396	0.017	B	0.15484	0.013	T	0.10520	-1.0626	10	0.17832	T	0.49	0.5734	9.7741	0.40607	0.7094:0.0:0.1067:0.1839	.	127	Q8N0W7	FMR1N_HUMAN	S	127	ENSP00000359498:N127S	ENSP00000359498:N127S	N	+	2	0	FMR1NB	146892515	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.497000	0.06428	-2.799000	0.00353	-1.033000	0.02402	AAT		0.373	FMR1NB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058667.1	NM_152578		7	23	7	23
UTY	7404	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	Y	15522901	15522901	+	Missense_Mutation	SNP	A	A	G			TCGA-HT-7688-01A-11D-2253-08	TCGA-HT-7688-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	35602eec-d9a6-4b1f-b4bf-0304d6f0337a	b1e48d0a-6c17-45b0-856c-58b9eba686c8	g.chrY:15522901A>G	ENST00000331397.4	-	6	1534	c.527T>C	c.(526-528)gTg>gCg	p.V176A	UTY_ENST00000382893.1_Missense_Mutation_p.V176A|UTY_ENST00000474365.1_5'UTR|UTY_ENST00000538878.1_Missense_Mutation_p.V176A|UTY_ENST00000362096.4_Missense_Mutation_p.V176A|UTY_ENST00000537580.1_Missense_Mutation_p.V176A|UTY_ENST00000382896.4_Missense_Mutation_p.V176A|UTY_ENST00000540140.1_Missense_Mutation_p.V176A|UTY_ENST00000545955.1_Missense_Mutation_p.V176A|UTY_ENST00000329134.5_Missense_Mutation_p.V176A	NM_001258267.1|NM_007125.4	NP_001245196.1|NP_009056.3	O14607	UTY_HUMAN	ubiquitously transcribed tetratricopeptide repeat containing, Y-linked	176					regulation of gene expression (GO:0010468)	nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|histone demethylase activity (H3-K27 specific) (GO:0071558)|metal ion binding (GO:0046872)			kidney(1)|lung(6)	7						GTCTGTGTTCACTTTGAACAT	0.413																																					Colon(103;1740 2135 40732 45171)											0																																										SO:0001583	missense	7404			AF000994	CCDS14783.1, CCDS14784.1, CCDS14785.1, CCDS59184.1, CCDS76073.1, CCDS76074.1, CCDS76075.1, CCDS76076.1, CCDS76077.1, CCDS76078.1, CCDS76079.1	Yq11.221	2013-11-04	2012-11-15		ENSG00000183878	ENSG00000183878		"""Tetratricopeptide (TTC) repeat domain containing"""	12638	protein-coding gene	gene with protein product		400009	"""ubiquitously transcribed tetratricopeptide repeat gene, Y chromosome"", ""ubiquitously transcribed tetratricopeptide repeat gene, Y-linked"""			8944031, 9499428	Standard	NM_182659		Approved	KDM6AL	uc022ckf.2	O14607	OTTHUMG00000036319	ENST00000331397.4:c.527T>C	Y.37:g.15522901A>G	ENSP00000328939:p.Val176Ala		A8K9Z3|E1U199|E1U1A0|F5H4V7|F8W8R7|O14608	Missense_Mutation	SNP	ENST00000331397.4	37	CCDS14783.1																																																																																				0.413	UTY-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000088394.1	NM_182660		22	37	22	37
TMEM175	84286	broad.mit.edu;ucsc.edu	37	4	944293	944293	+	Missense_Mutation	SNP	G	G	C			TCGA-HT-7688-01A-11D-2253-08	TCGA-HT-7688-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	35602eec-d9a6-4b1f-b4bf-0304d6f0337a	b1e48d0a-6c17-45b0-856c-58b9eba686c8	g.chr4:944293G>C	ENST00000264771.4	+	4	462	c.277G>C	c.(277-279)Gca>Cca	p.A93P	TMEM175_ENST00000508204.1_Missense_Mutation_p.A11P|TMEM175_ENST00000504180.1_3'UTR|TMEM175_ENST00000515740.1_5'UTR	NM_032326.2	NP_115702.1	Q9BSA9	TM175_HUMAN	transmembrane protein 175	93						integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)				NS(1)|endometrium(1)|large_intestine(2)|lung(6)|pancreas(1)|upper_aerodigestive_tract(3)	14			OV - Ovarian serous cystadenocarcinoma(23;0.0158)			AGTGGCCTGGGCAGCACACAC	0.597																																																0													84.0	79.0	81.0					4																	944293		2203	4300	6503	SO:0001583	missense	84286			BC005158	CCDS3341.1, CCDS75087.1, CCDS75088.1	4p16.3	2008-02-05			ENSG00000127419	ENSG00000127419			28709	protein-coding gene	gene with protein product						12477932	Standard	XM_005272301		Approved	MGC4618	uc003gbq.3	Q9BSA9	OTTHUMG00000118996	ENST00000264771.4:c.277G>C	4.37:g.944293G>C	ENSP00000264771:p.Ala93Pro		D3DVN4|Q8ND13	Missense_Mutation	SNP	ENST00000264771.4	37	CCDS3341.1	.	.	.	.	.	.	.	.	.	.	G	15.90	2.970715	0.53614	.	.	ENSG00000127419	ENST00000507319;ENST00000264771;ENST00000514453;ENST00000515492;ENST00000359768;ENST00000509508;ENST00000508204;ENST00000510493;ENST00000514546	T;T;T;T;T;T;T;T	0.47528	0.84;0.84;0.84;0.84;0.84;0.84;0.84;0.84	4.38	2.53	0.30540	.	0.149518	0.44285	D	0.000475	T	0.56411	0.1983	L	0.60455	1.87	0.37655	D	0.92257	D;D;D	0.69078	0.971;0.977;0.997	P;P;D	0.68621	0.9;0.816;0.959	T	0.56098	-0.8035	10	0.33940	T	0.23	-8.4511	6.6108	0.22751	0.2398:0.0:0.7602:0.0	.	11;93;11	D6RBE5;Q9BSA9;B3KR27	.;TM175_HUMAN;.	P	92;93;80;11;11;11;11;11;93	ENSP00000424746:A92P;ENSP00000264771:A93P;ENSP00000425181:A80P;ENSP00000425867:A11P;ENSP00000421750:A11P;ENSP00000423669:A11P;ENSP00000424208:A11P;ENSP00000425763:A93P	ENSP00000264771:A93P	A	+	1	0	TMEM175	934293	1.000000	0.71417	0.714000	0.30535	0.263000	0.26337	4.418000	0.59828	0.437000	0.26423	0.549000	0.68633	GCA		0.597	TMEM175-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239193.2	NM_032326		11	106	11	106
MBL2	4153	broad.mit.edu;ucsc.edu	37	10	54531233	54531233	+	Missense_Mutation	SNP	T	T	C			TCGA-HT-7688-01A-11D-2253-08	TCGA-HT-7688-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	35602eec-d9a6-4b1f-b4bf-0304d6f0337a	b1e48d0a-6c17-45b0-856c-58b9eba686c8	g.chr10:54531233T>C	ENST00000373968.3	-	1	227	c.163A>G	c.(163-165)Acc>Gcc	p.T55A		NM_000242.2	NP_000233.1	P11226	MBL2_HUMAN	mannose-binding lectin (protein C) 2, soluble	55	Collagen-like.				acute-phase response (GO:0006953)|complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|complement activation, lectin pathway (GO:0001867)|defense response to bacterium (GO:0042742)|defense response to Gram-positive bacterium (GO:0050830)|innate immune response (GO:0045087)|killing by host of symbiont cells (GO:0051873)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of viral process (GO:0048525)|opsonization (GO:0008228)|positive regulation of phagocytosis (GO:0050766)|response to oxidative stress (GO:0006979)	cell surface (GO:0009986)|collagen trimer (GO:0005581)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	calcium-dependent protein binding (GO:0048306)|mannose binding (GO:0005537)|receptor binding (GO:0005102)			breast(1)|endometrium(2)|lung(12)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	21						TCTCCCTTGGTGCCATCACGC	0.537																																																0													137.0	123.0	128.0					10																	54531233		2203	4300	6503	SO:0001583	missense	4153			AF360991	CCDS7247.1	10q11.2	2014-09-17	2011-02-02		ENSG00000165471	ENSG00000165471		"""Collectins"""	6922	protein-coding gene	gene with protein product		154545	"""mannose-binding lectin (protein C) 2, soluble (opsonic defect)"""	MBL		1675710, 1672848	Standard	NM_000242		Approved	COLEC1	uc001jjt.3	P11226	OTTHUMG00000150270	ENST00000373968.3:c.163A>G	10.37:g.54531233T>C	ENSP00000363079:p.Thr55Ala		Q4VB12|Q4VB13|Q4VB14|Q5SQS3|Q86SI4|Q96KE4|Q96TF7|Q96TF8|Q96TF9	Missense_Mutation	SNP	ENST00000373968.3	37	CCDS7247.1	.	.	.	.	.	.	.	.	.	.	T	0.009	-1.853802	0.00558	.	.	ENSG00000165471	ENST00000373968	D	0.83506	-1.73	3.99	-5.58	0.02512	.	2.420760	0.01340	N	0.011544	T	0.51702	0.1690	N	0.01454	-0.855	0.09310	N	1	B	0.06786	0.001	B	0.14023	0.01	T	0.54316	-0.8312	10	0.11794	T	0.64	0.3178	0.1657	0.00108	0.2504:0.1803:0.2482:0.3211	.	55	P11226	MBL2_HUMAN	A	55	ENSP00000363079:T55A	ENSP00000363079:T55A	T	-	1	0	MBL2	54201239	0.235000	0.23794	0.001000	0.08648	0.495000	0.33615	-0.219000	0.09228	-1.235000	0.02545	-1.093000	0.02169	ACC		0.537	MBL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048115.1	NM_000242		11	93	11	93
MKI67	4288	broad.mit.edu;ucsc.edu	37	10	129923863	129923863	+	Missense_Mutation	SNP	G	G	C	rs549241601		TCGA-HT-7688-01A-11D-2253-08	TCGA-HT-7688-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	35602eec-d9a6-4b1f-b4bf-0304d6f0337a	b1e48d0a-6c17-45b0-856c-58b9eba686c8	g.chr10:129923863G>C	ENST00000368654.3	-	2	444	c.69C>G	c.(67-69)agC>agG	p.S23R	MKI67_ENST00000368653.3_Missense_Mutation_p.S23R	NM_002417.4	NP_002408.3	P46013	KI67_HUMAN	marker of proliferation Ki-67	23					cell proliferation (GO:0008283)|cellular response to heat (GO:0034605)|DNA metabolic process (GO:0006259)|hyaluronan metabolic process (GO:0030212)|meiotic nuclear division (GO:0007126)|organ regeneration (GO:0031100)|response to organic cyclic compound (GO:0014070)	chromosome, centromeric region (GO:0000775)|condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)			NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(30)|lung(64)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|soft_tissue(1)|stomach(10)|upper_aerodigestive_tract(4)|urinary_tract(4)	159		all_epithelial(44;2.12e-05)|all_lung(145;0.00679)|Lung NSC(174;0.00998)|all_neural(114;0.0936)|Colorectal(57;0.14)|Breast(234;0.166)|Melanoma(40;0.203)				AGGTGCTGAGGCTCAGGGGAA	0.517																																																0													79.0	91.0	87.0					10																	129923863		2203	4300	6503	SO:0001583	missense	4288			X65550	CCDS7659.1, CCDS53588.1	10q26.2	2014-06-12	2013-10-10		ENSG00000148773	ENSG00000148773			7107	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 105"""	176741	"""antigen identified by monoclonal antibody Ki-67"""			2571566, 16206250	Standard	NM_002417		Approved	MIB-, PPP1R105	uc001lke.3	P46013	OTTHUMG00000019255	ENST00000368654.3:c.69C>G	10.37:g.129923863G>C	ENSP00000357643:p.Ser23Arg		Q5VWH2	Missense_Mutation	SNP	ENST00000368654.3	37	CCDS7659.1	.	.	.	.	.	.	.	.	.	.	G	14.30	2.492886	0.44352	.	.	ENSG00000148773	ENST00000368654;ENST00000368653;ENST00000537609;ENST00000368652;ENST00000538447	T;T	0.01335	5.0;5.08	3.91	0.642	0.17765	Forkhead-associated (FHA) domain (1);SMAD/FHA domain (1);	0.366803	0.24226	N	0.040393	T	0.02571	0.0078	L	0.34521	1.04	0.09310	N	1	D;P	0.71674	0.998;0.936	D;B	0.65684	0.937;0.262	T	0.47446	-0.9117	9	.	.	.	.	3.6319	0.08135	0.4371:0.1961:0.3669:0.0	.	23;23	P46013-2;P46013	.;KI67_HUMAN	R	23	ENSP00000357643:S23R;ENSP00000357642:S23R	.	S	-	3	2	MKI67	129813853	1.000000	0.71417	0.153000	0.22517	0.272000	0.26649	0.889000	0.28282	0.039000	0.15632	0.655000	0.94253	AGC		0.517	MKI67-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050999.1	NM_002417		14	122	14	122
HOXC4	3221	broad.mit.edu;ucsc.edu	37	12	54447735	54447735	+	Missense_Mutation	SNP	C	C	G			TCGA-HT-7688-01A-11D-2253-08	TCGA-HT-7688-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	35602eec-d9a6-4b1f-b4bf-0304d6f0337a	b1e48d0a-6c17-45b0-856c-58b9eba686c8	g.chr12:54447735C>G	ENST00000430889.2	+	1	75	c.29C>G	c.(28-30)tCt>tGt	p.S10C	HOXC4_ENST00000609810.1_Missense_Mutation_p.S10C|HOXC4_ENST00000303406.4_Missense_Mutation_p.S10C	NM_153633.2	NP_705897.1	P09017	HXC4_HUMAN	homeobox C4	10					multicellular organismal development (GO:0007275)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(1)|kidney(2)|large_intestine(4)|lung(3)|ovary(1)|prostate(1)|urinary_tract(1)	13						TTGATGGACTCTAACTACATC	0.423																																																0													93.0	92.0	92.0					12																	54447735		2203	4300	6503	SO:0001583	missense	3221				CCDS8873.1	12q13.13	2011-06-20	2005-12-22		ENSG00000198353	ENSG00000198353		"""Homeoboxes / ANTP class : HOXL subclass"""	5126	protein-coding gene	gene with protein product		142974	"""homeo box C4"""	HOX3, HOX3E		1973146, 1358459	Standard	NM_014620		Approved		uc001sex.3	P09017	OTTHUMG00000160036	ENST00000430889.2:c.29C>G	12.37:g.54447735C>G	ENSP00000399808:p.Ser10Cys			Missense_Mutation	SNP	ENST00000430889.2	37	CCDS8873.1	.	.	.	.	.	.	.	.	.	.	C	18.56	3.650783	0.67472	.	.	ENSG00000198353	ENST00000303406;ENST00000430889	T;T	0.49432	0.78;0.78	3.41	3.41	0.39046	.	0.066141	0.64402	D	0.000008	T	0.68476	0.3005	M	0.81802	2.56	0.80722	D	1	D	0.76494	0.999	D	0.74674	0.984	T	0.75365	-0.3343	10	0.87932	D	0	.	14.7795	0.69754	0.0:1.0:0.0:0.0	.	10	P09017	HXC4_HUMAN	C	10	ENSP00000305973:S10C;ENSP00000399808:S10C	ENSP00000305973:S10C	S	+	2	0	HOXC4	52734002	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.240000	0.78192	2.187000	0.69744	0.462000	0.41574	TCT		0.423	HOXC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358963.1			10	76	10	76
ARID1A	8289	broad.mit.edu;hgsc.bcm.edu	37	1	27100176	27100176	+	Frame_Shift_Del	DEL	C	C	-	rs377622327		TCGA-HT-7688-01A-11D-2253-08	TCGA-HT-7688-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	35602eec-d9a6-4b1f-b4bf-0304d6f0337a	b1e48d0a-6c17-45b0-856c-58b9eba686c8	g.chr1:27100176delC	ENST00000324856.7	+	16	4343	c.3972delC	c.(3970-3972)tacfs	p.Y1324fs	ARID1A_ENST00000374152.2_Frame_Shift_Del_p.Y941fs|ARID1A_ENST00000457599.2_Frame_Shift_Del_p.Y1324fs|ARID1A_ENST00000540690.1_5'UTR	NM_006015.4	NP_006006.3	O14497	ARI1A_HUMAN	AT rich interactive domain 1A (SWI-like)	1324					androgen receptor signaling pathway (GO:0030521)|ATP-dependent chromatin remodeling (GO:0043044)|cardiac chamber development (GO:0003205)|chromatin remodeling (GO:0006338)|chromatin-mediated maintenance of transcription (GO:0048096)|forebrain development (GO:0030900)|glucocorticoid receptor signaling pathway (GO:0042921)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|nucleosome disassembly (GO:0006337)|nucleosome mobilization (GO:0042766)|optic cup formation involved in camera-type eye development (GO:0003408)|placenta blood vessel development (GO:0060674)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|transcription coactivator activity (GO:0003713)	p.Y1324*(1)	ARID1A/MAST2_ENST00000361297(2)	NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(13)|central_nervous_system(6)|cervix(2)|endometrium(56)|haematopoietic_and_lymphoid_tissue(8)|kidney(10)|large_intestine(41)|liver(31)|lung(34)|ovary(130)|pancreas(18)|prostate(8)|skin(9)|stomach(14)|upper_aerodigestive_tract(4)|urinary_tract(24)	411		all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242)		CTAGCCGCTACCCCCCgcagc	0.597			"""Mis, N, F, S, D"""		"""clear cell ovarian carcinoma, RCC"""																																		Rec	yes		1	1p35.3	8289	AT rich interactive domain 1A (SWI-like)		E	1	Substitution - Nonsense(1)	endometrium(1)											53.0	59.0	57.0					1																	27100176		2203	4300	6503	SO:0001589	frameshift_variant	8289			AB001895	CCDS285.1, CCDS44091.1	1p36.1-p35	2014-09-17	2006-11-08	2004-01-30	ENSG00000117713	ENSG00000117713		"""-"""	11110	protein-coding gene	gene with protein product		603024	"""SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily f, member 1"", ""AT rich interactive domain 1A (SWI- like)"""	C1orf4, SMARCF1		9630625, 9434167	Standard	NM_139135		Approved	B120, P270, C10rf4, BAF250, BAF250a	uc001bmv.1	O14497	OTTHUMG00000004004	ENST00000324856.7:c.3972delC	1.37:g.27100176delC	ENSP00000320485:p.Tyr1324fs		D3DPL1|Q53FK9|Q5T0W1|Q5T0W2|Q5T0W3|Q8NFD6|Q96T89|Q9BY33|Q9HBJ5|Q9UPZ1	Frame_Shift_Del	DEL	ENST00000324856.7	37	CCDS285.1																																																																																				0.597	ARID1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011437.2	NM_139135		23	129	23	129
CAD	790	broad.mit.edu;hgsc.bcm.edu	37	2	27462334	27462334	+	Frame_Shift_Del	DEL	G	G	-			TCGA-HT-7688-01A-11D-2253-08	TCGA-HT-7688-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	35602eec-d9a6-4b1f-b4bf-0304d6f0337a	b1e48d0a-6c17-45b0-856c-58b9eba686c8	g.chr2:27462334delG	ENST00000403525.1	+	32	5344	c.5200delG	c.(5200-5202)gggfs	p.G1734fs	CAD_ENST00000264705.4_Frame_Shift_Del_p.G1797fs			O76075	DFFB_HUMAN	carbamoyl-phosphate synthetase 2, aspartate transcarbamylase, and dihydroorotase	0					apoptotic chromosome condensation (GO:0030263)|apoptotic DNA fragmentation (GO:0006309)|apoptotic process (GO:0006915)|brain development (GO:0007420)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)	cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	deoxyribonuclease activity (GO:0004536)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)			NS(1)|breast(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(19)|lung(40)|ovary(6)|pancreas(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	92	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CTATATCGATGGGCAGGTACG	0.567																																																0													71.0	61.0	64.0					2																	27462334		2203	4300	6503	SO:0001589	frameshift_variant	790			D78586	CCDS1742.1	2p22-p21	2012-10-02			ENSG00000084774	ENSG00000084774	2.1.3.2, 3.5.2.-		1424	protein-coding gene	gene with protein product		114010				8619816, 2565865	Standard	NM_004341		Approved		uc002rji.3	P27708	OTTHUMG00000097070	ENST00000403525.1:c.5200delG	2.37:g.27462334delG	ENSP00000384510:p.Gly1734fs		O60521|Q5SR22|Q9BYI4|Q9BYI5|Q9BYI6	Frame_Shift_Del	DEL	ENST00000403525.1	37																																																																																					0.567	CAD-002	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000324970.1			25	69	25	69
FBN2	2201	broad.mit.edu;hgsc.bcm.edu	37	5	127782200	127782203	+	Frame_Shift_Del	DEL	TGTT	TGTT	-			TCGA-HT-7688-01A-11D-2253-08	TCGA-HT-7688-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	35602eec-d9a6-4b1f-b4bf-0304d6f0337a	b1e48d0a-6c17-45b0-856c-58b9eba686c8	g.chr5:127782200_127782203delTGTT	ENST00000508053.1	-	13	1897_1900	c.923_926delAACA	c.(922-927)aaacagfs	p.KQ308fs	FBN2_ENST00000508989.1_Frame_Shift_Del_p.KQ275fs|FBN2_ENST00000262464.4_Frame_Shift_Del_p.KQ308fs			P35556	FBN2_HUMAN	fibrillin 2	308	EGF-like 4; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				anatomical structure morphogenesis (GO:0009653)|bone trabecula formation (GO:0060346)|embryonic limb morphogenesis (GO:0030326)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of bone mineralization (GO:0030501)|positive regulation of osteoblast differentiation (GO:0045669)|sequestering of TGFbeta in extracellular matrix (GO:0035583)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(37)|liver(1)|lung(89)|ovary(9)|pancreas(2)|prostate(6)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	197		all_cancers(142;0.0216)|Prostate(80;0.0551)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0821)|Epithelial(69;0.146)		AGTTTCACTCTGTTTGTGACCAGC	0.426																																																0																																										SO:0001589	frameshift_variant	2201			U03272	CCDS34222.1	5q23-q31	2008-08-01	2008-08-01			ENSG00000138829			3604	protein-coding gene	gene with protein product	"""fibrillin 5"""	612570	"""congenital contractural arachnodactyly"""	CCA		1852206, 8120105	Standard	NM_001999		Approved	DA9	uc003kuu.3	P35556		ENST00000508053.1:c.923_926delAACA	5.37:g.127782200_127782203delTGTT	ENSP00000424571:p.Lys308fs		B4DU01|Q59ES6	Frame_Shift_Del	DEL	ENST00000508053.1	37	CCDS34222.1																																																																																				0.426	FBN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371618.2	NM_001999		16	75	16	75
EPB41L2	2037	broad.mit.edu;hgsc.bcm.edu	37	6	131229973	131229976	+	Frame_Shift_Del	DEL	TCTT	TCTT	-			TCGA-HT-7688-01A-11D-2253-08	TCGA-HT-7688-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	35602eec-d9a6-4b1f-b4bf-0304d6f0337a	b1e48d0a-6c17-45b0-856c-58b9eba686c8	g.chr6:131229973_131229976delTCTT	ENST00000337057.3	-	5	1019_1022	c.838_841delAAGA	c.(838-843)aagagafs	p.KR280fs	EPB41L2_ENST00000368128.2_Frame_Shift_Del_p.KR280fs|EPB41L2_ENST00000445890.2_Frame_Shift_Del_p.KR280fs|EPB41L2_ENST00000528282.1_Frame_Shift_Del_p.KR280fs|EPB41L2_ENST00000529208.1_Frame_Shift_Del_p.KR280fs|EPB41L2_ENST00000525271.1_Frame_Shift_Del_p.KR280fs|EPB41L2_ENST00000392427.3_Frame_Shift_Del_p.KR280fs|EPB41L2_ENST00000530481.1_Frame_Shift_Del_p.KR280fs|EPB41L2_ENST00000527659.1_Frame_Shift_Del_p.KR280fs|EPB41L2_ENST00000525193.1_Frame_Shift_Del_p.KR280fs|EPB41L2_ENST00000527411.1_Frame_Shift_Del_p.KR280fs|EPB41L2_ENST00000530148.1_5'UTR	NM_001431.3	NP_001422.1	O43491	E41L2_HUMAN	erythrocyte membrane protein band 4.1-like 2	280	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				cortical actin cytoskeleton organization (GO:0030866)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|spectrin (GO:0008091)	structural molecule activity (GO:0005198)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(7)|kidney(2)|large_intestine(7)|lung(23)|prostate(1)|skin(2)	44	Breast(56;0.0639)			OV - Ovarian serous cystadenocarcinoma(155;0.0271)|GBM - Glioblastoma multiforme(226;0.0355)		CTCAGTTGTCTCTTTATTTCTTTA	0.284																																																0																																										SO:0001589	frameshift_variant	2037			AF027299	CCDS5141.1, CCDS47474.1, CCDS56450.1, CCDS59037.1	6q23	2008-08-29			ENSG00000079819	ENSG00000079819			3379	protein-coding gene	gene with protein product		603237				9598318, 9828140	Standard	NM_001431		Approved	4.1-G	uc003qch.2	O43491	OTTHUMG00000015560	ENST00000337057.3:c.838_841delAAGA	6.37:g.131229973_131229976delTCTT	ENSP00000338481:p.Lys280fs		B4DHI8|E9PPD9|Q5T4F0|Q68DV2	Frame_Shift_Del	DEL	ENST00000337057.3	37	CCDS5141.1																																																																																				0.284	EPB41L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042204.3			16	38	16	38
NCOA4	8031	broad.mit.edu;hgsc.bcm.edu	37	10	51585027	51585029	+	In_Frame_Del	DEL	AAG	AAG	-			TCGA-HT-7688-01A-11D-2253-08	TCGA-HT-7688-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	35602eec-d9a6-4b1f-b4bf-0304d6f0337a	b1e48d0a-6c17-45b0-856c-58b9eba686c8	g.chr10:51585027_51585029delAAG	ENST00000443446.1	+	8	1355_1357	c.1126_1128delAAG	c.(1126-1128)aagdel	p.K377del	NCOA4_ENST00000374087.4_In_Frame_Del_p.K377del|NCOA4_ENST00000438493.1_In_Frame_Del_p.K393del|NCOA4_ENST00000430396.2_In_Frame_Del_p.K277del|NCOA4_ENST00000374082.1_In_Frame_Del_p.K377del|NCOA4_ENST00000452682.1_In_Frame_Del_p.K393del|NCOA4_ENST00000344348.6_In_Frame_Del_p.K377del|NCOA4_ENST00000414907.2_In_Frame_Del_p.K211del	NM_001145262.1	NP_001138734.1	Q13772	NCOA4_HUMAN	nuclear receptor coactivator 4	377					androgen receptor signaling pathway (GO:0030521)|male gonad development (GO:0008584)|positive regulation of transcription, DNA-templated (GO:0045893)|response to hormone (GO:0009725)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|transcription coactivator activity (GO:0003713)			NS(1)|central_nervous_system(1)|kidney(1)|large_intestine(1)|skin(1)	5						CTTGGAGGCCAAGAAACCATTGT	0.522			T	RET	papillary thyroid																																		Dom	yes		10	10q11.2	8031	nuclear receptor coactivator 4 - PTC3 (ELE1)		E	0																																										SO:0001651	inframe_deletion	8031			L49399	CCDS73092.1, CCDS73093.1, CCDS73094.1	10q11.2	2014-04-10			ENSG00000138293	ENSG00000266412			7671	protein-coding gene	gene with protein product	"""RET-activating gene ELE1"""	601984				8290261, 8643607, 24695223	Standard	NM_001145260		Approved	ARA70, RFG, ELE1, PTC3, DKFZp762E1112	uc009xon.3	Q13772	OTTHUMG00000188314	ENST00000443446.1:c.1126_1128delAAG	10.37:g.51585027_51585029delAAG	ENSP00000390713:p.Lys377del		A8K8W5|B4E260|E9PAV7|J3KQN8|Q14239	In_Frame_Del	DEL	ENST00000443446.1	37	CCDS7237.1																																																																																				0.522	NCOA4-204	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048052.1	NM_005437		13	22	13	22
ARID5B	84159	broad.mit.edu;hgsc.bcm.edu	37	10	63845531	63845531	+	Frame_Shift_Del	DEL	A	A	-			TCGA-HT-7688-01A-11D-2253-08	TCGA-HT-7688-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	35602eec-d9a6-4b1f-b4bf-0304d6f0337a	b1e48d0a-6c17-45b0-856c-58b9eba686c8	g.chr10:63845531delA	ENST00000279873.7	+	9	1680	c.1270delA	c.(1270-1272)aaafs	p.K424fs	ARID5B_ENST00000309334.5_Frame_Shift_Del_p.K181fs	NM_032199.2	NP_115575.1	Q14865	ARI5B_HUMAN	AT rich interactive domain 5B (MRF1-like)	424					adipose tissue development (GO:0060612)|adrenal gland development (GO:0030325)|cell development (GO:0048468)|face morphogenesis (GO:0060325)|fat cell differentiation (GO:0045444)|fat pad development (GO:0060613)|female gonad development (GO:0008585)|fibroblast migration (GO:0010761)|kidney development (GO:0001822)|liver development (GO:0001889)|male gonad development (GO:0008584)|multicellular organism growth (GO:0035264)|muscle organ morphogenesis (GO:0048644)|negative regulation of transcription, DNA-templated (GO:0045892)|palate development (GO:0060021)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|post-embryonic development (GO:0009791)|skeletal system morphogenesis (GO:0048705)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(2)|endometrium(13)|kidney(3)|large_intestine(7)|lung(9)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	44	Prostate(12;0.016)|all_hematologic(501;0.215)					CAAACCTCGGAAACAGGAGAA	0.358																																																0													124.0	131.0	129.0					10																	63845531		2203	4300	6503	SO:0001589	frameshift_variant	84159			M73837	CCDS31208.1, CCDS58082.1	10q11.22	2013-02-07			ENSG00000150347	ENSG00000150347		"""-"""	17362	protein-coding gene	gene with protein product		608538				11483573, 11478881	Standard	NM_032199		Approved	FLJ21150, MRF2	uc001jlt.2	Q14865	OTTHUMG00000018298	ENST00000279873.7:c.1270delA	10.37:g.63845531delA	ENSP00000279873:p.Lys424fs		B4DLB3|Q05DG6|Q32Q59|Q5VST4|Q6NZ42|Q7Z3M4|Q8N421|Q9H786	Frame_Shift_Del	DEL	ENST00000279873.7	37	CCDS31208.1																																																																																				0.358	ARID5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048233.1	XM_084482		58	91	58	91
CDON	50937	broad.mit.edu;hgsc.bcm.edu	37	11	125891236	125891237	+	Frame_Shift_Del	DEL	AA	AA	-			TCGA-HT-7688-01A-11D-2253-08	TCGA-HT-7688-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	35602eec-d9a6-4b1f-b4bf-0304d6f0337a	b1e48d0a-6c17-45b0-856c-58b9eba686c8	g.chr11:125891236_125891237delAA	ENST00000392693.3	-	3	382_383	c.255_256delTT	c.(253-258)ctttctfs	p.S86fs	CDON_ENST00000263577.7_Frame_Shift_Del_p.S86fs	NM_001243597.1|NM_016952.4	NP_001230526.1|NP_058648.4	Q4KMG0	CDON_HUMAN	cell adhesion associated, oncogene regulated	86	Ig-like C2-type 1.				anterior/posterior pattern specification (GO:0009952)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cerebral cortex development (GO:0021987)|embryonic body morphogenesis (GO:0010172)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|lens development in camera-type eye (GO:0002088)|muscle cell differentiation (GO:0042692)|myoblast fusion (GO:0007520)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neural precursor cell proliferation (GO:2000179)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of skeletal muscle tissue development (GO:0048643)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of protein heterodimerization activity (GO:0043497)|skeletal muscle satellite cell differentiation (GO:0014816)|smoothened signaling pathway (GO:0007224)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|lung(9)|ovary(3)|prostate(2)|skin(4)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	61	all_hematologic(175;0.177)	Breast(109;0.00157)|Lung NSC(97;0.0127)|all_lung(97;0.0133)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.51e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0604)		GAGTTGAGAGAAAGAATTGTCA	0.475																																																0																																										SO:0001589	frameshift_variant	50937			AF004841	CCDS8468.1, CCDS58192.1	11q24.2	2013-02-11	2012-12-07		ENSG00000064309	ENSG00000064309		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	17104	protein-coding gene	gene with protein product	"""cell adhesion molecule-related/down-regulated by oncogenes"""	608707	"""Cdon homolog (mouse)"""			9214393	Standard	NM_016952		Approved	ORCAM, CDO, CDON1	uc009zbw.3	Q4KMG0	OTTHUMG00000165862	ENST00000392693.3:c.255_256delTT	11.37:g.125891236_125891237delAA	ENSP00000376458:p.Ser86fs		O14631	Frame_Shift_Del	DEL	ENST00000392693.3	37	CCDS58192.1																																																																																				0.475	CDON-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386749.2	NM_016952		19	73	19	73
PTPRR	5801	broad.mit.edu;hgsc.bcm.edu	37	12	71050530	71050532	+	In_Frame_Del	DEL	CTT	CTT	-			TCGA-HT-7688-01A-11D-2253-08	TCGA-HT-7688-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	35602eec-d9a6-4b1f-b4bf-0304d6f0337a	b1e48d0a-6c17-45b0-856c-58b9eba686c8	g.chr12:71050530_71050532delCTT	ENST00000283228.2	-	13	2284_2286	c.1832_1834delAAG	c.(1831-1836)gaagga>gga	p.E611del	PTPRR_ENST00000440835.2_In_Frame_Del_p.E366del|PTPRR_ENST00000378778.1_In_Frame_Del_p.E405del|PTPRR_ENST00000342084.4_In_Frame_Del_p.E499del|PTPRR_ENST00000537619.2_5'UTR|PTPRR_ENST00000549308.1_In_Frame_Del_p.E366del	NM_002849.3	NP_002840.2	Q15256	PTPRR_HUMAN	protein tyrosine phosphatase, receptor type, R	611	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				ERBB2 signaling pathway (GO:0038128)|in utero embryonic development (GO:0001701)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(22)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	41			GBM - Glioblastoma multiforme(2;5.67e-07)|Lung(24;0.00283)|OV - Ovarian serous cystadenocarcinoma(12;0.00578)|LUSC - Lung squamous cell carcinoma(43;0.132)	COAD - Colon adenocarcinoma(1;0.136)		TCCACAACTCCTTCTTCTTTCAG	0.433																																																0																																										SO:0001651	inframe_deletion	5801			D64053	CCDS8998.1, CCDS44945.1, CCDS55847.1, CCDS55848.1	12q15	2011-10-07			ENSG00000153233	ENSG00000153233		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"""	9680	protein-coding gene	gene with protein product		602853		PTPRQ		7557444, 10393441	Standard	NM_002849		Approved	PTPBR7, PTP-SL, EC-PTP, PCPTP1	uc001swi.2	Q15256	OTTHUMG00000169502	ENST00000283228.2:c.1832_1834delAAG	12.37:g.71050536_71050538delCTT	ENSP00000283228:p.Glu611del		B2R5Z7|B7Z3J1|F5GXR7|O00342|Q92682|Q9UE65	In_Frame_Del	DEL	ENST00000283228.2	37	CCDS8998.1																																																																																				0.433	PTPRR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404485.1	NM_002849		43	159	43	159
C14orf37	145407	broad.mit.edu;hgsc.bcm.edu	37	14	58605972	58605974	+	In_Frame_Del	DEL	CCT	CCT	-			TCGA-HT-7688-01A-11D-2253-08	TCGA-HT-7688-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	35602eec-d9a6-4b1f-b4bf-0304d6f0337a	b1e48d0a-6c17-45b0-856c-58b9eba686c8	g.chr14:58605972_58605974delCCT	ENST00000267485.7	-	2	297_299	c.103_105delAGG	c.(103-105)aggdel	p.R35del	C14orf37_ENST00000334342.5_5'UTR	NM_001001872.2	NP_001001872.2	Q86TY3	CN037_HUMAN	chromosome 14 open reading frame 37	35						integral component of membrane (GO:0016021)				breast(7)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(16)|pancreas(1)|skin(1)	33						GTGCTATCTCCCTCCTCCTTTCT	0.478																																																0																																										SO:0001651	inframe_deletion	0				CCDS32089.1	14q23.1	2012-09-03			ENSG00000139971	ENSG00000139971			19846	protein-coding gene	gene with protein product							Standard	NM_001001872		Approved		uc001xdc.3	Q86TY3	OTTHUMG00000171173	ENST00000267485.7:c.103_105delAGG	14.37:g.58605978_58605980delCCT	ENSP00000267485:p.Arg35del		A8K8Z8|Q6P5Q1|Q86TY1	In_Frame_Del	DEL	ENST00000267485.7	37	CCDS32089.1																																																																																				0.478	C14orf37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412059.1	NM_001001872		36	110	36	110
SMARCA4	6597	broad.mit.edu;hgsc.bcm.edu	37	19	11106926	11106928	+	In_Frame_Del	DEL	AGA	AGA	-			TCGA-HT-7688-01A-11D-2253-08	TCGA-HT-7688-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	35602eec-d9a6-4b1f-b4bf-0304d6f0337a	b1e48d0a-6c17-45b0-856c-58b9eba686c8	g.chr19:11106926_11106928delAGA	ENST00000429416.3	+	11	1912_1914	c.1631_1633delAGA	c.(1630-1635)cagaag>cag	p.K546del	SMARCA4_ENST00000413806.3_In_Frame_Del_p.K546del|SMARCA4_ENST00000344626.4_In_Frame_Del_p.K546del|SMARCA4_ENST00000589677.1_In_Frame_Del_p.K546del|SMARCA4_ENST00000541122.2_In_Frame_Del_p.K546del|SMARCA4_ENST00000358026.2_In_Frame_Del_p.K546del|SMARCA4_ENST00000590574.1_In_Frame_Del_p.K546del|SMARCA4_ENST00000444061.3_In_Frame_Del_p.K546del|SMARCA4_ENST00000450717.3_In_Frame_Del_p.K546del	NM_001128844.1	NP_001122316.1	P51532	SMCA4_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4	546			Missing (in MRD16). {ECO:0000269|PubMed:22426308}.		aortic smooth muscle cell differentiation (GO:0035887)|ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|blastocyst growth (GO:0001832)|blastocyst hatching (GO:0001835)|cell morphogenesis (GO:0000902)|chromatin remodeling (GO:0006338)|definitive erythrocyte differentiation (GO:0060318)|DNA methylation on cytosine within a CG sequence (GO:0010424)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic organ morphogenesis (GO:0048562)|epidermis morphogenesis (GO:0048730)|extracellular matrix organization (GO:0030198)|forebrain development (GO:0030900)|glial cell fate determination (GO:0007403)|heart trabecula formation (GO:0060347)|hindbrain development (GO:0030902)|histone H3 acetylation (GO:0043966)|keratinocyte differentiation (GO:0030216)|lens fiber cell development (GO:0070307)|liver development (GO:0001889)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of cell growth (GO:0030308)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter during mitosis (GO:0007070)|negative regulation of transcription, DNA-templated (GO:0045892)|neural retina development (GO:0003407)|nucleosome disassembly (GO:0006337)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of DNA binding (GO:0043388)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|vasculogenesis (GO:0001570)	extracellular space (GO:0005615)|heterochromatin (GO:0000792)|membrane (GO:0016020)|nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nuclear euchromatin (GO:0005719)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perichromatin fibrils (GO:0005726)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)	androgen receptor binding (GO:0050681)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|protein N-terminus binding (GO:0047485)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription coactivator activity (GO:0001105)|Tat protein binding (GO:0030957)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)	p.?(1)		adrenal_gland(1)|autonomic_ganglia(1)|breast(6)|central_nervous_system(23)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|liver(4)|lung(60)|ovary(10)|pancreas(7)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	163		all_lung(6;0.0512)|Lung NSC(9;0.0568)				CTCATCGACCAGAAGAAGGACAA	0.576			"""F, N, Mis"""		NSCLC																																		Rec	yes		19	19p13.2	6597	"""SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4"""		E	1	Unknown(1)	lung(1)																																								SO:0001651	inframe_deletion	6597			D26156	CCDS12253.1, CCDS45972.1, CCDS45973.1, CCDS54217.1, CCDS54218.1	19p13.3	2014-09-17	2006-11-09		ENSG00000127616	ENSG00000127616			11100	protein-coding gene	gene with protein product	"""SNF2-like 4"", ""global transcription activator homologous sequence"", ""sucrose nonfermenting-like 4"", ""mitotic growth and transcription activator"", ""BRM/SWI2-related gene 1"", ""homeotic gene regulator"", ""nuclear protein GRB1"", ""brahma protein-like 1"", ""ATP-dependent helicase SMARCA4"""	603254		SNF2L4		8208605	Standard	NM_003072		Approved	hSNF2b, BRG1, BAF190, SNF2, SWI2, SNF2-BETA, SNF2LB, FLJ39786	uc010dxo.3	P51532	OTTHUMG00000169272	ENST00000429416.3:c.1631_1633delAGA	19.37:g.11106929_11106931delAGA	ENSP00000395654:p.Lys546del		B1A8Z4|B1A8Z5|B1A8Z6|B1A8Z7|E9PBR8|O95052|Q9HBD3	In_Frame_Del	DEL	ENST00000429416.3	37	CCDS12253.1																																																																																				0.576	SMARCA4-007	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000452638.2	NM_003072		29	145	29	145
ATRX	546	broad.mit.edu	37	X	76875860	76875861	+	Splice_Site	DEL	CA	CA	-			TCGA-HT-7688-01A-11D-2253-08	TCGA-HT-7688-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	35602eec-d9a6-4b1f-b4bf-0304d6f0337a	b1e48d0a-6c17-45b0-856c-58b9eba686c8	g.chrX:76875860_76875861delCA	ENST00000373344.5	-	20	5487		c.e20+1		ATRX_ENST00000480283.1_Splice_Site|ATRX_ENST00000395603.3_Splice_Site	NM_000489.3	NP_000480.3	P46100	ATRX_HUMAN	alpha thalassemia/mental retardation syndrome X-linked						ATP catabolic process (GO:0006200)|cellular response to hydroxyurea (GO:0072711)|chromatin remodeling (GO:0006338)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA duplex unwinding (GO:0032508)|DNA methylation (GO:0006306)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication-independent nucleosome assembly (GO:0006336)|forebrain development (GO:0030900)|negative regulation of telomeric RNA transcription from RNA pol II promoter (GO:1901581)|nucleosome assembly (GO:0006334)|positive regulation of nuclear cell cycle DNA replication (GO:0010571)|positive regulation of telomere maintenance (GO:0032206)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|replication fork processing (GO:0031297)|seminiferous tubule development (GO:0072520)|Sertoli cell development (GO:0060009)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nuclear heterochromatin (GO:0005720)|nucleolus (GO:0005730)|nucleus (GO:0005634)|SWI/SNF superfamily-type complex (GO:0070603)|telomeric heterochromatin (GO:0031933)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|chromo shadow domain binding (GO:0070087)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA translocase activity (GO:0015616)|helicase activity (GO:0004386)|histone binding (GO:0042393)|methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)	p.?(1)		bone(1)|breast(6)|central_nervous_system(31)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(15)|kidney(14)|large_intestine(1)|liver(1)|lung(40)|ovary(2)|pancreas(13)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	145						GATATTAACTCACACTCAATTA	0.317			"""Mis, F, N"""		"""Pancreatic neuroendocrine tumors, paediatric GBM"""		ATR-X (alpha thalassemia/mental retardation) syndrome																																Rec	yes		X	Xq21.1	546	alpha thalassemia/mental retardation syndrome X-linked	yes	E	1	Unknown(1)	bone(1)																																								SO:0001630	splice_region_variant	546			U72937	CCDS14434.1, CCDS14435.1	Xq21.1	2014-06-17	2010-06-24		ENSG00000085224	ENSG00000085224			886	protein-coding gene	gene with protein product	"""RAD54 homolog (S. cerevisiae)"""	300032	"""alpha thalassemia/mental retardation syndrome X-linked (RAD54 (S. cerevisiae) homolog)"", ""Juberg-Marsidi syndrome"""	RAD54, JMS		7874112, 1415255, 8503439, 8630485	Standard	NM_000489		Approved	XH2, XNP	uc004ecp.4	P46100	OTTHUMG00000022686	ENST00000373344.5:c.5272+1TG>-	X.37:g.76875862_76875863delCA			D3DTE2|P51068|Q15886|Q59FB5|Q59H31|Q5H9A2|Q5JWI4|Q7Z2J1|Q9H0Z1|Q9NTS3	Splice_Site	DEL	ENST00000373344.5	37	CCDS14434.1																																																																																				0.317	ATRX-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058860.2	NM_000489	Intron	9	34	9	34
