#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_AAChange	i_ACHILLES_Lineage_Results_Top_Genes	i_BAM_File	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_Codon	i_COSMIC_Gene	i_COSMIC_Gene_Freq	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ChromChange	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Drug_Target	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Exon	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_Genome_Plus_Minus_10_Bp	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_Mutation_Status	i_NTotCov_SOL	i_NVarCov_SOL	i_ORegAnno_bin	i_Sequence_Source	i_Sequencer	i_Sequencing_Phase	i_TTotCov_SOL	i_TVarCov_SOL	i_Transcript_Id	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_dbSNPPopFreq	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
PTEN	5728	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	10	89720806	89720806	+	Frame_Shift_Del	DEL	T	T	-	rs398123330		TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr10:89720806delT	ENST00000371953.3	+	8	2314	c.957delT	c.(955-957)actfs	p.T319fs	PTEN_ENST00000472832.1_3'UTR	NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog	319	C2 tensin-type. {ECO:0000255|PROSITE- ProRule:PRU00589}.		Missing (in glioma; reduced tumor suppressor activity; fails to inactivate AKT/PKB). {ECO:0000269|PubMed:9090379}.		activation of mitotic anaphase-promoting complex activity (GO:0007092)|aging (GO:0007568)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|brain morphogenesis (GO:0048854)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle tissue development (GO:0048738)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|central nervous system myelin maintenance (GO:0032286)|central nervous system neuron axonogenesis (GO:0021955)|dendritic spine morphogenesis (GO:0060997)|dentate gyrus development (GO:0021542)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|innate immune response (GO:0045087)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|learning or memory (GO:0007611)|locomotor rhythm (GO:0045475)|locomotory behavior (GO:0007626)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|male mating behavior (GO:0060179)|maternal behavior (GO:0042711)|memory (GO:0007613)|multicellular organismal response to stress (GO:0033555)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell aging (GO:0090344)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031658)|negative regulation of dendritic spine morphogenesis (GO:0061002)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myelination (GO:0031642)|negative regulation of organ growth (GO:0046621)|negative regulation of phagocytosis (GO:0050765)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of ribosome biogenesis (GO:0090071)|negative regulation of synaptic vesicle clustering (GO:2000808)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell proliferation (GO:0008284)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|postsynaptic density assembly (GO:0097107)|prepulse inhibition (GO:0060134)|presynaptic membrane assembly (GO:0097105)|prostate gland growth (GO:0060736)|protein dephosphorylation (GO:0006470)|protein kinase B signaling (GO:0043491)|protein stabilization (GO:0050821)|regulation of B cell apoptotic process (GO:0002902)|regulation of cellular component size (GO:0032535)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of myeloid cell apoptotic process (GO:0033032)|regulation of neuron projection development (GO:0010975)|regulation of protein stability (GO:0031647)|response to arsenic-containing substance (GO:0046685)|response to ATP (GO:0033198)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse maturation (GO:0060074)|T cell receptor signaling pathway (GO:0050852)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|myelin sheath adaxonal region (GO:0035749)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)	anaphase-promoting complex binding (GO:0010997)|enzyme binding (GO:0019899)|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity (GO:0051717)|lipid binding (GO:0008289)|magnesium ion binding (GO:0000287)|PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity (GO:0051800)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.0?(37)|p.T319fs*1(24)|p.L318fs*2(11)|p.R55fs*1(5)|p.T319fs*24(4)|p.?(2)|p.N212fs*1(2)|p.Y27fs*1(2)|p.T319del(2)|p.T319_K332del(1)|p.G165_*404del(1)|p.L316fs*1(1)|p.T319fs*4(1)|p.T319fs*5(1)|p.W274_F341del(1)|p.V317_K322del(1)		NS(28)|autonomic_ganglia(2)|biliary_tract(6)|bone(5)|breast(92)|central_nervous_system(676)|cervix(26)|endometrium(1068)|eye(8)|haematopoietic_and_lymphoid_tissue(137)|kidney(24)|large_intestine(98)|liver(20)|lung(91)|meninges(2)|oesophagus(2)|ovary(82)|pancreas(6)|prostate(129)|salivary_gland(5)|skin(127)|soft_tissue(19)|stomach(30)|testis(1)|thyroid(29)|upper_aerodigestive_tract(29)|urinary_tract(12)|vulva(17)	2771		all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132)	KIRC - Kidney renal clear cell carcinoma(1;0.214)	UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218)		TAGTACTTACTTTAACAAAAA	0.333		31	"""D, Mis, N, F, S"""		"""glioma,  prostate, endometrial"""	"""harmartoma, glioma,  prostate, endometrial"""			Proteus syndrome;Juvenile Polyposis;Hereditary Mixed Polyposis Syndrome type 1;Cowden syndrome;Bannayan-Riley-Ruvalcaba syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)																											p.T319fs		.	yes	Rec	yes	"""Cowden Syndrome, Bannayan-Riley-Ruvalcaba syndrome"""	10	10q23.3	5728	phosphatase and tensin homolog gene		"""L, E, M, O"""	.,6	.	3652	96	Deletion - Frameshift(50)|Whole gene deletion(37)|Deletion - In frame(6)|Unknown(2)|Insertion - Frameshift(1)	central_nervous_system(25)|endometrium(22)|prostate(17)|skin(8)|lung(4)|breast(4)|ovary(4)|large_intestine(3)|haematopoietic_and_lymphoid_tissue(3)|soft_tissue(2)|urinary_tract(2)|liver(2)	c.956delC						.						89.0	90.0	90.0					10																	89720806		2203	4299	6502	SO:0001589	frameshift_variant	5728	exon8	Familial Cancer Database	Incl.: Encephalocraniocutaneous Lipomatosis, ECCL, Proteus-like s.;incl.: Juvenile Polyposis of the Stomach;HMPS1, Colorectal Adenoma Carcinoma syndrome, CRAC, CRAC1;CS, Cowden disease, Multiple Hamartoma Syndrome, incl.: Lhermitte-Duclos; part of PTEN hamartoma tumour syndrome (PHTS) / PTEN-MATCHS, Cowden-like syndrome;subset of PTEN-Hamartoma Tumor Syndrome; incl.: Ruvalcaba-Myhre-Smith s.	ACTTACTTTAACA	U92436	CCDS31238.1	10q23	2014-09-17	2008-07-31		ENSG00000171862	ENSG00000171862		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"""	9588	protein-coding gene	gene with protein product	"""mutated in multiple advanced cancers 1"""	601728		BZS, MHAM		9090379	Standard	NM_000314		Approved	MMAC1, TEP1, PTEN1	uc001kfb.3	P60484	OTTHUMG00000018688	ENST00000371953.3:c.957delT	10.37:g.89720806delT	ENSP00000361021:p.Thr319fs	Somatic	112	0		WXS	Illumina HiSeq	.	61	16	NM_000314	B2R904|F2YHV0|O00633|O02679|Q6ICT7	Frame_Shift_Del	DEL	ENST00000371953.3	37	CCDS31238.1																																																																																			.		0.333	PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049241.1	NM_000314	
WNK4	65266	hgsc.bcm.edu	37	17	40946837	40946838	+	Frame_Shift_Ins	INS	-	-	TC			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr17:40946837_40946838insTC	ENST00000246914.5	+	14	2419_2420	c.2398_2399insTC	c.(2398-2400)ttcfs	p.F800fs		NM_032387.4	NP_115763.2	Q96J92	WNK4_HUMAN	WNK lysine deficient protein kinase 4	800					chloride transport (GO:0006821)|distal tubule morphogenesis (GO:0072156)|intracellular signal transduction (GO:0035556)|ion homeostasis (GO:0050801)|ion transport (GO:0006811)|negative regulation of pancreatic juice secretion (GO:0090188)|protein localization (GO:0008104)|protein phosphorylation (GO:0006468)|regulation of cellular process (GO:0050794)|renal sodium ion absorption (GO:0070294)	cytoplasm (GO:0005737)|tight junction (GO:0005923)	ATP binding (GO:0005524)|chloride channel inhibitor activity (GO:0019869)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(10)|ovary(3)|prostate(1)|skin(5)|stomach(1)	35		Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.0749)		CTGGACAGCCTTCTCCACCTCC	0.569																																					p.F800fs	Esophageal Squamous(6;201 374 4964 23855 42828)	.											.	.	.	0			c.2398_2399insTC						.																																			SO:0001589	frameshift_variant	65266	exon14			ACAGCCTTCTCCA	AJ309861	CCDS11439.1	17q21-q22	2005-01-19	2005-01-19	2005-01-19		ENSG00000126562			14544	protein-coding gene	gene with protein product		601844	"""protein kinase, lysine deficient 4"""	PRKWNK4			Standard	NM_032387		Approved		uc002ibj.3	Q96J92		ENST00000246914.5:c.2401_2402dupTC	17.37:g.40946840_40946841dupTC	ENSP00000246914:p.Phe800fs	Somatic	56	0		WXS	Illumina HiSeq	.	39	0	NM_032387	B0LPI0|Q8N8X3|Q8N8Z2|Q96DT8|Q9BYS5	Frame_Shift_Ins	INS	ENST00000246914.5	37	CCDS11439.1																																																																																			.		0.569	WNK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452389.1		
PBRM1	55193	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	3	52712524	52712533	+	Frame_Shift_Del	DEL	TGGTGCCCTA	TGGTGCCCTA	-			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	TGGTGCCCTA	TGGTGCCCTA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr3:52712524_52712533delTGGTGCCCTA	ENST00000296302.7	-	2	220_229	c.219_228delTAGGGCACCA	c.(217-228)attagggcaccafs	p.IRAP73fs	PBRM1_ENST00000409057.1_Frame_Shift_Del_p.IRAP73fs|PBRM1_ENST00000410007.1_Frame_Shift_Del_p.IRAP73fs|PBRM1_ENST00000409114.3_Frame_Shift_Del_p.IRAP73fs|PBRM1_ENST00000394830.3_Frame_Shift_Del_p.IRAP73fs|PBRM1_ENST00000356770.4_Frame_Shift_Del_p.IRAP73fs|PBRM1_ENST00000337303.4_Frame_Shift_Del_p.IRAP73fs|PBRM1_ENST00000409767.1_Frame_Shift_Del_p.IRAP73fs			Q86U86	PB1_HUMAN	polybromo 1	73	Bromo 1. {ECO:0000255|PROSITE- ProRule:PRU00035}.				chromatin remodeling (GO:0006338)|heart development (GO:0007507)|mitotic nuclear division (GO:0007067)|negative regulation of cell proliferation (GO:0008285)|placenta development (GO:0001890)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	kinetochore (GO:0000776)|nuclear chromosome (GO:0000228)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)	p.F72fs*1(3)|p.A75V(3)		breast(5)|endometrium(5)|kidney(301)|liver(1)|lung(22)|pancreas(1)	335				BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)		ACCTTCGCTTTGGTGCCCTAATGAAGAGCT	0.452			"""Mis, N, F, S, D, O"""		"""clear cell renal carcinoma, breast"""																																p.74_77del		.		Rec	yes		3	3p21	55193	polybromo 1		E	.	.	.	6	Substitution - Missense(3)|Deletion - Frameshift(3)	kidney(3)|endometrium(3)	c.220_229del						.																																			SO:0001589	frameshift_variant	55193	exon3			TCGCTTTGGTGCC	BC015323	CCDS43099.1	3p21	2007-03-29			ENSG00000163939	ENSG00000163939			30064	protein-coding gene	gene with protein product		606083				11078522, 11483580	Standard	NM_018313		Approved	BAF180, PB1	uc003der.2	Q86U86	OTTHUMG00000152663	ENST00000296302.7:c.219_228delTAGGGCACCA	3.37:g.52712524_52712533delTGGTGCCCTA	ENSP00000296302:p.Ile73fs	Somatic	71	0		WXS	Illumina HiSeq	.	28	14	NM_018313	A1L381|A1L382|A4FUJ7|Q1RMD1|Q1RMD2|Q96MS2|Q9H2T3|Q9H2T4|Q9H2T5|Q9H301|Q9H314	Frame_Shift_Del	DEL	ENST00000296302.7	37																																																																																				.		0.452	PBRM1-008	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000327232.1	NM_018165	
DCUN1D3	123879	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	16	20871607	20871607	+	Frame_Shift_Del	DEL	T	T	-			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr16:20871607delT	ENST00000324344.4	-	3	801	c.516delA	c.(514-516)gaafs	p.E172fs	ERI2_ENST00000564349.1_Intron|DCUN1D3_ENST00000563934.1_Frame_Shift_Del_p.E172fs	NM_173475.2	NP_775746.1	Q8IWE4	DCNL3_HUMAN	DCN1, defective in cullin neddylation 1, domain containing 3	172	DCUN1. {ECO:0000255|PROSITE- ProRule:PRU00574}.				negative regulation of cell growth (GO:0030308)|positive regulation of apoptotic process (GO:0043065)|response to gamma radiation (GO:0010332)|response to UV-C (GO:0010225)	perinuclear region of cytoplasm (GO:0048471)				NS(2)|breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(3)|ovary(2)	14				GBM - Glioblastoma multiforme(48;0.249)		CTTGTTTGGCTTCTGTTAAGA	0.468																																					p.A173fs		.											.	.	.	0			c.517delG						.						98.0	99.0	99.0					16																	20871607		2201	4300	6501	SO:0001589	frameshift_variant	123879	exon3			TTTGGCTTCTGTT	BC040442	CCDS10592.1	16p12.3	2013-06-10	2013-06-10		ENSG00000188215	ENSG00000188215			28734	protein-coding gene	gene with protein product			"""DCN1, defective in cullin neddylation 1, domain containing 3 (S. cerevisiae)"""			15988528	Standard	NM_173475		Approved	MGC48972, FLJ41725, DKFZp686O0290	uc002dhz.3	Q8IWE4	OTTHUMG00000131553	ENST00000324344.4:c.516delA	16.37:g.20871607delT	ENSP00000319482:p.Glu172fs	Somatic	57	0		WXS	Illumina HiSeq	.	38	21	NM_173475	B3KVY4	Frame_Shift_Del	DEL	ENST00000324344.4	37	CCDS10592.1																																																																																			.		0.468	DCUN1D3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254415.2	NM_173475	
GIMAP8	155038	hgsc.bcm.edu	37	7	150174405	150174406	+	Frame_Shift_Ins	INS	-	-	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr7:150174405_150174406insC	ENST00000307271.3	+	5	2109_2110	c.1535_1536insC	c.(1534-1539)gaggagfs	p.EE512fs		NM_175571.2	NP_783161.1	Q8ND71	GIMA8_HUMAN	GTPase, IMAP family member 8	512	AIG1-type G 3.					cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	GTP binding (GO:0005525)			breast(3)|central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(11)|lung(26)|ovary(2)|skin(7)|stomach(1)|urinary_tract(1)	62			OV - Ovarian serous cystadenocarcinoma(82;0.0218)	UCEC - Uterine corpus endometrioid carcinoma (81;0.17)		CGGTTAGAAGAGGAGGTCAAGC	0.53																																					p.E512fs		.											.	.	.	0			c.1535_1536insC						.																																			SO:0001589	frameshift_variant	155038	exon5			TAGAAGAGGAGGT	AL834361	CCDS34777.1	7q36.1	2014-04-04			ENSG00000171115	ENSG00000171115		"""GTPases, IMAP"""	21792	protein-coding gene	gene with protein product	"""immune-associated nucleotide-binding protein 9"""					15474311	Standard	XM_005249951		Approved	DKFZp667I133, hIAN6, IAN9	uc003whj.3	Q8ND71	OTTHUMG00000158327	Exception_encountered	7.37:g.150174405_150174406insC	ENSP00000305107:p.Glu512fs	Somatic	63	0		WXS	Illumina HiSeq	.	34	14	NM_175571		Frame_Shift_Ins	INS	ENST00000307271.3	37	CCDS34777.1																																																																																			.		0.530	GIMAP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350701.1	NM_175571	
SAE1	10055	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	19	47712448	47712450	+	In_Frame_Del	DEL	CTT	CTT	-			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	CTT	CTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr19:47712448_47712450delCTT	ENST00000270225.7	+	9	1049_1051	c.981_983delCTT	c.(979-984)aacttc>aac	p.F331del	SAE1_ENST00000540850.1_In_Frame_Del_p.F157del|SAE1_ENST00000413379.3_In_Frame_Del_p.L259del|SAE1_ENST00000598840.1_In_Frame_Del_p.F250del|SAE1_ENST00000392776.3_3'UTR	NM_005500.2	NP_005491.1	Q9UBE0	SAE1_HUMAN	SUMO1 activating enzyme subunit 1	331					cellular protein metabolic process (GO:0044267)|positive regulation of catalytic activity (GO:0043085)|post-translational protein modification (GO:0043687)|protein sumoylation (GO:0016925)|protein ubiquitination (GO:0016567)|regulation of mitotic cell cycle (GO:0007346)|SMT3-dependent protein catabolic process (GO:0019950)	cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP-dependent protein binding (GO:0043008)|enzyme activator activity (GO:0008047)|protein C-terminus binding (GO:0008022)|protein heterodimerization activity (GO:0046982)|ubiquitin activating enzyme activity (GO:0004839)			endometrium(3)|large_intestine(5)|lung(4)|ovary(1)	13		all_cancers(25;1.13e-05)|all_lung(116;0.000192)|all_epithelial(76;0.000274)|Lung NSC(112;0.000446)|all_neural(266;0.0652)|Ovarian(192;0.15)		all cancers(93;0.00013)|OV - Ovarian serous cystadenocarcinoma(262;0.000146)|Epithelial(262;0.00697)|GBM - Glioblastoma multiforme(486;0.0278)		CTCACAACAACTTCTTCTTCTTC	0.493																																					p.327_328del		.											.	.	.	0			c.980_982del						.																																			SO:0001651	inframe_deletion	10055	exon9			CAACAACTTCTTC	BC018271	CCDS12696.1, CCDS54284.1, CCDS54285.1	19q13.32	2013-09-26				ENSG00000142230		"""Ubiquitin-like modifier activating enzymes"""	30660	protein-coding gene	gene with protein product	"""activator Of sumo 1"""	613294				10187858, 9920803, 10217437	Standard	NM_005500		Approved	AOS1, FLJ3091, Sua1	uc002pgc.3	Q9UBE0		ENST00000270225.7:c.981_983delCTT	19.37:g.47712457_47712459delCTT	ENSP00000270225:p.Phe331del	Somatic	57	0		WXS	Illumina HiSeq	.	37	13	NM_005500	B2RDP5|B3KMQ2|F5GXX7|G3XAK6|O95717|Q9P020	In_Frame_Del	DEL	ENST00000270225.7	37	CCDS12696.1																																																																																			.		0.493	SAE1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466775.1	NM_005500	
STK11IP	114790	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	2	220474091	220474091	+	Frame_Shift_Del	DEL	C	C	-			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr2:220474091delC	ENST00000456909.1	+	17	2023	c.1933delC	c.(1933-1935)cttfs	p.L645fs	STK11IP_ENST00000295641.10_Frame_Shift_Del_p.L656fs			Q8N1F8	S11IP_HUMAN	serine/threonine kinase 11 interacting protein	656					protein localization (GO:0008104)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal membrane (GO:0005765)	protein kinase binding (GO:0019901)			breast(2)|endometrium(5)|kidney(1)|large_intestine(2)|lung(10)|ovary(1)|prostate(1)|urinary_tract(1)	23		Renal(207;0.0183)		Epithelial(149;2.69e-07)|all cancers(144;5.91e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		TCAGGAGCTGCTTGCCGTGTT	0.647																																					p.L655fs		.											.	.	.	0			c.1965delG						.						32.0	37.0	36.0					2																	220474091		2040	4202	6242	SO:0001589	frameshift_variant	114790	exon17			GAGCTGCTTGCCG	AF450267	CCDS46521.1	2q35	2008-06-03			ENSG00000144589	ENSG00000144589			19184	protein-coding gene	gene with protein product	"""LKB1 interacting protein"""	607172				11741830	Standard	NM_052902		Approved	LIP1, KIAA1898, LKB1IP, STK11IP1	uc002vml.3	Q8N1F8	OTTHUMG00000059239	ENST00000456909.1:c.1933delC	2.37:g.220474091delC	ENSP00000389383:p.Leu645fs	Somatic	74	0		WXS	Illumina HiSeq	.	62	25	NM_052902	Q8NAW9|Q8WXE4|Q96CN3|Q96PY9	Frame_Shift_Del	DEL	ENST00000456909.1	37																																																																																				.		0.647	STK11IP-001	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000131432.1	NM_052902	
P4HA2	8974	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	5	131530672	131530672	+	Frame_Shift_Del	DEL	C	C	-			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr5:131530672delC	ENST00000401867.1	-	15	2052	c.1484delG	c.(1483-1485)ggtfs	p.G495fs	P4HA2_ENST00000379086.1_Frame_Shift_Del_p.G493fs|P4HA2-AS1_ENST00000417667.1_RNA|P4HA2_ENST00000360568.3_Frame_Shift_Del_p.G493fs|P4HA2_ENST00000379104.2_Frame_Shift_Del_p.G495fs|P4HA2_ENST00000379100.2_Frame_Shift_Del_p.G493fs|P4HA2_ENST00000166534.4_Frame_Shift_Del_p.G495fs			O15460	P4HA2_HUMAN	prolyl 4-hydroxylase, alpha polypeptide II	495	Fe2OG dioxygenase. {ECO:0000255|PROSITE- ProRule:PRU00805}.				peptidyl-proline hydroxylation to 4-hydroxy-L-proline (GO:0018401)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|procollagen-proline 4-dioxygenase complex (GO:0016222)	electron carrier activity (GO:0009055)|iron ion binding (GO:0005506)|L-ascorbic acid binding (GO:0031418)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen (GO:0016702)|procollagen-proline 4-dioxygenase activity (GO:0004656)			breast(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(8)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)	24		all_cancers(142;0.103)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)		L-Proline(DB00172)|Succinic acid(DB00139)	TCGGTAGTCACCTTCCCCGCT	0.552																																					p.G495fs	Esophageal Squamous(68;117 1135 17362 19256 34242)	.											.	.	.	0			c.1485delT						.						224.0	178.0	193.0					5																	131530672		2203	4300	6503	SO:0001589	frameshift_variant	8974	exon14			TAGTCACCTTCCC	U90441	CCDS4151.1, CCDS34230.1	5q31	2008-12-09	2008-12-09		ENSG00000072682	ENSG00000072682	1.14.11.2		8547	protein-coding gene	gene with protein product	"""4-PH alpha 2"", ""collagen prolyl 4-hydroxylase alpha(II)"""	600608	"""procollagen-proline, 2-oxoglutarate 4-dioxygenase (proline 4-hydroxylase), alpha polypeptide II"""			9211872, 9149945	Standard	NM_001142598		Approved	C-P4Halpha(II)	uc003kwl.3	O15460	OTTHUMG00000059647	ENST00000401867.1:c.1484delG	5.37:g.131530672delC	ENSP00000384999:p.Gly495fs	Somatic	48	0		WXS	Illumina HiSeq	.	45	26	NM_004199	D3DQ85|D3DQ86|Q8WWN0	Frame_Shift_Del	DEL	ENST00000401867.1	37	CCDS4151.1																																																																																			.		0.552	P4HA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000132653.4	NM_004199	
KIAA1109	84162	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	4	123168345	123168360	+	Frame_Shift_Del	DEL	AACCTGGTAGAACATC	AACCTGGTAGAACATC	-	rs200065287		TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	AACCTGGTAGAACATC	AACCTGGTAGAACATC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr4:123168345_123168360delAACCTGGTAGAACATC	ENST00000264501.4	+	35	5718_5733	c.5345_5360delAACCTGGTAGAACATC	c.(5344-5361)gaacctggtagaacatcafs	p.EPGRTS1782fs	KIAA1109_ENST00000455637.1_Frame_Shift_Del_p.EPGRTS1782fs|KIAA1109_ENST00000388738.3_Frame_Shift_Del_p.EPGRTS1782fs			Q2LD37	K1109_HUMAN	KIAA1109	1782					regulation of cell growth (GO:0001558)|regulation of epithelial cell differentiation (GO:0030856)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)		p.P1783T(2)		breast(7)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(6)|large_intestine(33)|liver(4)|lung(74)|ovary(9)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(6)|urinary_tract(3)	172						AACAATGCAGAACCTGGTAGAACATCAAATTTTGAT	0.356																																					p.1782_1787del		.											.	.	.	2	Substitution - Missense(2)	breast(2)	c.5344_5359del						.																																			SO:0001589	frameshift_variant	84162	exon33			ATGCAGAACCTGG	AL137384	CCDS43267.1	4q28.1	2012-07-09			ENSG00000138688	ENSG00000138688			26953	protein-coding gene	gene with protein product	"""fragile site-associated"""	611565				16386706	Standard	NM_015312		Approved	FLJ21404, FSA, KIAA1371, Tweek	uc003ieh.3	Q2LD37	OTTHUMG00000150116	ENST00000264501.4:c.5345_5360delAACCTGGTAGAACATC	4.37:g.123168345_123168360delAACCTGGTAGAACATC	ENSP00000264501:p.Glu1782fs	Somatic	161	0		WXS	Illumina HiSeq	.	34	16	NM_015312	Q4W598|Q5CZA9|Q6ZS70|Q6ZV75|Q86XA5|Q8WVD8|Q9H742|Q9NT48|Q9NTC3|Q9NTI4|Q9P2H6|Q9UPP3	Frame_Shift_Del	DEL	ENST00000264501.4	37	CCDS43267.1																																																																																			.		0.356	KIAA1109-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316415.1	NM_020797	
GC	2638	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	4	72629209	72629228	+	Splice_Site	DEL	AGCTGGAGTCTCTAGAAAAC	AGCTGGAGTCTCTAGAAAAC	-	rs111676899|rs376096638		TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	AGCTGGAGTCTCTAGAAAAC	AGCTGGAGTCTCTAGAAAAC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr4:72629209_72629228delAGCTGGAGTCTCTAGAAAAC	ENST00000273951.8	-	6	950_960	c.607_617delGTTTTCTAGAGACTCCAGCT	c.(607-618)gttttctagaga>a	p.VF*R203fs	GC_ENST00000513476.1_Splice_Site_p.VF*R203fs|GC_ENST00000504199.1_Splice_Site_p.VF*R222fs|GC_ENST00000503472.1_5'UTR	NM_000583.3|NM_001204306.1	NP_000574.2|NP_001191235.1	P02774	VTDB_HUMAN	group-specific component (vitamin D binding protein)	203	Albumin 1. {ECO:0000255|PROSITE- ProRule:PRU00769}.				small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D metabolic process (GO:0042359)|vitamin transport (GO:0051180)	blood microparticle (GO:0072562)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)	actin binding (GO:0003779)|calcidiol binding (GO:1902118)|vitamin D binding (GO:0005499)|vitamin transporter activity (GO:0051183)			endometrium(5)|kidney(1)|large_intestine(4)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(4)	45		all_hematologic(202;0.107)	Lung(101;0.148)		Alfacalcidol(DB01436)|Cholecalciferol(DB00169)	TAAATGTTTAAGCTGGAGTCTCTAGAAAACAAGTGAAAGA	0.341																																					p.222_225del		.											.	.	.	0			c.664_675del						.																																			SO:0001630	splice_region_variant	2638	exon7			TGTTTAAGCTGGA	L10641	CCDS3550.1, CCDS56332.1	4q12-q13	2008-08-29			ENSG00000145321	ENSG00000145321			4187	protein-coding gene	gene with protein product		139200				558959	Standard	NM_000583		Approved	DBP, VDBP, hDBP	uc010iif.3	P02774	OTTHUMG00000129915	ENST00000273951.8:c.607-1GTTTTCTAGAGACTCCAGCT>-	4.37:g.72629209_72629228delAGCTGGAGTCTCTAGAAAAC		Somatic	71	0		WXS	Illumina HiSeq	.	24	11	NM_001204307	B4DPP2|D6RAK8|Q16309|Q16310|Q53F31|Q6GTG1	In_Frame_Del	DEL	ENST00000273951.8	37	CCDS3550.1																																																																																			.		0.341	GC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252167.2		Frame_Shift_Del
APBB3	10307	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	5	139938329	139938329	+	Frame_Shift_Del	DEL	C	C	-			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr5:139938329delC	ENST00000357560.4	-	13	1745	c.1302delG	c.(1300-1302)cggfs	p.R434fs	SRA1_ENST00000520427.1_5'Flank|APBB3_ENST00000358580.5_3'UTR|APBB3_ENST00000356738.2_Frame_Shift_Del_p.R439fs|APBB3_ENST00000508496.2_Frame_Shift_Del_p.R211fs|APBB3_ENST00000412920.3_Frame_Shift_Del_p.R432fs|APBB3_ENST00000354402.5_Frame_Shift_Del_p.R441fs|SRA1_ENST00000336283.6_5'Flank	NM_006051.3|NM_133173.2	NP_006042.3|NP_573419.2	O95704	APBB3_HUMAN	amyloid beta (A4) precursor protein-binding, family B, member 3	434	PID 2. {ECO:0000255|PROSITE- ProRule:PRU00148}.					actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(2)|prostate(1)	11			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TCCGCTTGAGCCGCAGGCGGG	0.667																																					p.L442fs		.											.	.	.	0			c.1324delC						.						26.0	32.0	30.0					5																	139938329		2198	4293	6491	SO:0001589	frameshift_variant	10307	exon12			CTTGAGCCGCAGG	AB018247	CCDS4227.1, CCDS4228.1, CCDS4229.1, CCDS47279.1	5q31	2008-02-05			ENSG00000113108	ENSG00000113108			20708	protein-coding gene	gene with protein product		602711				9407065	Standard	NM_133172		Approved	FE65L2	uc003lgd.1	O95704	OTTHUMG00000129504	ENST00000357560.4:c.1302delG	5.37:g.139938329delC	ENSP00000350171:p.Arg434fs	Somatic	34	0		WXS	Illumina HiSeq	.	33	12	NM_006051	B3KQN9|Q08AG4|Q96Q18|Q9BYD4|Q9NYX6|Q9NYX7|Q9NYX8	Frame_Shift_Del	DEL	ENST00000357560.4	37	CCDS4229.1																																																																																			.		0.667	APBB3-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251677.2	NM_006051	
DAZAP1	26528	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	19	1428934	1428956	+	Frame_Shift_Del	DEL	GCTGCCAATGGCTGGGCAGGCCA	GCTGCCAATGGCTGGGCAGGCCA	-			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	GCTGCCAATGGCTGGGCAGGCCA	GCTGCCAATGGCTGGGCAGGCCA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr19:1428934_1428956delGCTGCCAATGGCTGGGCAGGCCA	ENST00000233078.4	+	8	801_823	c.640_662delGCTGCCAATGGCTGGGCAGGCCA	c.(640-663)gctgccaatggctgggcaggccagfs	p.AANGWAGQ214fs	DAZAP1_ENST00000336761.6_Frame_Shift_Del_p.AANGWAGQ214fs	NM_018959.2	NP_061832.2	Q96EP5	DAZP1_HUMAN	DAZ associated protein 1	214					cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|maternal placenta development (GO:0001893)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|RNA stem-loop binding (GO:0035613)			breast(2)|endometrium(2)|large_intestine(1)|lung(3)|upper_aerodigestive_tract(1)	9		Acute lymphoblastic leukemia(61;3.02e-13)|all_hematologic(61;4.32e-09)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		TGTGCCCAACGCTGCCAATGGCTGGGCAGGCCAGCCCCCGCCC	0.664																																					p.213_221del		.											.	.	.	0			c.639_661del						.																																			SO:0001589	frameshift_variant	26528	exon8			CCCAACGCTGCCA		CCDS12065.1, CCDS12066.1	19p13.3	2013-07-16			ENSG00000071626	ENSG00000071626		"""RNA binding motif (RRM) containing"""	2683	protein-coding gene	gene with protein product	"""deleted in azoospermia associated protein 1"""	607430				10857750, 23658607	Standard	XM_005259530		Approved	MGC19907	uc002lsn.3	Q96EP5		ENST00000233078.4:c.640_662delGCTGCCAATGGCTGGGCAGGCCA	19.37:g.1428934_1428956delGCTGCCAATGGCTGGGCAGGCCA	ENSP00000233078:p.Ala214fs	Somatic	142	0		WXS	Illumina HiSeq	.	90	14	NM_018959	Q96MJ3|Q9NRR9	Frame_Shift_Del	DEL	ENST00000233078.4	37	CCDS12065.1																																																																																			.		0.664	DAZAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449522.3	NM_170711	
APBB3	10307	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	5	139938337	139938338	+	Frame_Shift_Del	DEL	GG	GG	-	rs143692635	byFrequency	TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	GG	GG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr5:139938337_139938338delGG	ENST00000357560.4	-	13	1736_1737	c.1293_1294delCC	c.(1291-1296)gcccgcfs	p.R432fs	SRA1_ENST00000520427.1_5'Flank|APBB3_ENST00000358580.5_3'UTR|APBB3_ENST00000356738.2_Frame_Shift_Del_p.R437fs|APBB3_ENST00000508496.2_Frame_Shift_Del_p.R209fs|APBB3_ENST00000412920.3_Frame_Shift_Del_p.R430fs|APBB3_ENST00000354402.5_Frame_Shift_Del_p.R439fs|SRA1_ENST00000336283.6_5'Flank	NM_006051.3|NM_133173.2	NP_006042.3|NP_573419.2	O95704	APBB3_HUMAN	amyloid beta (A4) precursor protein-binding, family B, member 3	432	PID 2. {ECO:0000255|PROSITE- ProRule:PRU00148}.					actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(2)|prostate(1)	11			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AGCCGCAGGCGGGCACGGGCCT	0.658																																					p.439_439del		.											.	.	.	0			c.1315_1316del						.																																			SO:0001589	frameshift_variant	10307	exon12			GCAGGCGGGCACG	AB018247	CCDS4227.1, CCDS4228.1, CCDS4229.1, CCDS47279.1	5q31	2008-02-05			ENSG00000113108	ENSG00000113108			20708	protein-coding gene	gene with protein product		602711				9407065	Standard	NM_133172		Approved	FE65L2	uc003lgd.1	O95704	OTTHUMG00000129504	ENST00000357560.4:c.1293_1294delCC	5.37:g.139938337_139938338delGG	ENSP00000350171:p.Arg432fs	Somatic	34	0		WXS	Illumina HiSeq	.	25	12	NM_006051	B3KQN9|Q08AG4|Q96Q18|Q9BYD4|Q9NYX6|Q9NYX7|Q9NYX8	Frame_Shift_Del	DEL	ENST00000357560.4	37	CCDS4229.1																																																																																			.		0.658	APBB3-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251677.2	NM_006051	
ALB	213	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	4	74274503	74274507	+	Frame_Shift_Del	DEL	GAAGA	GAAGA	-			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	GAAGA	GAAGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr4:74274503_74274507delGAAGA	ENST00000295897.4	+	4	552_556	c.463_467delGAAGA	c.(463-468)gaagagfs	p.EE155fs	ALB_ENST00000509063.1_Frame_Shift_Del_p.EE155fs|ALB_ENST00000401494.3_Intron|ALB_ENST00000505649.1_3'UTR|ALB_ENST00000415165.2_Intron|ALB_ENST00000503124.1_Intron	NM_000477.5	NP_000468.1	Q8TES7	FBF1_HUMAN	albumin	0					apical junction assembly (GO:0043297)|cilium assembly (GO:0042384)|establishment of epithelial cell polarity (GO:0090162)	cell junction (GO:0030054)|centriole (GO:0005814)|ciliary transition fiber (GO:0097539)|spindle pole (GO:0000922)				NS(1)|endometrium(4)|kidney(1)|large_intestine(6)|liver(9)|lung(16)|ovary(3)|prostate(2)|skin(4)|stomach(1)|urinary_tract(1)	48	Breast(15;0.00102)		Epithelial(6;4.8e-05)|OV - Ovarian serous cystadenocarcinoma(6;0.000263)|all cancers(17;0.000472)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			TCATGACAATGAAGAGACATTTTTG	0.366																																					p.154_156del		.											.	.	.	0			c.462_466del						.																																			SO:0001589	frameshift_variant	213	exon4			GACAATGAAGAGA	V00494	CCDS3555.1	4q13.3	2008-02-05	2006-06-30	2006-06-30	ENSG00000163631	ENSG00000163631			399	protein-coding gene	gene with protein product		103600				6292049, 6192711	Standard	NM_000477		Approved		uc003hgs.4	P02768	OTTHUMG00000129919	ENST00000295897.4:c.463_467delGAAGA	4.37:g.74274503_74274507delGAAGA	ENSP00000295897:p.Glu155fs	Somatic	70	0		WXS	Illumina HiSeq	.	26	13	NM_000477	B5MEM5|Q96IF6|Q96JG4|Q96MA8	Frame_Shift_Del	DEL	ENST00000295897.4	37	CCDS3555.1																																																																																			.		0.366	ALB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252173.3	NM_000477	
GIMAP8	155038	hgsc.bcm.edu	37	7	150174406	150174407	+	Frame_Shift_Ins	INS	-	-	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr7:150174406_150174407insA	ENST00000307271.3	+	5	2110_2111	c.1536_1537insA	c.(1537-1539)gagfs	p.E513fs		NM_175571.2	NP_783161.1	Q8ND71	GIMA8_HUMAN	GTPase, IMAP family member 8	513	AIG1-type G 3.					cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	GTP binding (GO:0005525)			breast(3)|central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(11)|lung(26)|ovary(2)|skin(7)|stomach(1)|urinary_tract(1)	62			OV - Ovarian serous cystadenocarcinoma(82;0.0218)	UCEC - Uterine corpus endometrioid carcinoma (81;0.17)		GGTTAGAAGAGGAGGTCAAGCG	0.535																																					p.E512fs		.											.	.	.	0			c.1536_1537insA						.																																			SO:0001589	frameshift_variant	155038	exon5			AGAAGAGGAGGTC	AL834361	CCDS34777.1	7q36.1	2014-04-04			ENSG00000171115	ENSG00000171115		"""GTPases, IMAP"""	21792	protein-coding gene	gene with protein product	"""immune-associated nucleotide-binding protein 9"""					15474311	Standard	XM_005249951		Approved	DKFZp667I133, hIAN6, IAN9	uc003whj.3	Q8ND71	OTTHUMG00000158327	Exception_encountered	7.37:g.150174406_150174407insA	ENSP00000305107:p.Glu513fs	Somatic	64	0		WXS	Illumina HiSeq	.	35	14	NM_175571		Frame_Shift_Ins	INS	ENST00000307271.3	37	CCDS34777.1																																																																																			.		0.535	GIMAP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350701.1	NM_175571	
UGT2B15	7366	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	4	69520862	69520862	+	Frame_Shift_Del	DEL	T	T	-			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr4:69520862delT	ENST00000338206.5	-	4	1053	c.1044delA	c.(1042-1044)ttafs	p.L348fs		NM_001076.3	NP_001067.2	P54855	UDB15_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide B15	348					cellular glucuronidation (GO:0052695)|steroid metabolic process (GO:0008202)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	glucuronosyltransferase activity (GO:0015020)									Acetaminophen(DB00316)|Dabigatran etexilate(DB06695)|Ezetimibe(DB00973)|Lorazepam(DB00186)|Morphine(DB00295)|Oxazepam(DB00842)|Valproic Acid(DB00313)	TATTGGAACCTAAAGTATTTG	0.368																																					p.G349fs		.											.	.	.	0			c.1045delG						.						183.0	185.0	184.0					4																	69520862		2203	4296	6499	SO:0001589	frameshift_variant	7366	exon4			GGAACCTAAAGTA	AF180322	CCDS3524.1	4q13	2008-02-05	2005-07-20		ENSG00000196620	ENSG00000196620		"""UDP glucuronosyltransferases"""	12546	protein-coding gene	gene with protein product		600069	"""UDP glycosyltransferase 2 family, polypeptide B15"""			7835904	Standard	NM_001076		Approved	UGT2B8	uc021xow.1	P54855	OTTHUMG00000161507	ENST00000338206.5:c.1044delA	4.37:g.69520862delT	ENSP00000341045:p.Leu348fs	Somatic	146	0		WXS	Illumina HiSeq	.	53	35	NM_001076	A6NDX0|A6NNJ4|A8K054|P23765|Q9UK63	Frame_Shift_Del	DEL	ENST00000338206.5	37	CCDS3524.1																																																																																			.		0.368	UGT2B15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365172.1	NM_001076	
GIGYF2	26058	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	2	233660789	233660809	+	In_Frame_Del	DEL	GGCTTATCTCCAAGACAGTGC	GGCTTATCTCCAAGACAGTGC	-			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	GGCTTATCTCCAAGACAGTGC	GGCTTATCTCCAAGACAGTGC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr2:233660789_233660809delGGCTTATCTCCAAGACAGTGC	ENST00000409547.1	+	16	1808_1828	c.1497_1517delGGCTTATCTCCAAGACAGTGC	c.(1495-1518)gtggcttatctccaagacagtgca>gta	p.AYLQDSA500del	GIGYF2_ENST00000373566.3_In_Frame_Del_p.AYLQDSA522del|GIGYF2_ENST00000409480.1_In_Frame_Del_p.AYLQDSA522del|GIGYF2_ENST00000409196.3_In_Frame_Del_p.AYLQDSA494del|GIGYF2_ENST00000452341.2_In_Frame_Del_p.AYLQDSA331del|GIGYF2_ENST00000373563.4_In_Frame_Del_p.AYLQDSA500del|GIGYF2_ENST00000409451.3_In_Frame_Del_p.AYLQDSA521del	NM_015575.3	NP_056390.2	Q6Y7W6	PERQ2_HUMAN	GRB10 interacting GYF protein 2	500					adult locomotory behavior (GO:0008344)|cell death (GO:0008219)|cellular protein metabolic process (GO:0044267)|feeding behavior (GO:0007631)|homeostasis of number of cells within a tissue (GO:0048873)|insulin-like growth factor receptor signaling pathway (GO:0048009)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|musculoskeletal movement (GO:0050881)|negative regulation of translation (GO:0017148)|neuromuscular process controlling balance (GO:0050885)|post-embryonic development (GO:0009791)|spinal cord motor neuron differentiation (GO:0021522)	membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)	p.L502L(1)		NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(11)|kidney(2)|large_intestine(17)|lung(11)|ovary(5)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	63		Breast(86;0.00279)|all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0271)|Lung NSC(271;0.0839)		Epithelial(121;7.37e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000472)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Lung(119;0.0118)|GBM - Glioblastoma multiforme(43;0.0145)		AGAAAATGGTGGCTTATCTCCAAGACAGTGCACTAGATGAT	0.385																																					p.520_527del		.											.	.	.	1	Substitution - coding silent(1)	breast(1)	c.1559_1579del						.																																			SO:0001651	inframe_deletion	26058	exon16			AATGGTGGCTTAT	U80751	CCDS33401.1, CCDS46542.1, CCDS46543.1	2q37.1	2011-07-06	2008-02-11	2008-02-11	ENSG00000204120	ENSG00000204120		"""Trinucleotide (CAG) repeat containing"""	11960	protein-coding gene	gene with protein product	"""GYF domain containing 2"""	612003	"""PERQ amino acid rich, with GYF domain 2"", ""PERQ amino acid rich, with GYF domain 3"", ""trinucleotide repeat containing 15"", ""Parkinson disease (autosomal recessive, early onset) 11"""	PERQ2, PERQ3, TNRC15, PARK11		9225980, 9734811, 12771153, 18358451, 19279319	Standard	NM_015575		Approved	KIAA0642, GYF2	uc002vtk.4	Q6Y7W6	OTTHUMG00000153237	ENST00000409547.1:c.1497_1517delGGCTTATCTCCAAGACAGTGC	2.37:g.233660789_233660809delGGCTTATCTCCAAGACAGTGC	ENSP00000386537:p.Ala500_Ala506del	Somatic	67	0		WXS	Illumina HiSeq	.	29	11	NM_001103147	A6H8W4|B9EG55|E9PBB0|O75137|Q7Z2Z8|Q7Z3I2|Q96HU4|Q9NV82	In_Frame_Del	DEL	ENST00000409547.1	37	CCDS33401.1																																																																																			.		0.385	GIGYF2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000330316.2	NM_001103146	
GUSB	2990	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	7	65425957	65425973	+	Frame_Shift_Del	DEL	TTCCAGTATCTCTCTCG	TTCCAGTATCTCTCTCG	-	rs121918184|rs372550726		TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	TTCCAGTATCTCTCTCG	TTCCAGTATCTCTCTCG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr7:65425957_65425973delTTCCAGTATCTCTCTCG	ENST00000304895.4	-	12	1997_2013	c.1867_1883delCGAGAGAGATACTGGAA	c.(1867-1884)cgagagagatactggaagfs	p.RERYWK623fs	GUSB_ENST00000421103.1_Frame_Shift_Del_p.RERYWK477fs|GUSB_ENST00000345660.6_Frame_Shift_Del_p.RERYWK572fs	NM_000181.3	NP_000172.2	P08236	BGLR_HUMAN	glucuronidase, beta	623					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan catabolic process (GO:0030214)|hyaluronan metabolic process (GO:0030212)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)	beta-glucuronidase activity (GO:0004566)			breast(1)|cervix(2)|kidney(2)|large_intestine(4)|lung(10)|skin(1)	20						ATTGGCAATCTTCCAGTATCTCTCTCGCAAAAGGAAC	0.461																																					p.623_628del		.											GUSB,NS,carcinoma,0,1	GUSB	0	0			c.1868_1884del	GRCh37	CD962032|CM930361|CM980963	GUSB	D|M	rs121918184	.																																			SO:0001589	frameshift_variant	2990	exon12			GCAATCTTCCAGT	M15182	CCDS5530.1, CCDS64665.1	7q11.21	2012-10-02			ENSG00000169919	ENSG00000169919	3.2.1.31		4696	protein-coding gene	gene with protein product		611499				3468507	Standard	NM_000181		Approved		uc003tun.3	P08236	OTTHUMG00000023735	ENST00000304895.4:c.1867_1883delCGAGAGAGATACTGGAA	7.37:g.65425957_65425973delTTCCAGTATCTCTCTCG	ENSP00000302728:p.Arg623fs	Somatic	113	0		WXS	Illumina HiSeq	.	47	11	NM_000181	B4E1F6|E9PCV0|Q549U0|Q96CL9	Frame_Shift_Del	DEL	ENST00000304895.4	37	CCDS5530.1																																																																																			.		0.461	GUSB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251637.3	NM_000181	
FCGR1B	2210	hgsc.bcm.edu;broad.mit.edu	37	1	120934442	120934442	+	Frame_Shift_Del	DEL	T	T	-			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr1:120934442delT	ENST00000369384.4	-	3	288	c.246delA	c.(244-246)gaafs	p.E82fs	FCGR1B_ENST00000472543.1_5'UTR|RP11-439A17.9_ENST00000457996.1_RNA|RP11-439A17.10_ENST00000426275.1_RNA|FCGR1B_ENST00000369383.4_Intron	NM_001017986.3	NP_001017986.1	Q92637	FCGRB_HUMAN	Fc fragment of IgG, high affinity Ib, receptor (CD64)	82	Ig-like C2-type 1.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|Fc receptor signaling pathway (GO:0038093)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)	clathrin-coated endocytic vesicle membrane (GO:0030669)|early endosome membrane (GO:0031901)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	immunoglobulin receptor activity (GO:0019763)			breast(1)|endometrium(1)|lung(2)	4	all_neural(166;0.181)	all_lung(203;7.27e-05)|Lung NSC(69;0.000389)|all_epithelial(167;0.068)		Lung(183;0.0327)|LUSC - Lung squamous cell carcinoma(189;0.19)	Intravenous Immunoglobulin(DB00028)	GGCACCTGTATTCACCACTGT	0.542																																					p.Y83fs		.											.	.	.	0			c.247delT						.						8.0	9.0	9.0					1																	120934442		2117	4186	6303	SO:0001589	frameshift_variant	2210	exon3			CCTGTATTCACCA		CCDS72844.1, CCDS72845.1, CCDS72846.1	1p11.2	2013-01-11	2005-02-02		ENSG00000198019	ENSG00000198019		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	3614	protein-coding gene	gene with protein product		601502	"""Fc fragment of IgG, high affinity Ib, receptor for (CD64)"""			8697799, 9763663	Standard	NM_001017986		Approved	CD64b	uc001eip.3	Q92637	OTTHUMG00000040903	ENST00000369384.4:c.246delA	1.37:g.120934442delT	ENSP00000358391:p.Glu82fs	Somatic	136	0		WXS	Illumina HiSeq	.	87	14	NM_001244910	Q7KZ13|Q92638	Frame_Shift_Del	DEL	ENST00000369384.4	37	CCDS30821.1																																																																																			.		0.542	FCGR1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098241.1		
VPS41	27072	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	7	38860830	38860830	+	Frame_Shift_Del	DEL	A	A	-			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr7:38860830delA	ENST00000310301.4	-	6	411	c.357delT	c.(355-357)tttfs	p.F119fs	VPS41_ENST00000395969.2_Frame_Shift_Del_p.F94fs	NM_014396.3	NP_055211.2	P49754	VPS41_HUMAN	vacuolar protein sorting 41 homolog (S. cerevisiae)	119					Golgi vesicle transport (GO:0048193)|intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	cytosol (GO:0005829)|early endosome (GO:0005769)|Golgi-associated vesicle (GO:0005798)|HOPS complex (GO:0030897)|late endosome (GO:0005770)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)	zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(5)|kidney(4)|large_intestine(5)|lung(17)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(4)	44						AAGTCTCGTGAAATTCTTCTC	0.363																																					p.H120fs		.											.	.	.	0			c.358delC						.						97.0	101.0	100.0					7																	38860830		2203	4300	6503	SO:0001589	frameshift_variant	27072	exon6			CTCGTGAAATTCT	U87309	CCDS5457.1, CCDS5458.2	7p14.1-p13	2009-05-08	2006-12-19		ENSG00000006715	ENSG00000006715			12713	protein-coding gene	gene with protein product		605485	"""vacuolar protein sorting 41 (yeast homolog)"", ""vacuolar protein sorting 41 (yeast)"""			9159129	Standard	NM_080631		Approved	HVSP41	uc003tgy.3	P49754	OTTHUMG00000023629	ENST00000310301.4:c.357delT	7.37:g.38860830delA	ENSP00000309457:p.Phe119fs	Somatic	65	0		WXS	Illumina HiSeq	.	49	21	NM_014396	E9PF36|Q86TP8|Q99851|Q99852	Frame_Shift_Del	DEL	ENST00000310301.4	37	CCDS5457.1																																																																																			.		0.363	VPS41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226986.3		
CYP3A5	1577	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	7	99247826	99247826	+	Frame_Shift_Del	DEL	G	G	-			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr7:99247826delG	ENST00000222982.4	-	12	1382	c.1283delC	c.(1282-1284)cctfs	p.P428fs	CYP3A5_ENST00000339843.2_3'UTR|CYP3A5_ENST00000343703.5_Frame_Shift_Del_p.P418fs	NM_000777.3	NP_000768.1	P20815	CP3A5_HUMAN	cytochrome P450, family 3, subfamily A, polypeptide 5	428					alkaloid catabolic process (GO:0009822)|drug catabolic process (GO:0042737)|oxidative demethylation (GO:0070989)|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)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity (GO:0016491)|oxygen binding (GO:0019825)			NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	16	all_epithelial(64;2.77e-08)|Lung NSC(181;0.00396)|all_lung(186;0.00659)|Esophageal squamous(72;0.0166)				ado-trastuzumab emtansine(DB05773)|Alfentanil(DB00802)|Alprazolam(DB00404)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Amprenavir(DB00701)|Apixaban(DB06605)|Aprepitant(DB00673)|Argatroban(DB00278)|Aripiprazole(DB01238)|Artemether(DB06697)|Astemizole(DB00637)|Atorvastatin(DB01076)|Axitinib(DB06626)|Azelastine(DB00972)|Beclomethasone(DB00394)|Boceprevir(DB08873)|Brentuximab vedotin(DB08870)|Buprenorphine(DB00921)|Buspirone(DB00490)|Cabazitaxel(DB06772)|Caffeine(DB00201)|Carbamazepine(DB00564)|Chloramphenicol(DB00446)|Chloroquine(DB00608)|Chlorphenamine(DB01114)|Cilostazol(DB01166)|Cimetidine(DB00501)|Ciprofloxacin(DB00537)|Cisapride(DB00604)|Clarithromycin(DB01211)|Clonidine(DB00575)|Clopidogrel(DB00758)|Cocaine(DB00907)|Codeine(DB00318)|Crizotinib(DB08865)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dapsone(DB00250)|Dasatinib(DB01254)|Daunorubicin(DB00694)|Delavirdine(DB00705)|Dexamethasone(DB01234)|Dextromethorphan(DB00514)|Diazepam(DB00829)|Diltiazem(DB00343)|Disulfiram(DB00822)|Docetaxel(DB01248)|Dolutegravir(DB08930)|Domperidone(DB01184)|Dutasteride(DB01126)|Enzalutamide(DB08899)|Eplerenone(DB00700)|Erlotinib(DB00530)|Erythromycin(DB00199)|Estradiol(DB00783)|Estrone(DB00655)|Ethosuximide(DB00593)|Etoposide(DB00773)|Felodipine(DB01023)|Fentanyl(DB00813)|Finasteride(DB01216)|Fluconazole(DB00196)|Fluoxetine(DB00472)|Flutamide(DB00499)|Fluticasone Propionate(DB00588)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Gefitinib(DB00317)|Gestodene(DB06730)|Granisetron(DB00889)|Halofantrine(DB01218)|Haloperidol(DB00502)|Hydrocortisone(DB00741)|Ifosfamide(DB01181)|Iloperidone(DB04946)|Imatinib(DB00619)|Indinavir(DB00224)|Irinotecan(DB00762)|Itraconazole(DB01167)|Ketoconazole(DB01026)|Lapatinib(DB01259)|Lercanidipine(DB00528)|Levomethadyl Acetate(DB01227)|Lidocaine(DB00281)|Losartan(DB00678)|Lovastatin(DB00227)|Methadone(DB00333)|Midazolam(DB00683)|Mifepristone(DB00834)|Modafinil(DB00745)|Mycophenolate mofetil(DB00688)|Nateglinide(DB00731)|Nefazodone(DB01149)|Nelfinavir(DB00220)|Nevirapine(DB00238)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Norethindrone(DB00717)|Norfloxacin(DB01059)|Nortriptyline(DB00540)|Ondansetron(DB00904)|Oxazepam(DB00842)|Oxcarbazepine(DB00776)|Oxybutynin(DB01062)|Oxycodone(DB00497)|Paclitaxel(DB01229)|Paliperidone(DB01267)|Pentamidine(DB00738)|Perampanel(DB08883)|Phenelzine(DB00780)|Phenobarbital(DB01174)|Phenytoin(DB00252)|Pimozide(DB01100)|Ponatinib(DB08901)|Pravastatin(DB00175)|Praziquantel(DB01058)|Progesterone(DB00396)|Propranolol(DB00571)|Quetiapine(DB01224)|Quinacrine(DB01103)|Quinine(DB00468)|Ranitidine(DB00863)|Reserpine(DB00206)|Rifampicin(DB01045)|Rifapentine(DB01201)|Risperidone(DB00734)|Ritonavir(DB00503)|Rivaroxaban(DB06228)|Rosuvastatin(DB01098)|Salmeterol(DB00938)|Saquinavir(DB01232)|Saxagliptin(DB06335)|Sildenafil(DB00203)|Simvastatin(DB00641)|Sirolimus(DB00877)|Sorafenib(DB00398)|Sulfasalazine(DB00795)|Sunitinib(DB01268)|Tacrolimus(DB00864)|Tamoxifen(DB00675)|Telithromycin(DB00976)|Temsirolimus(DB06287)|Teniposide(DB00444)|Testosterone(DB00624)|Thalidomide(DB01041)|Trazodone(DB00656)|Tretinoin(DB00755)|Triazolam(DB00897)|Troleandomycin(DB01361)|Udenafil(DB06267)|Valproic Acid(DB00313)|Vardenafil(DB00862)|Verapamil(DB00661)|Vincristine(DB00541)|Voriconazole(DB00582)|Zalcitabine(DB00943)|Zaleplon(DB00962)|Ziprasidone(DB00246)|Zolpidem(DB00425)	GTATATGTAAGGATCTATGCT	0.388																																					p.P428fs		.											.	.	.	0			c.1284delT						.						312.0	269.0	284.0					7																	99247826		2203	4300	6503	SO:0001589	frameshift_variant	1577	exon12			ATGTAAGGATCTA	L26985	CCDS5672.1, CCDS55134.1	7q21.1	2007-12-14	2003-01-14		ENSG00000106258	ENSG00000106258		"""Cytochrome P450s"""	2638	protein-coding gene	gene with protein product		605325	"""cytochrome P450, subfamily IIIA (niphedipine oxidase), polypeptide 5"""				Standard	NR_033808		Approved	PCN3, P450PCN3, CP35		P20815	OTTHUMG00000156724	ENST00000222982.4:c.1283delC	7.37:g.99247826delG	ENSP00000222982:p.Pro428fs	Somatic	121	0		WXS	Illumina HiSeq	.	61	22	NM_000777	A4D289|B7Z5I7|Q53WY8|Q75MV0|Q9HB56	Frame_Shift_Del	DEL	ENST00000222982.4	37	CCDS5672.1																																																																																			.		0.388	CYP3A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345469.1		
ELMOD1	55531	hgsc.bcm.edu	37	11	107518233	107518234	+	In_Frame_Ins	INS	-	-	GGATTTCTA			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr11:107518233_107518234insGGATTTCTA	ENST00000265840.7	+	7	725_726	c.460_461insGGATTTCTA	c.(460-462)cgg>cGGATTTCTAgg	p.154_154R>RISR	ELMOD1_ENST00000443271.2_In_Frame_Ins_p.154_154R>RISR|ELMOD1_ENST00000531234.1_In_Frame_Ins_p.148_148R>RISR	NM_018712.3	NP_061182.3	Q8N336	ELMD1_HUMAN	ELMO/CED-12 domain containing 1	154	ELMO. {ECO:0000255|PROSITE- ProRule:PRU00664}.				phagocytosis (GO:0006909)|positive regulation of GTPase activity (GO:0043547)	cytoskeleton (GO:0005856)	GTPase activator activity (GO:0005096)			endometrium(2)|large_intestine(5)|liver(2)|lung(7)|pancreas(2)|prostate(1)	19		Melanoma(852;0.000288)|Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00301)|all_epithelial(67;0.00304)|Breast(348;0.104)		BRCA - Breast invasive adenocarcinoma(274;3.4e-05)|Epithelial(105;0.00027)|all cancers(92;0.00481)		ACTGGAATCTCGGATTTCTAAG	0.386																																					p.R154delinsRISR		.											.	.	.	0			c.460_461insGGATTTCTA						.																																			SO:0001652	inframe_insertion	55531	exon7			GAATCTCGGATTT	AL359601	CCDS44723.1, CCDS44724.1	11q23.1	2012-10-15	2006-01-20		ENSG00000110675	ENSG00000110675			25334	protein-coding gene	gene with protein product		615456	"""ELMO domain containing 1"""			12477932	Standard	NM_018712		Approved	DKFZp547C176	uc010rvs.2	Q8N336	OTTHUMG00000166361	ENST00000265840.7:c.461_469dupGGATTTCTA	11.37:g.107518234_107518242dupGGATTTCTA	Exception_encountered	Somatic	98	0		WXS	Illumina HiSeq	.	54	0	NM_018712	B4E167|G5E9S5|Q9NPW3	In_Frame_Ins	INS	ENST00000265840.7	37	CCDS44723.1																																																																																			.		0.386	ELMOD1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389406.1	NM_018712	
APBB3	10307	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	5	139938333	139938335	+	In_Frame_Del	DEL	AGG	AGG	-			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	AGG	AGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr5:139938333_139938335delAGG	ENST00000357560.4	-	13	1739_1741	c.1296_1298delCCT	c.(1294-1299)cgcctg>cgg	p.L433del	SRA1_ENST00000520427.1_5'Flank|APBB3_ENST00000358580.5_3'UTR|APBB3_ENST00000356738.2_In_Frame_Del_p.L438del|APBB3_ENST00000508496.2_In_Frame_Del_p.L210del|APBB3_ENST00000412920.3_In_Frame_Del_p.L431del|APBB3_ENST00000354402.5_In_Frame_Del_p.L440del|SRA1_ENST00000336283.6_5'Flank	NM_006051.3|NM_133173.2	NP_006042.3|NP_573419.2	O95704	APBB3_HUMAN	amyloid beta (A4) precursor protein-binding, family B, member 3	433	PID 2. {ECO:0000255|PROSITE- ProRule:PRU00148}.					actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(2)|prostate(1)	11			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTTGAGCCGCAGGCGGGCACGGG	0.655																																					p.440_440del		.											.	.	.	0			c.1318_1320del						.																																			SO:0001651	inframe_deletion	10307	exon12			AGCCGCAGGCGGG	AB018247	CCDS4227.1, CCDS4228.1, CCDS4229.1, CCDS47279.1	5q31	2008-02-05			ENSG00000113108	ENSG00000113108			20708	protein-coding gene	gene with protein product		602711				9407065	Standard	NM_133172		Approved	FE65L2	uc003lgd.1	O95704	OTTHUMG00000129504	ENST00000357560.4:c.1296_1298delCCT	5.37:g.139938333_139938335delAGG	ENSP00000350171:p.Leu433del	Somatic	34	0		WXS	Illumina HiSeq	.	25	12	NM_006051	B3KQN9|Q08AG4|Q96Q18|Q9BYD4|Q9NYX6|Q9NYX7|Q9NYX8	In_Frame_Del	DEL	ENST00000357560.4	37	CCDS4229.1																																																																																			.		0.655	APBB3-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251677.2	NM_006051	
IPO13	9670	hgsc.bcm.edu	37	1	44423802	44423803	+	In_Frame_Ins	INS	-	-	TGC			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr1:44423802_44423803insTGC	ENST00000372343.3	+	8	2356_2357	c.1694_1695insTGC	c.(1693-1698)tatgct>taTGCtgct	p.567_568insA		NM_014652.3	NP_055467.3	O94829	IPO13_HUMAN	importin 13	567					protein import into nucleus (GO:0006606)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(6)|lung(13)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	40	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0821)				CTGCCTCCCTATGCTGCCAACA	0.55																																					p.Y565delinsYA		.											.	.	.	0			c.1694_1695insTGC						.																																			SO:0001652	inframe_insertion	9670	exon8			CTCCCTATGCTGC	AB018267	CCDS503.1	1p34.1	2008-02-05			ENSG00000117408	ENSG00000117408		"""Importins"""	16853	protein-coding gene	gene with protein product		610411				9872452, 11447110	Standard	NM_014652		Approved	IMP13, KIAA0724, RANBP13	uc001ckx.3	O94829	OTTHUMG00000008297	ENST00000372343.3:c.1698_1700dupTGC	1.37:g.44423806_44423808dupTGC	ENSP00000361418:p.Ala567_Ala567dup	Somatic	27	0		WXS	Illumina HiSeq	.	30	10	NM_014652	D3DPY4|Q5T4X3|Q7LC04|Q96HS3|Q9H8N3|Q9UFR1	In_Frame_Ins	INS	ENST00000372343.3	37	CCDS503.1																																																																																			.		0.550	IPO13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022846.1	NM_014652	
ZNF721	170960	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	4	435664	435674	+	Frame_Shift_Del	DEL	GGGTTTCTCTC	GGGTTTCTCTC	-	rs576154356		TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	GGGTTTCTCTC	GGGTTTCTCTC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr4:435664_435674delGGGTTTCTCTC	ENST00000338977.5	-	2	2594_2604	c.2546_2556delGAGAGAAACCC	c.(2545-2556)ggagagaaacccfs	p.GEKP849fs	ZNF721_ENST00000507078.1_Intron|ABCA11P_ENST00000451020.2_RNA|ZNF721_ENST00000506646.1_Intron|ZNF721_ENST00000511833.2_Frame_Shift_Del_p.GEKP861fs			Q8TF20	ZN721_HUMAN	zinc finger protein 721	849					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.K863T(1)|p.K633T(1)		endometrium(2)|kidney(2)|large_intestine(15)|lung(6)|ovary(1)|skin(1)|stomach(5)|urinary_tract(1)	33						CACATGTGTAGGGTTTCTCTCCAGTATGAAT	0.412																																					p.861_865del		.											.	.	.	2	Substitution - Missense(2)	large_intestine(2)	c.2583_2593del						.																																			SO:0001589	frameshift_variant	170960	exon3			TGTGTAGGGTTTC	AK092362	CCDS46991.1	4p16.3	2013-01-08			ENSG00000182903	ENSG00000182903		"""Zinc fingers, C2H2-type"", ""-"""	29425	protein-coding gene	gene with protein product						11853319	Standard	NM_133474		Approved	KIAA1982	uc003gag.4	Q8TF20		ENST00000338977.5:c.2546_2556delGAGAGAAACCC	4.37:g.435664_435674delGGGTTTCTCTC	ENSP00000340524:p.Gly849fs	Somatic	85	0		WXS	Illumina HiSeq	.	51	13	NM_133474	Q69YG7	Frame_Shift_Del	DEL	ENST00000338977.5	37																																																																																				.		0.412	ZNF721-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000357939.1	NM_133474	
PRDM9	56979	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	5	23527639	23527654	+	Frame_Shift_Del	DEL	CAATAAGTCACACCTC	CAATAAGTCACACCTC	-	rs202203985|rs201595671|rs200479090|rs199802267|rs201134410|rs200487743	byFrequency	TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	CAATAAGTCACACCTC	CAATAAGTCACACCTC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr5:23527639_23527654delCAATAAGTCACACCTC	ENST00000296682.3	+	11	2624_2639	c.2442_2457delCAATAAGTCACACCTC	c.(2440-2457)agcaataagtcacacctcfs	p.SNKSHL814fs		NM_020227.2	NP_064612.2	Q9NQV7	PRDM9_HUMAN	PR domain containing 9	814					meiotic gene conversion (GO:0006311)|positive regulation of meiosis I (GO:0060903)|positive regulation of reciprocal meiotic recombination (GO:0010845)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)	histone methyltransferase activity (H3-K4 specific) (GO:0042800)|metal ion binding (GO:0046872)|recombination hotspot binding (GO:0010844)|sequence-specific DNA binding (GO:0043565)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(15)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(27)|lung(87)|ovary(6)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(11)	172						GGGGCTTTAGCAATAAGTCACACCTCCTCAGACACC	0.569										HNSCC(3;0.000094)																											p.814_819del		.											.	.	.	0			c.2441_2456del						.																																			SO:0001589	frameshift_variant	56979	exon11			CTTTAGCAATAAG	AF275816	CCDS43307.1	5p14.2	2014-06-03			ENSG00000164256	ENSG00000164256		"""-"", ""Zinc fingers, C2H2-type"""	13994	protein-coding gene	gene with protein product	"""PR-domain containing protein 9"""	609760	"""minisatellite binding protein 3, 115kDa"", ""minisatellite binding protein 3 (115kD)"""	MSBP3		10668202, 2062643, 24634223	Standard	NM_020227		Approved	PFM6, ZNF899	uc003jgo.3	Q9NQV7	OTTHUMG00000161918	ENST00000296682.3:c.2442_2457delCAATAAGTCACACCTC	5.37:g.23527639_23527654delCAATAAGTCACACCTC	ENSP00000296682:p.Ser814fs	Somatic	95	0		WXS	Illumina HiSeq	.	69	16	NM_020227	B4DX22|Q27Q50	Frame_Shift_Del	DEL	ENST00000296682.3	37	CCDS43307.1																																																																																			.		0.569	PRDM9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366375.1	NM_020227	
SLC12A7	10723	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	5	1093708	1093730	+	Frame_Shift_Del	DEL	GTTGGTGTAGTTGGCCAGCTTGT	GTTGGTGTAGTTGGCCAGCTTGT	-			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	GTTGGTGTAGTTGGCCAGCTTGT	GTTGGTGTAGTTGGCCAGCTTGT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr5:1093708_1093730delGTTGGTGTAGTTGGCCAGCTTGT	ENST00000264930.5	-	3	303_325	c.260_282delACAAGCTGGCCAACTACACCAAC	c.(259-282)aacaagctggccaactacaccaacfs	p.NKLANYTN87fs		NM_006598.2	NP_006589.2	Q9Y666	S12A7_HUMAN	solute carrier family 12 (potassium/chloride transporter), member 7	87					cell volume homeostasis (GO:0006884)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transport (GO:0006811)|potassium ion transport (GO:0006813)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	potassium:chloride symporter activity (GO:0015379)|protein kinase binding (GO:0019901)			breast(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(14)|ovary(2)|prostate(1)|skin(4)|urinary_tract(2)	32	Lung NSC(6;2.47e-13)|all_lung(6;1.67e-12)|all_epithelial(6;5.44e-09)		Epithelial(17;0.000497)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|all cancers(22;0.00241)|Lung(60;0.165)		Potassium Chloride(DB00761)	CCTGGCTCAGGTTGGTGTAGTTGGCCAGCTTGTTGAGCAGCGA	0.709																																					p.87_95del		.											.	.	.	0			c.261_283del						.																																			SO:0001589	frameshift_variant	10723	exon3			GCTCAGGTTGGTG	AF105365	CCDS34129.1	5p15	2013-07-18	2013-07-18		ENSG00000113504	ENSG00000113504		"""Solute carriers"""	10915	protein-coding gene	gene with protein product		604879				10347194	Standard	NM_006598		Approved	KCC4, DKFZP434F076	uc003jbu.3	Q9Y666	OTTHUMG00000161931	ENST00000264930.5:c.260_282delACAAGCTGGCCAACTACACCAAC	5.37:g.1093708_1093730delGTTGGTGTAGTTGGCCAGCTTGT	ENSP00000264930:p.Asn87fs	Somatic	56	0		WXS	Illumina HiSeq	.	26	10	NM_006598	A6NDS8|Q4G0F3|Q96I81|Q9H7I3|Q9H7I7|Q9UFW2	Frame_Shift_Del	DEL	ENST00000264930.5	37	CCDS34129.1																																																																																			.		0.709	SLC12A7-001	KNOWN	non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366446.2	NM_006598	
CYP3A5	1577	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	7	99247829	99247829	+	Frame_Shift_Del	DEL	T	T	-			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr7:99247829delT	ENST00000222982.4	-	12	1379	c.1280delA	c.(1279-1281)gatfs	p.D427fs	CYP3A5_ENST00000339843.2_3'UTR|CYP3A5_ENST00000343703.5_Frame_Shift_Del_p.D417fs	NM_000777.3	NP_000768.1	P20815	CP3A5_HUMAN	cytochrome P450, family 3, subfamily A, polypeptide 5	427					alkaloid catabolic process (GO:0009822)|drug catabolic process (GO:0042737)|oxidative demethylation (GO:0070989)|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)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity (GO:0016491)|oxygen binding (GO:0019825)			NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	16	all_epithelial(64;2.77e-08)|Lung NSC(181;0.00396)|all_lung(186;0.00659)|Esophageal squamous(72;0.0166)				ado-trastuzumab emtansine(DB05773)|Alfentanil(DB00802)|Alprazolam(DB00404)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Amprenavir(DB00701)|Apixaban(DB06605)|Aprepitant(DB00673)|Argatroban(DB00278)|Aripiprazole(DB01238)|Artemether(DB06697)|Astemizole(DB00637)|Atorvastatin(DB01076)|Axitinib(DB06626)|Azelastine(DB00972)|Beclomethasone(DB00394)|Boceprevir(DB08873)|Brentuximab vedotin(DB08870)|Buprenorphine(DB00921)|Buspirone(DB00490)|Cabazitaxel(DB06772)|Caffeine(DB00201)|Carbamazepine(DB00564)|Chloramphenicol(DB00446)|Chloroquine(DB00608)|Chlorphenamine(DB01114)|Cilostazol(DB01166)|Cimetidine(DB00501)|Ciprofloxacin(DB00537)|Cisapride(DB00604)|Clarithromycin(DB01211)|Clonidine(DB00575)|Clopidogrel(DB00758)|Cocaine(DB00907)|Codeine(DB00318)|Crizotinib(DB08865)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dapsone(DB00250)|Dasatinib(DB01254)|Daunorubicin(DB00694)|Delavirdine(DB00705)|Dexamethasone(DB01234)|Dextromethorphan(DB00514)|Diazepam(DB00829)|Diltiazem(DB00343)|Disulfiram(DB00822)|Docetaxel(DB01248)|Dolutegravir(DB08930)|Domperidone(DB01184)|Dutasteride(DB01126)|Enzalutamide(DB08899)|Eplerenone(DB00700)|Erlotinib(DB00530)|Erythromycin(DB00199)|Estradiol(DB00783)|Estrone(DB00655)|Ethosuximide(DB00593)|Etoposide(DB00773)|Felodipine(DB01023)|Fentanyl(DB00813)|Finasteride(DB01216)|Fluconazole(DB00196)|Fluoxetine(DB00472)|Flutamide(DB00499)|Fluticasone Propionate(DB00588)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Gefitinib(DB00317)|Gestodene(DB06730)|Granisetron(DB00889)|Halofantrine(DB01218)|Haloperidol(DB00502)|Hydrocortisone(DB00741)|Ifosfamide(DB01181)|Iloperidone(DB04946)|Imatinib(DB00619)|Indinavir(DB00224)|Irinotecan(DB00762)|Itraconazole(DB01167)|Ketoconazole(DB01026)|Lapatinib(DB01259)|Lercanidipine(DB00528)|Levomethadyl Acetate(DB01227)|Lidocaine(DB00281)|Losartan(DB00678)|Lovastatin(DB00227)|Methadone(DB00333)|Midazolam(DB00683)|Mifepristone(DB00834)|Modafinil(DB00745)|Mycophenolate mofetil(DB00688)|Nateglinide(DB00731)|Nefazodone(DB01149)|Nelfinavir(DB00220)|Nevirapine(DB00238)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Norethindrone(DB00717)|Norfloxacin(DB01059)|Nortriptyline(DB00540)|Ondansetron(DB00904)|Oxazepam(DB00842)|Oxcarbazepine(DB00776)|Oxybutynin(DB01062)|Oxycodone(DB00497)|Paclitaxel(DB01229)|Paliperidone(DB01267)|Pentamidine(DB00738)|Perampanel(DB08883)|Phenelzine(DB00780)|Phenobarbital(DB01174)|Phenytoin(DB00252)|Pimozide(DB01100)|Ponatinib(DB08901)|Pravastatin(DB00175)|Praziquantel(DB01058)|Progesterone(DB00396)|Propranolol(DB00571)|Quetiapine(DB01224)|Quinacrine(DB01103)|Quinine(DB00468)|Ranitidine(DB00863)|Reserpine(DB00206)|Rifampicin(DB01045)|Rifapentine(DB01201)|Risperidone(DB00734)|Ritonavir(DB00503)|Rivaroxaban(DB06228)|Rosuvastatin(DB01098)|Salmeterol(DB00938)|Saquinavir(DB01232)|Saxagliptin(DB06335)|Sildenafil(DB00203)|Simvastatin(DB00641)|Sirolimus(DB00877)|Sorafenib(DB00398)|Sulfasalazine(DB00795)|Sunitinib(DB01268)|Tacrolimus(DB00864)|Tamoxifen(DB00675)|Telithromycin(DB00976)|Temsirolimus(DB06287)|Teniposide(DB00444)|Testosterone(DB00624)|Thalidomide(DB01041)|Trazodone(DB00656)|Tretinoin(DB00755)|Triazolam(DB00897)|Troleandomycin(DB01361)|Udenafil(DB06267)|Valproic Acid(DB00313)|Vardenafil(DB00862)|Verapamil(DB00661)|Vincristine(DB00541)|Voriconazole(DB00582)|Zalcitabine(DB00943)|Zaleplon(DB00962)|Ziprasidone(DB00246)|Zolpidem(DB00425)	TATGTAAGGATCTATGCTGTC	0.388																																					p.D427fs		.											.	.	.	0			c.1281delT						.						310.0	267.0	282.0					7																	99247829		2203	4300	6503	SO:0001589	frameshift_variant	1577	exon12			TAAGGATCTATGC	L26985	CCDS5672.1, CCDS55134.1	7q21.1	2007-12-14	2003-01-14		ENSG00000106258	ENSG00000106258		"""Cytochrome P450s"""	2638	protein-coding gene	gene with protein product		605325	"""cytochrome P450, subfamily IIIA (niphedipine oxidase), polypeptide 5"""				Standard	NR_033808		Approved	PCN3, P450PCN3, CP35		P20815	OTTHUMG00000156724	ENST00000222982.4:c.1280delA	7.37:g.99247829delT	ENSP00000222982:p.Asp427fs	Somatic	117	0		WXS	Illumina HiSeq	.	62	22	NM_000777	A4D289|B7Z5I7|Q53WY8|Q75MV0|Q9HB56	Frame_Shift_Del	DEL	ENST00000222982.4	37	CCDS5672.1																																																																																			.		0.388	CYP3A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345469.1		
NDUFA13	51079	hgsc.bcm.edu	37	19	19638817	19638818	+	Splice_Site	INS	-	-	G	rs111375911		TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr19:19638817_19638818insG	ENST00000507754.4	+	5	801_802	c.317_318insG	c.(316-321)gtgggg>gtGgggg	p.VG106fs	NDUFA13_ENST00000503283.1_Intron|YJEFN3_ENST00000514277.4_5'Flank|NDUFA13_ENST00000428459.2_3'UTR|YJEFN3_ENST00000436027.5_5'Flank|CTC-260F20.3_ENST00000555938.1_Intron|CTC-260F20.3_ENST00000586674.1_3'UTR|NDUFA13_ENST00000252576.5_Splice_Site_p.VG189fs|YJEFN3_ENST00000608404.1_Intron|NDUFA13_ENST00000512771.3_Splice_Site_p.VG106fs			Q9P0J0	NDUAD_HUMAN	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 13	106	Important for inducing cell death.				apoptotic signaling pathway (GO:0097190)|cellular metabolic process (GO:0044237)|cellular response to interferon-beta (GO:0035458)|cellular response to retinoic acid (GO:0071300)|negative regulation of cell growth (GO:0030308)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of peptidase activity (GO:0010952)|positive regulation of protein catabolic process (GO:0045732)|protein import into mitochondrial inner membrane (GO:0045039)|reactive oxygen species metabolic process (GO:0072593)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial membrane (GO:0031966)|mitochondrial respiratory chain (GO:0005746)|mitochondrial respiratory chain complex I (GO:0005747)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|NADH dehydrogenase (ubiquinone) activity (GO:0008137)|NADH dehydrogenase activity (GO:0003954)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(4)|ovary(1)	12						TCCCCACAGGTGGGGGAGTCTG	0.658																																					p.V106fs		.											.	.	.	0			c.317_318insG						.																																			SO:0001630	splice_region_variant	51079	exon5			CACAGGTGGGGGA	AF261134	CCDS12404.1, CCDS12404.2	19p13.11	2011-07-04			ENSG00000186010	ENSG00000186010		"""Mitochondrial respiratory chain complex / Complex I"""	17194	protein-coding gene	gene with protein product	"""complex I B16.6 subunit"""	609435				12837546, 10924506, 15367666	Standard	NM_015965		Approved	CGI-39, CDA016, GRIM-19, GRIM19, B16.6		Q9P0J0	OTTHUMG00000162211	ENST00000507754.4:c.316-1->G	19.37:g.19638822_19638822dupG		Somatic	89	0		WXS	Illumina HiSeq	.	52	12	NM_015965	B4DF76|K7EK58|Q6PKI0|Q9H2L3|Q9Y327	Frame_Shift_Ins	INS	ENST00000507754.4	37	CCDS12404.2																																																																																			.		0.658	NDUFA13-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367916.6	NM_015965	Frame_Shift_Ins
PEAK1	79834	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	15	77450866	77450885	+	Frame_Shift_Del	DEL	TACAAGGGTTCGGGTCCATA	TACAAGGGTTCGGGTCCATA	-	rs555412505		TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	TACAAGGGTTCGGGTCCATA	TACAAGGGTTCGGGTCCATA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr15:77450866_77450885delTACAAGGGTTCGGGTCCATA	ENST00000560626.2	-	5	3766_3785	c.3291_3310delTATGGACCCGAACCCTTGTA	c.(3289-3312)cctatggacccgaacccttgtagtfs	p.MDPNPCS1098fs	PEAK1_ENST00000312493.4_Frame_Shift_Del_p.MDPNPCS1098fs			Q9H792	PEAK1_HUMAN	pseudopodium-enriched atypical kinase 1	1098					cell migration (GO:0016477)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein autophosphorylation (GO:0046777)|substrate adhesion-dependent cell spreading (GO:0034446)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)										TATGTTGCACTACAAGGGTTCGGGTCCATAGGATCTGAAA	0.427																																					p.1098_1104del		.											.	.	.	0			c.3292_3311del						.																																			SO:0001589	frameshift_variant	0	exon6			TTGCACTACAAGG		CCDS42062.1	15q24.3	2013-09-27			ENSG00000173517	ENSG00000173517			29431	protein-coding gene	gene with protein product		614248				16879967, 20534451	Standard	NM_024776		Approved	KIAA2002, sgk269		Q9H792	OTTHUMG00000172618	ENST00000560626.2:c.3291_3310delTATGGACCCGAACCCTTGTA	15.37:g.77450866_77450885delTACAAGGGTTCGGGTCCATA	ENSP00000452796:p.Met1098fs	Somatic	86	0		WXS	Illumina HiSeq	.	47	13	NM_024776	Q6ZS78|Q8NAZ4|Q8NCM3|Q8TEG7	Frame_Shift_Del	DEL	ENST00000560626.2	37	CCDS42062.1																																																																																			.		0.427	PEAK1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419483.3		
TEX2	55852	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	17	62272276	62272283	+	Frame_Shift_Del	DEL	GATTTTCT	GATTTTCT	-			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	GATTTTCT	GATTTTCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr17:62272276_62272283delGATTTTCT	ENST00000583097.1	-	3	1989_1996	c.1817_1824delAGAAAATC	c.(1816-1824)cagaaaatcfs	p.QKI606fs	TEX2_ENST00000584379.1_Frame_Shift_Del_p.QKI606fs|TEX2_ENST00000258991.3_Frame_Shift_Del_p.QKI606fs			Q8IWB9	TEX2_HUMAN	testis expressed 2	606					signal transduction (GO:0007165)|sphingolipid metabolic process (GO:0006665)	integral component of membrane (GO:0016021)				breast(3)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(15)|ovary(1)|pancreas(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	41			BRCA - Breast invasive adenocarcinoma(8;1.33e-10)	READ - Rectum adenocarcinoma(1115;0.0689)		AGAGGTCATAGATTTTCTGGCTGATGTA	0.433																																					p.606_609del		.											.	.	.	0			c.1818_1825del						.																																			SO:0001589	frameshift_variant	55852	exon3			GTCATAGATTTTC	AB051525	CCDS11658.1, CCDS74131.1	17q23.3	2007-03-13	2007-03-13			ENSG00000136478			30884	protein-coding gene	gene with protein product	"""transmembrane protein 96"""		"""testis expressed sequence 2"""			11214970	Standard	XM_005257507		Approved	HT008, TMEM96, KIAA1738	uc002jee.3	Q8IWB9		ENST00000583097.1:c.1817_1824delAGAAAATC	17.37:g.62272276_62272283delGATTTTCT	ENSP00000462665:p.Gln606fs	Somatic	68	0		WXS	Illumina HiSeq	.	37	11	NM_018469	Q6AHZ5|Q8N3L0|Q9C0C5	Frame_Shift_Del	DEL	ENST00000583097.1	37																																																																																				.		0.433	TEX2-003	KNOWN	alternative_5_UTR|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000443745.1	NM_018469	
CYP3A5	1577	hgsc.bcm.edu	37	7	99247827	99247829	+	In_Frame_Del	DEL	GAT	GAT	-			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	GAT	GAT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr7:99247827_99247829delGAT	ENST00000222982.4	-	12	1379_1381	c.1280_1282delATC	c.(1279-1284)gatcct>gct	p.427_428DP>A	CYP3A5_ENST00000339843.2_3'UTR|CYP3A5_ENST00000343703.5_In_Frame_Del_p.417_418DP>A	NM_000777.3	NP_000768.1	P20815	CP3A5_HUMAN	cytochrome P450, family 3, subfamily A, polypeptide 5	427					alkaloid catabolic process (GO:0009822)|drug catabolic process (GO:0042737)|oxidative demethylation (GO:0070989)|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)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity (GO:0016491)|oxygen binding (GO:0019825)			NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	16	all_epithelial(64;2.77e-08)|Lung NSC(181;0.00396)|all_lung(186;0.00659)|Esophageal squamous(72;0.0166)				ado-trastuzumab emtansine(DB05773)|Alfentanil(DB00802)|Alprazolam(DB00404)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Amprenavir(DB00701)|Apixaban(DB06605)|Aprepitant(DB00673)|Argatroban(DB00278)|Aripiprazole(DB01238)|Artemether(DB06697)|Astemizole(DB00637)|Atorvastatin(DB01076)|Axitinib(DB06626)|Azelastine(DB00972)|Beclomethasone(DB00394)|Boceprevir(DB08873)|Brentuximab vedotin(DB08870)|Buprenorphine(DB00921)|Buspirone(DB00490)|Cabazitaxel(DB06772)|Caffeine(DB00201)|Carbamazepine(DB00564)|Chloramphenicol(DB00446)|Chloroquine(DB00608)|Chlorphenamine(DB01114)|Cilostazol(DB01166)|Cimetidine(DB00501)|Ciprofloxacin(DB00537)|Cisapride(DB00604)|Clarithromycin(DB01211)|Clonidine(DB00575)|Clopidogrel(DB00758)|Cocaine(DB00907)|Codeine(DB00318)|Crizotinib(DB08865)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dapsone(DB00250)|Dasatinib(DB01254)|Daunorubicin(DB00694)|Delavirdine(DB00705)|Dexamethasone(DB01234)|Dextromethorphan(DB00514)|Diazepam(DB00829)|Diltiazem(DB00343)|Disulfiram(DB00822)|Docetaxel(DB01248)|Dolutegravir(DB08930)|Domperidone(DB01184)|Dutasteride(DB01126)|Enzalutamide(DB08899)|Eplerenone(DB00700)|Erlotinib(DB00530)|Erythromycin(DB00199)|Estradiol(DB00783)|Estrone(DB00655)|Ethosuximide(DB00593)|Etoposide(DB00773)|Felodipine(DB01023)|Fentanyl(DB00813)|Finasteride(DB01216)|Fluconazole(DB00196)|Fluoxetine(DB00472)|Flutamide(DB00499)|Fluticasone Propionate(DB00588)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Gefitinib(DB00317)|Gestodene(DB06730)|Granisetron(DB00889)|Halofantrine(DB01218)|Haloperidol(DB00502)|Hydrocortisone(DB00741)|Ifosfamide(DB01181)|Iloperidone(DB04946)|Imatinib(DB00619)|Indinavir(DB00224)|Irinotecan(DB00762)|Itraconazole(DB01167)|Ketoconazole(DB01026)|Lapatinib(DB01259)|Lercanidipine(DB00528)|Levomethadyl Acetate(DB01227)|Lidocaine(DB00281)|Losartan(DB00678)|Lovastatin(DB00227)|Methadone(DB00333)|Midazolam(DB00683)|Mifepristone(DB00834)|Modafinil(DB00745)|Mycophenolate mofetil(DB00688)|Nateglinide(DB00731)|Nefazodone(DB01149)|Nelfinavir(DB00220)|Nevirapine(DB00238)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Norethindrone(DB00717)|Norfloxacin(DB01059)|Nortriptyline(DB00540)|Ondansetron(DB00904)|Oxazepam(DB00842)|Oxcarbazepine(DB00776)|Oxybutynin(DB01062)|Oxycodone(DB00497)|Paclitaxel(DB01229)|Paliperidone(DB01267)|Pentamidine(DB00738)|Perampanel(DB08883)|Phenelzine(DB00780)|Phenobarbital(DB01174)|Phenytoin(DB00252)|Pimozide(DB01100)|Ponatinib(DB08901)|Pravastatin(DB00175)|Praziquantel(DB01058)|Progesterone(DB00396)|Propranolol(DB00571)|Quetiapine(DB01224)|Quinacrine(DB01103)|Quinine(DB00468)|Ranitidine(DB00863)|Reserpine(DB00206)|Rifampicin(DB01045)|Rifapentine(DB01201)|Risperidone(DB00734)|Ritonavir(DB00503)|Rivaroxaban(DB06228)|Rosuvastatin(DB01098)|Salmeterol(DB00938)|Saquinavir(DB01232)|Saxagliptin(DB06335)|Sildenafil(DB00203)|Simvastatin(DB00641)|Sirolimus(DB00877)|Sorafenib(DB00398)|Sulfasalazine(DB00795)|Sunitinib(DB01268)|Tacrolimus(DB00864)|Tamoxifen(DB00675)|Telithromycin(DB00976)|Temsirolimus(DB06287)|Teniposide(DB00444)|Testosterone(DB00624)|Thalidomide(DB01041)|Trazodone(DB00656)|Tretinoin(DB00755)|Triazolam(DB00897)|Troleandomycin(DB01361)|Udenafil(DB06267)|Valproic Acid(DB00313)|Vardenafil(DB00862)|Verapamil(DB00661)|Vincristine(DB00541)|Voriconazole(DB00582)|Zalcitabine(DB00943)|Zaleplon(DB00962)|Ziprasidone(DB00246)|Zolpidem(DB00425)	TATATGTAAGGATCTATGCTGTC	0.384																																					p.427_428del		.											.	.	.	0			c.1281_1283del						.																																			SO:0001651	inframe_deletion	1577	exon12			TGTAAGGATCTAT	L26985	CCDS5672.1, CCDS55134.1	7q21.1	2007-12-14	2003-01-14		ENSG00000106258	ENSG00000106258		"""Cytochrome P450s"""	2638	protein-coding gene	gene with protein product		605325	"""cytochrome P450, subfamily IIIA (niphedipine oxidase), polypeptide 5"""				Standard	NR_033808		Approved	PCN3, P450PCN3, CP35		P20815	OTTHUMG00000156724	ENST00000222982.4:c.1280_1282delATC	7.37:g.99247827_99247829delGAT	ENSP00000222982:p.Asp427_Pro428delinsAla	Somatic	123	0		WXS	Illumina HiSeq	.	61	0	NM_000777	A4D289|B7Z5I7|Q53WY8|Q75MV0|Q9HB56	In_Frame_Del	DEL	ENST00000222982.4	37	CCDS5672.1																																																																																			.		0.384	CYP3A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345469.1		
PRDX1	5052	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	1	45984678	45984687	+	Frame_Shift_Del	DEL	GGGGCAGGGT	GGGGCAGGGT	-	rs11544934		TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	GGGGCAGGGT	GGGGCAGGGT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr1:45984678_45984687delGGGGCAGGGT	ENST00000262746.1	-	2	368_377	c.29_38delACCCTGCCCC	c.(28-39)caccctgcccccfs	p.HPAP10fs	PRDX1_ENST00000319248.8_Frame_Shift_Del_p.HPAP10fs|PRDX1_ENST00000372079.1_Frame_Shift_Del_p.HPAP10fs|PRDX1_ENST00000483583.1_5'UTR	NM_002574.3|NM_181696.2	NP_002565.1|NP_859047.1	Q06830	PRDX1_HUMAN	peroxiredoxin 1	10	Thioredoxin. {ECO:0000255|PROSITE- ProRule:PRU00691}.				cell proliferation (GO:0008283)|erythrocyte homeostasis (GO:0034101)|hydrogen peroxide catabolic process (GO:0042744)|natural killer cell mediated cytotoxicity (GO:0042267)|regulation of NF-kappaB import into nucleus (GO:0042345)|regulation of stress-activated MAPK cascade (GO:0032872)|removal of superoxide radicals (GO:0019430)|retina homeostasis (GO:0001895)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|nuclear euchromatin (GO:0005719)|nucleolus (GO:0005730)|nucleus (GO:0005634)|peroxisomal matrix (GO:0005782)	heme binding (GO:0020037)|peroxidase activity (GO:0004601)|poly(A) RNA binding (GO:0044822)|thioredoxin peroxidase activity (GO:0008379)			breast(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(5)|skin(1)	12	Acute lymphoblastic leukemia(166;0.155)					TTTGAAGTTGGGGGCAGGGTGCCCAATTTT	0.414																																					p.10_13del		.											.	.	.	0			c.30_39del						.																																			SO:0001589	frameshift_variant	5052	exon2			AAGTTGGGGGCAG	BC021683	CCDS522.1	1p34.1	2008-02-05			ENSG00000117450	ENSG00000117450			9352	protein-coding gene	gene with protein product		176763		PAGA		8496166	Standard	NM_181697		Approved	NKEFA	uc021omw.1	Q06830	OTTHUMG00000007738	ENST00000262746.1:c.29_38delACCCTGCCCC	1.37:g.45984678_45984687delGGGGCAGGGT	ENSP00000262746:p.His10fs	Somatic	100	0		WXS	Illumina HiSeq	.	49	10	NM_181696	B5BU26|D3DPZ8|P35703|Q2V576|Q5T154|Q5T155	Frame_Shift_Del	DEL	ENST00000262746.1	37	CCDS522.1																																																																																			.		0.414	PRDX1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020845.1	NM_181697	
TGFBR2	7048	hgsc.bcm.edu;bcgsc.ca	37	3	30664759	30664775	+	Intron	DEL	AGACATAGTAAAGTATC	AGACATAGTAAAGTATC	-	rs184395862|rs555904329|rs138262219	byFrequency	TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	AGACATAGTAAAGTATC	AGACATAGTAAAGTATC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr3:30664759_30664775delAGACATAGTAAAGTATC	ENST00000295754.5	+	1	476				TGFBR2_ENST00000359013.4_Splice_Site_p.RHS55fs	NM_003242.5	NP_003233.4	P37173	TGFR2_HUMAN	transforming growth factor, beta receptor II (70/80kDa)						activation of protein kinase activity (GO:0032147)|aging (GO:0007568)|apoptotic process (GO:0006915)|blood vessel development (GO:0001568)|brain development (GO:0007420)|bronchus morphogenesis (GO:0060434)|cartilage development (GO:0051216)|common-partner SMAD protein phosphorylation (GO:0007182)|digestive tract development (GO:0048565)|embryo implantation (GO:0007566)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic hemopoiesis (GO:0035162)|gastrulation (GO:0007369)|heart development (GO:0007507)|in utero embryonic development (GO:0001701)|lens development in camera-type eye (GO:0002088)|lens fiber cell apoptotic process (GO:1990086)|lung lobe morphogenesis (GO:0060463)|mammary gland morphogenesis (GO:0060443)|myeloid dendritic cell differentiation (GO:0043011)|negative regulation of cardiac muscle cell proliferation (GO:0060044)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|organ regeneration (GO:0031100)|palate development (GO:0060021)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|patterning of blood vessels (GO:0001569)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of angiogenesis (GO:0045766)|positive regulation of B cell tolerance induction (GO:0002663)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of NK T cell differentiation (GO:0051138)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of skeletal muscle tissue regeneration (GO:0043415)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of T cell tolerance induction (GO:0002666)|positive regulation of tolerance induction to self antigen (GO:0002651)|protein phosphorylation (GO:0006468)|receptor-mediated endocytosis (GO:0006898)|regulation of cell proliferation (GO:0042127)|response to cholesterol (GO:0070723)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|response to glucose (GO:0009749)|response to mechanical stimulus (GO:0009612)|response to nutrient (GO:0007584)|smoothened signaling pathway (GO:0007224)|trachea formation (GO:0060440)|transforming growth factor beta receptor signaling pathway (GO:0007179)|vasculogenesis (GO:0001570)|wound healing (GO:0042060)	caveola (GO:0005901)|cytosol (GO:0005829)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|transforming growth factor beta receptor homodimeric complex (GO:0070022)	ATP binding (GO:0005524)|glycosaminoglycan binding (GO:0005539)|metal ion binding (GO:0046872)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|SMAD binding (GO:0046332)|transforming growth factor beta binding (GO:0050431)|transforming growth factor beta receptor activity, type II (GO:0005026)|transforming growth factor beta-activated receptor activity (GO:0005024)|transmembrane receptor protein serine/threonine kinase activity (GO:0004675)|type I transforming growth factor beta receptor binding (GO:0034713)|type III transforming growth factor beta receptor binding (GO:0034714)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(15)|lung(10)|ovary(3)|pancreas(12)|skin(1)|stomach(5)|upper_aerodigestive_tract(2)	53						CCATCCACTGAGACATAGTAAAGTATCATTAATTAAT	0.346																																					p.54_57del		.											.	.	.	0			c.162_169del						.																																			SO:0001627	intron_variant	7048	exon2			CCACTGAGACATA		CCDS2648.1, CCDS33727.1	3p22	2014-09-17	2002-08-29		ENSG00000163513	ENSG00000163513			11773	protein-coding gene	gene with protein product		190182	"""transforming growth factor, beta receptor II (70-80kD)"""	MFS2		1319842, 15235604	Standard	NM_001024847		Approved		uc003cen.3	P37173	OTTHUMG00000130569	ENST00000295754.5:c.94+16290AGACATAGTAAAGTATC>-	3.37:g.30664759_30664775delAGACATAGTAAAGTATC		Somatic	99	0		WXS	Illumina HiSeq	.	20	4	NM_001024847	B4DTV5|Q15580|Q6DKT6|Q99474	Frame_Shift_Del	DEL	ENST00000295754.5	37	CCDS2648.1																																																																																			.		0.346	TGFBR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252994.2		
BAIAP3	8938	hgsc.bcm.edu	37	16	1393405	1393430	+	Frame_Shift_Del	DEL	TCAGCAGCCGCCACCATCAAACCTGC	TCAGCAGCCGCCACCATCAAACCTGC	-	rs576394425|rs545400434|rs199910590		TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	TCAGCAGCCGCCACCATCAAACCTGC	TCAGCAGCCGCCACCATCAAACCTGC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr16:1393405_1393430delTCAGCAGCCGCCACCATCAAACCTGC	ENST00000324385.5	+	15	1540_1565	c.1382_1407delTCAGCAGCCGCCACCATCAAACCTGC	c.(1381-1407)gtcagcagccgccaccatcaaacctgcfs	p.VSSRHHQTC461fs	BAIAP3_ENST00000562208.1_Frame_Shift_Del_p.VSSRHHQTC403fs|BAIAP3_ENST00000568887.1_Frame_Shift_Del_p.VSSRHHQTC398fs|BAIAP3_ENST00000426824.3_Frame_Shift_Del_p.VSSRHHQTC426fs|BAIAP3_ENST00000421665.2_Frame_Shift_Del_p.VSSRHHQTC390fs|BAIAP3_ENST00000397488.2_Frame_Shift_Del_p.VSSRHHQTC443fs|BAIAP3_ENST00000397489.1_Frame_Shift_Del_p.VSSRHHQTC443fs	NM_003933.4	NP_003924.2	O94812	BAIP3_HUMAN	BAI1-associated protein 3	461					G-protein coupled receptor signaling pathway (GO:0007186)|neurotransmitter secretion (GO:0007269)		protein C-terminus binding (GO:0008022)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(1)|lung(25)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	42		Hepatocellular(780;0.0893)				CACTGGCAGGTCAGCAGCCGCCACCATCAAACCTGCACGCTGGACT	0.65																																					p.461_469del		.											.	.	.	0			c.1381_1406del						.																																			SO:0001589	frameshift_variant	8938	exon15			GGCAGGTCAGCAG	AB017111	CCDS10434.1, CCDS55978.1, CCDS55979.1, CCDS58402.1, CCDS58403.1, CCDS66894.1	16p13.3	2008-07-04			ENSG00000007516	ENSG00000007516			948	protein-coding gene	gene with protein product		604009				9790924	Standard	NM_003933		Approved	BAP3, KIAA0734	uc002clk.2	O94812	OTTHUMG00000047833	ENST00000324385.5:c.1382_1407delTCAGCAGCCGCCACCATCAAACCTGC	16.37:g.1393405_1393430delTCAGCAGCCGCCACCATCAAACCTGC	ENSP00000324510:p.Val461fs	Somatic	95	0		WXS	Illumina HiSeq	.	50	0	NM_003933	A2A2B2|B2RCD7|B4DGS5|B4DIK3|B4DRK9|B4DRP1|E7EUB9|H3BUH8|H3BVI3|H7C2Q1|O94839|Q2M226|Q658J2|Q76N05|Q96RZ3|Q9UJK1	Frame_Shift_Del	DEL	ENST00000324385.5	37	CCDS10434.1																																																																																			.		0.650	BAIAP3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000109056.3		
ZNF720	124411	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	16	31734032	31734052	+	In_Frame_Del	DEL	GGGATGTGATGTTAGAGAACT	GGGATGTGATGTTAGAGAACT	-			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	GGGATGTGATGTTAGAGAACT	GGGATGTGATGTTAGAGAACT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr16:31734032_31734052delGGGATGTGATGTTAGAGAACT	ENST00000316491.9	+	2	288_308	c.89_109delGGGATGTGATGTTAGAGAACT	c.(88-111)ggggatgtgatgttagagaactac>gac	p.30_37GDVMLENY>D	ZNF720_ENST00000539915.1_Intron|ZNF720_ENST00000398696.3_Intron|ZNF720_ENST00000399681.3_5'UTR|ZNF720_ENST00000531864.2_Intron|ZNF720_ENST00000534369.1_Intron	NM_001130913.1	NP_001124385.1	Q7Z2F6	ZN720_HUMAN	zinc finger protein 720	30	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)	intracellular (GO:0005622)	nucleic acid binding (GO:0003676)			endometrium(1)|kidney(1)|lung(1)|stomach(1)	4						CTTTTATATGGGGATGTGATGTTAGAGAACTACGGAAACCT	0.403																																					p.30_36del		.											.	.	.	0			c.88_108del						.																																			SO:0001651	inframe_deletion	124411	exon2			TATATGGGGATGT	AK128671	CCDS45473.1	16p11.2	2013-01-08				ENSG00000197302		"""Zinc fingers, C2H2-type"", ""-"""	26987	protein-coding gene	gene with protein product							Standard	NM_001130913		Approved		uc002ecq.3	Q7Z2F6		ENST00000316491.9:c.89_109delGGGATGTGATGTTAGAGAACT	16.37:g.31734032_31734052delGGGATGTGATGTTAGAGAACT	ENSP00000319222:p.Gly30_Tyr37delinsAsp	Somatic	117	0		WXS	Illumina HiSeq	.	62	0	NM_001130913	Q6ZQX1	In_Frame_Del	DEL	ENST00000316491.9	37	CCDS45473.1																																																																																			.		0.403	ZNF720-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000394883.3	NM_001004300	
ACADVL	37	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	17	7124970	7124983	+	Frame_Shift_Del	DEL	GAAAGAAAAATACC	GAAAGAAAAATACC	-	rs371407903|rs530082418		TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	GAAAGAAAAATACC	GAAAGAAAAATACC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr17:7124970_7124983delGAAAGAAAAATACC	ENST00000356839.5	+	7	770_783	c.591_604delGAAAGAAAAATACC	c.(589-606)cagaaagaaaaatacctcfs	p.QKEKYL197fs	MIR324_ENST00000362183.1_RNA|DLG4_ENST00000399510.2_5'Flank|ACADVL_ENST00000581562.1_Intron|ACADVL_ENST00000543245.2_Frame_Shift_Del_p.QKEKYL220fs|ACADVL_ENST00000350303.5_Frame_Shift_Del_p.QKEKYL175fs	NM_000018.3|NM_001270448.1	NP_000009.1|NP_001257377.1	P49748	ACADV_HUMAN	acyl-CoA dehydrogenase, very long chain	197	Catalytic.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular lipid metabolic process (GO:0044255)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|energy derivation by oxidation of organic compounds (GO:0015980)|epithelial cell differentiation (GO:0030855)|fatty acid beta-oxidation (GO:0006635)|fatty acid beta-oxidation using acyl-CoA dehydrogenase (GO:0033539)|negative regulation of fatty acid biosynthetic process (GO:0045717)|negative regulation of fatty acid oxidation (GO:0046322)|regulation of cholesterol metabolic process (GO:0090181)|small molecule metabolic process (GO:0044281)|temperature homeostasis (GO:0001659)	cytoplasm (GO:0005737)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	acyl-CoA dehydrogenase activity (GO:0003995)|flavin adenine dinucleotide binding (GO:0050660)|long-chain-acyl-CoA dehydrogenase activity (GO:0004466)			breast(2)|cervix(2)|endometrium(6)|kidney(1)|large_intestine(2)|liver(2)|lung(1)|ovary(4)|skin(1)	21						CAAAGGCCCAGAAAGAAAAATACCTCCCCAAGCT	0.556																																					p.220_224del		.											.	.	.	0			c.659_672del	GRCh37	CM034379	ACADVL	M		.																																			SO:0001589	frameshift_variant	37	exon8			GGCCCAGAAAGAA	BC012912	CCDS11090.1, CCDS42249.1, CCDS58509.1	17p13.1	2010-04-30	2010-04-30		ENSG00000072778	ENSG00000072778			92	protein-coding gene	gene with protein product		609575	"""acyl-Coenzyme A dehydrogenase, very long chain"""			8921384	Standard	NM_000018		Approved	VLCAD, LCACD, ACAD6	uc002gev.4	P49748	OTTHUMG00000102157	ENST00000356839.5:c.591_604delGAAAGAAAAATACC	17.37:g.7124970_7124983delGAAAGAAAAATACC	ENSP00000349297:p.Gln197fs	Somatic	41	0		WXS	Illumina HiSeq	.	20	9	NM_001270447	B4DEB6|F5H2A9|O76056|Q8WUL0	Frame_Shift_Del	DEL	ENST00000356839.5	37	CCDS11090.1																																																																																			.		0.556	ACADVL-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000220001.5	NM_000018	
TBC1D10B	26000	hgsc.bcm.edu;broad.mit.edu	37	16	30369466	30369486	+	In_Frame_Del	DEL	CCGCTCCTTCTCCTGTTTCTG	CCGCTCCTTCTCCTGTTTCTG	-	rs144176745|rs549120802		TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	CCGCTCCTTCTCCTGTTTCTG	CCGCTCCTTCTCCTGTTTCTG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr16:30369466_30369486delCCGCTCCTTCTCCTGTTTCTG	ENST00000409939.3	-	9	2286_2306	c.2206_2226delCAGAAACAGGAGAAGGAGCGG	c.(2206-2226)cagaaacaggagaaggagcggdel	p.QKQEKER736del	RP11-347C12.10_ENST00000563252.1_lincRNA|CD2BP2_ENST00000305596.3_5'Flank	NM_015527.3	NP_056342.3	Q4KMP7	TB10B_HUMAN	TBC1 domain family, member 10B	736					positive regulation of Rab GTPase activity (GO:0032851)|regulation of Rab GTPase activity (GO:0032313)|retrograde transport, endosome to Golgi (GO:0042147)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	Rab GTPase activator activity (GO:0005097)			endometrium(2)|kidney(1)|lung(2)|urinary_tract(1)	6			Colorectal(24;0.193)			gctccttctcccgctccttctcctgtttctgccgctccttc	0.584																																					p.736_743del		.											.	.	.	0			c.2207_2227del						.																																			SO:0001651	inframe_deletion	26000	exon9			CTTCTCCCGCTCC	BC063112	CCDS10676.2	16p11.2	2013-07-09			ENSG00000169221	ENSG00000169221			24510	protein-coding gene	gene with protein product		613620				20404108	Standard	NM_015527		Approved	DKFZP434P1750, Rab27A-GAPbeta, FLJ13130, EPI64B	uc002dxt.3	Q4KMP7	OTTHUMG00000132396	ENST00000409939.3:c.2206_2226delCAGAAACAGGAGAAGGAGCGG	16.37:g.30369466_30369486delCCGCTCCTTCTCCTGTTTCTG	ENSP00000386538:p.Gln736_Arg742del	Somatic	77	0		WXS	Illumina HiSeq	.	58	2	NM_015527	B9A6L0|Q6IN54|Q6P530|Q71RG7|Q86VC5|Q9H8Z2|Q9NUN6|Q9UFP2	In_Frame_Del	DEL	ENST00000409939.3	37	CCDS10676.2																																																																																			.		0.584	TBC1D10B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255527.3	NM_015527	
R3HDM2	22864	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	12	57682695	57682711	+	Splice_Site	DEL	TGTTGGTTAACATCAAA	TGTTGGTTAACATCAAA	-			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	TGTTGGTTAACATCAAA	TGTTGGTTAACATCAAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr12:57682695_57682711delTGTTGGTTAACATCAAA	ENST00000347140.3	-	12	1233		c.e12-2		R3HDM2_ENST00000402412.1_Intron|R3HDM2_ENST00000413953.2_Intron|R3HDM2_ENST00000358907.2_Splice_Site|RP11-123K3.4_ENST00000548184.1_Intron|R3HDM2_ENST00000403821.2_Splice_Site			Q9Y2K5	R3HD2_HUMAN	R3H domain containing 2							nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(3)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	22						TTGGAGAGTCTGTTGGTTAACATCAAAGAAAAGCATC	0.364																																					.		.											.	.	.	0			.						.																																			SO:0001630	splice_region_variant	22864	.			AGAGTCTGTTGGT	AB023219	CCDS8937.2	12q13.3	2012-11-19			ENSG00000179912	ENSG00000179912			29167	protein-coding gene	gene with protein product							Standard	NM_014925		Approved	KIAA1002	uc009zpm.1	Q9Y2K5	OTTHUMG00000171568	ENST00000347140.3:c.843-2TTTGATGTTAACCAACA>-	12.37:g.57682695_57682711delTGTTGGTTAACATCAAA		Somatic	90	0		WXS	Illumina HiSeq	.	44	6	.	Q2M1T9|Q3ZCT5	Splice_Site	DEL	ENST00000347140.3	37	CCDS8937.2																																																																																			.		0.364	R3HDM2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326570.2	NM_014925	Intron
ATF6B	1388	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	6	32086802	32086813	+	In_Frame_Del	DEL	CAGTACTGCTTG	CAGTACTGCTTG	-			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	CAGTACTGCTTG	CAGTACTGCTTG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr6:32086802_32086813delCAGTACTGCTTG	ENST00000375203.3	-	10	1104_1115	c.1072_1083delCAAGCAGTACTG	c.(1072-1083)caagcagtactgdel	p.QAVL358del	ATF6B_ENST00000375201.4_In_Frame_Del_p.QAVL355del	NM_001136153.1|NM_004381.4	NP_001129625.1|NP_004372.3	Q99941	ATF6B_HUMAN	activating transcription factor 6 beta	358	bZIP. {ECO:0000255|PROSITE- ProRule:PRU00978}.				response to unfolded protein (GO:0006986)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(11)|prostate(2)|skin(1)|urinary_tract(1)	22						GGTTGTCAGCCAGTACTGCTTGCAGCCGAGCC	0.613																																					p.358_362del		.											.	.	.	0			c.1073_1084del						.																																			SO:0001651	inframe_deletion	1388	exon10			GTCAGCCAGTACT		CCDS47408.1, CCDS4737.1	6p21.3	2013-01-10	2008-10-21	2008-10-21	ENSG00000213676	ENSG00000213676		"""basic leucine zipper proteins"""	2349	protein-coding gene	gene with protein product		600984	"""cAMP responsive element binding protein-like 1"""	CREBL1		11256944, 14973138	Standard	NM_004381		Approved	G13	uc003nzn.3	Q99941	OTTHUMG00000031296	ENST00000375203.3:c.1072_1083delCAAGCAGTACTG	6.37:g.32086802_32086813delCAGTACTGCTTG	ENSP00000364349:p.Gln358_Leu361del	Somatic	58	0		WXS	Illumina HiSeq	.	44	19	NM_004381	B0UYX6|Q13269|Q14343|Q14345|Q5SSW7|Q99635|Q99637|Q9H3V9|Q9H3W1|Q9NPL0	In_Frame_Del	DEL	ENST00000375203.3	37	CCDS4737.1																																																																																			.		0.613	ATF6B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000076638.2		
COX20	116228	hgsc.bcm.edu	37	1	245006151	245006152	+	Intron	INS	-	-	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr1:245006151_245006152insA	ENST00000411948.2	+	4	614				HNRNPU-AS1_ENST00000489705.1_RNA|COX20_ENST00000498262.1_Intron|HNRNPU-AS1_ENST00000475997.1_RNA|COX20_ENST00000366528.3_Intron	NM_198076.4	NP_932342.1	Q5RI15	COX20_HUMAN	COX20 cytochrome C oxidase assembly factor							integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)											TTTTTCCTAATAAAAAAAGAAT	0.292																																					.		.											.	.	.	0			.						.																																			SO:0001627	intron_variant	284702	.			TCCTAATAAAAAA	BC062419	CCDS31080.1	1q44	2013-05-24	2013-05-23	2012-02-24	ENSG00000203667	ENSG00000203667		"""Mitochondrial respiratory chain complex assembly factors"""	26970	protein-coding gene	gene with protein product		614698	"""family with sequence similarity 36, member A"", ""COX20 Cox2 chaperone homolog (S. cerevisiae)"""	FAM36A		22356826, 23125284	Standard	NM_198076		Approved	FLJ43269	uc001iar.3	Q5RI15	OTTHUMG00000040401	ENST00000411948.2:c.222-191->A	1.37:g.245006158_245006158dupA		Somatic	25	0		WXS	Illumina HiSeq	.	33	18	.	Q8WV86	RNA	INS	ENST00000411948.2	37	CCDS31080.1																																																																																			.		0.292	COX20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097174.1	NM_198076	
MPDZ	8777	hgsc.bcm.edu;bcgsc.ca	37	9	13175817	13175837	+	In_Frame_Del	DEL	GCATGACACACTCAGCATTAC	GCATGACACACTCAGCATTAC	-	rs374056827|rs371781743|rs367967232		TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	GCATGACACACTCAGCATTAC	GCATGACACACTCAGCATTAC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr9:13175817_13175837delGCATGACACACTCAGCATTAC	ENST00000319217.7	-	21	3216_3236	c.2969_2989delGTAATGCTGAGTGTGTCATGC	c.(2968-2991)tgtaatgctgagtgtgtcatgctt>ttt	p.990_997CNAECVML>F	MPDZ_ENST00000541718.1_In_Frame_Del_p.990_997CNAECVML>F|MPDZ_ENST00000536827.1_In_Frame_Del_p.990_997CNAECVML>F|MPDZ_ENST00000381022.2_In_Frame_Del_p.990_997CNAECVML>F|MPDZ_ENST00000381015.4_In_Frame_Del_p.990_997CNAECVML>F|MPDZ_ENST00000447879.1_In_Frame_Del_p.990_997CNAECVML>F|MPDZ_ENST00000546205.1_In_Frame_Del_p.990_997CNAECVML>F	NM_001261406.1	NP_001248335.1	O75970	MPDZ_HUMAN	multiple PDZ domain protein	990					cell adhesion (GO:0007155)|myelination (GO:0042552)|viral process (GO:0016032)	apical plasma membrane (GO:0016324)|apicolateral plasma membrane (GO:0016327)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|neuron projection (GO:0043005)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)|tight junction (GO:0005923)	protein C-terminus binding (GO:0008022)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(14)|lung(15)|ovary(5)|prostate(7)|stomach(1)|urinary_tract(2)	61				GBM - Glioblastoma multiforme(50;2.03e-06)		ACATTTTGAAGCATGACACACTCAGCATTACAGGCCAGGGA	0.394																																					p.990_997del		.											.	.	.	0			c.2970_2990del						.																																			SO:0001651	inframe_deletion	8777	exon21			TTTGAAGCATGAC	AF093419	CCDS47951.1, CCDS59119.1, CCDS59120.1	9p23	2008-05-15			ENSG00000107186	ENSG00000107186			7208	protein-coding gene	gene with protein product		603785					Standard	NM_003829		Approved	MUPP1	uc003zlb.4	O75970	OTTHUMG00000021031	ENST00000319217.7:c.2969_2989delGTAATGCTGAGTGTGTCATGC	9.37:g.13175817_13175837delGCATGACACACTCAGCATTAC	ENSP00000320006:p.Cys990_Leu997delinsPhe	Somatic	84	0		WXS	Illumina HiSeq	.	42	0	NM_001261406	A6NLC2|B2RTS3|B7ZMI4|O43798|Q4LE30|Q5CZ80|Q5JTX3|Q5JTX6|Q5JTX7|Q5JUC3|Q5JUC4|Q5VZ62|Q8N790	In_Frame_Del	DEL	ENST00000319217.7	37																																																																																				.		0.394	MPDZ-001	KNOWN	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000055485.2	NM_003829	
CDKN1A	1026	hgsc.bcm.edu	37	6	36652119	36652192	+	Frame_Shift_Del	DEL	GGGCCCCGGCGAGGCCGGGATGAGTTGGGAGGAGGCAGGCGGCCTGGCACCTCACCTGCTCTGCTGCAGGGGAC	GGGCCCCGGCGAGGCCGGGATGAGTTGGGAGGAGGCAGGCGGCCTGGCACCTCACCTGCTCTGCTGCAGGGGAC	-	rs368592299|rs566071526|rs367848692|rs374965936|rs143676546|rs34916193|rs569995916|rs565736236|rs548336812|rs144146573|rs200191871|rs376278884	byFrequency	TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	GGGCCCCGGCGAGGCCGGGATGAGTTGGGAGGAGGCAGGCGGCCTGGCACCTCACCTGCTCTGCTGCAGGGGAC	GGGCCCCGGCGAGGCCGGGATGAGTTGGGAGGAGGCAGGCGGCCTGGCACCTCACCTGCTCTGCTGCAGGGGAC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr6:36652119_36652192delGGGCCCCGGCGAGGCCGGGATGAGTTGGGAGGAGGCAGGCGGCCTGGCACCTCACCTGCTCTGCTGCAGGGGAC	ENST00000405375.1	+	2	476_549	c.241_314delGGGCCCCGGCGAGGCCGGGATGAGTTGGGAGGAGGCAGGCGGCCTGGCACCTCACCTGCTCTGCTGCAGGGGAC	c.(241-315)gggccccggcgaggccgggatgagttgggaggaggcaggcggcctggcacctcacctgctctgctgcaggggacafs	p.GPRRGRDELGGGRRPGTSPALLQGT81fs	CDKN1A_ENST00000478800.1_3'UTR|CDKN1A_ENST00000373711.2_Frame_Shift_Del_p.GPRRGRDELGGGRRPGTSPALLQGT81fs|CDKN1A_ENST00000244741.5_Frame_Shift_Del_p.GPRRGRDELGGGRRPGTSPALLQGT81fs|CDKN1A_ENST00000448526.2_Frame_Shift_Del_p.GPRRGRDELGGGRRPGTSPALLQGT115fs	NM_001220778.1	NP_001207707.1	P38936	CDN1A_HUMAN	cyclin-dependent kinase inhibitor 1A (p21, Cip1)	81					cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to extracellular stimulus (GO:0031668)|cellular response to ionizing radiation (GO:0071479)|cellular senescence (GO:0090398)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle (GO:0000278)|mitotic cell cycle arrest (GO:0071850)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of gene expression (GO:0010629)|negative regulation of phosphorylation (GO:0042326)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ regeneration (GO:0031100)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of programmed cell death (GO:0043068)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|protein phosphorylation (GO:0006468)|Ras protein signal transduction (GO:0007265)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of DNA biosynthetic process (GO:2000278)|regulation of protein import into nucleus, translocation (GO:0033158)|response to arsenic-containing substance (GO:0046685)|response to corticosterone (GO:0051412)|response to drug (GO:0042493)|response to hyperoxia (GO:0055093)|response to organonitrogen compound (GO:0010243)|response to toxic substance (GO:0009636)|response to UV (GO:0009411)|stress-induced premature senescence (GO:0090400)	cyclin-dependent protein kinase holoenzyme complex (GO:0000307)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PCNA-p21 complex (GO:0070557)	cyclin-dependent protein kinase activating kinase activity (GO:0019912)|cyclin-dependent protein serine/threonine kinase inhibitor activity (GO:0004861)|metal ion binding (GO:0046872)|ubiquitin protein ligase binding (GO:0031625)	p.R86W(1)|p.R93S(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|liver(1)|lung(3)|ovary(1)|urinary_tract(5)	15						CCTTCCCACGGGGCCCCGGCGAGGCCGGGATGAGTTGGGAGGAGGCAGGCGGCCTGGCACCTCACCTGCTCTGCTGCAGGGGACAGCAGAGGAA	0.65																																					p.80_105del		.											.	.	.	2	Substitution - Missense(2)	lung(1)|kidney(1)	c.240_313del	GRCh37	CM065058	CDKN1A	M	rs34916193	.																																			SO:0001589	frameshift_variant	1026	exon2			CCCACGGGGCCCC	U03106	CCDS4824.1	6p21.1	2009-01-21			ENSG00000124762	ENSG00000124762			1784	protein-coding gene	gene with protein product		116899		CDKN1			Standard	NM_000389		Approved	P21, CIP1, WAF1, SDI1, CAP20, p21CIP1, p21Cip1/Waf1	uc021yzb.1	P38936	OTTHUMG00000014603	ENST00000405375.1:c.241_314delGGGCCCCGGCGAGGCCGGGATGAGTTGGGAGGAGGCAGGCGGCCTGGCACCTCACCTGCTCTGCTGCAGGGGAC	6.37:g.36652119_36652192delGGGCCCCGGCGAGGCCGGGATGAGTTGGGAGGAGGCAGGCGGCCTGGCACCTCACCTGCTCTGCTGCAGGGGAC	ENSP00000384849:p.Gly81fs	Somatic	37	0		WXS	Illumina HiSeq	.	35	0	NM_000389	Q14010|Q6FI05|Q9BUT4	Frame_Shift_Del	DEL	ENST00000405375.1	37	CCDS4824.1																																																																																			.		0.650	CDKN1A-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040354.1	NM_078467	
SENP2	59343	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	3	185329428	185329449	+	Splice_Site	DEL	GTGTTTCTAAGTTCTCAAAGAA	GTGTTTCTAAGTTCTCAAAGAA	-	rs542566238		TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	GTGTTTCTAAGTTCTCAAAGAA	GTGTTTCTAAGTTCTCAAAGAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr3:185329428_185329449delGTGTTTCTAAGTTCTCAAAGAA	ENST00000296257.5	+	8	962_973	c.722_733delGTGTTTCTAAGTTCTCAAAGAA	c.(721-735)agtgtttctaagttc>atc	p.SVSKF241fs	SENP2_ENST00000545472.1_Splice_Site_p.SVSKF231fs|SENP2_ENST00000427465.2_Splice_Site_p.SVSKF65fs	NM_021627.2	NP_067640.2	Q9HC62	SENP2_HUMAN	SUMO1/sentrin/SMT3 specific peptidase 2	241					cellular protein metabolic process (GO:0044267)|dorsal/ventral axis specification (GO:0009950)|heart development (GO:0007507)|labyrinthine layer development (GO:0060711)|mRNA transport (GO:0051028)|negative regulation of chromatin binding (GO:0035562)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|negative regulation of protein binding (GO:0032091)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-translational protein modification (GO:0043687)|protein desumoylation (GO:0016926)|protein sumoylation (GO:0016925)|protein transport (GO:0015031)|regulation of DNA endoreduplication (GO:0032875)|regulation of G1/S transition of mitotic cell cycle (GO:2000045)|regulation of Wnt signaling pathway (GO:0030111)|spongiotrophoblast layer development (GO:0060712)|trophoblast giant cell differentiation (GO:0060707)|Wnt signaling pathway (GO:0016055)	cytoplasmic vesicle (GO:0031410)|nuclear pore (GO:0005643)|nucleoplasm (GO:0005654)|PML body (GO:0016605)	SUMO-specific protease activity (GO:0016929)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(5)|skin(3)	12	all_cancers(143;1.28e-10)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(80;1.31e-21)			CTCACTTTTTGTGTTTCTAAGTTCTCAAAGAAGTCAGATGGA	0.392																																					p.241_244del		.											.	.	.	0			c.723_732del						.																																			SO:0001630	splice_region_variant	59343	exon8			CTTTTTGTGTTTC	AF151697	CCDS33902.1	3q28	2005-08-17	2005-08-17		ENSG00000163904	ENSG00000163904			23116	protein-coding gene	gene with protein product		608261	"""SUMO1/sentrin/SMT3 specific protease 2"""			11896061, 11489887	Standard	XM_005247690		Approved	SMT3IP2, KIAA1331, DKFZp762A2316, AXAM2	uc003fpn.3	Q9HC62	OTTHUMG00000156658	ENST00000296257.5:c.723-1GTGTTTCTAAGTTCTCAAAGAA>-	3.37:g.185329428_185329449delGTGTTTCTAAGTTCTCAAAGAA		Somatic	58	0		WXS	Illumina HiSeq	.	38	8	NM_021627	B4DQ42|Q8IW97|Q96SR2|Q9P2L5	Frame_Shift_Del	DEL	ENST00000296257.5	37	CCDS33902.1																																																																																			.		0.392	SENP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345159.1	NM_021627	Frame_Shift_Del
PDE4DIP	9659	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	1	144922029	144922029	+	Missense_Mutation	SNP	G	G	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr1:144922029G>C	ENST00000369354.3	-	9	1189	c.1000C>G	c.(1000-1002)Cca>Gca	p.P334A	PDE4DIP_ENST00000313431.9_Missense_Mutation_p.P497A|PDE4DIP_ENST00000313382.9_Missense_Mutation_p.P400A|PDE4DIP_ENST00000369349.3_Missense_Mutation_p.P334A|PDE4DIP_ENST00000369359.4_Missense_Mutation_p.P471A|PDE4DIP_ENST00000369356.4_Missense_Mutation_p.P334A|PDE4DIP_ENST00000369351.3_Missense_Mutation_p.P334A|PDE4DIP_ENST00000479408.2_Missense_Mutation_p.P121A|PDE4DIP_ENST00000529945.1_Missense_Mutation_p.P497A|PDE4DIP_ENST00000530740.1_Missense_Mutation_p.P471A			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	334					cellular protein complex assembly (GO:0043623)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|myofibril (GO:0030016)|nucleus (GO:0005634)	enzyme binding (GO:0019899)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(12)|lung(106)|ovary(8)|prostate(7)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	176				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		TGCTGAGCTGGAGAAGTACCC	0.458			T	PDGFRB	MPD																																p.P497A		.		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	.	.	.	0			c.C1489G						.						126.0	137.0	133.0					1																	144922029		2203	4296	6499	SO:0001583	missense	9659	exon5			GAGCTGGAGAAGT	AB007923, AB007946	CCDS72887.1, CCDS72888.1, CCDS72889.1, CCDS72890.1, CCDS72891.1, CCDS72892.1, CCDS72893.1, CCDS72894.1	1q21.1	2008-07-31	2008-07-31		ENSG00000178104	ENSG00000178104			15580	protein-coding gene	gene with protein product	"""myomegalin"""	608117	"""cardiomyopathy associated 2"""	CMYA2		9455484, 11134006	Standard	NM_022359		Approved	KIAA0477, KIAA0454, MMGL	uc021ouh.1	Q5VU43	OTTHUMG00000013846	ENST00000369354.3:c.1000C>G	1.37:g.144922029G>C	ENSP00000358360:p.Pro334Ala	Somatic	75	0		WXS	Illumina HiSeq	.	65	11	NM_001002811	A2RU15|O75042|O75065|Q2YDC1|Q5VU42|Q5VU44|Q5VU45|Q5VU46|Q5VU47|Q5VU48|Q5VU49|Q68DU2|Q6AZ93|Q6PK88|Q86T40|Q86TB2|Q8N3W0|Q8TAY9|Q9HCP2|Q9HCP3|Q9HCP4|Q9HCP5	Missense_Mutation	SNP	ENST00000369354.3	37	CCDS30824.1	.	.	.	.	.	.	.	.	.	.	G	7.920	0.738363	0.15574	.	.	ENSG00000178104	ENST00000313382;ENST00000369354;ENST00000369356;ENST00000369353;ENST00000530740;ENST00000369359;ENST00000369351;ENST00000369349;ENST00000313431;ENST00000529945;ENST00000479408	T;T;T;T;T;T;T;T;T;T	0.11063	4.82;4.92;4.92;4.92;4.92;3.93;3.93;2.82;2.83;2.81	5.68	2.74	0.32292	.	.	.	.	.	T	0.03783	0.0107	L	0.29908	0.895	0.80722	D	1	B;B;B;P;B	0.44241	0.0;0.001;0.0;0.829;0.003	B;B;B;P;B	0.46543	0.001;0.004;0.001;0.52;0.004	T	0.47623	-0.9103	9	0.15952	T	0.53	.	9.3565	0.38171	0.076:0.274:0.65:0.0	.	497;334;497;400;334	E9PL24;Q5VU43-7;Q5VU43-2;Q5VU43-3;Q5VU43	.;.;.;.;MYOME_HUMAN	A	400;334;334;497;471;471;334;334;497;497;121	ENSP00000327209:P400A;ENSP00000358360:P334A;ENSP00000358363:P334A;ENSP00000435654:P471A;ENSP00000358366:P471A;ENSP00000358357:P334A;ENSP00000358355:P334A;ENSP00000316434:P497A;ENSP00000433392:P497A;ENSP00000436791:P121A	ENSP00000327209:P400A	P	-	1	0	PDE4DIP	143633386	0.981000	0.34729	0.239000	0.24122	0.368000	0.29767	2.136000	0.42121	0.306000	0.22856	-0.172000	0.13284	CCA	.		0.458	PDE4DIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000038858.2	NM_022359	
PRDM13	59336	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	6	100062584	100062584	+	Silent	SNP	A	A	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr6:100062584A>G	ENST00000369215.4	+	4	2378	c.2073A>G	c.(2071-2073)acA>acG	p.T691T		NM_021620.3	NP_067633.2	Q9H4Q3	PRD13_HUMAN	PR domain containing 13	691					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neurogenesis (GO:0022008)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(9)|prostate(1)	17		all_cancers(76;1.64e-05)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(107;0.0128)|Colorectal(196;0.069)|Lung NSC(302;0.186)		BRCA - Breast invasive adenocarcinoma(108;0.0598)		TCTGCTTCACAGACGACCAGA	0.692																																					p.T691T		.											.	.	.	0			c.A2073G						.						30.0	33.0	32.0					6																	100062584		1678	3740	5418	SO:0001819	synonymous_variant	59336	exon4			CTTCACAGACGAC	AY004253	CCDS43487.1	6q16.2	2012-03-28			ENSG00000112238	ENSG00000112238			13998	protein-coding gene	gene with protein product							Standard	NM_021620		Approved		uc003pqg.1	Q9H4Q3	OTTHUMG00000015269	ENST00000369215.4:c.2073A>G	6.37:g.100062584A>G		Somatic	14	0		WXS	Illumina HiSeq	.	11	6	NM_021620	Q5TGC1|Q5TGC2	Silent	SNP	ENST00000369215.4	37	CCDS43487.1																																																																																			.		0.692	PRDM13-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041619.2		
FSTL4	23105	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	5	132561381	132561381	+	Silent	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr5:132561381T>G	ENST00000265342.7	-	9	1395	c.1146A>C	c.(1144-1146)tcA>tcC	p.S382S	FSTL4_ENST00000507112.1_5'UTR|CTB-49A3.2_ENST00000502776.1_RNA|CTB-49A3.2_ENST00000509051.1_RNA	NM_015082.1	NP_055897.1	Q6MZW2	FSTL4_HUMAN	follistatin-like 4	382	Ig-like 2.					extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(8)|skin(2)|upper_aerodigestive_tract(1)	23		all_cancers(142;0.244)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			ACATCTGAGTTGAGACATCCA	0.522																																					p.S382S		.											.	.	.	0			c.A1146C						.						147.0	136.0	140.0					5																	132561381		2203	4300	6503	SO:0001819	synonymous_variant	23105	exon9			CTGAGTTGAGACA	AB028984	CCDS34238.1	5q31.1	2013-01-29			ENSG00000053108	ENSG00000053108		"""EF-hand domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	21389	protein-coding gene	gene with protein product						10470851, 15527507	Standard	NM_015082		Approved	KIAA1061	uc003kyn.1	Q6MZW2	OTTHUMG00000162729	ENST00000265342.7:c.1146A>C	5.37:g.132561381T>G		Somatic	90	0		WXS	Illumina HiSeq	.	63	33	NM_015082	Q8TBU0|Q9UPU1	Silent	SNP	ENST00000265342.7	37	CCDS34238.1																																																																																			.		0.522	FSTL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370212.1	XM_048786	
LIMD1	8994	hgsc.bcm.edu;ucsc.edu	37	3	45719739	45719739	+	3'UTR	SNP	C	C	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr3:45719739C>G	ENST00000273317.4	+	0	3240				LIMD1-AS1_ENST00000429798.1_RNA|LIMD1-AS1_ENST00000427644.1_RNA	NM_014240.2	NP_055055.1	Q9UGP4	LIMD1_HUMAN	LIM domains containing 1						cell migration (GO:0016477)|cytoplasmic mRNA processing body assembly (GO:0033962)|cytoskeleton organization (GO:0007010)|gene silencing by miRNA (GO:0035195)|multicellular organismal development (GO:0007275)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of hippo signaling (GO:0035331)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of transcription, DNA-templated (GO:0045892)|osteoblast development (GO:0002076)|phosphorylation (GO:0016310)|positive regulation of gene silencing by miRNA (GO:2000637)|regulation of cell shape (GO:0008360)|regulation of transcription, DNA-templated (GO:0006355)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	adherens junction (GO:0005912)|cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|RISC complex (GO:0016442)	transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|skin(1)	10				BRCA - Breast invasive adenocarcinoma(193;0.011)|KIRC - Kidney renal clear cell carcinoma(197;0.0264)|Kidney(197;0.0315)		AGAGCTTCACCAAATCACAGA	0.423																																					.		.											.	.	.	0			.						.																																			SO:0001624	3_prime_UTR_variant	644714	.			CTTCACCAAATCA	AJ132408	CCDS2729.1	3p21.31	2008-02-01			ENSG00000144791	ENSG00000144791			6612	protein-coding gene	gene with protein product		604543				10647888	Standard	NM_014240		Approved		uc003coq.3	Q9UGP4	OTTHUMG00000133453	ENST00000273317.4:c.*1188C>G	3.37:g.45719739C>G		Somatic	74	0		WXS	Illumina HiSeq	.	23	14	.	Q17RQ1|Q9BQQ9|Q9NQ47	RNA	SNP	ENST00000273317.4	37	CCDS2729.1																																																																																			.		0.423	LIMD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257327.1	NM_014240	
SETX	23064	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	9	135204542	135204542	+	Missense_Mutation	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr9:135204542A>C	ENST00000224140.5	-	10	2625	c.2443T>G	c.(2443-2445)Ttg>Gtg	p.L815V	SETX_ENST00000393220.1_Missense_Mutation_p.L815V|SETX_ENST00000372169.2_Missense_Mutation_p.L815V	NM_015046.5	NP_055861.3	Q7Z333	SETX_HUMAN	senataxin	815					cell death (GO:0008219)|circadian rhythm (GO:0007623)|DNA duplex unwinding (GO:0032508)|double-strand break repair (GO:0006302)|RNA processing (GO:0006396)|termination of RNA polymerase II transcription (GO:0006369)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)			breast(7)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(25)|liver(1)|lung(36)|ovary(2)|prostate(2)|skin(1)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	97		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;6.82e-06)|Epithelial(140;0.000171)		GATACAGTCAAATTTTCATCT	0.343																																					p.L815V		.											.	.	.	0			c.T2443G						.						73.0	68.0	69.0					9																	135204542		2202	4299	6501	SO:0001583	missense	23064	exon10			CAGTCAAATTTTC	AB014525	CCDS6947.1	9q34	2014-09-17	2005-11-29	2005-11-29	ENSG00000107290	ENSG00000107290			445	protein-coding gene	gene with protein product		608465	"""amyotrophic lateral sclerosis 4"", ""spinocerebellar ataxia, recessive, non-Friedreich type 1"""	ALS4, SCAR1		9497266, 11022012	Standard	NM_015046		Approved	KIAA0625, AOA2	uc004cbk.3	Q7Z333	OTTHUMG00000020834	ENST00000224140.5:c.2443T>G	9.37:g.135204542A>C	ENSP00000224140:p.Leu815Val	Somatic	13	0		WXS	Illumina HiSeq	.	10	5	NM_015046	A2A396|B2RPB2|B5ME16|C9JQ10|O75120|Q3KQX4|Q5JUJ1|Q68DW5|Q6AZD7|Q7Z3J6|Q8WX33|Q9H9D1|Q9NVP9	Missense_Mutation	SNP	ENST00000224140.5	37	CCDS6947.1	.	.	.	.	.	.	.	.	.	.	A	9.624	1.134706	0.21123	.	.	ENSG00000107290	ENST00000224140;ENST00000372169;ENST00000393220	D;D;D	0.86627	-2.06;-2.15;-1.76	5.52	0.275	0.15659	.	8.965640	0.00166	N	0.000010	T	0.75997	0.3926	L	0.27053	0.805	0.09310	N	1	B;B;B	0.13145	0.007;0.001;0.007	B;B;B	0.10450	0.005;0.002;0.005	T	0.63673	-0.6584	10	0.02654	T	1	.	4.4586	0.11656	0.086:0.4116:0.3564:0.146	.	815;815;815	Q7Z333-3;Q7Z333;Q7Z333-4	.;SETX_HUMAN;.	V	815	ENSP00000224140:L815V;ENSP00000361242:L815V;ENSP00000376913:L815V	ENSP00000224140:L815V	L	-	1	2	SETX	134194363	.	.	0.026000	0.17262	0.083000	0.17756	.	.	0.087000	0.17167	-0.177000	0.13119	TTG	.		0.343	SETX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054774.3	NM_015046	
ABCC3	8714	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	17	48745811	48745811	+	Silent	SNP	G	G	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr17:48745811G>C	ENST00000285238.8	+	14	1883	c.1803G>C	c.(1801-1803)cgG>cgC	p.R601R		NM_003786.3	NP_003777.2	O15438	MRP3_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 3	601					bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|organic anion transmembrane transporter activity (GO:0008514)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(11)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	33			BRCA - Breast invasive adenocarcinoma(22;3.05e-09)		Cisplatin(DB00515)|Clotrimazole(DB00257)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Doxorubicin(DB00997)|Etoposide(DB00773)|Ezetimibe(DB00973)|Fluorouracil(DB00544)|Folic Acid(DB00158)|Gadoxetate(DB08884)|Glutathione(DB00143)|Glyburide(DB01016)|Indomethacin(DB00328)|Lamivudine(DB00709)|Leucovorin(DB00650)|Methotrexate(DB00563)|Metyrapone(DB01011)|Nifedipine(DB01115)|Omeprazole(DB00338)|Phenobarbital(DB01174)|Probenecid(DB01032)|Rifampicin(DB01045)|Sulfinpyrazone(DB01138)|Verapamil(DB00661)|Vincristine(DB00541)	CTCTGAAACGGATCCAGCAAT	0.592																																					p.R601R		.											.	.	.	0			c.G1803C						.						102.0	96.0	98.0					17																	48745811		2203	4300	6503	SO:0001819	synonymous_variant	8714	exon14			GAAACGGATCCAG	Y17151	CCDS32681.1, CCDS45739.1	17q21	2012-03-14			ENSG00000108846	ENSG00000108846		"""ATP binding cassette transporters / subfamily C"""	54	protein-coding gene	gene with protein product	"""canalicular multispecific organic anion transporter 2"""	604323				8894702, 9827529	Standard	NM_003786		Approved	MRP3, cMOAT2, EST90757, MLP2, MOAT-D	uc002isl.3	O15438	OTTHUMG00000162245	ENST00000285238.8:c.1803G>C	17.37:g.48745811G>C		Somatic	82	0		WXS	Illumina HiSeq	.	46	16	NM_003786	B2RPA9|D3DTX9|O60265|O60922|O75621|O95078|O95289|O95290|Q86X85|Q9UN52	Silent	SNP	ENST00000285238.8	37	CCDS32681.1																																																																																			.		0.592	ABCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368083.2	NM_020038	
ISL2	64843	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	15	76632810	76632810	+	Silent	SNP	C	C	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr15:76632810C>A	ENST00000290759.4	+	4	865	c.705C>A	c.(703-705)atC>atA	p.I235I	RP11-685G9.2_ENST00000559539.1_RNA	NM_145805.1	NP_665804.1	Q96A47	ISL2_HUMAN	ISL LIM homeobox 2	235					negative regulation of neuron differentiation (GO:0045665)|neuron development (GO:0048666)|peripheral nervous system neuron development (GO:0048935)|regulation of transcription, DNA-templated (GO:0006355)|retinal ganglion cell axon guidance (GO:0031290)|spinal cord motor neuron cell fate specification (GO:0021520)|visceral motor neuron differentiation (GO:0021524)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)			breast(1)|kidney(1)|lung(2)|ovary(1)|skin(1)	6						CGCGGGTCATCCGCGTCTGGT	0.622																																					p.I235I	GBM(97;953 1391 16164 31496 36951)	.											.	.	.	0			c.C705A						.						35.0	40.0	38.0					15																	76632810		2196	4291	6487	SO:0001819	synonymous_variant	64843	exon4			GGTCATCCGCGTC	AK001022	CCDS10290.1	15q24.3	2012-03-09	2007-07-13		ENSG00000159556	ENSG00000159556		"""Homeoboxes / LIM class"""	18524	protein-coding gene	gene with protein product		609481	"""ISL2 transcription factor, LIM/homeodomain, (islet-2)"""				Standard	NM_145805		Approved	FLJ10160	uc002bbw.1	Q96A47	OTTHUMG00000143723	ENST00000290759.4:c.705C>A	15.37:g.76632810C>A		Somatic	71	0		WXS	Illumina HiSeq	.	63	21	NM_145805	B3KM37	Silent	SNP	ENST00000290759.4	37	CCDS10290.1																																																																																			.		0.622	ISL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000289779.1		
RCOR1	23186	hgsc.bcm.edu	37	14	103173699	103173699	+	Missense_Mutation	SNP	G	G	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr14:103173699G>A	ENST00000570597.1	+	5	501	c.501G>A	c.(499-501)atG>atA	p.M167I	RCOR1_ENST00000262241.6_Missense_Mutation_p.M170I			Q9UKL0	RCOR1_HUMAN	REST corepressor 1	167	ELM2. {ECO:0000255|PROSITE- ProRule:PRU00512}.|Interaction with HDAC1.				blood coagulation (GO:0007596)|histone H4 deacetylation (GO:0070933)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|viral process (GO:0016032)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)	12						CTCTTGGGATGCTCTTCTGGC	0.348																																					p.M170I		.											.	.	.	0			c.G510A						.						116.0	116.0	116.0					14																	103173699		2203	4300	6503	SO:0001583	missense	23186	exon5			TGGGATGCTCTTC	AF155595	CCDS9974.1, CCDS9974.2	14q32.33	2004-04-16	2004-04-16	2004-04-16		ENSG00000089902			17441	protein-coding gene	gene with protein product		607675	"""REST corepressor"""	RCOR		10449787	Standard	NM_015156		Approved	COREST, KIAA0071	uc001ymb.4	Q9UKL0		ENST00000570597.1:c.501G>A	14.37:g.103173699G>A	ENSP00000459789:p.Met167Ile	Somatic	69	0		WXS	Illumina HiSeq	.	45	3	NM_015156	Q15044|Q6P2I9|Q86VG5	Missense_Mutation	SNP	ENST00000570597.1	37		.	.	.	.	.	.	.	.	.	.	G	27.9	4.872915	0.91664	.	.	ENSG00000089902	ENST00000262241	.	.	.	4.98	4.98	0.66077	ELM2 domain (1);	0.000000	0.85682	D	0.000000	T	0.77538	0.4145	M	0.70595	2.14	0.80722	D	1	P	0.50528	0.936	P	0.61201	0.885	T	0.80353	-0.1418	9	0.87932	D	0	-24.1451	18.6211	0.91321	0.0:0.0:1.0:0.0	.	167	Q9UKL0	RCOR1_HUMAN	I	167	.	ENSP00000262241:M167I	M	+	3	0	RCOR1	102243452	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.779000	0.99018	2.480000	0.83734	0.655000	0.94253	ATG	.		0.348	RCOR1-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_015156	
XYLB	9942	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	3	38401886	38401886	+	Missense_Mutation	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr3:38401886T>G	ENST00000207870.3	+	3	287	c.197T>G	c.(196-198)cTa>cGa	p.L66R	XYLB_ENST00000542835.1_Intron	NM_005108.3	NP_005099.2	O75191	XYLB_HUMAN	xylulokinase homolog (H. influenzae)	66					carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|D-xylose metabolic process (GO:0042732)|generation of precursor metabolites and energy (GO:0006091)|xylulose catabolic process (GO:0005998)|xylulose metabolic process (GO:0005997)	extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|xylulokinase activity (GO:0004856)			endometrium(3)|kidney(3)|large_intestine(3)|liver(1)|lung(12)|ovary(1)|prostate(1)	24				KIRC - Kidney renal clear cell carcinoma(284;0.00372)|Kidney(284;0.00405)		TCTCCAGTACTAATGTGGGTC	0.537																																					p.L66R		.											.	.	.	0			c.T197G						.						257.0	199.0	218.0					3																	38401886		2203	4300	6503	SO:0001583	missense	9942	exon3			CAGTACTAATGTG	AB015046	CCDS2678.1	3p22-p21.3	2006-12-18	2001-12-04		ENSG00000093217	ENSG00000093217			12839	protein-coding gene	gene with protein product		604049	"""xylulokinase (H. influenzae) homolog"""			9763671	Standard	NM_005108		Approved	FLJ10343, FLJ12539	uc003cic.2	O75191	OTTHUMG00000131294	ENST00000207870.3:c.197T>G	3.37:g.38401886T>G	ENSP00000207870:p.Leu66Arg	Somatic	37	0		WXS	Illumina HiSeq	.	13	11	NM_005108	B2RAW4|B4DDT2|B9EH64	Missense_Mutation	SNP	ENST00000207870.3	37	CCDS2678.1	.	.	.	.	.	.	.	.	.	.	T	20.9	4.059854	0.76074	.	.	ENSG00000093217	ENST00000207870	T	0.44482	0.92	5.32	5.32	0.75619	Carbohydrate kinase, FGGY, N-terminal (1);	0.151906	0.45361	D	0.000376	T	0.47173	0.1431	M	0.69523	2.12	0.80722	D	1	B	0.34290	0.447	B	0.40009	0.316	T	0.41179	-0.9523	10	0.26408	T	0.33	.	13.5419	0.61679	0.0:0.0:0.0:1.0	.	66	O75191	XYLB_HUMAN	R	66	ENSP00000207870:L66R	ENSP00000207870:L66R	L	+	2	0	XYLB	38376890	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	4.892000	0.63193	2.152000	0.67230	0.533000	0.62120	CTA	.		0.537	XYLB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254062.2	NM_005108	
UROD	7389	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	45478646	45478646	+	Missense_Mutation	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr1:45478646T>G	ENST00000246337.4	+	2	207	c.88T>G	c.(88-90)Tac>Gac	p.Y30D	UROD_ENST00000494399.1_3'UTR|HECTD3_ENST00000372172.4_5'Flank	NM_000374.4	NP_000365.3	P06132	DCUP_HUMAN	uroporphyrinogen decarboxylase	30					heme biosynthetic process (GO:0006783)|porphyrin-containing compound metabolic process (GO:0006778)|protoporphyrinogen IX biosynthetic process (GO:0006782)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	uroporphyrinogen decarboxylase activity (GO:0004853)			endometrium(1)|large_intestine(1)|lung(1)|upper_aerodigestive_tract(1)	4	Acute lymphoblastic leukemia(166;0.155)					GGAAACAGACTACACTCCCGT	0.547									Porphyria Cutanea Tarda, Type II																												p.Y30D		.											.	.	.	0			c.T88G						.						54.0	50.0	52.0					1																	45478646		2203	4300	6503	SO:0001583	missense	7389	exon2	Familial Cancer Database	PCT-II	ACAGACTACACTC	BC001778	CCDS518.1	1p34	2012-10-02			ENSG00000126088	ENSG00000126088	4.1.1.37		12591	protein-coding gene	gene with protein product		613521				3015909, 3460962	Standard	NM_000374		Approved		uc001cna.2	P06132	OTTHUMG00000008949	ENST00000246337.4:c.88T>G	1.37:g.45478646T>G	ENSP00000246337:p.Tyr30Asp	Somatic	72	0		WXS	Illumina HiSeq	.	26	11	NM_000374	A8K762|Q16863|Q16883|Q53YB8|Q53ZP6|Q6IB28|Q9BUZ0	Missense_Mutation	SNP	ENST00000246337.4	37	CCDS518.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	15.90|15.90	2.968361|2.968361	0.53614|0.53614	.|.	.|.	ENSG00000126088|ENSG00000126088	ENST00000428106|ENST00000246337;ENST00000434478;ENST00000372135;ENST00000372139	.|D;D	.|0.94376	.|-3.34;-3.41	6.07|6.07	6.07|6.07	0.98685|0.98685	.|Uroporphyrinogen decarboxylase (URO-D) (1);	.|0.100341	.|0.64402	.|D	.|0.000002	D|D	0.95427|0.95427	0.8515|0.8515	M|M	0.78285|0.78285	2.405|2.405	0.40573|0.40573	D|D	0.981325|0.981325	.|D;P	.|0.58970	.|0.984;0.853	.|P;P	.|0.62184	.|0.899;0.791	D|D	0.95294|0.95294	0.8397|0.8397	5|10	.|0.52906	.|T	.|0.07	-10.9656|-10.9656	8.5313|8.5313	0.33335|0.33335	0.0:0.1458:0.0:0.8542|0.0:0.1458:0.0:0.8542	.|.	.|30;30	.|B4DHV6;P06132	.|.;DCUP_HUMAN	R|D	23|30;30;30;23	.|ENSP00000246337:Y30D;ENSP00000404489:Y30D	.|ENSP00000246337:Y30D	L|Y	+|+	2|1	0|0	UROD|UROD	45251233|45251233	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	2.597000|2.597000	0.46214|0.46214	2.326000|2.326000	0.78906|0.78906	0.533000|0.533000	0.62120|0.62120	CTA|TAC	.		0.547	UROD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024803.1	NM_000374	
IL33	90865	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	9	6254494	6254494	+	Missense_Mutation	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr9:6254494A>C	ENST00000381434.3	+	6	566	c.553A>C	c.(553-555)Acc>Ccc	p.T185P	IL33_ENST00000456383.2_Missense_Mutation_p.T143P|IL33_ENST00000417746.2_Missense_Mutation_p.T59P	NM_033439.3	NP_254274.1	O95760	IL33_HUMAN	interleukin 33	185					extrinsic apoptotic signaling pathway (GO:0097191)|negative regulation of immunoglobulin secretion (GO:0051025)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of leukocyte migration (GO:0002686)|negative regulation of T-helper 1 type immune response (GO:0002826)|positive regulation of chemokine secretion (GO:0090197)|positive regulation of immunoglobulin secretion (GO:0051024)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interleukin-13 production (GO:0032736)|positive regulation of interleukin-4 production (GO:0032753)|positive regulation of interleukin-5 production (GO:0032754)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of macrophage activation (GO:0043032)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type 2 immune response (GO:0002830)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|cytoplasmic vesicle (GO:0031410)|extracellular space (GO:0005615)|nucleus (GO:0005634)	cytokine activity (GO:0005125)			breast(3)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(4)|stomach(1)|urinary_tract(1)	16		Acute lymphoblastic leukemia(23;0.158)|Prostate(43;0.167)		GBM - Glioblastoma multiforme(50;0.0161)|Lung(218;0.105)		GTTAATGGTAACCCTGAGTCC	0.303																																					p.T185P		.											.	.	.	0			c.A553C						.						76.0	74.0	75.0					9																	6254494		2203	4300	6503	SO:0001583	missense	90865	exon7			ATGGTAACCCTGA	AB024518	CCDS6468.1, CCDS56563.1, CCDS56564.1	9p24.1	2014-01-28	2006-11-20	2006-11-20	ENSG00000137033	ENSG00000137033		"""Interleukins and interleukin receptors"""	16028	protein-coding gene	gene with protein product	"""DVS27-related protein"", ""nuclear factor for high endothelial venules"", ""interleukin-1 family, member 11"""	608678	"""chromosome 9 open reading frame 26 (NF-HEV)"""	C9orf26		10566975, 12819012	Standard	NM_033439		Approved	DVS27, DKFZp586H0523, NF-HEV, IL1F11	uc003zjt.3	O95760	OTTHUMG00000019516	ENST00000381434.3:c.553A>C	9.37:g.6254494A>C	ENSP00000370842:p.Thr185Pro	Somatic	73	0		WXS	Illumina HiSeq	.	34	16	NM_033439	B2R8L1|B4DJ35|B4E1Q9|D3DRI5|E7EAX4|Q2YEJ5	Missense_Mutation	SNP	ENST00000381434.3	37	CCDS6468.1	.	.	.	.	.	.	.	.	.	.	A	9.992	1.231057	0.22626	.	.	ENSG00000137033	ENST00000417746;ENST00000456383;ENST00000381434	T;T;T	0.46451	0.87;0.87;0.87	4.71	2.2	0.27929	.	0.868933	0.10081	N	0.718491	T	0.21227	0.0511	N	0.08118	0	0.09310	N	1	B;B;B	0.29552	0.051;0.248;0.248	B;B;B	0.28139	0.058;0.086;0.086	T	0.17349	-1.0372	10	0.56958	D	0.05	-11.3276	4.5547	0.12131	0.7027:0.1961:0.1013:0.0	.	59;143;185	B4DJ35;B4E1Q9;O95760	.;.;IL33_HUMAN	P	59;143;185	ENSP00000394039:T59P;ENSP00000414238:T143P;ENSP00000370842:T185P	ENSP00000370842:T185P	T	+	1	0	IL33	6244494	0.840000	0.29493	0.218000	0.23776	0.777000	0.43975	1.454000	0.35178	0.929000	0.37192	-0.274000	0.10170	ACC	.		0.303	IL33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051655.1	NM_033439	
SKP2	6502	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	5	36181926	36181926	+	Silent	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr5:36181926T>G	ENST00000274255.6	+	10	1264	c.1068T>G	c.(1066-1068)ctT>ctG	p.L356L	SKP2_ENST00000274254.5_Intron|SKP2_ENST00000546211.1_Silent_p.L142L|SKP2_ENST00000508514.1_Silent_p.L149L	NM_005983.3	NP_005974.2	Q13309	SKP2_HUMAN	S-phase kinase-associated protein 2, E3 ubiquitin protein ligase	356					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell proliferation (GO:0008283)|cellular response to cell-matrix adhesion (GO:0071460)|G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of smooth muscle cell proliferation (GO:0048661)|protein polyubiquitination (GO:0000209)|regulation of cell cycle (GO:0051726)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SCF ubiquitin ligase complex (GO:0019005)	identical protein binding (GO:0042802)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|central_nervous_system(2)|ovary(1)	4	all_lung(31;5.63e-05)		Epithelial(62;0.0396)|Lung(74;0.111)|all cancers(62;0.115)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			CCAGTGAACTTGGAGAAATTC	0.363																																					p.L356L		.											.	.	.	0			c.T1068G						.						101.0	110.0	107.0					5																	36181926		2203	4300	6503	SO:0001819	synonymous_variant	6502	exon10			TGAACTTGGAGAA	U33761	CCDS3915.1, CCDS3916.1, CCDS58944.1	5p13	2012-02-23	2012-02-23		ENSG00000145604	ENSG00000145604		"""F-boxes / Leucine-rich repeats"""	10901	protein-coding gene	gene with protein product		601436	"""S-phase kinase-associated protein 2 (p45)"""			8646875	Standard	NM_005983		Approved	FBXL1, FBL1, p45	uc003jkc.2	Q13309	OTTHUMG00000131106	ENST00000274255.6:c.1068T>G	5.37:g.36181926T>G		Somatic	72	0		WXS	Illumina HiSeq	.	95	18	NM_005983	A8K5E0|B4DJT4|Q8TDZ0|Q8TDZ1|Q9BV69	Silent	SNP	ENST00000274255.6	37	CCDS3916.1																																																																																			.		0.363	SKP2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253769.2	NM_005983	
PPP1R3C	5507	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	10	93390426	93390426	+	Missense_Mutation	SNP	T	T	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr10:93390426T>C	ENST00000238994.5	-	2	296	c.212A>G	c.(211-213)cAg>cGg	p.Q71R		NM_005398.5	NP_005389.1			protein phosphatase 1, regulatory subunit 3C											breast(1)|endometrium(1)|large_intestine(5)|lung(4)|upper_aerodigestive_tract(1)	12		Colorectal(252;0.235)				CCAGTCATTCTGTGATTTGGC	0.458																																					p.Q71R		.											.	.	.	0			c.A212G						.						172.0	169.0	170.0					10																	93390426		2203	4300	6503	SO:0001583	missense	5507	exon2			TCATTCTGTGATT	Y18207	CCDS7416.1	10q23-q24	2012-04-17	2011-10-04	2001-08-01	ENSG00000119938	ENSG00000119938		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	9293	protein-coding gene	gene with protein product	"""Phosphatase 1, regulatory inhibitor subunit 5"", ""protein targeting to glycogen"""	602999	"""protein phosphatase 1, regulatory (inhibitor) subunit 3C"""	PPP1R5		8985175	Standard	NM_005398		Approved	PTG	uc001kho.3	Q9UQK1	OTTHUMG00000018745	ENST00000238994.5:c.212A>G	10.37:g.93390426T>C	ENSP00000238994:p.Gln71Arg	Somatic	88	0		WXS	Illumina HiSeq	.	51	29	NM_005398		Missense_Mutation	SNP	ENST00000238994.5	37	CCDS7416.1	.	.	.	.	.	.	.	.	.	.	T	5.080	0.200389	0.09652	.	.	ENSG00000119938	ENST00000238994;ENST00000438999	T	0.42131	0.98	5.79	5.79	0.91817	.	0.428734	0.24384	N	0.038988	T	0.27134	0.0665	L	0.31664	0.95	0.19300	N	0.99998	B	0.14012	0.009	B	0.08055	0.003	T	0.16188	-1.0411	10	0.17369	T	0.5	-11.806	7.2004	0.25877	0.0:0.0726:0.1478:0.7797	.	71	Q9UQK1	PPR3C_HUMAN	R	71	ENSP00000238994:Q71R	ENSP00000238994:Q71R	Q	-	2	0	PPP1R3C	93380406	0.979000	0.34478	0.999000	0.59377	0.951000	0.60555	0.724000	0.25954	2.207000	0.71202	0.533000	0.62120	CAG	.		0.458	PPP1R3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049372.1	NM_005398	
MALAT1	378938	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	11	65268625	65268625	+	lincRNA	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr11:65268625T>G	ENST00000534336.1	+	0	3393				AP000769.7_ENST00000602344.1_lincRNA	NR_002819.2		Q9UHZ2	MALAT_HUMAN	metastasis associated lung adenocarcinoma transcript 1 (non-protein coding)																		TGTTTTTACTTCCTCACCCTG	0.383																																					.		.											.	.	.	0			.						.						57.0	64.0	62.0					11																	65268625		874	1988	2862			378938	.			TTTACTTCCTCAC	AF001540		11q13.1	2013-12-11	2007-11-20		ENSG00000251562	ENSG00000251562		"""Long non-coding RNAs"", ""-"""	29665	non-coding RNA	RNA, long non-coding	"""metastasis associated in lung adenocarcinoma transcript 1"", ""non-protein coding RNA 47"", ""hepcarcin"", ""nuclear enriched abundant transcript 2"", ""nuclear paraspeckle assembly transcript 2 (non-protein coding)"", ""long intergenic non-protein coding RNA 47"""	607924				12970751, 22560368	Standard	NR_002819		Approved	PRO1073, MALAT-1, NCRNA00047, HCN, NEAT2, LINC00047, mascRNA	uc010roh.3	Q9UHZ2	OTTHUMG00000166322		11.37:g.65268625T>G		Somatic	91	0		WXS	Illumina HiSeq	.	47	26	.		RNA	SNP	ENST00000534336.1	37																																																																																				.		0.383	MALAT1-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000389143.1	NR_002819	
C1S	716	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	12	7177759	7177759	+	Missense_Mutation	SNP	G	G	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr12:7177759G>A	ENST00000406697.1	+	15	2499	c.1871G>A	c.(1870-1872)gGc>gAc	p.G624D	C1S_ENST00000360817.5_Missense_Mutation_p.G624D|C1S_ENST00000328916.3_Missense_Mutation_p.G624D|C1S_ENST00000402681.3_Missense_Mutation_p.G457D			P09871	C1S_HUMAN	complement component 1, s subcomponent	624	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|innate immune response (GO:0045087)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|serine-type endopeptidase activity (GO:0004252)			breast(1)|endometrium(5)|kidney(2)|large_intestine(8)|liver(4)|lung(8)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	33					Abciximab(DB00054)|Adalimumab(DB00051)|Basiliximab(DB00074)|Cetuximab(DB00002)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Muromonab(DB00075)|Rituximab(DB00073)|Trastuzumab(DB00072)	GGAGAGAAGGGCATGGATAGC	0.512																																					p.G624D	GBM(156;750 1943 12971 24779 31015)	.											.	.	.	0			c.G1871A						.						132.0	135.0	134.0					12																	7177759		2203	4300	6503	SO:0001583	missense	716	exon12			AGAAGGGCATGGA		CCDS31735.1	12p13	2014-09-17			ENSG00000182326	ENSG00000182326	3.4.21.42	"""Complement system"""	1247	protein-coding gene	gene with protein product		120580					Standard	NM_201442		Approved		uc001qsl.3	P09871	OTTHUMG00000150305	ENST00000406697.1:c.1871G>A	12.37:g.7177759G>A	ENSP00000385035:p.Gly624Asp	Somatic	94	0		WXS	Illumina HiSeq	.	46	27	NM_201442	D3DUT4|Q9UCU7|Q9UCU8|Q9UCU9|Q9UCV0|Q9UCV1|Q9UCV2|Q9UCV3|Q9UCV4|Q9UCV5|Q9UM14	Missense_Mutation	SNP	ENST00000406697.1	37	CCDS31735.1	.	.	.	.	.	.	.	.	.	.	G	17.25	3.342991	0.61073	.	.	ENSG00000182326	ENST00000406697;ENST00000328916;ENST00000360817;ENST00000382222;ENST00000402681	T;T;T;T	0.79653	-1.29;-1.29;-1.29;-1.29	5.01	4.12	0.48240	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.000000	0.43416	D	0.000563	D	0.84460	0.5477	L	0.48174	1.505	0.45318	D	0.998316	D	0.69078	0.997	D	0.66716	0.946	D	0.85467	0.1170	10	0.87932	D	0	.	11.3954	0.49838	0.088:0.0:0.912:0.0	.	624	P09871	C1S_HUMAN	D	624;624;624;618;457	ENSP00000385035:G624D;ENSP00000328173:G624D;ENSP00000354057:G624D;ENSP00000384171:G457D	ENSP00000328173:G624D	G	+	2	0	C1S	7048020	1.000000	0.71417	0.031000	0.17742	0.543000	0.35085	5.439000	0.66556	1.332000	0.45431	0.561000	0.74099	GGC	.		0.512	C1S-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317481.1	NM_001734	
AGO3	192669	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	36506015	36506015	+	Silent	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr1:36506015A>C	ENST00000373191.4	+	16	2494	c.2145A>C	c.(2143-2145)cgA>cgC	p.R715R	AGO3_ENST00000246314.6_Silent_p.R481R	NM_024852.3	NP_079128.2	Q9H9G7	AGO3_HUMAN	argonaute RISC catalytic component 3	715	Piwi. {ECO:0000255|HAMAP-Rule:MF_03032}.				epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|innate immune response (GO:0045087)|mRNA catabolic process (GO:0006402)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)|regulation of stem cell proliferation (GO:0072091)	cytosol (GO:0005829)|membrane (GO:0016020)|micro-ribonucleoprotein complex (GO:0035068)|RISC complex (GO:0016442)	miRNA binding (GO:0035198)|poly(A) RNA binding (GO:0044822)										ATCACACTCGATTATTTTGTG	0.378																																					p.R715R		.											.	.	.	0			c.A2145C						.						136.0	127.0	130.0					1																	36506015		2202	4300	6502	SO:0001819	synonymous_variant	192669	exon16			CACTCGATTATTT	AB046787	CCDS399.1, CCDS400.1	1p34	2013-06-03	2013-02-15	2013-02-15	ENSG00000126070	ENSG00000126070		"""Argonaute/PIWI family"""	18421	protein-coding gene	gene with protein product	"""argonaute 3"""	607355	"""eukaryotic translation initiation factor 2C, 3"""	EIF2C3		12906857	Standard	NM_024852		Approved	hAGO3, FLJ12765	uc001bzp.3	Q9H9G7	OTTHUMG00000184172	ENST00000373191.4:c.2145A>C	1.37:g.36506015A>C		Somatic	59	0		WXS	Illumina HiSeq	.	45	17	NM_024852	B1ALI0|Q5TA55|Q9H1U6	Silent	SNP	ENST00000373191.4	37	CCDS399.1																																																																																			.		0.378	AGO3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019831.4	NM_024852	
MYO7A	4647	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	11	76885944	76885944	+	Missense_Mutation	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr11:76885944A>C	ENST00000409709.3	+	17	2350	c.2078A>C	c.(2077-2079)aAg>aCg	p.K693T	MYO7A_ENST00000409893.1_Missense_Mutation_p.K693T|MYO7A_ENST00000409619.2_Missense_Mutation_p.K682T|MYO7A_ENST00000458637.2_Missense_Mutation_p.K693T	NM_000260.3	NP_000251.3	Q13402	MYO7A_HUMAN	myosin VIIA	693	Myosin motor.				actin filament-based movement (GO:0030048)|auditory receptor cell stereocilium organization (GO:0060088)|equilibrioception (GO:0050957)|eye photoreceptor cell development (GO:0042462)|intracellular protein transport (GO:0006886)|lysosome organization (GO:0007040)|metabolic process (GO:0008152)|phagolysosome assembly (GO:0001845)|pigment granule transport (GO:0051904)|post-embryonic organ morphogenesis (GO:0048563)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|lysosomal membrane (GO:0005765)|melanosome (GO:0042470)|myosin VII complex (GO:0031477)|photoreceptor connecting cilium (GO:0032391)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|stereocilium (GO:0032420)|synapse (GO:0045202)	actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|spectrin binding (GO:0030507)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(32)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	64						CCAGGTGTGAAGCCGGCCTAC	0.592																																					p.K693T		.											.	.	.	0			c.A2078C						.						48.0	52.0	51.0					11																	76885944		2045	4177	6222	SO:0001583	missense	4647	exon17			GTGTGAAGCCGGC	U39226	CCDS53683.1, CCDS53684.1, CCDS53685.1	11q13.5	2013-01-08	2005-09-12		ENSG00000137474	ENSG00000137474		"""A-kinase anchor proteins"", ""Myosins / Myosin superfamily : Class VII"""	7606	protein-coding gene	gene with protein product		276903	"""myosin VIIA (Usher syndrome 1B (autosomal recessive, severe))"""	USH1B, DFNB2, DFNA11		8884266	Standard	NM_000260		Approved	NSRD2	uc001oyb.2	Q13402	OTTHUMG00000152822	ENST00000409709.3:c.2078A>C	11.37:g.76885944A>C	ENSP00000386331:p.Lys693Thr	Somatic	25	0		WXS	Illumina HiSeq	.	35	13	NM_001127179	B9A011|F8VUN5|P78427|Q13321|Q14785|Q92821|Q92822	Missense_Mutation	SNP	ENST00000409709.3	37	CCDS53683.1	.	.	.	.	.	.	.	.	.	.	A	16.18	3.051133	0.55218	.	.	ENSG00000137474	ENST00000409709;ENST00000409893;ENST00000458637;ENST00000409619;ENST00000358342;ENST00000343356;ENST00000341717;ENST00000343419	D;D;D;D	0.86865	-2.18;-2.18;-2.18;-2.18	5.21	5.21	0.72293	Myosin head, motor domain (2);	0.000000	0.85682	D	0.000000	D	0.86694	0.5994	N	0.25647	0.755	0.58432	D	0.999999	P;B;P	0.47191	0.891;0.024;0.605	P;B;P	0.55508	0.777;0.022;0.601	D	0.85944	0.1460	10	0.33940	T	0.23	.	15.091	0.72195	1.0:0.0:0.0:0.0	.	693;693;693	B9A012;F8VUN5;Q13402	.;.;MYO7A_HUMAN	T	693;693;693;682;692;692;569;692	ENSP00000386331:K693T;ENSP00000386689:K693T;ENSP00000392185:K693T;ENSP00000386635:K682T	ENSP00000345075:K569T	K	+	2	0	MYO7A	76563592	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	8.866000	0.92307	1.972000	0.57404	0.391000	0.25812	AAG	.		0.592	MYO7A-001	KNOWN	non_canonical_conserved|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000328133.1	NM_000260	
MEIS2	4212	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	15	37329152	37329152	+	Missense_Mutation	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr15:37329152A>C	ENST00000561208.1	-	8	1181	c.763T>G	c.(763-765)Tta>Gta	p.L255V	MEIS2_ENST00000397620.2_Missense_Mutation_p.L167V|MEIS2_ENST00000397624.3_Missense_Mutation_p.L167V|MEIS2_ENST00000338564.5_Missense_Mutation_p.L255V|MEIS2_ENST00000340545.5_Missense_Mutation_p.L242V|MEIS2_ENST00000444725.1_Missense_Mutation_p.L255V|MEIS2_ENST00000559085.1_Missense_Mutation_p.L242V|MEIS2_ENST00000382766.2_Missense_Mutation_p.L255V|MEIS2_ENST00000219869.9_Missense_Mutation_p.L109V|MEIS2_ENST00000559561.1_Missense_Mutation_p.L255V|MEIS2_ENST00000557796.2_Missense_Mutation_p.L242V|MEIS2_ENST00000424352.2_Missense_Mutation_p.L255V			O14770	MEIS2_HUMAN	Meis homeobox 2	255	Asp/Glu-rich (acidic).				eye development (GO:0001654)|negative regulation of myeloid cell differentiation (GO:0045638)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|pancreas development (GO:0031016)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to growth factor (GO:0070848)|response to mechanical stimulus (GO:0009612)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription cofactor activity (GO:0003712)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(7)|lung(17)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	36		all_epithelial(112;9.77e-14)|Lung NSC(122;1.42e-09)|all_lung(180;2.2e-08)|Ovarian(310;0.134)|Melanoma(134;0.155)		all cancers(64;9.33e-21)|GBM - Glioblastoma multiforme(113;1.71e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0288)		CTGTTGTCTAAACCATCCCCT	0.418																																					p.L255V		.											.	.	.	0			c.T763G						.						137.0	121.0	127.0					15																	37329152		2201	4297	6498	SO:0001583	missense	4212	exon8			TGTCTAAACCATC	AF017418	CCDS10044.1, CCDS10045.1, CCDS42014.1, CCDS45217.1, CCDS45218.1, CCDS45219.1, CCDS45220.1	15q14	2011-06-20	2007-02-15		ENSG00000134138	ENSG00000134138		"""Homeoboxes / TALE class"""	7001	protein-coding gene	gene with protein product		601740	"""Meis (mouse) homolog 2"", ""Meis1, myeloid ecotropic viral integration site 1 homolog 2 (mouse)"""			9383298	Standard	NM_172315		Approved	MRG1, HsT18361	uc001zjr.4	O14770	OTTHUMG00000129781	ENST00000561208.1:c.763T>G	15.37:g.37329152A>C	ENSP00000453793:p.Leu255Val	Somatic	80	0		WXS	Illumina HiSeq	.	45	16	NM_170676	A6NJI5|A8MWD5|B3KP98|B3KPQ6|Q96DI2|Q96KI4|Q96KI5|Q9NRS1|Q9NRS2|Q9NRS3	Missense_Mutation	SNP	ENST00000561208.1	37	CCDS10044.1	.	.	.	.	.	.	.	.	.	.	A	2.882	-0.231572	0.05983	.	.	ENSG00000134138	ENST00000314177;ENST00000338564;ENST00000382766;ENST00000424352;ENST00000444725;ENST00000340545;ENST00000397624;ENST00000397620;ENST00000219869	T;D;D;D;D;D;D;D	0.89415	1.87;-2.24;-2.24;-2.14;-2.2;-2.2;-2.2;-2.51	5.14	1.47	0.22746	.	0.000000	0.64402	D	0.000001	D	0.89812	0.6823	L	0.55834	1.745	0.58432	D	0.999991	B;D;P;P;B;B;P;B	0.54047	0.212;0.964;0.589;0.498;0.426;0.118;0.651;0.053	B;P;B;B;B;B;B;B	0.60789	0.059;0.879;0.223;0.23;0.053;0.034;0.424;0.04	D	0.85864	0.1412	10	0.33141	T	0.24	-5.3547	8.9998	0.36074	0.7828:0.0:0.2172:0.0	.	242;255;255;255;255;109;167;242	Q96DI2;O14770-4;O14770;O14770-3;O14770-2;B3KP81;B3KPQ6;B3KP98	.;.;MEIS2_HUMAN;.;.;.;.;.	V	255;255;255;255;255;242;242;167;109	ENSP00000326296:L255V;ENSP00000341400:L255V;ENSP00000372216:L255V;ENSP00000404185:L255V;ENSP00000391887:L255V;ENSP00000339549:L242V;ENSP00000380745:L167V;ENSP00000219869:L109V	ENSP00000219869:L109V	L	-	1	2	MEIS2	35116444	1.000000	0.71417	0.999000	0.59377	0.998000	0.95712	4.343000	0.59348	0.343000	0.23821	0.528000	0.53228	TTA	.		0.418	MEIS2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252003.2	NM_170677	
RREB1	6239	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	6	7249158	7249158	+	Missense_Mutation	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr6:7249158T>G	ENST00000349384.6	+	12	5335	c.5021T>G	c.(5020-5022)cTg>cGg	p.L1674R	RREB1_ENST00000379933.3_Missense_Mutation_p.L1674R|RREB1_ENST00000334984.6_Missense_Mutation_p.L1463R|RREB1_ENST00000379938.2_Missense_Mutation_p.L1729R	NM_001003698.3	NP_001003698.1	Q92766	RREB1_HUMAN	ras responsive element binding protein 1	1674					multicellular organismal development (GO:0007275)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|Ras protein signal transduction (GO:0007265)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear body (GO:0016604)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(5)|lung(18)|ovary(5)|pancreas(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	58	Ovarian(93;0.0398)	all_hematologic(90;0.0384)|Prostate(151;0.191)				CACCCAATCCTGGCCACAGCT	0.652																																					p.L1729R		.											.	.	.	0			c.T5186G						.						6.0	7.0	7.0					6																	7249158		2130	4201	6331	SO:0001583	missense	6239	exon13			CAATCCTGGCCAC	U26914	CCDS34335.1, CCDS34336.1, CCDS54963.1	6p25	2013-01-08			ENSG00000124782	ENSG00000124782		"""Zinc fingers, C2H2-type"""	10449	protein-coding gene	gene with protein product	"""hindsight homolog (drosophila)"""	602209				9367691, 18394891	Standard	NM_001003698		Approved	HNT	uc003mxb.3	Q92766	OTTHUMG00000014201	ENST00000349384.6:c.5021T>G	6.37:g.7249158T>G	ENSP00000305560:p.Leu1674Arg	Somatic	45	0		WXS	Illumina HiSeq	.	28	14	NM_001003699	A2RRF5|E2GM80|E2GM81|O75567|O75568|Q5VYB2|Q6BEP5|Q6BEP6|Q6BEP8|Q86SU2|Q9Y474	Missense_Mutation	SNP	ENST00000349384.6	37	CCDS34336.1	.	.	.	.	.	.	.	.	.	.	T	6.171	0.399711	0.11696	.	.	ENSG00000124782	ENST00000379933;ENST00000379938;ENST00000349384;ENST00000334984	T;T;T;T	0.39787	1.75;1.63;1.75;1.06	4.79	2.41	0.29592	.	.	.	.	.	T	0.44138	0.1279	M	0.67953	2.075	0.09310	N	1	D;D;D	0.89917	0.989;0.994;1.0	P;P;D	0.87578	0.885;0.77;0.998	T	0.26916	-1.0089	9	0.87932	D	0	-6.205	7.5154	0.27598	0.0:0.1709:0.0:0.8291	.	1463;1674;1729	Q92766-3;Q92766;Q92766-2	.;RREB1_HUMAN;.	R	1674;1729;1674;1463	ENSP00000369265:L1674R;ENSP00000369270:L1729R;ENSP00000305560:L1674R;ENSP00000335574:L1463R	ENSP00000335574:L1463R	L	+	2	0	RREB1	7194157	0.998000	0.40836	0.009000	0.14445	0.030000	0.12068	2.771000	0.47670	0.229000	0.21039	0.260000	0.18958	CTG	.		0.652	RREB1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000352985.1		
RHPN1	114822	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	8	144462004	144462004	+	Silent	SNP	A	A	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr8:144462004A>G	ENST00000289013.6	+	9	1052	c.951A>G	c.(949-951)gcA>gcG	p.A317A		NM_052924.2	NP_443156.2	Q8TCX5	RHPN1_HUMAN	rhophilin, Rho GTPase binding protein 1	317	BRO1. {ECO:0000255|PROSITE- ProRule:PRU00526}.				signal transduction (GO:0007165)		small GTPase regulator activity (GO:0005083)			endometrium(1)|large_intestine(1)|lung(7)	9	all_cancers(97;7.39e-11)|all_epithelial(106;5.44e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000459)|Ovarian(258;0.0212)|Acute lymphoblastic leukemia(118;0.155)		Colorectal(110;0.107)|BRCA - Breast invasive adenocarcinoma(115;0.156)			GGCAGGTGGCAGCCGAGTACA	0.662																																					p.A317A		.											.	.	.	0			c.A951G						.						18.0	28.0	25.0					8																	144462004		2080	4153	6233	SO:0001819	synonymous_variant	114822	exon9			GGTGGCAGCCGAG	AB067516	CCDS47927.1	8q24.3	2003-02-06			ENSG00000158106	ENSG00000158106			19973	protein-coding gene	gene with protein product		601031				11572484	Standard	NM_052924		Approved	KIAA1929, RHPN, ODF5	uc003yyb.3	Q8TCX5	OTTHUMG00000165006	ENST00000289013.6:c.951A>G	8.37:g.144462004A>G		Somatic	45	0		WXS	Illumina HiSeq	.	37	20	NM_052924	Q8TAV1|Q96PV9	Silent	SNP	ENST00000289013.6	37	CCDS47927.1																																																																																			.		0.662	RHPN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381417.1		
CPSF1	29894	hgsc.bcm.edu;bcgsc.ca	37	8	145623960	145623960	+	Silent	SNP	G	G	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr8:145623960G>A	ENST00000349769.3	-	18	1801	c.1707C>T	c.(1705-1707)ggC>ggT	p.G569G	MIR1234_ENST00000408875.1_RNA	NM_013291.2	NP_037423.2	Q10570	CPSF1_HUMAN	cleavage and polyadenylation specific factor 1, 160kDa	569					gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA cleavage (GO:0006379)|mRNA export from nucleus (GO:0006406)|mRNA polyadenylation (GO:0006378)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	mRNA cleavage and polyadenylation specificity factor complex (GO:0005847)|nucleoplasm (GO:0005654)	mRNA 3'-UTR binding (GO:0003730)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(15)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	38	all_cancers(97;6.64e-12)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.88e-41)|Epithelial(56;1.67e-40)|all cancers(56;1.2e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0323)|Colorectal(110;0.055)			CGTGTCTGCGGCCGTCGTCGT	0.682																																					p.G569G	NSCLC(133;1088 1848 27708 34777 35269)	.											.	.	.	0			c.C1707T						.						104.0	105.0	105.0					8																	145623960		2203	4300	6503	SO:0001819	synonymous_variant	29894	exon18			TCTGCGGCCGTCG	U37012	CCDS34966.1	8q24	2014-05-06	2002-08-29		ENSG00000071894	ENSG00000071894			2324	protein-coding gene	gene with protein product		606027	"""cleavage and polyadenylation specific factor 1, 160kD subunit"""			7651824, 7590244	Standard	NM_013291		Approved		uc003zcj.3	Q10570	OTTHUMG00000174612	ENST00000349769.3:c.1707C>T	8.37:g.145623960G>A		Somatic	97	0		WXS	Illumina HiSeq	.	71	4	NM_013291	Q96AF0	Silent	SNP	ENST00000349769.3	37	CCDS34966.1																																																																																			.		0.682	CPSF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382422.2	NM_013291	
SNED1	25992	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	2	242008393	242008393	+	Missense_Mutation	SNP	C	C	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr2:242008393C>A	ENST00000310397.8	+	23	3262	c.3262C>A	c.(3262-3264)Cac>Aac	p.H1088N	SNED1_ENST00000342631.6_Missense_Mutation_p.H1088N|SNED1_ENST00000401884.1_Missense_Mutation_p.H1088N|SNED1_ENST00000405547.3_Missense_Mutation_p.H1088N	NM_001080437.1	NP_001073906.1	Q8TER0	SNED1_HUMAN	sushi, nidogen and EGF-like domains 1	1088	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell-matrix adhesion (GO:0007160)	extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|central_nervous_system(3)|kidney(2)|large_intestine(6)|lung(4)|ovary(3)|prostate(3)|upper_aerodigestive_tract(1)	24		all_cancers(19;7.48e-31)|all_epithelial(40;1.35e-12)|Breast(86;0.000148)|Renal(207;0.00528)|Ovarian(221;0.104)|Esophageal squamous(248;0.131)|all_lung(227;0.17)|all_hematologic(139;0.182)|Melanoma(123;0.238)		Epithelial(32;6.46e-32)|all cancers(36;6.23e-29)|OV - Ovarian serous cystadenocarcinoma(60;2.1e-14)|Kidney(56;6.35e-09)|KIRC - Kidney renal clear cell carcinoma(57;5.98e-08)|BRCA - Breast invasive adenocarcinoma(100;3.66e-06)|Lung(119;0.00072)|LUSC - Lung squamous cell carcinoma(224;0.00553)|Colorectal(34;0.0162)|COAD - Colon adenocarcinoma(134;0.109)		GGGAGAGGAGCACCCCACAGA	0.657																																					p.H1088N		.											.	.	.	0			c.C3262A						.						21.0	26.0	24.0					2																	242008393		2054	4136	6190	SO:0001583	missense	25992	exon23			GAGGAGCACCCCA	AK074062	CCDS46562.1	2q37.3	2014-01-28			ENSG00000162804	ENSG00000162804		"""Fibronectin type III domain containing"""	24696	protein-coding gene	gene with protein product						12477932	Standard	NM_001080437		Approved	FLJ00133, SST3, Snep	uc002wah.1	Q8TER0	OTTHUMG00000151803	ENST00000310397.8:c.3262C>A	2.37:g.242008393C>A	ENSP00000308893:p.His1088Asn	Somatic	73	0		WXS	Illumina HiSeq	.	70	27	NM_001080437	B5MDC3|B7WNK6|B7WPM0|Q336F4|Q336F5|Q8N369|Q8TEP7	Missense_Mutation	SNP	ENST00000310397.8	37	CCDS46562.1	.	.	.	.	.	.	.	.	.	.	C	13.30	2.194592	0.38806	.	.	ENSG00000162804	ENST00000401884;ENST00000405547;ENST00000310397;ENST00000342631	T;T;T;T	0.53206	0.63;0.63;0.63;0.63	5.25	3.39	0.38822	Fibronectin, type III (2);	0.595365	0.15726	N	0.247678	T	0.26376	0.0644	N	0.24115	0.695	0.09310	N	0.999998	P;P;B	0.39665	0.682;0.491;0.332	B;B;B	0.33620	0.158;0.085;0.167	T	0.10245	-1.0638	10	0.08837	T	0.75	.	9.1399	0.36897	0.1471:0.7755:0.0:0.0774	.	1088;1088;1088	Q8TER0-5;B5MEF5;Q8TER0	.;.;SNED1_HUMAN	N	1088	ENSP00000384871:H1088N;ENSP00000386007:H1088N;ENSP00000308893:H1088N;ENSP00000342992:H1088N	ENSP00000308893:H1088N	H	+	1	0	SNED1	241657066	0.000000	0.05858	0.002000	0.10522	0.842000	0.47809	0.117000	0.15583	0.551000	0.29008	0.585000	0.79938	CAC	.		0.657	SNED1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323935.2	XM_059482	
SLC25A27	9481	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	6	46630146	46630146	+	Silent	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr6:46630146T>G	ENST00000371347.5	+	4	669	c.417T>G	c.(415-417)gtT>gtG	p.V139V	SLC25A27_ENST00000411689.2_Silent_p.V139V|SLC25A27_ENST00000452689.2_Silent_p.V53V|SLC25A27_ENST00000604908.1_3'UTR	NM_001204051.1|NM_004277.4	NP_001190980.1|NP_004268.3	O95847	UCP4_HUMAN	solute carrier family 25, member 27	139					cellular triglyceride homeostasis (GO:0035356)|generation of precursor metabolites and energy (GO:0006091)|inner ear development (GO:0048839)|negative regulation of apoptotic process (GO:0043066)|negative regulation of mitochondrial calcium ion concentration (GO:0051562)|negative regulation of mitochondrial membrane potential (GO:0010917)|neuron death (GO:0070997)|positive regulation of cell proliferation (GO:0008284)|regulation of glucose import (GO:0046324)|transport (GO:0006810)	apical part of cell (GO:0045177)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)				central_nervous_system(1)|kidney(1)|lung(4)|prostate(1)|urinary_tract(1)	8			Lung(136;0.192)			TGGCTGGTGTTATTGGCCAGT	0.388																																					p.V139V		.											.	.	.	0			c.T417G						.						100.0	96.0	97.0					6																	46630146		1863	4096	5959	SO:0001819	synonymous_variant	9481	exon4			TGGTGTTATTGGC	AK090871	CCDS43470.1, CCDS56431.1	6p12.3	2013-05-22			ENSG00000153291	ENSG00000153291		"""Solute carriers"""	21065	protein-coding gene	gene with protein product		613725				10025957, 10772343	Standard	NM_004277		Approved	UCP4, FLJ33552	uc003oyh.3	O95847	OTTHUMG00000014786	ENST00000371347.5:c.417T>G	6.37:g.46630146T>G		Somatic	71	0		WXS	Illumina HiSeq	.	67	15	NM_001204051	F5GWR4|Q5VTS9|Q8N518	Silent	SNP	ENST00000371347.5	37	CCDS43470.1																																																																																			.		0.388	SLC25A27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040791.1	NM_004277	
ATP9B	374868	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	18	76903819	76903819	+	Missense_Mutation	SNP	A	A	T	rs552823277	byFrequency	TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr18:76903819A>T	ENST00000426216.2	+	6	702	c.685A>T	c.(685-687)Agt>Tgt	p.S229C	ATP9B_ENST00000307671.7_Missense_Mutation_p.S229C|ATP9B_ENST00000591464.1_3'UTR	NM_198531.3	NP_940933.3	O43861	ATP9B_HUMAN	ATPase, class II, type 9B	229					establishment of protein localization to Golgi (GO:0072600)|phospholipid translocation (GO:0045332)	integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|trans-Golgi network (GO:0005802)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(15)|ovary(3)|prostate(1)|skin(2)|stomach(1)	38		Esophageal squamous(42;0.018)|Melanoma(33;0.0964)|Prostate(75;0.171)		OV - Ovarian serous cystadenocarcinoma(15;1.44e-07)|BRCA - Breast invasive adenocarcinoma(31;0.0405)		GCAAGTTAAGAGTTCAGACAT	0.308																																					p.S229C		.											.	.	.	0			c.A685T						.						174.0	186.0	182.0					18																	76903819		2203	4300	6503	SO:0001583	missense	374868	exon6			GTTAAGAGTTCAG	R51412	CCDS12014.1	18q23	2010-04-20	2007-09-19		ENSG00000166377	ENSG00000166377		"""ATPases / P-type"""	13541	protein-coding gene	gene with protein product		614446	"""ATPase, Class II, type 9B"""			9548971, 11015572	Standard	NM_198531		Approved	ATPIIB	uc002lmx.3	O43861	OTTHUMG00000132898	ENST00000426216.2:c.685A>T	18.37:g.76903819A>T	ENSP00000398076:p.Ser229Cys	Somatic	129	0		WXS	Illumina HiSeq	.	63	27	NM_198531	O60872|Q08AD8|Q08AD9	Missense_Mutation	SNP	ENST00000426216.2	37	CCDS12014.1	.	.	.	.	.	.	.	.	.	.	A	19.46	3.832147	0.71258	.	.	ENSG00000166377	ENST00000542323;ENST00000426216;ENST00000307671	D;D	0.91407	-2.84;-2.84	5.07	5.07	0.68467	ATPase, P-type, ATPase-associated domain (1);ATPase,  P-type, cytoplasmic transduction domain A (1);	0.000000	0.85682	D	0.000000	D	0.93559	0.7944	M	0.80982	2.52	0.80722	D	1	P;P	0.46912	0.886;0.862	P;P	0.54174	0.744;0.627	D	0.93966	0.7245	10	0.59425	D	0.04	.	13.0688	0.59048	1.0:0.0:0.0:0.0	.	229;229	O43861;O43861-2	ATP9B_HUMAN;.	C	152;229;229	ENSP00000398076:S229C;ENSP00000304500:S229C	ENSP00000304500:S229C	S	+	1	0	ATP9B	75004807	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.431000	0.80335	1.924000	0.55735	0.533000	0.62120	AGT	.		0.308	ATP9B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256402.3	NM_198531	
ZBED4	9889	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	22	50278233	50278233	+	Missense_Mutation	SNP	A	A	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr22:50278233A>T	ENST00000216268.5	+	2	1400	c.923A>T	c.(922-924)cAc>cTc	p.H308L		NM_014838.2	NP_055653.2	O75132	ZBED4_HUMAN	zinc finger, BED-type containing 4	308						cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(3)|kidney(2)|large_intestine(11)|lung(20)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	44		all_cancers(38;8.58e-10)|all_epithelial(38;1.15e-08)|all_lung(38;0.000109)|Lung NSC(38;0.0018)|Breast(42;0.00191)|Ovarian(80;0.0164)|Lung SC(80;0.164)		UCEC - Uterine corpus endometrioid carcinoma (28;0.168)|BRCA - Breast invasive adenocarcinoma(115;0.2)|LUAD - Lung adenocarcinoma(64;0.247)		GTCTGCATTCACTGCATGAAC	0.582																																					p.H308L		.											.	.	.	0			c.A923T						.						87.0	89.0	89.0					22																	50278233		2203	4300	6503	SO:0001583	missense	9889	exon2			GCATTCACTGCAT	AB014537	CCDS33677.1	22q13.33	2013-05-03			ENSG00000100426	ENSG00000100426		"""Zinc fingers, BED-type"""	20721	protein-coding gene	gene with protein product		612552				23533661	Standard	NM_014838		Approved	KIAA0637	uc003bix.2	O75132	OTTHUMG00000150291	ENST00000216268.5:c.923A>T	22.37:g.50278233A>T	ENSP00000216268:p.His308Leu	Somatic	27	0		WXS	Illumina HiSeq	.	17	7	NM_014838	B2RZH1|Q1ECU0|Q9UGG8	Missense_Mutation	SNP	ENST00000216268.5	37	CCDS33677.1	.	.	.	.	.	.	.	.	.	.	A	23.2	4.393421	0.83011	.	.	ENSG00000100426	ENST00000216268	T	0.41065	1.01	5.41	5.41	0.78517	Zinc finger, BED-type predicted (3);	0.000000	0.85682	D	0.000000	T	0.52613	0.1745	L	0.28115	0.83	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.57318	-0.7832	10	0.87932	D	0	-17.5629	15.6061	0.76672	1.0:0.0:0.0:0.0	.	308	O75132	ZBED4_HUMAN	L	308	ENSP00000216268:H308L	ENSP00000216268:H308L	H	+	2	0	ZBED4	48664237	1.000000	0.71417	1.000000	0.80357	0.468000	0.32798	6.475000	0.73582	2.273000	0.75805	0.528000	0.53228	CAC	.		0.582	ZBED4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317408.2	NM_014838	
SPAG4	6676	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	20	34205495	34205495	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr20:34205495G>T	ENST00000374273.3	+	3	575	c.463G>T	c.(463-465)Gtc>Ttc	p.V155F	SPAG4_ENST00000462896.1_3'UTR	NM_003116.1	NP_003107.1	Q9NPE6	SPAG4_HUMAN	sperm associated antigen 4	155					spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|motile cilium (GO:0031514)	structural molecule activity (GO:0005198)			NS(1)|cervix(5)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)	21	Lung NSC(9;0.0053)|all_lung(11;0.00785)		BRCA - Breast invasive adenocarcinoma(18;0.0127)			AGACGTGCTGGTCAGCATGTA	0.657																																					p.V155F		.											.	.	.	0			c.G463T						.						30.0	28.0	29.0					20																	34205495		2203	4300	6503	SO:0001583	missense	6676	exon3			GTGCTGGTCAGCA	AF043344	CCDS13259.1	20q11.2	2010-04-23			ENSG00000061656	ENSG00000061656			11214	protein-coding gene	gene with protein product	"""acrosomal protein ACR55"", ""Sad1 and UNC84 domain containing 4"", ""cancer/testis antigen 127"""	603038				9691178, 10373309	Standard	NM_003116		Approved	SUN4, CT127	uc002xdb.1	Q9NPE6	OTTHUMG00000032352	ENST00000374273.3:c.463G>T	20.37:g.34205495G>T	ENSP00000363391:p.Val155Phe	Somatic	48	0		WXS	Illumina HiSeq	.	22	10	NM_003116	O43648	Missense_Mutation	SNP	ENST00000374273.3	37	CCDS13259.1	.	.	.	.	.	.	.	.	.	.	G	14.72	2.619419	0.46736	.	.	ENSG00000061656	ENST00000374273;ENST00000454819	T;T	0.14144	2.53;2.53	4.5	1.38	0.22167	.	0.354583	0.23945	N	0.043018	T	0.10680	0.0261	M	0.70595	2.14	0.37612	D	0.920952	B;P	0.39216	0.437;0.664	B;B	0.30572	0.117;0.117	T	0.25779	-1.0122	10	0.12766	T	0.61	-7.5926	6.6696	0.23060	0.0954:0.3371:0.5675:0.0	.	30;155	C9JJZ6;Q9NPE6	.;SPAG4_HUMAN	F	155;30	ENSP00000363391:V155F;ENSP00000396670:V30F	ENSP00000363391:V155F	V	+	1	0	SPAG4	33668909	0.998000	0.40836	1.000000	0.80357	0.932000	0.56968	0.466000	0.22019	0.369000	0.24510	0.561000	0.74099	GTC	.		0.657	SPAG4-001	KNOWN	mRNA_start_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078896.1	NM_003116	
KDM3A	55818	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	2	86697428	86697428	+	Missense_Mutation	SNP	G	G	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr2:86697428G>A	ENST00000409556.1	+	12	1986	c.1621G>A	c.(1621-1623)Gca>Aca	p.A541T	KDM3A_ENST00000312912.5_Missense_Mutation_p.A541T|KDM3A_ENST00000485171.1_3'UTR|KDM3A_ENST00000542128.1_Missense_Mutation_p.A489T|KDM3A_ENST00000409064.1_Missense_Mutation_p.A541T			Q9Y4C1	KDM3A_HUMAN	lysine (K)-specific demethylase 3A	541					androgen receptor signaling pathway (GO:0030521)|formaldehyde biosynthetic process (GO:0046293)|histone H3-K9 demethylation (GO:0033169)|histone H3-K9 dimethylation (GO:0036123)|hormone-mediated signaling pathway (GO:0009755)|negative regulation of histone H3-K9 methylation (GO:0051573)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|spermatid nucleus elongation (GO:0007290)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|core promoter binding (GO:0001047)|dioxygenase activity (GO:0051213)|iron ion binding (GO:0005506)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			NS(1)|breast(3)|central_nervous_system(2)|endometrium(5)|kidney(5)|large_intestine(7)|liver(1)|lung(13)|ovary(1)|prostate(3)|skin(1)|stomach(3)|upper_aerodigestive_tract(2)	47						GAACATCGTGGCACAGTTGCC	0.507																																					p.A541T	NSCLC(96;1150 1523 6936 46253 49736)	.											.	.	.	0			c.G1621A						.						151.0	133.0	139.0					2																	86697428		2203	4300	6503	SO:0001583	missense	55818	exon11			ATCGTGGCACAGT	AB018285	CCDS1990.1	2p11.2	2011-07-01	2009-04-06	2009-04-06	ENSG00000115548	ENSG00000115548		"""Chromatin-modifying enzymes / K-demethylases"""	20815	protein-coding gene	gene with protein product	"""jumonji C domain-containing histone demethylase 2A"""	611512	"""jumonji domain containing 1"", ""jumonji domain containing 1A"""	JMJD1, JMJD1A		9872452	Standard	NM_018433		Approved	TSGA, KIAA0742, JHMD2A	uc010ytj.2	Q9Y4C1	OTTHUMG00000130204	ENST00000409556.1:c.1621G>A	2.37:g.86697428G>A	ENSP00000386660:p.Ala541Thr	Somatic	86	0		WXS	Illumina HiSeq	.	53	19	NM_001146688	D6W5M3|Q53S72|Q68D47|Q68UT9|Q6N050|Q8IY08	Missense_Mutation	SNP	ENST00000409556.1	37	CCDS1990.1	.	.	.	.	.	.	.	.	.	.	G	19.48	3.834889	0.71373	.	.	ENSG00000115548	ENST00000409556;ENST00000540058;ENST00000312912;ENST00000409064;ENST00000542128	T;T;T;T	0.67865	-0.29;-0.29;-0.29;-0.29	5.86	5.86	0.93980	.	0.075086	0.56097	D	0.000038	T	0.63931	0.2553	L	0.40543	1.245	0.43426	D	0.995588	P;B	0.40332	0.713;0.104	B;B	0.43783	0.431;0.04	T	0.66988	-0.5784	10	0.72032	D	0.01	.	14.0194	0.64545	0.0:0.2502:0.7498:0.0	.	489;541	F5H070;Q9Y4C1	.;KDM3A_HUMAN	T	541;541;541;541;489	ENSP00000386660:A541T;ENSP00000323659:A541T;ENSP00000386516:A541T;ENSP00000438324:A489T	ENSP00000323659:A541T	A	+	1	0	KDM3A	86550939	1.000000	0.71417	0.426000	0.26672	0.927000	0.56198	5.703000	0.68340	2.778000	0.95560	0.655000	0.94253	GCA	.		0.507	KDM3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252522.2	NM_018433	
GALNT4	8693	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	12	89916734	89916734	+	Nonsense_Mutation	SNP	C	C	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr12:89916734C>T	ENST00000529983.2	-	1	1849	c.1593G>A	c.(1591-1593)tgG>tgA	p.W531*	GALNT4_ENST00000413530.1_Nonsense_Mutation_p.W359*|POC1B-GALNT4_ENST00000547474.1_3'UTR|POC1B_ENST00000549035.1_Intron|RP11-734K2.4_ENST00000605233.1_RNA|POC1B_ENST00000541909.1_Intron|POC1B_ENST00000313546.3_Intron|POC1B-GALNT4_ENST00000548729.1_Nonsense_Mutation_p.W528*|POC1B_ENST00000549504.1_Intron|POC1B_ENST00000393179.4_Intron	NM_003774.4	NP_003765.2	Q8N4A0	GALT4_HUMAN	polypeptide N-acetylgalactosaminyltransferase 4	531	Ricin B-type lectin. {ECO:0000255|PROSITE-ProRule:PRU00174}.				carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			endometrium(4)|kidney(2)|lung(5)|prostate(2)|upper_aerodigestive_tract(1)	14						CTTTAAAATGCCAAATAATGT	0.428																																					p.W531X		.											.	.	.	0			c.G1593A						.						85.0	82.0	83.0					12																	89916734		1843	4093	5936	SO:0001587	stop_gained	8693	exon1			AAAATGCCAAATA	Y08564	CCDS53817.1	12q21.33	2014-03-13	2014-03-13		ENSG00000257594	ENSG00000257594	2.4.1.41	"""Glycosyltransferase family 2 domain containing"""	4126	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase 4"""	603565	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 4 (GalNAc-T4)"""			9804815	Standard	NM_003774		Approved	GalNAc-T4	uc001tbd.3	Q8N4A0	OTTHUMG00000166292	ENST00000529983.2:c.1593G>A	12.37:g.89916734C>T	ENSP00000436604:p.Trp531*	Somatic	57	0		WXS	Illumina HiSeq	.	39	18	NM_003774	B2R775|B4DMX6|O00208	Nonsense_Mutation	SNP	ENST00000529983.2	37	CCDS53817.1	.	.	.	.	.	.	.	.	.	.	C	39	7.716071	0.98450	.	.	ENSG00000259075;ENSG00000259075;ENSG00000257594	ENST00000548729;ENST00000413530;ENST00000529983	.	.	.	5.93	5.93	0.95920	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	19.3377	0.94326	0.0:1.0:0.0:0.0	.	.	.	.	X	528;359;531	.	ENSP00000436604:W531X	W	-	3	0	GALNT4;RP11-1109F11.4	88440865	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	7.256000	0.78350	2.814000	0.96858	0.591000	0.81541	TGG	.		0.428	GALNT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388973.2	NM_003774	
TTL	150465	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	2	113258837	113258837	+	Missense_Mutation	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr2:113258837A>C	ENST00000233336.6	+	4	715	c.524A>C	c.(523-525)aAc>aCc	p.N175T		NM_153712.4	NP_714923.1	Q8NG68	TTL_HUMAN	tubulin tyrosine ligase	175	TTL. {ECO:0000255|PROSITE- ProRule:PRU00568}.				cellular protein modification process (GO:0006464)|microtubule cytoskeleton organization (GO:0000226)|regulation of axon extension (GO:0030516)		ATP binding (GO:0005524)|tubulin-tyrosine ligase activity (GO:0004835)			breast(1)|large_intestine(2)|ovary(1)	4		Ovarian(717;0.024)		BRCA - Breast invasive adenocarcinoma(221;6.17e-07)|STAD - Stomach adenocarcinoma(1183;0.00644)		TTCATAGACAACCAGGGCCAA	0.463			T	ETV6	ALL																																p.N175T		.		Dom	yes		2	2q13	150465	tubulin tyrosine ligase		L	.	.	.	0			c.A524C						.						87.0	81.0	83.0					2																	113258837		2203	4300	6503	SO:0001583	missense	150465	exon4			TAGACAACCAGGG		CCDS2096.1	2q13	2010-04-21			ENSG00000114999	ENSG00000114999	6.3.2.25		21586	protein-coding gene	gene with protein product		608291				11431336	Standard	NM_153712		Approved	MGC46235	uc002thu.3	Q8NG68	OTTHUMG00000131316	ENST00000233336.6:c.524A>C	2.37:g.113258837A>C	ENSP00000233336:p.Asn175Thr	Somatic	240	0		WXS	Illumina HiSeq	.	123	54	NM_153712	Q585T3|Q7Z302|Q8N426	Missense_Mutation	SNP	ENST00000233336.6	37	CCDS2096.1	.	.	.	.	.	.	.	.	.	.	A	10.41	1.342450	0.24339	.	.	ENSG00000114999	ENST00000233336	T	0.05382	3.45	5.45	1.54	0.23209	.	0.471637	0.23896	N	0.043489	T	0.05318	0.0141	L	0.46614	1.455	0.36209	D	0.851239	B	0.06786	0.001	B	0.08055	0.003	T	0.37197	-0.9716	10	0.19590	T	0.45	.	5.7354	0.18063	0.5879:0.2635:0.1486:0.0	.	175	Q8NG68	TTL_HUMAN	T	175	ENSP00000233336:N175T	ENSP00000233336:N175T	N	+	2	0	TTL	112975308	1.000000	0.71417	0.995000	0.50966	0.993000	0.82548	4.773000	0.62331	0.022000	0.15160	0.374000	0.22700	AAC	.		0.463	TTL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254085.2	NM_153712	
TTC41P	253724	hgsc.bcm.edu	37	12	104264191	104264191	+	IGR	SNP	A	A	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr12:104264191A>G								RP11-650K20.3 (25749 upstream) : RP11-642P15.1 (43613 downstream)																							CTGCAGCACTAGAATGGAAAG	0.338																																					.		.											.	.	.	0			.						.																																			SO:0001628	intergenic_variant	0	.			AGCACTAGAATGG																													12.37:g.104264191A>G		Somatic	56	0		WXS	Illumina HiSeq	.	29	15	.		RNA	SNP		37																																																																																				.	0	0.338								
TMTC4	84899	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	13	101320946	101320946	+	Missense_Mutation	SNP	G	G	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr13:101320946G>A	ENST00000376234.3	-	2	238	c.49C>T	c.(49-51)Ctt>Ttt	p.L17F	TMTC4_ENST00000342624.5_Missense_Mutation_p.L36F|TMTC4_ENST00000328767.5_Missense_Mutation_p.L17F	NM_001079669.1	NP_001073137.1	Q5T4D3	TMTC4_HUMAN	transmembrane and tetratricopeptide repeat containing 4	17						integral component of membrane (GO:0016021)				breast(3)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(14)|ovary(2)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	34	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)					AATGGAGGAAGAACAGAAGAT	0.473																																					p.L36F		.											TMTC4,NS,carcinoma,0,1	TMTC4	0	0			c.C106T						.						123.0	113.0	116.0					13																	101320946		1982	4157	6139	SO:0001583	missense	84899	exon3			GAGGAAGAACAGA		CCDS9497.2, CCDS41904.1, CCDS66575.1	13q32.3	2013-01-10	2006-01-06		ENSG00000125247	ENSG00000125247		"""Tetratricopeptide (TTC) repeat domain containing"""	25904	protein-coding gene	gene with protein product							Standard	XM_005254082		Approved	FLJ14624, FLJ22153	uc001vot.3	Q5T4D3	OTTHUMG00000017289	ENST00000376234.3:c.49C>T	13.37:g.101320946G>A	ENSP00000365408:p.Leu17Phe	Somatic	89	0		WXS	Illumina HiSeq	.	47	19	NM_032813	A6NLI7|B7Z666|Q5T4D4|Q5T4D5|Q5T4D6|Q8WV63|Q96SU8	Missense_Mutation	SNP	ENST00000376234.3	37	CCDS41904.1	.	.	.	.	.	.	.	.	.	.	g	16.60	3.167661	0.57476	.	.	ENSG00000125247	ENST00000376234;ENST00000342624;ENST00000328767;ENST00000475272;ENST00000423847	T;T;T	0.56275	0.83;0.83;0.47	5.66	4.79	0.61399	.	0.059289	0.64402	D	0.000001	T	0.66277	0.2773	M	0.77486	2.375	0.29151	N	0.878372	D;B;P	0.53619	0.961;0.039;0.629	P;B;B	0.52758	0.708;0.013;0.177	T	0.67658	-0.5614	10	0.87932	D	0	.	16.0464	0.80724	0.0:0.0:0.8654:0.1346	.	17;17;36	B7Z666;Q5T4D3;Q5T4D3-3	.;TMTC4_HUMAN;.	F	17;36;17;36;17	ENSP00000365408:L17F;ENSP00000343871:L36F;ENSP00000365409:L17F	ENSP00000365409:L17F	L	-	1	0	TMTC4	100118947	1.000000	0.71417	0.137000	0.22149	0.152000	0.21847	5.739000	0.68622	2.676000	0.91093	0.558000	0.71614	CTT	.		0.473	TMTC4-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045649.2	NM_032813	
DDB2	1643	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	11	47256429	47256429	+	Missense_Mutation	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr11:47256429T>G	ENST00000256996.4	+	6	1019	c.824T>G	c.(823-825)gTt>gGt	p.V275G	DDB2_ENST00000378600.3_Intron|DDB2_ENST00000378603.3_Missense_Mutation_p.V211G|DDB2_ENST00000378601.3_Intron	NM_000107.2	NP_000098.1	Q92466	DDB2_HUMAN	damage-specific DNA binding protein 2, 48kDa	275					DNA repair (GO:0006281)|histone H2A monoubiquitination (GO:0035518)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|protein autoubiquitination (GO:0051865)|protein polyubiquitination (GO:0000209)|pyrimidine dimer repair (GO:0006290)|response to UV (GO:0009411)|UV-damage excision repair (GO:0070914)	Cul4B-RING E3 ubiquitin ligase complex (GO:0031465)|nucleoplasm (GO:0005654)|protein complex (GO:0043234)	damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)			breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)|skin(1)	17						CTGCGCCAGGTTAGAGGGAAA	0.547			"""Mis, N"""			"""skin basal cell, skin squamous cell, melanoma"""		Direct reversal of damage;Nucleotide excision repair (NER)	Xeroderma Pigmentosum																												p.V275G		.	yes	Rec		Xeroderma pigmentosum (E)	11	11p12	1643	damage-specific DNA binding protein 2		E	.	.	.	0			c.T824G						.						48.0	47.0	47.0					11																	47256429		2201	4298	6499	SO:0001583	missense	1643	exon6	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV	GCCAGGTTAGAGG		CCDS7927.1, CCDS73284.1	11p12-p11	2014-09-17	2002-08-29			ENSG00000134574		"""WD repeat domain containing"""	2718	protein-coding gene	gene with protein product	"""xeroderma pigmentosum group E protein"", ""UV-damaged DNA-binding protein 2"", ""DDB p48 subunit"""	600811	"""damage-specific DNA binding protein 2 (48kD)"""			8407967, 8530102	Standard	NM_000107		Approved	DDBB, UV-DDB2, FLJ34321	uc001neb.2	Q92466		ENST00000256996.4:c.824T>G	11.37:g.47256429T>G	ENSP00000256996:p.Val275Gly	Somatic	35	0		WXS	Illumina HiSeq	.	30	11	NM_000107	B2R875|Q76E54|Q76E55|Q76E56|Q76E57	Missense_Mutation	SNP	ENST00000256996.4	37	CCDS7927.1	.	.	.	.	.	.	.	.	.	.	T	22.6	4.317251	0.81469	.	.	ENSG00000134574	ENST00000256996;ENST00000378603	T;T	0.66280	-0.15;-0.2	5.57	5.57	0.84162	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.214317	0.47455	D	0.000228	T	0.42765	0.1217	N	0.02345	-0.59	0.80722	D	1	D;D	0.60575	0.988;0.962	P;B	0.45037	0.467;0.205	T	0.59263	-0.7487	10	0.62326	D	0.03	-20.5596	15.7325	0.77817	0.0:0.0:0.0:1.0	.	211;275	Q92466-4;Q92466	.;DDB2_HUMAN	G	275;211	ENSP00000256996:V275G;ENSP00000367866:V211G	ENSP00000256996:V275G	V	+	2	0	DDB2	47213005	1.000000	0.71417	0.996000	0.52242	0.997000	0.91878	7.703000	0.84585	2.116000	0.64780	0.460000	0.39030	GTT	.		0.547	DDB2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_000107	
PANX1	24145	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	11	93886741	93886741	+	Missense_Mutation	SNP	A	A	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr11:93886741A>T	ENST00000227638.3	+	2	651	c.266A>T	c.(265-267)cAg>cTg	p.Q89L	PANX1_ENST00000436171.2_Missense_Mutation_p.Q89L	NM_015368.3	NP_056183.2	Q96RD7	PANX1_HUMAN	pannexin 1	89					calcium ion transport (GO:0006816)|cation transport (GO:0006812)|innate immune response (GO:0045087)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of interleukin-1 alpha secretion (GO:0050717)|positive regulation of interleukin-1 beta secretion (GO:0050718)|protein hexamerization (GO:0034214)|response to ATP (GO:0033198)|response to ischemia (GO:0002931)|synaptic transmission (GO:0007268)	bleb (GO:0032059)|endoplasmic reticulum (GO:0005783)|gap junction (GO:0005921)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	calcium channel activity (GO:0005262)|gap junction hemi-channel activity (GO:0055077)|leak channel activity (GO:0022840)|receptor binding (GO:0005102)			endometrium(2)|large_intestine(2)|lung(13)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)			Probenecid(DB01032)	GCGGCTGTTCAGCAGAAGAAC	0.463																																					p.Q89L		.											.	.	.	0			c.A266T						.						138.0	128.0	131.0					11																	93886741		2201	4298	6499	SO:0001583	missense	24145	exon2			CTGTTCAGCAGAA	AF093239	CCDS8296.1	11q14-q21	2011-12-02			ENSG00000110218	ENSG00000110218		"""Ion channels / Pannexins"""	8599	protein-coding gene	gene with protein product	"""innexin"""	608420				14597722	Standard	NM_015368		Approved	MRS1, UNQ2529, PX1	uc001per.3	Q96RD7	OTTHUMG00000167757	ENST00000227638.3:c.266A>T	11.37:g.93886741A>T	ENSP00000227638:p.Gln89Leu	Somatic	43	0		WXS	Illumina HiSeq	.	27	14	NM_015368	O75968|Q543A0|Q6UW26|Q96AM9|Q96L77|Q96RS5	Missense_Mutation	SNP	ENST00000227638.3	37	CCDS8296.1	.	.	.	.	.	.	.	.	.	.	A	13.67	2.306754	0.40795	.	.	ENSG00000110218	ENST00000227638;ENST00000436171	T;T	0.29917	1.55;1.55	4.58	4.58	0.56647	.	0.139560	0.47093	D	0.000251	T	0.38427	0.1040	M	0.66939	2.045	0.58432	D	0.999999	P;P	0.49559	0.925;0.908	P;B	0.48270	0.572;0.436	T	0.18272	-1.0342	10	0.26408	T	0.33	-7.2132	12.9567	0.58432	1.0:0.0:0.0:0.0	.	89;89	Q96RD7;Q96RD7-2	PANX1_HUMAN;.	L	89	ENSP00000227638:Q89L;ENSP00000411461:Q89L	ENSP00000227638:Q89L	Q	+	2	0	PANX1	93526389	1.000000	0.71417	0.986000	0.45419	0.357000	0.29423	7.862000	0.87013	1.697000	0.51169	0.533000	0.62120	CAG	.		0.463	PANX1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396121.1	NM_015368	
EPB41L4A	64097	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	5	111594968	111594968	+	Silent	SNP	G	G	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr5:111594968G>A	ENST00000261486.5	-	9	1029	c.753C>T	c.(751-753)caC>caT	p.H251H	RP11-526F3.1_ENST00000504004.1_RNA	NM_022140.3	NP_071423	Q9HCS5	E41LA_HUMAN	erythrocyte membrane protein band 4.1 like 4A	251	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.					cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)				breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(10)|ovary(1)|prostate(2)|skin(1)	34		all_cancers(142;4.93e-06)|all_epithelial(76;2.28e-08)|Prostate(80;0.000244)|Colorectal(10;0.000788)|Ovarian(225;0.0448)|Lung NSC(167;0.126)|all_lung(232;0.135)		OV - Ovarian serous cystadenocarcinoma(64;6.24e-09)|Epithelial(69;1.43e-07)|all cancers(49;2.78e-05)|COAD - Colon adenocarcinoma(37;0.0467)|Colorectal(14;0.0791)		TCTCCTTGAAGTGAACCTTTG	0.388																																					p.H251H		.											.	.	.	0			c.C753T						.						160.0	142.0	148.0					5																	111594968		1817	4091	5908	SO:0001819	synonymous_variant	64097	exon9			CTTGAAGTGAACC	AB030240	CCDS43350.1	5q21.3	2008-02-05			ENSG00000129595	ENSG00000129595			13278	protein-coding gene	gene with protein product		612141				10874211	Standard	XM_005272043		Approved	NBL4	uc003kpv.1	Q9HCS5	OTTHUMG00000162902	ENST00000261486.5:c.753C>T	5.37:g.111594968G>A		Somatic	77	0		WXS	Illumina HiSeq	.	73	20	NM_022140	A4FUI6	Silent	SNP	ENST00000261486.5	37	CCDS43350.1																																																																																			.		0.388	EPB41L4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370969.1		
ATXN7L3B	552889	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	12	74932077	74932077	+	Missense_Mutation	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr12:74932077A>C	ENST00000519948.2	+	1	527	c.185A>C	c.(184-186)cAg>cCg	p.Q62P	RP11-56G10.2_ENST00000550926.1_RNA	NM_001136262.1	NP_001129734.1	Q96GX2	A7L3B_HUMAN	ataxin 7-like 3B	62																	TTTGGCATTCAGCCAGTGGAA	0.572																																					p.Q62P		.											.	.	.	0			c.A185C						.						123.0	109.0	113.0					12																	74932077		692	1591	2283	SO:0001583	missense	552889	exon1			GCATTCAGCCAGT		CCDS53815.1	12q21	2013-02-15			ENSG00000253719	ENSG00000253719			37931	protein-coding gene	gene with protein product		615579					Standard	NM_001136262		Approved		uc001sxd.4	Q96GX2	OTTHUMG00000163936	ENST00000519948.2:c.185A>C	12.37:g.74932077A>C	ENSP00000430000:p.Gln62Pro	Somatic	71	0		WXS	Illumina HiSeq	.	37	14	NM_001136262		Missense_Mutation	SNP	ENST00000519948.2	37	CCDS53815.1	.	.	.	.	.	.	.	.	.	.	A	15.96	2.986232	0.53934	.	.	ENSG00000253719	ENST00000519948	.	.	.	4.89	2.55	0.30701	.	.	.	.	.	T	0.29028	0.0721	.	.	.	0.28834	N	0.896978	B	0.06786	0.001	B	0.04013	0.001	T	0.25606	-1.0127	7	0.87932	D	0	.	4.4599	0.11661	0.6971:0.2025:0.1004:0.0	.	62	Q96GX2	A7L3B_HUMAN	P	62	.	ENSP00000430000:Q62P	Q	+	2	0	ATXN7L3B	73218344	0.997000	0.39634	0.999000	0.59377	0.990000	0.78478	1.861000	0.39438	0.937000	0.37394	0.482000	0.46254	CAG	.		0.572	ATXN7L3B-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376473.1	NM_001136262	
TYRP1	7306	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	9	12708981	12708981	+	Silent	SNP	G	G	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr9:12708981G>T	ENST00000388918.5	+	8	1542	c.1413G>T	c.(1411-1413)cgG>cgT	p.R471R	RP11-3L8.3_ENST00000417638.1_RNA|TYRP1_ENST00000473504.1_3'UTR|TYRP1_ENST00000381136.2_Silent_p.R181R|TYRP1_ENST00000381137.2_Silent_p.R180R	NM_000550.2	NP_000541.1	P17643	TYRP1_HUMAN	tyrosinase-related protein 1	471					acetoacetic acid metabolic process (GO:0043438)|melanin biosynthetic process (GO:0042438)|melanocyte differentiation (GO:0030318)|melanosome organization (GO:0032438)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|melanosome (GO:0042470)|melanosome membrane (GO:0033162)	copper ion binding (GO:0005507)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, another compound as one donor, and incorporation of one atom of oxygen (GO:0016716)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			NS(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(10)|stomach(1)	22		all_cancers(3;3.1e-05)|all_lung(3;1.7e-06)|Lung NSC(3;2.09e-06)|all_epithelial(3;0.000695)|all_hematologic(3;0.0033)|Acute lymphoblastic leukemia(23;0.0744)		GBM - Glioblastoma multiforme(50;9.85e-06)		AAATAGGTCGGGAGTTTAGTG	0.353									Oculocutaneous Albinism																												p.R471R		.											.	.	.	0			c.G1413T						.						139.0	130.0	133.0					9																	12708981		2202	4300	6502	SO:0001819	synonymous_variant	7306	exon8	Familial Cancer Database		AGGTCGGGAGTTT	L33830	CCDS34990.1	9p23	2013-01-08			ENSG00000107165	ENSG00000107165			12450	protein-coding gene	gene with protein product		115501		TYRP, CAS2		9434945	Standard	NM_000550		Approved	GP75, CATB, TRP, b-PROTEIN, OCA3	uc003zkv.4	P17643	OTTHUMG00000021034	ENST00000388918.5:c.1413G>T	9.37:g.12708981G>T		Somatic	40	0		WXS	Illumina HiSeq	.	30	17	NM_000550	P78468|P78469|Q13721|Q15679	Silent	SNP	ENST00000388918.5	37	CCDS34990.1																																																																																			.		0.353	TYRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055502.3	NM_000550	
FBXO5	26271	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	6	153296425	153296425	+	Silent	SNP	A	A	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr6:153296425A>G	ENST00000229758.3	-	2	493	c.435T>C	c.(433-435)agT>agC	p.S145S	FBXO5_ENST00000367241.3_Silent_p.S99S|FBXO5_ENST00000477822.1_5'Flank	NM_012177.3	NP_036309.1	Q9UKT4	FBX5_HUMAN	F-box protein 5	145	Interaction with EVI5.				anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|G1/S transition of mitotic cell cycle (GO:0000082)|inhibition of mitotic anaphase-promoting complex activity (GO:0060565)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|microtubule polymerization (GO:0046785)|mitotic cell cycle (GO:0000278)|negative regulation of meiosis (GO:0045835)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|oocyte maturation (GO:0001556)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|regulation of mitotic cell cycle (GO:0007346)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|spindle assembly involved in female meiosis I (GO:0007057)|vesicle organization (GO:0016050)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)			breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(3)|prostate(2)|upper_aerodigestive_tract(1)	15		Ovarian(120;0.125)		OV - Ovarian serous cystadenocarcinoma(155;4.38e-10)|BRCA - Breast invasive adenocarcinoma(81;0.0893)		AGGAATAGCCACTGTCTTCAT	0.428																																					p.S145S	NSCLC(121;372 1757 17721 17977 29669)	.											.	.	.	0			c.T435C						.						169.0	170.0	170.0					6																	153296425		2203	4300	6503	SO:0001819	synonymous_variant	26271	exon2			ATAGCCACTGTCT	AF129535	CCDS5242.1, CCDS47501.1	6q25-q26	2008-02-05	2004-06-15		ENSG00000112029	ENSG00000112029		"""F-boxes /  ""other"""""	13584	protein-coding gene	gene with protein product		606013	"""F-box only protein 5"""			10531035, 10531037	Standard	NM_012177		Approved	FBX5, Fbxo31, EMI1	uc003qpg.3	Q9UKT4	OTTHUMG00000015854	ENST00000229758.3:c.435T>C	6.37:g.153296425A>G		Somatic	52	0		WXS	Illumina HiSeq	.	39	20	NM_012177	B3KNX5|Q5TF47|Q8WV29|Q9UGC8	Silent	SNP	ENST00000229758.3	37	CCDS5242.1																																																																																			.		0.428	FBXO5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042757.1		
SMYD2	56950	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	214503534	214503534	+	Silent	SNP	C	C	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr1:214503534C>A	ENST00000366957.5	+	8	751	c.729C>A	c.(727-729)ctC>ctA	p.L243L	SMYD2_ENST00000491455.1_3'UTR|SMYD2_ENST00000415093.2_Silent_p.L243L	NM_020197.2	NP_064582.2	Q9NRG4	SMYD2_HUMAN	SET and MYND domain containing 2	243					negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|peptidyl-lysine dimethylation (GO:0018027)|peptidyl-lysine monomethylation (GO:0018026)|regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043516)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	histone methyltransferase activity (H3-K36 specific) (GO:0046975)|metal ion binding (GO:0046872)|p53 binding (GO:0002039)|protein-lysine N-methyltransferase activity (GO:0016279)|RNA polymerase II core binding (GO:0000993)			breast(2)|endometrium(3)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|upper_aerodigestive_tract(1)	14				OV - Ovarian serous cystadenocarcinoma(81;0.0122)|all cancers(67;0.0209)|GBM - Glioblastoma multiforme(131;0.106)|Epithelial(68;0.144)		ATATTGATCTCCTGTACCCAA	0.438																																					p.L243L		.											.	.	.	0			c.C729A						.						84.0	75.0	78.0					1																	214503534		2203	4300	6503	SO:0001819	synonymous_variant	56950	exon8			TGATCTCCTGTAC	AF226053	CCDS31022.1	1q32.3	2011-07-01			ENSG00000143499	ENSG00000143499		"""Zinc fingers, MYND-type"", ""Chromatin-modifying enzymes / K-methyltransferases"""	20982	protein-coding gene	gene with protein product		610663					Standard	NM_020197		Approved	HSKM-B, ZMYND14, KMT3C	uc021pix.1	Q9NRG4	OTTHUMG00000037066	ENST00000366957.5:c.729C>A	1.37:g.214503534C>A		Somatic	100	0		WXS	Illumina HiSeq	.	157	34	NM_020197	B2R9P9|I6L9H7|Q4V765|Q5VSH9|Q96AI4	Silent	SNP	ENST00000366957.5	37	CCDS31022.1																																																																																			.		0.438	SMYD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089998.1	NM_020197	
RAD17	5884	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	5	68680714	68680714	+	Missense_Mutation	SNP	T	T	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr5:68680714T>A	ENST00000509734.1	+	7	1310	c.632T>A	c.(631-633)aTg>aAg	p.M211K	RAD17_ENST00000345306.6_Missense_Mutation_p.M200K|RAD17_ENST00000305138.4_Missense_Mutation_p.M200K|RAD17_ENST00000358030.2_Missense_Mutation_p.M35K|RAD17_ENST00000504177.1_Intron|RAD17_ENST00000361732.2_Missense_Mutation_p.M200K|RAD17_ENST00000354312.3_Missense_Mutation_p.M200K|RAD17_ENST00000380774.3_Missense_Mutation_p.M211K|RAD17_ENST00000521422.1_Missense_Mutation_p.M35K|RAD17_ENST00000282891.6_Missense_Mutation_p.M114K|RAD17_ENST00000354868.5_Missense_Mutation_p.M200K			O75943	RAD17_HUMAN	RAD17 homolog (S. pombe)	211					cellular response to DNA damage stimulus (GO:0006974)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA replication checkpoint (GO:0000076)|mitotic cell cycle checkpoint (GO:0007093)|negative regulation of DNA replication (GO:0008156)|regulation of phosphorylation (GO:0042325)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)						Lung NSC(167;5.19e-05)|Prostate(74;0.0143)|Ovarian(174;0.0448)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;9.36e-57)|Epithelial(20;1.21e-52)|all cancers(19;3.34e-48)|Lung(70;0.0183)		AAGTTACAAATGCTTGGAGAT	0.323								Other conserved DNA damage response genes																													p.M211K		.											.	.	.	0			c.T632A						.						62.0	64.0	63.0					5																	68680714		2203	4300	6503	SO:0001583	missense	5884	exon5			TACAAATGCTTGG	AF085736	CCDS4003.1, CCDS4004.1, CCDS4005.1, CCDS47226.1	5q13	2010-09-24	2001-11-28		ENSG00000152942	ENSG00000152942			9807	protein-coding gene	gene with protein product		603139	"""RAD1 (S. pombe) homolog"""			9869296, 9660800	Standard	NM_133343		Approved	Rad24, RAD17Sp, CCYC	uc003jwo.3	O75943	OTTHUMG00000099357	ENST00000509734.1:c.632T>A	5.37:g.68680714T>A	ENSP00000426191:p.Met211Lys	Somatic	74	0		WXS	Illumina HiSeq	.	61	33	NM_133339	A8K8X2|D3DWA5|O75714|Q7Z3S4|Q9UNK7|Q9UNR7|Q9UNR8|Q9UPF5	Missense_Mutation	SNP	ENST00000509734.1	37	CCDS4003.1	.	.	.	.	.	.	.	.	.	.	T	22.5	4.297485	0.81025	.	.	ENSG00000152942	ENST00000361732;ENST00000509734;ENST00000354868;ENST00000521422;ENST00000354312;ENST00000345306;ENST00000512785;ENST00000305138;ENST00000282891;ENST00000358030;ENST00000380774	T;T;T;T;T;T;T;T;T;T;T	0.19669	2.13;2.13;2.13;2.13;2.13;2.13;2.13;2.13;2.13;2.13;2.13	5.05	5.05	0.67936	ATPase, AAA+ type, core (1);	0.038087	0.85682	D	0.000000	T	0.42653	0.1212	M	0.65975	2.015	0.58432	D	0.999999	D;D;D	0.64830	0.994;0.979;0.993	D;P;P	0.65323	0.934;0.846;0.891	T	0.36696	-0.9737	10	0.66056	D	0.02	-26.5306	14.0716	0.64863	0.0:0.0:0.0:1.0	.	211;114;200	O75943;O75943-4;O75943-2	RAD17_HUMAN;.;.	K	200;211;200;35;200;200;35;200;114;35;211	ENSP00000355226:M200K;ENSP00000426191:M211K;ENSP00000346938:M200K;ENSP00000427743:M35K;ENSP00000346271:M200K;ENSP00000311227:M200K;ENSP00000427673:M35K;ENSP00000303134:M200K;ENSP00000282891:M114K;ENSP00000350725:M35K;ENSP00000370151:M211K	ENSP00000282891:M114K	M	+	2	0	RAD17	68716470	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	6.503000	0.73699	2.032000	0.59987	0.254000	0.18369	ATG	.		0.323	RAD17-008	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369171.1	NM_133344	
RUNDC3A	10900	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	17	42395541	42395541	+	Missense_Mutation	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr17:42395541T>G	ENST00000426726.3	+	11	1550	c.1276T>G	c.(1276-1278)Ttc>Gtc	p.F426V	AC003102.3_ENST00000588097.1_RNA	NM_001144825.1	NP_001138297.1	Q59EK9	RUN3A_HUMAN	RUN domain containing 3A	426					positive regulation of cGMP biosynthetic process (GO:0030828)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	guanylate cyclase activator activity (GO:0030250)|small GTPase regulator activity (GO:0005083)			large_intestine(1)|lung(1)|ovary(2)	4		Prostate(33;0.0233)		BRCA - Breast invasive adenocarcinoma(366;0.189)		CCTGGCGAGCTTCAAATCCAA	0.672																																					p.F426V	Pancreas(82;1061 1416 11136 20771 23901)	.											.	.	.	0			c.T1276G						.						49.0	50.0	50.0					17																	42395541		692	1591	2283	SO:0001583	missense	10900	exon11			GCGAGCTTCAAAT	AF055026	CCDS45698.1, CCDS45699.1, CCDS59294.1	17q21.31	2008-02-05			ENSG00000108309	ENSG00000108309			16984	protein-coding gene	gene with protein product		605448				9523700	Standard	NM_006695		Approved	RPIP8, RAP2IP	uc002igl.4	Q59EK9	OTTHUMG00000169259	ENST00000426726.3:c.1276T>G	17.37:g.42395541T>G	ENSP00000410862:p.Phe426Val	Somatic	82	0		WXS	Illumina HiSeq	.	27	10	NM_001144825	B2R974|O15483|O60651|Q7Z3S2|Q9UF50	Missense_Mutation	SNP	ENST00000426726.3	37	CCDS45698.1	.	.	.	.	.	.	.	.	.	.	T	16.59	3.167036	0.57476	.	.	ENSG00000108309	ENST00000426726	T	0.21734	1.99	4.81	4.81	0.61882	.	.	.	.	.	T	0.10208	0.0250	N	0.08118	0	0.80722	D	1	B	0.20261	0.043	B	0.19946	0.027	T	0.13176	-1.0519	9	0.41790	T	0.15	-14.4968	5.9081	0.19012	0.0:0.1821:0.0:0.8179	.	426	Q59EK9	RUN3A_HUMAN	V	426	ENSP00000410862:F426V	ENSP00000410862:F426V	F	+	1	0	RUNDC3A	39751067	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.354000	0.59417	2.005000	0.58758	0.459000	0.35465	TTC	.		0.672	RUNDC3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403173.2	NM_006695	
RABGAP1	23637	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	9	125836700	125836700	+	Missense_Mutation	SNP	T	T	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr9:125836700T>C	ENST00000373647.4	+	17	2380	c.2246T>C	c.(2245-2247)tTa>tCa	p.L749S	RABGAP1_ENST00000373643.5_Missense_Mutation_p.L88S	NM_012197.3	NP_036329.3	Q9Y3P9	RBGP1_HUMAN	RAB GTPase activating protein 1	749	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.				cell cycle (GO:0007049)|positive regulation of GTPase activity (GO:0043547)|regulation of GTP catabolic process (GO:0033124)	centrosome (GO:0005813)|cytosol (GO:0005829)|microtubule associated complex (GO:0005875)	DNA binding (GO:0003677)|GTPase activator activity (GO:0005096)|Rab GTPase activator activity (GO:0005097)|Rab GTPase binding (GO:0017137)|tubulin binding (GO:0015631)			breast(3)|endometrium(3)|kidney(5)|large_intestine(8)|lung(11)|ovary(3)|prostate(4)|stomach(3)|upper_aerodigestive_tract(1)	41						GACCTGCTTTTATGTGAGGTA	0.428																																					p.L749S		.											.	.	.	0			c.T2246C						.						120.0	103.0	109.0					9																	125836700		2203	4300	6503	SO:0001583	missense	23637	exon17			TGCTTTTATGTGA	AJ011679	CCDS6848.2	9q34.11	2013-07-09			ENSG00000011454	ENSG00000011454			17155	protein-coding gene	gene with protein product	"""rab6 GTPase activating protein (GAP and centrosome-associated)"", ""TBC1 domain family, member 11"""	615882				10202141	Standard	NM_012197		Approved	GAPCenA, TBC1D11	uc011lzh.2	Q9Y3P9	OTTHUMG00000020633	ENST00000373647.4:c.2246T>C	9.37:g.125836700T>C	ENSP00000362751:p.Leu749Ser	Somatic	80	0		WXS	Illumina HiSeq	.	57	22	NM_012197	B9A6L2|Q05CW2|Q6ZMY1|Q9HA28|Q9P0E2|Q9UG67	Missense_Mutation	SNP	ENST00000373647.4	37	CCDS6848.2	.	.	.	.	.	.	.	.	.	.	T	28.6	4.931524	0.92389	.	.	ENSG00000011454	ENST00000373647;ENST00000373643	T;T	0.36157	1.27;1.27	6.16	6.16	0.99307	Rab-GAP/TBC domain (4);	0.000000	0.64402	D	0.000009	T	0.75852	0.3906	H	0.98466	4.24	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.85590	0.1245	10	0.87932	D	0	-10.9532	15.9872	0.80168	0.0:0.0:0.0:1.0	.	749	Q9Y3P9	RBGP1_HUMAN	S	749;88	ENSP00000362751:L749S;ENSP00000362747:L88S	ENSP00000362747:L88S	L	+	2	0	RABGAP1	124876521	0.999000	0.42202	0.989000	0.46669	0.998000	0.95712	7.698000	0.84413	2.367000	0.80283	0.528000	0.53228	TTA	.		0.428	RABGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053976.3	NM_012197	
STKLD1	169436	hgsc.bcm.edu;bcgsc.ca	37	9	136270413	136270413	+	Silent	SNP	G	G	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr9:136270413G>A	ENST00000371957.3	+	18	2018	c.1911G>A	c.(1909-1911)aaG>aaA	p.K637K	C9orf96_ENST00000371955.1_Silent_p.K170K	NM_153710.3	NP_714921.4	Q8NE28	STKL1_HUMAN		637							ATP binding (GO:0005524)|protein kinase activity (GO:0004672)			autonomic_ganglia(1)|central_nervous_system(3)|endometrium(1)|kidney(1)|large_intestine(5)|lung(10)|ovary(2)|stomach(2)	25				OV - Ovarian serous cystadenocarcinoma(145;1.06e-07)|Epithelial(140;1.28e-06)|all cancers(34;1.46e-05)		GTAGTATGAAGGCCCTGCTCC	0.632																																					p.K637K		.											.	.	.	0			c.G1911A						.						51.0	45.0	47.0					9																	136270413		2203	4300	6503	SO:0001819	synonymous_variant	169436	exon18			TATGAAGGCCCTG																												ENST00000371957.3:c.1911G>A	9.37:g.136270413G>A		Somatic	17	0		WXS	Illumina HiSeq	.	6	4	NM_153710	Q5T8U8|Q6ZMP6|Q6ZMQ5	Silent	SNP	ENST00000371957.3	37	CCDS35169.1																																																																																			.		0.632	C9orf96-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054855.1		
ST7-OT4	338069	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	7	116595119	116595119	+	5'UTR	SNP	A	A	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr7:116595119A>T	ENST00000397750.3	+	0	522				ST7_ENST00000393451.3_Intron|ST7-OT4_ENST00000397751.1_5'UTR|ST7-AS1_ENST00000456775.1_RNA|ST7-OT4_ENST00000466018.1_3'UTR|ST7_ENST00000265437.5_Intron|ST7_ENST00000323984.3_Intron|ST7_ENST00000393449.1_Intron|ST7_ENST00000393446.2_Intron					ST7 overlapping transcript 4																		AGCCCTTTTGAGTCTGTCATC	0.468																																					.		.											.	.	.	0			.						.																																			SO:0001623	5_prime_UTR_variant	338069	.			CTTTTGAGTCTGT	BM413623		7q31.2	2013-03-06	2013-03-06	2011-08-19	ENSG00000214188	ENSG00000214188		"""Long non-coding RNAs"", ""-"""	18835	other	unknown	"""non-protein coding RNA 42"""		"""ST7 overlapping transcript 4 (non-protein coding)"""	ST7OT4		12213198	Standard	NR_002329		Approved	NCRNA00042	uc003vip.1		OTTHUMG00000063631	ENST00000397750.3:c.-20A>T	7.37:g.116595119A>T		Somatic	50	0		WXS	Illumina HiSeq	.	26	11	.		RNA	SNP	ENST00000397750.3	37																																																																																				.		0.468	ST7-OT4-001	PUTATIVE	basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000137763.3	NR_002329	
NDUFA13	51079	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	19	19638823	19638823	+	Missense_Mutation	SNP	A	A	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr19:19638823A>G	ENST00000507754.4	+	5	807	c.323A>G	c.(322-324)gAg>gGg	p.E108G	NDUFA13_ENST00000503283.1_Intron|YJEFN3_ENST00000514277.4_5'Flank|NDUFA13_ENST00000428459.2_3'UTR|YJEFN3_ENST00000436027.5_5'Flank|CTC-260F20.3_ENST00000555938.1_Intron|CTC-260F20.3_ENST00000586674.1_3'UTR|NDUFA13_ENST00000252576.5_Missense_Mutation_p.E191G|YJEFN3_ENST00000608404.1_Intron|NDUFA13_ENST00000512771.3_Missense_Mutation_p.E108G			Q9P0J0	NDUAD_HUMAN	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 13	108	Important for inducing cell death.				apoptotic signaling pathway (GO:0097190)|cellular metabolic process (GO:0044237)|cellular response to interferon-beta (GO:0035458)|cellular response to retinoic acid (GO:0071300)|negative regulation of cell growth (GO:0030308)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of peptidase activity (GO:0010952)|positive regulation of protein catabolic process (GO:0045732)|protein import into mitochondrial inner membrane (GO:0045039)|reactive oxygen species metabolic process (GO:0072593)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial membrane (GO:0031966)|mitochondrial respiratory chain (GO:0005746)|mitochondrial respiratory chain complex I (GO:0005747)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|NADH dehydrogenase (ubiquinone) activity (GO:0008137)|NADH dehydrogenase activity (GO:0003954)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(4)|ovary(1)	12						CAGGTGGGGGAGTCTGTGTTC	0.647																																					p.E108G		.											.	.	.	0			c.A323G						.						39.0	37.0	38.0					19																	19638823		2203	4299	6502	SO:0001583	missense	51079	exon5			TGGGGGAGTCTGT	AF261134	CCDS12404.1, CCDS12404.2	19p13.11	2011-07-04			ENSG00000186010	ENSG00000186010		"""Mitochondrial respiratory chain complex / Complex I"""	17194	protein-coding gene	gene with protein product	"""complex I B16.6 subunit"""	609435				12837546, 10924506, 15367666	Standard	NM_015965		Approved	CGI-39, CDA016, GRIM-19, GRIM19, B16.6		Q9P0J0	OTTHUMG00000162211	ENST00000507754.4:c.323A>G	19.37:g.19638823A>G	ENSP00000423673:p.Glu108Gly	Somatic	89	0		WXS	Illumina HiSeq	.	53	18	NM_015965	B4DF76|K7EK58|Q6PKI0|Q9H2L3|Q9Y327	Missense_Mutation	SNP	ENST00000507754.4	37	CCDS12404.2	.	.	.	.	.	.	.	.	.	.	A	16.03	3.007832	0.54361	.	.	ENSG00000186010	ENST00000507754;ENST00000252576	D;D	0.85773	-2.03;-2.03	4.7	4.7	0.59300	.	0.000000	0.64402	D	0.000002	D	0.92469	0.7609	M	0.88640	2.97	0.80722	D	1	D;D	0.89917	1.0;0.998	D;D	0.77557	0.99;0.957	D	0.93256	0.6639	10	0.87932	D	0	.	10.6087	0.45408	1.0:0.0:0.0:0.0	.	108;108	B4DF76;Q9P0J0	.;NDUAD_HUMAN	G	108;191	ENSP00000423673:E108G;ENSP00000252576:E191G	ENSP00000252576:E191G	E	+	2	0	NDUFA13	19499823	1.000000	0.71417	0.621000	0.29145	0.043000	0.13939	6.361000	0.73070	1.785000	0.52413	0.477000	0.44152	GAG	.		0.647	NDUFA13-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367916.6	NM_015965	
MME	4311	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	3	154858051	154858051	+	Missense_Mutation	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr3:154858051A>C	ENST00000460393.1	+	10	1047	c.927A>C	c.(925-927)caA>caC	p.Q309H	MME_ENST00000462745.1_Missense_Mutation_p.Q309H|MME_ENST00000492661.1_Missense_Mutation_p.Q309H|MME_ENST00000360490.2_Missense_Mutation_p.Q309H|MME_ENST00000493237.1_Missense_Mutation_p.Q309H	NM_000902.3|NM_007287.2	NP_000893.2|NP_009218.2	P08473	NEP_HUMAN	membrane metallo-endopeptidase	309					angiotensin maturation (GO:0002003)|beta-amyloid metabolic process (GO:0050435)|cellular protein metabolic process (GO:0044267)|cellular response to cytokine stimulus (GO:0071345)|cellular response to UV-A (GO:0071492)|cellular response to UV-B (GO:0071493)|creatinine metabolic process (GO:0046449)|kidney development (GO:0001822)|peptide metabolic process (GO:0006518)|proteolysis (GO:0006508)|replicative senescence (GO:0090399)|sensory perception of pain (GO:0019233)	axon (GO:0030424)|brush border (GO:0005903)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|neuron projection terminus (GO:0044306)|plasma membrane (GO:0005886)|synapse (GO:0045202)|synaptic vesicle (GO:0008021)	endopeptidase activity (GO:0004175)|metalloendopeptidase activity (GO:0004222)|peptide binding (GO:0042277)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(31)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	64		all_neural(597;0.00391)|Myeloproliferative disorder(1037;0.0122)	LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.135)		Candoxatril(DB00616)|Liraglutide(DB06655)	CCCAGATCCAAAATAACTTTT	0.328																																					p.Q309H		.											.	.	.	0			c.A927C						.						70.0	64.0	66.0					3																	154858051		2203	4299	6502	SO:0001583	missense	4311	exon10			GATCCAAAATAAC		CCDS3172.1	3q25.2	2012-01-31	2007-02-21		ENSG00000196549	ENSG00000196549	3.4.24.11	"""CD molecules"""	7154	protein-coding gene	gene with protein product	"""neutral endopeptidase"", ""enkephalinase"", ""neprilysin"""	120520					Standard	NM_007287		Approved	CALLA, CD10, NEP	uc003fad.1	P08473	OTTHUMG00000158455	ENST00000460393.1:c.927A>C	3.37:g.154858051A>C	ENSP00000418525:p.Gln309His	Somatic	52	0		WXS	Illumina HiSeq	.	76	46	NM_007287	A8K6U6|D3DNJ9|Q3MIX4	Missense_Mutation	SNP	ENST00000460393.1	37	CCDS3172.1	.	.	.	.	.	.	.	.	.	.	A	10.39	1.337927	0.24253	.	.	ENSG00000196549	ENST00000492661;ENST00000460393;ENST00000462745;ENST00000493237;ENST00000360490	T;T;T;T;T	0.76186	-1.0;-1.0;-1.0;-1.0;-1.0	5.23	-2.01	0.07410	Peptidase M13 (1);	0.425465	0.27826	N	0.017688	T	0.78310	0.4263	L	0.58510	1.815	0.28134	N	0.930077	D	0.54772	0.968	D	0.65874	0.939	T	0.72513	-0.4270	10	0.87932	D	0	-11.212	8.7403	0.34554	0.4355:0.1147:0.4498:0.0	.	309	P08473	NEP_HUMAN	H	309	ENSP00000420389:Q309H;ENSP00000418525:Q309H;ENSP00000419653:Q309H;ENSP00000417079:Q309H;ENSP00000353679:Q309H	ENSP00000353679:Q309H	Q	+	3	2	MME	156340745	0.342000	0.24809	0.046000	0.18839	0.020000	0.10135	0.237000	0.17985	-0.505000	0.06568	0.533000	0.62120	CAA	.		0.328	MME-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351076.1	NM_000902	
MAST1	22983	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	19	12975632	12975632	+	Missense_Mutation	SNP	G	G	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr19:12975632G>A	ENST00000251472.4	+	13	1415	c.1376G>A	c.(1375-1377)tGt>tAt	p.C459Y		NM_014975.2	NP_055790.1			microtubule associated serine/threonine kinase 1											NS(1)|cervix(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(9)|lung(20)|ovary(5)|prostate(5)|skin(3)	56						GGCGGCGACTGTGCCACCCTG	0.542																																					p.C459Y		.											.	.	.	0			c.G1376A						.						81.0	78.0	79.0					19																	12975632		2203	4300	6503	SO:0001583	missense	22983	exon13			GCGACTGTGCCAC	AB023190	CCDS32921.1	19p13.2	2008-02-05				ENSG00000105613			19034	protein-coding gene	gene with protein product		612256					Standard	NM_014975		Approved	SAST, KIAA0973	uc002mvm.3	Q9Y2H9		ENST00000251472.4:c.1376G>A	19.37:g.12975632G>A	ENSP00000251472:p.Cys459Tyr	Somatic	44	0		WXS	Illumina HiSeq	.	29	10	NM_014975		Missense_Mutation	SNP	ENST00000251472.4	37	CCDS32921.1	.	.	.	.	.	.	.	.	.	.	G	17.60	3.429009	0.62844	.	.	ENSG00000105613	ENST00000251472;ENST00000542153	T	0.24350	1.86	4.39	4.39	0.52855	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.36963	0.0986	N	0.22421	0.69	0.80722	D	1	D	0.76494	0.999	D	0.87578	0.998	T	0.32798	-0.9893	10	0.87932	D	0	-15.5488	14.8264	0.70117	0.0:0.0:1.0:0.0	.	459	Q9Y2H9	MAST1_HUMAN	Y	459	ENSP00000251472:C459Y	ENSP00000251472:C459Y	C	+	2	0	MAST1	12836632	1.000000	0.71417	1.000000	0.80357	0.473000	0.32948	9.813000	0.99286	2.181000	0.69327	0.561000	0.74099	TGT	.		0.542	MAST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451733.2	NM_014975	
APOL2	23780	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	22	36624205	36624205	+	Missense_Mutation	SNP	G	G	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr22:36624205G>A	ENST00000249066.6	-	6	735	c.259C>T	c.(259-261)Cgg>Tgg	p.R87W	APOL2_ENST00000358502.5_Missense_Mutation_p.R87W|APOL2_ENST00000451256.2_Missense_Mutation_p.R199W	NM_145637.1	NP_663612.1	Q9BQE5	APOL2_HUMAN	apolipoprotein L, 2	87					acute-phase response (GO:0006953)|cholesterol metabolic process (GO:0008203)|lipid metabolic process (GO:0006629)|lipid transport (GO:0006869)|lipoprotein metabolic process (GO:0042157)|maternal process involved in female pregnancy (GO:0060135)|multicellular organismal development (GO:0007275)	endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|membrane (GO:0016020)	high-density lipoprotein particle binding (GO:0008035)|lipid binding (GO:0008289)|receptor binding (GO:0005102)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(1)|skin(1)|urinary_tract(2)	9						CTTTTCAACCGAGGAAACTCT	0.502																																					p.R87W		.											.	.	.	0			c.C259T						.						131.0	142.0	138.0					22																	36624205		2197	4297	6494	SO:0001583	missense	23780	exon5			TCAACCGAGGAAA	AF324224	CCDS43014.1	22q12.3	2013-09-20			ENSG00000128335	ENSG00000128335		"""Apolipoproteins"""	619	protein-coding gene	gene with protein product	"""apolipoprotein L-II"""	607252				10591208, 11374903	Standard	NM_145637		Approved	APOL-II	uc003apa.3	Q9BQE5	OTTHUMG00000150634	ENST00000249066.6:c.259C>T	22.37:g.36624205G>A	ENSP00000249066:p.Arg87Trp	Somatic	43	0		WXS	Illumina HiSeq	.	30	12	NM_030882	B0QYK7|O95915|Q59GW9|Q5TH96|Q969T6|Q9BT28|Q9UGT1|Q9UH10	Missense_Mutation	SNP	ENST00000249066.6	37	CCDS43014.1	.	.	.	.	.	.	.	.	.	.	G	14.29	2.490857	0.44249	.	.	ENSG00000128335	ENST00000358502;ENST00000249066;ENST00000451256;ENST00000529194	T;T;T;T	0.03717	3.83;3.83;3.83;3.83	3.66	-2.09	0.07232	.	0.978229	0.08412	N	0.949636	T	0.12390	0.0301	M	0.71036	2.16	0.09310	N	1	D;D	0.89917	1.0;0.999	D;D	0.69824	0.966;0.941	T	0.20874	-1.0262	10	0.62326	D	0.03	.	6.0865	0.19970	0.0:0.3373:0.3194:0.3433	.	199;87	B4E1T5;Q9BQE5	.;APOL2_HUMAN	W	87;87;199;87	ENSP00000351292:R87W;ENSP00000249066:R87W;ENSP00000403153:R199W;ENSP00000431231:R87W	ENSP00000249066:R87W	R	-	1	2	APOL2	34954151	0.000000	0.05858	0.005000	0.12908	0.004000	0.04260	-1.323000	0.02692	-0.016000	0.14127	-0.688000	0.03733	CGG	.		0.502	APOL2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000319279.1	NM_145637	
KIAA0247	9766	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	14	70175521	70175521	+	Missense_Mutation	SNP	G	G	A	rs368679025		TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr14:70175521G>A	ENST00000342745.4	+	5	899	c.586G>A	c.(586-588)Gta>Ata	p.V196I		NM_014734.3	NP_055549.1	Q92537	K0247_HUMAN	KIAA0247	196						integral component of membrane (GO:0016021)				endometrium(1)|kidney(1)|lung(4)|ovary(3)|upper_aerodigestive_tract(1)	10				all cancers(60;0.00155)|BRCA - Breast invasive adenocarcinoma(234;0.0164)|OV - Ovarian serous cystadenocarcinoma(108;0.0196)		TGACCCCAGAGTACAGATTGT	0.592																																					p.V196I		.											.	.	.	0			c.G586A						.	G	ILE/VAL	0,4406		0,0,2203	83.0	80.0	81.0		586	4.5	1.0	14		81	1,8599	1.2+/-3.3	0,1,4299	no	missense	KIAA0247	NM_014734.3	29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	196/304	70175521	1,13005	2203	4300	6503	SO:0001583	missense	9766	exon5			CCCAGAGTACAGA	D87434	CCDS9796.1	14q24.1	2012-11-29			ENSG00000100647	ENSG00000100647			19956	protein-coding gene	gene with protein product						9039502	Standard	NM_014734		Approved		uc001xlk.3	Q92537	OTTHUMG00000171234	ENST00000342745.4:c.586G>A	14.37:g.70175521G>A	ENSP00000344424:p.Val196Ile	Somatic	30	0		WXS	Illumina HiSeq	.	16	6	NM_014734		Missense_Mutation	SNP	ENST00000342745.4	37	CCDS9796.1	.	.	.	.	.	.	.	.	.	.	G	14.65	2.598084	0.46318	0.0	1.16E-4	ENSG00000100647	ENST00000342745	T	0.68025	-0.3	5.4	4.5	0.54988	.	0.057714	0.64402	D	0.000002	T	0.57272	0.2042	L	0.38531	1.155	0.58432	D	0.999993	B	0.14012	0.009	B	0.17433	0.018	T	0.57659	-0.7773	10	0.56958	D	0.05	-13.9175	13.5149	0.61535	0.075:0.0:0.925:0.0	.	196	Q92537	K0247_HUMAN	I	196	ENSP00000344424:V196I	ENSP00000344424:V196I	V	+	1	0	KIAA0247	69245274	1.000000	0.71417	1.000000	0.80357	0.389000	0.30415	6.436000	0.73417	2.513000	0.84729	0.563000	0.77884	GTA	.		0.592	KIAA0247-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412453.1	NM_014734	
EXOC1	55763	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	4	56759748	56759748	+	Silent	SNP	A	A	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr4:56759748A>G	ENST00000381295.2	+	15	2103	c.1755A>G	c.(1753-1755)aaA>aaG	p.K585K	EXOC1_ENST00000349598.6_Silent_p.K570K|EXOC1_ENST00000346134.7_Silent_p.K585K	NM_001024924.1	NP_001020095.1	Q9NV70	EXOC1_HUMAN	exocyst complex component 1	585					cellular protein metabolic process (GO:0044267)|exocytosis (GO:0006887)|membrane organization (GO:0061024)|protein transport (GO:0015031)	exocyst (GO:0000145)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(3)|lung(14)|ovary(2)|skin(4)|upper_aerodigestive_tract(1)	35	Glioma(25;0.08)|all_neural(26;0.101)					TGATGATTAAAATATTTCGCT	0.338																																					p.K585K		.											.	.	.	0			c.A1755G						.						97.0	96.0	97.0					4																	56759748		2203	4300	6503	SO:0001819	synonymous_variant	55763	exon15			GATTAAAATATTT	AK027047	CCDS3502.1, CCDS3503.1	4q12	2013-01-22	2005-11-01	2005-11-01	ENSG00000090989	ENSG00000090989			30380	protein-coding gene	gene with protein product		607879	"""SEC3-like 1 (S. cerevisiae)"""	SEC3L1		11042152, 11406615	Standard	XM_005265747		Approved	SEC3, FLJ10893, BM-102, Sec3p	uc003hbf.1	Q9NV70	OTTHUMG00000102165	ENST00000381295.2:c.1755A>G	4.37:g.56759748A>G		Somatic	61	0		WXS	Illumina HiSeq	.	28	16	NM_018261	Q504V4|Q8WUE7|Q96T15|Q9NZE4	Silent	SNP	ENST00000381295.2	37	CCDS3502.1																																																																																			.		0.338	EXOC1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361799.1	NM_018261	
TENM2	57451	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	5	167671562	167671562	+	Silent	SNP	C	C	T	rs368288670		TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr5:167671562C>T	ENST00000518659.1	+	26	5697	c.5658C>T	c.(5656-5658)agC>agT	p.S1886S	TENM2_ENST00000545108.1_Silent_p.S1885S|TENM2_ENST00000520394.1_Silent_p.S1647S|TENM2_ENST00000519204.1_Silent_p.S1765S|TENM2_ENST00000403607.2_Silent_p.S1710S	NM_001122679.1	NP_001116151.1	Q9NT68	TEN2_HUMAN	teneurin transmembrane protein 2	1886					axon guidance (GO:0007411)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|heterophilic cell-cell adhesion (GO:0007157)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of filopodium assembly (GO:0051491)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cell-cell junction (GO:0005911)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|endoplasmic reticulum (GO:0005783)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)										TGCCCAGCAGCGGGCTGGCAG	0.572																																					p.S1877S		.											ODZ2_ENST00000519204,NS,carcinoma,0,3	ODZ2_ENST00000519204	0	0			c.C5631T						.	C		0,3882		0,0,1941	56.0	62.0	60.0		5631	-3.2	0.9	5		60	8,8248		0,8,4120	no	coding-synonymous	ODZ2	NM_001122679.1		0,8,6061	TT,TC,CC		0.0969,0.0,0.0659		1877/2766	167671562	8,12130	1941	4128	6069	SO:0001819	synonymous_variant	57451	exon26			CAGCAGCGGGCTG	AB032953		5q35	2012-10-02	2012-10-02	2012-10-02	ENSG00000145934	ENSG00000145934			29943	protein-coding gene	gene with protein product		610119	"""odz, odd Oz/ten-m homolog 2 (Drosophila)"""	ODZ2		10625539	Standard	NM_001122679		Approved	KIAA1127, Ten-M2	uc010jjd.3	Q9NT68	OTTHUMG00000162928	ENST00000518659.1:c.5658C>T	5.37:g.167671562C>T		Somatic	27	0		WXS	Illumina HiSeq	.	24	5	NM_001122679	Q9ULU2	Silent	SNP	ENST00000518659.1	37																																																																																				.		0.572	TENM2-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000376096.1	NM_001122679	
GCNT2	2651	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	6	10621588	10621588	+	Silent	SNP	T	T	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr6:10621588T>C	ENST00000379597.3	+	2	1486	c.930T>C	c.(928-930)gtT>gtC	p.V310V	GCNT2_ENST00000397423.2_3'UTR|GCNT2_ENST00000316170.3_Silent_p.V308V|GCNT2_ENST00000410107.1_Silent_p.V24V|GCNT2_ENST00000495262.1_Silent_p.V310V|GCNT2_ENST00000265012.4_Silent_p.V310V			Q8N0V5	GNT2A_HUMAN	glucosaminyl (N-acetyl) transferase 2, I-branching enzyme (I blood group)	310					maintenance of lens transparency (GO:0036438)|negative regulation of cell-substrate adhesion (GO:0010812)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of heterotypic cell-cell adhesion (GO:0034116)|positive regulation of protein kinase B signaling (GO:0051897)|posttranscriptional regulation of gene expression (GO:0010608)|protein glycosylation (GO:0006486)|transforming growth factor beta receptor signaling pathway (GO:0007179)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	N-acetyllactosaminide beta-1,6-N-acetylglucosaminyltransferase activity (GO:0008109)			endometrium(2)|kidney(1)|large_intestine(5)|lung(2)|ovary(2)	12	Ovarian(93;0.107)|Breast(50;0.148)	all_hematologic(90;0.107)		KIRC - Kidney renal clear cell carcinoma(1;0.099)|Kidney(1;0.119)		TTGCAGGTGTTCCTGGCTCTA	0.468																																					p.V310V		.											.	.	.	0			c.T930C						.						89.0	78.0	82.0					6																	10621588		2203	4300	6503	SO:0001819	synonymous_variant	2651	exon4			AGGTGTTCCTGGC	L41605	CCDS4512.1, CCDS4513.1, CCDS34338.1	6p24.2	2014-07-18	2006-02-23		ENSG00000111846	ENSG00000111846	2.4.1.150	"""Blood group antigens"", ""Glucosaminyl (N-acetyl) transferase and xylosyltransferase family"""	4204	protein-coding gene	gene with protein product	"""Ii blood group"", ""unassigned linkage group 3"""	600429	"""glucosaminyl (N-acetyl) transferase 5"", ""glucosaminyl (N-acetyl) transferase 2, I-branching enzyme"", ""glucosaminyl (N-acetyl) transferase 2, I-branching enzyme (Ii blood group)"", ""cataract, congenital"""	NACGT1, II, GCNT5, CCAT		8449405, 9915862	Standard	NM_145649		Approved	IGNT, NAGCT1, bA421M1.1, bA360O19.2, ULG3	uc003mze.3	Q06430	OTTHUMG00000014244	ENST00000379597.3:c.930T>C	6.37:g.10621588T>C		Somatic	44	0		WXS	Illumina HiSeq	.	25	9	NM_145649		Silent	SNP	ENST00000379597.3	37	CCDS34338.1																																																																																			.		0.468	GCNT2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327912.3	NM_145649	
SKIDA1	387640	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	10	21805461	21805461	+	Missense_Mutation	SNP	T	T	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr10:21805461T>C	ENST00000449193.2	-	4	3543	c.1291A>G	c.(1291-1293)Agc>Ggc	p.S431G	SKIDA1_ENST00000487107.1_5'Flank|SKIDA1_ENST00000444772.3_Missense_Mutation_p.S352G	NM_207371.3	NP_997254.3	Q1XH10	SKDA1_HUMAN	SKI/DACH domain containing 1	350						nucleus (GO:0005634)											GAGGCCCCGCTGCccccctcc	0.612																																					p.S431G		.											.	.	.	0			c.A1291G						.						6.0	8.0	7.0					10																	21805461		2053	4151	6204	SO:0001583	missense	387640	exon4			CCCCGCTGCCCCC	AK131456	CCDS44363.1	10p12.31	2012-06-13	2012-06-13	2012-06-13	ENSG00000180592	ENSG00000180592			32697	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 140"""	C10orf140			Standard	NM_207371		Approved	FLJ45187	uc021pnx.1	Q1XH10	OTTHUMG00000017797	ENST00000449193.2:c.1291A>G	10.37:g.21805461T>C	ENSP00000410041:p.Ser431Gly	Somatic	36	0		WXS	Illumina HiSeq	.	30	15	NM_207371	B1ANA5|Q6ZMX4|Q8N3C3	Missense_Mutation	SNP	ENST00000449193.2	37	CCDS44363.1	.	.	.	.	.	.	.	.	.	.	T	5.784	0.328994	0.10956	.	.	ENSG00000180592	ENST00000449193;ENST00000444772	.	.	.	5.09	5.09	0.68999	.	0.930262	0.09165	N	0.839669	T	0.28267	0.0698	L	0.27053	0.805	0.29154	N	0.878201	P	0.47762	0.9	B	0.40940	0.344	T	0.03597	-1.1021	9	0.23302	T	0.38	-11.9417	12.3741	0.55271	0.0:0.0:0.0:1.0	.	431	E9PAX1	.	G	431;352	.	ENSP00000442432:S352G	S	-	1	0	C10orf140	21845467	0.997000	0.39634	1.000000	0.80357	0.997000	0.91878	1.031000	0.30165	1.919000	0.55581	0.454000	0.30748	AGC	.		0.612	SKIDA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286950.2	NM_207371	
ZSWIM3	140831	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	20	44506452	44506452	+	Missense_Mutation	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr20:44506452T>G	ENST00000255152.2	+	2	1464	c.1255T>G	c.(1255-1257)Ttt>Gtt	p.F419V	ZSWIM3_ENST00000454862.2_Missense_Mutation_p.F413V	NM_080752.3	NP_542790.2	Q96MP5	ZSWM3_HUMAN	zinc finger, SWIM-type containing 3	419							zinc ion binding (GO:0008270)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(15)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)	35		Myeloproliferative disorder(115;0.0122)				CATCCTCTGCTTTGTGGATTA	0.502																																					p.F419V		.											.	.	.	0			c.T1255G						.						75.0	65.0	68.0					20																	44506452		2203	4300	6503	SO:0001583	missense	140831	exon2			CTCTGCTTTGTGG	AL008726	CCDS13381.1	20q13.12	2014-06-13	2003-12-17	2003-12-19	ENSG00000132801	ENSG00000132801		"""Zinc fingers, SWIM-type"""	16157	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 174"""		"""chromosome 20 open reading frame 164"""	C20orf164			Standard	NM_080752		Approved	dJ337O18.7, PPP1R174	uc002xqd.3	Q96MP5	OTTHUMG00000032627	ENST00000255152.2:c.1255T>G	20.37:g.44506452T>G	ENSP00000255152:p.Phe419Val	Somatic	47	0		WXS	Illumina HiSeq	.	26	10	NM_080752	Q9BR13	Missense_Mutation	SNP	ENST00000255152.2	37	CCDS13381.1	.	.	.	.	.	.	.	.	.	.	T	17.43	3.387138	0.61956	.	.	ENSG00000132801	ENST00000255152;ENST00000454862	T;T	0.27104	1.73;1.69	5.41	4.3	0.51218	.	0.174502	0.41194	D	0.000923	T	0.22044	0.0531	L	0.32530	0.975	0.36228	D	0.852477	P;P	0.46395	0.877;0.799	B;B	0.43360	0.417;0.115	T	0.17410	-1.0370	10	0.49607	T	0.09	-13.0007	10.9175	0.47146	0.0:0.0736:0.0:0.9264	.	413;419	E7ETT6;Q96MP5	.;ZSWM3_HUMAN	V	419;413	ENSP00000255152:F419V;ENSP00000406313:F413V	ENSP00000255152:F419V	F	+	1	0	ZSWIM3	43939859	0.993000	0.37304	1.000000	0.80357	0.998000	0.95712	2.455000	0.44988	1.077000	0.40990	0.533000	0.62120	TTT	.		0.502	ZSWIM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079540.1	NM_080752	
TENM1	10178	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	X	123805577	123805577	+	Missense_Mutation	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chrX:123805577T>G	ENST00000371130.3	-	6	1187	c.1124A>C	c.(1123-1125)tAc>tCc	p.Y375S	TENM1_ENST00000422452.2_Missense_Mutation_p.Y375S	NM_014253.3	NP_055068.2	Q9UKZ4	TEN1_HUMAN	teneurin transmembrane protein 1	375					immune response (GO:0006955)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neuropeptide signaling pathway (GO:0007218)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|response to stress (GO:0006950)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|nuclear matrix (GO:0016363)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	heparin binding (GO:0008201)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)										AATTGGAGAGTAAGTAGTGTC	0.408																																					p.Y375S		.											.	.	.	0			c.A1124C						.						180.0	157.0	165.0					X																	123805577		2203	4300	6503	SO:0001583	missense	10178	exon6			GGAGAGTAAGTAG	AF100772	CCDS14609.1, CCDS55488.1	Xq25	2012-10-02	2012-10-02	2012-10-02	ENSG00000009694	ENSG00000009694			8117	protein-coding gene	gene with protein product		300588	"""tenascin M"", ""odz, odd Oz/ten-m homolog 1 (Drosophila)"""	ODZ3, TNM, ODZ1		10331952, 10341219	Standard	NM_001163278		Approved	TEN-M1	uc010nqy.3	Q9UKZ4	OTTHUMG00000022721	ENST00000371130.3:c.1124A>C	X.37:g.123805577T>G	ENSP00000360171:p.Tyr375Ser	Somatic	58	0		WXS	Illumina HiSeq	.	35	30	NM_001163278	B2RTR5|Q5JZ17	Missense_Mutation	SNP	ENST00000371130.3	37	CCDS14609.1	.	.	.	.	.	.	.	.	.	.	T	10.50	1.367523	0.24771	.	.	ENSG00000009694	ENST00000371130;ENST00000422452	T;T	0.27402	1.67;1.67	5.97	5.97	0.96955	.	0.321148	0.29631	N	0.011612	T	0.16300	0.0392	N	0.11427	0.14	0.43304	D	0.995305	B;B;B	0.22604	0.003;0.008;0.072	B;B;B	0.18871	0.002;0.002;0.023	T	0.15350	-1.0440	10	0.20519	T	0.43	.	10.5658	0.45171	0.1459:0.0:0.0:0.8541	.	374;375;375	B7ZMH4;B2RTR5;Q9UKZ4	.;.;TEN1_HUMAN	S	375	ENSP00000360171:Y375S;ENSP00000403954:Y375S	ENSP00000360171:Y375S	Y	-	2	0	ODZ1	123633258	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.983000	0.49345	1.999000	0.58509	0.481000	0.45027	TAC	.		0.408	TENM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058985.1	NM_014253	
TAP1	6890	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	6	32820888	32820888	+	Missense_Mutation	SNP	G	G	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr6:32820888G>A	ENST00000354258.4	-	1	867	c.706C>T	c.(706-708)Ctt>Ttt	p.L236F	PSMB9_ENST00000453265.2_5'Flank|PSMB9_ENST00000374859.2_5'Flank|PSMB9_ENST00000395330.1_Intron|TAP1_ENST00000425148.2_5'Flank	NM_000593.5	NP_000584.2	Q03518	TAP1_HUMAN	transporter 1, ATP-binding cassette, sub-family B (MDR/TAP)	236					antigen processing and presentation of endogenous peptide antigen via MHC class I (GO:0019885)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytosol to ER transport (GO:0046967)|defense response (GO:0006952)|intracellular transport of viral protein in host cell (GO:0019060)|peptide transport (GO:0015833)|transmembrane transport (GO:0055085)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrion (GO:0005739)|TAP complex (GO:0042825)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|MHC class Ib protein binding (GO:0023029)|peptide antigen binding (GO:0042605)|peptide transporter activity (GO:0015197)|protein homodimerization activity (GO:0042803)|TAP1 binding (GO:0046978)|TAP2 binding (GO:0046979)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(10)|lung(4)|prostate(1)|skin(1)	21					Lapatinib(DB01259)	CAGCCTAGAAGCCGACGCACA	0.672																																					p.L236F		.											.	.	.	0			c.C706T						.						20.0	23.0	22.0					6																	32820888		1508	2708	4216	SO:0001583	missense	6890	exon1			CTAGAAGCCGACG		CCDS4758.1	6p21.3	2014-09-17			ENSG00000168394	ENSG00000168394		"""ATP binding cassette transporters / subfamily B"""	43	protein-coding gene	gene with protein product		170260		ABCB2		1529427, 1946428	Standard	NM_000593		Approved	PSF1, RING4, D6S114E	uc003ocg.3	Q03518	OTTHUMG00000031067	ENST00000354258.4:c.706C>T	6.37:g.32820888G>A	ENSP00000346206:p.Leu236Phe	Somatic	50	0		WXS	Illumina HiSeq	.	43	12	NM_000593	Q16149|Q96CP4	Missense_Mutation	SNP	ENST00000354258.4	37	CCDS4758.1	.	.	.	.	.	.	.	.	.	.	G	16.72	3.200762	0.58234	.	.	ENSG00000168394	ENST00000354258	D	0.84873	-1.91	4.52	1.67	0.24075	ABC transporter, transmembrane domain, type 1 (1);	.	.	.	.	T	0.76357	0.3976	M	0.84948	2.725	0.38584	D	0.950259	P	0.37398	0.593	B	0.38194	0.267	T	0.73464	-0.3974	9	0.87932	D	0	-0.0037	3.5282	0.07766	0.2138:0.0:0.5791:0.2071	.	236	Q03518	TAP1_HUMAN	F	236	ENSP00000346206:L236F	ENSP00000346206:L236F	L	-	1	0	TAP1	32928866	0.998000	0.40836	0.001000	0.08648	0.404000	0.30871	2.949000	0.49074	0.136000	0.18733	0.637000	0.83480	CTT	.		0.672	TAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076087.2	NM_000593	
SIPA1	6494	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	11	65416935	65416935	+	Missense_Mutation	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr11:65416935T>G	ENST00000394224.3	+	10	2805	c.2509T>G	c.(2509-2511)Tcg>Gcg	p.S837A	SIPA1_ENST00000394227.3_Missense_Mutation_p.S735A|MIR4489_ENST00000578869.1_RNA|SIPA1_ENST00000534313.1_Missense_Mutation_p.S837A|SIPA1_ENST00000527525.1_Missense_Mutation_p.S735A	NM_153253.29	NP_694985.29	Q96FS4	SIPA1_HUMAN	signal-induced proliferation-associated 1	837					cell proliferation (GO:0008283)|cellular response to water deprivation (GO:0042631)|cytoskeleton organization (GO:0007010)|intracellular signal transduction (GO:0035556)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell growth (GO:0030308)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Rap GTPase activity (GO:0032854)|signal transduction (GO:0007165)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|protein complex (GO:0043234)|transport vesicle (GO:0030133)	GTPase activator activity (GO:0005096)|Rap GTPase activator activity (GO:0046582)			cervix(1)|endometrium(2)|large_intestine(2)|lung(3)|prostate(1)|urinary_tract(1)	10						CAGCCAGAACTCGCTGTCACC	0.627																																					p.S837A		.											.	.	.	0			c.T2509G						.						53.0	48.0	50.0					11																	65416935		2200	4295	6495	SO:0001583	missense	6494	exon10			CAGAACTCGCTGT	AH006363, BC010492, BM677738	CCDS8108.1	11q13.3	2008-09-12	2008-09-12		ENSG00000213445	ENSG00000213445			10885	protein-coding gene	gene with protein product		602180				9027487	Standard	NM_006747		Approved	SPA1	uc001ofb.2	Q96FS4	OTTHUMG00000166541	ENST00000394224.3:c.2509T>G	11.37:g.65416935T>G	ENSP00000377771:p.Ser837Ala	Somatic	31	0		WXS	Illumina HiSeq	.	31	13	NM_006747	O14518|O60484|O60618|Q2YD83	Missense_Mutation	SNP	ENST00000394224.3	37	CCDS8108.1	.	.	.	.	.	.	.	.	.	.	T	10.08	1.252588	0.22880	.	.	ENSG00000213445	ENST00000534313;ENST00000527525;ENST00000394224;ENST00000394227	D;D;D;D	0.82526	-1.61;-1.62;-1.61;-1.62	4.63	-4.51	0.03483	.	1.491090	0.04737	U	0.422154	T	0.66607	0.2806	L	0.27053	0.805	0.09310	N	1	B;B	0.18741	0.03;0.003	B;B	0.21917	0.037;0.01	T	0.50233	-0.8852	10	0.15499	T	0.54	-7.0856	2.3133	0.04192	0.1457:0.4101:0.149:0.2951	.	735;837	F6RY50;Q96FS4	.;SIPA1_HUMAN	A	837;735;837;735	ENSP00000436269:S837A;ENSP00000433686:S735A;ENSP00000377771:S837A;ENSP00000377774:S735A	ENSP00000377771:S837A	S	+	1	0	SIPA1	65173511	0.000000	0.05858	0.086000	0.20670	0.702000	0.40608	-0.025000	0.12413	-0.351000	0.08249	0.379000	0.24179	TCG	.		0.627	SIPA1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390356.1	NM_006747	
VPS41	27072	hgsc.bcm.edu	37	7	38791865	38791865	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr7:38791865G>T	ENST00000310301.4	-	22	1891	c.1837C>A	c.(1837-1839)Cat>Aat	p.H613N	VPS41_ENST00000395969.2_Missense_Mutation_p.H588N	NM_014396.3	NP_055211.2	P49754	VPS41_HUMAN	vacuolar protein sorting 41 homolog (S. cerevisiae)	613					Golgi vesicle transport (GO:0048193)|intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	cytosol (GO:0005829)|early endosome (GO:0005769)|Golgi-associated vesicle (GO:0005798)|HOPS complex (GO:0030897)|late endosome (GO:0005770)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)	zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(5)|kidney(4)|large_intestine(5)|lung(17)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(4)	44						TGTTTTTCATGGTAACGCTGC	0.408																																					p.H613N		.											.	.	.	0			c.C1837A						.						199.0	187.0	191.0					7																	38791865		2203	4300	6503	SO:0001583	missense	27072	exon22			TTTCATGGTAACG	U87309	CCDS5457.1, CCDS5458.2	7p14.1-p13	2009-05-08	2006-12-19		ENSG00000006715	ENSG00000006715			12713	protein-coding gene	gene with protein product		605485	"""vacuolar protein sorting 41 (yeast homolog)"", ""vacuolar protein sorting 41 (yeast)"""			9159129	Standard	NM_080631		Approved	HVSP41	uc003tgy.3	P49754	OTTHUMG00000023629	ENST00000310301.4:c.1837C>A	7.37:g.38791865G>T	ENSP00000309457:p.His613Asn	Somatic	147	0		WXS	Illumina HiSeq	.	83	3	NM_014396	E9PF36|Q86TP8|Q99851|Q99852	Missense_Mutation	SNP	ENST00000310301.4	37	CCDS5457.1	.	.	.	.	.	.	.	.	.	.	G	29.5	5.015351	0.93404	.	.	ENSG00000006715	ENST00000310301;ENST00000395969	T;T	0.18502	2.21;2.21	5.57	5.57	0.84162	Tetratricopeptide-like helical (1);	0.000000	0.85682	D	0.000000	T	0.50548	0.1622	M	0.88450	2.955	0.80722	D	1	D;D;D	0.89917	1.0;0.999;0.999	D;D;D	0.91635	0.999;0.997;0.997	T	0.52139	-0.8615	10	0.36615	T	0.2	-18.7415	19.5404	0.95271	0.0:0.0:1.0:0.0	.	613;588;613	B2RB94;E9PF36;P49754	.;.;VPS41_HUMAN	N	613;588	ENSP00000309457:H613N;ENSP00000379297:H588N	ENSP00000309457:H613N	H	-	1	0	VPS41	38758390	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.787000	0.99055	2.623000	0.88846	0.585000	0.79938	CAT	.		0.408	VPS41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226986.3		
PAIP2	51247	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	5	138700374	138700374	+	Missense_Mutation	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr5:138700374T>G	ENST00000394795.2	+	3	1251	c.260T>G	c.(259-261)aTc>aGc	p.I87S	CTB-43P18.1_ENST00000503553.3_RNA|PAIP2_ENST00000511706.1_Intron|PAIP2_ENST00000510080.1_Missense_Mutation_p.I87S|PAIP2_ENST00000265192.4_Missense_Mutation_p.I87S|PAIP2_ENST00000511381.1_3'UTR			Q9BPZ3	PAIP2_HUMAN	poly(A) binding protein interacting protein 2	87					memory (GO:0007613)|negative regulation of translational initiation (GO:0045947)|regulation of long-term synaptic potentiation (GO:1900271)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)	mRNA binding (GO:0003729)|translation repressor activity (GO:0030371)			kidney(1)|large_intestine(2)|lung(2)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			ATGGACCAAATCCAAGACCAG	0.378																																					p.I87S		.											.	.	.	0			c.T260G						.						112.0	98.0	103.0					5																	138700374		2203	4300	6503	SO:0001583	missense	51247	exon3			ACCAAATCCAAGA	AF151052	CCDS4211.1	5q32	2008-02-05			ENSG00000120727	ENSG00000120727			17970	protein-coding gene	gene with protein product		605604				11172725, 16804161	Standard	NM_016480		Approved	PAIP2A	uc003led.3	Q9BPZ3	OTTHUMG00000129227	ENST00000394795.2:c.260T>G	5.37:g.138700374T>G	ENSP00000378275:p.Ile87Ser	Somatic	60	0		WXS	Illumina HiSeq	.	49	17	NM_001033112	B2RBI1|D3DQC6|Q49A06|Q9H0Y5|Q9P0Q8	Missense_Mutation	SNP	ENST00000394795.2	37	CCDS4211.1	.	.	.	.	.	.	.	.	.	.	T	17.06	3.292429	0.59976	.	.	ENSG00000120727	ENST00000507755;ENST00000265192;ENST00000394795;ENST00000510080	.	.	.	5.79	4.62	0.57501	.	0.059705	0.64402	D	0.000002	T	0.37999	0.1024	L	0.38175	1.15	0.41765	D	0.989736	B	0.33549	0.417	B	0.17098	0.017	T	0.23583	-1.0184	9	0.45353	T	0.12	-13.0963	11.331	0.49477	0.0:0.0714:0.0:0.9286	.	87	Q9BPZ3	PAIP2_HUMAN	S	87	.	ENSP00000265192:I87S	I	+	2	0	PAIP2	138728273	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.851000	0.75425	1.023000	0.39654	0.533000	0.62120	ATC	.		0.378	PAIP2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373002.1	NM_016480	
SAMD4A	23034	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	14	55169112	55169112	+	Missense_Mutation	SNP	T	T	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr14:55169112T>C	ENST00000554335.1	+	3	1192	c.529T>C	c.(529-531)Tat>Cat	p.Y177H	SAMD4A_ENST00000555112.1_3'UTR|SAMD4A_ENST00000251091.5_Missense_Mutation_p.Y177H|SAMD4A_ENST00000392067.3_Missense_Mutation_p.Y177H|SAMD4A_ENST00000357634.3_Missense_Mutation_p.Y176H			Q9UPU9	SMAG1_HUMAN	sterile alpha motif domain containing 4A	177					negative regulation of translation (GO:0017148)|positive regulation of translation (GO:0045727)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|neuron projection (GO:0043005)|synapse (GO:0045202)	poly(A) RNA binding (GO:0044822)|translation repressor activity (GO:0030371)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(10)|prostate(1)|skin(1)	29						GACACACTACTATCACCAAAG	0.522																																					p.Y177H		.											.	.	.	0			c.T529C						.						65.0	61.0	62.0					14																	55169112		2203	4300	6503	SO:0001583	missense	23034	exon2			CACTACTATCACC	AB028976	CCDS32084.1, CCDS55917.1, CCDS55918.1, CCDS32084.2, CCDS55917.2	14q22.2	2013-01-10	2006-01-27	2006-01-27	ENSG00000020577	ENSG00000020577		"""Sterile alpha motif (SAM) domain containing"""	23023	protein-coding gene	gene with protein product	"""smaug homolog (Drosophila)"""	610747	"""sterile alpha motif domain containing 4"""	SAMD4		16221671	Standard	NM_001161577		Approved	KIAA1053, DKFZP434H0350, Smaug, SMG, SMGA, hSmaug1	uc001xbb.4	Q9UPU9	OTTHUMG00000170999	ENST00000554335.1:c.529T>C	14.37:g.55169112T>C	ENSP00000452535:p.Tyr177His	Somatic	30	0		WXS	Illumina HiSeq	.	31	16	NM_015589	A8MPZ5|Q0VA96|Q6PEW4	Missense_Mutation	SNP	ENST00000554335.1	37	CCDS32084.2	.	.	.	.	.	.	.	.	.	.	T	12.61	1.990353	0.35131	.	.	ENSG00000020577	ENST00000554335;ENST00000392067;ENST00000305831;ENST00000251091;ENST00000357634	T;T;T;T	0.73681	-0.73;-0.73;-0.77;-0.73	6.17	5.04	0.67666	.	0.205098	0.43260	D	0.000591	T	0.52565	0.1742	N	0.13043	0.29	0.22226	N	0.999275	B;B;B	0.18461	0.028;0.004;0.006	B;B;B	0.13407	0.009;0.003;0.004	T	0.30327	-0.9982	10	0.15952	T	0.53	-16.3418	7.8067	0.29206	0.0:0.0688:0.1397:0.7915	.	76;177;177	Q9UPU9-2;Q9UPU9-3;Q9UPU9	.;.;SMAG1_HUMAN	H	177;177;177;176;176	ENSP00000452535:Y177H;ENSP00000375919:Y177H;ENSP00000251091:Y176H;ENSP00000350261:Y176H	ENSP00000306381:Y177H	Y	+	1	0	SAMD4A	54238862	1.000000	0.71417	1.000000	0.80357	0.739000	0.42172	3.859000	0.55987	2.371000	0.80710	0.533000	0.62120	TAT	.		0.522	SAMD4A-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000411186.1	NM_015589	
MIR9-3	407051	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	15	89911321	89911321	+	RNA	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr15:89911321A>C	ENST00000385084.1	+	0	74					NR_029692.1				microRNA 9-3																		GATAACCGAAAGTAGAAATGA	0.622																																					.		.											.	.	.	0			.						.						33.0	36.0	35.0					15																	89911321		1565	3581	5146			407051	.			ACCGAAAGTAGAA			15q26.1	2011-09-12		2008-12-18	ENSG00000207819	ENSG00000207819		"""ncRNAs / Micro RNAs"""	31646	non-coding RNA	RNA, micro		611188		MIRN9-3			Standard	NR_029692		Approved	hsa-mir-9-3					15.37:g.89911321A>C		Somatic	103	0		WXS	Illumina HiSeq	.	101	53	.		RNA	SNP	ENST00000385084.1	37																																																																																				.		0.622	MIR9-3-201	KNOWN	basic	miRNA	miRNA		NR_029692	
VWC2L	402117	hgsc.bcm.edu	37	2	215279158	215279158	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr2:215279158G>T	ENST00000312504.5	+	2	1043	c.241G>T	c.(241-243)Gat>Tat	p.D81Y	VWC2L_ENST00000427124.1_Missense_Mutation_p.D81Y|AC107218.3_ENST00000412896.1_RNA|AC107218.3_ENST00000437883.1_RNA	NM_001080500.2	NP_001073969.1	B2RUY7	VWC2L_HUMAN	von Willebrand factor C domain containing protein 2-like	81	VWFC 1. {ECO:0000255|PROSITE- ProRule:PRU00220}.				negative regulation of BMP signaling pathway (GO:0030514)|positive regulation of neuron differentiation (GO:0045666)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|extracellular space (GO:0005615)|synapse (GO:0045202)				breast(1)|endometrium(1)|large_intestine(3)|lung(10)|prostate(1)	16						CTGTGCTCTAGATGGACCTGT	0.458																																					p.D81Y		.											VWC2L,NS,carcinoma,0,1	VWC2L	0	0			c.G241T						.						90.0	91.0	90.0					2																	215279158		1936	4131	6067	SO:0001583	missense	402117	exon2			GCTCTAGATGGAC	AB374231	CCDS46509.1	2q34-q35	2011-01-25	2011-01-25		ENSG00000174453	ENSG00000174453			37203	protein-coding gene	gene with protein product			"""von Willebrand factor C domain-containing protein 2-like"""				Standard	NM_001080500		Approved		uc002vet.2	B2RUY7	OTTHUMG00000154811	ENST00000312504.5:c.241G>T	2.37:g.215279158G>T	ENSP00000308976:p.Asp81Tyr	Somatic	91	0		WXS	Illumina HiSeq	.	68	3	NM_001080500	A6NC69|B2RUW7|B7X8X1	Missense_Mutation	SNP	ENST00000312504.5	37	CCDS46509.1	.	.	.	.	.	.	.	.	.	.	G	27.3	4.815823	0.90790	.	.	ENSG00000174453	ENST00000312504;ENST00000427124	T;T	0.65916	-0.18;-0.18	6.08	6.08	0.98989	.	0.000000	0.85682	D	0.000000	T	0.71221	0.3314	N	0.24115	0.695	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.991	T	0.73180	-0.4064	10	0.72032	D	0.01	-7.0145	20.6634	0.99662	0.0:0.0:1.0:0.0	.	81;81	B7ZW27;B2RUY7	.;VWC2L_HUMAN	Y	81	ENSP00000308976:D81Y;ENSP00000403779:D81Y	ENSP00000308976:D81Y	D	+	1	0	VWC2L	214987403	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.827000	0.99397	2.894000	0.99253	0.655000	0.94253	GAT	.		0.458	VWC2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337175.1	NM_001080500	
ANKFY1	51479	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	17	4098471	4098471	+	Splice_Site	SNP	G	G	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr17:4098471G>C	ENST00000341657.4	-	10	1209	c.1174C>G	c.(1174-1176)Cta>Gta	p.L392V	ANKFY1_ENST00000570535.1_Splice_Site_p.L434V|ANKFY1_ENST00000574367.1_Splice_Site_p.L392V|Y_RNA_ENST00000384660.1_RNA|ANKFY1_ENST00000433651.1_Splice_Site_p.L392V	NM_016376.3	NP_057460.3	Q9P2R3	ANFY1_HUMAN	ankyrin repeat and FYVE domain containing 1	392					endosomal vesicle fusion (GO:0034058)|endosome localization (GO:0032439)|Golgi to lysosome transport (GO:0090160)|positive regulation of pinocytosis (GO:0048549)|retrograde transport, endosome to Golgi (GO:0042147)	early endosome (GO:0005769)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|macropinosome (GO:0044354)|membrane (GO:0016020)	metal ion binding (GO:0046872)|phosphatidylinositol phosphate binding (GO:1901981)|Rab GTPase binding (GO:0017137)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(11)|liver(1)|lung(5)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	32						TCTAAATCTAGTCTGAAAAGC	0.453																																					p.L434V		.											.	.	.	0			c.C1300G						.						47.0	49.0	49.0					17																	4098471		1995	4177	6172	SO:0001630	splice_region_variant	51479	exon10			AATCTAGTCTGAA	AB033081	CCDS42236.1, CCDS58502.1	17p13.3	2013-01-10			ENSG00000185722	ENSG00000185722		"""Zinc fingers, FYVE domain containing"", ""BTB/POZ domain containing"", ""Ankyrin repeat domain containing"""	20763	protein-coding gene	gene with protein product		607927				10940552, 17273843	Standard	NM_016376		Approved	ANKHZN, KIAA1255, ZFYVE14, BTBD23	uc002fxn.3	Q9P2R3	OTTHUMG00000177727	ENST00000341657.4:c.1173-1C>G	17.37:g.4098471G>C		Somatic	46	0		WXS	Illumina HiSeq	.	16	6	NM_001257999	A8KA65|Q5RKV4|Q9ULG5	Missense_Mutation	SNP	ENST00000341657.4	37		.	.	.	.	.	.	.	.	.	.	G	7.363	0.625177	0.14257	.	.	ENSG00000185722	ENST00000341657;ENST00000535427;ENST00000433651	T;T	0.63913	-0.07;0.7	5.21	-2.54	0.06307	Ankyrin repeat-containing domain (4);	0.000000	0.64402	D	0.000003	T	0.33498	0.0865	N	0.10685	0.025	0.37963	D	0.933037	P;B;B;B;P	0.45902	0.868;0.359;0.406;0.3;0.493	B;B;B;B;B	0.41946	0.343;0.157;0.371;0.164;0.214	T	0.49273	-0.8957	10	0.05351	T	0.99	-2.6211	13.6893	0.62535	0.3978:0.0:0.6022:0.0	.	333;392;392;392;434	F5H754;Q9P2R3-3;Q9P2R3;Q9P2R3-2;Q9P2R3-4	.;.;ANFY1_HUMAN;.;.	V	392;333;392	ENSP00000343362:L392V;ENSP00000416005:L392V	ENSP00000343362:L392V	L	-	1	2	ANKFY1	4045220	0.024000	0.19004	0.021000	0.16686	0.813000	0.45954	0.313000	0.19415	-0.372000	0.07992	-0.302000	0.09304	CTA	.		0.453	ANKFY1-008	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000438702.1	NM_016376	Missense_Mutation
MARCH6	10299	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	5	10433774	10433774	+	Missense_Mutation	SNP	C	C	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr5:10433774C>T	ENST00000274140.5	+	26	2843	c.2711C>T	c.(2710-2712)cCt>cTt	p.P904L	MARCH6_ENST00000449913.2_Missense_Mutation_p.P856L|MARCH6_ENST00000503788.1_Missense_Mutation_p.P799L|MARCH6_ENST00000510792.1_Missense_Mutation_p.P602L	NM_005885.3	NP_005876.2	O60337	MARH6_HUMAN	membrane-associated ring finger (C3HC4) 6, E3 ubiquitin protein ligase	904					protein K48-linked ubiquitination (GO:0070936)	integral component of endoplasmic reticulum membrane (GO:0030176)|membrane (GO:0016020)	enzyme binding (GO:0019899)|ligase activity (GO:0016874)|ubiquitin conjugating enzyme binding (GO:0031624)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(7)|lung(35)|ovary(1)|urinary_tract(3)	54						TCTCCACCACCTCCACAGTCA	0.448																																					p.P904L		.											.	.	.	0			c.C2711T						.						217.0	174.0	189.0					5																	10433774		2203	4300	6503	SO:0001583	missense	10299	exon26			CACCACCTCCACA	AB011169	CCDS34135.1, CCDS59487.1, CCDS59488.1	5p15.2	2013-01-09	2012-02-23		ENSG00000145495	ENSG00000145495		"""MARCH membrane-associated ring fingers"", ""RING-type (C3HC4) zinc fingers"""	30550	protein-coding gene	gene with protein product		613297	"""membrane-associated ring finger (C3HC4) 6"""			14722266	Standard	NM_001270660		Approved	TEB4, MARCH-VI, RNF176	uc003jet.2	O60337	OTTHUMG00000162027	ENST00000274140.5:c.2711C>T	5.37:g.10433774C>T	ENSP00000274140:p.Pro904Leu	Somatic	79	0		WXS	Illumina HiSeq	.	114	87	NM_005885	A5PKZ4|B4DKJ2|B4DT33|D3DTC8|O14670|Q86X77	Missense_Mutation	SNP	ENST00000274140.5	37	CCDS34135.1	.	.	.	.	.	.	.	.	.	.	C	14.48	2.549262	0.45383	.	.	ENSG00000145495	ENST00000449913;ENST00000503788;ENST00000274140;ENST00000510792	T;T;T;T	0.42513	1.98;0.97;1.98;0.97	5.61	3.84	0.44239	.	0.104471	0.64402	D	0.000003	T	0.31358	0.0794	L	0.36672	1.1	0.50171	D	0.99985	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.04013	0.001;0.0;0.001;0.0	T	0.05835	-1.0861	10	0.27785	T	0.31	-10.7604	10.8515	0.46773	0.1309:0.8016:0.0:0.0676	.	799;856;484;904	B4DKJ2;B4DT33;B2RBJ1;O60337	.;.;.;MARH6_HUMAN	L	856;799;904;602	ENSP00000414643:P856L;ENSP00000425930:P799L;ENSP00000274140:P904L;ENSP00000424512:P602L	ENSP00000274140:P904L	P	+	2	0	MARCH6	10486774	0.992000	0.36948	0.085000	0.20634	0.677000	0.39632	4.505000	0.60421	0.736000	0.32559	0.563000	0.77884	CCT	.		0.448	MARCH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366919.2	NM_005885	
IDE	3416	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	10	94223499	94223499	+	Missense_Mutation	SNP	T	T	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr10:94223499T>C	ENST00000265986.6	-	21	2806	c.2750A>G	c.(2749-2751)aAt>aGt	p.N917S	IDE_ENST00000496903.1_5'UTR|IDE_ENST00000371581.5_Missense_Mutation_p.N362S	NM_004969.3	NP_004960.2	P14735	IDE_HUMAN	insulin-degrading enzyme	917					beta-amyloid metabolic process (GO:0050435)|bradykinin catabolic process (GO:0010815)|determination of adult lifespan (GO:0008340)|hormone catabolic process (GO:0042447)|insulin catabolic process (GO:1901143)|insulin metabolic process (GO:1901142)|insulin receptor signaling pathway (GO:0008286)|negative regulation of proteolysis (GO:0045861)|positive regulation of protein oligomerization (GO:0032461)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|protein homotetramerization (GO:0051289)|proteolysis (GO:0006508)|proteolysis involved in cellular protein catabolic process (GO:0051603)|ubiquitin homeostasis (GO:0010992)|viral process (GO:0016032)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic proteasome complex (GO:0031597)|extracellular space (GO:0005615)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|beta-amyloid binding (GO:0001540)|beta-endorphin binding (GO:0031626)|glycoprotein binding (GO:0001948)|insulin binding (GO:0043559)|metalloendopeptidase activity (GO:0004222)|peptide binding (GO:0042277)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|ubiquitin binding (GO:0043130)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(10)|liver(1)|lung(10)|ovary(2)|urinary_tract(2)	33					"""""""Insulin(DB00071)|Bacitracin(DB00626)|Insulin Regular(DB00030)"""	TCTGTCAAAATTATATTGCTG	0.373																																					p.N917S		.											.	.	.	0			c.A2750G						.						132.0	130.0	131.0					10																	94223499		2203	4300	6503	SO:0001583	missense	3416	exon21			TCAAAATTATATT	M21188	CCDS7421.1, CCDS53554.1	10q23-q25	2007-03-27			ENSG00000119912	ENSG00000119912			5381	protein-coding gene	gene with protein product	"""insulysin"""	146680				2293021	Standard	NM_004969		Approved		uc001kia.3	P14735	OTTHUMG00000018759	ENST00000265986.6:c.2750A>G	10.37:g.94223499T>C	ENSP00000265986:p.Asn917Ser	Somatic	79	0		WXS	Illumina HiSeq	.	46	21	NM_004969	B2R721|B7ZAU2|D3DR35|Q5T5N2	Missense_Mutation	SNP	ENST00000265986.6	37	CCDS7421.1	.	.	.	.	.	.	.	.	.	.	T	13.87	2.367143	0.41902	.	.	ENSG00000119912	ENST00000265986;ENST00000371581	T;T	0.32272	1.49;1.46	5.61	5.61	0.85477	Metalloenzyme, LuxS/M16 peptidase-like, metal-binding (1);	0.110594	0.64402	D	0.000017	T	0.39009	0.1062	M	0.61703	1.905	0.54753	D	0.999987	P;D	0.58970	0.777;0.984	B;P	0.49953	0.292;0.627	T	0.20405	-1.0276	10	0.10111	T	0.7	-13.7353	16.0994	0.81158	0.0:0.0:0.0:1.0	.	917;362	P14735;B3KSB8	IDE_HUMAN;.	S	917;362	ENSP00000265986:N917S;ENSP00000360637:N362S	ENSP00000265986:N917S	N	-	2	0	IDE	94213479	1.000000	0.71417	1.000000	0.80357	0.485000	0.33311	7.760000	0.85248	2.261000	0.74972	0.533000	0.62120	AAT	.		0.373	IDE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049393.1	NM_004969	
MARCH2	51257	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	19	8486775	8486775	+	Silent	SNP	C	C	T	rs368370666		TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr19:8486775C>T	ENST00000602117.1	+	2	506	c.51C>T	c.(49-51)tcC>tcT	p.S17S	RP11-886P16.6_ENST00000595706.1_RNA|MARCH2_ENST00000381035.4_Silent_p.S17S|MARCH2_ENST00000601283.1_Silent_p.S17S|MARCH2_ENST00000215555.2_Silent_p.S17S|MARCH2_ENST00000393944.1_Silent_p.S17S			Q9P0N8	MARH2_HUMAN	membrane-associated ring finger (C3HC4) 2, E3 ubiquitin protein ligase	17					endocytosis (GO:0006897)|protein ubiquitination (GO:0016567)	cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(1)|lung(3)|ovary(3)|skin(1)|urinary_tract(1)	10						GTGACTGCTCCGGCAGCCCTG	0.677													C|||	1	0.000199681	0.0	0.0	5008	,	,		16433	0.0		0.0	False		,,,				2504	0.001				p.S17S		.											.	.	.	0			c.C51T						.	C	,,	0,4406		0,0,2203	50.0	50.0	50.0		51,51,51	-5.2	0.8	19		50	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous	MARCH2	NM_001005415.1,NM_001005416.1,NM_016496.4	,,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,,	17/247,17/177,17/247	8486775	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	51257	exon2			CTGCTCCGGCAGC	AF151074	CCDS12202.1, CCDS32894.1	19p13.2	2013-01-09	2012-02-23			ENSG00000099785		"""MARCH membrane-associated ring fingers"", ""RING-type (C3HC4) zinc fingers"""	28038	protein-coding gene	gene with protein product		613332	"""membrane-associated ring finger (C3HC4) 2"""			11042152, 14722266	Standard	NM_016496		Approved	HSPC240, MARCH-II, RNF172	uc002mjw.3	Q9P0N8		ENST00000602117.1:c.51C>T	19.37:g.8486775C>T		Somatic	67	0		WXS	Illumina HiSeq	.	47	21	NM_001005415	A6NP10|Q5H785|Q8N5A3|Q96B78	Silent	SNP	ENST00000602117.1	37	CCDS12202.1																																																																																			.		0.677	MARCH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460361.2	NM_016496	
SF3B1	23451	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	2	198288622	198288622	+	Silent	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr2:198288622A>C	ENST00000335508.6	-	2	196	c.105T>G	c.(103-105)tcT>tcG	p.S35S	SF3B1_ENST00000487698.1_Silent_p.S35S|SF3B1_ENST00000409915.4_Silent_p.S35S|SF3B1_ENST00000414963.2_Silent_p.S35S	NM_012433.2	NP_036565.2	O75533	SF3B1_HUMAN	splicing factor 3b, subunit 1, 155kDa	35					anterior/posterior pattern specification (GO:0009952)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U12-type spliceosomal complex (GO:0005689)	chromatin binding (GO:0003682)|poly(A) RNA binding (GO:0044822)			NS(35)|breast(10)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(524)|kidney(4)|large_intestine(10)|lung(19)|ovary(1)|pancreas(4)|prostate(6)|salivary_gland(1)|skin(4)|testis(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	633			OV - Ovarian serous cystadenocarcinoma(117;0.246)			AATAACCTGTAGAATCGAGGC	0.398			Mis		myelodysplastic syndrome																																p.S35S		.		Dom	yes		2	2q33.1	23451	"""splicing factor 3b, subunit 1, 155kDa"""		L	.	.	.	0			c.T105G						.						96.0	86.0	89.0					2																	198288622		2203	4300	6503	SO:0001819	synonymous_variant	23451	exon2			ACCTGTAGAATCG	AF054284	CCDS33356.1, CCDS46479.1	2q33.1	2014-09-17	2002-08-29		ENSG00000115524	ENSG00000115524			10768	protein-coding gene	gene with protein product		605590	"""splicing factor 3b, subunit 1, 155kD"""			9585501	Standard	XM_005246428		Approved	SAP155, SF3b155, PRPF10, Prp10, Hsh155	uc002uue.3	O75533	OTTHUMG00000154447	ENST00000335508.6:c.105T>G	2.37:g.198288622A>C		Somatic	67	0		WXS	Illumina HiSeq	.	39	19	NM_012433	E9PCH3	Silent	SNP	ENST00000335508.6	37	CCDS33356.1																																																																																			.		0.398	SF3B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335245.2		
LOC101927795	101927795	hgsc.bcm.edu	37	2	201642244	201642244	+	RNA	SNP	A	A	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr2:201642244A>T	ENST00000447972.3	-	0	1754				AOX2P_ENST00000467645.1_RNA|RNU1-133P_ENST00000364867.1_RNA																							gagtcacttaagaggagtcaa	0.413																																					.		.											.	.	.	0			.						.																																					344454	.			CACTTAAGAGGAG																													2.37:g.201642244A>T		Somatic	10	0		WXS	Illumina HiSeq	.	5	4	.		RNA	SNP	ENST00000447972.3	37																																																																																				.		0.413	AC007163.6-001	KNOWN	basic	antisense	antisense	OTTHUMT00000335879.3		
ATP6V1G1	9550	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	9	117359886	117359886	+	Missense_Mutation	SNP	G	G	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr9:117359886G>A	ENST00000374050.3	+	3	313	c.220G>A	c.(220-222)Gag>Aag	p.E74K		NM_004888.3	NP_004879.1	O75348	VATG1_HUMAN	ATPase, H+ transporting, lysosomal 13kDa, V1 subunit G1	74					cellular iron ion homeostasis (GO:0006879)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|proton transport (GO:0015992)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)|vacuolar proton-transporting V-type ATPase complex (GO:0016471)	ATPase binding (GO:0051117)|hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances (GO:0016820)			endometrium(1)|lung(2)|prostate(1)|skin(1)	5						CACTGAAGTGGAGAAGGAGAC	0.517																																					p.E74K		.											.	.	.	0			c.G220A						.						106.0	91.0	96.0					9																	117359886		2203	4300	6503	SO:0001583	missense	9550	exon3			GAAGTGGAGAAGG	AF038954	CCDS6807.1	9q33.1	2010-04-21	2006-01-13	2002-05-10	ENSG00000136888	ENSG00000136888		"""ATPases / V-type"""	864	protein-coding gene	gene with protein product		607296	"""ATPase, H+ transporting, lysosomal (vacuolar proton pump), member J"", ""ATPase, H+ transporting, lysosomal 13kDa, V1 subunit G isoform 1"""	ATP6J, ATP6G1		9653160	Standard	NM_004888		Approved	ATP6GL, Vma10, ATP6G, DKFZp547P234	uc004bjc.3	O75348	OTTHUMG00000021023	ENST00000374050.3:c.220G>A	9.37:g.117359886G>A	ENSP00000363162:p.Glu74Lys	Somatic	54	0		WXS	Illumina HiSeq	.	52	16	NM_004888	Q6IB33	Missense_Mutation	SNP	ENST00000374050.3	37	CCDS6807.1	.	.	.	.	.	.	.	.	.	.	G	24.4	4.532207	0.85812	.	.	ENSG00000136888	ENST00000374050	T	0.47869	0.83	6.17	6.17	0.99709	.	0.042296	0.85682	D	0.000000	T	0.55162	0.1903	L	0.57130	1.785	0.80722	D	1	B	0.30763	0.294	B	0.38755	0.281	T	0.47761	-0.9092	10	0.41790	T	0.15	.	20.8794	0.99867	0.0:0.0:1.0:0.0	.	74	O75348	VATG1_HUMAN	K	74	ENSP00000363162:E74K	ENSP00000363162:E74K	E	+	1	0	ATP6V1G1	116399707	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.062000	0.93920	2.941000	0.99782	0.655000	0.94253	GAG	.		0.517	ATP6V1G1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055454.1	NM_004888	
TYK2	7297	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	19	10463198	10463198	+	Missense_Mutation	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr19:10463198T>G	ENST00000525621.1	-	23	3711	c.3230A>C	c.(3229-3231)aAg>aCg	p.K1077T	TYK2_ENST00000529422.1_Intron|TYK2_ENST00000264818.6_Missense_Mutation_p.K1077T|TYK2_ENST00000524462.1_Missense_Mutation_p.K892T	NM_003331.4	NP_003322.3	P29597	TYK2_HUMAN	tyrosine kinase 2	1077	Protein kinase 2. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cytokine-mediated signaling pathway (GO:0019221)|intracellular signal transduction (GO:0035556)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein phosphorylation (GO:0006468)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|growth hormone receptor binding (GO:0005131)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)			breast(1)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(11)|kidney(6)|large_intestine(3)|lung(19)|ovary(4)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	64			OV - Ovarian serous cystadenocarcinoma(20;1.77e-09)|Epithelial(33;3.92e-06)|all cancers(31;8.95e-06)			ATAGTAGAACTTATACTCCTT	0.627																																					p.K1077T		.											.	.	.	0			c.A3230C						.						78.0	78.0	78.0					19																	10463198		2203	4300	6503	SO:0001583	missense	7297	exon23			TAGAACTTATACT		CCDS12236.1	19p13.2	2014-09-17			ENSG00000105397	ENSG00000105397	2.7.10.1		12440	protein-coding gene	gene with protein product		176941				2156206	Standard	NM_003331		Approved	JTK1	uc002moc.4	P29597	OTTHUMG00000166373	ENST00000525621.1:c.3230A>C	19.37:g.10463198T>G	ENSP00000431885:p.Lys1077Thr	Somatic	67	0		WXS	Illumina HiSeq	.	36	14	NM_003331	Q6QB10|Q96CH0	Missense_Mutation	SNP	ENST00000525621.1	37	CCDS12236.1	.	.	.	.	.	.	.	.	.	.	T	19.70	3.877326	0.72294	.	.	ENSG00000105397	ENST00000524462;ENST00000525621;ENST00000264818;ENST00000543792;ENST00000529739	D;D;D;D	0.83250	-1.7;-1.7;-1.7;-1.7	5.35	5.35	0.76521	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.575727	0.15511	N	0.258537	D	0.84110	0.5400	N	0.21282	0.65	0.58432	D	0.999999	D	0.65815	0.995	D	0.69654	0.965	T	0.81660	-0.0832	9	.	.	.	-32.0253	13.3337	0.60505	0.0:0.0:0.0:1.0	.	1077	P29597	TYK2_HUMAN	T	892;1077;1077;824;100	ENSP00000433203:K892T;ENSP00000431885:K1077T;ENSP00000264818:K1077T;ENSP00000436155:K100T	.	K	-	2	0	TYK2	10324198	1.000000	0.71417	1.000000	0.80357	0.599000	0.36880	3.737000	0.55060	2.046000	0.60703	0.449000	0.29647	AAG	.		0.627	TYK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389443.1		
EDEM2	55741	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	20	33722567	33722567	+	Missense_Mutation	SNP	A	A	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr20:33722567A>G	ENST00000374492.3	-	6	781	c.676T>C	c.(676-678)Tgg>Cgg	p.W226R	EDEM2_ENST00000374491.3_Missense_Mutation_p.W189R|EDEM2_ENST00000541621.1_5'UTR|EDEM2_ENST00000542871.1_Intron|EDEM2_ENST00000540582.1_Missense_Mutation_p.W185R	NM_018217.2	NP_060687.2	Q9BV94	EDEM2_HUMAN	ER degradation enhancer, mannosidase alpha-like 2	226					cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)|response to unfolded protein (GO:0006986)	endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(10)|prostate(1)|stomach(1)|upper_aerodigestive_tract(2)	22			BRCA - Breast invasive adenocarcinoma(18;0.00936)			CGGCTCTCCCAGAGGCGCATC	0.577																																					p.W226R	Esophageal Squamous(51;906 1021 24535 36410 39145)	.											.	.	.	0			c.T676C						.						79.0	73.0	75.0					20																	33722567		2203	4300	6503	SO:0001583	missense	55741	exon6			TCTCCCAGAGGCG	AK001645	CCDS13247.1, CCDS46592.1	20q11.22	2006-03-31	2006-03-31	2006-03-31	ENSG00000088298	ENSG00000088298			15877	protein-coding gene	gene with protein product		610302	"""chromosome 20 open reading frame 31"""	C20orf49, C20orf31		15537790, 15579471	Standard	NM_018217		Approved	FLJ10783, bA4204.1	uc002xbo.2	Q9BV94	OTTHUMG00000032322	ENST00000374492.3:c.676T>C	20.37:g.33722567A>G	ENSP00000363616:p.Trp226Arg	Somatic	28	0		WXS	Illumina HiSeq	.	29	13	NM_018217	B4DTG9|Q6GU33|Q6IA89|Q6UWZ4|Q9H4U0|Q9H886|Q9NTL9|Q9NVE6	Missense_Mutation	SNP	ENST00000374492.3	37	CCDS13247.1	.	.	.	.	.	.	.	.	.	.	A	27.5	4.839954	0.91117	.	.	ENSG00000088298	ENST00000374491;ENST00000374492;ENST00000540582	T;T;T	0.72051	-0.62;-0.62;-0.62	5.87	5.87	0.94306	.	0.000000	0.85682	D	0.000000	D	0.82866	0.5130	M	0.68728	2.09	0.80722	D	1	D;D;D	0.76494	0.999;0.998;0.998	D;D;D	0.72625	0.975;0.963;0.978	D	0.84551	0.0644	10	0.87932	D	0	-10.4425	16.5764	0.84681	1.0:0.0:0.0:0.0	.	185;189;226	F5GZ44;Q9BV94-2;Q9BV94	.;.;EDEM2_HUMAN	R	189;226;185	ENSP00000363615:W189R;ENSP00000363616:W226R;ENSP00000441548:W185R	ENSP00000363615:W189R	W	-	1	0	EDEM2	33186228	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.056000	0.93881	2.371000	0.80710	0.533000	0.62120	TGG	.		0.577	EDEM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078842.2	NM_018217	
AOX1	316	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	2	201478642	201478642	+	Missense_Mutation	SNP	T	T	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr2:201478642T>C	ENST00000374700.2	+	15	1805	c.1564T>C	c.(1564-1566)Ttc>Ctc	p.F522L	AOX1_ENST00000485106.1_3'UTR	NM_001159.3	NP_001150.3	Q06278	AOXA_HUMAN	aldehyde oxidase 1	522					inflammatory response (GO:0006954)|reactive oxygen species metabolic process (GO:0072593)|small molecule metabolic process (GO:0044281)|vitamin B6 metabolic process (GO:0042816)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	2 iron, 2 sulfur cluster binding (GO:0051537)|aldehyde oxidase activity (GO:0004031)|electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|iron ion binding (GO:0005506)|molybdopterin cofactor binding (GO:0043546)|NAD binding (GO:0051287)|UDP-N-acetylmuramate dehydrogenase activity (GO:0008762)|xanthine dehydrogenase activity (GO:0004854)			breast(5)|endometrium(3)|kidney(4)|large_intestine(13)|lung(38)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	81					Allopurinol(DB00437)|Aminocaproic Acid(DB00513)|Brimonidine(DB00484)|Famciclovir(DB00426)|Menadione(DB00170)|Mercaptopurine(DB01033)|Methotrexate(DB00563)|Pyrazinamide(DB00339)|Raloxifene(DB00481)|Zaleplon(DB00962)|Zonisamide(DB00909)	CATCATCAGCTTCCTCTTCAA	0.458																																					p.F522L		.											.	.	.	0			c.T1564C						.						101.0	98.0	99.0					2																	201478642		2203	4300	6503	SO:0001583	missense	316	exon15			ATCAGCTTCCTCT	AF017060	CCDS33360.1	2q33	2008-05-20			ENSG00000138356	ENSG00000138356			553	protein-coding gene	gene with protein product		602841				7570184	Standard	NM_001159		Approved	AO, AOH1	uc002uvx.3	Q06278	OTTHUMG00000154536	ENST00000374700.2:c.1564T>C	2.37:g.201478642T>C	ENSP00000363832:p.Phe522Leu	Somatic	30	0		WXS	Illumina HiSeq	.	11	6	NM_001159	O14765|Q53RR8|Q53TV3|Q9BYF0|Q9UPG6	Missense_Mutation	SNP	ENST00000374700.2	37	CCDS33360.1	.	.	.	.	.	.	.	.	.	.	T	13.62	2.290765	0.40494	.	.	ENSG00000138356	ENST00000374700	T	0.23754	1.89	5.33	5.33	0.75918	CO dehydrogenase flavoprotein, C-terminal (3);	0.211604	0.49916	N	0.000136	T	0.24967	0.0606	L	0.44542	1.39	0.53688	D	0.999973	B	0.20164	0.042	B	0.29785	0.107	T	0.05683	-1.0870	10	0.12766	T	0.61	-29.1181	15.4598	0.75346	0.0:0.0:0.0:1.0	.	522	Q06278	ADO_HUMAN	L	522	ENSP00000363832:F522L	ENSP00000363832:F522L	F	+	1	0	AOX1	201186887	1.000000	0.71417	1.000000	0.80357	0.888000	0.51559	3.123000	0.50453	2.234000	0.73211	0.533000	0.62120	TTC	.		0.458	AOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335844.1	NM_001159	
RUSC1	23623	hgsc.bcm.edu;ucsc.edu	37	1	155290956	155290956	+	Intron	SNP	G	G	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr1:155290956G>T	ENST00000368352.5	+	1	65				RUSC1-AS1_ENST00000543656.1_RNA|RUSC1_ENST00000368354.3_Intron|RUSC1-AS1_ENST00000446880.1_RNA|RUSC1-AS1_ENST00000450199.1_RNA|RUSC1_ENST00000368347.4_5'Flank|RUSC1-AS1_ENST00000443642.1_RNA	NM_001105203.1	NP_001098673.1	Q9BVN2	RUSC1_HUMAN	RUN and SH3 domain containing 1						positive regulation of signal transduction (GO:0009967)|protein polyubiquitination (GO:0000209)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)	actin binding (GO:0003779)|SH3/SH2 adaptor activity (GO:0005070)			breast(2)|endometrium(2)|kidney(2)|large_intestine(2)|liver(2)|lung(7)|ovary(2)|skin(1)|urinary_tract(1)	21	Hepatocellular(266;0.0877)|all_hematologic(923;0.145)		Epithelial(20;1.55e-10)|all cancers(21;4.15e-10)|BRCA - Breast invasive adenocarcinoma(34;0.000549)|LUSC - Lung squamous cell carcinoma(543;0.127)			GCGCAGGCTGGAGCCCGGCCG	0.602																																					p.L108L		.											.	.	.	0			c.C324A						.						37.0	53.0	48.0					1																	155290956		2077	4206	6283	SO:0001627	intron_variant	284618	exon2			AGGCTGGAGCCCG	AB026894	CCDS1112.1, CCDS41410.1, CCDS41411.1, CCDS41412.1	1q21-q22	2011-04-28			ENSG00000160753	ENSG00000160753			17153	protein-coding gene	gene with protein product						10760598	Standard	NM_001105203		Approved	NESCA	uc001fkj.2	Q9BVN2	OTTHUMG00000013910	ENST00000368352.5:c.-87+174G>T	1.37:g.155290956G>T		Somatic	44	0		WXS	Illumina HiSeq	.	40	4	NM_001039517	B3KWM9|Q5T9U9|Q5T9V0|Q5T9V1|Q5T9V2|Q9UPY4|Q9Y4T5	Silent	SNP	ENST00000368352.5	37	CCDS41410.1																																																																																			.		0.602	RUSC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039071.1		
MYOM1	8736	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	18	3067439	3067439	+	Missense_Mutation	SNP	T	T	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr18:3067439T>A	ENST00000356443.4	-	38	5212	c.4879A>T	c.(4879-4881)Agg>Tgg	p.R1627W	MYOM1_ENST00000261606.7_Missense_Mutation_p.R1531W|MYOM1_ENST00000400569.3_Missense_Mutation_p.R1627W	NM_003803.3|NM_019856.1	NP_003794.3|NP_062830.1	P52179	MYOM1_HUMAN	myomesin 1	1627	Ig-like C2-type 5.				muscle contraction (GO:0006936)	M band (GO:0031430)|striated muscle myosin thick filament (GO:0005863)	identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|structural constituent of muscle (GO:0008307)			NS(2)|autonomic_ganglia(1)|central_nervous_system(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(20)|ovary(4)|pancreas(1)|prostate(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	77						TACGCGGTCCTCCCAGCCTCG	0.597																																					p.R1627W		.											.	.	.	0			c.A4879T						.						69.0	74.0	72.0					18																	3067439		2203	4300	6503	SO:0001583	missense	8736	exon38			CGGTCCTCCCAGC	AF185573	CCDS45823.1, CCDS45824.1	18p11.31	2014-09-17	2012-10-17		ENSG00000101605	ENSG00000101605		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	7613	protein-coding gene	gene with protein product	"""skelemin"""	603508	"""myomesin 1 (skelemin) (185kD)"", ""myomesin 1 (skelemin) 185kDa"", ""myomesin 1, 185kDa"""			9806852	Standard	NM_019856		Approved		uc002klp.3	P52179	OTTHUMG00000178209	ENST00000356443.4:c.4879A>T	18.37:g.3067439T>A	ENSP00000348821:p.Arg1627Trp	Somatic	59	0		WXS	Illumina HiSeq	.	27	11	NM_003803	Q14BD6|Q6H969|Q6ZUU0	Missense_Mutation	SNP	ENST00000356443.4	37	CCDS45824.1	.	.	.	.	.	.	.	.	.	.	T	16.84	3.233211	0.58777	.	.	ENSG00000101605	ENST00000356443;ENST00000400569;ENST00000261606	T;T;T	0.67865	-0.29;-0.29;-0.29	5.79	5.79	0.91817	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.045733	0.85682	D	0.000000	T	0.71500	0.3347	L	0.36672	1.1	0.27088	N	0.962912	D;P	0.53885	0.963;0.814	P;B	0.56916	0.809;0.29	T	0.68667	-0.5348	10	0.87932	D	0	.	16.1329	0.81458	0.0:0.0:0.0:1.0	.	1531;1627	P52179-2;P52179	.;MYOM1_HUMAN	W	1627;1627;1531	ENSP00000348821:R1627W;ENSP00000383413:R1627W;ENSP00000261606:R1531W	ENSP00000261606:R1531W	R	-	1	2	MYOM1	3057439	1.000000	0.71417	0.710000	0.30468	0.017000	0.09413	8.040000	0.89188	2.208000	0.71279	0.533000	0.62120	AGG	.		0.597	MYOM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441037.2	NM_003803	
DOCK10	55619	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	2	225738772	225738772	+	Missense_Mutation	SNP	C	C	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr2:225738772C>A	ENST00000258390.7	-	11	1265	c.1198G>T	c.(1198-1200)Gcc>Tcc	p.A400S	DOCK10_ENST00000409592.3_Missense_Mutation_p.A394S	NM_014689.2	NP_055504.2	Q96BY6	DOC10_HUMAN	dedicator of cytokinesis 10	400					regulation of cell migration (GO:0030334)|small GTPase mediated signal transduction (GO:0007264)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(3)|cervix(1)|endometrium(6)|kidney(10)|large_intestine(16)|lung(40)|ovary(2)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	87		Renal(207;0.0113)|all_lung(227;0.0486)|Lung NSC(271;0.0653)|all_hematologic(139;0.14)		Epithelial(121;2.37e-10)|all cancers(144;2.26e-07)|Lung(261;0.0143)|LUSC - Lung squamous cell carcinoma(224;0.0178)		GAGTTGAGGGCTTTACAGATG	0.378																																					p.A400S		.											.	.	.	0			c.G1198T						.						134.0	121.0	125.0					2																	225738772		1860	4099	5959	SO:0001583	missense	55619	exon11			TGAGGGCTTTACA	AB014594	CCDS46528.1, CCDS74661.1	2q36.3	2013-01-10			ENSG00000135905	ENSG00000135905		"""Pleckstrin homology (PH) domain containing"""	23479	protein-coding gene	gene with protein product	"""zizimin3"""	611518				12432077	Standard	NM_014689		Approved	ZIZ3, KIAA0694	uc010fwz.1	Q96BY6	OTTHUMG00000153428	ENST00000258390.7:c.1198G>T	2.37:g.225738772C>A	ENSP00000258390:p.Ala400Ser	Somatic	81	0		WXS	Illumina HiSeq	.	45	13	NM_014689	B3FL70|O75178|Q9NW06|Q9NXI8	Missense_Mutation	SNP	ENST00000258390.7	37	CCDS46528.1	.	.	.	.	.	.	.	.	.	.	C	1.429	-0.570657	0.03910	.	.	ENSG00000135905	ENST00000409592;ENST00000258390	T;T	0.35789	1.29;1.29	5.87	1.5	0.22942	.	0.157081	0.64402	D	0.000016	T	0.08980	0.0222	N	0.01086	-1.025	0.31393	N	0.677643	B;B;B	0.10296	0.0;0.003;0.0	B;B;B	0.14578	0.003;0.011;0.002	T	0.37865	-0.9687	10	0.02654	T	1	.	6.4538	0.21918	0.2157:0.5614:0.0:0.2229	.	400;400;394	Q96BY6;Q96BY6-2;B3FL70	DOC10_HUMAN;.;.	S	394;400	ENSP00000386694:A394S;ENSP00000258390:A400S	ENSP00000258390:A400S	A	-	1	0	DOCK10	225447016	1.000000	0.71417	0.998000	0.56505	0.349000	0.29174	3.353000	0.52247	0.199000	0.20427	-1.814000	0.00607	GCC	.		0.378	DOCK10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331246.1		
C9orf85	138241	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	9	74526743	74526743	+	Silent	SNP	G	G	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr9:74526743G>A	ENST00000377031.3	+	1	283	c.93G>A	c.(91-93)gtG>gtA	p.V31V	C9orf85_ENST00000486911.2_Silent_p.V31V|C9orf85_ENST00000334731.2_Silent_p.V31V|ABHD17B_ENST00000377041.2_5'Flank|ABHD17B_ENST00000333421.6_5'Flank			Q96MD7	CI085_HUMAN	chromosome 9 open reading frame 85	31	Lys-rich.									kidney(2)|large_intestine(1)|lung(4)	7						ATAAAAGTGTGCAGACCAAGG	0.522																																					p.V31V		.											.	.	.	0			c.G93A						.						124.0	117.0	119.0					9																	74526743		2203	4300	6503	SO:0001819	synonymous_variant	138241	exon1			AAGTGTGCAGACC	BC010179	CCDS6639.1	9q21.2	2012-03-16			ENSG00000155621	ENSG00000155621			28784	protein-coding gene	gene with protein product						12477932	Standard	NM_182505		Approved	MGC61599	uc004ain.3	Q96MD7	OTTHUMG00000020002	ENST00000377031.3:c.93G>A	9.37:g.74526743G>A		Somatic	47	0		WXS	Illumina HiSeq	.	34	16	NM_182505	Q5W0N1|Q5W0N3|Q6PJW9|Q86U95	Silent	SNP	ENST00000377031.3	37																																																																																				.		0.522	C9orf85-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000052628.2	NM_182505	
IPO11	51194	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	5	61747688	61747688	+	Missense_Mutation	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr5:61747688A>C	ENST00000325324.6	+	5	613	c.444A>C	c.(442-444)ttA>ttC	p.L148F	KIF2A_ENST00000509663.2_Intron|IPO11_ENST00000409296.3_Missense_Mutation_p.L188F	NM_016338.4	NP_057422.3	Q9UI26	IPO11_HUMAN	importin 11	148					ribosomal protein import into nucleus (GO:0006610)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein transporter activity (GO:0008565)			endometrium(2)|kidney(3)|large_intestine(5)|lung(14)|skin(4)|stomach(2)	30		Lung NSC(810;8.99e-06)|Prostate(74;0.0235)|Ovarian(174;0.0511)|Breast(144;0.077)		Lung(70;0.0613)		ACAGAGCATTACTTACCTTCT	0.383																																					p.L188F		.											.	.	.	0			c.A564C						.						149.0	137.0	141.0					5																	61747688		2203	4300	6503	SO:0001583	missense	51194	exon5			AGCATTACTTACC	AF111109	CCDS34167.1, CCDS47217.1	5q12.1	2008-09-19			ENSG00000086200	ENSG00000086200		"""Importins"""	20628	protein-coding gene	gene with protein product		610889					Standard	NM_016338		Approved	RanBP11	uc011cqr.2	Q9UI26	OTTHUMG00000154400	ENST00000325324.6:c.444A>C	5.37:g.61747688A>C	ENSP00000316651:p.Leu148Phe	Somatic	73	0		WXS	Illumina HiSeq	.	66	18	NM_001134779	A6NGJ5|B4DZ73|D3DW98|Q8N5R2|Q9NSJ6|Q9NVB1	Missense_Mutation	SNP	ENST00000325324.6	37	CCDS34167.1	.	.	.	.	.	.	.	.	.	.	A	15.56	2.868485	0.51588	.	.	ENSG00000086200	ENST00000514647;ENST00000325324;ENST00000506200;ENST00000409296	T;T;T;T	0.75367	-0.93;-0.93;-0.93;-0.93	5.36	-2.91	0.05631	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.77738	0.4175	L	0.60067	1.865	0.80722	D	1	D;D	0.67145	0.996;0.993	P;P	0.60541	0.876;0.755	T	0.76756	-0.2842	10	0.51188	T	0.08	.	12.7556	0.57333	0.5041:0.0:0.4959:0.0	.	188;148	Q9UI26-2;Q9UI26	.;IPO11_HUMAN	F	148;148;148;188	ENSP00000427129:L148F;ENSP00000316651:L148F;ENSP00000427274:L148F;ENSP00000386992:L188F	ENSP00000316651:L148F	L	+	3	2	IPO11	61783445	1.000000	0.71417	0.935000	0.37517	0.986000	0.74619	0.851000	0.27751	-0.455000	0.07054	-0.911000	0.02809	TTA	.		0.383	IPO11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335062.1	NM_016338	
SPRY4	81848	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	5	141694180	141694180	+	Missense_Mutation	SNP	C	C	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr5:141694180C>A	ENST00000434127.2	-	2	737	c.494G>T	c.(493-495)tGt>tTt	p.C165F	SPRY4_ENST00000503582.1_5'Flank|SPRY4_ENST00000344120.4_Missense_Mutation_p.C188F	NM_001127496.1	NP_001120968.1	Q9C004	SPY4_HUMAN	sprouty homolog 4 (Drosophila)	165	Cys-rich.				multicellular organismal development (GO:0007275)|negative regulation of MAP kinase activity (GO:0043407)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)				breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(3)|lung(7)|ovary(1)	18		all_hematologic(541;0.118)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTTGCATTTACACTTCCCACA	0.632									Testicular Cancer, Familial Clustering of																												p.C188F		.											.	.	.	0			c.G563T						.						67.0	70.0	69.0					5																	141694180		2203	4300	6503	SO:0001583	missense	81848	exon3	Familial Cancer Database		CATTTACACTTCC	AF227516	CCDS4274.1, CCDS47296.1	5q31.3	2010-08-05			ENSG00000187678	ENSG00000187678			15533	protein-coding gene	gene with protein product		607984				16465403	Standard	NM_030964		Approved		uc010jgi.1	Q9C004	OTTHUMG00000129663	ENST00000434127.2:c.494G>T	5.37:g.141694180C>A	ENSP00000399468:p.Cys165Phe	Somatic	30	0		WXS	Illumina HiSeq	.	40	11	NM_030964	A4FVB2|A4FVB3|Q6QIX2|Q9C003	Missense_Mutation	SNP	ENST00000434127.2	37	CCDS47296.1	.	.	.	.	.	.	.	.	.	.	C	21.8	4.206648	0.79127	.	.	ENSG00000187678	ENST00000344120;ENST00000434127	T;T	0.65178	-0.14;-0.14	5.32	5.32	0.75619	.	0.000000	0.85682	D	0.000000	D	0.82728	0.5100	M	0.86420	2.815	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.85824	0.1387	10	0.87932	D	0	-7.0511	18.9994	0.92828	0.0:1.0:0.0:0.0	.	165	Q9C004	SPY4_HUMAN	F	188;165	ENSP00000344967:C188F;ENSP00000399468:C165F	ENSP00000344967:C188F	C	-	2	0	SPRY4	141674364	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.456000	0.80751	2.486000	0.83907	0.561000	0.74099	TGT	.		0.632	SPRY4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370652.1		
DXO	1797	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	6	31938791	31938791	+	Nonsense_Mutation	SNP	C	C	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr6:31938791C>A	ENST00000375349.3	-	3	901	c.490G>T	c.(490-492)Gaa>Taa	p.E164*	STK19_ENST00000375331.2_5'Flank|DXO_ENST00000337523.5_Nonsense_Mutation_p.E164*|STK19_ENST00000375333.2_5'Flank|DXO_ENST00000478221.1_5'UTR|DXO_ENST00000375356.3_Nonsense_Mutation_p.E164*			O77932	DXO_HUMAN	decapping exoribonuclease	164					metabolic process (GO:0008152)|mRNA catabolic process (GO:0006402)|nuclear mRNA surveillance (GO:0071028)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|RNA destabilization (GO:0050779)	nucleus (GO:0005634)	5'-3' exonuclease activity (GO:0008409)|magnesium ion binding (GO:0000287)|mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|RNA pyrophosphohydrolase activity (GO:0034353)										GTCTCCACTTCACTCAGGTAT	0.602																																					p.E164X		.											.	.	.	0			c.G490T						.						88.0	102.0	97.0					6																	31938791		1510	2707	4217	SO:0001587	stop_gained	1797	exon3			CCACTTCACTCAG	AF059252	CCDS4732.1	6p21.3	2013-09-11	2013-09-11	2013-09-11	ENSG00000204348	ENSG00000204348			2992	protein-coding gene	gene with protein product		605996	"""DOM-3 (C. elegans) homolog Z"", ""dom-3 homolog Z (C. elegans)"""	DOM3Z		9799600, 23523372	Standard	NM_005510		Approved		uc003nyp.1	O77932	OTTHUMG00000031272	ENST00000375349.3:c.490G>T	6.37:g.31938791C>A	ENSP00000364498:p.Glu164*	Somatic	73	0		WXS	Illumina HiSeq	.	54	28	NM_005510	A2CER3|B0UZ80|O15004|O78127|O78128|Q5ST60|Q6IPZ2|Q9NPK4	Nonsense_Mutation	SNP	ENST00000375349.3	37	CCDS4732.1	.	.	.	.	.	.	.	.	.	.	C	37	6.007131	0.97195	.	.	ENSG00000204348	ENST00000337523;ENST00000375349;ENST00000375356	.	.	.	4.71	4.71	0.59529	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.17369	T	0.5	-21.2717	16.5761	0.84648	0.0:1.0:0.0:0.0	.	.	.	.	X	164	.	ENSP00000337759:E164X	E	-	1	0	DOM3Z	32046770	1.000000	0.71417	1.000000	0.80357	0.393000	0.30537	6.993000	0.76245	2.434000	0.82447	0.561000	0.74099	GAA	.		0.602	DXO-006	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076592.3		
AHCYL1	10768	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	1	110555049	110555049	+	Missense_Mutation	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr1:110555049A>C	ENST00000369799.5	+	4	809	c.442A>C	c.(442-444)Ata>Cta	p.I148L	AHCYL1_ENST00000393614.4_Missense_Mutation_p.I101L|AHCYL1_ENST00000359172.3_Missense_Mutation_p.I101L|AHCYL1_ENST00000475081.1_3'UTR	NM_001242673.1|NM_001242674.1|NM_006621.5	NP_001229602.1|NP_001229603.1|NP_006612.2	O43865	SAHH2_HUMAN	adenosylhomocysteinase-like 1	148					mRNA polyadenylation (GO:0006378)|one-carbon metabolic process (GO:0006730)|positive regulation of sodium ion transport (GO:0010765)|protein export from nucleus (GO:0006611)|regulation of anion transport (GO:0044070)|regulation of ion transmembrane transporter activity (GO:0032412)|regulation of mRNA 3'-end processing (GO:0031440)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)	adenosylhomocysteinase activity (GO:0004013)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(6)|ovary(1)|prostate(2)	18		all_epithelial(167;3.58e-05)|all_lung(203;0.000116)|Lung NSC(277;0.000233)		Lung(183;0.0259)|Colorectal(144;0.123)|all cancers(265;0.134)|Epithelial(280;0.141)|LUSC - Lung squamous cell carcinoma(189;0.143)		TGGTGCTAAAATAGTGGGCTG	0.453																																					p.I148L		.											.	.	.	0			c.A442C						.						79.0	81.0	80.0					1																	110555049		2203	4300	6503	SO:0001583	missense	10768	exon4			GCTAAAATAGTGG	U82761	CCDS818.1, CCDS55620.1	1p13	2014-06-12	2009-06-12		ENSG00000168710	ENSG00000168710			344	protein-coding gene	gene with protein product	"""inositol 1,4,5-trisphosphate receptor-binding protein"", ""protein phosphatase 1, regulatory subunit 78"""	607826	"""S-adenosylhomocysteine hydrolase-like 1"""			11904675, 16754674, 12525476	Standard	NM_006621		Approved	XPVKONA, IRBIT, PPP1R78	uc001dyx.3	O43865	OTTHUMG00000011652	ENST00000369799.5:c.442A>C	1.37:g.110555049A>C	ENSP00000358814:p.Ile148Leu	Somatic	15	0		WXS	Illumina HiSeq	.	7	7	NM_006621	B4E168|Q2TAJ6|Q502W8|Q5VSM0|Q6P171|Q96PK4|Q9UG84	Missense_Mutation	SNP	ENST00000369799.5	37	CCDS818.1	.	.	.	.	.	.	.	.	.	.	A	34	5.315335	0.95655	.	.	ENSG00000168710	ENST00000369799;ENST00000359172;ENST00000393614	D;D;D	0.82433	-1.61;-1.61;-1.61	5.71	5.71	0.89125	.	0.042806	0.85682	D	0.000000	D	0.88489	0.6450	M	0.85777	2.775	0.80722	D	1	B	0.21309	0.054	P	0.46275	0.51	D	0.88296	0.2946	10	0.87932	D	0	-24.3066	16.0042	0.80349	1.0:0.0:0.0:0.0	.	148	O43865	SAHH2_HUMAN	L	148;101;101	ENSP00000358814:I148L;ENSP00000352092:I101L;ENSP00000377238:I101L	ENSP00000352092:I101L	I	+	1	0	AHCYL1	110356572	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.474000	0.81024	2.171000	0.68590	0.528000	0.53228	ATA	.		0.453	AHCYL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032243.1		
THSD7A	221981	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	7	11419301	11419301	+	Missense_Mutation	SNP	A	A	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr7:11419301A>T	ENST00000423059.4	-	25	4797	c.4546T>A	c.(4546-4548)Tct>Act	p.S1516T	AC004538.3_ENST00000599875.1_RNA|AC004538.3_ENST00000421121.1_RNA|AC004538.3_ENST00000595972.1_RNA|AC004538.3_ENST00000428967.1_RNA|AC004538.3_ENST00000445839.1_RNA	NM_015204.2	NP_056019.1	Q9UPZ6	THS7A_HUMAN	thrombospondin, type I, domain containing 7A	1516					angiogenesis (GO:0001525)|cell differentiation (GO:0030154)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(5)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(7)|lung(68)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(11)	113				UCEC - Uterine corpus endometrioid carcinoma (126;0.163)		GGGTTACAAGACCTGTCGGCA	0.473										HNSCC(18;0.044)																											p.S1516T		.											.	.	.	0			c.T4546A						.						78.0	78.0	78.0					7																	11419301		2009	4163	6172	SO:0001583	missense	221981	exon24			TACAAGACCTGTC		CCDS47543.1	7p21.3	2006-10-16			ENSG00000005108	ENSG00000005108			22207	protein-coding gene	gene with protein product		612249					Standard	NM_015204		Approved	KIAA0960	uc021zzn.1	Q9UPZ6	OTTHUMG00000152346	ENST00000423059.4:c.4546T>A	7.37:g.11419301A>T	ENSP00000406482:p.Ser1516Thr	Somatic	70	0		WXS	Illumina HiSeq	.	48	20	NM_015204		Missense_Mutation	SNP	ENST00000423059.4	37	CCDS47543.1	.	.	.	.	.	.	.	.	.	.	A	22.2	4.263885	0.80358	.	.	ENSG00000005108	ENST00000262042;ENST00000423059	T	0.59224	0.28	5.73	5.73	0.89815	.	0.000000	0.85682	D	0.000000	T	0.64832	0.2634	L	0.55481	1.735	0.58432	D	0.999999	D;D	0.55605	0.972;0.972	P;P	0.55455	0.694;0.776	T	0.60105	-0.7328	10	0.16420	T	0.52	.	16.017	0.80445	1.0:0.0:0.0:0.0	.	1516;1516	Q9UPZ6;C9JL67	THS7A_HUMAN;.	T	1516	ENSP00000406482:S1516T	ENSP00000262042:S1516T	S	-	1	0	THSD7A	11385826	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.555000	0.90693	2.182000	0.69389	0.455000	0.32223	TCT	.		0.473	THSD7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325944.4	XM_928187.2	
CCDC170	80129	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	6	151869440	151869440	+	Splice_Site	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr6:151869440T>G	ENST00000239374.7	+	5	689	c.590T>G	c.(589-591)cTt>cGt	p.L197R	CCDC170_ENST00000367290.5_Splice_Site_p.L197R	NM_025059.3	NP_079335.2	Q8IYT3	CC170_HUMAN	coiled-coil domain containing 170	197																	TCTCTTCAGCTTAGAGACCTG	0.333																																					p.L197R		.											.	.	.	0			c.T590G						.						51.0	47.0	48.0					6																	151869440		1828	4079	5907	SO:0001630	splice_region_variant	80129	exon5			TTCAGCTTAGAGA	AK026958	CCDS43515.1	6q25.1	2012-03-26	2012-03-26	2012-03-26	ENSG00000120262	ENSG00000120262			21177	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 97"""	C6orf97			Standard	NM_025059		Approved	FLJ23305, bA282P11.1	uc003qol.3	Q8IYT3	OTTHUMG00000015839	ENST00000239374.7:c.589-1T>G	6.37:g.151869440T>G		Somatic	91	0		WXS	Illumina HiSeq	.	91	44	NM_025059	Q5VXB7|Q6P9E4|Q96KA9|Q9H5M3	Missense_Mutation	SNP	ENST00000239374.7	37	CCDS43515.1	.	.	.	.	.	.	.	.	.	.	T	21.1	4.091488	0.76756	.	.	ENSG00000120262	ENST00000239374;ENST00000367290	T;T	0.09163	3.01;3.01	5.48	5.48	0.80851	.	0.071637	0.53938	D	0.000046	T	0.15478	0.0373	M	0.63428	1.95	0.38628	D	0.95131	D	0.55605	0.972	P	0.53988	0.739	T	0.00735	-1.1588	10	0.72032	D	0.01	-3.179	15.5654	0.76287	0.0:0.0:0.0:1.0	.	197	Q8IYT3	CF097_HUMAN	R	197	ENSP00000239374:L197R;ENSP00000356259:L197R	ENSP00000239374:L197R	L	+	2	0	C6orf97	151911133	1.000000	0.71417	0.990000	0.47175	0.934000	0.57294	3.933000	0.56545	2.075000	0.62263	0.477000	0.44152	CTT	.		0.333	CCDC170-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000042727.2	NM_025059	Missense_Mutation
AMACR	23600	hgsc.bcm.edu	37	5	34004595	34004595	+	Intron	SNP	C	C	T	rs369179060|rs34401823	byFrequency	TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr5:34004595C>T	ENST00000335606.6	-	3	641				AMACR_ENST00000426255.2_Intron|AMACR_ENST00000382072.2_Intron|AMACR_ENST00000512079.1_Intron|RP11-1084J3.4_ENST00000382079.3_Intron|AMACR_ENST00000502637.1_Intron|AMACR_ENST00000382068.3_Intron|AMACR_ENST00000382085.3_Intron|AMACR_ENST00000441713.2_Intron|AMACR_ENST00000514195.1_Intron	NM_001167595.1|NM_014324.5	NP_001161067.1|NP_055139.4	Q9UHK6	AMACR_HUMAN	alpha-methylacyl-CoA racemase						bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	alpha-methylacyl-CoA racemase activity (GO:0008111)|receptor binding (GO:0005102)			endometrium(3)|kidney(1)|large_intestine(4)|lung(9)|stomach(1)|urinary_tract(1)	19						TATCTCTTGTCTTCTTCTTCA	0.318																																					.		.											.	.	.	0			.						.																																			SO:0001627	intron_variant	0	.			TCTTGTCTTCTTC	AF047020	CCDS3902.1, CCDS3903.1, CCDS54836.1	5p13.2	2012-05-16			ENSG00000242110	ENSG00000242110	5.1.99.4		451	protein-coding gene	gene with protein product		604489				9307041	Standard	NM_014324		Approved	RACE	uc003jij.3	Q9UHK6	OTTHUMG00000090734	ENST00000335606.6:c.552+83G>A	5.37:g.34004595C>T		Somatic	43	0		WXS	Illumina HiSeq	.	48	6	.	A5YM47|B8Y916|B8Y918|F8W9N1|O43673|Q3KT79|Q96GH1|Q9Y3Q1	RNA	SNP	ENST00000335606.6	37	CCDS3902.1																																																																																			.		0.318	AMACR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207467.1	NM_014324	
RNPS1	10921	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	16	2314620	2314620	+	Missense_Mutation	SNP	T	T	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr16:2314620T>C	ENST00000565678.1	-	2	570	c.25A>G	c.(25-27)Aag>Gag	p.K9E	RNPS1_ENST00000569598.2_Missense_Mutation_p.K9E|RNPS1_ENST00000320225.5_Missense_Mutation_p.K9E|RNPS1_ENST00000561718.1_Intron|RNPS1_ENST00000301730.8_Missense_Mutation_p.K9E|RNPS1_ENST00000566458.1_Intron|RNPS1_ENST00000568631.1_Missense_Mutation_p.K9E|RNPS1_ENST00000566397.1_5'Flank|RNPS1_ENST00000567147.1_Intron|RNPS1_ENST00000397086.2_Missense_Mutation_p.K9E			Q15287	RNPS1_HUMAN	RNA binding protein S1, serine-rich domain	9	Lys-rich.|Necessary for interaction with SRP54, nuclear localization and exon-skipping.|Necessary for interaction with the cleaved p110 isoform of CDC2L1.				gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|positive regulation of apoptotic process (GO:0043065)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)	ASAP complex (GO:0061574)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	mRNA 3'-UTR binding (GO:0003730)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			endometrium(1)|large_intestine(1)|lung(4)|ovary(2)|urinary_tract(1)	9						AGCAAGCTCTTCTTTTTCACT	0.423																																					p.K9E		.											.	.	.	0			c.A25G						.						122.0	118.0	120.0					16																	2314620		2198	4300	6498	SO:0001583	missense	10921	exon2			AGCTCTTCTTTTT	AF015608	CCDS10465.1, CCDS66907.1, CCDS73811.1	16p13.3	2013-02-12	2001-11-28		ENSG00000205937	ENSG00000205937		"""RNA binding motif (RRM) containing"""	10080	protein-coding gene	gene with protein product		606447	"""RNA-binding protein S1, serine-rich domain"""			9580558, 8543184	Standard	XM_005255048		Approved		uc002cpu.3	Q15287	OTTHUMG00000128828	ENST00000565678.1:c.25A>G	16.37:g.2314620T>C	ENSP00000457723:p.Lys9Glu	Somatic	18	0		WXS	Illumina HiSeq	.	26	16	NM_006711	A8K1P0|B4DDU8|B4DZU7|B7ZA17|O75308|Q32P25|Q8WY42|Q9NYG3	Missense_Mutation	SNP	ENST00000565678.1	37	CCDS10465.1	.	.	.	.	.	.	.	.	.	.	T	16.75	3.208799	0.58343	.	.	ENSG00000205937	ENST00000320225;ENST00000397086;ENST00000301730	T;T;T	0.07021	3.23;3.23;3.23	5.91	5.91	0.95273	.	0.209735	0.42548	N	0.000698	T	0.08313	0.0207	L	0.34521	1.04	0.80722	D	1	B	0.23854	0.092	B	0.12156	0.007	T	0.09422	-1.0675	10	0.87932	D	0	-27.1145	12.7337	0.57212	0.0:0.0:0.0:1.0	.	9	Q15287	RNPS1_HUMAN	E	9	ENSP00000315859:K9E;ENSP00000380275:K9E;ENSP00000301730:K9E	ENSP00000301730:K9E	K	-	1	0	RNPS1	2254621	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.587000	0.53957	2.263000	0.75096	0.450000	0.29827	AAG	.		0.423	RNPS1-007	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435415.1	NM_080594	
DDX11	1663	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	12	31256769	31256769	+	Silent	SNP	G	G	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr12:31256769G>A	ENST00000407793.2	+	27	2966	c.2715G>A	c.(2713-2715)ctG>ctA	p.L905L	DDX11_ENST00000228264.6_Silent_p.*881*|DDX11_ENST00000545668.1_Silent_p.L905L|DDX11_ENST00000251758.5_3'UTR|DDX11_ENST00000350437.4_Silent_p.*857*|DDX11_ENST00000542838.1_Silent_p.*907*	NM_030653.3|NM_152438.1	NP_085911.2|NP_689651.1	Q96FC9	DDX11_HUMAN	DEAD/H (Asp-Glu-Ala-Asp/His) box helicase 11	905					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|ATP catabolic process (GO:0006200)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|sister chromatid cohesion (GO:0007062)|viral process (GO:0016032)	midbody (GO:0030496)|nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle pole (GO:0000922)	4 iron, 4 sulfur cluster binding (GO:0051539)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA-dependent ATPase activity (GO:0008094)|double-stranded DNA binding (GO:0003690)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(11)|large_intestine(5)|lung(23)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	57	all_cancers(9;1.77e-11)|all_lung(12;6.21e-11)|all_epithelial(9;6.49e-11)|Lung NSC(12;1.06e-08)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Lung SC(12;0.0592)|Esophageal squamous(101;0.233)					GCCTCTTCCTGATGGGCAACC	0.582										Multiple Myeloma(12;0.14)																											p.X907X		.											.	.	.	0			c.G2720A						.						87.0	90.0	89.0					12																	31256769		2203	4299	6502	SO:0001819	synonymous_variant	1663	exon27			CTTCCTGATGGGC	U75969	CCDS8721.1, CCDS41767.1, CCDS44856.1, CCDS58224.1	12p11.21	2012-02-23	2012-02-23		ENSG00000013573	ENSG00000013573		"""DEAD-boxes"""	2736	protein-coding gene	gene with protein product	"""CHL1-like helicase homolog (S. cerevisiae)"""	601150	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11 (S.cerevisiae CHL1-like helicase)"", ""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11"""				Standard	NM_030653		Approved	CHLR1, KRG2, CHL1, ChlR1, WABS	uc001rjv.2	Q96FC9	OTTHUMG00000168435	ENST00000407793.2:c.2715G>A	12.37:g.31256769G>A		Somatic	65	0		WXS	Illumina HiSeq	.	48	25	NM_030653	Q13333|Q86VQ4|Q86W62|Q92498|Q92770|Q92998|Q92999	Silent	SNP	ENST00000407793.2	37	CCDS44856.1																																																																																			.		0.582	DDX11-202	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000399728.1	NM_030653	
PAIP2	51247	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	5	138700372	138700372	+	Missense_Mutation	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr5:138700372A>C	ENST00000394795.2	+	3	1249	c.258A>C	c.(256-258)caA>caC	p.Q86H	CTB-43P18.1_ENST00000503553.3_RNA|PAIP2_ENST00000511706.1_Intron|PAIP2_ENST00000510080.1_Missense_Mutation_p.Q86H|PAIP2_ENST00000265192.4_Missense_Mutation_p.Q86H|PAIP2_ENST00000511381.1_3'UTR			Q9BPZ3	PAIP2_HUMAN	poly(A) binding protein interacting protein 2	86					memory (GO:0007613)|negative regulation of translational initiation (GO:0045947)|regulation of long-term synaptic potentiation (GO:1900271)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)	mRNA binding (GO:0003729)|translation repressor activity (GO:0030371)			kidney(1)|large_intestine(2)|lung(2)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			CTATGGACCAAATCCAAGACC	0.378																																					p.Q86H		.											.	.	.	0			c.A258C						.						112.0	98.0	103.0					5																	138700372		2203	4300	6503	SO:0001583	missense	51247	exon3			GGACCAAATCCAA	AF151052	CCDS4211.1	5q32	2008-02-05			ENSG00000120727	ENSG00000120727			17970	protein-coding gene	gene with protein product		605604				11172725, 16804161	Standard	NM_016480		Approved	PAIP2A	uc003led.3	Q9BPZ3	OTTHUMG00000129227	ENST00000394795.2:c.258A>C	5.37:g.138700372A>C	ENSP00000378275:p.Gln86His	Somatic	60	0		WXS	Illumina HiSeq	.	48	16	NM_001033112	B2RBI1|D3DQC6|Q49A06|Q9H0Y5|Q9P0Q8	Missense_Mutation	SNP	ENST00000394795.2	37	CCDS4211.1	.	.	.	.	.	.	.	.	.	.	A	15.62	2.888586	0.52014	.	.	ENSG00000120727	ENST00000507755;ENST00000265192;ENST00000394795;ENST00000510080	.	.	.	5.79	3.38	0.38709	.	0.118969	0.64402	D	0.000020	T	0.54224	0.1845	L	0.59436	1.845	0.38896	D	0.957215	B	0.11235	0.004	B	0.06405	0.002	T	0.54583	-0.8272	9	0.48119	T	0.1	-24.895	7.9596	0.30064	0.7904:0.1383:0.0713:0.0	.	86	Q9BPZ3	PAIP2_HUMAN	H	86	.	ENSP00000265192:Q86H	Q	+	3	2	PAIP2	138728271	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.118000	0.57884	0.984000	0.38629	0.533000	0.62120	CAA	.		0.378	PAIP2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373002.1	NM_016480	
CHD8	57680	hgsc.bcm.edu	37	14	21896185	21896185	+	Silent	SNP	G	G	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr14:21896185G>T	ENST00000557364.1	-	4	1707	c.1444C>A	c.(1444-1446)Cga>Aga	p.R482R	RN7SL650P_ENST00000583681.1_RNA|CHD8_ENST00000399982.2_Silent_p.R482R|CHD8_ENST00000555962.1_Intron|CHD8_ENST00000430710.3_Silent_p.R203R			Q9HCK8	CHD8_HUMAN	chromodomain helicase DNA binding protein 8	482					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)	p.R482*(1)		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)		TTTAAGACTCGAGGTATGTTC	0.542																																					p.R482R		.											CHD8,NS,carcinoma,0,1	CHD8	0	1	Substitution - Nonsense(1)	prostate(1)	c.C1444A						.						135.0	132.0	133.0					14																	21896185		2025	4175	6200	SO:0001819	synonymous_variant	57680	exon3			AGACTCGAGGTAT	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.1444C>A	14.37:g.21896185G>T		Somatic	33	0		WXS	Illumina HiSeq	.	29	2	NM_001170629	Q4G0D8|Q68DQ0|Q6DKH9|Q6P440|Q6ZNL7|Q8N3Z9|Q8NCY4|Q8TBR9|Q96F26	Silent	SNP	ENST00000557364.1	37	CCDS53885.1																																																																																			.		0.542	CHD8-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410436.1	NM_020920	
ATAD3B	83858	hgsc.bcm.edu	37	1	1417592	1417592	+	Missense_Mutation	SNP	G	G	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr1:1417592G>A	ENST00000308647.7	+	6	705	c.589G>A	c.(589-591)Gcc>Acc	p.A197T	ATAD3B_ENST00000378736.3_3'UTR|ATAD3B_ENST00000378741.3_Missense_Mutation_p.A29T	NM_031921.4	NP_114127.3	Q5T9A4	ATD3B_HUMAN	ATPase family, AAA domain containing 3B	197						mitochondrial inner membrane (GO:0005743)	ATP binding (GO:0005524)			endometrium(2)|large_intestine(1)|lung(3)|ovary(1)|skin(2)|urinary_tract(1)	10	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;9.48e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)		Epithelial(90;1.79e-36)|OV - Ovarian serous cystadenocarcinoma(86;3.94e-22)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.00461)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.145)		CCGGGCGCGCGCCAAGGCCGA	0.657																																					p.A197T		.											ATAD3B_ENST00000378741,NS,carcinoma,0,2	ATAD3B_ENST00000378741	0	0			c.G589A						.						30.0	34.0	33.0					1																	1417592		2202	4295	6497	SO:0001583	missense	83858	exon6			GCGCGCGCCAAGG	AL834179	CCDS30.1	1p36.33	2010-04-21		2007-02-08	ENSG00000160072	ENSG00000160072		"""ATPases / AAA-type"""	24007	protein-coding gene	gene with protein product		612317				10574462	Standard	XM_005244806		Approved	TOB3, KIAA1273	uc001afv.3	Q5T9A4	OTTHUMG00000000577	ENST00000308647.7:c.589G>A	1.37:g.1417592G>A	ENSP00000311766:p.Ala197Thr	Somatic	68	0		WXS	Illumina HiSeq	.	53	3	NM_031921	A8K3H1|Q6ZRB5|Q9BUK4|Q9ULE7	Missense_Mutation	SNP	ENST00000308647.7	37	CCDS30.1	.	.	.	.	.	.	.	.	.	.	.	11.43	1.635807	0.29068	.	.	ENSG00000160072	ENST00000378741;ENST00000378737;ENST00000308647;ENST00000378736	T	0.17370	2.28	2.38	1.45	0.22620	ATPase family AAA domain-containing protein 3, domain of unknown function DUF3523 (1);	0.113072	0.64402	N	0.000016	T	0.26593	0.0650	M	0.85777	2.775	0.53005	D	0.999965	B;B;P	0.35411	0.087;0.208;0.5	B;B;B	0.41466	0.044;0.11;0.358	T	0.03112	-1.1071	10	0.46703	T	0.11	.	8.5026	0.33168	0.1237:0.0:0.8763:0.0	.	151;118;197	Q5T9A4-3;G3V1I6;Q5T9A4	.;.;ATD3B_HUMAN	T	29;12;197;29	ENSP00000311766:A197T	ENSP00000311766:A197T	A	+	1	0	ATAD3B	1407455	1.000000	0.71417	0.944000	0.38274	0.024000	0.10985	7.271000	0.78506	0.343000	0.23821	-1.111000	0.02071	GCC	.		0.657	ATAD3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001369.2	NM_031921	
ZNF569	148266	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	19	37904939	37904939	+	Silent	SNP	A	A	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr19:37904939A>G	ENST00000316950.6	-	6	1178	c.621T>C	c.(619-621)atT>atC	p.I207I	ZNF569_ENST00000392150.2_Silent_p.I48I|ZNF569_ENST00000392149.2_Silent_p.I207I	NM_152484.2	NP_689697.2	Q5MCW4	ZN569_HUMAN	zinc finger protein 569	207					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(5)|endometrium(4)|large_intestine(16)|lung(11)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	40			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			CTCCAGTATGAATTCTCAGAT	0.373																																					p.I207I		.											.	.	.	0			c.T621C						.						63.0	65.0	65.0					19																	37904939		2203	4300	6503	SO:0001819	synonymous_variant	148266	exon6			AGTATGAATTCTC	AL833408	CCDS12503.1	19q13.12	2013-09-20			ENSG00000196437	ENSG00000196437		"""Zinc fingers, C2H2-type"", ""-"""	24737	protein-coding gene	gene with protein product		613904				12477932	Standard	NM_152484		Approved	FLJ32053, ZAP1	uc002ogi.3	Q5MCW4	OTTHUMG00000048172	ENST00000316950.6:c.621T>C	19.37:g.37904939A>G		Somatic	92	0		WXS	Illumina HiSeq	.	61	26	NM_152484	A8K1S2|Q15925|Q17RR6|Q96MQ2	Silent	SNP	ENST00000316950.6	37	CCDS12503.1																																																																																			.		0.373	ZNF569-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109594.2	NM_152484	
STRBP	55342	hgsc.bcm.edu;ucsc.edu	37	9	125873860	125873860	+	Intron	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr9:125873860A>C	ENST00000530364.1	-	2	31				MIR600HG_ENST00000385007.1_RNA			Q96SI9	STRBP_HUMAN	spermatid perinuclear RNA binding protein						cellular component movement (GO:0006928)|mechanosensory behavior (GO:0007638)|multicellular organismal development (GO:0007275)|spermatid development (GO:0007286)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)	DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)|single-stranded RNA binding (GO:0003727)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(6)|prostate(1)|skin(2)	26						CTTGTCTGTAAGTAACTCCAC	0.567																																					.		.											.	.	.	0			.						.						20.0	23.0	22.0					9																	125873860		1561	3566	5127	SO:0001627	intron_variant	693185	.			TCTGTAAGTAACT	AK002169	CCDS6851.1, CCDS55337.1	9q33.1-q33.3	2008-08-29	2001-11-28		ENSG00000165209	ENSG00000165209			16462	protein-coding gene	gene with protein product		611138	"""spermatid perinuclear RNA-binding protein"", ""interleukin enhancer binding factor 3-like"""	ILF3L			Standard	NM_018387		Approved	FLJ11307, SPNR	uc004bns.3	Q96SI9	OTTHUMG00000020636	ENST00000530364.1:c.255-1828T>G	9.37:g.125873860A>C		Somatic	41	0		WXS	Illumina HiSeq	.	37	17	.	Q32NB9|Q9BUE1|Q9BXG4|Q9H0B4|Q9H7V1|Q9NUK4	RNA	SNP	ENST00000530364.1	37																																																																																				.		0.567	STRBP-009	PUTATIVE	basic	processed_transcript	protein_coding	OTTHUMT00000392598.1		
C2CD2	25966	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	21	43327893	43327893	+	Splice_Site	SNP	C	C	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr21:43327893C>T	ENST00000380486.3	-	9	1260	c.1019G>A	c.(1018-1020)gGt>gAt	p.G340D	C2CD2_ENST00000329623.7_Splice_Site_p.G185D	NM_015500.1	NP_056315.1	Q9Y426	CU025_HUMAN	C2 calcium-dependent domain containing 2	340	C2.					cytosol (GO:0005829)|extracellular region (GO:0005576)|nucleus (GO:0005634)				endometrium(2)|kidney(1)|large_intestine(4)|lung(3)|ovary(3)|prostate(1)|stomach(1)	15						CGCCAGCAGACCTGAAAAGAT	0.622																																					p.G340D		.											.	.	.	0			c.G1019A						.						32.0	36.0	35.0					21																	43327893		2203	4300	6503	SO:0001630	splice_region_variant	25966	exon9			AGCAGACCTGAAA	AB047784	CCDS13677.1, CCDS42933.1	21q22.3	2008-11-24	2007-10-17	2007-10-17	ENSG00000157617	ENSG00000157617			1266	protein-coding gene	gene with protein product	"""TMEM24-like"""		"""chromosome 21 open reading frame 25"""	C21orf25		15289880	Standard	NM_015500		Approved	TMEM24L, DKFZP586F0422, C21orf258	uc002yzw.3	Q9Y426	OTTHUMG00000086779	ENST00000380486.3:c.1019-1G>A	21.37:g.43327893C>T		Somatic	80	0		WXS	Illumina HiSeq	.	27	4	NM_015500	Q5R2V7|Q6AHX8|Q9NSE6	Missense_Mutation	SNP	ENST00000380486.3	37	CCDS42933.1	.	.	.	.	.	.	.	.	.	.	C	9.968	1.224585	0.22457	.	.	ENSG00000157617	ENST00000329623;ENST00000380486	T;T	0.66280	-0.2;-0.2	5.51	4.63	0.57726	C2 calcium-dependent membrane targeting (1);C2 calcium/lipid-binding domain, CaLB (1);	0.752570	0.12879	N	0.431590	T	0.54951	0.1890	L	0.50333	1.59	0.44719	D	0.99771	B;B	0.24768	0.111;0.028	B;B	0.26094	0.066;0.039	T	0.43669	-0.9377	10	0.08179	T	0.78	.	13.4264	0.61028	0.0:0.8096:0.1904:0.0	.	185;340	Q6P6D1;Q9Y426	.;CU025_HUMAN	D	185;340	ENSP00000329302:G185D;ENSP00000369853:G340D	ENSP00000329302:G185D	G	-	2	0	C2CD2	42200962	0.608000	0.26966	0.485000	0.27403	0.199000	0.23934	0.894000	0.28350	1.337000	0.45525	0.650000	0.86243	GGT	.		0.622	C2CD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195228.2	NM_015500	Missense_Mutation
CTSB	1508	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	8	11704585	11704585	+	Missense_Mutation	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr8:11704585A>C	ENST00000353047.6	-	8	1022	c.769T>G	c.(769-771)Tcg>Gcg	p.S257A	CTSB_ENST00000533455.1_Missense_Mutation_p.S257A|CTSB_ENST00000525076.1_5'Flank|CTSB_ENST00000453527.2_Missense_Mutation_p.S257A|CTSB_ENST00000345125.3_Missense_Mutation_p.S257A|CTSB_ENST00000534510.1_Missense_Mutation_p.S257A|CTSB_ENST00000434271.1_Missense_Mutation_p.S257A|CTSB_ENST00000530640.2_Missense_Mutation_p.S257A|CTSB_ENST00000415599.2_3'UTR|CTSB_ENST00000531089.1_Missense_Mutation_p.S257A|RP11-589N15.2_ENST00000602711.1_RNA	NM_001908.3	NP_001899.1	P07858	CATB_HUMAN	cathepsin B	257					cellular response to thyroid hormone stimulus (GO:0097067)|collagen catabolic process (GO:0030574)|decidualization (GO:0046697)|epithelial cell differentiation (GO:0030855)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|innate immune response (GO:0045087)|proteolysis (GO:0006508)|proteolysis involved in cellular protein catabolic process (GO:0051603)|regulation of apoptotic process (GO:0042981)|regulation of catalytic activity (GO:0050790)|toll-like receptor signaling pathway (GO:0002224)	endolysosome lumen (GO:0036021)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|intracellular membrane-bounded organelle (GO:0043231)|lysosome (GO:0005764)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|perinuclear region of cytoplasm (GO:0048471)	collagen binding (GO:0005518)|cysteine-type endopeptidase activity (GO:0004197)|cysteine-type peptidase activity (GO:0008234)|peptidase activity (GO:0008233)|proteoglycan binding (GO:0043394)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(5)|lung(1)	16	all_epithelial(15;0.205)		STAD - Stomach adenocarcinoma(15;0.00546)	COAD - Colon adenocarcinoma(149;0.184)		AGGAAGTCCGAATACACAGAG	0.542																																					p.S257A		.											.	.	.	0			c.T769G						.						95.0	86.0	89.0					8																	11704585		2203	4300	6503	SO:0001583	missense	1508	exon10			AGTCCGAATACAC	M14221	CCDS5986.1	8p23.1	2012-10-02			ENSG00000164733	ENSG00000164733	3.4.22.1	"""Cathepsins"""	2527	protein-coding gene	gene with protein product		116810				8112600, 3463996	Standard	XM_006716244		Approved		uc003wuq.3	P07858	OTTHUMG00000090799	ENST00000353047.6:c.769T>G	8.37:g.11704585A>C	ENSP00000345672:p.Ser257Ala	Somatic	62	0		WXS	Illumina HiSeq	.	43	14	NM_147780	B3KQR5|B3KRR5|Q503A6|Q96D87	Missense_Mutation	SNP	ENST00000353047.6	37	CCDS5986.1	.	.	.	.	.	.	.	.	.	.	A	4.044	0.005874	0.07866	.	.	ENSG00000164733	ENST00000434271;ENST00000540571;ENST00000353047;ENST00000530640;ENST00000531089;ENST00000453527;ENST00000345125;ENST00000533455;ENST00000534510;ENST00000541328	D;D;D;D;D;D;D;D	0.84223	-1.82;-1.82;-1.82;-1.82;-1.82;-1.82;-1.82;-1.82	5.71	-1.39	0.08997	Peptidase C1A, papain C-terminal (2);	0.629214	0.16336	N	0.218916	T	0.67636	0.2914	N	0.16098	0.37	0.21256	N	0.999749	B;B;B;B;B	0.11235	0.004;0.0;0.001;0.0;0.003	B;B;B;B;B	0.18871	0.023;0.007;0.012;0.002;0.014	T	0.52071	-0.8624	10	0.12103	T	0.63	.	9.5641	0.39387	0.1857:0.6388:0.0:0.1755	.	194;257;163;257;194	B3KUJ8;A8K2H4;B4DMY4;P07858;F5H2P9	.;.;.;CATB_HUMAN;.	A	257;194;257;257;257;257;257;257;257;163	ENSP00000415889:S257A;ENSP00000345672:S257A;ENSP00000435105:S257A;ENSP00000433215:S257A;ENSP00000409917:S257A;ENSP00000342070:S257A;ENSP00000432244:S257A;ENSP00000434217:S257A	ENSP00000342070:S257A	S	-	1	0	CTSB	11741994	0.000000	0.05858	0.000000	0.03702	0.022000	0.10575	0.894000	0.28350	-0.161000	0.10983	-0.429000	0.05907	TCG	.		0.542	CTSB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207586.3	NM_147780	
ELN	2006	hgsc.bcm.edu	37	7	73474785	73474785	+	Silent	SNP	T	T	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr7:73474785T>C	ENST00000252034.7	+	25	2100	c.1701T>C	c.(1699-1701)ggT>ggC	p.G567G	ELN_ENST00000380584.4_Silent_p.G519G|ELN_ENST00000380575.4_Silent_p.G538G|ELN_ENST00000458204.1_Silent_p.G557G|ELN_ENST00000414324.1_Silent_p.G543G|ELN_ENST00000320492.7_Silent_p.G486G|ELN_ENST00000429192.1_Silent_p.G553G|ELN_ENST00000357036.5_Silent_p.G572G|ELN_ENST00000380553.4_Silent_p.G431G|ELN_ENST00000380562.4_Silent_p.G573G|ELN_ENST00000358929.4_Silent_p.G602G|ELN_ENST00000320399.6_Silent_p.G567G|ELN_ENST00000445912.1_Silent_p.G567G|CTB-51J22.1_ENST00000435932.1_RNA|ELN_ENST00000380576.5_Silent_p.G548G	NM_000501.2|NM_001278915.1	NP_000492.2|NP_001265844.1	P15502	ELN_HUMAN	elastin	0	Ala-rich.				blood circulation (GO:0008015)|blood vessel remodeling (GO:0001974)|cell proliferation (GO:0008283)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|organ morphogenesis (GO:0009887)|regulation of actin filament polymerization (GO:0030833)|respiratory gaseous exchange (GO:0007585)|skeletal muscle tissue development (GO:0007519)|stress fiber assembly (GO:0043149)	elastic fiber (GO:0071953)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix binding (GO:0050840)|extracellular matrix constituent conferring elasticity (GO:0030023)|extracellular matrix structural constituent (GO:0005201)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(10)|ovary(4)|pancreas(2)|prostate(1)|skin(2)|stomach(1)	32		Lung NSC(55;0.159)				TTGGTGCTGGTGTTCCTGGAC	0.617			T	PAX5	B-ALL		"""Supravalvular Aortic Stenosis, Cutis laxa , Williams-Beuren Syndrome"""																														p.G572G		.		Dom	yes		7	7q11.23	2006	elastin	yes	L	.	.	.	0			c.T1716C						.						347.0	345.0	346.0					7																	73474785		2203	4300	6503	SO:0001819	synonymous_variant	2006	exon25			TGCTGGTGTTCCT		CCDS5562.2, CCDS43598.1, CCDS43599.1, CCDS47611.1, CCDS47612.1, CCDS64673.1, CCDS64674.1, CCDS64675.1, CCDS64676.1, CCDS64677.1, CCDS64678.1, CCDS75616.1, CCDS75617.1	7q11.1-q21.1	2008-08-01	2008-08-01		ENSG00000049540	ENSG00000049540			3327	protein-coding gene	gene with protein product	"""tropoelastin"", ""supravalvular aortic stenosis"", ""Williams-Beuren syndrome"""	130160				8096434	Standard	NM_001278939		Approved	WBS, WS, SVAS	uc003tzn.3	P15502	OTTHUMG00000150229	ENST00000252034.7:c.1701T>C	7.37:g.73474785T>C		Somatic	31	0		WXS	Illumina HiSeq	.	16	4	NM_001081754	B3KTS6|O15336|O15337|Q14233|Q14234|Q14235|Q14238|Q6P0L4|Q6ZWJ6|Q75MU5|Q7Z316|Q7Z3F5|Q9UMF5	Silent	SNP	ENST00000252034.7	37	CCDS5562.2																																																																																			.		0.617	ELN-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000316913.1	NM_000501	
CYBB	1536	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	X	37653034	37653034	+	Missense_Mutation	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chrX:37653034T>G	ENST00000378588.4	+	5	521	c.454T>G	c.(454-456)Tat>Gat	p.Y152D	CYBB_ENST00000545017.1_Missense_Mutation_p.Y120D|CYBB_ENST00000536160.1_Intron|TM4SF2_ENST00000465127.1_Intron	NM_000397.3	NP_000388.2	P04839	CY24B_HUMAN	cytochrome b-245, beta polypeptide	152	Ferric oxidoreductase.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|hydrogen peroxide biosynthetic process (GO:0050665)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interaction with host (GO:0051701)|oxidation-reduction process (GO:0055114)|phagosome maturation (GO:0090382)|respiratory burst (GO:0045730)|response to drug (GO:0042493)|response to nutrient (GO:0007584)|superoxide anion generation (GO:0042554)|superoxide metabolic process (GO:0006801)	dendrite (GO:0030425)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|mitochondrion (GO:0005739)|NADPH oxidase complex (GO:0043020)|neuronal cell body (GO:0043025)|phagocytic vesicle membrane (GO:0030670)|rough endoplasmic reticulum (GO:0005791)	flavin adenine dinucleotide binding (GO:0050660)|heme binding (GO:0020037)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|superoxide-generating NADPH oxidase activity (GO:0016175)|voltage-gated ion channel activity (GO:0005244)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(20)|prostate(2)|skin(2)	32					Dextromethorphan(DB00514)	AAATGAAAGTTATCTCAATTT	0.373																																					p.Y152D		.											.	.	.	0			c.T454G						.						100.0	85.0	90.0					X																	37653034		2202	4300	6502	SO:0001583	missense	1536	exon5			GAAAGTTATCTCA	X04011	CCDS14242.1	Xp21.1	2014-09-17	2008-07-29		ENSG00000165168	ENSG00000165168		"""Cytochrome b genes"""	2578	protein-coding gene	gene with protein product		300481	"""chronic granulomatous disease"""	CGD			Standard	NM_000397		Approved	GP91-PHOX, NOX2	uc004ddr.2	P04839	OTTHUMG00000033175	ENST00000378588.4:c.454T>G	X.37:g.37653034T>G	ENSP00000367851:p.Tyr152Asp	Somatic	33	0		WXS	Illumina HiSeq	.	25	20	NM_000397	A8K138|Q2PP16	Missense_Mutation	SNP	ENST00000378588.4	37	CCDS14242.1	.	.	.	.	.	.	.	.	.	.	T	11.69	1.712394	0.30322	.	.	ENSG00000165168	ENST00000378588;ENST00000545017	D;D	0.91011	-2.77;-2.77	5.67	5.67	0.87782	Flavoprotein transmembrane component (1);	0.156902	0.64402	D	0.000015	D	0.93959	0.8066	M	0.62154	1.92	0.80722	D	1	D;D	0.61697	0.973;0.99	P;D	0.65773	0.847;0.938	D	0.94527	0.7732	10	0.87932	D	0	.	14.9689	0.71217	0.0:0.0:0.0:1.0	.	120;152	F5GWD2;P04839	.;CY24B_HUMAN	D	152;120	ENSP00000367851:Y152D;ENSP00000441896:Y120D	ENSP00000367851:Y152D	Y	+	1	0	CYBB	37537974	1.000000	0.71417	0.794000	0.32065	0.048000	0.14542	6.382000	0.73167	1.917000	0.55516	0.483000	0.47432	TAT	.		0.373	CYBB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080881.1		
SLC17A3	10786	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	6	25850686	25850686	+	Splice_Site	SNP	C	C	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr6:25850686C>T	ENST00000360657.3	-	7	1045		c.e7+1		SLC17A3_ENST00000361703.6_Splice_Site|SLC17A3_ENST00000397060.4_Splice_Site			O00476	NPT4_HUMAN	solute carrier family 17 (organic anion transporter), member 3						drug transmembrane transport (GO:0006855)|drug transport (GO:0015893)|glucose-6-phosphate transport (GO:0015760)|ion transmembrane transport (GO:0034220)|organic acid transport (GO:0015849)|organic anion transport (GO:0015711)|phosphate ion transmembrane transport (GO:0035435)|phosphate ion transport (GO:0006817)|regulation of anion transport (GO:0044070)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|toxin transport (GO:1901998)|transmembrane transport (GO:0055085)|urate metabolic process (GO:0046415)|urate transport (GO:0015747)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	drug transmembrane transporter activity (GO:0015238)|efflux transmembrane transporter activity (GO:0015562)|organic anion transmembrane transporter activity (GO:0008514)|sodium:phosphate symporter activity (GO:0005436)|toxin transporter activity (GO:0019534)|urate transmembrane transporter activity (GO:0015143)|voltage-gated anion channel activity (GO:0008308)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(10)|prostate(1)	20						AACATACTCACGTCTCTGATG	0.403																																					.		.											.	.	.	0			c.759+1G>A						.						180.0	139.0	153.0					6																	25850686		2203	4300	6503	SO:0001630	splice_region_variant	10786	exon8			TACTCACGTCTCT	U90545	CCDS4566.2, CCDS47385.1	6p22.2	2013-07-18	2013-07-18		ENSG00000124564	ENSG00000124564		"""Solute carriers"""	10931	protein-coding gene	gene with protein product		611034	"""solute carrier family 17 (sodium phosphate), member 3"""			9149941	Standard	NM_006632		Approved	NPT4	uc003nfk.4	O00476	OTTHUMG00000014412	ENST00000360657.3:c.759+1G>A	6.37:g.25850686C>T		Somatic	45	0		WXS	Illumina HiSeq	.	40	24	NM_006632	B7WNJ5|B7Z511|Q8WWC7|Q9H533	Splice_Site	SNP	ENST00000360657.3	37	CCDS4566.2	.	.	.	.	.	.	.	.	.	.	C	7.632	0.679015	0.14841	.	.	ENSG00000124564	ENST00000397060;ENST00000360657;ENST00000361703	.	.	.	3.53	2.66	0.31614	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	6.9028	0.24293	0.0:0.873:0.0:0.127	.	.	.	.	.	-1	.	.	.	-	.	.	SLC17A3	25958665	0.996000	0.38824	0.999000	0.59377	0.323000	0.28346	4.283000	0.58977	1.050000	0.40346	-0.237000	0.12165	.	.		0.403	SLC17A3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000040070.2		Intron
SYNCRIP	10492	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	6	86351134	86351134	+	Silent	SNP	T	T	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr6:86351134T>C	ENST00000369622.3	-	2	524	c.24A>G	c.(22-24)ggA>ggG	p.G8G	SYNCRIP_ENST00000355238.6_Silent_p.G8G	NM_001159675.1|NM_006372.4	NP_001153147.1|NP_006363.4	O60506	HNRPQ_HUMAN	synaptotagmin binding, cytoplasmic RNA interacting protein	8					cellular response to interferon-gamma (GO:0071346)|CRD-mediated mRNA stabilization (GO:0070934)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of translation (GO:0017148)|osteoblast differentiation (GO:0001649)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|viral process (GO:0016032)	catalytic step 2 spliceosome (GO:0071013)|CRD-mediated mRNA stability complex (GO:0070937)|endoplasmic reticulum (GO:0005783)|GAIT complex (GO:0097452)|histone pre-mRNA 3'end processing complex (GO:0071204)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) binding (GO:0008143)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			autonomic_ganglia(1)|breast(2)|central_nervous_system(4)|endometrium(3)|kidney(2)|large_intestine(5)|liver(1)|lung(10)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	33		all_cancers(76;0.000137)|Acute lymphoblastic leukemia(125;3.66e-08)|Prostate(29;8.2e-07)|all_hematologic(105;8.61e-05)|all_epithelial(107;0.0297)		BRCA - Breast invasive adenocarcinoma(108;0.0389)		CAGTACCATTTCCATTAACAT	0.363																																					p.G8G		.											.	.	.	0			c.A24G						.						79.0	71.0	74.0					6																	86351134		2203	4300	6503	SO:0001819	synonymous_variant	10492	exon2			ACCATTTCCATTA	AF037448	CCDS5005.1, CCDS55041.1, CCDS75491.1	6q14-q15	2013-05-23			ENSG00000135316	ENSG00000135316		"""RNA binding motif (RRM) containing"""	16918	protein-coding gene	gene with protein product	"""heterogeneous nuclear ribonucleoprotein Q"""					9847309, 11352648	Standard	NM_006372		Approved	NSAP1, GRY-RBP, dJ3J17.2, HNRPQ1, hnRNP-Q, HNRNPQ	uc003pla.2	O60506	OTTHUMG00000015141	ENST00000369622.3:c.24A>G	6.37:g.86351134T>C		Somatic	66	0		WXS	Illumina HiSeq	.	56	28	NM_006372	E1P501|E1P502|Q53H05|Q5TCG2|Q5TCG3|Q8IW78|Q8N599|Q96LC1|Q96LC2|Q9Y583	Silent	SNP	ENST00000369622.3	37	CCDS5005.1																																																																																			.		0.363	SYNCRIP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041396.1	NM_006372	
MEX3C	51320	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	18	48703410	48703410	+	5'UTR	SNP	C	C	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr18:48703410C>T	ENST00000591040.1	-	0	579							Q5U5Q3	MEX3C_HUMAN	mex-3 RNA binding family member C						chondrocyte hypertrophy (GO:0003415)|energy homeostasis (GO:0097009)|regulation of fat cell differentiation (GO:0045598)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(2)|lung(11)|ovary(1)|skin(1)	17		Colorectal(6;0.003)|all_epithelial(6;0.0473)		Colorectal(16;0.0175)|READ - Rectum adenocarcinoma(32;0.15)		CTAGGAGGAACAGGATTGGAG	0.443																																					p.V431I		.											.	.	.	0			c.G1291A						.						87.0	84.0	85.0					18																	48703410		2203	4300	6503	SO:0001623	5_prime_UTR_variant	51320	exon2			GAGGAACAGGATT	BC041122	CCDS11951.2	18q21.1	2013-08-21	2013-08-21	2007-07-18	ENSG00000176624	ENSG00000176624		"""RING-type (C3HC4) zinc fingers"", ""Mex-3 homologs"""	28040	protein-coding gene	gene with protein product		611005	"""ring finger and KH domain containing 2"", ""mex-3 homolog C (C. elegans)"""	RKHD2		17267406	Standard	NM_016626		Approved	FLJ38871, RNF194	uc002lfc.4	Q5U5Q3	OTTHUMG00000132693	ENST00000591040.1:c.-220G>A	18.37:g.48703410C>T		Somatic	26	0		WXS	Illumina HiSeq	.	12	6	NM_016626	A1L022|Q9NZE3	Missense_Mutation	SNP	ENST00000591040.1	37		.	.	.	.	.	.	.	.	.	.	C	10.72	1.430022	0.25726	.	.	ENSG00000176624	ENST00000406189	T	0.30182	1.54	5.97	5.97	0.96955	.	0.721984	0.13795	N	0.362243	T	0.13457	0.0326	N	0.02011	-0.69	0.27694	N	0.94602	B	0.29716	0.255	B	0.29598	0.104	T	0.15037	-1.0451	10	0.21540	T	0.41	-4.9166	12.5252	0.56083	0.0:0.9233:0.0:0.0767	.	431	Q5U5Q3	MEX3C_HUMAN	I	431	ENSP00000385610:V431I	ENSP00000385610:V431I	V	-	1	0	MEX3C	46957408	0.351000	0.24887	0.997000	0.53966	0.983000	0.72400	1.013000	0.29937	2.836000	0.97738	0.655000	0.94253	GTT	.		0.443	MEX3C-003	KNOWN	mRNA_end_NF|basic	processed_transcript	protein_coding	OTTHUMT00000449559.1	NM_016626	
BCOR	54880	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	X	39921601	39921601	+	Missense_Mutation	SNP	A	A	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chrX:39921601A>G	ENST00000378444.4	-	10	4447	c.4219T>C	c.(4219-4221)Tat>Cat	p.Y1407H	BCOR_ENST00000378463.1_Missense_Mutation_p.Y250H|BCOR_ENST00000342274.4_Missense_Mutation_p.Y1373H|BCOR_ENST00000378455.4_Missense_Mutation_p.Y1355H|BCOR_ENST00000397354.3_Missense_Mutation_p.Y1373H	NM_001123385.1	NP_001116857.1	Q6W2J9	BCOR_HUMAN	BCL6 corepressor	1407					heart development (GO:0007507)|histone H2A monoubiquitination (GO:0035518)|negative regulation of bone mineralization (GO:0030502)|negative regulation of histone H3-K36 methylation (GO:0000415)|negative regulation of histone H3-K4 methylation (GO:0051572)|negative regulation of tooth mineralization (GO:0070171)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|odontogenesis (GO:0042476)|palate development (GO:0060021)|specification of axis polarity (GO:0065001)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	heat shock protein binding (GO:0031072)|histone deacetylase binding (GO:0042826)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			breast(4)|central_nervous_system(11)|cervix(1)|endometrium(24)|eye(6)|haematopoietic_and_lymphoid_tissue(33)|kidney(2)|large_intestine(11)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	126						GACAGATCATAGTCCGAACTG	0.577			"""F, N, S, T"""	RARA	"""retinoblastoma, AML, APL(translocation)"""		oculo-facio-cardio-dental genetic																														p.Y1407H		.		Rec	yes		X	Xp11.4	54880	BCL6 corepressor	yes		.	.	.	0			c.T4219C						.						92.0	64.0	73.0					X																	39921601		2202	4300	6502	SO:0001583	missense	54880	exon10			GATCATAGTCCGA	AF317391	CCDS14250.1, CCDS48092.1, CCDS48093.1	Xp11.4	2014-09-17	2010-06-10		ENSG00000183337	ENSG00000183337		"""Ankyrin repeat domain containing"""	20893	protein-coding gene	gene with protein product		300485	"""BCL6 co-repressor"""			10898795	Standard	NM_017745		Approved	FLJ20285, KIAA1575	uc004den.4	Q6W2J9	OTTHUMG00000024100	ENST00000378444.4:c.4219T>C	X.37:g.39921601A>G	ENSP00000367705:p.Tyr1407His	Somatic	72	0		WXS	Illumina HiSeq	.	28	23	NM_001123385	D3DWB3|D3DWB4|Q29RF6|Q6P4B6|Q7Z2K7|Q8TEB4|Q96DB3|Q9H232|Q9H233|Q9HCJ7|Q9NXF2	Missense_Mutation	SNP	ENST00000378444.4	37	CCDS48093.1	.	.	.	.	.	.	.	.	.	.	A	8.236	0.805658	0.16467	.	.	ENSG00000183337	ENST00000413905;ENST00000378463;ENST00000378455;ENST00000397354;ENST00000378444;ENST00000342274;ENST00000442018	T;T;T;T;T;T;T	0.68765	-0.35;1.03;1.1;1.08;1.08;1.08;-0.31	5.71	5.71	0.89125	.	.	.	.	.	T	0.61223	0.2330	N	0.14661	0.345	0.09310	N	0.999997	D;D;D	0.57571	0.98;0.98;0.98	P;P;P	0.56700	0.804;0.646;0.804	T	0.52449	-0.8574	9	0.25751	T	0.34	-9.4165	10.5765	0.45229	0.7061:0.2939:0.0:0.0	.	1355;1407;1373	Q6W2J9-4;Q6W2J9;Q6W2J9-2	.;BCOR_HUMAN;.	H	277;250;1355;1373;1407;1373;80	ENSP00000408006:Y277H;ENSP00000367724:Y250H;ENSP00000367716:Y1355H;ENSP00000380512:Y1373H;ENSP00000367705:Y1407H;ENSP00000345923:Y1373H;ENSP00000387552:Y80H	ENSP00000345923:Y1373H	Y	-	1	0	BCOR	39806545	1.000000	0.71417	0.109000	0.21407	0.764000	0.43329	4.034000	0.57289	1.902000	0.55061	0.486000	0.48141	TAT	.		0.577	BCOR-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060666.2	NM_017745	
SVEP1	79987	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	9	113205826	113205826	+	Splice_Site	SNP	A	A	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr9:113205826A>T	ENST00000401783.2	-	27	4974	c.4638T>A	c.(4636-4638)ccT>ccA	p.P1546P	SVEP1_ENST00000302728.8_Silent_p.P1546P|SVEP1_ENST00000467821.1_5'UTR|SVEP1_ENST00000374469.1_Splice_Site_p.P1523P	NM_153366.3	NP_699197.3	Q4LDE5	SVEP1_HUMAN	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	1546	Pentaxin.			P -> PGMF (in Ref. 1; CAF04067). {ECO:0000305}.	cell adhesion (GO:0007155)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|chromatin binding (GO:0003682)			NS(1)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|cervix(2)|endometrium(19)|kidney(8)|large_intestine(24)|lung(58)|ovary(7)|prostate(7)|skin(1)|stomach(4)|upper_aerodigestive_tract(5)|urinary_tract(4)	147						AAAACATACCAGGTATGGGCA	0.418																																					p.P1546P		.											.	.	.	0			c.T4638A						.						60.0	62.0	62.0					9																	113205826		1932	4136	6068	SO:0001630	splice_region_variant	79987	exon27			CATACCAGGTATG	AK027870		9q31-q32	2008-02-05	2005-03-15	2005-03-17	ENSG00000165124	ENSG00000165124			15985	protein-coding gene	gene with protein product		611691	"""chromosome 9 open reading frame 13"""	C9orf13			Standard	NM_153366		Approved	bA427L11.3, POLYDOM, FLJ13529	uc010mtz.3	Q4LDE5	OTTHUMG00000020482	ENST00000401783.2:c.4639+1T>A	9.37:g.113205826A>T		Somatic	31	0		WXS	Illumina HiSeq	.	20	5	NM_153366	Q0P675|Q5D213|Q5T938|Q5VTE4|Q5VTE5|Q7Z387|Q7Z3G3|Q8NBT9|Q96JU7|Q9H284|Q9H8J9	Silent	SNP	ENST00000401783.2	37	CCDS48004.1																																																																																			.		0.418	SVEP1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			Silent
RABL6	55684	hgsc.bcm.edu	37	9	139734291	139734291	+	Missense_Mutation	SNP	C	C	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr9:139734291C>T	ENST00000311502.7	+	13	2140	c.1904C>T	c.(1903-1905)gCc>gTc	p.A635V	RABL6_ENST00000371663.4_Missense_Mutation_p.A636V|RABL6_ENST00000371675.3_Missense_Mutation_p.A520V|RABL6_ENST00000357466.2_Intron|RABL6_ENST00000432842.2_3'UTR			Q3YEC7	RABL6_HUMAN	RAB, member RAS oncogene family-like 6	635					small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	GTP binding (GO:0005525)										CTGGAGGAGGCCGGACCCAAG	0.677																																					p.A636V		.											.	.	.	0			c.C1907T						.						21.0	27.0	25.0					9																	139734291		1934	4113	6047	SO:0001583	missense	55684	exon13			AGGAGGCCGGACC	AK094382	CCDS48058.1, CCDS55352.1, CCDS55353.1	9q34.3	2012-06-28	2012-06-28	2012-06-28	ENSG00000196642	ENSG00000196642			24703	protein-coding gene	gene with protein product	"""Rab-like protein 1"", ""partner of ARF"""	610615	"""chromosome 9 open reading frame 86"""	C9orf86		14702039, 16582619, 17962191, 19433581	Standard	NM_024718		Approved	FLJ10101, FLJ13045, pp8875, bA216L13.9, Parf, RBEL1	uc004cjj.1	Q3YEC7	OTTHUMG00000020947	ENST00000311502.7:c.1904C>T	9.37:g.139734291C>T	ENSP00000311134:p.Ala635Val	Somatic	94	0		WXS	Illumina HiSeq	.	70	4	NM_001173988	A8QVZ7|A8QVZ8|C6K8I4|C6K8I5|Q4F968|Q5T5R7|Q8IWK1|Q8TCL4|Q8WU94|Q96SR8|Q9BU21|Q9H935	Missense_Mutation	SNP	ENST00000311502.7	37	CCDS48058.1	.	.	.	.	.	.	.	.	.	.	.	6.853	0.526698	0.13066	.	.	ENSG00000196642	ENST00000371663;ENST00000311502;ENST00000371675;ENST00000435930	T;T;T;T	0.65178	-0.11;-0.11;-0.11;-0.14	4.72	3.81	0.43845	.	0.640675	0.15773	N	0.245330	T	0.45994	0.1370	L	0.34521	1.04	0.09310	N	1	B;B;B	0.29552	0.248;0.058;0.035	B;B;B	0.32090	0.14;0.04;0.018	T	0.28744	-1.0034	10	0.17832	T	0.49	-0.8971	5.3765	0.16168	0.1996:0.6926:0.0:0.1079	.	429;636;635	B1AMX5;Q3YEC7-2;Q3YEC7	.;.;PARF_HUMAN	V	636;635;520;429	ENSP00000360727:A636V;ENSP00000311134:A635V;ENSP00000360740:A520V;ENSP00000408442:A429V	ENSP00000311134:A635V	A	+	2	0	C9orf86	138854112	0.000000	0.05858	0.005000	0.12908	0.047000	0.14425	0.118000	0.15605	0.943000	0.37553	0.561000	0.74099	GCC	.		0.677	RABL6-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000055141.4	NM_024718	
STAT2	6773	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	12	56743381	56743381	+	Missense_Mutation	SNP	T	T	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr12:56743381T>A	ENST00000314128.4	-	14	1272	c.1249A>T	c.(1249-1251)Agc>Tgc	p.S417C	STAT2_ENST00000557235.1_Missense_Mutation_p.S413C|STAT2_ENST00000556539.1_5'UTR|RNU7-40P_ENST00000516397.1_RNA|STAT2_ENST00000418572.2_Missense_Mutation_p.S413C			P52630	STAT2_HUMAN	signal transducer and activator of transcription 2, 113kDa	417					cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|JAK-STAT cascade (GO:0007259)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|transcription, DNA-templated (GO:0006351)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			NS(1)|endometrium(2)|kidney(5)|large_intestine(7)|liver(2)|lung(10)|ovary(1)|skin(3)	31						ACCTTATTGCTGCCCTTTCCT	0.552																																					p.S417C		.											.	.	.	0			c.A1249T						.						136.0	124.0	128.0					12																	56743381		2203	4300	6503	SO:0001583	missense	6773	exon14			TATTGCTGCCCTT	BC051284	CCDS8917.1, CCDS55836.1	12q13.2	2013-02-14	2002-08-29			ENSG00000170581		"""SH2 domain containing"""	11363	protein-coding gene	gene with protein product		600556	"""signal transducer and activator of transcription 2, 113kD"""			7885841	Standard	NM_005419		Approved	STAT113	uc001slc.3	P52630		ENST00000314128.4:c.1249A>T	12.37:g.56743381T>A	ENSP00000315768:p.Ser417Cys	Somatic	50	0		WXS	Illumina HiSeq	.	34	13	NM_005419	B4DLC7|G3V2M6|Q16430|Q16431|Q9UDL4	Missense_Mutation	SNP	ENST00000314128.4	37	CCDS8917.1	.	.	.	.	.	.	.	.	.	.	T	14.22	2.471644	0.43942	.	.	ENSG00000170581	ENST00000314128;ENST00000557235;ENST00000553337;ENST00000418572	D;D;D	0.87571	-2.27;-2.27;-2.27	5.16	1.16	0.20824	STAT transcription factor, DNA-binding, subdomain (1);STAT transcription factor, DNA-binding (1);p53-like transcription factor, DNA-binding (1);	0.499987	0.22912	N	0.054126	T	0.76898	0.4052	L	0.32530	0.975	0.24330	N	0.995006	B;B;B	0.14805	0.009;0.011;0.004	B;B;B	0.17722	0.019;0.012;0.007	T	0.64723	-0.6340	10	0.46703	T	0.11	-0.645	5.2859	0.15700	0.2849:0.0822:0.0:0.6329	.	413;413;417	B4DLC8;G3V2M6;P52630	.;.;STAT2_HUMAN	C	417;413;219;413	ENSP00000315768:S417C;ENSP00000450751:S413C;ENSP00000387354:S413C	ENSP00000315768:S417C	S	-	1	0	STAT2	55029648	0.682000	0.27624	0.990000	0.47175	0.964000	0.63967	0.842000	0.27627	0.356000	0.24157	0.460000	0.39030	AGC	.		0.552	STAT2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410277.1	NM_005419	
UTP14C	9724	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	13	52598853	52598853	+	De_novo_Start_OutOfFrame	SNP	G	G	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr13:52598853G>A	ENST00000521776.2	+	0	27				ALG11_ENST00000521508.1_Silent_p.K329K|ALG11_ENST00000519151.1_3'UTR|ALG11_ENST00000523764.1_Intron	NM_021645.5	NP_067677.4	Q5TAP6	UT14C_HUMAN	UTP14, U3 small nucleolar ribonucleoprotein, homolog C (yeast)						cell differentiation (GO:0030154)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|rRNA processing (GO:0006364)|spermatogenesis (GO:0007283)	nucleus (GO:0005634)|small-subunit processome (GO:0032040)				breast(4)|cervix(1)|endometrium(1)|large_intestine(10)|lung(10)|ovary(3)|skin(1)|stomach(1)|urinary_tract(1)	32		Breast(56;0.00173)|Lung NSC(96;0.0108)|Prostate(109;0.0412)|Hepatocellular(98;0.152)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(99;2.3e-08)		TGAATAAGAAGATGGTTGAGT	0.448																																					p.K329K		.											.	.	.	0			c.G987A						.						105.0	105.0	105.0					13																	52598853		2203	4300	6503			440138	exon3			TAAGAAGATGGTT	D87455	CCDS31978.1	13q12.2-q13.3	2010-11-23	2004-06-15	2004-06-16	ENSG00000253797	ENSG00000253797			20321	protein-coding gene	gene with protein product		608969	"""KIAA0266"""	KIAA0266		9039502, 16354793	Standard	NM_021645		Approved	2700066J21Rik	uc021rjw.1	Q5TAP6	OTTHUMG00000164353	ENST00000521776.2:c.-707G>A	13.37:g.52598853G>A		Somatic	60	0		WXS	Illumina HiSeq	.	38	17	NM_001004127	Q5FWG3|Q92555	Silent	SNP	ENST00000521776.2	37	CCDS31978.1																																																																																			.		0.448	UTP14C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045049.2	NM_021645	
ACSM2B	348158	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	16	20554487	20554487	+	Missense_Mutation	SNP	C	C	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr16:20554487C>T	ENST00000329697.6	-	11	1547	c.1379G>A	c.(1378-1380)gGa>gAa	p.G460E	ACSM2B_ENST00000567288.1_5'Flank|ACSM2B_ENST00000565322.1_Missense_Mutation_p.G381E|ACSM2B_ENST00000567001.1_Missense_Mutation_p.G460E|ACSM2B_ENST00000565232.1_Missense_Mutation_p.G460E	NM_001105069.1	NP_001098539.1	Q68CK6	ACS2B_HUMAN	acyl-CoA synthetase medium-chain family member 2B	460					fatty acid metabolic process (GO:0006631)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|butyrate-CoA ligase activity (GO:0047760)|metal ion binding (GO:0046872)			breast(4)|central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(4)|lung(33)|ovary(1)|prostate(1)|skin(5)	57						ATCTGCCCGTCCCATAAACTG	0.498																																					p.G460E		.											.	.	.	0			c.G1379A						.						331.0	349.0	343.0					16																	20554487		2200	4299	6499	SO:0001583	missense	348158	exon12			GCCCGTCCCATAA	AY160217	CCDS10586.1	16p12.3	2014-08-08	2007-06-20	2007-06-20	ENSG00000066813	ENSG00000066813		"""Acyl-CoA synthetase family"""	30931	protein-coding gene	gene with protein product	"""xenobiotic/medium chain fatty acid:CoA ligase"""	614359	"""acyl-CoA synthetase medium-chain family member 2"""	ACSM2		12616642	Standard	NM_182617		Approved	HXMA, HYST1046	uc002dhk.4	Q68CK6	OTTHUMG00000131555	ENST00000329697.6:c.1379G>A	16.37:g.20554487C>T	ENSP00000327453:p.Gly460Glu	Somatic	195	0		WXS	Illumina HiSeq	.	164	52	NM_182617	Q86YT1	Missense_Mutation	SNP	ENST00000329697.6	37	CCDS10586.1	.	.	.	.	.	.	.	.	.	.	C	14.10	2.434782	0.43224	.	.	ENSG00000066813	ENST00000329697	T	0.64438	-0.1	3.1	3.1	0.35709	AMP-dependent synthetase/ligase (1);	0.000000	0.41396	U	0.000897	T	0.79370	0.4434	M	0.83118	2.625	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.83861	0.0268	10	0.87932	D	0	-15.5025	14.3347	0.66581	0.0:1.0:0.0:0.0	.	460;460	A8K051;Q68CK6	.;ACS2B_HUMAN	E	460	ENSP00000327453:G460E	ENSP00000327453:G460E	G	-	2	0	ACSM2B	20461988	0.980000	0.34600	0.537000	0.28052	0.180000	0.23129	4.198000	0.58419	1.743000	0.51761	0.508000	0.49915	GGA	.		0.498	ACSM2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254417.2	NM_182617	
RALGPS2	55103	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	178745908	178745908	+	Silent	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr1:178745908A>C	ENST00000367635.3	+	2	347	c.9A>C	c.(7-9)ctA>ctC	p.L3L	RALGPS2_ENST00000367634.2_Silent_p.L3L	NM_152663.3	NP_689876.2	Q86X27	RGPS2_HUMAN	Ral GEF with PH domain and SH3 binding motif 2	3					small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(11)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	29						GCATGGACCTAATGAACGGGC	0.423																																					p.L3L		.											.	.	.	0			c.A9C						.						126.0	101.0	110.0					1																	178745908		2203	4300	6503	SO:0001819	synonymous_variant	55103	exon2			GGACCTAATGAAC	AK098470	CCDS1325.1, CCDS65733.1	1q24	2013-01-11			ENSG00000116191	ENSG00000116191		"""Pleckstrin homology (PH) domain containing"""	30279	protein-coding gene	gene with protein product						10747847, 12102558	Standard	NM_152663		Approved	KIAA0351, FLJ10244, FLJ25604	uc001glz.3	Q86X27	OTTHUMG00000035076	ENST00000367635.3:c.9A>C	1.37:g.178745908A>C		Somatic	53	0		WXS	Illumina HiSeq	.	53	34	NM_152663	B7Z7B1|Q5T5Z1|Q5VZ67|Q9NW78	Silent	SNP	ENST00000367635.3	37	CCDS1325.1																																																																																			.		0.423	RALGPS2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084926.2	NM_152663	
PYGM	5837	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	11	64514795	64514795	+	Missense_Mutation	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr11:64514795T>G	ENST00000164139.3	-	18	2611	c.2213A>C	c.(2212-2214)gAg>gCg	p.E738A	RASGRP2_ENST00000394430.1_5'Flank|RASGRP2_ENST00000354024.3_5'Flank|RASGRP2_ENST00000377489.1_5'Flank|PYGM_ENST00000377432.3_Missense_Mutation_p.E650A|RASGRP2_ENST00000377487.1_5'Flank|RASGRP2_ENST00000377497.3_5'Flank	NM_005609.2	NP_005600.1	P11217	PYGM_HUMAN	phosphorylase, glycogen, muscle	738					carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|glycogen metabolic process (GO:0005977)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	glycogen phosphorylase activity (GO:0008184)|nucleotide binding (GO:0000166)|pyridoxal phosphate binding (GO:0030170)			cervix(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(21)|ovary(3)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						CTGCCGAAGCTCAGGAATGCG	0.557																																					p.E738A		.											.	.	.	0			c.A2213C						.						141.0	116.0	124.0					11																	64514795		2201	4297	6498	SO:0001583	missense	5837	exon18			CGAAGCTCAGGAA		CCDS8079.1, CCDS53659.1	11q12-q13.2	2013-03-01	2008-07-31		ENSG00000068976	ENSG00000068976	2.4.1.1	"""Glycogen phosphorylases"""	9726	protein-coding gene	gene with protein product	"""McArdle syndrome"", ""glycogen storage disease type V"", ""glycogen phosphorylase, muscle form"""	608455	"""phosphorylase, glycogen; muscle"""				Standard	NM_005609		Approved		uc001oax.4	P11217	OTTHUMG00000066835	ENST00000164139.3:c.2213A>C	11.37:g.64514795T>G	ENSP00000164139:p.Glu738Ala	Somatic	23	0		WXS	Illumina HiSeq	.	21	13	NM_005609	A0AVK1|A6NDY6	Missense_Mutation	SNP	ENST00000164139.3	37	CCDS8079.1	.	.	.	.	.	.	.	.	.	.	T	16.29	3.081001	0.55753	.	.	ENSG00000068976	ENST00000377432;ENST00000164139;ENST00000540450	D;D	0.93076	-3.16;-3.16	4.62	4.62	0.57501	.	0.000000	0.47852	D	0.000217	D	0.91202	0.7228	L	0.53729	1.69	0.80722	D	1	B;B	0.23316	0.083;0.006	B;B	0.29077	0.098;0.058	D	0.89281	0.3612	10	0.52906	T	0.07	-25.4673	12.0153	0.53311	0.0:0.0:0.0:1.0	.	650;738	A6NDY6;P11217	.;PYGM_HUMAN	A	650;738;719	ENSP00000366650:E650A;ENSP00000164139:E738A	ENSP00000164139:E738A	E	-	2	0	PYGM	64271371	1.000000	0.71417	0.972000	0.41901	0.794000	0.44872	7.805000	0.86005	1.954000	0.56735	0.379000	0.24179	GAG	.		0.557	PYGM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143254.2	NM_005609	
DLL1	28514	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	6	170597586	170597586	+	Splice_Site	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr6:170597586T>G	ENST00000366756.3	-	4	746		c.e4-2		FAM120B_ENST00000540480.1_5'Flank	NM_005618.3	NP_005609.3	O00548	DLL1_HUMAN	delta-like 1 (Drosophila)						cell differentiation (GO:0030154)|cell fate determination (GO:0001709)|cell-cell signaling (GO:0007267)|compartment pattern specification (GO:0007386)|determination of left/right symmetry (GO:0007368)|heart looping (GO:0001947)|hemopoiesis (GO:0030097)|inner ear development (GO:0048839)|left/right axis specification (GO:0070986)|loop of Henle development (GO:0072070)|negative regulation of auditory receptor cell differentiation (GO:0045608)|negative regulation of interleukin-10 production (GO:0032693)|negative regulation of myeloid cell differentiation (GO:0045638)|neuronal stem cell maintenance (GO:0097150)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|proximal tubule development (GO:0072014)|regulation of cell adhesion (GO:0030155)|somite specification (GO:0001757)	cytoplasmic vesicle (GO:0031410)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|Notch binding (GO:0005112)			NS(2)|breast(1)|endometrium(1)|large_intestine(7)|lung(17)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	33		Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246)		OV - Ovarian serous cystadenocarcinoma(33;6.71e-23)|BRCA - Breast invasive adenocarcinoma(81;4.81e-06)|GBM - Glioblastoma multiforme(31;0.0584)		CTGGGTTTTCTACGGGGAGAA	0.642																																					.		.											.	.	.	0			c.413-2A>C						.						30.0	32.0	31.0					6																	170597586		2203	4300	6503	SO:0001630	splice_region_variant	28514	exon5			GTTTTCTACGGGG	AF003522	CCDS5313.1	6q13-q22.33	2008-07-28	2001-12-03		ENSG00000198719	ENSG00000198719			2908	protein-coding gene	gene with protein product		606582	"""delta (Drosophila)-like 1"""				Standard	NM_005618		Approved		uc003qxm.3	O00548	OTTHUMG00000016078	ENST00000366756.3:c.413-2A>C	6.37:g.170597586T>G		Somatic	33	0		WXS	Illumina HiSeq	.	28	11	NM_005618	B2RAK7|B5M0B3|Q9NU41|Q9UJV2	Splice_Site	SNP	ENST00000366756.3	37	CCDS5313.1	.	.	.	.	.	.	.	.	.	.	T	11.63	1.697211	0.30142	.	.	ENSG00000198719	ENST00000366756	.	.	.	4.44	4.44	0.53790	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.9523	0.64126	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	DLL1	170439511	1.000000	0.71417	0.885000	0.34714	0.034000	0.12701	7.442000	0.80503	1.885000	0.54596	0.456000	0.33151	.	.		0.642	DLL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043254.1		Intron
YDJC	150223	hgsc.bcm.edu;bcgsc.ca	37	22	21982727	21982727	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr22:21982727G>T	ENST00000292778.6	-	5	1001	c.952C>A	c.(952-954)Ctg>Atg	p.L318M	YDJC_ENST00000398873.3_3'UTR	NM_001017964.1	NP_001017964.1	A8MPS7	YDJC_HUMAN	YdjC homolog (bacterial)	318					carbohydrate metabolic process (GO:0005975)		hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds (GO:0016810)					Colorectal(54;0.105)					GAGGGTTCCAGGAAGGGTTCC	0.612																																					p.L318M		.											.	.	.	0			c.C952A						.						102.0	109.0	107.0					22																	21982727		2203	4300	6503	SO:0001583	missense	150223	exon5			GTTCCAGGAAGGG		CCDS33613.1	22q11.21	2008-02-26			ENSG00000161179	ENSG00000161179			27158	protein-coding gene	gene with protein product						18177738	Standard	XM_005261347		Approved		uc002zvb.2	A8MPS7	OTTHUMG00000150822	ENST00000292778.6:c.952C>A	22.37:g.21982727G>T	ENSP00000292778:p.Leu318Met	Somatic	59	0		WXS	Illumina HiSeq	.	48	4	NM_001017964	Q2YDT4|Q4V9R7	Missense_Mutation	SNP	ENST00000292778.6	37	CCDS33613.1	.	.	.	.	.	.	.	.	.	.	G	20.9	4.065904	0.76187	.	.	ENSG00000161179	ENST00000292778	T	0.53206	0.63	4.02	-2.0	0.07433	.	0.789333	0.10385	N	0.681097	T	0.33440	0.0863	L	0.36672	1.1	0.18873	N	0.999988	B	0.34015	0.435	B	0.36289	0.221	T	0.34601	-0.9822	10	0.87932	D	0	.	3.9827	0.09501	0.3111:0.355:0.334:0.0	.	318	A8MPS7	YDJC_HUMAN	M	318	ENSP00000292778:L318M	ENSP00000292778:L318M	L	-	1	2	YDJC	20312727	0.000000	0.05858	0.012000	0.15200	0.936000	0.57629	-0.225000	0.09151	-0.175000	0.10725	0.650000	0.86243	CTG	.		0.612	YDJC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320213.1		
MTBP	27085	hgsc.bcm.edu	37	8	121519076	121519076	+	Missense_Mutation	SNP	C	C	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr8:121519076C>T	ENST00000305949.1	+	16	1903	c.1858C>T	c.(1858-1860)Ctt>Ttt	p.L620F		NM_022045.4	NP_071328.2	Q96DY7	MTBP_HUMAN	MDM2 binding protein	620	Interaction with MDM2. {ECO:0000250}.				cell cycle arrest (GO:0007050)|mitotic spindle checkpoint (GO:0071174)|negative regulation of cell proliferation (GO:0008285)|protein localization to kinetochore (GO:0034501)|traversing start control point of mitotic cell cycle (GO:0007089)	chromatin (GO:0000785)|kinetochore (GO:0000776)				NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	30	Lung NSC(37;5.68e-08)|Ovarian(258;0.00769)|all_neural(195;0.0804)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00503)			CATTGGAGATCTTCAACCTTT	0.358																																					p.L620F		.											MTBP,NS,carcinoma,0,1	MTBP	0	0			c.C1858T						.						84.0	81.0	82.0					8																	121519076		2203	4300	6503	SO:0001583	missense	27085	exon16			GGAGATCTTCAAC		CCDS6333.1	8q24.1-q24.2	2014-03-03	2014-03-03		ENSG00000172167	ENSG00000172167			7417	protein-coding gene	gene with protein product		605927	"""MDM2 (mouse double minute 2)-binding protein, 104kD"", ""Mdm2, transformed 3T3 cell double minute 2, p53 binding protein (mouse) binding protein, 104kDa"""			10906133, 11060448	Standard	NM_022045		Approved		uc003ypc.2	Q96DY7	OTTHUMG00000165040	ENST00000305949.1:c.1858C>T	8.37:g.121519076C>T	ENSP00000303398:p.Leu620Phe	Somatic	83	0		WXS	Illumina HiSeq	.	66	3	NM_022045	B4DUR5|Q9HA89	Missense_Mutation	SNP	ENST00000305949.1	37	CCDS6333.1	.	.	.	.	.	.	.	.	.	.	C	13.62	2.292136	0.40594	.	.	ENSG00000172167	ENST00000305949	.	.	.	5.18	5.18	0.71444	.	0.000000	0.64402	D	0.000001	T	0.79964	0.4537	M	0.76328	2.33	0.58432	D	0.999994	D	0.89917	1.0	D	0.91635	0.999	T	0.82250	-0.0550	9	0.72032	D	0.01	-19.3702	18.6686	0.91501	0.0:1.0:0.0:0.0	.	620	Q96DY7	MTBP_HUMAN	F	620	.	ENSP00000303398:L620F	L	+	1	0	MTBP	121588257	1.000000	0.71417	1.000000	0.80357	0.132000	0.20833	3.957000	0.56730	2.431000	0.82371	0.313000	0.20887	CTT	.		0.358	MTBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381530.1	NM_022045	
TNC	3371	hgsc.bcm.edu	37	9	117797604	117797604	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr9:117797604G>T	ENST00000350763.4	-	22	6077	c.5666C>A	c.(5665-5667)tCt>tAt	p.S1889Y	TNC_ENST00000423613.2_Missense_Mutation_p.S1616Y|TNC_ENST00000341037.4_Missense_Mutation_p.S1707Y|TNC_ENST00000346706.3_Missense_Mutation_p.S1343Y|TNC_ENST00000345230.3_Missense_Mutation_p.S1252Y|TNC_ENST00000535648.1_Missense_Mutation_p.S1434Y|TNC_ENST00000542877.1_Missense_Mutation_p.S1526Y|TNC_ENST00000340094.3_Missense_Mutation_p.S1525Y|TNC_ENST00000537320.1_Missense_Mutation_p.S1252Y	NM_002160.3	NP_002151.2	P24821	TENA_HUMAN	tenascin C	1889	Fibronectin type-III 15. {ECO:0000255|PROSITE-ProRule:PRU00316}.				bud outgrowth involved in lung branching (GO:0060447)|cell adhesion (GO:0007155)|cellular response to prostaglandin D stimulus (GO:0071799)|cellular response to retinoic acid (GO:0071300)|cellular response to vitamin D (GO:0071305)|extracellular matrix organization (GO:0030198)|mesenchymal-epithelial cell signaling involved in prostate gland development (GO:0060739)|negative regulation of cell adhesion (GO:0007162)|neuromuscular junction development (GO:0007528)|odontogenesis of dentin-containing tooth (GO:0042475)|osteoblast differentiation (GO:0001649)|peripheral nervous system axon regeneration (GO:0014012)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|prostate gland epithelium morphogenesis (GO:0060740)|response to ethanol (GO:0045471)|response to fibroblast growth factor (GO:0071774)|response to mechanical stimulus (GO:0009612)|response to wounding (GO:0009611)|wound healing (GO:0042060)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|interstitial matrix (GO:0005614)|membrane (GO:0016020)	syndecan binding (GO:0045545)			NS(3)|breast(5)|central_nervous_system(4)|endometrium(8)|kidney(6)|large_intestine(32)|liver(1)|lung(39)|ovary(1)|pancreas(2)|prostate(5)|skin(5)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	120						GTCTCTTGGAGAATCGAGGTC	0.512																																					p.S1889Y		.											TNC,NS,malignant_melanoma,0,1	TNC	0	0			c.C5666A						.						68.0	68.0	68.0					9																	117797604		2203	4300	6503	SO:0001583	missense	3371	exon22			CTTGGAGAATCGA		CCDS6811.1	9q33.1	2014-01-28	2008-07-31	2002-06-07	ENSG00000041982	ENSG00000041982		"""Fibrinogen C domain containing"", ""Fibronectin type III domain containing"""	5318	protein-coding gene	gene with protein product	"""hexabrachion (tenascin)"""	187380	"""hexabrachion (tenascin C, cytotactin)"", ""deafness, autosomal dominant 56"""	HXB, DFNA56		1704365, 1707164, 23936043	Standard	NM_002160		Approved	TN, MGC167029	uc004bjj.4	P24821	OTTHUMG00000021010	ENST00000350763.4:c.5666C>A	9.37:g.117797604G>T	ENSP00000265131:p.Ser1889Tyr	Somatic	56	0		WXS	Illumina HiSeq	.	44	2	NM_002160	C9IYT7|C9J575|C9J6D9|C9J848|Q14583|Q15567|Q5T7S3	Missense_Mutation	SNP	ENST00000350763.4	37	CCDS6811.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	22.0|22.0	4.230446|4.230446	0.79688|0.79688	.|.	.|.	ENSG00000041982|ENSG00000041982	ENST00000544972|ENST00000340094;ENST00000535648;ENST00000346706;ENST00000345230;ENST00000350763;ENST00000442945;ENST00000341037;ENST00000423613;ENST00000537320;ENST00000542877	.|T;T;T;T;T;T;T;T;T	.|0.58060	.|0.36;0.36;0.36;0.36;0.36;0.36;0.36;0.36;0.36	5.97|5.97	5.97|5.97	0.96955|0.96955	.|Fibronectin, type III (4);Immunoglobulin-like fold (1);	.|0.309163	.|0.38217	.|N	.|0.001779	T|T	0.67353|0.67353	0.2884|0.2884	L|L	0.52905|0.52905	1.665|1.665	0.23776|0.23776	N|N	0.996871|0.996871	.|D;P	.|0.64830	.|0.994;0.9	.|D;P	.|0.66196	.|0.942;0.793	T|T	0.62315|0.62315	-0.6880|-0.6880	5|10	.|0.72032	.|D	.|0.01	.|.	15.8476|15.8476	0.78903|0.78903	0.0:0.135:0.865:0.0|0.0:0.135:0.865:0.0	.|.	.|1616;1889	.|E9PC84;P24821	.|.;TENA_HUMAN	L|Y	451|1525;1434;1343;1252;1889;961;1707;1616;1252;1526	.|ENSP00000344400:S1525Y;ENSP00000438152:S1434Y;ENSP00000344555:S1343Y;ENSP00000345861:S1252Y;ENSP00000265131:S1889Y;ENSP00000339553:S1707Y;ENSP00000411406:S1616Y;ENSP00000443478:S1252Y;ENSP00000442242:S1526Y	.|ENSP00000344400:S1525Y	F|S	-|-	3|2	2|0	TNC|TNC	116837425|116837425	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.901000|0.901000	0.52897|0.52897	6.308000|6.308000	0.72820|0.72820	2.819000|2.819000	0.97034|0.97034	0.655000|0.655000	0.94253|0.94253	TTC|TCT	.		0.512	TNC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055418.2	NM_002160	
LINC00710	254312	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	10	10989451	10989451	+	RNA	SNP	A	A	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr10:10989451A>G	ENST00000428520.2	-	0	226					NR_015413.1				long intergenic non-protein coding RNA 710																		ATGAAACATCATTTGTAACTG	0.373																																					.		.											.	.	.	0			.						.																																					254312	.			AACATCATTTGTA			10p14	2012-12-05			ENSG00000229240	ENSG00000229240		"""Long non-coding RNAs"""	27386	non-coding RNA	RNA, long non-coding							Standard	NR_015413		Approved		uc009xiu.3		OTTHUMG00000017661		10.37:g.10989451A>G		Somatic	110	0		WXS	Illumina HiSeq	.	41	19	.		RNA	SNP	ENST00000428520.2	37																																																																																				.		0.373	LINC00710-001	KNOWN	basic	lincRNA	processed_transcript	OTTHUMT00000046746.3	NR_015413	
GPR98	84059	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	5	90079733	90079733	+	Missense_Mutation	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr5:90079733A>C	ENST00000405460.2	+	67	13608	c.13512A>C	c.(13510-13512)agA>agC	p.R4504S	GPR98_ENST00000425867.2_Missense_Mutation_p.R165S	NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	4504					detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|G-protein coupled receptor signaling pathway (GO:0007186)|inner ear receptor stereocilium organization (GO:0060122)|maintenance of organ identity (GO:0048496)|nervous system development (GO:0007399)|neurological system process (GO:0050877)|neuropeptide signaling pathway (GO:0007218)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|stereocilia ankle link complex (GO:0002142)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(4)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(18)|large_intestine(46)|liver(2)|lung(80)|ovary(12)|pancreas(5)|prostate(1)|skin(50)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(6)	269		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		TAGTGAGCAGAATCATAATAG	0.428																																					p.R4504S		.											.	.	.	0			c.A13512C						.						61.0	59.0	60.0					5																	90079733		1839	4084	5923	SO:0001583	missense	84059	exon67			GAGCAGAATCATA	AB014586	CCDS47246.1	5q13	2014-08-08	2006-05-26	2006-05-26	ENSG00000164199	ENSG00000164199		"""-"", ""GPCR / Class B : Orphans"""	17416	protein-coding gene	gene with protein product		602851	"""monogenic, audiogenic seizure susceptibility 1 homolog (mouse)"""	USH2C, MASS1		10976914, 14740321	Standard	NM_032119		Approved	DKFZp761P0710, KIAA0686, FEB4, VLGR1b	uc003kju.3	Q8WXG9	OTTHUMG00000162668	ENST00000405460.2:c.13512A>C	5.37:g.90079733A>C	ENSP00000384582:p.Arg4504Ser	Somatic	91	0		WXS	Illumina HiSeq	.	66	21	NM_032119	O75171|Q8TF58|Q9H0X5|Q9UL61	Missense_Mutation	SNP	ENST00000405460.2	37	CCDS47246.1	.	.	.	.	.	.	.	.	.	.	A	8.573	0.880526	0.17467	.	.	ENSG00000164199	ENST00000405460;ENST00000296619;ENST00000425867	T;T	0.26660	1.72;1.72	5.97	0.742	0.18341	.	0.254076	0.44483	D	0.000460	T	0.20210	0.0486	M	0.70595	2.14	0.21445	N	0.999685	B;P;P	0.48764	0.335;0.915;0.465	B;B;B	0.36666	0.086;0.23;0.178	T	0.18085	-1.0348	10	0.38643	T	0.18	.	6.1939	0.20540	0.5871:0.1256:0.2874:0.0	.	165;4504;165	E7EML1;Q8WXG9;Q8WXG9-2	.;GPR98_HUMAN;.	S	4504;4504;165	ENSP00000384582:R4504S;ENSP00000392618:R165S	ENSP00000296619:R4504S	R	+	3	2	GPR98	90115489	0.999000	0.42202	0.690000	0.30148	0.338000	0.28826	1.734000	0.38166	0.168000	0.19655	-0.250000	0.11733	AGA	.		0.428	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119	
ZC3H6	376940	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	2	113079392	113079392	+	Missense_Mutation	SNP	A	A	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr2:113079392A>G	ENST00000409871.1	+	8	1437	c.1036A>G	c.(1036-1038)Aaa>Gaa	p.K346E	ZC3H6_ENST00000343936.4_Missense_Mutation_p.K346E	NM_198581.2	NP_940983.2	P61129	ZC3H6_HUMAN	zinc finger CCCH-type containing 6	346							metal ion binding (GO:0046872)			central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(9)|lung(12)|ovary(4)|prostate(2)	35						AGACAACTGTAAATTTTCCCA	0.308																																					p.K346E		.											.	.	.	0			c.A1036G						.						47.0	42.0	43.0					2																	113079392		1801	4067	5868	SO:0001583	missense	376940	exon8			AACTGTAAATTTT	AK123404	CCDS46393.1	2q13	2012-07-05	2005-06-02	2005-06-02	ENSG00000188177	ENSG00000188177		"""Zinc fingers, CCCH-type domain containing"""	24762	protein-coding gene	gene with protein product			"""zinc finger CCCH-type domain containing 6"""	ZC3HDC6			Standard	NM_198581		Approved	FLJ41410, FLJ45877, KIAA2035	uc002thq.1	P61129	OTTHUMG00000153286	ENST00000409871.1:c.1036A>G	2.37:g.113079392A>G	ENSP00000386764:p.Lys346Glu	Somatic	125	0		WXS	Illumina HiSeq	.	73	38	NM_198581	A9JR71|Q6ZW96	Missense_Mutation	SNP	ENST00000409871.1	37	CCDS46393.1	.	.	.	.	.	.	.	.	.	.	A	28.7	4.946368	0.92593	.	.	ENSG00000188177	ENST00000409871;ENST00000343936;ENST00000542974	T;T	0.40756	1.02;1.02	5.54	5.54	0.83059	Zinc finger, CCCH-type (2);	0.000000	0.85682	D	0.000000	T	0.53318	0.1789	L	0.31845	0.965	0.80722	D	1	D	0.69078	0.997	D	0.70016	0.967	T	0.52449	-0.8574	10	0.45353	T	0.12	-25.9529	15.9801	0.80102	1.0:0.0:0.0:0.0	.	346	P61129	ZC3H6_HUMAN	E	346;346;323	ENSP00000386764:K346E;ENSP00000340298:K346E	ENSP00000340298:K346E	K	+	1	0	ZC3H6	112795863	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.887000	0.92456	2.230000	0.72887	0.528000	0.53228	AAA	.		0.308	ZC3H6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330551.1	NM_198581	
HNRNPM	4670	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	19	8527458	8527458	+	Missense_Mutation	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr19:8527458A>C	ENST00000325495.4	+	3	370	c.329A>C	c.(328-330)aAg>aCg	p.K110T	HNRNPM_ENST00000348943.3_Missense_Mutation_p.K110T	NM_005968.4	NP_005959.2	P52272	HNRPM_HUMAN	heterogeneous nuclear ribonucleoprotein M	110	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				alternative mRNA splicing, via spliceosome (GO:0000380)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|extracellular matrix (GO:0031012)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|paraspeckles (GO:0042382)|spliceosomal complex (GO:0005681)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein domain specific binding (GO:0019904)|RNA binding (GO:0003723)			endometrium(5)|kidney(2)|large_intestine(7)|lung(10)|ovary(1)	25						GCTGAAGGAAAGTCAAGGGTA	0.418																																					p.K110T		.											.	.	.	0			c.A329C						.						263.0	237.0	246.0					19																	8527458		2203	4300	6503	SO:0001583	missense	4670	exon3			AAGGAAAGTCAAG	L03532	CCDS12203.1, CCDS12204.1	19p13.2	2013-06-12		2008-04-18	ENSG00000099783	ENSG00000099783		"""RNA binding motif (RRM) containing"""	5046	protein-coding gene	gene with protein product	"""CEA receptor"""	160994		NAGR1, HNRPM		8441656, 7558047	Standard	NM_005968		Approved	HTGR1, HNRNPM4, HNRPM4, CEAR	uc010dwe.3	P52272	OTTHUMG00000182383	ENST00000325495.4:c.329A>C	19.37:g.8527458A>C	ENSP00000325376:p.Lys110Thr	Somatic	86	0		WXS	Illumina HiSeq	.	65	21	NM_031203	Q15584|Q8WZ44|Q96H56|Q9BWL9|Q9Y492	Missense_Mutation	SNP	ENST00000325495.4	37	CCDS12203.1	.	.	.	.	.	.	.	.	.	.	A	18.40	3.616099	0.66672	.	.	ENSG00000099783	ENST00000325495;ENST00000348943	T;T	0.17854	2.25;2.25	5.82	5.82	0.92795	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.047544	0.85682	D	0.000000	T	0.42404	0.1201	M	0.71581	2.175	0.80722	D	1	P;D;P	0.89917	0.558;1.0;0.77	P;D;P	0.85130	0.796;0.997;0.474	T	0.33111	-0.9881	10	0.87932	D	0	.	15.0018	0.71479	1.0:0.0:0.0:0.0	.	110;110;110	P52272;P52272-2;B4DEG4	HNRPM_HUMAN;.;.	T	110	ENSP00000325376:K110T;ENSP00000325732:K110T	ENSP00000325376:K110T	K	+	2	0	HNRNPM	8433458	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.962000	0.93254	2.225000	0.72522	0.459000	0.35465	AAG	.		0.418	HNRNPM-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460894.1		
FAM21EP	100421577	hgsc.bcm.edu	37	10	51816497	51816497	+	RNA	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr10:51816497A>C	ENST00000456967.1	-	0	1570					NR_038275.1																						GAATTATTAAAATGCTGCAGA	0.428																																					.		.											.	.	.	0			.						.																																					0	.			TATTAAAATGCTG																													10.37:g.51816497A>C		Somatic	216	0		WXS	Illumina HiSeq	.	102	49	.		RNA	SNP	ENST00000456967.1	37																																																																																				.		0.428	RP11-324H6.5-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000048059.1		
ZNF526	116115	hgsc.bcm.edu	37	19	42729173	42729173	+	Silent	SNP	C	C	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr19:42729173C>T	ENST00000301215.3	+	3	843	c.618C>T	c.(616-618)tgC>tgT	p.C206C		NM_133444.1	NP_597701.1	Q8TF50	ZN526_HUMAN	zinc finger protein 526	206	Glu-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			autonomic_ganglia(1)|cervix(1)|endometrium(4)|large_intestine(3)|lung(9)|prostate(1)|skin(3)	22		Prostate(69;0.0704)				CTACCCTCTGCGCCACCCCTG	0.587																																					p.C206C		.											ZNF526,NS,carcinoma,0,1	ZNF526	0	0			c.C618T						.						140.0	132.0	135.0					19																	42729173		2203	4300	6503	SO:0001819	synonymous_variant	116115	exon3			CCTCTGCGCCACC	AB075831	CCDS12598.1	19q13.31	2013-01-08				ENSG00000167625		"""Zinc fingers, C2H2-type"""	29415	protein-coding gene	gene with protein product		614387				11853319	Standard	NM_133444		Approved	KIAA1951, MGC4267	uc002osz.1	Q8TF50		ENST00000301215.3:c.618C>T	19.37:g.42729173C>T		Somatic	27	0		WXS	Illumina HiSeq	.	19	2	NM_133444	B3KV29|Q69YI2|Q96E24	Silent	SNP	ENST00000301215.3	37	CCDS12598.1																																																																																			.		0.587	ZNF526-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463681.2	XM_057401	
ZFYVE9	9372	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	52732359	52732359	+	Missense_Mutation	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr1:52732359A>C	ENST00000371591.1	+	5	2442	c.2311A>C	c.(2311-2313)Agc>Cgc	p.S771R	ZFYVE9_ENST00000357206.2_Intron|ZFYVE9_ENST00000287727.3_Missense_Mutation_p.S771R	NM_004799.2|NM_007324.2	NP_004790.2|NP_015563.2	O95405	ZFYV9_HUMAN	zinc finger, FYVE domain containing 9	771	SBD.				endocytosis (GO:0006897)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|proteolysis (GO:0006508)|SMAD protein complex assembly (GO:0007183)|SMAD protein import into nucleus (GO:0007184)|transforming growth factor beta receptor signaling pathway (GO:0007179)	early endosome (GO:0005769)|early endosome membrane (GO:0031901)	1-phosphatidylinositol binding (GO:0005545)|metal ion binding (GO:0046872)|serine-type peptidase activity (GO:0008236)			breast(1)|central_nervous_system(4)|endometrium(3)|kidney(1)|large_intestine(12)|lung(17)|ovary(2)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(6)	53						GAGTGCCTCAAGCCAGAGCCC	0.483																																					p.S771R		.											.	.	.	0			c.A2311C						.						171.0	155.0	160.0					1																	52732359		2203	4300	6503	SO:0001583	missense	9372	exon6			GCCTCAAGCCAGA	AF104304	CCDS563.1, CCDS564.1	1p32.3	2014-06-13	2004-05-21	2004-05-26	ENSG00000157077	ENSG00000157077		"""Zinc fingers, FYVE domain containing"""	6775	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 173"""	603755	"""MAD, mothers against decapentaplegic homolog (Drosophila) interacting protein, receptor activation anchor"""	MADHIP		9865696	Standard	NM_007324		Approved	SMADIP, SARA, PPP1R173	uc001cto.4	O95405	OTTHUMG00000008061	ENST00000371591.1:c.2311A>C	1.37:g.52732359A>C	ENSP00000360647:p.Ser771Arg	Somatic	69	0		WXS	Illumina HiSeq	.	57	19	NM_004799	Q5T0F6|Q5T0F7|Q9UNE1|Q9Y5R7	Missense_Mutation	SNP	ENST00000371591.1	37	CCDS563.1	.	.	.	.	.	.	.	.	.	.	A	16.33	3.092358	0.55968	.	.	ENSG00000157077	ENST00000287727;ENST00000371591	T;T	0.39787	1.06;1.06	5.25	5.25	0.73442	Smad anchor for receptor activation, Smad-binding domain (1);Zinc finger, FYVE/PHD-type (1);	0.178892	0.47455	D	0.000232	T	0.34919	0.0914	N	0.03608	-0.345	0.39922	D	0.974163	D	0.58970	0.984	D	0.63192	0.912	T	0.39231	-0.9624	10	0.33940	T	0.23	.	9.6481	0.39881	0.9222:0.0:0.0778:0.0	.	771	O95405	ZFYV9_HUMAN	R	771	ENSP00000287727:S771R;ENSP00000360647:S771R	ENSP00000287727:S771R	S	+	1	0	ZFYVE9	52504947	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.122000	0.71608	1.975000	0.57531	0.533000	0.62120	AGC	.		0.483	ZFYVE9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022083.1	NM_007324	
SYDE2	84144	hgsc.bcm.edu;broad.mit.edu	37	1	85666679	85666679	+	Start_Codon_SNP	SNP	T	T	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr1:85666679T>C	ENST00000341460.5	-	1	50	c.1A>G	c.(1-3)Atg>Gtg	p.M1V		NM_032184.1	NP_115560.1	Q5VT97	SYDE2_HUMAN	synapse defective 1, Rho GTPase, homolog 2 (C. elegans)	1					activation of Rho GTPase activity (GO:0032862)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho GTPase activator activity (GO:0005100)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(8)|ovary(1)	20				all cancers(265;0.0126)|Epithelial(280;0.0336)		AGGTCGTGCATGGCCTGGATC	0.751																																					p.M1V		.											.	.	.	0			c.A1G						.						4.0	4.0	4.0					1																	85666679		1168	2475	3643	SO:0001582	initiator_codon_variant	84144	exon1			CGTGCATGGCCTG	AL834286	CCDS44169.1	1p22.3	2008-02-05		2005-08-09	ENSG00000097096	ENSG00000097096			25841	protein-coding gene	gene with protein product							Standard	NM_032184		Approved	FLJ13815	uc009wcm.3	Q5VT97	OTTHUMG00000009956	ENST00000341460.5:c.1A>G	1.37:g.85666679T>C	ENSP00000340594:p.Met1Val	Somatic	9	0		WXS	Illumina HiSeq	.	14	6	NM_032184	Q5VT96|Q8NDB8|Q9H8A6	Missense_Mutation	SNP	ENST00000341460.5	37	CCDS44169.1	.	.	.	.	.	.	.	.	.	.	T	18.67	3.672900	0.67928	.	.	ENSG00000097096	ENST00000341460	T	0.07327	3.2	4.51	4.51	0.55191	.	.	.	.	.	T	0.04452	0.0122	.	.	.	0.46874	D	0.99923	B;P	0.44816	0.139;0.844	B;B	0.38803	0.075;0.282	T	0.24835	-1.0149	8	0.87932	D	0	.	12.7969	0.57564	0.0:0.0:0.0:1.0	.	1;1	Q5VT97;Q5VT97-2	SYDE2_HUMAN;.	V	1	ENSP00000340594:M1V	ENSP00000340594:M1V	M	-	1	0	SYDE2	85439267	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.110000	0.57831	1.678000	0.50952	0.402000	0.26972	ATG	.		0.751	SYDE2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127989.2		Missense_Mutation
PRKAB2	5565	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	146639504	146639504	+	Silent	SNP	C	C	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr1:146639504C>G	ENST00000254101.3	-	3	303	c.165G>C	c.(163-165)ggG>ggC	p.G55G	PRKAB2_ENST00000425272.2_Intron	NM_005399.3	NP_005390.1	O43741	AAKB2_HUMAN	protein kinase, AMP-activated, beta 2 non-catalytic subunit	55					carnitine shuttle (GO:0006853)|cell cycle arrest (GO:0007050)|cellular lipid metabolic process (GO:0044255)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|insulin receptor signaling pathway (GO:0008286)|membrane organization (GO:0061024)|protein phosphorylation (GO:0006468)|regulation of fatty acid biosynthetic process (GO:0042304)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	AMP-activated protein kinase complex (GO:0031588)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)	identical protein binding (GO:0042802)			NS(1)|endometrium(1)|large_intestine(2)|lung(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	11	all_hematologic(923;0.0487)				Acetylsalicylic acid(DB00945)|Adenosine monophosphate(DB00131)	ACTCTTTGTCCCCAGGGAGCT	0.517																																					p.G55G		.											.	.	.	0			c.G165C						.						142.0	152.0	149.0					1																	146639504		2203	4300	6503	SO:0001819	synonymous_variant	5565	exon3			TTTGTCCCCAGGG	BC053610	CCDS925.1	1q21.2	2008-02-05			ENSG00000131791	ENSG00000131791			9379	protein-coding gene	gene with protein product	"""AMPK beta 2"""	602741				8557660	Standard	NM_005399		Approved		uc001epe.3	O43741	OTTHUMG00000014032	ENST00000254101.3:c.165G>C	1.37:g.146639504C>G		Somatic	35	0		WXS	Illumina HiSeq	.	46	25	NM_005399	A8K9V5|B4DH06|Q5VXY0	Silent	SNP	ENST00000254101.3	37	CCDS925.1																																																																																			.		0.517	PRKAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039471.1	NM_005399	
CSNK1G2	1455	hgsc.bcm.edu	37	19	1953510	1953510	+	Intron	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr19:1953510A>C	ENST00000255641.8	+	1	230				CSNK1G2-AS1_ENST00000586395.1_RNA|CSNK1G2-AS1_ENST00000314315.3_RNA	NM_001319.6	NP_001310.3	P78368	KC1G2_HUMAN	casein kinase 1, gamma 2						protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|peptide binding (GO:0042277)|protein serine/threonine kinase activity (GO:0004674)			endometrium(1)|kidney(1)|lung(3)|prostate(1)|skin(1)|stomach(1)	8		Ovarian(11;2.11e-07)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CATAATCTGAATTTTGGGAAA	0.522																																					.	Ovarian(91;880 1392 21236 36928 37598)	.											.	.	.	0			.						.						82.0	77.0	79.0					19																	1953510		2091	4215	6306	SO:0001627	intron_variant	255193	.			ATCTGAATTTTGG	AF001177	CCDS12077.1	19p13.3	2013-01-17			ENSG00000133275	ENSG00000133275			2455	protein-coding gene	gene with protein product		602214				9403068	Standard	NM_001319		Approved	CK1g2	uc002lul.4	P78368		ENST00000255641.8:c.-266+12093A>C	19.37:g.1953510A>C		Somatic	50	0		WXS	Illumina HiSeq	.	28	13	.	B5BU42|O00704|Q8WUB1	RNA	SNP	ENST00000255641.8	37	CCDS12077.1																																																																																			.		0.522	CSNK1G2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449287.1	NM_001319	
PIKFYVE	200576	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	2	209189656	209189656	+	Missense_Mutation	SNP	C	C	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr2:209189656C>G	ENST00000264380.4	+	19	2511	c.2353C>G	c.(2353-2355)Cga>Gga	p.R785G		NM_015040.3	NP_055855.2	Q9Y2I7	FYV1_HUMAN	phosphoinositide kinase, FYVE finger containing	785					cellular protein metabolic process (GO:0044267)|intracellular signal transduction (GO:0035556)|myelin assembly (GO:0032288)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phospholipid metabolic process (GO:0006644)|protein localization to nucleus (GO:0034504)|retrograde transport, endosome to Golgi (GO:0042147)|small molecule metabolic process (GO:0044281)	cell-cell junction (GO:0005911)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|early endosome membrane (GO:0031901)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|late endosome membrane (GO:0031902)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|vesicle membrane (GO:0012506)	1-phosphatidylinositol-3-phosphate 5-kinase activity (GO:0000285)|1-phosphatidylinositol-4-phosphate 5-kinase activity (GO:0016308)|ATP binding (GO:0005524)|phosphatidylinositol-3,5-bisphosphate 5-phosphatase activity (GO:0043813)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(14)|kidney(6)|large_intestine(25)|lung(40)|ovary(7)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	107						ACGAATCAGTCGAATGACCCA	0.353																																					p.R785G		.											.	.	.	0			c.C2353G						.						125.0	121.0	122.0					2																	209189656		2203	4300	6503	SO:0001583	missense	200576	exon19			ATCAGTCGAATGA	AB023198	CCDS2382.1, CCDS33368.1, CCDS54431.1	2q34	2014-01-15	2009-04-17	2009-04-17	ENSG00000115020	ENSG00000115020		"""Zinc fingers, FYVE domain containing"""	23785	protein-coding gene	gene with protein product	"""zinc finger, FYVE domain containing 29"""	609414	"""phosphatidylinositol-3-phosphate/phosphatidylinositol 5-kinase, type III"""	PIP5K3		9858586, 12270933	Standard	NM_015040		Approved	MGC40423, KIAA0981, PIKfyve, PIP5K, p235, ZFYVE29, FAB1	uc002vcz.3	Q9Y2I7	OTTHUMG00000132945	ENST00000264380.4:c.2353C>G	2.37:g.209189656C>G	ENSP00000264380:p.Arg785Gly	Somatic	79	0		WXS	Illumina HiSeq	.	54	19	NM_015040	Q08AR7|Q08AR8|Q53ST3|Q53T36|Q8N5H0|Q8NB67	Missense_Mutation	SNP	ENST00000264380.4	37	CCDS2382.1	.	.	.	.	.	.	.	.	.	.	C	17.82	3.484294	0.63962	.	.	ENSG00000115020	ENST00000264380;ENST00000392200;ENST00000452564	T;T	0.69685	-0.42;-0.42	5.62	4.74	0.60224	.	0.078596	0.52532	D	0.000062	D	0.84844	0.5562	M	0.90814	3.15	0.80722	D	1	D;D	0.71674	0.978;0.998	P;D	0.79108	0.792;0.992	D	0.88645	0.3178	10	0.87932	D	0	-17.2161	16.2805	0.82673	0.1336:0.8664:0.0:0.0	.	785;729	Q9Y2I7;E9PDH4	FYV1_HUMAN;.	G	785;361;729	ENSP00000264380:R785G;ENSP00000405736:R729G	ENSP00000264380:R785G	R	+	1	2	PIKFYVE	208897901	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	3.991000	0.56973	1.489000	0.48450	0.650000	0.86243	CGA	.		0.353	PIKFYVE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256477.2	NM_015040	
ABI3	51225	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	17	47299925	47299925	+	Missense_Mutation	SNP	T	T	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr17:47299925T>C	ENST00000225941.1	+	8	1447	c.949T>C	c.(949-951)Tac>Cac	p.Y317H	ABI3_ENST00000419580.2_Missense_Mutation_p.Y311H	NM_001135186.1|NM_016428.2	NP_001128658.1|NP_057512	Q9P2A4	ABI3_HUMAN	ABI family, member 3	317	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				cellular component movement (GO:0006928)|regulation of cell migration (GO:0030334)	cytoplasm (GO:0005737)|intracellular (GO:0005622)|lamellipodium (GO:0030027)|membrane (GO:0016020)				breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	12			Epithelial(5;6.37e-06)|all cancers(6;6.36e-05)			GGTGACACTGTACCCATACAC	0.597										HNSCC(55;0.14)																											p.Y317H		.											.	.	.	0			c.T949C						.						126.0	91.0	103.0					17																	47299925		2203	4300	6503	SO:0001583	missense	51225	exon8			ACACTGTACCCAT	AB037886	CCDS11546.1, CCDS45725.1	17q21.3	2011-03-04	2008-09-12		ENSG00000108798	ENSG00000108798			29859	protein-coding gene	gene with protein product		606363				10978530, 11956071	Standard	NM_001135186		Approved	NESH, SSH3BP3	uc002iop.1	Q9P2A4	OTTHUMG00000161306	ENST00000225941.1:c.949T>C	17.37:g.47299925T>C	ENSP00000225941:p.Tyr317His	Somatic	32	0		WXS	Illumina HiSeq	.	24	10	NM_016428	C9IZN8|Q9H0P6	Missense_Mutation	SNP	ENST00000225941.1	37	CCDS11546.1	.	.	.	.	.	.	.	.	.	.	T	16.85	3.235592	0.58886	.	.	ENSG00000108798	ENST00000225941;ENST00000419580	T;T	0.55760	0.5;0.5	5.17	4.07	0.47477	Src homology-3 domain (5);	0.083490	0.49916	N	0.000136	T	0.55529	0.1926	M	0.82193	2.58	0.80722	D	1	B;B	0.27316	0.145;0.175	B;B	0.29524	0.062;0.103	T	0.56829	-0.7914	10	0.72032	D	0.01	-10.8905	9.4854	0.38926	0.0:0.0828:0.0:0.9172	.	311;317	Q9P2A4-2;Q9P2A4	.;ABI3_HUMAN	H	317;311	ENSP00000225941:Y317H;ENSP00000406651:Y311H	ENSP00000225941:Y317H	Y	+	1	0	ABI3	44654924	1.000000	0.71417	1.000000	0.80357	0.924000	0.55760	5.673000	0.68109	0.780000	0.33566	0.379000	0.24179	TAC	.		0.597	ABI3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364475.1	NM_016428	
SLC3A2	6520	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	11	62649510	62649510	+	Missense_Mutation	SNP	C	C	A	rs138578664		TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr11:62649510C>A	ENST00000377890.2	+	5	1041	c.873C>A	c.(871-873)gaC>gaA	p.D291E	SLC3A2_ENST00000338663.7_Missense_Mutation_p.D190E|SLC3A2_ENST00000535296.1_Missense_Mutation_p.D260E|SLC3A2_ENST00000377891.2_Missense_Mutation_p.D292E|SLC3A2_ENST00000377892.1_Missense_Mutation_p.D322E|SLC3A2_ENST00000377889.2_Missense_Mutation_p.D229E|SLC3A2_ENST00000536981.1_5'UTR|SLC3A2_ENST00000538682.1_3'UTR	NM_002394.5	NP_002385.3	P08195	4F2_HUMAN	solute carrier family 3 (amino acid transporter heavy chain), member 2	291					amino acid transport (GO:0006865)|blood coagulation (GO:0007596)|calcium ion transport (GO:0006816)|carbohydrate metabolic process (GO:0005975)|cell growth (GO:0016049)|ion transport (GO:0006811)|leucine import (GO:0060356)|leukocyte migration (GO:0050900)|response to exogenous dsRNA (GO:0043330)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|tryptophan transport (GO:0015827)	cell junction (GO:0030054)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium:sodium antiporter activity (GO:0005432)|catalytic activity (GO:0003824)|cation binding (GO:0043169)|double-stranded RNA binding (GO:0003725)|neutral amino acid transmembrane transporter activity (GO:0015175)|poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(3)|large_intestine(2)|lung(12)|ovary(1)|prostate(1)|skin(2)	22						AAGATTTTGACAGTCTCTTGC	0.473																																					p.D292E		.											.	.	.	0			c.C876A						.						102.0	97.0	98.0					11																	62649510		2201	4298	6499	SO:0001583	missense	6520	exon5			TTTTGACAGTCTC		CCDS8039.2, CCDS31588.1, CCDS31589.1, CCDS31590.1	11q12-q22	2013-07-19	2013-07-19		ENSG00000168003	ENSG00000168003		"""Solute carriers"""	11026	protein-coding gene	gene with protein product	"""antigen identified by monoclonal antibodies 4F2, TRA1.10, TROP4, and T43"", ""antigen defined by monoclonal antibody 4F2"", ""heavy chain"", ""4F2 heavy chain"", ""CD98 heavy chain"", ""monoclonal antibody 44D7"", ""4F2 cell-surface antigen heavy chain"", ""lymphocyte activation antigen 4F2 large subunit"""	158070	"""solute carrier family 3 (activators of dibasic and neutral amino acid transport), member 2"""	MDU1		3036867	Standard	NM_001012662		Approved	4T2HC, 4F2, NACAE, CD98, CD98HC, 4F2HC	uc001nwd.3	P08195	OTTHUMG00000074091	ENST00000377890.2:c.873C>A	11.37:g.62649510C>A	ENSP00000367122:p.Asp291Glu	Somatic	60	0		WXS	Illumina HiSeq	.	44	16	NM_001012662	Q13543	Missense_Mutation	SNP	ENST00000377890.2	37	CCDS8039.2	.	.	.	.	.	.	.	.	.	.	C	8.235	0.805568	0.16467	.	.	ENSG00000168003	ENST00000377892;ENST00000377891;ENST00000377890;ENST00000542007;ENST00000377889;ENST00000535296;ENST00000338663;ENST00000422606	D;D;D;D;D;D	0.98178	-4.77;-4.77;-4.77;-4.77;-4.77;-4.77	5.53	-5.15	0.02866	Glycoside hydrolase, subgroup, catalytic domain (1);Glycosyl hydrolase, family 13, catalytic domain (1);Glycoside hydrolase, superfamily (1);	1.425730	0.03714	N	0.250819	D	0.92087	0.7492	N	0.12527	0.23	0.09310	N	1	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.04013	0.0;0.0;0.001;0.0;0.001	D	0.88735	0.3239	10	0.17369	T	0.5	-2.8851	2.2957	0.04150	0.4408:0.2329:0.1933:0.133	.	229;260;291;190;322	P08195-3;F5GZS6;P08195;P08195-2;P08195-4	.;.;4F2_HUMAN;.;.	E	322;292;291;292;229;260;190;172	ENSP00000367124:D322E;ENSP00000367123:D292E;ENSP00000367122:D291E;ENSP00000367121:D229E;ENSP00000444236:D260E;ENSP00000340815:D190E	ENSP00000340815:D190E	D	+	3	2	SLC3A2	62406086	0.000000	0.05858	0.002000	0.10522	0.904000	0.53231	-1.897000	0.01603	-0.958000	0.03622	-0.169000	0.13324	GAC	.		0.473	SLC3A2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000157306.1	NM_001012661	
OR2L2	26246	hgsc.bcm.edu	37	1	248202347	248202347	+	Missense_Mutation	SNP	C	C	T	rs143360089		TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr1:248202347C>T	ENST00000366479.2	+	1	874	c.778C>T	c.(778-780)Cgt>Tgt	p.R260C	OR2L13_ENST00000366478.2_Intron	NM_001004686.2	NP_001004686.1	Q8NH16	OR2L2_HUMAN	olfactory receptor, family 2, subfamily L, member 2	260						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(28)|ovary(1)|skin(4)|urinary_tract(1)	42	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0278)			TACCTATGTACGTCCAAGATC	0.493													c|||	1	0.000199681	0.0	0.0	5008	,	,		20656	0.0		0.0	False		,,,				2504	0.001				p.R260C		.											OR2L2,right_upper_lobe,carcinoma,0,2	OR2L2	0	0			c.C778T						.	C	CYS/ARG,	1,4405		0,1,2202	152.0	137.0	142.0		778,	-3.0	0.0	1	dbSNP_134	142	2,8598		0,2,4298	no	missense,intron	OR2L2,OR2L13	NM_001004686.2,NM_175911.2	180,	0,3,6500	TT,TC,CC		0.0233,0.0227,0.0231	benign,	260/313,	248202347	3,13003	2203	4300	6503	SO:0001583	missense	26246	exon1			TATGTACGTCCAA	X64978	CCDS31103.1	1q44	2012-08-09			ENSG00000203663	ENSG00000203663		"""GPCR / Class A : Olfactory receptors"""	8266	protein-coding gene	gene with protein product				OR2L4P, OR2L12		1370859	Standard	NM_001004686		Approved	HTPCRH07, HSHTPCRH07	uc001idw.3	Q8NH16	OTTHUMG00000040214	ENST00000366479.2:c.778C>T	1.37:g.248202347C>T	ENSP00000355435:p.Arg260Cys	Somatic	76	0		WXS	Illumina HiSeq	.	71	3	NM_001004686	Q2M3T5	Missense_Mutation	SNP	ENST00000366479.2	37	CCDS31103.1	.	.	.	.	.	.	.	.	.	.	.	7.215	0.596219	0.13875	2.27E-4	2.33E-4	ENSG00000203663	ENST00000366479	T	0.35789	1.29	1.9	-3.02	0.05446	GPCR, rhodopsin-like superfamily (1);	1.359230	0.05838	N	0.618748	T	0.23492	0.0568	.	.	.	0.09310	N	1	B	0.22276	0.067	B	0.24269	0.052	T	0.32214	-0.9915	9	0.51188	T	0.08	.	3.5316	0.07778	0.2785:0.466:0.0:0.2555	.	260	Q8NH16	OR2L2_HUMAN	C	260	ENSP00000355435:R260C	ENSP00000355435:R260C	R	+	1	0	OR2L2	246268970	0.000000	0.05858	0.001000	0.08648	0.131000	0.20780	-0.744000	0.04839	-0.417000	0.07461	0.194000	0.17425	CGT	0.000		0.493	OR2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096871.1	NM_001004686	
CTC1	80169	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	17	8140773	8140773	+	Nonsense_Mutation	SNP	T	T	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr17:8140773T>A	ENST00000315684.8	-	5	719	c.712A>T	c.(712-714)Aaa>Taa	p.K238*	CTC1_ENST00000581671.1_5'UTR	NM_025099.5	NP_079375.3	Q2NKJ3	CTC1_HUMAN	CTS telomere maintenance complex component 1	238					bone marrow development (GO:0048539)|cellular response to DNA damage stimulus (GO:0006974)|hematopoietic stem cell proliferation (GO:0071425)|multicellular organism growth (GO:0035264)|positive regulation of DNA replication (GO:0045740)|positive regulation of fibroblast proliferation (GO:0048146)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|replicative senescence (GO:0090399)|spleen development (GO:0048536)|telomere maintenance (GO:0000723)|telomere maintenance via telomere lengthening (GO:0010833)|thymus development (GO:0048538)	nuclear chromosome, telomeric region (GO:0000784)|nucleus (GO:0005634)|Stn1-Ten1 complex (GO:0070188)	single-stranded DNA binding (GO:0003697)			NS(1)|endometrium(6)|kidney(3)|large_intestine(6)|lung(8)|ovary(1)|skin(4)	29						TGTTTACTTTTCACCAGAGCA	0.493																																					p.K238X		.											.	.	.	0			c.A712T						.						112.0	113.0	113.0					17																	8140773		2028	4173	6201	SO:0001587	stop_gained	80169	exon5			TACTTTTCACCAG	AL831955	CCDS42259.1	17p13.1	2011-02-21	2011-02-21	2011-02-21	ENSG00000178971	ENSG00000178971			26169	protein-coding gene	gene with protein product	"""conserved telomere maintenance component 1"", ""alpha accessory factor 132"", ""conserved telomere capping protein 1"""	613129	"""tmp494178"", ""chromosome 17 open reading frame 68"""	C17orf68		19854130, 19854131	Standard	NM_025099		Approved	FLJ22170, AAF132	uc002gkq.4	Q2NKJ3		ENST00000315684.8:c.712A>T	17.37:g.8140773T>A	ENSP00000313759:p.Lys238*	Somatic	66	0		WXS	Illumina HiSeq	.	29	13	NM_025099	B3KR66|C9JEX5|Q1PCD1|Q2TBE3|Q8N3S6|Q9H6L0	Nonsense_Mutation	SNP	ENST00000315684.8	37	CCDS42259.1	.	.	.	.	.	.	.	.	.	.	T	16.26	3.073233	0.55646	.	.	ENSG00000178971	ENST00000315684	.	.	.	4.82	3.72	0.42706	.	1.029370	0.07662	N	0.933959	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	0.0173	7.5885	0.28006	0.0:0.0979:0.0:0.9021	.	.	.	.	X	238	.	ENSP00000313759:K238X	K	-	1	0	CTC1	8081498	0.018000	0.18449	0.596000	0.28811	0.472000	0.32918	0.839000	0.27586	0.930000	0.37217	0.329000	0.21502	AAA	.		0.493	CTC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000442012.1	NM_025099	
CTTNBP2NL	55917	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	1	112999663	112999663	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr1:112999663G>T	ENST00000271277.6	+	6	1774	c.1549G>T	c.(1549-1551)Ggg>Tgg	p.G517W	CTTNBP2NL_ENST00000607039.1_3'UTR	NM_018704.2	NP_061174.1	Q9P2B4	CT2NL_HUMAN	CTTNBP2 N-terminal like	517					negative regulation of transmembrane transport (GO:0034763)|negative regulation of transporter activity (GO:0032410)|protein dephosphorylation (GO:0006470)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)	protein phosphatase 2A binding (GO:0051721)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(5)|lung(13)|ovary(1)|prostate(1)|stomach(1)|urinary_tract(1)	29		all_cancers(81;0.00064)|all_epithelial(167;0.000415)|all_lung(203;0.00045)|Lung NSC(69;0.000705)		Lung(183;0.0234)|all cancers(265;0.0246)|Epithelial(280;0.0342)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		TAGCCAACAAGGGCCAATCAA	0.532																																					p.G517W		.											.	.	.	0			c.G1549T						.						106.0	98.0	101.0					1																	112999663		2203	4300	6503	SO:0001583	missense	55917	exon6			CAACAAGGGCCAA	AB037854	CCDS845.1	1p13.2	2008-02-05			ENSG00000143079	ENSG00000143079			25330	protein-coding gene	gene with protein product		615100				10718198	Standard	NM_018704		Approved	DKFZp547A023	uc001ebx.3	Q9P2B4	OTTHUMG00000011154	ENST00000271277.6:c.1549G>T	1.37:g.112999663G>T	ENSP00000271277:p.Gly517Trp	Somatic	46	0		WXS	Illumina HiSeq	.	9	6	NM_018704	B3KMS5|Q96B40	Missense_Mutation	SNP	ENST00000271277.6	37	CCDS845.1	.	.	.	.	.	.	.	.	.	.	G	15.73	2.919392	0.52653	.	.	ENSG00000143079	ENST00000271277	T	0.26957	1.7	5.35	5.35	0.76521	.	0.163747	0.53938	D	0.000047	T	0.29190	0.0726	L	0.47716	1.5	0.45580	D	0.998529	D	0.62365	0.991	P	0.60415	0.874	T	0.02950	-1.1090	10	0.72032	D	0.01	-23.8138	12.0776	0.53653	0.0799:0.0:0.9201:0.0	.	517	Q9P2B4	CT2NL_HUMAN	W	517	ENSP00000271277:G517W	ENSP00000271277:G517W	G	+	1	0	CTTNBP2NL	112801186	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	3.021000	0.49651	2.502000	0.84385	0.462000	0.41574	GGG	.		0.532	CTTNBP2NL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030686.1	NM_018704	
MAGEH1	28986	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	X	55479371	55479371	+	Silent	SNP	T	T	G	rs267606487		TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chrX:55479371T>G	ENST00000342972.1	+	1	834	c.564T>G	c.(562-564)tcT>tcG	p.S188S	hsa-mir-4536-2_ENST00000583537.1_RNA	NM_014061.3	NP_054780.2	Q9H213	MAGH1_HUMAN	melanoma antigen family H, 1	188	MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.				apoptotic process (GO:0006915)	cytoplasm (GO:0005737)				central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(6)|ovary(1)|skin(2)	15						ACCGATGCTCTAAAGACTGGC	0.507																																					p.S188S		.											.	.	.	0			c.T564G						.						103.0	97.0	99.0					X																	55479371		2203	4300	6503	SO:0001819	synonymous_variant	28986	exon1			ATGCTCTAAAGAC	AF320912	CCDS14369.1	Xp11.22	2008-02-05			ENSG00000187601	ENSG00000187601			24092	protein-coding gene	gene with protein product		300548				12414813, 9485030	Standard	NM_014061		Approved	APR1	uc004dum.3	Q9H213	OTTHUMG00000021655	ENST00000342972.1:c.564T>G	X.37:g.55479371T>G		Somatic	30	0		WXS	Illumina HiSeq	.	15	14	NM_014061	B2R8V9|Q5JRJ3|Q9Y5M2	Silent	SNP	ENST00000342972.1	37	CCDS14369.1																																																																																			.		0.507	MAGEH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056868.1	NM_014061	
TTC39C	125488	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	18	21694602	21694602	+	Missense_Mutation	SNP	T	T	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr18:21694602T>A	ENST00000317571.3	+	7	1305	c.1069T>A	c.(1069-1071)Tat>Aat	p.Y357N	RP11-799B12.2_ENST00000583782.1_RNA|TTC39C_ENST00000304621.6_Missense_Mutation_p.Y296N|TTC39C_ENST00000540918.2_Missense_Mutation_p.Y50N	NM_001135993.1	NP_001129465.1	Q8N584	TT39C_HUMAN	tetratricopeptide repeat domain 39C	357										breast(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|skin(1)	19						TGTCTGTCTGTATGAAATTGG	0.378																																					p.Y357N		.											.	.	.	0			c.T1069A						.						156.0	138.0	144.0					18																	21694602		2203	4300	6503	SO:0001583	missense	125488	exon7			TGTCTGTATGAAA	AK091080	CCDS32804.1, CCDS45839.1, CCDS58616.1	18q11.2	2014-02-07	2008-06-23	2008-06-23	ENSG00000168234	ENSG00000168234		"""Tetratricopeptide (TTC) repeat domain containing"""	26595	protein-coding gene	gene with protein product			"""chromosome 18 open reading frame 17"""	C18orf17		14702039	Standard	NM_153211		Approved	FLJ33761, HsT2697	uc002kuw.3	Q8N584	OTTHUMG00000179403	ENST00000317571.3:c.1069T>A	18.37:g.21694602T>A	ENSP00000323645:p.Tyr357Asn	Somatic	59	0		WXS	Illumina HiSeq	.	37	16	NM_001135993	B7WP63|J3QRR1|Q0VAJ2|Q8N284	Missense_Mutation	SNP	ENST00000317571.3	37	CCDS45839.1	.	.	.	.	.	.	.	.	.	.	T	22.6	4.308134	0.81247	.	.	ENSG00000168234	ENST00000304621;ENST00000317571;ENST00000540918	T;T;T	0.49432	0.78;0.78;0.78	5.17	5.17	0.71159	Tetratricopeptide-like helical (1);	0.000000	0.85682	D	0.000000	T	0.67011	0.2848	M	0.72894	2.215	0.80722	D	1	D	0.89917	1.0	D	0.79784	0.993	T	0.70396	-0.4883	10	0.62326	D	0.03	-10.2203	14.2711	0.66152	0.0:0.0:0.0:1.0	.	357	Q8N584	TT39C_HUMAN	N	296;357;50	ENSP00000306598:Y296N;ENSP00000323645:Y357N;ENSP00000443016:Y50N	ENSP00000306598:Y296N	Y	+	1	0	TTC39C	19948600	1.000000	0.71417	0.997000	0.53966	0.956000	0.61745	7.368000	0.79567	2.086000	0.62901	0.533000	0.62120	TAT	.		0.378	TTC39C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446107.1	NM_153211	
RFWD3	55159	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	16	74670304	74670304	+	Missense_Mutation	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr16:74670304A>C	ENST00000361070.4	-	8	1463	c.1366T>G	c.(1366-1368)Tgt>Ggt	p.C456G	RFWD3_ENST00000571750.1_Missense_Mutation_p.C456G	NM_018124.3	NP_060594.3	Q6PCD5	RFWD3_HUMAN	ring finger and WD repeat domain 3	456					DNA repair (GO:0006281)|mitotic G1 DNA damage checkpoint (GO:0031571)|protein ubiquitination (GO:0016567)|regulation of DNA damage checkpoint (GO:2000001)|response to ionizing radiation (GO:0010212)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|MDM2/MDM4 family protein binding (GO:0097371)|p53 binding (GO:0002039)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(12)|ovary(1)|skin(2)|stomach(1)|urinary_tract(1)	26						AGAGCATCACAGTATGCCATG	0.502																																					p.C456G		.											.	.	.	0			c.T1366G						.						144.0	135.0	138.0					16																	74670304		2198	4300	6498	SO:0001583	missense	55159	exon8			CATCACAGTATGC	AK001382	CCDS32486.1	16q22.3	2013-01-09						"""WD repeat domain containing"", ""RING-type (C3HC4) zinc fingers"""	25539	protein-coding gene	gene with protein product		614151				21504906	Standard	XM_005256021		Approved	FLJ10520, RNF201	uc002fda.3	Q6PCD5		ENST00000361070.4:c.1366T>G	16.37:g.74670304A>C	ENSP00000354361:p.Cys456Gly	Somatic	52	0		WXS	Illumina HiSeq	.	37	19	NM_018124	A8K585|B2RE35|D3DUJ8|Q5XKR3|Q9H9Q3|Q9NVT4	Missense_Mutation	SNP	ENST00000361070.4	37	CCDS32486.1	.	.	.	.	.	.	.	.	.	.	A	13.16	2.154791	0.38021	.	.	ENSG00000168411	ENST00000361070	T	0.18810	2.19	5.61	5.61	0.85477	WD40/YVTN repeat-like-containing domain (1);	0.044156	0.85682	D	0.000000	T	0.27967	0.0689	M	0.81682	2.555	0.80722	D	1	B	0.14012	0.009	B	0.16289	0.015	T	0.15809	-1.0424	10	0.12430	T	0.62	-7.473	15.794	0.78394	1.0:0.0:0.0:0.0	.	456	Q6PCD5	RFWD3_HUMAN	G	456	ENSP00000354361:C456G	ENSP00000354361:C456G	C	-	1	0	RFWD3	73227805	1.000000	0.71417	0.437000	0.26809	0.914000	0.54420	5.876000	0.69667	2.126000	0.65437	0.533000	0.62120	TGT	.		0.502	RFWD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436506.2	NM_018124	
COPA	1314	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	160263008	160263008	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr1:160263008G>T	ENST00000241704.7	-	27	3000	c.2771C>A	c.(2770-2772)tCt>tAt	p.S924Y	COPA_ENST00000368069.3_Missense_Mutation_p.S933Y	NM_001098398.1|NM_004371.3	NP_001091868.1|NP_004362.2	P53621	COPA_HUMAN	coatomer protein complex, subunit alpha	924					COPI coating of Golgi vesicle (GO:0048205)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|pancreatic juice secretion (GO:0030157)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	COPI vesicle coat (GO:0030126)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(5)|kidney(5)|large_intestine(2)|lung(25)|ovary(1)|prostate(3)|skin(1)|stomach(1)|urinary_tract(2)	46	all_cancers(52;8.15e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			TGGAAGCTGAGAGTTATTACA	0.453																																					p.S933Y		.											.	.	.	0			c.C2798A						.						83.0	86.0	85.0					1																	160263008		2203	4300	6503	SO:0001583	missense	1314	exon27			AGCTGAGAGTTAT	U24105	CCDS1202.1, CCDS41424.1	1q23.2	2014-01-30			ENSG00000122218	ENSG00000122218		"""WD repeat domain containing"", ""Endogenous ligands"""	2230	protein-coding gene	gene with protein product	"""proxenin"", ""xenin"""	601924				8647451	Standard	NM_004371		Approved	HEP-COP	uc001fvv.4	P53621	OTTHUMG00000033111	ENST00000241704.7:c.2771C>A	1.37:g.160263008G>T	ENSP00000241704:p.Ser924Tyr	Somatic	89	0		WXS	Illumina HiSeq	.	103	66	NM_001098398	Q5T201|Q8IXZ9	Missense_Mutation	SNP	ENST00000241704.7	37	CCDS1202.1	.	.	.	.	.	.	.	.	.	.	G	26.5	4.746442	0.89663	.	.	ENSG00000122218	ENST00000368069;ENST00000241704	T;T	0.60040	0.22;0.22	5.34	5.34	0.76211	Coatomer, alpha subunit, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.76449	0.3989	M	0.85630	2.765	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	T	0.78792	-0.2065	10	0.87932	D	0	-19.5953	18.1326	0.89606	0.0:0.0:1.0:0.0	.	924;933	P53621;P53621-2	COPA_HUMAN;.	Y	933;924	ENSP00000357048:S933Y;ENSP00000241704:S924Y	ENSP00000241704:S924Y	S	-	2	0	COPA	158529632	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.964000	0.93389	2.937000	0.99478	0.650000	0.86243	TCT	.		0.453	COPA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080638.1	NM_004371	
RAPSN	5913	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	11	47464331	47464331	+	Silent	SNP	C	C	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr11:47464331C>G	ENST00000298854.2	-	3	780	c.567G>C	c.(565-567)gcG>gcC	p.A189A	RAPSN_ENST00000529341.1_Silent_p.A189A|RAPSN_ENST00000352508.3_Silent_p.A189A|RAPSN_ENST00000524487.1_Intron|RNU6-1302P_ENST00000516518.1_RNA|RAPSN_ENST00000528356.1_5'Flank	NM_005055.4	NP_005046.2	Q13702	RAPSN_HUMAN	receptor-associated protein of the synapse	189			A -> V (in FADS). {ECO:0000269|PubMed:18252226}.		positive regulation of neuron apoptotic process (GO:0043525)|synaptic transmission (GO:0007268)|synaptic transmission, cholinergic (GO:0007271)	cell junction (GO:0030054)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|neuromuscular junction (GO:0031594)|postsynaptic membrane (GO:0045211)	acetylcholine receptor binding (GO:0033130)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(3)|lung(6)|ovary(2)	12						CAAGCTCTGCCGCCTTGCAGG	0.607																																					p.A189A		.											.	.	.	0			c.G567C						.						87.0	81.0	83.0					11																	47464331		2201	4298	6499	SO:0001819	synonymous_variant	5913	exon3			CTCTGCCGCCTTG		CCDS7936.1, CCDS7937.1	11p11.2	2009-04-28	2007-02-23		ENSG00000165917	ENSG00000165917		"""RING-type (C3HC4) zinc fingers"""	9863	protein-coding gene	gene with protein product	"""rapsyn"""	601592	"""receptor-associated protein of the synapse, 43kD"""			8812503	Standard	NM_005055		Approved	RNF205, CMS1D, CMS1E	uc001nfi.2	Q13702	OTTHUMG00000166891	ENST00000298854.2:c.567G>C	11.37:g.47464331C>G		Somatic	47	0		WXS	Illumina HiSeq	.	25	12	NM_032645	Q8TDF3|Q9BTD9	Silent	SNP	ENST00000298854.2	37	CCDS7936.1																																																																																			.		0.607	RAPSN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391726.1		
RARRES3	5920	hgsc.bcm.edu	37	11	63304427	63304427	+	Intron	SNP	T	T	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr11:63304427T>C	ENST00000255688.3	+	1	57				RARRES3_ENST00000439013.2_Intron|RARRES3_ENST00000354445.2_5'Flank|RARRES3_ENST00000537871.1_Intron	NM_004585.3	NP_004576.2	Q9UL19	HRSL4_HUMAN	retinoic acid receptor responder (tazarotene induced) 3						lipid catabolic process (GO:0016042)|negative regulation of cell proliferation (GO:0008285)|phospholipid metabolic process (GO:0006644)	integral component of membrane (GO:0016021)	phospholipase A2 activity (GO:0004623)			kidney(1)|large_intestine(1)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)	6						CAGTCCAGGCTCCTGGCCTTG	0.532																																					.		.											.	.	.	0			.						.						54.0	50.0	51.0					11																	63304427		692	1591	2283	SO:0001627	intron_variant	100500917	.			CCAGGCTCCTGGC		CCDS41662.1	11q23	2008-05-02			ENSG00000133321	ENSG00000133321			9869	protein-coding gene	gene with protein product		605092				9270552	Standard	NM_004585		Approved	TIG3, HRASLS4	uc001nxf.4	Q9UL19	OTTHUMG00000167850	ENST00000255688.3:c.9+78T>C	11.37:g.63304427T>C		Somatic	50	0		WXS	Illumina HiSeq	.	29	15	.	B2R599|B4DDW2|E7ENZ7|O95200	RNA	SNP	ENST00000255688.3	37	CCDS41662.1																																																																																			.		0.532	RARRES3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396629.1		
PCDHGB1	56104	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	5	140730180	140730180	+	Missense_Mutation	SNP	T	T	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr5:140730180T>C	ENST00000523390.1	+	1	353	c.353T>C	c.(352-354)gTt>gCt	p.V118A	PCDHGA1_ENST00000517417.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA3_ENST00000253812.6_Intron	NM_018922.2|NM_032095.1	NP_061745.1|NP_115266.1	Q9Y5G3	PCDGD_HUMAN	protocadherin gamma subfamily B, 1	118	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(6)|lung(3)|ovary(2)|prostate(1)	16			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CACGTGGTTGTTGTAATCCAA	0.423																																					p.V118A		.											.	.	.	0			c.T353C						.						65.0	65.0	65.0					5																	140730180		1879	4112	5991	SO:0001583	missense	56104	exon1			TGGTTGTTGTAAT	AF152517	CCDS54923.1, CCDS75330.1	5q31	2010-01-26				ENSG00000254221		"""Cadherins / Protocadherins : Clustered"""	8708	other	protocadherin	"""protocadherin gamma subfamily B, 1, isoform 2"""	606299				10380929	Standard	NM_018922		Approved	PCDH-GAMMA-B1		Q9Y5G3		ENST00000523390.1:c.353T>C	5.37:g.140730180T>C	ENSP00000429273:p.Val118Ala	Somatic	63	0		WXS	Illumina HiSeq	.	61	16	NM_018922	Q3SY75|Q9Y5C8	Missense_Mutation	SNP	ENST00000523390.1	37	CCDS54923.1	.	.	.	.	.	.	.	.	.	.	.	21.9	4.215012	0.79352	.	.	ENSG00000254221	ENST00000523390	T	0.59364	0.27	5.46	5.46	0.80206	Cadherin (3);Cadherin conserved site (1);Cadherin-like (1);	.	.	.	.	D	0.85487	0.5708	H	0.98866	4.355	0.33189	D	0.550622	D;D	0.64830	0.994;0.989	D;P	0.70935	0.971;0.887	D	0.93494	0.6838	9	0.87932	D	0	.	15.4972	0.75662	0.0:0.0:0.0:1.0	.	118;118	Q9Y5G3-2;Q9Y5G3	.;PCDGD_HUMAN	A	118	ENSP00000429273:V118A	ENSP00000429273:V118A	V	+	2	0	PCDHGB1	140710364	1.000000	0.71417	0.064000	0.19789	0.816000	0.46133	7.558000	0.82253	2.197000	0.70478	0.460000	0.39030	GTT	.		0.423	PCDHGB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374740.1	NM_018922	
DNAJC14	85406	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	12	56215774	56215774	+	Missense_Mutation	SNP	G	G	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr12:56215774G>A	ENST00000357606.3	-	8	2385	c.2096C>T	c.(2095-2097)cCc>cTc	p.P699L	DNAJC14_ENST00000317269.3_Missense_Mutation_p.P699L|DNAJC14_ENST00000317287.5_Missense_Mutation_p.P699L|RP11-762I7.5_ENST00000546837.1_Intron|RP11-762I7.5_ENST00000552719.1_Intron			Q6Y2X3	DJC14_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 14	699					protein transport (GO:0015031)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				breast(2)|kidney(1)|large_intestine(8)|lung(7)|ovary(3)|prostate(1)|skin(1)	23						ACGTTGGAAGGGCCTCCTCAC	0.557																																					p.P699L		.											.	.	.	0			c.C2096T						.						149.0	138.0	142.0					12																	56215774		2203	4300	6503	SO:0001583	missense	85406	exon7			TGGAAGGGCCTCC	AF141342	CCDS8894.1	12q12	2011-09-02				ENSG00000135392		"""Heat shock proteins / DNAJ (HSP40)"""	24581	protein-coding gene	gene with protein product		606092				11331877, 11984006	Standard	NM_032364		Approved	DNAJ, DRIP78, HDJ3, LIP6, FLJ32792	uc001shu.2	Q6Y2X3		ENST00000357606.3:c.2096C>T	12.37:g.56215774G>A	ENSP00000350223:p.Pro699Leu	Somatic	47	0		WXS	Illumina HiSeq	.	38	18	NM_032364	A5YM67|Q17RY2|Q66K17|Q96N59|Q96T63	Missense_Mutation	SNP	ENST00000357606.3	37	CCDS8894.1	.	.	.	.	.	.	.	.	.	.	G	18.93	3.726787	0.69074	.	.	ENSG00000135392	ENST00000357606;ENST00000317269;ENST00000537962;ENST00000317287	T;T;T	0.66099	-0.19;-0.19;-0.19	5.63	5.63	0.86233	.	0.000000	0.85682	D	0.000000	T	0.69450	0.3112	N	0.24115	0.695	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.72683	-0.4219	10	0.87932	D	0	-11.261	17.551	0.87875	0.0:0.0:1.0:0.0	.	699	Q6Y2X3	DJC14_HUMAN	L	699;699;409;699	ENSP00000350223:P699L;ENSP00000316240:P699L;ENSP00000317500:P699L	ENSP00000316240:P699L	P	-	2	0	DNAJC14	54502041	1.000000	0.71417	1.000000	0.80357	0.559000	0.35586	7.707000	0.84623	2.830000	0.97506	0.585000	0.79938	CCC	.		0.557	DNAJC14-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409095.1	NM_032364	
ZNF821	55565	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	16	71901864	71901864	+	Silent	SNP	G	G	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr16:71901864G>A	ENST00000565601.1	-	3	524	c.117C>T	c.(115-117)ggC>ggT	p.G39G	ZNF821_ENST00000446827.2_Intron|ZNF821_ENST00000425432.1_Silent_p.G39G|ATXN1L_ENST00000569119.1_Intron|ZNF821_ENST00000313565.6_Intron|ZNF821_ENST00000564943.1_5'UTR|ZNF821_ENST00000564134.1_Silent_p.G39G	NM_001201553.1	NP_001188482.1	O75541	ZN821_HUMAN	zinc finger protein 821	39					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|kidney(1)|large_intestine(5)|lung(4)|ovary(2)	13						GTCGCTGACTGCCAAGGTCTC	0.478																																					p.G39G		.											.	.	.	0			c.C117T						.																																			SO:0001819	synonymous_variant	55565	exon4			CTGACTGCCAAGG	AF070588	CCDS32481.1, CCDS56006.1, CCDS73911.1	16q22.3	2008-05-02				ENSG00000102984		"""Zinc fingers, C2H2-type"""	28043	protein-coding gene	gene with protein product						8619474, 9110174	Standard	NM_017530		Approved		uc021tlb.1	O75541		ENST00000565601.1:c.117C>T	16.37:g.71901864G>A		Somatic	36	0		WXS	Illumina HiSeq	.	20	5	NM_001201556	A6NK48|B4DKK4|D3DWS3	Silent	SNP	ENST00000565601.1	37	CCDS56006.1																																																																																			.		0.478	ZNF821-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434180.1	NM_017530	
ZNF850	342892	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	19	37241073	37241073	+	Missense_Mutation	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr19:37241073A>C	ENST00000591344.1	-	5	1027	c.869T>G	c.(868-870)tTt>tGt	p.F290C	ZNF850_ENST00000589390.1_Intron	NM_001193552.1|NM_001267779.1	NP_001180481.1|NP_001254708.1	A8MQ14	ZN850_HUMAN	zinc finger protein 850	290					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)										GCCAGAAGTAAAAGATTTCCC	0.383																																					p.F290C		.											.	.	.	0			c.T869G						.																																			SO:0001583	missense	342892	exon5			GAAGTAAAAGATT	BC052603	CCDS59379.1, CCDS74350.1	19q13.12	2013-01-08	2010-08-02	2010-08-02		ENSG00000267041		"""Zinc fingers, C2H2-type"", ""-"""	27994	protein-coding gene	gene with protein product			"""zinc finger protein 850 pseudogene"", ""zinc finger protein 850 (pseudogene)"""	ZNF850P		12477932	Standard	NM_001193552		Approved		uc010efc.3	A8MQ14		ENST00000591344.1:c.869T>G	19.37:g.37241073A>C	ENSP00000464976:p.Phe290Cys	Somatic	105	0		WXS	Illumina HiSeq	.	63	22	NM_001193552		Missense_Mutation	SNP	ENST00000591344.1	37	CCDS59379.1																																																																																			.		0.383	ZNF850-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453557.1	XM_001720258	
ZNF354A	6940	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	5	178154001	178154001	+	Splice_Site	SNP	C	C	G	rs539667926		TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr5:178154001C>G	ENST00000335815.2	-	3	356	c.159G>C	c.(157-159)ctG>ctC	p.L53L		NM_005649.2	NP_005640.2	O60765	Z354A_HUMAN	zinc finger protein 354A	53	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|sensory perception of sound (GO:0007605)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|large_intestine(7)|lung(3)|ovary(2)|skin(2)|stomach(2)	19	all_cancers(89;0.000536)|Renal(175;0.000159)|all_epithelial(37;0.000221)|Lung NSC(126;0.00308)|all_lung(126;0.00536)	all_cancers(40;0.0452)|all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.185)		TTTCCTTACCCAGTGAGACCA	0.453																																					p.L53L		.											.	.	.	0			c.G159C						.						95.0	97.0	96.0					5																	178154001		2203	4300	6503	SO:0001630	splice_region_variant	6940	exon3			CTTACCCAGTGAG	AF116030	CCDS4438.1	5q35.3	2013-01-08		2001-11-23	ENSG00000169131	ENSG00000169131		"""Zinc fingers, C2H2-type"", ""-"""	11628	protein-coding gene	gene with protein product		602444		TCF17		9465904	Standard	NM_005649		Approved	KID-1, EZNF, HKL1, KID1	uc003mjj.3	O60765	OTTHUMG00000130895	ENST00000335815.2:c.160+1G>C	5.37:g.178154001C>G		Somatic	138	0		WXS	Illumina HiSeq	.	97	56	NM_005649	Q9UNJ8	Silent	SNP	ENST00000335815.2	37	CCDS4438.1																																																																																			.		0.453	ZNF354A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253481.1	NM_005649	Silent
EIF4E2	9470	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	2	233422641	233422641	+	Silent	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr2:233422641T>G	ENST00000258416.3	+	3	856	c.183T>G	c.(181-183)acT>acG	p.T61T	EIF4E2_ENST00000409394.1_Intron|EIF4E2_ENST00000409514.1_Silent_p.T61T|EIF4E2_ENST00000409322.1_Intron|EIF4E2_ENST00000409495.1_Silent_p.T61T|EIF4E2_ENST00000409098.1_Silent_p.T61T|EIF4E2_ENST00000409167.3_Intron	NM_004846.2	NP_004837.1	O60573	IF4E2_HUMAN	eukaryotic translation initiation factor 4E family member 2	61					cytokine-mediated signaling pathway (GO:0019221)|in utero embryonic development (GO:0001701)|negative regulation of translation (GO:0017148)	cytosol (GO:0005829)|mRNA cap binding complex (GO:0005845)	poly(A) RNA binding (GO:0044822)|RNA cap binding (GO:0000339)|translation factor activity, nucleic acid binding (GO:0008135)|translation initiation factor activity (GO:0003743)|ubiquitin protein ligase binding (GO:0031625)			endometrium(2)|kidney(1)|large_intestine(2)|lung(3)	8		all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0449)|Lung NSC(271;0.132)		Epithelial(121;2.3e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000912)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.00942)		ACAACTACACTTTTTGGTACT	0.522																																					p.T61T		.											.	.	.	0			c.T183G						.						113.0	110.0	111.0					2																	233422641		2203	4300	6503	SO:0001819	synonymous_variant	9470	exon3			CTACACTTTTTGG	AF038957	CCDS2496.1, CCDS63158.1, CCDS63159.1, CCDS74671.1	2q37.1	2008-02-05	2006-11-13	2004-10-30	ENSG00000135930	ENSG00000135930			3293	protein-coding gene	gene with protein product		605895	"""eukaryotic translation initiation factor 4E-like 3"""	EIF4EL3		9653160, 9582349	Standard	XM_005246975		Approved	IF4e, 4EHP	uc002vta.3	O60573	OTTHUMG00000133256	ENST00000258416.3:c.183T>G	2.37:g.233422641T>G		Somatic	60	0		WXS	Illumina HiSeq	.	34	15	NM_004846	B8ZZJ9|O75349	Silent	SNP	ENST00000258416.3	37	CCDS2496.1																																																																																			.		0.522	EIF4E2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257033.2	NM_004846	
PDZD2	23037	hgsc.bcm.edu	37	5	31983419	31983419	+	Missense_Mutation	SNP	A	A	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr5:31983419A>G	ENST00000438447.1	+	3	1023	c.635A>G	c.(634-636)aAg>aGg	p.K212R	PDZD2_ENST00000282493.3_Missense_Mutation_p.K212R			O15018	PDZD2_HUMAN	PDZ domain containing 2	212					cell adhesion (GO:0007155)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|nucleus (GO:0005634)				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						ACTGCGAAAAAGGGGAAACGA	0.532																																					p.K212R		.											.	.	.	0			c.A635G						.						92.0	90.0	90.0					5																	31983419		2203	4300	6503	SO:0001583	missense	23037	exon2			CGAAAAAGGGGAA	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.635A>G	5.37:g.31983419A>G	ENSP00000402033:p.Lys212Arg	Somatic	82	0		WXS	Illumina HiSeq	.	100	4	NM_178140	Q9BXD4	Missense_Mutation	SNP	ENST00000438447.1	37	CCDS34137.1	.	.	.	.	.	.	.	.	.	.	A	16.78	3.218375	0.58560	.	.	ENSG00000133401	ENST00000438447;ENST00000382161;ENST00000282493	T;T	0.65549	-0.16;-0.16	5.23	5.23	0.72850	.	0.000000	0.51477	D	0.000092	T	0.63965	0.2556	L	0.27053	0.805	0.35131	D	0.767995	D;D	0.67145	0.979;0.996	P;P	0.60609	0.628;0.877	T	0.71527	-0.4566	10	0.39692	T	0.17	.	13.1224	0.59334	1.0:0.0:0.0:0.0	.	38;212	B4E3P2;O15018	.;PDZD2_HUMAN	R	212	ENSP00000402033:K212R;ENSP00000282493:K212R	ENSP00000282493:K212R	K	+	2	0	PDZD2	32019176	1.000000	0.71417	0.777000	0.31699	0.130000	0.20726	7.898000	0.87363	2.198000	0.70561	0.528000	0.53228	AAG	.		0.532	PDZD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366608.1		
IGF2BP2	10644	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	3	185542734	185542734	+	Silent	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr3:185542734A>C	ENST00000382199.2	-	1	110	c.15T>G	c.(13-15)ctT>ctG	p.L5L	IGF2BP2_ENST00000457616.2_Silent_p.L5L|IGF2BP2_ENST00000346192.3_Silent_p.L5L	NM_006548.4	NP_006539.3	Q9Y6M1	IF2B2_HUMAN	insulin-like growth factor 2 mRNA binding protein 2	5	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				anatomical structure morphogenesis (GO:0009653)|gene expression (GO:0010467)|mRNA transport (GO:0051028)|negative regulation of translation (GO:0017148)|regulation of cytokine biosynthetic process (GO:0042035)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|nucleus (GO:0005634)	mRNA 3'-UTR binding (GO:0003730)|mRNA 5'-UTR binding (GO:0048027)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|translation regulator activity (GO:0045182)			breast(3)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(7)|prostate(1)|skin(3)	20	all_cancers(143;5.84e-11)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(80;7.41e-21)			TCCCGATGTAAAGCTTGTTCA	0.692																																					p.L5L		.											.	.	.	0			c.T15G						.						24.0	26.0	25.0					3																	185542734		2202	4300	6502	SO:0001819	synonymous_variant	10644	exon1			GATGTAAAGCTTG	BC021290	CCDS3273.2, CCDS33903.1	3q27.2	2013-02-12			ENSG00000073792	ENSG00000073792		"""RNA binding motif (RRM) containing"""	28867	protein-coding gene	gene with protein product	"""IGF II mRNA binding protein 2"""	608289				10190901, 9891060	Standard	NM_001007225		Approved	IMP-2	uc003fpo.3	Q9Y6M1	OTTHUMG00000074025	ENST00000382199.2:c.15T>G	3.37:g.185542734A>C		Somatic	136	0		WXS	Illumina HiSeq	.	112	31	NM_001007225	A0A4Z0|B3FTN2|B3FTN3|B3FTN4	Silent	SNP	ENST00000382199.2	37	CCDS3273.2																																																																																			.		0.692	IGF2BP2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000157087.2	NM_006548	
NUTM2B-AS1	101060691	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	10	81444371	81444371	+	RNA	SNP	C	C	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr10:81444371C>A	ENST00000600376.1	-	0	54				RP11-119F19.2_ENST00000596088.1_RNA																							AATTGGAGATCCCCAGCCCAA	0.562																																					.		.											.	.	.	0			.						.																																					650623	.			GGAGATCCCCAGC																													10.37:g.81444371C>A		Somatic	38	0		WXS	Illumina HiSeq	.	33	14	.		RNA	SNP	ENST00000600376.1	37																																																																																				.		0.562	RP11-119F19.2-004	KNOWN	basic	antisense	antisense	OTTHUMT00000461766.1		
CCBE1	147372	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	18	57106936	57106936	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr18:57106936G>T	ENST00000439986.4	-	8	925	c.888C>A	c.(886-888)caC>caA	p.H296Q	CCBE1_ENST00000398179.2_Intron	NM_133459.3	NP_597716.1	Q6UXH8	CCBE1_HUMAN	collagen and calcium binding EGF domains 1	296					lymphangiogenesis (GO:0001946)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of lymphangiogenesis (GO:1901492)|positive regulation of protein processing (GO:0010954)|positive regulation of vascular endothelial growth factor signaling pathway (GO:1900748)|positive regulation vascular endothelial growth factor production (GO:0010575)|sprouting angiogenesis (GO:0002040)|venous blood vessel morphogenesis (GO:0048845)	collagen trimer (GO:0005581)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|protease binding (GO:0002020)			NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|liver(1)|lung(6)|ovary(1)|prostate(1)|skin(3)	24		Colorectal(73;0.175)				CTTGCTTAATGTGGGACAGAT	0.577																																					p.H296Q	NSCLC(137;1340 1860 15773 39604 51087)|Esophageal Squamous(139;339 1777 2926 19691 38524)	.											.	.	.	0			c.C888A						.						82.0	86.0	85.0					18																	57106936		2203	4300	6503	SO:0001583	missense	147372	exon8			CTTAATGTGGGAC	AB075863	CCDS32838.1	18q21.32	2005-01-18				ENSG00000183287			29426	protein-coding gene	gene with protein product		612753				11853319, 12975309	Standard	NM_133459		Approved	FLJ30681, KIAA1983	uc002lib.3	Q6UXH8		ENST00000439986.4:c.888C>A	18.37:g.57106936G>T	ENSP00000404464:p.His296Gln	Somatic	48	0		WXS	Illumina HiSeq	.	37	4	NM_133459	Q6MZX5|Q86SS2|Q8TF19	Missense_Mutation	SNP	ENST00000439986.4	37	CCDS32838.1	.	.	.	.	.	.	.	.	.	.	G	12.76	2.035886	0.35893	.	.	ENSG00000183287	ENST00000439986	T	0.68331	-0.32	4.33	3.44	0.39384	.	0.045542	0.85682	D	0.000000	T	0.44891	0.1315	N	0.17248	0.465	0.80722	D	1	B;P	0.40332	0.447;0.713	B;B	0.39562	0.078;0.303	T	0.28106	-1.0054	10	0.33141	T	0.24	-23.1284	4.5045	0.11881	0.2111:0.1872:0.6017:0.0	.	296;105	Q6UXH8;Q6UXH8-3	CCBE1_HUMAN;.	Q	296	ENSP00000404464:H296Q	ENSP00000404464:H296Q	H	-	3	2	CCBE1	55257916	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	1.486000	0.35530	0.897000	0.36392	0.650000	0.86243	CAC	.		0.577	CCBE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449685.2	NM_133459	
PHF20L1	51105	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	8	133858086	133858086	+	Missense_Mutation	SNP	T	T	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr8:133858086T>C	ENST00000395386.2	+	21	3271	c.2972T>C	c.(2971-2973)tTg>tCg	p.L991S	AF230666.2_ENST00000429151.1_RNA|AF230666.2_ENST00000608375.1_RNA|PHF20L1_ENST00000220847.7_Missense_Mutation_p.L378S|PHF20L1_ENST00000395390.2_Missense_Mutation_p.L966S	NM_016018.4	NP_057102.4	A8MW92	P20L1_HUMAN	PHD finger protein 20-like 1	991							zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|large_intestine(1)|lung(10)|ovary(2)	15	all_neural(3;2.72e-06)|Medulloblastoma(3;7.08e-05)|Ovarian(258;0.00438)|Esophageal squamous(12;0.00507)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;4.46e-05)			CTTGCAAGATTGCCCCAACTT	0.413																																					p.L991S		.											.	.	.	0			c.T2972C						.						109.0	100.0	103.0					8																	133858086		1899	4111	6010	SO:0001583	missense	51105	exon21			CAAGATTGCCCCA	AF230666	CCDS6367.2, CCDS6368.1, CCDS75791.1	8q24.22	2014-03-24			ENSG00000129292	ENSG00000129292		"""Tudor domain containing"", ""Zinc fingers, PHD-type"""	24280	protein-coding gene	gene with protein product	"""tudor domain containing 20B"""					10810093, 24492612	Standard	NM_016018		Approved	CGI-72, FLJ13649, MGC64923, FLJ21615, TDRD20B	uc003ytt.3	A8MW92	OTTHUMG00000148656	ENST00000395386.2:c.2972T>C	8.37:g.133858086T>C	ENSP00000378784:p.Leu991Ser	Somatic	65	0		WXS	Illumina HiSeq	.	19	7	NM_016018	A8MZC9|Q86U89|Q86W43|Q96BT0|Q9H702|Q9HBK3|Q9NYR3|Q9Y381	Missense_Mutation	SNP	ENST00000395386.2	37	CCDS6367.2	.	.	.	.	.	.	.	.	.	.	T	19.08	3.757211	0.69648	.	.	ENSG00000129292	ENST00000395386;ENST00000220847;ENST00000395390	T;T	0.56776	0.47;0.44	5.4	5.4	0.78164	.	0.310769	0.21975	U	0.066383	T	0.72423	0.3458	M	0.73962	2.25	0.40764	D	0.98303	D;D	0.89917	1.0;0.999	D;D	0.91635	0.999;0.997	T	0.76735	-0.2850	10	0.87932	D	0	.	14.8926	0.70620	0.0:0.0:0.0:1.0	.	966;991	F8W9L8;A8MW92	.;P20L1_HUMAN	S	991;378;966	ENSP00000378784:L991S;ENSP00000378788:L966S	ENSP00000220847:L378S	L	+	2	0	PHF20L1	133927268	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.655000	0.83696	2.178000	0.69098	0.533000	0.62120	TTG	.		0.413	PHF20L1-008	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000308949.3	NM_016018	
ZNF134	7693	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	19	58132575	58132575	+	Missense_Mutation	SNP	A	A	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr19:58132575A>T	ENST00000396161.5	+	3	1398	c.1088A>T	c.(1087-1089)cAg>cTg	p.Q363L		NM_003435.3	NP_003426.3	P52741	ZN134_HUMAN	zinc finger protein 134	363					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(3)|prostate(1)	11		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0265)		ATTGCACACCAGAGGGTTCAC	0.443																																					p.Q363L		.											.	.	.	0			c.A1088T						.						104.0	110.0	108.0					19																	58132575		2181	4283	6464	SO:0001583	missense	7693	exon3			CACACCAGAGGGT	U09412	CCDS42638.1	19q13.4	2013-01-08	2006-06-13			ENSG00000213762		"""Zinc fingers, C2H2-type"""	12918	protein-coding gene	gene with protein product		604076	"""zinc finger protein 134 (clone pHZ-15)"""			7557990	Standard	NM_003435		Approved	pHZ-15	uc002qpn.2	P52741		ENST00000396161.5:c.1088A>T	19.37:g.58132575A>T	ENSP00000379464:p.Gln363Leu	Somatic	75	0		WXS	Illumina HiSeq	.	40	20	NM_003435	Q9Y4B2	Missense_Mutation	SNP	ENST00000396161.5	37	CCDS42638.1	.	.	.	.	.	.	.	.	.	.	A	22.3	4.275179	0.80580	.	.	ENSG00000213762	ENST00000418193;ENST00000541849;ENST00000396161	T	0.14391	2.51	4.43	4.43	0.53597	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.22975	0.0555	N	0.26042	0.785	0.27665	N	0.946952	D	0.67145	0.996	D	0.63597	0.916	T	0.04885	-1.0920	9	0.87932	D	0	.	13.037	0.58877	1.0:0.0:0.0:0.0	.	363	P52741	ZN134_HUMAN	L	430;283;363	ENSP00000379464:Q363L	ENSP00000379464:Q363L	Q	+	2	0	ZNF134	62824387	0.010000	0.17322	1.000000	0.80357	0.995000	0.86356	1.519000	0.35888	1.973000	0.57446	0.533000	0.62120	CAG	.		0.443	ZNF134-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466808.1	NM_003435	
FER1L6	654463	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	8	125110056	125110056	+	Silent	SNP	T	T	G	rs372723456		TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr8:125110056T>G	ENST00000522917.1	+	37	5021	c.4815T>G	c.(4813-4815)acT>acG	p.T1605T	FER1L6-AS2_ENST00000520031.1_RNA|FER1L6_ENST00000399018.1_Silent_p.T1605T	NM_001039112.2	NP_001034201.2	Q2WGJ9	FR1L6_HUMAN	fer-1-like family member 6	1605	C2 6. {ECO:0000255|PROSITE- ProRule:PRU00041}.					integral component of membrane (GO:0016021)				NS(2)|breast(3)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(18)|liver(1)|lung(49)|ovary(5)|prostate(3)|skin(8)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(1)	118	Lung NSC(37;4.1e-12)|Ovarian(258;0.00438)|all_neural(195;0.0741)		STAD - Stomach adenocarcinoma(47;0.00186)			TCTGGAACACTGAAGATGTCA	0.418																																					p.T1605T		.											.	.	.	0			c.T4815G						.						111.0	104.0	106.0					8																	125110056		1962	4160	6122	SO:0001819	synonymous_variant	654463	exon37			GAACACTGAAGAT	AB196633	CCDS43767.1	8q24.13	2014-06-27	2014-06-27		ENSG00000214814	ENSG00000214814			28065	protein-coding gene	gene with protein product			"""fer-1-like 6 (C. elegans)"""				Standard	NM_001039112		Approved	C8ORFK23	uc003yqw.3	Q2WGJ9	OTTHUMG00000164998	ENST00000522917.1:c.4815T>G	8.37:g.125110056T>G		Somatic	50	0		WXS	Illumina HiSeq	.	36	16	NM_001039112		Silent	SNP	ENST00000522917.1	37	CCDS43767.1																																																																																			.		0.418	FER1L6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381400.1	NM_001039112	
CDH13	1012	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	16	83816933	83816933	+	Missense_Mutation	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr16:83816933T>G	ENST00000566620.1	+	13	2280	c.1990T>G	c.(1990-1992)Tca>Gca	p.S664A	CDH13_ENST00000428848.3_Missense_Mutation_p.S625A|CDH13_ENST00000268613.10_Missense_Mutation_p.S711A	NM_001220488.1|NM_001220489.1|NM_001220490.1|NM_001257.4	NP_001207417.1|NP_001207418.1|NP_001207419.1|NP_001248.1	P55290	CAD13_HUMAN	cadherin 13	664	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|calcium-dependent cell-cell adhesion (GO:0016339)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|endothelial cell migration (GO:0043542)|homophilic cell adhesion (GO:0007156)|keratinocyte proliferation (GO:0043616)|lamellipodium assembly (GO:0030032)|localization within membrane (GO:0051668)|low-density lipoprotein particle mediated signaling (GO:0055096)|mitotic cell cycle (GO:0000278)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell proliferation (GO:0008285)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|Rac protein signal transduction (GO:0016601)|regulation of cell growth (GO:0001558)|regulation of endocytosis (GO:0030100)|regulation of epidermal growth factor receptor signaling pathway (GO:0042058)|Rho protein signal transduction (GO:0007266)|sprouting angiogenesis (GO:0002040)	anchored component of membrane (GO:0031225)|caveola (GO:0005901)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	adiponectin binding (GO:0055100)|cadherin binding (GO:0045296)|calcium ion binding (GO:0005509)|lipoprotein particle binding (GO:0071813)|low-density lipoprotein particle binding (GO:0030169)			large_intestine(1)	1		all_cancers(2;1.34e-11)|all_epithelial(2;4.3e-09)		COAD - Colon adenocarcinoma(5;0.0268)		GGTGACAGATTCAGGGAAACC	0.512																																					p.S711A		.											.	.	.	0			c.T2131G						.						94.0	90.0	91.0					16																	83816933		1979	4175	6154	SO:0001583	missense	1012	exon14			ACAGATTCAGGGA	U59288	CCDS56009.1, CCDS56010.1, CCDS58485.1, CCDS58486.1, CCDS58487.1	16q23.3	2013-08-27	2013-08-27			ENSG00000140945		"""Cadherins / Major cadherins"""	1753	protein-coding gene	gene with protein product	"""T-cadherin"", ""H-cadherin (heart)"""	601364				8673923, 9468307	Standard	NM_001257		Approved	CDHH	uc010vns.2	P55290		ENST00000566620.1:c.1990T>G	16.37:g.83816933T>G	ENSP00000454435:p.Ser664Ala	Somatic	65	0		WXS	Illumina HiSeq	.	44	24	NM_001220488	A8W476|A8W477|B7Z590|C9JRI6|J3KN62|Q6GTW4|Q8TBX3	Missense_Mutation	SNP	ENST00000566620.1	37	CCDS58486.1	.	.	.	.	.	.	.	.	.	.	T	16.13	3.036660	0.54896	.	.	ENSG00000140945	ENST00000268613;ENST00000428848;ENST00000536143;ENST00000538855;ENST00000539548;ENST00000540531	T	0.51574	0.7	5.19	5.19	0.71726	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.68393	0.2996	M	0.77712	2.385	0.80722	D	1	D;D;D	0.69078	0.997;0.973;0.992	D;D;D	0.76071	0.983;0.93;0.987	T	0.71248	-0.4649	9	0.49607	T	0.09	.	14.2364	0.65929	0.0:0.0:0.0:1.0	.	625;711;664	B7Z590;B7Z9B1;P55290	.;.;CAD13_HUMAN	A	711;664;625;366;223;354	ENSP00000268613:S711A	ENSP00000268613:S711A	S	+	1	0	CDH13	82374434	1.000000	0.71417	1.000000	0.80357	0.085000	0.17905	7.185000	0.77714	1.953000	0.56701	0.533000	0.62120	TCA	.		0.512	CDH13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432917.1	NM_001257	
DGAT1	8694	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	8	145541987	145541987	+	Missense_Mutation	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr8:145541987A>C	ENST00000332324.4	-	7	886	c.613T>G	c.(613-615)Ttc>Gtc	p.F205V	DGAT1_ENST00000527438.1_5'Flank|DGAT1_ENST00000531896.1_Missense_Mutation_p.F205V	NM_012079.4	NP_036211.2	O75907	DGAT1_HUMAN	diacylglycerol O-acyltransferase 1	205					acylglycerol acyl-chain remodeling (GO:0036155)|cellular lipid metabolic process (GO:0044255)|diacylglycerol metabolic process (GO:0046339)|glycerophospholipid biosynthetic process (GO:0046474)|lipid storage (GO:0019915)|long-chain fatty-acyl-CoA metabolic process (GO:0035336)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|triglyceride metabolic process (GO:0006641)|very-low-density lipoprotein particle assembly (GO:0034379)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	diacylglycerol O-acyltransferase activity (GO:0004144)|retinol O-fatty-acyltransferase activity (GO:0050252)|transferase activity, transferring acyl groups (GO:0016746)			breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)	9	all_cancers(97;6.64e-12)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;3.94e-40)|Epithelial(56;7.67e-40)|all cancers(56;7.88e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0441)|Colorectal(110;0.055)			AGCTTGAGGAAGAGGATGGTG	0.692																																					p.F205V		.											.	.	.	0			c.T613G						.						36.0	35.0	35.0					8																	145541987		2203	4295	6498	SO:0001583	missense	8694	exon7			TGAGGAAGAGGAT	AF059202	CCDS6420.1	8q24.3	2014-05-06	2010-06-24	2001-11-09	ENSG00000185000	ENSG00000185000	2.3.1.20		2843	protein-coding gene	gene with protein product		604900	"""diacylglycerol O-acyltransferase homolog 1 (mouse)"""			9756920	Standard	NM_012079		Approved	ARGP1, DGAT	uc003zbv.3	O75907	OTTHUMG00000174606	ENST00000332324.4:c.613T>G	8.37:g.145541987A>C	ENSP00000332258:p.Phe205Val	Somatic	30	0		WXS	Illumina HiSeq	.	19	6	NM_012079	B2RWQ2|D3DWL6|Q96BB8	Missense_Mutation	SNP	ENST00000332324.4	37	CCDS6420.1	.	.	.	.	.	.	.	.	.	.	A	26.5	4.740525	0.89573	.	.	ENSG00000185000	ENST00000332324;ENST00000526479;ENST00000531896	T	0.71341	-0.56	5.46	5.46	0.80206	.	0.000000	0.85682	D	0.000000	T	0.80449	0.4625	L	0.60904	1.88	0.58432	D	0.999999	D;P	0.69078	0.997;0.951	D;P	0.69307	0.963;0.801	T	0.82303	-0.0524	10	0.72032	D	0.01	-23.1006	13.4781	0.61320	1.0:0.0:0.0:0.0	.	205;205	E9PS80;O75907	.;DGAT1_HUMAN	V	205	ENSP00000332258:F205V	ENSP00000332258:F205V	F	-	1	0	DGAT1	145512795	1.000000	0.71417	1.000000	0.80357	0.831000	0.47069	4.024000	0.57218	2.072000	0.62099	0.454000	0.30748	TTC	.		0.692	DGAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382059.3	NM_012079	
POTEKP	440915	hgsc.bcm.edu;bcgsc.ca	37	2	132354664	132354664	+	IGR	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr2:132354664A>C								CCDC74A (63425 upstream) : RNU6-617P (5698 downstream)																							ATGTTGCTGGAACATGGCACT	0.373																																					.		.											.	.	.	0			.						.																																			SO:0001628	intergenic_variant	100873780	.			TGCTGGAACATGG																													2.37:g.132354664A>C		Somatic	357	0		WXS	Illumina HiSeq	.	198	91	.		RNA	SNP		37																																																																																				.	0	0.373								
GOLGA3	2802	hgsc.bcm.edu	37	12	133351864	133351864	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr12:133351864G>T	ENST00000450791.2	-	21	4189	c.4006C>A	c.(4006-4008)Cag>Aag	p.Q1336K	GOLGA3_ENST00000456883.2_Missense_Mutation_p.Q1336K|GOLGA3_ENST00000204726.3_Missense_Mutation_p.Q1336K			Q08378	GOGA3_HUMAN	golgin A3	1336	Gln-rich.				intra-Golgi vesicle-mediated transport (GO:0006891)	cytosol (GO:0005829)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extrinsic component of Golgi membrane (GO:0090498)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi transport complex (GO:0017119)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	transporter activity (GO:0005215)			breast(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(4)|lung(33)|ovary(3)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	64	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0176)|Lung NSC(355;0.204)		OV - Ovarian serous cystadenocarcinoma(86;2.27e-08)|Epithelial(86;3.34e-07)|all cancers(50;9.4e-06)		AGGTCTTCCTGGGCCATCTCC	0.443																																					p.Q1336K		.											GOLGA3,NS,carcinoma,0,1	GOLGA3	0	0			c.C4006A						.						94.0	85.0	88.0					12																	133351864		2203	4300	6503	SO:0001583	missense	2802	exon22			CTTCCTGGGCCAT	AF485338	CCDS9281.1, CCDS53846.1	12q24.33	2010-02-12	2010-02-12		ENSG00000090615	ENSG00000090615			4426	protein-coding gene	gene with protein product	"""SY2/SY10 protein"", ""Golgi complex-associated protein of 170 kD"""	602581	"""golgi autoantigen, golgin subfamily a, 3"""			8315394, 15829563	Standard	NM_001172557		Approved	golgin-160, GCP170, MEA-2	uc001ukz.1	Q08378	OTTHUMG00000168023	ENST00000450791.2:c.4006C>A	12.37:g.133351864G>T	ENSP00000410378:p.Gln1336Lys	Somatic	48	0		WXS	Illumina HiSeq	.	43	2	NM_005895	A5PKX6|O43241|Q6P9C7|Q86XW3|Q8TDA9|Q8WZA3	Missense_Mutation	SNP	ENST00000450791.2	37	CCDS9281.1	.	.	.	.	.	.	.	.	.	.	G	13.41	2.229233	0.39399	.	.	ENSG00000090615	ENST00000204726;ENST00000450791;ENST00000456883	T;T;T	0.77620	-1.11;-1.11;1.97	6.07	5.15	0.70609	.	0.165252	0.56097	D	0.000036	T	0.66015	0.2747	L	0.34521	1.04	0.80722	D	1	B;B	0.32040	0.003;0.353	B;B	0.32022	0.007;0.139	T	0.61377	-0.7075	10	0.07813	T	0.8	.	15.5362	0.76004	0.0:0.0:0.7569:0.2431	.	1336;1336	Q08378-2;Q08378	.;GOGA3_HUMAN	K	1336	ENSP00000204726:Q1336K;ENSP00000410378:Q1336K;ENSP00000409303:Q1336K	ENSP00000204726:Q1336K	Q	-	1	0	GOLGA3	131861937	1.000000	0.71417	0.905000	0.35620	0.411000	0.31082	5.183000	0.65065	2.884000	0.98904	0.655000	0.94253	CAG	.		0.443	GOLGA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397569.2	NM_005895	
AKR7L	246181	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	1	19597309	19597309	+	RNA	SNP	A	A	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr1:19597309A>G	ENST00000429712.1	-	0	454				AKR7L_ENST00000420396.2_RNA			Q8NHP1	ARK74_HUMAN	aldo-keto reductase family 7-like							extracellular vesicular exosome (GO:0070062)	oxidoreductase activity (GO:0016491)			breast(1)|endometrium(2)|ovary(1)|prostate(1)|urinary_tract(1)	6						AGGTGCATGTAGATAGAAGAG	0.612																																					.		.											.	.	.	0			.						.						59.0	55.0	56.0					1																	19597309		2203	4300	6503			246181	.			GCATGTAGATAGA			1p36.1-p35	2008-12-09			ENSG00000211454	ENSG00000211454			24056	protein-coding gene	gene with protein product		608478				12879023	Standard	NR_040288		Approved	AFAR3	uc021ohn.1	Q8NHP1	OTTHUMG00000002520		1.37:g.19597309A>G		Somatic	47	0		WXS	Illumina HiSeq	.	27	10	.	Q5U614	RNA	SNP	ENST00000429712.1	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	15.15|15.15	2.747611|2.747611	0.49257|0.49257	.|.	.|.	ENSG00000211454|ENSG00000211454	ENST00000429712;ENST00000388886|ENST00000457194	.|.	.|.	.|.	4.1|4.1	4.1|4.1	0.47936|0.47936	NADP-dependent oxidoreductase domain (3);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.63438|0.63438	0.2511|0.2511	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.97110|.	1.0;1.0|.	T|T	0.62562|0.62562	-0.6828|-0.6828	8|4	0.87932|.	D|.	0|.	.|.	12.3303|12.3303	0.55035|0.55035	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	112;112|.	F8W7D9;Q8NHP1|.	.;ARK74_HUMAN|.	P|H	112|68	.|.	ENSP00000373538:L112P|.	L|Y	-|-	2|1	0|0	AKR7L|AKR7L	19469896|19469896	1.000000|1.000000	0.71417|0.71417	0.160000|0.160000	0.22671|0.22671	0.176000|0.176000	0.22953|0.22953	8.431000|8.431000	0.90285|0.90285	1.855000|1.855000	0.53841|0.53841	0.455000|0.455000	0.32223|0.32223	CTA|TAC	.		0.612	AKR7L-001	KNOWN	basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000007163.3	NM_201252	
UBR5	51366	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	8	103299714	103299714	+	Missense_Mutation	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr8:103299714T>G	ENST00000520539.1	-	37	5510	c.4904A>C	c.(4903-4905)aAt>aCt	p.N1635T	UBR5_ENST00000220959.4_Missense_Mutation_p.N1635T|UBR5_ENST00000521922.1_Missense_Mutation_p.N1629T|UBR5_ENST00000519528.1_5'Flank	NM_001282873.1|NM_015902.5	NP_001269802.1|NP_056986.2	O95071	UBR5_HUMAN	ubiquitin protein ligase E3 component n-recognin 5	1635					cell proliferation (GO:0008283)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|negative regulation of double-strand break repair (GO:2000780)|negative regulation of histone H2A K63-linked ubiquitination (GO:1901315)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of protein import into nucleus, translocation (GO:0033160)|progesterone receptor signaling pathway (GO:0050847)|protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ligase activity (GO:0016874)|RNA binding (GO:0003723)|ubiquitin-protein transferase activity (GO:0004842)|ubiquitin-ubiquitin ligase activity (GO:0034450)|zinc ion binding (GO:0008270)			NS(1)|breast(13)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(8)|large_intestine(19)|liver(1)|lung(51)|ovary(6)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	124	all_cancers(14;8e-07)|all_epithelial(15;2.18e-08)|Lung NSC(17;2.55e-05)|all_lung(17;8.85e-05)		OV - Ovarian serous cystadenocarcinoma(57;0.000442)			CCCACTAGCATTATCTTGGTT	0.433																																					p.N1635T	Ovarian(131;96 1741 5634 7352 27489)	.											.	.	.	0			c.A4904C						.						202.0	150.0	168.0					8																	103299714		2203	4300	6503	SO:0001583	missense	51366	exon37			CTAGCATTATCTT	AF006010	CCDS34933.1, CCDS64946.1	8q22	2008-06-23	2007-06-19	2007-06-19	ENSG00000104517	ENSG00000104517		"""Ubiquitin protein ligase E3 component n-recognins"""	16806	protein-coding gene	gene with protein product		608413	"""E3 ubiquitin protein ligase, HECT domain containing, 1"""	EDD1		10030672, 16055722	Standard	NM_015902		Approved	DD5, HYD, EDD, KIAA0896	uc003ykr.2	O95071	OTTHUMG00000164755	ENST00000520539.1:c.4904A>C	8.37:g.103299714T>G	ENSP00000429084:p.Asn1635Thr	Somatic	26	0		WXS	Illumina HiSeq	.	26	10	NM_015902	B2RP24|J3KMW7|O94970|Q9NPL3	Missense_Mutation	SNP	ENST00000520539.1	37	CCDS34933.1	.	.	.	.	.	.	.	.	.	.	T	22.1	4.238025	0.79800	.	.	ENSG00000104517	ENST00000520539;ENST00000220959;ENST00000521922	T;T;T	0.44482	0.93;0.93;0.92	5.96	5.96	0.96718	.	0.000000	0.85682	D	0.000000	T	0.53981	0.1830	L	0.36672	1.1	0.80722	D	1	D;D	0.57899	0.981;0.981	D;D	0.67900	0.954;0.954	T	0.49011	-0.8983	10	0.35671	T	0.21	.	16.4245	0.83810	0.0:0.0:0.0:1.0	.	1629;1635	E7EMW7;O95071	.;UBR5_HUMAN	T	1635;1635;1629	ENSP00000429084:N1635T;ENSP00000220959:N1635T;ENSP00000427819:N1629T	ENSP00000220959:N1635T	N	-	2	0	UBR5	103368890	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.991000	0.88244	2.283000	0.76528	0.533000	0.62120	AAT	.		0.433	UBR5-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000380075.2	NM_015902	
PLXNA2	5362	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	208200667	208200667	+	Missense_Mutation	SNP	T	T	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr1:208200667T>A	ENST00000367033.3	-	32	6363	c.5606A>T	c.(5605-5607)gAg>gTg	p.E1869V	PLXNA2_ENST00000483048.1_5'UTR	NM_025179.3	NP_079455.3	O75051	PLXA2_HUMAN	plexin A2	1869					axon guidance (GO:0007411)|centrosome localization (GO:0051642)|cerebellar granule cell precursor tangential migration (GO:0021935)|limb bud formation (GO:0060174)|neural tube development (GO:0021915)|pharyngeal system development (GO:0060037)|regulation of cell migration (GO:0030334)|semaphorin-plexin signaling pathway (GO:0071526)|somitogenesis (GO:0001756)	integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)			NS(1)|breast(3)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(28)|ovary(3)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)	80				OV - Ovarian serous cystadenocarcinoma(81;0.199)		CTCATCCTGCTCTAGGGCCCC	0.542																																					p.E1869V		.											.	.	.	0			c.A5606T						.						70.0	69.0	69.0					1																	208200667		2203	4300	6503	SO:0001583	missense	5362	exon32			TCCTGCTCTAGGG	X87831	CCDS31013.1	1q32.2	2008-07-18			ENSG00000076356	ENSG00000076356		"""Plexins"""	9100	protein-coding gene	gene with protein product	"""plexin 2"", ""plexin-A2"", ""semaphorin receptor OCT"", ""transmembrane protein OCT"""	601054		PLXN2		8570614	Standard	NM_025179		Approved	OCT, FLJ11751, FLJ30634, KIAA0463	uc001hgz.3	O75051	OTTHUMG00000036564	ENST00000367033.3:c.5606A>T	1.37:g.208200667T>A	ENSP00000356000:p.Glu1869Val	Somatic	20	0		WXS	Illumina HiSeq	.	22	14	NM_025179	A2RTX9|B2RMX7|Q6UX61|Q96GN9|Q9BRL1|Q9UIW1	Missense_Mutation	SNP	ENST00000367033.3	37	CCDS31013.1	.	.	.	.	.	.	.	.	.	.	T	29.0	4.966710	0.92855	.	.	ENSG00000076356	ENST00000367033	T	0.01234	5.13	5.27	5.27	0.74061	.	0.049469	0.85682	D	0.000000	T	0.05227	0.0139	M	0.84219	2.685	0.80722	D	1	P;P	0.52170	0.951;0.8	P;B	0.47603	0.551;0.37	T	0.08973	-1.0696	10	0.87932	D	0	.	15.2098	0.73214	0.0:0.0:0.0:1.0	.	1869;139	O75051;Q9HAE7	PLXA2_HUMAN;.	V	1869	ENSP00000356000:E1869V	ENSP00000356000:E1869V	E	-	2	0	PLXNA2	206267290	1.000000	0.71417	0.988000	0.46212	0.987000	0.75469	7.751000	0.85126	1.997000	0.58415	0.533000	0.62120	GAG	.		0.542	PLXNA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088932.6	NM_025179	
ANKFY1	51479	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	17	4113218	4113218	+	Silent	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr17:4113218T>G	ENST00000341657.4	-	5	518	c.483A>C	c.(481-483)ctA>ctC	p.L161L	ANKFY1_ENST00000570535.1_Silent_p.L203L|ANKFY1_ENST00000574367.1_Silent_p.L161L|ANKFY1_ENST00000433651.1_Silent_p.L161L	NM_016376.3	NP_057460.3	Q9P2R3	ANFY1_HUMAN	ankyrin repeat and FYVE domain containing 1	161					endosomal vesicle fusion (GO:0034058)|endosome localization (GO:0032439)|Golgi to lysosome transport (GO:0090160)|positive regulation of pinocytosis (GO:0048549)|retrograde transport, endosome to Golgi (GO:0042147)	early endosome (GO:0005769)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|macropinosome (GO:0044354)|membrane (GO:0016020)	metal ion binding (GO:0046872)|phosphatidylinositol phosphate binding (GO:1901981)|Rab GTPase binding (GO:0017137)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(11)|liver(1)|lung(5)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	32						TGACATTCACTAGAGACATAA	0.418																																					p.L203L		.											.	.	.	0			c.A609C						.						113.0	110.0	111.0					17																	4113218		1957	4141	6098	SO:0001819	synonymous_variant	51479	exon5			ATTCACTAGAGAC	AB033081	CCDS42236.1, CCDS58502.1	17p13.3	2013-01-10			ENSG00000185722	ENSG00000185722		"""Zinc fingers, FYVE domain containing"", ""BTB/POZ domain containing"", ""Ankyrin repeat domain containing"""	20763	protein-coding gene	gene with protein product		607927				10940552, 17273843	Standard	NM_016376		Approved	ANKHZN, KIAA1255, ZFYVE14, BTBD23	uc002fxn.3	Q9P2R3	OTTHUMG00000177727	ENST00000341657.4:c.483A>C	17.37:g.4113218T>G		Somatic	44	0		WXS	Illumina HiSeq	.	20	12	NM_001257999	A8KA65|Q5RKV4|Q9ULG5	Silent	SNP	ENST00000341657.4	37																																																																																				.		0.418	ANKFY1-008	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000438702.1	NM_016376	
IRF6	3664	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	209974658	209974658	+	Missense_Mutation	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr1:209974658T>G	ENST00000367021.3	-	3	273	c.101A>C	c.(100-102)aAa>aCa	p.K34T	IRF6_ENST00000542854.1_Intron	NM_006147.3	NP_006138.1	O14896	IRF6_HUMAN	interferon regulatory factor 6	34					cell cycle arrest (GO:0007050)|cell development (GO:0048468)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|keratinocyte differentiation (GO:0030216)|keratinocyte proliferation (GO:0043616)|mammary gland epithelial cell differentiation (GO:0060644)|negative regulation of cell proliferation (GO:0008285)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	DNA binding (GO:0003677)|regulatory region DNA binding (GO:0000975)|sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(1)|large_intestine(4)|lung(12)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(4)	28				OV - Ovarian serous cystadenocarcinoma(81;0.0351)		CTGGAAGCGTTTAGAGTCCCT	0.547										HNSCC(57;0.16)																											p.K34T		.											.	.	.	0			c.A101C						.						87.0	93.0	91.0					1																	209974658		2203	4300	6503	SO:0001583	missense	3664	exon3			AAGCGTTTAGAGT	AL022398	CCDS1492.1, CCDS55681.1	1q32.2-q32.3	2011-02-10			ENSG00000117595	ENSG00000117595			6121	protein-coding gene	gene with protein product		607199	"""Van der Woude syndrome"""	VWS, LPS		12219090	Standard	NM_006147		Approved	OFC6, VWS1	uc001hhq.2	O14896	OTTHUMG00000036521	ENST00000367021.3:c.101A>C	1.37:g.209974658T>G	ENSP00000355988:p.Lys34Thr	Somatic	147	0		WXS	Illumina HiSeq	.	183	27	NM_006147	B4DLE2|D3DT90|F5GWX8|G0ZTL0	Missense_Mutation	SNP	ENST00000367021.3	37	CCDS1492.1	.	.	.	.	.	.	.	.	.	.	T	19.36	3.812956	0.70912	.	.	ENSG00000117595	ENST00000367021;ENST00000456314	D;D	0.97505	-4.41;-4.41	6.17	5.05	0.67936	Interferon regulatory factor, conserved site (1);Winged helix-turn-helix transcription repressor DNA-binding (1);Interferon regulatory factor DNA-binding domain (3);	0.083148	0.85682	D	0.000000	D	0.94879	0.8345	N	0.11673	0.155	0.80722	D	1	D	0.56287	0.975	P	0.59221	0.854	D	0.93431	0.6785	9	.	.	.	.	12.092	0.53733	0.0:0.0663:0.0:0.9337	.	34	O14896	IRF6_HUMAN	T	34	ENSP00000355988:K34T;ENSP00000403855:K34T	.	K	-	2	0	IRF6	208041281	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.818000	0.69236	1.160000	0.42584	0.533000	0.62120	AAA	.		0.547	IRF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088827.1	NM_006147	
POR	5447	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	7	75615316	75615316	+	Missense_Mutation	SNP	T	T	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr7:75615316T>A	ENST00000461988.1	+	14	1850	c.1745T>A	c.(1744-1746)cTg>cAg	p.L582Q	POR_ENST00000419840.1_Intron|POR_ENST00000394893.1_Missense_Mutation_p.L582Q|POR_ENST00000545601.1_Missense_Mutation_p.L390Q|POR_ENST00000450476.1_Missense_Mutation_p.L481Q|TMEM120A_ENST00000338761.4_RNA|TMEM120A_ENST00000493111.2_RNA|POR_ENST00000439269.1_Missense_Mutation_p.L320Q	NM_000941.2	NP_000932.3	P16435	NCPR_HUMAN	P450 (cytochrome) oxidoreductase	579					carnitine metabolic process (GO:0009437)|cellular organofluorine metabolic process (GO:0090346)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|cellular response to peptide hormone stimulus (GO:0071375)|demethylation (GO:0070988)|fatty acid oxidation (GO:0019395)|flavonoid metabolic process (GO:0009812)|internal peptidyl-lysine acetylation (GO:0018393)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of lipase activity (GO:0060192)|nitrate catabolic process (GO:0043602)|nitric oxide catabolic process (GO:0046210)|oxidation-reduction process (GO:0055114)|positive regulation of cholesterol biosynthetic process (GO:0045542)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of monooxygenase activity (GO:0032770)|positive regulation of smoothened signaling pathway (GO:0045880)|positive regulation of steroid hormone biosynthetic process (GO:0090031)|regulation of growth plate cartilage chondrocyte proliferation (GO:0003420)|response to drug (GO:0042493)|response to nutrient (GO:0007584)	endoplasmic reticulum (GO:0005783)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|mitochondrion (GO:0005739)	cytochrome-b5 reductase activity, acting on NAD(P)H (GO:0004128)|electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|FMN binding (GO:0010181)|hydrolase activity (GO:0016787)|iron ion binding (GO:0005506)|iron-cytochrome-c reductase activity (GO:0047726)|NADP binding (GO:0050661)|NADPH-hemoprotein reductase activity (GO:0003958)|nitric oxide dioxygenase activity (GO:0008941)			central_nervous_system(1)|endometrium(2)|kidney(2)|lung(3)|ovary(1)	9					Benzphetamine(DB00865)|Daunorubicin(DB00694)|Doxorubicin(DB00997)|Ethylmorphine(DB01466)|Flavin adenine dinucleotide(DB03147)|Lipoic Acid(DB00166)|Mitomycin(DB00305)|Nilutamide(DB00665)|Nitrofurantoin(DB00698)	CGGGAGGAGCTGGCGCAGTTC	0.692																																					p.L582Q		.											.	.	.	0			c.T1745A						.						17.0	23.0	21.0					7																	75615316		2023	4130	6153	SO:0001583	missense	5447	exon14			AGGAGCTGGCGCA	AF258341	CCDS5579.1	7q11.2	2006-12-05			ENSG00000127948	ENSG00000127948			9208	protein-coding gene	gene with protein product		124015				2516426	Standard	NM_000941		Approved	CYPOR, FLJ26468	uc003udy.3	P16435	OTTHUMG00000130413	ENST00000461988.1:c.1745T>A	7.37:g.75615316T>A	ENSP00000419970:p.Leu582Gln	Somatic	26	0		WXS	Illumina HiSeq	.	9	4	NM_000941	Q16455|Q197M5|Q8N181|Q9H3M8|Q9UDT3	Missense_Mutation	SNP	ENST00000461988.1	37	CCDS5579.1	.	.	.	.	.	.	.	.	.	.	T	18.10	3.549631	0.65311	.	.	ENSG00000127948	ENST00000461988;ENST00000394893;ENST00000545601;ENST00000450476;ENST00000439269	D;D;D;D;D	0.90504	-2.68;-2.68;-2.68;-2.68;-2.68	3.59	3.59	0.41128	Oxidoreductase FAD/NAD(P)-binding (1);Flavoprotein pyridine nucleotide cytochrome reductase (1);	0.000000	0.64402	D	0.000002	D	0.96812	0.8959	H	0.98111	4.15	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.81914	0.988;0.995;0.994;0.995	D	0.97481	1.0047	10	0.87932	D	0	-32.2452	12.3556	0.55174	0.0:0.0:0.0:1.0	.	579;481;390;588	P16435;E7EVY7;F5H468;Q59ED7	NCPR_HUMAN;.;.;.	Q	582;582;390;481;320	ENSP00000419970:L582Q;ENSP00000378355:L582Q;ENSP00000446149:L390Q;ENSP00000416572:L481Q;ENSP00000412490:L320Q	ENSP00000378355:L582Q	L	+	2	0	POR	75453252	1.000000	0.71417	0.997000	0.53966	0.579000	0.36224	7.401000	0.79962	1.863000	0.54032	0.459000	0.35465	CTG	.		0.692	POR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252796.7	NM_000941	
DNAJC9	23234	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	10	75006528	75006528	+	Missense_Mutation	SNP	T	T	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr10:75006528T>C	ENST00000372950.4	-	2	1911	c.239A>G	c.(238-240)gAg>gGg	p.E80G	DNAJC9-AS1_ENST00000440197.2_RNA|MRPS16_ENST00000479005.1_5'Flank|DNAJC9-AS1_ENST00000513954.1_RNA|MRPS16_ENST00000416782.2_3'UTR	NM_015190.3	NP_056005.1	Q8WXX5	DNJC9_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 9	80	J. {ECO:0000255|PROSITE- ProRule:PRU00286}.				social behavior (GO:0035176)	nucleus (GO:0005634)				endometrium(2)|kidney(1)|large_intestine(2)|stomach(1)	6	Prostate(51;0.0119)					TGTTCCCTGCTCATCGTACAC	0.522																																					p.E80G		.											.	.	.	0			c.A239G						.						97.0	87.0	90.0					10																	75006528		2203	4300	6503	SO:0001583	missense	23234	exon2			CCCTGCTCATCGT	AF327347	CCDS7322.1	10q22.3	2011-09-02			ENSG00000213551	ENSG00000213551		"""Heat shock proteins / DNAJ (HSP40)"""	19123	protein-coding gene	gene with protein product		611206					Standard	NM_015190		Approved	JDD1, SB73	uc001jtr.3	Q8WXX5	OTTHUMG00000018461	ENST00000372950.4:c.239A>G	10.37:g.75006528T>C	ENSP00000362041:p.Glu80Gly	Somatic	67	0		WXS	Illumina HiSeq	.	48	14	NM_015190	B2RMW6	Missense_Mutation	SNP	ENST00000372950.4	37	CCDS7322.1	.	.	.	.	.	.	.	.	.	.	T	36	5.616309	0.96649	.	.	ENSG00000213551	ENST00000372950	T	0.73363	-0.74	5.49	5.49	0.81192	Heat shock protein DnaJ, N-terminal (3);	0.046192	0.85682	D	0.000000	D	0.85809	0.5783	M	0.81179	2.53	0.80722	D	1	D	0.89917	1.0	D	0.75020	0.985	D	0.87535	0.2455	10	0.66056	D	0.02	.	13.5326	0.61631	0.0:0.0:0.0:1.0	.	80	Q8WXX5	DNJC9_HUMAN	G	80	ENSP00000362041:E80G	ENSP00000362041:E80G	E	-	2	0	DNAJC9	74676534	1.000000	0.71417	1.000000	0.80357	0.871000	0.50021	7.988000	0.88194	2.088000	0.63022	0.482000	0.46254	GAG	.		0.522	DNAJC9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048643.1	NM_015190	
FAH	2184	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	15	80464579	80464579	+	Missense_Mutation	SNP	A	A	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr15:80464579A>G	ENST00000407106.1	+	9	850	c.695A>G	c.(694-696)aAc>aGc	p.N232S	FAH_ENST00000261755.5_Missense_Mutation_p.N232S|FAH_ENST00000561421.1_Missense_Mutation_p.N232S|FAH_ENST00000539156.1_Missense_Mutation_p.N162S|FAH_ENST00000558627.1_3'UTR			P16930	FAAA_HUMAN	fumarylacetoacetate hydrolase (fumarylacetoacetase)	232					arginine catabolic process (GO:0006527)|cellular nitrogen compound metabolic process (GO:0034641)|L-phenylalanine catabolic process (GO:0006559)|small molecule metabolic process (GO:0044281)|tyrosine catabolic process (GO:0006572)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	fumarylacetoacetase activity (GO:0004334)|metal ion binding (GO:0046872)			endometrium(2)|kidney(1)|large_intestine(5)|lung(8)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						GTCCTTATGAACGACTGGAGT	0.512									Tyrosinemia, type 1																												p.N232S		.											.	.	.	0			c.A695G						.						88.0	85.0	86.0					15																	80464579		2203	4300	6503	SO:0001583	missense	2184	exon8	Familial Cancer Database	Fumarylacetoacetase Deficiency, Hepatorenal Tyrosinemia, Hereditary Tyrosinemia 1, HT1	TTATGAACGACTG	M55150	CCDS10314.1	15q25.1	2012-08-30			ENSG00000103876	ENSG00000103876	3.7.1.2		3579	protein-coding gene	gene with protein product		613871				1998338, 2336361	Standard	NM_000137		Approved		uc002bfm.2	P16930	OTTHUMG00000144187	ENST00000407106.1:c.695A>G	15.37:g.80464579A>G	ENSP00000385080:p.Asn232Ser	Somatic	43	0		WXS	Illumina HiSeq	.	24	11	NM_000137	B2R9X1|D3DW95|Q53XA7	Missense_Mutation	SNP	ENST00000407106.1	37	CCDS10314.1	.	.	.	.	.	.	.	.	.	.	A	18.38	3.612343	0.66672	.	.	ENSG00000103876	ENST00000407106;ENST00000261755;ENST00000539156	D;D;D	0.96685	-4.09;-4.09;-4.09	4.87	4.87	0.63330	Fumarylacetoacetase, C-terminal-related (2);Fumarylacetoacetase, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.98692	0.9561	H	0.96861	3.895	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	D	0.99521	1.0958	10	0.87932	D	0	-35.0169	13.4495	0.61163	1.0:0.0:0.0:0.0	.	232	P16930	FAAA_HUMAN	S	232;232;162	ENSP00000385080:N232S;ENSP00000261755:N232S;ENSP00000454271:N162S	ENSP00000261755:N232S	N	+	2	0	FAH	78251634	1.000000	0.71417	0.999000	0.59377	0.561000	0.35649	8.320000	0.89995	1.831000	0.53308	0.459000	0.35465	AAC	.		0.512	FAH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000291392.2		
ZNF606	80095	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	19	58491019	58491019	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr19:58491019G>T	ENST00000341164.4	-	7	1649	c.1029C>A	c.(1027-1029)aaC>aaA	p.N343K	ZNF606_ENST00000536132.1_Missense_Mutation_p.N253K	NM_025027.3	NP_079303.2	Q8WXB4	ZN606_HUMAN	zinc finger protein 606	343					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(2)|endometrium(4)|kidney(1)|large_intestine(5)|lung(10)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	26		Colorectal(82;5.46e-05)|all_neural(62;0.0182)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0168)		AATTATACTGGTTTTCTCCAA	0.318																																					p.N343K		.											.	.	.	0			c.C1029A						.						110.0	112.0	112.0					19																	58491019		2203	4299	6502	SO:0001583	missense	80095	exon7			ATACTGGTTTTCT	AB058755	CCDS12968.1	19q13.43	2013-01-08			ENSG00000166704	ENSG00000166704		"""Zinc fingers, C2H2-type"", ""-"""	25879	protein-coding gene	gene with protein product		613905		ZNF328		11347906	Standard	XM_005259276		Approved	FLJ14260, KIAA1852	uc002qqw.3	Q8WXB4	OTTHUMG00000169804	ENST00000341164.4:c.1029C>A	19.37:g.58491019G>T	ENSP00000343617:p.Asn343Lys	Somatic	101	0		WXS	Illumina HiSeq	.	46	16	NM_025027	A8KAN2|Q8NE04|Q96JH5	Missense_Mutation	SNP	ENST00000341164.4	37	CCDS12968.1	.	.	.	.	.	.	.	.	.	.	G	0.033	-1.324664	0.01309	.	.	ENSG00000166704	ENST00000341164;ENST00000536132;ENST00000551380	T;T;T	0.10477	2.87;2.87;2.87	4.29	2.17	0.27698	Zinc finger, C2H2 (1);	0.000000	0.48767	D	0.000171	T	0.01421	0.0046	N	0.00146	-1.995	0.29252	N	0.871893	B	0.09022	0.002	B	0.06405	0.002	T	0.39014	-0.9634	10	0.02654	T	1	.	1.5325	0.02539	0.1897:0.1646:0.4764:0.1693	.	343	Q8WXB4	ZN606_HUMAN	K	343;253;343	ENSP00000343617:N343K;ENSP00000445624:N253K;ENSP00000446972:N343K	ENSP00000343617:N343K	N	-	3	2	ZNF606	63182831	0.954000	0.32549	1.000000	0.80357	0.996000	0.88848	-0.512000	0.06313	0.751000	0.32900	0.655000	0.94253	AAC	.		0.318	ZNF606-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405961.1	NM_025027	
NOTCH4	4855	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	6	32166895	32166895	+	Missense_Mutation	SNP	G	G	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr6:32166895G>A	ENST00000375023.3	-	24	4481	c.4343C>T	c.(4342-4344)cCt>cTt	p.P1448L	NOTCH4_ENST00000443903.2_5'Flank	NM_004557.3	NP_004548.3	Q99466	NOTC4_HUMAN	notch 4	1448					cell differentiation (GO:0030154)|cell fate determination (GO:0001709)|embryo development (GO:0009790)|endothelial cell morphogenesis (GO:0001886)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|mammary gland development (GO:0030879)|morphogenesis of a branching structure (GO:0001763)|negative regulation of cell differentiation (GO:0045596)|negative regulation of endothelial cell differentiation (GO:0045602)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|patterning of blood vessels (GO:0001569)|positive regulation of transcription of Notch receptor target (GO:0007221)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cell surface (GO:0009986)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|protein heterodimerization activity (GO:0046982)|receptor activity (GO:0004872)			NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(4)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(47)|ovary(5)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(1)	100						GCACAGCACAGGCCAGGGAAG	0.617																																					p.P1448L		.											.	.	.	0			c.C4343T						.						13.0	15.0	14.0					6																	32166895		1505	2695	4200	SO:0001583	missense	4855	exon24			AGCACAGGCCAGG		CCDS34420.1	6p21.3	2013-01-10	2010-06-24		ENSG00000204301	ENSG00000204301		"""Ankyrin repeat domain containing"""	7884	protein-coding gene	gene with protein product		164951	"""Notch (Drosophila) homolog 4"", ""Notch homolog 4 (Drosophila)"""	INT3		7835890	Standard	NM_004557		Approved		uc003obb.3	Q99466	OTTHUMG00000031044	ENST00000375023.3:c.4343C>T	6.37:g.32166895G>A	ENSP00000364163:p.Pro1448Leu	Somatic	23	0		WXS	Illumina HiSeq	.	25	8	NM_004557	B0V183|B0V1X5|O00306|Q5SSY7|Q99458|Q99940|Q9H3S8|Q9UII9|Q9UIJ0	Missense_Mutation	SNP	ENST00000375023.3	37	CCDS34420.1	.	.	.	.	.	.	.	.	.	.	G	7.024	0.559331	0.13436	.	.	ENSG00000204301	ENST00000375023	T	0.80909	-1.43	5.2	4.34	0.51931	.	0.000000	0.43747	D	0.000523	T	0.49575	0.1565	L	0.27053	0.805	0.80722	D	1	B;B	0.18461	0.0;0.028	B;B	0.15870	0.001;0.014	T	0.48768	-0.9006	10	0.11182	T	0.66	.	11.3409	0.49533	0.0876:0.0:0.9124:0.0	.	1448;1447	Q99466;B0S882	NOTC4_HUMAN;.	L	1448	ENSP00000364163:P1448L	ENSP00000364163:P1448L	P	-	2	0	NOTCH4	32274873	1.000000	0.71417	0.983000	0.44433	0.996000	0.88848	4.490000	0.60319	1.431000	0.47355	0.555000	0.69702	CCT	.		0.617	NOTCH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076045.2		
MYH9	4627	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	22	36717867	36717867	+	Splice_Site	SNP	C	C	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr22:36717867C>A	ENST00000216181.5	-	7	936		c.e7-1			NM_002473.4	NP_002464.1	P35579	MYH9_HUMAN	myosin, heavy chain 9, non-muscle						actin cytoskeleton reorganization (GO:0031532)|actin filament-based movement (GO:0030048)|actomyosin structure organization (GO:0031032)|angiogenesis (GO:0001525)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|blood vessel endothelial cell migration (GO:0043534)|cytokinesis (GO:0000910)|establishment of meiotic spindle localization (GO:0051295)|establishment of T cell polarity (GO:0001768)|in utero embryonic development (GO:0001701)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|meiotic spindle organization (GO:0000212)|membrane protein ectodomain proteolysis (GO:0006509)|monocyte differentiation (GO:0030224)|myoblast fusion (GO:0007520)|platelet aggregation (GO:0070527)|platelet formation (GO:0030220)|protein transport (GO:0015031)|regulation of cell shape (GO:0008360)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|uropod organization (GO:0032796)	actin cytoskeleton (GO:0015629)|actomyosin (GO:0042641)|actomyosin contractile ring (GO:0005826)|cell leading edge (GO:0031252)|cell-cell adherens junction (GO:0005913)|cleavage furrow (GO:0032154)|cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|immunological synapse (GO:0001772)|membrane (GO:0016020)|myosin II complex (GO:0016460)|myosin II filament (GO:0097513)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|ruffle (GO:0001726)|spindle (GO:0005819)|stress fiber (GO:0001725)|uropod (GO:0001931)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)|motor activity (GO:0003774)|poly(A) RNA binding (GO:0044822)|protein anchor (GO:0043495)|protein homodimerization activity (GO:0042803)			NS(1)|breast(8)|central_nervous_system(3)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(16)|lung(29)|ovary(4)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(6)|urinary_tract(3)	86						TGAATTTGCCCTAAGTAAGAA	0.527			T	ALK	ALCL		"""Deafness, autosomal dominant 17, Epstein syndrome, Fechtner syndrome, May-Hegglin anomaly, Sebastian syndrome"""		Hereditary Macrothrombocytopenia, MYH9-associated																												.		.		Dom	yes		22	22q13.1	4627	"""myosin, heavy polypeptide 9, non-muscle"""	yes	L	.	.	.	0			c.706-1G>T						.						109.0	97.0	101.0					22																	36717867		2203	4300	6503	SO:0001630	splice_region_variant	4627	exon8	Familial Cancer Database	MYHIIA syndrome, incl. Fechtner Syndrome, FTNS, and May-Hegglin Anomaly, MHA	TTTGCCCTAAGTA		CCDS13927.1	22q13.1	2014-09-17	2006-09-29		ENSG00000100345	ENSG00000100345		"""Myosins / Myosin superfamily : Class II"""	7579	protein-coding gene	gene with protein product	"""nonmuscle myosin heavy chain II-A"""	160775	"""myosin, heavy polypeptide 9, non-muscle"""	DFNA17		1860190, 11023810	Standard	NM_002473		Approved	NMMHCA, NMHC-II-A, MHA, FTNS, EPSTS	uc003apg.3	P35579	OTTHUMG00000030429	ENST00000216181.5:c.706-1G>T	22.37:g.36717867C>A		Somatic	69	0		WXS	Illumina HiSeq	.	37	14	NM_002473	A8K6E4|O60805|Q60FE2|Q86T83	Splice_Site	SNP	ENST00000216181.5	37	CCDS13927.1	.	.	.	.	.	.	.	.	.	.	C	12.36	1.913688	0.33815	.	.	ENSG00000100345	ENST00000337818;ENST00000216181	.	.	.	5.22	5.22	0.72569	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.914	0.88943	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	MYH9	35047813	1.000000	0.71417	0.996000	0.52242	0.161000	0.22273	7.818000	0.86416	2.586000	0.87340	0.561000	0.74099	.	.		0.527	MYH9-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000259110.3	NM_002473	Intron
GLUD1P3	2749	hgsc.bcm.edu	37	10	75488004	75488004	+	RNA	SNP	A	A	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr10:75488004A>G	ENST00000507952.1	+	0	0				RP11-464F9.1_ENST00000399449.3_RNA|BMS1P4_ENST00000584747.1_RNA|RP11-574K11.28_ENST00000580790.1_RNA					glutamate dehydrogenase 1 pseudogene 3																		ATGTTTTGGTAAAAGCCACAC	0.428																																					.		.											.	.	.	0			.						.																																					729096	.			TTTGGTAAAAGCC	X66316		10q22.2	2012-04-17	2010-01-18	2010-01-18	ENSG00000250959	ENSG00000250959			4338	pseudogene	pseudogene			"""glutamate dehydrogenase pseudogene 3"", ""chromosome 10 open reading frame 102"""	GLUDP3, C10orf102		8486350	Standard	NR_048575		Approved	Em:AC022400.11	uc031pvx.1		OTTHUMG00000018477		10.37:g.75488004A>G		Somatic	119	0		WXS	Illumina HiSeq	.	54	15	.		RNA	SNP	ENST00000507952.1	37																																																																																				.		0.428	GLUD1P3-002	KNOWN	basic|exp_conf	processed_transcript	pseudogene	OTTHUMT00000416578.1		
RP11-690P14.4	0	hgsc.bcm.edu	37	10	97751346	97751346	+	Intron	SNP	G	G	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr10:97751346G>T	ENST00000475252.2	+	6	755				CC2D2B_ENST00000371198.2_Intron|ENTPD1-AS1_ENST00000452728.1_RNA|ENTPD1-AS1_ENST00000454638.1_RNA|ENTPD1-AS1_ENST00000416301.1_RNA|ENTPD1-AS1_ENST00000451364.1_RNA																							ATCATAACATGAAATATAATG	0.249																																					.		.											.	.	.	0			.						.																																			SO:0001627	intron_variant	0	.			TAACATGAAATAT																												ENST00000475252.2:c.516+128G>T	10.37:g.97751346G>T		Somatic	84	0		WXS	Illumina HiSeq	.	56	20	.		RNA	SNP	ENST00000475252.2	37																																																																																				.		0.249	RP11-690P14.4-001	KNOWN	mRNA_start_NF|cds_start_NF|basic|appris_principal|readthrough_transcript	nonsense_mediated_decay	protein_coding	OTTHUMT00000468152.1		
DENND4C	55667	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	9	19316816	19316816	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr9:19316816G>T	ENST00000380432.2	+	8	1111	c.1078G>T	c.(1078-1080)Gat>Tat	p.D360Y	DENND4C_ENST00000602925.1_Missense_Mutation_p.D596Y|DENND4C_ENST00000434457.2_Missense_Mutation_p.D596Y			Q5VZ89	DEN4C_HUMAN	DENN/MADD domain containing 4C	360	dDENN. {ECO:0000255|PROSITE- ProRule:PRU00306}.				cellular response to insulin stimulus (GO:0032869)|positive regulation of Rab GTPase activity (GO:0032851)|protein localization to plasma membrane (GO:0072659)|protein transport (GO:0015031)	cytosol (GO:0005829)|insulin-responsive compartment (GO:0032593)|plasma membrane (GO:0005886)|retromer complex (GO:0030904)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(1)|endometrium(8)|kidney(1)|large_intestine(7)|liver(2)|lung(13)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	40						CACAGCTGCTGATTCATTGTT	0.363																																					p.D596Y		.											.	.	.	0			c.G1786T						.						94.0	104.0	101.0					9																	19316816		2203	4300	6503	SO:0001583	missense	55667	exon12			GCTGCTGATTCAT	AK000693	CCDS6491.2, CCDS6491.3	9p22.1	2012-10-03	2006-01-27	2006-01-27	ENSG00000137145	ENSG00000137145		"""DENN/MADD domain containing"""	26079	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 55B"", ""chromosome 9 open reading frame 55"""	C9orf55B, C9orf55		12906859	Standard	NM_017925		Approved	FLJ20686, bA513M16.3	uc031tcw.1	Q5VZ89	OTTHUMG00000019627	ENST00000380432.2:c.1078G>T	9.37:g.19316816G>T	ENSP00000369797:p.Asp360Tyr	Somatic	42	0		WXS	Illumina HiSeq	.	28	13	NM_017925	A2A3R1|A2A3R2|A2A3R3|A2A3R9|Q6AI48|Q6ZUB3|Q8NCY7|Q9H6N4|Q9NUT1|Q9NWA5|Q9NWT3	Missense_Mutation	SNP	ENST00000380432.2	37		.	.	.	.	.	.	.	.	.	.	G	18.42	3.620991	0.66787	.	.	ENSG00000137145	ENST00000380437	.	.	.	5.13	5.13	0.70059	dDENN (3);	0.047414	0.85682	D	0.000000	T	0.75177	0.3814	L	0.47716	1.5	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.76854	-0.2805	9	0.72032	D	0.01	-20.6408	18.7716	0.91894	0.0:0.0:1.0:0.0	.	360	Q5VZ89	DEN4C_HUMAN	Y	360	.	ENSP00000369802:D360Y	D	+	1	0	DENND4C	19306816	1.000000	0.71417	0.990000	0.47175	0.994000	0.84299	4.515000	0.60489	2.672000	0.90937	0.460000	0.39030	GAT	.		0.363	DENND4C-201	KNOWN	basic	protein_coding	protein_coding		NM_017925	
AMBP	259	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	9	116840382	116840382	+	Silent	SNP	A	A	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr9:116840382A>G	ENST00000265132.3	-	1	370	c.108T>C	c.(106-108)aaT>aaC	p.N36N		NM_001633.3	NP_001624.1	P02760	AMBP_HUMAN	alpha-1-microglobulin/bikunin precursor	36					cell adhesion (GO:0007155)|female pregnancy (GO:0007565)|heme catabolic process (GO:0042167)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of immune response (GO:0050777)|negative regulation of JNK cascade (GO:0046329)|protein catabolic process (GO:0030163)|protein-chromophore linkage (GO:0018298)|viral process (GO:0016032)	blood microparticle (GO:0072562)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)	calcium channel inhibitor activity (GO:0019855)|calcium oxalate binding (GO:0046904)|heme binding (GO:0020037)|IgA binding (GO:0019862)|protein homodimerization activity (GO:0042803)|serine-type endopeptidase inhibitor activity (GO:0004867)|small molecule binding (GO:0036094)			breast(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(4)|skin(1)	11					Human Serum Albumin(DB00062)|Serum albumin iodonated(DB00064)	CCCGAGAGATATTGAAGTTTT	0.652																																					p.N36N		.											.	.	.	0			c.T108C						.						126.0	135.0	132.0					9																	116840382		2203	4300	6503	SO:0001819	synonymous_variant	259	exon1			AGAGATATTGAAG	X04494	CCDS6800.1	9q32-q33	2014-01-22			ENSG00000106927	ENSG00000106927		"""Lipocalins"""	453	protein-coding gene	gene with protein product	"""growth-inhibiting protein 19"", ""uristatin"", ""complex-forming glycoprotein heterogeneous in charge"", ""bikunin"", ""inter-alpha-trypsin inhibitor light chain"", ""protein HC"", ""uronic-acid-rich protein"", ""trypstatin"""	176870		ITI, ITIL		1708673, 1385302	Standard	NM_001633		Approved	UTI, HCP, EDC1, HI30, IATIL, ITILC	uc004bie.4	P02760	OTTHUMG00000020534	ENST00000265132.3:c.108T>C	9.37:g.116840382A>G		Somatic	36	0		WXS	Illumina HiSeq	.	19	9	NM_001633	P00977|P02759|P78491|Q2TU33|Q5TBD7|Q9UC58|Q9UDI8	Silent	SNP	ENST00000265132.3	37	CCDS6800.1																																																																																			.		0.652	AMBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053758.2	NM_001633	
ASPRV1	151516	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	2	70188309	70188309	+	Missense_Mutation	SNP	G	G	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr2:70188309G>A	ENST00000320256.4	-	1	1088	c.512C>T	c.(511-513)gCc>gTc	p.A171V	PCBP1-AS1_ENST00000419542.1_RNA|PCBP1-AS1_ENST00000457076.1_RNA|PCBP1-AS1_ENST00000596259.1_RNA|PCBP1-AS1_ENST00000418564.1_RNA|PCBP1-AS1_ENST00000413436.1_RNA|PCBP1-AS1_ENST00000435880.2_RNA	NM_152792.2	NP_690005.2			aspartic peptidase, retroviral-like 1											endometrium(3)|large_intestine(4)|lung(6)|ovary(1)	14						GACCCCAAAGGCCTTCAGGAG	0.577																																					p.A171V		.											.	.	.	0			c.C512T						.						42.0	45.0	44.0					2																	70188309		2203	4300	6503	SO:0001583	missense	151516	exon1			CCAAAGGCCTTCA	AK055994	CCDS1897.1	2p13.3	2008-02-20			ENSG00000244617	ENSG00000244617			26321	protein-coding gene	gene with protein product	"""Skin ASpartic Protease"""	611765				16098038, 16565508	Standard	NM_152792		Approved	Taps, SASPase, FLJ25084	uc002sfz.4	Q53RT3	OTTHUMG00000129647	ENST00000320256.4:c.512C>T	2.37:g.70188309G>A	ENSP00000315383:p.Ala171Val	Somatic	35	0		WXS	Illumina HiSeq	.	22	10	NM_152792		Missense_Mutation	SNP	ENST00000320256.4	37	CCDS1897.1	.	.	.	.	.	.	.	.	.	.	G	11.50	1.657994	0.29425	.	.	ENSG00000244617	ENST00000320256	T	0.50813	0.73	5.35	3.47	0.39725	.	0.911151	0.09078	N	0.851783	T	0.36580	0.0972	L	0.27053	0.805	0.09310	N	1	B	0.26935	0.164	B	0.25405	0.06	T	0.25222	-1.0138	10	0.34782	T	0.22	-1.6393	11.268	0.49122	0.0:0.0:0.6982:0.3018	.	171	Q53RT3	APRV1_HUMAN	V	171	ENSP00000315383:A171V	ENSP00000315383:A171V	A	-	2	0	ASPRV1	70041813	0.700000	0.27796	0.081000	0.20488	0.582000	0.36321	1.843000	0.39259	0.563000	0.29222	0.561000	0.74099	GCC	.		0.577	ASPRV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334161.1	NM_152792	
ATP7B	540	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	13	52539138	52539138	+	Missense_Mutation	SNP	T	T	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr13:52539138T>A	ENST00000242839.4	-	5	1895	c.1739A>T	c.(1738-1740)cAc>cTc	p.H580L	ATP7B_ENST00000542656.1_Intron|ATP7B_ENST00000400370.3_Intron|ATP7B_ENST00000344297.5_Missense_Mutation_p.H580L|ATP7B_ENST00000418097.2_Missense_Mutation_p.H580L|ATP7B_ENST00000482841.1_5'UTR|ATP7B_ENST00000400366.3_Missense_Mutation_p.H469L|ATP7B_ENST00000448424.2_Missense_Mutation_p.H580L	NM_000053.3	NP_000044.2	P35670	ATP7B_HUMAN	ATPase, Cu++ transporting, beta polypeptide	580	HMA 6. {ECO:0000255|PROSITE- ProRule:PRU00280}.				cellular copper ion homeostasis (GO:0006878)|cellular zinc ion homeostasis (GO:0006882)|copper ion import (GO:0015677)|copper ion transport (GO:0006825)|intracellular copper ion transport (GO:0015680)|ion transmembrane transport (GO:0034220)|lactation (GO:0007595)|response to copper ion (GO:0046688)|sequestering of calcium ion (GO:0051208)|transmembrane transport (GO:0055085)	Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|membrane (GO:0016020)|mitochondrion (GO:0005739)|trans-Golgi network (GO:0005802)	ATP binding (GO:0005524)|copper ion binding (GO:0005507)|copper-exporting ATPase activity (GO:0004008)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(7)|lung(23)|ovary(1)|prostate(3)|skin(4)|stomach(2)	55		Breast(56;0.000207)|Lung NSC(96;0.000845)|Prostate(109;0.0235)|Hepatocellular(98;0.065)|all_neural(104;0.19)		GBM - Glioblastoma multiforme(99;5.25e-08)	Carboplatin(DB00958)|Cisplatin(DB00515)|Oxaliplatin(DB00526)	CTCTATGTTGTGGACACAGGA	0.522									Wilson disease																												p.H580L		.											.	.	.	0			c.A1739T						.						90.0	92.0	92.0					13																	52539138		2060	4206	6266	SO:0001583	missense	540	exon5	Familial Cancer Database		ATGTTGTGGACAC	U11700	CCDS41892.1, CCDS45049.1, CCDS58293.1	13q14.3	2012-10-22	2005-11-29		ENSG00000123191	ENSG00000123191	3.6.3.4	"""ATPases / P-type"""	870	protein-coding gene	gene with protein product	"""Wilson disease"", ""copper pump 2"", ""copper-transporting ATPase 2"""	606882	"""ATPase, Cu++ transporting, beta polypeptide (Wilson disease)"""	WND		8298641, 8298639	Standard	NM_000053		Approved		uc001vfw.2	P35670	OTTHUMG00000017406	ENST00000242839.4:c.1739A>T	13.37:g.52539138T>A	ENSP00000242839:p.His580Leu	Somatic	103	0		WXS	Illumina HiSeq	.	75	26	NM_000053	Q16318|Q16319|Q4U3V3|Q59FJ9|Q5T7X7	Missense_Mutation	SNP	ENST00000242839.4	37	CCDS41892.1	.	.	.	.	.	.	.	.	.	.	T	34	5.312918	0.95655	.	.	ENSG00000123191	ENST00000242839;ENST00000400366;ENST00000344297;ENST00000448424;ENST00000418097	D;D;D;D;D	0.85411	-1.98;-1.98;-1.98;-1.98;-1.98	5.95	5.95	0.96441	Heavy metal-associated domain, HMA (3);Heavy metal-associated domain, copper ion-binding (1);Heavy-metal-associated, conserved site (1);	0.000000	0.85682	D	0.000000	D	0.87581	0.6213	N	0.21508	0.67	0.80722	D	1	D;D;D;D;D;D	0.89917	0.985;0.997;1.0;0.997;0.996;0.997	D;D;D;D;D;D	0.91635	0.971;0.943;0.999;0.955;0.943;0.985	D	0.88671	0.3195	10	0.52906	T	0.07	-23.8462	16.4237	0.83790	0.0:0.0:0.0:1.0	.	580;580;580;469;580;580	E7ET55;B7ZLR4;F5H748;P35670-3;P35670-2;P35670	.;.;.;.;.;ATP7B_HUMAN	L	580;469;580;580;580	ENSP00000242839:H580L;ENSP00000383217:H469L;ENSP00000342559:H580L;ENSP00000416738:H580L;ENSP00000393343:H580L	ENSP00000242839:H580L	H	-	2	0	ATP7B	51437139	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.649000	0.83500	2.279000	0.76181	0.533000	0.62120	CAC	.		0.522	ATP7B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045981.1	NM_000053	
ZNF91	7644	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	19	23544752	23544752	+	Missense_Mutation	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr19:23544752A>C	ENST00000300619.7	-	4	1234	c.1029T>G	c.(1027-1029)atT>atG	p.I343M	ZNF91_ENST00000599743.1_Intron|ZNF91_ENST00000397082.2_Missense_Mutation_p.I311M	NM_003430.2	NP_003421.2	Q05481	ZNF91_HUMAN	zinc finger protein 91	343					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)						all_lung(12;0.0349)|Lung NSC(12;0.0538)|all_epithelial(12;0.0611)				CTCCAGTATGAATTCTCTTAT	0.368																																					p.I343M		.											.	.	.	0			c.T1029G						.						55.0	58.0	57.0					19																	23544752		2060	4225	6285	SO:0001583	missense	7644	exon4			AGTATGAATTCTC	M61871	CCDS42541.1, CCDS74322.1	19p12	2014-02-04	2006-05-12		ENSG00000167232	ENSG00000167232		"""Zinc fingers, C2H2-type"", ""-"""	13166	protein-coding gene	gene with protein product		603971	"""zinc finger protein 91 (HPF7, HTF10)"""			2023909, 2505992	Standard	XR_430154		Approved	HPF7, HTF10	uc002nre.3	Q05481	OTTHUMG00000183268	ENST00000300619.7:c.1029T>G	19.37:g.23544752A>C	ENSP00000300619:p.Ile343Met	Somatic	67	0		WXS	Illumina HiSeq	.	33	14	NM_003430	A8K5E1|B7Z6G6	Missense_Mutation	SNP	ENST00000300619.7	37	CCDS42541.1	.	.	.	.	.	.	.	.	.	.	A	7.961	0.747075	0.15710	.	.	ENSG00000167232	ENST00000300619;ENST00000397082	T;T	0.01025	5.43;5.43	2.15	-4.3	0.03710	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.02193	0.0068	L	0.52011	1.625	0.09310	N	0.999998	D;B	0.89917	1.0;0.051	D;B	0.79784	0.993;0.053	T	0.19877	-1.0292	9	0.87932	D	0	.	1.5581	0.02589	0.2001:0.3117:0.3335:0.1547	.	311;343	Q05481-2;Q05481	.;ZNF91_HUMAN	M	343;311	ENSP00000300619:I343M;ENSP00000380272:I311M	ENSP00000300619:I343M	I	-	3	3	ZNF91	23336592	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-1.217000	0.02979	-1.928000	0.01059	-1.767000	0.00664	ATT	.		0.368	ZNF91-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465891.1	NM_003430	
PLGLA	285189	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	2	107007431	107007431	+	RNA	SNP	G	G	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr2:107007431G>C	ENST00000484422.1	+	0	280							Q15195	PLGA_HUMAN	plasminogen-like A (pseudogene)							extracellular region (GO:0005576)											ACAAAAAATGGCATCACCTGT	0.448																																					.		.											.	.	.	0			.						.																																					285189	.			AAAATGGCATCAC	U67178, M86872, M86873		2q12.2	2013-03-28	2013-03-28	2008-02-07	ENSG00000240935	ENSG00000240935			9074	pseudogene	pseudogene		612212	"""plasminogen pseudogene 2"", ""plasminogen-like A1"", ""plasminogen-like A"""	PLGP2, PLGLA1		1986355	Standard	NR_003506		Approved		uc002tdp.4	Q15195	OTTHUMG00000153188		2.37:g.107007431G>C		Somatic	411	0		WXS	Illumina HiSeq	.	229	68	.		RNA	SNP	ENST00000484422.1	37																																																																																				.		0.448	PLGLA-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000331219.1	NR_003506.2	
MLF1	4291	hgsc.bcm.edu	37	3	158315944	158315944	+	Nonsense_Mutation	SNP	G	G	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr3:158315944G>T	ENST00000355893.5	+	4	493	c.355G>T	c.(355-357)Gaa>Taa	p.E119*	MLF1_ENST00000471745.1_Nonsense_Mutation_p.E109*|MLF1_ENST00000478894.2_Nonsense_Mutation_p.E109*|MLF1_ENST00000469452.1_Intron|MLF1_ENST00000392822.3_Nonsense_Mutation_p.E150*|MLF1_ENST00000359117.5_Nonsense_Mutation_p.E94*|MLF1_ENST00000482628.1_Nonsense_Mutation_p.E94*|MLF1_ENST00000497004.1_3'UTR|MLF1_ENST00000484955.1_Nonsense_Mutation_p.E94*	NM_022443.4	NP_071888.1	P58340	MLF1_HUMAN	myeloid leukemia factor 1	119	Interaction with COPS3.				cell cycle arrest (GO:0007050)|myeloid progenitor cell differentiation (GO:0002318)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|protein domain specific binding (GO:0019904)			large_intestine(3)	3		Melanoma(1037;0.000458)|Prostate(884;0.0235)|all_neural(597;0.0299)	Lung(72;0.00199)|LUSC - Lung squamous cell carcinoma(72;0.00256)			AATAGGAGATGAACCGCCAAA	0.383			T	NPM1	AML																																p.E150X		.		Dom	yes		3	3q25.1	4291	myeloid leukemia factor 1		L	.	.	.	0			c.G448T						.						78.0	80.0	79.0					3																	158315944		2203	4300	6503	SO:0001587	stop_gained	4291	exon6			GGAGATGAACCGC	L49054	CCDS3182.1, CCDS46945.1, CCDS56286.1, CCDS56287.1, CCDS56288.1	3q25	2008-07-18			ENSG00000178053	ENSG00000178053			7125	protein-coding gene	gene with protein product	"""myeloid leukemia factor 1 variant 1"", ""myeloid leukemia factor 1 variant 2"", ""myeloid leukemia factor 1 variant 3"""	601402				8570204	Standard	NM_022443		Approved		uc003fcb.3	P58340	OTTHUMG00000158775	ENST00000355893.5:c.355G>T	3.37:g.158315944G>T	ENSP00000348157:p.Glu119*	Somatic	93	0		WXS	Illumina HiSeq	.	91	4	NM_001195432	E9PEU9|Q2TLE3|Q2TLE5|Q8N8F8|Q96MH1	Nonsense_Mutation	SNP	ENST00000355893.5	37	CCDS3182.1	.	.	.	.	.	.	.	.	.	.	G	36	5.884057	0.97062	.	.	ENSG00000178053	ENST00000491767;ENST00000355893;ENST00000484955;ENST00000359117;ENST00000498592;ENST00000477042;ENST00000471745;ENST00000482628;ENST00000478894;ENST00000392822;ENST00000466246	.	.	.	5.44	5.44	0.79542	.	0.059885	0.64402	D	0.000004	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.56958	D	0.05	-30.0223	19.2725	0.94016	0.0:0.0:1.0:0.0	.	.	.	.	X	45;119;94;94;74;109;109;94;109;150;134	.	ENSP00000348157:E119X	E	+	1	0	MLF1	159798638	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	8.921000	0.92784	2.561000	0.86390	0.563000	0.77884	GAA	.		0.383	MLF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352164.3	NM_022443	
AHNAK	79026	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	11	62299800	62299800	+	Missense_Mutation	SNP	T	T	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr11:62299800T>A	ENST00000378024.4	-	5	2363	c.2089A>T	c.(2089-2091)Atc>Ttc	p.I697F	AHNAK_ENST00000257247.7_Intron|AHNAK_ENST00000530124.1_Intron	NM_001620.1	NP_001611.1	Q09666	AHNK_HUMAN	AHNAK nucleoprotein	697					protein oligomerization (GO:0051259)|regulation of RNA splicing (GO:0043484)|regulation of voltage-gated calcium channel activity (GO:1901385)	actin cytoskeleton (GO:0015629)|cell-cell contact zone (GO:0044291)|costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|vesicle (GO:0031982)	poly(A) RNA binding (GO:0044822)|S100 protein binding (GO:0044548)|structural molecule activity conferring elasticity (GO:0097493)			NS(3)|autonomic_ganglia(1)|breast(10)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(33)|large_intestine(40)|liver(1)|lung(108)|ovary(13)|pancreas(4)|prostate(5)|skin(16)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	268		Melanoma(852;0.155)				GGCATGGAGATCTTTGGTGTC	0.478																																					p.I697F		.											.	.	.	0			c.A2089T						.						204.0	189.0	194.0					11																	62299800		2202	4299	6501	SO:0001583	missense	79026	exon5			TGGAGATCTTTGG	M80899	CCDS31584.1, CCDS44625.1	11q12-q13	2008-02-05	2007-03-30		ENSG00000124942	ENSG00000124942			347	protein-coding gene	gene with protein product	"""desmoyokin"""	103390	"""AHNAK nucleoprotein (desmoyokin)"""			7987395, 12153988	Standard	NM_024060		Approved	MGC5395	uc001ntl.3	Q09666	OTTHUMG00000167558	ENST00000378024.4:c.2089A>T	11.37:g.62299800T>A	ENSP00000367263:p.Ile697Phe	Somatic	48	0		WXS	Illumina HiSeq	.	28	15	NM_001620	A1A586	Missense_Mutation	SNP	ENST00000378024.4	37	CCDS31584.1	.	.	.	.	.	.	.	.	.	.	T	11.52	1.663885	0.29515	.	.	ENSG00000124942	ENST00000378024	T	0.01258	5.09	4.75	1.13	0.20643	.	.	.	.	.	T	0.02571	0.0078	M	0.68952	2.095	0.31294	N	0.689092	P	0.36789	0.57	B	0.41571	0.36	T	0.17776	-1.0358	9	0.52906	T	0.07	-4.4465	5.7706	0.18251	0.0:0.1529:0.142:0.7051	.	697	Q09666	AHNK_HUMAN	F	697	ENSP00000367263:I697F	ENSP00000367263:I697F	I	-	1	0	AHNAK	62056376	0.232000	0.23762	0.988000	0.46212	0.662000	0.39071	0.501000	0.22578	0.030000	0.15379	-0.475000	0.04921	ATC	.		0.478	AHNAK-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395572.1	NM_024060	
GUSB	2990	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	7	65425890	65425890	+	Silent	SNP	A	A	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr7:65425890A>G	ENST00000304895.4	-	12	2080	c.1950T>C	c.(1948-1950)ttT>ttC	p.F650F	GUSB_ENST00000421103.1_Silent_p.F504F|GUSB_ENST00000345660.6_Silent_p.F599F	NM_000181.3	NP_000172.2	P08236	BGLR_HUMAN	glucuronidase, beta	650					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan catabolic process (GO:0030214)|hyaluronan metabolic process (GO:0030212)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)	beta-glucuronidase activity (GO:0004566)			breast(1)|cervix(2)|kidney(2)|large_intestine(4)|lung(10)|skin(1)	20						TTGCTCAAGTAAACAGGCTGT	0.522																																					p.F650F		.											.	.	.	0			c.T1950C						.						219.0	188.0	199.0					7																	65425890		2203	4300	6503	SO:0001819	synonymous_variant	2990	exon12			TCAAGTAAACAGG	M15182	CCDS5530.1, CCDS64665.1	7q11.21	2012-10-02			ENSG00000169919	ENSG00000169919	3.2.1.31		4696	protein-coding gene	gene with protein product		611499				3468507	Standard	NM_000181		Approved		uc003tun.3	P08236	OTTHUMG00000023735	ENST00000304895.4:c.1950T>C	7.37:g.65425890A>G		Somatic	107	0		WXS	Illumina HiSeq	.	59	30	NM_000181	B4E1F6|E9PCV0|Q549U0|Q96CL9	Silent	SNP	ENST00000304895.4	37	CCDS5530.1																																																																																			.		0.522	GUSB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251637.3	NM_000181	
TMC4	147798	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	19	54672203	54672203	+	Missense_Mutation	SNP	T	T	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr19:54672203T>A	ENST00000376591.4	-	4	795	c.664A>T	c.(664-666)Acc>Tcc	p.T222S	TMC4_ENST00000476013.2_5'UTR|TMC4_ENST00000301187.4_Missense_Mutation_p.T216S	NM_001145303.1|NM_144686.2	NP_001138775|NP_653287.2	Q7Z404	TMC4_HUMAN	transmembrane channel-like 4	222					ion transport (GO:0006811)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				breast(2)|endometrium(7)|large_intestine(4)|lung(6)|pancreas(1)|skin(1)|urinary_tract(1)	22	all_cancers(19;0.0065)|all_epithelial(19;0.00348)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)					AAGAGCTGGGTGGCAAAGGTG	0.662											OREG0025670	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.T222S		.											.	.	.	0			c.A664T						.						19.0	16.0	17.0					19																	54672203		2058	4051	6109	SO:0001583	missense	147798	exon4			GCTGGGTGGCAAA	AY236492	CCDS12882.1, CCDS46174.1	19q13.42	2008-02-05			ENSG00000167608	ENSG00000167608			22998	protein-coding gene	gene with protein product						12812529, 12906855	Standard	XM_005277069		Approved		uc010erf.3	Q7Z404	OTTHUMG00000066485	ENST00000376591.4:c.664A>T	19.37:g.54672203T>A	ENSP00000365776:p.Thr222Ser	Somatic	68	0	1002	WXS	Illumina HiSeq	.	39	13	NM_001145303	Q7Z5M3|Q8N5E4|Q8TBS7	Missense_Mutation	SNP	ENST00000376591.4	37	CCDS46174.1	.	.	.	.	.	.	.	.	.	.	T	2.214	-0.380088	0.05000	.	.	ENSG00000167608	ENST00000301187;ENST00000376591;ENST00000446291	T;T;T	0.45276	0.9;0.9;0.9	4.03	-2.24	0.06909	.	0.525281	0.18785	N	0.131215	T	0.18593	0.0446	L	0.31526	0.94	0.09310	N	0.999996	B;B	0.18863	0.031;0.004	B;B	0.14578	0.011;0.006	T	0.31392	-0.9945	10	0.02654	T	1	-7.0421	3.455	0.07512	0.4455:0.2861:0.0:0.2683	.	222;216	Q7Z404;Q7Z404-1	TMC4_HUMAN;.	S	216;222;126	ENSP00000301187:T216S;ENSP00000365776:T222S;ENSP00000416444:T126S	ENSP00000301187:T216S	T	-	1	0	TMC4	59364015	0.001000	0.12720	0.278000	0.24718	0.527000	0.34593	-0.438000	0.06905	-0.538000	0.06281	-0.379000	0.06801	ACC	.		0.662	TMC4-011	NOVEL	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000156164.2		
ZSCAN32	54925	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	16	3434880	3434880	+	Silent	SNP	A	A	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr16:3434880A>G	ENST00000396852.4	-	6	1120	c.813T>C	c.(811-813)tcT>tcC	p.S271S	ZSCAN32_ENST00000422427.2_Silent_p.S59S|ZSCAN32_ENST00000304926.3_Silent_p.S59S|ZSCAN32_ENST00000396846.3_Silent_p.S271S|ZSCAN32_ENST00000573830.1_5'UTR|ZSCAN32_ENST00000439568.2_5'UTR|ZSCAN32_ENST00000574940.1_Silent_p.S271S	NM_001284527.1|NM_001284529.1	NP_001271456.1|NP_001271458.1	Q9NX65	ZSC32_HUMAN	zinc finger and SCAN domain containing 32	271	KRAB.				regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)										CATAAAATTGAGAACTACTAA	0.507																																					p.S59S		.											.	.	.	0			c.T177C						.						73.0	79.0	77.0					16																	3434880		2197	4300	6497	SO:0001819	synonymous_variant	54925	exon5			AAATTGAGAACTA	AK000424	CCDS10503.1, CCDS66920.1, CCDS66921.1	16p13.3	2013-01-09	2013-01-09	2013-01-09	ENSG00000140987	ENSG00000140987		"""-"", ""Zinc fingers, C2H2-type"""	20812	protein-coding gene	gene with protein product			"""zinc finger protein 434"""	ZNF434			Standard	XM_005255402		Approved	FLJ20417	uc002cux.4	Q9NX65	OTTHUMG00000129357	ENST00000396852.4:c.813T>C	16.37:g.3434880A>G		Somatic	34	0		WXS	Illumina HiSeq	.	23	12	NM_017810	B4DWL5|C9JB03|Q6WMU8|Q7Z6G2|Q8NFX8|Q9BU74	Silent	SNP	ENST00000396852.4	37																																																																																				.		0.507	ZSCAN32-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000251509.2	NM_017810	
MAGED1	9500	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	X	51644872	51644872	+	Missense_Mutation	SNP	C	C	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chrX:51644872C>A	ENST00000375722.1	+	12	2435	c.2183C>A	c.(2182-2184)tCc>tAc	p.S728Y	MAGED1_ENST00000375772.3_Missense_Mutation_p.S728Y|MAGED1_ENST00000494718.1_3'UTR|MAGED1_ENST00000326587.7_Missense_Mutation_p.S728Y|MAGED1_ENST00000375695.2_Missense_Mutation_p.S784Y			Q9Y5V3	MAGD1_HUMAN	melanoma antigen family D, 1	728					apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|circadian regulation of gene expression (GO:0032922)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of apoptotic process (GO:0042981)|regulation of circadian rhythm (GO:0042752)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	transcription coactivator activity (GO:0003713)			breast(1)|endometrium(4)|large_intestine(10)|lung(13)|ovary(3)|upper_aerodigestive_tract(1)	32	Ovarian(276;0.236)					GATCCCTGGTCCAGAATTCCA	0.542										Multiple Myeloma(10;0.10)																											p.S784Y		.											.	.	.	0			c.C2351A						.						97.0	94.0	95.0					X																	51644872		2203	4300	6503	SO:0001583	missense	9500	exon13			CCTGGTCCAGAAT	AF124440	CCDS14337.1, CCDS35279.1	Xp11.23	2008-08-01			ENSG00000179222	ENSG00000179222			6813	protein-coding gene	gene with protein product		300224				10409427	Standard	NM_006986		Approved	NRAGE, DLXIN-1	uc004dpn.3	Q9Y5V3	OTTHUMG00000021540	ENST00000375722.1:c.2183C>A	X.37:g.51644872C>A	ENSP00000364874:p.Ser728Tyr	Somatic	36	0		WXS	Illumina HiSeq	.	28	27	NM_001005333	Q5VSH6|Q8IZ84|Q8WY92|Q9H352|Q9HBT4|Q9UF36	Missense_Mutation	SNP	ENST00000375722.1	37	CCDS14337.1	.	.	.	.	.	.	.	.	.	.	C	13.50	2.254694	0.39896	.	.	ENSG00000179222	ENST00000375772;ENST00000375722;ENST00000326587;ENST00000375695	T;T;T;T	0.04360	3.69;3.69;3.69;3.64	4.09	4.09	0.47781	.	0.163615	0.29565	N	0.011786	T	0.08223	0.0205	N	0.19112	0.55	0.34291	D	0.68321	D;D	0.64830	0.994;0.978	P;P	0.59424	0.857;0.675	T	0.16928	-1.0386	10	0.87932	D	0	.	10.6836	0.45830	0.0:1.0:0.0:0.0	.	784;728	Q9Y5V3-2;Q9Y5V3	.;MAGD1_HUMAN	Y	728;728;728;784	ENSP00000364927:S728Y;ENSP00000364874:S728Y;ENSP00000325333:S728Y;ENSP00000364847:S784Y	ENSP00000325333:S728Y	S	+	2	0	MAGED1	51661612	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.833000	0.48159	2.284000	0.76573	0.513000	0.50165	TCC	.		0.542	MAGED1-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056593.1	NM_001005332	
TMEM184A	202915	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	7	1587391	1587391	+	Silent	SNP	C	C	T	rs548246825		TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr7:1587391C>T	ENST00000297477.5	-	8	1315	c.999G>A	c.(997-999)aaG>aaA	p.K333K	TMEM184A_ENST00000449955.1_5'Flank	NM_001097620.1	NP_001091089.1	Q6ZMB5	T184A_HUMAN	transmembrane protein 184A	333					germ-line sex determination (GO:0018992)|regulation of protein localization (GO:0032880)|regulation of secretion (GO:0051046)	early endosome membrane (GO:0031901)|integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(1)|lung(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	12		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0178)|OV - Ovarian serous cystadenocarcinoma(56;5.88e-15)		GTGAATTCTCCTTCTTCTCTG	0.637																																					p.K333K		.											.	.	.	0			c.G999A						.						48.0	56.0	54.0					7																	1587391		2131	4258	6389	SO:0001819	synonymous_variant	202915	exon8			ATTCTCCTTCTTC		CCDS43537.1	7p22.3	2008-05-02			ENSG00000164855	ENSG00000164855			28797	protein-coding gene	gene with protein product						12477932	Standard	NM_001097620		Approved	MGC9712	uc003skv.4	Q6ZMB5	OTTHUMG00000119025	ENST00000297477.5:c.999G>A	7.37:g.1587391C>T		Somatic	80	0		WXS	Illumina HiSeq	.	48	23	NM_001097620	Q8TBQ6	Silent	SNP	ENST00000297477.5	37	CCDS43537.1																																																																																			.		0.637	TMEM184A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239229.4	NM_152689	
TCP11L1	55346	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	11	33094146	33094146	+	Missense_Mutation	SNP	G	G	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr11:33094146G>A	ENST00000334274.4	+	10	1854	c.1454G>A	c.(1453-1455)cGc>cAc	p.R485H	TCP11L1_ENST00000324357.9_Missense_Mutation_p.R264H|TCP11L1_ENST00000531632.2_Missense_Mutation_p.R485H|TCP11L1_ENST00000432887.1_Missense_Mutation_p.R485H	NM_018393.3	NP_060863.3	Q9NUJ3	T11L1_HUMAN	t-complex 11, testis-specific-like 1	485						microtubule (GO:0005874)				kidney(1)|liver(2)|lung(2)|skin(1)	6						AAATTTGCTCGCCTGGTCAAC	0.512																																					p.R485H		.											.	.	.	0			c.G1454A						.						189.0	170.0	177.0					11																	33094146		2202	4298	6500	SO:0001583	missense	55346	exon10			TTGCTCGCCTGGT	BC041696	CCDS7882.1	11p13	2014-08-12	2012-09-20		ENSG00000176148	ENSG00000176148			25655	protein-coding gene	gene with protein product			"""t-complex 11 (mouse) like 1"""				Standard	NM_001145541		Approved	FLJ11336	uc010rei.2	Q9NUJ3	OTTHUMG00000165303	ENST00000334274.4:c.1454G>A	11.37:g.33094146G>A	ENSP00000335595:p.Arg485His	Somatic	67	0		WXS	Illumina HiSeq	.	45	10	NM_001145541	D3DR01|Q8IVX4	Missense_Mutation	SNP	ENST00000334274.4	37	CCDS7882.1	.	.	.	.	.	.	.	.	.	.	G	32	5.180621	0.94846	.	.	ENSG00000176148	ENST00000334274;ENST00000531632;ENST00000432887;ENST00000324357	T;T;T;T	0.11930	2.73;2.73;2.73;2.73	5.41	5.41	0.78517	.	0.000000	0.85682	D	0.000000	T	0.45875	0.1364	M	0.86953	2.85	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.51156	-0.8741	10	0.59425	D	0.04	-10.7262	19.1776	0.93609	0.0:0.0:1.0:0.0	.	485	Q9NUJ3	T11L1_HUMAN	H	485;485;485;264	ENSP00000335595:R485H;ENSP00000433067:R485H;ENSP00000395070:R485H;ENSP00000316279:R264H	ENSP00000316279:R264H	R	+	2	0	TCP11L1	33050722	1.000000	0.71417	0.997000	0.53966	0.965000	0.64279	9.387000	0.97232	2.530000	0.85305	0.313000	0.20887	CGC	.		0.512	TCP11L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383377.4	NM_018393	
ZNF529	57711	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	19	37038201	37038201	+	Missense_Mutation	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr19:37038201T>G	ENST00000591340.1	-	5	1417	c.1259A>C	c.(1258-1260)aAa>aCa	p.K420T	ZNF529_ENST00000334116.7_Missense_Mutation_p.K315T	NM_020951.4	NP_066002.3	Q6P280	ZN529_HUMAN	zinc finger protein 529	420					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(1)	1	Esophageal squamous(110;0.198)					TTTATAGGGTTTTTCACCAGT	0.363																																					p.K420T		.											.	.	.	0			c.A1259C						.						99.0	110.0	106.0					19																	37038201		2143	4282	6425	SO:0001583	missense	57711	exon6			TAGGGTTTTTCAC	AK025110	CCDS54256.1	19q13.13	2014-08-22			ENSG00000186020	ENSG00000186020		"""Zinc fingers, C2H2-type"", ""-"""	29328	protein-coding gene	gene with protein product						10997877	Standard	NM_020951		Approved	KIAA1615	uc002oeh.4	Q6P280	OTTHUMG00000180714	ENST00000591340.1:c.1259A>C	19.37:g.37038201T>G	ENSP00000465578:p.Lys420Thr	Somatic	69	0		WXS	Illumina HiSeq	.	20	9	NM_001145649	K7EKE1|Q9H731|Q9HCF7	Missense_Mutation	SNP	ENST00000591340.1	37	CCDS54256.1	.	.	.	.	.	.	.	.	.	.	T	15.87	2.959860	0.53400	.	.	ENSG00000186020	ENST00000334116	.	.	.	3.19	2.15	0.27550	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.65386	0.2686	M	0.80746	2.51	0.26294	N	0.978085	D;D	0.89917	0.997;1.0	D;D	0.72982	0.94;0.979	T	0.53920	-0.8370	8	0.87932	D	0	.	7.123	0.25456	0.0:0.1183:0.0:0.8817	.	315;387	Q6P280-2;Q6P280	.;ZN529_HUMAN	T	420	.	ENSP00000334695:K420T	K	-	2	0	ZNF529	41730041	0.003000	0.15002	0.991000	0.47740	0.988000	0.76386	0.199000	0.17237	0.315000	0.23110	0.482000	0.46254	AAA	.		0.363	ZNF529-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452730.1	NM_020951	
WHSC1L1	54904	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	8	38205356	38205356	+	Missense_Mutation	SNP	A	A	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr8:38205356A>G	ENST00000317025.8	-	2	851	c.334T>C	c.(334-336)Tat>Cat	p.Y112H	WHSC1L1_ENST00000316985.3_Missense_Mutation_p.Y112H|WHSC1L1_ENST00000527502.1_Missense_Mutation_p.Y112H|WHSC1L1_ENST00000433384.2_Missense_Mutation_p.Y112H	NM_023034.1	NP_075447.1	Q9BZ95	NSD3_HUMAN	Wolf-Hirschhorn syndrome candidate 1-like 1	112					histone lysine methylation (GO:0034968)|histone methylation (GO:0016571)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(3)|kidney(3)|large_intestine(2)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	24	Colorectal(12;0.000442)|Esophageal squamous(3;0.0725)	all_lung(54;0.00787)|Lung NSC(58;0.0295)|Hepatocellular(245;0.065)	Epithelial(3;3.12e-43)|all cancers(3;1.72e-38)|BRCA - Breast invasive adenocarcinoma(5;2.84e-27)|LUSC - Lung squamous cell carcinoma(2;2.79e-25)|Lung(2;5.03e-23)|COAD - Colon adenocarcinoma(9;0.0511)			TCTGAATGATAATAGTCAGTG	0.428			T	NUP98	AML																																p.Y112H		.		Dom	yes		8	8p12	54904	Wolf-Hirschhorn syndrome candidate 1-like 1 (NSD3)		L	.	.	.	0			c.T334C						.						136.0	134.0	134.0					8																	38205356		2203	4300	6503	SO:0001583	missense	54904	exon2			AATGATAATAGTC	AF332469	CCDS6105.1, CCDS43729.1	8p11.2	2013-05-20			ENSG00000147548	ENSG00000147548			12767	protein-coding gene	gene with protein product		607083				10802047, 23269674	Standard	NM_023034		Approved	FLJ20353, NSD3	uc003xli.3	Q9BZ95		ENST00000317025.8:c.334T>C	8.37:g.38205356A>G	ENSP00000313983:p.Tyr112His	Somatic	96	0		WXS	Illumina HiSeq	.	68	28	NM_017778	B7ZL11|D3DSX1|Q1RMD3|Q3B796|Q6ZSA5|Q9BYU8|Q9BYU9|Q9H2M8|Q9H9W9|Q9NXA6	Missense_Mutation	SNP	ENST00000317025.8	37	CCDS43729.1	.	.	.	.	.	.	.	.	.	.	A	21.2	4.112321	0.77210	.	.	ENSG00000147548	ENST00000433384;ENST00000317025;ENST00000527502;ENST00000316985;ENST00000529223	D;D;D;T;T	0.95518	-3.71;-3.73;-3.73;-0.27;0.75	5.69	5.69	0.88448	.	0.000000	0.44097	U	0.000497	D	0.96765	0.8944	L	0.54323	1.7	0.49687	D	0.999813	D;D;D;D	0.71674	0.991;0.995;0.998;0.991	P;P;D;P	0.68192	0.77;0.885;0.956;0.77	D	0.97338	0.9955	10	0.72032	D	0.01	.	15.9429	0.79771	1.0:0.0:0.0:0.0	.	112;112;112;112	B7ZL11;Q9BZ95-2;Q9BZ95-3;Q9BZ95	.;.;.;NSD3_HUMAN	H	112	ENSP00000393284:Y112H;ENSP00000313983:Y112H;ENSP00000434730:Y112H;ENSP00000313410:Y112H;ENSP00000435422:Y112H	ENSP00000313410:Y112H	Y	-	1	0	WHSC1L1	38324513	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.009000	0.70745	2.147000	0.66899	0.533000	0.62120	TAT	.		0.428	WHSC1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381924.3	NM_023034	
RGS3	5998	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	9	116356551	116356551	+	Intron	SNP	A	A	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr9:116356551A>G	ENST00000374140.2	+	23	3289				RGS3_ENST00000374134.3_Intron|RGS3_ENST00000462143.1_Intron|RGS3_ENST00000343817.5_Intron|RGS3_ENST00000462403.1_Missense_Mutation_p.T118A|RGS3_ENST00000394646.3_Intron|RGS3_ENST00000350696.5_Intron|RGS3_ENST00000342620.5_Intron	NM_001282923.1|NM_144488.4	NP_001269852.1|NP_652759.3	P49796	RGS3_HUMAN	regulator of G-protein signaling 3						inactivation of MAPK activity (GO:0000188)|positive regulation of GTPase activity (GO:0043547)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)			cervix(1)|endometrium(3)|kidney(5)|large_intestine(11)|lung(22)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	48						GGGGGGCCCTACAGAGATGCT	0.657																																					p.T118A		.											.	.	.	0			c.A352G						.						37.0	45.0	43.0					9																	116356551		2201	4298	6499	SO:0001627	intron_variant	5998	exon1			GGCCCTACAGAGA	AF006610	CCDS6797.1, CCDS6798.1, CCDS35113.1, CCDS35114.1, CCDS43869.1, CCDS65111.1	9q32	2008-02-05	2007-08-14		ENSG00000138835	ENSG00000138835		"""Regulators of G-protein signaling"""	9999	protein-coding gene	gene with protein product		602189	"""regulator of G-protein signalling 3"""			8602223, 11034339	Standard	NM_001276260		Approved	C2PA, FLJ20370, PDZ-RGS3	uc004bhq.4	P49796	OTTHUMG00000021048	ENST00000374140.2:c.3081-159A>G	9.37:g.116356551A>G		Somatic	17	0		WXS	Illumina HiSeq	.	14	6	NM_144489	A6NHA0|A8K0V1|B3KUB2|Q5VXB8|Q5VXC1|Q5VZ05|Q5VZ06|Q6ZRM5|Q8IUQ1|Q8NC47|Q8NFN4|Q8NFN5|Q8NFN6|Q8TD59|Q8TD68|Q8WV02|Q8WXA0	Missense_Mutation	SNP	ENST00000374140.2	37	CCDS43869.1	.	.	.	.	.	.	.	.	.	.	A	15.39	2.820467	0.50633	.	.	ENSG00000138835	ENST00000462403	T	0.57595	0.39	5.23	-9.78	0.00496	.	.	.	.	.	T	0.16471	0.0396	N	0.02011	-0.69	0.22412	N	0.999129	B	0.02656	0.0	B	0.01281	0.0	T	0.11060	-1.0603	9	0.35671	T	0.21	.	1.816	0.03100	0.1717:0.2137:0.3717:0.2429	.	118	Q5VZ06	.	A	118	ENSP00000436168:T118A	ENSP00000436168:T118A	T	+	1	0	RGS3	115396372	0.000000	0.05858	0.119000	0.21687	0.961000	0.63080	-0.857000	0.04286	-1.116000	0.02969	0.456000	0.33151	ACA	.		0.657	RGS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055561.3	NM_017790	
DRG2	1819	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	17	18009784	18009784	+	Missense_Mutation	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr17:18009784A>C	ENST00000225729.3	+	12	1130	c.992A>C	c.(991-993)aAg>aCg	p.K331T	MYO15A_ENST00000205890.5_5'Flank|DRG2_ENST00000583355.1_Missense_Mutation_p.Q137H|DRG2_ENST00000395726.4_Splice_Site_p.K331T	NM_001388.4	NP_001379.1	P55039	DRG2_HUMAN	developmentally regulated GTP binding protein 2	331					signal transduction (GO:0007165)	cytoplasm (GO:0005737)|membrane (GO:0016020)|mitochondrion (GO:0005739)	GTP binding (GO:0005525)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(3)|ovary(1)|prostate(1)|skin(1)|urinary_tract(2)	14	all_neural(463;0.228)					AGCCAGTTCAAGTACGCCCTG	0.597																																					p.K331T		.											.	.	.	0			c.A992C						.						90.0	79.0	83.0					17																	18009784		2203	4300	6503	SO:0001583	missense	1819	exon12			AGTTCAAGTACGC	X80754	CCDS11191.1	17p13-p12	2008-07-18	2001-11-28		ENSG00000108591	ENSG00000108591			3030	protein-coding gene	gene with protein product		602986	"""developmentally regulated GTP-binding protein 2"""			9605870, 7929244	Standard	NM_001388		Approved		uc002gsh.2	P55039	OTTHUMG00000059399	ENST00000225729.3:c.992A>C	17.37:g.18009784A>C	ENSP00000225729:p.Lys331Thr	Somatic	41	0		WXS	Illumina HiSeq	.	20	6	NM_001388	B2R8G5|Q53Y50|Q9BWB2	Missense_Mutation	SNP	ENST00000225729.3	37	CCDS11191.1	.	.	.	.	.	.	.	.	.	.	A	23.1	4.380489	0.82792	.	.	ENSG00000108591	ENST00000395726;ENST00000225729	T;T	0.32988	1.43;1.61	5.29	4.21	0.49690	TGS-like (1);TGS (1);	0.000000	0.85682	D	0.000000	T	0.66577	0.2803	H	0.96916	3.905	0.28888	N	0.894033	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.70000	-0.4992	10	0.87932	D	0	-7.7015	10.6302	0.45532	0.9247:0.0:0.0753:0.0	.	331;331	A8MZF9;P55039	.;DRG2_HUMAN	T	331	ENSP00000379076:K331T;ENSP00000225729:K331T	ENSP00000225729:K331T	K	+	2	0	DRG2	17950509	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.089000	0.94137	0.866000	0.35629	0.459000	0.35465	AAG	.		0.597	DRG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132075.3	NM_001388	
INTS10	55174	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	8	19700398	19700398	+	Missense_Mutation	SNP	T	T	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr8:19700398T>C	ENST00000397977.3	+	14	2077	c.1679T>C	c.(1678-1680)aTc>aCc	p.I560T		NM_018142.2	NP_060612.2	Q9NVR2	INT10_HUMAN	integrator complex subunit 10	560					snRNA processing (GO:0016180)	integrator complex (GO:0032039)				breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(8)|ovary(2)|prostate(1)|urinary_tract(1)	20				Colorectal(111;0.057)|COAD - Colon adenocarcinoma(73;0.215)		AGCAAGGCTATCATGCCATAC	0.343																																					p.I560T		.											.	.	.	0			c.T1679C						.						155.0	144.0	147.0					8																	19700398		1871	4128	5999	SO:0001583	missense	55174	exon14			AGGCTATCATGCC	AK001431	CCDS6011.2	8p21.3	2006-04-26	2006-03-15	2006-03-15	ENSG00000104613	ENSG00000104613			25548	protein-coding gene	gene with protein product		611353	"""chromosome 8 open reading frame 35"""	C8orf35		16239144	Standard	XM_005273558		Approved	FLJ10569, INT10	uc003wzj.3	Q9NVR2	OTTHUMG00000131065	ENST00000397977.3:c.1679T>C	8.37:g.19700398T>C	ENSP00000381064:p.Ile560Thr	Somatic	71	0		WXS	Illumina HiSeq	.	34	16	NM_018142	Q6IA93|Q7L538|Q7L8C8|Q9H3W8	Missense_Mutation	SNP	ENST00000397977.3	37	CCDS6011.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	18.40|18.40	3.615876|3.615876	0.66672|0.66672	.|.	.|.	ENSG00000104613|ENSG00000104613	ENST00000397977|ENST00000520670	T|.	0.50813|.	0.73|.	5.39|5.39	5.39|5.39	0.77823|0.77823	.|.	0.233115|.	0.45606|.	D|.	0.000342|.	T|T	0.61714|0.61714	0.2369|0.2369	L|L	0.48642|0.48642	1.525|1.525	0.42521|0.42521	D|D	0.993006|0.993006	B|.	0.33238|.	0.403|.	B|.	0.25291|.	0.059|.	T|T	0.60296|0.60296	-0.7291|-0.7291	9|5	.|.	.|.	.|.	-12.6702|-12.6702	14.2317|14.2317	0.65898|0.65898	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	560|.	Q9NVR2|.	INT10_HUMAN|.	T|P	560|50	ENSP00000381064:I560T|.	.|.	I|S	+|+	2|1	0|0	INTS10|INTS10	19744678|19744678	1.000000|1.000000	0.71417|0.71417	0.341000|0.341000	0.25589|0.25589	0.990000|0.990000	0.78478|0.78478	7.320000|7.320000	0.79064|0.79064	2.032000|2.032000	0.59987|0.59987	0.533000|0.533000	0.62120|0.62120	ATC|TCA	.		0.343	INTS10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253724.2	NM_018142	
JMJD1C	221037	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	10	64968449	64968449	+	Silent	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr10:64968449T>G	ENST00000399262.2	-	10	3198	c.2980A>C	c.(2980-2982)Agg>Cgg	p.R994R	JMJD1C_ENST00000399251.1_Silent_p.R775R|JMJD1C_ENST00000542921.1_Silent_p.R812R|JMJD1C_ENST00000402544.1_Silent_p.R775R	NM_032776.1	NP_116165.1	Q15652	JHD2C_HUMAN	jumonji domain containing 1C	994					blood coagulation (GO:0007596)|chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	intracellular (GO:0005622)|nucleoplasm (GO:0005654)	dioxygenase activity (GO:0051213)|metal ion binding (GO:0046872)|thyroid hormone receptor binding (GO:0046966)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(8)|large_intestine(9)|lung(27)|ovary(6)|prostate(4)|skin(4)|stomach(3)|upper_aerodigestive_tract(3)	77	Prostate(12;0.0119)|all_hematologic(501;0.191)					ACAAAATGCCTATGTAAGTGA	0.413																																					p.R994R		.											.	.	.	0			c.A2980C						.						147.0	136.0	140.0					10																	64968449		1894	4115	6009	SO:0001819	synonymous_variant	221037	exon10			AATGCCTATGTAA	L40411	CCDS41532.1, CCDS60538.1	10q22.1	2011-05-25	2004-03-31	2004-04-01	ENSG00000171988	ENSG00000171988			12313	protein-coding gene	gene with protein product		604503	"""thyroid hormone receptor interactor 8"""	TRIP8		7776974	Standard	XM_005269624		Approved	DKFZp761F0118, KIAA1380, FLJ14374	uc001jmn.3	Q15652	OTTHUMG00000018311	ENST00000399262.2:c.2980A>C	10.37:g.64968449T>G		Somatic	47	0		WXS	Illumina HiSeq	.	38	11	NM_032776	A0T124|Q5SQZ8|Q5SQZ9|Q5SR00|Q7Z3E7|Q8N3U0|Q96KB9|Q9P2G7	Silent	SNP	ENST00000399262.2	37	CCDS41532.1																																																																																			.		0.413	JMJD1C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048249.2	NM_004241	
CTNND1	1500	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	11	57569260	57569260	+	Missense_Mutation	SNP	C	C	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr11:57569260C>T	ENST00000399050.4	+	7	1548	c.1012C>T	c.(1012-1014)Cct>Tct	p.P338S	CTNND1_ENST00000399039.4_Missense_Mutation_p.P338S|CTNND1_ENST00000532844.1_Missense_Mutation_p.P284S|CTNND1_ENST00000361796.4_Missense_Mutation_p.P338S|CTNND1_ENST00000533667.1_Missense_Mutation_p.P15S|CTNND1_ENST00000426142.2_Missense_Mutation_p.P237S|CTNND1_ENST00000532245.1_Missense_Mutation_p.P237S|CTNND1_ENST00000526938.1_Missense_Mutation_p.P338S|CTNND1_ENST00000528232.1_Missense_Mutation_p.P237S|CTNND1_ENST00000527467.1_Missense_Mutation_p.P15S|CTNND1_ENST00000529873.1_Missense_Mutation_p.P284S|CTNND1_ENST00000524630.1_Missense_Mutation_p.P338S|CTNND1_ENST00000526357.1_Missense_Mutation_p.P284S|CTNND1_ENST00000529526.1_Missense_Mutation_p.P284S|CTNND1_ENST00000530748.1_Missense_Mutation_p.P284S|CTNND1_ENST00000358694.6_Missense_Mutation_p.P338S|CTNND1_ENST00000361391.6_Missense_Mutation_p.P338S|CTNND1_ENST00000428599.2_Missense_Mutation_p.P338S|CTNND1_ENST00000534579.1_Missense_Mutation_p.P284S|CTNND1_ENST00000525902.1_Missense_Mutation_p.P15S|CTNND1_ENST00000532463.1_Missense_Mutation_p.P237S|CTNND1_ENST00000529919.1_Missense_Mutation_p.P338S|CTNND1_ENST00000415361.2_Missense_Mutation_p.P237S|CTNND1_ENST00000530094.1_Missense_Mutation_p.P237S|CTNND1_ENST00000360682.6_Missense_Mutation_p.P338S|CTNND1_ENST00000532787.1_Missense_Mutation_p.P237S|CTNND1_ENST00000529986.1_Missense_Mutation_p.P237S|CTNND1_ENST00000528621.1_Missense_Mutation_p.P284S|CTNND1_ENST00000526772.1_Missense_Mutation_p.P15S|CTNND1_ENST00000361332.4_Missense_Mutation_p.P338S|CTNND1_ENST00000532649.1_Missense_Mutation_p.P284S|CTNND1_ENST00000531014.1_Missense_Mutation_p.P15S	NM_001085458.1	NP_001078927.1	O60716	CTND1_HUMAN	catenin (cadherin-associated protein), delta 1	338					adherens junction organization (GO:0034332)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|regulation of transcription, DNA-templated (GO:0006355)|single organismal cell-cell adhesion (GO:0016337)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|midbody (GO:0030496)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|synapse (GO:0045202)|zonula adherens (GO:0005915)	cadherin binding (GO:0045296)|receptor binding (GO:0005102)			breast(5)|endometrium(8)|kidney(4)|large_intestine(7)|liver(2)|lung(16)|ovary(1)|upper_aerodigestive_tract(2)	45		all_epithelial(135;0.155)				CTACTGGGCTCCTTTGGCCCA	0.502																																					p.P338S		.											.	.	.	0			c.C1012T						.						78.0	75.0	76.0					11																	57569260		1932	4150	6082	SO:0001583	missense	1500	exon7			TGGGCTCCTTTGG	AB002382	CCDS44604.1, CCDS44605.1, CCDS44606.1, CCDS44607.1, CCDS44608.1, CCDS44609.1, CCDS53632.1, CCDS53633.1, CCDS53634.1, CCDS55763.1, CCDS55764.1, CCDS55765.1, CCDS55766.1, CCDS55767.1, CCDS73290.1	11q12.1	2013-02-14				ENSG00000198561		"""Armadillo repeat containing"""	2515	protein-coding gene	gene with protein product		601045		CTNND		8808291	Standard	NM_001085460		Approved	KIAA0384, p120, p120cas, p120ctn	uc001nmc.4	O60716		ENST00000399050.4:c.1012C>T	11.37:g.57569260C>T	ENSP00000382004:p.Pro338Ser	Somatic	29	0		WXS	Illumina HiSeq	.	20	9	NM_001085461	A8K939|O15088|O60713|O60714|O60715|O60935|Q6DHZ7|Q6RBX8|Q9UP71|Q9UP72|Q9UP73	Missense_Mutation	SNP	ENST00000399050.4	37	CCDS44604.1	.	.	.	.	.	.	.	.	.	.	C	24.0	4.481579	0.84747	.	.	ENSG00000198561	ENST00000524630;ENST00000529919;ENST00000399039;ENST00000533189;ENST00000360682;ENST00000361796;ENST00000529526;ENST00000426142;ENST00000399050;ENST00000361391;ENST00000361332;ENST00000532463;ENST00000529986;ENST00000358694;ENST00000532787;ENST00000533667;ENST00000532649;ENST00000528621;ENST00000530748;ENST00000428599;ENST00000527467;ENST00000528232;ENST00000531014;ENST00000526772;ENST00000529873;ENST00000525902;ENST00000532844;ENST00000526357;ENST00000530094;ENST00000415361;ENST00000532245;ENST00000534579;ENST00000526938;ENST00000534647	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.79352	-0.52;-0.52;-0.52;-1.26;-0.9;-0.52;-0.52;-0.42;-0.55;-0.88;-0.54;-0.42;-0.42;-0.52;-0.75;-1.07;-0.52;-0.52;-0.53;-0.52;-0.68;-0.43;-0.68;-0.63;-0.87;-0.63;-0.55;-0.54;-0.52;-0.52;-0.42;-0.52;-0.88;1.95	4.74	4.74	0.60224	Armadillo-like helical (1);	0.224208	0.46758	D	0.000262	D	0.84638	0.5516	L	0.54323	1.7	0.58432	D	0.999999	D;D;D;D;D;D;D;D;D	0.89917	1.0;1.0;0.999;1.0;1.0;1.0;0.985;1.0;0.999	D;D;P;D;D;D;P;D;P	0.71870	0.955;0.955;0.903;0.975;0.955;0.955;0.861;0.955;0.903	D	0.85133	0.0976	10	0.51188	T	0.08	-1.8524	15.6813	0.77371	0.0:1.0:0.0:0.0	.	338;338;338;237;284;284;338;338;338	O60716-3;O60716-2;O60716;O60716-18;O60716-14;O60716-10;O60716-5;F8WA43;C9JZR2	.;.;CTND1_HUMAN;.;.;.;.;.;.	S	338;338;338;15;338;338;284;237;338;338;338;237;237;338;237;15;284;284;284;338;15;237;15;15;284;15;284;284;237;237;237;284;338;260	ENSP00000436543:P338S;ENSP00000434808:P338S;ENSP00000381996:P338S;ENSP00000435242:P15S;ENSP00000353902:P338S;ENSP00000354907:P338S;ENSP00000436323:P284S;ENSP00000409930:P237S;ENSP00000382004:P338S;ENSP00000354785:P338S;ENSP00000354823:P338S;ENSP00000432075:P237S;ENSP00000437156:P237S;ENSP00000351527:P338S;ENSP00000434949:P237S;ENSP00000437051:P15S;ENSP00000435379:P284S;ENSP00000432243:P284S;ENSP00000436744:P284S;ENSP00000413586:P338S;ENSP00000434900:P15S;ENSP00000435266:P237S;ENSP00000432623:P15S;ENSP00000433158:P15S;ENSP00000435494:P284S;ENSP00000434672:P15S;ENSP00000433276:P284S;ENSP00000433334:P284S;ENSP00000437327:P237S;ENSP00000403518:P237S;ENSP00000434017:P237S;ENSP00000435789:P284S;ENSP00000432041:P338S;ENSP00000434202:P260S	ENSP00000351527:P338S	P	+	1	0	CTNND1	57325836	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.169000	0.64984	2.441000	0.82636	0.557000	0.71058	CCT	.		0.502	CTNND1-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000393944.1	NM_001331	
PROSER2	254427	hgsc.bcm.edu	37	10	11908455	11908455	+	Intron	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr10:11908455T>G	ENST00000277570.5	+	3	292				PROSER2-AS1_ENST00000453242.1_RNA|PROSER2-AS1_ENST00000445498.1_RNA|PROSER2_ENST00000474155.1_Intron	NM_153256.3	NP_694988.3	Q86WR7	PRSR2_HUMAN	proline and serine rich 2																		CAATCCCAACTTTGCTTCAGC	0.522																																					.		.											.	.	.	0			.						.																																			SO:0001627	intron_variant	219731	.			CCCAACTTTGCTT	BC017269	CCDS7085.1	10p14	2014-02-19	2014-02-19	2012-12-05	ENSG00000148426	ENSG00000148426			23728	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 47"", ""proline and serine-rich protein 2"""	C10orf47		12477932	Standard	NM_153256		Approved	MGC35403	uc001ikx.3	Q86WR7	OTTHUMG00000017673	ENST00000277570.5:c.139-75T>G	10.37:g.11908455T>G		Somatic	29	0		WXS	Illumina HiSeq	.	16	8	.	D3DRR8|Q5W0J9|Q5W0K0|Q5W0K1|Q5W0K2|Q6PJC8|Q8N317	RNA	SNP	ENST00000277570.5	37	CCDS7085.1																																																																																			.		0.522	PROSER2-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090189.2	NM_153256	
STPG1	90529	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	24718155	24718155	+	Missense_Mutation	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr1:24718155A>C	ENST00000374409.1	-	3	339	c.85T>G	c.(85-87)Tat>Gat	p.Y29D	STPG1_ENST00000440416.1_Intron|STPG1_ENST00000337248.4_Missense_Mutation_p.Y29D|STPG1_ENST00000468303.1_5'UTR|STPG1_ENST00000003583.8_Intron	NM_001199012.1	NP_001185941.1	Q5TH74	STPG1_HUMAN	sperm-tail PG-rich repeat containing 1	29					apoptotic process (GO:0006915)	cytoplasm (GO:0005737)|nucleus (GO:0005634)											TGTGTTGGATATGCAGCAGTA	0.313											OREG0013240	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.Y29D		.											.	.	.	0			c.T85G						.																																			SO:0001583	missense	90529	exon3			TTGGATATGCAGC	BC047705	CCDS253.1, CCDS55581.1	1p36.11	2012-10-31	2012-07-30	2012-07-30	ENSG00000001460	ENSG00000001460			28070	protein-coding gene	gene with protein product	"""O6-methylguanine-induced apoptosis 2"""	615826	"""chromosome 1 open reading frame 201"""	C1orf201		23028632	Standard	NM_001199012		Approved	FLJ33340, MAPO2	uc001bjc.3	Q5TH74	OTTHUMG00000003297	ENST00000374409.1:c.85T>G	1.37:g.24718155A>C	ENSP00000363530:p.Tyr29Asp	Somatic	104	0	773	WXS	Illumina HiSeq	.	39	14	NM_001199012	Q49AP0|Q6P3R4|Q86VU9|Q8WVQ3	Missense_Mutation	SNP	ENST00000374409.1	37	CCDS55581.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	17.49|17.49	3.402607|3.402607	0.62288|0.62288	.|.	.|.	ENSG00000001460|ENSG00000001460	ENST00000435187|ENST00000374409;ENST00000337248;ENST00000437986	.|.	.|.	.|.	5.29|5.29	4.16|4.16	0.48862|0.48862	.|.	.|0.999748	.|0.08090	.|N	.|0.999477	T|T	0.69097|0.69097	0.3073|0.3073	M|M	0.64997|0.64997	1.995|1.995	0.80722|0.80722	D|D	1|1	.|D	.|0.69078	.|0.997	.|D	.|0.64237	.|0.923	T|T	0.62576|0.62576	-0.6825|-0.6825	5|9	.|0.37606	.|T	.|0.19	-13.9155|-13.9155	7.2689|7.2689	0.26246|0.26246	0.9021:0.0:0.0979:0.0|0.9021:0.0:0.0979:0.0	.|.	.|29	.|Q5TH74	.|CA201_HUMAN	Q|D	5|29	.|.	.|ENSP00000337461:Y29D	H|Y	-|-	3|1	2|0	C1orf201|C1orf201	24590742|24590742	0.992000|0.992000	0.36948|0.36948	1.000000|1.000000	0.80357|0.80357	0.951000|0.951000	0.60555|0.60555	1.895000|1.895000	0.39778|0.39778	2.131000|2.131000	0.65755|0.65755	0.533000|0.533000	0.62120|0.62120	CAT|TAT	.		0.313	STPG1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009172.1	NM_178122	
FCHO2	115548	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	5	72378651	72378651	+	Splice_Site	SNP	A	A	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr5:72378651A>T	ENST00000430046.2	+	24	2360	c.2244A>T	c.(2242-2244)ggA>ggT	p.G748G	FCHO2_ENST00000512348.1_Splice_Site_p.G715G|FCHO2_ENST00000341845.6_Splice_Site_p.G748G	NM_001146032.1|NM_138782.2	NP_001139504.1|NP_620137.2	Q0JRZ9	FCHO2_HUMAN	FCH domain only 2	748	MHD. {ECO:0000255|PROSITE- ProRule:PRU00404}.|Mediates interaction with DAB2, EPS15, EPS15R and ITSN1.				clathrin coat assembly (GO:0048268)|clathrin-mediated endocytosis (GO:0072583)|membrane invagination (GO:0010324)|protein localization to plasma membrane (GO:0072659)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|plasma membrane (GO:0005886)	phosphatidylinositol binding (GO:0035091)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylserine binding (GO:0001786)			cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(4)|ovary(1)|prostate(1)	17		Lung NSC(167;0.0465)|Ovarian(174;0.0908)|Prostate(461;0.165)		OV - Ovarian serous cystadenocarcinoma(47;4.6e-53)		CAGAAAATGGAGGTAAGTGTG	0.313																																					p.G748G		.											.	.	.	0			c.A2244T						.						78.0	73.0	75.0					5																	72378651		1807	4065	5872	SO:0001630	splice_region_variant	115548	exon24			AAATGGAGGTAAG	AL831971	CCDS47230.1, CCDS54868.1	5q13.2	2005-08-15			ENSG00000157107	ENSG00000157107			25180	protein-coding gene	gene with protein product		613438				15254787	Standard	NM_138782		Approved		uc003kcl.3	Q0JRZ9	OTTHUMG00000162413	ENST00000430046.2:c.2245+1A>T	5.37:g.72378651A>T		Somatic	140	0		WXS	Illumina HiSeq	.	105	63	NM_138782	A8K6W7|B2RNQ9|B4DHK0|E9PG79|Q0JTJ3|Q96CF5	Silent	SNP	ENST00000430046.2	37	CCDS47230.1																																																																																			.		0.313	FCHO2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000368795.3	XM_291142	Silent
TOP2A	7153	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	17	38574040	38574040	+	Missense_Mutation	SNP	C	C	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr17:38574040C>T	ENST00000423485.1	-	1	162	c.4G>A	c.(4-6)Gaa>Aaa	p.E2K		NM_001067.3	NP_001058.2	P11388	TOP2A_HUMAN	topoisomerase (DNA) II alpha 170kDa	2					apoptotic chromosome condensation (GO:0030263)|ATP catabolic process (GO:0006200)|cellular response to DNA damage stimulus (GO:0006974)|chromosome segregation (GO:0007059)|DNA ligation (GO:0006266)|DNA topological change (GO:0006265)|DNA unwinding involved in DNA replication (GO:0006268)|embryonic cleavage (GO:0040016)|hematopoietic progenitor cell differentiation (GO:0002244)|mitotic cell cycle (GO:0000278)|mitotic DNA integrity checkpoint (GO:0044774)|mitotic recombination (GO:0006312)|positive regulation of apoptotic process (GO:0043065)|positive regulation of single stranded viral RNA replication via double stranded DNA intermediate (GO:0045870)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral genome replication (GO:0045070)|resolution of meiotic recombination intermediates (GO:0000712)|sister chromatid segregation (GO:0000819)	condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|DNA topoisomerase complex (ATP-hydrolyzing) (GO:0009330)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA binding, bending (GO:0008301)|DNA topoisomerase type II (ATP-hydrolyzing) activity (GO:0003918)|DNA-dependent ATPase activity (GO:0008094)|drug binding (GO:0008144)|enzyme binding (GO:0019899)|histone deacetylase binding (GO:0042826)|magnesium ion binding (GO:0000287)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase C binding (GO:0005080)|ubiquitin binding (GO:0043130)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(9)|ovary(5)|pancreas(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)	39		Breast(137;0.00328)	STAD - Stomach adenocarcinoma(5;0.00183)		Amsacrine(DB00276)|Ciprofloxacin(DB00537)|Dactinomycin(DB00970)|Daunorubicin(DB00694)|Dexrazoxane(DB00380)|Doxorubicin(DB00997)|Enoxacin(DB00467)|Epirubicin(DB00445)|Etoposide(DB00773)|Fleroxacin(DB04576)|Idarubicin(DB01177)|Levofloxacin(DB01137)|Lomefloxacin(DB00978)|Lucanthone(DB04967)|Mitoxantrone(DB01204)|Moxifloxacin(DB00218)|Norfloxacin(DB01059)|Ofloxacin(DB01165)|Pefloxacin(DB00487)|Podofilox(DB01179)|Sparfloxacin(DB01208)|Teniposide(DB00444)|Trovafloxacin(DB00685)|Valrubicin(DB00385)	GGTGACACTTCCATGGTGACG	0.667																																					p.E2K		.											.	.	.	0			c.G4A						.						28.0	35.0	33.0					17																	38574040		1925	4106	6031	SO:0001583	missense	7153	exon1			ACACTTCCATGGT		CCDS45672.1	17q21-q22	2008-08-06	2002-08-29		ENSG00000131747	ENSG00000131747	5.99.1.2		11989	protein-coding gene	gene with protein product		126430	"""topoisomerase (DNA) II alpha (170kD)"""	TOP2			Standard	NM_001067		Approved		uc002huq.3	P11388	OTTHUMG00000155008	ENST00000423485.1:c.4G>A	17.37:g.38574040C>T	ENSP00000411532:p.Glu2Lys	Somatic	94	0		WXS	Illumina HiSeq	.	74	30	NM_001067	B2RTS1|Q71UN1|Q71UQ5|Q9HB24|Q9HB25|Q9HB26|Q9UP44|Q9UQP9	Missense_Mutation	SNP	ENST00000423485.1	37	CCDS45672.1	.	.	.	.	.	.	.	.	.	.	C	19.82	3.898148	0.72639	.	.	ENSG00000131747	ENST00000423485;ENST00000357601	T	0.22945	1.93	5.03	5.03	0.67393	.	.	.	.	.	T	0.19604	0.0471	N	0.22421	0.69	0.21386	N	0.999709	B	0.26635	0.155	B	0.18263	0.021	T	0.12041	-1.0563	9	0.66056	D	0.02	.	14.0488	0.64722	0.0:1.0:0.0:0.0	.	2	P11388	TOP2A_HUMAN	K	2	ENSP00000411532:E2K	ENSP00000350217:E2K	E	-	1	0	TOP2A	35827566	1.000000	0.71417	1.000000	0.80357	0.669000	0.39330	2.111000	0.41883	2.771000	0.95319	0.561000	0.74099	GAA	.		0.667	TOP2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338035.1		
NPR2	4882	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	9	35792667	35792667	+	Missense_Mutation	SNP	A	A	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr9:35792667A>G	ENST00000342694.2	+	1	517	c.262A>G	c.(262-264)Aag>Gag	p.K88E		NM_003995.3	NP_003986.2	P20594	ANPRB_HUMAN	natriuretic peptide receptor 2	88					bone development (GO:0060348)|cell surface receptor signaling pathway (GO:0007166)|cellular response to granulocyte macrophage colony-stimulating factor stimulus (GO:0097011)|cGMP biosynthetic process (GO:0006182)|intracellular signal transduction (GO:0035556)|negative regulation of meiotic cell cycle (GO:0051447)|negative regulation of oocyte maturation (GO:1900194)|ossification (GO:0001503)|receptor guanylyl cyclase signaling pathway (GO:0007168)|regulation of blood pressure (GO:0008217)|signal transduction (GO:0007165)|single organism reproductive process (GO:0044702)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|hormone binding (GO:0042562)|natriuretic peptide receptor activity (GO:0016941)|peptide hormone binding (GO:0017046)|protein kinase activity (GO:0004672)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(14)|ovary(2)|prostate(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	45	all_epithelial(49;0.161)		LUSC - Lung squamous cell carcinoma(32;0.00521)|Lung(28;0.00697)|STAD - Stomach adenocarcinoma(86;0.194)		Erythrityl Tetranitrate(DB01613)|Nesiritide(DB04899)	TGTGGACCTCAAGCTGTACCA	0.662																																					p.K88E		.											.	.	.	0			c.A262G						.						113.0	103.0	107.0					9																	35792667		2203	4300	6503	SO:0001583	missense	4882	exon1			GACCTCAAGCTGT	AJ005282	CCDS6590.1	9p21-p12	2014-03-03	2014-03-03		ENSG00000159899	ENSG00000159899			7944	protein-coding gene	gene with protein product	"""guanylate cyclase B"""	108961	"""acromesomelic dysplasia, Maroteaux type"", ""atrionatriuretic peptide receptor B"", ""natriuretic peptide receptor B"""	ANPRB, NPRB, AMDM		9634515, 15146390	Standard	XM_005251478		Approved	GUCY2B, ANPb	uc003zyd.3	P20594	OTTHUMG00000019871	ENST00000342694.2:c.262A>G	9.37:g.35792667A>G	ENSP00000341083:p.Lys88Glu	Somatic	68	0		WXS	Illumina HiSeq	.	41	12	NM_003995	B0ZBF2|B0ZBF3|D3DRP3|D3DRP4|O60871|Q4VAK7|Q5TCV2|Q8TA93|Q9UQ50	Missense_Mutation	SNP	ENST00000342694.2	37	CCDS6590.1	.	.	.	.	.	.	.	.	.	.	A	16.06	3.015037	0.54468	.	.	ENSG00000159899	ENST00000342694	T	0.74002	-0.8	3.93	3.93	0.45458	Extracellular ligand-binding receptor (1);	0.000000	0.46442	D	0.000298	T	0.78400	0.4277	M	0.69358	2.11	0.53688	D	0.999971	B;P	0.52692	0.18;0.955	B;P	0.54759	0.2;0.76	T	0.76296	-0.3011	10	0.29301	T	0.29	.	10.9604	0.47383	1.0:0.0:0.0:0.0	.	88;88	P20594-2;P20594	.;ANPRB_HUMAN	E	88	ENSP00000341083:K88E	ENSP00000341083:K88E	K	+	1	0	NPR2	35782667	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.289000	0.51747	1.773000	0.52216	0.460000	0.39030	AAG	.		0.662	NPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052345.1		
ZNF410	57862	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	14	74387683	74387683	+	Splice_Site	SNP	G	G	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr14:74387683G>A	ENST00000555044.1	+	9	1198	c.1004G>A	c.(1003-1005)gGa>gAa	p.G335E	ZNF410_ENST00000442160.3_Splice_Site_p.G352E|ZNF410_ENST00000540593.1_Splice_Site_p.G262E|RP5-1021I20.5_ENST00000554009.1_RNA|RP5-1021I20.4_ENST00000556551.2_3'UTR|RP5-1021I20.5_ENST00000555916.1_RNA|ZNF410_ENST00000334521.4_Splice_Site_p.G282E|ZNF410_ENST00000324593.6_Splice_Site_p.G335E	NM_001242928.1|NM_021188.2	NP_001229857.1|NP_067011.1	Q86VK4	ZN410_HUMAN	zinc finger protein 410	335					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(1)|endometrium(1)|large_intestine(3)|lung(5)|prostate(1)|skin(1)|urinary_tract(1)	13				BRCA - Breast invasive adenocarcinoma(234;0.00369)		CCTGTTTCAGGAGAGAAGCCT	0.473																																					p.G352E		.											.	.	.	0			c.G1055A						.						109.0	101.0	104.0					14																	74387683		2203	4300	6503	SO:0001630	splice_region_variant	57862	exon10			TTTCAGGAGAGAA	U90919	CCDS9821.1, CCDS55929.1, CCDS55930.1, CCDS55931.1	14q24.3	2013-01-08				ENSG00000119725		"""Zinc fingers, C2H2-type"""	20144	protein-coding gene	gene with protein product						12370286	Standard	NM_001242924		Approved	APA1, APA-1	uc010arz.2	Q86VK4		ENST00000555044.1:c.1004-1G>A	14.37:g.74387683G>A		Somatic	49	0		WXS	Illumina HiSeq	.	26	7	NM_001242924	B4DDV5|B4DR78|O00153|Q9BQ19	Missense_Mutation	SNP	ENST00000555044.1	37	CCDS9821.1	.	.	.	.	.	.	.	.	.	.	G	23.0	4.361792	0.82353	.	.	ENSG00000119725	ENST00000540593;ENST00000324593;ENST00000458102;ENST00000442160;ENST00000555044;ENST00000334521;ENST00000554316	T;T;T;T;T;T	0.25749	1.78;1.78;1.78;1.78;1.78;1.78	4.86	4.86	0.63082	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.42548	D	0.000686	T	0.48352	0.1495	L	0.58810	1.83	0.80722	D	1	D;D;D;D;D;D	0.89917	0.983;1.0;1.0;0.999;1.0;0.983	P;D;D;D;D;P	0.97110	0.822;1.0;0.999;0.998;1.0;0.822	T	0.32402	-0.9908	9	.	.	.	.	18.1415	0.89641	0.0:0.0:1.0:0.0	.	335;262;352;335;324;335	B2RCP6;B4DR78;B4DDV5;Q86VK4-3;B4DPE9;Q86VK4	.;.;.;.;.;ZN410_HUMAN	E	262;335;324;352;335;282;66	ENSP00000442228:G262E;ENSP00000323293:G335E;ENSP00000407130:G352E;ENSP00000451763:G335E;ENSP00000334170:G282E;ENSP00000451748:G66E	.	G	+	2	0	ZNF410	73457436	1.000000	0.71417	1.000000	0.80357	0.852000	0.48524	7.594000	0.82698	2.683000	0.91414	0.563000	0.77884	GGA	.		0.473	ZNF410-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412597.1	NM_021188	Missense_Mutation
CDIPT	10423	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	16	29874145	29874145	+	Missense_Mutation	SNP	T	T	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr16:29874145T>C	ENST00000219789.6	-	1	912	c.34A>G	c.(34-36)Aac>Gac	p.N12D	CDIPT_ENST00000569956.1_Missense_Mutation_p.N12D|CDIPT_ENST00000570016.1_Missense_Mutation_p.N12D|CDIPT_ENST00000566113.1_Missense_Mutation_p.N12D|CDIPT_ENST00000561555.1_5'Flank|CDIPT-AS1_ENST00000565014.1_RNA|CDIPT-AS1_ENST00000398859.3_RNA|CDIPT_ENST00000563415.1_Missense_Mutation_p.N12D	NM_006319.3	NP_006310.1	O14735	CDIPT_HUMAN	CDP-diacylglycerol--inositol 3-phosphatidyltransferase	12					CDP-diacylglycerol metabolic process (GO:0046341)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	alcohol binding (GO:0043178)|carbohydrate binding (GO:0030246)|CDP-diacylglycerol-inositol 3-phosphatidyltransferase activity (GO:0003881)|diacylglycerol binding (GO:0019992)|manganese ion binding (GO:0030145)			endometrium(1)|lung(3)	4						CCGATGAGGTTGGGCACGAAC	0.697																																					p.N12D		.											.	.	.	0			c.A34G						.						102.0	104.0	104.0					16																	29874145		2197	4300	6497	SO:0001583	missense	10423	exon1			TGAGGTTGGGCAC	AF014807	CCDS10657.1, CCDS67002.1	16p11.2	2012-11-19	2010-04-29		ENSG00000103502	ENSG00000103502	2.7.8.11		1769	protein-coding gene	gene with protein product	"""phosphatidylinositol synthase"""	605893	"""CDP-diacylglycerol--inositol 3-phosphatidyltransferase (phosphatidylinositol synthase)"""			9407135	Standard	NM_006319		Approved	PIS1, PIS	uc002dum.3	O14735	OTTHUMG00000177144	ENST00000219789.6:c.34A>G	16.37:g.29874145T>C	ENSP00000219789:p.Asn12Asp	Somatic	43	0		WXS	Illumina HiSeq	.	23	11	NM_006319	B4DUV0|H3BTV1|Q6FGU1|Q6ZN70	Missense_Mutation	SNP	ENST00000219789.6	37	CCDS10657.1	.	.	.	.	.	.	.	.	.	.	T	24.8	4.576437	0.86645	.	.	ENSG00000103502	ENST00000219789	T	0.57436	0.4	5.24	4.13	0.48395	.	0.045687	0.85682	D	0.000000	T	0.81809	0.4901	H	0.98996	4.395	0.58432	D	0.999998	D;D	0.89917	0.998;1.0	P;D	0.87578	0.9;0.998	D	0.85314	0.1080	10	0.87932	D	0	-22.8614	9.9159	0.41434	0.1527:0.0:0.0:0.8473	.	12;12	B4DUV0;O14735	.;CDIPT_HUMAN	D	12	ENSP00000219789:N12D	ENSP00000219789:N12D	N	-	1	0	CDIPT	29781646	1.000000	0.71417	1.000000	0.80357	0.712000	0.41017	4.658000	0.61497	0.911000	0.36747	-0.496000	0.04628	AAC	.		0.697	CDIPT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255147.3	NM_006319	
UTP14C	9724	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	13	52603174	52603174	+	Missense_Mutation	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr13:52603174A>C	ENST00000521776.2	+	2	967	c.234A>C	c.(232-234)gaA>gaC	p.E78D	ALG11_ENST00000521508.1_3'UTR|ALG11_ENST00000523764.1_3'UTR	NM_021645.5	NP_067677.4	Q5TAP6	UT14C_HUMAN	UTP14, U3 small nucleolar ribonucleoprotein, homolog C (yeast)	78					cell differentiation (GO:0030154)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|rRNA processing (GO:0006364)|spermatogenesis (GO:0007283)	nucleus (GO:0005634)|small-subunit processome (GO:0032040)				breast(4)|cervix(1)|endometrium(1)|large_intestine(10)|lung(10)|ovary(3)|skin(1)|stomach(1)|urinary_tract(1)	32		Breast(56;0.00173)|Lung NSC(96;0.0108)|Prostate(109;0.0412)|Hepatocellular(98;0.152)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(99;2.3e-08)		TCAGTTCTGAAGGATCAGGAG	0.438																																					p.E78D		.											.	.	.	0			c.A234C						.						188.0	194.0	192.0					13																	52603174		2203	4300	6503	SO:0001583	missense	9724	exon2			TTCTGAAGGATCA	D87455	CCDS31978.1	13q12.2-q13.3	2010-11-23	2004-06-15	2004-06-16	ENSG00000253797	ENSG00000253797			20321	protein-coding gene	gene with protein product		608969	"""KIAA0266"""	KIAA0266		9039502, 16354793	Standard	NM_021645		Approved	2700066J21Rik	uc021rjw.1	Q5TAP6	OTTHUMG00000164353	ENST00000521776.2:c.234A>C	13.37:g.52603174A>C	ENSP00000428619:p.Glu78Asp	Somatic	87	0		WXS	Illumina HiSeq	.	60	27	NM_021645	Q5FWG3|Q92555	Missense_Mutation	SNP	ENST00000521776.2	37	CCDS31978.1	.	.	.	.	.	.	.	.	.	.	A	13.96	2.391568	0.42410	.	.	ENSG00000253797	ENST00000521776	T	0.18657	2.2	2.28	-3.21	0.05140	.	0.234782	0.49305	D	0.000141	T	0.29914	0.0748	M	0.71581	2.175	0.36748	D	0.882615	D	0.55800	0.973	P	0.62382	0.901	T	0.25745	-1.0123	10	0.46703	T	0.11	-5.3239	2.5993	0.04862	0.4568:0.0:0.1397:0.4035	.	78	Q5TAP6	UT14C_HUMAN	D	78	ENSP00000428619:E78D	ENSP00000428619:E78D	E	+	3	2	UTP14C	51501175	0.232000	0.23762	0.925000	0.36789	0.983000	0.72400	0.321000	0.19558	-0.846000	0.04174	0.368000	0.22195	GAA	.		0.438	UTP14C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045049.2	NM_021645	
TPCN1	53373	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	12	113664590	113664590	+	5'UTR	SNP	G	G	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr12:113664590G>A	ENST00000335509.6	+	0	247				TPCN1_ENST00000541517.1_Missense_Mutation_p.R50K|TPCN1_ENST00000550785.1_Missense_Mutation_p.R50K	NM_017901.4	NP_060371.2	Q9ULQ1	TPC1_HUMAN	two pore segment channel 1						calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|membrane depolarization during action potential (GO:0086010)|transmembrane transport (GO:0055085)	endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)|NAADP-sensitive calcium-release channel activity (GO:0072345)|voltage-gated calcium channel activity (GO:0005245)			cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(16)|ovary(2)|prostate(3)|skin(3)|urinary_tract(1)	40						GGCTTTGAAAGGGAGCTCAAA	0.453																																					p.R50K		.											.	.	.	0			c.G149A						.						50.0	48.0	49.0					12																	113664590		692	1591	2283	SO:0001623	5_prime_UTR_variant	53373	exon3			TTGAAAGGGAGCT	AB032995	CCDS31908.1, CCDS44985.1	12q24.21	2011-07-05			ENSG00000186815	ENSG00000186815		"""Voltage-gated ion channels / Two-pore channels"""	18182	protein-coding gene	gene with protein product		609666				10574461, 10753632, 16382101	Standard	XM_005253905		Approved	KIAA1169, FLJ20612, TPC1	uc001tux.3	Q9ULQ1	OTTHUMG00000169625	ENST00000335509.6:c.-68G>A	12.37:g.113664590G>A		Somatic	29	0		WXS	Illumina HiSeq	.	33	11	NM_001143819	A7E258|Q86XS9|Q8NC20	Missense_Mutation	SNP	ENST00000335509.6	37	CCDS31908.1	.	.	.	.	.	.	.	.	.	.	G	12.39	1.923396	0.33908	.	.	ENSG00000186815	ENST00000547275;ENST00000552985;ENST00000551096;ENST00000550785;ENST00000541517	T;T;T;T;T	0.44482	0.92;0.92;0.92;0.92;0.92	4.72	0.434	0.16539	.	.	.	.	.	T	0.15696	0.0378	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.29397	-1.0013	9	0.05833	T	0.94	.	3.4594	0.07527	0.3451:0.2016:0.4533:0.0	.	50	Q9ULQ1-3	.	K	33;64;50;50;50	ENSP00000449560:R33K;ENSP00000447569:R64K;ENSP00000447263:R50K;ENSP00000448083:R50K;ENSP00000438125:R50K	ENSP00000438125:R50K	R	+	2	0	TPCN1	112148973	0.079000	0.21365	0.040000	0.18447	0.837000	0.47467	0.098000	0.15189	0.195000	0.20347	-0.502000	0.04539	AGG	.		0.453	TPCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405156.3	NM_017901	
OR51S1	119692	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	11	4870320	4870320	+	Missense_Mutation	SNP	A	A	C	rs139571388	byFrequency	TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr11:4870320A>C	ENST00000322101.2	-	1	194	c.119T>G	c.(118-120)aTt>aGt	p.I40S	MMP26_ENST00000380390.1_Intron|MMP26_ENST00000477339.1_Intron	NM_001004758.1	NP_001004758.1	Q8NGJ8	O51S1_HUMAN	olfactory receptor, family 51, subfamily S, member 1	40						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(15)|ovary(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	33		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;5.06e-12)|BRCA - Breast invasive adenocarcinoma(625;0.00438)|LUSC - Lung squamous cell carcinoma(625;0.19)		GTAGACAGCAATGAGGGGCAA	0.582																																					p.I40S		.											.	.	.	0			c.T119G						.						106.0	91.0	96.0					11																	4870320		2201	4298	6499	SO:0001583	missense	119692	exon1			ACAGCAATGAGGG	AB065796	CCDS31362.1	11p15.4	2012-08-09			ENSG00000176922	ENSG00000176922		"""GPCR / Class A : Olfactory receptors"""	15204	protein-coding gene	gene with protein product							Standard	NM_001004758		Approved		uc010qyo.2	Q8NGJ8	OTTHUMG00000066506	ENST00000322101.2:c.119T>G	11.37:g.4870320A>C	ENSP00000322754:p.Ile40Ser	Somatic	44	0		WXS	Illumina HiSeq	.	25	8	NM_001004758	B9EGZ1|Q6IFI2	Missense_Mutation	SNP	ENST00000322101.2	37	CCDS31362.1	.	.	.	.	.	.	.	.	.	.	A	5.909	0.351814	0.11182	.	.	ENSG00000176922	ENST00000322101	T	0.03181	4.02	5.45	4.27	0.50696	.	0.492235	0.17106	N	0.186796	T	0.02230	0.0069	N	0.08118	0	0.09310	N	1	B	0.14438	0.01	B	0.12156	0.007	T	0.39623	-0.9605	10	0.51188	T	0.08	-10.4057	6.9781	0.24688	0.7694:0.1518:0.0788:0.0	.	40	Q8NGJ8	O51S1_HUMAN	S	40	ENSP00000322754:I40S	ENSP00000322754:I40S	I	-	2	0	OR51S1	4826896	0.000000	0.05858	0.005000	0.12908	0.009000	0.06853	0.755000	0.26405	2.289000	0.77006	0.460000	0.39030	ATT	.		0.582	OR51S1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142179.1	NM_001004758	
NUP98	4928	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	11	3774605	3774605	+	Missense_Mutation	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr11:3774605A>C	ENST00000324932.7	-	11	1628	c.1208T>G	c.(1207-1209)tTt>tGt	p.F403C	NUP98_ENST00000359171.4_Missense_Mutation_p.F403C|NUP98_ENST00000355260.3_Missense_Mutation_p.F403C|NUP98_ENST00000397004.4_Missense_Mutation_p.F403C|NUP98_ENST00000397007.4_Missense_Mutation_p.F420C	NM_016320.4|NM_139132.3	NP_057404.2|NP_624358.2	P52948	NUP98_HUMAN	nucleoporin 98kDa	420	FG repeats 2.|Gly/Thr-rich.				carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|DNA replication (GO:0006260)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|nuclear pore complex assembly (GO:0051292)|nuclear pore organization (GO:0006999)|nucleocytoplasmic transport (GO:0006913)|protein import into nucleus, docking (GO:0000059)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|nuclear envelope (GO:0005635)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)|nuclear pore outer ring (GO:0031080)|nucleoplasm (GO:0005654)	peptide binding (GO:0042277)|structural constituent of nuclear pore (GO:0017056)|transporter activity (GO:0005215)			NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(1)|endometrium(5)|kidney(5)|large_intestine(13)|liver(1)|lung(15)|ovary(2)|prostate(2)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	66		Medulloblastoma(188;0.0025)|Breast(177;0.00328)|all_neural(188;0.0227)		BRCA - Breast invasive adenocarcinoma(625;0.0403)|LUSC - Lung squamous cell carcinoma(625;0.116)|Lung(200;0.199)		TTTACTTCCAAAAATACTATT	0.413			T	"""HOXA9, NSD1, WHSC1L1, DDX10, TOP1, HOXD13, PMX1, HOXA13, HOXD11, HOXA11, RAP1GDS1, HOXC11"""	AML																																p.F420C		.		Dom	yes		11	11p15	4928	nucleoporin 98kDa		L	.	.	.	0			c.T1259G						.						81.0	81.0	81.0					11																	3774605		2201	4298	6499	SO:0001583	missense	4928	exon11			CTTCCAAAAATAC	AF071076, AF231130, BC012906, BG773331	CCDS7746.1, CCDS31347.1, CCDS41605.1, CCDS41606.1	11p15	2008-02-26	2002-08-29		ENSG00000110713	ENSG00000110713			8068	protein-coding gene	gene with protein product		601021	"""nucleoporin 98kD"""			9166830	Standard	NM_139131		Approved	NUP96	uc001lyh.3	P52948	OTTHUMG00000011846	ENST00000324932.7:c.1208T>G	11.37:g.3774605A>C	ENSP00000316032:p.Phe403Cys	Somatic	111	0		WXS	Illumina HiSeq	.	59	29	NM_005387	Q8IUT2|Q8WYB0|Q96E54|Q9H3Q4|Q9NT02|Q9UF57|Q9UHX0|Q9Y6J4|Q9Y6J5	Missense_Mutation	SNP	ENST00000324932.7	37	CCDS7746.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	A|A|A	21.9|21.9|21.9	4.212263|4.212263|4.212263	0.79240|0.79240|0.79240	.|.|.	.|.|.	ENSG00000110713|ENSG00000110713|ENSG00000110713	ENST00000324932;ENST00000359171;ENST00000355260;ENST00000397004;ENST00000397007|ENST00000527104|ENST00000529379	.|.|.	.|.|.	.|.|.	5.34|5.34|5.34	5.34|5.34|5.34	0.76211|0.76211|0.76211	.|.|.	0.000000|0.000000|.	0.85682|0.85682|.	D|D|.	0.000000|0.000000|.	D|D|D	0.84674|0.84674|0.84674	0.5524|0.5524|0.5524	M|M|M	0.92691|0.92691|0.92691	3.335|3.335|3.335	0.58432|0.58432|0.58432	D|D|D	0.999997|0.999997|0.999997	D;D;D;D|.|.	0.89917|.|.	1.0;1.0;1.0;1.0|.|.	D;D;D;D|.|.	0.91635|.|.	0.997;0.997;0.999;0.999|.|.	D|D|D	0.88634|0.88634|0.88634	0.3171|0.3171|0.3171	9|6|5	0.48119|.|.	T|.|.	0.1|.|.	.|.|.	14.4955|14.4955|14.4955	0.67683|0.67683|0.67683	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.|.	420;403;403;403|.|.	P52948-3;P52948-4;P52948-2;P52948-5|.|.	.;.;.;.|.|.	C|L|V	403;403;403;403;420|22|52	.|.|.	ENSP00000316032:F403C|.|.	F|F|L	-|-|-	2|3|1	0|2|2	NUP98|NUP98|NUP98	3731181|3731181|3731181	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.998000|0.998000|0.998000	0.95712|0.95712|0.95712	7.387000|7.387000|7.387000	0.79785|0.79785|0.79785	2.023000|2.023000|2.023000	0.59567|0.59567|0.59567	0.533000|0.533000|0.533000	0.62120|0.62120|0.62120	TTT|TTT|TTG	.		0.413	NUP98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032766.3	NM_016320	
NUDT22	84304	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	11	63994325	63994325	+	Silent	SNP	C	C	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr11:63994325C>G	ENST00000279206.3	+	2	357	c.201C>G	c.(199-201)acC>acG	p.T67T	TRPT1_ENST00000546089.1_5'Flank|TRPT1_ENST00000546133.1_5'Flank|NUDT22_ENST00000441250.2_Silent_p.T67T|TRPT1_ENST00000541278.1_5'Flank|TRPT1_ENST00000394547.3_5'Flank|TRPT1_ENST00000394546.2_5'Flank|TRPT1_ENST00000540472.1_5'Flank|TRPT1_ENST00000317459.6_5'Flank|RP11-783K16.14_ENST00000534988.1_RNA	NM_001128612.2|NM_032344.2	NP_001122084.1|NP_115720	Q9BRQ3	NUD22_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 22	67							hydrolase activity (GO:0016787)			breast(1)|endometrium(1)|large_intestine(2)|lung(4)	8						ACTCAGCCACCCTGGCGCCTA	0.657																																					p.T67T		.											.	.	.	0			c.C201G						.						52.0	55.0	54.0					11																	63994325		2201	4297	6498	SO:0001819	synonymous_variant	84304	exon2			AGCCACCCTGGCG	BC006129	CCDS8061.1, CCDS44640.1	11q13.1	2008-02-05			ENSG00000149761	ENSG00000149761		"""Nudix motif containing"""	28189	protein-coding gene	gene with protein product						12477932	Standard	NM_032344		Approved	MGC13045	uc009ype.4	Q9BRQ3	OTTHUMG00000167791	ENST00000279206.3:c.201C>G	11.37:g.63994325C>G		Somatic	69	0		WXS	Illumina HiSeq	.	58	23	NM_001128613	C9JY06|Q71RD5	Silent	SNP	ENST00000279206.3	37	CCDS8061.1																																																																																			.		0.657	NUDT22-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396304.2	NM_032344	
C19orf54	284325	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	19	41248653	41248653	+	Silent	SNP	A	A	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr19:41248653A>T	ENST00000378313.2	-	6	860	c.741T>A	c.(739-741)gcT>gcA	p.A247A	C19orf54_ENST00000594163.1_5'Flank|C19orf54_ENST00000470681.1_3'UTR|C19orf54_ENST00000598485.2_Intron|C19orf54_ENST00000598729.1_Silent_p.A75A|C19orf54_ENST00000339153.3_Silent_p.A75A	NM_198476.3	NP_940878.3	Q5BKX5	CS054_HUMAN	chromosome 19 open reading frame 54	247										breast(1)|lung(1)|urinary_tract(2)	4			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)			GACTGGGCACAGCCCGAACAC	0.662																																					p.A247A		.											.	.	.	0			c.T741A						.						21.0	21.0	21.0					19																	41248653		2203	4296	6499	SO:0001819	synonymous_variant	284325	exon6			GGGCACAGCCCGA	AK123126	CCDS12564.2	19q13.2	2012-10-26			ENSG00000188493	ENSG00000188493			24758	protein-coding gene	gene with protein product							Standard	NM_198476		Approved	FLJ41131	uc002oou.1	Q5BKX5	OTTHUMG00000150174	ENST00000378313.2:c.741T>A	19.37:g.41248653A>T		Somatic	12	0		WXS	Illumina HiSeq	.	26	15	NM_198476	A8MSZ5|B4DNU7	Silent	SNP	ENST00000378313.2	37	CCDS12564.2																																																																																			.		0.662	C19orf54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316701.1	NM_198476	
MYOM1	8736	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	18	3067473	3067473	+	Silent	SNP	T	T	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr18:3067473T>A	ENST00000356443.4	-	38	5178	c.4845A>T	c.(4843-4845)tcA>tcT	p.S1615S	MYOM1_ENST00000261606.7_Silent_p.S1519S|MYOM1_ENST00000400569.3_Silent_p.S1615S	NM_003803.3|NM_019856.1	NP_003794.3|NP_062830.1	P52179	MYOM1_HUMAN	myomesin 1	1615	Ig-like C2-type 5.			SD -> QT (in Ref. 5; CAA48833). {ECO:0000305}.	muscle contraction (GO:0006936)	M band (GO:0031430)|striated muscle myosin thick filament (GO:0005863)	identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|structural constituent of muscle (GO:0008307)			NS(2)|autonomic_ganglia(1)|central_nervous_system(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(20)|ovary(4)|pancreas(1)|prostate(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	77						AGTGGTCGTCTGAGGCCAGGG	0.587																																					p.S1615S		.											.	.	.	0			c.A4845T						.						58.0	63.0	61.0					18																	3067473		2203	4299	6502	SO:0001819	synonymous_variant	8736	exon38			GTCGTCTGAGGCC	AF185573	CCDS45823.1, CCDS45824.1	18p11.31	2014-09-17	2012-10-17		ENSG00000101605	ENSG00000101605		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	7613	protein-coding gene	gene with protein product	"""skelemin"""	603508	"""myomesin 1 (skelemin) (185kD)"", ""myomesin 1 (skelemin) 185kDa"", ""myomesin 1, 185kDa"""			9806852	Standard	NM_019856		Approved		uc002klp.3	P52179	OTTHUMG00000178209	ENST00000356443.4:c.4845A>T	18.37:g.3067473T>A		Somatic	51	0		WXS	Illumina HiSeq	.	20	9	NM_003803	Q14BD6|Q6H969|Q6ZUU0	Silent	SNP	ENST00000356443.4	37	CCDS45824.1																																																																																			.		0.587	MYOM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441037.2	NM_003803	
FBXO28	23219	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	224345385	224345385	+	Silent	SNP	A	A	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr1:224345385A>G	ENST00000366862.5	+	5	1087	c.1044A>G	c.(1042-1044)cgA>cgG	p.R348R	FBXO28_ENST00000424254.2_3'UTR	NM_015176.3	NP_055991.1	Q9NVF7	FBX28_HUMAN	F-box protein 28	348										endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(3)|ovary(2)|skin(1)	10	Breast(184;0.206)			GBM - Glioblastoma multiforme(131;0.0363)		CTCGGAAACGAAAAAAGGCCA	0.468																																					p.R348R		.											.	.	.	0			c.A1044G						.						69.0	74.0	72.0					1																	224345385		2203	4300	6503	SO:0001819	synonymous_variant	23219	exon5			GAAACGAAAAAAG	AK001628	CCDS1539.1, CCDS44320.1	1q42.12	2011-08-12			ENSG00000143756	ENSG00000143756		"""F-boxes /  ""other"""""	29046	protein-coding gene	gene with protein product	"""centromere protein 30"""	609100				9455484	Standard	NM_015176		Approved	FLJ10766, KIAA0483, Fbx28, CENP-30	uc001hoh.3	Q9NVF7	OTTHUMG00000037495	ENST00000366862.5:c.1044A>G	1.37:g.224345385A>G		Somatic	63	0		WXS	Illumina HiSeq	.	60	42	NM_015176	E9PEM8|O75070	Silent	SNP	ENST00000366862.5	37	CCDS1539.1																																																																																			.		0.468	FBXO28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091283.2	NM_015176	
ASIC4	55515	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	2	220397059	220397059	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr2:220397059G>T	ENST00000347842.3	+	4	1273	c.1259G>T	c.(1258-1260)tGg>tTg	p.W420L	ASIC4_ENST00000358078.4_Missense_Mutation_p.W420L|ASIC4_ENST00000473709.1_3'UTR	NM_182847.2	NP_878267.2	Q96FT7	ASIC4_HUMAN	acid-sensing (proton-gated) ion channel family member 4	420					ion transmembrane transport (GO:0034220)|sodium ion transmembrane transport (GO:0035725)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)	ion channel activity (GO:0005216)|sodium channel activity (GO:0005272)|sodium ion transmembrane transporter activity (GO:0015081)										CCCCAGCCCTGGGGCAACTGC	0.637																																					p.W420L		.											.	.	.	0			c.G1259T						.						43.0	45.0	44.0					2																	220397059		2203	4300	6503	SO:0001583	missense	55515	exon4			AGCCCTGGGGCAA	AJ271643	CCDS2442.1	2q36.1	2012-02-22	2012-02-22	2012-02-22	ENSG00000072182	ENSG00000072182		"""Ion channels / Acid-sensing (proton-gated) ion channels"""	21263	protein-coding gene	gene with protein product		606715	"""amiloride-sensitive cation channel 4, pituitary"", ""amiloride-sensitive cation channel family member 4, pituitary"""	ACCN4		10852210	Standard	NM_182847		Approved	BNAC4	uc002vma.3	Q96FT7	OTTHUMG00000058928	ENST00000347842.3:c.1259G>T	2.37:g.220397059G>T	ENSP00000326627:p.Trp420Leu	Somatic	34	0		WXS	Illumina HiSeq	.	12	6	NM_182847	Q53SB7|Q6GMS1|Q6PIN9|Q9NQA4	Missense_Mutation	SNP	ENST00000347842.3	37	CCDS2442.1	.	.	.	.	.	.	.	.	.	.	G	26.6	4.749668	0.89753	.	.	ENSG00000072182	ENST00000347842;ENST00000358078	T;T	0.65178	-0.14;-0.14	4.1	4.1	0.47936	.	0.000000	0.85682	D	0.000000	D	0.82958	0.5150	M	0.92317	3.295	0.80722	D	1	B;D	0.65815	0.097;0.995	B;D	0.69142	0.085;0.962	D	0.88054	0.2789	10	0.87932	D	0	-11.8795	16.5064	0.84273	0.0:0.0:1.0:0.0	.	420;420	Q96FT7;Q96FT7-4	ACCN4_HUMAN;.	L	420	ENSP00000326627:W420L;ENSP00000350786:W420L	ENSP00000326627:W420L	W	+	2	0	ACCN4	220105303	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.513000	0.98010	2.305000	0.77605	0.561000	0.74099	TGG	.		0.637	ASIC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000130263.1	NM_018674	
CCDC83	220047	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	11	85630420	85630420	+	Missense_Mutation	SNP	T	T	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr11:85630420T>A	ENST00000342404.3	+	11	1325	c.1109T>A	c.(1108-1110)gTg>gAg	p.V370E	CCDC83_ENST00000376067.1_Missense_Mutation_p.V270E|CCDC83_ENST00000280245.4_Missense_Mutation_p.V401E|RP11-90K17.2_ENST00000531414.1_RNA			Q8IWF9	CCD83_HUMAN	coiled-coil domain containing 83	370										breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(12)|skin(3)|upper_aerodigestive_tract(2)	29		Acute lymphoblastic leukemia(157;4.88e-06)|all_hematologic(158;0.00572)				CCCCTGGGAGTGAAGCTTATG	0.423																																					p.V401E		.											.	.	.	0			c.T1202A						.						133.0	129.0	130.0					11																	85630420		2203	4299	6502	SO:0001583	missense	220047	exon12			TGGGAGTGAAGCT	AK124113	CCDS8271.1, CCDS66196.1	11q14.1-q14.2	2014-01-21			ENSG00000150676	ENSG00000150676			28535	protein-coding gene	gene with protein product						12477932	Standard	XM_005273842		Approved	MGC34732, FLJ42119, CT148	uc001pbg.1	Q8IWF9	OTTHUMG00000166978	ENST00000342404.3:c.1109T>A	11.37:g.85630420T>A	ENSP00000344512:p.Val370Glu	Somatic	87	0		WXS	Illumina HiSeq	.	70	30	NM_173556	B2RA49|Q6X7T2|Q6ZVT5|Q8N9Y1	Missense_Mutation	SNP	ENST00000342404.3	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	23.2|23.2	4.387093|4.387093	0.82902|0.82902	.|.	.|.	ENSG00000150676|ENSG00000150676	ENST00000280245;ENST00000376067;ENST00000342404|ENST00000526729	T;T;T|.	0.49139|.	0.79;0.79;0.79|.	5.62|5.62	5.62|5.62	0.85841|0.85841	.|.	0.306181|.	0.28279|.	N|.	0.015931|.	T|.	0.63177|.	0.2489|.	M|M	0.70595|0.70595	2.14|2.14	0.30934|0.30934	N|N	0.726625|0.726625	D;D;D|.	0.89917|.	0.999;0.999;1.0|.	D;D;D|.	0.70716|.	0.967;0.948;0.97|.	T|.	0.67292|.	-0.5707|.	9|.	.|.	.|.	.|.	-15.2766|-15.2766	12.5134|12.5134	0.56017|0.56017	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	270;370;401|.	Q8IWF9-3;Q8IWF9;Q8IWF9-2|.	.;CCD83_HUMAN;.|.	E|R	401;270;370|275	ENSP00000280245:V401E;ENSP00000365235:V270E;ENSP00000344512:V370E|.	.|.	V|X	+|+	2|1	0|0	CCDC83|CCDC83	85308068|85308068	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.945000|0.945000	0.59286|0.59286	1.570000|1.570000	0.36439|0.36439	2.277000|2.277000	0.76020|0.76020	0.528000|0.528000	0.53228|0.53228	GTG|TGA	.		0.423	CCDC83-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000392215.1	NM_173556	
SNX29	92017	hgsc.bcm.edu;ucsc.edu	37	16	12220546	12220546	+	Nonsense_Mutation	SNP	G	G	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr16:12220546G>T	ENST00000566228.1	+	12	1528	c.1459G>T	c.(1459-1461)Gag>Tag	p.E487*	SNX29_ENST00000306030.3_Nonsense_Mutation_p.E102*|SNX29_ENST00000323433.4_Nonsense_Mutation_p.E102*	NM_032167.3	NP_115543.3	Q8TEQ0	SNX29_HUMAN	sorting nexin 29	487						extracellular vesicular exosome (GO:0070062)	phosphatidylinositol binding (GO:0035091)			endometrium(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)	7						GCTGGAGGAGGAGAACAGGTA	0.473																																					p.E487X		.											.	.	.	0			c.G1459T						.						138.0	140.0	139.0					16																	12220546		2003	4178	6181	SO:0001587	stop_gained	92017	exon12			GAGGAGGAGAACA	AK074072	CCDS10553.2	16p13.13-p13.12	2011-08-16			ENSG00000048471	ENSG00000048471		"""Sorting nexins"""	30542	protein-coding gene	gene with protein product			"""RUN domain containing 2A"""	RUNDC2A		16782399	Standard	XM_005255682		Approved	FLJ12363	uc002dby.5	Q8TEQ0		ENST00000566228.1:c.1459G>T	16.37:g.12220546G>T	ENSP00000456480:p.Glu487*	Somatic	59	0		WXS	Illumina HiSeq	.	31	4	NM_032167	B5MDW2|Q8N2X2|Q9HA26	Nonsense_Mutation	SNP	ENST00000566228.1	37	CCDS10553.2	.	.	.	.	.	.	.	.	.	.	G	37	6.039100	0.97226	.	.	ENSG00000048471	ENST00000306030;ENST00000323433	.	.	.	4.36	4.36	0.52297	.	0.224346	0.37530	N	0.002047	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.25106	T	0.35	-22.2265	11.1914	0.48687	0.0:0.1871:0.8129:0.0	.	.	.	.	X	102	.	ENSP00000306940:E102X	E	+	1	0	SNX29	12128047	1.000000	0.71417	0.990000	0.47175	0.710000	0.40934	2.863000	0.48396	2.379000	0.81126	0.650000	0.86243	GAG	.		0.473	SNX29-005	PUTATIVE	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422622.1		
HK2	3099	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	2	75100419	75100419	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr2:75100419G>T	ENST00000290573.2	+	5	1112	c.512G>T	c.(511-513)tGg>tTg	p.W171L	HK2_ENST00000409174.1_Missense_Mutation_p.W143L	NM_000189.4	NP_000180.2	P52789	HXK2_HUMAN	hexokinase 2	171	Hexokinase type-1 1.|Regulatory.				apoptotic mitochondrial changes (GO:0008637)|carbohydrate metabolic process (GO:0005975)|cellular glucose homeostasis (GO:0001678)|glucose 6-phosphate metabolic process (GO:0051156)|glucose metabolic process (GO:0006006)|glucose transport (GO:0015758)|glycolytic process (GO:0006096)|hexose transport (GO:0008645)|lactation (GO:0007595)|regulation of glucose import (GO:0046324)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)	ATP binding (GO:0005524)|fructokinase activity (GO:0008865)|glucokinase activity (GO:0004340)|glucose binding (GO:0005536)|hexokinase activity (GO:0004396)|mannokinase activity (GO:0019158)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(22)|ovary(2)|prostate(1)|skin(2)|stomach(1)|urinary_tract(1)	43						CTGGTCTCATGGACCAAGGGA	0.527																																					p.W171L		.											.	.	.	0			c.G512T						.						117.0	122.0	121.0					2																	75100419		2203	4300	6503	SO:0001583	missense	3099	exon5			TCTCATGGACCAA		CCDS1956.1	2p13	2010-03-19			ENSG00000159399	ENSG00000159399	2.7.1.1		4923	protein-coding gene	gene with protein product		601125					Standard	NM_000189		Approved		uc002snd.3	P52789	OTTHUMG00000129972	ENST00000290573.2:c.512G>T	2.37:g.75100419G>T	ENSP00000290573:p.Trp171Leu	Somatic	37	0		WXS	Illumina HiSeq	.	35	19	NM_000189	D6W5J2|Q8WU87|Q9UN82	Missense_Mutation	SNP	ENST00000290573.2	37	CCDS1956.1	.	.	.	.	.	.	.	.	.	.	G	25.5	4.642043	0.87859	.	.	ENSG00000159399	ENST00000290573;ENST00000535740;ENST00000409174	D;D	0.99660	-6.32;-6.32	5.1	5.1	0.69264	Hexokinase, conserved site (1);Hexokinase, N-terminal (1);	0.000000	0.85682	D	0.000000	D	0.99789	0.9911	H	0.97240	3.965	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97050	0.9763	10	0.87932	D	0	-17.9825	16.3899	0.83531	0.0:0.0:1.0:0.0	.	171	P52789	HXK2_HUMAN	L	171;171;143	ENSP00000290573:W171L;ENSP00000387140:W143L	ENSP00000290573:W171L	W	+	2	0	HK2	74953927	1.000000	0.71417	0.998000	0.56505	0.862000	0.49288	9.597000	0.98273	2.802000	0.96397	0.561000	0.74099	TGG	.		0.527	HK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252238.2	NM_000189	
FSHB	2488	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	11	30255127	30255127	+	Missense_Mutation	SNP	A	A	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr11:30255127A>G	ENST00000417547.1	+	3	209	c.170A>G	c.(169-171)tAt>tGt	p.Y57C	FSHB_ENST00000533718.1_Missense_Mutation_p.Y57C|FSHB_ENST00000254122.3_Missense_Mutation_p.Y57C	NM_001018080.1	NP_001018090.1	P01225	FSHB_HUMAN	follicle stimulating hormone, beta polypeptide	57					cellular protein metabolic process (GO:0044267)|female gamete generation (GO:0007292)|female pregnancy (GO:0007565)|follicle-stimulating hormone signaling pathway (GO:0042699)|peptide hormone processing (GO:0016486)|positive regulation of bone resorption (GO:0045780)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|progesterone biosynthetic process (GO:0006701)|regulation of osteoclast differentiation (GO:0045670)|Sertoli cell proliferation (GO:0060011)|signal transduction (GO:0007165)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	hormone activity (GO:0005179)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(5)|ovary(3)|skin(1)	12						GATCTGGTGTATAAGGACCCA	0.438																																					p.Y57C		.											.	.	.	0			c.A170G						.						76.0	73.0	74.0					11																	30255127		2202	4299	6501	SO:0001583	missense	2488	exon3			TGGTGTATAAGGA		CCDS7868.1	11p13	2013-02-26				ENSG00000131808		"""Endogenous ligands"""	3964	protein-coding gene	gene with protein product	"""follitropin, beta chain"", ""follicle-stimulating hormone beta subunit"""	136530				2885163, 3151250	Standard	NM_000510		Approved		uc001msm.3	P01225		ENST00000417547.1:c.170A>G	11.37:g.30255127A>G	ENSP00000416606:p.Tyr57Cys	Somatic	70	0		WXS	Illumina HiSeq	.	48	12	NM_000510	A2TF08|A5JVV3|Q14D61	Missense_Mutation	SNP	ENST00000417547.1	37	CCDS7868.1	.	.	.	.	.	.	.	.	.	.	A	11.71	1.720518	0.30503	.	.	ENSG00000131808	ENST00000254122;ENST00000417547;ENST00000533718	D;D;D	0.83506	-1.73;-1.73;-1.73	6.17	4.99	0.66335	Cystine knot (1);	0.218618	0.39687	N	0.001300	D	0.83741	0.5320	M	0.88105	2.93	0.26108	N	0.980724	B	0.06786	0.001	B	0.14578	0.011	T	0.76547	-0.2919	10	0.54805	T	0.06	.	8.4963	0.33130	0.7356:0.1352:0.0:0.1293	.	57	P01225	FSHB_HUMAN	C	57	ENSP00000254122:Y57C;ENSP00000416606:Y57C;ENSP00000433424:Y57C	ENSP00000254122:Y57C	Y	+	2	0	FSHB	30211703	0.424000	0.25490	0.998000	0.56505	0.978000	0.69477	1.884000	0.39668	2.371000	0.80710	0.533000	0.62120	TAT	.		0.438	FSHB-003	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389757.1	NM_000510	
BMP4	652	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	14	54418732	54418732	+	Missense_Mutation	SNP	C	C	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr14:54418732C>G	ENST00000245451.4	-	3	602	c.209G>C	c.(208-210)cGc>cCc	p.R70P	BMP4_ENST00000559087.1_Missense_Mutation_p.R70P|BMP4_ENST00000417573.1_Missense_Mutation_p.R70P|BMP4_ENST00000558984.1_Missense_Mutation_p.R70P	NM_001202.3	NP_001193.2	P12644	BMP4_HUMAN	bone morphogenetic protein 4	70					activation of MAPKK activity (GO:0000186)|anterior/posterior axis specification (GO:0009948)|blood vessel endothelial cell proliferation involved in sprouting angiogenesis (GO:0002043)|BMP signaling pathway (GO:0030509)|BMP signaling pathway involved in heart induction (GO:0003130)|BMP signaling pathway involved in nephric duct formation (GO:0071893)|BMP signaling pathway involved in renal system segmentation (GO:0061151)|BMP signaling pathway involved in ureter morphogenesis (GO:0061149)|branching involved in prostate gland morphogenesis (GO:0060442)|branching involved in ureteric bud morphogenesis (GO:0001658)|branching morphogenesis of an epithelial tube (GO:0048754)|bronchus development (GO:0060433)|bud dilation involved in lung branching (GO:0060503)|bud elongation involved in lung branching (GO:0060449)|cardiac septum development (GO:0003279)|cellular response to growth factor stimulus (GO:0071363)|chondrocyte differentiation (GO:0002062)|cloacal septation (GO:0060197)|common-partner SMAD protein phosphorylation (GO:0007182)|cranial suture morphogenesis (GO:0060363)|deltoid tuberosity development (GO:0035993)|dorsal/ventral neural tube patterning (GO:0021904)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic digit morphogenesis (GO:0042733)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic skeletal joint morphogenesis (GO:0060272)|endocardial cushion development (GO:0003197)|endochondral ossification (GO:0001958)|epithelial cell proliferation involved in lung morphogenesis (GO:0060502)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|epithelial-mesenchymal cell signaling (GO:0060684)|erythrocyte differentiation (GO:0030218)|extracellular matrix organization (GO:0030198)|germ cell development (GO:0007281)|glomerular capillary formation (GO:0072104)|glomerular visceral epithelial cell development (GO:0072015)|hematopoietic progenitor cell differentiation (GO:0002244)|inner ear receptor cell differentiation (GO:0060113)|intermediate mesodermal cell differentiation (GO:0048392)|kidney development (GO:0001822)|lens induction in camera-type eye (GO:0060235)|lung alveolus development (GO:0048286)|lung morphogenesis (GO:0060425)|lymphoid progenitor cell differentiation (GO:0002320)|macrophage differentiation (GO:0030225)|mammary gland formation (GO:0060592)|mesenchymal cell differentiation involved in kidney development (GO:0072161)|mesenchymal cell proliferation involved in ureter development (GO:0072198)|mesenchymal cell proliferation involved in ureteric bud development (GO:0072138)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|mesodermal cell fate determination (GO:0007500)|mesonephros development (GO:0001823)|metanephric collecting duct development (GO:0072205)|monocyte differentiation (GO:0030224)|negative regulation of apoptotic process (GO:0043066)|negative regulation of branch elongation involved in ureteric bud branching by BMP signaling pathway (GO:0072097)|negative regulation of branching involved in ureteric bud morphogenesis (GO:0090191)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell death (GO:0060548)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell proliferation involved in heart morphogenesis (GO:2000137)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of glomerular mesangial cell proliferation (GO:0072125)|negative regulation of glomerulus development (GO:0090194)|negative regulation of immature T cell proliferation in thymus (GO:0033088)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of mesenchymal cell proliferation involved in ureter development (GO:0072200)|negative regulation of metanephric comma-shaped body morphogenesis (GO:2000007)|negative regulation of metanephric S-shaped body morphogenesis (GO:2000005)|negative regulation of mitosis (GO:0045839)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of phosphorylation (GO:0042326)|negative regulation of prostatic bud formation (GO:0060686)|negative regulation of striated muscle tissue development (GO:0045843)|negative regulation of T cell differentiation in thymus (GO:0033085)|negative regulation of thymocyte apoptotic process (GO:0070244)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|neuron fate commitment (GO:0048663)|odontogenesis (GO:0042476)|odontogenesis of dentin-containing tooth (GO:0042475)|osteoblast differentiation (GO:0001649)|pituitary gland development (GO:0021983)|positive chemotaxis (GO:0050918)|positive regulation of apoptotic process (GO:0043065)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of bone mineralization (GO:0030501)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of cardiac muscle fiber development (GO:0055020)|positive regulation of cartilage development (GO:0061036)|positive regulation of cell death (GO:0010942)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of DNA-dependent DNA replication (GO:2000105)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of epidermal cell differentiation (GO:0045606)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of kidney development (GO:0090184)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of ossification (GO:0045778)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of protein binding (GO:0032092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|post-embryonic development (GO:0009791)|protein localization to nucleus (GO:0034504)|pulmonary artery endothelial tube morphogenesis (GO:0061155)|regulation of branching involved in prostate gland morphogenesis (GO:0060687)|regulation of cell fate commitment (GO:0010453)|regulation of odontogenesis of dentin-containing tooth (GO:0042487)|regulation of pathway-restricted SMAD protein phosphorylation (GO:0060393)|regulation of smooth muscle cell differentiation (GO:0051150)|renal system development (GO:0072001)|renal system process (GO:0003014)|secondary heart field specification (GO:0003139)|SMAD protein signal transduction (GO:0060395)|smooth muscle tissue development (GO:0048745)|smoothened signaling pathway (GO:0007224)|specification of organ position (GO:0010159)|specification of ureteric bud anterior/posterior symmetry by BMP signaling pathway (GO:0072101)|steroid hormone mediated signaling pathway (GO:0043401)|telencephalon development (GO:0021537)|telencephalon regionalization (GO:0021978)|tendon cell differentiation (GO:0035990)|trachea development (GO:0060438)|trachea formation (GO:0060440)|type B pancreatic cell development (GO:0003323)|ureter epithelial cell differentiation (GO:0072192)|ureter smooth muscle cell differentiation (GO:0072193)|ureteric bud development (GO:0001657)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	BMP receptor binding (GO:0070700)|chemoattractant activity (GO:0042056)|cytokine activity (GO:0005125)|heparin binding (GO:0008201)			breast(1)|endometrium(3)|large_intestine(2)|lung(9)|prostate(3)|urinary_tract(1)	19						AGGCTGCGGGCGGCGGCGCAG	0.632																																					p.R70P		.											BMP4,colon,carcinoma,0,2	BMP4	0	0			c.G209C						.						42.0	45.0	44.0					14																	54418732		2203	4300	6503	SO:0001583	missense	652	exon3			TGCGGGCGGCGGC	AF035427	CCDS9715.1	14q22-q23	2014-01-30			ENSG00000125378	ENSG00000125378		"""Bone morphogenetic proteins"", ""Endogenous ligands"""	1071	protein-coding gene	gene with protein product		112262		BMP2B		7558046, 7579580	Standard	NM_001202		Approved		uc010aoh.3	P12644	OTTHUMG00000140303	ENST00000245451.4:c.209G>C	14.37:g.54418732C>G	ENSP00000245451:p.Arg70Pro	Somatic	32	0		WXS	Illumina HiSeq	.	25	15	NM_130851	Q9UM80	Missense_Mutation	SNP	ENST00000245451.4	37	CCDS9715.1	.	.	.	.	.	.	.	.	.	.	C	31	5.076408	0.94000	.	.	ENSG00000125378	ENST00000245451;ENST00000417573	T;T	0.70045	-0.45;-0.45	5.2	5.2	0.72013	Transforming growth factor-beta, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.79936	0.4532	L	0.58969	1.84	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.81280	-0.1004	10	0.87932	D	0	.	17.9081	0.88926	0.0:1.0:0.0:0.0	.	70	P12644	BMP4_HUMAN	P	70	ENSP00000245451:R70P;ENSP00000394165:R70P	ENSP00000245451:R70P	R	-	2	0	BMP4	53488482	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.558000	0.82253	2.717000	0.92951	0.655000	0.94253	CGC	.		0.632	BMP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276894.2	NM_001202	
UBXN4	23190	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	2	136513166	136513166	+	Missense_Mutation	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr2:136513166T>G	ENST00000272638.9	+	5	724	c.413T>G	c.(412-414)tTt>tGt	p.F138C	UBXN4_ENST00000490163.1_3'UTR	NM_014607.3	NP_055422.1	Q92575	UBXN4_HUMAN	UBX domain protein 4	138					response to unfolded protein (GO:0006986)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nucleus (GO:0005634)				NS(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(9)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	24						TCTGCGTCATTTGAACCTAAC	0.403																																					p.F138C		.											.	.	.	0			c.T413G						.						98.0	93.0	95.0					2																	136513166		1858	4105	5963	SO:0001583	missense	23190	exon5			CGTCATTTGAACC	D87684	CCDS42761.1	2q21.3-q22.1	2008-07-25	2008-07-25	2008-07-25	ENSG00000144224	ENSG00000144224		"""UBX domain containing"""	14860	protein-coding gene	gene with protein product	"""erasin"""	611216	"""UBX domain-containing 2"", ""UBX domain containing 2"""	UBXDC1, UBXD2		16968747	Standard	NM_014607		Approved	KIAA0242	uc002tur.3	Q92575	OTTHUMG00000153577	ENST00000272638.9:c.413T>G	2.37:g.136513166T>G	ENSP00000272638:p.Phe138Cys	Somatic	40	0		WXS	Illumina HiSeq	.	21	7	NM_014607	A8K9W4|Q4ZG56|Q8IYM5	Missense_Mutation	SNP	ENST00000272638.9	37	CCDS42761.1	.	.	.	.	.	.	.	.	.	.	T	10.90	1.480285	0.26598	.	.	ENSG00000144224	ENST00000272638;ENST00000430594	T	0.42900	0.96	5.51	1.44	0.22558	.	0.801112	0.11437	N	0.564202	T	0.25531	0.0621	N	0.22421	0.69	0.30261	N	0.793124	B	0.02656	0.0	B	0.01281	0.0	T	0.20472	-1.0274	10	0.38643	T	0.18	.	5.3289	0.15922	0.2734:0.0:0.2978:0.4289	.	138	Q92575	UBXN4_HUMAN	C	138;120	ENSP00000272638:F138C	ENSP00000272638:F138C	F	+	2	0	UBXN4	136229636	0.095000	0.21747	0.997000	0.53966	0.667000	0.39255	-0.030000	0.12308	0.344000	0.23847	0.455000	0.32223	TTT	.		0.403	UBXN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331696.1	NM_014607	
SIK1	150094	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	21	44845977	44845977	+	Missense_Mutation	SNP	C	C	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr21:44845977C>G	ENST00000270162.6	-	2	214	c.82G>C	c.(82-84)Gac>Cac	p.D28H		NM_173354.3	NP_775490.2	P57059	SIK1_HUMAN	salt-inducible kinase 1	28	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cardiac muscle cell differentiation (GO:0055007)|cell cycle (GO:0007049)|entrainment of circadian clock by photoperiod (GO:0043153)|intracellular signal transduction (GO:0035556)|negative regulation of CREB transcription factor activity (GO:0032792)|negative regulation of gluconeogenesis (GO:0045721)|negative regulation of triglyceride biosynthetic process (GO:0010868)|positive regulation of anoikis (GO:2000210)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of cell differentiation (GO:0045595)|regulation of mitotic cell cycle (GO:0007346)|regulation of myotube differentiation (GO:0010830)|regulation of sodium ion transport (GO:0002028)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	14-3-3 protein binding (GO:0071889)|ATP binding (GO:0005524)|cAMP response element binding protein binding (GO:0008140)|magnesium ion binding (GO:0000287)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|skin(2)|testis(2)|urinary_tract(1)	21					Dabrafenib(DB08912)	CGCTCGATGTCGTAAAAACCC	0.677																																					p.D28H		.											.	.	.	0			c.G82C						.						22.0	24.0	23.0					21																	44845977		2199	4295	6494	SO:0001583	missense	150094	exon2			CGATGTCGTAAAA	BC038504	CCDS33575.1	21q22.3	2008-12-23	2008-12-23	2008-12-23	ENSG00000142178	ENSG00000142178			11142	protein-coding gene	gene with protein product	"""myocardial SNF1-like kinase"""	605705	"""SNF1-like kinase"""	SNF1LK		7893599	Standard	NM_173354		Approved	msk	uc002zdf.2	P57059	OTTHUMG00000086874	ENST00000270162.6:c.82G>C	21.37:g.44845977C>G	ENSP00000270162:p.Asp28His	Somatic	82	0		WXS	Illumina HiSeq	.	44	31	NM_173354	A6NC84|Q5R2V5|Q6ZNL8|Q86YJ2	Missense_Mutation	SNP	ENST00000270162.6	37	CCDS33575.1	.	.	.	.	.	.	.	.	.	.	C	30	5.053041	0.93793	.	.	ENSG00000142178	ENST00000270162	T	0.65178	-0.14	3.7	3.7	0.42460	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.059368	0.64402	D	0.000003	T	0.67040	0.2851	N	0.20881	0.62	0.80722	D	1	D	0.71674	0.998	D	0.74674	0.984	T	0.72953	-0.4135	10	0.72032	D	0.01	.	15.5171	0.75833	0.0:1.0:0.0:0.0	.	28	P57059	SIK1_HUMAN	H	28	ENSP00000270162:D28H	ENSP00000270162:D28H	D	-	1	0	SIK1	43670405	1.000000	0.71417	0.991000	0.47740	0.915000	0.54546	7.297000	0.78799	1.611000	0.50210	0.558000	0.71614	GAC	.		0.677	SIK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195654.1	NM_173354	
NEK6	10783	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	9	127113221	127113221	+	Missense_Mutation	SNP	A	A	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr9:127113221A>G	ENST00000320246.5	+	10	1082	c.937A>G	c.(937-939)Acc>Gcc	p.T313A	PSMB7_ENST00000498485.1_5'Flank|NEK6_ENST00000539416.1_Missense_Mutation_p.T338A|AL137846.1_ENST00000583657.1_RNA|NEK6_ENST00000373600.3_Missense_Mutation_p.T347A|NEK6_ENST00000394199.2_Missense_Mutation_p.T347A|NEK6_ENST00000540326.1_Missense_Mutation_p.T331A|NEK6_ENST00000546191.1_Missense_Mutation_p.T313A|NEK6_ENST00000545174.1_Missense_Mutation_p.T313A|NEK6_ENST00000373603.1_Missense_Mutation_p.T313A	NM_014397.5	NP_055212.2	Q9HC98	NEK6_HUMAN	NIMA-related kinase 6	313					apoptotic process (GO:0006915)|chromosome segregation (GO:0007059)|cytokinesis (GO:0000910)|G2 DNA damage checkpoint (GO:0031572)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope disassembly (GO:0007077)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of cellular senescence (GO:2000772)|regulation of mitotic cell cycle (GO:0007346)|regulation of mitotic metaphase/anaphase transition (GO:0030071)|signal transduction (GO:0007165)|spindle assembly (GO:0051225)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule (GO:0005874)|nucleus (GO:0005634)	ATP binding (GO:0005524)|kinesin binding (GO:0019894)|magnesium ion binding (GO:0000287)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|signal transducer activity (GO:0004871)			endometrium(1)|kidney(1)|large_intestine(4)|lung(4)|ovary(2)|prostate(1)|skin(1)|stomach(1)	15						GATGTCCAGCACCTGAGCGTG	0.557																																					p.T347A	NSCLC(122;934 1785 18647 44295 45571)	.											.	.	.	0			c.A1039G						.						97.0	69.0	79.0					9																	127113221		2203	4300	6503	SO:0001583	missense	10783	exon11			TCCAGCACCTGAG	AF087909	CCDS6854.1, CCDS48015.1, CCDS55338.1, CCDS55339.1	9q33.3-q34.11	2012-11-15	2012-11-15		ENSG00000119408	ENSG00000119408			7749	protein-coding gene	gene with protein product	"""putative serine-threonine protein kinase"""	604884	"""NIMA (never in mitosis gene a)-related kinase 6"""			10702691	Standard	NM_001145001		Approved	SID6-1512	uc004boh.3	Q9HC98	OTTHUMG00000020650	ENST00000320246.5:c.937A>G	9.37:g.127113221A>G	ENSP00000319734:p.Thr313Ala	Somatic	29	0		WXS	Illumina HiSeq	.	23	12	NM_001166171	B7Z2D9|Q5TBG3|Q5TBG9|Q6FG86|Q6IAR3|Q96E83|Q9ULX2	Missense_Mutation	SNP	ENST00000320246.5	37	CCDS6854.1	.	.	.	.	.	.	.	.	.	.	A	10.84	1.464883	0.26335	.	.	ENSG00000119408	ENST00000373603;ENST00000540326;ENST00000373600;ENST00000320246;ENST00000373601;ENST00000545174;ENST00000394199;ENST00000546191;ENST00000539416	T;T;T;T;T;T;T;T	0.70399	-0.45;-0.45;-0.47;-0.45;-0.45;-0.47;-0.45;-0.48	5.38	4.24	0.50183	.	0.000000	0.85682	D	0.000000	T	0.56529	0.1991	L	0.27053	0.805	0.44652	D	0.997639	B;B;B;B	0.21452	0.033;0.056;0.034;0.056	B;B;B;B	0.21360	0.034;0.034;0.015;0.034	T	0.51996	-0.8634	10	0.46703	T	0.11	.	10.2832	0.43552	0.9232:0.0:0.0768:0.0	.	338;347;313;331	Q9HC98-4;Q9HC98-2;Q9HC98;Q9HC98-3	.;.;NEK6_HUMAN;.	A	313;331;347;313;245;313;347;313;338	ENSP00000362705:T313A;ENSP00000441469:T331A;ENSP00000362702:T347A;ENSP00000319734:T313A;ENSP00000442636:T313A;ENSP00000377749:T347A;ENSP00000441426:T313A;ENSP00000439651:T338A	ENSP00000319734:T313A	T	+	1	0	NEK6	126153042	1.000000	0.71417	0.997000	0.53966	0.015000	0.08874	8.962000	0.93254	0.899000	0.36444	0.528000	0.53228	ACC	.		0.557	NEK6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054016.1	NM_014397	
LRRC37A6P	387646	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	10	27538087	27538087	+	lincRNA	SNP	T	T	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr10:27538087T>C	ENST00000574842.1	+	0	255				LRRC37A6P_ENST00000284414.4_RNA																							GCTGTAGTCTTCTCCAGGGCT	0.527																																					.		.											.	.	.	0			.						.						74.0	67.0	69.0					10																	27538087		692	1591	2283			387646	.			TAGTCTTCTCCAG																													10.37:g.27538087T>C		Somatic	173	0		WXS	Illumina HiSeq	.	116	46	.		RNA	SNP	ENST00000574842.1	37																																																																																				.		0.527	RP11-85G18.6-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000436904.1		
RHAG	6005	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	6	49574864	49574864	+	Splice_Site	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr6:49574864T>G	ENST00000371175.4	-	8	1163	c.1137A>C	c.(1135-1137)acA>acC	p.T379T	RHAG_ENST00000229810.7_Splice_Site_p.R339R	NM_000324.2	NP_000315.2	Q02094	RHAG_HUMAN	Rh-associated glycoprotein	379					ammonium transmembrane transport (GO:0072488)|ammonium transport (GO:0015696)|bicarbonate transport (GO:0015701)|carbon dioxide transport (GO:0015670)|cellular ion homeostasis (GO:0006873)|erythrocyte development (GO:0048821)|multicellular organismal iron ion homeostasis (GO:0060586)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ammonium transmembrane transporter activity (GO:0008519)|ankyrin binding (GO:0030506)			NS(1)|breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(24)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	39	Lung NSC(77;0.0255)					TATGCTGACCTGTCATCAGAC	0.398																																					p.T379T	Ovarian(176;476 2003 7720 43408 44749)	.											.	.	.	0			c.A1137C						.						76.0	74.0	75.0					6																	49574864		2203	4300	6503	SO:0001630	splice_region_variant	6005	exon8			CTGACCTGTCATC		CCDS4927.1	6p12.3	2014-07-19	2006-02-23		ENSG00000112077	ENSG00000112077		"""CD molecules"", ""Blood group antigens"", ""Solute carriers"""	10006	protein-coding gene	gene with protein product		180297	"""Rhesus blood group-associated glycoprotein"""			9479501	Standard	NM_000324		Approved	RH50A, CD241, SLC42A1	uc003ozk.4	Q02094	OTTHUMG00000016377	ENST00000371175.4:c.1138+1A>C	6.37:g.49574864T>G		Somatic	66	0		WXS	Illumina HiSeq	.	39	29	NM_000324	B2R8T8|O43514|O43515|Q7L8L3|Q9H454	Silent	SNP	ENST00000371175.4	37	CCDS4927.1																																																																																			.		0.398	RHAG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043806.1		Silent
ARSE	415	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	X	2876371	2876371	+	Silent	SNP	C	C	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chrX:2876371C>G	ENST00000381134.3	-	3	195	c.129G>C	c.(127-129)ctG>ctC	p.L43L	ARSE_ENST00000540563.1_Intron|ARSE_ENST00000496095.1_5'Flank|ARSE_ENST00000545496.1_Silent_p.L68L	NM_000047.2	NP_000038.2	P51690	ARSE_HUMAN	arylsulfatase E (chondrodysplasia punctata 1)	43					cellular protein metabolic process (GO:0044267)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(2)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	17		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				CGTCCGCCATCAGAAGAAGGA	0.557																																					p.L43L		.											.	.	.	0			c.G129C						.						113.0	80.0	91.0					X																	2876371		2203	4300	6503	SO:0001819	synonymous_variant	415	exon3			CGCCATCAGAAGA	X83573	CCDS14122.1, CCDS75948.1, CCDS75949.1	Xp22.33	2013-02-14			ENSG00000157399	ENSG00000157399		"""Arylsulfatase family"""	719	protein-coding gene	gene with protein product		300180		CDPX, CDPX1		7720070	Standard	NM_000047		Approved		uc004crc.4	P51690	OTTHUMG00000137358	ENST00000381134.3:c.129G>C	X.37:g.2876371C>G		Somatic	27	0		WXS	Illumina HiSeq	.	16	15	NM_000047	Q53FT2|Q53FU8	Silent	SNP	ENST00000381134.3	37	CCDS14122.1																																																																																			.		0.557	ARSE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055643.1	NM_000047	
Unknown	0	hgsc.bcm.edu	37	18	27878877	27878877	+	IGR	SNP	C	C	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr18:27878877C>T								RP11-784B15.1 (760519 upstream) : RP11-675P14.1 (414363 downstream)																							ATAATGTCTTCTGTGTAAACC	0.303																																					.		.											.	.	.	0			.						.						84.0	78.0	80.0					18																	27878877		1567	3575	5142	SO:0001628	intergenic_variant	100302131	.			TGTCTTCTGTGTA																													18.37:g.27878877C>T		Somatic	152	0		WXS	Illumina HiSeq	.	97	4	.		RNA	SNP		37																																																																																				.	0	0.303								
RBM10	8241	hgsc.bcm.edu	37	X	47030429	47030429	+	Silent	SNP	T	T	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chrX:47030429T>C	ENST00000377604.3	+	4	946	c.204T>C	c.(202-204)gaT>gaC	p.D68D	RBM10_ENST00000329236.7_Intron|RBM10_ENST00000345781.6_Intron	NM_001204467.1|NM_001204468.1|NM_005676.4	NP_001191396.1|NP_001191397.1|NP_005667.2	P98175	RBM10_HUMAN	RNA binding motif protein 10	68					3'-UTR-mediated mRNA stabilization (GO:0070935)|mRNA processing (GO:0006397)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of smooth muscle cell apoptotic process (GO:0034393)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	identical protein binding (GO:0042802)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein complex binding (GO:0032403)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(8)|large_intestine(10)|liver(1)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	48						TCGGCCAGGATTCCTACGAGG	0.687																																					p.D133D	Melanoma(171;120 2705 19495 39241)	.											.	.	.	0			c.T399C						.						15.0	15.0	15.0					X																	47030429		2198	4273	6471	SO:0001819	synonymous_variant	8241	exon4			CCAGGATTCCTAC	U35373	CCDS14274.1, CCDS56600.1, CCDS75969.1	Xp11.3	2014-06-09			ENSG00000182872	ENSG00000182872		"""Zinc fingers, RAN-binding domain containing"", ""G patch domain containing"", ""RNA binding motif (RRM) containing"""	9896	protein-coding gene	gene with protein product		300080				8590280, 8808293	Standard	NM_005676		Approved	DXS8237E, KIAA0122, GPATC9, ZRANB5, GPATCH9	uc004dhi.3	P98175	OTTHUMG00000021432	ENST00000377604.3:c.204T>C	X.37:g.47030429T>C		Somatic	6	0		WXS	Illumina HiSeq	.	10	8	NM_001204468	C4AM81|Q14136|Q5JRR2|Q9BTE4|Q9BTX0|Q9NTB1	Silent	SNP	ENST00000377604.3	37	CCDS14274.1																																																																																			.		0.687	RBM10-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056381.1	NM_005676	
SPINK5	11005	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	5	147498034	147498034	+	Missense_Mutation	SNP	A	A	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr5:147498034A>T	ENST00000256084.7	+	23	2189	c.2147A>T	c.(2146-2148)aAt>aTt	p.N716I	SPINK5_ENST00000398454.1_Missense_Mutation_p.N716I|SPINK5_ENST00000359874.3_Missense_Mutation_p.N716I	NM_006846.3	NP_006837.2	Q9NQ38	ISK5_HUMAN	serine peptidase inhibitor, Kazal type 5	716	Kazal-like 11. {ECO:0000255|PROSITE- ProRule:PRU00798}.				anagen (GO:0042640)|epidermal cell differentiation (GO:0009913)|epithelial cell differentiation (GO:0030855)|extracellular matrix organization (GO:0030198)|hair cell differentiation (GO:0035315)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of immune response (GO:0050777)|negative regulation of proteolysis (GO:0045861)|negative regulation of serine-type peptidase activity (GO:1902572)|regulation of cell adhesion (GO:0030155)|regulation of T cell differentiation (GO:0045580)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|epidermal lamellar body (GO:0097209)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|perinuclear region of cytoplasm (GO:0048471)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(16)|ovary(4)|prostate(1)|skin(5)|stomach(8)|upper_aerodigestive_tract(2)	64			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CAAATGAAAAATGGAAGACTC	0.403																																					p.N716I		.											.	.	.	0			c.A2147T						.						130.0	131.0	130.0					5																	147498034		1923	4119	6042	SO:0001583	missense	11005	exon23			TGAAAAATGGAAG	AJ228139	CCDS43382.1, CCDS47300.1, CCDS47301.1	5q31-q32	2014-09-17	2005-08-17		ENSG00000133710	ENSG00000133710		"""Serine peptidase inhibitors, Kazal type"""	15464	protein-coding gene	gene with protein product	"""lymphoepithelial Kazal-type-related inhibitor"""	605010	"""serine protease inhibitor, Kazal type 5"""			10419450	Standard	NM_001127698		Approved	VAKTI, LEKTI, LETKI, NETS, NS, FLJ21544, FLJ97536, FLJ97596, FLJ99794, DKFZp686K19184	uc003loy.2	Q9NQ38	OTTHUMG00000134305	ENST00000256084.7:c.2147A>T	5.37:g.147498034A>T	ENSP00000256084:p.Asn716Ile	Somatic	79	0		WXS	Illumina HiSeq	.	70	12	NM_001127699	A8MYE8|B7WPB7|D6REN5|O75770|Q3LX95|Q3LX96|Q3LX97|Q96PP2|Q96PP3	Missense_Mutation	SNP	ENST00000256084.7	37	CCDS43382.1	.	.	.	.	.	.	.	.	.	.	A	13.83	2.355169	0.41700	.	.	ENSG00000133710	ENST00000398454;ENST00000359874;ENST00000508733;ENST00000256084	T;T;T;T	0.08720	3.06;3.06;3.06;3.06	5.75	4.59	0.56863	Proteinase inhibitor I1, Kazal (1);	0.625437	0.15012	N	0.285511	T	0.14184	0.0343	M	0.62266	1.93	0.25185	N	0.990175	P;P;P;P	0.47034	0.527;0.889;0.823;0.794	B;P;B;P	0.47941	0.288;0.562;0.359;0.562	T	0.09751	-1.0660	10	0.38643	T	0.18	-7.7572	8.8087	0.34954	0.9149:0.0:0.0851:0.0	.	697;716;716;716	B4DWS3;Q9NQ38-3;Q9NQ38;Q9NQ38-2	.;.;ISK5_HUMAN;.	I	716;716;697;716	ENSP00000381472:N716I;ENSP00000352936:N716I;ENSP00000421519:N697I;ENSP00000256084:N716I	ENSP00000256084:N716I	N	+	2	0	SPINK5	147478227	0.264000	0.24093	0.819000	0.32651	0.393000	0.30537	2.370000	0.44240	1.122000	0.41944	0.533000	0.62120	AAT	.		0.403	SPINK5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000259215.2	NM_001127698	
BIRC6	57448	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	2	32678936	32678936	+	Missense_Mutation	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr2:32678936T>G	ENST00000421745.2	+	23	4813	c.4679T>G	c.(4678-4680)cTt>cGt	p.L1560R		NM_016252.3	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat containing 6	1560					apoptotic process (GO:0006915)|labyrinthine layer development (GO:0060711)|mitotic nuclear division (GO:0007067)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of cell proliferation (GO:0042127)|regulation of cytokinesis (GO:0032465)|spongiotrophoblast layer development (GO:0060712)	endosome (GO:0005768)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|spindle pole (GO:0000922)|trans-Golgi network (GO:0005802)	acid-amino acid ligase activity (GO:0016881)|cysteine-type endopeptidase inhibitor activity (GO:0004869)|ubiquitin-protein transferase activity (GO:0004842)			NS(4)|breast(8)|central_nervous_system(3)|endometrium(21)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(31)|lung(65)|ovary(7)|pancreas(1)|prostate(5)|skin(5)|stomach(1)|urinary_tract(5)	172	Acute lymphoblastic leukemia(172;0.155)					CTCACTGGACTTTTGGAAGTT	0.398																																					p.L1560R	Pancreas(94;175 1509 16028 18060 45422)	.											BIRC6_ENST00000421745,NS,carcinoma,0,2	BIRC6_ENST00000421745	0	0			c.T4679G						.						198.0	179.0	185.0					2																	32678936		2203	4300	6503	SO:0001583	missense	57448	exon23			CTGGACTTTTGGA	AF265555	CCDS33175.2	2p22.3	2011-01-25	2011-01-25		ENSG00000115760	ENSG00000115760		"""Baculoviral IAP repeat containing"", ""Ubiquitin-conjugating enzymes E2"""	13516	protein-coding gene	gene with protein product	"""apollon"""	605638	"""baculoviral IAP repeat-containing 6"""			10544019	Standard	NM_016252		Approved	BRUCE	uc010ezu.3	Q9NR09	OTTHUMG00000150528	ENST00000421745.2:c.4679T>G	2.37:g.32678936T>G	ENSP00000393596:p.Leu1560Arg	Somatic	115	0		WXS	Illumina HiSeq	.	63	25	NM_016252	Q9ULD1	Missense_Mutation	SNP	ENST00000421745.2	37	CCDS33175.2	.	.	.	.	.	.	.	.	.	.	T	28.9	4.959819	0.92791	.	.	ENSG00000115760	ENST00000421745	D	0.88354	-2.37	5.57	5.57	0.84162	.	0.000000	0.64402	D	0.000002	D	0.94016	0.8083	M	0.73598	2.24	0.80722	D	1	D	0.71674	0.998	D	0.80764	0.994	D	0.94676	0.7861	10	0.87932	D	0	.	15.7375	0.77856	0.0:0.0:0.0:1.0	.	1560	Q9NR09	BIRC6_HUMAN	R	1560	ENSP00000393596:L1560R	ENSP00000393596:L1560R	L	+	2	0	BIRC6	32532440	1.000000	0.71417	0.996000	0.52242	0.956000	0.61745	7.977000	0.88081	2.124000	0.65301	0.477000	0.44152	CTT	.		0.398	BIRC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318769.3	NM_016252	
PCF11	51585	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	11	82877732	82877732	+	Missense_Mutation	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr11:82877732A>C	ENST00000298281.4	+	5	2245	c.1793A>C	c.(1792-1794)aAa>aCa	p.K598T		NM_015885.3	NP_056969.2	O94913	PCF11_HUMAN	PCF11 cleavage and polyadenylation factor subunit	598					gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA cleavage (GO:0006379)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	mRNA cleavage factor complex (GO:0005849)|nucleoplasm (GO:0005654)				cervix(1)|endometrium(3)|kidney(4)|large_intestine(1)|lung(22)|ovary(1)|urinary_tract(1)	33						AAAAGATGGAAATCTGGTTGG	0.338																																					p.K598T		.											.	.	.	0			c.A1793C						.						75.0	77.0	76.0					11																	82877732		1737	3792	5529	SO:0001583	missense	51585	exon5			GATGGAAATCTGG	AB020631	CCDS44689.1	11q13	2013-07-02	2013-07-02		ENSG00000165494	ENSG00000165494			30097	protein-coding gene	gene with protein product		608876	"""PCF11, cleavage and polyadenylation factor II subunit, homolog (S. cerevisiae)"", ""PCF11, cleavage and polyadenylation factor subunit, homolog (S. cerevisiae)"""			11060040	Standard	NM_015885		Approved	KIAA0824	uc001ozx.4	O94913	OTTHUMG00000167031	ENST00000298281.4:c.1793A>C	11.37:g.82877732A>C	ENSP00000298281:p.Lys598Thr	Somatic	162	0		WXS	Illumina HiSeq	.	124	44	NM_015885	A6H8W7|O43671|Q6P0X8	Missense_Mutation	SNP	ENST00000298281.4	37	CCDS44689.1	.	.	.	.	.	.	.	.	.	.	A	17.09	3.300870	0.60195	.	.	ENSG00000165494	ENST00000298281;ENST00000530660;ENST00000530304	T;T;T	0.55413	1.49;0.56;0.52	6.07	6.07	0.98685	.	0.000000	0.64402	D	0.000005	T	0.58352	0.2116	L	0.29908	0.895	0.41517	D	0.98837	D;D	0.76494	0.999;0.993	P;P	0.60012	0.867;0.813	T	0.56183	-0.8021	9	.	.	.	.	16.6406	0.85098	1.0:0.0:0.0:0.0	.	598;598	E9PQ01;O94913	.;PCF11_HUMAN	T	598	ENSP00000298281:K598T;ENSP00000434540:K598T;ENSP00000431567:K598T	.	K	+	2	0	PCF11	82555380	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.626000	0.74253	2.326000	0.78906	0.533000	0.62120	AAA	.		0.338	PCF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392548.2	NM_015885	
NRCAM	4897	hgsc.bcm.edu	37	7	107824716	107824716	+	Nonsense_Mutation	SNP	G	G	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr7:107824716G>T	ENST00000425651.2	-	19	2272	c.2273C>A	c.(2272-2274)tCa>tAa	p.S758*	NRCAM_ENST00000379028.3_Nonsense_Mutation_p.S758*|NRCAM_ENST00000379024.4_Nonsense_Mutation_p.S739*|NRCAM_ENST00000351718.4_Nonsense_Mutation_p.S742*|NRCAM_ENST00000413765.2_Nonsense_Mutation_p.S739*|NRCAM_ENST00000379022.4_Nonsense_Mutation_p.S758*	NM_001037132.2	NP_001032209.1	Q92823	NRCAM_HUMAN	neuronal cell adhesion molecule	758	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				angiogenesis (GO:0001525)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|axonogenesis (GO:0007409)|central nervous system development (GO:0007417)|clustering of voltage-gated sodium channels (GO:0045162)|heterotypic cell-cell adhesion (GO:0034113)|neuron migration (GO:0001764)|neuronal action potential propagation (GO:0019227)|positive regulation of neuron differentiation (GO:0045666)|protein localization (GO:0008104)|regulation of axon extension (GO:0030516)|retinal ganglion cell axon guidance (GO:0031290)|single organismal cell-cell adhesion (GO:0016337)|synapse assembly (GO:0007416)	axon initial segment (GO:0043194)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|synapse (GO:0045202)	ankyrin binding (GO:0030506)			breast(4)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(8)|liver(1)|lung(36)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(4)	65						ATCAGGCTCTGATCCCAGTCC	0.388																																					p.S758X		.											.	.	.	0			c.C2273A						.						87.0	75.0	79.0					7																	107824716		2203	4300	6503	SO:0001587	stop_gained	4897	exon19			GGCTCTGATCCCA		CCDS5751.1, CCDS47686.1, CCDS55153.1, CCDS75652.1	7q31	2013-02-11			ENSG00000091129	ENSG00000091129		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	7994	protein-coding gene	gene with protein product	"""NgCAM-related cell adhesion molecule"""	601581				8812479	Standard	NM_001037132		Approved	KIAA0343, Bravo	uc022aka.1	Q92823	OTTHUMG00000154973	ENST00000425651.2:c.2273C>A	7.37:g.107824716G>T	ENSP00000401244:p.Ser758*	Somatic	77	0		WXS	Illumina HiSeq	.	51	4	NM_001037132	A4D0S3|E9PDA4|O15051|O15179|Q14BM2|Q9UHI3|Q9UHI4	Nonsense_Mutation	SNP	ENST00000425651.2	37	CCDS47686.1	.	.	.	.	.	.	.	.	.	.	G	44	11.036853	0.99507	.	.	ENSG00000091129	ENST00000379032;ENST00000379028;ENST00000413765;ENST00000537765;ENST00000351718;ENST00000379024;ENST00000425651;ENST00000379022;ENST00000445979	.	.	.	5.46	5.46	0.80206	.	0.183641	0.46442	D	0.000300	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.06891	T	0.86	.	19.321	0.94240	0.0:0.0:1.0:0.0	.	.	.	.	X	758;758;739;758;742;739;758;758;742	.	ENSP00000325269:S742X	S	-	2	0	NRCAM	107611952	1.000000	0.71417	0.986000	0.45419	0.989000	0.77384	7.884000	0.87274	2.548000	0.85928	0.591000	0.81541	TCA	.		0.388	NRCAM-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337942.2	NM_001037132	
UBE2F	140739	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	2	238934042	238934042	+	Silent	SNP	A	A	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr2:238934042A>G	ENST00000272930.4	+	6	536	c.342A>G	c.(340-342)gaA>gaG	p.E114E	UBE2F_ENST00000414443.1_Silent_p.E82E|UBE2F_ENST00000409953.1_Silent_p.E90E|UBE2F_ENST00000409332.1_Silent_p.E92E|UBE2F-SCLY_ENST00000449191.1_Intron|UBE2F_ENST00000409633.1_Silent_p.E114E	NM_001278305.1|NM_080678.2	NP_001265234.1|NP_542409.1	Q969M7	UBE2F_HUMAN	ubiquitin-conjugating enzyme E2F (putative)	114					protein neddylation (GO:0045116)		ATP binding (GO:0005524)|NEDD8 ligase activity (GO:0019788)			endometrium(1)|large_intestine(1)	2		Breast(86;0.0042)|Renal(207;0.00571)|Ovarian(221;0.17)|all_hematologic(139;0.182)		Epithelial(121;6.7e-23)|OV - Ovarian serous cystadenocarcinoma(60;1.52e-11)|Kidney(56;3.53e-09)|KIRC - Kidney renal clear cell carcinoma(57;9.79e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000136)|Lung(119;0.0126)|LUSC - Lung squamous cell carcinoma(224;0.0301)		AGACAGGGGAAATATGTCTGA	0.453																																					p.E114E		.											.	.	.	0			c.A342G						.						219.0	198.0	205.0					2																	238934042		2203	4300	6503	SO:0001819	synonymous_variant	140739	exon6			AGGGGAAATATGT	BC010549	CCDS2523.1, CCDS63175.1, CCDS63176.1, CCDS63177.1	2q37.3	2008-02-05	2005-12-15		ENSG00000184182	ENSG00000184182		"""Ubiquitin-conjugating enzymes E2"""	12480	protein-coding gene	gene with protein product	"""NEDD8 conjugating enzyme"""					12477932	Standard	NM_080678		Approved	NCE2	uc031rrz.1	Q969M7	OTTHUMG00000133341	ENST00000272930.4:c.342A>G	2.37:g.238934042A>G		Somatic	39	0		WXS	Illumina HiSeq	.	27	13	NM_080678	A8K1Z8|B4DDT9|B4DFI1|B4DMK3|B4DZU2|B8ZZG2|C9J212|H9KVB9	Silent	SNP	ENST00000272930.4	37	CCDS2523.1																																																																																			.		0.453	UBE2F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257171.2	NM_080678	
SNX14	57231	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	6	86235879	86235879	+	Missense_Mutation	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr6:86235879T>G	ENST00000314673.3	-	21	2248	c.2072A>C	c.(2071-2073)cAa>cCa	p.Q691P	SNX14_ENST00000346348.3_Missense_Mutation_p.Q638P|SNX14_ENST00000508980.1_5'UTR|SNX14_ENST00000513865.1_Intron|SNX14_ENST00000369627.2_Missense_Mutation_p.Q682P|SNX14_ENST00000505648.1_Missense_Mutation_p.Q639P	NM_153816.3	NP_722523.1	Q9Y5W7	SNX14_HUMAN	sorting nexin 14	691					protein transport (GO:0015031)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	integral component of membrane (GO:0016021)	phosphatidylinositol binding (GO:0035091)			NS(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(11)|skin(1)	22		all_cancers(76;4.83e-07)|Acute lymphoblastic leukemia(125;3.3e-08)|Prostate(29;2.55e-07)|all_hematologic(105;3.66e-05)|all_epithelial(107;0.000695)|Lung NSC(302;0.197)|all_lung(197;0.24)		BRCA - Breast invasive adenocarcinoma(108;0.0423)		ATCAAGAAATTGTGTTTCCCC	0.333																																					p.Q691P		.											.	.	.	0			c.A2072C						.						37.0	37.0	37.0					6																	86235879		2203	4299	6502	SO:0001583	missense	57231	exon21			AGAAATTGTGTTT	AF121863	CCDS5003.1, CCDS5004.1, CCDS75490.1	6q15	2008-10-22			ENSG00000135317	ENSG00000135317		"""Sorting nexins"""	14977	protein-coding gene	gene with protein product						11485546, 11736640	Standard	XM_005248738		Approved	RGS-PX2	uc003pkr.3	Q9Y5W7	OTTHUMG00000015140	ENST00000314673.3:c.2072A>C	6.37:g.86235879T>G	ENSP00000313121:p.Gln691Pro	Somatic	57	0		WXS	Illumina HiSeq	.	69	19	NM_153816	B4DI55|Q4VBR3|Q5TCF9|Q5TCG0|Q6NUI7|Q6PI37|Q9BSD1	Missense_Mutation	SNP	ENST00000314673.3	37	CCDS5004.1	.	.	.	.	.	.	.	.	.	.	T	18.61	3.660962	0.67700	.	.	ENSG00000135317	ENST00000346348;ENST00000369628;ENST00000314673;ENST00000505648;ENST00000369627;ENST00000515216;ENST00000418862	T;T;T;T;T;T	0.30714	1.52;1.52;1.52;1.52;1.52;1.52	5.01	3.83	0.44106	Phox homologous domain (1);	0.057622	0.64402	N	0.000001	T	0.35624	0.0938	L	0.54323	1.7	0.58432	D	0.999999	D;D;D;D	0.89917	1.0;0.999;0.999;0.998	D;D;D;D	0.69824	0.966;0.931;0.925;0.953	T	0.14559	-1.0468	10	0.51188	T	0.08	-10.3507	11.8996	0.52675	0.0:0.0:0.1461:0.8539	.	682;638;691;639	Q9Y5W7-4;Q9Y5W7-2;Q9Y5W7;Q9Y5W7-3	.;.;SNX14_HUMAN;.	P	638;148;691;639;682;609;56	ENSP00000257769:Q638P;ENSP00000313121:Q691P;ENSP00000427380:Q639P;ENSP00000358641:Q682P;ENSP00000425630:Q609P;ENSP00000391981:Q56P	ENSP00000313121:Q691P	Q	-	2	0	SNX14	86292598	1.000000	0.71417	0.936000	0.37596	0.960000	0.62799	7.459000	0.80802	0.731000	0.32448	-0.316000	0.08728	CAA	.		0.333	SNX14-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041393.2	NM_153816	
SLC12A8	84561	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	3	124826699	124826699	+	Missense_Mutation	SNP	T	T	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr3:124826699T>A	ENST00000393469.4	-	9	1380	c.1331A>T	c.(1330-1332)gAg>gTg	p.E444V	SLC12A8_ENST00000430155.2_Missense_Mutation_p.E245V|SLC12A8_ENST00000423114.2_Missense_Mutation_p.E473V|SLC12A8_ENST00000469902.1_Missense_Mutation_p.E444V|SLC12A8_ENST00000465475.1_5'UTR|SLC12A8_ENST00000314584.7_Missense_Mutation_p.E197V	NM_001195483.1	NP_001182412	A0AV02	S12A8_HUMAN	solute carrier family 12, member 8	444					potassium ion transport (GO:0006813)	integral component of membrane (GO:0016021)	symporter activity (GO:0015293)			endometrium(2)|kidney(2)|lung(12)	16						GGCAGGTCCCTCAGAGCCGTA	0.602																																					p.E444V		.											.	.	.	0			c.A1331T						.						67.0	67.0	67.0					3																	124826699		1928	4135	6063	SO:0001583	missense	84561	exon10			GGTCCCTCAGAGC		CCDS43143.1	3q21.2	2013-07-18	2013-07-18		ENSG00000221955	ENSG00000221955		"""Solute carriers"""	15595	protein-coding gene	gene with protein product	"""solute carrier family 12 (sodium/potassium/chloride transporters), member 8"", ""cation-chloride cotransporter 9"""	611316				11863360	Standard	NM_024628		Approved	CCC9	uc003ehv.4	A0AV02	OTTHUMG00000159483	ENST00000393469.4:c.1331A>T	3.37:g.124826699T>A	ENSP00000377112:p.Glu444Val	Somatic	18	0		WXS	Illumina HiSeq	.	14	6	NM_024628	C9JJJ2|Q68D04|Q6I9Z2|Q6P4C0|Q7Z3A6|Q86WK0|Q8NFX9|Q8WUI3|Q96RF9|Q9H5P9	Missense_Mutation	SNP	ENST00000393469.4	37	CCDS43143.1	.	.	.	.	.	.	.	.	.	.	T	16.42	3.119042	0.56505	.	.	ENSG00000221955	ENST00000430155;ENST00000393469;ENST00000423114;ENST00000469902;ENST00000314584	D;D;D;D;D	0.89123	-1.98;-2.46;-2.47;-2.46;-1.58	5.28	1.6	0.23607	.	.	.	.	.	D	0.90807	0.7113	L	0.57536	1.79	0.09310	N	1	D;P;P;D	0.71674	0.998;0.82;0.586;0.985	P;B;B;P	0.60949	0.881;0.19;0.146;0.735	T	0.81433	-0.0935	9	0.54805	T	0.06	.	9.0865	0.36584	0.0:0.2131:0.0:0.7869	.	197;473;444;245	A0AV02-4;A0AV02-2;A0AV02;A0AV02-3	.;.;S12A8_HUMAN;.	V	245;444;473;444;197	ENSP00000415713:E245V;ENSP00000377112:E444V;ENSP00000404243:E473V;ENSP00000418783:E444V;ENSP00000323632:E197V	ENSP00000323632:E197V	E	-	2	0	SLC12A8	126309389	0.508000	0.26154	0.050000	0.19076	0.836000	0.47400	0.921000	0.28718	0.475000	0.27415	0.533000	0.62120	GAG	.		0.602	SLC12A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355711.4	NM_024628	
ZNF91	7644	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	19	23544197	23544197	+	Silent	SNP	T	T	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr19:23544197T>C	ENST00000300619.7	-	4	1789	c.1584A>G	c.(1582-1584)agA>agG	p.R528R	ZNF91_ENST00000599743.1_Intron|ZNF91_ENST00000596528.1_5'Flank|ZNF91_ENST00000397082.2_Silent_p.R496R	NM_003430.2	NP_003421.2	Q05481	ZNF91_HUMAN	zinc finger protein 91	528					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)						all_lung(12;0.0349)|Lung NSC(12;0.0538)|all_epithelial(12;0.0611)				TTAAGGATTGTCTAAAAGCTT	0.343																																					p.R528R		.											.	.	.	0			c.A1584G						.						39.0	41.0	40.0					19																	23544197		2047	4231	6278	SO:0001819	synonymous_variant	7644	exon4			GGATTGTCTAAAA	M61871	CCDS42541.1, CCDS74322.1	19p12	2014-02-04	2006-05-12		ENSG00000167232	ENSG00000167232		"""Zinc fingers, C2H2-type"", ""-"""	13166	protein-coding gene	gene with protein product		603971	"""zinc finger protein 91 (HPF7, HTF10)"""			2023909, 2505992	Standard	XR_430154		Approved	HPF7, HTF10	uc002nre.3	Q05481	OTTHUMG00000183268	ENST00000300619.7:c.1584A>G	19.37:g.23544197T>C		Somatic	88	0		WXS	Illumina HiSeq	.	43	21	NM_003430	A8K5E1|B7Z6G6	Silent	SNP	ENST00000300619.7	37	CCDS42541.1																																																																																			.		0.343	ZNF91-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465891.1	NM_003430	
VTRNA2-1	100126299	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	5	135416270	135416270	+	lincRNA	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr5:135416270T>G	ENST00000602301.1	-	0	16					NR_030583.2				vault RNA 2-1																		GGTAACCGCTTGAGCTAACTC	0.552																																					.		.											.	.	.	0			.						.						55.0	53.0	54.0					5																	135416270		1568	3582	5150			100126299	.			ACCGCTTGAGCTA			5q31.1	2013-05-03	2011-04-11	2011-04-11	ENSG00000202030	ENSG00000270123		"""Vault RNAs (vtRNAs)"""	37054	non-coding RNA	RNA, vault		614938	"""microRNA 886"", ""vault RNA 2"""	MIR886, MIRN886, VTRNA2		19298825, 19491402, 22926522, 22058117	Standard	NR_030583		Approved	vtRNA2, hvg-5, CBL-3, hsa-mir-886, nc886	uc021ydy.1				5.37:g.135416270T>G		Somatic	33	0		WXS	Illumina HiSeq	.	22	13	.		RNA	SNP	ENST00000602301.1	37																																																																																				.		0.552	VTRNA2-1-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000467708.1	NR_030583	
IGSF9B	22997	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	11	133802005	133802005	+	Silent	SNP	G	G	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr11:133802005G>A	ENST00000321016.8	-	8	1301	c.1071C>T	c.(1069-1071)gtC>gtT	p.V357V	IGSF9B_ENST00000533871.2_Silent_p.V357V			Q9UPX0	TUTLB_HUMAN	immunoglobulin superfamily, member 9B	357	Ig-like 4.				homophilic cell adhesion (GO:0007156)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)	dendrite (GO:0030425)|inhibitory synapse (GO:0060077)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)				breast(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(18)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	44	all_hematologic(175;0.127)	all_cancers(12;1.58e-21)|all_epithelial(12;5.17e-16)|all_lung(97;1.6e-05)|Lung NSC(97;3.86e-05)|Breast(109;0.000126)|Medulloblastoma(222;0.0245)|all_neural(223;0.0505)|Esophageal squamous(93;0.0559)		Epithelial(10;7.19e-10)|BRCA - Breast invasive adenocarcinoma(10;9.69e-09)|all cancers(11;1.23e-08)|OV - Ovarian serous cystadenocarcinoma(99;0.00328)|Lung(977;0.221)		TGTTCCACTTGACCACGGTGG	0.612																																					p.V357V		.											.	.	.	0			c.C1071T						.						66.0	82.0	77.0					11																	133802005		2149	4239	6388	SO:0001819	synonymous_variant	22997	exon8			CCACTTGACCACG	AK097578	CCDS61010.1	11q25	2013-02-11	2005-10-12	2005-11-20				"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	32326	protein-coding gene	gene with protein product		613773					Standard	NM_001277285		Approved	KIAA1030	uc031qfh.1	Q9UPX0		ENST00000321016.8:c.1071C>T	11.37:g.133802005G>A		Somatic	39	0		WXS	Illumina HiSeq	.	20	11	NM_014987	G5EA26	Silent	SNP	ENST00000321016.8	37																																																																																				.		0.612	IGSF9B-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		XM_290502	
PPP4R1	9989	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	18	9559465	9559465	+	Missense_Mutation	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr18:9559465A>C	ENST00000400556.3	-	14	2053	c.1980T>G	c.(1978-1980)aaT>aaG	p.N660K	PPP4R1_ENST00000400555.3_Missense_Mutation_p.N643K	NM_001042388.2	NP_001035847.1	Q8TF05	PP4R1_HUMAN	protein phosphatase 4, regulatory subunit 1	660					dephosphorylation (GO:0016311)|protein phosphorylation (GO:0006468)|regulation of catalytic activity (GO:0050790)|signal transduction (GO:0007165)	protein phosphatase 4 complex (GO:0030289)	protein phosphatase type 4 regulator activity (GO:0030362)			large_intestine(1)|skin(2)	3						GGCAGTGCCAATTCTGTCTTC	0.502																																					p.N660K	Melanoma(188;1232 2082 5061 11948 35994)	.											.	.	.	0			c.T1980G						.						219.0	202.0	207.0					18																	9559465		2021	4182	6203	SO:0001583	missense	9989	exon14			GTGCCAATTCTGT	AF111106	CCDS42412.1, CCDS42413.1	18p11.22	2010-06-18			ENSG00000154845	ENSG00000154845		"""Serine/threonine phosphatases / Protein phosphatase 4, regulatory subunits"""	9320	protein-coding gene	gene with protein product		604908				10026142	Standard	NM_001042388		Approved	PP4R1	uc002koe.2	Q8TF05	OTTHUMG00000137466	ENST00000400556.3:c.1980T>G	18.37:g.9559465A>C	ENSP00000383402:p.Asn660Lys	Somatic	33	0		WXS	Illumina HiSeq	.	29	15	NM_001042388	Q99774|Q9UNQ7	Missense_Mutation	SNP	ENST00000400556.3	37	CCDS42412.1	.	.	.	.	.	.	.	.	.	.	A	16.54	3.150577	0.57151	.	.	ENSG00000154845	ENST00000400556;ENST00000400555	T;T	0.32988	1.43;1.43	5.57	-1.04	0.10068	Armadillo-like helical (1);Armadillo-type fold (1);	0.247888	0.42053	D	0.000777	T	0.35566	0.0936	M	0.65975	2.015	0.46458	D	0.999052	B;P;B	0.42010	0.369;0.768;0.172	B;P;B	0.45232	0.131;0.474;0.171	T	0.18808	-1.0325	9	.	.	.	-28.2103	14.8346	0.70172	0.0934:0.0:0.9066:0.0	.	643;660;643	A8K923;Q8TF05;Q8TF05-2	.;PP4R1_HUMAN;.	K	660;643	ENSP00000383402:N660K;ENSP00000383401:N643K	.	N	-	3	2	PPP4R1	9549465	1.000000	0.71417	0.976000	0.42696	0.873000	0.50193	2.516000	0.45520	-0.568000	0.06038	-0.263000	0.10527	AAT	.		0.502	PPP4R1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000268571.1	NM_005134	
SUPT20H	55578	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	13	37583918	37583918	+	Missense_Mutation	SNP	G	G	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr13:37583918G>A	ENST00000350612.6	-	26	2451	c.2231C>T	c.(2230-2232)gCt>gTt	p.A744V	SUPT20H_ENST00000475892.1_Silent_p.G788G|SUPT20H_ENST00000464744.1_Silent_p.G710G|SUPT20H_ENST00000356185.3_Silent_p.G710G|SUPT20H_ENST00000360252.4_Silent_p.G710G	NM_001014286.2	NP_001014308.2	Q8NEM7	SP20H_HUMAN	suppressor of Ty 20 homolog (S. cerevisiae)	744	Gln-rich.				autophagy (GO:0006914)|chromatin organization (GO:0006325)|gastrulation (GO:0007369)	SAGA complex (GO:0000124)|SAGA-type complex (GO:0070461)	transcription cofactor activity (GO:0003712)										TGCTGCCATAGCCATTTGATG	0.473																																					p.A744V		.											.	.	.	0			c.C2231T						.						110.0	101.0	104.0					13																	37583918		2203	4300	6503	SO:0001583	missense	55578	exon26			GCCATAGCCATTT	AF093250	CCDS9362.1, CCDS31959.1, CCDS61311.1	13q13	2012-11-29	2012-11-29	2012-11-29	ENSG00000102710	ENSG00000102710			20596	protein-coding gene	gene with protein product	"""p38 interacting protein"", ""transcription factor (p38 interacting protein)"""	613417	"""chromosome 13 open reading frame 19"", ""family with sequence similarity 48, member A"""	C13orf19, FAM48A		12070015 , 16685401	Standard	NM_001278480		Approved	SPT20, bA421P11.4, P38IP	uc001uwg.3	Q8NEM7	OTTHUMG00000016747	ENST00000350612.6:c.2231C>T	13.37:g.37583918G>A	ENSP00000218894:p.Ala744Val	Somatic	76	0		WXS	Illumina HiSeq	.	39	21	NM_001014286	E7ER46|Q71RF3|Q9Y6A6	Missense_Mutation	SNP	ENST00000350612.6	37	CCDS31959.1	.	.	.	.	.	.	.	.	.	.	G	9.351	1.065521	0.20067	.	.	ENSG00000102710	ENST00000350612	T	0.32988	1.43	5.76	5.76	0.90799	.	0.121925	0.37219	N	0.002192	T	0.25865	0.0630	L	0.50333	1.59	0.80722	D	1	B	0.06786	0.001	B	0.08055	0.003	T	0.06935	-1.0799	10	0.12766	T	0.61	0.7452	10.9946	0.47569	0.1273:0.0:0.8727:0.0	.	744	Q8NEM7	FA48A_HUMAN	V	744	ENSP00000218894:A744V	ENSP00000218894:A744V	A	-	2	0	FAM48A	36481918	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	4.003000	0.57061	2.733000	0.93635	0.467000	0.42956	GCT	.		0.473	SUPT20H-016	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354766.1	NM_017569	
B3GNT1	11041	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	11	66114615	66114615	+	Silent	SNP	C	C	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr11:66114615C>A	ENST00000311181.4	-	1	548	c.402G>T	c.(400-402)ctG>ctT	p.L134L	BRMS1_ENST00000425825.2_5'Flank|BRMS1_ENST00000359957.3_5'Flank|RP11-867G23.8_ENST00000531602.1_5'Flank	NM_006876.2	NP_006867.1	O43505	B3GN1_HUMAN	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 1	134					axon guidance (GO:0007411)|carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|poly-N-acetyllactosamine biosynthetic process (GO:0030311)|protein glycosylation (GO:0006486)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)	N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase activity (GO:0008532)			breast(2)|kidney(1)|large_intestine(2)|lung(6)|urinary_tract(1)	12						GCACCGTGGCCAGCTGCGCCT	0.711																																					p.L134L		.											.	.	.	0			c.G402T						.						10.0	9.0	9.0					11																	66114615		2177	4262	6439	SO:0001819	synonymous_variant	11041	exon1			CGTGGCCAGCTGC	AF029893	CCDS8136.1	11q13.2	2014-07-08	2006-04-12	2006-04-12	ENSG00000174684	ENSG00000174684	2.4.1.149	"""Beta 3-glycosyltransferases"""	15685	protein-coding gene	gene with protein product	"""N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase"""	605517	"""UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 6"""	B3GNT6		9405606	Standard	NM_006876		Approved	iGNT, iGAT, iGnT, BETA3GNTI, B3GN-T1	uc001ohr.3	O43505	OTTHUMG00000167082	ENST00000311181.4:c.402G>T	11.37:g.66114615C>A		Somatic	22	0		WXS	Illumina HiSeq	.	16	8	NM_006876	Q4TTN0	Silent	SNP	ENST00000311181.4	37	CCDS8136.1																																																																																			.		0.711	B3GNT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392959.1	NM_006876	
PTPMT1	114971	hgsc.bcm.edu	37	11	47591273	47591273	+	Nonsense_Mutation	SNP	G	G	T	rs200800213		TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr11:47591273G>T	ENST00000326674.9	+	3	299	c.277G>T	c.(277-279)Gag>Tag	p.E93*	PTPMT1_ENST00000527079.2_3'UTR|PTPMT1_ENST00000426530.2_Intron|NDUFS3_ENST00000533507.1_Intron|PTPMT1_ENST00000534775.1_Missense_Mutation_p.R129L|PTPMT1_ENST00000326656.8_Intron	NM_175732.2	NP_783859.1	Q8WUK0	PTPM1_HUMAN	protein tyrosine phosphatase, mitochondrial 1	93					cardiolipin biosynthetic process (GO:0032049)|glycerophospholipid biosynthetic process (GO:0046474)|inositol phosphate dephosphorylation (GO:0046855)|phosphatidylglycerol biosynthetic process (GO:0006655)|phospholipid metabolic process (GO:0006644)|protein dephosphorylation (GO:0006470)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	phosphatidylglycerophosphatase activity (GO:0008962)|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity (GO:0004439)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.E93K(1)		breast(1)|kidney(1)|large_intestine(2)|lung(1)|skin(1)	6						ACTAGGAGTCGAGCAGCTGCG	0.522																																					p.E93X		.											PTPMT1,NS,carcinoma,0,1	PTPMT1	0	1	Substitution - Missense(1)	breast(1)	c.G277T						.						67.0	69.0	69.0					11																	47591273		1973	4169	6142	SO:0001587	stop_gained	114971	exon3			GGAGTCGAGCAGC	BC014048	CCDS41643.1, CCDS44593.1	11p11.2	2011-06-09			ENSG00000110536	ENSG00000110536	3.1.3.36	"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Atypical dual specificity phosphatases"""	26965	protein-coding gene	gene with protein product		609538				12477932	Standard	NM_175732		Approved	PLIP, DUSP23, MOSP	uc001nfs.4	Q8WUK0	OTTHUMG00000166892	ENST00000326674.9:c.277G>T	11.37:g.47591273G>T	ENSP00000325958:p.Glu93*	Somatic	48	0		WXS	Illumina HiSeq	.	33	3	NM_175732	E9PAT8|Q7Z557|Q96CR2|Q9BXV8	Nonsense_Mutation	SNP	ENST00000326674.9	37	CCDS41643.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	23.6|23.6	4.433444|4.433444	0.83776|0.83776	.|.	.|.	ENSG00000110536|ENSG00000110536	ENST00000326674|ENST00000534775	.|.	.|.	.|.	5.2|5.2	5.2|5.2	0.72013|0.72013	.|.	0.000000|.	0.64402|.	U|.	0.000001|.	.|T	.|0.61961	.|0.2389	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|P	.|0.45768	.|0.866	.|P	.|0.45971	.|0.499	.|T	.|0.73126	.|-0.4081	.|6	0.29301|0.87932	T|D	0.29|0	-11.7343|-11.7343	16.9249|16.9249	0.86173|0.86173	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|129	.|E9PQM0	.|.	X|L	93|129	.|.	ENSP00000325958:E93X|ENSP00000436160:R129L	E|R	+|+	1|2	0|0	PTPMT1|PTPMT1	47547849|47547849	1.000000|1.000000	0.71417|0.71417	0.967000|0.967000	0.41034|0.41034	0.949000|0.949000	0.60115|0.60115	7.320000|7.320000	0.79064|0.79064	2.443000|2.443000	0.82685|0.82685	0.462000|0.462000	0.41574|0.41574	GAG|CGA	.		0.522	PTPMT1-002	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391746.1	XM_374879	
MRPL11	65003	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	11	66203493	66203493	+	Missense_Mutation	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr11:66203493T>G	ENST00000310999.7	-	5	657	c.564A>C	c.(562-564)gaA>gaC	p.E188D	MRPL11_ENST00000329819.4_3'UTR|MRPL11_ENST00000524576.1_5'UTR|MRPL11_ENST00000430466.2_Missense_Mutation_p.E162D	NM_016050.3	NP_057134.1	Q9Y3B7	RM11_HUMAN	mitochondrial ribosomal protein L11	188					translation (GO:0006412)	mitochondrial ribosome (GO:0005761)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			endometrium(3)|lung(2)|ovary(1)|prostate(1)	7						TCTTGGCAGCTTCTTCTTGGG	0.527																																					p.E188D		.											.	.	.	0			c.A564C						.						61.0	55.0	57.0					11																	66203493		2200	4295	6495	SO:0001583	missense	65003	exon5			GGCAGCTTCTTCT	AB051338	CCDS8139.1, CCDS8140.1, CCDS44655.1	11q13.2	2012-11-14			ENSG00000174547	ENSG00000174547		"""Mitochondrial ribosomal proteins / large subunits"""	14042	protein-coding gene	gene with protein product		611826					Standard	XR_247672		Approved		uc001ohz.4	Q9Y3B7	OTTHUMG00000167097	ENST00000310999.7:c.564A>C	11.37:g.66203493T>G	ENSP00000308897:p.Glu188Asp	Somatic	40	0		WXS	Illumina HiSeq	.	28	8	NM_016050	A6NLT0|A8K219|Q32P46|Q96Q73	Missense_Mutation	SNP	ENST00000310999.7	37	CCDS8139.1	.	.	.	.	.	.	.	.	.	.	T	12.65	2.002176	0.35320	.	.	ENSG00000174547	ENST00000310999;ENST00000430466	.	.	.	5.13	2.74	0.32292	.	0.295571	0.36815	N	0.002395	T	0.20251	0.0487	N	0.08118	0	0.80722	D	1	D;P	0.54601	0.967;0.902	B;B	0.42738	0.396;0.301	T	0.03364	-1.1044	9	0.52906	T	0.07	-10.3092	4.5368	0.12038	0.0:0.3663:0.0:0.6337	.	162;188	Q9Y3B7-2;Q9Y3B7	.;RM11_HUMAN	D	188;162	.	ENSP00000308897:E188D	E	-	3	2	MRPL11	65960069	0.996000	0.38824	1.000000	0.80357	0.464000	0.32679	0.345000	0.19979	0.777000	0.33496	0.454000	0.30748	GAA	.		0.527	MRPL11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393098.2	NM_016050	
IRF6	3664	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	209969704	209969704	+	Missense_Mutation	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr1:209969704A>C	ENST00000367021.3	-	4	540	c.368T>G	c.(367-369)aTc>aGc	p.I123S	IRF6_ENST00000542854.1_Missense_Mutation_p.I28S	NM_006147.3	NP_006138.1	O14896	IRF6_HUMAN	interferon regulatory factor 6	123					cell cycle arrest (GO:0007050)|cell development (GO:0048468)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|keratinocyte differentiation (GO:0030216)|keratinocyte proliferation (GO:0043616)|mammary gland epithelial cell differentiation (GO:0060644)|negative regulation of cell proliferation (GO:0008285)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	DNA binding (GO:0003677)|regulatory region DNA binding (GO:0000975)|sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(1)|large_intestine(4)|lung(12)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(4)	28				OV - Ovarian serous cystadenocarcinoma(81;0.0351)		TGGGTTAATGATCGAGCCCTG	0.522										HNSCC(57;0.16)																											p.I123S		.											.	.	.	0			c.T368G						.						83.0	78.0	80.0					1																	209969704		2203	4300	6503	SO:0001583	missense	3664	exon4			TTAATGATCGAGC	AL022398	CCDS1492.1, CCDS55681.1	1q32.2-q32.3	2011-02-10			ENSG00000117595	ENSG00000117595			6121	protein-coding gene	gene with protein product		607199	"""Van der Woude syndrome"""	VWS, LPS		12219090	Standard	NM_006147		Approved	OFC6, VWS1	uc001hhq.2	O14896	OTTHUMG00000036521	ENST00000367021.3:c.368T>G	1.37:g.209969704A>C	ENSP00000355988:p.Ile123Ser	Somatic	36	0		WXS	Illumina HiSeq	.	28	6	NM_006147	B4DLE2|D3DT90|F5GWX8|G0ZTL0	Missense_Mutation	SNP	ENST00000367021.3	37	CCDS1492.1	.	.	.	.	.	.	.	.	.	.	A	13.62	2.292251	0.40594	.	.	ENSG00000117595	ENST00000367021;ENST00000542854;ENST00000456314	D;D;D	0.97688	-4.37;-3.87;-4.49	5.63	5.63	0.86233	.	0.319207	0.28332	N	0.015736	D	0.93341	0.7877	N	0.14661	0.345	0.53688	D	0.999974	B	0.18461	0.028	B	0.09377	0.004	D	0.90833	0.4718	9	.	.	.	.	15.5434	0.76074	1.0:0.0:0.0:0.0	.	123	O14896	IRF6_HUMAN	S	123;28;123	ENSP00000355988:I123S;ENSP00000440532:I28S;ENSP00000403855:I123S	.	I	-	2	0	IRF6	208036327	1.000000	0.71417	0.982000	0.44146	0.860000	0.49131	4.992000	0.63889	2.145000	0.66743	0.533000	0.62120	ATC	.		0.522	IRF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088827.1	NM_006147	
RBM4	5936	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	11	66410945	66410945	+	Missense_Mutation	SNP	C	C	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr11:66410945C>T	ENST00000409406.1	+	2	1214	c.437C>T	c.(436-438)tCc>tTc	p.S146F	RBM4_ENST00000506523.2_Intron|RBM14-RBM4_ENST00000412278.2_Missense_Mutation_p.S121F|RBM4_ENST00000396053.4_Intron|RBM14-RBM4_ENST00000500635.2_Intron|RBM4_ENST00000578778.1_Intron|RBM4_ENST00000408993.2_Missense_Mutation_p.S146F|RBM4_ENST00000514361.3_Missense_Mutation_p.S121F|RBM4_ENST00000398692.4_Intron|RBM4_ENST00000530235.1_Intron|RBM4_ENST00000310092.7_Missense_Mutation_p.S146F|RBM4_ENST00000503028.2_Missense_Mutation_p.S146F			Q9BWF3	RBM4_HUMAN	RNA binding motif protein 4	146	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.				cap-independent translational initiation (GO:0002190)|cell differentiation (GO:0030154)|circadian regulation of translation (GO:0097167)|entrainment of circadian clock by photoperiod (GO:0043153)|IRES-dependent translational initiation (GO:0002192)|mRNA processing (GO:0006397)|negative regulation of translation (GO:0017148)|negative regulation of translation in response to stress (GO:0032055)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|negative regulation of translational initiation (GO:0045947)|positive regulation of muscle cell differentiation (GO:0051149)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of nucleocytoplasmic transport (GO:0046822)|response to arsenic-containing substance (GO:0046685)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|stress-activated MAPK cascade (GO:0051403)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|nuclear speck (GO:0016607)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	miRNA binding (GO:0035198)|mRNA 3'-UTR binding (GO:0003730)|mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|pre-mRNA intronic binding (GO:0097157)|pre-mRNA intronic pyrimidine-rich binding (GO:0097158)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			endometrium(3)|large_intestine(4)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13				Lung(977;0.0112)|LUSC - Lung squamous cell carcinoma(976;0.0266)		GTGCAGTTGTCCACCAGCCGG	0.572																																					p.S146F		.											.	.	.	0			c.C437T						.						58.0	64.0	62.0					11																	66410945		2180	4284	6464	SO:0001583	missense	5936	exon3			AGTTGTCCACCAG	U89505	CCDS41676.1, CCDS55776.1, CCDS55777.1	11q13	2013-02-12			ENSG00000173933	ENSG00000173933		"""Zinc fingers, CCHC domain containing"", ""RNA binding motif (RRM) containing"""	9901	protein-coding gene	gene with protein product		602571				9169144, 16260624	Standard	NM_002896		Approved	LARK, RBM4A, ZCRB3A, ZCCHC21		Q9BWF3	OTTHUMG00000154171	ENST00000409406.1:c.437C>T	11.37:g.66410945C>T	ENSP00000386894:p.Ser146Phe	Somatic	43	0		WXS	Illumina HiSeq	.	33	14	NM_002896	B3KUN0|B4E1U0|E7EQS3|O02916|Q4VC48|Q6P1P2|Q8WU85	Missense_Mutation	SNP	ENST00000409406.1	37	CCDS41676.1	.	.	.	.	.	.	.	.	.	.	C	23.7	4.445037	0.83993	.	.	ENSG00000248643;ENSG00000248643;ENSG00000248643;ENSG00000173933;ENSG00000173933;ENSG00000173933;ENSG00000173933	ENST00000412278;ENST00000503028;ENST00000514361;ENST00000310092;ENST00000408993;ENST00000510173;ENST00000409406	T;T;T;T;T;T	0.75477	0.34;-0.94;-0.94;-0.94;-0.94;-0.94	6.06	6.06	0.98353	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (1);	0.000000	0.85682	U	0.000000	D	0.89420	0.6710	M	0.91872	3.25	0.80722	D	1	D;D	0.71674	0.998;0.998	D;P	0.79784	0.993;0.905	D	0.90815	0.4704	10	0.87932	D	0	-5.0469	18.1147	0.89549	0.0:1.0:0.0:0.0	.	121;146	B0LM41;Q9BWF3	.;RBM4_HUMAN	F	121;146;146;146;146;146;146	ENSP00000388552:S121F;ENSP00000425760:S146F;ENSP00000309166:S146F;ENSP00000386561:S146F;ENSP00000422301:S146F;ENSP00000386894:S146F	ENSP00000388552:S121F	S	+	2	0	RBM4;RBM14-RBM4	66167521	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.200000	0.77838	2.882000	0.98803	0.655000	0.94253	TCC	.		0.572	RBM4-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334212.1	NM_002896	
COL4A3	1285	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	2	228118346	228118346	+	Missense_Mutation	SNP	A	A	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr2:228118346A>G	ENST00000396578.3	+	13	919	c.757A>G	c.(757-759)Aac>Gac	p.N253D	AC097662.2_ENST00000437673.1_RNA|AC097662.2_ENST00000396588.2_RNA|AC097662.2_ENST00000439598.2_RNA|AC097662.2_ENST00000606119.1_RNA	NM_000091.4	NP_000082.2	Q01955	CO4A3_HUMAN	collagen, type IV, alpha 3 (Goodpasture antigen)	253	Triple-helical region.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|axon guidance (GO:0007411)|blood circulation (GO:0008015)|cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|collagen catabolic process (GO:0030574)|endothelial cell apoptotic process (GO:0072577)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glomerular basement membrane development (GO:0032836)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell proliferation (GO:0008285)|negative regulation of endopeptidase activity (GO:0010951)|sensory perception of sound (GO:0007605)	basement membrane (GO:0005604)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent (GO:0005201)|integrin binding (GO:0005178)|metalloendopeptidase inhibitor activity (GO:0008191)|structural molecule activity (GO:0005198)			NS(4)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(24)|ovary(1)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	55		all_lung(227;0.00101)|Lung NSC(271;0.00278)|Renal(207;0.0112)|Ovarian(221;0.0129)|all_hematologic(139;0.211)|Esophageal squamous(248;0.247)		Epithelial(121;1.17e-46)|all cancers(144;6.87e-42)|Lung(261;0.0137)|LUSC - Lung squamous cell carcinoma(224;0.0187)		TGGCCCAGATAACAGAACGGT	0.463																																					p.N253D		.											.	.	.	0			c.A757G						.						303.0	282.0	289.0					2																	228118346		1935	4140	6075	SO:0001583	missense	1285	exon13			CCAGATAACAGAA		CCDS42829.1	2q36-q37	2014-09-17			ENSG00000169031	ENSG00000169031		"""Collagens"""	2204	protein-coding gene	gene with protein product	"""tumstatin"""	120070				1737849	Standard	NM_000091		Approved		uc002vom.2	Q01955	OTTHUMG00000149891	ENST00000396578.3:c.757A>G	2.37:g.228118346A>G	ENSP00000379823:p.Asn253Asp	Somatic	46	0		WXS	Illumina HiSeq	.	35	14	NM_000091	Q53QQ1|Q53R14|Q53RW8|Q9BQT2|Q9NYC4|Q9UDJ9|Q9UDK9|Q9UDL0|Q9UDL1	Missense_Mutation	SNP	ENST00000396578.3	37	CCDS42829.1	.	.	.	.	.	.	.	.	.	.	A	15.02	2.708495	0.48517	.	.	ENSG00000169031	ENST00000396578;ENST00000328380;ENST00000335583;ENST00000396574;ENST00000315699	D	0.94138	-3.36	5.59	5.59	0.84812	.	0.324946	0.25894	N	0.027604	D	0.92648	0.7664	N	0.15975	0.35	0.26153	N	0.980112	D;D;P;D	0.76494	0.998;0.996;0.611;0.999	D;D;B;P	0.76071	0.941;0.987;0.31;0.874	D	0.87097	0.2176	10	0.66056	D	0.02	.	12.157	0.54083	1.0:0.0:0.0:0.0	.	253;253;253;253	Q01955-5;Q01955-4;Q01955-2;Q01955	.;.;.;CO4A3_HUMAN	D	253	ENSP00000379823:N253D	ENSP00000323334:N253D	N	+	1	0	COL4A3	227826590	0.990000	0.36364	0.858000	0.33744	0.832000	0.47134	3.322000	0.52007	2.124000	0.65301	0.533000	0.62120	AAC	.		0.463	COL4A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331409.2	NM_000091	
GATAD1	57798	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	7	92078113	92078113	+	Missense_Mutation	SNP	A	A	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr7:92078113A>T	ENST00000287957.3	+	2	574	c.297A>T	c.(295-297)aaA>aaT	p.K99N		NM_021167.4	NP_066990.3	Q8WUU5	GATD1_HUMAN	GATA zinc finger domain containing 1	99						nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|lung(3)	6	all_cancers(62;1.63e-10)|all_epithelial(64;8.33e-10)|Breast(17;0.00311)|all_lung(186;0.0498)|Lung NSC(181;0.0676)		STAD - Stomach adenocarcinoma(171;4.51e-05)|GBM - Glioblastoma multiforme(5;8.83e-05)|all cancers(6;0.000136)|Lung(22;0.123)|Epithelial(20;0.179)|LUSC - Lung squamous cell carcinoma(200;0.225)			GAAACACTAAATACAAATCTG	0.363																																					p.K99N		.											.	.	.	0			c.A297T						.						94.0	101.0	98.0					7																	92078113		2203	4300	6503	SO:0001583	missense	57798	exon2			CACTAAATACAAA		CCDS5625.1	7q21-q22	2014-09-17			ENSG00000157259	ENSG00000157259		"""GATA zinc finger domain containing"""	29941	protein-coding gene	gene with protein product	"""ocular development associated gene"""	614518				12062807	Standard	NM_021167		Approved	ODAG, RG083M05.2, FLJ22489	uc003ulx.2	Q8WUU5	OTTHUMG00000131201	ENST00000287957.3:c.297A>T	7.37:g.92078113A>T	ENSP00000287957:p.Lys99Asn	Somatic	74	0		WXS	Illumina HiSeq	.	37	14	NM_021167	B2RE37|D6W5Q5|Q8N5Y5|Q99995|Q9H689	Missense_Mutation	SNP	ENST00000287957.3	37	CCDS5625.1	.	.	.	.	.	.	.	.	.	.	A	23.2	4.389356	0.82902	.	.	ENSG00000157259	ENST00000287957	T	0.64085	-0.08	5.37	-2.88	0.05682	.	0.000000	0.85682	D	0.000000	T	0.66761	0.2822	L	0.41710	1.295	0.58432	D	0.999995	D	0.71674	0.998	D	0.76071	0.987	T	0.66456	-0.5919	10	0.56958	D	0.05	-10.3007	13.7756	0.63050	0.4538:0.0:0.5462:0.0	.	99	Q8WUU5	GATD1_HUMAN	N	99	ENSP00000287957:K99N	ENSP00000287957:K99N	K	+	3	2	GATAD1	91916049	0.679000	0.27596	0.990000	0.47175	0.993000	0.82548	-0.073000	0.11468	-0.393000	0.07739	0.378000	0.23410	AAA	.		0.363	GATAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253929.2	NM_021167	
ERCC2	2068	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	19	45855787	45855787	+	Missense_Mutation	SNP	C	C	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr19:45855787C>A	ENST00000391945.4	-	21	2100	c.2023G>T	c.(2023-2025)Ggc>Tgc	p.G675C	ERCC2_ENST00000391944.3_Missense_Mutation_p.G597C	NM_000400.3	NP_000391.1	P18074	ERCC2_HUMAN	excision repair cross-complementation group 2	675			G -> R (in XP-D/CS; severe form). {ECO:0000269|PubMed:7825573}.		7-methylguanosine mRNA capping (GO:0006370)|aging (GO:0007568)|apoptotic process (GO:0006915)|ATP catabolic process (GO:0006200)|bone mineralization (GO:0030282)|cell proliferation (GO:0008283)|central nervous system myelin formation (GO:0032289)|chromosome segregation (GO:0007059)|DNA duplex unwinding (GO:0032508)|DNA repair (GO:0006281)|embryonic cleavage (GO:0040016)|erythrocyte maturation (GO:0043249)|extracellular matrix organization (GO:0030198)|gene expression (GO:0010467)|hair cell differentiation (GO:0035315)|hair follicle maturation (GO:0048820)|hematopoietic stem cell differentiation (GO:0060218)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|nucleotide-excision repair, DNA incision (GO:0033683)|positive regulation of DNA binding (GO:0043388)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of viral transcription (GO:0050434)|post-embryonic development (GO:0009791)|protein phosphorylation (GO:0006468)|regulation of mitotic cell cycle phase transition (GO:1901990)|response to hypoxia (GO:0001666)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)|spinal cord development (GO:0021510)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|UV protection (GO:0009650)|viral process (GO:0016032)	cytoplasm (GO:0005737)|holo TFIIH complex (GO:0005675)|MMXD complex (GO:0071817)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	4 iron, 4 sulfur cluster binding (GO:0051539)|5'-3' DNA helicase activity (GO:0043139)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)|protein N-terminus binding (GO:0047485)			large_intestine(4)|lung(2)|ovary(1)|pancreas(1)|stomach(1)	9		Ovarian(192;0.0728)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0226)		ACCATGAGGCCGTAGTCCGTC	0.597			"""Mis, N, F, S"""			"""skin basal cell, skin squamous cell, melanoma"""		Nucleotide excision repair (NER)	Xeroderma Pigmentosum																												p.G675C		.	yes	Rec		Xeroderma pigmentosum (D)	19	19q13.2-q13.3	2068	"""excision repair cross-complementing rodent repair deficiency, complementation group 2 (xeroderma pigmentosum D)"""		E	ERCC2_ENST00000391945,bladder,carcinoma,0,1	ERCC2_ENST00000391945	0	0			c.G2023T	GRCh37	CM950364	ERCC2	M		.						76.0	66.0	70.0					19																	45855787		2203	4300	6503	SO:0001583	missense	2068	exon21	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV	TGAGGCCGTAGTC		CCDS33049.1, CCDS46112.1	19q13.3	2014-09-17	2014-03-07		ENSG00000104884	ENSG00000104884	3.6.4.12	"""General transcription factor IIH complex subunits"""	3434	protein-coding gene	gene with protein product	"""excision repair cross-complementing rodent repair deficiency, complementation group 2 protein"", ""TFIIH basal transcription factor complex helicase XPB subunit"""	126340	"""xeroderma pigmentosum complementary group D"", ""excision repair cross-complementing rodent repair deficiency, complementation group 2"""	XPD		8413672, 2184031	Standard	NM_000400		Approved	MAG, EM9, MGC102762, MGC126218, MGC126219, TFIIH	uc002pbj.2	P18074	OTTHUMG00000048190	ENST00000391945.4:c.2023G>T	19.37:g.45855787C>A	ENSP00000375809:p.Gly675Cys	Somatic	44	0		WXS	Illumina HiSeq	.	43	21	NM_000400	Q2TB78|Q2YDY2|Q7KZU6|Q8N721	Missense_Mutation	SNP	ENST00000391945.4	37	CCDS33049.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.073639	0.76415	.	.	ENSG00000104884	ENST00000391941;ENST00000391942;ENST00000391945;ENST00000391944	D;D	0.82344	-1.6;-1.6	5.14	5.14	0.70334	Helicase, ATP-dependent, c2 type (1);	0.110771	0.64402	D	0.000010	D	0.95149	0.8428	H	0.99156	4.45	0.80722	D	1	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.97110	1.0;0.999;1.0	D	0.97267	0.9908	10	0.87932	D	0	-35.7354	16.0952	0.81114	0.0:1.0:0.0:0.0	.	597;675;368	E7EVE9;P18074;Q6ZNQ5	.;ERCC2_HUMAN;.	C	625;651;675;597	ENSP00000375809:G675C;ENSP00000375808:G597C	ENSP00000375805:G625C	G	-	1	0	ERCC2	50547627	1.000000	0.71417	0.979000	0.43373	0.488000	0.33401	6.923000	0.75817	2.391000	0.81399	0.561000	0.74099	GGC	.		0.597	ERCC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109626.2	NM_000400	
ABCA13	154664	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	7	48443439	48443439	+	Silent	SNP	G	G	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr7:48443439G>A	ENST00000435803.1	+	39	12057	c.12033G>A	c.(12031-12033)cgG>cgA	p.R4011R		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	4011	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(13)|central_nervous_system(8)|endometrium(25)|haematopoietic_and_lymphoid_tissue(4)|kidney(20)|large_intestine(51)|lung(100)|ovary(5)|pancreas(2)|prostate(22)|skin(10)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	270						CTTGCTCCCGGCATAGCCTGT	0.557																																					p.R4011R		.											.	.	.	0			c.G12033A						.						59.0	59.0	59.0					7																	48443439		2011	4178	6189	SO:0001819	synonymous_variant	154664	exon39			CTCCCGGCATAGC	AY204751	CCDS47584.1	7p12.3	2012-03-14			ENSG00000179869	ENSG00000179869		"""ATP binding cassette transporters / subfamily A"""	14638	protein-coding gene	gene with protein product		607807				12697998	Standard	NM_152701		Approved	FLJ33876, FLJ33951	uc003toq.2	Q86UQ4	OTTHUMG00000155840	ENST00000435803.1:c.12033G>A	7.37:g.48443439G>A		Somatic	50	0		WXS	Illumina HiSeq	.	36	15	NM_152701	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Silent	SNP	ENST00000435803.1	37	CCDS47584.1																																																																																			.		0.557	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701	
TIMMDC1	51300	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	3	119217752	119217752	+	Missense_Mutation	SNP	C	C	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr3:119217752C>T	ENST00000494664.1	+	1	374	c.172C>T	c.(172-174)Ctc>Ttc	p.L58F	TIMMDC1_ENST00000493694.1_Missense_Mutation_p.L58F|RP11-190C22.8_ENST00000609598.1_lincRNA	NM_016589.3	NP_057673.2	Q9NPL8	TIDC1_HUMAN	translocase of inner mitochondrial membrane domain containing 1	58						integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|nucleus (GO:0005634)				autonomic_ganglia(1)|kidney(2)|large_intestine(2)|lung(7)|ovary(1)|stomach(1)|urinary_tract(1)	15						ATGGGACCGCCTCCGGGAGCT	0.617																																					p.L58F		.											.	.	.	0			c.C172T						.						69.0	77.0	74.0					3																	119217752		2203	4300	6503	SO:0001583	missense	51300	exon1			GACCGCCTCCGGG	AF210057	CCDS33831.1	3q13.33	2013-12-05	2011-07-05	2011-07-05	ENSG00000113845	ENSG00000113845			1321	protein-coding gene	gene with protein product		615534	"""chromosome 3 open reading frame 1"""	C3orf1		11092749	Standard	NM_016589		Approved	FLJ22597	uc003ecn.3	Q9NPL8	OTTHUMG00000159388	ENST00000494664.1:c.172C>T	3.37:g.119217752C>T	ENSP00000418803:p.Leu58Phe	Somatic	46	0		WXS	Illumina HiSeq	.	46	16	NM_016589	D3DN81|Q6IAJ7|Q6UWU6|Q9NPR3|Q9NPS5|Q9P0Y6	Missense_Mutation	SNP	ENST00000494664.1	37	CCDS33831.1	.	.	.	.	.	.	.	.	.	.	C	18.48	3.633254	0.67015	.	.	ENSG00000113845	ENST00000494664;ENST00000493694;ENST00000466984	T;T;T	0.58506	0.99;0.33;0.42	4.99	4.99	0.66335	.	0.254472	0.39544	N	0.001330	T	0.75413	0.3846	M	0.78801	2.425	0.29670	N	0.842561	D	0.89917	1.0	D	0.83275	0.996	T	0.73480	-0.3969	10	0.72032	D	0.01	-11.9778	13.9526	0.64129	0.0:1.0:0.0:0.0	.	58	Q9NPL8	TIDC1_HUMAN	F	58	ENSP00000418803:L58F;ENSP00000419510:L58F;ENSP00000420122:L58F	ENSP00000264244:L58F	L	+	1	0	TIMMDC1	120700442	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	2.616000	0.46376	2.752000	0.94435	0.557000	0.71058	CTC	.		0.617	TIMMDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355077.3	NM_016589	
SYS1	90196	hgsc.bcm.edu;ucsc.edu	37	20	43996521	43996521	+	3'UTR	SNP	G	G	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr20:43996521G>A	ENST00000243918.5	+	0	1528				SYS1-DBNDD2_ENST00000475242.1_Intron|SYS1-DBNDD2_ENST00000452133.1_Intron|SYS1_ENST00000426004.1_Intron	NM_033542.3	NP_291020.1	Q8N2H4	SYS1_HUMAN	Sys1 golgi trafficking protein						protein transport (GO:0015031)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)				cervix(1)|endometrium(2)|large_intestine(2)|prostate(1)|skin(1)	7		Myeloproliferative disorder(115;0.0122)				GGAATGACCAGGCACCCAGCT	0.488																																					.		.											.	.	.	0			.						.																																			SO:0001624	3_prime_UTR_variant	90196	.			TGACCAGGCACCC	AL021578	CCDS13351.1, CCDS56192.1	20q13.12	2014-05-07	2014-05-07	2006-11-06	ENSG00000204070	ENSG00000204070			16162	protein-coding gene	gene with protein product		612979	"""chromosome 20 open reading frame 169"", ""SYS1 Golgi-localized integral membrane protein homolog (S. cerevisiae)"""	C20orf169		15077113	Standard	NM_001197129		Approved	dJ453C12.4	uc002xnv.3	Q8N2H4	OTTHUMG00000032579	ENST00000243918.5:c.*766G>A	20.37:g.43996521G>A		Somatic	36	0		WXS	Illumina HiSeq	.	15	10	.	C9JFB3|E1P620|Q5QPU7|Q96SD8|Q9BQZ2|Q9BQZ4|Q9H1F7	RNA	SNP	ENST00000243918.5	37	CCDS13351.1																																																																																			.		0.488	SYS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079453.2	NM_033542	
Unknown	0	hgsc.bcm.edu	37	13	41438002	41438002	+	IGR	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr13:41438002T>G								TPTE2P5 (8875 upstream) : SUGT1P3 (48020 downstream)																							CTGGGCACACTTCTGAACAAA	0.493																																					.		.											.	.	.	0			.						.																																			SO:0001628	intergenic_variant	100616668	.			GCACACTTCTGAA																													13.37:g.41438002T>G		Somatic	26	0		WXS	Illumina HiSeq	.	14	5	.		RNA	SNP		37																																																																																				.	0	0.493								
PTK2	5747	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	8	141669627	141669627	+	Missense_Mutation	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr8:141669627T>G	ENST00000522684.1	-	32	3326	c.3097A>C	c.(3097-3099)Aac>Cac	p.N1033H	PTK2_ENST00000519465.1_Missense_Mutation_p.N661H|PTK2_ENST00000395218.2_Missense_Mutation_p.N1046H|PTK2_ENST00000517887.1_Missense_Mutation_p.N1077H|PTK2_ENST00000538769.1_Missense_Mutation_p.N701H|PTK2_ENST00000517712.1_Missense_Mutation_p.N96H|PTK2_ENST00000519419.1_Missense_Mutation_p.N1077H|PTK2_ENST00000340930.3_Missense_Mutation_p.N1046H|PTK2_ENST00000535192.1_Missense_Mutation_p.N987H|PTK2_ENST00000430260.2_Missense_Mutation_p.N343H|PTK2_ENST00000521059.1_Missense_Mutation_p.N1033H	NM_153831.3	NP_722560.1	Q05397	FAK1_HUMAN	protein tyrosine kinase 2	1033	Interaction with ARHGEF28. {ECO:0000250}.|Interaction with TGFB1I1.				angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell motility (GO:0048870)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|central nervous system neuron axonogenesis (GO:0021955)|embryo development (GO:0009790)|endothelial cell migration (GO:0043542)|ephrin receptor signaling pathway (GO:0048013)|establishment of cell polarity (GO:0030010)|establishment of nucleus localization (GO:0040023)|extracellular matrix organization (GO:0030198)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|growth hormone receptor signaling pathway (GO:0060396)|heart morphogenesis (GO:0003007)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|microtubule cytoskeleton organization (GO:0000226)|negative regulation of anoikis (GO:2000811)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of organ growth (GO:0046621)|negative regulation of synapse assembly (GO:0051964)|netrin-activated signaling pathway (GO:0038007)|neuron migration (GO:0001764)|peptidyl-tyrosine phosphorylation (GO:0018108)|placenta development (GO:0001890)|platelet activation (GO:0030168)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|protein autophosphorylation (GO:0046777)|regulation of cell adhesion mediated by integrin (GO:0033628)|regulation of cell proliferation (GO:0042127)|regulation of cell shape (GO:0008360)|regulation of cytoskeleton organization (GO:0051493)|regulation of endothelial cell migration (GO:0010594)|regulation of focal adhesion assembly (GO:0051893)|regulation of osteoblast differentiation (GO:0045667)|regulation of Rho GTPase activity (GO:0032319)|signal complex assembly (GO:0007172)|transforming growth factor beta receptor signaling pathway (GO:0007179)|vasculogenesis (GO:0001570)	apical plasma membrane (GO:0016324)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|stress fiber (GO:0001725)	actin binding (GO:0003779)|ATP binding (GO:0005524)|JUN kinase binding (GO:0008432)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|SH2 domain binding (GO:0042169)|signal transducer activity (GO:0004871)			breast(1)|central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(6)|lung(23)|ovary(2)|prostate(1)|skin(3)|urinary_tract(1)	48	all_cancers(97;1.05e-15)|all_epithelial(106;2.09e-14)|Lung NSC(106;1.61e-06)|all_lung(105;2.5e-06)|Ovarian(258;0.01)|Acute lymphoblastic leukemia(118;0.155)	Ovarian(118;2.72e-05)|Breast(495;0.159)	BRCA - Breast invasive adenocarcinoma(115;0.137)			TCGAGTAAGTTTTTGGCATCC	0.507																																					p.N1055H		.											.	.	.	0			c.A3163C						.						182.0	134.0	150.0					8																	141669627		2203	4300	6503	SO:0001583	missense	5747	exon32			GTAAGTTTTTGGC	L13616	CCDS6381.1, CCDS56557.1	8q24.3	2013-02-18	2013-02-18		ENSG00000169398	ENSG00000169398	2.7.10.1	"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	9611	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 71"""	600758	"""PTK2 protein tyrosine kinase 2"""			8422239	Standard	NM_153831		Approved	FAK, FADK, FAK1, PPP1R71	uc003yvt.3	Q05397	OTTHUMG00000067438	ENST00000522684.1:c.3097A>C	8.37:g.141669627T>G	ENSP00000429911:p.Asn1033His	Somatic	45	0		WXS	Illumina HiSeq	.	21	9	NM_005607	B4E2N6|F5H4S4|Q14291|Q9UD85	Missense_Mutation	SNP	ENST00000522684.1	37	CCDS6381.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	24.5|24.5	4.538503|4.538503	0.85917|0.85917	.|.	.|.	ENSG00000169398|ENSG00000169398	ENST00000519654|ENST00000522684;ENST00000535192;ENST00000519465;ENST00000517887;ENST00000521059;ENST00000395214;ENST00000395218;ENST00000354438;ENST00000395221;ENST00000517712;ENST00000523539;ENST00000340930;ENST00000538769;ENST00000519419;ENST00000430260;ENST00000521986;ENST00000523435	T|T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.49139|0.47869	0.79|0.83;0.83;0.83;0.83;0.83;0.83;0.83;0.83;0.83;0.83;0.83;0.83;0.83;0.83	5.81|5.81	5.81|5.81	0.92471|0.92471	.|Focal adhesion kinase, targeting (FAT) domain (3);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.70369|0.70369	0.3216|0.3216	M|M	0.78049|0.78049	2.395|2.395	0.53688|0.53688	D|D	0.999973|0.999973	.|D;D;D;D;D;D;D;D;D;D	.|0.89917	.|1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	.|D;D;D;D;D;D;D;D;D;D	.|0.97110	.|0.999;0.999;1.0;0.999;1.0;0.999;1.0;1.0;1.0;1.0	T|T	0.74490|0.74490	-0.3648|-0.3648	7|10	0.46703|0.87932	T|D	0.11|0	.|.	16.2142|16.2142	0.82195|0.82195	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|1046;731;956;1033;1055;987;988;860;701;661	.|B4E2N6;B4DH13;Q59GN8;Q05397;Q658W2;Q8IYN9;Q59GM6;Q05397-2;Q8N9D7;E9PEI4	.|.;.;.;FAK1_HUMAN;.;.;.;.;.;.	T|H	997|1033;987;661;1077;1033;988;1046;957;731;96;705;1046;701;1077;343;734;107	ENSP00000429929:K997T|ENSP00000429911:N1033H;ENSP00000438009:N987H;ENSP00000429170:N661H;ENSP00000429082:N1077H;ENSP00000429474:N1033H;ENSP00000378644:N1046H;ENSP00000430916:N96H;ENSP00000428492:N705H;ENSP00000341189:N1046H;ENSP00000445742:N701H;ENSP00000429129:N1077H;ENSP00000403416:N343H;ENSP00000430603:N734H;ENSP00000430828:N107H	ENSP00000429929:K997T|ENSP00000341189:N1046H	K|N	-|-	2|1	0|0	PTK2|PTK2	141738809|141738809	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.997000|0.997000	0.91878|0.91878	7.782000|7.782000	0.85680|0.85680	2.230000|2.230000	0.72887|0.72887	0.529000|0.529000	0.55759|0.55759	AAA|AAC	.		0.507	PTK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378054.5	NM_005607	
CSMD2	114784	hgsc.bcm.edu	37	1	34285407	34285407	+	Missense_Mutation	SNP	C	C	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr1:34285407C>T	ENST00000373381.4	-	9	1407	c.1231G>A	c.(1231-1233)Gag>Aag	p.E411K		NM_001281956.1|NM_052896.3	NP_001268885.1|NP_443128.2	Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2	371	CUB 3. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(5)|breast(5)|central_nervous_system(3)|cervix(2)|endometrium(20)|haematopoietic_and_lymphoid_tissue(4)|kidney(9)|large_intestine(43)|lung(114)|ovary(8)|pancreas(1)|prostate(6)|skin(20)|upper_aerodigestive_tract(5)|urinary_tract(1)	246		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)				TCATAGCCCTCGTTGCAGGTG	0.607																																					p.E371K		.											CSMD2_ENST00000373381,NS,malignant_melanoma,0,4	CSMD2_ENST00000373381	0	0			c.G1111A						.						92.0	84.0	87.0					1																	34285407		2203	4300	6503	SO:0001583	missense	114784	exon9			AGCCCTCGTTGCA	AY210418	CCDS380.1, CCDS60082.1	1p34.3	2014-01-28			ENSG00000121904	ENSG00000121904			19290	protein-coding gene	gene with protein product		608398				11472063, 11572484	Standard	NM_001281956		Approved	KIAA1884	uc001bxn.1	Q7Z408	OTTHUMG00000011135	ENST00000373381.4:c.1231G>A	1.37:g.34285407C>T	ENSP00000362479:p.Glu411Lys	Somatic	60	0		WXS	Illumina HiSeq	.	43	2	NM_052896	B1AM50|E7EUA6|Q53TY4|Q5VT59|Q8N963|Q96Q03|Q9H4V7|Q9H4V8|Q9H4V9|Q9H4W0|Q9H4W1|Q9H4W2|Q9H4W3|Q9H4W4|Q9HCY5|Q9HCY6|Q9HCY7	Missense_Mutation	SNP	ENST00000373381.4	37		.	.	.	.	.	.	.	.	.	.	C	34	5.312322	0.95655	.	.	ENSG00000121904	ENST00000373381	T	0.66815	-0.23	5.7	5.7	0.88788	Complement control module (2);Sushi/SCR/CCP (3);	0.000000	0.85682	D	0.000000	T	0.77089	0.4079	L	0.56124	1.755	0.80722	D	1	D;D	0.65815	0.995;0.99	P;P	0.61328	0.887;0.709	T	0.74355	-0.3692	10	0.37606	T	0.19	.	18.8196	0.92090	0.0:1.0:0.0:0.0	.	371;411	Q7Z408;E7EUA6	CSMD2_HUMAN;.	K	411	ENSP00000362479:E411K	ENSP00000241312:E371K	E	-	1	0	CSMD2	34057994	1.000000	0.71417	0.995000	0.50966	0.991000	0.79684	7.793000	0.85851	2.675000	0.91044	0.655000	0.94253	GAG	.		0.607	CSMD2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_052896	
CP	1356	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	3	148899805	148899805	+	Silent	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr3:148899805A>C	ENST00000264613.6	-	14	2803	c.2541T>G	c.(2539-2541)acT>acG	p.T847T		NM_000096.3	NP_000087	P00450	CERU_HUMAN	ceruloplasmin (ferroxidase)	847	F5/8 type A 3.|Plastocyanin-like 5.				cellular iron ion homeostasis (GO:0006879)|copper ion transport (GO:0006825)|transmembrane transport (GO:0055085)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)	chaperone binding (GO:0051087)|copper ion binding (GO:0005507)|ferroxidase activity (GO:0004322)			breast(6)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(14)|ovary(1)|prostate(1)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	44		Prostate(884;0.00217)|Hepatocellular(537;0.00826)|Myeloproliferative disorder(1037;0.0122)|all_neural(597;0.0189)|Melanoma(1037;0.152)	LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)		Drotrecogin alfa(DB00055)	GTAATGTTGGAGTAACTGTAG	0.468																																					p.T847T		.											.	.	.	0			c.T2541G						.						134.0	132.0	133.0					3																	148899805		2203	4300	6503	SO:0001819	synonymous_variant	1356	exon14			TGTTGGAGTAACT	M13536	CCDS3141.1	3q23-q25	2010-07-01			ENSG00000047457	ENSG00000047457	1.16.3.1		2295	protein-coding gene	gene with protein product		117700					Standard	NM_000096		Approved		uc003ewy.4	P00450	OTTHUMG00000159563	ENST00000264613.6:c.2541T>G	3.37:g.148899805A>C		Somatic	82	0		WXS	Illumina HiSeq	.	57	35	NM_000096	Q14063|Q2PP18|Q9UKS4	Silent	SNP	ENST00000264613.6	37	CCDS3141.1																																																																																			.		0.468	CP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317498.1	NM_000096	
RAPGEF2	9693	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	4	160262761	160262761	+	Missense_Mutation	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr4:160262761T>G	ENST00000264431.4	+	14	2516	c.2097T>G	c.(2095-2097)gaT>gaG	p.D699E		NM_014247.2	NP_055062.1	Q9Y4G8	RPGF2_HUMAN	Rap guanine nucleotide exchange factor (GEF) 2	699					adenylate cyclase-activating adrenergic receptor signaling pathway (GO:0071880)|blood vessel development (GO:0001568)|brain-derived neurotrophic factor receptor signaling pathway (GO:0031547)|cAMP-mediated signaling (GO:0019933)|cellular response to cAMP (GO:0071320)|cellular response to cGMP (GO:0071321)|cellular response to nerve growth factor stimulus (GO:1990090)|establishment of endothelial barrier (GO:0061028)|forebrain neuron development (GO:0021884)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|MAPK cascade (GO:0000165)|negative regulation of cell proliferation (GO:0008285)|negative regulation of dendrite morphogenesis (GO:0050774)|negative regulation of melanin biosynthetic process (GO:0048022)|nerve growth factor signaling pathway (GO:0038180)|neuron migration (GO:0001764)|neuron projection development (GO:0031175)|neuropeptide signaling pathway (GO:0007218)|positive regulation of cAMP-dependent protein kinase activity (GO:2000481)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of dendritic cell apoptotic process (GO:2000670)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of neuron migration (GO:2001224)|positive regulation of neuron projection development (GO:0010976)|positive regulation of protein binding (GO:0032092)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of Rap GTPase activity (GO:0032854)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of vasculogenesis (GO:2001214)|Rap protein signal transduction (GO:0032486)|regulation of cell junction assembly (GO:1901888)|regulation of synaptic plasticity (GO:0048167)|small GTPase mediated signal transduction (GO:0007264)|ventricular system development (GO:0021591)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|membrane (GO:0016020)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|synapse (GO:0045202)	beta-1 adrenergic receptor binding (GO:0031697)|calcium ion binding (GO:0005509)|cAMP binding (GO:0030552)|diacylglycerol binding (GO:0019992)|PDZ domain binding (GO:0030165)|Rap GTPase activator activity (GO:0046582)|Rap guanyl-nucleotide exchange factor activity (GO:0017034)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|signal transducer activity (GO:0004871)|WW domain binding (GO:0050699)			breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|liver(1)|lung(29)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	70	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.0817)		TTTGTTCAGATGAAGATGCTC	0.388																																					p.D699E		.											.	.	.	0			c.T2097G						.						68.0	63.0	65.0					4																	160262761		1910	4138	6048	SO:0001583	missense	9693	exon14			TTCAGATGAAGAT	AB002311	CCDS43277.1	4q32.1	2004-03-01	2004-03-01	2004-03-01					16854	protein-coding gene	gene with protein product	"""Rap GEP"""	609530	"""PDZ domain containing guanine nucleotide exchange factor (GEF) 1"""	PDZGEF1		9205841, 10934204	Standard	NM_014247		Approved	PDZ-GEF1, RA-GEF, DKFZP586O1422, KIAA0313	uc003iqg.4	Q9Y4G8		ENST00000264431.4:c.2097T>G	4.37:g.160262761T>G	ENSP00000264431:p.Asp699Glu	Somatic	39	0		WXS	Illumina HiSeq	.	15	9	NM_014247	D3DP27	Missense_Mutation	SNP	ENST00000264431.4	37	CCDS43277.1	.	.	.	.	.	.	.	.	.	.	T	15.43	2.830257	0.50845	.	.	ENSG00000109756	ENST00000264431	T	0.29655	1.56	5.76	0.628	0.17681	Ras guanine nucleotide exchange factor, domain (1);	0.000000	0.85682	D	0.000000	T	0.46718	0.1407	M	0.62723	1.935	0.58432	D	0.999996	D	0.89917	1.0	D	0.77557	0.99	T	0.40327	-0.9569	10	0.87932	D	0	.	9.2956	0.37813	0.0:0.2855:0.0:0.7145	.	699	Q9Y4G8	RPGF2_HUMAN	E	699	ENSP00000264431:D699E	ENSP00000264431:D699E	D	+	3	2	RAPGEF2	160482211	0.992000	0.36948	0.995000	0.50966	0.263000	0.26337	0.229000	0.17833	0.168000	0.19655	-0.417000	0.06048	GAT	.		0.388	RAPGEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364980.2	NM_014247	
SLC47A2	146802	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	17	19606450	19606450	+	Missense_Mutation	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr17:19606450A>C	ENST00000325411.5	-	12	1207	c.1157T>G	c.(1156-1158)aTa>aGa	p.I386R	SLC47A2_ENST00000463318.1_Intron|SLC47A2_ENST00000350657.5_Missense_Mutation_p.I364R	NM_152908.3	NP_690872.2	Q86VL8	S47A2_HUMAN	solute carrier family 47 (multidrug and toxin extrusion), member 2	386					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	antiporter activity (GO:0015297)|drug transmembrane transporter activity (GO:0015238)			endometrium(2)|kidney(3)|large_intestine(2)|lung(1)|ovary(1)	9	all_cancers(12;2.3e-05)|all_epithelial(12;0.0024)|Breast(13;0.245)				Aciclovir(DB00787)	CAGGATGCTTATCAGGGTGCC	0.473																																					p.I386R		.											.	.	.	0			c.T1157G						.						68.0	65.0	66.0					17																	19606450		2203	4300	6503	SO:0001583	missense	146802	exon12			ATGCTTATCAGGG	AB250364	CCDS11211.1, CCDS58530.1	17p11.2	2013-07-17	2013-07-17		ENSG00000180638	ENSG00000180638		"""Solute carriers"""	26439	protein-coding gene	gene with protein product	"""multidrug and toxin extrusion 2"""	609833				16996621, 16807400	Standard	NM_152908		Approved	FLJ31196, MATE2, MATE2-K	uc002gwf.4	Q86VL8	OTTHUMG00000059464	ENST00000325411.5:c.1157T>G	17.37:g.19606450A>C	ENSP00000326671:p.Ile386Arg	Somatic	68	0		WXS	Illumina HiSeq	.	27	10	NM_152908	A0JBX9|A0P8Z7|Q63HJ9|Q8IV44|Q96NA1	Missense_Mutation	SNP	ENST00000325411.5	37	CCDS11211.1	.	.	.	.	.	.	.	.	.	.	A	17.53	3.412103	0.62511	.	.	ENSG00000180638	ENST00000350657;ENST00000325411;ENST00000433844	T;T;T	0.35605	1.3;1.3;1.3	4.71	4.71	0.59529	.	0.620143	0.15488	N	0.259723	T	0.54481	0.1861	M	0.73962	2.25	0.25445	N	0.988056	P;P;P	0.51147	0.942;0.942;0.907	P;P;P	0.56865	0.712;0.785;0.808	T	0.50499	-0.8821	10	0.87932	D	0	-12.2653	12.1347	0.53964	1.0:0.0:0.0:0.0	.	350;364;386	Q86VL8-3;Q86VL8-4;Q86VL8	.;.;S47A2_HUMAN	R	364;386;350	ENSP00000338084:I364R;ENSP00000326671:I386R;ENSP00000391848:I350R	ENSP00000326671:I386R	I	-	2	0	SLC47A2	19547042	0.249000	0.23941	0.003000	0.11579	0.015000	0.08874	5.843000	0.69424	1.759000	0.51996	0.450000	0.29827	ATA	.		0.473	SLC47A2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000132242.2	NM_152908	
OR2D3	120775	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	11	6943064	6943064	+	Missense_Mutation	SNP	C	C	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr11:6943064C>T	ENST00000317834.3	+	1	860	c.832C>T	c.(832-834)Cca>Tca	p.P278S		NM_001004684.1	NP_001004684.1	Q8NGH3	OR2D3_HUMAN	olfactory receptor, family 2, subfamily D, member 3	278						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(2)|large_intestine(7)|lung(12)|prostate(3)|skin(1)|stomach(1)	27		Medulloblastoma(188;0.0523)|all_neural(188;0.236)		Epithelial(150;4.78e-08)|BRCA - Breast invasive adenocarcinoma(625;0.129)		CTACATGCGACCAAACTCCAA	0.433																																					p.P278S		.											.	.	.	0			c.C832T						.						106.0	104.0	104.0					11																	6943064		2201	4296	6497	SO:0001583	missense	120775	exon1			ATGCGACCAAACT	BK004294	CCDS31417.1	11p15.4	2012-08-09			ENSG00000178358	ENSG00000178358		"""GPCR / Class A : Olfactory receptors"""	15146	protein-coding gene	gene with protein product							Standard	NM_001004684		Approved		uc010rav.2	Q8NGH3	OTTHUMG00000165742	ENST00000317834.3:c.832C>T	11.37:g.6943064C>T	ENSP00000320560:p.Pro278Ser	Somatic	57	0		WXS	Illumina HiSeq	.	41	17	NM_001004684	B2RP06|Q6IFG8|Q96R51	Missense_Mutation	SNP	ENST00000317834.3	37	CCDS31417.1	.	.	.	.	.	.	.	.	.	.	C	13.77	2.337104	0.41398	.	.	ENSG00000178358	ENST00000317834	T	0.00262	8.4	4.42	4.42	0.53409	GPCR, rhodopsin-like superfamily (1);	0.000000	0.44285	D	0.000461	T	0.00524	0.0017	M	0.77712	2.385	0.26862	N	0.967933	D	0.58620	0.983	P	0.62382	0.901	T	0.49881	-0.8892	10	0.87932	D	0	-34.5626	15.3409	0.74296	0.0:1.0:0.0:0.0	.	278	Q8NGH3	OR2D3_HUMAN	S	278	ENSP00000320560:P278S	ENSP00000320560:P278S	P	+	1	0	OR2D3	6899640	0.000000	0.05858	0.991000	0.47740	0.396000	0.30629	-0.131000	0.10482	2.752000	0.94435	0.655000	0.94253	CCA	.		0.433	OR2D3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385987.1	NM_001004684	
EGR4	1961	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	2	73518868	73518868	+	Missense_Mutation	SNP	C	C	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr2:73518868C>T	ENST00000545030.1	-	2	1561	c.1487G>A	c.(1486-1488)cGc>cAc	p.R496H	EGR4_ENST00000436467.2_Missense_Mutation_p.R393H	NM_001965.3	NP_001956.3	Q05215	EGR4_HUMAN	early growth response 4	496					cellular response to cAMP (GO:0071320)|cellular response to gonadotropin stimulus (GO:0071371)|negative regulation of apoptotic process (GO:0043066)|positive regulation of cell proliferation (GO:0008284)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(1)|large_intestine(3)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	11						CTCGTCGGAGCGCGCAAAGCT	0.687																																					p.R496H		.											.	.	.	0			c.G1487A						.						44.0	39.0	41.0					2																	73518868		2203	4300	6503	SO:0001583	missense	1961	exon2			TCGGAGCGCGCAA		CCDS1925.2	2p13	2013-01-08			ENSG00000135625	ENSG00000135625		"""Zinc fingers, C2H2-type"""	3241	protein-coding gene	gene with protein product		128992				1584812	Standard	NM_001965		Approved	NGFI-C, PAT133	uc010yrj.2	Q05215	OTTHUMG00000129774	ENST00000545030.1:c.1487G>A	2.37:g.73518868C>T	ENSP00000445626:p.Arg496His	Somatic	22	0		WXS	Illumina HiSeq	.	12	6	NM_001965	B2RAE3|G3V1T5|Q2Z1P5	Missense_Mutation	SNP	ENST00000545030.1	37	CCDS1925.2	.	.	.	.	.	.	.	.	.	.	C	27.4	4.824197	0.90955	.	.	ENSG00000135625	ENST00000545030;ENST00000436467	T;T	0.08370	3.1;3.1	4.79	4.79	0.61399	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.64402	D	0.000005	T	0.17959	0.0431	N	0.24115	0.695	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.83275	0.984;0.996	T	0.03077	-1.1075	10	0.87932	D	0	-19.7805	16.5595	0.84535	0.0:1.0:0.0:0.0	.	393;496	Q05215;G3V1T5	EGR4_HUMAN;.	H	496;393	ENSP00000445626:R496H;ENSP00000419687:R393H	ENSP00000419687:R393H	R	-	2	0	EGR4	73372376	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.602000	0.82796	2.478000	0.83669	0.655000	0.94253	CGC	.		0.687	EGR4-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_001965	
FARP2	9855	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	2	242433442	242433442	+	Missense_Mutation	SNP	G	G	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr2:242433442G>A	ENST00000264042.3	+	27	3237	c.3067G>A	c.(3067-3069)Ggg>Agg	p.G1023R	STK25_ENST00000316586.4_3'UTR|STK25_ENST00000478403.1_5'Flank	NM_014808.2	NP_055623.1	O94887	FARP2_HUMAN	FERM, RhoGEF and pleckstrin domain protein 2	1023	PH 2. {ECO:0000255|PROSITE- ProRule:PRU00145}.				actin cytoskeleton reorganization (GO:0031532)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|neuron remodeling (GO:0016322)|osteoclast differentiation (GO:0030316)|podosome assembly (GO:0071800)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|Rac protein signal transduction (GO:0016601)|regulation of integrin activation (GO:0033623)|regulation of Rac GTPase activity (GO:0032314)|semaphorin-plexin signaling pathway (GO:0071526)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extrinsic component of membrane (GO:0019898)	Rac guanyl-nucleotide exchange factor activity (GO:0030676)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(8)|lung(18)|ovary(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	43		all_cancers(19;4.88e-34)|all_epithelial(40;4.81e-14)|Breast(86;0.000141)|Renal(207;0.0143)|all_lung(227;0.0344)|Lung NSC(271;0.0886)|Ovarian(221;0.0905)|Esophageal squamous(248;0.131)|all_hematologic(139;0.182)|Melanoma(123;0.238)		Epithelial(32;1.81e-33)|all cancers(36;1.61e-30)|OV - Ovarian serous cystadenocarcinoma(60;6.83e-15)|Kidney(56;1.19e-08)|KIRC - Kidney renal clear cell carcinoma(57;8.98e-08)|BRCA - Breast invasive adenocarcinoma(100;1.49e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00125)|Colorectal(34;0.0199)|COAD - Colon adenocarcinoma(134;0.121)		GGTGATCCAGGGGGCCAGCAG	0.632																																					p.G1023R		.											.	.	.	0			c.G3067A						.						50.0	55.0	53.0					2																	242433442		2202	4298	6500	SO:0001583	missense	9855	exon27			ATCCAGGGGGCCA	AB018336	CCDS33424.1, CCDS63197.1	2q37.3	2013-01-10			ENSG00000006607	ENSG00000006607		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	16460	protein-coding gene	gene with protein product						9872452, 12351724	Standard	NM_001282984		Approved	KIAA0793, FIR, PLEKHC3, FRG	uc002wbi.2	O94887	OTTHUMG00000151574	ENST00000264042.3:c.3067G>A	2.37:g.242433442G>A	ENSP00000264042:p.Gly1023Arg	Somatic	57	0		WXS	Illumina HiSeq	.	49	19	NM_014808	B7Z6J8|F5GZ84|Q53QM5|Q8WU27|Q9UFE7	Missense_Mutation	SNP	ENST00000264042.3	37	CCDS33424.1	.	.	.	.	.	.	.	.	.	.	G	8.301	0.819991	0.16678	.	.	ENSG00000006607	ENST00000264042	T	0.74421	-0.84	4.73	-0.864	0.10666	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.336108	0.33438	N	0.004910	T	0.32793	0.0841	N	0.00446	-1.495	0.19775	N	0.999952	B	0.02656	0.0	B	0.06405	0.002	T	0.39165	-0.9627	10	0.32370	T	0.25	.	4.7145	0.12889	0.5669:0.1527:0.2804:0.0	.	1023	O94887	FARP2_HUMAN	R	1023	ENSP00000264042:G1023R	ENSP00000264042:G1023R	G	+	1	0	FARP2	242082115	0.843000	0.29541	0.000000	0.03702	0.021000	0.10359	2.287000	0.43505	-0.336000	0.08438	-0.345000	0.07892	GGG	.		0.632	FARP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323153.1		
BIRC3	330	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	11	102198793	102198793	+	Missense_Mutation	SNP	T	T	G	rs373892386		TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr11:102198793T>G	ENST00000263464.3	+	4	3714	c.964T>G	c.(964-966)Ttg>Gtg	p.L322V	BIRC3_ENST00000532808.1_Missense_Mutation_p.L322V	NM_001165.4	NP_001156.1	Q13489	BIRC3_HUMAN	baculoviral IAP repeat containing 3	322					apoptotic process (GO:0006915)|cell surface receptor signaling pathway (GO:0007166)|innate immune response (GO:0045087)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of necroptotic process (GO:0060546)|negative regulation of phosphorylation (GO:0042326)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|NIK/NF-kappaB signaling (GO:0038061)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of protein ubiquitination (GO:0031398)|protein heterooligomerization (GO:0051291)|protein ubiquitination (GO:0016567)|regulation of apoptotic process (GO:0042981)|regulation of cysteine-type endopeptidase activity (GO:2000116)|regulation of inflammatory response (GO:0050727)|regulation of innate immune response (GO:0045088)|regulation of necroptotic process (GO:0060544)|regulation of nucleotide-binding oligomerization domain containing signaling pathway (GO:0070424)|regulation of RIG-I signaling pathway (GO:0039535)|regulation of toll-like receptor signaling pathway (GO:0034121)|spermatogenesis (GO:0007283)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane raft (GO:0045121)|nucleus (GO:0005634)|protein complex (GO:0043234)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(3)|kidney(2)|large_intestine(7)|lung(5)|ovary(3)|skin(1)	21	all_cancers(8;0.00044)|all_epithelial(12;0.00348)|Lung NSC(15;0.227)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0093)	Lung(13;0.109)|LUSC - Lung squamous cell carcinoma(19;0.151)	BRCA - Breast invasive adenocarcinoma(274;0.0146)		GTGTGAGTACTTGATAAGAAT	0.313			T	MALT1	MALT																																p.L322V		.		Dom	yes		11	11q22-q23	330	baculoviral IAP repeat-containing 3		L	.	.	.	0			c.T964G						.	T	VAL/LEU,VAL/LEU	0,4406		0,0,2203	74.0	73.0	74.0		964,964	5.1	0.9	11		74	1,8597	1.2+/-3.3	0,1,4298	no	missense,missense	BIRC3	NM_001165.4,NM_182962.2	32,32	0,1,6501	GG,GT,TT		0.0116,0.0,0.0077	possibly-damaging,possibly-damaging	322/605,322/605	102198793	1,13003	2203	4299	6502	SO:0001583	missense	330	exon4			GAGTACTTGATAA	L49432	CCDS8315.1	11q22	2011-01-25	2011-01-25			ENSG00000023445		"""Baculoviral IAP repeat containing"", ""RING-type (C3HC4) zinc fingers"""	591	protein-coding gene	gene with protein product	"""apoptosis inhibitor 2"", ""TNFR2-TRAF signaling complex protein"", ""mammalian IAP homolog C"", ""inhibitor of apoptosis protein 1"""	601721	"""baculoviral IAP repeat-containing 3"""	API2		8552191, 8548810	Standard	NM_001165		Approved	cIAP2, hiap-1, MIHC, RNF49, MALT2, c-IAP2	uc001pgx.3	Q13489		ENST00000263464.3:c.964T>G	11.37:g.102198793T>G	ENSP00000263464:p.Leu322Val	Somatic	52	0		WXS	Illumina HiSeq	.	42	14	NM_001165	Q16628|Q9HC27|Q9UP46	Missense_Mutation	SNP	ENST00000263464.3	37	CCDS8315.1	.	.	.	.	.	.	.	.	.	.	T	16.77	3.215294	0.58452	0.0	1.16E-4	ENSG00000023445	ENST00000263464;ENST00000532808;ENST00000532609;ENST00000527309	T;T;T	0.71103	-0.54;-0.54;-0.42	5.14	5.14	0.70334	Baculoviral inhibition of apoptosis protein repeat (5);	0.063724	0.64402	D	0.000005	T	0.63486	0.2515	L	0.31578	0.945	0.80722	D	1	P	0.38922	0.651	P	0.45474	0.482	T	0.62868	-0.6763	10	0.37606	T	0.19	.	9.6814	0.40072	0.0:0.121:0.0:0.879	.	322	Q13489	BIRC3_HUMAN	V	322;322;171;126	ENSP00000263464:L322V;ENSP00000432907:L322V;ENSP00000431718:L126V	ENSP00000263464:L322V	L	+	1	2	BIRC3	101704003	1.000000	0.71417	0.879000	0.34478	0.986000	0.74619	0.794000	0.26958	2.285000	0.76669	0.533000	0.62120	TTG	.		0.313	BIRC3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394159.1	NM_001165	
C11orf52	91894	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	11	111796729	111796729	+	Missense_Mutation	SNP	C	C	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr11:111796729C>A	ENST00000278601.5	+	4	274	c.178C>A	c.(178-180)Caa>Aaa	p.Q60K	C11orf52_ENST00000527286.1_3'UTR|CRYAB_ENST00000527950.1_5'Flank|RNA5SP351_ENST00000459480.1_RNA|DIXDC1_ENST00000529225.1_5'Flank|HSPB2-C11orf52_ENST00000534100.1_3'UTR	NM_080659.2	NP_542390.2	Q96A22	CK052_HUMAN	chromosome 11 open reading frame 52	60						extracellular vesicular exosome (GO:0070062)				lung(2)|ovary(1)	3		all_cancers(61;8.8e-15)|all_epithelial(67;6.27e-09)|Melanoma(852;1.91e-06)|all_hematologic(158;0.000405)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0112)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		Epithelial(105;3.63e-07)|BRCA - Breast invasive adenocarcinoma(274;1.1e-06)|all cancers(92;6.7e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.0512)		GTTACAGCAGCAAGGGTCTCA	0.517																																					p.Q60K		.											.	.	.	0			c.C178A						.						125.0	93.0	104.0					11																	111796729		2201	4297	6498	SO:0001583	missense	91894	exon4			CAGCAGCAAGGGT	AK057948	CCDS8353.1	11q23.1	2006-02-06	2006-02-06		ENSG00000149300	ENSG00000149300			30531	protein-coding gene	gene with protein product							Standard	NM_080659		Approved	MGC14839, FLJ25219		Q96A22	OTTHUMG00000166888	ENST00000278601.5:c.178C>A	11.37:g.111796729C>A	ENSP00000278601:p.Gln60Lys	Somatic	53	0		WXS	Illumina HiSeq	.	26	6	NM_080659		Missense_Mutation	SNP	ENST00000278601.5	37	CCDS8353.1	.	.	.	.	.	.	.	.	.	.	C	11.99	1.804347	0.31869	.	.	ENSG00000149300	ENST00000278601	T	0.42513	0.97	4.72	0.61	0.17580	.	0.992547	0.08184	N	0.984957	T	0.23133	0.0559	N	0.14661	0.345	0.09310	N	1	B	0.12630	0.006	B	0.14023	0.01	T	0.22626	-1.0211	10	0.39692	T	0.17	1.1359	3.6902	0.08343	0.1726:0.5512:0.0:0.2762	.	60	Q96A22	CK052_HUMAN	K	60	ENSP00000278601:Q60K	ENSP00000278601:Q60K	Q	+	1	0	C11orf52	111301939	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	-0.110000	0.10824	-0.043000	0.13513	0.561000	0.74099	CAA	.		0.517	C11orf52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391673.1	NM_080659	
IKZF5	64376	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	10	124758099	124758099	+	Missense_Mutation	SNP	A	A	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr10:124758099A>T	ENST00000368886.5	-	3	363	c.43T>A	c.(43-45)Ttt>Att	p.F15I	IKZF5_ENST00000479103.1_5'UTR	NM_001271840.1	NP_001258769.1	Q9H5V7	IKZF5_HUMAN	IKAROS family zinc finger 5 (Pegasus)	15					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|lung(3)|prostate(1)	6		all_neural(114;0.169)|Colorectal(57;0.178)|Glioma(114;0.222)		Colorectal(40;0.0701)|COAD - Colon adenocarcinoma(40;0.0754)		TATTCCTGAAAATCTTTCACG	0.398																																					p.F15I		.											.	.	.	0			c.T43A						.						137.0	124.0	128.0					10																	124758099		1842	4089	5931	SO:0001583	missense	64376	exon3			CCTGAAAATCTTT	AF230808	CCDS41574.1	10q26	2011-05-31	2006-08-25	2006-08-25	ENSG00000095574	ENSG00000095574		"""Zinc fingers, C2H2-type"", ""IKAROS zinc fingers"""	14283	protein-coding gene	gene with protein product		606238	"""zinc finger protein, subfamily 1A, 5"", ""zinc finger protein, subfamily 1A, 5 (Pegasus)"""	ZNFN1A5		10978333	Standard	NM_001271840		Approved	Pegasus, FLJ22973	uc021qaj.2	Q9H5V7	OTTHUMG00000019192	ENST00000368886.5:c.43T>A	10.37:g.124758099A>T	ENSP00000357881:p.Phe15Ile	Somatic	78	0		WXS	Illumina HiSeq	.	60	22	NM_001271840	B3KVH7|D3DRE7|Q9H2T0	Missense_Mutation	SNP	ENST00000368886.5	37	CCDS41574.1	.	.	.	.	.	.	.	.	.	.	A	35	5.583448	0.96578	.	.	ENSG00000095574	ENST00000368886	T	0.09073	3.02	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	T	0.19406	0.0466	L	0.29908	0.895	0.80722	D	1	D	0.71674	0.998	D	0.76071	0.987	T	0.01428	-1.1357	10	0.39692	T	0.17	-27.6006	16.8222	0.85835	1.0:0.0:0.0:0.0	.	15	Q9H5V7	IKZF5_HUMAN	I	15	ENSP00000357881:F15I	ENSP00000357881:F15I	F	-	1	0	IKZF5	124748089	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.868000	0.92320	2.371000	0.80710	0.533000	0.62120	TTT	.		0.398	IKZF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050820.2	NM_022466	
MALAT1	378938	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	11	65266585	65266585	+	lincRNA	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr11:65266585A>C	ENST00000534336.1	+	0	1353				AP000769.7_ENST00000602344.1_lincRNA	NR_002819.2		Q9UHZ2	MALAT_HUMAN	metastasis associated lung adenocarcinoma transcript 1 (non-protein coding)																		ACCGCAGATAAGTTTTTTTCT	0.428																																					.		.											.	.	.	0			.						.						56.0	61.0	59.0					11																	65266585		874	1988	2862			378938	.			CAGATAAGTTTTT	AF001540		11q13.1	2013-12-11	2007-11-20		ENSG00000251562	ENSG00000251562		"""Long non-coding RNAs"", ""-"""	29665	non-coding RNA	RNA, long non-coding	"""metastasis associated in lung adenocarcinoma transcript 1"", ""non-protein coding RNA 47"", ""hepcarcin"", ""nuclear enriched abundant transcript 2"", ""nuclear paraspeckle assembly transcript 2 (non-protein coding)"", ""long intergenic non-protein coding RNA 47"""	607924				12970751, 22560368	Standard	NR_002819		Approved	PRO1073, MALAT-1, NCRNA00047, HCN, NEAT2, LINC00047, mascRNA	uc010roh.3	Q9UHZ2	OTTHUMG00000166322		11.37:g.65266585A>C		Somatic	54	0		WXS	Illumina HiSeq	.	38	17	.		RNA	SNP	ENST00000534336.1	37																																																																																				.		0.428	MALAT1-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000389143.1	NR_002819	
SUCO	51430	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	172558420	172558420	+	Missense_Mutation	SNP	C	C	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr1:172558420C>G	ENST00000263688.3	+	18	2398	c.2179C>G	c.(2179-2181)Caa>Gaa	p.Q727E	SUCO_ENST00000610051.1_Intron|SUCO_ENST00000367723.4_Missense_Mutation_p.Q878E|SUCO_ENST00000608151.1_Missense_Mutation_p.Q879E	NM_014283.3	NP_055098.1	Q9UBS9	SUCO_HUMAN	SUN domain containing ossification factor	727					multicellular organismal development (GO:0007275)|ossification (GO:0001503)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of osteoblast differentiation (GO:0045669)|regulation of bone remodeling (GO:0046850)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|rough endoplasmic reticulum (GO:0005791)											AAGCCATTCTCAAACTCTTTC	0.393																																					p.Q727E		.											.	.	.	0			c.C2179G						.						87.0	88.0	88.0					1																	172558420		2201	4299	6500	SO:0001583	missense	51430	exon18			CATTCTCAAACTC	AF097535	CCDS1303.1, CCDS65726.1, CCDS65727.1, CCDS72984.1	1q24	2012-07-10	2012-07-10	2012-07-10	ENSG00000094975	ENSG00000094975			1240	protein-coding gene	gene with protein product	"""SUN-like protein 1"", ""osteopotentia"""		"""chromosome 1 open reading frame 9"""	C1orf9		10673381, 20440000	Standard	NM_001282750		Approved	CH1, SLP1, OPT	uc001giq.4	Q9UBS9	OTTHUMG00000034839	ENST00000263688.3:c.2179C>G	1.37:g.172558420C>G	ENSP00000263688:p.Gln727Glu	Somatic	34	0		WXS	Illumina HiSeq	.	44	28	NM_014283	B2RNU4|Q9BQB9|Q9BXQ2|Q9UL04	Missense_Mutation	SNP	ENST00000263688.3	37	CCDS1303.1	.	.	.	.	.	.	.	.	.	.	C	14.96	2.691075	0.48097	.	.	ENSG00000094975	ENST00000367723;ENST00000263688	.	.	.	5.39	5.39	0.77823	.	0.406919	0.27513	N	0.019024	T	0.47116	0.1428	M	0.62723	1.935	0.40808	D	0.983392	P;B;B	0.35959	0.53;0.435;0.332	B;B;B	0.34652	0.187;0.15;0.142	T	0.49476	-0.8936	9	0.19147	T	0.46	-3.43	17.705	0.88306	0.0:1.0:0.0:0.0	.	727;879;727	B4DZJ3;Q5H945;Q9UBS9	.;.;OSPT_HUMAN	E	879;727	.	ENSP00000263688:Q727E	Q	+	1	0	C1orf9	170825043	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.765000	0.55272	2.517000	0.84864	0.655000	0.94253	CAA	.		0.393	SUCO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084273.1	NM_016227	
OR2A2	442361	hgsc.bcm.edu	37	7	143807373	143807373	+	Missense_Mutation	SNP	G	G	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr7:143807373G>A	ENST00000408979.2	+	1	767	c.698G>A	c.(697-699)cGc>cAc	p.R233H		NM_001005480.2	NP_001005480.2	Q6IF42	OR2A2_HUMAN	olfactory receptor, family 2, subfamily A, member 2	233						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|kidney(1)|large_intestine(2)|lung(13)|prostate(1)|skin(4)	22	Melanoma(164;0.0783)					AAGGAGGGCCGCATAAAGGCC	0.522																																					p.R233H		.											OR2A2,colon,carcinoma,0,1	OR2A2	0	0			c.G698A						.						104.0	108.0	107.0					7																	143807373		2071	4233	6304	SO:0001583	missense	442361	exon1			AGGGCCGCATAAA		CCDS43671.1	7q35	2013-09-20		2004-03-10	ENSG00000221989	ENSG00000221989		"""GPCR / Class A : Olfactory receptors"""	8230	protein-coding gene	gene with protein product				OR2A2P, OR2A17P			Standard	NM_001005480		Approved	OST008	uc011ktz.2	Q6IF42	OTTHUMG00000158001	ENST00000408979.2:c.698G>A	7.37:g.143807373G>A	ENSP00000386209:p.Arg233His	Somatic	59	0		WXS	Illumina HiSeq	.	31	2	NM_001005480	B2RN85|Q8NGT6	Missense_Mutation	SNP	ENST00000408979.2	37	CCDS43671.1	.	.	.	.	.	.	.	.	.	.	G	12.25	1.880455	0.33255	.	.	ENSG00000221989	ENST00000408979	T	0.00333	8.07	3.47	3.47	0.39725	GPCR, rhodopsin-like superfamily (1);	0.000000	0.33327	U	0.005027	T	0.00524	0.0017	M	0.89904	3.07	0.09310	N	1	P	0.35821	0.523	B	0.40940	0.344	T	0.08027	-1.0742	10	0.72032	D	0.01	-4.2634	12.7847	0.57498	0.0:0.0:1.0:0.0	.	233	Q6IF42	OR2A2_HUMAN	H	233	ENSP00000386209:R233H	ENSP00000386209:R233H	R	+	2	0	OR2A2	143438306	0.000000	0.05858	0.365000	0.25901	0.643000	0.38383	0.412000	0.21131	1.938000	0.56188	0.511000	0.50034	CGC	.		0.522	OR2A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349978.1		
LRRC8B	23507	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	90049514	90049514	+	Silent	SNP	T	T	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr1:90049514T>C	ENST00000330947.2	+	5	1665	c.1305T>C	c.(1303-1305)aaT>aaC	p.N435N	RP5-1007M22.2_ENST00000443562.1_RNA|LRRC8B_ENST00000358200.4_Silent_p.N435N|LRRC8B_ENST00000439853.1_Silent_p.N435N	NM_001134476.1	NP_001127948.1	Q6P9F7	LRC8B_HUMAN	leucine rich repeat containing 8 family, member B	435					ion transport (GO:0006811)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(6)|kidney(5)|large_intestine(2)|lung(5)|ovary(2)|prostate(2)|skin(1)|urinary_tract(1)	26		all_lung(203;0.17)		all cancers(265;0.00515)|Epithelial(280;0.0241)		TTCCAGACAATGTCTTTGAGT	0.443																																					p.N435N		.											.	.	.	0			c.T1305C						.						65.0	68.0	67.0					1																	90049514		2203	4300	6503	SO:0001819	synonymous_variant	23507	exon5			AGACAATGTCTTT	AF385436	CCDS724.1	1p22.2	2008-02-05			ENSG00000197147	ENSG00000197147			30692	protein-coding gene	gene with protein product	"""T cell activation leucine repeat rich protein"""	612888				9039502	Standard	NM_015350		Approved	TA-LRRP, KIAA0231	uc001dni.3	Q6P9F7	OTTHUMG00000010129	ENST00000330947.2:c.1305T>C	1.37:g.90049514T>C		Somatic	38	0		WXS	Illumina HiSeq	.	13	11	NM_015350	D3DT28|Q6UY21|Q8N106|Q92627	Silent	SNP	ENST00000330947.2	37	CCDS724.1																																																																																			.		0.443	LRRC8B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028008.1	NM_015350	
ASXL3	80816	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	18	31158612	31158612	+	Missense_Mutation	SNP	A	A	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr18:31158612A>G	ENST00000269197.5	+	1	17	c.17A>G	c.(16-18)aAg>aGg	p.K6R	RP11-258B16.1_ENST00000591558.1_lincRNA	NM_030632.1	NP_085135.1	Q9C0F0	ASXL3_HUMAN	additional sex combs like transcriptional regulator 3	6					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						GACAAGAGGAAGAAGAAGGAC	0.682																																					p.K6R		.											.	.	.	0			c.A17G						.						23.0	32.0	29.0					18																	31158612		1933	4145	6078	SO:0001583	missense	80816	exon1			AGAGGAAGAAGAA	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.17A>G	18.37:g.31158612A>G	ENSP00000269197:p.Lys6Arg	Somatic	176	0		WXS	Illumina HiSeq	.	110	41	NM_030632	Q6ZMX6|Q96MU3|Q9UFC5	Missense_Mutation	SNP	ENST00000269197.5	37	CCDS45847.1	.	.	.	.	.	.	.	.	.	.	a	9.322	1.058378	0.19987	.	.	ENSG00000141431	ENST00000269197	T	0.16743	2.32	2.19	2.19	0.27852	.	.	.	.	.	T	0.17831	0.0428	N	0.25485	0.75	0.25787	N	0.984662	D	0.57571	0.98	P	0.57009	0.811	T	0.05784	-1.0864	9	0.08381	T	0.77	.	9.4888	0.38946	1.0:0.0:0.0:0.0	.	6	Q9C0F0	ASXL3_HUMAN	R	6	ENSP00000269197:K6R	ENSP00000269197:K6R	K	+	2	0	ASXL3	29412610	1.000000	0.71417	0.999000	0.59377	0.159000	0.22180	4.055000	0.57441	0.861000	0.35504	0.328000	0.21473	AAG	.		0.682	ASXL3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441865.2		
AC006116.24	0	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	19	56888579	56888579	+	RNA	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr19:56888579T>G	ENST00000591836.1	-	0	74				ZNF542_ENST00000490123.1_RNA																							GTGAGAAACCTTACAAATGTA	0.423																																					.		.											.	.	.	0			.						.																																					147947	.			GAAACCTTACAAA																													19.37:g.56888579T>G		Somatic	34	0		WXS	Illumina HiSeq	.	40	22	.		RNA	SNP	ENST00000591836.1	37																																																																																				.		0.423	AC006116.24-001	KNOWN	basic	sense_intronic	sense_intronic	OTTHUMT00000459747.1		
KIF14	9928	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	200587439	200587439	+	Missense_Mutation	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr1:200587439A>C	ENST00000367350.4	-	2	851	c.413T>G	c.(412-414)aTa>aGa	p.I138R		NM_014875.2	NP_055690.1	Q15058	KIF14_HUMAN	kinesin family member 14	138	Required for PRC1-binding.				ATP catabolic process (GO:0006200)|cytoskeleton-dependent intracellular transport (GO:0030705)|establishment of protein localization (GO:0045184)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|negative regulation of integrin activation (GO:0033624)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of Rap protein signal transduction (GO:0032487)|substrate adhesion-dependent cell spreading (GO:0034446)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|PDZ domain binding (GO:0030165)			NS(1)|breast(5)|central_nervous_system(2)|endometrium(8)|kidney(8)|large_intestine(15)|lung(13)|ovary(3)|prostate(2)|skin(3)|urinary_tract(1)	61						GACAGAATCTATTTCAGCTGT	0.353																																					p.I138R		.											.	.	.	0			c.T413G						.						94.0	97.0	96.0					1																	200587439		2203	4300	6503	SO:0001583	missense	9928	exon2			GAATCTATTTCAG	D26361	CCDS30963.1	1q32.1	2008-03-03			ENSG00000118193	ENSG00000118193		"""Kinesins"""	19181	protein-coding gene	gene with protein product		611279				7584044	Standard	NM_014875		Approved	KIAA0042	uc010ppk.1	Q15058	OTTHUMG00000035723	ENST00000367350.4:c.413T>G	1.37:g.200587439A>C	ENSP00000356319:p.Ile138Arg	Somatic	72	0		WXS	Illumina HiSeq	.	67	43	NM_014875	Q14CI8|Q4G0A5|Q5T1W3	Missense_Mutation	SNP	ENST00000367350.4	37	CCDS30963.1	.	.	.	.	.	.	.	.	.	.	A	5.496	0.276456	0.10403	.	.	ENSG00000118193	ENST00000367350	T	0.72505	-0.66	1.94	-3.88	0.04205	.	.	.	.	.	T	0.38506	0.1043	N	0.08118	0	0.09310	N	1	B	0.06786	0.001	B	0.09377	0.004	T	0.17319	-1.0373	9	0.17369	T	0.5	.	0.7228	0.00943	0.4335:0.1765:0.2124:0.1776	.	138	Q15058	KIF14_HUMAN	R	138	ENSP00000356319:I138R	ENSP00000356319:I138R	I	-	2	0	KIF14	198854062	0.003000	0.15002	0.000000	0.03702	0.012000	0.07955	-0.631000	0.05496	-1.379000	0.02118	-0.755000	0.03482	ATA	.		0.353	KIF14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086878.1	NM_014875	
TBCEL	219899	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	11	120957511	120957511	+	Silent	SNP	T	T	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr11:120957511T>C	ENST00000529397.1	+	8	1081	c.981T>C	c.(979-981)taT>taC	p.Y327Y	TBCEL_ENST00000422003.2_Silent_p.Y327Y	NM_001130047.1	NP_001123519.1	Q5QJ74	TBCEL_HUMAN	tubulin folding cofactor E-like	327						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)			TECTA/TBCEL(2)	endometrium(3)|kidney(1)|large_intestine(2)|lung(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	14		Breast(109;0.00526)|Medulloblastoma(222;0.0523)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;5.89e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.121)		TCACTAAATATGGGAAGTTGG	0.423																																					p.Y327Y		.											.	.	.	0			c.T981C						.						81.0	75.0	77.0					11																	120957511		2203	4299	6502	SO:0001819	synonymous_variant	219899	exon8			TAAATATGGGAAG	BC020501	CCDS31692.1	11q23.3	2008-02-05	2006-11-21	2006-11-21		ENSG00000154114			28115	protein-coding gene	gene with protein product		610451	"""leucine rich repeat containing 35"", ""tubulin-specific chaperone e-like"""	LRRC35		15728251	Standard	NM_152715		Approved	MGC10233	uc001pxo.3	Q5QJ74		ENST00000529397.1:c.981T>C	11.37:g.120957511T>C		Somatic	55	0		WXS	Illumina HiSeq	.	36	5	NM_001130047	Q0VAN6	Silent	SNP	ENST00000529397.1	37	CCDS31692.1																																																																																			.		0.423	TBCEL-005	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000387688.1	NM_152715	
HOXA5	3202	hgsc.bcm.edu	37	7	27183301	27183301	+	5'Flank	SNP	G	G	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr7:27183301G>T	ENST00000222726.3	-	0	0				RP1-170O19.22_ENST00000467897.2_RNA|HOXA-AS3_ENST00000518848.1_RNA|HOXA6_ENST00000521478.1_5'Flank|HOXA-AS3_ENST00000521197.1_RNA|HOXA5_ENST00000520854.1_5'Flank	NM_019102.3	NP_061975.2	P20719	HXA5_HUMAN	homeobox A5						anterior/posterior pattern specification (GO:0009952)|bronchiole development (GO:0060435)|cell migration (GO:0016477)|cell-cell signaling involved in mammary gland development (GO:0060764)|embryonic skeletal system morphogenesis (GO:0048704)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|intestinal epithelial cell maturation (GO:0060574)|lung alveolus development (GO:0048286)|lung goblet cell differentiation (GO:0060480)|lung-associated mesenchyme development (GO:0060484)|mammary gland alveolus development (GO:0060749)|mammary gland epithelial cell differentiation (GO:0060644)|mesenchymal-epithelial cell signaling (GO:0060638)|multicellular organism growth (GO:0035264)|negative regulation of angiogenesis (GO:0016525)|negative regulation of erythrocyte differentiation (GO:0045647)|positive regulation of apoptotic process (GO:0043065)|positive regulation of myeloid cell differentiation (GO:0045639)|positive regulation of receptor biosynthetic process (GO:0010870)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of mammary gland epithelial cell proliferation (GO:0033599)|respiratory system process (GO:0003016)|thyroid gland development (GO:0030878)|trachea cartilage morphogenesis (GO:0060535)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|large_intestine(2)|lung(12)|skin(1)	16						CACAATTTATGATGAATTATG	0.423											OREG0017912	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									.	Colon(119;75 2200 7557 42868)	.											.	.	.	0			.						.																																			SO:0001631	upstream_gene_variant	100133311	.			ATTTATGATGAAT		CCDS5406.1	7p15.2	2011-06-20	2005-12-22		ENSG00000106004	ENSG00000106004		"""Homeoboxes / ANTP class : HOXL subclass"""	5106	protein-coding gene	gene with protein product		142952	"""homeo box A5"""	HOX1C, HOX1		1973146, 1358459	Standard	NM_019102		Approved		uc003syn.2	P20719	OTTHUMG00000023214		7.37:g.27183301G>T	Exception_encountered	Somatic	98	0	792	WXS	Illumina HiSeq	.	65	4	.	A4D179|O43367|Q96CY6	RNA	SNP	ENST00000222726.3	37	CCDS5406.1																																																																																			.		0.423	HOXA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358705.1		
ELAVL1	1994	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	19	8056616	8056616	+	Silent	SNP	A	A	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr19:8056616A>T	ENST00000407627.2	-	2	213	c.84T>A	c.(82-84)ccT>ccA	p.P28P	ELAVL1_ENST00000351593.5_Silent_p.P55P|ELAVL1_ENST00000596459.1_Silent_p.P28P|ELAVL1_ENST00000593807.1_Silent_p.P28P	NM_001419.2	NP_001410.2	Q15717	ELAV1_HUMAN	ELAV like RNA binding protein 1	28	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				3'-UTR-mediated mRNA stabilization (GO:0070935)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|mRNA stabilization (GO:0048255)|multicellular organismal development (GO:0007275)|positive regulation of translation (GO:0045727)|regulation of stem cell maintenance (GO:2000036)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	AU-rich element binding (GO:0017091)|double-stranded RNA binding (GO:0003725)|mRNA 3'-UTR AU-rich region binding (GO:0035925)|mRNA 3'-UTR binding (GO:0003730)|mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|RNA binding (GO:0003723)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	20						TCATGTTCTGAGGGAGGTAGT	0.433																																					p.P28P		.											.	.	.	0			c.T84A						.						179.0	155.0	163.0					19																	8056616		2203	4300	6503	SO:0001819	synonymous_variant	1994	exon2			GTTCTGAGGGAGG	U38175	CCDS12193.1	19p13.2	2013-10-03	2013-10-03			ENSG00000066044		"""RNA binding motif (RRM) containing"""	3312	protein-coding gene	gene with protein product	"""embryonic lethal, abnormal vision, drosophila, homolog-like 1"", ""Hu antigen R"""	603466	"""ELAV (embryonic lethal, abnormal vision, Drosophila)-like 1 (Hu antigen R)"""	HUR		8626503, 9003489	Standard	NM_001419		Approved	HuR, Hua, MelG	uc002mjb.3	Q15717		ENST00000407627.2:c.84T>A	19.37:g.8056616A>T		Somatic	67	0		WXS	Illumina HiSeq	.	52	21	NM_001419	B4DVB8|Q53XN6|Q9BTT1	Silent	SNP	ENST00000407627.2	37	CCDS12193.1																																																																																			.		0.433	ELAVL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461494.3	NM_001419	
BMP6	654	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	6	7880449	7880449	+	Missense_Mutation	SNP	A	A	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr6:7880449A>G	ENST00000283147.6	+	7	1574	c.1415A>G	c.(1414-1416)tAt>tGt	p.Y472C		NM_001718.4	NP_001709.1	P22004	BMP6_HUMAN	bone morphogenetic protein 6	472					BMP signaling pathway (GO:0030509)|cartilage development (GO:0051216)|cellular response to mechanical stimulus (GO:0071260)|endochondral ossification (GO:0001958)|eye development (GO:0001654)|growth (GO:0040007)|immune response (GO:0006955)|inflammatory response (GO:0006954)|kidney development (GO:0001822)|male genitalia development (GO:0030539)|osteoblast differentiation (GO:0001649)|positive regulation of aldosterone biosynthetic process (GO:0032349)|positive regulation of aldosterone secretion (GO:2000860)|positive regulation of bone mineralization (GO:0030501)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of DNA-dependent DNA replication (GO:2000105)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of protein secretion (GO:0050714)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to activity (GO:0014823)|response to glucocorticoid (GO:0051384)|response to iron ion (GO:0010039)|response to magnesium ion (GO:0032026)|response to retinoic acid (GO:0032526)|skeletal system development (GO:0001501)|SMAD protein signal transduction (GO:0060395)|type B pancreatic cell development (GO:0003323)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|membrane-bounded vesicle (GO:0031988)	BMP receptor binding (GO:0070700)|protein heterodimerization activity (GO:0046982)			breast(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(6)|ovary(1)|prostate(1)	23	Ovarian(93;0.0721)					AACCCCGAGTATGTCCCCAAA	0.433																																					p.Y472C		.											.	.	.	0			c.A1415G						.						185.0	195.0	192.0					6																	7880449		2203	4300	6503	SO:0001583	missense	654	exon7			CCGAGTATGTCCC	AF083030	CCDS4503.1	6p24-p23	2014-01-30	2003-10-06		ENSG00000153162	ENSG00000153162		"""Bone morphogenetic proteins"", ""Endogenous ligands"""	1073	protein-coding gene	gene with protein product		112266	"""vegetal related growth factor (TGFB-related)"""	VGR		1427904, 1453478	Standard	NM_001718		Approved	VGR1	uc003mxu.4	P22004	OTTHUMG00000014217	ENST00000283147.6:c.1415A>G	6.37:g.7880449A>G	ENSP00000283147:p.Tyr472Cys	Somatic	72	0		WXS	Illumina HiSeq	.	54	30	NM_001718	Q5TCP3	Missense_Mutation	SNP	ENST00000283147.6	37	CCDS4503.1	.	.	.	.	.	.	.	.	.	.	A	17.95	3.512738	0.64522	.	.	ENSG00000153162	ENST00000537240;ENST00000283147;ENST00000540959	D	0.83755	-1.76	5.65	5.65	0.86999	Transforming growth factor-beta, C-terminal (3);	0.051940	0.85682	D	0.000000	T	0.81683	0.4874	L	0.36672	1.1	0.58432	D	0.999991	D	0.58268	0.982	P	0.60682	0.878	T	0.81918	-0.0713	10	0.37606	T	0.19	.	15.8773	0.79173	1.0:0.0:0.0:0.0	.	472	P22004	BMP6_HUMAN	C	394;472;435	ENSP00000283147:Y472C	ENSP00000283147:Y472C	Y	+	2	0	BMP6	7825448	1.000000	0.71417	0.996000	0.52242	0.990000	0.78478	5.641000	0.67881	2.149000	0.67028	0.533000	0.62120	TAT	.		0.433	BMP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039794.1	NM_001718	
DHX40	79665	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	17	57643997	57643997	+	Missense_Mutation	SNP	G	G	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr17:57643997G>A	ENST00000251241.4	+	2	269	c.122G>A	c.(121-123)gGa>gAa	p.G41E	DHX40_ENST00000451169.2_De_novo_Start_OutOfFrame|DHX40_ENST00000425628.3_Missense_Mutation_p.G41E	NM_024612.4	NP_078888.4	Q8IX18	DHX40_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 40	41							ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|nucleic acid binding (GO:0003676)			endometrium(7)|large_intestine(6)|lung(6)|prostate(1)	20	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)					GAAGAGAAAGGATGCACGTCC	0.348																																					p.G41E		.											.	.	.	0			c.G122A						.						37.0	36.0	37.0					17																	57643997		2203	4300	6503	SO:0001583	missense	79665	exon2			AGAAAGGATGCAC	AF260270	CCDS11617.1, CCDS54150.1	17q22	2014-01-28	2003-06-13	2003-06-20		ENSG00000108406		"""DEAH-boxes"""	18018	protein-coding gene	gene with protein product		607570	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 40 (RNA helicase)"""	DDX40			Standard	NM_024612		Approved	ARG147, PAD, FLJ22060	uc002ixn.2	Q8IX18		ENST00000251241.4:c.122G>A	17.37:g.57643997G>A	ENSP00000251241:p.Gly41Glu	Somatic	103	0		WXS	Illumina HiSeq	.	58	18	NM_024612	B3KTJ5|C9JR60|Q5JPH4|Q8TC86|Q8WY53|Q9BXM1|Q9H6M9	Missense_Mutation	SNP	ENST00000251241.4	37	CCDS11617.1	.	.	.	.	.	.	.	.	.	.	G	11.42	1.634301	0.29068	.	.	ENSG00000108406	ENST00000251241;ENST00000538926;ENST00000425628	T;T	0.02656	4.23;4.21	5.47	4.5	0.54988	.	0.128058	0.35615	N	0.003085	T	0.01695	0.0054	N	0.08118	0	0.80722	D	1	B;B	0.22003	0.013;0.063	B;B	0.19666	0.025;0.026	T	0.56135	-0.8029	10	0.39692	T	0.17	.	6.3079	0.21149	0.0913:0.0:0.7245:0.1842	.	41;41	F5H625;Q8IX18	.;DHX40_HUMAN	E	41	ENSP00000251241:G41E;ENSP00000388749:G41E	ENSP00000251241:G41E	G	+	2	0	DHX40	54998779	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	2.317000	0.43770	2.567000	0.86603	0.561000	0.74099	GGA	.		0.348	DHX40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446095.1	NM_024612	
APBB3	10307	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	5	139939978	139939978	+	Missense_Mutation	SNP	G	G	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr5:139939978G>C	ENST00000357560.4	-	12	1587	c.1144C>G	c.(1144-1146)Cgt>Ggt	p.R382G	SRA1_ENST00000520427.1_5'Flank|APBB3_ENST00000358580.5_3'UTR|APBB3_ENST00000507279.1_5'Flank|APBB3_ENST00000356738.2_Missense_Mutation_p.R387G|APBB3_ENST00000508496.2_Missense_Mutation_p.R159G|APBB3_ENST00000412920.3_Missense_Mutation_p.R380G|APBB3_ENST00000354402.5_Missense_Mutation_p.R389G|SRA1_ENST00000336283.6_5'Flank	NM_006051.3|NM_133173.2	NP_006042.3|NP_573419.2	O95704	APBB3_HUMAN	amyloid beta (A4) precursor protein-binding, family B, member 3	382	PID 2. {ECO:0000255|PROSITE- ProRule:PRU00148}.					actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(2)|prostate(1)	11			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AAGCTCTGACGGCCCAGGTCA	0.602																																					p.R389G		.											.	.	.	0			c.C1165G						.						59.0	53.0	55.0					5																	139939978		2203	4300	6503	SO:0001583	missense	10307	exon11			TCTGACGGCCCAG	AB018247	CCDS4227.1, CCDS4228.1, CCDS4229.1, CCDS47279.1	5q31	2008-02-05			ENSG00000113108	ENSG00000113108			20708	protein-coding gene	gene with protein product		602711				9407065	Standard	NM_133172		Approved	FE65L2	uc003lgd.1	O95704	OTTHUMG00000129504	ENST00000357560.4:c.1144C>G	5.37:g.139939978G>C	ENSP00000350171:p.Arg382Gly	Somatic	67	0		WXS	Illumina HiSeq	.	40	5	NM_006051	B3KQN9|Q08AG4|Q96Q18|Q9BYD4|Q9NYX6|Q9NYX7|Q9NYX8	Missense_Mutation	SNP	ENST00000357560.4	37	CCDS4229.1	.	.	.	.	.	.	.	.	.	.	G	8.545	0.874245	0.17395	.	.	ENSG00000113108	ENST00000356738;ENST00000354402;ENST00000357560;ENST00000508496;ENST00000412920	T;T;T;T;T	0.27890	1.64;1.64;1.64;1.64;1.64	5.28	3.47	0.39725	.	0.490245	0.22961	N	0.053554	T	0.14743	0.0356	N	0.14661	0.345	0.37580	D	0.919766	B;B	0.24675	0.032;0.109	B;B	0.23018	0.016;0.043	T	0.12760	-1.0535	9	.	.	.	-0.011	5.424	0.16415	0.1534:0.0:0.5727:0.2739	.	380;387	O95704-2;O95704-3	.;.	G	387;389;382;159;380	ENSP00000349177:R387G;ENSP00000346378:R389G;ENSP00000350171:R382G;ENSP00000444013:R159G;ENSP00000402591:R380G	.	R	-	1	0	APBB3	139920162	0.087000	0.21565	0.999000	0.59377	0.999000	0.98932	1.089000	0.30890	0.596000	0.29794	0.655000	0.94253	CGT	.		0.602	APBB3-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251677.2	NM_006051	
ZNF699	374879	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	19	9407095	9407095	+	Missense_Mutation	SNP	G	G	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr19:9407095G>A	ENST00000591998.1	-	6	1213	c.985C>T	c.(985-987)Cac>Tac	p.H329Y	CTC-325H20.4_ENST00000591336.1_RNA|ZNF699_ENST00000308650.3_Missense_Mutation_p.H329Y			Q32M78	ZN699_HUMAN	zinc finger protein 699	329					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(7)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	24						TCTCCACTGTGAATTCTTTTG	0.408																																					p.H329Y		.											.	.	.	0			c.C985T						.						77.0	79.0	79.0					19																	9407095		2184	4288	6472	SO:0001583	missense	374879	exon5			CACTGTGAATTCT	BC109268	CCDS42495.1	19p13.2	2013-01-08				ENSG00000196110		"""Zinc fingers, C2H2-type"", ""-"""	24750	protein-coding gene	gene with protein product	hangover homolog (Drosophila)	609571				16940975	Standard	NM_198535		Approved	FLJ38144, hang	uc002mlc.1	Q32M78		ENST00000591998.1:c.985C>T	19.37:g.9407095G>A	ENSP00000467723:p.His329Tyr	Somatic	59	0		WXS	Illumina HiSeq	.	33	17	NM_198535	Q8N9A1	Missense_Mutation	SNP	ENST00000591998.1	37	CCDS42495.1	.	.	.	.	.	.	.	.	.	.	g	13.62	2.291476	0.40494	.	.	ENSG00000196110	ENST00000308650	T	0.67523	-0.27	3.17	3.17	0.36434	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.37053	N	0.002279	D	0.84588	0.5505	M	0.93898	3.47	0.34096	D	0.661334	D	0.89917	1.0	D	0.91635	0.999	D	0.90871	0.4746	10	0.72032	D	0.01	.	12.5826	0.56399	0.0:0.0:1.0:0.0	.	329	Q32M78	ZN699_HUMAN	Y	329	ENSP00000311596:H329Y	ENSP00000311596:H329Y	H	-	1	0	ZNF699	9268095	1.000000	0.71417	0.046000	0.18839	0.058000	0.15608	8.227000	0.89787	2.087000	0.62958	0.455000	0.32223	CAC	.		0.408	ZNF699-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449010.1	NM_198535	
AOX1	316	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	2	201531474	201531474	+	Splice_Site	SNP	A	A	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr2:201531474A>T	ENST00000374700.2	+	32	3849	c.3608A>T	c.(3607-3609)cAg>cTg	p.Q1203L	AOX1_ENST00000485106.1_3'UTR	NM_001159.3	NP_001150.3	Q06278	AOXA_HUMAN	aldehyde oxidase 1	1203					inflammatory response (GO:0006954)|reactive oxygen species metabolic process (GO:0072593)|small molecule metabolic process (GO:0044281)|vitamin B6 metabolic process (GO:0042816)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	2 iron, 2 sulfur cluster binding (GO:0051537)|aldehyde oxidase activity (GO:0004031)|electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|iron ion binding (GO:0005506)|molybdopterin cofactor binding (GO:0043546)|NAD binding (GO:0051287)|UDP-N-acetylmuramate dehydrogenase activity (GO:0008762)|xanthine dehydrogenase activity (GO:0004854)			breast(5)|endometrium(3)|kidney(4)|large_intestine(13)|lung(38)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	81					Allopurinol(DB00437)|Aminocaproic Acid(DB00513)|Brimonidine(DB00484)|Famciclovir(DB00426)|Menadione(DB00170)|Mercaptopurine(DB01033)|Methotrexate(DB00563)|Pyrazinamide(DB00339)|Raloxifene(DB00481)|Zaleplon(DB00962)|Zonisamide(DB00909)	GACATAGGCCAGGTACGTGTA	0.368																																					p.Q1203L		.											.	.	.	0			c.A3608T						.						101.0	96.0	98.0					2																	201531474		2203	4300	6503	SO:0001630	splice_region_variant	316	exon32			TAGGCCAGGTACG	AF017060	CCDS33360.1	2q33	2008-05-20			ENSG00000138356	ENSG00000138356			553	protein-coding gene	gene with protein product		602841				7570184	Standard	NM_001159		Approved	AO, AOH1	uc002uvx.3	Q06278	OTTHUMG00000154536	ENST00000374700.2:c.3609+1A>T	2.37:g.201531474A>T		Somatic	85	0		WXS	Illumina HiSeq	.	64	27	NM_001159	O14765|Q53RR8|Q53TV3|Q9BYF0|Q9UPG6	Missense_Mutation	SNP	ENST00000374700.2	37	CCDS33360.1	.	.	.	.	.	.	.	.	.	.	A	21.4	4.146144	0.77888	.	.	ENSG00000138356	ENST00000374700;ENST00000260930;ENST00000439380	T;T;T	0.67698	-0.28;-0.28;-0.28	5.09	5.09	0.68999	Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding (3);	0.111370	0.64402	D	0.000006	D	0.89132	0.6628	H	0.98936	4.375	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.93413	0.6770	10	0.87932	D	0	-46.0161	15.3271	0.74172	1.0:0.0:0.0:0.0	.	1203	Q06278	ADO_HUMAN	L	1203;89;43	ENSP00000363832:Q1203L;ENSP00000260930:Q89L;ENSP00000413326:Q43L	ENSP00000260930:Q89L	Q	+	2	0	AOX1	201239719	1.000000	0.71417	1.000000	0.80357	0.524000	0.34500	8.661000	0.91125	2.267000	0.75376	0.383000	0.25322	CAG	.		0.368	AOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335844.1	NM_001159	Missense_Mutation
XPNPEP1	7511	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	10	111643856	111643856	+	Missense_Mutation	SNP	A	A	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr10:111643856A>G	ENST00000502935.1	-	9	918	c.799T>C	c.(799-801)Tcc>Ccc	p.S267P	XPNPEP1_ENST00000430337.1_5'UTR|XPNPEP1_ENST00000369680.4_Missense_Mutation_p.S224P|XPNPEP1_ENST00000369683.1_Missense_Mutation_p.S153P|XPNPEP1_ENST00000322238.8_Missense_Mutation_p.S267P					X-prolyl aminopeptidase (aminopeptidase P) 1, soluble											endometrium(2)|kidney(9)|large_intestine(4)|lung(9)|ovary(3)|pancreas(2)|skin(1)|urinary_tract(1)	31		Breast(234;0.174)		Epithelial(162;1.64e-05)|all cancers(201;0.000564)|BRCA - Breast invasive adenocarcinoma(275;0.0721)		ATTGCGTAGGAGAAAAATACT	0.458											OREG0020527	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.S267P		.											.	.	.	0			c.T799C						.						193.0	190.0	191.0					10																	111643856		2203	4300	6503	SO:0001583	missense	7511	exon9			CGTAGGAGAAAAA		CCDS7560.1, CCDS7560.2, CCDS53576.1	10q25.3	2006-01-16	2002-07-17		ENSG00000108039	ENSG00000108039	3.4.11.9		12822	protein-coding gene	gene with protein product		602443	"""X-prolyl aminopeptidase (aminopeptidase P)-like"""	XPNPEP, XPNPEPL1, XPNPEPL			Standard	NM_020383		Approved		uc001kyp.2	Q9NQW7	OTTHUMG00000019029	ENST00000502935.1:c.799T>C	10.37:g.111643856A>G	ENSP00000421566:p.Ser267Pro	Somatic	40	0	1436	WXS	Illumina HiSeq	.	36	15	NM_001167604		Missense_Mutation	SNP	ENST00000502935.1	37	CCDS7560.2	.	.	.	.	.	.	.	.	.	.	A	22.5	4.300920	0.81136	.	.	ENSG00000108039	ENST00000502935;ENST00000369683;ENST00000322238;ENST00000369680;ENST00000403138;ENST00000423625	T;T;T;T;T	0.70516	-0.49;-0.49;-0.49;-0.49;-0.49	5.24	5.24	0.73138	.	0.055532	0.64402	D	0.000001	D	0.86623	0.5977	H	0.94808	3.585	0.42906	D	0.994248	D;D;D	0.76494	0.999;0.992;0.976	D;D;P	0.68192	0.956;0.925;0.714	D	0.89552	0.3800	10	0.87932	D	0	-14.7018	10.3877	0.44150	0.7841:0.2159:0.0:0.0	.	267;267;224	B4E2P4;G5E9Y2;Q9NQW7	.;.;XPP1_HUMAN	P	267;153;267;224;224;192	ENSP00000421566:S267P;ENSP00000358697:S153P;ENSP00000324011:S267P;ENSP00000358694:S224P;ENSP00000385388:S224P	ENSP00000324011:S267P	S	-	1	0	XPNPEP1	111633846	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	4.825000	0.62708	2.113000	0.64589	0.533000	0.62120	TCC	.		0.458	XPNPEP1-015	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000050264.2		
CYP4F22	126410	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	19	15651396	15651396	+	Silent	SNP	C	C	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr19:15651396C>T	ENST00000269703.3	+	8	1006	c.807C>T	c.(805-807)gaC>gaT	p.D269D	CYP4F22_ENST00000601005.2_Silent_p.D269D	NM_173483.3	NP_775754.2	Q6NT55	CP4FN_HUMAN	cytochrome P450, family 4, subfamily F, polypeptide 22	269						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						AGGCCTGTGACATGGTGCACC	0.632																																					p.D269D		.											.	.	.	0			c.C807T						.						71.0	66.0	68.0					19																	15651396		2203	4300	6503	SO:0001819	synonymous_variant	126410	exon8			CTGTGACATGGTG		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.807C>T	19.37:g.15651396C>T		Somatic	28	0		WXS	Illumina HiSeq	.	31	11	NM_173483	Q8N8H4	Silent	SNP	ENST00000269703.3	37	CCDS12331.1																																																																																			.		0.632	CYP4F22-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461338.2	NM_173483	
XKR4	114786	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	8	56015562	56015562	+	Missense_Mutation	SNP	A	A	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr8:56015562A>T	ENST00000327381.6	+	1	614	c.514A>T	c.(514-516)Agc>Tgc	p.S172C		NM_052898.1	NP_443130.1	Q5GH76	XKR4_HUMAN	XK, Kell blood group complex subunit-related family, member 4	172						integral component of membrane (GO:0016021)				NS(1)|autonomic_ganglia(1)|endometrium(1)|kidney(3)|large_intestine(4)|liver(2)|lung(12)|ovary(1)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	34			Epithelial(17;0.000117)|all cancers(17;0.000836)			GCACGATTTCAGCACCGAGGA	0.672											OREG0006933	type=TRANSCRIPTION FACTOR BINDING SITE|Gene=XKR4|TFbs=REST|Dataset=NRSF/REST ChIPSeq sites|EvidenceSubtype=Chromatin immunoprecipitation with tag sequencing (ChIP-TS)																									p.S172C		.											.	.	.	0			c.A514T						.						39.0	30.0	33.0					8																	56015562		2203	4297	6500	SO:0001583	missense	114786	exon1			GATTTCAGCACCG	AY534241	CCDS34893.1	8q12.1	2006-01-12	2006-01-12		ENSG00000206579	ENSG00000206579			29394	protein-coding gene	gene with protein product			"""X Kell blood group precursor-related family, member 4"""				Standard	NM_052898		Approved	KIAA1889	uc003xsf.3	Q5GH76	OTTHUMG00000164288	ENST00000327381.6:c.514A>T	8.37:g.56015562A>T	ENSP00000328326:p.Ser172Cys	Somatic	22	0	1012	WXS	Illumina HiSeq	.	23	11	NM_052898	Q96PZ8	Missense_Mutation	SNP	ENST00000327381.6	37	CCDS34893.1	.	.	.	.	.	.	.	.	.	.	A	21.0	4.079734	0.76528	.	.	ENSG00000206579	ENST00000327381;ENST00000543752	T	0.66460	-0.21	5.57	3.2	0.36748	.	0.373631	0.29178	N	0.012918	T	0.73598	0.3607	L	0.57536	1.79	0.35760	D	0.820064	D	0.69078	0.997	P	0.62649	0.905	T	0.79237	-0.1886	10	0.87932	D	0	-7.0293	8.9059	0.35523	0.7478:0.0:0.2522:0.0	.	172	Q5GH76	XKR4_HUMAN	C	172	ENSP00000328326:S172C	ENSP00000328326:S172C	S	+	1	0	XKR4	56178116	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.026000	0.49689	0.933000	0.37291	0.528000	0.53228	AGC	.		0.672	XKR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378129.2	NM_052898	
ARID1B	57492	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	6	157505453	157505453	+	Missense_Mutation	SNP	A	A	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr6:157505453A>G	ENST00000350026.5	+	12	3396	c.3395A>G	c.(3394-3396)tAt>tGt	p.Y1132C	ARID1B_ENST00000346085.5_Missense_Mutation_p.Y1145C|ARID1B_ENST00000275248.4_Missense_Mutation_p.Y1127C|ARID1B_ENST00000367148.1_Missense_Mutation_p.Y1185C	NM_017519.2	NP_059989.2	Q8NFD5	ARI1B_HUMAN	AT rich interactive domain 1B (SWI1-like)	1132	ARID. {ECO:0000255|PROSITE- ProRule:PRU00355}.				chromatin-mediated maintenance of transcription (GO:0048096)|nervous system development (GO:0007399)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)			NS(2)|breast(5)|central_nervous_system(4)|endometrium(12)|kidney(4)|large_intestine(11)|lung(30)|ovary(3)|pancreas(1)|prostate(4)|skin(2)|urinary_tract(3)	81		Breast(66;0.000162)|Ovarian(120;0.0265)		OV - Ovarian serous cystadenocarcinoma(65;3.19e-17)|BRCA - Breast invasive adenocarcinoma(81;1.01e-05)		AAAAAGCAGTATATTCAGTAC	0.517																																					p.Y1145C		.											.	.	.	0			c.A3434G						.						89.0	85.0	87.0					6																	157505453		2203	4296	6499	SO:0001583	missense	57492	exon13			AGCAGTATATTCA	AF521671	CCDS5251.1, CCDS5251.2, CCDS55072.1	6q25.3	2014-09-17			ENSG00000049618	ENSG00000049618		"""-"""	18040	protein-coding gene	gene with protein product		614556					Standard	NM_017519		Approved	KIAA1235, ELD/OSA1, p250R, BAF250b, DAN15, 6A3-5	uc003qqo.3	Q8NFD5	OTTHUMG00000015890	ENST00000350026.5:c.3395A>G	6.37:g.157505453A>G	ENSP00000055163:p.Tyr1132Cys	Somatic	81	0		WXS	Illumina HiSeq	.	80	25	NM_020732	Q5JRD1|Q5VYC4|Q8IZY8|Q8TEV0|Q8TF02|Q99491|Q9ULI5	Missense_Mutation	SNP	ENST00000350026.5	37	CCDS5251.2	.	.	.	.	.	.	.	.	.	.	A	25.4	4.632531	0.87660	.	.	ENSG00000049618	ENST00000346085;ENST00000350026;ENST00000367148;ENST00000275248;ENST00000354354;ENST00000414678;ENST00000319584;ENST00000400790	T;T;T;T;T;T;T	0.76448	-1.02;-1.02;-1.02;-1.02;-1.02;-1.02;-1.02	5.91	5.91	0.95273	ARID/BRIGHT DNA-binding domain (5);	0.000000	0.85682	D	0.000000	D	0.89646	0.6775	M	0.92923	3.36	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;1.0	D	0.92131	0.5712	10	0.87932	D	0	.	16.3483	0.83171	1.0:0.0:0.0:0.0	.	382;1132;1145;1127	Q8NFD5-4;Q8NFD5;Q8NFD5-2;G3XAA0	.;ARI1B_HUMAN;.;.	C	1145;1132;1185;1127;602;654;607;199	ENSP00000344546:Y1145C;ENSP00000055163:Y1132C;ENSP00000356116:Y1185C;ENSP00000275248:Y1127C;ENSP00000412835:Y654C;ENSP00000313006:Y607C;ENSP00000383596:Y199C	ENSP00000275248:Y1127C	Y	+	2	0	ARID1B	157547145	1.000000	0.71417	0.999000	0.59377	0.998000	0.95712	9.329000	0.96413	2.254000	0.74563	0.533000	0.62120	TAT	.		0.517	ARID1B-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000372723.1	NM_020732	
KCNU1	157855	hgsc.bcm.edu	37	8	36675277	36675277	+	Splice_Site	SNP	G	G	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr8:36675277G>T	ENST00000399881.3	+	10	1142	c.1105G>T	c.(1105-1107)Gaa>Taa	p.E369*		NM_001031836.2	NP_001027006.2	A8MYU2	KCNU1_HUMAN	potassium channel, subfamily U, member 1	369	RCK N-terminal.				multicellular organism reproduction (GO:0032504)|potassium ion transmembrane transport (GO:0071805)|single fertilization (GO:0007338)|sperm-egg recognition (GO:0035036)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	large conductance calcium-activated potassium channel activity (GO:0060072)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(9)|lung(31)|ovary(1)|urinary_tract(1)	57				KIRC - Kidney renal clear cell carcinoma(67;0.0504)|Kidney(114;0.0634)		TTTCCTGGGAGAGTAAGTATA	0.373																																					p.E369X		.											.	.	.	0			c.G1105T						.						125.0	113.0	117.0					8																	36675277		1851	4086	5937	SO:0001630	splice_region_variant	157855	exon10			CTGGGAGAGTAAG	BC028701	CCDS55220.1	8p11.2	2012-07-05				ENSG00000215262		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, calcium-activated"""	18867	protein-coding gene	gene with protein product		615215				16382103	Standard	NM_001031836		Approved	KCa5.1, Slo3, KCNMC1, Kcnma3	uc010lvw.3	A8MYU2		ENST00000399881.3:c.1106+1G>T	8.37:g.36675277G>T		Somatic	119	0		WXS	Illumina HiSeq	.	86	5	NM_001031836		Nonsense_Mutation	SNP	ENST00000399881.3	37	CCDS55220.1	.	.	.	.	.	.	.	.	.	.	G	38	6.834054	0.97873	.	.	ENSG00000215262	ENST00000399881	.	.	.	5.31	4.41	0.53225	.	0.000000	0.38111	U	0.001807	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.21540	T	0.41	-1.9162	12.4646	0.55751	0.0:0.0:0.8261:0.1739	.	.	.	.	X	369	.	ENSP00000382770:E369X	E	+	1	0	KCNU1	36794435	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	4.963000	0.63694	1.298000	0.44778	0.655000	0.94253	GAA	.		0.373	KCNU1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376631.1	NM_001031836	Nonsense_Mutation
ZNF281	23528	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	200376559	200376559	+	Missense_Mutation	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr1:200376559A>C	ENST00000294740.3	-	2	2399	c.2275T>G	c.(2275-2277)Ttg>Gtg	p.L759V	ZNF281_ENST00000367352.3_Missense_Mutation_p.L723V|ZNF281_ENST00000367353.1_Missense_Mutation_p.L759V	NM_001281293.1|NM_001281294.1|NM_012482.4	NP_001268222.1|NP_001268223.1|NP_036614.1	Q9Y2X9	ZN281_HUMAN	zinc finger protein 281	759					embryonic body morphogenesis (GO:0010172)|negative regulation of gene expression (GO:0010629)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|stem cell differentiation (GO:0048863)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	core promoter binding (GO:0001047)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)			breast(4)|endometrium(3)|kidney(3)|large_intestine(6)|lung(7)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	27						GAAGGTGTCAACTGCTGATGT	0.453																																					p.L759V		.											.	.	.	0			c.T2275G						.						55.0	55.0	55.0					1																	200376559		2203	4300	6503	SO:0001583	missense	23528	exon2			GTGTCAACTGCTG	AF125158	CCDS1402.1, CCDS60384.1	1q32.1	2012-08-08			ENSG00000162702	ENSG00000162702		"""Zinc fingers, C2H2-type"""	13075	protein-coding gene	gene with protein product						10448078	Standard	NM_012482		Approved	ZBP-99	uc001gve.3	Q9Y2X9	OTTHUMG00000035724	ENST00000294740.3:c.2275T>G	1.37:g.200376559A>C	ENSP00000294740:p.Leu759Val	Somatic	63	0		WXS	Illumina HiSeq	.	74	19	NM_012482	A6NF48|B3KMX2|Q5RKW5|Q9NY92	Missense_Mutation	SNP	ENST00000294740.3	37	CCDS1402.1	.	.	.	.	.	.	.	.	.	.	A	12.34	1.909682	0.33721	.	.	ENSG00000162702	ENST00000294740;ENST00000367353;ENST00000367352;ENST00000537759	T;T;T	0.08720	3.07;3.07;3.06	5.6	2.88	0.33553	.	0.000000	0.64402	D	0.000001	T	0.14657	0.0354	L	0.29908	0.895	0.48830	D	0.999717	D;D	0.76494	0.999;0.999	D;D	0.76071	0.987;0.987	T	0.03121	-1.1070	10	0.36615	T	0.2	5.2259	9.4078	0.38473	0.7748:0.0:0.2252:0.0	.	723;759	A6NF48;Q9Y2X9	.;ZN281_HUMAN	V	759;759;723;464	ENSP00000294740:L759V;ENSP00000356322:L759V;ENSP00000356321:L723V	ENSP00000294740:L759V	L	-	1	2	ZNF281	198643182	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	1.925000	0.40074	0.913000	0.36797	0.533000	0.62120	TTG	.		0.453	ZNF281-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000086879.2	NM_012482	
STAG2	10735	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	X	123200253	123200253	+	Missense_Mutation	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chrX:123200253A>C	ENST00000371160.1	+	23	2522	c.2232A>C	c.(2230-2232)caA>caC	p.Q744H	STAG2_ENST00000371145.3_Missense_Mutation_p.Q744H|STAG2_ENST00000354548.5_Missense_Mutation_p.Q675H|STAG2_ENST00000469481.1_Intron|STAG2_ENST00000218089.9_Missense_Mutation_p.Q744H|STAG2_ENST00000371157.3_Missense_Mutation_p.Q744H|STAG2_ENST00000371144.3_Missense_Mutation_p.Q744H	NM_001282418.1	NP_001269347.1	Q8N3U4	STAG2_HUMAN	stromal antigen 2	744					meiotic nuclear division (GO:0007126)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of DNA endoreduplication (GO:0032876)|sister chromatid cohesion (GO:0007062)|stem cell maintenance (GO:0019827)	actin cytoskeleton (GO:0015629)|chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	chromatin binding (GO:0003682)			breast(5)|central_nervous_system(4)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(9)|lung(21)|ovary(5)|prostate(2)|skin(5)|urinary_tract(4)	78						TCCTTTGGCAACTTGCTAAGA	0.343																																					p.Q744H		.											.	.	.	0			c.A2232C						.						99.0	81.0	87.0					X																	123200253		2203	4300	6503	SO:0001583	missense	10735	exon23			TTGGCAACTTGCT	Z75331	CCDS14607.1, CCDS43990.1	Xq25	2014-09-17			ENSG00000101972	ENSG00000101972			11355	protein-coding gene	gene with protein product		300826				9305759	Standard	NM_001042750		Approved	SA-2, SCC3B	uc004eua.3	Q8N3U4	OTTHUMG00000022725	ENST00000371160.1:c.2232A>C	X.37:g.123200253A>C	ENSP00000360202:p.Gln744His	Somatic	77	0		WXS	Illumina HiSeq	.	32	30	NM_001042749	B1AMT5|D3DTF5|O00540|Q5JTI6|Q68DE9|Q9H1N8	Missense_Mutation	SNP	ENST00000371160.1	37	CCDS14607.1	.	.	.	.	.	.	.	.	.	.	A	11.55	1.671992	0.29693	.	.	ENSG00000101972	ENST00000218089;ENST00000354548;ENST00000371160;ENST00000371157;ENST00000371145;ENST00000371144	T;T;T;T;T;T	0.32753	1.44;1.44;1.44;1.44;1.44;1.44	5.32	2.46	0.29980	Armadillo-type fold (1);	0.231129	0.44688	D	0.000426	T	0.20901	0.0503	L	0.31207	0.915	0.34869	D	0.743403	B;B	0.12013	0.005;0.001	B;B	0.17979	0.02;0.002	T	0.12243	-1.0555	10	0.41790	T	0.15	-5.9633	8.8581	0.35240	0.2633:0.0:0.7367:0.0	.	744;744	Q8N3U4-2;Q8N3U4	.;STAG2_HUMAN	H	744;675;744;744;744;744	ENSP00000218089:Q744H;ENSP00000346555:Q675H;ENSP00000360202:Q744H;ENSP00000360199:Q744H;ENSP00000360187:Q744H;ENSP00000360186:Q744H	ENSP00000218089:Q744H	Q	+	3	2	STAG2	123027934	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.075000	0.30716	0.144000	0.18951	0.486000	0.48141	CAA	.		0.343	STAG2-018	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000156159.2	NM_006603	
ZNF345	25850	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	19	37368144	37368144	+	Silent	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr19:37368144A>C	ENST00000529555.1	+	2	1200	c.412A>C	c.(412-414)Aga>Cga	p.R138R	ZNF345_ENST00000432005.2_Intron|ZNF345_ENST00000589046.1_Silent_p.R138R|ZNF345_ENST00000526123.1_Intron|ZNF345_ENST00000420450.1_Silent_p.R138R			Q14585	ZN345_HUMAN	zinc finger protein 345	138					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)|transcription from RNA polymerase III promoter (GO:0006383)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(1)|kidney(1)|large_intestine(13)|lung(5)|ovary(2)|prostate(1)	24	Esophageal squamous(110;0.183)		COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			TCACCATCAGAGAATTCATAC	0.423																																					p.R138R		.											.	.	.	0			c.A412C						.						65.0	66.0	66.0					19																	37368144		2203	4300	6503	SO:0001819	synonymous_variant	25850	exon4			CATCAGAGAATTC	X78933	CCDS12497.1	19q13.12	2013-01-08			ENSG00000251247	ENSG00000251247		"""Zinc fingers, C2H2-type"""	16367	protein-coding gene	gene with protein product						7865130	Standard	NM_003419		Approved	HZF10	uc002oey.4	Q14585	OTTHUMG00000048162	ENST00000529555.1:c.412A>C	19.37:g.37368144A>C		Somatic	74	0		WXS	Illumina HiSeq	.	35	12	NM_001242476		Silent	SNP	ENST00000529555.1	37	CCDS12497.1																																																																																			.		0.423	ZNF345-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388258.1		
OGT	8473	hgsc.bcm.edu	37	X	70787308	70787308	+	Intron	SNP	C	C	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chrX:70787308C>A	ENST00000373719.3	+	20	2806				OGT_ENST00000373701.3_Intron	NM_181672.2|NM_181673.2	NP_858058.1|NP_858059.1	O15294	OGT1_HUMAN	O-linked N-acetylglucosamine (GlcNAc) transferase						apoptotic process (GO:0006915)|cellular response to retinoic acid (GO:0071300)|chromatin organization (GO:0006325)|circadian regulation of gene expression (GO:0032922)|histone H3-K4 trimethylation (GO:0080182)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)|negative regulation of protein ubiquitination (GO:0031397)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of catalytic activity (GO:0043085)|positive regulation of granulocyte differentiation (GO:0030854)|positive regulation of histone H3-K27 methylation (GO:0061087)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of proteolysis (GO:0045862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein O-linked glycosylation (GO:0006493)|regulation of gluconeogenesis involved in cellular glucose homeostasis (GO:0090526)|regulation of glycolytic process (GO:0006110)|regulation of insulin receptor signaling pathway (GO:0046626)|regulation of Rac protein signal transduction (GO:0035020)|response to insulin (GO:0032868)|response to nutrient (GO:0007584)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|histone acetyltransferase complex (GO:0000123)|microtubule organizing center (GO:0005815)|mitochondrion (GO:0005739)|MLL5-L complex (GO:0070688)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	acetylglucosaminyltransferase activity (GO:0008375)|enzyme activator activity (GO:0008047)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|protein N-acetylglucosaminyltransferase activity (GO:0016262)|protein O-GlcNAc transferase activity (GO:0097363)			breast(6)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(5)|liver(3)|lung(9)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	Renal(35;0.156)					TTGAAAAAGGCAGATCTGCTA	0.393																																					.		.											.	.	.	0			.						.						30.0	30.0	30.0					X																	70787308		2203	4300	6503	SO:0001627	intron_variant	618	.			AAAAGGCAGATCT	U77413	CCDS14414.1, CCDS35502.1	Xq13	2013-07-24	2012-05-04		ENSG00000147162	ENSG00000147162	2.4.1.255	"""Tetratricopeptide (TTC) repeat domain containing"""	8127	protein-coding gene	gene with protein product	"""UDP-N-acetylglucosamine:polypeptide-N-acetylglucosaminyl transferase"""	300255	"""O-linked N-acetylglucosamine (GlcNAc) transferase (UDP-N-acetylglucosamine:polypeptide-N-acetylglucosaminyl transferase)"""			9083068	Standard	NM_181672		Approved	O-GLCNAC, HRNT1, MGC22921, FLJ23071	uc004eaa.2	O15294	OTTHUMG00000033316	ENST00000373719.3:c.2590-42C>A	X.37:g.70787308C>A		Somatic	84	0		WXS	Illumina HiSeq	.	49	38	.	Q7Z3K0|Q8WWM8|Q96CC1|Q9UG57	RNA	SNP	ENST00000373719.3	37	CCDS14414.1																																																																																			.		0.393	OGT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000081829.3	NM_003605, NM_181672	
SRP54	6729	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	14	35468824	35468824	+	Missense_Mutation	SNP	A	A	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr14:35468824A>G	ENST00000556994.1	+	4	536	c.139A>G	c.(139-141)Aaa>Gaa	p.K47E	SRP54_ENST00000555557.1_Intron|SRP54_ENST00000546080.1_Intron|SRP54_ENST00000555535.1_3'UTR|SRP54_ENST00000216774.6_Missense_Mutation_p.K47E			P61011	SRP54_HUMAN	signal recognition particle 54kDa	47	G-domain.				cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|GTP catabolic process (GO:0006184)|protein targeting to ER (GO:0045047)|response to drug (GO:0042493)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|SRP-dependent cotranslational protein targeting to membrane, signal sequence recognition (GO:0006617)|SRP-dependent cotranslational protein targeting to membrane, translocation (GO:0006616)|translation (GO:0006412)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleolus (GO:0005730)|nucleus (GO:0005634)|signal recognition particle, endoplasmic reticulum targeting (GO:0005786)	7S RNA binding (GO:0008312)|drug binding (GO:0008144)|endoplasmic reticulum signal peptide binding (GO:0030942)|GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)|ribonucleoprotein complex binding (GO:0043021)			NS(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	14	Breast(36;0.0545)|Hepatocellular(127;0.158)		LUAD - Lung adenocarcinoma(48;2.48e-05)|Lung(238;3.13e-05)|Epithelial(34;0.0314)|all cancers(34;0.0797)|BRCA - Breast invasive adenocarcinoma(188;0.243)	GBM - Glioblastoma multiforme(112;0.0396)		TGTTAATATTAAACTAGTGAA	0.323																																					p.K47E		.											.	.	.	0			c.A139G						.						106.0	111.0	110.0					14																	35468824		2203	4300	6503	SO:0001583	missense	6729	exon3			AATATTAAACTAG	X86373	CCDS9652.1, CCDS53893.1	14q13.2	2014-06-02	2002-08-29		ENSG00000100883	ENSG00000100883			11301	protein-coding gene	gene with protein product		604857	"""signal recognition particle 54kD"""			8722571	Standard	NM_003136		Approved		uc001wso.3	P61011	OTTHUMG00000140214	ENST00000556994.1:c.139A>G	14.37:g.35468824A>G	ENSP00000451818:p.Lys47Glu	Somatic	57	0		WXS	Illumina HiSeq	.	37	20	NM_003136	B2R759|B4DUW6|P13624	Missense_Mutation	SNP	ENST00000556994.1	37	CCDS9652.1	.	.	.	.	.	.	.	.	.	.	A	18.72	3.683535	0.68157	.	.	ENSG00000100883	ENST00000556994;ENST00000555746;ENST00000216774	.	.	.	5.64	5.64	0.86602	Signal recognition particle, SRP54 subunit, helical bundle (4);	0.000000	0.85682	D	0.000000	T	0.65281	0.2676	M	0.67397	2.05	0.80722	D	1	B	0.27700	0.186	B	0.33339	0.162	T	0.66416	-0.5929	9	0.66056	D	0.02	-20.663	15.862	0.79032	1.0:0.0:0.0:0.0	.	47	P61011	SRP54_HUMAN	E	47	.	ENSP00000216774:K47E	K	+	1	0	SRP54	34538575	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.133000	0.94460	2.145000	0.66743	0.460000	0.39030	AAA	.		0.323	SRP54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276643.2	NM_003136	
KIF1B	23095	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	1	10327609	10327609	+	Missense_Mutation	SNP	A	A	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr1:10327609A>G	ENST00000377086.1	+	6	803	c.601A>G	c.(601-603)Aaa>Gaa	p.K201E	KIF1B_ENST00000377081.1_Missense_Mutation_p.K201E|KIF1B_ENST00000377083.1_Missense_Mutation_p.K201E|KIF1B_ENST00000377093.4_Missense_Mutation_p.K201E|KIF1B_ENST00000263934.6_Missense_Mutation_p.K201E			O60333	KIF1B_HUMAN	kinesin family member 1B	201	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				anterograde axon cargo transport (GO:0008089)|apoptotic process (GO:0006915)|cytoskeleton-dependent intracellular transport (GO:0030705)|microtubule-based movement (GO:0007018)|mitochondrion transport along microtubule (GO:0047497)|neuromuscular synaptic transmission (GO:0007274)|neuron-neuron synaptic transmission (GO:0007270)|vesicle-mediated transport (GO:0016192)	cytoplasmic vesicle (GO:0031410)|cytoplasmic vesicle membrane (GO:0030659)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|kinesin binding (GO:0019894)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)			breast(2)|endometrium(7)|kidney(8)|large_intestine(9)|lung(29)|ovary(3)|prostate(3)|skin(5)|stomach(3)|upper_aerodigestive_tract(2)	71	Ovarian(185;0.203)	all_lung(284;1.31e-05)|Lung NSC(185;2.2e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0259)|Colorectal(212;9.79e-07)|COAD - Colon adenocarcinoma(227;0.000143)|BRCA - Breast invasive adenocarcinoma(304;0.000413)|Kidney(185;0.00134)|KIRC - Kidney renal clear cell carcinoma(229;0.0037)|STAD - Stomach adenocarcinoma(132;0.0113)|READ - Rectum adenocarcinoma(331;0.0642)		TGCTGGGAACAAAGCCAGGTA	0.463																																					p.K201E		.											.	.	.	0			c.A601G						.						90.0	71.0	78.0					1																	10327609		2203	4300	6503	SO:0001583	missense	23095	exon6			GGGAACAAAGCCA	AF257176	CCDS111.1, CCDS112.1	1p36.22	2014-09-17			ENSG00000054523	ENSG00000054523		"""Kinesins"", ""Pleckstrin homology (PH) domain containing"""	16636	protein-coding gene	gene with protein product		605995		CMT2A, CMT2		11389829, 10762626	Standard	NM_015074		Approved	KIAA0591, KLP, HMSNII	uc001aqw.4	O60333	OTTHUMG00000001817	ENST00000377086.1:c.601A>G	1.37:g.10327609A>G	ENSP00000366290:p.Lys201Glu	Somatic	63	0		WXS	Illumina HiSeq	.	19	12	NM_183416	A6NFS8|A6NKQ4|Q4VXC3|Q4VXC4|Q4VXC5|Q4VXC6|Q96Q94|Q9BV80|Q9P280	Missense_Mutation	SNP	ENST00000377086.1	37		.	.	.	.	.	.	.	.	.	.	A	28.2	4.903607	0.92035	.	.	ENSG00000054523	ENST00000355249;ENST00000263934;ENST00000377093;ENST00000377086;ENST00000377083;ENST00000377081	T;T;T;T;T	0.76060	-0.99;-0.99;-0.99;-0.99;-0.99	5.2	5.2	0.72013	Kinesin, motor domain (4);	0.105145	0.64402	D	0.000004	D	0.85647	0.5745	M	0.75777	2.31	0.80722	D	1	D;D;D;D;P;P;P	0.76494	0.999;0.999;0.997;0.998;0.553;0.939;0.92	D;D;D;D;B;P;P	0.91635	0.998;0.999;0.978;0.998;0.405;0.751;0.866	D	0.87587	0.2488	10	0.87932	D	0	.	15.3528	0.74402	1.0:0.0:0.0:0.0	.	201;201;201;201;201;201;201	Q4R9M9;Q4R9M7;Q4VXC4;Q4R9M8;O60333;O60333-2;O60333-3	.;.;.;.;KIF1B_HUMAN;.;.	E	201	ENSP00000263934:K201E;ENSP00000366297:K201E;ENSP00000366290:K201E;ENSP00000366287:K201E;ENSP00000366284:K201E	ENSP00000263934:K201E	K	+	1	0	KIF1B	10250196	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.287000	0.95975	2.098000	0.63641	0.477000	0.44152	AAA	.		0.463	KIF1B-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000005102.1		
SDCCAG8	10806	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	243663078	243663078	+	Silent	SNP	T	T	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr1:243663078T>A	ENST00000366541.3	+	18	2251	c.2133T>A	c.(2131-2133)tcT>tcA	p.S711S	AKT3_ENST00000366540.1_Silent_p.S455S|SDCCAG8_ENST00000343783.6_Silent_p.S566S|SDCCAG8_ENST00000355875.4_Silent_p.S668S|AKT3_ENST00000336199.5_Silent_p.S455S	NM_006642.3	NP_006633.1	Q86SQ7	SDCG8_HUMAN	serologically defined colon cancer antigen 8	711	Mediates interaction with OFD1.|Sufficient for homodimerization. {ECO:0000250}.				establishment of cell polarity (GO:0030010)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|tube formation (GO:0035148)	cell-cell junction (GO:0005911)|centriole (GO:0005814)|centrosome (GO:0005813)|cytosol (GO:0005829)				breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(17)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29	all_cancers(71;0.000545)|all_epithelial(71;0.000509)|all_lung(81;0.0821)|Ovarian(71;0.0919)|all_neural(11;0.101)|Breast(184;0.218)	all_cancers(173;0.00395)	all cancers(7;1.58e-07)|GBM - Glioblastoma multiforme(7;5.12e-06)|OV - Ovarian serous cystadenocarcinoma(106;0.00392)	COAD - Colon adenocarcinoma(196;0.145)		TGCCACAATCTGATTGCTGAC	0.353																																					p.S711S		.											.	.	.	0			c.T2133A						.						60.0	62.0	61.0					1																	243663078		2203	4300	6503	SO:0001819	synonymous_variant	10806	exon18			ACAATCTGATTGC	AF039690	CCDS31075.1	1q43	2011-08-02			ENSG00000054282	ENSG00000054282			10671	protein-coding gene	gene with protein product		613524				9610721, 20835237	Standard	NM_006642		Approved	NY-CO-8, CCCAP, SLSN7, NPHP10, BBS16	uc001hzw.3	Q86SQ7	OTTHUMG00000039996	ENST00000366541.3:c.2133T>A	1.37:g.243663078T>A		Somatic	56	0		WXS	Illumina HiSeq	.	64	28	NM_006642	O60527|Q3ZCR6|Q8N5F2|Q9P0F1	Silent	SNP	ENST00000366541.3	37	CCDS31075.1																																																																																			.		0.353	SDCCAG8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096485.1	NM_006642	
ZNF695	57116	hgsc.bcm.edu	37	1	247130468	247130468	+	Intron	SNP	G	G	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr1:247130468G>A	ENST00000487338.2	-	5	673				ZNF695_ENST00000498046.2_Intron	NM_001204221.1	NP_001191150	Q8IW36	ZN695_HUMAN	zinc finger protein 695						regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			endometrium(1)|large_intestine(1)|lung(9)|prostate(1)|urinary_tract(1)	13	all_cancers(71;4.01e-05)|all_epithelial(71;6.72e-06)|Ovarian(71;0.0173)|Breast(184;0.0318)|all_lung(81;0.0458)|Lung NSC(105;0.0518)	all_cancers(173;0.0266)	OV - Ovarian serous cystadenocarcinoma(106;0.00271)			tcgaactcccgacctcaggtg	0.512																																					.		.											.	.	.	0			.						.																																			SO:0001627	intron_variant	0	.			ACTCCCGACCTCA		CCDS44344.1, CCDS55694.1	1q44	2013-01-08			ENSG00000197472	ENSG00000197472		"""Zinc fingers, C2H2-type"", ""-"""	30954	protein-coding gene	gene with protein product						12477932	Standard	NM_020394		Approved	SBZF3	uc009xgu.3	Q8IW36	OTTHUMG00000040707	ENST00000487338.2:c.488+528C>T	1.37:g.247130468G>A		Somatic	14	0		WXS	Illumina HiSeq	.	14	12	.	Q5T0N9|Q5T0P1|Q5T0P3|Q7Z2W8|Q7Z648	RNA	SNP	ENST00000487338.2	37	CCDS55694.1																																																																																			.		0.512	ZNF695-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000098003.4	NM_020394	
BSCL2	26580	hgsc.bcm.edu	37	11	62460156	62460156	+	Silent	SNP	G	G	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr11:62460156G>A	ENST00000403550.1	-	5	975	c.552C>T	c.(550-552)taC>taT	p.Y184Y	BSCL2_ENST00000360796.5_Silent_p.Y248Y|BSCL2_ENST00000433053.1_Silent_p.Y248Y|BSCL2_ENST00000407022.3_Silent_p.Y184Y|BSCL2_ENST00000405837.1_Silent_p.Y248Y|BSCL2_ENST00000278893.7_Silent_p.Y184Y|BSCL2_ENST00000421906.1_Silent_p.Y184Y|BSCL2_ENST00000537604.1_5'Flank|LRRN4CL_ENST00000317449.4_5'Flank|HNRNPUL2-BSCL2_ENST00000403734.2_3'UTR			Q96G97	BSCL2_HUMAN	Berardinelli-Seip congenital lipodystrophy 2 (seipin)	184					cell death (GO:0008219)|fat cell differentiation (GO:0045444)|lipid catabolic process (GO:0016042)|lipid particle organization (GO:0034389)|lipid storage (GO:0019915)|negative regulation of lipid catabolic process (GO:0050995)	integral component of endoplasmic reticulum membrane (GO:0030176)		p.Y184*(1)		endometrium(2)|kidney(2)|large_intestine(2)|lung(4)|prostate(1)|skin(1)	12						TATAGTCTGCGTAGAGTTCCA	0.537																																					p.Y248Y		.											BSCL2,NS,carcinoma,0,1	BSCL2	0	1	Substitution - Nonsense(1)	endometrium(1)	c.C744T						.						110.0	97.0	101.0					11																	62460156		2202	4299	6501	SO:0001819	synonymous_variant	26580	exon5			GTCTGCGTAGAGT		CCDS8031.1, CCDS44627.1, CCDS55769.1	11q13	2014-09-17	2009-07-30		ENSG00000168000	ENSG00000168000			15832	protein-coding gene	gene with protein product		606158	"""spastic paraplegia 17 (Silver syndrome)"""	GNG3LG, SPG17		11479539, 14981520	Standard	NM_001122955		Approved		uc001nur.4	Q96G97	OTTHUMG00000150624	ENST00000403550.1:c.552C>T	11.37:g.62460156G>A		Somatic	36	0		WXS	Illumina HiSeq	.	20	2	NM_001122955	G3XAE4|Q567S1|Q96SV1|Q9BSQ0	Silent	SNP	ENST00000403550.1	37	CCDS8031.1																																																																																			.		0.537	BSCL2-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000319185.1	NM_032667	
PAFAH1B2	5049	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	11	117030734	117030734	+	Missense_Mutation	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr11:117030734T>G	ENST00000527958.1	+	3	325	c.166T>G	c.(166-168)Tat>Gat	p.Y56D	PAFAH1B2_ENST00000526888.1_Intron|PAFAH1B2_ENST00000419197.2_Missense_Mutation_p.Y56D|PAFAH1B2_ENST00000530272.1_Missense_Mutation_p.Y56D|PAFAH1B2_ENST00000529887.2_Missense_Mutation_p.Y56D	NM_002572.3	NP_002563.1	P68402	PA1B2_HUMAN	platelet-activating factor acetylhydrolase 1b, catalytic subunit 2 (30kDa)	56					brain development (GO:0007420)|lipid catabolic process (GO:0016042)|lipid metabolic process (GO:0006629)|positive regulation of macroautophagy (GO:0016239)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	1-alkyl-2-acetylglycerophosphocholine esterase activity (GO:0003847)			kidney(1)	1	all_hematologic(175;0.0487)	Medulloblastoma(222;0.0523)|Breast(348;0.056)|all_hematologic(192;0.232)		BRCA - Breast invasive adenocarcinoma(274;1.68e-05)|Epithelial(105;0.000162)|all cancers(92;0.00111)		AATGCAGCAATATGAGGTAAA	0.408			T	IGH@	MLCLS																																p.Y56D		.		Dom	yes		11	11q23	5049	"""platelet-activating factor acetylhydrolase, isoform Ib, beta subunit 30kDa"""		L	.	.	.	0			c.T166G						.						247.0	227.0	234.0					11																	117030734		2201	4296	6497	SO:0001583	missense	5049	exon3			CAGCAATATGAGG	D63390	CCDS8380.1, CCDS53713.1, CCDS53714.1, CCDS53715.1	11q23	2011-10-24	2010-02-10			ENSG00000168092			8575	protein-coding gene	gene with protein product	"""PAF-AH1b alpha 2 subunit"""	602508	"""platelet-activating factor acetylhydrolase, isoform Ib, beta subunit 30kDa"", ""platelet-activating factor acetylhydrolase, isoform Ib, subunit 2 (30kDa)"""			9144386, 9693049	Standard	NM_002572		Approved		uc001pqe.2	P68402		ENST00000527958.1:c.166T>G	11.37:g.117030734T>G	ENSP00000435289:p.Tyr56Asp	Somatic	69	0		WXS	Illumina HiSeq	.	46	15	NM_001184747	A8DPS5|A8DPS6|A8DPS7|E9PEJ5|E9PLP3|O00687|Q29459|Q6IBR6	Missense_Mutation	SNP	ENST00000527958.1	37	CCDS8380.1	.	.	.	.	.	.	.	.	.	.	T	18.68	3.675024	0.67928	.	.	ENSG00000168092	ENST00000527958;ENST00000419197;ENST00000529887;ENST00000530272	T;T;T	0.42131	0.98;0.99;0.99	5.72	4.53	0.55603	Esterase, SGNH hydrolase-type (1);Esterase, SGNH hydrolase-type, subgroup (1);Lipase, GDSL (1);	0.170349	0.53938	D	0.000057	T	0.43787	0.1263	N	0.20986	0.625	0.54753	D	0.999982	D;P;P	0.69078	0.997;0.591;0.951	P;P;P	0.60886	0.88;0.46;0.708	T	0.25916	-1.0118	10	0.34782	T	0.22	-2.1089	11.7457	0.51819	0.1319:0.0:0.0:0.8681	.	56;56;56	E9PLP3;A8DPS6;P68402	.;.;PA1B2_HUMAN	D	56	ENSP00000435289:Y56D;ENSP00000388742:Y56D;ENSP00000431365:Y56D	ENSP00000388742:Y56D	Y	+	1	0	PAFAH1B2	116535944	0.957000	0.32711	0.994000	0.49952	0.965000	0.64279	3.898000	0.56281	2.184000	0.69523	0.455000	0.32223	TAT	.		0.408	PAFAH1B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392826.1	NM_002572	
LOXL2	4017	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	8	23198669	23198669	+	Silent	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr8:23198669T>G	ENST00000389131.3	-	4	948	c.579A>C	c.(577-579)tcA>tcC	p.S193S	RP11-177H13.2_ENST00000519692.1_RNA	NM_002318.2	NP_002309.1	Q9Y4K0	LOXL2_HUMAN	lysyl oxidase-like 2	193	SRCR 2. {ECO:0000255|PROSITE- ProRule:PRU00196}.				aging (GO:0007568)|cell adhesion (GO:0007155)|cellular protein modification process (GO:0006464)|collagen fibril organization (GO:0030199)|endothelial cell migration (GO:0043542)|endothelial cell proliferation (GO:0001935)|epithelial to mesenchymal transition (GO:0001837)|histone modification (GO:0016570)|negative regulation of transcription, DNA-templated (GO:0045892)|oxidation-reduction process (GO:0055114)|positive regulation of chondrocyte differentiation (GO:0032332)|protein deamination (GO:0018277)|response to copper ion (GO:0046688)|response to hypoxia (GO:0001666)|sprouting angiogenesis (GO:0002040)|transcription, DNA-templated (GO:0006351)	basement membrane (GO:0005604)|chromosome (GO:0005694)|extracellular space (GO:0005615)|membrane (GO:0016020)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|electron carrier activity (GO:0009055)|methylated histone binding (GO:0035064)|oligosaccharide binding (GO:0070492)|protein-lysine 6-oxidase activity (GO:0004720)|scavenger receptor activity (GO:0005044)|transcription corepressor activity (GO:0003714)			breast(2)|endometrium(4)|kidney(3)|large_intestine(12)|lung(5)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	35		Prostate(55;0.0453)|Breast(100;0.143)		Colorectal(74;0.0288)|COAD - Colon adenocarcinoma(73;0.096)		TGCGGTAGGTTGAGAGGATGG	0.567																																					p.S193S		.											.	.	.	0			c.A579C						.						147.0	118.0	127.0					8																	23198669		2203	4300	6503	SO:0001819	synonymous_variant	4017	exon4			GTAGGTTGAGAGG	U89942	CCDS34864.1	8p21.3	2008-05-15				ENSG00000134013			6666	protein-coding gene	gene with protein product		606663				9722957	Standard	NM_002318		Approved	WS9-14	uc003xdh.1	Q9Y4K0		ENST00000389131.3:c.579A>C	8.37:g.23198669T>G		Somatic	41	0		WXS	Illumina HiSeq	.	41	16	NM_002318	B2R5Q0|Q53HV3|Q9BW70|Q9Y5Y8	Silent	SNP	ENST00000389131.3	37	CCDS34864.1																																																																																			.		0.567	LOXL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375603.1		
UPK3A	7380	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	22	45681856	45681856	+	Silent	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr22:45681856T>G	ENST00000216211.4	+	2	119	c.87T>G	c.(85-87)acT>acG	p.T29T	UPK3A_ENST00000396082.2_Silent_p.T29T	NM_006953.3	NP_008884.1	O75631	UPK3A_HUMAN	uroplakin 3A	29					cell morphogenesis (GO:0000902)|epithelial cell differentiation (GO:0030855)|kidney development (GO:0001822)|potassium ion homeostasis (GO:0055075)|sodium ion homeostasis (GO:0055078)|urea transport (GO:0015840)|urinary bladder development (GO:0060157)|water transport (GO:0006833)	apical plasma membrane (GO:0016324)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				kidney(1)|large_intestine(1)|lung(2)|skin(1)	5		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0178)		CCAGTGTGACTTTCGCCACCA	0.582																																					p.T29T		.											.	.	.	0			c.T87G						.						127.0	93.0	105.0					22																	45681856		2203	4300	6503	SO:0001819	synonymous_variant	7380	exon2			TGTGACTTTCGCC	AB010637	CCDS14064.1, CCDS54539.1	22q13.31	2005-11-14	2003-07-29	2003-07-30	ENSG00000100373	ENSG00000100373			12580	protein-coding gene	gene with protein product		611559	"""uroplakin 3"""	UPK3		9818021	Standard	NM_006953		Approved		uc003bfy.3	O75631	OTTHUMG00000151339	ENST00000216211.4:c.87T>G	22.37:g.45681856T>G		Somatic	37	0		WXS	Illumina HiSeq	.	21	5	NM_006953	B0QY25|O60261|Q32N05|Q5TII6	Silent	SNP	ENST00000216211.4	37	CCDS14064.1																																																																																			.		0.582	UPK3A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000322276.1	NM_006953	
ACLY	47	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	17	40049390	40049390	+	Silent	SNP	G	G	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr17:40049390G>A	ENST00000352035.2	-	15	1627	c.1497C>T	c.(1495-1497)gcC>gcT	p.A499A	ACLY_ENST00000590151.1_Silent_p.A499A|ACLY_ENST00000393896.2_Silent_p.A489A|ACLY_ENST00000353196.1_Silent_p.A489A|ACLY_ENST00000537919.1_Silent_p.A228A	NM_001096.2	NP_001087.2	P53396	ACLY_HUMAN	ATP citrate lyase	499					ATP catabolic process (GO:0006200)|cellular carbohydrate metabolic process (GO:0044262)|cellular lipid metabolic process (GO:0044255)|citrate metabolic process (GO:0006101)|coenzyme A metabolic process (GO:0015936)|energy reserve metabolic process (GO:0006112)|lipid biosynthetic process (GO:0008610)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|positive regulation of cellular metabolic process (GO:0031325)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	citrate lyase complex (GO:0009346)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATP citrate synthase activity (GO:0003878)|cofactor binding (GO:0048037)|metal ion binding (GO:0046872)|succinate-CoA ligase (ADP-forming) activity (GO:0004775)		NTN1/ACLY(2)	breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(5)|lung(4)|ovary(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	28		Breast(137;0.000143)				CCCACACAATGGCCTTGGTGT	0.612																																					p.A499A	Colon(64;807 1396 15971 30971)	.											.	.	.	0			c.C1497T						.						96.0	93.0	94.0					17																	40049390		2203	4300	6503	SO:0001819	synonymous_variant	47	exon15			CACAATGGCCTTG	X64330	CCDS11412.1, CCDS11413.1	17q21.2	2010-04-27			ENSG00000131473	ENSG00000131473	2.3.3.8		115	protein-coding gene	gene with protein product	"""ATP citrate synthase"""	108728				1371749, 8088842	Standard	NM_001096		Approved	ATPCL, CLATP, ACL	uc002hyg.3	P53396	OTTHUMG00000133507	ENST00000352035.2:c.1497C>T	17.37:g.40049390G>A		Somatic	39	0		WXS	Illumina HiSeq	.	27	15	NM_001096	B4DIM0|B4E3P0|Q13037|Q9BRL0	Silent	SNP	ENST00000352035.2	37	CCDS11412.1																																																																																			.		0.612	ACLY-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257465.1	NM_001096	
ITGB4	3691	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	17	73738739	73738739	+	Missense_Mutation	SNP	G	G	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr17:73738739G>C	ENST00000200181.3	+	25	3046	c.2859G>C	c.(2857-2859)gaG>gaC	p.E953D	ITGB4_ENST00000579662.1_Missense_Mutation_p.E953D|ITGB4_ENST00000449880.2_Missense_Mutation_p.E953D|ITGB4_ENST00000339591.3_Missense_Mutation_p.E953D|ITGB4_ENST00000450894.3_Missense_Mutation_p.E953D	NM_000213.3	NP_000204.3	P16144	ITB4_HUMAN	integrin, beta 4	953					amelogenesis (GO:0097186)|autophagy (GO:0006914)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell motility (GO:0048870)|cell-matrix adhesion (GO:0007160)|digestive tract development (GO:0048565)|extracellular matrix organization (GO:0030198)|filopodium assembly (GO:0046847)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|mesodermal cell differentiation (GO:0048333)|nail development (GO:0035878)|renal system development (GO:0072001)|response to wounding (GO:0009611)|skin development (GO:0043588)	basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|hemidesmosome (GO:0030056)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor binding (GO:0001664)|receptor activity (GO:0004872)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|liver(1)|lung(25)|skin(1)|urinary_tract(1)	43	all_cancers(13;1.5e-07)		all cancers(21;8.32e-07)|Epithelial(20;1.92e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00194)|Lung(188;0.132)|LUSC - Lung squamous cell carcinoma(166;0.154)			TCCGGCCTGAGGATGACGACG	0.662																																					p.E953D		.											.	.	.	0			c.G2859C						.						83.0	65.0	71.0					17																	73738739		2203	4300	6503	SO:0001583	missense	3691	exon25			GCCTGAGGATGAC		CCDS11727.1, CCDS32736.1, CCDS58599.1	17q25.1	2013-09-19			ENSG00000132470	ENSG00000132470		"""CD molecules"", ""Integrins"", ""Fibronectin type III domain containing"""	6158	protein-coding gene	gene with protein product		147557				2070796	Standard	XM_005257309		Approved	CD104	uc002jpg.3	P16144	OTTHUMG00000179814	ENST00000200181.3:c.2859G>C	17.37:g.73738739G>C	ENSP00000200181:p.Glu953Asp	Somatic	49	0		WXS	Illumina HiSeq	.	28	14	NM_001005731	A0AVL6|O14690|O14691|O15339|O15340|O15341|Q0VF97|Q9UIQ4	Missense_Mutation	SNP	ENST00000200181.3	37	CCDS11727.1	.	.	.	.	.	.	.	.	.	.	G	12.80	2.047580	0.36085	.	.	ENSG00000132470	ENST00000200181;ENST00000339591;ENST00000449880	T;T;T	0.75704	-0.96;-0.92;-0.92	5.52	0.983	0.19767	.	0.194847	0.43747	D	0.000526	T	0.47507	0.1449	N	0.12746	0.255	0.46279	D	0.998961	B;B;B	0.26120	0.142;0.049;0.088	B;B;B	0.24541	0.054;0.024;0.024	T	0.20739	-1.0266	10	0.32370	T	0.25	.	2.3637	0.04314	0.2339:0.105:0.4959:0.1652	.	953;953;953	P16144-3;A0AVL6;P16144	.;.;ITB4_HUMAN	D	953	ENSP00000200181:E953D;ENSP00000344079:E953D;ENSP00000400217:E953D	ENSP00000200181:E953D	E	+	3	2	ITGB4	71250334	0.994000	0.37717	0.989000	0.46669	0.762000	0.43233	0.194000	0.17135	0.723000	0.32274	0.655000	0.94253	GAG	.		0.662	ITGB4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000448334.1		
NPLOC4	55666	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	17	79563165	79563165	+	Missense_Mutation	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr17:79563165T>G	ENST00000331134.6	-	11	1312	c.1097A>C	c.(1096-1098)aAg>aCg	p.K366T	NPLOC4_ENST00000539314.1_Missense_Mutation_p.K205T|NPLOC4_ENST00000374747.5_Missense_Mutation_p.K366T	NM_017921.2	NP_060391.2	Q8TAT6	NPL4_HUMAN	nuclear protein localization 4 homolog (S. cerevisiae)	366					ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|Golgi organization (GO:0007030)|membrane fusion (GO:0061025)	endoplasmic reticulum (GO:0005783)|nuclear outer membrane-endoplasmic reticulum membrane network (GO:0042175)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)	11	all_neural(118;0.0878)|Melanoma(429;0.242)|all_lung(278;0.246)		BRCA - Breast invasive adenocarcinoma(99;0.0282)|OV - Ovarian serous cystadenocarcinoma(97;0.0739)			AGTAACAAACTTGGATCCAAA	0.418																																					p.K366T		.											.	.	.	0			c.A1097C						.						86.0	85.0	85.0					17																	79563165		1881	4112	5993	SO:0001583	missense	55666	exon11			ACAAACTTGGATC	AB040932	CCDS45812.1	17q25.3	2012-09-20			ENSG00000182446	ENSG00000182446			18261	protein-coding gene	gene with protein product		606590				11574150, 10811609	Standard	NM_017921		Approved	NPL4, FLJ20657, KIAA1499	uc002kas.3	Q8TAT6	OTTHUMG00000177990	ENST00000331134.6:c.1097A>C	17.37:g.79563165T>G	ENSP00000331487:p.Lys366Thr	Somatic	80	0		WXS	Illumina HiSeq	.	40	18	NM_017921	Q8N3J1|Q9H8V2|Q9H964|Q9NWR5|Q9P229	Missense_Mutation	SNP	ENST00000331134.6	37	CCDS45812.1	.	.	.	.	.	.	.	.	.	.	T	29.8	5.037422	0.93630	.	.	ENSG00000182446	ENST00000331134;ENST00000374747;ENST00000539314	.	.	.	5.63	5.63	0.86233	Nuclear pore localisation protein NPL4 (1);	0.000000	0.85682	D	0.000000	T	0.80834	0.4699	M	0.84082	2.675	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.999;1.0	T	0.83328	-0.0014	9	0.59425	D	0.04	-31.009	15.886	0.79247	0.0:0.0:0.0:1.0	.	205;366;366	B4DG89;Q8TAT6-2;Q8TAT6	.;.;NPL4_HUMAN	T	366;365;205	.	ENSP00000331487:K366T	K	-	2	0	NPLOC4	77173603	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.975000	0.88055	2.150000	0.67090	0.529000	0.55759	AAG	.		0.418	NPLOC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440140.1		
ZNF583	147949	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	19	56935139	56935139	+	Missense_Mutation	SNP	A	A	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr19:56935139A>G	ENST00000333201.9	+	5	1322	c.1112A>G	c.(1111-1113)cAg>cGg	p.Q371R	ZNF583_ENST00000291598.7_Missense_Mutation_p.Q371R|ZNF583_ENST00000585612.1_3'UTR	NM_001159861.1|NM_152478.2	NP_001153333.1|NP_689691.2	Q96ND8	ZN583_HUMAN	zinc finger protein 583	371					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(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(5)|ovary(2)|prostate(1)|skin(1)	26		Colorectal(82;0.000256)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0564)		ATTGTACATCAGAGAATTCAT	0.428																																					p.Q371R		.											.	.	.	0			c.A1112G						.						99.0	101.0	101.0					19																	56935139		2203	4300	6503	SO:0001583	missense	147949	exon5			TACATCAGAGAAT	AK055592	CCDS12943.1	19q13.43	2013-09-20			ENSG00000198440	ENSG00000198440		"""Zinc fingers, C2H2-type"", ""-"""	26427	protein-coding gene	gene with protein product							Standard	NM_152478		Approved	FLJ31030	uc010ygl.1	Q96ND8	OTTHUMG00000168874	ENST00000333201.9:c.1112A>G	19.37:g.56935139A>G	ENSP00000388502:p.Gln371Arg	Somatic	67	0		WXS	Illumina HiSeq	.	33	11	NM_001159861	O14850|Q2NKK3	Missense_Mutation	SNP	ENST00000333201.9	37	CCDS12943.1	.	.	.	.	.	.	.	.	.	.	A	16.61	3.172446	0.57584	.	.	ENSG00000198440	ENST00000291598;ENST00000333201	T;T	0.07327	3.2;3.2	4.33	4.33	0.51752	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.42172	D	0.000741	T	0.09024	0.0223	N	0.17901	0.54	0.24492	N	0.994293	P	0.39920	0.695	P	0.49665	0.618	T	0.22800	-1.0206	9	.	.	.	.	8.1728	0.31264	0.9031:0.0:0.0969:0.0	.	371	Q96ND8	ZN583_HUMAN	R	371	ENSP00000291598:Q371R;ENSP00000388502:Q371R	.	Q	+	2	0	ZNF583	61626951	0.000000	0.05858	1.000000	0.80357	0.973000	0.67179	0.842000	0.27627	1.953000	0.56701	0.379000	0.24179	CAG	.		0.428	ZNF583-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401453.1	NM_152478	
Unknown	0	hgsc.bcm.edu;ucsc.edu	37	13	19426389	19426389	+	IGR	SNP	T	T	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr13:19426389T>C								LINC00418 (132520 upstream) : RP11-38M15.11 (7577 downstream)																							AGCATGGATATCACTGTGAAC	0.393																																					.		.											.	.	.	0			.						.																																			SO:0001628	intergenic_variant	284232	.			TGGATATCACTGT																													13.37:g.19426389T>C		Somatic	52	0		WXS	Illumina HiSeq	.	26	10	.		RNA	SNP		37																																																																																				.	0	0.393								
QPRT	23475	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	16	29706151	29706151	+	Missense_Mutation	SNP	C	C	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr16:29706151C>G	ENST00000395384.4	+	2	341	c.180C>G	c.(178-180)ttC>ttG	p.F60L	QPRT_ENST00000219771.7_Intron|QPRT_ENST00000562473.1_Intron	NM_014298.3	NP_055113.2	Q15274	NADC_HUMAN	quinolinate phosphoribosyltransferase	60					NAD biosynthetic process (GO:0009435)|NAD metabolic process (GO:0019674)|protein oligomerization (GO:0051259)|quinolinate catabolic process (GO:0034213)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	nicotinate-nucleotide diphosphorylase (carboxylating) activity (GO:0004514)|protein homodimerization activity (GO:0042803)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)	9					Niacin(DB00627)	AGCCTTTCTTCGATGCCATAT	0.662																																					p.F60L		.											.	.	.	0			c.C180G						.						69.0	71.0	70.0					16																	29706151		2197	4300	6497	SO:0001583	missense	23475	exon2			TTTCTTCGATGCC	D78177	CCDS10651.1	16p11.2	2008-07-31	2008-07-31		ENSG00000103485	ENSG00000103485	2.4.2.19		9755	protein-coding gene	gene with protein product	"""nicotinate-nucleotide pyrophosphorylase (carboxylating)"""	606248				9473669	Standard	NM_014298		Approved	QPRTase	uc002dto.3	Q15274	OTTHUMG00000097770	ENST00000395384.4:c.180C>G	16.37:g.29706151C>G	ENSP00000378782:p.Phe60Leu	Somatic	51	0		WXS	Illumina HiSeq	.	30	13	NM_014298	Q53XW7|Q96G22|Q9BSG6	Missense_Mutation	SNP	ENST00000395384.4	37	CCDS10651.1	.	.	.	.	.	.	.	.	.	.	.	5.892	0.348777	0.11126	.	.	ENSG00000103485	ENST00000449759;ENST00000395384	T	0.29142	1.58	4.75	-8.14	0.01069	Quinolinate phosphoribosyl transferase, N-terminal (2);	0.000000	0.85682	D	0.000000	T	0.21841	0.0526	L	0.46819	1.47	0.58432	D	0.999998	B	0.12013	0.005	B	0.13407	0.009	T	0.23833	-1.0177	10	0.20046	T	0.44	-20.044	17.2825	0.87132	0.0:0.6193:0.0:0.3807	.	60	Q15274	NADC_HUMAN	L	60	ENSP00000378782:F60L	ENSP00000378782:F60L	F	+	3	2	QPRT	29613652	0.014000	0.17966	0.270000	0.24601	0.047000	0.14425	-1.863000	0.01651	-2.722000	0.00388	-2.159000	0.00328	TTC	.		0.662	QPRT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215011.2	NM_014298	
EEF1A1	1915	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	6	74229629	74229629	+	Missense_Mutation	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr6:74229629T>G	ENST00000316292.9	-	1	1112	c.121A>C	c.(121-123)Aaa>Caa	p.K41Q	EEF1A1_ENST00000331523.2_Missense_Mutation_p.K41Q|EEF1A1_ENST00000491404.1_5'Flank|EEF1A1_ENST00000309268.6_Missense_Mutation_p.K41Q	NM_001402.5	NP_001393.1	P68104	EF1A1_HUMAN	eukaryotic translation elongation factor 1 alpha 1	41	tr-type G.				cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|translation (GO:0006412)|translational elongation (GO:0006414)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|eukaryotic translation elongation factor 1 complex (GO:0005853)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|translation elongation factor activity (GO:0003746)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(6)|prostate(2)|skin(3)	18						TTCTCAAATTTTTCAATGGTT	0.413																																					p.K41Q		.											.	.	.	0			c.A121C						.						111.0	114.0	113.0					6																	74229629		2203	4300	6503	SO:0001583	missense	1915	exon2			CAAATTTTTCAAT	BC019669	CCDS4980.1	6q14.1	2010-06-30	2004-11-19		ENSG00000156508	ENSG00000156508			3189	protein-coding gene	gene with protein product		130590	"""leukocyte receptor cluster (LRC) member 7"""	EF1A, EEF1A, LENG7		8812466, 10941842	Standard	NM_001402		Approved	EE1A1	uc003phj.3	P68104	OTTHUMG00000015031	ENST00000316292.9:c.121A>C	6.37:g.74229629T>G	ENSP00000339063:p.Lys41Gln	Somatic	130	0		WXS	Illumina HiSeq	.	96	62	NM_001402	P04719|P04720|Q6IQ15	Missense_Mutation	SNP	ENST00000316292.9	37	CCDS4980.1	.	.	.	.	.	.	.	.	.	.	T	15.60	2.882343	0.51908	.	.	ENSG00000156508	ENST00000316292;ENST00000358190;ENST00000309268;ENST00000331523;ENST00000391977;ENST00000456206;ENST00000356303;ENST00000455918	T;T;T;T;T	0.71698	-0.59;-0.59;-0.59;-0.59;-0.59	4.15	4.15	0.48705	Protein synthesis factor, GTP-binding (2);	0.000000	0.85682	U	0.000000	T	0.63815	0.2543	M	0.71296	2.17	0.80722	D	1	B;P;P;P;P	0.37141	0.137;0.584;0.584;0.584;0.584	B;B;B;B;B	0.40864	0.07;0.177;0.177;0.177;0.342	T	0.72821	-0.4177	10	0.87932	D	0	.	13.6597	0.62359	0.0:0.0:0.0:1.0	.	41;41;41;41;41	A6PW80;P68104;Q53HR5;Q6IPS9;Q5VTE0	.;EF1A1_HUMAN;.;.;EF1A3_HUMAN	Q	41	ENSP00000339063:K41Q;ENSP00000339053:K41Q;ENSP00000330054:K41Q;ENSP00000348651:K41Q;ENSP00000392366:K41Q	ENSP00000339053:K41Q	K	-	1	0	EEF1A1	74286350	1.000000	0.71417	0.997000	0.53966	0.976000	0.68499	7.669000	0.83911	1.874000	0.54306	0.454000	0.30748	AAA	.		0.413	EEF1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041210.2	NM_001402	
ANKRD17	26057	hgsc.bcm.edu	37	4	73979583	73979583	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr4:73979583G>T	ENST00000358602.4	-	24	4443	c.4327C>A	c.(4327-4329)Caa>Aaa	p.Q1443K	ANKRD17_ENST00000330838.6_Missense_Mutation_p.Q1192K|ANKRD17_ENST00000514252.1_5'UTR|ANKRD17_ENST00000509867.2_Missense_Mutation_p.Q1330K	NM_032217.3	NP_115593.3	O75179	ANR17_HUMAN	ankyrin repeat domain 17	1443					blood vessel maturation (GO:0001955)|negative regulation of smooth muscle cell differentiation (GO:0051151)|viral process (GO:0016032)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(3)|breast(2)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(39)|ovary(6)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)	96	Breast(15;0.000295)		Epithelial(6;8.86e-07)|OV - Ovarian serous cystadenocarcinoma(6;6.22e-06)|all cancers(17;1.51e-05)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			TCTTTGGCTTGTACTATTGAC	0.353																																					p.Q1443K		.											ANKRD17,NS,lymphoid_neoplasm,0,1	ANKRD17	0	0			c.C4327A						.						145.0	145.0	145.0					4																	73979583		2203	4300	6503	SO:0001583	missense	26057	exon24			TGGCTTGTACTAT	AB014597	CCDS34003.1, CCDS34004.1, CCDS68721.1	4q21.1-q21.21	2013-01-10			ENSG00000132466	ENSG00000132466		"""Ankyrin repeat domain containing"""	23575	protein-coding gene	gene with protein product		615929				11165478	Standard	NM_032217		Approved	GTAR, KIAA0697, FLJ22206, NY-BR-16	uc003hgp.3	O75179	OTTHUMG00000160826	ENST00000358602.4:c.4327C>A	4.37:g.73979583G>T	ENSP00000351416:p.Gln1443Lys	Somatic	74	0		WXS	Illumina HiSeq	.	27	2	NM_032217	E7EUV3|G5E964|Q6PJ85|Q6PK85|Q6PKA2|Q86XI3|Q8NDR5|Q96I86|Q9H288|Q9H6J9	Missense_Mutation	SNP	ENST00000358602.4	37	CCDS34004.1	.	.	.	.	.	.	.	.	.	.	G	8.700	0.909537	0.17833	.	.	ENSG00000132466	ENST00000358602;ENST00000330838;ENST00000509867	T;T;T	0.62364	1.63;0.04;0.03	5.07	5.07	0.68467	.	0.000000	0.64402	D	0.000014	T	0.42404	0.1201	N	0.12569	0.235	0.42532	D	0.993048	B;B;B;B;B	0.18741	0.0;0.009;0.009;0.005;0.03	B;B;B;B;B	0.13407	0.001;0.006;0.006;0.002;0.009	T	0.42865	-0.9426	10	0.02654	T	1	.	18.8032	0.92027	0.0:0.0:1.0:0.0	.	964;1442;1192;1443;1330	B4DR08;O75179-2;G5E964;O75179;E7EUV3	.;.;.;ANR17_HUMAN;.	K	1443;1192;1330	ENSP00000351416:Q1443K;ENSP00000332265:Q1192K;ENSP00000427151:Q1330K	ENSP00000332265:Q1192K	Q	-	1	0	ANKRD17	74198447	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.020000	0.76419	2.501000	0.84356	0.555000	0.69702	CAA	.		0.353	ANKRD17-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000362475.1	NM_032217	
WNT3A	89780	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	1	228194881	228194881	+	Missense_Mutation	SNP	G	G	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr1:228194881G>C	ENST00000284523.1	+	1	130	c.52G>C	c.(52-54)Ggc>Cgc	p.G18R	WNT3A_ENST00000366753.2_Missense_Mutation_p.G18R	NM_033131.3	NP_149122.1	P56704	WNT3A_HUMAN	wingless-type MMTV integration site family, member 3A	18					axis elongation involved in somitogenesis (GO:0090245)|axon guidance (GO:0007411)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in cardiac muscle cell fate commitment (GO:0061317)|cell proliferation in forebrain (GO:0021846)|cellular protein localization (GO:0034613)|cellular response to retinoic acid (GO:0071300)|COP9 signalosome assembly (GO:0010387)|dorsal/ventral neural tube patterning (GO:0021904)|extracellular matrix organization (GO:0030198)|heart looping (GO:0001947)|hemopoiesis (GO:0030097)|hippocampus development (GO:0021766)|in utero embryonic development (GO:0001701)|inner ear morphogenesis (GO:0042472)|mammary gland development (GO:0030879)|negative regulation of axon extension involved in axon guidance (GO:0048843)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neurogenesis (GO:0050768)|negative regulation of neuron projection development (GO:0010977)|neuron differentiation (GO:0030182)|osteoblast differentiation (GO:0001649)|palate development (GO:0060021)|paraxial mesodermal cell fate commitment (GO:0048343)|platelet aggregation (GO:0070527)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of canonical Wnt signaling pathway involved in controlling type B pancreatic cell proliferation (GO:2000081)|positive regulation of cardiac muscle cell differentiation (GO:2000727)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-cell adhesion mediated by cadherin (GO:2000049)|positive regulation of collateral sprouting in absence of injury (GO:0048697)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of dermatome development (GO:0061184)|positive regulation of mesodermal cell fate specification (GO:0048337)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of protein binding (GO:0032092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of receptor internalization (GO:0002092)|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)|post-anal tail morphogenesis (GO:0036342)|regulation of microtubule cytoskeleton organization (GO:0070507)|skeletal muscle cell differentiation (GO:0035914)|spinal cord association neuron differentiation (GO:0021527)|Wnt signaling pathway involved in forebrain neuroblast division (GO:0021874)	cell surface (GO:0009986)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	frizzled binding (GO:0005109)|receptor agonist activity (GO:0048018)|transcription coactivator activity (GO:0003713)			kidney(1)|large_intestine(3)|lung(6)|ovary(1)|pancreas(1)	12		Prostate(94;0.0405)				GCAGGCTCTGGGCAGCTACCC	0.721																																					p.G18R		.											.	.	.	0			c.G52C						.						29.0	25.0	26.0					1																	228194881		2200	4299	6499	SO:0001583	missense	89780	exon1			GCTCTGGGCAGCT	AB060284	CCDS1564.1	1q42	2013-02-28			ENSG00000154342	ENSG00000154342		"""Wingless-type MMTV integration sites"", ""Endogenous ligands"""	15983	protein-coding gene	gene with protein product		606359				11414706	Standard	NM_033131		Approved		uc001hrq.2	P56704	OTTHUMG00000037593	ENST00000284523.1:c.52G>C	1.37:g.228194881G>C	ENSP00000284523:p.Gly18Arg	Somatic	41	0		WXS	Illumina HiSeq	.	54	33	NM_033131	Q3SY79|Q3SY80|Q969P2	Missense_Mutation	SNP	ENST00000284523.1	37	CCDS1564.1	.	.	.	.	.	.	.	.	.	.	G	8.781	0.928148	0.18131	.	.	ENSG00000154342	ENST00000284523;ENST00000366753	T;T	0.76448	-1.01;-1.02	3.36	2.43	0.29744	.	1.407350	0.04793	N	0.432047	T	0.60077	0.2241	N	0.08118	0	0.26601	N	0.973029	B;B	0.18461	0.012;0.028	B;B	0.14023	0.01;0.009	T	0.49899	-0.8890	10	0.34782	T	0.22	.	6.8535	0.24028	0.1391:0.0:0.8609:0.0	.	18;18	P56704;Q3SY79	WNT3A_HUMAN;.	R	18	ENSP00000284523:G18R;ENSP00000355715:G18R	ENSP00000284523:G18R	G	+	1	0	WNT3A	226261504	1.000000	0.71417	1.000000	0.80357	0.514000	0.34195	1.917000	0.39996	0.542000	0.28846	0.462000	0.41574	GGC	.		0.721	WNT3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091648.1	NM_033131	
WDFY3	23001	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	4	85687060	85687060	+	Missense_Mutation	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr4:85687060A>C	ENST00000295888.4	-	32	5498	c.5091T>G	c.(5089-5091)aaT>aaG	p.N1697K	WDFY3_ENST00000322366.6_Missense_Mutation_p.N1697K	NM_014991.4	NP_055806.2	Q8IZQ1	WDFY3_HUMAN	WD repeat and FYVE domain containing 3	1697					aggrephagy (GO:0035973)|positive regulation of macroautophagy (GO:0016239)	autophagic vacuole (GO:0005776)|cytoplasm (GO:0005737)|extrinsic component of membrane (GO:0019898)|inclusion body (GO:0016234)|nuclear envelope (GO:0005635)|PML body (GO:0016605)	1-phosphatidylinositol binding (GO:0005545)|beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity (GO:0003831)|metal ion binding (GO:0046872)			breast(5)|central_nervous_system(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(32)|lung(50)|ovary(3)|prostate(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	134		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000808)		GAATAGACTGATTACTTAGTA	0.398																																					p.N1697K		.											.	.	.	0			c.T5091G						.						143.0	136.0	139.0					4																	85687060		2203	4300	6503	SO:0001583	missense	23001	exon32			AGACTGATTACTT	AB023210	CCDS3609.1	4q21.3	2013-01-09			ENSG00000163625	ENSG00000163625		"""Zinc fingers, FYVE domain containing"", ""WD repeat domain containing"""	20751	protein-coding gene	gene with protein product						10231032	Standard	NM_014991		Approved	KIAA0993, ALFY, ZFYVE25	uc003hpd.3	Q8IZQ1	OTTHUMG00000130424	ENST00000295888.4:c.5091T>G	4.37:g.85687060A>C	ENSP00000295888:p.Asn1697Lys	Somatic	51	0		WXS	Illumina HiSeq	.	22	16	NM_014991	Q4W5K5|Q6P0Q5|Q8N1T2|Q8NAV6|Q96BS7|Q96D33|Q96N85|Q9Y2J7	Missense_Mutation	SNP	ENST00000295888.4	37	CCDS3609.1	.	.	.	.	.	.	.	.	.	.	A	18.44	3.623610	0.66901	.	.	ENSG00000163625	ENST00000322366;ENST00000295888	T;T	0.51574	0.7;0.7	5.81	-0.694	0.11294	.	0.000000	0.85682	D	0.000000	T	0.50922	0.1644	M	0.68593	2.085	0.80722	D	1	D	0.54207	0.965	P	0.53266	0.722	T	0.50759	-0.8790	10	0.20046	T	0.44	.	11.3347	0.49496	0.5006:0.0:0.4994:0.0	.	1697	Q8IZQ1	WDFY3_HUMAN	K	1697	ENSP00000318466:N1697K;ENSP00000295888:N1697K	ENSP00000295888:N1697K	N	-	3	2	WDFY3	85906084	1.000000	0.71417	0.998000	0.56505	0.820000	0.46376	1.967000	0.40491	-0.072000	0.12864	-0.256000	0.11100	AAT	.		0.398	WDFY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252811.2	NM_014991	
HRH2	3274	hgsc.bcm.edu	37	5	175111128	175111128	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr5:175111128G>T	ENST00000231683.2	+	1	2665	c.892G>T	c.(892-894)Ggg>Tgg	p.G298W	HRH2_ENST00000377291.2_Missense_Mutation_p.G298W	NM_022304.2	NP_071640.1	P25021	HRH2_HUMAN	histamine receptor H2	298					digestive tract development (GO:0048565)|epithelial cell morphogenesis (GO:0003382)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|gastrin-induced gastric acid secretion (GO:0001698)|gland development (GO:0048732)|histamine-induced gastric acid secretion (GO:0001697)|immune response (GO:0006955)|memory (GO:0007613)|positive regulation of vasoconstriction (GO:0045907)|regulation of synaptic plasticity (GO:0048167)|visual learning (GO:0008542)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	histamine receptor activity (GO:0004969)	p.G298W(1)		breast(1)|cervix(1)|endometrium(3)|large_intestine(6)|lung(10)|ovary(1)	22	all_cancers(89;0.00805)|Renal(175;0.000269)|Lung NSC(126;0.00419)|all_lung(126;0.00711)	Medulloblastoma(196;0.0208)|all_neural(177;0.0277)|all_hematologic(541;0.214)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)	Colorectal(1;0.0154)|COAD - Colon adenocarcinoma(1;0.149)	Amitriptyline(DB00321)|Asenapine(DB06216)|Betazole(DB00272)|Cimetidine(DB00501)|Doxepin(DB01142)|Epinastine(DB00751)|Famotidine(DB00927)|Histamine Phosphate(DB00667)|Loxapine(DB00408)|Methantheline(DB00940)|Nizatidine(DB00585)|Olanzapine(DB00334)|Ranitidine(DB00863)|Roxatidine acetate(DB08806)|Tolazoline(DB00797)	CTTCCGCACCGGGTACCAACA	0.567																																					p.G298W		.											HRH2_ENST00000377291,middle_lobe,carcinoma,0,3	HRH2_ENST00000377291	0	1	Substitution - Missense(1)	lung(1)	c.G892T						.						97.0	84.0	88.0					5																	175111128		2203	4300	6503	SO:0001583	missense	3274	exon2			CGCACCGGGTACC		CCDS4395.1, CCDS47344.1	5q35	2012-08-08			ENSG00000113749	ENSG00000113749		"""GPCR / Class A : Histamine receptors"""	5183	protein-coding gene	gene with protein product		142703				1714721	Standard	NM_022304		Approved		uc003mdc.4	P25021	OTTHUMG00000130660	ENST00000231683.2:c.892G>T	5.37:g.175111128G>T	ENSP00000231683:p.Gly298Trp	Somatic	28	0		WXS	Illumina HiSeq	.	36	2	NM_001131055	B5BUP7|Q14464|Q7Z5R9	Missense_Mutation	SNP	ENST00000231683.2	37	CCDS4395.1	.	.	.	.	.	.	.	.	.	.	G	17.04	3.286347	0.59867	.	.	ENSG00000113749	ENST00000377291;ENST00000231683	T;T	0.37915	1.17;1.17	5.21	5.21	0.72293	.	0.425026	0.24323	N	0.039529	T	0.37785	0.1016	N	0.08118	0	0.45108	D	0.998125	P;D	0.56746	0.811;0.977	P;P	0.58721	0.6;0.844	T	0.50329	-0.8841	10	0.87932	D	0	.	17.7435	0.88413	0.0:0.0:1.0:0.0	.	298;298	P25021;Q7Z5R9	HRH2_HUMAN;.	W	298	ENSP00000366506:G298W;ENSP00000231683:G298W	ENSP00000231683:G298W	G	+	1	0	HRH2	175043734	1.000000	0.71417	0.027000	0.17364	0.195000	0.23768	9.736000	0.98828	2.442000	0.82660	0.650000	0.86243	GGG	.		0.567	HRH2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253151.1		
EIF4G1	1981	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	3	184039802	184039802	+	Missense_Mutation	SNP	A	A	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr3:184039802A>T	ENST00000346169.2	+	10	1701	c.1430A>T	c.(1429-1431)gAg>gTg	p.E477V	EIF4G1_ENST00000434061.2_Missense_Mutation_p.E281V|EIF4G1_ENST00000392537.2_Missense_Mutation_p.E390V|EIF4G1_ENST00000427845.1_Missense_Mutation_p.E390V|EIF4G1_ENST00000382330.3_Missense_Mutation_p.E484V|EIF4G1_ENST00000352767.3_Missense_Mutation_p.E484V|EIF2B5_ENST00000444495.1_Intron|EIF4G1_ENST00000441154.1_Missense_Mutation_p.E313V|EIF4G1_ENST00000350481.5_Missense_Mutation_p.E313V|EIF4G1_ENST00000342981.4_Missense_Mutation_p.E477V|EIF4G1_ENST00000414031.1_Missense_Mutation_p.E437V|EIF4G1_ENST00000319274.6_Missense_Mutation_p.E477V|EIF4G1_ENST00000435046.2_Missense_Mutation_p.E281V|EIF4G1_ENST00000424196.1_Missense_Mutation_p.E484V|EIF4G1_ENST00000411531.1_Missense_Mutation_p.E437V	NM_198241.2	NP_937884	Q04637	IF4G1_HUMAN	eukaryotic translation initiation factor 4 gamma, 1	477					cell death (GO:0008219)|cellular protein metabolic process (GO:0044267)|cytokine-mediated signaling pathway (GO:0019221)|gene expression (GO:0010467)|insulin receptor signaling pathway (GO:0008286)|lung development (GO:0030324)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|regulation of translational initiation (GO:0006446)|response to ethanol (GO:0045471)|RNA metabolic process (GO:0016070)|translation (GO:0006412)|translational initiation (GO:0006413)|viral process (GO:0016032)	cytosol (GO:0005829)|eukaryotic translation initiation factor 4F complex (GO:0016281)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|translation factor activity, nucleic acid binding (GO:0008135)|translation initiation factor activity (GO:0003743)			central_nervous_system(1)|cervix(2)|endometrium(3)|kidney(5)|large_intestine(14)|lung(41)|ovary(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	75	all_cancers(143;1.06e-10)|Ovarian(172;0.0339)		Epithelial(37;1.53e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			gcTGAGAGTGAGAAAGGAGGA	0.532																																					p.E484V		.											.	.	.	0			c.A1451T						.						63.0	64.0	64.0					3																	184039802		2203	4300	6503	SO:0001583	missense	1981	exon11			AGAGTGAGAAAGG	D12686	CCDS3259.1, CCDS3260.1, CCDS3261.1, CCDS46970.1, CCDS46970.2, CCDS54687.1, CCDS54688.1	3q27.1	2013-09-19			ENSG00000114867	ENSG00000114867		"""Parkinson disease"""	3296	protein-coding gene	gene with protein product		600495		EIF4G, EIF4F		1429670, 9372926, 21907011	Standard	NM_182917		Approved	p220, PARK18	uc010hxy.3	Q04637	OTTHUMG00000156784	ENST00000346169.2:c.1430A>T	3.37:g.184039802A>T	ENSP00000316879:p.Glu477Val	Somatic	111	0		WXS	Illumina HiSeq	.	79	26	NM_001194946	D3DNT2|D3DNT4|D3DNT5|E9PFM1|G5E9S1|O43177|O95066|Q5HYG0|Q6ZN21|Q8N102	Missense_Mutation	SNP	ENST00000346169.2	37	CCDS3259.1	.	.	.	.	.	.	.	.	.	.	A	11.98	1.800720	0.31869	.	.	ENSG00000114867	ENST00000346169;ENST00000414031;ENST00000392537;ENST00000450424;ENST00000421110;ENST00000382330;ENST00000426123;ENST00000350481;ENST00000352767;ENST00000427845;ENST00000342981;ENST00000319274;ENST00000424196;ENST00000411531;ENST00000444861;ENST00000441154;ENST00000434061;ENST00000457456;ENST00000435046	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.64618	-0.11;-0.11;-0.11;-0.11;-0.11;-0.11;-0.11;-0.11;-0.11;-0.11;-0.11;-0.11;-0.11;-0.11;-0.11;-0.11;-0.11;0.94;-0.11	5.77	5.77	0.91146	.	0.429627	0.23813	N	0.044310	T	0.51109	0.1655	L	0.34521	1.04	0.51482	D	0.999923	B;B;B;B	0.27498	0.18;0.18;0.18;0.023	B;B;B;B	0.24155	0.051;0.051;0.051;0.044	T	0.48768	-0.9006	10	0.37606	T	0.19	-10.7873	13.4858	0.61364	1.0:0.0:0.0:0.0	.	484;477;477;484	E9PFM1;D3DNT2;Q04637;B2RU10	.;.;IF4G1_HUMAN;.	V	477;437;390;477;484;484;418;313;484;390;477;477;484;437;313;313;281;281;281	ENSP00000316879:E477V;ENSP00000391935:E437V;ENSP00000376320:E390V;ENSP00000391412:E477V;ENSP00000413159:E484V;ENSP00000371767:E484V;ENSP00000403269:E418V;ENSP00000317600:E313V;ENSP00000338020:E484V;ENSP00000407682:E390V;ENSP00000343450:E477V;ENSP00000323737:E477V;ENSP00000416255:E484V;ENSP00000395974:E437V;ENSP00000398145:E313V;ENSP00000399858:E313V;ENSP00000411826:E281V;ENSP00000399969:E281V;ENSP00000404754:E281V	ENSP00000323737:E477V	E	+	2	0	EIF4G1	185522496	1.000000	0.71417	1.000000	0.80357	0.884000	0.51177	3.704000	0.54815	2.205000	0.71048	0.460000	0.39030	GAG	.		0.532	EIF4G1-007	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000345733.1	NM_182917	
ABCB11	8647	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	2	169820752	169820752	+	Silent	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr2:169820752A>C	ENST00000263817.6	-	18	2266	c.2142T>G	c.(2140-2142)gtT>gtG	p.V714V		NM_003742.2	NP_003733.2	O95342	ABCBB_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 11	714					bile acid and bile salt transport (GO:0015721)|bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|canalicular bile acid transport (GO:0015722)|small molecule metabolic process (GO:0044281)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intercellular canaliculus (GO:0046581)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|bile acid-exporting ATPase activity (GO:0015432)|canalicular bile acid transmembrane transporter activity (GO:0015126)|sodium-exporting ATPase activity, phosphorylative mechanism (GO:0008554)|transporter activity (GO:0005215)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(16)|lung(26)|ovary(3)|stomach(1)	57					Adenosine triphosphate(DB00171)|Bosentan(DB00559)|Chlorpromazine(DB00477)|Cimetidine(DB00501)|Clofazimine(DB00845)|Cyclosporine(DB00091)|Daunorubicin(DB00694)|Dexamethasone(DB01234)|Digoxin(DB00390)|Doxorubicin(DB00997)|Ethinyl Estradiol(DB00977)|Fluorescein(DB00693)|Fusidic Acid(DB02703)|Glyburide(DB01016)|Ketoconazole(DB01026)|Novobiocin(DB01051)|Paclitaxel(DB01229)|Phenobarbital(DB01174)|Ponatinib(DB08901)|Pravastatin(DB00175)|Progesterone(DB00396)|Quinidine(DB00908)|Reserpine(DB00206)|Rifampicin(DB01045)|Rosuvastatin(DB01098)|Tamoxifen(DB00675)|Ursodeoxycholic acid(DB01586)|Verapamil(DB00661)|Vinblastine(DB00570)|Vincristine(DB00541)	TATGATCTACAACAGCTAATG	0.478																																					p.V714V		.											.	.	.	0			c.T2142G						.						67.0	85.0	79.0					2																	169820752		1927	4148	6075	SO:0001819	synonymous_variant	8647	exon18			ATCTACAACAGCT	AF091582	CCDS46444.1	2q24	2012-03-14			ENSG00000073734	ENSG00000073734		"""ATP binding cassette transporters / subfamily B"""	42	protein-coding gene	gene with protein product	"""ABC member 16, MDR/TAP subfamily"""	603201	"""progressive familial intrahepatic cholestasis 2"", ""bile salt export pump"""	BSEP, PFIC2		9806540	Standard	NM_003742		Approved	ABC16, SPGP, PFIC-2, PGY4	uc002ueo.1	O95342	OTTHUMG00000154039	ENST00000263817.6:c.2142T>G	2.37:g.169820752A>C		Somatic	58	0		WXS	Illumina HiSeq	.	50	24	NM_003742	Q53TL2|Q9UNB2	Silent	SNP	ENST00000263817.6	37	CCDS46444.1																																																																																			.		0.478	ABCB11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333616.2	NM_003742	
ST7L	54879	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	113140706	113140706	+	Missense_Mutation	SNP	T	T	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr1:113140706T>C	ENST00000358039.4	-	5	813	c.509A>G	c.(508-510)tAc>tGc	p.Y170C	ST7L_ENST00000543570.1_Missense_Mutation_p.Y153C|ST7L_ENST00000343210.7_Missense_Mutation_p.Y170C|ST7L_ENST00000463235.1_5'UTR|ST7L_ENST00000369666.1_Missense_Mutation_p.Y153C|ST7L_ENST00000538187.1_Missense_Mutation_p.Y114C|ST7L_ENST00000360743.4_Missense_Mutation_p.Y170C|ST7L_ENST00000369668.2_Missense_Mutation_p.Y170C|ST7L_ENST00000490067.1_Missense_Mutation_p.Y153C|ST7L_ENST00000544629.1_Intron|ST7L_ENST00000369669.1_De_novo_Start_OutOfFrame	NM_017744.4|NM_138727.3	NP_060214.2|NP_620055.1	Q8TDW4	ST7L_HUMAN	suppression of tumorigenicity 7 like	170					negative regulation of cell growth (GO:0030308)	integral component of membrane (GO:0016021)				endometrium(1)|kidney(4)|large_intestine(3)|lung(1)|prostate(2)|stomach(1)|urinary_tract(3)	15	Lung SC(450;0.246)	all_cancers(81;1.44e-07)|all_epithelial(167;7.64e-07)|all_lung(203;2.16e-05)|Lung NSC(69;3.86e-05)		Lung(183;0.0234)|all cancers(265;0.0246)|Epithelial(280;0.0342)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		CACCCAAGTGTATCTTTACCA	0.363																																					p.Y170C		.											.	.	.	0			c.A509G						.						155.0	148.0	150.0					1																	113140706		2203	4300	6503	SO:0001583	missense	54879	exon5			CAAGTGTATCTTT	AB081317	CCDS848.1, CCDS849.1, CCDS850.1, CCDS852.1	1p13.1	2008-06-06			ENSG00000007341	ENSG00000007341			18441	protein-coding gene	gene with protein product						12012006	Standard	NM_138729		Approved	FLJ20284, STLR, ST7R, FAM4B	uc001ecd.3	Q8TDW4	OTTHUMG00000011753	ENST00000358039.4:c.509A>G	1.37:g.113140706T>C	ENSP00000350734:p.Tyr170Cys	Somatic	98	0		WXS	Illumina HiSeq	.	38	28	NM_138729	A8K4S7|Q49AH6|Q5TEI4|Q5U5K6|Q6N067|Q7Z2Z0|Q7Z3C2|Q8N7P8|Q8TDW1|Q8TDW2|Q8TDW3|Q9NXF3	Missense_Mutation	SNP	ENST00000358039.4	37	CCDS848.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	20.3|20.3	3.967928|3.967928	0.74131|0.74131	.|.	.|.	ENSG00000007341|ENSG00000007341	ENST00000418497|ENST00000358039;ENST00000360743;ENST00000369673;ENST00000490067;ENST00000369668;ENST00000343210;ENST00000369666;ENST00000538187;ENST00000543570;ENST00000369665;ENST00000369664	.|T;T;T;T;T;T;T;T;T	.|0.25912	.|1.77;1.77;1.77;1.77;1.77;1.77;1.77;1.77;1.77	5.56|5.56	4.41|4.41	0.53225|0.53225	.|.	.|0.111778	.|0.64402	.|D	.|0.000006	T|T	0.39733|0.39733	0.1089|0.1089	M|M	0.78637|0.78637	2.42|2.42	0.80722|0.80722	D|D	1|1	.|D;D;D;D;D;D;D	.|0.76494	.|0.999;0.996;0.996;0.998;0.998;0.999;0.998	.|D;D;D;D;D;D;D	.|0.76575	.|0.988;0.94;0.952;0.952;0.952;0.967;0.981	T|T	0.43621|0.43621	-0.9380|-0.9380	5|10	.|0.87932	.|D	.|0	-1.3983|-1.3983	11.6068|11.6068	0.51037|0.51037	0.1337:0.0:0.0:0.8663|0.1337:0.0:0.0:0.8663	.|.	.|153;114;170;153;153;170;170	.|B7Z8V6;B7Z7D4;Q8TDW4-5;Q8TDW4-6;Q8TDW4-3;Q8TDW4-2;Q8TDW4	.|.;.;.;.;.;.;ST7L_HUMAN	A|C	42|170;170;48;153;170;170;153;114;153;48;114	.|ENSP00000350734:Y170C;ENSP00000353972:Y170C;ENSP00000417140:Y153C;ENSP00000358682:Y170C;ENSP00000345312:Y170C;ENSP00000358680:Y153C;ENSP00000444021:Y114C;ENSP00000444088:Y153C;ENSP00000358678:Y114C	.|ENSP00000345312:Y170C	T|Y	-|-	1|2	0|0	ST7L|ST7L	112942229|112942229	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.970000|0.970000	0.65996|0.65996	6.290000|6.290000	0.72712|0.72712	0.906000|0.906000	0.36621|0.36621	0.383000|0.383000	0.25322|0.25322	ACA|TAC	.		0.363	ST7L-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000032504.3		
ABCA13	154664	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	7	48315409	48315409	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr7:48315409G>T	ENST00000435803.1	+	17	6170	c.6146G>T	c.(6145-6147)aGt>aTt	p.S2049I		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	2049					transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(13)|central_nervous_system(8)|endometrium(25)|haematopoietic_and_lymphoid_tissue(4)|kidney(20)|large_intestine(51)|lung(100)|ovary(5)|pancreas(2)|prostate(22)|skin(10)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	270						ATTGAAAAAAGTGAAACACCT	0.348																																					p.S2049I		.											.	.	.	0			c.G6146T						.						35.0	33.0	34.0					7																	48315409		1830	4082	5912	SO:0001583	missense	154664	exon17			AAAAAAGTGAAAC	AY204751	CCDS47584.1	7p12.3	2012-03-14			ENSG00000179869	ENSG00000179869		"""ATP binding cassette transporters / subfamily A"""	14638	protein-coding gene	gene with protein product		607807				12697998	Standard	NM_152701		Approved	FLJ33876, FLJ33951	uc003toq.2	Q86UQ4	OTTHUMG00000155840	ENST00000435803.1:c.6146G>T	7.37:g.48315409G>T	ENSP00000411096:p.Ser2049Ile	Somatic	66	0		WXS	Illumina HiSeq	.	55	12	NM_152701	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Missense_Mutation	SNP	ENST00000435803.1	37	CCDS47584.1	.	.	.	.	.	.	.	.	.	.	G	7.720	0.696922	0.15106	.	.	ENSG00000179869	ENST00000435803	T	0.14893	2.47	4.44	0.188	0.15114	.	0.609366	0.15408	N	0.263931	T	0.13415	0.0325	L	0.50333	1.59	0.09310	N	1	B	0.16603	0.018	B	0.14023	0.01	T	0.29610	-1.0006	9	.	.	.	.	6.5984	0.22687	0.3811:0.0:0.505:0.114	.	2049	Q86UQ4	ABCAD_HUMAN	I	2049	ENSP00000411096:S2049I	.	S	+	2	0	ABCA13	48285955	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.425000	0.07017	-0.464000	0.06963	-1.626000	0.00786	AGT	.		0.348	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701	
CNTLN	54875	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	9	17273832	17273832	+	Silent	SNP	T	T	C	rs369987628		TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr9:17273832T>C	ENST00000380647.3	+	6	1035	c.951T>C	c.(949-951)ctT>ctC	p.L317L	CNTLN_ENST00000380641.4_Silent_p.L317L|CNTLN_ENST00000262360.5_Silent_p.L317L|CNTLN_ENST00000425824.1_Silent_p.L317L			Q9NXG0	CNTLN_HUMAN	centlein, centrosomal protein	317					centriole-centriole cohesion (GO:0010457)|protein localization to organelle (GO:0033365)	centriole (GO:0005814)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	phosphorelay sensor kinase activity (GO:0000155)|protein binding, bridging (GO:0030674)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)			breast(6)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|kidney(3)|large_intestine(10)|lung(17)|ovary(1)|pancreas(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	53				GBM - Glioblastoma multiforme(50;6.14e-10)		AGACTGAACTTATCCAGAAGG	0.303																																					p.L317L		.											.	.	.	0			c.T951C						.	T	,	1,3673		0,1,1836	110.0	109.0	109.0		951,951	-0.3	1.0	9		109	1,8153		0,1,4076	no	coding-synonymous,coding-synonymous	CNTLN	NM_001114395.1,NM_017738.2	,	0,2,5912	CC,CT,TT		0.0123,0.0272,0.0169	,	317/392,317/1407	17273832	2,11826	1837	4077	5914	SO:0001819	synonymous_variant	54875	exon6			TGAACTTATCCAG	AK000283	CCDS43789.1, CCDS47953.1	9p22.2-p22.1	2008-11-11	2008-02-08	2008-02-08	ENSG00000044459	ENSG00000044459			23432	protein-coding gene	gene with protein product		611870	"""chromosome 9 open reading frame 101"", ""chromosome 9 open reading frame 39"""	C9orf101, C9orf39		18086554	Standard	XM_005251492		Approved	FLJ20276, bA340N12.1, OTTHUMG00000019597	uc003zmy.3	Q9NXG0	OTTHUMG00000019599	ENST00000380647.3:c.951T>C	9.37:g.17273832T>C		Somatic	78	0		WXS	Illumina HiSeq	.	36	10	NM_017738	A5Z2X6|Q5VYJ0|Q8N1G9|Q9HAJ5	Silent	SNP	ENST00000380647.3	37	CCDS43789.1																																																																																			.		0.303	CNTLN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051793.3	NM_017738	
CTIF	9811	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	18	46385774	46385774	+	Silent	SNP	G	G	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr18:46385774G>C	ENST00000256413.3	+	12	1936	c.1641G>C	c.(1639-1641)ctG>ctC	p.L547L	CTIF_ENST00000382998.4_Silent_p.L549L	NM_014772.2	NP_055587.1	O43310	CTIF_HUMAN	CBP80/20-dependent translation initiation factor	547	MIF4G.				nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of translational initiation (GO:0006446)	cytoplasm (GO:0005737)|perinuclear region of cytoplasm (GO:0048471)	RNA binding (GO:0003723)			breast(2)|endometrium(1)|kidney(2)|large_intestine(3)|lung(14)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	31						CAGAGCTCCTGGCCAGCGCAC	0.622																																					p.L549L		.											.	.	.	0			c.G1647C						.						79.0	77.0	78.0					18																	46385774		2203	4300	6503	SO:0001819	synonymous_variant	9811	exon13			GCTCCTGGCCAGC	AB007887	CCDS11935.1, CCDS45864.1	18q21.1	2011-01-20	2011-01-20	2011-01-20	ENSG00000134030	ENSG00000134030			23925	protein-coding gene	gene with protein product		613178	"""KIAA0427"""	KIAA0427		9455477, 19648179	Standard	NM_014772		Approved		uc002ldd.3	O43310	OTTHUMG00000132656	ENST00000256413.3:c.1641G>C	18.37:g.46385774G>C		Somatic	21	0		WXS	Illumina HiSeq	.	15	6	NM_001142397	B3KTR8|Q8IVD5	Silent	SNP	ENST00000256413.3	37	CCDS11935.1																																																																																			.		0.622	CTIF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255907.1	NM_014772	
ZNF500	26048	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	16	4815793	4815793	+	Missense_Mutation	SNP	C	C	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr16:4815793C>G	ENST00000219478.6	-	2	486	c.187G>C	c.(187-189)Ggg>Cgg	p.G63R	ZNF500_ENST00000545009.1_Missense_Mutation_p.G63R			O60304	ZN500_HUMAN	zinc finger protein 500	63	SCAN box. {ECO:0000255|PROSITE- ProRule:PRU00187}.				transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(3)|large_intestine(3)|lung(7)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	21						TCCCGGGGCCCAGCCACCTCC	0.682																																					p.G63R		.											.	.	.	0			c.G187C						.						18.0	21.0	20.0					16																	4815793		2196	4298	6494	SO:0001583	missense	26048	exon2			GGGGCCCAGCCAC	AB011129	CCDS32383.1	16p13.3	2013-01-09				ENSG00000103199		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	23716	protein-coding gene	gene with protein product						9628581	Standard	XM_005255243		Approved	ZKSCAN18, KIAA0557, ZSCAN50	uc002cxp.1	O60304		ENST00000219478.6:c.187G>C	16.37:g.4815793C>G	ENSP00000219478:p.Gly63Arg	Somatic	48	0		WXS	Illumina HiSeq	.	22	9	NM_021646	A8K6X7|B4DNN9|Q0VAL2|Q96CQ8|Q9BTG0	Missense_Mutation	SNP	ENST00000219478.6	37	CCDS32383.1	.	.	.	.	.	.	.	.	.	.	C	17.21	3.330851	0.60853	.	.	ENSG00000103199	ENST00000545009;ENST00000219478	T;T	0.06294	3.32;3.32	4.16	3.2	0.36748	Retrovirus capsid, C-terminal (1);Transcription regulator SCAN (3);	.	.	.	.	T	0.12390	0.0301	M	0.87900	2.915	0.25354	N	0.988846	P;P	0.41366	0.747;0.747	B;B	0.38954	0.286;0.286	T	0.12760	-1.0535	9	0.72032	D	0.01	.	7.907	0.29767	0.0:0.8825:0.0:0.1175	.	63;63	B4DNN9;O60304	.;ZN500_HUMAN	R	63	ENSP00000445714:G63R;ENSP00000219478:G63R	ENSP00000219478:G63R	G	-	1	0	ZNF500	4755794	0.408000	0.25360	0.410000	0.26471	0.979000	0.70002	1.859000	0.39418	0.761000	0.33130	0.655000	0.94253	GGG	.		0.682	ZNF500-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432461.1	XM_085507	
LRRC16B	90668	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	14	24532678	24532678	+	Missense_Mutation	SNP	G	G	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr14:24532678G>A	ENST00000342740.5	+	31	3069	c.2915G>A	c.(2914-2916)aGg>aAg	p.R972K	LRRC16B_ENST00000334420.7_Missense_Mutation_p.R68K	NM_138360.3	NP_612369.3	Q8ND23	LR16B_HUMAN	leucine rich repeat containing 16B	972						cytoplasm (GO:0005737)				breast(3)|central_nervous_system(2)|cervix(3)|endometrium(7)|kidney(1)|large_intestine(9)|liver(1)|lung(15)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(4)	52				GBM - Glioblastoma multiforme(265;0.019)		TACAAACTAAGGCATCAAACA	0.602																																					p.R972K		.											.	.	.	0			c.G2915A						.						47.0	56.0	53.0					14																	24532678		2203	4300	6503	SO:0001583	missense	90668	exon31			AACTAAGGCATCA	AI017934	CCDS32054.1	14q11.2-q12	2010-09-10	2008-02-12	2008-02-12					20272	protein-coding gene	gene with protein product		614716	"""chromosome 14 open reading frame 121"""	C14orf121		19846667	Standard	NM_138360		Approved	BC008134, crml-1, CARMIL3	uc001wlj.2	Q8ND23		ENST00000342740.5:c.2915G>A	14.37:g.24532678G>A	ENSP00000340467:p.Arg972Lys	Somatic	22	0		WXS	Illumina HiSeq	.	19	14	NM_138360	Q8TEF7|Q96HS9	Missense_Mutation	SNP	ENST00000342740.5	37	CCDS32054.1	.	.	.	.	.	.	.	.	.	.	G	14.99	2.700986	0.48307	.	.	ENSG00000186648	ENST00000342740;ENST00000334420	T;T	0.39997	1.05;1.05	5.12	3.16	0.36331	.	0.122178	0.37669	N	0.001985	T	0.32194	0.0821	L	0.50333	1.59	0.31545	N	0.659475	B;B	0.14438	0.0;0.01	B;B	0.10450	0.001;0.005	T	0.33343	-0.9872	10	0.54805	T	0.06	-15.1777	4.3652	0.11222	0.1859:0.0:0.6339:0.1802	.	68;972	Q8ND23-2;Q8ND23	.;LR16B_HUMAN	K	972;68	ENSP00000340467:R972K;ENSP00000334701:R68K	ENSP00000334701:R68K	R	+	2	0	LRRC16B	23602518	1.000000	0.71417	0.995000	0.50966	0.985000	0.73830	2.483000	0.45233	1.289000	0.44618	-0.258000	0.10820	AGG	.		0.602	LRRC16B-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416527.1	NM_138360	
TTLL4	9654	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	2	219603258	219603258	+	Missense_Mutation	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr2:219603258T>G	ENST00000392102.1	+	3	1199	c.859T>G	c.(859-861)Ttg>Gtg	p.L287V	TTLL4_ENST00000258398.4_Missense_Mutation_p.L287V|TTLL4_ENST00000457313.1_Missense_Mutation_p.L122V|TTLL4_ENST00000442769.1_Missense_Mutation_p.L287V	NM_014640.4	NP_055455.3	Q14679	TTLL4_HUMAN	tubulin tyrosine ligase-like family, member 4	287					protein polyglutamylation (GO:0018095)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	ligase activity (GO:0016874)|tubulin binding (GO:0015631)			endometrium(3)|kidney(1)|large_intestine(6)|lung(21)|ovary(3)|skin(3)|upper_aerodigestive_tract(2)	39		Renal(207;0.0915)		Epithelial(149;5.03e-07)|all cancers(144;0.000106)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.0101)		CCATATCGCCTTGTCTACCGC	0.552																																					p.L287V	GBM(172;1818 2053 15407 20943 49753)	.											.	.	.	0			c.T859G						.						139.0	120.0	126.0					2																	219603258		2203	4300	6503	SO:0001583	missense	9654	exon3			ATCGCCTTGTCTA		CCDS2422.1	2p24.3-p24.1	2013-02-14			ENSG00000135912	ENSG00000135912		"""Tubulin tyrosine ligase-like family"""	28976	protein-coding gene	gene with protein product						11054573	Standard	NM_014640		Approved	KIAA0173	uc002viy.3	Q14679	OTTHUMG00000133081	ENST00000392102.1:c.859T>G	2.37:g.219603258T>G	ENSP00000375951:p.Leu287Val	Somatic	36	0		WXS	Illumina HiSeq	.	19	10	NM_014640	A8K6V5|Q8WW29	Missense_Mutation	SNP	ENST00000392102.1	37	CCDS2422.1	.	.	.	.	.	.	.	.	.	.	T	1.437	-0.568582	0.03910	.	.	ENSG00000135912	ENST00000457313;ENST00000392102;ENST00000442769;ENST00000258398	T;T;T;T	0.04406	3.83;4.08;3.63;4.08	4.54	-1.08	0.09936	.	1.516350	0.04177	N	0.325782	T	0.03871	0.0109	L	0.29908	0.895	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.001;0.001	T	0.44159	-0.9346	10	0.41790	T	0.15	.	0.9827	0.01440	0.1868:0.2835:0.1236:0.4061	.	122;287;287	E9PH58;E7EX20;Q14679	.;.;TTLL4_HUMAN	V	122;287;287;287	ENSP00000393332:L122V;ENSP00000375951:L287V;ENSP00000396555:L287V;ENSP00000258398:L287V	ENSP00000258398:L287V	L	+	1	2	TTLL4	219311502	0.001000	0.12720	0.005000	0.12908	0.052000	0.14988	-0.210000	0.09345	-0.417000	0.07461	-0.371000	0.07208	TTG	.		0.552	TTLL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256726.1	NM_014640	
GPR98	84059	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	5	90079724	90079724	+	Silent	SNP	A	A	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr5:90079724A>G	ENST00000405460.2	+	67	13599	c.13503A>G	c.(13501-13503)ctA>ctG	p.L4501L	GPR98_ENST00000425867.2_Silent_p.L162L	NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	4501					detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|G-protein coupled receptor signaling pathway (GO:0007186)|inner ear receptor stereocilium organization (GO:0060122)|maintenance of organ identity (GO:0048496)|nervous system development (GO:0007399)|neurological system process (GO:0050877)|neuropeptide signaling pathway (GO:0007218)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|stereocilia ankle link complex (GO:0002142)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(4)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(18)|large_intestine(46)|liver(2)|lung(80)|ovary(12)|pancreas(5)|prostate(1)|skin(50)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(6)	269		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		GGCGCCACCTAGTGAGCAGAA	0.438																																					p.L4501L		.											.	.	.	0			c.A13503G						.						59.0	57.0	58.0					5																	90079724		1839	4083	5922	SO:0001819	synonymous_variant	84059	exon67			CCACCTAGTGAGC	AB014586	CCDS47246.1	5q13	2014-08-08	2006-05-26	2006-05-26	ENSG00000164199	ENSG00000164199		"""-"", ""GPCR / Class B : Orphans"""	17416	protein-coding gene	gene with protein product		602851	"""monogenic, audiogenic seizure susceptibility 1 homolog (mouse)"""	USH2C, MASS1		10976914, 14740321	Standard	NM_032119		Approved	DKFZp761P0710, KIAA0686, FEB4, VLGR1b	uc003kju.3	Q8WXG9	OTTHUMG00000162668	ENST00000405460.2:c.13503A>G	5.37:g.90079724A>G		Somatic	91	0		WXS	Illumina HiSeq	.	62	37	NM_032119	O75171|Q8TF58|Q9H0X5|Q9UL61	Silent	SNP	ENST00000405460.2	37	CCDS47246.1																																																																																			.		0.438	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119	
TVP23B	51030	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	17	18702239	18702239	+	Missense_Mutation	SNP	T	T	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr17:18702239T>A	ENST00000307767.8	+	5	744	c.445T>A	c.(445-447)Ttc>Atc	p.F149I	TVP23B_ENST00000581733.1_Missense_Mutation_p.F85I|TVP23B_ENST00000476139.1_Missense_Mutation_p.F85I|TVP23B_ENST00000574226.1_Missense_Mutation_p.F149I	NM_016078.4	NP_057162.4	Q9NYZ1	TV23B_HUMAN	trans-golgi network vesicle protein 23 homolog B (S. cerevisiae)	149						integral component of membrane (GO:0016021)											ACTCTTCTCCTTCAGAGTAAA	0.393																																					p.F149I		.											.	.	.	0			c.T445A						.						185.0	182.0	183.0					17																	18702239		2203	4300	6503	SO:0001583	missense	51030	exon5			TTCTCCTTCAGAG	AF151906	CCDS42274.1	17p11.2	2012-11-29	2012-11-29	2012-11-29	ENSG00000171928	ENSG00000171928			20399	protein-coding gene	gene with protein product			"""family with sequence similarity 18, member B"", ""family with sequence similarity 18, member B1"""	FAM18B, FAM18B1		10810093	Standard	NM_016078		Approved	CGI-148, YDR084C	uc002gum.2	Q9NYZ1	OTTHUMG00000059052	ENST00000307767.8:c.445T>A	17.37:g.18702239T>A	ENSP00000305654:p.Phe149Ile	Somatic	125	0		WXS	Illumina HiSeq	.	72	39	NM_016078	A8K448|Q96HK5|Q9Y3E6	Missense_Mutation	SNP	ENST00000307767.8	37	CCDS42274.1	.	.	.	.	.	.	.	.	.	.	T	15.94	2.981598	0.53827	.	.	ENSG00000171928	ENST00000307767	T	0.44881	0.91	3.13	3.13	0.36017	.	0.050447	0.85682	D	0.000000	T	0.63379	0.2506	M	0.87456	2.885	0.58432	D	0.999993	D	0.59357	0.985	D	0.65773	0.938	T	0.67205	-0.5729	10	0.59425	D	0.04	-15.6554	9.3432	0.38093	0.0:0.0:0.0:1.0	.	149	Q9NYZ1	F18B1_HUMAN	I	149	ENSP00000305654:F149I	ENSP00000305654:F149I	F	+	1	0	FAM18B1	18642964	1.000000	0.71417	0.998000	0.56505	0.480000	0.33159	5.770000	0.68873	1.284000	0.44531	0.163000	0.16589	TTC	.		0.393	TVP23B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000130667.2	NM_016078	
CHAMP1	283489	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	13	115090640	115090640	+	Missense_Mutation	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr13:115090640A>C	ENST00000361283.1	+	3	1632	c.1323A>C	c.(1321-1323)aaA>aaC	p.K441N		NM_001164144.1|NM_001164145.1|NM_032436.2	NP_001157616.1|NP_001157617.1|NP_115812.1	Q96JM3	CHAP1_HUMAN	chromosome alignment maintaining phosphoprotein 1	441	Mediates interaction with MAD2L2.|Pro-rich.				attachment of spindle microtubules to kinetochore involved in mitotic sister chromatid segregation (GO:0051315)|protein localization to kinetochore (GO:0034501)|protein localization to microtubule (GO:0035372)|sister chromatid biorientation (GO:0031134)	condensed chromosome (GO:0000793)|condensed chromosome kinetochore (GO:0000777)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|spindle (GO:0005819)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)										AGCTCAGAAAACCCTCAGGGT	0.537																																					p.K441N		.											.	.	.	0			c.A1323C						.						93.0	106.0	102.0					13																	115090640		2203	4300	6503	SO:0001583	missense	283489	exon3			CAGAAAACCCTCA	AK074894	CCDS9545.1	13q34	2013-01-07	2011-10-07	2011-10-07	ENSG00000198824	ENSG00000198824		"""Zinc fingers, C2H2-type"""	20311	protein-coding gene	gene with protein product	"""chromosome alignment-maintaining phosphoprotein"""		"""chromosome 13 open reading frame 8"", ""zinc finger protein 828"""	C13orf8, ZNF828		21063390	Standard	NM_032436		Approved	CAMP, CHAMP	uc010ahb.3	Q96JM3	OTTHUMG00000017404	ENST00000361283.1:c.1323A>C	13.37:g.115090640A>C	ENSP00000354730:p.Lys441Asn	Somatic	59	0		WXS	Illumina HiSeq	.	33	16	NM_001164144	B3KU06|Q6P181|Q8NC88|Q9BST0	Missense_Mutation	SNP	ENST00000361283.1	37	CCDS9545.1	.	.	.	.	.	.	.	.	.	.	A	15.81	2.943526	0.53079	.	.	ENSG00000198824	ENST00000361283	T	0.02446	4.29	5.8	-0.871	0.10642	.	0.000000	0.64402	D	0.000010	T	0.09202	0.0227	M	0.63843	1.955	0.34696	D	0.726215	D	0.89917	1.0	D	0.74348	0.983	T	0.02345	-1.1173	9	.	.	.	-11.311	9.9317	0.41525	0.6328:0.0:0.3672:0.0	.	441	Q96JM3	ZN828_HUMAN	N	441	ENSP00000354730:K441N	.	K	+	3	2	ZNF828	114108742	0.988000	0.35896	0.983000	0.44433	0.952000	0.60782	0.123000	0.15708	-0.358000	0.08162	-0.256000	0.11100	AAA	.		0.537	CHAMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045977.2	NM_032436	
COL24A1	255631	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	86591498	86591498	+	Missense_Mutation	SNP	C	C	G	rs368053899|rs36031173		TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr1:86591498C>G	ENST00000370571.2	-	3	887	c.521G>C	c.(520-522)aGt>aCt	p.S174T	COL24A1_ENST00000436319.1_Missense_Mutation_p.S174T	NM_152890.5	NP_690850.2	Q17RW2	COOA1_HUMAN	collagen, type XXIV, alpha 1	174	Laminin G-like.				extracellular matrix organization (GO:0030198)|hematopoietic progenitor cell differentiation (GO:0002244)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)			NS(3)|central_nervous_system(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(9)|liver(1)|lung(56)|ovary(4)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	101				all cancers(265;0.0627)|Epithelial(280;0.0689)		CATTGAGACACTTTGGTTTCT	0.358																																					p.S174T		.											.	.	.	0			c.G521C						.						58.0	53.0	55.0					1																	86591498		1846	4086	5932	SO:0001583	missense	255631	exon3			GAGACACTTTGGT	AF410793	CCDS41353.1	1p22.3-p22.2	2013-01-16			ENSG00000171502	ENSG00000171502		"""Collagens"""	20821	protein-coding gene	gene with protein product		610025					Standard	NM_152890		Approved		uc001dlj.3	Q17RW2	OTTHUMG00000010629	ENST00000370571.2:c.521G>C	1.37:g.86591498C>G	ENSP00000359603:p.Ser174Thr	Somatic	33	0		WXS	Illumina HiSeq	.	12	12	NM_152890	C9J1X6|Q14BD7|Q59EX5|Q5VY50|Q7Z5L5	Missense_Mutation	SNP	ENST00000370571.2	37	CCDS41353.1	.	.	.	.	.	.	.	.	.	.	C	0.020	-1.436689	0.01108	.	.	ENSG00000171502	ENST00000370571;ENST00000436319	T;T	0.19250	2.16;2.16	5.82	-2.09	0.07232	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G, thrombospondin-type, N-terminal (1);Laminin G, subdomain 2 (1);	2.008790	0.02887	N	0.133601	T	0.01387	0.0045	N	0.02830	-0.485	0.09310	N	1	B;B	0.09022	0.002;0.0	B;B	0.08055	0.003;0.002	T	0.20907	-1.0261	10	0.02654	T	1	.	1.8197	0.03108	0.2369:0.2915:0.3347:0.1369	.	174;174	F8WDM8;Q17RW2	.;COOA1_HUMAN	T	174	ENSP00000359603:S174T;ENSP00000392531:S174T	ENSP00000359603:S174T	S	-	2	0	COL24A1	86364086	0.000000	0.05858	0.005000	0.12908	0.022000	0.10575	-0.078000	0.11375	-0.371000	0.08004	-1.041000	0.02371	AGT	.		0.358	COL24A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029335.4	NM_152890	
SEMA3D	223117	hgsc.bcm.edu	37	7	84651769	84651769	+	Missense_Mutation	SNP	T	T	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr7:84651769T>C	ENST00000284136.6	-	11	1395	c.1352A>G	c.(1351-1353)cAg>cGg	p.Q451R	SEMA3D_ENST00000484038.1_5'UTR	NM_152754.2	NP_689967.2	O95025	SEM3D_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3D	451	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				cell differentiation (GO:0030154)|nervous system development (GO:0007399)	extracellular region (GO:0005576)|membrane (GO:0016020)	receptor activity (GO:0004872)			NS(1)|breast(2)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(19)|lung(29)|ovary(3)|pancreas(1)|prostate(4)|skin(2)	73						CACCACTATCTGTGTCAGTCT	0.403																																					p.Q451R	Ovarian(63;442 1191 17318 29975 31528)	.											SEMA3D,NS,adenocarcinoma,0,1	SEMA3D	0	0			c.A1352G						.						277.0	244.0	256.0					7																	84651769		2203	4300	6503	SO:0001583	missense	223117	exon11			ACTATCTGTGTCA	BC029590	CCDS34676.1	7q21.11	2013-01-11			ENSG00000153993	ENSG00000153993		"""Semaphorins"", ""Immunoglobulin superfamily / V-set domain containing"""	10726	protein-coding gene	gene with protein product		609907					Standard	NM_152754		Approved	coll-2, Sema-Z2	uc003uic.3	O95025	OTTHUMG00000154569	ENST00000284136.6:c.1352A>G	7.37:g.84651769T>C	ENSP00000284136:p.Gln451Arg	Somatic	62	0		WXS	Illumina HiSeq	.	49	2	NM_152754	A6NK46|Q6UW77|Q8NCQ1	Missense_Mutation	SNP	ENST00000284136.6	37	CCDS34676.1	.	.	.	.	.	.	.	.	.	.	T	20.3	3.961558	0.74016	.	.	ENSG00000153993	ENST00000284136	T	0.11385	2.78	5.67	5.67	0.87782	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.100671	0.64402	D	0.000001	T	0.09642	0.0237	L	0.28192	0.835	0.80722	D	1	B	0.33494	0.414	B	0.29942	0.109	T	0.11108	-1.0601	10	0.56958	D	0.05	.	15.9171	0.79527	0.0:0.0:0.0:1.0	.	451	O95025	SEM3D_HUMAN	R	451	ENSP00000284136:Q451R	ENSP00000284136:Q451R	Q	-	2	0	SEMA3D	84489705	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.055000	0.64282	2.152000	0.67230	0.455000	0.32223	CAG	.		0.403	SEMA3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336084.2	NM_152754	
PCGF5	84333	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	10	93021177	93021177	+	Missense_Mutation	SNP	A	A	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr10:93021177A>G	ENST00000336126.5	+	7	801	c.569A>G	c.(568-570)tAt>tGt	p.Y190C	PCGF5_ENST00000543648.1_Missense_Mutation_p.Y190C	NM_001257101.1|NM_032373.4	NP_001244030.1|NP_115749.2	Q86SE9	PCGF5_HUMAN	polycomb group ring finger 5	190					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|nucleolus (GO:0005730)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)	zinc ion binding (GO:0008270)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(6)	12						CCAAGTTCTTATGAGGTAAGT	0.254																																					p.Y190C	Colon(178;732 2696 46441 50370)	.											.	.	.	0			c.A569G						.						18.0	21.0	20.0					10																	93021177		2165	4251	6416	SO:0001583	missense	84333	exon7			GTTCTTATGAGGT	AL832003	CCDS7413.1	10q23.33	2013-01-09	2005-01-17	2005-01-19	ENSG00000180628	ENSG00000180628		"""RING-type (C3HC4) zinc fingers"", ""Polycomb group ring fingers"""	28264	protein-coding gene	gene with protein product			"""ring finger protein (C3HC4 type) 159"""	RNF159		8076819	Standard	NM_001256549		Approved	MGC16202	uc001khh.4	Q86SE9	OTTHUMG00000018740	ENST00000336126.5:c.569A>G	10.37:g.93021177A>G	ENSP00000337500:p.Tyr190Cys	Somatic	224	0		WXS	Illumina HiSeq	.	157	63	NM_001256549	B7Z892|D3DR33|Q6PK47|Q86TD0	Missense_Mutation	SNP	ENST00000336126.5	37	CCDS7413.1	.	.	.	.	.	.	.	.	.	.	A	18.61	3.660452	0.67586	.	.	ENSG00000180628	ENST00000543648;ENST00000336126	T;T	0.46819	0.86;0.86	5.63	5.63	0.86233	.	0.000000	0.85682	D	0.000000	T	0.62865	0.2463	L	0.58810	1.83	0.80722	D	1	D	0.76494	0.999	D	0.64042	0.921	T	0.61525	-0.7045	10	0.38643	T	0.18	-22.1839	15.8457	0.78887	1.0:0.0:0.0:0.0	.	190	Q86SE9	PCGF5_HUMAN	C	190	ENSP00000445704:Y190C;ENSP00000337500:Y190C	ENSP00000337500:Y190C	Y	+	2	0	PCGF5	93011157	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.962000	0.93254	2.131000	0.65755	0.459000	0.35465	TAT	.		0.254	PCGF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049363.1	NM_032373	
C17orf70	80233	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	17	79514062	79514062	+	Silent	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr17:79514062A>C	ENST00000327787.8	-	5	2092	c.2046T>G	c.(2044-2046)acT>acG	p.T682T	C17orf70_ENST00000425898.2_Silent_p.T331T|C17orf70_ENST00000537152.1_Silent_p.T531T			Q0VG06	FP100_HUMAN	chromosome 17 open reading frame 70	682					DNA repair (GO:0006281)	cytoplasm (GO:0005737)|Fanconi anaemia nuclear complex (GO:0043240)|intermediate filament cytoskeleton (GO:0045111)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|central_nervous_system(1)|endometrium(1)|lung(11)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	19	all_neural(118;0.0878)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0282)|OV - Ovarian serous cystadenocarcinoma(97;0.0371)			GCTCCCGACAAGTTTCCAGAA	0.687																																					p.T682T		.											.	.	.	0			c.T2046G						.						10.0	14.0	13.0					17																	79514062		2188	4286	6474	SO:0001819	synonymous_variant	80233	exon5			CCGACAAGTTTCC	BC008883	CCDS32765.1, CCDS32765.2	17q25.3	2012-05-30			ENSG00000185504	ENSG00000185504			26171	protein-coding gene	gene with protein product	"""Fanconi anemia-associated protein, 100kDa"""	611301				17396147	Standard	NM_025161		Approved	FLJ22175, FAAP100	uc002kaq.3	Q0VG06	OTTHUMG00000167764	ENST00000327787.8:c.2046T>G	17.37:g.79514062A>C		Somatic	19	0		WXS	Illumina HiSeq	.	12	4	NM_025161	A6NNM1|Q8N3F7|Q9BV13|Q9H6K7|Q9H7E8	Silent	SNP	ENST00000327787.8	37	CCDS32765.2																																																																																			.		0.687	C17orf70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396170.1	NM_025161	
LIX1L	128077	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	145498117	145498117	+	Silent	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr1:145498117T>G	ENST00000369308.3	+	5	782	c.708T>G	c.(706-708)gtT>gtG	p.V236V	RP11-315I20.1_ENST00000597144.1_RNA|RP11-315I20.1_ENST00000599469.1_RNA|RP11-315I20.1_ENST00000437797.1_RNA|RP11-315I20.1_ENST00000598354.1_RNA|RP11-315I20.1_ENST00000599147.1_RNA|RP11-315I20.1_ENST00000421764.1_RNA|RP11-315I20.1_ENST00000599626.1_RNA|RP11-315I20.1_ENST00000412239.1_RNA|RP11-315I20.1_ENST00000595518.1_RNA|RP11-315I20.1_ENST00000598103.1_RNA|RP11-315I20.1_ENST00000600340.1_RNA|RP11-315I20.1_ENST00000595494.1_RNA|RP11-315I20.1_ENST00000448561.1_RNA|RP11-315I20.1_ENST00000601726.1_RNA	NM_153713.1	NP_714924.1	Q8IVB5	LIX1L_HUMAN	Lix1 homolog (chicken) like	236										large_intestine(4)|lung(6)|ovary(2)|skin(1)	13	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					TAATGACAGTTTTTCAACTGC	0.463																																					p.V236V		.											.	.	.	0			c.T708G						.						93.0	89.0	91.0					1																	145498117		2203	4300	6503	SO:0001819	synonymous_variant	128077	exon5			GACAGTTTTTCAA	AK128733	CCDS72873.1	1q21.1	2014-07-15	2014-07-15		ENSG00000152022	ENSG00000271601			28715	protein-coding gene	gene with protein product			"""Lix1 homolog (mouse) like"", ""Lix1 homolog (chicken)-like"""			12477932	Standard	NM_153713		Approved	MGC46719	uc001enr.3	Q8IVB5	OTTHUMG00000013741	ENST00000369308.3:c.708T>G	1.37:g.145498117T>G		Somatic	80	0		WXS	Illumina HiSeq	.	82	12	NM_153713	Q6AI36	Silent	SNP	ENST00000369308.3	37	CCDS915.1																																																																																			.		0.463	LIX1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038513.1	NM_153713	
ZBTB38	253461	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	3	141162287	141162287	+	Missense_Mutation	SNP	A	A	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr3:141162287A>T	ENST00000514251.1	+	4	1336	c.1057A>T	c.(1057-1059)Agc>Tgc	p.S353C	ZBTB38_ENST00000441582.2_Missense_Mutation_p.S353C|ZBTB38_ENST00000321464.5_Missense_Mutation_p.S354C					zinc finger and BTB domain containing 38											breast(3)|cervix(4)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(3)|lung(14)|ovary(3)|prostate(2)|skin(3)|urinary_tract(1)	41						AGCCTTTGACAGCAGCACTCT	0.512																																					p.S353C		.											.	.	.	0			c.A1057T						.						110.0	111.0	110.0					3																	141162287		1961	4149	6110	SO:0001583	missense	253461	exon8			TTTGACAGCAGCA	BC015444	CCDS43157.1	3q23	2014-06-13			ENSG00000177311	ENSG00000177311		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	26636	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 171"""	612218				12477932	Standard	NM_001080412		Approved	FLJ35036, CIBZ, ZNF921, PPP1R171	uc003etw.3	Q8NAP3	OTTHUMG00000160128	ENST00000514251.1:c.1057A>T	3.37:g.141162287A>T	ENSP00000426387:p.Ser353Cys	Somatic	33	0		WXS	Illumina HiSeq	.	35	17	NM_001080412		Missense_Mutation	SNP	ENST00000514251.1	37	CCDS43157.1	.	.	.	.	.	.	.	.	.	.	A	17.33	3.363438	0.61513	.	.	ENSG00000177311	ENST00000509883;ENST00000514251;ENST00000441582;ENST00000321464	T;T;T;T	0.61392	1.54;0.11;0.11;0.11	5.58	4.43	0.53597	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);	0.174774	0.50627	D	0.000102	T	0.48390	0.1497	L	0.33137	0.985	0.28019	N	0.934613	D;D	0.59357	0.985;0.985	P;P	0.49999	0.628;0.628	T	0.46119	-0.9214	9	.	.	.	-22.1241	4.5594	0.12152	0.7245:0.0:0.2755:0.0	.	354;353	B4DYR8;Q8NAP3	.;ZBT38_HUMAN	C	353;353;353;354	ENSP00000424254:S353C;ENSP00000426387:S353C;ENSP00000406955:S353C;ENSP00000372635:S354C	.	S	+	1	0	ZBTB38	142644977	1.000000	0.71417	0.889000	0.34880	0.941000	0.58515	4.223000	0.58587	2.110000	0.64415	0.482000	0.46254	AGC	.		0.512	ZBTB38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359329.2		
TPP1	1200	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	11	6637270	6637270	+	Silent	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr11:6637270T>G	ENST00000299427.6	-	9	1171	c.1111A>C	c.(1111-1113)Aga>Cga	p.R371R	TPP1_ENST00000533371.1_Silent_p.R128R|RP11-732A19.9_ENST00000545572.1_RNA|TPP1_ENST00000534644.1_5'Flank	NM_000391.3	NP_000382.3	P49638	TTPA_HUMAN	tripeptidyl peptidase I	0					embryonic placenta development (GO:0001892)|intermembrane transport (GO:0046909)|intracellular pH reduction (GO:0051452)|lipid metabolic process (GO:0006629)|negative regulation of cell death (GO:0060548)|negative regulation of establishment of blood-brain barrier (GO:0090212)|response to nutrient (GO:0007584)|response to pH (GO:0009268)|response to toxic substance (GO:0009636)|transport (GO:0006810)|vitamin E metabolic process (GO:0042360)|vitamin transport (GO:0051180)	cytosol (GO:0005829)|late endosome (GO:0005770)	phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|transporter activity (GO:0005215)|vitamin E binding (GO:0008431)			breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|lung(9)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23		Medulloblastoma(188;0.00263)|all_neural(188;0.026)		Epithelial(150;3.45e-09)|BRCA - Breast invasive adenocarcinoma(625;0.131)	Vitamin E(DB00163)	AACTGGTGTCTTCCAGAGACA	0.498																																					p.R371R		.											.	.	.	0			c.A1111C						.						109.0	95.0	100.0					11																	6637270		2201	4296	6497	SO:0001819	synonymous_variant	1200	exon9			GGTGTCTTCCAGA	AF017456	CCDS7770.1	11p15.4	2014-09-17	2004-12-09	2004-12-10	ENSG00000166340	ENSG00000166340			2073	protein-coding gene	gene with protein product	"""TPP I"""	607998	"""ceroid-lipofuscinosis, neuronal 2, late infantile (Jansky-Bielschowsky disease)"", ""spinocerebellar ataxia, autosomal recessive 7"""	CLN2, SCAR7		9653647, 23418007	Standard	NM_000391		Approved		uc001mel.1	O14773	OTTHUMG00000133404	ENST00000299427.6:c.1111A>C	11.37:g.6637270T>G		Somatic	63	0		WXS	Illumina HiSeq	.	40	17	NM_000391	Q71V64	Silent	SNP	ENST00000299427.6	37	CCDS7770.1																																																																																			.		0.498	TPP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257261.2		
CDC14A	8556	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	100983832	100983832	+	Missense_Mutation	SNP	A	A	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr1:100983832A>G	ENST00000336454.3	+	16	2136	c.1781A>G	c.(1780-1782)tAc>tGc	p.Y594C	CDC14A_ENST00000544534.1_3'UTR|CDC14A_ENST00000370125.2_3'UTR	NM_003672.3	NP_003663.2	Q9UNH5	CC14A_HUMAN	cell division cycle 14A	594					cell cycle (GO:0007049)|cell division (GO:0051301)|cell proliferation (GO:0008283)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	phosphoprotein phosphatase activity (GO:0004721)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			breast(1)|endometrium(5)|kidney(6)|large_intestine(6)|lung(10)|skin(2)|urinary_tract(1)	31		all_epithelial(167;3.71e-06)|all_lung(203;0.00097)|Lung NSC(277;0.001)		Epithelial(280;0.0676)|all cancers(265;0.127)|COAD - Colon adenocarcinoma(174;0.201)|Lung(183;0.227)|Colorectal(144;0.241)		TATGTTCATTACTAAGGCCTT	0.438																																					p.Y594C		.											.	.	.	0			c.A1781G						.						267.0	245.0	252.0					1																	100983832		2203	4300	6503	SO:0001583	missense	8556	exon16			TTCATTACTAAGG	AF000367	CCDS769.1, CCDS770.1, CCDS771.1	1p21	2013-01-17	2013-01-17		ENSG00000079335	ENSG00000079335		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : CDC14s"""	1718	protein-coding gene	gene with protein product		603504	"""CDC10 (cell division cycle 10, S. cerevisiae, homolog)"", ""CDC14 cell division cycle 14 homolog A (S. cerevisiae)"""			9367992, 10409437	Standard	NM_033312		Approved	Cdc14A1, Cdc14A2, cdc14	uc001dtf.2	Q9UNH5	OTTHUMG00000010987	ENST00000336454.3:c.1781A>G	1.37:g.100983832A>G	ENSP00000336739:p.Tyr594Cys	Somatic	72	0		WXS	Illumina HiSeq	.	33	22	NM_003672	A6MA65|B1AQ14|B1AQ15|O43171|O60727|O60728|Q52LH9|Q8IXX0	Missense_Mutation	SNP	ENST00000336454.3	37	CCDS769.1	.	.	.	.	.	.	.	.	.	.	A	17.72	3.459480	0.63401	.	.	ENSG00000079335	ENST00000336454	T	0.11930	2.73	5.62	5.62	0.85841	.	.	.	.	.	T	0.13586	0.0329	N	0.14661	0.345	0.80722	D	1	D	0.76494	0.999	D	0.80764	0.994	T	0.16129	-1.0413	9	0.72032	D	0.01	.	14.3917	0.66983	1.0:0.0:0.0:0.0	.	594	Q9UNH5	CC14A_HUMAN	C	594	ENSP00000336739:Y594C	ENSP00000336739:Y594C	Y	+	2	0	CDC14A	100756420	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	4.307000	0.59123	2.139000	0.66308	0.528000	0.53228	TAC	.		0.438	CDC14A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000030220.1	NM_033312	
ADH6	130	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	4	100130084	100130084	+	Splice_Site	SNP	A	A	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr4:100130084A>G	ENST00000237653.7	-	6	953	c.569T>C	c.(568-570)gTg>gCg	p.V190A	RP11-696N14.1_ENST00000506454.1_RNA|ADH6_ENST00000504257.1_5'UTR|ADH6_ENST00000407820.2_5'UTR|RP11-696N14.1_ENST00000506160.1_RNA|ADH6_ENST00000394897.1_Splice_Site_p.V190A|ADH6_ENST00000394899.2_Splice_Site_p.V190A|RP11-696N14.1_ENST00000500358.2_RNA	NM_000672.3	NP_000663	P28332	ADH6_HUMAN	alcohol dehydrogenase 6 (class V)	190					ethanol oxidation (GO:0006069)|response to ethanol (GO:0045471)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	alcohol dehydrogenase (NAD) activity (GO:0004022)|alcohol dehydrogenase activity, zinc-dependent (GO:0004024)|ethanol binding (GO:0035276)|zinc ion binding (GO:0008270)			breast(1)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)|skin(2)	20				OV - Ovarian serous cystadenocarcinoma(123;3.58e-08)	Abacavir(DB01048)	ACCTGGAGTCACCTAAACACA	0.448																																					p.V190A		.											.	.	.	0			c.T569C						.						152.0	157.0	155.0					4																	100130084		2203	4300	6503	SO:0001630	splice_region_variant	130	exon6			GGAGTCACCTAAA	AK092768	CCDS3647.1, CCDS43255.1	4q23	2008-02-05			ENSG00000172955	ENSG00000172955	1.1.1.1	"""Alcohol dehydrogenases"""	255	protein-coding gene	gene with protein product		103735				1881901	Standard	NM_000672		Approved	ADH-5	uc003huo.2	P28332	OTTHUMG00000131024	ENST00000237653.7:c.568-1T>C	4.37:g.100130084A>G		Somatic	28	0		WXS	Illumina HiSeq	.	9	6	NM_000672	B3KS45|Q58F53	Missense_Mutation	SNP	ENST00000237653.7	37	CCDS3647.1	.	.	.	.	.	.	.	.	.	.	A	15.00	2.702023	0.48307	.	.	ENSG00000172955	ENST00000394897;ENST00000394899;ENST00000237653;ENST00000508558	T;T;T;T	0.25912	3.66;1.77;1.77;3.52	4.72	3.51	0.40186	GroES-like (1);	0.000000	0.85682	D	0.000000	T	0.54631	0.1870	M	0.89840	3.065	0.80722	D	1	D;P;D	0.89917	1.0;0.936;0.993	D;P;D	0.76071	0.987;0.828;0.953	T	0.63730	-0.6571	10	0.87932	D	0	-31.024	10.8274	0.46640	0.9203:0.0:0.0797:0.0	.	190;190;190	E9PBI1;P28332;P28332-2	.;ADH6_HUMAN;.	A	190;190;190;126	ENSP00000378358:V190A;ENSP00000378359:V190A;ENSP00000237653:V190A;ENSP00000426187:V126A	ENSP00000237653:V190A	V	-	2	0	ADH6	100349107	1.000000	0.71417	0.276000	0.24689	0.037000	0.13140	6.304000	0.72800	1.880000	0.54463	0.460000	0.39030	GTG	.		0.448	ADH6-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000253665.1	NM_000672	Missense_Mutation
ATAD2B	54454	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	24118774	24118774	+	Nonsense_Mutation	SNP	G	G	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr2:24118774G>A	ENST00000238789.5	-	2	626	c.283C>T	c.(283-285)Caa>Taa	p.Q95*		NM_001242338.1|NM_017552.2	NP_001229267.1|NP_060022.1	Q9ULI0	ATD2B_HUMAN	ATPase family, AAA domain containing 2B	95						nucleus (GO:0005634)	ATP binding (GO:0005524)|lysine-acetylated histone binding (GO:0070577)			central_nervous_system(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GAATCAGGTTGTTTCAAAGTG	0.393																																					p.Q95X		.											.	.	.	0			c.C283T						.						109.0	102.0	104.0					2																	24118774		1940	4150	6090	SO:0001587	stop_gained	54454	exon2			CAGGTTGTTTCAA	AB033066	CCDS46227.1	2p24.1-p23.3	2010-04-21		2007-02-08	ENSG00000119778	ENSG00000119778		"""ATPases / AAA-type"""	29230	protein-coding gene	gene with protein product		615347					Standard	XM_005264372		Approved	KIAA1240	uc002rek.4	Q9ULI0	OTTHUMG00000151902	ENST00000238789.5:c.283C>T	2.37:g.24118774G>A	ENSP00000238789:p.Gln95*	Somatic	54	0		WXS	Illumina HiSeq	.	38	15	NM_001242338	B9ZVQ5|Q6ZNA6|Q8N9E7	Nonsense_Mutation	SNP	ENST00000238789.5	37	CCDS46227.1	.	.	.	.	.	.	.	.	.	.	G	38	6.846503	0.97881	.	.	ENSG00000119778	ENST00000238789;ENST00000439915	.	.	.	5.03	5.03	0.67393	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	18.7496	0.91809	0.0:0.0:1.0:0.0	.	.	.	.	X	95	.	ENSP00000238789:Q95X	Q	-	1	0	ATAD2B	23972278	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.631000	0.74277	2.513000	0.84729	0.655000	0.94253	CAA	.		0.393	ATAD2B-001	KNOWN	mRNA_end_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324333.1	NM_017552	
SMC4	10051	hgsc.bcm.edu;bcgsc.ca	37	3	160150976	160150976	+	Silent	SNP	C	C	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr3:160150976C>A	ENST00000357388.3	+	23	4144	c.3693C>A	c.(3691-3693)tcC>tcA	p.S1231S	SMC4_ENST00000462787.1_Silent_p.S1173S|SMC4_ENST00000469762.1_Silent_p.S1206S|SMC4_ENST00000360111.2_Silent_p.S1173S|RP11-432B6.3_ENST00000483754.1_Intron|SMC4_ENST00000344722.5_Silent_p.S1231S|TRIM59_ENST00000543469.1_3'UTR	NM_001002800.1	NP_001002800.1	Q9NTJ3	SMC4_HUMAN	structural maintenance of chromosomes 4	1231					kinetochore organization (GO:0051383)|meiotic chromosome condensation (GO:0010032)|meiotic chromosome segregation (GO:0045132)|mitotic cell cycle (GO:0000278)|mitotic chromosome condensation (GO:0007076)|mitotic sister chromatid segregation (GO:0000070)	condensin complex (GO:0000796)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein heterodimerization activity (GO:0046982)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(15)|lung(20)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	48			Lung(72;0.00334)|LUSC - Lung squamous cell carcinoma(72;0.00523)			AAAATGTGTCCATTGTTGCAT	0.338																																					p.S1231S		.											.	.	.	0			c.C3693A						.						120.0	119.0	119.0					3																	160150976		2203	4300	6503	SO:0001819	synonymous_variant	10051	exon22			TGTGTCCATTGTT	AF092564	CCDS3189.1, CCDS75046.1	3q26.1	2006-07-06	2006-07-06	2006-07-06	ENSG00000113810	ENSG00000113810		"""Structural maintenance of chromosomes proteins"""	14013	protein-coding gene	gene with protein product		605575	"""SMC4 (structural maintenance of chromosomes 4, yeast)-like 1"", ""SMC4 structural maintenance of chromosomes 4-like 1 (yeast)"""	SMC4L1		9789013, 10319587	Standard	NM_005496		Approved	hCAP-C, CAP-C	uc003fdh.3	Q9NTJ3	OTTHUMG00000159006	ENST00000357388.3:c.3693C>A	3.37:g.160150976C>A		Somatic	92	0		WXS	Illumina HiSeq	.	87	4	NM_005496	A6NLT9|D3DNL8|O95752|Q8NDL4|Q9UNT9	Silent	SNP	ENST00000357388.3	37	CCDS3189.1																																																																																			.		0.338	SMC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352862.1		
SREBF1	6720	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	17	17722483	17722483	+	Silent	SNP	A	A	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr17:17722483A>G	ENST00000261646.5	-	5	1096	c.912T>C	c.(910-912)ccT>ccC	p.P304P	SREBF1_ENST00000355815.4_Silent_p.P334P|SREBF1_ENST00000395757.1_Silent_p.P50P|SREBF1_ENST00000338854.5_Silent_p.P304P|SREBF1_ENST00000583732.1_5'UTR|SREBF1_ENST00000435530.2_Silent_p.P304P	NM_004176.4	NP_004167.3	P36956	SRBP1_HUMAN	sterol regulatory element binding transcription factor 1	304	Interaction with LMNA. {ECO:0000250}.				aging (GO:0007568)|cellular lipid metabolic process (GO:0044255)|cellular response to fatty acid (GO:0071398)|cellular response to starvation (GO:0009267)|cholesterol metabolic process (GO:0008203)|circadian rhythm (GO:0007623)|insulin receptor signaling pathway (GO:0008286)|lipid biosynthetic process (GO:0008610)|lipid metabolic process (GO:0006629)|lung development (GO:0030324)|negative regulation of insulin secretion (GO:0046676)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cholesterol biosynthetic process (GO:0045542)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of triglyceride biosynthetic process (GO:0010867)|regulation of fatty acid metabolic process (GO:0019217)|regulation of heart rate by chemical signal (GO:0003062)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to cAMP (GO:0051591)|response to drug (GO:0042493)|response to food (GO:0032094)|response to glucagon (GO:0033762)|response to glucose (GO:0009749)|response to progesterone (GO:0032570)|response to retinoic acid (GO:0032526)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|sterol response element binding (GO:0032810)			cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(5)|skin(1)|urinary_tract(1)	14						GCCGGTTGATAGGCAGCTTCT	0.632																																					p.P334P		.											.	.	.	0			c.T1002C						.						70.0	65.0	66.0					17																	17722483		2203	4300	6503	SO:0001819	synonymous_variant	6720	exon6			GTTGATAGGCAGC	BC057388	CCDS11189.1, CCDS32583.1	17p11.2	2013-05-21			ENSG00000072310	ENSG00000072310		"""Basic helix-loop-helix proteins"""	11289	protein-coding gene	gene with protein product		184756				8402897, 7759101	Standard	NM_001005291		Approved	SREBP1, bHLHd1, SREBP-1c	uc002grt.2	P36956	OTTHUMG00000059313	ENST00000261646.5:c.912T>C	17.37:g.17722483A>G		Somatic	37	0		WXS	Illumina HiSeq	.	18	5	NM_001005291	B0I4X3|B0I4X4|D3DXC4|Q16062|Q59F52|Q6P4R7|Q6PFW7|Q6PJ36|Q8TAK9	Silent	SNP	ENST00000261646.5	37	CCDS11189.1	.	.	.	.	.	.	.	.	.	.	A	10.36	1.329075	0.24167	.	.	ENSG00000072310	ENST00000395751	.	.	.	4.62	1.06	0.20224	.	.	.	.	.	T	0.46347	0.1388	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.28202	-1.0051	4	.	.	.	-20.5859	4.382	0.11299	0.2592:0.0:0.5848:0.156	.	.	.	.	H	312	.	.	Y	-	1	0	SREBF1	17663208	1.000000	0.71417	1.000000	0.80357	0.571000	0.35966	1.763000	0.38461	0.368000	0.24481	-0.337000	0.08149	TAT	.		0.632	SREBF1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131771.1	NM_004176	
TNFRSF10D	8793	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	8	23003411	23003411	+	Missense_Mutation	SNP	A	A	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr8:23003411A>G	ENST00000312584.3	-	5	600	c.506T>C	c.(505-507)gTc>gCc	p.V169A		NM_003840.4	NP_003831.2	Q9UBN6	TR10D_HUMAN	tumor necrosis factor receptor superfamily, member 10d, decoy with truncated death domain	169					apoptotic process (GO:0006915)|negative regulation of apoptotic process (GO:0043066)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	transmembrane signaling receptor activity (GO:0004888)			endometrium(1)|large_intestine(2)|lung(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	9		Prostate(55;0.0421)|Breast(100;0.067)		Colorectal(74;0.0147)|COAD - Colon adenocarcinoma(73;0.0612)		ACAATTACTGACCTTGACCAT	0.557																																					p.V169A		.											.	.	.	0			c.T506C						.						126.0	116.0	119.0					8																	23003411		2203	4300	6503	SO:0001583	missense	8793	exon5			TTACTGACCTTGA	AF029761	CCDS6038.1	8p21	2006-02-22			ENSG00000173530	ENSG00000173530		"""Tumor necrosis factor receptor superfamily"", ""CD molecules"""	11907	protein-coding gene	gene with protein product		603614				9382840, 9537512	Standard	NM_003840		Approved	DcR2, TRUNDD, TRAILR4, CD264	uc003xcz.2	Q9UBN6	OTTHUMG00000097845	ENST00000312584.3:c.506T>C	8.37:g.23003411A>G	ENSP00000310263:p.Val169Ala	Somatic	53	0		WXS	Illumina HiSeq	.	42	14	NM_003840	B2R8W0|Q9Y6Q4	Missense_Mutation	SNP	ENST00000312584.3	37	CCDS6038.1	.	.	.	.	.	.	.	.	.	.	a	6.722	0.502003	0.12822	.	.	ENSG00000173530	ENST00000312584	T	0.39997	1.05	1.99	-3.99	0.04069	TNFR/CD27/30/40/95 cysteine-rich region (4);	56.032600	0.02416	U	0.082087	T	0.55768	0.1941	M	0.66439	2.03	0.09310	N	1	D	0.76494	0.999	D	0.85130	0.997	T	0.56195	-0.8019	10	0.25751	T	0.34	.	3.2494	0.06808	0.4071:0.0:0.1571:0.4358	.	169	Q9UBN6	TR10D_HUMAN	A	169	ENSP00000310263:V169A	ENSP00000310263:V169A	V	-	2	0	TNFRSF10D	23059356	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.137000	0.01304	-2.345000	0.00621	-0.695000	0.03696	GTC	.		0.557	TNFRSF10D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215135.1		
CACNA1I	8911	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	22	40059833	40059833	+	Missense_Mutation	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr22:40059833A>C	ENST00000402142.3	+	19	3584	c.3584A>C	c.(3583-3585)gAg>gCg	p.E1195A	CACNA1I_ENST00000400164.3_Missense_Mutation_p.E1160A|CACNA1I_ENST00000404898.1_Missense_Mutation_p.E1160A|CACNA1I_ENST00000336649.4_Missense_Mutation_p.E1201A|CACNA1I_ENST00000401624.1_Missense_Mutation_p.E1195A|CACNA1I_ENST00000407673.1_Missense_Mutation_p.E1160A	NM_021096.3	NP_066919.2	Q9P0X4	CAC1I_HUMAN	calcium channel, voltage-dependent, T type, alpha 1I subunit	1195					axon guidance (GO:0007411)|calcium ion import (GO:0070509)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|signal transduction (GO:0007165)|sleep (GO:0030431)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	voltage-gated calcium channel activity (GO:0005245)			breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|liver(2)|lung(27)|ovary(1)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	60	Melanoma(58;0.0749)				Cinnarizine(DB00568)|Flunarizine(DB04841)|Paramethadione(DB00617)|Spironolactone(DB00421)|Verapamil(DB00661)|Zonisamide(DB00909)	CCTCAGATCGAGGCCGGCAGC	0.622																																					p.E1195A		.											.	.	.	0			c.A3584C						.						95.0	105.0	102.0					22																	40059833		2036	4177	6213	SO:0001583	missense	8911	exon19			AGATCGAGGCCGG	AF129133	CCDS46710.1, CCDS46711.1	22q13.1	2012-03-07	2007-02-16		ENSG00000100346	ENSG00000100346		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1396	protein-coding gene	gene with protein product		608230				10454147, 16382099	Standard	NM_021096		Approved	Cav3.3	uc003ayd.3	Q9P0X4	OTTHUMG00000151096	ENST00000402142.3:c.3584A>C	22.37:g.40059833A>C	ENSP00000385019:p.Glu1195Ala	Somatic	17	0		WXS	Illumina HiSeq	.	15	6	NM_021096	B0QY12|B0QY13|B0QY14|O95504|Q5JZ88|Q7Z6S9|Q8NFX6|Q9NZC8|Q9UH15|Q9UH30|Q9ULU9|Q9UNE6	Missense_Mutation	SNP	ENST00000402142.3	37	CCDS46710.1	.	.	.	.	.	.	.	.	.	.	A	15.87	2.960440	0.53400	.	.	ENSG00000100346	ENST00000402142;ENST00000404898;ENST00000401624;ENST00000407673;ENST00000336649;ENST00000400164	D;D;D;D;D;D	0.97642	-4.47;-4.47;-4.47;-4.47;-4.47;-4.47	5.4	5.4	0.78164	.	0.167707	0.52532	D	0.000065	D	0.97467	0.9171	L	0.41961	1.31	0.39452	D	0.967417	P;D;P;P	0.71674	0.792;0.998;0.792;0.895	B;D;B;P	0.81914	0.415;0.995;0.415;0.451	D	0.99372	1.0920	10	0.72032	D	0.01	.	15.423	0.75028	1.0:0.0:0.0:0.0	.	1160;1195;1160;1195	Q9P0X4-3;Q9P0X4-2;Q9P0X4-4;Q9P0X4	.;.;.;CAC1I_HUMAN	A	1195;1160;1195;1160;1201;1160	ENSP00000385019:E1195A;ENSP00000384093:E1160A;ENSP00000383887:E1195A;ENSP00000385680:E1160A;ENSP00000337829:E1201A;ENSP00000383028:E1160A	ENSP00000337829:E1201A	E	+	2	0	CACNA1I	38389779	1.000000	0.71417	0.983000	0.44433	0.281000	0.26958	4.977000	0.63792	2.039000	0.60335	0.459000	0.35465	GAG	.		0.622	CACNA1I-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000321290.1	NM_001003406	
C6orf132	647024	hgsc.bcm.edu	37	6	42074397	42074397	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr6:42074397G>T	ENST00000341865.4	-	4	1252	c.1253C>A	c.(1252-1254)cCc>cAc	p.P418H		NM_001164446.1	NP_001157918.1	Q5T0Z8	CF132_HUMAN	chromosome 6 open reading frame 132	418										breast(1)	1						CTGAGCACAGGGCAAAggagg	0.652																																					p.P418H		.											.	.	.	0			c.C1253A						.						3.0	3.0	3.0					6																	42074397		644	1479	2123	SO:0001583	missense	647024	exon4			GCACAGGGCAAAG		CCDS47428.1	6p21.1	2012-02-06			ENSG00000188112	ENSG00000188112			21288	protein-coding gene	gene with protein product							Standard	NM_001164446		Approved	bA7K24.2	uc003orw.2	Q5T0Z8	OTTHUMG00000014695	ENST00000341865.4:c.1253C>A	6.37:g.42074397G>T	ENSP00000341368:p.Pro418His	Somatic	9	0		WXS	Illumina HiSeq	.	20	4	NM_001164446	A6NI05	Missense_Mutation	SNP	ENST00000341865.4	37	CCDS47428.1	.	.	.	.	.	.	.	.	.	.	G	13.78	2.340360	0.41498	.	.	ENSG00000188112	ENST00000341865	T	0.62639	0.01	3.9	3.01	0.34805	.	.	.	.	.	T	0.43144	0.1234	L	0.29908	0.895	0.54753	D	0.999981	.	.	.	.	.	.	T	0.48031	-0.9070	7	0.87932	D	0	.	9.3604	0.38192	0.0:0.22:0.78:0.0	.	.	.	.	H	418	ENSP00000341368:P418H	ENSP00000341368:P418H	P	-	2	0	C6orf132	42182375	0.939000	0.31865	0.444000	0.26895	0.647000	0.38526	1.345000	0.33953	0.602000	0.29896	0.650000	0.86243	CCC	.		0.652	C6orf132-001	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000040548.2	NM_001164446	
ATP13A3	79572	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	3	194169221	194169221	+	Missense_Mutation	SNP	G	G	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr3:194169221G>A	ENST00000439040.1	-	12	1906	c.1115C>T	c.(1114-1116)aCt>aTt	p.T372I	ATP13A3_ENST00000256031.4_Missense_Mutation_p.T372I			Q9H7F0	AT133_HUMAN	ATPase type 13A3	372						integral component of membrane (GO:0016021)|membrane (GO:0016020)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|metal ion binding (GO:0046872)			NS(2)|endometrium(3)|kidney(3)|large_intestine(2)|lung(10)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	24	all_cancers(143;6.01e-09)|Ovarian(172;0.0634)	Melanoma(1037;0.211)	OV - Ovarian serous cystadenocarcinoma(49;3.83e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;5.98e-05)		GAGTTCTCCAGTGTAGAAACG	0.343																																					p.T372I		.											.	.	.	0			c.C1115T						.						155.0	139.0	144.0					3																	194169221		1863	4102	5965	SO:0001583	missense	79572	exon11			TCTCCAGTGTAGA	AJ306929	CCDS43187.1	3q29	2010-04-20			ENSG00000133657	ENSG00000133657		"""ATPases / P-type"""	24113	protein-coding gene	gene with protein product	"""ATPase family homolog up regulated in senescence cells"""	610232				11867234	Standard	NM_024524		Approved	AFURS1	uc003fty.4	Q9H7F0	OTTHUMG00000156034	ENST00000439040.1:c.1115C>T	3.37:g.194169221G>A	ENSP00000416508:p.Thr372Ile	Somatic	56	0		WXS	Illumina HiSeq	.	79	24	NM_024524	Q8NC11|Q96KS1	Missense_Mutation	SNP	ENST00000439040.1	37	CCDS43187.1	.	.	.	.	.	.	.	.	.	.	G	15.66	2.899837	0.52227	.	.	ENSG00000133657	ENST00000439040;ENST00000256031;ENST00000310773	D;D	0.86769	-2.17;-2.17	5.55	5.55	0.83447	ATPase, P-type, ATPase-associated domain (1);ATPase,  P-type, cytoplasmic transduction domain A (1);	0.198725	0.52532	D	0.000063	D	0.84929	0.5581	L	0.43757	1.38	0.52501	D	0.999951	B	0.02656	0.0	B	0.19946	0.027	T	0.79546	-0.1759	10	0.45353	T	0.12	-4.3982	19.567	0.95397	0.0:0.0:1.0:0.0	.	372	Q9H7F0	AT133_HUMAN	I	372;372;110	ENSP00000416508:T372I;ENSP00000256031:T372I	ENSP00000256031:T372I	T	-	2	0	ATP13A3	195650510	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.166000	0.64965	2.597000	0.87782	0.650000	0.86243	ACT	.		0.343	ATP13A3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342799.2	NM_024524	
TIMM23	100287932	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	10	51592574	51592574	+	Missense_Mutation	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr10:51592574A>C	ENST00000260867.4	-	7	683	c.560T>G	c.(559-561)cTt>cGt	p.L187R	TIMM23_ENST00000485812.1_5'UTR|TIMM23_ENST00000374065.3_Missense_Mutation_p.L150R|TIMM23_ENST00000374064.3_Missense_Mutation_p.L139R	NM_006327.3	NP_006318.1	O14925	TIM23_HUMAN	translocase of inner mitochondrial membrane 23 homolog (yeast)	187					cellular protein metabolic process (GO:0044267)|protein targeting to mitochondrion (GO:0006626)	integral component of mitochondrial inner membrane (GO:0031305)|mitochondrial inner membrane (GO:0005743)|mitochondrial inner membrane presequence translocase complex (GO:0005744)|mitochondrial intermembrane space (GO:0005758)|mitochondrion (GO:0005739)	P-P-bond-hydrolysis-driven protein transmembrane transporter activity (GO:0015450)			endometrium(1)|large_intestine(1)|pancreas(1)	3						GAGGCTGGTAAGTGTTAGTCC	0.453																																					p.L187R		.											.	.	.	0			c.T560G						.						141.0	134.0	136.0					10																	51592574		2203	4300	6503	SO:0001583	missense	100287932	exon7			CTGGTAAGTGTTA	AF030162	CCDS73091.1	10q11.21-q11.23	2010-03-17			ENSG00000138297				17312	protein-coding gene	gene with protein product		605034				10339406	Standard	NM_006327		Approved	TIM23	uc010qha.2	O14925	OTTHUMG00000018213	ENST00000260867.4:c.560T>G	10.37:g.51592574A>C	ENSP00000260867:p.Leu187Arg	Somatic	65	0		WXS	Illumina HiSeq	.	33	15	NM_006327	Q53FF8|Q5T1E6|Q6P5S5	Missense_Mutation	SNP	ENST00000260867.4	37	CCDS7238.1	.	.	.	.	.	.	.	.	.	.	A	12.69	2.014513	0.35511	.	.	ENSG00000138297	ENST00000260867;ENST00000374064;ENST00000374065	T;T;T	0.35789	1.29;1.29;1.29	5.28	4.15	0.48705	.	0.153324	0.43110	D	0.000611	T	0.58366	0.2117	M	0.81341	2.54	0.38949	D	0.9583	D;D	0.69078	0.992;0.997	D;D	0.68039	0.935;0.955	T	0.65274	-0.6208	10	0.87932	D	0	-9.3599	11.0443	0.47849	0.9275:0.0:0.0725:0.0	.	150;187	B1APJ0;O14925	.;TIM23_HUMAN	R	187;139;150	ENSP00000260867:L187R;ENSP00000363177:L139R;ENSP00000363178:L150R	ENSP00000260867:L187R	L	-	2	0	TIMM23	51262580	1.000000	0.71417	0.063000	0.19743	0.002000	0.02628	6.879000	0.75572	1.022000	0.39626	-0.371000	0.07208	CTT	.		0.453	TIMM23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048040.1	NM_006327.2	
DNAH6	1768	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	2	84930673	84930673	+	Missense_Mutation	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr2:84930673A>C	ENST00000237449.6	+	49	8224	c.8216A>C	c.(8215-8217)gAa>gCa	p.E2739A	DNAH6_ENST00000389394.3_Missense_Mutation_p.E2739A			Q9C0G6	DYH6_HUMAN	dynein, axonemal, heavy chain 6	2739	Stalk. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(2)|breast(9)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(3)|lung(14)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	57						GTGGATCAAGAAAGTGCCGAT	0.378																																					p.E2739A		.											.	.	.	0			c.A8216C						.						68.0	60.0	63.0					2																	84930673		692	1591	2283	SO:0001583	missense	1768	exon50			ATCAAGAAAGTGC	U61736	CCDS46348.1	2p11.2	2011-05-24	2006-09-04		ENSG00000115423	ENSG00000115423		"""Axonemal dyneins"""	2951	protein-coding gene	gene with protein product		603336	"""dynein, axonemal, heavy polypeptide 6"", ""dynein heavy chain-like 1"""	DNHL1		8812413	Standard	NM_001370		Approved	Dnahc6, HL-2, FLJ37357	uc010fgb.3	Q9C0G6	OTTHUMG00000128957	ENST00000237449.6:c.8216A>C	2.37:g.84930673A>C	ENSP00000237449:p.Glu2739Ala	Somatic	35	0		WXS	Illumina HiSeq	.	17	7	NM_001370	A0PJN9|B5MEE0|B7ZL99|O95493|Q53QZ1|Q53TE5|Q8N1W6|Q92861|Q96BL6|Q9H030|Q9H5E1	Missense_Mutation	SNP	ENST00000237449.6	37	CCDS46348.1	.	.	.	.	.	.	.	.	.	.	A	12.50	1.956623	0.34565	.	.	ENSG00000115423	ENST00000389394;ENST00000237449	T;T	0.77620	-1.11;-1.11	5.79	5.79	0.91817	Dynein heavy chain, coiled coil stalk (1);	.	.	.	.	T	0.62962	0.2471	N	0.16307	0.4	0.80722	D	1	B	0.15930	0.015	B	0.19946	0.027	T	0.59048	-0.7527	9	0.09843	T	0.71	.	15.1136	0.72380	1.0:0.0:0.0:0.0	.	2739	Q9C0G6	DYH6_HUMAN	A	2739	ENSP00000374045:E2739A;ENSP00000237449:E2739A	ENSP00000237449:E2739A	E	+	2	0	DNAH6	84784184	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.532000	0.81985	2.208000	0.71279	0.460000	0.39030	GAA	.		0.378	DNAH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328537.2	NM_001370	
CHEK2	11200	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	22	29130501	29130501	+	Missense_Mutation	SNP	T	T	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr22:29130501T>C	ENST00000405598.1	-	3	400	c.209A>G	c.(208-210)gAa>gGa	p.E70G	CHEK2_ENST00000382565.1_Missense_Mutation_p.E70G|CHEK2_ENST00000382566.1_Missense_Mutation_p.E70G|CHEK2_ENST00000382578.1_Missense_Mutation_p.E70G|CHEK2_ENST00000348295.3_Missense_Mutation_p.E70G|CHEK2_ENST00000402731.1_Missense_Mutation_p.E70G|CHEK2_ENST00000403642.1_Missense_Mutation_p.E70G|CHEK2_ENST00000544772.1_5'UTR|CHEK2_ENST00000328354.6_Missense_Mutation_p.E70G|CHEK2_ENST00000382580.2_Missense_Mutation_p.E70G|CHEK2_ENST00000404276.1_Missense_Mutation_p.E70G			O96017	CHK2_HUMAN	checkpoint kinase 2	70					cellular protein catabolic process (GO:0044257)|cellular response to DNA damage stimulus (GO:0006974)|DNA damage checkpoint (GO:0000077)|DNA damage induced protein phosphorylation (GO:0006975)|double-strand break repair (GO:0006302)|G2/M transition of mitotic cell cycle (GO:0000086)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|positive regulation of transcription, DNA-templated (GO:0045893)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|protein stabilization (GO:0050821)|regulation of protein catabolic process (GO:0042176)|regulation of transcription, DNA-templated (GO:0006355)|replicative senescence (GO:0090399)|response to gamma radiation (GO:0010332)|signal transduction in response to DNA damage (GO:0042770)|signal transduction involved in intra-S DNA damage checkpoint (GO:0072428)|spindle assembly involved in mitosis (GO:0090307)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)|PML body (GO:0016605)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(17)|endometrium(2)|kidney(11)|large_intestine(2)|lung(11)|ovary(1)|prostate(4)|stomach(2)	50						AGAATAGAGTTCCTGAGTGGA	0.552			F			breast		Direct reversal of damage;Other conserved DNA damage response genes																													p.E70G		.	yes	Rec		familial breast cancer	22	22q12.1	11200	CHK2 checkpoint homolog (S. pombe)		E	.	.	.	0			c.A209G						.						94.0	95.0	95.0					22																	29130501		2203	4300	6503	SO:0001583	missense	11200	exon2			TAGAGTTCCTGAG	AF086904	CCDS13843.1, CCDS13844.1, CCDS33629.1	22q12.1	2014-09-17	2011-11-11	2001-09-27	ENSG00000183765	ENSG00000183765			16627	protein-coding gene	gene with protein product		604373	"""CHK2 (checkpoint, S.pombe) homolog"", ""CHK2 checkpoint homolog (S. pombe)"""	RAD53		9836640, 10097108	Standard	NM_001257387		Approved	CDS1, CHK2, HuCds1, PP1425, bA444G7	uc003adt.1	O96017	OTTHUMG00000151023	ENST00000405598.1:c.209A>G	22.37:g.29130501T>C	ENSP00000386087:p.Glu70Gly	Somatic	52	0		WXS	Illumina HiSeq	.	17	12	NM_145862	A8K3Y9|B7ZBF3|B7ZBF4|B7ZBF5|Q6QA03|Q6QA04|Q6QA05|Q6QA06|Q6QA07|Q6QA08|Q6QA10|Q6QA11|Q6QA12|Q6QA13|Q9HBS5|Q9HCQ8|Q9UGF0|Q9UGF1	Missense_Mutation	SNP	ENST00000405598.1	37	CCDS13843.1	.	.	.	.	.	.	.	.	.	.	T	24.8	4.566118	0.86439	.	.	ENSG00000183765	ENST00000348295;ENST00000382578;ENST00000382565;ENST00000382563;ENST00000382566;ENST00000328354;ENST00000404276;ENST00000405598;ENST00000382580;ENST00000403642;ENST00000402731;ENST00000447421;ENST00000439200;ENST00000398017	T;T;T;D;T;T;T;T;T;T;T;T;D	0.94330	0.67;-0.29;-0.56;-3.4;-0.31;-0.31;-0.31;2.16;-0.29;0.67;0.15;2.16;-2.46	5.42	5.42	0.78866	.	0.169262	0.50627	D	0.000102	D	0.92182	0.7521	L	0.38175	1.15	0.50632	D	0.999888	P;P;P;P;P;D	0.53745	0.952;0.925;0.877;0.925;0.877;0.962	P;P;B;P;B;P	0.52343	0.461;0.54;0.339;0.54;0.339;0.696	D	0.90494	0.4469	10	0.23891	T	0.37	-10.427	14.9384	0.70975	0.0:0.0:0.0:1.0	.	70;70;70;70;70;70	O96017-7;O96017-4;A8JZZ5;O96017-12;O96017;O96017-9	.;.;.;.;CHK2_HUMAN;.	G	70;70;70;70;70;70;70;70;70;70;70;70;70;80	ENSP00000329012:E70G;ENSP00000372021:E70G;ENSP00000372006:E70G;ENSP00000372007:E70G;ENSP00000329178:E70G;ENSP00000385747:E70G;ENSP00000386087:E70G;ENSP00000372023:E70G;ENSP00000384919:E70G;ENSP00000384835:E70G;ENSP00000397478:E70G;ENSP00000408065:E70G;ENSP00000381099:E80G	ENSP00000329178:E70G	E	-	2	0	CHEK2	27460501	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.187000	0.65087	2.184000	0.69523	0.533000	0.62120	GAA	.		0.552	CHEK2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000321150.1	NM_001005735	
KCNH8	131096	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	3	19432012	19432012	+	Missense_Mutation	SNP	C	C	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr3:19432012C>A	ENST00000328405.2	+	6	1117	c.851C>A	c.(850-852)tCt>tAt	p.S284Y	KCNH8_ENST00000475063.1_3'UTR|KCNH8_ENST00000537696.1_5'Flank	NM_144633.2	NP_653234.2	Q96L42	KCNH8_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 8	284					potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	phosphorelay sensor kinase activity (GO:0000155)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|liver(3)|lung(37)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	77						GTCAGCAAGTCTGGCCAAGTT	0.358																																					p.S284Y	NSCLC(124;1625 1765 8018 24930 42026)	.											.	.	.	0			c.C851A						.						115.0	118.0	117.0					3																	19432012		2203	4300	6503	SO:0001583	missense	131096	exon6			GCAAGTCTGGCCA	AY053503	CCDS2632.1	3p24.3	2012-07-05			ENSG00000183960	ENSG00000183960		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	18864	protein-coding gene	gene with protein product		608260				16382104	Standard	NM_144633		Approved	Kv12.1, elk3	uc003cbk.1	Q96L42	OTTHUMG00000129891	ENST00000328405.2:c.851C>A	3.37:g.19432012C>A	ENSP00000328813:p.Ser284Tyr	Somatic	49	0		WXS	Illumina HiSeq	.	24	18	NM_144633	B7Z2I7|Q59GQ6	Missense_Mutation	SNP	ENST00000328405.2	37	CCDS2632.1	.	.	.	.	.	.	.	.	.	.	C	28.8	4.955420	0.92726	.	.	ENSG00000183960	ENST00000328405	D	0.97138	-4.26	5.78	5.78	0.91487	Ion transport (1);	0.000000	0.31747	U	0.007124	D	0.98036	0.9353	L	0.60957	1.885	0.80722	D	1	D;D	0.89917	0.998;1.0	D;D	0.83275	0.973;0.996	D	0.97766	1.0223	9	.	.	.	.	20.0085	0.97443	0.0:1.0:0.0:0.0	.	284;284	B7Z398;Q96L42	.;KCNH8_HUMAN	Y	284	ENSP00000328813:S284Y	.	S	+	2	0	KCNH8	19407016	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.818000	0.86416	2.723000	0.93209	0.650000	0.86243	TCT	.		0.358	KCNH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252139.2	NM_144633	
IL6ST	3572	hgsc.bcm.edu	37	5	55250698	55250698	+	Missense_Mutation	SNP	C	C	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr5:55250698C>T	ENST00000381298.2	-	11	1702	c.1390G>A	c.(1390-1392)Gca>Aca	p.A464T	IL6ST_ENST00000381286.3_Intron|IL6ST_ENST00000522633.2_3'UTR|IL6ST_ENST00000336909.5_Missense_Mutation_p.A464T|IL6ST_ENST00000536319.1_Intron|IL6ST_ENST00000381293.2_Intron|IL6ST_ENST00000381294.3_Intron|IL6ST_ENST00000502326.3_Missense_Mutation_p.A464T|IL6ST_ENST00000381287.4_3'UTR	NM_001190981.1|NM_002184.3|NM_175767.2	NP_001177910.1|NP_002175.2|NP_786943.1	P40189	IL6RB_HUMAN	interleukin 6 signal transducer	464	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.				ciliary neurotrophic factor-mediated signaling pathway (GO:0070120)|cytokine-mediated signaling pathway (GO:0019221)|glycogen metabolic process (GO:0005977)|interleukin-27-mediated signaling pathway (GO:0070106)|interleukin-6-mediated signaling pathway (GO:0070102)|leukemia inhibitory factor signaling pathway (GO:0048861)|negative regulation of apoptotic process (GO:0043066)|negative regulation of interleukin-6-mediated signaling pathway (GO:0070104)|oncostatin-M-mediated signaling pathway (GO:0038165)|positive regulation of acute inflammatory response (GO:0002675)|positive regulation of adaptive immune response (GO:0002821)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of cell proliferation (GO:0008284)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of Notch signaling pathway (GO:0008593)|response to cytokine (GO:0034097)|viral process (GO:0016032)	ciliary neurotrophic factor receptor complex (GO:0070110)|dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|interleukin-6 receptor complex (GO:0005896)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|oncostatin-M receptor complex (GO:0005900)|plasma membrane (GO:0005886)	ciliary neurotrophic factor receptor activity (GO:0004897)|ciliary neurotrophic factor receptor binding (GO:0005127)|growth factor binding (GO:0019838)|interleukin-11 receptor activity (GO:0004921)|interleukin-27 receptor activity (GO:0045509)|protein homodimerization activity (GO:0042803)			breast(2)|endometrium(5)|kidney(5)|large_intestine(4)|liver(2)|lung(1)|ovary(1)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	26		Lung NSC(810;8.69e-05)|Prostate(74;0.00308)|Breast(144;0.0544)|Ovarian(174;0.223)				ATACAGGGTGCTTTATCTGAT	0.398			O		hepatocellular ca																																p.A464T		.		Dom	yes		5	5q11	3572	"""interleukin 6 signal transducer (gp130, oncostatin M receptor)"""		E	.	.	.	0			c.G1390A						.						215.0	207.0	210.0					5																	55250698		2203	4300	6503	SO:0001583	missense	3572	exon11			AGGGTGCTTTATC	M57230	CCDS3971.1, CCDS47209.1, CCDS54856.1	5q11.2	2014-04-04	2014-04-04		ENSG00000134352	ENSG00000134352		"""Interleukins and interleukin receptors"", ""CD molecules"", ""Fibronectin type III domain containing"""	6021	protein-coding gene	gene with protein product	"""gp130, oncostatin M receptor"""	600694	"""interleukin 6 signal transducer (gp130, oncostatin M receptor)"""			2261637	Standard	NM_002184		Approved	GP130, CD130	uc003jqq.3	P40189	OTTHUMG00000097043	ENST00000381298.2:c.1390G>A	5.37:g.55250698C>T	ENSP00000370698:p.Ala464Thr	Somatic	77	0		WXS	Illumina HiSeq	.	80	4	NM_002184	A0N0L4|Q5FC04|Q9UQ41	Missense_Mutation	SNP	ENST00000381298.2	37	CCDS3971.1	.	.	.	.	.	.	.	.	.	.	C	6.865	0.528936	0.13127	.	.	ENSG00000134352	ENST00000381298;ENST00000336909	T;T	0.52295	0.67;0.67	5.94	-3.39	0.04868	Fibronectin, type III (3);Immunoglobulin-like fold (1);	1.794520	0.02285	N	0.069741	T	0.34193	0.0889	N	0.22421	0.69	0.09310	N	1	B;B	0.12630	0.006;0.006	B;B	0.08055	0.003;0.003	T	0.24799	-1.0150	10	0.15066	T	0.55	.	13.703	0.62620	0.2946:0.645:0.0603:0.0	.	464;464	Q17RA0;P40189	.;IL6RB_HUMAN	T	464	ENSP00000370698:A464T;ENSP00000338799:A464T	ENSP00000338799:A464T	A	-	1	0	IL6ST	55286455	0.000000	0.05858	0.000000	0.03702	0.325000	0.28411	-0.289000	0.08365	-0.403000	0.07622	-0.362000	0.07510	GCA	.		0.398	IL6ST-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000214146.3	NM_002184	
ZNF354C	30832	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	5	178506225	178506225	+	Missense_Mutation	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr5:178506225A>C	ENST00000315475.6	+	5	1098	c.792A>C	c.(790-792)agA>agC	p.R264S		NM_014594.1	NP_055409.1	Q86Y25	Z354C_HUMAN	zinc finger protein 354C	264					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|kidney(1)|large_intestine(10)|lung(13)|ovary(1)|urinary_tract(3)	30	all_cancers(89;0.00065)|all_epithelial(37;0.000153)|Renal(175;0.000159)|Lung NSC(126;0.00175)|all_lung(126;0.00309)	all_cancers(40;0.19)|all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.247)		CTCATCAGAGAATTCATACTG	0.383																																					p.R264S		.											.	.	.	0			c.A792C						.						58.0	62.0	61.0					5																	178506225		2203	4300	6503	SO:0001583	missense	30832	exon5			TCAGAGAATTCAT		CCDS4443.1	5q35	2013-01-08			ENSG00000177932	ENSG00000177932		"""Zinc fingers, C2H2-type"", ""-"""	16736	protein-coding gene	gene with protein product						10786630	Standard	NM_014594		Approved	KID3	uc003mju.3	Q86Y25	OTTHUMG00000130888	ENST00000315475.6:c.792A>C	5.37:g.178506225A>C	ENSP00000324064:p.Arg264Ser	Somatic	71	0		WXS	Illumina HiSeq	.	55	12	NM_014594	Q6P4P9|Q8NFX1	Missense_Mutation	SNP	ENST00000315475.6	37	CCDS4443.1	.	.	.	.	.	.	.	.	.	.	A	16.82	3.227680	0.58668	.	.	ENSG00000177932	ENST00000315475	T	0.02395	4.31	3.7	1.28	0.21552	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.08626	0.0214	L	0.55743	1.74	0.32373	N	0.555591	D	0.76494	0.999	D	0.69479	0.964	T	0.14392	-1.0474	9	0.72032	D	0.01	-19.838	6.4383	0.21835	0.7848:0.0:0.2151:0.0	.	264	Q86Y25	Z354C_HUMAN	S	264	ENSP00000324064:R264S	ENSP00000324064:R264S	R	+	3	2	ZNF354C	178438831	0.000000	0.05858	0.996000	0.52242	0.993000	0.82548	-0.144000	0.10280	0.152000	0.19188	0.482000	0.46254	AGA	.		0.383	ZNF354C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253473.2		
CYP2F1	1572	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	19	41633960	41633960	+	Silent	SNP	T	T	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr19:41633960T>A	ENST00000331105.2	+	10	1521	c.1449T>A	c.(1447-1449)ccT>ccA	p.P483P		NM_000774.3	NP_000765.2	P24903	CP2F1_HUMAN	cytochrome P450, family 2, subfamily F, polypeptide 1	483					naphthalene metabolic process (GO:0018931)|response to toxic substance (GO:0009636)|small molecule metabolic process (GO:0044281)|trichloroethylene metabolic process (GO:0018979)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|intracellular membrane-bounded organelle (GO:0043231)	aromatase activity (GO:0070330)|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, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen (GO:0016712)|oxygen binding (GO:0019825)			central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(4)|liver(2)|lung(11)|ovary(2)|skin(2)	29						TGCCGCGGCCTTTCCAGCTGT	0.657																																					p.P483P		.											.	.	.	0			c.T1449A						.						26.0	30.0	29.0					19																	41633960		2202	4300	6502	SO:0001819	synonymous_variant	1572	exon10			GCGGCCTTTCCAG	J02906	CCDS12572.1	19q13.1-q13.2	2008-02-05	2003-01-14		ENSG00000197446	ENSG00000197446		"""Cytochrome P450s"""	2632	protein-coding gene	gene with protein product		124070	"""cytochrome P450, subfamily IIF, polypeptide 1"""	CYP2F			Standard	NM_000774		Approved		uc002opu.1	P24903	OTTHUMG00000167412	ENST00000331105.2:c.1449T>A	19.37:g.41633960T>A		Somatic	81	0		WXS	Illumina HiSeq	.	49	23	NM_000774	A7KAU6|A7KAU7|A7KAU8|A7KAU9|A7KAV0|Q32MN5|Q8WWJ2	Silent	SNP	ENST00000331105.2	37	CCDS12572.1																																																																																			.		0.657	CYP2F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394527.2		
PLA2G4D	283748	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	15	42363325	42363325	+	Missense_Mutation	SNP	C	C	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr15:42363325C>A	ENST00000290472.3	-	17	1966	c.1872G>T	c.(1870-1872)tgG>tgT	p.W624C		NM_178034.3	NP_828848.3	Q86XP0	PA24D_HUMAN	phospholipase A2, group IVD (cytosolic)	624	PLA2c. {ECO:0000255|PROSITE- ProRule:PRU00555}.				glycerophospholipid biosynthetic process (GO:0046474)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid catabolic process (GO:0009395)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|membrane (GO:0016020)	metal ion binding (GO:0046872)|phospholipase A2 activity (GO:0004623)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(4)|lung(7)|ovary(1)|skin(2)|stomach(1)	27		all_cancers(109;6.37e-17)|all_epithelial(112;3.78e-15)|Lung NSC(122;5.01e-09)|all_lung(180;2.24e-08)|Melanoma(134;0.019)|Ovarian(310;0.143)|Colorectal(260;0.245)		OV - Ovarian serous cystadenocarcinoma(18;4.9e-17)|GBM - Glioblastoma multiforme(94;1.02e-06)		CCTGACCTGCCCAGGTGGAGA	0.647																																					p.W624C		.											.	.	.	0			c.G1872T						.						31.0	34.0	33.0					15																	42363325		2203	4297	6500	SO:0001583	missense	283748	exon17			ACCTGCCCAGGTG	AB090876	CCDS32203.1	15q14	2008-09-19				ENSG00000159337	3.1.1.4		30038	protein-coding gene	gene with protein product		612864				14709560	Standard	NM_178034		Approved	cPLA2delta	uc001zox.3	Q86XP0		ENST00000290472.3:c.1872G>T	15.37:g.42363325C>A	ENSP00000290472:p.Trp624Cys	Somatic	56	0		WXS	Illumina HiSeq	.	39	19	NM_178034	Q8N176	Missense_Mutation	SNP	ENST00000290472.3	37	CCDS32203.1	.	.	.	.	.	.	.	.	.	.	C	18.37	3.608083	0.66558	.	.	ENSG00000159337	ENST00000290472	T	0.17054	2.3	5.27	5.27	0.74061	Acyl transferase/acyl hydrolase/lysophospholipase (1);Lysophospholipase, catalytic domain (2);	0.082787	0.51477	D	0.000091	T	0.49762	0.1576	M	0.88842	2.985	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.58612	-0.7606	10	0.72032	D	0.01	-14.1271	16.6925	0.85325	0.0:1.0:0.0:0.0	.	624	Q86XP0	PA24D_HUMAN	C	624	ENSP00000290472:W624C	ENSP00000290472:W624C	W	-	3	0	PLA2G4D	40150617	1.000000	0.71417	1.000000	0.80357	0.751000	0.42716	5.158000	0.64917	2.471000	0.83476	0.655000	0.94253	TGG	.		0.647	PLA2G4D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419317.1	NM_178034	
ANKMY1	51281	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	2	241451322	241451322	+	Missense_Mutation	SNP	T	T	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr2:241451322T>C	ENST00000272972.3	-	10	2189	c.1975A>G	c.(1975-1977)Agg>Ggg	p.R659G	ANKMY1_ENST00000403283.1_Missense_Mutation_p.R597G|ANKMY1_ENST00000401804.1_Missense_Mutation_p.R748G|ANKMY1_ENST00000391987.1_Missense_Mutation_p.R659G|ANKMY1_ENST00000373320.4_Missense_Mutation_p.R429G|ANKMY1_ENST00000361678.4_Intron|ANKMY1_ENST00000373318.2_Missense_Mutation_p.R518G|ANKMY1_ENST00000406958.1_Missense_Mutation_p.R420G	NM_016552.2	NP_057636.2	Q9P2S6	ANKY1_HUMAN	ankyrin repeat and MYND domain containing 1	659							metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(5)|large_intestine(4)|lung(14)|ovary(1)|prostate(2)|skin(1)|urinary_tract(2)	30		all_epithelial(40;2.79e-15)|Breast(86;2.41e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0335)|Lung NSC(271;0.106)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;1.03e-30)|all cancers(36;4.78e-28)|OV - Ovarian serous cystadenocarcinoma(60;1.45e-14)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;7.8e-06)|Lung(119;0.00271)|LUSC - Lung squamous cell carcinoma(224;0.01)|Colorectal(34;0.0101)|COAD - Colon adenocarcinoma(134;0.0476)		AGAGCCGTCCTGCCCCCCTCC	0.682																																					p.R659G		.											.	.	.	0			c.A1975G						.						53.0	54.0	53.0					2																	241451322		2203	4300	6503	SO:0001583	missense	51281	exon10			CCGTCCTGCCCCC	AB034636	CCDS2535.1, CCDS2536.1, CCDS63184.1, CCDS63185.1, CCDS74681.1	2q37.3	2013-01-10			ENSG00000144504	ENSG00000144504		"""Zinc fingers, MYND-type"", ""Ankyrin repeat domain containing"""	20987	protein-coding gene	gene with protein product							Standard	XM_005247020		Approved	FLJ20499, ZMYND13	uc002vyz.1	Q9P2S6	OTTHUMG00000133355	ENST00000272972.3:c.1975A>G	2.37:g.241451322T>C	ENSP00000272972:p.Arg659Gly	Somatic	50	0		WXS	Illumina HiSeq	.	27	13	NM_016552	B2RB78|Q4ZFV3|Q8IYX5|Q8NDK5|Q9H0V8|Q9NX10	Missense_Mutation	SNP	ENST00000272972.3	37	CCDS2536.1	.	.	.	.	.	.	.	.	.	.	T	15.39	2.818232	0.50633	.	.	ENSG00000144504	ENST00000373318;ENST00000406958;ENST00000272972;ENST00000391987;ENST00000373320;ENST00000403283;ENST00000401804	T;T;T;T;T;T;T	0.72394	-0.19;-0.37;-0.65;-0.65;-0.37;-0.19;-0.59	3.43	-4.08	0.03963	Ankyrin repeat-containing domain (4);	0.089401	0.39834	U	0.001241	T	0.69860	0.3158	L	0.28400	0.85	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;0.999;1.0;1.0	D;D;D;D;D	0.91635	0.999;0.996;0.996;0.998;0.999	T	0.68051	-0.5511	10	0.48119	T	0.1	-34.3722	11.6184	0.51102	0.0:0.0:0.6935:0.3065	.	659;429;518;420;659	Q4ZFV3;Q9P2S6-4;Q6GPI0;B5MBY4;Q9P2S6	.;.;.;.;ANKY1_HUMAN	G	518;420;659;659;429;597;748	ENSP00000362415:R518G;ENSP00000384555:R420G;ENSP00000272972:R659G;ENSP00000375847:R659G;ENSP00000362417:R429G;ENSP00000383968:R597G;ENSP00000385887:R748G	ENSP00000272972:R659G	R	-	1	2	ANKMY1	241099995	0.817000	0.29147	0.861000	0.33841	0.600000	0.36913	-0.066000	0.11598	-0.791000	0.04486	0.377000	0.23210	AGG	.		0.682	ANKMY1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000257187.2	NM_017844	
PHF3	23469	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	6	64416712	64416712	+	Silent	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr6:64416712A>C	ENST00000262043.3	+	13	3997	c.3657A>C	c.(3655-3657)gcA>gcC	p.A1219A	PHF3_ENST00000393387.1_Silent_p.A1219A			Q92576	PHF3_HUMAN	PHD finger protein 3	1219					multicellular organismal development (GO:0007275)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	zinc ion binding (GO:0008270)			breast(7)|cervix(2)|endometrium(8)|kidney(7)|large_intestine(18)|lung(21)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(6)	75	all_cancers(3;0.0241)|all_epithelial(2;0.00306)|Lung NSC(77;0.121)		LUSC - Lung squamous cell carcinoma(74;0.0644)|Lung(124;0.148)			CTTCTGTGGCAAAATTTGTTA	0.418																																					p.A1219A	GBM(135;136 1820 29512 34071 46235)	.											.	.	.	0			c.A3657C						.						145.0	135.0	138.0					6																	64416712		2203	4300	6503	SO:0001819	synonymous_variant	23469	exon12			TGTGGCAAAATTT	AF091622	CCDS4966.1	6q12	2013-09-24			ENSG00000118482	ENSG00000118482		"""Zinc fingers, PHD-type"""	8921	protein-coding gene	gene with protein product		607789				11856869	Standard	XM_005248701		Approved		uc003pep.1	Q92576	OTTHUMG00000014952	ENST00000262043.3:c.3657A>C	6.37:g.64416712A>C		Somatic	94	0		WXS	Illumina HiSeq	.	72	19	NM_015153	A3KFI8|Q14CR5|Q5CZI1|Q5T1T6|Q9NQ16|Q9UI45	Silent	SNP	ENST00000262043.3	37	CCDS4966.1	.	.	.	.	.	.	.	.	.	.	A	10.80	1.452448	0.26074	.	.	ENSG00000118482	ENST00000505138	.	.	.	5.66	3.24	0.37175	.	.	.	.	.	T	0.46521	0.1397	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.42832	-0.9428	4	.	.	.	-19.8802	9.8078	0.40803	0.8593:0.0:0.1407:0.0	.	.	.	.	P	8	.	.	Q	+	2	0	PHF3	64474671	0.982000	0.34865	1.000000	0.80357	0.994000	0.84299	0.373000	0.20484	0.926000	0.37118	0.402000	0.26972	CAA	.		0.418	PHF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041086.2		
TAS2R9	50835	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	12	10962389	10962389	+	Missense_Mutation	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr12:10962389T>G	ENST00000240691.2	-	1	378	c.286A>C	c.(286-288)Agt>Cgt	p.S96R	TAS2R8_ENST00000240615.2_5'Flank	NM_023917.2	NP_076406.1	Q9NYW1	TA2R9_HUMAN	taste receptor, type 2, member 9	96					detection of chemical stimulus involved in sensory perception of taste (GO:0050912)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	taste receptor activity (GO:0008527)			endometrium(1)|kidney(1)|large_intestine(4)|lung(7)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17						AACCAGAGACTTGAATTATTG	0.388																																					p.S96R		.											.	.	.	0			c.A286C						.						98.0	95.0	96.0					12																	10962389		2203	4300	6503	SO:0001583	missense	50835	exon1			AGAGACTTGAATT	AF227135	CCDS8633.1	12p13	2012-08-22			ENSG00000121381	ENSG00000121381		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	14917	protein-coding gene	gene with protein product		604795				10761934, 10766242	Standard	NM_023917		Approved	T2R9, TRB6	uc001qyx.3	Q9NYW1	OTTHUMG00000168507	ENST00000240691.2:c.286A>C	12.37:g.10962389T>G	ENSP00000240691:p.Ser96Arg	Somatic	66	0		WXS	Illumina HiSeq	.	54	19	NM_023917	Q502V7|Q50KT0|Q50KT1|Q645W9	Missense_Mutation	SNP	ENST00000240691.2	37	CCDS8633.1	.	.	.	.	.	.	.	.	.	.	T	15.94	2.979958	0.53827	.	.	ENSG00000121381	ENST00000240691	T	0.55588	0.51	3.86	2.65	0.31530	GPCR, rhodopsin-like superfamily (1);	0.081973	0.45606	U	0.000359	T	0.75369	0.3840	M	0.93550	3.43	0.09310	N	1	D	0.76494	0.999	D	0.77004	0.989	T	0.66646	-0.5871	10	0.87932	D	0	.	8.5848	0.33651	0.0:0.0:0.1951:0.8049	.	96	Q9NYW1	TA2R9_HUMAN	R	96	ENSP00000240691:S96R	ENSP00000240691:S96R	S	-	1	0	TAS2R9	10853656	0.003000	0.15002	0.001000	0.08648	0.289000	0.27227	1.440000	0.35024	0.617000	0.30160	0.473000	0.43528	AGT	.		0.388	TAS2R9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399933.1		
HNRNPU	3192	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	245019773	245019773	+	Missense_Mutation	SNP	A	A	T	rs111577008		TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr1:245019773A>T	ENST00000283179.9	-	10	2061	c.1898T>A	c.(1897-1899)gTc>gAc	p.V633D	HNRNPU-AS1_ENST00000489705.1_RNA|HNRNPU-AS1_ENST00000475997.1_RNA|HNRNPU_ENST00000444376.2_Missense_Mutation_p.V614D			Q00839	HNRPU_HUMAN	heterogeneous nuclear ribonucleoprotein U (scaffold attachment factor A)	633					CRD-mediated mRNA stabilization (GO:0070934)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|osteoblast differentiation (GO:0001649)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|CRD-mediated mRNA stability complex (GO:0070937)|cytoplasmic ribonucleoprotein granule (GO:0036464)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			NS(1)|endometrium(2)|large_intestine(1)|lung(10)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20	all_cancers(71;6.97e-06)|all_epithelial(71;0.000104)|all_neural(11;0.0269)|Breast(184;0.0545)|Glioma(6;0.0724)|Ovarian(71;0.0761)|all_lung(81;0.0989)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.00868)			CATTTTGAGGACCGCATGTTC	0.363																																					p.V633D	NSCLC(33;911 1010 3329 23631 49995)	.											.	.	.	0			c.T1898A						.						186.0	190.0	189.0					1																	245019773		2203	4299	6502	SO:0001583	missense	3192	exon10			TTGAGGACCGCAT	X65488	CCDS31081.1, CCDS41479.1	1q44	2011-10-24		2007-08-16	ENSG00000153187	ENSG00000153187			5048	protein-coding gene	gene with protein product		602869		HNRPU		7509195, 8068679	Standard	NM_031844		Approved	SAF-A, hnRNPU	uc001iaz.1	Q00839	OTTHUMG00000040396	ENST00000283179.9:c.1898T>A	1.37:g.245019773A>T	ENSP00000283179:p.Val633Asp	Somatic	56	0		WXS	Illumina HiSeq	.	107	49	NM_031844	O75507|Q8N174|Q96HY9|Q9BQ09	Missense_Mutation	SNP	ENST00000283179.9	37	CCDS41479.1	.	.	.	.	.	.	.	.	.	.	A	24.8	4.567295	0.86439	.	.	ENSG00000153187	ENST00000444376;ENST00000283179;ENST00000427948	T;T	0.47528	0.84;0.84	5.79	5.79	0.91817	.	0.208574	0.42682	D	0.000676	T	0.65984	0.2744	L	0.60067	1.865	0.80722	D	1	D;D;D;D	0.89917	0.995;0.999;1.0;0.996	P;D;D;P	0.81914	0.879;0.986;0.995;0.897	T	0.68689	-0.5342	10	0.87932	D	0	-10.321	16.1299	0.81422	1.0:0.0:0.0:0.0	.	558;614;633;357	B3KX72;Q00839-2;Q00839;Q5RI19	.;.;HNRPU_HUMAN;.	D	614;633;558	ENSP00000393151:V614D;ENSP00000283179:V633D	ENSP00000283179:V633D	V	-	2	0	HNRNPU	243086396	1.000000	0.71417	0.995000	0.50966	0.990000	0.78478	9.282000	0.95840	2.215000	0.71742	0.528000	0.53228	GTC	.		0.363	HNRNPU-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000097163.3	NM_031844	
PAOX	196743	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	10	135193724	135193724	+	Missense_Mutation	SNP	T	T	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr10:135193724T>C	ENST00000278060.5	+	2	486	c.403T>C	c.(403-405)Tac>Cac	p.Y135H	PAOX_ENST00000480071.2_Missense_Mutation_p.Y135H|PAOX_ENST00000368539.4_Intron|AL360181.1_ENST00000597657.1_5'Flank|PAOX_ENST00000368535.2_3'UTR|PAOX_ENST00000357296.3_Missense_Mutation_p.Y135H	NM_152911.2	NP_690875.1	Q6QHF9	PAOX_HUMAN	polyamine oxidase (exo-N4-amino)	273					cellular nitrogen compound metabolic process (GO:0034641)|oxidation-reduction process (GO:0055114)|polyamine biosynthetic process (GO:0006596)|polyamine catabolic process (GO:0006598)|polyamine metabolic process (GO:0006595)|positive regulation of spermidine biosynthetic process (GO:1901307)|putrescine biosynthetic process (GO:0009446)|putrescine catabolic process (GO:0009447)|small molecule metabolic process (GO:0044281)|spermidine catabolic process (GO:0046203)|spermine catabolic process (GO:0046208)|xenobiotic metabolic process (GO:0006805)	peroxisomal matrix (GO:0005782)	N(1),N(12)-diacetylspermine:oxygen oxidoreductase (3-acetamidopropanal-forming) activity (GO:0052899)|N1-acetylspermidine:oxygen oxidoreductase (3-acetamidopropanal-forming) activity (GO:0052904)|N1-acetylspermine:oxygen oxidoreductase (3-acetamidopropanal-forming) activity (GO:0052903)|polyamine oxidase activity (GO:0046592)|receptor binding (GO:0005102)|spermidine:oxygen oxidoreductase (3-aminopropanal-forming) activity (GO:0052902)|spermine:oxygen oxidoreductase (spermidine-forming) activity (GO:0052901)			cervix(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(13)|ovary(1)|urinary_tract(2)	23		all_cancers(35;1.14e-09)|all_epithelial(44;5.79e-08)|Lung NSC(174;0.00263)|all_lung(145;0.0039)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.172)|Glioma(114;0.203)		all cancers(32;4.39e-07)|OV - Ovarian serous cystadenocarcinoma(35;1.21e-06)|Epithelial(32;1.94e-06)		GACTCTGTTCTACGGCCTGAT	0.677																																					p.Y135H		.											.	.	.	0			c.T403C						.						40.0	40.0	40.0					10																	135193724		2200	4298	6498	SO:0001583	missense	196743	exon2			CTGTTCTACGGCC	BC032778	CCDS7682.1, CCDS7683.1, CCDS7684.1	10q26.3	2003-11-13			ENSG00000148832	ENSG00000148832			20837	protein-coding gene	gene with protein product		615853				12660232	Standard	NM_207127		Approved	PAO	uc001lmv.3	Q6QHF9	OTTHUMG00000019318	ENST00000278060.5:c.403T>C	10.37:g.135193724T>C	ENSP00000278060:p.Tyr135His	Somatic	77	0		WXS	Illumina HiSeq	.	43	21	NM_207128	D3DXI6|Q5VWY0|Q6QHF5|Q6QHF6|Q6QHF7|Q6QHF8|Q6QHG0|Q6QHG1|Q6QHG2|Q6QHG3|Q6QHG4|Q6QHG5|Q6QHG6|Q86WP9|Q8N555|Q8NCX3	Missense_Mutation	SNP	ENST00000278060.5	37	CCDS7683.1	.	.	.	.	.	.	.	.	.	.	T	3.500	-0.102086	0.06967	.	.	ENSG00000148832	ENST00000368542;ENST00000278060;ENST00000357296;ENST00000480071;ENST00000368534	T;T;T	0.09445	2.98;2.98;2.98	4.88	3.75	0.43078	.	0.737030	0.13512	N	0.382425	T	0.09069	0.0224	L	0.41027	1.25	0.50813	D	0.999898	B;B;B	0.18461	0.028;0.005;0.015	B;B;B	0.15484	0.013;0.012;0.009	T	0.12967	-1.0527	10	0.16420	T	0.52	-13.718	8.6814	0.34212	0.0:0.0922:0.0:0.9078	.	135;135;135	Q6QHF9-5;Q6QHF9-4;Q6QHF9-2	.;.;.	H	135;135;135;135;6	ENSP00000278060:Y135H;ENSP00000349847:Y135H;ENSP00000435514:Y135H	ENSP00000278060:Y135H	Y	+	1	0	PAOX	135043714	0.000000	0.05858	0.161000	0.22692	0.203000	0.24098	-0.032000	0.12266	0.722000	0.32252	0.460000	0.39030	TAC	.		0.677	PAOX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051146.2	NM_152911	
ITPR2	3709	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	12	26816634	26816634	+	Missense_Mutation	SNP	T	T	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr12:26816634T>A	ENST00000381340.3	-	15	2113	c.1697A>T	c.(1696-1698)gAt>gTt	p.D566V		NM_002223.2	NP_002214.2	Q14571	ITPR2_HUMAN	inositol 1,4,5-trisphosphate receptor, type 2	566					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|cellular response to cAMP (GO:0071320)|cellular response to ethanol (GO:0071361)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|regulation of insulin secretion (GO:0050796)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	cell cortex (GO:0005938)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet dense tubular network membrane (GO:0031095)|receptor complex (GO:0043235)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion transmembrane transporter activity (GO:0015085)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|phosphatidylinositol binding (GO:0035091)		ETV6/ITPR2(2)	biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(20)|liver(1)|lung(51)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	125	Colorectal(261;0.0847)				Caffeine(DB00201)	TTTCCGGTAATCCTGCTGCGA	0.463																																					p.D566V		.											.	.	.	0			c.A1697T						.						234.0	236.0	235.0					12																	26816634		1866	4103	5969	SO:0001583	missense	3709	exon15			CGGTAATCCTGCT	D26350	CCDS41764.1	12p11.23	2014-07-18	2011-04-28		ENSG00000123104	ENSG00000123104		"""Ion channels / Inositol triphosphate receptors"""	6181	protein-coding gene	gene with protein product	"""cilia and flagella associated protein 48"""	600144	"""inositol 1,4,5-triphosphate receptor, type 2"""			8081734	Standard	XM_006719064		Approved	IP3R2, CFAP48	uc001rhg.3	Q14571	OTTHUMG00000169181	ENST00000381340.3:c.1697A>T	12.37:g.26816634T>A	ENSP00000370744:p.Asp566Val	Somatic	100	0		WXS	Illumina HiSeq	.	46	20	NM_002223	O94773	Missense_Mutation	SNP	ENST00000381340.3	37	CCDS41764.1	.	.	.	.	.	.	.	.	.	.	T	19.54	3.846275	0.71603	.	.	ENSG00000123104	ENST00000381340	D	0.90788	-2.73	4.57	4.57	0.56435	Intracellular calcium-release channel (1);	0.000000	0.85682	D	0.000000	D	0.95341	0.8488	M	0.84683	2.71	0.80722	D	1	D	0.69078	0.997	D	0.77557	0.99	D	0.95884	0.8901	10	0.66056	D	0.02	.	14.4356	0.67279	0.0:0.0:0.0:1.0	.	566	Q14571	ITPR2_HUMAN	V	566	ENSP00000370744:D566V	ENSP00000370744:D566V	D	-	2	0	ITPR2	26707901	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	6.114000	0.71560	2.058000	0.61347	0.533000	0.62120	GAT	.		0.463	ITPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402732.1	NM_002223	
NLRP8	126205	hgsc.bcm.edu;bcgsc.ca	37	19	56467321	56467321	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr19:56467321G>T	ENST00000291971.3	+	3	1968	c.1897G>T	c.(1897-1899)Gtc>Ttc	p.V633F	NLRP8_ENST00000590542.1_Missense_Mutation_p.V633F	NM_176811.2	NP_789781.2	Q86W28	NALP8_HUMAN	NLR family, pyrin domain containing 8	633					neuron death (GO:0070997)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)			breast(4)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(14)|ovary(5)|skin(2)|stomach(3)|upper_aerodigestive_tract(2)	35		Colorectal(82;0.000147)|Ovarian(87;0.17)		GBM - Glioblastoma multiforme(193;0.0695)		TCATAAAGTTGTCTTGAGAAT	0.463																																					p.V633F		.											.	.	.	0			c.G1897T						.						124.0	116.0	119.0					19																	56467321		2203	4300	6503	SO:0001583	missense	126205	exon3			AAAGTTGTCTTGA	AY154463	CCDS12937.1	19q13.43	2008-02-05	2006-12-08	2006-12-08		ENSG00000179709		"""Nucleotide-binding domain and leucine rich repeat containing"""	22940	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 8"""	609659	"""NACHT, leucine rich repeat and PYD containing 8"""	NALP8		12563287	Standard	NM_176811		Approved	NOD16, PAN4, CLR19.2	uc002qmh.3	Q86W28		ENST00000291971.3:c.1897G>T	19.37:g.56467321G>T	ENSP00000291971:p.Val633Phe	Somatic	94	0		WXS	Illumina HiSeq	.	54	4	NM_176811	Q7RTR4	Missense_Mutation	SNP	ENST00000291971.3	37	CCDS12937.1	.	.	.	.	.	.	.	.	.	.	G	10.66	1.413205	0.25465	.	.	ENSG00000179709	ENST00000291971	D	0.87571	-2.27	2.03	-3.94	0.04130	.	.	.	.	.	T	0.81631	0.4863	L	0.46157	1.445	0.09310	N	1	P;B	0.42785	0.79;0.08	P;B	0.44990	0.466;0.029	T	0.72481	-0.4280	9	0.54805	T	0.06	.	4.7461	0.13038	0.2735:0.2128:0.5137:0.0	.	633;633	Q86W28-2;Q86W28	.;NALP8_HUMAN	F	633	ENSP00000291971:V633F	ENSP00000291971:V633F	V	+	1	0	NLRP8	61159133	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-3.168000	0.00574	-1.137000	0.02888	-0.507000	0.04495	GTC	.		0.463	NLRP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457462.1	NM_176811	
RTP4	64108	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	3	187088734	187088734	+	Missense_Mutation	SNP	A	A	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr3:187088734A>T	ENST00000259030.2	+	2	424	c.314A>T	c.(313-315)gAg>gTg	p.E105V		NM_022147.2	NP_071430.2	Q96DX8	RTP4_HUMAN	receptor (chemosensory) transporter protein 4	105					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|protein targeting to membrane (GO:0006612)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|large_intestine(2)|lung(5)|skin(1)	11	all_cancers(143;4.66e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;5.56e-18)	GBM - Glioblastoma multiforme(93;0.0269)		GAGATGCCTGAGTTCTCCTCG	0.517																																					p.E105V		.											.	.	.	0			c.A314T						.						66.0	62.0	64.0					3																	187088734		2203	4300	6503	SO:0001583	missense	64108	exon2			TGCCTGAGTTCTC	BC013161	CCDS33910.1	3q27.3	2014-02-20	2006-11-21		ENSG00000136514	ENSG00000136514		"""Receptor transporter proteins"""	23992	protein-coding gene	gene with protein product	"""zinc finger, 3CxxC-type 4"""	609350	"""receptor transporter protein 4"""			16271481, 15550249, 16720576	Standard	NM_022147		Approved	IFRG28, Z3CXXC4	uc003frm.3	Q96DX8	OTTHUMG00000156459	ENST00000259030.2:c.314A>T	3.37:g.187088734A>T	ENSP00000259030:p.Glu105Val	Somatic	47	0		WXS	Illumina HiSeq	.	25	4	NM_022147	Q9H4F3	Missense_Mutation	SNP	ENST00000259030.2	37	CCDS33910.1	.	.	.	.	.	.	.	.	.	.	A	12.57	1.976224	0.34848	.	.	ENSG00000136514	ENST00000259030	T	0.22743	1.94	4.09	1.53	0.23141	.	1.196400	0.05679	N	0.590022	T	0.44456	0.1294	M	0.72894	2.215	0.09310	N	1	D	0.89917	1.0	D	0.77004	0.989	T	0.14337	-1.0476	10	0.48119	T	0.1	-8.0091	8.1328	0.31037	0.5927:0.4073:0.0:0.0	.	105	Q96DX8	RTP4_HUMAN	V	105	ENSP00000259030:E105V	ENSP00000259030:E105V	E	+	2	0	RTP4	188571428	0.000000	0.05858	0.027000	0.17364	0.457000	0.32468	-0.064000	0.11636	0.329000	0.23460	0.533000	0.62120	GAG	.		0.517	RTP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344260.1	NM_022147	
PSG5	5673	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	19	43690496	43690496	+	Missense_Mutation	SNP	G	G	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr19:43690496G>A	ENST00000366175.3	-	1	192	c.62C>T	c.(61-63)aCa>aTa	p.T21I	PSG5_ENST00000404580.1_Missense_Mutation_p.T21I|PSG5_ENST00000599812.1_Missense_Mutation_p.T21I|PSG5_ENST00000407356.1_Missense_Mutation_p.T21I|PSG5_ENST00000401992.1_5'UTR|PSG5_ENST00000342951.6_Missense_Mutation_p.T21I|PSG5_ENST00000407568.1_Missense_Mutation_p.T21I			Q15238	PSG5_HUMAN	pregnancy specific beta-1-glycoprotein 5	21					female pregnancy (GO:0007565)	extracellular region (GO:0005576)				breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(18)|prostate(1)|skin(6)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	35		Prostate(69;0.00899)				CTCCTCACCTGTGAGCAGGAG	0.577																																					p.T21I		.											.	.	.	0			c.C62T						.						85.0	85.0	85.0					19																	43690496		2203	4292	6495	SO:0001583	missense	5673	exon1			TCACCTGTGAGCA		CCDS12617.1	19q13.2	2013-01-29			ENSG00000204941	ENSG00000204941		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9522	protein-coding gene	gene with protein product	"""pregnancy-specific beta-1 glycoprotein"", ""pregnancy-specific beta 1 glycoprotein"""	176394				2735907	Standard	NM_002781		Approved	FL-NCA-3, PSG	uc002ovx.3	Q15238	OTTHUMG00000151539	ENST00000366175.3:c.62C>T	19.37:g.43690496G>A	ENSP00000382334:p.Thr21Ile	Somatic	97	0		WXS	Illumina HiSeq	.	70	26	NM_002781	Q15239|Q96QJ1|Q9UQ75	Missense_Mutation	SNP	ENST00000366175.3	37	CCDS12617.1	.	.	.	.	.	.	.	.	.	.	N	12.52	1.963046	0.34659	.	.	ENSG00000204941	ENST00000366175;ENST00000407356;ENST00000407568;ENST00000342951;ENST00000404580;ENST00000401992	T;T;T;T;T	0.01495	5.12;5.12;4.83;5.12;5.1	1.41	1.41	0.22369	.	.	.	.	.	T	0.08179	0.0204	M	0.84219	2.685	0.09310	N	1	P;P;P	0.52577	0.954;0.887;0.786	D;P;P	0.65323	0.934;0.823;0.823	T	0.09400	-1.0676	9	0.66056	D	0.02	.	6.2837	0.21021	0.0:0.0:1.0:0.0	.	21;21;21	E9PC55;Q15228;Q15238	.;.;PSG5_HUMAN	I	21	ENSP00000382334:T21I;ENSP00000386008:T21I;ENSP00000386053:T21I;ENSP00000344413:T21I;ENSP00000385250:T21I	ENSP00000344413:T21I	T	-	2	0	PSG5	48382336	0.998000	0.40836	0.108000	0.21378	0.121000	0.20230	1.962000	0.40442	1.099000	0.41499	0.184000	0.17185	ACA	.		0.577	PSG5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000323055.1	NM_002781	
UNC93A	54346	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	6	167717430	167717430	+	Missense_Mutation	SNP	A	A	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr6:167717430A>G	ENST00000230256.3	+	5	824	c.649A>G	c.(649-651)Atg>Gtg	p.M217V	UNC93A_ENST00000366829.2_Missense_Mutation_p.M175V	NM_018974.3	NP_061847.2	Q86WB7	UN93A_HUMAN	unc-93 homolog A (C. elegans)	217						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(7)|lung(20)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	40		Breast(66;7.62e-05)|Ovarian(120;0.105)		OV - Ovarian serous cystadenocarcinoma(33;2.22e-20)|BRCA - Breast invasive adenocarcinoma(81;6.17e-07)|GBM - Glioblastoma multiforme(31;0.00492)		GGCTGTCCTGATGATAGCTGC	0.507																																					p.M217V		.											.	.	.	0			c.A649G						.						145.0	127.0	133.0					6																	167717430		2203	4300	6503	SO:0001583	missense	54346	exon5			GTCCTGATGATAG	AJ508812	CCDS5300.1, CCDS47515.1	6q27	2014-05-16	2001-11-28		ENSG00000112494	ENSG00000112494			12570	protein-coding gene	gene with protein product		607995	"""unc93 (C.elegans) homolog A"""			12381271	Standard	NM_001143947		Approved	dJ366N23.2, dJ366N23.1	uc003qvq.3	Q86WB7	OTTHUMG00000016021	ENST00000230256.3:c.649A>G	6.37:g.167717430A>G	ENSP00000230256:p.Met217Val	Somatic	69	0		WXS	Illumina HiSeq	.	88	28	NM_018974	B3KRP5|Q4QQJ4|Q5JZD6	Missense_Mutation	SNP	ENST00000230256.3	37	CCDS5300.1	.	.	.	.	.	.	.	.	.	.	A	3.707	-0.060415	0.07317	.	.	ENSG00000112494	ENST00000230256;ENST00000366829	T;T	0.79653	-1.24;-1.29	4.58	1.65	0.23941	Major facilitator superfamily domain, general substrate transporter (1);	0.222050	0.38326	N	0.001738	T	0.34571	0.0902	N	0.04203	-0.255	0.24154	N	0.995686	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.34976	-0.9807	10	0.32370	T	0.25	-20.7848	6.6272	0.22837	0.1466:0.6908:0.0:0.1626	.	175;217	Q4QQJ4;Q86WB7	.;UN93A_HUMAN	V	217;175	ENSP00000230256:M217V;ENSP00000355794:M175V	ENSP00000230256:M217V	M	+	1	0	UNC93A	167637420	0.997000	0.39634	0.304000	0.25085	0.004000	0.04260	1.650000	0.37292	0.323000	0.23307	-0.648000	0.03929	ATG	.		0.507	UNC93A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043125.2	NM_018974	
COL28A1	340267	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	7	7476074	7476074	+	Silent	SNP	C	C	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr7:7476074C>G	ENST00000399429.3	-	23	1952	c.1812G>C	c.(1810-1812)ggG>ggC	p.G604G		NM_001037763.2	NP_001032852.2	Q2UY09	COSA1_HUMAN	collagen, type XXVIII, alpha 1	604					cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.G604G(1)		cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(23)|prostate(1)|skin(4)|stomach(1)|urinary_tract(1)	42		Ovarian(82;0.0789)		UCEC - Uterine corpus endometrioid carcinoma (126;0.228)		ATCCAGGTATCCCAGGTCCTC	0.393																																					p.G604G		.											COL28A1,NS,carcinoma,0,1	COL28A1	0	1	Substitution - coding silent(1)	lung(1)	c.G1812C						.						126.0	121.0	123.0					7																	7476074		1851	4102	5953	SO:0001819	synonymous_variant	340267	exon23			AGGTATCCCAGGT	AJ890451	CCDS43553.1	7p21.3	2013-01-16			ENSG00000215018	ENSG00000215018		"""Collagens"""	22442	protein-coding gene	gene with protein product		609996				16330543	Standard	NM_001037763		Approved		uc003src.1	Q2UY09	OTTHUMG00000150034	ENST00000399429.3:c.1812G>C	7.37:g.7476074C>G		Somatic	90	0		WXS	Illumina HiSeq	.	69	29	NM_001037763	A4D101|A4D106|A4D107|A8MVR2|B9EGX9|Q2UY07|Q2UY08	Silent	SNP	ENST00000399429.3	37	CCDS43553.1																																																																																			.		0.393	COL28A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315899.1	NM_001037763	
PCF11	51585	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	11	82877755	82877755	+	Splice_Site	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr11:82877755A>C	ENST00000298281.4	+	5	2268	c.1816A>C	c.(1816-1818)Agc>Cgc	p.S606R		NM_015885.3	NP_056969.2	O94913	PCF11_HUMAN	PCF11 cleavage and polyadenylation factor subunit	606					gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA cleavage (GO:0006379)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	mRNA cleavage factor complex (GO:0005849)|nucleoplasm (GO:0005654)				cervix(1)|endometrium(3)|kidney(4)|large_intestine(1)|lung(22)|ovary(1)|urinary_tract(1)	33						AGAAAATAAAAGGTATGATGT	0.323																																					p.S606R		.											.	.	.	0			c.A1816C						.						71.0	75.0	74.0					11																	82877755		1668	3590	5258	SO:0001630	splice_region_variant	51585	exon5			AATAAAAGGTATG	AB020631	CCDS44689.1	11q13	2013-07-02	2013-07-02		ENSG00000165494	ENSG00000165494			30097	protein-coding gene	gene with protein product		608876	"""PCF11, cleavage and polyadenylation factor II subunit, homolog (S. cerevisiae)"", ""PCF11, cleavage and polyadenylation factor subunit, homolog (S. cerevisiae)"""			11060040	Standard	NM_015885		Approved	KIAA0824	uc001ozx.4	O94913	OTTHUMG00000167031	ENST00000298281.4:c.1817+1A>C	11.37:g.82877755A>C		Somatic	166	0		WXS	Illumina HiSeq	.	130	62	NM_015885	A6H8W7|O43671|Q6P0X8	Missense_Mutation	SNP	ENST00000298281.4	37	CCDS44689.1	.	.	.	.	.	.	.	.	.	.	A	13.18	2.161686	0.38119	.	.	ENSG00000165494	ENST00000298281;ENST00000530660;ENST00000530304	T;T;T	0.46063	1.87;0.88;0.88	5.93	5.93	0.95920	.	0.078146	0.56097	D	0.000035	T	0.27798	0.0684	N	0.19112	0.55	0.34337	D	0.688379	P;B	0.48764	0.915;0.421	B;B	0.36922	0.236;0.08	T	0.37596	-0.9699	9	.	.	.	.	16.3839	0.83495	1.0:0.0:0.0:0.0	.	606;606	E9PQ01;O94913	.;PCF11_HUMAN	R	606	ENSP00000298281:S606R;ENSP00000434540:S606R;ENSP00000431567:S606R	.	S	+	1	0	PCF11	82555403	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	6.191000	0.72063	2.258000	0.74832	0.533000	0.62120	AGC	.		0.323	PCF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392548.2	NM_015885	Missense_Mutation
EZR	7430	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	6	159208198	159208198	+	Missense_Mutation	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr6:159208198A>C	ENST00000367075.3	-	4	302	c.134T>G	c.(133-135)tTt>tGt	p.F45C	EZR_ENST00000337147.7_Missense_Mutation_p.F45C|EZR_ENST00000476189.1_5'UTR|EZR_ENST00000392177.4_Intron	NM_001111077.1	NP_001104547.1	P15311	EZRI_HUMAN	ezrin	45	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				actin filament bundle assembly (GO:0051017)|axon guidance (GO:0007411)|cytoskeletal anchoring at plasma membrane (GO:0007016)|establishment of endothelial barrier (GO:0061028)|establishment or maintenance of apical/basal cell polarity (GO:0035088)|filopodium assembly (GO:0046847)|leukocyte cell-cell adhesion (GO:0007159)|membrane to membrane docking (GO:0022614)|positive regulation of gene expression (GO:0010628)|receptor internalization (GO:0031623)|regulation of cell shape (GO:0008360)	actin cytoskeleton (GO:0015629)|actin filament (GO:0005884)|apical part of cell (GO:0045177)|apical plasma membrane (GO:0016324)|astrocyte projection (GO:0097449)|basolateral plasma membrane (GO:0016323)|cell body (GO:0044297)|cell tip (GO:0051286)|ciliary basal body (GO:0036064)|cortical cytoskeleton (GO:0030863)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|membrane (GO:0016020)|membrane raft (GO:0045121)|microspike (GO:0044393)|microvillus (GO:0005902)|microvillus membrane (GO:0031528)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|Schwann cell microvillus (GO:0097454)|T-tubule (GO:0030315)|uropod (GO:0001931)|vesicle (GO:0031982)	actin filament binding (GO:0051015)|cell adhesion molecule binding (GO:0050839)|poly(A) RNA binding (GO:0044822)		EZR/ROS1(4)	breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(2)|lung(1)|ovary(1)|prostate(2)	15		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;2.16e-17)|BRCA - Breast invasive adenocarcinoma(81;6.58e-06)		GTGGAGGCCAAAGTACCACAC	0.468			T	ROS1	NSCLC																																p.F45C		.		Dom	yes		6	6q25.3	7430	ezrin		E	.	.	.	0			c.T134G						.						133.0	122.0	126.0					6																	159208198		2203	4300	6503	SO:0001583	missense	7430	exon3			AGGCCAAAGTACC	AF187552	CCDS5258.1	6q25.3	2010-12-10	2007-11-29	2007-11-29	ENSG00000092820	ENSG00000092820		"""A-kinase anchor proteins"""	12691	protein-coding gene	gene with protein product	"""cytovillin 2"""	123900	"""villin 2 (ezrin)"""	VIL2			Standard	NM_003379		Approved		uc003qrt.4	P15311	OTTHUMG00000015917	ENST00000367075.3:c.134T>G	6.37:g.159208198A>C	ENSP00000356042:p.Phe45Cys	Somatic	43	0		WXS	Illumina HiSeq	.	33	20	NM_003379	E1P5A8|P23714|Q4VX75|Q96CU8|Q9NSJ4	Missense_Mutation	SNP	ENST00000367075.3	37	CCDS5258.1	.	.	.	.	.	.	.	.	.	.	A	22.4	4.286577	0.80803	.	.	ENSG00000092820	ENST00000337147;ENST00000367075	D;D	0.87256	-2.23;-2.23	5.12	5.12	0.69794	FERM, N-terminal (1);Band 4.1 domain (1);FERM domain (1);	0.000000	0.85682	D	0.000000	D	0.95689	0.8598	H	0.99225	4.475	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.96595	0.9440	10	0.87932	D	0	.	10.9219	0.47169	0.8598:0.0:0.0:0.1402	.	45	P15311	EZRI_HUMAN	C	45	ENSP00000338934:F45C;ENSP00000356042:F45C	ENSP00000338934:F45C	F	-	2	0	EZR	159128186	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.076000	0.76806	2.139000	0.66308	0.533000	0.62120	TTT	.		0.468	EZR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042878.1	NM_003379	
KMT2A	4297	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	11	118365076	118365076	+	Missense_Mutation	SNP	A	A	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr11:118365076A>T	ENST00000389506.5	+	17	5243	c.5243A>T	c.(5242-5244)aAa>aTa	p.K1748I	KMT2A_ENST00000534358.1_Missense_Mutation_p.K1751I|KMT2A_ENST00000354520.4_Missense_Mutation_p.K1710I			Q03164	KMT2A_HUMAN	lysine (K)-specific methyltransferase 2A	1748	Bromo; divergent. {ECO:0000255|PROSITE- ProRule:PRU00035}.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|DNA methylation (GO:0006306)|embryonic hemopoiesis (GO:0035162)|histone H3-K4 methylation (GO:0051568)|histone H3-K4 trimethylation (GO:0080182)|histone H4-K16 acetylation (GO:0043984)|negative regulation of cell proliferation (GO:0008285)|positive regulation of cellular response to drug (GO:2001040)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transporter activity (GO:0032411)|protein complex assembly (GO:0006461)|regulation of histone H3-K4 methylation (GO:0051569)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|histone methyltransferase complex (GO:0035097)|MLL1 complex (GO:0071339)|nucleus (GO:0005634)	AT DNA binding (GO:0003680)|chromatin binding (GO:0003682)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|identical protein binding (GO:0042802)|lysine-acetylated histone binding (GO:0070577)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|unmethylated CpG binding (GO:0045322)|zinc ion binding (GO:0008270)										CCAGAAATTAAAAAAGCCAAC	0.333																																					p.K1751I		.											.	.	.	0			c.A5252T						.						120.0	106.0	110.0					11																	118365076		2200	4296	6496	SO:0001583	missense	4297	exon17			AAATTAAAAAAGC	L04284	CCDS31686.1, CCDS55791.1	11q23	2014-09-17	2013-05-09	2013-05-09	ENSG00000118058	ENSG00000118058		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	7132	protein-coding gene	gene with protein product		159555	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog)"", ""myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila)"""	MLL		1720549	Standard	NM_001197104		Approved	TRX1, HRX, ALL-1, HTRX1, CXXC7, MLL1A		Q03164	OTTHUMG00000166337	ENST00000389506.5:c.5243A>T	11.37:g.118365076A>T	ENSP00000374157:p.Lys1748Ile	Somatic	61	0		WXS	Illumina HiSeq	.	30	18	NM_001197104	E9PQG7|Q13743|Q13744|Q14845|Q16364|Q59FF2|Q6UBD1|Q9HBJ3|Q9UD94|Q9UMA3	Missense_Mutation	SNP	ENST00000389506.5	37	CCDS31686.1	.	.	.	.	.	.	.	.	.	.	A	18.19	3.569952	0.65765	.	.	ENSG00000118058	ENST00000534358;ENST00000389506;ENST00000354520;ENST00000359313	T;T;T	0.40476	1.03;1.03;1.03	6.07	6.07	0.98685	Bromodomain (4);	0.046649	0.85682	D	0.000000	T	0.48572	0.1507	N	0.14661	0.345	0.58432	D	0.999998	D;D	0.71674	0.997;0.998	D;D	0.68943	0.961;0.915	T	0.55879	-0.8071	10	0.72032	D	0.01	.	16.6406	0.85098	1.0:0.0:0.0:0.0	.	1751;1748	E9PQG7;Q03164	.;MLL1_HUMAN	I	1751;1748;1710;658	ENSP00000436786:K1751I;ENSP00000374157:K1748I;ENSP00000346516:K1710I	ENSP00000346516:K1710I	K	+	2	0	MLL	117870286	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	6.679000	0.74513	2.326000	0.78906	0.533000	0.62120	AAA	.		0.333	KMT2A-015	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399085.2	NM_005933	
MPDZ	8777	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	9	13190124	13190124	+	Missense_Mutation	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr9:13190124A>C	ENST00000319217.7	-	16	2390	c.2143T>G	c.(2143-2145)Tta>Gta	p.L715V	MPDZ_ENST00000541718.1_Missense_Mutation_p.L715V|MPDZ_ENST00000536827.1_Missense_Mutation_p.L715V|MPDZ_ENST00000381022.2_Missense_Mutation_p.L715V|MPDZ_ENST00000381015.4_Missense_Mutation_p.L715V|MPDZ_ENST00000447879.1_Missense_Mutation_p.L715V|MPDZ_ENST00000546205.1_Missense_Mutation_p.L715V	NM_001261406.1	NP_001248335.1	O75970	MPDZ_HUMAN	multiple PDZ domain protein	715	PDZ 5. {ECO:0000255|PROSITE- ProRule:PRU00143}.				cell adhesion (GO:0007155)|myelination (GO:0042552)|viral process (GO:0016032)	apical plasma membrane (GO:0016324)|apicolateral plasma membrane (GO:0016327)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|neuron projection (GO:0043005)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)|tight junction (GO:0005923)	protein C-terminus binding (GO:0008022)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(14)|lung(15)|ovary(5)|prostate(7)|stomach(1)|urinary_tract(2)	61				GBM - Glioblastoma multiforme(50;2.03e-06)		TGATAATCTAAAATGCTAAAA	0.378																																					p.L715V		.											.	.	.	0			c.T2143G						.						59.0	55.0	57.0					9																	13190124		1908	4125	6033	SO:0001583	missense	8777	exon16			AATCTAAAATGCT	AF093419	CCDS47951.1, CCDS59119.1, CCDS59120.1	9p23	2008-05-15			ENSG00000107186	ENSG00000107186			7208	protein-coding gene	gene with protein product		603785					Standard	NM_003829		Approved	MUPP1	uc003zlb.4	O75970	OTTHUMG00000021031	ENST00000319217.7:c.2143T>G	9.37:g.13190124A>C	ENSP00000320006:p.Leu715Val	Somatic	51	0		WXS	Illumina HiSeq	.	36	16	NM_003829	A6NLC2|B2RTS3|B7ZMI4|O43798|Q4LE30|Q5CZ80|Q5JTX3|Q5JTX6|Q5JTX7|Q5JUC3|Q5JUC4|Q5VZ62|Q8N790	Missense_Mutation	SNP	ENST00000319217.7	37		.	.	.	.	.	.	.	.	.	.	A	17.60	3.429925	0.62844	.	.	ENSG00000107186	ENST00000319217;ENST00000541718;ENST00000381022;ENST00000536827;ENST00000447879;ENST00000381015;ENST00000399902;ENST00000546205	T;T;T;T;T;T;T	0.24538	1.85;1.85;1.85;1.85;1.85;1.85;1.85	6.07	6.07	0.98685	.	0.000000	0.36972	N	0.002318	T	0.33440	0.0863	N	0.11756	0.17	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.998;0.998	T	0.22977	-1.0201	10	0.30854	T	0.27	.	16.3141	0.82909	1.0:0.0:0.0:0.0	.	715;715;715	B7ZMI4;O75970-3;O75970-2	.;.;.	V	715;715;715;715;715;715;665;715	ENSP00000320006:L715V;ENSP00000439807:L715V;ENSP00000370410:L715V;ENSP00000444151:L715V;ENSP00000415208:L715V;ENSP00000370403:L715V;ENSP00000446358:L715V	ENSP00000320006:L715V	L	-	1	2	MPDZ	13180124	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.094000	0.41719	2.326000	0.78906	0.533000	0.62120	TTA	.		0.378	MPDZ-001	KNOWN	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000055485.2	NM_003829	
ABCA17P	650655	hgsc.bcm.edu	37	16	2416852	2416852	+	RNA	SNP	G	G	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr16:2416852G>A	ENST00000469908.1	+	0	665					NR_003574.1				ATP-binding cassette, sub-family A (ABC1), member 17, pseudogene																		GCCAGTGTGGGCATCCTTCAT	0.498																																					.		.											.	.	.	0			.						.																																					650655	.			GTGTGGGCATCCT	DQ266102		16p13.3	2012-03-14	2010-03-12		ENSG00000238098	ENSG00000238098		"""ATP binding cassette transporters / subfamily A"""	32972	pseudogene	pseudogene						16968533	Standard	NR_003574		Approved		uc002cqc.1		OTTHUMG00000154348		16.37:g.2416852G>A		Somatic	26	0		WXS	Illumina HiSeq	.	17	9	.		RNA	SNP	ENST00000469908.1	37																																																																																				.		0.498	ABCA17P-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000334904.1	NR_003574	
PHF7	51533	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	3	52441997	52441997	+	5'Flank	SNP	A	A	C	rs113802540		TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr3:52441997A>C	ENST00000327906.3	+	0	0				BAP1_ENST00000460680.1_Missense_Mutation_p.F118V|BAP1_ENST00000296288.5_Missense_Mutation_p.F118V	NM_016483.4	NP_057567.3	Q9BWX1	PHF7_HUMAN	PHD finger protein 7							Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	zinc ion binding (GO:0008270)			breast(2)|large_intestine(4)|lung(3)	9				BRCA - Breast invasive adenocarcinoma(193;1.71e-05)|Kidney(197;0.00178)|KIRC - Kidney renal clear cell carcinoma(197;0.00201)|OV - Ovarian serous cystadenocarcinoma(275;0.0275)		CCCTTGGTGAAGTCCTTCATG	0.582																																					p.F118V		.											.	.	.	0			c.T352G						.						63.0	56.0	58.0					3																	52441997		2203	4300	6503	SO:0001631	upstream_gene_variant	8314	exon5			TGGTGAAGTCCTT	AY014283	CCDS2854.1, CCDS2855.1	3p21.31	2013-01-28			ENSG00000010318	ENSG00000010318		"""Zinc fingers, PHD-type"""	18458	protein-coding gene	gene with protein product						11042152, 11829468	Standard	NM_016483		Approved	NYD-SP6, HSPC226	uc003ddy.3	Q9BWX1	OTTHUMG00000158495		3.37:g.52441997A>C	Exception_encountered	Somatic	44	0		WXS	Illumina HiSeq	.	14	12	NM_004656	K4DI82	Missense_Mutation	SNP	ENST00000327906.3	37	CCDS2854.1	.	.	.	.	.	.	.	.	.	.	A	33	5.197747	0.94997	.	.	ENSG00000163930	ENST00000460680;ENST00000296288;ENST00000470173	T;T;T	0.56776	0.44;0.44;0.44	5.49	5.49	0.81192	Peptidase C12, ubiquitin carboxyl-terminal hydrolase 1 (3);	0.000000	0.85682	D	0.000000	T	0.71913	0.3396	M	0.83852	2.665	0.80722	D	1	D	0.56521	0.976	P	0.60012	0.867	T	0.76476	-0.2945	10	0.59425	D	0.04	-3.2432	15.5817	0.76448	1.0:0.0:0.0:0.0	.	118	Q92560	BAP1_HUMAN	V	118;118;39	ENSP00000417132:F118V;ENSP00000296288:F118V;ENSP00000417776:F39V	ENSP00000296288:F118V	F	-	1	0	BAP1	52417037	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.047000	0.93823	2.092000	0.63282	0.459000	0.35465	TTC	.		0.582	PHF7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351155.1	NM_016483	
NID1	4811	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	236175345	236175345	+	Splice_Site	SNP	T	T	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr1:236175345T>C	ENST00000264187.6	-	12	2487		c.e12-2		NID1_ENST00000366595.3_Intron	NM_002508.2	NP_002499.2	P14543	NID1_HUMAN	nidogen 1						basement membrane organization (GO:0071711)|cell-matrix adhesion (GO:0007160)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glomerular basement membrane development (GO:0032836)|positive regulation of cell-substrate adhesion (GO:0010811)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|cell periphery (GO:0071944)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|laminin binding (GO:0043236)|proteoglycan binding (GO:0043394)			breast(4)|endometrium(9)|kidney(1)|large_intestine(23)|lung(20)|pancreas(1)|prostate(4)|skin(3)|urinary_tract(1)	66	Ovarian(103;0.0544)|Breast(184;0.23)	all_cancers(173;0.00491)|Prostate(94;0.184)|Acute lymphoblastic leukemia(190;0.229)	OV - Ovarian serous cystadenocarcinoma(106;0.00162)		Urokinase(DB00013)	CATCTACATCTGTAAAACAGC	0.478																																					.		.											.	.	.	0			c.2405-2A>G						.						82.0	72.0	75.0					1																	236175345		2203	4300	6503	SO:0001630	splice_region_variant	4811	exon13			TACATCTGTAAAA	BC045606	CCDS1608.1	1q43	2011-05-08	2005-06-02	2005-06-02	ENSG00000116962	ENSG00000116962			7821	protein-coding gene	gene with protein product		131390	"""nidogen (enactin)"""	NID		2471408, 7557988	Standard	NM_002508		Approved	entactin	uc001hxo.3	P14543	OTTHUMG00000040071	ENST00000264187.6:c.2405-2A>G	1.37:g.236175345T>C		Somatic	21	0		WXS	Illumina HiSeq	.	31	16	NM_002508	Q14942|Q59FL2|Q5TAF2|Q5TAF3|Q86XD7	Splice_Site	SNP	ENST00000264187.6	37	CCDS1608.1	.	.	.	.	.	.	.	.	.	.	T	25.3	4.626823	0.87560	.	.	ENSG00000116962	ENST00000264187	.	.	.	5.77	5.77	0.91146	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.0773	0.72087	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	NID1	234241968	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.270000	0.78493	2.182000	0.69389	0.528000	0.53228	.	.		0.478	NID1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096647.2	NM_002508	Intron
RAB11B	9230	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	19	8467132	8467132	+	Silent	SNP	T	T	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr19:8467132T>C	ENST00000328024.6	+	3	617	c.399T>C	c.(397-399)gcT>gcC	p.A133A	RAB11B_ENST00000594216.1_Silent_p.A133A|RAB11B_ENST00000601897.1_Silent_p.A14A	NM_004218.3	NP_004209.2	Q15907	RB11B_HUMAN	RAB11B, member RAS oncogene family	133					cellular response to acidic pH (GO:0071468)|constitutive secretory pathway (GO:0045054)|establishment of protein localization to membrane (GO:0090150)|GTP catabolic process (GO:0006184)|insulin secretion involved in cellular response to glucose stimulus (GO:0035773)|melanosome transport (GO:0032402)|receptor recycling (GO:0001881)|regulated secretory pathway (GO:0045055)|regulation of anion transport (GO:0044070)|regulation of endocytic recycling (GO:2001135)|regulation of protein localization to cell surface (GO:2000008)|retrograde transport, endosome to plasma membrane (GO:1990126)|small GTPase mediated signal transduction (GO:0007264)|transferrin transport (GO:0033572)	cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|phagocytic vesicle (GO:0045335)|recycling endosome (GO:0055037)|recycling endosome membrane (GO:0055038)|synaptic vesicle (GO:0008021)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|myosin V binding (GO:0031489)			large_intestine(2)|lung(1)|ovary(1)	4						ACCTGCGGGCTGTGCCCACTG	0.647																																					p.A133A		.											.	.	.	0			c.T399C						.						39.0	24.0	29.0					19																	8467132		2190	4283	6473	SO:0001819	synonymous_variant	9230	exon3			GCGGGCTGTGCCC	X79780	CCDS12201.1	19p13.2	2012-07-02			ENSG00000185236	ENSG00000185236		"""RAB, member RAS oncogene"""	9761	protein-coding gene	gene with protein product		604198				7811277	Standard	NM_004218		Approved	H-YPT3	uc002mju.4	Q15907		ENST00000328024.6:c.399T>C	19.37:g.8467132T>C		Somatic	26	0		WXS	Illumina HiSeq	.	17	5	NM_004218	A5YM50|B2R7I4|B4DMK0|D6W671|Q2YDT2|Q5U0I1|Q6FHR0|Q6FI42|Q8NI07	Silent	SNP	ENST00000328024.6	37	CCDS12201.1																																																																																			.		0.647	RAB11B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460343.2	NM_004218	
C15orf52	388115	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	15	40628778	40628778	+	Missense_Mutation	SNP	C	C	T	rs370895955		TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr15:40628778C>T	ENST00000559313.1	-	9	1031	c.1016G>A	c.(1015-1017)cGa>cAa	p.R339Q	C15orf52_ENST00000397536.2_Missense_Mutation_p.R129Q	NM_207380.2	NP_997263.2	Q6ZUT6	CO052_HUMAN	chromosome 15 open reading frame 52	339							poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(9)|urinary_tract(1)	19		all_cancers(109;9.35e-19)|all_epithelial(112;1.18e-15)|Lung NSC(122;2.45e-11)|all_lung(180;6.47e-10)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;9.06e-06)|Colorectal(105;0.0107)|BRCA - Breast invasive adenocarcinoma(123;0.0505)|READ - Rectum adenocarcinoma(2;0.0649)|Lung(196;0.0781)|LUAD - Lung adenocarcinoma(183;0.0841)		CTGTTACCTTCGGGCCCTGCC	0.652																																					p.R339Q		.											C15orf52,right_lower_lobe,carcinoma,0,1	C15orf52	0	0			c.G1016A						.	C	GLN/ARG	0,4406		0,0,2203	89.0	84.0	86.0		1016	5.5	1.0	15		86	1,8599	1.2+/-3.3	0,1,4299	no	missense	C15orf52	NM_207380.2	43	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	339/535	40628778	1,13005	2203	4300	6503	SO:0001583	missense	388115	exon9			TACCTTCGGGCCC	AK124643	CCDS10055.2	15q15.1	2007-06-14			ENSG00000188549	ENSG00000188549			33488	protein-coding gene	gene with protein product							Standard	NM_207380		Approved	FLJ43339	uc001zlh.4	Q6ZUT6	OTTHUMG00000129981	ENST00000559313.1:c.1016G>A	15.37:g.40628778C>T	ENSP00000453969:p.Arg339Gln	Somatic	56	0		WXS	Illumina HiSeq	.	42	18	NM_207380	B9EIQ8|Q68DG9|Q6ZTM3|Q6ZU22	Missense_Mutation	SNP	ENST00000559313.1	37	CCDS10055.2	.	.	.	.	.	.	.	.	.	.	C	34	5.339046	0.95783	0.0	1.16E-4	ENSG00000188549	ENST00000382688;ENST00000397536	T	0.45668	0.89	5.52	5.52	0.82312	.	0.000000	0.64402	D	0.000015	T	0.63379	0.2506	M	0.71581	2.175	0.44234	D	0.997078	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.996	T	0.62909	-0.6754	10	0.46703	T	0.11	.	14.9467	0.71039	0.0:1.0:0.0:0.0	.	129;339	Q6ZUT6-2;Q6ZUT6	.;CO052_HUMAN	Q	339;129	ENSP00000380670:R129Q	ENSP00000372135:R339Q	R	-	2	0	C15orf52	38416070	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.823000	0.48081	2.609000	0.88269	0.462000	0.41574	CGA	.		0.652	C15orf52-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319567.2	NM_207380	
BCLAF1	9774	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	6	136597516	136597516	+	Missense_Mutation	SNP	A	A	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr6:136597516A>G	ENST00000531224.1	-	5	1399	c.1147T>C	c.(1147-1149)Tac>Cac	p.Y383H	BCLAF1_ENST00000527536.1_Missense_Mutation_p.Y383H|BCLAF1_ENST00000530767.1_Intron|BCLAF1_ENST00000527759.1_Missense_Mutation_p.Y381H|BCLAF1_ENST00000392348.2_Missense_Mutation_p.Y381H|BCLAF1_ENST00000353331.4_Missense_Mutation_p.Y381H	NM_001077441.1|NM_014739.2	NP_001070909.1|NP_055554.1	Q9NYF8	BCLF1_HUMAN	BCL2-associated transcription factor 1	383					apoptotic process (GO:0006915)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA-templated transcription, initiation (GO:2000144)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of response to DNA damage stimulus (GO:2001022)|regulation of DNA-templated transcription in response to stress (GO:0043620)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			haematopoietic_and_lymphoid_tissue(3)|large_intestine(4)|ovary(1)|skin(1)	9	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00226)|OV - Ovarian serous cystadenocarcinoma(155;0.00331)		TCACTGAAGTAATCTAGAGCT	0.433																																					p.Y383H	Colon(142;1534 1789 5427 7063 28491)	.											.	.	.	0			c.T1147C						.						253.0	271.0	265.0					6																	136597516		2203	4299	6502	SO:0001583	missense	9774	exon5			TGAAGTAATCTAG	AF249273	CCDS5177.1, CCDS47485.1, CCDS47486.1, CCDS75525.1	6q22-q23	2007-03-02			ENSG00000029363	ENSG00000029363			16863	protein-coding gene	gene with protein product		612588				8724849, 10330179	Standard	NM_001077440		Approved	KIAA0164, BTF	uc003qgx.1	Q9NYF8	OTTHUMG00000033323	ENST00000531224.1:c.1147T>C	6.37:g.136597516A>G	ENSP00000435210:p.Tyr383His	Somatic	210	0		WXS	Illumina HiSeq	.	149	31	NM_014739	A2RU75|B7ZM58|E1P586|Q14673|Q86WU6|Q86WY0	Missense_Mutation	SNP	ENST00000531224.1	37	CCDS5177.1	.	.	.	.	.	.	.	.	.	.	A	14.63	2.591436	0.46214	.	.	ENSG00000029363	ENST00000531224;ENST00000353331;ENST00000527536;ENST00000527759;ENST00000392348;ENST00000529826	T;T;T;T;T;T	0.13778	2.56;2.56;2.56;2.56;2.56;2.56	5.53	5.53	0.82687	.	0.105052	0.42964	D	0.000627	T	0.07098	0.0180	L	0.36672	1.1	0.80722	D	1	P;P;P	0.41848	0.763;0.763;0.763	B;B;B	0.41088	0.347;0.347;0.347	T	0.30995	-0.9959	10	0.25751	T	0.34	-6.0971	15.9539	0.79865	1.0:0.0:0.0:0.0	.	381;381;383	Q9NYF8-2;Q9NYF8-3;Q9NYF8	.;.;BCLF1_HUMAN	H	383;381;383;381;381;383	ENSP00000435210:Y383H;ENSP00000229446:Y381H;ENSP00000435441:Y383H;ENSP00000434826:Y381H;ENSP00000376159:Y381H;ENSP00000431734:Y383H	ENSP00000229446:Y381H	Y	-	1	0	BCLAF1	136639209	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.178000	0.77657	2.240000	0.73641	0.528000	0.53228	TAC	.		0.433	BCLAF1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042375.2	NM_014739	
SMARCC2	6601	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	12	56578658	56578658	+	Silent	SNP	C	C	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr12:56578658C>T	ENST00000267064.4	-	5	548	c.462G>A	c.(460-462)ggG>ggA	p.G154G	SMARCC2_ENST00000550164.1_Silent_p.G154G|SMARCC2_ENST00000394023.3_Silent_p.G154G|RP11-977G19.5_ENST00000553176.1_RNA|SMARCC2_ENST00000550859.1_5'UTR|SMARCC2_ENST00000347471.4_Silent_p.G154G	NM_003075.3	NP_003066.2	Q8TAQ2	SMRC2_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 2	154					ATP-dependent chromatin remodeling (GO:0043044)|chromatin remodeling (GO:0006338)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome disassembly (GO:0006337)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase II promoter involved in forebrain neuron fate commitment (GO:0021882)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)			breast(1)|central_nervous_system(3)|endometrium(6)|kidney(3)|large_intestine(3)|lung(20)|ovary(1)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(1)	41			OV - Ovarian serous cystadenocarcinoma(18;0.123)			CCTTTAATTTCCCTAGTAGTT	0.403																																					p.G154G		.											.	.	.	0			c.G462A						.						157.0	141.0	146.0					12																	56578658		2203	4300	6503	SO:0001819	synonymous_variant	6601	exon5			TAATTTCCCTAGT	U66616	CCDS8907.1, CCDS8908.1, CCDS55835.1	12q13.2	2008-05-14				ENSG00000139613			11105	protein-coding gene	gene with protein product		601734				8804307, 9693044	Standard	NM_001130420		Approved	BAF170, Rsc8, CRACC2	uc001skb.3	Q8TAQ2	OTTHUMG00000170288	ENST00000267064.4:c.462G>A	12.37:g.56578658C>T		Somatic	92	0		WXS	Illumina HiSeq	.	63	22	NM_139067	F8VTJ5|Q59GV3|Q92923|Q96E12|Q96GY4	Silent	SNP	ENST00000267064.4	37	CCDS8907.1																																																																																			.		0.403	SMARCC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408370.1		
OGFOD1	55239	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	16	56487225	56487225	+	Missense_Mutation	SNP	T	T	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr16:56487225T>A	ENST00000566157.1	+	2	328	c.205T>A	c.(205-207)Ttc>Atc	p.F69I	NUDT21_ENST00000300291.5_5'Flank|OGFOD1_ENST00000568397.1_Missense_Mutation_p.F69I	NM_018233.3	NP_060703.3	Q8N543	OGFD1_HUMAN	2-oxoglutarate and iron-dependent oxygenase domain containing 1	69					cell proliferation (GO:0008283)|peptidyl-proline hydroxylation (GO:0019511)|protein hydroxylation (GO:0018126)|regulation of translational termination (GO:0006449)|stress granule assembly (GO:0034063)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|nucleus (GO:0005634)	iron ion binding (GO:0005506)|L-ascorbic acid binding (GO:0031418)|peptidyl-proline 3-dioxygenase activity (GO:0031544)|peptidyl-proline dioxygenase activity (GO:0031543)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|skin(1)	8					Vitamin C(DB00126)	GATCCCAAACTTCATCCAAAG	0.368																																					p.F69I		.											.	.	.	0			c.T205A						.						104.0	103.0	103.0					16																	56487225		2198	4300	6498	SO:0001583	missense	55239	exon2			CCAAACTTCATCC	BC032919	CCDS10761.2	16q12.2	2010-11-23			ENSG00000087263	ENSG00000087263			25585	protein-coding gene	gene with protein product	"""TPA1, termination and polyadenylation 1, homolog (S. cerevisiae)"""	615857				10997877	Standard	NM_018233		Approved	KIAA1612, FLJ10826, TPA1	uc002ejb.3	Q8N543	OTTHUMG00000133237	ENST00000566157.1:c.205T>A	16.37:g.56487225T>A	ENSP00000457258:p.Phe69Ile	Somatic	118	0		WXS	Illumina HiSeq	.	81	36	NM_018233	H3BUQ2|Q9H7U5|Q9H9J9|Q9HA87|Q9HCG0|Q9NVB6	Missense_Mutation	SNP	ENST00000566157.1	37	CCDS10761.2	.	.	.	.	.	.	.	.	.	.	T	16.04	3.008888	0.54361	.	.	ENSG00000087263	ENST00000336111	.	.	.	4.93	3.83	0.44106	Prolyl 4-hydroxylase, alpha subunit (1);	0.048567	0.85682	D	0.000000	T	0.70343	0.3213	M	0.70595	2.14	0.58432	D	0.999995	D	0.76494	0.999	D	0.66847	0.947	T	0.67879	-0.5556	9	0.35671	T	0.21	-28.5138	11.0	0.47600	0.0:0.0:0.1568:0.8432	.	69	Q8N543	OGFD1_HUMAN	I	69	.	ENSP00000337196:F69I	F	+	1	0	OGFOD1	55044726	1.000000	0.71417	1.000000	0.80357	0.933000	0.57130	6.525000	0.73795	0.707000	0.31934	-0.389000	0.06534	TTC	.		0.368	OGFOD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256976.3	NM_018233	
SLC25A16	8034	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	10	70243272	70243272	+	Missense_Mutation	SNP	G	G	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr10:70243272G>A	ENST00000609923.1	-	9	1014	c.916C>T	c.(916-918)Ctt>Ttt	p.L306F	SLC25A16_ENST00000539557.1_Missense_Mutation_p.L208F|SLC25A16_ENST00000265870.3_5'UTR	NM_152707.3	NP_689920.1	P16260	GDC_HUMAN	solute carrier family 25 (mitochondrial carrier), member 16	306					coenzyme biosynthetic process (GO:0009108)|pantothenate metabolic process (GO:0015939)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)	antiporter activity (GO:0015297)			endometrium(1)|large_intestine(2)|lung(3)|upper_aerodigestive_tract(1)	7						ATGTAATTAAGAGATAAACCA	0.368																																					p.L306F		.											.	.	.	0			c.C916T						.						144.0	141.0	142.0					10																	70243272		2203	4300	6503	SO:0001583	missense	8034	exon9			AATTAAGAGATAA	M31659	CCDS7280.1	10q21.3-q22.1	2014-06-17	2014-06-17		ENSG00000122912	ENSG00000122912		"""Solute carriers"""	10986	protein-coding gene	gene with protein product	"""Graves disease autoantigen"""	139080				8444471, 2575220	Standard	NM_152707		Approved	GDA, D10S105E, HGT.1, ML7	uc001joi.3	P16260	OTTHUMG00000018354	ENST00000609923.1:c.916C>T	10.37:g.70243272G>A	ENSP00000476815:p.Leu306Phe	Somatic	69	0		WXS	Illumina HiSeq	.	52	20	NM_152707	Q8N2U1	Missense_Mutation	SNP	ENST00000609923.1	37	CCDS7280.1	.	.	.	.	.	.	.	.	.	.	G	27.0	4.794539	0.90453	.	.	ENSG00000122912	ENST00000265870;ENST00000539557	T;T	0.79653	-1.29;-1.29	5.67	5.67	0.87782	Mitochondrial carrier domain (2);	0.065640	0.64402	D	0.000006	D	0.90738	0.7093	M	0.90650	3.135	0.80722	D	1	D	0.62365	0.991	D	0.70487	0.969	D	0.90674	0.4600	10	0.40728	T	0.16	-9.1114	14.9135	0.70776	0.0703:0.0:0.9297:0.0	.	306	P16260	GDC_HUMAN	F	306;208	ENSP00000265870:L306F;ENSP00000443914:L208F	ENSP00000265870:L306F	L	-	1	0	SLC25A16	69913278	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.856000	0.86956	2.682000	0.91365	0.555000	0.69702	CTT	.		0.368	SLC25A16-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048347.2		
STAG1	10274	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	3	136059372	136059372	+	Silent	SNP	A	A	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr3:136059372A>G	ENST00000383202.2	-	32	3889	c.3633T>C	c.(3631-3633)gaT>gaC	p.D1211D	STAG1_ENST00000236698.5_Silent_p.D1174D|STAG1_ENST00000536929.1_Silent_p.D795D|STAG1_ENST00000434713.2_Silent_p.D951D	NM_005862.2	NP_005853.2	Q8WVM7	STAG1_HUMAN	stromal antigen 1	1211					chromosome segregation (GO:0007059)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	cell junction (GO:0030054)|chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(16)|lung(16)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	58						CTTCATTCATATCTTCTAACT	0.388																																					p.D1211D		.											.	.	.	0			c.T3633C						.						129.0	121.0	124.0					3																	136059372		2203	4300	6503	SO:0001819	synonymous_variant	10274	exon32			ATTCATATCTTCT	Z75330	CCDS3090.1	3q22.2-q22.3	2011-08-12			ENSG00000118007	ENSG00000118007			11354	protein-coding gene	gene with protein product		604358				9305759	Standard	XM_006713471		Approved	SA-1, SCC3A	uc003era.1	Q8WVM7	OTTHUMG00000159798	ENST00000383202.2:c.3633T>C	3.37:g.136059372A>G		Somatic	64	0		WXS	Illumina HiSeq	.	53	14	NM_005862	O00539|Q6P275	Silent	SNP	ENST00000383202.2	37	CCDS3090.1																																																																																			.		0.388	STAG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357366.1	NM_005862	
MPRIP	23164	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	17	17050634	17050634	+	Splice_Site	SNP	G	G	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr17:17050634G>T	ENST00000341712.4	+	11	1208	c.1208G>T	c.(1207-1209)tGg>tTg	p.W403L	MPRIP_ENST00000444976.1_Splice_Site_p.W365L|MPRIP_ENST00000395811.5_Splice_Site_p.W403L|MPRIP_ENST00000395804.3_Splice_Site_p.W403L			Q6WCQ1	MPRIP_HUMAN	myosin phosphatase Rho interacting protein	403	PH 2. {ECO:0000255|PROSITE- ProRule:PRU00145}.					actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)				biliary_tract(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(9)|ovary(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	31						CCCCTTTAGTGGAAGAAACAC	0.557																																					p.W403L		.											.	.	.	0			c.G1208T						.						175.0	162.0	166.0					17																	17050634		2203	4300	6503	SO:0001630	splice_region_variant	23164	exon11			TTTAGTGGAAGAA	BC014102	CCDS32578.1, CCDS42268.1	17p11.2	2013-01-10			ENSG00000133030	ENSG00000133030		"""Pleckstrin homology (PH) domain containing"""	30321	protein-coding gene	gene with protein product	"""Rho interacting protein 3"""	612935				10048485	Standard	NM_201274		Approved	RHOIP3, M-RIP, p116Rip	uc002gqy.2	Q6WCQ1	OTTHUMG00000059276	ENST00000341712.4:c.1207-1G>T	17.37:g.17050634G>T		Somatic	69	0		WXS	Illumina HiSeq	.	45	21	NM_015134	Q3KQZ5|Q5FB94|Q6DHW2|Q7Z5Y2|Q8N390|Q96G40	Missense_Mutation	SNP	ENST00000341712.4	37	CCDS32578.1	.	.	.	.	.	.	.	.	.	.	G	32	5.108428	0.94292	.	.	ENSG00000133030	ENST00000444976;ENST00000395811;ENST00000395804;ENST00000341712	T;T;T;T	0.79454	-1.27;-1.27;-1.27;-1.27	5.4	5.4	0.78164	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	.	.	.	.	D	0.91576	0.7339	M	0.93328	3.405	0.80722	D	1	P;D	0.89917	0.669;1.0	P;D	0.97110	0.506;1.0	D	0.93146	0.6545	9	0.72032	D	0.01	.	19.5418	0.95277	0.0:0.0:1.0:0.0	.	403;403	Q6WCQ1-2;Q6WCQ1	.;MPRIP_HUMAN	L	365;403;403;403	ENSP00000400189:W365L;ENSP00000379156:W403L;ENSP00000379149:W403L;ENSP00000342379:W403L	ENSP00000342379:W403L	W	+	2	0	MPRIP	16991359	1.000000	0.71417	1.000000	0.80357	0.914000	0.54420	9.720000	0.98763	2.701000	0.92244	0.655000	0.94253	TGG	.		0.557	MPRIP-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000131587.1	NM_015134	Missense_Mutation
NDUFV1	4723	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	11	67378874	67378874	+	Splice_Site	SNP	G	G	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr11:67378874G>C	ENST00000322776.6	+	7	1067	c.914G>C	c.(913-915)gGg>gCg	p.G305A	NDUFV1_ENST00000532303.1_Splice_Site_p.G204A|NDUFV1_ENST00000415352.2_Splice_Site_p.G298A|DOC2GP_ENST00000495263.1_RNA|NDUFV1_ENST00000526169.1_Intron|NDUFV1_ENST00000529927.1_Splice_Site_p.G296A	NM_001166102.1|NM_007103.3	NP_001159574.1|NP_009034.2	P49821	NDUV1_HUMAN	NADH dehydrogenase (ubiquinone) flavoprotein 1, 51kDa	305					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	4 iron, 4 sulfur cluster binding (GO:0051539)|FMN binding (GO:0010181)|metal ion binding (GO:0046872)|NAD binding (GO:0051287)|NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(1)|endometrium(3)|large_intestine(2)|lung(7)|prostate(1)|skin(2)	16						GGGGCCCCAGGGGGTGTCACG	0.657																																					p.G305A		.											.	.	.	0			c.G914C						.						36.0	38.0	38.0					11																	67378874		2200	4292	6492	SO:0001630	splice_region_variant	4723	exon7			CCCCAGGGGGTGT	AF092131	CCDS8173.1, CCDS53669.1	11q13	2011-07-04	2002-08-29		ENSG00000167792	ENSG00000167792	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7716	protein-coding gene	gene with protein product	"""complex I 51kDa subunit"", ""NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial"""	161015	"""NADH dehydrogenase (ubiquinone) flavoprotein 1 (51kD)"""			1478657	Standard	NM_007103		Approved	CI-51K	uc001omj.2	P49821	OTTHUMG00000166215	ENST00000322776.6:c.914-1G>C	11.37:g.67378874G>C		Somatic	52	0		WXS	Illumina HiSeq	.	32	15	NM_007103	O60924|O60940|Q16104|Q6IBR3|Q96BF8|Q96HS7	Missense_Mutation	SNP	ENST00000322776.6	37	CCDS8173.1	.	.	.	.	.	.	.	.	.	.	G	22.4	4.286648	0.80803	.	.	ENSG00000167792	ENST00000322776;ENST00000532303;ENST00000529927;ENST00000415352;ENST00000453836	T;T;T;T	0.70986	-0.53;-0.53;-0.53;-0.53	3.91	3.91	0.45181	Soluble ligand binding domain (1);	0.000000	0.85682	D	0.000000	D	0.89392	0.6702	H	0.98199	4.17	0.80722	D	1	D;D;D	0.76494	0.999;0.999;0.994	D;D;D	0.73708	0.981;0.971;0.968	D	0.93356	0.6722	10	0.87932	D	0	.	15.0207	0.71630	0.0:0.0:1.0:0.0	.	298;296;305	G3V0I5;P49821-2;P49821	.;.;NDUV1_HUMAN	A	305;204;296;298;176	ENSP00000322450:G305A;ENSP00000432015:G204A;ENSP00000436766:G296A;ENSP00000395368:G298A	ENSP00000322450:G305A	G	+	2	0	NDUFV1	67135450	1.000000	0.71417	0.996000	0.52242	0.963000	0.63663	7.623000	0.83113	2.173000	0.68751	0.491000	0.48974	GGG	.		0.657	NDUFV1-001	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388406.1	NM_007103	Missense_Mutation
CNN3	1266	hgsc.bcm.edu	37	1	95368727	95368727	+	Missense_Mutation	SNP	T	T	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr1:95368727T>C	ENST00000370206.4	-	3	580	c.197A>G	c.(196-198)cAg>cGg	p.Q66R	CNN3_ENST00000394202.4_Missense_Mutation_p.Q66R|CNN3_ENST00000545882.1_Missense_Mutation_p.Q25R|CNN3_ENST00000487539.1_5'UTR|CNN3_ENST00000538964.1_Missense_Mutation_p.Q66R	NM_001839.3	NP_001830.1	Q15417	CNN3_HUMAN	calponin 3, acidic	66	CH. {ECO:0000255|PROSITE- ProRule:PRU00044}.				actomyosin structure organization (GO:0031032)|epithelial cell differentiation (GO:0030855)	focal adhesion (GO:0005925)				breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(9)|prostate(1)|stomach(1)|urinary_tract(2)	18		all_lung(203;0.00206)|Lung NSC(277;0.00948)		all cancers(265;0.0325)|Epithelial(280;0.0861)		TGAGCCTGGCTGTAGCTTGTT	0.413																																					p.Q66R		.											.	.	.	0			c.A197G						.						89.0	86.0	87.0					1																	95368727		2203	4300	6503	SO:0001583	missense	1266	exon3			CCTGGCTGTAGCT	BC025372	CCDS30775.1, CCDS65592.1, CCDS65593.1	1p22-p21	2010-07-08			ENSG00000117519	ENSG00000117519			2157	protein-coding gene	gene with protein product		602374				8526917	Standard	NM_001839		Approved		uc001dqz.4	Q15417	OTTHUMG00000010783	ENST00000370206.4:c.197A>G	1.37:g.95368727T>C	ENSP00000359225:p.Gln66Arg	Somatic	121	0		WXS	Illumina HiSeq	.	22	10	NM_001839	B4DFK6|B4DP09|F8WA86|Q6FHA7	Missense_Mutation	SNP	ENST00000370206.4	37	CCDS30775.1	.	.	.	.	.	.	.	.	.	.	T	15.58	2.877036	0.51801	.	.	ENSG00000117519	ENST00000370206;ENST00000538964;ENST00000394202;ENST00000545882;ENST00000415017	D;D;D;D;D	0.94897	-3.55;-3.55;-3.55;-3.55;-3.55	5.61	5.61	0.85477	Calponin homology domain (5);	0.000000	0.85682	D	0.000000	D	0.94837	0.8332	L	0.48362	1.52	0.44221	D	0.997059	B;D	0.55800	0.096;0.973	B;D	0.79784	0.072;0.993	D	0.93849	0.7143	10	0.29301	T	0.29	-10.9227	15.8096	0.78547	0.0:0.0:0.0:1.0	.	66;66	F8WA86;Q15417	.;CNN3_HUMAN	R	66;66;66;25;25	ENSP00000359225:Q66R;ENSP00000437665:Q66R;ENSP00000377752:Q66R;ENSP00000440081:Q25R;ENSP00000401452:Q25R	ENSP00000359225:Q66R	Q	-	2	0	CNN3	95141315	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	4.782000	0.62396	2.132000	0.65825	0.533000	0.62120	CAG	.		0.413	CNN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029702.2	NM_001839	
ATP13A3	79572	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	3	194152559	194152559	+	Nonsense_Mutation	SNP	T	T	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr3:194152559T>A	ENST00000439040.1	-	22	3099	c.2308A>T	c.(2308-2310)Aaa>Taa	p.K770*	ATP13A3_ENST00000256031.4_Nonsense_Mutation_p.K770*			Q9H7F0	AT133_HUMAN	ATPase type 13A3	770						integral component of membrane (GO:0016021)|membrane (GO:0016020)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|metal ion binding (GO:0046872)			NS(2)|endometrium(3)|kidney(3)|large_intestine(2)|lung(10)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	24	all_cancers(143;6.01e-09)|Ovarian(172;0.0634)	Melanoma(1037;0.211)	OV - Ovarian serous cystadenocarcinoma(49;3.83e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;5.98e-05)		ATAATCACTTTATCCTGAGGT	0.383																																					p.K770X		.											.	.	.	0			c.A2308T						.						85.0	78.0	80.0					3																	194152559		1909	4134	6043	SO:0001587	stop_gained	79572	exon21			TCACTTTATCCTG	AJ306929	CCDS43187.1	3q29	2010-04-20			ENSG00000133657	ENSG00000133657		"""ATPases / P-type"""	24113	protein-coding gene	gene with protein product	"""ATPase family homolog up regulated in senescence cells"""	610232				11867234	Standard	NM_024524		Approved	AFURS1	uc003fty.4	Q9H7F0	OTTHUMG00000156034	ENST00000439040.1:c.2308A>T	3.37:g.194152559T>A	ENSP00000416508:p.Lys770*	Somatic	56	0		WXS	Illumina HiSeq	.	55	30	NM_024524	Q8NC11|Q96KS1	Nonsense_Mutation	SNP	ENST00000439040.1	37	CCDS43187.1	.	.	.	.	.	.	.	.	.	.	T	44	11.148052	0.99522	.	.	ENSG00000133657	ENST00000439040;ENST00000256031;ENST00000310773	.	.	.	5.71	5.71	0.89125	.	0.092234	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-8.1382	15.9856	0.80151	0.0:0.0:0.0:1.0	.	.	.	.	X	770;770;508	.	ENSP00000256031:K770X	K	-	1	0	ATP13A3	195633848	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	4.364000	0.59479	2.180000	0.69256	0.455000	0.32223	AAA	.		0.383	ATP13A3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342799.2	NM_024524	
GJA10	84694	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	6	90604202	90604202	+	Missense_Mutation	SNP	C	C	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr6:90604202C>G	ENST00000369352.1	+	1	15	c.15C>G	c.(13-15)aaC>aaG	p.N5K		NM_032602.1	NP_115991.1	P57773	CXA9_HUMAN	gap junction protein, alpha 10, 62kDa	5					cell communication (GO:0007154)	connexon complex (GO:0005922)|integral component of membrane (GO:0016021)				breast(2)|endometrium(2)|kidney(1)|large_intestine(10)|lung(17)|ovary(1)|skin(3)|urinary_tract(1)	37		all_cancers(76;5.71e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00527)		BRCA - Breast invasive adenocarcinoma(108;0.0915)		GGGACTGGAACTTATTGGGTG	0.433																																					p.N5K		.											.	.	.	0			c.C15G						.						164.0	171.0	168.0					6																	90604202		2203	4300	6503	SO:0001583	missense	84694	exon1			CTGGAACTTATTG	AF296766	CCDS5025.1	6q15-q16	2008-02-05			ENSG00000135355	ENSG00000135355		"""Ion channels / Gap junction proteins (connexins)"""	16995	protein-coding gene	gene with protein product	"""connexin 62"""	611924					Standard	NM_032602		Approved	CX62	uc011eaa.2	Q969M2	OTTHUMG00000015210	ENST00000369352.1:c.15C>G	6.37:g.90604202C>G	ENSP00000358358:p.Asn5Lys	Somatic	77	0		WXS	Illumina HiSeq	.	61	18	NM_032602	B2R722|B3KVQ2|Q5TA63|Q96KG0	Missense_Mutation	SNP	ENST00000369352.1	37	CCDS5025.1	.	.	.	.	.	.	.	.	.	.	C	16.09	3.024332	0.54683	.	.	ENSG00000135355	ENST00000369352	D	0.99014	-5.33	4.8	-1.72	0.08107	Connexin, N-terminal (1);	0.000000	0.85682	D	0.000000	D	0.97794	0.9276	L	0.40543	1.245	0.41527	D	0.988431	D	0.76494	0.999	D	0.79784	0.993	D	0.96104	0.9071	10	0.62326	D	0.03	.	10.1938	0.43043	0.0:0.4119:0.0:0.5881	.	5	Q969M2	CXA10_HUMAN	K	5	ENSP00000358358:N5K	ENSP00000358358:N5K	N	+	3	2	GJA10	90660923	0.305000	0.24481	0.940000	0.37924	0.997000	0.91878	-0.085000	0.11250	-0.258000	0.09446	0.563000	0.77884	AAC	.		0.433	GJA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041505.1	NM_032602	
TEPP	374739	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	16	58019375	58019375	+	Intron	SNP	G	G	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr16:58019375G>A	ENST00000441824.2	+	6	724				TEPP_ENST00000569996.1_Intron|TEPP_ENST00000290871.5_Missense_Mutation_p.C253Y	NM_199456.2	NP_955535.2	Q6URK8	TEPP_HUMAN	testis, prostate and placenta expressed							extracellular region (GO:0005576)				central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(3)|skin(1)|urinary_tract(1)	8						TATCCCTGCTGCCCGCCTCAG	0.682																																					p.C253Y		.											.	.	.	0			c.G758A						.						43.0	44.0	44.0					16																	58019375		2198	4300	6498	SO:0001627	intron_variant	374739	exon6			CCTGCTGCCCGCC	BC104458	CCDS10790.1, CCDS45496.1	16q13	2009-04-20			ENSG00000159648	ENSG00000159648			33745	protein-coding gene	gene with protein product		610264				14652002	Standard	NM_199456		Approved		uc002emv.4	Q6URK8	OTTHUMG00000133463	ENST00000441824.2:c.688-11G>A	16.37:g.58019375G>A		Somatic	76	0		WXS	Illumina HiSeq	.	46	16	NM_199046	Q6URK7	Missense_Mutation	SNP	ENST00000441824.2	37	CCDS45496.1	.	.	.	.	.	.	.	.	.	.	G	11.62	1.692938	0.30052	.	.	ENSG00000159648	ENST00000290871	T	0.48522	0.81	4.67	1.57	0.23409	.	1.713730	0.03374	N	0.199378	T	0.36880	0.0983	.	.	.	0.80722	D	1	P	0.46327	0.876	B	0.37888	0.26	T	0.29792	-1.0000	9	0.49607	T	0.09	-13.8937	3.7677	0.08629	0.2036:0.0:0.604:0.1924	.	253	Q6URK8-2	.	Y	253	ENSP00000290871:C253Y	ENSP00000290871:C253Y	C	+	2	0	TEPP	56576876	0.001000	0.12720	0.007000	0.13788	0.115000	0.19883	0.354000	0.20146	0.191000	0.20236	-0.311000	0.09066	TGC	.		0.682	TEPP-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000431966.1	NM_199456	
STAT1	6772	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	2	191859926	191859926	+	Missense_Mutation	SNP	T	T	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr2:191859926T>C	ENST00000361099.3	-	10	1192	c.805A>G	c.(805-807)Agt>Ggt	p.S269G	STAT1_ENST00000409465.1_Missense_Mutation_p.S269G|STAT1_ENST00000392323.2_Missense_Mutation_p.S271G|STAT1_ENST00000392322.3_Missense_Mutation_p.S269G|STAT1_ENST00000540176.1_3'UTR	NM_007315.3	NP_009330.1	P42224	STAT1_HUMAN	signal transducer and activator of transcription 1, 91kDa	269					apoptotic process (GO:0006915)|blood circulation (GO:0008015)|cellular response to insulin stimulus (GO:0032869)|cellular response to interferon-beta (GO:0035458)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|interferon-gamma-mediated signaling pathway (GO:0060333)|JAK-STAT cascade (GO:0007259)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|metanephric mesenchymal cell differentiation (GO:0072162)|metanephric mesenchymal cell proliferation involved in metanephros development (GO:0072136)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of macrophage fusion (GO:0034240)|negative regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003340)|negative regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072308)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of apoptotic process (GO:0042981)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|renal tubule development (GO:0061326)|response to cAMP (GO:0051591)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to exogenous dsRNA (GO:0043330)|response to hydrogen peroxide (GO:0042542)|response to mechanical stimulus (GO:0009612)|response to nutrient (GO:0007584)|response to peptide hormone (GO:0043434)|transcription from RNA polymerase II promoter (GO:0006366)|tumor necrosis factor-mediated signaling pathway (GO:0033209)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II core promoter sequence-specific DNA binding transcription factor activity (GO:0000983)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|tumor necrosis factor receptor binding (GO:0005164)			autonomic_ganglia(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(2)|large_intestine(6)|lung(13)|ovary(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	39			OV - Ovarian serous cystadenocarcinoma(117;0.00434)|Epithelial(96;0.0555)|all cancers(119;0.141)			TGCTGCAGACTCTCCGCAACT	0.423																																					p.S269G		.											.	.	.	0			c.A805G						.						122.0	106.0	111.0					2																	191859926		2203	4300	6503	SO:0001583	missense	6772	exon10			GCAGACTCTCCGC		CCDS2309.1, CCDS42793.1	2q32.2-q32.3	2014-09-17	2002-08-29		ENSG00000115415	ENSG00000115415		"""SH2 domain containing"""	11362	protein-coding gene	gene with protein product	"""transcription factor ISGF-3 components p91/p84"""	600555	"""signal transducer and activator of transcription 1, 91kD"""			7885841	Standard	NM_139266		Approved	STAT91, ISGF-3	uc002usj.2	P42224	OTTHUMG00000132699	ENST00000361099.3:c.805A>G	2.37:g.191859926T>C	ENSP00000354394:p.Ser269Gly	Somatic	67	0		WXS	Illumina HiSeq	.	35	11	NM_007315	A8K989|B2RCA0|D2KFR8|D3DPI7|Q53S88|Q53XW4|Q68D00|Q9UDL5	Missense_Mutation	SNP	ENST00000361099.3	37	CCDS2309.1	.	.	.	.	.	.	.	.	.	.	T	14.91	2.676398	0.47886	.	.	ENSG00000115415	ENST00000361099;ENST00000409465;ENST00000392322;ENST00000392323	T;T;T;T	0.61158	0.13;0.13;0.13;0.13	5.66	5.66	0.87406	STAT transcription factor, all-alpha (2);STAT transcription factor, coiled coil (1);	0.117089	0.85682	D	0.000000	T	0.61476	0.2350	M	0.74881	2.28	0.80722	D	1	B;B	0.24258	0.007;0.1	B;B	0.26310	0.018;0.068	T	0.62464	-0.6849	10	0.66056	D	0.02	-15.406	15.9051	0.79423	0.0:0.0:0.0:1.0	.	269;269	P42224-2;P42224	.;STAT1_HUMAN	G	269;269;269;271	ENSP00000354394:S269G;ENSP00000386244:S269G;ENSP00000376136:S269G;ENSP00000376137:S271G	ENSP00000354394:S269G	S	-	1	0	STAT1	191568171	1.000000	0.71417	1.000000	0.80357	0.758000	0.43043	4.839000	0.62810	2.151000	0.67156	0.455000	0.32223	AGT	.		0.423	STAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255997.3	NM_007315	
TTC12	54970	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	11	113230696	113230696	+	Missense_Mutation	SNP	C	C	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr11:113230696C>A	ENST00000529221.1	+	18	1685	c.1580C>A	c.(1579-1581)tCt>tAt	p.S527Y	TTC12_ENST00000393020.1_Missense_Mutation_p.S527Y|TTC12_ENST00000483239.2_Missense_Mutation_p.S533Y|TTC12_ENST00000478125.1_3'UTR|TTC12_ENST00000314756.3_Missense_Mutation_p.S527Y	NM_017868.3	NP_060338.3	Q9H892	TTC12_HUMAN	tetratricopeptide repeat domain 12	527										breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(12)|pancreas(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32		all_cancers(61;2.73e-16)|all_epithelial(67;8.64e-10)|Melanoma(852;1.46e-05)|all_hematologic(158;0.00014)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Prostate(24;0.183)|Renal(330;0.187)		BRCA - Breast invasive adenocarcinoma(274;5.3e-06)|Epithelial(105;8.37e-05)|all cancers(92;0.000694)		AGGTGCCTGTCTTTACTAAAC	0.453																																					p.S527Y		.											.	.	.	0			c.C1580A						.						82.0	73.0	76.0					11																	113230696		2200	4296	6496	SO:0001583	missense	54970	exon18			GCCTGTCTTTACT	AK000542	CCDS8360.2	11q23.2	2013-01-10			ENSG00000149292	ENSG00000149292		"""Tetratricopeptide (TTC) repeat domain containing"""	23700	protein-coding gene	gene with protein product		610732				12964006	Standard	XM_005271607		Approved	FLJ13859, FLJ20535, TPARM	uc001pnu.3	Q9H892	OTTHUMG00000142832	ENST00000529221.1:c.1580C>A	11.37:g.113230696C>A	ENSP00000433757:p.Ser527Tyr	Somatic	24	0		WXS	Illumina HiSeq	.	29	18	NM_017868	Q8N5H9|Q9NWY3	Missense_Mutation	SNP	ENST00000529221.1	37	CCDS8360.2	.	.	.	.	.	.	.	.	.	.	C	7.503	0.653070	0.14580	.	.	ENSG00000149292	ENST00000529221;ENST00000314756;ENST00000393020;ENST00000483239	T;T;T;T	0.51071	0.72;0.72;0.72;0.72	5.86	-0.752	0.11072	Armadillo-like helical (1);Armadillo-type fold (1);	1.300330	0.04602	N	0.398678	T	0.44829	0.1312	M	0.67953	2.075	0.09310	N	1	P;P	0.35411	0.5;0.5	B;B	0.33521	0.165;0.165	T	0.42699	-0.9436	10	0.66056	D	0.02	0.7299	5.7321	0.18047	0.0:0.5011:0.1259:0.373	.	527;527	A8K8G6;Q9H892	.;TTC12_HUMAN	Y	527;527;527;533	ENSP00000433757:S527Y;ENSP00000315160:S527Y;ENSP00000376743:S527Y;ENSP00000419652:S533Y	ENSP00000315160:S527Y	S	+	2	0	TTC12	112735906	0.017000	0.18338	0.006000	0.13384	0.108000	0.19459	-0.143000	0.10296	-0.103000	0.12175	-0.145000	0.13849	TCT	.		0.453	TTC12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286455.2	NM_017868	
ATF5	22809	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	19	50436094	50436094	+	Silent	SNP	C	C	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr19:50436094C>T	ENST00000423777.2	+	3	971	c.594C>T	c.(592-594)gcC>gcT	p.A198A	ATF5_ENST00000595125.1_Silent_p.A198A|CTC-326K19.6_ENST00000451973.1_Intron|MIR4751_ENST00000578027.1_RNA	NM_001193646.1	NP_001180575.1	Q9Y2D1	ATF5_HUMAN	activating transcription factor 5	198	Interaction with PTP4A1. {ECO:0000250}.				multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|negative regulation of astrocyte differentiation (GO:0048712)|olfactory bulb interneuron development (GO:0021891)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|transcription corepressor activity (GO:0003714)			NS(1)|endometrium(2)|large_intestine(1)|skin(3)	7		all_lung(116;0.00318)|all_neural(266;0.107)|Ovarian(192;0.17)		GBM - Glioblastoma multiforme(134;0.00221)|OV - Ovarian serous cystadenocarcinoma(262;0.017)	Pseudoephedrine(DB00852)	CTCGCCTGGCCCCCTACCCAC	0.672																																					p.A198A	GBM(48;768 989 9196 9511 26329)	.											.	.	.	0			c.C594T						.						32.0	24.0	27.0					19																	50436094		2202	4299	6501	SO:0001819	synonymous_variant	22809	exon4			CCTGGCCCCCTAC	AF101388	CCDS12789.1	19q13.33	2013-09-20			ENSG00000169136	ENSG00000169136		"""basic leucine zipper proteins"""	790	protein-coding gene	gene with protein product		606398				10373550	Standard	NM_012068		Approved		uc002prd.3	Q9Y2D1	OTTHUMG00000183065	ENST00000423777.2:c.594C>T	19.37:g.50436094C>T		Somatic	60	0		WXS	Illumina HiSeq	.	35	24	NM_012068	B3KND3|Q9BSA1|Q9UNQ3	Silent	SNP	ENST00000423777.2	37	CCDS12789.1																																																																																			.		0.672	ATF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464915.2		
DOC2GP	390213	hgsc.bcm.edu	37	11	67383064	67383064	+	lincRNA	SNP	G	G	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr11:67383064G>A	ENST00000533311.1	-	0	1662				DOC2GP_ENST00000495263.1_RNA																							GGCAGCAGTGGGGGCCTGGGG	0.642																																					.		.											.	.	.	0			.						.																																					390213	.			GCAGTGGGGGCCT																													11.37:g.67383064G>A		Somatic	46	0		WXS	Illumina HiSeq	.	25	10	.		RNA	SNP	ENST00000533311.1	37																																																																																				.		0.642	RP11-655M14.13-001	KNOWN	not_organism_supported|basic	lincRNA	lincRNA	OTTHUMT00000395005.1		
ACO1	48	hgsc.bcm.edu	37	9	32429463	32429463	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr9:32429463G>T	ENST00000309951.6	+	13	1669	c.1531G>T	c.(1531-1533)Ggg>Tgg	p.G511W	ACO1_ENST00000541043.1_Missense_Mutation_p.G412W|ACO1_ENST00000379923.1_Missense_Mutation_p.G511W	NM_002197.2	NP_002188.1	P21399	ACOC_HUMAN	aconitase 1, soluble	511					cellular iron ion homeostasis (GO:0006879)|citrate metabolic process (GO:0006101)|intestinal absorption (GO:0050892)|post-embryonic development (GO:0009791)|regulation of translation (GO:0006417)|response to iron(II) ion (GO:0010040)|tricarboxylic acid cycle (GO:0006099)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)	4 iron, 4 sulfur cluster binding (GO:0051539)|aconitate hydratase activity (GO:0003994)|iron-responsive element binding (GO:0030350)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)			breast(1)|endometrium(7)|kidney(5)|large_intestine(6)|lung(6)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	30			LUSC - Lung squamous cell carcinoma(29;0.00813)	GBM - Glioblastoma multiforme(74;3.94e-06)		TGGCAACAGTGGGCCTTTACC	0.463																																					p.G511W		.											.	.	.	0			c.G1531T						.						194.0	155.0	168.0					9																	32429463		2203	4300	6503	SO:0001583	missense	48	exon13			AACAGTGGGCCTT	M58510	CCDS6525.1	9p21.1	2013-05-21			ENSG00000122729	ENSG00000122729	4.2.1.3		117	protein-coding gene	gene with protein product	"""aconitate hydratase, cytoplasmic"""	100880		IREB1		2172968, 2771641	Standard	NM_002197		Approved	IRP1, IREBP	uc003zqw.4	P21399	OTTHUMG00000019740	ENST00000309951.6:c.1531G>T	9.37:g.32429463G>T	ENSP00000309477:p.Gly511Trp	Somatic	40	0		WXS	Illumina HiSeq	.	27	4	NM_002197	D3DRK7|Q14652|Q5VZA7	Missense_Mutation	SNP	ENST00000309951.6	37	CCDS6525.1	.	.	.	.	.	.	.	.	.	.	G	24.5	4.542796	0.86022	.	.	ENSG00000122729	ENST00000432017;ENST00000309951;ENST00000379923;ENST00000541043	T;T;T	0.49139	0.79;0.79;0.79	5.05	5.05	0.67936	Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha, subdomain 1/3 (1);Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha (2);	0.000000	0.85682	D	0.000000	T	0.81413	0.4817	H	0.98682	4.3	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.89186	0.3547	10	0.87932	D	0	-12.6372	17.1827	0.86858	0.0:0.0:1.0:0.0	.	547;511	Q59FI0;P21399	.;ACOC_HUMAN	W	547;511;511;412	ENSP00000309477:G511W;ENSP00000369255:G511W;ENSP00000438733:G412W	ENSP00000309477:G511W	G	+	1	0	ACO1	32419463	1.000000	0.71417	1.000000	0.80357	0.875000	0.50365	9.869000	0.99810	2.355000	0.79922	0.455000	0.32223	GGG	.		0.463	ACO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051998.3	NM_002197	
UBN2	254048	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	7	138968747	138968747	+	Silent	SNP	G	G	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr7:138968747G>A	ENST00000473989.3	+	15	3096	c.3096G>A	c.(3094-3096)tcG>tcA	p.S1032S	UBN2_ENST00000288561.8_Silent_p.S949S	NM_173569.3	NP_775840.3	Q6ZU65	UBN2_HUMAN	ubinuclein 2	1032	Ser-rich.					extracellular space (GO:0005615)|nucleus (GO:0005634)				NS(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(7)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	42						CTCCCTTCTCGATGGCTGCCT	0.542																																					p.S1032S		.											.	.	.	0			c.G3096A						.						85.0	94.0	91.0					7																	138968747		2034	4179	6213	SO:0001819	synonymous_variant	254048	exon15			CTTCTCGATGGCT	AK098644	CCDS43655.1, CCDS43655.2	7q34	2008-12-08			ENSG00000157741	ENSG00000157741			21931	protein-coding gene	gene with protein product		613841				19029251	Standard	NM_173569		Approved	FLJ25778, KIAA2030	uc011kqr.2	Q6ZU65	OTTHUMG00000157623	ENST00000473989.3:c.3096G>A	7.37:g.138968747G>A		Somatic	21	0		WXS	Illumina HiSeq	.	15	6	NM_173569	A4D1S2|Q2YDY4|Q6P1K0|Q86XN9|Q8N7D1	Silent	SNP	ENST00000473989.3	37	CCDS43655.2																																																																																			.		0.542	UBN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349272.3	NM_173569	
PPAP2A	8611	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	5	54763893	54763893	+	Missense_Mutation	SNP	A	A	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr5:54763893A>G	ENST00000307259.8	-	3	715	c.295T>C	c.(295-297)Tac>Cac	p.Y99H	PPAP2A_ENST00000264775.5_Missense_Mutation_p.Y100H|PPAP2A_ENST00000515132.1_5'UTR	NM_003711.2	NP_003702.2	O14494	LPP1_HUMAN	phosphatidic acid phosphatase type 2A	99					androgen receptor signaling pathway (GO:0030521)|germ cell migration (GO:0008354)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|lipid metabolic process (GO:0006629)|negative regulation of cell proliferation (GO:0008285)|phospholipid dephosphorylation (GO:0046839)|protein dephosphorylation (GO:0006470)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of lipid metabolic process (GO:0019216)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	phosphatidate phosphatase activity (GO:0008195)			breast(2)|endometrium(1)|large_intestine(1)|lung(2)|ovary(2)|prostate(1)	9		Lung NSC(810;4.08e-05)|Prostate(74;0.0181)|Breast(144;0.0544)				ATGGCTTTGTAAATAGTGGCT	0.403																																					p.Y100H		.											.	.	.	0			c.T298C						.						106.0	108.0	107.0					5																	54763893		2203	4300	6503	SO:0001583	missense	8611	exon3			CTTTGTAAATAGT	AB000888	CCDS34159.1, CCDS34160.1	5q11	2009-05-27			ENSG00000067113	ENSG00000067113	3.1.3.4		9228	protein-coding gene	gene with protein product		607124				9305923	Standard	NM_003711		Approved	PAP-2a, LPP1	uc003jpz.4	O14494	OTTHUMG00000162240	ENST00000307259.8:c.295T>C	5.37:g.54763893A>G	ENSP00000302229:p.Tyr99His	Somatic	55	0		WXS	Illumina HiSeq	.	48	28	NM_176895	B7ZKN8|G3XA95|O60457|O60463|Q17RZ4	Missense_Mutation	SNP	ENST00000307259.8	37	CCDS34159.1	.	.	.	.	.	.	.	.	.	.	A	24.5	4.537187	0.85812	.	.	ENSG00000067113	ENST00000264775;ENST00000307259	T;T	0.32272	1.48;1.46	5.73	5.73	0.89815	.	0.106801	0.64402	D	0.000003	T	0.66799	0.2826	M	0.93638	3.44	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	T	0.76556	-0.2916	10	0.87932	D	0	-24.7644	16.3554	0.83234	1.0:0.0:0.0:0.0	.	99;100	O14494;G3XA95	LPP1_HUMAN;.	H	100;99	ENSP00000264775:Y100H;ENSP00000302229:Y99H	ENSP00000264775:Y100H	Y	-	1	0	PPAP2A	54799650	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.910000	0.92685	2.323000	0.78572	0.467000	0.42956	TAC	.		0.403	PPAP2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368073.1		
ASH1L	55870	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	155447890	155447890	+	Missense_Mutation	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr1:155447890A>C	ENST00000368346.3	-	3	5410	c.4771T>G	c.(4771-4773)Ttc>Gtc	p.F1591V	ASH1L_ENST00000392403.3_Missense_Mutation_p.F1591V			Q9NR48	ASH1L_HUMAN	ash1 (absent, small, or homeotic)-like (Drosophila)	1591	Ser-rich.				cell-cell signaling (GO:0007267)|DNA packaging (GO:0006323)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|tight junction (GO:0005923)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|endometrium(12)|kidney(13)|large_intestine(28)|lung(39)|ovary(2)|pancreas(1)|prostate(6)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(4)	124	Hepatocellular(266;0.0997)|all_neural(408;0.129)|all_hematologic(923;0.145)		Epithelial(20;1.74e-08)|all cancers(21;3.29e-08)|BRCA - Breast invasive adenocarcinoma(34;0.021)			TTGGGAGTGAATCCTCCAAGG	0.488																																					p.F1591V		.											.	.	.	0			c.T4771G						.						93.0	94.0	94.0					1																	155447890		2203	4300	6503	SO:0001583	missense	55870	exon3			GAGTGAATCCTCC	AB037841	CCDS1113.2	1q22	2013-01-28			ENSG00000116539	ENSG00000116539		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	19088	protein-coding gene	gene with protein product		607999				10860993, 16545939	Standard	NM_018489		Approved	huASH1, ASH1, ASH1L1, KMT2H	uc001fkt.3	Q9NR48	OTTHUMG00000014011	ENST00000368346.3:c.4771T>G	1.37:g.155447890A>C	ENSP00000357330:p.Phe1591Val	Somatic	77	0		WXS	Illumina HiSeq	.	71	12	NM_018489	Q59GP1|Q5T714|Q5T715|Q9P2C7	Missense_Mutation	SNP	ENST00000368346.3	37		.	.	.	.	.	.	.	.	.	.	A	17.86	3.493690	0.64186	.	.	ENSG00000116539	ENST00000368346;ENST00000392403	D;D	0.88975	-2.44;-2.45	5.44	5.44	0.79542	.	0.074164	0.56097	D	0.000028	D	0.84474	0.5480	N	0.14661	0.345	0.80722	D	1	D;D	0.61697	0.982;0.99	P;P	0.58721	0.702;0.844	D	0.87876	0.2674	10	0.54805	T	0.06	.	15.3248	0.74150	1.0:0.0:0.0:0.0	.	1591;1591	Q9NR48;Q9NR48-2	ASH1L_HUMAN;.	V	1591	ENSP00000357330:F1591V;ENSP00000376204:F1591V	ENSP00000357330:F1591V	F	-	1	0	ASH1L	153714514	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.748000	0.62148	2.285000	0.76669	0.533000	0.62120	TTC	.		0.488	ASH1L-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000039400.1	NM_018489	
GOLGA8I	283796	hgsc.bcm.edu	37	15	23258877	23258877	+	Intron	SNP	T	T	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr15:23258877T>C	ENST00000450802.3	+	5	407					NM_001282468.1|NM_001282472.1|NM_001282484.1|NM_001282490.1|NM_001282493.1|NM_001282494.1	NP_001269397.1|NP_001269401.1|NP_001269413.1|NP_001269419.1|NP_001269422.1|NP_001269423.1	A6NC78	GOG8I_HUMAN	golgin A8 family, member I							Golgi apparatus (GO:0005794)|membrane (GO:0016020)											tctgtccttttctatcctata	0.473																																					.		.											.	.	.	0			.						.																																			SO:0001627	intron_variant	283796	.			TCCTTTTCTATCC	AK093104		15q11.2	2013-01-17	2012-10-05	2012-10-05	ENSG00000153666	ENSG00000277561			26660	other	unknown	"""FLJ35785"""		"""golgi autoantigen, golgin subfamily a, 9 pseudogene"", ""golgin A9, pseudogene"", ""golgin A8 family, member I, pseudogene"""	GOLGA9P, GOLGA8IP			Standard	NR_024074		Approved	FLJ35785	uc001yvh.1	A6NC78	OTTHUMG00000129149	ENST00000450802.3:c.310-379T>C	15.37:g.23258877T>C		Somatic	13	0		WXS	Illumina HiSeq	.	13	4	.		RNA	SNP	ENST00000450802.3	37																																																																																				.		0.473	GOLGA8I-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000251213.2	NR_024074	
NXPH4	11247	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	12	57619423	57619423	+	Missense_Mutation	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr12:57619423T>G	ENST00000349394.5	+	2	995	c.820T>G	c.(820-822)Ttc>Gtc	p.F274V	Y_RNA_ENST00000365197.1_RNA	NM_007224.3	NP_009155.1	O95158	NXPH4_HUMAN	neurexophilin 4	274	V (Cys-rich).				neuropeptide signaling pathway (GO:0007218)	extracellular region (GO:0005576)				NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|lung(2)|stomach(1)|upper_aerodigestive_tract(1)	10						TGCCAAGCCCTTCAAAGTCAT	0.572																																					p.F274V		.											.	.	.	0			c.T820G						.						58.0	65.0	62.0					12																	57619423		2203	4300	6503	SO:0001583	missense	11247	exon2			AAGCCCTTCAAAG	AF043469	CCDS8933.1	12q13.3	2014-09-04			ENSG00000182379	ENSG00000182379			8078	protein-coding gene	gene with protein product		604637				9570794	Standard	NM_007224		Approved	NPH4	uc009zpj.4	O95158	OTTHUMG00000171241	ENST00000349394.5:c.820T>G	12.37:g.57619423T>G	ENSP00000333593:p.Phe274Val	Somatic	27	0		WXS	Illumina HiSeq	.	12	7	NM_007224	A8K4I4|Q7Z6L3|Q8N462	Missense_Mutation	SNP	ENST00000349394.5	37	CCDS8933.1	.	.	.	.	.	.	.	.	.	.	T	19.36	3.812107	0.70797	.	.	ENSG00000182379	ENST00000349394	.	.	.	4.16	4.16	0.48862	.	0.000000	0.85682	D	0.000000	T	0.69415	0.3108	L	0.54323	1.7	0.58432	D	0.999997	D	0.71674	0.998	D	0.74023	0.982	T	0.72795	-0.4185	9	0.87932	D	0	-19.2694	12.3172	0.54964	0.0:0.0:0.0:1.0	.	274	O95158	NXPH4_HUMAN	V	274	.	ENSP00000333593:F274V	F	+	1	0	NXPH4	55905690	1.000000	0.71417	1.000000	0.80357	0.597000	0.36814	5.915000	0.69973	1.744000	0.51775	0.460000	0.39030	TTC	.		0.572	NXPH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412474.1	NM_007224	
CDR2L	30850	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	17	72997553	72997553	+	Missense_Mutation	SNP	G	G	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr17:72997553G>C	ENST00000337231.5	+	3	722	c.310G>C	c.(310-312)Gag>Cag	p.E104Q		NM_014603.2	NP_055418.2	Q86X02	CDR2L_HUMAN	cerebellar degeneration-related protein 2-like	104												all_lung(278;0.226)					GCTGGTGCTGGAGAGTAAGGC	0.672																																					p.E104Q		.											.	.	.	0			c.G310C						.						34.0	25.0	28.0					17																	72997553		2201	4292	6493	SO:0001583	missense	30850	exon3			GTGCTGGAGAGTA		CCDS11710.2	17q25.1	2006-03-28			ENSG00000109089	ENSG00000109089			29999	protein-coding gene	gene with protein product	"""paraneoplastic antigen"""						Standard	NM_014603		Approved	HUMPPA	uc002jml.4	Q86X02	OTTHUMG00000150435	ENST00000337231.5:c.310G>C	17.37:g.72997553G>C	ENSP00000336587:p.Glu104Gln	Somatic	57	0		WXS	Illumina HiSeq	.	22	11	NM_014603	B4DFA7|Q15175	Missense_Mutation	SNP	ENST00000337231.5	37	CCDS11710.2	.	.	.	.	.	.	.	.	.	.	G	34	5.374957	0.95923	.	.	ENSG00000109089	ENST00000337231	T	0.53423	0.62	5.08	5.08	0.68730	.	0.000000	0.85682	D	0.000000	T	0.67515	0.2901	M	0.86420	2.815	0.80722	D	1	D	0.61080	0.989	P	0.55923	0.787	T	0.68236	-0.5462	10	0.23891	T	0.37	-29.7136	18.8348	0.92157	0.0:0.0:1.0:0.0	.	104	Q86X02	CDR2L_HUMAN	Q	104	ENSP00000336587:E104Q	ENSP00000336587:E104Q	E	+	1	0	CDR2L	70509148	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	9.813000	0.99286	2.511000	0.84671	0.585000	0.79938	GAG	.		0.672	CDR2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318080.1	NM_014603	
STARD5	80765	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	15	81614763	81614763	+	Missense_Mutation	SNP	G	G	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr15:81614763G>C	ENST00000302824.6	-	3	293	c.268C>G	c.(268-270)Caa>Gaa	p.Q90E	RP11-761I4.3_ENST00000559781.1_RNA|STARD5_ENST00000559913.1_5'UTR|RP11-761I4.3_ENST00000560973.1_RNA	NM_181900.2	NP_871629.1	Q9NSY2	STAR5_HUMAN	StAR-related lipid transfer (START) domain containing 5	90	START. {ECO:0000255|PROSITE- ProRule:PRU00197}.				C21-steroid hormone biosynthetic process (GO:0006700)|lipid transport (GO:0006869)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)	cytosol (GO:0005829)	lipid binding (GO:0008289)			large_intestine(3)|ovary(1)|skin(1)|stomach(1)	6						GTGATGCTTTGGATAATTTCA	0.488																																					p.Q90E		.											.	.	.	0			c.C268G						.						148.0	126.0	134.0					15																	81614763		2203	4300	6503	SO:0001583	missense	80765	exon3			TGCTTTGGATAAT	AF480304	CCDS10318.1	15q26	2011-09-12	2007-08-16		ENSG00000172345	ENSG00000172345		"""StAR-related lipid transfer (START) domain containing"""	18065	protein-coding gene	gene with protein product		607050	"""START domain containing 5"""			12011452	Standard	NM_181900		Approved	MGC10327	uc002bgm.3	Q9NSY2	OTTHUMG00000147342	ENST00000302824.6:c.268C>G	15.37:g.81614763G>C	ENSP00000304032:p.Gln90Glu	Somatic	63	0		WXS	Illumina HiSeq	.	29	17	NM_181900	P59094	Missense_Mutation	SNP	ENST00000302824.6	37	CCDS10318.1	.	.	.	.	.	.	.	.	.	.	G	0.006	-2.020659	0.00418	.	.	ENSG00000172345	ENST00000302824	T	0.80824	-1.42	5.51	-5.63	0.02474	Lipid-binding START (3);START-like domain (1);	0.327500	0.31290	N	0.007905	T	0.56077	0.1961	N	0.03253	-0.375	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.46470	-0.9189	10	0.02654	T	1	-13.3989	24.4124	0.99990	0.0:0.5498:0.4502:0.0	.	90	Q9NSY2	STAR5_HUMAN	E	90	ENSP00000304032:Q90E	ENSP00000304032:Q90E	Q	-	1	0	STARD5	79401818	0.384000	0.25164	0.000000	0.03702	0.025000	0.11179	0.704000	0.25661	-0.828000	0.04273	-0.156000	0.13503	CAA	.		0.488	STARD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000303950.2		
HSPA8	3312	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	11	122931947	122931947	+	Missense_Mutation	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr11:122931947A>C	ENST00000532636.1	-	2	205	c.86T>G	c.(85-87)aTt>aGt	p.I29S	HSPA8_ENST00000534624.1_Missense_Mutation_p.I29S|SNORD14C_ENST00000365382.1_RNA|HSPA8_ENST00000526110.1_Missense_Mutation_p.I29S|HSPA8_ENST00000534319.1_5'Flank|SNORD14D_ENST00000384390.1_RNA|HSPA8_ENST00000453788.2_Missense_Mutation_p.I29S|HSPA8_ENST00000526862.1_5'Flank|HSPA8_ENST00000227378.3_Missense_Mutation_p.I29S|HSPA8_ENST00000533540.1_Missense_Mutation_p.I29S			P11142	HSP7C_HUMAN	heat shock 70kDa protein 8	29					ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|chaperone mediated protein folding requiring cofactor (GO:0051085)|clathrin coat disassembly (GO:0072318)|gene expression (GO:0010467)|membrane organization (GO:0061024)|mRNA metabolic process (GO:0016071)|mRNA processing (GO:0006397)|negative regulation of fibril organization (GO:1902904)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotransmitter secretion (GO:0007269)|post-Golgi vesicle-mediated transport (GO:0006892)|protein folding (GO:0006457)|protein refolding (GO:0042026)|regulation of cell cycle (GO:0051726)|response to unfolded protein (GO:0006986)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|synaptic transmission (GO:0007268)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	blood microparticle (GO:0072562)|clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane (GO:0061202)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|intracellular (GO:0005622)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|Prp19 complex (GO:0000974)|ribonucleoprotein complex (GO:0030529)|spliceosomal complex (GO:0005681)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled (GO:0042623)|enzyme binding (GO:0019899)|G-protein coupled receptor binding (GO:0001664)|heat shock protein binding (GO:0031072)|MHC class II protein complex binding (GO:0023026)|poly(A) RNA binding (GO:0044822)|ubiquitin protein ligase binding (GO:0031625)|unfolded protein binding (GO:0051082)			breast(1)|central_nervous_system(7)|endometrium(1)|kidney(9)|large_intestine(4)|lung(13)|upper_aerodigestive_tract(1)	36		Breast(109;0.00249)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0279)		ATCATTGGCAATTATCTCGAC	0.473																																					p.I29S	Colon(21;486 594 5900 6733 14272)	.											.	.	.	0			c.T86G						.						88.0	74.0	79.0					11																	122931947		2202	4299	6501	SO:0001583	missense	3312	exon2			TTGGCAATTATCT	Y00371	CCDS8440.1, CCDS44754.1	11q24.1	2011-09-02	2002-08-29		ENSG00000109971	ENSG00000109971		"""Heat shock proteins / HSP70"""	5241	protein-coding gene	gene with protein product		600816	"""heat shock 70kD protein 8"""	HSPA10		8530083, 3037489	Standard	NM_006597		Approved	HSC71, HSC70, HSP73	uc001pyo.3	P11142	OTTHUMG00000166030	ENST00000532636.1:c.86T>G	11.37:g.122931947A>C	ENSP00000437125:p.Ile29Ser	Somatic	33	0		WXS	Illumina HiSeq	.	21	13	NM_006597	Q9H3R6	Missense_Mutation	SNP	ENST00000532636.1	37	CCDS8440.1	.	.	.	.	.	.	.	.	.	.	A	25.8	4.677962	0.88445	.	.	ENSG00000109971	ENST00000532636;ENST00000533540;ENST00000534624;ENST00000453788;ENST00000227378;ENST00000526110;ENST00000525463;ENST00000525624;ENST00000534567;ENST00000527387;ENST00000532182;ENST00000524590;ENST00000530391	T;T;T;T;T;T;T;T;T;T;T;T;T	0.04758	4.78;4.78;4.78;4.78;4.78;4.78;3.56;4.78;4.78;4.78;4.78;4.78;4.78	4.42	4.42	0.53409	.	0.000000	0.85682	D	0.000000	T	0.45558	0.1348	H	0.99985	5.245	0.80722	D	1	D;D;D;D;D	0.89917	1.0;0.999;0.998;0.997;0.988	D;D;D;D;D	0.97110	1.0;0.999;0.999;0.998;0.999	T	0.74179	-0.3749	10	0.87932	D	0	-25.6586	13.9807	0.64304	1.0:0.0:0.0:0.0	.	29;29;29;29;29	B4DTX2;Q53GZ6;E7ET08;P11142-2;P11142	.;.;.;.;HSP7C_HUMAN	S	29	ENSP00000437125:I29S;ENSP00000437189:I29S;ENSP00000432083:I29S;ENSP00000404372:I29S;ENSP00000227378:I29S;ENSP00000433584:I29S;ENSP00000436762:I29S;ENSP00000435154:I29S;ENSP00000431641:I29S;ENSP00000436183:I29S;ENSP00000434415:I29S;ENSP00000434565:I29S;ENSP00000434851:I29S	ENSP00000227378:I29S	I	-	2	0	HSPA8	122437157	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	9.339000	0.96797	1.748000	0.51833	0.397000	0.26171	ATT	.		0.473	HSPA8-004	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000387515.1		
MSRB2	22921	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	10	23393156	23393156	+	Missense_Mutation	SNP	G	G	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr10:23393156G>C	ENST00000376510.3	+	2	305	c.202G>C	c.(202-204)Gaa>Caa	p.E68Q		NM_012228.3	NP_036360.3	Q9Y3D2	MSRB2_HUMAN	methionine sulfoxide reductase B2	68					actin filament polymerization (GO:0030041)|protein repair (GO:0030091)|regulation of transcription, DNA-templated (GO:0006355)|response to oxidative stress (GO:0006979)	mitochondrion (GO:0005739)	actin binding (GO:0003779)|peptide-methionine (R)-S-oxide reductase activity (GO:0033743)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(2)|lung(4)|skin(1)|urinary_tract(1)	9					L-Methionine(DB00134)	CGTCACAAGAGAAAAGGGAAC	0.488																																					p.E68Q	Esophageal Squamous(89;1240 1363 4973 30188 42299)	.											MSRB2,colon,carcinoma,0,1	MSRB2	0	0			c.G202C						.						79.0	77.0	77.0					10																	23393156		1939	4144	6083	SO:0001583	missense	22921	exon2			ACAAGAGAAAAGG	AF122004	CCDS41495.1	10p12	2004-12-07	2004-12-06	2004-12-07	ENSG00000148450	ENSG00000148450			17061	protein-coding gene	gene with protein product		613782	"""methionine sulfoxide reductase B"""	MSRB		8749308, 10375640	Standard	NM_012228		Approved	PILB, CGI-131, CBS1, CBS-1	uc001iro.3	Q9Y3D2	OTTHUMG00000017812	ENST00000376510.3:c.202G>C	10.37:g.23393156G>C	ENSP00000365693:p.Glu68Gln	Somatic	62	0		WXS	Illumina HiSeq	.	39	15	NM_012228	Q17R44|Q4G1C7|Q9Y5W6	Missense_Mutation	SNP	ENST00000376510.3	37	CCDS41495.1	.	.	.	.	.	.	.	.	.	.	G	12.91	2.080371	0.36662	.	.	ENSG00000148450	ENST00000376510	T	0.77620	-1.11	4.79	2.83	0.33086	Mss4-like (1);Methionine sulphoxide reductase B (3);	0.104020	0.64402	D	0.000006	T	0.63236	0.2494	L	0.37561	1.115	0.41138	D	0.985931	B	0.31241	0.315	B	0.33196	0.159	T	0.51803	-0.8659	10	0.09338	T	0.73	-8.1169	8.2325	0.31605	0.0:0.1724:0.6491:0.1785	.	68	Q9Y3D2	MSRB2_HUMAN	Q	68	ENSP00000365693:E68Q	ENSP00000365693:E68Q	E	+	1	0	MSRB2	23433162	1.000000	0.71417	0.269000	0.24586	0.319000	0.28217	2.297000	0.43593	0.632000	0.30432	0.557000	0.71058	GAA	.		0.488	MSRB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047205.1	NM_012228	
MCCC1	56922	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	3	182756844	182756844	+	Silent	SNP	T	T	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr3:182756844T>A	ENST00000265594.4	-	12	1493	c.1347A>T	c.(1345-1347)acA>acT	p.T449T	MCCC1_ENST00000539926.1_Silent_p.T314T|MCCC1_ENST00000489909.1_5'Flank|MCCC1_ENST00000492597.1_Silent_p.T340T	NM_020166.3	NP_064551.3	Q96RQ3	MCCA_HUMAN	methylcrotonoyl-CoA carboxylase 1 (alpha)	449	Biotin carboxylation.				biotin metabolic process (GO:0006768)|branched-chain amino acid catabolic process (GO:0009083)|cellular nitrogen compound metabolic process (GO:0034641)|leucine catabolic process (GO:0006552)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|biotin binding (GO:0009374)|biotin carboxylase activity (GO:0004075)|metal ion binding (GO:0046872)|methylcrotonoyl-CoA carboxylase activity (GO:0004485)			central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(9)|liver(1)|lung(17)|ovary(1)|pancreas(2)|prostate(1)|skin(2)	40	all_cancers(143;1.84e-14)|Ovarian(172;0.0355)		all cancers(12;1.8e-44)|Epithelial(37;3.23e-38)|LUSC - Lung squamous cell carcinoma(7;5.04e-25)|Lung(8;5.03e-23)|OV - Ovarian serous cystadenocarcinoma(80;5.07e-21)		Biotin(DB00121)	ACCTCAGTTTTGTCAATGCCG	0.507																																					p.T449T		.											.	.	.	0			c.A1347T						.						141.0	115.0	124.0					3																	182756844		2203	4300	6503	SO:0001819	synonymous_variant	56922	exon12			CAGTTTTGTCAAT	AF310972	CCDS3241.1	3q27.1	2010-04-30	2010-04-30		ENSG00000078070	ENSG00000078070	6.4.1.4		6936	protein-coding gene	gene with protein product		609010	"""methylcrotonoyl-Coenzyme A carboxylase 1 (alpha)"""			11170888	Standard	XR_241502		Approved	MCCA	uc003fle.3	Q96RQ3	OTTHUMG00000158355	ENST00000265594.4:c.1347A>T	3.37:g.182756844T>A		Somatic	47	0		WXS	Illumina HiSeq	.	58	15	NM_020166	Q59ES4|Q9H959|Q9NS97	Silent	SNP	ENST00000265594.4	37	CCDS3241.1																																																																																			.		0.507	MCCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350775.1	NM_020166	
ACVR2A	92	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	2	148676088	148676088	+	Missense_Mutation	SNP	G	G	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr2:148676088G>A	ENST00000241416.7	+	7	1525	c.889G>A	c.(889-891)Gct>Act	p.A297T	ACVR2A_ENST00000404590.1_Missense_Mutation_p.A297T|ACVR2A_ENST00000535787.1_Missense_Mutation_p.A189T	NM_001278579.1|NM_001278580.1|NM_001616.3	NP_001265508.1|NP_001265509.1|NP_001607.1	P27037	AVR2A_HUMAN	activin A receptor, type IIA	297	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activin receptor signaling pathway (GO:0032924)|anterior/posterior pattern specification (GO:0009952)|BMP signaling pathway (GO:0030509)|cellular response to BMP stimulus (GO:0071773)|determination of left/right symmetry (GO:0007368)|embryonic skeletal system development (GO:0048706)|gastrulation with mouth forming second (GO:0001702)|mesoderm development (GO:0007498)|penile erection (GO:0043084)|positive regulation of activin receptor signaling pathway (GO:0032927)|positive regulation of bone mineralization (GO:0030501)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of protein phosphorylation (GO:0001934)|regulation of BMP signaling pathway (GO:0030510)|regulation of nitric-oxide synthase activity (GO:0050999)|Sertoli cell proliferation (GO:0060011)|sperm ejaculation (GO:0042713)|spermatogenesis (GO:0007283)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|inhibin-betaglycan-ActRII complex (GO:0034673)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|coreceptor activity (GO:0015026)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|transforming growth factor beta-activated receptor activity (GO:0005024)|transmembrane receptor protein serine/threonine kinase activity (GO:0004675)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(5)|large_intestine(14)|liver(1)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(8)	45				BRCA - Breast invasive adenocarcinoma(221;0.0969)		AGAAACCATGGCTAGAGGATT	0.378																																					p.A297T		.											.	.	.	0			c.G889A						.						110.0	107.0	108.0					2																	148676088		2203	4300	6503	SO:0001583	missense	92	exon7			ACCATGGCTAGAG		CCDS33301.1, CCDS63030.1	2q22.2-q23.3	2008-02-05	2005-05-10	2005-05-10	ENSG00000121989	ENSG00000121989			173	protein-coding gene	gene with protein product		102581	"""activin A receptor, type II"""	ACVR2		1314589, 10702675	Standard	NM_001278579		Approved	ACTRII	uc002twh.3	P27037	OTTHUMG00000150603	ENST00000241416.7:c.889G>A	2.37:g.148676088G>A	ENSP00000241416:p.Ala297Thr	Somatic	87	0		WXS	Illumina HiSeq	.	35	25	NM_001616	B2RAB8|B4DWQ2|D3DP85|Q53TH4|Q6NWV2|Q92474	Missense_Mutation	SNP	ENST00000241416.7	37	CCDS33301.1	.	.	.	.	.	.	.	.	.	.	G	24.6	4.552266	0.86127	.	.	ENSG00000121989	ENST00000241416;ENST00000535787;ENST00000404590	D;D;D	0.94862	-3.54;-3.54;-3.54	5.39	3.55	0.40652	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.052637	0.85682	D	0.000000	D	0.96935	0.8999	M	0.87682	2.9	0.80722	D	1	D	0.64830	0.994	D	0.65323	0.934	D	0.96575	0.9426	10	0.72032	D	0.01	.	12.2827	0.54774	0.0:0.1297:0.7353:0.1351	.	297	P27037	AVR2A_HUMAN	T	297;189;297	ENSP00000241416:A297T;ENSP00000439988:A189T;ENSP00000384338:A297T	ENSP00000241416:A297T	A	+	1	0	ACVR2A	148392558	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.869000	0.99810	0.616000	0.30141	0.563000	0.77884	GCT	.		0.378	ACVR2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319051.1	NM_001616	
TMEM38A	79041	hgsc.bcm.edu	37	19	16790827	16790827	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr19:16790827G>T	ENST00000187762.2	+	2	248	c.157G>T	c.(157-159)Gcg>Tcg	p.A53S		NM_024074.1	NP_076979.1	Q9H6F2	TM38A_HUMAN	transmembrane protein 38A	53						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nuclear membrane (GO:0031965)|sarcoplasmic reticulum membrane (GO:0033017)	potassium channel activity (GO:0005267)			central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(6)|ovary(1)	15						CCACCCCATCGCGTCCTGGCT	0.602																																					p.A53S		.											TMEM38A,colon,carcinoma,-1,1	TMEM38A	-1	0			c.G157T						.						54.0	40.0	45.0					19																	16790827		2203	4300	6503	SO:0001583	missense	79041	exon2			CCCATCGCGTCCT	AK025981	CCDS12349.1	19p13.11	2013-05-23				ENSG00000072954			28462	protein-coding gene	gene with protein product		611235				17611541	Standard	NM_024074		Approved	MGC3169, TRIC-A	uc002nes.3	Q9H6F2		ENST00000187762.2:c.157G>T	19.37:g.16790827G>T	ENSP00000187762:p.Ala53Ser	Somatic	20	0		WXS	Illumina HiSeq	.	21	2	NM_024074	A8K9P9	Missense_Mutation	SNP	ENST00000187762.2	37	CCDS12349.1	.	.	.	.	.	.	.	.	.	.	g	13.95	2.388574	0.42308	.	.	ENSG00000072954	ENST00000187762	.	.	.	5.29	5.29	0.74685	.	0.000000	0.85682	D	0.000000	T	0.65883	0.2734	L	0.28608	0.87	0.80722	D	1	D	0.76494	0.999	D	0.77557	0.99	T	0.62723	-0.6794	9	0.30078	T	0.28	-14.3296	17.9316	0.88999	0.0:0.0:1.0:0.0	.	53	Q9H6F2	TM38A_HUMAN	S	53	.	ENSP00000187762:A53S	A	+	1	0	TMEM38A	16651827	1.000000	0.71417	0.397000	0.26308	0.074000	0.17049	9.324000	0.96373	2.474000	0.83562	0.561000	0.74099	GCG	.		0.602	TMEM38A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462841.1	NM_024074	
DDX19A	55308	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	16	70404165	70404165	+	Missense_Mutation	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr16:70404165A>C	ENST00000302243.7	+	10	1223	c.1060A>C	c.(1060-1062)Aaa>Caa	p.K354Q	DDX19A_ENST00000417604.2_Missense_Mutation_p.K323Q|DDX19A_ENST00000443119.2_Missense_Mutation_p.K264Q	NM_018332.3	NP_060802.1	Q9NUU7	DD19A_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 19A	354	C-terminal lobe. {ECO:0000250}.|Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				mRNA transport (GO:0051028)|positive regulation of apoptotic process (GO:0043065)|protein transport (GO:0015031)|response to zinc ion (GO:0010043)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear pore (GO:0005643)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|RNA binding (GO:0003723)			breast(1)|endometrium(1)|large_intestine(5)|lung(3)|urinary_tract(1)	11		Ovarian(137;0.221)				AGAGCTCTCAAAAGAAGGCCA	0.463																																					p.K354Q		.											.	.	.	0			c.A1060C						.						68.0	68.0	68.0					16																	70404165		2198	4298	6496	SO:0001583	missense	55308	exon10			CTCTCAAAAGAAG	AF183422	CCDS10889.1	16q22.1	2012-02-23	2012-02-23	2005-07-13	ENSG00000168872	ENSG00000168872		"""DEAD-boxes"""	25628	protein-coding gene	gene with protein product			"""DEAD (Asp-Glu-Ala-As) box polypeptide 19-like"""	DDX19L		12477932	Standard	NM_018332		Approved	FLJ11126		Q9NUU7	OTTHUMG00000137579	ENST00000302243.7:c.1060A>C	16.37:g.70404165A>C	ENSP00000306117:p.Lys354Gln	Somatic	81	0		WXS	Illumina HiSeq	.	30	17	NM_018332	B2RPL0|B4DRZ7|Q53FM0	Missense_Mutation	SNP	ENST00000302243.7	37	CCDS10889.1	.	.	.	.	.	.	.	.	.	.	A	11.21	1.571458	0.28003	.	.	ENSG00000168872	ENST00000302243;ENST00000302227;ENST00000417604;ENST00000443119	T;T;T	0.75821	-0.97;-0.97;-0.97	5.47	4.31	0.51392	Helicase, C-terminal (3);	0.142668	0.64402	D	0.000005	T	0.58652	0.2137	N	0.16790	0.44	0.41356	D	0.987399	B;B;B;B;B	0.31581	0.001;0.006;0.001;0.329;0.001	B;B;B;B;B	0.36608	0.003;0.026;0.003;0.229;0.005	T	0.55786	-0.8086	10	0.20519	T	0.43	.	10.3183	0.43751	0.8348:0.1652:0.0:0.0	.	264;323;189;354;355	B4DRZ7;B4DS24;Q59FQ9;Q9NUU7;Q7Z4W5	.;.;.;DD19A_HUMAN;.	Q	354;246;323;264	ENSP00000306117:K354Q;ENSP00000410243:K323Q;ENSP00000399208:K264Q	ENSP00000306209:K246Q	K	+	1	0	DDX19A	68961666	0.997000	0.39634	0.995000	0.50966	0.997000	0.91878	3.813000	0.55636	2.070000	0.61991	0.402000	0.26972	AAA	.		0.463	DDX19A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268967.2	NM_018332	
NOM1	64434	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	7	156745289	156745289	+	Missense_Mutation	SNP	A	A	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr7:156745289A>G	ENST00000275820.3	+	2	1124	c.1109A>G	c.(1108-1110)aAc>aGc	p.N370S		NM_138400.1	NP_612409.1	Q5C9Z4	NOM1_HUMAN	nucleolar protein with MIF4G domain 1	370	MIF4G. {ECO:0000255|PROSITE- ProRule:PRU00698}.					nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(5)|kidney(4)|large_intestine(9)|lung(7)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	31	Ovarian(565;0.218)	all_hematologic(28;0.0749)	OV - Ovarian serous cystadenocarcinoma(82;0.00301)	UCEC - Uterine corpus endometrioid carcinoma (81;0.169)		GGTCTACTTAACAGGTGACCT	0.413																																					p.N370S		.											NOM1,bladder,carcinoma,0,1	NOM1	0	0			c.A1109G						.						103.0	93.0	96.0					7																	156745289		2203	4300	6503	SO:0001583	missense	64434	exon2			TACTTAACAGGTG	AF107455	CCDS34787.1	7q36.3	2014-06-13	2005-03-30	2005-03-30	ENSG00000146909	ENSG00000146909			13244	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 113"""	611269	"""chromosome 7 open reading frame 3"""	C7orf3		10329000	Standard	XM_005249560		Approved	SGD1, PPP1R113	uc003wmy.3	Q5C9Z4	OTTHUMG00000152639	ENST00000275820.3:c.1109A>G	7.37:g.156745289A>G	ENSP00000275820:p.Asn370Ser	Somatic	114	0		WXS	Illumina HiSeq	.	71	31	NM_138400	Q96I08	Missense_Mutation	SNP	ENST00000275820.3	37	CCDS34787.1	.	.	.	.	.	.	.	.	.	.	A	15.38	2.816849	0.50633	.	.	ENSG00000146909	ENST00000275820	T	0.34667	1.35	4.69	4.69	0.59074	MIF4G-like, type 3 (2);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.67896	0.2942	M	0.93678	3.445	0.80722	D	1	D	0.71674	0.998	D	0.76575	0.988	T	0.77064	-0.2726	10	0.87932	D	0	-23.8178	12.7703	0.57417	1.0:0.0:0.0:0.0	.	370	Q5C9Z4	NOM1_HUMAN	S	370	ENSP00000275820:N370S	ENSP00000275820:N370S	N	+	2	0	NOM1	156438050	1.000000	0.71417	0.982000	0.44146	0.091000	0.18340	7.867000	0.87062	1.754000	0.51921	0.456000	0.33151	AAC	.		0.413	NOM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327098.1	NM_138400	
KIAA0125	9834	hgsc.bcm.edu;bcgsc.ca	37	14	106391361	106391361	+	IGR	SNP	T	T	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr14:106391361T>A	ENST00000449410.1	+	0	533				KIAA0125_ENST00000482999.1_3'UTR			Q9NZY2	K0125_HUMAN	KIAA0125																		ACTCCTCTCCTGGGCAACATT	0.632																																					.		.											.	.	.	0			.						.																																			SO:0001628	intergenic_variant	9834	.			CTCTCCTGGGCAA	AB019441		14q32.33	2014-04-01			ENSG00000226777	ENSG00000226777			19955	other	unknown			"""family with sequence similarity 30, member A"", ""chromosome 14 open reading frame 110"""	FAM30A, C14orf110		8590280	Standard	NR_026800		Approved	HSPC053	uc001ysq.3	Q9NZY2	OTTHUMG00000152318		14.37:g.106391361T>A		Somatic	72	0		WXS	Illumina HiSeq	.	44	13	.	C9J8W9	RNA	SNP	ENST00000449410.1	37																																																																																				.		0.632	KIAA0125-001	PUTATIVE	basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000325876.1	NM_014792	
CCDC168	643677	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	13	103383698	103383698	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr13:103383698G>T	ENST00000322527.2	-	1	5461	c.5462C>A	c.(5461-5463)aCt>aAt	p.T1821N		NM_001146197.1	NP_001139669.1	Q8NDH2	CC168_HUMAN	coiled-coil domain containing 168	1821																	TTTTGAAATAGTCCCTTTTGG	0.333																																					p.T6450N		.											.	.	.	0			c.C19349A						.						105.0	81.0	88.0					13																	103383698		692	1588	2280	SO:0001583	missense	643677	exon4			GAAATAGTCCCTT		CCDS73596.1	13q33.1	2014-06-17	2011-08-09	2011-08-09	ENSG00000175820	ENSG00000175820			26851	protein-coding gene	gene with protein product			"""chromosome 13 open reading frame 40"""	C13orf40			Standard	NM_001146197		Approved	FLJ40176	uc001vpm.3	Q8NDH2	OTTHUMG00000187287	ENST00000322527.2:c.5462C>A	13.37:g.103383698G>T	ENSP00000320232:p.Thr1821Asn	Somatic	89	0		WXS	Illumina HiSeq	.	46	14	NM_001146197	Q8N800	Missense_Mutation	SNP	ENST00000322527.2	37		.	.	.	.	.	.	.	.	.	.	G	13.37	2.218093	0.39201	.	.	ENSG00000175820	ENST00000322527	T	0.04502	3.61	5.0	2.16	0.27623	.	.	.	.	.	T	0.04003	0.0112	N	0.19112	0.55	0.09310	N	1	P	0.41848	0.763	B	0.41988	0.372	T	0.43376	-0.9395	9	0.41790	T	0.15	.	7.045	0.25040	0.0:0.17:0.4794:0.3506	.	1821	Q8NDH2	CC168_HUMAN	N	1821	ENSP00000320232:T1821N	ENSP00000320232:T1821N	T	-	2	0	CCDC168	102181699	0.002000	0.14202	0.003000	0.11579	0.004000	0.04260	0.526000	0.22971	1.295000	0.44724	0.655000	0.94253	ACT	.		0.333	CCDC168-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001146197	
LRP6	4040	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	12	12291295	12291295	+	Missense_Mutation	SNP	T	T	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr12:12291295T>C	ENST00000261349.4	-	16	3647	c.3571A>G	c.(3571-3573)Att>Gtt	p.I1191V	BCL2L14_ENST00000396369.1_Intron|LRP6_ENST00000543091.1_Missense_Mutation_p.I1191V	NM_002336.2	NP_002327.2	O75581	LRP6_HUMAN	low density lipoprotein receptor-related protein 6	1191	Beta-propeller 4.				anterior/posterior pattern specification (GO:0009952)|axis elongation involved in somitogenesis (GO:0090245)|bone morphogenesis (GO:0060349)|bone remodeling (GO:0046849)|branching involved in mammary gland duct morphogenesis (GO:0060444)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in cardiac neural crest cell differentiation involved in heart development (GO:0061310)|canonical Wnt signaling pathway involved in neural crest cell differentiation (GO:0044335)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in regulation of cell proliferation (GO:0044340)|cell migration involved in gastrulation (GO:0042074)|cellular response to cholesterol (GO:0071397)|cerebellum morphogenesis (GO:0021587)|cerebral cortex cell migration (GO:0021795)|cerebral cortex development (GO:0021987)|convergent extension (GO:0060026)|dopaminergic neuron differentiation (GO:0071542)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic pattern specification (GO:0009880)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|external genitalia morphogenesis (GO:0035261)|face morphogenesis (GO:0060325)|forebrain radial glial cell differentiation (GO:0021861)|formation of radial glial scaffolds (GO:0021943)|gastrulation with mouth forming second (GO:0001702)|heart looping (GO:0001947)|mammary placode formation (GO:0060596)|midbrain development (GO:0030901)|midbrain-hindbrain boundary development (GO:0030917)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of planar cell polarity pathway involved in cardiac muscle tissue morphogenesis (GO:2000151)|negative regulation of planar cell polarity pathway involved in cardiac right atrium morphogenesis (GO:2000162)|negative regulation of planar cell polarity pathway involved in neural tube closure (GO:2000168)|negative regulation of planar cell polarity pathway involved in outflow tract morphogenesis (GO:2000164)|negative regulation of planar cell polarity pathway involved in pericardium morphogenesis (GO:2000166)|negative regulation of planar cell polarity pathway involved in ventricular septum morphogenesis (GO:2000149)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|negative regulation of smooth muscle cell apoptotic process (GO:0034392)|neural crest cell differentiation (GO:0014033)|neural crest formation (GO:0014029)|neural tube closure (GO:0001843)|odontogenesis of dentin-containing tooth (GO:0042475)|palate development (GO:0060021)|pericardium morphogenesis (GO:0003344)|positive regulation of apoptotic process (GO:0043065)|positive regulation of bone resorption (GO:0045780)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell cycle (GO:0045787)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of ossification (GO:0045778)|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)|positive regulation of Wnt signaling pathway involved in dorsal/ventral axis specification (GO:2000055)|post-anal tail morphogenesis (GO:0036342)|primitive streak formation (GO:0090009)|receptor-mediated endocytosis of low-density lipoprotein particle involved in cholesterol transport (GO:0090118)|regulation of cell development (GO:0060284)|regulation of fat cell differentiation (GO:0045598)|regulation of ossification (GO:0030278)|response to folic acid (GO:0051593)|response to peptide hormone (GO:0043434)|single organismal cell-cell adhesion (GO:0016337)|synaptic transmission (GO:0007268)|thalamus development (GO:0021794)|toxin transport (GO:1901998)|trachea cartilage morphogenesis (GO:0060535)|Wnt signaling pathway (GO:0016055)|Wnt signaling pathway involved in dorsal/ventral axis specification (GO:0044332)|Wnt signaling pathway involved in forebrain neuroblast division (GO:0021874)|Wnt signaling pathway involved in somitogenesis (GO:0090244)	cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|synapse (GO:0045202)	apolipoprotein binding (GO:0034185)|coreceptor activity involved in Wnt signaling pathway (GO:0071936)|frizzled binding (GO:0005109)|identical protein binding (GO:0042802)|kinase inhibitor activity (GO:0019210)|low-density lipoprotein receptor activity (GO:0005041)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|toxin transporter activity (GO:0019534)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(19)|lung(28)|ovary(3)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	85		Prostate(47;0.0865)				ACTGCATGAATGTCACTAAGC	0.363																																					p.I1191V		.											.	.	.	0			c.A3571G						.						232.0	209.0	216.0					12																	12291295		2203	4300	6503	SO:0001583	missense	4040	exon16			CATGAATGTCACT	AF074264	CCDS8647.1	12p13.2	2013-05-29			ENSG00000070018	ENSG00000070018		"""Low density lipoprotein receptors"""	6698	protein-coding gene	gene with protein product		603507				9704021	Standard	NM_002336		Approved	ADCAD2	uc001rah.4	O75581	OTTHUMG00000168540	ENST00000261349.4:c.3571A>G	12.37:g.12291295T>C	ENSP00000261349:p.Ile1191Val	Somatic	60	0		WXS	Illumina HiSeq	.	34	18	NM_002336	Q17RZ2	Missense_Mutation	SNP	ENST00000261349.4	37	CCDS8647.1	.	.	.	.	.	.	.	.	.	.	T	18.38	3.610558	0.66558	.	.	ENSG00000070018	ENST00000261349;ENST00000543091	D;D	0.91180	-2.8;-2.8	5.74	5.74	0.90152	Six-bladed beta-propeller, TolB-like (1);	0.000000	0.64402	D	0.000008	D	0.94238	0.8150	M	0.70787	2.145	0.80722	D	1	P;B	0.42785	0.79;0.403	P;B	0.62560	0.904;0.175	D	0.92445	0.5965	10	0.22109	T	0.4	.	16.0271	0.80551	0.0:0.0:0.0:1.0	.	1191;1191	F5H7J9;O75581	.;LRP6_HUMAN	V	1191	ENSP00000261349:I1191V;ENSP00000442472:I1191V	ENSP00000261349:I1191V	I	-	1	0	LRP6	12182562	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.665000	0.83852	2.188000	0.69820	0.482000	0.46254	ATT	.		0.363	LRP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400137.1		
BTBD8	284697	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	92573559	92573559	+	Splice_Site	SNP	G	G	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr1:92573559G>T	ENST00000342818.3	+	4	898		c.e4+1		BTBD8_ENST00000540648.1_Splice_Site|BTBD8_ENST00000370382.3_Splice_Site	NM_183242.3	NP_899065.2	Q5XKL5	BTBD8_HUMAN	BTB (POZ) domain containing 8							nucleus (GO:0005634)				breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(8)|ovary(1)	16		all_lung(203;0.0484)|Lung NSC(277;0.126)|Glioma(108;0.222)		all cancers(265;0.0153)|Epithelial(280;0.0982)		AAGCTCACAGGTAAATAGACA	0.408																																					.		.											.	.	.	0			c.662+1G>T						.						165.0	163.0	163.0					1																	92573559		2203	4300	6503	SO:0001630	splice_region_variant	284697	exon4			TCACAGGTAAATA	AY346333	CCDS737.1	1p22.1	2013-01-08			ENSG00000189195	ENSG00000189195		"""BTB/POZ domain containing"""	21019	protein-coding gene	gene with protein product						14654994	Standard	NM_183242		Approved		uc001doo.3	Q5XKL5	OTTHUMG00000010289	ENST00000342818.3:c.662+1G>T	1.37:g.92573559G>T		Somatic	88	0		WXS	Illumina HiSeq	.	28	20	NM_183242	Q6V9S5	Splice_Site	SNP	ENST00000342818.3	37	CCDS737.1	.	.	.	.	.	.	.	.	.	.	G	19.96	3.923407	0.73213	.	.	ENSG00000189195	ENST00000370382;ENST00000342818;ENST00000540648	.	.	.	5.32	5.32	0.75619	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.8871	0.79258	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	BTBD8	92346147	1.000000	0.71417	1.000000	0.80357	0.929000	0.56500	5.535000	0.67173	2.480000	0.83734	0.591000	0.81541	.	.		0.408	BTBD8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028372.1	NM_183242	Intron
RAB6A	5870	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	11	73427372	73427372	+	Missense_Mutation	SNP	C	C	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr11:73427372C>G	ENST00000336083.3	-	5	780	c.325G>C	c.(325-327)Gat>Cat	p.D109H	RAB6A_ENST00000536566.1_Missense_Mutation_p.D76H|RAB6A_ENST00000310653.6_Missense_Mutation_p.D109H|RAB6A_ENST00000541588.1_Intron	NM_198896.1	NP_942599.1	P20340	RAB6A_HUMAN	RAB6A, member RAS oncogene family	109					antigen processing and presentation (GO:0019882)|early endosome to Golgi transport (GO:0034498)|GTP catabolic process (GO:0006184)|minus-end-directed organelle transport along microtubule (GO:0072385)|peptidyl-cysteine methylation (GO:0018125)|protein localization to Golgi apparatus (GO:0034067)|protein targeting to Golgi (GO:0000042)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|small GTPase mediated signal transduction (GO:0007264)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|trans-Golgi network (GO:0005802)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|myosin V binding (GO:0031489)|protein domain specific binding (GO:0019904)			large_intestine(2)|lung(2)	4						CTGACATCATCAATCCACTTT	0.403																																					p.D109H		.											.	.	.	0			c.G325C						.						160.0	139.0	146.0					11																	73427372		2200	4293	6493	SO:0001583	missense	5870	exon5			CATCATCAATCCA	AF130986	CCDS8223.1, CCDS8224.1, CCDS58155.1, CCDS58156.1	11q13.3	2008-08-08			ENSG00000175582	ENSG00000175582		"""RAB, member RAS oncogene"""	9786	protein-coding gene	gene with protein product		179513		RAB6			Standard	NM_001243718		Approved		uc001ouf.3	P20340	OTTHUMG00000134308	ENST00000336083.3:c.325G>C	11.37:g.73427372C>G	ENSP00000336850:p.Asp109His	Somatic	81	0		WXS	Illumina HiSeq	.	52	26	NM_002869	A8K133|B7Z772|F5H668|Q1W5D8|Q5U0A8|Q9UBE4	Missense_Mutation	SNP	ENST00000336083.3	37	CCDS8224.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	25.3|25.3	4.629171|4.629171	0.87560|0.87560	.|.	.|.	ENSG00000175582|ENSG00000175582	ENST00000310653;ENST00000336083;ENST00000393571;ENST00000536566;ENST00000539750|ENST00000541973;ENST00000400470	T;T;T|.	0.77750|.	-1.12;-1.12;-1.12|.	5.76|5.76	5.76|5.76	0.90799|0.90799	Small GTP-binding protein domain (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.66963|0.66963	0.2843|0.2843	L|L	0.39467|0.39467	1.215|1.215	0.80722|0.80722	D|D	1|1	P;D|.	0.56746|.	0.946;0.977|.	P;P|.	0.58873|.	0.847;0.762|.	T|T	0.61058|0.61058	-0.7139|-0.7139	10|5	0.87932|.	D|.	0|.	-5.0518|-5.0518	18.9443|18.9443	0.92616|0.92616	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	109;109|.	P20340;P20340-2|.	RAB6A_HUMAN;.|.	H|F	109;109;109;76;109|101;100	ENSP00000311449:D109H;ENSP00000336850:D109H;ENSP00000437863:D76H|.	ENSP00000311449:D109H|.	D|L	-|-	1|3	0|2	RAB6A|RAB6A	73105020|73105020	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	7.487000|7.487000	0.81328|0.81328	2.725000|2.725000	0.93324|0.93324	0.591000|0.591000	0.81541|0.81541	GAT|TTG	.		0.403	RAB6A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000259241.2		
CCDC74A	90557	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	2	132285743	132285743	+	Missense_Mutation	SNP	T	T	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr2:132285743T>C	ENST00000295171.6	+	1	338	c.200T>C	c.(199-201)aTg>aCg	p.M67T	CCDC74A_ENST00000478665.1_3'UTR|CCDC74A_ENST00000467992.2_5'Flank|CCDC74A_ENST00000409856.3_Missense_Mutation_p.M67T	NM_001258304.1|NM_001258305.1|NM_138770.2	NP_001245233.1|NP_001245234.1|NP_620125.1	Q96AQ1	CC74A_HUMAN	coiled-coil domain containing 74A	67										endometrium(4)|large_intestine(3)|lung(9)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19						CACTCGGAGATGCTGGCCAAG	0.647																																					p.M67T		.											.	.	.	0			c.T200C						.						37.0	36.0	36.0					2																	132285743		2203	4300	6503	SO:0001583	missense	90557	exon1			CGGAGATGCTGGC		CCDS2167.1, CCDS58732.1, CCDS74578.1	2q21.1	2008-02-05		2006-02-16	ENSG00000163040	ENSG00000163040			25197	protein-coding gene	gene with protein product						12477932	Standard	NM_138770		Approved	FLJ40345	uc002ttb.4	Q96AQ1	OTTHUMG00000131667	ENST00000295171.6:c.200T>C	2.37:g.132285743T>C	ENSP00000295171:p.Met67Thr	Somatic	95	0		WXS	Illumina HiSeq	.	70	17	NM_001258304	Q6P4I5	Missense_Mutation	SNP	ENST00000295171.6	37	CCDS2167.1	.	.	.	.	.	.	.	.	.	.	.	0.012	-1.660819	0.00772	.	.	ENSG00000163040	ENST00000295171;ENST00000409856	T;T	0.35605	1.3;1.3	2.79	1.89	0.25635	.	0.388346	0.18113	N	0.151289	T	0.06962	0.0177	N	0.00197	-1.87	0.80722	D	1	B;B;B	0.09022	0.002;0.001;0.0	B;B;B	0.04013	0.001;0.001;0.0	T	0.31223	-0.9951	10	0.05833	T	0.94	-4.4475	7.2041	0.25897	0.0:0.8509:0.0:0.1491	.	67;67;67	B4DZ94;Q96AQ1-2;Q96AQ1	.;.;CC74A_HUMAN	T	67	ENSP00000295171:M67T;ENSP00000387009:M67T	ENSP00000295171:M67T	M	+	2	0	CCDC74A	132002213	0.926000	0.31397	0.999000	0.59377	0.509000	0.34042	0.775000	0.26689	0.178000	0.19917	0.113000	0.15668	ATG	.		0.647	CCDC74A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254570.2	NM_138770	
NEFM	4741	hgsc.bcm.edu	37	8	24775376	24775376	+	Missense_Mutation	SNP	T	T	C	rs201305028		TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr8:24775376T>C	ENST00000221166.5	+	3	2790	c.2008T>C	c.(2008-2010)Tca>Cca	p.S670P	NEFM_ENST00000518131.1_Intron|NEFM_ENST00000433454.2_Missense_Mutation_p.S294P|NEFM_ENST00000437366.2_Missense_Mutation_p.S631P|NEFM_ENST00000521540.1_Intron			P07197	NFM_HUMAN	neurofilament, medium polypeptide	670	6 X 13 AA approximate tandem repeats of K-S-P-V-[PS]-K-S-P-V-E-E-[KA]-[GAK].|Tail.				axon cargo transport (GO:0008088)|microtubule cytoskeleton organization (GO:0000226)|neurofilament bundle assembly (GO:0033693)|regulation of axon diameter (GO:0031133)	axon (GO:0030424)|neurofibrillary tangle (GO:0097418)|neurofilament (GO:0005883)|neuromuscular junction (GO:0031594)	microtubule binding (GO:0008017)|structural constituent of cytoskeleton (GO:0005200)			breast(3)|endometrium(7)|kidney(4)|large_intestine(5)|lung(14)|ovary(1)|prostate(1)|urinary_tract(1)	36		Prostate(55;0.157)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0197)|Epithelial(17;2.44e-10)|Colorectal(74;0.0108)|COAD - Colon adenocarcinoma(73;0.0375)		GTCTCCTGTGTCAAAATCACC	0.483																																					p.S670P		.											NEFM,lower_third,carcinoma,-2,1	NEFM	-2	0			c.T2008C						.						87.0	90.0	89.0					8																	24775376		2203	4300	6503	SO:0001583	missense	4741	exon3			CCTGTGTCAAAAT	BC002421	CCDS6046.1, CCDS47831.1	8p21	2013-01-16	2008-09-19	2006-11-20	ENSG00000104722	ENSG00000104722		"""Intermediate filaments type IV"""	7734	protein-coding gene	gene with protein product		162250	"""neurofilament, medium polypeptide 150kDa"""	NEF3		1348579	Standard	NM_001105541		Approved	NFM, NF-M	uc003xed.4	P07197	OTTHUMG00000131990	ENST00000221166.5:c.2008T>C	8.37:g.24775376T>C	ENSP00000221166:p.Ser670Pro	Somatic	127	0		WXS	Illumina HiSeq	.	97	4	NM_005382	B4DGN2|E9PBF7|Q4QRK6	Missense_Mutation	SNP	ENST00000221166.5	37	CCDS6046.1	.	.	.	.	.	.	.	.	.	.	T	0.003	-2.443080	0.00180	.	.	ENSG00000104722	ENST00000221166;ENST00000437366;ENST00000433454	D;D;D	0.93763	-1.71;-1.65;-3.28	2.52	-5.05	0.02955	.	.	.	.	.	T	0.74122	0.3675	N	0.00926	-1.1	0.09310	N	1	B	0.10296	0.003	B	0.04013	0.001	T	0.65331	-0.6194	9	0.31617	T	0.26	.	3.2688	0.06874	0.267:0.0:0.2386:0.4944	.	670	P07197	NFM_HUMAN	P	670;631;294	ENSP00000221166:S670P;ENSP00000410137:S631P;ENSP00000412295:S294P	ENSP00000221166:S670P	S	+	1	0	NEFM	24831281	0.051000	0.20477	0.000000	0.03702	0.050000	0.14768	-0.304000	0.08199	-1.534000	0.01743	-1.344000	0.01245	TCA	.		0.483	NEFM-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254954.2	NM_005382	
BCL3	602	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	19	45254588	45254588	+	Missense_Mutation	SNP	C	C	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr19:45254588C>T	ENST00000164227.5	+	2	605	c.361C>T	c.(361-363)Ctt>Ttt	p.L121F		NM_005178.4	NP_005169.2	P20749	BCL3_HUMAN	B-cell CLL/lymphoma 3	121					antimicrobial humoral response (GO:0019730)|cellular response to DNA damage stimulus (GO:0006974)|defense response to bacterium (GO:0042742)|defense response to protozoan (GO:0042832)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|extracellular matrix organization (GO:0030198)|follicular dendritic cell differentiation (GO:0002268)|germinal center formation (GO:0002467)|humoral immune response mediated by circulating immunoglobulin (GO:0002455)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|maintenance of protein location in nucleus (GO:0051457)|marginal zone B cell differentiation (GO:0002315)|negative regulation of apoptotic process (GO:0043066)|negative regulation of interleukin-8 biosynthetic process (GO:0045415)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of tumor necrosis factor biosynthetic process (GO:0042536)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-10 biosynthetic process (GO:0045082)|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)|protein import into nucleus, translocation (GO:0000060)|regulation of apoptotic process (GO:0042981)|regulation of DNA binding (GO:0051101)|regulation of NF-kappaB import into nucleus (GO:0042345)|response to UV-C (GO:0010225)|response to virus (GO:0009615)|spleen development (GO:0048536)|T-helper 1 type immune response (GO:0042088)|T-helper 2 cell differentiation (GO:0045064)|transcription, DNA-templated (GO:0006351)	Bcl3-Bcl10 complex (GO:0032996)|Bcl3/NF-kappaB2 complex (GO:0033257)|cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|protein binding, bridging (GO:0030674)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			kidney(1)|large_intestine(2)|lung(2)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	10	Lung NSC(12;0.000698)|all_lung(12;0.002)	Ovarian(192;0.0728)				GGAACACCCCCTTTCTGCTGA	0.597			T	IGH@	CLL																																p.L121F		.		Dom	yes		19	19q13	602	B-cell CLL/lymphoma 3		L	.	.	.	0			c.C361T						.						121.0	99.0	107.0					19																	45254588		2203	4300	6503	SO:0001583	missense	602	exon2			CACCCCCTTTCTG	M31732	CCDS12642.2	19q13.1-q13.2	2013-01-10			ENSG00000069399	ENSG00000069399		"""Ankyrin repeat domain containing"""	998	protein-coding gene	gene with protein product	"""B-cell lymphoma 3-encoded protein"", ""B-cell leukemia/lymphoma 3"", ""chronic lymphatic leukemia protein"""	109560		D19S37, BCL4		1501714, 2180580	Standard	NM_005178		Approved		uc010xxe.2	P20749	OTTHUMG00000151517	ENST00000164227.5:c.361C>T	19.37:g.45254588C>T	ENSP00000164227:p.Leu121Phe	Somatic	32	0		WXS	Illumina HiSeq	.	23	17	NM_005178		Missense_Mutation	SNP	ENST00000164227.5	37	CCDS12642.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	19.80|19.80	3.894312|3.894312	0.72639|0.72639	.|.	.|.	ENSG00000069399|ENSG00000069399	ENST00000403534;ENST00000164227|ENST00000444487	T|T	0.49432|0.45668	0.78|0.89	5.19|5.19	3.03|3.03	0.35002|0.35002	.|.	0.000000|.	0.38381|.	N|.	0.001704|.	T|T	0.28466|0.28466	0.0704|0.0704	L|L	0.29908|0.29908	0.895|0.895	0.37252|0.37252	D|D	0.906628|0.906628	D|.	0.71674|.	0.998|.	D|.	0.83275|.	0.996|.	T|T	0.11084|0.11084	-1.0602|-1.0602	10|7	0.62326|0.02654	D|T	0.03|1	-16.5854|-16.5854	10.0819|10.0819	0.42395|0.42395	0.0:0.83:0.0:0.17|0.0:0.83:0.0:0.17	.|.	121|.	P20749|.	BCL3_HUMAN|.	F|L	81;121|4	ENSP00000164227:L121F|ENSP00000393731:P4L	ENSP00000164227:L121F|ENSP00000393731:P4L	L|P	+|+	1|2	0|0	BCL3|BCL3	49946428|49946428	0.969000|0.969000	0.33509|0.33509	0.992000|0.992000	0.48379|0.48379	0.846000|0.846000	0.48090|0.48090	1.334000|1.334000	0.33827|0.33827	1.193000|1.193000	0.43086|0.43086	0.455000|0.455000	0.32223|0.32223	CTT|CCT	.		0.597	BCL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322976.1	NM_005178	
OR6V1	346517	hgsc.bcm.edu;broad.mit.edu	37	7	142749878	142749878	+	Nonsense_Mutation	SNP	G	G	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr7:142749878G>A	ENST00000418316.1	+	1	462	c.441G>A	c.(439-441)tgG>tgA	p.W147*		NM_001001667.1	NP_001001667.1	Q8N148	OR6V1_HUMAN	olfactory receptor, family 6, subfamily V, member 1	147						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|kidney(2)|large_intestine(1)|lung(13)|ovary(1)|upper_aerodigestive_tract(1)	20	Melanoma(164;0.059)					GGGCTGCCTGGGCAGCTCCTT	0.572																																					p.W147X		.											.	.	.	0			c.G441A						.						71.0	78.0	76.0					7																	142749878		2110	4254	6364	SO:0001587	stop_gained	346517	exon1			TGCCTGGGCAGCT		CCDS47728.1	7q34	2014-05-06			ENSG00000225781	ENSG00000225781		"""GPCR / Class A : Olfactory receptors"""	15090	protein-coding gene	gene with protein product						12732197	Standard	NM_001001667		Approved	GPR138	uc011ksv.2	Q8N148	OTTHUMG00000158385	ENST00000418316.1:c.441G>A	7.37:g.142749878G>A	ENSP00000396085:p.Trp147*	Somatic	44	0		WXS	Illumina HiSeq	.	34	15	NM_001001667	A4D2I0|B9EH48|Q6IF70	Nonsense_Mutation	SNP	ENST00000418316.1	37	CCDS47728.1	.	.	.	.	.	.	.	.	.	.	G	23.1	4.371765	0.82573	.	.	ENSG00000225781	ENST00000418316	.	.	.	4.16	3.28	0.37604	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	9.925	0.41487	0.1007:0.0:0.8993:0.0	.	.	.	.	X	147	.	ENSP00000396085:W147X	W	+	3	0	OR6V1	142460000	0.921000	0.31238	0.943000	0.38184	0.786000	0.44442	1.634000	0.37123	0.988000	0.38734	-0.126000	0.14955	TGG	.		0.572	OR6V1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350860.1		
SYNJ2BP	55333	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	14	70839843	70839843	+	Silent	SNP	C	C	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr14:70839843C>T	ENST00000256366.4	-	4	384	c.303G>A	c.(301-303)caG>caA	p.Q101Q	SYNJ2BP-COX16_ENST00000555276.1_RNA|SYNJ2BP_ENST00000554216.1_5'UTR	NM_018373.2	NP_060843.2	P57105	SYJ2B_HUMAN	synaptojanin 2 binding protein	101					intracellular distribution of mitochondria (GO:0048312)|negative regulation of activin receptor signaling pathway (GO:0032926)|positive regulation of activin receptor signaling pathway (GO:0032927)|positive regulation of protein localization to cell surface (GO:2000010)|positive regulation of receptor internalization (GO:0002092)	cell surface (GO:0009986)|integral component of mitochondrial outer membrane (GO:0031307)|mitochondrion (GO:0005739)				central_nervous_system(1)|kidney(2)|large_intestine(1)|upper_aerodigestive_tract(1)	5				all cancers(60;0.00367)|BRCA - Breast invasive adenocarcinoma(234;0.00716)|OV - Ovarian serous cystadenocarcinoma(108;0.0377)		CATTCTGCACCTGTAACTGGA	0.468																																					p.Q101Q		.											.	.	.	0			c.G303A						.						113.0	93.0	100.0					14																	70839843		2203	4300	6503	SO:0001819	synonymous_variant	0	exon4			CTGCACCTGTAAC	AK002133	CCDS9803.1	14q24.2	2013-05-10			ENSG00000213463	ENSG00000213463			18955	protein-coding gene	gene with protein product	"""activin receptor interacting protein 5"""	609411				11882656	Standard	NM_018373		Approved	Arip2		P57105	OTTHUMG00000171240	ENST00000256366.4:c.303G>A	14.37:g.70839843C>T		Somatic	42	0		WXS	Illumina HiSeq	.	23	10	NM_001202547	Q49SH3|Q96IA4	Silent	SNP	ENST00000256366.4	37	CCDS9803.1																																																																																			.		0.468	SYNJ2BP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412472.1	NM_018373	
WBP2	23558	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	17	73847681	73847681	+	Nonsense_Mutation	SNP	T	T	A	rs149300980		TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr17:73847681T>A	ENST00000591399.1	-	3	560	c.136A>T	c.(136-138)Aag>Tag	p.K46*	WBP2_ENST00000254806.3_Nonsense_Mutation_p.K46*|WBP2_ENST00000344296.4_Nonsense_Mutation_p.K24*|WBP2_ENST00000590450.1_5'UTR|WBP2_ENST00000433525.2_Nonsense_Mutation_p.K46*|WBP2_ENST00000585462.1_Nonsense_Mutation_p.K24*|WBP2_ENST00000590221.1_Nonsense_Mutation_p.K46*			Q969T9	WBP2_HUMAN	WW domain binding protein 2	46	GRAM.				cellular response to estrogen stimulus (GO:0071391)|establishment of protein localization (GO:0045184)|positive regulation of gene expression, epigenetic (GO:0045815)|positive regulation of histone H3-K14 acetylation (GO:0071442)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nuclear chromatin (GO:0000790)	chromatin DNA binding (GO:0031490)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription coactivator activity (GO:0001105)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)	7			all cancers(21;2.61e-06)|Epithelial(20;2.92e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00092)|LUSC - Lung squamous cell carcinoma(166;0.154)			GTGCCTTTCTTGGTCCCTTTG	0.488																																					p.K46X		.											.	.	.	0			c.A136T						.						327.0	269.0	289.0					17																	73847681		2203	4300	6503	SO:0001587	stop_gained	23558	exon2			CTTTCTTGGTCCC	U79458	CCDS11731.1	17q25	2008-02-01				ENSG00000132471			12738	protein-coding gene	gene with protein product		606962				7644498	Standard	NM_012478		Approved	WBP-2	uc002jps.3	Q969T9		ENST00000591399.1:c.136A>T	17.37:g.73847681T>A	ENSP00000467579:p.Lys46*	Somatic	58	0		WXS	Illumina HiSeq	.	40	16	NM_012478	O95638	Nonsense_Mutation	SNP	ENST00000591399.1	37	CCDS11731.1	.	.	.	.	.	.	.	.	.	.	T	35	5.478913	0.96291	.	.	ENSG00000132471	ENST00000254806;ENST00000344296;ENST00000433525;ENST00000431190;ENST00000416574	.	.	.	4.72	4.72	0.59763	.	0.091855	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-10.8521	14.4925	0.67660	0.0:0.0:0.0:1.0	.	.	.	.	X	46;24;46;46;46	.	ENSP00000254806:K46X	K	-	1	0	WBP2	71359276	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.826000	0.86716	1.877000	0.54381	0.459000	0.35465	AAG	.		0.488	WBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448862.1	NM_012478	
MRPL2	51069	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	6	43022170	43022170	+	Missense_Mutation	SNP	T	T	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr6:43022170T>C	ENST00000388752.3	-	7	1184	c.760A>G	c.(760-762)Aaa>Gaa	p.K254E	MRPL2_ENST00000230413.5_3'UTR|CUL7_ENST00000265348.3_5'Flank|CUL7_ENST00000535468.1_5'Flank|MRPL2_ENST00000489623.1_3'UTR	NM_015950.3	NP_057034.2	Q5T653	RM02_HUMAN	mitochondrial ribosomal protein L2	254					translation (GO:0006412)	mitochondrion (GO:0005739)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			breast(1)|endometrium(2)|kidney(3)|large_intestine(1)|lung(2)	9		Ovarian(999;0.0014)	Colorectal(64;0.00237)|COAD - Colon adenocarcinoma(64;0.00473)|all cancers(41;0.00708)|OV - Ovarian serous cystadenocarcinoma(102;0.0442)	BRCA - Breast invasive adenocarcinoma(397;0.0026)		ATGACCCGTTTGTTATGATCA	0.567																																					p.K254E		.											.	.	.	0			c.A760G						.						82.0	66.0	71.0					6																	43022170		2203	4300	6503	SO:0001583	missense	51069	exon7			CCCGTTTGTTATG	AB051617	CCDS34454.1, CCDS75458.1	6p21.3	2012-09-13			ENSG00000112651	ENSG00000112651		"""Mitochondrial ribosomal proteins / large subunits"""	14056	protein-coding gene	gene with protein product		611822					Standard	XM_005249161		Approved	MRP-L14, RPML14, CGI-22	uc003ots.1	Q5T653	OTTHUMG00000014719	ENST00000388752.3:c.760A>G	6.37:g.43022170T>C	ENSP00000373404:p.Lys254Glu	Somatic	42	0		WXS	Illumina HiSeq	.	27	5	NM_015950	B2RC56|Q8WUL1|Q96Q56|Q9Y311	Missense_Mutation	SNP	ENST00000388752.3	37	CCDS34454.1	.	.	.	.	.	.	.	.	.	.	T	26.0	4.696513	0.88830	.	.	ENSG00000112651	ENST00000388752	T	0.41400	1.0	5.53	2.96	0.34315	Translation protein SH3-like (1);Ribosomal protein L2, domain 3 (1);Ribosomal protein L2, C-terminal (1);	0.097816	0.64402	D	0.000001	T	0.25938	0.0632	N	0.26092	0.79	0.80722	D	1	P	0.34562	0.457	P	0.47786	0.557	T	0.11012	-1.0605	10	0.39692	T	0.17	-10.3179	10.882	0.46944	0.0:0.0:0.314:0.686	.	254	Q5T653	RM02_HUMAN	E	254	ENSP00000373404:K254E	ENSP00000373404:K254E	K	-	1	0	MRPL2	43130148	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.738000	0.55067	0.906000	0.36621	0.460000	0.39030	AAA	.		0.567	MRPL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040577.2		
CYP20A1	57404	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	2	204111487	204111487	+	Missense_Mutation	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr2:204111487T>G	ENST00000356079.4	+	3	255	c.132T>G	c.(130-132)aaT>aaG	p.N44K	CYP20A1_ENST00000429815.2_Missense_Mutation_p.N44K|CYP20A1_ENST00000461371.1_Intron	NM_177538.2	NP_803882.1	Q6UW02	CP20A_HUMAN	cytochrome P450, family 20, subfamily A, polypeptide 1	44						integral component of membrane (GO:0016021)|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)			cervix(1)|large_intestine(2)|lung(6)|ovary(1)|skin(1)	11						GAGATGGTAATCTTCCAGATA	0.378																																					p.N44K		.											.	.	.	0			c.T132G						.						232.0	220.0	224.0					2																	204111487		2203	4300	6503	SO:0001583	missense	57404	exon3			TGGTAATCTTCCA	AK021770	CCDS2357.1	2q33	2008-02-05			ENSG00000119004	ENSG00000119004		"""Cytochrome P450s"""	20576	protein-coding gene	gene with protein product							Standard	NM_177538		Approved	CYP-M	uc002uzv.4	Q6UW02	OTTHUMG00000132854	ENST00000356079.4:c.132T>G	2.37:g.204111487T>G	ENSP00000348380:p.Asn44Lys	Somatic	79	0		WXS	Illumina HiSeq	.	29	13	NM_177538	Q4ZG61|Q8N4Q8|Q8WWA9|Q9HC04	Missense_Mutation	SNP	ENST00000356079.4	37	CCDS2357.1	.	.	.	.	.	.	.	.	.	.	T	18.07	3.542276	0.65198	.	.	ENSG00000119004	ENST00000356079;ENST00000421618;ENST00000429815;ENST00000443941	T;T;T	0.71461	-0.57;-0.57;-0.57	5.4	2.99	0.34606	.	0.000000	0.85682	D	0.000000	T	0.80539	0.4642	M	0.69823	2.125	0.51233	D	0.999918	D;D	0.89917	1.0;1.0	D;D	0.91635	0.993;0.999	T	0.79035	-0.1968	10	0.87932	D	0	-21.6818	8.8703	0.35311	0.0:0.3068:0.0:0.6932	.	44;44	E9PHG5;Q6UW02	.;CP20A_HUMAN	K	44	ENSP00000348380:N44K;ENSP00000407860:N44K;ENSP00000411341:N44K	ENSP00000348380:N44K	N	+	3	2	CYP20A1	203819732	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	0.727000	0.25999	0.355000	0.24131	0.460000	0.39030	AAT	.		0.378	CYP20A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256328.3	NM_020674	
ZNF204P	7754	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	6	27326564	27326564	+	IGR	SNP	G	G	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr6:27326564G>A								POM121L2 (46615 upstream) : ZNF391 (15829 downstream)																							AATTAGGGCTGAACAGAAACT	0.428																																					.		.											.	.	.	0			.						.																																			SO:0001628	intergenic_variant	7754	.			AGGGCTGAACAGA																													6.37:g.27326564G>A		Somatic	62	0		WXS	Illumina HiSeq	.	55	12	.		RNA	SNP		37																																																																																				.	0	0.428								
RPTN	126638	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	152129068	152129068	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr1:152129068G>T	ENST00000316073.3	-	3	571	c.507C>A	c.(505-507)caC>caA	p.H169Q		NM_001122965.1	NP_001116437.1	Q6XPR3	RPTN_HUMAN	repetin	169	Gln-rich.					cornified envelope (GO:0001533)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)	p.G159_H170delGQSEKQDRDSHH(1)		breast(2)|central_nervous_system(1)|endometrium(14)|kidney(2)|large_intestine(1)|lung(32)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	59						GCTGACTGTGGTGGGAATCTC	0.483																																					p.H169Q		.											.	.	.	1	Deletion - In frame(1)	stomach(1)	c.C507A						.						489.0	422.0	442.0					1																	152129068		1568	3582	5150	SO:0001583	missense	126638	exon3			ACTGTGGTGGGAA	AK096436	CCDS41397.1	1q21.3	2013-01-10			ENSG00000215853	ENSG00000215853		"""EF-hand domain containing"""	26809	protein-coding gene	gene with protein product		613259				15854042	Standard	NM_001122965		Approved	FLJ39117	uc001ezs.1	Q6XPR3	OTTHUMG00000154095	ENST00000316073.3:c.507C>A	1.37:g.152129068G>T	ENSP00000317895:p.His169Gln	Somatic	91	0		WXS	Illumina HiSeq	.	68	9	NM_001122965	B7ZBZ3	Missense_Mutation	SNP	ENST00000316073.3	37	CCDS41397.1	.	.	.	.	.	.	.	.	.	.	G	15.37	2.814040	0.50527	.	.	ENSG00000215853	ENST00000316073	T	0.12672	2.66	5.18	0.862	0.19056	.	0.766141	0.10635	U	0.651661	T	0.15609	0.0376	M	0.80616	2.505	0.09310	N	1	D	0.76494	0.999	D	0.67103	0.949	T	0.10567	-1.0624	10	0.25106	T	0.35	-0.3258	4.4843	0.11781	0.2824:0.1647:0.5528:0.0	.	169	Q6XPR3	RPTN_HUMAN	Q	169	ENSP00000317895:H169Q	ENSP00000317895:H169Q	H	-	3	2	RPTN	150395692	0.001000	0.12720	0.000000	0.03702	0.040000	0.13550	0.116000	0.15561	0.584000	0.29591	0.549000	0.68633	CAC	.		0.483	RPTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333867.1	XM_371312	
FLJ33360	401172	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	5	6337401	6337401	+	lincRNA	SNP	C	C	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr5:6337401C>A	ENST00000507444.1	-	0	4					NR_028351.1																						AGCAGGTGCTCCAAGAACGAT	0.567																																					.		.											.	.	.	0			.						.																																					0	.			GGTGCTCCAAGAA																													5.37:g.6337401C>A		Somatic	13	0		WXS	Illumina HiSeq	.	26	17	.		RNA	SNP	ENST00000507444.1	37																																																																																				.		0.567	CTD-2324F15.2-001	KNOWN	basic|exp_conf	lincRNA	lincRNA	OTTHUMT00000365707.1		
ARMC6	93436	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	19	19162649	19162649	+	Silent	SNP	T	T	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr19:19162649T>C	ENST00000535612.1	+	5	930	c.498T>C	c.(496-498)acT>acC	p.T166T	ARMC6_ENST00000546344.1_Silent_p.T73T|ARMC6_ENST00000269932.6_Silent_p.T141T|ARMC6_ENST00000392336.3_Silent_p.T166T|ARMC6_ENST00000392335.2_Silent_p.T141T	NM_001199196.1	NP_001186125.1	Q6NXE6	ARMC6_HUMAN	armadillo repeat containing 6	166					hematopoietic progenitor cell differentiation (GO:0002244)					NS(1)|endometrium(2)|kidney(1)|large_intestine(1)|liver(2)|lung(5)|ovary(1)|prostate(1)	14			OV - Ovarian serous cystadenocarcinoma(5;5.66e-06)|Epithelial(12;0.000391)			CGGTGCTGACTGATGGACAGC	0.622																																					p.T166T		.											.	.	.	0			c.T498C						.						69.0	55.0	59.0					19																	19162649		2203	4300	6503	SO:0001819	synonymous_variant	93436	exon5			GCTGACTGATGGA	BX648486	CCDS32965.1, CCDS56089.1	19p13	2013-02-14				ENSG00000105676		"""Armadillo repeat containing"""	25049	protein-coding gene	gene with protein product						12477932	Standard	NM_033415		Approved	MGC19595	uc002nlc.3	Q6NXE6		ENST00000535612.1:c.498T>C	19.37:g.19162649T>C		Somatic	21	0		WXS	Illumina HiSeq	.	18	9	NM_001199196	B4DI98|O94999|Q9BTH5	Silent	SNP	ENST00000535612.1	37	CCDS56089.1																																																																																			.		0.622	ARMC6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000403226.1	NM_033415	
RAPGEF3	10411	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	12	48131422	48131422	+	Silent	SNP	A	A	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr12:48131422A>T	ENST00000449771.2	-	28	2788	c.2700T>A	c.(2698-2700)gcT>gcA	p.A900A	RAPGEF3_ENST00000389212.3_Silent_p.A900A|RAPGEF3_ENST00000548919.1_Silent_p.A791A|RAPGEF3_ENST00000549151.1_Silent_p.A858A|RAPGEF3_ENST00000171000.4_Silent_p.A858A|RP1-197B17.3_ENST00000547799.1_lincRNA|RAPGEF3_ENST00000405493.2_Silent_p.A858A			O95398	RPGF3_HUMAN	Rap guanine nucleotide exchange factor (GEF) 3	900					angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cAMP-mediated signaling (GO:0019933)|cell proliferation (GO:0008283)|cellular response to cAMP (GO:0071320)|energy reserve metabolic process (GO:0006112)|establishment of endothelial barrier (GO:0061028)|platelet activation (GO:0030168)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cAMP catabolic process (GO:0030822)|positive regulation of Rap GTPase activity (GO:0032854)|positive regulation of stress fiber assembly (GO:0051496)|Rap protein signal transduction (GO:0032486)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cAMP-dependent protein kinase complex (GO:0005952)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cAMP binding (GO:0030552)|cAMP-dependent protein kinase regulator activity (GO:0008603)|guanyl-nucleotide exchange factor activity (GO:0005085)|Rap guanyl-nucleotide exchange factor activity (GO:0017034)			endometrium(1)|kidney(2)|large_intestine(4)|lung(9)|pancreas(1)|prostate(1)|skin(7)	25	Lung SC(27;0.192)			GBM - Glioblastoma multiforme(48;0.0375)		GCTGGACATAAGCCCAGGTGC	0.632																																					p.A900A		.											.	.	.	0			c.T2700A						.						55.0	51.0	53.0					12																	48131422		2203	4300	6503	SO:0001819	synonymous_variant	10411	exon28			GACATAAGCCCAG	AK092448	CCDS31784.1, CCDS41775.1	12q13.1	2006-04-12	2004-03-26		ENSG00000079337	ENSG00000079337			16629	protein-coding gene	gene with protein product	"""exchange protein directly activated by cAMP 1"""	606057	"""RAP guanine-nucleotide-exchange factor (GEF) 3"""			10777494, 9856955	Standard	NM_001098531		Approved	cAMP-GEFI, EPAC, bcm910	uc001rpz.4	O95398	OTTHUMG00000133667	ENST00000449771.2:c.2700T>A	12.37:g.48131422A>T		Somatic	50	0		WXS	Illumina HiSeq	.	43	16	NM_001098531	A8K2G5|E7EQC8|O95634|Q8WVN0	Silent	SNP	ENST00000449771.2	37	CCDS41775.1																																																																																			.		0.632	RAPGEF3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257848.1	NM_006105	
MARCH6	10299	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	5	10402698	10402698	+	Nonsense_Mutation	SNP	G	G	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr5:10402698G>A	ENST00000274140.5	+	14	1308	c.1176G>A	c.(1174-1176)tgG>tgA	p.W392*	MARCH6_ENST00000449913.2_Nonsense_Mutation_p.W344*|MARCH6_ENST00000503788.1_Nonsense_Mutation_p.W287*|MARCH6_ENST00000510792.1_Nonsense_Mutation_p.W90*	NM_005885.3	NP_005876.2	O60337	MARH6_HUMAN	membrane-associated ring finger (C3HC4) 6, E3 ubiquitin protein ligase	392					protein K48-linked ubiquitination (GO:0070936)	integral component of endoplasmic reticulum membrane (GO:0030176)|membrane (GO:0016020)	enzyme binding (GO:0019899)|ligase activity (GO:0016874)|ubiquitin conjugating enzyme binding (GO:0031624)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(7)|lung(35)|ovary(1)|urinary_tract(3)	54						TTTGTGGTTGGTGGCTGGATA	0.358																																					p.W392X		.											.	.	.	0			c.G1176A						.						382.0	365.0	371.0					5																	10402698		2203	4300	6503	SO:0001587	stop_gained	10299	exon14			TGGTTGGTGGCTG	AB011169	CCDS34135.1, CCDS59487.1, CCDS59488.1	5p15.2	2013-01-09	2012-02-23		ENSG00000145495	ENSG00000145495		"""MARCH membrane-associated ring fingers"", ""RING-type (C3HC4) zinc fingers"""	30550	protein-coding gene	gene with protein product		613297	"""membrane-associated ring finger (C3HC4) 6"""			14722266	Standard	NM_001270660		Approved	TEB4, MARCH-VI, RNF176	uc003jet.2	O60337	OTTHUMG00000162027	ENST00000274140.5:c.1176G>A	5.37:g.10402698G>A	ENSP00000274140:p.Trp392*	Somatic	93	0		WXS	Illumina HiSeq	.	121	18	NM_005885	A5PKZ4|B4DKJ2|B4DT33|D3DTC8|O14670|Q86X77	Nonsense_Mutation	SNP	ENST00000274140.5	37	CCDS34135.1	.	.	.	.	.	.	.	.	.	.	G	39	7.481141	0.98309	.	.	ENSG00000145495	ENST00000449913;ENST00000503788;ENST00000274140;ENST00000510792	.	.	.	5.85	5.85	0.93711	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-13.8348	20.1634	0.98142	0.0:0.0:1.0:0.0	.	.	.	.	X	344;287;392;90	.	ENSP00000274140:W392X	W	+	3	0	MARCH6	10455698	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.112000	0.94314	2.773000	0.95371	0.655000	0.94253	TGG	.		0.358	MARCH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366919.2	NM_005885	
C10orf62	414157	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	10	99350107	99350107	+	Silent	SNP	T	T	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr10:99350107T>C	ENST00000370640.3	+	1	658	c.453T>C	c.(451-453)gcT>gcC	p.A151A	PI4K2A_ENST00000370649.3_Intron|PI4K2A_ENST00000555577.1_Intron|HOGA1_ENST00000370647.4_Intron|HOGA1_ENST00000370646.4_Intron	NM_001009997.2	NP_001009997.2	Q5T681	CJ062_HUMAN	chromosome 10 open reading frame 62	151										endometrium(2)|kidney(1)|lung(1)	4		Colorectal(252;0.162)		Epithelial(162;9.58e-11)|all cancers(201;8.62e-09)		GGGCCATAGCTTACCAGCACT	0.602																																					p.A151A		.											.	.	.	0			c.T453C						.						68.0	67.0	67.0					10																	99350107		2203	4300	6503	SO:0001819	synonymous_variant	414157	exon1			CATAGCTTACCAG		CCDS31261.1	10q24.2	2012-05-31			ENSG00000203942	ENSG00000203942			23294	protein-coding gene	gene with protein product							Standard	NM_001009997		Approved	bA548K23.1	uc001koa.3	Q5T681	OTTHUMG00000018858	ENST00000370640.3:c.453T>C	10.37:g.99350107T>C		Somatic	50	0		WXS	Illumina HiSeq	.	35	15	NM_001009997	Q49A70|Q8N3Y6	Silent	SNP	ENST00000370640.3	37	CCDS31261.1																																																																																			.		0.602	C10orf62-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049723.1	NM_001009997	
TGFBR2	7048	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	3	30686364	30686364	+	Missense_Mutation	SNP	A	A	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr3:30686364A>G	ENST00000295754.5	+	2	602	c.220A>G	c.(220-222)Acc>Gcc	p.T74A	TGFBR2_ENST00000359013.4_Missense_Mutation_p.T99A	NM_003242.5	NP_003233.4	P37173	TGFR2_HUMAN	transforming growth factor, beta receptor II (70/80kDa)	74					activation of protein kinase activity (GO:0032147)|aging (GO:0007568)|apoptotic process (GO:0006915)|blood vessel development (GO:0001568)|brain development (GO:0007420)|bronchus morphogenesis (GO:0060434)|cartilage development (GO:0051216)|common-partner SMAD protein phosphorylation (GO:0007182)|digestive tract development (GO:0048565)|embryo implantation (GO:0007566)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic hemopoiesis (GO:0035162)|gastrulation (GO:0007369)|heart development (GO:0007507)|in utero embryonic development (GO:0001701)|lens development in camera-type eye (GO:0002088)|lens fiber cell apoptotic process (GO:1990086)|lung lobe morphogenesis (GO:0060463)|mammary gland morphogenesis (GO:0060443)|myeloid dendritic cell differentiation (GO:0043011)|negative regulation of cardiac muscle cell proliferation (GO:0060044)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|organ regeneration (GO:0031100)|palate development (GO:0060021)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|patterning of blood vessels (GO:0001569)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of angiogenesis (GO:0045766)|positive regulation of B cell tolerance induction (GO:0002663)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of NK T cell differentiation (GO:0051138)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of skeletal muscle tissue regeneration (GO:0043415)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of T cell tolerance induction (GO:0002666)|positive regulation of tolerance induction to self antigen (GO:0002651)|protein phosphorylation (GO:0006468)|receptor-mediated endocytosis (GO:0006898)|regulation of cell proliferation (GO:0042127)|response to cholesterol (GO:0070723)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|response to glucose (GO:0009749)|response to mechanical stimulus (GO:0009612)|response to nutrient (GO:0007584)|smoothened signaling pathway (GO:0007224)|trachea formation (GO:0060440)|transforming growth factor beta receptor signaling pathway (GO:0007179)|vasculogenesis (GO:0001570)|wound healing (GO:0042060)	caveola (GO:0005901)|cytosol (GO:0005829)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|transforming growth factor beta receptor homodimeric complex (GO:0070022)	ATP binding (GO:0005524)|glycosaminoglycan binding (GO:0005539)|metal ion binding (GO:0046872)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|SMAD binding (GO:0046332)|transforming growth factor beta binding (GO:0050431)|transforming growth factor beta receptor activity, type II (GO:0005026)|transforming growth factor beta-activated receptor activity (GO:0005024)|transmembrane receptor protein serine/threonine kinase activity (GO:0004675)|type I transforming growth factor beta receptor binding (GO:0034713)|type III transforming growth factor beta receptor binding (GO:0034714)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(15)|lung(10)|ovary(3)|pancreas(12)|skin(1)|stomach(5)|upper_aerodigestive_tract(2)	53						CTGCAGCATCACCTCCATCTG	0.418																																					p.T99A		.											.	.	.	0			c.A295G						.						75.0	67.0	70.0					3																	30686364		2203	4300	6503	SO:0001583	missense	7048	exon3			AGCATCACCTCCA		CCDS2648.1, CCDS33727.1	3p22	2014-09-17	2002-08-29		ENSG00000163513	ENSG00000163513			11773	protein-coding gene	gene with protein product		190182	"""transforming growth factor, beta receptor II (70-80kD)"""	MFS2		1319842, 15235604	Standard	NM_001024847		Approved		uc003cen.3	P37173	OTTHUMG00000130569	ENST00000295754.5:c.220A>G	3.37:g.30686364A>G	ENSP00000295754:p.Thr74Ala	Somatic	65	0		WXS	Illumina HiSeq	.	12	11	NM_001024847	B4DTV5|Q15580|Q6DKT6|Q99474	Missense_Mutation	SNP	ENST00000295754.5	37	CCDS2648.1	.	.	.	.	.	.	.	.	.	.	A	16.62	3.174179	0.57692	.	.	ENSG00000163513	ENST00000295754;ENST00000359013	D;D	0.84516	-1.86;-1.86	5.66	5.66	0.87406	Transforming growth factor beta receptor 2 ectodomain (1);	0.096340	0.64402	D	0.000001	T	0.81336	0.4801	L	0.41961	1.31	0.53688	D	0.999971	B;B	0.09022	0.0;0.002	B;B	0.19666	0.011;0.026	T	0.76482	-0.2943	10	0.39692	T	0.17	.	14.8777	0.70507	1.0:0.0:0.0:0.0	.	74;99	P37173;D2JYI1	TGFR2_HUMAN;.	A	74;99	ENSP00000295754:T74A;ENSP00000351905:T99A	ENSP00000295754:T74A	T	+	1	0	TGFBR2	30661368	1.000000	0.71417	0.995000	0.50966	0.950000	0.60333	5.410000	0.66381	2.147000	0.66899	0.533000	0.62120	ACC	.		0.418	TGFBR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252994.2		
SHBG	6462	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	17	7533491	7533491	+	Start_Codon_SNP	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr17:7533491A>C	ENST00000380450.4	+	1	32	c.1A>C	c.(1-3)Atg>Ctg	p.M1L	SHBG_ENST00000570547.1_Intron|SHBG_ENST00000575314.1_Intron|SHBG_ENST00000572262.1_Intron|SHBG_ENST00000574539.1_Intron|SHBG_ENST00000416273.3_Start_Codon_SNP_p.M1L|SAT2_ENST00000573566.1_5'Flank|SHBG_ENST00000576728.1_Intron|SAT2_ENST00000380466.2_5'Flank|SHBG_ENST00000572182.1_Intron|SHBG_ENST00000575903.1_Start_Codon_SNP_p.M1L|SHBG_ENST00000576478.1_Intron|SHBG_ENST00000441599.2_Start_Codon_SNP_p.M1L|SAT2_ENST00000269298.5_5'Flank|SHBG_ENST00000340624.5_Intron	NM_001040.3	NP_001031.2	P04278	SHBG_HUMAN	sex hormone-binding globulin	1					primary spermatocyte growth (GO:0007285)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	androgen binding (GO:0005497)	p.?(1)		cervix(1)|endometrium(2)|large_intestine(4)|lung(2)|skin(1)	10		all_cancers(10;0.0867)		READ - Rectum adenocarcinoma(115;0.168)	Danazol(DB01406)|Drostanolone(DB00858)|Estradiol(DB00783)|Estropipate(DB04574)|Fluoxymesterone(DB01185)|Hydrocortisone(DB00741)|Methyltestosterone(DB06710)|Mitotane(DB00648)|Norethindrone(DB00717)|Spironolactone(DB00421)|Testosterone(DB00624)|transdermal testosterone gel(DB05275)	GTGGCTGATTATGGAGAGCAG	0.612																																					p.M1L		.											.	.	.	1	Unknown(1)	haematopoietic_and_lymphoid_tissue(1)	c.A1C						.						54.0	49.0	51.0					17																	7533491		2203	4300	6503	SO:0001582	initiator_codon_variant	6462	exon1			CTGATTATGGAGA		CCDS11117.1, CCDS54082.1, CCDS54083.1, CCDS58513.1, CCDS73961.1, CCDS73962.1	17p13.1	2013-09-19			ENSG00000129214	ENSG00000129214			10839	protein-coding gene	gene with protein product	"""androgen binding protein"""	182205				2587256	Standard	NM_001146279		Approved	ABP, TEBG, MGC126834, MGC138391	uc002gie.2	P04278	OTTHUMG00000108153	ENST00000380450.4:c.1A>C	17.37:g.7533491A>C	ENSP00000369816:p.Met1Leu	Somatic	27	0		WXS	Illumina HiSeq	.	18	7	NM_001040	B0FWH4|E9PGW1|F5H5Z8|I3L1N7|P14689|Q16616|Q3MIL0|Q6ISD2	Missense_Mutation	SNP	ENST00000380450.4	37	CCDS11117.1	.	.	.	.	.	.	.	.	.	.	A	12.53	1.965655	0.34659	.	.	ENSG00000129214	ENST00000441599;ENST00000416273;ENST00000441313;ENST00000452698;ENST00000380450	T;D;D	0.89875	-1.45;-2.03;-2.58	4.52	2.23	0.28157	.	0.308756	0.31542	N	0.007469	D	0.82430	0.5035	.	.	.	0.58432	D	0.999995	B;B;B;B;B	0.25312	0.047;0.028;0.123;0.123;0.123	B;B;B;B;B	0.20577	0.013;0.006;0.02;0.03;0.02	T	0.75271	-0.3376	9	0.87932	D	0	-0.5135	6.1575	0.20346	0.7911:0.0:0.2089:0.0	.	1;1;1;1;1	F5H5Z8;E9PH59;E9PGW1;E9PGQ3;P04278	.;.;.;.;SHBG_HUMAN	L	1	ENSP00000393426:M1L;ENSP00000388867:M1L;ENSP00000369816:M1L	ENSP00000369816:M1L	M	+	1	0	SHBG	7474216	0.544000	0.26441	0.393000	0.26258	0.435000	0.31806	0.814000	0.27239	0.249000	0.21456	0.459000	0.35465	ATG	.		0.612	SHBG-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000226957.2	NM_001040	Missense_Mutation
FMN1	342184	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	15	33256352	33256352	+	Missense_Mutation	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr15:33256352T>G	ENST00000559047.1	-	6	3093	c.3094A>C	c.(3094-3096)Aaa>Caa	p.K1032Q	FMN1_ENST00000561249.1_Missense_Mutation_p.K934Q|FMN1_ENST00000334528.9_Missense_Mutation_p.K809Q			Q68DA7	FMN1_HUMAN	formin 1	1032	FH2. {ECO:0000255|PROSITE- ProRule:PRU00774}.				actin nucleation (GO:0045010)	actin filament (GO:0005884)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|lung(14)|ovary(2)|prostate(1)|upper_aerodigestive_tract(3)	29		all_lung(180;1.14e-07)		all cancers(64;3.05e-15)|Epithelial(43;1.67e-10)|GBM - Glioblastoma multiforme(186;4.95e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0262)		GACAGAGGTTTTTTCTTCTGT	0.373																																					p.K809Q		.											.	.	.	0			c.A2425C						.						189.0	171.0	176.0					15																	33256352		1808	4068	5876	SO:0001583	missense	342184	exon5			GAGGTTTTTTCTT	AH002864	CCDS45209.1, CCDS61581.1, CCDS61582.1	15q13.3	2013-06-13	2005-01-20	2005-01-22	ENSG00000248905	ENSG00000248905			3768	protein-coding gene	gene with protein product	"""limb deformity protein"""	136535	"""formin (limb deformity)"""	LD, FMN		1673046	Standard	NM_001277313		Approved	DKFZP686C2281, FLJ45135, MGC125288, MGC125289	uc031qrh.1	Q68DA7	OTTHUMG00000172201	ENST00000559047.1:c.3094A>C	15.37:g.33256352T>G	ENSP00000454047:p.Lys1032Gln	Somatic	105	0		WXS	Illumina HiSeq	.	68	28	NM_001103184	Q3B7I6|Q3ZAR4|Q6ZSY1	Missense_Mutation	SNP	ENST00000559047.1	37		.	.	.	.	.	.	.	.	.	.	T	17.94	3.510684	0.64522	.	.	ENSG00000248905	ENST00000334528	T	0.19250	2.16	5.06	5.06	0.68205	.	0.046086	0.85682	D	0.000000	T	0.46386	0.1390	M	0.77616	2.38	0.21802	N	0.999536	D	0.59767	0.986	D	0.66351	0.943	T	0.59547	-0.7434	9	0.62326	D	0.03	.	14.8008	0.69913	0.0:0.0:0.0:1.0	.	809	Q68DA7-5	.	Q	809	ENSP00000333950:K809Q	ENSP00000333950:K809Q	K	-	1	0	FMN1	31043644	1.000000	0.71417	1.000000	0.80357	0.661000	0.39034	7.699000	0.84547	1.890000	0.54733	0.460000	0.39030	AAA	.		0.373	FMN1-005	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000417414.1	NM_001103184	
ALOX12B	242	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	17	7976095	7976095	+	Silent	SNP	A	A	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr17:7976095A>G	ENST00000319144.4	-	15	2360	c.2100T>C	c.(2098-2100)tcT>tcC	p.S700S	ALOX12B_ENST00000577351.1_5'Flank	NM_001139.2	NP_001130.1	O75342	LX12B_HUMAN	arachidonate 12-lipoxygenase, 12R type	700	Lipoxygenase. {ECO:0000255|PROSITE- ProRule:PRU00726}.				arachidonic acid metabolic process (GO:0019369)|ceramide biosynthetic process (GO:0046513)|establishment of skin barrier (GO:0061436)|hepoxilin biosynthetic process (GO:0051122)|linoleic acid metabolic process (GO:0043651)|lipoxygenase pathway (GO:0019372)|oxidation-reduction process (GO:0055114)|positive regulation of gene expression (GO:0010628)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mucus secretion (GO:0070257)|protein lipidation (GO:0006497)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	cytosol (GO:0005829)	arachidonate 12-lipoxygenase activity (GO:0004052)|iron ion binding (GO:0005506)|linoleate 9S-lipoxygenase activity (GO:1990136)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen (GO:0016702)			endometrium(5)|kidney(1)|large_intestine(3)|lung(5)|prostate(1)|stomach(1)	16						GCTCCTAAATAGAAATGCTGT	0.493										Multiple Myeloma(8;0.094)																											p.S700S		.											.	.	.	0			c.T2100C						.						163.0	150.0	155.0					17																	7976095		2203	4300	6503	SO:0001819	synonymous_variant	242	exon15			CTAAATAGAAATG	AF038461	CCDS11129.1	17p13.1	2008-03-18			ENSG00000179477	ENSG00000179477	1.13.11.-	"""Arachidonate lipoxygenases"""	430	protein-coding gene	gene with protein product		603741				9618483	Standard	NM_001139		Approved	12R-LOX	uc002gjy.1	O75342	OTTHUMG00000108180	ENST00000319144.4:c.2100T>C	17.37:g.7976095A>G		Somatic	37	0		WXS	Illumina HiSeq	.	41	20	NM_001139		Silent	SNP	ENST00000319144.4	37	CCDS11129.1																																																																																			.		0.493	ALOX12B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226984.3		
ISX	91464	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	22	35481519	35481519	+	Nonsense_Mutation	SNP	C	C	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr22:35481519C>T	ENST00000308700.6	+	4	1523	c.571C>T	c.(571-573)Cag>Tag	p.Q191*	ISX_ENST00000404699.2_Nonsense_Mutation_p.Q191*	NM_001008494.1	NP_001008494.1	Q2M1V0	ISX_HUMAN	intestine-specific homeobox	191					regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of vitamin A metabolic process (GO:1901738)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(12)|ovary(3)|prostate(1)|skin(4)	26						GGCTCAAGATCAGCTGGCCTC	0.607																																					p.Q191X		.											.	.	.	0			c.C571T						.						173.0	135.0	148.0					22																	35481519		2203	4300	6503	SO:0001587	stop_gained	91464	exon4			CAAGATCAGCTGG	AK025181	CCDS33640.1	22q12.3	2011-06-20			ENSG00000175329	ENSG00000175329		"""Homeoboxes / PRD class"""	28084	protein-coding gene	gene with protein product		612019					Standard	NM_001008494		Approved	RAXLX	uc003anj.3	Q2M1V0	OTTHUMG00000150962	ENST00000308700.6:c.571C>T	22.37:g.35481519C>T	ENSP00000311492:p.Gln191*	Somatic	30	0		WXS	Illumina HiSeq	.	29	15	NM_001008494	Q68DJ5	Nonsense_Mutation	SNP	ENST00000308700.6	37	CCDS33640.1	.	.	.	.	.	.	.	.	.	.	C	44	10.906949	0.99487	.	.	ENSG00000175329	ENST00000308700;ENST00000404699	.	.	.	5.02	3.97	0.46021	.	0.159061	0.29940	N	0.010803	.	.	.	.	.	.	0.58432	D	0.999996	.	.	.	.	.	.	.	.	.	.	0.06099	T	0.92	.	10.6139	0.45439	0.1923:0.8077:0.0:0.0	.	.	.	.	X	191	.	ENSP00000311492:Q191X	Q	+	1	0	ISX	33811519	0.107000	0.21998	0.016000	0.15963	0.408000	0.30992	1.812000	0.38952	1.059000	0.40554	0.655000	0.94253	CAG	.		0.607	ISX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320662.1	NM_001008494	
MSH5	4439	hgsc.bcm.edu	37	6	31711843	31711843	+	Intron	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr6:31711843A>C	ENST00000375755.3	+	6	823				MSH5_ENST00000431848.2_5'Flank|MSH5_ENST00000482280.1_Intron|MSH5_ENST00000534153.4_Intron|MSH5_ENST00000375750.3_Intron|MSH5_ENST00000375740.3_Intron|MSH5-SAPCD1_ENST00000493662.2_Intron|MSH5_ENST00000375703.3_Intron|MSH5_ENST00000375742.3_Intron	NM_002441.4	NP_002432.1	O43196	MSH5_HUMAN	mutS homolog 5						ATP catabolic process (GO:0006200)|chiasma assembly (GO:0051026)|homologous chromosome segregation (GO:0045143)|mismatch repair (GO:0006298)|reciprocal meiotic recombination (GO:0007131)	synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|DNA-dependent ATPase activity (GO:0008094)|mismatched DNA binding (GO:0030983)			breast(1)|ovary(2)|skin(2)	5						GAGGCGGCACAAGTGCTAGGG	0.527								Direct reversal of damage;Mismatch excision repair (MMR)																													.		.											.	.	.	0			.						.						111.0	127.0	121.0					6																	31711843		1511	2709	4220	SO:0001627	intron_variant	100532732	.			CGGCACAAGTGCT	AF070071	CCDS4720.1, CCDS34409.1, CCDS34410.1, CCDS34409.2	6p21.3	2013-09-12	2013-09-12		ENSG00000204410	ENSG00000204410			7328	protein-coding gene	gene with protein product		603382	"""mutS (E. coli) homolog 5"", ""mutS homolog 5 (E. coli)"""			9740671, 9787078, 17977839	Standard	NM_002441		Approved		uc011hbg.2	O43196	OTTHUMG00000167551	ENST00000375755.3:c.537+41A>C	6.37:g.31711843A>C		Somatic	46	0		WXS	Illumina HiSeq	.	30	17	.	B0V033|B0V034|O60586|Q5BLU9|Q5SSR1|Q8IW44|Q9BQC7	RNA	SNP	ENST00000375755.3	37	CCDS4720.1																																																																																			.		0.527	MSH5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076243.4		
UBR5	51366	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	8	103299709	103299709	+	Missense_Mutation	SNP	T	T	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr8:103299709T>C	ENST00000520539.1	-	37	5515	c.4909A>G	c.(4909-4911)Agt>Ggt	p.S1637G	UBR5_ENST00000220959.4_Missense_Mutation_p.S1637G|UBR5_ENST00000521922.1_Missense_Mutation_p.S1631G|UBR5_ENST00000519528.1_5'Flank	NM_001282873.1|NM_015902.5	NP_001269802.1|NP_056986.2	O95071	UBR5_HUMAN	ubiquitin protein ligase E3 component n-recognin 5	1637					cell proliferation (GO:0008283)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|negative regulation of double-strand break repair (GO:2000780)|negative regulation of histone H2A K63-linked ubiquitination (GO:1901315)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of protein import into nucleus, translocation (GO:0033160)|progesterone receptor signaling pathway (GO:0050847)|protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ligase activity (GO:0016874)|RNA binding (GO:0003723)|ubiquitin-protein transferase activity (GO:0004842)|ubiquitin-ubiquitin ligase activity (GO:0034450)|zinc ion binding (GO:0008270)			NS(1)|breast(13)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(8)|large_intestine(19)|liver(1)|lung(51)|ovary(6)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	124	all_cancers(14;8e-07)|all_epithelial(15;2.18e-08)|Lung NSC(17;2.55e-05)|all_lung(17;8.85e-05)		OV - Ovarian serous cystadenocarcinoma(57;0.000442)			CTGCGCCCACTAGCATTATCT	0.438																																					p.S1637G	Ovarian(131;96 1741 5634 7352 27489)	.											.	.	.	0			c.A4909G						.						199.0	148.0	165.0					8																	103299709		2203	4300	6503	SO:0001583	missense	51366	exon37			GCCCACTAGCATT	AF006010	CCDS34933.1, CCDS64946.1	8q22	2008-06-23	2007-06-19	2007-06-19	ENSG00000104517	ENSG00000104517		"""Ubiquitin protein ligase E3 component n-recognins"""	16806	protein-coding gene	gene with protein product		608413	"""E3 ubiquitin protein ligase, HECT domain containing, 1"""	EDD1		10030672, 16055722	Standard	NM_015902		Approved	DD5, HYD, EDD, KIAA0896	uc003ykr.2	O95071	OTTHUMG00000164755	ENST00000520539.1:c.4909A>G	8.37:g.103299709T>C	ENSP00000429084:p.Ser1637Gly	Somatic	26	0		WXS	Illumina HiSeq	.	27	10	NM_015902	B2RP24|J3KMW7|O94970|Q9NPL3	Missense_Mutation	SNP	ENST00000520539.1	37	CCDS34933.1	.	.	.	.	.	.	.	.	.	.	T	32	5.147472	0.94603	.	.	ENSG00000104517	ENST00000520539;ENST00000220959;ENST00000521922	T;T;T	0.48836	0.8;0.8;0.8	5.96	5.96	0.96718	.	0.000000	0.85682	D	0.000000	T	0.61615	0.2361	L	0.50333	1.59	0.80722	D	1	P;P	0.49447	0.924;0.924	P;P	0.60682	0.878;0.878	T	0.60052	-0.7338	10	0.46703	T	0.11	.	16.4245	0.83810	0.0:0.0:0.0:1.0	.	1631;1637	E7EMW7;O95071	.;UBR5_HUMAN	G	1637;1637;1631	ENSP00000429084:S1637G;ENSP00000220959:S1637G;ENSP00000427819:S1631G	ENSP00000220959:S1637G	S	-	1	0	UBR5	103368885	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.991000	0.88244	2.283000	0.76528	0.533000	0.62120	AGT	.		0.438	UBR5-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000380075.2	NM_015902	
UTP20	27340	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	12	101705835	101705835	+	Missense_Mutation	SNP	T	T	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr12:101705835T>C	ENST00000261637.4	+	21	2507	c.2333T>C	c.(2332-2334)aTg>aCg	p.M778T		NM_014503.2	NP_055318.2	O75691	UTP20_HUMAN	UTP20, small subunit (SSU) processome component, homolog (yeast)	778					endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000480)|endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000447)|endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000472)|negative regulation of cell proliferation (GO:0008285)|rRNA processing (GO:0006364)	90S preribosome (GO:0030686)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|preribosome, small subunit precursor (GO:0030688)|small-subunit processome (GO:0032040)	poly(A) RNA binding (GO:0044822)			NS(3)|biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(26)|lung(30)|ovary(2)|prostate(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	88						CAGAATGATATGACAGATGAG	0.403																																					p.M778T		.											.	.	.	0			c.T2333C						.						109.0	114.0	112.0					12																	101705835		2203	4300	6503	SO:0001583	missense	27340	exon21			ATGATATGACAGA	AJ006778	CCDS9081.1	12q23	2006-02-11				ENSG00000120800			17897	protein-coding gene	gene with protein product	"""down regulated in metastasis"""	612822				9673349, 15590835, 12837249	Standard	NM_014503		Approved	DRIM	uc001tia.1	O75691	OTTHUMG00000170270	ENST00000261637.4:c.2333T>C	12.37:g.101705835T>C	ENSP00000261637:p.Met778Thr	Somatic	54	0		WXS	Illumina HiSeq	.	37	22	NM_014503	Q9H3H4	Missense_Mutation	SNP	ENST00000261637.4	37	CCDS9081.1	.	.	.	.	.	.	.	.	.	.	T	3.792	-0.043415	0.07452	.	.	ENSG00000120800	ENST00000261637	T	0.16324	2.35	5.07	-5.87	0.02297	Armadillo-type fold (1);	2.548160	0.00810	N	0.001488	T	0.04861	0.0131	N	0.00926	-1.1	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.33343	-0.9872	10	0.13853	T	0.58	8.0454	7.2386	0.26084	0.2089:0.4337:0.0:0.3574	.	778	O75691	UTP20_HUMAN	T	778	ENSP00000261637:M778T	ENSP00000261637:M778T	M	+	2	0	UTP20	100229966	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	0.232000	0.17891	-1.060000	0.03189	-0.250000	0.11733	ATG	.		0.403	UTP20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408242.1	NM_014503	
ZBTB21	49854	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	21	43412457	43412457	+	Missense_Mutation	SNP	C	C	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr21:43412457C>G	ENST00000310826.5	-	3	1931	c.1748G>C	c.(1747-1749)aGg>aCg	p.R583T	ZBTB21_ENST00000465968.1_Intron|ZBTB21_ENST00000398505.3_Intron|ZBTB21_ENST00000398511.3_Missense_Mutation_p.R583T|ZBTB21_ENST00000398499.1_Missense_Mutation_p.R583T	NM_001098402.1	NP_001091872.1	Q9ULJ3	ZBT21_HUMAN	zinc finger and BTB domain containing 21	583					negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|methyl-CpG binding (GO:0008327)										GGTGTGAAACCTCTTGTGACA	0.453																																					p.R583T		.											.	.	.	0			c.G1748C						.						154.0	150.0	151.0					21																	43412457		2203	4300	6503	SO:0001583	missense	49854	exon3			TGAAACCTCTTGT	AB033053	CCDS13678.1, CCDS42934.1	21q22.3	2013-01-09	2013-01-09	2013-01-09	ENSG00000173276	ENSG00000173276		"""-"", ""BTB/POZ domain containing"", ""Zinc fingers, C2H2-type"""	13083	protein-coding gene	gene with protein product			"""zinc finger protein 295"""	ZNF295			Standard	NM_020727		Approved	KIAA1227	uc002yzy.4	Q9ULJ3	OTTHUMG00000086789	ENST00000310826.5:c.1748G>C	21.37:g.43412457C>G	ENSP00000308759:p.Arg583Thr	Somatic	47	0		WXS	Illumina HiSeq	.	10	9	NM_001098402	Q5R2W1|Q5R2W2|Q6P4R0	Missense_Mutation	SNP	ENST00000310826.5	37	CCDS13678.1	.	.	.	.	.	.	.	.	.	.	C	15.82	2.944955	0.53079	.	.	ENSG00000173276	ENST00000310826;ENST00000398499;ENST00000398511	T;T;T	0.14516	2.5;2.5;2.5	5.68	5.68	0.88126	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (1);	0.000000	0.85682	D	0.000000	T	0.23171	0.0560	N	0.25647	0.755	0.50813	D	0.999894	D	0.89917	1.0	D	0.91635	0.999	T	0.01290	-1.1394	10	0.02654	T	1	-14.5011	19.7842	0.96430	0.0:1.0:0.0:0.0	.	583	Q9ULJ3	ZN295_HUMAN	T	583	ENSP00000308759:R583T;ENSP00000381512:R583T;ENSP00000381523:R583T	ENSP00000308759:R583T	R	-	2	0	ZNF295	42285526	1.000000	0.71417	0.963000	0.40424	0.998000	0.95712	7.289000	0.78701	2.676000	0.91093	0.591000	0.81541	AGG	.		0.453	ZBTB21-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195308.1	NM_020727	
ATXN7L3B	552889	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	12	74932028	74932028	+	Missense_Mutation	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr12:74932028T>G	ENST00000519948.2	+	1	478	c.136T>G	c.(136-138)Ttc>Gtc	p.F46V	RP11-56G10.2_ENST00000550926.1_RNA	NM_001136262.1	NP_001129734.1	Q96GX2	A7L3B_HUMAN	ataxin 7-like 3B	46																	GTGTGGCTACTTCTACCTGGA	0.542																																					p.F46V		.											.	.	.	0			c.T136G						.						160.0	146.0	150.0					12																	74932028		692	1591	2283	SO:0001583	missense	552889	exon1			GGCTACTTCTACC		CCDS53815.1	12q21	2013-02-15			ENSG00000253719	ENSG00000253719			37931	protein-coding gene	gene with protein product		615579					Standard	NM_001136262		Approved		uc001sxd.4	Q96GX2	OTTHUMG00000163936	ENST00000519948.2:c.136T>G	12.37:g.74932028T>G	ENSP00000430000:p.Phe46Val	Somatic	68	0		WXS	Illumina HiSeq	.	39	14	NM_001136262		Missense_Mutation	SNP	ENST00000519948.2	37	CCDS53815.1	.	.	.	.	.	.	.	.	.	.	T	17.31	3.356109	0.61293	.	.	ENSG00000253719	ENST00000519948	.	.	.	4.23	4.23	0.50019	.	.	.	.	.	T	0.75162	0.3812	.	.	.	0.50632	D	0.99988	D	0.69078	0.997	D	0.68483	0.958	T	0.77840	-0.2438	7	0.87932	D	0	.	10.0116	0.41990	0.0:0.0:0.0:1.0	.	46	Q96GX2	A7L3B_HUMAN	V	46	.	ENSP00000430000:F46V	F	+	1	0	ATXN7L3B	73218295	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	6.776000	0.75023	2.133000	0.65898	0.482000	0.46254	TTC	.		0.542	ATXN7L3B-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376473.1	NM_001136262	
LMBR1	64327	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	7	156589175	156589175	+	Missense_Mutation	SNP	G	G	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr7:156589175G>A	ENST00000353442.5	-	5	567	c.331C>T	c.(331-333)Ctt>Ttt	p.L111F	LMBR1_ENST00000354505.4_Missense_Mutation_p.L111F|LMBR1_ENST00000359422.4_5'UTR|LMBR1_ENST00000540390.1_Missense_Mutation_p.L90F	NM_022458.3	NP_071903.2	Q8WVP7	LMBR1_HUMAN	limb development membrane protein 1	111					embryonic digit morphogenesis (GO:0042733)	integral component of membrane (GO:0016021)				breast(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(9)|skin(1)	18	Ovarian(565;0.218)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.00231)	UCEC - Uterine corpus endometrioid carcinoma (81;0.208)		AGGGAAGCAAGATTCCACAAA	0.323																																					p.L111F		.											.	.	.	0			c.C331T						.						52.0	48.0	49.0					7																	156589175		2203	4300	6503	SO:0001583	missense	64327	exon5			AAGCAAGATTCCA	AF107454	CCDS5945.1	7q36.3	2013-08-05	2013-08-05	2005-07-25	ENSG00000105983	ENSG00000105983			13243	protein-coding gene	gene with protein product		605522	"""chromosome 7 open reading frame 2"", ""limb region 1 homolog (mouse)"""	C7orf2		10329000, 11090342	Standard	NM_022458		Approved	ACHP, FLJ11665, ZRS	uc003wmw.4	Q8WVP7	OTTHUMG00000151510	ENST00000353442.5:c.331C>T	7.37:g.156589175G>A	ENSP00000326604:p.Leu111Phe	Somatic	108	0		WXS	Illumina HiSeq	.	66	27	NM_022458	A4D242|Q8N3E3|Q96QZ5|Q9H5N0|Q9HAG9|Q9UDN5|Q9Y6U2	Missense_Mutation	SNP	ENST00000353442.5	37	CCDS5945.1	.	.	.	.	.	.	.	.	.	.	G	16.72	3.200137	0.58126	.	.	ENSG00000105983	ENST00000353442;ENST00000415428;ENST00000354505;ENST00000540390;ENST00000347571	T;T;T;T	0.32753	1.44;1.44;1.44;1.44	4.67	4.67	0.58626	LMBR1-like membrane protein (1);	0.000000	0.85682	D	0.000000	T	0.47581	0.1453	L	0.46157	1.445	0.80722	D	1	D;D;D	0.76494	0.999;0.989;0.999	D;P;D	0.87578	0.998;0.868;0.998	T	0.25502	-1.0130	10	0.16420	T	0.52	-14.0235	18.0086	0.89216	0.0:0.0:1.0:0.0	.	90;111;111	B7Z633;Q8WVP7-3;Q8WVP7	.;.;LMBR1_HUMAN	F	111;109;111;90;111	ENSP00000326604:L111F;ENSP00000408256:L109F;ENSP00000346500:L111F;ENSP00000445509:L90F	ENSP00000337803:L111F	L	-	1	0	LMBR1	156281936	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	8.925000	0.92832	2.326000	0.78906	0.485000	0.47835	CTT	.		0.323	LMBR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347939.3	NM_022458	
SENP5	205564	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	3	196626893	196626893	+	Missense_Mutation	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr3:196626893A>C	ENST00000323460.5	+	4	1967	c.1718A>C	c.(1717-1719)gAc>gCc	p.D573A	SENP5_ENST00000445299.2_Missense_Mutation_p.D573A|SENP5_ENST00000419026.1_Missense_Mutation_p.D63A	NM_152699.4	NP_689912.2	Q96HI0	SENP5_HUMAN	SUMO1/sentrin specific peptidase 5	573	Protease.				cell cycle (GO:0007049)|cell division (GO:0051301)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein sumoylation (GO:0016925)	intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	cysteine-type peptidase activity (GO:0008234)			NS(1)|breast(2)|endometrium(2)|kidney(3)|large_intestine(9)|lung(14)|skin(1)	32	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)|Breast(254;0.135)		Epithelial(36;3.14e-24)|all cancers(36;2.1e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.03e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.004)		GATATGGACGACCTGGCGACT	0.383																																					p.D573A	Ovarian(47;891 1095 11174 13858 51271)	.											.	.	.	0			c.A1718C						.						86.0	87.0	87.0					3																	196626893		2203	4300	6503	SO:0001583	missense	205564	exon4			TGGACGACCTGGC	BC030705	CCDS3322.1	3q29	2005-08-17	2005-08-17		ENSG00000119231	ENSG00000119231			28407	protein-coding gene	gene with protein product		612845	"""SUMO1/sentrin specific protease 5"""			12477932	Standard	NM_152699		Approved	MGC27076	uc003fwz.4	Q96HI0	OTTHUMG00000155527	ENST00000323460.5:c.1718A>C	3.37:g.196626893A>C	ENSP00000327197:p.Asp573Ala	Somatic	54	0		WXS	Illumina HiSeq	.	42	12	NM_152699	B4DY82|Q96SA5	Missense_Mutation	SNP	ENST00000323460.5	37	CCDS3322.1	.	.	.	.	.	.	.	.	.	.	A	24.6	4.548285	0.86127	.	.	ENSG00000119231	ENST00000323460;ENST00000445299;ENST00000419026	T;T;T	0.57907	0.37;0.93;0.37	5.84	5.84	0.93424	.	0.000000	0.85682	D	0.000000	T	0.68183	0.2973	L	0.54323	1.7	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.997;0.999	T	0.70321	-0.4904	10	0.72032	D	0.01	-14.7583	14.4783	0.67562	1.0:0.0:0.0:0.0	.	573;573	B4DY82;Q96HI0	.;SENP5_HUMAN	A	573;573;63	ENSP00000327197:D573A;ENSP00000390231:D573A;ENSP00000396927:D63A	ENSP00000327197:D573A	D	+	2	0	SENP5	198111290	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	8.511000	0.90535	2.367000	0.80283	0.528000	0.53228	GAC	.		0.383	SENP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340524.1	NM_152699	
FUS	2521	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	16	31201095	31201095	+	Missense_Mutation	SNP	C	C	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr16:31201095C>G	ENST00000254108.7	+	10	1151	c.1046C>G	c.(1045-1047)gCa>gGa	p.A349G	FUS_ENST00000474990.1_3'UTR|FUS_ENST00000568685.1_Missense_Mutation_p.A350G|FUS_ENST00000380244.3_Missense_Mutation_p.A348G	NM_001170634.1|NM_001170937.1|NM_004960.3	NP_001164105.1|NP_001164408.1|NP_004951.1	P35637	FUS_HUMAN	FUS RNA binding protein	349	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.				cell death (GO:0008219)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)		FUS/ERG(167)|FUS/DDIT3(631)|FUS/FEV(2)|FUS/ATF1(4)|FUS/CREB3L1(6)|FUS/CREB3L2(158)	breast(3)|endometrium(5)|kidney(3)|large_intestine(1)|lung(5)|prostate(3)|skin(1)|urinary_tract(1)	22		Renal(780;0.000219)|Breast(268;0.00957)|Hepatocellular(780;0.121)		GBM - Glioblastoma multiforme(240;2.31e-05)|Kidney(780;0.000209)		TCAGCTAAAGCAGCTATTGAC	0.493			T	"""DDIT3, ERG, FEV, ATF1, CREB3L2, CREB3L1"""	"""liposarcoma, AML, Ewing sarcoma, angiomatoid fibrous histiocytoma, fibromyxoid sarcoma"""																																p.A349G		.		Dom	yes		16	16p11.2	2521	"""fusion, derived from t(12;16) malignant liposarcoma"""		"""M, L"""	.	.	.	0			c.C1046G						.						126.0	123.0	124.0					16																	31201095		2197	4300	6497	SO:0001583	missense	2521	exon10			CTAAAGCAGCTAT	AF071213	CCDS10707.1, CCDS58454.1	16p11.2	2014-09-17	2014-05-09		ENSG00000089280	ENSG00000089280		"""RNA binding motif (RRM) containing"""	4010	protein-coding gene	gene with protein product	"""heterogeneous nuclear ribonucleoprotein P2"", ""translocated in liposarcoma"""	137070	"""fusion, derived from t(12;16) malignant liposarcoma"", ""amyotrophic lateral sclerosis 6"", ""fusion (involved in t(12;16) in malignant liposarcoma)"", ""fused in sarcoma"""	ALS6		2372777, 7503811, 19251628, 19251627	Standard	NM_004960		Approved	TLS, FUS1, hnRNP-P2, HNRNPP2	uc002ebe.2	P35637	OTTHUMG00000132395	ENST00000254108.7:c.1046C>G	16.37:g.31201095C>G	ENSP00000254108:p.Ala349Gly	Somatic	62	0		WXS	Illumina HiSeq	.	39	17	NM_004960	Q9H4A8	Missense_Mutation	SNP	ENST00000254108.7	37	CCDS10707.1	.	.	.	.	.	.	.	.	.	.	C	18.79	3.699304	0.68501	.	.	ENSG00000089280	ENST00000254108;ENST00000380244;ENST00000394533	T	0.18657	2.2	5.29	4.34	0.51931	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.000000	0.85682	D	0.000000	T	0.49677	0.1571	M	0.89353	3.025	0.80722	D	1	P;P;P;P;B;P	0.39737	0.685;0.685;0.685;0.635;0.04;0.685	P;P;P;P;B;P	0.57425	0.82;0.82;0.82;0.724;0.159;0.82	T	0.55679	-0.8103	10	0.87932	D	0	-0.0226	12.6937	0.56990	0.0:0.9187:0.0:0.0813	.	348;349;349;348;123;349	A8K4H1;Q8TBR3;Q6IBQ5;P35637-2;Q59H57;P35637	.;.;.;.;.;FUS_HUMAN	G	349;76;278	ENSP00000254108:A349G	ENSP00000254108:A349G	A	+	2	0	FUS	31108596	1.000000	0.71417	0.992000	0.48379	0.987000	0.75469	7.431000	0.80335	1.224000	0.43551	0.591000	0.81541	GCA	.		0.493	FUS-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255526.2	NM_004960	
GPR97	222487	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	16	57719585	57719585	+	Silent	SNP	C	C	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr16:57719585C>T	ENST00000333493.4	+	11	1448	c.1287C>T	c.(1285-1287)taC>taT	p.Y429Y	GPR97_ENST00000450388.3_Silent_p.Y309Y|GPR97_ENST00000327655.6_Silent_p.Y219Y|RP11-405F3.4_ENST00000563062.1_RNA	NM_170776.4	NP_740746.4	Q86Y34	GPR97_HUMAN	G protein-coupled receptor 97	429					neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(9)|lung(7)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30						CAACCATGTACGCCCTCTATA	0.597																																					p.Y429Y		.											.	.	.	0			c.C1287T						.						187.0	168.0	175.0					16																	57719585		2198	4300	6498	SO:0001819	synonymous_variant	222487	exon11			CATGTACGCCCTC	AY140959	CCDS10786.1	16q13	2014-08-08			ENSG00000182885	ENSG00000182885		"""-"", ""GPCR / Class B : Orphans"""	13728	protein-coding gene	gene with protein product						12435584, 222487	Standard	NM_170776		Approved	Pb99, PGR26	uc002emh.3	Q86Y34	OTTHUMG00000133458	ENST00000333493.4:c.1287C>T	16.37:g.57719585C>T		Somatic	70	0		WXS	Illumina HiSeq	.	33	18	NM_170776	Q6ZMF4|Q86SL9|Q8IZF1	Silent	SNP	ENST00000333493.4	37	CCDS10786.1																																																																																			.		0.597	GPR97-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257333.2	NM_170776	
LAMB3	3914	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	209801446	209801446	+	Missense_Mutation	SNP	C	C	G	rs145170416		TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr1:209801446C>G	ENST00000356082.4	-	11	1356	c.1222G>C	c.(1222-1224)Gag>Cag	p.E408Q	LAMB3_ENST00000391911.1_Missense_Mutation_p.E408Q|LAMB3_ENST00000367030.3_Missense_Mutation_p.E408Q	NM_000228.2	NP_000219.2	Q13751	LAMB3_HUMAN	laminin, beta 3	408	Laminin EGF-like 3. {ECO:0000255|PROSITE- ProRule:PRU00460}.				brown fat cell differentiation (GO:0050873)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	extracellular region (GO:0005576)|laminin-5 complex (GO:0005610)	structural molecule activity (GO:0005198)			NS(1)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(11)|lung(13)|ovary(1)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	45				OV - Ovarian serous cystadenocarcinoma(81;0.0519)		TCACAGCGCTCTCCCTGCACA	0.647											OREG0014217	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.E408Q		.											.	.	.	0			c.G1222C						.	C	GLN/GLU,GLN/GLU,GLN/GLU	0,4402		0,0,2201	67.0	47.0	53.0		1222,1222,1222	4.2	1.0	1	dbSNP_134	53	1,8597		0,1,4298	no	missense,missense,missense	LAMB3	NM_000228.2,NM_001017402.1,NM_001127641.1	29,29,29	0,1,6499	GG,GC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging	408/1173,408/1173,408/1173	209801446	1,12999	2201	4299	6500	SO:0001583	missense	3914	exon11			AGCGCTCTCCCTG	D37766	CCDS1487.1	1q32	2013-03-01	2002-08-29		ENSG00000196878	ENSG00000196878		"""Laminins"""	6490	protein-coding gene	gene with protein product		150310	"""laminin, beta 3 (nicein (125kD), kalinin (140kD), BM600 (125kD))"""	LAMNB1		8088808, 7774918	Standard	NM_001127641		Approved	nicein-125kDa, kalinin-140kDa, BM600-125kDa	uc001hhh.3	Q13751	OTTHUMG00000036360	ENST00000356082.4:c.1222G>C	1.37:g.209801446C>G	ENSP00000348384:p.Glu408Gln	Somatic	58	0	2185	WXS	Illumina HiSeq	.	58	44	NM_000228	D3DT88|O14947|Q14733|Q9UJK4|Q9UJL1	Missense_Mutation	SNP	ENST00000356082.4	37	CCDS1487.1	.	.	.	.	.	.	.	.	.	.	C	12.79	2.042211	0.35989	0.0	1.16E-4	ENSG00000196878	ENST00000391911;ENST00000356082;ENST00000367030	T;T;T	0.61627	0.09;0.09;0.09	5.12	4.18	0.49190	EGF-like, laminin (4);EGF-like region, conserved site (1);	0.112377	0.64402	D	0.000008	T	0.38268	0.1034	N	0.10837	0.055	0.23325	N	0.997902	B	0.33494	0.414	B	0.33690	0.168	T	0.19289	-1.0310	10	0.23891	T	0.37	.	14.7888	0.69824	0.1456:0.8544:0.0:0.0	.	408	Q13751	LAMB3_HUMAN	Q	408	ENSP00000375778:E408Q;ENSP00000348384:E408Q;ENSP00000355997:E408Q	ENSP00000348384:E408Q	E	-	1	0	LAMB3	207868069	0.852000	0.29690	0.994000	0.49952	0.739000	0.42172	1.805000	0.38883	1.247000	0.43917	0.456000	0.33151	GAG	0.000		0.647	LAMB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088525.2	NM_000228	
JMJD1C	221037	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	10	64966945	64966945	+	Missense_Mutation	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr10:64966945T>G	ENST00000399262.2	-	10	4702	c.4484A>C	c.(4483-4485)aAa>aCa	p.K1495T	JMJD1C_ENST00000399251.1_Missense_Mutation_p.K1276T|JMJD1C_ENST00000542921.1_Missense_Mutation_p.K1313T|JMJD1C_ENST00000402544.1_Missense_Mutation_p.K1276T	NM_032776.1	NP_116165.1	Q15652	JHD2C_HUMAN	jumonji domain containing 1C	1495					blood coagulation (GO:0007596)|chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	intracellular (GO:0005622)|nucleoplasm (GO:0005654)	dioxygenase activity (GO:0051213)|metal ion binding (GO:0046872)|thyroid hormone receptor binding (GO:0046966)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(8)|large_intestine(9)|lung(27)|ovary(6)|prostate(4)|skin(4)|stomach(3)|upper_aerodigestive_tract(3)	77	Prostate(12;0.0119)|all_hematologic(501;0.191)					ATTACTACTTTTATACTGAGC	0.408																																					p.K1495T		.											.	.	.	0			c.A4484C						.						102.0	96.0	98.0					10																	64966945		1883	4111	5994	SO:0001583	missense	221037	exon10			CTACTTTTATACT	L40411	CCDS41532.1, CCDS60538.1	10q22.1	2011-05-25	2004-03-31	2004-04-01	ENSG00000171988	ENSG00000171988			12313	protein-coding gene	gene with protein product		604503	"""thyroid hormone receptor interactor 8"""	TRIP8		7776974	Standard	XM_005269624		Approved	DKFZp761F0118, KIAA1380, FLJ14374	uc001jmn.3	Q15652	OTTHUMG00000018311	ENST00000399262.2:c.4484A>C	10.37:g.64966945T>G	ENSP00000382204:p.Lys1495Thr	Somatic	79	0		WXS	Illumina HiSeq	.	38	7	NM_032776	A0T124|Q5SQZ8|Q5SQZ9|Q5SR00|Q7Z3E7|Q8N3U0|Q96KB9|Q9P2G7	Missense_Mutation	SNP	ENST00000399262.2	37	CCDS41532.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	14.33|14.33	2.503389|2.503389	0.44558|0.44558	.|.	.|.	ENSG00000171988|ENSG00000171988	ENST00000327520|ENST00000399262;ENST00000402544;ENST00000399251;ENST00000542921	T|T;T;T;T	0.60548|0.56941	0.18|0.73;0.43;2.18;0.78	5.75|5.75	4.6|4.6	0.57074|0.57074	.|.	0.160488|0.160488	0.56097|0.56097	D|D	0.000038|0.000038	T|T	0.49184|0.49184	0.1542|0.1542	L|L	0.54323|0.54323	1.7|1.7	0.35707|0.35707	D|D	0.81606|0.81606	.|P;P;P	.|0.48911	.|0.917;0.917;0.917	.|P;P;P	.|0.46850	.|0.529;0.529;0.529	T|T	0.55811|0.55811	-0.8082|-0.8082	8|10	0.52906|0.23302	T|T	0.07|0.38	-12.1255|-12.1255	8.0873|8.0873	0.30780|0.30780	0.1217:0.0672:0.0:0.8111|0.1217:0.0672:0.0:0.8111	.|.	.|1036;1495;1313	.|A6PW35;Q15652;A0T124	.|.;JHD2C_HUMAN;.	Q|T	181|1495;1276;1276;1313	ENSP00000335929:K181Q|ENSP00000382204:K1495T;ENSP00000384990:K1276T;ENSP00000382195:K1276T;ENSP00000444682:K1313T	ENSP00000335929:K181Q|ENSP00000382195:K1276T	K|K	-|-	1|2	0|0	JMJD1C|JMJD1C	64636951|64636951	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.984000|0.984000	0.73092|0.73092	2.610000|2.610000	0.46325|0.46325	0.978000|0.978000	0.38470|0.38470	0.482000|0.482000	0.46254|0.46254	AAA|AAA	.		0.408	JMJD1C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048249.2	NM_004241	
ELN	2006	hgsc.bcm.edu	37	7	73474788	73474788	+	Silent	SNP	T	T	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr7:73474788T>C	ENST00000252034.7	+	25	2103	c.1704T>C	c.(1702-1704)gtT>gtC	p.V568V	ELN_ENST00000380584.4_Silent_p.V520V|ELN_ENST00000380575.4_Silent_p.V539V|ELN_ENST00000458204.1_Silent_p.V558V|ELN_ENST00000414324.1_Silent_p.V544V|ELN_ENST00000320492.7_Silent_p.V487V|ELN_ENST00000429192.1_Silent_p.V554V|ELN_ENST00000357036.5_Silent_p.V573V|ELN_ENST00000380553.4_Silent_p.V432V|ELN_ENST00000380562.4_Silent_p.V574V|ELN_ENST00000358929.4_Silent_p.V603V|ELN_ENST00000320399.6_Silent_p.V568V|ELN_ENST00000445912.1_Silent_p.V568V|CTB-51J22.1_ENST00000435932.1_RNA|ELN_ENST00000380576.5_Silent_p.V549V	NM_000501.2|NM_001278915.1	NP_000492.2|NP_001265844.1	P15502	ELN_HUMAN	elastin	0	Ala-rich.				blood circulation (GO:0008015)|blood vessel remodeling (GO:0001974)|cell proliferation (GO:0008283)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|organ morphogenesis (GO:0009887)|regulation of actin filament polymerization (GO:0030833)|respiratory gaseous exchange (GO:0007585)|skeletal muscle tissue development (GO:0007519)|stress fiber assembly (GO:0043149)	elastic fiber (GO:0071953)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix binding (GO:0050840)|extracellular matrix constituent conferring elasticity (GO:0030023)|extracellular matrix structural constituent (GO:0005201)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(10)|ovary(4)|pancreas(2)|prostate(1)|skin(2)|stomach(1)	32		Lung NSC(55;0.159)				GTGCTGGTGTTCCTGGACTTG	0.617			T	PAX5	B-ALL		"""Supravalvular Aortic Stenosis, Cutis laxa , Williams-Beuren Syndrome"""																														p.V573V		.		Dom	yes		7	7q11.23	2006	elastin	yes	L	.	.	.	0			c.T1719C						.						342.0	341.0	342.0					7																	73474788		2203	4300	6503	SO:0001819	synonymous_variant	2006	exon25			TGGTGTTCCTGGA		CCDS5562.2, CCDS43598.1, CCDS43599.1, CCDS47611.1, CCDS47612.1, CCDS64673.1, CCDS64674.1, CCDS64675.1, CCDS64676.1, CCDS64677.1, CCDS64678.1, CCDS75616.1, CCDS75617.1	7q11.1-q21.1	2008-08-01	2008-08-01		ENSG00000049540	ENSG00000049540			3327	protein-coding gene	gene with protein product	"""tropoelastin"", ""supravalvular aortic stenosis"", ""Williams-Beuren syndrome"""	130160				8096434	Standard	NM_001278939		Approved	WBS, WS, SVAS	uc003tzn.3	P15502	OTTHUMG00000150229	ENST00000252034.7:c.1704T>C	7.37:g.73474788T>C		Somatic	31	0		WXS	Illumina HiSeq	.	16	4	NM_001081754	B3KTS6|O15336|O15337|Q14233|Q14234|Q14235|Q14238|Q6P0L4|Q6ZWJ6|Q75MU5|Q7Z316|Q7Z3F5|Q9UMF5	Silent	SNP	ENST00000252034.7	37	CCDS5562.2																																																																																			.		0.617	ELN-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000316913.1	NM_000501	
COL20A1	57642	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	20	61926534	61926534	+	Missense_Mutation	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr20:61926534A>C	ENST00000358894.6	+	2	175	c.75A>C	c.(73-75)caA>caC	p.Q25H	COL20A1_ENST00000326996.6_Missense_Mutation_p.Q25H|COL20A1_ENST00000422202.1_Missense_Mutation_p.Q25H|COL20A1_ENST00000435874.1_Missense_Mutation_p.Q25H	NM_020882.2	NP_065933.2	Q9P218	COKA1_HUMAN	collagen, type XX, alpha 1	25					extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)				NS(3)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(21)|ovary(1)|prostate(3)|urinary_tract(2)	36	all_cancers(38;1.39e-10)					GAAGAGAGCAAGTTCAAGGTA	0.701																																					p.Q25H		.											.	.	.	0			c.A75C						.						15.0	19.0	18.0					20																	61926534		1985	4069	6054	SO:0001583	missense	57642	exon2			AGAGCAAGTTCAA	BC043183	CCDS46628.1	20q13.33	2014-02-12			ENSG00000101203	ENSG00000101203		"""Collagens"", ""Fibronectin type III domain containing"""	14670	protein-coding gene	gene with protein product						10819331	Standard	NM_020882		Approved	KIAA1510	uc011aau.2	Q9P218	OTTHUMG00000032964	ENST00000358894.6:c.75A>C	20.37:g.61926534A>C	ENSP00000351767:p.Gln25His	Somatic	96	0		WXS	Illumina HiSeq	.	68	23	NM_020882	Q4VXQ4|Q6PI59|Q8WUT2|Q96CY9|Q9BQU6|Q9BQU7	Missense_Mutation	SNP	ENST00000358894.6	37	CCDS46628.1	.	.	.	.	.	.	.	.	.	.	A	11.24	1.580267	0.28180	.	.	ENSG00000101203	ENST00000358894;ENST00000326996;ENST00000435874;ENST00000422202	D;D;D;D	0.88664	-2.35;-2.39;-2.41;-2.41	2.84	0.725	0.18242	Fibronectin, type III (2);	1.456920	0.04712	U	0.417852	T	0.78304	0.4262	N	0.24115	0.695	0.09310	N	1	P	0.43352	0.804	B	0.34652	0.187	T	0.68062	-0.5508	10	0.28530	T	0.3	.	5.3092	0.15821	0.324:0.0:0.676:0.0	.	25	Q9P218	COKA1_HUMAN	H	25	ENSP00000351767:Q25H;ENSP00000323077:Q25H;ENSP00000408690:Q25H;ENSP00000414753:Q25H	ENSP00000323077:Q25H	Q	+	3	2	COL20A1	61396979	0.005000	0.15991	0.080000	0.20451	0.017000	0.09413	0.052000	0.14163	0.051000	0.15978	0.260000	0.18958	CAA	.		0.701	COL20A1-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000144595.2	NM_020882	
CCT4	10575	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	2	62100224	62100224	+	Silent	SNP	A	A	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr2:62100224A>T	ENST00000394440.3	-	10	1334	c.1038T>A	c.(1036-1038)gcT>gcA	p.A346A	CCT4_ENST00000538252.1_Silent_p.A290A|CCT4_ENST00000461540.2_Intron|CCT4_ENST00000544185.1_Silent_p.A196A|AC107081.5_ENST00000425779.1_RNA|CCT4_ENST00000544079.1_Silent_p.A316A	NM_006430.3	NP_006421.2	P50991	TCPD_HUMAN	chaperonin containing TCP1, subunit 4 (delta)	346					'de novo' posttranslational protein folding (GO:0051084)|binding of sperm to zona pellucida (GO:0007339)|cellular protein metabolic process (GO:0044267)|protein folding (GO:0006457)	cell body (GO:0044297)|centrosome (GO:0005813)|chaperonin-containing T-complex (GO:0005832)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|nucleus (GO:0005634)|zona pellucida receptor complex (GO:0002199)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|unfolded protein binding (GO:0051082)			breast(1)|large_intestine(2)|lung(6)|ovary(2)	11	Lung NSC(7;0.035)|all_lung(7;0.0691)		LUSC - Lung squamous cell carcinoma(7;6.5e-06)|Epithelial(17;0.0647)|all cancers(80;0.221)			GGTCAATATGAGCAACTGGCT	0.368																																					p.A346A		.											.	.	.	0			c.T1038A						.						154.0	161.0	159.0					2																	62100224		2203	4300	6503	SO:0001819	synonymous_variant	10575	exon10			AATATGAGCAACT		CCDS33206.1, CCDS58711.1	2p15	2011-09-02			ENSG00000115484	ENSG00000115484		"""Heat Shock Proteins / Chaperonins"""	1617	protein-coding gene	gene with protein product		605142				9819444	Standard	NM_001256721		Approved	Cctd	uc002sbo.4	P50991	OTTHUMG00000152166	ENST00000394440.3:c.1038T>A	2.37:g.62100224A>T		Somatic	111	0		WXS	Illumina HiSeq	.	56	24	NM_006430	B2R6I3|B7Z8B1|F5H5W3|O14870|Q53QP9|Q96C51	Silent	SNP	ENST00000394440.3	37	CCDS33206.1																																																																																			.		0.368	CCT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325548.2		
BTNL9	153579	hgsc.bcm.edu;broad.mit.edu	37	5	180480244	180480244	+	Missense_Mutation	SNP	G	G	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr5:180480244G>C	ENST00000327705.9	+	5	1012	c.781G>C	c.(781-783)Gcg>Ccg	p.A261P	BTNL9_ENST00000511589.1_3'UTR|BTNL9_ENST00000376842.3_Missense_Mutation_p.A261P|BTNL9_ENST00000515271.1_Missense_Mutation_p.A192P|BTNL9_ENST00000376841.2_Missense_Mutation_p.A261P	NM_152547.4	NP_689760.2	Q6UXG8	BTNL9_HUMAN	butyrophilin-like 9	261						integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|kidney(4)|large_intestine(1)|lung(10)|ovary(1)	19	all_cancers(89;2.45e-05)|all_epithelial(37;3.77e-06)|Renal(175;0.000159)|Lung NSC(126;0.00211)|all_lung(126;0.00371)|Breast(19;0.114)	all_cancers(40;0.0801)|Medulloblastoma(196;0.0392)|all_neural(177;0.0529)|all_hematologic(541;0.191)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CGCGTTCGTCGCGACCCTGCC	0.736																																					p.A261P		.											.	.	.	0			c.G781C						.						14.0	18.0	17.0					5																	180480244		2168	4237	6405	SO:0001583	missense	153579	exon5			TTCGTCGCGACCC	AK057097	CCDS4460.2	5q35.3	2014-01-14			ENSG00000165810	ENSG00000165810		"""Immunoglobulin superfamily / V-set domain containing"", ""Butyrophilins"""	24176	protein-coding gene	gene with protein product							Standard	NM_152547		Approved	FLJ32535, BTN8	uc003mmt.3	Q6UXG8	OTTHUMG00000133152	ENST00000327705.9:c.781G>C	5.37:g.180480244G>C	ENSP00000330200:p.Ala261Pro	Somatic	8	0		WXS	Illumina HiSeq	.	8	4	NM_152547	A6NL42|Q6P660|Q96DM5	Missense_Mutation	SNP	ENST00000327705.9	37	CCDS4460.2	.	.	.	.	.	.	.	.	.	.	g	13.24	2.178366	0.38511	.	.	ENSG00000165810	ENST00000376841;ENST00000327705;ENST00000376842;ENST00000376850;ENST00000515271	T;T;T;T	0.42131	4.23;1.01;0.98;3.98	3.93	3.04	0.35103	.	.	.	.	.	T	0.24509	0.0594	N	0.12182	0.205	0.09310	N	1	P;B	0.45348	0.856;0.322	B;B	0.39706	0.307;0.179	T	0.04029	-1.0983	9	0.36615	T	0.2	.	10.191	0.43026	0.0:0.2039:0.7961:0.0	.	192;261	B7Z4Y8;Q6UXG8	.;BTNL9_HUMAN	P	261;261;261;261;192	ENSP00000366037:A261P;ENSP00000330200:A261P;ENSP00000366038:A261P;ENSP00000427345:A192P	ENSP00000330200:A261P	A	+	1	0	BTNL9	180412850	0.038000	0.19896	0.002000	0.10522	0.007000	0.05969	1.615000	0.36922	0.934000	0.37316	0.187000	0.17357	GCG	.		0.736	BTNL9-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000157342.3	NM_152547	
MYCBP2	23077	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	13	77672823	77672823	+	Silent	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr13:77672823A>C	ENST00000544440.2	-	56	8369	c.8352T>G	c.(8350-8352)ccT>ccG	p.P2784P	MYCBP2-AS1_ENST00000593933.1_RNA|MYCBP2_ENST00000357337.6_Silent_p.P2784P|MYCBP2_ENST00000407578.2_Silent_p.P2822P|MYCBP2_ENST00000482517.1_5'UTR|MYCBP2_ENST00000360084.5_Silent_p.P307P					MYC binding protein 2, E3 ubiquitin protein ligase											NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(51)|ovary(5)|pancreas(2)|prostate(5)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	118		Breast(118;0.212)|Acute lymphoblastic leukemia(28;0.22)		GBM - Glioblastoma multiforme(99;0.109)		TCTTTGGCTTAGGAGATGACA	0.502																																					p.P2822P		.											.	.	.	0			c.T8466G						.						106.0	107.0	107.0					13																	77672823		2203	4300	6503	SO:0001819	synonymous_variant	23077	exon56			TGGCTTAGGAGAT	AB020723		13q22	2012-02-23	2012-02-23		ENSG00000005810	ENSG00000005810			23386	protein-coding gene	gene with protein product		610392	"""MYC binding protein 2"""			9689053, 15057823	Standard	NM_015057		Approved	PAM, KIAA0916, FLJ10106	uc021rks.1	O75592	OTTHUMG00000017105	ENST00000544440.2:c.8352T>G	13.37:g.77672823A>C		Somatic	43	0		WXS	Illumina HiSeq	.	26	12	NM_015057		Silent	SNP	ENST00000544440.2	37																																																																																				.		0.502	MYCBP2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000045326.1	NM_015057	
MEF2D	4209	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	156450644	156450644	+	Silent	SNP	C	C	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr1:156450644C>T	ENST00000348159.4	-	4	858	c.378G>A	c.(376-378)ggG>ggA	p.G126G	MEF2D_ENST00000353795.3_Intron|MEF2D_ENST00000360595.3_Silent_p.G126G|MEF2D_ENST00000368240.2_Silent_p.G126G|MEF2D_ENST00000340875.5_Intron|MEF2D_ENST00000464356.2_Intron	NM_005920.2	NP_005911.1	Q14814	MEF2D_HUMAN	myocyte enhancer factor 2D	126					adult heart development (GO:0007512)|apoptotic process (GO:0006915)|chondrocyte differentiation (GO:0002062)|endochondral ossification (GO:0001958)|muscle organ development (GO:0007517)|nervous system development (GO:0007399)|osteoblast differentiation (GO:0001649)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|skeletal muscle cell differentiation (GO:0035914)|transcription from RNA polymerase II promoter (GO:0006366)	intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	activating transcription factor binding (GO:0033613)|histone deacetylase binding (GO:0042826)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(4)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|urinary_tract(1)	15	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					GCCGGAAGAGCCCGTCGAGCT	0.682											OREG0013874	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.G126G		.											.	.	.	0			c.G378A						.						40.0	46.0	44.0					1																	156450644		2203	4299	6502	SO:0001819	synonymous_variant	4209	exon4			GAAGAGCCCGTCG	BC054520	CCDS1143.1, CCDS60304.1	1q12-q23	2008-02-05	2007-04-24		ENSG00000116604	ENSG00000116604		"""Myocyte enhancer factors"""	6997	protein-coding gene	gene with protein product		600663				8269842	Standard	NM_005920		Approved		uc001fpb.4	Q14814	OTTHUMG00000033095	ENST00000348159.4:c.378G>A	1.37:g.156450644C>T		Somatic	44	0	1778	WXS	Illumina HiSeq	.	55	35	NM_005920	D3DVC0|Q14815|Q5T9U5|Q5T9U6	Silent	SNP	ENST00000348159.4	37	CCDS1143.1																																																																																			.		0.682	MEF2D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080562.2	NM_005920	
STAP2	55620	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	19	4327373	4327373	+	Silent	SNP	C	C	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr19:4327373C>T	ENST00000594605.1	-	7	723	c.600G>A	c.(598-600)gtG>gtA	p.V200V	STAP2_ENST00000600324.1_Silent_p.V200V|STAP2_ENST00000597593.1_5'UTR	NM_001013841.1	NP_001013863.1	Q9UGK3	STAP2_HUMAN	signal transducing adaptor family member 2	200	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.					cytoplasm (GO:0005737)|plasma membrane (GO:0005886)				central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(10)	23		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0339)|STAD - Stomach adenocarcinoma(1328;0.18)		AATGCCGGACCACGTGCGTCC	0.647																																					p.V200V		.											.	.	.	0			c.G600A						.						85.0	73.0	77.0					19																	4327373		2203	4300	6503	SO:0001819	synonymous_variant	55620	exon7			CCGGACCACGTGC	AJ245719	CCDS12128.1, CCDS45926.1	19p13.3	2011-05-03	2007-08-09		ENSG00000178078	ENSG00000178078			30430	protein-coding gene	gene with protein product		607881				10980601, 11441184	Standard	XM_005259592		Approved	STAP-2, BKS	uc002mac.3	Q9UGK3		ENST00000594605.1:c.600G>A	19.37:g.4327373C>T		Somatic	36	0		WXS	Illumina HiSeq	.	16	10	NM_001013841	A6NKK3|Q9NXI2	Silent	SNP	ENST00000594605.1	37	CCDS45926.1																																																																																			.		0.647	STAP2-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000458114.2	NM_001013841	
MRPL44	65080	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	2	224828637	224828637	+	Missense_Mutation	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr2:224828637T>G	ENST00000258383.3	+	3	882	c.813T>G	c.(811-813)ttT>ttG	p.F271L	AC073641.2_ENST00000425192.1_RNA	NM_022915.3	NP_075066.1	Q9H9J2	RM44_HUMAN	mitochondrial ribosomal protein L44	271	DRBM. {ECO:0000255|PROSITE- ProRule:PRU00266}.				mitochondrial translational elongation (GO:0070125)|RNA processing (GO:0006396)	mitochondrion (GO:0005739)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|ribonuclease III activity (GO:0004525)			breast(1)|central_nervous_system(1)|large_intestine(5)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	13		all_lung(227;0.00679)|Lung NSC(271;0.00855)|Renal(207;0.0112)|all_hematologic(139;0.189)		Epithelial(121;2.51e-10)|all cancers(144;7.89e-08)|Lung(261;0.00705)|LUSC - Lung squamous cell carcinoma(224;0.008)		CTTTGTATTTTGTTGGCTTAT	0.378																																					p.F271L		.											MRPL44,colon,carcinoma,0,1	MRPL44	0	0			c.T813G						.						97.0	96.0	96.0					2																	224828637		2203	4300	6503	SO:0001583	missense	65080	exon3			GTATTTTGTTGGC	AK022763	CCDS2459.1	2p24.3-p24.1	2012-09-13			ENSG00000135900	ENSG00000135900		"""Mitochondrial ribosomal proteins / large subunits"""	16650	protein-coding gene	gene with protein product	"""39S ribosomal protein L44, mitochondrial"""	611849					Standard	NM_022915		Approved	FLJ12701, FLJ13990	uc002vnr.4	Q9H9J2	OTTHUMG00000133164	ENST00000258383.3:c.813T>G	2.37:g.224828637T>G	ENSP00000258383:p.Phe271Leu	Somatic	117	0		WXS	Illumina HiSeq	.	66	29	NM_022915	Q53S16|Q6IA62|Q9H821	Missense_Mutation	SNP	ENST00000258383.3	37	CCDS2459.1	.	.	.	.	.	.	.	.	.	.	T	16.74	3.206106	0.58234	.	.	ENSG00000135900	ENST00000258383	T	0.41400	1.0	5.7	2.11	0.27256	Double-stranded RNA-binding (1);Double-stranded RNA-binding-like (1);	0.000000	0.85682	D	0.000000	T	0.34337	0.0894	L	0.36672	1.1	0.58432	D	0.99999	P	0.44090	0.826	P	0.48770	0.589	T	0.09271	-1.0682	10	0.11485	T	0.65	-14.2981	7.6628	0.28413	0.0:0.25:0.0:0.75	.	271	Q9H9J2	RM44_HUMAN	L	271	ENSP00000258383:F271L	ENSP00000258383:F271L	F	+	3	2	MRPL44	224536881	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.493000	0.35605	0.447000	0.26695	0.482000	0.46254	TTT	.		0.378	MRPL44-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256866.2	NM_022915	
NDUFB10	4716	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	16	2011155	2011155	+	Splice_Site	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr16:2011155A>C	ENST00000268668.6	+	2	249	c.132A>C	c.(130-132)gaA>gaC	p.E44D	NDUFB10_ENST00000543683.2_Splice_Site_p.E44D|SNORA10_ENST00000384084.1_RNA|NDUFB10_ENST00000569148.1_Splice_Site_p.E44D|SNORA64_ENST00000384674.1_RNA	NM_004548.2	NP_004539.1	O96000	NDUBA_HUMAN	NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 10, 22kDa	44					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			lung(1)|urinary_tract(1)	2						TCTTTGCAGAATTTATAGAGC	0.493																																					p.E44D		.											.	.	.	0			c.A132C						.						63.0	58.0	60.0					16																	2011155		2199	4300	6499	SO:0001630	splice_region_variant	4716	exon2			TGCAGAATTTATA	AF044954	CCDS10451.1	16p13.3	2011-07-04	2002-08-29		ENSG00000140990	ENSG00000140990		"""Mitochondrial respiratory chain complex / Complex I"""	7696	protein-coding gene	gene with protein product	"""complex I PDSW subunit"""	603843	"""NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 10 (22kD, PDSW)"""			9763677, 9878551	Standard	NM_004548		Approved	PDSW	uc002cni.2	O96000	OTTHUMG00000128709	ENST00000268668.6:c.131-1A>C	16.37:g.2011155A>C		Somatic	69	0		WXS	Illumina HiSeq	.	60	20	NM_004548	Q96II6	Missense_Mutation	SNP	ENST00000268668.6	37	CCDS10451.1	.	.	.	.	.	.	.	.	.	.	A	7.877	0.729356	0.15507	.	.	ENSG00000140990	ENST00000268668;ENST00000543683	.	.	.	4.74	-3.88	0.04205	.	0.235418	0.44285	D	0.000475	T	0.20373	0.0490	L	0.33293	1	0.29367	N	0.864295	B;B	0.15930	0.015;0.015	B;B	0.16289	0.01;0.015	T	0.03240	-1.1057	9	0.35671	T	0.21	.	0.7203	0.00939	0.2703:0.2951:0.2324:0.2022	.	44;44	Q96II6;O96000	.;NDUBA_HUMAN	D	44	.	ENSP00000268668:E44D	E	+	3	2	NDUFB10	1951156	0.080000	0.21391	0.985000	0.45067	0.171000	0.22731	-0.802000	0.04545	-0.200000	0.10300	-0.468000	0.05107	GAA	.		0.493	NDUFB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250614.2	NM_004548	Missense_Mutation
DAPK1	1612	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	9	90255340	90255340	+	Missense_Mutation	SNP	A	A	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr9:90255340A>G	ENST00000408954.3	+	8	1092	c.757A>G	c.(757-759)Aga>Gga	p.R253G	DAPK1_ENST00000469640.2_Missense_Mutation_p.R253G|DAPK1_ENST00000358077.5_Missense_Mutation_p.R253G|DAPK1_ENST00000491893.1_Missense_Mutation_p.R253G|DAPK1_ENST00000472284.1_Missense_Mutation_p.R253G	NM_004938.2	NP_004929.2	P53355	DAPK1_HUMAN	death-associated protein kinase 1	253	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cellular response to interferon-gamma (GO:0071346)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|intracellular signal transduction (GO:0035556)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of translation (GO:0017148)|positive regulation of apoptotic process (GO:0043065)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of apoptotic process (GO:0042981)|regulation of autophagy (GO:0010506)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)	ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|calmodulin-dependent protein kinase activity (GO:0004683)|identical protein binding (GO:0042802)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(27)|liver(2)|lung(17)|ovary(1)|prostate(2)|skin(3)|stomach(1)	72						AGATTTCATAAGAAGACTTCT	0.473									Chronic Lymphocytic Leukemia, Familial Clustering of																												p.R253G		.											.	.	.	0			c.A757G						.						85.0	86.0	86.0					9																	90255340		1932	4127	6059	SO:0001583	missense	1612	exon8	Familial Cancer Database	Familial CLL	TTCATAAGAAGAC	X76104	CCDS43842.1	9q34.1	2013-01-10			ENSG00000196730	ENSG00000196730		"""Ankyrin repeat domain containing"""	2674	protein-coding gene	gene with protein product		600831				8530096	Standard	XM_005251757		Approved	DAPK	uc004apd.3	P53355	OTTHUMG00000020150	ENST00000408954.3:c.757A>G	9.37:g.90255340A>G	ENSP00000386135:p.Arg253Gly	Somatic	60	0		WXS	Illumina HiSeq	.	38	17	NM_004938	B7ZLD2|B7ZLE7|Q14CQ7|Q1W5W0|Q68CP8|Q6ZRZ3|Q9BTL8	Missense_Mutation	SNP	ENST00000408954.3	37	CCDS43842.1	.	.	.	.	.	.	.	.	.	.	A	14.62	2.589494	0.46214	.	.	ENSG00000196730	ENST00000358077;ENST00000472284;ENST00000469640;ENST00000408954;ENST00000491893	T;T;T;T;T	0.65549	-0.16;-0.16;-0.16;-0.16;-0.16	5.1	5.1	0.69264	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	0.53938	D	0.000042	T	0.56934	0.2019	L	0.52759	1.655	0.43032	D	0.994603	P;P;B	0.40602	0.723;0.721;0.326	B;B;B	0.39805	0.31;0.285;0.084	T	0.61959	-0.6955	10	0.52906	T	0.07	.	11.9327	0.52855	0.8448:0.1551:0.0:0.0	.	253;253;253	B7ZLE7;B7Z454;P53355	.;.;DAPK1_HUMAN	G	253	ENSP00000350785:R253G;ENSP00000417076:R253G;ENSP00000418885:R253G;ENSP00000386135:R253G;ENSP00000419026:R253G	ENSP00000350785:R253G	R	+	1	2	DAPK1	89445160	0.911000	0.30947	1.000000	0.80357	0.999000	0.98932	0.927000	0.28818	2.129000	0.65627	0.533000	0.62120	AGA	.		0.473	DAPK1-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356843.1	NM_004938	
BIRC6	57448	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	2	32667184	32667184	+	Silent	SNP	T	T	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr2:32667184T>C	ENST00000421745.2	+	18	4130	c.3996T>C	c.(3994-3996)gtT>gtC	p.V1332V		NM_016252.3	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat containing 6	1332				V -> L (in Ref. 2; AAF75772). {ECO:0000305}.	apoptotic process (GO:0006915)|labyrinthine layer development (GO:0060711)|mitotic nuclear division (GO:0007067)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of cell proliferation (GO:0042127)|regulation of cytokinesis (GO:0032465)|spongiotrophoblast layer development (GO:0060712)	endosome (GO:0005768)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|spindle pole (GO:0000922)|trans-Golgi network (GO:0005802)	acid-amino acid ligase activity (GO:0016881)|cysteine-type endopeptidase inhibitor activity (GO:0004869)|ubiquitin-protein transferase activity (GO:0004842)			NS(4)|breast(8)|central_nervous_system(3)|endometrium(21)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(31)|lung(65)|ovary(7)|pancreas(1)|prostate(5)|skin(5)|stomach(1)|urinary_tract(5)	172	Acute lymphoblastic leukemia(172;0.155)					AGAAGCTTGTTAATACTCTTT	0.373																																					p.V1332V	Pancreas(94;175 1509 16028 18060 45422)	.											.	.	.	0			c.T3996C						.						59.0	63.0	62.0					2																	32667184		2203	4300	6503	SO:0001819	synonymous_variant	57448	exon18			GCTTGTTAATACT	AF265555	CCDS33175.2	2p22.3	2011-01-25	2011-01-25		ENSG00000115760	ENSG00000115760		"""Baculoviral IAP repeat containing"", ""Ubiquitin-conjugating enzymes E2"""	13516	protein-coding gene	gene with protein product	"""apollon"""	605638	"""baculoviral IAP repeat-containing 6"""			10544019	Standard	NM_016252		Approved	BRUCE	uc010ezu.3	Q9NR09	OTTHUMG00000150528	ENST00000421745.2:c.3996T>C	2.37:g.32667184T>C		Somatic	81	0		WXS	Illumina HiSeq	.	47	20	NM_016252	Q9ULD1	Silent	SNP	ENST00000421745.2	37	CCDS33175.2																																																																																			.		0.373	BIRC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318769.3	NM_016252	
ZNF204P	7754	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	6	27327423	27327423	+	IGR	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr6:27327423T>G								POM121L2 (47474 upstream) : ZNF391 (14970 downstream)																							CTTCCCACACTCACTGCATTT	0.403																																					.		.											.	.	.	0			.						.																																			SO:0001628	intergenic_variant	7754	.			CCACACTCACTGC																													6.37:g.27327423T>G		Somatic	65	0		WXS	Illumina HiSeq	.	53	14	.		RNA	SNP		37																																																																																				.	0	0.403								
DENND1A	57706	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	9	126414328	126414328	+	Missense_Mutation	SNP	T	T	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr9:126414328T>A	ENST00000373624.2	-	9	783	c.582A>T	c.(580-582)gaA>gaT	p.E194D	DENND1A_ENST00000394215.2_Missense_Mutation_p.E164D|DENND1A_ENST00000394219.3_Missense_Mutation_p.E162D|DENND1A_ENST00000473039.1_5'UTR|DENND1A_ENST00000373620.3_Missense_Mutation_p.E194D|DENND1A_ENST00000542603.1_5'UTR|DENND1A_ENST00000373618.1_Missense_Mutation_p.E162D	NM_020946.1	NP_065997.1	Q8TEH3	DEN1A_HUMAN	DENN/MADD domain containing 1A	194	DENN. {ECO:0000255|PROSITE- ProRule:PRU00304}.				endocytosis (GO:0006897)|positive regulation of Rab GTPase activity (GO:0032851)|protein transport (GO:0015031)|regulation of Rab protein signal transduction (GO:0032483)|synaptic vesicle endocytosis (GO:0048488)	cell junction (GO:0030054)|clathrin-coated vesicle (GO:0030136)|clathrin-coated vesicle membrane (GO:0030665)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|synapse (GO:0045202)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|liver(2)|lung(18)|ovary(2)|prostate(1)|skin(1)|stomach(1)	43						GTATCCGGCGTTCGTACAGCA	0.403																																					p.E194D		.											.	.	.	0			c.A582T						.						100.0	93.0	95.0					9																	126414328		2203	4300	6503	SO:0001583	missense	57706	exon9			CCGGCGTTCGTAC	AB046828	CCDS35133.1, CCDS35134.1	9q34.11	2012-10-03	2005-08-17	2005-08-17	ENSG00000119522	ENSG00000119522		"""DENN/MADD domain containing"""	29324	protein-coding gene	gene with protein product		613633	"""KIAA1608"""	KIAA1608		10997877	Standard	XM_005252109		Approved	FLJ21129, FAM31A	uc004bnz.1	Q8TEH3	OTTHUMG00000020643	ENST00000373624.2:c.582A>T	9.37:g.126414328T>A	ENSP00000362727:p.Glu194Asp	Somatic	38	0		WXS	Illumina HiSeq	.	21	7	NM_024820	A8MZA3|B1AM80|B7Z3C8|B7Z669|D3PFD3|Q05C88|Q5VWF0|Q6PJZ5|Q8IVD6|Q9H796	Missense_Mutation	SNP	ENST00000373624.2	37	CCDS35133.1	.	.	.	.	.	.	.	.	.	.	T	20.3	3.964299	0.74131	.	.	ENSG00000119522	ENST00000373624;ENST00000394219;ENST00000373620;ENST00000394215;ENST00000373618	T;T;T;T;T	0.26223	1.75;1.75;1.75;1.75;1.75	5.35	1.64	0.23874	DENN (3);	0.000000	0.85682	D	0.000000	T	0.56366	0.1980	M	0.93507	3.425	0.50171	D	0.99985	D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;0.999	D;D;D;D;D;D;D	0.87578	0.997;0.997;0.993;0.998;0.993;0.998;0.998	T	0.60094	-0.7330	10	0.87932	D	0	-14.5749	9.435	0.38632	0.0:0.3944:0.0:0.6056	.	162;194;162;164;194;194;92	Q8TEH3-6;Q8TEH3-7;Q8TEH3-4;Q8TEH3-5;Q8TEH3-2;Q8TEH3;Q9HCG4	.;.;.;.;.;DEN1A_HUMAN;.	D	194;162;194;164;162	ENSP00000362727:E194D;ENSP00000377766:E162D;ENSP00000362722:E194D;ENSP00000377763:E164D;ENSP00000362720:E162D	ENSP00000362720:E162D	E	-	3	2	DENND1A	125454149	0.745000	0.28261	1.000000	0.80357	0.995000	0.86356	-0.142000	0.10311	0.087000	0.17167	0.460000	0.39030	GAA	.		0.403	DENND1A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053997.1	NM_024820	
ANKRD13C	81573	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	70779446	70779446	+	Missense_Mutation	SNP	A	A	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr1:70779446A>T	ENST00000370944.4	-	5	1004	c.691T>A	c.(691-693)Tgg>Agg	p.W231R	ANKRD13C_ENST00000262346.6_Missense_Mutation_p.W196R	NM_030816.4	NP_110443.3	Q8N6S4	AN13C_HUMAN	ankyrin repeat domain 13C	231					protein retention in ER lumen (GO:0006621)|regulation of anoikis (GO:2000209)|regulation of receptor biosynthetic process (GO:0010869)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)	receptor binding (GO:0005102)			endometrium(3)|kidney(2)|large_intestine(2)|lung(8)|prostate(2)|skin(1)|urinary_tract(1)	19						TGAAAATCCCAGTGAAGTTCT	0.284																																					p.W231R		.											.	.	.	0			c.T691A						.						74.0	83.0	80.0					1																	70779446		2202	4289	6491	SO:0001583	missense	81573	exon5			AATCCCAGTGAAG		CCDS648.2	1p32.3-p31.3	2013-01-10			ENSG00000118454	ENSG00000118454		"""Ankyrin repeat domain containing"""	25374	protein-coding gene	gene with protein product		615125				11230166	Standard	NM_030816		Approved	DKFZP566D1346, dJ677H15.3	uc001dex.4	Q8N6S4	OTTHUMG00000009343	ENST00000370944.4:c.691T>A	1.37:g.70779446A>T	ENSP00000359982:p.Trp231Arg	Somatic	99	0		WXS	Illumina HiSeq	.	55	24	NM_030816	B3KQ97|Q5VYH4|Q5VYH5|Q6PJE4|Q9H0N9	Missense_Mutation	SNP	ENST00000370944.4	37	CCDS648.2	.	.	.	.	.	.	.	.	.	.	A	19.66	3.869372	0.72065	.	.	ENSG00000118454	ENST00000370944;ENST00000262346	T;T	0.60920	0.27;0.15	5.43	5.43	0.79202	Ankyrin repeat-containing domain (1);	0.115026	0.64402	D	0.000005	T	0.73110	0.3545	M	0.86178	2.8	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.998	T	0.79082	-0.1949	10	0.87932	D	0	.	13.7018	0.62613	1.0:0.0:0.0:0.0	.	196;231	Q8N6S4-2;Q8N6S4	.;AN13C_HUMAN	R	231;196	ENSP00000359982:W231R;ENSP00000262346:W196R	ENSP00000262346:W196R	W	-	1	0	ANKRD13C	70552034	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.251000	0.78297	2.056000	0.61249	0.482000	0.46254	TGG	.		0.284	ANKRD13C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025903.1	NM_030816	
ADAMTS5	11096	hgsc.bcm.edu	37	21	28296852	28296852	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr21:28296852G>T	ENST00000284987.5	-	8	2434	c.2313C>A	c.(2311-2313)ttC>ttA	p.F771L	AP001601.2_ENST00000426771.1_RNA	NM_007038.3	NP_008969.2	Q9UNA0	ATS5_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 5	771	Spacer.				defense response to bacterium (GO:0042742)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|proteolysis (GO:0006508)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.F771L(1)		breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(34)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)	72						AATAGGCAGTGAATCTAGTCT	0.428																																					p.F771L	Esophageal Squamous(53;683 1080 10100 14424 45938)	.											ADAMTS5,NS,carcinoma,0,1	ADAMTS5	0	1	Substitution - Missense(1)	kidney(1)	c.C2313A						.						163.0	162.0	162.0					21																	28296852		2203	4300	6503	SO:0001583	missense	11096	exon8			GGCAGTGAATCTA	AF142099	CCDS13579.1	21q21.3	2008-07-31	2008-07-31		ENSG00000154736	ENSG00000154736		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	221	protein-coding gene	gene with protein product	"""aggrecanase-2"""	605007	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 5 (aggrecanase-2)"""			10438522	Standard	NM_007038		Approved	ADMP-2, ADAMTS11	uc002ymg.3	Q9UNA0	OTTHUMG00000078686	ENST00000284987.5:c.2313C>A	21.37:g.28296852G>T	ENSP00000284987:p.Phe771Leu	Somatic	97	0		WXS	Illumina HiSeq	.	21	2	NM_007038	Q52LV4|Q9UKP2	Missense_Mutation	SNP	ENST00000284987.5	37	CCDS13579.1	.	.	.	.	.	.	.	.	.	.	G	16.09	3.023651	0.54683	.	.	ENSG00000154736	ENST00000284987	T	0.61980	0.06	5.93	5.0	0.66597	ADAM-TS Spacer 1 (1);	0.152162	0.64402	D	0.000010	T	0.47619	0.1455	N	0.22421	0.69	0.45194	D	0.998203	B	0.29552	0.248	B	0.30179	0.112	T	0.46816	-0.9164	10	0.45353	T	0.12	.	11.7861	0.52043	0.0676:0.1241:0.8083:0.0	.	771	Q9UNA0	ATS5_HUMAN	L	771	ENSP00000284987:F771L	ENSP00000284987:F771L	F	-	3	2	ADAMTS5	27218723	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	5.247000	0.65416	2.826000	0.97356	0.655000	0.94253	TTC	.		0.428	ADAMTS5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171648.1		
RB1CC1	9821	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	8	53568653	53568653	+	Silent	SNP	G	G	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr8:53568653G>A	ENST00000025008.5	-	15	4259	c.3736C>T	c.(3736-3738)Cta>Tta	p.L1246L	RB1CC1_ENST00000435644.2_Silent_p.L1246L|RB1CC1_ENST00000539297.1_Silent_p.L1246L|RB1CC1_ENST00000521611.1_Intron	NM_014781.4	NP_055596.3	Q8TDY2	RBCC1_HUMAN	RB1-inducible coiled-coil 1	1246					autophagic vacuole assembly (GO:0000045)|cell cycle (GO:0007049)|heart development (GO:0007507)|JNK cascade (GO:0007254)|liver development (GO:0001889)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell size (GO:0045793)|positive regulation of protein phosphorylation (GO:0001934)|regulation of autophagy (GO:0010506)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|pre-autophagosomal structure membrane (GO:0034045)|ULK1-ATG13-FIP200 complex (GO:0070969)				NS(2)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(9)|lung(19)|ovary(8)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)	60		all_cancers(86;0.137)|all_epithelial(80;0.00494)|Lung NSC(129;0.011)|all_lung(136;0.023)				AATTCTTTTAGGGCAGTCTGA	0.328																																					p.L1246L	GBM(180;1701 2102 13475 42023 52570)	.											.	.	.	0			c.C3736T						.						108.0	109.0	109.0					8																	53568653		2202	4298	6500	SO:0001819	synonymous_variant	9821	exon15			CTTTTAGGGCAGT	AB059622	CCDS34892.1, CCDS47856.1	8q11	2014-06-13				ENSG00000023287			15574	protein-coding gene	gene with protein product	"""200 kDa FAK family kinase-interacting protein"", ""phosphatase 1, regulatory subunit 131"""	606837				11850849, 7724523, 18443221	Standard	NM_014781		Approved	KIAA0203, Cc1, DRAGOU14, FIP200, ATG17, PPP1R131	uc003xre.4	Q8TDY2		ENST00000025008.5:c.3736C>T	8.37:g.53568653G>A		Somatic	55	0		WXS	Illumina HiSeq	.	55	26	NM_001083617	Q86YR4|Q8WVU9|Q92601	Silent	SNP	ENST00000025008.5	37	CCDS34892.1																																																																																			.		0.328	RB1CC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000378011.1	NM_014781	
TMCO1	54499	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	165728808	165728808	+	Silent	SNP	C	C	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr1:165728808C>T	ENST00000392129.6	-	3	312	c.162G>A	c.(160-162)aaG>aaA	p.K54K	TMCO1_ENST00000464650.1_5'UTR|TMCO1_ENST00000367881.5_Silent_p.K105K|TMCO1_ENST00000580248.1_5'UTR	NM_001256165.1|NM_019026.4	NP_001243094.1|NP_061899.2	Q9UM00	TMCO1_HUMAN	transmembrane and coiled-coil domains 1	54						endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)	9	all_hematologic(923;0.048)|Acute lymphoblastic leukemia(8;0.155)					TTATTGTTTCCTTCTTCTTTT	0.299																																					p.K105K		.											.	.	.	0			c.G315A						.						90.0	89.0	90.0					1																	165728808		2203	4298	6501	SO:0001819	synonymous_variant	54499	exon3			TGTTTCCTTCTTC	AB020980	CCDS1251.1, CCDS1251.2	1q22-q25	2008-02-05	2005-07-13	2005-07-13	ENSG00000143183	ENSG00000143183			18188	protein-coding gene	gene with protein product		614123	"""transmembrane and coiled-coil domains 4"""	TMCC4		8619474, 9110174	Standard	NM_019026		Approved	HP10122	uc001gdj.5	Q9UM00	OTTHUMG00000034672	ENST00000392129.6:c.162G>A	1.37:g.165728808C>T		Somatic	79	0		WXS	Illumina HiSeq	.	93	60	NM_019026	B2REA0|O75545|Q9BZS3|Q9BZU8	Silent	SNP	ENST00000392129.6	37																																																																																				.		0.299	TMCO1-008	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000467850.1	NM_019026	
SOAT1	6646	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	179312001	179312001	+	Silent	SNP	T	T	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr1:179312001T>C	ENST00000367619.3	+	9	1007	c.864T>C	c.(862-864)acT>acC	p.T288T	SOAT1_ENST00000540564.1_Silent_p.T230T|SOAT1_ENST00000535686.1_Silent_p.T24T|SOAT1_ENST00000539888.1_Silent_p.T223T	NM_003101.5	NP_003092.4	P35610	SOAT1_HUMAN	sterol O-acyltransferase 1	288					cholesterol efflux (GO:0033344)|cholesterol esterification (GO:0034435)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol storage (GO:0010878)|macrophage derived foam cell differentiation (GO:0010742)|positive regulation of amyloid precursor protein biosynthetic process (GO:0042986)|very-low-density lipoprotein particle assembly (GO:0034379)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	cholesterol binding (GO:0015485)|cholesterol O-acyltransferase activity (GO:0034736)|fatty-acyl-CoA binding (GO:0000062)|sterol O-acyltransferase activity (GO:0004772)			central_nervous_system(1)|endometrium(3)|large_intestine(1)|lung(10)|prostate(1)|skin(3)|stomach(1)	20					Ezetimibe(DB00973)|Hesperetin(DB01094)	TTCTAGGCACTGTTCCAATAC	0.403																																					p.T288T		.											.	.	.	0			c.T864C						.						164.0	154.0	157.0					1																	179312001		2203	4300	6503	SO:0001819	synonymous_variant	6646	exon9			AGGCACTGTTCCA	L21934	CCDS1330.1, CCDS58047.1, CCDS58048.1	1q25	2008-08-26	2008-08-26		ENSG00000057252	ENSG00000057252	2.3.1.26		11177	protein-coding gene	gene with protein product	"""acyl-Coenzyme A: cholesterol acyltransferase"""	102642	"""sterol O-acyltransferase (acyl-Coenzyme A: cholesterol acyltransferase) 1"""	SOAT, STAT		8407899	Standard	NM_003101		Approved	ACAT	uc001gml.3	P35610	OTTHUMG00000035253	ENST00000367619.3:c.864T>C	1.37:g.179312001T>C		Somatic	66	0		WXS	Illumina HiSeq	.	73	54	NM_003101	A6NC40|A8K3P4|A9Z1V7|B4DU95|Q5T0X4|Q8N1E4	Silent	SNP	ENST00000367619.3	37	CCDS1330.1																																																																																			.		0.403	SOAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085286.2	NM_003101	
NACAD	23148	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	7	45124486	45124486	+	Silent	SNP	G	G	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr7:45124486G>T	ENST00000490531.2	-	2	1312	c.1293C>A	c.(1291-1293)gcC>gcA	p.A431A		NM_001146334.1	NP_001139806.1	O15069	NACAD_HUMAN	NAC alpha domain containing	431					protein transport (GO:0015031)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|endometrium(2)|skin(2)	5						GCAGCCCCTTGGCCCCACCTC	0.622																																					p.A431A		.											.	.	.	0			c.C1293A						.						19.0	21.0	21.0					7																	45124486		692	1591	2283	SO:0001819	synonymous_variant	23148	exon2			CCCCTTGGCCCCA	AB002361	CCDS47582.1	7p13	2010-07-14			ENSG00000136274	ENSG00000136274			22196	protein-coding gene	gene with protein product							Standard	NM_001146334		Approved	KIAA0363	uc003tmt.3	O15069	OTTHUMG00000159170	ENST00000490531.2:c.1293C>A	7.37:g.45124486G>T		Somatic	26	0		WXS	Illumina HiSeq	.	13	5	NM_001146334		Silent	SNP	ENST00000490531.2	37	CCDS47582.1																																																																																			.		0.622	NACAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353652.2	NM_001146334	
C2CD2L	9854	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	11	118983266	118983266	+	Missense_Mutation	SNP	C	C	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr11:118983266C>T	ENST00000528586.1	+	5	473	c.403C>T	c.(403-405)Ctc>Ttc	p.L135F	C2CD2L_ENST00000336702.3_Missense_Mutation_p.L387F			O14523	C2C2L_HUMAN	C2CD2-like	387						integral component of membrane (GO:0016021)				NS(1)|endometrium(1)|large_intestine(2)|lung(8)|prostate(1)	13						GTTGTGCCCACTCACCCCAGG	0.652																																					p.L387F		.											.	.	.	0			c.C1159T						.						45.0	47.0	47.0					11																	118983266		2200	4295	6495	SO:0001583	missense	9854	exon9			TGCCCACTCACCC	AK025223	CCDS8413.1	11q23.3	2008-04-22	2008-04-22	2008-04-22		ENSG00000172375			29000	protein-coding gene	gene with protein product			"""transmembrane protein 24"""	TMEM24		15289880	Standard	XM_005271738		Approved	KIAA0285	uc001pvn.3	O14523		ENST00000528586.1:c.403C>T	11.37:g.118983266C>T	ENSP00000433600:p.Leu135Phe	Somatic	33	0		WXS	Illumina HiSeq	.	13	7	NM_014807	Q86UT7|Q86V04|Q8N522|Q8TBN4|Q96G10	Missense_Mutation	SNP	ENST00000528586.1	37		.	.	.	.	.	.	.	.	.	.	C	21.4	4.140784	0.77775	.	.	ENSG00000172375	ENST00000336702;ENST00000528586	T;T	0.59224	0.28;0.28	5.32	5.32	0.75619	C2 calcium/lipid-binding domain, CaLB (1);	0.060697	0.64402	D	0.000003	T	0.66396	0.2785	L	0.32530	0.975	0.52501	D	0.999952	D;D	0.67145	0.996;0.996	D;D	0.63793	0.918;0.918	T	0.68938	-0.5277	10	0.87932	D	0	-4.6111	18.1628	0.89714	0.0:1.0:0.0:0.0	.	387;387	O14523;O14523-2	C2C2L_HUMAN;.	F	387;135	ENSP00000338885:L387F;ENSP00000433600:L135F	ENSP00000338885:L387F	L	+	1	0	C2CD2L	118488476	0.991000	0.36638	1.000000	0.80357	0.976000	0.68499	2.468000	0.45102	2.778000	0.95560	0.655000	0.94253	CTC	.		0.652	C2CD2L-003	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000388199.2	NM_014807	
ATAD3C	219293	hgsc.bcm.edu	37	1	1398007	1398007	+	Silent	SNP	C	C	T	rs373872196		TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr1:1398007C>T	ENST00000378785.2	+	11	2003	c.1008C>T	c.(1006-1008)taC>taT	p.Y336Y		NM_001039211.2	NP_001034300.2	Q5T2N8	ATD3C_HUMAN	ATPase family, AAA domain containing 3C	336							ATP binding (GO:0005524)			autonomic_ganglia(1)|endometrium(1)|kidney(1)|lung(4)	7	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;9.48e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)		Epithelial(90;1.79e-36)|OV - Ovarian serous cystadenocarcinoma(86;3.94e-22)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.00461)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.145)		AGTTTGACTACGGGAGGAAGT	0.637																																					p.Y336Y		.											ATAD3C,colon,carcinoma,0,1	ATAD3C	0	0			c.C1008T						.	C		0,4402		0,0,2201	54.0	53.0	53.0		1008	-4.9	0.1	1		53	1,8577		0,1,4288	no	coding-synonymous	ATAD3C	NM_001039211.2		0,1,6489	TT,TC,CC		0.0117,0.0,0.0077		336/412	1398007	1,12979	2201	4289	6490	SO:0001819	synonymous_variant	219293	exon11			TGACTACGGGAGG	AK091918	CCDS44039.1	1p36.33	2010-04-21		2007-02-08	ENSG00000215915	ENSG00000215915		"""ATPases / AAA-type"""	32151	protein-coding gene	gene with protein product							Standard	NM_001039211		Approved	FLJ34599	uc001aft.2	Q5T2N8	OTTHUMG00000000531	ENST00000378785.2:c.1008C>T	1.37:g.1398007C>T		Somatic	88	0		WXS	Illumina HiSeq	.	48	2	NM_001039211	Q8N1Z5	Silent	SNP	ENST00000378785.2	37	CCDS44039.1																																																																																			.		0.637	ATAD3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001279.3	NM_001039211	
CEP350	9857	hgsc.bcm.edu	37	1	180023000	180023000	+	Missense_Mutation	SNP	T	T	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr1:180023000T>C	ENST00000367607.3	+	24	5523	c.5105T>C	c.(5104-5106)cTg>cCg	p.L1702P		NM_014810.4	NP_055625.4	Q5VT06	CE350_HUMAN	centrosomal protein 350kDa	1702					microtubule anchoring (GO:0034453)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(7)|lung(35)|ovary(4)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	66						TCTTCACTCCTGCGTCTCCGT	0.413																																					p.L1702P		.											.	.	.	0			c.T5105C						.						88.0	92.0	90.0					1																	180023000		2203	4300	6503	SO:0001583	missense	9857	exon24			CACTCCTGCGTCT	AF287356	CCDS1336.1	1q25.2	2014-02-20			ENSG00000135837	ENSG00000135837			24238	protein-coding gene	gene with protein product	"""centrosome associated protein 350"""					16314388, 15615782	Standard	NM_014810		Approved	KIAA0480, CAP350	uc001gnt.3	Q5VT06	OTTHUMG00000035269	ENST00000367607.3:c.5105T>C	1.37:g.180023000T>C	ENSP00000356579:p.Leu1702Pro	Somatic	79	0		WXS	Illumina HiSeq	.	98	4	NM_014810	O75068|Q8TDK3|Q8WY20	Missense_Mutation	SNP	ENST00000367607.3	37	CCDS1336.1	.	.	.	.	.	.	.	.	.	.	T	28.1	4.888321	0.91814	.	.	ENSG00000135837	ENST00000367607	T	0.74209	-0.82	5.98	5.98	0.97165	.	0.000000	0.35708	N	0.003040	T	0.80059	0.4554	L	0.32530	0.975	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	T	0.78484	-0.2186	9	.	.	.	.	16.1237	0.81377	0.0:0.0:0.0:1.0	.	1702;1702	E7EU22;Q5VT06	.;CE350_HUMAN	P	1702	ENSP00000356579:L1702P	.	L	+	2	0	CEP350	178289623	1.000000	0.71417	0.932000	0.37286	0.995000	0.86356	7.698000	0.84413	2.289000	0.77006	0.533000	0.62120	CTG	.		0.413	CEP350-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085315.2	NM_014810	
POTEF	728378	hgsc.bcm.edu	37	2	130832686	130832686	+	Missense_Mutation	SNP	G	G	A	rs376041561		TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr2:130832686G>A	ENST00000409914.2	-	17	2758	c.2359C>T	c.(2359-2361)Cac>Tac	p.H787Y	POTEF_ENST00000357462.5_Missense_Mutation_p.H787Y	NM_001099771.2	NP_001093241.1	A5A3E0	POTEF_HUMAN	POTE ankyrin domain family, member F	787	Actin-like.				retina homeostasis (GO:0001895)	blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)		p.H787N(1)		breast(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(4)|lung(28)|ovary(3)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	53						AAGGTGTGGTGCCAGATCTTC	0.592																																					p.H787Y		.											POTEF,NS,carcinoma,0,1	POTEF	0	1	Substitution - Missense(1)	lung(1)	c.C2359T						.						50.0	54.0	52.0					2																	130832686		2200	4297	6497	SO:0001583	missense	728378	exon17			TGTGGTGCCAGAT	EF523384	CCDS46409.1	2q21.1	2013-01-10	2008-11-26	2008-11-26	ENSG00000196604	ENSG00000196604		"""POTE ankyrin domain containing"", ""Ankyrin repeat domain containing"""	33905	protein-coding gene	gene with protein product			"""ANKRD26-like family C, member 1B"""	A26C1B		17101985	Standard	NM_001099771		Approved	POTEACTIN, POTE2alpha	uc010fmh.2	A5A3E0	OTTHUMG00000153628	ENST00000409914.2:c.2359C>T	2.37:g.130832686G>A	ENSP00000386786:p.His787Tyr	Somatic	77	0		WXS	Illumina HiSeq	.	52	3	NM_001099771	A6NC34	Missense_Mutation	SNP	ENST00000409914.2	37	CCDS46409.1	.	.	.	.	.	.	.	.	.	.	.	15.42	2.829377	0.50845	.	.	ENSG00000196604	ENST00000357462;ENST00000409914	D;D	0.97256	-4.31;-4.31	.	.	.	.	.	.	.	.	D	0.96793	0.8953	M	0.84846	2.72	0.80722	D	1	B	0.26120	0.142	B	0.40506	0.331	D	0.94238	0.7482	8	0.87932	D	0	.	5.9051	0.18992	8.0E-4:0.0:0.9992:0.0	.	787	A5A3E0	POTEF_HUMAN	Y	787	ENSP00000350052:H787Y;ENSP00000386786:H787Y	ENSP00000350052:H787Y	H	-	1	0	POTEF	130549156	1.000000	0.71417	0.225000	0.23894	0.227000	0.25037	6.509000	0.73725	0.119000	0.18210	0.121000	0.15741	CAC	.		0.592	POTEF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331889.2	NM_001099771	
ZCCHC8	55596	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	12	122973962	122973962	+	Missense_Mutation	SNP	C	C	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr12:122973962C>T	ENST00000336229.4	-	5	602	c.472G>A	c.(472-474)Gcc>Acc	p.A158T	SNORA9_ENST00000516383.1_RNA|ZCCHC8_ENST00000536306.1_5'UTR|ZCCHC8_ENST00000543897.1_5'UTR	NM_017612.3	NP_060082.2	Q6NZY4	ZCHC8_HUMAN	zinc finger, CCHC domain containing 8	158					mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			endometrium(4)|kidney(2)|large_intestine(8)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	23	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;5.25e-05)|Epithelial(86;0.000113)|BRCA - Breast invasive adenocarcinoma(302;0.202)		TTTTTAATGGCACAGGACTCT	0.393																																					p.A158T		.											.	.	.	0			c.G472A						.						122.0	120.0	120.0					12																	122973962		1858	4107	5965	SO:0001583	missense	55596	exon5			TAATGGCACAGGA	BC017704		12q24.31	2014-04-14				ENSG00000033030		"""Zinc fingers, CCHC domain containing"""	25265	protein-coding gene	gene with protein product						12477932	Standard	XM_005253581		Approved	DKFZp434E2220	uc001ucn.3	Q6NZY4		ENST00000336229.4:c.472G>A	12.37:g.122973962C>T	ENSP00000337313:p.Ala158Thr	Somatic	130	0		WXS	Illumina HiSeq	.	70	29	NM_017612	Q7L2P6|Q8N2K5|Q96SK7|Q9NSS2|Q9NSS3	Missense_Mutation	SNP	ENST00000336229.4	37		.	.	.	.	.	.	.	.	.	.	C	0.612	-0.824667	0.02755	.	.	ENSG00000033030	ENST00000336229	T	0.44083	0.93	5.59	0.591	0.17465	.	0.716205	0.14513	N	0.314999	T	0.18425	0.0442	N	0.14661	0.345	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.23476	-1.0187	10	0.10636	T	0.68	0.5935	3.6659	0.08255	0.3124:0.3047:0.0:0.3829	.	158	Q6NZY4	ZCHC8_HUMAN	T	158	ENSP00000337313:A158T	ENSP00000337313:A158T	A	-	1	0	ZCCHC8	121539915	0.085000	0.21516	0.001000	0.08648	0.032000	0.12392	0.355000	0.20163	0.042000	0.15717	0.305000	0.20034	GCC	.		0.393	ZCCHC8-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_017612	
CDC20B	166979	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	5	54442593	54442593	+	Missense_Mutation	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr5:54442593A>C	ENST00000381375.2	-	3	363	c.218T>G	c.(217-219)aTt>aGt	p.I73S	CDC20B_ENST00000334206.5_Missense_Mutation_p.I73S|CDC20B_ENST00000322374.6_Missense_Mutation_p.I73S|CDC20B_ENST00000331730.3_Missense_Mutation_p.I52S|CDC20B_ENST00000296733.1_Missense_Mutation_p.I73S			Q86Y33	CD20B_HUMAN	cell division cycle 20B	73										kidney(1)|large_intestine(5)|lung(7)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)	19		Lung NSC(810;0.000744)|Breast(144;0.159)|Prostate(74;0.194)	LUSC - Lung squamous cell carcinoma(15;0.225)			CCTTGTGGTAATGGGGCTACT	0.498											OREG0016610	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.I73S		.											.	.	.	0			c.T218G						.						118.0	109.0	112.0					5																	54442593		2203	4300	6503	SO:0001583	missense	166979	exon3			GTGGTAATGGGGC	AB086378	CCDS3966.1, CCDS47207.1, CCDS54852.1	5q11.2	2013-01-17	2013-01-17		ENSG00000164287	ENSG00000164287		"""WD repeat domain containing"""	24222	protein-coding gene	gene with protein product			"""CDC20 cell division cycle 20 homolog B (S. cerevisiae)"", ""cell division cycle 20 homolog B (S. cerevisiae)"""				Standard	NM_152623		Approved	FLJ37927	uc003jpo.2	Q86Y33	OTTHUMG00000131185	ENST00000381375.2:c.218T>G	5.37:g.54442593A>C	ENSP00000370781:p.Ile73Ser	Somatic	89	0	1000	WXS	Illumina HiSeq	.	65	23	NM_001170402	B7WNV8|B9EGL8|C9J6X8|C9JHE9|C9JKL5|Q86Y31|Q86Y32|Q8IUZ8|Q8N1S1|Q8NG56	Missense_Mutation	SNP	ENST00000381375.2	37	CCDS54852.1	.	.	.	.	.	.	.	.	.	.	A	12.61	1.989013	0.35131	.	.	ENSG00000164287	ENST00000334206;ENST00000296733;ENST00000381375;ENST00000322374;ENST00000331730	T;T;T;T;T	0.30182	3.17;3.17;3.17;3.17;1.54	4.7	4.7	0.59300	.	0.268702	0.26103	N	0.026334	T	0.38241	0.1033	L	0.59436	1.845	0.09310	N	1	D;P;P;P	0.57571	0.98;0.879;0.808;0.879	P;P;B;P	0.51229	0.663;0.626;0.422;0.626	T	0.24870	-1.0148	10	0.42905	T	0.14	-19.8367	10.7027	0.45937	1.0:0.0:0.0:0.0	.	73;73;73;73	Q86Y33-4;Q86Y33-3;Q86Y33;Q86Y33-2	.;.;CD20B_HUMAN;.	S	73;73;73;73;52	ENSP00000335664:I73S;ENSP00000296733:I73S;ENSP00000370781:I73S;ENSP00000315720:I73S;ENSP00000330566:I52S	ENSP00000296733:I73S	I	-	2	0	CDC20B	54478350	0.043000	0.20138	0.020000	0.16555	0.092000	0.18411	4.115000	0.57865	2.093000	0.63338	0.528000	0.53228	ATT	.		0.498	CDC20B-004	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000369715.1	NM_152623	
HMGCS2	3158	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	120302536	120302536	+	Silent	SNP	T	T	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr1:120302536T>A	ENST00000369406.3	-	3	685	c.636A>T	c.(634-636)ggA>ggT	p.G212G	HMGCS2_ENST00000544913.2_Intron|HMGCS2_ENST00000476640.1_5'UTR	NM_005518.3	NP_005509.1	P54868	HMCS2_HUMAN	3-hydroxy-3-methylglutaryl-CoA synthase 2 (mitochondrial)	212			G -> R (in HMGCS deficiency). {ECO:0000269|PubMed:11479731}.		cellular ketone body metabolic process (GO:0046950)|cellular lipid metabolic process (GO:0044255)|cholesterol biosynthetic process (GO:0006695)|isoprenoid biosynthetic process (GO:0008299)|ketone body biosynthetic process (GO:0046951)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	hydroxymethylglutaryl-CoA synthase activity (GO:0004421)			NS(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(1)|lung(13)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	28	all_cancers(5;6.38e-10)|all_epithelial(5;1.1e-10)|Melanoma(3;1.93e-05)|Breast(55;0.218)|all_neural(166;0.219)	all_lung(203;1.29e-06)|Lung NSC(69;9.35e-06)|all_epithelial(167;0.00124)		Lung(183;0.0112)|LUSC - Lung squamous cell carcinoma(189;0.0595)		TAGCCACAGCTCCGGCCCCAC	0.527																																					p.G212G		.											.	.	.	0			c.A636T						.						61.0	59.0	60.0					1																	120302536		2203	4300	6503	SO:0001819	synonymous_variant	3158	exon3			CACAGCTCCGGCC	BC044217	CCDS905.1, CCDS53353.1	1p13-p12	2014-09-17	2010-04-30		ENSG00000134240	ENSG00000134240			5008	protein-coding gene	gene with protein product		600234	"""3-hydroxy-3-methylglutaryl-Coenzyme A synthase 2 (mitochondrial)"""			7851882, 7893153	Standard	NM_005518		Approved		uc001eid.3	P54868	OTTHUMG00000012101	ENST00000369406.3:c.636A>T	1.37:g.120302536T>A		Somatic	25	0		WXS	Illumina HiSeq	.	14	6	NM_005518	B7Z8R3|D3Y5K6|Q5SZU2|Q6IBF4	Silent	SNP	ENST00000369406.3	37	CCDS905.1																																																																																			.		0.527	HMGCS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033469.2	NM_005518	
IL12B	3593	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	5	158749517	158749517	+	Missense_Mutation	SNP	G	G	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr5:158749517G>C	ENST00000231228.2	-	4	822	c.367C>G	c.(367-369)Ccc>Gcc	p.P123A		NM_002187.2	NP_002178.2	P29460	IL12B_HUMAN	interleukin 12B	123					cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular response to interferon-gamma (GO:0071346)|cellular response to lipopolysaccharide (GO:0071222)|defense response to Gram-negative bacterium (GO:0050829)|defense response to protozoan (GO:0042832)|defense response to virus (GO:0051607)|interferon-gamma biosynthetic process (GO:0042095)|natural killer cell activation (GO:0030101)|natural killer cell activation involved in immune response (GO:0002323)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of inflammatory response to antigenic stimulus (GO:0002862)|negative regulation of interleukin-10 production (GO:0032693)|negative regulation of interleukin-17 production (GO:0032700)|negative regulation of smooth muscle cell proliferation (GO:0048662)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of activation of JAK2 kinase activity (GO:0010535)|positive regulation of cell adhesion (GO:0045785)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of granulocyte macrophage colony-stimulating factor production (GO:0032725)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-17 production (GO:0032740)|positive regulation of lymphocyte proliferation (GO:0050671)|positive regulation of memory T cell differentiation (GO:0043382)|positive regulation of mononuclear cell proliferation (GO:0032946)|positive regulation of natural killer cell activation (GO:0032816)|positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target (GO:0002860)|positive regulation of natural killer cell proliferation (GO:0032819)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NK T cell activation (GO:0051135)|positive regulation of NK T cell proliferation (GO:0051142)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of smooth muscle cell apoptotic process (GO:0034393)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of T-helper 1 type immune response (GO:0002827)|positive regulation of T-helper 17 cell lineage commitment (GO:2000330)|positive regulation of T-helper 17 type immune response (GO:2000318)|positive regulation of tissue remodeling (GO:0034105)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat4 protein (GO:0042520)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|regulation of cytokine biosynthetic process (GO:0042035)|regulation of tyrosine phosphorylation of Stat1 protein (GO:0042510)|response to UV-B (GO:0010224)|sensory perception of pain (GO:0019233)|sexual reproduction (GO:0019953)|T-helper 1 type immune response (GO:0042088)|T-helper cell differentiation (GO:0042093)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|interleukin-12 complex (GO:0043514)|interleukin-23 complex (GO:0070743)|membrane (GO:0016020)	cytokine receptor activity (GO:0004896)|identical protein binding (GO:0042802)|interleukin-12 alpha subunit binding (GO:0042164)|interleukin-12 receptor binding (GO:0005143)|protein heterodimerization activity (GO:0046982)			cervix(1)|endometrium(1)|large_intestine(5)|lung(4)	11	Renal(175;0.00196)	Medulloblastoma(196;0.0354)|all_neural(177;0.138)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			TTATTTTTGGGTTCTGGATTT	0.383																																					p.P123A		.											.	.	.	0			c.C367G						.						70.0	71.0	71.0					5																	158749517		2203	4300	6503	SO:0001583	missense	3593	exon4			TTTTGGGTTCTGG	M65290	CCDS4346.1	5q31.1-q33.1	2014-09-17	2014-04-04		ENSG00000113302	ENSG00000113302		"""Interleukins and interleukin receptors"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5970	protein-coding gene	gene with protein product	"""natural killer cell stimulatory factor-2"", ""cytotoxic lymphocyte maturation factor 2, p40"", ""interleukin 12, p40"", ""natural killer cell stimulatory factor, 40 kD subunit"", ""interleukin-12 beta chain"", ""IL12, subunit p40"""	161561	"""interleukin 12B (natural killer cell stimulatory factor 2, cytotoxic lymphocyte maturation factor 2, p40)"""	NKSF2		1673147	Standard	NM_002187		Approved	CLMF, IL-12B, NKSF, CLMF2	uc003lxr.1	P29460	OTTHUMG00000130307	ENST00000231228.2:c.367C>G	5.37:g.158749517G>C	ENSP00000231228:p.Pro123Ala	Somatic	60	0		WXS	Illumina HiSeq	.	65	29	NM_002187		Missense_Mutation	SNP	ENST00000231228.2	37	CCDS4346.1	.	.	.	.	.	.	.	.	.	.	G	13.75	2.328886	0.41197	.	.	ENSG00000113302	ENST00000231228	T	0.23552	1.9	5.87	1.6	0.23607	Fibronectin, type III (1);	0.777388	0.12862	N	0.433016	T	0.23171	0.0560	M	0.62723	1.935	0.27613	N	0.94859	B	0.28783	0.222	B	0.16722	0.016	T	0.12941	-1.0528	10	0.46703	T	0.11	-4.8247	7.9342	0.29920	0.4162:0.0:0.5838:0.0	.	123	P29460	IL12B_HUMAN	A	123	ENSP00000231228:P123A	ENSP00000231228:P123A	P	-	1	0	IL12B	158682095	0.992000	0.36948	0.984000	0.44739	0.991000	0.79684	0.481000	0.22260	0.312000	0.23038	0.655000	0.94253	CCC	.		0.383	IL12B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252652.2	NM_002187	
TMEM128	85013	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	4	4242110	4242110	+	Silent	SNP	A	A	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr4:4242110A>G	ENST00000382753.4	-	3	345	c.336T>C	c.(334-336)taT>taC	p.Y112Y	TMEM128_ENST00000254742.2_Silent_p.Y88Y|TMEM128_ENST00000540397.1_Silent_p.Y112Y|TMEM128_ENST00000538516.1_Silent_p.Y112Y			Q5BJH2	TM128_HUMAN	transmembrane protein 128	112						integral component of membrane (GO:0016021)				endometrium(1)|kidney(1)	2				UCEC - Uterine corpus endometrioid carcinoma (64;0.166)		ACTTGACATCATATTCTCCAA	0.403																																					p.Y88Y		.											.	.	.	0			c.T264C						.						138.0	112.0	121.0					4																	4242110		2203	4300	6503	SO:0001819	synonymous_variant	85013	exon3			GACATCATATTCT	BC007729	CCDS3373.1, CCDS75099.1	4p16.3	2008-02-05			ENSG00000132406	ENSG00000132406			28201	protein-coding gene	gene with protein product							Standard	XM_005248034		Approved	MGC13159	uc003ghq.1	Q5BJH2	OTTHUMG00000125475	ENST00000382753.4:c.336T>C	4.37:g.4242110A>G		Somatic	85	0		WXS	Illumina HiSeq	.	79	37	NM_032927	B4DHS7|D3DVS3|Q5H9U6|Q96I94	Silent	SNP	ENST00000382753.4	37																																																																																				.		0.403	TMEM128-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000246798.2	NM_032927	
FAM69B	138311	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	9	139620610	139620610	+	IGR	SNP	T	T	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr9:139620610T>C	ENST00000371692.4	+	0	1668				SNHG7_ENST00000391185.1_RNA|SNHG7_ENST00000414282.1_RNA|SNHG7_ENST00000436596.1_RNA|SNHG7_ENST00000362567.2_RNA|SNHG7_ENST00000416970.1_RNA|SNHG7_ENST00000447221.1_RNA	NM_152421.3	NP_689634.2	Q5VUD6	FA69B_HUMAN	family with sequence similarity 69, member B							endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				NS(1)|endometrium(3)|large_intestine(2)|lung(1)|prostate(1)	8	all_cancers(76;0.0882)|all_epithelial(76;0.228)	Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;1.03e-05)|Epithelial(140;0.00013)		GCACTGAGTGTAGAAATCGCC	0.547																																					.		.											.	.	.	0			.						.						51.0	48.0	49.0					9																	139620610		876	1991	2867	SO:0001628	intergenic_variant	84973	.			TGAGTGTAGAAAT		CCDS7004.1	9q34.3	2012-08-03			ENSG00000165716	ENSG00000165716			28290	protein-coding gene	gene with protein product		614543				21334309	Standard	NM_152421		Approved	MGC20262, C9orf136	uc004cik.3	Q5VUD6	OTTHUMG00000020940		9.37:g.139620610T>C		Somatic	46	0		WXS	Illumina HiSeq	.	25	13	.	Q5VUD7|Q8N5N0|Q8WYU5	RNA	SNP	ENST00000371692.4	37	CCDS7004.1																																																																																			.		0.547	FAM69B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055102.1	NM_152421	
ATF4	468	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	22	39917554	39917554	+	Missense_Mutation	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr22:39917554A>C	ENST00000337304.2	+	1	986	c.104A>C	c.(103-105)gAt>gCt	p.D35A	ATF4_ENST00000396680.1_Missense_Mutation_p.D35A|ATF4_ENST00000404241.2_Missense_Mutation_p.D35A	NM_001675.2	NP_001666.2	P18848	ATF4_HUMAN	activating transcription factor 4	35					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular amino acid metabolic process (GO:0006520)|cellular protein metabolic process (GO:0044267)|circadian regulation of gene expression (GO:0032922)|endoplasmic reticulum unfolded protein response (GO:0030968)|gamma-aminobutyric acid signaling pathway (GO:0007214)|gluconeogenesis (GO:0006094)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|negative regulation of oxidative stress-induced neuron death (GO:1903204)|negative regulation of potassium ion transport (GO:0043267)|positive regulation of apoptotic process (GO:0043065)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to endoplasmic reticulum stress (GO:1990440)|positive regulation of transcription from RNA polymerase II promoter in response to oxidative stress (GO:0036091)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|response to endoplasmic reticulum stress (GO:0034976)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dendrite membrane (GO:0032590)|Lewy body core (GO:1990037)|neuron projection (GO:0043005)|nuclear periphery (GO:0034399)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	core promoter sequence-specific DNA binding (GO:0001046)|DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|endometrium(2)|large_intestine(2)|lung(5)|skin(1)	11	Melanoma(58;0.04)				Pseudoephedrine(DB00852)	GGTCTCTTAGATGATTACCTG	0.572																																					p.D35A		.											.	.	.	0			c.A104C						.						65.0	64.0	64.0					22																	39917554		2203	4300	6503	SO:0001583	missense	468	exon1			TCTTAGATGATTA	D90209	CCDS13996.1	22q13.1	2013-05-23	2013-05-23		ENSG00000128272	ENSG00000128272		"""basic leucine zipper proteins"""	786	protein-coding gene	gene with protein product	"""tax-responsive enhancer element B67"""	604064	"""activating transcription factor 4 (tax-responsive enhancer element B67)"""	TXREB		1847461, 1534408	Standard	NM_182810		Approved	TAXREB67, CREB-2	uc003axz.3	P18848	OTTHUMG00000151099	ENST00000337304.2:c.104A>C	22.37:g.39917554A>C	ENSP00000336790:p.Asp35Ala	Somatic	65	0		WXS	Illumina HiSeq	.	35	10	NM_001675	Q9UH31	Missense_Mutation	SNP	ENST00000337304.2	37	CCDS13996.1	.	.	.	.	.	.	.	.	.	.	A	19.00	3.741385	0.69304	.	.	ENSG00000128272	ENST00000404241;ENST00000337304;ENST00000396680	T;T;T	0.74002	-0.8;-0.8;-0.8	4.37	4.37	0.52481	.	0.445824	0.23556	N	0.046912	T	0.78947	0.4364	M	0.69823	2.125	0.47547	D	0.999458	P	0.48503	0.911	P	0.49387	0.609	T	0.82212	-0.0569	10	0.87932	D	0	-7.1823	13.5848	0.61924	1.0:0.0:0.0:0.0	.	35	P18848	ATF4_HUMAN	A	35	ENSP00000384587:D35A;ENSP00000336790:D35A;ENSP00000379912:D35A	ENSP00000336790:D35A	D	+	2	0	ATF4	38247500	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	6.318000	0.72866	1.614000	0.50241	0.459000	0.35465	GAT	.		0.572	ATF4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321305.1	NM_001675	
PIK3CB	5291	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	3	138407783	138407783	+	Missense_Mutation	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr3:138407783T>G	ENST00000477593.1	-	15	2143	c.2070A>C	c.(2068-2070)caA>caC	p.Q690H	PIK3CB_ENST00000289153.2_Missense_Mutation_p.Q690H|PIK3CB_ENST00000544716.1_Missense_Mutation_p.Q136H			P42338	PK3CB_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit beta	690	PIK helical. {ECO:0000255|PROSITE- ProRule:PRU00878}.				activation of MAPK activity (GO:0000187)|autophagy (GO:0006914)|blood coagulation (GO:0007596)|cell migration (GO:0016477)|cellular calcium ion homeostasis (GO:0006874)|chemotaxis (GO:0006935)|embryonic cleavage (GO:0040016)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|homophilic cell adhesion (GO:0007156)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|positive regulation of autophagy (GO:0010508)|regulation of cell-matrix adhesion (GO:0001952)|regulation of clathrin-mediated endocytosis (GO:2000369)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|T cell receptor signaling pathway (GO:0050852)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytosol (GO:0005829)|nucleus (GO:0005634)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)			NS(1)|breast(3)|endometrium(5)|kidney(2)|large_intestine(4)|lung(17)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(4)	41					Caffeine(DB00201)	TGACACCAAATTGTACTGAGA	0.388																																					p.Q690H		.											.	.	.	0			c.A2070C						.						87.0	77.0	80.0					3																	138407783		2203	4300	6503	SO:0001583	missense	5291	exon14			ACCAAATTGTACT		CCDS3104.1	3q22.3	2013-09-19	2012-07-13		ENSG00000051382	ENSG00000051382	2.7.1.153		8976	protein-coding gene	gene with protein product		602925	"""phosphoinositide-3-kinase, catalytic, beta polypeptide"""	PIK3C1		8246984	Standard	NM_006219		Approved		uc011bmq.3	P42338	OTTHUMG00000159893	ENST00000477593.1:c.2070A>C	3.37:g.138407783T>G	ENSP00000418143:p.Gln690His	Somatic	45	0		WXS	Illumina HiSeq	.	41	15	NM_006219	D3DNF0|Q24JU2	Missense_Mutation	SNP	ENST00000477593.1	37	CCDS3104.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	11.34|11.34	1.610776|1.610776	0.28712|0.28712	.|.	.|.	ENSG00000051382|ENSG00000051382	ENST00000493568|ENST00000477593;ENST00000544716;ENST00000289153	.|T;T;T	.|0.63417	.|-0.04;-0.04;-0.04	5.24|5.24	-7.58|-7.58	0.01313|0.01313	.|Phosphoinositide 3-kinase, accessory (PIK) domain (3);Armadillo-type fold (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.43831|0.43831	0.1265|0.1265	L|L	0.41415|0.41415	1.275|1.275	0.35219|0.35219	D|D	0.77587|0.77587	.|B;B;B	.|0.17465	.|0.001;0.001;0.022	.|B;B;B	.|0.14023	.|0.005;0.005;0.01	T|T	0.02398|0.02398	-1.1165|-1.1165	5|10	.|0.66056	.|D	.|0.02	-6.891|-6.891	10.3122|10.3122	0.43714|0.43714	0.0916:0.3148:0.0:0.5937|0.0916:0.3148:0.0:0.5937	.|.	.|690;277;136	.|P42338;B4DZI3;Q68DL0	.|PK3CB_HUMAN;.;.	T|H	322|690;136;690	.|ENSP00000418143:Q690H;ENSP00000438259:Q136H;ENSP00000289153:Q690H	.|ENSP00000289153:Q690H	N|Q	-|-	2|3	0|2	PIK3CB|PIK3CB	139890473|139890473	0.257000|0.257000	0.24022|0.24022	0.178000|0.178000	0.23040|0.23040	0.706000|0.706000	0.40770|0.40770	-0.257000|-0.257000	0.08745|0.08745	-1.356000|-1.356000	0.02183|0.02183	-1.064000|-1.064000	0.02280|0.02280	AAT|CAA	.		0.388	PIK3CB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358019.1		
USP2	9099	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	11	119243852	119243852	+	Silent	SNP	G	G	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr11:119243852G>A	ENST00000260187.2	-	2	633	c.339C>T	c.(337-339)ttC>ttT	p.F113F	USP2_ENST00000455332.2_Intron|RP11-334E6.3_ENST00000530918.2_RNA	NM_004205.4	NP_004196.4	O75604	UBP2_HUMAN	ubiquitin specific peptidase 2	113	Necessary for interaction with MDM4.				cell cycle (GO:0007049)|muscle organ development (GO:0007517)|negative regulation of skeletal muscle tissue development (GO:0048642)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of skeletal muscle tissue development (GO:0048643)|protein deubiquitination (GO:0016579)|protein stabilization (GO:0050821)|ubiquitin-dependent protein catabolic process (GO:0006511)	cell cortex (GO:0005938)|centrosome (GO:0005813)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	cyclin binding (GO:0030332)|cysteine-type endopeptidase activity (GO:0004197)|metal ion binding (GO:0046872)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			breast(2)|endometrium(2)|kidney(2)|large_intestine(5)|lung(5)|ovary(2)|prostate(3)|skin(2)|urinary_tract(1)	24		all_hematologic(192;4.65e-05)|Breast(348;0.0101)|all_neural(223;0.0218)|Medulloblastoma(222;0.0425)|Renal(330;0.157)		BRCA - Breast invasive adenocarcinoma(274;3.93e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.000513)|Colorectal(284;0.0116)|Lung(307;0.0853)|LUSC - Lung squamous cell carcinoma(976;0.0889)		CTCCATAAGGGAATCCGCTGC	0.612																																					p.F113F		.											.	.	.	0			c.C339T						.						88.0	97.0	94.0					11																	119243852		2199	4295	6494	SO:0001819	synonymous_variant	9099	exon2			ATAAGGGAATCCG	AF079564	CCDS8422.1, CCDS8423.1, CCDS58189.1	11q23.3	2008-02-05	2005-08-08			ENSG00000036672		"""Ubiquitin-specific peptidases"""	12618	protein-coding gene	gene with protein product		604725	"""ubiquitin specific protease 2"""			12838346	Standard	NM_004205		Approved	UBP41	uc001pwm.4	O75604		ENST00000260187.2:c.339C>T	11.37:g.119243852G>A		Somatic	36	0		WXS	Illumina HiSeq	.	18	8	NM_004205	B0YJB8|E9PPM2|Q8IUM2|Q8IW04|Q96MB9|Q9BQ21	Silent	SNP	ENST00000260187.2	37	CCDS8422.1																																																																																			.		0.612	USP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388361.2	NM_171997	
ODF2	4957	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	9	131256904	131256904	+	Missense_Mutation	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr9:131256904A>C	ENST00000434106.3	+	17	2231	c.1868A>C	c.(1867-1869)aAg>aCg	p.K623T	ODF2_ENST00000546203.1_Missense_Mutation_p.K604T|ODF2_ENST00000393527.3_Missense_Mutation_p.K599T|ODF2_ENST00000448249.3_Missense_Mutation_p.K542T|ODF2_ENST00000351030.3_Missense_Mutation_p.K618T|ODF2_ENST00000393533.2_Missense_Mutation_p.K623T|ODF2_ENST00000604420.1_Missense_Mutation_p.K623T|ODF2_ENST00000444119.2_Missense_Mutation_p.K599T|ODF2_ENST00000372791.3_Missense_Mutation_p.K604T|ODF2_ENST00000372814.3_Missense_Mutation_p.K667T|ODF2_ENST00000372807.5_Missense_Mutation_p.K618T	NM_153433.1	NP_702911.1	Q5BJF6	ODFP2_HUMAN	outer dense fiber of sperm tails 2	623					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|multicellular organismal development (GO:0007275)|regulation of cilium assembly (GO:1902017)|spermatid development (GO:0007286)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytosol (GO:0005829)|microtubule (GO:0005874)|nucleus (GO:0005634)|outer dense fiber (GO:0001520)|primary cilium (GO:0072372)	Rab GTPase binding (GO:0017137)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(7)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(7)|lung(8)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	37						TATGAGCGGAAGAACATCGAC	0.602																																					p.K687T		.											.	.	.	0			c.A2060C						.						77.0	69.0	72.0					9																	131256904		2203	4300	6503	SO:0001583	missense	4957	exon17			AGCGGAAGAACAT	AF012549	CCDS6902.1, CCDS56585.1, CCDS56586.1, CCDS56587.1, CCDS56588.1, CCDS56589.1, CCDS56590.1	9q34	2010-04-23	2002-10-21		ENSG00000136811	ENSG00000136811			8114	protein-coding gene	gene with protein product	"""cancer/testis antigen 134"""	602015	"""outer dense fibre of sperm tails 2"""			9045620, 10072582	Standard	NM_153435		Approved	ODF84, CT134	uc004bvc.3	Q5BJF6	OTTHUMG00000020748	ENST00000434106.3:c.1868A>C	9.37:g.131256904A>C	ENSP00000403453:p.Lys623Thr	Somatic	17	0		WXS	Illumina HiSeq	.	14	6	NM_153435	B1AND3|B4DRK4|B4DX73|B4DZ02|E7EWL2|F5H6J4|O14721|O60631|Q1W2J6|Q6UN26|Q7Z5I6|Q96FN2	Missense_Mutation	SNP	ENST00000434106.3	37	CCDS56588.1	.	.	.	.	.	.	.	.	.	.	A	22.3	4.266726	0.80358	.	.	ENSG00000136811	ENST00000393533;ENST00000372814;ENST00000351030;ENST00000372796;ENST00000303890;ENST00000448249;ENST00000546203;ENST00000372791	T;D;T;T;T;D;T;T	0.82619	1.33;-1.63;-0.02;-0.02;-0.02;-1.63;1.35;1.36	5.4	5.4	0.78164	.	0.095740	0.64402	D	0.000002	D	0.87609	0.6220	L	0.52573	1.65	0.42207	D	0.991794	D;D;D;D;D;D;D	0.76494	0.999;0.983;0.999;0.999;0.999;0.983;0.991	D;P;D;D;D;P;P	0.67725	0.929;0.798;0.929;0.953;0.929;0.798;0.798	D	0.87377	0.2354	10	0.41790	T	0.15	-30.6116	14.6101	0.68510	1.0:0.0:0.0:0.0	.	604;618;542;623;604;623;599	Q5BJF6-8;Q5BJF6-4;Q5BJF6-9;B4DX73;Q5BJF6-5;Q5BJF6;Q5BJF6-3	.;.;.;.;.;ODFP2_HUMAN;.	T	623;667;618;623;599;542;604;604	ENSP00000377166:K623T;ENSP00000361901:K667T;ENSP00000342581:K618T;ENSP00000361882:K623T;ENSP00000307781:K599T;ENSP00000396687:K542T;ENSP00000437579:K604T;ENSP00000361877:K604T	ENSP00000307781:K599T	K	+	2	0	ODF2	130296725	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	4.590000	0.61013	2.047000	0.60756	0.459000	0.35465	AAG	.		0.602	ODF2-011	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054449.3		
COL22A1	169044	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	8	139815133	139815133	+	Silent	SNP	C	C	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr8:139815133C>T	ENST00000303045.6	-	11	1985	c.1539G>A	c.(1537-1539)aaG>aaA	p.K513K	COL22A1_ENST00000435777.1_Silent_p.K513K	NM_152888.1	NP_690848.1	Q8NFW1	COMA1_HUMAN	collagen, type XXII, alpha 1	513	Collagen-like 1.|Gly-rich.|Pro-rich.				extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(14)|large_intestine(29)|lung(107)|ovary(13)|pancreas(1)|prostate(3)|skin(12)|upper_aerodigestive_tract(15)|urinary_tract(4)	211	all_epithelial(106;1.55e-12)|Lung NSC(106;1.67e-05)|all_lung(105;3.39e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0517)			CTTTCTCTCCCTTAGGTCCAG	0.587										HNSCC(7;0.00092)																											p.K513K		.											.	.	.	0			c.G1539A						.						153.0	128.0	136.0					8																	139815133		2203	4300	6503	SO:0001819	synonymous_variant	169044	exon11			CTCTCCCTTAGGT	AF406780	CCDS6376.1	8q24.3	2013-01-16			ENSG00000169436	ENSG00000169436		"""Collagens"""	22989	protein-coding gene	gene with protein product		610026					Standard	NM_152888		Approved		uc003yvd.3	Q8NFW1	OTTHUMG00000150035	ENST00000303045.6:c.1539G>A	8.37:g.139815133C>T		Somatic	38	0		WXS	Illumina HiSeq	.	28	13	NM_152888	B7ZMH0|C9K0G4|Q8IVT9	Silent	SNP	ENST00000303045.6	37	CCDS6376.1																																																																																			.		0.587	COL22A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000315905.2	XM_291257	
ACSL5	51703	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	10	114168254	114168254	+	Missense_Mutation	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr10:114168254A>C	ENST00000393081.1	+	6	814	c.507A>C	c.(505-507)gaA>gaC	p.E169D	ACSL5_ENST00000354273.4_Missense_Mutation_p.E169D|ACSL5_ENST00000433418.1_Missense_Mutation_p.E169D|ACSL5_ENST00000479936.1_3'UTR|ACSL5_ENST00000356116.1_Missense_Mutation_p.E225D|ACSL5_ENST00000354655.4_Missense_Mutation_p.E169D|ACSL5_ENST00000369410.3_5'Flank|RP11-324O2.3_ENST00000598447.1_RNA|RP11-324O2.3_ENST00000449782.2_RNA|RP11-324O2.3_ENST00000594870.2_RNA	NM_203380.1	NP_976314.1	Q9ULC5	ACSL5_HUMAN	acyl-CoA synthetase long-chain family member 5	169					cellular lipid metabolic process (GO:0044255)|long-chain fatty acid metabolic process (GO:0001676)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|regulation of extrinsic apoptotic signaling pathway (GO:2001236)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|long-chain fatty acid-CoA ligase activity (GO:0004467)			breast(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(6)|prostate(1)|skin(2)|stomach(1)	21		Colorectal(252;0.117)|Breast(234;0.222)		Epithelial(162;0.0343)|all cancers(201;0.137)		TGGGACCAGAAGCCATCGTAC	0.388																																					p.E225D		.											.	.	.	0			c.A675C						.						260.0	211.0	228.0					10																	114168254		2203	4300	6503	SO:0001583	missense	51703	exon6			ACCAGAAGCCATC	AB033899	CCDS7572.1, CCDS7573.1	10q25.1-q25.2	2004-06-21	2004-02-19	2004-02-20	ENSG00000197142	ENSG00000197142		"""Acyl-CoA synthetase family"""	16526	protein-coding gene	gene with protein product	"""FACL5 for fatty acid coenzyme A ligase 5"", ""long-chain acyl-CoA synthetase 5"", ""long-chain fatty acid coenzyme A ligase 5"", ""fatty-acid-Coenzyme A ligase, long-chain 5"""	605677	"""fatty-acid-Coenzyme A ligase, long-chain 5"""	FACL5		11127823	Standard	NM_016234		Approved	ACS5, ACS2	uc001kzu.3	Q9ULC5	OTTHUMG00000019060	ENST00000393081.1:c.507A>C	10.37:g.114168254A>C	ENSP00000376796:p.Glu169Asp	Somatic	93	0		WXS	Illumina HiSeq	.	57	23	NM_016234	A6GV77|D3DRB3|Q6UX44|Q9UIU4	Missense_Mutation	SNP	ENST00000393081.1	37	CCDS7573.1	.	.	.	.	.	.	.	.	.	.	A	11.12	1.544832	0.27563	.	.	ENSG00000197142	ENST00000354655;ENST00000393081;ENST00000356116;ENST00000433418;ENST00000354273	T;T;T;T;T	0.48836	0.8;0.8;0.8;0.8;0.8	5.92	-7.0	0.01599	AMP-dependent synthetase/ligase (1);	0.353602	0.34932	N	0.003565	T	0.19366	0.0465	L	0.31207	0.915	0.80722	D	1	B;B;B	0.20887	0.049;0.014;0.005	B;B;B	0.25405	0.06;0.016;0.019	T	0.41556	-0.9502	10	0.06494	T	0.89	-5.6934	1.0009	0.01477	0.2689:0.2954:0.1219:0.3139	.	169;225;169	A6GV77;Q9ULC5-3;Q9ULC5	.;.;ACSL5_HUMAN	D	169;169;225;169;169	ENSP00000346680:E169D;ENSP00000376796:E169D;ENSP00000348429:E225D;ENSP00000403647:E169D;ENSP00000346223:E169D	ENSP00000346223:E169D	E	+	3	2	ACSL5	114158244	0.512000	0.26186	0.731000	0.30826	0.980000	0.70556	-0.218000	0.09240	-1.338000	0.02233	0.523000	0.50628	GAA	.		0.388	ACSL5-203	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050386.1	NM_016234	
SMAD5	4090	hgsc.bcm.edu;ucsc.edu	37	5	135469456	135469456	+	Intron	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr5:135469456A>C	ENST00000514641.2	+	1	118				SMAD5_ENST00000545279.1_Intron|SMAD5_ENST00000545620.1_Intron|SMAD5-AS1_ENST00000297163.3_RNA			Q99717	SMAD5_HUMAN	SMAD family member 5						BMP signaling pathway (GO:0030509)|bone development (GO:0060348)|cardiac muscle contraction (GO:0060048)|cartilage development (GO:0051216)|cellular response to BMP stimulus (GO:0071773)|cellular response to organic cyclic compound (GO:0071407)|embryonic pattern specification (GO:0009880)|erythrocyte differentiation (GO:0030218)|germ cell development (GO:0007281)|intracellular signal transduction (GO:0035556)|Mullerian duct regression (GO:0001880)|osteoblast fate commitment (GO:0002051)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter involved in cellular response to chemical stimulus (GO:1901522)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ureteric bud development (GO:0001657)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)|transcription factor complex (GO:0005667)	metal ion binding (GO:0046872)|receptor signaling protein activity (GO:0005057)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transforming growth factor beta receptor, pathway-specific cytoplasmic mediator activity (GO:0030618)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|large_intestine(4)|lung(3)	8			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			TGGAGTTTGGAGCCTAAGCTT	0.483																																					.		.											.	.	.	0			.						.																																			SO:0001627	intron_variant	9597	.			GTTTGGAGCCTAA	U59913	CCDS75308.1	5q31	2008-02-05	2006-11-06	2004-05-26		ENSG00000113658		"""SMADs"""	6771	protein-coding gene	gene with protein product		603110	"""MAD, mothers against decapentaplegic homolog 5 (Drosophila)"", ""SMAD, mothers against DPP homolog 5 (Drosophila)"""	MADH5		8673135	Standard	NM_005903		Approved	Dwfc, JV5-1	uc003lbl.1	Q99717		ENST00000514641.2:c.118+805A>C	5.37:g.135469456A>C		Somatic	58	0		WXS	Illumina HiSeq	.	44	19	.	O14688|Q15798|Q9UQA1	RNA	SNP	ENST00000514641.2	37																																																																																				.		0.483	SMAD5-001	KNOWN	basic	processed_transcript	protein_coding	OTTHUMT00000372096.2	NM_005903	
GALNT4	8693	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	12	89917207	89917207	+	Missense_Mutation	SNP	T	T	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr12:89917207T>C	ENST00000529983.2	-	1	1376	c.1120A>G	c.(1120-1122)Aat>Gat	p.N374D	GALNT4_ENST00000413530.1_Missense_Mutation_p.N202D|POC1B-GALNT4_ENST00000547474.1_3'UTR|POC1B_ENST00000549035.1_Intron|RP11-734K2.4_ENST00000605233.1_RNA|POC1B_ENST00000541909.1_Intron|POC1B_ENST00000313546.3_Intron|POC1B-GALNT4_ENST00000548729.1_Missense_Mutation_p.N371D|POC1B_ENST00000549504.1_Intron|POC1B_ENST00000393179.4_Intron	NM_003774.4	NP_003765.2	Q8N4A0	GALT4_HUMAN	polypeptide N-acetylgalactosaminyltransferase 4	374					carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			endometrium(4)|kidney(2)|lung(5)|prostate(2)|upper_aerodigestive_tract(1)	14						TGTAGGAAATTGGGGCGAGCA	0.507																																					p.N374D		.											.	.	.	0			c.A1120G						.						73.0	72.0	72.0					12																	89917207		1911	4134	6045	SO:0001583	missense	8693	exon1			GGAAATTGGGGCG	Y08564	CCDS53817.1	12q21.33	2014-03-13	2014-03-13		ENSG00000257594	ENSG00000257594	2.4.1.41	"""Glycosyltransferase family 2 domain containing"""	4126	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase 4"""	603565	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 4 (GalNAc-T4)"""			9804815	Standard	NM_003774		Approved	GalNAc-T4	uc001tbd.3	Q8N4A0	OTTHUMG00000166292	ENST00000529983.2:c.1120A>G	12.37:g.89917207T>C	ENSP00000436604:p.Asn374Asp	Somatic	78	0		WXS	Illumina HiSeq	.	49	14	NM_003774	B2R775|B4DMX6|O00208	Missense_Mutation	SNP	ENST00000529983.2	37	CCDS53817.1	.	.	.	.	.	.	.	.	.	.	T	16.46	3.128252	0.56721	.	.	ENSG00000259075;ENSG00000259075;ENSG00000257594	ENST00000548729;ENST00000413530;ENST00000529983	T;T;T	0.59224	0.28;0.28;0.28	5.65	4.46	0.54185	.	.	.	.	.	T	0.49558	0.1564	L	0.28740	0.885	0.41908	D	0.990453	P;P	0.40970	0.734;0.615	P;B	0.44673	0.457;0.269	T	0.40924	-0.9537	9	0.30078	T	0.28	.	11.8587	0.52453	0.0:0.0:0.1465:0.8535	.	371;374	F8VUJ3;Q8N4A0	.;GALT4_HUMAN	D	371;202;374	ENSP00000447852:N371D;ENSP00000389686:N202D;ENSP00000436604:N374D	ENSP00000436604:N374D	N	-	1	0	GALNT4;RP11-1109F11.4	88441338	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	4.984000	0.63838	0.918000	0.36919	0.477000	0.44152	AAT	.		0.507	GALNT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388973.2	NM_003774	
TBR1	10716	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	2	162273323	162273323	+	Silent	SNP	C	C	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr2:162273323C>T	ENST00000389554.3	+	1	719	c.402C>T	c.(400-402)caC>caT	p.H134H	TBR1_ENST00000410035.1_5'Flank	NM_006593.2	NP_006584.1	Q16650	TBR1_HUMAN	T-box, brain, 1	134					axon guidance (GO:0007411)|brain development (GO:0007420)|hindbrain development (GO:0030902)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of neuron projection development (GO:0010975)|specification of organ identity (GO:0010092)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(6)|lung(15)|ovary(1)|prostate(1)|skin(3)	30						GACCGGCGCACCCCGCCTTCT	0.667																																					p.H134H		.											.	.	.	0			c.C402T						.						77.0	85.0	82.0					2																	162273323		2202	4298	6500	SO:0001819	synonymous_variant	10716	exon1			GGCGCACCCCGCC	U49250	CCDS33310.1	2q24.2	2011-06-13			ENSG00000136535	ENSG00000136535		"""T-boxes"""	11590	protein-coding gene	gene with protein product		604616				7619531	Standard	NM_006593		Approved		uc002ubw.1	Q16650	OTTHUMG00000153888	ENST00000389554.3:c.402C>T	2.37:g.162273323C>T		Somatic	39	0		WXS	Illumina HiSeq	.	27	15	NM_006593	B0AZS4|B2R6G5|Q14DC5|Q53TH0|Q56A81	Silent	SNP	ENST00000389554.3	37	CCDS33310.1																																																																																			.		0.667	TBR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332845.1	NM_006593	
ABCC2	1244	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	10	101544402	101544402	+	Missense_Mutation	SNP	C	C	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr10:101544402C>A	ENST00000370449.4	+	2	184	c.71C>A	c.(70-72)cCa>cAa	p.P24Q	ABCC2_ENST00000370434.1_Missense_Mutation_p.P24Q	NM_000392.3	NP_000383	Q92887	MRP2_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 2	24					cellular chloride ion homeostasis (GO:0030644)|drug transmembrane transport (GO:0006855)|prostaglandin transport (GO:0015732)|response to arsenic-containing substance (GO:0046685)|response to estrogen (GO:0043627)|response to heat (GO:0009408)|response to methotrexate (GO:0031427)|response to oxidative stress (GO:0006979)|thyroid hormone transport (GO:0070327)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|intercellular canaliculus (GO:0046581)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|organic anion transmembrane transporter activity (GO:0008514)			NS(1)|breast(5)|endometrium(9)|kidney(2)|large_intestine(20)|liver(1)|lung(20)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	67		Colorectal(252;0.234)		Epithelial(162;2.77e-10)|all cancers(201;2.47e-08)	Adenosine triphosphate(DB00171)|Aminohippurate(DB00345)|Arsenic trioxide(DB01169)|Atorvastatin(DB01076)|Canagliflozin(DB08907)|Carbamazepine(DB00564)|Carboplatin(DB00958)|Cisplatin(DB00515)|Clotrimazole(DB00257)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Daunorubicin(DB00694)|Dexamethasone(DB01234)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Eprosartan(DB00876)|Ethinyl Estradiol(DB00977)|Etoposide(DB00773)|Ezetimibe(DB00973)|Furosemide(DB00695)|Fusidic Acid(DB02703)|Gadoxetate(DB08884)|Glutathione(DB00143)|Glyburide(DB01016)|Indinavir(DB00224)|Indomethacin(DB00328)|Irinotecan(DB00762)|Ivermectin(DB00602)|Lamivudine(DB00709)|Leucovorin(DB00650)|Levetiracetam(DB01202)|Lomefloxacin(DB00978)|Lovastatin(DB00227)|Methotrexate(DB00563)|Mycophenolate mofetil(DB00688)|Nifedipine(DB01115)|Norgestimate(DB00957)|Ofloxacin(DB01165)|Olmesartan(DB00275)|Oxaliplatin(DB00526)|Paclitaxel(DB01229)|Phenobarbital(DB01174)|Phenytoin(DB00252)|Pitavastatin(DB08860)|Pranlukast(DB01411)|Pravastatin(DB00175)|Probenecid(DB01032)|Quinidine(DB00908)|Reserpine(DB00206)|Rifampicin(DB01045)|Ritonavir(DB00503)|Saquinavir(DB01232)|Simvastatin(DB00641)|Sorafenib(DB00398)|Sparfloxacin(DB01208)|Spironolactone(DB00421)|Sulfasalazine(DB00795)|Sulfinpyrazone(DB01138)|Sunitinib(DB01268)|Tamoxifen(DB00675)|Telmisartan(DB00966)|Tenofovir(DB00300)|Tetrahydrofolic acid(DB00116)|Ursodeoxycholic acid(DB01586)|Vasopressin(DB00067)|Verapamil(DB00661)|Vinblastine(DB00570)|Vincristine(DB00541)	GCAGACCTGCCACTTTGTTTT	0.517																																					p.P24Q		.											.	.	.	0			c.C71A						.						153.0	140.0	144.0					10																	101544402		2203	4300	6503	SO:0001583	missense	1244	exon2			ACCTGCCACTTTG	U63970	CCDS7484.1	10q24	2012-03-14			ENSG00000023839	ENSG00000023839		"""ATP binding cassette transporters / subfamily C"""	53	protein-coding gene	gene with protein product		601107	"""canalicular multispecific organic anion transporter 1"""	CMOAT		8797578, 9284939	Standard	XM_006717630		Approved	DJS, MRP2, cMRP	uc001kqf.2	Q92887	OTTHUMG00000018895	ENST00000370449.4:c.71C>A	10.37:g.101544402C>A	ENSP00000359478:p.Pro24Gln	Somatic	40	0		WXS	Illumina HiSeq	.	28	13	NM_000392	B2RMT8|Q14022|Q5T2B1|Q92500|Q92798|Q99663|Q9UMS2	Missense_Mutation	SNP	ENST00000370449.4	37	CCDS7484.1	.	.	.	.	.	.	.	.	.	.	C	24.6	4.547692	0.86022	.	.	ENSG00000023839	ENST00000370449;ENST00000370434	T;T	0.35048	1.33;1.33	5.7	5.7	0.88788	.	0.000000	0.85682	D	0.000000	T	0.62258	0.2413	M	0.83118	2.625	0.58432	D	0.999991	D	0.65815	0.995	P	0.61397	0.888	T	0.64141	-0.6477	10	0.49607	T	0.09	-13.2886	18.5934	0.91222	0.0:1.0:0.0:0.0	.	24	Q92887	MRP2_HUMAN	Q	24	ENSP00000359478:P24Q;ENSP00000359463:P24Q	ENSP00000359463:P24Q	P	+	2	0	ABCC2	101534392	1.000000	0.71417	0.998000	0.56505	0.955000	0.61496	6.466000	0.73543	2.685000	0.91497	0.561000	0.74099	CCA	.		0.517	ABCC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049825.1	NM_000392	
SREK1IP1	285672	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	5	64020374	64020374	+	Missense_Mutation	SNP	T	T	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr5:64020374T>A	ENST00000513458.4	-	5	472	c.305A>T	c.(304-306)gAg>gTg	p.E102V		NM_173829.3	NP_776190.1	Q8N9Q2	SR1IP_HUMAN	SREK1-interacting protein 1	102	Lys-rich.				mRNA processing (GO:0006397)|RNA splicing (GO:0008380)		nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|large_intestine(3)|ovary(1)	6						tGAAGTGTCCTCTTCAGTGGA	0.294																																					p.E102V		.											.	.	.	0			c.A305T						.						93.0	80.0	84.0					5																	64020374		2194	4292	6486	SO:0001583	missense	285672	exon5			GTGTCCTCTTCAG	AK094073	CCDS34171.1	5q12.3	2010-09-20	2010-09-20	2010-09-20	ENSG00000153006	ENSG00000153006			26716	protein-coding gene	gene with protein product	"""p18 splicing regulatory protein"""		"""SFRS12-interacting protein 1"""	SFRS12IP1		15456940	Standard	NM_173829		Approved	FLJ36754, P18SRP	uc003jtk.3	Q8N9Q2	OTTHUMG00000162291	ENST00000513458.4:c.305A>T	5.37:g.64020374T>A	ENSP00000427401:p.Glu102Val	Somatic	122	0		WXS	Illumina HiSeq	.	102	6	NM_173829	Q32NC8	Missense_Mutation	SNP	ENST00000513458.4	37	CCDS34171.1	.	.	.	.	.	.	.	.	.	.	T	14.60	2.583555	0.46006	.	.	ENSG00000153006	ENST00000513458	.	.	.	6.17	6.17	0.99709	.	0.330979	0.39020	N	0.001490	T	0.76357	0.3976	M	0.68593	2.085	0.46774	D	0.999199	D	0.71674	0.998	D	0.73708	0.981	T	0.77739	-0.2475	9	0.56958	D	0.05	-18.7424	13.214	0.59844	0.0:0.0:0.0:1.0	.	102	Q8N9Q2	SR1IP_HUMAN	V	102	.	ENSP00000427401:E102V	E	-	2	0	SREK1IP1	64056130	1.000000	0.71417	1.000000	0.80357	0.698000	0.40448	3.602000	0.54066	2.371000	0.80710	0.533000	0.62120	GAG	.		0.294	SREK1IP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368457.4	NM_173829	
SIPA1L3	23094	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	19	38689097	38689097	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr19:38689097G>T	ENST00000222345.6	+	19	5418	c.4909G>T	c.(4909-4911)Ggg>Tgg	p.G1637W	RN7SL663P_ENST00000578592.1_RNA|CTB-102L5.8_ENST00000598146.1_RNA	NM_015073.1	NP_055888.1	O60292	SI1L3_HUMAN	signal-induced proliferation-associated 1 like 3	1637					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)			CCTGGACCCTGGGCTGATGCC	0.682																																					p.G1637W		.											.	.	.	0			c.G4909T						.						70.0	79.0	76.0					19																	38689097		2201	4294	6495	SO:0001583	missense	23094	exon19			GACCCTGGGCTGA	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.4909G>T	19.37:g.38689097G>T	ENSP00000222345:p.Gly1637Trp	Somatic	22	0		WXS	Illumina HiSeq	.	21	12	NM_015073	Q2TV87	Missense_Mutation	SNP	ENST00000222345.6	37	CCDS33007.1	.	.	.	.	.	.	.	.	.	.	G	31	5.069197	0.93950	.	.	ENSG00000105738	ENST00000222345	T	0.38240	1.15	5.58	5.58	0.84498	.	0.000000	0.85682	D	0.000000	T	0.61825	0.2378	M	0.69523	2.12	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.64188	-0.6466	10	0.87932	D	0	-41.3964	18.3375	0.90294	0.0:0.0:1.0:0.0	.	1637	O60292	SI1L3_HUMAN	W	1637	ENSP00000222345:G1637W	ENSP00000222345:G1637W	G	+	1	0	SIPA1L3	43380937	1.000000	0.71417	0.959000	0.39883	0.970000	0.65996	9.214000	0.95140	2.625000	0.88918	0.650000	0.86243	GGG	.		0.682	SIPA1L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000156294.2	XM_032278	
PRICKLE4	29964	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	6	41751913	41751913	+	Missense_Mutation	SNP	C	C	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr6:41751913C>G	ENST00000394260.1	+	1	57	c.57C>G	c.(55-57)aaC>aaG	p.N19K	PRICKLE4_ENST00000394263.1_Missense_Mutation_p.N59K|PRICKLE4_ENST00000359201.5_Missense_Mutation_p.N59K|PRICKLE4_ENST00000458694.1_Missense_Mutation_p.N59K|PRICKLE4_ENST00000394259.1_Missense_Mutation_p.N19K			Q2TBC4	PRIC4_HUMAN	prickle homolog 4 (Drosophila)	19	PET. {ECO:0000255|PROSITE- ProRule:PRU00636}.					nucleus (GO:0005634)	zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)	13	Ovarian(28;0.0355)|Colorectal(47;0.121)		Epithelial(12;8.38e-05)|STAD - Stomach adenocarcinoma(11;0.000204)|Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)			TGGACACCAACCAAGCCCCCA	0.547																																					p.N59K		.											.	.	.	0			c.C177G						.						153.0	121.0	132.0					6																	41751913		2203	4300	6503	SO:0001583	missense	29964	exon4			CACCAACCAAGCC	AF216754	CCDS34449.1	6p21.1	2010-08-05	2007-09-18	2007-09-18	ENSG00000124593	ENSG00000124593			16805	protein-coding gene	gene with protein product		611389	"""chromosome 6 open reading frame 49"""	C6orf49		15702247	Standard	NM_013397		Approved	OEBT, DKFZp761H221	uc011duf.1	Q2TBC4	OTTHUMG00000014685	ENST00000394260.1:c.57C>G	6.37:g.41751913C>G	ENSP00000377803:p.Asn19Lys	Somatic	86	0		WXS	Illumina HiSeq	.	53	27	NM_013397	A2A3M0|A6PVU1|B3KQ15|Q5T3D4|Q9NSV1	Missense_Mutation	SNP	ENST00000394260.1	37		.	.	.	.	.	.	.	.	.	.	C	14.57	2.574031	0.45902	.	.	ENSG00000124593	ENST00000458694;ENST00000359201;ENST00000394263;ENST00000394259;ENST00000394260	T;T;T;T;T	0.69926	-0.2;-0.44;-0.2;-0.31;-0.07	4.54	2.76	0.32466	.	1.076960	0.07148	N	0.848582	T	0.29491	0.0735	N	0.22421	0.69	0.09310	N	1	P	0.37276	0.589	B	0.33960	0.173	T	0.20042	-1.0287	10	0.44086	T	0.13	-1.4749	6.5487	0.22420	0.0:0.7843:0.0:0.2157	.	59	Q2TBC4-3	.	K	59;59;59;19;19	ENSP00000404911:N59K;ENSP00000352128:N59K;ENSP00000377806:N59K;ENSP00000377802:N19K;ENSP00000377803:N19K	ENSP00000335185:N59K	N	+	3	2	PRICKLE4	41859891	0.000000	0.05858	0.001000	0.08648	0.510000	0.34073	-0.180000	0.09754	0.554000	0.29061	0.561000	0.74099	AAC	.		0.547	PRICKLE4-007	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000303948.1	NM_013397	
TAF2	6873	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	8	120754808	120754808	+	Silent	SNP	G	G	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr8:120754808G>C	ENST00000378164.2	-	25	3601	c.3303C>G	c.(3301-3303)ccC>ccG	p.P1101P		NM_003184.3	NP_003175	Q6P1X5	TAF2_HUMAN	TAF2 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 150kDa	1101					G2/M transition of mitotic cell cycle (GO:0000086)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to organic cyclic compound (GO:0014070)|transcription initiation from RNA polymerase II promoter (GO:0006367)	transcription factor TFIID complex (GO:0005669)|transcription factor TFTC complex (GO:0033276)	metallopeptidase activity (GO:0008237)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			NS(2)|breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(21)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	49	Lung NSC(37;9.35e-07)|Ovarian(258;0.011)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00185)			AACTCCACTGGGGTTTTGTGG	0.413																																					p.P1101P		.											.	.	.	0			c.C3303G						.						63.0	61.0	62.0					8																	120754808		2203	4300	6503	SO:0001819	synonymous_variant	6873	exon25			CCACTGGGGTTTT	AF040701	CCDS34937.1	8q24	2012-07-18	2002-08-29	2001-12-07	ENSG00000064313	ENSG00000064313			11536	protein-coding gene	gene with protein product		604912	"""TATA box binding protein (TBP)-associated factor, RNA polymerase II, B, 150kD"""	TAF2B		9774672, 9418870	Standard	NM_003184		Approved	TAFII150, CIF150	uc003you.3	Q6P1X5	OTTHUMG00000165009	ENST00000378164.2:c.3303C>G	8.37:g.120754808G>C		Somatic	151	0		WXS	Illumina HiSeq	.	93	18	NM_003184	B2RE82|O43487|O43604|O60668|Q86WW7|Q8IWK4	Silent	SNP	ENST00000378164.2	37	CCDS34937.1																																																																																			.		0.413	TAF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381436.1	NM_003184	
SF3A3	10946	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	38444662	38444662	+	Silent	SNP	G	G	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr1:38444662G>C	ENST00000373019.4	-	10	1780	c.825C>G	c.(823-825)ggC>ggG	p.G275G	SF3A3_ENST00000448721.2_Silent_p.G222G|SF3A3_ENST00000489537.1_5'UTR	NM_006802.2	NP_006793.1	Q12874	SF3A3_HUMAN	splicing factor 3a, subunit 3, 60kDa	275					gene expression (GO:0010467)|mRNA 3'-splice site recognition (GO:0000389)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|kidney(3)|large_intestine(1)|liver(1)|lung(3)|prostate(2)	12	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)				TTCCTTACCCGCCACATTTCA	0.368																																					p.G275G		.											.	.	.	0			c.C825G						.						57.0	64.0	62.0					1																	38444662		2203	4300	6503	SO:0001819	synonymous_variant	10946	exon10			TTACCCGCCACAT	U08815	CCDS428.1	1p34.3	2012-06-07	2002-08-29		ENSG00000183431	ENSG00000183431			10767	protein-coding gene	gene with protein product		605596	"""splicing factor 3a, subunit 3, 60kD"""			7816610, 8022796	Standard	NM_006802		Approved	SF3a60, SAP61, PRP9, PRPF9	uc001cci.3	Q12874	OTTHUMG00000004438	ENST00000373019.4:c.825C>G	1.37:g.38444662G>C		Somatic	104	0		WXS	Illumina HiSeq	.	63	28	NM_006802	D3DPT5|Q15460|Q5VT87	Silent	SNP	ENST00000373019.4	37	CCDS428.1																																																																																			.		0.368	SF3A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012976.1	NM_006802	
PRPF39	55015	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	14	45583442	45583442	+	Missense_Mutation	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr14:45583442A>C	ENST00000355765.6	+	12	1984	c.1814A>C	c.(1813-1815)aAa>aCa	p.K605T		NM_017922.3	NP_060392.3	Q86UA1	PRP39_HUMAN	pre-mRNA processing factor 39	605					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)				breast(2)|endometrium(2)|kidney(4)|lung(3)|ovary(1)	12						GATTCTTTAAAAAGGAAAGCA	0.333																																					p.K605T		.											.	.	.	0			c.A1814C						.						53.0	55.0	54.0					14																	45583442		2202	4297	6499	SO:0001583	missense	55015	exon12			CTTTAAAAAGGAA	AK000673	CCDS9682.2	14q21.1	2013-10-03	2013-10-03		ENSG00000185246	ENSG00000185246			20314	protein-coding gene	gene with protein product		614907	"""PRP39 pre-mRNA processing factor 39 homolog (yeast)"", ""PRP39 pre-mRNA processing factor 39 homolog (S. cerevisiae)"""				Standard	NM_017922		Approved	FLJ20666, FLJ11128	uc001wvz.4	Q86UA1	OTTHUMG00000140265	ENST00000355765.6:c.1814A>C	14.37:g.45583442A>C	ENSP00000348010:p.Lys605Thr	Somatic	147	0		WXS	Illumina HiSeq	.	94	33	NM_017922	Q08AL1|Q08AL2|Q9NUU5	Missense_Mutation	SNP	ENST00000355765.6	37	CCDS9682.2	.	.	.	.	.	.	.	.	.	.	A	19.17	3.775254	0.70107	.	.	ENSG00000185246	ENST00000355765	T	0.42900	0.96	5.66	5.66	0.87406	.	0.000000	0.85682	D	0.000000	T	0.61135	0.2323	L	0.59436	1.845	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.91635	0.999;0.972	T	0.63251	-0.6679	10	0.62326	D	0.03	-18.0472	14.7269	0.69351	1.0:0.0:0.0:0.0	.	209;605	Q86UA1-2;Q86UA1	.;PRP39_HUMAN	T	605	ENSP00000348010:K605T	ENSP00000348010:K605T	K	+	2	0	PRPF39	44653192	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.631000	0.90991	2.147000	0.66899	0.533000	0.62120	AAA	.		0.333	PRPF39-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319683.2		
CSNK1G2	1455	hgsc.bcm.edu	37	19	1953519	1953519	+	Intron	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr19:1953519A>C	ENST00000255641.8	+	1	230				CSNK1G2-AS1_ENST00000586395.1_RNA|CSNK1G2-AS1_ENST00000314315.3_RNA	NM_001319.6	NP_001310.3	P78368	KC1G2_HUMAN	casein kinase 1, gamma 2						protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|peptide binding (GO:0042277)|protein serine/threonine kinase activity (GO:0004674)			endometrium(1)|kidney(1)|lung(3)|prostate(1)|skin(1)|stomach(1)	8		Ovarian(11;2.11e-07)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		AATTTTGGGAAAATTGCCCCT	0.527																																					.	Ovarian(91;880 1392 21236 36928 37598)	.											.	.	.	0			.						.						81.0	76.0	78.0					19																	1953519		2096	4213	6309	SO:0001627	intron_variant	255193	.			TTGGGAAAATTGC	AF001177	CCDS12077.1	19p13.3	2013-01-17			ENSG00000133275	ENSG00000133275			2455	protein-coding gene	gene with protein product		602214				9403068	Standard	NM_001319		Approved	CK1g2	uc002lul.4	P78368		ENST00000255641.8:c.-266+12102A>C	19.37:g.1953519A>C		Somatic	49	0		WXS	Illumina HiSeq	.	27	14	.	B5BU42|O00704|Q8WUB1	RNA	SNP	ENST00000255641.8	37	CCDS12077.1																																																																																			.		0.527	CSNK1G2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449287.1	NM_001319	
FUZ	80199	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	19	50314691	50314691	+	Missense_Mutation	SNP	C	C	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr19:50314691C>A	ENST00000313777.4	-	5	584	c.421G>T	c.(421-423)Gac>Tac	p.D141Y	FUZ_ENST00000445575.2_Missense_Mutation_p.D141Y|FUZ_ENST00000526575.1_3'UTR|FUZ_ENST00000534008.1_5'UTR|AC006942.4_ENST00000600669.1_RNA|FUZ_ENST00000528094.1_Missense_Mutation_p.D105Y|FUZ_ENST00000533418.1_Missense_Mutation_p.D91Y	NM_025129.4	NP_079405.2	Q9BT04	FUZZY_HUMAN	fuzzy planar cell polarity protein	141					cilium assembly (GO:0042384)|embryonic body morphogenesis (GO:0010172)|embryonic skeletal system morphogenesis (GO:0048704)|establishment of planar polarity (GO:0001736)|hair follicle development (GO:0001942)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of fibroblast growth factor receptor signaling pathway involved in neural plate anterior/posterior pattern formation (GO:2000314)|negative regulation of neural crest formation (GO:0090301)|neural tube closure (GO:0001843)|nonmotile primary cilium assembly (GO:0035058)|positive regulation of cilium assembly (GO:0045724)|protein transport (GO:0015031)|regulation of smoothened signaling pathway (GO:0008589)|spinal cord dorsal/ventral patterning (GO:0021513)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)				endometrium(1)|lung(3)	4		all_lung(116;1.05e-05)|Lung NSC(112;3.77e-05)|all_neural(266;0.107)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00793)|GBM - Glioblastoma multiforme(134;0.0116)		AGCTCCGAGTCCCCCAGGAAG	0.567																																					p.D141Y		.											.	.	.	0			c.G421T						.						63.0	55.0	58.0					19																	50314691		2203	4300	6503	SO:0001583	missense	80199	exon5			CCGAGTCCCCCAG	BC016793	CCDS12781.1, CCDS54293.1	19q13.33	2013-03-05	2013-03-05			ENSG00000010361			26219	protein-coding gene	gene with protein product		610622	"""fuzzy homolog (Drosophila)"""			21761479	Standard	NM_001171937		Approved	FLJ22688, Fy	uc002ppq.2	Q9BT04		ENST00000313777.4:c.421G>T	19.37:g.50314691C>A	ENSP00000313309:p.Asp141Tyr	Somatic	52	0		WXS	Illumina HiSeq	.	26	13	NM_025129	B2RD86|B5MDH0|Q6PJY0|Q9H613	Missense_Mutation	SNP	ENST00000313777.4	37	CCDS12781.1	.	.	.	.	.	.	.	.	.	.	C	16.56	3.156461	0.57259	.	.	ENSG00000010361	ENST00000528094;ENST00000533418;ENST00000529634;ENST00000313777;ENST00000377092;ENST00000445575;ENST00000529004;ENST00000421740	T;T;T;T	0.20200	2.09;2.09;2.09;2.09	4.21	-0.733	0.11144	.	0.371978	0.28901	N	0.013773	T	0.19248	0.0462	L	0.46157	1.445	0.35560	D	0.80456	P;P;P	0.48016	0.904;0.874;0.828	B;P;P	0.48141	0.407;0.568;0.452	T	0.17715	-1.0360	10	0.59425	D	0.04	-17.0546	4.0439	0.09764	0.0:0.3405:0.3443:0.3152	.	141;105;141	B4DHF8;Q9BT04-3;Q9BT04	.;.;FUZZY_HUMAN	Y	105;91;141;141;41;141;91;141	ENSP00000435177:D105Y;ENSP00000431731:D91Y;ENSP00000313309:D141Y;ENSP00000408018:D141Y	ENSP00000313309:D141Y	D	-	1	0	FUZ	55006503	0.206000	0.23470	0.981000	0.43875	0.904000	0.53231	0.107000	0.15375	-0.209000	0.10156	0.462000	0.41574	GAC	.		0.567	FUZ-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393986.1	NM_025129	
ATAD5	79915	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	17	29220580	29220580	+	Nonsense_Mutation	SNP	T	T	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr17:29220580T>A	ENST00000321990.4	+	21	5087	c.4709T>A	c.(4708-4710)tTg>tAg	p.L1570*		NM_024857.3	NP_079133.3	Q96QE3	ATAD5_HUMAN	ATPase family, AAA domain containing 5	1570					cellular response to DNA damage stimulus (GO:0006974)	nucleus (GO:0005634)	ATP binding (GO:0005524)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(3)|large_intestine(18)|lung(13)|ovary(3)|pancreas(1)	51		all_hematologic(16;0.0202)|Acute lymphoblastic leukemia(14;0.0238)|Myeloproliferative disorder(56;0.0393)				AAGAAAACATTGGTAATATTA	0.368																																					p.L1570X		.											.	.	.	0			c.T4709A						.						41.0	45.0	44.0					17																	29220580		2203	4296	6499	SO:0001587	stop_gained	79915	exon21			AAACATTGGTAAT		CCDS11260.1	17q11.2	2010-04-21	2007-02-08	2007-02-08	ENSG00000176208	ENSG00000176208		"""ATPases / AAA-type"""	25752	protein-coding gene	gene with protein product	"""enhanced level of genomic instability 1 homolog (S. cerevisiae)"""	609534	"""chromosome 17 open reading frame 41"""	C17orf41		15983387, 11468690, 19755857	Standard	NM_024857		Approved	FLJ12735, FRAG1, ELG1	uc002hfs.1	Q96QE3	OTTHUMG00000132794	ENST00000321990.4:c.4709T>A	17.37:g.29220580T>A	ENSP00000313171:p.Leu1570*	Somatic	47	0		WXS	Illumina HiSeq	.	26	11	NM_024857	Q05DH0|Q69YR6|Q9H9I1	Nonsense_Mutation	SNP	ENST00000321990.4	37	CCDS11260.1	.	.	.	.	.	.	.	.	.	.	T	42	9.822497	0.99272	.	.	ENSG00000176208	ENST00000321990	.	.	.	6.08	6.08	0.98989	.	0.905145	0.09917	N	0.738999	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	12.2831	0.54776	0.1269:0.0:0.0:0.8731	.	.	.	.	X	1570	.	ENSP00000313171:L1570X	L	+	2	0	ATAD5	26244706	0.998000	0.40836	0.803000	0.32268	0.019000	0.09904	3.120000	0.50430	2.333000	0.79357	0.482000	0.46254	TTG	.		0.368	ATAD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256206.2	NM_024857	
CSPG4	1464	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	15	75968341	75968341	+	Silent	SNP	C	C	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr15:75968341C>T	ENST00000308508.5	-	10	6611	c.6519G>A	c.(6517-6519)gtG>gtA	p.V2173V	CTD-2026K11.1_ENST00000569467.1_RNA|AC105020.1_ENST00000435356.1_5'Flank	NM_001897.4	NP_001888.2	Q6UVK1	CSPG4_HUMAN	chondroitin sulfate proteoglycan 4	2173	Cysteine-containing.|Neurite growth inhibition. {ECO:0000250}.				activation of MAPK activity (GO:0000187)|angiogenesis (GO:0001525)|carbohydrate metabolic process (GO:0005975)|cell proliferation (GO:0008283)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|intracellular signal transduction (GO:0035556)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|small molecule metabolic process (GO:0044281)|tissue remodeling (GO:0048771)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell projection (GO:0042995)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)	protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)			breast(1)|cervix(2)|endometrium(5)|kidney(5)|large_intestine(3)|liver(2)|lung(18)|ovary(2)|pancreas(2)|prostate(4)|skin(4)	48						TGAGCAGGGCCACGCTGTAGG	0.682																																					p.V2173V		.											.	.	.	0			c.G6519A						.						18.0	18.0	18.0					15																	75968341		2192	4291	6483	SO:0001819	synonymous_variant	1464	exon10			CAGGGCCACGCTG	X96753, AY359468	CCDS10284.1	15q24.2	2010-04-19	2007-02-16		ENSG00000173546	ENSG00000173546		"""Proteoglycans / Cell surface : Other"""	2466	protein-coding gene	gene with protein product	"""melanoma-associated chondroitin sulfate proteoglycan"""	601172	"""chondroitin sulfate proteoglycan 4 (melanoma-associated)"""			8790396, 16407841	Standard	NM_001897		Approved	MCSPG, MEL-CSPG, MSK16, NG2, MCSP, HMW-MAA	uc002baw.3	Q6UVK1	OTTHUMG00000142836	ENST00000308508.5:c.6519G>A	15.37:g.75968341C>T		Somatic	50	0		WXS	Illumina HiSeq	.	36	18	NM_001897	D3DW77|Q92675	Silent	SNP	ENST00000308508.5	37	CCDS10284.1																																																																																			.		0.682	CSPG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286472.1	NM_001897	
ZFAND6	54469	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	15	80429825	80429825	+	Missense_Mutation	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr15:80429825T>G	ENST00000261749.6	+	7	904	c.482T>G	c.(481-483)tTt>tGt	p.F161C	ZFAND6_ENST00000561060.1_Missense_Mutation_p.F161C|ZFAND6_ENST00000559835.1_Missense_Mutation_p.F161C|ZFAND6_ENST00000558087.1_Missense_Mutation_p.F161C|ZFAND6_ENST00000558494.1_Missense_Mutation_p.F161C|ZFAND6_ENST00000559775.1_Missense_Mutation_p.F161C|ZFAND6_ENST00000559157.1_Missense_Mutation_p.F149C	NM_001242913.1|NM_001242914.1|NM_019006.3	NP_001229842.1|NP_001229843.1|NP_061879.2	Q6FIF0	ZFAN6_HUMAN	zinc finger, AN1-type domain 6	161					apoptotic process (GO:0006915)|cellular response to tumor necrosis factor (GO:0071356)|negative regulation of apoptotic process (GO:0043066)|protein targeting to peroxisome (GO:0006625)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)	cytoplasm (GO:0005737)	DNA binding (GO:0003677)|polyubiquitin binding (GO:0031593)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)	11						TTTCCAGGGTTTGAATGCCGG	0.383																																					p.F161C		.											.	.	.	0			c.T482G						.						121.0	103.0	109.0					15																	80429825		2203	4300	6503	SO:0001583	missense	54469	exon8			CAGGGTTTGAATG	BC005283	CCDS10313.1, CCDS58395.1	15q24.3	2013-01-09	2006-07-07	2006-07-07	ENSG00000086666	ENSG00000086666		"""Zinc fingers, AN1-type domain containing"""	30164	protein-coding gene	gene with protein product	"""protein associated with PRK1"""	610183	"""zinc finger, A20 domain containing 3"""	ZA20D3		11054541	Standard	NM_019006		Approved	ZFAND5B, AWP1	uc002bff.2	Q6FIF0	OTTHUMG00000144169	ENST00000261749.6:c.482T>G	15.37:g.80429825T>G	ENSP00000261749:p.Phe161Cys	Somatic	57	0		WXS	Illumina HiSeq	.	43	18	NM_001242913	D3DW92|D3DW94|O95792|Q9BQF7|Q9GZY3	Missense_Mutation	SNP	ENST00000261749.6	37	CCDS10313.1	.	.	.	.	.	.	.	.	.	.	T	18.82	3.705869	0.68615	.	.	ENSG00000086666	ENST00000261749	T	0.51325	0.71	5.23	5.23	0.72850	Zinc finger, AN1-type (4);	0.075689	0.53938	D	0.000047	T	0.77274	0.4106	H	0.94620	3.56	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	D	0.84463	0.0595	10	0.87932	D	0	.	15.4457	0.75228	0.0:0.0:0.0:1.0	.	149;161	Q6FIF0-2;Q6FIF0	.;ZFAN6_HUMAN	C	161	ENSP00000261749:F161C	ENSP00000261749:F161C	F	+	2	0	ZFAND6	78216880	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.785000	0.68998	2.107000	0.64212	0.533000	0.62120	TTT	.		0.383	ZFAND6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000291368.1	NM_019006	
MICAL3	57553	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	22	18379580	18379580	+	Silent	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr22:18379580A>C	ENST00000441493.2	-	8	1468	c.1116T>G	c.(1114-1116)acT>acG	p.T372T	MICAL3_ENST00000383094.3_Silent_p.T372T|MICAL3_ENST00000429452.1_Silent_p.T372T|MICAL3_ENST00000400561.2_Silent_p.T372T|MICAL3_ENST00000207726.7_Silent_p.T372T|MICAL3_ENST00000585038.1_Silent_p.T372T|MICAL3_ENST00000414725.2_Silent_p.T372T|MICAL3_ENST00000444520.1_Silent_p.T372T	NM_015241.2	NP_056056.2	Q7RTP6	MICA3_HUMAN	microtubule associated monooxygenase, calponin and LIM domain containing 3	372	Monooxygenase domain. {ECO:0000250}.				actin filament depolymerization (GO:0030042)|cytoskeleton organization (GO:0007010)|exocytosis (GO:0006887)|oxidation-reduction process (GO:0055114)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	actin binding (GO:0003779)|FAD binding (GO:0071949)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen (GO:0016709)|zinc ion binding (GO:0008270)			large_intestine(1)|lung(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	4		all_epithelial(15;0.198)		Lung(27;0.0427)		CATACATACAAGTGAAGTCAA	0.577											OREG0026285	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.T372T		.											.	.	.	0			c.T1116G						.						73.0	66.0	68.0					22																	18379580		1568	3582	5150	SO:0001819	synonymous_variant	57553	exon8			CATACAAGTGAAG	AB037785	CCDS46659.1, CCDS46660.1, CCDS46661.1	22q11.21	2013-03-26	2013-03-26		ENSG00000243156	ENSG00000243156			24694	protein-coding gene	gene with protein product		608882				12110185	Standard	NM_015241		Approved	KIAA0819	uc002zng.4	Q7RTP6	OTTHUMG00000150067	ENST00000441493.2:c.1116T>G	22.37:g.18379580A>C		Somatic	26	0	725	WXS	Illumina HiSeq	.	11	5	NM_015241	B2RXJ5|E9PEF0|O94909|Q5U4P4|Q6ICK4|Q96DF2|Q9P2I3	Silent	SNP	ENST00000441493.2	37	CCDS46659.1																																																																																			.		0.577	MICAL3-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447351.1		
LRRTM3	347731	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	10	68686686	68686686	+	Silent	SNP	T	T	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr10:68686686T>C	ENST00000361320.4	+	2	590	c.12T>C	c.(10-12)aaT>aaC	p.N4N	CTNNA3_ENST00000373744.4_Intron|CTNNA3_ENST00000433211.2_Intron	NM_178011.3	NP_821079.3	Q86VH5	LRRT3_HUMAN	leucine rich repeat transmembrane neuronal 3	4					positive regulation of beta-amyloid formation (GO:1902004)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)				breast(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(6)|lung(20)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	41						CAGGTTTCAATGTAATTAGGC	0.378																																					p.N4N		.											.	.	.	0			c.T12C						.						52.0	49.0	50.0					10																	68686686		2203	4300	6503	SO:0001819	synonymous_variant	347731	exon2			TTTCAATGTAATT	BX640611	CCDS7270.1	10q22.1	2007-01-22				ENSG00000198739			19410	protein-coding gene	gene with protein product		610869				12676565	Standard	XR_247527		Approved		uc001jmz.1	Q86VH5		ENST00000361320.4:c.12T>C	10.37:g.68686686T>C		Somatic	51	0		WXS	Illumina HiSeq	.	36	19	NM_178011	A8K2A3|Q2NKX7|Q6N0A3	Silent	SNP	ENST00000361320.4	37	CCDS7270.1																																																																																			.		0.378	LRRTM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048277.2	NM_178011	
ELL2	22936	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	5	95236433	95236433	+	Silent	SNP	A	A	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr5:95236433A>G	ENST00000237853.4	-	7	1267	c.918T>C	c.(916-918)ccT>ccC	p.P306P	ELL2_ENST00000431061.2_Intron	NM_012081.5	NP_036213.2	O00472	ELL2_HUMAN	elongation factor, RNA polymerase II, 2	306					regulation of transcription, DNA-templated (GO:0006355)|snRNA transcription from RNA polymerase II promoter (GO:0042795)|transcription elongation from RNA polymerase II promoter (GO:0006368)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(10)|pancreas(1)|prostate(2)	24		all_cancers(142;2.04e-06)|all_epithelial(76;3.1e-09)|all_lung(232;0.00309)|Lung NSC(167;0.00454)|Ovarian(225;0.0165)|Colorectal(57;0.0343)|Breast(839;0.198)		all cancers(79;2.16e-15)		TAGAACATACAGGAGATTCTG	0.398																																					p.P306P		.											.	.	.	0			c.T918C						.						75.0	74.0	74.0					5																	95236433		2203	4300	6503	SO:0001819	synonymous_variant	22936	exon7			ACATACAGGAGAT	U88629	CCDS4080.1	5q15	2010-11-29			ENSG00000118985	ENSG00000118985			17064	protein-coding gene	gene with protein product		601874				9108030	Standard	NM_012081		Approved		uc003klr.4	O00472	OTTHUMG00000122085	ENST00000237853.4:c.918T>C	5.37:g.95236433A>G		Somatic	57	0		WXS	Illumina HiSeq	.	66	20	NM_012081	B4DNK7	Silent	SNP	ENST00000237853.4	37	CCDS4080.1																																																																																			.		0.398	ELL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242846.1	NM_012081	
INPPL1	3636	hgsc.bcm.edu;broad.mit.edu	37	11	71939417	71939417	+	Missense_Mutation	SNP	G	G	A	rs142516692		TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr11:71939417G>A	ENST00000298229.2	+	3	476	c.272G>A	c.(271-273)cGc>cAc	p.R91H	INPPL1_ENST00000541756.1_5'UTR|INPPL1_ENST00000538751.1_5'UTR	NM_001567.3	NP_001558.3	O15357	SHIP2_HUMAN	inositol polyphosphate phosphatase-like 1	91	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				actin filament organization (GO:0007015)|cell adhesion (GO:0007155)|endochondral ossification (GO:0001958)|endocytosis (GO:0006897)|glucose metabolic process (GO:0006006)|immune system process (GO:0002376)|inositol phosphate metabolic process (GO:0043647)|negative regulation of cell proliferation (GO:0008285)|negative regulation of gene expression (GO:0010629)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|post-embryonic development (GO:0009791)|response to insulin (GO:0032868)|ruffle assembly (GO:0097178)|small molecule metabolic process (GO:0044281)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	hydrolase activity (GO:0016787)|SH2 domain binding (GO:0042169)			breast(2)|endometrium(9)|kidney(1)|large_intestine(7)|lung(12)|ovary(1)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	44						CCTGTGCGCCGCTTCCAGACC	0.662																																					p.R91H		.											INPPL1,NS,carcinoma,0,1	INPPL1	0	0			c.G272A						.	G	HIS/ARG	1,4399	2.1+/-5.4	0,1,2199	60.0	61.0	61.0		272	4.3	1.0	11	dbSNP_134	61	0,8586		0,0,4293	no	missense	INPPL1	NM_001567.3	29	0,1,6492	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging	91/1259	71939417	1,12985	2200	4293	6493	SO:0001583	missense	3636	exon3			TGCGCCGCTTCCA	Y14385	CCDS8213.1	11q23	2013-02-14			ENSG00000165458	ENSG00000165458		"""Sterile alpha motif (SAM) domain containing"", ""SH2 domain containing"""	6080	protein-coding gene	gene with protein product	"""51C protein"""	600829				8530088	Standard	NM_001567		Approved	SHIP2	uc001osf.3	O15357	OTTHUMG00000167879	ENST00000298229.2:c.272G>A	11.37:g.71939417G>A	ENSP00000298229:p.Arg91His	Somatic	35	0		WXS	Illumina HiSeq	.	29	3	NM_001567	B2RTX5|Q13577|Q13578	Missense_Mutation	SNP	ENST00000298229.2	37	CCDS8213.1	.	.	.	.	.	.	.	.	.	.	g	17.31	3.357146	0.61293	2.27E-4	0.0	ENSG00000165458	ENST00000298229	D	0.89123	-2.47	4.3	4.3	0.51218	SH2 motif (5);	0.504726	0.19148	N	0.121520	D	0.90854	0.7127	L	0.49778	1.585	0.80722	D	1	D	0.71674	0.998	D	0.66497	0.944	D	0.87366	0.2347	10	0.15952	T	0.53	.	13.6353	0.62219	0.0:0.0:1.0:0.0	.	91	O15357	SHIP2_HUMAN	H	91	ENSP00000298229:R91H	ENSP00000298229:R91H	R	+	2	0	INPPL1	71617065	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	4.371000	0.59523	2.236000	0.73375	0.561000	0.74099	CGC	0.000		0.662	INPPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396789.1	NM_001567	
UNC5D	137970	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	8	35544140	35544140	+	Missense_Mutation	SNP	A	A	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr8:35544140A>T	ENST00000404895.2	+	7	1325	c.997A>T	c.(997-999)Aca>Tca	p.T333S	UNC5D_ENST00000287272.2_Missense_Mutation_p.T277S|UNC5D_ENST00000453357.2_Missense_Mutation_p.T328S|UNC5D_ENST00000420357.1_Missense_Mutation_p.T277S|UNC5D_ENST00000416672.1_Missense_Mutation_p.T333S	NM_080872.2	NP_543148.2	Q6UXZ4	UNC5D_HUMAN	unc-5 homolog D (C. elegans)	333	TSP type-1 2. {ECO:0000255|PROSITE- ProRule:PRU00210}.				apoptotic process (GO:0006915)|axon guidance (GO:0007411)|pyramidal neuron differentiation (GO:0021859)|regulation of neuron migration (GO:2001222)|signal transduction (GO:0007165)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)				NS(2)|breast(7)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(14)|lung(56)|ovary(3)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(6)|urinary_tract(2)	112				READ - Rectum adenocarcinoma(1;1.31e-05)|Colorectal(1;0.000723)		CCGGGAGTGCACAGCACCACC	0.507																																					p.T333S		.											.	.	.	0			c.A997T						.						122.0	104.0	110.0					8																	35544140		2203	4300	6503	SO:0001583	missense	137970	exon7			GAGTGCACAGCAC	AB055056	CCDS6093.2	8p12	2013-01-11			ENSG00000156687	ENSG00000156687		"""Immunoglobulin superfamily / I-set domain containing"""	18634	protein-coding gene	gene with protein product						18402767	Standard	NM_080872		Approved	KIAA1777, Unc5h4	uc003xjr.2	Q6UXZ4	OTTHUMG00000157145	ENST00000404895.2:c.997A>T	8.37:g.35544140A>T	ENSP00000385143:p.Thr333Ser	Somatic	60	0		WXS	Illumina HiSeq	.	26	13	NM_080872	Q8WYP7	Missense_Mutation	SNP	ENST00000404895.2	37	CCDS6093.2	.	.	.	.	.	.	.	.	.	.	A	9.964	1.223648	0.22457	.	.	ENSG00000156687	ENST00000404895;ENST00000420357;ENST00000287272;ENST00000416672;ENST00000453357	T;T;T;T;T	0.51071	0.72;2.24;2.24;0.72;0.72	5.76	4.59	0.56863	.	0.272323	0.46145	N	0.000313	T	0.29684	0.0741	N	0.20357	0.565	0.80722	D	1	B;B;B	0.21381	0.055;0.046;0.026	B;B;B	0.20955	0.032;0.018;0.031	T	0.07424	-1.0773	10	0.24483	T	0.36	-13.2536	8.2393	0.31650	0.8135:0.0:0.0662:0.1203	.	333;328;333	C9J2B6;Q6UXZ4-2;Q6UXZ4	.;.;UNC5D_HUMAN	S	333;277;277;333;328	ENSP00000385143:T333S;ENSP00000392739:T277S;ENSP00000287272:T277S;ENSP00000412652:T333S;ENSP00000394303:T328S	ENSP00000287272:T277S	T	+	1	0	UNC5D	35663682	0.944000	0.32072	0.999000	0.59377	0.968000	0.65278	2.432000	0.44784	1.086000	0.41228	0.528000	0.53228	ACA	.		0.507	UNC5D-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000347586.2		
KCNAB2	8514	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	6101927	6101927	+	Missense_Mutation	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr1:6101927T>G	ENST00000164247.1	+	3	678	c.114T>G	c.(112-114)ttT>ttG	p.F38L	KCNAB2_ENST00000378087.3_Missense_Mutation_p.F38L|AL035406.1_ENST00000594544.1_5'Flank|KCNAB2_ENST00000378092.1_Intron|KCNAB2_ENST00000602612.1_Missense_Mutation_p.F38L|KCNAB2_ENST00000352527.1_Intron|KCNAB2_ENST00000341524.1_Missense_Mutation_p.F38L|KCNAB2_ENST00000378111.1_Missense_Mutation_p.F38L|KCNAB2_ENST00000378097.1_Missense_Mutation_p.F38L	NM_001199860.1	NP_001186789.1	Q13303	KCAB2_HUMAN	potassium voltage-gated channel, shaker-related subfamily, beta member 2	38					hematopoietic progenitor cell differentiation (GO:0002244)|protein heterooligomerization (GO:0051291)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|juxtaparanode region of axon (GO:0044224)|plasma membrane (GO:0005886)	potassium channel regulator activity (GO:0015459)|voltage-gated potassium channel activity (GO:0005249)			large_intestine(1)|lung(4)|skin(3)	8	Ovarian(185;0.0634)	all_cancers(23;5.85e-39)|all_epithelial(116;4.88e-22)|all_lung(118;4.21e-08)|Lung NSC(185;9.77e-07)|all_hematologic(16;2.78e-06)|all_neural(13;3.18e-06)|Acute lymphoblastic leukemia(12;0.000272)|Breast(487;0.000496)|Renal(390;0.0007)|Colorectal(325;0.00106)|Glioma(11;0.00203)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0393)|Medulloblastoma(700;0.211)		Epithelial(90;6.9e-37)|GBM - Glioblastoma multiforme(13;8.8e-31)|OV - Ovarian serous cystadenocarcinoma(86;1.45e-19)|Colorectal(212;2.46e-07)|COAD - Colon adenocarcinoma(227;2.07e-05)|Kidney(185;7.88e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.00131)|BRCA - Breast invasive adenocarcinoma(365;0.00133)|STAD - Stomach adenocarcinoma(132;0.00391)|READ - Rectum adenocarcinoma(331;0.0649)		AGCTCCAGTTTTACAGGTAAT	0.527											OREG0013028	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.F38L		.											.	.	.	0			c.T114G						.						97.0	98.0	98.0					1																	6101927		2203	4300	6503	SO:0001583	missense	8514	exon3			CCAGTTTTACAGG	U33429	CCDS55.1, CCDS56.1, CCDS55570.1, CCDS55571.1	1p36.3	2008-02-05			ENSG00000069424	ENSG00000069424		"""Potassium channels"", ""Aldo-keto reductases"""	6229	protein-coding gene	gene with protein product		601142				8838324	Standard	NM_003636		Approved	AKR6A5, KCNA2B, HKvbeta2.1, HKvbeta2.2	uc001aly.2	Q13303	OTTHUMG00000000795	ENST00000164247.1:c.114T>G	1.37:g.6101927T>G	ENSP00000164247:p.Phe38Leu	Somatic	158	0	631	WXS	Illumina HiSeq	.	35	24	NM_001199860	A0AVM9|A8K1A4|B0AZR7|O43659|Q5TG82|Q5TG83|Q6ZNE4|Q99411	Missense_Mutation	SNP	ENST00000164247.1	37	CCDS55.1	.	.	.	.	.	.	.	.	.	.	T	11.79	1.742997	0.30865	.	.	ENSG00000069424	ENST00000378111;ENST00000378097;ENST00000445501;ENST00000389632;ENST00000378087;ENST00000341524;ENST00000164247	T;T;T;T;T;T	0.42513	1.02;3.62;3.2;0.97;3.62;3.62	4.84	4.84	0.62591	.	.	.	.	.	T	0.20780	0.0500	N	0.08118	0	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.08994	-1.0695	9	0.20046	T	0.44	.	8.2645	0.31806	0.0:0.1002:0.0:0.8998	.	38;38	Q13303;Q2YD85	KCAB2_HUMAN;.	L	38	ENSP00000367351:F38L;ENSP00000367337:F38L;ENSP00000374283:F38L;ENSP00000367327:F38L;ENSP00000340824:F38L;ENSP00000164247:F38L	ENSP00000164247:F38L	F	+	3	2	KCNAB2	6024514	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	2.347000	0.44036	1.824000	0.53156	0.383000	0.25322	TTT	.		0.527	KCNAB2-006	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000002114.3	NM_172130	
STX3	6809	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	11	59554567	59554567	+	Nonsense_Mutation	SNP	A	A	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr11:59554567A>T	ENST00000337979.4	+	3	719	c.172A>T	c.(172-174)Aaa>Taa	p.K58*	STX3_ENST00000437946.2_Intron|STX3_ENST00000529177.1_Nonsense_Mutation_p.K58*|STX3_ENST00000535361.1_Nonsense_Mutation_p.K58*|STX3_ENST00000300150.7_Nonsense_Mutation_p.K27*	NM_001178040.1|NM_004177.4	NP_001171511.1|NP_004168.1	Q13277	STX3_HUMAN	syntaxin 3	58					exocytosis (GO:0006887)|intracellular protein transport (GO:0006886)|long-term synaptic potentiation (GO:0060291)|membrane fusion (GO:0061025)|neuron projection development (GO:0031175)|neurotransmitter transport (GO:0006836)	apical plasma membrane (GO:0016324)|azurophil granule (GO:0042582)|cell-cell junction (GO:0005911)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|SNARE complex (GO:0031201)|specific granule (GO:0042581)|vacuole (GO:0005773)	arachidonic acid binding (GO:0050544)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(3)|ovary(2)|skin(1)	13						GGAGGCTAAGAAACTCTACAG	0.418																																					p.K58X		.											.	.	.	0			c.A172T						.						161.0	143.0	149.0					11																	59554567		2201	4295	6496	SO:0001587	stop_gained	6809	exon3			GCTAAGAAACTCT	AJ002076	CCDS7975.1, CCDS53637.1	11q12.1	2008-02-05	2006-04-25	2006-04-25	ENSG00000166900	ENSG00000166900			11438	protein-coding gene	gene with protein product		600876	"""syntaxin 3A"""	STX3A		16598260, 16339081	Standard	NM_004177		Approved		uc001nog.3	Q13277	OTTHUMG00000167353	ENST00000337979.4:c.172A>T	11.37:g.59554567A>T	ENSP00000338562:p.Lys58*	Somatic	64	0		WXS	Illumina HiSeq	.	29	6	NM_004177	B4DME0|O43750|O43751|Q15360	Nonsense_Mutation	SNP	ENST00000337979.4	37	CCDS7975.1	.	.	.	.	.	.	.	.	.	.	A	42	9.505042	0.99190	.	.	ENSG00000166900	ENST00000300150;ENST00000337979;ENST00000535361;ENST00000529177;ENST00000528805	.	.	.	5.01	5.01	0.66863	.	0.092777	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-21.1909	13.5719	0.61851	1.0:0.0:0.0:0.0	.	.	.	.	X	27;58;58;58;10	.	ENSP00000300150:K27X	K	+	1	0	STX3	59311143	1.000000	0.71417	0.998000	0.56505	0.900000	0.52787	6.461000	0.73522	1.875000	0.54330	0.528000	0.53228	AAA	.		0.418	STX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394264.1	NM_004177	
PCF11	51585	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	11	82877699	82877699	+	Missense_Mutation	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr11:82877699A>C	ENST00000298281.4	+	5	2212	c.1760A>C	c.(1759-1761)aAc>aCc	p.N587T		NM_015885.3	NP_056969.2	O94913	PCF11_HUMAN	PCF11 cleavage and polyadenylation factor subunit	587					gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA cleavage (GO:0006379)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	mRNA cleavage factor complex (GO:0005849)|nucleoplasm (GO:0005654)				cervix(1)|endometrium(3)|kidney(4)|large_intestine(1)|lung(22)|ovary(1)|urinary_tract(1)	33						AATGTAGAAAACTGGCAAAGT	0.383																																					p.N587T		.											PCF11_ENST00000298281,colon,carcinoma,0,2	PCF11_ENST00000298281	0	0			c.A1760C						.						68.0	68.0	68.0					11																	82877699		1810	4019	5829	SO:0001583	missense	51585	exon5			TAGAAAACTGGCA	AB020631	CCDS44689.1	11q13	2013-07-02	2013-07-02		ENSG00000165494	ENSG00000165494			30097	protein-coding gene	gene with protein product		608876	"""PCF11, cleavage and polyadenylation factor II subunit, homolog (S. cerevisiae)"", ""PCF11, cleavage and polyadenylation factor subunit, homolog (S. cerevisiae)"""			11060040	Standard	NM_015885		Approved	KIAA0824	uc001ozx.4	O94913	OTTHUMG00000167031	ENST00000298281.4:c.1760A>C	11.37:g.82877699A>C	ENSP00000298281:p.Asn587Thr	Somatic	126	0		WXS	Illumina HiSeq	.	77	31	NM_015885	A6H8W7|O43671|Q6P0X8	Missense_Mutation	SNP	ENST00000298281.4	37	CCDS44689.1	.	.	.	.	.	.	.	.	.	.	A	15.62	2.888291	0.52014	.	.	ENSG00000165494	ENST00000298281;ENST00000530660;ENST00000530304	T;T;T	0.51817	1.66;0.73;0.69	6.07	3.77	0.43336	.	0.089474	0.48767	D	0.000180	T	0.51975	0.1706	L	0.29908	0.895	0.32337	N	0.560265	D;D	0.67145	0.996;0.993	P;D	0.70935	0.824;0.971	T	0.58317	-0.7657	9	.	.	.	.	10.3418	0.43882	0.8681:0.0:0.1319:0.0	.	587;587	E9PQ01;O94913	.;PCF11_HUMAN	T	587	ENSP00000298281:N587T;ENSP00000434540:N587T;ENSP00000431567:N587T	.	N	+	2	0	PCF11	82555347	0.999000	0.42202	0.999000	0.59377	0.983000	0.72400	3.003000	0.49505	0.541000	0.28827	0.533000	0.62120	AAC	.		0.383	PCF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392548.2	NM_015885	
MYRIP	25924	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	3	40231505	40231505	+	Missense_Mutation	SNP	G	G	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr3:40231505G>A	ENST00000302541.6	+	10	1558	c.1216G>A	c.(1216-1218)Gcc>Acc	p.A406T	MYRIP_ENST00000539167.1_Missense_Mutation_p.A219T|MYRIP_ENST00000459828.1_3'UTR|MYRIP_ENST00000425621.1_Missense_Mutation_p.A406T|MYRIP_ENST00000444716.1_Missense_Mutation_p.A406T|MYRIP_ENST00000396217.3_Missense_Mutation_p.A317T	NM_001284423.1|NM_001284426.1|NM_015460.2	NP_001271352.1|NP_001271355.1|NP_056275.2	Q8NFW9	MYRIP_HUMAN	myosin VIIA and Rab interacting protein	406	Myosin-binding.				intracellular protein transport (GO:0006886)|positive regulation of insulin secretion (GO:0032024)	actin cytoskeleton (GO:0015629)|dense core granule (GO:0031045)|exocyst (GO:0000145)|melanosome (GO:0042470)|perinuclear region of cytoplasm (GO:0048471)|photoreceptor outer segment (GO:0001750)|synapse (GO:0045202)	zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|liver(2)|lung(10)|ovary(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34				KIRC - Kidney renal clear cell carcinoma(284;0.174)|Kidney(284;0.206)		CTGGAGTGAGGCCTTGAGCAA	0.632																																					p.A406T		.											.	.	.	0			c.G1216A						.						103.0	93.0	96.0					3																	40231505		2203	4300	6503	SO:0001583	missense	25924	exon10			AGTGAGGCCTTGA	AF396687	CCDS2689.1, CCDS68390.1, CCDS68391.1, CCDS68392.1	3p21.33	2010-08-20			ENSG00000170011	ENSG00000170011		"""A-kinase anchor proteins"""	19156	protein-coding gene	gene with protein product	"""synaptotagmin-like protein homologue lacking C2 domains-c"", ""rab effector MYRIP"", ""Slp homologue lacking C2 domains"""	611790				11964381, 12221080	Standard	NM_001284425		Approved	DKFZp586F1018, exophilin-8, MyRIP, SLAC2-C, SLAC2C	uc003cka.3	Q8NFW9	OTTHUMG00000131392	ENST00000302541.6:c.1216G>A	3.37:g.40231505G>A	ENSP00000301972:p.Ala406Thr	Somatic	32	0		WXS	Illumina HiSeq	.	9	7	NM_015460	B3KWM3|B3KWW4|B7Z2H1|B7Z9V3|G3XAI8|Q32M41|Q32M42|Q569F7|Q8IUF5|Q9Y3V4	Missense_Mutation	SNP	ENST00000302541.6	37	CCDS2689.1	.	.	.	.	.	.	.	.	.	.	G	18.11	3.550106	0.65311	.	.	ENSG00000170011	ENST00000444716;ENST00000302541;ENST00000425621;ENST00000396217;ENST00000539167	T;T;T;T;T	0.29142	1.58;1.58;1.58;1.58;1.58	5.73	4.67	0.58626	Myelin-associated oligodendrocytic basic protein (MOBP) (1);	0.117372	0.64402	D	0.000019	T	0.35998	0.0951	L	0.46157	1.445	0.41289	D	0.986963	P;P;B	0.48834	0.916;0.513;0.17	P;B;B	0.50405	0.64;0.103;0.068	T	0.02676	-1.1125	9	.	.	.	.	12.876	0.57989	0.0919:0.0:0.9081:0.0	.	317;406;406	Q32M42;G3XAI8;Q8NFW9	.;.;MYRIP_HUMAN	T	406;406;406;317;219	ENSP00000398665:A406T;ENSP00000301972:A406T;ENSP00000389323:A406T;ENSP00000379519:A317T;ENSP00000438297:A219T	.	A	+	1	0	MYRIP	40206509	1.000000	0.71417	0.910000	0.35882	0.998000	0.95712	4.740000	0.62087	2.711000	0.92665	0.655000	0.94253	GCC	.		0.632	MYRIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254181.2	NM_015460	
NVL	4931	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	224477340	224477340	+	Missense_Mutation	SNP	A	A	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr1:224477340A>G	ENST00000281701.6	-	13	1680	c.1421T>C	c.(1420-1422)cTc>cCc	p.L474P	NVL_ENST00000391875.2_Missense_Mutation_p.L368P|NVL_ENST00000361463.3_Missense_Mutation_p.L368P|NVL_ENST00000340871.4_Missense_Mutation_p.L285P|NVL_ENST00000469075.1_Missense_Mutation_p.L383P|NVL_ENST00000482491.1_Missense_Mutation_p.L198P	NM_002533.3	NP_002524.2	O15381	NVL_HUMAN	nuclear VCP-like	474						membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)			breast(3)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(10)|lung(13)|ovary(1)|prostate(1)|skin(4)|soft_tissue(1)|urinary_tract(1)	42				GBM - Glioblastoma multiforme(131;0.00501)		CAGTGCCATGAGATCAGCACC	0.433																																					p.L474P		.											.	.	.	0			c.T1421C						.						80.0	73.0	75.0					1																	224477340		2203	4300	6503	SO:0001583	missense	4931	exon13			GCCATGAGATCAG	U78772	CCDS1541.1, CCDS1542.1, CCDS58062.1, CCDS58063.1	1q41-q42.2	2010-04-21			ENSG00000143748	ENSG00000143748		"""ATPases / AAA-type"""	8070	protein-coding gene	gene with protein product	"""Nuclear valosin-containing protein-like"", ""nuclear VCP-like protein"""	602426				9286697	Standard	NM_002533		Approved		uc001hok.3	O15381	OTTHUMG00000037536	ENST00000281701.6:c.1421T>C	1.37:g.224477340A>G	ENSP00000281701:p.Leu474Pro	Somatic	66	0		WXS	Illumina HiSeq	.	67	17	NM_002533	B4DMC4|B4DP98|Q96EM7	Missense_Mutation	SNP	ENST00000281701.6	37	CCDS1541.1	.	.	.	.	.	.	.	.	.	.	A	28.5	4.921939	0.92319	.	.	ENSG00000143748	ENST00000281701;ENST00000391875;ENST00000469075;ENST00000482491;ENST00000340871;ENST00000361463	D;D;D;D;D;D	0.96232	-1.64;-1.64;-1.64;-3.95;-1.64;-1.64	5.91	5.91	0.95273	.	0.000000	0.85682	D	0.000000	D	0.99023	0.9666	H	0.98786	4.33	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.83275	0.996;0.993;0.996	D	0.99194	1.0871	10	0.87932	D	0	-9.7541	16.3483	0.83171	1.0:0.0:0.0:0.0	.	285;383;474	B4DMC4;B4DP98;O15381	.;.;NVL_HUMAN	P	474;368;383;198;285;368	ENSP00000281701:L474P;ENSP00000375747:L368P;ENSP00000417826:L383P;ENSP00000417213:L198P;ENSP00000341362:L285P;ENSP00000354779:L368P	ENSP00000281701:L474P	L	-	2	0	NVL	222543963	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	9.204000	0.95041	2.254000	0.74563	0.533000	0.62120	CTC	.		0.433	NVL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000091453.2	NM_002533	
MYOM1	8736	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	18	3094261	3094261	+	Missense_Mutation	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr18:3094261T>G	ENST00000356443.4	-	26	4104	c.3771A>C	c.(3769-3771)aaA>aaC	p.K1257N	RNU7-25P_ENST00000516544.1_RNA|MYOM1_ENST00000261606.7_Missense_Mutation_p.K1161N|MYOM1_ENST00000400569.3_Missense_Mutation_p.K1257N	NM_003803.3|NM_019856.1	NP_003794.3|NP_062830.1	P52179	MYOM1_HUMAN	myomesin 1	1257					muscle contraction (GO:0006936)	M band (GO:0031430)|striated muscle myosin thick filament (GO:0005863)	identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|structural constituent of muscle (GO:0008307)			NS(2)|autonomic_ganglia(1)|central_nervous_system(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(20)|ovary(4)|pancreas(1)|prostate(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	77						GGACCTGGCCTTTCTCCAAAA	0.383																																					p.K1257N		.											.	.	.	0			c.A3771C						.						62.0	59.0	60.0					18																	3094261		1822	4075	5897	SO:0001583	missense	8736	exon26			CTGGCCTTTCTCC	AF185573	CCDS45823.1, CCDS45824.1	18p11.31	2014-09-17	2012-10-17		ENSG00000101605	ENSG00000101605		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	7613	protein-coding gene	gene with protein product	"""skelemin"""	603508	"""myomesin 1 (skelemin) (185kD)"", ""myomesin 1 (skelemin) 185kDa"", ""myomesin 1, 185kDa"""			9806852	Standard	NM_019856		Approved		uc002klp.3	P52179	OTTHUMG00000178209	ENST00000356443.4:c.3771A>C	18.37:g.3094261T>G	ENSP00000348821:p.Lys1257Asn	Somatic	233	0		WXS	Illumina HiSeq	.	132	56	NM_003803	Q14BD6|Q6H969|Q6ZUU0	Missense_Mutation	SNP	ENST00000356443.4	37	CCDS45824.1	.	.	.	.	.	.	.	.	.	.	T	11.35	1.611871	0.28712	.	.	ENSG00000101605	ENST00000356443;ENST00000400569;ENST00000261606	T;T;T	0.04454	3.62;3.62;3.62	5.55	1.28	0.21552	Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.15998	0.0385	M	0.70595	2.14	0.48185	D	0.999602	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	T	0.00409	-1.1757	10	0.30854	T	0.27	.	10.9193	0.47154	0.0:0.3084:0.0:0.6916	.	1161;1257	P52179-2;P52179	.;MYOM1_HUMAN	N	1257;1257;1161	ENSP00000348821:K1257N;ENSP00000383413:K1257N;ENSP00000261606:K1161N	ENSP00000261606:K1161N	K	-	3	2	MYOM1	3084261	1.000000	0.71417	0.996000	0.52242	0.736000	0.42039	1.130000	0.31393	-0.043000	0.13513	-2.096000	0.00365	AAA	.		0.383	MYOM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441037.2	NM_003803	
TTR	7276	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	18	29172884	29172884	+	Missense_Mutation	SNP	T	T	G	rs121918094		TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr18:29172884T>G	ENST00000237014.3	+	2	272	c.95T>G	c.(94-96)cTg>cGg	p.L32R		NM_000371.3	NP_000362.1	P02766	TTHY_HUMAN	transthyretin	32			L -> P (in AMYL-TTR). {ECO:0000269|PubMed:10071047, ECO:0000269|PubMed:17503405}.		extracellular matrix organization (GO:0030198)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|retinol metabolic process (GO:0042572)|transport (GO:0006810)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)	hormone binding (GO:0042562)|identical protein binding (GO:0042802)			cervix(1)|large_intestine(3)|lung(7)|ovary(1)|stomach(1)	13			OV - Ovarian serous cystadenocarcinoma(10;0.00523)		Diclofenac(DB00586)|Diethylstilbestrol(DB00255)|Diflunisal(DB00861)|Dimethyl sulfoxide(DB01093)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583)	AAGTGTCCTCTGATGGTCAAA	0.478																																					p.L32R		.											.	.	.	0			c.T95G	GRCh37	CM993974	TTR	M	rs121918094	.						136.0	115.0	122.0					18																	29172884		2203	4300	6503	SO:0001583	missense	7276	exon2			GTCCTCTGATGGT	M10605	CCDS11899.1	18q12.1	2014-09-17	2008-07-31		ENSG00000118271	ENSG00000118271			12405	protein-coding gene	gene with protein product		176300	"""prealbumin, amyloidosis type I"", ""carpal tunnel syndrome 1"""	PALB, CTS1		8309582	Standard	NM_000371		Approved	HsT2651, CTS	uc002kwx.4	P02766	OTTHUMG00000131984	ENST00000237014.3:c.95T>G	18.37:g.29172884T>G	ENSP00000237014:p.Leu32Arg	Somatic	43	0		WXS	Illumina HiSeq	.	39	14	NM_000371	Q549C7|Q6IB96|Q9UBZ6|Q9UCM9	Missense_Mutation	SNP	ENST00000237014.3	37	CCDS11899.1	.	.	.	.	.	.	.	.	.	.	T	24.0	4.482873	0.84747	.	.	ENSG00000118271	ENST00000237014;ENST00000432547;ENST00000541025	D	0.97731	-4.51	5.71	5.71	0.89125	Transthyretin/hydroxyisourate hydrolase, superfamily (4);	0.069633	0.64402	D	0.000016	D	0.99199	0.9722	H	0.96604	3.85	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.99044	1.0825	10	0.87932	D	0	-11.3537	15.9439	0.79779	0.0:0.0:0.0:1.0	.	32	P02766	TTHY_HUMAN	R	32	ENSP00000237014:L32R	ENSP00000237014:L32R	L	+	2	0	TTR	27426882	1.000000	0.71417	1.000000	0.80357	0.938000	0.57974	6.186000	0.72026	2.307000	0.77673	0.528000	0.53228	CTG	.		0.478	TTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254948.1	NM_000371	
NOXO1	124056	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	16	2030477	2030477	+	Missense_Mutation	SNP	A	A	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr16:2030477A>G	ENST00000397280.4	-	4	310	c.307T>C	c.(307-309)Tat>Cat	p.Y103H	NOXO1_ENST00000354249.4_Missense_Mutation_p.Y97H|NOXO1_ENST00000356120.4_Missense_Mutation_p.Y98H|AC005606.1_ENST00000598236.1_5'Flank|TBL3_ENST00000568546.1_3'UTR|NOXO1_ENST00000566005.1_Missense_Mutation_p.Y102H			Q8NFA2	NOXO1_HUMAN	NADPH oxidase organizer 1	103	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.				extracellular matrix disassembly (GO:0022617)|regulation of hydrogen peroxide metabolic process (GO:0010310)|regulation of respiratory burst (GO:0060263)|superoxide metabolic process (GO:0006801)	NADPH oxidase complex (GO:0043020)	enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|phosphatidylinositol binding (GO:0035091)|phospholipid binding (GO:0005543)|superoxide-generating NADPH oxidase activator activity (GO:0016176)			lung(2)	2					Ecabet(DB05265)	CTCCGAGAATAGGTTTCCAAC	0.652																																					p.Y103H	Pancreas(104;2811 2841 4129)|Esophageal Squamous(25;910 1225 43728)	.											.	.	.	0			c.T307C						.						18.0	24.0	22.0					16																	2030477		2189	4282	6471	SO:0001583	missense	124056	exon4			GAGAATAGGTTTC	AF532985	CCDS10454.1, CCDS10455.1, CCDS42101.1, CCDS58406.1	16p13.3	2008-02-05			ENSG00000196408	ENSG00000196408			19404	protein-coding gene	gene with protein product		611256					Standard	NM_144603		Approved	P41NOXA, P41NOXB, P41NOXC, SH3PXD5, SNX28	uc002cnx.4	Q8NFA2	OTTHUMG00000128707	ENST00000397280.4:c.307T>C	16.37:g.2030477A>G	ENSP00000380450:p.Tyr103His	Somatic	54	0		WXS	Illumina HiSeq	.	25	16	NM_172168	Q86YM1|Q8NFA3|Q96B73	Missense_Mutation	SNP	ENST00000397280.4	37	CCDS42101.1	.	.	.	.	.	.	.	.	.	.	A	17.99	3.522095	0.64747	.	.	ENSG00000196408	ENST00000354249;ENST00000356120;ENST00000397280	T;T;T	0.80033	-1.33;0.29;0.29	5.12	5.12	0.69794	Phox homologous domain (4);	0.000000	0.85682	D	0.000000	D	0.90807	0.7113	M	0.90082	3.085	0.58432	D	0.99999	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;1.0	D	0.92435	0.5957	10	0.87932	D	0	-19.9999	12.6575	0.56795	1.0:0.0:0.0:0.0	.	102;97;98;103	Q8NFA2-2;Q8NFA2-4;Q8NFA2-3;Q8NFA2	.;.;.;NOXO1_HUMAN	H	97;98;103	ENSP00000346195:Y97H;ENSP00000348435:Y98H;ENSP00000380450:Y103H	ENSP00000346195:Y97H	Y	-	1	0	NOXO1	1970478	0.695000	0.27747	0.615000	0.29064	0.076000	0.17211	3.000000	0.49481	1.920000	0.55613	0.459000	0.35465	TAT	.		0.652	NOXO1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250612.1		
ZNF69	7620	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	19	12014751	12014751	+	Silent	SNP	T	T	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr19:12014751T>C	ENST00000429654.2	+	3	362	c.222T>C	c.(220-222)taT>taC	p.Y74Y	ZNF69_ENST00000340180.5_Silent_p.Y60Y			Q9UC07	ZNF69_HUMAN	zinc finger protein 69	74	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(1)|skin(2)	4				Lung(535;0.011)		ACATTGAATATGAGTACCAAA	0.303																																					p.Y60Y		.											.	.	.	0			c.T180C						.						69.0	73.0	72.0					19																	12014751		2203	4298	6501	SO:0001819	synonymous_variant	7620	exon3			TGAATATGAGTAC	X60076	CCDS32914.1	19p13.2	2013-01-08	2006-05-12		ENSG00000198429	ENSG00000198429		"""Zinc fingers, C2H2-type"", ""-"""	13138	protein-coding gene	gene with protein product		194543	"""zinc finger protein 69 (Cos5)"""			1639391	Standard	NM_021915		Approved	Cos5	uc002mst.4	Q9UC07	OTTHUMG00000156526	ENST00000429654.2:c.222T>C	19.37:g.12014751T>C		Somatic	196	0		WXS	Illumina HiSeq	.	105	38	NM_021915	Q86VA7	Silent	SNP	ENST00000429654.2	37																																																																																				.		0.303	ZNF69-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000344082.1	NM_021915	
CRAT	1384	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	9	131864315	131864315	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr9:131864315G>T	ENST00000318080.2	-	6	946	c.652C>A	c.(652-654)Cac>Aac	p.H218N	CRAT_ENST00000464290.1_5'UTR|RP11-247A12.1_ENST00000434250.1_RNA	NM_000755.3|NM_001257363.1	NP_000746|NP_001244292.1	P43155	CACP_HUMAN	carnitine O-acetyltransferase	218					carnitine metabolic process, CoA-linked (GO:0019254)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	endoplasmic reticulum (GO:0005783)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	carnitine O-acetyltransferase activity (GO:0004092)|receptor binding (GO:0005102)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(4)|skin(1)|urinary_tract(2)	13				UCEC - Uterine corpus endometrioid carcinoma (4;0.0178)	L-Carnitine(DB00583)	CCGTCACTGTGGTACACATCC	0.577																																					p.H218N		.											.	.	.	0			c.C652A						.						95.0	80.0	85.0					9																	131864315		2203	4300	6503	SO:0001583	missense	1384	exon6			CACTGTGGTACAC	X78706	CCDS6919.1	9q34.1	2010-04-27	2010-04-27		ENSG00000095321	ENSG00000095321	2.3.1.7		2342	protein-coding gene	gene with protein product		600184	"""carnitine acetyltransferase"""			7829107	Standard	NM_000755		Approved	CAT1	uc004bxh.3	P43155	OTTHUMG00000147343	ENST00000318080.2:c.652C>A	9.37:g.131864315G>T	ENSP00000315013:p.His218Asn	Somatic	43	0		WXS	Illumina HiSeq	.	16	7	NM_000755	Q5T952|Q9BW16	Missense_Mutation	SNP	ENST00000318080.2	37	CCDS6919.1	.	.	.	.	.	.	.	.	.	.	G	2.203	-0.382448	0.04966	.	.	ENSG00000095321	ENST00000351352;ENST00000318080	T	0.39229	1.09	4.6	3.67	0.42095	.	0.098476	0.64402	N	0.000003	T	0.16896	0.0406	N	0.02736	-0.51	0.80722	D	1	B	0.06786	0.001	B	0.09377	0.004	T	0.06862	-1.0803	10	0.09590	T	0.72	-27.3184	10.5455	0.45058	0.0:0.0:0.5047:0.4953	.	218	P43155	CACP_HUMAN	N	218	ENSP00000315013:H218N	ENSP00000315013:H218N	H	-	1	0	CRAT	130904136	1.000000	0.71417	1.000000	0.80357	0.821000	0.46438	2.554000	0.45845	1.097000	0.41459	0.561000	0.74099	CAC	.		0.577	CRAT-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253700.1		
PCDHGA3	56112	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	5	140724331	140724331	+	Missense_Mutation	SNP	A	A	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr5:140724331A>T	ENST00000253812.6	+	1	731	c.731A>T	c.(730-732)cAg>cTg	p.Q244L	PCDHGA1_ENST00000517417.1_Intron|PCDHGA2_ENST00000394576.2_Intron	NM_018916.3|NM_032011.1	NP_061739.2|NP_114400.1	Q9Y5H0	PCDG3_HUMAN	protocadherin gamma subfamily A, 3	244	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ATGTTTACTCAGCCTGAGTAC	0.547																																					p.Q244L		.											.	.	.	0			c.A731T						.						58.0	60.0	59.0					5																	140724331		2176	4281	6457	SO:0001583	missense	56112	exon1			TTACTCAGCCTGA	AF152510	CCDS47290.1, CCDS75329.1	5q31	2010-01-26			ENSG00000254245	ENSG00000254245		"""Cadherins / Protocadherins : Clustered"""	8701	other	protocadherin		606290				10380929	Standard	NM_032011		Approved	PCDH-GAMMA-A3		Q9Y5H0	OTTHUMG00000163680	ENST00000253812.6:c.731A>T	5.37:g.140724331A>T	ENSP00000253812:p.Gln244Leu	Somatic	60	0		WXS	Illumina HiSeq	.	51	11	NM_032011	Q9Y5D4	Missense_Mutation	SNP	ENST00000253812.6	37	CCDS47290.1	.	.	.	.	.	.	.	.	.	.	.	11.55	1.672174	0.29693	.	.	ENSG00000254245	ENST00000253812	T	0.01705	4.68	5.65	3.29	0.37713	Cadherin (3);Cadherin-like (1);	0.260649	0.19597	U	0.110470	T	0.04227	0.0117	M	0.86097	2.795	0.26529	N	0.974297	B;B	0.19935	0.04;0.005	B;B	0.22753	0.041;0.013	T	0.12604	-1.0541	10	0.52906	T	0.07	.	9.636	0.39809	0.8582:0.0:0.1418:0.0	.	244;244	Q9Y5H0-2;Q9Y5H0	.;PCDG3_HUMAN	L	244	ENSP00000253812:Q244L	ENSP00000253812:Q244L	Q	+	2	0	PCDHGA3	140704515	0.755000	0.28372	0.725000	0.30721	0.683000	0.39861	5.208000	0.65203	0.526000	0.28541	-0.256000	0.11100	CAG	.		0.547	PCDHGA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377017.1	NM_018916	
TNK2	10188	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	3	195609127	195609127	+	Missense_Mutation	SNP	T	T	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr3:195609127T>A	ENST00000333602.6	-	6	1299	c.682A>T	c.(682-684)Act>Tct	p.T228S	TNK2_ENST00000316664.3_Missense_Mutation_p.T228S|TNK2_ENST00000428187.1_Missense_Mutation_p.T260S|TNK2_ENST00000392400.1_Missense_Mutation_p.T228S|TNK2_ENST00000381916.2_Missense_Mutation_p.T291S|TNK2_ENST00000468819.1_Intron	NM_005781.4	NP_005772.3	Q07912	ACK1_HUMAN	tyrosine kinase, non-receptor, 2	228	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell surface receptor signaling pathway (GO:0007166)|endocytosis (GO:0006897)|negative regulation of catalytic activity (GO:0043086)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphorylation (GO:0016310)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|regulation of clathrin-mediated endocytosis (GO:2000369)|small GTPase mediated signal transduction (GO:0007264)	axon (GO:0030424)|cell junction (GO:0030054)|clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|endosome (GO:0005768)|Grb2-EGFR complex (GO:0070436)|growth cone (GO:0030426)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|epidermal growth factor receptor binding (GO:0005154)|GTPase inhibitor activity (GO:0005095)|metal ion binding (GO:0046872)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)|WW domain binding (GO:0050699)			central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(11)|ovary(3)|prostate(4)|skin(2)|stomach(1)|urinary_tract(1)	29	all_cancers(143;6.48e-09)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;1.46e-22)|OV - Ovarian serous cystadenocarcinoma(49;8.3e-19)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;0.000757)	Adenosine triphosphate(DB00171)	CGGCTCAGAGTCCCCAGGAGG	0.622																																					p.T291S		.											.	.	.	0			c.A871T						.						81.0	71.0	74.0					3																	195609127		2203	4300	6503	SO:0001583	missense	10188	exon6			TCAGAGTCCCCAG	L13738	CCDS33927.1, CCDS33928.1	3q29	2013-09-02			ENSG00000061938	ENSG00000061938			19297	protein-coding gene	gene with protein product	"""activated Cdc42-associated kinase 1"""	606994				8497321, 14506255	Standard	XM_006713460		Approved	p21cdc42Hs, ACK, ACK1	uc003fvt.1	Q07912	OTTHUMG00000155737	ENST00000333602.6:c.682A>T	3.37:g.195609127T>A	ENSP00000329425:p.Thr228Ser	Somatic	70	0		WXS	Illumina HiSeq	.	48	16	NM_001010938	Q6ZMQ0|Q8N6U7|Q96H59	Missense_Mutation	SNP	ENST00000333602.6	37	CCDS33928.1	.	.	.	.	.	.	.	.	.	.	T	13.55	2.269541	0.40095	.	.	ENSG00000061938	ENST00000333602;ENST00000381916;ENST00000428187;ENST00000392400;ENST00000316664	D;D;D;D;D	0.82344	-1.6;-1.6;-1.6;-1.6;-1.6	4.74	4.74	0.60224	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.104975	0.64402	D	0.000004	T	0.75852	0.3906	L	0.37800	1.135	0.42229	D	0.991888	B;B;B;B	0.19706	0.032;0.019;0.038;0.004	B;B;B;B	0.21917	0.037;0.007;0.012;0.008	T	0.71862	-0.4464	10	0.32370	T	0.25	.	13.4876	0.61375	0.0:0.0:0.0:1.0	.	104;228;291;260	Q59FX1;Q07912;Q07912-3;C9J1X3	.;ACK1_HUMAN;.;.	S	228;291;260;228;228	ENSP00000329425:T228S;ENSP00000371341:T291S;ENSP00000392546:T260S;ENSP00000376201:T228S;ENSP00000323216:T228S	ENSP00000323216:T228S	T	-	1	0	TNK2	197093524	1.000000	0.71417	0.932000	0.37286	0.998000	0.95712	4.774000	0.62339	2.112000	0.64535	0.533000	0.62120	ACT	.		0.622	TNK2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341437.3	NM_005781	
RIT1	6016	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	155880452	155880452	+	Missense_Mutation	SNP	T	T	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr1:155880452T>A	ENST00000368323.3	-	2	305	c.101A>T	c.(100-102)aAg>aTg	p.K34M	RIT1_ENST00000368322.3_Missense_Mutation_p.K51M|RIT1_ENST00000539040.1_Intron	NM_006912.5	NP_008843.1	Q92963	RIT1_HUMAN	Ras-like without CAAX 1	34					GTP catabolic process (GO:0006184)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Ras protein signal transduction (GO:0007265)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	plasma membrane (GO:0005886)	calmodulin binding (GO:0005516)|GTP binding (GO:0005525)			breast(1)|kidney(1)|large_intestine(3)|lung(12)|skin(1)|urinary_tract(1)	19	Hepatocellular(266;0.133)|all_hematologic(923;0.145)|all_neural(408;0.195)		OV - Ovarian serous cystadenocarcinoma(3;1.79e-05)			CCTACCACTCTTCCCTACACC	0.463																																					p.K51M		.											RIT1,NS,malignant_melanoma,0,1	RIT1	0	0			c.A152T						.						147.0	150.0	149.0					1																	155880452		2203	4300	6503	SO:0001583	missense	6016	exon2			CCACTCTTCCCTA	AF084462	CCDS1123.1, CCDS58037.1, CCDS58036.1	1q21.2	2014-05-09	2002-09-11	2002-09-13	ENSG00000143622	ENSG00000143622			10023	protein-coding gene	gene with protein product	"""Ric-like, expressed in many tissues"", ""GTP-binding protein Roc1"""	609591	"""Ric (Drosophila)-like, expressed in many tissues"""	RIT		8824319, 8918462	Standard	NM_006912		Approved	RIBB, ROC1, MGC125864, MGC125865	uc031pqc.1	Q92963	OTTHUMG00000014104	ENST00000368323.3:c.101A>T	1.37:g.155880452T>A	ENSP00000357306:p.Lys34Met	Somatic	58	0		WXS	Illumina HiSeq	.	58	36	NM_001256821	B4DQE8|O00646|O00720|Q5VY89|Q5VY90	Missense_Mutation	SNP	ENST00000368323.3	37	CCDS1123.1	.	.	.	.	.	.	.	.	.	.	T	32	5.161017	0.94727	.	.	ENSG00000143622	ENST00000368323;ENST00000368322	D;D	0.96913	-4.17;-4.17	4.7	4.7	0.59300	Small GTP-binding protein domain (1);	0.000000	0.64402	D	0.000004	D	0.98947	0.9642	H	0.99582	4.64	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.98908	1.0779	10	0.87932	D	0	.	12.5409	0.56169	0.0:0.0:0.0:1.0	.	34	Q92963	RIT1_HUMAN	M	34;51	ENSP00000357306:K34M;ENSP00000357305:K51M	ENSP00000357305:K51M	K	-	2	0	RIT1	154147076	0.993000	0.37304	0.678000	0.29963	0.591000	0.36615	4.535000	0.60629	1.972000	0.57404	0.454000	0.30748	AAG	.		0.463	RIT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039593.1	NM_006912	
PCF11	51585	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	11	82877714	82877714	+	Missense_Mutation	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr11:82877714A>C	ENST00000298281.4	+	5	2227	c.1775A>C	c.(1774-1776)aAg>aCg	p.K592T		NM_015885.3	NP_056969.2	O94913	PCF11_HUMAN	PCF11 cleavage and polyadenylation factor subunit	592					gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA cleavage (GO:0006379)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	mRNA cleavage factor complex (GO:0005849)|nucleoplasm (GO:0005654)				cervix(1)|endometrium(3)|kidney(4)|large_intestine(1)|lung(22)|ovary(1)|urinary_tract(1)	33						CAAAGTTCCAAGTCTGCCAAA	0.363																																					p.K592T		.											.	.	.	0			c.A1775C						.						71.0	71.0	71.0					11																	82877714		1780	3942	5722	SO:0001583	missense	51585	exon5			GTTCCAAGTCTGC	AB020631	CCDS44689.1	11q13	2013-07-02	2013-07-02		ENSG00000165494	ENSG00000165494			30097	protein-coding gene	gene with protein product		608876	"""PCF11, cleavage and polyadenylation factor II subunit, homolog (S. cerevisiae)"", ""PCF11, cleavage and polyadenylation factor subunit, homolog (S. cerevisiae)"""			11060040	Standard	NM_015885		Approved	KIAA0824	uc001ozx.4	O94913	OTTHUMG00000167031	ENST00000298281.4:c.1775A>C	11.37:g.82877714A>C	ENSP00000298281:p.Lys592Thr	Somatic	137	0		WXS	Illumina HiSeq	.	107	48	NM_015885	A6H8W7|O43671|Q6P0X8	Missense_Mutation	SNP	ENST00000298281.4	37	CCDS44689.1	.	.	.	.	.	.	.	.	.	.	A	19.20	3.781222	0.70222	.	.	ENSG00000165494	ENST00000298281;ENST00000530660;ENST00000530304	T;T;T	0.52526	1.62;0.66;0.66	6.07	6.07	0.98685	.	0.000000	0.64402	D	0.000007	T	0.58595	0.2133	L	0.32530	0.975	0.51482	D	0.999927	D;D	0.76494	0.999;0.998	D;D	0.80764	0.994;0.987	T	0.55159	-0.8184	9	.	.	.	.	16.6406	0.85098	1.0:0.0:0.0:0.0	.	592;592	E9PQ01;O94913	.;PCF11_HUMAN	T	592	ENSP00000298281:K592T;ENSP00000434540:K592T;ENSP00000431567:K592T	.	K	+	2	0	PCF11	82555362	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	6.414000	0.73318	2.326000	0.78906	0.533000	0.62120	AAG	.		0.363	PCF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392548.2	NM_015885	
PIK3R1	5295	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	5	67522582	67522582	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr5:67522582G>T	ENST00000521381.1	+	2	695	c.79G>T	c.(79-81)Ggt>Tgt	p.G27C	PIK3R1_ENST00000396611.1_Missense_Mutation_p.G27C|PIK3R1_ENST00000274335.5_Missense_Mutation_p.G27C|PIK3R1_ENST00000521657.1_Missense_Mutation_p.G27C	NM_181523.2	NP_852664.1	P27986	P85A_HUMAN	phosphoinositide-3-kinase, regulatory subunit 1 (alpha)	27	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				B cell differentiation (GO:0030183)|blood coagulation (GO:0007596)|cellular response to UV (GO:0034644)|epidermal growth factor receptor signaling pathway (GO:0007173)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|growth hormone receptor signaling pathway (GO:0060396)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|leukocyte migration (GO:0050900)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of osteoclast differentiation (GO:0045671)|neurotrophin TRK receptor signaling pathway (GO:0048011)|NFAT protein import into nucleus (GO:0051531)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of cell migration (GO:0030335)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of glucose import (GO:0046326)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|protein phosphorylation (GO:0006468)|regulation of phosphatidylinositol 3-kinase activity (GO:0043551)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|membrane (GO:0016020)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	ErbB-3 class receptor binding (GO:0043125)|insulin binding (GO:0043559)|insulin receptor binding (GO:0005158)|insulin receptor substrate binding (GO:0043560)|insulin-like growth factor receptor binding (GO:0005159)|neurotrophin TRKA receptor binding (GO:0005168)|phosphatidylinositol 3-kinase binding (GO:0043548)|phosphatidylinositol 3-kinase regulator activity (GO:0035014)|protein phosphatase binding (GO:0019903)|transmembrane receptor protein tyrosine kinase adaptor activity (GO:0005068)	p.0?(1)		breast(12)|central_nervous_system(31)|cervix(1)|endometrium(68)|haematopoietic_and_lymphoid_tissue(5)|kidney(1)|large_intestine(32)|lung(10)|ovary(9)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	178		Lung NSC(167;1.99e-05)|Prostate(74;0.00308)|Ovarian(174;0.00473)|Colorectal(97;0.0176)		OV - Ovarian serous cystadenocarcinoma(47;3.76e-51)|Lung(70;0.0211)	Isoprenaline(DB01064)	CTTGCACTTGGGTGACATATT	0.428			"""Mis, F, O"""		"""gliobastoma, ovarian, colorectal"""					TCGA GBM(4;<1E-08)																											p.G27C		.		Rec	yes		5	5q13.1	5295	"""phosphoinositide-3-kinase, regulatory subunit 1 (alpha)"""		"""E, O"""	.	.	.	1	Whole gene deletion(1)	large_intestine(1)	c.G79T						.						82.0	82.0	82.0					5																	67522582		2203	4300	6503	SO:0001583	missense	5295	exon2			CACTTGGGTGACA	M61906	CCDS3993.1, CCDS3994.1, CCDS3995.1, CCDS56374.1	5q13.1	2014-09-17	2008-02-04		ENSG00000145675	ENSG00000145675		"""SH2 domain containing"""	8979	protein-coding gene	gene with protein product		171833				1314371, 18387942	Standard	NM_181524		Approved	GRB1, p85-ALPHA, p85	uc003jva.3	P27986	OTTHUMG00000131251	ENST00000521381.1:c.79G>T	5.37:g.67522582G>T	ENSP00000428056:p.Gly27Cys	Somatic	148	0		WXS	Illumina HiSeq	.	112	67	NM_181523	B3KT19|D3DWA0|E7EX19|Q15747|Q4VBZ7|Q53EM6|Q8IXA2|Q8N1C5	Missense_Mutation	SNP	ENST00000521381.1	37	CCDS3993.1	.	.	.	.	.	.	.	.	.	.	G	26.7	4.761898	0.89932	.	.	ENSG00000145675	ENST00000521381;ENST00000521657;ENST00000396611;ENST00000274335	T;T;T;T	0.38240	1.15;1.15;1.15;1.15	5.93	5.93	0.95920	Src homology-3 domain (3);Variant SH3 (1);	0.049268	0.85682	D	0.000000	T	0.76835	0.4043	H	0.98133	4.155	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.84965	0.0879	10	0.87932	D	0	-8.5186	20.3437	0.98782	0.0:0.0:1.0:0.0	.	27	P27986	P85A_HUMAN	C	27	ENSP00000428056:G27C;ENSP00000429277:G27C;ENSP00000379855:G27C;ENSP00000274335:G27C	ENSP00000274335:G27C	G	+	1	0	PIK3R1	67558338	1.000000	0.71417	0.999000	0.59377	0.974000	0.67602	9.869000	0.99810	2.815000	0.96918	0.561000	0.74099	GGT	.		0.428	PIK3R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254013.2	NM_181504	
ATP5S	27109	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	14	50789296	50789296	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr14:50789296G>T	ENST00000311459.7	+	3	600	c.220G>T	c.(220-222)Ggg>Tgg	p.G74W	ATP5S_ENST00000554438.1_3'UTR|ATP5S_ENST00000358473.1_Missense_Mutation_p.G46W|ATP5S_ENST00000245448.6_Missense_Mutation_p.G74W|ATP5S_ENST00000426751.2_Missense_Mutation_p.G74W	NM_001003803.2	NP_001003803.1	Q99766	ATP5S_HUMAN	ATP synthase, H+ transporting, mitochondrial Fo complex, subunit s (factor B)	74	N-terminal domain.				ATP biosynthetic process (GO:0006754)|hydrogen ion transmembrane transport (GO:1902600)|proton transport (GO:0015992)	mitochondrial inner membrane (GO:0005743)|proton-transporting ATP synthase complex, coupling factor F(o) (GO:0045263)	hydrogen ion transmembrane transporter activity (GO:0015078)|metal ion binding (GO:0046872)			breast(2)|kidney(1)|large_intestine(2)|liver(1)|lung(2)|ovary(1)|skin(2)|stomach(1)	12	all_epithelial(31;0.000636)|Breast(41;0.0102)			OV - Ovarian serous cystadenocarcinoma(311;0.0685)		GCTGCGCTGTGGGGCCATGGT	0.552																																					p.G74W		.											.	.	.	0			c.G220T						.						78.0	70.0	73.0					14																	50789296		2203	4300	6503	SO:0001583	missense	27109	exon3			CGCTGTGGGGCCA	U79253	CCDS32075.1, CCDS32076.1, CCDS45102.1	14q21.3	2011-04-13	2010-06-11			ENSG00000125375			18799	protein-coding gene	gene with protein product			"""ATP synthase, H+ transporting, mitochondrial F0 complex, subunit s (factor B)"""			11744738, 8619474	Standard	NM_015684		Approved	HSU79253, ATPW	uc001wxw.2	Q99766		ENST00000311459.7:c.220G>T	14.37:g.50789296G>T	ENSP00000308334:p.Gly74Trp	Somatic	45	0		WXS	Illumina HiSeq	.	15	5	NM_015684	A8K1U3|D9N156|Q8WWX3|Q96F77	Missense_Mutation	SNP	ENST00000311459.7	37	CCDS32075.1	.	.	.	.	.	.	.	.	.	.	G	31	5.074540	0.94000	.	.	ENSG00000125375;ENSG00000125375;ENSG00000125375;ENSG00000125375;ENSG00000258447	ENST00000245448;ENST00000426751;ENST00000311459;ENST00000358473;ENST00000553905	D;D;D;D	0.97906	-4.6;-4.6;-4.6;-4.6	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	D	0.98975	0.9651	M	0.88640	2.97	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;1.0	D	0.99585	1.0974	10	0.87932	D	0	-21.9751	20.017	0.97481	0.0:0.0:1.0:0.0	.	46;74;74;74	Q8WXQ4;Q99766-3;Q99766;Q99766-2	.;.;ATP5S_HUMAN;.	W	74;74;74;46;46	ENSP00000245448:G74W;ENSP00000389246:G74W;ENSP00000308334:G74W;ENSP00000351258:G46W	ENSP00000245448:G74W	G	+	1	0	RP11-247L20.2;ATP5S	49859046	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	9.841000	0.99482	2.723000	0.93209	0.585000	0.79938	GGG	.		0.552	ATP5S-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410761.1	NM_015684	
HOXA6	3203	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	7	27187127	27187127	+	Missense_Mutation	SNP	G	G	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr7:27187127G>C	ENST00000222728.3	-	1	266	c.242C>G	c.(241-243)tCt>tGt	p.S81C	RP1-170O19.22_ENST00000467897.2_RNA|HOXA-AS3_ENST00000518848.1_RNA|HOXA-AS3_ENST00000518947.2_RNA|HOXA-AS3_ENST00000521231.1_RNA|HOXA6_ENST00000521478.1_5'UTR|RP1-170O19.23_ENST00000498652.1_RNA|HOXA-AS3_ENST00000521197.1_RNA|HOXA-AS3_ENST00000524304.1_RNA	NM_024014.3	NP_076919.1	P31267	HXA6_HUMAN	homeobox A6	81					anterior/posterior pattern specification (GO:0009952)|embryonic skeletal system morphogenesis (GO:0048704)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|large_intestine(5)|lung(3)|ovary(1)	10						GTCCTTATCAGAATAGAAACA	0.607																																					p.S81C		.											.	.	.	0			c.C242G						.						45.0	46.0	45.0					7																	27187127		2203	4300	6503	SO:0001583	missense	3203	exon1			TTATCAGAATAGA		CCDS5407.1	7p15.2	2011-06-20	2005-12-22		ENSG00000106006	ENSG00000106006		"""Homeoboxes / ANTP class : HOXL subclass"""	5107	protein-coding gene	gene with protein product		142951	"""homeo box A6"""	HOX1B, HOX1		1973146, 1358459	Standard	NM_024014		Approved		uc003syo.2	P31267	OTTHUMG00000023216	ENST00000222728.3:c.242C>G	7.37:g.27187127G>C	ENSP00000222728:p.Ser81Cys	Somatic	52	0		WXS	Illumina HiSeq	.	32	13	NM_024014	A4D192|Q2M3G3|Q9UPM0	Missense_Mutation	SNP	ENST00000222728.3	37	CCDS5407.1	.	.	.	.	.	.	.	.	.	.	g	14.64	2.596849	0.46318	.	.	ENSG00000106006	ENST00000222728	D	0.91351	-2.83	4.89	4.89	0.63831	.	0.325822	0.24771	N	0.035727	D	0.90573	0.7045	M	0.63428	1.95	0.39495	D	0.968106	P	0.47762	0.9	B	0.43783	0.431	D	0.92392	0.5922	10	0.62326	D	0.03	.	18.0742	0.89422	0.0:0.0:1.0:0.0	.	81	P31267	HXA6_HUMAN	C	81	ENSP00000222728:S81C	ENSP00000222728:S81C	S	-	2	0	HOXA6	27153652	0.845000	0.29573	1.000000	0.80357	0.998000	0.95712	1.648000	0.37271	2.243000	0.73865	0.651000	0.88453	TCT	.		0.607	HOXA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358697.1		
SCFD1	23256	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	14	31097418	31097418	+	Missense_Mutation	SNP	C	C	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr14:31097418C>G	ENST00000458591.2	+	2	292	c.65C>G	c.(64-66)gCt>gGt	p.A22G	SCFD1_ENST00000541123.1_5'UTR|SCFD1_ENST00000396629.2_Intron|SCFD1_ENST00000421551.3_5'UTR|SCFD1_ENST00000544052.2_Intron	NM_016106.3	NP_057190.2	Q8WVM8	SCFD1_HUMAN	sec1 family domain containing 1	22					post-Golgi vesicle-mediated transport (GO:0006892)|protein transport (GO:0015031)|regulation of ER to Golgi vesicle-mediated transport (GO:0060628)|response to hypoxia (GO:0001666)|response to toxic substance (GO:0009636)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|vesicle docking involved in exocytosis (GO:0006904)	cis-Golgi network (GO:0005801)|endoplasmic reticulum (GO:0005783)|Golgi transport complex (GO:0017119)|Golgi-associated vesicle (GO:0005798)|plasma membrane (GO:0005886)	syntaxin binding (GO:0019905)			endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)	13	Hepatocellular(127;0.0877)		LUAD - Lung adenocarcinoma(48;0.00192)|Lung(238;0.0119)	GBM - Glioblastoma multiforme(265;0.0181)		TTTTCAGTGGCTTTGAAGCGT	0.318																																					p.A22G		.											.	.	.	0			c.C65G						.						78.0	81.0	80.0					14																	31097418		2203	4299	6502	SO:0001583	missense	23256	exon2			CAGTGGCTTTGAA	AF110646	CCDS9639.1, CCDS45092.1, CCDS58308.1	14q12	2006-04-04	2004-01-15	2004-01-16	ENSG00000092108	ENSG00000092108			20726	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 163"""	C14orf163			Standard	NM_016106		Approved	RA410, KIAA0917, STXBP1L2, SLY1	uc001wqm.2	Q8WVM8	OTTHUMG00000029420	ENST00000458591.2:c.65C>G	14.37:g.31097418C>G	ENSP00000390783:p.Ala22Gly	Somatic	101	0		WXS	Illumina HiSeq	.	56	21	NM_016106	A8K2Z5|B7Z4U7|B7Z594|O60754|O94990|Q7Z529|Q9BZI3|Q9UNL3|Q9Y6A8	Missense_Mutation	SNP	ENST00000458591.2	37	CCDS9639.1	.	.	.	.	.	.	.	.	.	.	C	18.63	3.665988	0.67700	.	.	ENSG00000092108	ENST00000458591	T	0.30981	1.51	5.54	5.54	0.83059	.	0.000000	0.85682	D	0.000000	T	0.23886	0.0578	N	0.08118	0	0.80722	D	1	B	0.24533	0.105	B	0.33521	0.165	T	0.14172	-1.0482	10	0.54805	T	0.06	-17.9096	18.4713	0.90776	0.0:1.0:0.0:0.0	.	22	Q8WVM8	SCFD1_HUMAN	G	22	ENSP00000390783:A22G	ENSP00000309417:A30G	A	+	2	0	SCFD1	30167169	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.325000	0.79124	2.601000	0.87937	0.655000	0.94253	GCT	.		0.318	SCFD1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276612.3	NM_182835	
ODF2	4957	hgsc.bcm.edu;broad.mit.edu	37	9	131256884	131256884	+	Missense_Mutation	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr9:131256884A>C	ENST00000434106.3	+	17	2211	c.1848A>C	c.(1846-1848)caA>caC	p.Q616H	ODF2_ENST00000546203.1_Missense_Mutation_p.Q597H|ODF2_ENST00000393527.3_Missense_Mutation_p.Q592H|ODF2_ENST00000448249.3_Missense_Mutation_p.Q535H|ODF2_ENST00000351030.3_Missense_Mutation_p.Q611H|ODF2_ENST00000393533.2_Missense_Mutation_p.Q616H|ODF2_ENST00000604420.1_Missense_Mutation_p.Q616H|ODF2_ENST00000444119.2_Missense_Mutation_p.Q592H|ODF2_ENST00000372791.3_Missense_Mutation_p.Q597H|ODF2_ENST00000372814.3_Missense_Mutation_p.Q660H|ODF2_ENST00000372807.5_Missense_Mutation_p.Q611H	NM_153433.1	NP_702911.1	Q5BJF6	ODFP2_HUMAN	outer dense fiber of sperm tails 2	616					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|multicellular organismal development (GO:0007275)|regulation of cilium assembly (GO:1902017)|spermatid development (GO:0007286)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytosol (GO:0005829)|microtubule (GO:0005874)|nucleus (GO:0005634)|outer dense fiber (GO:0001520)|primary cilium (GO:0072372)	Rab GTPase binding (GO:0017137)|structural molecule activity (GO:0005198)	p.Q616Q(1)|p.Q592Q(1)|p.Q660Q(1)		autonomic_ganglia(1)|breast(7)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(7)|lung(8)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	37						GCCAAGACCAACTGCAGGGCT	0.587																																					p.Q680H		.											ODF2_ENST00000372814,NS,carcinoma,0,2	ODF2_ENST00000372814	0	3	Substitution - coding silent(3)	kidney(3)	c.A2040C						.						77.0	67.0	71.0					9																	131256884		2203	4300	6503	SO:0001583	missense	4957	exon17			AGACCAACTGCAG	AF012549	CCDS6902.1, CCDS56585.1, CCDS56586.1, CCDS56587.1, CCDS56588.1, CCDS56589.1, CCDS56590.1	9q34	2010-04-23	2002-10-21		ENSG00000136811	ENSG00000136811			8114	protein-coding gene	gene with protein product	"""cancer/testis antigen 134"""	602015	"""outer dense fibre of sperm tails 2"""			9045620, 10072582	Standard	NM_153435		Approved	ODF84, CT134	uc004bvc.3	Q5BJF6	OTTHUMG00000020748	ENST00000434106.3:c.1848A>C	9.37:g.131256884A>C	ENSP00000403453:p.Gln616His	Somatic	16	0		WXS	Illumina HiSeq	.	13	4	NM_153435	B1AND3|B4DRK4|B4DX73|B4DZ02|E7EWL2|F5H6J4|O14721|O60631|Q1W2J6|Q6UN26|Q7Z5I6|Q96FN2	Missense_Mutation	SNP	ENST00000434106.3	37	CCDS56588.1	.	.	.	.	.	.	.	.	.	.	A	18.31	3.596863	0.66332	.	.	ENSG00000136811	ENST00000393533;ENST00000372814;ENST00000351030;ENST00000372796;ENST00000303890;ENST00000448249;ENST00000546203;ENST00000372791	T;D;D;D;D;D;T;T	0.83992	1.36;-1.79;-1.73;-1.73;-1.73;-1.79;1.38;1.38	5.4	3.55	0.40652	.	0.183924	0.48767	D	0.000164	D	0.83885	0.5351	L	0.43152	1.355	0.80722	D	1	D;D;D;D;D;D;D	0.71674	0.994;0.996;0.994;0.996;0.994;0.996;0.998	P;P;P;P;P;P;P	0.62560	0.861;0.892;0.861;0.904;0.861;0.892;0.892	T	0.83005	-0.0175	10	0.54805	T	0.06	-27.1705	7.5816	0.27967	0.26:0.0:0.74:0.0	.	597;611;535;616;597;616;592	Q5BJF6-8;Q5BJF6-4;Q5BJF6-9;B4DX73;Q5BJF6-5;Q5BJF6;Q5BJF6-3	.;.;.;.;.;ODFP2_HUMAN;.	H	616;660;611;616;592;535;597;597	ENSP00000377166:Q616H;ENSP00000361901:Q660H;ENSP00000342581:Q611H;ENSP00000361882:Q616H;ENSP00000307781:Q592H;ENSP00000396687:Q535H;ENSP00000437579:Q597H;ENSP00000361877:Q597H	ENSP00000307781:Q592H	Q	+	3	2	ODF2	130296705	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	1.590000	0.36654	1.257000	0.44085	-0.366000	0.07423	CAA	.		0.587	ODF2-011	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054449.3		
DNAJC16	23341	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	15855658	15855658	+	Silent	SNP	C	C	T	rs370972086	byFrequency	TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr1:15855658C>T	ENST00000375847.3	+	2	222	c.58C>T	c.(58-60)Ctg>Ttg	p.L20L	CASP9_ENST00000469637.1_5'Flank|DNAJC16_ENST00000375849.1_Silent_p.L20L|DNAJC16_ENST00000375838.1_Silent_p.L20L	NM_015291.2	NP_056106.1	Q9Y2G8	DJC16_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 16	20					cell redox homeostasis (GO:0045454)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(4)|lung(7)|urinary_tract(1)	18		Colorectal(325;0.00108)|Renal(390;0.00145)|Breast(348;0.00173)|all_lung(284;0.00459)|Lung NSC(340;0.00499)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0798)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;9.18e-07)|COAD - Colon adenocarcinoma(227;4.5e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000133)|KIRC - Kidney renal clear cell carcinoma(229;0.00262)|STAD - Stomach adenocarcinoma(313;0.00774)|READ - Rectum adenocarcinoma(331;0.0657)		GGTTCTGATCCTGCAAATTCT	0.448													C|||	2	0.000399361	0.0	0.0	5008	,	,		17330	0.002		0.0	False		,,,				2504	0.0				p.L20L		.											.	.	.	0			c.C58T						.						160.0	151.0	154.0					1																	15855658		2203	4300	6503	SO:0001819	synonymous_variant	23341	exon2			CTGATCCTGCAAA	AB023179	CCDS30606.1, CCDS72710.1	1p36.1	2011-09-02			ENSG00000116138	ENSG00000116138		"""Heat shock proteins / DNAJ (HSP40)"""	29157	protein-coding gene	gene with protein product							Standard	NM_015291		Approved	KIAA0962	uc001aws.3	Q9Y2G8	OTTHUMG00000002358	ENST00000375847.3:c.58C>T	1.37:g.15855658C>T		Somatic	106	0		WXS	Illumina HiSeq	.	81	34	NM_015291	Q68D57|Q86X32|Q8N5P4	Silent	SNP	ENST00000375847.3	37	CCDS30606.1																																																																																			.		0.448	DNAJC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006764.1	NM_015291	
DPY19L2P2	349152	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	7	102920615	102920615	+	RNA	SNP	T	T	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr7:102920615T>C	ENST00000312132.4	-	0	242							Q6ZN68	D19P2_HUMAN	DPY19L2 pseudogene 2							integral component of membrane (GO:0016021)	transferase activity, transferring glycosyl groups (GO:0016757)										CTAGTGGAGCTGGGTCAATTT	0.632																																					.		.											.	.	.	0			.						.																																					349152	.			TGGAGCTGGGTCA	AL834175		7q22.1	2013-09-12	2013-09-12		ENSG00000170629	ENSG00000170629			21764	pseudogene	pseudogene			"""dpy-19-like 2 pseudogene 2 (C. elegans)"""				Standard	NR_027768		Approved	DKFZp434E092, FLJ36166	uc003vbh.4	Q6ZN68	OTTHUMG00000157200		7.37:g.102920615T>C		Somatic	50	0		WXS	Illumina HiSeq	.	22	9	.	Q8N9V4|Q8ND62	RNA	SNP	ENST00000312132.4	37																																																																																				.		0.632	DPY19L2P2-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000347877.1	NM_182634	
TRAPPC9	83696	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	8	141415702	141415702	+	Nonsense_Mutation	SNP	T	T	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr8:141415702T>A	ENST00000438773.2	-	6	1115	c.982A>T	c.(982-984)Aaa>Taa	p.K328*	TRAPPC9_ENST00000389328.4_Nonsense_Mutation_p.K426*|TRAPPC9_ENST00000389327.3_Nonsense_Mutation_p.K319*	NM_001160372.1	NP_001153844.1	Q96Q05	TPPC9_HUMAN	trafficking protein particle complex 9	328					cell differentiation (GO:0030154)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)				breast(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(1)|lung(16)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	47						ATCGCCTCTTTATACTTGTCA	0.408																																					p.K426X		.											.	.	.	0			c.A1276T						.						155.0	132.0	140.0					8																	141415702		2203	4300	6503	SO:0001587	stop_gained	83696	exon6			CCTCTTTATACTT	BC006206	CCDS34946.1, CCDS55278.1	8q24.3	2010-10-22			ENSG00000167632	ENSG00000167632		"""Trafficking protein particle complex"""	30832	protein-coding gene	gene with protein product	"""TRAPP 120 kDa subunit"", ""tularik gene 1"""	611966				11572484	Standard	NM_031466		Approved	IKBKBBP, NIBP, KIAA1882, T1, TRS120, MRT13	uc003yvh.2	Q96Q05	OTTHUMG00000164187	ENST00000438773.2:c.982A>T	8.37:g.141415702T>A	ENSP00000405060:p.Lys328*	Somatic	67	0		WXS	Illumina HiSeq	.	38	16	NM_031466	Q4VTT3|Q658K7|Q6P149|Q6ZQT3|Q7L5C4|Q86Y21|Q96SL2|Q9BQA2	Nonsense_Mutation	SNP	ENST00000438773.2	37	CCDS55278.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	32|32	5.163705|5.163705	0.94727|0.94727	.|.	.|.	ENSG00000167632|ENSG00000167632	ENST00000389328;ENST00000389327;ENST00000438773|ENST00000520857	.|.	.|.	.|.	5.7|5.7	5.7|5.7	0.88788|0.88788	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	.|.	.|.	.|.	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	0.02654|.	T|.	1|.	.|.	14.9535|14.9535	0.71094|0.71094	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|.	.|.	.|.	X|L	426;319;328|171	.|.	ENSP00000373978:K319X|.	K|X	-|-	1|2	0|2	TRAPPC9|TRAPPC9	141484884|141484884	1.000000|1.000000	0.71417|0.71417	0.935000|0.935000	0.37517|0.37517	0.969000|0.969000	0.65631|0.65631	5.284000|5.284000	0.65627|0.65627	2.175000|2.175000	0.68902|0.68902	0.533000|0.533000	0.62120|0.62120	AAA|TAA	.		0.408	TRAPPC9-002	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000377749.1	NM_031466	
RPRD1B	58490	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	20	36694651	36694651	+	Missense_Mutation	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr20:36694651A>C	ENST00000373433.4	+	6	1226	c.824A>C	c.(823-825)aAa>aCa	p.K275T		NM_021215.3	NP_067038.1	Q9NQG5	RPR1B_HUMAN	regulation of nuclear pre-mRNA domain containing 1B	275					dephosphorylation of RNA polymerase II C-terminal domain (GO:0070940)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell cycle process (GO:0010564)|transcription, DNA-templated (GO:0006351)	DNA-directed RNA polymerase II, holoenzyme (GO:0016591)|nucleus (GO:0005634)	RNA polymerase II core binding (GO:0000993)			endometrium(3)|kidney(1)|large_intestine(2)|lung(4)|pancreas(1)|skin(1)	12						AAGGAGAAAAAACTAGAGGTG	0.488																																					p.K275T		.											.	.	.	0			c.A824C						.						68.0	77.0	74.0					20																	36694651		2203	4300	6503	SO:0001583	missense	58490	exon6			AGAAAAAACTAGA	AL109823	CCDS13301.1	20q11.21-q12	2012-02-09	2008-08-15	2008-07-28	ENSG00000101413	ENSG00000101413			16209	protein-coding gene	gene with protein product		614694	"""chromosome 20 open reading frame 77"""	C20orf77		22231121	Standard	NM_021215		Approved	dJ1057B20.2, DKFZp434P0735, CREPT, FLJ44520, NET60	uc002xho.4	Q9NQG5	OTTHUMG00000032434	ENST00000373433.4:c.824A>C	20.37:g.36694651A>C	ENSP00000362532:p.Lys275Thr	Somatic	48	0		WXS	Illumina HiSeq	.	30	10	NM_021215	Q1WDE7|Q6PKF4	Missense_Mutation	SNP	ENST00000373433.4	37	CCDS13301.1	.	.	.	.	.	.	.	.	.	.	A	19.06	3.754525	0.69648	.	.	ENSG00000101413	ENST00000373433;ENST00000449186	.	.	.	5.35	5.35	0.76521	.	0.040629	0.85682	D	0.000000	T	0.52419	0.1733	L	0.55743	1.74	0.80722	D	1	P	0.39883	0.693	B	0.36378	0.223	T	0.55140	-0.8187	9	0.39692	T	0.17	-16.7168	14.958	0.71131	1.0:0.0:0.0:0.0	.	275	Q9NQG5	RPR1B_HUMAN	T	275;157	.	ENSP00000362532:K275T	K	+	2	0	RPRD1B	36128065	1.000000	0.71417	0.997000	0.53966	0.910000	0.53928	7.310000	0.78947	2.371000	0.80710	0.533000	0.62120	AAA	.		0.488	RPRD1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079142.2	NM_021215	
NDN	4692	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	15	23931983	23931983	+	Missense_Mutation	SNP	C	C	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr15:23931983C>T	ENST00000331837.4	-	1	467	c.382G>A	c.(382-384)Gtc>Atc	p.V128I		NM_002487.2	NP_002478.1	Q99608	NECD_HUMAN	necdin, melanoma antigen (MAGE) family member	128	MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.				axon extension (GO:0048675)|axonal fasciculation (GO:0007413)|central nervous system development (GO:0007417)|genetic imprinting (GO:0071514)|glial cell migration (GO:0008347)|multicellular organismal homeostasis (GO:0048871)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neuron migration (GO:0001764)|neurotrophin TRK receptor signaling pathway (GO:0048011)|post-embryonic development (GO:0009791)|regulation of growth (GO:0040008)|regulation of transcription, DNA-templated (GO:0006355)|respiratory system process (GO:0003016)|sensory perception of pain (GO:0019233)|transcription, DNA-templated (GO:0006351)	cell projection (GO:0042995)|centrosome (GO:0005813)|cytosol (GO:0005829)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(2)|endometrium(3)|kidney(2)|large_intestine(5)|lung(23)|ovary(1)|prostate(2)|skin(1)	39		all_cancers(20;1.78e-24)|all_epithelial(15;7.75e-22)|Lung NSC(15;2.96e-18)|all_lung(15;2.8e-17)|Breast(32;0.000625)|Colorectal(260;0.14)		all cancers(64;8.37e-11)|Epithelial(43;9.29e-10)|BRCA - Breast invasive adenocarcinoma(123;0.00179)|GBM - Glioblastoma multiforme(186;0.018)|Lung(196;0.153)		CTGCCGATGACATCTTTCACC	0.597									Prader-Willi syndrome																												p.V128I		.											.	.	.	0			c.G382A						.						90.0	84.0	86.0					15																	23931983		2203	4300	6503	SO:0001583	missense	4692	exon1	Familial Cancer Database	Prader-Labhart-Willi syndrome	CGATGACATCTTT	U35139	CCDS10014.1	15q11-q12	2012-12-07	2012-12-07		ENSG00000182636	ENSG00000182636			7675	protein-coding gene	gene with protein product	"""Prader-Willi syndrome chromosome region"""	602117	"""necdin (mouse) homolog"", ""necdin homolog (mouse)"""			9302265	Standard	NM_002487		Approved	HsT16328, PWCR	uc001ywk.3	Q99608	OTTHUMG00000129161	ENST00000331837.4:c.382G>A	15.37:g.23931983C>T	ENSP00000332643:p.Val128Ile	Somatic	39	0		WXS	Illumina HiSeq	.	26	13	NM_002487	B2R6Z5	Missense_Mutation	SNP	ENST00000331837.4	37	CCDS10014.1	.	.	.	.	.	.	.	.	.	.	C	16.09	3.024009	0.54683	.	.	ENSG00000182636	ENST00000331837	T	0.05513	3.43	3.87	2.94	0.34122	.	0.000000	0.64402	D	0.000001	T	0.06371	0.0164	N	0.13327	0.33	0.34848	D	0.741379	P	0.45715	0.865	P	0.54706	0.759	T	0.42531	-0.9446	10	0.19147	T	0.46	.	6.4168	0.21721	0.0:0.87:0.0:0.13	.	128	Q99608	NECD_HUMAN	I	128	ENSP00000332643:V128I	ENSP00000332643:V128I	V	-	1	0	NDN	21483076	1.000000	0.71417	0.999000	0.59377	0.993000	0.82548	1.263000	0.33004	2.110000	0.64415	0.561000	0.74099	GTC	.		0.597	NDN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251226.2	NM_002487	
ANKRD42	338699	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	11	82935942	82935942	+	Missense_Mutation	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr11:82935942T>G	ENST00000393392.2	+	6	710	c.548T>G	c.(547-549)cTa>cGa	p.L183R	ANKRD42_ENST00000260047.6_Missense_Mutation_p.L210R|ANKRD42_ENST00000533342.1_Missense_Mutation_p.L211R|ANKRD42_ENST00000531895.1_Missense_Mutation_p.L211R	NM_182603.2	NP_872409.2	Q8N9B4	ANR42_HUMAN	ankyrin repeat domain 42	183					positive regulation of cytokine production involved in inflammatory response (GO:1900017)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)	nucleus (GO:0005634)				central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(6)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	18						TTCAAATTCCTAGTCAGTAGA	0.338																																					p.L183R		.											.	.	.	0			c.T548G						.						84.0	86.0	86.0					11																	82935942		2203	4300	6503	SO:0001583	missense	338699	exon6			AATTCCTAGTCAG	AK095193	CCDS8265.1, CCDS73355.1, CCDS73356.1	11q14.1	2014-06-12			ENSG00000137494	ENSG00000137494		"""Ankyrin repeat domain containing"""	26752	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 79"""						Standard	XM_005273971		Approved	FLJ37874, SARP, PPP1R79	uc001ozz.1	Q8N9B4	OTTHUMG00000167075	ENST00000393392.2:c.548T>G	11.37:g.82935942T>G	ENSP00000377051:p.Leu183Arg	Somatic	112	0		WXS	Illumina HiSeq	.	81	34	NM_182603	Q49A49	Missense_Mutation	SNP	ENST00000393392.2	37	CCDS8265.1	.	.	.	.	.	.	.	.	.	.	T	21.0	4.080183	0.76528	.	.	ENSG00000137494	ENST00000545672;ENST00000260047;ENST00000531895;ENST00000393392;ENST00000533342	T;T;T;T	0.80824	-1.42;-1.42;-1.42;-1.42	5.67	5.67	0.87782	Ankyrin repeat-containing domain (4);	0.000000	0.47455	D	0.000221	D	0.91576	0.7339	M	0.91663	3.23	0.48571	D	0.999671	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.999;0.999;0.999	D	0.93239	0.6624	9	.	.	.	-2.8408	14.8967	0.70649	0.0:0.0:0.0:1.0	.	211;475;302;183	E9PIL2;A1DRY3;A1XPJ0;Q8N9B4	.;.;.;ANR42_HUMAN	R	530;210;211;183;211	ENSP00000260047:L210R;ENSP00000434666:L211R;ENSP00000377051:L183R;ENSP00000435790:L211R	.	L	+	2	0	ANKRD42	82613590	1.000000	0.71417	1.000000	0.80357	0.933000	0.57130	5.427000	0.66483	2.154000	0.67381	0.533000	0.62120	CTA	.		0.338	ANKRD42-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000392934.1	NM_182603	
CHD1	1105	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	5	98240741	98240741	+	Missense_Mutation	SNP	T	T	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr5:98240741T>C	ENST00000284049.3	-	2	264	c.115A>G	c.(115-117)Agt>Ggt	p.S39G		NM_001270.2	NP_001261.2	O14646	CHD1_HUMAN	chromodomain helicase DNA binding protein 1	39	Ser-rich.				chromatin modification (GO:0016568)|DNA duplex unwinding (GO:0032508)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|methylated histone binding (GO:0035064)			NS(1)|breast(4)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(12)|ovary(2)|pancreas(1)|prostate(7)|skin(3)|urinary_tract(2)	49		all_cancers(142;5.36e-08)|all_epithelial(76;6.97e-11)|Lung NSC(167;0.000693)|Prostate(80;0.000986)|all_lung(232;0.00119)|Ovarian(225;0.024)|Colorectal(57;0.117)		COAD - Colon adenocarcinoma(37;0.0717)	Epirubicin(DB00445)	CCATCACTACTGCTTCCAGAA	0.448																																					p.S39G		.											.	.	.	0			c.A115G						.						120.0	124.0	123.0					5																	98240741		2203	4300	6503	SO:0001583	missense	1105	exon2			CACTACTGCTTCC	AF006513	CCDS34204.1	5q15-q21	2008-07-18			ENSG00000153922	ENSG00000153922			1915	protein-coding gene	gene with protein product		602118				8460153, 9326634	Standard	XM_005271866		Approved		uc003knf.3	O14646	OTTHUMG00000162744	ENST00000284049.3:c.115A>G	5.37:g.98240741T>C	ENSP00000284049:p.Ser39Gly	Somatic	40	0		WXS	Illumina HiSeq	.	23	10	NM_001270	Q17RZ3	Missense_Mutation	SNP	ENST00000284049.3	37	CCDS34204.1	.	.	.	.	.	.	.	.	.	.	T	19.08	3.757632	0.69648	.	.	ENSG00000153922	ENST00000284049;ENST00000540681	D	0.90069	-2.61	4.85	4.85	0.62838	.	0.000000	0.39274	U	0.001413	D	0.91882	0.7430	M	0.66939	2.045	0.80722	D	1	P	0.49447	0.924	P	0.60682	0.878	D	0.89410	0.3702	10	0.13108	T	0.6	.	15.141	0.72609	0.0:0.0:0.0:1.0	.	39	O14646	CHD1_HUMAN	G	39	ENSP00000284049:S39G	ENSP00000284049:S39G	S	-	1	0	CHD1	98268641	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.568000	0.82369	2.120000	0.65058	0.460000	0.39030	AGT	.		0.448	CHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370295.1	NM_001270	
CTR9	9646	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	11	10785962	10785962	+	Silent	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr11:10785962T>G	ENST00000361367.2	+	11	1818	c.1392T>G	c.(1390-1392)ctT>ctG	p.L464L		NM_014633.3	NP_055448.1	Q6PD62	CTR9_HUMAN	CTR9, Paf1/RNA polymerase II complex component	464					cellular response to lipopolysaccharide (GO:0071222)|endodermal cell fate commitment (GO:0001711)|histone H2B ubiquitination (GO:0033523)|histone H3-K4 trimethylation (GO:0080182)|histone monoubiquitination (GO:0010390)|interleukin-6-mediated signaling pathway (GO:0070102)|JAK-STAT cascade (GO:0007259)|negative regulation of myeloid cell differentiation (GO:0045638)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of histone H3-K79 methylation (GO:2001162)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	Cdc73/Paf1 complex (GO:0016593)|transcriptionally active chromatin (GO:0035327)				breast(4)|central_nervous_system(2)|cervix(1)|endometrium(7)|kidney(3)|large_intestine(7)|lung(12)|ovary(2)|pancreas(1)|stomach(1)	40				all cancers(16;1.64e-07)|Epithelial(150;2.47e-07)|BRCA - Breast invasive adenocarcinoma(625;0.111)		ATTTTAGACTTGGAAACCTAG	0.398																																					p.L464L		.											.	.	.	0			c.T1392G						.						92.0	94.0	93.0					11																	10785962		2201	4294	6495	SO:0001819	synonymous_variant	9646	exon11			TAGACTTGGAAAC	D63875	CCDS7805.1	11p15.3	2013-07-03	2013-07-03	2006-05-22	ENSG00000198730	ENSG00000198730		"""Tetratricopeptide (TTC) repeat domain containing"""	16850	protein-coding gene	gene with protein product		609366	"""SH2 domain binding protein 1 (tetratricopeptide repeat containing)"", ""Ctr9, Paf1/RNA polymerase II complex component, homolog (S. cerevisiae)"""	SH2BP1		8590280, 8636124	Standard	NM_014633		Approved	KIAA0155, TSBP, p150TSP	uc001mja.3	Q6PD62	OTTHUMG00000165789	ENST00000361367.2:c.1392T>G	11.37:g.10785962T>G		Somatic	62	0		WXS	Illumina HiSeq	.	42	17	NM_014633	D3DQV8|Q15015	Silent	SNP	ENST00000361367.2	37	CCDS7805.1																																																																																			.		0.398	CTR9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386215.1	NM_014633	
RPTN	126638	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	152129066	152129066	+	Missense_Mutation	SNP	T	T	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr1:152129066T>C	ENST00000316073.3	-	3	573	c.509A>G	c.(508-510)cAc>cGc	p.H170R		NM_001122965.1	NP_001116437.1	Q6XPR3	RPTN_HUMAN	repetin	170	Gln-rich.					cornified envelope (GO:0001533)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)	p.G159_H170delGQSEKQDRDSHH(1)		breast(2)|central_nervous_system(1)|endometrium(14)|kidney(2)|large_intestine(1)|lung(32)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	59						AGGCTGACTGTGGTGGGAATC	0.483																																					p.H170R		.											.,15	.	123	1	Deletion - In frame(1)	stomach(1)	c.A509G						.						486.0	419.0	440.0					1																	152129066		1568	3582	5150	SO:0001583	missense	126638	exon3			TGACTGTGGTGGG	AK096436	CCDS41397.1	1q21.3	2013-01-10			ENSG00000215853	ENSG00000215853		"""EF-hand domain containing"""	26809	protein-coding gene	gene with protein product		613259				15854042	Standard	NM_001122965		Approved	FLJ39117	uc001ezs.1	Q6XPR3	OTTHUMG00000154095	ENST00000316073.3:c.509A>G	1.37:g.152129066T>C	ENSP00000317895:p.His170Arg	Somatic	94	0		WXS	Illumina HiSeq	.	70	10	NM_001122965	B7ZBZ3	Missense_Mutation	SNP	ENST00000316073.3	37	CCDS41397.1	.	.	.	.	.	.	.	.	.	.	T	9.768	1.171947	0.21704	.	.	ENSG00000215853	ENST00000316073	T	0.13196	2.61	5.18	1.25	0.21368	.	1.717380	0.04185	N	0.327283	T	0.03434	0.0099	L	0.34521	1.04	0.09310	N	1	B	0.11235	0.004	B	0.08055	0.003	T	0.41124	-0.9526	10	0.25106	T	0.35	0.0335	7.7237	0.28746	0.0:0.2679:0.0:0.7321	.	170	Q6XPR3	RPTN_HUMAN	R	170	ENSP00000317895:H170R	ENSP00000317895:H170R	H	-	2	0	RPTN	150395690	0.000000	0.05858	0.001000	0.08648	0.025000	0.11179	0.035000	0.13797	0.241000	0.21283	0.448000	0.29417	CAC	.		0.483	RPTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333867.1	XM_371312	
SLC16A10	117247	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	6	111498823	111498823	+	Silent	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr6:111498823A>C	ENST00000368851.5	+	3	1072	c.897A>C	c.(895-897)ggA>ggC	p.G299G	SLC16A10_ENST00000368850.3_5'UTR|SLC16A10_ENST00000465319.1_3'UTR	NM_018593.4	NP_061063.2	Q8TF71	MOT10_HUMAN	solute carrier family 16 (aromatic amino acid transporter), member 10	299					amino acid transport (GO:0006865)|aromatic amino acid transport (GO:0015801)|ion transport (GO:0006811)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|prostate(2)	12		all_cancers(87;0.00172)|Acute lymphoblastic leukemia(125;2.27e-07)|all_hematologic(75;1.38e-05)|all_epithelial(87;0.0313)|Colorectal(196;0.0466)		OV - Ovarian serous cystadenocarcinoma(136;0.0703)|Epithelial(106;0.12)|all cancers(137;0.132)	Droxidopa(DB06262)|Glycine(DB00145)|L-Alanine(DB00160)|L-Arginine(DB00125)|L-Asparagine(DB00174)|L-Aspartic Acid(DB00128)|L-Cysteine(DB00151)|L-Cystine(DB00138)|L-DOPA(DB01235)|L-Glutamine(DB00130)|L-Histidine(DB00117)|L-Isoleucine(DB00167)|L-Leucine(DB00149)|L-Lysine(DB00123)|L-Methionine(DB00134)|L-Phenylalanine(DB00120)|L-Proline(DB00172)|L-Serine(DB00133)|L-Threonine(DB00156)|L-Tryptophan(DB00150)|L-Tyrosine(DB00135)|L-Valine(DB00161)|Liothyronine(DB00279)|Liotrix(DB01583)|Pyruvic acid(DB00119)	GGGCAGTTGGAATACCACTTG	0.383																																					p.G299G		.											.	.	.	0			c.A897C						.						91.0	88.0	89.0					6																	111498823		2203	4300	6503	SO:0001819	synonymous_variant	117247	exon3			AGTTGGAATACCA	AF116652	CCDS5089.1	6q21-q22	2014-01-28	2013-07-18		ENSG00000112394	ENSG00000112394		"""Solute carriers"""	17027	protein-coding gene	gene with protein product		607550	"""solute carrier family 16 (monocarboxylic acid transporters), member 10"""			11278508, 11827462	Standard	NM_018593		Approved	TAT1, MCT10	uc003pus.3	Q8TF71	OTTHUMG00000015371	ENST00000368851.5:c.897A>C	6.37:g.111498823A>C		Somatic	11	0		WXS	Illumina HiSeq	.	13	6	NM_018593	B3KWY0|Q6ZMG0|Q8WVI5	Silent	SNP	ENST00000368851.5	37	CCDS5089.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	9.030|9.030	0.987111|0.987111	0.18889|0.18889	.|.	.|.	ENSG00000112394|ENSG00000112394	ENST00000419619;ENST00000439288|ENST00000535637	.|.	.|.	.|.	5.41|5.41	2.83|2.83	0.33086|0.33086	.|.	.|.	.|.	.|.	.|.	T|T	0.41119|0.41119	0.1145|0.1145	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.33189|0.33189	-0.9878|-0.9878	4|5	.|0.39692	.|T	.|0.17	.|.	5.4609|5.4609	0.16615|0.16615	0.5966:0.1362:0.2671:0.0|0.5966:0.1362:0.2671:0.0	.|.	.|.	.|.	.|.	A|H	185|299	.|.	.|ENSP00000439389:N299H	E|N	+|+	2|1	0|0	SLC16A10|SLC16A10	111605516|111605516	0.781000|0.781000	0.28676|0.28676	1.000000|1.000000	0.80357|0.80357	0.963000|0.963000	0.63663|0.63663	0.001000|0.001000	0.13038|0.13038	0.357000|0.357000	0.24183|0.24183	0.460000|0.460000	0.39030|0.39030	GAA|AAT	.		0.383	SLC16A10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041822.2		
CNBD2	140894	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	20	34568459	34568459	+	Missense_Mutation	SNP	T	T	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr20:34568459T>A	ENST00000373973.3	+	4	495	c.322T>A	c.(322-324)Tgt>Agt	p.C108S	CNBD2_ENST00000538900.1_Missense_Mutation_p.C108S|CNBD2_ENST00000349339.1_Missense_Mutation_p.C108S			Q96M20	CNBD2_HUMAN	cyclic nucleotide binding domain containing 2	108																	CCAGGCCGTCTGTAACATCTT	0.552																																					p.C108S		.											.	.	.	0			c.T322A						.						106.0	87.0	93.0					20																	34568459		2203	4300	6503	SO:0001583	missense	140894	exon4			GCCGTCTGTAACA	AL359828	CCDS13270.1, CCDS56189.1	20q11.23	2012-11-15	2012-11-15	2012-11-15	ENSG00000149646	ENSG00000149646			16145	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 152"", ""cyclic nucleotide (cNMP) binding domain containing 1"""	C20orf152, CNMPD1		11780052	Standard	NM_080834		Approved	dJ954P9.1	uc002xer.1	Q96M20	OTTHUMG00000032371	ENST00000373973.3:c.322T>A	20.37:g.34568459T>A	ENSP00000363084:p.Cys108Ser	Somatic	50	0		WXS	Illumina HiSeq	.	45	22	NM_080834	Q14C79|Q5JWY7|Q5T3S1|Q9BR36|Q9BWY5	Missense_Mutation	SNP	ENST00000373973.3	37		.	.	.	.	.	.	.	.	.	.	T	15.63	2.890669	0.52014	.	.	ENSG00000149646	ENST00000373973;ENST00000349339;ENST00000538900	D;D;D	0.83755	-1.76;-1.76;-1.76	5.15	4.04	0.47022	Cyclic nucleotide-binding-like (1);RmlC-like jelly roll fold (1);	0.152029	0.46758	D	0.000274	D	0.85695	0.5756	M	0.66939	2.045	0.31495	N	0.665472	D;D	0.62365	0.988;0.991	P;P	0.59595	0.709;0.86	T	0.83263	-0.0047	10	0.33940	T	0.23	-10.3153	6.7961	0.23727	0.0:0.1828:0.0:0.8172	.	108;108	Q96M20;Q96M20-2	CT152_HUMAN;.	S	108	ENSP00000363084:C108S;ENSP00000340954:C108S;ENSP00000442729:C108S	ENSP00000340954:C108S	C	+	1	0	C20orf152	34031873	0.215000	0.23574	0.225000	0.23894	0.004000	0.04260	0.724000	0.25954	0.799000	0.34018	-0.290000	0.09829	TGT	.		0.552	CNBD2-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000078960.2	NM_080834	
FAM208B	54906	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	10	5803315	5803315	+	Missense_Mutation	SNP	T	T	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr10:5803315T>C	ENST00000328090.5	+	19	7680	c.7055T>C	c.(7054-7056)aTt>aCt	p.I2352T		NM_017782.4	NP_060252	Q5VWN6	F208B_HUMAN	family with sequence similarity 208, member B	2352																	GCAAATATCATTGAATTGCTT	0.343																																					p.I2352T		.											.	.	.	0			c.T7055C						.						120.0	113.0	115.0					10																	5803315		1883	4112	5995	SO:0001583	missense	54906	exon19			ATATCATTGAATT	BX649177	CCDS41485.1	10p15.1	2011-09-14	2011-09-14	2011-09-14	ENSG00000108021	ENSG00000108021			23484	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 18"""	C10orf18		12477932	Standard	NM_017782		Approved	FLJ20360, bA318E3.2, KIAA2006	uc001iij.3	Q5VWN6	OTTHUMG00000017605	ENST00000328090.5:c.7055T>C	10.37:g.5803315T>C	ENSP00000328426:p.Ile2352Thr	Somatic	76	0		WXS	Illumina HiSeq	.	38	18	NM_017782	Q2YD91|Q5VWN5|Q6ZRQ8|Q8IVG4|Q9BUZ7|Q9H5J9|Q9H7A4|Q9H996|Q9NXA1	Missense_Mutation	SNP	ENST00000328090.5	37	CCDS41485.1	.	.	.	.	.	.	.	.	.	.	T	14.47	2.543879	0.45280	.	.	ENSG00000108021	ENST00000328090;ENST00000442808	T	0.46819	0.86	6.06	4.93	0.64822	.	0.374660	0.25869	N	0.027766	T	0.42040	0.1185	M	0.72118	2.19	0.34363	D	0.691188	P	0.38788	0.647	B	0.28553	0.091	T	0.60652	-0.7221	10	0.87932	D	0	.	9.5778	0.39468	0.0:0.1413:0.0:0.8587	.	2352	Q5VWN6	F208B_HUMAN	T	2352;1547	ENSP00000328426:I2352T	ENSP00000328426:I2352T	I	+	2	0	C10orf18	5843321	0.143000	0.22626	0.779000	0.31741	0.223000	0.24884	2.874000	0.48483	1.120000	0.41904	0.528000	0.53228	ATT	.		0.343	FAM208B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046571.2	NM_017782	
VWA8	23078	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	13	42357983	42357983	+	Missense_Mutation	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr13:42357983T>G	ENST00000379310.3	-	19	2293	c.2225A>C	c.(2224-2226)aAt>aCt	p.N742T	VWA8_ENST00000281496.6_Missense_Mutation_p.N742T	NM_015058.1	NP_055873.1	A3KMH1	VWA8_HUMAN	von Willebrand factor A domain containing 8	742						extracellular region (GO:0005576)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)										CTCATGTGCATTATAGATCGG	0.378																																					p.N742T		.											.	.	.	0			c.A2225C						.						140.0	118.0	126.0					13																	42357983		2203	4300	6503	SO:0001583	missense	23078	exon19			TGTGCATTATAGA	AB011136	CCDS31963.1, CCDS41881.1	13q14.11	2013-11-18	2012-08-02	2012-08-02	ENSG00000102763	ENSG00000102763			29071	protein-coding gene	gene with protein product			"""KIAA0564"""	KIAA0564		9628581	Standard	NM_015058		Approved		uc001uyj.3	A3KMH1	OTTHUMG00000016799	ENST00000379310.3:c.2225A>C	13.37:g.42357983T>G	ENSP00000368612:p.Asn742Thr	Somatic	83	0		WXS	Illumina HiSeq	.	54	14	NM_015058	O60310|Q5JTP6|Q5VW08|Q7Z6I9|Q86YC9|Q8N3E4	Missense_Mutation	SNP	ENST00000379310.3	37	CCDS41881.1	.	.	.	.	.	.	.	.	.	.	T	8.362	0.833330	0.16820	.	.	ENSG00000102763	ENST00000251030;ENST00000379310;ENST00000281496	T;T	0.11495	2.95;2.77	5.95	4.76	0.60689	.	0.060477	0.85682	D	0.000000	T	0.09468	0.0233	L	0.43923	1.385	0.52501	D	0.999957	B	0.06786	0.001	B	0.14578	0.011	T	0.10154	-1.0642	10	0.09590	T	0.72	.	11.3559	0.49615	0.0:0.0723:0.0:0.9277	.	742	A3KMH1	K0564_HUMAN	T	646;742;742	ENSP00000368612:N742T;ENSP00000281496:N742T	ENSP00000251030:N646T	N	-	2	0	KIAA0564	41255983	1.000000	0.71417	0.982000	0.44146	0.617000	0.37484	2.835000	0.48175	1.060000	0.40578	0.460000	0.39030	AAT	.		0.378	VWA8-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354828.2	NM_015058	
SETD1B	23067	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	12	122243775	122243775	+	Missense_Mutation	SNP	A	A	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr12:122243775A>G	ENST00000604567.1	+	4	376	c.308A>G	c.(307-309)aAg>aGg	p.K103R	RHOF_ENST00000545544.1_5'Flank|SETD1B_ENST00000542440.1_Missense_Mutation_p.K103R|SETD1B_ENST00000267197.5_Missense_Mutation_p.K103R			Q9UPS6	SET1B_HUMAN	SET domain containing 1B	103	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.				histone H3-K4 methylation (GO:0051568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)|Set1C/COMPASS complex (GO:0048188)	histone-lysine N-methyltransferase activity (GO:0018024)|nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			NS(1)|endometrium(6)|kidney(2)|prostate(2)	11						GTGCCTCCGAAGCAGGTGACA	0.517																																					p.K103R		.											.	.	.	0			c.A308G						.						76.0	67.0	69.0					12																	122243775		692	1591	2283	SO:0001583	missense	23067	exon3			CTCCGAAGCAGGT	AB028999	CCDS53838.1	12q24.31	2013-02-12			ENSG00000139718	ENSG00000139718		"""Chromatin-modifying enzymes / K-methyltransferases"", ""RNA binding motif (RRM) containing"""	29187	protein-coding gene	gene with protein product		611055				10470851, 17355966	Standard	NM_015048		Approved	KIAA1076, Set1B, KMT2G	uc001ubi.3	Q9UPS6	OTTHUMG00000169080	ENST00000604567.1:c.308A>G	12.37:g.122243775A>G	ENSP00000474253:p.Lys103Arg	Somatic	53	0		WXS	Illumina HiSeq	.	28	12	NM_015048	F6MFW1	Missense_Mutation	SNP	ENST00000604567.1	37		.	.	.	.	.	.	.	.	.	.	A	19.05	3.751794	0.69533	.	.	ENSG00000139718	ENST00000542440;ENST00000267197	T;T	0.39056	1.1;1.1	4.39	4.39	0.52855	RNA recognition motif domain (1);	.	.	.	.	T	0.45478	0.1344	N	0.12569	0.235	0.58432	D	0.999999	D	0.67145	0.996	D	0.76575	0.988	T	0.52786	-0.8529	9	0.54805	T	0.06	.	13.9141	0.63885	1.0:0.0:0.0:0.0	.	103	Q9UPS6	SET1B_HUMAN	R	103	ENSP00000442924:K103R;ENSP00000267197:K103R	ENSP00000267197:K103R	K	+	2	0	SETD1B	120728158	1.000000	0.71417	0.998000	0.56505	0.960000	0.62799	9.276000	0.95745	1.761000	0.52028	0.379000	0.24179	AAG	.		0.517	SETD1B-002	PUTATIVE	non_canonical_U12|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000468264.1	XM_037523	
PLEKHH3	79990	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	17	40823409	40823409	+	Missense_Mutation	SNP	G	G	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr17:40823409G>A	ENST00000591022.1	-	8	1631	c.1244C>T	c.(1243-1245)gCc>gTc	p.A415V	PLEKHH3_ENST00000412503.1_Missense_Mutation_p.A415V|PLEKHH3_ENST00000293349.6_Missense_Mutation_p.A415V|PLEKHH3_ENST00000456950.2_5'UTR	NM_024927.4	NP_079203	Q7Z736	PKHH3_HUMAN	pleckstrin homology domain containing, family H (with MyTH4 domain) member 3	415	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				signal transduction (GO:0007165)	cytoskeleton (GO:0005856)|extracellular space (GO:0005615)				endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|ovary(1)|prostate(2)|skin(2)	13		Breast(137;0.00116)		BRCA - Breast invasive adenocarcinoma(366;0.14)		CACAGCACAGGCACCAGCCCC	0.677																																					p.A415V		.											.	.	.	0			c.C1244T						.						36.0	29.0	32.0					17																	40823409		2202	4298	6500	SO:0001583	missense	79990	exon8			GCACAGGCACCAG	BC052978	CCDS11434.1	17q21.2	2013-01-11				ENSG00000068137		"""Pleckstrin homology (PH) domain containing"""	26105	protein-coding gene	gene with protein product						12477932	Standard	NM_024927		Approved	FLJ21019	uc002iau.3	Q7Z736		ENST00000591022.1:c.1244C>T	17.37:g.40823409G>A	ENSP00000468678:p.Ala415Val	Somatic	113	0		WXS	Illumina HiSeq	.	57	22	NM_024927	C9JQ76|Q59H20|Q96B28|Q9H7D6|Q9NT18	Missense_Mutation	SNP	ENST00000591022.1	37	CCDS11434.1	.	.	.	.	.	.	.	.	.	.	G	23.1	4.379841	0.82682	.	.	ENSG00000068137	ENST00000456950;ENST00000293349;ENST00000412503	T;T	0.16457	2.34;2.34	4.99	4.99	0.66335	Band 4.1 domain (1);FERM domain (1);Ras-association (1);	0.000000	0.46442	D	0.000294	T	0.27697	0.0681	L	0.29908	0.895	0.43512	D	0.995773	D;D	0.63880	0.993;0.99	D;P	0.63033	0.91;0.87	T	0.02238	-1.1190	10	0.22706	T	0.39	-19.6906	17.911	0.88934	0.0:0.0:1.0:0.0	.	415;415	Q7Z736-2;Q7Z736	.;PKHH3_HUMAN	V	77;415;415	ENSP00000293349:A415V;ENSP00000411885:A415V	ENSP00000293349:A415V	A	-	2	0	PLEKHH3	38076935	1.000000	0.71417	0.999000	0.59377	0.825000	0.46686	5.396000	0.66297	2.337000	0.79520	0.561000	0.74099	GCC	.		0.677	PLEKHH3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000452332.1	NM_024927	
BARHL2	343472	hgsc.bcm.edu	37	1	91182194	91182194	+	Missense_Mutation	SNP	C	C	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr1:91182194C>G	ENST00000370445.4	-	1	600	c.559G>C	c.(559-561)Gag>Cag	p.E187Q		NM_020063.1	NP_064447.1	Q9NY43	BARH2_HUMAN	BarH-like homeobox 2	187					cell fate determination (GO:0001709)|neuron differentiation (GO:0030182)|neuron migration (GO:0001764)|positive regulation of translation (GO:0045727)|regulation of axon extension (GO:0030516)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)			cervix(2)|endometrium(1)|kidney(3)|large_intestine(5)|lung(9)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	24		all_lung(203;0.0263)|Lung SC(238;0.128)		all cancers(265;0.000897)|Epithelial(280;0.00516)|OV - Ovarian serous cystadenocarcinoma(397;0.211)		TCCTCCTGCTCGAGCTTTGGC	0.622																																					p.E187Q	GBM(199;3561 4100 22440)	.											BARHL2,colon,carcinoma,0,1	BARHL2	0	0			c.G559C						.						77.0	64.0	68.0					1																	91182194		2203	4300	6503	SO:0001583	missense	343472	exon1			CCTGCTCGAGCTT	AJ251753	CCDS730.1	1p22.2	2011-07-08	2007-07-09		ENSG00000143032	ENSG00000143032		"""Homeoboxes / ANTP class : NKL subclass"""	954	protein-coding gene	gene with protein product		605212	"""BarH (Drosophila)-like 2"""				Standard	NM_020063		Approved		uc001dns.3	Q9NY43	OTTHUMG00000010020	ENST00000370445.4:c.559G>C	1.37:g.91182194C>G	ENSP00000359474:p.Glu187Gln	Somatic	44	0		WXS	Illumina HiSeq	.	12	2	NM_020063	A0AVP2|Q7Z4N7	Missense_Mutation	SNP	ENST00000370445.4	37	CCDS730.1	.	.	.	.	.	.	.	.	.	.	C	20.7	4.032423	0.75504	.	.	ENSG00000143032	ENST00000370445	D	0.90444	-2.67	5.71	5.71	0.89125	.	0.046677	0.85682	D	0.000000	D	0.87617	0.6222	N	0.08118	0	0.80722	D	1	D	0.69078	0.997	D	0.77004	0.989	D	0.88078	0.2805	10	0.30078	T	0.28	.	18.4286	0.90617	0.0:1.0:0.0:0.0	.	187	Q9NY43	BARH2_HUMAN	Q	187	ENSP00000359474:E187Q	ENSP00000359474:E187Q	E	-	1	0	BARHL2	90954782	1.000000	0.71417	0.997000	0.53966	0.997000	0.91878	7.263000	0.78421	2.688000	0.91661	0.655000	0.94253	GAG	.		0.622	BARHL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027728.2		
CNTROB	116840	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	17	7840511	7840511	+	Silent	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr17:7840511T>G	ENST00000563694.1	+	7	1783	c.858T>G	c.(856-858)tcT>tcG	p.S286S	CNTROB_ENST00000565740.1_Silent_p.S286S|CNTROB_ENST00000380255.3_Silent_p.S286S|CNTROB_ENST00000380262.3_Silent_p.S286S	NM_053051.3	NP_444279.2	Q8N137	CNTRB_HUMAN	centrobin, centrosomal BRCA2 interacting protein	286					centriole replication (GO:0007099)|centrosome separation (GO:0051299)|cytokinesis (GO:0000910)	centriole (GO:0005814)|centrosome (GO:0005813)|cytoplasm (GO:0005737)	protein domain specific binding (GO:0019904)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(8)|lung(9)	25		Prostate(122;0.173)				AAAGCCTTTCTGAGGCCATGG	0.488																																					p.S286S		.											.	.	.	0			c.T858G						.						152.0	154.0	153.0					17																	7840511		2203	4300	6503	SO:0001819	synonymous_variant	116840	exon7			CCTTTCTGAGGCC	AF331638	CCDS32557.1, CCDS11126.1	17p13.1	2006-03-15				ENSG00000170037			29616	protein-coding gene	gene with protein product	"""centrobin"""	611425				11984006, 16275750	Standard	NM_001037144		Approved	LIP8, PP1221	uc002gjp.3	Q8N137		ENST00000563694.1:c.858T>G	17.37:g.7840511T>G		Somatic	74	0		WXS	Illumina HiSeq	.	60	31	NM_001037144	A6NHQ1|Q331K3|Q69YV7|Q8NCB8|Q8WXV3|Q96CQ7|Q9C060	Silent	SNP	ENST00000563694.1	37	CCDS11126.1																																																																																			.		0.488	CNTROB-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000421372.1	NM_053051	
ZCCHC4	29063	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	4	25363483	25363483	+	Silent	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr4:25363483A>C	ENST00000302874.4	+	9	1038	c.1014A>C	c.(1012-1014)gtA>gtC	p.V338V		NM_024936.2	NP_079212.2	Q9H5U6	ZCHC4_HUMAN	zinc finger, CCHC domain containing 4	338							methyltransferase activity (GO:0008168)|nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(3)|lung(2)|ovary(2)|pancreas(1)	9		Breast(46;0.0503)				CTTTCTAGGTAGATTATGATA	0.333																																					p.V338V		.											.	.	.	0			c.A1014C						.						44.0	43.0	43.0					4																	25363483		1811	4077	5888	SO:0001819	synonymous_variant	29063	exon9			CTAGGTAGATTAT	AF161537	CCDS43218.1	4p15.31	2014-02-18			ENSG00000168228	ENSG00000168228		"""Zinc fingers, CCHC domain containing"""	22917	protein-coding gene	gene with protein product	"""zinc finger, GRF-type containing 4"""	611792				11042152	Standard	NM_024936		Approved	HSPC052, FLJ23024, ZGRF4	uc003grl.4	Q9H5U6	OTTHUMG00000160563	ENST00000302874.4:c.1014A>C	4.37:g.25363483A>C		Somatic	95	0		WXS	Illumina HiSeq	.	77	33	NM_024936	B2RXF6|B4DRD8|B7ZW20|Q5IW78|Q96AN7	Silent	SNP	ENST00000302874.4	37	CCDS43218.1																																																																																			.		0.333	ZCCHC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361151.1		
PHC3	80012	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	3	169820688	169820688	+	Missense_Mutation	SNP	T	T	A	rs537605155		TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr3:169820688T>A	ENST00000494943.1	-	13	2535	c.2467A>T	c.(2467-2469)Agt>Tgt	p.S823C	PHC3_ENST00000467570.1_Missense_Mutation_p.S782C|PHC3_ENST00000495893.2_Missense_Mutation_p.S835C			Q8NDX5	PHC3_HUMAN	polyhomeotic homolog 3 (Drosophila)	823					multicellular organismal development (GO:0007275)	actin cytoskeleton (GO:0015629)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(12)|ovary(1)|upper_aerodigestive_tract(2)	26	all_cancers(22;2.67e-22)|all_epithelial(15;4.73e-27)|all_lung(20;6.31e-17)|Lung NSC(18;2.61e-16)|Ovarian(172;0.000337)|Breast(254;0.169)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.0655)			TTCCAACGACTAAGTGCAAAT	0.388																																					p.S835C		.											.	.	.	0			c.A2503T						.						43.0	42.0	42.0					3																	169820688		1869	4088	5957	SO:0001583	missense	80012	exon13			AACGACTAAGTGC		CCDS46952.1	3q26.32	2014-01-28	2006-09-12		ENSG00000173889	ENSG00000173889		"""Sterile alpha motif (SAM) domain containing"""	15682	protein-coding gene	gene with protein product	"""early development regulator 3"", ""polyhomeotic like 3"""		"""polyhomeotic like 3 (Drosophila)"""			12167701, 12384788	Standard	NM_024947		Approved	EDR3, FLJ12967, FLJ12729, HPH3	uc003fgl.2	Q8NDX5	OTTHUMG00000158777	ENST00000494943.1:c.2467A>T	3.37:g.169820688T>A	ENSP00000420271:p.Ser823Cys	Somatic	70	0		WXS	Illumina HiSeq	.	63	27	NM_024947	A2RRP9|Q5HYF0|Q6NSG2|Q8NFT7|Q8NFZ1|Q8TBM2|Q9H971|Q9H9I4	Missense_Mutation	SNP	ENST00000494943.1	37		.	.	.	.	.	.	.	.	.	.	T	17.86	3.493599	0.64186	.	.	ENSG00000173889	ENST00000494943;ENST00000495893;ENST00000467570	T;T;T	0.44083	0.93;0.93;0.93	5.47	4.31	0.51392	.	0.129995	0.52532	D	0.000061	T	0.44030	0.1274	L	0.50333	1.59	0.80722	D	1	B;D;D	0.63046	0.102;0.985;0.992	B;B;P	0.49502	0.051;0.408;0.613	T	0.27020	-1.0086	9	.	.	.	-3.931	11.3578	0.49625	0.0:0.0714:0.0:0.9286	.	782;823;835	E7EX82;Q8NDX5;Q8NDX5-7	.;PHC3_HUMAN;.	C	823;835;782	ENSP00000420271:S823C;ENSP00000420294:S835C;ENSP00000419089:S782C	.	S	-	1	0	PHC3	171303382	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	3.171000	0.50824	0.907000	0.36646	0.528000	0.53228	AGT	.		0.388	PHC3-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000352182.3	NM_024947	
EIF4G1	1981	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	3	184040641	184040641	+	Missense_Mutation	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr3:184040641A>C	ENST00000346169.2	+	13	2099	c.1828A>C	c.(1828-1830)Aaa>Caa	p.K610Q	EIF4G1_ENST00000434061.2_Missense_Mutation_p.K414Q|EIF4G1_ENST00000392537.2_Missense_Mutation_p.K523Q|EIF4G1_ENST00000427845.1_Missense_Mutation_p.K523Q|EIF4G1_ENST00000382330.3_Missense_Mutation_p.K617Q|EIF4G1_ENST00000352767.3_Missense_Mutation_p.K617Q|EIF2B5_ENST00000444495.1_Intron|EIF4G1_ENST00000441154.1_Missense_Mutation_p.K446Q|EIF4G1_ENST00000350481.5_Missense_Mutation_p.K446Q|EIF4G1_ENST00000342981.4_Missense_Mutation_p.K610Q|EIF4G1_ENST00000414031.1_Missense_Mutation_p.K570Q|SNORD66_ENST00000390856.1_RNA|EIF4G1_ENST00000319274.6_Missense_Mutation_p.K610Q|EIF4G1_ENST00000435046.2_Missense_Mutation_p.K414Q|EIF4G1_ENST00000424196.1_Missense_Mutation_p.K617Q|EIF4G1_ENST00000411531.1_Missense_Mutation_p.K570Q	NM_198241.2	NP_937884	Q04637	IF4G1_HUMAN	eukaryotic translation initiation factor 4 gamma, 1	610	EIF4E-binding.|MIF4G. {ECO:0000255|PROSITE- ProRule:PRU00698}.				cell death (GO:0008219)|cellular protein metabolic process (GO:0044267)|cytokine-mediated signaling pathway (GO:0019221)|gene expression (GO:0010467)|insulin receptor signaling pathway (GO:0008286)|lung development (GO:0030324)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|regulation of translational initiation (GO:0006446)|response to ethanol (GO:0045471)|RNA metabolic process (GO:0016070)|translation (GO:0006412)|translational initiation (GO:0006413)|viral process (GO:0016032)	cytosol (GO:0005829)|eukaryotic translation initiation factor 4F complex (GO:0016281)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|translation factor activity, nucleic acid binding (GO:0008135)|translation initiation factor activity (GO:0003743)			central_nervous_system(1)|cervix(2)|endometrium(3)|kidney(5)|large_intestine(14)|lung(41)|ovary(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	75	all_cancers(143;1.06e-10)|Ovarian(172;0.0339)		Epithelial(37;1.53e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			AGAGGAGAAAAAACGTTACGA	0.458																																					p.K617Q		.											.	.	.	0			c.A1849C						.						167.0	159.0	162.0					3																	184040641		2203	4300	6503	SO:0001583	missense	1981	exon14			GAGAAAAAACGTT	D12686	CCDS3259.1, CCDS3260.1, CCDS3261.1, CCDS46970.1, CCDS46970.2, CCDS54687.1, CCDS54688.1	3q27.1	2013-09-19			ENSG00000114867	ENSG00000114867		"""Parkinson disease"""	3296	protein-coding gene	gene with protein product		600495		EIF4G, EIF4F		1429670, 9372926, 21907011	Standard	NM_182917		Approved	p220, PARK18	uc010hxy.3	Q04637	OTTHUMG00000156784	ENST00000346169.2:c.1828A>C	3.37:g.184040641A>C	ENSP00000316879:p.Lys610Gln	Somatic	67	0		WXS	Illumina HiSeq	.	54	15	NM_001194946	D3DNT2|D3DNT4|D3DNT5|E9PFM1|G5E9S1|O43177|O95066|Q5HYG0|Q6ZN21|Q8N102	Missense_Mutation	SNP	ENST00000346169.2	37	CCDS3259.1	.	.	.	.	.	.	.	.	.	.	A	22.1	4.243445	0.79912	.	.	ENSG00000114867	ENST00000346169;ENST00000414031;ENST00000392537;ENST00000450424;ENST00000421110;ENST00000382330;ENST00000426123;ENST00000350481;ENST00000352767;ENST00000427845;ENST00000342981;ENST00000319274;ENST00000424196;ENST00000411531;ENST00000444861;ENST00000441154;ENST00000434061;ENST00000435046	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.47869	0.83;0.83;0.83;0.83;0.83;0.83;0.83;0.83;0.83;0.83;0.83;0.83;0.83;0.83;0.83;0.83;0.83;0.83	5.4	5.4	0.78164	.	0.000000	0.85682	D	0.000000	T	0.71264	0.3319	M	0.87269	2.87	0.80722	D	1	D;D;D;D	0.76494	0.999;0.999;0.999;0.999	D;D;D;D	0.70935	0.971;0.971;0.971;0.971	T	0.73363	-0.4006	10	0.35671	T	0.21	-23.5912	15.5933	0.76558	1.0:0.0:0.0:0.0	.	617;610;610;617	E9PFM1;D3DNT2;Q04637;B2RU10	.;.;IF4G1_HUMAN;.	Q	610;570;523;610;617;617;551;446;617;523;610;610;617;570;446;446;414;414	ENSP00000316879:K610Q;ENSP00000391935:K570Q;ENSP00000376320:K523Q;ENSP00000391412:K610Q;ENSP00000413159:K617Q;ENSP00000371767:K617Q;ENSP00000403269:K551Q;ENSP00000317600:K446Q;ENSP00000338020:K617Q;ENSP00000407682:K523Q;ENSP00000343450:K610Q;ENSP00000323737:K610Q;ENSP00000416255:K617Q;ENSP00000395974:K570Q;ENSP00000398145:K446Q;ENSP00000399858:K446Q;ENSP00000411826:K414Q;ENSP00000404754:K414Q	ENSP00000323737:K610Q	K	+	1	0	EIF4G1	185523335	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	8.761000	0.91691	2.270000	0.75569	0.460000	0.39030	AAA	.		0.458	EIF4G1-007	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000345733.1	NM_182917	
SNHG14	104472715	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	15	25321133	25321133	+	RNA	SNP	A	A	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr15:25321133A>G	ENST00000549804.2	+	0	1109				SNORD116-9_ENST00000384000.1_RNA|SNORD116-12_ENST00000384468.1_RNA|SNORD116-10_ENST00000363791.1_RNA|SNHG14_ENST00000551077.1_RNA|SNORD116-11_ENST00000383882.1_RNA					small nucleolar RNA host gene 14 (non-protein coding)																		AATGAGTGAAAACTTTATACT	0.458																																					.		.											.	.	.	0			.						.						107.0	97.0	100.0					15																	25321133		876	1991	2867			100033423	.			AGTGAAAACTTTA			15q11.2	2014-01-17	2011-08-22	2011-08-22	ENSG00000224078	ENSG00000224078		"""Long non-coding RNAs"""	37462	non-coding RNA	RNA, long non-coding	"""non-protein coding RNA 214"""		"""UBE3A antisense RNA 1 (non-protein coding)"""	UBE3A-AS1		23771028	Standard			Approved	NCRNA00214, UBE3A-AS			OTTHUMG00000056661		15.37:g.25321133A>G		Somatic	97	0		WXS	Illumina HiSeq	.	52	27	.		RNA	SNP	ENST00000549804.2	37																																																																																				.		0.458	SNHG14-012	KNOWN	non_canonical_other|basic	antisense	processed_transcript	OTTHUMT00000408278.2		
ZBTB16	7704	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	11	114121244	114121244	+	Silent	SNP	A	A	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr11:114121244A>T	ENST00000335953.4	+	7	2369	c.1989A>T	c.(1987-1989)atA>atT	p.I663I	RP11-64D24.2_ENST00000544925.1_RNA|ZBTB16_ENST00000392996.2_Silent_p.I663I|ZBTB16_ENST00000535379.1_3'UTR	NM_006006.4	NP_005997.2	Q05516	ZBT16_HUMAN	zinc finger and BTB domain containing 16	663					anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|cartilage development (GO:0051216)|central nervous system development (GO:0007417)|embryonic digit morphogenesis (GO:0042733)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic pattern specification (GO:0009880)|forelimb morphogenesis (GO:0035136)|hemopoiesis (GO:0030097)|male germ-line stem cell asymmetric division (GO:0048133)|mesonephros development (GO:0001823)|myeloid cell differentiation (GO:0030099)|negative regulation of cell proliferation (GO:0008285)|negative regulation of myeloid cell differentiation (GO:0045638)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cartilage development (GO:0061036)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of NK T cell differentiation (GO:0051138)|positive regulation of ossification (GO:0045778)|positive regulation of transcription, DNA-templated (GO:0045893)|protein localization to nucleus (GO:0034504)|protein ubiquitination (GO:0016567)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|nuclear body (GO:0016604)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)|transcriptional repressor complex (GO:0017053)	DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|large_intestine(2)|skin(1)|upper_aerodigestive_tract(2)	6		all_cancers(61;3.79e-18)|all_epithelial(67;2.32e-10)|all_hematologic(158;2.96e-05)|Melanoma(852;0.000362)|Acute lymphoblastic leukemia(157;0.00108)|Breast(348;0.0104)|all_neural(223;0.0294)|Prostate(24;0.0318)|Medulloblastoma(222;0.0438)		BRCA - Breast invasive adenocarcinoma(274;6.75e-06)|Epithelial(105;0.000181)|all cancers(92;0.0018)		ACTGGAGGATAGAGAAGACGT	0.597																																					p.I663I		.											.	.	.	0			c.A1989T						.						65.0	62.0	63.0					11																	114121244		2201	4296	6497	SO:0001819	synonymous_variant	7704	exon7			GAGGATAGAGAAG	Z19002	CCDS8367.1	11q23	2013-10-17	2004-07-16	2004-07-16	ENSG00000109906	ENSG00000109906		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	12930	protein-coding gene	gene with protein product	"""promyelocytic leukaemia zinc finger"""	176797	"""zinc finger protein 145 (Kruppel-like, expressed in promyelocytic leukemia)"""	ZNF145			Standard	XM_006718899		Approved	PLZF	uc001poq.3	Q05516	OTTHUMG00000168243	ENST00000335953.4:c.1989A>T	11.37:g.114121244A>T		Somatic	32	0		WXS	Illumina HiSeq	.	17	10	NM_006006	Q8TAL4	Silent	SNP	ENST00000335953.4	37	CCDS8367.1																																																																																			.		0.597	ZBTB16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398940.1	NM_006006	
TAS1R2	80834	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	19166611	19166611	+	Missense_Mutation	SNP	C	C	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr1:19166611C>T	ENST00000375371.3	-	6	2023	c.2002G>A	c.(2002-2004)Gcc>Acc	p.A668T		NM_152232.2	NP_689418.2	Q8TE23	TS1R2_HUMAN	taste receptor, type 1, member 2	668					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)	TAGCTGTAGGCGCGTGGGAAG	0.567																																					p.A668T		.											TAS1R2,caecum,carcinoma,0,1	TAS1R2	0	0			c.G2002A						.						132.0	141.0	138.0					1																	19166611		2203	4300	6503	SO:0001583	missense	80834	exon6			TGTAGGCGCGTGG		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.2002G>A	1.37:g.19166611C>T	ENSP00000364520:p.Ala668Thr	Somatic	35	0		WXS	Illumina HiSeq	.	42	19	NM_152232	Q5TZ19	Missense_Mutation	SNP	ENST00000375371.3	37	CCDS187.1	.	.	.	.	.	.	.	.	.	.	C	15.51	2.856063	0.51376	.	.	ENSG00000179002	ENST00000375371	D	0.88046	-2.33	5.22	5.22	0.72569	GPCR, family 3, C-terminal (2);	0.138235	0.32687	N	0.005767	D	0.92688	0.7676	M	0.83953	2.67	0.41111	D	0.985741	D	0.76494	0.999	D	0.71870	0.975	D	0.91194	0.4986	10	0.22109	T	0.4	.	14.2737	0.66166	0.0:1.0:0.0:0.0	.	668	Q8TE23	TS1R2_HUMAN	T	668	ENSP00000364520:A668T	ENSP00000364520:A668T	A	-	1	0	TAS1R2	19039198	0.084000	0.21492	0.745000	0.31077	0.640000	0.38277	0.904000	0.28491	2.438000	0.82558	0.561000	0.74099	GCC	.		0.567	TAS1R2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000006953.1		
C9orf152	401546	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	9	112963453	112963453	+	Missense_Mutation	SNP	C	C	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr9:112963453C>A	ENST00000400613.4	-	2	1104	c.495G>T	c.(493-495)atG>atT	p.M165I	C9orf152_ENST00000473442.1_Intron	NM_001012993.2	NP_001013011.2	Q5JTZ5	CI152_HUMAN	chromosome 9 open reading frame 152	165										NS(1)|endometrium(1)|large_intestine(1)|lung(1)|skin(1)|stomach(1)	6						CTTGCTGAGTCATCTGATTGG	0.502																																					p.M165I		.											.	.	.	0			c.G495T						.						203.0	185.0	191.0					9																	112963453		2203	4300	6503	SO:0001583	missense	401546	exon2			CTGAGTCATCTGA	BX648620	CCDS35102.2	9q31.3	2012-04-03			ENSG00000188959	ENSG00000188959			31455	protein-coding gene	gene with protein product							Standard	NM_001012993		Approved	bA470J20.2	uc011lwk.2	Q5JTZ5	OTTHUMG00000020478	ENST00000400613.4:c.495G>T	9.37:g.112963453C>A	ENSP00000383456:p.Met165Ile	Somatic	53	0		WXS	Illumina HiSeq	.	30	13	NM_001012993	A8MWT6	Missense_Mutation	SNP	ENST00000400613.4	37	CCDS35102.2	.	.	.	.	.	.	.	.	.	.	C	10.77	1.444487	0.25987	.	.	ENSG00000188959	ENST00000400613	.	.	.	4.33	0.115	0.14643	.	1.626060	0.03324	N	0.192407	T	0.30479	0.0766	L	0.27053	0.805	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.21793	-1.0235	9	0.46703	T	0.11	0.7061	5.3784	0.16178	0.0:0.5828:0.1496:0.2676	.	165	Q5JTZ5	CI152_HUMAN	I	165	.	ENSP00000383456:M165I	M	-	3	0	C9orf152	112003274	0.004000	0.15560	0.000000	0.03702	0.006000	0.05464	0.098000	0.15189	0.027000	0.15297	-0.302000	0.09304	ATG	.		0.502	C9orf152-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053602.2	NM_001012993	
FLJ26850	400710	hgsc.bcm.edu	37	19	50563715	50563715	+	RNA	SNP	G	G	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr19:50563715G>A	ENST00000527209.1	+	0	606					NR_027257.1																						GACCGATAGTGACATGCCAAG	0.522																																					.		.											.	.	.	0			.						.																																					0	.			GATAGTGACATGC																													19.37:g.50563715G>A		Somatic	36	0		WXS	Illumina HiSeq	.	27	9	.		RNA	SNP	ENST00000527209.1	37																																																																																				.		0.522	CTD-2126E3.1-001	KNOWN	basic	sense_overlapping	sense_overlapping	OTTHUMT00000384643.1		
RABGAP1	23637	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	9	125760961	125760961	+	Silent	SNP	C	C	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr9:125760961C>G	ENST00000373647.4	+	10	1424	c.1290C>G	c.(1288-1290)gtC>gtG	p.V430V		NM_012197.3	NP_036329.3	Q9Y3P9	RBGP1_HUMAN	RAB GTPase activating protein 1	430					cell cycle (GO:0007049)|positive regulation of GTPase activity (GO:0043547)|regulation of GTP catabolic process (GO:0033124)	centrosome (GO:0005813)|cytosol (GO:0005829)|microtubule associated complex (GO:0005875)	DNA binding (GO:0003677)|GTPase activator activity (GO:0005096)|Rab GTPase activator activity (GO:0005097)|Rab GTPase binding (GO:0017137)|tubulin binding (GO:0015631)			breast(3)|endometrium(3)|kidney(5)|large_intestine(8)|lung(11)|ovary(3)|prostate(4)|stomach(3)|upper_aerodigestive_tract(1)	41						AGACAAAAGTCCGCGTTTGCT	0.368																																					p.V430V		.											.	.	.	0			c.C1290G						.						116.0	120.0	118.0					9																	125760961		2203	4300	6503	SO:0001819	synonymous_variant	23637	exon10			AAAAGTCCGCGTT	AJ011679	CCDS6848.2	9q34.11	2013-07-09			ENSG00000011454	ENSG00000011454			17155	protein-coding gene	gene with protein product	"""rab6 GTPase activating protein (GAP and centrosome-associated)"", ""TBC1 domain family, member 11"""	615882				10202141	Standard	NM_012197		Approved	GAPCenA, TBC1D11	uc011lzh.2	Q9Y3P9	OTTHUMG00000020633	ENST00000373647.4:c.1290C>G	9.37:g.125760961C>G		Somatic	200	0		WXS	Illumina HiSeq	.	110	39	NM_012197	B9A6L2|Q05CW2|Q6ZMY1|Q9HA28|Q9P0E2|Q9UG67	Silent	SNP	ENST00000373647.4	37	CCDS6848.2																																																																																			.		0.368	RABGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053976.3	NM_012197	
WBP4	11193	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	13	41636805	41636805	+	Missense_Mutation	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr13:41636805A>C	ENST00000379487.3	+	2	428	c.28A>C	c.(28-30)Aag>Cag	p.K10Q	WBP4_ENST00000542082.1_Missense_Mutation_p.K10Q	NM_007187.3	NP_009118.1	O75554	WBP4_HUMAN	WW domain binding protein 4	10					mRNA cis splicing, via spliceosome (GO:0045292)	nuclear speck (GO:0016607)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|spliceosomal complex (GO:0005681)	nucleic acid binding (GO:0003676)|proline-rich region binding (GO:0070064)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|liver(2)|lung(2)|prostate(1)|skin(1)	12		Lung NSC(96;3.55e-06)|Breast(139;0.00123)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(98;0.114)		all cancers(112;3.11e-09)|Epithelial(112;3.37e-06)|OV - Ovarian serous cystadenocarcinoma(117;8.3e-05)|GBM - Glioblastoma multiforme(144;0.00102)|BRCA - Breast invasive adenocarcinoma(63;0.07)		GTCACAGCCAAAGAAATTCTG	0.373																																					p.K10Q		.											.	.	.	0			c.A28C						.						117.0	112.0	114.0					13																	41636805		2203	4300	6503	SO:0001583	missense	11193	exon2			CAGCCAAAGAAAT	AF071185	CCDS9375.1	13q13.3	2012-10-17	2012-10-17		ENSG00000120688	ENSG00000120688			12739	protein-coding gene	gene with protein product	"""formin binding protein 21"""	604981				9724750	Standard	NM_007187		Approved	FBP21, MGC117310	uc001uxt.3	O75554	OTTHUMG00000016784	ENST00000379487.3:c.28A>C	13.37:g.41636805A>C	ENSP00000368801:p.Lys10Gln	Somatic	113	0		WXS	Illumina HiSeq	.	59	25	NM_007187	B7Z4M2|Q32P29	Missense_Mutation	SNP	ENST00000379487.3	37	CCDS9375.1	.	.	.	.	.	.	.	.	.	.	A	26.3	4.724574	0.89298	.	.	ENSG00000120688	ENST00000379487;ENST00000542082	.	.	.	5.06	5.06	0.68205	Zinc finger, U1-C type (1);Zinc finger, U1-type (1);	0.048439	0.85682	D	0.000000	T	0.77890	0.4198	M	0.71206	2.165	0.54753	D	0.999982	D;D	0.89917	1.0;1.0	D;D	0.91635	0.993;0.999	T	0.80772	-0.1233	9	0.72032	D	0.01	-4.9023	14.8369	0.70190	1.0:0.0:0.0:0.0	.	10;10	B7Z4M2;O75554	.;WBP4_HUMAN	Q	10	.	ENSP00000368801:K10Q	K	+	1	0	WBP4	40534805	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.278000	0.89899	1.903000	0.55091	0.459000	0.35465	AAG	.		0.373	WBP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044655.2	NM_007187	
SUPT6H	6830	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	17	27005649	27005649	+	Missense_Mutation	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr17:27005649A>C	ENST00000314616.6	+	10	1486	c.1203A>C	c.(1201-1203)gaA>gaC	p.E401D	SUPT6H_ENST00000347486.4_Missense_Mutation_p.E401D	NM_003170.3	NP_003161.2	Q7KZ85	SPT6H_HUMAN	suppressor of Ty 6 homolog (S. cerevisiae)	401	Interaction with IWS1. {ECO:0000250}.|Interaction with KDM6A. {ECO:0000250}.|Interaction with PAAF1.				chromatin remodeling (GO:0006338)|mRNA processing (GO:0006397)|mRNA transport (GO:0051028)|negative regulation of histone H3-K27 methylation (GO:0061086)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|regulation of isotype switching (GO:0045191)|regulation of mRNA export from nucleus (GO:0010793)|regulation of mRNA processing (GO:0050684)|regulation of muscle cell differentiation (GO:0051147)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone binding (GO:0042393)|hydrolase activity, acting on ester bonds (GO:0016788)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(4)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(15)|lung(21)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	64	Lung NSC(42;0.00431)					AGTGGGATGAAAAGGTAATGT	0.522																																					p.E401D		.											.	.	.	0			c.A1203C						.						102.0	98.0	100.0					17																	27005649		2203	4300	6503	SO:0001583	missense	6830	exon10			GGATGAAAAGGTA	U38658	CCDS32596.1	17q11.2	2013-02-14	2001-11-28			ENSG00000109111		"""SH2 domain containing"""	11470	protein-coding gene	gene with protein product		601333	"""suppressor of Ty (S.cerevisiae) 6 homolog"""			8786132	Standard	XM_005258026		Approved	KIAA0162, SPT6H	uc002hby.3	Q7KZ85		ENST00000314616.6:c.1203A>C	17.37:g.27005649A>C	ENSP00000319104:p.Glu401Asp	Somatic	82	0		WXS	Illumina HiSeq	.	41	15	NM_003170	A7E2B4|Q15737|Q6GMQ4|Q7KYW9|Q7LDK4|Q8N526|Q92775|Q96AH3|Q9BTH9|Q9BTI2	Missense_Mutation	SNP	ENST00000314616.6	37	CCDS32596.1	.	.	.	.	.	.	.	.	.	.	A	21.3	4.127258	0.77549	.	.	ENSG00000109111	ENST00000314616;ENST00000347486	T;T	0.45276	0.9;0.9	5.65	2.09	0.27110	.	0.000000	0.85682	D	0.000000	T	0.49898	0.1584	M	0.71581	2.175	0.58432	D	0.999999	D	0.59767	0.986	P	0.58210	0.835	T	0.49570	-0.8926	10	0.13470	T	0.59	-19.8912	8.6783	0.34191	0.6436:0.0:0.3564:0.0	.	401	Q7KZ85	SPT6H_HUMAN	D	401	ENSP00000319104:E401D;ENSP00000338143:E401D	ENSP00000319104:E401D	E	+	3	2	SUPT6H	24029776	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	1.140000	0.31516	0.419000	0.25927	0.533000	0.62120	GAA	.		0.522	SUPT6H-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446422.2	NM_003170	
POM121C	100101267	hgsc.bcm.edu	37	7	75045150	75045150	+	IGR	SNP	G	G	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr7:75045150G>C	ENST00000257665.5	-	0	5700				NSUN5P1_ENST00000393633.2_RNA			A8CG34	P121C_HUMAN	POM121 transmembrane nucleoporin C						mRNA transport (GO:0051028)|protein transport (GO:0015031)	endoplasmic reticulum (GO:0005783)|nuclear pore (GO:0005643)				central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|prostate(1)|skin(1)|urinary_tract(1)	14						taatgggcttgggaccctgga	0.527																																					.		.											.	.	.	0			.						.																																			SO:0001628	intergenic_variant	155400	.			GGGCTTGGGACCC		CCDS47617.1	7q11.23	2012-03-13	2012-03-13		ENSG00000135213	ENSG00000272391			34005	protein-coding gene	gene with protein product		615754	"""POM121 membrane glycoprotein C"""			17900573	Standard	NM_001099415		Approved		uc003udk.4	A8CG34	OTTHUMG00000156238		7.37:g.75045150G>C		Somatic	48	0		WXS	Illumina HiSeq	.	45	16	.	O75115|Q9Y2N3|Q9Y4S7	RNA	SNP	ENST00000257665.5	37																																																																																				.		0.527	POM121C-003	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000343919.2	NM_001099415	
MUC5B	727897	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	11	1263842	1263842	+	Missense_Mutation	SNP	C	C	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr11:1263842C>G	ENST00000529681.1	+	31	5790	c.5732C>G	c.(5731-5733)aCc>aGc	p.T1911S	RP11-532E4.2_ENST00000532061.2_RNA|MUC5B_ENST00000447027.1_Missense_Mutation_p.T1914S	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	1911	11 X approximate tandem repeats, Ser/Thr- rich.|7 X Cys-rich subdomain repeats.|Thr-rich.				cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to retinoic acid (GO:0071300)|epithelial cell differentiation (GO:0030855)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to lipopolysaccharide (GO:0032496)|response to ozone (GO:0010193)|response to sulfur dioxide (GO:0010477)|response to vitamin A (GO:0033189)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				cervix(2)|endometrium(36)|kidney(9)|lung(89)|urinary_tract(1)	137		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)		ACAAAGCCGACCACAACAGCC	0.652																																					p.T1911S		.											.	.	.	0			c.C5732G						.						98.0	125.0	116.0					11																	1263842		2174	4244	6418	SO:0001583	missense	727897	exon31			AGCCGACCACAAC	U95031, AF086604	CCDS44515.1, CCDS44515.2	11p15.5	2007-01-19	2006-03-14			ENSG00000117983		"""Mucins"""	7516	protein-coding gene	gene with protein product		600770	"""mucin 5, subtype B, tracheobronchial"""	MUC5		9804771	Standard	NM_002458		Approved	MG1	uc001lta.3	Q9HC84		ENST00000529681.1:c.5732C>G	11.37:g.1263842C>G	ENSP00000436812:p.Thr1911Ser	Somatic	78	0		WXS	Illumina HiSeq	.	53	24	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	37	CCDS44515.2	.	.	.	.	.	.	.	.	.	.	c	7.483	0.649022	0.14516	.	.	ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637;ENST00000406844	T;T	0.20200	2.09;2.29	2.65	0.594	0.17485	.	.	.	.	.	T	0.07999	0.0200	N	0.10707	0.03	0.09310	N	1	P;P	0.43477	0.808;0.808	B;B	0.30646	0.118;0.118	T	0.21245	-1.0251	9	0.87932	D	0	.	7.1149	0.25411	0.0:0.7215:0.1719:0.1066	.	2604;1914	A7Y9J9;E9PBJ0	.;.	S	1911;1914;1912;1981	ENSP00000436812:T1911S;ENSP00000415793:T1914S	ENSP00000343037:T1912S	T	+	2	0	MUC5B	1220418	0.000000	0.05858	0.004000	0.12327	0.010000	0.07245	-0.775000	0.04679	0.371000	0.24564	-1.285000	0.01374	ACC	.		0.652	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
SMG1	23049	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	16	18865012	18865012	+	Missense_Mutation	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr16:18865012T>G	ENST00000446231.2	-	31	5073	c.4661A>C	c.(4660-4662)aAc>aCc	p.N1554T	SMG1_ENST00000389467.3_Missense_Mutation_p.N1554T			Q96Q15	SMG1_HUMAN	SMG1 phosphatidylinositol 3-kinase-related kinase	1554	FAT. {ECO:0000255|PROSITE- ProRule:PRU00534}.|Interaction with SMG8 and SMG9.				DNA repair (GO:0006281)|gene expression (GO:0010467)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol phosphorylation (GO:0046854)|protein autophosphorylation (GO:0046777)|response to stress (GO:0006950)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(8)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(37)|ovary(1)|skin(1)|stomach(4)|urinary_tract(1)	92						ACCTGTGAAGTTCTGTTGGTG	0.413																																					p.N1554T		.											.	.	.	0			c.A4661C						.						118.0	110.0	113.0					16																	18865012		1874	4105	5979	SO:0001583	missense	23049	exon31			GTGAAGTTCTGTT	AB061371	CCDS45430.1	16p12.3	2013-07-02	2013-07-02		ENSG00000157106	ENSG00000157106			30045	protein-coding gene	gene with protein product	"""phosphatidylinositol 3-kinase-related kinase"""	607032	"""smg-1 homolog, phosphatidylinositol 3-kinase-related kinase (C. elegans)"""			9455477, 11331269, 17229728	Standard	NM_015092		Approved	LIP, KIAA0421, ATX	uc002dfm.3	Q96Q15	OTTHUMG00000166900	ENST00000446231.2:c.4661A>C	16.37:g.18865012T>G	ENSP00000402515:p.Asn1554Thr	Somatic	94	0		WXS	Illumina HiSeq	.	52	15	NM_015092	O43305|Q13284|Q8NFX2|Q96QV0|Q96RW3	Missense_Mutation	SNP	ENST00000446231.2	37	CCDS45430.1	.	.	.	.	.	.	.	.	.	.	T	11.15	1.555137	0.27739	.	.	ENSG00000157106	ENST00000446231;ENST00000389467	T;T	0.01152	5.26;5.26	5.35	4.25	0.50352	PIK-related kinase (1);Armadillo-type fold (1);	0.183165	0.37530	N	0.002051	T	0.01092	0.0036	N	0.19112	0.55	0.28774	N	0.900213	B	0.17038	0.02	B	0.14578	0.011	T	0.39251	-0.9623	10	0.39692	T	0.17	.	11.2317	0.48916	0.0:0.0722:0.0:0.9278	.	1554	Q96Q15	SMG1_HUMAN	T	1554	ENSP00000402515:N1554T;ENSP00000374118:N1554T	ENSP00000374118:N1554T	N	-	2	0	SMG1	18772513	1.000000	0.71417	0.994000	0.49952	0.439000	0.31926	1.945000	0.40273	0.985000	0.38656	-0.415000	0.06103	AAC	.		0.413	SMG1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000391817.1	NM_015092	
LINC00283	100874057	hgsc.bcm.edu	37	13	103400137	103400137	+	RNA	SNP	C	C	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr13:103400137C>T	ENST00000430111.1	+	0	3894									long intergenic non-protein coding RNA 283																		ATGGACTATTCTCCAAAATAG	0.418																																					p.E970E		.											.	.	.	0			c.G2910A						.						297.0	251.0	265.0					13																	103400137		692	1591	2283			643677	exon4			ACTATTCTCCAAA			13q33.1	2012-10-12	2011-08-10	2011-08-10	ENSG00000231633	ENSG00000231633		"""Long non-coding RNAs"""	38809	non-coding RNA	RNA, long non-coding			"""non-protein coding RNA 283"""	NCRNA00283			Standard			Approved				OTTHUMG00000017311		13.37:g.103400137C>T		Somatic	119	0		WXS	Illumina HiSeq	.	77	4	NM_001146197		Silent	SNP	ENST00000430111.1	37																																																																																				.		0.418	LINC00283-001	KNOWN	not_organism_supported|basic	antisense	antisense	OTTHUMT00000045714.1		
LIMD1	8994	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	3	45637209	45637209	+	Missense_Mutation	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr3:45637209T>G	ENST00000273317.4	+	1	859	c.838T>G	c.(838-840)Ttg>Gtg	p.L280V	LIMD1_ENST00000440097.1_Missense_Mutation_p.L280V|LIMD1_ENST00000465039.1_Intron	NM_014240.2	NP_055055.1	Q9UGP4	LIMD1_HUMAN	LIM domains containing 1	280					cell migration (GO:0016477)|cytoplasmic mRNA processing body assembly (GO:0033962)|cytoskeleton organization (GO:0007010)|gene silencing by miRNA (GO:0035195)|multicellular organismal development (GO:0007275)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of hippo signaling (GO:0035331)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of transcription, DNA-templated (GO:0045892)|osteoblast development (GO:0002076)|phosphorylation (GO:0016310)|positive regulation of gene silencing by miRNA (GO:2000637)|regulation of cell shape (GO:0008360)|regulation of transcription, DNA-templated (GO:0006355)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	adherens junction (GO:0005912)|cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|RISC complex (GO:0016442)	transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|skin(1)	10				BRCA - Breast invasive adenocarcinoma(193;0.011)|KIRC - Kidney renal clear cell carcinoma(197;0.0264)|Kidney(197;0.0315)		TTCCCCAAACTTGGAGAACGG	0.632																																					p.L280V		.											.	.	.	0			c.T838G						.						49.0	52.0	51.0					3																	45637209		2203	4300	6503	SO:0001583	missense	8994	exon1			CCAAACTTGGAGA	AJ132408	CCDS2729.1	3p21.31	2008-02-01			ENSG00000144791	ENSG00000144791			6612	protein-coding gene	gene with protein product		604543				10647888	Standard	NM_014240		Approved		uc003coq.3	Q9UGP4	OTTHUMG00000133453	ENST00000273317.4:c.838T>G	3.37:g.45637209T>G	ENSP00000273317:p.Leu280Val	Somatic	77	0		WXS	Illumina HiSeq	.	22	16	NM_014240	Q17RQ1|Q9BQQ9|Q9NQ47	Missense_Mutation	SNP	ENST00000273317.4	37	CCDS2729.1	.	.	.	.	.	.	.	.	.	.	T	0.182	-1.060968	0.01950	.	.	ENSG00000144791	ENST00000440097;ENST00000273317	T;T	0.57436	0.4;0.59	4.92	1.77	0.24775	.	2.112880	0.02562	N	0.096917	T	0.39517	0.1081	N	0.19112	0.55	0.09310	N	1	B	0.32245	0.361	B	0.32864	0.154	T	0.24728	-1.0152	10	0.16896	T	0.51	.	9.2562	0.37584	0.0:0.7341:0.0:0.2659	.	280	Q9UGP4	LIMD1_HUMAN	V	280	ENSP00000394537:L280V;ENSP00000273317:L280V	ENSP00000273317:L280V	L	+	1	2	LIMD1	45612213	0.010000	0.17322	0.013000	0.15412	0.038000	0.13279	0.187000	0.16998	0.028000	0.15324	-0.379000	0.06801	TTG	.		0.632	LIMD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257327.1	NM_014240	
APMAP	57136	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	20	24954309	24954309	+	Silent	SNP	G	G	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr20:24954309G>A	ENST00000217456.2	-	4	683	c.393C>T	c.(391-393)acC>acT	p.T131T	APMAP_ENST00000447138.1_Silent_p.T131T|RNU6-1257P_ENST00000384625.1_RNA	NM_020531.2	NP_065392.1	Q9HDC9	APMAP_HUMAN	adipocyte plasma membrane associated protein	131					biosynthetic process (GO:0009058)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	arylesterase activity (GO:0004064)|strictosidine synthase activity (GO:0016844)										ACCGGGCAATGGTCTCTATTT	0.443																																					p.T131T		.											.	.	.	0			c.C393T						.						108.0	94.0	98.0					20																	24954309		2203	4300	6503	SO:0001819	synonymous_variant	57136	exon4			GGCAATGGTCTCT	AB033767	CCDS13166.1	20p11.2	2012-07-20	2012-07-20	2012-07-20	ENSG00000101474	ENSG00000101474			13238	protein-coding gene	gene with protein product		615884	"""chromosome 20 open reading frame 3"""	C20orf3		10945474, 11583587, 20552250	Standard	NM_020531		Approved	BSCv	uc002wty.3	Q9HDC9	OTTHUMG00000032107	ENST00000217456.2:c.393C>T	20.37:g.24954309G>A		Somatic	69	0		WXS	Illumina HiSeq	.	61	21	NM_020531	A8K514|B4DXG1|Q6UVZ8|Q9GZS8|Q9NUB2	Silent	SNP	ENST00000217456.2	37	CCDS13166.1	.	.	.	.	.	.	.	.	.	.	G	8.781	0.928185	0.18131	.	.	ENSG00000101474	ENST00000451442	.	.	.	5.43	-0.777	0.10981	.	.	.	.	.	T	0.39911	0.1096	.	.	.	0.58432	D	0.999996	.	.	.	.	.	.	T	0.23976	-1.0173	4	.	.	.	-3.085	1.1563	0.01797	0.1745:0.1484:0.2261:0.451	.	.	.	.	L	116	.	.	P	-	2	0	C20orf3	24902309	0.049000	0.20398	0.828000	0.32881	0.813000	0.45954	-0.091000	0.11146	-0.191000	0.10448	-0.137000	0.14449	CCA	.		0.443	APMAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078380.2	NM_020531	
FBXO5	26271	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	6	153296461	153296461	+	Missense_Mutation	SNP	T	T	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr6:153296461T>C	ENST00000229758.3	-	2	457	c.399A>G	c.(397-399)atA>atG	p.I133M	FBXO5_ENST00000367241.3_Missense_Mutation_p.I87M|FBXO5_ENST00000477822.1_5'Flank	NM_012177.3	NP_036309.1	Q9UKT4	FBX5_HUMAN	F-box protein 5	133					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|G1/S transition of mitotic cell cycle (GO:0000082)|inhibition of mitotic anaphase-promoting complex activity (GO:0060565)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|microtubule polymerization (GO:0046785)|mitotic cell cycle (GO:0000278)|negative regulation of meiosis (GO:0045835)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|oocyte maturation (GO:0001556)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|regulation of mitotic cell cycle (GO:0007346)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|spindle assembly involved in female meiosis I (GO:0007057)|vesicle organization (GO:0016050)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)	p.I133M(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(3)|prostate(2)|upper_aerodigestive_tract(1)	15		Ovarian(120;0.125)		OV - Ovarian serous cystadenocarcinoma(155;4.38e-10)|BRCA - Breast invasive adenocarcinoma(81;0.0893)		CTAGTGCTTCTATTTCATTTG	0.413																																					p.I133M	NSCLC(121;372 1757 17721 17977 29669)	.											FBXO5,mouth,carcinoma,0,1	FBXO5	0	1	Substitution - Missense(1)	upper_aerodigestive_tract(1)	c.A399G						.						189.0	185.0	187.0					6																	153296461		2203	4300	6503	SO:0001583	missense	26271	exon2			TGCTTCTATTTCA	AF129535	CCDS5242.1, CCDS47501.1	6q25-q26	2008-02-05	2004-06-15		ENSG00000112029	ENSG00000112029		"""F-boxes /  ""other"""""	13584	protein-coding gene	gene with protein product		606013	"""F-box only protein 5"""			10531035, 10531037	Standard	NM_012177		Approved	FBX5, Fbxo31, EMI1	uc003qpg.3	Q9UKT4	OTTHUMG00000015854	ENST00000229758.3:c.399A>G	6.37:g.153296461T>C	ENSP00000229758:p.Ile133Met	Somatic	60	0		WXS	Illumina HiSeq	.	40	11	NM_012177	B3KNX5|Q5TF47|Q8WV29|Q9UGC8	Missense_Mutation	SNP	ENST00000229758.3	37	CCDS5242.1	.	.	.	.	.	.	.	.	.	.	T	1.683	-0.506083	0.04231	.	.	ENSG00000112029	ENST00000229758;ENST00000367241	T;T	0.36878	1.23;1.23	5.4	1.59	0.23543	.	0.806942	0.11865	N	0.522005	T	0.10423	0.0255	L	0.35414	1.06	0.09310	N	0.999999	B	0.19817	0.039	B	0.19148	0.024	T	0.30357	-0.9981	10	0.41790	T	0.15	-0.7707	7.0706	0.25177	0.0:0.2103:0.1265:0.6631	.	133	Q9UKT4	FBX5_HUMAN	M	133;87	ENSP00000229758:I133M;ENSP00000356210:I87M	ENSP00000229758:I133M	I	-	3	3	FBXO5	153338154	0.037000	0.19845	0.627000	0.29227	0.150000	0.21749	0.068000	0.14531	0.477000	0.27464	0.533000	0.62120	ATA	.		0.413	FBXO5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042757.1		
NID1	4811	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	236175334	236175334	+	Missense_Mutation	SNP	T	T	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr1:236175334T>A	ENST00000264187.6	-	12	2496	c.2414A>T	c.(2413-2415)gAa>gTa	p.E805V	NID1_ENST00000366595.3_Intron	NM_002508.2	NP_002499.2	P14543	NID1_HUMAN	nidogen 1	805	EGF-like 5; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				basement membrane organization (GO:0071711)|cell-matrix adhesion (GO:0007160)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glomerular basement membrane development (GO:0032836)|positive regulation of cell-substrate adhesion (GO:0010811)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|cell periphery (GO:0071944)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|laminin binding (GO:0043236)|proteoglycan binding (GO:0043394)			breast(4)|endometrium(9)|kidney(1)|large_intestine(23)|lung(20)|pancreas(1)|prostate(4)|skin(3)|urinary_tract(1)	66	Ovarian(103;0.0544)|Breast(184;0.23)	all_cancers(173;0.00491)|Prostate(94;0.184)|Acute lymphoblastic leukemia(190;0.229)	OV - Ovarian serous cystadenocarcinoma(106;0.00162)		Urokinase(DB00013)	TGGCTGGCATTCATCTACATC	0.483																																					p.E805V		.											.	.	.	0			c.A2414T						.						96.0	79.0	85.0					1																	236175334		2203	4300	6503	SO:0001583	missense	4811	exon12			TGGCATTCATCTA	BC045606	CCDS1608.1	1q43	2011-05-08	2005-06-02	2005-06-02	ENSG00000116962	ENSG00000116962			7821	protein-coding gene	gene with protein product		131390	"""nidogen (enactin)"""	NID		2471408, 7557988	Standard	NM_002508		Approved	entactin	uc001hxo.3	P14543	OTTHUMG00000040071	ENST00000264187.6:c.2414A>T	1.37:g.236175334T>A	ENSP00000264187:p.Glu805Val	Somatic	21	0		WXS	Illumina HiSeq	.	34	18	NM_002508	Q14942|Q59FL2|Q5TAF2|Q5TAF3|Q86XD7	Missense_Mutation	SNP	ENST00000264187.6	37	CCDS1608.1	.	.	.	.	.	.	.	.	.	.	T	25.2	4.611780	0.87258	.	.	ENSG00000116962	ENST00000264187	D	0.99800	-6.8	5.77	5.77	0.91146	EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (1);Epidermal growth factor-like, type 3 (1);	0.000000	0.85682	D	0.000000	D	0.99840	0.9927	H	0.95294	3.65	0.80722	D	1	D	0.76494	0.999	D	0.71414	0.973	D	0.96690	0.9510	10	0.87932	D	0	.	15.0773	0.72087	0.0:0.0:0.0:1.0	.	805	P14543	NID1_HUMAN	V	805	ENSP00000264187:E805V	ENSP00000264187:E805V	E	-	2	0	NID1	234241957	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	7.270000	0.78493	2.182000	0.69389	0.528000	0.53228	GAA	.		0.483	NID1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096647.2	NM_002508	
RAB27B	5874	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	18	52556641	52556641	+	Nonsense_Mutation	SNP	C	C	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr18:52556641C>A	ENST00000262094.5	+	6	1175	c.654C>A	c.(652-654)tgC>tgA	p.C218*	RP11-839G9.1_ENST00000588466.1_RNA	NM_004163.4	NP_004154.2	O00194	RB27B_HUMAN	RAB27B, member RAS oncogene family	218					multivesicular body sorting pathway (GO:0071985)|positive regulation of exocytosis (GO:0045921)|protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)	apical plasma membrane (GO:0016324)|extracellular vesicular exosome (GO:0070062)|Golgi stack (GO:0005795)|multivesicular body membrane (GO:0032585)|trans-Golgi network transport vesicle (GO:0030140)|zymogen granule membrane (GO:0042589)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|protein domain specific binding (GO:0019904)			large_intestine(3)|lung(3)|skin(1)	7				Colorectal(16;0.0273)|READ - Rectum adenocarcinoma(59;0.219)		AATGTATCTGCTAGACTCTAC	0.393																																					p.C218X		.											.	.	.	0			c.C654A						.						62.0	61.0	61.0					18																	52556641		2203	4300	6503	SO:0001587	stop_gained	5874	exon6			TATCTGCTAGACT	U57093	CCDS11958.1	18q21.2	2006-12-18			ENSG00000041353	ENSG00000041353		"""RAB, member RAS oncogene"""	9767	protein-coding gene	gene with protein product		603869				9066979	Standard	NM_004163		Approved		uc002lfr.3	O00194	OTTHUMG00000132710	ENST00000262094.5:c.654C>A	18.37:g.52556641C>A	ENSP00000262094:p.Cys218*	Somatic	68	0		WXS	Illumina HiSeq	.	36	11	NM_004163	B2RAB0|Q9BZB6	Nonsense_Mutation	SNP	ENST00000262094.5	37	CCDS11958.1	.	.	.	.	.	.	.	.	.	.	C	22.6	4.314672	0.81358	.	.	ENSG00000041353	ENST00000262094	.	.	.	5.61	3.83	0.44106	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	9.7603	0.40528	0.0:0.7747:0.0:0.2253	.	.	.	.	X	218	.	ENSP00000262094:C218X	C	+	3	2	RAB27B	50707639	0.994000	0.37717	1.000000	0.80357	0.872000	0.50106	0.304000	0.19228	0.845000	0.35118	0.655000	0.94253	TGC	.		0.393	RAB27B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256008.3	NM_004163	
PCF11	51585	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	11	82877696	82877696	+	Missense_Mutation	SNP	A	A	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr11:82877696A>G	ENST00000298281.4	+	5	2209	c.1757A>G	c.(1756-1758)gAa>gGa	p.E586G		NM_015885.3	NP_056969.2	O94913	PCF11_HUMAN	PCF11 cleavage and polyadenylation factor subunit	586					gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA cleavage (GO:0006379)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	mRNA cleavage factor complex (GO:0005849)|nucleoplasm (GO:0005654)		p.N587fs*33(1)		cervix(1)|endometrium(3)|kidney(4)|large_intestine(1)|lung(22)|ovary(1)|urinary_tract(1)	33						GAGAATGTAGAAAACTGGCAA	0.393																																					p.E586G		.											PCF11_ENST00000298281,bladder,carcinoma,+1,1	PCF11_ENST00000298281	+1	1	Deletion - Frameshift(1)	NS(1)	c.A1757G						.						67.0	67.0	67.0					11																	82877696		1807	4027	5834	SO:0001583	missense	51585	exon5			ATGTAGAAAACTG	AB020631	CCDS44689.1	11q13	2013-07-02	2013-07-02		ENSG00000165494	ENSG00000165494			30097	protein-coding gene	gene with protein product		608876	"""PCF11, cleavage and polyadenylation factor II subunit, homolog (S. cerevisiae)"", ""PCF11, cleavage and polyadenylation factor subunit, homolog (S. cerevisiae)"""			11060040	Standard	NM_015885		Approved	KIAA0824	uc001ozx.4	O94913	OTTHUMG00000167031	ENST00000298281.4:c.1757A>G	11.37:g.82877696A>G	ENSP00000298281:p.Glu586Gly	Somatic	124	0		WXS	Illumina HiSeq	.	77	30	NM_015885	A6H8W7|O43671|Q6P0X8	Missense_Mutation	SNP	ENST00000298281.4	37	CCDS44689.1	.	.	.	.	.	.	.	.	.	.	A	20.3	3.971908	0.74246	.	.	ENSG00000165494	ENST00000298281;ENST00000530660;ENST00000530304	T;T;T	0.52983	1.62;0.66;0.64	6.07	6.07	0.98685	.	0.095438	0.46145	D	0.000315	T	0.48822	0.1521	L	0.29908	0.895	0.48762	D	0.999705	D;P	0.60575	0.988;0.457	P;B	0.52343	0.696;0.129	T	0.38887	-0.9640	9	.	.	.	.	16.6406	0.85098	1.0:0.0:0.0:0.0	.	586;586	E9PQ01;O94913	.;PCF11_HUMAN	G	586	ENSP00000298281:E586G;ENSP00000434540:E586G;ENSP00000431567:E586G	.	E	+	2	0	PCF11	82555344	1.000000	0.71417	0.997000	0.53966	0.975000	0.68041	6.337000	0.72958	2.326000	0.78906	0.533000	0.62120	GAA	.		0.393	PCF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392548.2	NM_015885	
XKR4	114786	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	8	56015559	56015559	+	Missense_Mutation	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr8:56015559T>G	ENST00000327381.6	+	1	611	c.511T>G	c.(511-513)Ttc>Gtc	p.F171V		NM_052898.1	NP_443130.1	Q5GH76	XKR4_HUMAN	XK, Kell blood group complex subunit-related family, member 4	171						integral component of membrane (GO:0016021)				NS(1)|autonomic_ganglia(1)|endometrium(1)|kidney(3)|large_intestine(4)|liver(2)|lung(12)|ovary(1)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	34			Epithelial(17;0.000117)|all cancers(17;0.000836)			TGTGCACGATTTCAGCACCGA	0.672											OREG0006933	type=TRANSCRIPTION FACTOR BINDING SITE|Gene=XKR4|TFbs=REST|Dataset=NRSF/REST ChIPSeq sites|EvidenceSubtype=Chromatin immunoprecipitation with tag sequencing (ChIP-TS)																									p.F171V		.											.	.	.	0			c.T511G						.						41.0	31.0	34.0					8																	56015559		2203	4298	6501	SO:0001583	missense	114786	exon1			CACGATTTCAGCA	AY534241	CCDS34893.1	8q12.1	2006-01-12	2006-01-12		ENSG00000206579	ENSG00000206579			29394	protein-coding gene	gene with protein product			"""X Kell blood group precursor-related family, member 4"""				Standard	NM_052898		Approved	KIAA1889	uc003xsf.3	Q5GH76	OTTHUMG00000164288	ENST00000327381.6:c.511T>G	8.37:g.56015559T>G	ENSP00000328326:p.Phe171Val	Somatic	22	0	1012	WXS	Illumina HiSeq	.	23	9	NM_052898	Q96PZ8	Missense_Mutation	SNP	ENST00000327381.6	37	CCDS34893.1	.	.	.	.	.	.	.	.	.	.	T	25.6	4.658821	0.88154	.	.	ENSG00000206579	ENST00000327381;ENST00000543752	T	0.62639	0.01	5.57	5.57	0.84162	.	0.191099	0.44902	D	0.000405	T	0.65893	0.2735	L	0.36672	1.1	0.48185	D	0.999603	D	0.53619	0.961	P	0.54924	0.764	T	0.67027	-0.5774	10	0.48119	T	0.1	-1.1774	15.7316	0.77810	0.0:0.0:0.0:1.0	.	171	Q5GH76	XKR4_HUMAN	V	171	ENSP00000328326:F171V	ENSP00000328326:F171V	F	+	1	0	XKR4	56178113	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.430000	0.80321	2.118000	0.64928	0.528000	0.53228	TTC	.		0.672	XKR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378129.2	NM_052898	
UBR2	23304	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	6	42644579	42644579	+	Silent	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr6:42644579T>G	ENST00000372899.1	+	40	4704	c.4446T>G	c.(4444-4446)gcT>gcG	p.A1482A	UBR2_ENST00000372901.1_Silent_p.A1482A|UBR2_ENST00000372883.3_3'UTR	NM_015255.2	NP_056070.1	Q8IWV8	UBR2_HUMAN	ubiquitin protein ligase E3 component n-recognin 2	1482					cellular response to leucine (GO:0071233)|chromatin silencing (GO:0006342)|histone H2A ubiquitination (GO:0033522)|male meiosis I (GO:0007141)|negative regulation of TOR signaling (GO:0032007)|spermatogenesis (GO:0007283)|ubiquitin-dependent protein catabolic process (GO:0006511)	chromatin (GO:0000785)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ubiquitin ligase complex (GO:0000151)	leucine binding (GO:0070728)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(10)|kidney(7)|large_intestine(14)|lung(22)|ovary(3)|pancreas(1)|skin(5)	64	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)|all cancers(41;0.004)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.196)			CAGTTCTTGCTTTGTATAAAA	0.358																																					p.A1482A		.											.	.	.	0			c.T4446G						.						134.0	122.0	126.0					6																	42644579		2203	4300	6503	SO:0001819	synonymous_variant	23304	exon40			TCTTGCTTTGTAT	BC024217	CCDS4870.1, CCDS55001.1	6p21.1	2008-06-23	2005-01-10	2005-01-12	ENSG00000024048	ENSG00000024048		"""Ubiquitin protein ligase E3 component n-recognins"""	21289	protein-coding gene	gene with protein product		609134	"""chromosome 6 open reading frame 133"""	C6orf133			Standard	NM_015255		Approved	bA49A4.1, dJ392M17.3, KIAA0349	uc011dur.2	Q8IWV8	OTTHUMG00000014703	ENST00000372899.1:c.4446T>G	6.37:g.42644579T>G		Somatic	71	0		WXS	Illumina HiSeq	.	50	31	NM_015255	O15057|Q4VXK2|Q5TFH6|Q6P2I2|Q6ZUD0	Silent	SNP	ENST00000372899.1	37	CCDS4870.1																																																																																			.		0.358	UBR2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040558.2	NM_015255	
DST	667	hgsc.bcm.edu	37	6	56406143	56406143	+	Intron	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr6:56406143A>C	ENST00000361203.3	-	58	15983				DST_ENST00000312431.6_Intron|DST_ENST00000446842.2_Intron|DST_ENST00000340834.4_5'Flank|DST_ENST00000244364.6_Intron|DST_ENST00000421834.2_Intron|DST_ENST00000370754.5_Intron|DST_ENST00000370769.4_Intron|DST_ENST00000370788.2_Intron			Q03001	DYST_HUMAN	dystonin						axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell motility (GO:0048870)|cytoplasmic microtubule organization (GO:0031122)|cytoskeleton organization (GO:0007010)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|maintenance of cell polarity (GO:0030011)|microtubule cytoskeleton organization (GO:0000226)|regulation of microtubule polymerization or depolymerization (GO:0031110)|response to wounding (GO:0009611)|retrograde axon cargo transport (GO:0008090)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integral component of membrane (GO:0016021)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|neurofilament cytoskeleton (GO:0060053)|nucleus (GO:0005634)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|microtubule plus-end binding (GO:0051010)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)			NS(1)|breast(5)|central_nervous_system(8)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(43)|ovary(7)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	105	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			ATAAAGAACTAACATCCAGTG	0.398																																					.		.											.	.	.	0			.						.																																			SO:0001627	intron_variant	100873774	.			AGAACTAACATCC	M22942, M69225	CCDS4959.1, CCDS47443.1, CCDS75474.1	6p12.1	2013-01-10	2004-06-25	2004-07-01	ENSG00000151914	ENSG00000151914		"""EF-hand domain containing"""	1090	protein-coding gene	gene with protein product		113810	"""bullous pemphigoid antigen 1, 230/240kDa"""	BPAG1		2461961, 2276744	Standard	NM_001144770		Approved	BP240, KIAA0728, FLJ21489, FLJ13425, FLJ32235, FLJ30627, CATX-15, BPA, MACF2	uc021zba.2	Q03001	OTTHUMG00000014913	ENST00000361203.3:c.15976-4405T>G	6.37:g.56406143A>C		Somatic	70	0		WXS	Illumina HiSeq	.	63	16	.	B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	RNA	SNP	ENST00000361203.3	37																																																																																				.		0.398	DST-004	NOVEL	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000041021.3	NM_001723	
FST	10468	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	5	52779381	52779381	+	Missense_Mutation	SNP	A	A	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr5:52779381A>G	ENST00000256759.3	+	3	708	c.325A>G	c.(325-327)Aac>Gac	p.N109D	FST_ENST00000396947.3_Missense_Mutation_p.N109D	NM_013409.2	NP_037541.1	P19883	FST_HUMAN	follistatin	109	Follistatin-like 1.				BMP signaling pathway (GO:0030509)|female gonad development (GO:0008585)|gamete generation (GO:0007276)|hair follicle morphogenesis (GO:0031069)|hematopoietic progenitor cell differentiation (GO:0002244)|keratinocyte proliferation (GO:0043616)|negative regulation of activin receptor signaling pathway (GO:0032926)|negative regulation of cell differentiation (GO:0045596)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|odontogenesis of dentin-containing tooth (GO:0042475)|pattern specification process (GO:0007389)|positive regulation of hair follicle development (GO:0051798)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|nucleus (GO:0005634)	activin binding (GO:0048185)|signal transducer activity (GO:0004871)			breast(1)|endometrium(1)|large_intestine(4)|lung(7)|prostate(1)|urinary_tract(1)	15		Ovarian(174;1.78e-06)|Lung NSC(810;3.55e-06)|Breast(144;4.08e-05)				ATGCCGAATGAACAAGAAGAA	0.527																																					p.N109D		.											.	.	.	0			c.A325G						.						80.0	77.0	78.0					5																	52779381		2203	4300	6503	SO:0001583	missense	10468	exon3			CGAATGAACAAGA	M19481	CCDS3959.1, CCDS43315.1	5q11.2	2008-02-05			ENSG00000134363	ENSG00000134363			3971	protein-coding gene	gene with protein product		136470				10411917, 3380788	Standard	NM_006350		Approved	FS	uc003jpd.3	P19883	OTTHUMG00000131183	ENST00000256759.3:c.325A>G	5.37:g.52779381A>G	ENSP00000256759:p.Asn109Asp	Somatic	84	0		WXS	Illumina HiSeq	.	79	22	NM_013409	B5BU94|Q9BTH0	Missense_Mutation	SNP	ENST00000256759.3	37	CCDS3959.1	.	.	.	.	.	.	.	.	.	.	A	34	5.371881	0.95923	.	.	ENSG00000134363	ENST00000256759;ENST00000511025;ENST00000396947	T;T	0.28454	1.61;1.84	5.66	5.66	0.87406	Follistatin-like, N-terminal (1);Follistatin/Osteonectin EGF domain (1);	0.000000	0.85682	D	0.000000	T	0.46833	0.1413	L	0.57536	1.79	0.80722	D	1	D	0.53885	0.963	P	0.58130	0.833	T	0.27536	-1.0071	10	0.29301	T	0.29	-34.9635	15.8956	0.79333	1.0:0.0:0.0:0.0	.	109	P19883	FST_HUMAN	D	109	ENSP00000256759:N109D;ENSP00000380151:N109D	ENSP00000256759:N109D	N	+	1	0	FST	52815138	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.305000	0.96197	2.154000	0.67381	0.402000	0.26972	AAC	.		0.527	FST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253906.1	NM_013409	
ZNF598	90850	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	16	2052709	2052709	+	Missense_Mutation	SNP	A	A	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr16:2052709A>G	ENST00000563630.1	-	4	567	c.325T>C	c.(325-327)Tac>Cac	p.Y109H	ZNF598_ENST00000431526.1_Missense_Mutation_p.Y164H|ZNF598_ENST00000562103.1_Missense_Mutation_p.Y109H			Q86UK7	ZN598_HUMAN	zinc finger protein 598	164							poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|lung(7)|skin(1)|urinary_tract(1)	16						TTGCGCGAGTACCACTTGCGC	0.642																																					p.Y164H		.											.	.	.	0			c.T490C						.						31.0	35.0	34.0					16																	2052709		2120	4240	6360	SO:0001583	missense	90850	exon6			GCGAGTACCACTT	BC029270		16p13.3	2008-05-02				ENSG00000167962		"""Zinc fingers, C2H2-type"""	28079	protein-coding gene	gene with protein product							Standard	NM_178167		Approved	FLJ00086	uc002cof.2	Q86UK7		ENST00000563630.1:c.325T>C	16.37:g.2052709A>G	ENSP00000455882:p.Tyr109His	Somatic	10	0		WXS	Illumina HiSeq	.	18	12	NM_178167	Q8IW49|Q8N3D9|Q96FG3|Q9H7J3	Missense_Mutation	SNP	ENST00000563630.1	37		.	.	.	.	.	.	.	.	.	.	.	25.4	4.635300	0.87760	.	.	ENSG00000167962	ENST00000431526	T	0.14893	2.47	4.98	4.98	0.66077	.	0.000000	0.85682	D	0.000000	T	0.45196	0.1330	M	0.82716	2.605	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.51458	-0.8703	10	0.87932	D	0	-32.4357	13.8277	0.63361	1.0:0.0:0.0:0.0	.	164	Q86UK7	ZN598_HUMAN	H	164	ENSP00000411409:Y164H	ENSP00000411409:Y164H	Y	-	1	0	ZNF598	1992710	1.000000	0.71417	1.000000	0.80357	0.899000	0.52679	8.905000	0.92613	1.871000	0.54225	0.459000	0.35465	TAC	.		0.642	ZNF598-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000434439.1	NM_178167	
PPAP2A	8611	hgsc.bcm.edu;ucsc.edu	37	5	54826126	54826126	+	Intron	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr5:54826126T>G	ENST00000307259.8	-	1	479				PPAP2A_ENST00000264775.5_Intron|PPAP2A_ENST00000515132.1_Intron	NM_003711.2	NP_003702.2	O14494	LPP1_HUMAN	phosphatidic acid phosphatase type 2A						androgen receptor signaling pathway (GO:0030521)|germ cell migration (GO:0008354)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|lipid metabolic process (GO:0006629)|negative regulation of cell proliferation (GO:0008285)|phospholipid dephosphorylation (GO:0046839)|protein dephosphorylation (GO:0006470)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of lipid metabolic process (GO:0019216)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	phosphatidate phosphatase activity (GO:0008195)			breast(2)|endometrium(1)|large_intestine(1)|lung(2)|ovary(2)|prostate(1)	9		Lung NSC(810;4.08e-05)|Prostate(74;0.0181)|Breast(144;0.0544)				CTGGCTAGGATCTCCCCAAGG	0.368																																					.		.											.	.	.	0			.						.																																			SO:0001627	intron_variant	379013	.			CTAGGATCTCCCC	AB000888	CCDS34159.1, CCDS34160.1	5q11	2009-05-27			ENSG00000067113	ENSG00000067113	3.1.3.4		9228	protein-coding gene	gene with protein product		607124				9305923	Standard	NM_003711		Approved	PAP-2a, LPP1	uc003jpz.4	O14494	OTTHUMG00000162240	ENST00000307259.8:c.58+4273A>C	5.37:g.54826126T>G		Somatic	72	0		WXS	Illumina HiSeq	.	55	9	.	B7ZKN8|G3XA95|O60457|O60463|Q17RZ4	RNA	SNP	ENST00000307259.8	37	CCDS34159.1																																																																																			.		0.368	PPAP2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368073.1		
CARD11	84433	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	7	2977638	2977638	+	Missense_Mutation	SNP	A	A	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr7:2977638A>G	ENST00000396946.4	-	8	1449	c.1046T>C	c.(1045-1047)cTc>cCc	p.L349P		NM_032415.4	NP_115791.3	Q9BXL7	CAR11_HUMAN	caspase recruitment domain family, member 11	349					Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|nucleotide phosphorylation (GO:0046939)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cytokine production (GO:0001819)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of T cell proliferation (GO:0042102)|regulation of apoptotic process (GO:0042981)|regulation of B cell differentiation (GO:0045577)|regulation of T cell differentiation (GO:0045580)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|thymic T cell selection (GO:0045061)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|immunological synapse (GO:0001772)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	CARD domain binding (GO:0050700)|guanylate kinase activity (GO:0004385)			NS(1)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(62)|kidney(11)|large_intestine(13)|lung(31)|ovary(4)|prostate(5)|skin(7)|upper_aerodigestive_tract(2)	150		Ovarian(82;0.0115)		OV - Ovarian serous cystadenocarcinoma(56;8.44e-14)		CGAGCACTTGAGCTCCAGGTC	0.542			Mis		DLBCL																																p.L349P		.		Dom	yes		7	7p22	84433	"""caspase recruitment domain family, member 11"""		L	.	.	.	0			c.T1046C						.						157.0	133.0	141.0					7																	2977638		2203	4300	6503	SO:0001583	missense	84433	exon8			CACTTGAGCTCCA	AF322641	CCDS5336.2	7p22	2014-09-17			ENSG00000198286	ENSG00000198286			16393	protein-coding gene	gene with protein product	"""card-maguk protein 1"", ""bcl10-interacting maguk protein 3"""	607210				11278692, 11356195	Standard	NM_032415		Approved	CARMA1, BIMP3	uc003smv.3	Q9BXL7	OTTHUMG00000023023	ENST00000396946.4:c.1046T>C	7.37:g.2977638A>G	ENSP00000380150:p.Leu349Pro	Somatic	33	0		WXS	Illumina HiSeq	.	14	4	NM_032415	A4D1Z7|Q2NKN7|Q548H3	Missense_Mutation	SNP	ENST00000396946.4	37	CCDS5336.2	.	.	.	.	.	.	.	.	.	.	A	22.1	4.246676	0.80024	.	.	ENSG00000198286	ENST00000396946	T	0.37058	1.22	5.0	5.0	0.66597	.	0.000000	0.64402	D	0.000004	T	0.51483	0.1677	L	0.52364	1.645	0.80722	D	1	D	0.61080	0.989	D	0.63703	0.917	T	0.53885	-0.8375	10	0.66056	D	0.02	-26.5461	13.8813	0.63684	1.0:0.0:0.0:0.0	.	349	Q9BXL7	CAR11_HUMAN	P	349	ENSP00000380150:L349P	ENSP00000380150:L349P	L	-	2	0	CARD11	2944164	1.000000	0.71417	0.999000	0.59377	0.985000	0.73830	9.048000	0.93830	1.878000	0.54408	0.482000	0.46254	CTC	.		0.542	CARD11-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059344.4	NM_032415	
MUC5B	727897	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	11	1280229	1280229	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr11:1280229G>T	ENST00000529681.1	+	44	16709	c.16651G>T	c.(16651-16653)Gac>Tac	p.D5551Y	MUC5B_ENST00000447027.1_Missense_Mutation_p.D5554Y	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	5551	VWFC 3. {ECO:0000255|PROSITE- ProRule:PRU00220}.				cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to retinoic acid (GO:0071300)|epithelial cell differentiation (GO:0030855)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to lipopolysaccharide (GO:0032496)|response to ozone (GO:0010193)|response to sulfur dioxide (GO:0010477)|response to vitamin A (GO:0033189)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				cervix(2)|endometrium(36)|kidney(9)|lung(89)|urinary_tract(1)	137		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)		CCTCTCTGGGGACACCCAGGA	0.647																																					p.D5551Y		.											.	.	.	0			c.G16651T						.						36.0	45.0	42.0					11																	1280229		1946	4099	6045	SO:0001583	missense	727897	exon44			TCTGGGGACACCC	U95031, AF086604	CCDS44515.1, CCDS44515.2	11p15.5	2007-01-19	2006-03-14			ENSG00000117983		"""Mucins"""	7516	protein-coding gene	gene with protein product		600770	"""mucin 5, subtype B, tracheobronchial"""	MUC5		9804771	Standard	NM_002458		Approved	MG1	uc001lta.3	Q9HC84		ENST00000529681.1:c.16651G>T	11.37:g.1280229G>T	ENSP00000436812:p.Asp5551Tyr	Somatic	82	0		WXS	Illumina HiSeq	.	57	20	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	37	CCDS44515.2	.	.	.	.	.	.	.	.	.	.	G	10.44	1.349619	0.24426	.	.	ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637;ENST00000546052;ENST00000406844;ENST00000526859	T;T	0.18960	2.18;2.37	4.8	3.87	0.44632	.	.	.	.	.	T	0.36608	0.0973	L	0.60455	1.87	0.09310	N	1	D;D	0.65815	0.995;0.995	D;D	0.68353	0.957;0.957	T	0.15235	-1.0444	9	0.87932	D	0	.	5.5697	0.17190	0.1009:0.0:0.7007:0.1984	.	5888;5554	A7Y9J9;E9PBJ0	.;.	Y	5551;5554;5495;450;5263;96	ENSP00000436812:D5551Y;ENSP00000415793:D5554Y	ENSP00000343037:D5495Y	D	+	1	0	MUC5B	1236805	0.000000	0.05858	0.005000	0.12908	0.273000	0.26683	0.413000	0.21148	2.381000	0.81170	0.561000	0.74099	GAC	.		0.647	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
STK32C	282974	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	10	134039116	134039116	+	Missense_Mutation	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr10:134039116A>C	ENST00000368622.1	-	6	717	c.336T>G	c.(334-336)caT>caG	p.H112Q	STK32C_ENST00000368625.4_Missense_Mutation_p.H242Q					serine/threonine kinase 32C											breast(1)|endometrium(2)|large_intestine(2)|lung(15)|ovary(2)|skin(1)	23		all_cancers(35;2.72e-11)|all_epithelial(44;2.33e-08)|Lung NSC(174;0.000855)|all_lung(145;0.00146)|all_neural(114;0.0299)|Breast(234;0.106)|Colorectal(31;0.112)|Melanoma(40;0.124)|Glioma(114;0.203)		Epithelial(32;3.99e-05)|all cancers(32;5.58e-05)|OV - Ovarian serous cystadenocarcinoma(35;9.96e-05)|BRCA - Breast invasive adenocarcinoma(275;0.222)		TCAGGTGTGCATGTCCTGTGC	0.622																																					p.H229Q		.											.	.	.	0			c.T687G						.						203.0	176.0	185.0					10																	134039116		2203	4300	6503	SO:0001583	missense	282974	exon6			GTGTGCATGTCCT	AK057849	CCDS7666.1	10q26.3	2004-07-22			ENSG00000165752	ENSG00000165752			21332	protein-coding gene	gene with protein product							Standard	NM_173575		Approved	PKE, MGC23665, YANK3	uc001lle.1	Q86UX6	OTTHUMG00000019285	ENST00000368622.1:c.336T>G	10.37:g.134039116A>C	ENSP00000357611:p.His112Gln	Somatic	32	0		WXS	Illumina HiSeq	.	17	7	NM_173575		Missense_Mutation	SNP	ENST00000368622.1	37		.	.	.	.	.	.	.	.	.	.	A	12.41	1.930756	0.34096	.	.	ENSG00000165752	ENST00000368622;ENST00000298630;ENST00000368625	T;T;T	0.63913	-0.07;-0.07;-0.07	4.45	-6.97	0.01616	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	0.000005	T	0.70369	0.3216	L	0.61387	1.9	0.45607	D	0.998548	D;D;D	0.76494	0.996;0.999;0.998	D;D;D	0.81914	0.975;0.991;0.995	T	0.76498	-0.2937	10	0.87932	D	0	.	15.1965	0.73096	0.6734:0.0:0.3266:0.0	.	242;168;229	B7Z7J1;F2Z300;Q86UX6	.;.;ST32C_HUMAN	Q	112;229;242	ENSP00000357611:H112Q;ENSP00000298630:H229Q;ENSP00000357614:H242Q	ENSP00000298630:H229Q	H	-	3	2	STK32C	133889106	0.036000	0.19791	0.155000	0.22561	0.222000	0.24845	-0.594000	0.05733	-1.494000	0.01833	-0.973000	0.02599	CAT	.		0.622	STK32C-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000051068.2	NM_173575	
ACSM5	54988	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	16	20451133	20451133	+	Silent	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr16:20451133A>C	ENST00000331849.4	+	13	1695	c.1548A>C	c.(1546-1548)gcA>gcC	p.A516A	CTD-2194A8.2_ENST00000575772.1_RNA|CTD-2194A8.2_ENST00000574654.1_RNA	NM_017888.2	NP_060358.2	Q6NUN0	ACSM5_HUMAN	acyl-CoA synthetase medium-chain family member 5	516					fatty acid metabolic process (GO:0006631)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|butyrate-CoA ligase activity (GO:0047760)|GTP binding (GO:0005525)|metal ion binding (GO:0046872)	p.A516A(1)		breast(1)|endometrium(6)|kidney(2)|large_intestine(6)|lung(28)|ovary(3)|prostate(1)|skin(3)|urinary_tract(1)	51						TGGTAAAGGCATTTATAGTCC	0.453																																					p.A516A		.											ACSM5,NS,carcinoma,0,1	ACSM5	0	1	Substitution - coding silent(1)	prostate(1)	c.A1548C						.						77.0	77.0	77.0					16																	20451133		2203	4296	6499	SO:0001819	synonymous_variant	54988	exon13			AAAGGCATTTATA		CCDS10585.1	16p12.3	2007-10-17			ENSG00000183549	ENSG00000183549		"""Acyl-CoA synthetase family"""	26060	protein-coding gene	gene with protein product		614361				17762044	Standard	NM_017888		Approved	FLJ20581	uc002dhe.3	Q6NUN0	OTTHUMG00000131551	ENST00000331849.4:c.1548A>C	16.37:g.20451133A>C		Somatic	98	0		WXS	Illumina HiSeq	.	72	22	NM_017888	Q96AV1|Q96CX8|Q9NWV3	Silent	SNP	ENST00000331849.4	37	CCDS10585.1																																																																																			.		0.453	ACSM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254413.1	NM_017888	
C18orf63	644041	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	18	72020689	72020689	+	Missense_Mutation	SNP	A	A	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr18:72020689A>T	ENST00000579455.1	+	12	1516	c.1187A>T	c.(1186-1188)aAg>aTg	p.K396M		NM_001174123.1	NP_001167594.1	Q68DL7	CR063_HUMAN	chromosome 18 open reading frame 63	396										breast(1)	1						CAGGGTAGAAAGAAATCCCTG	0.468																																					p.K396M		.											.	.	.	0			c.A1187T						.																																			SO:0001583	missense	644041	exon12			GTAGAAAGAAATC		CCDS54189.1	18q22.3	2012-10-24			ENSG00000206043	ENSG00000206043			40037	protein-coding gene	gene with protein product							Standard	NM_001174123		Approved	DKFZP781G0119	uc002llj.3	Q68DL7	OTTHUMG00000178987	ENST00000579455.1:c.1187A>T	18.37:g.72020689A>T	ENSP00000464330:p.Lys396Met	Somatic	58	0		WXS	Illumina HiSeq	.	36	20	NM_001174123	A6NME8	Missense_Mutation	SNP	ENST00000579455.1	37	CCDS54189.1	.	.	.	.	.	.	.	.	.	.	A	1.973	-0.436022	0.04636	.	.	ENSG00000206043	ENST00000382675	.	.	.	5.51	-1.74	0.08056	.	0.718426	0.12574	N	0.457050	T	0.23171	0.0560	M	0.68317	2.08	0.09310	N	1	P	0.43938	0.822	B	0.30855	0.121	T	0.26326	-1.0106	9	0.66056	D	0.02	-8.9454	1.2191	0.01920	0.3551:0.1488:0.3321:0.164	.	396	Q68DL7	CR063_HUMAN	M	396	.	ENSP00000372122:K396M	K	+	2	0	C18orf63	70171669	0.004000	0.15560	0.000000	0.03702	0.009000	0.06853	0.381000	0.20619	0.052000	0.16007	0.533000	0.62120	AAG	.		0.468	C18orf63-001	KNOWN	non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444246.2	NM_001174123	
PRDM4	11108	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	12	108145645	108145645	+	Missense_Mutation	SNP	T	T	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr12:108145645T>C	ENST00000228437.5	-	5	1132	c.673A>G	c.(673-675)Atc>Gtc	p.I225V	PRDM4_ENST00000547268.1_5'Flank|RP11-864J10.4_ENST00000546714.1_RNA	NM_012406.3	NP_036538.3	Q9UKN5	PRDM4_HUMAN	PR domain containing 4	225					cell proliferation (GO:0008283)|negative regulation of cell cycle (GO:0045786)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|methyltransferase activity (GO:0008168)|zinc ion binding (GO:0008270)			biliary_tract(1)|breast(2)|endometrium(1)|kidney(2)|large_intestine(3)|lung(6)|prostate(2)|skin(2)|urinary_tract(1)	20						CCATTTGGGATTTGGGAATGC	0.502																																					p.I225V		.											.	.	.	0			c.A673G						.						128.0	110.0	116.0					12																	108145645		2203	4300	6503	SO:0001583	missense	11108	exon5			TTGGGATTTGGGA	AF144757	CCDS9115.1	12q23-q24.1	2013-01-08				ENSG00000110851		"""Zinc fingers, C2H2-type"""	9348	protein-coding gene	gene with protein product		605780				10552934	Standard	NM_012406		Approved	PFM1	uc001tmp.3	Q9UKN5	OTTHUMG00000169914	ENST00000228437.5:c.673A>G	12.37:g.108145645T>C	ENSP00000228437:p.Ile225Val	Somatic	44	0		WXS	Illumina HiSeq	.	23	6	NM_012406	Q9UFA6	Missense_Mutation	SNP	ENST00000228437.5	37	CCDS9115.1	.	.	.	.	.	.	.	.	.	.	T	13.94	2.387315	0.42308	.	.	ENSG00000110851	ENST00000228437	T	0.09723	2.95	5.93	5.93	0.95920	.	0.244651	0.45606	D	0.000347	T	0.07954	0.0199	N	0.14661	0.345	0.35293	D	0.782354	B	0.06786	0.001	B	0.10450	0.005	T	0.12578	-1.0542	10	0.72032	D	0.01	.	12.2529	0.54608	0.0:0.0:0.1416:0.8584	.	225	Q9UKN5	PRDM4_HUMAN	V	225	ENSP00000228437:I225V	ENSP00000228437:I225V	I	-	1	0	PRDM4	106669775	1.000000	0.71417	0.984000	0.44739	0.989000	0.77384	2.882000	0.48546	2.263000	0.75096	0.533000	0.62120	ATC	.		0.502	PRDM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406546.1	NM_012406	
FBXO6	26270	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	11733376	11733376	+	Missense_Mutation	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr1:11733376A>C	ENST00000376753.4	+	5	687	c.552A>C	c.(550-552)aaA>aaC	p.K184N		NM_018438.5	NP_060908.1	Q9NRD1	FBX6_HUMAN	F-box protein 6	184	FBA. {ECO:0000255|PROSITE- ProRule:PRU00482}.				DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|glycoprotein catabolic process (GO:0006516)|proteolysis (GO:0006508)|response to unfolded protein (GO:0006986)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)	cytoplasm (GO:0005737)|SCF ubiquitin ligase complex (GO:0019005)	carbohydrate binding (GO:0030246)|glycoprotein binding (GO:0001948)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|large_intestine(1)|lung(1)|ovary(1)|upper_aerodigestive_tract(2)	6	Ovarian(185;0.249)	Lung NSC(185;4.15e-05)|all_lung(284;4.76e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.25e-06)|COAD - Colon adenocarcinoma(227;0.000251)|BRCA - Breast invasive adenocarcinoma(304;0.000297)|Kidney(185;0.000747)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.00727)|READ - Rectum adenocarcinoma(331;0.0649)		ACCAACTCAAAGTGCAGCTGG	0.622																																					p.K184N	NSCLC(54;506 1562 46490 51389)	.											.	.	.	0			c.A552C						.						70.0	60.0	64.0					1																	11733376		2203	4300	6503	SO:0001583	missense	26270	exon5			ACTCAAAGTGCAG	AF129536	CCDS133.1	1p36.22	2008-05-14	2004-06-15		ENSG00000116663	ENSG00000116663		"""F-boxes /  ""other"""""	13585	protein-coding gene	gene with protein product		605647	"""F-box only protein 6"""			10531035, 10945468	Standard	NM_018438		Approved	FBX6, FBG2, FBS2, Fbx6b	uc001aso.3	Q9NRD1	OTTHUMG00000002229	ENST00000376753.4:c.552A>C	1.37:g.11733376A>C	ENSP00000365944:p.Lys184Asn	Somatic	43	0		WXS	Illumina HiSeq	.	17	11	NM_018438	B1AK42|B2RC88|Q9UKT3	Missense_Mutation	SNP	ENST00000376753.4	37	CCDS133.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	0.971|0.971	-0.700314|-0.700314	0.03279|0.03279	.|.	.|.	ENSG00000116663|ENSG00000116663	ENST00000376753|ENST00000449067	T|T	0.28666|0.27890	1.6|1.64	5.69|5.69	-11.4|-11.4	0.00090|0.00090	Galactose-binding domain-like (1);F-box associated (FBA) domain (2);|.	1.040950|1.040950	0.07480|0.07480	N|N	0.903676|0.903676	T|T	0.11196|0.11196	0.0273|0.0273	N|N	0.25890|0.25890	0.77|0.77	0.09310|0.09310	N|N	0.999991|0.999991	P|.	0.38195|.	0.622|.	B|.	0.42245|.	0.381|.	T|T	0.13202|0.13202	-1.0518|-1.0518	10|8	0.15499|0.13108	T|T	0.54|0.6	.|.	0.4713|0.4713	0.00532|0.00532	0.3536:0.2149:0.2155:0.216|0.3536:0.2149:0.2155:0.216	.|.	184|.	Q9NRD1|.	FBX6_HUMAN|.	N|T	184|140	ENSP00000365944:K184N|ENSP00000388781:K140T	ENSP00000365944:K184N|ENSP00000388781:K140T	K|K	+|+	3|2	2|0	FBXO6|FBXO6	11655963|11655963	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.006000|0.006000	0.05464|0.05464	-3.614000|-3.614000	0.00414|0.00414	-2.980000|-2.980000	0.00283|0.00283	-1.342000|-1.342000	0.01247|0.01247	AAA|AAG	.		0.622	FBXO6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006332.1	NM_018438	
C2orf71	388939	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	2	29295281	29295281	+	Missense_Mutation	SNP	T	T	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr2:29295281T>A	ENST00000331664.5	-	1	1846	c.1847A>T	c.(1846-1848)cAg>cTg	p.Q616L		NM_001029883.2	NP_001025054.1	A6NGG8	CB071_HUMAN	chromosome 2 open reading frame 71	616					response to stimulus (GO:0050896)|visual perception (GO:0007601)	primary cilium (GO:0072372)				NS(2)|breast(5)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(11)|lung(20)|ovary(2)|prostate(6)|skin(3)|stomach(1)	60						GAGGTCCCTCTGGACCCTTCG	0.632																																					p.Q616L		.											.	.	.	0			c.A1847T						.						33.0	35.0	35.0					2																	29295281		2028	4182	6210	SO:0001583	missense	388939	exon1			TCCCTCTGGACCC		CCDS42669.1	2p23.2	2014-01-28			ENSG00000179270	ENSG00000179270			34383	protein-coding gene	gene with protein product		613425				20398886	Standard	NM_001029883		Approved	FLJ34931, RP54	uc002rmt.2	A6NGG8	OTTHUMG00000152024	ENST00000331664.5:c.1847A>T	2.37:g.29295281T>A	ENSP00000332809:p.Gln616Leu	Somatic	18	0		WXS	Illumina HiSeq	.	14	7	NM_001029883		Missense_Mutation	SNP	ENST00000331664.5	37	CCDS42669.1	.	.	.	.	.	.	.	.	.	.	T	25.5	4.640159	0.87760	.	.	ENSG00000179270	ENST00000331664	T	0.36157	1.27	5.32	5.32	0.75619	.	0.000000	0.85682	D	0.000000	T	0.59985	0.2234	M	0.71581	2.175	0.50313	D	0.999869	D	0.89917	1.0	D	0.91635	0.999	T	0.64262	-0.6449	10	0.72032	D	0.01	-19.1155	15.3007	0.73949	0.0:0.0:0.0:1.0	.	616	A6NGG8	CB071_HUMAN	L	616	ENSP00000332809:Q616L	ENSP00000332809:Q616L	Q	-	2	0	C2orf71	29148785	1.000000	0.71417	1.000000	0.80357	0.896000	0.52359	7.268000	0.78473	2.023000	0.59567	0.459000	0.35465	CAG	.		0.632	C2orf71-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000324924.3	NM_001029883	
ASCC3	10973	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	6	101100758	101100758	+	Missense_Mutation	SNP	G	G	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr6:101100758G>C	ENST00000369162.2	-	18	3175	c.2831C>G	c.(2830-2832)cCa>cGa	p.P944R		NM_006828.2	NP_006819.2	Q8N3C0	ASCC3_HUMAN	activating signal cointegrator 1 complex subunit 3	944					cell proliferation (GO:0008283)|DNA dealkylation involved in DNA repair (GO:0006307)|DNA duplex unwinding (GO:0032508)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular (GO:0005622)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent 3'-5' DNA helicase activity (GO:0043140)|poly(A) RNA binding (GO:0044822)			breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(20)|liver(1)|lung(36)|ovary(6)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	92		all_cancers(76;1.45e-07)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(87;0.00149)|Hepatocellular(1;0.0893)|Colorectal(196;0.13)		BRCA - Breast invasive adenocarcinoma(108;0.0539)|all cancers(137;0.103)|GBM - Glioblastoma multiforme(226;0.199)		TCTTAATGTTGGGTCAATCTA	0.323																																					p.P944R		.											.	.	.	0			c.C2831G						.						68.0	65.0	66.0					6																	101100758		2202	4300	6502	SO:0001583	missense	10973	exon18			AATGTTGGGTCAA	AJ223948	CCDS5046.1, CCDS5047.1, CCDS75497.1	6q16	2008-02-05		2004-07-28	ENSG00000112249	ENSG00000112249			18697	protein-coding gene	gene with protein product	"""RNA helicase family"""	614217	"""helicase, ATP binding 1"""	HELIC1		10218103	Standard	NM_006828		Approved	RNAH, ASC1p200, dJ121G13.4, dJ467N11.1	uc003pqk.3	Q8N3C0	OTTHUMG00000015279	ENST00000369162.2:c.2831C>G	6.37:g.101100758G>C	ENSP00000358159:p.Pro944Arg	Somatic	128	0		WXS	Illumina HiSeq	.	89	5	NM_006828	E7EW23|O43738|Q4G1A0|Q5VTN2|Q9H1I9|Q9H5A2|Q9NTR0	Missense_Mutation	SNP	ENST00000369162.2	37	CCDS5046.1	.	.	.	.	.	.	.	.	.	.	G	22.3	4.271521	0.80469	.	.	ENSG00000112249	ENST00000369162	T	0.59083	0.29	5.68	4.79	0.61399	.	0.109417	0.64402	N	0.000005	T	0.67135	0.2861	M	0.64630	1.985	0.80722	D	1	D	0.89917	1.0	D	0.73380	0.98	T	0.72683	-0.4219	10	0.66056	D	0.02	.	16.7566	0.85501	0.0:0.1293:0.8707:0.0	.	944	Q8N3C0	HELC1_HUMAN	R	944	ENSP00000358159:P944R	ENSP00000358159:P944R	P	-	2	0	ASCC3	101207479	1.000000	0.71417	1.000000	0.80357	0.949000	0.60115	7.856000	0.86956	1.476000	0.48215	0.591000	0.81541	CCA	.		0.323	ASCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041632.2	NM_006828	
ZFAND2B	130617	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	2	220072980	220072980	+	Missense_Mutation	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr2:220072980T>G	ENST00000289528.5	+	5	632	c.437T>G	c.(436-438)cTt>cGt	p.L146R	ZFAND2B_ENST00000409206.1_Missense_Mutation_p.L146R|ZFAND2B_ENST00000409594.1_Missense_Mutation_p.L146R|ZFAND2B_ENST00000409319.1_3'UTR|ZFAND2B_ENST00000409217.1_Missense_Mutation_p.L146R|ZFAND2B_ENST00000409097.1_Missense_Mutation_p.L146R|ZFAND2B_ENST00000444522.2_Missense_Mutation_p.L146R|ZFAND2B_ENST00000409336.1_Missense_Mutation_p.L146R	NM_001270998.1|NM_001270999.1|NM_138802.2	NP_001257927.1|NP_001257928.1|NP_620157.1	Q8WV99	ZFN2B_HUMAN	zinc finger, AN1-type domain 2B	146						endoplasmic reticulum (GO:0005783)	zinc ion binding (GO:0008270)			endometrium(2)|kidney(4)|lung(4)|upper_aerodigestive_tract(1)	11		Renal(207;0.0915)		Epithelial(149;1.16e-06)|all cancers(144;0.000191)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		CCCTACAGACTTGCTGCCATC	0.522																																					p.L146R		.											.	.	.	0			c.T437G						.						69.0	58.0	61.0					2																	220072980		2203	4300	6503	SO:0001583	missense	130617	exon5			ACAGACTTGCTGC	AK074571	CCDS2435.1, CCDS74656.1	2q35	2010-04-23	2005-08-22		ENSG00000158552	ENSG00000158552		"""Zinc fingers, AN1-type domain containing"""	25206	protein-coding gene	gene with protein product	"""arsenite inducible RNA associated protein-like"""	613474	"""zinc finger, AN1-type 2B"""			18467495	Standard	NM_138802		Approved	AIRAPL	uc002vka.4	Q8WV99	OTTHUMG00000133135	ENST00000289528.5:c.437T>G	2.37:g.220072980T>G	ENSP00000289528:p.Leu146Arg	Somatic	43	0		WXS	Illumina HiSeq	.	19	10	NM_138802	Q8NB98	Missense_Mutation	SNP	ENST00000289528.5	37	CCDS2435.1	.	.	.	.	.	.	.	.	.	.	T	12.25	1.882652	0.33255	.	.	ENSG00000158552	ENST00000409206;ENST00000409594;ENST00000289528;ENST00000422255;ENST00000409097;ENST00000409336;ENST00000409217;ENST00000444522	T;T;T;T;T;T;T;T	0.47177	0.88;0.88;0.89;0.85;0.85;0.89;0.89;0.85	5.18	5.18	0.71444	Zinc finger, AN1-type (1);	0.386815	0.27240	N	0.020277	T	0.50769	0.1635	L	0.59436	1.845	0.39174	D	0.962644	D;B;B	0.61697	0.99;0.415;0.08	P;B;B	0.50754	0.649;0.137;0.017	T	0.50874	-0.8776	10	0.25106	T	0.35	-7.4008	11.3405	0.49531	0.0:0.0:0.0:1.0	.	37;146;146	B3KQB0;Q8WV99;B4DEN4	.;ZFN2B_HUMAN;.	R	146	ENSP00000386824:L146R;ENSP00000386399:L146R;ENSP00000289528:L146R;ENSP00000409931:L146R;ENSP00000387179:L146R;ENSP00000386898:L146R;ENSP00000386370:L146R;ENSP00000411334:L146R	ENSP00000289528:L146R	L	+	2	0	ZFAND2B	219781224	0.995000	0.38212	1.000000	0.80357	0.793000	0.44817	1.443000	0.35057	2.165000	0.68154	0.533000	0.62120	CTT	.		0.522	ZFAND2B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256824.2	NM_138802	
ESPN	83715	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	6511978	6511978	+	Missense_Mutation	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr1:6511978T>G	ENST00000377828.1	+	10	2315	c.2147T>G	c.(2146-2148)cTc>cGc	p.L716R	ESPN_ENST00000461727.1_Missense_Mutation_p.L150R|ESPN_ENST00000416731.1_Missense_Mutation_p.L150R|ESPN_ENST00000475228.1_3'UTR	NM_031475.2	NP_113663.2	B1AK53	ESPN_HUMAN	espin	716	Pro-rich.				locomotory behavior (GO:0007626)|negative regulation of cytoskeleton organization (GO:0051494)|parallel actin filament bundle assembly (GO:0030046)|positive regulation of filopodium assembly (GO:0051491)|sensory perception of sound (GO:0007605)	brush border (GO:0005903)|cytoplasm (GO:0005737)|filamentous actin (GO:0031941)|microvillus (GO:0005902)|stereocilium bundle tip (GO:0032426)	actin filament binding (GO:0051015)|SH3 domain binding (GO:0017124)			NS(1)|breast(2)|cervix(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|prostate(1)|skin(1)	17	Ovarian(185;0.0386)|all_lung(157;0.154)	all_cancers(23;3.6e-37)|all_epithelial(116;2.56e-22)|all_lung(118;7.57e-07)|Lung NSC(185;4.26e-06)|all_hematologic(16;6.92e-06)|Colorectal(325;4.47e-05)|Acute lymphoblastic leukemia(12;4.92e-05)|Breast(487;7.61e-05)|Renal(390;0.0007)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0392)		Epithelial(90;1.82e-35)|GBM - Glioblastoma multiforme(13;3e-28)|Kidney(185;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(229;5.63e-08)|Colorectal(212;7e-08)|COAD - Colon adenocarcinoma(227;1.41e-05)|BRCA - Breast invasive adenocarcinoma(365;0.000109)|STAD - Stomach adenocarcinoma(132;0.00167)|Lung(427;0.0108)|LUSC - Lung squamous cell carcinoma(448;0.0253)|READ - Rectum adenocarcinoma(331;0.0419)		CAGCCGCTGCTCAATGGAAGC	0.677																																					p.L716R		.											.	.	.	0			c.T2147G						.						19.0	21.0	20.0					1																	6511978		2200	4300	6500	SO:0001583	missense	83715	exon10			CGCTGCTCAATGG	AF134401	CCDS70.1	1p36.31	2013-01-10			ENSG00000187017	ENSG00000187017		"""Ankyrin repeat domain containing"""	13281	protein-coding gene	gene with protein product		606351	"""deafness, autosomal recessive 36"""	DFNB36		10975527, 15286153	Standard	NM_031475		Approved		uc001amy.3	B1AK53	OTTHUMG00000000753	ENST00000377828.1:c.2147T>G	1.37:g.6511978T>G	ENSP00000367059:p.Leu716Arg	Somatic	78	0		WXS	Illumina HiSeq	.	23	18	NM_031475	Q6XYB2|Q9H0A2|Q9Y329	Missense_Mutation	SNP	ENST00000377828.1	37	CCDS70.1	.	.	.	.	.	.	.	.	.	.	T	12.12	1.842223	0.32513	.	.	ENSG00000187017	ENST00000377828;ENST00000416731	T;D	0.84442	-0.38;-1.85	5.14	5.14	0.70334	.	0.378748	0.27151	N	0.020688	D	0.88396	0.6425	L	0.40543	1.245	0.32805	D	0.500669	D;D	0.89917	1.0;0.973	D;P	0.91635	0.999;0.8	D	0.89717	0.3916	10	0.37606	T	0.19	-24.8726	13.774	0.63041	0.0:0.0:0.0:1.0	.	150;716	B1AK53-2;B1AK53	.;ESPN_HUMAN	R	716;150	ENSP00000367059:L716R;ENSP00000399239:L150R	ENSP00000367059:L716R	L	+	2	0	ESPN	6434565	0.197000	0.23362	1.000000	0.80357	0.240000	0.25518	1.584000	0.36589	1.943000	0.56356	0.402000	0.26972	CTC	.		0.677	ESPN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001887.3	NM_031475	
PTPN3	5774	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	9	112168774	112168774	+	Missense_Mutation	SNP	G	G	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr9:112168774G>A	ENST00000374541.2	-	18	1864	c.1760C>T	c.(1759-1761)tCa>tTa	p.S587L	PTPN3_ENST00000262539.3_Missense_Mutation_p.S433L|PTPN3_ENST00000412145.1_Missense_Mutation_p.S456L|PTPN3_ENST00000446349.1_Missense_Mutation_p.S411L|PTPN3_ENST00000394827.3_Missense_Mutation_p.S55L	NM_001145368.1|NM_002829.3	NP_001138840.1|NP_002820.3	P26045	PTN3_HUMAN	protein tyrosine phosphatase, non-receptor type 3	587					negative regulation of membrane protein ectodomain proteolysis (GO:0051045)|negative regulation of mitotic cell cycle (GO:0045930)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of membrane depolarization during action potential (GO:0098902)|regulation of sodium ion transmembrane transporter activity (GO:2000649)	cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytoskeleton (GO:0005856)	ATPase binding (GO:0051117)|phosphotyrosine binding (GO:0001784)|protein tyrosine phosphatase activity (GO:0004725)|sodium channel regulator activity (GO:0017080)			breast(1)|endometrium(2)|kidney(2)|large_intestine(8)|liver(1)|lung(14)|ovary(4)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	41						CAGCTCCCGTGAGTGGGACTC	0.582																																					p.S587L		.											.	.	.	0			c.C1760T						.						132.0	123.0	126.0					9																	112168774		2203	4300	6503	SO:0001583	missense	5774	exon18			TCCCGTGAGTGGG		CCDS6776.1, CCDS48000.1, CCDS48001.1	9q31	2011-06-09			ENSG00000070159	ENSG00000070159		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"""	9655	protein-coding gene	gene with protein product		176877				1648725	Standard	NM_002829		Approved	PTPH1	uc004bed.2	P26045	OTTHUMG00000020475	ENST00000374541.2:c.1760C>T	9.37:g.112168774G>A	ENSP00000363667:p.Ser587Leu	Somatic	51	0		WXS	Illumina HiSeq	.	31	13	NM_002829	A0AUW9|E7EN99|E9PGU7	Missense_Mutation	SNP	ENST00000374541.2	37	CCDS6776.1	.	.	.	.	.	.	.	.	.	.	G	23.5	4.419003	0.83559	.	.	ENSG00000070159	ENST00000394831;ENST00000412145;ENST00000446349;ENST00000374541;ENST00000394827;ENST00000262539	T;T;T;T;T	0.72167	-0.49;-0.45;-0.63;3.91;-0.4	5.74	4.82	0.62117	PDZ/DHR/GLGF (3);	0.292396	0.36932	N	0.002333	T	0.76140	0.3946	M	0.75615	2.305	0.43183	D	0.995	B;B;B	0.26635	0.155;0.096;0.045	B;B;B	0.36504	0.226;0.216;0.201	T	0.77091	-0.2716	10	0.87932	D	0	.	16.583	0.84719	0.0:0.1306:0.8694:0.0	.	433;542;587	B7Z3H5;B7Z9V1;P26045	.;.;PTN3_HUMAN	L	587;456;411;587;55;433	ENSP00000416654:S456L;ENSP00000395384:S411L;ENSP00000363667:S587L;ENSP00000378304:S55L;ENSP00000262539:S433L	ENSP00000262539:S433L	S	-	2	0	PTPN3	111208595	1.000000	0.71417	0.961000	0.40146	0.981000	0.71138	6.454000	0.73493	1.390000	0.46547	0.561000	0.74099	TCA	.		0.582	PTPN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053598.4		
SYNE2	23224	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	14	64565493	64565493	+	Missense_Mutation	SNP	T	T	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr14:64565493T>A	ENST00000344113.4	+	63	12547	c.12335T>A	c.(12334-12336)cTg>cAg	p.L4112Q	SYNE2_ENST00000555002.1_Missense_Mutation_p.L746Q|SYNE2_ENST00000554584.1_Missense_Mutation_p.L4145Q|ESR2_ENST00000542956.1_Intron|SYNE2_ENST00000394768.2_Missense_Mutation_p.L497Q|SYNE2_ENST00000357395.3_Missense_Mutation_p.L497Q|SYNE2_ENST00000358025.3_Missense_Mutation_p.L4112Q	NM_015180.4	NP_055995.4	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	4112					centrosome localization (GO:0051642)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment or maintenance of cell polarity (GO:0007163)|fibroblast migration (GO:0010761)|nuclear envelope organization (GO:0006998)|nuclear migration (GO:0007097)|nuclear migration along microfilament (GO:0031022)|positive regulation of cell migration (GO:0030335)|protein localization to nucleus (GO:0034504)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intermediate filament cytoskeleton (GO:0045111)|lamellipodium membrane (GO:0031258)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nuclear lumen (GO:0031981)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)|SUN-KASH complex (GO:0034993)|Z disc (GO:0030018)	actin binding (GO:0003779)			NS(5)|breast(17)|central_nervous_system(3)|cervix(8)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(21)|large_intestine(34)|lung(75)|ovary(10)|pancreas(2)|prostate(8)|skin(8)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(4)	224				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)		ATGTCTTACCTGGCAGCAGTC	0.458																																					p.L4112Q		.											.	.	.	0			c.T12335A						.						117.0	114.0	115.0					14																	64565493		2203	4300	6503	SO:0001583	missense	23224	exon63			CTTACCTGGCAGC	AB023228	CCDS9761.2, CCDS41963.1, CCDS45124.1, CCDS45125.1	14q22.1-q22.3	2014-09-17			ENSG00000054654	ENSG00000054654			17084	protein-coding gene	gene with protein product	"""nuclear envelope spectrin repeat-2"", ""nucleus and actin connecting element"""	608442				10231032, 10878022	Standard	NM_182910		Approved	SYNE-2, DKFZP434H2235, Nesprin-2, NUANCE, NUA, KIAA1011, Nesp2	uc001xgl.3	Q8WXH0	OTTHUMG00000140349	ENST00000344113.4:c.12335T>A	14.37:g.64565493T>A	ENSP00000341781:p.Leu4112Gln	Somatic	42	0		WXS	Illumina HiSeq	.	44	19	NM_182914	Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	Missense_Mutation	SNP	ENST00000344113.4	37	CCDS41963.1	.	.	.	.	.	.	.	.	.	.	T	10.83	1.460155	0.26248	.	.	ENSG00000054654	ENST00000358025;ENST00000357395;ENST00000344113;ENST00000554584;ENST00000261678;ENST00000555002;ENST00000394768;ENST00000553308	T;T;T;T;T;T	0.62788	0.37;3.67;0.37;-0.0;3.72;3.67	5.52	4.35	0.52113	.	0.161089	0.29609	N	0.011666	T	0.64983	0.2648	L	0.34521	1.04	0.58432	D	0.999999	D;D;D;D	0.71674	0.997;0.994;0.998;0.965	D;P;D;P	0.66716	0.943;0.871;0.946;0.66	T	0.64935	-0.6290	10	0.49607	T	0.09	.	8.4987	0.33144	0.0:0.092:0.0:0.908	.	497;4146;4112;4112	Q8WXH0-7;D4YW74;Q8WXH0;Q8WXH0-2	.;.;SYNE2_HUMAN;.	Q	4112;497;4112;4145;4145;746;497;4	ENSP00000350719:L4112Q;ENSP00000349969:L497Q;ENSP00000341781:L4112Q;ENSP00000452570:L4145Q;ENSP00000450831:L746Q;ENSP00000378249:L497Q	ENSP00000261678:L4145Q	L	+	2	0	SYNE2	63635246	1.000000	0.71417	0.958000	0.39756	0.163000	0.22366	2.538000	0.45710	2.228000	0.72767	0.533000	0.62120	CTG	.		0.458	SYNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276994.2	NM_182914	
PLXNB2	23654	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	22	50720113	50720113	+	Missense_Mutation	SNP	T	T	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr22:50720113T>A	ENST00000449103.1	-	21	3544	c.3404A>T	c.(3403-3405)gAg>gTg	p.E1135V	PLXNB2_ENST00000496720.1_5'Flank|PLXNB2_ENST00000359337.4_Missense_Mutation_p.E1135V			O15031	PLXB2_HUMAN	plexin B2	1135					brain development (GO:0007420)|neural tube closure (GO:0001843)|neuroblast proliferation (GO:0007405)|positive regulation of axonogenesis (GO:0050772)|regulation of cell shape (GO:0008360)|regulation of neuron migration (GO:2001222)|regulation of protein phosphorylation (GO:0001932)|regulation of Rho GTPase activity (GO:0032319)|semaphorin-plexin signaling pathway (GO:0071526)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)	GTPase activator activity (GO:0005096)|semaphorin receptor activity (GO:0017154)			breast(2)|central_nervous_system(4)|cervix(2)|endometrium(11)|kidney(4)|large_intestine(3)|liver(1)|lung(20)|ovary(5)|prostate(6)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	66		all_cancers(38;5.78e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)		GGTGCAGCGCTCGGCACCCAC	0.672																																					p.E1135V		.											.	.	.	0			c.A3404T						.						26.0	31.0	29.0					22																	50720113		2163	4253	6416	SO:0001583	missense	23654	exon21			CAGCGCTCGGCAC		CCDS43035.1	22q13.33	2008-06-12			ENSG00000196576	ENSG00000196576		"""Plexins"""	9104	protein-coding gene	gene with protein product		604293				10520995, 12183458	Standard	NM_012401		Approved	MM1, KIAA0315, PLEXB2	uc003bkv.4	O15031	OTTHUMG00000150219	ENST00000449103.1:c.3404A>T	22.37:g.50720113T>A	ENSP00000409171:p.Glu1135Val	Somatic	34	0		WXS	Illumina HiSeq	.	24	12	NM_012401	A6QRH0|Q7KZU3|Q9BSU7	Missense_Mutation	SNP	ENST00000449103.1	37	CCDS43035.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	12.83|12.83	2.056799|2.056799	0.36277|0.36277	.|.	.|.	ENSG00000196576|ENSG00000196576	ENST00000449103;ENST00000359337|ENST00000427829	T;T|.	0.03607|.	3.87;3.87|.	4.23|4.23	4.23|4.23	0.50019|0.50019	Immunoglobulin-like fold (1);|.	0.000000|.	0.53938|.	D|.	0.000049|.	T|T	0.52885|0.52885	0.1762|0.1762	L|L	0.40543|0.40543	1.245|1.245	0.43545|0.43545	D|D	0.995842|0.995842	B|.	0.23185|.	0.081|.	B|.	0.20955|.	0.032|.	T|T	0.49113|0.49113	-0.8973|-0.8973	10|5	0.27785|.	T|.	0.31|.	.|.	8.2663|8.2663	0.31815|0.31815	0.0:0.09:0.0:0.91|0.0:0.09:0.0:0.91	.|.	1135|.	O15031|.	PLXB2_HUMAN|.	V|C	1135|153	ENSP00000409171:E1135V;ENSP00000352288:E1135V|.	ENSP00000352288:E1135V|.	E|S	-|-	2|1	0|0	PLXNB2|PLXNB2	49062240|49062240	0.399000|0.399000	0.25287|0.25287	1.000000|1.000000	0.80357|0.80357	0.826000|0.826000	0.46750|0.46750	0.821000|0.821000	0.27338|0.27338	1.788000|1.788000	0.52465|0.52465	0.402000|0.402000	0.26972|0.26972	GAG|AGC	.		0.672	PLXNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316874.3	NM_012401	
ERC2	26059	hgsc.bcm.edu	37	3	56026205	56026205	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr3:56026205G>T	ENST00000288221.6	-	11	2390	c.2135C>A	c.(2134-2136)gCg>gAg	p.A712E		NM_015576.1	NP_056391.1	O15083	ERC2_HUMAN	ELKS/RAB6-interacting/CAST family member 2	712						cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|growth cone (GO:0030426)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)				breast(2)|endometrium(5)|large_intestine(6)|liver(1)|lung(14)|ovary(2)|urinary_tract(1)	31				KIRC - Kidney renal clear cell carcinoma(284;0.0667)|Kidney(284;0.0873)|OV - Ovarian serous cystadenocarcinoma(275;0.219)		GTAGTAAGACGCCTCTTTATC	0.458																																					p.A712E		.											ERC2_ENST00000288221,caecum,carcinoma,0,2	ERC2_ENST00000288221	0	0			c.C2135A						.						194.0	188.0	190.0					3																	56026205		1902	4128	6030	SO:0001583	missense	26059	exon11			TAAGACGCCTCTT	AB002376	CCDS46851.1	3p14.3	2006-08-14			ENSG00000187672	ENSG00000187672			31922	protein-coding gene	gene with protein product							Standard	NM_015576		Approved	CAST, CAST1, KIAA0378, SPBC110, Spc110, ELKSL	uc003dhr.1	O15083	OTTHUMG00000158390	ENST00000288221.6:c.2135C>A	3.37:g.56026205G>T	ENSP00000288221:p.Ala712Glu	Somatic	60	0		WXS	Illumina HiSeq	.	20	2	NM_015576	Q2T9F6|Q86TK4	Missense_Mutation	SNP	ENST00000288221.6	37	CCDS46851.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	16.05|16.05	3.011828|3.011828	0.54468|0.54468	.|.	.|.	ENSG00000187672|ENSG00000187672	ENST00000288221|ENST00000492584	T|.	0.47177|.	0.85|.	5.47|5.47	5.47|5.47	0.80525|0.80525	.|.	0.064020|.	0.64402|.	D|.	0.000003|.	T|T	0.41719|0.41719	0.1171|0.1171	N|N	0.14661|0.14661	0.345|0.345	0.39447|0.39447	D|D	0.967342|0.967342	P|.	0.35793|.	0.521|.	B|.	0.37451|.	0.25|.	T|T	0.35201|0.35201	-0.9798|-0.9798	10|5	0.54805|.	T|.	0.06|.	-11.4437|-11.4437	12.6507|12.6507	0.56759|0.56759	0.0754:0.0:0.9246:0.0|0.0754:0.0:0.9246:0.0	.|.	712|.	O15083|.	ERC2_HUMAN|.	E|S	712|363	ENSP00000288221:A712E|.	ENSP00000288221:A712E|.	A|R	-|-	2|1	0|0	ERC2|ERC2	56001245|56001245	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.980000|0.980000	0.70556|0.70556	7.483000|7.483000	0.81158|0.81158	2.582000|2.582000	0.87167|0.87167	0.591000|0.591000	0.81541|0.81541	GCG|CGT	.		0.458	ERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350884.2	NM_015576	
OCRL	4952	hgsc.bcm.edu;broad.mit.edu	37	X	128724136	128724136	+	Silent	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chrX:128724136T>G	ENST00000371113.4	+	24	2760	c.2595T>G	c.(2593-2595)acT>acG	p.T865T	OCRL_ENST00000357121.5_Silent_p.T857T	NM_000276.3	NP_000267.2	Q01968	OCRL_HUMAN	oculocerebrorenal syndrome of Lowe	865	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				cilium assembly (GO:0042384)|in utero embryonic development (GO:0001701)|inositol phosphate metabolic process (GO:0043647)|lipid metabolic process (GO:0006629)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|positive regulation of Rac GTPase activity (GO:0032855)|regulation of Rac GTPase activity (GO:0032314)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|Golgi stack (GO:0005795)|Golgi-associated vesicle (GO:0005798)|nucleus (GO:0005634)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	inositol phosphate phosphatase activity (GO:0052745)|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity (GO:0004439)|Rac GTPase activator activity (GO:0030675)|Rac GTPase binding (GO:0048365)			breast(1)|endometrium(3)|kidney(4)|large_intestine(11)|lung(24)|ovary(2)|upper_aerodigestive_tract(3)	48						CTCTCTTCACTAGTCTTCTCC	0.532																																					p.T865T		.											.	.	.	0			c.T2595G						.						212.0	196.0	201.0					X																	128724136		2203	4300	6503	SO:0001819	synonymous_variant	4952	exon24			CTTCACTAGTCTT	U57627	CCDS35393.1, CCDS35394.1	Xq25	2014-06-18			ENSG00000122126	ENSG00000122126			8108	protein-coding gene	gene with protein product		300535					Standard	NM_001587		Approved	OCRL1	uc004euq.3	Q01968	OTTHUMG00000022706	ENST00000371113.4:c.2595T>G	X.37:g.128724136T>G		Somatic	13	0		WXS	Illumina HiSeq	.	9	8	NM_000276	A6NKI1|A8KAP2|B7ZLX2|O60800|Q15684|Q15774|Q4VY09|Q4VY10|Q5JQF1|Q5JQF2|Q9UJG5|Q9UMA5	Silent	SNP	ENST00000371113.4	37	CCDS35393.1																																																																																			.		0.532	OCRL-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058917.1	NM_000276	
MTUS1	57509	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	8	17510965	17510965	+	Missense_Mutation	SNP	T	T	C	rs570318137		TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr8:17510965T>C	ENST00000262102.6	-	11	3481	c.3257A>G	c.(3256-3258)gAt>gGt	p.D1086G	MTUS1_ENST00000519263.1_Missense_Mutation_p.D1032G|MTUS1_ENST00000297488.6_Missense_Mutation_p.D252G|MTUS1_ENST00000381869.3_Missense_Mutation_p.D1032G|MTUS1_ENST00000381861.3_Missense_Mutation_p.D333G|MTUS1_ENST00000544260.1_Missense_Mutation_p.D231G|MTUS1_ENST00000400046.1_Missense_Mutation_p.D158G|MTUS1_ENST00000518713.1_5'UTR	NM_001001924.2	NP_001001924.1	Q9ULD2	MTUS1_HUMAN	microtubule associated tumor suppressor 1	1086					cellular response to peptide hormone stimulus (GO:0071375)|regulation of macrophage chemotaxis (GO:0010758)	extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(14)|lung(8)|ovary(1)|skin(2)|urinary_tract(1)	36				Colorectal(111;0.0778)		AGAAAGTAAATCTTCAAGCGA	0.333													T|||	1	0.000199681	0.0008	0.0	5008	,	,		17885	0.0		0.0	False		,,,				2504	0.0				p.D1086G		.											.	.	.	0			c.A3257G						.						72.0	66.0	68.0					8																	17510965		1804	4073	5877	SO:0001583	missense	57509	exon11			AGTAAATCTTCAA	AL096842	CCDS43716.1, CCDS43717.1, CCDS43718.1, CCDS43719.1, CCDS55204.1	8p22	2013-01-17	2009-10-20		ENSG00000129422	ENSG00000129422			29789	protein-coding gene	gene with protein product	"""AT2 receptor-interacting protein"", ""AT2R binding protein"", ""mitochondrial tumor suppressor gene 1"""	609589	"""mitochondrial tumor suppressor 1"""			10574462, 12692079	Standard	NM_001001931		Approved	MTSG1, KIAA1288, DKFZp586D1519, FLJ14295, ATIP1, MP44, ATBP, ICIS	uc003wxv.3	Q9ULD2	OTTHUMG00000163756	ENST00000262102.6:c.3257A>G	8.37:g.17510965T>C	ENSP00000262102:p.Asp1086Gly	Somatic	96	0		WXS	Illumina HiSeq	.	59	25	NM_001001924	A8K135|B2RBJ6|B3KWJ9|B4DH03|B9EGA1|D3DSP8|Q63HJ6|Q659F4|Q6PK49|Q6URW7|Q8N4M6|Q8WTT9|Q9H7T2	Missense_Mutation	SNP	ENST00000262102.6	37	CCDS43717.1	.	.	.	.	.	.	.	.	.	.	T	22.6	4.305986	0.81247	.	.	ENSG00000129422	ENST00000381869;ENST00000544260;ENST00000400046;ENST00000297488;ENST00000381861;ENST00000262102;ENST00000519263	T;T;T;T;T;T;T	0.35973	1.28;1.28;2.16;1.28;1.28;1.28;1.28	5.32	5.32	0.75619	.	0.208536	0.49916	D	0.000133	T	0.48077	0.1480	M	0.69823	2.125	0.80722	D	1	P;P;B;P	0.44776	0.843;0.746;0.39;0.532	P;P;B;B	0.47346	0.487;0.544;0.329;0.423	T	0.53837	-0.8382	10	0.72032	D	0.01	-16.7254	15.611	0.76716	0.0:0.0:0.0:1.0	.	1032;1086;333;252	Q9ULD2-2;Q9ULD2;Q9ULD2-6;Q9ULD2-3	.;MTUS1_HUMAN;.;.	G	1032;231;158;252;333;1086;1032	ENSP00000371293:D1032G;ENSP00000445738:D231G;ENSP00000382921:D158G;ENSP00000297488:D252G;ENSP00000371285:D333G;ENSP00000262102:D1086G;ENSP00000430167:D1032G	ENSP00000262102:D1086G	D	-	2	0	MTUS1	17555245	1.000000	0.71417	0.892000	0.35008	0.960000	0.62799	2.410000	0.44592	2.150000	0.67090	0.383000	0.25322	GAT	.		0.333	MTUS1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000375247.1	XM_372031	
CAPRIN1	4076	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	11	34074072	34074072	+	Silent	SNP	C	C	T	rs370335951	byFrequency	TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr11:34074072C>T	ENST00000341394.4	+	2	294	c.105C>T	c.(103-105)gcC>gcT	p.A35A	CAPRIN1_ENST00000530820.1_Silent_p.A35A|CAPRIN1_ENST00000532820.1_Silent_p.A35A|CAPRIN1_ENST00000389645.3_Silent_p.A35A|CAPRIN1_ENST00000529307.1_5'Flank	NM_005898.4	NP_005889.3	Q14444	CAPR1_HUMAN	cell cycle associated protein 1	35					negative regulation of translation (GO:0017148)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of dendritic spine morphogenesis (GO:0061003)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytoplasmic stress granule (GO:0010494)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(2)|endometrium(2)|kidney(1)|large_intestine(6)|lung(5)|ovary(1)|prostate(1)	18		Acute lymphoblastic leukemia(5;0.00045)|all_hematologic(20;0.0016)				ccggggccgccgcgccggcTT	0.716																																					p.A35A		.											.	.	.	0			c.C105T						.						6.0	9.0	8.0					11																	34074072		2034	3996	6030	SO:0001819	synonymous_variant	4076	exon2			GGCCGCCGCGCCG	BC001731	CCDS31453.1, CCDS31454.1	11p13	2010-08-03	2007-03-27	2007-03-27	ENSG00000135387	ENSG00000135387			6743	protein-coding gene	gene with protein product	"""cytoplasmic activation/proliferation-associated protein-1"""	601178	"""membrane component, chromosome 11, surface marker 1"", ""GPI-anchored membrane protein 1"""	M11S1, GPIAP1		7657653, 16177067, 17210633, 14764709, 15471883	Standard	NM_005898		Approved	caprin-1, RNG105	uc001mvh.1	Q14444	OTTHUMG00000166248	ENST00000341394.4:c.105C>T	11.37:g.34074072C>T		Somatic	42	0		WXS	Illumina HiSeq	.	32	15	NM_203364	A6NMY7|D3DR06|Q15074|Q6IMN4|Q6IMN7|Q9BV09	Silent	SNP	ENST00000341394.4	37	CCDS31453.1																																																																																			.		0.716	CAPRIN1-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000388680.2	NM_005898	
CDK12	51755	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	17	37687154	37687154	+	Missense_Mutation	SNP	C	C	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr17:37687154C>T	ENST00000447079.4	+	14	4091	c.4058C>T	c.(4057-4059)aCt>aTt	p.T1353I	CDK12_ENST00000430627.2_Missense_Mutation_p.T1344I	NM_015083.1|NM_016507.2	NP_055898.1|NP_057591.2	Q9NYV4	CDK12_HUMAN	cyclin-dependent kinase 12	1353					mRNA processing (GO:0006397)|phosphorylation of RNA polymerase II C-terminal domain (GO:0070816)|protein autophosphorylation (GO:0046777)|regulation of MAP kinase activity (GO:0043405)|RNA splicing (GO:0008380)	cyclin K-CDK12 complex (GO:0002944)|nuclear cyclin-dependent protein kinase holoenzyme complex (GO:0019908)|nuclear speck (GO:0016607)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cyclin binding (GO:0030332)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein kinase activity (GO:0004672)|RNA polymerase II carboxy-terminal domain kinase activity (GO:0008353)			NS(4)|breast(3)|endometrium(5)|kidney(4)|large_intestine(11)|lung(23)|ovary(11)|prostate(4)|skin(2)|urinary_tract(3)	70						GCCATTGACACTGATGAACGA	0.547			"""Mis, N, F"""		serous ovarian					TCGA Ovarian(9;0.13)																											p.T1353I		.		Rec	yes		17	17q12	51755	cyclin-dependent kinase 12		E	.	.	.	0			c.C4058T						.						81.0	77.0	78.0					17																	37687154		2203	4300	6503	SO:0001583	missense	51755	exon14			TTGACACTGATGA	AF227198	CCDS11337.1, CCDS45666.1	17q12	2011-10-25	2009-12-16	2009-12-16	ENSG00000167258	ENSG00000167258		"""Cyclin-dependent kinases"""	24224	protein-coding gene	gene with protein product	"""CDC2 related protein kinase 7"""	615514	"""Cdc2-related kinase, arginine/serine-rich"""	CRKRS		10048485, 11683387, 19884882	Standard	XM_005257456		Approved	CRK7, CRKR, KIAA0904	uc010cvv.3	Q9NYV4	OTTHUMG00000133214	ENST00000447079.4:c.4058C>T	17.37:g.37687154C>T	ENSP00000398880:p.Thr1353Ile	Somatic	60	0		WXS	Illumina HiSeq	.	29	12	NM_016507	A7E2B2|B4DYX4|B9EIQ6|O94978	Missense_Mutation	SNP	ENST00000447079.4	37	CCDS11337.1	.	.	.	.	.	.	.	.	.	.	C	9.422	1.083218	0.20309	.	.	ENSG00000167258	ENST00000430627;ENST00000447079	T;T	0.68624	-0.34;-0.32	5.45	5.45	0.79879	.	0.000000	0.50627	D	0.000106	T	0.44435	0.1293	N	0.08118	0	0.27724	N	0.94502	B;B	0.24426	0.063;0.103	B;B	0.24269	0.023;0.052	T	0.35798	-0.9774	10	0.56958	D	0.05	-11.7716	8.1005	0.30854	0.0:0.8371:0.0:0.1629	.	1353;1344	Q9NYV4;Q9NYV4-2	CDK12_HUMAN;.	I	1344;1353	ENSP00000407720:T1344I;ENSP00000398880:T1353I	ENSP00000407720:T1344I	T	+	2	0	CDK12	34940680	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	1.943000	0.40253	2.836000	0.97738	0.655000	0.94253	ACT	.		0.547	CDK12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256941.4	NM_016507	
LOC101927795	101927795	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	2	201642727	201642727	+	RNA	SNP	C	C	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr2:201642727C>G	ENST00000447972.3	-	0	1754				AOX2P_ENST00000467645.1_RNA|RNU1-133P_ENST00000364867.1_RNA																							GTGTCCTGTACTCTCGGAGCC	0.458																																					.		.											.	.	.	0			.						.																																					344454	.			CCTGTACTCTCGG																													2.37:g.201642727C>G		Somatic	50	0		WXS	Illumina HiSeq	.	35	15	.		RNA	SNP	ENST00000447972.3	37																																																																																				.		0.458	AC007163.6-001	KNOWN	basic	antisense	antisense	OTTHUMT00000335879.3		
MYO18A	399687	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	17	27493528	27493528	+	Missense_Mutation	SNP	C	C	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr17:27493528C>T	ENST00000527372.1	-	2	611	c.431G>A	c.(430-432)cGt>cAt	p.R144H	MYO18A_ENST00000354329.4_Missense_Mutation_p.R144H|MYO18A_ENST00000533112.1_Missense_Mutation_p.R144H|MYO18A_ENST00000531253.1_Missense_Mutation_p.R144H	NM_078471.3	NP_510880.2	Q92614	MY18A_HUMAN	myosin XVIIIA	144	Mediates nucleotide-independent binding to F-actin and interaction with GOLPH3.				actomyosin structure organization (GO:0031032)|cell migration (GO:0016477)|DNA metabolic process (GO:0006259)|Golgi organization (GO:0007030)|Golgi vesicle budding (GO:0048194)|negative regulation of apoptotic process (GO:0043066)|positive regulation of protein secretion (GO:0050714)	actomyosin (GO:0042641)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|myosin complex (GO:0016459)|trans-Golgi network (GO:0005802)	actin filament binding (GO:0051015)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|motor activity (GO:0003774)|poly(A) RNA binding (GO:0044822)			NS(1)|cervix(1)|endometrium(6)|kidney(6)|lung(20)|urinary_tract(2)	36			Epithelial(11;4.97e-05)|BRCA - Breast invasive adenocarcinoma(11;0.000221)|all cancers(11;0.000234)|Colorectal(6;0.0102)|COAD - Colon adenocarcinoma(6;0.031)			ATCCCGGCTACGCTGGGAGAA	0.622																																					p.R144H	Esophageal Squamous(182;472 2015 7001 15270 22562)	.											.	.	.	0			c.G431A						.						23.0	28.0	27.0					17																	27493528		2063	4200	6263	SO:0001583	missense	399687	exon2			CGGCTACGCTGGG	D86970	CCDS45641.1, CCDS45642.1	17q11.2	2011-09-27			ENSG00000196535	ENSG00000196535		"""Myosins / Myosin superfamily : Class XVIII"""	31104	protein-coding gene	gene with protein product		610067				12761286	Standard	NM_078471		Approved	KIAA0216, MysPDZ	uc002hdt.1	Q92614	OTTHUMG00000166360	ENST00000527372.1:c.431G>A	17.37:g.27493528C>T	ENSP00000437073:p.Arg144His	Somatic	37	0		WXS	Illumina HiSeq	.	35	16	NM_078471	Q5H9U3|Q5W9F9|Q5W9G1|Q8IXP8	Missense_Mutation	SNP	ENST00000527372.1	37	CCDS45642.1	.	.	.	.	.	.	.	.	.	.	C	17.27	3.346137	0.61073	.	.	ENSG00000196535	ENST00000354329;ENST00000359450;ENST00000533112;ENST00000531253;ENST00000527372	D;D;D;D	0.88975	-2.35;-2.45;-2.34;-2.35	5.11	5.11	0.69529	.	0.125411	0.49305	D	0.000142	T	0.80417	0.4619	N	0.19112	0.55	0.31507	N	0.664121	D;D;D	0.61697	0.957;0.983;0.99	P;P;B	0.45449	0.481;0.481;0.374	T	0.80692	-0.1269	10	0.44086	T	0.13	.	6.1101	0.20096	0.0:0.782:0.0:0.218	.	144;144;144	Q92614-3;Q92614-4;Q92614	.;.;MY18A_HUMAN	H	144	ENSP00000346291:R144H;ENSP00000435932:R144H;ENSP00000434228:R144H;ENSP00000437073:R144H	ENSP00000346291:R144H	R	-	2	0	MYO18A	24517654	0.896000	0.30565	0.987000	0.45799	0.996000	0.88848	1.642000	0.37207	2.660000	0.90430	0.467000	0.42956	CGT	.		0.622	MYO18A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389396.1	NM_078471	
INTS7	25896	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	212118230	212118230	+	Missense_Mutation	SNP	C	C	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr1:212118230C>T	ENST00000366994.3	-	19	2601	c.2497G>A	c.(2497-2499)Gga>Aga	p.G833R	INTS7_ENST00000440600.2_Missense_Mutation_p.G784R|INTS7_ENST00000366993.3_Missense_Mutation_p.G819R|INTS7_ENST00000366992.3_Missense_Mutation_p.G813R|INTS7_ENST00000469606.1_5'UTR	NM_001199811.1|NM_001199812.1|NM_015434.3	NP_001186740.1|NP_001186741.1|NP_056249.1	Q9NVH2	INT7_HUMAN	integrator complex subunit 7	833					cellular response to ionizing radiation (GO:0071479)|DNA damage checkpoint (GO:0000077)|snRNA processing (GO:0016180)	chromosome (GO:0005694)|integrator complex (GO:0032039)				NS(1)|breast(1)|kidney(1)|large_intestine(8)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	20				OV - Ovarian serous cystadenocarcinoma(81;0.00584)|all cancers(67;0.0318)|Epithelial(68;0.0852)		TGAACCACTCCCTCTACCTTT	0.502																																					p.G833R		.											.	.	.	0			c.G2497A						.						137.0	126.0	130.0					1																	212118230		2203	4300	6503	SO:0001583	missense	25896	exon19			CCACTCCCTCTAC	AK022509	CCDS1501.1, CCDS55684.1, CCDS55683.1, CCDS55685.1	1q32.3	2008-02-05	2006-03-15	2006-03-15	ENSG00000143493	ENSG00000143493			24484	protein-coding gene	gene with protein product		611350	"""chromosome 1 open reading frame 73"""	C1orf73		16239144	Standard	NM_015434		Approved	DKFZP434B168, INT7	uc001hiw.2	Q9NVH2	OTTHUMG00000037119	ENST00000366994.3:c.2497G>A	1.37:g.212118230C>T	ENSP00000355961:p.Gly833Arg	Somatic	64	0		WXS	Illumina HiSeq	.	46	28	NM_015434	B4DLZ6|B7WNP6|B7WPB6|Q8N4K7|Q8WUH5|Q9H9V3|Q9NVU5|Q9UFC6|Q9UFM3	Missense_Mutation	SNP	ENST00000366994.3	37	CCDS1501.1	.	.	.	.	.	.	.	.	.	.	C	33	5.256311	0.95336	.	.	ENSG00000143493	ENST00000366994;ENST00000366993;ENST00000366992;ENST00000440600	D;D;D;D	0.85088	-1.86;-1.94;-1.87;-1.92	5.56	5.56	0.83823	.	0.046832	0.85682	D	0.000000	D	0.92008	0.7468	M	0.69358	2.11	0.80722	D	1	D;D;D;D	0.89917	0.979;0.992;1.0;1.0	P;P;D;D	0.97110	0.747;0.838;0.999;1.0	D	0.92378	0.5911	10	0.87932	D	0	-20.4574	19.5159	0.95165	0.0:1.0:0.0:0.0	.	784;813;819;833	B4DLZ6;Q9NVH2-3;Q9NVH2-2;Q9NVH2	.;.;.;INT7_HUMAN	R	833;819;813;784	ENSP00000355961:G833R;ENSP00000355960:G819R;ENSP00000355959:G813R;ENSP00000388908:G784R	ENSP00000355959:G813R	G	-	1	0	INTS7	210184853	1.000000	0.71417	0.999000	0.59377	0.990000	0.78478	7.442000	0.80503	2.621000	0.88768	0.655000	0.94253	GGA	.		0.502	INTS7-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090142.1	NM_015434	
TAF1D	79101	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	11	93469419	93469419	+	Missense_Mutation	SNP	A	A	C	rs554467119		TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr11:93469419A>C	ENST00000448108.2	-	6	1395	c.745T>G	c.(745-747)Tta>Gta	p.L249V	TAF1D_ENST00000546088.1_5'Flank|SNORA40_ENST00000388090.1_RNA|MIR1304_ENST00000408243.1_RNA|SNORD5_ENST00000459342.1_RNA|SNORA18_ENST00000384416.1_RNA	NM_024116.3	NP_077021.1	Q9H5J8	TAF1D_HUMAN	TATA box binding protein (TBP)-associated factor, RNA polymerase I, D, 41kDa	249					gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)	microtubule organizing center (GO:0005815)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)			large_intestine(1)|lung(3)|prostate(1)|skin(2)	7						TCTTCTTCTAAGTATACACTC	0.358																																					p.L249V		.											.	.	.	0			c.T745G						.						103.0	99.0	100.0					11																	93469419		2201	4297	6498	SO:0001583	missense	79101	exon6			CTTCTAAGTATAC		CCDS8293.1	11q21	2012-05-30	2008-09-30	2008-09-30	ENSG00000166012	ENSG00000166012			28759	protein-coding gene	gene with protein product		612823	"""Josephin domain containing 3"""	JOSD3		15520167, 17318177	Standard	NM_024116		Approved	MGC5306, TAF(I)41	uc001pec.3	Q9H5J8	OTTHUMG00000167451	ENST00000448108.2:c.745T>G	11.37:g.93469419A>C	ENSP00000410409:p.Leu249Val	Somatic	105	0		WXS	Illumina HiSeq	.	64	25	NM_024116	Q6I9Y6	Missense_Mutation	SNP	ENST00000448108.2	37	CCDS8293.1	.	.	.	.	.	.	.	.	.	.	A	7.504	0.653242	0.14580	.	.	ENSG00000166012	ENST00000448108	.	.	.	4.81	-3.46	0.04767	.	0.648268	0.12540	N	0.459982	T	0.18299	0.0439	L	0.34521	1.04	0.09310	N	1	B	0.31318	0.319	B	0.26416	0.069	T	0.11012	-1.0605	9	0.44086	T	0.13	-11.2881	1.8018	0.03073	0.3435:0.164:0.354:0.1384	.	249	Q9H5J8	TAF1D_HUMAN	V	249	.	ENSP00000314971:L249V	L	-	1	2	TAF1D	93109067	0.001000	0.12720	0.000000	0.03702	0.027000	0.11550	0.035000	0.13797	-0.759000	0.04684	-0.441000	0.05720	TTA	.		0.358	TAF1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394662.2	NM_024116	
UIMC1	51720	hgsc.bcm.edu	37	5	176396234	176396234	+	Silent	SNP	G	G	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr5:176396234G>A	ENST00000377227.4	-	6	654	c.522C>T	c.(520-522)aaC>aaT	p.N174N	UIMC1_ENST00000511320.1_Silent_p.N174N|UIMC1_ENST00000506128.1_Silent_p.N174N|UIMC1_ENST00000377219.2_Silent_p.N174N|UIMC1_ENST00000503273.1_5'Flank			Q96RL1	UIMC1_HUMAN	ubiquitin interaction motif containing 1	174	Necessary for interaction with NR6A1 N- terminus.				double-strand break repair (GO:0006302)|G2 DNA damage checkpoint (GO:0031572)|histone H2A K63-linked deubiquitination (GO:0070537)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of DNA repair (GO:0045739)|response to ionizing radiation (GO:0010212)|transcription, DNA-templated (GO:0006351)	BRCA1-A complex (GO:0070531)|nucleus (GO:0005634)	histone binding (GO:0042393)|K63-linked polyubiquitin binding (GO:0070530)	p.N174N(1)		NS(1)|endometrium(2)|kidney(3)|large_intestine(3)|lung(5)|ovary(4)|pancreas(1)|prostate(1)|skin(1)	21	all_cancers(89;7.96e-05)|Renal(175;0.000269)|Lung NSC(126;0.00476)|all_lung(126;0.00806)	Medulloblastoma(196;0.0145)|all_neural(177;0.0325)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CCTCAGCCTCGTTTCCCTGAC	0.502																																					p.N174N		.											UIMC1,NS,carcinoma,0,1	UIMC1	0	1	Substitution - coding silent(1)	endometrium(1)	c.C522T						.						85.0	87.0	86.0					5																	176396234		2203	4300	6503	SO:0001819	synonymous_variant	51720	exon6			AGCCTCGTTTCCC	AF349313	CCDS4408.1	5q35.2	2008-02-05			ENSG00000087206	ENSG00000087206			30298	protein-coding gene	gene with protein product	"""receptor associated protein 80"""	609433				12080054	Standard	NM_001199297		Approved	RAP80	uc021yin.1	Q96RL1	OTTHUMG00000130852	ENST00000377227.4:c.522C>T	5.37:g.176396234G>A		Somatic	81	0		WXS	Illumina HiSeq	.	71	3	NM_016290	A8MSA1|B3KMZ1|B4E3N2|Q5XKQ1|Q7Z3W7|Q8N5B9|Q9BZR1|Q9BZR5|Q9UHX7	Silent	SNP	ENST00000377227.4	37	CCDS4408.1																																																																																			.		0.502	UIMC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253422.1	NM_016290	
GLG1	2734	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	16	74525044	74525044	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr16:74525044G>T	ENST00000422840.2	-	8	1303	c.1304C>A	c.(1303-1305)tCt>tAt	p.S435Y	GLG1_ENST00000447066.2_Missense_Mutation_p.S424Y|GLG1_ENST00000205061.5_Missense_Mutation_p.S435Y	NM_001145667.1	NP_001139139.1	Q92896	GSLG1_HUMAN	golgi glycoprotein 1	435					blood coagulation (GO:0007596)|bone morphogenesis (GO:0060349)|leukocyte migration (GO:0050900)|negative regulation of protein processing (GO:0010955)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|regulation of chondrocyte differentiation (GO:0032330)	extracellular matrix (GO:0031012)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)			breast(2)|cervix(2)|endometrium(6)|kidney(8)|large_intestine(6)|lung(28)|ovary(3)|prostate(1)|skin(1)	57						AGGGCTCAGAGAAAAGTCTTC	0.488																																					p.S435Y		.											.	.	.	0			c.C1304A						.						194.0	154.0	167.0					16																	74525044		2198	4300	6498	SO:0001583	missense	2734	exon8			CTCAGAGAAAAGT		CCDS32485.1, CCDS45526.1, CCDS45527.1	16q22-q23	2010-02-12	2010-02-12			ENSG00000090863			4316	protein-coding gene	gene with protein product		600753	"""golgi apparatus protein 1"""			8530051, 7531823	Standard	NM_012201		Approved	MG-160, ESL-1, CFR-1	uc002fcx.3	Q92896		ENST00000422840.2:c.1304C>A	16.37:g.74525044G>T	ENSP00000405984:p.Ser435Tyr	Somatic	46	0		WXS	Illumina HiSeq	.	28	10	NM_001145667	B7Z8Y4|D3DUJ7|Q13221|Q6P9D1	Missense_Mutation	SNP	ENST00000422840.2	37	CCDS45527.1	.	.	.	.	.	.	.	.	.	.	G	29.7	5.029866	0.93575	.	.	ENSG00000090863	ENST00000205061;ENST00000447066;ENST00000422840	.	.	.	5.71	5.71	0.89125	.	0.000000	0.85682	D	0.000000	T	0.76919	0.4055	L	0.53249	1.67	0.80722	D	1	D;D;D	0.71674	0.998;0.995;0.994	D;D;D	0.77557	0.99;0.954;0.944	T	0.75836	-0.3177	9	0.51188	T	0.08	-6.9227	19.8636	0.96797	0.0:0.0:1.0:0.0	.	435;435;424	Q92896;Q92896-2;B7Z8Y4	GSLG1_HUMAN;.;.	Y	435;424;435	.	ENSP00000205061:S435Y	S	-	2	0	GLG1	73082545	1.000000	0.71417	0.955000	0.39395	0.993000	0.82548	9.605000	0.98321	2.694000	0.91930	0.655000	0.94253	TCT	.		0.488	GLG1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000435750.1	NM_012201	
REEP6	92840	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	19	1490288	1490288	+	5'Flank	SNP	G	G	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr19:1490288G>A	ENST00000233596.3	+	0	0				PCSK4_ENST00000587784.1_Intron|PCSK4_ENST00000300954.5_Missense_Mutation_p.R20C	NM_138393.1	NP_612402.1	Q96HR9	REEP6_HUMAN	receptor accessory protein 6						regulation of intracellular transport (GO:0032386)	apical part of cell (GO:0045177)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)				lung(1)|ovary(1)	2		Acute lymphoblastic leukemia(61;5.61e-13)|all_hematologic(61;2.65e-08)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GCCCGGGGGCGGACAAGGGCC	0.746																																					p.R20C		.											.	.	.	0			c.C58T						.						5.0	6.0	6.0					19																	1490288		2108	4138	6246	SO:0001631	upstream_gene_variant	54760	exon1			GGGGGCGGACAAG	BC008201	CCDS12070.1	19p13.3	2012-12-20	2006-02-08	2006-02-07	ENSG00000115255	ENSG00000115255		"""Receptor accessory proteins"""	30078	protein-coding gene	gene with protein product	"""polyposis locus protein 1-like 1"", ""deleted in polyposis 1-like 1"""	609346	"""chromosome 19 open reading frame 32"""	C19orf32		16271481, 15550249	Standard	NM_138393		Approved	DP1L1, FLJ25383	uc002ltc.3	Q96HR9	OTTHUMG00000180072		19.37:g.1490288G>A	Exception_encountered	Somatic	89	0		WXS	Illumina HiSeq	.	66	28	NM_017573	B2RE01|D6W5Z0|Q96LM0	Missense_Mutation	SNP	ENST00000233596.3	37	CCDS12070.1	.	.	.	.	.	.	.	.	.	.	g	9.638	1.138236	0.21123	.	.	ENSG00000115257	ENST00000300954	T	0.69435	-0.4	3.31	-6.62	0.01813	.	1.617810	0.04195	N	0.329028	T	0.36026	0.0952	N	0.02539	-0.55	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.24190	-1.0167	10	0.38643	T	0.18	.	7.1918	0.25831	0.5261:0.2048:0.2691:0.0	.	20	Q6UW60	PCSK4_HUMAN	C	20	ENSP00000300954:R20C	ENSP00000300954:R20C	R	-	1	0	PCSK4	1441288	0.000000	0.05858	0.068000	0.19968	0.011000	0.07611	-1.638000	0.02013	-0.731000	0.04862	-2.032000	0.00423	CGC	.		0.746	REEP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449623.1	NM_138393	
CHAF1A	10036	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	19	4442934	4442934	+	Missense_Mutation	SNP	C	C	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr19:4442934C>T	ENST00000301280.5	+	15	2884	c.2783C>T	c.(2782-2784)cCg>cTg	p.P928L		NM_005483.2	NP_005474	Q13111	CAF1A_HUMAN	chromatin assembly factor 1, subunit A (p150)	928	Binds to p60.				cell cycle (GO:0007049)|chromatin assembly (GO:0031497)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA replication-dependent nucleosome assembly (GO:0006335)|protein complex assembly (GO:0006461)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	CAF-1 complex (GO:0033186)|nuclear chromatin (GO:0000790)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|chromo shadow domain binding (GO:0070087)|identical protein binding (GO:0042802)|unfolded protein binding (GO:0051082)			breast(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(6)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|urinary_tract(1)	27		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0148)|STAD - Stomach adenocarcinoma(1328;0.18)		GTCCAAGCCCCGTGTGGAGCC	0.692								Chromatin Structure																													p.P928L		.											.	.	.	0			c.C2783T						.						21.0	23.0	22.0					19																	4442934		2201	4295	6496	SO:0001583	missense	10036	exon15			AAGCCCCGTGTGG	U20979	CCDS32875.1	19p13.3	2008-07-16				ENSG00000167670			1910	protein-coding gene	gene with protein product	"""chromatin assembly factor I (150 kDa)"""	601246				7600578	Standard	NM_005483		Approved	CAF1P150, CAF1B, CAF-1, CAF1, P150, MGC71229	uc002mal.3	Q13111		ENST00000301280.5:c.2783C>T	19.37:g.4442934C>T	ENSP00000301280:p.Pro928Leu	Somatic	94	0		WXS	Illumina HiSeq	.	43	12	NM_005483	Q6NXG5|Q7Z7K3|Q9UJY8	Missense_Mutation	SNP	ENST00000301280.5	37	CCDS32875.1	.	.	.	.	.	.	.	.	.	.	C	14.60	2.585076	0.46110	.	.	ENSG00000167670	ENST00000301280	T	0.30182	1.54	4.0	2.91	0.33838	.	.	.	.	.	T	0.35913	0.0948	L	0.51422	1.61	0.09310	N	1	D	0.69078	0.997	P	0.50708	0.648	T	0.13683	-1.0500	9	0.87932	D	0	-11.5465	8.9521	0.35796	0.2227:0.7773:0.0:0.0	.	928	Q13111	CAF1A_HUMAN	L	928	ENSP00000301280:P928L	ENSP00000301280:P928L	P	+	2	0	CHAF1A	4393934	0.000000	0.05858	0.003000	0.11579	0.031000	0.12232	-0.079000	0.11357	0.754000	0.32968	0.313000	0.20887	CCG	.		0.692	CHAF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458310.2	NM_005483	
RIMBP3	85376	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	22	20458094	20458094	+	Missense_Mutation	SNP	C	C	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr22:20458094C>G	ENST00000426804.1	-	1	3692	c.3208G>C	c.(3208-3210)Gga>Cga	p.G1070R	SCARNA17_ENST00000516762.1_RNA|RN7SKP131_ENST00000363006.1_RNA|SCARNA18_ENST00000516215.1_RNA	NM_015672.1	NP_056487.1	Q9UFD9	RIM3A_HUMAN	RIMS binding protein 3	1070	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.									breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(3)|lung(1)|prostate(1)|skin(1)|urinary_tract(1)	13	Colorectal(54;0.0993)|Melanoma(16;0.165)		LUSC - Lung squamous cell carcinoma(15;0.0405)|Lung(15;0.224)			GACATAGTTCCCCAATACACC	0.662																																					p.G1070R		.											.	.	.	0			c.G3208C						.						68.0	88.0	81.0					22																	20458094		2115	4241	6356	SO:0001583	missense	85376	exon1			TAGTTCCCCAATA	AB051453	CCDS46665.1	22q11.21	2014-05-06			ENSG00000196622	ENSG00000275793			29344	protein-coding gene	gene with protein product		612699				11258795, 17855024	Standard	NM_015672		Approved	KIAA1666, RIMBP3.1, RIMBP3A	uc002zsd.4	Q9UFD9	OTTHUMG00000188355	ENST00000426804.1:c.3208G>C	22.37:g.20458094C>G	ENSP00000391564:p.Gly1070Arg	Somatic	283	0		WXS	Illumina HiSeq	.	177	31	NM_015672	Q8IYP7|Q9BY94|Q9UFQ5	Missense_Mutation	SNP	ENST00000426804.1	37	CCDS46665.1	.	.	.	.	.	.	.	.	.	.	C	10.02	1.235036	0.22626	.	.	ENSG00000196622	ENST00000355186;ENST00000426804	T	0.60797	0.16	3.56	1.23	0.21249	Fibronectin, type III (1);	0.226733	0.35555	N	0.003129	T	0.34513	0.0900	N	0.22421	0.69	0.09310	N	1	B	0.32160	0.358	B	0.26517	0.07	T	0.23226	-1.0194	10	0.59425	D	0.04	-3.7359	5.0801	0.14651	0.0:0.5265:0.3451:0.1284	.	976	Q9UFD9	RIM3A_HUMAN	R	976;1070	ENSP00000391564:G1070R	ENSP00000347318:G976R	G	-	1	0	RIMBP3	18838094	0.003000	0.15002	0.388000	0.26195	0.483000	0.33249	0.495000	0.22483	0.841000	0.35020	0.398000	0.26397	GGA	.		0.662	RIMBP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318945.2	NM_015672	
ITGB4	3691	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	17	73751914	73751914	+	Missense_Mutation	SNP	A	A	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr17:73751914A>G	ENST00000200181.3	+	35	4878	c.4691A>G	c.(4690-4692)tAc>tGc	p.Y1564C	ITGB4_ENST00000579662.1_Missense_Mutation_p.Y1494C|GALK1_ENST00000225614.2_Intron|ITGB4_ENST00000449880.2_Missense_Mutation_p.Y1547C|ITGB4_ENST00000339591.3_Missense_Mutation_p.Y1547C|ITGB4_ENST00000450894.3_Missense_Mutation_p.Y1494C	NM_000213.3	NP_000204.3	P16144	ITB4_HUMAN	integrin, beta 4	1564	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				amelogenesis (GO:0097186)|autophagy (GO:0006914)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell motility (GO:0048870)|cell-matrix adhesion (GO:0007160)|digestive tract development (GO:0048565)|extracellular matrix organization (GO:0030198)|filopodium assembly (GO:0046847)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|mesodermal cell differentiation (GO:0048333)|nail development (GO:0035878)|renal system development (GO:0072001)|response to wounding (GO:0009611)|skin development (GO:0043588)	basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|hemidesmosome (GO:0030056)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor binding (GO:0001664)|receptor activity (GO:0004872)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|liver(1)|lung(25)|skin(1)|urinary_tract(1)	43	all_cancers(13;1.5e-07)		all cancers(21;8.32e-07)|Epithelial(20;1.92e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00194)|Lung(188;0.132)|LUSC - Lung squamous cell carcinoma(166;0.154)			AGTGTGGAGTACCAGCTGCTG	0.677																																					p.Y1564C		.											.	.	.	0			c.A4691G						.						23.0	24.0	24.0					17																	73751914		2202	4297	6499	SO:0001583	missense	3691	exon35			TGGAGTACCAGCT		CCDS11727.1, CCDS32736.1, CCDS58599.1	17q25.1	2013-09-19			ENSG00000132470	ENSG00000132470		"""CD molecules"", ""Integrins"", ""Fibronectin type III domain containing"""	6158	protein-coding gene	gene with protein product		147557				2070796	Standard	XM_005257309		Approved	CD104	uc002jpg.3	P16144	OTTHUMG00000179814	ENST00000200181.3:c.4691A>G	17.37:g.73751914A>G	ENSP00000200181:p.Tyr1564Cys	Somatic	20	0		WXS	Illumina HiSeq	.	23	10	NM_000213	A0AVL6|O14690|O14691|O15339|O15340|O15341|Q0VF97|Q9UIQ4	Missense_Mutation	SNP	ENST00000200181.3	37	CCDS11727.1	.	.	.	.	.	.	.	.	.	.	A	14.89	2.671825	0.47781	.	.	ENSG00000132470	ENST00000200181;ENST00000339591;ENST00000449880	T;T;T	0.61274	0.12;0.12;0.12	5.43	5.43	0.79202	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.64402	D	0.000001	T	0.71728	0.3374	L	0.53671	1.685	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	T	0.72646	-0.4230	10	0.49607	T	0.09	.	15.4761	0.75481	1.0:0.0:0.0:0.0	.	1547;1494;1564	P16144-3;A0AVL6;P16144	.;.;ITB4_HUMAN	C	1564;1547;1547	ENSP00000200181:Y1564C;ENSP00000344079:Y1547C;ENSP00000400217:Y1547C	ENSP00000200181:Y1564C	Y	+	2	0	ITGB4	71263509	1.000000	0.71417	1.000000	0.80357	0.865000	0.49528	9.339000	0.96797	2.078000	0.62432	0.459000	0.35465	TAC	.		0.677	ITGB4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000448334.1		
HPS3	84343	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	3	148894184	148894184	+	IGR	SNP	T	T	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr3:148894184T>C	ENST00000296051.2	+	0	4665				CP_ENST00000264613.6_Missense_Mutation_p.S1012G	NM_032383.3	NP_115759.2	Q969F9	HPS3_HUMAN	Hermansky-Pudlak syndrome 3						organelle organization (GO:0006996)|pigmentation (GO:0043473)	BLOC-2 complex (GO:0031084)				breast(2)|endometrium(2)|kidney(1)|large_intestine(7)|lung(12)|ovary(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	34			LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)			ACATCAGAACTATAAACTCCC	0.368									Hermansky-Pudlak syndrome																												p.S1012G		.											.	.	.	0			c.A3034G						.						82.0	82.0	82.0					3																	148894184		2203	4299	6502	SO:0001628	intergenic_variant	1356	exon18	Familial Cancer Database	HPS, HPS1-8	CAGAACTATAAAC	AY033141	CCDS3140.1	3q24	2014-06-18			ENSG00000163755	ENSG00000163755			15597	protein-coding gene	gene with protein product		606118				11455388	Standard	NM_032383		Approved	SUTAL	uc003ewu.1	Q969F9	OTTHUMG00000159548		3.37:g.148894184T>C		Somatic	59	0		WXS	Illumina HiSeq	.	49	17	NM_000096	A8K6G6|Q8WTV6|Q96AP1|Q96MR3|Q9H608	Missense_Mutation	SNP	ENST00000296051.2	37	CCDS3140.1	.	.	.	.	.	.	.	.	.	.	T	12.87	2.068033	0.36470	.	.	ENSG00000047457	ENST00000479771;ENST00000264613;ENST00000494544	D;D;D	0.99706	-6.47;-6.47;-6.47	5.62	1.97	0.26223	Cupredoxin (2);Multicopper oxidase, type 2 (1);	0.338989	0.33346	N	0.005020	D	0.98128	0.9382	N	0.20986	0.625	0.09310	N	0.999997	P	0.42584	0.784	B	0.37780	0.258	D	0.94683	0.7867	10	0.72032	D	0.01	-5.5326	14.584	0.68310	0.0:0.0:0.7128:0.2872	.	1012	P00450	CERU_HUMAN	G	147;1012;795	ENSP00000420367:S147G;ENSP00000264613:S1012G;ENSP00000420545:S795G	ENSP00000264613:S1012G	S	-	1	0	CP	150376874	0.989000	0.36119	0.274000	0.24659	0.737000	0.42083	2.080000	0.41586	0.368000	0.24481	0.528000	0.53228	AGT	.		0.368	HPS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356151.1	NM_032383	
SENP1	29843	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	12	48501972	48501972	+	5'Flank	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr12:48501972A>C	ENST00000004980.5	-	0	0				SENP1_ENST00000549518.1_5'Flank|PFKM_ENST00000340802.6_Missense_Mutation_p.K67T|SENP1_ENST00000551330.1_5'Flank|SENP1_ENST00000448372.1_5'Flank|SENP1_ENST00000339976.6_5'Flank			Q9P0U3	SENP1_HUMAN	SUMO1/sentrin specific peptidase 1						activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic signaling pathway (GO:0097190)|cellular protein metabolic process (GO:0044267)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-translational protein modification (GO:0043687)|protein desumoylation (GO:0016926)|protein sumoylation (GO:0016925)|proteolysis (GO:0006508)|regulation of definitive erythrocyte differentiation (GO:0010724)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	endopeptidase activity (GO:0004175)|SUMO-specific protease activity (GO:0016929)			large_intestine(3)|lung(1)|pancreas(2)|stomach(1)	7		Acute lymphoblastic leukemia(13;0.108)|all_hematologic(14;0.214)				CCTGTTTTCAAAACTGGTGAG	0.418																																					p.K67T		.											.	.	.	0			c.A200C						.						171.0	149.0	155.0					12																	48501972		1568	3582	5150	SO:0001631	upstream_gene_variant	5213	exon3			TTTTCAAAACTGG	AF149770	CCDS44868.1, CCDS44868.2	12q13.1	2008-02-05	2005-08-17			ENSG00000079387			17927	protein-coding gene	gene with protein product		612157	"""SUMO1/sentrin specific protease 1"""			10652325, 14563852	Standard	NM_001267595		Approved		uc009zkx.4	Q9P0U3	OTTHUMG00000169896		12.37:g.48501972A>C	Exception_encountered	Somatic	61	0		WXS	Illumina HiSeq	.	44	17	NM_001166686	A8K7P5|Q86XC8	Missense_Mutation	SNP	ENST00000004980.5	37	CCDS44868.2	.	.	.	.	.	.	.	.	.	.	A	14.37	2.515563	0.44763	.	.	ENSG00000152556	ENST00000550257;ENST00000340802;ENST00000546755;ENST00000549366;ENST00000552792;ENST00000548288	D;T;D;D;D	0.86562	-2.12;-1.42;-2.14;-2.13;-2.13	4.05	-1.54	0.08584	.	1.145590	0.06408	N	0.719985	T	0.75613	0.3873	N	0.14661	0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.56751	-0.7927	10	0.18276	T	0.48	0.0324	11.8501	0.52407	0.3451:0.6549:0.0:0.0	.	67	Q6ZTT1	.	T	70;67;67;67;67;67	ENSP00000447997:K70T;ENSP00000345771:K67T;ENSP00000449622:K67T;ENSP00000448940:K67T;ENSP00000448018:K67T	ENSP00000345771:K67T	K	+	2	0	PFKM	46788239	0.002000	0.14202	0.001000	0.08648	0.200000	0.23975	0.194000	0.17135	-0.238000	0.09724	-0.466000	0.05196	AAA	.		0.418	SENP1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000406471.1	NM_014554	
ELMSAN1	91748	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	14	74189546	74189546	+	Missense_Mutation	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr14:74189546T>G	ENST00000286523.5	-	10	3361	c.2579A>C	c.(2578-2580)cAg>cCg	p.Q860P	ELMSAN1_ENST00000394071.2_Missense_Mutation_p.Q860P	NM_194278.3	NP_919254.2	Q6PJG2	EMSA1_HUMAN	ELM2 and Myb/SANT-like domain containing 1	860	SANT. {ECO:0000255|PROSITE- ProRule:PRU00624}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)										GGTCTTGGTCTGGATCTGGTT	0.517																																					p.Q860P		.											.	.	.	0			c.A2579C						.						177.0	165.0	169.0					14																	74189546		2203	4300	6503	SO:0001583	missense	91748	exon10			TTGGTCTGGATCT	BF971739	CCDS9819.1	14q24.3	2012-09-25	2012-09-25	2012-09-25	ENSG00000156030	ENSG00000156030			19853	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 117"", ""chromosome 14 open reading frame 43"""	C14orf117, C14orf43			Standard	NM_194278		Approved	LSR68	uc001xou.3	Q6PJG2	OTTHUMG00000150359	ENST00000286523.5:c.2579A>C	14.37:g.74189546T>G	ENSP00000286523:p.Gln860Pro	Somatic	64	0		WXS	Illumina HiSeq	.	50	20	NM_194278	Q6PK13|Q6PK59|Q6ZS23	Missense_Mutation	SNP	ENST00000286523.5	37	CCDS9819.1	.	.	.	.	.	.	.	.	.	.	T	20.7	4.040982	0.75732	.	.	ENSG00000156030	ENST00000394071;ENST00000286523;ENST00000423556;ENST00000435371	T;T;T;T	0.29917	1.55;1.55;1.55;1.55	5.38	5.38	0.77491	SANT domain, DNA binding (1);Homeodomain-like (1);SANT, eukarya (1);	0.101180	0.41605	D	0.000842	T	0.24890	0.0604	N	0.03948	-0.315	0.41263	D	0.986797	D;D	0.59357	0.967;0.985	B;P	0.53006	0.326;0.715	T	0.33266	-0.9875	10	0.46703	T	0.11	-17.679	15.3898	0.74735	0.0:0.0:0.0:1.0	.	860;860	A0PJD3;Q6PJG2	.;CN043_HUMAN	P	860	ENSP00000377634:Q860P;ENSP00000286523:Q860P;ENSP00000407767:Q860P;ENSP00000402380:Q860P	ENSP00000286523:Q860P	Q	-	2	0	C14orf43	73259299	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.365000	0.52335	2.051000	0.60960	0.459000	0.35465	CAG	.		0.517	ELMSAN1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317793.1	NM_194278	
TMEM132D	121256	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	12	129566387	129566387	+	Missense_Mutation	SNP	T	T	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr12:129566387T>A	ENST00000422113.2	-	7	2166	c.1840A>T	c.(1840-1842)Atg>Ttg	p.M614L	TMEM132D_ENST00000389441.4_Missense_Mutation_p.M152L	NM_133448.2	NP_597705.2	Q14C87	T132D_HUMAN	transmembrane protein 132D	614					negative regulation of phosphatase activity (GO:0010923)	integral component of membrane (GO:0016021)				NS(1)|breast(6)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(33)|liver(1)|lung(69)|ovary(10)|pancreas(2)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(2)	152	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0934)|Breast(359;0.133)		OV - Ovarian serous cystadenocarcinoma(86;0.000288)|Epithelial(86;0.0116)|all cancers(50;0.0246)		TCCACCTGCATGAAGTCATTT	0.572																																					p.M614L		.											.	.	.	0			c.A1840T						.						57.0	54.0	55.0					12																	129566387		2203	4300	6503	SO:0001583	missense	121256	exon7			CCTGCATGAAGTC	AB061814	CCDS9266.1	12q24.32-q24.33	2014-06-13			ENSG00000151952	ENSG00000151952			29411	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 153"""	611257				11853319, 12966072	Standard	NM_133448		Approved	KIAA1944, MOLT, PPP1R153	uc009zyl.1	Q14C87	OTTHUMG00000168400	ENST00000422113.2:c.1840A>T	12.37:g.129566387T>A	ENSP00000408581:p.Met614Leu	Somatic	45	0		WXS	Illumina HiSeq	.	26	8	NM_133448	Q14C96|Q76M59|Q8N1W9|Q8N3Q5|Q8TF57	Missense_Mutation	SNP	ENST00000422113.2	37	CCDS9266.1	.	.	.	.	.	.	.	.	.	.	T	11.07	1.529997	0.27387	.	.	ENSG00000151952	ENST00000389441;ENST00000422113	T;T	0.12147	2.71;2.71	4.63	2.23	0.28157	.	0.187945	0.47455	D	0.000222	T	0.11452	0.0279	L	0.46157	1.445	0.34320	D	0.686447	B;B	0.06786	0.001;0.001	B;B	0.11329	0.002;0.006	T	0.18587	-1.0332	9	.	.	.	-41.1316	8.943	0.35742	0.0:0.1529:0.0:0.8471	.	614;152	Q14C87;Q14C87-2	T132D_HUMAN;.	L	152;614	ENSP00000374092:M152L;ENSP00000408581:M614L	.	M	-	1	0	TMEM132D	128132340	1.000000	0.71417	1.000000	0.80357	0.838000	0.47535	0.567000	0.23608	0.156000	0.19299	-1.144000	0.01866	ATG	.		0.572	TMEM132D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399592.1	NM_133448	
Unknown	0	hgsc.bcm.edu	37	X	103165052	103165052	+	IGR	SNP	A	A	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chrX:103165052A>T								RNA5SP511 (59212 upstream) : LL0XNC01-116E7.2 (6952 downstream)																							TATTTCCAGTAAGTTTCATTG	0.338																																					.		.											.	.	.	0			.						.																																			SO:0001628	intergenic_variant	100302155	.			TCCAGTAAGTTTC																													X.37:g.103165052A>T		Somatic	15	0		WXS	Illumina HiSeq	.	5	5	.		RNA	SNP		37																																																																																				.	0	0.338								
POLE	5426	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	12	133202837	133202837	+	Missense_Mutation	SNP	C	C	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr12:133202837C>A	ENST00000320574.5	-	46	6440	c.6397G>T	c.(6397-6399)Gtg>Ttg	p.V2133L	POLE_ENST00000535270.1_Missense_Mutation_p.V2106L	NM_006231.2	NP_006222.2	Q07864	DPOE1_HUMAN	polymerase (DNA directed), epsilon, catalytic subunit	2133					base-excision repair, gap-filling (GO:0006287)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA synthesis involved in DNA repair (GO:0000731)|G1/S transition of mitotic cell cycle (GO:0000082)|in utero embryonic development (GO:0001701)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	cytoplasm (GO:0005737)|epsilon DNA polymerase complex (GO:0008622)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	4 iron, 4 sulfur cluster binding (GO:0051539)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|nucleotide binding (GO:0000166)|zinc ion binding (GO:0008270)			NS(2)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(41)|ovary(3)|pancreas(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	89	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0416)		OV - Ovarian serous cystadenocarcinoma(86;5.22e-08)|Epithelial(86;4.03e-07)|all cancers(50;1.18e-05)	Cladribine(DB00242)	CCGACATCCACCAGGCGAAGC	0.602								DNA polymerases (catalytic subunits)																													p.V2133L		.											.	.	.	0			c.G6397T						.						94.0	73.0	80.0					12																	133202837		2203	4300	6503	SO:0001583	missense	5426	exon46			CATCCACCAGGCG		CCDS9278.1	12q24.3	2014-09-17	2012-05-18		ENSG00000177084	ENSG00000177084		"""DNA polymerases"""	9177	protein-coding gene	gene with protein product	"""DNA polymerase epsilon catalytic subunit A"""	174762	"""polymerase (DNA directed), epsilon"""			8020968	Standard	NM_006231		Approved	POLE1	uc001uks.1	Q07864	OTTHUMG00000168045	ENST00000320574.5:c.6397G>T	12.37:g.133202837C>A	ENSP00000322570:p.Val2133Leu	Somatic	20	0		WXS	Illumina HiSeq	.	10	4	NM_006231	Q13533|Q86VH9	Missense_Mutation	SNP	ENST00000320574.5	37	CCDS9278.1	.	.	.	.	.	.	.	.	.	.	C	15.39	2.819270	0.50633	.	.	ENSG00000177084	ENST00000434528;ENST00000320574;ENST00000455752;ENST00000320557;ENST00000535270	T;T;T	0.22945	1.93;1.93;1.93	4.81	3.92	0.45320	.	0.062472	0.64402	D	0.000006	T	0.18173	0.0436	L	0.28458	0.855	0.46586	D	0.999111	B;B	0.16166	0.002;0.016	B;B	0.12156	0.004;0.007	T	0.04203	-1.0969	10	0.37606	T	0.19	.	10.202	0.43089	0.0:0.825:0.0:0.175	.	2133;343	Q07864;B3KS74	DPOE1_HUMAN;.	L	343;2133;2144;48;2106	ENSP00000322570:V2133L;ENSP00000406383:V2144L;ENSP00000445753:V2106L	ENSP00000322473:V48L	V	-	1	0	POLE	131712910	1.000000	0.71417	0.992000	0.48379	0.823000	0.46562	2.905000	0.48727	1.249000	0.43950	0.555000	0.69702	GTG	.		0.602	POLE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397689.2	NM_006231	
DMXL1	1657	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	5	118486011	118486011	+	Missense_Mutation	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr5:118486011A>C	ENST00000311085.8	+	18	4569	c.4489A>C	c.(4489-4491)Agt>Cgt	p.S1497R	DMXL1_ENST00000539542.1_Missense_Mutation_p.S1497R	NM_005509.4	NP_005500.4	Q9Y485	DMXL1_HUMAN	Dmx-like 1	1497										breast(3)|central_nervous_system(1)|endometrium(14)|kidney(4)|large_intestine(20)|liver(6)|lung(28)|ovary(2)|prostate(5)|skin(2)|upper_aerodigestive_tract(1)	86		all_cancers(142;0.0314)|all_epithelial(76;0.00559)|Prostate(80;0.11)|Breast(839;0.231)		OV - Ovarian serous cystadenocarcinoma(64;0.000563)|Epithelial(69;0.00179)|all cancers(49;0.0243)		ACTTCATTCTAGTTTACCAGG	0.443																																					p.S1497R		.											.	.	.	0			c.A4489C						.						133.0	130.0	131.0					5																	118486011		2202	4300	6502	SO:0001583	missense	1657	exon18			CATTCTAGTTTAC	AJ005821	CCDS4125.1, CCDS75289.1	5q22	2013-01-10			ENSG00000172869	ENSG00000172869		"""WD repeat domain containing"""	2937	protein-coding gene	gene with protein product		605671				10708522	Standard	NM_005509		Approved		uc003ksd.2	Q9Y485	OTTHUMG00000128898	ENST00000311085.8:c.4489A>C	5.37:g.118486011A>C	ENSP00000309690:p.Ser1497Arg	Somatic	51	0		WXS	Illumina HiSeq	.	45	21	NM_005509		Missense_Mutation	SNP	ENST00000311085.8	37	CCDS4125.1	.	.	.	.	.	.	.	.	.	.	A	12.75	2.031892	0.35893	.	.	ENSG00000172869	ENST00000311085;ENST00000539542	T;T	0.42513	0.97;0.97	5.42	5.42	0.78866	.	0.000000	0.85682	D	0.000000	T	0.38134	0.1029	L	0.39020	1.185	0.80722	D	1	P;P	0.48350	0.909;0.767	B;P	0.45406	0.425;0.479	T	0.08868	-1.0701	10	0.18276	T	0.48	-19.0541	15.7495	0.77972	1.0:0.0:0.0:0.0	.	1497;1497	F5H269;Q9Y485	.;DMXL1_HUMAN	R	1497	ENSP00000309690:S1497R;ENSP00000439479:S1497R	ENSP00000309690:S1497R	S	+	1	0	DMXL1	118513910	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.910000	0.92685	2.184000	0.69523	0.455000	0.32223	AGT	.		0.443	DMXL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250862.1	NM_005509	
INTS2	57508	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	17	59952332	59952332	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr17:59952332G>T	ENST00000444766.3	-	19	2623	c.2548C>A	c.(2548-2550)Cag>Aag	p.Q850K	Y_RNA_ENST00000365491.1_RNA|INTS2_ENST00000251334.6_Missense_Mutation_p.Q842K	NM_020748.2	NP_065799	Q9H0H0	INT2_HUMAN	integrator complex subunit 2	850					snRNA processing (GO:0016180)	integral component of membrane (GO:0016021)|integrator complex (GO:0032039)|intracellular (GO:0005622)|membrane (GO:0016020)				NS(1)|breast(2)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(6)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	38						AGGTCATTCTGAGTATACTTT	0.363																																					p.Q850K		.											.	.	.	0			c.C2548A						.						56.0	55.0	55.0					17																	59952332		1871	4102	5973	SO:0001583	missense	57508	exon19			CATTCTGAGTATA	AB033113	CCDS45750.1	17q23.2	2006-04-26	2006-03-15	2006-03-15		ENSG00000108506			29241	protein-coding gene	gene with protein product		611346	"""KIAA1287"""	KIAA1287		16239144	Standard	NR_026641		Approved	INT2	uc002izn.3	Q9H0H0		ENST00000444766.3:c.2548C>A	17.37:g.59952332G>T	ENSP00000414237:p.Gln850Lys	Somatic	58	0		WXS	Illumina HiSeq	.	52	20	NM_020748	Q9ULD3	Missense_Mutation	SNP	ENST00000444766.3	37	CCDS45750.1	.	.	.	.	.	.	.	.	.	.	G	23.1	4.377422	0.82682	.	.	ENSG00000108506	ENST00000444766;ENST00000251334	T	0.43294	0.95	5.11	5.11	0.69529	.	0.000000	0.85682	D	0.000000	T	0.61173	0.2326	L	0.61218	1.895	0.80722	D	1	P	0.43578	0.811	P	0.60789	0.879	T	0.57027	-0.7881	9	.	.	.	-7.2956	17.8928	0.88877	0.0:0.0:1.0:0.0	.	850	Q9H0H0	INT2_HUMAN	K	850;849	ENSP00000414237:Q850K	.	Q	-	1	0	INTS2	57307114	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.182000	0.94881	2.521000	0.84997	0.650000	0.86243	CAG	.		0.363	INTS2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000445368.1	NM_020748	
RPS24	6229	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	10	79814760	79814760	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr10:79814760G>T	ENST00000440692.1	+	5	1004	c.862G>T	c.(862-864)Ggc>Tgc	p.G288C		NM_001142285.1	NP_001135757.1	P62847	RS24_HUMAN	ribosomal protein S24	0					cellular protein metabolic process (GO:0044267)|erythrocyte homeostasis (GO:0034101)|gene expression (GO:0010467)|maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000462)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|ribosomal small subunit biogenesis (GO:0042274)|RNA metabolic process (GO:0016070)|rRNA processing (GO:0006364)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic small ribosomal subunit (GO:0022627)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|small ribosomal subunit (GO:0015935)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)|translation initiation factor binding (GO:0031369)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|ovary(2)|skin(1)	5	all_cancers(46;0.0343)|all_epithelial(25;0.000959)|Breast(12;0.00113)|Prostate(51;0.0095)		Epithelial(14;0.00128)|OV - Ovarian serous cystadenocarcinoma(4;0.00248)|all cancers(16;0.00428)			ctctggtctgggccactaatg	0.547																																					p.G288C		.											.	.	.	0			c.G862T						.						33.0	31.0	32.0					10																	79814760		692	1591	2283	SO:0001583	missense	6229	exon5			GGTCTGGGCCACT	AB007159	CCDS7355.1, CCDS7356.1, CCDS44443.1	10q22	2011-04-06			ENSG00000138326	ENSG00000138326		"""S ribosomal proteins"""	10411	protein-coding gene	gene with protein product		602412				9027498, 9582194	Standard	NM_001142283		Approved	S24	uc001jzs.3	P62847	OTTHUMG00000018549	ENST00000440692.1:c.862G>T	10.37:g.79814760G>T	ENSP00000414321:p.Gly288Cys	Somatic	23	0		WXS	Illumina HiSeq	.	24	12	NM_001142285	E7EPK6|P16632|Q5T0P7|Q5T0P8|Q7Z3D1	Missense_Mutation	SNP	ENST00000440692.1	37	CCDS44443.1	.	.	.	.	.	.	.	.	.	.	G	7.410	0.634532	0.14322	.	.	ENSG00000138326	ENST00000440692	.	.	.	1.86	-0.0979	0.13631	.	.	.	.	.	T	0.15998	0.0385	N	0.08118	0	0.09310	N	1	P	0.52463	0.953	P	0.47075	0.536	T	0.10894	-1.0610	7	.	.	.	.	3.9315	0.09288	0.4426:0.0:0.5574:0.0	.	288	E7EPK6	.	C	288	.	.	G	+	1	0	RPS24	79484766	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.231000	0.09069	-0.018000	0.14079	-0.222000	0.12452	GGC	.		0.547	RPS24-202	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_001026	
MYOM1	8736	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	18	3067471	3067471	+	Missense_Mutation	SNP	T	T	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr18:3067471T>A	ENST00000356443.4	-	38	5180	c.4847A>T	c.(4846-4848)gAc>gTc	p.D1616V	MYOM1_ENST00000261606.7_Missense_Mutation_p.D1520V|MYOM1_ENST00000400569.3_Missense_Mutation_p.D1616V	NM_003803.3|NM_019856.1	NP_003794.3|NP_062830.1	P52179	MYOM1_HUMAN	myomesin 1	1616	Ig-like C2-type 5.			SD -> QT (in Ref. 5; CAA48833). {ECO:0000305}.	muscle contraction (GO:0006936)	M band (GO:0031430)|striated muscle myosin thick filament (GO:0005863)	identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|structural constituent of muscle (GO:0008307)			NS(2)|autonomic_ganglia(1)|central_nervous_system(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(20)|ovary(4)|pancreas(1)|prostate(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	77						GCAGTGGTCGTCTGAGGCCAG	0.582																																					p.D1616V		.											.	.	.	0			c.A4847T						.						59.0	64.0	62.0					18																	3067471		2203	4299	6502	SO:0001583	missense	8736	exon38			TGGTCGTCTGAGG	AF185573	CCDS45823.1, CCDS45824.1	18p11.31	2014-09-17	2012-10-17		ENSG00000101605	ENSG00000101605		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	7613	protein-coding gene	gene with protein product	"""skelemin"""	603508	"""myomesin 1 (skelemin) (185kD)"", ""myomesin 1 (skelemin) 185kDa"", ""myomesin 1, 185kDa"""			9806852	Standard	NM_019856		Approved		uc002klp.3	P52179	OTTHUMG00000178209	ENST00000356443.4:c.4847A>T	18.37:g.3067471T>A	ENSP00000348821:p.Asp1616Val	Somatic	48	0		WXS	Illumina HiSeq	.	22	10	NM_003803	Q14BD6|Q6H969|Q6ZUU0	Missense_Mutation	SNP	ENST00000356443.4	37	CCDS45824.1	.	.	.	.	.	.	.	.	.	.	T	15.20	2.763118	0.49574	.	.	ENSG00000101605	ENST00000356443;ENST00000400569;ENST00000261606	T;T;T	0.47177	0.85;0.85;0.85	5.79	2.1	0.27182	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.142496	0.64402	D	0.000009	T	0.63698	0.2533	M	0.88377	2.95	0.39421	D	0.966929	P;P	0.52316	0.897;0.952	P;P	0.55222	0.72;0.771	T	0.66184	-0.5987	10	0.52906	T	0.07	.	9.6942	0.40147	0.0:0.1958:0.0:0.8042	.	1520;1616	P52179-2;P52179	.;MYOM1_HUMAN	V	1616;1616;1520	ENSP00000348821:D1616V;ENSP00000383413:D1616V;ENSP00000261606:D1520V	ENSP00000261606:D1520V	D	-	2	0	MYOM1	3057471	1.000000	0.71417	0.000000	0.03702	0.125000	0.20455	5.184000	0.65070	0.125000	0.18397	0.533000	0.62120	GAC	.		0.582	MYOM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441037.2	NM_003803	
GRIN2A	2903	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	16	9857878	9857878	+	Nonsense_Mutation	SNP	C	C	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr16:9857878C>A	ENST00000396573.2	-	14	3832	c.3523G>T	c.(3523-3525)Gaa>Taa	p.E1175*	GRIN2A_ENST00000535259.1_Nonsense_Mutation_p.E1018*|GRIN2A_ENST00000330684.3_Nonsense_Mutation_p.E1175*|GRIN2A_ENST00000404927.2_Nonsense_Mutation_p.E1175*|GRIN2A_ENST00000562109.1_Nonsense_Mutation_p.E1175*|GRIN2A_ENST00000396575.2_Nonsense_Mutation_p.E1175*	NM_000833.3	NP_000824.1	Q12879	NMDE1_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2A	1175			E -> K (found in a cutaneous malignant melanoma sample; somatic mutation). {ECO:0000269|PubMed:21499247}.		directional locomotion (GO:0033058)|dopamine metabolic process (GO:0042417)|glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|learning or memory (GO:0007611)|memory (GO:0007613)|negative regulation of protein catabolic process (GO:0042177)|neurogenesis (GO:0022008)|positive regulation of apoptotic process (GO:0043065)|protein localization (GO:0008104)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of sensory perception of pain (GO:0051930)|regulation of synaptic plasticity (GO:0048167)|response to amphetamine (GO:0001975)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to wounding (GO:0009611)|sensory perception of pain (GO:0019233)|serotonin metabolic process (GO:0042428)|sleep (GO:0030431)|startle response (GO:0001964)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)|visual learning (GO:0008542)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|synaptic vesicle (GO:0008021)	calcium channel activity (GO:0005262)|extracellular-glutamate-gated ion channel activity (GO:0005234)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|zinc ion binding (GO:0008270)	p.E1175K(1)		NS(7)|breast(5)|cervix(1)|endometrium(11)|kidney(6)|large_intestine(36)|lung(71)|ovary(4)|prostate(9)|skin(45)|upper_aerodigestive_tract(2)|urinary_tract(1)	198					Acamprosate(DB00659)|Acetylcysteine(DB06151)|Atomoxetine(DB00289)|Felbamate(DB00949)|Gabapentin(DB00996)|Glycine(DB00145)|Halothane(DB01159)|Ketobemidone(DB06738)|Memantine(DB01043)|Milnacipran(DB04896)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	AGCCCCTCTTCATTATGCAAG	0.557																																					p.E1175X		.											GRIN2A,NS,carcinoma,0,2	GRIN2A	0	1	Substitution - Missense(1)	skin(1)	c.G3523T						.						194.0	190.0	191.0					16																	9857878		2197	4300	6497	SO:0001587	stop_gained	2903	exon14			CCTCTTCATTATG		CCDS10539.1, CCDS45407.1	16p13.2	2012-08-29			ENSG00000183454	ENSG00000183454		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4585	protein-coding gene	gene with protein product		138253		NMDAR2A		9480759	Standard	XM_005255267		Approved	GluN2A	uc002czo.4	Q12879	OTTHUMG00000129721	ENST00000396573.2:c.3523G>T	16.37:g.9857878C>A	ENSP00000379818:p.Glu1175*	Somatic	55	0		WXS	Illumina HiSeq	.	41	16	NM_000833	O00669|Q17RZ6	Nonsense_Mutation	SNP	ENST00000396573.2	37	CCDS10539.1	.	.	.	.	.	.	.	.	.	.	C	33	5.241064	0.95272	.	.	ENSG00000183454	ENST00000396573;ENST00000404927;ENST00000535259;ENST00000330684;ENST00000396575	.	.	.	5.19	5.19	0.71726	.	0.352416	0.34828	N	0.003657	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.7092	0.88317	0.0:1.0:0.0:0.0	.	.	.	.	X	1175;1175;1018;1175;1175	.	.	E	-	1	0	GRIN2A	9765379	0.925000	0.31364	0.312000	0.25196	0.012000	0.07955	2.693000	0.47027	2.406000	0.81754	0.650000	0.86243	GAA	.		0.557	GRIN2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251930.3		
IMP3	55272	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	15	75932170	75932170	+	Missense_Mutation	SNP	C	C	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr15:75932170C>T	ENST00000314852.2	-	2	1283	c.340G>A	c.(340-342)Gtg>Atg	p.V114M	IMP3_ENST00000403490.1_Missense_Mutation_p.V114M|IMP3_ENST00000565349.1_5'Flank|CTD-2026K11.2_ENST00000564683.1_RNA			Q8TCT8	SPP2A_HUMAN	IMP3, U3 small nucleolar ribonucleoprotein	0	PA.				membrane protein ectodomain proteolysis (GO:0006509)|membrane protein intracellular domain proteolysis (GO:0031293)|regulation of immune response (GO:0050776)	extracellular vesicular exosome (GO:0070062)|Golgi-associated vesicle membrane (GO:0030660)|integral component of cytoplasmic side of endoplasmic reticulum membrane (GO:0071458)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	aspartic-type endopeptidase activity (GO:0004190)|protein homodimerization activity (GO:0042803)			large_intestine(1)	1						TTGAGGAGCACGGTGGGGAGG	0.682																																					p.V114M		.											.	.	.	0			c.G340A						.						24.0	25.0	25.0					15																	75932170		2197	4286	6483	SO:0001583	missense	55272	exon1			GGAGCACGGTGGG	AB051628	CCDS10282.1	15q24	2014-02-19	2014-02-19	2005-07-14	ENSG00000177971	ENSG00000177971			14497	protein-coding gene	gene with protein product		612980	"""mitochondrial ribosomal protein S4"", ""chromosome 15 open reading frame 12"", ""IMP3, U3 small nucleolar ribonucleoprotein, homolog (yeast)"""	MRPS4, C15orf12		11543634, 12655004	Standard	NM_018285		Approved	FLJ10968, BRMS2	uc010bkl.2	Q9NV31	OTTHUMG00000142840	ENST00000314852.2:c.340G>A	15.37:g.75932170C>T	ENSP00000326981:p.Val114Met	Somatic	37	0		WXS	Illumina HiSeq	.	23	10	NM_018285	B2RDS0|Q8TAW1|Q96SZ8	Missense_Mutation	SNP	ENST00000314852.2	37	CCDS10282.1	.	.	.	.	.	.	.	.	.	.	C	21.1	4.090834	0.76756	.	.	ENSG00000177971	ENST00000314852;ENST00000403490	T;T	0.50277	0.75;0.75	5.65	4.71	0.59529	RNA-binding S4 (4);	0.208959	0.43579	D	0.000559	T	0.45337	0.1337	L	0.58669	1.825	0.41969	D	0.99074	P	0.50943	0.94	B	0.42995	0.404	T	0.49322	-0.8952	10	0.49607	T	0.09	-15.7935	11.4299	0.50034	0.1865:0.8135:0.0:0.0	.	114	Q9NV31	IMP3_HUMAN	M	114	ENSP00000326981:V114M;ENSP00000385217:V114M	ENSP00000326981:V114M	V	-	1	0	IMP3	73719225	0.998000	0.40836	0.997000	0.53966	0.636000	0.38137	1.506000	0.35747	1.564000	0.49628	0.655000	0.94253	GTG	.		0.682	IMP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286476.1	NM_018285	
PTEN	5728	hgsc.bcm.edu;bcgsc.ca	37	10	89720807	89720807	+	Missense_Mutation	SNP	T	T	G	rs398123330		TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr10:89720807T>G	ENST00000371953.3	+	8	2315	c.958T>G	c.(958-960)Tta>Gta	p.L320V	PTEN_ENST00000472832.1_3'UTR	NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog	320	C2 tensin-type. {ECO:0000255|PROSITE- ProRule:PRU00589}.				activation of mitotic anaphase-promoting complex activity (GO:0007092)|aging (GO:0007568)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|brain morphogenesis (GO:0048854)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle tissue development (GO:0048738)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|central nervous system myelin maintenance (GO:0032286)|central nervous system neuron axonogenesis (GO:0021955)|dendritic spine morphogenesis (GO:0060997)|dentate gyrus development (GO:0021542)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|innate immune response (GO:0045087)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|learning or memory (GO:0007611)|locomotor rhythm (GO:0045475)|locomotory behavior (GO:0007626)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|male mating behavior (GO:0060179)|maternal behavior (GO:0042711)|memory (GO:0007613)|multicellular organismal response to stress (GO:0033555)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell aging (GO:0090344)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031658)|negative regulation of dendritic spine morphogenesis (GO:0061002)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myelination (GO:0031642)|negative regulation of organ growth (GO:0046621)|negative regulation of phagocytosis (GO:0050765)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of ribosome biogenesis (GO:0090071)|negative regulation of synaptic vesicle clustering (GO:2000808)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell proliferation (GO:0008284)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|postsynaptic density assembly (GO:0097107)|prepulse inhibition (GO:0060134)|presynaptic membrane assembly (GO:0097105)|prostate gland growth (GO:0060736)|protein dephosphorylation (GO:0006470)|protein kinase B signaling (GO:0043491)|protein stabilization (GO:0050821)|regulation of B cell apoptotic process (GO:0002902)|regulation of cellular component size (GO:0032535)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of myeloid cell apoptotic process (GO:0033032)|regulation of neuron projection development (GO:0010975)|regulation of protein stability (GO:0031647)|response to arsenic-containing substance (GO:0046685)|response to ATP (GO:0033198)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse maturation (GO:0060074)|T cell receptor signaling pathway (GO:0050852)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|myelin sheath adaxonal region (GO:0035749)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)	anaphase-promoting complex binding (GO:0010997)|enzyme binding (GO:0019899)|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity (GO:0051717)|lipid binding (GO:0008289)|magnesium ion binding (GO:0000287)|PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity (GO:0051800)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.0?(37)|p.T319fs*1(24)|p.R55fs*1(5)|p.T319fs*24(4)|p.?(2)|p.N212fs*1(2)|p.Y27fs*1(2)|p.T319_K332del(1)|p.G165_*404del(1)|p.L320V(1)|p.L316fs*1(1)|p.T319fs*4(1)|p.T319fs*5(1)|p.W274_F341del(1)|p.V317_K322del(1)		NS(28)|autonomic_ganglia(2)|biliary_tract(6)|bone(5)|breast(92)|central_nervous_system(676)|cervix(26)|endometrium(1068)|eye(8)|haematopoietic_and_lymphoid_tissue(137)|kidney(24)|large_intestine(98)|liver(20)|lung(91)|meninges(2)|oesophagus(2)|ovary(82)|pancreas(6)|prostate(129)|salivary_gland(5)|skin(127)|soft_tissue(19)|stomach(30)|testis(1)|thyroid(29)|upper_aerodigestive_tract(29)|urinary_tract(12)|vulva(17)	2771		all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132)	KIRC - Kidney renal clear cell carcinoma(1;0.214)	UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218)		AGTACTTACTTTAACAAAAAA	0.328		31	"""D, Mis, N, F, S"""		"""glioma,  prostate, endometrial"""	"""harmartoma, glioma,  prostate, endometrial"""			Proteus syndrome;Juvenile Polyposis;Hereditary Mixed Polyposis Syndrome type 1;Cowden syndrome;Bannayan-Riley-Ruvalcaba syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)																											p.L320V		.	yes	Rec	yes	"""Cowden Syndrome, Bannayan-Riley-Ruvalcaba syndrome"""	10	10q23.3	5728	phosphatase and tensin homolog gene		"""L, E, M, O"""	PTEN,caecum,carcinoma,-1,1	PTEN	-1	84	Deletion - Frameshift(39)|Whole gene deletion(37)|Deletion - In frame(4)|Unknown(2)|Insertion - Frameshift(1)|Substitution - Missense(1)	central_nervous_system(19)|endometrium(18)|prostate(17)|skin(8)|lung(4)|breast(4)|ovary(4)|large_intestine(3)|haematopoietic_and_lymphoid_tissue(3)|soft_tissue(2)|urinary_tract(2)	c.T958G						.						89.0	90.0	89.0					10																	89720807		2203	4299	6502	SO:0001583	missense	5728	exon8	Familial Cancer Database	Incl.: Encephalocraniocutaneous Lipomatosis, ECCL, Proteus-like s.;incl.: Juvenile Polyposis of the Stomach;HMPS1, Colorectal Adenoma Carcinoma syndrome, CRAC, CRAC1;CS, Cowden disease, Multiple Hamartoma Syndrome, incl.: Lhermitte-Duclos; part of PTEN hamartoma tumour syndrome (PHTS) / PTEN-MATCHS, Cowden-like syndrome;subset of PTEN-Hamartoma Tumor Syndrome; incl.: Ruvalcaba-Myhre-Smith s.	CTTACTTTAACAA	U92436	CCDS31238.1	10q23	2014-09-17	2008-07-31		ENSG00000171862	ENSG00000171862		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"""	9588	protein-coding gene	gene with protein product	"""mutated in multiple advanced cancers 1"""	601728		BZS, MHAM		9090379	Standard	NM_000314		Approved	MMAC1, TEP1, PTEN1	uc001kfb.3	P60484	OTTHUMG00000018688	ENST00000371953.3:c.958T>G	10.37:g.89720807T>G	ENSP00000361021:p.Leu320Val	Somatic	114	0		WXS	Illumina HiSeq	.	60	19	NM_000314	B2R904|F2YHV0|O00633|O02679|Q6ICT7	Missense_Mutation	SNP	ENST00000371953.3	37	CCDS31238.1	.	.	.	.	.	.	.	.	.	.	T	19.22	3.784683	0.70222	.	.	ENSG00000171862	ENST00000371953	D	0.89485	-2.52	5.37	3.03	0.35002	Tensin phosphatase, C2 domain (2);C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.85682	D	0.000000	D	0.92133	0.7506	M	0.75264	2.295	0.58432	D	0.999998	D	0.67145	0.996	D	0.65573	0.936	D	0.89797	0.3972	9	.	.	.	-7.0909	8.2636	0.31799	0.0:0.2352:0.0:0.7648	.	320	P60484	PTEN_HUMAN	V	320	ENSP00000361021:L320V	.	L	+	1	2	PTEN	89710787	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.997000	0.49457	0.357000	0.24183	0.482000	0.46254	TTA	.		0.328	PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049241.1	NM_000314	
NUB1	51667	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	7	151072981	151072981	+	Silent	SNP	T	T	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr7:151072981T>A	ENST00000355851.4	+	13	1520	c.1443T>A	c.(1441-1443)ccT>ccA	p.P481P	NUB1_ENST00000568733.1_Silent_p.P505P|NUB1_ENST00000413040.2_Silent_p.P491P|NUB1_ENST00000566856.1_Silent_p.P467P|WDR86_ENST00000463000.1_5'Flank	NM_001243351.1	NP_001230280.1	Q9Y5A7	NUB1_HUMAN	negative regulator of ubiquitin-like proteins 1	481					positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|protein ubiquitination (GO:0016567)|response to interferon-gamma (GO:0034341)|response to tumor necrosis factor (GO:0034612)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)				endometrium(1)|large_intestine(7)|lung(3)	11			OV - Ovarian serous cystadenocarcinoma(82;0.00569)	UCEC - Uterine corpus endometrioid carcinoma (81;0.172)		ATTCCAATCCTGAAACCGACA	0.488																																					p.P505P		.											.	.	.	0			c.T1515A						.						230.0	230.0	230.0					7																	151072981		1970	4151	6121	SO:0001819	synonymous_variant	51667	exon13			CAATCCTGAAACC	AF300717	CCDS47751.1, CCDS47751.2, CCDS59089.1	7q36	2006-07-27			ENSG00000013374	ENSG00000013374			17623	protein-coding gene	gene with protein product	"""NEDD8 ultimate buster-1"""	607981				10508479, 11259415	Standard	NM_001243351		Approved	BS4, NYREN18	uc003wjx.3	Q9Y5A7	OTTHUMG00000157365	ENST00000355851.4:c.1443T>A	7.37:g.151072981T>A		Somatic	87	0		WXS	Illumina HiSeq	.	87	35	NM_001243351	O95422|Q75MR9|Q8IX22|Q9BXR2	Silent	SNP	ENST00000355851.4	37		.	.	.	.	.	.	.	.	.	.	T	3.996	-0.003453	0.07773	.	.	ENSG00000013374	ENST00000460712	.	.	.	5.29	1.6	0.23607	.	.	.	.	.	T	0.53753	0.1816	.	.	.	0.42626	D	0.993367	.	.	.	.	.	.	T	0.42682	-0.9437	4	.	.	.	-1.0148	6.3375	0.21304	0.0:0.0814:0.3315:0.5871	.	.	.	.	Q	68	.	.	L	+	2	0	NUB1	150703914	0.630000	0.27155	0.076000	0.20297	0.329000	0.28539	-0.025000	0.12413	0.117000	0.18138	0.459000	0.35465	CTG	.		0.488	NUB1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_016118	
UBFD1	56061	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	16	23578342	23578342	+	Missense_Mutation	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr16:23578342A>C	ENST00000395878.3	+	6	1152	c.771A>C	c.(769-771)aaA>aaC	p.K257N	UBFD1_ENST00000219638.4_Missense_Mutation_p.K481N|CTD-2196E14.6_ENST00000568262.2_RNA|UBFD1_ENST00000567212.1_Missense_Mutation_p.K248N	NM_019116.2	NP_061989.2	O14562	UBFD1_HUMAN	ubiquitin family domain containing 1	257							poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(1)|large_intestine(2)|lung(3)	7				GBM - Glioblastoma multiforme(48;0.0331)		GCTCCATAAAAAATGTGGTCA	0.478																																					p.K257N	Melanoma(22;290 1069 22358 48158)	.											.	.	.	0			c.A771C						.						124.0	122.0	123.0					16																	23578342		1896	4114	6010	SO:0001583	missense	56061	exon6			CATAAAAAATGTG	AK124139	CCDS10613.2	16p12.1	2008-11-05			ENSG00000103353	ENSG00000103353			30565	protein-coding gene	gene with protein product	"""ubiquitin-binding protein homolog"""					10493829	Standard	XM_006721064		Approved	FLJ42145, FLJ38870, UBPH	uc002dlv.3	O14562	OTTHUMG00000128855	ENST00000395878.3:c.771A>C	16.37:g.23578342A>C	ENSP00000379217:p.Lys257Asn	Somatic	56	0		WXS	Illumina HiSeq	.	47	16	NM_019116	A8MW58|D3DWF2	Missense_Mutation	SNP	ENST00000395878.3	37	CCDS10613.2	.	.	.	.	.	.	.	.	.	.	A	24.1	4.492336	0.84962	.	.	ENSG00000103353	ENST00000219638;ENST00000395878;ENST00000399462	.	.	.	4.9	2.38	0.29361	.	0.000000	0.85682	D	0.000000	T	0.71126	0.3303	M	0.80982	2.52	0.54753	D	0.999983	D	0.76494	0.999	D	0.66196	0.942	T	0.69953	-0.5005	9	0.87932	D	0	-4.4863	7.7214	0.28733	0.7923:0.0:0.2077:0.0	.	257	O14562	UBFD1_HUMAN	N	481;257;134	.	ENSP00000219638:K481N	K	+	3	2	UBFD1	23485843	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	1.972000	0.40540	0.225000	0.20959	0.459000	0.35465	AAA	.		0.478	UBFD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250795.2	NM_019116	
ATAD2B	54454	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	2	24103602	24103602	+	Missense_Mutation	SNP	T	T	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr2:24103602T>C	ENST00000238789.5	-	7	1151	c.808A>G	c.(808-810)Ata>Gta	p.I270V		NM_001242338.1|NM_017552.2	NP_001229267.1|NP_060022.1	Q9ULI0	ATD2B_HUMAN	ATPase family, AAA domain containing 2B	270						nucleus (GO:0005634)	ATP binding (GO:0005524)|lysine-acetylated histone binding (GO:0070577)			central_nervous_system(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TCAACTTCTATATCTCCATCC	0.368																																					p.I270V		.											.	.	.	0			c.A808G						.						176.0	149.0	157.0					2																	24103602		1833	4100	5933	SO:0001583	missense	54454	exon7			CTTCTATATCTCC	AB033066	CCDS46227.1	2p24.1-p23.3	2010-04-21		2007-02-08	ENSG00000119778	ENSG00000119778		"""ATPases / AAA-type"""	29230	protein-coding gene	gene with protein product		615347					Standard	XM_005264372		Approved	KIAA1240	uc002rek.4	Q9ULI0	OTTHUMG00000151902	ENST00000238789.5:c.808A>G	2.37:g.24103602T>C	ENSP00000238789:p.Ile270Val	Somatic	67	0		WXS	Illumina HiSeq	.	42	16	NM_001242338	B9ZVQ5|Q6ZNA6|Q8N9E7	Missense_Mutation	SNP	ENST00000238789.5	37	CCDS46227.1	.	.	.	.	.	.	.	.	.	.	T	11.63	1.696353	0.30052	.	.	ENSG00000119778	ENST00000238789;ENST00000442596;ENST00000439915	D;T	0.91237	-2.81;0.92	5.02	5.02	0.67125	.	.	.	.	.	D	0.85461	0.5702	L	0.40543	1.245	0.27869	N	0.940119	B;B	0.30146	0.27;0.042	B;B	0.30316	0.114;0.01	T	0.76984	-0.2756	9	0.30854	T	0.27	.	9.5829	0.39499	0.0:0.0787:0.0:0.9213	.	284;270	C9JG15;Q9ULI0	.;ATD2B_HUMAN	V	270;122;284	ENSP00000238789:I270V;ENSP00000403177:I284V	ENSP00000238789:I270V	I	-	1	0	ATAD2B	23957106	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.877000	0.63086	2.034000	0.60081	0.528000	0.53228	ATA	.		0.368	ATAD2B-001	KNOWN	mRNA_end_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324333.1	NM_017552	
KIF1B	23095	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	1	10327615	10327615	+	Splice_Site	SNP	A	A	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr1:10327615A>T	ENST00000377086.1	+	6	809	c.607A>T	c.(607-609)Agg>Tgg	p.R203W	KIF1B_ENST00000377081.1_Splice_Site_p.R203W|KIF1B_ENST00000377083.1_Splice_Site_p.R203W|KIF1B_ENST00000377093.4_Splice_Site_p.R203W|KIF1B_ENST00000263934.6_Splice_Site_p.R203W			O60333	KIF1B_HUMAN	kinesin family member 1B	203	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				anterograde axon cargo transport (GO:0008089)|apoptotic process (GO:0006915)|cytoskeleton-dependent intracellular transport (GO:0030705)|microtubule-based movement (GO:0007018)|mitochondrion transport along microtubule (GO:0047497)|neuromuscular synaptic transmission (GO:0007274)|neuron-neuron synaptic transmission (GO:0007270)|vesicle-mediated transport (GO:0016192)	cytoplasmic vesicle (GO:0031410)|cytoplasmic vesicle membrane (GO:0030659)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|kinesin binding (GO:0019894)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)			breast(2)|endometrium(7)|kidney(8)|large_intestine(9)|lung(29)|ovary(3)|prostate(3)|skin(5)|stomach(3)|upper_aerodigestive_tract(2)	71	Ovarian(185;0.203)	all_lung(284;1.31e-05)|Lung NSC(185;2.2e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0259)|Colorectal(212;9.79e-07)|COAD - Colon adenocarcinoma(227;0.000143)|BRCA - Breast invasive adenocarcinoma(304;0.000413)|Kidney(185;0.00134)|KIRC - Kidney renal clear cell carcinoma(229;0.0037)|STAD - Stomach adenocarcinoma(132;0.0113)|READ - Rectum adenocarcinoma(331;0.0642)		GAACAAAGCCAGGTATGGTAG	0.453																																					p.R203W		.											.	.	.	0			c.A607T						.						85.0	67.0	73.0					1																	10327615		2203	4300	6503	SO:0001630	splice_region_variant	23095	exon6			AAAGCCAGGTATG	AF257176	CCDS111.1, CCDS112.1	1p36.22	2014-09-17			ENSG00000054523	ENSG00000054523		"""Kinesins"", ""Pleckstrin homology (PH) domain containing"""	16636	protein-coding gene	gene with protein product		605995		CMT2A, CMT2		11389829, 10762626	Standard	NM_015074		Approved	KIAA0591, KLP, HMSNII	uc001aqw.4	O60333	OTTHUMG00000001817	ENST00000377086.1:c.608+1A>T	1.37:g.10327615A>T		Somatic	54	0		WXS	Illumina HiSeq	.	20	12	NM_183416	A6NFS8|A6NKQ4|Q4VXC3|Q4VXC4|Q4VXC5|Q4VXC6|Q96Q94|Q9BV80|Q9P280	Missense_Mutation	SNP	ENST00000377086.1	37		.	.	.	.	.	.	.	.	.	.	A	31	5.069790	0.93950	.	.	ENSG00000054523	ENST00000355249;ENST00000263934;ENST00000377093;ENST00000377086;ENST00000377083;ENST00000377081	D;D;D;D;D	0.82619	-1.63;-1.63;-1.63;-1.63;-1.63	5.44	5.44	0.79542	Kinesin, motor domain (4);	0.000000	0.85682	D	0.000000	D	0.95987	0.8693	H	0.99951	5.03	0.80722	D	1	D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0;1.0;1.0	D	0.98281	1.0508	10	0.87932	D	0	.	15.7836	0.78286	1.0:0.0:0.0:0.0	.	203;203;203;203;203;203;203	Q4R9M9;Q4R9M7;Q4VXC4;Q4R9M8;O60333;O60333-2;O60333-3	.;.;.;.;KIF1B_HUMAN;.;.	W	203	ENSP00000263934:R203W;ENSP00000366297:R203W;ENSP00000366290:R203W;ENSP00000366287:R203W;ENSP00000366284:R203W	ENSP00000263934:R203W	R	+	1	2	KIF1B	10250202	1.000000	0.71417	1.000000	0.80357	0.932000	0.56968	7.459000	0.80802	2.190000	0.69967	0.477000	0.44152	AGG	.		0.453	KIF1B-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000005102.1		Missense_Mutation
SLC10A7	84068	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	4	147363937	147363937	+	Missense_Mutation	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr4:147363937A>C	ENST00000507030.1	-	5	432	c.433T>G	c.(433-435)Ttg>Gtg	p.L145V	SLC10A7_ENST00000432059.2_Intron|SLC10A7_ENST00000264986.3_3'UTR|SLC10A7_ENST00000394059.4_Missense_Mutation_p.L145V|SLC10A7_ENST00000511315.1_5'UTR|SLC10A7_ENST00000511374.1_3'UTR|SLC10A7_ENST00000335472.7_Missense_Mutation_p.L145V|SLC10A7_ENST00000394062.3_Missense_Mutation_p.L145V			Q0GE19	NTCP7_HUMAN	solute carrier family 10, member 7	145					sodium ion transport (GO:0006814)	integral component of membrane (GO:0016021)	symporter activity (GO:0015293)			endometrium(1)|kidney(3)|large_intestine(3)|lung(8)|skin(1)	16	all_hematologic(180;0.151)					TTACTTACCAAAAAACTTCCA	0.289																																					p.L145V		.											.	.	.	0			c.T433G						.						44.0	43.0	44.0					4																	147363937		2195	4288	6483	SO:0001583	missense	84068	exon5			TTACCAAAAAACT	AY346324	CCDS3768.1, CCDS34073.1, CCDS75198.1	4q31.2	2013-07-18	2013-07-18	2006-12-19	ENSG00000120519	ENSG00000120519		"""Solute carriers"""	23088	protein-coding gene	gene with protein product		611459	"""chromosome 4 open reading frame 13"""	C4orf13		15932064	Standard	NM_032128		Approved	MGC25043, DKFZp566M114, DKFZp313H0531, DKFZp779O2438	uc003ikr.2	Q0GE19	OTTHUMG00000161437	ENST00000507030.1:c.433T>G	4.37:g.147363937A>C	ENSP00000421275:p.Leu145Val	Somatic	235	0		WXS	Illumina HiSeq	.	69	54	NM_032128	A7E2E6|A7MAX9|Q0VAP9|Q45NG1|Q45NG2|Q5H9S6|Q6P4E6|Q8IZ62|Q8NBP8|Q9H0M9	Missense_Mutation	SNP	ENST00000507030.1	37	CCDS34073.1	.	.	.	.	.	.	.	.	.	.	A	12.85	2.061068	0.36373	.	.	ENSG00000120519	ENST00000335472;ENST00000507030;ENST00000394062;ENST00000394059	.	.	.	5.96	4.78	0.61160	.	0.000000	0.85682	D	0.000000	T	0.64560	0.2609	M	0.79805	2.47	0.80722	D	1	P;P;P	0.48998	0.752;0.801;0.918	P;B;B	0.46452	0.517;0.344;0.362	T	0.68454	-0.5404	9	0.56958	D	0.05	-17.3784	11.9777	0.53103	0.9325:0.0:0.0675:0.0	.	145;145;145	Q0GE19;Q0GE19-5;Q0GE19-2	NTCP7_HUMAN;.;.	V	145	.	ENSP00000334594:L145V	L	-	1	2	SLC10A7	147583387	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.270000	0.51600	1.081000	0.41110	0.477000	0.44152	TTG	.		0.289	SLC10A7-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000366932.1	NM_032128	
SRGAP1	57522	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	12	64505656	64505656	+	Silent	SNP	T	T	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr12:64505656T>C	ENST00000355086.3	+	17	2558	c.2034T>C	c.(2032-2034)caT>caC	p.H678H	RP11-196H14.4_ENST00000535806.1_RNA|SRGAP1_ENST00000357825.3_Silent_p.H655H|SRGAP1_ENST00000543397.1_Silent_p.H615H	NM_020762.2	NP_065813.1	Q7Z6B7	SRGP1_HUMAN	SLIT-ROBO Rho GTPase activating protein 1	678	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				axon guidance (GO:0007411)|cell migration (GO:0016477)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho GTPase activator activity (GO:0005100)			breast(4)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(26)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	65			GBM - Glioblastoma multiforme(3;0.000139)|BRCA - Breast invasive adenocarcinoma(9;0.225)	GBM - Glioblastoma multiforme(28;0.0608)		GCCAGGCACATGTGAATGAAA	0.443																																					p.H678H		.											.	.	.	0			c.T2034C						.						164.0	143.0	150.0					12																	64505656		2203	4300	6503	SO:0001819	synonymous_variant	57522	exon17			GGCACATGTGAAT	AB037725	CCDS8967.1	12q13.13	2011-07-04			ENSG00000196935	ENSG00000196935		"""Rho GTPase activating proteins"""	17382	protein-coding gene	gene with protein product		606523				11672528	Standard	NM_020762		Approved	KIAA1304, ARHGAP13	uc010ssp.1	Q7Z6B7	OTTHUMG00000168750	ENST00000355086.3:c.2034T>C	12.37:g.64505656T>C		Somatic	69	0		WXS	Illumina HiSeq	.	48	28	NM_020762	Q9H8A3|Q9P2P2	Silent	SNP	ENST00000355086.3	37	CCDS8967.1																																																																																			.		0.443	SRGAP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000400896.1		
ZNF345	25850	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	19	37368149	37368149	+	Missense_Mutation	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr19:37368149T>G	ENST00000529555.1	+	2	1205	c.417T>G	c.(415-417)atT>atG	p.I139M	ZNF345_ENST00000432005.2_Intron|ZNF345_ENST00000589046.1_Missense_Mutation_p.I139M|ZNF345_ENST00000526123.1_Intron|ZNF345_ENST00000420450.1_Missense_Mutation_p.I139M			Q14585	ZN345_HUMAN	zinc finger protein 345	139					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)|transcription from RNA polymerase III promoter (GO:0006383)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(1)|kidney(1)|large_intestine(13)|lung(5)|ovary(2)|prostate(1)	24	Esophageal squamous(110;0.183)		COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			ATCAGAGAATTCATACTGGTG	0.423																																					p.I139M		.											.	.	.	0			c.T417G						.						66.0	66.0	66.0					19																	37368149		2203	4300	6503	SO:0001583	missense	25850	exon4			GAGAATTCATACT	X78933	CCDS12497.1	19q13.12	2013-01-08			ENSG00000251247	ENSG00000251247		"""Zinc fingers, C2H2-type"""	16367	protein-coding gene	gene with protein product						7865130	Standard	NM_003419		Approved	HZF10	uc002oey.4	Q14585	OTTHUMG00000048162	ENST00000529555.1:c.417T>G	19.37:g.37368149T>G	ENSP00000431202:p.Ile139Met	Somatic	73	0		WXS	Illumina HiSeq	.	37	14	NM_001242476		Missense_Mutation	SNP	ENST00000529555.1	37	CCDS12497.1	.	.	.	.	.	.	.	.	.	.	T	13.74	2.326255	0.41197	.	.	ENSG00000251247	ENST00000420450;ENST00000529555	T;T	0.18810	2.19;2.19	3.93	0.381	0.16228	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.23611	0.0571	L	0.33624	1.015	0.21802	N	0.999538	D	0.59357	0.985	P	0.60949	0.881	T	0.11842	-1.0571	8	.	.	.	.	2.4474	0.04509	0.3077:0.2349:0.0:0.4574	.	139	Q14585	ZN345_HUMAN	M	139	ENSP00000431216:I139M;ENSP00000431202:I139M	.	I	+	3	3	ZNF345	42059989	0.000000	0.05858	1.000000	0.80357	0.997000	0.91878	-1.430000	0.02434	0.207000	0.20607	0.459000	0.35465	ATT	.		0.423	ZNF345-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388258.1		
ANKRD36BP2	645784	hgsc.bcm.edu	37	2	89072724	89072724	+	RNA	SNP	G	G	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr2:89072724G>T	ENST00000393525.3	+	0	401									ankyrin repeat domain 36B pseudogene 2																		GATATTTAAGGCATAAGACAG	0.313																																					.		.											.	.	.	0			.						.																																					645784	.			TTTAAGGCATAAG			2q11.2	2010-09-30			ENSG00000230006	ENSG00000230006			33607	pseudogene	pseudogene							Standard	NR_015424		Approved		uc010fhg.4		OTTHUMG00000151690		2.37:g.89072724G>T		Somatic	12	0		WXS	Illumina HiSeq	.	14	4	.		RNA	SNP	ENST00000393525.3	37																																																																																				.		0.313	ANKRD36BP2-003	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000323523.1		
RHPN1	114822	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	8	144450431	144450431	+	5'Flank	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr8:144450431A>C	ENST00000289013.6	+	0	0				RHPN1-AS1_ENST00000518049.1_RNA|RHPN1-AS1_ENST00000596598.1_RNA	NM_052924.2	NP_443156.2	Q8TCX5	RHPN1_HUMAN	rhophilin, Rho GTPase binding protein 1						signal transduction (GO:0007165)		small GTPase regulator activity (GO:0005083)			endometrium(1)|large_intestine(1)|lung(7)	9	all_cancers(97;7.39e-11)|all_epithelial(106;5.44e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000459)|Ovarian(258;0.0212)|Acute lymphoblastic leukemia(118;0.155)		Colorectal(110;0.107)|BRCA - Breast invasive adenocarcinoma(115;0.156)			CGGTTTTGGAAGCAGGACGAC	0.632																																					.		.											.	.	.	0			.						.						84.0	91.0	89.0					8																	144450431		692	1591	2283	SO:0001631	upstream_gene_variant	78998	.			TTTGGAAGCAGGA	AB067516	CCDS47927.1	8q24.3	2003-02-06			ENSG00000158106	ENSG00000158106			19973	protein-coding gene	gene with protein product		601031				11572484	Standard	NM_052924		Approved	KIAA1929, RHPN, ODF5	uc003yyb.3	Q8TCX5	OTTHUMG00000165006		8.37:g.144450431A>C	Exception_encountered	Somatic	151	0		WXS	Illumina HiSeq	.	88	31	.	Q8TAV1|Q96PV9	RNA	SNP	ENST00000289013.6	37	CCDS47927.1																																																																																			.		0.632	RHPN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381417.1		
FKBP8	23770	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	19	18648519	18648519	+	Silent	SNP	C	C	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr19:18648519C>T	ENST00000596558.2	-	6	943	c.834G>A	c.(832-834)ctG>ctA	p.L278L	FKBP8_ENST00000453489.2_Silent_p.L307L|FKBP8_ENST00000610101.1_Silent_p.L119L|FKBP8_ENST00000222308.4_Silent_p.L278L|FKBP8_ENST00000597960.3_Silent_p.L279L|FKBP8_ENST00000608443.1_Silent_p.L279L|AC005387.2_ENST00000596596.1_RNA			Q14318	FKBP8_HUMAN	FK506 binding protein 8, 38kDa	278					apoptotic process (GO:0006915)|camera-type eye development (GO:0043010)|cell fate specification (GO:0001708)|chaperone-mediated protein folding (GO:0061077)|dorsal/ventral neural tube patterning (GO:0021904)|intracellular signal transduction (GO:0035556)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|positive regulation of BMP signaling pathway (GO:0030513)|protein peptidyl-prolyl isomerization (GO:0000413)|regulation of gene expression (GO:0010468)|smoothened signaling pathway (GO:0007224)|viral process (GO:0016032)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|membrane (GO:0016020)|mitochondrial envelope (GO:0005740)	FK506 binding (GO:0005528)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(3)|ovary(2)|prostate(1)	15						GCGAGGCCGCCAGGTTGTTCA	0.617																																					p.L279L		.											.	.	.	0			c.G837A						.						88.0	69.0	75.0					19																	18648519		2203	4300	6503	SO:0001819	synonymous_variant	23770	exon6			GGCCGCCAGGTTG	L37033	CCDS32961.1	19p12	2013-01-10	2002-08-29		ENSG00000105701	ENSG00000105701		"""Tetratricopeptide (TTC) repeat domain containing"""	3724	protein-coding gene	gene with protein product	"""FK506-binding protein 8 (38kD)"""	604840	"""FK506-binding protein 8 (38kD)"""			7543869	Standard	NM_012181		Approved	FKBP38, FKBPr38	uc002njj.1	Q14318		ENST00000596558.2:c.834G>A	19.37:g.18648519C>T		Somatic	67	0		WXS	Illumina HiSeq	.	48	21	NM_012181	C8C9T5|Q53GU3|Q7Z349|Q86YK6	Silent	SNP	ENST00000596558.2	37																																																																																				.		0.617	FKBP8-002	KNOWN	alternative_5_UTR|NAGNAG_splice_site|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000466374.3	NM_012181	
SYT1	6857	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	12	79685872	79685872	+	Missense_Mutation	SNP	C	C	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr12:79685872C>T	ENST00000261205.4	+	6	1093	c.436C>T	c.(436-438)Ctt>Ttt	p.L146F	SYT1_ENST00000552744.1_Missense_Mutation_p.L146F|SYT1_ENST00000457153.2_Missense_Mutation_p.L143F|SYT1_ENST00000393240.3_Missense_Mutation_p.L146F	NM_005639.2	NP_005630.1	P21579	SYT1_HUMAN	synaptotagmin I	146	Phospholipid binding. {ECO:0000305}.				calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|detection of calcium ion (GO:0005513)|glutamate secretion (GO:0014047)|neurotransmitter secretion (GO:0007269)|positive regulation of calcium ion-dependent exocytosis (GO:0045956)|positive regulation of synaptic transmission (GO:0050806)|positive regulation of vesicle fusion (GO:0031340)|protein homooligomerization (GO:0051260)|regulation of exocytosis (GO:0017157)|regulation of regulated secretory pathway (GO:1903305)|regulation of synaptic transmission, glutamatergic (GO:0051966)|synaptic transmission (GO:0007268)|synaptic vesicle exocytosis (GO:0016079)|vesicle docking (GO:0048278)	cell junction (GO:0030054)|clathrin-sculpted acetylcholine transport vesicle membrane (GO:0060201)|clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane (GO:0061202)|clathrin-sculpted glutamate transport vesicle membrane (GO:0060203)|clathrin-sculpted monoamine transport vesicle membrane (GO:0070083)|dense core granule (GO:0031045)|endocytic vesicle membrane (GO:0030666)|excitatory synapse (GO:0060076)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)|synaptic vesicle (GO:0008021)|synaptic vesicle membrane (GO:0030672)	1-phosphatidylinositol binding (GO:0005545)|calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|low-density lipoprotein particle receptor binding (GO:0050750)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylserine binding (GO:0001786)|SNARE binding (GO:0000149)|syntaxin-1 binding (GO:0017075)|transporter activity (GO:0005215)			NS(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(11)|ovary(1)|pancreas(2)|skin(6)	25						ACTGGGAAAACTTCAGTATTC	0.363																																					p.L146F		.											.	.	.	0			c.C436T						.						117.0	128.0	125.0					12																	79685872		2203	4300	6503	SO:0001583	missense	6857	exon7			GGAAAACTTCAGT		CCDS9017.1	12q21.2	2013-09-20			ENSG00000067715	ENSG00000067715		"""Synaptotagmins"""	11509	protein-coding gene	gene with protein product		185605		SYT, SVP65		1840599	Standard	NM_001135805		Approved	P65	uc001syv.3	P21579	OTTHUMG00000134326	ENST00000261205.4:c.436C>T	12.37:g.79685872C>T	ENSP00000261205:p.Leu146Phe	Somatic	84	0		WXS	Illumina HiSeq	.	59	20	NM_001135805	Q6AI31	Missense_Mutation	SNP	ENST00000261205.4	37	CCDS9017.1	.	.	.	.	.	.	.	.	.	.	C	16.01	3.001334	0.54254	.	.	ENSG00000067715	ENST00000393240;ENST00000261205;ENST00000457153;ENST00000552744;ENST00000552624;ENST00000446242	T;T;T;T;T;T	0.11169	2.8;2.8;2.8;2.8;2.8;2.8	5.66	5.66	0.87406	C2 calcium/lipid-binding domain, CaLB (1);	0.060292	0.64402	D	0.000004	T	0.35828	0.0945	M	0.84846	2.72	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.66602	0.945;0.945	T	0.14980	-1.0453	10	0.87932	D	0	.	14.4664	0.67488	0.1826:0.8174:0.0:0.0	.	146;146	Q6AI31;P21579	.;SYT1_HUMAN	F	146;146;143;146;143;146	ENSP00000376932:L146F;ENSP00000261205:L146F;ENSP00000391056:L143F;ENSP00000447575:L146F;ENSP00000448861:L143F;ENSP00000401559:L146F	ENSP00000261205:L146F	L	+	1	0	SYT1	78210003	1.000000	0.71417	1.000000	0.80357	0.822000	0.46500	3.808000	0.55598	2.665000	0.90641	0.650000	0.86243	CTT	.		0.363	SYT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000259415.1	NM_005639	
ZNF525	170958	hgsc.bcm.edu;ucsc.edu	37	19	53885337	53885337	+	IGR	SNP	A	A	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr19:53885337A>G	ENST00000355326.3	+	0	594				ZNF525_ENST00000475179.1_Intron|ZNF525_ENST00000467003.1_3'UTR|ZNF525_ENST00000593918.1_Intron|ZNF525_ENST00000474037.1_3'UTR			Q8N782	ZN525_HUMAN	zinc finger protein 525						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(3)|kidney(3)|lung(3)	9						GATTGTGGCAAGATCTTCAGT	0.333																																					.		.											.	.	.	0			.						.																																			SO:0001628	intergenic_variant	170958	.			GTGGCAAGATCTT	AB075859		19q13.42	2013-01-16			ENSG00000203326	ENSG00000203326		"""Zinc fingers, C2H2-type"", ""-"""	29423	protein-coding gene	gene with protein product						11853319	Standard	NR_003699		Approved	KIAA1979	uc010eqn.3	Q8N782	OTTHUMG00000158277		19.37:g.53885337A>G		Somatic	61	0		WXS	Illumina HiSeq	.	23	6	.	Q8TF23	RNA	SNP	ENST00000355326.3	37																																																																																				.		0.333	ZNF525-201	KNOWN	basic	protein_coding	protein_coding		NR_003699	
DNAH7	56171	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	2	196822115	196822115	+	Missense_Mutation	SNP	A	A	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr2:196822115A>G	ENST00000312428.6	-	19	3048	c.2948T>C	c.(2947-2949)gTc>gCc	p.V983A		NM_018897.2	NP_061720.2	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7	983	Stem. {ECO:0000250}.				cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)	axonemal dynein complex (GO:0005858)|cilium (GO:0005929)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|microtubule motor activity (GO:0003777)			NS(4)|breast(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(28)|liver(3)|lung(100)|ovary(4)|prostate(5)|skin(26)|upper_aerodigestive_tract(2)|urinary_tract(3)	205						CGTGGCTTGGACTTTGAGCCA	0.493																																					p.V983A		.											.	.	.	0			c.T2948C						.						69.0	67.0	68.0					2																	196822115		1904	4134	6038	SO:0001583	missense	56171	exon19			GCTTGGACTTTGA	AF327442	CCDS42794.1	2q33.1	2013-01-10	2006-09-04		ENSG00000118997	ENSG00000118997		"""Axonemal dyneins"", ""EF-hand domain containing"""	18661	protein-coding gene	gene with protein product		610061	"""dynein, axonemal, heavy polypeptide 7"""			9373155, 11877439	Standard	NM_018897		Approved	KIAA0944	uc002utj.4	Q8WXX0	OTTHUMG00000154438	ENST00000312428.6:c.2948T>C	2.37:g.196822115A>G	ENSP00000311273:p.Val983Ala	Somatic	55	0		WXS	Illumina HiSeq	.	33	17	NM_018897	B8ZZX8|O00433|O95492|Q4G152|Q53QX7|Q53S64|Q53T02|Q68CY5|Q8N1Z2|Q9UMS3|Q9Y2F3	Missense_Mutation	SNP	ENST00000312428.6	37	CCDS42794.1	.	.	.	.	.	.	.	.	.	.	A	27.6	4.847975	0.91277	.	.	ENSG00000118997	ENST00000312428	T	0.67698	-0.28	5.43	5.43	0.79202	Dynein heavy chain, domain-2 (1);	0.062472	0.64402	D	0.000006	D	0.86264	0.5891	M	0.94063	3.49	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.89859	0.4015	10	0.72032	D	0.01	.	15.7782	0.78240	1.0:0.0:0.0:0.0	.	983	Q8WXX0	DYH7_HUMAN	A	983	ENSP00000311273:V983A	ENSP00000311273:V983A	V	-	2	0	DNAH7	196530360	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	9.261000	0.95576	2.193000	0.70182	0.459000	0.35465	GTC	.		0.493	DNAH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335202.3	NM_018897	
PGBD2	267002	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	249211007	249211007	+	Missense_Mutation	SNP	T	T	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr1:249211007T>C	ENST00000329291.5	+	3	371	c.224T>C	c.(223-225)cTg>cCg	p.L75P	PGBD2_ENST00000539153.1_Missense_Mutation_p.L72P|PGBD2_ENST00000462488.1_Intron|PGBD2_ENST00000355360.4_Intron	NM_170725.2	NP_733843.1	Q6P3X8	PGBD2_HUMAN	piggyBac transposable element derived 2	75										NS(1)|endometrium(3)|lung(6)|ovary(1)|skin(3)	14	all_cancers(71;3.33e-06)|all_epithelial(71;2.41e-06)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.0458)|Lung NSC(105;0.0494)|Melanoma(84;0.199)	all_cancers(173;0.012)	OV - Ovarian serous cystadenocarcinoma(106;0.00989)			GGCAGTGTGCTGCATGCTTCA	0.557																																					p.L75P		.											.	.	.	0			c.T224C						.						74.0	68.0	70.0					1																	249211007		2203	4300	6503	SO:0001583	missense	267002	exon3			GTGTGCTGCATGC	AF229602	CCDS31128.1, CCDS31129.1	1q	2008-02-05			ENSG00000185220	ENSG00000185220			19399	protein-coding gene	gene with protein product							Standard	XM_005270333		Approved		uc001ifh.3	Q6P3X8	OTTHUMG00000040424	ENST00000329291.5:c.224T>C	1.37:g.249211007T>C	ENSP00000331643:p.Leu75Pro	Somatic	26	0		WXS	Illumina HiSeq	.	38	22	NM_170725	B3KVR8|Q6MZF8	Missense_Mutation	SNP	ENST00000329291.5	37	CCDS31128.1	.	.	.	.	.	.	.	.	.	.	T	17.81	3.479670	0.63849	.	.	ENSG00000185220	ENST00000329291;ENST00000539153	T;T	0.15139	2.45;2.45	3.84	3.84	0.44239	.	.	.	.	.	T	0.33847	0.0877	L	0.58101	1.795	0.45066	D	0.998082	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	T	0.03103	-1.1072	9	0.49607	T	0.09	-15.2169	9.2192	0.37366	0.0:0.0:0.0:1.0	.	72;75	F5H4U7;Q6P3X8	.;PGBD2_HUMAN	P	75;72	ENSP00000331643:L75P;ENSP00000439950:L72P	ENSP00000331643:L75P	L	+	2	0	PGBD2	247177630	1.000000	0.71417	0.598000	0.28837	0.234000	0.25298	2.728000	0.47319	1.751000	0.51876	0.533000	0.62120	CTG	.		0.557	PGBD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000097318.1		
CASKIN1	57524	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	16	2233907	2233907	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr16:2233907G>T	ENST00000343516.6	-	15	1544	c.1452C>A	c.(1450-1452)ttC>ttA	p.F484L	CASKIN1_ENST00000564289.1_Intron	NM_020764.3	NP_065815.1	Q8WXD9	CSKI1_HUMAN	CASK interacting protein 1	484	SAM 1. {ECO:0000255|PROSITE- ProRule:PRU00184}.				signal transduction (GO:0007165)	cytoplasm (GO:0005737)				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|liver(1)|lung(7)|ovary(4)|prostate(5)|skin(3)	28						GCTGCAGCTGGAACGCGGTGA	0.682																																					p.F484L		.											.	.	.	0			c.C1452A						.						34.0	44.0	41.0					16																	2233907		2144	4270	6414	SO:0001583	missense	57524	exon15			CAGCTGGAACGCG	AF451977	CCDS42103.1	16p13.3	2013-01-10				ENSG00000167971		"""Sterile alpha motif (SAM) domain containing"", ""Ankyrin repeat domain containing"""	20879	protein-coding gene	gene with protein product		612184				12040031	Standard	NM_020764		Approved	KIAA1306, ANKS5A	uc010bsg.1	Q8WXD9		ENST00000343516.6:c.1452C>A	16.37:g.2233907G>T	ENSP00000345436:p.Phe484Leu	Somatic	78	0		WXS	Illumina HiSeq	.	51	21	NM_020764	Q9P2P0	Missense_Mutation	SNP	ENST00000343516.6	37	CCDS42103.1	.	.	.	.	.	.	.	.	.	.	G	15.27	2.782902	0.49891	.	.	ENSG00000167971	ENST00000343516;ENST00000382453	T	0.37915	1.17	4.01	3.05	0.35203	Sterile alpha motif domain (2);Sterile alpha motif/pointed domain (2);Sterile alpha motif, type 1 (1);	.	.	.	.	T	0.37237	0.0996	N	0.16098	0.37	0.54753	D	0.999986	D	0.76494	0.999	D	0.71656	0.974	T	0.26292	-1.0107	9	0.72032	D	0.01	-14.3793	7.7754	0.29035	0.1941:0.0:0.8059:0.0	.	484	Q8WXD9	CSKI1_HUMAN	L	484;313	ENSP00000345436:F484L	ENSP00000345436:F484L	F	-	3	2	CASKIN1	2173908	1.000000	0.71417	1.000000	0.80357	0.237000	0.25408	4.786000	0.62425	1.030000	0.39839	0.297000	0.19635	TTC	.		0.682	CASKIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435055.1	NM_020764	
WDR33	55339	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	2	128471295	128471295	+	Missense_Mutation	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr2:128471295T>G	ENST00000322313.4	-	18	3328	c.3170A>C	c.(3169-3171)gAt>gCt	p.D1057A		NM_018383.4	NP_060853.3	Q9C0J8	WDR33_HUMAN	WD repeat domain 33	1057					mRNA processing (GO:0006397)|postreplication repair (GO:0006301)|spermatogenesis (GO:0007283)	collagen trimer (GO:0005581)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(3)|endometrium(2)|kidney(2)|large_intestine(9)|lung(17)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	39	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0695)		TTCCCTGTGATCAGGGGGAAA	0.662																																					p.D1057A		.											.	.	.	0			c.A3170C						.						59.0	64.0	62.0					2																	128471295		2203	4300	6503	SO:0001583	missense	55339	exon18			CTGTGATCAGGGG		CCDS2150.1, CCDS42746.1, CCDS46407.1	2q21.1	2013-01-09			ENSG00000136709	ENSG00000136709		"""WD repeat domain containing"""	25651	protein-coding gene	gene with protein product						11162572	Standard	NM_001006622		Approved	FLJ11294, WDC146, NET14	uc002tpg.2	Q9C0J8	OTTHUMG00000131534	ENST00000322313.4:c.3170A>C	2.37:g.128471295T>G	ENSP00000325377:p.Asp1057Ala	Somatic	73	0		WXS	Illumina HiSeq	.	55	25	NM_018383	Q05DP8|Q53FG9|Q587J1|Q69YF7|Q6NUQ0|Q9NUL1	Missense_Mutation	SNP	ENST00000322313.4	37	CCDS2150.1	.	.	.	.	.	.	.	.	.	.	T	23.2	4.391935	0.83011	.	.	ENSG00000136709	ENST00000322313	D	0.90004	-2.6	5.81	5.81	0.92471	.	0.000000	0.64402	D	0.000002	T	0.79058	0.4382	N	0.08118	0	0.80722	D	1	P	0.37781	0.608	B	0.33960	0.173	T	0.82764	-0.0296	10	0.72032	D	0.01	-12.7067	16.1592	0.81686	0.0:0.0:0.0:1.0	.	1057	Q9C0J8	WDR33_HUMAN	A	1057	ENSP00000325377:D1057A	ENSP00000325377:D1057A	D	-	2	0	WDR33	128187765	0.998000	0.40836	0.993000	0.49108	0.987000	0.75469	6.066000	0.71185	2.210000	0.71456	0.533000	0.62120	GAT	.		0.662	WDR33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331141.2	NM_018383	
WWP2	11060	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	16	69874107	69874107	+	Missense_Mutation	SNP	T	T	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr16:69874107T>A	ENST00000359154.2	+	5	520	c.419T>A	c.(418-420)tTc>tAc	p.F140Y	WWP2_ENST00000569174.1_Missense_Mutation_p.F140Y|WWP2_ENST00000544162.1_3'UTR|WWP2_ENST00000542271.1_Missense_Mutation_p.F24Y|WWP2_ENST00000448661.1_Missense_Mutation_p.F140Y|WWP2_ENST00000356003.2_Missense_Mutation_p.F140Y	NM_001270454.1|NM_007014.4	NP_001257383.1|NP_008945.2	O00308	WWP2_HUMAN	WW domain containing E3 ubiquitin protein ligase 2	140					cellular protein modification process (GO:0006464)|negative regulation of gene expression (GO:0010629)|negative regulation of protein transport (GO:0051224)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transporter activity (GO:0032410)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein autoubiquitination (GO:0051865)|protein K63-linked ubiquitination (GO:0070534)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of ion transmembrane transport (GO:0034765)|regulation of membrane potential (GO:0042391)|regulation of potassium ion transmembrane transporter activity (GO:1901016)|viral entry into host cell (GO:0046718)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	ligase activity (GO:0016874)|RNA polymerase II transcription factor binding (GO:0001085)|transcription factor binding (GO:0008134)|ubiquitin-protein transferase activity (GO:0004842)			breast(4)|endometrium(2)|kidney(2)|large_intestine(11)|lung(13)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	42						CTGACAATTTTCCTGGACGGG	0.572																																					p.F140Y		.											.	.	.	0			c.T419A						.						118.0	98.0	104.0					16																	69874107		2198	4300	6498	SO:0001583	missense	11060	exon5			CAATTTTCCTGGA	BC013645	CCDS10885.1, CCDS58475.1, CCDS58476.1, CCDS58477.1	16q22.1	2008-02-05			ENSG00000198373	ENSG00000198373			16804	protein-coding gene	gene with protein product		602308				9169421, 12167593	Standard	NM_007014		Approved	AIP2	uc002exv.2	O00308	OTTHUMG00000137573	ENST00000359154.2:c.419T>A	16.37:g.69874107T>A	ENSP00000352069:p.Phe140Tyr	Somatic	49	0		WXS	Illumina HiSeq	.	34	16	NM_001270454	A6NEP1|B2R706|B4DTL5|F5H213|H3BRF3|I3RSG8|Q6ZTQ5|Q96CZ2|Q9BWN6	Missense_Mutation	SNP	ENST00000359154.2	37	CCDS10885.1	.	.	.	.	.	.	.	.	.	.	T	16.15	3.041858	0.55003	.	.	ENSG00000198373	ENST00000359154;ENST00000448661;ENST00000356003;ENST00000544162;ENST00000542271	T;T;T;T	0.31247	1.56;1.56;1.56;1.5	5.37	5.37	0.77165	C2 calcium/lipid-binding domain, CaLB (1);	0.052911	0.85682	D	0.000000	T	0.16769	0.0403	N	0.19112	0.55	0.41348	D	0.987349	P	0.39282	0.666	B	0.28553	0.091	T	0.08743	-1.0707	9	.	.	.	.	13.1034	0.59233	0.0:0.0:0.0:1.0	.	140	O00308	WWP2_HUMAN	Y	140;140;140;27;24	ENSP00000352069:F140Y;ENSP00000396871:F140Y;ENSP00000348283:F140Y;ENSP00000445616:F24Y	.	F	+	2	0	WWP2	68431608	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.407000	0.59754	2.032000	0.59987	0.533000	0.62120	TTC	.		0.572	WWP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268954.1	NM_007014	
TTC39A	22996	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	51754561	51754561	+	Silent	SNP	A	A	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr1:51754561A>G	ENST00000447632.2	-	17	1716	c.1668T>C	c.(1666-1668)ctT>ctC	p.L556L	TTC39A_ENST00000262675.7_Silent_p.L493L|TTC39A_ENST00000530004.1_Silent_p.L164L|TTC39A_ENST00000534098.1_5'UTR|TTC39A_ENST00000371750.5_Silent_p.L521L|TTC39A_ENST00000413473.2_Silent_p.L524L|TTC39A_ENST00000451380.1_Silent_p.L520L			Q5SRH9	TT39A_HUMAN	tetratricopeptide repeat domain 39A	556								p.0?(2)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(3)|lung(2)|prostate(2)|skin(3)|urinary_tract(1)	17						CTTGCTCCATAAGCAGCAGGG	0.493																																					p.L524L		.											.	.	.	2	Whole gene deletion(2)	thyroid(1)|central_nervous_system(1)	c.T1572C						.						61.0	62.0	62.0					1																	51754561		1910	4127	6037	SO:0001819	synonymous_variant	22996	exon17			CTCCATAAGCAGC	AB007921	CCDS44143.1, CCDS44144.1, CCDS72789.1, CCDS72790.1	1p32.3	2013-01-11	2008-06-23	2008-06-23	ENSG00000085831	ENSG00000085831		"""Tetratricopeptide (TTC) repeat domain containing"""	18657	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 34"""	C1orf34		9455484, 9461476	Standard	XM_005270643		Approved	KIAA0452, DEME-6	uc010onf.2	Q5SRH9	OTTHUMG00000008193	ENST00000447632.2:c.1668T>C	1.37:g.51754561A>G		Somatic	54	0		WXS	Illumina HiSeq	.	21	10	NM_001144832	B7Z782|E7EQY9|G3XAF8|O43417|O75040|Q5SRH5|Q5SRH6|Q5SRH7|Q5SRH8|Q5SRI0|Q5SRI1|Q5SRI2|Q5T7S1|Q6PIU8|Q9BT24	Silent	SNP	ENST00000447632.2	37																																																																																				.		0.493	TTC39A-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000022434.2		
ZNF74	7625	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	22	20760929	20760929	+	Missense_Mutation	SNP	G	G	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr22:20760929G>A	ENST00000400451.2	+	5	2120	c.1606G>A	c.(1606-1608)Gcc>Acc	p.A536T	ZNF74_ENST00000356671.5_Missense_Mutation_p.A536T|ZNF74_ENST00000403682.3_3'UTR|ZNF74_ENST00000357502.5_3'UTR|ZNF74_ENST00000405993.1_Missense_Mutation_p.A504T	NM_003426.3	NP_003417.2	Q16587	ZNF74_HUMAN	zinc finger protein 74	536					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	actin cytoskeleton (GO:0015629)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(4)|lung(7)|ovary(1)|skin(1)|urinary_tract(1)	19	Melanoma(16;0.000465)|Ovarian(15;0.0025)|Colorectal(54;0.0221)|all_neural(72;0.219)	Lung SC(17;0.0262)|all_lung(157;0.248)	LUSC - Lung squamous cell carcinoma(15;0.00102)|Lung(15;0.0173)			GTGCGGCAGAGCCTTCAGCCA	0.547																																					p.A536T		.											.	.	.	0			c.G1606A						.						73.0	82.0	79.0					22																	20760929		2203	4300	6503	SO:0001583	missense	7625	exon5			GGCAGAGCCTTCA	X71623	CCDS42982.1, CCDS58794.1	22q11.2	2013-01-08	2006-05-12		ENSG00000185252	ENSG00000185252		"""Zinc fingers, C2H2-type"", ""-"""	13144	protein-coding gene	gene with protein product		194548	"""zinc finger protein 74 (Cos52)"""			1639391, 10591208	Standard	NM_003426		Approved	Cos52, Zfp520, ZNF520	uc010gsm.4	Q16587	OTTHUMG00000150687	ENST00000400451.2:c.1606G>A	22.37:g.20760929G>A	ENSP00000383301:p.Ala536Thr	Somatic	74	0		WXS	Illumina HiSeq	.	32	16	NM_003426	B5MCE3|B7Z5Y2|Q6IBV2|Q6PJP1|Q9UC04|Q9UF05|Q9UF06|Q9UF07	Missense_Mutation	SNP	ENST00000400451.2	37	CCDS42982.1	.	.	.	.	.	.	.	.	.	.	G	13.12	2.143075	0.37825	.	.	ENSG00000185252	ENST00000400451;ENST00000356671;ENST00000405993	T;T;T	0.16897	2.31;2.31;2.31	4.15	3.11	0.35812	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.39985	N	0.001207	T	0.09113	0.0225	N	0.04335	-0.225	0.20926	N	0.99983	P	0.43788	0.817	P	0.45998	0.5	T	0.12142	-1.0559	10	0.35671	T	0.21	-28.9002	6.9753	0.24672	0.2071:0.0:0.7929:0.0	.	536	Q16587	ZNF74_HUMAN	T	536;536;504	ENSP00000383301:A536T;ENSP00000349098:A536T;ENSP00000385855:A504T	ENSP00000349098:A536T	A	+	1	0	ZNF74	19090929	0.006000	0.16342	0.885000	0.34714	0.695000	0.40330	0.290000	0.18975	1.300000	0.44818	0.655000	0.94253	GCC	.		0.547	ZNF74-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319648.2	NM_003426	
ZFHX3	463	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	16	72831573	72831573	+	Missense_Mutation	SNP	T	T	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr16:72831573T>C	ENST00000268489.5	-	9	5680	c.5008A>G	c.(5008-5010)Agt>Ggt	p.S1670G	ZFHX3_ENST00000397992.5_Missense_Mutation_p.S756G	NM_006885.3	NP_008816.3	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3	1670					brain development (GO:0007420)|cell cycle arrest (GO:0007050)|muscle organ development (GO:0007517)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of myoblast differentiation (GO:0045663)|regulation of neuron differentiation (GO:0045664)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	enzyme binding (GO:0019899)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			NS(3)|breast(7)|cervix(2)|endometrium(18)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(22)|liver(1)|lung(46)|ovary(5)|pancreas(1)|prostate(15)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(11)	153		Ovarian(137;0.13)				ATGCCAGCACTGCTTGGATTG	0.532																																					p.S1670G		.											.	.	.	0			c.A5008G						.						126.0	105.0	112.0					16																	72831573		2198	4300	6498	SO:0001583	missense	463	exon9			CAGCACTGCTTGG	D10250	CCDS10908.1, CCDS54035.1	16q22.3	2012-03-09	2007-08-09	2007-08-09	ENSG00000140836	ENSG00000140836		"""Zinc fingers, C2H2-type"", ""Homeoboxes / ZF class"""	777	protein-coding gene	gene with protein product		104155	"""AT-binding transcription factor 1"""	ATBF1		1719379, 7592926	Standard	NM_006885		Approved	ZNF927	uc002fck.3	Q15911	OTTHUMG00000137599	ENST00000268489.5:c.5008A>G	16.37:g.72831573T>C	ENSP00000268489:p.Ser1670Gly	Somatic	38	0		WXS	Illumina HiSeq	.	22	10	NM_006885	D3DWS8|O15101|Q13719	Missense_Mutation	SNP	ENST00000268489.5	37	CCDS10908.1	.	.	.	.	.	.	.	.	.	.	T	0.400	-0.919081	0.02396	.	.	ENSG00000140836	ENST00000268489;ENST00000397992	T;T	0.74421	-0.84;-0.82	5.87	3.59	0.41128	.	0.207947	0.33419	N	0.004934	T	0.54013	0.1832	N	0.14661	0.345	0.36339	D	0.859373	B	0.06786	0.001	B	0.06405	0.002	T	0.49000	-0.8984	10	0.23302	T	0.38	.	9.191	0.37200	0.0:0.0642:0.1241:0.8118	.	1670	Q15911	ZFHX3_HUMAN	G	1670;756	ENSP00000268489:S1670G;ENSP00000438926:S756G	ENSP00000268489:S1670G	S	-	1	0	ZFHX3	71389074	0.998000	0.40836	0.543000	0.28128	0.011000	0.07611	2.172000	0.42463	0.540000	0.28808	-0.313000	0.08912	AGT	.		0.532	ZFHX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269008.1	NM_006885	
IREB2	3658	hgsc.bcm.edu	37	15	78770699	78770699	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr15:78770699G>T	ENST00000258886.8	+	10	1405	c.1256G>T	c.(1255-1257)cGa>cTa	p.R419L	RP11-650L12.1_ENST00000560094.1_RNA	NM_004136.2	NP_004127	P48200	IREB2_HUMAN	iron-responsive element binding protein 2	419					aging (GO:0007568)|cellular iron ion homeostasis (GO:0006879)|cellular response to hypoxia (GO:0071456)|erythrocyte homeostasis (GO:0034101)|intestinal absorption (GO:0050892)|iron ion transport (GO:0006826)|osteoclast differentiation (GO:0030316)|post-embryonic development (GO:0009791)|protoporphyrinogen IX biosynthetic process (GO:0006782)|response to iron(II) ion (GO:0010040)|response to retinoic acid (GO:0032526)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)	4 iron, 4 sulfur cluster binding (GO:0051539)|iron-responsive element binding (GO:0030350)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)|translation repressor activity (GO:0030371)	p.R419Q(3)		central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|liver(1)|lung(14)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	41				UCEC - Uterine corpus endometrioid carcinoma (272;0.232)		AAATTGTTTCGAAATGACCAG	0.393																																					p.R419L	NSCLC(200;764 2208 35157 49871 50830)	.											IREB2,rectum,carcinoma,0,3	IREB2	0	3	Substitution - Missense(3)	large_intestine(2)|endometrium(1)	c.G1256T						.						92.0	90.0	90.0					15																	78770699		2196	4293	6489	SO:0001583	missense	3658	exon10			TGTTTCGAAATGA	M58511	CCDS10302.1	15q25.1	2013-09-20			ENSG00000136381	ENSG00000136381			6115	protein-coding gene	gene with protein product		147582				2172968	Standard	NM_004136		Approved	IRP2	uc002bdr.2	P48200	OTTHUMG00000143861	ENST00000258886.8:c.1256G>T	15.37:g.78770699G>T	ENSP00000258886:p.Arg419Leu	Somatic	61	0		WXS	Illumina HiSeq	.	38	2	NM_004136	A8KAC7|E1CJT9|H0YKU0|Q13095|Q1HE21|Q59FQ7|Q8WVK6|Q9UF17	Missense_Mutation	SNP	ENST00000258886.8	37	CCDS10302.1	.	.	.	.	.	.	.	.	.	.	G	23.8	4.461827	0.84425	.	.	ENSG00000136381	ENST00000258886	T	0.16597	2.33	5.37	4.38	0.52667	Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha (2);Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha, subdomain 2 (1);	0.101689	0.64402	D	0.000004	T	0.43853	0.1266	M	0.85710	2.77	0.80722	D	1	D	0.89917	1.0	D	0.75484	0.986	T	0.46317	-0.9200	10	0.62326	D	0.03	-15.4669	11.2102	0.48793	0.0954:0.0:0.9046:0.0	.	419	P48200	IREB2_HUMAN	L	419	ENSP00000258886:R419L	ENSP00000258886:R419L	R	+	2	0	IREB2	76557754	1.000000	0.71417	0.989000	0.46669	0.998000	0.95712	5.168000	0.64978	1.249000	0.43950	0.591000	0.81541	CGA	.		0.393	IREB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000290109.3	NM_004136	
TLE4	7091	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	9	82188691	82188691	+	Missense_Mutation	SNP	C	C	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr9:82188691C>G	ENST00000376552.2	+	2	1151	c.133C>G	c.(133-135)Caa>Gaa	p.Q45E	TLE4_ENST00000376520.4_Missense_Mutation_p.Q45E|TLE4_ENST00000265284.6_Missense_Mutation_p.Q45E|TLE4_ENST00000376544.3_Missense_Mutation_p.Q45E|TLE4_ENST00000376534.4_5'UTR|TLE4_ENST00000376537.4_Missense_Mutation_p.Q45E	NM_007005.3	NP_008936.2	Q04727	TLE4_HUMAN	transducin-like enhancer of split 4	45	Gln-rich (Q domain).				negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|Wnt signaling pathway (GO:0016055)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|transcription corepressor activity (GO:0003714)			breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(10)|lung(12)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	39						TTTACAGGCTCAATACCACAG	0.418																																					p.Q45E		.											.	.	.	0			c.C133G						.						88.0	83.0	84.0					9																	82188691		1906	4123	6029	SO:0001583	missense	7091	exon2			CAGGCTCAATACC	M99439	CCDS43837.1, CCDS65069.1, CCDS65070.1, CCDS75851.1	9q21.32	2014-03-07	2014-03-07		ENSG00000106829	ENSG00000106829		"""WD repeat domain containing"""	11840	protein-coding gene	gene with protein product		605132	"""transducin-like enhancer of split 4, homolog of Drosophila E(sp1)"", ""transducin-like enhancer of split 4 (E(sp1) homolog, Drosophila)"""			8365415	Standard	XM_005252167		Approved	E(spI), ESG, GRG4	uc004alc.3	Q04727	OTTHUMG00000020072	ENST00000376552.2:c.133C>G	9.37:g.82188691C>G	ENSP00000365735:p.Gln45Glu	Somatic	51	0		WXS	Illumina HiSeq	.	41	14	NM_007005	F8W6T6|Q3ZCS1|Q5T1Y2|Q6PCB3|Q9BZ07|Q9BZ08|Q9BZ09|Q9NSL3|Q9ULF9	Missense_Mutation	SNP	ENST00000376552.2	37	CCDS43837.1	.	.	.	.	.	.	.	.	.	.	C	16.78	3.218321	0.58560	.	.	ENSG00000106829	ENST00000376552;ENST00000376544;ENST00000376520;ENST00000399288;ENST00000435650;ENST00000414465;ENST00000376537;ENST00000265284;ENST00000425506;ENST00000428713	T;T;T;T;T;T;T;T;T	0.60672	0.24;0.17;0.17;0.54;2.53;0.17;0.44;0.53;0.98	4.7	4.7	0.59300	Groucho/TLE, N-terminal Q-rich domain (1);	0.000000	0.85682	D	0.000000	T	0.80859	0.4704	M	0.93808	3.46	0.80722	D	1	P;D;P	0.57257	0.941;0.979;0.953	P;P;P	0.61477	0.72;0.889;0.816	D	0.87055	0.2149	10	0.87932	D	0	-9.2223	17.6488	0.88157	0.0:1.0:0.0:0.0	.	45;45;45	F8W6T6;Q04727-2;Q04727	.;.;TLE4_HUMAN	E	45;45;45;45;45;45;45;45;43;30	ENSP00000365735:Q45E;ENSP00000365727:Q45E;ENSP00000365703:Q45E;ENSP00000415423:Q45E;ENSP00000397822:Q45E;ENSP00000365720:Q45E;ENSP00000265284:Q45E;ENSP00000412567:Q43E;ENSP00000409313:Q30E	ENSP00000265284:Q45E	Q	+	1	0	TLE4	81378511	1.000000	0.71417	0.998000	0.56505	0.981000	0.71138	7.550000	0.82173	2.162000	0.67917	0.462000	0.41574	CAA	.		0.418	TLE4-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052792.4	XM_212237	
PPIEL	728448	hgsc.bcm.edu	37	1	40019783	40019783	+	IGR	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr1:40019783A>C								RP11-69E11.4 (7924 upstream) : PABPC4 (6704 downstream)																							caggaaggcaagtaaagagtc	0.448																																					.		.											.	.	.	0			.						.																																			SO:0001628	intergenic_variant	728448	.			AAGGCAAGTAAAG																													1.37:g.40019783A>C		Somatic	7	0		WXS	Illumina HiSeq	.	6	4	.		RNA	SNP		37																																																																																				.	0	0.448								
IMPA1	3612	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	8	82588479	82588479	+	Missense_Mutation	SNP	A	A	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr8:82588479A>T	ENST00000256108.5	-	5	803	c.338T>A	c.(337-339)gTa>gAa	p.V113E	IMPA1_ENST00000449740.2_Missense_Mutation_p.V172E|IMPA1_ENST00000523710.1_5'UTR|IMPA1_ENST00000311489.4_Missense_Mutation_p.V113E	NM_005536.3	NP_005527.1	P29218	IMPA1_HUMAN	inositol(myo)-1(or 4)-monophosphatase 1	113					inositol biosynthetic process (GO:0006021)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|phosphate-containing compound metabolic process (GO:0006796)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	identical protein binding (GO:0042802)|inositol monophosphate 1-phosphatase activity (GO:0008934)|inositol monophosphate 3-phosphatase activity (GO:0052832)|inositol monophosphate 4-phosphatase activity (GO:0052833)|inositol monophosphate phosphatase activity (GO:0052834)|lithium ion binding (GO:0031403)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|protein homodimerization activity (GO:0042803)			NS(1)|cervix(1)|large_intestine(4)|lung(7)|prostate(2)|skin(2)|stomach(1)	18					Lithium(DB01356)	CTTTTTATTTACAGCAAAGCC	0.244																																					p.V172E		.											.	.	.	0			c.T515A						.						29.0	30.0	29.0					8																	82588479		2191	4258	6449	SO:0001583	missense	3612	exon6			TTATTTACAGCAA		CCDS6231.1, CCDS47883.1, CCDS47884.1	8q21.1-q21.3	2008-01-28			ENSG00000133731	ENSG00000133731	3.1.3.25		6050	protein-coding gene	gene with protein product		602064		IMPA		1377913	Standard	NM_005536		Approved		uc011lfq.1	P29218	OTTHUMG00000164682	ENST00000256108.5:c.338T>A	8.37:g.82588479A>T	ENSP00000256108:p.Val113Glu	Somatic	275	0		WXS	Illumina HiSeq	.	178	70	NM_001144878	B2R733|B4DLN3|B7Z6Q4|J3KQT7|Q9UK71	Missense_Mutation	SNP	ENST00000256108.5	37	CCDS6231.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	28.7|28.7	4.938996|4.938996	0.92526|0.92526	.|.	.|.	ENSG00000133731|ENSG00000133731	ENST00000523942|ENST00000256108;ENST00000311489;ENST00000449740;ENST00000519964;ENST00000521360;ENST00000522997;ENST00000518202	.|T;T;T;T;T;T;T	.|0.50548	.|0.74;0.74;0.74;0.74;0.74;0.74;0.74	4.38|4.38	4.38|4.38	0.52667|0.52667	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	.|T	.|0.65647	.|0.2711	M|M	0.69463|0.69463	2.115|2.115	0.80722|0.80722	D|D	1|1	.|D;D;D	.|0.89917	.|0.999;1.0;0.999	.|D;D;D	.|0.85130	.|0.992;0.997;0.994	.|T	.|0.69555	.|-0.5114	.|10	0.51188|0.72032	T|D	0.08|0.01	-17.4011|-17.4011	13.2598|13.2598	0.60098|0.60098	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|113;172;113	.|B4DLN3;B7Z6Q4;P29218	.|.;.;IMPA1_HUMAN	X|E	137|113;113;172;105;78;172;144	.|ENSP00000256108:V113E;ENSP00000311803:V113E;ENSP00000408526:V172E;ENSP00000429322:V105E;ENSP00000430283:V78E;ENSP00000430081:V172E;ENSP00000429516:V144E	ENSP00000428425:C108X|ENSP00000256108:V113E	C|V	-|-	3|2	2|0	IMPA1|IMPA1	82751034|82751034	1.000000|1.000000	0.71417|0.71417	0.993000|0.993000	0.49108|0.49108	0.977000|0.977000	0.68977|0.68977	8.109000|8.109000	0.89561|0.89561	1.602000|1.602000	0.50124|0.50124	0.448000|0.448000	0.29417|0.29417	TGT|GTA	.		0.244	IMPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379723.1		
HNRNPA1	3178	hgsc.bcm.edu	37	12	54678037	54678037	+	Intron	SNP	T	T	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr12:54678037T>C	ENST00000340913.6	+	10	1116				HNRNPA1_ENST00000330752.8_Intron|HNRNPA1_ENST00000546500.1_Intron|HNRNPA1_ENST00000547276.1_Intron|RP11-968A15.8_ENST00000553061.1_RNA	NM_002136.2|NM_031157.2	NP_002127.1|NP_112420.1	P09651	ROA1_HUMAN	heterogeneous nuclear ribonucleoprotein A1						cell death (GO:0008219)|gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|mRNA transport (GO:0051028)|nuclear export (GO:0051168)|nuclear import (GO:0051170)|RNA export from nucleus (GO:0006405)|RNA splicing (GO:0008380)|viral process (GO:0016032)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|spliceosomal complex (GO:0005681)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)|single-stranded RNA binding (GO:0003727)			endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	20						AATTGTACTTTTCAGGTGGCT	0.348																																					.	Colon(83;502 1289 8436 16406 24870)	.											.	.	.	0			.						.						62.0	60.0	61.0					12																	54678037		1837	4096	5933	SO:0001627	intron_variant	664709	.			GTACTTTTCAGGT	BC009600	CCDS41793.1, CCDS44909.1	12q13.1	2013-10-11		2007-08-16	ENSG00000135486	ENSG00000135486		"""RNA binding motif (RRM) containing"""	5031	protein-coding gene	gene with protein product		164017		HNRPA1		1733858	Standard	XR_245923		Approved	hnRNPA1, hnRNP-A1	uc001sfl.3	P09651		ENST00000340913.6:c.1064-5T>C	12.37:g.54678037T>C		Somatic	108	0		WXS	Illumina HiSeq	.	66	35	.	A8K4Z8|Q3MIB7|Q6PJZ7	RNA	SNP	ENST00000340913.6	37	CCDS44909.1																																																																																			.		0.348	HNRNPA1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000405480.1	NM_031157	
C1orf140	400804	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	221507263	221507263	+	lincRNA	SNP	G	G	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr1:221507263G>A	ENST00000439004.1	-	0	498					NR_024236.1																						TAGACCTGCAGTATCCACAAA	0.473																																					.		.											.	.	.	0			.						.						151.0	125.0	133.0					1																	221507263		692	1591	2283			0	.			CCTGCAGTATCCA																													1.37:g.221507263G>A		Somatic	53	0		WXS	Illumina HiSeq	.	81	26	.		RNA	SNP	ENST00000439004.1	37																																																																																				.		0.473	RP11-421L10.1-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000091116.2		
MUC4	4585	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	3	195509900	195509900	+	Missense_Mutation	SNP	C	C	T	rs557314271		TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr3:195509900C>T	ENST00000463781.3	-	2	9010	c.8551G>A	c.(8551-8553)Gtc>Atc	p.V2851I	MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.V2851I	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GCGTCGGTGACAGGAAGAGGG	0.587																																					p.V2851I		.											.	.	.	0			c.G8551A						.																																			SO:0001583	missense	4585	exon2			CGGTGACAGGAAG	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.8551G>A	3.37:g.195509900C>T	ENSP00000417498:p.Val2851Ile	Somatic	149	0		WXS	Illumina HiSeq	.	97	38	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	c	2.825	-0.243965	0.05906	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.32023	1.47;1.47	.	.	.	.	.	.	.	.	T	0.30262	0.0759	N	0.19112	0.55	0.09310	N	1	P	0.52170	0.951	P	0.62560	0.904	T	0.18209	-1.0344	7	.	.	.	.	5.5911	0.17301	0.0:0.6581:0.3419:0.0	.	2723	E7ESK3	.	I	2851	ENSP00000417498:V2851I;ENSP00000420243:V2851I	.	V	-	1	0	MUC4	196994679	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.511000	0.00446	-0.000000	0.14550	0.000000	0.15137	GTC	.		0.587	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
WDR61	80349	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	15	78582401	78582401	+	Silent	SNP	A	A	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr15:78582401A>G	ENST00000267973.2	-	6	631	c.360T>C	c.(358-360)taT>taC	p.Y120Y	WDR61_ENST00000558311.1_Silent_p.Y120Y|WDR61_ENST00000558459.1_Silent_p.Y27Y			Q9GZS3	WDR61_HUMAN	WD repeat domain 61	120					histone H3-K4 trimethylation (GO:0080182)|negative regulation of myeloid cell differentiation (GO:0045638)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of histone H3-K79 methylation (GO:2001162)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	Cdc73/Paf1 complex (GO:0016593)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|Ski complex (GO:0055087)|transcriptionally active chromatin (GO:0035327)				central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(3)|ovary(1)|skin(1)	9						CTGTGGCCAGATACTGGGAAT	0.393																																					p.Y120Y		.											.	.	.	0			c.T360C						.						52.0	48.0	49.0					15																	78582401		2196	4293	6489	SO:0001819	synonymous_variant	80349	exon6			GGCCAGATACTGG		CCDS10300.1	15q25.1	2013-01-09			ENSG00000140395	ENSG00000140395		"""WD repeat domain containing"""	30300	protein-coding gene	gene with protein product		609540				12477932	Standard	NM_025234		Approved	REC14	uc002bdn.3	Q9GZS3	OTTHUMG00000143735	ENST00000267973.2:c.360T>C	15.37:g.78582401A>G		Somatic	76	0		WXS	Illumina HiSeq	.	49	25	NM_025234	D3DW84|Q6IA22|Q7Z4X4	Silent	SNP	ENST00000267973.2	37	CCDS10300.1																																																																																			.		0.393	WDR61-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000289803.3	NM_025234	
COL8A2	1296	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	36565701	36565701	+	Missense_Mutation	SNP	T	T	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr1:36565701T>C	ENST00000397799.1	-	3	367	c.143A>G	c.(142-144)cAg>cGg	p.Q48R	COL8A2_ENST00000303143.4_Missense_Mutation_p.Q48R|COL8A2_ENST00000481785.1_Intron			P25067	CO8A2_HUMAN	collagen, type VIII, alpha 2	48	Nonhelical region (NC2).				angiogenesis (GO:0001525)|camera-type eye morphogenesis (GO:0048593)|collagen catabolic process (GO:0030574)|epithelial cell proliferation (GO:0050673)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|single organismal cell-cell adhesion (GO:0016337)	basement membrane (GO:0005604)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|protein binding, bridging (GO:0030674)			NS(2)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(1)|lung(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	17		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				AGGTCCTTTCTGCATGGGCTG	0.672											OREG0013361	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.Q48R		.											.	.	.	0			c.A143G						.						67.0	64.0	65.0					1																	36565701		2203	4300	6503	SO:0001583	missense	1296	exon1			CCTTTCTGCATGG	M60832	CCDS403.1, CCDS72756.1	1p34.2-p32.3	2014-02-14			ENSG00000171812	ENSG00000171812		"""Collagens"""	2216	protein-coding gene	gene with protein product		120252		FECD		11689488	Standard	XM_005270477		Approved	PPCD, FECD1, PPCD2	uc001bzv.2	P25067	OTTHUMG00000007665	ENST00000397799.1:c.143A>G	1.37:g.36565701T>C	ENSP00000380901:p.Gln48Arg	Somatic	70	0	863	WXS	Illumina HiSeq	.	55	17	NM_005202	Q5JV31|Q8TEJ5	Missense_Mutation	SNP	ENST00000397799.1	37	CCDS403.1	.	.	.	.	.	.	.	.	.	.	T	13.21	2.169481	0.38315	.	.	ENSG00000171812	ENST00000303143;ENST00000397799;ENST00000373172	D;D	0.90844	-2.74;-2.74	4.37	1.73	0.24493	.	0.258372	0.36519	N	0.002552	T	0.78717	0.4327	N	0.20845	0.615	0.80722	D	1	B	0.14012	0.009	B	0.10450	0.005	T	0.64769	-0.6329	10	0.10902	T	0.67	.	7.2843	0.26328	0.5291:0.0:0.0:0.4709	.	48	P25067	CO8A2_HUMAN	R	48	ENSP00000305913:Q48R;ENSP00000380901:Q48R	ENSP00000305913:Q48R	Q	-	2	0	COL8A2	36338288	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	3.659000	0.54489	0.674000	0.31244	0.402000	0.26972	CAG	.		0.672	COL8A2-003	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313674.1	NM_005202	
SLX4	84464	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	16	3656611	3656611	+	Missense_Mutation	SNP	C	C	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr16:3656611C>A	ENST00000294008.3	-	3	1264	c.624G>T	c.(622-624)ttG>ttT	p.L208F		NM_032444.2	NP_115820.2	Q8IY92	SLX4_HUMAN	SLX4 structure-specific endonuclease subunit	208	Interaction with SLX4IP, ERCC4 and MSH2.				DNA catabolic process, endonucleolytic (GO:0000737)|DNA double-strand break processing involved in repair via single-strand annealing (GO:0010792)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|double-strand break repair via homologous recombination (GO:0000724)|nucleotide-excision repair (GO:0006289)|positive regulation of catalytic activity (GO:0043085)|response to intra-S DNA damage checkpoint signaling (GO:0072429)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|Slx1-Slx4 complex (GO:0033557)	5'-flap endonuclease activity (GO:0017108)|enzyme activator activity (GO:0008047)			breast(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(20)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	76						GCTGTAGGACCAATTGTGCTG	0.572								Direct reversal of damage																													p.L208F		.											.	.	.	0			c.G624T						.						196.0	195.0	196.0					16																	3656611		2197	4300	6497	SO:0001583	missense	84464	exon3			TAGGACCAATTGT	AB058687	CCDS10506.2	16p13.3	2014-09-17	2013-06-05	2010-09-13	ENSG00000188827	ENSG00000188827		"""Fanconi anemia, complementation groups"", ""BTB/POZ domain containing"""	23845	protein-coding gene	gene with protein product	"""Fanconi anemia, complementation group P"""	613278	"""BTB (POZ) domain containing 12"", ""SLX4 structure-specific endonuclease subunit homolog (S. cerevisiae)"""	BTBD12		11347906, 19595721	Standard	NM_032444		Approved	KIAA1784, KIAA1987, FANCP	uc002cvp.2	Q8IY92	OTTHUMG00000074089	ENST00000294008.3:c.624G>T	16.37:g.3656611C>A	ENSP00000294008:p.Leu208Phe	Somatic	45	0		WXS	Illumina HiSeq	.	43	23	NM_032444	Q69YT8|Q8TF15|Q96JP1	Missense_Mutation	SNP	ENST00000294008.3	37	CCDS10506.2	.	.	.	.	.	.	.	.	.	.	C	15.51	2.855282	0.51376	.	.	ENSG00000188827	ENST00000294008	T	0.01572	4.76	5.16	0.833	0.18875	.	0.312631	0.26820	N	0.022339	T	0.04952	0.0133	L	0.55990	1.75	0.31797	N	0.628891	D	0.76494	0.999	D	0.68192	0.956	T	0.15636	-1.0430	10	0.87932	D	0	.	4.5166	0.11937	0.1272:0.6025:0.1236:0.1467	.	208	Q8IY92	SLX4_HUMAN	F	208	ENSP00000294008:L208F	ENSP00000294008:L208F	L	-	3	2	SLX4	3596612	1.000000	0.71417	0.531000	0.27976	0.265000	0.26407	1.283000	0.33237	0.263000	0.21812	-0.181000	0.13052	TTG	.		0.572	SLX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157301.3	NM_032444	
ODF2	4957	hgsc.bcm.edu	37	9	131256844	131256844	+	Missense_Mutation	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr9:131256844T>G	ENST00000434106.3	+	17	2171	c.1808T>G	c.(1807-1809)cTg>cGg	p.L603R	ODF2_ENST00000546203.1_Missense_Mutation_p.L584R|ODF2_ENST00000393527.3_Missense_Mutation_p.L579R|ODF2_ENST00000448249.3_Missense_Mutation_p.L522R|ODF2_ENST00000351030.3_Missense_Mutation_p.L598R|ODF2_ENST00000393533.2_Missense_Mutation_p.L603R|ODF2_ENST00000604420.1_Missense_Mutation_p.L603R|ODF2_ENST00000444119.2_Missense_Mutation_p.L579R|ODF2_ENST00000372791.3_Missense_Mutation_p.L584R|ODF2_ENST00000372814.3_Missense_Mutation_p.L647R|ODF2_ENST00000372807.5_Missense_Mutation_p.L598R	NM_153433.1	NP_702911.1	Q5BJF6	ODFP2_HUMAN	outer dense fiber of sperm tails 2	603					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|multicellular organismal development (GO:0007275)|regulation of cilium assembly (GO:1902017)|spermatid development (GO:0007286)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytosol (GO:0005829)|microtubule (GO:0005874)|nucleus (GO:0005634)|outer dense fiber (GO:0001520)|primary cilium (GO:0072372)	Rab GTPase binding (GO:0017137)|structural molecule activity (GO:0005198)	p.L579P(1)|p.L603P(1)|p.L647P(1)		autonomic_ganglia(1)|breast(7)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(7)|lung(8)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	37						CCTGACATCCTGAAGATCACG	0.562																																					p.L667R		.											ODF2_ENST00000372814,NS,carcinoma,0,2	ODF2_ENST00000372814	0	3	Substitution - Missense(3)	endometrium(3)	c.T2000G						.						65.0	57.0	60.0					9																	131256844		2203	4300	6503	SO:0001583	missense	4957	exon17			ACATCCTGAAGAT	AF012549	CCDS6902.1, CCDS56585.1, CCDS56586.1, CCDS56587.1, CCDS56588.1, CCDS56589.1, CCDS56590.1	9q34	2010-04-23	2002-10-21		ENSG00000136811	ENSG00000136811			8114	protein-coding gene	gene with protein product	"""cancer/testis antigen 134"""	602015	"""outer dense fibre of sperm tails 2"""			9045620, 10072582	Standard	NM_153435		Approved	ODF84, CT134	uc004bvc.3	Q5BJF6	OTTHUMG00000020748	ENST00000434106.3:c.1808T>G	9.37:g.131256844T>G	ENSP00000403453:p.Leu603Arg	Somatic	19	0		WXS	Illumina HiSeq	.	7	2	NM_153435	B1AND3|B4DRK4|B4DX73|B4DZ02|E7EWL2|F5H6J4|O14721|O60631|Q1W2J6|Q6UN26|Q7Z5I6|Q96FN2	Missense_Mutation	SNP	ENST00000434106.3	37	CCDS56588.1	.	.	.	.	.	.	.	.	.	.	T	22.9	4.345641	0.82022	.	.	ENSG00000136811	ENST00000393533;ENST00000372814;ENST00000351030;ENST00000372796;ENST00000303890;ENST00000448249;ENST00000546203;ENST00000372791	T;D;D;D;D;D;T;T	0.83837	0.47;-1.57;-1.77;-1.77;-1.77;-1.57;0.58;0.6	5.4	5.4	0.78164	.	0.000000	0.85682	D	0.000000	D	0.89836	0.6830	M	0.73217	2.22	0.80722	D	1	D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D	0.87578	0.995;0.995;0.995;0.997;0.995;0.998;0.995	D	0.89327	0.3644	10	0.39692	T	0.17	-11.5259	14.6101	0.68510	0.0:0.0:0.0:1.0	.	584;598;522;603;584;603;579	Q5BJF6-8;Q5BJF6-4;Q5BJF6-9;B4DX73;Q5BJF6-5;Q5BJF6;Q5BJF6-3	.;.;.;.;.;ODFP2_HUMAN;.	R	603;647;598;603;579;522;584;584	ENSP00000377166:L603R;ENSP00000361901:L647R;ENSP00000342581:L598R;ENSP00000361882:L603R;ENSP00000307781:L579R;ENSP00000396687:L522R;ENSP00000437579:L584R;ENSP00000361877:L584R	ENSP00000307781:L579R	L	+	2	0	ODF2	130296665	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	6.449000	0.73473	2.047000	0.60756	0.459000	0.35465	CTG	.		0.562	ODF2-011	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054449.3		
PTGER2	5732	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	14	52781389	52781389	+	Missense_Mutation	SNP	A	A	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr14:52781389A>G	ENST00000245457.5	+	1	277	c.123A>G	c.(121-123)atA>atG	p.I41M	PTGER2_ENST00000557436.1_Intron	NM_000956.3	NP_000947.2	P43116	PE2R2_HUMAN	prostaglandin E receptor 2 (subtype EP2), 53kDa	41					adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|cellular response to prostaglandin E stimulus (GO:0071380)|G-protein coupled receptor signaling pathway (GO:0007186)|regulation of cell proliferation (GO:0042127)|response to lipopolysaccharide (GO:0032496)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	prostaglandin E receptor activity (GO:0004957)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(7)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	15	Breast(41;0.0639)|all_epithelial(31;0.0729)				Alprostadil(DB00770)|Dinoprostone(DB00917)|Misoprostol(DB00929)	GGAACCTCATAGCACTGGCGC	0.697																																					p.I41M		.											.	.	.	0			c.A123G						.						19.0	24.0	23.0					14																	52781389		2199	4298	6497	SO:0001583	missense	5732	exon1			CCTCATAGCACTG		CCDS9708.1	14q22	2012-08-08	2002-08-29		ENSG00000125384	ENSG00000125384		"""GPCR / Class A : Prostanoid receptors"""	9594	protein-coding gene	gene with protein product		176804	"""prostaglandin E receptor 2 (subtype EP2), 53kD"""			8250933, 7759114	Standard	NM_000956		Approved	EP2	uc001wzr.3	P43116	OTTHUMG00000140300	ENST00000245457.5:c.123A>G	14.37:g.52781389A>G	ENSP00000245457:p.Ile41Met	Somatic	73	0		WXS	Illumina HiSeq	.	41	21	NM_000956	D3DSC0|Q52LG8	Missense_Mutation	SNP	ENST00000245457.5	37	CCDS9708.1	.	.	.	.	.	.	.	.	.	.	A	13.42	2.230577	0.39399	.	.	ENSG00000125384	ENST00000245457	T	0.38401	1.14	5.19	-1.54	0.08584	GPCR, rhodopsin-like superfamily (1);	0.500239	0.22190	N	0.063383	T	0.24661	0.0598	L	0.56769	1.78	0.40053	D	0.975792	B	0.22480	0.07	B	0.19148	0.024	T	0.07501	-1.0769	10	0.41790	T	0.15	-25.3127	1.4275	0.02326	0.2413:0.4066:0.1152:0.2369	.	41	P43116	PE2R2_HUMAN	M	41	ENSP00000245457:I41M	ENSP00000245457:I41M	I	+	3	3	PTGER2	51851139	0.001000	0.12720	0.998000	0.56505	0.983000	0.72400	-1.370000	0.02575	0.031000	0.15407	-0.254000	0.11334	ATA	.		0.697	PTGER2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276890.1		
SLMO2	51012	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	20	57611616	57611616	+	Silent	SNP	T	T	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr20:57611616T>C	ENST00000355937.4	-	5	553	c.375A>G	c.(373-375)acA>acG	p.T125T	SLMO2_ENST00000371033.5_Silent_p.T95T	NM_016045.2	NP_057129.2	Q9Y3B1	SLMO2_HUMAN	slowmo homolog 2 (Drosophila)	125	PRELI/MSF1. {ECO:0000255|PROSITE- ProRule:PRU00158}.				phospholipid transport (GO:0015914)	mitochondrial intermembrane space (GO:0005758)	phosphatidic acid transporter activity (GO:1990050)	p.T125T(1)		endometrium(1)|lung(2)|skin(2)	5	all_lung(29;0.00711)		Colorectal(105;0.109)			TGGCTTCTTGTGTCAAAACAG	0.383																																					p.T125T		.											SLMO2,NS,carcinoma,0,1	SLMO2	0	1	Substitution - coding silent(1)	lung(1)	c.A375G						.						107.0	96.0	99.0					20																	57611616		1879	4111	5990	SO:0001819	synonymous_variant	51012	exon5			TTCTTGTGTCAAA	AF151865	CCDS42893.1, CCDS58783.1	20q13.32	2008-10-22	2007-02-06	2007-02-06	ENSG00000101166	ENSG00000101166			15892	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 45"""	C20orf45			Standard	NM_016045		Approved	dJ543J19.5, PRELID3B	uc002yam.3	Q9Y3B1	OTTHUMG00000032856	ENST00000355937.4:c.375A>G	20.37:g.57611616T>C		Somatic	75	0		WXS	Illumina HiSeq	.	44	23	NM_016045	E1P5I8|Q5JX17|Q9NUL0	Silent	SNP	ENST00000355937.4	37	CCDS42893.1																																																																																			.		0.383	SLMO2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079897.2	NM_016045	
MED28	80306	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	4	17621579	17621579	+	Missense_Mutation	SNP	A	A	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr4:17621579A>G	ENST00000237380.7	+	2	239	c.215A>G	c.(214-216)gAa>gGa	p.E72G		NM_025205.3	NP_079481.2	Q9H204	MED28_HUMAN	mediator complex subunit 28	72					negative regulation of smooth muscle cell differentiation (GO:0051151)|regulation of transcription, DNA-templated (GO:0006355)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)	cortical actin cytoskeleton (GO:0030864)|mediator complex (GO:0016592)|membrane (GO:0016020)				lung(6)|skin(2)	8						GATCAGGAAGAAATTCGAACC	0.393																																					p.E72G		.											.	.	.	0			c.A215G						.						132.0	120.0	124.0					4																	17621579		2203	4300	6503	SO:0001583	missense	80306	exon2			AGGAAGAAATTCG	AF317678	CCDS33963.1	4p16	2007-07-30	2007-07-30		ENSG00000118579	ENSG00000118579			24628	protein-coding gene	gene with protein product		610311	"""mediator of RNA polymerase II transcription, subunit 28 homolog (S. cerevisiae)"""			11779215, 15467741	Standard	NM_025205		Approved	EG1, DKFZP434N185, magicin	uc003gpi.1	Q9H204	OTTHUMG00000161980	ENST00000237380.7:c.215A>G	4.37:g.17621579A>G	ENSP00000237380:p.Glu72Gly	Somatic	83	0		WXS	Illumina HiSeq	.	76	7	NM_025205	Q9BZJ5	Missense_Mutation	SNP	ENST00000237380.7	37	CCDS33963.1	.	.	.	.	.	.	.	.	.	.	A	32	5.121725	0.94385	.	.	ENSG00000118579	ENST00000237380;ENST00000503945	.	.	.	5.79	5.79	0.91817	.	0.047766	0.85682	D	0.000000	T	0.77425	0.4128	M	0.64170	1.965	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.79669	-0.1707	9	0.87932	D	0	-6.3248	16.1415	0.81528	1.0:0.0:0.0:0.0	.	72	Q9H204	MED28_HUMAN	G	72;69	.	ENSP00000237380:E72G	E	+	2	0	MED28	17230677	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.888000	0.92464	2.198000	0.70561	0.533000	0.62120	GAA	.		0.393	MED28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360055.3	NM_025205	
IRS1	3667	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	2	227661428	227661428	+	Missense_Mutation	SNP	C	C	T	rs577419348		TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr2:227661428C>T	ENST00000305123.5	-	1	3047	c.2027G>A	c.(2026-2028)gGa>gAa	p.G676E	IRS1_ENST00000498335.1_5'Flank	NM_005544.2	NP_005535.1	P35568	IRS1_HUMAN	insulin receptor substrate 1	676					cellular response to insulin stimulus (GO:0032869)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose homeostasis (GO:0042593)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|lipid catabolic process (GO:0016042)|mammary gland development (GO:0030879)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of insulin secretion (GO:0046676)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of fatty acid beta-oxidation (GO:0032000)|positive regulation of glucose import (GO:0046326)|positive regulation of glucose import in response to insulin stimulus (GO:2001275)|positive regulation of glucose metabolic process (GO:0010907)|positive regulation of glycogen biosynthetic process (GO:0045725)|positive regulation of insulin receptor signaling pathway (GO:0046628)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|protein kinase B signaling (GO:0043491)|protein localization to nucleus (GO:0034504)|regulation of gene expression (GO:0010468)|response to insulin (GO:0032868)|response to peptide hormone (GO:0043434)|signal transduction (GO:0007165)	caveola (GO:0005901)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|insulin receptor complex (GO:0005899)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	insulin receptor binding (GO:0005158)|insulin-like growth factor receptor binding (GO:0005159)|phosphatidylinositol 3-kinase binding (GO:0043548)|protein kinase C binding (GO:0005080)|SH2 domain binding (GO:0042169)|signal transducer activity (GO:0004871)|transmembrane receptor protein tyrosine kinase adaptor activity (GO:0005068)			autonomic_ganglia(1)|breast(2)|central_nervous_system(4)|endometrium(5)|kidney(4)|large_intestine(10)|lung(33)|ovary(6)|pancreas(1)|prostate(1)|urinary_tract(2)	69		Renal(207;0.023)|all_lung(227;0.0994)|all_hematologic(139;0.118)|Esophageal squamous(248;0.23)		Epithelial(121;3.03e-11)|all cancers(144;2.42e-08)|Lung(261;0.00712)|LUSC - Lung squamous cell carcinoma(224;0.0137)		gGGGCCACCTCCAATGTCAGG	0.607											OREG0015248	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	1	0.000199681	0.0	0.0	5008	,	,		17270	0.0		0.0	False		,,,				2504	0.001				p.G676E		.											.	.	.	0			c.G2027A						.						51.0	53.0	52.0					2																	227661428		2203	4300	6503	SO:0001583	missense	3667	exon1			CCACCTCCAATGT		CCDS2463.1	2q36	2013-01-10			ENSG00000169047	ENSG00000169047		"""Pleckstrin homology (PH) domain containing"""	6125	protein-coding gene	gene with protein product		147545				1648180	Standard	NM_005544		Approved	HIRS-1	uc002voh.4	P35568	OTTHUMG00000133179	ENST00000305123.5:c.2027G>A	2.37:g.227661428C>T	ENSP00000304895:p.Gly676Glu	Somatic	25	0	2321	WXS	Illumina HiSeq	.	24	13	NM_005544		Missense_Mutation	SNP	ENST00000305123.5	37	CCDS2463.1	.	.	.	.	.	.	.	.	.	.	C	19.60	3.858205	0.71834	.	.	ENSG00000169047	ENST00000305123	T	0.55930	0.49	4.81	1.69	0.24217	.	0.713937	0.12683	N	0.447811	T	0.23688	0.0573	N	0.03608	-0.345	0.09310	N	0.999998	B	0.27498	0.18	B	0.22601	0.04	T	0.14144	-1.0483	10	0.02654	T	1	-1.3629	12.0974	0.53763	0.0:0.4397:0.5603:0.0	.	676	P35568	IRS1_HUMAN	E	676	ENSP00000304895:G676E	ENSP00000304895:G676E	G	-	2	0	IRS1	227369672	0.001000	0.12720	0.607000	0.28956	0.911000	0.54048	0.873000	0.28052	0.558000	0.29135	0.561000	0.74099	GGA	.		0.607	IRS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256886.3	NM_005544	
RET	5979	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	10	43601837	43601837	+	Missense_Mutation	SNP	C	C	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr10:43601837C>T	ENST00000355710.3	+	5	1113	c.881C>T	c.(880-882)gCc>gTc	p.A294V	RET_ENST00000340058.5_Missense_Mutation_p.A294V	NM_020975.4	NP_066124.1	P07949	RET_HUMAN	ret proto-oncogene	294					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|cellular response to retinoic acid (GO:0071300)|embryonic epithelial tube formation (GO:0001838)|enteric nervous system development (GO:0048484)|homophilic cell adhesion (GO:0007156)|innervation (GO:0060384)|lymphocyte migration into lymphoid organs (GO:0097021)|MAPK cascade (GO:0000165)|membrane protein proteolysis (GO:0033619)|neural crest cell migration (GO:0001755)|neuron cell-cell adhesion (GO:0007158)|neuron maturation (GO:0042551)|peptidyl-tyrosine phosphorylation (GO:0018108)|Peyer's patch morphogenesis (GO:0061146)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of cell migration (GO:0030335)|positive regulation of cell size (GO:0045793)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of metanephric glomerulus development (GO:0072300)|positive regulation of neuron maturation (GO:0014042)|positive regulation of neuron projection development (GO:0010976)|positive regulation of transcription, DNA-templated (GO:0045893)|posterior midgut development (GO:0007497)|protein phosphorylation (GO:0006468)|regulation of axonogenesis (GO:0050770)|regulation of cell adhesion (GO:0030155)|response to drug (GO:0042493)|response to pain (GO:0048265)|retina development in camera-type eye (GO:0060041)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|ureter maturation (GO:0035799)|ureteric bud development (GO:0001657)	endosome membrane (GO:0010008)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|protein tyrosine kinase activity (GO:0004713)|receptor activity (GO:0004872)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)		CCDC6/RET(4)|KIF5B/RET(79)	NS(2)|adrenal_gland(26)|breast(5)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(7)|kidney(2)|large_intestine(14)|lung(27)|ovary(5)|prostate(3)|skin(1)|thyroid(504)|upper_aerodigestive_tract(1)|urinary_tract(1)	607		Ovarian(717;0.0423)			Cabozantinib(DB08875)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)	ACCGTGGTGGCCACGCTGCGT	0.642		1	"""T, Mis, N, F"""	"""H4, PRKAR1A, NCOA4, PCM1, GOLGA5, TRIM33, KTN1, TRIM27, HOOK3, KIF5B, CCDC6"""	"""medullary thyroid,  papillary thyroid, pheochromocytoma, NSCLC"""	"""medullary thyroid,  papillary thyroid, pheochromocytoma"""	Hirschsprung disease		Multiple Endocrine Neoplasia, type 2B;Multiple Endocrine Neoplasia, type 2A;Familial Medullary Thyroid Carcinoma																												p.A294V	Melanoma(102;360 522 3376 9752 9881 14372 17251 18341 20876 24662 34807 43144 48149)	.	yes	Dom	yes	Multiple endocrine neoplasia 2A/2B	10	10q11.2	5979	ret proto-oncogene	yes	"""E, O"""	.	.	.	0			c.C881T						.						49.0	36.0	41.0					10																	43601837		2203	4300	6503	SO:0001583	missense	5979	exon5	Familial Cancer Database	MEN2B, Wagenmann-Froboese s.;MEN2A, Sipple disease, incl MEN2C;FMTC	TGGTGGCCACGCT	BC004257	CCDS7200.1, CCDS53525.1	10q11.2	2014-09-17	2007-02-16		ENSG00000165731	ENSG00000165731		"""Cadherins / Cadherin-related"""	9967	protein-coding gene	gene with protein product	"""cadherin-related family member 16"""	164761	"""multiple endocrine neoplasia and medullary thyroid carcinoma 1"", ""Hirschsprung disease 1"""	HSCR1, MEN2A, MTC1, MEN2B		2687772, 1611909	Standard	NM_020975		Approved	PTC, CDHF12, RET51, CDHR16	uc001jal.3	P07949	OTTHUMG00000018024	ENST00000355710.3:c.881C>T	10.37:g.43601837C>T	ENSP00000347942:p.Ala294Val	Somatic	47	0		WXS	Illumina HiSeq	.	20	10	NM_020630	A8K6Z2|Q15250|Q9BTB0|Q9H4A2	Missense_Mutation	SNP	ENST00000355710.3	37	CCDS7200.1	.	.	.	.	.	.	.	.	.	.	C	14.02	2.411434	0.42817	.	.	ENSG00000165731	ENST00000355710;ENST00000340058;ENST00000535749	T;T	0.81163	-1.36;-1.46	5.05	5.05	0.67936	.	0.161832	0.52532	D	0.000061	T	0.81931	0.4927	L	0.56769	1.78	0.09310	N	1	P;P;P	0.48764	0.77;0.745;0.915	B;B;P	0.50896	0.357;0.287;0.653	T	0.76154	-0.3063	10	0.56958	D	0.05	.	11.5882	0.50931	0.0:0.8203:0.1797:0.0	.	40;294;294	B4DGX8;P07949;P07949-2	.;RET_HUMAN;.	V	294	ENSP00000347942:A294V;ENSP00000344798:A294V	ENSP00000344798:A294V	A	+	2	0	RET	42921843	0.975000	0.34042	0.080000	0.20451	0.009000	0.06853	3.107000	0.50329	2.618000	0.88619	0.467000	0.42956	GCC	.		0.642	RET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047694.2	NM_020975	
TRAM1	23471	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	8	71495450	71495450	+	Missense_Mutation	SNP	C	C	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr8:71495450C>A	ENST00000262213.2	-	10	1169	c.1000G>T	c.(1000-1002)Gtg>Ttg	p.V334L	TRAM1_ENST00000536748.1_Missense_Mutation_p.V303L|TRAM1_ENST00000521049.1_5'Flank|TRAM1_ENST00000521425.1_Missense_Mutation_p.V248L	NM_014294.5	NP_055109.1	Q15629	TRAM1_HUMAN	translocation associated membrane protein 1	334					cellular protein metabolic process (GO:0044267)|cotranslational protein targeting to membrane (GO:0006613)|gene expression (GO:0010467)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|viral process (GO:0016032)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			endometrium(2)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)	17			Epithelial(68;0.00679)|all cancers(69;0.0324)|OV - Ovarian serous cystadenocarcinoma(28;0.0509)			TTCTTCTTCACAGCTGGTGCC	0.383																																					p.V334L	Ovarian(85;984 1334 5116 12432 40638)	.											.	.	.	0			c.G1000T						.						131.0	119.0	123.0					8																	71495450		2203	4300	6503	SO:0001583	missense	23471	exon10			TCTTCACAGCTGG	X63679	CCDS6207.1	8q13.1	2004-01-22			ENSG00000067167	ENSG00000067167			20568	protein-coding gene	gene with protein product		605190				1315422	Standard	NM_014294		Approved	TRAM, TRAMP	uc003xyo.2	Q15629	OTTHUMG00000164428	ENST00000262213.2:c.1000G>T	8.37:g.71495450C>A	ENSP00000262213:p.Val334Leu	Somatic	62	0		WXS	Illumina HiSeq	.	24	11	NM_014294	B4E0K2	Missense_Mutation	SNP	ENST00000262213.2	37	CCDS6207.1	.	.	.	.	.	.	.	.	.	.	C	10.31	1.313908	0.23908	.	.	ENSG00000067167	ENST00000521425;ENST00000262213;ENST00000536748	T;T;T	0.42900	0.96;1.55;1.55	5.21	4.34	0.51931	.	0.889339	0.09919	N	0.738667	T	0.26412	0.0645	N	0.11756	0.17	0.37503	D	0.916835	B	0.09022	0.002	B	0.08055	0.003	T	0.09618	-1.0666	10	0.33940	T	0.23	.	9.5977	0.39584	0.0:0.7841:0.1415:0.0744	.	334	Q15629	TRAM1_HUMAN	L	248;334;303	ENSP00000428052:V248L;ENSP00000262213:V334L;ENSP00000439359:V303L	ENSP00000262213:V334L	V	-	1	0	TRAM1	71658004	0.998000	0.40836	0.912000	0.35992	0.958000	0.62258	0.910000	0.28571	1.445000	0.47624	-0.140000	0.14226	GTG	.		0.383	TRAM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378738.1	NM_014294	
ASCC2	84164	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	22	30186459	30186459	+	Splice_Site	SNP	C	C	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr22:30186459C>A	ENST00000397771.2	-	20	2278	c.2101G>T	c.(2101-2103)Ggg>Tgg	p.G701W	ASCC2_ENST00000542393.1_Splice_Site_p.G625W|ASCC2_ENST00000307790.3_Splice_Site_p.G701W			Q9H1I8	ASCC2_HUMAN	activating signal cointegrator 1 complex subunit 2	701					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)					endometrium(3)|large_intestine(3)|lung(9)|prostate(1)|skin(1)|urinary_tract(1)	18			OV - Ovarian serous cystadenocarcinoma(5;0.000103)|Epithelial(10;0.0169)|all cancers(5;0.0259)			AATGCTCACCCTTTCTTGGCG	0.602																																					p.G701W		.											.	.	.	0			c.G2101T						.						51.0	46.0	47.0					22																	30186459		2203	4300	6503	SO:0001630	splice_region_variant	84164	exon19			CTCACCCTTTCTT	AY013289	CCDS13869.1, CCDS56226.1	22q12.1	2004-07-27			ENSG00000100325	ENSG00000100325			24103	protein-coding gene	gene with protein product	"""ASC 1 complex subunit P100"""	614216				12077347, 9847074	Standard	NM_032204		Approved	ASC1p100, FLJ21588, DKFZp586O0223	uc003agr.3	Q9H1I8	OTTHUMG00000067658	ENST00000397771.2:c.2102+1G>T	22.37:g.30186459C>A		Somatic	42	0		WXS	Illumina HiSeq	.	17	10	NM_032204	B7Z8E0|F5H6J9|Q4TT54|Q8TAZ0|Q9H711|Q9H9D6	Missense_Mutation	SNP	ENST00000397771.2	37	CCDS13869.1	.	.	.	.	.	.	.	.	.	.	C	21.1	4.096367	0.76870	.	.	ENSG00000100325	ENST00000307790;ENST00000397771;ENST00000542393	T;T;T	0.14893	2.47;2.47;2.48	5.76	5.76	0.90799	.	0.050481	0.85682	D	0.000000	T	0.44414	0.1292	M	0.71036	2.16	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.29458	-1.0011	10	0.87932	D	0	-33.7584	18.5398	0.91023	0.0:1.0:0.0:0.0	.	625;701	F5H6J9;Q9H1I8	.;ASCC2_HUMAN	W	701;701;625	ENSP00000305502:G701W;ENSP00000380877:G701W;ENSP00000437570:G625W	ENSP00000305502:G701W	G	-	1	0	ASCC2	28516459	1.000000	0.71417	0.996000	0.52242	0.510000	0.34073	6.687000	0.74552	2.713000	0.92767	0.655000	0.94253	GGG	.		0.602	ASCC2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322127.1	NM_032204	Missense_Mutation
PSD3	23362	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	8	18662106	18662106	+	Missense_Mutation	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr8:18662106T>G	ENST00000327040.8	-	6	1938	c.1836A>C	c.(1834-1836)gaA>gaC	p.E612D	PSD3_ENST00000523619.1_Missense_Mutation_p.E547D|PSD3_ENST00000440756.2_Missense_Mutation_p.E612D|PSD3_ENST00000286485.8_Missense_Mutation_p.E78D	NM_015310.3	NP_056125.3	Q9NYI0	PSD3_HUMAN	pleckstrin and Sec7 domain containing 3	612	SEC7. {ECO:0000255|PROSITE- ProRule:PRU00189}.				neuron differentiation (GO:0030182)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)	cell junction (GO:0030054)|postsynaptic membrane (GO:0045211)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(8)|ovary(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20				Colorectal(111;0.0281)|READ - Rectum adenocarcinoma(644;0.183)		GTTTGCTAAATTCGTTGCTAT	0.383																																					p.E612D		.											.	.	.	0			c.A1836C						.						98.0	102.0	100.0					8																	18662106		2203	4300	6503	SO:0001583	missense	23362	exon6			GCTAAATTCGTTG	AF243495	CCDS34854.1, CCDS43720.1	8p21.3	2013-01-10			ENSG00000156011	ENSG00000156011		"""Pleckstrin homology (PH) domain containing"""	19093	protein-coding gene	gene with protein product		614440					Standard	NM_206909		Approved	KIAA0942, HCA67, EFA6R, DKFZp761K1423	uc003wza.3	Q9NYI0	OTTHUMG00000163711	ENST00000327040.8:c.1836A>C	8.37:g.18662106T>G	ENSP00000324127:p.Glu612Asp	Somatic	103	0		WXS	Illumina HiSeq	.	66	23	NM_015310	A6NFQ4|E9KL50|Q6B003|Q9Y2F1	Missense_Mutation	SNP	ENST00000327040.8	37	CCDS43720.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	10.60|10.60	1.395887|1.395887	0.25205|0.25205	.|.	.|.	ENSG00000156011|ENSG00000156011	ENST00000327040;ENST00000440756;ENST00000286485;ENST00000523619;ENST00000519851|ENST00000520858;ENST00000521027	T;T;T;T;T|.	0.55930|.	0.49;0.49;0.49;0.49;0.49|.	6.07|6.07	4.93|4.93	0.64822|0.64822	.|.	0.180315|.	0.49305|.	D|.	0.000150|.	T|T	0.39989|0.39989	0.1099|0.1099	N|N	0.22421|0.22421	0.69|0.69	0.37667|0.37667	D|D	0.922976|0.922976	B;B|.	0.15141|.	0.012;0.001|.	B;B|.	0.18871|.	0.023;0.005|.	T|T	0.39121|0.39121	-0.9629|-0.9629	10|5	0.02654|.	T|.	1|.	.|.	5.8376|5.8376	0.18615|0.18615	0.0:0.0825:0.1696:0.7478|0.0:0.0825:0.1696:0.7478	.|.	612;78|.	E9KL50;Q9NYI0-3|.	.;.|.	D|L	612;612;78;547;53|45;60	ENSP00000324127:E612D;ENSP00000401704:E612D;ENSP00000286485:E78D;ENSP00000430640:E547D;ENSP00000429069:E53D|.	ENSP00000286485:E78D|.	E|I	-|-	3|1	2|0	PSD3|PSD3	18706386|18706386	0.987000|0.987000	0.35691|0.35691	1.000000|1.000000	0.80357|0.80357	0.807000|0.807000	0.45602|0.45602	0.082000|0.082000	0.14847|0.14847	2.326000|2.326000	0.78906|0.78906	0.533000|0.533000	0.62120|0.62120	GAA|ATT	.		0.383	PSD3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000374867.1	NM_015310	
SYCP2	10388	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	20	58470491	58470491	+	Splice_Site	SNP	C	C	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr20:58470491C>T	ENST00000357552.3	-	20	1891		c.e20+1		SYCP2_ENST00000371001.2_Splice_Site			Q9BX26	SYCP2_HUMAN	synaptonemal complex protein 2						female meiotic division (GO:0007143)|fertilization (GO:0009566)|male genitalia morphogenesis (GO:0048808)|male meiosis (GO:0007140)|negative regulation of apoptotic process (GO:0043066)|synaptonemal complex assembly (GO:0007130)	lateral element (GO:0000800)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	DNA binding (GO:0003677)			NS(4)|breast(2)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(14)|lung(12)|ovary(4)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	53	all_lung(29;0.00344)		BRCA - Breast invasive adenocarcinoma(7;1.19e-09)			GGTAAAGTTACTTTGTCTATA	0.313																																					.		.											.	.	.	0			c.1665+1G>A						.						130.0	125.0	127.0					20																	58470491		2203	4300	6503	SO:0001630	splice_region_variant	10388	exon20			AAGTTACTTTGTC	Y08982	CCDS13482.1	20q13.33	2007-07-02			ENSG00000196074	ENSG00000196074			11490	protein-coding gene	gene with protein product		604105				10341103, 9592139	Standard	NM_014258		Approved	SCP2	uc002yaz.3	Q9BX26	OTTHUMG00000032872	ENST00000357552.3:c.1665+1G>A	20.37:g.58470491C>T		Somatic	51	0		WXS	Illumina HiSeq	.	41	15	NM_014258	A2RUE5|O75763|Q5JX11|Q9NTX8|Q9UG27	Splice_Site	SNP	ENST00000357552.3	37	CCDS13482.1	.	.	.	.	.	.	.	.	.	.	C	12.79	2.042142	0.35989	.	.	ENSG00000196074	ENST00000371001;ENST00000357552;ENST00000446834	.	.	.	4.15	4.15	0.48705	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.2307	0.54486	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	SYCP2	57903886	0.989000	0.36119	1.000000	0.80357	0.459000	0.32528	2.344000	0.44010	2.579000	0.87056	0.585000	0.79938	.	.		0.313	SYCP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079930.3	NM_014258	Intron
NLRP5	126206	hgsc.bcm.edu	37	19	56527149	56527149	+	Missense_Mutation	SNP	G	G	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr19:56527149G>A	ENST00000390649.3	+	4	550	c.550G>A	c.(550-552)Gag>Aag	p.E184K		NM_153447.4	NP_703148.4	P59047	NALP5_HUMAN	NLR family, pyrin domain containing 5	184					cellular protein complex assembly (GO:0043623)|cellular protein localization (GO:0034613)|embryo implantation (GO:0007566)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|neuron death (GO:0070997)|organ morphogenesis (GO:0009887)|regulation of protein stability (GO:0031647)|regulation of RNA stability (GO:0043487)	apical cortex (GO:0045179)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|protein complex (GO:0043234)	ATP binding (GO:0005524)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|ovary(5)|skin(2)|stomach(4)|upper_aerodigestive_tract(2)	25		Colorectal(82;3.46e-05)|Ovarian(87;0.0481)|Renal(1328;0.157)		GBM - Glioblastoma multiforme(193;0.0326)		cacagctgcagagacaaaaga	0.393																																					p.E184K		.											NLRP5_ENST00000390649,colon,carcinoma,0,1	NLRP5_ENST00000390649	0	0			c.G550A						.						75.0	70.0	72.0					19																	56527149		1900	4098	5998	SO:0001583	missense	126206	exon4			GCTGCAGAGACAA	AY154460	CCDS12938.1	19q13.43	2008-10-30	2006-12-08	2006-12-08	ENSG00000171487	ENSG00000171487		"""Nucleotide-binding domain and leucine rich repeat containing"""	21269	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 5"""	609658	"""NACHT, leucine rich repeat and PYD containing 5"""	NALP5		12563287, 11925379	Standard	NM_153447		Approved	PYPAF8, MATER, PAN11, CLR19.8	uc002qmj.3	P59047	OTTHUMG00000149887	ENST00000390649.3:c.550G>A	19.37:g.56527149G>A	ENSP00000375063:p.Glu184Lys	Somatic	49	0		WXS	Illumina HiSeq	.	41	2	NM_153447	A8MTY4|Q86W29	Missense_Mutation	SNP	ENST00000390649.3	37	CCDS12938.1	.	.	.	.	.	.	.	.	.	.	G	3.680	-0.065784	0.07273	.	.	ENSG00000171487	ENST00000390649	T	0.72282	-0.64	0.109	0.109	0.14578	.	.	.	.	.	T	0.38957	0.1060	N	0.08118	0	0.09310	N	1	P	0.35011	0.48	B	0.24974	0.057	T	0.22765	-1.0207	8	0.11794	T	0.64	.	.	.	.	.	184	P59047	NALP5_HUMAN	K	184	ENSP00000375063:E184K	ENSP00000375063:E184K	E	+	1	0	NLRP5	61218961	0.065000	0.20965	0.050000	0.19076	0.051000	0.14879	0.218000	0.17622	0.181000	0.19994	0.184000	0.17185	GAG	.		0.393	NLRP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313735.1	NM_153447	
ARMC4	55130	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	10	28196701	28196701	+	Missense_Mutation	SNP	A	A	G	rs150213638		TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr10:28196701A>G	ENST00000305242.5	-	17	2593	c.2501T>C	c.(2500-2502)aTt>aCt	p.I834T	ARMC4_ENST00000545014.1_Missense_Mutation_p.I359T|ARMC4_ENST00000537576.1_Missense_Mutation_p.I526T	NM_018076.2	NP_060546.2	Q5T2S8	ARMC4_HUMAN	armadillo repeat containing 4	834					cell projection organization (GO:0030030)|cilium movement (GO:0003341)|left/right axis specification (GO:0070986)|outer dynein arm assembly (GO:0036158)|ventricular system development (GO:0021591)	axoneme (GO:0005930)|ciliary base (GO:0097546)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)				NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(17)|liver(1)|lung(17)|ovary(5)|prostate(3)|skin(8)|stomach(2)|urinary_tract(3)	75						TAAGCGATCAATTATCCTATC	0.398																																					p.I834T		.											.	.	.	0			c.T2501C						.	A	THR/ILE	0,4406		0,0,2203	101.0	90.0	94.0		2501	5.7	1.0	10	dbSNP_134	94	1,8599	1.2+/-3.3	0,1,4299	no	missense	ARMC4	NM_018076.2	89	0,1,6502	GG,GA,AA		0.0116,0.0,0.0077	probably-damaging	834/1045	28196701	1,13005	2203	4300	6503	SO:0001583	missense	55130	exon17			CGATCAATTATCC	AL136859	CCDS7157.1	10p12.1-p11.23	2014-02-03			ENSG00000169126	ENSG00000169126		"""Armadillo repeat containing"""	25583	protein-coding gene	gene with protein product		615408				11230166	Standard	XM_005252485		Approved	FLJ10817, FLJ10376, DKFZP434P1735, CILD23	uc001itz.3	Q5T2S8	OTTHUMG00000017867	ENST00000305242.5:c.2501T>C	10.37:g.28196701A>G	ENSP00000306410:p.Ile834Thr	Somatic	71	0		WXS	Illumina HiSeq	.	59	20	NM_018076	A8K906|B7Z7I1|Q9H0C0	Missense_Mutation	SNP	ENST00000305242.5	37	CCDS7157.1	.	.	.	.	.	.	.	.	.	.	A	18.70	3.679946	0.68042	0.0	1.16E-4	ENSG00000169126	ENST00000537576;ENST00000305242;ENST00000545014	D;D;D	0.95001	-3.58;-3.58;-3.58	5.74	5.74	0.90152	Armadillo-like helical (1);Armadillo-type fold (1);	0.044446	0.85682	D	0.000000	D	0.97711	0.9249	M	0.89904	3.07	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.83275	0.992;0.996	D	0.98628	1.0670	10	0.87932	D	0	-28.2121	16.0343	0.80612	1.0:0.0:0.0:0.0	.	359;834	B7Z7I1;Q5T2S8	.;ARMC4_HUMAN	T	526;834;359	ENSP00000443208:I526T;ENSP00000306410:I834T;ENSP00000441076:I359T	ENSP00000306410:I834T	I	-	2	0	ARMC4	28236707	1.000000	0.71417	1.000000	0.80357	0.743000	0.42351	9.053000	0.93860	2.198000	0.70561	0.533000	0.62120	ATT	0.000		0.398	ARMC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047339.1	NM_018076	
CDH23	64072	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	10	73569791	73569791	+	Silent	SNP	C	C	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr10:73569791C>T	ENST00000224721.6	+	60	8957	c.8952C>T	c.(8950-8952)ctC>ctT	p.L2984L	CDH23_ENST00000398788.3_Silent_p.L739L|CDH23_ENST00000475158.1_3'UTR	NM_022124.5	NP_071407.4	Q9H251	CAD23_HUMAN	cadherin-related 23	2979					calcium ion transport (GO:0006816)|calcium-dependent cell-cell adhesion (GO:0016339)|cytosolic calcium ion homeostasis (GO:0051480)|equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(6)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(27)|lung(49)|ovary(3)|pancreas(1)|prostate(7)|stomach(7)|upper_aerodigestive_tract(3)	133						TCCACCTGCTCTCCAACATCA	0.612																																					p.L2979L		.											.	.	.	0			c.C8937T						.						60.0	61.0	60.0					10																	73569791		2071	4184	6255	SO:0001819	synonymous_variant	64072	exon59			CCTGCTCTCCAAC	AY010111	CCDS53540.1, CCDS73146.1	10q22.1	2014-08-08	2010-01-25		ENSG00000107736	ENSG00000107736		"""Cadherins / Cadherin-related"""	13733	protein-coding gene	gene with protein product	"""cadherin-related family member 23"""	605516	"""cadherin related 23"", ""cadherin-like 23"""	DFNB12, USH1D		11090341	Standard	NM_022124		Approved	CDHR23	uc001jrx.4	Q9H251	OTTHUMG00000019347	ENST00000224721.6:c.8952C>T	10.37:g.73569791C>T		Somatic	10	0		WXS	Illumina HiSeq	.	13	6	NM_022124	C4IXS9|F6U049|Q5QGS1|Q5QGS2|Q5QGS5|Q5QGS6|Q5XKN2|Q6UWW1|Q96JL3|Q9H4K9	Silent	SNP	ENST00000224721.6	37																																																																																				.		0.612	CDH23-001	PUTATIVE	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051227.4	NM_052836	
MROH7	374977	hgsc.bcm.edu	37	1	55168304	55168304	+	Silent	SNP	G	G	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr1:55168304G>A	ENST00000421030.2	+	21	3735	c.3450G>A	c.(3448-3450)gtG>gtA	p.V1150V	MROH7_ENST00000454855.2_Silent_p.V668V|MROH7_ENST00000409996.1_Silent_p.V718V|MROH7-TTC4_ENST00000414150.2_Silent_p.V1150V	NM_001039464.2	NP_001034553	Q68CQ1	MROH7_HUMAN	maestro heat-like repeat family member 7	1150						extracellular space (GO:0005615)|integral component of membrane (GO:0016021)											AGAAGTGTGTGAAGACCCTGT	0.443																																					p.V1150V		.											.	.	.	0			c.G3450A						.						109.0	105.0	106.0					1																	55168304		1893	4125	6018	SO:0001819	synonymous_variant	374977	exon21			GTGTGTGAAGACC	AL832492	CCDS41342.2	1p32.3	2012-12-19	2012-12-19	2012-12-19	ENSG00000184313	ENSG00000184313		"""maestro heat-like repeat containing"""	24802	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 175"", ""HEAT repeat containing 8"""	C1orf175, HEATR8		12477932	Standard	NM_001039464		Approved	FLJ46354	uc010ooe.1	Q68CQ1	OTTHUMG00000009890	ENST00000421030.2:c.3450G>A	1.37:g.55168304G>A		Somatic	71	0		WXS	Illumina HiSeq	.	50	4	NM_001039464	A0AUX8|Q5TA99|Q6ZP40|Q6ZRH6|Q8N311|Q8NA14	Silent	SNP	ENST00000421030.2	37	CCDS41342.2																																																																																			.		0.443	MROH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346978.1	NM_198547	
ZNF695	57116	hgsc.bcm.edu	37	1	247130470	247130470	+	Intron	SNP	C	C	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr1:247130470C>A	ENST00000487338.2	-	5	673				ZNF695_ENST00000498046.2_Intron	NM_001204221.1	NP_001191150	Q8IW36	ZN695_HUMAN	zinc finger protein 695						regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			endometrium(1)|large_intestine(1)|lung(9)|prostate(1)|urinary_tract(1)	13	all_cancers(71;4.01e-05)|all_epithelial(71;6.72e-06)|Ovarian(71;0.0173)|Breast(184;0.0318)|all_lung(81;0.0458)|Lung NSC(105;0.0518)	all_cancers(173;0.0266)	OV - Ovarian serous cystadenocarcinoma(106;0.00271)			gaactcccgacctcaggtgat	0.502																																					.		.											.	.	.	0			.						.																																			SO:0001627	intron_variant	0	.			TCCCGACCTCAGG		CCDS44344.1, CCDS55694.1	1q44	2013-01-08			ENSG00000197472	ENSG00000197472		"""Zinc fingers, C2H2-type"", ""-"""	30954	protein-coding gene	gene with protein product						12477932	Standard	NM_020394		Approved	SBZF3	uc009xgu.3	Q8IW36	OTTHUMG00000040707	ENST00000487338.2:c.488+526G>T	1.37:g.247130470C>A		Somatic	14	0		WXS	Illumina HiSeq	.	14	12	.	Q5T0N9|Q5T0P1|Q5T0P3|Q7Z2W8|Q7Z648	RNA	SNP	ENST00000487338.2	37	CCDS55694.1																																																																																			.		0.502	ZNF695-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000098003.4	NM_020394	
ZC3H15	55854	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	2	187351163	187351163	+	Silent	SNP	A	A	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr2:187351163A>G	ENST00000337859.6	+	1	281	c.54A>G	c.(52-54)aaA>aaG	p.K18K	ZC3H15_ENST00000544130.1_5'UTR	NM_018471.2	NP_060941.2	Q8WU90	ZC3HF_HUMAN	zinc finger CCCH-type containing 15	18					cytokine-mediated signaling pathway (GO:0019221)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(1)|kidney(1)|large_intestine(4)|lung(5)|skin(1)	15			OV - Ovarian serous cystadenocarcinoma(117;0.0148)|Epithelial(96;0.0922)|all cancers(119;0.233)			CGGAGCAAAAAAAGAAGGAGA	0.622																																					p.K18K		.											.	.	.	0			c.A54G						.						57.0	73.0	68.0					2																	187351163		1898	4100	5998	SO:0001819	synonymous_variant	55854	exon1			GCAAAAAAAGAAG		CCDS42791.1	2q32.1	2012-07-05			ENSG00000065548	ENSG00000065548		"""Zinc fingers, CCCH-type domain containing"""	29528	protein-coding gene	gene with protein product	"""likely ortholog of mouse immediate early response, erythropoietin 4"""					10880228	Standard	NM_018471		Approved	LEREPO4	uc002upo.3	Q8WU90	OTTHUMG00000154251	ENST00000337859.6:c.54A>G	2.37:g.187351163A>G		Somatic	59	0		WXS	Illumina HiSeq	.	52	23	NM_018471	B4DMW2|D3DPG7|Q5QTQ4|Q8WZ06|Q9NUZ3|Q9NZ37|Q9P079	Silent	SNP	ENST00000337859.6	37	CCDS42791.1																																																																																			.		0.622	ZC3H15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334547.2	NM_018471	
FRAS1	80144	hgsc.bcm.edu	37	4	79204119	79204119	+	Nonsense_Mutation	SNP	C	C	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr4:79204119C>A	ENST00000325942.6	+	12	1693	c.1253C>A	c.(1252-1254)tCa>tAa	p.S418*	FRAS1_ENST00000264895.6_Nonsense_Mutation_p.S418*|FRAS1_ENST00000264899.6_Nonsense_Mutation_p.S418*	NM_001166133.1	NP_001159605.1	Q86XX4	FRAS1_HUMAN	Fraser extracellular matrix complex subunit 1	418					cell communication (GO:0007154)|embryonic limb morphogenesis (GO:0030326)|metanephros morphogenesis (GO:0003338)|morphogenesis of an epithelium (GO:0002009)|palate development (GO:0060021)|protein transport (GO:0015031)|skin development (GO:0043588)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sublamina densa (GO:0061618)	metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(5)|lung(54)|prostate(7)|skin(2)|urinary_tract(4)	103						GACTGCACATCAGGTGGGTCC	0.512																																					p.S418X		.											FRAS1_ENST00000325942,NS,carcinoma,0,3	FRAS1_ENST00000325942	0	0			c.C1253A						.						50.0	53.0	52.0					4																	79204119		1997	4164	6161	SO:0001587	stop_gained	80144	exon12			GCACATCAGGTGG	AB040933	CCDS54772.1	4q21.21	2014-06-25	2014-06-25		ENSG00000138759	ENSG00000138759			19185	protein-coding gene	gene with protein product		607830	"""Fraser syndrome 1"""			12766769, 3118036	Standard	NM_025074		Approved	FLJ22031, FLJ14927, KIAA1500	uc003hlb.2	Q86XX4	OTTHUMG00000160856	ENST00000325942.6:c.1253C>A	4.37:g.79204119C>A	ENSP00000326330:p.Ser418*	Somatic	46	0		WXS	Illumina HiSeq	.	19	3	NM_001166133	A2RRR8|Q86UZ4|Q8N3U9|Q8NAU7|Q96JW7|Q9H6N9|Q9P228	Nonsense_Mutation	SNP	ENST00000325942.6	37	CCDS54772.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	21.6|21.6	4.168677|4.168677	0.78339|0.78339	.|.	.|.	ENSG00000138759|ENSG00000138759	ENST00000502446|ENST00000325942;ENST00000264895;ENST00000264899;ENST00000534913	.|.	.|.	.|.	5.6|5.6	4.67|4.67	0.58626|0.58626	.|.	.|1.016850	.|0.07870	.|N	.|0.967691	T|.	0.42494|.	0.1205|.	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.29305|.	-1.0016|.	3|.	.|0.09084	.|T	.|0.74	.|.	14.0839|14.0839	0.64942|0.64942	0.0:0.9223:0.0:0.0777|0.0:0.9223:0.0:0.0777	.|.	.|.	.|.	.|.	K|X	347|418;418;418;158	.|.	.|ENSP00000264895:S418X	Q|S	+|+	1|2	0|0	FRAS1|FRAS1	79423143|79423143	0.994000|0.994000	0.37717|0.37717	0.885000|0.885000	0.34714|0.34714	0.316000|0.316000	0.28119|0.28119	3.343000|3.343000	0.52167|0.52167	1.200000|1.200000	0.43188|0.43188	0.563000|0.563000	0.77884|0.77884	CAG|TCA	.		0.512	FRAS1-001	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000362706.2		
B2M	567	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	15	45007705	45007705	+	Missense_Mutation	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr15:45007705A>C	ENST00000558401.1	+	2	222	c.152A>C	c.(151-153)cAt>cCt	p.H51P	B2M_ENST00000559916.1_Missense_Mutation_p.H51P|B2M_ENST00000559220.1_Intron|B2M_ENST00000544417.1_Missense_Mutation_p.H51P	NM_004048.2	NP_004039.1	P61769	B2MG_HUMAN	beta-2-microglobulin	51	Ig-like C1-type.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent (GO:0002481)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|innate immune response (GO:0045087)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|protein refolding (GO:0042026)|regulation of defense response to virus by virus (GO:0050690)|regulation of immune response (GO:0050776)|response to cadmium ion (GO:0046686)|response to drug (GO:0042493)|response to molecule of bacterial origin (GO:0002237)|retina homeostasis (GO:0001895)|T cell differentiation in thymus (GO:0033077)|viral process (GO:0016032)	cytoplasm (GO:0005737)|early endosome lumen (GO:0031905)|early endosome membrane (GO:0031901)|endoplasmic reticulum lumen (GO:0005788)|ER to Golgi transport vesicle membrane (GO:0012507)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)			breast(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(30)|kidney(8)|large_intestine(6)|lung(6)|ovary(2)|skin(2)|urinary_tract(1)	59		all_cancers(109;1.88e-13)|all_epithelial(112;2.13e-11)|Lung NSC(122;2.22e-07)|all_lung(180;1.81e-06)|Melanoma(134;0.0122)		all cancers(107;4.16e-21)|GBM - Glioblastoma multiforme(94;8.97e-07)|COAD - Colon adenocarcinoma(120;0.0357)|Colorectal(105;0.0377)|Lung(196;0.0903)|LUSC - Lung squamous cell carcinoma(244;0.192)		TCTGGGTTTCATCCATCCGAC	0.418																																					p.H51P		.											.	.	.	0			c.A152C						.						190.0	193.0	192.0					15																	45007705		2198	4298	6496	SO:0001583	missense	567	exon2			GGTTTCATCCATC	AB021288	CCDS10113.1	15q21-q22.2	2013-01-11			ENSG00000166710	ENSG00000166710		"""Immunoglobulin superfamily / C1-set domain containing"""	914	protein-coding gene	gene with protein product		109700					Standard	NM_004048		Approved		uc001zuc.3	P61769	OTTHUMG00000131247	ENST00000558401.1:c.152A>C	15.37:g.45007705A>C	ENSP00000452780:p.His51Pro	Somatic	109	0		WXS	Illumina HiSeq	.	55	18	NM_004048	P01884|Q540F8|Q6IAT8|Q9UCK0|Q9UD48|Q9UDF4	Missense_Mutation	SNP	ENST00000558401.1	37	CCDS10113.1	.	.	.	.	.	.	.	.	.	.	A	21.7	4.187758	0.78789	.	.	ENSG00000166710	ENST00000349264;ENST00000544417;ENST00000396754	T	0.03065	4.06	6.03	6.03	0.97812	Immunoglobulin-like (1);Immunoglobulin C1-set (2);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.26666	0.0652	H	0.94423	3.535	0.58432	D	0.999999	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.996;0.999;0.997	T	0.16217	-1.0410	10	0.87932	D	0	.	12.95	0.58394	1.0:0.0:0.0:0.0	.	51;51;51	F5H6I0;A6XMH4;P61769	.;.;B2MG_HUMAN	P	51	ENSP00000437604:H51P	ENSP00000340858:H51P	H	+	2	0	B2M	42794997	1.000000	0.71417	0.999000	0.59377	0.700000	0.40528	6.818000	0.75257	2.308000	0.77769	0.533000	0.62120	CAT	.		0.418	B2M-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254007.2	NM_004048	
RFC2	5982	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	7	73661064	73661064	+	Missense_Mutation	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr7:73661064T>G	ENST00000055077.3	-	5	422	c.362A>C	c.(361-363)aAa>aCa	p.K121T	RFC2_ENST00000352131.3_Intron	NM_181471.1	NP_852136.1	P35250	RFC2_HUMAN	replication factor C (activator 1) 2, 40kDa	121					DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA strand elongation involved in DNA replication (GO:0006271)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	DNA replication factor C complex (GO:0005663)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|DNA binding (GO:0003677)			central_nervous_system(1)|endometrium(2)|large_intestine(1)|liver(1)|lung(3)	8						AGCAAACATTTTAATTTTATT	0.398																																					p.K121T		.											.	.	.	0			c.A362C						.						172.0	158.0	163.0					7																	73661064		2203	4300	6503	SO:0001583	missense	5982	exon5			AACATTTTAATTT		CCDS5567.1, CCDS5568.1, CCDS75618.1	7q11.23	2010-04-21	2002-08-29		ENSG00000049541	ENSG00000049541		"""ATPases / AAA-type"""	9970	protein-coding gene	gene with protein product	"""activator 1"""	600404	"""replication factor C (activator 1) 2 (40kD)"""			1313560, 7774928	Standard	NM_181471		Approved	A1, RFC40	uc003uaj.3	P35250	OTTHUMG00000023239	ENST00000055077.3:c.362A>C	7.37:g.73661064T>G	ENSP00000055077:p.Lys121Thr	Somatic	66	0		WXS	Illumina HiSeq	.	56	29	NM_181471	B5BU07|D3DXG3|P32846|Q9BU93	Missense_Mutation	SNP	ENST00000055077.3	37	CCDS5568.1	.	.	.	.	.	.	.	.	.	.	t	26.8	4.771119	0.90108	.	.	ENSG00000049541	ENST00000055077	T	0.44083	0.93	5.12	5.12	0.69794	ATPase, AAA-type, core (1);ATPase, AAA+ type, core (1);	0.000000	0.85682	D	0.000000	T	0.68943	0.3056	M	0.88450	2.955	0.80722	D	1	D	0.63046	0.992	D	0.75020	0.985	T	0.76055	-0.3099	10	0.87932	D	0	.	14.0527	0.64747	0.0:0.0:0.0:1.0	.	121	P35250	RFC2_HUMAN	T	121	ENSP00000055077:K121T	ENSP00000055077:K121T	K	-	2	0	RFC2	73299000	1.000000	0.71417	0.999000	0.59377	0.934000	0.57294	7.706000	0.84615	2.064000	0.61679	0.519000	0.50382	AAA	.		0.398	RFC2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252459.2	NM_181471	
PLD1	5337	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	3	171394504	171394504	+	Splice_Site	SNP	C	C	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr3:171394504C>T	ENST00000351298.4	-	18	2242		c.e18+1		PLD1_ENST00000340989.4_Splice_Site|PLD1_ENST00000342215.6_Splice_Site|PLD1_ENST00000356327.5_Splice_Site	NM_002662.4	NP_002653.1	Q13393	PLD1_HUMAN	phospholipase D1, phosphatidylcholine-specific						chemotaxis (GO:0006935)|defense response to Gram-positive bacterium (GO:0050830)|glycerophospholipid biosynthetic process (GO:0046474)|lipid catabolic process (GO:0016042)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylglycerol biosynthetic process (GO:0006655)|phospholipid metabolic process (GO:0006644)|Ras protein signal transduction (GO:0007265)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	N-acylphosphatidylethanolamine-specific phospholipase D activity (GO:0070290)|phosphatidylinositol binding (GO:0035091)|phospholipase D activity (GO:0004630)			breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(15)|lung(27)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	63	all_cancers(22;4.53e-19)|Ovarian(172;0.00197)|Breast(254;0.186)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)		Choline(DB00122)	CATCCAAGTACTTTTGTGAAG	0.527																																					.	NSCLC(149;2174 3517 34058)	.											.	.	.	0			c.2001+1G>A						.						94.0	90.0	91.0					3																	171394504		2203	4300	6503	SO:0001630	splice_region_variant	5337	exon18			CAAGTACTTTTGT	U38545	CCDS3216.1, CCDS46957.1	3q26	2013-01-10	2006-02-17		ENSG00000075651	ENSG00000075651	3.1.4.4	"""Pleckstrin homology (PH) domain containing"""	9067	protein-coding gene	gene with protein product	"""choline phosphatase 1"""	602382				9858822, 8530346	Standard	NM_002662		Approved		uc003fhs.3	Q13393	OTTHUMG00000156947	ENST00000351298.4:c.2115+1G>A	3.37:g.171394504C>T		Somatic	61	0		WXS	Illumina HiSeq	.	30	16	NM_001130081		Splice_Site	SNP	ENST00000351298.4	37	CCDS3216.1	.	.	.	.	.	.	.	.	.	.	C	19.90	3.913339	0.72983	.	.	ENSG00000075651	ENST00000356327;ENST00000351298;ENST00000342215;ENST00000340989	.	.	.	5.81	5.81	0.92471	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.089	0.97809	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	PLD1	172877198	1.000000	0.71417	0.999000	0.59377	0.617000	0.37484	7.818000	0.86416	2.752000	0.94435	0.557000	0.71058	.	.		0.527	PLD1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000346730.2	NM_002662	Intron
MDN1	23195	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	6	90449961	90449961	+	Missense_Mutation	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr6:90449961T>G	ENST00000369393.3	-	32	4700	c.4585A>C	c.(4585-4587)Aaa>Caa	p.K1529Q	MDN1_ENST00000428876.1_Missense_Mutation_p.K1529Q			Q9NU22	MDN1_HUMAN	MDN1, midasin homolog (yeast)	1529					ATP catabolic process (GO:0006200)|protein complex assembly (GO:0006461)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|unfolded protein binding (GO:0051082)			NS(1)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(22)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(52)|liver(1)|lung(83)|ovary(10)|pancreas(1)|prostate(10)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	218		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)		ACCTCCTTTTTTCCAAAGTCA	0.383																																					p.K1529Q		.											.	.	.	0			c.A4585C						.						91.0	91.0	91.0					6																	90449961		2203	4300	6503	SO:0001583	missense	23195	exon32			CCTTTTTTCCAAA	AF503925	CCDS5024.1	6q15	2014-01-28			ENSG00000112159	ENSG00000112159			18302	protein-coding gene	gene with protein product						9205841, 12102729	Standard	XM_005248699		Approved	KIAA0301	uc003pnn.1	Q9NU22	OTTHUMG00000015213	ENST00000369393.3:c.4585A>C	6.37:g.90449961T>G	ENSP00000358400:p.Lys1529Gln	Somatic	86	0		WXS	Illumina HiSeq	.	100	56	NM_014611	O15019|Q5T794	Missense_Mutation	SNP	ENST00000369393.3	37	CCDS5024.1	.	.	.	.	.	.	.	.	.	.	t	17.55	3.416809	0.62511	.	.	ENSG00000112159	ENST00000369393;ENST00000428876	T;T	0.40225	1.04;1.04	5.22	5.22	0.72569	ATPase, AAA+ type, core (1);ATPase, dynein-related, AAA domain (1);	0.000000	0.85682	D	0.000000	T	0.65101	0.2659	M	0.90814	3.15	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.73319	-0.4020	10	0.59425	D	0.04	.	15.4726	0.75453	0.0:0.0:0.0:1.0	.	1529	Q9NU22	MDN1_HUMAN	Q	1529	ENSP00000358400:K1529Q;ENSP00000413970:K1529Q	ENSP00000358400:K1529Q	K	-	1	0	MDN1	90506682	1.000000	0.71417	1.000000	0.80357	0.819000	0.46315	7.904000	0.87408	2.120000	0.65058	0.458000	0.33432	AAA	.		0.383	MDN1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041514.2		
VWA5B1	127731	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	20656759	20656759	+	Silent	SNP	C	C	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr1:20656759C>T	ENST00000375079.2	+	10	1537	c.1341C>T	c.(1339-1341)gtC>gtT	p.V447V	VWA5B1_ENST00000375083.4_Silent_p.V447V|VWA5B1_ENST00000289815.8_Silent_p.V447V|VWA5B1_ENST00000289825.4_Silent_p.V164V	NM_001039500.2	NP_001034589.2	Q5TIE3	VW5B1_HUMAN	von Willebrand factor A domain containing 5B1	447	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.					extracellular region (GO:0005576)				central_nervous_system(1)|endometrium(3)|kidney(1)|prostate(1)|skin(1)	7						TCAAGTGGGTCATCAGGCAGC	0.582																																					p.V447V		.											.	.	.	0			c.C1341T						.						82.0	82.0	82.0					1																	20656759		692	1591	2283	SO:0001819	synonymous_variant	127731	exon10			GTGGGTCATCAGG	AK125833, AK057346		1p36.12	2014-02-12			ENSG00000158816	ENSG00000158816			26538	protein-coding gene	gene with protein product							Standard	NM_001039500		Approved	FLJ32784	uc009vps.2	Q5TIE3	OTTHUMG00000002835	ENST00000375079.2:c.1341C>T	1.37:g.20656759C>T		Somatic	32	0		WXS	Illumina HiSeq	.	22	10	NM_001039500	A4IF35|A4IF36|Q3ZCM4|Q6ZUB4|Q96M71	Silent	SNP	ENST00000375079.2	37																																																																																				.		0.582	VWA5B1-001	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000007945.4	XM_001722222	
ROMO1	140823	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	20	34287659	34287659	+	Silent	SNP	G	G	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr20:34287659G>A	ENST00000374078.1	+	2	285	c.105G>A	c.(103-105)gcG>gcA	p.A35A	NFS1_ENST00000374085.1_5'Flank|NFS1_ENST00000306750.3_5'Flank|NFS1_ENST00000397425.1_5'Flank|ROMO1_ENST00000374072.1_Silent_p.A35A|ROMO1_ENST00000374077.3_Silent_p.A35A|NFS1_ENST00000541387.1_5'Flank|NFS1_ENST00000374092.4_5'Flank|NFS1_ENST00000540053.1_5'Flank|ROMO1_ENST00000397416.1_Silent_p.A35A|ROMO1_ENST00000336695.4_Silent_p.A35A	NM_080748.2	NP_542786.1	P60602	ROMO1_HUMAN	reactive oxygen species modulator 1	35					cellular response to reactive oxygen species (GO:0034614)|defense response to bacterium (GO:0042742)|positive regulation of cell proliferation (GO:0008284)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|replicative cell aging (GO:0001302)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)				cervix(1)	1						CGGCCGGGGCGCTCTTCGGCA	0.672											OREG0004048	type=REGULATORY REGION|Gene=NFS1|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																									p.A35A		.											.	.	.	0			c.G105A						.						84.0	89.0	88.0					20																	34287659		2203	4299	6502	SO:0001819	synonymous_variant	140823	exon2			CGGGGCGCTCTTC	AK000548	CCDS13264.1	20q11.22	2008-09-30	2008-09-30	2008-09-30	ENSG00000125995	ENSG00000125995			16185	protein-coding gene	gene with protein product	"""mitochondrial targeting GXXXG protein"""		"""chromosome 20 open reading frame 52"""	C20orf52		18313394, 17537404, 16842742	Standard	NM_080748		Approved	bA353C18.2, MTGMP	uc002xdy.3	P60602	OTTHUMG00000032360	ENST00000374078.1:c.105G>A	20.37:g.34287659G>A		Somatic	83	0	846	WXS	Illumina HiSeq	.	58	25	NM_080748	A7M872|E1P5R9|E9KL28|Q3MHD5|Q5QP16|Q9CQ98|Q9H1N2	Silent	SNP	ENST00000374078.1	37	CCDS13264.1																																																																																			.		0.672	ROMO1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000126404.1	NM_080748	
MRPL35	51318	hgsc.bcm.edu	37	2	86437740	86437740	+	Silent	SNP	C	C	T	rs1052060		TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr2:86437740C>T	ENST00000337109.4	+	4	550	c.516C>T	c.(514-516)taC>taT	p.Y172Y	MRPL35_ENST00000254644.8_Intron|MRPL35_ENST00000605125.1_3'UTR|MRPL35_ENST00000409180.1_Intron	NM_016622.3	NP_057706.2	Q9NZE8	RM35_HUMAN	mitochondrial ribosomal protein L35	172					translation (GO:0006412)	mitochondrial ribosome (GO:0005761)	structural constituent of ribosome (GO:0003735)	p.Y172Y(1)		cervix(1)|endometrium(1)|kidney(3)|large_intestine(1)|lung(4)|skin(1)|stomach(1)|urinary_tract(2)	14						GAAACTGGTACGTTGATGATC	0.373													C|||	1	0.000199681	0.0	0.0014	5008	,	,		17403	0.0		0.0	False		,,,				2504	0.0				p.Y172Y		.											MRPL35,NS,carcinoma,0,1	MRPL35	0	1	Substitution - coding silent(1)	lung(1)	c.C516T						.						101.0	94.0	96.0					2																	86437740		2203	4300	6503	SO:0001819	synonymous_variant	51318	exon4			CTGGTACGTTGAT	AF208849	CCDS1987.1, CCDS1988.1	2p11.2	2012-09-13			ENSG00000132313	ENSG00000132313		"""Mitochondrial ribosomal proteins / large subunits"""	14489	protein-coding gene	gene with protein product		611841				11042152, 11551941	Standard	NM_016622		Approved		uc002srg.4	Q9NZE8	OTTHUMG00000037385	ENST00000337109.4:c.516C>T	2.37:g.86437740C>T		Somatic	69	0		WXS	Illumina HiSeq	.	42	2	NM_016622	A6NKV6|B2RB93|Q658U7|Q8WWA2	Silent	SNP	ENST00000337109.4	37	CCDS1988.1																																																																																			.		0.373	MRPL35-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000091002.2	NM_016622	
GZF1	64412	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	20	23345474	23345474	+	Missense_Mutation	SNP	A	A	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr20:23345474A>G	ENST00000338121.5	+	2	531	c.454A>G	c.(454-456)Agc>Ggc	p.S152G	GZF1_ENST00000542987.1_Intron|GZF1_ENST00000544236.1_Intron|GZF1_ENST00000377051.2_Missense_Mutation_p.S152G			Q9H116	GZF1_HUMAN	GDNF-inducible zinc finger protein 1	152					branching involved in ureteric bud morphogenesis (GO:0001658)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001206)|sequence-specific DNA binding (GO:0043565)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(7)|prostate(1)|urinary_tract(2)	24	Lung NSC(19;0.0605)|Colorectal(13;0.0993)|all_lung(19;0.135)					GGTGGAGGTGAGCAGTGGCTC	0.498																																					p.S152G		.											.	.	.	0			c.A454G						.						62.0	67.0	65.0					20																	23345474		2203	4300	6503	SO:0001583	missense	64412	exon1			GAGGTGAGCAGTG	AK025447	CCDS13151.1	20p11.21	2013-01-09	2006-09-19	2006-09-19	ENSG00000125812	ENSG00000125812		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	15808	protein-coding gene	gene with protein product		613842	"""zinc finger protein 336"""	ZNF336		14522971, 16049025	Standard	NM_022482		Approved	dJ322G13.2, ZBTB23	uc002wsz.3	Q9H116	OTTHUMG00000032069	ENST00000338121.5:c.454A>G	20.37:g.23345474A>G	ENSP00000338290:p.Ser152Gly	Somatic	39	0		WXS	Illumina HiSeq	.	17	5	NM_022482	A8K199|B2RBC3|B3KPL4|B4DF58|D3DW39|Q54A22|Q96N08|Q9BQK9|Q9H117|Q9H6W6	Missense_Mutation	SNP	ENST00000338121.5	37	CCDS13151.1	.	.	.	.	.	.	.	.	.	.	A	1.741	-0.491755	0.04322	.	.	ENSG00000125812	ENST00000338121;ENST00000377051	T;T	0.10477	2.87;2.87	4.62	2.2	0.27929	.	0.265765	0.32533	N	0.005974	T	0.05823	0.0152	N	0.19112	0.55	0.09310	N	0.999999	B	0.06786	0.001	B	0.06405	0.002	T	0.37430	-0.9706	10	0.23891	T	0.37	.	6.4133	0.21702	0.5884:0.0:0.4116:0.0	.	152	Q9H116	GZF1_HUMAN	G	152	ENSP00000338290:S152G;ENSP00000366250:S152G	ENSP00000338290:S152G	S	+	1	0	GZF1	23293474	0.002000	0.14202	0.009000	0.14445	0.026000	0.11368	1.180000	0.32005	0.775000	0.33450	-0.417000	0.06048	AGC	.		0.498	GZF1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078333.1	NM_022482	
PXMP4	11264	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	20	32295759	32295759	+	Missense_Mutation	SNP	A	A	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr20:32295759A>G	ENST00000409299.3	-	4	484	c.392T>C	c.(391-393)tTg>tCg	p.L131S	PXMP4_ENST00000344022.3_Missense_Mutation_p.C65R|PXMP4_ENST00000217398.3_Missense_Mutation_p.C138R	NM_007238.4	NP_009169.3	Q9Y6I8	PXMP4_HUMAN	peroxisomal membrane protein 4, 24kDa	131						integral component of membrane (GO:0016021)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)				NS(1)|endometrium(2)|large_intestine(2)|lung(8)	13						GACGCGTGACAACAGGTACAT	0.488																																					p.L131S		.											.	.	.	0			c.T392C						.						50.0	48.0	49.0					20																	32295759		2203	4300	6503	SO:0001583	missense	11264	exon4			CGTGACAACAGGT	AF072864	CCDS13225.1, CCDS13226.1	20q11.22	2008-07-02	2002-08-29		ENSG00000101417	ENSG00000101417			15920	protein-coding gene	gene with protein product	"""24 kDa peroxisomal intrinsic membrane protein"""		"""peroxisomal membrane protein 4 (24kD)"""			10366717	Standard	NM_183397		Approved	PMP24	uc002wzv.3	Q9Y6I8	OTTHUMG00000032273	ENST00000409299.3:c.392T>C	20.37:g.32295759A>G	ENSP00000386385:p.Leu131Ser	Somatic	39	0		WXS	Illumina HiSeq	.	36	16	NM_007238	A2A2I7|Q9H0T4	Missense_Mutation	SNP	ENST00000409299.3	37	CCDS13225.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	a|a	10.88|10.88	1.476755|1.476755	0.26511|0.26511	.|.	.|.	ENSG00000101417|ENSG00000101417	ENST00000344022;ENST00000217398|ENST00000409299	.|T	.|0.29655	.|1.56	5.93|5.93	2.23|2.23	0.28157|0.28157	.|.	.|0.465348	.|0.22770	.|N	.|0.055845	T|T	0.39462|0.39462	0.1079|0.1079	.|.	.|.	.|.	0.09310|0.09310	N|N	1|1	B;B|P	0.11235|0.48589	0.004;0.001|0.912	B;B|P	0.09377|0.55303	0.004;0.002|0.773	T|T	0.14924|0.14924	-1.0455|-1.0455	7|9	0.62326|0.45353	D|T	0.03|0.12	-4.8709|-4.8709	7.3291|7.3291	0.26571|0.26571	0.6301:0.0:0.3699:0.0|0.6301:0.0:0.3699:0.0	.|.	138;65|131	B4DWH1;A2A2I7|Q9Y6I8	.;.|PXMP4_HUMAN	R|S	65;138|131	.|ENSP00000386385:L131S	ENSP00000217398:C138R|ENSP00000386385:L131S	C|L	-|-	1|2	0|0	PXMP4|PXMP4	31759420|31759420	0.939000|0.939000	0.31865|0.31865	0.000000|0.000000	0.03702|0.03702	0.557000|0.557000	0.35523|0.35523	3.714000|3.714000	0.54889|0.54889	0.136000|0.136000	0.18733|0.18733	0.519000|0.519000	0.50382|0.50382	TGT|TTG	.		0.488	PXMP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078739.2	NM_007238	
USP34	9736	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	2	61523963	61523963	+	Missense_Mutation	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr2:61523963A>C	ENST00000398571.2	-	30	4302	c.4226T>G	c.(4225-4227)aTg>aGg	p.M1409R		NM_014709.3	NP_055524.3	Q70CQ2	UBP34_HUMAN	ubiquitin specific peptidase 34	1409					positive regulation of canonical Wnt signaling pathway (GO:0090263)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|ubiquitin-dependent protein catabolic process (GO:0006511)|Wnt signaling pathway (GO:0016055)		cysteine-type endopeptidase activity (GO:0004197)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			autonomic_ganglia(1)|breast(14)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(24)|lung(52)|ovary(8)|prostate(10)|skin(6)|urinary_tract(2)	138			Epithelial(17;0.229)			CTGGAATGCCATCAACATATT	0.428																																					p.M1409R		.											.	.	.	0			c.T4226G						.						185.0	178.0	180.0					2																	61523963		1918	4140	6058	SO:0001583	missense	9736	exon30			AATGCCATCAACA	AB011142	CCDS42686.1	2p16.1-p15	2005-08-08	2005-08-08		ENSG00000115464	ENSG00000115464		"""Ubiquitin-specific peptidases"""	20066	protein-coding gene	gene with protein product		615295	"""ubiquitin specific protease 34"""			12838346	Standard	NM_014709		Approved	KIAA0570, KIAA0729	uc002sbe.3	Q70CQ2	OTTHUMG00000152265	ENST00000398571.2:c.4226T>G	2.37:g.61523963A>C	ENSP00000381577:p.Met1409Arg	Somatic	73	0		WXS	Illumina HiSeq	.	41	15	NM_014709	A8MWD0|B3KWU9|O60316|O94834|Q3B777|Q6P6C9|Q7L8P6|Q8N3T9|Q8TBW2|Q9UGA1	Missense_Mutation	SNP	ENST00000398571.2	37	CCDS42686.1	.	.	.	.	.	.	.	.	.	.	A	8.939	0.965294	0.18583	.	.	ENSG00000115464	ENST00000263989;ENST00000398569;ENST00000398571	T	0.02890	4.12	5.55	-0.0147	0.13979	.	0.302638	0.37761	N	0.001958	T	0.00998	0.0033	N	0.01874	-0.695	0.26183	N	0.979692	B	0.02656	0.0	B	0.06405	0.002	T	0.47156	-0.9139	10	0.19147	T	0.46	.	4.1772	0.10358	0.3894:0.0:0.2895:0.3211	.	1409	Q70CQ2	UBP34_HUMAN	R	1257;1257;1409	ENSP00000381577:M1409R	ENSP00000263989:M1257R	M	-	2	0	USP34	61377467	1.000000	0.71417	0.998000	0.56505	0.994000	0.84299	3.073000	0.50057	0.076000	0.16826	0.528000	0.53228	ATG	.		0.428	USP34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325650.4		
SLC12A1	6557	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	15	48580290	48580290	+	Nonsense_Mutation	SNP	A	A	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr15:48580290A>T	ENST00000558405.1	+	21	2694	c.2680A>T	c.(2680-2682)Aaa>Taa	p.K894*	SLC12A1_ENST00000380993.3_Nonsense_Mutation_p.K894*|SLC12A1_ENST00000396577.3_Nonsense_Mutation_p.K894*			Q13621	S12A1_HUMAN	solute carrier family 12 (sodium/potassium/chloride transporter), member 1	894					cell death (GO:0008219)|chemical homeostasis (GO:0048878)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|kidney development (GO:0001822)|potassium ion transport (GO:0006813)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	sodium:potassium:chloride symporter activity (GO:0008511)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|lung(30)|ovary(1)|prostate(2)|skin(1)	59		all_lung(180;0.00219)		all cancers(107;1.76e-09)|GBM - Glioblastoma multiforme(94;1.48e-06)	Bumetanide(DB00887)|Chlormerodrin(DB00534)|Chlorthalidone(DB00310)|Ethacrynic acid(DB00903)|Furosemide(DB00695)|Hydroflumethiazide(DB00774)|Methyclothiazide(DB00232)|Potassium Chloride(DB00761)|Quinethazone(DB01325)|Torasemide(DB00214)|Trichlormethiazide(DB01021)	GTTCAACCAGAAACTGGTGGA	0.403																																					p.K894X		.											.	.	.	0			c.A2680T						.						64.0	60.0	62.0					15																	48580290		2198	4297	6495	SO:0001587	stop_gained	6557	exon22			AACCAGAAACTGG		CCDS10129.2, CCDS53940.1	15q15-q21	2013-07-18	2013-07-18		ENSG00000074803	ENSG00000074803		"""Solute carriers"""	10910	protein-coding gene	gene with protein product		600839				8640224	Standard	NM_000338		Approved	NKCC2	uc010bem.3	Q13621	OTTHUMG00000131495	ENST00000558405.1:c.2680A>T	15.37:g.48580290A>T	ENSP00000453409:p.Lys894*	Somatic	78	0		WXS	Illumina HiSeq	.	56	24	NM_001184832	A8JYA2|E9PDW4	Nonsense_Mutation	SNP	ENST00000558405.1	37	CCDS10129.2	.	.	.	.	.	.	.	.	.	.	A	37	6.201723	0.97371	.	.	ENSG00000074803	ENST00000380993;ENST00000396577	.	.	.	5.87	4.68	0.58851	.	0.184455	0.56097	D	0.000027	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	12.5503	0.56223	0.7584:0.2416:0.0:0.0	.	.	.	.	X	894	.	ENSP00000370381:K894X	K	+	1	0	SLC12A1	46367582	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.663000	0.61532	2.371000	0.80710	0.533000	0.62120	AAA	.		0.403	SLC12A1-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417131.1		
PKD1L2	114780	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	16	81248669	81248669	+	RNA	SNP	A	A	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr16:81248669A>T	ENST00000525539.1	-	0	593				PKD1L2_ENST00000337114.4_RNA	NM_052892.3	NP_443124.3	Q7Z442	PK1L2_HUMAN	polycystic kidney disease 1-like 2						ion transport (GO:0006811)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(20)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44						GATCTGAAGGACGCCCGGCAT	0.647											OREG0023964	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R198R		.											.	.	.	0			c.T594A						.						18.0	23.0	21.0					16																	81248669		2003	4163	6166			114780	exon3			TGAAGGACGCCCG	AY164483	CCDS61998.1, CCDS61999.1	16q23.2	2014-09-11			ENSG00000166473	ENSG00000166473			21715	protein-coding gene	gene with protein product		607894				12782129	Standard	NM_052892		Approved	KIAA1879	uc002fgf.1	Q7Z442	OTTHUMG00000166126		16.37:g.81248669A>T		Somatic	51	0	1204	WXS	Illumina HiSeq	.	32	13	NM_001076780	Q6UEE1|Q6ZN46|Q6ZSP2|Q8N1H9|Q96CL2|Q96Q08	Silent	SNP	ENST00000525539.1	37																																																																																				.		0.647	PKD1L2-001	KNOWN	non_canonical_polymorphism|basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000387972.2		
CYP3A5	1577	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	7	99247744	99247744	+	Silent	SNP	T	T	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr7:99247744T>C	ENST00000222982.4	-	12	1464	c.1365A>G	c.(1363-1365)ctA>ctG	p.L455L	CYP3A5_ENST00000339843.2_3'UTR|CYP3A5_ENST00000343703.5_Silent_p.L445L	NM_000777.3	NP_000768.1	P20815	CP3A5_HUMAN	cytochrome P450, family 3, subfamily A, polypeptide 5	455					alkaloid catabolic process (GO:0009822)|drug catabolic process (GO:0042737)|oxidative demethylation (GO:0070989)|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)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity (GO:0016491)|oxygen binding (GO:0019825)			NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	16	all_epithelial(64;2.77e-08)|Lung NSC(181;0.00396)|all_lung(186;0.00659)|Esophageal squamous(72;0.0166)				ado-trastuzumab emtansine(DB05773)|Alfentanil(DB00802)|Alprazolam(DB00404)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Amprenavir(DB00701)|Apixaban(DB06605)|Aprepitant(DB00673)|Argatroban(DB00278)|Aripiprazole(DB01238)|Artemether(DB06697)|Astemizole(DB00637)|Atorvastatin(DB01076)|Axitinib(DB06626)|Azelastine(DB00972)|Beclomethasone(DB00394)|Boceprevir(DB08873)|Brentuximab vedotin(DB08870)|Buprenorphine(DB00921)|Buspirone(DB00490)|Cabazitaxel(DB06772)|Caffeine(DB00201)|Carbamazepine(DB00564)|Chloramphenicol(DB00446)|Chloroquine(DB00608)|Chlorphenamine(DB01114)|Cilostazol(DB01166)|Cimetidine(DB00501)|Ciprofloxacin(DB00537)|Cisapride(DB00604)|Clarithromycin(DB01211)|Clonidine(DB00575)|Clopidogrel(DB00758)|Cocaine(DB00907)|Codeine(DB00318)|Crizotinib(DB08865)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dapsone(DB00250)|Dasatinib(DB01254)|Daunorubicin(DB00694)|Delavirdine(DB00705)|Dexamethasone(DB01234)|Dextromethorphan(DB00514)|Diazepam(DB00829)|Diltiazem(DB00343)|Disulfiram(DB00822)|Docetaxel(DB01248)|Dolutegravir(DB08930)|Domperidone(DB01184)|Dutasteride(DB01126)|Enzalutamide(DB08899)|Eplerenone(DB00700)|Erlotinib(DB00530)|Erythromycin(DB00199)|Estradiol(DB00783)|Estrone(DB00655)|Ethosuximide(DB00593)|Etoposide(DB00773)|Felodipine(DB01023)|Fentanyl(DB00813)|Finasteride(DB01216)|Fluconazole(DB00196)|Fluoxetine(DB00472)|Flutamide(DB00499)|Fluticasone Propionate(DB00588)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Gefitinib(DB00317)|Gestodene(DB06730)|Granisetron(DB00889)|Halofantrine(DB01218)|Haloperidol(DB00502)|Hydrocortisone(DB00741)|Ifosfamide(DB01181)|Iloperidone(DB04946)|Imatinib(DB00619)|Indinavir(DB00224)|Irinotecan(DB00762)|Itraconazole(DB01167)|Ketoconazole(DB01026)|Lapatinib(DB01259)|Lercanidipine(DB00528)|Levomethadyl Acetate(DB01227)|Lidocaine(DB00281)|Losartan(DB00678)|Lovastatin(DB00227)|Methadone(DB00333)|Midazolam(DB00683)|Mifepristone(DB00834)|Modafinil(DB00745)|Mycophenolate mofetil(DB00688)|Nateglinide(DB00731)|Nefazodone(DB01149)|Nelfinavir(DB00220)|Nevirapine(DB00238)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Norethindrone(DB00717)|Norfloxacin(DB01059)|Nortriptyline(DB00540)|Ondansetron(DB00904)|Oxazepam(DB00842)|Oxcarbazepine(DB00776)|Oxybutynin(DB01062)|Oxycodone(DB00497)|Paclitaxel(DB01229)|Paliperidone(DB01267)|Pentamidine(DB00738)|Perampanel(DB08883)|Phenelzine(DB00780)|Phenobarbital(DB01174)|Phenytoin(DB00252)|Pimozide(DB01100)|Ponatinib(DB08901)|Pravastatin(DB00175)|Praziquantel(DB01058)|Progesterone(DB00396)|Propranolol(DB00571)|Quetiapine(DB01224)|Quinacrine(DB01103)|Quinine(DB00468)|Ranitidine(DB00863)|Reserpine(DB00206)|Rifampicin(DB01045)|Rifapentine(DB01201)|Risperidone(DB00734)|Ritonavir(DB00503)|Rivaroxaban(DB06228)|Rosuvastatin(DB01098)|Salmeterol(DB00938)|Saquinavir(DB01232)|Saxagliptin(DB06335)|Sildenafil(DB00203)|Simvastatin(DB00641)|Sirolimus(DB00877)|Sorafenib(DB00398)|Sulfasalazine(DB00795)|Sunitinib(DB01268)|Tacrolimus(DB00864)|Tamoxifen(DB00675)|Telithromycin(DB00976)|Temsirolimus(DB06287)|Teniposide(DB00444)|Testosterone(DB00624)|Thalidomide(DB01041)|Trazodone(DB00656)|Tretinoin(DB00755)|Triazolam(DB00897)|Troleandomycin(DB01361)|Udenafil(DB06267)|Valproic Acid(DB00313)|Vardenafil(DB00862)|Verapamil(DB00661)|Vincristine(DB00541)|Voriconazole(DB00582)|Zalcitabine(DB00943)|Zaleplon(DB00962)|Ziprasidone(DB00246)|Zolpidem(DB00425)	GGACTCTGATTAGAGCAAGTT	0.383																																					p.L455L		.											.	.	.	0			c.A1365G						.						218.0	194.0	202.0					7																	99247744		2203	4297	6500	SO:0001819	synonymous_variant	1577	exon12			TCTGATTAGAGCA	L26985	CCDS5672.1, CCDS55134.1	7q21.1	2007-12-14	2003-01-14		ENSG00000106258	ENSG00000106258		"""Cytochrome P450s"""	2638	protein-coding gene	gene with protein product		605325	"""cytochrome P450, subfamily IIIA (niphedipine oxidase), polypeptide 5"""				Standard	NR_033808		Approved	PCN3, P450PCN3, CP35		P20815	OTTHUMG00000156724	ENST00000222982.4:c.1365A>G	7.37:g.99247744T>C		Somatic	152	0		WXS	Illumina HiSeq	.	103	10	NM_000777	A4D289|B7Z5I7|Q53WY8|Q75MV0|Q9HB56	Silent	SNP	ENST00000222982.4	37	CCDS5672.1																																																																																			.		0.383	CYP3A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345469.1		
HIRA	7290	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	22	19373053	19373053	+	Silent	SNP	A	A	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr22:19373053A>G	ENST00000263208.5	-	12	1576	c.1320T>C	c.(1318-1320)gaT>gaC	p.D440D	HIRA_ENST00000340170.4_Silent_p.D440D|HIRA_ENST00000541063.1_Silent_p.D396D|HIRA_ENST00000546308.1_Silent_p.D396D	NM_003325.3	NP_003316.3	P54198	HIRA_HUMAN	histone cell cycle regulator	440	Interaction with ASF1A.|Interaction with CCNA1.|Required for repression of histone gene transcription.				anatomical structure morphogenesis (GO:0009653)|chromatin modification (GO:0016568)|DNA replication-independent nucleosome assembly (GO:0006336)|gastrulation (GO:0007369)|muscle cell differentiation (GO:0042692)|osteoblast differentiation (GO:0001649)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(14)|ovary(2)|prostate(1)|skin(1)	37	Colorectal(54;0.0993)					CCTTCCTGATATCTTCAAGAC	0.597																																					p.D440D		.											.	.	.	0			c.T1320C						.						79.0	72.0	74.0					22																	19373053		2203	4300	6503	SO:0001819	synonymous_variant	7290	exon12			CCTGATATCTTCA	X75296	CCDS13759.1	22q11.2	2013-05-03	2013-05-03		ENSG00000100084	ENSG00000100084		"""WD repeat domain containing"""	4916	protein-coding gene	gene with protein product	"""DiGeorge critical region gene 1"""	600237	"""HIR (histone cell cycle regulation defective) homolog A (S. cerevisiae)"", ""HIR histone cell cycle regulation defective homolog A (S. cerevisiae)"""	TUPLE1		8111380, 7633437, 9731536	Standard	NM_003325		Approved	DGCR1, TUP1	uc002zpf.1	P54198	OTTHUMG00000150134	ENST00000263208.5:c.1320T>C	22.37:g.19373053A>G		Somatic	26	0		WXS	Illumina HiSeq	.	20	10	NM_003325	Q05BU9|Q8IXN2	Silent	SNP	ENST00000263208.5	37	CCDS13759.1																																																																																			.		0.597	HIRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316488.2	NM_003325	
IGF2R	3482	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	6	160511104	160511104	+	Silent	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr6:160511104A>C	ENST00000356956.1	+	44	6772	c.6624A>C	c.(6622-6624)ggA>ggC	p.G2208G		NM_000876.2	NP_000867	P11717	MPRI_HUMAN	insulin-like growth factor 2 receptor	2208					insulin-like growth factor receptor signaling pathway (GO:0048009)|liver development (GO:0001889)|organ regeneration (GO:0031100)|positive regulation of apoptotic process (GO:0043065)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|response to retinoic acid (GO:0032526)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)	cell surface (GO:0009986)|clathrin coat (GO:0030118)|endocytic vesicle (GO:0030139)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)|nuclear envelope lumen (GO:0005641)|perinuclear region of cytoplasm (GO:0048471)|trans-Golgi network transport vesicle (GO:0030140)	G-protein coupled receptor activity (GO:0004930)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|insulin-like growth factor-activated receptor activity (GO:0005010)|mannose binding (GO:0005537)|phosphoprotein binding (GO:0051219)|receptor activity (GO:0004872)|retinoic acid binding (GO:0001972)|transporter activity (GO:0005215)			breast(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(27)|lung(31)|ovary(3)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	95		Breast(66;0.000777)|Ovarian(120;0.0305)		OV - Ovarian serous cystadenocarcinoma(65;2.45e-17)|BRCA - Breast invasive adenocarcinoma(81;1.09e-05)	Mecasermin(DB01277)	GGAAAGTTGGAACCTCTGACA	0.478																																					p.G2208G		.											.	.	.	0			c.A6624C						.						74.0	68.0	70.0					6																	160511104		2203	4300	6503	SO:0001819	synonymous_variant	3482	exon44			AGTTGGAACCTCT	J03528	CCDS5273.1	6q25.3	2014-09-16			ENSG00000197081	ENSG00000197081		"""CD molecules"""	5467	protein-coding gene	gene with protein product	"""cation-independent mannose-6 phosphate receptor"""	147280					Standard	NM_000876		Approved	CD222, MPRI, MPR1, CIMPR, M6P-R	uc003qta.3	P11717	OTTHUMG00000015945	ENST00000356956.1:c.6624A>C	6.37:g.160511104A>C		Somatic	80	0		WXS	Illumina HiSeq	.	68	18	NM_000876	Q7Z7G9|Q96PT5	Silent	SNP	ENST00000356956.1	37	CCDS5273.1																																																																																			.		0.478	IGF2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042931.1	NM_000876	
PRG4	10216	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	186277684	186277684	+	Missense_Mutation	SNP	A	A	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr1:186277684A>G	ENST00000445192.2	+	7	2878	c.2833A>G	c.(2833-2835)Aca>Gca	p.T945A	PRG4_ENST00000367485.4_Missense_Mutation_p.T852A|PRG4_ENST00000367486.3_Missense_Mutation_p.T902A|PRG4_ENST00000367484.3_Missense_Mutation_p.T474A|PRG4_ENST00000367483.4_Missense_Mutation_p.T904A	NM_005807.3	NP_005798.2	Q92954	PRG4_HUMAN	proteoglycan 4	945					cell proliferation (GO:0008283)|hematopoietic stem cell proliferation (GO:0071425)|immune response (GO:0006955)|negative regulation of interleukin-6 biosynthetic process (GO:0045409)|regulation of cell proliferation (GO:0042127)	extracellular space (GO:0005615)	polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(33)|prostate(7)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(1)	102						AGCAACTACAACAGAAAAAAC	0.378																																					p.T945A		.											.	.	.	0			c.A2833G						.						208.0	224.0	219.0					1																	186277684		2203	4300	6503	SO:0001583	missense	10216	exon7			ACTACAACAGAAA	U70136	CCDS1369.1, CCDS44287.1, CCDS44288.1	1q25-q31	2008-07-18	2004-11-15		ENSG00000116690	ENSG00000116690			9364	protein-coding gene	gene with protein product	"""lubricin"", ""megakaryocyte stimulating factor"", ""articular superficial zone protein"", ""Jacobs camptodactyly-arthropathy-pericarditis syndrome"", ""camptodactyly, arthropathy, coxa vara, pericarditis syndrome"", ""bG174L6.2 (MSF: megakaryocyte stimulating factor )"""	604283	"""proteoglycan 4, (megakaryocyte stimulating factor, articular superficial zone protein, camptodactyly, arthropathy, coxa vara, pericarditis syndrome)"""	CACP		10545950, 9920774	Standard	NM_005807		Approved	JCAP, SZP, MSF, HAPO, bG174L6.2, FLJ32635	uc001gru.4	Q92954	OTTHUMG00000035574	ENST00000445192.2:c.2833A>G	1.37:g.186277684A>G	ENSP00000399679:p.Thr945Ala	Somatic	76	0		WXS	Illumina HiSeq	.	94	54	NM_005807	Q6DNC4|Q6DNC5|Q6ZMZ5|Q9BX49	Missense_Mutation	SNP	ENST00000445192.2	37	CCDS1369.1	.	.	.	.	.	.	.	.	.	.	A	8.502	0.864593	0.17250	.	.	ENSG00000116690	ENST00000367486;ENST00000367484;ENST00000367482;ENST00000367483;ENST00000367485;ENST00000445192	T;T;T;T;T	0.04758	3.56;3.59;3.68;3.57;3.68	3.53	-2.87	0.05700	.	1.069190	0.07425	U	0.894627	T	0.02418	0.0074	N	0.17474	0.49	0.09310	N	1	B;B;B;B	0.25312	0.123;0.047;0.028;0.047	B;B;B;B	0.16289	0.015;0.009;0.004;0.009	T	0.48364	-0.9042	10	0.10636	T	0.68	1.6111	5.2784	0.15663	0.5017:0.2609:0.2373:0.0	.	811;852;945;904	Q92954-4;Q92954-3;Q92954;Q92954-2	.;.;PRG4_HUMAN;.	A	902;474;811;904;852;945	ENSP00000356456:T902A;ENSP00000356454:T474A;ENSP00000356453:T904A;ENSP00000356455:T852A;ENSP00000399679:T945A	ENSP00000356452:T811A	T	+	1	0	PRG4	184544307	0.157000	0.22836	0.001000	0.08648	0.155000	0.21991	0.568000	0.23623	-0.523000	0.06409	0.352000	0.21897	ACA	.		0.378	PRG4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000086346.1	NM_005807	
SBF2	81846	hgsc.bcm.edu	37	11	9801363	9801363	+	3'UTR	SNP	G	G	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr11:9801363G>A	ENST00000256190.8	-	0	6289				SBF2-AS1_ENST00000525636.1_RNA|SBF2-AS1_ENST00000499953.2_RNA|SBF2-AS1_ENST00000498905.2_RNA|SBF2-AS1_ENST00000527406.1_RNA|SBF2-AS1_ENST00000534671.1_RNA	NM_030962.3	NP_112224.1	Q86WG5	MTMRD_HUMAN	SET binding factor 2						cell death (GO:0008219)|myelination (GO:0042552)|positive regulation of Rab GTPase activity (GO:0032851)|protein tetramerization (GO:0051262)	membrane (GO:0016020)|vacuolar membrane (GO:0005774)	phosphatase activity (GO:0016791)|phosphatase regulator activity (GO:0019208)|phosphatidylinositol binding (GO:0035091)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(4)|endometrium(8)|kidney(2)|large_intestine(8)|lung(16)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	48				all cancers(16;2.88e-11)|Epithelial(150;3.61e-10)|BRCA - Breast invasive adenocarcinoma(625;0.00887)		TTTTCCATCAGAATAATGCTG	0.468																																					.		.											.	.	.	0			.						.																																			SO:0001624	3_prime_UTR_variant	81846	.			CCATCAGAATAAT	AB051553	CCDS31427.1	11p15.3	2014-09-17	2004-11-12	2004-11-12	ENSG00000133812	ENSG00000133812		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"", ""DENN/MADD domain containing"", ""Pleckstrin homology (PH) domain containing"""	2135	protein-coding gene	gene with protein product	"""myotubularin related 13"""	607697	"""Charcot-Marie-Tooth neuropathy 4B2 (autosomal recessive, with myelin outfolding)"", ""DENN/MADD domain containing 7B"""	CMT4B2		10644431	Standard	NM_030962		Approved	KIAA1766, MTMR13, DENND7B	uc001mib.2	Q86WG5	OTTHUMG00000165890	ENST00000256190.8:c.*602C>T	11.37:g.9801363G>A		Somatic	15	0		WXS	Illumina HiSeq	.	18	4	.	Q3MJF0|Q68DQ3|Q6P459|Q6PJD1|Q7Z325|Q7Z621|Q86VE2|Q96FE2|Q9C097	RNA	SNP	ENST00000256190.8	37	CCDS31427.1																																																																																			.		0.468	SBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386911.2	NM_030962	
FOXA2	3170	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	20	22563329	22563329	+	Missense_Mutation	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr20:22563329T>G	ENST00000377115.4	-	3	714	c.533A>C	c.(532-534)aAg>aCg	p.K178T	FOXA2_ENST00000419308.2_Missense_Mutation_p.K184T	NM_153675.2	NP_710141.1	Q9Y261	FOXA2_HUMAN	forkhead box A2	178					adult locomotory behavior (GO:0008344)|cell development (GO:0048468)|cell differentiation in hindbrain (GO:0021533)|cell fate specification (GO:0001708)|chromatin modification (GO:0016568)|connective tissue development (GO:0061448)|dopaminergic neuron differentiation (GO:0071542)|dorsal/ventral neural tube patterning (GO:0021904)|ectoderm formation (GO:0001705)|endocrine pancreas development (GO:0031018)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|in utero embryonic development (GO:0001701)|lung epithelial cell differentiation (GO:0060487)|negative regulation of detection of glucose (GO:2000971)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|negative regulation of glucokinase activity (GO:0033132)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter by glucose (GO:0000433)|neuron fate specification (GO:0048665)|positive regulation of cell-cell adhesion mediated by cadherin (GO:2000049)|positive regulation of embryonic development (GO:0040019)|positive regulation of gastrulation (GO:2000543)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of smoothened signaling pathway (GO:0045880)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter by glucose (GO:0000432)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of transcription, DNA-templated (GO:0045893)|primitive streak formation (GO:0090009)|regulation of blood coagulation (GO:0030193)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|regulation of steroid metabolic process (GO:0019218)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase II promoter involved in detection of glucose (GO:2000976)|response to interleukin-6 (GO:0070741)|signal transduction involved in regulation of gene expression (GO:0023019)|somite rostral/caudal axis specification (GO:0032525)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|central_nervous_system(3)|endometrium(7)|kidney(2)|large_intestine(1)|lung(3)|ovary(2)|prostate(2)|urinary_tract(1)	22	Lung NSC(19;0.188)					CGTCAGCATCTTGTTGGGGCT	0.612																																					p.K184T		.											.	.	.	0			c.A551C						.						133.0	115.0	121.0					20																	22563329		2203	4300	6503	SO:0001583	missense	3170	exon2			AGCATCTTGTTGG	AF147787	CCDS13147.1, CCDS46585.1	20p11	2008-04-10		2002-09-20	ENSG00000125798	ENSG00000125798		"""Forkhead boxes"""	5022	protein-coding gene	gene with protein product		600288	"""hepatocyte nuclear factor 3, beta"""	HNF3B		9119385, 11875061	Standard	NM_153675		Approved		uc002wsm.3	Q9Y261	OTTHUMG00000032041	ENST00000377115.4:c.533A>C	20.37:g.22563329T>G	ENSP00000366319:p.Lys178Thr	Somatic	50	0		WXS	Illumina HiSeq	.	54	21	NM_021784	Q8WUW4|Q96DF7	Missense_Mutation	SNP	ENST00000377115.4	37	CCDS13147.1	.	.	.	.	.	.	.	.	.	.	T	20.6	4.009805	0.75046	.	.	ENSG00000125798	ENST00000377115;ENST00000419308;ENST00000319993;ENST00000444877	D;D;D	0.96334	-3.98;-3.98;-3.98	4.98	4.98	0.66077	Winged helix-turn-helix transcription repressor DNA-binding (1);Transcription factor, fork head (3);	0.000000	0.64402	U	0.000006	D	0.98651	0.9548	H	0.95982	3.75	0.80722	D	1	D;D	0.76494	0.992;0.999	P;D	0.74023	0.882;0.982	D	0.99675	1.0997	10	0.87932	D	0	.	14.3356	0.66586	0.0:0.0:0.0:1.0	.	178;184	Q9Y261;B0ZTD4	FOXA2_HUMAN;.	T	178;178;184;64	ENSP00000366319:K178T;ENSP00000400341:K178T;ENSP00000315955:K184T	ENSP00000315955:K184T	K	-	2	0	FOXA2	22511329	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.971000	0.88012	1.867000	0.54127	0.468000	0.43344	AAG	.		0.612	FOXA2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000078289.1		
KIAA1462	57608	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	10	30315724	30315724	+	Missense_Mutation	SNP	G	G	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr10:30315724G>C	ENST00000375377.1	-	3	3454	c.3353C>G	c.(3352-3354)gCc>gGc	p.A1118G		NM_020848.2	NP_065899.1	Q9P266	JCAD_HUMAN	KIAA1462	1118					cell adhesion (GO:0007155)	cell-cell junction (GO:0005911)				breast(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|lung(23)|ovary(6)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)	75						TGGGGTGCAGGCACTTGCATC	0.637																																					p.A1118G		.											.	.	.	0			c.C3353G						.						43.0	46.0	45.0					10																	30315724		2001	4179	6180	SO:0001583	missense	57608	exon3			GTGCAGGCACTTG	AB040895	CCDS41500.1	10p12.1	2013-04-23			ENSG00000165757	ENSG00000165757			29283	protein-coding gene	gene with protein product	"""junctional protein associated with coronary artery disease"""	614398				10819331, 21884682	Standard	NM_020848		Approved	JCAD	uc001iux.3	Q9P266	OTTHUMG00000017885	ENST00000375377.1:c.3353C>G	10.37:g.30315724G>C	ENSP00000364526:p.Ala1118Gly	Somatic	39	0		WXS	Illumina HiSeq	.	20	11	NM_020848	Q5HYA7|Q5T992|Q86WZ9|Q9BYJ2	Missense_Mutation	SNP	ENST00000375377.1	37	CCDS41500.1	.	.	.	.	.	.	.	.	.	.	G	16.51	3.143708	0.57044	.	.	ENSG00000165757	ENST00000375377	T	0.15017	2.46	4.79	2.91	0.33838	.	0.716055	0.13614	N	0.374894	T	0.20536	0.0494	M	0.61703	1.905	0.09310	N	1	B	0.27679	0.185	B	0.29716	0.106	T	0.16012	-1.0417	10	0.62326	D	0.03	-8.4635	10.2699	0.43477	0.0753:0.1364:0.7883:0.0	.	1118	Q9P266	K1462_HUMAN	G	1118	ENSP00000364526:A1118G	ENSP00000364526:A1118G	A	-	2	0	KIAA1462	30355730	0.001000	0.12720	0.008000	0.14137	0.014000	0.08584	0.810000	0.27183	0.536000	0.28733	0.462000	0.41574	GCC	.		0.637	KIAA1462-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047409.1	NM_020848	
CCDC144A	9720	hgsc.bcm.edu	37	17	16705681	16705681	+	3'UTR	SNP	G	G	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr17:16705681G>A	ENST00000443444.2	+	0	6826				RP11-219A15.2_ENST00000582895.1_lincRNA|RP11-219A15.4_ENST00000602730.1_RNA|USP32P1_ENST00000393005.2_RNA|RP11-219A15.1_ENST00000448331.3_3'UTR			A2RUR9	C144A_HUMAN	coiled-coil domain containing 144A																		CAAAAAGATGGCAGACACAAG	0.443																																					.		.											.	.	.	0			.						.																																			SO:0001624	3_prime_UTR_variant	162632	.			AAGATGGCAGACA	BC133019	CCDS45621.1	17p11.2	2008-10-23			ENSG00000170160	ENSG00000170160			29072	protein-coding gene	gene with protein product						9628581, 11997339	Standard	NM_014695		Approved	KIAA0565, FLJ43983	uc002gqk.1	A2RUR9	OTTHUMG00000059178	ENST00000443444.2:c.*2402G>A	17.37:g.16705681G>A		Somatic	176	0		WXS	Illumina HiSeq	.	113	43	.	O60311|Q6ZU57	RNA	SNP	ENST00000443444.2	37	CCDS45621.1																																																																																			.		0.443	CCDC144A-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding			
SLC2A2	6514	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	3	170715825	170715825	+	Missense_Mutation	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr3:170715825A>C	ENST00000314251.3	-	11	1521	c.1442T>G	c.(1441-1443)tTt>tGt	p.F481C	SLC2A2_ENST00000382808.4_Missense_Mutation_p.F362C	NM_000340.1	NP_000331.1	P11168	GTR2_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 2	481					carbohydrate metabolic process (GO:0005975)|endocrine pancreas development (GO:0031018)|energy reserve metabolic process (GO:0006112)|glucose transport (GO:0015758)|hexose transmembrane transport (GO:0035428)|hexose transport (GO:0008645)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	brush border (GO:0005903)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	D-glucose transmembrane transporter activity (GO:0055056)|dehydroascorbic acid transporter activity (GO:0033300)|glucose transmembrane transporter activity (GO:0005355)|hexose transmembrane transporter activity (GO:0015149)			central_nervous_system(1)|endometrium(2)|large_intestine(9)|lung(9)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24	all_cancers(22;1.41e-19)|all_lung(20;1.59e-15)|Lung NSC(18;7.08e-15)|Ovarian(172;0.00197)|Breast(254;0.122)		LUSC - Lung squamous cell carcinoma(14;1.1e-14)|Lung(28;2.99e-14)		Streptozocin(DB00428)	AACTTTAAAAAATGTGAACAG	0.433																																					p.F481C		.											.	.	.	0			c.T1442G						.						45.0	49.0	48.0					3																	170715825		2202	4300	6502	SO:0001583	missense	6514	exon11			TTAAAAAATGTGA	J03810	CCDS3215.1	3q26.2-q27	2013-05-22			ENSG00000163581	ENSG00000163581		"""Solute carriers"""	11006	protein-coding gene	gene with protein product		138160		GLUT2		1852621	Standard	NM_000340		Approved		uc003fhe.1	P11168	OTTHUMG00000158997	ENST00000314251.3:c.1442T>G	3.37:g.170715825A>C	ENSP00000323568:p.Phe481Cys	Somatic	40	0		WXS	Illumina HiSeq	.	47	22	NM_000340	A8K481|B2R936|B7Z547|F8W8V8|Q9UCW9	Missense_Mutation	SNP	ENST00000314251.3	37	CCDS3215.1	.	.	.	.	.	.	.	.	.	.	A	19.64	3.865619	0.71949	.	.	ENSG00000163581	ENST00000314251;ENST00000382808	T;T	0.76186	-1.0;-1.0	6.17	3.65	0.41850	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.195940	0.56097	D	0.000033	D	0.83658	0.5302	M	0.81682	2.555	0.40130	D	0.976703	D	0.59767	0.986	D	0.64687	0.928	D	0.85151	0.0986	10	0.72032	D	0.01	.	9.9466	0.41613	0.5217:0.0:0.0:0.4783	.	481	P11168	GTR2_HUMAN	C	481;362	ENSP00000323568:F481C;ENSP00000372258:F362C	ENSP00000323568:F481C	F	-	2	0	SLC2A2	172198519	0.997000	0.39634	0.977000	0.42913	0.962000	0.63368	2.493000	0.45320	1.120000	0.41904	0.533000	0.62120	TTT	.		0.433	SLC2A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352834.1	NM_000340	
ZFYVE9	9372	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	52732339	52732339	+	Missense_Mutation	SNP	A	A	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr1:52732339A>G	ENST00000371591.1	+	5	2422	c.2291A>G	c.(2290-2292)gAg>gGg	p.E764G	ZFYVE9_ENST00000357206.2_Intron|ZFYVE9_ENST00000287727.3_Missense_Mutation_p.E764G	NM_004799.2|NM_007324.2	NP_004790.2|NP_015563.2	O95405	ZFYV9_HUMAN	zinc finger, FYVE domain containing 9	764					endocytosis (GO:0006897)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|proteolysis (GO:0006508)|SMAD protein complex assembly (GO:0007183)|SMAD protein import into nucleus (GO:0007184)|transforming growth factor beta receptor signaling pathway (GO:0007179)	early endosome (GO:0005769)|early endosome membrane (GO:0031901)	1-phosphatidylinositol binding (GO:0005545)|metal ion binding (GO:0046872)|serine-type peptidase activity (GO:0008236)			breast(1)|central_nervous_system(4)|endometrium(3)|kidney(1)|large_intestine(12)|lung(17)|ovary(2)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(6)	53						CAAGCCTGGGAGAACATGATG	0.448																																					p.E764G		.											.	.	.	0			c.A2291G						.						158.0	144.0	149.0					1																	52732339		2203	4300	6503	SO:0001583	missense	9372	exon6			CCTGGGAGAACAT	AF104304	CCDS563.1, CCDS564.1	1p32.3	2014-06-13	2004-05-21	2004-05-26	ENSG00000157077	ENSG00000157077		"""Zinc fingers, FYVE domain containing"""	6775	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 173"""	603755	"""MAD, mothers against decapentaplegic homolog (Drosophila) interacting protein, receptor activation anchor"""	MADHIP		9865696	Standard	NM_007324		Approved	SMADIP, SARA, PPP1R173	uc001cto.4	O95405	OTTHUMG00000008061	ENST00000371591.1:c.2291A>G	1.37:g.52732339A>G	ENSP00000360647:p.Glu764Gly	Somatic	61	0		WXS	Illumina HiSeq	.	60	18	NM_004799	Q5T0F6|Q5T0F7|Q9UNE1|Q9Y5R7	Missense_Mutation	SNP	ENST00000371591.1	37	CCDS563.1	.	.	.	.	.	.	.	.	.	.	A	19.31	3.803913	0.70682	.	.	ENSG00000157077	ENST00000287727;ENST00000371591	T;T	0.42900	0.96;0.96	5.45	5.45	0.79879	Zinc finger, FYVE/PHD-type (1);	0.000000	0.64402	D	0.000001	T	0.54351	0.1853	L	0.33485	1.01	0.58432	D	0.999999	D	0.89917	1.0	D	0.76071	0.987	T	0.58405	-0.7642	10	0.87932	D	0	.	15.5095	0.75769	1.0:0.0:0.0:0.0	.	764	O95405	ZFYV9_HUMAN	G	764	ENSP00000287727:E764G;ENSP00000360647:E764G	ENSP00000287727:E764G	E	+	2	0	ZFYVE9	52504927	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.830000	0.92063	2.065000	0.61736	0.496000	0.49642	GAG	.		0.448	ZFYVE9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022083.1	NM_007324	
HSD17B14	51171	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	19	49339067	49339067	+	Missense_Mutation	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr19:49339067T>G	ENST00000263278.4	-	2	388	c.122A>C	c.(121-123)aAg>aCg	p.K41T	HSD17B14_ENST00000599157.1_Missense_Mutation_p.K41T	NM_016246.2	NP_057330.2	Q9BPX1	DHB14_HUMAN	hydroxysteroid (17-beta) dehydrogenase 14	41					steroid catabolic process (GO:0006706)	cytosol (GO:0005829)	estradiol 17-beta-dehydrogenase activity (GO:0004303)|testosterone 17-beta-dehydrogenase (NADP+) activity (GO:0047045)			large_intestine(3)|lung(1)|skin(1)	5		all_epithelial(76;7e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000341)|all cancers(93;0.000764)|GBM - Glioblastoma multiforme(486;0.0233)|Epithelial(262;0.0346)		CTCACCATCCTTGTCGCAGAT	0.612											OREG0025610	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.K41T		.											.	.	.	0			c.A122C						.						99.0	83.0	89.0					19																	49339067		2203	4299	6502	SO:0001583	missense	51171	exon2			CCATCCTTGTCGC	AF126781	CCDS12736.1	19q13.33	2011-09-14	2006-11-22	2006-11-22		ENSG00000087076		"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"""	23238	protein-coding gene	gene with protein product	"""retinal short-chain dehydrogenase/reductase 3"", ""short chain dehydrogenase/reductase family 47C, member 1"""	612832	"""dehydrogenase/reductase (SDR family) member 10"""	DHRS10		10800688, 17067289, 19027726	Standard	XM_005258969		Approved	retSDR3, SDR47C1	uc002pkv.1	Q9BPX1		ENST00000263278.4:c.122A>C	19.37:g.49339067T>G	ENSP00000263278:p.Lys41Thr	Somatic	36	0	961	WXS	Illumina HiSeq	.	22	9	NM_016246	Q9UKU3	Missense_Mutation	SNP	ENST00000263278.4	37	CCDS12736.1	.	.	.	.	.	.	.	.	.	.	-	7.168	0.587023	0.13749	.	.	ENSG00000087076	ENST00000263278	T	0.21191	2.02	2.96	2.96	0.34315	NAD(P)-binding domain (1);	0.286281	0.27966	N	0.017129	T	0.10121	0.0248	N	0.11154	0.105	0.34385	D	0.693501	B	0.24186	0.099	B	0.27887	0.084	T	0.18967	-1.0320	10	0.22706	T	0.39	.	7.7492	0.28888	0.0:0.0:0.0:1.0	.	41	Q9BPX1	DHB14_HUMAN	T	41	ENSP00000263278:K41T	ENSP00000263278:K41T	K	-	2	0	HSD17B14	54030879	1.000000	0.71417	0.998000	0.56505	0.065000	0.16274	2.091000	0.41691	1.593000	0.50029	0.370000	0.22315	AAG	.		0.612	HSD17B14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466212.1	NM_016246	
DPY19L2P2	349152	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	7	102920595	102920595	+	RNA	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr7:102920595T>G	ENST00000312132.4	-	0	262							Q6ZN68	D19P2_HUMAN	DPY19L2 pseudogene 2							integral component of membrane (GO:0016021)	transferase activity, transferring glycosyl groups (GO:0016757)										TCCTTGTTTCTTCATAATTCC	0.627																																					.		.											.	.	.	0			.						.																																					349152	.			TGTTTCTTCATAA	AL834175		7q22.1	2013-09-12	2013-09-12		ENSG00000170629	ENSG00000170629			21764	pseudogene	pseudogene			"""dpy-19-like 2 pseudogene 2 (C. elegans)"""				Standard	NR_027768		Approved	DKFZp434E092, FLJ36166	uc003vbh.4	Q6ZN68	OTTHUMG00000157200		7.37:g.102920595T>G		Somatic	63	0		WXS	Illumina HiSeq	.	32	10	.	Q8N9V4|Q8ND62	RNA	SNP	ENST00000312132.4	37																																																																																				.		0.627	DPY19L2P2-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000347877.1	NM_182634	
AGFG1	3267	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	2	228401415	228401415	+	Missense_Mutation	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr2:228401415T>G	ENST00000310078.8	+	9	1540	c.1280T>G	c.(1279-1281)tTt>tGt	p.F427C	AGFG1_ENST00000409315.1_Missense_Mutation_p.F406C|AGFG1_ENST00000409171.1_Missense_Mutation_p.F427C|AGFG1_ENST00000373671.3_Missense_Mutation_p.F387C|AGFG1_ENST00000409979.2_Missense_Mutation_p.F451C	NM_001135188.1|NM_001135189.1|NM_004504.4	NP_001128660.1|NP_001128661.1|NP_004495.2	P52594	AGFG1_HUMAN	ArfGAP with FG repeats 1	427					cell differentiation (GO:0030154)|mRNA export from nucleus (GO:0006406)|multicellular organismal development (GO:0007275)|regulation of ARF GTPase activity (GO:0032312)|spermatogenesis (GO:0007283)	cytoplasmic vesicle (GO:0031410)|intracellular membrane-bounded organelle (GO:0043231)|nuclear pore (GO:0005643)	ARF GTPase activator activity (GO:0008060)|DNA binding (GO:0003677)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|large_intestine(5)|liver(2)|lung(2)|ovary(1)|prostate(1)|skin(4)|stomach(1)	18						CCTGCTCCATTTGGAGGTATG	0.388																																					p.F451C		.											.	.	.	0			c.T1352G						.						103.0	101.0	102.0					2																	228401415		2203	4300	6503	SO:0001583	missense	3267	exon10			CTCCATTTGGAGG		CCDS2467.1, CCDS46533.1, CCDS46534.1, CCDS46535.1	2q36	2009-11-30	2008-09-22	2008-09-22	ENSG00000173744	ENSG00000173744		"""ADP-ribosylation factor GTPase activating proteins"""	5175	protein-coding gene	gene with protein product		600862	"""HIV-1 Rev binding protein"""	HRB		7637788	Standard	NM_004504		Approved	RIP, RAB	uc002vpd.2	P52594	OTTHUMG00000133186	ENST00000310078.8:c.1280T>G	2.37:g.228401415T>G	ENSP00000312059:p.Phe427Cys	Somatic	51	0		WXS	Illumina HiSeq	.	38	15	NM_001135187	B3KUL1|E9PHX7|Q15277|Q4VAS0|Q4VAS1|Q4VAS3|Q53QT8|Q53R11	Missense_Mutation	SNP	ENST00000310078.8	37	CCDS2467.1	.	.	.	.	.	.	.	.	.	.	T	20.4	3.975992	0.74360	.	.	ENSG00000173744	ENST00000409979;ENST00000542592;ENST00000310078;ENST00000409315;ENST00000373671;ENST00000409171	T;T;T;T;T	0.48201	0.82;1.54;1.34;1.52;1.53	5.97	5.97	0.96955	.	0.000000	0.85682	D	0.000000	T	0.62024	0.2394	L	0.47716	1.5	0.54753	D	0.999983	D;D;D;D	0.89917	1.0;0.999;0.999;1.0	D;D;D;D	0.87578	0.998;0.995;0.993;0.996	T	0.59568	-0.7430	10	0.38643	T	0.18	-9.6196	15.026	0.71669	0.0:0.0:0.0:1.0	.	387;427;451;427	P52594-2;P52594-3;E9PHX7;P52594	.;.;.;AGFG1_HUMAN	C	451;436;427;406;387;427	ENSP00000387282:F451C;ENSP00000312059:F427C;ENSP00000387154:F406C;ENSP00000362775:F387C;ENSP00000387218:F427C	ENSP00000312059:F427C	F	+	2	0	AGFG1	228109659	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	6.168000	0.71908	2.289000	0.77006	0.482000	0.46254	TTT	.		0.388	AGFG1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256895.2	NM_004504	
DNAJB13	374407	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	11	73679407	73679407	+	Silent	SNP	A	A	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr11:73679407A>G	ENST00000339764.1	+	6	1375	c.624A>G	c.(622-624)ccA>ccG	p.P208P	RP11-167N4.2_ENST00000537019.1_RNA|DNAJB13_ENST00000543947.1_Silent_p.P33P|DNAJB13_ENST00000537753.1_Silent_p.P33P	NM_153614.2	NP_705842.2	P59910	DJB13_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 13	208					protein folding (GO:0006457)					large_intestine(3)|lung(2)	5	Breast(11;7.42e-05)					ACATCATCCCAGCAGACATCA	0.542																																					p.P208P		.											.	.	.	0			c.A624G						.						162.0	119.0	133.0					11																	73679407		2200	4293	6493	SO:0001819	synonymous_variant	374407	exon6			CATCCCAGCAGAC	AF516185	CCDS8227.1	11q13.3	2011-09-02	2010-04-21		ENSG00000187726	ENSG00000187726		"""Heat shock proteins / DNAJ (HSP40)"""	30718	protein-coding gene	gene with protein product	"""radial spoke 16 homolog A (Chlamydomonas)"""	610263	"""DnaJ (Hsp40) related, subfamily B, member 13"""				Standard	NM_153614		Approved	TSARG6, RSPH16A	uc001ouo.3	P59910	OTTHUMG00000168093	ENST00000339764.1:c.624A>G	11.37:g.73679407A>G		Somatic	43	0		WXS	Illumina HiSeq	.	48	12	NM_153614	B3LEP4|Q8IZW5	Silent	SNP	ENST00000339764.1	37	CCDS8227.1	.	.	.	.	.	.	.	.	.	.	a	14.75	2.629279	0.46944	.	.	ENSG00000187726	ENST00000542350	.	.	.	5.23	-1.07	0.09968	.	.	.	.	.	T	0.43166	0.1235	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.24404	-1.0161	4	.	.	.	.	3.659	0.08232	0.4886:0.0:0.2573:0.2542	.	.	.	.	G	109	.	.	S	+	1	0	DNAJB13	73357055	0.058000	0.20735	0.979000	0.43373	0.977000	0.68977	-0.680000	0.05197	-0.371000	0.08004	0.359000	0.22050	AGC	.		0.542	DNAJB13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398100.1	NM_153614	
AIM1	202	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	6	107006479	107006479	+	Missense_Mutation	SNP	C	C	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr6:107006479C>T	ENST00000369066.3	+	16	5097	c.4610C>T	c.(4609-4611)tCt>tTt	p.S1537F	AIM1_ENST00000535438.1_Missense_Mutation_p.S356F	NM_001624.2	NP_001615	Q9UMX9	S45A2_HUMAN	absent in melanoma 1	0					developmental pigmentation (GO:0048066)|melanin biosynthetic process (GO:0042438)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)				breast(8)|central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(7)|large_intestine(13)|lung(20)|ovary(5)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	69	Breast(9;0.0138)|all_epithelial(6;0.169)	all_cancers(87;4.67e-25)|all_epithelial(87;5.46e-21)|Acute lymphoblastic leukemia(125;2.15e-07)|all_hematologic(75;5.28e-06)|Colorectal(196;3.46e-05)|all_lung(197;5.94e-05)|Lung NSC(302;7.26e-05)|Ovarian(999;0.00473)	Epithelial(6;0.00114)|all cancers(7;0.00726)|BRCA - Breast invasive adenocarcinoma(8;0.0114)|OV - Ovarian serous cystadenocarcinoma(5;0.0305)	all cancers(137;1.73e-50)|Epithelial(106;2.42e-48)|OV - Ovarian serous cystadenocarcinoma(136;1.51e-27)|BRCA - Breast invasive adenocarcinoma(108;0.00104)|GBM - Glioblastoma multiforme(226;0.00858)		CAAATACGCTCTGTTCAGGTT	0.388																																					p.S1537F		.											.	.	.	0			c.C4610T						.						115.0	101.0	106.0					6																	107006479		2203	4300	6503	SO:0001583	missense	202	exon16			TACGCTCTGTTCA	U83115	CCDS34506.1	6q21	2014-01-29			ENSG00000112297	ENSG00000112297			356	protein-coding gene	gene with protein product	"""suppression of tumorigenicity 4"", ""beta-gamma crystallin domain containing 1"""	601797	"""suppression of tumorigenicity 4 (malignant melanoma)"""	ST4		1680551, 12693952	Standard	NM_001624		Approved	CRYBG1	uc003prh.3	Q9Y4K1	OTTHUMG00000015302	ENST00000369066.3:c.4610C>T	6.37:g.107006479C>T	ENSP00000358062:p.Ser1537Phe	Somatic	45	0		WXS	Illumina HiSeq	.	40	10	NM_001624	Q6P2P0|Q9BTM3	Missense_Mutation	SNP	ENST00000369066.3	37	CCDS34506.1	.	.	.	.	.	.	.	.	.	.	C	22.0	4.228946	0.79688	.	.	ENSG00000112297	ENST00000369066;ENST00000535438	D;D	0.93426	-3.22;-3.22	5.81	5.81	0.92471	Beta/gamma crystallin (4);Gamma-crystallin-related (1);	0.000000	0.85682	D	0.000000	D	0.98128	0.9382	H	0.97023	3.925	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	D	0.98821	1.0747	10	0.87932	D	0	.	20.0826	0.97783	0.0:1.0:0.0:0.0	.	356;1537	B4DU04;Q9Y4K1	.;AIM1_HUMAN	F	1537;356	ENSP00000358062:S1537F;ENSP00000439183:S356F	ENSP00000358062:S1537F	S	+	2	0	AIM1	107113172	1.000000	0.71417	1.000000	0.80357	0.599000	0.36880	6.602000	0.74141	2.746000	0.94184	0.655000	0.94253	TCT	.		0.388	AIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041669.1		
REL	5966	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	2	61149151	61149151	+	Silent	SNP	G	G	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr2:61149151G>C	ENST00000295025.8	+	11	1661	c.1341G>C	c.(1339-1341)ctG>ctC	p.L447L	REL_ENST00000394479.3_Silent_p.L415L	NM_002908.2	NP_002899.1	Q04864	REL_HUMAN	v-rel avian reticuloendotheliosis viral oncogene homolog	447					cytokine production (GO:0001816)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|negative regulation of neuron death (GO:1901215)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-12 biosynthetic process (GO:0045084)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|transcription factor complex (GO:0005667)	RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(1)|large_intestine(5)|lung(3)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	16	all_hematologic(2;0.0797)	Ovarian(717;0.0728)	LUSC - Lung squamous cell carcinoma(5;6.2e-08)|Lung(5;1.65e-06)|Epithelial(17;0.064)|all cancers(80;0.221)			CACCATTCCTGAGAATACCTG	0.468			A		Hodgkin Lymphoma																																p.L447L		.		Dom	yes		2	2p13-p12	5966	v-rel reticuloendotheliosis viral oncogene homolog (avian)		L	.	.	.	0			c.G1341C						.						95.0	88.0	90.0					2																	61149151		2203	4300	6503	SO:0001819	synonymous_variant	5966	exon11			ATTCCTGAGAATA	M11595	CCDS1864.1, CCDS74515.1	2p13-p12	2013-07-09	2013-07-09		ENSG00000162924	ENSG00000162924			9954	protein-coding gene	gene with protein product		164910				1577270	Standard	XM_005264470		Approved	I-Rel, c-Rel	uc002sam.1	Q04864	OTTHUMG00000129418	ENST00000295025.8:c.1341G>C	2.37:g.61149151G>C		Somatic	53	0		WXS	Illumina HiSeq	.	35	17	NM_002908	Q17RU2|Q2PNZ7|Q6LDY0	Silent	SNP	ENST00000295025.8	37	CCDS1864.1																																																																																			.		0.468	REL-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251576.3	NM_002908	
JMJD1C	221037	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	10	64966863	64966863	+	Silent	SNP	T	T	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr10:64966863T>A	ENST00000399262.2	-	10	4784	c.4566A>T	c.(4564-4566)gtA>gtT	p.V1522V	JMJD1C_ENST00000399251.1_Silent_p.V1303V|JMJD1C_ENST00000542921.1_Silent_p.V1340V|JMJD1C_ENST00000402544.1_Silent_p.V1303V	NM_032776.1	NP_116165.1	Q15652	JHD2C_HUMAN	jumonji domain containing 1C	1522					blood coagulation (GO:0007596)|chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	intracellular (GO:0005622)|nucleoplasm (GO:0005654)	dioxygenase activity (GO:0051213)|metal ion binding (GO:0046872)|thyroid hormone receptor binding (GO:0046966)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(8)|large_intestine(9)|lung(27)|ovary(6)|prostate(4)|skin(4)|stomach(3)|upper_aerodigestive_tract(3)	77	Prostate(12;0.0119)|all_hematologic(501;0.191)					TACTACAGATTACAGTGCTAT	0.418																																					p.V1522V		.											.	.	.	0			c.A4566T						.						130.0	122.0	124.0					10																	64966863		1886	4099	5985	SO:0001819	synonymous_variant	221037	exon10			ACAGATTACAGTG	L40411	CCDS41532.1, CCDS60538.1	10q22.1	2011-05-25	2004-03-31	2004-04-01	ENSG00000171988	ENSG00000171988			12313	protein-coding gene	gene with protein product		604503	"""thyroid hormone receptor interactor 8"""	TRIP8		7776974	Standard	XM_005269624		Approved	DKFZp761F0118, KIAA1380, FLJ14374	uc001jmn.3	Q15652	OTTHUMG00000018311	ENST00000399262.2:c.4566A>T	10.37:g.64966863T>A		Somatic	89	0		WXS	Illumina HiSeq	.	29	17	NM_032776	A0T124|Q5SQZ8|Q5SQZ9|Q5SR00|Q7Z3E7|Q8N3U0|Q96KB9|Q9P2G7	Silent	SNP	ENST00000399262.2	37	CCDS41532.1	.	.	.	.	.	.	.	.	.	.	T	4.022	0.001472	0.07819	.	.	ENSG00000171988	ENST00000327520	.	.	.	5.97	-2.12	0.07165	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	0.999995	.	.	.	.	.	.	.	.	.	.	.	.	.	-3.8662	2.645	0.04981	0.1025:0.3428:0.2509:0.3038	.	.	.	.	L	208	.	.	X	-	2	2	JMJD1C	64636869	0.018000	0.18449	0.995000	0.50966	0.992000	0.81027	0.021000	0.13489	-0.058000	0.13177	0.482000	0.46254	TAA	.		0.418	JMJD1C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048249.2	NM_004241	
ZFAND2A	90637	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	7	1197813	1197813	+	Missense_Mutation	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr7:1197813T>G	ENST00000316495.3	-	2	295	c.36A>C	c.(34-36)gaA>gaC	p.E12D	AC091729.9_ENST00000423008.1_RNA|ZFAND2A_ENST00000401903.1_Missense_Mutation_p.E12D|ZFAND2A_ENST00000478137.1_5'Flank|AC091729.9_ENST00000413706.1_RNA|AC091729.9_ENST00000422230.1_RNA	NM_182491.2	NP_872297.2	Q8N6M9	ZFN2A_HUMAN	zinc finger, AN1-type domain 2A	12					cellular response to arsenic-containing substance (GO:0071243)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|proteasome complex (GO:0000502)	zinc ion binding (GO:0008270)			lung(2)|ovary(1)	3		Ovarian(82;0.11)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0178)|OV - Ovarian serous cystadenocarcinoma(56;1.82e-15)		TGCAAGTCTTTTCTGAACAAT	0.398																																					p.E12D		.											.	.	.	0			c.A36C						.						250.0	267.0	261.0					7																	1197813		2203	4300	6503	SO:0001583	missense	90637	exon2			AGTCTTTTCTGAA	BC029558	CCDS5323.1	7p22.3	2010-04-23			ENSG00000178381	ENSG00000178381		"""Zinc fingers, AN1-type domain containing"""	28073	protein-coding gene	gene with protein product	"""arsenite inducible RNA associated protein"""	610699				20185824	Standard	NM_182491		Approved	AIRAP	uc003skc.3	Q8N6M9	OTTHUMG00000119019	ENST00000316495.3:c.36A>C	7.37:g.1197813T>G	ENSP00000314619:p.Glu12Asp	Somatic	49	0		WXS	Illumina HiSeq	.	21	7	NM_182491	A4D220	Missense_Mutation	SNP	ENST00000316495.3	37	CCDS5323.1	.	.	.	.	.	.	.	.	.	.	T	19.63	3.864386	0.71949	.	.	ENSG00000178381	ENST00000401903;ENST00000397083;ENST00000316495	T;T;T	0.43688	0.94;0.94;0.94	5.21	1.56	0.23342	Zinc finger, AN1-type (4);	0.000000	0.85682	D	0.000000	T	0.57932	0.2087	M	0.82923	2.615	0.54753	D	0.999983	D;D	0.63880	0.971;0.993	P;P	0.62089	0.898;0.842	T	0.54576	-0.8273	10	0.48119	T	0.1	-37.7492	7.3881	0.26895	0.0:0.3605:0.0:0.6395	.	12;12	A8MYA3;Q8N6M9	.;ZFN2A_HUMAN	D	12	ENSP00000386031:E12D;ENSP00000380273:E12D;ENSP00000314619:E12D	ENSP00000314619:E12D	E	-	3	2	ZFAND2A	1164339	0.978000	0.34361	0.893000	0.35052	0.995000	0.86356	0.462000	0.21956	0.034000	0.15491	0.533000	0.62120	GAA	.		0.398	ZFAND2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239220.2	NM_182491	
SPTBN5	51332	hgsc.bcm.edu;broad.mit.edu	37	15	42168834	42168834	+	Missense_Mutation	SNP	T	T	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr15:42168834T>C	ENST00000320955.6	-	20	4090	c.3863A>G	c.(3862-3864)cAg>cGg	p.Q1288R		NM_016642.2	NP_057726.4	Q9NRC6	SPTN5_HUMAN	spectrin, beta, non-erythrocytic 5	1288					actin cytoskeleton organization (GO:0030036)|actin filament capping (GO:0051693)|axon guidance (GO:0007411)|Golgi organization (GO:0007030)|lysosomal transport (GO:0007041)|protein homooligomerization (GO:0051260)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|photoreceptor connecting cilium (GO:0032391)|photoreceptor disc membrane (GO:0097381)|spectrin (GO:0008091)	actin binding (GO:0003779)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|kinesin binding (GO:0019894)|myosin tail binding (GO:0032029)|protein self-association (GO:0043621)|spectrin binding (GO:0030507)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(6)|lung(18)|ovary(5)|prostate(8)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	62		all_cancers(109;1.84e-17)|all_epithelial(112;1.12e-15)|Lung NSC(122;7.6e-10)|all_lung(180;4.15e-09)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.173)		all cancers(2;4.33e-34)|Epithelial(2;1.72e-25)|OV - Ovarian serous cystadenocarcinoma(18;8.32e-20)|GBM - Glioblastoma multiforme(94;4.69e-07)|Colorectal(2;0.00104)|COAD - Colon adenocarcinoma(120;0.0405)|READ - Rectum adenocarcinoma(92;0.0908)		ACTCTGCAGCTGCTCTCTGAC	0.667																																					p.Q1253R		.											.	.	.	0			c.A3758G						.						22.0	25.0	24.0					15																	42168834		1991	4141	6132	SO:0001583	missense	51332	exon20			TGCAGCTGCTCTC	AF233523	CCDS61599.1	15q21	2010-08-17			ENSG00000137877	ENSG00000137877			15680	protein-coding gene	gene with protein product	"""beta V spectrin"""	605916				10764729	Standard	NM_016642		Approved	HUSPECV, BSPECV, HUBSPECV	uc001zos.4	Q9NRC6		ENST00000320955.6:c.3863A>G	15.37:g.42168834T>C	ENSP00000317790:p.Gln1288Arg	Somatic	14	0		WXS	Illumina HiSeq	.	19	11	NM_016642		Missense_Mutation	SNP	ENST00000320955.6	37		.	.	.	.	.	.	.	.	.	.	.	0.170	-1.072753	0.01918	.	.	ENSG00000137877	ENST00000320955	T	0.41758	0.99	4.64	1.11	0.20524	.	0.262232	0.28470	N	0.015222	T	0.18383	0.0441	N	0.21142	0.635	0.09310	N	0.999997	B	0.14438	0.01	B	0.14023	0.01	T	0.21449	-1.0245	10	0.05721	T	0.95	.	2.3297	0.04232	0.2535:0.225:0.0:0.5215	.	1288	Q9NRC6	SPTN5_HUMAN	R	1288	ENSP00000317790:Q1288R	ENSP00000317790:Q1288R	Q	-	2	0	SPTBN5	39956126	0.022000	0.18835	0.991000	0.47740	0.529000	0.34654	-0.493000	0.06459	0.133000	0.18654	0.402000	0.26972	CAG	.		0.667	SPTBN5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000420237.1	NM_016642	
AP3S2	10239	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	15	90431760	90431760	+	Missense_Mutation	SNP	A	A	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr15:90431760A>G	ENST00000336418.4	-	3	658	c.266T>C	c.(265-267)cTc>cCc	p.L89P	C15orf38-AP3S2_ENST00000560224.1_5'UTR|RNU6-1111P_ENST00000391118.1_RNA|AP3S2_ENST00000558011.1_Missense_Mutation_p.L89P|AP3S2_ENST00000560940.1_Missense_Mutation_p.L89P|C15orf38-AP3S2_ENST00000398333.3_Missense_Mutation_p.L290P	NM_005829.4	NP_005820.1	P59780	AP3S2_HUMAN	adaptor-related protein complex 3, sigma 2 subunit	89					anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|intracellular protein transport (GO:0006886)	AP-3 adaptor complex (GO:0030123)|cytoplasmic vesicle (GO:0031410)|Golgi apparatus (GO:0005794)	protein transporter activity (GO:0008565)			NS(1)|kidney(1)|lung(2)|ovary(1)|urinary_tract(1)	6	Lung NSC(78;0.0181)|all_lung(78;0.0384)		BRCA - Breast invasive adenocarcinoma(143;0.0107)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.223)			TACCTGGATGAGGTCCAAGAT	0.453																																					p.L290P		.											.	.	.	0			c.T869C						.						79.0	73.0	75.0					15																	90431760		2200	4299	6499	SO:0001583	missense	100526783	exon7			TGGATGAGGTCCA	X99459	CCDS10357.1	15q26.1	2010-08-13			ENSG00000157823	ENSG00000157823			571	protein-coding gene	gene with protein product		602416				9118953	Standard	NM_005829		Approved	sigma3b		P59780	OTTHUMG00000149811	ENST00000336418.4:c.266T>C	15.37:g.90431760A>G	ENSP00000338777:p.Leu89Pro	Somatic	56	0		WXS	Illumina HiSeq	.	20	12	NM_001199058	B2R677|B4DGQ3|O09077|O09149|Q53H83|Q99589	Missense_Mutation	SNP	ENST00000336418.4	37	CCDS10357.1	.	.	.	.	.	.	.	.	.	.	A	25.3	4.628898	0.87560	.	.	ENSG00000157823;ENSG00000157823;ENSG00000250021	ENST00000336418;ENST00000423566;ENST00000398333	T;T	0.55760	0.57;0.5	5.56	5.56	0.83823	Longin-like (1);AP complex, mu/sigma subunit (1);	0.152719	0.45126	D	0.000383	T	0.82250	0.4996	H	0.97983	4.12	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.88386	0.3005	10	0.87932	D	0	-17.3722	13.6945	0.62569	1.0:0.0:0.0:0.0	.	290;89	E2QRD5;P59780	.;AP3S2_HUMAN	P	89;89;290	ENSP00000338777:L89P;ENSP00000381377:L290P	ENSP00000338777:L89P	L	-	2	0	C15orf38-AP3S2;AP3S2	88232764	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	8.617000	0.90927	2.330000	0.79161	0.533000	0.62120	CTC	.		0.453	AP3S2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313422.1		
DNAJB6	10049	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	7	157208727	157208727	+	Missense_Mutation	SNP	A	A	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr7:157208727A>G	ENST00000262177.4	+	10	1121	c.916A>G	c.(916-918)Aag>Gag	p.K306E	DNAJB6_ENST00000494267.1_3'UTR|DNAJB6_ENST00000452797.2_Missense_Mutation_p.K257E|DNAJB6_ENST00000443280.1_Missense_Mutation_p.K191E	NM_058246.3	NP_490647.1	O75190	DNJB6_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 6	306					intermediate filament organization (GO:0045109)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of inclusion body assembly (GO:0090084)|positive regulation of ATPase activity (GO:0032781)|protein folding (GO:0006457)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|Z disc (GO:0030018)	ATPase activator activity (GO:0001671)|chaperone binding (GO:0051087)|heat shock protein binding (GO:0031072)|unfolded protein binding (GO:0051082)			central_nervous_system(1)|lung(1)|ovary(2)|stomach(1)	5	all_neural(206;0.181)	all_epithelial(9;0.000606)|all_hematologic(28;0.00287)|Acute lymphoblastic leukemia(9;0.0647)|Ovarian(593;0.196)	OV - Ovarian serous cystadenocarcinoma(82;0.00399)	UCEC - Uterine corpus endometrioid carcinoma (81;0.172)		AGAAGGTGGCaagaggaagaa	0.502																																					p.K306E	Esophageal Squamous(46;195 967 1350 20350 43814)	.											.	.	.	0			c.A916G						.						135.0	123.0	127.0					7																	157208727		2203	4300	6503	SO:0001583	missense	10049	exon10			GGTGGCAAGAGGA	AB014888	CCDS5946.1, CCDS47755.1	7q36.3	2014-02-03			ENSG00000105993	ENSG00000105993		"""Heat shock proteins / DNAJ (HSP40)"""	14888	protein-coding gene	gene with protein product		611332	"""limb girdle muscular dystrophy 1D (autosomal dominant)"""	LGMD1D		10319584, 9915854, 22366786	Standard	NM_005494		Approved	MRJ	uc003wnk.3	O75190	OTTHUMG00000157242	ENST00000262177.4:c.916A>G	7.37:g.157208727A>G	ENSP00000262177:p.Lys306Glu	Somatic	79	0		WXS	Illumina HiSeq	.	32	13	NM_058246	A4D232|A8K7D8|A8KAG0|B4DN73|E9PCZ2|O95806|Q53EN8|Q59EF2|Q6FIC8|Q75MA2|Q9UIK6	Missense_Mutation	SNP	ENST00000262177.4	37	CCDS5946.1	.	.	.	.	.	.	.	.	.	.	A	14.38	2.519431	0.44866	.	.	ENSG00000105993	ENST00000262177;ENST00000452797;ENST00000443280	T;T;T	0.66995	0.26;-0.22;-0.24	4.46	3.29	0.37713	.	2.482380	0.02140	N	0.057085	T	0.64204	0.2577	L	0.57536	1.79	0.28102	N	0.931373	B;P;B;B	0.41393	0.023;0.748;0.384;0.176	B;B;B;B	0.36959	0.019;0.237;0.048;0.07	T	0.51529	-0.8694	10	0.39692	T	0.17	.	7.9667	0.30102	0.9022:0.0:0.0978:0.0	.	191;257;306;306	E9PH18;B4DN73;A8KAG0;O75190	.;.;.;DNJB6_HUMAN	E	306;257;191	ENSP00000262177:K306E;ENSP00000402270:K257E;ENSP00000396267:K191E	ENSP00000262177:K306E	K	+	1	0	DNAJB6	156901488	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	4.876000	0.63079	0.669000	0.31146	0.482000	0.46254	AAG	.		0.502	DNAJB6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000348119.2		
CNTLN	54875	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	9	17273829	17273829	+	Missense_Mutation	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr9:17273829A>C	ENST00000380647.3	+	6	1032	c.948A>C	c.(946-948)gaA>gaC	p.E316D	CNTLN_ENST00000380641.4_Missense_Mutation_p.E316D|CNTLN_ENST00000262360.5_Missense_Mutation_p.E316D|CNTLN_ENST00000425824.1_Missense_Mutation_p.E316D			Q9NXG0	CNTLN_HUMAN	centlein, centrosomal protein	316					centriole-centriole cohesion (GO:0010457)|protein localization to organelle (GO:0033365)	centriole (GO:0005814)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	phosphorelay sensor kinase activity (GO:0000155)|protein binding, bridging (GO:0030674)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)			breast(6)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|kidney(3)|large_intestine(10)|lung(17)|ovary(1)|pancreas(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	53				GBM - Glioblastoma multiforme(50;6.14e-10)		AACAGACTGAACTTATCCAGA	0.308																																					p.E316D		.											.	.	.	0			c.A948C						.						110.0	110.0	110.0					9																	17273829		1837	4078	5915	SO:0001583	missense	54875	exon6			GACTGAACTTATC	AK000283	CCDS43789.1, CCDS47953.1	9p22.2-p22.1	2008-11-11	2008-02-08	2008-02-08	ENSG00000044459	ENSG00000044459			23432	protein-coding gene	gene with protein product		611870	"""chromosome 9 open reading frame 101"", ""chromosome 9 open reading frame 39"""	C9orf101, C9orf39		18086554	Standard	XM_005251492		Approved	FLJ20276, bA340N12.1, OTTHUMG00000019597	uc003zmy.3	Q9NXG0	OTTHUMG00000019599	ENST00000380647.3:c.948A>C	9.37:g.17273829A>C	ENSP00000370021:p.Glu316Asp	Somatic	78	0		WXS	Illumina HiSeq	.	35	10	NM_017738	A5Z2X6|Q5VYJ0|Q8N1G9|Q9HAJ5	Missense_Mutation	SNP	ENST00000380647.3	37	CCDS43789.1	.	.	.	.	.	.	.	.	.	.	A	14.12	2.442009	0.43326	.	.	ENSG00000044459	ENST00000380647;ENST00000425824;ENST00000262360;ENST00000380641	T;T;T;T	0.11495	2.77;2.77;3.0;2.77	4.73	3.49	0.39957	.	.	.	.	.	T	0.11965	0.0291	M	0.64997	1.995	0.30858	N	0.733787	B;B;B	0.31318	0.106;0.106;0.319	B;B;B	0.28991	0.097;0.097;0.069	T	0.03374	-1.1043	9	0.27082	T	0.32	.	9.7598	0.40526	0.8269:0.1731:0.0:0.0	.	316;316;316	C9J1F9;Q9NXG0-2;Q9NXG0-3	.;.;.	D	316	ENSP00000370021:E316D;ENSP00000392798:E316D;ENSP00000262360:E316D;ENSP00000370015:E316D	ENSP00000262360:E316D	E	+	3	2	CNTLN	17263829	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	1.316000	0.33620	1.881000	0.54492	0.254000	0.18369	GAA	.		0.308	CNTLN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051793.3	NM_017738	
CIDEB	27141	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	14	24777048	24777048	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr14:24777048G>T	ENST00000336557.5	-	4	1319	c.17C>A	c.(16-18)gCt>gAt	p.A6D	CIDEB_ENST00000555817.1_5'Flank|NOP9_ENST00000267425.3_3'UTR|LTB4R2_ENST00000533293.1_5'Flank|CIDEB_ENST00000554411.1_Missense_Mutation_p.A6D|CIDEB_ENST00000258807.5_Missense_Mutation_p.A6D|LTB4R2_ENST00000528054.1_5'Flank|LTB4R2_ENST00000543919.1_5'Flank			Q9UHD4	CIDEB_HUMAN	cell death-inducing DFFA-like effector b	6					apoptotic process (GO:0006915)|execution phase of apoptosis (GO:0097194)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|regulation of apoptotic process (GO:0042981)	cytosol (GO:0005829)|lipid particle (GO:0005811)	identical protein binding (GO:0042802)			NS(1)|endometrium(1)|kidney(1)|large_intestine(3)|urinary_tract(1)	7				GBM - Glioblastoma multiforme(265;0.0181)		GGGGTTCAGAGCTGAGAGGTA	0.547											OREG0022623	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A6D		.											.	.	.	0			c.C17A						.						179.0	140.0	153.0					14																	24777048		2203	4299	6502	SO:0001583	missense	27141	exon3			TTCAGAGCTGAGA	AF190901	CCDS32056.1	14q12	2012-09-20			ENSG00000136305	ENSG00000136305			1977	protein-coding gene	gene with protein product		604441				10619428, 10837461	Standard	XM_005267540		Approved		uc001woo.3	Q9UHD4	OTTHUMG00000171555	ENST00000336557.5:c.17C>A	14.37:g.24777048G>T	ENSP00000337731:p.Ala6Asp	Somatic	54	0	774	WXS	Illumina HiSeq	.	35	10	NM_014430	D3DS73|Q546V8|Q9NNW9	Missense_Mutation	SNP	ENST00000336557.5	37	CCDS32056.1	.	.	.	.	.	.	.	.	.	.	G	12.19	1.864734	0.32977	.	.	ENSG00000136305	ENST00000554411;ENST00000336557;ENST00000258807;ENST00000541830	T;T;T	0.45276	0.9;0.9;0.9	4.93	3.07	0.35406	.	1.014060	0.07862	N	0.966471	T	0.38532	0.1044	L	0.50333	1.59	0.58432	D	0.999999	B	0.21520	0.057	B	0.26969	0.075	T	0.22068	-1.0227	10	0.46703	T	0.11	-8.4268	6.1878	0.20508	0.0949:0.0:0.7209:0.1842	.	6	Q9UHD4	CIDEB_HUMAN	D	6	ENSP00000451089:A6D;ENSP00000337731:A6D;ENSP00000258807:A6D	ENSP00000258807:A6D	A	-	2	0	CIDEB	23846888	0.918000	0.31147	0.858000	0.33744	0.864000	0.49448	1.963000	0.40452	0.769000	0.33313	0.491000	0.48974	GCT	.		0.547	CIDEB-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414120.1		
DDB2	1643	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	11	47256385	47256385	+	Silent	SNP	A	A	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr11:47256385A>G	ENST00000256996.4	+	6	975	c.780A>G	c.(778-780)acA>acG	p.T260T	DDB2_ENST00000378600.3_Intron|DDB2_ENST00000378603.3_Silent_p.T196T|DDB2_ENST00000378601.3_Intron	NM_000107.2	NP_000098.1	Q92466	DDB2_HUMAN	damage-specific DNA binding protein 2, 48kDa	260					DNA repair (GO:0006281)|histone H2A monoubiquitination (GO:0035518)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|protein autoubiquitination (GO:0051865)|protein polyubiquitination (GO:0000209)|pyrimidine dimer repair (GO:0006290)|response to UV (GO:0009411)|UV-damage excision repair (GO:0070914)	Cul4B-RING E3 ubiquitin ligase complex (GO:0031465)|nucleoplasm (GO:0005654)|protein complex (GO:0043234)	damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)			breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)|skin(1)	17						TCCTGGCCACAGCCTCCGTAG	0.532			"""Mis, N"""			"""skin basal cell, skin squamous cell, melanoma"""		Direct reversal of damage;Nucleotide excision repair (NER)	Xeroderma Pigmentosum																												p.T260T		.	yes	Rec		Xeroderma pigmentosum (E)	11	11p12	1643	damage-specific DNA binding protein 2		E	.	.	.	0			c.A780G						.						52.0	50.0	51.0					11																	47256385		2201	4298	6499	SO:0001819	synonymous_variant	1643	exon6	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV	GGCCACAGCCTCC		CCDS7927.1, CCDS73284.1	11p12-p11	2014-09-17	2002-08-29			ENSG00000134574		"""WD repeat domain containing"""	2718	protein-coding gene	gene with protein product	"""xeroderma pigmentosum group E protein"", ""UV-damaged DNA-binding protein 2"", ""DDB p48 subunit"""	600811	"""damage-specific DNA binding protein 2 (48kD)"""			8407967, 8530102	Standard	NM_000107		Approved	DDBB, UV-DDB2, FLJ34321	uc001neb.2	Q92466		ENST00000256996.4:c.780A>G	11.37:g.47256385A>G		Somatic	35	0		WXS	Illumina HiSeq	.	33	16	NM_000107	B2R875|Q76E54|Q76E55|Q76E56|Q76E57	Silent	SNP	ENST00000256996.4	37	CCDS7927.1																																																																																			.		0.532	DDB2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_000107	
MAP3K2	10746	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	2	128087578	128087578	+	Missense_Mutation	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr2:128087578T>G	ENST00000409947.1	-	7	667	c.385A>C	c.(385-387)Aat>Cat	p.N129H	MAP3K2_ENST00000344908.5_Missense_Mutation_p.N129H			Q9Y2U5	M3K2_HUMAN	mitogen-activated protein kinase kinase kinase 2	129					activation of JUN kinase activity (GO:0007257)|activation of MAPK activity (GO:0000187)|cellular response to mechanical stimulus (GO:0071260)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|MAP kinase kinase kinase activity (GO:0004709)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)			central_nervous_system(1)|large_intestine(1)|lung(3)|ovary(2)	7	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0706)	Bosutinib(DB06616)	GGTTCTAAATTAGTAGCCTAC	0.363																																					p.N129H		.											.	.	.	0			c.A385C						.						120.0	116.0	117.0					2																	128087578		1820	4074	5894	SO:0001583	missense	10746	exon6			CTAAATTAGTAGC	AF111105	CCDS46404.1	2q21.1	2011-06-09			ENSG00000169967	ENSG00000169967		"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	6854	protein-coding gene	gene with protein product	"""MAP/ERK kinase kinase 2"""	609487		MEKK2		8621389, 10085062	Standard	NM_006609		Approved	MEKK2B	uc002toj.2	Q9Y2U5	OTTHUMG00000153397	ENST00000409947.1:c.385A>C	2.37:g.128087578T>G	ENSP00000387246:p.Asn129His	Somatic	135	0		WXS	Illumina HiSeq	.	72	32	NM_006609	B9EG87|Q53QL9|Q53S75|Q59GZ6|Q8NC32|Q9NYK3	Missense_Mutation	SNP	ENST00000409947.1	37	CCDS46404.1	.	.	.	.	.	.	.	.	.	.	t	8.660	0.900254	0.17686	.	.	ENSG00000169967	ENST00000409947;ENST00000344908	T;T	0.66815	-0.23;-0.23	5.6	4.44	0.53790	.	0.573963	0.19863	N	0.104362	T	0.50820	0.1638	N	0.08118	0	0.26145	N	0.980222	B	0.20261	0.043	B	0.32022	0.139	T	0.50389	-0.8834	10	0.46703	T	0.11	.	13.2634	0.60120	0.0:0.0:0.1326:0.8674	.	129	Q9Y2U5	M3K2_HUMAN	H	129	ENSP00000387246:N129H;ENSP00000343463:N129H	ENSP00000343463:N129H	N	-	1	0	MAP3K2	127804048	1.000000	0.71417	0.995000	0.50966	0.333000	0.28666	3.375000	0.52410	1.057000	0.40506	-0.264000	0.10439	AAT	.		0.363	MAP3K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331014.1	NM_006609	
GPR21	2844	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	9	125797792	125797792	+	Missense_Mutation	SNP	A	A	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr9:125797792A>G	ENST00000373642.1	+	1	987	c.947A>G	c.(946-948)aAg>aGg	p.K316R	RABGAP1_ENST00000493854.1_Intron|RABGAP1_ENST00000373647.4_Intron|RABGAP1_ENST00000373643.5_Intron	NM_005294.1	NP_005285.1	Q99679	GPR21_HUMAN	G protein-coupled receptor 21	316					G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|negative regulation of insulin receptor signaling pathway (GO:0046627)|positive regulation of multicellular organism growth (GO:0040018)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)			endometrium(3)|large_intestine(3)|lung(4)|ovary(1)|skin(1)|stomach(1)|urinary_tract(2)	15						AGAGGACTAAAGCGCCTCTCA	0.453																																					p.K316R		.											.	.	.	0			c.A947G						.						84.0	85.0	85.0					9																	125797792		2203	4300	6503	SO:0001583	missense	2844	exon2			GACTAAAGCGCCT	BC066885	CCDS6849.1	9q33	2012-08-21			ENSG00000188394	ENSG00000188394		"""GPCR / Class A : Orphans"""	4476	protein-coding gene	gene with protein product		601909					Standard	NM_005294		Approved		uc011lzk.3	Q99679	OTTHUMG00000020631	ENST00000373642.1:c.947A>G	9.37:g.125797792A>G	ENSP00000362746:p.Lys316Arg	Somatic	39	0		WXS	Illumina HiSeq	.	32	13	NM_005294	B2R8W9|Q6NXU2	Missense_Mutation	SNP	ENST00000373642.1	37	CCDS6849.1	.	.	.	.	.	.	.	.	.	.	A	1.564	-0.536031	0.04082	.	.	ENSG00000188394	ENST00000373642	T	0.38077	1.16	6.03	4.87	0.63330	.	0.305702	0.27375	U	0.019659	T	0.17874	0.0429	N	0.08118	0	0.80722	D	1	B	0.16166	0.016	B	0.13407	0.009	T	0.05767	-1.0865	10	0.08179	T	0.78	-3.0148	12.3676	0.55236	0.8656:0.0:0.0:0.1344	.	316	Q99679	GPR21_HUMAN	R	316	ENSP00000362746:K316R	ENSP00000362746:K316R	K	+	2	0	GPR21	124837613	1.000000	0.71417	0.997000	0.53966	0.976000	0.68499	4.910000	0.63321	1.065000	0.40693	-0.438000	0.05819	AAG	.		0.453	GPR21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053965.1	NM_005294	
VNN1	8876	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	6	133034964	133034964	+	Splice_Site	SNP	C	C	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr6:133034964C>T	ENST00000367928.4	-	1	224		c.e1+1			NM_004666.2	NP_004657.2	O95497	VNN1_HUMAN	vanin 1						acute inflammatory response (GO:0002526)|cellular component movement (GO:0006928)|chronic inflammatory response (GO:0002544)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|pantothenate metabolic process (GO:0015939)|positive regulation of T cell differentiation in thymus (GO:0033089)|response to oxidative stress (GO:0006979)|single organismal cell-cell adhesion (GO:0016337)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	GPI anchor binding (GO:0034235)|pantetheine hydrolase activity (GO:0017159)			NS(2)|endometrium(3)|kidney(2)|large_intestine(8)|lung(10)|ovary(4)|prostate(1)|upper_aerodigestive_tract(1)	31	Breast(56;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.0027)|GBM - Glioblastoma multiforme(226;0.0189)		AGAGATGGTACCTGATCTGCT	0.488																																					.		.											.	.	.	0			c.210+1G>A						.						160.0	137.0	145.0					6																	133034964		2203	4300	6503	SO:0001630	splice_region_variant	8876	exon2			ATGGTACCTGATC	AJ132099	CCDS5159.1	6q23-q24	2013-02-13			ENSG00000112299	ENSG00000112299	3.5.1.92	"""Vanins"""	12705	protein-coding gene	gene with protein product		603570				9790769	Standard	NM_004666		Approved	Tiff66	uc003qdo.3	O95497	OTTHUMG00000015587	ENST00000367928.4:c.210+1G>A	6.37:g.133034964C>T		Somatic	58	0		WXS	Illumina HiSeq	.	35	13	NM_004666	A8K310|Q4JFW6|Q4VAS7|Q4VAS8|Q4VAS9|Q9UF16|Q9UJF4	Splice_Site	SNP	ENST00000367928.4	37	CCDS5159.1	.	.	.	.	.	.	.	.	.	.	C	12.73	2.025700	0.35701	.	.	ENSG00000112299	ENST00000367928	.	.	.	5.2	5.2	0.72013	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.5078	0.87750	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	VNN1	133076657	1.000000	0.71417	1.000000	0.80357	0.284000	0.27059	3.555000	0.53727	2.434000	0.82447	0.555000	0.69702	.	.		0.488	VNN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042263.1		Intron
MARVELD3	91862	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	16	71668439	71668439	+	Missense_Mutation	SNP	C	C	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr16:71668439C>G	ENST00000268485.3	+	3	983	c.939C>G	c.(937-939)atC>atG	p.I313M	MARVELD3_ENST00000565261.1_Intron|MARVELD3_ENST00000299952.4_Intron|MARVELD3_ENST00000567501.1_3'UTR	NM_052858.4	NP_443090.4	Q96A59	MALD3_HUMAN	MARVEL domain containing 3	313	MARVEL. {ECO:0000255|PROSITE- ProRule:PRU00581}.				cell-cell junction organization (GO:0045216)|tight junction assembly (GO:0070830)	cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|tight junction (GO:0005923)				NS(1)|endometrium(3)|large_intestine(5)|lung(6)|skin(2)	17		Ovarian(137;0.125)				ACATGCTCATCGCGGGGGGGT	0.582																																					p.I313M		.											.	.	.	0			c.C939G						.						84.0	80.0	82.0					16																	71668439		2198	4300	6498	SO:0001583	missense	91862	exon3			GCTCATCGCGGGG	BC013376	CCDS10904.1, CCDS32478.1, CCDS59270.1	16q22.2	2008-02-05	2004-07-12	2004-07-14	ENSG00000140832	ENSG00000140832			30525	protein-coding gene	gene with protein product		614094	"""MARVEL (membrane-associating) domain containing 3"""	MRVLDC3			Standard	NM_001017967		Approved		uc002fat.4	Q96A59	OTTHUMG00000137591	ENST00000268485.3:c.939C>G	16.37:g.71668439C>G	ENSP00000268485:p.Ile313Met	Somatic	34	0		WXS	Illumina HiSeq	.	18	7	NM_052858	A8K820|H3BQM5|Q96MJ4	Missense_Mutation	SNP	ENST00000268485.3	37	CCDS10904.1	.	.	.	.	.	.	.	.	.	.	C	8.904	0.957118	0.18507	.	.	ENSG00000140832	ENST00000268485	T	0.51325	0.71	5.55	-11.1	0.00147	Marvel (1);	.	.	.	.	T	0.40398	0.1115	M	0.64997	1.995	0.80722	D	1	P	0.45715	0.865	B	0.42062	0.374	T	0.72469	-0.4284	9	0.59425	D	0.04	.	14.0483	0.64719	0.0:0.5698:0.1695:0.2607	.	313	Q96A59	MALD3_HUMAN	M	313	ENSP00000268485:I313M	ENSP00000268485:I313M	I	+	3	3	MARVELD3	70225940	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-4.054000	0.00304	-2.793000	0.00355	-0.882000	0.02950	ATC	.		0.582	MARVELD3-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000268991.2	NM_052858	
CARNS1	57571	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	11	67186527	67186527	+	Missense_Mutation	SNP	A	A	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr11:67186527A>G	ENST00000307823.3	+	4	748	c.296A>G	c.(295-297)cAg>cGg	p.Q99R	CARNS1_ENST00000531040.1_Missense_Mutation_p.Q222R|CARNS1_ENST00000423745.2_Missense_Mutation_p.Q99R|CARNS1_ENST00000445895.2_Missense_Mutation_p.Q222R	NM_020811.1	NP_065862.1	A5YM72	CRNS1_HUMAN	carnosine synthase 1	99					ATP catabolic process (GO:0006200)|carnosine biosynthetic process (GO:0035499)		ATP binding (GO:0005524)|ATPase activity (GO:0016887)|carnosine synthase activity (GO:0047730)|metal ion binding (GO:0046872)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(7)	11						TTGCTGGCCCAGCAGGGTGGT	0.687																																					p.Q222R		.											.	.	.	0			c.A665G						.						5.0	7.0	7.0					11																	67186527		2022	4140	6162	SO:0001583	missense	57571	exon5			TGGCCCAGCAGGG		CCDS44658.1, CCDS53667.1	11q13.1	2010-03-25	2010-03-25	2010-03-25	ENSG00000172508	ENSG00000172508			29268	protein-coding gene	gene with protein product		613368	"""ATP-grasp domain containing 1"""	ATPGD1		20097752	Standard	NM_020811		Approved	KIAA1394	uc010rpr.2	A5YM72		ENST00000307823.3:c.296A>G	11.37:g.67186527A>G	ENSP00000308268:p.Gln99Arg	Somatic	52	0		WXS	Illumina HiSeq	.	29	12	NM_001166222	A8K1M3|B4DFC6|E9PK38|F5H427|Q8N467|Q9P2F3	Missense_Mutation	SNP	ENST00000307823.3	37	CCDS44658.1	.	.	.	.	.	.	.	.	.	.	A	12.47	1.947033	0.34377	.	.	ENSG00000172508	ENST00000531040;ENST00000307823;ENST00000542831;ENST00000539452;ENST00000423745;ENST00000445895	T;T;T;T	0.32988	1.43;1.44;1.44;1.46	4.38	1.95	0.26073	.	.	.	.	.	T	0.17959	0.0431	N	0.19112	0.55	0.21740	N	0.999563	B;B;B	0.09022	0.002;0.001;0.002	B;B;B	0.08055	0.003;0.001;0.003	T	0.22103	-1.0226	9	0.62326	D	0.03	.	4.8046	0.13314	0.6642:0.1582:0.1777:0.0	.	222;99;238	F5H427;A5YM72;A5YM72-3	.;CRNS1_HUMAN;.	R	222;99;222;238;99;222	ENSP00000431670:Q222R;ENSP00000308268:Q99R;ENSP00000401519:Q99R;ENSP00000389009:Q222R	ENSP00000308268:Q99R	Q	+	2	0	CARNS1	66943103	0.031000	0.19500	0.986000	0.45419	0.792000	0.44763	0.952000	0.29149	0.203000	0.20529	0.459000	0.35465	CAG	.		0.687	CARNS1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000395501.1	NM_020811	
LINC00472	79940	hgsc.bcm.edu	37	6	72128283	72128283	+	lincRNA	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr6:72128283A>C	ENST00000426635.2	-	0	770				RP3-331H24.5_ENST00000602823.1_lincRNA	NR_026807.1		Q9H8W2	CF155_HUMAN	long intergenic non-protein coding RNA 472																		TCTCCACTAAAGCATGATCAT	0.318																																					.		.											.	.	.	0			.						.																																					79940	.			CACTAAAGCATGA			6q13	2012-10-12	2011-08-31	2011-08-31	ENSG00000233237	ENSG00000233237		"""Long non-coding RNAs"""	21380	non-coding RNA	RNA, long non-coding			"""chromosome 6 open reading frame 155"""	C6orf155			Standard	XR_426058		Approved	dJ288M22.3, FLJ13189	uc003pfz.1	Q9H8W2	OTTHUMG00000015006		6.37:g.72128283A>C		Somatic	44	0		WXS	Illumina HiSeq	.	46	9	.	E1P533|Q5TG13	RNA	SNP	ENST00000426635.2	37																																																																																				.		0.318	LINC00472-004	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000041168.3	NM_024882	
ZHX2	22882	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	8	123965153	123965153	+	Missense_Mutation	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr8:123965153A>C	ENST00000314393.4	+	3	2238	c.1403A>C	c.(1402-1404)gAg>gCg	p.E468A		NM_014943.3	NP_055758.1	Q9Y6X8	ZHX2_HUMAN	zinc fingers and homeoboxes 2	468	Required for interaction with NFYA.				mRNA catabolic process (GO:0006402)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(15)|ovary(1)|prostate(1)|skin(4)|stomach(3)|urinary_tract(1)	45	Lung NSC(37;2e-09)|Ovarian(258;0.0205)|Hepatocellular(40;0.105)		STAD - Stomach adenocarcinoma(47;0.00527)			GACGATGCCGAGGTTTACCGG	0.567																																					p.E468A	Esophageal Squamous(94;1056 1388 11767 13799 49639)	.											.	.	.	0			c.A1403C						.						96.0	100.0	98.0					8																	123965153		2203	4300	6503	SO:0001583	missense	22882	exon3			ATGCCGAGGTTTA	AB020661	CCDS6336.1	8q24.13	2012-03-09	2004-01-23		ENSG00000178764	ENSG00000178764		"""Zinc fingers, C2H2-type"", ""Homeoboxes / ZF class"""	18513	protein-coding gene	gene with protein product		609185	"""zinc-fingers and homeoboxes 2"""			10048485, 12741956	Standard	XM_005250837		Approved	KIAA0854	uc003ypk.1	Q9Y6X8	OTTHUMG00000165077	ENST00000314393.4:c.1403A>C	8.37:g.123965153A>C	ENSP00000314709:p.Glu468Ala	Somatic	16	0		WXS	Illumina HiSeq	.	16	5	NM_014943		Missense_Mutation	SNP	ENST00000314393.4	37	CCDS6336.1	.	.	.	.	.	.	.	.	.	.	A	19.79	3.892150	0.72524	.	.	ENSG00000178764	ENST00000314393	D	0.93488	-3.23	5.94	5.94	0.96194	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);	0.102836	0.64402	D	0.000004	D	0.95749	0.8617	L	0.55834	1.745	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.96101	0.9069	10	0.72032	D	0.01	-23.4284	16.3979	0.83621	1.0:0.0:0.0:0.0	.	468	Q9Y6X8	ZHX2_HUMAN	A	468	ENSP00000314709:E468A	ENSP00000314709:E468A	E	+	2	0	ZHX2	124034334	1.000000	0.71417	0.997000	0.53966	0.779000	0.44077	7.161000	0.77505	2.279000	0.76181	0.459000	0.35465	GAG	.		0.567	ZHX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381709.1	NM_014943	
RP11-377D9.3	0	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	12	13157460	13157460	+	lincRNA	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr12:13157460T>G	ENST00000543321.1	+	0	31																											AAGTGGAATTTCGACATGGAT	0.413																																					.		.											.	.	.	0			.						.																																					93164	.			GGAATTTCGACAT																													12.37:g.13157460T>G		Somatic	16	0		WXS	Illumina HiSeq	.	10	4	.		RNA	SNP	ENST00000543321.1	37																																																																																				.		0.413	RP11-377D9.3-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000401005.1		
KIAA0319L	79932	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	36020083	36020083	+	Missense_Mutation	SNP	T	T	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr1:36020083T>C	ENST00000325722.3	-	2	244	c.10A>G	c.(10-12)Agg>Ggg	p.R4G	NCDN_ENST00000373253.3_5'Flank	NM_024874.4	NP_079150.3	Q8IZA0	K319L_HUMAN	KIAA0319-like	4						cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|kidney(3)|large_intestine(7)|lung(12)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|urinary_tract(1)	34		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				ACTCCCAGCCTCTTCTCCATG	0.428																																					p.R4G		.											.	.	.	0			c.A10G						.						70.0	70.0	70.0					1																	36020083		2203	4300	6503	SO:0001583	missense	79932	exon2			CCAGCCTCTTCTC	AY163234	CCDS390.1	1p34.3	2008-10-24			ENSG00000142687	ENSG00000142687			30071	protein-coding gene	gene with protein product		613535				11347906	Standard	NM_024874		Approved	KIAA1837	uc001byx.3	Q8IZA0	OTTHUMG00000004370	ENST00000325722.3:c.10A>G	1.37:g.36020083T>C	ENSP00000318406:p.Arg4Gly	Somatic	76	0		WXS	Illumina HiSeq	.	47	21	NM_024874	B1AN13|D3DPR8|O95010|Q6PJJ7|Q7L1C9|Q8N2B3|Q8NDA0|Q8WY39|Q8WYZ5|Q96IC3|Q96JJ0|Q9BUW6|Q9H7V0	Missense_Mutation	SNP	ENST00000325722.3	37	CCDS390.1	.	.	.	.	.	.	.	.	.	.	T	14.46	2.542869	0.45280	.	.	ENSG00000142687	ENST00000325722;ENST00000426982;ENST00000440579;ENST00000373258;ENST00000469892;ENST00000494948	T;T;T;T;T	0.56103	3.01;3.0;2.43;1.11;0.48	5.32	1.54	0.23209	.	0.391150	0.24220	N	0.040450	T	0.32164	0.0820	N	0.14661	0.345	0.21579	N	0.999639	B;B;B	0.30068	0.253;0.267;0.02	B;B;B	0.31337	0.128;0.04;0.027	T	0.19192	-1.0313	10	0.54805	T	0.06	0.0276	7.6546	0.28369	0.0:0.0748:0.2631:0.6622	.	4;4;4	B4DYG9;B1AN14;Q8IZA0	.;.;K319L_HUMAN	G	4	ENSP00000318406:R4G;ENSP00000395883:R4G;ENSP00000407576:R4G;ENSP00000362355:R4G;ENSP00000419396:R4G	ENSP00000318406:R4G	R	-	1	2	KIAA0319L	35792670	0.994000	0.37717	0.158000	0.22627	0.836000	0.47400	1.416000	0.34759	0.038000	0.15604	-1.871000	0.00553	AGG	.		0.428	KIAA0319L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012684.2	NM_024874	
KIR3DX1	90011	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	19	55054772	55054772	+	Missense_Mutation	SNP	G	G	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr19:55054772G>A	ENST00000335056.3	+	8	1117	c.1079G>A	c.(1078-1080)aGa>aAa	p.R360K	KIR3DX1_ENST00000482404.1_3'UTR			Q9H7L2	KI3X1_HUMAN	killer cell immunoglobulin-like receptor, three domains, X1	0						extracellular region (GO:0005576)				endometrium(1)|kidney(2)|large_intestine(4)|lung(14)|ovary(1)|pancreas(1)|skin(1)	24				GBM - Glioblastoma multiforme(193;0.099)		AGACACAGGAGATCATATATG	0.537																																					.	Colon(183;529 2002 28270 32358 35845)|Esophageal Squamous(50;443 1006 2278 10294 37938)	.											.	.	.	0			.						.																																			SO:0001583	missense	90011	.			ACAGGAGATCATA	BC033195		19q13.42	2013-03-26	2006-09-12	2006-09-12	ENSG00000104970	ENSG00000104970		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	25043	other	unknown			"""leukocyte receptor cluster (LRC) member 12"""	LENG12		11441184	Standard	NR_026716		Approved	FLJ00060	uc010erm.2	Q9H7L2	OTTHUMG00000065696	ENST00000335056.3:c.1079G>A	19.37:g.55054772G>A	ENSP00000335388:p.Arg360Lys	Somatic	35	0		WXS	Illumina HiSeq	.	25	13	.	B7WNL0|Q8N0S4	RNA	SNP	ENST00000335056.3	37		.	.	.	.	.	.	.	.	.	.	G	10.10	1.256871	0.22965	.	.	ENSG00000104970	ENST00000335056	T	0.00538	6.71	2.33	-4.67	0.03319	.	.	.	.	.	T	0.00440	0.0014	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.41680	-0.9495	6	0.87932	D	0	.	0.2896	0.00256	0.2624:0.2914:0.2198:0.2264	.	.	.	.	K	360	ENSP00000335388:R360K	ENSP00000335388:R360K	R	+	2	0	KIR3DX1	59746584	0.005000	0.15991	0.000000	0.03702	0.002000	0.02628	-0.275000	0.08525	-1.198000	0.02669	-0.136000	0.14681	AGA	.		0.537	KIR3DX1-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000140800.2	NR_026716	
PUM1	9698	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	31437700	31437700	+	Missense_Mutation	SNP	T	T	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr1:31437700T>C	ENST00000257075.5	-	14	2237	c.2144A>G	c.(2143-2145)gAc>gGc	p.D715G	PUM1_ENST00000373742.2_Missense_Mutation_p.D656G|PUM1_ENST00000423018.2_Missense_Mutation_p.D571G|PUM1_ENST00000426105.2_Missense_Mutation_p.D715G|PUM1_ENST00000490546.1_5'Flank|PUM1_ENST00000373747.3_Missense_Mutation_p.D716G|PUM1_ENST00000440538.2_Missense_Mutation_p.D689G|PUM1_ENST00000424085.2_Missense_Mutation_p.D473G|PUM1_ENST00000373741.4_Missense_Mutation_p.D751G	NM_014676.2	NP_055491.1	Q14671	PUM1_HUMAN	pumilio RNA-binding family member 1	715	Ser-rich.				membrane organization (GO:0061024)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of translation (GO:0006417)	cytosol (GO:0005829)	poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(2)|endometrium(8)|kidney(4)|large_intestine(8)|lung(17)|ovary(2)|pancreas(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	48		Colorectal(325;0.0211)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0308)|all_neural(195;0.0381)|Breast(348;0.0848)|Medulloblastoma(700;0.123)		STAD - Stomach adenocarcinoma(196;0.0232)|READ - Rectum adenocarcinoma(331;0.0681)		CTTATAAAGGTCACTGCTGCC	0.507																																					p.D715G		.											.	.	.	0			c.A2144G						.						80.0	83.0	82.0					1																	31437700		2203	4300	6503	SO:0001583	missense	9698	exon14			TAAAGGTCACTGC	AF315592	CCDS338.1, CCDS44099.1	1p35.2	2013-09-02	2013-09-02		ENSG00000134644	ENSG00000134644			14957	protein-coding gene	gene with protein product		607204	"""pumilio (Drosophila) homolog 1"", ""pumilio homolog 1 (Drosophila)"""				Standard	NM_001020658		Approved	PUMH1, KIAA0099	uc001bsh.1	Q14671	OTTHUMG00000003795	ENST00000257075.5:c.2144A>G	1.37:g.31437700T>C	ENSP00000257075:p.Asp715Gly	Somatic	69	0		WXS	Illumina HiSeq	.	65	34	NM_014676	A8K6W4|B4DG92|D3DPN3|E9PCJ0|Q53HH5|Q5VXY7|Q9HAN1	Missense_Mutation	SNP	ENST00000257075.5	37	CCDS338.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	20.6|20.6	4.012615|4.012615	0.75161|0.75161	.|.	.|.	ENSG00000134644|ENSG00000134644	ENST00000424085;ENST00000257075;ENST00000373747;ENST00000373749;ENST00000426105;ENST00000440538;ENST00000373741;ENST00000423018;ENST00000373742|ENST00000498419	T;T;T;T;T;T;T;T|.	0.20738|.	2.11;2.05;2.32;2.31;2.4;2.31;2.4;2.05|.	5.54|5.54	5.54|5.54	0.83059|0.83059	.|.	0.085177|.	0.85682|.	D|.	0.000000|.	T|.	0.62998|.	0.2474|.	L|L	0.48642|0.48642	1.525|1.525	0.80722|0.80722	D|D	1|1	D;P;P;D;D;B;D|.	0.60160|.	0.987;0.949;0.935;0.97;0.987;0.264;0.987|.	P;P;P;P;P;B;P|.	0.55345|.	0.759;0.599;0.599;0.774;0.759;0.074;0.759|.	T|.	0.60362|.	-0.7278|.	10|.	0.33141|.	T|.	0.24|.	-5.2391|-5.2391	15.6674|15.6674	0.77242|0.77242	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	656;571;751;689;715;715;715|.	B4DG92;E7EWT3;Q5T1Z8;Q14671-2;Q14671;E9PCJ0;Q53HH5|.	.;.;.;.;PUM1_HUMAN;.;.|.	G|W	473;715;716;453;715;689;751;571;656|426	ENSP00000400141:D473G;ENSP00000257075:D715G;ENSP00000362852:D716G;ENSP00000391723:D715G;ENSP00000401777:D689G;ENSP00000362846:D751G;ENSP00000399440:D571G;ENSP00000362847:D656G|.	ENSP00000257075:D715G|.	D|X	-|-	2|3	0|0	PUM1|PUM1	31210287|31210287	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	8.035000|8.035000	0.88872|0.88872	2.116000|2.116000	0.64780|0.64780	0.533000|0.533000	0.62120|0.62120	GAC|TGA	.		0.507	PUM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000010671.1		
MPDZ	8777	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	9	13176276	13176276	+	Silent	SNP	A	A	G	rs540572504		TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr9:13176276A>G	ENST00000319217.7	-	20	3037	c.2790T>C	c.(2788-2790)acT>acC	p.T930T	MPDZ_ENST00000541718.1_Silent_p.T930T|MPDZ_ENST00000536827.1_Silent_p.T930T|MPDZ_ENST00000381022.2_Silent_p.T930T|MPDZ_ENST00000381015.4_Silent_p.T930T|MPDZ_ENST00000447879.1_Silent_p.T930T|MPDZ_ENST00000546205.1_Silent_p.T930T	NM_001261406.1	NP_001248335.1	O75970	MPDZ_HUMAN	multiple PDZ domain protein	930					cell adhesion (GO:0007155)|myelination (GO:0042552)|viral process (GO:0016032)	apical plasma membrane (GO:0016324)|apicolateral plasma membrane (GO:0016327)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|neuron projection (GO:0043005)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)|tight junction (GO:0005923)	protein C-terminus binding (GO:0008022)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(14)|lung(15)|ovary(5)|prostate(7)|stomach(1)|urinary_tract(2)	61				GBM - Glioblastoma multiforme(50;2.03e-06)		AGTCATTTATAGTAAAGCCAG	0.388													A|||	1	0.000199681	0.0	0.0014	5008	,	,		18196	0.0		0.0	False		,,,				2504	0.0				p.T930T		.											.	.	.	0			c.T2790C						.						114.0	98.0	103.0					9																	13176276		1871	4114	5985	SO:0001819	synonymous_variant	8777	exon20			ATTTATAGTAAAG	AF093419	CCDS47951.1, CCDS59119.1, CCDS59120.1	9p23	2008-05-15			ENSG00000107186	ENSG00000107186			7208	protein-coding gene	gene with protein product		603785					Standard	NM_003829		Approved	MUPP1	uc003zlb.4	O75970	OTTHUMG00000021031	ENST00000319217.7:c.2790T>C	9.37:g.13176276A>G		Somatic	81	0		WXS	Illumina HiSeq	.	44	22	NM_003829	A6NLC2|B2RTS3|B7ZMI4|O43798|Q4LE30|Q5CZ80|Q5JTX3|Q5JTX6|Q5JTX7|Q5JUC3|Q5JUC4|Q5VZ62|Q8N790	Silent	SNP	ENST00000319217.7	37																																																																																				.		0.388	MPDZ-001	KNOWN	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000055485.2	NM_003829	
GTF3C1	2975	hgsc.bcm.edu	37	16	27549552	27549552	+	Missense_Mutation	SNP	C	C	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr16:27549552C>T	ENST00000356183.4	-	3	572	c.557G>A	c.(556-558)cGg>cAg	p.R186Q	GTF3C1_ENST00000561623.1_Missense_Mutation_p.R186Q	NM_001520.3	NP_001511.2	Q12789	TF3C1_HUMAN	general transcription factor IIIC, polypeptide 1, alpha 220kDa	186					5S class rRNA transcription from RNA polymerase III type 1 promoter (GO:0042791)|gene expression (GO:0010467)|rRNA transcription (GO:0009303)|transcription from RNA polymerase III promoter (GO:0006383)|transcription, DNA-templated (GO:0006351)|tRNA transcription (GO:0009304)|tRNA transcription from RNA polymerase III promoter (GO:0042797)	membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|transcription factor TFIIIC complex (GO:0000127)	DNA binding (GO:0003677)			breast(2)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(14)|liver(3)|lung(28)|ovary(2)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)	80						CCACCTGGACCGGCCTAGCCG	0.577																																					p.R186Q		.											GTF3C1,right_upper_lobe,carcinoma,+1,1	GTF3C1	+1	0			c.G557A						.						63.0	65.0	64.0					16																	27549552		2197	4300	6497	SO:0001583	missense	2975	exon3			CTGGACCGGCCTA	U06485	CCDS32414.1, CCDS66988.1	16p12	2010-03-23	2002-08-29			ENSG00000077235		"""General transcription factors"""	4664	protein-coding gene	gene with protein product		603246	"""general transcription factor IIIC, polypeptide 1 (alpha subunit, 220kD )"""			8164661, 8127861	Standard	NM_001520		Approved	TFIIIC220	uc002dov.2	Q12789		ENST00000356183.4:c.557G>A	16.37:g.27549552C>T	ENSP00000348510:p.Arg186Gln	Somatic	63	0		WXS	Illumina HiSeq	.	42	2	NM_001520	B2RP21|Q12838|Q6DKN9|Q9Y4W9	Missense_Mutation	SNP	ENST00000356183.4	37	CCDS32414.1	.	.	.	.	.	.	.	.	.	.	C	36	5.882578	0.97062	.	.	ENSG00000077235	ENST00000356183	T	0.46063	0.88	5.73	5.73	0.89815	.	0.069937	0.64402	D	0.000015	T	0.68256	0.2981	M	0.78456	2.415	0.44402	D	0.997315	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	T	0.69316	-0.5177	10	0.66056	D	0.02	-1.9192	19.8705	0.96849	0.0:1.0:0.0:0.0	.	186;186	Q12789;Q12789-3	TF3C1_HUMAN;.	Q	186	ENSP00000348510:R186Q	ENSP00000348510:R186Q	R	-	2	0	GTF3C1	27457053	1.000000	0.71417	1.000000	0.80357	0.935000	0.57460	7.411000	0.80078	2.861000	0.98227	0.655000	0.94253	CGG	.		0.577	GTF3C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433856.1	NM_001520	
USP12	219333	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	13	27669906	27669906	+	Silent	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr13:27669906T>G	ENST00000282344.6	-	4	661	c.405A>C	c.(403-405)acA>acC	p.T135T		NM_182488.3	NP_872294.2	O75317	UBP12_HUMAN	ubiquitin specific peptidase 12	135	USP.				protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type endopeptidase activity (GO:0004197)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			breast(3)|endometrium(3)|kidney(1)|large_intestine(2)|lung(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17		Lung SC(185;0.0161)		all cancers(112;0.0508)|GBM - Glioblastoma multiforme(144;0.168)|Epithelial(112;0.244)|OV - Ovarian serous cystadenocarcinoma(117;0.246)		TATCAGCAATTGTATTTAGTA	0.294																																					p.T135T	Ovarian(37;808 911 7590 44442 44991)	.											.	.	.	0			c.A405C						.						56.0	57.0	57.0					13																	27669906		2203	4296	6499	SO:0001819	synonymous_variant	219333	exon4			AGCAATTGTATTT	AL049221	CCDS31952.1	13q12.13	2010-05-12	2005-08-08	2003-10-08	ENSG00000152484	ENSG00000152484		"""Ubiquitin-specific peptidases"""	20485	protein-coding gene	gene with protein product			"""ubiquitin specific protease 12 like 1"", ""ubiquitin specific protease 12"""	USP12L1		12838346	Standard	NM_182488		Approved		uc001uqy.3	O75317	OTTHUMG00000016626	ENST00000282344.6:c.405A>C	13.37:g.27669906T>G		Somatic	250	0		WXS	Illumina HiSeq	.	123	47	NM_182488	A8K0X0|Q5VZV3|Q8TC49	Silent	SNP	ENST00000282344.6	37	CCDS31952.1																																																																																			.		0.294	USP12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044264.1	NM_182488	
SEPT7P2	641977	hgsc.bcm.edu;bcgsc.ca	37	7	45805412	45805412	+	RNA	SNP	C	C	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr7:45805412C>G	ENST00000429741.1	-	0	295									septin 7 pseudogene 2																		CCAGATTCACCTAAAAGAAAT	0.343																																					.		.											.	.	.	0			.						.																																					641977	.			ATTCACCTAAAAG	AL133216		7p12.3	2010-03-24	2010-03-24	2010-03-24	ENSG00000214765	ENSG00000214765			32339	pseudogene	pseudogene		611563	"""septin 7B"", ""septin 13"""	SEPT7B, SEPT13		15915442	Standard	NR_024271		Approved	DKFZp313J1114	uc003tnf.4		OTTHUMG00000155423		7.37:g.45805412C>G		Somatic	224	0		WXS	Illumina HiSeq	.	120	48	.		RNA	SNP	ENST00000429741.1	37																																																																																				.		0.343	SEPT7P2-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000340060.1	NR_024271	
BCAP29	55973	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	7	107258885	107258885	+	3'UTR	SNP	C	C	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr7:107258885C>A	ENST00000005259.4	+	0	1142				BCAP29_ENST00000445771.2_Missense_Mutation_p.F294L|BCAP29_ENST00000379117.2_3'UTR|BCAP29_ENST00000379119.2_Missense_Mutation_p.F294L|BCAP29_ENST00000494086.1_3'UTR|BCAP29_ENST00000465919.1_3'UTR	NM_018844.3	NP_061332.2	Q9UHQ4	BAP29_HUMAN	B-cell receptor-associated protein 29						apoptotic process (GO:0006915)|ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)|osteoblast differentiation (GO:0001649)|protein localization to endoplasmic reticulum exit site (GO:0070973)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				cervix(1)|kidney(1)|large_intestine(4)|lung(4)|ovary(2)|skin(1)|urinary_tract(1)	14						AATTTAAGTTCAGAAAAATGC	0.294																																					p.F294L		.											.	.	.	0			c.C882A						.						53.0	56.0	55.0					7																	107258885		2202	4292	6494	SO:0001624	3_prime_UTR_variant	55973	exon8			TAAGTTCAGAAAA		CCDS34730.1, CCDS34731.1	7q22.3	2012-09-20			ENSG00000075790	ENSG00000075790			24131	protein-coding gene	gene with protein product						12477932	Standard	NM_018844		Approved	BAP29, DKFZp686M2086	uc011kma.1	Q9UHQ4	OTTHUMG00000154770	ENST00000005259.4:c.*77C>A	7.37:g.107258885C>A		Somatic	116	0		WXS	Illumina HiSeq	.	59	29	NM_001008405	G5E9L4|O95003	Missense_Mutation	SNP	ENST00000005259.4	37	CCDS34731.1	.	.	.	.	.	.	.	.	.	.	C	13.92	2.379785	0.42207	.	.	ENSG00000075790	ENST00000445771;ENST00000379119	.	.	.	4.64	0.348	0.16026	.	0.482463	0.15500	N	0.259093	T	0.15696	0.0378	N	0.08118	0	0.09310	N	0.999999	B	0.09022	0.002	B	0.11329	0.006	T	0.16217	-1.0410	9	0.87932	D	0	-24.1803	3.1818	0.06587	0.1996:0.4842:0.0:0.3162	.	294	G5E9L4	.	L	294	.	ENSP00000368414:F294L	F	+	3	2	BCAP29	107046121	0.004000	0.15560	0.398000	0.26321	0.429000	0.31625	-0.414000	0.07114	0.202000	0.20498	0.655000	0.94253	TTC	.		0.294	BCAP29-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000337011.2	NM_018844	
COG8	84342	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	16	69370532	69370532	+	Missense_Mutation	SNP	T	T	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr16:69370532T>A	ENST00000306875.4	-	2	575	c.461A>T	c.(460-462)gAa>gTa	p.E154V	RP11-343C2.9_ENST00000563634.1_Missense_Mutation_p.E29V|COG8_ENST00000562081.1_Missense_Mutation_p.E154V|NIP7_ENST00000254940.5_5'Flank|RP11-343C2.12_ENST00000562949.1_5'Flank|RP11-343C2.7_ENST00000564737.1_3'UTR|NIP7_ENST00000569637.2_5'Flank	NM_032382.4	NP_115758.3	Q96MW5	COG8_HUMAN	component of oligomeric golgi complex 8	154					protein transport (GO:0015031)	Golgi transport complex (GO:0017119)|membrane (GO:0016020)				breast(3)|kidney(1)|large_intestine(2)|ovary(2)|skin(1)	9						CTCCAGTATTTCCAAAATTTC	0.498																																					p.E154V		.											.	.	.	0			c.A461T						.						111.0	103.0	106.0					16																	69370532		2198	4300	6498	SO:0001583	missense	84342	exon2			AGTATTTCCAAAA	AK025968	CCDS10876.1	16q22.1	2011-05-31			ENSG00000213380	ENSG00000213380		"""Components of oligomeric golgi complex"""	18623	protein-coding gene	gene with protein product		606979				11980916	Standard	NM_032382		Approved	FLJ22315, DOR1	uc002ewy.2	Q96MW5	OTTHUMG00000154277	ENST00000306875.4:c.461A>T	16.37:g.69370532T>A	ENSP00000305459:p.Glu154Val	Somatic	32	0		WXS	Illumina HiSeq	.	23	5	NM_032382	Q0VAK2|Q8WVV6|Q9H6F8	Missense_Mutation	SNP	ENST00000306875.4	37	CCDS10876.1	.	.	.	.	.	.	.	.	.	.	T	24.2	4.505768	0.85282	.	.	ENSG00000213380	ENST00000306875	T	0.56611	0.45	5.79	5.79	0.91817	Cullin repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.77212	0.4097	M	0.88906	2.99	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.997	T	0.81022	-0.1121	10	0.54805	T	0.06	-4.7032	16.1189	0.81329	0.0:0.0:0.0:1.0	.	181;154	B4DYU2;Q96MW5	.;COG8_HUMAN	V	154	ENSP00000305459:E154V	ENSP00000305459:E154V	E	-	2	0	COG8	67928033	1.000000	0.71417	1.000000	0.80357	0.636000	0.38137	7.640000	0.83355	2.201000	0.70794	0.460000	0.39030	GAA	.		0.498	COG8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268948.2	NM_032382	
ATP8B3	148229	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	19	1811727	1811727	+	Silent	SNP	A	A	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr19:1811727A>T	ENST00000310127.6	-	2	247	c.9T>A	c.(7-9)acT>acA	p.T3T	ATP8B3_ENST00000539485.1_Silent_p.T3T|ATP8B3_ENST00000526092.2_Intron|ATP8B3_ENST00000525591.1_Intron	NM_138813.3	NP_620168.1	O60423	AT8B3_HUMAN	ATPase, aminophospholipid transporter, class I, type 8B, member 3	3					binding of sperm to zona pellucida (GO:0007339)	acrosomal vesicle (GO:0001669)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(9)|ovary(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	23		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GAGCGGGGCCAGTGCCCATTC	0.662																																					p.T3T		.											.	.	.	0			c.T9A						.						25.0	29.0	27.0					19																	1811727		1993	4136	6129	SO:0001819	synonymous_variant	148229	exon2			GGGGCCAGTGCCC	AA827939	CCDS45901.1, CCDS54196.1	19p13.3	2010-04-28	2010-04-28		ENSG00000130270	ENSG00000130270		"""ATPases / P-type"""	13535	protein-coding gene	gene with protein product	"""aminophospholipid translocase ATP8B3"", ""potential phospholipid-transporting ATPase IK"""	605866	"""ATPase, Class I, type 8B, member 3"", ""ATPase, class I, type 8B, member 3"""			11015572	Standard	NM_138813		Approved	ATPIK	uc002ltw.4	O60423	OTTHUMG00000166189	ENST00000310127.6:c.9T>A	19.37:g.1811727A>T		Somatic	16	0		WXS	Illumina HiSeq	.	14	10	NM_138813	Q7Z485|Q8IVB8|Q8N4Y8|Q96M22	Silent	SNP	ENST00000310127.6	37	CCDS45901.1																																																																																			.		0.662	ATP8B3-002	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000388279.1	NM_138813	
FMO6P	388714	hgsc.bcm.edu	37	1	171116923	171116923	+	Intron	SNP	G	G	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr1:171116923G>T	ENST00000236166.3	+	4	737							O60774	FMO6_HUMAN	flavin containing monooxygenase 6 pseudogene							endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	flavin adenine dinucleotide binding (GO:0050660)|N,N-dimethylaniline monooxygenase activity (GO:0004499)|NADP binding (GO:0050661)										TGACGTAAAGGTTTTGGGAAA	0.493																																					.		.											.	.	.	0			.						.																																			SO:0001627	intron_variant	388714	.			GTAAAGGTTTTGG	AK130511		1q24.3	2011-08-04	2006-12-04	2006-12-04	ENSG00000117507	ENSG00000117507			24024	pseudogene	pseudogene			"""flavin containing monooxygenase 6"""	FMO6		15077013	Standard	NR_002601		Approved		uc001ghj.1	O60774	OTTHUMG00000035503	ENST00000236166.3:c.627+16G>T	1.37:g.171116923G>T		Somatic	68	0		WXS	Illumina HiSeq	.	77	16	.		RNA	SNP	ENST00000236166.3	37																																																																																				.		0.493	FMO6P-003	NOVEL	not_organism_supported|basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000385941.4	XM_371326	
ATXN10	25814	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	22	46125305	46125305	+	Splice_Site	SNP	A	A	G	rs547165095		TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr22:46125305A>G	ENST00000252934.5	+	7	994	c.729A>G	c.(727-729)agA>agG	p.R243R	ATXN10_ENST00000381061.4_Splice_Site_p.R179R	NM_013236.3	NP_037368.1	Q9UBB4	ATX10_HUMAN	ataxin 10	243					cell death (GO:0008219)|nervous system development (GO:0007399)|neuron projection development (GO:0031175)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|extracellular space (GO:0005615)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)				central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(3)|ovary(1)|skin(1)	10		Ovarian(80;0.00973)|all_neural(38;0.0417)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0223)		TGTTTTACAGAGTTACACTGT	0.343																																					p.R243R		.											.	.	.	0			c.A729G						.						125.0	107.0	113.0					22																	46125305		2203	4300	6503	SO:0001630	splice_region_variant	25814	exon7			TTACAGAGTTACA	AK095309	CCDS14070.1, CCDS54540.1	22q13	2013-02-15	2004-08-12	2004-08-12	ENSG00000130638	ENSG00000130638		"""Ataxins"""	10549	protein-coding gene	gene with protein product		611150	"""spinocerebellar ataxia 10"""	SCA10		9973298	Standard	NM_013236		Approved	E46L, FLJ37990	uc003bgm.2	Q9UBB4	OTTHUMG00000150451	ENST00000252934.5:c.729-1A>G	22.37:g.46125305A>G		Somatic	40	0		WXS	Illumina HiSeq	.	15	7	NM_013236	A6NLC4|B4DG05|O14998|O15009|Q6I9X4	Silent	SNP	ENST00000252934.5	37	CCDS14070.1																																																																																			.		0.343	ATXN10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318142.2	NM_013236	Silent
CALCB	797	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	11	15096669	15096669	+	Missense_Mutation	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr11:15096669T>G	ENST00000533448.1	+	3	260	c.149T>G	c.(148-150)cTg>cGg	p.L50R	CALCB_ENST00000324229.6_Missense_Mutation_p.L50R|CALCB_ENST00000523376.1_Missense_Mutation_p.L61R			P10092	CALCB_HUMAN	calcitonin-related polypeptide beta	50					cellular calcium ion homeostasis (GO:0006874)|signal transduction (GO:0007165)	extracellular region (GO:0005576)	neuropeptide hormone activity (GO:0005184)			endometrium(1)|large_intestine(1)|lung(1)|skin(2)	5						CGCCTCCTGCTGGCTGCACTG	0.627											OREG0020793	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L50R		.											.	.	.	0			c.T149G						.						58.0	61.0	60.0					11																	15096669		2200	4294	6494	SO:0001583	missense	797	exon3			TCCTGCTGGCTGC		CCDS7820.1	11p14.2-p12	2013-02-25	2008-02-20			ENSG00000175868		"""Endogenous ligands"""	1438	protein-coding gene	gene with protein product		114160	"""calcitonin 2"""	CALC2			Standard	NM_000728		Approved	FLJ30166, CGRP-II	uc001mlx.1	P10092		ENST00000533448.1:c.149T>G	11.37:g.15096669T>G	ENSP00000433490:p.Leu50Arg	Somatic	48	0	700	WXS	Illumina HiSeq	.	31	13	NM_000728	A8K573|D3DQX4|Q569I0|Q9UCN9	Missense_Mutation	SNP	ENST00000533448.1	37	CCDS7820.1	.	.	.	.	.	.	.	.	.	.	T	23.0	4.359586	0.82353	.	.	ENSG00000175868	ENST00000523376;ENST00000324229;ENST00000533448	T;T;T	0.26223	1.75;1.75;1.75	5.4	4.26	0.50523	.	0.180007	0.27327	N	0.019878	T	0.54319	0.1851	M	0.90483	3.12	0.38099	D	0.937193	D	0.60160	0.987	D	0.63597	0.916	T	0.66400	-0.5933	10	0.87932	D	0	-22.8629	11.9707	0.53062	0.13:0.0:0.0:0.87	.	50	P10092	CALCB_HUMAN	R	61;50;50	ENSP00000428882:L61R;ENSP00000346017:L50R;ENSP00000433490:L50R	ENSP00000346017:L50R	L	+	2	0	CALCB	15053245	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.188000	0.77739	0.969000	0.38237	0.454000	0.30748	CTG	.		0.627	CALCB-003	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387433.1	NM_000728	
TMEM256-PLSCR3	100529211	hgsc.bcm.edu	37	17	7297797	7297797	+	5'UTR	SNP	T	T	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr17:7297797T>C	ENST00000574401.1	-	0	329				TMEM256-PLSCR3_ENST00000576201.1_5'UTR|TMEM256-PLSCR3_ENST00000576362.1_5'Flank|C17orf61-PLSCR3_ENST00000573331.1_3'UTR|TMEM256-PLSCR3_ENST00000324822.11_5'UTR|TMEM256-PLSCR3_ENST00000535512.1_5'UTR	NM_020360.3	NP_065093.2			TMEM256-PLSCR3 readthrough (NMD candidate)																		CCCGCTCACCTGGAGCCCCCA	0.746																																					.		.											.	.	.	0			.						.																																			SO:0001623	5_prime_UTR_variant	57048	.			CTCACCTGGAGCC			17p13.1	2013-09-25			ENSG00000187838	ENSG00000187838			49186	other	readthrough							Standard	NR_037719		Approved				OTTHUMG00000178150	ENST00000574401.1:c.-163A>G	17.37:g.7297797T>C		Somatic	35	0		WXS	Illumina HiSeq	.	14	6	.		RNA	SNP	ENST00000574401.1	37	CCDS42253.1																																																																																			.		0.746	TMEM256-PLSCR3-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440806.2		
PPFIBP2	8495	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	11	7669733	7669733	+	Missense_Mutation	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr11:7669733A>C	ENST00000299492.4	+	18	2150	c.1762A>C	c.(1762-1764)Acc>Ccc	p.T588P	PPFIBP2_ENST00000533792.1_Missense_Mutation_p.T430P|PPFIBP2_ENST00000530181.1_Missense_Mutation_p.T445P|PPFIBP2_ENST00000528883.1_Missense_Mutation_p.T476P|PPFIBP2_ENST00000530582.1_3'UTR	NM_003621.3	NP_003612	Q8ND30	LIPB2_HUMAN	PTPRF interacting protein, binding protein 2 (liprin beta 2)	588	SAM 1. {ECO:0000255|PROSITE- ProRule:PRU00184}.				cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|intracellular (GO:0005622)|presynaptic active zone (GO:0048786)	DNA binding (GO:0003677)|integrase activity (GO:0008907)			breast(8)|cervix(1)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	32				Epithelial(150;2.01e-07)|BRCA - Breast invasive adenocarcinoma(625;0.236)		TTCTGGCCACACCTTATTGAC	0.577																																					p.T588P		.											.	.	.	0			c.A1762C						.						176.0	140.0	152.0					11																	7669733		2201	4296	6497	SO:0001583	missense	8495	exon18			GGCCACACCTTAT	AF034803	CCDS31419.1, CCDS58116.1, CCDS58117.1	11p15.4	2013-01-10			ENSG00000166387	ENSG00000166387		"""Sterile alpha motif (SAM) domain containing"""	9250	protein-coding gene	gene with protein product		603142				9624153	Standard	NM_003621		Approved	Cclp1	uc001mfj.5	Q8ND30	OTTHUMG00000165617	ENST00000299492.4:c.1762A>C	11.37:g.7669733A>C	ENSP00000299492:p.Thr588Pro	Somatic	31	0		WXS	Illumina HiSeq	.	10	7	NM_003621	B7Z433|E9PK77|O75337|Q8WW26	Missense_Mutation	SNP	ENST00000299492.4	37	CCDS31419.1	.	.	.	.	.	.	.	.	.	.	A	21.9	4.216144	0.79352	.	.	ENSG00000166387	ENST00000299492;ENST00000533792;ENST00000541115;ENST00000528883;ENST00000530181	T;T;T;T	0.52057	0.68;0.68;0.68;0.68	5.87	5.87	0.94306	Sterile alpha motif domain (2);Sterile alpha motif/pointed domain (2);Sterile alpha motif, type 1 (1);	0.000000	0.85682	D	0.000000	T	0.72317	0.3445	M	0.87758	2.905	0.58432	D	0.999998	D;D;D;D;D;D	0.89917	1.0;0.997;1.0;0.999;0.999;1.0	D;P;D;D;D;D	0.91635	0.994;0.905;0.99;0.968;0.998;0.999	T	0.76517	-0.2930	10	0.54805	T	0.06	-15.5192	14.2326	0.65903	1.0:0.0:0.0:0.0	.	476;476;511;430;445;588	E9PK77;B7Z433;F5GWB0;E9PP16;E9PMU1;Q8ND30	.;.;.;.;.;LIPB2_HUMAN	P	588;430;511;476;445	ENSP00000299492:T588P;ENSP00000436498:T430P;ENSP00000435469:T476P;ENSP00000437321:T445P	ENSP00000299492:T588P	T	+	1	0	PPFIBP2	7626309	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	7.353000	0.79414	2.248000	0.74166	0.533000	0.62120	ACC	.		0.577	PPFIBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385345.2	NM_003621	
RSU1P2	100133308	hgsc.bcm.edu	37	10	45601831	45601831	+	RNA	SNP	T	T	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr10:45601831T>C	ENST00000423875.1	-	0	1373									Ras suppressor protein 1 pseudogene 2																		ATCAGCAGTTTCTAAGACACG	0.458																																					.		.											.	.	.	0			.						.																																					100133308	.			GCAGTTTCTAAGA			10q11.21	2013-06-03			ENSG00000242848	ENSG00000232554			44391	pseudogene	pseudogene							Standard	NR_024472		Approved		uc009xmq.2		OTTHUMG00000185442		10.37:g.45601831T>C		Somatic	6	0		WXS	Illumina HiSeq	.	10	7	.		RNA	SNP	ENST00000423875.1	37																																																																																				.		0.458	RSU1P2-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000471233.1		
HOOK1	51361	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	60330334	60330334	+	Missense_Mutation	SNP	C	C	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr1:60330334C>T	ENST00000371208.3	+	17	1914	c.1657C>T	c.(1657-1659)Cat>Tat	p.H553Y	HOOK1_ENST00000465876.1_Intron|HOOK1_ENST00000395561.2_Missense_Mutation_p.H511Y	NM_015888.4	NP_056972.1	Q9UJC3	HOOK1_HUMAN	hook microtubule-tethering protein 1	553	Sufficient for interaction with microtubules.				early endosome to late endosome transport (GO:0045022)|endosome organization (GO:0007032)|endosome to lysosome transport (GO:0008333)|lysosome organization (GO:0007040)|multicellular organismal development (GO:0007275)|protein transport (GO:0015031)|spermatid development (GO:0007286)	FHF complex (GO:0070695)|microtubule (GO:0005874)	identical protein binding (GO:0042802)	p.H553N(1)		biliary_tract(1)|breast(2)|endometrium(3)|kidney(2)|large_intestine(5)|lung(14)|ovary(1)|urinary_tract(1)	29	all_cancers(7;0.000129)					GTTGGAAGCTCATATGTAAGT	0.318																																					p.H553Y		.											.	.	.	1	Substitution - Missense(1)	lung(1)	c.C1657T						.						63.0	74.0	70.0					1																	60330334		2203	4299	6502	SO:0001583	missense	51361	exon17			GAAGCTCATATGT	AF044923	CCDS612.1	1p32.1	2013-08-21	2013-08-21		ENSG00000134709	ENSG00000134709			19884	protein-coding gene	gene with protein product		607820	"""hook homolog 1 (Drosophila)"""			9927460	Standard	XM_005270922		Approved	HK1	uc001czo.3	Q9UJC3	OTTHUMG00000008990	ENST00000371208.3:c.1657C>T	1.37:g.60330334C>T	ENSP00000360252:p.His553Tyr	Somatic	144	0		WXS	Illumina HiSeq	.	97	38	NM_015888	A8K8E9|A8MU44|B4DX15|O60561|Q5TG44	Missense_Mutation	SNP	ENST00000371208.3	37	CCDS612.1	.	.	.	.	.	.	.	.	.	.	C	21.0	4.081949	0.76528	.	.	ENSG00000134709	ENST00000371208;ENST00000395561	T;T	0.20463	2.07;2.07	5.83	5.83	0.93111	.	0.045329	0.85682	D	0.000000	T	0.45256	0.1333	M	0.79123	2.44	0.54753	D	0.999988	D	0.76494	0.999	D	0.74023	0.982	T	0.41787	-0.9489	10	0.02654	T	1	.	20.1338	0.98010	0.0:1.0:0.0:0.0	.	553	Q9UJC3	HOOK1_HUMAN	Y	553;511	ENSP00000360252:H553Y;ENSP00000378928:H511Y	ENSP00000360252:H553Y	H	+	1	0	HOOK1	60102922	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.077000	0.71275	2.770000	0.95276	0.655000	0.94253	CAT	.		0.318	HOOK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024934.1	NM_015888	
Unknown	0	hgsc.bcm.edu	37	2	132349305	132349305	+	IGR	SNP	C	C	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr2:132349305C>T								CCDC74A (58066 upstream) : RNU6-617P (11057 downstream)																							GCTGCCTCTTCTGTGAAGAAG	0.542																																					.		.											.	.	.	0			.						.																																			SO:0001628	intergenic_variant	100873780	.			CCTCTTCTGTGAA																													2.37:g.132349305C>T		Somatic	187	0		WXS	Illumina HiSeq	.	94	38	.		RNA	SNP		37																																																																																				.	0	0.542								
UPP2	151531	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	2	158977952	158977952	+	Missense_Mutation	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr2:158977952T>G	ENST00000005756.4	+	5	680	c.486T>G	c.(484-486)gaT>gaG	p.D162E	UPP2_ENST00000460456.1_Intron|UPP2_ENST00000409859.4_Missense_Mutation_p.D219E|UPP2_ENST00000605860.1_Missense_Mutation_p.D219E	NM_173355.3	NP_775491.1	O95045	UPP2_HUMAN	uridine phosphorylase 2	162					nucleobase-containing small molecule metabolic process (GO:0055086)|nucleoside metabolic process (GO:0009116)|nucleotide catabolic process (GO:0009166)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside catabolic process (GO:0046135)|pyrimidine nucleoside salvage (GO:0043097)|small molecule metabolic process (GO:0044281)|UMP salvage (GO:0044206)|uridine metabolic process (GO:0046108)	cytosol (GO:0005829)|type III intermediate filament (GO:0045098)	uridine phosphorylase activity (GO:0004850)			breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(11)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	31					Fluorouracil(DB00544)	TAATAACGGATATAGCTGTAG	0.398																																					p.D219E		.											.	.	.	0			c.T657G						.						218.0	223.0	221.0					2																	158977952		2203	4299	6502	SO:0001583	missense	151531	exon7			AACGGATATAGCT	AY225131	CCDS2207.1, CCDS46435.1	2q24.2	2008-02-05			ENSG00000007001	ENSG00000007001			23061	protein-coding gene	gene with protein product						12849978	Standard	NM_173355		Approved	UPASE2, UP2, UDRPASE2	uc002tzo.3	O95045	OTTHUMG00000131969	ENST00000005756.4:c.486T>G	2.37:g.158977952T>G	ENSP00000005756:p.Asp162Glu	Somatic	116	0		WXS	Illumina HiSeq	.	71	24	NM_001135098	B3KV87	Missense_Mutation	SNP	ENST00000005756.4	37	CCDS2207.1	.	.	.	.	.	.	.	.	.	.	T	0.011	-1.702355	0.00719	.	.	ENSG00000007001	ENST00000409859;ENST00000005756	D;D	0.87966	-2.32;-2.32	5.52	-2.81	0.05805	Nucleoside phosphorylase domain (1);	0.097549	0.64402	D	0.000002	T	0.74718	0.3753	L	0.32530	0.975	0.32777	N	0.50296	B	0.10296	0.003	B	0.12156	0.007	T	0.63915	-0.6529	10	0.06625	T	0.88	.	13.0204	0.58784	0.0:0.6223:0.0:0.3777	.	162	O95045	UPP2_HUMAN	E	219;162	ENSP00000387230:D219E;ENSP00000005756:D162E	ENSP00000005756:D162E	D	+	3	2	UPP2	158686198	0.001000	0.12720	0.001000	0.08648	0.044000	0.14063	-0.531000	0.06171	-0.383000	0.07858	0.459000	0.35465	GAT	.		0.398	UPP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254929.2	NM_173355	
DST	667	hgsc.bcm.edu	37	6	56406150	56406150	+	Intron	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr6:56406150A>C	ENST00000361203.3	-	58	15983				DST_ENST00000312431.6_Intron|DST_ENST00000446842.2_Intron|DST_ENST00000340834.4_5'Flank|DST_ENST00000244364.6_Intron|DST_ENST00000421834.2_Intron|DST_ENST00000370754.5_Intron|DST_ENST00000370769.4_Intron|DST_ENST00000370788.2_Intron			Q03001	DYST_HUMAN	dystonin						axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell motility (GO:0048870)|cytoplasmic microtubule organization (GO:0031122)|cytoskeleton organization (GO:0007010)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|maintenance of cell polarity (GO:0030011)|microtubule cytoskeleton organization (GO:0000226)|regulation of microtubule polymerization or depolymerization (GO:0031110)|response to wounding (GO:0009611)|retrograde axon cargo transport (GO:0008090)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integral component of membrane (GO:0016021)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|neurofilament cytoskeleton (GO:0060053)|nucleus (GO:0005634)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|microtubule plus-end binding (GO:0051010)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)			NS(1)|breast(5)|central_nervous_system(8)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(43)|ovary(7)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	105	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			ACTAACATCCAGTGTTCTGTG	0.393																																					.		.											.	.	.	0			.						.																																			SO:0001627	intron_variant	100873774	.			ACATCCAGTGTTC	M22942, M69225	CCDS4959.1, CCDS47443.1, CCDS75474.1	6p12.1	2013-01-10	2004-06-25	2004-07-01	ENSG00000151914	ENSG00000151914		"""EF-hand domain containing"""	1090	protein-coding gene	gene with protein product		113810	"""bullous pemphigoid antigen 1, 230/240kDa"""	BPAG1		2461961, 2276744	Standard	NM_001144770		Approved	BP240, KIAA0728, FLJ21489, FLJ13425, FLJ32235, FLJ30627, CATX-15, BPA, MACF2	uc021zba.2	Q03001	OTTHUMG00000014913	ENST00000361203.3:c.15976-4412T>G	6.37:g.56406150A>C		Somatic	68	0		WXS	Illumina HiSeq	.	59	14	.	B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	RNA	SNP	ENST00000361203.3	37																																																																																				.		0.393	DST-004	NOVEL	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000041021.3	NM_001723	
Unknown	0	hgsc.bcm.edu	37	2	139655835	139655835	+	IGR	SNP	T	T	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr2:139655835T>C								RN7SKP286 (34370 upstream) : AC062021.1 (467899 downstream)																							TTCTTGCAAGTATGAAGCTCA	0.303																																					.		.											.	.	.	0			.						.																																			SO:0001628	intergenic_variant	647012	.			TGCAAGTATGAAG																													2.37:g.139655835T>C		Somatic	13	0		WXS	Illumina HiSeq	.	14	6	.		RNA	SNP		37																																																																																				.	0	0.303								
CNTN2	6900	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	205027329	205027329	+	Missense_Mutation	SNP	A	A	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr1:205027329A>T	ENST00000331830.4	+	4	520	c.236A>T	c.(235-237)gAg>gTg	p.E79V		NM_005076.3	NP_005067.1	Q02246	CNTN2_HUMAN	contactin 2 (axonal)	79	Ig-like C2-type 1.				adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|cell adhesion (GO:0007155)|cellular protein localization (GO:0034613)|central nervous system myelination (GO:0022010)|cerebral cortex GABAergic interneuron migration (GO:0021853)|clustering of voltage-gated potassium channels (GO:0045163)|establishment of protein localization to juxtaparanode region of axon (GO:0071206)|learning (GO:0007612)|microtubule cytoskeleton organization (GO:0000226)|negative regulation of neuron differentiation (GO:0045665)|positive regulation of adenosine receptor signaling pathway (GO:0060168)|positive regulation of protein processing (GO:0010954)|presynaptic membrane organization (GO:0097090)|receptor internalization (GO:0031623)|regulation of astrocyte differentiation (GO:0048710)|regulation of axon diameter (GO:0031133)|regulation of neuronal synaptic plasticity (GO:0048168)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|juxtaparanode region of axon (GO:0044224)|myelin sheath (GO:0043209)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|synapse (GO:0045202)|voltage-gated potassium channel complex (GO:0008076)	carbohydrate binding (GO:0030246)|identical protein binding (GO:0042802)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(11)|lung(23)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	54	all_cancers(21;0.144)|Breast(84;0.0437)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.158)			AATGGTACCGAGATGAAGCTG	0.612																																					p.E79V	Melanoma(183;2548 2817 37099 41192)	.											.	.	.	0			c.A236T						.						26.0	26.0	26.0					1																	205027329		2203	4300	6503	SO:0001583	missense	6900	exon4			GTACCGAGATGAA	X67734	CCDS1449.1	1q32.1	2013-02-11			ENSG00000184144	ENSG00000184144		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	2172	protein-coding gene	gene with protein product		190197		TAX, AXT		8307567, 8586965	Standard	NM_005076		Approved	TAG-1, TAX1	uc001hbr.3	Q02246	OTTHUMG00000037105	ENST00000331830.4:c.236A>T	1.37:g.205027329A>T	ENSP00000330633:p.Glu79Val	Somatic	31	0		WXS	Illumina HiSeq	.	33	21	NM_005076	P78432|Q5T054	Missense_Mutation	SNP	ENST00000331830.4	37	CCDS1449.1	.	.	.	.	.	.	.	.	.	.	A	23.0	4.363463	0.82353	.	.	ENSG00000184144	ENST00000331830	T	0.13089	2.62	5.3	5.3	0.74995	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.116790	0.37669	N	0.001989	T	0.17238	0.0414	L	0.45744	1.44	0.80722	D	1	P	0.38335	0.627	B	0.41374	0.355	T	0.01734	-1.1285	10	0.39692	T	0.17	.	14.8945	0.70633	1.0:0.0:0.0:0.0	.	79	Q02246	CNTN2_HUMAN	V	79	ENSP00000330633:E79V	ENSP00000330633:E79V	E	+	2	0	CNTN2	203293952	1.000000	0.71417	0.977000	0.42913	0.784000	0.44337	5.761000	0.68801	1.982000	0.57802	0.533000	0.62120	GAG	.		0.612	CNTN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090080.3	NM_005076	
ATXN10	25814	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	22	46125307	46125307	+	Missense_Mutation	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr22:46125307T>G	ENST00000252934.5	+	7	996	c.731T>G	c.(730-732)gTt>gGt	p.V244G	ATXN10_ENST00000381061.4_Missense_Mutation_p.V180G	NM_013236.3	NP_037368.1	Q9UBB4	ATX10_HUMAN	ataxin 10	244					cell death (GO:0008219)|nervous system development (GO:0007399)|neuron projection development (GO:0031175)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|extracellular space (GO:0005615)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)				central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(3)|ovary(1)|skin(1)	10		Ovarian(80;0.00973)|all_neural(38;0.0417)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0223)		TTTTACAGAGTTACACTGTTA	0.353																																					p.V244G		.											.	.	.	0			c.T731G						.						130.0	110.0	116.0					22																	46125307		2203	4300	6503	SO:0001583	missense	25814	exon7			ACAGAGTTACACT	AK095309	CCDS14070.1, CCDS54540.1	22q13	2013-02-15	2004-08-12	2004-08-12	ENSG00000130638	ENSG00000130638		"""Ataxins"""	10549	protein-coding gene	gene with protein product		611150	"""spinocerebellar ataxia 10"""	SCA10		9973298	Standard	NM_013236		Approved	E46L, FLJ37990	uc003bgm.2	Q9UBB4	OTTHUMG00000150451	ENST00000252934.5:c.731T>G	22.37:g.46125307T>G	ENSP00000252934:p.Val244Gly	Somatic	39	0		WXS	Illumina HiSeq	.	15	7	NM_013236	A6NLC4|B4DG05|O14998|O15009|Q6I9X4	Missense_Mutation	SNP	ENST00000252934.5	37	CCDS14070.1	.	.	.	.	.	.	.	.	.	.	T	14.88	2.666383	0.47677	.	.	ENSG00000130638	ENST00000381061;ENST00000252934;ENST00000396011	.	.	.	5.26	5.26	0.73747	Armadillo-type fold (1);	0.126283	0.53938	D	0.000059	T	0.68128	0.2967	L	0.58101	1.795	0.80722	D	1	D;D	0.57899	0.981;0.96	P;P	0.60345	0.873;0.723	T	0.69068	-0.5243	9	0.48119	T	0.1	-6.4763	13.0497	0.58948	0.0:0.0:0.0:1.0	.	180;244	A6NLC4;Q9UBB4	.;ATX10_HUMAN	G	180;244;244	.	ENSP00000252934:V244G	V	+	2	0	ATXN10	44503971	0.998000	0.40836	0.738000	0.30950	0.104000	0.19210	4.275000	0.58927	2.202000	0.70862	0.533000	0.62120	GTT	.		0.353	ATXN10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318142.2	NM_013236	
ZNF513	130557	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	2	27601102	27601102	+	Silent	SNP	G	G	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr2:27601102G>A	ENST00000323703.6	-	4	1134	c.936C>T	c.(934-936)ttC>ttT	p.F312F	ZNF513_ENST00000491924.1_Intron|ZNF513_ENST00000407879.1_Silent_p.F250F	NM_144631.5	NP_653232.3	Q8N8E2	ZN513_HUMAN	zinc finger protein 513	312					regulation of transcription, DNA-templated (GO:0006355)|response to stimulus (GO:0050896)|retina development in camera-type eye (GO:0060041)|transcription, DNA-templated (GO:0006351)|visual perception (GO:0007601)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|transcription regulatory region DNA binding (GO:0044212)			endometrium(5)|kidney(1)|large_intestine(2)|lung(7)|ovary(2)	17	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					AGGTCCAAGGGAATAGCAGCT	0.652																																					p.F312F		.											.	.	.	0			c.C936T						.						39.0	41.0	40.0					2																	27601102		2203	4300	6503	SO:0001819	synonymous_variant	130557	exon4			CCAAGGGAATAGC	AL833946	CCDS1751.1, CCDS56114.1	2p23.3	2014-01-28			ENSG00000163795	ENSG00000163795		"""Zinc fingers, C2H2-type"""	26498	protein-coding gene	gene with protein product		613598				12477932	Standard	NM_001201459		Approved	FLJ32203, RP58	uc002rkk.3	Q8N8E2	OTTHUMG00000097783	ENST00000323703.6:c.936C>T	2.37:g.27601102G>A		Somatic	51	0		WXS	Illumina HiSeq	.	21	14	NM_144631	A8K3S5|B7WP71|Q3ZCU1|Q68CJ1|Q86UZ3|Q8NDL8|Q96ML3	Silent	SNP	ENST00000323703.6	37	CCDS1751.1																																																																																			.		0.652	ZNF513-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215026.2	NM_144631	
PAX8	7849	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	2	114002103	114002103	+	Missense_Mutation	SNP	C	C	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr2:114002103C>T	ENST00000429538.3	-	4	484	c.290G>A	c.(289-291)cGc>cAc	p.R97H	AC016683.6_ENST00000422956.2_RNA|PAX8_ENST00000397647.3_Missense_Mutation_p.R97H|PAX8_ENST00000263335.7_Missense_Mutation_p.R97H|AC016683.6_ENST00000436293.2_RNA|AC016683.6_ENST00000553869.2_RNA|AC016683.6_ENST00000445745.1_RNA|AC016683.6_ENST00000556070.1_RNA|AC016683.6_ENST00000451179.1_RNA|PAX8_ENST00000348715.5_Missense_Mutation_p.R97H|AC016683.6_ENST00000333145.5_RNA|PAX8_ENST00000263334.5_Missense_Mutation_p.R97H	NM_003466.3	NP_003457.1	Q06710	PAX8_HUMAN	paired box 8	97	Paired. {ECO:0000255|PROSITE- ProRule:PRU00381}.				anatomical structure morphogenesis (GO:0009653)|branching involved in ureteric bud morphogenesis (GO:0001658)|cellular response to gonadotropin stimulus (GO:0071371)|central nervous system development (GO:0007417)|inner ear morphogenesis (GO:0042472)|kidney development (GO:0001822)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|mesonephros development (GO:0001823)|metanephric comma-shaped body morphogenesis (GO:0072278)|metanephric distal convoluted tubule development (GO:0072221)|metanephric epithelium development (GO:0072207)|metanephric nephron tubule formation (GO:0072289)|metanephric S-shaped body morphogenesis (GO:0072284)|negative regulation of apoptotic process involved in metanephric collecting duct development (GO:1900215)|negative regulation of apoptotic process involved in metanephric nephron tubule development (GO:1900218)|negative regulation of mesenchymal cell apoptotic process involved in metanephric nephron morphogenesis (GO:0072305)|negative regulation of mesenchymal cell apoptotic process involved in metanephros development (GO:1900212)|otic vesicle development (GO:0071599)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0072108)|positive regulation of metanephric DCT cell differentiation (GO:2000594)|positive regulation of thyroid hormone generation (GO:2000611)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|pronephric field specification (GO:0039003)|pronephros development (GO:0048793)|regulation of apoptotic process (GO:0042981)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)|regulation of thyroid-stimulating hormone secretion (GO:2000612)|thyroid gland development (GO:0030878)|thyroid-stimulating hormone signaling pathway (GO:0038194)|transcription, DNA-templated (GO:0006351)|urogenital system development (GO:0001655)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding transcription factor activity (GO:0003700)|thyroid-stimulating hormone receptor activity (GO:0004996)|transcription regulatory region DNA binding (GO:0044212)		PAX8/PPARG(117)	breast(1)|endometrium(4)|kidney(2)|large_intestine(1)|liver(1)|lung(9)|ovary(1)|skin(1)	20						AGGGTTCTGGCGTTTGTAGTC	0.587			T	PPARG	follicular thyroid		Thyroid dysgenesis																														p.R97H	Ovarian(188;7 2067 9084 29802 29892)	.		Dom	yes		2	2q12-q14	7849	paired box gene 8	yes	E	.	.	.	0			c.G290A						.						185.0	203.0	197.0					2																	114002103		2193	4298	6491	SO:0001583	missense	7849	exon4			TTCTGGCGTTTGT	X69699	CCDS42735.1, CCDS42736.1, CCDS46398.1, CCDS46399.1	2q13	2011-06-20	2007-07-12		ENSG00000125618	ENSG00000125618		"""Paired boxes"", ""Homeoboxes / PRD class"""	8622	protein-coding gene	gene with protein product		167415	"""paired box gene 8"""			8431641, 7981748	Standard	NM_003466		Approved		uc010yxt.2	Q06710	OTTHUMG00000128529	ENST00000429538.3:c.290G>A	2.37:g.114002103C>T	ENSP00000395498:p.Arg97His	Somatic	40	0		WXS	Illumina HiSeq	.	33	17	NM_013952	Q09155|Q16337|Q16338|Q16339|Q4ZG35|Q96J49	Missense_Mutation	SNP	ENST00000429538.3	37	CCDS46398.1	.	.	.	.	.	.	.	.	.	.	C	23.4	4.410121	0.83340	.	.	ENSG00000125618	ENST00000263335;ENST00000397647;ENST00000348715;ENST00000429538;ENST00000263334	D;D;D;D;D	0.99479	-5.98;-5.98;-5.98;-5.98;-5.98	5.32	4.43	0.53597	Paired box protein, N-terminal (3);Winged helix-turn-helix transcription repressor DNA-binding (1);Homeodomain-like (1);	0.053373	0.64402	D	0.000001	D	0.99357	0.9774	M	0.70787	2.145	0.80722	D	1	P;D;D;P;P	0.89917	0.879;1.0;1.0;0.923;0.744	B;P;D;B;B	0.78314	0.126;0.881;0.991;0.171;0.171	D	0.98945	1.0792	10	0.87932	D	0	.	13.7248	0.62752	0.0:0.8443:0.1557:0.0	.	97;97;97;97;97	Q06710-2;Q06710-3;Q06710;Q06710-5;Q06710-4	.;.;PAX8_HUMAN;.;.	H	97	ENSP00000263335:R97H;ENSP00000380768:R97H;ENSP00000314750:R97H;ENSP00000395498:R97H;ENSP00000263334:R97H	ENSP00000263334:R97H	R	-	2	0	PAX8	113718573	1.000000	0.71417	0.857000	0.33713	0.951000	0.60555	4.973000	0.63763	1.224000	0.43551	0.655000	0.94253	CGC	.		0.587	PAX8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250353.5		
ZBTB37	84614	hgsc.bcm.edu	37	1	173836681	173836681	+	5'Flank	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr1:173836681T>G	ENST00000367701.5	+	0	0				GAS5_ENST00000363146.1_RNA|ZBTB37_ENST00000367702.1_5'Flank|ZBTB37_ENST00000367704.1_5'Flank|ZBTB37_ENST00000432989.1_5'Flank|GAS5_ENST00000363859.1_RNA|ZBTB37_ENST00000427304.1_5'Flank|SNORD78_ENST00000385582.1_RNA|GAS5_ENST00000385578.2_RNA|GAS5_ENST00000364822.2_RNA|GAS5_ENST00000364084.1_RNA			Q5TC79	ZBT37_HUMAN	zinc finger and BTB domain containing 37						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|skin(1)|urinary_tract(4)	13						AATGGAAATATTGGTGACACT	0.527																																					.		.											.	.	.	0			.						.																																			SO:0001631	upstream_gene_variant	60674	.			GAAATATTGGTGA	AK057310	CCDS1312.1, CCDS44278.1	1q24.2	2013-01-08			ENSG00000185278	ENSG00000185278		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	28365	protein-coding gene	gene with protein product						12477932	Standard	NM_032522		Approved	MGC2629, ZNF908	uc009wwp.1	Q5TC79	OTTHUMG00000037274		1.37:g.173836681T>G	Exception_encountered	Somatic	23	0		WXS	Illumina HiSeq	.	21	4	.	Q5TC80|Q96M87|Q9BQ88	RNA	SNP	ENST00000367701.5	37	CCDS44278.1																																																																																			.		0.527	ZBTB37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090729.2	NM_032522	
PLEKHG4	25894	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	16	67319000	67319000	+	Missense_Mutation	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr16:67319000T>G	ENST00000360461.5	+	12	4612	c.2077T>G	c.(2077-2079)Tgc>Ggc	p.C693G	PLEKHG4_ENST00000379344.3_Missense_Mutation_p.C693G|PLEKHG4_ENST00000427155.2_Missense_Mutation_p.C693G|PLEKHG4_ENST00000450733.1_Missense_Mutation_p.C612G	NM_001129727.1|NM_015432.3	NP_001123199.1|NP_056247.1	Q58EX7	PKHG4_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 4	693							Rho guanyl-nucleotide exchange factor activity (GO:0005089)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(14)|ovary(2)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	37				OV - Ovarian serous cystadenocarcinoma(108;0.00376)|Epithelial(162;0.0173)|all cancers(182;0.116)|Kidney(780;0.119)		TGCCTGCCACTGCCACCATGC	0.652																																					p.C693G		.											.	.	.	0			c.T2077G						.						23.0	24.0	24.0					16																	67319000		2152	4241	6393	SO:0001583	missense	25894	exon13			TGCCACTGCCACC	AK024475	CCDS32466.1, CCDS45512.1	16q22.1	2013-01-11						"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	24501	protein-coding gene	gene with protein product	"""puratrophin-1"""	609526	"""spinocerebellar ataxia 4"""	SCA4		16491300, 16001362	Standard	NM_015432		Approved	DKFZP434I216, ARHGEF44	uc010cef.3	Q58EX7		ENST00000360461.5:c.2077T>G	16.37:g.67319000T>G	ENSP00000353646:p.Cys693Gly	Somatic	61	0		WXS	Illumina HiSeq	.	35	16	NM_001129728	Q4G0J8|Q4H485|Q56A69|Q9H7K4|Q9UFW0	Missense_Mutation	SNP	ENST00000360461.5	37	CCDS32466.1	.	.	.	.	.	.	.	.	.	.	T	0.628	-0.818452	0.02776	.	.	ENSG00000196155	ENST00000360461;ENST00000427155;ENST00000379344;ENST00000450733	T;T;T;T	0.08458	3.09;3.09;3.09;3.1	4.48	-4.28	0.03732	.	0.732224	0.11277	N	0.580767	T	0.03564	0.0102	N	0.12746	0.255	0.09310	N	0.999999	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.44802	-0.9304	10	0.21540	T	0.41	.	7.0933	0.25295	0.0:0.1793:0.4647:0.356	.	612;693	Q58EX7-2;Q58EX7	.;PKHG4_HUMAN	G	693;693;693;612	ENSP00000353646:C693G;ENSP00000401118:C693G;ENSP00000368649:C693G;ENSP00000398030:C612G	ENSP00000353646:C693G	C	+	1	0	PLEKHG4	65876501	0.000000	0.05858	0.248000	0.24265	0.043000	0.13939	-0.307000	0.08167	-0.386000	0.07821	-1.122000	0.02009	TGC	.		0.652	PLEKHG4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421395.2	NM_015432	
SNX14	57231	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	6	86267770	86267770	+	Missense_Mutation	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr6:86267770A>C	ENST00000314673.3	-	7	734	c.558T>G	c.(556-558)atT>atG	p.I186M	SNX14_ENST00000346348.3_Missense_Mutation_p.I142M|SNX14_ENST00000508980.1_5'UTR|SNX14_ENST00000513865.1_Missense_Mutation_p.I186M|SNX14_ENST00000369627.2_Missense_Mutation_p.I186M|SNX14_ENST00000505648.1_Missense_Mutation_p.I134M|RP11-321N4.5_ENST00000503906.1_3'UTR	NM_153816.3	NP_722523.1	Q9Y5W7	SNX14_HUMAN	sorting nexin 14	186	PXA. {ECO:0000255|PROSITE- ProRule:PRU00147, ECO:0000255|PROSITE- ProRule:PRU00553}.				protein transport (GO:0015031)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	integral component of membrane (GO:0016021)	phosphatidylinositol binding (GO:0035091)			NS(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(11)|skin(1)	22		all_cancers(76;4.83e-07)|Acute lymphoblastic leukemia(125;3.3e-08)|Prostate(29;2.55e-07)|all_hematologic(105;3.66e-05)|all_epithelial(107;0.000695)|Lung NSC(302;0.197)|all_lung(197;0.24)		BRCA - Breast invasive adenocarcinoma(108;0.0423)		TAATAGATGGAATATCCACCT	0.279																																					p.I186M		.											.	.	.	0			c.T558G						.						103.0	105.0	104.0					6																	86267770		2201	4286	6487	SO:0001583	missense	57231	exon7			AGATGGAATATCC	AF121863	CCDS5003.1, CCDS5004.1, CCDS75490.1	6q15	2008-10-22			ENSG00000135317	ENSG00000135317		"""Sorting nexins"""	14977	protein-coding gene	gene with protein product						11485546, 11736640	Standard	XM_005248738		Approved	RGS-PX2	uc003pkr.3	Q9Y5W7	OTTHUMG00000015140	ENST00000314673.3:c.558T>G	6.37:g.86267770A>C	ENSP00000313121:p.Ile186Met	Somatic	80	0		WXS	Illumina HiSeq	.	83	19	NM_153816	B4DI55|Q4VBR3|Q5TCF9|Q5TCG0|Q6NUI7|Q6PI37|Q9BSD1	Missense_Mutation	SNP	ENST00000314673.3	37	CCDS5004.1	.	.	.	.	.	.	.	.	.	.	A	18.61	3.661294	0.67700	.	.	ENSG00000135317	ENST00000346348;ENST00000314673;ENST00000513865;ENST00000505648;ENST00000369627;ENST00000515216;ENST00000509338;ENST00000514419	T;T;T;T;T;T	0.32023	1.84;1.9;1.47;1.9;1.89;1.88	5.63	0.492	0.16872	Phox-associated domain (2);	0.050982	0.85682	D	0.000000	T	0.14830	0.0358	L	0.36672	1.1	0.80722	D	1	P;P;P;P	0.50710	0.896;0.938;0.915;0.896	P;P;P;P	0.49387	0.575;0.576;0.609;0.575	T	0.02610	-1.1134	10	0.32370	T	0.25	-18.0338	9.0915	0.36614	0.6968:0.0:0.3032:0.0	.	186;142;186;134	Q9Y5W7-4;Q9Y5W7-2;Q9Y5W7;Q9Y5W7-3	.;.;SNX14_HUMAN;.	M	142;186;186;134;186;113;90;185	ENSP00000257769:I142M;ENSP00000313121:I186M;ENSP00000420938:I186M;ENSP00000427380:I134M;ENSP00000358641:I186M;ENSP00000425630:I113M	ENSP00000313121:I186M	I	-	3	3	SNX14	86324489	0.997000	0.39634	1.000000	0.80357	0.998000	0.95712	0.662000	0.25038	0.140000	0.18849	0.533000	0.62120	ATT	.		0.279	SNX14-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041393.2	NM_153816	
HIRA	7290	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	22	19344493	19344493	+	Silent	SNP	G	G	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr22:19344493G>A	ENST00000263208.5	-	19	2572	c.2316C>T	c.(2314-2316)ctC>ctT	p.L772L	HIRA_ENST00000340170.4_Intron|HIRA_ENST00000541063.1_Silent_p.L728L|HIRA_ENST00000546308.1_Silent_p.L728L	NM_003325.3	NP_003316.3	P54198	HIRA_HUMAN	histone cell cycle regulator	772	Interaction with PAX3. {ECO:0000250}.|Interaction with histone H2B.|Interaction with histone H4.				anatomical structure morphogenesis (GO:0009653)|chromatin modification (GO:0016568)|DNA replication-independent nucleosome assembly (GO:0006336)|gastrulation (GO:0007369)|muscle cell differentiation (GO:0042692)|osteoblast differentiation (GO:0001649)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(14)|ovary(2)|prostate(1)|skin(1)	37	Colorectal(54;0.0993)					GGGATGGCAGGAGGATGGGAG	0.587																																					p.L772L		.											.	.	.	0			c.C2316T						.						281.0	217.0	239.0					22																	19344493		2203	4300	6503	SO:0001819	synonymous_variant	7290	exon19			TGGCAGGAGGATG	X75296	CCDS13759.1	22q11.2	2013-05-03	2013-05-03		ENSG00000100084	ENSG00000100084		"""WD repeat domain containing"""	4916	protein-coding gene	gene with protein product	"""DiGeorge critical region gene 1"""	600237	"""HIR (histone cell cycle regulation defective) homolog A (S. cerevisiae)"", ""HIR histone cell cycle regulation defective homolog A (S. cerevisiae)"""	TUPLE1		8111380, 7633437, 9731536	Standard	NM_003325		Approved	DGCR1, TUP1	uc002zpf.1	P54198	OTTHUMG00000150134	ENST00000263208.5:c.2316C>T	22.37:g.19344493G>A		Somatic	20	0		WXS	Illumina HiSeq	.	12	8	NM_003325	Q05BU9|Q8IXN2	Silent	SNP	ENST00000263208.5	37	CCDS13759.1																																																																																			.		0.587	HIRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316488.2	NM_003325	
OR4Q3	441669	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	14	20216384	20216384	+	Missense_Mutation	SNP	C	C	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr14:20216384C>G	ENST00000331723.1	+	1	798	c.798C>G	c.(796-798)ttC>ttG	p.F266L		NM_172194.1	NP_751944.1	Q8NH05	OR4Q3_HUMAN	olfactory receptor, family 4, subfamily Q, member 3	266						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(2)|breast(4)|endometrium(3)|kidney(2)|large_intestine(1)|lung(28)|pancreas(1)|skin(4)|upper_aerodigestive_tract(2)	47	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)		TCTGCAGCTTCTCTGTGGATA	0.443																																					p.F266L		.											.	.	.	0			c.C798G						.						165.0	168.0	167.0					14																	20216384		2203	4300	6503	SO:0001583	missense	441669	exon1			CAGCTTCTCTGTG	AF179768	CCDS32020.1	14p13	2012-08-09				ENSG00000182652		"""GPCR / Class A : Olfactory receptors"""	15426	protein-coding gene	gene with protein product				OR4Q4			Standard	NM_172194		Approved	C14orf13	uc010tkt.2	Q8NH05		ENST00000331723.1:c.798C>G	14.37:g.20216384C>G	ENSP00000330049:p.Phe266Leu	Somatic	37	0		WXS	Illumina HiSeq	.	27	6	NM_172194	Q6IEX4	Missense_Mutation	SNP	ENST00000331723.1	37	CCDS32020.1	.	.	.	.	.	.	.	.	.	.	.	4.669	0.124358	0.08931	.	.	ENSG00000182652	ENST00000331723	T	0.00054	8.8	4.35	1.17	0.20885	GPCR, rhodopsin-like superfamily (1);	0.000000	0.42294	U	0.000726	T	0.00073	0.0002	N	0.17838	0.53	0.09310	N	1	B	0.14012	0.009	B	0.23574	0.047	T	0.12372	-1.0550	10	0.09590	T	0.72	.	5.2315	0.15424	0.0:0.6163:0.1667:0.2171	.	266	Q8NH05	OR4Q3_HUMAN	L	266	ENSP00000330049:F266L	ENSP00000330049:F266L	F	+	3	2	OR4Q3	19286224	0.000000	0.05858	1.000000	0.80357	0.697000	0.40408	0.427000	0.21379	0.415000	0.25817	-0.366000	0.07423	TTC	.		0.443	OR4Q3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409818.2		
CTR9	9646	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	11	10789426	10789426	+	Missense_Mutation	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr11:10789426A>C	ENST00000361367.2	+	14	2186	c.1760A>C	c.(1759-1761)aAg>aCg	p.K587T		NM_014633.3	NP_055448.1	Q6PD62	CTR9_HUMAN	CTR9, Paf1/RNA polymerase II complex component	587					cellular response to lipopolysaccharide (GO:0071222)|endodermal cell fate commitment (GO:0001711)|histone H2B ubiquitination (GO:0033523)|histone H3-K4 trimethylation (GO:0080182)|histone monoubiquitination (GO:0010390)|interleukin-6-mediated signaling pathway (GO:0070102)|JAK-STAT cascade (GO:0007259)|negative regulation of myeloid cell differentiation (GO:0045638)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of histone H3-K79 methylation (GO:2001162)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	Cdc73/Paf1 complex (GO:0016593)|transcriptionally active chromatin (GO:0035327)				breast(4)|central_nervous_system(2)|cervix(1)|endometrium(7)|kidney(3)|large_intestine(7)|lung(12)|ovary(2)|pancreas(1)|stomach(1)	40				all cancers(16;1.64e-07)|Epithelial(150;2.47e-07)|BRCA - Breast invasive adenocarcinoma(625;0.111)		GGGCAGAAGAAGTTTGAGAGG	0.443																																					p.K587T		.											.	.	.	0			c.A1760C						.						240.0	238.0	238.0					11																	10789426		2201	4294	6495	SO:0001583	missense	9646	exon14			AGAAGAAGTTTGA	D63875	CCDS7805.1	11p15.3	2013-07-03	2013-07-03	2006-05-22	ENSG00000198730	ENSG00000198730		"""Tetratricopeptide (TTC) repeat domain containing"""	16850	protein-coding gene	gene with protein product		609366	"""SH2 domain binding protein 1 (tetratricopeptide repeat containing)"", ""Ctr9, Paf1/RNA polymerase II complex component, homolog (S. cerevisiae)"""	SH2BP1		8590280, 8636124	Standard	NM_014633		Approved	KIAA0155, TSBP, p150TSP	uc001mja.3	Q6PD62	OTTHUMG00000165789	ENST00000361367.2:c.1760A>C	11.37:g.10789426A>C	ENSP00000355013:p.Lys587Thr	Somatic	89	0		WXS	Illumina HiSeq	.	57	25	NM_014633	D3DQV8|Q15015	Missense_Mutation	SNP	ENST00000361367.2	37	CCDS7805.1	.	.	.	.	.	.	.	.	.	.	A	19.46	3.831970	0.71258	.	.	ENSG00000198730	ENST00000361367	T	0.58652	0.32	5.56	5.56	0.83823	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.000000	0.85682	D	0.000000	T	0.58032	0.2094	L	0.53249	1.67	0.80722	D	1	P	0.45569	0.861	P	0.45639	0.488	T	0.55068	-0.8198	10	0.22109	T	0.4	-25.3637	15.6945	0.77484	1.0:0.0:0.0:0.0	.	587	Q6PD62	CTR9_HUMAN	T	587	ENSP00000355013:K587T	ENSP00000355013:K587T	K	+	2	0	CTR9	10746002	1.000000	0.71417	1.000000	0.80357	0.609000	0.37215	9.238000	0.95380	2.116000	0.64780	0.383000	0.25322	AAG	.		0.443	CTR9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386215.1	NM_014633	
NBPF10	100132406	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	1	145299899	145299899	+	Silent	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr1:145299899T>G	ENST00000369338.1	+	2	325	c.135T>G	c.(133-135)acT>acG	p.T45T	RP11-458D21.5_ENST00000468030.1_3'UTR|NBPF10_ENST00000342960.5_Silent_p.T316T|NBPF10_ENST00000369339.3_Intron			Q6P3W6	NBPFA_HUMAN	neuroblastoma breakpoint family, member 10	316						cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)			NS(3)|breast(1)|central_nervous_system(3)|endometrium(12)|kidney(23)|lung(15)|ovary(1)|prostate(7)|skin(6)|urinary_tract(2)	73	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		GTTTTCTAACTCAACTGTCCG	0.428																																					p.T316T		.											.	.	.	0			c.T948G						.						43.0	31.0	34.0					1																	145299899		692	1591	2283	SO:0001819	synonymous_variant	100132406	exon6			TCTAACTCAACTG	BC021111		1q21.1	2013-01-17			ENSG00000163386	ENSG00000271425		"""neuroblastoma breakpoint family"""	31992	protein-coding gene	gene with protein product		614000				16079250	Standard	NM_001039703		Approved	AG1		Q6P3W6	OTTHUMG00000013757	ENST00000369338.1:c.135T>G	1.37:g.145299899T>G		Somatic	663	1		WXS	Illumina HiSeq	.	613	151	NM_001039703	Q5RHC0|Q9NWN6	Silent	SNP	ENST00000369338.1	37																																																																																				.		0.428	NBPF10-003	KNOWN	not_best_in_genome_evidence|basic	protein_coding	protein_coding	OTTHUMT00000038552.1	NM_001039703	
MYLK	4638	hgsc.bcm.edu;ucsc.edu	37	3	123332738	123332738	+	3'UTR	SNP	T	T	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr3:123332738T>C	ENST00000360304.3	-	0	6240				MYLK-AS1_ENST00000470449.1_RNA|MYLK_ENST00000578202.1_3'UTR|MYLK_ENST00000359169.1_3'UTR|MYLK_ENST00000418370.2_3'UTR|MYLK-AS1_ENST00000485162.1_RNA|MYLK_ENST00000360772.3_3'UTR|MYLK-AS1_ENST00000463408.1_RNA	NM_053025.3	NP_444253.3	Q15746	MYLK_HUMAN	myosin light chain kinase						actin filament organization (GO:0007015)|aorta smooth muscle tissue morphogenesis (GO:0060414)|bleb assembly (GO:0032060)|cellular hypotonic response (GO:0071476)|muscle contraction (GO:0006936)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cell migration (GO:0030335)|positive regulation of wound healing (GO:0090303)|protein phosphorylation (GO:0006468)|smooth muscle contraction (GO:0006939)|tonic smooth muscle contraction (GO:0014820)	cell-cell junction (GO:0005911)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|lamellipodium (GO:0030027)|stress fiber (GO:0001725)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)|metal ion binding (GO:0046872)|myosin light chain kinase activity (GO:0004687)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(24)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(37)|ovary(7)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	113		Lung NSC(201;0.0496)		GBM - Glioblastoma multiforme(114;0.0736)		CTAGCTGCACTAGTATCTTAA	0.378																																					.		.											.	.	.	0			.						.																																			SO:0001624	3_prime_UTR_variant	4638	.			CTGCACTAGTATC	X85337	CCDS3023.1, CCDS43141.1, CCDS46896.1, CCDS46897.1, CCDS58849.1	3q21	2013-02-11	2008-01-23		ENSG00000065534	ENSG00000065534	2.7.11.18	"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	7590	protein-coding gene	gene with protein product	"""smooth muscle myosin light chain kinase"""	600922	"""myosin, light polypeptide kinase"""			8575746	Standard	NM_053026		Approved	MLCK, smMLCK, MYLK1, MLCK1	uc003ego.3	Q15746	OTTHUMG00000141304	ENST00000360304.3:c.*214A>G	3.37:g.123332738T>C		Somatic	65	0		WXS	Illumina HiSeq	.	61	16	.	B4DUE3|D3DN97|O95796|O95797|O95798|O95799|Q14844|Q16794|Q17S15|Q3ZCP9|Q5MY99|Q5MYA0|Q6P2N0|Q7Z4J0|Q9C0L5|Q9UBG5|Q9UBY6|Q9UIT9	RNA	SNP	ENST00000360304.3	37	CCDS46896.1																																																																																			.		0.378	MYLK-203	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_053025	
SF3B2	10992	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	11	65820161	65820161	+	Missense_Mutation	SNP	G	G	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr11:65820161G>A	ENST00000322535.6	+	2	200	c.151G>A	c.(151-153)Gtg>Atg	p.V51M	SF3B2_ENST00000528302.1_Missense_Mutation_p.V51M|snoU13_ENST00000459530.1_RNA	NM_006842.2	NP_006833.2	Q13435	SF3B2_HUMAN	splicing factor 3b, subunit 2, 145kDa	51	SAP. {ECO:0000255|PROSITE- ProRule:PRU00186}.				gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|viral process (GO:0016032)	catalytic step 2 spliceosome (GO:0071013)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U12-type spliceosomal complex (GO:0005689)	poly(A) RNA binding (GO:0044822)			breast(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|liver(2)|lung(14)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	41						CGAGGAGCTGGTGGAGCGGCT	0.662																																					p.V51M		.											.	.	.	0			c.G151A						.						43.0	48.0	46.0					11																	65820161		2201	4296	6497	SO:0001583	missense	10992	exon2			GAGCTGGTGGAGC	U41371	CCDS31612.1	11q13	2010-07-21	2002-08-29		ENSG00000087365	ENSG00000087365			10769	protein-coding gene	gene with protein product		605591	"""splicing factor 3b, subunit 2, 145kD"""			8566756	Standard	XM_005273726		Approved	SAP145, SF3b1, Cus1, SF3b145	uc001ogy.1	Q13435	OTTHUMG00000166751	ENST00000322535.6:c.151G>A	11.37:g.65820161G>A	ENSP00000318861:p.Val51Met	Somatic	49	0		WXS	Illumina HiSeq	.	30	11	NM_006842	A8K485|B4DT19|Q7L4T5|Q7Z627|Q969K1|Q96CM6|Q9BWD2	Missense_Mutation	SNP	ENST00000322535.6	37	CCDS31612.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	27.5|27.5	4.836835|4.836835	0.91117|0.91117	.|.	.|.	ENSG00000087365|ENSG00000087365	ENST00000528302;ENST00000322535;ENST00000533595;ENST00000524627;ENST00000355456;ENST00000530322|ENST00000533421	.|.	.|.	.|.	5.39|5.39	4.44|4.44	0.53790|0.53790	DNA-binding SAP (4);|.	0.239442|.	0.40640|.	N|.	0.001042|.	T|.	0.30978|.	0.0782|.	N|N	0.08118|0.08118	0|0	0.35466|0.35466	D|D	0.796973|0.796973	P;D|.	0.55385|.	0.57;0.971|.	P;P|.	0.55303|.	0.486;0.773|.	T|.	0.30880|.	-0.9963|.	9|.	0.87932|.	D|.	0|.	-31.4995|-31.4995	11.4642|11.4642	0.50227|0.50227	0.0:0.0:0.8216:0.1784|0.0:0.0:0.8216:0.1784	.|.	51;51|.	Q13435;E9PJ04|.	SF3B2_HUMAN;.|.	M|X	51;51;51;51;53;46|1	.|.	ENSP00000318861:V51M|.	V|W	+|+	1|3	0|0	SF3B2|SF3B2	65576737|65576737	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	3.440000|3.440000	0.52886|0.52886	2.804000|2.804000	0.96469|0.96469	0.655000|0.655000	0.94253|0.94253	GTG|TGG	.		0.662	SF3B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391352.2		
PDIA2	64714	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	16	334725	334725	+	Missense_Mutation	SNP	T	T	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr16:334725T>C	ENST00000219406.6	+	3	491	c.473T>C	c.(472-474)cTg>cCg	p.L158P	PDIA2_ENST00000404312.1_Missense_Mutation_p.L158P	NM_006849.2	NP_006840.2	Q13087	PDIA2_HUMAN	protein disulfide isomerase family A, member 2	158					cell redox homeostasis (GO:0045454)|peptidyl-proline hydroxylation (GO:0019511)|protein folding (GO:0006457)|protein retention in ER lumen (GO:0006621)|regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902175)|response to endoplasmic reticulum stress (GO:0034976)	endoplasmic reticulum (GO:0005783)	protein disulfide isomerase activity (GO:0003756)|steroid binding (GO:0005496)			breast(1)|central_nervous_system(4)|kidney(3)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	17		all_cancers(16;6.71e-07)|all_epithelial(16;1.59e-06)|Hepatocellular(16;0.000105)|Lung NSC(18;0.00769)|all_lung(18;0.0186)				GCCATGCGGCTGGAGGACGAG	0.716																																					p.L158P		.											.	.	.	0			c.T473C						.						8.0	14.0	12.0					16																	334725		2050	4127	6177	SO:0001583	missense	64714	exon3			TGCGGCTGGAGGA	U19948	CCDS42089.1	16p13.3	2009-11-20	2005-06-29	2005-03-03	ENSG00000185615	ENSG00000185615	5.3.4.1	"""Protein disulfide isomerases"""	14180	protein-coding gene	gene with protein product		608012	"""protein disulfide isomerase, pancreatic"", ""protein disulfide isomerase-associated 2"""	PDIP		8561901	Standard	NM_006849		Approved	PDA2, PDI, PDIR	uc002cgo.1	Q13087	OTTHUMG00000064891	ENST00000219406.6:c.473T>C	16.37:g.334725T>C	ENSP00000219406:p.Leu158Pro	Somatic	22	0		WXS	Illumina HiSeq	.	19	5	NM_006849	A6ZJ64|B4DI27|Q2WGM4|Q4TT67|Q6B010|Q96KJ6|Q9BW95	Missense_Mutation	SNP	ENST00000219406.6	37	CCDS42089.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	t|t	14.07|14.07	2.426712|2.426712	0.43020|0.43020	.|.	.|.	ENSG00000185615|ENSG00000185615	ENST00000219406;ENST00000455994;ENST00000404312|ENST00000456379	T;T|.	0.04156|.	3.69;3.72|.	3.75|3.75	3.75|3.75	0.43078|0.43078	Thioredoxin-like fold (1);|.	0.000000|.	0.64402|.	D|.	0.000003|.	T|T	0.79770|0.79770	0.4503|0.4503	M|M	0.91354|0.91354	3.2|3.2	0.80722|0.80722	D|D	1|1	D|.	0.89917|.	1.0|.	D|.	0.77557|.	0.99|.	D|D	0.83707|0.83707	0.0185|0.0185	10|5	0.66056|.	D|.	0.02|.	.|.	11.5573|11.5573	0.50755|0.50755	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	158|.	Q13087|.	PDIA2_HUMAN|.	P|R	158;127;158|155	ENSP00000219406:L158P;ENSP00000384410:L158P|.	ENSP00000219406:L158P|.	L|W	+|+	2|1	0|0	PDIA2|PDIA2	274726|274726	1.000000|1.000000	0.71417|0.71417	0.760000|0.760000	0.31359|0.31359	0.185000|0.185000	0.23345|0.23345	3.419000|3.419000	0.52728|0.52728	1.567000|1.567000	0.49668|0.49668	0.375000|0.375000	0.23000|0.23000	CTG|TGG	.		0.716	PDIA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139315.3	NM_006849	
DDX12P	440081	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	12	9571135	9571135	+	IGR	SNP	T	T	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr12:9571135T>C								RP13-735L24.1 (20922 upstream) : SNORA75 (26518 downstream)																							GGCAGCGCTCTGGACTCCACA	0.587																																					.		.											.	.	.	0			.						.																																			SO:0001628	intergenic_variant	440081	.			GCGCTCTGGACTC																													12.37:g.9571135T>C		Somatic	74	0		WXS	Illumina HiSeq	.	45	8	.		RNA	SNP		37																																																																																				.	0	0.587								
ECM2	1842	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	9	95277473	95277473	+	Missense_Mutation	SNP	A	A	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr9:95277473A>G	ENST00000344604.5	-	4	643	c.494T>C	c.(493-495)cTa>cCa	p.L165P	ECM2_ENST00000444490.2_Intron|CENPP_ENST00000375587.3_Intron	NM_001197295.1|NM_001393.3	NP_001184224.1|NP_001384.1	O94769	ECM2_HUMAN	extracellular matrix protein 2, female organ and adipocyte specific	165					cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)|positive regulation of cell-substrate adhesion (GO:0010811)	interstitial matrix (GO:0005614)|proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|integrin binding (GO:0005178)			breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	27						ACCACTGAGTAGAGAATAGGA	0.338																																					p.L165P		.											.	.	.	0			c.T494C						.						32.0	31.0	31.0					9																	95277473		2203	4300	6503	SO:0001583	missense	1842	exon4			CTGAGTAGAGAAT	AB011792	CCDS6698.1, CCDS56578.1	9q22.3	2008-07-21			ENSG00000106823	ENSG00000106823			3154	protein-coding gene	gene with protein product	"""matrix glycoprotein SC1/ECM2"""	603479				9790758	Standard	NM_001393		Approved		uc011lty.2	O94769	OTTHUMG00000020226	ENST00000344604.5:c.494T>C	9.37:g.95277473A>G	ENSP00000344758:p.Leu165Pro	Somatic	30	0		WXS	Illumina HiSeq	.	21	12	NM_001393	B2R730|E2PU11|Q5T9F2|Q7Z3D0	Missense_Mutation	SNP	ENST00000344604.5	37	CCDS6698.1	.	.	.	.	.	.	.	.	.	.	A	8.292	0.817854	0.16607	.	.	ENSG00000106823	ENST00000344604	T	0.52526	0.66	5.32	0.266	0.15617	.	1.039030	0.07647	N	0.931225	T	0.26484	0.0647	N	0.14661	0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.19224	-1.0312	10	0.29301	T	0.29	.	3.7834	0.08689	0.5971:0.0:0.2529:0.15	.	165	O94769	ECM2_HUMAN	P	165	ENSP00000344758:L165P	ENSP00000344758:L165P	L	-	2	0	ECM2	94317294	0.000000	0.05858	0.000000	0.03702	0.942000	0.58702	0.704000	0.25661	-0.120000	0.11809	-0.280000	0.10049	CTA	.		0.338	ECM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053091.1	NM_001393	
ODF2	4957	hgsc.bcm.edu	37	9	131256878	131256878	+	Silent	SNP	A	A	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr9:131256878A>G	ENST00000434106.3	+	17	2205	c.1842A>G	c.(1840-1842)caA>caG	p.Q614Q	ODF2_ENST00000546203.1_Silent_p.Q595Q|ODF2_ENST00000393527.3_Silent_p.Q590Q|ODF2_ENST00000448249.3_Silent_p.Q533Q|ODF2_ENST00000351030.3_Silent_p.Q609Q|ODF2_ENST00000393533.2_Silent_p.Q614Q|ODF2_ENST00000604420.1_Silent_p.Q614Q|ODF2_ENST00000444119.2_Silent_p.Q590Q|ODF2_ENST00000372791.3_Silent_p.Q595Q|ODF2_ENST00000372814.3_Silent_p.Q658Q|ODF2_ENST00000372807.5_Silent_p.Q609Q	NM_153433.1	NP_702911.1	Q5BJF6	ODFP2_HUMAN	outer dense fiber of sperm tails 2	614					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|multicellular organismal development (GO:0007275)|regulation of cilium assembly (GO:1902017)|spermatid development (GO:0007286)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytosol (GO:0005829)|microtubule (GO:0005874)|nucleus (GO:0005634)|outer dense fiber (GO:0001520)|primary cilium (GO:0072372)	Rab GTPase binding (GO:0017137)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(7)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(7)|lung(8)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	37						CTGAGTGCCAAGACCAACTGC	0.582																																					p.Q678Q		.											.	.	.	0			c.A2034G						.						77.0	66.0	70.0					9																	131256878		2203	4300	6503	SO:0001819	synonymous_variant	4957	exon17			GTGCCAAGACCAA	AF012549	CCDS6902.1, CCDS56585.1, CCDS56586.1, CCDS56587.1, CCDS56588.1, CCDS56589.1, CCDS56590.1	9q34	2010-04-23	2002-10-21		ENSG00000136811	ENSG00000136811			8114	protein-coding gene	gene with protein product	"""cancer/testis antigen 134"""	602015	"""outer dense fibre of sperm tails 2"""			9045620, 10072582	Standard	NM_153435		Approved	ODF84, CT134	uc004bvc.3	Q5BJF6	OTTHUMG00000020748	ENST00000434106.3:c.1842A>G	9.37:g.131256878A>G		Somatic	17	0		WXS	Illumina HiSeq	.	12	6	NM_153435	B1AND3|B4DRK4|B4DX73|B4DZ02|E7EWL2|F5H6J4|O14721|O60631|Q1W2J6|Q6UN26|Q7Z5I6|Q96FN2	Silent	SNP	ENST00000434106.3	37	CCDS56588.1																																																																																			.		0.582	ODF2-011	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054449.3		
ATP8B1	5205	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	18	55336582	55336582	+	Nonsense_Mutation	SNP	T	T	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr18:55336582T>A	ENST00000283684.4	-	17	2064	c.2065A>T	c.(2065-2067)Aaa>Taa	p.K689*	RP11-35G9.3_ENST00000592201.1_RNA|ATP8B1_ENST00000536015.1_Nonsense_Mutation_p.K689*|RP11-35G9.5_ENST00000588925.1_RNA|RP11-35G9.3_ENST00000599199.1_RNA|RP11-35G9.3_ENST00000591854.1_RNA			O43520	AT8B1_HUMAN	ATPase, aminophospholipid transporter, class I, type 8B, member 1	689			Missing (in PFIC1). {ECO:0000269|PubMed:9500542}.		bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|drug transmembrane transport (GO:0006855)|inner ear receptor cell development (GO:0060119)|ion transmembrane transport (GO:0034220)|negative regulation of transcription, DNA-templated (GO:0045892)|phospholipid translocation (GO:0045332)|regulation of microvillus assembly (GO:0032534)|sensory perception of sound (GO:0007605)|transmembrane transport (GO:0055085)|vestibulocochlear nerve formation (GO:0021650)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)	ATP binding (GO:0005524)|cardiolipin binding (GO:1901612)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			breast(6)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(11)|lung(19)|ovary(3)|prostate(1)	53		Colorectal(73;0.229)				TCATATACTTTATCCAGAGCT	0.328																																					p.K689X		.											.	.	.	0			c.A2065T						.						72.0	78.0	76.0					18																	55336582		2203	4300	6503	SO:0001587	stop_gained	5205	exon18			ATACTTTATCCAG	AF038007	CCDS11965.1	18q21	2010-04-28	2010-04-28		ENSG00000081923	ENSG00000081923		"""ATPases / P-type"""	3706	protein-coding gene	gene with protein product		602397	"""ATPase, Class I, type 8B, member 1"", ""ATPase, class I, type 8B, member 1"""	FIC1, BRIC, PFIC1		9500542, 7655458	Standard	NM_005603		Approved	ATPIC, PFIC	uc002lgw.3	O43520	OTTHUMG00000132739	ENST00000283684.4:c.2065A>T	18.37:g.55336582T>A	ENSP00000283684:p.Lys689*	Somatic	156	0		WXS	Illumina HiSeq	.	109	47	NM_005603	Q9BTP8	Nonsense_Mutation	SNP	ENST00000283684.4	37	CCDS11965.1	.	.	.	.	.	.	.	.	.	.	T	38	6.960921	0.97964	.	.	ENSG00000081923	ENST00000283684;ENST00000536015	.	.	.	5.91	4.72	0.59763	.	0.239575	0.43747	D	0.000539	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	12.8014	0.57588	0.0:0.0:0.1368:0.8632	.	.	.	.	X	689	.	ENSP00000283684:K689X	K	-	1	0	ATP8B1	53487580	1.000000	0.71417	1.000000	0.80357	0.862000	0.49288	1.161000	0.31773	1.013000	0.39391	0.533000	0.62120	AAA	.		0.328	ATP8B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256097.1	NM_005603	
PPP1R16A	84988	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	8	145725522	145725522	+	Missense_Mutation	SNP	T	T	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr8:145725522T>A	ENST00000292539.4	+	5	1437	c.520T>A	c.(520-522)Tat>Aat	p.Y174N	GPT_ENST00000528431.1_5'Flank|CTD-2517M22.14_ENST00000532766.1_RNA|CTD-2517M14.5_ENST00000569326.1_RNA|PPP1R16A_ENST00000435887.1_Missense_Mutation_p.Y174N			Q96I34	PP16A_HUMAN	protein phosphatase 1, regulatory subunit 16A	174						plasma membrane (GO:0005886)				NS(1)|endometrium(1)|kidney(2)|lung(3)|prostate(1)	8	all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055)			GAACATGCCCTATGACCTGTG	0.672																																					p.Y174N		.											.	.	.	0			c.T520A						.						127.0	81.0	97.0					8																	145725522		2200	4298	6498	SO:0001583	missense	84988	exon4			ATGCCCTATGACC		CCDS6429.1	8q24.3	2013-01-10	2011-10-04		ENSG00000160972	ENSG00000160972		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Ankyrin repeat domain containing"""	14941	protein-coding gene	gene with protein product		609172	"""protein phosphatase 1, regulatory (inhibitor) subunit 16A"""			11948623	Standard	NM_032902		Approved	MGC14333, MYPT3	uc003zdf.3	Q96I34	OTTHUMG00000165173	ENST00000292539.4:c.520T>A	8.37:g.145725522T>A	ENSP00000292539:p.Tyr174Asn	Somatic	66	0		WXS	Illumina HiSeq	.	42	14	NM_032902	D3DWM5	Missense_Mutation	SNP	ENST00000292539.4	37	CCDS6429.1	.	.	.	.	.	.	.	.	.	.	T	27.5	4.835988	0.91117	.	.	ENSG00000160972	ENST00000292539;ENST00000435887	T;T	0.53206	0.63;0.63	5.26	5.26	0.73747	Ankyrin repeat-containing domain (3);	0.000000	0.85682	D	0.000000	T	0.65217	0.2670	M	0.62723	1.935	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.68640	-0.5355	10	0.87932	D	0	.	13.1298	0.59375	0.0:0.0:0.0:1.0	.	174	Q96I34	PP16A_HUMAN	N	174	ENSP00000292539:Y174N;ENSP00000391126:Y174N	ENSP00000292539:Y174N	Y	+	1	0	PPP1R16A	145696330	0.993000	0.37304	0.983000	0.44433	0.837000	0.47467	2.768000	0.47645	1.996000	0.58369	0.459000	0.35465	TAT	.		0.672	PPP1R16A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382459.1	NM_032902	
SCUBE2	57758	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	11	9047293	9047293	+	Missense_Mutation	SNP	C	C	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr11:9047293C>T	ENST00000309263.3	-	20	2795	c.2723G>A	c.(2722-2724)gGg>gAg	p.G908E	SCUBE2_ENST00000450649.2_Missense_Mutation_p.G716E|RP11-467K18.2_ENST00000531592.1_RNA|SCUBE2_ENST00000457346.2_Missense_Mutation_p.G937E|SCUBE2_ENST00000520467.1_Missense_Mutation_p.G880E			Q9NQ36	SCUB2_HUMAN	signal peptide, CUB domain, EGF-like 2	908	CUB. {ECO:0000255|PROSITE- ProRule:PRU00059}.					extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			breast(1)|endometrium(5)|kidney(3)|large_intestine(15)|liver(1)|lung(10)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	42				all cancers(16;8.57e-09)|Epithelial(150;4.42e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0116)		AGCGCTGTTCCCTTCATTGGA	0.502																																					p.G880E		.											.	.	.	0			c.G2639A						.						184.0	161.0	168.0					11																	9047293		2201	4296	6497	SO:0001583	missense	57758	exon20			CTGTTCCCTTCAT	AK131552	CCDS7797.1, CCDS7797.2, CCDS53599.1	11p15.4	2014-09-04			ENSG00000175356	ENSG00000175356			30425	protein-coding gene	gene with protein product		611747				12270931, 11528127	Standard	NM_020974		Approved	Cegf1, Cegb1, FLJ16792	uc001mhi.2	Q9NQ36	OTTHUMG00000163880	ENST00000309263.3:c.2723G>A	11.37:g.9047293C>T	ENSP00000310658:p.Gly908Glu	Somatic	58	0		WXS	Illumina HiSeq	.	46	20	NM_020974	Q2NKQ8|Q6ZWI1	Missense_Mutation	SNP	ENST00000309263.3	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	34|34	5.328539|5.328539	0.95733|0.95733	.|.	.|.	ENSG00000175356|ENSG00000175356	ENST00000457346;ENST00000309263;ENST00000450649;ENST00000520467|ENST00000519202	T;T;T;T|T	0.34275|0.17528	2.34;2.34;1.37;2.34|2.27	5.39|5.39	5.39|5.39	0.77823|0.77823	CUB (5);|.	0.000000|0.000000	0.85682|0.85682	D|D	0.000000|0.000000	T|T	0.20577|0.20577	0.0495|0.0495	N|N	0.16201|0.16201	0.385|0.385	0.80722|0.80722	D|D	1|1	D;D;D|.	0.89917|.	1.0;0.998;1.0|.	D;D;D|.	0.97110|.	1.0;0.984;0.998|.	T|T	0.04140|0.04140	-1.0974|-1.0974	10|8	0.72032|0.52906	D|T	0.01|0.07	.|.	19.5154|19.5154	0.95162|0.95162	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	716;880;908|.	Q9NQ36-3;Q9NQ36-2;Q9NQ36|.	.;.;SCUB2_HUMAN|.	E|R	937;908;716;880|91	ENSP00000390481:G937E;ENSP00000310658:G908E;ENSP00000415187:G716E;ENSP00000429969:G880E|ENSP00000432828:G91R	ENSP00000310658:G908E|ENSP00000432828:G91R	G|G	-|-	2|1	0|0	SCUBE2|SCUBE2	9003869|9003869	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.982000|0.982000	0.71751|0.71751	4.773000|4.773000	0.62331|0.62331	2.685000|2.685000	0.91497|0.91497	0.655000|0.655000	0.94253|0.94253	GGG|GGA	.		0.502	SCUBE2-005	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000385812.2	NM_020974	
UBN1	29855	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	16	4920542	4920542	+	Missense_Mutation	SNP	A	A	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr16:4920542A>G	ENST00000396658.4	+	9	2040	c.1337A>G	c.(1336-1338)cAg>cGg	p.Q446R	UBN1_ENST00000545171.1_Missense_Mutation_p.Q446R|UBN1_ENST00000262376.6_Missense_Mutation_p.Q446R|UBN1_ENST00000590769.1_Missense_Mutation_p.Q446R|UBN1_ENST00000585857.1_3'UTR	NM_016936.3	NP_058632.2	Q9NPG3	UBN1_HUMAN	ubinuclein 1	446					chromatin modification (GO:0016568)|DNA replication-independent nucleosome assembly (GO:0006336)|negative regulation of phosphatase activity (GO:0010923)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|viral process (GO:0016032)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|tight junction (GO:0005923)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(6)|kidney(4)|large_intestine(10)|lung(12)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	38						GAGCCTCTCCAGAAGCTCAAG	0.567																																					p.Q446R		.											.	.	.	0			c.A1337G						.						44.0	39.0	41.0					16																	4920542		2197	4300	6497	SO:0001583	missense	29855	exon10			CTCTCCAGAAGCT	AF108460	CCDS10525.1, CCDS73822.1	16p13.3	2010-11-09			ENSG00000118900	ENSG00000118900			12506	protein-coding gene	gene with protein product		609771				10725330	Standard	XM_005255277		Approved		uc002cyb.3	Q9NPG3	OTTHUMG00000129531	ENST00000396658.4:c.1337A>G	16.37:g.4920542A>G	ENSP00000379894:p.Gln446Arg	Somatic	26	0		WXS	Illumina HiSeq	.	12	5	NM_001079514	B7Z6D3|D3DUE8|Q13079|Q9P1P7	Missense_Mutation	SNP	ENST00000396658.4	37	CCDS10525.1	.	.	.	.	.	.	.	.	.	.	A	15.33	2.803042	0.50315	.	.	ENSG00000118900	ENST00000262376;ENST00000545171;ENST00000396658	T;T;T	0.44083	0.93;0.93;0.93	5.23	5.23	0.72850	.	0.061049	0.64402	D	0.000002	T	0.30039	0.0752	L	0.31664	0.95	0.35912	D	0.83117	B;B	0.30634	0.244;0.288	B;B	0.29267	0.061;0.1	T	0.39292	-0.9621	10	0.44086	T	0.13	-15.9275	9.6179	0.39704	0.9217:0.0:0.0783:0.0	.	446;446	Q9NPG3-2;Q9NPG3	.;UBN1_HUMAN	R	446	ENSP00000262376:Q446R;ENSP00000442379:Q446R;ENSP00000379894:Q446R	ENSP00000262376:Q446R	Q	+	2	0	UBN1	4860543	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.071000	0.57556	1.983000	0.57843	0.533000	0.62120	CAG	.		0.567	UBN1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251719.1	NM_016936	
DCAF7	10238	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	17	61660866	61660866	+	Missense_Mutation	SNP	T	T	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr17:61660866T>C	ENST00000310827.4	+	5	749	c.532T>C	c.(532-534)Tat>Cat	p.Y178H	DCAF7_ENST00000415273.2_Intron|DCAF7_ENST00000431926.1_Intron|DCAF7_ENST00000577702.1_3'UTR	NM_005828.3	NP_005819.3	P61962	DCAF7_HUMAN	DDB1 and CUL4 associated factor 7	178					multicellular organismal development (GO:0007275)|protein ubiquitination (GO:0016567)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)|cytoplasm (GO:0005737)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)|protein complex (GO:0043234)				endometrium(6)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)	18						CCAACAGGTCTATGATATTGC	0.522																																					p.Y178H		.											.	.	.	0			c.T532C						.						48.0	49.0	49.0					17																	61660866		1955	4147	6102	SO:0001583	missense	10238	exon5			CAGGTCTATGATA	U94747	CCDS74127.1	17q23.3	2013-01-09	2009-07-17	2009-07-17		ENSG00000136485		"""WD repeat domain containing"", ""DDB1 and CUL4 associated factors"""	30915	protein-coding gene	gene with protein product	"""seven-WD-repeat protein of the AN11 family-1"", ""human anthocyanin"""	605973	"""WD repeat domain 68"""	WDR68		9192870, 20940704	Standard	NM_005828		Approved	HAN11, SWAN-1	uc002jbc.4	P61962		ENST00000310827.4:c.532T>C	17.37:g.61660866T>C	ENSP00000308344:p.Tyr178His	Somatic	108	0		WXS	Illumina HiSeq	.	63	27	NM_005828	B4E039|D3DU14|O15491|Q9DAE4	Missense_Mutation	SNP	ENST00000310827.4	37		.	.	.	.	.	.	.	.	.	.	T	15.14	2.746512	0.49257	.	.	ENSG00000136485	ENST00000310827	T	0.60548	0.18	5.29	4.21	0.49690	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	0.56572	0.1994	L	0.46819	1.47	0.80722	D	1	B	0.27823	0.19	B	0.40375	0.327	T	0.52064	-0.8625	10	0.30854	T	0.27	-22.3377	11.6764	0.51432	0.1327:0.0:0.0:0.8673	.	178	P61962	DCAF7_HUMAN	H	178	ENSP00000308344:Y178H	ENSP00000308344:Y178H	Y	+	1	0	DCAF7	59014598	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.846000	0.86887	1.011000	0.39340	0.533000	0.62120	TAT	.		0.522	DCAF7-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_005828	
MLLT4	4301	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	6	168348587	168348587	+	Missense_Mutation	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr6:168348587A>C	ENST00000447894.2	+	27	3587	c.3587A>C	c.(3586-3588)aAg>aCg	p.K1196T	MLLT4_ENST00000507679.1_3'UTR|MLLT4_ENST00000366806.2_Missense_Mutation_p.K1196T|MLLT4_ENST00000392112.1_Missense_Mutation_p.K1179T|MLLT4_ENST00000400822.3_Missense_Mutation_p.K1195T|MLLT4_ENST00000351017.4_Missense_Mutation_p.K1203T|MLLT4_ENST00000392108.3_Missense_Mutation_p.K1196T|MLLT4_ENST00000344191.4_Missense_Mutation_p.K1196T			P55196	AFAD_HUMAN	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 4	1196					adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cell-cell signaling (GO:0007267)|signal transduction (GO:0007165)	apical part of cell (GO:0045177)|cell junction (GO:0030054)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein C-terminus binding (GO:0008022)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(13)|large_intestine(10)|lung(19)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	65		Breast(66;1.07e-05)|Ovarian(120;0.024)		Epithelial(4;2.38e-32)|OV - Ovarian serous cystadenocarcinoma(33;9.99e-23)|BRCA - Breast invasive adenocarcinoma(4;1.2e-11)|GBM - Glioblastoma multiforme(31;0.00117)		ACAACAGCGAAGATAACATCT	0.433			T	MLL	AL																																p.K1196T		.		Dom	yes		6	6q27	4301	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 4 (AF6)"""		L	MLLT4_ENST00000392108,NS,carcinoma,0,3	MLLT4_ENST00000392108	0	0			c.A3587C						.						97.0	87.0	90.0					6																	168348587		2203	4300	6503	SO:0001583	missense	4301	exon27			CAGCGAAGATAAC	AB011399	CCDS47517.1, CCDS75553.1	6q27	2008-02-05	2001-11-28		ENSG00000130396	ENSG00000130396			7137	protein-coding gene	gene with protein product		159559	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 4"""			8242616	Standard	NM_001040000		Approved	AF-6, AF6	uc021zij.1	P55196	OTTHUMG00000016031	ENST00000447894.2:c.3587A>C	6.37:g.168348587A>C	ENSP00000404595:p.Lys1196Thr	Somatic	37	0		WXS	Illumina HiSeq	.	19	9	NM_001040000	O75087|O75088|O75089|Q59FP0|Q5TIG6|Q5TIG7|Q9NSN7|Q9NU92	Missense_Mutation	SNP	ENST00000447894.2	37		.	.	.	.	.	.	.	.	.	.	A	19.79	3.893151	0.72524	.	.	ENSG00000130396	ENST00000344191;ENST00000351017;ENST00000392108;ENST00000366806;ENST00000392112;ENST00000341575;ENST00000400822;ENST00000447894	T;T;T;T;T;T;T	0.05382	3.68;3.55;3.66;3.65;3.45;3.56;3.55	5.88	4.72	0.59763	.	0.000000	0.85682	D	0.000000	T	0.13286	0.0322	M	0.73962	2.25	0.53688	D	0.999975	P;D;D;D	0.89917	0.7;1.0;0.997;0.99	B;D;P;P	0.91635	0.132;0.999;0.899;0.855	T	0.01776	-1.1276	10	0.35671	T	0.21	-3.5762	11.9508	0.52954	0.9324:0.0:0.0676:0.0	.	1196;1195;1196;1180	P55196;P55196-5;P55196-6;P55196-2	AFAD_HUMAN;.;.;.	T	1196;1203;1196;1196;1179;1196;1195;1196	ENSP00000341118:K1196T;ENSP00000252692:K1203T;ENSP00000375956:K1196T;ENSP00000355771:K1196T;ENSP00000375960:K1179T;ENSP00000383623:K1195T;ENSP00000404595:K1196T	ENSP00000345834:K1196T	K	+	2	0	MLLT4	168091436	1.000000	0.71417	0.967000	0.41034	0.933000	0.57130	5.451000	0.66632	1.045000	0.40225	0.533000	0.62120	AAG	.		0.433	MLLT4-013	PUTATIVE	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000372077.1	NM_005936	
COPA	1314	hgsc.bcm.edu;ucsc.edu	37	1	160269048	160269048	+	Silent	SNP	G	G	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr1:160269048G>A	ENST00000241704.7	-	18	1903	c.1674C>T	c.(1672-1674)caC>caT	p.H558H	COPA_ENST00000368069.3_Silent_p.H567H	NM_001098398.1|NM_004371.3	NP_001091868.1|NP_004362.2	P53621	COPA_HUMAN	coatomer protein complex, subunit alpha	558					COPI coating of Golgi vesicle (GO:0048205)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|pancreatic juice secretion (GO:0030157)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	COPI vesicle coat (GO:0030126)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(5)|kidney(5)|large_intestine(2)|lung(25)|ovary(1)|prostate(3)|skin(1)|stomach(1)|urinary_tract(2)	46	all_cancers(52;8.15e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			GAATGATCCCGTGGTCCCTAA	0.493																																					p.H567H		.											.	.	.	0			c.C1701T						.						89.0	82.0	84.0					1																	160269048		2203	4300	6503	SO:0001819	synonymous_variant	1314	exon18			GATCCCGTGGTCC	U24105	CCDS1202.1, CCDS41424.1	1q23.2	2014-01-30			ENSG00000122218	ENSG00000122218		"""WD repeat domain containing"", ""Endogenous ligands"""	2230	protein-coding gene	gene with protein product	"""proxenin"", ""xenin"""	601924				8647451	Standard	NM_004371		Approved	HEP-COP	uc001fvv.4	P53621	OTTHUMG00000033111	ENST00000241704.7:c.1674C>T	1.37:g.160269048G>A		Somatic	22	0		WXS	Illumina HiSeq	.	40	4	NM_001098398	Q5T201|Q8IXZ9	Silent	SNP	ENST00000241704.7	37	CCDS1202.1																																																																																			.		0.493	COPA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080638.1	NM_004371	
ZNRF3	84133	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	22	29440787	29440787	+	Missense_Mutation	SNP	A	A	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr22:29440787A>G	ENST00000544604.2	+	5	828	c.653A>G	c.(652-654)gAc>gGc	p.D218G	ZNRF3_ENST00000406323.3_Missense_Mutation_p.D118G|ZNRF3_ENST00000402174.1_Missense_Mutation_p.D118G|ZNRF3_ENST00000332811.4_Missense_Mutation_p.D118G	NM_001206998.1	NP_001193927.1	Q9ULT6	ZNRF3_HUMAN	zinc and ring finger 3	218					canonical Wnt signaling pathway (GO:0060070)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of non-canonical Wnt signaling pathway (GO:2000051)|protein ubiquitination (GO:0016567)|stem cell proliferation (GO:0072089)|ubiquitin-dependent protein catabolic process (GO:0006511)|Wnt receptor catabolic process (GO:0038018)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	integral component of plasma membrane (GO:0005887)	frizzled binding (GO:0005109)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|liver(4)|lung(9)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	28						GAATACTTTGACATGGGGATT	0.527																																					p.D218G		.											.	.	.	0			c.A653G						.						166.0	170.0	169.0					22																	29440787		2000	4168	6168	SO:0001583	missense	84133	exon5			ACTTTGACATGGG	AB051436	CCDS42999.1, CCDS56225.1	22q12.1	2013-01-09			ENSG00000183579	ENSG00000183579		"""RING-type (C3HC4) zinc fingers"""	18126	protein-coding gene	gene with protein product		612062				10574461	Standard	NM_032173		Approved	KIAA1133, BK747E2.3, FLJ22057, RNF203	uc003aeg.3	Q9ULT6	OTTHUMG00000151009	ENST00000544604.2:c.653A>G	22.37:g.29440787A>G	ENSP00000443824:p.Asp218Gly	Somatic	75	0		WXS	Illumina HiSeq	.	20	14	NM_001206998	B3KU18|Q6ICH1|Q6NTF8|Q8WU18	Missense_Mutation	SNP	ENST00000544604.2	37	CCDS56225.1	.	.	.	.	.	.	.	.	.	.	A	24.9	4.581779	0.86748	.	.	ENSG00000183579	ENST00000544604;ENST00000332811;ENST00000402174;ENST00000406323	T;T;T;T	0.10099	3.05;2.91;2.91;2.91	5.56	5.56	0.83823	.	0.000000	0.85682	D	0.000000	T	0.21881	0.0527	L	0.29908	0.895	0.58432	D	0.999999	D	0.76494	0.999	D	0.70716	0.97	T	0.01099	-1.1452	10	0.59425	D	0.04	-7.4001	14.9129	0.70773	1.0:0.0:0.0:0.0	.	218	Q9ULT6	ZNRF3_HUMAN	G	218;118;118;118	ENSP00000443824:D218G;ENSP00000328614:D118G;ENSP00000384456:D118G;ENSP00000384553:D118G	ENSP00000328614:D118G	D	+	2	0	ZNRF3	27770787	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.603000	0.90871	2.125000	0.65367	0.533000	0.62120	GAC	.		0.527	ZNRF3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320943.2	XM_290972	
CHRM2	1129	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	7	136700368	136700368	+	Silent	SNP	C	C	T	rs531986911		TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr7:136700368C>T	ENST00000445907.2	+	3	1284	c.756C>T	c.(754-756)gaC>gaT	p.D252D	CHRM2_ENST00000401861.1_Silent_p.D252D|hsa-mir-490_ENST00000592183.1_RNA|CHRM2_ENST00000402486.3_Silent_p.D252D|hsa-mir-490_ENST00000593789.1_RNA|CHRM2_ENST00000397608.3_Silent_p.D252D|hsa-mir-490_ENST00000586239.1_RNA|CHRM2_ENST00000320658.5_Silent_p.D252D|CHRM2_ENST00000453373.1_Silent_p.D252D|hsa-mir-490_ENST00000425981.2_RNA|hsa-mir-490_ENST00000439694.1_RNA|hsa-mir-490_ENST00000598184.1_RNA|hsa-mir-490_ENST00000597642.1_RNA	NM_001006627.1|NM_001006629.1	NP_001006628.1|NP_001006630.1	P08172	ACM2_HUMAN	cholinergic receptor, muscarinic 2	252					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|nervous system development (GO:0007399)|phospholipase C-activating G-protein coupled acetylcholine receptor signaling pathway (GO:0007207)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|regulation of heart contraction (GO:0008016)|response to virus (GO:0009615)	cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	G-protein coupled acetylcholine receptor activity (GO:0016907)			central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(13)|liver(1)|lung(29)|ovary(4)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	68					Aclidinium(DB08897)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Anisotropine Methylbromide(DB00517)|Aripiprazole(DB01238)|Atropine(DB00572)|Bethanechol(DB01019)|Brompheniramine(DB00835)|Carbachol(DB00411)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Clozapine(DB00363)|Cocaine(DB00907)|Cryptenamine(DB00785)|Cyproheptadine(DB00434)|Darifenacin(DB00496)|Desipramine(DB01151)|Dicyclomine(DB00804)|Dimetindene(DB08801)|Diphenidol(DB01231)|Disopyramide(DB00280)|Doxacurium chloride(DB01135)|Doxepin(DB01142)|Ethopropazine(DB00392)|Fesoterodine(DB06702)|Flavoxate(DB01148)|Gallamine Triethiodide(DB00483)|Glycopyrrolate(DB00986)|Homatropine Methylbromide(DB00725)|Hyoscyamine(DB00424)|Imipramine(DB00458)|Ipratropium bromide(DB00332)|Ketamine(DB01221)|Loxapine(DB00408)|Maprotiline(DB00934)|Methotrimeprazine(DB01403)|Methylscopolamine bromide(DB00462)|Metixene(DB00340)|Metocurine(DB01336)|Mivacurium(DB01226)|Nicardipine(DB00622)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Oxybutynin(DB01062)|Oxyphencyclimine(DB00383)|Pancuronium(DB01337)|Paroxetine(DB00715)|Pethidine(DB00454)|Pilocarpine(DB01085)|Pipecuronium(DB01338)|Procyclidine(DB00387)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Quetiapine(DB01224)|Rocuronium(DB00728)|Scopolamine(DB00747)|Solifenacin(DB01591)|Succinylcholine(DB00202)|Tiotropium(DB01409)|Tolterodine(DB01036)|Triflupromazine(DB00508)|Trihexyphenidyl(DB00376)|Trimipramine(DB00726)|Tropicamide(DB00809)|Ziprasidone(DB00246)	CCAGCAGTGACGATGGCCTGG	0.507													C|||	1	0.000199681	0.0008	0.0	5008	,	,		19521	0.0		0.0	False		,,,				2504	0.0				p.D252D		.											CHRM2,colon,carcinoma,+2,1	CHRM2	+2	0			c.C756T						.						56.0	58.0	57.0					7																	136700368		2203	4300	6503	SO:0001819	synonymous_variant	1129	exon3			CAGTGACGATGGC		CCDS5843.1	7q35-q36	2014-09-17			ENSG00000181072	ENSG00000181072		"""Cholinergic receptors"", ""GPCR / Class A : Cholinergic receptors, muscarinic"""	1951	protein-coding gene	gene with protein product	"""acetylcholine receptor, muscarinic 2"""	118493					Standard	NM_000739		Approved		uc003vtl.1	P08172	OTTHUMG00000155658	ENST00000445907.2:c.756C>T	7.37:g.136700368C>T		Somatic	45	0		WXS	Illumina HiSeq	.	25	11	NM_001006632	Q4VBK6|Q9P1X9	Silent	SNP	ENST00000445907.2	37	CCDS5843.1																																																																																			.		0.507	CHRM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341010.1		
ERBB2	2064	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	17	37883077	37883077	+	Missense_Mutation	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr17:37883077T>G	ENST00000269571.5	+	25	3139	c.2980T>G	c.(2980-2982)Ttg>Gtg	p.L994V	ERBB2_ENST00000445658.2_Missense_Mutation_p.L718V|MIEN1_ENST00000474210.1_5'Flank|ERBB2_ENST00000406381.2_Missense_Mutation_p.L964V|ERBB2_ENST00000540147.1_Missense_Mutation_p.L964V|ERBB2_ENST00000584601.1_Missense_Mutation_p.L964V|MIR4728_ENST00000580969.1_RNA|ERBB2_ENST00000541774.1_Missense_Mutation_p.L979V|ERBB2_ENST00000584450.1_Missense_Mutation_p.L994V			P04626	ERBB2_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 2	994					axon guidance (GO:0007411)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|enzyme linked receptor protein signaling pathway (GO:0007167)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|motor neuron axon guidance (GO:0008045)|myelination (GO:0042552)|negative regulation of immature T cell proliferation in thymus (GO:0033088)|neuromuscular junction development (GO:0007528)|neurotrophin TRK receptor signaling pathway (GO:0048011)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine phosphorylation (GO:0018108)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell growth (GO:0030307)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of transcription from RNA polymerase I promoter (GO:0045943)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of angiogenesis (GO:0045765)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of microtubule-based process (GO:0032886)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|transcription, DNA-templated (GO:0006351)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|ErbB-3 class receptor binding (GO:0043125)|identical protein binding (GO:0042802)|protein C-terminus binding (GO:0008022)|protein dimerization activity (GO:0046983)|protein heterodimerization activity (GO:0046982)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|RNA polymerase I core binding (GO:0001042)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(16)|central_nervous_system(17)|endometrium(6)|haematopoietic_and_lymphoid_tissue(8)|kidney(4)|large_intestine(16)|liver(3)|lung(125)|ovary(18)|pancreas(1)|prostate(4)|skin(1)|stomach(14)|upper_aerodigestive_tract(9)|urinary_tract(4)	247	all_cancers(6;1.06e-93)|all_epithelial(6;2.33e-113)|Breast(7;9.37e-100)|Lung NSC(9;9.76e-10)|all_lung(9;5.34e-09)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052)	Ovarian(249;0.0547)|Colorectal(1115;0.234)	UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|Epithelial(3;9.42e-64)|all cancers(3;5.61e-57)|BRCA - Breast invasive adenocarcinoma(8;2.5e-45)|STAD - Stomach adenocarcinoma(3;9.03e-13)|Colorectal(5;6.23e-08)|COAD - Colon adenocarcinoma(5;8.58e-06)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|OV - Ovarian serous cystadenocarcinoma(8;0.0917)|LUSC - Lung squamous cell carcinoma(15;0.171)	UCEC - Uterine corpus endometrioid carcinoma (308;0.0767)	ado-trastuzumab emtansine(DB05773)|Afatinib(DB08916)|Lapatinib(DB01259)|Pertuzumab(DB06366)|Trastuzumab(DB00072)	GAATGAGGACTTGGGCCCAGC	0.617		1	"""A, Mis, O"""		"""breast, ovarian, other tumour types, NSCLC, gastric"""					TCGA GBM(5;<1E-08)																											p.L994V		.		Dom	yes		17	17q21.1	2064	"""v-erb-b2 erythroblastic leukemia viral oncogene homolog 2, neuro/glioblastoma derived oncogene homolog (avian)"""		E	.	.	.	0			c.T2980G						.						71.0	71.0	71.0					17																	37883077		2203	4300	6503	SO:0001583	missense	2064	exon25			GAGGACTTGGGCC	X03363	CCDS32642.1, CCDS45667.1, CCDS74052.1	17q11.2-q12	2014-09-17	2013-07-09			ENSG00000141736		"""CD molecules"""	3430	protein-coding gene	gene with protein product	"""neuro/glioblastoma derived oncogene homolog"""	164870	"""v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 2 (neuro/glioblastoma derived oncogene homolog)"""	NGL			Standard	XM_005257140		Approved	NEU, HER-2, CD340, HER2	uc002hso.3	P04626		ENST00000269571.5:c.2980T>G	17.37:g.37883077T>G	ENSP00000269571:p.Leu994Val	Somatic	34	0		WXS	Illumina HiSeq	.	18	8	NM_004448	B2RZG3|B4DHN3|Q14256|Q6LDV1|Q9UMK4|X5D2V5	Missense_Mutation	SNP	ENST00000269571.5	37	CCDS32642.1	.	.	.	.	.	.	.	.	.	.	T	11.85	1.762908	0.31228	.	.	ENSG00000141736	ENST00000406381;ENST00000541774;ENST00000445658;ENST00000269571;ENST00000540147	T;T;T;T;T	0.76186	-1.0;-1.0;-0.98;-1.0;-1.0	5.35	-6.07	0.02158	Protein kinase-like domain (1);	.	.	.	.	T	0.60534	0.2276	L	0.46157	1.445	0.44508	D	0.997455	B;B;B	0.23806	0.0;0.091;0.068	B;B;B	0.22601	0.001;0.027;0.04	T	0.17167	-1.0378	9	0.45353	T	0.12	.	8.1316	0.31031	0.3345:0.4832:0.0:0.1823	.	718;979;994	B4DTR1;P04626-4;P04626	.;.;ERBB2_HUMAN	V	964;979;718;994;964	ENSP00000385185:L964V;ENSP00000446466:L979V;ENSP00000404047:L718V;ENSP00000269571:L994V;ENSP00000443562:L964V	ENSP00000269571:L994V	L	+	1	2	ERBB2	35136603	0.003000	0.15002	0.514000	0.27761	0.985000	0.73830	-0.308000	0.08156	-1.454000	0.01926	0.533000	0.62120	TTG	.		0.617	ERBB2-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445621.2		
RPS12	6206	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	6	133137642	133137642	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr6:133137642G>T	ENST00000230050.3	+	4	384	c.174G>T	c.(172-174)gaG>gaT	p.E58D	SNORD101_ENST00000384027.1_RNA|SNORA33_ENST00000363664.1_RNA|SNORD100_ENST00000408573.1_RNA	NM_001016.3	NP_001007.2	P25398	RS12_HUMAN	ribosomal protein S12	58					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytosol (GO:0005829)|cytosolic small ribosomal subunit (GO:0022627)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			endometrium(1)|kidney(13)|lung(3)|urinary_tract(1)	18	Breast(56;0.214)			OV - Ovarian serous cystadenocarcinoma(155;0.00284)|GBM - Glioblastoma multiforme(226;0.0256)		ACTGTGATGAGCCTATGTATG	0.423																																					p.E58D		.											.	.	.	0			c.G174T						.						145.0	139.0	141.0					6																	133137642		2203	4298	6501	SO:0001583	missense	6206	exon4			TGATGAGCCTATG	X53505	CCDS5164.1	6q23	2011-04-05			ENSG00000112306	ENSG00000112306		"""S ribosomal proteins"""	10385	protein-coding gene	gene with protein product		603660				1861993, 9582194	Standard	NM_001016		Approved	S12	uc003qdx.3	P25398	OTTHUMG00000015593	ENST00000230050.3:c.174G>T	6.37:g.133137642G>T	ENSP00000230050:p.Glu58Asp	Somatic	36	0		WXS	Illumina HiSeq	.	19	9	NM_001016	Q76M58	Missense_Mutation	SNP	ENST00000230050.3	37	CCDS5164.1	.	.	.	.	.	.	.	.	.	.	G	19.26	3.793497	0.70452	.	.	ENSG00000112306	ENST00000230050	T	0.59502	0.26	5.91	2.73	0.32206	Ribosomal protein L7Ae/L30e/S12e/Gadd45 (1);	0.045134	0.85682	D	0.000000	T	0.57710	0.2072	M	0.82823	2.61	0.80722	D	1	P	0.43938	0.822	P	0.51079	0.658	T	0.61850	-0.6978	10	0.48119	T	0.1	-21.7349	10.7172	0.46019	0.2701:0.0:0.7299:0.0	.	58	P25398	RS12_HUMAN	D	58	ENSP00000230050:E58D	ENSP00000230050:E58D	E	+	3	2	RPS12	133179335	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.265000	0.33027	0.790000	0.33803	0.655000	0.94253	GAG	.		0.423	RPS12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042270.2	NM_001016	
PAPPA2	60676	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	176811561	176811561	+	Missense_Mutation	SNP	C	C	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr1:176811561C>G	ENST00000367662.3	+	23	6511	c.5347C>G	c.(5347-5349)Cgg>Ggg	p.R1783G		NM_020318.2	NP_064714.2	Q9BXP8	PAPP2_HUMAN	pappalysin 2	1783					bone morphogenesis (GO:0060349)|cell differentiation (GO:0030154)|cellular protein metabolic process (GO:0044267)|proteolysis (GO:0006508)|regulation of cell growth (GO:0001558)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|membrane (GO:0016020)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(3)|breast(3)|central_nervous_system(7)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(19)|lung(136)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|upper_aerodigestive_tract(8)|urinary_tract(1)	226						GTGCACCTGCCGGGACCCCAA	0.512																																					p.R1783G		.											PAPPA2,colon,carcinoma,-1,2	PAPPA2	-1	0			c.C5347G						.						90.0	89.0	89.0					1																	176811561		1903	4129	6032	SO:0001583	missense	60676	exon23			ACCTGCCGGGACC	BG354569	CCDS41438.1, CCDS41439.1	1q23-q25	2008-05-23	2004-07-07	2004-07-09	ENSG00000116183	ENSG00000116183			14615	protein-coding gene	gene with protein product			"""placenta-specific 3"""	PLAC3		11018262, 11264294	Standard	NM_021936		Approved	PAPPE, PAPP-A2	uc001gkz.3	Q9BXP8	OTTHUMG00000035025	ENST00000367662.3:c.5347C>G	1.37:g.176811561C>G	ENSP00000356634:p.Arg1783Gly	Somatic	43	0		WXS	Illumina HiSeq	.	61	16	NM_020318	A9Z1Y8|Q96PH7|Q96PH8|Q9H4C9	Missense_Mutation	SNP	ENST00000367662.3	37	CCDS41438.1	.	.	.	.	.	.	.	.	.	.	C	23.2	4.387203	0.82902	.	.	ENSG00000116183	ENST00000367662	T	0.02015	4.5	5.51	4.59	0.56863	.	0.000000	0.64402	D	0.000001	T	0.10294	0.0252	M	0.61703	1.905	0.80722	D	1	D	0.89917	1.0	D	0.71656	0.974	T	0.00926	-1.1512	10	0.87932	D	0	-9.368	14.5915	0.68368	0.1474:0.8526:0.0:0.0	.	1783	Q9BXP8	PAPP2_HUMAN	G	1783	ENSP00000356634:R1783G	ENSP00000356634:R1783G	R	+	1	2	PAPPA2	175078184	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	6.724000	0.74747	1.311000	0.45024	-0.181000	0.13052	CGG	.		0.512	PAPPA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084763.1		
NCOR1	9611	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	17	15976773	15976773	+	Missense_Mutation	SNP	T	T	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr17:15976773T>C	ENST00000268712.3	-	28	4038	c.3781A>G	c.(3781-3783)Agg>Ggg	p.R1261G	NCOR1_ENST00000395857.3_Intron|NCOR1_ENST00000395851.1_Missense_Mutation_p.R1277G	NM_006311.3	NP_006302.2	O75376	NCOR1_HUMAN	nuclear receptor corepressor 1	1261	Interaction with ETO.				CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation (GO:0002361)|cellular lipid metabolic process (GO:0044255)|cholesterol homeostasis (GO:0042632)|chromatin modification (GO:0016568)|circadian regulation of gene expression (GO:0032922)|definitive erythrocyte differentiation (GO:0060318)|gene expression (GO:0010467)|negative regulation of JNK cascade (GO:0046329)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of histone deacetylation (GO:0031065)|regulation of fatty acid transport (GO:2000191)|regulation of glycolytic process by negative regulation of transcription from RNA polymerase II promoter (GO:0072362)|regulation of lipid transport by negative regulation of transcription from RNA polymerase II promoter (GO:0072368)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|spindle assembly (GO:0051225)|thalamus development (GO:0021794)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)|transcription factor complex (GO:0005667)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|histone deacetylase binding (GO:0042826)|histone deacetylase regulator activity (GO:0035033)|nuclear hormone receptor binding (GO:0035257)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)			NS(2)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(17)|lung(26)|ovary(1)|prostate(7)|skin(2)|upper_aerodigestive_tract(6)|urinary_tract(10)	107				UCEC - Uterine corpus endometrioid carcinoma (92;0.101)		GGAGACTCCCTCATTGACATC	0.368																																					p.R1277G		.											.	.	.	0			c.A3829G						.						178.0	157.0	164.0					17																	15976773		2203	4300	6503	SO:0001583	missense	9611	exon27			ACTCCCTCATTGA	AF044209	CCDS11175.1, CCDS54094.1, CCDS54095.1	17p11.2	2014-06-12	2010-06-10		ENSG00000141027	ENSG00000141027			7672	protein-coding gene	gene with protein product	"""thyroid hormone- and retinoic acid receptor-associated corepressor 1"", ""protein phosphatase 1, regulatory subunit 109"""	600849	"""nuclear receptor co-repressor 1"""			7566114, 9724795	Standard	NM_006311		Approved	N-CoR, hCIT529I10, TRAC1, hN-CoR, KIAA1047, MGC104216, PPP1R109	uc002gpo.3	O75376	OTTHUMG00000059309	ENST00000268712.3:c.3781A>G	17.37:g.15976773T>C	ENSP00000268712:p.Arg1261Gly	Somatic	80	0		WXS	Illumina HiSeq	.	59	28	NM_001190440	B3DLF8|E9PGV6|Q86YY0|Q9UPV5|Q9UQ18	Missense_Mutation	SNP	ENST00000268712.3	37	CCDS11175.1	.	.	.	.	.	.	.	.	.	.	T	12.25	1.880299	0.33162	.	.	ENSG00000141027	ENST00000268712;ENST00000395851;ENST00000395849	T;T	0.52526	0.66;0.66	6.07	6.07	0.98685	.	0.000000	0.85682	D	0.000000	T	0.51601	0.1684	N	0.14661	0.345	0.80722	D	1	D;D;D;D	0.67145	0.996;0.993;0.979;0.988	D;D;P;P	0.77557	0.99;0.977;0.628;0.794	T	0.58864	-0.7561	10	0.87932	D	0	-11.2234	12.9307	0.58284	0.0:0.0:0.1347:0.8653	.	72;1168;1261;1277	B4DZ48;E7EVK1;O75376;O75376-2	.;.;NCOR1_HUMAN;.	G	1261;1277;1168	ENSP00000268712:R1261G;ENSP00000379192:R1277G	ENSP00000268712:R1261G	R	-	1	2	NCOR1	15917498	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	2.821000	0.48065	2.326000	0.78906	0.533000	0.62120	AGG	.		0.368	NCOR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131751.5	NM_006311	
HAMP	57817	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	19	35775743	35775743	+	Missense_Mutation	SNP	A	A	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr19:35775743A>G	ENST00000598398.1	+	3	438	c.142A>G	c.(142-144)Agc>Ggc	p.S48G	HAMP_ENST00000222304.3_Missense_Mutation_p.S48G	NM_021175.2	NP_066998.1	P81172	HEPC_HUMAN	hepcidin antimicrobial peptide	48					cellular iron ion homeostasis (GO:0006879)|defense response to bacterium (GO:0042742)|defense response to fungus (GO:0050832)|immune response (GO:0006955)|killing of cells of other organism (GO:0031640)	apical cortex (GO:0045179)|extracellular region (GO:0005576)				breast(1)|central_nervous_system(1)|large_intestine(1)|lung(1)	4	all_lung(56;2.37e-08)|Lung NSC(56;3.66e-08)|Esophageal squamous(110;0.162)		Epithelial(14;7.4e-20)|OV - Ovarian serous cystadenocarcinoma(14;6.47e-19)|all cancers(14;4.17e-17)|LUSC - Lung squamous cell carcinoma(66;0.0417)			AGCCAGGGCCAGCTGGATGGT	0.632																																					p.S48G		.											.	.	.	0			c.A142G						.						104.0	101.0	102.0					19																	35775743		2203	4300	6503	SO:0001583	missense	57817	exon2			AGGGCCAGCTGGA	AF309489	CCDS12454.1	19q13.1	2014-09-17				ENSG00000105697			15598	protein-coding gene	gene with protein product		606464				11034317, 11113132	Standard	NM_021175		Approved	LEAP-1, HEPC, HFE2B, LEAP1	uc002nyw.3	P81172		ENST00000598398.1:c.142A>G	19.37:g.35775743A>G	ENSP00000471894:p.Ser48Gly	Somatic	37	0		WXS	Illumina HiSeq	.	33	12	NM_021175	Q1HE14|Q9BY68	Missense_Mutation	SNP	ENST00000598398.1	37	CCDS12454.1	.	.	.	.	.	.	.	.	.	.	A	0.073	-1.198985	0.01581	.	.	ENSG00000105697	ENST00000222304	D	0.88201	-2.35	4.51	-5.16	0.02857	.	1.094660	0.06924	N	0.809964	T	0.71467	0.3343	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.64356	-0.6427	9	0.02654	T	1	-2.2616	10.3388	0.43864	0.2035:0.1319:0.6646:0.0	.	48	P81172	HEPC_HUMAN	G	48	ENSP00000222304:S48G	ENSP00000222304:S48G	S	+	1	0	HAMP	40467583	0.000000	0.05858	0.000000	0.03702	0.154000	0.21943	-0.756000	0.04777	-0.902000	0.03886	-2.455000	0.00206	AGC	.		0.632	HAMP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466067.1	NM_021175	
HPSE	10855	hgsc.bcm.edu;bcgsc.ca	37	4	84222115	84222115	+	Silent	SNP	G	G	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr4:84222115G>T	ENST00000405413.2	-	12	1606	c.1470C>A	c.(1468-1470)tcC>tcA	p.S490S	HPSE_ENST00000513463.1_Silent_p.S432S|HPSE_ENST00000311412.5_Silent_p.S490S|HPSE_ENST00000512196.1_Silent_p.S416S	NM_006665.5	NP_006656.2	Q9Y251	HPSE_HUMAN	heparanase	490					carbohydrate metabolic process (GO:0005975)|cell-matrix adhesion (GO:0007160)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan catabolic process (GO:0030200)|positive regulation of blood coagulation (GO:0030194)|positive regulation of hair follicle development (GO:0051798)|positive regulation of osteoblast proliferation (GO:0033690)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation vascular endothelial growth factor production (GO:0010575)|proteoglycan metabolic process (GO:0006029)|regulation of hair follicle development (GO:0051797)|small molecule metabolic process (GO:0044281)|vascular wound healing (GO:0061042)	extracellular region (GO:0005576)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)|membrane raft (GO:0045121)|nucleus (GO:0005634)	beta-glucuronidase activity (GO:0004566)|heparanase activity (GO:0030305)|protein dimerization activity (GO:0046983)|syndecan binding (GO:0045545)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(2)|skin(1)|urinary_tract(2)	20		Hepatocellular(203;0.114)		COAD - Colon adenocarcinoma(81;0.141)	Dalteparin(DB06779)|Heparin(DB01109)	TTACTTACTTGGAAAGTAATC	0.358																																					p.S490S		.											.	.	.	0			c.C1470A						.						78.0	81.0	80.0					4																	84222115		2203	4300	6503	SO:0001819	synonymous_variant	10855	exon11			TTACTTGGAAAGT	AF144325	CCDS3602.1, CCDS54774.1, CCDS56337.1	4q21.3	2008-02-05			ENSG00000173083	ENSG00000173083			5164	protein-coding gene	gene with protein product		604724				10395325, 10395326	Standard	NM_006665		Approved	HPA, HSE1, HPSE1	uc003hoj.4	Q9Y251	OTTHUMG00000130425	ENST00000405413.2:c.1470C>A	4.37:g.84222115G>T		Somatic	144	0		WXS	Illumina HiSeq	.	56	4	NM_001098540	A9JIG7|C7F7I3|C7F7I4|E9PCA9|E9PGR1|Q53GE5|Q9UL39	Silent	SNP	ENST00000405413.2	37	CCDS3602.1																																																																																			.		0.358	HPSE-001	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252812.2	NM_006665	
TYMP	1890	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	22	50967621	50967621	+	Missense_Mutation	SNP	C	C	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr22:50967621C>T	ENST00000252029.3	-	3	523	c.361G>A	c.(361-363)Gtg>Atg	p.V121M	TYMP_ENST00000395680.1_Missense_Mutation_p.V121M|TYMP_ENST00000395678.3_Missense_Mutation_p.V121M|TYMP_ENST00000395681.1_Missense_Mutation_p.V121M|SCO2_ENST00000543927.1_5'Flank	NM_001113755.2|NM_001113756.2|NM_001257988.1|NM_001257989.1|NM_001953.4	NP_001107227.1|NP_001107228.1|NP_001244917.1|NP_001244918.1|NP_001944.1	P19971	TYPH_HUMAN	thymidine phosphorylase	121					angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|chemotaxis (GO:0006935)|DNA replication (GO:0006260)|mitochondrial genome maintenance (GO:0000002)|nucleobase-containing small molecule metabolic process (GO:0055086)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside catabolic process (GO:0046135)|pyrimidine nucleoside salvage (GO:0043097)|pyrimidine nucleotide metabolic process (GO:0006220)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	phosphorylase activity (GO:0004645)|platelet-derived growth factor receptor binding (GO:0005161)|pyrimidine-nucleoside phosphorylase activity (GO:0016154)|thymidine phosphorylase activity (GO:0009032)|transferase activity, transferring pentosyl groups (GO:0016763)			large_intestine(1)|lung(2)|ovary(1)|prostate(1)	5		all_cancers(38;4.58e-14)|all_epithelial(38;1.12e-12)|all_lung(38;3.07e-05)|Breast(42;6.27e-05)|Lung NSC(38;0.000813)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.206)|LUAD - Lung adenocarcinoma(64;0.247)	Capecitabine(DB01101)|Cidofovir(DB00369)|Floxuridine(DB00322)|Fluorouracil(DB00544)|Trifluridine(DB00432)	TTGTCACCCACACCCCCTGTG	0.637																																					p.V121M		.											.	.	.	0			c.G361A						.						56.0	53.0	54.0					22																	50967621		2203	4300	6503	SO:0001583	missense	1890	exon3			CACCCACACCCCC	M63193	CCDS14096.1, CCDS58811.1	22q13	2014-09-17	2008-01-21	2008-01-21	ENSG00000025708	ENSG00000025708	2.4.2.4		3148	protein-coding gene	gene with protein product	"""gliostatin"""	131222	"""endothelial cell growth factor 1 (platelet-derived)"""	MNGIE, ECGF1		1590793, 11733540	Standard	NM_001113755		Approved		uc003bme.5	P19971	OTTHUMG00000150249	ENST00000252029.3:c.361G>A	22.37:g.50967621C>T	ENSP00000252029:p.Val121Met	Somatic	62	0		WXS	Illumina HiSeq	.	46	21	NM_001257989	A8MW15|H9KVA0|Q13390|Q8WVB7	Missense_Mutation	SNP	ENST00000252029.3	37	CCDS14096.1	.	.	.	.	.	.	.	.	.	.	C	23.4	4.410499	0.83340	.	.	ENSG00000025708	ENST00000395680;ENST00000395681;ENST00000252029;ENST00000395678;ENST00000425169	D;D;D;D;D	0.98493	-4.96;-4.96;-4.96;-4.96;-4.96	5.21	5.21	0.72293	Glycosyl transferase, family 3 (3);	0.000000	0.64402	D	0.000001	D	0.99363	0.9776	H	0.97682	4.055	0.47094	D	0.999318	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;1.0	D	0.98521	1.0623	10	0.87932	D	0	-7.4255	16.2524	0.82492	0.0:1.0:0.0:0.0	.	121;121;121;121	B4DVR2;B2RBL3;E5KRG5;P19971	.;.;.;TYPH_HUMAN	M	121	ENSP00000379037:V121M;ENSP00000379038:V121M;ENSP00000252029:V121M;ENSP00000379036:V121M;ENSP00000395875:V121M	ENSP00000252029:V121M	V	-	1	0	TYMP	49314487	1.000000	0.71417	0.424000	0.26647	0.568000	0.35870	6.836000	0.75349	2.441000	0.82636	0.561000	0.74099	GTG	.		0.637	TYMP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317081.1	NM_001953	
MCOLN1	57192	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	19	7591678	7591678	+	Missense_Mutation	SNP	G	G	C	rs147878118		TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr19:7591678G>C	ENST00000264079.6	+	4	562	c.437G>C	c.(436-438)cGg>cCg	p.R146P		NM_020533.2	NP_065394.1	Q9GZU1	MCLN1_HUMAN	mucolipin 1	146					calcium ion transmembrane transport (GO:0070588)|cation transport (GO:0006812)|cellular iron ion homeostasis (GO:0006879)|ion transmembrane transport (GO:0034220)|release of sequestered calcium ion into cytosol (GO:0051209)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	cation channel activity (GO:0005261)|NAADP-sensitive calcium-release channel activity (GO:0072345)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18						TCACTGGGCCGGTATGCGTAT	0.667																																					p.R146P		.											.	.	.	0			c.G437C						.						123.0	84.0	97.0					19																	7591678		2203	4300	6503	SO:0001583	missense	57192	exon4			TGGGCCGGTATGC	AF249319	CCDS12180.1	19p13.2	2011-12-16				ENSG00000090674		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	13356	protein-coding gene	gene with protein product		605248				16382100	Standard	NM_020533		Approved	TRPML1, ML4, MLIV, MST080, MSTP080, TRPM-L1	uc002mgo.3	Q9GZU1		ENST00000264079.6:c.437G>C	19.37:g.7591678G>C	ENSP00000264079:p.Arg146Pro	Somatic	58	0		WXS	Illumina HiSeq	.	36	17	NM_020533	D6W647|Q7Z4F7|Q9H292|Q9H4B3|Q9H4B5	Missense_Mutation	SNP	ENST00000264079.6	37	CCDS12180.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	11.06|11.06	1.527639|1.527639	0.27299|0.27299	.|.	.|.	ENSG00000090674|ENSG00000090674	ENST00000394321|ENST00000264079	.|T	.|0.50548	.|0.74	5.24|5.24	1.97|1.97	0.26223|0.26223	.|.	.|0.305584	.|0.36665	.|N	.|0.002466	T|T	0.28599|0.28599	0.0708|0.0708	N|N	0.21142|0.21142	0.635|0.635	0.20764|0.20764	N|N	0.999858|0.999858	D|B	0.54964|0.14012	0.969|0.009	P|B	0.47162|0.10450	0.54|0.005	T|T	0.17868|0.17868	-1.0355|-1.0355	8|10	0.87932|0.17832	D|T	0|0.49	.|.	8.9883|8.9883	0.36008|0.36008	0.2415:0.0:0.7585:0.0|0.2415:0.0:0.7585:0.0	.|.	33|146	Q9GZU1-2|Q9GZU1	.|MCLN1_HUMAN	R|P	33|146	.|ENSP00000264079:R146P	ENSP00000377856:G33R|ENSP00000264079:R146P	G|R	+|+	1|2	0|0	MCOLN1|MCOLN1	7497678|7497678	0.036000|0.036000	0.19791|0.19791	0.555000|0.555000	0.28281|0.28281	0.763000|0.763000	0.43281|0.43281	1.571000|1.571000	0.36450|0.36450	0.237000|0.237000	0.21200|0.21200	0.655000|0.655000	0.94253|0.94253	GGT|CGG	.		0.667	MCOLN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458974.2	NM_020533	
BCO2	83875	hgsc.bcm.edu	37	11	112065435	112065435	+	Silent	SNP	G	G	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr11:112065435G>T	ENST00000357685.5	+	5	828	c.693G>T	c.(691-693)ctG>ctT	p.L231L	BCO2_ENST00000393032.2_Silent_p.L197L|BCO2_ENST00000526088.1_Silent_p.L197L|BCO2_ENST00000531169.1_Silent_p.L197L|BCO2_ENST00000361053.4_Intron|BCO2_ENST00000438022.1_Silent_p.L197L|BCO2_ENST00000532593.1_Silent_p.L126L|AP002884.3_ENST00000532612.1_Intron			Q9BYV7	BCDO2_HUMAN	beta-carotene oxygenase 2	231			L -> P (in dbSNP:rs10891338). {ECO:0000269|PubMed:11278918, ECO:0000269|PubMed:14702039, ECO:0000269|Ref.1}.		carotene catabolic process (GO:0016121)|carotene metabolic process (GO:0016119)|carotenoid metabolic process (GO:0016116)|oxidation-reduction process (GO:0055114)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of reactive oxygen species metabolic process (GO:2000377)|retinal metabolic process (GO:0042574)|retinoic acid metabolic process (GO:0042573)	intracellular (GO:0005622)|mitochondrion (GO:0005739)	metal ion binding (GO:0046872)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen (GO:0016702)			NS(1)|breast(1)|kidney(3)|large_intestine(1)|lung(9)|skin(1)	16						ATTATGACCTGGATGGAACAG	0.408																																					p.L231L	GBM(177;1916 2099 21049 29541 39946)	.											BCO2,NS,carcinoma,0,1	BCO2	0	0			c.G693T						.						167.0	155.0	159.0					11																	112065435		2201	4297	6498	SO:0001819	synonymous_variant	83875	exon5			TGACCTGGATGGA	AJ290393	CCDS8358.2, CCDS41716.1, CCDS58181.1, CCDS58182.1, CCDS58183.1	11q23.1	2014-05-12	2008-04-15	2008-04-15	ENSG00000197580	ENSG00000197580	1.13.11.71		18503	protein-coding gene	gene with protein product	"""beta-carotene 9',10' oxygenase"", ""carotenoid-9',10'-cleaving dioxygenase"""	611740	"""beta-carotene dioxygenase 2"""	BCDO2		11278918, 15983114, 15949678	Standard	NM_031938		Approved	FLJ34464, B-DIOX-II	uc001pnf.3	Q9BYV7	OTTHUMG00000167155	ENST00000357685.5:c.693G>T	11.37:g.112065435G>T		Somatic	58	0		WXS	Illumina HiSeq	.	33	2	NM_031938	B0YIX5|B4DNC3|E9PBI8|E9PJJ1|Q8IUS0|Q96JC8|Q96JY5	Silent	SNP	ENST00000357685.5	37	CCDS8358.2																																																																																			.		0.408	BCO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256570.3	NM_001037290	
ZNF630	57232	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	X	47918881	47918881	+	Missense_Mutation	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chrX:47918881T>G	ENST00000409324.3	-	5	1176	c.950A>C	c.(949-951)aAa>aCa	p.K317T	ZNF630_ENST00000276054.4_Missense_Mutation_p.K193T|ZNF630-AS1_ENST00000436124.1_RNA|ZNF630_ENST00000442455.3_Missense_Mutation_p.K303T	NM_001037735.2	NP_001032824.2	Q2M218	ZN630_HUMAN	zinc finger protein 630	317					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|large_intestine(6)|lung(11)|ovary(1)	19						TTCATAGGGTTTCTCCCCAGT	0.423																																					p.K317T		.											.	.	.	0			c.A950C						.						62.0	55.0	58.0					X																	47918881		2194	4291	6485	SO:0001583	missense	57232	exon5			TAGGGTTTCTCCC	AK000580	CCDS35237.2, CCDS75971.1	Xp11.3-p11.1	2013-01-08			ENSG00000221994	ENSG00000221994		"""Zinc fingers, C2H2-type"", ""-"""	28855	protein-coding gene	gene with protein product		300819					Standard	NM_001037735		Approved	BC037316, dJ54B20.2, FLJ20573, MGC138344	uc004div.4	Q2M218	OTTHUMG00000021463	ENST00000409324.3:c.950A>C	X.37:g.47918881T>G	ENSP00000386393:p.Lys317Thr	Somatic	33	0		WXS	Illumina HiSeq	.	27	24	NM_001037735	F8WAG4|Q5H8Z5	Missense_Mutation	SNP	ENST00000409324.3	37	CCDS35237.2	.	.	.	.	.	.	.	.	.	.	.	14.52	2.560402	0.45590	.	.	ENSG00000221994	ENST00000442455;ENST00000276054;ENST00000409324	T;T;T	0.24908	1.83;1.83;1.83	2.31	2.31	0.28768	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.51126	0.1656	M	0.87456	2.885	0.25174	N	0.990259	D	0.76494	0.999	D	0.73708	0.981	T	0.31503	-0.9941	9	0.72032	D	0.01	.	7.6956	0.28592	0.0:0.0:0.0:1.0	.	317	Q2M218	ZN630_HUMAN	T	303;193;317	ENSP00000393163:K303T;ENSP00000354683:K193T;ENSP00000386393:K317T	ENSP00000354683:K193T	K	-	2	0	ZNF630	47803825	0.311000	0.24536	0.644000	0.29465	0.679000	0.39708	0.487000	0.22356	0.961000	0.38030	0.441000	0.28932	AAA	.		0.423	ZNF630-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327254.1	NM_001037735	
GBP1P1	400759	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	1	89889824	89889824	+	RNA	SNP	T	T	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr1:89889824T>C	ENST00000513638.1	+	0	565					NR_003133.2				guanylate binding protein 1, interferon-inducible pseudogene 1																		CAGTGGAACGTGTGAAAGCTG	0.433																																					.		.											.	.	.	0			.						.																																					400759	.			GGAACGTGTGAAA			1p22.2	2011-03-09			ENSG00000225492	ENSG00000225492			39561	pseudogene	pseudogene							Standard	NR_003133		Approved		uc009wcy.1		OTTHUMG00000010128		1.37:g.89889824T>C		Somatic	67	0		WXS	Illumina HiSeq	.	9	4	.		RNA	SNP	ENST00000513638.1	37																																																																																				.		0.433	GBP1P1-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000360073.1	NR_003133	
NHLRC2	374354	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	10	115657896	115657896	+	Missense_Mutation	SNP	T	T	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr10:115657896T>C	ENST00000369301.3	+	6	1279	c.1067T>C	c.(1066-1068)tTa>tCa	p.L356S		NM_198514.3	NP_940916.2	Q8NBF2	NHLC2_HUMAN	NHL repeat containing 2	356										breast(1)|endometrium(2)|kidney(4)|large_intestine(3)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	15				Epithelial(162;0.017)|all cancers(201;0.0187)		GGTGACATTTTATGGATAGCC	0.373																																					p.L356S		.											.	.	.	0			c.T1067C						.						40.0	41.0	41.0					10																	115657896		2203	4300	6503	SO:0001583	missense	374354	exon6			ACATTTTATGGAT	AK090631	CCDS7585.1	10q26.11	2006-03-31			ENSG00000196865	ENSG00000196865			24731	protein-coding gene	gene with protein product						12477932	Standard	NM_198514		Approved	FLJ25621, FLJ20147, FLJ33312, MGC45492, DKFZp779F115	uc001lax.2	Q8NBF2	OTTHUMG00000019078	ENST00000369301.3:c.1067T>C	10.37:g.115657896T>C	ENSP00000358307:p.Leu356Ser	Somatic	229	0		WXS	Illumina HiSeq	.	108	45	NM_198514	Q8N1H1|Q8N5A6	Missense_Mutation	SNP	ENST00000369301.3	37	CCDS7585.1	.	.	.	.	.	.	.	.	.	.	T	24.4	4.529598	0.85706	.	.	ENSG00000196865	ENST00000369301	D	0.92495	-3.05	5.92	5.92	0.95590	Six-bladed beta-propeller, TolB-like (1);	0.000000	0.64402	D	0.000002	D	0.96935	0.8999	M	0.92880	3.355	0.58432	D	0.999991	D	0.89917	1.0	D	0.91635	0.999	D	0.97760	1.0220	10	0.87932	D	0	-9.7543	14.9492	0.71057	0.0:0.0:0.0:1.0	.	356	Q8NBF2	NHLC2_HUMAN	S	356	ENSP00000358307:L356S	ENSP00000358307:L356S	L	+	2	0	NHLRC2	115647886	1.000000	0.71417	0.934000	0.37439	0.940000	0.58332	7.809000	0.86057	2.277000	0.76020	0.528000	0.53228	TTA	.		0.373	NHLRC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050446.1	NM_198514	
CDC42BPB	9578	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	14	103410551	103410551	+	Missense_Mutation	SNP	G	G	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr14:103410551G>A	ENST00000361246.2	-	30	4373	c.4085C>T	c.(4084-4086)cCa>cTa	p.P1362L		NM_006035.3	NP_006026.3			CDC42 binding protein kinase beta (DMPK-like)											NS(1)|breast(4)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(11)|liver(1)|lung(14)|ovary(2)|prostate(2)|skin(3)|stomach(1)	49		Melanoma(154;0.155)		Colorectal(3;0.0129)|READ - Rectum adenocarcinoma(2;0.0419)|Epithelial(152;0.0474)|all cancers(159;0.199)		TCTGTGGAATGGCTTCGTTCT	0.577																																					p.P1362L		.											.	.	.	0			c.C4085T						.						71.0	68.0	69.0					14																	103410551		2203	4299	6502	SO:0001583	missense	9578	exon30			TGGAATGGCTTCG	AF128625	CCDS9978.1	14q32.32	2010-05-12	2001-11-28		ENSG00000198752	ENSG00000198752			1738	protein-coding gene	gene with protein product		614062	"""CDC42-binding protein kinase beta (DMPK-like)"""			10198171	Standard	NM_006035		Approved	MRCKB, KIAA1124	uc001ymi.1	Q9Y5S2		ENST00000361246.2:c.4085C>T	14.37:g.103410551G>A	ENSP00000355237:p.Pro1362Leu	Somatic	29	0		WXS	Illumina HiSeq	.	19	6	NM_006035		Missense_Mutation	SNP	ENST00000361246.2	37	CCDS9978.1	.	.	.	.	.	.	.	.	.	.	G	17.54	3.414385	0.62511	.	.	ENSG00000198752	ENST00000361246;ENST00000541396	T	0.04917	3.53	5.24	5.24	0.73138	Citron-like (3);	0.000000	0.85682	D	0.000000	T	0.12518	0.0304	M	0.69248	2.105	0.80722	D	1	B;B	0.17465	0.022;0.013	B;B	0.25140	0.058;0.036	T	0.04065	-1.0980	10	0.42905	T	0.14	.	19.1847	0.93639	0.0:0.0:1.0:0.0	.	1362;1362	A9JR72;Q9Y5S2	.;MRCKB_HUMAN	L	1362;473	ENSP00000355237:P1362L	ENSP00000355237:P1362L	P	-	2	0	CDC42BPB	102480304	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	9.568000	0.98166	2.603000	0.88011	0.655000	0.94253	CCA	.		0.577	CDC42BPB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415711.1	NM_006035	
PIK3R4	30849	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	3	130452666	130452666	+	Silent	SNP	A	A	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr3:130452666A>G	ENST00000356763.3	-	4	1733	c.1176T>C	c.(1174-1176)tgT>tgC	p.C392C		NM_014602.2	NP_055417.1	Q99570	PI3R4_HUMAN	phosphoinositide-3-kinase, regulatory subunit 4	392					innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|protein phosphorylation (GO:0006468)|small molecule metabolic process (GO:0044281)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)	axoneme (GO:0005930)|cytosol (GO:0005829)|late endosome (GO:0005770)|membrane (GO:0016020)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(6)|kidney(6)|large_intestine(16)|lung(28)|ovary(6)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|urinary_tract(1)	77						GTTTGGAATCACAGTATTTAA	0.398																																					p.C392C		.											.	.	.	0			c.T1176C						.						133.0	130.0	131.0					3																	130452666		2203	4300	6503	SO:0001819	synonymous_variant	30849	exon4			GGAATCACAGTAT	Y08991	CCDS3067.1	3q22.1	2013-01-10	2008-02-04		ENSG00000196455	ENSG00000196455		"""WD repeat domain containing"""	8982	protein-coding gene	gene with protein product		602610				8999962	Standard	NM_014602		Approved	VPS15, p150	uc003enj.3	Q99570	OTTHUMG00000159645	ENST00000356763.3:c.1176T>C	3.37:g.130452666A>G		Somatic	83	0		WXS	Illumina HiSeq	.	61	20	NM_014602	Q2TBF4	Silent	SNP	ENST00000356763.3	37	CCDS3067.1																																																																																			.		0.398	PIK3R4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356668.1	NM_014602	
YEATS2	55689	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	3	183528369	183528369	+	Nonstop_Mutation	SNP	T	T	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr3:183528369T>C	ENST00000305135.5	+	31	4462	c.4267T>C	c.(4267-4269)Tga>Cga	p.*1423R	YEATS2-AS1_ENST00000609871.1_RNA|YEATS2-AS1_ENST00000609195.1_RNA|YEATS2-AS1_ENST00000425008.3_RNA	NM_018023.4	NP_060493.3	Q9ULM3	YETS2_HUMAN	YEATS domain containing 2	0					chromatin organization (GO:0006325)|histone H3 acetylation (GO:0043966)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)	Ada2/Gcn5/Ada3 transcription activator complex (GO:0005671)|mitotic spindle (GO:0072686)	TBP-class protein binding (GO:0017025)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(24)|ovary(3)|prostate(2)|skin(3)	49	all_cancers(143;6.55e-10)|Ovarian(172;0.0303)		all cancers(12;2.38e-42)|Epithelial(37;1.9e-36)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)			TGAGGACCAGTGAGCGGAGTG	0.488																																					p.X1423R		.											.	.	.	0			c.T4267C						.						68.0	64.0	65.0					3																	183528369		2019	4172	6191	SO:0001578	stop_lost	55689	exon31			GACCAGTGAGCGG	AB033023	CCDS43175.1	3q27.3	2004-08-18			ENSG00000163872	ENSG00000163872			25489	protein-coding gene	gene with protein product		613373				10574462	Standard	NM_018023		Approved	FLJ10201, FLJ12841, FLJ13308, KIAA1197	uc003fly.2	Q9ULM3	OTTHUMG00000156898	ENST00000305135.5:c.4267T>C	3.37:g.183528369T>C	ENSP00000306983:p.*1423Argext*3	Somatic	42	0		WXS	Illumina HiSeq	.	32	12	NM_018023	A7E2B9|D3DNS9|Q641P6|Q9NW96	Missense_Mutation	SNP	ENST00000305135.5	37	CCDS43175.1	.	.	.	.	.	.	.	.	.	.	T	16.20	3.055858	0.55325	.	.	ENSG00000163872	ENST00000421660;ENST00000305135	.	.	.	5.51	5.51	0.81932	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	0.999998	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.4914	0.67654	0.0:0.0:0.0:1.0	.	.	.	.	R	1423	.	.	X	+	1	0	YEATS2	185011063	1.000000	0.71417	0.988000	0.46212	0.539000	0.34962	4.677000	0.61634	2.210000	0.71456	0.533000	0.62120	TGA	.		0.488	YEATS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346507.2	NM_018023	
MRPS16	51021	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	10	75011619	75011619	+	Missense_Mutation	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr10:75011619T>G	ENST00000372945.3	-	2	386	c.176A>C	c.(175-177)aAc>aCc	p.N59T	RP11-152N13.5_ENST00000457147.1_RNA|DNAJC9-AS1_ENST00000440197.2_RNA|TTC18_ENST00000493787.1_5'Flank|DNAJC9_ENST00000372950.4_5'Flank|RP11-152N13.5_ENST00000457758.1_RNA|RP11-152N13.5_ENST00000394864.2_RNA|MRPS16_ENST00000372940.3_Missense_Mutation_p.N59T|MRPS16_ENST00000479005.1_5'UTR|DNAJC9-AS1_ENST00000513954.1_RNA|MRPS16_ENST00000416782.2_Missense_Mutation_p.N59T	NM_016065.3	NP_057149.1	Q9Y3D3	RT16_HUMAN	mitochondrial ribosomal protein S16	59					translation (GO:0006412)	mitochondrial small ribosomal subunit (GO:0005763)	structural constituent of ribosome (GO:0003735)			large_intestine(2)|lung(2)	4	Prostate(51;0.0119)					TCCATGACTGTTGGGCAATGG	0.547																																					p.N59T		.											.	.	.	0			c.A176C						.						115.0	106.0	109.0					10																	75011619		2203	4300	6503	SO:0001583	missense	51021	exon2			TGACTGTTGGGCA	AB051351	CCDS7323.1	10q22.1	2012-09-13			ENSG00000182180	ENSG00000182180		"""Mitochondrial ribosomal proteins / small subunits"""	14048	protein-coding gene	gene with protein product		609204				10810093	Standard	NM_016065		Approved	CGI-132	uc001jts.1	Q9Y3D3	OTTHUMG00000018454	ENST00000372945.3:c.176A>C	10.37:g.75011619T>G	ENSP00000362036:p.Asn59Thr	Somatic	76	0		WXS	Illumina HiSeq	.	47	21	NM_016065	B4E032|Q96Q60	Missense_Mutation	SNP	ENST00000372945.3	37	CCDS7323.1	.	.	.	.	.	.	.	.	.	.	T	21.2	4.106269	0.77096	.	.	ENSG00000182180	ENST00000416782;ENST00000372945;ENST00000372940	T;T;T	0.47177	0.87;0.85;0.9	5.33	5.33	0.75918	Ribosomal protein S16 domain (2);	0.000000	0.85682	U	0.000000	T	0.64713	0.2623	M	0.71296	2.17	0.80722	D	1	D	0.89917	1.0	D	0.75020	0.985	T	0.62572	-0.6826	10	0.25106	T	0.35	-14.2755	13.2804	0.60210	0.0:0.0:0.0:1.0	.	59	Q9Y3D3	RT16_HUMAN	T	59	ENSP00000408812:N59T;ENSP00000362036:N59T;ENSP00000362031:N59T	ENSP00000362031:N59T	N	-	2	0	MRPS16	74681625	1.000000	0.71417	0.998000	0.56505	0.634000	0.38068	7.283000	0.78640	2.020000	0.59435	0.533000	0.62120	AAC	.		0.547	MRPS16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048616.1		
PLRG1	5356	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	4	155463385	155463385	+	Missense_Mutation	SNP	G	G	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr4:155463385G>A	ENST00000499023.2	-	8	767	c.641C>T	c.(640-642)cCt>cTt	p.P214L	PLRG1_ENST00000302078.5_Missense_Mutation_p.P205L|PLRG1_ENST00000393905.2_Missense_Mutation_p.P214L|RNU6-1285P_ENST00000363480.1_RNA	NM_001201564.1|NM_002669.3	NP_001188493.1|NP_002660.1	O43660	PLRG1_HUMAN	pleiotropic regulator 1	214					mRNA splicing, via spliceosome (GO:0000398)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|protein localization to nucleus (GO:0034504)|regulation of RNA biosynthetic process (GO:2001141)|signal transduction (GO:0007165)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)	signal transducer activity (GO:0004871)|transcription corepressor activity (GO:0003714)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(11)|skin(1)|urinary_tract(1)	22	all_hematologic(180;0.215)	Renal(120;0.0854)				CTGATTTCCAGGTTCCACAGC	0.368																																					p.P214L		.											.	.	.	0			c.C641T						.						118.0	104.0	109.0					4																	155463385		2203	4300	6503	SO:0001583	missense	5356	exon8			TTTCCAGGTTCCA	AF044333	CCDS34083.1, CCDS56341.1	4q31.2-q32.1	2013-01-10	2011-05-19		ENSG00000171566	ENSG00000171566		"""WD repeat domain containing"""	9089	protein-coding gene	gene with protein product	"""transport and golgi organization 4 homolog (Drosophila)"""	605961	"""pleiotropic regulator 1 (PRL1, Arabidopsis homolog)"", ""pleiotropic regulator 1 (PRL1 homolog, Arabidopsis)"""				Standard	NM_002669		Approved	PRL1, Prp46, PRPF46, Cwc1, TANGO4	uc003iny.3	O43660	OTTHUMG00000161411	ENST00000499023.2:c.641C>T	4.37:g.155463385G>A	ENSP00000424417:p.Pro214Leu	Somatic	46	0		WXS	Illumina HiSeq	.	9	7	NM_002669	B3KMK4|Q3KQY5|Q8WUD8	Missense_Mutation	SNP	ENST00000499023.2	37	CCDS34083.1	.	.	.	.	.	.	.	.	.	.	G	36	5.688798	0.96784	.	.	ENSG00000171566	ENST00000499023;ENST00000393905;ENST00000302078;ENST00000504341	T;T;T	0.71222	-0.55;-0.55;-0.55	6.07	6.07	0.98685	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	D	0.85583	0.5730	M	0.77712	2.385	0.80722	D	1	D;D	0.76494	0.998;0.999	D;D	0.77557	0.954;0.99	D	0.85550	0.1221	10	0.72032	D	0.01	-21.4001	20.6593	0.99626	0.0:0.0:1.0:0.0	.	205;214	O43660-2;O43660	.;PLRG1_HUMAN	L	214;214;205;212	ENSP00000424417:P214L;ENSP00000377483:P214L;ENSP00000303191:P205L	ENSP00000303191:P205L	P	-	2	0	PLRG1	155682835	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.869000	0.99810	2.885000	0.99019	0.655000	0.94253	CCT	.		0.368	PLRG1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364824.1	NM_002669	
PCDHGA4	56111	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	5	140736182	140736182	+	Missense_Mutation	SNP	T	T	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr5:140736182T>C	ENST00000571252.1	+	1	1415	c.1415T>C	c.(1414-1416)tTa>tCa	p.L472S	PCDHGB1_ENST00000523390.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA3_ENST00000253812.6_Intron	NM_018917.2	NP_061740	Q9Y5G9	PCDG4_HUMAN	protocadherin gamma subfamily A, 4	472	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(1)|kidney(1)|lung(3)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCCTCCATCTTATCTATGACT	0.512																																					p.L472S		.											.	.	.	0			c.T1415C						.						120.0	125.0	123.0					5																	140736182		2073	4244	6317	SO:0001583	missense	56111	exon1			CCATCTTATCTAT	AF152511	CCDS58979.1, CCDS58979.2, CCDS75331.1	5q31	2010-01-26						"""Cadherins / Protocadherins : Clustered"""	8702	other	protocadherin		606291				10380929	Standard	NM_018917		Approved	PCDH-GAMMA-A4		Q9Y5G9		ENST00000571252.1:c.1415T>C	5.37:g.140736182T>C	ENSP00000458570:p.Leu472Ser	Somatic	46	0		WXS	Illumina HiSeq	.	24	14	NM_018917	Q9Y5D3	Missense_Mutation	SNP	ENST00000571252.1	37	CCDS58979.1																																																																																			.		0.512	PCDHGA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437959.1	NM_018917	
DMXL2	23312	hgsc.bcm.edu	37	15	51741202	51741202	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr15:51741202G>T	ENST00000251076.5	-	43	9377	c.9090C>A	c.(9088-9090)aaC>aaA	p.N3030K	RP11-707P17.1_ENST00000561007.1_RNA|DMXL2_ENST00000449909.3_Missense_Mutation_p.N2394K|DMXL2_ENST00000543779.2_Missense_Mutation_p.N3031K	NM_001174116.1|NM_015263.3	NP_001167587.1|NP_056078.2	Q8TDJ6	DMXL2_HUMAN	Dmx-like 2	3030						cell junction (GO:0030054)|extracellular space (GO:0005615)|membrane (GO:0016020)|synaptic vesicle (GO:0008021)	Rab GTPase binding (GO:0017137)			breast(4)|central_nervous_system(1)|cervix(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(26)|liver(1)|lung(28)|ovary(7)|prostate(7)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	101				all cancers(107;0.00494)		CAAGAATTCTGTTAGGGATGT	0.408																																					p.N3031K		.											DMXL2,bladder,carcinoma,0,1	DMXL2	0	0			c.C9093A						.						55.0	51.0	52.0					15																	51741202		2196	4293	6489	SO:0001583	missense	23312	exon43			AATTCTGTTAGGG	AB020663	CCDS10141.1, CCDS53945.1, CCDS53946.1	15q21.2	2013-01-10			ENSG00000104093	ENSG00000104093		"""WD repeat domain containing"""	2938	protein-coding gene	gene with protein product	"""rabconnectin 3"""	612186					Standard	NM_001174116		Approved	RC3, KIAA0856	uc010ufy.2	Q8TDJ6	OTTHUMG00000131749	ENST00000251076.5:c.9090C>A	15.37:g.51741202G>T	ENSP00000251076:p.Asn3030Lys	Somatic	63	0		WXS	Illumina HiSeq	.	32	2	NM_001174116	B2RTR3|B7ZMH3|F5GWF1|O94938	Missense_Mutation	SNP	ENST00000251076.5	37	CCDS10141.1	.	.	.	.	.	.	.	.	.	.	G	11.24	1.580689	0.28180	.	.	ENSG00000104093	ENST00000251076;ENST00000543779;ENST00000449909;ENST00000436119	T;T;T	0.25414	1.93;1.93;1.8	5.6	-2.15	0.07102	.	1.305650	0.04866	N	0.445067	T	0.22244	0.0536	L	0.42245	1.32	0.09310	N	0.999996	B;B;B;B	0.32324	0.01;0.364;0.006;0.168	B;B;B;B	0.33121	0.022;0.077;0.01;0.158	T	0.35425	-0.9789	10	0.44086	T	0.13	.	7.4996	0.27509	0.417:0.0:0.4465:0.1365	.	3031;2394;3030;3031	F5GWF1;B2RTR3;Q8TDJ6;B7ZMH3	.;.;DMXL2_HUMAN;.	K	3030;3031;2394;596	ENSP00000251076:N3030K;ENSP00000441858:N3031K;ENSP00000400855:N2394K	ENSP00000251076:N3030K	N	-	3	2	DMXL2	49528494	0.141000	0.22595	0.013000	0.15412	0.973000	0.67179	0.544000	0.23253	-0.320000	0.08640	-0.251000	0.11542	AAC	.		0.408	DMXL2-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254671.2	NM_015263	
ERN1	2081	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	17	62142632	62142632	+	Silent	SNP	A	A	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr17:62142632A>G	ENST00000433197.3	-	9	953	c.858T>C	c.(856-858)gtT>gtC	p.V286V	ERN1_ENST00000577567.1_5'Flank	NM_001433.3	NP_001424.3			endoplasmic reticulum to nucleus signaling 1											central_nervous_system(4)|kidney(1)|lung(2)|ovary(1)|stomach(1)	9						AGTATTTCCCAACATACAGAG	0.502																																					p.V286V		.											.	.	.	0			c.T858C						.						52.0	51.0	51.0					17																	62142632		1922	4135	6057	SO:0001819	synonymous_variant	2081	exon9			TTTCCCAACATAC	AF059198	CCDS45762.1	17q23	2011-08-12	2007-08-14			ENSG00000178607			3449	protein-coding gene	gene with protein product	"""inositol-requiring enzyme 1"""	604033	"""ER to nucleus signalling 1"""			9637683	Standard	NM_001433		Approved	IRE1, IRE1P	uc002jdz.2	O75460		ENST00000433197.3:c.858T>C	17.37:g.62142632A>G		Somatic	63	0		WXS	Illumina HiSeq	.	24	9	NM_001433		Silent	SNP	ENST00000433197.3	37	CCDS45762.1																																																																																			.		0.502	ERN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443734.2	NM_001433	
SHANK2	22941	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	11	70332549	70332549	+	Silent	SNP	C	C	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr11:70332549C>T	ENST00000423696.2	-	15	2748	c.2712G>A	c.(2710-2712)gaG>gaA	p.E904E	SHANK2_ENST00000449833.2_Silent_p.E688E|SHANK2_ENST00000338508.4_Silent_p.E1284E|SHANK2_ENST00000409161.1_Silent_p.E687E			Q9UPX8	SHAN2_HUMAN	SH3 and multiple ankyrin repeat domains 2	904					adult behavior (GO:0030534)|learning (GO:0007612)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|vocalization behavior (GO:0071625)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|cell junction (GO:0030054)|ciliary membrane (GO:0060170)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|growth cone (GO:0030426)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	GKAP/Homer scaffold activity (GO:0030160)|ionotropic glutamate receptor binding (GO:0035255)			NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(30)|ovary(3)|pancreas(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	62			LUSC - Lung squamous cell carcinoma(11;4.72e-09)|STAD - Stomach adenocarcinoma(18;0.071)			CCAGGTCGGTCTCGTACTTGT	0.612																																					p.E695E		.											.	.	.	0			c.G2085A						.						104.0	102.0	102.0					11																	70332549		2200	4294	6494	SO:0001819	synonymous_variant	22941	exon10			GTCGGTCTCGTAC	AF141901		11q13.2	2013-01-10			ENSG00000162105	ENSG00000162105		"""Sterile alpha motif (SAM) domain containing"", ""Ankyrin repeat domain containing"""	14295	protein-coding gene	gene with protein product		603290	"""cortactin binding protein 1"""	CORTBP1		10506216	Standard	XM_005277930		Approved	CTTNBP1, ProSAP1, SHANK, SPANK-3	uc001oqc.3	Q9UPX8	OTTHUMG00000154615	ENST00000423696.2:c.2712G>A	11.37:g.70332549C>T		Somatic	35	0		WXS	Illumina HiSeq	.	30	13	NM_133266	C0SPG8|C0SPG9|Q3Y8G9|Q52LK2|Q9UKP1	Silent	SNP	ENST00000423696.2	37																																																																																				.		0.612	SHANK2-203	KNOWN	basic	protein_coding	protein_coding		NM_012309	
KIAA0754	643314	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	39879568	39879568	+	Missense_Mutation	SNP	A	A	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr1:39879568A>T	ENST00000530275.1	+	1	3418	c.3223A>T	c.(3223-3225)Acc>Tcc	p.T1075S	MACF1_ENST00000361689.2_Intron|MACF1_ENST00000372915.3_Intron|MACF1_ENST00000564288.1_Intron|MACF1_ENST00000539005.1_Intron|MACF1_ENST00000317713.7_Intron|MACF1_ENST00000567887.1_Intron|MACF1_ENST00000289893.4_Intron|MACF1_ENST00000545844.1_Intron	NM_015038.1	NP_055853.1	O94854	K0754_HUMAN	KIAA0754	1075	Ala-rich.									central_nervous_system(1)|large_intestine(6)|skin(1)	8	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			TATGGTGGCCACCCTAGAGGA	0.642																																					p.T1211S		.											.	.	.	0			c.A3631T						.						14.0	17.0	16.0					1																	39879568		1938	4145	6083	SO:0001583	missense	643314	exon1			GTGGCCACCCTAG			1p34.2	2009-07-09				ENSG00000255103			29111	protein-coding gene	gene with protein product						9872452	Standard	NM_015038		Approved		uc009vvt.1	O94854		ENST00000530275.1:c.3223A>T	1.37:g.39879568A>T	ENSP00000431179:p.Thr1075Ser	Somatic	45	0		WXS	Illumina HiSeq	.	42	10	NM_015038	E9PMC2|Q6ZSB2	Missense_Mutation	SNP	ENST00000530275.1	37		.	.	.	.	.	.	.	.	.	.	A	10.91	1.483824	0.26598	.	.	ENSG00000255103	ENST00000530275	T	0.25749	1.78	3.36	0.609	0.17575	.	.	.	.	.	T	0.09949	0.0244	N	0.14661	0.345	0.09310	N	1	B	0.13145	0.007	B	0.10450	0.005	T	0.36768	-0.9734	9	0.02654	T	1	.	3.1095	0.06353	0.6091:0.0:0.1248:0.2661	.	1075	O94854	K0754_HUMAN	S	1075	ENSP00000431179:T1075S	ENSP00000431179:T1075S	T	+	1	0	RP4-562N20.1	39652155	0.000000	0.05858	0.019000	0.16419	0.059000	0.15707	-0.580000	0.05827	0.068000	0.16574	0.155000	0.16302	ACC	.		0.642	KIAA0754-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000392100.1	NM_015038	
HAUS4	54930	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	14	23416891	23416891	+	Missense_Mutation	SNP	C	C	T	rs551628708		TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr14:23416891C>T	ENST00000206474.7	-	8	1010	c.758G>A	c.(757-759)cGg>cAg	p.R253Q	HAUS4_ENST00000554446.1_5'UTR|HAUS4_ENST00000342454.8_Missense_Mutation_p.R208Q|HAUS4_ENST00000555367.1_Missense_Mutation_p.R208Q|HAUS4_ENST00000397409.4_Missense_Mutation_p.R127Q|HAUS4_ENST00000347758.2_Missense_Mutation_p.R127Q|HAUS4_ENST00000555986.1_Missense_Mutation_p.R208Q|RP11-298I3.1_ENST00000548819.1_RNA|HAUS4_ENST00000490506.1_Missense_Mutation_p.R129Q|RP11-298I3.5_ENST00000555074.1_Silent_p.P82P|HAUS4_ENST00000541587.1_Missense_Mutation_p.R253Q|RP11-298I3.1_ENST00000548322.1_RNA			Q9H6D7	HAUS4_HUMAN	HAUS augmin-like complex, subunit 4	253					centrosome organization (GO:0051297)|mitotic nuclear division (GO:0007067)|spindle assembly (GO:0051225)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|HAUS complex (GO:0070652)|microtubule (GO:0005874)				breast(3)|cervix(1)|endometrium(2)|lung(6)|ovary(1)|skin(1)	14						AGTCTTCAGCCGGTGTTCTTG	0.517																																					p.R253Q		.											.	.	.	0			c.G758A						.						92.0	88.0	89.0					14																	23416891		2203	4300	6503	SO:0001583	missense	54930	exon8			TTCAGCCGGTGTT	AK000431	CCDS9580.1, CCDS53886.1	14q11.1	2011-10-24	2009-04-20	2009-04-20	ENSG00000092036	ENSG00000092036		"""HAUS augmin-like complex subunits"""	20163	protein-coding gene	gene with protein product		613431	"""chromosome 14 open reading frame 94"""	C14orf94		19427217	Standard	NM_017815		Approved	FLJ20424	uc001wht.3	Q9H6D7	OTTHUMG00000028710	ENST00000206474.7:c.758G>A	14.37:g.23416891C>T	ENSP00000206474:p.Arg253Gln	Somatic	79	0		WXS	Illumina HiSeq	.	59	31	NM_001166269	B7WP17|D3DS34|Q86T15|Q86T16|Q86U43|Q9NX59	Missense_Mutation	SNP	ENST00000206474.7	37	CCDS9580.1	.	.	.	.	.	.	.	.	.	.	C	32	5.159954	0.94727	.	.	ENSG00000092036;ENSG00000092036;ENSG00000092036;ENSG00000092036;ENSG00000092036;ENSG00000092036;ENSG00000092036;ENSG00000092036;ENSG00000092036;ENSG00000259132	ENST00000206474;ENST00000490506;ENST00000541587;ENST00000342454;ENST00000347758;ENST00000397409;ENST00000555367;ENST00000555986;ENST00000555040;ENST00000555074	.	.	.	5.11	5.11	0.69529	.	0.000000	0.85682	D	0.000000	T	0.76499	0.3996	M	0.63843	1.955	0.45025	D	0.998045	D;D;D	0.76494	0.998;0.997;0.999	D;P;D	0.77557	0.986;0.786;0.99	T	0.79115	-0.1936	9	0.87932	D	0	-23.0366	15.5002	0.75691	0.0:1.0:0.0:0.0	.	208;127;253	Q9H6D7-4;Q9H6D7-2;Q9H6D7	.;.;HAUS4_HUMAN	Q	253;129;253;208;127;127;208;208;253;30	.	ENSP00000206474:R253Q	R	-	2	0	RP11-298I3.5;HAUS4	22486731	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	3.120000	0.50430	2.375000	0.81037	0.585000	0.79938	CGG	.		0.517	HAUS4-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071680.3		
CMTR1	23070	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	6	37441251	37441251	+	Silent	SNP	T	T	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr6:37441251T>C	ENST00000373451.4	+	17	1859	c.1695T>C	c.(1693-1695)acT>acC	p.T565T		NM_015050.2	NP_055865.1	Q8N1G2	CMTR1_HUMAN	cap methyltransferase 1	565					7-methylguanosine mRNA capping (GO:0006370)|cap1 mRNA methylation (GO:0097309)|mRNA methylation (GO:0080009)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	mRNA (nucleoside-2'-O-)-methyltransferase activity (GO:0004483)|nucleic acid binding (GO:0003676)										TGCAGGGCACTGAGATTGACA	0.572																																					p.T565T		.											.	.	.	0			c.T1695C						.						126.0	113.0	117.0					6																	37441251		2203	4300	6503	SO:0001819	synonymous_variant	23070	exon17			GGGCACTGAGATT	BC031890	CCDS4835.1	6p21.2	2013-07-23	2013-07-23	2013-07-23	ENSG00000137200	ENSG00000137200	2.1.1.57	"""G patch domain containing"""	21077	protein-coding gene	gene with protein product			"""KIAA0082"", ""FtsJ methyltransferase domain containing 2"""	KIAA0082, FTSJD2		20713356	Standard	NM_015050		Approved	MTr1, ISG95	uc003ons.3	Q8N1G2	OTTHUMG00000014624	ENST00000373451.4:c.1695T>C	6.37:g.37441251T>C		Somatic	23	0		WXS	Illumina HiSeq	.	35	18	NM_015050	A8K949|Q14670|Q96FJ9	Silent	SNP	ENST00000373451.4	37	CCDS4835.1																																																																																			.		0.572	CMTR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040408.1	NM_015050	
FAM64A	54478	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	17	6351018	6351018	+	Missense_Mutation	SNP	C	C	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr17:6351018C>T	ENST00000250056.8	+	3	613	c.530C>T	c.(529-531)tCa>tTa	p.S177L	FAM64A_ENST00000572447.1_Missense_Mutation_p.S177L|FAM64A_ENST00000570337.2_Missense_Mutation_p.S177L|FAM64A_ENST00000571373.1_Missense_Mutation_p.S177L|FAM64A_ENST00000572595.2_Missense_Mutation_p.S208L|FAM64A_ENST00000576056.1_Missense_Mutation_p.S177L	NM_001195228.1	NP_001182157.1	Q9BSJ6	FA64A_HUMAN	family with sequence similarity 64, member A	177					mitotic nuclear division (GO:0007067)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)				breast(1)|kidney(1)|large_intestine(3)|lung(1)|skin(1)	7				COAD - Colon adenocarcinoma(228;0.141)		TTACGGCGATCAAGGCGGGAG	0.657																																					p.S177L		.											.	.	.	0			c.C530T						.						31.0	33.0	32.0					17																	6351018		2203	4299	6502	SO:0001583	missense	54478	exon3			GGCGATCAAGGCG		CCDS32541.1, CCDS56016.1	17p13.2	2013-10-11			ENSG00000129195	ENSG00000129195			25483	protein-coding gene	gene with protein product	"""CALM interacting protein expressed in thymus and spleen"""					19383357, 16491119	Standard	NM_019013		Approved	FLJ10156, FLJ10491, CATS	uc002gcw.2	Q9BSJ6	OTTHUMG00000177832	ENST00000250056.8:c.530C>T	17.37:g.6351018C>T	ENSP00000250056:p.Ser177Leu	Somatic	57	0		WXS	Illumina HiSeq	.	28	15	NM_019013	Q96CT4|Q9NVV1|Q9NWB5	Missense_Mutation	SNP	ENST00000250056.8	37	CCDS56016.1	.	.	.	.	.	.	.	.	.	.	C	10.58	1.389806	0.25118	.	.	ENSG00000129195	ENST00000250056;ENST00000308855	T	0.40756	1.02	4.9	2.47	0.30058	.	0.517250	0.18793	N	0.131007	T	0.28665	0.0710	L	0.41824	1.3	0.09310	N	1	B;B	0.11235	0.002;0.004	B;B	0.12156	0.007;0.004	T	0.19712	-1.0297	10	0.20046	T	0.44	-0.862	6.2057	0.20602	0.0:0.7166:0.0:0.2834	.	177;177	Q9BSJ6;Q9BSJ6-2	FA64A_HUMAN;.	L	177	ENSP00000250056:S177L	ENSP00000250056:S177L	S	+	2	0	FAM64A	6291742	0.013000	0.17824	0.008000	0.14137	0.085000	0.17905	0.552000	0.23376	0.433000	0.26313	0.563000	0.77884	TCA	.		0.657	FAM64A-008	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000439156.1	NM_019013	
ACVR1B	91	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	12	52377793	52377793	+	Silent	SNP	C	C	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr12:52377793C>A	ENST00000257963.4	+	5	899	c.822C>A	c.(820-822)acC>acA	p.T274T	ACVR1B_ENST00000542485.1_Silent_p.T222T|ACVR1B_ENST00000426655.2_Silent_p.T274T|ACVR1B_ENST00000541224.1_Silent_p.T315T|ACVR1B_ENST00000415850.2_Silent_p.T274T	NM_004302.4|NM_020328.3	NP_004293.1|NP_064733.3	P36896	ACV1B_HUMAN	activin A receptor, type IB	274	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activin receptor signaling pathway (GO:0032924)|central nervous system development (GO:0007417)|development of primary female sexual characteristics (GO:0046545)|extrinsic apoptotic signaling pathway (GO:0097191)|G1/S transition of mitotic cell cycle (GO:0000082)|hair follicle development (GO:0001942)|in utero embryonic development (GO:0001701)|negative regulation of cell growth (GO:0030308)|nodal signaling pathway (GO:0038092)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of activin receptor signaling pathway (GO:0032927)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of trophoblast cell migration (GO:1901165)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	activin receptor activity, type I (GO:0016361)|ATP binding (GO:0005524)|inhibin binding (GO:0034711)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|SMAD binding (GO:0046332)|transforming growth factor beta-activated receptor activity (GO:0005024)|transmembrane receptor protein serine/threonine kinase activity (GO:0004675)|ubiquitin protein ligase binding (GO:0031625)			breast(5)|endometrium(4)|kidney(5)|large_intestine(12)|lung(10)|ovary(1)|pancreas(6)|prostate(1)	44				BRCA - Breast invasive adenocarcinoma(357;0.104)	Adenosine triphosphate(DB00171)	ATAATGGCACCTGGACACAGC	0.443																																					p.T315T		.											.	.	.	0			c.C945A						.						104.0	88.0	94.0					12																	52377793		2203	4300	6503	SO:0001819	synonymous_variant	91	exon6			TGGCACCTGGACA		CCDS8816.1, CCDS44893.1, CCDS44894.1, CCDS44893.2, CCDS44894.2	12q13	2006-11-09			ENSG00000135503	ENSG00000135503			172	protein-coding gene	gene with protein product		601300		ACVRLK4		8397373	Standard	NM_020327		Approved	ALK4, SKR2, ActRIB	uc010snn.2	P36896	OTTHUMG00000167920	ENST00000257963.4:c.822C>A	12.37:g.52377793C>A		Somatic	53	0		WXS	Illumina HiSeq	.	42	22	NM_020328	B7Z5L8|B7Z5W5|Q15479|Q15480|Q15481|Q15482	Silent	SNP	ENST00000257963.4	37	CCDS8816.1																																																																																			.		0.443	ACVR1B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397000.1	NM_020328	
C1orf174	339448	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	3807598	3807598	+	Silent	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr1:3807598T>G	ENST00000361605.3	-	3	251	c.153A>C	c.(151-153)acA>acC	p.T51T	C1orf174_ENST00000486765.1_5'UTR	NM_207356.2	NP_997239.2	Q8IYL3	CA174_HUMAN	chromosome 1 open reading frame 174	51						nucleus (GO:0005634)				endometrium(1)|large_intestine(5)|lung(4)|prostate(1)	11	all_cancers(77;0.0395)|Ovarian(185;0.0634)|all_lung(157;0.222)|Lung NSC(156;0.227)	all_cancers(23;5.09e-25)|all_epithelial(116;9.35e-17)|all_lung(118;1.09e-06)|Lung NSC(185;0.000139)|all_neural(13;0.00287)|Renal(390;0.00357)|Breast(487;0.00446)|Hepatocellular(190;0.0219)|all_hematologic(16;0.027)|Colorectal(325;0.0276)|Myeloproliferative disorder(586;0.0393)|Lung SC(97;0.0743)|Ovarian(437;0.127)		Epithelial(90;1.55e-39)|OV - Ovarian serous cystadenocarcinoma(86;5.99e-23)|GBM - Glioblastoma multiforme(42;2.22e-17)|Colorectal(212;1.08e-05)|COAD - Colon adenocarcinoma(227;5.49e-05)|Kidney(185;0.000342)|BRCA - Breast invasive adenocarcinoma(365;0.000365)|KIRC - Kidney renal clear cell carcinoma(229;0.00549)|STAD - Stomach adenocarcinoma(132;0.00644)|Lung(427;0.19)		TTCGCGTGTCTGTGGCTTTGT	0.423																																					p.T51T		.											.	.	.	0			c.A153C						.						88.0	100.0	96.0					1																	3807598		2201	4295	6496	SO:0001819	synonymous_variant	339448	exon3			CGTGTCTGTGGCT	BC035643	CCDS53.1	1p36.32	2012-07-25			ENSG00000198912	ENSG00000198912			27915	protein-coding gene	gene with protein product						12477932	Standard	NM_207356		Approved	RP13-531C17.2	uc001alf.3	Q8IYL3	OTTHUMG00000003739	ENST00000361605.3:c.153A>C	1.37:g.3807598T>G		Somatic	73	0		WXS	Illumina HiSeq	.	42	17	NM_207356	A8K0C8|A8MUG9|Q5SR20|Q6NX36	Silent	SNP	ENST00000361605.3	37	CCDS53.1																																																																																			.		0.423	C1orf174-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010539.1	NM_207356	
GABRA4	2557	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	4	46930297	46930297	+	Missense_Mutation	SNP	T	T	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr4:46930297T>C	ENST00000264318.3	-	9	2592	c.1610A>G	c.(1609-1611)tAt>tGt	p.Y537C		NM_000809.3|NM_001204266.1|NM_001204267.1	NP_000800.2|NP_001191195.1|NP_001191196.1	P48169	GBRA4_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha 4	537					central nervous system development (GO:0007417)|gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|regulation of response to drug (GO:2001023)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	benzodiazepine receptor activity (GO:0008503)|chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(17)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	45					Acamprosate(DB00659)|Alprazolam(DB00404)|Amobarbital(DB01351)|Amoxapine(DB00543)|Aprobarbital(DB01352)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Chlordiazepoxide(DB00475)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Flumazenil(DB01205)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Secobarbital(DB00418)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Thiopental(DB00599)|Topiramate(DB00273)|Triazolam(DB00897)	AACAACCCAATAAACCATGTT	0.378																																					p.Y537C	Ovarian(6;283 369 8234 12290 33402)	.											.	.	.	0			c.A1610G						.						65.0	68.0	67.0					4																	46930297		2203	4299	6502	SO:0001583	missense	2557	exon9			ACCCAATAAACCA		CCDS3473.1	4p12	2012-06-22			ENSG00000109158	ENSG00000109158		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4078	protein-coding gene	gene with protein product	"""GABA(A) receptor, alpha 4"""	137141				7607683	Standard	NM_000809		Approved		uc021xnz.1	P48169	OTTHUMG00000099431	ENST00000264318.3:c.1610A>G	4.37:g.46930297T>C	ENSP00000264318:p.Tyr537Cys	Somatic	109	0		WXS	Illumina HiSeq	.	103	28	NM_000809	Q8IYR7	Missense_Mutation	SNP	ENST00000264318.3	37	CCDS3473.1	.	.	.	.	.	.	.	.	.	.	T	22.8	4.343019	0.82022	.	.	ENSG00000109158	ENST00000264318	D	0.88201	-2.35	5.82	5.82	0.92795	Neurotransmitter-gated ion-channel transmembrane domain (2);	0.000000	0.85682	D	0.000000	D	0.93167	0.7824	L	0.57536	1.79	0.58432	D	0.999991	D	0.89917	1.0	D	0.97110	1.0	D	0.93785	0.7087	10	0.87932	D	0	.	15.3777	0.74625	0.0:0.0:0.0:1.0	.	537	P48169	GBRA4_HUMAN	C	537	ENSP00000264318:Y537C	ENSP00000264318:Y537C	Y	-	2	0	GABRA4	46625054	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	7.950000	0.87804	2.232000	0.73038	0.528000	0.53228	TAT	.		0.378	GABRA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216893.1		
STK39	27347	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	2	169038515	169038515	+	Missense_Mutation	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr2:169038515T>G	ENST00000355999.4	-	2	999	c.294A>C	c.(292-294)aaA>aaC	p.K98N		NM_013233.2	NP_037365.2	Q9UEW8	STK39_HUMAN	serine threonine kinase 39	98	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cellular hypotonic response (GO:0071476)|intracellular signal transduction (GO:0035556)|negative regulation of potassium ion transmembrane transport (GO:1901380)|negative regulation of potassium ion transmembrane transporter activity (GO:1901017)|negative regulation of rubidium ion transmembrane transporter activity (GO:2000687)|negative regulation of rubidium ion transport (GO:2000681)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of potassium ion transport (GO:0043268)|protein phosphorylation (GO:0006468)|regulation of inflammatory response (GO:0050727)|response to stress (GO:0006950)|signal transduction by phosphorylation (GO:0023014)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein serine/threonine kinase activity (GO:0004702)			central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(3)|prostate(2)|skin(2)	13						TGGTCTGGCATTTTTCCAAGT	0.443																																					p.K98N		.											.,2	.	95	0			c.A294C						.						243.0	226.0	232.0					2																	169038515		1932	4116	6048	SO:0001583	missense	27347	exon2			CTGGCATTTTTCC	AF099989	CCDS42770.1	2q24.3	2010-06-25	2010-06-25		ENSG00000198648	ENSG00000198648			17717	protein-coding gene	gene with protein product	"""STE20/SPS1 homolog (yeast)"""	607648				10980603	Standard	NM_013233		Approved	DCHT, SPAK	uc002uea.3	Q9UEW8	OTTHUMG00000133745	ENST00000355999.4:c.294A>C	2.37:g.169038515T>G	ENSP00000348278:p.Lys98Asn	Somatic	48	0		WXS	Illumina HiSeq	.	32	14	NM_013233	O14774|Q53S90|Q53SL7|Q53SS1|Q9UER4|X5D9C8	Missense_Mutation	SNP	ENST00000355999.4	37	CCDS42770.1	.	.	.	.	.	.	.	.	.	.	T	23.2	4.392197	0.83011	.	.	ENSG00000198648	ENST00000355999	T	0.66280	-0.2	6.17	3.77	0.43336	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.66538	0.2799	L	0.31371	0.925	0.53005	D	0.999967	D	0.76494	0.999	D	0.80764	0.994	T	0.66779	-0.5837	10	0.87932	D	0	0.4881	9.983	0.41824	0.0:0.1394:0.0:0.8606	.	98	Q9UEW8	STK39_HUMAN	N	98	ENSP00000348278:K98N	ENSP00000348278:K98N	K	-	3	2	STK39	168746761	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.180000	0.50895	0.542000	0.28846	0.533000	0.62120	AAA	.		0.443	STK39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258112.2	NM_013233	
LARP4	113251	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	12	50855117	50855117	+	Missense_Mutation	SNP	T	T	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr12:50855117T>C	ENST00000398473.2	+	11	1433	c.1321T>C	c.(1321-1323)Tat>Cat	p.Y441H	LARP4_ENST00000522085.1_Missense_Mutation_p.Y441H|LARP4_ENST00000293618.8_Intron|LARP4_ENST00000347328.5_Missense_Mutation_p.Y370H|LARP4_ENST00000429001.3_Missense_Mutation_p.Y447H|LARP4_ENST00000518444.1_Missense_Mutation_p.Y440H|LARP4_ENST00000518561.1_Missense_Mutation_p.Y371H	NM_052879.4|NM_199188.2	NP_443111.4|NP_954658.2	Q71RC2	LARP4_HUMAN	La ribonucleoprotein domain family, member 4	441					cytoskeleton organization (GO:0007010)|regulation of cell morphogenesis (GO:0022604)	membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(3)|kidney(2)|large_intestine(2)|liver(2)|lung(7)|ovary(1)|skin(2)|urinary_tract(1)	23						GAATGGGGACTATGGTAGGGG	0.403																																					p.Y441H		.											.	.	.	0			c.T1321C						.						74.0	69.0	71.0					12																	50855117		1849	4094	5943	SO:0001583	missense	113251	exon11			GGGGACTATGGTA	AY004310	CCDS41782.1, CCDS44879.1, CCDS44880.1, CCDS44879.2, CCDS53789.1, CCDS53790.1	12q13.12	2005-08-09			ENSG00000161813	ENSG00000161813		"""La ribonucleoprotein domain containing"""	24320	protein-coding gene	gene with protein product						12477932	Standard	NM_052879		Approved	PP13296	uc001rwp.2	Q71RC2	OTTHUMG00000163724	ENST00000398473.2:c.1321T>C	12.37:g.50855117T>C	ENSP00000381490:p.Tyr441His	Somatic	56	0		WXS	Illumina HiSeq	.	34	15	NM_001170804	A8K6T1|E9PDG5|G3XAA8|G5E976|Q5CZ97|Q6ZV14|Q96NF9	Missense_Mutation	SNP	ENST00000398473.2	37	CCDS41782.1	.	.	.	.	.	.	.	.	.	.	T	16.24	3.068415	0.55539	.	.	ENSG00000161813	ENST00000429001;ENST00000398473;ENST00000522085;ENST00000518444;ENST00000518561;ENST00000520064;ENST00000347328	T;T;T;T;T;T	0.45276	1.57;1.57;0.91;1.57;0.9;1.57	4.37	4.37	0.52481	.	1.366970	0.04449	N	0.372274	T	0.54319	0.1851	L	0.47716	1.5	0.80722	D	1	D;P;P;P;P	0.57571	0.98;0.759;0.891;0.895;0.923	P;P;P;P;P	0.56700	0.804;0.579;0.549;0.526;0.521	T	0.31888	-0.9927	10	0.42905	T	0.14	.	10.4443	0.44483	0.0:0.0:0.1636:0.8364	.	342;440;370;441;447	Q71RC2-2;Q71RC2-3;G5E976;Q71RC2;Q71RC2-4	.;.;.;LARP4_HUMAN;.	H	447;441;441;440;371;342;370	ENSP00000415464:Y447H;ENSP00000381490:Y441H;ENSP00000429781:Y441H;ENSP00000429077:Y440H;ENSP00000430851:Y371H;ENSP00000340901:Y370H	ENSP00000340901:Y370H	Y	+	1	0	LARP4	49141384	1.000000	0.71417	1.000000	0.80357	0.873000	0.50193	1.865000	0.39479	1.914000	0.55421	0.379000	0.24179	TAT	.		0.403	LARP4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000374981.1	NM_052879	
TNRC6A	27327	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	16	24826538	24826538	+	Silent	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr16:24826538T>G	ENST00000395799.3	+	19	4872	c.4743T>G	c.(4741-4743)acT>acG	p.T1581T	TNRC6A_ENST00000315183.7_Silent_p.T1532T|TNRC6A_ENST00000432286.2_Silent_p.T59T|CTD-2515A14.1_ENST00000568895.1_RNA	NM_014494.2	NP_055309.2	Q8NDV7	TNR6A_HUMAN	trinucleotide repeat containing 6A	1581					cellular response to starvation (GO:0009267)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|innate immune response (GO:0045087)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|micro-ribonucleoprotein complex (GO:0035068)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(13)|kidney(5)|large_intestine(13)|liver(1)|lung(20)|ovary(3)|skin(2)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	64				GBM - Glioblastoma multiforme(48;0.0394)		ACAGCAGTACTTCACCAGCCA	0.448																																					p.T1581T		.											.	.	.	0			c.T4743G						.						81.0	80.0	80.0					16																	24826538		2197	4300	6497	SO:0001819	synonymous_variant	27327	exon19			CAGTACTTCACCA	U80739	CCDS10624.2	16p11.2	2009-09-22	2004-12-17	2004-12-17	ENSG00000090905	ENSG00000090905		"""Trinucleotide (CAG) repeat containing"""	11969	protein-coding gene	gene with protein product		610739	"""trinucleotide repeat containing 6"""	TNRC6		9225980	Standard	NM_014494		Approved	CAGH26, KIAA1460, GW182	uc002dmm.3	Q8NDV7	OTTHUMG00000096999	ENST00000395799.3:c.4743T>G	16.37:g.24826538T>G		Somatic	65	0		WXS	Illumina HiSeq	.	39	31	NM_014494	C9JAR8|O15408|Q658L5|Q6NVB5|Q8NEZ0|Q8TBT8|Q8TCR0|Q9NV59|Q9P268	Silent	SNP	ENST00000395799.3	37	CCDS10624.2	.	.	.	.	.	.	.	.	.	.	T	9.901	1.206778	0.22205	.	.	ENSG00000090905	ENST00000450465	.	.	.	5.92	4.83	0.62350	.	.	.	.	.	T	0.58977	0.2160	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.56068	-0.8040	4	.	.	.	-0.416	8.1894	0.31359	0.0:0.2667:0.0:0.7333	.	.	.	.	V	472	.	.	F	+	1	0	TNRC6A	24734039	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	0.840000	0.27600	1.073000	0.40885	0.533000	0.62120	TTC	.		0.448	TNRC6A-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214081.1	NM_020847	
HSPA12B	116835	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	20	3730721	3730721	+	Missense_Mutation	SNP	C	C	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr20:3730721C>A	ENST00000254963.2	+	11	1293	c.1148C>A	c.(1147-1149)gCc>gAc	p.A383D	HSPA12B_ENST00000542646.1_Missense_Mutation_p.A217D	NM_001197327.1|NM_052970.4	NP_001184256.1|NP_443202.3	Q96MM6	HS12B_HUMAN	heat shock 70kD protein 12B	383							ATP binding (GO:0005524)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|prostate(1)|skin(1)	14						CGGCCGGCAGCCTGGGTAGAT	0.637																																					p.A383D		.											.	.	.	0			c.C1148A						.						18.0	17.0	18.0					20																	3730721		2199	4295	6494	SO:0001583	missense	116835	exon11			CGGCAGCCTGGGT	AK056712	CCDS13061.1	20p13	2011-09-02	2003-04-10	2003-04-10	ENSG00000132622	ENSG00000132622		"""Heat shock proteins / HSP70"""	16193	protein-coding gene	gene with protein product		610702	"""chromosome 20 open reading frame 60"""	C20orf60		12552099	Standard	NM_052970		Approved	dJ1009E24.2	uc002wjd.3	Q96MM6	OTTHUMG00000031755	ENST00000254963.2:c.1148C>A	20.37:g.3730721C>A	ENSP00000254963:p.Ala383Asp	Somatic	47	0		WXS	Illumina HiSeq	.	18	5	NM_052970	D3DVX7|Q2TAK3|Q9BR52	Missense_Mutation	SNP	ENST00000254963.2	37	CCDS13061.1	.	.	.	.	.	.	.	.	.	.	C	20.2	3.957103	0.73902	.	.	ENSG00000132622	ENST00000254963;ENST00000542646;ENST00000399701	T;T;T	0.11930	2.73;2.73;2.73	5.21	5.21	0.72293	.	0.111349	0.64402	D	0.000014	T	0.26666	0.0652	L	0.47190	1.495	0.80722	D	1	B;D	0.63046	0.097;0.992	B;D	0.64410	0.061;0.925	T	0.01810	-1.1269	10	0.11794	T	0.64	.	16.6243	0.84952	0.0:1.0:0.0:0.0	.	382;383	B7ZLP2;Q96MM6	.;HS12B_HUMAN	D	383;217;297	ENSP00000254963:A383D;ENSP00000441506:A217D;ENSP00000382608:A297D	ENSP00000254963:A383D	A	+	2	0	HSPA12B	3678721	1.000000	0.71417	0.999000	0.59377	0.932000	0.56968	7.419000	0.80179	2.592000	0.87571	0.551000	0.68910	GCC	.		0.637	HSPA12B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077756.2	NM_052970	
CDC20B	166979	hgsc.bcm.edu;ucsc.edu	37	5	54468121	54468121	+	Intron	SNP	A	A	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr5:54468121A>G	ENST00000381375.2	-	2	272				MIR449B_ENST00000384995.1_RNA|CDC20B_ENST00000334206.5_Intron|CDC20B_ENST00000322374.6_Intron|CDC20B_ENST00000331730.3_Intron|CDC20B_ENST00000296733.1_Intron|MIR449C_ENST00000516047.1_RNA|MIR449A_ENST00000362113.1_RNA			Q86Y33	CD20B_HUMAN	cell division cycle 20B											kidney(1)|large_intestine(5)|lung(7)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)	19		Lung NSC(810;0.000744)|Breast(144;0.159)|Prostate(74;0.194)	LUSC - Lung squamous cell carcinoma(15;0.225)			GAGTGCAACTAGCAACTGTTA	0.458																																					.		.											.	.	.	0			.						.						65.0	63.0	63.0					5																	54468121		692	1591	2283	SO:0001627	intron_variant	100313923	.			GCAACTAGCAACT	AB086378	CCDS3966.1, CCDS47207.1, CCDS54852.1	5q11.2	2013-01-17	2013-01-17		ENSG00000164287	ENSG00000164287		"""WD repeat domain containing"""	24222	protein-coding gene	gene with protein product			"""CDC20 cell division cycle 20 homolog B (S. cerevisiae)"", ""cell division cycle 20 homolog B (S. cerevisiae)"""				Standard	NM_152623		Approved	FLJ37927	uc003jpo.2	Q86Y33	OTTHUMG00000131185	ENST00000381375.2:c.126+294T>C	5.37:g.54468121A>G		Somatic	40	0		WXS	Illumina HiSeq	.	28	14	.	B7WNV8|B9EGL8|C9J6X8|C9JHE9|C9JKL5|Q86Y31|Q86Y32|Q8IUZ8|Q8N1S1|Q8NG56	RNA	SNP	ENST00000381375.2	37	CCDS54852.1																																																																																			.		0.458	CDC20B-004	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000369715.1	NM_152623	
PARD6G-AS1	100130522	hgsc.bcm.edu;ucsc.edu	37	18	77906016	77906016	+	5'UTR	SNP	A	A	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr18:77906016A>T	ENST00000586421.1	+	0	209				AC139100.2_ENST00000589574.1_5'UTR|AC139100.2_ENST00000585422.1_5'UTR|AC139100.2_ENST00000587254.1_5'UTR|AC139100.2_ENST00000588226.1_5'UTR																							gcccacgggcagcggggaaga	0.642																																					.		.											.	.	.	0			.						.																																			SO:0001623	5_prime_UTR_variant	100130522	.			ACGGGCAGCGGGG																												ENST00000586421.1:c.-26A>T	18.37:g.77906016A>T		Somatic	15	0		WXS	Illumina HiSeq	.	20	7	.		RNA	SNP	ENST00000586421.1	37																																																																																				.		0.642	AC139100.2-001	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000451060.1		
MACROD2	140733	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	20	16025251	16025251	+	Missense_Mutation	SNP	C	C	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr20:16025251C>A	ENST00000310348.4	+	17	1267	c.1267C>A	c.(1267-1269)Cca>Aca	p.P423T	MACROD2_ENST00000217246.4_Intron|MACROD2_ENST00000378058.3_Missense_Mutation_p.P188T|MACROD2_ENST00000402914.1_Missense_Mutation_p.P188T|MACROD2_ENST00000407045.3_Missense_Mutation_p.P74T			A1Z1Q3	MACD2_HUMAN	MACRO domain containing 2	423					brain development (GO:0007420)|cellular response to DNA damage stimulus (GO:0006974)|protein de-ADP-ribosylation (GO:0051725)|purine nucleoside metabolic process (GO:0042278)	nucleus (GO:0005634)	deacetylase activity (GO:0019213)|hydrolase activity, acting on glycosyl bonds (GO:0016798)			breast(2)|kidney(4)|large_intestine(5)|lung(8)|skin(1)	20		all_neural(2;0.0381)|Acute lymphoblastic leukemia(2;0.175)				GGTAAATGACCCAACAGAGAG	0.333																																					p.P188T		.											.	.	.	0			c.C562A						.						94.0	87.0	90.0					20																	16025251		2203	4300	6503	SO:0001583	missense	140733	exon13			AATGACCCAACAG	BC101218	CCDS13120.2, CCDS33443.1	20p12.1	2011-04-28	2007-07-24	2007-07-24	ENSG00000172264	ENSG00000172264			16126	protein-coding gene	gene with protein product		611567	"""chromosome 20 open reading frame 133"""	C20orf133			Standard	NM_080676		Approved	dJ631M13.5	uc002wot.3	A1Z1Q3	OTTHUMG00000031919	ENST00000310348.4:c.1267C>A	20.37:g.16025251C>A	ENSP00000309809:p.Pro423Thr	Somatic	105	0		WXS	Illumina HiSeq	.	61	19	NM_001033087	A6NFF7|B0QZ39|B3KWV0|Q0P6D5|Q495E0|Q5W199|Q6ZN71	Missense_Mutation	SNP	ENST00000310348.4	37	CCDS13120.2	.	.	.	.	.	.	.	.	.	.	C	15.98	2.993755	0.54041	.	.	ENSG00000172264	ENST00000310348;ENST00000402914;ENST00000378058;ENST00000407045	T;T;T	0.62941	1.36;-0.01;-0.01	5.81	3.84	0.44239	.	.	.	.	.	T	0.59891	0.2227	.	.	.	0.27311	N	0.95732	P;B	0.40211	0.707;0.18	B;B	0.43301	0.415;0.03	T	0.51371	-0.8714	8	0.41790	T	0.15	.	12.9883	0.58604	0.293:0.707:0.0:0.0	.	74;423	A1Z1Q3-6;A1Z1Q3	.;MACD2_HUMAN	T	423;188;188;74	ENSP00000309809:P423T;ENSP00000385290:P188T;ENSP00000367297:P188T	ENSP00000309809:P423T	P	+	1	0	MACROD2	15973251	0.931000	0.31567	1.000000	0.80357	0.897000	0.52465	0.672000	0.25187	0.752000	0.32923	0.655000	0.94253	CCA	.		0.333	MACROD2-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_080676	
CAPN1	823	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	11	64950279	64950279	+	Missense_Mutation	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr11:64950279A>C	ENST00000527323.1	+	1	347	c.107A>C	c.(106-108)aAg>aCg	p.K36T	CAPN1_ENST00000533820.1_Missense_Mutation_p.K36T|AP003068.23_ENST00000526623.1_5'Flank|CAPN1_ENST00000527469.1_3'UTR|CAPN1_ENST00000279247.6_Missense_Mutation_p.K36T|CAPN1_ENST00000533129.1_Missense_Mutation_p.K36T|CAPN1_ENST00000524773.1_Missense_Mutation_p.K36T			P07384	CAN1_HUMAN	calpain 1, (mu/I) large subunit	36					extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of cell proliferation (GO:0008284)|proteolysis (GO:0006508)|receptor catabolic process (GO:0032801)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)			breast(2)|endometrium(1)|large_intestine(2)|lung(5)|ovary(1)|prostate(1)|skin(1)	13		Lung NSC(402;0.094)|Melanoma(852;0.16)		Lung(977;0.00168)|LUSC - Lung squamous cell carcinoma(976;0.00813)		AATGCCATCAAGTACCTGGGC	0.642																																					p.K36T		.											.	.	.	0			c.A107C						.						36.0	42.0	40.0					11																	64950279		2096	4210	6306	SO:0001583	missense	823	exon2			CCATCAAGTACCT	X04366	CCDS44644.1	11q13	2013-01-10			ENSG00000014216	ENSG00000014216	3.4.22.52	"""EF-hand domain containing"""	1476	protein-coding gene	gene with protein product		114220				3017764, 2209092	Standard	NM_005186		Approved	muCANP, muCL, CANP, CANPL1	uc009yqd.2	P07384	OTTHUMG00000165614	ENST00000527323.1:c.107A>C	11.37:g.64950279A>C	ENSP00000431984:p.Lys36Thr	Somatic	48	0		WXS	Illumina HiSeq	.	18	10	NM_001198869	Q2TTR0|Q6DHV4	Missense_Mutation	SNP	ENST00000527323.1	37	CCDS44644.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	25.1|25.1	4.600592|4.600592	0.87055|0.87055	.|.	.|.	ENSG00000014216|ENSG00000014216	ENST00000528396;ENST00000529133;ENST00000533820;ENST00000530571;ENST00000527739;ENST00000526966;ENST00000533129;ENST00000524773;ENST00000279247;ENST00000532285;ENST00000534373;ENST00000531068;ENST00000527699;ENST00000533909;ENST00000527323|ENST00000259755	T;T;T;T;T;T;T;T;D;T;T;T;T;T|.	0.97505|.	0.93;0.93;2.3;0.93;0.93;2.3;2.3;2.3;-4.41;0.93;0.93;0.93;0.93;2.3|.	4.89|4.89	4.89|4.89	0.63831|0.63831	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.69342|0.69342	0.3100|0.3100	M|M	0.72894|0.72894	2.215|2.215	0.52099|0.52099	D|D	0.999944|0.999944	P|.	0.42993|.	0.797|.	P|.	0.44732|.	0.459|.	T|T	0.66284|0.66284	-0.5962|-0.5962	10|6	0.59425|0.22109	D|T	0.04|0.4	.|.	12.5064|12.5064	0.55984|0.55984	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	36|.	P07384|.	CAN1_HUMAN|.	T|R	36|6	ENSP00000435847:K36T;ENSP00000432512:K36T;ENSP00000435272:K36T;ENSP00000433823:K36T;ENSP00000431528:K36T;ENSP00000431686:K36T;ENSP00000434176:K36T;ENSP00000279247:K36T;ENSP00000436693:K36T;ENSP00000431793:K36T;ENSP00000435092:K36T;ENSP00000431172:K36T;ENSP00000435198:K36T;ENSP00000431984:K36T|.	ENSP00000279247:K36T|ENSP00000259755:S6R	K|S	+|+	2|1	0|0	CAPN1|CAPN1	64706855|64706855	0.981000|0.981000	0.34729|0.34729	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	1.576000|1.576000	0.36504|0.36504	2.061000|2.061000	0.61500|0.61500	0.533000|0.533000	0.62120|0.62120	AAG|AGT	.		0.642	CAPN1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385325.1		
LRP6	4040	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	12	12279634	12279634	+	Missense_Mutation	SNP	A	A	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr12:12279634A>T	ENST00000261349.4	-	20	4379	c.4303T>A	c.(4303-4305)Tct>Act	p.S1435T	LRP6_ENST00000540415.1_Intron|BCL2L14_ENST00000396369.1_Intron|LRP6_ENST00000543091.1_Missense_Mutation_p.S1390T	NM_002336.2	NP_002327.2	O75581	LRP6_HUMAN	low density lipoprotein receptor-related protein 6	1435					anterior/posterior pattern specification (GO:0009952)|axis elongation involved in somitogenesis (GO:0090245)|bone morphogenesis (GO:0060349)|bone remodeling (GO:0046849)|branching involved in mammary gland duct morphogenesis (GO:0060444)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in cardiac neural crest cell differentiation involved in heart development (GO:0061310)|canonical Wnt signaling pathway involved in neural crest cell differentiation (GO:0044335)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in regulation of cell proliferation (GO:0044340)|cell migration involved in gastrulation (GO:0042074)|cellular response to cholesterol (GO:0071397)|cerebellum morphogenesis (GO:0021587)|cerebral cortex cell migration (GO:0021795)|cerebral cortex development (GO:0021987)|convergent extension (GO:0060026)|dopaminergic neuron differentiation (GO:0071542)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic pattern specification (GO:0009880)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|external genitalia morphogenesis (GO:0035261)|face morphogenesis (GO:0060325)|forebrain radial glial cell differentiation (GO:0021861)|formation of radial glial scaffolds (GO:0021943)|gastrulation with mouth forming second (GO:0001702)|heart looping (GO:0001947)|mammary placode formation (GO:0060596)|midbrain development (GO:0030901)|midbrain-hindbrain boundary development (GO:0030917)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of planar cell polarity pathway involved in cardiac muscle tissue morphogenesis (GO:2000151)|negative regulation of planar cell polarity pathway involved in cardiac right atrium morphogenesis (GO:2000162)|negative regulation of planar cell polarity pathway involved in neural tube closure (GO:2000168)|negative regulation of planar cell polarity pathway involved in outflow tract morphogenesis (GO:2000164)|negative regulation of planar cell polarity pathway involved in pericardium morphogenesis (GO:2000166)|negative regulation of planar cell polarity pathway involved in ventricular septum morphogenesis (GO:2000149)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|negative regulation of smooth muscle cell apoptotic process (GO:0034392)|neural crest cell differentiation (GO:0014033)|neural crest formation (GO:0014029)|neural tube closure (GO:0001843)|odontogenesis of dentin-containing tooth (GO:0042475)|palate development (GO:0060021)|pericardium morphogenesis (GO:0003344)|positive regulation of apoptotic process (GO:0043065)|positive regulation of bone resorption (GO:0045780)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell cycle (GO:0045787)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of ossification (GO:0045778)|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)|positive regulation of Wnt signaling pathway involved in dorsal/ventral axis specification (GO:2000055)|post-anal tail morphogenesis (GO:0036342)|primitive streak formation (GO:0090009)|receptor-mediated endocytosis of low-density lipoprotein particle involved in cholesterol transport (GO:0090118)|regulation of cell development (GO:0060284)|regulation of fat cell differentiation (GO:0045598)|regulation of ossification (GO:0030278)|response to folic acid (GO:0051593)|response to peptide hormone (GO:0043434)|single organismal cell-cell adhesion (GO:0016337)|synaptic transmission (GO:0007268)|thalamus development (GO:0021794)|toxin transport (GO:1901998)|trachea cartilage morphogenesis (GO:0060535)|Wnt signaling pathway (GO:0016055)|Wnt signaling pathway involved in dorsal/ventral axis specification (GO:0044332)|Wnt signaling pathway involved in forebrain neuroblast division (GO:0021874)|Wnt signaling pathway involved in somitogenesis (GO:0090244)	cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|synapse (GO:0045202)	apolipoprotein binding (GO:0034185)|coreceptor activity involved in Wnt signaling pathway (GO:0071936)|frizzled binding (GO:0005109)|identical protein binding (GO:0042802)|kinase inhibitor activity (GO:0019210)|low-density lipoprotein receptor activity (GO:0005041)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|toxin transporter activity (GO:0019534)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(19)|lung(28)|ovary(3)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	85		Prostate(47;0.0865)				CCTGGAAGAGATCCTGACAAA	0.448																																					p.S1435T		.											.	.	.	0			c.T4303A						.						142.0	118.0	126.0					12																	12279634		2203	4300	6503	SO:0001583	missense	4040	exon20			GAAGAGATCCTGA	AF074264	CCDS8647.1	12p13.2	2013-05-29			ENSG00000070018	ENSG00000070018		"""Low density lipoprotein receptors"""	6698	protein-coding gene	gene with protein product		603507				9704021	Standard	NM_002336		Approved	ADCAD2	uc001rah.4	O75581	OTTHUMG00000168540	ENST00000261349.4:c.4303T>A	12.37:g.12279634A>T	ENSP00000261349:p.Ser1435Thr	Somatic	76	0		WXS	Illumina HiSeq	.	34	14	NM_002336	Q17RZ2	Missense_Mutation	SNP	ENST00000261349.4	37	CCDS8647.1	.	.	.	.	.	.	.	.	.	.	A	15.65	2.896002	0.52121	.	.	ENSG00000070018	ENST00000261349;ENST00000543091	T;T	0.54071	0.59;0.59	5.7	5.7	0.88788	.	0.000000	0.64402	D	0.000009	T	0.57975	0.2090	L	0.27053	0.805	0.80722	D	1	D;B	0.56035	0.974;0.004	D;B	0.70487	0.969;0.01	T	0.51834	-0.8655	10	0.13470	T	0.59	.	15.96	0.79923	1.0:0.0:0.0:0.0	.	1390;1435	F5H7J9;O75581	.;LRP6_HUMAN	T	1435;1390	ENSP00000261349:S1435T;ENSP00000442472:S1390T	ENSP00000261349:S1435T	S	-	1	0	LRP6	12170901	1.000000	0.71417	0.971000	0.41717	0.996000	0.88848	8.907000	0.92634	2.165000	0.68154	0.460000	0.39030	TCT	.		0.448	LRP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400137.1		
ATE1	11101	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	10	123670610	123670610	+	Missense_Mutation	SNP	T	T	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr10:123670610T>C	ENST00000224652.6	-	5	479	c.394A>G	c.(394-396)Aat>Gat	p.N132D	ATE1_ENST00000369043.3_Missense_Mutation_p.N132D|ATE1_ENST00000535655.1_5'UTR|ATE1_ENST00000540606.1_Missense_Mutation_p.N125D|ATE1_ENST00000369040.3_Missense_Mutation_p.N36D|ATE1_ENST00000543447.1_Missense_Mutation_p.N17D	NM_001001976.1	NP_001001976.1	O95260	ATE1_HUMAN	arginyltransferase 1	132					protein arginylation (GO:0016598)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	arginyltransferase activity (GO:0004057)			endometrium(2)|kidney(2)|large_intestine(2)|lung(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	14		all_neural(114;0.061)|Lung NSC(174;0.095)|all_lung(145;0.124)|Breast(234;0.212)				TCCAGTTTATTTATCAATGCA	0.368																																					p.N132D		.											.	.	.	0			c.A394G						.						121.0	124.0	123.0					10																	123670610		2203	4300	6503	SO:0001583	missense	11101	exon5			GTTTATTTATCAA	AF079098	CCDS31299.1, CCDS31300.1, CCDS73211.1, CCDS73212.1, CCDS73213.1	10q26	2013-05-08			ENSG00000107669	ENSG00000107669	2.3.2.8		782	protein-coding gene	gene with protein product		607103				16002466, 16943202	Standard	XM_005269458		Approved		uc001lfq.3	O95260	OTTHUMG00000019178	ENST00000224652.6:c.394A>G	10.37:g.123670610T>C	ENSP00000224652:p.Asn132Asp	Somatic	31	0		WXS	Illumina HiSeq	.	26	6	NM_001001976	O95261|Q5SQQ3|Q8WW04	Missense_Mutation	SNP	ENST00000224652.6	37	CCDS31300.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	13.37|13.37	2.216263|2.216263	0.39201|0.39201	.|.	.|.	ENSG00000107669|ENSG00000107669	ENST00000423243|ENST00000369043;ENST00000224652;ENST00000369040;ENST00000540606;ENST00000543447;ENST00000455628	.|.	.|.	.|.	5.78|5.78	5.78|5.78	0.91487|0.91487	.|.	.|0.401742	.|0.26951	.|N	.|0.021679	T|T	0.53769|0.53769	0.1817|0.1817	L|L	0.45137|0.45137	1.4|1.4	0.80722|0.80722	D|D	1|1	.|B;B;B;B	.|0.14012	.|0.009;0.004;0.009;0.007	.|B;B;B;B	.|0.20384	.|0.029;0.006;0.006;0.012	T|T	0.49513|0.49513	-0.8932|-0.8932	5|9	.|0.13853	.|T	.|0.58	-21.2161|-21.2161	14.6826|14.6826	0.69028|0.69028	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|125;36;132;132	.|F5GXE4;B4E107;O95260;O95260-2	.|.;.;ATE1_HUMAN;.	R|D	128|132;132;36;125;17;125	.|.	.|ENSP00000224652:N132D	K|N	-|-	2|1	0|0	ATE1|ATE1	123660600|123660600	1.000000|1.000000	0.71417|0.71417	0.963000|0.963000	0.40424|0.40424	0.915000|0.915000	0.54546|0.54546	4.488000|4.488000	0.60300|0.60300	2.207000|2.207000	0.71202|0.71202	0.460000|0.460000	0.39030|0.39030	AAA|AAT	.		0.368	ATE1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_001001976	
CRYBG3	131544	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	3	97594051	97594051	+	Missense_Mutation	SNP	C	C	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr3:97594051C>G	ENST00000419587.2	+	4	4180	c.4013C>G	c.(4012-4014)gCt>gGt	p.A1338G	CRYBG3_ENST00000182096.4_5'Flank			Q68DQ2	CRBG3_HUMAN	beta-gamma crystallin domain containing 3	1338							carbohydrate binding (GO:0030246)			breast(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(10)|stomach(1)|upper_aerodigestive_tract(2)	32						GAACTTCAGGCTAATACTTCA	0.348																																					p.A1338G		.											.	.	.	0			c.C4013G						.																																			SO:0001583	missense	131544	exon4			TTCAGGCTAATAC			3q11.2	2008-09-30			ENSG00000080200	ENSG00000080200			34427	protein-coding gene	gene with protein product							Standard	NM_153605		Approved	DKFZp667G2110	uc021xbn.2	Q68DQ2	OTTHUMG00000159187	ENST00000419587.2:c.4013C>G	3.37:g.97594051C>G	ENSP00000391551:p.Ala1338Gly	Somatic	72	0		WXS	Illumina HiSeq	.	63	17	NM_153605	B4DLE8|F6VHI2|Q4G0V8|Q7Z4R9|Q86VD0|Q8N262|Q8N7F1|Q8NDQ8	Missense_Mutation	SNP	ENST00000419587.2	37		.	.	.	.	.	.	.	.	.	.	C	13.16	2.155077	0.38021	.	.	ENSG00000233280	ENST00000419587	.	.	.	5.54	2.67	0.31697	.	.	.	.	.	T	0.38558	0.1045	N	0.19112	0.55	.	.	.	D	0.59767	0.986	P	0.56398	0.797	T	0.49021	-0.8982	7	0.62326	D	0.03	.	6.8136	0.23819	0.1413:0.7095:0.0:0.1493	.	1338	B4DLE8	.	G	1338	.	ENSP00000391551:A1338G	A	+	2	0	AC110491.1	99076741	0.211000	0.23529	0.543000	0.28128	0.213000	0.24496	0.640000	0.24705	0.340000	0.23745	0.561000	0.74099	GCT	.		0.348	CRYBG3-001	PUTATIVE	mRNA_end_NF|cds_end_NF|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000469328.1	NM_153605	
MCMBP	79892	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	10	121587136	121587136	+	IGR	SNP	T	T	A	rs552783556		TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr10:121587136T>A	ENST00000360003.3	-	0	4113				INPP5F_ENST00000361976.2_Silent_p.V1081V|INPP5F_ENST00000369080.3_Silent_p.V471V	NM_001256378.1|NM_001256379.1|NM_024834.3	NP_001243307.1|NP_001243308.1|NP_079110.1	Q9BTE3	MCMBP_HUMAN	minichromosome maintenance complex binding protein						DNA-dependent DNA replication (GO:0006261)|mitotic nuclear division (GO:0007067)|sister chromatid cohesion (GO:0007062)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	chromatin binding (GO:0003682)			breast(1)|endometrium(3)|large_intestine(4)|lung(9)|ovary(2)|skin(2)	21						TGGTCCAGGTTGCTAGTATTA	0.458													T|||	1	0.000199681	0.0	0.0	5008	,	,		18513	0.0		0.0	False		,,,				2504	0.001				p.V1081V		.											.	.	.	0			c.T3243A						.						92.0	93.0	92.0					10																	121587136		2203	4300	6503	SO:0001628	intergenic_variant	22876	exon20			CCAGGTTGCTAGT	BC007219	CCDS7617.1, CCDS58099.1	10q26.13	2013-10-11	2011-01-05	2011-01-05	ENSG00000197771	ENSG00000197771			25782	protein-coding gene	gene with protein product		610909	"""chromosome 10 open reading frame 119"""	C10orf119		17296731	Standard	NM_024834		Approved	FLJ13081, MCM-BP	uc001ler.3	Q9BTE3	OTTHUMG00000019159		10.37:g.121587136T>A		Somatic	87	0		WXS	Illumina HiSeq	.	56	22	NM_014937	B3KSP7|Q6IA56|Q9BVT9|Q9H916	Silent	SNP	ENST00000360003.3	37	CCDS7617.1																																																																																			.		0.458	MCMBP-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000050684.1	NM_024834	
PRMT7	54496	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	16	68380156	68380156	+	Silent	SNP	T	T	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr16:68380156T>C	ENST00000339507.5	+	11	1994	c.1164T>C	c.(1162-1164)acT>acC	p.T388T	PRMT7_ENST00000441236.1_Silent_p.T338T|PRMT7_ENST00000449359.3_Silent_p.T338T|PRMT7_ENST00000348497.4_Silent_p.T314T			Q9NVM4	ANM7_HUMAN	protein arginine methyltransferase 7	388	SAM-dependent MTase PRMT-type 2. {ECO:0000255|PROSITE-ProRule:PRU01015}.				cell differentiation (GO:0030154)|DNA methylation involved in gamete generation (GO:0043046)|histone arginine methylation (GO:0034969)|histone methylation (GO:0016571)|peptidyl-arginine methylation (GO:0018216)|peptidyl-arginine methylation, to asymmetrical-dimethyl arginine (GO:0019919)|peptidyl-arginine methylation, to symmetrical-dimethyl arginine (GO:0019918)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of protein binding (GO:0043393)|regulation of transcription, DNA-templated (GO:0006355)|spliceosomal snRNP assembly (GO:0000387)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	[myelin basic protein]-arginine N-methyltransferase activity (GO:0016277)|histone binding (GO:0042393)|histone methyltransferase activity (H4-R3 specific) (GO:0044020)|histone-arginine N-methyltransferase activity (GO:0008469)|protein-arginine omega-N asymmetric methyltransferase activity (GO:0035242)|protein-arginine omega-N monomethyltransferase activity (GO:0035241)|protein-arginine omega-N symmetric methyltransferase activity (GO:0035243)|ribonucleoprotein complex binding (GO:0043021)|S-adenosylmethionine-dependent methyltransferase activity (GO:0008757)			endometrium(3)|kidney(2)|large_intestine(3)|lung(10)|pancreas(1)|urinary_tract(1)	20		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0155)|Epithelial(162;0.0629)		AGGACAGAACTGATCGATACG	0.557																																					p.T388T		.											.	.	.	0			c.T1164C						.						79.0	76.0	77.0					16																	68380156		2198	4300	6498	SO:0001819	synonymous_variant	54496	exon11			CAGAACTGATCGA	AK001502	CCDS10866.1, CCDS54033.1	16q22.1	2008-02-05			ENSG00000132600	ENSG00000132600		"""Protein arginine methyltransferases"""	25557	protein-coding gene	gene with protein product		610087				15044439	Standard	NM_001184824		Approved	FLJ10640, KIAA1933	uc002evy.2	Q9NVM4	OTTHUMG00000137556	ENST00000339507.5:c.1164T>C	16.37:g.68380156T>C		Somatic	26	0		WXS	Illumina HiSeq	.	20	10	NM_019023	B3KPR0|B3KUG9|B4E379|Q96PV5|Q9H9L0	Silent	SNP	ENST00000339507.5	37	CCDS10866.1																																																																																			.		0.557	PRMT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268892.3	NM_019023	
NDEL1	81565	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	17	8354204	8354204	+	Missense_Mutation	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr17:8354204A>C	ENST00000334527.7	+	6	830	c.633A>C	c.(631-633)caA>caC	p.Q211H	NDEL1_ENST00000299734.7_Missense_Mutation_p.Q211H|NDEL1_ENST00000585098.1_Intron|NDEL1_ENST00000380025.4_Missense_Mutation_p.Q211H|NDEL1_ENST00000402554.3_Missense_Mutation_p.Q211H	NM_030808.4	NP_110435.1	Q9GZM8	NDEL1_HUMAN	nudE neurodevelopment protein 1-like 1	211	Interaction with CENPF.|Interaction with KATNA1. {ECO:0000250}.|Interaction with NEFL. {ECO:0000250}.|Interaction with YWHAE. {ECO:0000250}.				activation of Cdc42 GTPase activity (GO:0032864)|central nervous system neuron axonogenesis (GO:0021955)|centrosome localization (GO:0051642)|cerebral cortex radially oriented cell migration (GO:0021799)|chromosome segregation (GO:0007059)|inner cell mass cell proliferation (GO:0001833)|mitotic cell cycle (GO:0000278)|mitotic centrosome separation (GO:0007100)|neurofilament cytoskeleton organization (GO:0060052)|neuron migration (GO:0001764)|neuron projection extension (GO:1990138)|nuclear envelope disassembly (GO:0051081)|positive regulation of axon extension (GO:0045773)|positive regulation of axon regeneration (GO:0048680)|retrograde axon cargo transport (GO:0008090)|vesicle transport along microtubule (GO:0047496)	axon hillock (GO:0043203)|cell leading edge (GO:0031252)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|kinetochore (GO:0000776)|microtubule (GO:0005874)|neurofilament cytoskeleton (GO:0060053)|nuclear envelope (GO:0005635)|nucleolus (GO:0005730)	oligopeptidase activity (GO:0070012)			large_intestine(6)|lung(4)|skin(3)	13						CCGCCGTCCAAGCATCACTTT	0.473																																					p.Q211H		.											.	.	.	0			c.A633C						.						77.0	69.0	71.0					17																	8354204		2203	4300	6503	SO:0001583	missense	81565	exon6			CGTCCAAGCATCA	AF182078	CCDS11143.1, CCDS32564.1	17p13.1	2013-08-06	2013-08-06	2003-04-16	ENSG00000166579	ENSG00000166579			17620	protein-coding gene	gene with protein product		607538	"""nudE nuclear distribution gene E homolog (A. nidulans)-like 1"", ""nudE nuclear distribution E homolog (A. nidulans)-like 1"""			11163260, 11163259	Standard	NM_001025579		Approved	NUDEL, MITAP1, NDE1L1, NDE2	uc002glj.4	Q9GZM8	OTTHUMG00000108193	ENST00000334527.7:c.633A>C	17.37:g.8354204A>C	ENSP00000333982:p.Gln211His	Somatic	54	0		WXS	Illumina HiSeq	.	35	18	NM_001025579	B3KP93|D3DTS0|J3QT32|Q86T80|Q8TAR7|Q9UH50	Missense_Mutation	SNP	ENST00000334527.7	37	CCDS11143.1	.	.	.	.	.	.	.	.	.	.	A	16.51	3.144647	0.57044	.	.	ENSG00000166579	ENST00000299734;ENST00000380025;ENST00000402554;ENST00000334527	.	.	.	4.98	-7.49	0.01355	NUDE protein, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.65249	0.2673	M	0.73962	2.25	0.58432	D	0.999994	B;B	0.24618	0.012;0.107	B;B	0.27608	0.035;0.081	T	0.49523	-0.8931	9	0.51188	T	0.08	-3.9645	22.5354	0.99973	0.1857:0.0:0.8143:0.0	.	211;211	Q9GZM8;A6NIZ0	NDEL1_HUMAN;.	H	211;211;266;211	.	ENSP00000299734:Q211H	Q	+	3	2	NDEL1	8294929	0.890000	0.30428	0.454000	0.27019	0.992000	0.81027	-0.060000	0.11712	-1.417000	0.02017	0.533000	0.62120	CAA	.		0.473	NDEL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226999.2	NM_030808	
AXIN2	8313	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	17	63526145	63526145	+	Silent	SNP	C	C	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr17:63526145C>A	ENST00000375702.5	-	9	2394	c.2286G>T	c.(2284-2286)gtG>gtT	p.V762V	AXIN2_ENST00000307078.5_Silent_p.V827V			Q9Y2T1	AXIN2_HUMAN	axin 2	827	DIX. {ECO:0000255|PROSITE- ProRule:PRU00069}.				bone mineralization (GO:0030282)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to organic cyclic compound (GO:0071407)|chondrocyte differentiation involved in endochondral bone morphogenesis (GO:0003413)|dorsal/ventral axis specification (GO:0009950)|intramembranous ossification (GO:0001957)|maintenance of DNA repeat elements (GO:0043570)|mRNA stabilization (GO:0048255)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catenin import into nucleus (GO:0035414)|negative regulation of cell proliferation (GO:0008285)|negative regulation of osteoblast differentiation (GO:0045668)|odontogenesis (GO:0042476)|positive regulation of cell death (GO:0010942)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of GTPase activity (GO:0043547)|positive regulation of protein phosphorylation (GO:0001934)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of chondrocyte development (GO:0061181)|regulation of mismatch repair (GO:0032423)|secondary heart field specification (GO:0003139)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|Wnt signaling pathway involved in somitogenesis (GO:0090244)	beta-catenin destruction complex (GO:0030877)|cell cortex (GO:0005938)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoplasmic microtubule (GO:0005881)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	armadillo repeat domain binding (GO:0070016)|beta-catenin binding (GO:0008013)|enzyme binding (GO:0019899)|GTPase activator activity (GO:0005096)|protein kinase binding (GO:0019901)|ubiquitin protein ligase binding (GO:0031625)			NS(1)|central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(10)|lung(10)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	34						ACATCGGGAGCACCGTCTCAT	0.502									Oligodontia, Ectodermal Dysplasia and Colorectal Polyp syndrome																												p.V827V		.											.	.	.	0			c.G2481T						.						135.0	117.0	123.0					17																	63526145		2203	4300	6503	SO:0001819	synonymous_variant	8313	exon11	Familial Cancer Database	Oligodontia-Colorectal Cancer syndrome, Tooth Agenesis-Colorectal Cancer Syndrome	CGGGAGCACCGTC	AF078165	CCDS11662.1	17q24.1	2014-09-17	2008-08-01		ENSG00000168646				904	protein-coding gene	gene with protein product	"""conductin"", ""axil"""	604025				10049590	Standard	NM_004655		Approved	MGC126582, DKFZp781B0869	uc002jfi.3	Q9Y2T1	OTTHUMG00000179353	ENST00000375702.5:c.2286G>T	17.37:g.63526145C>A		Somatic	38	0		WXS	Illumina HiSeq	.	22	6	NM_004655	Q3MJ88|Q9H3M6|Q9UH84	Silent	SNP	ENST00000375702.5	37																																																																																				.		0.502	AXIN2-004	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000445901.1	NM_004655	
LAP3	51056	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	4	17600083	17600083	+	Missense_Mutation	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr4:17600083A>C	ENST00000226299.4	+	10	1356	c.1082A>C	c.(1081-1083)gAt>gCt	p.D361A	AC006160.5_ENST00000511010.1_RNA|LAP3_ENST00000606142.1_Missense_Mutation_p.D330A|LAP3_ENST00000503467.1_3'UTR	NM_015907.2	NP_056991.2	P28838	AMPL_HUMAN	leucine aminopeptidase 3	361					proteolysis (GO:0006508)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|trans-Golgi network (GO:0005802)	aminopeptidase activity (GO:0004177)|manganese ion binding (GO:0030145)|metalloexopeptidase activity (GO:0008235)			endometrium(4)|kidney(1)|large_intestine(4)|lung(10)|urinary_tract(1)	20						CTGCAGGTTGATAACACTGAT	0.478																																					p.D361A		.											.	.	.	0			c.A1082C						.						145.0	119.0	128.0					4																	17600083		2203	4300	6503	SO:0001583	missense	51056	exon10			AGGTTGATAACAC	AF061738	CCDS3422.1	4p15.33	2012-07-25	2003-09-12		ENSG00000002549	ENSG00000002549	3.4.11.1		18449	protein-coding gene	gene with protein product		170250	"""peptidase S"""	PEPS		6350155, 689684	Standard	NM_015907		Approved	LAPEP, LAP	uc003gph.1	P28838	OTTHUMG00000048214	ENST00000226299.4:c.1082A>C	4.37:g.17600083A>C	ENSP00000226299:p.Asp361Ala	Somatic	77	0		WXS	Illumina HiSeq	.	56	8	NM_015907	B3KMQ3|Q6IAM6|Q6P0L6|Q9UQE3	Missense_Mutation	SNP	ENST00000226299.4	37	CCDS3422.1	.	.	.	.	.	.	.	.	.	.	A	23.6	4.440120	0.83993	.	.	ENSG00000002549	ENST00000226299	T	0.42513	0.97	5.05	5.05	0.67936	Peptidase M17, leucyl aminopeptidase, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.64438	0.2598	M	0.80332	2.49	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	T	0.63998	-0.6510	10	0.24483	T	0.36	-29.4045	15.0951	0.72226	1.0:0.0:0.0:0.0	.	361	P28838	AMPL_HUMAN	A	361	ENSP00000226299:D361A	ENSP00000226299:D361A	D	+	2	0	LAP3	17209181	1.000000	0.71417	0.751000	0.31187	0.904000	0.53231	8.738000	0.91569	2.011000	0.59026	0.460000	0.39030	GAT	.		0.478	LAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250365.1		
OR5H14	403273	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	3	97868425	97868425	+	Missense_Mutation	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr3:97868425T>G	ENST00000437310.1	+	1	256	c.196T>G	c.(196-198)Tta>Gta	p.L66V	RP11-343D2.11_ENST00000508964.1_RNA	NM_001005514.1	NP_001005514.1	A6NHG9	O5H14_HUMAN	olfactory receptor, family 5, subfamily H, member 14	66						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(3)|lung(17)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	31						CCTTGGGAATTTAGCTTTTGT	0.398																																					p.L66V		.											.	.	.	0			c.T196G						.						316.0	320.0	319.0					3																	97868425		2203	4300	6503	SO:0001583	missense	403273	exon1			GGGAATTTAGCTT		CCDS33798.1	3q11.2	2013-09-23			ENSG00000236032	ENSG00000236032		"""GPCR / Class A : Olfactory receptors"""	31286	protein-coding gene	gene with protein product							Standard	NM_001005514		Approved		uc003dsg.1	A6NHG9	OTTHUMG00000160079	ENST00000437310.1:c.196T>G	3.37:g.97868425T>G	ENSP00000401706:p.Leu66Val	Somatic	151	0		WXS	Illumina HiSeq	.	104	20	NM_001005514	B9EH15	Missense_Mutation	SNP	ENST00000437310.1	37	CCDS33798.1	.	.	.	.	.	.	.	.	.	.	T	11.39	1.624128	0.28889	.	.	ENSG00000236032	ENST00000437310	T	0.00587	6.38	2.49	1.27	0.21489	GPCR, rhodopsin-like superfamily (1);	0.000000	0.34853	N	0.003626	T	0.02848	0.0085	H	0.96430	3.82	0.09310	N	1	D	0.64830	0.994	P	0.61201	0.885	T	0.28038	-1.0056	10	0.87932	D	0	.	4.493	0.11822	0.0:0.327:0.0:0.673	.	66	A6NHG9	O5H14_HUMAN	V	66	ENSP00000401706:L66V	ENSP00000401706:L66V	L	+	1	2	OR5H14	99351115	0.000000	0.05858	0.010000	0.14722	0.024000	0.10985	-1.563000	0.02154	0.198000	0.20407	0.164000	0.16699	TTA	.		0.398	OR5H14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359112.1		
TMEM39B	55116	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	1	32560448	32560448	+	Missense_Mutation	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr1:32560448T>G	ENST00000336294.5	+	7	1137	c.991T>G	c.(991-993)Tcc>Gcc	p.S331A	TMEM39B_ENST00000456834.2_3'UTR|TMEM39B_ENST00000427288.1_Missense_Mutation_p.S216A|TMEM39B_ENST00000373634.4_Missense_Mutation_p.S132A|TMEM39B_ENST00000487305.1_3'UTR	NM_018056.2	NP_060526.2	Q9GZU3	TM39B_HUMAN	transmembrane protein 39B	331						integral component of membrane (GO:0016021)				endometrium(2)|kidney(1)|lung(5)|ovary(1)|prostate(2)	11		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Ovarian(437;0.101)|Breast(348;0.174)				CATCAGCACCTCCGTGATCCT	0.607																																					p.S331A		.											.	.	.	0			c.T991G						.						106.0	92.0	97.0					1																	32560448		2203	4300	6503	SO:0001583	missense	55116	exon7			AGCACCTCCGTGA	AL136695	CCDS351.2	1p35.1	2008-02-05			ENSG00000121775	ENSG00000121775			25510	protein-coding gene	gene with protein product						12477932	Standard	NM_018056		Approved	FLJ10315	uc010ogv.2	Q9GZU3	OTTHUMG00000004020	ENST00000336294.5:c.991T>G	1.37:g.32560448T>G	ENSP00000338165:p.Ser331Ala	Somatic	13	0		WXS	Illumina HiSeq	.	22	8	NM_018056	B4DKN8|B4DQE6|B4DTN8|D3DPP4|Q6IA44	Missense_Mutation	SNP	ENST00000336294.5	37	CCDS351.2	.	.	.	.	.	.	.	.	.	.	T	16.65	3.181629	0.57800	.	.	ENSG00000121775	ENST00000336294;ENST00000373634;ENST00000427288	.	.	.	4.59	4.59	0.56863	.	0.181218	0.49916	D	0.000123	T	0.68165	0.2971	L	0.57536	1.79	0.54753	D	0.999986	P;D;P	0.60160	0.737;0.987;0.737	B;P;B	0.61592	0.396;0.891;0.396	T	0.66826	-0.5825	9	0.33141	T	0.24	-1.6818	14.4184	0.67165	0.0:0.0:0.0:1.0	.	331;216;204	Q9GZU3;B4DTN8;Q9NW51	TM39B_HUMAN;.;.	A	331;132;216	.	ENSP00000338165:S331A	S	+	1	0	TMEM39B	32333035	1.000000	0.71417	0.665000	0.29768	0.849000	0.48306	7.382000	0.79729	2.048000	0.60808	0.533000	0.62120	TCC	.		0.607	TMEM39B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011489.2	NM_018056	
USP28	57646	hgsc.bcm.edu	37	11	113683165	113683165	+	Missense_Mutation	SNP	C	C	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr11:113683165C>A	ENST00000003302.4	-	16	1873	c.1805G>T	c.(1804-1806)tGg>tTg	p.W602L	USP28_ENST00000544967.1_Missense_Mutation_p.W310L|USP28_ENST00000260188.5_Missense_Mutation_p.W602L|USP28_ENST00000545540.1_Missense_Mutation_p.W477L	NM_020886.2	NP_065937.1	Q96RU2	UBP28_HUMAN	ubiquitin specific peptidase 28	602	USP.				cell proliferation (GO:0008283)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|protein deubiquitination (GO:0016579)|response to ionizing radiation (GO:0010212)|ubiquitin-dependent protein catabolic process (GO:0006511)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			breast(4)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(12)|lung(24)|ovary(1)|prostate(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	59		all_cancers(61;3.74e-18)|all_epithelial(67;3.75e-11)|Melanoma(852;1.46e-05)|all_hematologic(158;4.65e-05)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|Prostate(24;0.0153)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;3.93e-06)|Epithelial(105;0.000122)|all cancers(92;0.00104)		GATATAGGCCCAATAGTGTCC	0.443																																					p.W602L	Melanoma(4;162 555 7664)|GBM(79;500 2010 17506)|Esophageal Squamous(9;463 924 15765)	.											USP28,NS,carcinoma,0,1	USP28	0	0			c.G1805T						.						136.0	140.0	139.0					11																	113683165		2201	4296	6497	SO:0001583	missense	57646	exon16			TAGGCCCAATAGT	AB040948	CCDS31680.1, CCDS73394.1	11q23	2008-04-11	2005-08-08		ENSG00000048028	ENSG00000048028		"""Ubiquitin-specific peptidases"""	12625	protein-coding gene	gene with protein product		610748	"""ubiquitin specific protease 28"""			12838346, 11597335	Standard	XM_005271630		Approved	KIAA1515	uc001poh.3	Q96RU2	OTTHUMG00000168205	ENST00000003302.4:c.1805G>T	11.37:g.113683165C>A	ENSP00000003302:p.Trp602Leu	Somatic	31	0		WXS	Illumina HiSeq	.	24	2	NM_020886	B0YJC0|B0YJC1|Q9P213	Missense_Mutation	SNP	ENST00000003302.4	37	CCDS31680.1	.	.	.	.	.	.	.	.	.	.	C	29.3	4.991744	0.93106	.	.	ENSG00000048028	ENST00000003302;ENST00000260188;ENST00000544967;ENST00000545540;ENST00000538475	T;T;T;T;T	0.28454	1.61;1.61;1.61;1.61;1.61	5.38	5.38	0.77491	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.000000	0.85682	D	0.000000	T	0.56277	0.1974	M	0.67953	2.075	0.80722	D	1	D;D;D	0.60575	0.984;0.988;0.98	P;D;P	0.72338	0.866;0.977;0.79	T	0.58457	-0.7633	10	0.72032	D	0.01	-8.4685	19.1336	0.93417	0.0:1.0:0.0:0.0	.	477;602;310	B4E3L3;Q96RU2;G3V1N5	.;UBP28_HUMAN;.	L	602;602;310;477;306	ENSP00000003302:W602L;ENSP00000260188:W602L;ENSP00000442431:W310L;ENSP00000444991:W477L;ENSP00000442257:W306L	ENSP00000003302:W602L	W	-	2	0	USP28	113188375	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.487000	0.81328	2.504000	0.84457	0.655000	0.94253	TGG	.		0.443	USP28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398789.1		
KIAA0754	643314	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	39879575	39879575	+	Missense_Mutation	SNP	A	A	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr1:39879575A>T	ENST00000530275.1	+	1	3425	c.3230A>T	c.(3229-3231)gAg>gTg	p.E1077V	MACF1_ENST00000361689.2_Intron|MACF1_ENST00000372915.3_Intron|MACF1_ENST00000564288.1_Intron|MACF1_ENST00000539005.1_Intron|MACF1_ENST00000317713.7_Intron|MACF1_ENST00000567887.1_Intron|MACF1_ENST00000289893.4_Intron|MACF1_ENST00000545844.1_Intron	NM_015038.1	NP_055853.1	O94854	K0754_HUMAN	KIAA0754	1077	Ala-rich.									central_nervous_system(1)|large_intestine(6)|skin(1)	8	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			GCCACCCTAGAGGAATTCACT	0.637																																					p.E1213V		.											.	.	.	0			c.A3638T						.						14.0	16.0	16.0					1																	39879575		1945	4154	6099	SO:0001583	missense	643314	exon1			CCCTAGAGGAATT			1p34.2	2009-07-09				ENSG00000255103			29111	protein-coding gene	gene with protein product						9872452	Standard	NM_015038		Approved		uc009vvt.1	O94854		ENST00000530275.1:c.3230A>T	1.37:g.39879575A>T	ENSP00000431179:p.Glu1077Val	Somatic	46	0		WXS	Illumina HiSeq	.	40	9	NM_015038	E9PMC2|Q6ZSB2	Missense_Mutation	SNP	ENST00000530275.1	37		.	.	.	.	.	.	.	.	.	.	A	11.81	1.750148	0.30955	.	.	ENSG00000255103	ENST00000530275	T	0.25749	1.78	3.21	-6.41	0.01938	.	.	.	.	.	T	0.10852	0.0265	N	0.14661	0.345	0.09310	N	1	B	0.20671	0.047	B	0.16289	0.015	T	0.25847	-1.0120	9	0.44086	T	0.13	.	4.168	0.10315	0.2864:0.0:0.4162:0.2973	.	1077	O94854	K0754_HUMAN	V	1077	ENSP00000431179:E1077V	ENSP00000431179:E1077V	E	+	2	0	RP4-562N20.1	39652162	0.011000	0.17503	0.000000	0.03702	0.053000	0.15095	-0.160000	0.10041	-1.407000	0.02043	0.155000	0.16302	GAG	.		0.637	KIAA0754-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000392100.1	NM_015038	
BCAN	63827	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	156622046	156622046	+	Missense_Mutation	SNP	A	A	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr1:156622046A>G	ENST00000329117.5	+	8	1640	c.1304A>G	c.(1303-1305)gAa>gGa	p.E435G	RP11-284F21.7_ENST00000448869.1_RNA|BCAN_ENST00000361588.5_Missense_Mutation_p.E435G	NM_021948.4	NP_068767.3	Q96GW7	PGCB_HUMAN	brevican	435	Glu-rich.				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|hippocampus development (GO:0021766)|small molecule metabolic process (GO:0044281)	anchored component of membrane (GO:0031225)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)	carbohydrate binding (GO:0030246)|hyaluronic acid binding (GO:0005540)			cervix(1)|endometrium(6)|kidney(3)|large_intestine(6)|lung(29)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	55	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					CTAGAATTTGAAACACAATCC	0.493																																					p.E435G		.											.	.	.	0			c.A1304G						.						60.0	59.0	59.0					1																	156622046		2203	4299	6502	SO:0001583	missense	63827	exon8			AATTTGAAACACA	BC027971	CCDS1149.1, CCDS1150.1	1q31	2013-05-07			ENSG00000132692	ENSG00000132692		"""Immunoglobulin superfamily / V-set domain containing"", ""Proteoglycans / Extracellular Matrix : Hyalectans"""	23059	protein-coding gene	gene with protein product	"""chondroitin sulfate proteoglycan 7"", ""brevican proteoglycan"""	600347				11054543, 11873941	Standard	NM_021948		Approved	BEHAB, MGC13038, CSPG7	uc001fpp.3	Q96GW7	OTTHUMG00000033322	ENST00000329117.5:c.1304A>G	1.37:g.156622046A>G	ENSP00000331210:p.Glu435Gly	Somatic	90	0		WXS	Illumina HiSeq	.	62	16	NM_198427	D3DVC2|Q5SZ10|Q5T3I5|Q8TBB9|Q9HBK1|Q9HBK4	Missense_Mutation	SNP	ENST00000329117.5	37	CCDS1149.1	.	.	.	.	.	.	.	.	.	.	A	4.723	0.134390	0.09032	.	.	ENSG00000132692	ENST00000255029;ENST00000329117;ENST00000361588	T;T	0.16743	2.32;3.0	4.85	3.7	0.42460	.	0.322091	0.23920	N	0.043249	T	0.03477	0.0100	N	0.19112	0.55	0.29206	N	0.874903	B;B	0.06786	0.001;0.001	B;B	0.04013	0.001;0.001	T	0.29243	-1.0018	10	0.41790	T	0.15	-5.9363	5.7536	0.18160	0.8784:0.0:0.1216:0.0	.	435;435	Q96GW7;Q96GW7-2	PGCB_HUMAN;.	G	374;435;435	ENSP00000331210:E435G;ENSP00000354925:E435G	ENSP00000255029:E374G	E	+	2	0	BCAN	154888670	0.996000	0.38824	0.944000	0.38274	0.054000	0.15201	2.590000	0.46154	2.032000	0.59987	0.459000	0.35465	GAA	.		0.493	BCAN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000081844.2	NM_021948	
TSNAX	7257	hgsc.bcm.edu	37	1	231678136	231678136	+	Intron	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr1:231678136A>C	ENST00000366639.4	+	4	394				TSNAX-DISC1_ENST00000602962.1_Intron|TSNAX_ENST00000602825.1_Intron	NM_005999.2	NP_005990.1	Q99598	TSNAX_HUMAN	translin-associated factor X						cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|protein transport (GO:0015031)|spermatogenesis (GO:0007283)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|protein transporter activity (GO:0008565)|sequence-specific DNA binding (GO:0043565)			endometrium(1)|kidney(1)|large_intestine(2)|lung(5)	9		all_cancers(173;0.0395)|Acute lymphoblastic leukemia(190;3.76e-06)|Prostate(94;0.116)				AATGCATACAATATTTAGCCC	0.289																																					.		.											.	.	.	0			.						.																																			SO:0001627	intron_variant	0	.			CATACAATATTTA	X95073	CCDS1596.1	1q42.2	2008-02-05			ENSG00000116918	ENSG00000116918			12380	protein-coding gene	gene with protein product		602964				9013868	Standard	NM_005999		Approved	TRAX	uc001huw.3	Q99598	OTTHUMG00000039486	ENST00000366639.4:c.237-91A>C	1.37:g.231678136A>C		Somatic	55	0		WXS	Illumina HiSeq	.	86	19	.	B1APC6	RNA	SNP	ENST00000366639.4	37	CCDS1596.1																																																																																			.		0.289	TSNAX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095267.2	NM_005999	
DGKB	1607	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	7	14613961	14613961	+	Missense_Mutation	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr7:14613961T>G	ENST00000403951.2	-	20	2068	c.1649A>C	c.(1648-1650)gAc>gCc	p.D550A	DGKB_ENST00000258767.5_Missense_Mutation_p.D550A|DGKB_ENST00000403963.1_5'UTR|DGKB_ENST00000402815.1_Missense_Mutation_p.D549A|DGKB_ENST00000399322.3_Missense_Mutation_p.D550A|DGKB_ENST00000407950.1_Missense_Mutation_p.D542A|DGKB_ENST00000406247.3_Missense_Mutation_p.D550A|DGKB_ENST00000444700.2_Missense_Mutation_p.D531A			Q9Y6T7	DGKB_HUMAN	diacylglycerol kinase, beta 90kDa	550	DAGKc. {ECO:0000255|PROSITE- ProRule:PRU00783}.				blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|platelet activation (GO:0030168)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|diacylglycerol kinase activity (GO:0004143)|NAD+ kinase activity (GO:0003951)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|liver(1)|lung(34)|ovary(4)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	72						GTTTTCAATGTCTTTTAGAAT	0.348																																					p.D550A		.											.	.	.	0			c.A1649C						.						189.0	169.0	175.0					7																	14613961		1843	4102	5945	SO:0001583	missense	1607	exon19			TCAATGTCTTTTA	AB018261	CCDS47547.1, CCDS47548.1	7p21.2	2013-01-10	2002-08-29		ENSG00000136267	ENSG00000136267	2.7.1.107	"""EF-hand domain containing"""	2850	protein-coding gene	gene with protein product		604070	"""diacylglycerol kinase, beta (90kD)"""	DAGK2		7689223	Standard	NM_004080		Approved	KIAA0718, DGK, DGK-BETA	uc003ssz.3	Q9Y6T7	OTTHUMG00000152477	ENST00000403951.2:c.1649A>C	7.37:g.14613961T>G	ENSP00000385780:p.Asp550Ala	Somatic	49	0		WXS	Illumina HiSeq	.	31	13	NM_145695	A4D116|A4D117|A8MXU2|O75241|Q2M377|Q75MF9|Q75MU7|Q86UI5|Q86UM9|Q9UQ29	Missense_Mutation	SNP	ENST00000403951.2	37	CCDS47547.1	.	.	.	.	.	.	.	.	.	.	T	20.4	3.984638	0.74474	.	.	ENSG00000136267	ENST00000403951;ENST00000399322;ENST00000258767;ENST00000402815;ENST00000407950;ENST00000444700;ENST00000406247	T;T;T;T;T;T;T	0.22336	1.96;1.96;1.96;1.96;1.96;1.96;1.96	5.29	4.15	0.48705	Diacylglycerol kinase, catalytic domain (3);	0.057816	0.64402	D	0.000003	T	0.33673	0.0871	L	0.41492	1.28	0.51233	D	0.999917	D;P;P;D	0.65815	0.995;0.876;0.876;0.982	D;P;P;P	0.68483	0.958;0.757;0.757;0.883	T	0.02333	-1.1175	10	0.51188	T	0.08	.	10.7913	0.46434	0.0:0.0742:0.0:0.9258	.	549;531;550;550	B7ZL83;C9JTC0;Q9Y6T7-2;Q9Y6T7	.;.;.;DGKB_HUMAN	A	550;550;550;549;542;531;550	ENSP00000385780:D550A;ENSP00000382260:D550A;ENSP00000258767:D550A;ENSP00000384909:D549A;ENSP00000385031:D542A;ENSP00000388451:D531A;ENSP00000386066:D550A	ENSP00000258767:D550A	D	-	2	0	DGKB	14580486	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	6.294000	0.72738	0.869000	0.35703	0.459000	0.35465	GAC	.		0.348	DGKB-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000326356.2	NM_004080	
CSMD1	64478	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	8	2886950	2886950	+	Silent	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr8:2886950A>C	ENST00000520002.1	-	52	8304	c.7749T>G	c.(7747-7749)gcT>gcG	p.A2583A	CSMD1_ENST00000537824.1_Silent_p.A2582A|CSMD1_ENST00000602723.1_Silent_p.A2583A|CSMD1_ENST00000400186.3_Silent_p.A2583A|CSMD1_ENST00000602557.1_Silent_p.A2583A|CSMD1_ENST00000542608.1_Silent_p.A2582A			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	2583	Sushi 16. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		GCAATACTTGAGCACCGTACT	0.542																																					p.A2582A		.											.	.	.	0			c.T7746G						.						67.0	64.0	65.0					8																	2886950		1995	4167	6162	SO:0001819	synonymous_variant	64478	exon51			TACTTGAGCACCG			8p23.2	2012-04-17			ENSG00000183117	ENSG00000183117		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	14026	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 24"""	608397					Standard	NM_033225		Approved	KIAA1890, PPP1R24	uc022aqr.1	Q96PZ7	OTTHUMG00000163605	ENST00000520002.1:c.7749T>G	8.37:g.2886950A>C		Somatic	31	0		WXS	Illumina HiSeq	.	19	8	NM_033225	Q0H0J5|Q96QU9|Q96RM4	Silent	SNP	ENST00000520002.1	37		.	.	.	.	.	.	.	.	.	.	A	5.139	0.211268	0.09757	.	.	ENSG00000183117	ENST00000335551	.	.	.	4.88	-8.82	0.00810	.	.	.	.	.	T	0.32912	0.0845	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.38845	-0.9642	4	.	.	.	.	0.9577	0.01389	0.2547:0.2996:0.2509:0.1948	.	.	.	.	A	2000	.	.	S	-	1	0	CSMD1	2874357	0.977000	0.34250	0.080000	0.20451	0.331000	0.28603	0.228000	0.17814	-2.000000	0.00965	0.482000	0.46254	TCA	.		0.542	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225	
PALLD	23022	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	4	169824935	169824935	+	Missense_Mutation	SNP	A	A	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr4:169824935A>G	ENST00000505667.1	+	15	2673	c.2500A>G	c.(2500-2502)Atc>Gtc	p.I834V	PALLD_ENST00000335742.7_Missense_Mutation_p.I659V|CBR4_ENST00000509108.1_Intron|PALLD_ENST00000512127.1_Missense_Mutation_p.I435V|PALLD_ENST00000507735.1_Missense_Mutation_p.I330V|PALLD_ENST00000261509.6_Missense_Mutation_p.I817V			Q8WX93	PALLD_HUMAN	palladin, cytoskeletal associated protein	1041	Interaction with ACTN.|Pro-rich.				cytoskeleton organization (GO:0007010)	actin filament (GO:0005884)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	muscle alpha-actinin binding (GO:0051371)			breast(4)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(6)|liver(2)|lung(18)|ovary(3)|prostate(3)|skin(4)	48		Prostate(90;0.00996)|Renal(120;0.0203)|Melanoma(52;0.144)		GBM - Glioblastoma multiforme(119;0.204)		TGGGAAGCAGATCTCTCCAAA	0.398									Pancreatic Cancer, Familial Clustering of																												p.I834V	Esophageal Squamous(109;1482 1532 18347 40239 51172)	.											.	.	.	0			c.A2500G						.						88.0	85.0	86.0					4																	169824935		2203	4300	6503	SO:0001583	missense	23022	exon15	Familial Cancer Database	incl.: Hereditary Pancreatic Adenocarcinoma, Insulin-Dependent Diabetes Mellitus - Exocrine Insufficiency - Familial Pancreatic Cancer, PNCA1	AAGCAGATCTCTC	AB023209	CCDS34098.1, CCDS54818.1, CCDS54819.1, CCDS54820.1	4q32.3	2013-01-11			ENSG00000129116	ENSG00000129116		"""Immunoglobulin superfamily / I-set domain containing"""	17068	protein-coding gene	gene with protein product		608092				10231032, 10931874	Standard	NM_001166108		Approved	KIAA0992, SIH002, CGI-151	uc011cjx.2	Q8WX93	OTTHUMG00000161097	ENST00000505667.1:c.2500A>G	4.37:g.169824935A>G	ENSP00000425556:p.Ile834Val	Somatic	64	0		WXS	Illumina HiSeq	.	28	19	NM_001166108	B3KTG2|B5MD56|B7ZMM5|Q7L3E0|Q7Z3W0|Q86WE8|Q8N1M2|Q9UGA0|Q9UQF5|Q9Y2J6|Q9Y3E9	Missense_Mutation	SNP	ENST00000505667.1	37	CCDS54818.1	.	.	.	.	.	.	.	.	.	.	A	13.14	2.148535	0.37923	.	.	ENSG00000129116	ENST00000261509;ENST00000335742;ENST00000505667;ENST00000512127;ENST00000393726;ENST00000507735	T;T;T;T;T;T	0.68025	-0.3;-0.3;-0.3;-0.3;-0.3;-0.3	5.36	4.18	0.49190	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.32328	U	0.006253	T	0.55401	0.1918	L	0.31845	0.965	0.80722	D	1	B;B;B;B	0.25048	0.117;0.079;0.02;0.117	B;B;B;B	0.29716	0.106;0.068;0.068;0.106	T	0.50145	-0.8862	10	0.32370	T	0.25	.	11.2148	0.48819	0.9287:0.0:0.0713:0.0	.	834;1041;435;817	B7ZMM5;Q8WX93;B3KTG2;B2RTX2	.;PALLD_HUMAN;.;.	V	817;659;834;435;110;330	ENSP00000261509:I817V;ENSP00000336735:I659V;ENSP00000425556:I834V;ENSP00000426947:I435V;ENSP00000377327:I110V;ENSP00000424016:I330V	ENSP00000261509:I817V	I	+	1	0	PALLD	170061510	1.000000	0.71417	1.000000	0.80357	0.319000	0.28217	6.155000	0.71833	1.053000	0.40415	-0.256000	0.11100	ATC	.		0.398	PALLD-002	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000363762.1	NM_016081	
ZBTB11	27107	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	3	101395620	101395620	+	Missense_Mutation	SNP	G	G	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr3:101395620G>C	ENST00000312938.4	-	1	719	c.139C>G	c.(139-141)Ctg>Gtg	p.L47V	ZBTB11_ENST00000461821.1_Missense_Mutation_p.L47V|ZBTB11-AS1_ENST00000536865.1_RNA|ZBTB11-AS1_ENST00000609682.1_RNA	NM_014415.3	NP_055230.2	O95625	ZBT11_HUMAN	zinc finger and BTB domain containing 11	47					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(1)|endometrium(6)|kidney(2)|large_intestine(7)|lung(14)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	37						TGGTAATACAGAGTCCCGCCG	0.677																																					p.L47V		.											.	.	.	0			c.C139G						.						12.0	13.0	13.0					3																	101395620		2191	4273	6464	SO:0001583	missense	27107	exon1			AATACAGAGTCCC	U69274	CCDS2943.1	3q12.3	2013-01-09			ENSG00000066422	ENSG00000066422		"""-"", ""BTB/POZ domain containing"", ""Zinc fingers, C2H2-type"""	16740	protein-coding gene	gene with protein product							Standard	NM_014415		Approved	ZNF-U69274, ZNF913	uc003dve.4	O95625	OTTHUMG00000159133	ENST00000312938.4:c.139C>G	3.37:g.101395620G>C	ENSP00000326200:p.Leu47Val	Somatic	17	0		WXS	Illumina HiSeq	.	27	10	NM_014415	Q2NKP9	Missense_Mutation	SNP	ENST00000312938.4	37	CCDS2943.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	18.40|18.40	3.615603|3.615603	0.66672|0.66672	.|.	.|.	ENSG00000066422|ENSG00000256628	ENST00000312938;ENST00000461821|ENST00000536865	T;T|.	0.50001|.	0.76;0.76|.	5.72|5.72	-0.347|-0.347	0.12617|0.12617	.|.	.|0.593832	.|0.12591	.|U	.|0.455556	T|T	0.63803|0.63803	0.2542|0.2542	M|M	0.69358|0.69358	2.11|2.11	0.32193|0.32193	N|N	0.578842|0.578842	D;D|D	0.76494|0.65815	0.998;0.999|0.995	D;D|P	0.78314|0.60415	0.975;0.991|0.874	T|T	0.68334|0.68334	-0.5436|-0.5436	9|9	0.87932|0.87932	D|D	0|0	-7.2738|-7.2738	10.7012|10.7012	0.45928|0.45928	0.3705:0.0:0.6295:0.0|0.3705:0.0:0.6295:0.0	.|.	47;47|44	C9J2L2;O95625|Q9BTX9	.;ZBT11_HUMAN|YC010_HUMAN	V|H	47|44	ENSP00000326200:L47V;ENSP00000417369:L47V|.	ENSP00000326200:L47V|ENSP00000444544:Q44H	L|Q	-|+	1|3	2|2	ZBTB11|AC084198.1	102878310|102878310	0.010000|0.010000	0.17322|0.17322	0.027000|0.027000	0.17364|0.17364	0.914000|0.914000	0.54420|0.54420	0.038000|0.038000	0.13862|0.13862	-0.388000|-0.388000	0.07797|0.07797	-0.218000|-0.218000	0.12543|0.12543	CTG|CAG	.		0.677	ZBTB11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353441.2	NM_014415	
ORM1	5004	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	9	117086362	117086362	+	Missense_Mutation	SNP	A	A	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr9:117086362A>G	ENST00000259396.8	+	3	400	c.322A>G	c.(322-324)Aga>Gga	p.R108G	ORM1_ENST00000538816.1_3'UTR|ORM1_ENST00000477456.1_3'UTR	NM_000607.2	NP_000598.2	P02763	A1AG1_HUMAN	orosomucoid 1	108					acute-phase response (GO:0006953)|inflammatory response (GO:0006954)|regulation of immune system process (GO:0002682)|transport (GO:0006810)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				endometrium(2)|large_intestine(4)|lung(2)	8		Myeloproliferative disorder(63;0.163)			Abiraterone(DB05812)|Acenocoumarol(DB01418)|Ajmaline(DB01426)|Alfentanil(DB00802)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Aprindine(DB01429)|Bupropion(DB01156)|Canagliflozin(DB08907)|Celecoxib(DB00482)|Chlorpromazine(DB00477)|Desipramine(DB01151)|Disopyramide(DB00280)|Doxazosin(DB00590)|Doxepin(DB01142)|Erlotinib(DB00530)|Fluoxetine(DB00472)|Gefitinib(DB00317)|Imatinib(DB00619)|Imipramine(DB00458)|Ivacaftor(DB08820)|Maprotiline(DB00934)|Mirabegron(DB08893)|Nateglinide(DB00731)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Oxycodone(DB00497)|Penbutolol(DB01359)|Pethidine(DB00454)|Phenprocoumon(DB00946)|Pitavastatin(DB08860)|Prazosin(DB00457)|Propranolol(DB00571)|Quinidine(DB00908)|Saquinavir(DB01232)|Tacrolimus(DB00864)|Tamsulosin(DB00706)|Telaprevir(DB05521)|Thalidomide(DB01041)|Trazodone(DB00656)|Vandetanib(DB05294)|Vemurafenib(DB08881)|Vismodegib(DB08828)|Warfarin(DB00682)	GACCATCTCCAGATACGGTGA	0.567																																					p.R108G		.											.	.	.	0			c.A322G						.						123.0	131.0	129.0					9																	117086362		2203	4300	6503	SO:0001583	missense	5004	exon3			ATCTCCAGATACG		CCDS6803.1	9q32	2013-09-19			ENSG00000229314	ENSG00000229314		"""Lipocalins"""	8498	protein-coding gene	gene with protein product		138600					Standard	NM_000607		Approved		uc004bik.4	P02763	OTTHUMG00000021012	ENST00000259396.8:c.322A>G	9.37:g.117086362A>G	ENSP00000259396:p.Arg108Gly	Somatic	37	0		WXS	Illumina HiSeq	.	23	8	NM_000607	B7ZKQ5|Q5T539|Q5U067|Q8TC16	Missense_Mutation	SNP	ENST00000259396.8	37	CCDS6803.1	.	.	.	.	.	.	.	.	.	.	A	10.22	1.290708	0.23564	.	.	ENSG00000229314	ENST00000259396	T	0.07800	3.16	3.39	-0.283	0.12874	Calycin-like (1);Lipocalin/cytosolic fatty-acid binding protein domain (1);Calycin (1);	0.729034	0.13178	N	0.407765	T	0.06508	0.0167	L	0.36672	1.1	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.31833	-0.9929	10	0.72032	D	0.01	-0.4749	5.7846	0.18326	0.6202:0.0:0.3798:0.0	.	108	P02763	A1AG1_HUMAN	G	108	ENSP00000259396:R108G	ENSP00000259396:R108G	R	+	1	2	ORM1	116126183	0.020000	0.18652	0.001000	0.08648	0.060000	0.15804	2.102000	0.41796	-0.055000	0.13244	0.260000	0.18958	AGA	.		0.567	ORM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055426.1		
HNRNPA1	3178	hgsc.bcm.edu	37	12	54675101	54675101	+	Intron	SNP	T	T	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr12:54675101T>C	ENST00000340913.6	+	2	68				HNRNPA1_ENST00000330752.8_Intron|HNRNPA1_ENST00000546500.1_Intron|HNRNPA1_ENST00000547276.1_Intron|RP11-968A15.8_ENST00000553061.1_RNA|CBX5_ENST00000209875.4_5'Flank|RP11-968A15.2_ENST00000547177.1_RNA	NM_002136.2|NM_031157.2	NP_002127.1|NP_112420.1	P09651	ROA1_HUMAN	heterogeneous nuclear ribonucleoprotein A1						cell death (GO:0008219)|gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|mRNA transport (GO:0051028)|nuclear export (GO:0051168)|nuclear import (GO:0051170)|RNA export from nucleus (GO:0006405)|RNA splicing (GO:0008380)|viral process (GO:0016032)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|spliceosomal complex (GO:0005681)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)|single-stranded RNA binding (GO:0003727)			endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	20						GTGTCTAGTTTTTCTTTTCCT	0.493																																					.	Colon(83;502 1289 8436 16406 24870)	.											.	.	.	0			.						.																																			SO:0001627	intron_variant	664709	.			CTAGTTTTTCTTT	BC009600	CCDS41793.1, CCDS44909.1	12q13.1	2013-10-11		2007-08-16	ENSG00000135486	ENSG00000135486		"""RNA binding motif (RRM) containing"""	5031	protein-coding gene	gene with protein product		164017		HNRPA1		1733858	Standard	XR_245923		Approved	hnRNPA1, hnRNP-A1	uc001sfl.3	P09651		ENST00000340913.6:c.16-69T>C	12.37:g.54675101T>C		Somatic	83	0		WXS	Illumina HiSeq	.	30	12	.	A8K4Z8|Q3MIB7|Q6PJZ7	RNA	SNP	ENST00000340913.6	37	CCDS44909.1																																																																																			.		0.493	HNRNPA1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000405480.1	NM_031157	
ARL8A	127829	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	202107156	202107156	+	Missense_Mutation	SNP	A	A	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr1:202107156A>G	ENST00000272217.2	-	3	383	c.215T>C	c.(214-216)aTt>aCt	p.I72T	ARL8A_ENST00000486225.1_5'UTR	NM_001256129.1|NM_138795.3	NP_001243058.1|NP_620150.1	Q96BM9	ARL8A_HUMAN	ADP-ribosylation factor-like 8A	72					chromosome segregation (GO:0007059)|GTP catabolic process (GO:0006184)|mitotic nuclear division (GO:0007067)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|midbody (GO:0030496)|spindle midzone (GO:0051233)	alpha-tubulin binding (GO:0043014)|beta-tubulin binding (GO:0048487)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)			large_intestine(1)|lung(2)|ovary(2)|skin(1)	6						CTGTCCCCCAATGTCCCAGAG	0.597																																					p.I72T		.											.	.	.	0			c.T215C						.						63.0	55.0	58.0					1																	202107156		2203	4300	6503	SO:0001583	missense	127829	exon3			CCCCCAATGTCCC	BC015408	CCDS1421.1, CCDS73004.1	1q32.1	2014-05-09	2005-11-03	2005-11-03	ENSG00000143862	ENSG00000143862		"""ADP-ribosylation factors-like"", ""ADP-ribosylation factors"""	25192	protein-coding gene	gene with protein product			"""ADP-ribosylation factor-like 10B"""	ARL10B		8889548	Standard	NM_001256129		Approved	FLJ45195, Gie2	uc001gxk.2	Q96BM9	OTTHUMG00000035923	ENST00000272217.2:c.215T>C	1.37:g.202107156A>G	ENSP00000272217:p.Ile72Thr	Somatic	31	0		WXS	Illumina HiSeq	.	38	27	NM_138795	B3KXD0	Missense_Mutation	SNP	ENST00000272217.2	37	CCDS1421.1	.	.	.	.	.	.	.	.	.	.	A	23.1	4.379776	0.82682	.	.	ENSG00000143862	ENST00000272217	T	0.68181	-0.31	4.55	4.55	0.56014	Small GTP-binding protein domain (1);	0.060552	0.64402	D	0.000006	T	0.76062	0.3935	L	0.47716	1.5	0.80722	D	1	D	0.69078	0.997	D	0.85130	0.997	T	0.78758	-0.2079	10	0.87932	D	0	-6.4729	13.5562	0.61761	1.0:0.0:0.0:0.0	.	72	Q96BM9	ARL8A_HUMAN	T	72	ENSP00000272217:I72T	ENSP00000272217:I72T	I	-	2	0	ARL8A	200373779	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.431000	0.80335	1.682000	0.51000	0.383000	0.25322	ATT	.		0.597	ARL8A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087493.1	NM_138795	
UBE3D	90025	hgsc.bcm.edu	37	6	83667047	83667047	+	Missense_Mutation	SNP	C	C	T	rs557165335		TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr6:83667047C>T	ENST00000369747.3	-	9	1255	c.1133G>A	c.(1132-1134)cGt>cAt	p.R378H		NM_198920.1	NP_944602.1	Q7Z6J8	UBE3D_HUMAN	ubiquitin protein ligase E3D	378	HECT-like.				protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)										GGAATTCACACGGCGAAGGGA	0.463													T|||	1	0.000199681	0.0	0.0	5008	,	,		17808	0.001		0.0	False		,,,				2504	0.0				p.R378H		.											UBE2CBP,NS,carcinoma,0,1	UBE2CBP	0	0			c.G1133A						.						118.0	97.0	104.0					6																	83667047		2203	4300	6503	SO:0001583	missense	90025	exon9			TTCACACGGCGAA	AL137544	CCDS34491.1	6q15	2012-02-24	2012-02-24	2012-02-24	ENSG00000118420	ENSG00000118420			21381	protein-coding gene	gene with protein product	"""UBCH10 binding protein with a hect-like domain"""	612495	"""chromosome 6 open reading frame 157"", ""ubiquitin-conjugating enzyme E2C binding protein"""	C6orf157, UBE2CBP		15749827	Standard	NM_198920		Approved	DKFZp434A1520, H10BH, YJR141W	uc003pjp.2	Q7Z6J8	OTTHUMG00000015108	ENST00000369747.3:c.1133G>A	6.37:g.83667047C>T	ENSP00000358762:p.Arg378His	Somatic	58	0		WXS	Illumina HiSeq	.	47	2	NM_198920	B4DP63|Q5T4W2|Q6IPR4|Q75UG0|Q9NT42	Missense_Mutation	SNP	ENST00000369747.3	37	CCDS34491.1	.	.	.	.	.	.	.	.	.	.	T	0.816	-0.750263	0.03041	.	.	ENSG00000118420	ENST00000369747	T	0.28895	1.59	5.57	-8.9	0.00782	.	0.689394	0.16128	N	0.228309	T	0.03434	0.0099	N	0.14661	0.345	0.09310	N	0.999996	B	0.06786	0.001	B	0.06405	0.002	T	0.27331	-1.0077	10	0.15499	T	0.54	10.6038	10.3705	0.44051	0.2054:0.6096:0.0:0.1851	.	378	Q7Z6J8	UB2CB_HUMAN	H	378	ENSP00000358762:R378H	ENSP00000358762:R378H	R	-	2	0	UBE2CBP	83723766	0.000000	0.05858	0.002000	0.10522	0.013000	0.08279	-1.325000	0.02687	-2.392000	0.00585	-1.390000	0.01156	CGT	.		0.463	UBE3D-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041347.7	NM_198920	
PUM1	9698	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	31437697	31437697	+	Missense_Mutation	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr1:31437697A>C	ENST00000257075.5	-	14	2240	c.2147T>G	c.(2146-2148)cTt>cGt	p.L716R	PUM1_ENST00000373742.2_Missense_Mutation_p.L657R|PUM1_ENST00000423018.2_Missense_Mutation_p.L572R|PUM1_ENST00000426105.2_Missense_Mutation_p.L716R|PUM1_ENST00000490546.1_5'Flank|PUM1_ENST00000373747.3_Missense_Mutation_p.L717R|PUM1_ENST00000440538.2_Missense_Mutation_p.L690R|PUM1_ENST00000424085.2_Missense_Mutation_p.L474R|PUM1_ENST00000373741.4_Missense_Mutation_p.L752R	NM_014676.2	NP_055491.1	Q14671	PUM1_HUMAN	pumilio RNA-binding family member 1	716	Ser-rich.				membrane organization (GO:0061024)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of translation (GO:0006417)	cytosol (GO:0005829)	poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(2)|endometrium(8)|kidney(4)|large_intestine(8)|lung(17)|ovary(2)|pancreas(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	48		Colorectal(325;0.0211)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0308)|all_neural(195;0.0381)|Breast(348;0.0848)|Medulloblastoma(700;0.123)		STAD - Stomach adenocarcinoma(196;0.0232)|READ - Rectum adenocarcinoma(331;0.0681)		CCTCTTATAAAGGTCACTGCT	0.512																																					p.L716R		.											.	.	.	0			c.T2147G						.						83.0	85.0	84.0					1																	31437697		2203	4300	6503	SO:0001583	missense	9698	exon14			TTATAAAGGTCAC	AF315592	CCDS338.1, CCDS44099.1	1p35.2	2013-09-02	2013-09-02		ENSG00000134644	ENSG00000134644			14957	protein-coding gene	gene with protein product		607204	"""pumilio (Drosophila) homolog 1"", ""pumilio homolog 1 (Drosophila)"""				Standard	NM_001020658		Approved	PUMH1, KIAA0099	uc001bsh.1	Q14671	OTTHUMG00000003795	ENST00000257075.5:c.2147T>G	1.37:g.31437697A>C	ENSP00000257075:p.Leu716Arg	Somatic	68	0		WXS	Illumina HiSeq	.	66	32	NM_014676	A8K6W4|B4DG92|D3DPN3|E9PCJ0|Q53HH5|Q5VXY7|Q9HAN1	Missense_Mutation	SNP	ENST00000257075.5	37	CCDS338.1	.	.	.	.	.	.	.	.	.	.	A	17.33	3.362747	0.61403	.	.	ENSG00000134644	ENST00000424085;ENST00000257075;ENST00000373747;ENST00000373749;ENST00000426105;ENST00000440538;ENST00000373741;ENST00000423018;ENST00000373742	T;T;T;T;T;T;T;T	0.20463	2.14;2.07;2.34;2.34;2.42;2.33;2.46;2.08	5.54	4.38	0.52667	.	0.122285	0.64402	D	0.000020	T	0.33933	0.0880	L	0.48642	1.525	0.58432	D	0.999992	D;D;P;D;P;B;P	0.69078	0.985;0.995;0.865;0.997;0.716;0.159;0.716	P;D;B;D;P;B;P	0.69479	0.783;0.922;0.397;0.964;0.602;0.224;0.501	T	0.03503	-1.1030	10	0.18710	T	0.47	-3.1937	11.7192	0.51672	0.8675:0.0:0.0:0.1324	.	657;572;752;690;716;716;716	B4DG92;E7EWT3;Q5T1Z8;Q14671-2;Q14671;E9PCJ0;Q53HH5	.;.;.;.;PUM1_HUMAN;.;.	R	474;716;717;454;716;690;752;572;657	ENSP00000400141:L474R;ENSP00000257075:L716R;ENSP00000362852:L717R;ENSP00000391723:L716R;ENSP00000401777:L690R;ENSP00000362846:L752R;ENSP00000399440:L572R;ENSP00000362847:L657R	ENSP00000257075:L716R	L	-	2	0	PUM1	31210284	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.880000	0.63107	0.900000	0.36469	0.533000	0.62120	CTT	.		0.512	PUM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000010671.1		
FSCN1	6624	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	7	5632703	5632703	+	Missense_Mutation	SNP	T	T	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr7:5632703T>C	ENST00000382361.3	+	1	250	c.136T>C	c.(136-138)Tgg>Cgg	p.W46R	FSCN1_ENST00000340250.6_Intron	NM_003088.3	NP_003079.1	Q16658	FSCN1_HUMAN	fascin actin-bundling protein 1	46					actin cytoskeleton organization (GO:0030036)|actin filament bundle assembly (GO:0051017)|cell migration (GO:0016477)|cell motility (GO:0048870)|cell proliferation (GO:0008283)	actin cytoskeleton (GO:0015629)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|invadopodium (GO:0071437)|stress fiber (GO:0001725)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|drug binding (GO:0008144)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|kidney(3)|large_intestine(1)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)	9		Ovarian(82;0.0694)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0986)|OV - Ovarian serous cystadenocarcinoma(56;1.21e-13)		GAAGCAGATCTGGACGCTGGA	0.672																																					p.W46R		.											.	.	.	0			c.T136C						.						12.0	11.0	11.0					7																	5632703		2167	4252	6419	SO:0001583	missense	6624	exon1			CAGATCTGGACGC	U03057	CCDS5342.1	7p22	2014-02-03	2014-02-03	2002-09-20	ENSG00000075618	ENSG00000075618		"""Fascins"""	11148	protein-coding gene	gene with protein product	"""Singed, drosophila, homolog-like"", ""actin bundling protein"""	602689	"""singed (Drosophila)-like (sea urchin fascin homolog like)"", ""fascin homolog 1, actin-bundling protein (Strongylocentrotus purpuratus)"""	SNL		8068206, 10783262	Standard	NM_003088		Approved	p55, FLJ38511	uc003sou.3	Q16658	OTTHUMG00000090599	ENST00000382361.3:c.136T>C	7.37:g.5632703T>C	ENSP00000371798:p.Trp46Arg	Somatic	53	0		WXS	Illumina HiSeq	.	35	14	NM_003088	A6NI89|B2RE97|Q96IC5|Q96IH1|Q9BRF1	Missense_Mutation	SNP	ENST00000382361.3	37	CCDS5342.1	.	.	.	.	.	.	.	.	.	.	T	14.65	2.599844	0.46318	.	.	ENSG00000075618	ENST00000382361	T	0.31510	1.49	3.37	3.37	0.38596	Fascin domain (1);Actin cross-linking (1);	0.074988	0.64402	D	0.000019	T	0.59878	0.2226	M	0.91249	3.19	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.67007	-0.5779	10	0.87932	D	0	-3.9623	9.7912	0.40706	0.0:0.0:0.0:1.0	.	46	Q16658	FSCN1_HUMAN	R	46	ENSP00000371798:W46R	ENSP00000371798:W46R	W	+	1	0	FSCN1	5599229	1.000000	0.71417	1.000000	0.80357	0.314000	0.28054	5.631000	0.67812	1.413000	0.46997	0.379000	0.24179	TGG	.		0.672	FSCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207153.3	NM_003088	
GDPD4	220032	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	11	76954813	76954813	+	Silent	SNP	G	G	A	rs199737312		TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr11:76954813G>A	ENST00000376217.2	-	12	1417	c.1167C>T	c.(1165-1167)tcC>tcT	p.S389S	GDPD4_ENST00000315938.4_Silent_p.S389S			Q6W3E5	GDPD4_HUMAN	glycerophosphodiester phosphodiesterase domain containing 4	389	GP-PDE.				glycerol metabolic process (GO:0006071)|lipid metabolic process (GO:0006629)	integral component of membrane (GO:0016021)	glycerophosphodiester phosphodiesterase activity (GO:0008889)|metal ion binding (GO:0046872)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(8)|prostate(1)|skin(1)	20						GGGTTTCAATGGATACTAAAC	0.413													G|||	1	0.000199681	0.0	0.0	5008	,	,		16134	0.0		0.0	False		,,,				2504	0.001				p.S389S		.											.	.	.	0			c.C1167T						.						115.0	107.0	110.0					11																	76954813		2200	4292	6492	SO:0001819	synonymous_variant	220032	exon12			TTCAATGGATACT	AY326450	CCDS8249.1	11q13.5	2008-02-05			ENSG00000178795	ENSG00000178795			24849	protein-coding gene	gene with protein product							Standard	NM_182833		Approved	GDE6	uc001oyf.3	Q6W3E5	OTTHUMG00000165136	ENST00000376217.2:c.1167C>T	11.37:g.76954813G>A		Somatic	138	0		WXS	Illumina HiSeq	.	68	22	NM_182833	Q7Z5B0	Silent	SNP	ENST00000376217.2	37																																																																																				0.001		0.413	GDPD4-002	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000382075.1	NM_182833	
LRP1	4035	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	12	57584755	57584755	+	Missense_Mutation	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr12:57584755A>C	ENST00000243077.3	+	43	7665	c.7199A>C	c.(7198-7200)aAg>aCg	p.K2400T		NM_002332.2	NP_002323.2	Q07954	LRP1_HUMAN	low density lipoprotein receptor-related protein 1	2400					aging (GO:0007568)|aorta morphogenesis (GO:0035909)|apoptotic cell clearance (GO:0043277)|beta-amyloid clearance (GO:0097242)|cell proliferation (GO:0008283)|cholesterol metabolic process (GO:0008203)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of platelet-derived growth factor receptor-beta signaling pathway (GO:2000587)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of Wnt signaling pathway (GO:0030178)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of lipid transport (GO:0032370)|positive regulation of protein transport (GO:0051222)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|receptor-mediated endocytosis (GO:0006898)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cholesterol transport (GO:0032374)|regulation of phospholipase A2 activity (GO:0032429)|retinoid metabolic process (GO:0001523)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	apolipoprotein binding (GO:0034185)|calcium ion binding (GO:0005509)|lipoprotein particle receptor binding (GO:0070325)|lipoprotein transporter activity (GO:0042954)|poly(A) RNA binding (GO:0044822)|protein complex binding (GO:0032403)|receptor activity (GO:0004872)			NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(33)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(26)|lung(58)|ovary(10)|pancreas(2)|prostate(11)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	184				BRCA - Breast invasive adenocarcinoma(357;0.0103)	Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031)	ACCCTGGACAAGATCGAGCGG	0.642																																					p.K2400T		.											.	.	.	0			c.A7199C						.						84.0	67.0	73.0					12																	57584755		2203	4300	6503	SO:0001583	missense	4035	exon43			TGGACAAGATCGA	X13916	CCDS8932.1	12q13.3	2013-05-28	2010-01-26		ENSG00000123384	ENSG00000123384		"""CD molecules"", ""Low density lipoprotein receptors"""	6692	protein-coding gene	gene with protein product		107770	"""alpha-2-macroglobulin receptor"""	APR, A2MR		2548950	Standard	NM_002332		Approved	LRP, CD91, LRP1A, APOER	uc001snd.3	Q07954	OTTHUMG00000044412	ENST00000243077.3:c.7199A>C	12.37:g.57584755A>C	ENSP00000243077:p.Lys2400Thr	Somatic	16	0		WXS	Illumina HiSeq	.	14	7	NM_002332	Q2PP12|Q86SW0|Q8IVG8	Missense_Mutation	SNP	ENST00000243077.3	37	CCDS8932.1	.	.	.	.	.	.	.	.	.	.	a	29.5	5.009151	0.93346	.	.	ENSG00000123384	ENST00000243077	D	0.96073	-3.9	4.93	4.93	0.64822	Six-bladed beta-propeller, TolB-like (1);	0.000000	0.64402	D	0.000001	D	0.96228	0.8770	L	0.48877	1.53	0.80722	D	1	D	0.71674	0.998	D	0.80764	0.994	D	0.95512	0.8587	10	0.37606	T	0.19	.	13.7412	0.62849	1.0:0.0:0.0:0.0	.	2400	Q07954	LRP1_HUMAN	T	2400	ENSP00000243077:K2400T	ENSP00000243077:K2400T	K	+	2	0	LRP1	55871022	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	9.119000	0.94362	2.070000	0.61991	0.439000	0.28862	AAG	.		0.642	LRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412772.2	NM_002332	
DIP2C	22982	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	10	387246	387246	+	Silent	SNP	G	G	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr10:387246G>T	ENST00000280886.6	-	29	3564	c.3477C>A	c.(3475-3477)gcC>gcA	p.A1159A		NM_014974.2	NP_055789.1	Q9Y2E4	DIP2C_HUMAN	DIP2 disco-interacting protein 2 homolog C (Drosophila)	1159						nucleus (GO:0005634)	catalytic activity (GO:0003824)			breast(8)|endometrium(6)|kidney(10)|large_intestine(13)|lung(26)|ovary(3)|prostate(6)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(4)	81		all_cancers(4;0.00336)|all_lung(4;0.00732)|Lung NSC(4;0.00785)|all_epithelial(10;0.0159)|Colorectal(49;0.235)	OV - Ovarian serous cystadenocarcinoma(33;0.136)	Epithelial(11;0.0123)|all cancers(11;0.0467)|Lung(33;0.0864)|OV - Ovarian serous cystadenocarcinoma(14;0.106)		AACGGCAGAAGGCACTGGTGG	0.552																																					p.A1159A		.											.	.	.	0			c.C3477A						.						144.0	118.0	127.0					10																	387246		2203	4300	6503	SO:0001819	synonymous_variant	22982	exon29			GCAGAAGGCACTG	BC035216	CCDS7054.1	10p15.3	2006-01-13	2006-01-13	2006-01-13	ENSG00000151240	ENSG00000151240			29150	protein-coding gene	gene with protein product		611380	"""KIAA0934"""	KIAA0934			Standard	NM_014974		Approved		uc001ifp.3	Q9Y2E4	OTTHUMG00000017532	ENST00000280886.6:c.3477C>A	10.37:g.387246G>T		Somatic	71	0		WXS	Illumina HiSeq	.	38	14	NM_014974	B4DPI5|Q5SS78	Silent	SNP	ENST00000280886.6	37	CCDS7054.1																																																																																			.		0.552	DIP2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046389.1	NM_014974	
NREP	9315	hgsc.bcm.edu;ucsc.edu	37	5	111065333	111065333	+	3'UTR	SNP	T	T	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr5:111065333T>A	ENST00000379671.3	-	0	1756				NREP_ENST00000447165.2_3'UTR|NREP_ENST00000509025.1_Intron|NREP_ENST00000257435.7_3'UTR|NREP_ENST00000446294.2_3'UTR|STARD4-AS1_ENST00000513221.1_RNA|STARD4-AS1_ENST00000500779.2_RNA|NREP_ENST00000507742.1_5'Flank	NM_001142478.1	NP_001135950.1	Q16612	NREP_HUMAN	neuronal regeneration related protein						axon regeneration (GO:0031103)|regulation of neuron differentiation (GO:0045664)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)	cytoplasm (GO:0005737)|nucleus (GO:0005634)											GAACAAGGCCTGCCCTGTCAA	0.423																																					.		.											.	.	.	0			.						.																																			SO:0001624	3_prime_UTR_variant	100505678	.			AAGGCCTGCCCTG	AF119859	CCDS4105.1, CCDS47255.1	5q22.1	2012-12-07	2012-12-07	2012-01-23	ENSG00000134986	ENSG00000134986			16834	protein-coding gene	gene with protein product	"""neuronal protein 3.1"""	607332	"""chromosome 5 open reading frame 13"", ""neuronal regeneration related protein homolog (rat)"""	C5orf13		8261136, 10981724, 15485502	Standard	NM_004772		Approved	P311, D4S114, PRO1873, PTZ17, SEZ17	uc011cvr.2	Q16612	OTTHUMG00000128795	ENST00000379671.3:c.*1285A>T	5.37:g.111065333T>A		Somatic	88	0		WXS	Illumina HiSeq	.	59	32	.	B2RDN8|B7Z5D2|D3DSZ8	RNA	SNP	ENST00000379671.3	37	CCDS4105.1																																																																																			.		0.423	NREP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250722.1	NM_004772	
UBAP2	55833	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	9	33927945	33927945	+	Missense_Mutation	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr9:33927945A>C	ENST00000379238.1	-	20	2338	c.2221T>G	c.(2221-2223)Ttc>Gtc	p.F741V	UBAP2_ENST00000539807.1_Missense_Mutation_p.F496V|UBAP2_ENST00000418786.2_Silent_p.P665P|UBAP2_ENST00000379235.1_5'UTR|UBAP2_ENST00000360802.1_Missense_Mutation_p.F741V|UBAP2_ENST00000379239.4_Missense_Mutation_p.F474V|UBAP2_ENST00000449054.1_Missense_Mutation_p.F741V					ubiquitin associated protein 2											endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(13)|ovary(3)|stomach(1)	32			LUSC - Lung squamous cell carcinoma(29;0.00575)	GBM - Glioblastoma multiforme(74;0.168)		GCCGTGGAGAAGGTGGCTGAG	0.617																																					p.F741V		.											.	.	.	0			c.T2221G						.						82.0	72.0	75.0					9																	33927945		2203	4300	6503	SO:0001583	missense	55833	exon20			TGGAGAAGGTGGC	AB040924	CCDS6547.1, CCDS75828.1	9p11.2	2008-02-05			ENSG00000137073	ENSG00000137073			14185	protein-coding gene	gene with protein product						8871400	Standard	NM_018449		Approved	KIAA1491, bA176F3.5, FLJ22435	uc003ztq.1	Q5T6F2	OTTHUMG00000000427	ENST00000379238.1:c.2221T>G	9.37:g.33927945A>C	ENSP00000368540:p.Phe741Val	Somatic	47	0		WXS	Illumina HiSeq	.	24	10	NM_018449		Missense_Mutation	SNP	ENST00000379238.1	37	CCDS6547.1	.	.	.	.	.	.	.	.	.	.	A	10.99	1.508101	0.27036	.	.	ENSG00000137073	ENST00000379238;ENST00000449054;ENST00000360802;ENST00000431417;ENST00000379239;ENST00000539807;ENST00000351580	T;T;T;T;T	0.35605	1.3;1.3;1.3;1.3;1.3	5.57	5.57	0.84162	.	0.432253	0.29314	N	0.012504	T	0.38081	0.1027	M	0.74881	2.28	0.80722	D	1	P;P;P;P;B	0.35575	0.51;0.51;0.51;0.51;0.376	B;B;B;B;B	0.32864	0.154;0.154;0.154;0.154;0.073	T	0.24584	-1.0156	10	0.16896	T	0.51	-10.8851	15.3872	0.74711	1.0:0.0:0.0:0.0	.	666;496;474;650;741	F5H4D5;F5H2U4;A6NCA8;F5H2C8;Q5T6F2	.;.;.;.;UBAP2_HUMAN	V	741;741;741;650;474;496;177	ENSP00000368540:F741V;ENSP00000416932:F741V;ENSP00000354039:F741V;ENSP00000368541:F474V;ENSP00000439329:F496V	ENSP00000259602:F177V	F	-	1	0	UBAP2	33917945	1.000000	0.71417	0.995000	0.50966	0.057000	0.15508	5.019000	0.64060	2.119000	0.64992	0.533000	0.62120	TTC	.		0.617	UBAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001071.1	NM_018449	
TAS2R9	50835	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	12	10962375	10962375	+	Silent	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr12:10962375A>C	ENST00000240691.2	-	1	392	c.300T>G	c.(298-300)acT>acG	p.T100T	TAS2R8_ENST00000240615.2_5'Flank	NM_023917.2	NP_076406.1	Q9NYW1	TA2R9_HUMAN	taste receptor, type 2, member 9	100					detection of chemical stimulus involved in sensory perception of taste (GO:0050912)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	taste receptor activity (GO:0008527)			endometrium(1)|kidney(1)|large_intestine(4)|lung(7)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17						TGAGGCAAGAAGTAAACCAGA	0.398																																					p.T100T		.											.	.	.	0			c.T300G						.						91.0	90.0	90.0					12																	10962375		2203	4300	6503	SO:0001819	synonymous_variant	50835	exon1			GCAAGAAGTAAAC	AF227135	CCDS8633.1	12p13	2012-08-22			ENSG00000121381	ENSG00000121381		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	14917	protein-coding gene	gene with protein product		604795				10761934, 10766242	Standard	NM_023917		Approved	T2R9, TRB6	uc001qyx.3	Q9NYW1	OTTHUMG00000168507	ENST00000240691.2:c.300T>G	12.37:g.10962375A>C		Somatic	72	0		WXS	Illumina HiSeq	.	56	17	NM_023917	Q502V7|Q50KT0|Q50KT1|Q645W9	Silent	SNP	ENST00000240691.2	37	CCDS8633.1																																																																																			.		0.398	TAS2R9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399933.1		
DCTN6	10671	hgsc.bcm.edu	37	8	30013852	30013852	+	5'UTR	SNP	C	C	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr8:30013852C>G	ENST00000221114.3	+	0	40				DCTN6_ENST00000520829.1_5'Flank|RP11-51J9.5_ENST00000607315.1_lincRNA	NM_006571.3	NP_006562.1	O00399	DCTN6_HUMAN	dynactin 6						antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|mitotic spindle organization (GO:0007052)	centrosome (GO:0005813)|cytosol (GO:0005829)|dynactin complex (GO:0005869)|kinetochore (GO:0000776)				endometrium(1)|lung(1)|ovary(1)|prostate(1)	4				KIRC - Kidney renal clear cell carcinoma(542;0.099)|Kidney(114;0.119)		GGAATTATCGCTCTACCCAGG	0.597																																					.		.											.	.	.	0			.						.						71.0	55.0	60.0					8																	30013852		2203	4297	6500	SO:0001623	5_prime_UTR_variant	10671	.			TTATCGCTCTACC	D84145	CCDS6076.1	8p12-p11	2003-03-20			ENSG00000104671	ENSG00000104671			16964	protein-coding gene	gene with protein product		612963				9168138	Standard	NM_006571		Approved	WS-3	uc003xhy.3	O00399	OTTHUMG00000163828	ENST00000221114.3:c.-48C>G	8.37:g.30013852C>G		Somatic	56	0		WXS	Illumina HiSeq	.	40	12	.	B2RAC1	RNA	SNP	ENST00000221114.3	37	CCDS6076.1																																																																																			.		0.597	DCTN6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375815.2	NM_006571	
BFSP1	631	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	20	17475396	17475396	+	Missense_Mutation	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr20:17475396A>C	ENST00000377873.3	-	8	1360	c.1321T>G	c.(1321-1323)Ttt>Gtt	p.F441V	BFSP1_ENST00000377868.2_Missense_Mutation_p.F316V|BFSP1_ENST00000544874.1_Missense_Mutation_p.F302V|BFSP1_ENST00000536626.1_Missense_Mutation_p.F302V	NM_001195.3	NP_001186.1	Q12934	BFSP1_HUMAN	beaded filament structural protein 1, filensin	441	Tail.				cell maturation (GO:0048469)|lens fiber cell development (GO:0070307)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|intermediate filament (GO:0005882)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	structural constituent of cytoskeleton (GO:0005200)|structural constituent of eye lens (GO:0005212)			central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(7)|prostate(2)|skin(1)|stomach(1)	18						AGTTTCCCAAAGCCTTTGCTT	0.498																																					p.F441V		.											.	.	.	0			c.T1321G						.						127.0	125.0	126.0					20																	17475396		2203	4300	6503	SO:0001583	missense	631	exon8			TCCCAAAGCCTTT	Y16717	CCDS13126.1, CCDS54448.1, CCDS63229.1	20p12.1	2014-06-05			ENSG00000125864	ENSG00000125864		"""Intermediate filaments type VI, eye lens intermediate filaments"""	1040	protein-coding gene	gene with protein product		603307				9787085	Standard	NM_001161705		Approved	CP94, CP115, LIFL-H, filensin	uc002wpo.3	Q12934	OTTHUMG00000031940	ENST00000377873.3:c.1321T>G	20.37:g.17475396A>C	ENSP00000367104:p.Phe441Val	Somatic	27	0		WXS	Illumina HiSeq	.	27	15	NM_001195	F5H0G1|O43595|O76034|O95676|Q8IVZ6|Q9HBX4	Missense_Mutation	SNP	ENST00000377873.3	37	CCDS13126.1	.	.	.	.	.	.	.	.	.	.	A	15.81	2.944423	0.53079	.	.	ENSG00000125864	ENST00000377873;ENST00000377868;ENST00000536626;ENST00000544874	T;T;T;T	0.54866	0.55;0.55;0.55;0.55	5.21	5.21	0.72293	.	0.108147	0.64402	D	0.000004	T	0.67458	0.2895	L	0.60455	1.87	0.53688	D	0.999979	D;D	0.76494	0.983;0.999	P;D	0.69142	0.755;0.962	T	0.70784	-0.4778	10	0.72032	D	0.01	-9.0027	13.9173	0.63908	1.0:0.0:0.0:0.0	.	316;441	Q12934-2;Q12934	.;BFSP1_HUMAN	V	441;316;302;302	ENSP00000367104:F441V;ENSP00000367099:F316V;ENSP00000442522:F302V;ENSP00000439870:F302V	ENSP00000367099:F316V	F	-	1	0	BFSP1	17423396	1.000000	0.71417	0.989000	0.46669	0.020000	0.10135	6.819000	0.75262	1.948000	0.56530	0.533000	0.62120	TTT	.		0.498	BFSP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078119.6	NM_001195	
PTDSS2	81490	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	11	488603	488603	+	Silent	SNP	G	G	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr11:488603G>A	ENST00000308020.5	+	8	986	c.810G>A	c.(808-810)ctG>ctA	p.L270L		NM_030783.1	NP_110410.1	Q9BVG9	PTSS2_HUMAN	phosphatidylserine synthase 2	270					glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylserine biosynthetic process (GO:0006659)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	CDP-diacylglycerol-serine O-phosphatidyltransferase activity (GO:0003882)			autonomic_ganglia(1)|breast(1)|cervix(2)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|skin(1)	9		all_cancers(49;1.59e-06)|all_epithelial(84;0.000256)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;2.76e-26)|Epithelial(43;2.56e-25)|OV - Ovarian serous cystadenocarcinoma(40;7.54e-20)|BRCA - Breast invasive adenocarcinoma(625;8.76e-05)|Lung(200;0.0407)|LUSC - Lung squamous cell carcinoma(625;0.0735)	Phosphatidylserine(DB00144)	GGCTGTCCCTGAAGACGTACA	0.632																																					p.L270L		.											.	.	.	0			c.G810A						.						103.0	83.0	90.0					11																	488603		2202	4300	6502	SO:0001819	synonymous_variant	81490	exon8			GTCCCTGAAGACG	BC001210	CCDS7696.1	11p15	2008-05-02			ENSG00000174915	ENSG00000174915			15463	protein-coding gene	gene with protein product		612793				14984733	Standard	NM_030783		Approved	PSS2	uc001lpj.3	Q9BVG9	OTTHUMG00000119087	ENST00000308020.5:c.810G>A	11.37:g.488603G>A		Somatic	35	0		WXS	Illumina HiSeq	.	19	8	NM_030783		Silent	SNP	ENST00000308020.5	37	CCDS7696.1																																																																																			.		0.632	PTDSS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239301.2		
PCDHB7	56129	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	5	140554443	140554443	+	Missense_Mutation	SNP	C	C	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr5:140554443C>T	ENST00000231137.3	+	1	2201	c.2027C>T	c.(2026-2028)gCg>gTg	p.A676V	PCDHB8_ENST00000239444.2_5'Flank	NM_018940.2	NP_061763.1	Q9Y5E2	PCDB7_HUMAN	protocadherin beta 7	676					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(20)|lung(54)|ovary(5)|prostate(7)|skin(7)|upper_aerodigestive_tract(4)|urinary_tract(1)	119			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CTCCCGGAGGCGGCCCCGGAC	0.692																																					p.A676V		.											.	.	.	0			c.C2027T						.						48.0	79.0	68.0					5																	140554443		2185	4283	6468	SO:0001583	missense	56129	exon1			CGGAGGCGGCCCC	AF152500	CCDS4249.1	5q31	2010-01-26			ENSG00000113212	ENSG00000113212		"""Cadherins / Protocadherins : Clustered"""	8692	other	protocadherin		606333				10380929	Standard	NM_018940		Approved	PCDH-BETA7	uc003lit.3	Q9Y5E2	OTTHUMG00000129608	ENST00000231137.3:c.2027C>T	5.37:g.140554443C>T	ENSP00000231137:p.Ala676Val	Somatic	201	0		WXS	Illumina HiSeq	.	146	18	NM_018940	A1L3Y8	Missense_Mutation	SNP	ENST00000231137.3	37	CCDS4249.1	.	.	.	.	.	.	.	.	.	.	C	4.037	0.004475	0.07866	.	.	ENSG00000113212	ENST00000231137	T	0.51817	0.69	3.77	-3.6	0.04570	.	.	.	.	.	T	0.17704	0.0425	N	0.10707	0.03	0.09310	N	1	B	0.15473	0.013	B	0.10450	0.005	T	0.31641	-0.9936	9	0.02654	T	1	.	4.7814	0.13204	0.0:0.2545:0.3902:0.3553	.	676	Q9Y5E2	PCDB7_HUMAN	V	676	ENSP00000231137:A676V	ENSP00000231137:A676V	A	+	2	0	PCDHB7	140534627	0.000000	0.05858	0.077000	0.20336	0.306000	0.27790	-0.419000	0.07071	-0.428000	0.07339	0.449000	0.29647	GCG	.		0.692	PCDHB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251803.2	NM_018940	
CHD7	55636	hgsc.bcm.edu	37	8	61713037	61713037	+	Missense_Mutation	SNP	G	G	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr8:61713037G>A	ENST00000423902.2	+	5	2808	c.2329G>A	c.(2329-2331)Gct>Act	p.A777T	CHD7_ENST00000524602.1_Intron|CHD7_ENST00000525508.1_Missense_Mutation_p.A777T	NM_017780.3	NP_060250.2	Q9P2D1	CHD7_HUMAN	chromodomain helicase DNA binding protein 7	777					adult heart development (GO:0007512)|adult walking behavior (GO:0007628)|artery morphogenesis (GO:0048844)|blood circulation (GO:0008015)|central nervous system development (GO:0007417)|chromatin modification (GO:0016568)|cognition (GO:0050890)|cranial nerve development (GO:0021545)|embryonic hindlimb morphogenesis (GO:0035116)|epithelium development (GO:0060429)|face development (GO:0060324)|female genitalia development (GO:0030540)|genitalia development (GO:0048806)|heart morphogenesis (GO:0003007)|in utero embryonic development (GO:0001701)|inner ear morphogenesis (GO:0042472)|limb development (GO:0060173)|nose development (GO:0043584)|olfactory behavior (GO:0042048)|olfactory bulb development (GO:0021772)|olfactory nerve development (GO:0021553)|palate development (GO:0060021)|positive regulation of multicellular organism growth (GO:0040018)|regulation of growth hormone secretion (GO:0060123)|regulation of neurogenesis (GO:0050767)|regulation of transcription, DNA-templated (GO:0006355)|retina development in camera-type eye (GO:0060041)|rRNA processing (GO:0006364)|semicircular canal morphogenesis (GO:0048752)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|T cell differentiation (GO:0030217)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)	p.556_871dup(1)		NS(1)|breast(6)|central_nervous_system(8)|cervix(2)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(16)|lung(49)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|urinary_tract(3)	123		all_cancers(86;0.2)|all_lung(136;0.0402)|Lung NSC(129;0.0459)|all_epithelial(80;0.0477)	BRCA - Breast invasive adenocarcinoma(89;0.143)			TGATGCAGATGCTGCTGGGAG	0.473																																					p.A777T		.											CHD7_ENST00000423902,NS,carcinoma,0,2	CHD7_ENST00000423902	0	1	Insertion - In frame(1)	lung(1)	c.G2329A						.						53.0	55.0	55.0					8																	61713037		2012	4206	6218	SO:0001583	missense	55636	exon5			GCAGATGCTGCTG	AB037837	CCDS47865.1	8q12.2	2014-09-17				ENSG00000171316			20626	protein-coding gene	gene with protein product		608892	"""CHARGE association"""	CRG		15300250, 18834967	Standard	NM_017780		Approved	KIAA1416, FLJ20357, FLJ20361	uc003xue.3	Q9P2D1		ENST00000423902.2:c.2329G>A	8.37:g.61713037G>A	ENSP00000392028:p.Ala777Thr	Somatic	85	0		WXS	Illumina HiSeq	.	55	2	NM_017780	D0VBA5|E9PNZ2|Q05DI5|Q2TAN4|Q66K35|Q7Z6C0|Q7Z7Q2|Q9NXA0|Q9NXA3	Missense_Mutation	SNP	ENST00000423902.2	37	CCDS47865.1	.	.	.	.	.	.	.	.	.	.	G	12.22	1.872203	0.33069	.	.	ENSG00000171316	ENST00000307121;ENST00000423902;ENST00000525508	T;T	0.54479	0.57;0.57	5.81	4.94	0.65067	Chromo domain-like (1);	0.170964	0.39759	N	0.001266	T	0.31136	0.0787	N	0.08118	0	0.45046	D	0.998061	B	0.26318	0.146	B	0.25987	0.065	T	0.11446	-1.0587	10	0.13470	T	0.59	-8.6027	13.351	0.60601	0.0729:0.0:0.9271:0.0	.	777	Q9P2D1	CHD7_HUMAN	T	777	ENSP00000392028:A777T;ENSP00000436027:A777T	ENSP00000307304:A777T	A	+	1	0	CHD7	61875591	1.000000	0.71417	0.997000	0.53966	0.998000	0.95712	4.342000	0.59341	1.452000	0.47756	0.655000	0.94253	GCT	.		0.473	CHD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383468.2	XM_098762	
SNX5	27131	hgsc.bcm.edu	37	20	17936035	17936035	+	Missense_Mutation	SNP	C	C	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr20:17936035C>T	ENST00000377768.3	-	4	553	c.241G>A	c.(241-243)Gaa>Aaa	p.E81K	SNX5_ENST00000377759.4_Missense_Mutation_p.E81K|SNX5_ENST00000483485.1_5'UTR	NM_152227.1	NP_689413.1	Q9Y5X3	SNX5_HUMAN	sorting nexin 5	81	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.				intracellular protein transport (GO:0006886)|pinocytosis (GO:0006907)	cytoplasmic vesicle (GO:0031410)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|extrinsic component of endosome membrane (GO:0031313)|macropinocytic cup (GO:0070685)	phosphatidylinositol binding (GO:0035091)			endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|prostate(1)	11						TCTGTTGTTTCAATAAGAGTG	0.383																																					p.E81K		.											.	.	.	0			c.G241A						.						77.0	72.0	74.0					20																	17936035		2203	4300	6503	SO:0001583	missense	27131	exon3			TTGTTTCAATAAG	AF121855	CCDS13130.1	20p11	2008-05-22			ENSG00000089006	ENSG00000089006		"""Sorting nexins"""	14969	protein-coding gene	gene with protein product		605937				10600472, 17148574	Standard	NM_152227		Approved		uc002wqc.3	Q9Y5X3	OTTHUMG00000031953	ENST00000377768.3:c.241G>A	20.37:g.17936035C>T	ENSP00000366998:p.Glu81Lys	Somatic	38	0		WXS	Illumina HiSeq	.	40	4	NM_014426	B7ZKN3|D3DW26|Q52LC4|Q7KZN0|Q9BWP0	Missense_Mutation	SNP	ENST00000377768.3	37	CCDS13130.1	.	.	.	.	.	.	.	.	.	.	C	27.5	4.833621	0.91036	.	.	ENSG00000089006	ENST00000377768;ENST00000377759;ENST00000419004	T;T;T	0.38887	1.11;1.11;1.11	5.57	5.57	0.84162	Phox homologous domain (5);	0.000000	0.85682	D	0.000000	T	0.61862	0.2381	M	0.66297	2.02	0.80722	D	1	D;B	0.55172	0.97;0.326	P;B	0.59115	0.852;0.276	T	0.62751	-0.6788	10	0.66056	D	0.02	.	19.9024	0.96993	0.0:1.0:0.0:0.0	.	102;81	B7Z476;Q9Y5X3	.;SNX5_HUMAN	K	81;81;46	ENSP00000366998:E81K;ENSP00000366988:E81K;ENSP00000406731:E46K	ENSP00000366988:E81K	E	-	1	0	SNX5	17884035	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	7.818000	0.86416	2.775000	0.95449	0.650000	0.86243	GAA	.		0.383	SNX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078137.4		
C1QBP	708	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	17	5341560	5341560	+	Missense_Mutation	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr17:5341560T>G	ENST00000225698.4	-	2	347	c.266A>C	c.(265-267)gAa>gCa	p.E89A	C1QBP_ENST00000574444.1_5'UTR	NM_001212.3	NP_001203.1	Q07021	C1QBP_HUMAN	complement component 1, q subcomponent binding protein	89	C1q binding.				apoptotic process (GO:0006915)|blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|complement activation, classical pathway (GO:0006958)|immune response (GO:0006955)|innate immune response (GO:0045087)|mature ribosome assembly (GO:0042256)|mRNA processing (GO:0006397)|negative regulation of defense response to virus (GO:0050687)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of MDA-5 signaling pathway (GO:0039534)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|negative regulation of RIG-I signaling pathway (GO:0039536)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|phosphatidylinositol 3-kinase signaling (GO:0014065)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of dendritic cell chemotaxis (GO:2000510)|positive regulation of mitochondrial translation (GO:0070131)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive regulation of trophoblast cell migration (GO:1901165)|regulation of complement activation (GO:0030449)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|membrane (GO:0016020)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	adrenergic receptor binding (GO:0031690)|complement component C1q binding (GO:0001849)|hyaluronic acid binding (GO:0005540)|kininogen binding (GO:0030984)|mitochondrial ribosome binding (GO:0097177)|mRNA binding (GO:0003729)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)			lung(2)|ovary(1)	3					Hyaluronan(DB08818)	CTCCTTAATTTCATCACTCAG	0.388																																					p.E89A		.											.	.	.	0			c.A266C						.						75.0	76.0	76.0					17																	5341560		2203	4300	6503	SO:0001583	missense	708	exon2			TTAATTTCATCAC	X75913	CCDS11071.1	17p13.3	2009-05-07				ENSG00000108561			1243	protein-coding gene	gene with protein product	"""C1q globular domain-binding protein"", ""hyaluronan-binding protein 1"", ""splicing factor SF2-associated protein"""	601269		HABP1		8567680, 8195709	Standard	NM_001212		Approved	gC1Q-R, gC1qR, p32, SF2p32	uc002gby.1	Q07021		ENST00000225698.4:c.266A>C	17.37:g.5341560T>G	ENSP00000225698:p.Glu89Ala	Somatic	110	0		WXS	Illumina HiSeq	.	75	27	NM_001212	Q2HXR8|Q9NNY8	Missense_Mutation	SNP	ENST00000225698.4	37	CCDS11071.1	.	.	.	.	.	.	.	.	.	.	T	22.3	4.266942	0.80469	.	.	ENSG00000108561	ENST00000225698	.	.	.	4.77	4.77	0.60923	.	0.000000	0.85682	D	0.000000	T	0.81851	0.4910	M	0.89715	3.055	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.85815	0.1382	9	0.87932	D	0	-22.9607	13.2777	0.60196	0.0:0.0:0.0:1.0	.	89	Q07021	C1QBP_HUMAN	A	89	.	ENSP00000225698:E89A	E	-	2	0	C1QBP	5282284	1.000000	0.71417	1.000000	0.80357	0.761000	0.43186	7.630000	0.83225	2.003000	0.58678	0.528000	0.53228	GAA	.		0.388	C1QBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439388.1	NM_001212	
RNF19B	127544	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	33409664	33409664	+	Missense_Mutation	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr1:33409664T>G	ENST00000373456.7	-	6	1360	c.1361A>C	c.(1360-1362)aAa>aCa	p.K454T	RNF19B_ENST00000356990.5_Missense_Mutation_p.K453T|RNF19B_ENST00000235150.4_Missense_Mutation_p.K453T	NM_153341.2	NP_699172.2	Q6ZMZ0	RN19B_HUMAN	ring finger protein 19B	454					interferon-gamma secretion (GO:0072643)|natural killer cell mediated cytotoxicity (GO:0042267)|protein ubiquitination (GO:0016567)	cytolytic granule (GO:0044194)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			endometrium(4)|kidney(2)|large_intestine(3)|lung(4)	13		Myeloproliferative disorder(586;0.0393)|all_neural(195;0.186)				TTTCACTCCTTTTCCGTTGGC	0.403																																					p.K454T		.											.	.	.	0			c.A1361C						.						103.0	93.0	96.0					1																	33409664		2203	4300	6503	SO:0001583	missense	127544	exon6			ACTCCTTTTCCGT	AK074486	CCDS372.2, CCDS44107.1, CCDS72754.1	1p35.1	2010-05-11	2007-08-20	2007-08-20	ENSG00000116514	ENSG00000116514		"""RING-type (C3HC4) zinc fingers"""	26886	protein-coding gene	gene with protein product		610872	"""IBR domain containing 3"""	IBRDC3		12477932	Standard	XM_006710356		Approved	FLJ90005	uc010oho.2	Q6ZMZ0	OTTHUMG00000004013	ENST00000373456.7:c.1361A>C	1.37:g.33409664T>G	ENSP00000362555:p.Lys454Thr	Somatic	62	0		WXS	Illumina HiSeq	.	46	22	NM_153341	B7ZLB2|E9PAW6|G3XA82|Q0VG77|Q5TH44|Q5TH45|Q6P6A4|Q8N2S8|Q8WUF3	Missense_Mutation	SNP	ENST00000373456.7	37	CCDS372.2	.	.	.	.	.	.	.	.	.	.	T	15.16	2.751549	0.49257	.	.	ENSG00000116514	ENST00000373456;ENST00000356990;ENST00000235150;ENST00000405457	T;T;T	0.33438	1.41;1.45;1.41	5.5	5.5	0.81552	.	0.048336	0.85682	D	0.000000	T	0.43456	0.1248	L	0.35854	1.095	0.36642	D	0.876918	D;D;P	0.59767	0.986;0.958;0.82	D;P;B	0.63703	0.917;0.613;0.328	T	0.49899	-0.8890	10	0.51188	T	0.08	.	14.4879	0.67629	0.0:0.0:0.0:1.0	.	453;454;453	G3XA82;Q6ZMZ0;E9PAW6	.;RN19B_HUMAN;.	T	454;453;453;352	ENSP00000362555:K454T;ENSP00000349482:K453T;ENSP00000235150:K453T	ENSP00000235150:K453T	K	-	2	0	RNF19B	33182251	0.995000	0.38212	1.000000	0.80357	0.995000	0.86356	3.062000	0.49971	2.216000	0.71823	0.533000	0.62120	AAA	.		0.403	RNF19B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011465.3	NM_153341	
DISC1	27185	hgsc.bcm.edu	37	1	231829484	231829484	+	Intron	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr1:231829484T>G	ENST00000602281.1	+	2	120				TSNAX-DISC1_ENST00000602962.1_Intron|DISC1_ENST00000537876.1_Intron|DISC1_ENST00000539444.1_Intron|DISC1_ENST00000366633.3_Intron|DISC1_ENST00000317586.4_Intron|DISC1_ENST00000366636.4_Intron|DISC1_ENST00000439617.2_Intron|DISC1_ENST00000602873.1_Intron|DISC1_ENST00000535983.1_Intron|DISC1_ENST00000366637.3_Intron	NM_001164542.1|NM_001164544.1	NP_001158014.1|NP_001158016.1	Q9NRI5	DISC1_HUMAN	disrupted in schizophrenia 1						canonical Wnt signaling pathway (GO:0060070)|cell proliferation in forebrain (GO:0021846)|cellular protein localization (GO:0034613)|cerebral cortex radially oriented cell migration (GO:0021799)|microtubule cytoskeleton organization (GO:0000226)|mitochondrial calcium ion homeostasis (GO:0051560)|neuron migration (GO:0001764)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of neuron projection development (GO:0010975)|regulation of synapse maturation (GO:0090128)|TOR signaling (GO:0031929)	cell junction (GO:0030054)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|postsynaptic membrane (GO:0045211)				breast(1)|cervix(1)|kidney(1)|large_intestine(1)|liver(2)|lung(6)|skin(2)|upper_aerodigestive_tract(1)	15		all_cancers(173;0.0208)|Prostate(94;0.0975)				GAGATGACCTTTAAACCTAGG	0.473																																					.		.											.	.	.	0			.						.																																			SO:0001627	intron_variant	0	.			TGACCTTTAAACC	AF222980	CCDS31055.1, CCDS31056.1, CCDS53482.1, CCDS53483.1, CCDS53484.1, CCDS59205.1, CCDS59206.1, CCDS59207.1	1q42.1	2008-02-05			ENSG00000162946	ENSG00000162946			2888	protein-coding gene	gene with protein product		605210				10814723	Standard	NM_001164550		Approved		uc010pxh.2	Q9NRI5	OTTHUMG00000037835	ENST00000602281.1:c.68-88T>G	1.37:g.231829484T>G		Somatic	11	0		WXS	Illumina HiSeq	.	17	4	.	A6NLH2|C4P091|C4P095|C4P0A1|C4P0A3|C4P0B3|C4P0B6|C4P0C1|C9J6D0|O75045|Q5VT44|Q5VT45|Q8IXJ0|Q8IXJ1|Q9BX19|Q9NRI3|Q9NRI4	RNA	SNP	ENST00000602281.1	37	CCDS59205.1																																																																																			.		0.473	DISC1-019	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000467451.1	NM_018662	
RSU1P2	100133308	hgsc.bcm.edu	37	10	45601819	45601819	+	RNA	SNP	T	T	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr10:45601819T>C	ENST00000423875.1	-	0	1373									Ras suppressor protein 1 pseudogene 2																		GGGTCATCTTTCATCAGCAGT	0.473																																					.		.											.	.	.	0			.						.																																					100133308	.			CATCTTTCATCAG			10q11.21	2013-06-03			ENSG00000242848	ENSG00000232554			44391	pseudogene	pseudogene							Standard	NR_024472		Approved		uc009xmq.2		OTTHUMG00000185442		10.37:g.45601819T>C		Somatic	6	0		WXS	Illumina HiSeq	.	8	6	.		RNA	SNP	ENST00000423875.1	37																																																																																				.		0.473	RSU1P2-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000471233.1		
IARS	3376	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	9	95005505	95005505	+	Missense_Mutation	SNP	C	C	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr9:95005505C>A	ENST00000375643.3	-	28	3259	c.2993G>T	c.(2992-2994)cGc>cTc	p.R998L	IARS_ENST00000375627.1_Missense_Mutation_p.R51L|IARS_ENST00000443024.2_Missense_Mutation_p.R998L|IARS_ENST00000474340.1_5'UTR|IARS_ENST00000375629.3_Missense_Mutation_p.R51L|IARS_ENST00000447699.2_Missense_Mutation_p.R888L	NM_013417.2	NP_038203.2	P41252	SYIC_HUMAN	isoleucyl-tRNA synthetase	998					gene expression (GO:0010467)|isoleucyl-tRNA aminoacylation (GO:0006428)|osteoblast differentiation (GO:0001649)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	aminoacyl-tRNA editing activity (GO:0002161)|ATP binding (GO:0005524)|isoleucine-tRNA ligase activity (GO:0004822)			breast(3)|endometrium(2)|kidney(4)|large_intestine(7)|lung(14)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	35					L-Isoleucine(DB00167)	AACCTTTTTGCGAAGTTTCTG	0.408											OREG0019313	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R998L		.											.	.	.	0			c.G2993T						.						126.0	102.0	110.0					9																	95005505		2203	4300	6503	SO:0001583	missense	3376	exon28			TTTTTGCGAAGTT	AB209234	CCDS6694.1	9q21	2011-07-01	2007-02-26		ENSG00000196305	ENSG00000196305	6.1.1.5	"""Aminoacyl tRNA synthetases / Class I"""	5330	protein-coding gene	gene with protein product	"""isoleucine tRNA ligase 1, cytoplasmic"""	600709				8812440	Standard	NM_002161		Approved	ILRS, IARS1	uc004aru.4	P41252	OTTHUMG00000020219	ENST00000375643.3:c.2993G>T	9.37:g.95005505C>A	ENSP00000364794:p.Arg998Leu	Somatic	27	0	1309	WXS	Illumina HiSeq	.	13	6	NM_013417	A8KAE9|Q5TCD0|Q7Z3T4|Q9H588	Missense_Mutation	SNP	ENST00000375643.3	37	CCDS6694.1	.	.	.	.	.	.	.	.	.	.	C	34	5.379456	0.95945	.	.	ENSG00000196305	ENST00000375643;ENST00000375629;ENST00000443024;ENST00000447699;ENST00000375660;ENST00000375627;ENST00000449893	T;T;T	0.44482	0.92;0.92;0.92	5.69	5.69	0.88448	.	0.000000	0.85682	D	0.000000	T	0.77150	0.4088	H	0.96269	3.795	0.80722	D	1	D;P;P	0.89917	1.0;0.956;0.902	D;P;P	0.78314	0.991;0.897;0.836	D	0.84377	0.0547	10	0.87932	D	0	-11.5555	19.4031	0.94639	0.0:1.0:0.0:0.0	.	508;998;843	F5H1M4;P41252;Q6P0M4	.;SYIC_HUMAN;.	L	998;51;998;888;998;51;230	ENSP00000364794:R998L;ENSP00000406448:R998L;ENSP00000415020:R888L	ENSP00000364778:R51L	R	-	2	0	IARS	94045326	1.000000	0.71417	1.000000	0.80357	0.900000	0.52787	7.380000	0.79704	2.676000	0.91093	0.462000	0.41574	CGC	.		0.408	IARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053059.2	NM_002161	
ZNF770	54989	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	15	35274078	35274078	+	Silent	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr15:35274078T>G	ENST00000356321.4	-	3	1902	c.1558A>C	c.(1558-1560)Aga>Cga	p.R520R		NM_014106.3	NP_054825.2	Q6IQ21	ZN770_HUMAN	zinc finger protein 770	520					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(7)|lung(11)|ovary(1)	29		Lung NSC(122;4.59e-10)|all_lung(180;8.78e-09)		all cancers(64;1.97e-18)|GBM - Glioblastoma multiforme(113;2.11e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0643)		TGTTCATGTCTTTTTAAGTGA	0.333																																					p.R520R		.											.	.	.	0			c.A1558C						.						61.0	62.0	62.0					15																	35274078		2201	4298	6499	SO:0001819	synonymous_variant	54989	exon3			CATGTCTTTTTAA	BC071603	CCDS10042.1	15q14	2013-01-08			ENSG00000198146	ENSG00000198146		"""Zinc fingers, C2H2-type"""	26061	protein-coding gene	gene with protein product							Standard	NM_014106		Approved	FLJ20582, PRO1914	uc001ziw.3	Q6IQ21	OTTHUMG00000129689	ENST00000356321.4:c.1558A>C	15.37:g.35274078T>G		Somatic	72	0		WXS	Illumina HiSeq	.	41	16	NM_014106	Q6ZMZ6|Q9NWV2	Silent	SNP	ENST00000356321.4	37	CCDS10042.1																																																																																			.		0.333	ZNF770-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251896.2	NM_014106	
TMEM245	23731	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	9	111798539	111798539	+	Silent	SNP	A	A	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr9:111798539A>G	ENST00000374586.3	-	16	2377	c.2346T>C	c.(2344-2346)ttT>ttC	p.F782F		NM_032012.3	NP_114401.2	Q9H330	TM245_HUMAN	transmembrane protein 245	782						integral component of membrane (GO:0016021)											GCAAGAGATGAAAAATCAACA	0.438																																					p.F782F		.											.	.	.	0			c.T2346C						.						99.0	98.0	98.0					9																	111798539		1939	4139	6078	SO:0001819	synonymous_variant	23731	exon16			GAGATGAAAAATC	AF153415	CCDS43858.1	9q31	2012-03-06	2012-03-06	2012-03-06	ENSG00000106771	ENSG00000106771			1363	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 5"""	C9orf5		10564813	Standard	NM_032012		Approved	CG-2	uc004bdt.4	Q9H330	OTTHUMG00000020469	ENST00000374586.3:c.2346T>C	9.37:g.111798539A>G		Somatic	127	0		WXS	Illumina HiSeq	.	79	24	NM_032012	B4DSW7|Q5JTQ5|Q5SS43|Q6ZME3|Q8NDJ5|Q96CG6	Silent	SNP	ENST00000374586.3	37	CCDS43858.1	.	.	.	.	.	.	.	.	.	.	A	9.660	1.143855	0.21205	.	.	ENSG00000106771	ENST00000413712	.	.	.	5.52	3.21	0.36854	.	.	.	.	.	T	0.57257	0.2041	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.49881	-0.8892	4	.	.	.	-18.7779	7.8194	0.29280	0.6946:0.0:0.3054:0.0	.	.	.	.	P	375	.	.	S	-	1	0	C9orf5	110838360	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.402000	0.44521	0.416000	0.25844	0.528000	0.53228	TCA	.		0.438	TMEM245-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053587.2	NM_032012	
PPAP2A	8611	hgsc.bcm.edu;ucsc.edu	37	5	54826106	54826106	+	Intron	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr5:54826106T>G	ENST00000307259.8	-	1	479				PPAP2A_ENST00000264775.5_Intron|PPAP2A_ENST00000515132.1_Intron	NM_003711.2	NP_003702.2	O14494	LPP1_HUMAN	phosphatidic acid phosphatase type 2A						androgen receptor signaling pathway (GO:0030521)|germ cell migration (GO:0008354)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|lipid metabolic process (GO:0006629)|negative regulation of cell proliferation (GO:0008285)|phospholipid dephosphorylation (GO:0046839)|protein dephosphorylation (GO:0006470)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of lipid metabolic process (GO:0019216)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	phosphatidate phosphatase activity (GO:0008195)			breast(2)|endometrium(1)|large_intestine(1)|lung(2)|ovary(2)|prostate(1)	9		Lung NSC(810;4.08e-05)|Prostate(74;0.0181)|Breast(144;0.0544)				CTAACGAAATTTCTGGTAATC	0.373																																					.		.											.	.	.	0			.						.																																			SO:0001627	intron_variant	379013	.			CGAAATTTCTGGT	AB000888	CCDS34159.1, CCDS34160.1	5q11	2009-05-27			ENSG00000067113	ENSG00000067113	3.1.3.4		9228	protein-coding gene	gene with protein product		607124				9305923	Standard	NM_003711		Approved	PAP-2a, LPP1	uc003jpz.4	O14494	OTTHUMG00000162240	ENST00000307259.8:c.58+4293A>C	5.37:g.54826106T>G		Somatic	91	0		WXS	Illumina HiSeq	.	66	14	.	B7ZKN8|G3XA95|O60457|O60463|Q17RZ4	RNA	SNP	ENST00000307259.8	37	CCDS34159.1																																																																																			.		0.373	PPAP2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368073.1		
HDAC6	10013	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	X	48661354	48661354	+	Missense_Mutation	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chrX:48661354A>C	ENST00000334136.5	+	3	348	c.170A>C	c.(169-171)aAg>aCg	p.K57T	HDAC6_ENST00000469223.1_3'UTR|HDAC6_ENST00000376619.2_Missense_Mutation_p.K57T|HDAC6_ENST00000444343.2_Missense_Mutation_p.K71T|HDAC6_ENST00000413163.2_Missense_Mutation_p.K2T			Q9UBN7	HDAC6_HUMAN	histone deacetylase 6	57					aggresome assembly (GO:0070842)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to misfolded protein (GO:0071218)|cellular response to topologically incorrect protein (GO:0035967)|histone deacetylation (GO:0016575)|Hsp90 deacetylation (GO:0070846)|intracellular protein transport (GO:0006886)|lysosome localization (GO:0032418)|macroautophagy (GO:0016236)|misfolded or incompletely synthesized protein catabolic process (GO:0006515)|negative regulation of hydrogen peroxide metabolic process (GO:0010727)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of oxidoreductase activity (GO:0051354)|negative regulation of protein complex disassembly (GO:0043242)|negative regulation of proteolysis (GO:0045861)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-lysine deacetylation (GO:0034983)|polyubiquitinated misfolded protein transport (GO:0070845)|positive regulation of chaperone-mediated protein complex assembly (GO:0090035)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of hydrogen peroxide-mediated programmed cell death (GO:1901300)|positive regulation of receptor biosynthetic process (GO:0010870)|positive regulation of signal transduction (GO:0009967)|protein complex disassembly (GO:0043241)|protein deacetylation (GO:0006476)|protein polyubiquitination (GO:0000209)|regulation of androgen receptor signaling pathway (GO:0060765)|regulation of establishment of protein localization (GO:0070201)|regulation of gene expression, epigenetic (GO:0040029)|regulation of microtubule-based movement (GO:0060632)|regulation of receptor activity (GO:0010469)|response to growth factor (GO:0070848)|response to misfolded protein (GO:0051788)|response to organic substance (GO:0010033)|response to toxic substance (GO:0009636)|transcription, DNA-templated (GO:0006351)|tubulin deacetylation (GO:0090042)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)	aggresome (GO:0016235)|axon (GO:0030424)|caveola (GO:0005901)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|dendrite (GO:0030425)|histone deacetylase complex (GO:0000118)|inclusion body (GO:0016234)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|nucleus (GO:0005634)|perikaryon (GO:0043204)|perinuclear region of cytoplasm (GO:0048471)	alpha-tubulin binding (GO:0043014)|beta-catenin binding (GO:0008013)|core promoter binding (GO:0001047)|dynein complex binding (GO:0070840)|enzyme binding (GO:0019899)|histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|Hsp90 protein binding (GO:0051879)|microtubule binding (GO:0008017)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|polyubiquitin binding (GO:0031593)|tau protein binding (GO:0048156)|tubulin deacetylase activity (GO:0042903)|zinc ion binding (GO:0008270)			breast(2)|endometrium(6)|kidney(5)|large_intestine(8)|lung(9)|ovary(3)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	40					Vorinostat(DB02546)	GGCAAAATGAAGAAGCTCGGC	0.498																																					p.K57T	Pancreas(112;205 1675 2305 8976 15959)	.											.	.	.	0			c.A170C						.						73.0	58.0	63.0					X																	48661354		2203	4300	6503	SO:0001583	missense	10013	exon3			AAATGAAGAAGCT	AF132609	CCDS14306.1	Xp11.23	2014-06-12			ENSG00000094631	ENSG00000094631			14064	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 90"""	300272				10220385, 10048485	Standard	NM_006044		Approved	KIAA0901, JM21, HD6, FLJ16239, PPP1R90	uc004dks.1	Q9UBN7	OTTHUMG00000034496	ENST00000334136.5:c.170A>C	X.37:g.48661354A>C	ENSP00000334061:p.Lys57Thr	Somatic	18	0		WXS	Illumina HiSeq	.	8	7	NM_006044	O94975|Q6NT75|Q7L3E5|Q96CY0	Missense_Mutation	SNP	ENST00000334136.5	37	CCDS14306.1	.	.	.	.	.	.	.	.	.	.	A	19.93	3.917993	0.73098	.	.	ENSG00000094631	ENST00000423941;ENST00000376643;ENST00000444343;ENST00000376610;ENST00000334136;ENST00000376619;ENST00000436813;ENST00000413163;ENST00000441703;ENST00000426196;ENST00000443563;ENST00000440653	T;T;T;T	0.65732	0.02;0.03;0.03;-0.17	4.42	3.25	0.37280	.	0.467933	0.20797	N	0.085508	T	0.63082	0.2481	L	0.32530	0.975	0.26508	N	0.974647	D;P;D;D	0.76494	0.998;0.759;0.99;0.999	P;B;P;D	0.83275	0.878;0.19;0.815;0.996	T	0.52230	-0.8603	10	0.45353	T	0.12	-20.3335	3.1598	0.06516	0.6749:0.0:0.1149:0.2102	.	47;2;57;57	B4DZN1;E7EUZ1;Q9UBN7;Q9BRX7	.;.;HDAC6_HUMAN;.	T	57;57;71;57;57;57;57;2;57;57;57;57	ENSP00000398566:K71T;ENSP00000334061:K57T;ENSP00000365804:K57T;ENSP00000398801:K2T	ENSP00000334061:K57T	K	+	2	0	HDAC6	48546298	1.000000	0.71417	1.000000	0.80357	0.942000	0.58702	1.806000	0.38892	0.654000	0.30846	0.486000	0.48141	AAG	.		0.498	HDAC6-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083394.2	NM_006044	
AIFM3	150209	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	22	21333952	21333952	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr22:21333952G>T	ENST00000399167.2	+	18	1853	c.1613G>T	c.(1612-1614)gGg>gTg	p.G538V	AIFM3_ENST00000335375.5_Missense_Mutation_p.G526V|LZTR1_ENST00000215739.8_5'Flank|AIFM3_ENST00000440238.2_Missense_Mutation_p.G538V|XXbac-B135H6.18_ENST00000610278.1_lincRNA|LZTR1_ENST00000479606.1_3'UTR|LZTR1_ENST00000389355.3_5'Flank|AIFM3_ENST00000399163.2_Missense_Mutation_p.G538V|AIFM3_ENST00000405089.1_Missense_Mutation_p.G544V|AIFM3_ENST00000465606.1_3'UTR|AIFM3_ENST00000333607.6_Missense_Mutation_p.G538V	NM_144704.2	NP_653305.1	Q96NN9	AIFM3_HUMAN	apoptosis-inducing factor, mitochondrion-associated, 3	538					cell redox homeostasis (GO:0045454)|execution phase of apoptosis (GO:0097194)	endoplasmic reticulum (GO:0005783)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	2 iron, 2 sulfur cluster binding (GO:0051537)|flavin adenine dinucleotide binding (GO:0050660)|metal ion binding (GO:0046872)|oxidoreductase activity (GO:0016491)			breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(5)|ovary(3)|prostate(1)|skin(2)|urinary_tract(1)	21	all_cancers(11;3.71e-26)|all_epithelial(7;1.59e-23)|Lung NSC(8;3.06e-15)|all_lung(8;5.05e-14)|Melanoma(16;0.000465)|Ovarian(15;0.0028)|Colorectal(54;0.0332)|all_neural(72;0.142)	Lung SC(17;0.0367)	LUSC - Lung squamous cell carcinoma(15;0.000204)|Lung(15;0.00494)|Epithelial(17;0.195)			ATCATCCAGGGGGATCTGGAG	0.622																																					p.G544V		.											.	.	.	0			c.G1631T						.						116.0	121.0	119.0					22																	21333952		2203	4300	6503	SO:0001583	missense	150209	exon18			TCCAGGGGGATCT	AK094844	CCDS13786.1, CCDS33605.1, CCDS54503.1	22q11.21	2007-05-03			ENSG00000183773	ENSG00000183773			26398	protein-coding gene	gene with protein product						15764604	Standard	NM_144704		Approved	AIFL, FLJ30473		Q96NN9	OTTHUMG00000150804	ENST00000399167.2:c.1613G>T	22.37:g.21333952G>T	ENSP00000382120:p.Gly538Val	Somatic	69	0		WXS	Illumina HiSeq	.	46	21	NM_001146288	B7WP37|D3DX37|D3DX38|Q6ZT44|Q8N1V3|Q8N5E0	Missense_Mutation	SNP	ENST00000399167.2	37	CCDS13786.1	.	.	.	.	.	.	.	.	.	.	G	27.9	4.873202	0.91664	.	.	ENSG00000183773	ENST00000399167;ENST00000399163;ENST00000405089;ENST00000335375;ENST00000440238;ENST00000333607	T;T;T;T;T;T	0.58940	0.3;0.3;0.3;0.3;0.3;0.3	4.27	4.27	0.50696	FAD/NAD-linked reductase, dimerisation (1);Pyridine nucleotide-disulphide oxidoreductase, dimerisation (1);	0.000000	0.85682	D	0.000000	T	0.81254	0.4784	M	0.93150	3.385	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0	D	0.86393	0.1737	10	0.87932	D	0	-8.1634	14.5733	0.68226	0.0:0.0:1.0:0.0	.	526;526;544;538;538	B7Z9S7;B7Z376;Q96NN9-2;Q96NN9-3;Q96NN9	.;.;.;.;AIFM3_HUMAN	V	538;538;544;526;538;538	ENSP00000382120:G538V;ENSP00000382116:G538V;ENSP00000385800:G544V;ENSP00000335369:G526V;ENSP00000390798:G538V;ENSP00000327671:G538V	ENSP00000327671:G538V	G	+	2	0	AIFM3	19663952	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.669000	0.91163	2.378000	0.81104	0.561000	0.74099	GGG	.		0.622	AIFM3-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000320150.1	NM_144704	
BLOC1S3	388552	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	19	45683097	45683097	+	Silent	SNP	C	C	A	rs540921310		TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr19:45683097C>A	ENST00000433642.2	+	2	639	c.543C>A	c.(541-543)cgC>cgA	p.R181R	TRAPPC6A_ENST00000006275.4_5'Flank|TRAPPC6A_ENST00000585934.1_5'Flank|AC005779.2_ENST00000593083.1_Silent_p.R6R|TRAPPC6A_ENST00000588062.1_5'Flank|TRAPPC6A_ENST00000592647.1_5'Flank|BLOC1S3_ENST00000587722.1_Silent_p.R181R	NM_212550.3	NP_997715.1	Q6QNY0	BL1S3_HUMAN	biogenesis of lysosomal organelles complex-1, subunit 3	181					anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|endosome to melanosome transport (GO:0035646)|eye development (GO:0001654)|melanosome organization (GO:0032438)|melanosome transport (GO:0032402)|membrane organization (GO:0061024)|neuron projection development (GO:0031175)|pigmentation (GO:0043473)|platelet activation (GO:0030168)|platelet dense granule organization (GO:0060155)|positive regulation of natural killer cell activation (GO:0032816)|post-Golgi vesicle-mediated transport (GO:0006892)|response to drug (GO:0042493)|secretion of lysosomal enzymes (GO:0033299)	BLOC-1 complex (GO:0031083)|cytosol (GO:0005829)|transport vesicle (GO:0030133)				ovary(1)|skin(1)	2		Ovarian(192;0.0728)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.00863)|GBM - Glioblastoma multiforme(486;0.231)		CTGGCTGCCGCCTGCTGCCGG	0.711									Hermansky-Pudlak syndrome																												p.R181R		.											.	.	.	0			c.C543A						.						14.0	14.0	14.0					19																	45683097		1685	3416	5101	SO:0001819	synonymous_variant	388552	exon2	Familial Cancer Database	HPS, HPS1-8	CTGCCGCCTGCTG	AY531266	CCDS12656.1	19q13.32	2012-08-01	2008-08-11			ENSG00000189114		"""Biogenesis of lysosomal organelles complex-1 subunits"""	20914	protein-coding gene	gene with protein product	"""BLOC-1 subunit 3"", ""Biogenesis of Lysosome-related Organelles complex-1 Subunit 3"", ""Hermansky-Pudlak syndrome 8"""	609762				15102850	Standard	NM_212550		Approved	BLOS3, HPS8	uc002pax.4	Q6QNY0		ENST00000433642.2:c.543C>A	19.37:g.45683097C>A		Somatic	26	0		WXS	Illumina HiSeq	.	8	6	NM_212550	B2RXB8	Silent	SNP	ENST00000433642.2	37	CCDS12656.1																																																																																			.		0.711	BLOC1S3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457559.1	NM_212550	
MUC4	4585	hgsc.bcm.edu	37	3	195511212	195511212	+	Missense_Mutation	SNP	G	G	C	rs549429405	byFrequency	TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr3:195511212G>C	ENST00000463781.3	-	2	7698	c.7239C>G	c.(7237-7239)caC>caG	p.H2413Q	MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.H2413Q	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GATGGGTGGCGTGACCTGTGG	0.592																																					p.H2413Q		.											MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4_ENST00000463781	0	0			c.C7239G						.						42.0	42.0	42.0					3																	195511212		668	1587	2255	SO:0001583	missense	4585	exon2			GGTGGCGTGACCT	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.7239C>G	3.37:g.195511212G>C	ENSP00000417498:p.His2413Gln	Somatic	240	2		WXS	Illumina HiSeq	.	133	5	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	G	5.745	0.321952	0.10900	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.26810	1.71;1.75	.	.	.	.	.	.	.	.	T	0.13586	0.0329	N	0.19112	0.55	0.09310	N	1	B	0.18610	0.029	B	0.04013	0.001	T	0.30909	-0.9962	7	.	.	.	.	6.6894	0.23163	2.0E-4:0.0:0.9998:0.0	.	2413	E7ESK3	.	Q	2413	ENSP00000417498:H2413Q;ENSP00000420243:H2413Q	.	H	-	3	2	MUC4	196995607	0.000000	0.05858	0.003000	0.11579	0.000000	0.00434	0.313000	0.19415	0.482000	0.27582	0.000000	0.15137	CAC	.		0.592	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
PUM2	23369	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	2	20482963	20482963	+	Missense_Mutation	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr2:20482963T>G	ENST00000361078.2	-	11	1487	c.1465A>C	c.(1465-1467)Agt>Cgt	p.S489R	PUM2_ENST00000338086.5_Missense_Mutation_p.S489R|PUM2_ENST00000319801.5_Missense_Mutation_p.S489R|PUM2_ENST00000536417.1_Missense_Mutation_p.S433R|PUM2_ENST00000403432.1_Missense_Mutation_p.S489R			Q8TB72	PUM2_HUMAN	pumilio RNA-binding family member 2	489					regulation of translation (GO:0006417)|stress granule assembly (GO:0034063)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|nuclear membrane (GO:0031965)|perinuclear region of cytoplasm (GO:0048471)	poly(A) RNA binding (GO:0044822)			breast(2)|central_nervous_system(1)|endometrium(6)|kidney(4)|large_intestine(7)|lung(13)|ovary(2)|prostate(4)|urinary_tract(3)	42	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GTAAGGCTACTTGCAGTTCCT	0.438																																					p.S489R		.											.	.	.	0			c.A1465C						.						57.0	60.0	59.0					2																	20482963		2203	4300	6503	SO:0001583	missense	23369	exon11			GGCTACTTGCAGT	AF315591	CCDS1698.1, CCDS74486.1, CCDS74487.1	2p22-p21	2013-09-02	2013-09-02		ENSG00000055917	ENSG00000055917			14958	protein-coding gene	gene with protein product		607205	"""pumilio (Drosphila) homolog 2"", ""pumilio homolog 2 (Drosophila)"""			9039502, 12459267, 12511597	Standard	XM_005262607		Approved	PUMH2, KIAA0235	uc002rds.1	Q8TB72	OTTHUMG00000122098	ENST00000361078.2:c.1465A>C	2.37:g.20482963T>G	ENSP00000354370:p.Ser489Arg	Somatic	86	0		WXS	Illumina HiSeq	.	38	13	NM_015317	B3KSL0|B4E2B6|D6W527|O00234|Q53TV7|Q8WY43|Q9HAN2	Missense_Mutation	SNP	ENST00000361078.2	37		.	.	.	.	.	.	.	.	.	.	T	16.95	3.264572	0.59431	.	.	ENSG00000055917	ENST00000338086;ENST00000361078;ENST00000319801;ENST00000440577;ENST00000403432;ENST00000536417	T;T;T;T;T;T	0.18338	2.22;2.48;2.52;2.25;2.22;2.22	6.03	6.03	0.97812	.	0.226219	0.50627	D	0.000105	T	0.10895	0.0266	N	0.08118	0	0.33939	D	0.642968	B;B;B	0.22983	0.023;0.023;0.078	B;B;B	0.22152	0.017;0.018;0.038	T	0.19063	-1.0317	10	0.29301	T	0.29	-7.0223	16.5602	0.84551	0.0:0.0:0.0:1.0	.	433;489;489	B4E2B6;B7ZL34;Q8TB72-3	.;.;.	R	489;489;489;380;489;433	ENSP00000338173:S489R;ENSP00000354370:S489R;ENSP00000326746:S489R;ENSP00000409905:S380R;ENSP00000385992:S489R;ENSP00000440093:S433R	ENSP00000326746:S489R	S	-	1	0	PUM2	20346444	1.000000	0.71417	0.998000	0.56505	0.796000	0.44982	3.976000	0.56867	2.313000	0.78055	0.454000	0.30748	AGT	.		0.438	PUM2-202	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015317	
SNX30	401548	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	9	115598546	115598546	+	Missense_Mutation	SNP	A	A	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr9:115598546A>G	ENST00000374232.3	+	5	835	c.671A>G	c.(670-672)gAg>gGg	p.E224G		NM_001012994.1	NP_001013012.1	Q5VWJ9	SNX30_HUMAN	sorting nexin family member 30	224					apoptotic process (GO:0006915)|intracellular protein transport (GO:0006886)	endosome (GO:0005768)	phosphatidylinositol binding (GO:0035091)			large_intestine(1)|lung(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	8						AGAATGGGCGAGTCAGTCAAG	0.502																																					p.E224G		.											.	.	.	0			c.A671G						.						140.0	134.0	136.0					9																	115598546		2007	4177	6184	SO:0001583	missense	401548	exon5			TGGGCGAGTCAGT	AK126644	CCDS43865.1	9q33.1	2014-02-12			ENSG00000148158	ENSG00000148158		"""Sorting nexins"""	23685	protein-coding gene	gene with protein product							Standard	NM_001012994		Approved	ATG24A	uc004bgj.4	Q5VWJ9	OTTHUMG00000020512	ENST00000374232.3:c.671A>G	9.37:g.115598546A>G	ENSP00000363349:p.Glu224Gly	Somatic	38	0		WXS	Illumina HiSeq	.	14	6	NM_001012994		Missense_Mutation	SNP	ENST00000374232.3	37	CCDS43865.1	.	.	.	.	.	.	.	.	.	.	A	28.0	4.877495	0.91664	.	.	ENSG00000148158	ENST00000374232	T	0.28255	1.62	5.8	5.8	0.92144	.	0.051355	0.85682	D	0.000000	T	0.52677	0.1749	L	0.56769	1.78	0.80722	D	1	D	0.76494	0.999	D	0.75484	0.986	T	0.52011	-0.8632	10	0.54805	T	0.06	.	16.1405	0.81519	1.0:0.0:0.0:0.0	.	224	Q5VWJ9	SNX30_HUMAN	G	224	ENSP00000363349:E224G	ENSP00000363349:E224G	E	+	2	0	SNX30	114638367	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	9.315000	0.96313	2.214000	0.71695	0.533000	0.62120	GAG	.		0.502	SNX30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053700.1		
FRAS1	80144	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	4	79360216	79360216	+	Missense_Mutation	SNP	A	A	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr4:79360216A>G	ENST00000325942.6	+	40	5967	c.5527A>G	c.(5527-5529)Acg>Gcg	p.T1843A	FRAS1_ENST00000264895.6_Missense_Mutation_p.T1843A	NM_001166133.1	NP_001159605.1	Q86XX4	FRAS1_HUMAN	Fraser extracellular matrix complex subunit 1	1843					cell communication (GO:0007154)|embryonic limb morphogenesis (GO:0030326)|metanephros morphogenesis (GO:0003338)|morphogenesis of an epithelium (GO:0002009)|palate development (GO:0060021)|protein transport (GO:0015031)|skin development (GO:0043588)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sublamina densa (GO:0061618)	metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(5)|lung(54)|prostate(7)|skin(2)|urinary_tract(4)	103						TGACCTTATCACGGTAAACAA	0.398																																					p.T1843A		.											.	.	.	0			c.A5527G						.						203.0	197.0	199.0					4																	79360216		1887	4107	5994	SO:0001583	missense	80144	exon40			CTTATCACGGTAA	AB040933	CCDS54772.1	4q21.21	2014-06-25	2014-06-25		ENSG00000138759	ENSG00000138759			19185	protein-coding gene	gene with protein product		607830	"""Fraser syndrome 1"""			12766769, 3118036	Standard	NM_025074		Approved	FLJ22031, FLJ14927, KIAA1500	uc003hlb.2	Q86XX4	OTTHUMG00000160856	ENST00000325942.6:c.5527A>G	4.37:g.79360216A>G	ENSP00000326330:p.Thr1843Ala	Somatic	25	0		WXS	Illumina HiSeq	.	13	7	NM_001166133	A2RRR8|Q86UZ4|Q8N3U9|Q8NAU7|Q96JW7|Q9H6N9|Q9P228	Missense_Mutation	SNP	ENST00000325942.6	37	CCDS54772.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	12.82|12.82	2.053442|2.053442	0.36181|0.36181	.|.	.|.	ENSG00000138759|ENSG00000138759	ENST00000510944;ENST00000512123|ENST00000325942;ENST00000264895;ENST00000545316	.|T;T	.|0.28895	.|1.59;1.59	5.92|5.92	5.92|5.92	0.95590|0.95590	.|.	.|0.107675	.|0.64402	.|D	.|0.000007	T|T	0.26666|0.26666	0.0652|0.0652	L|L	0.47016|0.47016	1.485|1.485	0.80722|0.80722	D|D	1|1	.|B;B	.|0.27013	.|0.166;0.163	.|B;B	.|0.23716	.|0.017;0.048	T|T	0.05920|0.05920	-1.0856|-1.0856	5|10	.|0.22109	.|T	.|0.4	.|.	12.2044|12.2044	0.54345|0.54345	0.932:0.0:0.068:0.0|0.932:0.0:0.068:0.0	.|.	.|1843;1843	.|E9PHH6;A2RRR8	.|.;.	R|A	292;71|1843;1843;263	.|ENSP00000326330:T1843A;ENSP00000264895:T1843A	.|ENSP00000264895:T1843A	H|T	+|+	2|1	0|0	FRAS1|FRAS1	79579240|79579240	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.986000|0.986000	0.74619|0.74619	3.417000|3.417000	0.52714|0.52714	2.270000|2.270000	0.75569|0.75569	0.477000|0.477000	0.44152|0.44152	CAC|ACG	.		0.398	FRAS1-001	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000362706.2		
TRIM55	84675	hgsc.bcm.edu	37	8	67049405	67049405	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr8:67049405G>T	ENST00000315962.4	+	4	956	c.583G>T	c.(583-585)Gac>Tac	p.D195Y	TRIM55_ENST00000350034.4_Missense_Mutation_p.D195Y|TRIM55_ENST00000353317.5_Missense_Mutation_p.D195Y|TRIM55_ENST00000276573.7_Missense_Mutation_p.D195Y	NM_184085.1	NP_908973.1	Q9BYV6	TRI55_HUMAN	tripartite motif containing 55	195					signal transduction (GO:0007165)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)	identical protein binding (GO:0042802)|signal transducer activity (GO:0004871)|zinc ion binding (GO:0008270)	p.D195N(1)		breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(13)|ovary(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(2)	39		Lung NSC(129;0.138)|all_lung(136;0.221)	Epithelial(68;0.0136)|all cancers(69;0.0582)|BRCA - Breast invasive adenocarcinoma(89;0.0628)|OV - Ovarian serous cystadenocarcinoma(28;0.0904)			CCAGCTGGAAGACACCTGCAA	0.527																																					p.D195Y		.											TRIM55,trunk,malignant_melanoma,0,1	TRIM55	0	1	Substitution - Missense(1)	skin(1)	c.G583T						.						106.0	88.0	94.0					8																	67049405		2203	4300	6503	SO:0001583	missense	84675	exon4			CTGGAAGACACCT	AJ291712	CCDS6184.1, CCDS6185.1, CCDS6186.1, CCDS6187.1	8q13.1	2013-01-09	2011-01-25	2004-11-17	ENSG00000147573	ENSG00000147573		"""RING-type (C3HC4) zinc fingers"", ""Tripartite motif containing / Tripartite motif containing"""	14215	protein-coding gene	gene with protein product		606469	"""ring finger protein 29"", ""tripartite motif-containing 55"""	RNF29		11243782	Standard	NM_033058		Approved	MURF-2	uc003xvv.3	Q9BYV6	OTTHUMG00000164473	ENST00000315962.4:c.583G>T	8.37:g.67049405G>T	ENSP00000323913:p.Asp195Tyr	Somatic	28	0		WXS	Illumina HiSeq	.	23	2	NM_184086	B3KRC0|B3KRJ3|Q53XX3|Q8IUD9|Q8IUE4|Q96DV2|Q96DV3|Q9BYV5	Missense_Mutation	SNP	ENST00000315962.4	37	CCDS6184.1	.	.	.	.	.	.	.	.	.	.	G	23.4	4.409787	0.83340	.	.	ENSG00000147573	ENST00000315962;ENST00000353317;ENST00000276573;ENST00000350034	T;T;T;T	0.40225	1.54;1.55;1.54;1.04	5.4	4.52	0.55395	.	0.142501	0.64402	D	0.000007	T	0.56615	0.1997	L	0.52905	1.665	0.44834	D	0.997848	D;D;P;P	0.55800	0.973;0.96;0.806;0.927	P;P;P;P	0.61592	0.847;0.891;0.498;0.785	T	0.60954	-0.7160	10	0.87932	D	0	.	14.4498	0.67376	0.0712:0.0:0.9288:0.0	.	195;195;195;195	Q9BYV6-4;Q9BYV6-2;Q9BYV6;Q9BYV6-3	.;.;TRI55_HUMAN;.	Y	195	ENSP00000323913:D195Y;ENSP00000297348:D195Y;ENSP00000276573:D195Y;ENSP00000332302:D195Y	ENSP00000276573:D195Y	D	+	1	0	TRIM55	67211959	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	5.541000	0.67212	1.409000	0.46915	0.655000	0.94253	GAC	.		0.527	TRIM55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378921.1	NM_184085	
CYC1	1537	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	8	145151139	145151139	+	Nonsense_Mutation	SNP	G	G	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr8:145151139G>T	ENST00000318911.4	+	3	512	c.439G>T	c.(439-441)Gag>Tag	p.E147*		NM_001916.3	NP_001907	P08574	CY1_HUMAN	cytochrome c-1	147	Cytochrome c.				cellular metabolic process (GO:0044237)|respiratory electron transport chain (GO:0022904)|response to glucagon (GO:0033762)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|respiratory chain (GO:0070469)	electron transporter, transferring electrons from CoQH2-cytochrome c reductase complex and cytochrome c oxidase complex activity (GO:0045155)|heme binding (GO:0020037)|iron ion binding (GO:0005506)			endometrium(1)|kidney(1)|large_intestine(2)|lung(8)|ovary(1)|prostate(2)	15	all_cancers(97;2.87e-11)|all_epithelial(106;2.16e-09)|Lung NSC(106;5.89e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;3.38e-41)|Epithelial(56;8.71e-40)|all cancers(56;3e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			TGAAGCTAAGGAGCTGGCTGC	0.622											OREG0019052	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.E147X		.											.	.	.	0			c.G439T						.						147.0	159.0	155.0					8																	145151139		2203	4300	6503	SO:0001587	stop_gained	1537	exon3			GCTAAGGAGCTGG	BC001006	CCDS6415.1	8q24	2011-07-04			ENSG00000179091	ENSG00000179091		"""Mitochondrial respiratory chain complex / Complex III"""	2579	protein-coding gene	gene with protein product		123980					Standard	NM_001916		Approved	UQCR4	uc003zaz.4	P08574	OTTHUMG00000165242	ENST00000318911.4:c.439G>T	8.37:g.145151139G>T	ENSP00000317159:p.Glu147*	Somatic	38	0	1692	WXS	Illumina HiSeq	.	22	7	NM_001916	Q5U062|Q6FHS7	Nonsense_Mutation	SNP	ENST00000318911.4	37	CCDS6415.1	.	.	.	.	.	.	.	.	.	.	G	15.04	2.715908	0.48622	.	.	ENSG00000179091	ENST00000318911	.	.	.	4.34	4.34	0.51931	.	0.213849	0.39834	N	0.001255	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	-10.7161	12.2253	0.54457	0.0:0.0:1.0:0.0	.	.	.	.	X	147	.	ENSP00000317159:E147X	E	+	1	0	CYC1	145223127	1.000000	0.71417	0.197000	0.23402	0.112000	0.19704	1.735000	0.38176	2.266000	0.75297	0.561000	0.74099	GAG	.		0.622	CYC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382895.1	NM_001916	
TM4SF18	116441	hgsc.bcm.edu;bcgsc.ca	37	3	149051002	149051002	+	Silent	SNP	T	T	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr3:149051002T>C	ENST00000296059.2	-	2	433	c.168A>G	c.(166-168)tcA>tcG	p.S56S	TM4SF18_ENST00000470080.1_Silent_p.S56S|RP11-206M11.7_ENST00000489011.1_RNA	NM_138786.3	NP_620141.1	Q96CE8	T4S18_HUMAN	transmembrane 4 L six family member 18	56						integral component of membrane (GO:0016021)				lung(1)|ovary(1)|prostate(1)	3			LUSC - Lung squamous cell carcinoma(72;0.0378)|Lung(72;0.048)			CCATGATGCCTGAGAAACAGA	0.378																																					p.S56S		.											.	.	.	0			c.A168G						.						122.0	115.0	117.0					3																	149051002		2203	4300	6503	SO:0001819	synonymous_variant	116441	exon1			GATGCCTGAGAAA	BC014339	CCDS3142.1	3q25.1	2005-08-09			ENSG00000163762	ENSG00000163762			25181	protein-coding gene	gene with protein product						10975581	Standard	NM_001184723		Approved	L6D	uc021xfl.1	Q96CE8	OTTHUMG00000159582	ENST00000296059.2:c.168A>G	3.37:g.149051002T>C		Somatic	49	0		WXS	Illumina HiSeq	.	48	4	NM_001184723	B2R8K0|D3DNH5	Silent	SNP	ENST00000296059.2	37	CCDS3142.1																																																																																			.		0.378	TM4SF18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356326.1	NM_138786	
SRSF1	6426	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	17	56082914	56082914	+	Silent	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr17:56082914T>G	ENST00000258962.4	-	4	808	c.600A>C	c.(598-600)ccA>ccC	p.P200P	SRSF1_ENST00000584773.1_Silent_p.P200P|SRSF1_ENST00000582730.2_3'UTR|RP11-159D12.5_ENST00000578794.1_5'Flank|SRSF1_ENST00000581497.1_5'Flank|SRSF1_ENST00000585096.1_Intron	NM_006924.4	NP_008855.1	Q07955	SRSF1_HUMAN	serine/arginine-rich splicing factor 1	200	Arg/Ser-rich (RS domain).|Interacts with SAFB1.				cardiac muscle contraction (GO:0060048)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|mRNA 3'-end processing (GO:0031124)|mRNA 5'-splice site recognition (GO:0000395)|mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|mRNA splice site selection (GO:0006376)|mRNA splicing, via spliceosome (GO:0000398)|regulation of mRNA splicing, via spliceosome (GO:0048024)|regulation of mRNA stability (GO:0043488)|regulation of transcription, DNA-templated (GO:0006355)|regulation of translation (GO:0006417)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(1)|lung(7)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	24						TTCCATAACTTGGACTTCTGG	0.473																																					p.P200P		.											.	.	.	0			c.A600C						.						133.0	130.0	131.0					17																	56082914		2203	4300	6503	SO:0001819	synonymous_variant	6426	exon4			ATAACTTGGACTT		CCDS11600.1, CCDS58580.1	17q22	2013-02-12	2010-06-22	2010-06-22	ENSG00000136450	ENSG00000136450		"""Serine/arginine-rich splicing factors"", ""RNA binding motif (RRM) containing"""	10780	protein-coding gene	gene with protein product	"""splicing factor 2"", ""pre-mRNA-splicing factor SF2, P33 subunit"", ""alternate splicing factor"", ""SR splicing factor 1"""	600812	"""splicing factor, arginine/serine-rich 1"""	SFRS1		8530103, 20516191	Standard	NM_006924		Approved	ASF, SF2, SRp30a, SF2p33, MGC5228	uc002ivi.3	Q07955		ENST00000258962.4:c.600A>C	17.37:g.56082914T>G		Somatic	31	0		WXS	Illumina HiSeq	.	31	10	NM_006924	B2R6Z7|D3DTZ3|Q13809	Silent	SNP	ENST00000258962.4	37	CCDS11600.1																																																																																			.		0.473	SRSF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443335.1	NM_006924	
WWP1	11059	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	8	87454934	87454934	+	Missense_Mutation	SNP	A	A	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr8:87454934A>G	ENST00000517970.1	+	18	2232	c.1925A>G	c.(1924-1926)cAg>cGg	p.Q642R	WWP1_ENST00000349423.2_Missense_Mutation_p.Q424R|WWP1_ENST00000265428.4_Missense_Mutation_p.Q642R|WWP1_ENST00000341922.2_Missense_Mutation_p.Q512R	NM_007013.3	NP_008944.1	Q9H0M0	WWP1_HUMAN	WW domain containing E3 ubiquitin protein ligase 1	642	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				central nervous system development (GO:0007417)|ion transmembrane transport (GO:0034220)|negative regulation of transcription, DNA-templated (GO:0045892)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|signal transduction (GO:0007165)|transmembrane transport (GO:0055085)|viral entry into host cell (GO:0046718)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ubiquitin ligase complex (GO:0000151)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			endometrium(3)|kidney(2)|large_intestine(9)|liver(4)|lung(10)|prostate(2)|urinary_tract(1)	31						TATTGTCTGCAGATAAATCCA	0.338																																					p.Q642R		.											.	.	.	0			c.A1925G						.						130.0	118.0	122.0					8																	87454934		2203	4300	6503	SO:0001583	missense	11059	exon18			GTCTGCAGATAAA	AY043361	CCDS6242.1	8q21.3	2013-07-22			ENSG00000123124	ENSG00000123124			17004	protein-coding gene	gene with protein product		602307				9169421, 9647693	Standard	NM_007013		Approved	AIP5, DKFZP434D2111	uc003ydt.3	Q9H0M0	OTTHUMG00000163690	ENST00000517970.1:c.1925A>G	8.37:g.87454934A>G	ENSP00000427793:p.Gln642Arg	Somatic	99	0		WXS	Illumina HiSeq	.	48	22	NM_007013	O00307|Q5YLC1|Q96BP4	Missense_Mutation	SNP	ENST00000517970.1	37	CCDS6242.1	.	.	.	.	.	.	.	.	.	.	A	25.9	4.684661	0.88639	.	.	ENSG00000123124	ENST00000517970;ENST00000265428;ENST00000341922;ENST00000349423	T;T;T;T	0.57907	0.37;0.37;0.37;0.37	5.4	5.4	0.78164	HECT (4);	0.000000	0.85682	D	0.000000	T	0.66519	0.2797	M	0.83483	2.645	0.80722	D	1	B;P	0.41366	0.093;0.747	B;P	0.47705	0.157;0.555	T	0.72724	-0.4207	10	0.87932	D	0	.	15.4113	0.74923	1.0:0.0:0.0:0.0	.	424;642	Q9H0M0-6;Q9H0M0	.;WWP1_HUMAN	R	642;642;512;424	ENSP00000427793:Q642R;ENSP00000265428:Q642R;ENSP00000340564:Q512R;ENSP00000342665:Q424R	ENSP00000265428:Q642R	Q	+	2	0	WWP1	87524050	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	9.287000	0.95975	2.027000	0.59764	0.477000	0.44152	CAG	.		0.338	WWP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374755.1	NM_007013	
AMZ2P1	201283	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	17	62971482	62971482	+	RNA	SNP	C	C	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr17:62971482C>T	ENST00000430983.1	-	0	204					NR_026903.1				archaelysin family metallopeptidase 2 pseudogene 1																		CCAGGAGCCTCTGGAAAGGCC	0.697																																					.		.											.	.	.	0			.						.																																					201283	.			GAGCCTCTGGAAA	AK056627		17q24.1	2012-10-16	2010-04-08		ENSG00000214174	ENSG00000214174			26491	pseudogene	pseudogene							Standard	NR_026903		Approved	FLJ32065	uc002jfb.3		OTTHUMG00000132075		17.37:g.62971482C>T		Somatic	41	0		WXS	Illumina HiSeq	.	39	16	.		RNA	SNP	ENST00000430983.1	37																																																																																				.		0.697	AMZ2P1-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000255102.1	NM_153032	
ZNF184	7738	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	6	27420544	27420544	+	Missense_Mutation	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr6:27420544A>C	ENST00000211936.6	-	6	1078	c.794T>G	c.(793-795)cTt>cGt	p.L265R	ZNF184_ENST00000377419.1_Missense_Mutation_p.L265R	NM_007149.2	NP_009080.2	Q99676	ZN184_HUMAN	zinc finger protein 184	265					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(4)|kidney(9)|large_intestine(13)|lung(14)|ovary(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	48						ATGGTTTATAAGGTTTTCACT	0.373																																					p.L265R		.											.	.	.	0			c.T794G						.						103.0	109.0	107.0					6																	27420544		2203	4300	6503	SO:0001583	missense	7738	exon6			TTTATAAGGTTTT	U66561	CCDS4624.1	6p21.3	2013-01-08	2006-06-28		ENSG00000096654	ENSG00000096654		"""Zinc fingers, C2H2-type"", ""-"""	12975	protein-coding gene	gene with protein product		602277	"""zinc finger protein 184 (Kruppel-like)"""				Standard	NM_007149		Approved		uc003nji.3	Q99676	OTTHUMG00000014478	ENST00000211936.6:c.794T>G	6.37:g.27420544A>C	ENSP00000211936:p.Leu265Arg	Somatic	48	0		WXS	Illumina HiSeq	.	55	24	NM_007149	B2R715|O60792|Q8TBA9	Missense_Mutation	SNP	ENST00000211936.6	37	CCDS4624.1	.	.	.	.	.	.	.	.	.	.	A	16.71	3.198407	0.58126	.	.	ENSG00000096654	ENST00000211936;ENST00000377419;ENST00000341087	T;T	0.53640	0.61;0.61	4.99	3.76	0.43208	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.42548	D	0.000688	T	0.53417	0.1795	M	0.64404	1.975	0.37666	D	0.922958	D	0.89917	1.0	D	0.87578	0.998	T	0.58880	-0.7558	10	0.72032	D	0.01	.	9.4274	0.38588	0.8416:0.0:0.0:0.1584	.	265	Q99676	ZN184_HUMAN	R	265	ENSP00000211936:L265R;ENSP00000366636:L265R	ENSP00000211936:L265R	L	-	2	0	ZNF184	27528523	0.998000	0.40836	1.000000	0.80357	0.993000	0.82548	5.668000	0.68074	2.093000	0.63338	0.374000	0.22700	CTT	.		0.373	ZNF184-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040146.1	NM_007149	
CALCR	799	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	7	93073026	93073026	+	Missense_Mutation	SNP	G	G	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr7:93073026G>A	ENST00000394441.1	-	8	1007	c.692C>T	c.(691-693)gCc>gTc	p.A231V	CALCR_ENST00000426151.1_Missense_Mutation_p.A231V|CALCR_ENST00000359558.2_Missense_Mutation_p.A265V|CALCR_ENST00000360249.4_Missense_Mutation_p.A247V|CALCR_ENST00000421592.1_Missense_Mutation_p.A247V	NM_001164738.1	NP_001158210.1	P30988	CALCR_HUMAN	calcitonin receptor	265					adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|protein localization to plasma membrane (GO:0072659)|protein transport (GO:0015031)|receptor internalization (GO:0031623)|response to glucocorticoid (GO:0051384)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcitonin binding (GO:0032841)|calcitonin receptor activity (GO:0004948)|protein transporter activity (GO:0008565)|receptor activity (GO:0004872)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(27)|ovary(3)|pancreas(1)|skin(3)	45	all_cancers(62;3.18e-12)|all_epithelial(64;1.34e-11)|Breast(17;0.000675)|Lung NSC(181;0.207)		STAD - Stomach adenocarcinoma(171;0.000244)		Pramlintide(DB01278)|Salmon Calcitonin(DB00017)	ATAGTTGCAGGCCATCATGTA	0.443																																					p.A265V		.											.	.	.	0			c.C794T						.						137.0	127.0	130.0					7																	93073026		2203	4300	6503	SO:0001583	missense	799	exon11			TTGCAGGCCATCA	L00587	CCDS5631.1, CCDS55125.1	7q21.3	2012-08-10			ENSG00000004948	ENSG00000004948		"""GPCR / Class B : Calcitonin receptors"""	1440	protein-coding gene	gene with protein product		114131				1331173	Standard	NM_001742		Approved	CTR	uc003umw.2	P30988	OTTHUMG00000023599	ENST00000394441.1:c.692C>T	7.37:g.93073026G>A	ENSP00000377959:p.Ala231Val	Somatic	54	0		WXS	Illumina HiSeq	.	33	14	NM_001164737	A4D1G6|F5H605|O14585|Q13941|Q5ZGL8|Q659U6|Q6DJU8|Q6T712	Missense_Mutation	SNP	ENST00000394441.1	37	CCDS5631.1	.	.	.	.	.	.	.	.	.	.	G	12.92	2.081735	0.36758	.	.	ENSG00000004948	ENST00000359558;ENST00000360249;ENST00000421592;ENST00000394441;ENST00000426151	T;T;T;T;T	0.42131	0.98;0.98;0.98;0.98;0.98	4.94	3.02	0.34903	.	.	.	.	.	T	0.24928	0.0605	N	0.11000	0.08	0.29282	N	0.869943	B;B	0.25390	0.125;0.002	B;B	0.29077	0.098;0.012	T	0.19192	-1.0313	9	0.52906	T	0.07	.	8.0843	0.30762	0.0937:0.325:0.5813:0.0	.	265;231	F5H605;A4D1G6	.;.	V	265;247;247;231;231	ENSP00000352561:A265V;ENSP00000353385:A247V;ENSP00000399552:A247V;ENSP00000377959:A231V;ENSP00000389295:A231V	ENSP00000352561:A265V	A	-	2	0	CALCR	92910962	1.000000	0.71417	0.224000	0.23877	0.976000	0.68499	4.535000	0.60629	1.466000	0.48025	0.557000	0.71058	GCC	.		0.443	CALCR-002	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254661.2	NM_001742	
ANXA9	8416	hgsc.bcm.edu	37	1	150956496	150956496	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr1:150956496G>T	ENST00000368947.4	+	5	694	c.218G>T	c.(217-219)aGa>aTa	p.R73I	ANXA9_ENST00000474997.1_3'UTR	NM_003568.2	NP_003559.2	O76027	ANXA9_HUMAN	annexin A9	73					single organismal cell-cell adhesion (GO:0016337)|synaptic transmission (GO:0007268)	cell surface (GO:0009986)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	acetylcholine receptor activity (GO:0015464)|calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|phosphatidylserine binding (GO:0001786)|phospholipid binding (GO:0005543)|protein homodimerization activity (GO:0042803)			endometrium(1)|large_intestine(1)|lung(4)|skin(2)	8	all_lung(15;1.09e-34)|Lung NSC(24;1.1e-30)|Lung SC(34;0.00202)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211)			AACCGGAGCAGAGAGCAAAGG	0.587																																					p.R73I		.											ANXA9,NS,carcinoma,0,1	ANXA9	0	0			c.G218T						.						79.0	59.0	66.0					1																	150956496		2203	4300	6503	SO:0001583	missense	8416	exon5			GGAGCAGAGAGCA	AJ009985	CCDS975.2	1q21.2	2008-02-05			ENSG00000143412	ENSG00000143412		"""Annexins"""	547	protein-coding gene	gene with protein product		603319		ANX31		9742942, 9931420	Standard	NM_003568		Approved		uc001ewa.2	O76027	OTTHUMG00000035063	ENST00000368947.4:c.218G>T	1.37:g.150956496G>T	ENSP00000357943:p.Arg73Ile	Somatic	36	0		WXS	Illumina HiSeq	.	36	2	NM_003568	Q5SZF1|Q6FI55|Q9BS00|Q9HBJ6	Missense_Mutation	SNP	ENST00000368947.4	37	CCDS975.2	.	.	.	.	.	.	.	.	.	.	G	24.0	4.487705	0.84854	.	.	ENSG00000143412	ENST00000368947	T	0.03301	3.98	5.52	3.54	0.40534	Annexin repeat, conserved site (1);	0.173147	0.51477	D	0.000093	T	0.02230	0.0069	N	0.20530	0.585	0.44771	D	0.997775	D	0.55385	0.971	P	0.55161	0.77	T	0.57528	-0.7796	10	0.49607	T	0.09	.	7.048	0.25056	0.0924:0.1735:0.7341:0.0	.	73	O76027	ANXA9_HUMAN	I	73	ENSP00000357943:R73I	ENSP00000357943:R73I	R	+	2	0	ANXA9	149223120	0.994000	0.37717	1.000000	0.80357	0.914000	0.54420	2.074000	0.41529	1.322000	0.45245	0.655000	0.94253	AGA	.		0.587	ANXA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084895.2	NM_003568	
USPL1	10208	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	13	31205128	31205128	+	Missense_Mutation	SNP	A	A	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr13:31205128A>G	ENST00000255304.4	+	4	727	c.385A>G	c.(385-387)Att>Gtt	p.I129V	USPL1_ENST00000465952.1_3'UTR	NM_005800.4	NP_005791.3	Q5W0Q7	USPL1_HUMAN	ubiquitin specific peptidase like 1	129					Cajal body organization (GO:0030576)|cell proliferation (GO:0008283)|protein desumoylation (GO:0016926)	Cajal body (GO:0015030)|extracellular space (GO:0005615)	SUMO binding (GO:0032183)|SUMO-specific isopeptidase activity (GO:0070140)			breast(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(15)|pancreas(3)|skin(3)	34		Lung SC(185;0.0257)|Breast(139;0.203)		all cancers(112;0.0306)|Epithelial(112;0.131)|OV - Ovarian serous cystadenocarcinoma(117;0.134)		TAGAAATTATATTGCTATTGA	0.368																																					p.I129V	Ovarian(60;318 1180 1554 28110 31601)	.											.	.	.	0			c.A385G						.						61.0	63.0	63.0					13																	31205128		2203	4300	6503	SO:0001583	missense	10208	exon4			AATTATATTGCTA	X59131	CCDS9336.1	13q12-q14	2012-11-14	2005-11-24	2005-11-24	ENSG00000132952	ENSG00000132952			20294	protein-coding gene	gene with protein product			"""chromosome 13 open reading frame 22"""	C13orf22		22878415	Standard	NM_005800		Approved	bA121O19.1, D13S106E	uc001utc.2	Q5W0Q7	OTTHUMG00000016675	ENST00000255304.4:c.385A>G	13.37:g.31205128A>G	ENSP00000255304:p.Ile129Val	Somatic	59	0		WXS	Illumina HiSeq	.	44	20	NM_005800	Q14109|Q6AI45|Q8IY30|Q8IYE8	Missense_Mutation	SNP	ENST00000255304.4	37	CCDS9336.1	.	.	.	.	.	.	.	.	.	.	A	4.024	0.001900	0.07819	.	.	ENSG00000132952	ENST00000255304	T	0.06528	3.29	6.07	-12.1	0.00011	.	2.127980	0.01502	N	0.017556	T	0.02767	0.0083	L	0.27053	0.805	0.09310	N	1	B	0.06786	0.001	B	0.08055	0.003	T	0.42716	-0.9435	10	0.02654	T	1	0.4784	3.8531	0.08963	0.2446:0.3791:0.284:0.0922	.	129	Q5W0Q7	USPL1_HUMAN	V	129	ENSP00000255304:I129V	ENSP00000255304:I129V	I	+	1	0	USPL1	30103128	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.281000	0.08456	-2.102000	0.00845	0.533000	0.62120	ATT	.		0.368	USPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044369.1	NM_005800	
C8orf33	65265	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	8	146277985	146277985	+	Missense_Mutation	SNP	T	T	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr8:146277985T>C	ENST00000331434.6	+	2	134	c.20T>C	c.(19-21)cTt>cCt	p.L7P		NM_023080.2	NP_075568.1	Q9H7E9	CH033_HUMAN	chromosome 8 open reading frame 33	7										endometrium(1)|large_intestine(1)|lung(4)|urinary_tract(1)	7	all_cancers(97;8.72e-12)|all_epithelial(106;1.07e-10)|Lung NSC(106;7.18e-05)|all_lung(105;0.00021)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		Epithelial(56;9.1e-38)|all cancers(56;7.37e-33)|BRCA - Breast invasive adenocarcinoma(115;0.0424)|Colorectal(110;0.055)	GBM - Glioblastoma multiforme(99;0.243)		CTGGGACATCTTGCTGGGGAG	0.701																																					p.L7P		.											.	.	.	0			c.T20C						.						50.0	66.0	60.0					8																	146277985		2203	4299	6502	SO:0001583	missense	65265	exon2			GACATCTTGCTGG		CCDS34974.1	8q24.3	2012-04-11			ENSG00000182307	ENSG00000182307			26104	protein-coding gene	gene with protein product							Standard	NM_023080		Approved	FLJ20989	uc003zfc.4	Q9H7E9	OTTHUMG00000165256	ENST00000331434.6:c.20T>C	8.37:g.146277985T>C	ENSP00000330361:p.Leu7Pro	Somatic	91	0		WXS	Illumina HiSeq	.	78	28	NM_023080	A6NGC0|Q96BT8	Missense_Mutation	SNP	ENST00000331434.6	37	CCDS34974.1	.	.	.	.	.	.	.	.	.	.	.	10.80	1.452768	0.26074	.	.	ENSG00000182307	ENST00000331434	.	.	.	2.87	1.91	0.25777	.	0.201576	0.28989	N	0.013483	T	0.05914	0.0154	N	0.00289	-1.7	0.19300	N	0.999978	B	0.02656	0.0	B	0.01281	0.0	T	0.38286	-0.9668	8	.	.	.	0.0066	5.8167	0.18495	0.0:0.8446:0.0:0.1554	.	7	Q9H7E9	CH033_HUMAN	P	7	.	.	L	+	2	0	C8orf33	146248789	0.000000	0.05858	0.051000	0.19133	0.050000	0.14768	-0.243000	0.08915	0.743000	0.32719	-0.182000	0.12963	CTT	.		0.701	C8orf33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382995.1	NM_023080	
PCDHGA6	56109	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	5	140755037	140755037	+	Missense_Mutation	SNP	G	G	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr5:140755037G>A	ENST00000517434.1	+	1	1387	c.1387G>A	c.(1387-1389)Gaa>Aaa	p.E463K	PCDHGB3_ENST00000576222.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGB2_ENST00000522605.1_Intron	NM_018919.2|NM_032086.1	NP_061742.1|NP_114475.1	Q9Y5G7	PCDG6_HUMAN	protocadherin gamma subfamily A, 6	463	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|large_intestine(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTATGTCCTTGAAAACAACCC	0.527																																					p.E463K		.											PCDHGA6_ENST00000517434,NS,carcinoma,0,1	PCDHGA6_ENST00000517434	0	0			c.G1387A						.						138.0	151.0	147.0					5																	140755037		2038	4213	6251	SO:0001583	missense	56109	exon1			GTCCTTGAAAACA	AF152513	CCDS54926.1, CCDS75335.1	5q31	2010-01-26				ENSG00000253731		"""Cadherins / Protocadherins : Clustered"""	8704	other	protocadherin		606293				10380929	Standard	NM_018919		Approved	PCDH-GAMMA-A6		Q9Y5G7		ENST00000517434.1:c.1387G>A	5.37:g.140755037G>A	ENSP00000429601:p.Glu463Lys	Somatic	21	0		WXS	Illumina HiSeq	.	30	13	NM_018919	A6H8K7|B2RN55|Q9Y5D1	Missense_Mutation	SNP	ENST00000517434.1	37	CCDS54926.1	.	.	.	.	.	.	.	.	.	.	.	17.51	3.406921	0.62399	.	.	ENSG00000253731	ENST00000517434	T	0.76316	-1.01	5.13	5.13	0.70059	Cadherin (4);Cadherin-like (1);	0.000000	0.31301	U	0.007895	D	0.93458	0.7913	H	0.98965	4.385	0.44194	D	0.997015	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.95691	0.8740	10	0.87932	D	0	.	19.1356	0.93426	0.0:0.0:1.0:0.0	.	463;463	Q9Y5G7-2;Q9Y5G7	.;PCDG6_HUMAN	K	463	ENSP00000429601:E463K	ENSP00000429601:E463K	E	+	1	0	PCDHGA6	140735221	1.000000	0.71417	1.000000	0.80357	0.065000	0.16274	7.831000	0.86748	2.826000	0.97356	0.655000	0.94253	GAA	.		0.527	PCDHGA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374743.1	NM_018919	
UHMK1	127933	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	162467956	162467956	+	Missense_Mutation	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr1:162467956T>G	ENST00000489294.1	+	1	324	c.166T>G	c.(166-168)Ttc>Gtc	p.F56V	UHMK1_ENST00000545294.1_Intron|UHMK1_ENST00000538489.1_Missense_Mutation_p.F56V|UHMK1_ENST00000282169.8_3'UTR	NM_175866.4	NP_787062.1	Q8TAS1	UHMK1_HUMAN	U2AF homology motif (UHM) kinase 1	56	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159, ECO:0000305}.				cell cycle arrest (GO:0007050)|neuron projection development (GO:0031175)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of translational initiation (GO:0045948)|protein autophosphorylation (GO:0046777)|regulation of protein export from nucleus (GO:0046825)	axon (GO:0030424)|dendrite cytoplasm (GO:0032839)|neuronal ribonucleoprotein granule (GO:0071598)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|ribonucleoprotein complex binding (GO:0043021)|RNA binding (GO:0003723)|transferase activity (GO:0016740)			endometrium(1)|large_intestine(2)|lung(6)|prostate(2)	11	all_hematologic(112;0.115)		BRCA - Breast invasive adenocarcinoma(70;0.126)			CCTCAAGCAGTTCTTGCCGCC	0.667																																					p.F56V		.											.	.	.	0			c.T166G						.						12.0	15.0	14.0					1																	162467956		2194	4296	6490	SO:0001583	missense	127933	exon1			AAGCAGTTCTTGC	BC026046	CCDS1239.1, CCDS53423.1, CCDS53424.1	1q23.1	2013-02-12			ENSG00000152332	ENSG00000152332		"""RNA binding motif (RRM) containing"""	19683	protein-coding gene	gene with protein product		608849				12093740, 12782393	Standard	NM_175866		Approved	KIS, Kist	uc001gcc.2	Q8TAS1	OTTHUMG00000031373	ENST00000489294.1:c.166T>G	1.37:g.162467956T>G	ENSP00000420270:p.Phe56Val	Somatic	24	0		WXS	Illumina HiSeq	.	29	19	NM_175866	A8K8K4|G3V1M1|Q96C22	Missense_Mutation	SNP	ENST00000489294.1	37	CCDS1239.1	.	.	.	.	.	.	.	.	.	.	T	26.1	4.702466	0.88924	.	.	ENSG00000152332	ENST00000538489;ENST00000489294	T;T	0.18338	2.22;2.22	4.94	4.94	0.65067	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.64402	D	0.000001	T	0.07007	0.0178	N	0.04373	-0.215	.	.	.	D;D	0.56287	0.968;0.975	D;D	0.74023	0.969;0.982	T	0.10474	-1.0628	9	0.05436	T	0.98	-12.4638	11.1664	0.48545	0.0:0.0:0.0:1.0	.	56;56	Q8TAS1-2;Q8TAS1	.;UHMK1_HUMAN	V	56	ENSP00000446416:F56V;ENSP00000420270:F56V	ENSP00000420270:F56V	F	+	1	0	UHMK1	160734580	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.766000	0.62279	2.192000	0.70111	0.533000	0.62120	TTC	.		0.667	UHMK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076788.1	NM_175866	
ZFAND2B	130617	hgsc.bcm.edu;broad.mit.edu	37	2	220072731	220072731	+	Silent	SNP	T	T	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr2:220072731T>C	ENST00000289528.5	+	4	600	c.405T>C	c.(403-405)tcT>tcC	p.S135S	ZFAND2B_ENST00000409206.1_Silent_p.S135S|ZFAND2B_ENST00000409594.1_Silent_p.S135S|ZFAND2B_ENST00000409412.1_Silent_p.S135S|ZFAND2B_ENST00000409319.1_Silent_p.S135S|ZFAND2B_ENST00000409097.1_Silent_p.S135S|ZFAND2B_ENST00000409217.1_Silent_p.S135S|ZFAND2B_ENST00000444522.2_Silent_p.S135S|ZFAND2B_ENST00000409336.1_Silent_p.S135S	NM_001270998.1|NM_001270999.1|NM_138802.2	NP_001257927.1|NP_001257928.1|NP_620157.1	Q8WV99	ZFN2B_HUMAN	zinc finger, AN1-type domain 2B	135						endoplasmic reticulum (GO:0005783)	zinc ion binding (GO:0008270)			endometrium(2)|kidney(4)|lung(4)|upper_aerodigestive_tract(1)	11		Renal(207;0.0915)		Epithelial(149;1.16e-06)|all cancers(144;0.000191)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		ATGATTGCTCTGGGGAGGGGC	0.552																																					p.S135S		.											.	.	.	0			c.T405C						.						77.0	82.0	80.0					2																	220072731		2202	4300	6502	SO:0001819	synonymous_variant	130617	exon4			TTGCTCTGGGGAG	AK074571	CCDS2435.1, CCDS74656.1	2q35	2010-04-23	2005-08-22		ENSG00000158552	ENSG00000158552		"""Zinc fingers, AN1-type domain containing"""	25206	protein-coding gene	gene with protein product	"""arsenite inducible RNA associated protein-like"""	613474	"""zinc finger, AN1-type 2B"""			18467495	Standard	NM_138802		Approved	AIRAPL	uc002vka.4	Q8WV99	OTTHUMG00000133135	ENST00000289528.5:c.405T>C	2.37:g.220072731T>C		Somatic	11	0		WXS	Illumina HiSeq	.	9	4	NM_138802	Q8NB98	Silent	SNP	ENST00000289528.5	37	CCDS2435.1																																																																																			.		0.552	ZFAND2B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256824.2	NM_138802	
WDFY4	57705	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	10	50025455	50025455	+	Splice_Site	SNP	G	G	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr10:50025455G>A	ENST00000325239.5	+	31	5532		c.e31+1		WDFY4_ENST00000413659.2_Splice_Site	NM_020945.1	NP_065996.1	Q6ZS81	WDFY4_HUMAN	WDFY family member 4							integral component of membrane (GO:0016021)				NS(2)|breast(5)|central_nervous_system(4)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|lung(3)|pancreas(2)|prostate(5)|skin(6)|stomach(1)	48						AGCCCAAAAGGTAGGACATGC	0.597																																					.		.											.	.	.	0			c.5505+1G>A						.						23.0	29.0	27.0					10																	50025455		692	1591	2283	SO:0001630	splice_region_variant	57705	exon32			CAAAAGGTAGGAC	AK074085	CCDS44385.1	10q11.23	2013-01-10			ENSG00000128815	ENSG00000128815		"""WD repeat domain containing"""	29323	protein-coding gene	gene with protein product		613316	"""chromosome 10 open reading frame 64"""	C10orf64		10997877	Standard	NM_020945		Approved	KIAA1607, Em:AC060234.3, FLJ45748	uc001jha.4	Q6ZS81	OTTHUMG00000018180	ENST00000325239.5:c.5505+1G>A	10.37:g.50025455G>A		Somatic	45	0		WXS	Illumina HiSeq	.	34	12	NM_020945	B9ZVP2|Q86WZ4|Q8N4A3|Q8TEN7|Q96BE1|Q9H7H8|Q9HCG5	Splice_Site	SNP	ENST00000325239.5	37	CCDS44385.1	.	.	.	.	.	.	.	.	.	.	G	14.03	2.414646	0.42817	.	.	ENSG00000128815	ENST00000426033;ENST00000325239;ENST00000312002;ENST00000374161	.	.	.	5.46	5.46	0.80206	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.0343	0.80612	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	WDFY4	49695461	1.000000	0.71417	1.000000	0.80357	0.232000	0.25224	7.142000	0.77339	2.577000	0.86979	0.655000	0.94253	.	.		0.597	WDFY4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		XM_033379	Intron
ARHGAP19	84986	hgsc.bcm.edu	37	10	98988750	98988750	+	Intron	SNP	T	T	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr10:98988750T>C	ENST00000358531.4	-	11	1503				ARHGAP19_ENST00000371027.1_Intron|ARHGAP19_ENST00000355366.5_Intron|ARHGAP19-SLIT1_ENST00000453547.2_Intron|ARHGAP19_ENST00000487035.1_Intron|ARHGAP19-SLIT1_ENST00000316676.8_Intron	NM_001204300.1|NM_032900.5	NP_001191229.1|NP_116289.4	Q14CB8	RHG19_HUMAN	Rho GTPase activating protein 19						regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|nucleus (GO:0005634)	GTPase activator activity (GO:0005096)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|prostate(1)|stomach(2)|urinary_tract(1)	13		Colorectal(252;0.0854)		Epithelial(162;7.65e-09)|all cancers(201;4.49e-07)		aataaccatctggtgaatgaa	0.438																																					.		.											.	.	.	0			.						.																																			SO:0001627	intron_variant	0	.			ACCATCTGGTGAA	AK074122	CCDS7454.2, CCDS58092.1, CCDS73175.1	10q24.2	2011-06-29			ENSG00000213390	ENSG00000213390		"""Rho GTPase activating proteins"""	23724	protein-coding gene	gene with protein product		611587					Standard	NM_032900		Approved	FLJ00194, MGC14258	uc001knb.3	Q14CB8	OTTHUMG00000018845	ENST00000358531.4:c.1474+153A>G	10.37:g.98988750T>C		Somatic	58	0		WXS	Illumina HiSeq	.	35	12	.	A1XCP1|B4DZR1|Q14CF2|Q5J8M2|Q5T460|Q5T462|Q68DG6|Q8N9X1|Q8NF34|Q8TEK1	RNA	SNP	ENST00000358531.4	37	CCDS7454.2																																																																																			.		0.438	ARHGAP19-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049647.2	NM_032900	
SLC27A5	10998	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	19	59009967	59009967	+	Missense_Mutation	SNP	A	A	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr19:59009967A>T	ENST00000263093.2	-	10	2097	c.1988T>A	c.(1987-1989)tTt>tAt	p.F663Y	SLC27A5_ENST00000594786.1_Missense_Mutation_p.F68Y|SLC27A5_ENST00000599700.1_5'UTR|SLC27A5_ENST00000601355.1_Missense_Mutation_p.F579Y	NM_012254.2	NP_036386.1	Q9Y2P5	S27A5_HUMAN	solute carrier family 27 (fatty acid transporter), member 5	663					bile acid and bile salt transport (GO:0015721)|bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|ketone body biosynthetic process (GO:0046951)|plasma membrane long-chain fatty acid transport (GO:0015911)|small molecule metabolic process (GO:0044281)|triglyceride mobilization (GO:0006642)|very long-chain fatty acid metabolic process (GO:0000038)	basal plasma membrane (GO:0009925)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|protein complex (GO:0043234)	ATP binding (GO:0005524)|cholate-CoA ligase activity (GO:0047747)|fatty acid transporter activity (GO:0015245)|very long-chain fatty acid-CoA ligase activity (GO:0031957)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(7)|ovary(1)|skin(1)|urinary_tract(1)	19		all_cancers(17;4.4e-22)|all_epithelial(17;2.15e-16)|Lung NSC(17;1.24e-06)|all_lung(17;5.41e-06)|Colorectal(82;3.46e-05)|Renal(17;0.00179)|all_neural(62;0.00607)|Ovarian(87;0.0443)|Breast(46;0.0928)|Medulloblastoma(540;0.184)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0168)|Lung(386;0.181)		GTCCAGTACAAACAGAGGGTC	0.602																																					p.F663Y		.											.	.	.	0			c.T1988A						.						156.0	130.0	139.0					19																	59009967		2203	4300	6503	SO:0001583	missense	10998	exon10			AGTACAAACAGAG	AF064255	CCDS12983.1	19q13.43	2013-07-15			ENSG00000083807	ENSG00000083807		"""Acyl-CoA synthetase family"", ""Solute carriers"""	10999	protein-coding gene	gene with protein product	"""fatty-acid-Coenzyme A ligase, very long-chain 3"""	603314				10479480, 10749848	Standard	NM_012254		Approved	FATP5, VLACSR, VLCS-H2, VLCSH2, FACVL3, FLJ22987, ACSVL6, ACSB	uc002qtc.2	Q9Y2P5	OTTHUMG00000183543	ENST00000263093.2:c.1988T>A	19.37:g.59009967A>T	ENSP00000263093:p.Phe663Tyr	Somatic	37	0		WXS	Illumina HiSeq	.	25	10	NM_012254	B3KVP6|B4DPQ1	Missense_Mutation	SNP	ENST00000263093.2	37	CCDS12983.1	.	.	.	.	.	.	.	.	.	.	A	0.017	-1.507175	0.00984	.	.	ENSG00000083807	ENST00000263093	T	0.48836	0.8	4.85	0.912	0.19349	.	0.192654	0.45361	N	0.000379	T	0.15305	0.0369	N	0.01817	-0.705	0.20074	N	0.999939	B	0.10296	0.003	B	0.12156	0.007	T	0.34675	-0.9819	10	0.02654	T	1	-11.064	8.142	0.31089	0.3907:0.0:0.0:0.6093	.	663	Q9Y2P5	S27A5_HUMAN	Y	663	ENSP00000263093:F663Y	ENSP00000263093:F663Y	F	-	2	0	SLC27A5	63701779	0.367000	0.25023	0.015000	0.15790	0.037000	0.13140	0.646000	0.24797	0.250000	0.21479	0.533000	0.62120	TTT	.		0.602	SLC27A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467060.1	NM_012254	
CDH19	28513	hgsc.bcm.edu	37	18	64172343	64172343	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr18:64172343G>T	ENST00000262150.2	-	12	2317	c.2025C>A	c.(2023-2025)agC>agA	p.S675R	CDH19_ENST00000540086.1_3'UTR	NM_021153.3	NP_066976.1	Q96JQ0	PCD16_HUMAN	cadherin 19, type 2	0	Cadherin 6. {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)			NS(1)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(13)|lung(22)|ovary(1)|prostate(3)|skin(7)	61		Esophageal squamous(42;0.0132)				TGATCTCAGCGCTTGTGGTTT	0.478																																					p.S675R		.											CDH19,right_lower_lobe,carcinoma,0,1	CDH19	0	0			c.C2025A						.						173.0	163.0	166.0					18																	64172343		2203	4300	6503	SO:0001583	missense	28513	exon12			CTCAGCGCTTGTG	AJ007607	CCDS11994.1, CCDS59325.1	18q22.1	2010-01-26			ENSG00000071991	ENSG00000071991		"""Cadherins / Major cadherins"""	1758	protein-coding gene	gene with protein product		603016				10995570	Standard	NM_021153		Approved	CDH7	uc002lkc.2	Q9H159	OTTHUMG00000132802	ENST00000262150.2:c.2025C>A	18.37:g.64172343G>T	ENSP00000262150:p.Ser675Arg	Somatic	38	0		WXS	Illumina HiSeq	.	33	3	NM_021153	O15098	Missense_Mutation	SNP	ENST00000262150.2	37	CCDS11994.1	.	.	.	.	.	.	.	.	.	.	G	0.057	-1.233881	0.01505	.	.	ENSG00000071991	ENST00000262150	T	0.76316	-1.01	5.18	-3.92	0.04155	Cadherin, cytoplasmic domain (1);	0.810448	0.11650	N	0.542874	T	0.38188	0.1031	N	0.01705	-0.755	0.09310	N	1	B	0.06786	0.001	B	0.09377	0.004	T	0.41556	-0.9502	10	0.06891	T	0.86	.	0.9049	0.01282	0.2056:0.31:0.2074:0.2769	.	675	Q9H159	CAD19_HUMAN	R	675	ENSP00000262150:S675R	ENSP00000262150:S675R	S	-	3	2	CDH19	62323323	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-3.135000	0.00588	-0.812000	0.04363	-0.219000	0.12488	AGC	.		0.478	CDH19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256219.1	NM_021153	
SLC5A10	125206	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	17	18880179	18880179	+	Silent	SNP	C	C	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr17:18880179C>A	ENST00000395645.3	+	9	877	c.859C>A	c.(859-861)Cga>Aga	p.R287R	SLC5A10_ENST00000395643.2_Silent_p.R260R|FAM83G_ENST00000388995.6_Intron|SLC5A10_ENST00000395647.2_Silent_p.R287R|FAM83G_ENST00000585154.2_Intron|SLC5A10_ENST00000417251.2_Silent_p.R287R|SLC5A10_ENST00000395642.1_Silent_p.R204R|FAM83G_ENST00000345041.4_Intron|SLC5A10_ENST00000317977.6_Silent_p.R204R	NM_001042450.2	NP_001035915.1	A0PJK1	SC5AA_HUMAN	solute carrier family 5 (sodium/sugar cotransporter), member 10	287					sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(3)|ovary(3)|prostate(3)|skin(3)	24						CATCGTGCAGCGATCACTGTC	0.622																																					p.R287R		.											.	.	.	0			c.C859A						.						118.0	82.0	94.0					17																	18880179		2203	4300	6503	SO:0001819	synonymous_variant	125206	exon9			GTGCAGCGATCAC		CCDS11201.2, CCDS42275.1, CCDS59277.1, CCDS59278.1, CCDS74008.1	17p11.2	2013-07-19	2013-07-19		ENSG00000154025	ENSG00000154025		"""Solute carriers"""	23155	protein-coding gene	gene with protein product			"""solute carrier family 5 (sodium/glucose cotransporter), member 10"""				Standard	NM_152351		Approved	SGLT5	uc002gut.2	A0PJK1	OTTHUMG00000178143	ENST00000395645.3:c.859C>A	17.37:g.18880179C>A		Somatic	35	0		WXS	Illumina HiSeq	.	33	7	NM_001042450	A8MUC9|B4DPI0|B7WPR4|Q6P5X0|Q8IXM4|Q96LQ1	Silent	SNP	ENST00000395645.3	37	CCDS42275.1																																																																																			.		0.622	SLC5A10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132129.2	NM_152351	
PLXNA4	91584	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	7	131887488	131887488	+	Missense_Mutation	SNP	G	G	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr7:131887488G>A	ENST00000359827.3	-	12	3465	c.2503C>T	c.(2503-2505)Cgc>Tgc	p.R835C	PLXNA4_ENST00000321063.4_Missense_Mutation_p.R835C			Q9HCM2	PLXA4_HUMAN	plexin A4	835	PSI 3.				anterior commissure morphogenesis (GO:0021960)|axon guidance (GO:0007411)|chemorepulsion of branchiomotor axon (GO:0021793)|facial nerve structural organization (GO:0021612)|glossopharyngeal nerve morphogenesis (GO:0021615)|postganglionic parasympathetic nervous system development (GO:0021784)|regulation of axon extension involved in axon guidance (GO:0048841)|regulation of negative chemotaxis (GO:0050923)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|sympathetic nervous system development (GO:0048485)|trigeminal nerve structural organization (GO:0021637)|vagus nerve morphogenesis (GO:0021644)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)			NS(1)|breast(1)|endometrium(3)|kidney(4)|large_intestine(14)|lung(17)|ovary(1)|prostate(2)|skin(1)|stomach(1)	45						CAGTGCTGGCGCAGGGTGCAC	0.652																																					p.R835C		.											.	.	.	0			c.C2503T						.						25.0	28.0	27.0					7																	131887488		2087	4221	6308	SO:0001583	missense	91584	exon12			GCTGGCGCAGGGT	AB046770, AK123428	CCDS5826.1, CCDS43646.1, CCDS43647.1	7q32.3	2007-09-26	2007-09-26	2007-09-26	ENSG00000221866	ENSG00000221866		"""Plexins"""	9102	protein-coding gene	gene with protein product		604280	"""plexin A4, A"", ""plexin A4, B"""	PLXNA4A, PLXNA4B			Standard	NM_181775		Approved	KIAA1550, DKFZp434G0625PRO34003, FAYV2820	uc003vra.4	Q9HCM2	OTTHUMG00000155108	ENST00000359827.3:c.2503C>T	7.37:g.131887488G>A	ENSP00000352882:p.Arg835Cys	Somatic	79	0		WXS	Illumina HiSeq	.	69	33	NM_020911	A4D1N6|E9PAM2|Q6UWC6|Q6ZW89|Q8N969|Q8ND00|Q8NEN3|Q9NTD4	Missense_Mutation	SNP	ENST00000359827.3	37	CCDS43646.1	.	.	.	.	.	.	.	.	.	.	G	19.28	3.798130	0.70567	.	.	ENSG00000221866	ENST00000321063;ENST00000359827	T;T	0.18657	2.2;2.2	4.5	3.61	0.41365	.	0.057135	0.64402	D	0.000003	T	0.44435	0.1293	M	0.83223	2.63	0.51767	D	0.999933	D	0.76494	0.999	D	0.63283	0.913	T	0.49093	-0.8975	10	0.72032	D	0.01	.	11.1637	0.48531	0.0:0.0:0.482:0.518	.	835	Q9HCM2	PLXA4_HUMAN	C	835	ENSP00000323194:R835C;ENSP00000352882:R835C	ENSP00000323194:R835C	R	-	1	0	PLXNA4	131538028	0.923000	0.31300	0.997000	0.53966	0.978000	0.69477	1.538000	0.36094	1.109000	0.41680	0.561000	0.74099	CGC	.		0.652	PLXNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338422.2	NM_181775	
PIK3R1	5295	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	5	67569785	67569785	+	Missense_Mutation	SNP	T	T	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr5:67569785T>C	ENST00000521381.1	+	4	1062	c.446T>C	c.(445-447)cTa>cCa	p.L149P	PIK3R1_ENST00000396611.1_Missense_Mutation_p.L149P|PIK3R1_ENST00000274335.5_Missense_Mutation_p.L149P|PIK3R1_ENST00000521657.1_Missense_Mutation_p.L149P	NM_181523.2	NP_852664.1	P27986	P85A_HUMAN	phosphoinositide-3-kinase, regulatory subunit 1 (alpha)	149	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				B cell differentiation (GO:0030183)|blood coagulation (GO:0007596)|cellular response to UV (GO:0034644)|epidermal growth factor receptor signaling pathway (GO:0007173)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|growth hormone receptor signaling pathway (GO:0060396)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|leukocyte migration (GO:0050900)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of osteoclast differentiation (GO:0045671)|neurotrophin TRK receptor signaling pathway (GO:0048011)|NFAT protein import into nucleus (GO:0051531)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of cell migration (GO:0030335)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of glucose import (GO:0046326)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|protein phosphorylation (GO:0006468)|regulation of phosphatidylinositol 3-kinase activity (GO:0043551)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|membrane (GO:0016020)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	ErbB-3 class receptor binding (GO:0043125)|insulin binding (GO:0043559)|insulin receptor binding (GO:0005158)|insulin receptor substrate binding (GO:0043560)|insulin-like growth factor receptor binding (GO:0005159)|neurotrophin TRKA receptor binding (GO:0005168)|phosphatidylinositol 3-kinase binding (GO:0043548)|phosphatidylinositol 3-kinase regulator activity (GO:0035014)|protein phosphatase binding (GO:0019903)|transmembrane receptor protein tyrosine kinase adaptor activity (GO:0005068)	p.?(2)|p.0?(1)		breast(12)|central_nervous_system(31)|cervix(1)|endometrium(68)|haematopoietic_and_lymphoid_tissue(5)|kidney(1)|large_intestine(32)|lung(10)|ovary(9)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	178		Lung NSC(167;1.99e-05)|Prostate(74;0.00308)|Ovarian(174;0.00473)|Colorectal(97;0.0176)		OV - Ovarian serous cystadenocarcinoma(47;3.76e-51)|Lung(70;0.0211)	Isoprenaline(DB01064)	TGTTCAACTCTATACAGAACA	0.473			"""Mis, F, O"""		"""gliobastoma, ovarian, colorectal"""					TCGA GBM(4;<1E-08)																											p.L149P		.		Rec	yes		5	5q13.1	5295	"""phosphoinositide-3-kinase, regulatory subunit 1 (alpha)"""		"""E, O"""	.	.	.	3	Unknown(2)|Whole gene deletion(1)	large_intestine(1)|lung(1)|breast(1)	c.T446C						.						211.0	196.0	201.0					5																	67569785		2203	4300	6503	SO:0001583	missense	5295	exon4			CAACTCTATACAG	M61906	CCDS3993.1, CCDS3994.1, CCDS3995.1, CCDS56374.1	5q13.1	2014-09-17	2008-02-04		ENSG00000145675	ENSG00000145675		"""SH2 domain containing"""	8979	protein-coding gene	gene with protein product		171833				1314371, 18387942	Standard	NM_181524		Approved	GRB1, p85-ALPHA, p85	uc003jva.3	P27986	OTTHUMG00000131251	ENST00000521381.1:c.446T>C	5.37:g.67569785T>C	ENSP00000428056:p.Leu149Pro	Somatic	42	0		WXS	Illumina HiSeq	.	29	9	NM_181523	B3KT19|D3DWA0|E7EX19|Q15747|Q4VBZ7|Q53EM6|Q8IXA2|Q8N1C5	Missense_Mutation	SNP	ENST00000521381.1	37	CCDS3993.1	.	.	.	.	.	.	.	.	.	.	T	21.0	4.075147	0.76415	.	.	ENSG00000145675	ENST00000521381;ENST00000521657;ENST00000396611;ENST00000274335;ENST00000520675	T;T;T;T;T	0.56275	0.47;0.47;0.47;0.47;0.47	5.67	5.67	0.87782	Rho GTPase-activating protein domain (4);Rho GTPase activation protein (1);	0.000000	0.64402	D	0.000002	T	0.73179	0.3554	M	0.83774	2.66	0.80722	D	1	D	0.60575	0.988	P	0.62885	0.908	T	0.78117	-0.2329	10	0.87932	D	0	-7.1638	15.9173	0.79531	0.0:0.0:0.0:1.0	.	149	P27986	P85A_HUMAN	P	149;149;149;149;51	ENSP00000428056:L149P;ENSP00000429277:L149P;ENSP00000379855:L149P;ENSP00000274335:L149P;ENSP00000428566:L51P	ENSP00000274335:L149P	L	+	2	0	PIK3R1	67605541	1.000000	0.71417	0.953000	0.39169	0.988000	0.76386	5.959000	0.70339	2.170000	0.68504	0.533000	0.62120	CTA	.		0.473	PIK3R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254013.2	NM_181504	
TMCC1	23023	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	3	129546839	129546839	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr3:129546839G>T	ENST00000393238.3	-	3	723	c.383C>A	c.(382-384)cCa>cAa	p.P128Q	TMCC1_ENST00000426664.2_Missense_Mutation_p.P14Q	NM_001017395.3	NP_001017395.2	O94876	TMCC1_HUMAN	transmembrane and coiled-coil domain family 1	128						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)			PLXND1/TMCC1(4)	breast(1)|endometrium(3)|large_intestine(8)|lung(12)|skin(1)	25						TGGGGCCTCTGGCTTGCCCCG	0.562																																					p.P128Q		.											.	.	.	0			c.C383A						.						102.0	93.0	96.0					3																	129546839		2203	4300	6503	SO:0001583	missense	23023	exon3			GCCTCTGGCTTGC	AB018322	CCDS33855.1	3q21.3	2010-04-19	2005-07-13		ENSG00000172765	ENSG00000172765		"""Transmembrane and coiled-coil domain containing"""	29116	protein-coding gene	gene with protein product			"""transmembrane and coiled-coil domains 1"""			9872452	Standard	NR_033361		Approved	KIAA0779	uc021xdy.1	O94876	OTTHUMG00000159579	ENST00000393238.3:c.383C>A	3.37:g.129546839G>T	ENSP00000376930:p.Pro128Gln	Somatic	50	0		WXS	Illumina HiSeq	.	36	14	NM_001017395	A8K5Y3|B4DE04|Q68E06|Q8IXM8	Missense_Mutation	SNP	ENST00000393238.3	37	CCDS33855.1	.	.	.	.	.	.	.	.	.	.	G	11.81	1.750509	0.31046	.	.	ENSG00000172765	ENST00000393238;ENST00000426664;ENST00000505616	T;T;T	0.42900	1.58;1.59;0.96	5.98	5.98	0.97165	.	0.387744	0.26159	N	0.025989	T	0.31389	0.0795	N	0.14661	0.345	0.80722	D	1	B	0.19583	0.037	B	0.20384	0.029	T	0.07731	-1.0757	10	0.59425	D	0.04	-0.0774	17.3499	0.87321	0.0:0.1246:0.8754:0.0	.	128	O94876	TMCC1_HUMAN	Q	128;14;14	ENSP00000376930:P128Q;ENSP00000389892:P14Q;ENSP00000422544:P14Q	ENSP00000376930:P128Q	P	-	2	0	TMCC1	131029529	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.247000	0.65416	2.838000	0.97847	0.591000	0.81541	CCA	.		0.562	TMCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356418.2	NM_015008	
CELF3	11189	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	151687099	151687099	+	Missense_Mutation	SNP	C	C	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr1:151687099C>T	ENST00000290583.4	-	2	992	c.199G>A	c.(199-201)Gcc>Acc	p.A67T	RIIAD1_ENST00000326413.3_Intron|AL589765.1_ENST00000442233.2_Intron|CELF3_ENST00000290585.4_Missense_Mutation_p.A67T	NM_001172648.1|NM_007185.4	NP_001166119.1|NP_009116.3	Q5SZQ8	CELF3_HUMAN	CUGBP, Elav-like family member 3	67	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				mRNA splicing, via spliceosome (GO:0000398)|positive regulation of mRNA splicing, via spliceosome (GO:0048026)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing (GO:0008380)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)	21						TCGTGCAGGGCGCTCTGGGCC	0.642																																					p.A67T		.											.	.	.	0			c.G199A						.						39.0	33.0	35.0					1																	151687099		2195	4280	6475	SO:0001583	missense	11189	exon2			GCAGGGCGCTCTG	U80759	CCDS1002.1, CCDS53367.1	1q21	2013-02-12	2010-02-19	2010-02-19	ENSG00000159409	ENSG00000159409		"""Trinucleotide (CAG) repeat containing"", ""RNA binding motif (RRM) containing"""	11967	protein-coding gene	gene with protein product	"""expanded repeat domain, CAG/CTG 4"", ""CAG repeat domain"", ""CUG-BP and ETR-3 like factor 3"""	612678	"""trinucleotide repeat containing 4"""	TNRC4		9225980	Standard	XM_005244859		Approved	CAGH4, BRUNOL1, ERDA4, MGC57297	uc001eys.2	Q5SZQ8	OTTHUMG00000013064	ENST00000290583.4:c.199G>A	1.37:g.151687099C>T	ENSP00000290583:p.Ala67Thr	Somatic	52	0		WXS	Illumina HiSeq	.	60	47	NM_007185	B7ZKK6|O15414|Q499Y6|Q5SZQ7|Q6NVK0|Q8IZ98|Q9BZC2|Q9HB30	Missense_Mutation	SNP	ENST00000290583.4	37	CCDS1002.1	.	.	.	.	.	.	.	.	.	.	C	32	5.147308	0.94603	.	.	ENSG00000159409	ENST00000290585;ENST00000290583;ENST00000368833	T;T	0.17691	2.26;2.26	4.64	4.64	0.57946	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.128879	0.51477	D	0.000094	T	0.25344	0.0616	L	0.46670	1.46	0.80722	D	1	B;P;D;D	0.76494	0.208;0.792;0.999;0.997	B;B;D;P	0.81914	0.154;0.171;0.995;0.845	T	0.00875	-1.1531	10	0.51188	T	0.08	-11.6468	15.041	0.71791	0.0:1.0:0.0:0.0	.	67;67;67;67	Q5SZQ7;Q5SZQ8-2;Q5SZQ8;Q5SZQ8-3	.;.;CELF3_HUMAN;.	T	67	ENSP00000290585:A67T;ENSP00000290583:A67T	ENSP00000290583:A67T	A	-	1	0	CELF3	149953723	1.000000	0.71417	0.996000	0.52242	0.986000	0.74619	5.602000	0.67612	2.400000	0.81607	0.563000	0.77884	GCC	.		0.642	CELF3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000036663.2	NM_007185	
BTNL9	153579	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	5	180477173	180477173	+	Silent	SNP	C	C	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr5:180477173C>G	ENST00000327705.9	+	4	771	c.540C>G	c.(538-540)ccC>ccG	p.P180P	BTNL9_ENST00000376842.3_Silent_p.P180P|BTNL9_ENST00000515271.1_Silent_p.P111P|BTNL9_ENST00000376841.2_Silent_p.P180P	NM_152547.4	NP_689760.2	Q6UXG8	BTNL9_HUMAN	butyrophilin-like 9	180						integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|kidney(4)|large_intestine(1)|lung(10)|ovary(1)	19	all_cancers(89;2.45e-05)|all_epithelial(37;3.77e-06)|Renal(175;0.000159)|Lung NSC(126;0.00211)|all_lung(126;0.00371)|Breast(19;0.114)	all_cancers(40;0.0801)|Medulloblastoma(196;0.0392)|all_neural(177;0.0529)|all_hematologic(541;0.191)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			GCTGGTACCCCAAGCCTAAGG	0.587																																					p.P180P		.											.	.	.	0			c.C540G						.						83.0	84.0	84.0					5																	180477173		2203	4300	6503	SO:0001819	synonymous_variant	153579	exon4			GTACCCCAAGCCT	AK057097	CCDS4460.2	5q35.3	2014-01-14			ENSG00000165810	ENSG00000165810		"""Immunoglobulin superfamily / V-set domain containing"", ""Butyrophilins"""	24176	protein-coding gene	gene with protein product							Standard	NM_152547		Approved	FLJ32535, BTN8	uc003mmt.3	Q6UXG8	OTTHUMG00000133152	ENST00000327705.9:c.540C>G	5.37:g.180477173C>G		Somatic	37	0		WXS	Illumina HiSeq	.	38	21	NM_152547	A6NL42|Q6P660|Q96DM5	Silent	SNP	ENST00000327705.9	37	CCDS4460.2																																																																																			.		0.587	BTNL9-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000157342.3	NM_152547	
PXN	5829	hgsc.bcm.edu;ucsc.edu	37	12	120649932	120649932	+	3'UTR	SNP	G	G	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr12:120649932G>C	ENST00000228307.7	-	0	2102				PXN_ENST00000267257.7_3'UTR|PXN-AS1_ENST00000542265.1_RNA|PXN_ENST00000397506.3_3'UTR|PXN-AS1_ENST00000539446.1_RNA|PXN_ENST00000424649.2_3'UTR|PXN_ENST00000538144.1_5'Flank|PXN-AS1_ENST00000535200.1_RNA|PXN-AS1_ENST00000542314.1_RNA|PXN_ENST00000536957.1_3'UTR|PXN_ENST00000458477.2_3'UTR|PXN-AS1_ENST00000538804.1_RNA	NM_001080855.2	NP_001074324.1	P49023	PAXI_HUMAN	paxillin						activation of MAPK activity (GO:0000187)|branching morphogenesis of an epithelial tube (GO:0048754)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cellular component movement (GO:0006928)|cellular response to reactive oxygen species (GO:0034614)|cytoskeleton organization (GO:0007010)|epidermal growth factor receptor signaling pathway (GO:0007173)|focal adhesion assembly (GO:0048041)|growth hormone receptor signaling pathway (GO:0060396)|integrin-mediated signaling pathway (GO:0007229)|lamellipodium assembly (GO:0030032)|muscle contraction (GO:0006936)|peptidyl-tyrosine phosphorylation (GO:0018108)|regulation of cell shape (GO:0008360)|signal complex assembly (GO:0007172)|signal transduction (GO:0007165)|substrate adhesion-dependent cell spreading (GO:0034446)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|microtubule associated complex (GO:0005875)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|stress fiber (GO:0001725)	beta-catenin binding (GO:0008013)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)			breast(1)|endometrium(5)|kidney(2)|large_intestine(1)|lung(5)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					GGGCCCAGAGGCTCTGGCAGG	0.662																																					.		.											.	.	.	0			.						.																																			SO:0001624	3_prime_UTR_variant	5829	.			CCAGAGGCTCTGG	U14588	CCDS44996.1, CCDS44997.1, CCDS44998.1, CCDS58281.1	12q24	2006-01-23			ENSG00000089159	ENSG00000089159			9718	protein-coding gene	gene with protein product		602505				7534286	Standard	NM_001080855		Approved		uc001txv.3	P49023	OTTHUMG00000169169	ENST00000228307.7:c.*185C>G	12.37:g.120649932G>C		Somatic	55	0		WXS	Illumina HiSeq	.	38	23	.	B2RAI3|B7ZMB4|O14970|O14971|O60360|Q5HYA4	RNA	SNP	ENST00000228307.7	37	CCDS44997.1																																																																																			.		0.662	PXN-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000402679.4	NM_002859	
HRH1	3269	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	3	11301253	11301253	+	Missense_Mutation	SNP	A	A	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr3:11301253A>G	ENST00000397056.1	+	3	721	c.530A>G	c.(529-531)gAg>gGg	p.E177G	HRH1_ENST00000438284.2_Missense_Mutation_p.E177G|HRH1_ENST00000431010.2_Missense_Mutation_p.E177G	NM_000861.3|NM_001098211.1	NP_000852.1|NP_001091681.1	P35367	HRH1_HUMAN	histamine receptor H1	177					cellular response to histamine (GO:0071420)|eosinophil chemotaxis (GO:0048245)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)|inositol phosphate-mediated signaling (GO:0048016)|memory (GO:0007613)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of inositol trisphosphate biosynthetic process (GO:0032962)|positive regulation of vasoconstriction (GO:0045907)|regulation of synaptic plasticity (GO:0048167)|regulation of vascular permeability (GO:0043114)|visual learning (GO:0008542)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|histamine receptor activity (GO:0004969)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(4)|large_intestine(3)|lung(11)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	25					Aceprometazine(DB01615)|Alcaftadine(DB06766)|Alimemazine(DB01246)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Antazoline(DB08799)|Aripiprazole(DB01238)|Asenapine(DB06216)|Astemizole(DB00637)|Azatadine(DB00719)|Azelastine(DB00972)|Benzatropine(DB00245)|Bepotastine(DB04890)|Betahistine(DB06698)|Bromodiphenhydramine(DB01237)|Brompheniramine(DB00835)|Buclizine(DB00354)|Carbinoxamine(DB00748)|Cetirizine(DB00341)|Chlorcyclizine(DB08936)|Chloropyramine(DB08800)|Chlorphenamine(DB01114)|Chlorpromazine(DB00477)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Citalopram(DB00215)|Clemastine(DB00283)|Clofedanol(DB04837)|Clozapine(DB00363)|Cyclizine(DB01176)|Cyproheptadine(DB00434)|Desipramine(DB01151)|Desloratadine(DB00967)|Dexbrompheniramine(DB00405)|Dimenhydrinate(DB00985)|Dimetindene(DB08801)|Diphenhydramine(DB01075)|Diphenylpyraline(DB01146)|Doxepin(DB01142)|Doxylamine(DB00366)|Emedastine(DB01084)|Epinastine(DB00751)|Escitalopram(DB01175)|Fexofenadine(DB00950)|Flunarizine(DB04841)|Histamine Phosphate(DB00667)|Hydroxyzine(DB00557)|Iloperidone(DB04946)|Imipramine(DB00458)|Isothipendyl(DB08802)|Ketotifen(DB00920)|Levocabastine(DB01106)|Loratadine(DB00455)|Loxapine(DB00408)|Maprotiline(DB00934)|Meclizine(DB00737)|Mepyramine(DB06691)|Mequitazine(DB01071)|Methdilazine(DB00902)|Methotrimeprazine(DB01403)|Mianserin(DB06148)|Mirtazapine(DB00370)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Olopatadine(DB00768)|Orphenadrine(DB01173)|Paliperidone(DB01267)|Phenindamine(DB01619)|Pheniramine(DB01620)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Quetiapine(DB01224)|Risperidone(DB00734)|Tolazoline(DB00797)|Trazodone(DB00656)|Trimipramine(DB00726)|Tripelennamine(DB00792)|Triprolidine(DB00427)|Ziprasidone(DB00246)	GTGCGCCGAGAGGACAAGTGT	0.522																																					p.E177G		.											.	.	.	0			c.A530G						.						178.0	150.0	159.0					3																	11301253		2203	4300	6503	SO:0001583	missense	3269	exon3			GCCGAGAGGACAA		CCDS2604.1	3p25	2012-11-12			ENSG00000196639	ENSG00000196639		"""GPCR / Class A : Histamine receptors"""	5182	protein-coding gene	gene with protein product		600167				8003029	Standard	NM_001098211		Approved		uc010hds.3	P35367	OTTHUMG00000129719	ENST00000397056.1:c.530A>G	3.37:g.11301253A>G	ENSP00000380247:p.Glu177Gly	Somatic	26	0		WXS	Illumina HiSeq	.	7	5	NM_000861	A8K047|Q6P9E5	Missense_Mutation	SNP	ENST00000397056.1	37	CCDS2604.1	.	.	.	.	.	.	.	.	.	.	A	10.46	1.357276	0.24598	.	.	ENSG00000196639	ENST00000438284;ENST00000431010;ENST00000397056	T;T;T	0.36157	1.27;1.27;1.27	5.98	4.81	0.61882	GPCR, rhodopsin-like superfamily (1);	0.466272	0.24467	N	0.038270	T	0.32763	0.0840	L	0.52364	1.645	0.18873	N	0.999985	B	0.22541	0.071	B	0.29663	0.105	T	0.16100	-1.0414	10	0.33940	T	0.23	-3.7866	9.2442	0.37515	0.8119:0.1226:0.0655:0.0	.	177	P35367	HRH1_HUMAN	G	177	ENSP00000406705:E177G;ENSP00000397028:E177G;ENSP00000380247:E177G	ENSP00000380247:E177G	E	+	2	0	HRH1	11276253	0.001000	0.12720	0.006000	0.13384	0.603000	0.37013	0.658000	0.24979	2.289000	0.77006	0.533000	0.62120	GAG	.		0.522	HRH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251928.2		
MUC4	4585	hgsc.bcm.edu	37	3	195512373	195512373	+	Silent	SNP	G	G	T	rs112774151|rs63118461		TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr3:195512373G>T	ENST00000463781.3	-	2	6537	c.6078C>A	c.(6076-6078)tcC>tcA	p.S2026S	MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Silent_p.S2026S	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.S2026_T2027insS(3)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		TGTCACCAGTGGATGCTGAGG	0.577																																					p.S2026S		.											.,4	.	1505	3	Insertion - In frame(3)	large_intestine(2)|breast(1)	c.C6078A						.						25.0	24.0	24.0					3																	195512373		684	1580	2264	SO:0001819	synonymous_variant	4585	exon2			ACCAGTGGATGCT	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.6078C>A	3.37:g.195512373G>T		Somatic	149	0		WXS	Illumina HiSeq	.	67	3	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Silent	SNP	ENST00000463781.3	37	CCDS54700.1																																																																																			.		0.577	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
MLLT4	4301	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	6	168307886	168307886	+	Silent	SNP	T	T	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr6:168307886T>C	ENST00000447894.2	+	13	1686	c.1686T>C	c.(1684-1686)tcT>tcC	p.S562S	MLLT4_ENST00000366806.2_Silent_p.S562S|MLLT4_ENST00000392112.1_Silent_p.S546S|MLLT4_ENST00000400822.3_Silent_p.S561S|MLLT4_ENST00000351017.4_Silent_p.S562S|MLLT4_ENST00000392108.3_Silent_p.S562S|MLLT4_ENST00000344191.4_Silent_p.S562S			P55196	AFAD_HUMAN	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 4	562					adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cell-cell signaling (GO:0007267)|signal transduction (GO:0007165)	apical part of cell (GO:0045177)|cell junction (GO:0030054)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein C-terminus binding (GO:0008022)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(13)|large_intestine(10)|lung(19)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	65		Breast(66;1.07e-05)|Ovarian(120;0.024)		Epithelial(4;2.38e-32)|OV - Ovarian serous cystadenocarcinoma(33;9.99e-23)|BRCA - Breast invasive adenocarcinoma(4;1.2e-11)|GBM - Glioblastoma multiforme(31;0.00117)		GAGTGTCGTCTGCCTCTAGCA	0.522			T	MLL	AL																																p.S562S		.		Dom	yes		6	6q27	4301	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 4 (AF6)"""		L	.	.	.	0			c.T1686C						.						122.0	115.0	117.0					6																	168307886		2203	4300	6503	SO:0001819	synonymous_variant	4301	exon13			GTCGTCTGCCTCT	AB011399	CCDS47517.1, CCDS75553.1	6q27	2008-02-05	2001-11-28		ENSG00000130396	ENSG00000130396			7137	protein-coding gene	gene with protein product		159559	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 4"""			8242616	Standard	NM_001040000		Approved	AF-6, AF6	uc021zij.1	P55196	OTTHUMG00000016031	ENST00000447894.2:c.1686T>C	6.37:g.168307886T>C		Somatic	39	0		WXS	Illumina HiSeq	.	23	9	NM_001040000	O75087|O75088|O75089|Q59FP0|Q5TIG6|Q5TIG7|Q9NSN7|Q9NU92	Silent	SNP	ENST00000447894.2	37		.	.	.	.	.	.	.	.	.	.	T	3.092	-0.186769	0.06340	.	.	ENSG00000130396	ENST00000423229	.	.	.	5.14	-9.41	0.00613	.	.	.	.	.	T	0.15955	0.0384	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.45483	-0.9258	4	.	.	.	-2.1552	0.5994	0.00742	0.2426:0.2955:0.1814:0.2805	.	.	.	.	R	261	.	.	C	+	1	0	MLLT4	168050735	0.001000	0.12720	0.017000	0.16124	0.274000	0.26718	-1.741000	0.01837	-1.120000	0.02953	-0.280000	0.10049	TGC	.		0.522	MLLT4-013	PUTATIVE	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000372077.1	NM_005936	
KIAA2018	205717	hgsc.bcm.edu	37	3	113376107	113376107	+	Silent	SNP	C	C	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr3:113376107C>T	ENST00000478658.1	-	5	4439	c.4422G>A	c.(4420-4422)caG>caA	p.Q1474Q	KIAA2018_ENST00000316407.4_Silent_p.Q1474Q|KIAA2018_ENST00000491165.1_Intron			Q68DE3	K2018_HUMAN	KIAA2018	1474	Gln-rich.					membrane (GO:0016020)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|DNA binding (GO:0003677)|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity (GO:0004571)			NS(1)|breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|liver(1)|lung(30)|ovary(8)|skin(5)|upper_aerodigestive_tract(4)|urinary_tract(2)	80						gttgttgttgctgttgctgct	0.493																																					p.Q1474Q		.											KIAA2018,colon,carcinoma,0,1	KIAA2018	0	0			c.G4422A						.						88.0	96.0	93.0					3																	113376107		2193	4279	6472	SO:0001819	synonymous_variant	205717	exon7			TTGTTGCTGTTGC	AB095938	CCDS43133.1	3q13.2	2014-01-02			ENSG00000176542	ENSG00000176542			30494	protein-coding gene	gene with protein product							Standard	XM_005247208		Approved		uc003eam.3	Q68DE3	OTTHUMG00000159322	ENST00000478658.1:c.4422G>A	3.37:g.113376107C>T		Somatic	22	1		WXS	Illumina HiSeq	.	23	5	NM_001009899	Q7Z3L9|Q8IVF3|Q9H8T4	Silent	SNP	ENST00000478658.1	37	CCDS43133.1																																																																																			.		0.493	KIAA2018-003	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354591.1	NM_001009899	
TBCCD1	55171	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	3	186269020	186269020	+	Missense_Mutation	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr3:186269020T>G	ENST00000424280.1	-	7	2072	c.1593A>C	c.(1591-1593)gaA>gaC	p.E531D	TBCCD1_ENST00000479590.1_5'Flank|TBCCD1_ENST00000338733.5_Missense_Mutation_p.E531D|TBCCD1_ENST00000446782.1_Missense_Mutation_p.E435D	NM_001134415.1	NP_001127887.1	Q9NVR7	TBCC1_HUMAN	TBCC domain containing 1	531					cell morphogenesis (GO:0000902)|cytoskeleton organization (GO:0007010)|maintenance of centrosome location (GO:0051661)|maintenance of Golgi location (GO:0051684)|regulation of cell migration (GO:0030334)|regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)|spindle pole centrosome (GO:0031616)				breast(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(4)|ovary(1)|skin(1)	17	all_cancers(143;3.75e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;4.3e-21)	GBM - Glioblastoma multiforme(93;0.0474)		TAATCAACCATTCATAAAACT	0.408																																					p.E531D		.											.	.	.	0			c.A1593C						.						133.0	120.0	125.0					3																	186269020		2203	4300	6503	SO:0001583	missense	55171	exon7			CAACCATTCATAA	BC025748	CCDS3276.1, CCDS75061.1	3q27.3	2006-03-09			ENSG00000113838	ENSG00000113838			25546	protein-coding gene	gene with protein product						12477932	Standard	NM_001134415		Approved	FLJ10560	uc003fqg.3	Q9NVR7	OTTHUMG00000156613	ENST00000424280.1:c.1593A>C	3.37:g.186269020T>G	ENSP00000411253:p.Glu531Asp	Somatic	71	0		WXS	Illumina HiSeq	.	48	16	NM_001134415	B3KW69|D3DNU6|G5E9J4	Missense_Mutation	SNP	ENST00000424280.1	37	CCDS3276.1	.	.	.	.	.	.	.	.	.	.	T	14.44	2.534777	0.45073	.	.	ENSG00000113838	ENST00000424280;ENST00000338733;ENST00000446782	D;D;D	0.83992	-1.78;-1.78;-1.79	5.39	-0.0894	0.13669	.	0.059514	0.64402	D	0.000002	T	0.72407	0.3456	L	0.50333	1.59	0.43536	D	0.995829	B;B	0.33549	0.404;0.417	B;B	0.32583	0.148;0.075	T	0.59700	-0.7405	10	0.17832	T	0.49	-17.424	8.3533	0.32316	0.0:0.4093:0.0:0.5907	.	435;531	G5E9J4;Q9NVR7	.;TBCC1_HUMAN	D	531;531;435	ENSP00000411253:E531D;ENSP00000341652:E531D;ENSP00000397091:E435D	ENSP00000341652:E531D	E	-	3	2	TBCCD1	187751714	0.894000	0.30519	0.998000	0.56505	0.981000	0.71138	-0.083000	0.11286	-0.054000	0.13266	0.528000	0.53228	GAA	.		0.408	TBCCD1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344774.1	NM_018138	
DHH	50846	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	12	49483683	49483683	+	Missense_Mutation	SNP	A	A	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr12:49483683A>G	ENST00000266991.2	-	3	1456	c.1150T>C	c.(1150-1152)Tct>Cct	p.S384P	RP11-386G11.8_ENST00000548030.1_RNA|RP11-386G11.8_ENST00000553174.1_RNA	NM_021044.2	NP_066382.1	O43323	DHH_HUMAN	desert hedgehog	384					cell-cell signaling (GO:0007267)|Leydig cell differentiation (GO:0033327)|male sex determination (GO:0030238)|myelination (GO:0042552)|regulation of steroid biosynthetic process (GO:0050810)|response to estradiol (GO:0032355)|spermatid development (GO:0007286)	extracellular region (GO:0005576)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|peptidase activity (GO:0008233)|zinc ion binding (GO:0008270)			breast(1)|large_intestine(3)|lung(4)	8						AGGAGCCGAGAGTACCAATGC	0.667																																					p.S384P		.											.	.	.	0			c.T1150C						.						10.0	12.0	12.0					12																	49483683		2199	4294	6493	SO:0001583	missense	50846	exon3			GCCGAGAGTACCA	AB010994	CCDS8779.1	12q13.1	2010-06-24	2010-06-24			ENSG00000139549			2865	protein-coding gene	gene with protein product		605423	"""desert hedgehog (Drosophila) homolog"""			10773676, 10640830	Standard	NM_021044		Approved	HHG-3, MGC35145	uc001rtf.3	O43323	OTTHUMG00000170408	ENST00000266991.2:c.1150T>C	12.37:g.49483683A>G	ENSP00000266991:p.Ser384Pro	Somatic	51	0		WXS	Illumina HiSeq	.	28	13	NM_021044	Q15794	Missense_Mutation	SNP	ENST00000266991.2	37	CCDS8779.1	.	.	.	.	.	.	.	.	.	.	a	13.24	2.177513	0.38413	.	.	ENSG00000139549	ENST00000266991	D	0.99422	-5.88	4.77	4.77	0.60923	Peptidase C46, hedgehog protein, hint region (1);	0.200343	0.42420	D	0.000710	D	0.98679	0.9557	L	0.28458	0.855	0.35720	D	0.817089	D	0.65815	0.995	P	0.60345	0.873	D	0.99947	1.1485	10	0.27785	T	0.31	-15.8194	13.7159	0.62695	1.0:0.0:0.0:0.0	.	384	O43323	DHH_HUMAN	P	384	ENSP00000266991:S384P	ENSP00000266991:S384P	S	-	1	0	DHH	47769950	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.902000	0.69869	2.144000	0.66660	0.454000	0.30748	TCT	.		0.667	DHH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408973.1	NM_021044	
ADCY3	109	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	2	25043665	25043665	+	Silent	SNP	G	G	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr2:25043665G>A	ENST00000260600.5	-	20	4031	c.3180C>T	c.(3178-3180)caC>caT	p.H1060H	ADCY3_ENST00000405392.1_Silent_p.H647H|CENPO_ENST00000380834.2_3'UTR|CENPO_ENST00000473706.1_3'UTR	NM_004036.3	NP_004027.2	O60266	ADCY3_HUMAN	adenylate cyclase 3	1060					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|neurotrophin TRK receptor signaling pathway (GO:0048011)|sensory perception of smell (GO:0007608)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cilium (GO:0005929)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)			NS(1)|breast(5)|endometrium(7)|kidney(1)|large_intestine(7)|lung(14)|ovary(3)|prostate(4)|skin(2)	44	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.203)					AGATGTCGTAGTGTGGTTTCC	0.567																																					p.H1060H		.											.	.	.	0			c.C3180T						.						170.0	141.0	151.0					2																	25043665		2203	4300	6503	SO:0001819	synonymous_variant	109	exon20			GTCGTAGTGTGGT	AF033861	CCDS1715.1	2p23.3	2013-02-04			ENSG00000138031	ENSG00000138031	4.6.1.1	"""Adenylate cyclases"""	234	protein-coding gene	gene with protein product		600291				9920776	Standard	NM_004036		Approved	AC3	uc002rfs.4	O60266	OTTHUMG00000094765	ENST00000260600.5:c.3180C>T	2.37:g.25043665G>A		Somatic	83	0		WXS	Illumina HiSeq	.	54	21	NM_004036	B3KT86|Q53T54|Q9UDB1	Silent	SNP	ENST00000260600.5	37	CCDS1715.1																																																																																			.		0.567	ADCY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211574.2		
PLGLA	285189	hgsc.bcm.edu	37	2	107003012	107003012	+	RNA	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr2:107003012A>C	ENST00000484422.1	+	0	103							Q15195	PLGA_HUMAN	plasminogen-like A (pseudogene)							extracellular region (GO:0005576)											ATAGTATGTGAAGCCATACTA	0.333																																					.		.											.	.	.	0			.						.																																					285189	.			TATGTGAAGCCAT	U67178, M86872, M86873		2q12.2	2013-03-28	2013-03-28	2008-02-07	ENSG00000240935	ENSG00000240935			9074	pseudogene	pseudogene		612212	"""plasminogen pseudogene 2"", ""plasminogen-like A1"", ""plasminogen-like A"""	PLGP2, PLGLA1		1986355	Standard	NR_003506		Approved		uc002tdp.4	Q15195	OTTHUMG00000153188		2.37:g.107003012A>C		Somatic	158	0		WXS	Illumina HiSeq	.	92	42	.		RNA	SNP	ENST00000484422.1	37																																																																																				.		0.333	PLGLA-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000331219.1	NR_003506.2	
TMEM150C	441027	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	4	83411279	83411279	+	Missense_Mutation	SNP	T	T	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr4:83411279T>C	ENST00000515780.2	-	7	680	c.476A>G	c.(475-477)gAa>gGa	p.E159G	TMEM150C_ENST00000508701.1_3'UTR|TMEM150C_ENST00000449862.2_Missense_Mutation_p.E159G			B9EJG8	T150C_HUMAN	transmembrane protein 150C	159						integral component of membrane (GO:0016021)				ovary(1)	1						TCTCCGTCCTTCATTCTTGAT	0.473																																					p.E159G		.											.	.	.	0			c.A476G						.						192.0	195.0	194.0					4																	83411279		1939	4148	6087	SO:0001583	missense	441027	exon7			CGTCCTTCATTCT	BC147027	CCDS47087.1	4q21.22	2010-06-25			ENSG00000249242	ENSG00000249242			37263	protein-coding gene	gene with protein product							Standard	NM_001080506		Approved	FLJ12993	uc003hmy.1	B9EJG8	OTTHUMG00000161083	ENST00000515780.2:c.476A>G	4.37:g.83411279T>C	ENSP00000420919:p.Glu159Gly	Somatic	56	0		WXS	Illumina HiSeq	.	25	22	NM_001080506	B7Z4J5|B7Z4L3|B7Z692|B7Z6X6	Missense_Mutation	SNP	ENST00000515780.2	37	CCDS47087.1	.	.	.	.	.	.	.	.	.	.	T	19.22	3.785380	0.70337	.	.	ENSG00000249242	ENST00000449862;ENST00000515780	T;T	0.43294	0.95;0.95	5.62	5.62	0.85841	.	.	.	.	.	T	0.47893	0.1470	N	0.20766	0.605	0.80722	D	1	D	0.76494	0.999	D	0.79108	0.992	T	0.38415	-0.9662	9	0.18276	T	0.48	-7.5965	15.8218	0.78654	0.0:0.0:0.0:1.0	.	159	B9EJG8	T150C_HUMAN	G	159	ENSP00000403438:E159G;ENSP00000420919:E159G	ENSP00000403438:E159G	E	-	2	0	TMEM150C	83630303	1.000000	0.71417	1.000000	0.80357	0.518000	0.34316	7.040000	0.76551	2.131000	0.65755	0.379000	0.24179	GAA	.		0.473	TMEM150C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363685.2	NM_001080506	
PDIK1L	149420	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	26448622	26448622	+	Missense_Mutation	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr1:26448622A>C	ENST00000374271.4	+	4	867	c.580A>C	c.(580-582)Agt>Cgt	p.S194R	PDIK1L_ENST00000374269.1_Missense_Mutation_p.S194R	NM_001243532.1|NM_001243533.1|NM_152835.4	NP_001230461.1|NP_001230462.1|NP_690048.1	Q8N165	PDK1L_HUMAN	PDLIM1 interacting kinase 1 like	194	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.					nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			large_intestine(3)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)	7		Colorectal(325;0.000147)|Renal(390;0.00211)|Lung NSC(340;0.00239)|all_lung(284;0.00366)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.051)|Breast(348;0.0589)|all_neural(195;0.0687)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;7.32e-26)|Colorectal(126;1.24e-08)|COAD - Colon adenocarcinoma(152;9.31e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.000735)|BRCA - Breast invasive adenocarcinoma(304;0.000973)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.015)|READ - Rectum adenocarcinoma(331;0.0649)		TTTTGGTCTAAGTAAAGTTTG	0.448																																					p.S194R		.											.	.	.	0			c.A580C						.						112.0	109.0	110.0					1																	26448622		2203	4300	6503	SO:0001583	missense	149420	exon3			GGTCTAAGTAAAG	AF411102	CCDS274.1	1p35.1	2008-02-05			ENSG00000175087	ENSG00000175087			18981	protein-coding gene	gene with protein product		610785				14631099	Standard	NM_152835		Approved	CLIK1L	uc009vsb.3	Q8N165	OTTHUMG00000007511	ENST00000374271.4:c.580A>C	1.37:g.26448622A>C	ENSP00000363389:p.Ser194Arg	Somatic	43	0		WXS	Illumina HiSeq	.	22	14	NM_001243532	B2R777|D3DPK2|Q5T2I0|Q8NDB3	Missense_Mutation	SNP	ENST00000374271.4	37	CCDS274.1	.	.	.	.	.	.	.	.	.	.	A	19.84	3.902196	0.72754	.	.	ENSG00000175087	ENST00000374271;ENST00000374269	T;T	0.28454	1.61;1.61	5.81	5.81	0.92471	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.63534	0.2519	M	0.90425	3.115	0.44462	D	0.99739	D	0.76494	0.999	D	0.81914	0.995	T	0.71258	-0.4646	9	.	.	.	-15.5587	15.8235	0.78678	1.0:0.0:0.0:0.0	.	194	Q8N165	PDK1L_HUMAN	R	194	ENSP00000363389:S194R;ENSP00000363387:S194R	.	S	+	1	0	PDIK1L	26321209	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.339000	0.96797	2.219000	0.72066	0.533000	0.62120	AGT	.		0.448	PDIK1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019752.1	NM_152835	
TTLL9	164395	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	20	30486300	30486300	+	Missense_Mutation	SNP	C	C	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr20:30486300C>G	ENST00000375938.4	+	4	391	c.138C>G	c.(136-138)ttC>ttG	p.F46L	TTLL9_ENST00000375921.2_5'UTR|TTLL9_ENST00000535842.1_Missense_Mutation_p.F46L|TTLL9_ENST00000310998.4_5'UTR|TTLL9_ENST00000375922.4_5'UTR|RNU1-94P_ENST00000362627.1_RNA|TTLL9_ENST00000375934.4_Missense_Mutation_p.F28L			Q3SXZ7	TTLL9_HUMAN	tubulin tyrosine ligase-like family, member 9	46	TTL. {ECO:0000255|PROSITE- ProRule:PRU00568}.				cellular protein modification process (GO:0006464)	cilium (GO:0005929)|cytoplasm (GO:0005737)|microtubule (GO:0005874)	ligase activity (GO:0016874)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	26			Colorectal(19;0.00306)|COAD - Colon adenocarcinoma(19;0.0347)			CGATCCGGTTCAAGACCACCC	0.527																																					p.F46L		.											.	.	.	0			c.C138G						.						110.0	109.0	109.0					20																	30486300		2043	4193	6236	SO:0001583	missense	164395	exon4			CCGGTTCAAGACC	AL031658	CCDS42863.1	20q11	2013-02-14	2005-07-28	2005-07-28		ENSG00000131044		"""Tubulin tyrosine ligase-like family"""	16118	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 125"""	C20orf125		15890843	Standard	NM_001008409		Approved	dJ310O13.1	uc010gdx.1	Q3SXZ7		ENST00000375938.4:c.138C>G	20.37:g.30486300C>G	ENSP00000365105:p.Phe46Leu	Somatic	26	0		WXS	Illumina HiSeq	.	33	17	NM_001008409	A6NH06|A6NIS5|B3KSG8|Q3SXZ8|Q5JYS3|Q5JYS4	Missense_Mutation	SNP	ENST00000375938.4	37	CCDS42863.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.072290	0.76415	.	.	ENSG00000131044	ENST00000375938;ENST00000535842;ENST00000375935;ENST00000375934	T;T;T	0.10192	3.84;3.84;2.9	5.44	5.44	0.79542	.	0.258505	0.42294	D	0.000722	T	0.26448	0.0646	M	0.92459	3.31	0.80722	D	1	D	0.54207	0.965	B	0.43950	0.437	T	0.34800	-0.9814	10	0.62326	D	0.03	.	14.8279	0.70128	0.0:1.0:0.0:0.0	.	46	Q3SXZ7	TTLL9_HUMAN	L	46;46;28;28	ENSP00000365105:F46L;ENSP00000442515:F46L;ENSP00000365100:F28L	ENSP00000365100:F28L	F	+	3	2	TTLL9	29949961	1.000000	0.71417	1.000000	0.80357	0.772000	0.43724	4.310000	0.59141	2.578000	0.87016	0.558000	0.71614	TTC	.		0.527	TTLL9-205	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001008409	
GRIK5	2901	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	19	42525501	42525501	+	Missense_Mutation	SNP	G	G	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr19:42525501G>A	ENST00000262895.3	-	14	1822	c.1823C>T	c.(1822-1824)tCg>tTg	p.S608L	GRIK5_ENST00000301218.4_Missense_Mutation_p.S608L|GRIK5_ENST00000593562.1_Missense_Mutation_p.S608L	NM_002088.4	NP_002079.3	Q16478	GRIK5_HUMAN	glutamate receptor, ionotropic, kainate 5	608					cellular response to glucose stimulus (GO:0071333)|establishment of localization in cell (GO:0051649)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|positive regulation of neuron apoptotic process (GO:0043525)|protein retention in ER lumen (GO:0006621)|receptor clustering (GO:0043113)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of synaptic vesicle fusion to presynaptic membrane (GO:0031630)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)	cell junction (GO:0030054)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|kainate selective glutamate receptor complex (GO:0032983)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|terminal bouton (GO:0043195)	extracellular-glutamate-gated ion channel activity (GO:0005234)|kainate selective glutamate receptor activity (GO:0015277)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|liver(1)|lung(11)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	35		Prostate(69;0.059)				CATGATCTCCGAGCCCTGCTG	0.657																																					p.S608L		.											.	.	.	0			c.C1823T						.						34.0	32.0	33.0					19																	42525501		2203	4300	6503	SO:0001583	missense	2901	exon14			ATCTCCGAGCCCT		CCDS12595.1	19q13.2	2012-08-29			ENSG00000105737	ENSG00000105737		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4583	protein-coding gene	gene with protein product		600283		GRIK2		7527545	Standard	NM_002088		Approved	GluK5, KA2	uc002osj.2	Q16478	OTTHUMG00000044573	ENST00000262895.3:c.1823C>T	19.37:g.42525501G>A	ENSP00000262895:p.Ser608Leu	Somatic	63	0		WXS	Illumina HiSeq	.	36	17	NM_002088	Q8WWG8	Missense_Mutation	SNP	ENST00000262895.3	37	CCDS12595.1	.	.	.	.	.	.	.	.	.	.	G	27.9	4.872873	0.91587	.	.	ENSG00000105737	ENST00000262895;ENST00000301218	T;T	0.52754	0.65;0.65	4.51	4.51	0.55191	Ionotropic glutamate receptor (2);	0.000000	0.64402	D	0.000002	T	0.60573	0.2279	M	0.85462	2.755	0.46874	D	0.999234	P	0.52842	0.956	P	0.47376	0.545	T	0.71994	-0.4424	10	0.87932	D	0	.	16.0191	0.80468	0.0:0.0:1.0:0.0	.	608	Q16478	GRIK5_HUMAN	L	608	ENSP00000262895:S608L;ENSP00000301218:S608L	ENSP00000262895:S608L	S	-	2	0	GRIK5	47217341	1.000000	0.71417	0.998000	0.56505	0.981000	0.71138	9.835000	0.99442	2.055000	0.61198	0.563000	0.77884	TCG	.		0.657	GRIK5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463453.1		
AP3S2	10239	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	15	90431767	90431767	+	Missense_Mutation	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr15:90431767A>C	ENST00000336418.4	-	3	651	c.259T>G	c.(259-261)Ttg>Gtg	p.L87V	C15orf38-AP3S2_ENST00000560224.1_5'UTR|RNU6-1111P_ENST00000391118.1_RNA|AP3S2_ENST00000558011.1_Missense_Mutation_p.L87V|AP3S2_ENST00000560940.1_Missense_Mutation_p.L87V|C15orf38-AP3S2_ENST00000398333.3_Missense_Mutation_p.L288V	NM_005829.4	NP_005820.1	P59780	AP3S2_HUMAN	adaptor-related protein complex 3, sigma 2 subunit	87					anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|intracellular protein transport (GO:0006886)	AP-3 adaptor complex (GO:0030123)|cytoplasmic vesicle (GO:0031410)|Golgi apparatus (GO:0005794)	protein transporter activity (GO:0008565)			NS(1)|kidney(1)|lung(2)|ovary(1)|urinary_tract(1)	6	Lung NSC(78;0.0181)|all_lung(78;0.0384)		BRCA - Breast invasive adenocarcinoma(143;0.0107)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.223)			ATGAGGTCCAAGATTCCAAGT	0.453																																					p.L288V		.											.	.	.	0			c.T862G						.						81.0	76.0	78.0					15																	90431767		2200	4299	6499	SO:0001583	missense	100526783	exon7			GGTCCAAGATTCC	X99459	CCDS10357.1	15q26.1	2010-08-13			ENSG00000157823	ENSG00000157823			571	protein-coding gene	gene with protein product		602416				9118953	Standard	NM_005829		Approved	sigma3b		P59780	OTTHUMG00000149811	ENST00000336418.4:c.259T>G	15.37:g.90431767A>C	ENSP00000338777:p.Leu87Val	Somatic	60	0		WXS	Illumina HiSeq	.	23	19	NM_001199058	B2R677|B4DGQ3|O09077|O09149|Q53H83|Q99589	Missense_Mutation	SNP	ENST00000336418.4	37	CCDS10357.1	.	.	.	.	.	.	.	.	.	.	A	19.96	3.924103	0.73213	.	.	ENSG00000157823;ENSG00000157823;ENSG00000250021	ENST00000336418;ENST00000423566;ENST00000398333	T;T	0.57595	0.46;0.39	5.56	4.44	0.53790	Longin-like (1);AP complex, mu/sigma subunit (1);	0.098040	0.44902	D	0.000415	T	0.78201	0.4246	H	0.97682	4.055	0.26507	N	0.974663	D;D	0.64830	0.993;0.994	D;D	0.67548	0.952;0.927	T	0.73845	-0.3854	10	0.87932	D	0	-24.0644	6.806	0.23779	0.8257:0.0:0.1743:0.0	.	288;87	E2QRD5;P59780	.;AP3S2_HUMAN	V	87;87;288	ENSP00000338777:L87V;ENSP00000381377:L288V	ENSP00000338777:L87V	L	-	1	2	C15orf38-AP3S2;AP3S2	88232771	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	1.747000	0.38298	1.130000	0.42092	0.533000	0.62120	TTG	.		0.453	AP3S2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313422.1		
NAGLU	4669	hgsc.bcm.edu	37	17	40689478	40689478	+	Missense_Mutation	SNP	G	G	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr17:40689478G>A	ENST00000225927.2	+	2	547	c.446G>A	c.(445-447)cGc>cAc	p.R149H	RP11-400F19.8_ENST00000585572.1_RNA	NM_000263.3	NP_000254.2	P54802	ANAG_HUMAN	N-acetylglucosaminidase, alpha	149					carbohydrate metabolic process (GO:0005975)|cerebellar Purkinje cell layer development (GO:0021680)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|inner ear receptor cell development (GO:0060119)|locomotor rhythm (GO:0045475)|lysosome organization (GO:0007040)|middle ear morphogenesis (GO:0042474)|nervous system development (GO:0007399)|retinal rod cell development (GO:0046548)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)	alpha-N-acetylglucosaminidase activity (GO:0004561)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(1)|ovary(2)|skin(1)	12		all_cancers(22;1.58e-05)|Breast(137;0.000153)|all_epithelial(22;0.000344)		BRCA - Breast invasive adenocarcinoma(366;0.13)	N-Acetyl-D-glucosamine(DB00141)	GACTGGGCCCGCTGGGAGCGA	0.627																																					p.R149H		.											NAGLU,colon,carcinoma,0,1	NAGLU	0	0			c.G446A						.						134.0	118.0	124.0					17																	40689478		2203	4300	6503	SO:0001583	missense	4669	exon2			GGGCCCGCTGGGA		CCDS11427.1	17q21.2	2010-07-27	2010-07-27		ENSG00000108784	ENSG00000108784	3.2.1.50		7632	protein-coding gene	gene with protein product	"""Sanfilippo disease IIIB"""	609701					Standard	XM_006721920		Approved	NAG	uc002hzv.3	P54802		ENST00000225927.2:c.446G>A	17.37:g.40689478G>A	ENSP00000225927:p.Arg149His	Somatic	51	0		WXS	Illumina HiSeq	.	26	2	NM_000263		Missense_Mutation	SNP	ENST00000225927.2	37	CCDS11427.1	.	.	.	.	.	.	.	.	.	.	G	28.2	4.901269	0.92035	.	.	ENSG00000108784	ENST00000225927	D	0.98987	-5.3	4.3	3.33	0.38152	Alpha-N-acetylglucosaminidase, tim-barrel domain (1);	0.000000	0.85682	D	0.000000	D	0.99345	0.9770	M	0.93375	3.41	0.49483	D	0.999795	D	0.89917	1.0	D	0.74348	0.983	D	0.99078	1.0836	10	0.87932	D	0	-20.5556	11.4866	0.50356	0.09:0.0:0.91:0.0	.	149	P54802	ANAG_HUMAN	H	149	ENSP00000225927:R149H	ENSP00000225927:R149H	R	+	2	0	NAGLU	37943004	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.396000	0.73234	1.142000	0.42291	-0.254000	0.11334	CGC	.		0.627	NAGLU-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450385.1	NM_000263	
GIPC3	126326	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	19	3589910	3589910	+	Splice_Site	SNP	G	G	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr19:3589910G>T	ENST00000322315.5	+	5	832	c.787G>T	c.(787-789)Gcg>Tcg	p.A263S		NM_133261.2	NP_573568.1	Q8TF64	GIPC3_HUMAN	GIPC PDZ domain containing family, member 3	263										breast(2)|endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)	10				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0025)|STAD - Stomach adenocarcinoma(1328;0.18)		CCCCGAGCTGGGTAAGGGGCC	0.672																																					p.A263S		.											.	.	.	0			c.G787T						.						52.0	54.0	54.0					19																	3589910		2203	4299	6502	SO:0001630	splice_region_variant	126326	exon5			GAGCTGGGTAAGG	AB073738	CCDS32871.1	19p13.3	2011-11-29				ENSG00000179855			18183	protein-coding gene	gene with protein product		608792	"""chromosome 19 open reading frame 64"", ""deafness, autosomal recessive 72"", ""deafness, autosomal recessive 15"""	C19orf64, DFNB72, DFNB15		11836571, 21326233	Standard	NM_133261		Approved	DFNB95	uc002lyd.4	Q8TF64		ENST00000322315.5:c.787+1G>T	19.37:g.3589910G>T		Somatic	66	0		WXS	Illumina HiSeq	.	40	20	NM_133261	O75227	Missense_Mutation	SNP	ENST00000322315.5	37	CCDS32871.1	.	.	.	.	.	.	.	.	.	.	g	22.2	4.262268	0.80358	.	.	ENSG00000179855	ENST00000322315	D	0.88277	-2.36	4.48	3.43	0.39272	.	0.059022	0.64402	D	0.000003	D	0.91506	0.7318	L	0.52759	1.655	0.80722	D	1	D	0.63880	0.993	D	0.72625	0.978	D	0.90215	0.4267	10	0.44086	T	0.13	-28.8747	12.2548	0.54617	0.0:0.1729:0.8271:0.0	.	263	Q8TF64	GIPC3_HUMAN	S	263	ENSP00000319254:A263S	ENSP00000319254:A263S	A	+	1	0	GIPC3	3540910	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.293000	0.78740	0.871000	0.35750	0.486000	0.48141	GCG	.		0.672	GIPC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394577.1	NM_133261	Missense_Mutation
RPS6KA3	6197	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	X	20183169	20183169	+	Missense_Mutation	SNP	T	T	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chrX:20183169T>C	ENST00000379565.3	-	18	1819	c.1612A>G	c.(1612-1614)Aga>Gga	p.R538G	RPS6KA3_ENST00000479809.1_Intron|RPS6KA3_ENST00000544447.1_Missense_Mutation_p.R510G|RPS6KA3_ENST00000379548.4_Missense_Mutation_p.R508G|RPS6KA3_ENST00000540702.1_Missense_Mutation_p.R509G	NM_004586.2	NP_004577.1	P51812	KS6A3_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide 3	538	Protein kinase 2. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axon guidance (GO:0007411)|cell cycle (GO:0007049)|central nervous system development (GO:0007417)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell growth (GO:0030307)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of DNA-templated transcription in response to stress (GO:0043620)|regulation of translation in response to stress (GO:0043555)|response to lipopolysaccharide (GO:0032496)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)|stress-activated MAPK cascade (GO:0051403)|synaptic transmission (GO:0007268)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|magnesium ion binding (GO:0000287)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(4)|central_nervous_system(4)|endometrium(3)|kidney(2)|large_intestine(5)|liver(14)|lung(7)|ovary(1)|stomach(1)	41					Acetylsalicylic acid(DB00945)	TTCAAGTCTCTATGAACCACC	0.333																																					p.R538G		.											.	.	.	0			c.A1612G						.						75.0	70.0	72.0					X																	20183169		2203	4300	6503	SO:0001583	missense	6197	exon18			AGTCTCTATGAAC	U08316	CCDS14197.1	Xp22.2-p22.1	2013-06-03	2002-08-29		ENSG00000177189	ENSG00000177189			10432	protein-coding gene	gene with protein product		300075	"""ribosomal protein S6 kinase, 90kD, polypeptide 3"", ""mental retardation, X-linked 19"", ""Coffin-Lowry syndrome"""	MRX19, CLS		8141249, 11896450, 16879200	Standard	XM_005274573		Approved	RSK, RSK2, HU-3	uc004czu.3	P51812	OTTHUMG00000021231	ENST00000379565.3:c.1612A>G	X.37:g.20183169T>C	ENSP00000368884:p.Arg538Gly	Somatic	93	0		WXS	Illumina HiSeq	.	48	41	NM_004586	B2R9V4|Q4VAP3|Q59H26|Q5JPK8|Q7Z3Z7	Missense_Mutation	SNP	ENST00000379565.3	37	CCDS14197.1	.	.	.	.	.	.	.	.	.	.	T	17.13	3.311211	0.60414	.	.	ENSG00000177189	ENST00000379565;ENST00000544447;ENST00000379548;ENST00000540702	T;T;T;T	0.60548	0.18;0.18;0.18;0.18	5.67	5.67	0.87782	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.79713	0.4493	M	0.89785	3.06	0.80722	D	1	D;D;P;D	0.76494	0.999;0.999;0.907;0.999	D;D;P;D	0.70227	0.968;0.946;0.7;0.968	D	0.83512	0.0081	10	0.54805	T	0.06	.	14.9165	0.70801	0.0:0.0:0.0:1.0	.	509;508;510;538	B4DG22;F5GYC4;B7ZB17;P51812	.;.;.;KS6A3_HUMAN	G	538;510;508;509	ENSP00000368884:R538G;ENSP00000440220:R510G;ENSP00000368865:R508G;ENSP00000444837:R509G	ENSP00000368865:R508G	R	-	1	2	RPS6KA3	20093090	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.186000	0.42593	1.905000	0.55150	0.486000	0.48141	AGA	.		0.333	RPS6KA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056011.3	NM_004586	
KCNMA1	3778	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	10	79011006	79011006	+	Missense_Mutation	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr10:79011006T>G	ENST00000286628.8	-	3	548	c.549A>C	c.(547-549)ttA>ttC	p.L183F	KCNMA1_ENST00000372443.1_Missense_Mutation_p.L183F|KCNMA1_ENST00000372440.1_Missense_Mutation_p.L183F|KCNMA1_ENST00000286627.5_Missense_Mutation_p.L183F|KCNMA1_ENST00000404771.3_Missense_Mutation_p.L183F|KCNMA1_ENST00000354353.5_Missense_Mutation_p.L183F|KCNMA1_ENST00000406533.3_Missense_Mutation_p.L183F|KCNMA1_ENST00000404857.1_Missense_Mutation_p.L183F	NM_001161352.1	NP_001154824.1	Q12791	KCMA1_HUMAN	potassium large conductance calcium-activated channel, subfamily M, alpha member 1	183					blood coagulation (GO:0007596)|cellular potassium ion homeostasis (GO:0030007)|micturition (GO:0060073)|negative regulation of cell volume (GO:0045794)|positive regulation of apoptotic process (GO:0043065)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of membrane potential (GO:0042391)|response to calcium ion (GO:0051592)|response to carbon monoxide (GO:0034465)|response to hypoxia (GO:0001666)|response to osmotic stress (GO:0006970)|smooth muscle contraction involved in micturition (GO:0060083)|synaptic transmission (GO:0007268)	apical plasma membrane (GO:0016324)|caveola (GO:0005901)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	actin binding (GO:0003779)|calcium-activated potassium channel activity (GO:0015269)|large conductance calcium-activated potassium channel activity (GO:0060072)|metal ion binding (GO:0046872)|voltage-gated potassium channel activity (GO:0005249)			breast(1)|cervix(2)|endometrium(6)|kidney(3)|large_intestine(17)|lung(23)|ovary(2)|pancreas(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	68	all_cancers(46;0.203)|all_epithelial(25;0.00604)|Prostate(51;0.0198)		OV - Ovarian serous cystadenocarcinoma(4;0.0586)|Epithelial(14;0.081)|all cancers(16;0.183)		Bendroflumethiazide(DB00436)|Chlorzoxazone(DB00356)|Cromoglicic acid(DB01003)|Diazoxide(DB01119)|Halothane(DB01159)|Hydrochlorothiazide(DB00999)|Hydroflumethiazide(DB00774)|Miconazole(DB01110)|Procaine(DB00721)	GAGCAAAGACTAAGACAACCT	0.383											OREG0020289	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L183F		.											.	.	.	0			c.A549C						.						120.0	121.0	121.0					10																	79011006		2203	4300	6503	SO:0001583	missense	3778	exon3			AAAGACTAAGACA	U11717	CCDS7352.1, CCDS60569.1, CCDS60571.1, CCDS60572.1, CCDS73156.1	10q22	2012-07-05			ENSG00000156113	ENSG00000156113		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, calcium-activated"""	6284	protein-coding gene	gene with protein product	"""BK channel alpha subunit"""	600150		SLO		7987297, 16382103	Standard	NM_002247		Approved	KCa1.1, mSLO1	uc001jxn.3	Q12791	OTTHUMG00000018543	ENST00000286628.8:c.549A>C	10.37:g.79011006T>G	ENSP00000286628:p.Leu183Phe	Somatic	76	0	1187	WXS	Illumina HiSeq	.	42	14	NM_001161352	F8WA96|Q12886|Q12917|Q12921|Q12960|Q13150|Q5JQ23|Q5SQR9|Q96LG8|Q9UBB0|Q9UCX0|Q9UQK6	Missense_Mutation	SNP	ENST00000286628.8	37		.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	T|T|T	17.84|17.84|17.84	3.488547|3.488547|3.488547	0.64074|0.64074|0.64074	.|.|.	.|.|.	ENSG00000156113|ENSG00000156113|ENSG00000156113	ENST00000372440;ENST00000372408;ENST00000372437;ENST00000457953;ENST00000404771;ENST00000372443;ENST00000286627;ENST00000286628;ENST00000406533;ENST00000354353;ENST00000404857|ENST00000372421|ENST00000372403	D;D;D;D;D;D;D;D;D|.|.	0.97888|.|.	-4.59;-4.59;-4.59;-4.59;-4.59;-4.59;-4.59;-4.59;-4.59|.|.	5.33|5.33|5.33	1.7|1.7|1.7	0.24286|0.24286|0.24286	.|.|.	0.263417|.|.	0.30969|.|.	N|.|.	0.008504|.|.	T|T|.	0.60011|0.60011|.	0.2236|0.2236|.	M|M|M	0.64404|0.64404|0.64404	1.975|1.975|1.975	0.54753|0.54753|0.54753	D|D|D	0.999983|0.999983|0.999983	D;D;D;D;D|.|.	0.71674|.|.	0.97;0.982;0.97;0.998;0.97|.|.	D;D;D;D;D|.|.	0.72982|.|.	0.934;0.97;0.934;0.979;0.934|.|.	T|T|.	0.53158|0.53158|.	-0.8478|-0.8478|.	10|5|.	0.87932|.|.	D|.|.	0|.|.	-7.3448|-7.3448|-7.3448	8.1678|8.1678|8.1678	0.31237|0.31237|0.31237	0.0:0.2253:0.0:0.7747|0.0:0.2253:0.0:0.7747|0.0:0.2253:0.0:0.7747	.|.|.	183;183;183;183;183|.|.	B7ZMF5;Q12791-2;Q12791;Q12791-5;Q5SVJ7|.|.	.;.;KCMA1_HUMAN;.;.|.|.	F|R|S	183;120;118;157;120;183;183;157;183;183;183|172|134	ENSP00000361517:L183F;ENSP00000361485:L120F;ENSP00000361514:L118F;ENSP00000396608:L157F;ENSP00000361520:L183F;ENSP00000286627:L183F;ENSP00000385552:L183F;ENSP00000346321:L183F;ENSP00000385806:L183F|.|.	ENSP00000286627:L183F|.|.	L|S|X	-|-|-	3|1|2	2|0|0	KCNMA1|KCNMA1|KCNMA1	78681012|78681012|78681012	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.988000|0.988000|0.988000	0.76386|0.76386|0.76386	2.347000|2.347000|2.347000	0.44036|0.44036|0.44036	0.105000|0.105000|0.105000	0.17753|0.17753|0.17753	-0.297000|-0.297000|-0.297000	0.09499|0.09499|0.09499	TTA|AGT|TAG	.		0.383	KCNMA1-009	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000048885.3	NM_002247	
HBS1L	10767	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	6	135358028	135358028	+	Intron	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr6:135358028T>G	ENST00000367837.5	-	4	637				HBS1L_ENST00000367822.5_Missense_Mutation_p.K523Q|HBS1L_ENST00000445176.2_Intron|HBS1L_ENST00000314674.3_Intron|HBS1L_ENST00000415177.2_Intron|HBS1L_ENST00000367824.4_Intron|HBS1L_ENST00000367826.2_Intron|HBS1L_ENST00000367820.2_Intron	NM_001145158.1|NM_006620.3	NP_001138630.1|NP_006611.1	Q9Y450	HBS1L_HUMAN	HBS1-like translational GTPase						signal transduction (GO:0007165)|translation (GO:0006412)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|translation elongation factor activity (GO:0003746)			NS(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	20	Colorectal(23;0.221)			OV - Ovarian serous cystadenocarcinoma(155;0.0046)|GBM - Glioblastoma multiforme(68;0.00702)		TTCCCTAGCTTTGAACTTAGA	0.388																																					p.K523Q		.											.	.	.	0			c.A1567C						.						41.0	38.0	39.0					6																	135358028		692	1591	2283	SO:0001627	intron_variant	10767	exon5			CTAGCTTTGAACT	U87791	CCDS5173.1, CCDS47479.1, CCDS47480.1	6q23.3	2014-04-30	2014-04-30		ENSG00000112339	ENSG00000112339			4834	protein-coding gene	gene with protein product	"""eRF3 family member"""	612450	"""HBS1 (S. cerevisiae)-like"", ""HBS1-like (S. cerevisiae)"""			9872408, 23667253	Standard	NM_006620		Approved	ERFS, HBS1, HSPC276, KIAA1038, DKFZp434g247, EF-1a, eRF3c	uc003qez.2	Q9Y450	OTTHUMG00000015626	ENST00000367837.5:c.430+2682A>C	6.37:g.135358028T>G		Somatic	111	0		WXS	Illumina HiSeq	.	70	15	NM_001145207	B7Z365|Q4VX89|Q4VX90|Q5T7G3|Q8NDW9|Q9UPW3	Missense_Mutation	SNP	ENST00000367837.5	37	CCDS5173.1	.	.	.	.	.	.	.	.	.	.	T	9.944	1.218310	0.22373	.	.	ENSG00000112339	ENST00000367822	.	.	.	5.32	4.16	0.48862	.	.	.	.	.	T	0.56140	0.1965	.	.	.	0.80722	D	1	D	0.56746	0.977	P	0.56648	0.803	T	0.61964	-0.6954	7	0.59425	D	0.04	.	7.775	0.29033	0.0:0.1536:0.0:0.8464	.	523	Q9Y450-2	.	Q	523	.	ENSP00000356796:K523Q	K	-	1	0	HBS1L	135399721	1.000000	0.71417	1.000000	0.80357	0.082000	0.17680	2.644000	0.46613	2.139000	0.66308	0.533000	0.62120	AAG	.		0.388	HBS1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042339.2		
NUP98	4928	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	11	3774554	3774554	+	Missense_Mutation	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr11:3774554A>C	ENST00000324932.7	-	11	1679	c.1259T>G	c.(1258-1260)tTt>tGt	p.F420C	NUP98_ENST00000359171.4_Missense_Mutation_p.F420C|NUP98_ENST00000355260.3_Missense_Mutation_p.F420C|NUP98_ENST00000397004.4_Missense_Mutation_p.F420C|NUP98_ENST00000397007.4_Missense_Mutation_p.F437C	NM_016320.4|NM_139132.3	NP_057404.2|NP_624358.2	P52948	NUP98_HUMAN	nucleoporin 98kDa	437	FG repeats 2.|Gly/Thr-rich.				carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|DNA replication (GO:0006260)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|nuclear pore complex assembly (GO:0051292)|nuclear pore organization (GO:0006999)|nucleocytoplasmic transport (GO:0006913)|protein import into nucleus, docking (GO:0000059)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|nuclear envelope (GO:0005635)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)|nuclear pore outer ring (GO:0031080)|nucleoplasm (GO:0005654)	peptide binding (GO:0042277)|structural constituent of nuclear pore (GO:0017056)|transporter activity (GO:0005215)			NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(1)|endometrium(5)|kidney(5)|large_intestine(13)|liver(1)|lung(15)|ovary(2)|prostate(2)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	66		Medulloblastoma(188;0.0025)|Breast(177;0.00328)|all_neural(188;0.0227)		BRCA - Breast invasive adenocarcinoma(625;0.0403)|LUSC - Lung squamous cell carcinoma(625;0.116)|Lung(200;0.199)		ACCTGTTCCAAATCCTGCACC	0.423			T	"""HOXA9, NSD1, WHSC1L1, DDX10, TOP1, HOXD13, PMX1, HOXA13, HOXD11, HOXA11, RAP1GDS1, HOXC11"""	AML																																p.F437C		.		Dom	yes		11	11p15	4928	nucleoporin 98kDa		L	.	.	.	0			c.T1310G						.						86.0	80.0	82.0					11																	3774554		2201	4298	6499	SO:0001583	missense	4928	exon11			GTTCCAAATCCTG	AF071076, AF231130, BC012906, BG773331	CCDS7746.1, CCDS31347.1, CCDS41605.1, CCDS41606.1	11p15	2008-02-26	2002-08-29		ENSG00000110713	ENSG00000110713			8068	protein-coding gene	gene with protein product		601021	"""nucleoporin 98kD"""			9166830	Standard	NM_139131		Approved	NUP96	uc001lyh.3	P52948	OTTHUMG00000011846	ENST00000324932.7:c.1259T>G	11.37:g.3774554A>C	ENSP00000316032:p.Phe420Cys	Somatic	89	0		WXS	Illumina HiSeq	.	42	19	NM_005387	Q8IUT2|Q8WYB0|Q96E54|Q9H3Q4|Q9NT02|Q9UF57|Q9UHX0|Q9Y6J4|Q9Y6J5	Missense_Mutation	SNP	ENST00000324932.7	37	CCDS7746.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	A|A|A	21.4|21.4|21.4	4.141666|4.141666|4.141666	0.77775|0.77775|0.77775	.|.|.	.|.|.	ENSG00000110713|ENSG00000110713|ENSG00000110713	ENST00000324932;ENST00000359171;ENST00000355260;ENST00000397004;ENST00000397007|ENST00000527104|ENST00000529379	.|.|.	.|.|.	.|.|.	5.34|5.34|5.34	5.34|5.34|5.34	0.76211|0.76211|0.76211	.|.|.	0.000000|.|.	0.85682|.|.	D|.|.	0.000000|.|.	T|T|T	0.78457|0.78457|0.78457	0.4286|0.4286|0.4286	M|M|M	0.85777|0.85777|0.85777	2.775|2.775|2.775	0.58432|0.58432|0.58432	D|D|D	0.999997|0.999997|0.999997	D;D;D;D|.|.	0.89917|.|.	1.0;0.999;1.0;1.0|.|.	D;D;D;D|.|.	0.91635|.|.	0.997;0.947;0.999;0.999|.|.	T|T|T	0.81309|0.81309|0.81309	-0.0991|-0.0991|-0.0991	9|5|5	0.45353|.|.	T|.|.	0.12|.|.	.|.|.	14.4955|14.4955|14.4955	0.67683|0.67683|0.67683	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.|.	437;420;420;420|.|.	P52948-3;P52948-4;P52948-2;P52948-5|.|.	.;.;.;.|.|.	C|M|V	420;420;420;420;437|39|69	.|.|.	ENSP00000316032:F420C|.|.	F|I|L	-|-|-	2|3|1	0|3|2	NUP98|NUP98|NUP98	3731130|3731130|3731130	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.991000|0.991000|0.991000	0.79684|0.79684|0.79684	7.387000|7.387000|7.387000	0.79785|0.79785|0.79785	2.023000|2.023000|2.023000	0.59567|0.59567|0.59567	0.533000|0.533000|0.533000	0.62120|0.62120|0.62120	TTT|ATT|TTG	.		0.423	NUP98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032766.3	NM_016320	
EP300	2033	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	22	41574848	41574848	+	Missense_Mutation	SNP	G	G	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr22:41574848G>A	ENST00000263253.7	+	31	8352	c.7133G>A	c.(7132-7134)aGc>aAc	p.S2378N	RP1-85F18.5_ENST00000420537.1_RNA|RP1-85F18.6_ENST00000415054.1_RNA	NM_001429.3	NP_001420.2	Q09472	EP300_HUMAN	E1A binding protein p300	2378					apoptotic process (GO:0006915)|cellular response to hypoxia (GO:0071456)|chromatin organization (GO:0006325)|circadian rhythm (GO:0007623)|G2/M transition of mitotic cell cycle (GO:0000086)|heart development (GO:0007507)|histone H2B acetylation (GO:0043969)|histone H4 acetylation (GO:0043967)|innate immune response (GO:0045087)|internal peptidyl-lysine acetylation (GO:0018393)|internal protein amino acid acetylation (GO:0006475)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|lung development (GO:0030324)|mitotic cell cycle (GO:0000278)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of protein binding (GO:0032092)|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 type I interferon production (GO:0032481)|regulation of androgen receptor signaling pathway (GO:0060765)|regulation of cell cycle (GO:0051726)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)|regulation of tubulin deacetylation (GO:0090043)|response to estrogen (GO:0043627)|response to hypoxia (GO:0001666)|skeletal muscle tissue development (GO:0007519)|somitogenesis (GO:0001756)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	acetyltransferase activity (GO:0016407)|activating transcription factor binding (GO:0033613)|androgen receptor binding (GO:0050681)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|lysine N-acetyltransferase activity, acting on acetyl phosphate as donor (GO:0004468)|nuclear hormone receptor binding (GO:0035257)|pre-mRNA intronic binding (GO:0097157)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transferase activity, transferring acyl groups (GO:0016746)|zinc ion binding (GO:0008270)			NS(2)|breast(11)|central_nervous_system(7)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(31)|kidney(5)|large_intestine(31)|liver(2)|lung(33)|ovary(2)|pancreas(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(16)	171						CAGCTTGCTAGCAATCCAGGC	0.537			"""T,  N, F, Mis, O"""	"""MLL, RUNXBP2"""	"""colorectal, breast, pancreatic, AML, ALL, DLBCL"""				Rubinstein-Taybi syndrome																												p.S2378N		.		Rec	yes		22	22q13	2033	300 kd E1A-Binding protein gene		"""L, E"""	.	.	.	0			c.G7133A						.						49.0	50.0	50.0					22																	41574848		2203	4300	6503	SO:0001583	missense	2033	exon31	Familial Cancer Database	Broad Thumb-Hallux syndrome	TTGCTAGCAATCC	U01877	CCDS14010.1	22q13.2	2011-07-01			ENSG00000100393	ENSG00000100393		"""Chromatin-modifying enzymes / K-acetyltransferases"""	3373	protein-coding gene	gene with protein product	"""histone acetyltransferase p300"""	602700				7523245	Standard	NM_001429		Approved	p300, KAT3B	uc003azl.4	Q09472	OTTHUMG00000150937	ENST00000263253.7:c.7133G>A	22.37:g.41574848G>A	ENSP00000263253:p.Ser2378Asn	Somatic	62	0		WXS	Illumina HiSeq	.	38	14	NM_001429	B1AKC2	Missense_Mutation	SNP	ENST00000263253.7	37	CCDS14010.1	.	.	.	.	.	.	.	.	.	.	G	8.220	0.802224	0.16397	.	.	ENSG00000100393	ENST00000263253	D	0.84146	-1.81	5.65	3.57	0.40892	.	0.106281	0.41097	D	0.000951	T	0.68044	0.2958	N	0.11064	0.09	0.31949	N	0.609974	B	0.02656	0.0	B	0.04013	0.001	T	0.60707	-0.7210	10	0.12430	T	0.62	-2.2404	10.1606	0.42849	0.2126:0.0:0.7874:0.0	.	2378	Q09472	EP300_HUMAN	N	2378	ENSP00000263253:S2378N	ENSP00000263253:S2378N	S	+	2	0	EP300	39904794	1.000000	0.71417	0.997000	0.53966	0.886000	0.51366	3.244000	0.51399	0.748000	0.32831	-0.150000	0.13652	AGC	.		0.537	EP300-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320600.1	NM_001429	
GPR155	151556	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	2	175346540	175346540	+	Missense_Mutation	SNP	A	A	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr2:175346540A>G	ENST00000392552.2	-	2	383	c.145T>C	c.(145-147)Tgc>Cgc	p.C49R	GPR155_ENST00000295500.4_Missense_Mutation_p.C49R|GPR155_ENST00000392551.2_Missense_Mutation_p.C49R	NM_001267051.1|NM_152529.6	NP_001253980.1|NP_689742.4	Q7Z3F1	GP155_HUMAN	G protein-coupled receptor 155	49					cognition (GO:0050890)|intracellular signal transduction (GO:0035556)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				breast(2)|endometrium(5)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|stomach(2)|urinary_tract(2)	26						ATGCCAAAGCATTCCAGTAAG	0.433																																					p.C49R		.											.	.	.	0			c.T145C						.						99.0	92.0	94.0					2																	175346540		2203	4300	6503	SO:0001583	missense	151556	exon2			CAAAGCATTCCAG	AY255528	CCDS2259.1, CCDS74605.1	2q31.1	2012-04-10			ENSG00000163328	ENSG00000163328			22951	protein-coding gene	gene with protein product						12679517	Standard	NM_001033045		Approved	DEPDC3, DEP.7, FLJ31819, PGR22	uc002uiu.4	Q7Z3F1	OTTHUMG00000132336	ENST00000392552.2:c.145T>C	2.37:g.175346540A>G	ENSP00000376335:p.Cys49Arg	Somatic	35	0		WXS	Illumina HiSeq	.	26	17	NM_001267051	B2RCI2|D3DPE2|Q4G0Y6|Q53SJ3|Q53TA8|Q69YG8|Q86SP9|Q8N261|Q8N639|Q8N8K3|Q96MV6	Missense_Mutation	SNP	ENST00000392552.2	37	CCDS2259.1	.	.	.	.	.	.	.	.	.	.	A	22.1	4.243739	0.79912	.	.	ENSG00000163328	ENST00000392552;ENST00000392551;ENST00000295500	T;T;T	0.52526	0.66;0.66;0.66	5.79	5.79	0.91817	.	0.000000	0.85682	D	0.000000	T	0.72700	0.3493	M	0.84433	2.695	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.77816	-0.2447	10	0.87932	D	0	-9.3762	16.1199	0.81342	1.0:0.0:0.0:0.0	.	49	Q7Z3F1	GP155_HUMAN	R	49	ENSP00000376335:C49R;ENSP00000376334:C49R;ENSP00000295500:C49R	ENSP00000295500:C49R	C	-	1	0	GPR155	175054786	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.305000	0.96197	2.194000	0.70268	0.533000	0.62120	TGC	.		0.433	GPR155-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255455.1	NM_152529	
LRP6	4040	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	12	12279840	12279840	+	Missense_Mutation	SNP	G	G	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr12:12279840G>A	ENST00000261349.4	-	20	4173	c.4097C>T	c.(4096-4098)cCa>cTa	p.P1366L	LRP6_ENST00000540415.1_Intron|BCL2L14_ENST00000396369.1_Intron|LRP6_ENST00000543091.1_Missense_Mutation_p.P1321L	NM_002336.2	NP_002327.2	O75581	LRP6_HUMAN	low density lipoprotein receptor-related protein 6	1366					anterior/posterior pattern specification (GO:0009952)|axis elongation involved in somitogenesis (GO:0090245)|bone morphogenesis (GO:0060349)|bone remodeling (GO:0046849)|branching involved in mammary gland duct morphogenesis (GO:0060444)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in cardiac neural crest cell differentiation involved in heart development (GO:0061310)|canonical Wnt signaling pathway involved in neural crest cell differentiation (GO:0044335)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in regulation of cell proliferation (GO:0044340)|cell migration involved in gastrulation (GO:0042074)|cellular response to cholesterol (GO:0071397)|cerebellum morphogenesis (GO:0021587)|cerebral cortex cell migration (GO:0021795)|cerebral cortex development (GO:0021987)|convergent extension (GO:0060026)|dopaminergic neuron differentiation (GO:0071542)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic pattern specification (GO:0009880)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|external genitalia morphogenesis (GO:0035261)|face morphogenesis (GO:0060325)|forebrain radial glial cell differentiation (GO:0021861)|formation of radial glial scaffolds (GO:0021943)|gastrulation with mouth forming second (GO:0001702)|heart looping (GO:0001947)|mammary placode formation (GO:0060596)|midbrain development (GO:0030901)|midbrain-hindbrain boundary development (GO:0030917)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of planar cell polarity pathway involved in cardiac muscle tissue morphogenesis (GO:2000151)|negative regulation of planar cell polarity pathway involved in cardiac right atrium morphogenesis (GO:2000162)|negative regulation of planar cell polarity pathway involved in neural tube closure (GO:2000168)|negative regulation of planar cell polarity pathway involved in outflow tract morphogenesis (GO:2000164)|negative regulation of planar cell polarity pathway involved in pericardium morphogenesis (GO:2000166)|negative regulation of planar cell polarity pathway involved in ventricular septum morphogenesis (GO:2000149)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|negative regulation of smooth muscle cell apoptotic process (GO:0034392)|neural crest cell differentiation (GO:0014033)|neural crest formation (GO:0014029)|neural tube closure (GO:0001843)|odontogenesis of dentin-containing tooth (GO:0042475)|palate development (GO:0060021)|pericardium morphogenesis (GO:0003344)|positive regulation of apoptotic process (GO:0043065)|positive regulation of bone resorption (GO:0045780)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell cycle (GO:0045787)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of ossification (GO:0045778)|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)|positive regulation of Wnt signaling pathway involved in dorsal/ventral axis specification (GO:2000055)|post-anal tail morphogenesis (GO:0036342)|primitive streak formation (GO:0090009)|receptor-mediated endocytosis of low-density lipoprotein particle involved in cholesterol transport (GO:0090118)|regulation of cell development (GO:0060284)|regulation of fat cell differentiation (GO:0045598)|regulation of ossification (GO:0030278)|response to folic acid (GO:0051593)|response to peptide hormone (GO:0043434)|single organismal cell-cell adhesion (GO:0016337)|synaptic transmission (GO:0007268)|thalamus development (GO:0021794)|toxin transport (GO:1901998)|trachea cartilage morphogenesis (GO:0060535)|Wnt signaling pathway (GO:0016055)|Wnt signaling pathway involved in dorsal/ventral axis specification (GO:0044332)|Wnt signaling pathway involved in forebrain neuroblast division (GO:0021874)|Wnt signaling pathway involved in somitogenesis (GO:0090244)	cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|synapse (GO:0045202)	apolipoprotein binding (GO:0034185)|coreceptor activity involved in Wnt signaling pathway (GO:0071936)|frizzled binding (GO:0005109)|identical protein binding (GO:0042802)|kinase inhibitor activity (GO:0019210)|low-density lipoprotein receptor activity (GO:0005041)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|toxin transporter activity (GO:0019534)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(19)|lung(28)|ovary(3)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	85		Prostate(47;0.0865)				CTGTGGTGCTGGTTCTTCAGT	0.378																																					p.P1366L		.											.	.	.	0			c.C4097T						.						85.0	81.0	82.0					12																	12279840		2203	4300	6503	SO:0001583	missense	4040	exon20			GGTGCTGGTTCTT	AF074264	CCDS8647.1	12p13.2	2013-05-29			ENSG00000070018	ENSG00000070018		"""Low density lipoprotein receptors"""	6698	protein-coding gene	gene with protein product		603507				9704021	Standard	NM_002336		Approved	ADCAD2	uc001rah.4	O75581	OTTHUMG00000168540	ENST00000261349.4:c.4097C>T	12.37:g.12279840G>A	ENSP00000261349:p.Pro1366Leu	Somatic	95	0		WXS	Illumina HiSeq	.	64	23	NM_002336	Q17RZ2	Missense_Mutation	SNP	ENST00000261349.4	37	CCDS8647.1	.	.	.	.	.	.	.	.	.	.	G	24.7	4.555892	0.86231	.	.	ENSG00000070018	ENST00000261349;ENST00000543091	D;D	0.94417	-3.31;-3.42	5.84	5.84	0.93424	.	0.000000	0.64402	D	0.000009	D	0.96485	0.8853	L	0.57536	1.79	0.80722	D	1	D;D	0.76494	0.999;0.998	D;D	0.80764	0.994;0.987	D	0.94497	0.7706	10	0.23891	T	0.37	.	20.1368	0.98032	0.0:0.0:1.0:0.0	.	1321;1366	F5H7J9;O75581	.;LRP6_HUMAN	L	1366;1321	ENSP00000261349:P1366L;ENSP00000442472:P1321L	ENSP00000261349:P1366L	P	-	2	0	LRP6	12171107	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	7.277000	0.78572	2.751000	0.94390	0.563000	0.77884	CCA	.		0.378	LRP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400137.1		
BMP5	653	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	6	55638874	55638874	+	Missense_Mutation	SNP	C	C	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr6:55638874C>A	ENST00000370830.3	-	4	1698	c.1000G>T	c.(1000-1002)Gac>Tac	p.D334Y	BMP5_ENST00000446683.2_Missense_Mutation_p.D334Y	NM_021073.2	NP_066551.1	P22003	BMP5_HUMAN	bone morphogenetic protein 5	334					cartilage development (GO:0051216)|growth (GO:0040007)|male genitalia development (GO:0030539)|negative regulation of aldosterone biosynthetic process (GO:0032348)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cortisol biosynthetic process (GO:2000065)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of insulin-like growth factor receptor signaling pathway (GO:0043569)|negative regulation of mononuclear cell migration (GO:0071676)|negative regulation of steroid biosynthetic process (GO:0010894)|ossification (GO:0001503)|pattern specification process (GO:0007389)|positive regulation of dendrite development (GO:1900006)|positive regulation of DNA-dependent DNA replication (GO:2000105)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|skeletal system development (GO:0001501)|type B pancreatic cell development (GO:0003323)	extracellular space (GO:0005615)|membrane-bounded vesicle (GO:0031988)	BMP receptor binding (GO:0070700)			cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(6)|lung(19)|ovary(2)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)	45	Lung NSC(77;0.0462)		LUSC - Lung squamous cell carcinoma(124;0.181)			CTGGAGGAGTCCTGATGAGAG	0.473																																					p.D334Y		.											.	.	.	0			c.G1000T						.						161.0	141.0	148.0					6																	55638874		2203	4299	6502	SO:0001583	missense	653	exon4			AGGAGTCCTGATG		CCDS4958.1	6p12.1	2014-01-30			ENSG00000112175	ENSG00000112175		"""Bone morphogenetic proteins"", ""Endogenous ligands"""	1072	protein-coding gene	gene with protein product		112265				1427904, 11580864	Standard	NM_021073		Approved		uc003pcq.3	P22003	OTTHUMG00000014903	ENST00000370830.3:c.1000G>T	6.37:g.55638874C>A	ENSP00000359866:p.Asp334Tyr	Somatic	86	0		WXS	Illumina HiSeq	.	84	46	NM_021073	B4E0Y4|Q9H547|Q9NTM5	Missense_Mutation	SNP	ENST00000370830.3	37	CCDS4958.1	.	.	.	.	.	.	.	.	.	.	C	22.8	4.334373	0.81801	.	.	ENSG00000112175	ENST00000370830;ENST00000446683	T;T	0.73575	-0.76;-0.38	5.73	5.73	0.89815	.	0.358596	0.34652	N	0.003783	T	0.71550	0.3353	L	0.32530	0.975	0.53688	D	0.999974	P;P	0.51147	0.942;0.942	P;P	0.52909	0.713;0.713	T	0.75317	-0.3360	10	0.87932	D	0	.	19.8944	0.96949	0.0:1.0:0.0:0.0	.	334;334	B4E0Y4;P22003	.;BMP5_HUMAN	Y	334	ENSP00000359866:D334Y;ENSP00000391818:D334Y	ENSP00000359866:D334Y	D	-	1	0	BMP5	55746833	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.030000	0.49720	2.694000	0.91930	0.643000	0.83706	GAC	.		0.473	BMP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041000.1		
MREG	55686	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	2	216809713	216809713	+	Missense_Mutation	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr2:216809713A>C	ENST00000263268.6	-	5	813	c.518T>G	c.(517-519)cTc>cGc	p.L173R		NM_018000.2	NP_060470.2	Q8N565	MREG_HUMAN	melanoregulin	173						plasma membrane (GO:0005886)				large_intestine(1)|lung(2)	3		Renal(323;0.0328)		Epithelial(149;4.64e-07)|all cancers(144;5.56e-05)|LUSC - Lung squamous cell carcinoma(224;0.00832)|Lung(261;0.0111)		AAGTGCAATGAGACGGTCCTG	0.458																																					p.L173R		.											.	.	.	0			c.T518G						.						43.0	41.0	42.0					2																	216809713		1886	4124	6010	SO:0001583	missense	55686	exon5			GCAATGAGACGGT	AK000978	CCDS46513.1	2q35	2013-09-27			ENSG00000118242	ENSG00000118242			25478	protein-coding gene	gene with protein product		609207				19240024, 22275436	Standard	NM_018000		Approved	FLJ10116, DSU, WDT2	uc002vfo.3	Q8N565	OTTHUMG00000154828	ENST00000263268.6:c.518T>G	2.37:g.216809713A>C	ENSP00000263268:p.Leu173Arg	Somatic	19	0		WXS	Illumina HiSeq	.	18	9	NM_018000	Q53R89|Q53TC1|Q5XKB6|Q9NWC9|Q9P1S1	Missense_Mutation	SNP	ENST00000263268.6	37	CCDS46513.1	.	.	.	.	.	.	.	.	.	.	A	21.0	4.076031	0.76415	.	.	ENSG00000118242	ENST00000236976;ENST00000263268;ENST00000439791;ENST00000424992	T	0.68903	-0.36	6.17	5.01	0.66863	.	0.000000	0.85682	D	0.000000	T	0.63283	0.2498	M	0.62723	1.935	0.51012	D	0.999902	B	0.23249	0.082	B	0.22386	0.039	T	0.62224	-0.6899	10	0.87932	D	0	-12.6509	10.5378	0.45016	0.8378:0.1622:0.0:0.0	.	173	Q8N565	MREG_HUMAN	R	173;173;119;119	ENSP00000263268:L173R	ENSP00000236976:L173R	L	-	2	0	MREG	216517958	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.963000	0.70372	1.130000	0.42092	0.533000	0.62120	CTC	.		0.458	MREG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337297.1	NM_018000	
CDK2	1017	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	12	56361718	56361718	+	Splice_Site	SNP	A	A	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr12:56361718A>G	ENST00000266970.4	+	2	434	c.194A>G	c.(193-195)aAg>aGg	p.K65R	PMEL_ENST00000548689.1_5'Flank|CDK2_ENST00000440311.2_Intron|PMEL_ENST00000552882.1_5'Flank|RP11-973D8.4_ENST00000554022.1_RNA|CDK2_ENST00000553376.1_Splice_Site_p.K65R|PMEL_ENST00000449260.2_5'Flank|PMEL_ENST00000548747.1_5'Flank|PMEL_ENST00000539511.1_5'Flank|PMEL_ENST00000550447.1_5'Flank|PMEL_ENST00000536427.1_5'Flank|CDK2_ENST00000354056.4_Splice_Site_p.K65R|PMEL_ENST00000548493.1_5'Flank|PMEL_ENST00000360714.4_5'Flank|CDK2_ENST00000556656.1_3'UTR|PMEL_ENST00000550464.1_5'Flank	NM_001798.3	NP_001789.2	P24941	CDK2_HUMAN	cyclin-dependent kinase 2	65	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|blood coagulation (GO:0007596)|cellular response to nitric oxide (GO:0071732)|centrosome duplication (GO:0051298)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|histone phosphorylation (GO:0016572)|meiotic nuclear division (GO:0007126)|mitotic cell cycle (GO:0000278)|mitotic G1 DNA damage checkpoint (GO:0031571)|mitotic nuclear division (GO:0007067)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA-dependent DNA replication initiation (GO:0032298)|positive regulation of transcription, DNA-templated (GO:0045893)|potassium ion transport (GO:0006813)|Ras protein signal transduction (GO:0007265)|regulation of gene silencing (GO:0060968)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	Cajal body (GO:0015030)|centrosome (GO:0005813)|chromosome, telomeric region (GO:0000781)|condensed chromosome (GO:0000793)|cyclin-dependent protein kinase holoenzyme complex (GO:0000307)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)|X chromosome (GO:0000805)|Y chromosome (GO:0000806)	ATP binding (GO:0005524)|cyclin binding (GO:0030332)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|metal ion binding (GO:0046872)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(7)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	18			UCEC - Uterine corpus endometrioid carcinoma (6;0.123)|OV - Ovarian serous cystadenocarcinoma(18;0.235)		Bosutinib(DB06616)	AATATTGTCAAGTAAGTATGC	0.478																																					p.K65R		.											.	.	.	0			c.A194G						.						134.0	122.0	126.0					12																	56361718		2203	4300	6503	SO:0001630	splice_region_variant	1017	exon2			TTGTCAAGTAAGT	M68520	CCDS8898.1, CCDS8899.1	12q13	2011-11-08				ENSG00000123374		"""Cyclin-dependent kinases"""	1771	protein-coding gene	gene with protein product		116953				1717994, 8275715	Standard	NM_001798		Approved		uc001sit.4	P24941		ENST00000266970.4:c.194+1A>G	12.37:g.56361718A>G		Somatic	52	0		WXS	Illumina HiSeq	.	52	22	NM_052827	A8K7C6|O75100	Missense_Mutation	SNP	ENST00000266970.4	37	CCDS8898.1	.	.	.	.	.	.	.	.	.	.	A	7.362	0.624967	0.14257	.	.	ENSG00000123374	ENST00000266970;ENST00000553376;ENST00000354056	T;T;T	0.43294	0.95;0.95;0.95	5.52	5.52	0.82312	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.28665	0.0710	L	0.28649	0.875	0.58432	D	0.999998	B;B	0.02656	0.0;0.0	B;B	0.08055	0.002;0.003	T	0.11372	-1.0590	10	0.02654	T	1	-10.722	14.9334	0.70935	1.0:0.0:0.0:0.0	.	65;65	P24941-2;P24941	.;CDK2_HUMAN	R	65	ENSP00000266970:K65R;ENSP00000452514:K65R;ENSP00000243067:K65R	ENSP00000266970:K65R	K	+	2	0	CDK2	54647985	1.000000	0.71417	1.000000	0.80357	0.687000	0.40016	3.101000	0.50283	2.242000	0.73789	0.402000	0.26972	AAG	.		0.478	CDK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409650.1		Missense_Mutation
TMPRSS11B	132724	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	4	69093790	69093790	+	Splice_Site	SNP	T	T	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr4:69093790T>C	ENST00000332644.5	-	10	1251	c.1090A>G	c.(1090-1092)Aat>Gat	p.N364D		NM_182502.3	NP_872308.2	Q86T26	TM11B_HUMAN	transmembrane protease, serine 11B	364	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	serine-type endopeptidase activity (GO:0004252)			breast(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(14)|ovary(1)|skin(1)	27						CCAGAATCATTCTAGAAGAAG	0.388																																					p.N364D		.											.	.	.	0			c.A1090G						.						50.0	47.0	48.0					4																	69093790		2203	4300	6503	SO:0001630	splice_region_variant	132724	exon10			AATCATTCTAGAA	BX537945	CCDS3521.1	4q13.2	2010-04-13			ENSG00000185873	ENSG00000185873		"""Serine peptidases / Transmembrane"""	25398	protein-coding gene	gene with protein product							Standard	NM_182502		Approved		uc003hdw.4	Q86T26	OTTHUMG00000129301	ENST00000332644.5:c.1090-1A>G	4.37:g.69093790T>C		Somatic	71	0		WXS	Illumina HiSeq	.	16	11	NM_182502	A8K4D9	Missense_Mutation	SNP	ENST00000332644.5	37	CCDS3521.1	.	.	.	.	.	.	.	.	.	.	T	19.16	3.773244	0.69992	.	.	ENSG00000185873	ENST00000332644	D	0.88431	-2.38	4.78	-5.89	0.02282	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	1.237600	0.05786	N	0.609412	T	0.69984	0.3172	N	0.01576	-0.805	0.23787	N	0.996842	B	0.17038	0.02	B	0.19391	0.025	T	0.61118	-0.7127	10	0.72032	D	0.01	.	7.6364	0.28270	0.0:0.4729:0.2649:0.2622	.	364	Q86T26	TM11B_HUMAN	D	364	ENSP00000330475:N364D	ENSP00000330475:N364D	N	-	1	0	TMPRSS11B	68776385	0.065000	0.20965	0.053000	0.19242	0.959000	0.62525	0.303000	0.19210	-0.890000	0.03945	0.528000	0.53228	AAT	.		0.388	TMPRSS11B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251431.2	NM_182502	Missense_Mutation
PAQR9	344838	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	3	142681920	142681920	+	Missense_Mutation	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr3:142681920A>C	ENST00000340634.3	-	1	258	c.259T>G	c.(259-261)Ttc>Gtc	p.F87V	RP11-372E1.6_ENST00000493825.1_RNA|RP11-372E1.6_ENST00000595774.1_RNA|RP11-372E1.6_ENST00000594095.1_RNA|RP11-372E1.6_ENST00000593321.1_RNA|RP11-372E1.6_ENST00000607937.1_RNA|RP11-372E1.6_ENST00000497652.1_RNA|RP11-372E1.6_ENST00000598787.1_RNA|RP11-372E1.6_ENST00000478823.1_RNA|RP11-372E1.6_ENST00000598139.1_RNA|RP11-372E1.6_ENST00000608686.1_RNA|RP11-372E1.6_ENST00000608349.1_RNA|RP11-372E1.6_ENST00000595248.1_RNA	NM_198504.2	NP_940906.1	Q6ZVX9	PAQR9_HUMAN	progestin and adipoQ receptor family member IX	87						integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			endometrium(2)|large_intestine(7)|lung(12)|prostate(1)	22						TGCGTCCAGAAGTTGAGCGTC	0.632																																					p.F87V		.											.	.	.	0			c.T259G						.						98.0	99.0	99.0					3																	142681920		2203	4300	6503	SO:0001583	missense	344838	exon1			TCCAGAAGTTGAG	AY424287	CCDS3128.1	3q23	2008-05-02			ENSG00000188582	ENSG00000188582			30131	protein-coding gene	gene with protein product		614580					Standard	NM_198504		Approved	FLJ41938	uc003evg.3	Q6ZVX9	OTTHUMG00000159313	ENST00000340634.3:c.259T>G	3.37:g.142681920A>C	ENSP00000341564:p.Phe87Val	Somatic	14	0		WXS	Illumina HiSeq	.	14	4	NM_198504	Q147T6	Missense_Mutation	SNP	ENST00000340634.3	37	CCDS3128.1	.	.	.	.	.	.	.	.	.	.	A	11.14	1.549692	0.27652	.	.	ENSG00000188582	ENST00000340634	T	0.25085	1.82	4.64	4.64	0.57946	.	0.063541	0.64402	D	0.000005	T	0.16769	0.0403	N	0.17594	0.5	0.49483	D	0.999795	B	0.27140	0.169	B	0.34991	0.193	T	0.03000	-1.1084	10	0.06099	T	0.92	-26.5171	14.0273	0.64592	1.0:0.0:0.0:0.0	.	87	Q6ZVX9	PAQR9_HUMAN	V	87	ENSP00000341564:F87V	ENSP00000341564:F87V	F	-	1	0	PAQR9	144164610	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.717000	0.68446	1.854000	0.53819	0.460000	0.39030	TTC	.		0.632	PAQR9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354538.1	NM_198504	
VNN1	8876	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	6	133014343	133014343	+	Missense_Mutation	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr6:133014343A>C	ENST00000367928.4	-	4	659	c.646T>G	c.(646-648)Ttc>Gtc	p.F216V		NM_004666.2	NP_004657.2	O95497	VNN1_HUMAN	vanin 1	216	CN hydrolase. {ECO:0000255|PROSITE- ProRule:PRU00054}.				acute inflammatory response (GO:0002526)|cellular component movement (GO:0006928)|chronic inflammatory response (GO:0002544)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|pantothenate metabolic process (GO:0015939)|positive regulation of T cell differentiation in thymus (GO:0033089)|response to oxidative stress (GO:0006979)|single organismal cell-cell adhesion (GO:0016337)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	GPI anchor binding (GO:0034235)|pantetheine hydrolase activity (GO:0017159)			NS(2)|endometrium(3)|kidney(2)|large_intestine(8)|lung(10)|ovary(4)|prostate(1)|upper_aerodigestive_tract(1)	31	Breast(56;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.0027)|GBM - Glioblastoma multiforme(226;0.0189)		GGATCATGGAAGAGTATATCA	0.413																																					p.F216V		.											.	.	.	0			c.T646G						.						115.0	104.0	108.0					6																	133014343		2203	4300	6503	SO:0001583	missense	8876	exon4			CATGGAAGAGTAT	AJ132099	CCDS5159.1	6q23-q24	2013-02-13			ENSG00000112299	ENSG00000112299	3.5.1.92	"""Vanins"""	12705	protein-coding gene	gene with protein product		603570				9790769	Standard	NM_004666		Approved	Tiff66	uc003qdo.3	O95497	OTTHUMG00000015587	ENST00000367928.4:c.646T>G	6.37:g.133014343A>C	ENSP00000356905:p.Phe216Val	Somatic	82	0		WXS	Illumina HiSeq	.	103	29	NM_004666	A8K310|Q4JFW6|Q4VAS7|Q4VAS8|Q4VAS9|Q9UF16|Q9UJF4	Missense_Mutation	SNP	ENST00000367928.4	37	CCDS5159.1	.	.	.	.	.	.	.	.	.	.	A	25.3	4.628369	0.87560	.	.	ENSG00000112299	ENST00000367928	D	0.89617	-2.54	6.07	6.07	0.98685	Nitrilase/cyanide hydratase and apolipoprotein N-acyltransferase (4);	0.063751	0.64402	D	0.000003	D	0.95802	0.8634	H	0.95850	3.73	0.58432	D	0.999997	D	0.53885	0.963	D	0.64321	0.924	D	0.96936	0.9684	10	0.87932	D	0	-29.5065	16.6288	0.85011	1.0:0.0:0.0:0.0	.	216	O95497	VNN1_HUMAN	V	216	ENSP00000356905:F216V	ENSP00000356905:F216V	F	-	1	0	VNN1	133056036	1.000000	0.71417	0.997000	0.53966	0.997000	0.91878	7.497000	0.81536	2.326000	0.78906	0.533000	0.62120	TTC	.		0.413	VNN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042263.1		
KIF3A	11127	hgsc.bcm.edu	37	5	132038286	132038286	+	Missense_Mutation	SNP	C	C	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr5:132038286C>A	ENST00000378746.4	-	12	1859	c.1641G>T	c.(1639-1641)aaG>aaT	p.K547N	KIF3A_ENST00000487055.1_5'UTR|KIF3A_ENST00000403231.1_Missense_Mutation_p.K574N|KIF3A_ENST00000378735.1_Missense_Mutation_p.K550N|AC004237.1_ENST00000431165.1_RNA	NM_007054.5	NP_008985.3	Q9Y496	KIF3A_HUMAN	kinesin family member 3A	547					anterior/posterior pattern specification (GO:0009952)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|determination of left/right symmetry (GO:0007368)|dorsal/ventral neural tube patterning (GO:0021904)|epidermal stem cell homeostasis (GO:0036334)|epidermis development (GO:0008544)|heart development (GO:0007507)|in utero embryonic development (GO:0001701)|inner ear receptor stereocilium organization (GO:0060122)|kidney development (GO:0001822)|membrane organization (GO:0061024)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|neurogenesis (GO:0022008)|organelle organization (GO:0006996)|plus-end-directed vesicle transport along microtubule (GO:0072383)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of receptor-mediated endocytosis (GO:0048260)|smoothened signaling pathway (GO:0007224)	centrosome (GO:0005813)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intraciliary transport particle (GO:0030990)|kinesin II complex (GO:0016939)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|neuron projection (GO:0043005)|photoreceptor connecting cilium (GO:0032391)|primary cilium (GO:0072372)|synaptic vesicle (GO:0008021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)|spectrin binding (GO:0030507)	p.K547N(1)		endometrium(1)|kidney(4)|large_intestine(8)|lung(3)|ovary(1)|pancreas(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)	25		all_cancers(142;0.0751)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			TCCAAACTTTCTTTAACTTCT	0.363																																					p.K547N		.											KIF3A,colon,carcinoma,0,1	KIF3A	0	1	Substitution - Missense(1)	large_intestine(1)	c.G1641T						.						166.0	165.0	165.0					5																	132038286		2203	4300	6503	SO:0001583	missense	11127	exon12			AACTTTCTTTAAC	AF041853	CCDS34235.1, CCDS75295.1, CCDS75296.1	5q31	2012-08-01			ENSG00000131437	ENSG00000131437		"""Kinesins"""	6319	protein-coding gene	gene with protein product	"""kinesin family protein 3A"""	604683				1054846	Standard	XM_005271868		Approved	FLA10, KLP-20	uc003kxo.3	Q9Y496	OTTHUMG00000059725	ENST00000378746.4:c.1641G>T	5.37:g.132038286C>A	ENSP00000368020:p.Lys547Asn	Somatic	57	0		WXS	Illumina HiSeq	.	53	3	NM_007054	A8MSW9|Q59EN1|Q86XE9|Q9Y6V4	Missense_Mutation	SNP	ENST00000378746.4	37	CCDS34235.1	.	.	.	.	.	.	.	.	.	.	C	19.25	3.791892	0.70452	.	.	ENSG00000131437	ENST00000378746;ENST00000378735;ENST00000541316;ENST00000450441;ENST00000403231	T;T;T;T	0.10099	2.91;3.65;2.93;2.91	5.7	2.98	0.34508	.	0.000000	0.85682	D	0.000000	T	0.29491	0.0735	M	0.79011	2.435	0.58432	D	0.999999	D;D;D;D	0.58268	0.981;0.981;0.982;0.981	D;D;P;D	0.67231	0.95;0.95;0.637;0.95	T	0.00807	-1.1558	10	0.46703	T	0.11	.	10.9563	0.47360	0.0:0.7986:0.0:0.2014	.	574;574;547;573	E9PES4;B4DHG8;Q9Y496;Q2UVF2	.;.;KIF3A_HUMAN;.	N	547;550;574;75;574	ENSP00000368020:K547N;ENSP00000368009:K550N;ENSP00000405619:K75N;ENSP00000385808:K574N	ENSP00000368009:K550N	K	-	3	2	KIF3A	132066185	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	2.728000	0.47319	0.351000	0.24027	0.655000	0.94253	AAG	.		0.363	KIF3A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000132788.3	NM_007054	
EDEM2	55741	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	20	33722569	33722569	+	Missense_Mutation	SNP	A	A	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr20:33722569A>G	ENST00000374492.3	-	6	779	c.674T>C	c.(673-675)cTc>cCc	p.L225P	EDEM2_ENST00000374491.3_Missense_Mutation_p.L188P|EDEM2_ENST00000541621.1_5'UTR|EDEM2_ENST00000542871.1_Intron|EDEM2_ENST00000540582.1_Missense_Mutation_p.L184P	NM_018217.2	NP_060687.2	Q9BV94	EDEM2_HUMAN	ER degradation enhancer, mannosidase alpha-like 2	225					cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)|response to unfolded protein (GO:0006986)	endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(10)|prostate(1)|stomach(1)|upper_aerodigestive_tract(2)	22			BRCA - Breast invasive adenocarcinoma(18;0.00936)			GCTCTCCCAGAGGCGCATCAA	0.577																																					p.L225P	Esophageal Squamous(51;906 1021 24535 36410 39145)	.											.	.	.	0			c.T674C						.						80.0	73.0	75.0					20																	33722569		2203	4300	6503	SO:0001583	missense	55741	exon6			TCCCAGAGGCGCA	AK001645	CCDS13247.1, CCDS46592.1	20q11.22	2006-03-31	2006-03-31	2006-03-31	ENSG00000088298	ENSG00000088298			15877	protein-coding gene	gene with protein product		610302	"""chromosome 20 open reading frame 31"""	C20orf49, C20orf31		15537790, 15579471	Standard	NM_018217		Approved	FLJ10783, bA4204.1	uc002xbo.2	Q9BV94	OTTHUMG00000032322	ENST00000374492.3:c.674T>C	20.37:g.33722569A>G	ENSP00000363616:p.Leu225Pro	Somatic	28	0		WXS	Illumina HiSeq	.	28	12	NM_018217	B4DTG9|Q6GU33|Q6IA89|Q6UWZ4|Q9H4U0|Q9H886|Q9NTL9|Q9NVE6	Missense_Mutation	SNP	ENST00000374492.3	37	CCDS13247.1	.	.	.	.	.	.	.	.	.	.	A	28.6	4.933915	0.92458	.	.	ENSG00000088298	ENST00000374491;ENST00000374492;ENST00000540582	T;T;T	0.57752	0.38;0.38;0.38	5.87	5.87	0.94306	.	0.000000	0.85682	D	0.000000	D	0.82747	0.5104	H	0.97516	4.02	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.996;0.998;0.999	D	0.88914	0.3361	10	0.87932	D	0	-20.9402	16.5764	0.84681	1.0:0.0:0.0:0.0	.	184;188;225	F5GZ44;Q9BV94-2;Q9BV94	.;.;EDEM2_HUMAN	P	188;225;184	ENSP00000363615:L188P;ENSP00000363616:L225P;ENSP00000441548:L184P	ENSP00000363615:L188P	L	-	2	0	EDEM2	33186230	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.056000	0.93881	2.371000	0.80710	0.533000	0.62120	CTC	.		0.577	EDEM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078842.2	NM_018217	
LEO1	123169	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	15	52242142	52242142	+	Missense_Mutation	SNP	C	C	T	rs367614131		TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr15:52242142C>T	ENST00000299601.5	-	10	1721	c.1661G>A	c.(1660-1662)cGc>cAc	p.R554H	LEO1_ENST00000315141.5_Missense_Mutation_p.R494H	NM_138792.2	NP_620147.1	Q8WVC0	LEO1_HUMAN	Leo1, Paf1/RNA polymerase II complex component, homolog (S. cerevisiae)	554					endodermal cell fate commitment (GO:0001711)|histone H2B ubiquitination (GO:0033523)|histone monoubiquitination (GO:0010390)|mRNA polyadenylation (GO:0006378)|negative regulation of myeloid cell differentiation (GO:0045638)|positive regulation of mRNA 3'-end processing (GO:0031442)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	Cdc73/Paf1 complex (GO:0016593)				endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(5)|skin(1)	14				all cancers(107;0.00264)		TCTCATTCGGCGCTGCTGAGA	0.498																																					p.R554H	Esophageal Squamous(40;229 896 18505 32465 43844)|Ovarian(53;886 1123 14462 18432 23189)	.											.	.	.	0			c.G1661A						.	C	HIS/ARG	0,4390		0,0,2195	73.0	66.0	68.0		1661	5.7	1.0	15		68	1,8585		0,1,4292	no	missense	LEO1	NM_138792.2	29	0,1,6487	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	554/667	52242142	1,12975	2195	4293	6488	SO:0001583	missense	123169	exon10			ATTCGGCGCTGCT	AY302186	CCDS10146.1, CCDS66767.1	15q21.2	2008-02-05			ENSG00000166477	ENSG00000166477			30401	protein-coding gene	gene with protein product		610507				15632063	Standard	NM_001286430		Approved		uc002abo.3	Q8WVC0	OTTHUMG00000131843	ENST00000299601.5:c.1661G>A	15.37:g.52242142C>T	ENSP00000299601:p.Arg554His	Somatic	47	0		WXS	Illumina HiSeq	.	34	18	NM_138792	Q96N99	Missense_Mutation	SNP	ENST00000299601.5	37	CCDS10146.1	.	.	.	.	.	.	.	.	.	.	.	35	5.551873	0.96501	0.0	1.16E-4	ENSG00000166477	ENST00000299601;ENST00000538386;ENST00000315141	.	.	.	5.71	5.71	0.89125	.	0.097400	0.64402	D	0.000003	T	0.79540	0.4463	M	0.73430	2.235	0.80722	D	1	P;D	0.89917	0.782;1.0	B;D	0.67231	0.336;0.95	T	0.79862	-0.1624	9	0.56958	D	0.05	.	19.8505	0.96738	0.0:1.0:0.0:0.0	.	494;554	Q8WVC0-2;Q8WVC0	.;LEO1_HUMAN	H	554;532;494	.	ENSP00000299601:R554H	R	-	2	0	LEO1	50029434	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.703000	0.84585	2.688000	0.91661	0.655000	0.94253	CGC	.		0.498	LEO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254791.2	NM_138792	
COL5A1	1289	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	9	137650127	137650127	+	Silent	SNP	C	C	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr9:137650127C>T	ENST00000371817.3	+	18	2334	c.1920C>T	c.(1918-1920)ggC>ggT	p.G640G		NM_000093.3|NM_001278074.1	NP_000084.3|NP_001265003.1	P20908	CO5A1_HUMAN	collagen, type V, alpha 1	640	Triple-helical region.				axon guidance (GO:0007411)|blood vessel development (GO:0001568)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|collagen biosynthetic process (GO:0032964)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular fibril organization (GO:0043206)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|eye morphogenesis (GO:0048592)|heart morphogenesis (GO:0003007)|integrin biosynthetic process (GO:0045112)|negative regulation of endodermal cell differentiation (GO:1903225)|regulation of cellular component organization (GO:0051128)|skin development (GO:0043588)|tendon development (GO:0035989)|wound healing, spreading of epidermal cells (GO:0035313)	basement membrane (GO:0005604)|collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)|proteoglycan binding (GO:0043394)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(26)|liver(2)|lung(36)|ovary(4)|pancreas(4)|prostate(5)|skin(10)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	115		Myeloproliferative disorder(178;0.0341)		all cancers(34;2.28e-08)|OV - Ovarian serous cystadenocarcinoma(145;6.03e-08)|Epithelial(140;6.4e-08)|GBM - Glioblastoma multiforme(294;0.131)		GGTTGCCAGGCGAGAAGGGCC	0.627																																					p.G640G		.											.	.	.	0			c.C1920T						.						108.0	97.0	101.0					9																	137650127		2203	4300	6503	SO:0001819	synonymous_variant	1289	exon18			GCCAGGCGAGAAG	D90279	CCDS6982.1, CCDS75932.1	9q34.2-q34.3	2014-09-17			ENSG00000130635	ENSG00000130635		"""Collagens"""	2209	protein-coding gene	gene with protein product	"""alpha 1 type V collagen"""	120215				1572660	Standard	NM_001278074		Approved		uc031tfl.1	P20908	OTTHUMG00000020891	ENST00000371817.3:c.1920C>T	9.37:g.137650127C>T		Somatic	23	0		WXS	Illumina HiSeq	.	17	11	NM_000093	Q15094|Q5SUX4	Silent	SNP	ENST00000371817.3	37	CCDS6982.1																																																																																			.		0.627	COL5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054954.2	NM_000093	
BRWD1	54014	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	21	40665822	40665822	+	Missense_Mutation	SNP	T	T	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr21:40665822T>C	ENST00000333229.2	-	8	1073	c.746A>G	c.(745-747)gAt>gGt	p.D249G	BRWD1_ENST00000380800.3_Missense_Mutation_p.D249G|BRWD1_ENST00000342449.3_Missense_Mutation_p.D249G	NM_018963.4	NP_061836.2	Q9NSI6	BRWD1_HUMAN	bromodomain and WD repeat domain containing 1	249					cytoskeleton organization (GO:0007010)|regulation of cell shape (GO:0008360)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				cervix(2)|endometrium(6)|kidney(8)|large_intestine(14)|liver(2)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(7)|urinary_tract(2)	58		Prostate(19;8.44e-08)|all_epithelial(19;0.223)				AATAATTTTATCACAGCTCCC	0.408																																					p.D249G	Melanoma(170;988 1986 4794 16843 39731)	.											.	.	.	0			c.A746G						.						115.0	107.0	110.0					21																	40665822		2203	4300	6503	SO:0001583	missense	54014	exon8			ATTTTATCACAGC	AJ002572	CCDS13662.1, CCDS13663.1, CCDS33557.1	21q22.2	2013-05-21	2005-05-13	2005-05-13	ENSG00000185658	ENSG00000185658		"""WD repeat domain containing"""	12760	protein-coding gene	gene with protein product			"""chromosome 21 open reading frame 107"", ""WD repeat domain 9"""	C21orf107, WDR9			Standard	NM_033656		Approved	FLJ11315, N143	uc002yxk.2	Q9NSI6	OTTHUMG00000066030	ENST00000333229.2:c.746A>G	21.37:g.40665822T>C	ENSP00000330753:p.Asp249Gly	Somatic	71	0		WXS	Illumina HiSeq	.	18	16	NM_018963	C9JK25|O43721|Q5R2V0|Q5R2V1|Q6P2D1|Q8TCV3|Q96QG9|Q96QH0|Q9NUK1	Missense_Mutation	SNP	ENST00000333229.2	37	CCDS13662.1	.	.	.	.	.	.	.	.	.	.	T	25.6	4.658017	0.88154	.	.	ENSG00000185658	ENST00000333229;ENST00000342449;ENST00000380800	D;D;D	0.89270	-2.49;-2.49;-2.49	5.03	5.03	0.67393	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.076280	0.53938	D	0.000044	D	0.95268	0.8465	M	0.90814	3.15	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.994	D	0.96189	0.9136	10	0.87932	D	0	-13.5988	14.7747	0.69724	0.0:0.0:0.0:1.0	.	249;249	Q9NSI6-2;Q9NSI6	.;BRWD1_HUMAN	G	249	ENSP00000330753:D249G;ENSP00000344333:D249G;ENSP00000370178:D249G	ENSP00000330753:D249G	D	-	2	0	BRWD1	39587692	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.903000	0.87398	1.890000	0.54733	0.533000	0.62120	GAT	.		0.408	BRWD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141398.3	NM_033656	
ITIH1	3697	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	3	52812387	52812387	+	Missense_Mutation	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr3:52812387A>C	ENST00000273283.2	+	3	194	c.170A>C	c.(169-171)aAa>aCa	p.K57T	ITIH1_ENST00000542827.1_Missense_Mutation_p.K57T|ITIH1_ENST00000537050.1_5'Flank|ITIH1_ENST00000540715.1_5'Flank	NM_002215.3	NP_002206.2	P19827	ITIH1_HUMAN	inter-alpha-trypsin inhibitor heavy chain 1	57	VIT. {ECO:0000255|PROSITE- ProRule:PRU00801}.				hyaluronan metabolic process (GO:0030212)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|serine-type endopeptidase inhibitor activity (GO:0004867)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(16)|lung(18)|ovary(4)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	52				BRCA - Breast invasive adenocarcinoma(193;7.04e-05)|Kidney(197;0.000659)|KIRC - Kidney renal clear cell carcinoma(197;0.000795)|OV - Ovarian serous cystadenocarcinoma(275;0.0498)		CGGAGTTTGAAAGTCAACTGC	0.547																																					p.K57T		.											.	.	.	0			c.A170C						.						145.0	137.0	140.0					3																	52812387		2203	4300	6503	SO:0001583	missense	3697	exon3			GTTTGAAAGTCAA		CCDS2864.1, CCDS54595.1	3p21.1	2011-10-26	2011-10-26		ENSG00000055957	ENSG00000055957			6166	protein-coding gene	gene with protein product		147270	"""inter-alpha (globulin) inhibitor, H1 polypeptide"""			1385302, 10100603	Standard	NM_002215		Approved	H1P, IATIH, ITIH	uc003dfs.3	P19827	OTTHUMG00000150312	ENST00000273283.2:c.170A>C	3.37:g.52812387A>C	ENSP00000273283:p.Lys57Thr	Somatic	49	0		WXS	Illumina HiSeq	.	16	9	NM_002215	A8K9N5|B2RAH9|B7Z558|B7Z8C0|F5H165|F5H7Y8|P78455|Q01746|Q562G1	Missense_Mutation	SNP	ENST00000273283.2	37	CCDS2864.1	.	.	.	.	.	.	.	.	.	.	A	21.3	4.122318	0.77436	.	.	ENSG00000055957	ENST00000542827;ENST00000273283	T;T	0.23754	1.89;1.89	5.65	4.49	0.54785	Vault protein inter-alpha-trypsin (2);Vault protein inter-alpha-trypsin, metazoa (1);	0.276820	0.39834	N	0.001258	T	0.33556	0.0867	L	0.48218	1.51	0.80722	D	1	D	0.54601	0.967	P	0.54706	0.759	T	0.02975	-1.1087	10	0.39692	T	0.17	-18.3131	10.2147	0.43162	0.9257:0.0:0.0743:0.0	.	57	P19827	ITIH1_HUMAN	T	57	ENSP00000442584:K57T;ENSP00000273283:K57T	ENSP00000273283:K57T	K	+	2	0	ITIH1	52787427	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.270000	0.51600	1.149000	0.42402	0.533000	0.62120	AAA	.		0.547	ITIH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317522.1	NM_002215	
TSPAN12	23554	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	7	120496757	120496757	+	Missense_Mutation	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr7:120496757A>C	ENST00000222747.3	-	2	668	c.61T>G	c.(61-63)Ttt>Gtt	p.F21V	TSPAN12_ENST00000415871.1_Missense_Mutation_p.F21V	NM_012338.3	NP_036470.1	O95859	TSN12_HUMAN	tetraspanin 12	21					angiogenesis (GO:0001525)|cell surface receptor signaling pathway (GO:0007166)|regulation of angiogenesis (GO:0045765)|retina layer formation (GO:0010842)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)				endometrium(3)|kidney(1)|lung(4)|ovary(1)|skin(1)	10	all_neural(327;0.117)					CTTACCCAAAAGAGCAGATTG	0.537																																					p.F21V		.											.	.	.	0			c.T61G						.						104.0	89.0	94.0					7																	120496757		2203	4300	6503	SO:0001583	missense	23554	exon2			CCCAAAAGAGCAG	AF124522	CCDS5777.1	7q31.31	2013-02-14	2005-03-21	2005-03-21	ENSG00000106025	ENSG00000106025		"""Tetraspanins"""	21641	protein-coding gene	gene with protein product		613138	"""transmembrane 4 superfamily member 12"""	TM4SF12			Standard	NM_012338		Approved	NET-2	uc003vjk.3	O95859	OTTHUMG00000156980	ENST00000222747.3:c.61T>G	7.37:g.120496757A>C	ENSP00000222747:p.Phe21Val	Somatic	63	0		WXS	Illumina HiSeq	.	52	18	NM_012338	A4D0V8|B4DRG6|Q549U9|Q8N5Y0	Missense_Mutation	SNP	ENST00000222747.3	37	CCDS5777.1	.	.	.	.	.	.	.	.	.	.	A	22.7	4.325459	0.81580	.	.	ENSG00000106025	ENST00000222747;ENST00000415871;ENST00000441017;ENST00000433758;ENST00000424710;ENST00000430985	T;T;T;T;T;T	0.80824	-1.42;-1.42;-1.42;-1.42;-1.42;-1.42	4.95	4.95	0.65309	.	0.000000	0.85682	D	0.000000	D	0.89283	0.6671	M	0.84156	2.68	0.80722	D	1	D	0.67145	0.996	D	0.66084	0.941	D	0.91037	0.4868	10	0.87932	D	0	-9.3101	14.307	0.66391	1.0:0.0:0.0:0.0	.	21	O95859	TSN12_HUMAN	V	21	ENSP00000222747:F21V;ENSP00000397699:F21V;ENSP00000411158:F21V;ENSP00000399059:F21V;ENSP00000404942:F21V;ENSP00000388819:F21V	ENSP00000222747:F21V	F	-	1	0	TSPAN12	120283993	1.000000	0.71417	0.958000	0.39756	0.914000	0.54420	6.251000	0.72441	1.865000	0.54081	0.533000	0.62120	TTT	.		0.537	TSPAN12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346951.1	NM_012338	
PJA2	9867	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	5	108714025	108714025	+	Missense_Mutation	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr5:108714025T>G	ENST00000361189.2	-	4	1402	c.1163A>C	c.(1162-1164)gAa>gCa	p.E388A	PJA2_ENST00000511624.1_5'Flank|PJA2_ENST00000361557.3_Missense_Mutation_p.E388A	NM_014819.4	NP_055634.3	O43164	PJA2_HUMAN	praja ring finger 2, E3 ubiquitin protein ligase	388					long-term memory (GO:0007616)|protein ubiquitination (GO:0016567)|regulation of protein kinase A signaling (GO:0010738)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	ligase activity (GO:0016874)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(2)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	21		all_cancers(142;4.4e-06)|all_epithelial(76;8.17e-08)|Prostate(80;0.00676)|Lung NSC(167;0.0436)|Ovarian(225;0.0443)|all_lung(232;0.053)|Colorectal(57;0.0946)|Breast(839;0.151)		OV - Ovarian serous cystadenocarcinoma(64;3.46e-10)|Epithelial(69;6.02e-09)|COAD - Colon adenocarcinoma(37;0.224)		ATTTTCTGTTTCCCTTTGTGT	0.408																																					p.E388A		.											.	.	.	0			c.A1163C						.						205.0	191.0	195.0					5																	108714025		2202	4300	6502	SO:0001583	missense	9867	exon4			TCTGTTTCCCTTT	AB007898	CCDS4099.1	5q22.1	2013-01-09	2012-02-23	2003-06-05	ENSG00000198961	ENSG00000198961		"""RING-type (C3HC4) zinc fingers"""	17481	protein-coding gene	gene with protein product			"""ring finger protein 131"", ""praja ring finger 2"""	RNF131			Standard	NM_014819		Approved	KIAA0438, Neurodap1	uc003kos.4	O43164	OTTHUMG00000128750	ENST00000361189.2:c.1163A>C	5.37:g.108714025T>G	ENSP00000354775:p.Glu388Ala	Somatic	80	0		WXS	Illumina HiSeq	.	76	20	NM_014819	A8K6U4|D3DSZ5|Q68D49|Q8N1G5	Missense_Mutation	SNP	ENST00000361189.2	37	CCDS4099.1	.	.	.	.	.	.	.	.	.	.	T	8.713	0.912580	0.17907	.	.	ENSG00000198961	ENST00000361189;ENST00000361557	T;T	0.05580	3.42;3.42	5.43	5.43	0.79202	.	0.427911	0.23688	N	0.045550	T	0.09423	0.0232	L	0.55481	1.735	0.09310	N	1	B	0.25850	0.136	B	0.30029	0.11	T	0.13575	-1.0504	10	0.59425	D	0.04	-11.7591	11.7435	0.51807	0.0:0.0:0.1471:0.8529	.	388	O43164	PJA2_HUMAN	A	388	ENSP00000354775:E388A;ENSP00000355284:E388A	ENSP00000354775:E388A	E	-	2	0	PJA2	108741924	0.956000	0.32656	0.178000	0.23040	0.404000	0.30871	5.370000	0.66144	2.197000	0.70478	0.533000	0.62120	GAA	.		0.408	PJA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250663.1	NM_014819	
ZFC3H1	196441	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	12	72057114	72057114	+	Missense_Mutation	SNP	A	A	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr12:72057114A>G	ENST00000378743.3	-	1	635	c.277T>C	c.(277-279)Tct>Cct	p.S93P	ZFC3H1_ENST00000552037.1_Missense_Mutation_p.S93P|THAP2_ENST00000547843.1_5'Flank|THAP2_ENST00000308086.2_5'UTR|ZFC3H1_ENST00000548100.1_Missense_Mutation_p.S93P|ZFC3H1_ENST00000549407.1_5'UTR	NM_144982.4	NP_659419.3	O60293	ZC3H1_HUMAN	zinc finger, C3H1-type containing	93	Ser-rich.				RNA processing (GO:0006396)	extracellular space (GO:0005615)|intracellular (GO:0005622)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(12)|lung(31)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	69						CCCCGCTCAGACGCGTGCCGC	0.647											OREG0021993	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.S93P		.											.	.	.	0			c.T277C						.						62.0	69.0	67.0					12																	72057114		1956	4137	6093	SO:0001583	missense	196441	exon1			GCTCAGACGCGTG	AB011118	CCDS41813.1	12q21.1	2013-01-25	2008-10-01	2008-10-01		ENSG00000133858		"""Zinc finger, C3H1-type containing"""	28328	protein-coding gene	gene with protein product			"""proline/serine-rich coiled-coil 2"", ""coiled-coil domain containing 131"""	PSRC2, CCDC131		9628581	Standard	NM_144982		Approved	MGC23401, KIAA0546	uc001swo.2	O60293	OTTHUMG00000169545	ENST00000378743.3:c.277T>C	12.37:g.72057114A>G	ENSP00000368017:p.Ser93Pro	Somatic	95	0	1134	WXS	Illumina HiSeq	.	49	19	NM_144982	Q6GMU1|Q6P2S9|Q6ZV36|Q96BE7	Missense_Mutation	SNP	ENST00000378743.3	37	CCDS41813.1	.	.	.	.	.	.	.	.	.	.	A	11.73	1.724467	0.30593	.	.	ENSG00000133858	ENST00000378743;ENST00000548100;ENST00000552037	T	0.33216	1.42	4.33	1.82	0.25136	.	0.417097	0.19575	N	0.111011	T	0.14056	0.0340	N	0.14661	0.345	0.80722	D	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.08055	0.003;0.001;0.0	T	0.10291	-1.0636	10	0.23891	T	0.37	.	4.37	0.11242	0.4709:0.402:0.1271:0.0	.	93;93;93	G3V1X1;O60293-4;O60293	.;.;ZC3H1_HUMAN	P	93	ENSP00000368017:S93P	ENSP00000368017:S93P	S	-	1	0	ZFC3H1	70343381	0.988000	0.35896	0.938000	0.37757	0.987000	0.75469	1.478000	0.35442	0.254000	0.21573	0.454000	0.30748	TCT	.		0.647	ZFC3H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404751.1	NM_144982	
ZFP2	80108	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	5	178359047	178359047	+	Missense_Mutation	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr5:178359047A>C	ENST00000361362.2	+	5	1263	c.733A>C	c.(733-735)Aat>Cat	p.N245H	ZFP2_ENST00000520301.1_Missense_Mutation_p.N245H|ZFP2_ENST00000523286.1_Missense_Mutation_p.N245H|ZFP2_ENST00000503510.2_Missense_Mutation_p.N245H	NM_030613.2	NP_085116.2	Q6ZN57	ZFP2_HUMAN	ZFP2 zinc finger protein	245					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(2)|kidney(1)|large_intestine(7)|liver(1)|lung(2)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|stomach(1)	20	all_cancers(89;0.000639)|all_epithelial(37;0.000109)|Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)	all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.00655)|GBM - Glioblastoma multiforme(465;0.0302)|OV - Ovarian serous cystadenocarcinoma(192;0.0615)|Epithelial(171;0.111)		CTATGAATGTAATGAATGTGG	0.378																																					p.N245H		.											.	.	.	0			c.A733C						.						60.0	63.0	62.0					5																	178359047		2203	4300	6503	SO:0001583	missense	80108	exon5			GAATGTAATGAAT	AK025281	CCDS4440.1	5q35.3	2013-01-08	2012-11-27		ENSG00000198939	ENSG00000198939		"""Zinc fingers, C2H2-type"""	26138	protein-coding gene	gene with protein product			"""zinc finger protein 2 homolog (mouse)"""				Standard	NM_030613		Approved	FLJ21628, ZNF751	uc003mjn.1	Q6ZN57	OTTHUMG00000130885	ENST00000361362.2:c.733A>C	5.37:g.178359047A>C	ENSP00000354453:p.Asn245His	Somatic	68	0		WXS	Illumina HiSeq	.	69	41	NM_030613	A5PLN5|B7ZM23|Q9H6Z6	Missense_Mutation	SNP	ENST00000361362.2	37	CCDS4440.1	.	.	.	.	.	.	.	.	.	.	a	13.79	2.342512	0.41498	.	.	ENSG00000198939	ENST00000361362;ENST00000520301;ENST00000523286;ENST00000503510	T;T;T;T	0.03860	3.78;3.78;3.78;3.78	4.85	3.62	0.41486	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.34460	N	0.003951	T	0.03915	0.0110	N	0.25201	0.72	0.09310	N	1	B	0.25667	0.131	B	0.22152	0.038	T	0.35450	-0.9788	10	0.62326	D	0.03	-9.2371	10.007	0.41964	0.831:0.169:0.0:0.0	.	245	Q6ZN57	ZFP2_HUMAN	H	245	ENSP00000354453:N245H;ENSP00000430980:N245H;ENSP00000430531:N245H;ENSP00000438114:N245H	ENSP00000354453:N245H	N	+	1	0	ZFP2	178291653	0.000000	0.05858	0.527000	0.27925	0.876000	0.50452	-1.259000	0.02861	2.023000	0.59567	0.477000	0.44152	AAT	.		0.378	ZFP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253470.2	NM_030613	
OVCH1	341350	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	12	29639246	29639246	+	Missense_Mutation	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr12:29639246A>C	ENST00000318184.5	-	8	927	c.928T>G	c.(928-930)Tca>Gca	p.S310A	OVCH1-AS1_ENST00000551108.1_Intron|OVCH1-AS1_ENST00000549411.1_Intron	NM_183378.2	NP_899234.2	Q7RTY7	OVCH1_HUMAN	ovochymase 1	310	CUB 1. {ECO:0000255|PROSITE- ProRule:PRU00059}.					extracellular region (GO:0005576)	metal ion binding (GO:0046872)|serine-type endopeptidase activity (GO:0004252)			NS(2)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(15)|lung(43)|ovary(5)|pancreas(3)|prostate(2)|skin(1)|soft_tissue(1)|stomach(3)	92	Lung NSC(12;1.84e-09)|Acute lymphoblastic leukemia(23;0.00885)|all_hematologic(23;0.0155)					ATATACCTTGAGCCCACTTTT	0.408																																					p.S310A		.											.	.	.	0			c.T928G						.						87.0	83.0	84.0					12																	29639246		1827	4089	5916	SO:0001583	missense	341350	exon8			ACCTTGAGCCCAC	BN000128		12p11.23	2012-11-08			ENSG00000187950	ENSG00000187950			23080	protein-coding gene	gene with protein product						12838346	Standard	NM_183378		Approved	OVCH	uc001rix.1	Q7RTY7	OTTHUMG00000167741	ENST00000318184.5:c.928T>G	12.37:g.29639246A>C	ENSP00000326708:p.Ser310Ala	Somatic	215	0		WXS	Illumina HiSeq	.	133	58	NM_183378		Missense_Mutation	SNP	ENST00000318184.5	37		.	.	.	.	.	.	.	.	.	.	a	0.013	-1.620826	0.00820	.	.	ENSG00000187950	ENST00000318184	D	0.86097	-2.07	1.94	-1.1	0.09872	.	.	.	.	.	T	0.62913	0.2467	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.47209	-0.9135	9	0.17369	T	0.5	.	2.2077	0.03940	0.3232:0.0:0.4319:0.2449	.	310	Q7RTY7	OVCH1_HUMAN	A	310	ENSP00000326708:S310A	ENSP00000326708:S310A	S	-	1	0	OVCH1	29530513	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.065000	0.11617	-0.361000	0.08125	-2.513000	0.00187	TCA	.		0.408	OVCH1-001	KNOWN	non_canonical_TEC|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000395997.2	NM_183378	
RABL6	55684	hgsc.bcm.edu;broad.mit.edu	37	9	139734973	139734973	+	Nonstop_Mutation	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr9:139734973A>C	ENST00000311502.7	+	15	2425	c.2189A>C	c.(2188-2190)tAg>tCg	p.*730S	RABL6_ENST00000371663.4_Nonstop_Mutation_p.*731S|RABL6_ENST00000371675.3_Nonstop_Mutation_p.*615S|RABL6_ENST00000357466.2_Silent_p.L372L			Q3YEC7	RABL6_HUMAN	RAB, member RAS oncogene family-like 6	0					small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	GTP binding (GO:0005525)										GAGGAGCTCTAGGCCGGCGTG	0.741																																					p.X731S		.											.	.	.	0			c.A2192C						.						2.0	2.0	2.0					9																	139734973		1294	2807	4101	SO:0001578	stop_lost	55684	exon15			AGCTCTAGGCCGG	AK094382	CCDS48058.1, CCDS55352.1, CCDS55353.1	9q34.3	2012-06-28	2012-06-28	2012-06-28	ENSG00000196642	ENSG00000196642			24703	protein-coding gene	gene with protein product	"""Rab-like protein 1"", ""partner of ARF"""	610615	"""chromosome 9 open reading frame 86"""	C9orf86		14702039, 16582619, 17962191, 19433581	Standard	NM_024718		Approved	FLJ10101, FLJ13045, pp8875, bA216L13.9, Parf, RBEL1	uc004cjj.1	Q3YEC7	OTTHUMG00000020947	ENST00000311502.7:c.2189A>C	9.37:g.139734973A>C	ENSP00000311134:p.*730Serext*97	Somatic	9	0		WXS	Illumina HiSeq	.	11	5	NM_001173988	A8QVZ7|A8QVZ8|C6K8I4|C6K8I5|Q4F968|Q5T5R7|Q8IWK1|Q8TCL4|Q8WU94|Q96SR8|Q9BU21|Q9H935	Missense_Mutation	SNP	ENST00000311502.7	37	CCDS48058.1	.	.	.	.	.	.	.	.	.	.	.	7.438	0.640158	0.14386	.	.	ENSG00000196642	ENST00000371663;ENST00000311502;ENST00000371675	.	.	.	2.9	2.9	0.33743	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	9.2214	0.37379	1.0:0.0:0.0:0.0	.	.	.	.	S	731;730;615	.	.	X	+	2	0	C9orf86	138854794	0.398000	0.25279	0.981000	0.43875	0.134000	0.20937	3.963000	0.56773	1.320000	0.45209	0.379000	0.24179	TAG	.		0.741	RABL6-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000055141.4	NM_024718	
TDO2	6999	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	4	156831267	156831267	+	Silent	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr4:156831267T>G	ENST00000536354.2	+	6	586	c.522T>G	c.(520-522)ccT>ccG	p.P174P		NM_005651.3	NP_005642.1			tryptophan 2,3-dioxygenase											breast(3)|endometrium(1)|large_intestine(4)|lung(7)|prostate(1)|skin(1)|urinary_tract(1)	18	all_hematologic(180;0.24)	Renal(120;0.0854)		KIRC - Kidney renal clear cell carcinoma(143;0.0455)|Kidney(143;0.0568)|COAD - Colon adenocarcinoma(41;0.141)		TGAGAGTCCCTTATAACAGAA	0.378																																					p.P174P	Colon(57;928 1036 2595 6946 26094)	.											.	.	.	0			c.T522G						.						95.0	100.0	98.0					4																	156831267		2203	4300	6503	SO:0001819	synonymous_variant	6999	exon6			AGTCCCTTATAAC		CCDS34086.1	4q31-q32	2008-02-05				ENSG00000151790	1.13.11.11		11708	protein-coding gene	gene with protein product		191070					Standard	NM_005651		Approved	TDO, TPH2	uc003ipf.2	P48775		ENST00000536354.2:c.522T>G	4.37:g.156831267T>G		Somatic	105	0		WXS	Illumina HiSeq	.	30	24	NM_005651		Silent	SNP	ENST00000536354.2	37	CCDS34086.1																																																																																			.		0.378	TDO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366209.3	NM_005651	
SNX5	27131	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	20	17928287	17928287	+	Missense_Mutation	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr20:17928287A>C	ENST00000377768.3	-	12	1233	c.921T>G	c.(919-921)gaT>gaG	p.D307E	SNX5_ENST00000377759.4_Missense_Mutation_p.D307E|SNX5_ENST00000483485.1_5'UTR	NM_152227.1	NP_689413.1	Q9Y5X3	SNX5_HUMAN	sorting nexin 5	307	BAR.				intracellular protein transport (GO:0006886)|pinocytosis (GO:0006907)	cytoplasmic vesicle (GO:0031410)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|extrinsic component of endosome membrane (GO:0031313)|macropinocytic cup (GO:0070685)	phosphatidylinositol binding (GO:0035091)			endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|prostate(1)	11						TGTATAAGAGATCCTGGGAAA	0.413																																					p.D307E		.											.	.	.	0			c.T921G						.						60.0	56.0	57.0					20																	17928287		2203	4299	6502	SO:0001583	missense	27131	exon11			TAAGAGATCCTGG	AF121855	CCDS13130.1	20p11	2008-05-22			ENSG00000089006	ENSG00000089006		"""Sorting nexins"""	14969	protein-coding gene	gene with protein product		605937				10600472, 17148574	Standard	NM_152227		Approved		uc002wqc.3	Q9Y5X3	OTTHUMG00000031953	ENST00000377768.3:c.921T>G	20.37:g.17928287A>C	ENSP00000366998:p.Asp307Glu	Somatic	99	0		WXS	Illumina HiSeq	.	40	20	NM_014426	B7ZKN3|D3DW26|Q52LC4|Q7KZN0|Q9BWP0	Missense_Mutation	SNP	ENST00000377768.3	37	CCDS13130.1	.	.	.	.	.	.	.	.	.	.	A	16.12	3.033418	0.54896	.	.	ENSG00000089006	ENST00000377768;ENST00000377759	T;T	0.55760	0.5;0.5	5.31	1.75	0.24633	Vps5 C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.46560	0.1399	M	0.64170	1.965	0.80722	D	1	P;P	0.41597	0.756;0.565	B;P	0.44647	0.401;0.456	T	0.45264	-0.9273	10	0.07175	T	0.84	-9.5112	8.5888	0.33674	0.6794:0.0:0.3206:0.0	.	328;307	B7Z476;Q9Y5X3	.;SNX5_HUMAN	E	307	ENSP00000366998:D307E;ENSP00000366988:D307E	ENSP00000366988:D307E	D	-	3	2	SNX5	17876287	1.000000	0.71417	1.000000	0.80357	0.934000	0.57294	2.375000	0.44283	0.400000	0.25396	0.528000	0.53228	GAT	.		0.413	SNX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078137.4		
ADAM30	11085	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	120436670	120436670	+	Missense_Mutation	SNP	C	C	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr1:120436670C>A	ENST00000369400.1	-	1	2448	c.2290G>T	c.(2290-2292)Gca>Tca	p.A764S		NM_021794.3	NP_068566.2	Q9UKF2	ADA30_HUMAN	ADAM metallopeptidase domain 30	764	5 X 9 AA approximate repeats.				binding of sperm to zona pellucida (GO:0007339)|multicellular organism reproduction (GO:0032504)|single fertilization (GO:0007338)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(11)|lung(16)|ovary(2)|skin(2)	38	all_cancers(5;7.07e-10)|all_epithelial(5;1.62e-10)|all_neural(166;0.153)|Breast(55;0.234)	all_lung(203;1.55e-06)|Lung NSC(69;1.04e-05)|all_epithelial(167;0.00138)		Lung(183;0.0204)|LUSC - Lung squamous cell carcinoma(189;0.117)		CCAGTTTTTGCTTTAGATTCT	0.363																																					p.A764S		.											.	.	.	0			c.G2290T						.						302.0	314.0	310.0					1																	120436670		2203	4300	6503	SO:0001583	missense	11085	exon1			TTTTTGCTTTAGA	AF171932	CCDS907.1	1p12	2012-05-16	2005-08-18		ENSG00000134249	ENSG00000134249		"""ADAM metallopeptidase domain containing"""	208	protein-coding gene	gene with protein product		604779	"""a disintegrin and metalloproteinase domain 30"""				Standard	NM_021794		Approved	svph4	uc001eij.3	Q9UKF2	OTTHUMG00000012176	ENST00000369400.1:c.2290G>T	1.37:g.120436670C>A	ENSP00000358407:p.Ala764Ser	Somatic	165	0		WXS	Illumina HiSeq	.	103	55	NM_021794	A8K8W8|Q5T3X6|Q9UKF1	Missense_Mutation	SNP	ENST00000369400.1	37	CCDS907.1	.	.	.	.	.	.	.	.	.	.	C	5.633	0.301485	0.10678	.	.	ENSG00000134249	ENST00000369400	T	0.01159	5.25	1.74	-2.25	0.06888	.	.	.	.	.	T	0.00300	0.0009	N	0.19112	0.55	0.09310	N	1	B	0.20887	0.049	B	0.10450	0.005	T	0.40478	-0.9561	9	0.48119	T	0.1	.	3.3825	0.07260	0.3725:0.4566:0.0:0.1709	.	764	Q9UKF2	ADA30_HUMAN	S	764	ENSP00000358407:A764S	ENSP00000358407:A764S	A	-	1	0	ADAM30	120238193	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.871000	0.04223	-0.236000	0.09753	0.655000	0.94253	GCA	.		0.363	ADAM30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033678.1	NM_021794	
ITPR3	3710	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	6	33631568	33631568	+	Missense_Mutation	SNP	C	C	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr6:33631568C>G	ENST00000374316.5	+	12	2119	c.1059C>G	c.(1057-1059)tgC>tgG	p.C353W	ITPR3_ENST00000605930.1_Missense_Mutation_p.C353W			Q14573	ITPR3_HUMAN	inositol 1,4,5-trisphosphate receptor, type 3	353	MIR 4. {ECO:0000255|PROSITE- ProRule:PRU00131}.				activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|calcium ion transport into cytosol (GO:0060402)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|long-term synaptic potentiation (GO:0060291)|memory (GO:0007613)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|regulation of insulin secretion (GO:0050796)|response to calcium ion (GO:0051592)|sensory perception of bitter taste (GO:0050913)|sensory perception of sweet taste (GO:0050916)|sensory perception of umami taste (GO:0050917)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	apical part of cell (GO:0045177)|brush border (GO:0005903)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|myelin sheath (GO:0043209)|neuronal cell body (GO:0043025)|nuclear outer membrane (GO:0005640)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|platelet dense tubular network membrane (GO:0031095)|receptor complex (GO:0043235)	inositol 1,3,4,5 tetrakisphosphate binding (GO:0043533)|inositol 1,4,5 trisphosphate binding (GO:0070679)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|inositol hexakisphosphate binding (GO:0000822)|intracellular ligand-gated calcium channel activity (GO:0005218)|phosphatidylinositol binding (GO:0035091)			NS(1)|breast(6)|central_nervous_system(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|liver(1)|lung(24)|ovary(8)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	85					Caffeine(DB00201)	TCAAGTACTGCCTGGTGGCTG	0.597																																					p.C353W		.											ITPR3_ENST00000374316,NS,carcinoma,0,2	ITPR3_ENST00000374316	0	0			c.C1059G						.						71.0	68.0	69.0					6																	33631568		2203	4300	6503	SO:0001583	missense	3710	exon11			GTACTGCCTGGTG	D26351	CCDS4783.1	6p21.31	2011-11-24	2011-04-28		ENSG00000096433	ENSG00000096433		"""Ion channels / Inositol triphosphate receptors"""	6182	protein-coding gene	gene with protein product		147267	"""inositol 1,4,5-triphosphate receptor, type 3"""			8081734, 8288584	Standard	NM_002224		Approved	IP3R3	uc021ywr.1	Q14573	OTTHUMG00000014532	ENST00000374316.5:c.1059C>G	6.37:g.33631568C>G	ENSP00000363435:p.Cys353Trp	Somatic	63	0		WXS	Illumina HiSeq	.	43	9	NM_002224	Q14649|Q5TAQ2	Missense_Mutation	SNP	ENST00000374316.5	37	CCDS4783.1	.	.	.	.	.	.	.	.	.	.	C	12.06	1.823667	0.32237	.	.	ENSG00000096433	ENST00000374316	D	0.86956	-2.19	4.63	2.63	0.31362	MIR motif (2);MIR (2);	0.122450	0.56097	D	0.000033	T	0.62563	0.2438	L	0.34521	1.04	0.32237	N	0.573176	B	0.16603	0.018	B	0.15484	0.013	T	0.52328	-0.8590	10	0.38643	T	0.18	-16.4408	3.8073	0.08782	0.2176:0.5469:0.139:0.0966	.	353	Q14573	ITPR3_HUMAN	W	353	ENSP00000363435:C353W	ENSP00000363435:C353W	C	+	3	2	ITPR3	33739546	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	2.604000	0.46274	1.131000	0.42111	0.491000	0.48974	TGC	.		0.597	ITPR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040204.2	NM_002224	
UTRN	7402	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	6	144744760	144744760	+	Missense_Mutation	SNP	A	A	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr6:144744760A>T	ENST00000367545.3	+	4	310	c.310A>T	c.(310-312)Aat>Tat	p.N104Y		NM_007124.2	NP_009055.2	P46939	UTRO_HUMAN	utrophin	104	Actin-binding.|CH 1. {ECO:0000255|PROSITE- ProRule:PRU00044}.				aging (GO:0007568)|muscle cell differentiation (GO:0042692)|muscle contraction (GO:0006936)|muscle organ development (GO:0007517)|neuron projection morphogenesis (GO:0048812)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of sodium ion transmembrane transporter activity (GO:2000649)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dystrophin-associated glycoprotein complex (GO:0016010)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane (GO:0016020)|membrane raft (GO:0045121)|myofibril (GO:0030016)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|protein kinase binding (GO:0019901)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(1)|cervix(2)|endometrium(21)|kidney(10)|large_intestine(29)|lung(56)|ovary(5)|pancreas(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	148		Ovarian(120;0.218)		OV - Ovarian serous cystadenocarcinoma(155;5.72e-07)|GBM - Glioblastoma multiforme(68;4.9e-05)|Colorectal(48;0.213)		ACATCAGAACAATGTAAGTGT	0.418																																					p.N104Y		.											.	.	.	0			c.A310T						.						182.0	162.0	169.0					6																	144744760		2203	4300	6503	SO:0001583	missense	7402	exon4			CAGAACAATGTAA	AK023675	CCDS34547.1	6q24	2008-02-05	2006-12-13		ENSG00000152818	ENSG00000152818			12635	protein-coding gene	gene with protein product		128240	"""utrophin (homologous to dystrophin)"""	DMDL		1426262	Standard	NM_007124		Approved	DRP, DRP1	uc003qkt.3	P46939	OTTHUMG00000015746	ENST00000367545.3:c.310A>T	6.37:g.144744760A>T	ENSP00000356515:p.Asn104Tyr	Somatic	40	0		WXS	Illumina HiSeq	.	21	15	NM_007124	Q5SYY1|Q5SZ57|Q9UJ40	Missense_Mutation	SNP	ENST00000367545.3	37	CCDS34547.1	.	.	.	.	.	.	.	.	.	.	A	19.57	3.852217	0.71719	.	.	ENSG00000152818	ENST00000367529;ENST00000367545;ENST00000421035	D;D	0.95447	-3.71;-3.71	5.61	5.61	0.85477	Calponin homology domain (5);	0.000000	0.53938	D	0.000055	D	0.97498	0.9181	M	0.88450	2.955	0.80722	D	1	D	0.67145	0.996	P	0.62885	0.908	D	0.98104	1.0416	10	0.66056	D	0.02	.	15.8165	0.78604	1.0:0.0:0.0:0.0	.	104	P46939	UTRO_HUMAN	Y	104;104;109	ENSP00000356515:N104Y;ENSP00000396276:N109Y	ENSP00000356499:N104Y	N	+	1	0	UTRN	144786453	1.000000	0.71417	0.999000	0.59377	0.893000	0.52053	6.487000	0.73633	2.143000	0.66587	0.455000	0.32223	AAT	.		0.418	UTRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042551.1		
MCEE	84693	hgsc.bcm.edu;broad.mit.edu	37	2	71351654	71351654	+	Missense_Mutation	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr2:71351654T>G	ENST00000244217.5	-	2	77	c.60A>C	c.(58-60)caA>caC	p.Q20H	AC007881.1_ENST00000578636.1_RNA	NM_032601.3	NP_115990.3	Q96PE7	MCEE_HUMAN	methylmalonyl CoA epimerase	20					cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|L-methylmalonyl-CoA metabolic process (GO:0046491)|short-chain fatty acid catabolic process (GO:0019626)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)	metal ion binding (GO:0046872)|methylmalonyl-CoA epimerase activity (GO:0004493)			kidney(1)|large_intestine(2)|lung(3)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	9						GAATGGGAGCTTGAAGTCTGG	0.398																																					p.Q20H		.											.	.	.	0			c.A60C						.						73.0	80.0	78.0					2																	71351654		2203	4300	6503	SO:0001583	missense	84693	exon2			GGGAGCTTGAAGT	AF364547	CCDS1915.1	2p13.3	2011-05-12			ENSG00000124370	ENSG00000124370	5.1.99.1		16732	protein-coding gene	gene with protein product	"""glyoxalase domain containing 2"""	608419				16697227, 16752391, 16843692	Standard	NM_032601		Approved	GLOD2	uc002shs.2	Q96PE7	OTTHUMG00000129709	ENST00000244217.5:c.60A>C	2.37:g.71351654T>G	ENSP00000244217:p.Gln20His	Somatic	14	0		WXS	Illumina HiSeq	.	7	4	NM_032601	Q53TP1|Q8WW63	Missense_Mutation	SNP	ENST00000244217.5	37	CCDS1915.1	.	.	.	.	.	.	.	.	.	.	T	9.416	1.081659	0.20309	.	.	ENSG00000124370	ENST00000244217	T	0.64991	-0.13	5.33	-9.86	0.00473	.	0.645442	0.16801	N	0.198985	T	0.31295	0.0792	L	0.28192	0.835	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.21177	-1.0253	10	0.14656	T	0.56	-6.2894	3.445	0.07477	0.1882:0.4648:0.0956:0.2514	.	20	Q96PE7	MCEE_HUMAN	H	20	ENSP00000244217:Q20H	ENSP00000244217:Q20H	Q	-	3	2	MCEE	71205162	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-0.615000	0.05597	-2.191000	0.00756	-1.134000	0.01955	CAA	.		0.398	MCEE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251917.3	NM_032601	
NOD2	64127	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	16	50733483	50733483	+	Missense_Mutation	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr16:50733483T>G	ENST00000300589.2	+	2	263	c.158T>G	c.(157-159)tTc>tGc	p.F53C	NOD2_ENST00000526417.2_3'UTR	NM_022162.1	NP_071445.1	Q9HC29	NOD2_HUMAN	nucleotide-binding oligomerization domain containing 2	53	CARD 1. {ECO:0000255|PROSITE- ProRule:PRU00046}.				activation of MAPK activity (GO:0000187)|activation of MAPK activity involved in innate immune response (GO:0035419)|cellular response to muramyl dipeptide (GO:0071225)|cellular response to peptidoglycan (GO:0071224)|cytokine production involved in immune response (GO:0002367)|defense response (GO:0006952)|defense response to bacterium (GO:0042742)|defense response to Gram-positive bacterium (GO:0050830)|detection of bacterium (GO:0016045)|detection of biotic stimulus (GO:0009595)|detection of muramyl dipeptide (GO:0032498)|immunoglobulin production involved in immunoglobulin mediated immune response (GO:0002381)|innate immune response (GO:0045087)|innate immune response in mucosa (GO:0002227)|intracellular signal transduction (GO:0035556)|JNK cascade (GO:0007254)|macrophage inflammatory protein-1 alpha production (GO:0071608)|maintenance of gastrointestinal epithelium (GO:0030277)|microglial cell activation involved in immune response (GO:0002282)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of inflammatory response to antigenic stimulus (GO:0002862)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of interleukin-18 production (GO:0032701)|negative regulation of interleukin-2 production (GO:0032703)|negative regulation of macrophage apoptotic process (GO:2000110)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of T cell mediated immunity (GO:0002710)|negative regulation of toll-like receptor 2 signaling pathway (GO:0034136)|negative regulation of tumor necrosis factor production (GO:0032720)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing 2 signaling pathway (GO:0070431)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of B cell activation (GO:0050871)|positive regulation of biosynthetic process of antibacterial peptides active against Gram-positive bacteria (GO:0006965)|positive regulation of dendritic cell antigen processing and presentation (GO:0002606)|positive regulation of dendritic cell cytokine production (GO:0002732)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of gamma-delta T cell activation (GO:0046645)|positive regulation of humoral immune response mediated by circulating immunoglobulin (GO:0002925)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-1 beta production (GO:0032731)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-17 production (GO:0032740)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of JNK cascade (GO:0046330)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of oxidoreductase activity (GO:0051353)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phagocytosis (GO:0050766)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of prostaglandin-E synthase activity (GO:2000363)|positive regulation of prostaglandin-endoperoxide synthase activity (GO:0060585)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of stress-activated MAPK cascade (GO:0032874)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of type 2 immune response (GO:0002830)|protein oligomerization (GO:0051259)|regulation of inflammatory response (GO:0050727)|regulation of neutrophil chemotaxis (GO:0090022)|response to exogenous dsRNA (GO:0043330)|response to lipopolysaccharide (GO:0032496)|response to muramyl dipeptide (GO:0032495)|response to nutrient (GO:0007584)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|vesicle (GO:0031982)	ATP binding (GO:0005524)|CARD domain binding (GO:0050700)|enzyme binding (GO:0019899)|muramyl dipeptide binding (GO:0032500)|peptidoglycan binding (GO:0042834)|protein kinase binding (GO:0019901)			cervix(1)|endometrium(5)|kidney(3)|large_intestine(7)|lung(30)|ovary(3)|skin(3)	52		all_cancers(37;0.0156)				CTGGAAGGCTTCGAGAGTGTC	0.622																																					p.F53C		.											.	.	.	0			c.T158G						.						83.0	88.0	86.0					16																	50733483		2198	4300	6498	SO:0001583	missense	64127	exon2			AAGGCTTCGAGAG	AF178930	CCDS10746.1	16q12	2014-09-17	2006-12-08	2006-12-08	ENSG00000167207	ENSG00000167207		"""Nucleotide-binding domain and leucine rich repeat containing"""	5331	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 2"", ""NOD-like receptor C2"", ""NLR family, CARD domain containing 2"""	605956	"""caspase recruitment domain family, member 15"""	IBD1, CARD15		7809109, 8587604	Standard	XM_005256084		Approved	BLAU, CD, PSORAS1, CLR16.3, NLRC2	uc002egm.1	Q9HC29	OTTHUMG00000133171	ENST00000300589.2:c.158T>G	16.37:g.50733483T>G	ENSP00000300589:p.Phe53Cys	Somatic	131	0		WXS	Illumina HiSeq	.	63	28	NM_022162	E2JEQ6|Q96RH5|Q96RH6|Q96RH8	Missense_Mutation	SNP	ENST00000300589.2	37	CCDS10746.1	.	.	.	.	.	.	.	.	.	.	T	20.4	3.983703	0.74474	.	.	ENSG00000167207	ENST00000526417;ENST00000531674;ENST00000300589	T;T	0.15718	2.4;2.4	5.34	5.34	0.76211	DEATH-like (2);Caspase Recruitment (3);	0.000000	0.56097	D	0.000039	T	0.34803	0.0910	L	0.50333	1.59	0.39879	D	0.973611	D	0.89917	1.0	D	0.91635	0.999	T	0.13710	-1.0499	10	0.87932	D	0	.	11.7152	0.51647	0.0:0.0:0.0:1.0	.	53	Q9HC29	NOD2_HUMAN	C	26;26;53	ENSP00000431681:F26C;ENSP00000300589:F53C	ENSP00000300589:F53C	F	+	2	0	NOD2	49290984	0.992000	0.36948	0.972000	0.41901	0.958000	0.62258	4.145000	0.58065	2.035000	0.60131	0.533000	0.62120	TTC	.		0.622	NOD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256876.2	NM_022162	
APOB	338	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	2	21235170	21235170	+	Missense_Mutation	SNP	A	A	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr2:21235170A>G	ENST00000233242.1	-	26	4697	c.4570T>C	c.(4570-4572)Tcc>Ccc	p.S1524P		NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	1524					artery morphogenesis (GO:0048844)|blood coagulation (GO:0007596)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to tumor necrosis factor (GO:0071356)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle remodeling (GO:0034374)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol biosynthetic process (GO:0045540)|response to carbohydrate (GO:0009743)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to virus (GO:0009615)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|triglyceride catabolic process (GO:0019433)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	actin cytoskeleton (GO:0015629)|chylomicron (GO:0042627)|chylomicron remnant (GO:0034360)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome lumen (GO:0031904)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate-density lipoprotein particle (GO:0034363)|intracellular membrane-bounded organelle (GO:0043231)|low-density lipoprotein particle (GO:0034362)|mature chylomicron (GO:0034359)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|lipase binding (GO:0035473)|low-density lipoprotein particle receptor binding (GO:0050750)|phospholipid binding (GO:0005543)			NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					AGGTAGGAGGAGTTAAACCTC	0.488																																					p.S1524P		.											.	.	.	0			c.T4570C						.						126.0	126.0	126.0					2																	21235170		2203	4300	6503	SO:0001583	missense	338	exon26			AGGAGGAGTTAAA	M14162	CCDS1703.1	2p24-p23	2013-05-29	2013-05-29		ENSG00000084674	ENSG00000084674		"""Apolipoproteins"""	603	protein-coding gene	gene with protein product		107730	"""apolipoprotein B (including Ag(x) antigen)"""				Standard	NM_000384		Approved		uc002red.3	P04114	OTTHUMG00000090785	ENST00000233242.1:c.4570T>C	2.37:g.21235170A>G	ENSP00000233242:p.Ser1524Pro	Somatic	63	0		WXS	Illumina HiSeq	.	39	18	NM_000384	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Missense_Mutation	SNP	ENST00000233242.1	37	CCDS1703.1	.	.	.	.	.	.	.	.	.	.	A	21.0	4.079031	0.76528	.	.	ENSG00000084674	ENST00000233242;ENST00000535079	T	0.01252	5.1	5.88	5.88	0.94601	.	0.000000	0.56097	D	0.000022	T	0.07007	0.0178	L	0.59436	1.845	0.80722	D	1	D	0.89917	1.0	D	0.73380	0.98	T	0.16778	-1.0391	10	0.51188	T	0.08	.	16.3009	0.82811	1.0:0.0:0.0:0.0	.	1524	P04114	APOB_HUMAN	P	1524	ENSP00000233242:S1524P	ENSP00000233242:S1524P	S	-	1	0	APOB	21088675	1.000000	0.71417	1.000000	0.80357	0.926000	0.56050	5.542000	0.67218	2.246000	0.74042	0.533000	0.62120	TCC	.		0.488	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1		
GPR98	84059	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	5	90079728	90079728	+	Missense_Mutation	SNP	A	A	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr5:90079728A>G	ENST00000405460.2	+	67	13603	c.13507A>G	c.(13507-13509)Agc>Ggc	p.S4503G	GPR98_ENST00000425867.2_Missense_Mutation_p.S164G	NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	4503					detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|G-protein coupled receptor signaling pathway (GO:0007186)|inner ear receptor stereocilium organization (GO:0060122)|maintenance of organ identity (GO:0048496)|nervous system development (GO:0007399)|neurological system process (GO:0050877)|neuropeptide signaling pathway (GO:0007218)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|stereocilia ankle link complex (GO:0002142)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(4)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(18)|large_intestine(46)|liver(2)|lung(80)|ovary(12)|pancreas(5)|prostate(1)|skin(50)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(6)	269		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		CCACCTAGTGAGCAGAATCAT	0.428																																					p.S4503G		.											GPR98,NS,carcinoma,0,2	GPR98	0	0			c.A13507G						.						60.0	58.0	59.0					5																	90079728		1838	4082	5920	SO:0001583	missense	84059	exon67			CTAGTGAGCAGAA	AB014586	CCDS47246.1	5q13	2014-08-08	2006-05-26	2006-05-26	ENSG00000164199	ENSG00000164199		"""-"", ""GPCR / Class B : Orphans"""	17416	protein-coding gene	gene with protein product		602851	"""monogenic, audiogenic seizure susceptibility 1 homolog (mouse)"""	USH2C, MASS1		10976914, 14740321	Standard	NM_032119		Approved	DKFZp761P0710, KIAA0686, FEB4, VLGR1b	uc003kju.3	Q8WXG9	OTTHUMG00000162668	ENST00000405460.2:c.13507A>G	5.37:g.90079728A>G	ENSP00000384582:p.Ser4503Gly	Somatic	92	0		WXS	Illumina HiSeq	.	66	58	NM_032119	O75171|Q8TF58|Q9H0X5|Q9UL61	Missense_Mutation	SNP	ENST00000405460.2	37	CCDS47246.1	.	.	.	.	.	.	.	.	.	.	A	14.18	2.457100	0.43634	.	.	ENSG00000164199	ENST00000405460;ENST00000296619;ENST00000425867	T;T	0.26518	1.73;1.73	5.97	4.79	0.61399	.	0.177930	0.64402	D	0.000011	T	0.30198	0.0757	M	0.70595	2.14	0.27864	N	0.940298	P;B;P	0.39480	0.546;0.156;0.675	B;B;B	0.39379	0.202;0.054;0.298	T	0.26744	-1.0094	10	0.62326	D	0.03	.	10.3547	0.43956	0.7168:0.0:0.0:0.2832	.	164;4503;164	E7EML1;Q8WXG9;Q8WXG9-2	.;GPR98_HUMAN;.	G	4503;4503;164	ENSP00000384582:S4503G;ENSP00000392618:S164G	ENSP00000296619:S4503G	S	+	1	0	GPR98	90115484	1.000000	0.71417	1.000000	0.80357	0.902000	0.53008	2.854000	0.48325	1.028000	0.39785	0.533000	0.62120	AGC	.		0.428	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119	
OR4N2	390429	hgsc.bcm.edu;bcgsc.ca	37	14	20295956	20295956	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr14:20295956G>T	ENST00000315947.1	+	1	349	c.349G>T	c.(349-351)Gtg>Ttg	p.V117L	OR4N2_ENST00000568211.1_Missense_Mutation_p.V117L	NM_001004723.1	NP_001004723.1	Q8NGD1	OR4N2_HUMAN	olfactory receptor, family 4, subfamily N, member 2	117						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|liver(1)|lung(32)|ovary(2)|prostate(1)|skin(2)|stomach(2)	52	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)		ACTCCTTGTTGTGATGGCCTT	0.512																																					p.V117L		.											.	.	.	0			c.G349T						.						133.0	143.0	140.0					14																	20295956		2203	4298	6501	SO:0001583	missense	390429	exon1			CTTGTTGTGATGG		CCDS32022.1	14q11.2	2013-09-23				ENSG00000176294		"""GPCR / Class A : Olfactory receptors"""	14742	protein-coding gene	gene with protein product							Standard	NM_001004723		Approved		uc010tkv.2	Q8NGD1		ENST00000315947.1:c.349G>T	14.37:g.20295956G>T	ENSP00000319601:p.Val117Leu	Somatic	175	0		WXS	Illumina HiSeq	.	126	29	NM_001004723	Q6IEY9|Q6IFA2	Missense_Mutation	SNP	ENST00000315947.1	37	CCDS32022.1	.	.	.	.	.	.	.	.	.	.	.	16.71	3.199348	0.58126	.	.	ENSG00000176294	ENST00000557677;ENST00000315947	T;T	0.05139	3.49;3.49	4.53	1.57	0.23409	GPCR, rhodopsin-like superfamily (1);	0.000000	0.44688	D	0.000424	T	0.07324	0.0185	L	0.35487	1.065	0.09310	N	1	D	0.61080	0.989	P	0.51701	0.677	T	0.24225	-1.0166	10	0.41790	T	0.15	-14.2389	5.4387	0.16496	0.17:0.0:0.6693:0.1606	.	117	Q8NGD1	OR4N2_HUMAN	L	117	ENSP00000452022:V117L;ENSP00000319601:V117L	ENSP00000319601:V117L	V	+	1	0	OR4N2	19365796	0.024000	0.19004	0.586000	0.28679	0.973000	0.67179	1.989000	0.40707	0.214000	0.20742	0.591000	0.81541	GTG	.		0.512	OR4N2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409821.2		
RECK	8434	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	9	36091179	36091179	+	Silent	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr9:36091179T>G	ENST00000377966.3	+	10	1490	c.924T>G	c.(922-924)ctT>ctG	p.L308L		NM_021111.2	NP_066934.1	O95980	RECK_HUMAN	reversion-inducing-cysteine-rich protein with kazal motifs	308	5 X Knot repeats.				blood vessel maturation (GO:0001955)|embryo implantation (GO:0007566)|extracellular matrix organization (GO:0030198)|negative regulation of endopeptidase activity (GO:0010951)	anchored component of membrane (GO:0031225)|membrane (GO:0016020)|plasma membrane (GO:0005886)	endopeptidase inhibitor activity (GO:0004866)|metalloendopeptidase inhibitor activity (GO:0008191)|serine-type endopeptidase inhibitor activity (GO:0004867)			cervix(1)|endometrium(7)|kidney(3)|large_intestine(6)|lung(10)|ovary(1)|pancreas(1)|skin(2)|stomach(1)	32			LUSC - Lung squamous cell carcinoma(32;0.112)|STAD - Stomach adenocarcinoma(86;0.228)			GCACTAAACTTTACAGCATGA	0.408																																					p.L308L		.											.	.	.	0			c.T924G						.						125.0	115.0	119.0					9																	36091179		2203	4300	6503	SO:0001819	synonymous_variant	8434	exon10			TAAACTTTACAGC	E13833	CCDS6597.1	9p13.3	2008-05-15			ENSG00000122707	ENSG00000122707			11345	protein-coding gene	gene with protein product		605227		ST15		9789069	Standard	NM_021111		Approved	hRECK	uc003zyv.3	O95980	OTTHUMG00000019898	ENST00000377966.3:c.924T>G	9.37:g.36091179T>G		Somatic	62	0		WXS	Illumina HiSeq	.	54	28	NM_021111	B2RNS1|Q5W0K6|Q8WX37	Silent	SNP	ENST00000377966.3	37	CCDS6597.1																																																																																			.		0.408	RECK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052409.1		
SRCAP	10847	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	16	30734428	30734428	+	Missense_Mutation	SNP	C	C	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr16:30734428C>T	ENST00000262518.4	+	24	4422	c.4037C>T	c.(4036-4038)cCc>cTc	p.P1346L	SRCAP_ENST00000344771.4_Missense_Mutation_p.P1188L|SRCAP_ENST00000395059.2_Missense_Mutation_p.P1284L	NM_006662.2	NP_006653.2	Q6ZRS2	SRCAP_HUMAN	Snf2-related CREBBP activator protein	1346	Pro-rich.				histone acetylation (GO:0016573)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|histone acetyltransferase activity (GO:0004402)|transcription coactivator activity (GO:0003713)			NS(1)|breast(3)|cervix(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(22)|liver(3)|lung(62)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(5)	136			Colorectal(24;0.198)			AATCCACGCCCCACGTTAACC	0.637																																					p.P1346L		.											.	.	.	0			c.C4037T						.						83.0	83.0	83.0					16																	30734428		2197	4300	6497	SO:0001583	missense	10847	exon24			CACGCCCCACGTT	AB002307	CCDS10689.2	16p11.2	2009-08-06			ENSG00000080603	ENSG00000080603			16974	protein-coding gene	gene with protein product	"""Swi2/Snf2-related ATPase homolog (S. cerevisiae)"", ""domino homolog 1 (Drosophila)"""	611421				10347196, 9205841	Standard	NM_006662		Approved	KIAA0309, EAF1, SWR1, DOMO1	uc002dze.1	Q6ZRS2	OTTHUMG00000132393	ENST00000262518.4:c.4037C>T	16.37:g.30734428C>T	ENSP00000262518:p.Pro1346Leu	Somatic	78	0		WXS	Illumina HiSeq	.	46	22	NM_006662	B0JZA6|O15026|Q7Z744|Q9Y5L9	Missense_Mutation	SNP	ENST00000262518.4	37	CCDS10689.2	.	.	.	.	.	.	.	.	.	.	C	13.03	2.114683	0.37339	.	.	ENSG00000080603	ENST00000262518;ENST00000395059;ENST00000344771	D;D;D	0.91180	-2.61;-2.8;-2.74	5.83	5.83	0.93111	.	0.000000	0.56097	D	0.000035	D	0.83083	0.5177	N	0.14661	0.345	0.42852	D	0.994081	B;B;B	0.33637	0.2;0.42;0.296	B;B;B	0.28465	0.051;0.09;0.041	D	0.84084	0.0386	10	0.72032	D	0.01	-12.9346	17.0352	0.86473	0.0:1.0:0.0:0.0	.	1188;1284;1346	Q6ZRS2-3;Q6ZRS2-2;Q6ZRS2	.;.;SRCAP_HUMAN	L	1346;1284;1188	ENSP00000262518:P1346L;ENSP00000378499:P1284L;ENSP00000343042:P1188L	ENSP00000262518:P1346L	P	+	2	0	SRCAP	30641929	0.009000	0.17119	1.000000	0.80357	0.998000	0.95712	1.165000	0.31822	2.769000	0.95229	0.655000	0.94253	CCC	.		0.637	SRCAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255523.1	NM_006662	
TBX3	6926	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	12	115114210	115114210	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr12:115114210G>T	ENST00000257566.3	-	6	1396	c.1007C>A	c.(1006-1008)tCt>tAt	p.S336Y	TBX3_ENST00000349155.2_Missense_Mutation_p.S316Y	NM_016569.3	NP_057653.3	O15119	TBX3_HUMAN	T-box 3	336					anterior/posterior axis specification, embryo (GO:0008595)|atrioventricular bundle cell differentiation (GO:0003167)|blood vessel development (GO:0001568)|branching involved in mammary gland duct morphogenesis (GO:0060444)|cardiac muscle cell fate commitment (GO:0060923)|cell aging (GO:0007569)|cellular senescence (GO:0090398)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|female genitalia development (GO:0030540)|follicle-stimulating hormone secretion (GO:0046884)|forelimb morphogenesis (GO:0035136)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|limbic system development (GO:0021761)|luteinizing hormone secretion (GO:0032275)|male genitalia development (GO:0030539)|mammary gland development (GO:0030879)|mammary placode formation (GO:0060596)|mesoderm morphogenesis (GO:0048332)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epithelial cell differentiation (GO:0030857)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|organ morphogenesis (GO:0009887)|outflow tract morphogenesis (GO:0003151)|palate development (GO:0060021)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell proliferation (GO:0008284)|positive regulation of stem cell proliferation (GO:2000648)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|sinoatrial node cell development (GO:0060931)|skeletal system development (GO:0001501)|specification of organ position (GO:0010159)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)|ventricular septum morphogenesis (GO:0060412)	nucleus (GO:0005634)	RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(5)|endometrium(1)|kidney(1)|large_intestine(6)|lung(21)|ovary(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	47	Medulloblastoma(191;0.163)|all_neural(191;0.178)			BRCA - Breast invasive adenocarcinoma(302;0.0574)		GGACTCATCAGAGGTCCCATT	0.512																																					p.S336Y		.											.	.	.	0			c.C1007A						.						163.0	148.0	153.0					12																	115114210		2203	4300	6503	SO:0001583	missense	6926	exon6			TCATCAGAGGTCC	BC025258	CCDS9175.1, CCDS9176.1	12q24.21	2013-09-05	2008-07-31		ENSG00000135111	ENSG00000135111		"""T-boxes"""	11602	protein-coding gene	gene with protein product		601621	"""ulnar mammary syndrome"""	UMS		8988164	Standard	NM_005996		Approved	TBX3-ISO, XHL	uc001tvt.1	O15119	OTTHUMG00000169586	ENST00000257566.3:c.1007C>A	12.37:g.115114210G>T	ENSP00000257566:p.Ser336Tyr	Somatic	52	0		WXS	Illumina HiSeq	.	30	13	NM_016569	Q8TB20|Q9UKF8	Missense_Mutation	SNP	ENST00000257566.3	37	CCDS9176.1	.	.	.	.	.	.	.	.	.	.	G	20.5	4.007725	0.75046	.	.	ENSG00000135111	ENST00000349155;ENST00000257566;ENST00000361100	D;D	0.89617	-2.53;-2.54	4.99	4.99	0.66335	Transcription factor, T-box, region of unknown function (1);	0.309700	0.32134	N	0.006537	D	0.93284	0.7860	L	0.59436	1.845	0.80722	D	1	D;D	0.69078	0.981;0.997	D;D	0.83275	0.947;0.996	D	0.94065	0.7330	10	0.87932	D	0	.	17.2495	0.87038	0.0:0.0:1.0:0.0	.	316;336	O15119-2;O15119	.;TBX3_HUMAN	Y	316;336;336	ENSP00000257567:S316Y;ENSP00000257566:S336Y	ENSP00000257566:S336Y	S	-	2	0	TBX3	113598593	1.000000	0.71417	0.904000	0.35570	0.354000	0.29330	9.127000	0.94417	2.297000	0.77311	0.655000	0.94253	TCT	.		0.512	TBX3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000404947.2	NM_016569, NM_005996	
DNAI1	27019	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	9	34500833	34500833	+	Missense_Mutation	SNP	T	T	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr9:34500833T>C	ENST00000242317.4	+	11	1186	c.1015T>C	c.(1015-1017)Tgc>Cgc	p.C339R		NM_001281428.1|NM_012144.2	NP_001268357.1|NP_036276.1	Q9UI46	DNAI1_HUMAN	dynein, axonemal, intermediate chain 1	339					cell projection organization (GO:0030030)|epithelial cilium movement (GO:0003351)|metabolic process (GO:0008152)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dynein complex (GO:0030286)|microtubule (GO:0005874)	motor activity (GO:0003774)			autonomic_ganglia(1)|endometrium(7)|kidney(1)|large_intestine(8)|lung(13)|prostate(1)|skin(2)|urinary_tract(1)	34	all_epithelial(49;0.244)		LUSC - Lung squamous cell carcinoma(29;0.0107)|STAD - Stomach adenocarcinoma(86;0.212)	GBM - Glioblastoma multiforme(74;0.0222)		CACTGCCCTCTGCTGGTAAGT	0.552									Kartagener syndrome		OREG0019152	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.C339R		.											.	.	.	0			c.T1015C						.						58.0	58.0	58.0					9																	34500833		2203	4300	6503	SO:0001583	missense	27019	exon11	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	GCCCTCTGCTGGT	AF091619	CCDS6557.1, CCDS75829.1	9p13.3	2013-02-19	2006-09-04		ENSG00000122735	ENSG00000122735		"""Axonemal dyneins"", ""WD repeat domain containing"""	2954	protein-coding gene	gene with protein product		604366	"""dynein, axonemal, intermediate polypeptide 1"""			10577904, 21953912	Standard	NM_012144		Approved	DIC1, PCD, CILD1	uc003zum.3	Q9UI46	OTTHUMG00000019825	ENST00000242317.4:c.1015T>C	9.37:g.34500833T>C	ENSP00000242317:p.Cys339Arg	Somatic	48	0	848	WXS	Illumina HiSeq	.	33	10	NM_012144	B7Z7U1|Q5T8G7|Q8NHQ7|Q9UEZ8	Missense_Mutation	SNP	ENST00000242317.4	37	CCDS6557.1	.	.	.	.	.	.	.	.	.	.	T	15.30	2.793100	0.50102	.	.	ENSG00000122735	ENST00000242317	T	0.76709	-1.04	4.99	4.99	0.66335	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.233360	0.45606	D	0.000343	T	0.76644	0.4016	M	0.78049	2.395	0.80722	D	1	B	0.12630	0.006	B	0.13407	0.009	T	0.72786	-0.4188	10	0.28530	T	0.3	.	12.9332	0.58299	0.0:0.0:0.0:1.0	.	339	Q9UI46	DNAI1_HUMAN	R	339	ENSP00000242317:C339R	ENSP00000242317:C339R	C	+	1	0	DNAI1	34490833	1.000000	0.71417	1.000000	0.80357	0.860000	0.49131	7.222000	0.78025	1.999000	0.58509	0.379000	0.24179	TGC	.		0.552	DNAI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052192.1		
MRTO4	51154	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	1	19584345	19584345	+	Silent	SNP	A	A	G	rs140351482		TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr1:19584345A>G	ENST00000330263.4	+	6	657	c.360A>G	c.(358-360)acA>acG	p.T120T		NM_016183.3	NP_057267.2	Q9UKD2	MRT4_HUMAN	mRNA turnover 4 homolog (S. cerevisiae)	120					ribosome biogenesis (GO:0042254)	nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|large_intestine(1)|liver(2)|ovary(1)|pancreas(1)|stomach(1)	8		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000321)|Lung NSC(340;0.000398)|Breast(348;0.00049)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00462)|BRCA - Breast invasive adenocarcinoma(304;1.87e-05)|Kidney(64;0.000171)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|GBM - Glioblastoma multiforme(114;0.00301)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)		CGAAATACACAGAAATGGACT	0.577																																					p.T120T	GBM(192;2418 3032 7540 48714)	.											.	.	.	0			c.A360G						.						78.0	79.0	79.0					1																	19584345		2203	4300	6503	SO:0001819	synonymous_variant	51154	exon6			ATACACAGAAATG	AK027569	CCDS191.1	1p36.13	2008-02-05	2006-12-21	2007-01-05	ENSG00000053372	ENSG00000053372			18477	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 33"", ""MRT4, mRNA turnover 4, homolog (S. cerevisiae)"""	C1orf33			Standard	NM_016183		Approved	dJ657E11.4, MRT4	uc001bbs.3	Q9UKD2	OTTHUMG00000002496	ENST00000330263.4:c.360A>G	1.37:g.19584345A>G		Somatic	55	0		WXS	Illumina HiSeq	.	28	7	NM_016183	B3KNB3|Q5TG55|Q96SS6|Q9BPV9	Silent	SNP	ENST00000330263.4	37	CCDS191.1																																																																																			.		0.577	MRTO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007075.2	NM_016183	
VAMP5	10791	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	2	85820227	85820227	+	Missense_Mutation	SNP	A	A	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr2:85820227A>T	ENST00000306384.4	+	3	381	c.298A>T	c.(298-300)Agt>Tgt	p.S100C	RNF181_ENST00000306368.4_5'Flank|RNF181_ENST00000441634.1_5'Flank	NM_006634.2	NP_006625.1	O95183	VAMP5_HUMAN	vesicle-associated membrane protein 5	100					cell differentiation (GO:0030154)|Golgi to plasma membrane protein transport (GO:0043001)|muscle organ development (GO:0007517)|skeletal muscle tissue development (GO:0007519)	cell surface (GO:0009986)|cytoplasmic vesicle membrane (GO:0030659)|extracellular vesicular exosome (GO:0070062)|integral component of organelle membrane (GO:0031301)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|late endosome (GO:0005770)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)				NS(1)|large_intestine(3)|lung(1)	5						CAGTGACAGCAGTAGTGCCCC	0.597																																					p.S100C		.											.	.	.	0			c.A298T						.						230.0	180.0	197.0					2																	85820227		2203	4300	6503	SO:0001583	missense	10791	exon3			GACAGCAGTAGTG	AF054825	CCDS1980.1	2p11.2	2013-02-13	2012-10-17		ENSG00000168899	ENSG00000168899		"""Vesicle-associated membrane proteins"""	12646	protein-coding gene	gene with protein product	"""myobrevin"""	607029				9725904	Standard	NM_006634		Approved		uc002spu.1	O95183	OTTHUMG00000130169	ENST00000306384.4:c.298A>T	2.37:g.85820227A>T	ENSP00000305647:p.Ser100Cys	Somatic	36	0		WXS	Illumina HiSeq	.	19	7	NM_006634	Q9P0T2	Missense_Mutation	SNP	ENST00000306384.4	37	CCDS1980.1	.	.	.	.	.	.	.	.	.	.	A	14.93	2.683457	0.47991	.	.	ENSG00000168899	ENST00000306384	.	.	.	4.55	2.04	0.26737	.	1.005910	0.08003	N	0.989143	T	0.49966	0.1588	M	0.66939	2.045	0.09310	N	1	D	0.63046	0.992	P	0.52710	0.707	T	0.36601	-0.9741	9	0.72032	D	0.01	.	4.7446	0.13031	0.7051:0.1921:0.1028:0.0	.	100	O95183	VAMP5_HUMAN	C	100	.	ENSP00000305647:S100C	S	+	1	0	VAMP5	85673738	0.001000	0.12720	0.007000	0.13788	0.778000	0.44026	1.002000	0.29796	0.764000	0.33197	-0.313000	0.08912	AGT	.		0.597	VAMP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252484.2	NM_006634	
GPR98	84059	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	5	90079731	90079731	+	Missense_Mutation	SNP	A	A	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr5:90079731A>G	ENST00000405460.2	+	67	13606	c.13510A>G	c.(13510-13512)Aga>Gga	p.R4504G	GPR98_ENST00000425867.2_Missense_Mutation_p.R165G	NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	4504					detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|G-protein coupled receptor signaling pathway (GO:0007186)|inner ear receptor stereocilium organization (GO:0060122)|maintenance of organ identity (GO:0048496)|nervous system development (GO:0007399)|neurological system process (GO:0050877)|neuropeptide signaling pathway (GO:0007218)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|stereocilia ankle link complex (GO:0002142)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(4)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(18)|large_intestine(46)|liver(2)|lung(80)|ovary(12)|pancreas(5)|prostate(1)|skin(50)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(6)	269		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		CCTAGTGAGCAGAATCATAAT	0.428																																					p.R4504G		.											GPR98,caecum,carcinoma,0,1	GPR98	0	0			c.A13510G						.						61.0	59.0	59.0					5																	90079731		1836	4084	5920	SO:0001583	missense	84059	exon67			GTGAGCAGAATCA	AB014586	CCDS47246.1	5q13	2014-08-08	2006-05-26	2006-05-26	ENSG00000164199	ENSG00000164199		"""-"", ""GPCR / Class B : Orphans"""	17416	protein-coding gene	gene with protein product		602851	"""monogenic, audiogenic seizure susceptibility 1 homolog (mouse)"""	USH2C, MASS1		10976914, 14740321	Standard	NM_032119		Approved	DKFZp761P0710, KIAA0686, FEB4, VLGR1b	uc003kju.3	Q8WXG9	OTTHUMG00000162668	ENST00000405460.2:c.13510A>G	5.37:g.90079731A>G	ENSP00000384582:p.Arg4504Gly	Somatic	89	0		WXS	Illumina HiSeq	.	66	58	NM_032119	O75171|Q8TF58|Q9H0X5|Q9UL61	Missense_Mutation	SNP	ENST00000405460.2	37	CCDS47246.1	.	.	.	.	.	.	.	.	.	.	A	12.45	1.940715	0.34283	.	.	ENSG00000164199	ENST00000405460;ENST00000296619;ENST00000425867	T;T	0.27557	1.66;1.66	5.97	4.86	0.63082	.	0.254076	0.44483	D	0.000460	T	0.36054	0.0953	M	0.70595	2.14	0.23492	N	0.997562	P;P;P	0.52842	0.501;0.956;0.634	B;B;B	0.44224	0.157;0.444;0.3	T	0.41448	-0.9508	10	0.52906	T	0.07	.	12.1772	0.54192	0.773:0.227:0.0:0.0	.	165;4504;165	E7EML1;Q8WXG9;Q8WXG9-2	.;GPR98_HUMAN;.	G	4504;4504;165	ENSP00000384582:R4504G;ENSP00000392618:R165G	ENSP00000296619:R4504G	R	+	1	2	GPR98	90115487	1.000000	0.71417	0.984000	0.44739	0.632000	0.37999	2.852000	0.48310	2.275000	0.75901	0.533000	0.62120	AGA	.		0.428	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119	
UBR3	130507	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	2	170734063	170734063	+	Missense_Mutation	SNP	A	A	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr2:170734063A>G	ENST00000272793.5	+	4	954	c.904A>G	c.(904-906)Agc>Ggc	p.S302G	UBR3_ENST00000418381.1_Missense_Mutation_p.S302G			Q6ZT12	UBR3_HUMAN	ubiquitin protein ligase E3 component n-recognin 3 (putative)	302					embryo development (GO:0009790)|in utero embryonic development (GO:0001701)|olfactory behavior (GO:0042048)|sensory perception of smell (GO:0007608)|suckling behavior (GO:0001967)|ubiquitin-dependent protein catabolic process (GO:0006511)	integral component of membrane (GO:0016021)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(9)|liver(1)|lung(8)|ovary(1)|prostate(3)|stomach(1)	33						AGCTTTAAAGAGCTCTGGACT	0.348																																					p.S302G		.											.	.	.	0			c.A904G						.						209.0	182.0	190.0					2																	170734063		692	1591	2283	SO:0001583	missense	130507	exon4			TTAAAGAGCTCTG	AL834144	CCDS2238.2	2q31.1	2008-06-23	2008-06-23	2007-11-29	ENSG00000144357	ENSG00000144357		"""Ubiquitin protein ligase E3 component n-recognins"""	30467	protein-coding gene	gene with protein product		613831	"""zinc finger protein 650"""	ZNF650		17462990	Standard	NM_172070		Approved	KIAA2024, DKFZp434P117, FLJ37422	uc010zdi.2	Q6ZT12	OTTHUMG00000132229	ENST00000272793.5:c.904A>G	2.37:g.170734063A>G	ENSP00000272793:p.Ser302Gly	Somatic	85	0		WXS	Illumina HiSeq	.	55	30	NM_172070	B4DZR7|Q2KHN5|Q6ZR55|Q6ZSC2|Q8IVE7|Q8ND96	Missense_Mutation	SNP	ENST00000272793.5	37		.	.	.	.	.	.	.	.	.	.	A	13.85	2.358965	0.41801	.	.	ENSG00000144357	ENST00000272793;ENST00000442603;ENST00000418381	T;T	0.53640	0.61;0.61	5.58	4.44	0.53790	.	.	.	.	.	T	0.22126	0.0533	N	0.08118	0	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.15694	-1.0428	9	0.23302	T	0.38	.	3.2536	0.06823	0.6514:0.0:0.3486:0.0	.	302	Q6ZT12	UBR3_HUMAN	G	302	ENSP00000272793:S302G;ENSP00000396068:S302G	ENSP00000272793:S302G	S	+	1	0	UBR3	170442309	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.041000	0.64196	2.119000	0.64992	0.482000	0.46254	AGC	.		0.348	UBR3-001	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000255290.2	NM_172070	
SAP30L	79685	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	5	153835544	153835544	+	Missense_Mutation	SNP	A	A	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr5:153835544A>T	ENST00000297109.6	+	4	1156	c.508A>T	c.(508-510)Agt>Tgt	p.S170C	SAP30L_ENST00000440364.2_Missense_Mutation_p.S129C|SAP30L_ENST00000426761.2_Missense_Mutation_p.S124C	NM_024632.5	NP_078908.1	Q9HAJ7	SP30L_HUMAN	SAP30-like	170					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|lung(3)	4	Renal(175;0.00488)	Medulloblastoma(196;0.0523)	Kidney(363;8.21e-05)|KIRC - Kidney renal clear cell carcinoma(527;0.000577)			GAGTAACAAGAGTAGACTGGA	0.448																																					p.S170C		.											.	.	.	0			c.A508T						.						159.0	145.0	150.0					5																	153835544		2203	4300	6503	SO:0001583	missense	79685	exon4			AACAAGAGTAGAC	AY341060	CCDS4326.1, CCDS47321.1, CCDS47322.1	5q33.2	2008-02-05			ENSG00000164576	ENSG00000164576			25663	protein-coding gene	gene with protein product		610398				14680513	Standard	NM_001131062		Approved	FLJ11526, NS4ATP2	uc003lvk.3	Q9HAJ7	OTTHUMG00000130146	ENST00000297109.6:c.508A>T	5.37:g.153835544A>T	ENSP00000297109:p.Ser170Cys	Somatic	56	0		WXS	Illumina HiSeq	.	61	14	NM_024632	E9PAU7|E9PAY2	Missense_Mutation	SNP	ENST00000297109.6	37	CCDS4326.1	.	.	.	.	.	.	.	.	.	.	A	23.7	4.443561	0.83993	.	.	ENSG00000164576	ENST00000297109;ENST00000440364;ENST00000426761	.	.	.	5.91	5.91	0.95273	.	0.000000	0.85682	D	0.000000	T	0.73682	0.3618	L	0.44542	1.39	0.80722	D	1	D;D;D	0.89917	0.999;0.999;1.0	D;D;D	0.75484	0.962;0.962;0.986	T	0.76085	-0.3088	9	0.87932	D	0	-12.3715	16.3453	0.83126	1.0:0.0:0.0:0.0	.	124;129;170	E9PAY2;E9PAU7;Q9HAJ7	.;.;SP30L_HUMAN	C	170;129;124	.	ENSP00000297109:S170C	S	+	1	0	SAP30L	153815737	1.000000	0.71417	0.998000	0.56505	0.546000	0.35178	9.125000	0.94402	2.261000	0.74972	0.533000	0.62120	AGT	.		0.448	SAP30L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252454.3	NM_024632	
ATG2A	23130	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	11	64679638	64679638	+	Missense_Mutation	SNP	G	G	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr11:64679638G>C	ENST00000377264.3	-	8	1118	c.1006C>G	c.(1006-1008)Cag>Gag	p.Q336E	ATG2A_ENST00000421419.2_Missense_Mutation_p.Q336E	NM_015104.2	NP_055919.2	Q2TAZ0	ATG2A_HUMAN	autophagy related 2A	336					autophagic vacuole assembly (GO:0000045)|cellular response to nitrogen starvation (GO:0006995)|mitochondrion degradation (GO:0000422)|nucleophagy (GO:0044804)	extrinsic component of membrane (GO:0019898)|lipid particle (GO:0005811)|pre-autophagosomal structure (GO:0000407)				breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(19)|ovary(3)|prostate(5)|skin(1)|stomach(1)|urinary_tract(3)	55						TGCAGCTGCTGGTTCAGGTCC	0.632																																					p.Q336E		.											.	.	.	0			c.C1006G						.						59.0	64.0	63.0					11																	64679638		2201	4297	6498	SO:0001583	missense	23130	exon8			GCTGCTGGTTCAG		CCDS31602.1	11q13.1	2014-02-12	2012-06-06		ENSG00000110046	ENSG00000110046			29028	protein-coding gene	gene with protein product			"""ATG2 autophagy related 2 homolog A (S. cerevisiae)"""			21887408	Standard	NM_015104		Approved	KIAA0404	uc001obx.3	Q2TAZ0	OTTHUMG00000066831	ENST00000377264.3:c.1006C>G	11.37:g.64679638G>C	ENSP00000366475:p.Gln336Glu	Somatic	56	0		WXS	Illumina HiSeq	.	29	15	NM_015104	O43154|Q14DM2|Q6ZTV2|Q7Z6K8|Q8IVY5|Q8TAI8|Q96HH7	Missense_Mutation	SNP	ENST00000377264.3	37	CCDS31602.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	16.31|16.31	3.086361|3.086361	0.55861|0.55861	.|.	.|.	ENSG00000110046|ENSG00000110046	ENST00000418259|ENST00000421419;ENST00000377264;ENST00000227459	.|T;T	.|0.06371	.|3.31;3.31	4.07|4.07	3.14|3.14	0.36123|0.36123	.|.	.|0.143795	.|0.46145	.|N	.|0.000311	T|T	0.07548|0.07548	0.0190|0.0190	L|L	0.47716|0.47716	1.5|1.5	0.33924|0.33924	D|D	0.64117|0.64117	.|P	.|0.38504	.|0.634	.|B	.|0.38880	.|0.284	T|T	0.24941|0.24941	-1.0146|-1.0146	5|10	.|0.36615	.|T	.|0.2	.|.	11.7994|11.7994	0.52118|0.52118	0.0:0.179:0.821:0.0|0.0:0.179:0.821:0.0	.|.	.|336	.|Q2TAZ0	.|ATG2A_HUMAN	R|E	137|336	.|ENSP00000410522:Q336E;ENSP00000366475:Q336E	.|ENSP00000227459:Q336E	P|Q	-|-	2|1	0|0	ATG2A|ATG2A	64436214|64436214	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.985000|0.985000	0.73830|0.73830	4.372000|4.372000	0.59530|0.59530	1.062000|1.062000	0.40625|0.40625	0.561000|0.561000	0.74099|0.74099	CCA|CAG	.		0.632	ATG2A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000143224.1	NM_015104	
STRBP	55342	hgsc.bcm.edu;ucsc.edu	37	9	125874010	125874010	+	Intron	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr9:125874010T>G	ENST00000530364.1	-	2	31				MIR600HG_ENST00000385007.1_RNA			Q96SI9	STRBP_HUMAN	spermatid perinuclear RNA binding protein						cellular component movement (GO:0006928)|mechanosensory behavior (GO:0007638)|multicellular organismal development (GO:0007275)|spermatid development (GO:0007286)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)	DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)|single-stranded RNA binding (GO:0003727)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(6)|prostate(1)|skin(2)	26						CGGCTCCAGTTTGTCAGTTTC	0.512																																					.		.											.	.	.	0			.						.																																			SO:0001627	intron_variant	81571	.			TCCAGTTTGTCAG	AK002169	CCDS6851.1, CCDS55337.1	9q33.1-q33.3	2008-08-29	2001-11-28		ENSG00000165209	ENSG00000165209			16462	protein-coding gene	gene with protein product		611138	"""spermatid perinuclear RNA-binding protein"", ""interleukin enhancer binding factor 3-like"""	ILF3L			Standard	NM_018387		Approved	FLJ11307, SPNR	uc004bns.3	Q96SI9	OTTHUMG00000020636	ENST00000530364.1:c.255-1978A>C	9.37:g.125874010T>G		Somatic	53	0		WXS	Illumina HiSeq	.	37	12	.	Q32NB9|Q9BUE1|Q9BXG4|Q9H0B4|Q9H7V1|Q9NUK4	RNA	SNP	ENST00000530364.1	37																																																																																				.		0.512	STRBP-009	PUTATIVE	basic	processed_transcript	protein_coding	OTTHUMT00000392598.1		
KRT10	3858	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	17	38976869	38976869	+	Missense_Mutation	SNP	C	C	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr17:38976869C>A	ENST00000269576.5	-	3	770	c.761G>T	c.(760-762)gGc>gTc	p.G254V	TMEM99_ENST00000496847.1_Intron|TMEM99_ENST00000301665.3_Intron	NM_000421.3	NP_000412	P13645	K1C10_HUMAN	keratin 10	254	Coil 1B.|Gly-rich.|Rod.				cellular response to calcium ion (GO:0071277)|keratinocyte differentiation (GO:0030216)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)|membrane (GO:0016020)|nucleus (GO:0005634)	structural constituent of epidermis (GO:0030280)			NS(2)|kidney(1)|large_intestine(3)|lung(4)|prostate(1)	11		Breast(137;0.000301)				CCTACGCAGGCCGTTGATGTC	0.502																																					p.G254V		.											.	.	.	0			c.G761T						.						104.0	100.0	102.0					17																	38976869		2203	4300	6503	SO:0001583	missense	3858	exon3			CGCAGGCCGTTGA	J04029	CCDS11377.1	17q21.2	2013-06-20	2008-08-01		ENSG00000186395	ENSG00000186395		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6413	protein-coding gene	gene with protein product	"""cytokeratin 10"", ""epidermolytic hyperkeratosis"""	148080	"""keratosis palmaris et plantaris"""	KPP		2461420, 16831889	Standard	NM_000421		Approved	K10, CK10	uc002hvi.3	P13645	OTTHUMG00000133368	ENST00000269576.5:c.761G>T	17.37:g.38976869C>A	ENSP00000269576:p.Gly254Val	Somatic	40	0		WXS	Illumina HiSeq	.	28	12	NM_000421	Q14664|Q8N175	Missense_Mutation	SNP	ENST00000269576.5	37	CCDS11377.1	.	.	.	.	.	.	.	.	.	.	C	19.93	3.917935	0.73098	.	.	ENSG00000186395	ENST00000269576	D	0.83075	-1.68	5.84	5.84	0.93424	Filament (1);	0.000000	0.36932	N	0.002326	D	0.92289	0.7554	M	0.82716	2.605	0.80722	D	1	D	0.76494	0.999	D	0.87578	0.998	D	0.92543	0.6043	10	0.87932	D	0	.	20.1533	0.98095	0.0:1.0:0.0:0.0	.	254	P13645	K1C10_HUMAN	V	254	ENSP00000269576:G254V	ENSP00000269576:G254V	G	-	2	0	KRT10	36230395	0.001000	0.12720	0.660000	0.29694	0.930000	0.56654	1.336000	0.33850	2.758000	0.94735	0.655000	0.94253	GGC	.		0.502	KRT10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257875.1	NM_000421	
AL356693.1	0	broad.mit.edu	37	1	5875969	5875984	+	RNA	DEL	ATTGAAAGTAATGGCA	ATTGAAAGTAATGGCA	-			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr1:5875969_5875984delATTGAAAGTAATGGCA	ENST00000401226.2	-	0	35_50																											ggtttttgccattgaaagtaatggcaaaaaccgcaa	0.319																																					.													.	.	.	0			.						.																																					0	.			TTTGCCATTGAAA																													1.37:g.5875969_5875984delATTGAAAGTAATGGCA		Somatic	12	0		WXS	Illumina GAIIx	Phase_I	10	2	.		RNA	DEL	ENST00000401226.2	37																																																																																				.		0.319	AL356693.1-201	NOVEL	basic	miRNA	miRNA			
ANO7P1	101927546	broad.mit.edu	37	1	16543166	16543179	+	RNA	DEL	CTTACCCTGAGCCA	CTTACCCTGAGCCA	-	rs221024	byFrequency	TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr1:16543166_16543179delCTTACCCTGAGCCA	ENST00000475369.1	-	0	202									anoctamin 7 pseudogene 1																		tcatggagcgcttaccctgagccaaaccctaacc	0.472																																					.													.	.	.	0			.						.																																					0	.			GGAGCGCTTACCC			1p36.13	2014-02-13	2012-10-24	2012-10-24	ENSG00000237276	ENSG00000237276			32248	pseudogene	pseudogene			"""transmembrane protein 16M"", ""chromosome 1 open reading frame 224"", ""anoctamin 7-like 1"""	TMEM16M, C1orf224, ANO7L1			Standard	XM_006711098		Approved				OTTHUMG00000002221		1.37:g.16543166_16543179delCTTACCCTGAGCCA		Somatic	40	0		WXS	Illumina GAIIx	Phase_I	32	11	.		RNA	DEL	ENST00000475369.1	37																																																																																				.		0.472	ANO7P1-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000006295.2		
ATAD3C	219293	broad.mit.edu	37	1	1389795	1389795	+	Missense_Mutation	SNP	A	A	T	rs1610766	byFrequency	TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr1:1389795A>T	ENST00000378785.2	+	4	1288	c.293A>T	c.(292-294)tAc>tTc	p.Y98F		NM_001039211.2	NP_001034300.2	Q5T2N8	ATD3C_HUMAN	ATPase family, AAA domain containing 3C	98							ATP binding (GO:0005524)			autonomic_ganglia(1)|endometrium(1)|kidney(1)|lung(4)	7	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;9.48e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)		Epithelial(90;1.79e-36)|OV - Ovarian serous cystadenocarcinoma(86;3.94e-22)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.00461)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.145)		ACTGGCCGCTACATCGAGGCT	0.682													N|||	4	0.000798722	0.003	0.0	5008	,	,		15291	0.0		0.0	False		,,,				2504	0.0				p.Y98F													.	ATAD3C	23	0			c.A293T						.						25.0	46.0	40.0					1																	1389795		692	1591	2283	SO:0001583	missense	219293	exon4			GCCGCTACATCGA	AK091918	CCDS44039.1	1p36.33	2010-04-21		2007-02-08	ENSG00000215915	ENSG00000215915		"""ATPases / AAA-type"""	32151	protein-coding gene	gene with protein product							Standard	NM_001039211		Approved	FLJ34599	uc001aft.2	Q5T2N8	OTTHUMG00000000531	ENST00000378785.2:c.293A>T	1.37:g.1389795A>T	ENSP00000368062:p.Tyr98Phe	Somatic	57	0		WXS	Illumina GAIIx	Phase_I	43	9	NM_001039211	Q8N1Z5	Missense_Mutation	SNP	ENST00000378785.2	37	CCDS44039.1	.	.	.	.	.	.	.	.	.	.	.	3.552	-0.091432	0.07053	.	.	ENSG00000215915	ENST00000378785	D	0.94758	-3.51	2.47	1.27	0.21489	ATPase family AAA domain-containing protein 3, domain of unknown function DUF3523 (1);	0.355383	0.30193	N	0.010200	D	0.87684	0.6239	L	0.28115	0.83	0.40679	D	0.982285	B	0.17667	0.023	B	0.22880	0.042	T	0.74548	-0.3629	10	0.26408	T	0.33	.	7.4476	0.27219	0.8022:0.0:0.0:0.1978	rs1610766	98	Q5T2N8	ATD3C_HUMAN	F	98	ENSP00000368062:Y98F	ENSP00000368062:Y98F	Y	+	2	0	ATAD3C	1379658	1.000000	0.71417	0.016000	0.15963	0.003000	0.03518	4.072000	0.57563	-0.303000	0.08856	-1.645000	0.00762	TAC	.		0.682	ATAD3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001279.3	NM_001039211	
CNN3	1266	broad.mit.edu;bcgsc.ca	37	1	95368720	95368720	+	Frame_Shift_Del	DEL	G	G	-			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr1:95368720delG	ENST00000370206.4	-	3	587	c.204delC	c.(202-204)ggcfs	p.G68fs	CNN3_ENST00000394202.4_Frame_Shift_Del_p.G68fs|CNN3_ENST00000545882.1_Frame_Shift_Del_p.G27fs|CNN3_ENST00000487539.1_5'UTR|CNN3_ENST00000538964.1_Frame_Shift_Del_p.G68fs	NM_001839.3	NP_001830.1	Q15417	CNN3_HUMAN	calponin 3, acidic	68	CH. {ECO:0000255|PROSITE- ProRule:PRU00044}.				actomyosin structure organization (GO:0031032)|epithelial cell differentiation (GO:0030855)	focal adhesion (GO:0005925)				breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(9)|prostate(1)|stomach(1)|urinary_tract(2)	18		all_lung(203;0.00206)|Lung NSC(277;0.00948)		all cancers(265;0.0325)|Epithelial(280;0.0861)		TCTTCACTGAGCCTGGCTGTA	0.408																																					p.G68fs													.	CNN3	23	0			c.204delC						.						93.0	90.0	91.0					1																	95368720		2203	4300	6503	SO:0001589	frameshift_variant	1266	exon3			CACTGAGCCTGGC	BC025372	CCDS30775.1, CCDS65592.1, CCDS65593.1	1p22-p21	2010-07-08			ENSG00000117519	ENSG00000117519			2157	protein-coding gene	gene with protein product		602374				8526917	Standard	NM_001839		Approved		uc001dqz.4	Q15417	OTTHUMG00000010783	ENST00000370206.4:c.204delC	1.37:g.95368720delG	ENSP00000359225:p.Gly68fs	Somatic	116	0		WXS	Illumina GAIIx	Phase_I	23	8	NM_001839	B4DFK6|B4DP09|F8WA86|Q6FHA7	Frame_Shift_Del	DEL	ENST00000370206.4	37	CCDS30775.1																																																																																			.		0.408	CNN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029702.2	NM_001839	
GPATCH2	55105	broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	217783668	217783668	+	Missense_Mutation	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr1:217783668A>C	ENST00000366935.3	-	5	1203	c.1093T>G	c.(1093-1095)Tca>Gca	p.S365A	GPATCH2_ENST00000366934.3_Missense_Mutation_p.S365A	NM_018040.2	NP_060510.1	Q9NW75	GPTC2_HUMAN	G patch domain containing 2	365					negative regulation of phosphatase activity (GO:0010923)		nucleic acid binding (GO:0003676)			NS(1)|breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(17)|ovary(1)|prostate(1)|skin(3)|stomach(1)	35				OV - Ovarian serous cystadenocarcinoma(81;0.0397)|all cancers(67;0.0744)|GBM - Glioblastoma multiforme(131;0.0872)		CCTACCATTGAAGTTGGAGTC	0.343																																					p.S365A													.	GPATCH2	53	0			c.T1093G						.						101.0	105.0	104.0					1																	217783668		2203	4300	6503	SO:0001583	missense	55105	exon5			CCATTGAAGTTGG	AK001114	CCDS1518.1, CCDS73031.1	1q41	2013-01-28		2006-12-13	ENSG00000092978	ENSG00000092978		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""G patch domain containing"""	25499	protein-coding gene	gene with protein product	"""cancer/testis antigen 110"", ""protein phosphatase 1, regulatory subunit 30"""			GPATC2		19432882, 15375528	Standard	XM_005273174		Approved	FLJ10252, CT110, PPP1R30	uc001hlf.1	Q9NW75	OTTHUMG00000000527	ENST00000366935.3:c.1093T>G	1.37:g.217783668A>C	ENSP00000355902:p.Ser365Ala	Somatic	119	1		WXS	Illumina GAIIx	Phase_I	140	31	NM_018040	Q5VYK7|Q5VYK8|Q86YE7	Missense_Mutation	SNP	ENST00000366935.3	37	CCDS1518.1	.	.	.	.	.	.	.	.	.	.	A	0.952	-0.705997	0.03255	.	.	ENSG00000092978	ENST00000366935;ENST00000366934	T;T	0.44881	1.53;0.91	6.08	2.5	0.30297	.	0.335609	0.30510	N	0.009478	T	0.17619	0.0423	N	0.10874	0.06	0.26537	N	0.974157	B;B	0.06786	0.001;0.001	B;B	0.04013	0.001;0.001	T	0.08452	-1.0721	10	0.36615	T	0.2	.	0.4445	0.00491	0.4095:0.2106:0.1618:0.2181	.	365;365	Q9NW75-2;Q9NW75	.;GPTC2_HUMAN	A	365	ENSP00000355902:S365A;ENSP00000355901:S365A	ENSP00000355901:S365A	S	-	1	0	GPATCH2	215850291	1.000000	0.71417	0.997000	0.53966	0.991000	0.79684	0.951000	0.29135	0.511000	0.28236	-0.468000	0.05107	TCA	.		0.343	GPATCH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001272.1	NM_018040	
MFSD2A	84879	broad.mit.edu	37	1	40431616	40431616	+	Missense_Mutation	SNP	A	A	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr1:40431616A>G	ENST00000372809.5	+	6	826	c.683A>G	c.(682-684)gAc>gGc	p.D228G	MFSD2A_ENST00000372811.5_Missense_Mutation_p.D215G|MFSD2A_ENST00000420632.2_Missense_Mutation_p.D59G|MFSD2A_ENST00000480630.1_3'UTR	NM_001136493.1	NP_001129965.1	Q8NA29	NLS1_HUMAN	major facilitator superfamily domain containing 2A	228					establishment of blood-brain barrier (GO:0060856)|fatty acid transport (GO:0015908)|lipid transport across blood brain barrier (GO:1990379)|transcytosis (GO:0045056)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	phospholipid transporter activity (GO:0005548)|symporter activity (GO:0015293)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(3)|lung(6)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	24						TGTTTCCAGGACCTCAATAGC	0.577																																					p.D228G													.	MFSD2A	53	0			c.A683G						.						126.0	99.0	108.0					1																	40431616		2203	4300	6503	SO:0001583	missense	84879	exon6			TCCAGGACCTCAA	AK093223	CCDS446.1, CCDS44118.1, CCDS72762.1	1p34.2	2009-09-08	2009-09-08	2009-09-08	ENSG00000168389	ENSG00000168389			25897	protein-coding gene	gene with protein product		614397	"""major facilitator superfamily domain containing 2"""	MFSD2		18694395	Standard	XM_005271285		Approved	FLJ14490	uc001cev.3	Q8NA29	OTTHUMG00000009293	ENST00000372809.5:c.683A>G	1.37:g.40431616A>G	ENSP00000361895:p.Asp228Gly	Somatic	25	0		WXS	Illumina GAIIx	Phase_I	16	3	NM_001136493	A8K675|Q6UWU5|Q96F59|Q9BRC8	Missense_Mutation	SNP	ENST00000372809.5	37	CCDS44118.1	.	.	.	.	.	.	.	.	.	.	A	8.021	0.759723	0.15846	.	.	ENSG00000168389	ENST00000372811;ENST00000420632;ENST00000434861;ENST00000372809	D;D;D;D	0.86297	-2.1;-2.1;-2.1;-2.1	5.94	3.6	0.41247	Major facilitator superfamily domain, general substrate transporter (1);	0.895788	0.10030	N	0.724829	T	0.70202	0.3197	N	0.03608	-0.345	0.09310	N	1	B;B;B	0.06786	0.001;0.001;0.0	B;B;B	0.11329	0.005;0.006;0.003	T	0.56974	-0.7890	10	0.23891	T	0.37	-1.4567	6.1585	0.20350	0.7434:0.0:0.1354:0.1212	.	178;228;215	B4DNN7;Q8NA29;Q8NA29-2	.;MFS2A_HUMAN;.	G	215;59;213;228	ENSP00000361898:D215G;ENSP00000391261:D59G;ENSP00000407606:D213G;ENSP00000361895:D228G	ENSP00000361895:D228G	D	+	2	0	MFSD2A	40204203	0.343000	0.24818	0.067000	0.19924	0.692000	0.40212	0.751000	0.26348	0.476000	0.27440	0.460000	0.39030	GAC	.		0.577	MFSD2A-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000025756.1	NM_032793	
HIST3H2BB	128312	broad.mit.edu	37	1	228646009	228646009	+	Missense_Mutation	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr1:228646009T>G	ENST00000369160.2	+	1	202	c.179T>G	c.(178-180)aTg>aGg	p.M60R	HIST3H2A_ENST00000366695.2_5'Flank	NM_175055.2	NP_778225.1	Q8N257	H2B3B_HUMAN	histone cluster 3, H2bb	60					chromatin organization (GO:0006325)	nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			skin(1)	1		Prostate(94;0.183)				TCCAAGGCCATGGGCATCATG	0.602																																					p.M60R													.	HIST3H2BB	23	0			c.T179G						.						97.0	92.0	94.0					1																	228646009		2203	4296	6499	SO:0001583	missense	128312	exon1			AGGCCATGGGCAT	AY131981	CCDS1574.1	1q42.13	2011-01-27	2006-10-11		ENSG00000196890	ENSG00000196890		"""Histones / Replication-dependent"""	20514	protein-coding gene	gene with protein product		615046	"""histone 3, H2bb"""			12408966	Standard	NM_175055		Approved		uc001hsz.3	Q8N257	OTTHUMG00000040045	ENST00000369160.2:c.179T>G	1.37:g.228646009T>G	ENSP00000375736:p.Met60Arg	Somatic	134	0		WXS	Illumina GAIIx	Phase_I	196	4	NM_175055	A4FU05|Q3ZCP6|Q5TA30	Missense_Mutation	SNP	ENST00000369160.2	37	CCDS1574.1	.	.	.	.	.	.	.	.	.	.	.	17.13	3.311325	0.60414	.	.	ENSG00000196890	ENST00000369160	T	0.70045	-0.45	3.94	3.94	0.45596	Histone-fold (2);Histone core (1);	0.000000	0.56097	D	0.000032	T	0.80706	0.4674	H	0.99590	4.645	0.58432	D	0.999999	B	0.18741	0.03	B	0.21546	0.035	D	0.83766	0.0217	10	0.87932	D	0	.	11.4739	0.50286	0.0:0.0:0.0:1.0	.	60	Q8N257	H2B3B_HUMAN	R	60	ENSP00000375736:M60R	ENSP00000375736:M60R	M	+	2	0	HIST3H2BB	226712632	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	7.313000	0.78978	2.016000	0.59253	0.477000	0.44152	ATG	.		0.602	HIST3H2BB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096597.1	NM_175055	
KIAA1804	84451	broad.mit.edu	37	1	233464401	233464409	+	In_Frame_Del	DEL	CCGAGCGCT	CCGAGCGCT	-			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr1:233464401_233464409delCCGAGCGCT	ENST00000366624.3	+	1	888_896	c.627_635delCCGAGCGCT	c.(625-636)aaccgagcgctg>aag	p.209_212NRAL>K	MLK4_ENST00000366623.3_In_Frame_Del_p.209_212NRAL>K	NM_032435.2	NP_115811.2																					GAGCGCTCAACCGAGCGCTGGCCGCTGCC	0.756																																					p.209_212del													.	KIAA1804	129	0			c.627_635del						.																																			SO:0001651	inframe_deletion	0	exon1			GCTCAACCGAGCG																												ENST00000366624.3:c.627_635delCCGAGCGCT	1.37:g.233464401_233464409delCCGAGCGCT	ENSP00000355583:p.Asn209_Leu212delinsLys	Somatic	8	0		WXS	Illumina GAIIx	Phase_I	8	4	NM_032435		In_Frame_Del	DEL	ENST00000366624.3	37	CCDS1598.1																																																																																			.		0.756	MLK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092495.1		
TRNP1	388610	broad.mit.edu	37	1	27320310	27320310	+	Frame_Shift_Del	DEL	G	G	-			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr1:27320310delG	ENST00000522111.2	+	1	113	c.33delG	c.(31-33)ccgfs	p.P11fs		NM_001013642.2	NP_001013664	Q6NT89	TRNP1_HUMAN	TMF1-regulated nuclear protein 1	11					cell cycle (GO:0007049)|cerebellar cortex morphogenesis (GO:0021696)|neural precursor cell proliferation (GO:0061351)|regulation of cell cycle (GO:0051726)|regulation of cell proliferation (GO:0042127)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nuclear euchromatin (GO:0005719)|nucleus (GO:0005634)	DNA binding (GO:0003677)										CCTGCGGCCCGGGGGCCCAGG	0.736																																					p.P11fs													.	TRNP1	2	0			c.33delG						.						1.0	2.0	2.0					1																	27320310		976	2524	3500	SO:0001589	frameshift_variant	388610	exon1			CGGCCCGGGGGCC	AI366714, AL356390, BC069216, CH471059	CCDS41289.1	1p36.11	2012-10-03	2009-02-19	2009-02-19	ENSG00000253368	ENSG00000253368			34348	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 225"""	C1orf225		12477932	Standard	NM_001013642		Approved	LOC388610	uc001bnj.4	Q6NT89	OTTHUMG00000004277	ENST00000522111.2:c.33delG	1.37:g.27320310delG	ENSP00000429216:p.Pro11fs	Somatic	13	0		WXS	Illumina GAIIx	Phase_I	6	2	NM_001013642		Frame_Shift_Del	DEL	ENST00000522111.2	37	CCDS41289.1																																																																																			.		0.736	TRNP1-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012346.3	NM_001013642	
THRAP3	9967	broad.mit.edu;bcgsc.ca	37	1	36759444	36759456	+	Splice_Site	DEL	AATTTTAGGAGAA	AATTTTAGGAGAA	-			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr1:36759444_36759456delAATTTTAGGAGAA	ENST00000354618.5	+	8	2254_2259	c.2030_2035delAATTTTAGGAGAA	c.(2029-2037)aaattttag>aag	p.F*678fs	THRAP3_ENST00000466743.1_3'UTR|THRAP3_ENST00000469141.2_Splice_Site_p.F*678fs	NM_005119.3	NP_005110.2	Q9Y2W1	TR150_HUMAN	thyroid hormone receptor associated protein 3	678	Required for mRNA decay activity.				androgen receptor signaling pathway (GO:0030521)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|mRNA processing (GO:0006397)|mRNA stabilization (GO:0048255)|nuclear-transcribed mRNA catabolic process (GO:0000956)|positive regulation of mRNA splicing, via spliceosome (GO:0048026)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing (GO:0008380)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|phosphoprotein binding (GO:0051219)|poly(A) RNA binding (GO:0044822)|receptor activity (GO:0004872)|RNA polymerase II transcription cofactor activity (GO:0001104)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			breast(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(12)|ovary(5)|stomach(1)	37		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				TTGTATTTTCAATTTTAGGAGAATAGACATTTC	0.357			T	USP6	aneurysmal bone cysts																																p.677_679del	Pancreas(129;785 1795 20938 23278 32581)			Dom	yes		1	1p34.3	9967	thyroid hormone receptor associated protein 3 (TRAP150)		M	.	THRAP3	93	0			c.2031_2035del						.																																			SO:0001630	splice_region_variant	9967	exon8			ATTTTCAATTTTA	AF117756	CCDS405.1	1p34.3	2008-02-05			ENSG00000054118	ENSG00000054118			22964	protein-coding gene	gene with protein product		603809					Standard	NM_005119		Approved	TRAP150	uc001cae.4	Q9Y2W1	OTTHUMG00000007866	ENST00000354618.5:c.2031-1AATTTTAGGAGAA>-	1.37:g.36759444_36759456delAATTTTAGGAGAA		Somatic	101	0		WXS	Illumina GAIIx	Phase_I	39	7	NM_005119	D3DPS5|Q5VTK6	Splice_Site	DEL	ENST00000354618.5	37	CCDS405.1																																																																																			.		0.357	THRAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021688.2	NM_005119	Frame_Shift_Del
PLEKHA6	22874	broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	204236606	204236606	+	Missense_Mutation	SNP	T	T	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr1:204236606T>C	ENST00000272203.3	-	5	593	c.277A>G	c.(277-279)Aaa>Gaa	p.K93E	PLEKHA6_ENST00000414478.1_Missense_Mutation_p.K93E	NM_014935.4	NP_055750.2	Q9Y2H5	PKHA6_HUMAN	pleckstrin homology domain containing, family A member 6	93	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.									breast(2)|endometrium(6)|kidney(1)|large_intestine(9)|lung(21)|ovary(3)|pancreas(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	53	all_cancers(21;0.0222)|Breast(84;0.179)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|BRCA - Breast invasive adenocarcinoma(75;0.0833)|Kidney(21;0.0934)|Epithelial(59;0.229)			AGCTCACCTTTATAGTAGAAG	0.582																																					p.K93E													.	PLEKHA6	115	0			c.A277G						.						92.0	70.0	77.0					1																	204236606		2203	4300	6503	SO:0001583	missense	22874	exon5			CACCTTTATAGTA	AB023186	CCDS1444.1	1q32	2013-01-10			ENSG00000143850	ENSG00000143850		"""Pleckstrin homology (PH) domain containing"""	17053	protein-coding gene	gene with protein product		607771				11001876	Standard	NM_014935		Approved	PEPP3, KIAA0969	uc001hau.4	Q9Y2H5	OTTHUMG00000036057	ENST00000272203.3:c.277A>G	1.37:g.204236606T>C	ENSP00000272203:p.Lys93Glu	Somatic	38	0		WXS	Illumina GAIIx	Phase_I	31	18	NM_014935	A7MD51|Q5VTI6	Missense_Mutation	SNP	ENST00000272203.3	37	CCDS1444.1	.	.	.	.	.	.	.	.	.	.	T	21.4	4.143627	0.77888	.	.	ENSG00000143850	ENST00000272203;ENST00000414478	T;T	0.78003	-1.14;-1.14	5.51	5.51	0.81932	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.047987	0.85682	D	0.000000	D	0.87124	0.6099	M	0.70842	2.15	0.80722	D	1	D	0.53312	0.959	D	0.72625	0.978	D	0.88403	0.3016	10	0.72032	D	0.01	.	15.2951	0.73898	0.0:0.0:0.0:1.0	.	93	Q9Y2H5	PKHA6_HUMAN	E	93	ENSP00000272203:K93E;ENSP00000402046:K93E	ENSP00000272203:K93E	K	-	1	0	PLEKHA6	202503229	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	6.511000	0.73733	2.086000	0.62901	0.448000	0.29417	AAA	.		0.582	PLEKHA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087889.3	NM_014935	
AC074323.1	0	broad.mit.edu;bcgsc.ca	37	10	80510398	80510398	+	RNA	DEL	T	T	-			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr10:80510398delT	ENST00000411311.1	+	0	40																											gtaattgcggtttttgccatt	0.333																																					.													.	.	.	0			.						.																																					0	.			TTGCGGTTTTTGC																													10.37:g.80510398delT		Somatic	52	0		WXS	Illumina GAIIx	Phase_I	36	14	.		RNA	DEL	ENST00000411311.1	37																																																																																				.		0.333	AC074323.1-201	NOVEL	basic	miRNA	miRNA			
HNRNPF	3185	broad.mit.edu	37	10	43882519	43882526	+	Frame_Shift_Del	DEL	ACATTCCG	ACATTCCG	-	rs201947175|rs17849827		TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr10:43882519_43882526delACATTCCG	ENST00000544000.1	-	4	1214_1221	c.807_814delCGGAATGT	c.(805-816)tccggaatgtatfs	p.GMY270fs	HNRNPF_ENST00000443950.2_Frame_Shift_Del_p.GMY270fs|HNRNPF_ENST00000356053.3_Frame_Shift_Del_p.GMY270fs|HNRNPF_ENST00000337970.3_Frame_Shift_Del_p.GMY270fs|HNRNPF_ENST00000357065.4_Frame_Shift_Del_p.GMY270fs|HNRNPF_ENST00000498176.1_5'Flank	NM_001098207.1	NP_001091677.1	P52597	HNRPF_HUMAN	heterogeneous nuclear ribonucleoprotein F	270					gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|regulation of RNA splicing (GO:0043484)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|single-stranded RNA binding (GO:0003727)			breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(10)|prostate(1)|urinary_tract(1)	19						CTGTGGTCATACATTCCGGAGAGACAGT	0.582																																					p.269_272del													.	HNRNPF	57	0			c.807_814del						.																																			SO:0001589	frameshift_variant	3185	exon4			GGTCATACATTCC		CCDS7204.1	10q11.21	2013-02-12		2008-04-18	ENSG00000169813	ENSG00000169813		"""RNA binding motif (RRM) containing"""	5039	protein-coding gene	gene with protein product		601037		HNRPF		7499401	Standard	NM_001098208		Approved		uc001jas.2	P52597	OTTHUMG00000018029	ENST00000544000.1:c.807_814delCGGAATGT	10.37:g.43882519_43882526delACATTCCG	ENSP00000438061:p.Gly270fs	Somatic	18	0		WXS	Illumina GAIIx	Phase_I	13	5	NM_001098204	B3KM84|Q5T0N2|Q96AU2	Frame_Shift_Del	DEL	ENST00000544000.1	37	CCDS7204.1																																																																																			.		0.582	HNRNPF-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047705.2		
HPSE2	60495	broad.mit.edu	37	10	100904026	100904026	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr10:100904026G>T	ENST00000370552.3	-	3	638	c.579C>A	c.(577-579)ttC>ttA	p.F193L	HPSE2_ENST00000370549.1_Missense_Mutation_p.F193L|HPSE2_ENST00000370546.1_Missense_Mutation_p.F193L|HPSE2_ENST00000404542.1_Intron	NM_021828.4	NP_068600.4	Q8WWQ2	HPSE2_HUMAN	heparanase 2 (inactive)	193					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	intracellular (GO:0005622)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	heparan sulfate proteoglycan binding (GO:0043395)|heparanase activity (GO:0030305)			NS(1)|breast(1)|endometrium(3)|kidney(2)|large_intestine(14)|lung(15)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	40				Epithelial(162;1.8e-09)|all cancers(201;4.72e-07)		AAGTATTGGAGAATTGCTCCT	0.423																																					p.F193L													.	HPSE2	203	0			c.C579A						.						108.0	104.0	105.0					10																	100904026		2203	4300	6503	SO:0001583	missense	60495	exon3			ATTGGAGAATTGC	AF282885	CCDS7477.1, CCDS53567.1, CCDS53568.1	10q23-q24	2014-05-09	2014-05-09		ENSG00000172987	ENSG00000172987			18374	protein-coding gene	gene with protein product		613469	"""urofacial syndrome"", ""heparanase 2"""	UFS		11027606, 20605132, 9199567, 20576607	Standard	NM_021828		Approved	HPA2, HPR2	uc001kpn.2	Q8WWQ2	OTTHUMG00000018880	ENST00000370552.3:c.579C>A	10.37:g.100904026G>T	ENSP00000359583:p.Phe193Leu	Somatic	19	0		WXS	Illumina GAIIx	Phase_I	12	3	NM_001166246	Q5VUH4|Q5VUH5|Q5VUH6|Q8WWQ1|Q9HB37|Q9HB38|Q9HB39	Missense_Mutation	SNP	ENST00000370552.3	37	CCDS7477.1	.	.	.	.	.	.	.	.	.	.	G	10.31	1.314293	0.23908	.	.	ENSG00000172987	ENST00000370552;ENST00000370549;ENST00000370546	T;T;T	0.28666	7.25;1.6;7.25	5.97	5.06	0.68205	Glycoside hydrolase, superfamily (1);	0.260739	0.34700	N	0.003749	T	0.08802	0.0218	N	0.00707	-1.245	0.80722	D	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.06405	0.001;0.001;0.002	T	0.16158	-1.0412	10	0.11485	T	0.65	-5.1364	9.6581	0.39939	0.1973:0.0:0.8027:0.0	.	193;193;193	Q8WWQ2-2;Q8WWQ2-3;Q8WWQ2	.;.;HPSE2_HUMAN	L	193	ENSP00000359583:F193L;ENSP00000359580:F193L;ENSP00000359577:F193L	ENSP00000359577:F193L	F	-	3	2	HPSE2	100894016	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.775000	0.38584	1.529000	0.49120	0.655000	0.94253	TTC	.		0.423	HPSE2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049789.1	NM_021828	
PPP3CB	5532	broad.mit.edu	37	10	75255630	75255630	+	Silent	SNP	C	C	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr10:75255630C>A	ENST00000360663.5	-	1	129	c.18G>T	c.(16-18)ccG>ccT	p.P6P	RP11-137L10.6_ENST00000593790.1_RNA|PPP3CB_ENST00000394822.2_Silent_p.P6P|PPP3CB_ENST00000545874.1_5'UTR|PPP3CB_ENST00000394829.2_Silent_p.P6P|PPP3CB_ENST00000342558.3_Silent_p.P6P|RP11-137L10.6_ENST00000600607.1_RNA|RP11-137L10.6_ENST00000596320.1_RNA|RP11-137L10.6_ENST00000422977.1_RNA|RP11-137L10.6_ENST00000597958.1_RNA|RP11-137L10.6_ENST00000442133.4_RNA|RP11-137L10.6_ENST00000595935.1_RNA|USP54_ENST00000497106.1_5'Flank|RP11-137L10.6_ENST00000600887.1_RNA|PPP3CB_ENST00000394828.2_Silent_p.P6P|RP11-137L10.6_ENST00000600206.1_RNA|RP11-137L10.6_ENST00000595069.1_RNA			P16298	PP2BB_HUMAN	protein phosphatase 3, catalytic subunit, beta isozyme	6	Catalytic.				axon extension (GO:0048675)|calcium ion-dependent exocytosis (GO:0017156)|cellular response to drug (GO:0035690)|dephosphorylation (GO:0016311)|Fc-epsilon receptor signaling pathway (GO:0038095)|heart development (GO:0007507)|innate immune response (GO:0045087)|learning (GO:0007612)|locomotion involved in locomotory behavior (GO:0031987)|memory (GO:0007613)|negative regulation of T cell mediated cytotoxicity (GO:0001915)|positive regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0035774)|positive regulation of transcription, DNA-templated (GO:0045893)|protein dephosphorylation (GO:0006470)|protein phosphorylation (GO:0006468)|regulation of insulin secretion (GO:0050796)|regulation of synaptic plasticity (GO:0048167)|response to cytokine (GO:0034097)|signal transduction (GO:0007165)|social behavior (GO:0035176)|T cell activation (GO:0042110)|T cell differentiation (GO:0030217)|T cell homeostasis (GO:0043029)|T cell proliferation (GO:0042098)	calcineurin complex (GO:0005955)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|calmodulin-dependent protein phosphatase activity (GO:0033192)|drug binding (GO:0008144)|enzyme binding (GO:0019899)|protein dimerization activity (GO:0046983)|protein phosphatase 2B binding (GO:0030346)|protein serine/threonine phosphatase activity (GO:0004722)			breast(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(7)|skin(1)|urinary_tract(1)	22	Prostate(51;0.0119)					CAGCCCGGGCCGGCTCCGGGG	0.811																																					p.P6P													.	PPP3CB	68	0			c.G18T						.						1.0	1.0	1.0					10																	75255630		125	447	572	SO:0001819	synonymous_variant	5532	exon1			CCGGGCCGGCTCC	M29551	CCDS7328.1, CCDS44436.1, CCDS44437.1	10q22.2	2010-03-17	2010-03-05		ENSG00000107758	ENSG00000107758	3.1.3.16	"""Serine/threonine phosphatases / Protein phosphatase, catalytic subunits"""	9315	protein-coding gene	gene with protein product	"""calcineurin A beta"", ""protein phosphatase 2B, catalytic subunit, beta isoform"""	114106	"""protein phosphatase 3 (formerly 2B), catalytic subunit, beta isoform (calcineurin A beta)"", ""protein phosphatase 3 (formerly 2B), catalytic subunit, beta isoform"""	CALNB		1659808, 2558868	Standard	XM_005269944		Approved	CALNA2, CNA2, PP2Bbeta	uc001juf.3	P16298	OTTHUMG00000018472	ENST00000360663.5:c.18G>T	10.37:g.75255630C>A		Somatic	16	0		WXS	Illumina GAIIx	Phase_I	17	10	NM_001142354	P16299|Q5F2F9|Q8N1F0|Q8N3W4	Silent	SNP	ENST00000360663.5	37	CCDS7328.1																																																																																			.		0.811	PPP3CB-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000048669.1	NM_021132	
MGEA5	10724	broad.mit.edu;bcgsc.ca	37	10	103577755	103577755	+	Missense_Mutation	SNP	T	T	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr10:103577755T>C	ENST00000361464.3	-	1	420	c.25A>G	c.(25-27)Acg>Gcg	p.T9A	MGEA5_ENST00000370094.3_Missense_Mutation_p.T9A|KCNIP2-AS1_ENST00000412353.1_RNA|MGEA5_ENST00000357797.5_Missense_Mutation_p.T9A|MGEA5_ENST00000439817.1_Missense_Mutation_p.T9A|MGEA5_ENST00000419011.2_Missense_Mutation_p.T9A	NM_012215.3	NP_036347.1	O60502	OGA_HUMAN	meningioma expressed antigen 5 (hyaluronidase)	9					aging (GO:0007568)|dATP metabolic process (GO:0046060)|glycoprotein catabolic process (GO:0006516)|N-acetylglucosamine metabolic process (GO:0006044)|necrotic cell death (GO:0070265)|negative regulation of cardiac muscle adaptation (GO:0010616)|negative regulation of protein glycosylation (GO:0060051)|positive regulation of calcium ion transport into cytosol (GO:0010524)|positive regulation of cell killing (GO:0031343)|positive regulation of DNA metabolic process (GO:0051054)|positive regulation of glucose import (GO:0046326)|positive regulation of growth hormone secretion (GO:0060124)|positive regulation of insulin secretion (GO:0032024)|positive regulation of mitochondrial depolarization (GO:0051901)|positive regulation of protein complex disassembly (GO:0043243)|positive regulation of proteolysis (GO:0045862)|protein targeting to membrane (GO:0006612)|response to steroid hormone (GO:0048545)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	histone acetyltransferase activity (GO:0004402)|hyalurononglucosaminidase activity (GO:0004415)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(11)|ovary(2)|skin(1)|urinary_tract(1)	23		Colorectal(252;0.207)		Epithelial(162;4.67e-09)|all cancers(201;2.54e-07)		TCCTCCAACGTCGCTTGACTC	0.711																																					p.T9A													.	MGEA5	53	0			c.A25G						.						16.0	15.0	15.0					10																	103577755		2198	4299	6497	SO:0001583	missense	10724	exon1			CCAACGTCGCTTG	AF036144	CCDS7520.1, CCDS44471.1	10q24.1-q24.3	2008-08-01			ENSG00000198408	ENSG00000198408			7056	protein-coding gene	gene with protein product	"""nuclear cytoplasmic O-GlcNAcase and acetyltransferase"""	604039				9811929, 16356930	Standard	NM_012215		Approved	MEA5, NCOAT, OGA	uc001ktv.2	O60502	OTTHUMG00000018939	ENST00000361464.3:c.25A>G	10.37:g.103577755T>C	ENSP00000354850:p.Thr9Ala	Somatic	28	0		WXS	Illumina GAIIx	Phase_I	20	5	NM_001142434	B7WPB9|D3DR79|E9PGF9|O75166|Q86WV0|Q8IV98|Q9BVA5|Q9HAR0	Missense_Mutation	SNP	ENST00000361464.3	37	CCDS7520.1	.	.	.	.	.	.	.	.	.	.	T	4.126	0.021694	0.08006	.	.	ENSG00000198408	ENST00000439817;ENST00000361464;ENST00000357797;ENST00000370094;ENST00000419011	T;T;T;T;T	0.38887	1.76;1.72;1.75;1.72;1.11	4.83	1.84	0.25277	.	0.555501	0.18746	N	0.132309	T	0.14270	0.0345	N	0.04508	-0.205	0.25055	N	0.991109	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.31308	-0.9948	10	0.02654	T	1	-0.6107	4.6203	0.12447	0.0:0.487:0.1519:0.3611	.	9;9;9;9	E9PGF9;O60502-2;O60502-3;O60502	.;.;.;NCOAT_HUMAN	A	9	ENSP00000409973:T9A;ENSP00000354850:T9A;ENSP00000350445:T9A;ENSP00000359112:T9A;ENSP00000407081:T9A	ENSP00000350445:T9A	T	-	1	0	MGEA5	103567745	1.000000	0.71417	0.999000	0.59377	0.870000	0.49936	1.202000	0.32271	0.190000	0.20209	-0.366000	0.07423	ACG	.		0.711	MGEA5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049987.1	NM_012215	
C11orf88	399949	broad.mit.edu;bcgsc.ca	37	11	111385536	111385536	+	Silent	SNP	T	T	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr11:111385536T>A	ENST00000375618.4	+	1	27	c.27T>A	c.(25-27)ccT>ccA	p.P9P	C11orf88_ENST00000529167.1_Silent_p.P9P|BTG4_ENST00000525791.1_5'Flank|MIR34B_ENST00000385076.1_RNA|MIR34C_ENST00000384831.1_RNA|RP11-794P6.6_ENST00000530283.1_RNA|C11orf88_ENST00000332814.6_Silent_p.P9P|BTG4_ENST00000356018.2_5'Flank	NM_001100388.1	NP_001093858.1	Q6PI97	CK088_HUMAN	chromosome 11 open reading frame 88	9										endometrium(1)|large_intestine(3)|lung(2)	6						GCGAAGAACCTAGCGGCCGAA	0.617											OREG0021329	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.P9P													.	C11orf88	37	0			c.T27A						.						49.0	55.0	53.0					11																	111385536		1858	4092	5950	SO:0001819	synonymous_variant	399949	exon1			AGAACCTAGCGGC	BC039505, AK128145	CCDS41712.1, CCDS41713.1	11q23.1	2012-08-10			ENSG00000183644	ENSG00000183644			25061	protein-coding gene	gene with protein product	"""hypothetical gene supported by BC039505"""					12477932	Standard	NM_001100388		Approved	FLJ46266	uc009yyd.3	Q6PI97	OTTHUMG00000166720	ENST00000375618.4:c.27T>A	11.37:g.111385536T>A		Somatic	42	1	1434	WXS	Illumina GAIIx	Phase_I	39	14	NM_001100388	E9PAN0|Q6ZRL3	Silent	SNP	ENST00000375618.4	37	CCDS41713.1																																																																																			.		0.617	C11orf88-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000391181.1	NM_001100388	
FAM99B	100132464	broad.mit.edu	37	11	1706483	1706491	+	RNA	DEL	CCAGGCTGA	CCAGGCTGA	-			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr11:1706483_1706491delCCAGGCTGA	ENST00000382166.2	-	0	192					NR_026642.1				family with sequence similarity 99, member B (non-protein coding)																		CCCTCAGCCTCCAGGCTGACCAGGCTTCC	0.646																																					.													.	.	.	0			.						.																																					0	.			CAGCCTCCAGGCT	CR627417		11p15.5	2012-10-16	2011-08-31		ENSG00000205865	ENSG00000205865		"""Long non-coding RNAs"""	32369	non-coding RNA	RNA, long non-coding			"""family with sequence similarity 99, member B"""				Standard	NR_026642		Approved	DKFZp781M09150	uc010qxa.1		OTTHUMG00000057552		11.37:g.1706483_1706491delCCAGGCTGA		Somatic	18	0		WXS	Illumina GAIIx	Phase_I	11	2	.		RNA	DEL	ENST00000382166.2	37																																																																																				.		0.646	FAM99B-001	KNOWN	basic	antisense	antisense	OTTHUMT00000127917.1		
KBTBD4	55709	broad.mit.edu;ucsc.edu;bcgsc.ca	37	11	47594521	47594521	+	Missense_Mutation	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr11:47594521A>C	ENST00000526005.1	-	4	1671	c.1518T>G	c.(1516-1518)atT>atG	p.I506M	PTPMT1_ENST00000527079.2_3'UTR|NDUFS3_ENST00000533507.1_Intron|KBTBD4_ENST00000430070.2_Missense_Mutation_p.I522M|KBTBD4_ENST00000533290.1_Missense_Mutation_p.I531M|KBTBD4_ENST00000395288.2_Missense_Mutation_p.I506M			Q9NVX7	KBTB4_HUMAN	kelch repeat and BTB (POZ) domain containing 4	506										NS(1)|breast(1)|central_nervous_system(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(5)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	24						GCAGCACCTTAATACCTCTTG	0.507																																					p.I522M													.	KBTBD4	55	0			c.T1566G						.						95.0	67.0	76.0					11																	47594521		2201	4298	6499	SO:0001583	missense	55709	exon4			CACCTTAATACCT	AF151086	CCDS7940.1, CCDS44594.1	11p11.2	2013-01-08	2003-12-12	2003-12-17	ENSG00000123444	ENSG00000123444		"""BTB/POZ domain containing"""	23761	protein-coding gene	gene with protein product			"""BTB and kelch domain containing 4"""	BKLHD4		11042152	Standard	NM_018095		Approved	FLJ10450, HSPC252	uc001nfz.3	Q9NVX7	OTTHUMG00000166894	ENST00000526005.1:c.1518T>G	11.37:g.47594521A>C	ENSP00000433340:p.Ile506Met	Somatic	51	0		WXS	Illumina GAIIx	Phase_I	28	6	NM_018095	D3DQS1|D3DQS2|Q6IA85|Q9BUC3|Q9NV76	Missense_Mutation	SNP	ENST00000526005.1	37	CCDS7940.1	.	.	.	.	.	.	.	.	.	.	A	11.74	1.729824	0.30684	.	.	ENSG00000123444	ENST00000526005;ENST00000533290;ENST00000395288;ENST00000430070	T;T;T;T	0.74002	-0.71;-0.8;-0.71;-0.78	6.04	-1.99	0.07457	.	0.093369	0.64402	D	0.000001	T	0.59985	0.2234	N	0.19112	0.55	0.47584	D	0.999469	B;B;B	0.31859	0.343;0.077;0.232	B;B;B	0.36289	0.221;0.023;0.11	T	0.55970	-0.8056	10	0.59425	D	0.04	-6.3232	14.1734	0.65525	0.227:0.0:0.773:0.0	.	522;506;531	Q9NVX7-2;Q9NVX7;B3KRH9	.;KBTB4_HUMAN;.	M	506;531;506;522	ENSP00000433340:I506M;ENSP00000436713:I531M;ENSP00000378703:I506M;ENSP00000415106:I522M	ENSP00000378703:I506M	I	-	3	3	KBTBD4	47551097	1.000000	0.71417	0.993000	0.49108	0.993000	0.82548	2.264000	0.43302	-0.273000	0.09246	0.459000	0.35465	ATT	.		0.507	KBTBD4-003	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000391763.1	NM_016506	
FADS1	3992	broad.mit.edu	37	11	61584238	61584238	+	Missense_Mutation	SNP	C	C	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr11:61584238C>A	ENST00000350997.7	-	1	396	c.164G>T	c.(163-165)aGg>aTg	p.R55M	FADS1_ENST00000433932.1_5'Flank|MIR1908_ENST00000410394.1_RNA|FADS2_ENST00000257261.6_Intron|FADS2_ENST00000522639.1_Intron|FADS2_ENST00000517839.1_Intron|FADS1_ENST00000541683.1_5'Flank|FADS2_ENST00000522056.1_Intron|FADS1_ENST00000542506.1_5'Flank|FADS2_ENST00000574708.1_Intron	NM_013402.4	NP_037534.3	O60427	FADS1_HUMAN	fatty acid desaturase 1	0	Cytochrome b5 heme-binding. {ECO:0000255|PROSITE-ProRule:PRU00279}.				alpha-linolenic acid metabolic process (GO:0036109)|cell-cell signaling (GO:0007267)|cellular lipid metabolic process (GO:0044255)|cellular response to starvation (GO:0009267)|icosanoid biosynthetic process (GO:0046456)|linoleic acid metabolic process (GO:0043651)|phospholipid biosynthetic process (GO:0008654)|regulation of cell differentiation (GO:0045595)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|unsaturated fatty acid biosynthetic process (GO:0006636)|unsaturated fatty acid metabolic process (GO:0033559)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|mitochondrion (GO:0005739)	C-5 sterol desaturase activity (GO:0000248)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxidoreductase activity (GO:0016491)			central_nervous_system(1)|endometrium(1)|lung(1)|urinary_tract(1)	4					Alpha-Linolenic Acid(DB00132)|Icosapent(DB00159)	CATAGCTGGCCTGGCGACGCC	0.761																																					p.R55M													.	FADS1	19	0			c.G164T						.						2.0	3.0	3.0					11																	61584238		1475	3343	4818	SO:0001583	missense	3992	exon1			GCTGGCCTGGCGA		CCDS8011.2	11q12-q13.1	2013-01-25			ENSG00000149485	ENSG00000149485	1.14.19.3	"""Fatty acid desaturases"""	3574	protein-coding gene	gene with protein product	"""delta-5 desaturase"""	606148		LLCDL1			Standard	NM_013402		Approved	D5D, FADSD5, TU12, FADS6	uc010rlm.2	O60427	OTTHUMG00000157155	ENST00000350997.7:c.164G>T	11.37:g.61584238C>A	ENSP00000322229:p.Arg55Met	Somatic	22	0		WXS	Illumina GAIIx	Phase_I	14	5	NM_013402	A8K0I7|B2RAI0|Q53GM5|Q8N3A6|Q8NCC7|Q8NCG0|Q96I39|Q96SV3|Q96T10|Q9NRP8|Q9NYX1	Missense_Mutation	SNP	ENST00000350997.7	37	CCDS8011.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	17.26|17.26	3.345407|3.345407	0.61073|0.61073	.|.	.|.	ENSG00000149485|ENSG00000149485	ENST00000491310|ENST00000350997	.|T	.|0.58797	.|0.31	3.3|3.3	-0.845|-0.845	0.10737|0.10737	.|.	.|.	.|.	.|.	.|.	T|T	0.35595|0.35595	0.0937|0.0937	N|N	0.08118|0.08118	0|0	0.09310|0.09310	N|N	0.99999|0.99999	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.30707|0.30707	-0.9969|-0.9969	5|7	.|0.48119	.|T	.|0.1	.|.	8.0557|8.0557	0.30604|0.30604	0.0:0.6348:0.0:0.3652|0.0:0.6348:0.0:0.3652	.|.	.|.	.|.	.|.	C|M	5|55	.|ENSP00000322229:R55M	.|ENSP00000322229:R55M	G|R	-|-	1|2	0|0	FADS1|FADS1	61340814|61340814	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.081000|0.081000	0.17604|0.17604	-0.243000|-0.243000	0.08915|0.08915	-0.159000|-0.159000	0.11021|0.11021	-0.254000|-0.254000	0.11334|0.11334	GGC|AGG	.		0.761	FADS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347648.2	NM_013402	
MALAT1	378938	broad.mit.edu;ucsc.edu	37	11	65268621	65268621	+	lincRNA	SNP	T	T	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr11:65268621T>C	ENST00000534336.1	+	0	3389				AP000769.7_ENST00000602344.1_lincRNA	NR_002819.2		Q9UHZ2	MALAT_HUMAN	metastasis associated lung adenocarcinoma transcript 1 (non-protein coding)																		GACCTGTTTTTACTTCCTCAC	0.388																																					.													.	MALAT1	3	0			.						.						59.0	65.0	63.0					11																	65268621		874	1988	2862			0	.			TGTTTTTACTTCC	AF001540		11q13.1	2013-12-11	2007-11-20		ENSG00000251562	ENSG00000251562		"""Long non-coding RNAs"", ""-"""	29665	non-coding RNA	RNA, long non-coding	"""metastasis associated in lung adenocarcinoma transcript 1"", ""non-protein coding RNA 47"", ""hepcarcin"", ""nuclear enriched abundant transcript 2"", ""nuclear paraspeckle assembly transcript 2 (non-protein coding)"", ""long intergenic non-protein coding RNA 47"""	607924				12970751, 22560368	Standard	NR_002819		Approved	PRO1073, MALAT-1, NCRNA00047, HCN, NEAT2, LINC00047, mascRNA	uc010roh.3	Q9UHZ2	OTTHUMG00000166322		11.37:g.65268621T>C		Somatic	91	0		WXS	Illumina GAIIx	Phase_I	45	25	.		RNA	SNP	ENST00000534336.1	37																																																																																				.		0.388	MALAT1-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000389143.1	NR_002819	
DLAT	1737	broad.mit.edu;ucsc.edu;bcgsc.ca	37	11	111933226	111933226	+	Silent	SNP	G	G	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr11:111933226G>A	ENST00000280346.6	+	14	2570	c.1911G>A	c.(1909-1911)aaG>aaA	p.K637K	DLAT_ENST00000537636.1_Silent_p.K408K|DLAT_ENST00000393051.1_Silent_p.K532K	NM_001931.4	NP_001922.2	P10515	ODP2_HUMAN	dihydrolipoamide S-acetyltransferase	637	Catalytic. {ECO:0000250}.				cellular metabolic process (GO:0044237)|glucose metabolic process (GO:0006006)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	mitochondrial matrix (GO:0005759)|mitochondrial pyruvate dehydrogenase complex (GO:0005967)|mitochondrion (GO:0005739)	dihydrolipoyllysine-residue acetyltransferase activity (GO:0004742)			breast(2)|endometrium(1)|kidney(3)|large_intestine(4)|lung(10)|ovary(1)|skin(1)	22		all_cancers(61;4.53e-11)|all_epithelial(67;2.76e-06)|Melanoma(852;9.42e-06)|all_hematologic(158;0.000885)|Acute lymphoblastic leukemia(157;0.000966)|Breast(348;0.0512)|Medulloblastoma(222;0.0523)|all_neural(223;0.0663)		Epithelial(105;4.87e-07)|BRCA - Breast invasive adenocarcinoma(274;6.83e-07)|all cancers(92;9.63e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.0557)		AGTTTAGAAAGTACCTTGAAA	0.408																																					p.K637K													.	DLAT	39	0			c.G1911A						.						136.0	139.0	138.0					11																	111933226		2201	4297	6498	SO:0001819	synonymous_variant	1737	exon14			TAGAAAGTACCTT	Y00978	CCDS8354.1	11q23.1	2008-02-05	2008-02-04		ENSG00000150768	ENSG00000150768	2.3.1.12		2896	protein-coding gene	gene with protein product	"""E2 component of pyruvate dehydrogenase complex"""	608770		DLTA		8102256	Standard	NM_001931		Approved	PDC-E2	uc001pmo.3	P10515	OTTHUMG00000133751	ENST00000280346.6:c.1911G>A	11.37:g.111933226G>A		Somatic	156	1		WXS	Illumina GAIIx	Phase_I	90	35	NM_001931	Q16783|Q53EP3	Silent	SNP	ENST00000280346.6	37	CCDS8354.1																																																																																			.		0.408	DLAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258167.1	NM_001931	
RDX	5962	broad.mit.edu;ucsc.edu;bcgsc.ca	37	11	110124822	110124822	+	Missense_Mutation	SNP	A	A	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr11:110124822A>T	ENST00000343115.4	-	9	1127	c.808T>A	c.(808-810)Tat>Aat	p.Y270N	RDX_ENST00000530301.1_Intron|RDX_ENST00000544551.1_Missense_Mutation_p.Y134N|RDX_ENST00000528498.1_Missense_Mutation_p.Y270N|RDX_ENST00000405097.1_Missense_Mutation_p.Y270N|RDX_ENST00000528900.1_Intron	NM_001260494.1|NM_002906.3	NP_001247423.1|NP_002897.1	P35241	RADI_HUMAN	radixin	270	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				actin filament capping (GO:0051693)|apical protein localization (GO:0045176)|establishment of endothelial barrier (GO:0061028)|microvillus assembly (GO:0030033)|positive regulation of gene expression (GO:0010628)	apical part of cell (GO:0045177)|cell tip (GO:0051286)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|stereocilium (GO:0032420)|T-tubule (GO:0030315)	poly(A) RNA binding (GO:0044822)			endometrium(3)|kidney(2)|large_intestine(3)|lung(8)|skin(1)|urinary_tract(1)	18		all_cancers(61;7.18e-13)|all_epithelial(67;2.61e-07)|Melanoma(852;1.46e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;3.95e-05)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Breast(348;0.0544)		Epithelial(105;1.13e-06)|BRCA - Breast invasive adenocarcinoma(274;9.75e-06)|all cancers(92;5.9e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0248)		CGAGGTGCATAAAACACAAAA	0.343																																					p.Y270N	Esophageal Squamous(55;25 1062 11040 28755 44273)												.	RDX	59	0			c.T808A						.						71.0	64.0	66.0					11																	110124822		2201	4298	6499	SO:0001583	missense	5962	exon9			GTGCATAAAACAC	BC020751	CCDS8343.1, CCDS58171.1, CCDS58172.1, CCDS58173.1, CCDS58174.1	11q23	2008-03-17				ENSG00000137710			9944	protein-coding gene	gene with protein product		179410	"""deafness, autosomal recessive 24"""	DFNB24		8486357, 17226784	Standard	NM_001260492		Approved		uc031qdy.1	P35241		ENST00000343115.4:c.808T>A	11.37:g.110124822A>T	ENSP00000342830:p.Tyr270Asn	Somatic	71	0		WXS	Illumina GAIIx	Phase_I	40	18	NM_001260493	A7YIJ8|A7YIK0|A7YIK3|B7Z9U6|F5H1A7|Q86Y61	Missense_Mutation	SNP	ENST00000343115.4	37	CCDS8343.1	.	.	.	.	.	.	.	.	.	.	A	20.5	3.995571	0.74703	.	.	ENSG00000137710	ENST00000528498;ENST00000429481;ENST00000405097;ENST00000343115;ENST00000544551	D;D;D;D	0.87966	-2.32;-2.32;-2.32;-2.32	5.72	5.72	0.89469	FERM, C-terminal PH-like domain (1);FERM domain (1);Pleckstrin homology-type (1);	0.000000	0.85682	D	0.000000	D	0.90089	0.6904	L	0.41961	1.31	0.80722	D	1	P;D;B	0.63046	0.523;0.992;0.052	B;D;B	0.66351	0.218;0.943;0.241	D	0.88790	0.3277	10	0.32370	T	0.25	.	16.0055	0.80359	1.0:0.0:0.0:0.0	.	134;270;270	F5H1A7;A7YIJ8;P35241	.;.;RADI_HUMAN	N	270;270;270;270;134	ENSP00000432112:Y270N;ENSP00000384136:Y270N;ENSP00000342830:Y270N;ENSP00000445826:Y134N	ENSP00000342830:Y270N	Y	-	1	0	RDX	109630032	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.274000	0.95731	2.184000	0.69523	0.533000	0.62120	TAT	.		0.343	RDX-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000390535.2	NM_002906	
NLRX1	79671	broad.mit.edu;bcgsc.ca	37	11	119050924	119050924	+	Missense_Mutation	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr11:119050924T>G	ENST00000409109.1	+	7	2781	c.2194T>G	c.(2194-2196)Ttg>Gtg	p.L732V	NLRX1_ENST00000525863.1_Missense_Mutation_p.L732V|NLRX1_ENST00000409265.4_Missense_Mutation_p.L732V|NLRX1_ENST00000409991.1_Missense_Mutation_p.L732V|NLRX1_ENST00000292199.2_Missense_Mutation_p.L732V	NM_001282144.1	NP_001269073.1	Q86UT6	NLRX1_HUMAN	NLR family member X1	732	Required for the repression of MAVS- induced interferon signaling.				innate immune response (GO:0045087)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of inflammatory response (GO:0050728)|negative regulation of innate immune response (GO:0045824)|negative regulation of interferon-beta production (GO:0032688)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of RIG-I signaling pathway (GO:0039536)|negative regulation of type I interferon production (GO:0032480)|viral process (GO:0016032)	mitochondrial outer membrane (GO:0005741)	ATP binding (GO:0005524)			cervix(1)|endometrium(2)|kidney(2)|lung(10)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)	22	all_hematologic(175;0.0977)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.7e-05)		TGAGGTGAACTTGGCCTCCTG	0.627																																					p.L732V													.	NLRX1	128	0			c.T2194G						.						49.0	46.0	47.0					11																	119050924		2200	4295	6495	SO:0001583	missense	79671	exon7			GTGAACTTGGCCT	AB094095	CCDS8416.1	11q23.3	2007-02-07			ENSG00000160703	ENSG00000160703		"""Nucleotide-binding domain and leucine rich repeat containing"""	29890	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat containing X1"", ""NOD-like receptor X1"", ""NLR family, X1"""	611947				12766759	Standard	XM_005271669		Approved	NOD9, CLR11.3	uc001pvw.3	Q86UT6	OTTHUMG00000154476	ENST00000409109.1:c.2194T>G	11.37:g.119050924T>G	ENSP00000387334:p.Leu732Val	Somatic	21	0		WXS	Illumina GAIIx	Phase_I	8	3	NM_024618	A8K6Q1|B3KPK2|B3KTA2|Q7RTR3|Q96D51|Q9H724	Missense_Mutation	SNP	ENST00000409109.1	37	CCDS8416.1	.	.	.	.	.	.	.	.	.	.	T	14.16	2.452222	0.43531	.	.	ENSG00000160703	ENST00000409991;ENST00000292199;ENST00000409265;ENST00000409109;ENST00000525863	T;T;T;T;T	0.74526	-0.85;-0.85;-0.85;-0.85;-0.85	5.17	2.89	0.33648	.	0.087215	0.45867	D	0.000328	T	0.63792	0.2541	L	0.32530	0.975	0.39671	D	0.97075	P;P	0.38827	0.649;0.598	B;B	0.42495	0.359;0.389	T	0.67764	-0.5586	10	0.87932	D	0	.	6.5796	0.22585	0.0:0.2238:0.0:0.7762	.	732;732	Q86UT6-2;Q86UT6	.;NLRX1_HUMAN	V	732	ENSP00000386851:L732V;ENSP00000292199:L732V;ENSP00000386858:L732V;ENSP00000387334:L732V;ENSP00000433442:L732V	ENSP00000292199:L732V	L	+	1	2	NLRX1	118556134	1.000000	0.71417	1.000000	0.80357	0.273000	0.26683	2.681000	0.46926	1.958000	0.56883	0.260000	0.18958	TTG	.		0.627	NLRX1-004	PUTATIVE	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335403.1	NM_170722	
LOC100507431	100507431	broad.mit.edu;ucsc.edu	37	11	130731697	130731697	+	lincRNA	SNP	C	C	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr11:130731697C>T	ENST00000533812.2	-	0	919																											TGTGAATTTCCGTTGAACACG	0.498											OREG0021520	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									.													.	.	.	0			.						.																																					0	.			AATTTCCGTTGAA																													11.37:g.130731697C>T		Somatic	58	0	1582	WXS	Illumina GAIIx	Phase_I	41	15	.		RNA	SNP	ENST00000533812.2	37		.	.	.	.	.	.	.	.	.	.	C	10.50	1.366696	0.24771	.	.	ENSG00000254842	ENST00000533812	.	.	.	3.1	-5.42	0.02640	.	.	.	.	.	T	0.19087	0.0458	.	.	.	.	.	.	B	0.14438	0.01	B	0.04013	0.001	T	0.30031	-0.9992	6	0.87932	D	0	.	0.9325	0.01338	0.161:0.3061:0.1642:0.3687	.	32	G5EA22	.	Q	32	.	ENSP00000436275:R32Q	R	-	2	0	RP11-890B15.2	130236907	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.150000	0.10189	-1.045000	0.03250	-0.423000	0.05987	CGG	.		0.498	RP11-890B15.2-001	KNOWN	basic|exp_conf	lincRNA	lincRNA	OTTHUMT00000385642.2		
A2M	2	broad.mit.edu	37	12	9264989	9264989	+	Nonsense_Mutation	SNP	G	G	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr12:9264989G>T	ENST00000318602.7	-	3	721	c.414C>A	c.(412-414)taC>taA	p.Y138*		NM_000014.4	NP_000005	P01023	A2MG_HUMAN	alpha-2-macroglobulin	138					blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of complement activation, lectin pathway (GO:0001869)|negative regulation of endopeptidase activity (GO:0010951)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|stem cell differentiation (GO:0048863)	blood microparticle (GO:0072562)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|platelet alpha granule lumen (GO:0031093)	calcium-dependent protein binding (GO:0048306)|enzyme binding (GO:0019899)|growth factor binding (GO:0019838)|interleukin-1 binding (GO:0019966)|interleukin-8 binding (GO:0019959)|protease binding (GO:0002020)|receptor binding (GO:0005102)|serine-type endopeptidase inhibitor activity (GO:0004867)|tumor necrosis factor binding (GO:0043120)			breast(1)|central_nervous_system(6)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(17)|lung(30)|ovary(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	77					Bacitracin(DB00626)|Becaplermin(DB00102)|Ocriplasmin(DB08888)	GCCCTGGTTTGTAGATTGATT	0.448																																					p.Y138X													.	A2M	180	0			c.C414A						.						99.0	93.0	95.0					12																	9264989		1933	4158	6091	SO:0001587	stop_gained	2	exon3			TGGTTTGTAGATT	BX647329, X68728, M11313	CCDS44827.1	12p13.31	2010-02-24			ENSG00000175899	ENSG00000175899			7	protein-coding gene	gene with protein product		103950					Standard	XM_006719056		Approved	FWP007, S863-7, CPAMD5	uc001qvk.1	P01023	OTTHUMG00000150267	ENST00000318602.7:c.414C>A	12.37:g.9264989G>T	ENSP00000323929:p.Tyr138*	Somatic	91	0		WXS	Illumina GAIIx	Phase_I	61	3	NM_000014	Q13677|Q59F47|Q5QTS0|Q68DN2|Q6PIY3|Q6PN97	Nonsense_Mutation	SNP	ENST00000318602.7	37	CCDS44827.1	.	.	.	.	.	.	.	.	.	.	G	17.78	3.472401	0.63737	.	.	ENSG00000175899	ENST00000318602;ENST00000540099;ENST00000404455	.	.	.	5.53	2.73	0.32206	.	0.000000	0.64402	D	0.000007	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	7.5016	0.27522	0.2678:0.0:0.7322:0.0	.	.	.	.	X	138;153;138	.	ENSP00000323929:Y138X	Y	-	3	2	A2M	9156256	1.000000	0.71417	1.000000	0.80357	0.577000	0.36160	1.326000	0.33735	0.308000	0.22923	0.650000	0.86243	TAC	.		0.448	A2M-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317233.2	NM_000014	
CFAP54	144535	broad.mit.edu;ucsc.edu;bcgsc.ca	37	12	96883547	96883547	+	Missense_Mutation	SNP	G	G	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr12:96883547G>C	ENST00000524981.4	+	1	183	c.160G>C	c.(160-162)Gac>Cac	p.D54H	C12orf55_ENST00000298953.3_Missense_Mutation_p.D54H			Q96N23	CL055_HUMAN		54																	CTGCCCCGAGGACTCATTGCC	0.617											OREG0022044	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									.													.	.	.	0			.						.																																			SO:0001583	missense	144535	.			CCCGAGGACTCAT																												ENST00000524981.4:c.160G>C	12.37:g.96883547G>C	ENSP00000431759:p.Asp54His	Somatic	139	0	1324	WXS	Illumina GAIIx	Phase_I	77	31	.		Missense_Mutation	SNP	ENST00000524981.4	37		.	.	.	.	.	.	.	.	.	.	G	23.6	4.437804	0.83885	.	.	ENSG00000188596	ENST00000553778;ENST00000524981;ENST00000298953	T;T	0.27402	1.67;1.74	4.89	1.93	0.25924	.	0.919749	0.09306	N	0.820275	T	0.30448	0.0765	L	0.51422	1.61	0.18873	N	0.999985	P	0.47677	0.899	P	0.44921	0.464	T	0.15694	-1.0428	10	0.51188	T	0.08	-0.0845	6.6189	0.22792	0.3229:0.0:0.6771:0.0	.	54	G3V4Y4	.	H	54	ENSP00000452066:D54H;ENSP00000298953:D54H	ENSP00000298953:D54H	D	+	1	0	C12orf63	95407678	0.001000	0.12720	0.139000	0.22197	0.894000	0.52154	0.431000	0.21444	0.610000	0.30035	0.561000	0.74099	GAC	.		0.617	C12orf55-003	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000395046.4		
RARG	5916	broad.mit.edu	37	12	53607314	53607314	+	Silent	SNP	T	T	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr12:53607314T>A	ENST00000425354.2	-	8	1471	c.984A>T	c.(982-984)acA>acT	p.T328T	RARG_ENST00000394426.1_Silent_p.T328T|RARG_ENST00000327550.3_Silent_p.T256T|RARG_ENST00000543762.1_5'UTR|RARG_ENST00000543726.1_Silent_p.T306T|RARG_ENST00000338561.5_Silent_p.T317T	NM_000966.5	NP_000957.1	P13631	RARG_HUMAN	retinoic acid receptor, gamma	328	Ligand-binding.				anterior/posterior pattern specification (GO:0009952)|canonical Wnt signaling pathway (GO:0060070)|cellular response to retinoic acid (GO:0071300)|embryonic camera-type eye development (GO:0031076)|embryonic eye morphogenesis (GO:0048048)|embryonic hindlimb morphogenesis (GO:0035116)|face development (GO:0060324)|gene expression (GO:0010467)|glandular epithelial cell development (GO:0002068)|growth plate cartilage chondrocyte growth (GO:0003430)|Harderian gland development (GO:0070384)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cartilage development (GO:0061037)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell proliferation (GO:0008284)|positive regulation of programmed cell death (GO:0043068)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|prostate gland epithelium morphogenesis (GO:0060740)|regulation of cell size (GO:0008361)|regulation of myelination (GO:0031641)|response to retinoic acid (GO:0032526)|retinal pigment epithelium development (GO:0003406)|retinoic acid receptor signaling pathway (GO:0048384)|trachea cartilage development (GO:0060534)|transcription initiation from RNA polymerase II promoter (GO:0006367)	integral component of membrane (GO:0016021)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|retinoic acid receptor activity (GO:0003708)|retinoid X receptor binding (GO:0046965)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			breast(3)|endometrium(3)|kidney(1)|large_intestine(6)|lung(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20					Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Tazarotene(DB00799)|Tretinoin(DB00755)	TGAGCAGCCCTGTCTCGGTGT	0.642											OREG0021862	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.T328T													.	RARG	53	0			c.A984T						.						45.0	44.0	44.0					12																	53607314		2203	4300	6503	SO:0001819	synonymous_variant	5916	exon8			CAGCCCTGTCTCG	M57707	CCDS8850.1, CCDS41790.1, CCDS58236.1, CCDS58237.1	12q13	2013-01-16			ENSG00000172819	ENSG00000172819		"""Nuclear hormone receptors"""	9866	protein-coding gene	gene with protein product		180190				1849262	Standard	NM_001042728		Approved	RARC, NR1B3	uc001scf.3	P13631	OTTHUMG00000048077	ENST00000425354.2:c.984A>T	12.37:g.53607314T>A		Somatic	21	0	993	WXS	Illumina GAIIx	Phase_I	12	3	NM_000966	B7Z492|B7Z4F1|B7ZAE4|J3KNP6|P22932|Q15281|Q52LZ8|Q9BYX8|Q9H1I3|Q9UJ38	Silent	SNP	ENST00000425354.2	37	CCDS8850.1																																																																																			.		0.642	RARG-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000109404.2	NM_000966	
TIMELESS	8914	broad.mit.edu	37	12	56822671	56822671	+	Missense_Mutation	SNP	G	G	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr12:56822671G>A	ENST00000553532.1	-	11	1450	c.1300C>T	c.(1300-1302)Cgc>Tgc	p.R434C	TIMELESS_ENST00000229201.4_Missense_Mutation_p.R433C|TIMELESS_ENST00000554616.1_Intron					timeless circadian clock											NS(1)|breast(2)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(8)|lung(14)|ovary(7)|pancreas(2)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	49						ACTCACCGGCGTGCCCAGGAG	0.512																																					p.R434C													.	TIMELESS	107	0			c.C1300T						.						92.0	80.0	84.0					12																	56822671		2203	4300	6503	SO:0001583	missense	8914	exon11			ACCGGCGTGCCCA	AF098162	CCDS8918.1	12q13.3	2012-12-14	2012-12-14		ENSG00000111602	ENSG00000111602			11813	protein-coding gene	gene with protein product	"""Tof1 homolog (S. cerevisiae)"", ""timeless circadian clock 1"""	603887	"""timeless (Drosophila) homolog"", ""timeless homolog (Drosophila)"""			9856465	Standard	NM_003920		Approved	hTIM, TIM, TIM1	uc001slf.2	Q9UNS1	OTTHUMG00000170600	ENST00000553532.1:c.1300C>T	12.37:g.56822671G>A	ENSP00000450607:p.Arg434Cys	Somatic	17	0		WXS	Illumina GAIIx	Phase_I	15	4	NM_003920		Missense_Mutation	SNP	ENST00000553532.1	37	CCDS8918.1	.	.	.	.	.	.	.	.	.	.	G	15.67	2.902474	0.52227	.	.	ENSG00000111602	ENST00000229201;ENST00000553532	T;T	0.10382	2.88;2.89	4.95	4.06	0.47325	.	0.057662	0.64402	N	0.000001	T	0.14960	0.0361	M	0.83012	2.62	0.80722	D	1	B;B	0.28026	0.198;0.125	B;B	0.21546	0.035;0.015	T	0.02132	-1.1208	10	0.48119	T	0.1	.	8.1353	0.31050	0.0851:0.0:0.7578:0.1572	.	433;434	Q9UNS1-2;Q9UNS1	.;TIM_HUMAN	C	433;434	ENSP00000229201:R433C;ENSP00000450607:R434C	ENSP00000229201:R434C	R	-	1	0	TIMELESS	55108938	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	4.347000	0.59373	1.217000	0.43442	0.462000	0.41574	CGC	.		0.512	TIMELESS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000409771.1	NM_003920	
PSMD9	5715	broad.mit.edu	37	12	122326825	122326825	+	Silent	SNP	C	C	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr12:122326825C>T	ENST00000541212.1	+	1	189	c.63C>T	c.(61-63)agC>agT	p.S21S	PSMD9_ENST00000261817.2_Silent_p.S21S|RP11-87C12.2_ENST00000546333.1_Silent_p.S21S|PSMD9_ENST00000542602.1_Silent_p.S21S|PSMD9_ENST00000340175.5_Silent_p.S21S			O00233	PSMD9_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 9	21					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of insulin secretion (GO:0046676)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of insulin secretion (GO:0032024)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|proteasome regulatory particle assembly (GO:0070682)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome regulatory particle (GO:0005838)	bHLH transcription factor binding (GO:0043425)|transcription coactivator activity (GO:0003713)			endometrium(1)|large_intestine(1)|lung(1)	3	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)			OV - Ovarian serous cystadenocarcinoma(86;0.000117)|Epithelial(86;0.000415)|BRCA - Breast invasive adenocarcinoma(302;0.231)		TGACTGTCAGCGACGTCCAGG	0.662											OREG0022209	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.S21S													.	PSMD9	8	0			c.C63T						.						34.0	21.0	26.0					12																	122326825		2201	4299	6500	SO:0001819	synonymous_variant	5715	exon1			TGTCAGCGACGTC	AB003177	CCDS9225.1, CCDS58284.1	12q24.31-q24.32	2008-05-22			ENSG00000110801	ENSG00000110801		"""Proteasome (prosome, macropain) subunits"""	9567	protein-coding gene	gene with protein product		603146				9653651	Standard	NM_002813		Approved	p27, Rpn4	uc001ubl.4	O00233	OTTHUMG00000168945	ENST00000541212.1:c.63C>T	12.37:g.122326825C>T		Somatic	68	0	1518	WXS	Illumina GAIIx	Phase_I	38	3	NM_001261400	B2RD35|G3V1Q6|Q9BQ42	Silent	SNP	ENST00000541212.1	37	CCDS9225.1																																																																																			.		0.662	PSMD9-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000401686.1	NM_002813	
LRRC63	220416	broad.mit.edu;ucsc.edu;bcgsc.ca	37	13	46802187	46802187	+	Missense_Mutation	SNP	C	C	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr13:46802187C>T	ENST00000595396.1	+	2	626	c.626C>T	c.(625-627)tCt>tTt	p.S209F	LRRC63_ENST00000446175.1_Missense_Mutation_p.S209F			Q05C16	LRC63_HUMAN	leucine rich repeat containing 63	209										lung(1)|ovary(1)	2						ATGACTGTATCTATGAAACCA	0.433																																					.													.	.	.	0			.						.																																			SO:0001583	missense	220416	.			CTGTATCTATGAA		CCDS61325.1	13q14.12	2014-02-12			ENSG00000173988	ENSG00000173988			34296	protein-coding gene	gene with protein product							Standard	NM_001282460		Approved	RP11-139H14.4	uc001vbc.3	Q05C16	OTTHUMG00000016866	ENST00000595396.1:c.626C>T	13.37:g.46802187C>T	ENSP00000469337:p.Ser209Phe	Somatic	85	0		WXS	Illumina GAIIx	Phase_I	51	22	.	Q5TBN0	Missense_Mutation	SNP	ENST00000595396.1	37		.	.	.	.	.	.	.	.	.	.	C	13.30	2.196911	0.38806	.	.	ENSG00000173988	ENST00000378805;ENST00000446175	T;T	0.01430	4.9;4.94	3.93	3.08	0.35506	.	1.008330	0.07971	N	0.984034	T	0.01800	0.0057	N	0.24115	0.695	0.09310	N	1	P	0.50943	0.94	P	0.44732	0.459	T	0.55617	-0.8113	10	0.51188	T	0.08	-9.6642	9.0753	0.36517	0.2184:0.7816:0.0:0.0	.	209	Q05C16	LRC63_HUMAN	F	209	ENSP00000368082:S209F;ENSP00000408828:S209F	ENSP00000368082:S209F	S	+	2	0	LRRC63	45700188	0.000000	0.05858	0.010000	0.14722	0.003000	0.03518	0.163000	0.16520	1.207000	0.43291	0.591000	0.81541	TCT	.		0.433	LRRC63-002	NOVEL	not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000463266.1	XM_001718341	
ADAM21	8747	broad.mit.edu;bcgsc.ca	37	14	70924269	70924269	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr14:70924269G>T	ENST00000603540.1	+	2	311	c.53G>T	c.(52-54)tGg>tTg	p.W18L	ADAM21_ENST00000267499.3_Missense_Mutation_p.W18L|RP11-486O13.4_ENST00000556646.1_lincRNA	NM_003813.3	NP_003804.2	Q9UKJ8	ADA21_HUMAN	ADAM metallopeptidase domain 21	18					binding of sperm to zona pellucida (GO:0007339)|multicellular organism reproduction (GO:0032504)|single fertilization (GO:0007338)	axon (GO:0030424)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(10)|lung(10)|pancreas(1)|prostate(1)|skin(2)|stomach(1)	31				all cancers(60;0.00326)|BRCA - Breast invasive adenocarcinoma(234;0.00646)|OV - Ovarian serous cystadenocarcinoma(108;0.0401)		CTGCTGCTCTGGCTTGGGGTA	0.532																																					p.W18L													.	ADAM21	181	0			c.G53T						.						91.0	107.0	102.0					14																	70924269		2203	4300	6503	SO:0001583	missense	8747	exon2			TGCTCTGGCTTGG	AF029900	CCDS9804.1	14q24.1	2008-09-05	2005-08-18		ENSG00000139985	ENSG00000139985		"""ADAM metallopeptidase domain containing"""	200	protein-coding gene	gene with protein product		603713	"""a disintegrin and metalloproteinase domain 21"""			9469942	Standard	NM_003813		Approved	ADAM31	uc001xmd.3	Q9UKJ8		ENST00000603540.1:c.53G>T	14.37:g.70924269G>T	ENSP00000474385:p.Trp18Leu	Somatic	27	0		WXS	Illumina GAIIx	Phase_I	11	6	NM_003813	O43507|Q2VPC6|Q32MR0	Missense_Mutation	SNP	ENST00000603540.1	37	CCDS9804.1	.	.	.	.	.	.	.	.	.	.	G	11.03	1.517700	0.27123	.	.	ENSG00000139985	ENST00000267499	T	0.01025	5.43	3.77	1.89	0.25635	.	0.259259	0.20634	U	0.088524	T	0.00608	0.0020	N	0.08118	0	0.09310	N	1	B	0.06786	0.001	B	0.14023	0.01	T	0.48811	-0.9002	10	0.48119	T	0.1	.	5.0295	0.14402	0.1711:0.0:0.6447:0.1842	.	18	Q9UKJ8	ADA21_HUMAN	L	18	ENSP00000267499:W18L	ENSP00000267499:W18L	W	+	2	0	ADAM21	69994022	0.020000	0.18652	0.853000	0.33588	0.169000	0.22640	0.563000	0.23547	0.912000	0.36772	-0.261000	0.10672	TGG	.		0.532	ADAM21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413008.3		
ASB2	51676	broad.mit.edu;ucsc.edu;bcgsc.ca	37	14	94401066	94401066	+	Missense_Mutation	SNP	A	A	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr14:94401066A>G	ENST00000315988.4	-	8	2188	c.1700T>C	c.(1699-1701)cTc>cCc	p.L567P	ASB2_ENST00000555019.1_Missense_Mutation_p.L615P	NM_016150.4	NP_057234.2	Q96Q27	ASB2_HUMAN	ankyrin repeat and SOCS box containing 2	567	SOCS box. {ECO:0000255|PROSITE- ProRule:PRU00194}.				intracellular signal transduction (GO:0035556)|myoblast differentiation (GO:0045445)|protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|signal transduction (GO:0007165)|skeletal muscle cell differentiation (GO:0035914)	Cul5-RING ubiquitin ligase complex (GO:0031466)	ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(8)|ovary(2)|pancreas(1)|prostate(3)|skin(1)|soft_tissue(1)|urinary_tract(1)	27		all_cancers(154;0.13)		COAD - Colon adenocarcinoma(157;0.217)|Epithelial(152;0.232)		GGTGTCTAGGAGTTTTATACG	0.537																																					p.L615P													.	ASB2	71	0			c.T1844C						.						106.0	107.0	107.0					14																	94401066		2203	4300	6503	SO:0001583	missense	51676	exon10			TCTAGGAGTTTTA	AF159164	CCDS9915.1, CCDS55940.1	14q31-q32	2013-01-10	2011-01-25					"""Ankyrin repeat domain containing"""	16012	protein-coding gene	gene with protein product		605759	"""ankyrin repeat and SOCS box-containing 2"""				Standard	NM_016150		Approved	ASB-2	uc001ycd.3	Q96Q27		ENST00000315988.4:c.1700T>C	14.37:g.94401066A>G	ENSP00000320675:p.Leu567Pro	Somatic	81	2		WXS	Illumina GAIIx	Phase_I	58	25	NM_001202429	B2RDP9|B4E166|Q9NSU5|Q9Y567	Missense_Mutation	SNP	ENST00000315988.4	37	CCDS9915.1	.	.	.	.	.	.	.	.	.	.	A	15.28	2.787806	0.49997	.	.	ENSG00000100628	ENST00000555019;ENST00000434324;ENST00000315988	T;T	0.47869	0.83;0.83	5.16	5.16	0.70880	SOCS protein, C-terminal (3);	0.165190	0.39909	N	0.001236	T	0.71693	0.3370	M	0.87269	2.87	0.58432	D	0.999998	D;D	0.89917	1.0;0.999	D;D	0.97110	1.0;0.959	T	0.74396	-0.3679	10	0.36615	T	0.2	-17.7588	15.0105	0.71547	1.0:0.0:0.0:0.0	.	615;567	B4E166;Q96Q27	.;ASB2_HUMAN	P	615;583;567	ENSP00000451575:L615P;ENSP00000320675:L567P	ENSP00000320675:L567P	L	-	2	0	ASB2	93470819	0.977000	0.34250	1.000000	0.80357	0.985000	0.73830	2.384000	0.44362	1.951000	0.56629	0.402000	0.26972	CTC	.		0.537	ASB2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000412845.1		
AHNAK2	113146	broad.mit.edu	37	14	105414880	105414880	+	Missense_Mutation	SNP	T	T	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr14:105414880T>C	ENST00000333244.5	-	7	7027	c.6908A>G	c.(6907-6909)gAc>gGc	p.D2303G	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	2303						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)				cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			CAGGGACATGTCCCCCTCCAG	0.602																																					p.D2303G													.	AHNAK2	719	0			c.A6908G						.						175.0	193.0	187.0					14																	105414880		2036	4197	6233	SO:0001583	missense	113146	exon7			GACATGTCCCCCT	AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"""chromosome 14 open reading frame 78"""	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.6908A>G	14.37:g.105414880T>C	ENSP00000353114:p.Asp2303Gly	Somatic	131	0		WXS	Illumina GAIIx	Phase_I	74	3	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	.	.	.	.	.	.	.	.	.	.	N	15.85	2.953458	0.53293	.	.	ENSG00000185567	ENST00000333244	T	0.01279	5.06	3.76	3.76	0.43208	.	.	.	.	.	T	0.03390	0.0098	M	0.87180	2.865	0.18873	N	0.999986	B	0.27765	0.188	B	0.27796	0.083	T	0.25779	-1.0122	9	0.26408	T	0.33	.	10.0825	0.42399	0.0:0.0:0.1682:0.8318	.	2303	Q8IVF2	AHNK2_HUMAN	G	2303	ENSP00000353114:D2303G	ENSP00000353114:D2303G	D	-	2	0	AHNAK2	104485925	0.770000	0.28543	0.018000	0.16275	0.025000	0.11179	3.465000	0.53064	1.329000	0.45376	0.254000	0.18369	GAC	.		0.602	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
KIAA0125	9834	broad.mit.edu	37	14	106382684	106382684	+	5'Flank	SNP	G	G	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr14:106382684G>T	ENST00000449410.1	+	0	0				IGHD3-3_ENST00000390590.1_RNA|IGHD1-1_ENST00000454908.1_RNA|KIAA0125_ENST00000429431.1_5'Flank|IGHD2-2_ENST00000390591.1_RNA			Q9NZY2	K0125_HUMAN	KIAA0125																		GTGTCACTGTGGGCATAGCAG	0.592																																					.													.	.	.	0			.						.						76.0	77.0	77.0					14																	106382684		1889	4098	5987	SO:0001631	upstream_gene_variant	0	.			CACTGTGGGCATA	AB019441		14q32.33	2014-04-01			ENSG00000226777	ENSG00000226777			19955	other	unknown			"""family with sequence similarity 30, member A"", ""chromosome 14 open reading frame 110"""	FAM30A, C14orf110		8590280	Standard	NR_026800		Approved	HSPC053	uc001ysq.3	Q9NZY2	OTTHUMG00000152318		14.37:g.106382684G>T	Exception_encountered	Somatic	127	1		WXS	Illumina GAIIx	Phase_I	74	29	.	C9J8W9	RNA	SNP	ENST00000449410.1	37																																																																																				.		0.592	KIAA0125-001	PUTATIVE	basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000325876.1	NM_014792	
PSMC1	5700	broad.mit.edu;bcgsc.ca	37	14	90736595	90736609	+	In_Frame_Del	DEL	CGCATCTTTCAGATT	CGCATCTTTCAGATT	-			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr14:90736595_90736609delCGCATCTTTCAGATT	ENST00000261303.8	+	10	1190_1204	c.1087_1101delCGCATCTTTCAGATT	c.(1087-1101)cgcatctttcagattdel	p.RIFQI363del	PSMC1_ENST00000543772.2_In_Frame_Del_p.RIFQI290del	NM_002802.2	NP_002793.2	P62191	PRS4_HUMAN	proteasome (prosome, macropain) 26S subunit, ATPase, 1	363					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|ATP catabolic process (GO:0006200)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)|proteasome regulatory particle (GO:0005838)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|poly(A) RNA binding (GO:0044822)			endometrium(2)|kidney(2)|upper_aerodigestive_tract(2)	6		all_cancers(154;0.142)		COAD - Colon adenocarcinoma(157;0.21)		GACGAAGAAGCGCATCTTTCAGATTCACACAAGCA	0.502																																					p.363_367del													.	PSMC1	27	0			c.1087_1101del						.																																			SO:0001651	inframe_deletion	5700	exon10			AAGAAGCGCATCT	L02426	CCDS32139.1	14q32.11	2010-04-21			ENSG00000100764	ENSG00000100764		"""Proteasome (prosome, macropain) subunits"", ""ATPases / AAA-type"""	9547	protein-coding gene	gene with protein product		602706				9473509	Standard	NM_002802		Approved	S4, p56	uc001xyf.3	P62191		ENST00000261303.8:c.1087_1101delCGCATCTTTCAGATT	14.37:g.90736595_90736609delCGCATCTTTCAGATT	ENSP00000261303:p.Arg363_Ile367del	Somatic	68	0		WXS	Illumina GAIIx	Phase_I	28	6	NM_002802	B4DR63|P49014|Q03527|Q6IAW0|Q6NW36|Q96AZ3	In_Frame_Del	DEL	ENST00000261303.8	37	CCDS32139.1																																																																																			.		0.502	PSMC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411253.1	NM_002802	
IGHV3-48	28424	broad.mit.edu;ucsc.edu;bcgsc.ca	37	14	106993973	106993973	+	RNA	SNP	C	C	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr14:106993973C>T	ENST00000390624.2	-	0	270									immunoglobulin heavy variable 3-48																		AAACCCACTCCAGCCCCTTCC	0.527																																					.													.	.	.	0			.						.						120.0	134.0	130.0					14																	106993973		1843	4086	5929			0	.			CCACTCCAGCCCC	M99675		14q32.33	2012-02-08			ENSG00000211964	ENSG00000211964		"""Immunoglobulins / IGH locus"""	5606	other	immunoglobulin gene							Standard	NG_001019		Approved				OTTHUMG00000151959		14.37:g.106993973C>T		Somatic	114	0		WXS	Illumina GAIIx	Phase_I	48	23	.		RNA	SNP	ENST00000390624.2	37																																																																																				.		0.527	IGHV3-48-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal	IG_V_gene	IG_V_gene	OTTHUMT00000324605.1	NG_001019	
NPIPB7	440350	broad.mit.edu	37	16	28468222	28468222	+	Silent	SNP	T	T	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr16:28468222T>A	ENST00000452313.1	-	7	876	c.768A>T	c.(766-768)atA>atT	p.I256I	RP11-57A19.5_ENST00000602838.1_lincRNA			O75200	NPIB7_HUMAN	nuclear pore complex interacting protein family, member B7	256	Pro-rich.					extracellular region (GO:0005576)											AGTTATCAGTTATAGAATGTT	0.502																																					.													.	.	.	0			.						.																																			SO:0001819	synonymous_variant	0	.			ATCAGTTATAGAA	BC156858, AC002425		16p11.2	2013-06-11	2013-06-11	2013-06-11	ENSG00000233232	ENSG00000233232			33832	other	unknown			"""nuclear pore complex interacting protein-like 1"""	NPIPL1			Standard	NG_023370		Approved	LOC440350	uc010vcq.2	O75200	OTTHUMG00000156915	ENST00000452313.1:c.768A>T	16.37:g.28468222T>A		Somatic	122	0		WXS	Illumina GAIIx	Phase_I	63	16	.	E7ERT9	Silent	SNP	ENST00000452313.1	37																																																																																				.		0.502	NPIPB7-001	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000346596.1	NG_023370	
SNX29P2	440352	broad.mit.edu	37	16	29449546	29449582	+	lincRNA	DEL	TAAACATTAAAAGACAGTTACTTTCAGCTGGCCAAAA	TAAACATTAAAAGACAGTTACTTTCAGCTGGCCAAAA	-	rs544276913		TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr16:29449546_29449582delTAAACATTAAAAGACAGTTACTTTCAGCTGGCCAAAA	ENST00000398878.3	+	0	5991				snoU13_ENST00000458775.1_RNA			Q8IUI4	S29P2_HUMAN	sorting nexin 29 pseudogene 2																		CGAGAGCTATTAAACATTAAAAGACAGTTACTTTCAGCTGGCCAAAAGAAATTATAT	0.397																																					.													.	.	.	0			.						.																																					0	.			AGCTATTAAACAT	BX648280		16p11.2	2014-03-21	2011-08-16	2011-08-16	ENSG00000198106	ENSG00000198106			31914	pseudogene	pseudogene			"""RUN domain containing 2C"""	RUNDC2C			Standard	NR_002939		Approved		uc021tfw.1	Q8IUI4			16.37:g.29449546_29449582delTAAACATTAAAAGACAGTTACTTTCAGCTGGCCAAAA		Somatic	329	0		WXS	Illumina GAIIx	Phase_I	158	5	.		RNA	DEL	ENST00000398878.3	37																																																																																				.		0.397	SNX29P2-202	KNOWN	basic	lincRNA	lincRNA		NR_002939	
LINC01566	283914	broad.mit.edu;bcgsc.ca	37	16	34624256	34624256	+	lincRNA	SNP	C	C	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr16:34624256C>T	ENST00000569242.1	+	0	2102					NR_027079.1																						TGCAGCTGAACCATCTGTTTT	0.383																																					.													.	.	.	0			.						.																																					0	.			GCTGAACCATCTG																													16.37:g.34624256C>T		Somatic	19	0		WXS	Illumina GAIIx	Phase_I	11	3	.		RNA	SNP	ENST00000569242.1	37																																																																																				.		0.383	RP11-488I20.3-002	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000431678.1		
PDP2	57546	broad.mit.edu	37	16	66918662	66918662	+	Missense_Mutation	SNP	T	T	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr16:66918662T>C	ENST00000311765.2	+	2	809	c.475T>C	c.(475-477)Tat>Cat	p.Y159H	PDP2_ENST00000568720.1_Intron	NM_020786.2	NP_065837.1	Q9P2J9	PDP2_HUMAN	pyruvate dehyrogenase phosphatase catalytic subunit 2	159					cellular metabolic process (GO:0044237)|peptidyl-threonine dephosphorylation (GO:0035970)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)	[pyruvate dehydrogenase (lipoamide)] phosphatase activity (GO:0004741)|magnesium-dependent protein serine/threonine phosphatase activity (GO:0004724)|metal ion binding (GO:0046872)			kidney(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|urinary_tract(1)	12		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.088)|Epithelial(162;0.204)		GCTCTTCTACTATGTGGCAGT	0.542																																					p.Y159H													.	PDP2	39	0			c.T475C						.						91.0	68.0	76.0					16																	66918662		2200	4300	6500	SO:0001583	missense	57546	exon2			TTCTACTATGTGG	AB037769	CCDS10822.1	16q22.1	2012-04-17			ENSG00000172840	ENSG00000172840		"""Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"""	30263	protein-coding gene	gene with protein product	"""protein phosphatase 2C, magnesium-dependent, catalytic subunit 2"""	615499				9651365	Standard	NM_020786		Approved	KIAA1348, PPM2C2	uc002eqk.2	Q9P2J9	OTTHUMG00000137512	ENST00000311765.2:c.475T>C	16.37:g.66918662T>C	ENSP00000309548:p.Tyr159His	Somatic	10	0		WXS	Illumina GAIIx	Phase_I	9	3	NM_020786	A8K924	Missense_Mutation	SNP	ENST00000311765.2	37	CCDS10822.1	.	.	.	.	.	.	.	.	.	.	T	22.3	4.269859	0.80469	.	.	ENSG00000172840	ENST00000311765	T	0.09350	2.99	5.74	5.74	0.90152	Protein phosphatase 2C-like (4);	0.000000	0.85682	D	0.000000	T	0.39682	0.1087	M	0.87682	2.9	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.34700	-0.9818	10	0.51188	T	0.08	-11.9154	16.338	0.83073	0.0:0.0:0.0:1.0	.	159	Q9P2J9	PDP2_HUMAN	H	159	ENSP00000309548:Y159H	ENSP00000309548:Y159H	Y	+	1	0	PDP2	65476163	1.000000	0.71417	0.989000	0.46669	0.996000	0.88848	7.977000	0.88081	2.319000	0.78375	0.528000	0.53228	TAT	.		0.542	PDP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268831.2	NM_020786	
ABCA9	10350	broad.mit.edu;bcgsc.ca	37	17	67014691	67014706	+	Frame_Shift_Del	DEL	GGGATAAAGCTAATAC	GGGATAAAGCTAATAC	-			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr17:67014691_67014706delGGGATAAAGCTAATAC	ENST00000340001.4	-	20	2826_2841	c.2615_2630delGTATTAGCTTTATCCC	c.(2614-2631)ggtattagctttatccctfs	p.GISFIP872fs	ABCA9_ENST00000453985.2_Frame_Shift_Del_p.GISFIP872fs|ABCA9-AS1_ENST00000458677.1_RNA|ABCA9_ENST00000370732.2_Frame_Shift_Del_p.GISFIP872fs	NM_080283.3	NP_525022.2	Q8IUA7	ABCA9_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 9	872					transport (GO:0006810)	integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			NS(2)|breast(4)|central_nervous_system(3)|endometrium(8)|kidney(3)|large_intestine(21)|lung(35)|ovary(4)|prostate(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	91	Breast(10;1.47e-12)					CAAAAGTTGAGGGATAAAGCTAATACCAAAAAGCAA	0.333																																					p.872_877del													.	ABCA9	192	0			c.2615_2630del						.																																			SO:0001589	frameshift_variant	10350	exon20			AGTTGAGGGATAA	AF423307	CCDS11681.1	17q24	2012-03-14			ENSG00000154258	ENSG00000154258		"""ATP binding cassette transporters / subfamily A"""	39	protein-coding gene	gene with protein product		612507					Standard	XM_005256934		Approved	EST640918	uc002jhu.3	Q8IUA7	OTTHUMG00000140371	ENST00000340001.4:c.2615_2630delGTATTAGCTTTATCCC	17.37:g.67014691_67014706delGGGATAAAGCTAATAC	ENSP00000342216:p.Gly872fs	Somatic	49	0		WXS	Illumina GAIIx	Phase_I	23	6	NM_080283	Q6P655|Q8N2S4|Q8WWZ5|Q96MD8	Frame_Shift_Del	DEL	ENST00000340001.4	37	CCDS11681.1																																																																																			.		0.333	ABCA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277072.2	NM_172386	
ZNF594	84622	broad.mit.edu	37	17	5096766	5096766	+	5'Flank	DEL	A	A	-			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr17:5096766delA	ENST00000575779.1	-	0	0				RP11-333E1.1_ENST00000575601.1_RNA|RP11-333E1.1_ENST00000571689.1_RNA	NM_032530.1	NP_115919.1	Q96JF6	ZN594_HUMAN	zinc finger protein 594						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(3)|lung(10)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	33						tcaaaaaaataaaaaaaaaaa	0.507																																					.													.	.	.	0			.						.																																			SO:0001631	upstream_gene_variant	0	.			AAAAATAAAAAAA	AB058774	CCDS42241.1	17p13	2013-01-08			ENSG00000180626	ENSG00000180626		"""Zinc fingers, C2H2-type"""	29392	protein-coding gene	gene with protein product						11347906	Standard	NM_032530		Approved	KIAA1871	uc010cla.1	Q96JF6	OTTHUMG00000132059		17.37:g.5096766delA	Exception_encountered	Somatic	17	0		WXS	Illumina GAIIx	Phase_I	5	1	.	Q6RFS0	RNA	DEL	ENST00000575779.1	37	CCDS42241.1																																																																																			.		0.507	ZNF594-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255082.2	XM_290737	
ELP5	23587	broad.mit.edu;bcgsc.ca	37	17	7156115	7156124	+	Frame_Shift_Del	DEL	CTCTTGAAGG	CTCTTGAAGG	-			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr17:7156115_7156124delCTCTTGAAGG	ENST00000396628.2	+	2	338_347	c.121_130delCTCTTGAAGG	c.(121-132)ctcttgaaggcgfs	p.LLKA41fs	CTDNEP1_ENST00000574322.1_5'Flank|ELP5_ENST00000396627.2_Frame_Shift_Del_p.LLKA41fs|ELP5_ENST00000573657.1_Frame_Shift_Del_p.LLKA41fs|CTDNEP1_ENST00000318988.6_5'Flank|CTDNEP1_ENST00000572043.1_5'Flank|ELP5_ENST00000574255.1_Frame_Shift_Del_p.LLKA41fs|RP1-4G17.5_ENST00000577138.1_Intron|CTDNEP1_ENST00000573600.1_5'Flank|ELP5_ENST00000356683.2_Frame_Shift_Del_p.LLKA41fs|ELP5_ENST00000574993.1_Frame_Shift_Del_p.LLKA41fs|ELP5_ENST00000354429.2_Frame_Shift_Del_p.LLKA41fs	NM_203414.1	NP_981959.1	Q8TE02	ELP5_HUMAN	elongator acetyltransferase complex subunit 5	41					chromatin organization (GO:0006325)|positive regulation of cell migration (GO:0030335)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|Elongator holoenzyme complex (GO:0033588)|nucleus (GO:0005634)											GGGGCGCAGTCTCTTGAAGGCGCTTGTCAA	0.576																																					p.41_44del													.	.	.	0			c.121_130del						.																																			SO:0001589	frameshift_variant	23587	exon2			CGCAGTCTCTTGA	BC002762	CCDS11094.1, CCDS11095.1	17p13.1	2012-08-14	2012-08-08	2012-08-08	ENSG00000170291	ENSG00000170291		"""Elongator acetyltransferase complex subunits"""	30617	protein-coding gene	gene with protein product	"""dermal papilla derived protein 6"", ""S-phase 2 protein"""	615019	"""chromosome 17 open reading frame 81"""	C17orf81		22854966	Standard	NM_203415		Approved	DERP6	uc002gfi.1	Q8TE02	OTTHUMG00000177974	ENST00000396628.2:c.121_130delCTCTTGAAGG	17.37:g.7156115_7156124delCTCTTGAAGG	ENSP00000379869:p.Leu41fs	Somatic	47	0		WXS	Illumina GAIIx	Phase_I	19	6	NM_203414	A8K1M5|D3DTN9|Q659B6|Q7Z2T4|Q8TDR9|Q9BUB2|Q9Y2Q4	Frame_Shift_Del	DEL	ENST00000396628.2	37	CCDS11094.1																																																																																			.		0.576	ELP5-003	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000440111.1	NM_015362	
PER1	5187	broad.mit.edu;bcgsc.ca	37	17	8051527	8051527	+	Missense_Mutation	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr17:8051527T>G	ENST00000317276.4	-	9	1336	c.1099A>C	c.(1099-1101)Agc>Cgc	p.S367R	PER1_ENST00000354903.5_Missense_Mutation_p.S351R|PER1_ENST00000581082.1_Missense_Mutation_p.S347R|PER1_ENST00000578089.1_5'Flank	NM_002616.2	NP_002607.2	O15534	PER1_HUMAN	period circadian clock 1	367	PAS 2. {ECO:0000255|PROSITE- ProRule:PRU00140}.				circadian regulation of gene expression (GO:0032922)|circadian regulation of translation (GO:0097167)|circadian rhythm (GO:0007623)|entrainment of circadian clock (GO:0009649)|entrainment of circadian clock by photoperiod (GO:0043153)|histone H3 acetylation (GO:0043966)|histone H3 deacetylation (GO:0070932)|histone H4 acetylation (GO:0043967)|negative regulation of glucocorticoid receptor signaling pathway (GO:2000323)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of JNK cascade (GO:0046329)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|posttranscriptional regulation of gene expression (GO:0010608)|regulation of circadian rhythm (GO:0042752)|regulation of cytokine production involved in inflammatory response (GO:1900015)|regulation of hair cycle (GO:0042634)|regulation of p38MAPK cascade (GO:1900744)|regulation of sodium ion transport (GO:0002028)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|E-box binding (GO:0070888)|kinase binding (GO:0019900)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|signal transducer activity (GO:0004871)|transcription factor binding transcription factor activity (GO:0000989)|ubiquitin protein ligase binding (GO:0031625)			breast(4)|central_nervous_system(1)|endometrium(2)|kidney(7)|large_intestine(3)|lung(15)|ovary(4)|pancreas(1)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	47						AAGAGGCAGCTGGGTGTGTGC	0.597			T	ETV6	"""AML, CMML"""			Other conserved DNA damage response genes																													p.S367R				Dom	yes		17	17p13.1-17p12	5187	period homolog 1 (Drosophila)		L	.	PER1	104	0			c.A1099C						.						101.0	92.0	95.0					17																	8051527		2203	4300	6503	SO:0001583	missense	5187	exon9			GGCAGCTGGGTGT	AB002107	CCDS11131.1	17p13.1	2012-12-13	2012-12-13			ENSG00000179094			8845	protein-coding gene	gene with protein product		602260	"""period (Drosophila) homolog 1"", ""period homolog 1 (Drosophila)"""	PER		9323128	Standard	NM_002616		Approved	RIGUI	uc002gkd.3	O15534		ENST00000317276.4:c.1099A>C	17.37:g.8051527T>G	ENSP00000314420:p.Ser367Arg	Somatic	19	0		WXS	Illumina GAIIx	Phase_I	12	6	NM_002616	B2RPA8|B4DI49|D3DTR3	Missense_Mutation	SNP	ENST00000317276.4	37	CCDS11131.1	.	.	.	.	.	.	.	.	.	.	T	21.2	4.106789	0.77096	.	.	ENSG00000179094	ENST00000317276;ENST00000354903	T;T	0.16897	2.31;2.31	5.34	5.34	0.76211	PAS (1);	0.000000	0.85682	D	0.000000	T	0.45094	0.1325	M	0.85945	2.785	0.54753	D	0.999989	D;D	0.71674	0.998;0.996	D;D	0.71656	0.94;0.974	T	0.51293	-0.8724	10	0.72032	D	0.01	-18.5265	13.2765	0.60189	0.0:0.0:0.0:1.0	.	351;367	B4DI49;O15534	.;PER1_HUMAN	R	367;351	ENSP00000314420:S367R;ENSP00000346979:S351R	ENSP00000314420:S367R	S	-	1	0	PER1	7992252	0.992000	0.36948	1.000000	0.80357	0.931000	0.56810	2.298000	0.43602	2.025000	0.59659	0.460000	0.39030	AGC	.		0.597	PER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441481.2		
PER1	5187	broad.mit.edu	37	17	8051559	8051559	+	Missense_Mutation	SNP	T	T	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr17:8051559T>C	ENST00000317276.4	-	9	1304	c.1067A>G	c.(1066-1068)gAc>gGc	p.D356G	PER1_ENST00000354903.5_Missense_Mutation_p.D340G|PER1_ENST00000581082.1_Missense_Mutation_p.D336G|PER1_ENST00000578089.1_5'Flank	NM_002616.2	NP_002607.2	O15534	PER1_HUMAN	period circadian clock 1	356	PAS 2. {ECO:0000255|PROSITE- ProRule:PRU00140}.				circadian regulation of gene expression (GO:0032922)|circadian regulation of translation (GO:0097167)|circadian rhythm (GO:0007623)|entrainment of circadian clock (GO:0009649)|entrainment of circadian clock by photoperiod (GO:0043153)|histone H3 acetylation (GO:0043966)|histone H3 deacetylation (GO:0070932)|histone H4 acetylation (GO:0043967)|negative regulation of glucocorticoid receptor signaling pathway (GO:2000323)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of JNK cascade (GO:0046329)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|posttranscriptional regulation of gene expression (GO:0010608)|regulation of circadian rhythm (GO:0042752)|regulation of cytokine production involved in inflammatory response (GO:1900015)|regulation of hair cycle (GO:0042634)|regulation of p38MAPK cascade (GO:1900744)|regulation of sodium ion transport (GO:0002028)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|E-box binding (GO:0070888)|kinase binding (GO:0019900)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|signal transducer activity (GO:0004871)|transcription factor binding transcription factor activity (GO:0000989)|ubiquitin protein ligase binding (GO:0031625)			breast(4)|central_nervous_system(1)|endometrium(2)|kidney(7)|large_intestine(3)|lung(15)|ovary(4)|pancreas(1)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	47						AATCCTCTTGTCAGGGGGTAT	0.602			T	ETV6	"""AML, CMML"""			Other conserved DNA damage response genes																													p.D356G				Dom	yes		17	17p13.1-17p12	5187	period homolog 1 (Drosophila)		L	.	PER1	104	0			c.A1067G						.						88.0	82.0	84.0					17																	8051559		2203	4300	6503	SO:0001583	missense	5187	exon9			CTCTTGTCAGGGG	AB002107	CCDS11131.1	17p13.1	2012-12-13	2012-12-13			ENSG00000179094			8845	protein-coding gene	gene with protein product		602260	"""period (Drosophila) homolog 1"", ""period homolog 1 (Drosophila)"""	PER		9323128	Standard	NM_002616		Approved	RIGUI	uc002gkd.3	O15534		ENST00000317276.4:c.1067A>G	17.37:g.8051559T>C	ENSP00000314420:p.Asp356Gly	Somatic	16	0		WXS	Illumina GAIIx	Phase_I	12	4	NM_002616	B2RPA8|B4DI49|D3DTR3	Missense_Mutation	SNP	ENST00000317276.4	37	CCDS11131.1	.	.	.	.	.	.	.	.	.	.	T	18.40	3.615723	0.66672	.	.	ENSG00000179094	ENST00000317276;ENST00000354903	T;T	0.40476	2.4;1.03	5.34	5.34	0.76211	PAS (1);	0.154450	0.53938	D	0.000042	T	0.64394	0.2594	M	0.77313	2.365	0.58432	D	0.999999	P;D	0.69078	0.714;0.997	B;D	0.73380	0.289;0.98	T	0.69320	-0.5176	10	0.87932	D	0	-23.4602	13.2765	0.60189	0.0:0.0:0.0:1.0	.	340;356	B4DI49;O15534	.;PER1_HUMAN	G	356;340	ENSP00000314420:D356G;ENSP00000346979:D340G	ENSP00000314420:D356G	D	-	2	0	PER1	7992284	1.000000	0.71417	0.995000	0.50966	0.488000	0.33401	7.973000	0.88032	2.025000	0.59659	0.460000	0.39030	GAC	.		0.602	PER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441481.2		
FLII	2314	broad.mit.edu	37	17	18156676	18156676	+	Missense_Mutation	SNP	T	T	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr17:18156676T>A	ENST00000327031.4	-	9	1177	c.952A>T	c.(952-954)Aac>Tac	p.N318Y	FLII_ENST00000545457.2_Missense_Mutation_p.N264Y|FLII_ENST00000379450.4_Missense_Mutation_p.N233Y|FLII_ENST00000584444.1_5'UTR|FLII_ENST00000578558.1_Missense_Mutation_p.N318Y|FLII_ENST00000579294.1_Missense_Mutation_p.N307Y	NM_002018.3	NP_002009.1	Q13045	FLII_HUMAN	flightless I homolog (Drosophila)	318	Interaction with LRRFIP1 and LRRFIP2.				multicellular organismal development (GO:0007275)|muscle contraction (GO:0006936)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|microtubule organizing center (GO:0005815)|nucleus (GO:0005634)	actin binding (GO:0003779)			central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(6)|lung(11)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	32	all_neural(463;0.228)					TCTTCCAGGTTGGTGAGCTTG	0.567																																					p.N318Y													.	FLII	79	0			c.A952T						.						74.0	66.0	69.0					17																	18156676		2203	4300	6503	SO:0001583	missense	2314	exon9			CCAGGTTGGTGAG	U01184	CCDS11192.1, CCDS58521.1, CCDS58522.1	17p11.2	2008-07-18	2001-11-28		ENSG00000177731	ENSG00000177731			3750	protein-coding gene	gene with protein product		600362	"""flightless I (Drosophila) homolog"""			7825574	Standard	NM_002018		Approved	FLI, FLIL, Fli1, MGC39265	uc002gsr.2	Q13045	OTTHUMG00000059389	ENST00000327031.4:c.952A>T	17.37:g.18156676T>A	ENSP00000324573:p.Asn318Tyr	Somatic	30	0		WXS	Illumina GAIIx	Phase_I	11	4	NM_002018	B4DIL0|F5H407|J3QLG3	Missense_Mutation	SNP	ENST00000327031.4	37	CCDS11192.1	.	.	.	.	.	.	.	.	.	.	T	12.10	1.836900	0.32421	.	.	ENSG00000177731	ENST00000327031;ENST00000545457;ENST00000379450	T;T	0.27720	1.65;1.65	5.78	1.08	0.20341	.	0.259366	0.49916	D	0.000123	T	0.28167	0.0695	M	0.62016	1.91	0.34030	D	0.653751	B;B;P;B;B	0.50272	0.162;0.162;0.933;0.245;0.357	B;B;P;B;B	0.45232	0.172;0.172;0.474;0.092;0.306	T	0.36915	-0.9728	10	0.59425	D	0.04	-11.1909	3.1159	0.06375	0.1146:0.1256:0.12:0.6398	.	233;233;318;318;287	E7EPM0;B4DIL0;F5H407;Q13045;B4DIX0	.;.;.;FLII_HUMAN;.	Y	318;318;233	ENSP00000324573:N318Y;ENSP00000368763:N233Y	ENSP00000324573:N318Y	N	-	1	0	FLII	18097401	1.000000	0.71417	0.946000	0.38457	0.305000	0.27757	3.315000	0.51951	-0.101000	0.12219	-0.264000	0.10439	AAC	.		0.567	FLII-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132032.2	NM_002018	
ABCC3	8714	broad.mit.edu;ucsc.edu;bcgsc.ca	37	17	48753044	48753044	+	Silent	SNP	C	C	A	rs371874263		TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr17:48753044C>A	ENST00000285238.8	+	21	2847	c.2767C>A	c.(2767-2769)Cgg>Agg	p.R923R	ABCC3_ENST00000510891.1_3'UTR	NM_003786.3	NP_003777.2	O15438	MRP3_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 3	923					bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|organic anion transmembrane transporter activity (GO:0008514)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(11)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	33			BRCA - Breast invasive adenocarcinoma(22;3.05e-09)		Cisplatin(DB00515)|Clotrimazole(DB00257)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Doxorubicin(DB00997)|Etoposide(DB00773)|Ezetimibe(DB00973)|Fluorouracil(DB00544)|Folic Acid(DB00158)|Gadoxetate(DB08884)|Glutathione(DB00143)|Glyburide(DB01016)|Indomethacin(DB00328)|Lamivudine(DB00709)|Leucovorin(DB00650)|Methotrexate(DB00563)|Metyrapone(DB01011)|Nifedipine(DB01115)|Omeprazole(DB00338)|Phenobarbital(DB01174)|Probenecid(DB01032)|Rifampicin(DB01045)|Sulfinpyrazone(DB01138)|Verapamil(DB00661)|Vincristine(DB00541)	GCCTGTACCCCGGAGGCACCT	0.652																																					p.R923R													.	ABCC3	138	0			c.C2767A						.						25.0	25.0	25.0					17																	48753044		2196	4294	6490	SO:0001819	synonymous_variant	8714	exon21			GTACCCCGGAGGC	Y17151	CCDS32681.1, CCDS45739.1	17q21	2012-03-14			ENSG00000108846	ENSG00000108846		"""ATP binding cassette transporters / subfamily C"""	54	protein-coding gene	gene with protein product	"""canalicular multispecific organic anion transporter 2"""	604323				8894702, 9827529	Standard	NM_003786		Approved	MRP3, cMOAT2, EST90757, MLP2, MOAT-D	uc002isl.3	O15438	OTTHUMG00000162245	ENST00000285238.8:c.2767C>A	17.37:g.48753044C>A		Somatic	24	0		WXS	Illumina GAIIx	Phase_I	13	8	NM_003786	B2RPA9|D3DTX9|O60265|O60922|O75621|O95078|O95289|O95290|Q86X85|Q9UN52	Silent	SNP	ENST00000285238.8	37	CCDS32681.1	.	.	.	.	.	.	.	.	.	.	C	4.801	0.148971	0.09185	.	.	ENSG00000108846	ENST00000513745	D	0.88975	-2.45	5.67	-4.36	0.03645	.	.	.	.	.	D	0.82360	0.5020	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.66272	-0.5965	6	0.13108	T	0.6	-12.9521	17.0214	0.86434	0.7886:0.2114:0.0:0.0	.	.	.	.	Q	71	ENSP00000421755:P71Q	ENSP00000421755:P71Q	P	+	2	0	ABCC3	46108043	0.096000	0.21769	0.000000	0.03702	0.006000	0.05464	0.169000	0.16641	-0.233000	0.09797	-0.182000	0.12963	CCG	.		0.652	ABCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368083.2	NM_020038	
CDH2	1000	broad.mit.edu	37	18	25565702	25565702	+	Missense_Mutation	SNP	C	C	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr18:25565702C>T	ENST00000269141.3	-	12	2188	c.1765G>A	c.(1765-1767)Gga>Aga	p.G589R	CDH2_ENST00000399380.3_Missense_Mutation_p.G558R	NM_001792.3	NP_001783.2	P19022	CADH2_HUMAN	cadherin 2, type 1, N-cadherin (neuronal)	589	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|blood vessel morphogenesis (GO:0048514)|calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell migration (GO:0016477)|cell-cell adhesion mediated by cadherin (GO:0044331)|cell-cell junction organization (GO:0045216)|glial cell differentiation (GO:0010001)|heterophilic cell-cell adhesion (GO:0007157)|homophilic cell adhesion (GO:0007156)|muscle cell differentiation (GO:0042692)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|neuronal stem cell maintenance (GO:0097150)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of muscle cell differentiation (GO:0051149)|striated muscle cell differentiation (GO:0051146)	apical plasma membrane (GO:0016324)|catenin complex (GO:0016342)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intercalated disc (GO:0014704)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|synapse (GO:0045202)	alpha-catenin binding (GO:0045294)|beta-catenin binding (GO:0008013)|calcium ion binding (GO:0005509)|gamma-catenin binding (GO:0045295)			NS(1)|breast(5)|cervix(2)|endometrium(7)|kidney(3)|large_intestine(22)|lung(32)|ovary(4)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	82						TGCAGCGTTCCTGTTCCACTC	0.403																																					p.G589R													.	CDH2	194	0			c.G1765A						.						66.0	69.0	68.0					18																	25565702		2203	4300	6503	SO:0001583	missense	1000	exon12			GCGTTCCTGTTCC	S42303	CCDS11891.1	18q12.1	2010-01-26			ENSG00000170558	ENSG00000170558		"""CD molecules"", ""Cadherins / Major cadherins"""	1759	protein-coding gene	gene with protein product	"""N-cadherin"""	114020		NCAD		2384753, 7731968, 2216790	Standard	NM_001792		Approved	CDHN, CD325	uc002kwg.2	P19022	OTTHUMG00000059940	ENST00000269141.3:c.1765G>A	18.37:g.25565702C>T	ENSP00000269141:p.Gly589Arg	Somatic	32	0		WXS	Illumina GAIIx	Phase_I	14	4	NM_001792	A8MWK3|B0YIY6|Q14923|Q8N173	Missense_Mutation	SNP	ENST00000269141.3	37	CCDS11891.1	.	.	.	.	.	.	.	.	.	.	C	23.3	4.397738	0.83120	.	.	ENSG00000170558	ENST00000269141;ENST00000399380	T;T	0.53857	0.6;0.6	5.96	5.96	0.96718	Cadherin (5);Cadherin-like (1);	0.000000	0.85682	D	0.000000	T	0.75708	0.3886	M	0.79343	2.45	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.76743	-0.2847	10	0.87932	D	0	.	20.394	0.98981	0.0:1.0:0.0:0.0	.	558;589	A8MWK3;P19022	.;CADH2_HUMAN	R	589;558	ENSP00000269141:G589R;ENSP00000382312:G558R	ENSP00000269141:G589R	G	-	1	0	CDH2	23819700	1.000000	0.71417	0.989000	0.46669	0.997000	0.91878	7.487000	0.81328	2.830000	0.97506	0.585000	0.79938	GGA	.		0.403	CDH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133246.3	NM_001792	
FBL	2091	broad.mit.edu	37	19	40331279	40331279	+	Silent	SNP	G	G	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr19:40331279G>A	ENST00000221801.3	-	2	272	c.159C>T	c.(157-159)ggC>ggT	p.G53G	FBL_ENST00000593503.1_5'Flank	NM_001436.3	NP_001427.2	P22087	FBRL_HUMAN	fibrillarin	53	DMA/Gly-rich.				histone glutamine methylation (GO:1990258)|osteoblast differentiation (GO:0001649)|rRNA processing (GO:0006364)|snoRNA metabolic process (GO:0016074)|tRNA processing (GO:0008033)	box C/D snoRNP complex (GO:0031428)|Cajal body (GO:0015030)|extracellular vesicular exosome (GO:0070062)|granular component (GO:0001652)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	histone-glutamine methyltransferase activity (GO:1990259)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			endometrium(1)|kidney(1)|large_intestine(4)|lung(2)|ovary(1)	9	all_cancers(60;5.79e-06)|all_lung(34;5.2e-08)|Lung NSC(34;6.14e-08)|Ovarian(47;0.06)	Renal(1328;0.000518)|Hepatocellular(1079;0.0893)	Epithelial(26;5.74e-25)|OV - Ovarian serous cystadenocarcinoma(5;3.13e-24)|all cancers(26;8.59e-23)	GBM - Glioblastoma multiforme(1328;0.000826)|STAD - Stomach adenocarcinoma(1328;0.138)		ctcctccaccgccgccgccgc	0.657																																					p.G53G													.	FBL	37	0			c.C159T						.						18.0	21.0	20.0					19																	40331279		2201	4299	6500	SO:0001819	synonymous_variant	2091	exon2			TCCACCGCCGCCG	AC005393	CCDS12545.1	19q13.1	2010-02-17			ENSG00000105202	ENSG00000105202			3599	protein-coding gene	gene with protein product		134795				1846968, 2026646	Standard	NM_001436		Approved	RNU3IP1, FLRN, FIB	uc002omn.3	P22087		ENST00000221801.3:c.159C>T	19.37:g.40331279G>A		Somatic	82	2		WXS	Illumina GAIIx	Phase_I	62	5	NM_001436	B5BUE8|O75259|Q6IAT5|Q9UPI6	Silent	SNP	ENST00000221801.3	37	CCDS12545.1																																																																																			.		0.657	FBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462509.4	NM_001436	
PPP5C	5536	broad.mit.edu;ucsc.edu;bcgsc.ca	37	19	46891939	46891939	+	Missense_Mutation	SNP	G	G	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr19:46891939G>A	ENST00000012443.4	+	11	1409	c.1306G>A	c.(1306-1308)Gtg>Atg	p.V436M	AC007193.8_ENST00000598616.1_RNA|PPP5C_ENST00000391919.1_Missense_Mutation_p.V308M	NM_006247.3	NP_006238.1	P53041	PPP5_HUMAN	protein phosphatase 5, catalytic subunit	436	Catalytic.				cell death (GO:0008219)|DNA repair (GO:0006281)|mitotic nuclear division (GO:0007067)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|protein dephosphorylation (GO:0006470)|protein heterooligomerization (GO:0051291)|response to morphine (GO:0043278)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)	identical protein binding (GO:0042802)|lipid binding (GO:0008289)|metal ion binding (GO:0046872)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|RNA binding (GO:0003723)|signal transducer activity (GO:0004871)			endometrium(4)|kidney(1)|large_intestine(5)|liver(2)|lung(4)|ovary(1)|pancreas(1)	18		Ovarian(192;0.0731)|all_neural(266;0.196)		OV - Ovarian serous cystadenocarcinoma(262;0.000196)|all cancers(93;0.00192)|GBM - Glioblastoma multiforme(486;0.0499)|Epithelial(262;0.0504)		GGGCTACGAGGTGGCTCACGG	0.577																																					p.V436M													.	PPP5C	44	0			c.G1306A						.						121.0	105.0	111.0					19																	46891939		2203	4300	6503	SO:0001583	missense	5536	exon11			TACGAGGTGGCTC		CCDS12684.1	19q13.3	2013-01-10			ENSG00000011485	ENSG00000011485	3.1.3.16	"""Serine/threonine phosphatases / Protein phosphatase, catalytic subunits"", ""Tetratricopeptide (TTC) repeat domain containing"""	9322	protein-coding gene	gene with protein product		600658		PPP5		8666404	Standard	NM_006247		Approved	PP5	uc002pem.3	P53041	OTTHUMG00000134287	ENST00000012443.4:c.1306G>A	19.37:g.46891939G>A	ENSP00000012443:p.Val436Met	Somatic	24	0		WXS	Illumina GAIIx	Phase_I	12	5	NM_006247	Q16722|Q53XV2	Missense_Mutation	SNP	ENST00000012443.4	37	CCDS12684.1	.	.	.	.	.	.	.	.	.	.	G	14.46	2.543299	0.45280	.	.	ENSG00000011485	ENST00000012443;ENST00000451918;ENST00000391919	T;T	0.65549	-0.16;-0.16	5.09	5.09	0.68999	Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase (2);	0.000000	0.85682	D	0.000000	T	0.54743	0.1877	L	0.60957	1.885	0.80722	D	1	P;P	0.43477	0.784;0.808	B;B	0.31390	0.129;0.085	T	0.63216	-0.6687	10	0.51188	T	0.08	-19.6586	15.9745	0.80049	0.0:0.0:1.0:0.0	.	436;436	B2R6R6;P53041	.;PPP5_HUMAN	M	436;423;308	ENSP00000012443:V436M;ENSP00000375786:V308M	ENSP00000012443:V436M	V	+	1	0	PPP5C	51583779	1.000000	0.71417	1.000000	0.80357	0.035000	0.12851	9.180000	0.94867	2.367000	0.80283	0.561000	0.74099	GTG	.		0.577	PPP5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258969.2	NM_006247	
SPHK2	56848	broad.mit.edu;ucsc.edu;bcgsc.ca	37	19	49132945	49132945	+	Missense_Mutation	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr19:49132945A>C	ENST00000245222.4	+	7	2246	c.1880A>C	c.(1879-1881)gAg>gCg	p.E627A	SPHK2_ENST00000599029.1_Missense_Mutation_p.E591A|SPHK2_ENST00000443164.1_Missense_Mutation_p.E689A|SPHK2_ENST00000600537.1_Missense_Mutation_p.E568A|SPHK2_ENST00000340932.3_Missense_Mutation_p.E589A|SPHK2_ENST00000598088.1_Missense_Mutation_p.E627A|SPHK2_ENST00000599748.1_Missense_Mutation_p.E591A	NM_001204158.2|NM_001243876.1|NM_020126.4	NP_001191087.1|NP_001230805.1|NP_064511.2	Q9NRA0	SPHK2_HUMAN	sphingosine kinase 2	627					blood vessel development (GO:0001568)|brain development (GO:0007420)|cell proliferation (GO:0008283)|lipid phosphorylation (GO:0046834)|negative regulation of apoptotic process (GO:0043066)|positive regulation of cell proliferation (GO:0008284)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|small molecule metabolic process (GO:0044281)|sphinganine-1-phosphate biosynthetic process (GO:0006669)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|sphingosine metabolic process (GO:0006670)	cytosol (GO:0005829)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	ATP binding (GO:0005524)|D-erythro-sphingosine kinase activity (GO:0017050)|diacylglycerol kinase activity (GO:0004143)|NAD+ kinase activity (GO:0003951)|Ras GTPase binding (GO:0017016)|sphinganine kinase activity (GO:0008481)			NS(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(4)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	19		all_lung(116;0.000125)|Lung NSC(112;0.000202)|all_epithelial(76;0.000283)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000102)|all cancers(93;0.000117)|GBM - Glioblastoma multiforme(486;0.00627)|Epithelial(262;0.0158)		GAGCAGGTGGAGTATGGGCCG	0.677																																					p.E627A													.	SPHK2	62	0			c.A1880C						.						19.0	18.0	18.0					19																	49132945		2201	4297	6498	SO:0001583	missense	56848	exon7			AGGTGGAGTATGG	AF245447	CCDS12727.1, CCDS59404.1, CCDS59405.1, CCDS74414.1	19q13.33	2013-09-20			ENSG00000063176	ENSG00000063176			18859	protein-coding gene	gene with protein product		607092				10751414, 17895250	Standard	NM_020126		Approved		uc002pjs.3	Q9NRA0	OTTHUMG00000183318	ENST00000245222.4:c.1880A>C	19.37:g.49132945A>C	ENSP00000245222:p.Glu627Ala	Somatic	26	0		WXS	Illumina GAIIx	Phase_I	13	5	NM_020126	A0T4C8|B4DU87|Q9BRN1|Q9H0Q2|Q9NWU7	Missense_Mutation	SNP	ENST00000245222.4	37	CCDS12727.1	.	.	.	.	.	.	.	.	.	.	A	21.1	4.095359	0.76870	.	.	ENSG00000063176	ENST00000245222;ENST00000406269;ENST00000340932;ENST00000443164	T;T;T	0.13778	2.56;2.56;2.56	4.78	4.78	0.61160	.	0.129958	0.51477	D	0.000090	T	0.13329	0.0323	L	0.34521	1.04	0.34390	D	0.694095	P;P;D	0.58620	0.9;0.47;0.983	B;B;P	0.46796	0.284;0.109;0.527	T	0.20240	-1.0281	10	0.20519	T	0.43	-50.5664	12.5766	0.56367	1.0:0.0:0.0:0.0	.	568;689;627	B4DU87;A0T4C8;Q9NRA0	.;.;SPHK2_HUMAN	A	627;600;589;689	ENSP00000245222:E627A;ENSP00000341091:E589A;ENSP00000413369:E689A	ENSP00000245222:E627A	E	+	2	0	SPHK2	53824757	0.999000	0.42202	1.000000	0.80357	0.973000	0.67179	1.991000	0.40727	2.142000	0.66516	0.454000	0.30748	GAG	.		0.677	SPHK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466153.1		
ZNF177	7730	broad.mit.edu;bcgsc.ca	37	19	9491917	9491917	+	Silent	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr19:9491917A>C	ENST00000589262.1	+	6	976	c.910A>C	c.(910-912)Aga>Cga	p.R304R	ZNF177_ENST00000343499.4_Silent_p.R144R|ZNF177_ENST00000434737.2_Silent_p.R304R|ZNF177_ENST00000446085.4_3'UTR|ZNF177_ENST00000541595.2_Silent_p.R144R|ZNF177_ENST00000590616.1_Intron|ZNF177_ENST00000602738.1_Silent_p.R144R|ZNF177_ENST00000602856.1_3'UTR	NM_001172651.1	NP_001166122.1	Q13360	ZN177_HUMAN	zinc finger protein 177	304					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	blood microparticle (GO:0072562)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(2)|large_intestine(1)|lung(4)|ovary(1)|prostate(2)|stomach(2)	13						GAAACACATGAGATCTCATAC	0.443																																					p.R304R													.	ZNF177	57	0			c.A910C						.						94.0	87.0	90.0					19																	9491917		2203	4300	6503	SO:0001819	synonymous_variant	7730	exon6			CACATGAGATCTC	U37263, BC012012	CCDS12212.1, CCDS54214.1	19p13.2	2013-01-08						"""Zinc fingers, C2H2-type"", ""-"""	12966	protein-coding gene	gene with protein product		601276					Standard	NM_003451		Approved		uc021uon.1	Q13360		ENST00000589262.1:c.910A>C	19.37:g.9491917A>C		Somatic	49	1		WXS	Illumina GAIIx	Phase_I	30	12	NM_001172651	B4DY57|E9PDG0|I3L0I4|Q96ER2	Silent	SNP	ENST00000589262.1	37	CCDS54214.1																																																																																			.		0.443	ZNF177-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000449028.1	NM_003451	
SPHK2	56848	broad.mit.edu;ucsc.edu	37	19	49132949	49132949	+	Nonsense_Mutation	SNP	T	T	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr19:49132949T>A	ENST00000245222.4	+	7	2250	c.1884T>A	c.(1882-1884)taT>taA	p.Y628*	SPHK2_ENST00000599029.1_Nonsense_Mutation_p.Y592*|SPHK2_ENST00000443164.1_Nonsense_Mutation_p.Y690*|SPHK2_ENST00000600537.1_Nonsense_Mutation_p.Y569*|SPHK2_ENST00000340932.3_Nonsense_Mutation_p.Y590*|SPHK2_ENST00000598088.1_Nonsense_Mutation_p.Y628*|SPHK2_ENST00000599748.1_Nonsense_Mutation_p.Y592*	NM_001204158.2|NM_001243876.1|NM_020126.4	NP_001191087.1|NP_001230805.1|NP_064511.2	Q9NRA0	SPHK2_HUMAN	sphingosine kinase 2	628					blood vessel development (GO:0001568)|brain development (GO:0007420)|cell proliferation (GO:0008283)|lipid phosphorylation (GO:0046834)|negative regulation of apoptotic process (GO:0043066)|positive regulation of cell proliferation (GO:0008284)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|small molecule metabolic process (GO:0044281)|sphinganine-1-phosphate biosynthetic process (GO:0006669)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|sphingosine metabolic process (GO:0006670)	cytosol (GO:0005829)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	ATP binding (GO:0005524)|D-erythro-sphingosine kinase activity (GO:0017050)|diacylglycerol kinase activity (GO:0004143)|NAD+ kinase activity (GO:0003951)|Ras GTPase binding (GO:0017016)|sphinganine kinase activity (GO:0008481)			NS(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(4)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	19		all_lung(116;0.000125)|Lung NSC(112;0.000202)|all_epithelial(76;0.000283)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000102)|all cancers(93;0.000117)|GBM - Glioblastoma multiforme(486;0.00627)|Epithelial(262;0.0158)		AGGTGGAGTATGGGCCGCTAC	0.672																																					p.Y628X													.	SPHK2	62	0			c.T1884A						.						19.0	18.0	18.0					19																	49132949		2200	4297	6497	SO:0001587	stop_gained	56848	exon7			GGAGTATGGGCCG	AF245447	CCDS12727.1, CCDS59404.1, CCDS59405.1, CCDS74414.1	19q13.33	2013-09-20			ENSG00000063176	ENSG00000063176			18859	protein-coding gene	gene with protein product		607092				10751414, 17895250	Standard	NM_020126		Approved		uc002pjs.3	Q9NRA0	OTTHUMG00000183318	ENST00000245222.4:c.1884T>A	19.37:g.49132949T>A	ENSP00000245222:p.Tyr628*	Somatic	25	0		WXS	Illumina GAIIx	Phase_I	13	5	NM_020126	A0T4C8|B4DU87|Q9BRN1|Q9H0Q2|Q9NWU7	Nonsense_Mutation	SNP	ENST00000245222.4	37	CCDS12727.1	.	.	.	.	.	.	.	.	.	.	T	39	7.812081	0.98504	.	.	ENSG00000063176	ENST00000245222;ENST00000406269;ENST00000340932;ENST00000443164	.	.	.	4.78	-5.62	0.02481	.	0.138680	0.49916	D	0.000135	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-38.2219	12.907	0.58158	0.0:0.1924:0.0:0.8076	.	.	.	.	X	628;601;590;690	.	ENSP00000245222:Y628X	Y	+	3	2	SPHK2	53824761	0.000000	0.05858	0.986000	0.45419	0.977000	0.68977	-3.229000	0.00549	-0.538000	0.06281	0.454000	0.30748	TAT	.		0.672	SPHK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466153.1		
KCNF1	3754	broad.mit.edu;bcgsc.ca	37	2	11053983	11053983	+	Frame_Shift_Del	DEL	C	C	-			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr2:11053983delC	ENST00000295082.1	+	1	1921	c.1431delC	c.(1429-1431)atcfs	p.I477fs		NM_002236.4	NP_002227.2	Q9H3M0	KCNF1_HUMAN	potassium voltage-gated channel, subfamily F, member 1	477					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)			NS(1)|endometrium(2)|large_intestine(2)|lung(10)|ovary(2)|skin(1)|urinary_tract(1)	19	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.191)			Epithelial(75;0.115)|OV - Ovarian serous cystadenocarcinoma(76;0.128)		ACACCTTCATCCCCCTCCTGA	0.662																																					p.I477fs													.	KCNF1	70	0			c.1431delC						.						22.0	28.0	26.0					2																	11053983		2189	4274	6463	SO:0001589	frameshift_variant	3754	exon1			CTTCATCCCCCTC	AF033382	CCDS1676.1	2p25	2011-07-05			ENSG00000162975	ENSG00000162975		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6246	protein-coding gene	gene with protein product		603787		KCNF		9434767, 16382104	Standard	NM_002236		Approved	Kv5.1, kH1, IK8	uc002rax.3	Q9H3M0	OTTHUMG00000119054	ENST00000295082.1:c.1431delC	2.37:g.11053983delC	ENSP00000295082:p.Ile477fs	Somatic	50	0		WXS	Illumina GAIIx	Phase_I	32	8	NM_002236	O43527|Q585L3	Frame_Shift_Del	DEL	ENST00000295082.1	37	CCDS1676.1																																																																																			.		0.662	KCNF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239265.1	NM_002236	
LOC101927533	101927533	broad.mit.edu	37	2	65894933	65894933	+	lincRNA	DEL	A	A	-			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr2:65894933delA	ENST00000377977.3	+	0	862				AC007389.4_ENST00000583614.1_RNA																							TCAGAGGTTTAAAAAAAAAAA	0.517																																					.													.	.	.	0			.						.																																					0	.			AGGTTTAAAAAAA																													2.37:g.65894933delA		Somatic	3	0		WXS	Illumina GAIIx	Phase_I	8	2	.		RNA	DEL	ENST00000377977.3	37																																																																																				.		0.517	AC074391.1-010	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000470883.1		
LIMS1	3987	broad.mit.edu	37	2	109150329	109150329	+	5'Flank	SNP	A	A	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr2:109150329A>G	ENST00000544547.1	+	0	0				AC012487.2_ENST00000440975.1_RNA|AC012487.2_ENST00000322353.3_RNA	NM_001193483.2	NP_001180412.1	P48059	LIMS1_HUMAN	LIM and senescent cell antigen-like domains 1						cell aging (GO:0007569)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cell-matrix adhesion (GO:0007160)|cellular response to transforming growth factor beta stimulus (GO:0071560)|chordate embryonic development (GO:0043009)|establishment or maintenance of cell polarity (GO:0007163)|negative regulation of apoptotic process (GO:0043066)|negative regulation of hepatocyte proliferation (GO:2000346)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of integrin-mediated signaling pathway (GO:2001046)|protein heterooligomerization (GO:0051291)|single organismal cell-cell adhesion (GO:0016337)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	zinc ion binding (GO:0008270)			breast(2)|endometrium(2)|kidney(1)|large_intestine(1)|lung(4)	10						TCAGGCACCCAGCGGTGACCG	0.597																																					.													.	LIMS1	38	0			.						.																																			SO:0001631	upstream_gene_variant	0	.			GCACCCAGCGGTG		CCDS2078.1, CCDS54382.1, CCDS54383.1, CCDS54384.1, CCDS54385.1	2q12.3	2008-05-23			ENSG00000169756	ENSG00000169756			6616	protein-coding gene	gene with protein product		602567				7517666, 10022929	Standard	NM_001193482		Approved	PINCH, PINCH1	uc002tek.4	P48059	OTTHUMG00000130983		2.37:g.109150329A>G	Exception_encountered	Somatic	8	0		WXS	Illumina GAIIx	Phase_I	11	4	.	B2RAJ4|B7Z483|B7Z7R3|B7Z907|Q53TE0|Q9BS44	RNA	SNP	ENST00000544547.1	37	CCDS54382.1																																																																																			.		0.597	LIMS1-203	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_004987	
AL133247.2	0	broad.mit.edu	37	2	31751121	31751121	+	RNA	SNP	A	A	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr2:31751121A>G	ENST00000435713.1	+	0	0				SRD5A2_ENST00000405650.1_RNA																							GACACCACTCAGAATCCCCAG	0.458																																					.													.	.	.	0			.						.																																					6716	.			CCACTCAGAATCC																													2.37:g.31751121A>G		Somatic	34	0		WXS	Illumina GAIIx	Phase_I	29	8	.		RNA	SNP	ENST00000435713.1	37																																																																																				.		0.458	AL133247.2-001	KNOWN	basic|exp_conf	antisense	antisense	OTTHUMT00000325125.1		
STRN	6801	broad.mit.edu;bcgsc.ca	37	2	37084999	37084999	+	Splice_Site	SNP	C	C	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr2:37084999C>G	ENST00000263918.4	-	14	1845	c.1837G>C	c.(1837-1839)Gaa>Caa	p.E613Q	STRN_ENST00000379213.2_Splice_Site_p.E564Q	NM_003162.3	NP_003153.2	O43815	STRN_HUMAN	striatin, calmodulin binding protein	613					dendrite development (GO:0016358)|locomotory behavior (GO:0007626)|negative regulation of cell proliferation (GO:0008285)|tight junction assembly (GO:0070830)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|tight junction (GO:0005923)	armadillo repeat domain binding (GO:0070016)|calmodulin binding (GO:0005516)|estrogen receptor binding (GO:0030331)|protein complex binding (GO:0032403)|protein phosphatase 2A binding (GO:0051721)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(16)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	33		Ovarian(717;0.0129)|all_hematologic(82;0.21)				AAGTATGTACCTTTAGTATCA	0.338																																					p.E613Q													.	STRN	71	0			c.G1837C						.						39.0	41.0	40.0					2																	37084999		2203	4300	6503	SO:0001630	splice_region_variant	6801	exon14			ATGTACCTTTAGT	AJ223814	CCDS1784.1	2p22.2	2013-01-10	2001-11-28		ENSG00000115808	ENSG00000115808		"""WD repeat domain containing"""	11424	protein-coding gene	gene with protein product		614765	"""striatin, calmodulin-binding protein"""			9693043, 8769426	Standard	NM_003162		Approved	SG2NA	uc002rpn.3	O43815	OTTHUMG00000100959	ENST00000263918.4:c.1837+1G>C	2.37:g.37084999C>G		Somatic	50	0		WXS	Illumina GAIIx	Phase_I	14	7	NM_003162	Q3KP65|Q53TQ8|Q9NP38	Splice_Site	SNP	ENST00000263918.4	37	CCDS1784.1	.	.	.	.	.	.	.	.	.	.	C	15.22	2.768968	0.49680	.	.	ENSG00000115808	ENST00000263918;ENST00000538092;ENST00000379213	T;T	0.29397	1.57;1.57	4.76	4.76	0.60689	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.270973	0.42548	D	0.000696	T	0.34948	0.0915	L	0.45470	1.425	0.54753	D	0.999985	P;B	0.35745	0.518;0.036	B;B	0.41619	0.361;0.09	T	0.07539	-1.0767	9	.	.	.	-9.7776	18.1307	0.89600	0.0:1.0:0.0:0.0	.	564;613	O43815-2;O43815	.;STRN_HUMAN	Q	613;588;564	ENSP00000263918:E613Q;ENSP00000368513:E564Q	.	E	-	1	0	STRN	36938503	1.000000	0.71417	1.000000	0.80357	0.861000	0.49209	4.298000	0.59067	2.363000	0.80096	0.484000	0.47621	GAA	.		0.338	STRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218568.1		Missense_Mutation
SPTBN1	6711	broad.mit.edu;bcgsc.ca	37	2	54857084	54857084	+	Missense_Mutation	SNP	A	A	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr2:54857084A>G	ENST00000356805.4	+	15	3006	c.2725A>G	c.(2725-2727)Aac>Gac	p.N909D	SPTBN1_ENST00000333896.5_Missense_Mutation_p.N896D	NM_003128.2	NP_003119.2	Q01082	SPTB2_HUMAN	spectrin, beta, non-erythrocytic 1	909					actin filament capping (GO:0051693)|axon guidance (GO:0007411)|Golgi to plasma membrane protein transport (GO:0043001)|membrane assembly (GO:0071709)|mitotic cytokinesis (GO:0000281)|plasma membrane organization (GO:0007009)|protein targeting to plasma membrane (GO:0072661)	axolemma (GO:0030673)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|protein complex (GO:0043234)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin binding (GO:0003779)|ankyrin binding (GO:0030506)|phospholipid binding (GO:0005543)|poly(A) RNA binding (GO:0044822)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|breast(8)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(11)|lung(27)|ovary(4)|prostate(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	82			Lung(47;0.24)			TGCAGTGGTGAACCAGATTGC	0.542																																					p.N909D													.	SPTBN1	378	0			c.A2725G						.						80.0	74.0	76.0					2																	54857084		2203	4300	6503	SO:0001583	missense	0	exon15			GTGGTGAACCAGA		CCDS33198.1, CCDS33199.1	2p21	2013-01-10			ENSG00000115306	ENSG00000115306		"""Pleckstrin homology (PH) domain containing"""	11275	protein-coding gene	gene with protein product		182790					Standard	NM_003128		Approved		uc002rxu.3	Q01082	OTTHUMG00000133746	ENST00000356805.4:c.2725A>G	2.37:g.54857084A>G	ENSP00000349259:p.Asn909Asp	Somatic	20	0		WXS	Illumina GAIIx	Phase_I	6	3	NM_003128	B2RP63|O60837|Q16057|Q53R99|Q59ER3|Q8IX99	Missense_Mutation	SNP	ENST00000356805.4	37	CCDS33198.1	.	.	.	.	.	.	.	.	.	.	A	26.1	4.704172	0.88924	.	.	ENSG00000115306	ENST00000356805;ENST00000333896	T;T	0.52983	0.64;0.64	5.78	5.78	0.91487	.	0.000000	0.85682	D	0.000000	T	0.71409	0.3336	M	0.88640	2.97	0.58432	D	0.999996	P;P	0.48764	0.915;0.849	P;P	0.59012	0.584;0.85	T	0.77552	-0.2545	10	0.87932	D	0	.	16.1138	0.81283	1.0:0.0:0.0:0.0	.	896;909	Q01082-3;Q01082	.;SPTB2_HUMAN	D	909;896	ENSP00000349259:N909D;ENSP00000334156:N896D	ENSP00000334156:N896D	N	+	1	0	SPTBN1	54710588	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	9.281000	0.95811	2.220000	0.72140	0.533000	0.62120	AAC	.		0.542	SPTBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258115.3		
MERTK	10461	broad.mit.edu	37	2	112656268	112656268	+	De_novo_Start_OutOfFrame	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr2:112656268T>G	ENST00000295408.4	+	0	213				MERTK_ENST00000421804.2_De_novo_Start_OutOfFrame|MERTK_ENST00000409780.1_De_novo_Start_InFrame			Q12866	MERTK_HUMAN	MER proto-oncogene, tyrosine kinase						apoptotic cell clearance (GO:0043277)|blood coagulation (GO:0007596)|cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|leukocyte migration (GO:0050900)|natural killer cell differentiation (GO:0001779)|negative regulation of lymphocyte activation (GO:0051250)|peptidyl-tyrosine phosphorylation (GO:0018108)|phagocytosis (GO:0006909)|platelet activation (GO:0030168)|positive regulation of phagocytosis (GO:0050766)|protein kinase B signaling (GO:0043491)|protein phosphorylation (GO:0006468)|retina development in camera-type eye (GO:0060041)|secretion by cell (GO:0032940)|spermatogenesis (GO:0007283)|substrate adhesion-dependent cell spreading (GO:0034446)|vagina development (GO:0060068)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|rhabdomere (GO:0016028)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(1)|endometrium(3)|kidney(2)|large_intestine(6)|liver(1)|lung(18)|pancreas(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(10)	46						GGGACGTCCATCTGTCCATCC	0.721																																					.													.	MERTK	112	0			.						.						6.0	9.0	8.0					2																	112656268		2139	4214	6353			10461	.			CGTCCATCTGTCC	U08023	CCDS2094.1	2q14.1	2014-06-26	2014-06-26		ENSG00000153208	ENSG00000153208		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	7027	protein-coding gene	gene with protein product		604705	"""c-mer proto-oncogene tyrosine kinase"""			8086340, 10343112	Standard	XM_005263565		Approved	mer, RP38	uc002thk.1	Q12866	OTTHUMG00000131278	ENST00000295408.4:c.-45T>G	2.37:g.112656268T>G		Somatic	9	0		WXS	Illumina GAIIx	Phase_I	5	2	.	Q9HBB4	Translation_Start_Site	SNP	ENST00000295408.4	37	CCDS2094.1																																																																																			.		0.721	MERTK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254046.2		
WDFY1	57590	broad.mit.edu;bcgsc.ca	37	2	224758968	224758968	+	Missense_Mutation	SNP	C	C	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr2:224758968C>T	ENST00000233055.4	-	8	916	c.814G>A	c.(814-816)Gat>Aat	p.D272N		NM_020830.3	NP_065881.1	Q8IWB7	WDFY1_HUMAN	WD repeat and FYVE domain containing 1	272						cytosol (GO:0005829)|early endosome (GO:0005769)|nucleus (GO:0005634)	1-phosphatidylinositol binding (GO:0005545)|zinc ion binding (GO:0008270)			NS(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(6)|prostate(2)	18		all_lung(227;0.00682)|Lung NSC(271;0.00859)|Renal(207;0.0112)|all_hematologic(139;0.189)		Epithelial(121;5.34e-10)|all cancers(144;1.67e-07)|Lung(261;0.00807)|LUSC - Lung squamous cell carcinoma(224;0.00843)		CTGCTAACATCCATGTTCCAC	0.567																																					p.D272N													.	WDFY1	46	0			c.G814A						.						191.0	140.0	157.0					2																	224758968		2203	4300	6503	SO:0001583	missense	57590	exon8			TAACATCCATGTT	AB037856	CCDS33387.1	2q36.2	2013-01-09	2003-03-13		ENSG00000085449	ENSG00000085449		"""Zinc fingers, FYVE domain containing"", ""WD repeat domain containing"""	20451	protein-coding gene	gene with protein product			"""WD40 and FYVE domain containing 1"""			11739631	Standard	NM_020830		Approved	KIAA1435, FENS-1, WDF1, ZFYVE17	uc002vnq.3	Q8IWB7	OTTHUMG00000153370	ENST00000233055.4:c.814G>A	2.37:g.224758968C>T	ENSP00000233055:p.Asp272Asn	Somatic	47	0		WXS	Illumina GAIIx	Phase_I	34	16	NM_020830	Q53S17|Q9H9D5|Q9P2B3	Missense_Mutation	SNP	ENST00000233055.4	37	CCDS33387.1	.	.	.	.	.	.	.	.	.	.	C	24.4	4.523155	0.85600	.	.	ENSG00000085449	ENST00000233055	T	0.28895	1.59	5.73	5.73	0.89815	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.046925	0.85682	D	0.000000	T	0.45236	0.1332	L	0.32530	0.975	0.80722	D	1	D	0.63880	0.993	D	0.74674	0.984	T	0.08700	-1.0709	10	0.18276	T	0.48	-24.6381	19.9093	0.97021	0.0:1.0:0.0:0.0	.	272	Q8IWB7	WDFY1_HUMAN	N	272	ENSP00000233055:D272N	ENSP00000233055:D272N	D	-	1	0	WDFY1	224467212	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.176000	0.77643	2.713000	0.92767	0.655000	0.94253	GAT	.		0.567	WDFY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330908.1	NM_020830	
ADAM33	80332	broad.mit.edu	37	20	3654549	3654549	+	Missense_Mutation	SNP	T	T	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr20:3654549T>C	ENST00000356518.2	-	9	989	c.748A>G	c.(748-750)Act>Gct	p.T250A	ADAM33_ENST00000466620.1_5'Flank|ADAM33_ENST00000379861.4_Missense_Mutation_p.T250A|ADAM33_ENST00000350009.2_Missense_Mutation_p.T250A	NM_025220.2	NP_079496.1	Q9BZ11	ADA33_HUMAN	ADAM metallopeptidase domain 33	250	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				proteolysis (GO:0006508)	integral component of membrane (GO:0016021)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(17)|ovary(1)|skin(3)	29						ATGTCCAGAGTCCTGAGAAGC	0.706																																					p.T250A													.	ADAM33	76	0			c.A748G						.						9.0	11.0	11.0					20																	3654549		2161	4209	6370	SO:0001583	missense	80332	exon9			CCAGAGTCCTGAG	AL117415, AB055891	CCDS13058.1, CCDS63219.1	20p13	2010-04-06	2005-08-18		ENSG00000149451	ENSG00000149451		"""ADAM metallopeptidase domain containing"""	15478	protein-coding gene	gene with protein product		607114	"""a disintegrin and metalloproteinase domain 33"", ""chromosome 20 open reading frame 153"""	C20orf153		11814695	Standard	XM_005260843		Approved	DKFZp434K0521, dJ964F7.1	uc002wit.3	Q9BZ11	OTTHUMG00000031758	ENST00000356518.2:c.748A>G	20.37:g.3654549T>C	ENSP00000348912:p.Thr250Ala	Somatic	17	0		WXS	Illumina GAIIx	Phase_I	11	7	NM_025220	A0A1K6|Q5JT75|Q5JT76|Q8N0W6	Missense_Mutation	SNP	ENST00000356518.2	37	CCDS13058.1	.	.	.	.	.	.	.	.	.	.	T	10.79	1.448464	0.26074	.	.	ENSG00000149451	ENST00000356518;ENST00000379861;ENST00000350009;ENST00000439201	T;T;T	0.17054	2.3;2.3;2.3	5.3	4.16	0.48862	Metallopeptidase, catalytic domain (1);Peptidase M12B, ADAM/reprolysin (2);	.	.	.	.	T	0.10252	0.0251	N	0.05510	-0.035	0.32729	N	0.509217	B;B;B;B;B	0.32862	0.387;0.039;0.046;0.033;0.033	B;B;B;B;B	0.39068	0.289;0.035;0.018;0.03;0.03	T	0.14392	-1.0474	9	0.34782	T	0.22	.	7.6245	0.28204	0.3699:0.0:0.0:0.6301	.	250;262;250;250;250	B4DTZ3;B4E1Y6;Q9BZ11-2;Q9BZ11;A2A2L3	.;.;.;ADA33_HUMAN;.	A	250	ENSP00000348912:T250A;ENSP00000369190:T250A;ENSP00000322550:T250A	ENSP00000322550:T250A	T	-	1	0	ADAM33	3602549	1.000000	0.71417	0.998000	0.56505	0.647000	0.38526	1.204000	0.32296	2.008000	0.58898	0.379000	0.24179	ACT	.		0.706	ADAM33-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000077763.2	NM_025220	
MMP9	4318	broad.mit.edu;bcgsc.ca	37	20	44643002	44643008	+	Splice_Site	DEL	GCCCGCA	GCCCGCA	-			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr20:44643002_44643008delGCCCGCA	ENST00000372330.3	+	12	1920		c.e12-1		RP11-465L10.10_ENST00000535913.1_RNA	NM_004994.2	NP_004985.2	P14780	MMP9_HUMAN	matrix metallopeptidase 9 (gelatinase B, 92kDa gelatinase, 92kDa type IV collagenase)						collagen catabolic process (GO:0030574)|embryo implantation (GO:0007566)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|leukocyte migration (GO:0050900)|macrophage differentiation (GO:0030225)|negative regulation of cation channel activity (GO:2001258)|ossification (GO:0001503)|positive regulation of apoptotic process (GO:0043065)|positive regulation of keratinocyte migration (GO:0051549)|positive regulation of receptor binding (GO:1900122)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	collagen binding (GO:0005518)|identical protein binding (GO:0042802)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(2)|endometrium(4)|large_intestine(14)|liver(2)|lung(17)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(3)	46		Myeloproliferative disorder(115;0.0122)			Captopril(DB01197)|Glucosamine(DB01296)|Marimastat(DB00786)|Minocycline(DB01017)	CTCCGCGCCTGCCCGCAGGTTCGACGT	0.729											OREG0025990	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									.													.	MMP9	84	0			.						.																																			SO:0001630	splice_region_variant	4318	.			GCGCCTGCCCGCA		CCDS13390.1	20q12-q13	2008-01-07	2005-08-08		ENSG00000100985	ENSG00000100985	3.4.24.35		7176	protein-coding gene	gene with protein product		120361	"""matrix metalloproteinase 9 (gelatinase B, 92kD gelatinase, 92kD type IV collagenase)"", ""matrix metalloproteinase 9 (gelatinase B, 92kDa gelatinase, 92kDa type IV collagenase)"""	CLG4B		2158484	Standard	NM_004994		Approved		uc002xqz.3	P14780	OTTHUMG00000033044	ENST00000372330.3:c.1902-1GCCCGCA>-	20.37:g.44643002_44643008delGCCCGCA		Somatic	43	0	925	WXS	Illumina GAIIx	Phase_I	28	7	.	B2R7V9|Q3LR70|Q8N725|Q9H4Z1|Q9UCJ9|Q9UCL1|Q9UDK2	Splice_Site	DEL	ENST00000372330.3	37	CCDS13390.1																																																																																			.		0.729	MMP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080337.1		Intron
SLC23A2	9962	broad.mit.edu;ucsc.edu;bcgsc.ca	37	20	4839936	4839936	+	Splice_Site	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr20:4839936T>G	ENST00000379333.1	-	16	2111	c.1719A>C	c.(1717-1719)ccA>ccC	p.P573P	SLC23A2_ENST00000338244.1_Splice_Site_p.P573P|SLC23A2_ENST00000424750.2_Splice_Site_p.P459P	NM_203327.1	NP_976072.1	Q9UGH3	S23A2_HUMAN	solute carrier family 23 (ascorbic acid transporter), member 2	573					L-ascorbic acid metabolic process (GO:0019852)|L-ascorbic acid transport (GO:0015882)|molecular hydrogen transport (GO:0015993)|nucleobase transport (GO:0015851)|nucleobase-containing compound metabolic process (GO:0006139)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)|transepithelial L-ascorbic acid transport (GO:0070904)|vitamin metabolic process (GO:0006766)|vitamin transmembrane transport (GO:0035461)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	L-ascorbate:sodium symporter activity (GO:0008520)|L-ascorbic acid transporter activity (GO:0015229)|nucleobase transmembrane transporter activity (GO:0015205)|sodium-dependent L-ascorbate transmembrane transporter activity (GO:0070890)|sodium-dependent multivitamin transmembrane transporter activity (GO:0008523)			endometrium(1)|kidney(3)|large_intestine(9)|lung(7)|ovary(3)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	27						ACCACGTACCTGGGATGGTGT	0.363																																					p.P573P													.	SLC23A2	62	0			c.A1719C						.						148.0	140.0	142.0					20																	4839936		2203	4300	6503	SO:0001630	splice_region_variant	9962	exon16			CGTACCTGGGATG	AF058319	CCDS13085.1	20p13	2013-07-18	2013-07-18	2003-03-21	ENSG00000089057	ENSG00000089057		"""Solute carriers"""	10973	protein-coding gene	gene with protein product		603791	"""solute carrier family 23 (nucleobase transporters), member 1"""	SLC23A1		9804989, 10331392	Standard	NM_005116		Approved	SVCT2, KIAA0238, YSPL2	uc002wlh.1	Q9UGH3	OTTHUMG00000031793	ENST00000379333.1:c.1720+1A>C	20.37:g.4839936T>G		Somatic	133	0		WXS	Illumina GAIIx	Phase_I	78	31	NM_203327	B4DJZ1|Q8WWR4|Q92512|Q96D54|Q9UNU1|Q9UP85	Splice_Site	SNP	ENST00000379333.1	37	CCDS13085.1																																																																																			.		0.363	SLC23A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077832.1		Silent
RALGAPB	57148	broad.mit.edu	37	20	37117260	37117260	+	Splice_Site	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr20:37117260A>C	ENST00000262879.6	+	2	469	c.185A>C	c.(184-186)gAa>gCa	p.E62A	RALGAPB_ENST00000397042.3_Splice_Site_p.E62A|RALGAPB_ENST00000397040.1_Splice_Site_p.E62A|RALGAPB_ENST00000397038.1_5'UTR|RALGAPB_ENST00000537204.1_Splice_Site_p.E62A			Q86X10	RLGPB_HUMAN	Ral GTPase activating protein, beta subunit (non-catalytic)	62					activation of Ral GTPase activity (GO:0032859)|membrane organization (GO:0061024)|Ral protein signal transduction (GO:0032484)|regulation of exocyst localization (GO:0060178)		protein heterodimerization activity (GO:0046982)|Ral GTPase activator activity (GO:0017123)			breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(29)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	65						ACTGACAAAGAAGTAAGTGTT	0.353																																					p.E62A													.	RALGAPB	134	0			c.A185C						.						108.0	103.0	105.0					20																	37117260		2203	4300	6503	SO:0001630	splice_region_variant	57148	exon2			ACAAAGAAGTAAG	AB033045	CCDS13305.1, CCDS63272.1	20q11.23	2009-09-09	2009-09-09	2009-09-09	ENSG00000170471	ENSG00000170471			29221	protein-coding gene	gene with protein product			"""KIAA1219"""	KIAA1219		19520869	Standard	XM_005260462		Approved	DKFZp781M2411, RalGAPbeta	uc002xiw.3	Q86X10	OTTHUMG00000140270	ENST00000262879.6:c.186+1A>C	20.37:g.37117260A>C		Somatic	46	0		WXS	Illumina GAIIx	Phase_I	17	4	NM_020336	A2A2E8|A2A2E9|Q5TG31|Q8N3D1|Q8WWC0|Q9H3X8|Q9UJR1|Q9ULK1|Q9Y3G9	Splice_Site	SNP	ENST00000262879.6	37	CCDS13305.1	.	.	.	.	.	.	.	.	.	.	A	27.9	4.868576	0.91587	.	.	ENSG00000170471	ENST00000262879;ENST00000397042;ENST00000304939;ENST00000537204;ENST00000397040	.	.	.	5.68	5.68	0.88126	.	0.047041	0.85682	D	0.000000	T	0.78886	0.4354	M	0.73962	2.25	0.80722	D	1	B;D;D;D	0.56035	0.008;0.974;0.974;0.974	B;D;D;D	0.70487	0.034;0.969;0.969;0.969	T	0.80752	-0.1242	9	0.62326	D	0.03	.	16.2322	0.82352	1.0:0.0:0.0:0.0	.	62;62;62;62	B4E2E8;Q86X10-4;A2A2E9;Q86X10	.;.;.;RLGPB_HUMAN	A	62	.	ENSP00000262879:E62A	E	+	2	0	RALGAPB	36550674	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.826000	0.92034	2.288000	0.76882	0.528000	0.53228	GAA	.		0.353	RALGAPB-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000079191.1	NM_020336	Missense_Mutation
BAGE2	85319	broad.mit.edu	37	21	11043037	11043039	+	RNA	DEL	TGC	TGC	-	rs2770437|rs60544723|rs149525628|rs560954938	byFrequency	TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr21:11043037_11043039delTGC	ENST00000470054.1	-	0	774							Q86Y30	BAGE2_HUMAN	B melanoma antigen family, member 2							extracellular region (GO:0005576)								Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		ttgctgttgttgctgttgttgtt	0.453														1753	0.35004	0.2118	0.4222	5008	,	,		128618	0.4038		0.4264	False		,,,				2504	0.3517				.													.	.	.	0			.						.																																					85319	.			TGTTGTTGCTGTT	AF218570		21p	2009-03-13			ENSG00000187172	ENSG00000187172			15723	protein-coding gene	gene with protein product	"""cancer/testis antigen family 2, member 2"""					12461691	Standard	NM_182482		Approved	CT2.2		Q86Y30	OTTHUMG00000074128		21.37:g.11043037_11043039delTGC		Somatic	5	0		WXS	Illumina GAIIx	Phase_I	6	2	.	A8K925|Q08ER0	RNA	DEL	ENST00000470054.1	37																																																																																				.		0.453	BAGE2-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000157417.3	NM_182482	
BTG3	10950	broad.mit.edu;ucsc.edu;bcgsc.ca	37	21	18966436	18966436	+	Missense_Mutation	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr21:18966436T>G	ENST00000348354.6	-	5	990	c.734A>C	c.(733-735)aAt>aCt	p.N245T	BTG3_ENST00000339775.6_Missense_Mutation_p.N289T	NM_006806.4	NP_006797.3	Q14201	BTG3_HUMAN	BTG family, member 3	245					negative regulation of cell proliferation (GO:0008285)|negative regulation of mitotic cell cycle (GO:0045930)	cytoplasm (GO:0005737)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(4)	8				Epithelial(23;0.000283)|all cancers(11;0.0012)|Lung(58;0.0191)|OV - Ovarian serous cystadenocarcinoma(11;0.0206)|COAD - Colon adenocarcinoma(22;0.0315)|LUSC - Lung squamous cell carcinoma(23;0.0703)|Colorectal(24;0.0971)		CATGTGAGGATTAATCCAGTG	0.388																																					p.N289T													.	BTG3	27	0			c.A866C						.						105.0	85.0	92.0					21																	18966436		2203	4299	6502	SO:0001583	missense	10950	exon6			TGAGGATTAATCC	D64110	CCDS13569.1, CCDS46636.1	21q21.1	2006-12-16			ENSG00000154640	ENSG00000154640			1132	protein-coding gene	gene with protein product		605674				9632145	Standard	NM_006806		Approved	ANA, tob55	uc002ykk.3	Q14201	OTTHUMG00000074501	ENST00000348354.6:c.734A>C	21.37:g.18966436T>G	ENSP00000284879:p.Asn245Thr	Somatic	91	0		WXS	Illumina GAIIx	Phase_I	36	23	NM_001130914	D3DSC4|Q53XV1|Q96ET7	Missense_Mutation	SNP	ENST00000348354.6	37	CCDS13569.1	.	.	.	.	.	.	.	.	.	.	T	15.70	2.911072	0.52439	.	.	ENSG00000154640	ENST00000339775;ENST00000348354	.	.	.	3.88	2.7	0.31948	.	0.308672	0.26915	N	0.021850	T	0.26629	0.0651	N	0.19112	0.55	0.23243	N	0.998057	P;B	0.52316	0.952;0.0	P;B	0.47402	0.546;0.0	T	0.06862	-1.0803	9	0.66056	D	0.02	-15.2504	7.3894	0.26901	0.0:0.0:0.2226:0.7774	.	289;245	Q14201-2;Q14201	.;BTG3_HUMAN	T	289;245	.	ENSP00000344609:N289T	N	-	2	0	BTG3	17888307	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.421000	0.52742	0.824000	0.34613	0.482000	0.46254	AAT	.		0.388	BTG3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000158196.1	NM_006806	
PFKL	5211	broad.mit.edu;bcgsc.ca	37	21	45746699	45746699	+	Missense_Mutation	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr21:45746699T>G	ENST00000349048.4	+	22	2352	c.2297T>G	c.(2296-2298)cTg>cGg	p.L766R	AP001062.8_ENST00000422357.1_RNA|PFKL_ENST00000403390.1_Missense_Mutation_p.L813R	NM_002626.4	NP_002617.3	P17858	PFKAL_HUMAN	phosphofructokinase, liver	766	C-terminal regulatory PFK domain 2.				carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|fructose 1,6-bisphosphate metabolic process (GO:0030388)|fructose 6-phosphate metabolic process (GO:0006002)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|negative regulation of insulin secretion (GO:0046676)|protein homotetramerization (GO:0051289)|protein oligomerization (GO:0051259)|response to glucose (GO:0009749)|small molecule metabolic process (GO:0044281)	6-phosphofructokinase complex (GO:0005945)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	6-phosphofructokinase activity (GO:0003872)|ATP binding (GO:0005524)|fructose binding (GO:0070061)|fructose-6-phosphate binding (GO:0070095)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|metal ion binding (GO:0046872)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(10)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	23				Colorectal(79;0.0811)		TCAGGGGAGCTGGAGCACGTG	0.672																																					p.L766R													.	PFKL	65	0			c.T2297G						.						32.0	28.0	30.0					21																	45746699		2194	4295	6489	SO:0001583	missense	5211	exon22			GGGAGCTGGAGCA		CCDS33582.1	21q22.3	1992-12-17			ENSG00000141959	ENSG00000141959	2.7.1.11		8876	protein-coding gene	gene with protein product		171860					Standard	NR_024108		Approved		uc002zel.3	P17858	OTTHUMG00000086910	ENST00000349048.4:c.2297T>G	21.37:g.45746699T>G	ENSP00000269848:p.Leu766Arg	Somatic	94	3		WXS	Illumina GAIIx	Phase_I	23	17	NM_002626	Q96A64|Q96IH4|Q9BR91	Missense_Mutation	SNP	ENST00000349048.4	37	CCDS33582.1	.	.	.	.	.	.	.	.	.	.	T	14.24	2.475584	0.43942	.	.	ENSG00000141959	ENST00000349048;ENST00000534847;ENST00000403390	D;D	0.83755	-1.69;-1.76	3.86	3.86	0.44501	.	0.124769	0.53938	U	0.000058	D	0.86986	0.6065	L	0.52905	1.665	0.41152	D	0.986039	B;D	0.56035	0.09;0.974	B;D	0.63488	0.069;0.915	D	0.87744	0.2587	10	0.66056	D	0.02	-17.672	11.6617	0.51349	0.0:0.0:0.0:1.0	.	766;813	P17858;P17858-2	K6PL_HUMAN;.	R	766;559;813	ENSP00000269848:L766R;ENSP00000384038:L813R	ENSP00000269848:L766R	L	+	2	0	PFKL	44571127	1.000000	0.71417	0.998000	0.56505	0.476000	0.33039	7.604000	0.82830	1.381000	0.46364	0.383000	0.25322	CTG	.		0.672	PFKL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195805.1		
CDC42EP1	11135	broad.mit.edu	37	22	37964736	37964736	+	Missense_Mutation	SNP	A	A	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr22:37964736A>G	ENST00000249014.4	+	3	1505	c.1085A>G	c.(1084-1086)cAg>cGg	p.Q362R		NM_152243.2	NP_689449.1	Q00587	BORG5_HUMAN	CDC42 effector protein (Rho GTPase binding) 1	362					positive regulation of pseudopodium assembly (GO:0031274)|regulation of cell shape (GO:0008360)|Rho protein signal transduction (GO:0007266)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)				endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(2)|lung(4)|prostate(5)	15	Melanoma(58;0.0574)					AGGGCGCCCCAGGCAGGCAGC	0.647																																					p.Q362R													.	CDC42EP1	53	0			c.A1085G						.						22.0	27.0	25.0					22																	37964736		2203	4300	6503	SO:0001583	missense	11135	exon3			CGCCCCAGGCAGG	M88338	CCDS13949.1	22q13.1	2008-06-11			ENSG00000128283	ENSG00000128283			17014	protein-coding gene	gene with protein product	"""55 kDa bone marrow stromal/endothelial cell protein"", ""serum constituent protein"""	606084				1629197, 10430899	Standard	NM_152243		Approved	MSE55, CEP1, Borg5	uc003asz.4	Q00587	OTTHUMG00000150591	ENST00000249014.4:c.1085A>G	22.37:g.37964736A>G	ENSP00000249014:p.Gln362Arg	Somatic	14	0		WXS	Illumina GAIIx	Phase_I	8	3	NM_152243	A8K825|Q96GN1	Missense_Mutation	SNP	ENST00000249014.4	37	CCDS13949.1	.	.	.	.	.	.	.	.	.	.	A	1.910	-0.451018	0.04572	.	.	ENSG00000128283	ENST00000249014	T	0.28895	1.59	4.57	-7.04	0.01578	.	1.673740	0.03305	N	0.189655	T	0.16727	0.0402	L	0.27053	0.805	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.37103	-0.9720	10	0.05959	T	0.93	1.0E-4	9.6851	0.40094	0.1643:0.4232:0.4125:0.0	.	362	Q00587	BORG5_HUMAN	R	362	ENSP00000249014:Q362R	ENSP00000249014:Q362R	Q	+	2	0	CDC42EP1	36294682	0.000000	0.05858	0.151000	0.22473	0.164000	0.22412	-0.402000	0.07223	-1.138000	0.02884	-0.441000	0.05720	CAG	.		0.647	CDC42EP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318993.1	NM_152243	
TOP3B	8940	broad.mit.edu	37	22	22318376	22318376	+	Missense_Mutation	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr22:22318376T>G	ENST00000398793.2	-	11	1557	c.1123A>C	c.(1123-1125)Atc>Ctc	p.I375L	TOP3B_ENST00000413067.2_Missense_Mutation_p.I104L|TOP3B_ENST00000357179.5_Missense_Mutation_p.I375L	NM_003935.3	NP_003926.1	O95985	TOP3B_HUMAN	topoisomerase (DNA) III beta	375					chromosome segregation (GO:0007059)|DNA topological change (GO:0006265)	condensed chromosome (GO:0000793)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA topoisomerase activity (GO:0003916)|DNA topoisomerase type I activity (GO:0003917)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(4)|lung(9)|ovary(1)	26	Colorectal(54;0.105)			READ - Rectum adenocarcinoma(21;0.145)		GGGCGGTTGATACCTTCTGCT	0.602																																					p.I375L													.	TOP3B	107	0			c.A1123C						.						63.0	65.0	64.0					22																	22318376		2203	4300	6503	SO:0001583	missense	8940	exon11			GGTTGATACCTTC	AF017146	CCDS13797.1	22q11.22	2011-05-24			ENSG00000100038	ENSG00000100038			11993	protein-coding gene	gene with protein product		603582				9786842, 9074928	Standard	XM_005261811		Approved		uc002zvs.3	O95985	OTTHUMG00000167438	ENST00000398793.2:c.1123A>C	22.37:g.22318376T>G	ENSP00000381773:p.Ile375Leu	Somatic	15	0		WXS	Illumina GAIIx	Phase_I	10	3	NM_003935	A0M8Q3|Q9BUP5	Missense_Mutation	SNP	ENST00000398793.2	37	CCDS13797.1	.	.	.	.	.	.	.	.	.	.	T	11.05	1.523790	0.27299	.	.	ENSG00000100038	ENST00000357179;ENST00000398793;ENST00000413067	T;T;T	0.21191	2.02;2.02;2.02	4.95	3.9	0.45041	DNA topoisomerase, type IA, core domain (1);DNA topoisomerase, type IA, central region, subdomain 3 (1);DNA topoisomerase, type IA, central (1);DNA topoisomerase, type IA, DNA-binding (1);	0.113744	0.64402	D	0.000018	T	0.11153	0.0272	N	0.17474	0.49	0.58432	D	0.999999	B;B	0.09022	0.002;0.002	B;B	0.11329	0.006;0.003	T	0.08827	-1.0703	10	0.07325	T	0.83	.	10.8156	0.46573	0.0:0.0754:0.0:0.9246	.	375;375	O95985;O95985-2	TOP3B_HUMAN;.	L	375;375;104	ENSP00000349705:I375L;ENSP00000381773:I375L;ENSP00000393118:I104L	ENSP00000349705:I375L	I	-	1	0	TOP3B	20648376	0.298000	0.24417	0.989000	0.46669	0.656000	0.38851	0.586000	0.23894	0.883000	0.36040	0.459000	0.35465	ATC	.		0.602	TOP3B-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320251.1	NM_003935	
BMS1P20	96610	broad.mit.edu	37	22	22663052	22663052	+	RNA	SNP	T	T	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr22:22663052T>C	ENST00000426066.1	+	0	500					NR_027293.1				BMS1 pseudogene 20																		AATTTTGGGGTTCCTGTTAGC	0.308																																					.													.	.	.	0			.						.																																					0	.			TTGGGGTTCCTGT			22q11.22	2013-09-20			ENSG00000236850	ENSG00000236850			49153	pseudogene	pseudogene							Standard	XR_430414		Approved				OTTHUMG00000151046		22.37:g.22663052T>C		Somatic	221	1		WXS	Illumina GAIIx	Phase_I	87	6	.		RNA	SNP	ENST00000426066.1	37																																																																																				.		0.308	BMS1P20-001	KNOWN	basic|readthrough_transcript	processed_transcript	processed_transcript	OTTHUMT00000473090.1		
EP300	2033	broad.mit.edu	37	22	41513219	41513219	+	Missense_Mutation	SNP	C	C	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr22:41513219C>G	ENST00000263253.7	+	2	1342	c.123C>G	c.(121-123)caC>caG	p.H41Q		NM_001429.3	NP_001420.2	Q09472	EP300_HUMAN	E1A binding protein p300	41	Interaction with ALX1.|Interaction with RORA.				apoptotic process (GO:0006915)|cellular response to hypoxia (GO:0071456)|chromatin organization (GO:0006325)|circadian rhythm (GO:0007623)|G2/M transition of mitotic cell cycle (GO:0000086)|heart development (GO:0007507)|histone H2B acetylation (GO:0043969)|histone H4 acetylation (GO:0043967)|innate immune response (GO:0045087)|internal peptidyl-lysine acetylation (GO:0018393)|internal protein amino acid acetylation (GO:0006475)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|lung development (GO:0030324)|mitotic cell cycle (GO:0000278)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of protein binding (GO:0032092)|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 type I interferon production (GO:0032481)|regulation of androgen receptor signaling pathway (GO:0060765)|regulation of cell cycle (GO:0051726)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)|regulation of tubulin deacetylation (GO:0090043)|response to estrogen (GO:0043627)|response to hypoxia (GO:0001666)|skeletal muscle tissue development (GO:0007519)|somitogenesis (GO:0001756)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	acetyltransferase activity (GO:0016407)|activating transcription factor binding (GO:0033613)|androgen receptor binding (GO:0050681)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|lysine N-acetyltransferase activity, acting on acetyl phosphate as donor (GO:0004468)|nuclear hormone receptor binding (GO:0035257)|pre-mRNA intronic binding (GO:0097157)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transferase activity, transferring acyl groups (GO:0016746)|zinc ion binding (GO:0008270)			NS(2)|breast(11)|central_nervous_system(7)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(31)|kidney(5)|large_intestine(31)|liver(2)|lung(33)|ovary(2)|pancreas(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(16)	171						ACTTGGAGCACGACTTACCAG	0.368			"""T,  N, F, Mis, O"""	"""MLL, RUNXBP2"""	"""colorectal, breast, pancreatic, AML, ALL, DLBCL"""				Rubinstein-Taybi syndrome																												p.H41Q				Rec	yes		22	22q13	2033	300 kd E1A-Binding protein gene		"""L, E"""	.	EP300	367	0			c.C123G						.						72.0	72.0	72.0					22																	41513219		2203	4300	6503	SO:0001583	missense	2033	exon2	Familial Cancer Database	Broad Thumb-Hallux syndrome	GGAGCACGACTTA	U01877	CCDS14010.1	22q13.2	2011-07-01			ENSG00000100393	ENSG00000100393		"""Chromatin-modifying enzymes / K-acetyltransferases"""	3373	protein-coding gene	gene with protein product	"""histone acetyltransferase p300"""	602700				7523245	Standard	NM_001429		Approved	p300, KAT3B	uc003azl.4	Q09472	OTTHUMG00000150937	ENST00000263253.7:c.123C>G	22.37:g.41513219C>G	ENSP00000263253:p.His41Gln	Somatic	52	0		WXS	Illumina GAIIx	Phase_I	35	12	NM_001429	B1AKC2	Missense_Mutation	SNP	ENST00000263253.7	37	CCDS14010.1	.	.	.	.	.	.	.	.	.	.	C	13.53	2.266190	0.40095	.	.	ENSG00000100393	ENST00000263253	D	0.82711	-1.64	6.16	-5.19	0.02832	.	0.000000	0.49916	D	0.000123	T	0.69052	0.3068	N	0.17723	0.515	0.38705	D	0.953088	P	0.38440	0.631	B	0.38378	0.272	T	0.61778	-0.6993	10	0.49607	T	0.09	-11.5288	15.6194	0.76793	0.0:0.0752:0.0755:0.8493	.	41	Q09472	EP300_HUMAN	Q	41	ENSP00000263253:H41Q	ENSP00000263253:H41Q	H	+	3	2	EP300	39843165	0.342000	0.24809	0.754000	0.31244	0.968000	0.65278	-0.453000	0.06778	-1.650000	0.01506	-0.802000	0.03209	CAC	.		0.368	EP300-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320600.1	NM_001429	
ITPR1	3708	broad.mit.edu	37	3	4878503	4878503	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr3:4878503G>T	ENST00000443694.2	+	58	8029	c.8029G>T	c.(8029-8031)Gtc>Ttc	p.V2677F	ITPR1_ENST00000463980.1_3'UTR|ITPR1_ENST00000423119.2_Missense_Mutation_p.V2644F|ITPR1_ENST00000544951.1_Missense_Mutation_p.V655F|ITPR1_ENST00000354582.6_Missense_Mutation_p.V2677F|ITPR1_ENST00000302640.8_Missense_Mutation_p.V2677F|ITPR1_ENST00000357086.4_Missense_Mutation_p.V2644F|ITPR1_ENST00000456211.2_Missense_Mutation_p.V2629F|AC018816.3_ENST00000441894.1_Intron|AC018816.3_ENST00000449914.1_Intron			Q14643	ITPR1_HUMAN	inositol 1,4,5-trisphosphate receptor, type 1	2692					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|calcium ion transport (GO:0006816)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|negative regulation of calcium-mediated signaling (GO:0050849)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|post-embryonic development (GO:0009791)|regulation of insulin secretion (GO:0050796)|release of sequestered calcium ion into cytosol (GO:0051209)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|voluntary musculoskeletal movement (GO:0050882)	calcineurin complex (GO:0005955)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear inner membrane (GO:0005637)|nucleolus (GO:0005730)|platelet dense granule membrane (GO:0031088)|platelet dense tubular network (GO:0031094)|platelet dense tubular network membrane (GO:0031095)|postsynaptic density (GO:0014069)|sarcoplasmic reticulum (GO:0016529)	calcium channel inhibitor activity (GO:0019855)|calcium ion transmembrane transporter activity (GO:0015085)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|intracellular ligand-gated calcium channel activity (GO:0005218)|phosphatidylinositol binding (GO:0035091)			NS(1)|autonomic_ganglia(1)|breast(10)|endometrium(15)|kidney(6)|large_intestine(27)|liver(1)|lung(27)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|urinary_tract(2)	106				Epithelial(13;0.0199)|OV - Ovarian serous cystadenocarcinoma(96;0.0361)|all cancers(10;0.0982)	Caffeine(DB00201)	CATGTCATTGGTCAGCAGTGA	0.428																																					p.V2677F													.	ITPR1	659	0			c.G8029T						.						26.0	26.0	26.0					3																	4878503		1922	4133	6055	SO:0001583	missense	3708	exon60			TCATTGGTCAGCA	D26070	CCDS46740.1, CCDS46740.2, CCDS54550.1, CCDS54551.1	3p26.1	2014-06-12	2011-04-28			ENSG00000150995		"""Ion channels / Inositol triphosphate receptors"""	6180	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 94"""	147265	"""spinocerebellar ataxia 15"", ""spinocerebellar ataxia 16"", ""spinocerebellar ataxia 29"""	SCA15, SCA16, SCA29		7945203, 7500840, 17590087, 17932120, 22986007	Standard	NM_001099952		Approved	Insp3r1, IP3R1, ACV, PPP1R94	uc003bqc.3	Q14643		ENST00000443694.2:c.8029G>T	3.37:g.4878503G>T	ENSP00000401671:p.Val2677Phe	Somatic	44	0		WXS	Illumina GAIIx	Phase_I	25	4	NM_001168272	E7EPX7|E9PDE9|Q14660|Q99897	Missense_Mutation	SNP	ENST00000443694.2	37	CCDS54551.1	.	.	.	.	.	.	.	.	.	.	G	33	5.264713	0.95399	.	.	ENSG00000150995	ENST00000356617;ENST00000302640;ENST00000354582;ENST00000423119;ENST00000426160;ENST00000357086;ENST00000456211;ENST00000544951;ENST00000443694	T;T;T;T;T;D;T	0.83075	0.98;0.98;0.98;0.98;0.98;-1.68;0.98	6.06	6.06	0.98353	.	0.000000	0.85682	D	0.000000	D	0.90160	0.6925	L	0.59436	1.845	0.80722	D	1	D;D;D	0.69078	0.988;0.991;0.997	D;P;D	0.74674	0.921;0.73;0.984	D	0.89199	0.3556	10	0.56958	D	0.05	.	20.6208	0.99490	0.0:0.0:1.0:0.0	.	655;2692;2644	B7ZMI3;Q14643;G5E9P1	.;ITPR1_HUMAN;.	F	2692;2677;2677;2644;1138;2644;2629;655;2677	ENSP00000306253:V2677F;ENSP00000346595:V2677F;ENSP00000405934:V2644F;ENSP00000349597:V2644F;ENSP00000397885:V2629F;ENSP00000440564:V655F;ENSP00000401671:V2677F	ENSP00000306253:V2677F	V	+	1	0	ITPR1	4853503	1.000000	0.71417	1.000000	0.80357	0.714000	0.41099	9.766000	0.98957	2.882000	0.98803	0.655000	0.94253	GTC	.		0.428	ITPR1-004	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337982.3	NM_002222	
MON1A	84315	broad.mit.edu;bcgsc.ca	37	3	49967045	49967045	+	Frame_Shift_Del	DEL	T	T	-			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr3:49967045delT	ENST00000296473.3	-	1	533	c.275delA	c.(274-276)aacfs	p.N92fs	MON1A_ENST00000455683.2_Frame_Shift_Del_p.N92fs|MON1A_ENST00000483022.1_5'UTR|MON1A_ENST00000417270.1_5'UTR	NM_032355.3	NP_115731.2	Q86VX9	MON1A_HUMAN	MON1 secretory trafficking family member A	0										breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|ovary(2)|prostate(1)	13				BRCA - Breast invasive adenocarcinoma(193;4.62e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.00551)|Kidney(197;0.00621)		AACTCACCTGTTTCTCAGAGG	0.657																																					p.N92fs													.	MON1A	41	0			c.275delA						.						33.0	33.0	33.0					3																	49967045		692	1590	2282	SO:0001589	frameshift_variant	84315	exon1			CACCTGTTTCTCA	AK074404	CCDS2808.2, CCDS46830.1	3p21.31	2013-08-21	2013-08-21		ENSG00000164077	ENSG00000164077			28207	protein-coding gene	gene with protein product		611464	"""MON1 homolog A (yeast)"""			12477932	Standard	NM_032355		Approved	MGC13272, SAND1	uc003cxz.3	Q86VX9	OTTHUMG00000156737	ENST00000296473.3:c.275delA	3.37:g.49967045delT	ENSP00000296473:p.Asn92fs	Somatic	37	0		WXS	Illumina GAIIx	Phase_I	12	9	NM_032355	B2RDQ1|G5E9N1|Q8NAV7|Q9BRF3	Frame_Shift_Del	DEL	ENST00000296473.3	37	CCDS2808.2																																																																																			.		0.657	MON1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345534.2	NM_032355	
FAM86DP	692099	broad.mit.edu	37	3	75471400	75471400	+	RNA	SNP	C	C	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr3:75471400C>T	ENST00000459803.1	-	0	1741					NR_024241.1				family with sequence similarity 86, member D, pseudogene																		TGGCCAGAAGCTGAAATGACG	0.577																																					.													.	.	.	0			.						.																																					0	.			CAGAAGCTGAAAT	BC016686		3p12.3	2010-06-04	2010-06-04	2010-06-04	ENSG00000244026	ENSG00000244026			32659	pseudogene	pseudogene			"""family with sequence similarity 86, member D"""	FAM86D			Standard	NR_024241		Approved		uc003dpp.4		OTTHUMG00000158855		3.37:g.75471400C>T		Somatic	126	0		WXS	Illumina GAIIx	Phase_I	48	3	.		RNA	SNP	ENST00000459803.1	37																																																																																				.		0.577	FAM86DP-003	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000352425.1	NR_024241	
C3orf56	285311	broad.mit.edu;ucsc.edu;bcgsc.ca	37	3	126916189	126916189	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr3:126916189G>T	ENST00000398112.1	+	2	901	c.661G>T	c.(661-663)Gac>Tac	p.D221Y		NM_001007534.2	NP_001007535.1	Q8N813	CC056_HUMAN	chromosome 3 open reading frame 56	221										breast(1)|endometrium(2)|kidney(1)|lung(5)	9				GBM - Glioblastoma multiforme(114;0.142)		TTCTCAGCTGGACCCGGGCTG	0.632																																					.													.	.	.	0			.						.						22.0	24.0	23.0					3																	126916189		1883	4090	5973	SO:0001583	missense	285311	.			CAGCTGGACCCGG	AK097460	CCDS63757.1	3q21.3	2012-08-08			ENSG00000214324	ENSG00000214324			32481	protein-coding gene	gene with protein product						14702039	Standard	NM_001007534		Approved	FLJ40141	uc003eji.1	Q8N813	OTTHUMG00000159593	ENST00000398112.1:c.661G>T	3.37:g.126916189G>T	ENSP00000381182:p.Asp221Tyr	Somatic	63	0		WXS	Illumina GAIIx	Phase_I	57	13	.	B2RNW5	Missense_Mutation	SNP	ENST00000398112.1	37		.	.	.	.	.	.	.	.	.	.	G	7.961	0.747074	0.15710	.	.	ENSG00000214324	ENST00000398112	.	.	.	2.06	-3.65	0.04502	.	.	.	.	.	T	0.24084	0.0583	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.26326	-1.0106	7	0.72032	D	0.01	.	0.3491	0.00346	0.3786:0.1932:0.2336:0.1946	.	221	Q8N813	CC056_HUMAN	Y	221	.	ENSP00000381182:D221Y	D	+	1	0	C3orf56	128398879	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-1.151000	0.03175	-1.129000	0.02918	0.585000	0.79938	GAC	.		0.632	C3orf56-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000356354.1		
ST6GAL1	6480	broad.mit.edu;ucsc.edu;bcgsc.ca	37	3	186760575	186760575	+	Missense_Mutation	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr3:186760575A>C	ENST00000169298.3	+	4	758	c.84A>C	c.(82-84)gaA>gaC	p.E28D	ST6GAL1_ENST00000448044.1_Missense_Mutation_p.E28D|ST6GAL1_ENST00000457772.2_Intron	NM_173216.2	NP_775323.1	P15907	SIAT1_HUMAN	ST6 beta-galactosamide alpha-2,6-sialyltranferase 1	28					cellular protein metabolic process (GO:0044267)|humoral immune response (GO:0006959)|N-acetylneuraminate metabolic process (GO:0006054)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|sialylation (GO:0097503)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)	beta-galactoside alpha-2,6-sialyltransferase activity (GO:0003835)|sialyltransferase activity (GO:0008373)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(1)	7	all_cancers(143;2.33e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;8.53e-19)	GBM - Glioblastoma multiforme(93;0.0939)		TGTGGAAGGAAAAGAAGAAAG	0.428																																					p.E28D													ST6GAL1,right_lower_lobe,carcinoma,+2,1	ST6GAL1	36	0			c.A84C						.						146.0	146.0	146.0					3																	186760575		2203	4300	6503	SO:0001583	missense	6480	exon3			GAAGGAAAAGAAG	X62822	CCDS3285.1, CCDS46973.1	3q27-q28	2013-02-26	2003-01-14	2005-02-07	ENSG00000073849	ENSG00000073849	2.4.99.1		10860	protein-coding gene	gene with protein product	"""ST6Gal I"""	109675	"""sialyltransferase 1 (beta-galactoside alpha-2,6-sialytransferase)"""	SIAT1		2408023	Standard	NM_003032		Approved		uc003frd.3	P15907	OTTHUMG00000156500	ENST00000169298.3:c.84A>C	3.37:g.186760575A>C	ENSP00000169298:p.Glu28Asp	Somatic	58	0		WXS	Illumina GAIIx	Phase_I	42	17	NM_003032	A8KA14|B2R513|D3DNV3	Missense_Mutation	SNP	ENST00000169298.3	37	CCDS3285.1	.	.	.	.	.	.	.	.	.	.	A	20.9	4.066477	0.76187	.	.	ENSG00000073849	ENST00000169298;ENST00000430309;ENST00000417392;ENST00000438590;ENST00000448408;ENST00000440338;ENST00000448044;ENST00000416235;ENST00000423451;ENST00000446170	T;T	0.32023	1.47;1.47	5.07	-0.0638	0.13775	.	0.138959	0.64402	D	0.000004	T	0.43656	0.1257	M	0.63843	1.955	0.80722	D	1	D	0.67145	0.996	D	0.65773	0.938	T	0.25537	-1.0129	10	0.66056	D	0.02	-10.0786	7.6207	0.28183	0.606:0.0:0.394:0.0	.	28	P15907	SIAT1_HUMAN	D	28	ENSP00000169298:E28D;ENSP00000389337:E28D	ENSP00000169298:E28D	E	+	3	2	ST6GAL1	188243269	0.997000	0.39634	0.996000	0.52242	0.966000	0.64601	0.332000	0.19751	-0.166000	0.10890	0.459000	0.35465	GAA	.		0.428	ST6GAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344399.1	NM_173216	
RP11-143P4.2	0	broad.mit.edu	37	3	192871852	192871852	+	lincRNA	DEL	T	T	-	rs34765749|rs397875444	byFrequency	TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr3:192871852delT	ENST00000414895.1	-	0	425																											TTTAGTTAACTTTTTTTTTTT	0.279													|||unknown(HR)	534	0.106629	0.2307	0.0879	5008	,	,		16966	0.0893		0.0239	False		,,,				2504	0.0552				.													.	.	.	0			.						.																																					0	.			GTTAACTTTTTTT																													3.37:g.192871852delT		Somatic	4	0		WXS	Illumina GAIIx	Phase_I	7	3	.		RNA	DEL	ENST00000414895.1	37																																																																																				T|0.500;-|0.500		0.279	RP11-143P4.2-001	KNOWN	basic|exp_conf	lincRNA	lincRNA	OTTHUMT00000343029.1		
LOC220729	220729	broad.mit.edu;bcgsc.ca	37	3	197351427	197351427	+	RNA	SNP	A	A	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr3:197351427A>T	ENST00000418868.1	-	0	127					NR_003266.2																						AAAGACATCCAGATCGTATTA	0.438																																					.													.	.	.	0			.						.																																					0	.			ACATCCAGATCGT																													3.37:g.197351427A>T		Somatic	126	0		WXS	Illumina GAIIx	Phase_I	119	24	.		RNA	SNP	ENST00000418868.1	37																																																																																				.		0.438	AC024560.3-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000340283.1		
CWH43	80157	broad.mit.edu	37	4	48988658	48988658	+	Intron	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr4:48988658T>G	ENST00000226432.4	+	1	226				CWH43_ENST00000513409.1_De_novo_Start_OutOfFrame	NM_025087.2	NP_079363.2	Q9H720	PG2IP_HUMAN	cell wall biogenesis 43 C-terminal homolog (S. cerevisiae)						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						CTGAAGGGAATAAAGGAAAAG	0.577																																					.													.	CWH43	101	0			.						.																																			SO:0001627	intron_variant	80157	.			AGGGAATAAAGGA		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.43+169T>G	4.37:g.48988658T>G		Somatic	23	0		WXS	Illumina GAIIx	Phase_I	26	3	.	B2RPD7	Translation_Start_Site	SNP	ENST00000226432.4	37	CCDS3486.1																																																																																			.		0.577	CWH43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250496.2	NM_025087	
HOPX	84525	broad.mit.edu;bcgsc.ca	37	4	57547691	57547691	+	De_novo_Start_InFrame	SNP	T	T	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr4:57547691T>C	ENST00000337881.7	-	0	374				HOPX_ENST00000381260.3_Intron|HOPX_ENST00000556376.2_5'Flank|HOPX_ENST00000605395.1_5'Flank|HOPX_ENST00000420433.1_De_novo_Start_OutOfFrame|HOPX_ENST00000554144.1_De_novo_Start_OutOfFrame	NM_139212.3	NP_631958.1	Q9BPY8	HOP_HUMAN	HOP homeobox						heart development (GO:0007507)|histone deacetylation (GO:0016575)|lung alveolus development (GO:0048286)|negative regulation of cell differentiation (GO:0045596)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of skeletal muscle tissue regeneration (GO:0043415)|positive regulation of striated muscle cell differentiation (GO:0051155)|regulation of heart contraction (GO:0008016)|regulation of protein binding (GO:0043393)|transcription, DNA-templated (GO:0006351)|trophectodermal cell differentiation (GO:0001829)	nucleus (GO:0005634)	DNA binding (GO:0003677)			large_intestine(2)|lung(5)|skin(1)	8	Glioma(25;0.08)|all_neural(26;0.101)					TTCTCGTCACTATCTTCTCGT	0.483																																					.													.	HOPX	28	0			.						.																																					84525	.			CGTCACTATCTTC		CCDS3507.1, CCDS47062.1, CCDS54767.1	4q12	2011-06-20			ENSG00000171476	ENSG00000171476		"""Homeoboxes / PRD class"""	24961	protein-coding gene	gene with protein product	"""homeobox only domain"""	607275				12297045	Standard	NM_032495		Approved	LAGY, HOP, OB1, NECC1, SMAP31	uc003hbz.2	Q9BPY8	OTTHUMG00000128768		4.37:g.57547691T>C		Somatic	15	0		WXS	Illumina GAIIx	Phase_I	2	2	.	A8K0Z2|E9PB55|G3V294|Q8N0V6|Q96CI1	Translation_Start_Site	SNP	ENST00000337881.7	37	CCDS3507.1																																																																																			.		0.483	HOPX-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250689.4		
GUSBP1	728411	broad.mit.edu	37	5	21491214	21491224	+	RNA	DEL	GAACCTGGGAG	GAACCTGGGAG	-			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr5:21491214_21491224delGAACCTGGGAG	ENST00000607545.1	+	0	179					NR_027026.1		Q15486	GUSP1_HUMAN	glucuronidase, beta pseudogene 1						carbohydrate metabolic process (GO:0005975)|nervous system development (GO:0007399)|skeletal system development (GO:0001501)		hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)										agaatcacttgaacctgggaggcagaggttt	0.45																																					.													.	.	.	0			.						.																																					0	.			TCACTTGAACCTG	BC064850, X75940		5p14.3	2012-10-04			ENSG00000183666	ENSG00000183666			13670	pseudogene	pseudogene						8565635	Standard	NR_027026		Approved		uc010iub.3	Q15486	OTTHUMG00000162474		5.37:g.21491214_21491224delGAACCTGGGAG		Somatic	194	0		WXS	Illumina GAIIx	Phase_I	169	20	.	A6NLY8|A8K1B7|Q969T8|Q9BUH2	RNA	DEL	ENST00000607545.1	37																																																																																				.		0.450	GUSBP1-006	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000470546.1	NG_008324	
LOC102724392	102724392	broad.mit.edu;bcgsc.ca	37	5	70741487	70741487	+	lincRNA	SNP	C	C	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr5:70741487C>G	ENST00000502659.2	-	0	682				RP11-136K7.1_ENST00000510180.1_lincRNA																							TTGAAATTTTCTCTGTGAACG	0.443																																					.													.	.	.	0			.						.																																					0	.			AATTTTCTCTGTG																													5.37:g.70741487C>G		Somatic	59	0		WXS	Illumina GAIIx	Phase_I	50	14	.		RNA	SNP	ENST00000502659.2	37																																																																																				.		0.443	RP11-136K7.2-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000374679.1		
RAD50	10111	broad.mit.edu;bcgsc.ca	37	5	131931434	131931434	+	Silent	SNP	G	G	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr5:131931434G>A	ENST00000265335.6	+	13	2526	c.2139G>A	c.(2137-2139)aaG>aaA	p.K713K	RAD50_ENST00000378823.3_Silent_p.K574K			Q92878	RAD50_HUMAN	RAD50 homolog (S. cerevisiae)	713	Zinc-hook. {ECO:0000255|PROSITE- ProRule:PRU00471}.				cellular response to DNA damage stimulus (GO:0006974)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA duplex unwinding (GO:0032508)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|positive regulation of kinase activity (GO:0033674)|positive regulation of protein autophosphorylation (GO:0031954)|reciprocal meiotic recombination (GO:0007131)|regulation of mitotic recombination (GO:0000019)|telomere maintenance (GO:0000723)|telomere maintenance via telomerase (GO:0007004)	membrane (GO:0016020)|Mre11 complex (GO:0030870)|nuclear chromosome, telomeric region (GO:0000784)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|pronucleus (GO:0045120)|site of double-strand break (GO:0035861)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|nuclease activity (GO:0004518)|protein binding, bridging (GO:0030674)|zinc ion binding (GO:0008270)			breast(3)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(10)|liver(1)|lung(8)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	36		all_cancers(142;0.0368)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			ATAAACTCAAGTCAACAGAAT	0.433								Homologous recombination																													p.K713K													.	RAD50	246	0			c.G2139A						.						75.0	71.0	73.0					5																	131931434		2203	4300	6503	SO:0001819	synonymous_variant	10111	exon13			ACTCAAGTCAACA	Z75311	CCDS34233.1	5q23-q31	2008-05-30	2001-11-28		ENSG00000113522	ENSG00000113522			9816	protein-coding gene	gene with protein product		604040	"""RAD50 (S. cerevisiae) homolog"""			8756642, 9705271	Standard	NM_005732		Approved	hRad50, RAD50-2	uc003kxi.3	Q92878	OTTHUMG00000059613	ENST00000265335.6:c.2139G>A	5.37:g.131931434G>A		Somatic	24	0		WXS	Illumina GAIIx	Phase_I	24	13	NM_005732	B9EGF5|O43254|Q6GMT7|Q6P5X3|Q9UP86	Silent	SNP	ENST00000265335.6	37	CCDS34233.1																																																																																			.		0.433	RAD50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132566.5	NM_005732	
ZC3H12D	340152	broad.mit.edu	37	6	149772005	149772005	+	Silent	SNP	T	T	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr6:149772005T>C	ENST00000409806.3	-	6	1716	c.1398A>G	c.(1396-1398)tcA>tcG	p.S466S	ZC3H12D_ENST00000416573.2_3'UTR|ZC3H12D_ENST00000389942.5_Silent_p.S466S|ZC3H12D_ENST00000498662.1_5'Flank			A2A288	ZC12D_HUMAN	zinc finger CCCH-type containing 12D	466					negative regulation of cell growth (GO:0030308)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(1)|prostate(1)	6		Ovarian(120;0.0907)		OV - Ovarian serous cystadenocarcinoma(155;1.23e-11)|GBM - Glioblastoma multiforme(68;0.0921)		TCGCGTACACTGAAAGTCCCC	0.751																																					p.S466S													.	ZC3H12D	21	0			c.A1398G						.						7.0	14.0	12.0					6																	149772005		677	1576	2253	SO:0001819	synonymous_variant	340152	exon6			GTACACTGAAAGT			6q25.1	2012-07-05	2005-06-30	2005-06-30	ENSG00000178199	ENSG00000178199		"""Zinc fingers, CCCH-type domain containing"""	21175	protein-coding gene	gene with protein product	"""MCP induced protein 4"""	611106	"""chromosome 6 open reading frame 95"""	C6orf95		18178554	Standard	NM_207360		Approved	dJ281H8.1, MCPIP4	uc010kid.3	A2A288	OTTHUMG00000015786	ENST00000409806.3:c.1398A>G	6.37:g.149772005T>C		Somatic	12	0		WXS	Illumina GAIIx	Phase_I	9	4	NM_207360	A1L178|B2RXF4|B7WNU7|B9ZZP9|B9ZZQ0|Q6ZRW2	Silent	SNP	ENST00000409806.3	37																																																																																				.		0.751	ZC3H12D-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000286400.2	NM_207360	
INHBA	3624	broad.mit.edu;bcgsc.ca	37	7	41729636	41729636	+	Missense_Mutation	SNP	C	C	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr7:41729636C>T	ENST00000242208.4	-	3	1139	c.893G>A	c.(892-894)cGg>cAg	p.R298Q	AC005027.3_ENST00000416150.1_RNA|INHBA_ENST00000464515.1_5'UTR|INHBA_ENST00000442711.1_Missense_Mutation_p.R298Q	NM_002192.2	NP_002183.1	P08476	INHBA_HUMAN	inhibin, beta A	298					activin receptor signaling pathway (GO:0032924)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|cellular response to cholesterol (GO:0071397)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|defense response (GO:0006952)|endodermal cell differentiation (GO:0035987)|erythrocyte differentiation (GO:0030218)|extrinsic apoptotic signaling pathway (GO:0097191)|eyelid development in camera-type eye (GO:0061029)|G1/S transition of mitotic cell cycle (GO:0000082)|growth (GO:0040007)|hair follicle development (GO:0001942)|hematopoietic progenitor cell differentiation (GO:0002244)|hemoglobin biosynthetic process (GO:0042541)|male gonad development (GO:0008584)|mesodermal cell differentiation (GO:0048333)|negative regulation of B cell differentiation (GO:0045578)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of follicle-stimulating hormone secretion (GO:0046882)|negative regulation of interferon-gamma biosynthetic process (GO:0045077)|negative regulation of macrophage differentiation (GO:0045650)|negative regulation of phosphorylation (GO:0042326)|nervous system development (GO:0007399)|odontogenesis (GO:0042476)|ovarian follicle development (GO:0001541)|palate development (GO:0060021)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of follicle-stimulating hormone secretion (GO:0046881)|positive regulation of ovulation (GO:0060279)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|progesterone secretion (GO:0042701)|regulation of follicle-stimulating hormone secretion (GO:0046880)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to drug (GO:0042493)	activin A complex (GO:0043509)|extracellular region (GO:0005576)|inhibin A complex (GO:0043512)	cytokine activity (GO:0005125)|growth factor activity (GO:0008083)|hormone activity (GO:0005179)|identical protein binding (GO:0042802)|peptide hormone binding (GO:0017046)|type II activin receptor binding (GO:0070699)			biliary_tract(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(15)|lung(26)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	55						TTCAGACTGCCGGGCCTGCAG	0.572										TSP Lung(11;0.080)																											p.R298Q													.	INHBA	118	0			c.G893A						.						91.0	93.0	92.0					7																	41729636		2203	4300	6503	SO:0001583	missense	3624	exon3			GACTGCCGGGCCT		CCDS5464.1	7p15-p13	2014-01-30	2007-07-30		ENSG00000122641	ENSG00000122641		"""Endogenous ligands"""	6066	protein-coding gene	gene with protein product		147290	"""inhibin, beta A (activin A, activin AB alpha polypeptide)"""			3345731	Standard	NM_002192		Approved		uc003thr.3	P08476	OTTHUMG00000023574	ENST00000242208.4:c.893G>A	7.37:g.41729636C>T	ENSP00000242208:p.Arg298Gln	Somatic	39	1		WXS	Illumina GAIIx	Phase_I	15	10	NM_002192	Q14599	Missense_Mutation	SNP	ENST00000242208.4	37	CCDS5464.1	.	.	.	.	.	.	.	.	.	.	.	14.47	2.545477	0.45280	.	.	ENSG00000122641	ENST00000242208;ENST00000442711	T;T	0.79454	-1.27;-1.27	5.82	5.82	0.92795	.	0.200435	0.46442	D	0.000283	T	0.66799	0.2826	L	0.28400	0.85	0.49299	D	0.999775	P	0.42827	0.791	B	0.30401	0.115	T	0.70475	-0.4861	10	0.48119	T	0.1	-21.7563	20.0937	0.97831	0.0:1.0:0.0:0.0	.	298	P08476	INHBA_HUMAN	Q	298	ENSP00000242208:R298Q;ENSP00000397197:R298Q	ENSP00000242208:R298Q	R	-	2	0	INHBA	41696161	1.000000	0.71417	0.996000	0.52242	0.986000	0.74619	3.998000	0.57024	2.762000	0.94881	0.484000	0.47621	CGG	.		0.572	INHBA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250793.1		
LINC00174	285908	broad.mit.edu	37	7	65842005	65842005	+	lincRNA	SNP	C	C	T	rs540658465	byFrequency	TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr7:65842005C>T	ENST00000421767.1	-	0	3727					NR_026873.1				long intergenic non-protein coding RNA 174																		AGGAGCTGGGCTTGTGGCGCC	0.731													C|||	2	0.000399361	0.0008	0.0	5008	,	,		10734	0.0		0.001	False		,,,				2504	0.0				.													.	.	.	0			.						.						2.0	3.0	2.0					7																	65842005		1455	3201	4656			0	.			GCTGGGCTTGTGG	AK091213		7q11.21	2013-12-05	2013-12-05	2013-12-05	ENSG00000179406	ENSG00000179406		"""Long non-coding RNAs"""	27788	non-coding RNA	RNA, long non-coding			"""non-protein coding RNA 174"""	NCRNA00174			Standard	NR_026873		Approved		uc003tux.4		OTTHUMG00000156590		7.37:g.65842005C>T		Somatic	10	0		WXS	Illumina GAIIx	Phase_I	9	4	.		RNA	SNP	ENST00000421767.1	37																																																																																				.		0.731	LINC00174-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000344721.1	NR_026873	
RABGEF1	27342	broad.mit.edu;ucsc.edu;bcgsc.ca	37	7	66270137	66270137	+	Missense_Mutation	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr7:66270137A>C	ENST00000284957.5	+	8	908	c.831A>C	c.(829-831)gaA>gaC	p.E277D	KCTD7_ENST00000380828.2_Missense_Mutation_p.E317D|RABGEF1_ENST00000450873.2_Missense_Mutation_p.E277D|KCTD7_ENST00000510829.2_Missense_Mutation_p.E277D|KCTD7_ENST00000451741.2_Missense_Mutation_p.E277D|RABGEF1_ENST00000484547.2_3'UTR|RABGEF1_ENST00000439720.2_Missense_Mutation_p.E290D|RABGEF1_ENST00000437078.2_Missense_Mutation_p.E291D			Q9UJ41	RABX5_HUMAN	RAB guanine nucleotide exchange factor (GEF) 1	494					endocytosis (GO:0006897)|positive regulation of Rab GTPase activity (GO:0032851)|protein targeting to membrane (GO:0006612)	early endosome (GO:0005769)	DNA binding (GO:0003677)|Rab GTPase binding (GO:0017137)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)|zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(5)|lung(9)|ovary(1)|stomach(1)	27						ATATCATTGAAATGGATTCCA	0.408																																					p.E277D													.	RABGEF1	56	0			c.A831C						.						76.0	68.0	71.0					7																	66270137		2203	4300	6503	SO:0001583	missense	154881	exon8			CATTGAAATGGAT	AJ250042	CCDS5535.1, CCDS69308.1, CCDS75610.1	7q11.21	2010-07-09			ENSG00000154710	ENSG00000154710			17676	protein-coding gene	gene with protein product		609700				12505986, 11098082	Standard	NM_014504		Approved	rabex-5, RABEX5	uc003tvh.3	Q9UJ41	OTTHUMG00000129547	ENST00000284957.5:c.831A>C	7.37:g.66270137A>C	ENSP00000284957:p.Glu277Asp	Somatic	59	1		WXS	Illumina GAIIx	Phase_I	36	10	NM_014504	B4DZM7|Q3HKR2|Q3HKR3|Q53FG0	Missense_Mutation	SNP	ENST00000284957.5	37	CCDS5535.1	.	.	.	.	.	.	.	.	.	.	.	20.7	4.039725	0.75732	.	.	ENSG00000243335;ENSG00000243335;ENSG00000243335;ENSG00000243335;ENSG00000243335;ENSG00000154710;ENSG00000154710;ENSG00000154710;ENSG00000154710	ENST00000380827;ENST00000380828;ENST00000510829;ENST00000451741;ENST00000539561;ENST00000284957;ENST00000450873;ENST00000439720;ENST00000437078	T;T;T;T;T;T;T	0.30714	1.52;1.52;1.52;1.52;1.52;1.52;1.52	5.49	0.46	0.16684	Vacuolar sorting protein 9, subgroup (1);Vacuolar sorting protein 9 (2);	0.000000	0.85682	D	0.000000	T	0.43590	0.1254	M	0.71581	2.175	0.58432	D	0.999998	P;B;P	0.46064	0.864;0.235;0.872	P;B;P	0.57620	0.618;0.278;0.824	T	0.21449	-1.0245	10	0.39692	T	0.17	-28.2779	8.7144	0.34403	0.3445:0.0:0.6555:0.0	.	291;111;494	B4DZM7;B3KMF1;Q9UJ41	.;.;RABX5_HUMAN	D	361;317;277;277;193;277;277;290;291	ENSP00000370208:E317D;ENSP00000421124:E277D;ENSP00000398177:E277D;ENSP00000284957:E277D;ENSP00000415815:E277D;ENSP00000403429:E290D;ENSP00000390480:E291D	ENSP00000370207:E361D	E	+	3	2	RABGEF1;KCTD7	65907572	0.666000	0.27475	1.000000	0.80357	0.997000	0.91878	-0.148000	0.10219	0.087000	0.17167	0.533000	0.62120	GAA	.		0.408	RABGEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251737.3	NM_014504	
TNFRSF10C	8794	broad.mit.edu;bcgsc.ca	37	8	22960538	22960569	+	5'UTR	DEL	CCTACCGTTAGGGAACTCTGGGGACAGAGCGC	CCTACCGTTAGGGAACTCTGGGGACAGAGCGC	-	rs139576559|rs534839554|rs41308122	byFrequency	TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr8:22960538_22960569delCCTACCGTTAGGGAACTCTGGGGACAGAGCGC	ENST00000356864.3	+	0	436_467				TNFRSF10C_ENST00000540813.1_5'UTR|TNFRSF10C_ENST00000397703.2_Frame_Shift_Del_p.LPLGNSGDRAP9fs|TNFRSF10C_ENST00000520607.1_Intron	NM_003841.3	NP_003832	O14798	TR10C_HUMAN	tumor necrosis factor receptor superfamily, member 10c, decoy without an intracellular domain						apoptotic process (GO:0006915)|signal transduction (GO:0007165)	anchored component of membrane (GO:0031225)|integral component of plasma membrane (GO:0005887)	transmembrane signaling receptor activity (GO:0004888)			endometrium(1)|large_intestine(6)|lung(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	15		Prostate(55;0.0421)|Breast(100;0.067)		Colorectal(74;0.0147)|COAD - Colon adenocarcinoma(73;0.0612)		AGGAGCGCTTCCTACCGTTAGGGAACTCTGGGGACAGAGCGCCCCGGCCGCC	0.608																																					.													.	.	.	0			.						.																																			SO:0001623	5_prime_UTR_variant	8794	.			GCGCTTCCTACCG	AF012536	CCDS6037.1	8p22-p21	2006-02-22			ENSG00000173535	ENSG00000173535		"""Tumor necrosis factor receptor superfamily"", ""CD molecules"""	11906	protein-coding gene	gene with protein product		603613				9314565, 9325248	Standard	NM_003841		Approved	DcR1, TRAILR3, LIT, TRID, CD263	uc003xcy.3	O14798	OTTHUMG00000097844	ENST00000356864.3:c.-66CCTACCGTTAGGGAACTCTGGGGACAGAGCGC>-	8.37:g.22960538_22960569delCCTACCGTTAGGGAACTCTGGGGACAGAGCGC		Somatic	78	0		WXS	Illumina GAIIx	Phase_I	37	6	.	O14755|Q08AS6|Q6FH98|Q6UXM5	Frame_Shift_Del	DEL	ENST00000356864.3	37	CCDS6037.1																																																																																			.		0.608	TNFRSF10C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215134.3		
BNIP3L	665	broad.mit.edu	37	8	26240232	26240232	+	5'Flank	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr8:26240232A>C	ENST00000380629.2	+	0	0				SDAD1P1_ENST00000519902.1_RNA|BNIP3L_ENST00000523515.1_5'Flank|BNIP3L_ENST00000520409.1_5'Flank	NM_004331.2	NP_004322.1	O60238	BNI3L_HUMAN	BCL2/adenovirus E1B 19kDa interacting protein 3-like						defense response to virus (GO:0051607)|mitochondrial outer membrane permeabilization (GO:0097345)|mitochondrial protein catabolic process (GO:0035694)|negative regulation of apoptotic process (GO:0043066)|positive regulation of apoptotic process (GO:0043065)|viral process (GO:0016032)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|intrinsic component of membrane (GO:0031224)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)	identical protein binding (GO:0042802)|lamin binding (GO:0005521)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			large_intestine(3)|lung(1)	4		all_cancers(63;0.086)|Ovarian(32;2.61e-05)|all_epithelial(46;0.0514)|Prostate(55;0.157)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0019)|Epithelial(17;1.59e-12)|all cancers(2;3.75e-11)|OV - Ovarian serous cystadenocarcinoma(2;2.57e-08)|Colorectal(74;0.135)		TAAGAGGTAGAAAACAGATGC	0.547																																					.													.	BNIP3L	7	0			.						.																																			SO:0001631	upstream_gene_variant	0	.			AGGTAGAAAACAG	AB004788	CCDS6050.1	8p21	2014-05-13	2002-08-29		ENSG00000104765	ENSG00000104765			1085	protein-coding gene	gene with protein product		605368	"""BCL2/adenovirus E1B 19kD-interacting protein 3-like"""			9523198, 9973195	Standard	NM_004331		Approved	Nix, BNIP3a	uc003xex.1	O60238	OTTHUMG00000099433		8.37:g.26240232A>C	Exception_encountered	Somatic	22	1		WXS	Illumina GAIIx	Phase_I	5	2	.	B0AZS9|Q5JW63|Q8NF87	RNA	SNP	ENST00000380629.2	37	CCDS6050.1																																																																																			.		0.547	BNIP3L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216895.1	NM_004331	
MIR548H4	100313884	broad.mit.edu;ucsc.edu;bcgsc.ca	37	8	26906407	26906407	+	RNA	SNP	T	T	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr8:26906407T>C	ENST00000408689.1	-	0	73					NR_031680.1				microRNA 548h-4																		aattgcggtttttgtcattaa	0.328																																					.													.	.	.	0			.						.						8.0	8.0	8.0					8																	26906407		1450	3187	4637			0	.			GCGGTTTTTGTCA			8p21.2	2011-09-12		2008-12-18	ENSG00000221616	ENSG00000221616		"""ncRNAs / Micro RNAs"""	35345	non-coding RNA	RNA, micro				MIRN548H4			Standard	NR_031680		Approved	hsa-mir-548h-4	uc021spl.1				8.37:g.26906407T>C		Somatic	41	0		WXS	Illumina GAIIx	Phase_I	32	15	.		RNA	SNP	ENST00000408689.1	37																																																																																				.		0.328	MIR548H4-201	KNOWN	basic	miRNA	miRNA		NR_031680	
PARP10	84875	broad.mit.edu	37	8	145059959	145059959	+	Silent	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr8:145059959A>C	ENST00000313028.7	-	3	460	c.366T>G	c.(364-366)ccT>ccG	p.P122P	PARP10_ENST00000524918.1_Silent_p.P122P|PARP10_ENST00000533665.1_5'UTR|PARP10_ENST00000525773.1_Silent_p.P134P	NM_032789.3	NP_116178.2	Q53GL7	PAR10_HUMAN	poly (ADP-ribose) polymerase family, member 10	122					negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of gene expression (GO:0010629)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein import into nucleus, translocation (GO:0033159)|negative regulation of protein K63-linked ubiquitination (GO:1900045)|negative regulation of viral genome replication (GO:0045071)|protein ADP-ribosylation (GO:0006471)|protein auto-ADP-ribosylation (GO:0070213)|protein poly-ADP-ribosylation (GO:0070212)|regulation of chromatin assembly (GO:0010847)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	K63-linked polyubiquitin binding (GO:0070530)|NAD+ ADP-ribosyltransferase activity (GO:0003950)			NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(5)|lung(9)|ovary(4)|pancreas(1)|upper_aerodigestive_tract(2)	27	all_cancers(97;8.2e-11)|all_epithelial(106;1.1e-09)|Lung NSC(106;5.89e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.31e-40)|Epithelial(56;1.16e-39)|all cancers(56;6.43e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			AGGCACAGCAAGGCTGTACTG	0.687																																					p.P122P													.	PARP10	57	0			c.T366G						.						23.0	29.0	27.0					8																	145059959		2133	4248	6381	SO:0001819	synonymous_variant	84875	exon3			ACAGCAAGGCTGT	AK027370	CCDS34960.1	8q24	2010-02-16				ENSG00000178685		"""Poly (ADP-ribose) polymerases"""	25895	protein-coding gene	gene with protein product		609564				15273990	Standard	NM_032789		Approved	FLJ14464	uc003zal.4	Q53GL7		ENST00000313028.7:c.366T>G	8.37:g.145059959A>C		Somatic	30	0		WXS	Illumina GAIIx	Phase_I	19	3	NM_032789	Q8N2I0|Q8WV05|Q96CH7|Q96K72	Silent	SNP	ENST00000313028.7	37	CCDS34960.1																																																																																			.		0.687	PARP10-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000383866.1	NM_032789	
CPSF1	29894	broad.mit.edu;bcgsc.ca	37	8	145618578	145618578	+	Silent	SNP	G	G	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr8:145618578G>A	ENST00000349769.3	-	38	4381	c.4287C>T	c.(4285-4287)atC>atT	p.I1429I	MIR939_ENST00000401314.1_RNA|CPSF1_ENST00000531727.1_5'UTR	NM_013291.2	NP_037423.2	Q10570	CPSF1_HUMAN	cleavage and polyadenylation specific factor 1, 160kDa	1429					gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA cleavage (GO:0006379)|mRNA export from nucleus (GO:0006406)|mRNA polyadenylation (GO:0006378)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	mRNA cleavage and polyadenylation specificity factor complex (GO:0005847)|nucleoplasm (GO:0005654)	mRNA 3'-UTR binding (GO:0003730)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(15)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	38	all_cancers(97;6.64e-12)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.88e-41)|Epithelial(56;1.67e-40)|all cancers(56;1.2e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0323)|Colorectal(110;0.055)			AGTCGTCCAGGATCTGCAGGG	0.677																																					p.I1429I	NSCLC(133;1088 1848 27708 34777 35269)												.	CPSF1	92	0			c.C4287T						.						21.0	16.0	18.0					8																	145618578		2078	4055	6133	SO:0001819	synonymous_variant	29894	exon38			GTCCAGGATCTGC	U37012	CCDS34966.1	8q24	2014-05-06	2002-08-29		ENSG00000071894	ENSG00000071894			2324	protein-coding gene	gene with protein product		606027	"""cleavage and polyadenylation specific factor 1, 160kD subunit"""			7651824, 7590244	Standard	NM_013291		Approved		uc003zcj.3	Q10570	OTTHUMG00000174612	ENST00000349769.3:c.4287C>T	8.37:g.145618578G>A		Somatic	33	1		WXS	Illumina GAIIx	Phase_I	30	10	NM_013291	Q96AF0	Silent	SNP	ENST00000349769.3	37	CCDS34966.1																																																																																			.		0.677	CPSF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382422.2	NM_013291	
C9orf131	138724	broad.mit.edu;bcgsc.ca	37	9	35042287	35042287	+	Frame_Shift_Del	DEL	G	G	-			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr9:35042287delG	ENST00000312292.5	+	1	83	c.36delG	c.(34-36)aagfs	p.K12fs	C9orf131_ENST00000421362.2_Intron|C9orf131_ENST00000354479.5_Intron	NM_001040410.1|NM_203299.2	NP_001035500.1|NP_976044.2	Q5VYM1	CI131_HUMAN	chromosome 9 open reading frame 131	12										cervix(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(23)|prostate(2)|skin(2)|stomach(1)	39	all_epithelial(49;0.22)		LUSC - Lung squamous cell carcinoma(32;0.00117)|Lung(28;0.00309)			TTGGGGCTAAGGGGGATATGG	0.547																																					p.K12fs													.	C9orf131	71	0			c.36delG						.						45.0	43.0	44.0					9																	35042287		2203	4300	6503	SO:0001589	frameshift_variant	138724	exon1			GGCTAAGGGGGAT	BC045643	CCDS6572.2, CCDS47961.1, CCDS47962.1	9p13.3	2008-02-05			ENSG00000174038	ENSG00000174038			31418	protein-coding gene	gene with protein product							Standard	NM_001287391		Approved	MGC41945	uc003zvw.3	Q5VYM1	OTTHUMG00000019853	ENST00000312292.5:c.36delG	9.37:g.35042287delG	ENSP00000308279:p.Lys12fs	Somatic	32	0		WXS	Illumina GAIIx	Phase_I	18	8	NM_001040410	A6NLE6|E9PB26|Q86XC6|Q9UF74	Frame_Shift_Del	DEL	ENST00000312292.5	37	CCDS6572.2																																																																																			.		0.547	C9orf131-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052283.5	NM_203299	
CNTRL	11064	broad.mit.edu;bcgsc.ca	37	9	123937475	123937475	+	Silent	SNP	A	A	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr9:123937475A>T	ENST00000373855.1	+	43	7187	c.6927A>T	c.(6925-6927)acA>acT	p.T2309T	CNTRL_ENST00000373850.1_Silent_p.T1757T|CNTRL_ENST00000238341.5_Silent_p.T2309T|CNTRL_ENST00000373845.2_3'UTR			Q7Z7A1	CNTRL_HUMAN	centriolin	2309	Sufficient for interaction with HOOK2.				cell division (GO:0051301)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)				haematopoietic_and_lymphoid_tissue(2)|large_intestine(9)|lung(2)|ovary(4)|skin(3)	20						CTTCCCTCACAGAGGACTCTC	0.443																																					p.T2309T													.	CNTRL	161	0			c.A6927T						.						83.0	76.0	78.0					9																	123937475		2203	4300	6503	SO:0001819	synonymous_variant	11064	exon41			CCTCACAGAGGAC	AF513978	CCDS35118.1	9q33.2	2014-02-20	2011-05-23	2011-05-23	ENSG00000119397	ENSG00000119397			1858	protein-coding gene	gene with protein product		605496	"""centrosomal protein 1"", ""centrosomal protein 110kDa"""	CEP1, CEP110		10688839	Standard	XM_005251679		Approved		uc004bkx.1	Q7Z7A1	OTTHUMG00000020581	ENST00000373855.1:c.6927A>T	9.37:g.123937475A>T		Somatic	40	1		WXS	Illumina GAIIx	Phase_I	31	10	NM_007018	A2A2Y1|B2RP67|Q3MN79|Q5FWF8|Q5JVD0|Q6MZR3|Q6PKC1|Q8TEP3|Q9Y489	Silent	SNP	ENST00000373855.1	37	CCDS35118.1																																																																																			.		0.443	CNTRL-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250216.1	NM_007018	
GARNL3	84253	broad.mit.edu	37	9	130026087	130026087	+	5'Flank	SNP	G	G	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr9:130026087G>A	ENST00000373387.4	+	0	0				GARNL3_ENST00000314904.5_5'Flank|GARNL3_ENST00000435213.2_De_novo_Start_InFrame	NM_032293.4	NP_115669.3	Q5VVW2	GARL3_HUMAN	GTPase activating Rap/RanGAP domain-like 3						regulation of small GTPase mediated signal transduction (GO:0051056)		GTPase activator activity (GO:0005096)|small GTPase regulator activity (GO:0005083)			NS(1)|central_nervous_system(1)|endometrium(6)|large_intestine(5)|lung(24)|ovary(1)|skin(1)|urinary_tract(2)	41						TCTGTGAAATGGTGGAAGCAG	0.423																																					.													.	GARNL3	83	0			.						.																																			SO:0001631	upstream_gene_variant	84253	.			TGAAATGGTGGAA	BC034983	CCDS6869.2, CCDS69663.1	9q34.13	2009-09-14	2004-08-09		ENSG00000136895	ENSG00000136895			25425	protein-coding gene	gene with protein product			"""GTPase activating RANGAP domain-like 3"""			11230166	Standard	NM_032293		Approved	DKFZp761J1523, bA356B19.1	uc011mae.2	Q5VVW2	OTTHUMG00000020700		9.37:g.130026087G>A	Exception_encountered	Somatic	8	0		WXS	Illumina GAIIx	Phase_I	12	5	.	B4DEP7|B7Z3Q6|Q8IYU1|Q8N951|Q8ND89|Q9BQH6	Translation_Start_Site	SNP	ENST00000373387.4	37	CCDS6869.2																																																																																			.		0.423	GARNL3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054151.3	NM_032293	
LCN12	286256	broad.mit.edu	37	9	139848199	139848199	+	Missense_Mutation	SNP	A	A	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr9:139848199A>G	ENST00000371633.3	+	3	299	c.299A>G	c.(298-300)cAg>cGg	p.Q100R	LCN12_ENST00000466277.1_3'UTR	NM_178536.3	NP_848631.2	Q6JVE5	LCN12_HUMAN	lipocalin 12	100					lipid metabolic process (GO:0006629)	extracellular region (GO:0005576)	retinoic acid binding (GO:0001972)|transporter activity (GO:0005215)			endometrium(1)|kidney(1)|lung(1)|prostate(2)	5	all_cancers(76;0.11)	Myeloproliferative disorder(178;0.0511)	STAD - Stomach adenocarcinoma(284;0.19)	OV - Ovarian serous cystadenocarcinoma(145;7.8e-06)|Epithelial(140;0.000106)		CCGGCAGCCCAGCCTGGGCAG	0.637																																					p.Q100R													.	LCN12	11	0			c.A299G						.						33.0	36.0	35.0					9																	139848199		2065	4187	6252	SO:0001583	missense	286256	exon3			CAGCCCAGCCTGG	BC041168	CCDS7018.2	9q34	2011-10-24	2007-12-18		ENSG00000184925	ENSG00000184925		"""Lipocalins"""	28733	protein-coding gene	gene with protein product		612905				15363845	Standard	XM_005266068		Approved	MGC48935	uc004ckb.3	Q6JVE5	OTTHUMG00000020968	ENST00000371633.3:c.299A>G	9.37:g.139848199A>G	ENSP00000360696:p.Gln100Arg	Somatic	61	0		WXS	Illumina GAIIx	Phase_I	38	5	NM_178536	A2AMJ7	Missense_Mutation	SNP	ENST00000371633.3	37	CCDS7018.2	.	.	.	.	.	.	.	.	.	.	A	9.439	1.087473	0.20390	.	.	ENSG00000184925	ENST00000371633;ENST00000371632	T;D	0.82433	3.14;-1.61	2.37	2.37	0.29283	Calycin-like (1);Lipocalin/cytosolic fatty-acid binding protein domain (1);Calycin (1);	0.275120	0.19496	N	0.112843	T	0.70351	0.3214	N	0.25825	0.765	0.09310	N	1	B;B	0.25850	0.136;0.108	B;B	0.29353	0.101;0.039	T	0.60276	-0.7295	10	0.41790	T	0.15	-17.8383	6.6229	0.22812	1.0:0.0:0.0:0.0	.	100;100	Q8IW14;Q6JVE5	.;LCN12_HUMAN	R	100;34	ENSP00000360696:Q100R;ENSP00000360695:Q34R	ENSP00000360695:Q34R	Q	+	2	0	LCN12	138968020	0.003000	0.15002	0.206000	0.23566	0.009000	0.06853	0.277000	0.18734	1.329000	0.45376	0.260000	0.18958	CAG	.		0.637	LCN12-015	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257990.1	NM_178536	
TOR4A	54863	broad.mit.edu	37	9	140174311	140174311	+	Silent	SNP	C	C	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr9:140174311C>T	ENST00000357503.2	+	2	1366	c.1170C>T	c.(1168-1170)cgC>cgT	p.R390R		NM_017723.2	NP_060193.2	Q9NXH8	TOR4A_HUMAN	torsin family 4, member A	390					chaperone mediated protein folding requiring cofactor (GO:0051085)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)										ACCAGGCCCGCGCGGAGAACC	0.672																																					p.R390R													.	.	.	0			c.C1170T						.						11.0	14.0	13.0					9																	140174311		2189	4287	6476	SO:0001819	synonymous_variant	54863	exon2			GGCCCGCGCGGAG	AK023361	CCDS7041.1	9q34.3	2012-04-03	2012-04-03	2012-04-03	ENSG00000198113	ENSG00000198113			25981	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 167"""	C9orf167			Standard	NM_017723		Approved	FLJ20245	uc004cmn.3	Q9NXH8	OTTHUMG00000131779	ENST00000357503.2:c.1170C>T	9.37:g.140174311C>T		Somatic	13	0		WXS	Illumina GAIIx	Phase_I	4	3	NM_017723	A2BFA4	Silent	SNP	ENST00000357503.2	37	CCDS7041.1																																																																																			.		0.672	TOR4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254711.1	NM_017723	
ARSD	414	broad.mit.edu	37	X	2836254	2836254	+	Missense_Mutation	SNP	C	C	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chrX:2836254C>T	ENST00000381154.1	-	5	529	c.454G>A	c.(454-456)Ggt>Agt	p.G152S	ARSD_ENST00000217890.6_5'UTR	NM_001669.3	NP_001660.2	P51689	ARSD_HUMAN	arylsulfatase D	152					cellular protein metabolic process (GO:0044267)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)			large_intestine(3)|lung(3)	6		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				CAATTCACACCCTGGTGCCAT	0.532																																					p.G152S													.	ARSD	47	0			c.G454A						.						25.0	15.0	19.0					X																	2836254		2188	4276	6464	SO:0001583	missense	414	exon5			TCACACCCTGGTG	X83572	CCDS35196.1	Xp22.3	2013-02-14			ENSG00000006756	ENSG00000006756		"""Arylsulfatase family"""	717	protein-coding gene	gene with protein product		300002				7720070	Standard	NM_001669		Approved		uc004cqy.3	P51689	OTTHUMG00000021077	ENST00000381154.1:c.454G>A	X.37:g.2836254C>T	ENSP00000370546:p.Gly152Ser	Somatic	25	0		WXS	Illumina GAIIx	Phase_I	16	3	NM_001669	Q9UHJ8	Missense_Mutation	SNP	ENST00000381154.1	37	CCDS35196.1	.	.	.	.	.	.	.	.	.	.	c	17.09	3.300164	0.60195	.	.	ENSG00000006756	ENST00000381154;ENST00000217890	D	0.95412	-3.7	3.47	3.47	0.39725	Alkaline phosphatase-like, alpha/beta/alpha (1);Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	0.000000	0.85682	U	0.000000	D	0.98213	0.9409	H	0.94462	3.54	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.99470	1.0945	10	0.87932	D	0	.	14.5312	0.67926	0.0:1.0:0.0:0.0	.	152;152	E9PAW5;P51689	.;ARSD_HUMAN	S	152	ENSP00000370546:G152S	ENSP00000217890:G152S	G	-	1	0	ARSD	2846254	1.000000	0.71417	0.870000	0.34147	0.063000	0.16089	6.346000	0.72999	1.394000	0.46624	0.420000	0.28162	GGT	.		0.532	ARSD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055636.1		
STS	412	broad.mit.edu;bcgsc.ca	37	X	7177472	7177482	+	Frame_Shift_Del	DEL	TGGGATCTCTT	TGGGATCTCTT	-			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chrX:7177472_7177482delTGGGATCTCTT	ENST00000217961.4	+	5	700_710	c.480_490delTGGGATCTCTT	c.(478-492)tatgggatctctttgfs	p.GISL161fs		NM_000351.4	NP_000342.2	P08842	STS_HUMAN	steroid sulfatase (microsomal), isozyme S	161					cellular protein metabolic process (GO:0044267)|epidermis development (GO:0008544)|female pregnancy (GO:0007565)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)|steroid catabolic process (GO:0006706)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|lysosome (GO:0005764)|membrane (GO:0016020)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|steryl-sulfatase activity (GO:0004773)|sulfuric ester hydrolase activity (GO:0008484)			NS(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(6)|lung(10)|prostate(2)|skin(1)	27		Colorectal(8;0.0136)|Medulloblastoma(8;0.184)			Norelgestromin(DB06713)	ATTATTTCTATGGGATCTCTTTGACCAATCT	0.536									Ichthyosis																												p.160_164del													.	STS	64	0			c.480_490del						.																																			SO:0001589	frameshift_variant	412	exon5	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	TTTCTATGGGATC	M16505	CCDS14127.1	Xp22.32	2013-06-10	2007-07-19		ENSG00000101846	ENSG00000101846	3.1.6.2	"""Arylsulfatase family"""	11425	protein-coding gene	gene with protein product	"""arylsulfatase C"""	300747	"""steroid sulfatase (microsomal), arylsulfatase C, isozyme S"""	ARSC1			Standard	NM_000351		Approved	ARSC	uc004cry.4	P08842	OTTHUMG00000021102	ENST00000217961.4:c.480_490delTGGGATCTCTT	X.37:g.7177472_7177482delTGGGATCTCTT	ENSP00000217961:p.Gly161fs	Somatic	17	0		WXS	Illumina GAIIx	Phase_I	6	4	NM_000351	B2RA47	Frame_Shift_Del	DEL	ENST00000217961.4	37	CCDS14127.1																																																																																			.		0.536	STS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055686.1	NM_000351	
ADCK2	90956	ucsc.edu	37	7	140373610	140373610	+	Silent	SNP	G	G	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr7:140373610G>A	ENST00000072869.4	+	1	658	c.480G>A	c.(478-480)tcG>tcA	p.S160S	ADCK2_ENST00000476491.1_Silent_p.S160S	NM_052853.3	NP_443085.2	Q7Z695	ADCK2_HUMAN	aarF domain containing kinase 2	160						integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			cervix(1)|kidney(2)|large_intestine(2)|lung(5)|prostate(1)|skin(4)	15	Melanoma(164;0.00956)					ATCTGTTTTCGGAGGCTTTCT	0.602																																					p.S160S													.	ADCK2	37	0			c.G480A						.						46.0	53.0	51.0					7																	140373610		2203	4300	6503	SO:0001819	synonymous_variant	90956	exon1			GTTTTCGGAGGCT	AF131745	CCDS5861.1	7q34	2003-07-21			ENSG00000133597	ENSG00000133597			19039	protein-coding gene	gene with protein product							Standard	NM_052853		Approved	MGC20727	uc003vvy.1	Q7Z695	OTTHUMG00000157409	ENST00000072869.4:c.480G>A	7.37:g.140373610G>A		Somatic	45	0		WXS	Illumina HiSeq		33	4	NM_052853	Q96CN6|Q9Y6T5	Silent	SNP	ENST00000072869.4	37	CCDS5861.1																																																																																			.		0.602	ADCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348734.1	NM_052853	
PSKH2	85481	ucsc.edu;bcgsc.ca	37	8	87060845	87060845	+	Missense_Mutation	SNP	G	G	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr8:87060845G>A	ENST00000276616.2	-	3	1078	c.1004C>T	c.(1003-1005)gCc>gTc	p.A335V		NM_033126.1	NP_149117.1	Q96QS6	KPSH2_HUMAN	protein serine kinase H2	335							ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|kidney(11)|large_intestine(2)|lung(26)|ovary(1)|prostate(1)|stomach(3)|urinary_tract(1)	47			STAD - Stomach adenocarcinoma(118;0.129)			TCGGGATATGGCCCTCTGGAG	0.537																																					p.A335V													.	PSKH2	79	0			c.C1004T						.						102.0	109.0	107.0					8																	87060845		2203	4300	6503	SO:0001583	missense	85481	exon3			GATATGGCCCTCT	AY037806	CCDS6240.1	8q21.13	2004-06-03				ENSG00000147613			18997	protein-coding gene	gene with protein product							Standard	NM_033126		Approved		uc011lfy.2	Q96QS6		ENST00000276616.2:c.1004C>T	8.37:g.87060845G>A	ENSP00000276616:p.Ala335Val	Somatic	79	0		WXS	Illumina HiSeq		43	5	NM_033126	A0AV22	Missense_Mutation	SNP	ENST00000276616.2	37	CCDS6240.1	.	.	.	.	.	.	.	.	.	.	G	13.71	2.319347	0.41096	.	.	ENSG00000147613	ENST00000276616	T	0.38560	1.13	4.98	2.0	0.26442	Protein kinase-like domain (1);	.	.	.	.	T	0.16769	0.0403	N	0.02011	-0.69	0.23889	N	0.996551	B	0.02656	0.0	B	0.06405	0.002	T	0.20009	-1.0288	9	0.45353	T	0.12	.	6.2429	0.20801	0.4088:0.0:0.5912:0.0	.	335	Q96QS6	KPSH2_HUMAN	V	335	ENSP00000276616:A335V	ENSP00000276616:A335V	A	-	2	0	PSKH2	87129961	1.000000	0.71417	0.962000	0.40283	0.845000	0.48019	1.577000	0.36515	0.073000	0.16731	0.650000	0.86243	GCC	.		0.537	PSKH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374628.1	NM_033126	
FERMT3	83706	ucsc.edu;bcgsc.ca	37	11	63986820	63986820	+	Missense_Mutation	SNP	C	C	T	rs560195082	byFrequency	TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr11:63986820C>T	ENST00000279227.5	+	7	979	c.884C>T	c.(883-885)gCc>gTc	p.A295V	FERMT3_ENST00000345728.5_Missense_Mutation_p.A295V	NM_178443.2	NP_848537.1	Q86UX7	URP2_HUMAN	fermitin family member 3	295	FERM.				integrin activation (GO:0033622)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|platelet aggregation (GO:0070527)|regulation of cell-cell adhesion mediated by integrin (GO:0033632)|substrate adhesion-dependent cell spreading (GO:0034446)	cell junction (GO:0030054)|cell projection (GO:0042995)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|podosome (GO:0002102)	integrin binding (GO:0005178)			breast(1)|cervix(1)|endometrium(4)|large_intestine(2)|lung(6)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	18						ATGGTGTTTGCCGCCCTGCAG	0.667													C|||	3	0.000599042	0.0	0.0	5008	,	,		18564	0.0		0.0	False		,,,				2504	0.0031				p.A295V													.	FERMT3	51	0			c.C884T						.						32.0	30.0	31.0					11																	63986820		2199	4295	6494	SO:0001583	missense	83706	exon7			TGTTTGCCGCCCT	L25343	CCDS8059.1, CCDS8060.1	11q13.1	2014-09-17	2010-06-24		ENSG00000149781	ENSG00000149781		"""Fermitins"", ""Pleckstrin homology (PH) domain containing"""	23151	protein-coding gene	gene with protein product	"""kindlin-3"""	607901	"""fermitin family homolog 3 (Drosophila)"""				Standard	NM_178443		Approved	URP2, KIND3, MIG2B, MGC10966, MIG-2, UNC112C	uc001nym.2	Q86UX7	OTTHUMG00000167790	ENST00000279227.5:c.884C>T	11.37:g.63986820C>T	ENSP00000279227:p.Ala295Val	Somatic	28	0		WXS	Illumina HiSeq		32	4	NM_031471	Q8IUA1|Q8N207|Q9BT48	Missense_Mutation	SNP	ENST00000279227.5	37	CCDS8060.1	.	.	.	.	.	.	.	.	.	.	C	17.16	3.317941	0.60524	.	.	ENSG00000149781	ENST00000345728;ENST00000279227	D;D	0.88431	-2.38;-2.38	5.18	5.18	0.71444	Band 4.1 domain (1);FERM central domain (2);	0.066212	0.64402	D	0.000018	D	0.92919	0.7747	M	0.64997	1.995	0.80722	D	1	D;D	0.67145	0.979;0.996	P;D	0.65233	0.743;0.933	D	0.92275	0.5828	9	.	.	.	-12.6066	17.8499	0.88742	0.0:1.0:0.0:0.0	.	295;295	Q86UX7-2;Q86UX7	.;URP2_HUMAN	V	295	ENSP00000339950:A295V;ENSP00000279227:A295V	.	A	+	2	0	FERMT3	63743396	1.000000	0.71417	0.760000	0.31359	0.027000	0.11550	5.956000	0.70315	2.595000	0.87683	0.655000	0.94253	GCC	.		0.667	FERMT3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000396297.1	NM_031471	
ESPL1	9700	ucsc.edu	37	12	53677189	53677189	+	Nonsense_Mutation	SNP	C	C	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr12:53677189C>T	ENST00000257934.4	+	16	3035	c.2944C>T	c.(2944-2946)Cag>Tag	p.Q982*	ESPL1_ENST00000552462.1_Nonsense_Mutation_p.Q982*	NM_012291.4	NP_036423.4	Q14674	ESPL1_HUMAN	extra spindle pole bodies homolog 1 (S. cerevisiae)	982					apoptotic process (GO:0006915)|cytokinesis (GO:0000910)|establishment of mitotic spindle localization (GO:0040001)|homologous chromosome segregation (GO:0045143)|meiotic spindle organization (GO:0000212)|mitotic cell cycle (GO:0000278)|mitotic sister chromatid segregation (GO:0000070)|negative regulation of sister chromatid cohesion (GO:0045875)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)	centrosome (GO:0005813)|cytosol (GO:0005829)|nucleus (GO:0005634)	catalytic activity (GO:0003824)|cysteine-type peptidase activity (GO:0008234)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(10)|large_intestine(12)|lung(21)|ovary(2)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(8)	70						ACAAAAATGGCAGGTTCTTTC	0.537																																					p.Q982X	Colon(53;1069 1201 2587 5382)												.	ESPL1	158	0			c.C2944T						.						96.0	101.0	99.0					12																	53677189		2203	4300	6503	SO:0001587	stop_gained	9700	exon16			AAATGGCAGGTTC	D79987	CCDS8852.1	12q13.13	2014-08-04	2013-05-03		ENSG00000135476	ENSG00000135476	3.4.22.49		16856	protein-coding gene	gene with protein product	"""separin"", ""separase"", ""separin, cysteine protease"""	604143	"""extra spindle poles like 1 (S. cerevisiae)"""			8724849, 16258266	Standard	NM_012291		Approved	KIAA0165, ESP1, SEPA	uc001sck.2	Q14674	OTTHUMG00000169674	ENST00000257934.4:c.2944C>T	12.37:g.53677189C>T	ENSP00000257934:p.Gln982*	Somatic	61	1		WXS	Illumina HiSeq		31	4	NM_012291		Nonsense_Mutation	SNP	ENST00000257934.4	37	CCDS8852.1	.	.	.	.	.	.	.	.	.	.	C	41	8.929351	0.99006	.	.	ENSG00000135476	ENST00000257934;ENST00000552671;ENST00000552462	.	.	.	5.12	5.12	0.69794	.	0.056851	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.62326	D	0.03	.	17.4979	0.87723	0.0:1.0:0.0:0.0	.	.	.	.	X	982;657;982	.	ENSP00000257934:Q982X	Q	+	1	0	ESPL1	51963456	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.129000	0.64739	2.667000	0.90743	0.655000	0.94253	CAG	.		0.537	ESPL1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406899.2	NM_012291	
C16orf93	90835	ucsc.edu	37	16	30770351	30770351	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr16:30770351G>T	ENST00000543610.1	-	8	1760	c.799C>A	c.(799-801)Cca>Aca	p.P267T	C16orf93_ENST00000541260.1_Missense_Mutation_p.P332T|PHKG2_ENST00000563588.1_3'UTR|PHKG2_ENST00000424889.3_Intron|RNF40_ENST00000324685.6_5'Flank	NM_001014979.2	NP_001014979.2	A1A4V9	CP093_HUMAN	chromosome 16 open reading frame 93	267										breast(2)|central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(6)	11						GGCTCTGGTGGGGCCACTGTC	0.542																																					p.P267T													.	C16orf93	33	0			c.C799A						.						180.0	165.0	170.0					16																	30770351		2197	4300	6497	SO:0001583	missense	90835	exon8			CTGGTGGGGCCAC	BC042548	CCDS32434.1, CCDS32434.2, CCDS55993.1	16p11.2	2012-10-10			ENSG00000196118	ENSG00000196118			28078	protein-coding gene	gene with protein product							Standard	NM_001195620		Approved	MGC104706	uc002dzm.3	A1A4V9	OTTHUMG00000167926	ENST00000543610.1:c.799C>A	16.37:g.30770351G>T	ENSP00000437532:p.Pro267Thr	Somatic	35	0		WXS	Illumina HiSeq		33	4	NM_001014979	A1A4V8|F5GX13|Q569G2	Missense_Mutation	SNP	ENST00000543610.1	37	CCDS32434.2	.	.	.	.	.	.	.	.	.	.	G	5.529	0.282560	0.10458	.	.	ENSG00000196118	ENST00000354963;ENST00000543610	.	.	.	4.3	-0.584	0.11702	.	0.644098	0.15491	N	0.259545	T	0.19287	0.0463	N	0.08118	0	0.09310	N	1	B;B;B	0.16396	0.001;0.017;0.0	B;B;B	0.17433	0.002;0.018;0.0	T	0.25882	-1.0119	9	0.17832	T	0.49	-4.0053	9.7202	0.40297	0.0:0.5973:0.2644:0.1383	.	230;39;267	A1A4V9-2;A1A4V9-3;A1A4V9	.;.;CP093_HUMAN	T	230;267	.	ENSP00000347050:P230T	P	-	1	0	C16orf93	30677852	0.001000	0.12720	0.011000	0.14972	0.003000	0.03518	-0.331000	0.07914	-0.043000	0.13513	0.655000	0.94253	CCA	.		0.542	C16orf93-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397089.1	NM_001014979	
RNF165	494470	ucsc.edu	37	18	44015312	44015312	+	Silent	SNP	C	C	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr18:44015312C>T	ENST00000269439.7	+	3	489	c.438C>T	c.(436-438)ggC>ggT	p.G146G	RNF165_ENST00000543885.1_Intron	NM_152470.2	NP_689683.2	Q6ZSG1	RN165_HUMAN	ring finger protein 165	146							zinc ion binding (GO:0008270)			NS(1)|large_intestine(4)|lung(6)	11				READ - Rectum adenocarcinoma(1;0.0873)		TCGACTTCGGCCAACTGCAGA	0.637																																					p.G146G													.	RNF165	34	0			c.C438T						.						63.0	55.0	58.0					18																	44015312		2203	4300	6503	SO:0001819	synonymous_variant	494470	exon3			CTTCGGCCAACTG	BC012190	CCDS32823.1, CCDS58621.1	18q21.1	2014-01-03			ENSG00000141622	ENSG00000141622		"""RING-type (C3HC4) zinc fingers"""	31696	protein-coding gene	gene with protein product							Standard	NR_046357		Approved	ARKL2, RNF111L2	uc002lcb.1	Q6ZSG1		ENST00000269439.7:c.438C>T	18.37:g.44015312C>T		Somatic	34	0		WXS	Illumina HiSeq		25	4	NM_152470	B3KVD1	Silent	SNP	ENST00000269439.7	37	CCDS32823.1																																																																																			.		0.637	RNF165-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445358.1	NM_152470	
GZF1	64412	ucsc.edu	37	20	23345235	23345235	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr20:23345235G>T	ENST00000338121.5	+	2	292	c.215G>T	c.(214-216)gGt>gTt	p.G72V	GZF1_ENST00000542987.1_Intron|GZF1_ENST00000544236.1_Intron|GZF1_ENST00000377051.2_Missense_Mutation_p.G72V			Q9H116	GZF1_HUMAN	GDNF-inducible zinc finger protein 1	72	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.				branching involved in ureteric bud morphogenesis (GO:0001658)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001206)|sequence-specific DNA binding (GO:0043565)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(7)|prostate(1)|urinary_tract(2)	24	Lung NSC(19;0.0605)|Colorectal(13;0.0993)|all_lung(19;0.135)					AGTGTGGATGGTACTAGGACT	0.453																																					p.G72V													.	GZF1	61	0			c.G215T						.						93.0	91.0	92.0					20																	23345235		2203	4300	6503	SO:0001583	missense	64412	exon1			TGGATGGTACTAG	AK025447	CCDS13151.1	20p11.21	2013-01-09	2006-09-19	2006-09-19	ENSG00000125812	ENSG00000125812		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	15808	protein-coding gene	gene with protein product		613842	"""zinc finger protein 336"""	ZNF336		14522971, 16049025	Standard	NM_022482		Approved	dJ322G13.2, ZBTB23	uc002wsz.3	Q9H116	OTTHUMG00000032069	ENST00000338121.5:c.215G>T	20.37:g.23345235G>T	ENSP00000338290:p.Gly72Val	Somatic	93	0		WXS	Illumina HiSeq		51	5	NM_022482	A8K199|B2RBC3|B3KPL4|B4DF58|D3DW39|Q54A22|Q96N08|Q9BQK9|Q9H117|Q9H6W6	Missense_Mutation	SNP	ENST00000338121.5	37	CCDS13151.1	.	.	.	.	.	.	.	.	.	.	G	11.82	1.752216	0.31046	.	.	ENSG00000125812	ENST00000338121;ENST00000377051	T;T	0.71698	-0.59;-0.59	5.33	4.39	0.52855	BTB/POZ-like (2);BTB/POZ (1);BTB/POZ fold (2);	0.225394	0.30859	N	0.008723	T	0.72779	0.3503	L	0.29908	0.895	0.80722	D	1	D	0.63880	0.993	P	0.61201	0.885	T	0.75022	-0.3464	10	0.59425	D	0.04	.	12.8603	0.57910	0.0783:0.0:0.9217:0.0	.	72	Q9H116	GZF1_HUMAN	V	72	ENSP00000338290:G72V;ENSP00000366250:G72V	ENSP00000338290:G72V	G	+	2	0	GZF1	23293235	0.998000	0.40836	0.028000	0.17463	0.004000	0.04260	4.355000	0.59424	1.270000	0.44297	0.650000	0.86243	GGT	.		0.453	GZF1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078333.1	NM_022482	
CNN3	1266	bcgsc.ca	37	1	95368702	95368706	+	Frame_Shift_Del	DEL	GTTGA	GTTGA	-	rs374270794		TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	GTTGA	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr1:95368702_95368706delGTTGA	ENST00000370206.4	-	3	601_605	c.218_222delTCAAC	c.(217-222)gtcaacfs	p.VN73fs	CNN3_ENST00000394202.4_Frame_Shift_Del_p.VN73fs|CNN3_ENST00000545882.1_Frame_Shift_Del_p.VN32fs|CNN3_ENST00000487539.1_5'UTR|CNN3_ENST00000538964.1_Frame_Shift_Del_p.VN73fs	NM_001839.3	NP_001830.1	Q15417	CNN3_HUMAN	calponin 3, acidic	73	CH. {ECO:0000255|PROSITE- ProRule:PRU00044}.				actomyosin structure organization (GO:0031032)|epithelial cell differentiation (GO:0030855)	focal adhesion (GO:0005925)				breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(9)|prostate(1)|stomach(1)|urinary_tract(2)	18		all_lung(203;0.00206)|Lung NSC(277;0.00948)		all cancers(265;0.0325)|Epithelial(280;0.0861)		GTGAGGACTCGTTGACCTTCTTCAC	0.395																																					p.73_74del													.	CNN3	23	0			c.218_222del						.																																			SO:0001589	frameshift_variant	1266	exon3			GGACTCGTTGACC	BC025372	CCDS30775.1, CCDS65592.1, CCDS65593.1	1p22-p21	2010-07-08			ENSG00000117519	ENSG00000117519			2157	protein-coding gene	gene with protein product		602374				8526917	Standard	NM_001839		Approved		uc001dqz.4	Q15417	OTTHUMG00000010783	ENST00000370206.4:c.218_222delTCAAC	1.37:g.95368702_95368706delGTTGA	ENSP00000359225:p.Val73fs	Somatic	119	0		WXS	Illumina HiSeq	Phase_1	25	0	NM_001839	B4DFK6|B4DP09|F8WA86|Q6FHA7	Frame_Shift_Del	DEL	ENST00000370206.4	37	CCDS30775.1																																																																																			.		0.395	CNN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029702.2	NM_001839	
CNN3	1266	bcgsc.ca	37	1	95368708	95368712	+	Frame_Shift_Del	DEL	CTTCT	CTTCT	-	rs201766980		TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	CTTCT	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr1:95368708_95368712delCTTCT	ENST00000370206.4	-	3	595_599	c.212_216delAGAAG	c.(211-216)aagaagfs	p.KK71fs	CNN3_ENST00000394202.4_Frame_Shift_Del_p.KK71fs|CNN3_ENST00000545882.1_Frame_Shift_Del_p.KK30fs|CNN3_ENST00000487539.1_5'UTR|CNN3_ENST00000538964.1_Frame_Shift_Del_p.KK71fs	NM_001839.3	NP_001830.1	Q15417	CNN3_HUMAN	calponin 3, acidic	71	CH. {ECO:0000255|PROSITE- ProRule:PRU00044}.				actomyosin structure organization (GO:0031032)|epithelial cell differentiation (GO:0030855)	focal adhesion (GO:0005925)				breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(9)|prostate(1)|stomach(1)|urinary_tract(2)	18		all_lung(203;0.00206)|Lung NSC(277;0.00948)		all cancers(265;0.0325)|Epithelial(280;0.0861)		ACTCGTTGACCTTCTTCACTGAGCC	0.395																																					p.71_72del													.	CNN3	23	0			c.212_216del						.																																			SO:0001589	frameshift_variant	1266	exon3			GTTGACCTTCTTC	BC025372	CCDS30775.1, CCDS65592.1, CCDS65593.1	1p22-p21	2010-07-08			ENSG00000117519	ENSG00000117519			2157	protein-coding gene	gene with protein product		602374				8526917	Standard	NM_001839		Approved		uc001dqz.4	Q15417	OTTHUMG00000010783	ENST00000370206.4:c.212_216delAGAAG	1.37:g.95368708_95368712delCTTCT	ENSP00000359225:p.Lys71fs	Somatic	120	0		WXS	Illumina HiSeq	Phase_1	20	5	NM_001839	B4DFK6|B4DP09|F8WA86|Q6FHA7	Frame_Shift_Del	DEL	ENST00000370206.4	37	CCDS30775.1																																																																																			.		0.395	CNN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029702.2	NM_001839	
PRDM9	56979	bcgsc.ca	37	5	23527721	23527727	+	Frame_Shift_Del	DEL	CGCAATA	CGCAATA	-	rs201643800		TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	CGCAATA	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr5:23527721_23527727delCGCAATA	ENST00000296682.3	+	11	2706_2712	c.2524_2530delCGCAATA	c.(2524-2532)cgcaataagfs	p.RNK842fs		NM_020227.2	NP_064612.2	Q9NQV7	PRDM9_HUMAN	PR domain containing 9	842					meiotic gene conversion (GO:0006311)|positive regulation of meiosis I (GO:0060903)|positive regulation of reciprocal meiotic recombination (GO:0010845)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)	histone methyltransferase activity (H3-K4 specific) (GO:0042800)|metal ion binding (GO:0046872)|recombination hotspot binding (GO:0010844)|sequence-specific DNA binding (GO:0043565)	p.N843D(2)|p.R842H(1)		NS(1)|breast(1)|central_nervous_system(3)|endometrium(15)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(27)|lung(87)|ovary(6)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(11)	172						GCGGGGCTTTCGCAATAAGTCACACCT	0.585										HNSCC(3;0.000094)																											p.842_844del													PRDM9,brain,primitive_neuroectodermal_tumour-medulloblastoma,-1,1	PRDM9	344	3	Substitution - Missense(3)	skin(2)|central_nervous_system(1)	c.2524_2530del						.																																			SO:0001589	frameshift_variant	56979	exon11			GGCTTTCGCAATA	AF275816	CCDS43307.1	5p14.2	2014-06-03			ENSG00000164256	ENSG00000164256		"""-"", ""Zinc fingers, C2H2-type"""	13994	protein-coding gene	gene with protein product	"""PR-domain containing protein 9"""	609760	"""minisatellite binding protein 3, 115kDa"", ""minisatellite binding protein 3 (115kD)"""	MSBP3		10668202, 2062643, 24634223	Standard	NM_020227		Approved	PFM6, ZNF899	uc003jgo.3	Q9NQV7	OTTHUMG00000161918	ENST00000296682.3:c.2524_2530delCGCAATA	5.37:g.23527721_23527727delCGCAATA	ENSP00000296682:p.Arg842fs	Somatic	74	0		WXS	Illumina HiSeq	Phase_1	81	6	NM_020227	B4DX22|Q27Q50	Frame_Shift_Del	DEL	ENST00000296682.3	37	CCDS43307.1																																																																																			.		0.585	PRDM9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366375.1	NM_020227	
PRDM9	56979	bcgsc.ca	37	5	23527730	23527738	+	In_Frame_Del	DEL	TCACACCTC	TCACACCTC	-	rs561307345		TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	TCACACCTC	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr5:23527730_23527738delTCACACCTC	ENST00000296682.3	+	11	2715_2723	c.2533_2541delTCACACCTC	c.(2533-2541)tcacacctcdel	p.SHL845del		NM_020227.2	NP_064612.2	Q9NQV7	PRDM9_HUMAN	PR domain containing 9	845					meiotic gene conversion (GO:0006311)|positive regulation of meiosis I (GO:0060903)|positive regulation of reciprocal meiotic recombination (GO:0010845)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)	histone methyltransferase activity (H3-K4 specific) (GO:0042800)|metal ion binding (GO:0046872)|recombination hotspot binding (GO:0010844)|sequence-specific DNA binding (GO:0043565)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(15)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(27)|lung(87)|ovary(6)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(11)	172						TCGCAATAAGTCACACCTCCTCAGACACC	0.574										HNSCC(3;0.000094)																											p.845_847del													.	PRDM9	344	0			c.2533_2541del						.																																			SO:0001651	inframe_deletion	56979	exon11			AATAAGTCACACC	AF275816	CCDS43307.1	5p14.2	2014-06-03			ENSG00000164256	ENSG00000164256		"""-"", ""Zinc fingers, C2H2-type"""	13994	protein-coding gene	gene with protein product	"""PR-domain containing protein 9"""	609760	"""minisatellite binding protein 3, 115kDa"", ""minisatellite binding protein 3 (115kD)"""	MSBP3		10668202, 2062643, 24634223	Standard	NM_020227		Approved	PFM6, ZNF899	uc003jgo.3	Q9NQV7	OTTHUMG00000161918	ENST00000296682.3:c.2533_2541delTCACACCTC	5.37:g.23527730_23527738delTCACACCTC	ENSP00000296682:p.Ser845_Leu847del	Somatic	79	0		WXS	Illumina HiSeq	Phase_1	77	6	NM_020227	B4DX22|Q27Q50	In_Frame_Del	DEL	ENST00000296682.3	37	CCDS43307.1																																																																																			.		0.574	PRDM9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366375.1	NM_020227	
CYP2E1	1571	bcgsc.ca	37	10	135340926	135340949	+	In_Frame_Del	DEL	CCTGCTGGTGTGGGCGGCCTTCCT	CCTGCTGGTGTGGGCGGCCTTCCT	-	rs543066971|rs563043306|rs367957731|rs375169910		TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	CCTGCTGGTGTGGGCGGCCTTCCT	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr10:135340926_135340949delCCTGCTGGTGTGGGCGGCCTTCCT	ENST00000463117.2	+	3	299_322	c.27_50delCCTGCTGGTGTGGGCGGCCTTCCT	c.(25-51)gccctgctggtgtgggcggccttcctc>gcc	p.LLVWAAFL10del	SPRN_ENST00000541506.1_Intron|CYP2E1_ENST00000252945.3_In_Frame_Del_p.LLVWAAFL10del			P05181	CP2E1_HUMAN	cytochrome P450, family 2, subfamily E, polypeptide 1	10					drug metabolic process (GO:0017144)|heterocycle metabolic process (GO:0046483)|monoterpenoid metabolic process (GO:0016098)|oxidation-reduction process (GO:0055114)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to organonitrogen compound (GO:0010243)|response to ozone (GO:0010193)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|triglyceride metabolic process (GO:0006641)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|Golgi membrane (GO:0000139)|intrinsic component of endoplasmic reticulum membrane (GO:0031227)|mitochondrion (GO:0005739)	enzyme binding (GO:0019899)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity (GO:0016491)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen (GO:0016709)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen (GO:0016712)|oxygen binding (GO:0019825)	p.A14V(1)		NS(1)|central_nervous_system(3)|endometrium(1)|kidney(4)|large_intestine(6)|liver(2)|lung(7)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	30		all_cancers(35;1.14e-09)|all_epithelial(44;5.79e-08)|Lung NSC(174;0.00263)|all_lung(145;0.0039)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.172)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;1.12e-06)|all cancers(32;1.43e-06)|Epithelial(32;1.71e-06)	Acetaminophen(DB00316)|Aldesleukin(DB00041)|Almotriptan(DB00918)|Alosetron(DB00969)|Aminophylline(DB01223)|Amitriptyline(DB00321)|Antipyrine(DB01435)|Azelastine(DB00972)|Benzyl alcohol(DB06770)|Bifonazole(DB04794)|Bromazepam(DB01558)|Brompheniramine(DB00835)|Bupropion(DB01156)|Caffeine(DB00201)|Carbinoxamine(DB00748)|Carvedilol(DB01136)|Chlorpromazine(DB00477)|Chlorzoxazone(DB00356)|Cimetidine(DB00501)|Citalopram(DB00215)|Clevidipine(DB04920)|Clofibrate(DB00636)|Clomifene(DB00882)|Clonazepam(DB01068)|Clotrimazole(DB00257)|Clozapine(DB00363)|Colchicine(DB01394)|Dacarbazine(DB00851)|Dalfampridine(DB06637)|Dapsone(DB00250)|Desipramine(DB01151)|Dexamethasone(DB01234)|Dexfenfluramine(DB01191)|Dexmedetomidine(DB00633)|Dextromethorphan(DB00514)|Diazepam(DB00829)|Diclofenac(DB00586)|Diethylstilbestrol(DB00255)|Disulfiram(DB00822)|Econazole(DB01127)|Enflurane(DB00228)|Enfuvirtide(DB00109)|Estrone(DB00655)|Ethanol(DB00898)|Ethanolamine Oleate(DB06689)|Ethosuximide(DB00593)|Etoposide(DB00773)|Etoricoxib(DB01628)|Felbamate(DB00949)|Fingolimod(DB08868)|Flunitrazepam(DB01544)|Fluphenazine(DB00623)|Flurazepam(DB00690)|Fluvoxamine(DB00176)|Folic Acid(DB00158)|Fomepizole(DB01213)|Glucosamine(DB01296)|Halothane(DB01159)|Hexobarbital(DB01355)|Iloperidone(DB04946)|Imipramine(DB00458)|Isoflurane(DB00753)|Isoniazid(DB00951)|Isosorbide Dinitrate(DB00883)|Itraconazole(DB01167)|Menadione(DB00170)|Meprobamate(DB00371)|Methazolamide(DB00703)|Methimazole(DB00763)|Methotrimeprazine(DB01403)|Methoxyflurane(DB01028)|Metyrapone(DB01011)|Mexiletine(DB00379)|Miconazole(DB01110)|Midazolam(DB00683)|Mitoxantrone(DB01204)|Nicardipine(DB00622)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nitrazepam(DB01595)|Nortriptyline(DB00540)|Ondansetron(DB00904)|Orphenadrine(DB01173)|Oxaliplatin(DB00526)|Paramethadione(DB00617)|Phenelzine(DB00780)|Phenobarbital(DB01174)|Pilocarpine(DB01085)|Pimozide(DB01100)|Proguanil(DB01131)|Propofol(DB00818)|Quinidine(DB00908)|Quinine(DB00468)|Rifampicin(DB01045)|Ritonavir(DB00503)|Rufinamide(DB06201)|S-Adenosylmethionine(DB00118)|Selegiline(DB01037)|Sevoflurane(DB01236)|Sildenafil(DB00203)|Streptozocin(DB00428)|Sulfadiazine(DB00359)|Sulfanilamide(DB00259)|Tamoxifen(DB00675)|Thalidomide(DB01041)|Theobromine(DB01412)|Theophylline(DB00277)|Thiopental(DB00599)|Thioridazine(DB00679)|Ticlopidine(DB00208)|Tioconazole(DB01007)|Trabectedin(DB05109)|Tranylcypromine(DB00752)|Trimethadione(DB00347)|Ursodeoxycholic acid(DB01586)|Zafirlukast(DB00549)|Zopiclone(DB01198)	TCACCGTGGCCCTGCTGGTGTGGGCGGCCTTCCTCCTGCTGGTG	0.607									Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of																												p.9_17del													.	CYP2E1	69	1	Substitution - Missense(1)	large_intestine(1)	c.27_50del						.																																			SO:0001651	inframe_deletion	1571	exon1	Familial Cancer Database	incl.: Familial Head and Neck Cancer	CGTGGCCCTGCTG	J02843	CCDS7686.1	10q26.3	2013-05-03	2003-01-14	2002-09-13	ENSG00000130649	ENSG00000130649		"""Cytochrome P450s"""	2631	protein-coding gene	gene with protein product		124040	"""cytochrome P450, subfamily IIE (ethanol-inducible), polypeptide 1"""	CYP2E			Standard	NM_000773		Approved		uc001lnj.1	P05181	OTTHUMG00000019322	ENST00000463117.2:c.27_50delCCTGCTGGTGTGGGCGGCCTTCCT	10.37:g.135340926_135340949delCCTGCTGGTGTGGGCGGCCTTCCT	ENSP00000440689:p.Leu10_Leu17del	Somatic	72	0		WXS	Illumina HiSeq	Phase_1	25	6	NM_000773	Q5VZD5|Q6NWT9|Q9UK47	In_Frame_Del	DEL	ENST00000463117.2	37	CCDS7686.1																																																																																			.		0.607	CYP2E1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051161.2	NM_000773	
LINC01219	104355220	bcgsc.ca	37	11	2016914	2016914	+	lincRNA	DEL	G	G	-			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr11:2016914delG	ENST00000418612.1	+	0	1444				H19_ENST00000390168.4_RNA																							GTCCGCCGCAGGGGGTGGCCA	0.622																																					.													.	H19	1	0			.						.						38.0	40.0	40.0					11																	2016914		875	1990	2865			283120	.			GCCGCAGGGGGTG																													11.37:g.2016914delG		Somatic	38	0		WXS	Illumina HiSeq	Phase_1	19	7	.		RNA	DEL	ENST00000418612.1	37																																																																																				.		0.622	AC051649.6-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000034754.1		
MSRB3	253827	bcgsc.ca	37	12	65672596	65672601	+	In_Frame_Del	DEL	CCTCTG	CCTCTG	-	rs377713148		TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	CCTCTG	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr12:65672596_65672601delCCTCTG	ENST00000355192.3	+	1	174_179	c.48_53delCCTCTG	c.(46-54)tccctctgc>tcc	p.LC21del	MSRB3_ENST00000308259.5_5'UTR|RP11-305O6.3_ENST00000545709.1_RNA|MSRB3_ENST00000535664.1_5'UTR|MSRB3_ENST00000538725.1_3'UTR|MSRB3_ENST00000540804.1_In_Frame_Del_p.LC21del	NM_198080.3	NP_932346.1	Q8IXL7	MSRB3_HUMAN	methionine sulfoxide reductase B3	21					protein repair (GO:0030091)|response to oxidative stress (GO:0006979)	endoplasmic reticulum (GO:0005783)|mitochondrion (GO:0005739)	peptide-methionine (R)-S-oxide reductase activity (GO:0033743)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(4)|lung(3)|prostate(1)|skin(1)	13			LUAD - Lung adenocarcinoma(6;0.0234)|LUSC - Lung squamous cell carcinoma(43;0.0975)	GBM - Glioblastoma multiforme(28;0.131)		tctgcctctccctctgcctctgcctc	0.738																																					p.16_18del													MSRB3_ENST00000355192,rectum,carcinoma,+2,1	MSRB3	80	0			c.48_53del						.																																			SO:0001651	inframe_deletion	253827	exon1			CCTCTCCCTCTGC	BX640871	CCDS8973.1, CCDS31853.1	12q14.3	2011-11-29			ENSG00000174099	ENSG00000174099			27375	protein-coding gene	gene with protein product		613719	"""deafness, autosomal recessive 74"""	DFNB74		21185009	Standard	NM_198080		Approved	FLJ36866, DKFZp686C1178	uc021qzy.1	Q8IXL7	OTTHUMG00000168866	ENST00000355192.3:c.48_53delCCTCTG	12.37:g.65672602_65672607delCCTCTG	ENSP00000347324:p.Leu21_Cys22del	Somatic	76	0		WXS	Illumina HiSeq	Phase_1	66	3	NM_198080	B4DR19|B7ZAQ0|Q6UXS2	In_Frame_Del	DEL	ENST00000355192.3	37	CCDS8973.1																																																																																			.		0.738	MSRB3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000401421.1	NM_198080	
EMC4	51234	bcgsc.ca	37	15	34517724	34517724	+	Intron	DEL	T	T	-			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr15:34517724delT	ENST00000267750.4	+	2	202				EMC4_ENST00000557879.1_Intron|EMC4_ENST00000249209.4_Intron|EMC4_ENST00000559421.1_Intron|EMC4_ENST00000559078.1_Intron	NM_016454.2	NP_057538.1	Q5J8M3	EMC4_HUMAN	ER membrane protein complex subunit 4						apoptotic process (GO:0006915)	ER membrane protein complex (GO:0072546)|integral component of membrane (GO:0016021)											AGTTTCTTGGTTTGGTTTTTT	0.478																																					.													.	.	.	0			.						.						141.0	139.0	139.0					15																	34517724		2201	4298	6499	SO:0001627	intron_variant	51234	.			TCTTGGTTTGGTT	BC016348	CCDS10035.1, CCDS66732.1	15q14	2012-05-23	2012-05-23	2012-05-23	ENSG00000128463	ENSG00000128463			28032	protein-coding gene	gene with protein product			"""transmembrane protein 85"""	TMEM85		18586032, 22119785	Standard	NM_001286420		Approved	FLJ90746, MGC24415, PIG17	uc001zhq.3	Q5J8M3	OTTHUMG00000129411	ENST00000267750.4:c.87-13T>-	15.37:g.34517724delT		Somatic	92	0		WXS	Illumina HiSeq	Phase_1	65	11	.	A8K3A9|B4DJQ4|Q96KX9|Q9BUI5|Q9P0T9	Frame_Shift_Del	DEL	ENST00000267750.4	37	CCDS10035.1																																																																																			.		0.478	EMC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251568.1	NM_016454	
CLPX	10845	bcgsc.ca	37	15	65447200	65447212	+	Frame_Shift_Del	DEL	CATCTAGGCTATG	CATCTAGGCTATG	-	rs141503742		TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	CATCTAGGCTATG	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr15:65447200_65447212delCATCTAGGCTATG	ENST00000300107.3	-	11	1707_1719	c.1519_1531delCATAGCCTAGATG	c.(1519-1533)catagcctagatgagfs	p.HSLDE507fs		NM_006660.3	NP_006651.2	O76031	CLPX_HUMAN	caseinolytic mitochondrial matrix peptidase chaperone subunit	507					ATP catabolic process (GO:0006200)|positive regulation of peptidase activity (GO:0010952)|protein folding (GO:0006457)|proteolysis involved in cellular protein catabolic process (GO:0051603)	endopeptidase Clp complex (GO:0009368)|mitochondrial endopeptidase Clp complex (GO:0009841)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|metal ion binding (GO:0046872)|peptidase activator activity (GO:0016504)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(4)|prostate(1)|skin(2)	16						AGTGTTTTCTCATCTAGGCTATGCAATGGAACC	0.408																																					p.507_511del													.	CLPX	49	0			c.1519_1531del						.																																			SO:0001589	frameshift_variant	10845	exon11			TTTTCTCATCTAG	AJ006267	CCDS10202.1	15q22.31	2013-09-12	2013-09-12		ENSG00000166855	ENSG00000166855		"""ATPases / AAA-type"""	2088	protein-coding gene	gene with protein product		615611	"""ClpX (caseinolytic protease X, E. coli) homolog"", ""ClpX caseinolytic protease X homolog (E. coli)"", ""ClpX caseinolytic peptidase X homolog (E. coli)"""			22841477	Standard	NM_006660		Approved		uc002aom.3	O76031	OTTHUMG00000133139	ENST00000300107.3:c.1519_1531delCATAGCCTAGATG	15.37:g.65447200_65447212delCATCTAGGCTATG	ENSP00000300107:p.His507fs	Somatic	61	0		WXS	Illumina HiSeq	Phase_1	30	3	NM_006660	A1L428|A8K8F1|B9EGI8|Q9H4D9	Frame_Shift_Del	DEL	ENST00000300107.3	37	CCDS10202.1																																																																																			.		0.408	CLPX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256828.2	NM_006660	
BAIAP3	8938	bcgsc.ca	37	16	1393409	1393430	+	Frame_Shift_Del	DEL	CAGCCGCCACCATCAAACCTGC	CAGCCGCCACCATCAAACCTGC	-	rs576394425|rs545400434		TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	CAGCCGCCACCATCAAACCTGC	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr16:1393409_1393430delCAGCCGCCACCATCAAACCTGC	ENST00000324385.5	+	15	1544_1565	c.1386_1407delCAGCCGCCACCATCAAACCTGC	c.(1384-1407)agcagccgccaccatcaaacctgcfs	p.SSRHHQTC462fs	BAIAP3_ENST00000562208.1_Frame_Shift_Del_p.SSRHHQTC404fs|BAIAP3_ENST00000568887.1_Frame_Shift_Del_p.SSRHHQTC399fs|BAIAP3_ENST00000426824.3_Frame_Shift_Del_p.SSRHHQTC427fs|BAIAP3_ENST00000421665.2_Frame_Shift_Del_p.SSRHHQTC391fs|BAIAP3_ENST00000397488.2_Frame_Shift_Del_p.SSRHHQTC444fs|BAIAP3_ENST00000397489.1_Frame_Shift_Del_p.SSRHHQTC444fs	NM_003933.4	NP_003924.2	O94812	BAIP3_HUMAN	BAI1-associated protein 3	462					G-protein coupled receptor signaling pathway (GO:0007186)|neurotransmitter secretion (GO:0007269)		protein C-terminus binding (GO:0008022)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(1)|lung(25)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	42		Hepatocellular(780;0.0893)				GGCAGGTCAGCAGCCGCCACCATCAAACCTGCACGCTGGACT	0.649																																					p.462_469del													.	BAIAP3	88	0			c.1386_1407del						.																																			SO:0001589	frameshift_variant	8938	exon15			GGTCAGCAGCCGC	AB017111	CCDS10434.1, CCDS55978.1, CCDS55979.1, CCDS58402.1, CCDS58403.1, CCDS66894.1	16p13.3	2008-07-04			ENSG00000007516	ENSG00000007516			948	protein-coding gene	gene with protein product		604009				9790924	Standard	NM_003933		Approved	BAP3, KIAA0734	uc002clk.2	O94812	OTTHUMG00000047833	ENST00000324385.5:c.1386_1407delCAGCCGCCACCATCAAACCTGC	16.37:g.1393409_1393430delCAGCCGCCACCATCAAACCTGC	ENSP00000324510:p.Ser462fs	Somatic	67	0		WXS	Illumina HiSeq	Phase_1	26	3	NM_003933	A2A2B2|B2RCD7|B4DGS5|B4DIK3|B4DRK9|B4DRP1|E7EUB9|H3BUH8|H3BVI3|H7C2Q1|O94839|Q2M226|Q658J2|Q76N05|Q96RZ3|Q9UJK1	Frame_Shift_Del	DEL	ENST00000324385.5	37	CCDS10434.1																																																																																			.		0.649	BAIAP3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000109056.3		
FUS	2521	bcgsc.ca	37	16	31195693	31195698	+	In_Frame_Del	DEL	GGTGGA	GGTGGA	-	rs375535815|rs78117286		TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	GGTGGA	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr16:31195693_31195698delGGTGGA	ENST00000254108.7	+	5	604_609	c.499_504delGGTGGA	c.(499-504)ggtggadel	p.GG173del	FUS_ENST00000568685.1_In_Frame_Del_p.GG173del|RP11-388M20.6_ENST00000564743.1_RNA|FUS_ENST00000380244.3_In_Frame_Del_p.GG172del	NM_001170634.1|NM_001170937.1|NM_004960.3	NP_001164105.1|NP_001164408.1|NP_004951.1	P35637	FUS_HUMAN	FUS RNA binding protein	173	Gly-rich.				cell death (GO:0008219)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)		FUS/ERG(167)|FUS/DDIT3(631)|FUS/FEV(2)|FUS/ATF1(4)|FUS/CREB3L1(6)|FUS/CREB3L2(158)	breast(3)|endometrium(5)|kidney(3)|large_intestine(1)|lung(5)|prostate(3)|skin(1)|urinary_tract(1)	22		Renal(780;0.000219)|Breast(268;0.00957)|Hepatocellular(780;0.121)		GBM - Glioblastoma multiforme(240;2.31e-05)|Kidney(780;0.000209)		CAGCAgtggtggtggaggtggaggtg	0.485			T	"""DDIT3, ERG, FEV, ATF1, CREB3L2, CREB3L1"""	"""liposarcoma, AML, Ewing sarcoma, angiomatoid fibrous histiocytoma, fibromyxoid sarcoma"""																																p.167_168del				Dom	yes		16	16p11.2	2521	"""fusion, derived from t(12;16) malignant liposarcoma"""		"""M, L"""	.	FUS	52	0			c.499_504del						.																																			SO:0001651	inframe_deletion	2521	exon5			AGTGGTGGTGGAG	AF071213	CCDS10707.1, CCDS58454.1	16p11.2	2014-09-17	2014-05-09		ENSG00000089280	ENSG00000089280		"""RNA binding motif (RRM) containing"""	4010	protein-coding gene	gene with protein product	"""heterogeneous nuclear ribonucleoprotein P2"", ""translocated in liposarcoma"""	137070	"""fusion, derived from t(12;16) malignant liposarcoma"", ""amyotrophic lateral sclerosis 6"", ""fusion (involved in t(12;16) in malignant liposarcoma)"", ""fused in sarcoma"""	ALS6		2372777, 7503811, 19251628, 19251627	Standard	NM_004960		Approved	TLS, FUS1, hnRNP-P2, HNRNPP2	uc002ebe.2	P35637	OTTHUMG00000132395	ENST00000254108.7:c.499_504delGGTGGA	16.37:g.31195699_31195704delGGTGGA	ENSP00000254108:p.Gly173_Gly174del	Somatic	43	0		WXS	Illumina HiSeq	Phase_1	23	7	NM_004960	Q9H4A8	In_Frame_Del	DEL	ENST00000254108.7	37	CCDS10707.1																																																																																			.		0.485	FUS-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255526.2	NM_004960	
LOC101928303	101928303	bcgsc.ca	37	1	26536413	26536413	+	IGR	SNP	C	C	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr1:26536413C>T								CATSPER4 (6954 upstream) : RP11-231P20.2 (15397 downstream)																							CCAGCTGCTCCTCCAACCTCT	0.433																																					.													.	.	.	0			.						.																																			SO:0001628	intergenic_variant	0	.			CTGCTCCTCCAAC																													1.37:g.26536413C>T		Somatic	31	0		WXS	Illumina HiSeq	Phase_1	25	10	.		RNA	SNP		37																																																																																				.	0	0.433								
Unknown	0	bcgsc.ca	37	1	146791337	146791337	+	IGR	SNP	C	C	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr1:146791337C>A								CHD1L (23894 upstream) : Y_RNA (100588 downstream)																							TAGGGTCTGACGAAAAGACTG	0.453																																					.													.	.	.	0			.						.																																			SO:0001628	intergenic_variant	0	.			GTCTGACGAAAAG																													1.37:g.146791337C>A		Somatic	25	0		WXS	Illumina HiSeq	Phase_1	14	8	.		RNA	SNP		37																																																																																				.	0	0.453								
PHBP11	644214	bcgsc.ca	37	1	224044438	224044438	+	IGR	SNP	G	G	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr1:224044438G>T								TP53BP2 (10764 upstream) : RP11-504P24.8 (94657 downstream)																							AGCTGCCTTGGAGTCGCCCTC	0.567																																					.													.	.	.	0			.						.																																			SO:0001628	intergenic_variant	644214	.			GCCTTGGAGTCGC																													1.37:g.224044438G>T		Somatic	25	0		WXS	Illumina HiSeq	Phase_1	15	4	.		RNA	SNP		37																																																																																				.	0	0.567								
AC073218.1	0	bcgsc.ca	37	2	34628769	34628769	+	lincRNA	SNP	T	T	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr2:34628769T>A	ENST00000422558.1	+	0	475				AC011748.1_ENST00000390736.2_RNA																							aattgcggtttttggcatcac	0.274																																					.													.	.	.	0			.						.																																					0	.			GCGGTTTTTGGCA																													2.37:g.34628769T>A		Somatic	44	0		WXS	Illumina HiSeq	Phase_1	28	14	.		RNA	SNP	ENST00000422558.1	37																																																																																				.		0.274	AC073218.1-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000325415.1		
CEP68	23177	bcgsc.ca	37	2	65299502	65299502	+	Silent	SNP	G	G	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr2:65299502G>A	ENST00000377990.2	+	3	1475	c.1272G>A	c.(1270-1272)cgG>cgA	p.R424R	CEP68_ENST00000260569.4_Silent_p.R424R|CEP68_ENST00000546106.1_Silent_p.R424R|CEP68_ENST00000497039.1_3'UTR|CEP68_ENST00000537589.1_Silent_p.R36R|RAB1A_ENST00000494188.1_Intron	NM_015147.2	NP_055962.2	Q76N32	CEP68_HUMAN	centrosomal protein 68kDa	424					centriole-centriole cohesion (GO:0010457)|centrosome organization (GO:0051297)|protein localization to organelle (GO:0033365)	centrosome (GO:0005813)|cytoplasm (GO:0005737)	protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)			breast(1)|endometrium(6)|kidney(8)|large_intestine(5)|lung(8)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	32						CGAAGGACCGGCTGACTATAG	0.632																																					p.R424R													.	CEP68	69	0			c.G1272A						.						57.0	58.0	58.0					2																	65299502		2203	4300	6503	SO:0001819	synonymous_variant	23177	exon3			GGACCGGCTGACT	BC004873	CCDS1880.2	2p14	2014-02-20	2005-12-01	2005-12-01	ENSG00000011523	ENSG00000011523			29076	protein-coding gene	gene with protein product			"""KIAA0582"""	KIAA0582		9628581, 9847074, 14654843	Standard	NM_015147		Approved		uc002sdl.4	Q76N32	OTTHUMG00000129538	ENST00000377990.2:c.1272G>A	2.37:g.65299502G>A		Somatic	21	0		WXS	Illumina HiSeq	Phase_1	14	3	NM_015147	B4DRQ1|D6W5F1|D6W5F2|O60326|Q9BQ18|Q9UDM9	Silent	SNP	ENST00000377990.2	37	CCDS1880.2																																																																																			.		0.632	CEP68-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251727.2	NM_015147	
IGKV1OR2-108	28862	bcgsc.ca	37	2	114164265	114164265	+	RNA	SNP	T	T	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr2:114164265T>C	ENST00000542081.1	+	0	103									immunoglobulin kappa variable 1/OR2-108 (non-functional)																		TGGGTTATCCTGGTATCAGCA	0.567																																					.													.	.	.	0			.						.																																					0	.			TTATCCTGGTATC	X51887		2q12-q14	2013-12-06	2008-09-11		ENSG00000231292	ENSG00000231292		"""Immunoglobulins / IGK orphons"""	5767	other	immunoglobulin gene	"""immunoglobulin orphon (transposed element) 1"""	147185	"""immunoglobulin kappa variable 1/OR2-108"""			2114012	Standard			Approved	IGKV1/OR2-108, IGKV1OR2108, IGO1			OTTHUMG00000153338		2.37:g.114164265T>C		Somatic	127	0		WXS	Illumina HiSeq	Phase_1	60	22	.		RNA	SNP	ENST00000542081.1	37																																																																																				.		0.567	IGKV1OR2-108-201	KNOWN	basic|appris_principal	IG_V_gene	IG_V_gene			
AC122136.1	0	bcgsc.ca	37	2	216743614	216743614	+	RNA	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr2:216743614A>C	ENST00000390766.1	-	0	28																											aagggcaaaaatcgcaattac	0.358																																					.													.	.	.	0			.						.																																					0	.			GCAAAAATCGCAA																													2.37:g.216743614A>C		Somatic	56	0		WXS	Illumina HiSeq	Phase_1	23	11	.		RNA	SNP	ENST00000390766.1	37																																																																																				.		0.358	AC122136.1-201	NOVEL	basic	miRNA	miRNA			
STK11IP	114790	bcgsc.ca	37	2	220474092	220474092	+	Missense_Mutation	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr2:220474092T>G	ENST00000456909.1	+	17	2024	c.1934T>G	c.(1933-1935)cTt>cGt	p.L645R	STK11IP_ENST00000295641.10_Missense_Mutation_p.L656R			Q8N1F8	S11IP_HUMAN	serine/threonine kinase 11 interacting protein	656					protein localization (GO:0008104)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal membrane (GO:0005765)	protein kinase binding (GO:0019901)			breast(2)|endometrium(5)|kidney(1)|large_intestine(2)|lung(10)|ovary(1)|prostate(1)|urinary_tract(1)	23		Renal(207;0.0183)		Epithelial(149;2.69e-07)|all cancers(144;5.91e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		CAGGAGCTGCTTGCCGTGTTG	0.647																																					p.L656R													.	STK11IP	152	0			c.T1967G						.						32.0	37.0	35.0					2																	220474092		2038	4198	6236	SO:0001583	missense	114790	exon17			AGCTGCTTGCCGT	AF450267	CCDS46521.1	2q35	2008-06-03			ENSG00000144589	ENSG00000144589			19184	protein-coding gene	gene with protein product	"""LKB1 interacting protein"""	607172				11741830	Standard	NM_052902		Approved	LIP1, KIAA1898, LKB1IP, STK11IP1	uc002vml.3	Q8N1F8	OTTHUMG00000059239	ENST00000456909.1:c.1934T>G	2.37:g.220474092T>G	ENSP00000389383:p.Leu645Arg	Somatic	71	0		WXS	Illumina HiSeq	Phase_1	61	27	NM_052902	Q8NAW9|Q8WXE4|Q96CN3|Q96PY9	Missense_Mutation	SNP	ENST00000456909.1	37		.	.	.	.	.	.	.	.	.	.	T	17.93	3.507984	0.64410	.	.	ENSG00000144589	ENST00000456909;ENST00000295641	T;T	0.07688	3.18;3.17	5.1	5.1	0.69264	.	0.237832	0.36303	N	0.002677	T	0.26376	0.0644	M	0.71581	2.175	0.47584	D	0.999467	D;D	0.76494	0.999;0.999	D;D	0.91635	0.999;0.999	T	0.00738	-1.1587	10	0.87932	D	0	-15.9226	11.237	0.48946	0.0:0.0:0.0:1.0	.	656;656	Q8N1F8-2;Q8N1F8	.;S11IP_HUMAN	R	645;656	ENSP00000389383:L645R;ENSP00000295641:L656R	ENSP00000295641:L656R	L	+	2	0	STK11IP	220182336	0.986000	0.35501	0.945000	0.38365	0.664000	0.39144	2.216000	0.42871	2.145000	0.66743	0.533000	0.62120	CTT	.		0.647	STK11IP-001	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000131432.1	NM_052902	
HSPA9P1	266724	bcgsc.ca	37	2	222828423	222828423	+	IGR	SNP	G	G	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr2:222828423G>C								AC068489.1 (321890 upstream) : PAX3 (236183 downstream)																							GCAACTGAACGAGAAGGCTCT	0.423																																					.													.	.	.	0			.						.																																			SO:0001628	intergenic_variant	266724	.			CTGAACGAGAAGG																													2.37:g.222828423G>C		Somatic	24	0		WXS	Illumina HiSeq	Phase_1	13	3	.		RNA	SNP		37																																																																																				.	0	0.423								
MIR1324	100302212	bcgsc.ca	37	3	75679969	75679969	+	RNA	SNP	G	G	A	rs556136335	byFrequency	TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr3:75679969G>A	ENST00000408868.1	+	0	56					NR_031714.1				microRNA 1324																		CCTTCCCTCTGGGTACCAGAC	0.507																																					.													.	.	.	0			.						.						77.0	75.0	76.0					3																	75679969		1568	3578	5146			100302212	.			CCCTCTGGGTACC			3	2011-09-12		2008-12-18	ENSG00000221795	ENSG00000221795		"""ncRNAs / Micro RNAs"""	35377	non-coding RNA	RNA, micro				MIRN1324			Standard	NR_031714		Approved	hsa-mir-1324	uc021xar.1				3.37:g.75679969G>A		Somatic	680	1		WXS	Illumina HiSeq	Phase_1	378	17	.		RNA	SNP	ENST00000408868.1	37																																																																																				.		0.507	MIR1324-201	KNOWN	basic	miRNA	miRNA		NR_031714	
CLDN1	9076	bcgsc.ca	37	3	190030784	190030784	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr3:190030784G>T	ENST00000295522.3	-	2	533	c.265C>A	c.(265-267)Ctc>Atc	p.L89I		NM_021101.4	NP_066924.1	O95832	CLD1_HUMAN	claudin 1	89					calcium-independent cell-cell adhesion (GO:0016338)|cell adhesion (GO:0007155)|cell-cell junction organization (GO:0045216)|establishment of skin barrier (GO:0061436)|viral process (GO:0016032)	apical plasma membrane (GO:0016324)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lateral plasma membrane (GO:0016328)|tight junction (GO:0005923)	identical protein binding (GO:0042802)|structural molecule activity (GO:0005198)			lung(9)	9	all_cancers(143;2.95e-10)|Ovarian(172;0.0512)		Lung(62;2.23e-05)|LUSC - Lung squamous cell carcinoma(58;3.15e-05)	GBM - Glioblastoma multiforme(93;0.015)		ACTCCCAGGAGGATGCCAACC	0.463																																					p.L89I													.	CLDN1	23	0			c.C265A						.						230.0	213.0	219.0					3																	190030784		2203	4300	6503	SO:0001583	missense	9076	exon2			CCAGGAGGATGCC	AF101051	CCDS3295.1	3q28-q29	2008-07-18			ENSG00000163347	ENSG00000163347		"""Claudins"""	2032	protein-coding gene	gene with protein product	"""senescence-associated epithelial membrane protein 1"""	603718				10828592, 9892664	Standard	NM_021101		Approved	SEMP1, ILVASC	uc003fsh.3	O95832	OTTHUMG00000156214	ENST00000295522.3:c.265C>A	3.37:g.190030784G>T	ENSP00000295522:p.Leu89Ile	Somatic	45	0		WXS	Illumina HiSeq	Phase_1	47	4	NM_021101		Missense_Mutation	SNP	ENST00000295522.3	37	CCDS3295.1	.	.	.	.	.	.	.	.	.	.	G	10.04	1.241309	0.22711	.	.	ENSG00000163347	ENST00000295522;ENST00000545382	D	0.86432	-2.12	5.95	2.82	0.32997	.	0.121948	0.56097	D	0.000025	T	0.77837	0.4190	N	0.20530	0.585	0.48341	D	0.999635	B	0.22541	0.071	B	0.33960	0.173	T	0.66826	-0.5825	10	0.23302	T	0.38	.	8.7407	0.34556	0.1546:0.0:0.715:0.1304	.	89	O95832	CLD1_HUMAN	I	89;44	ENSP00000295522:L89I	ENSP00000295522:L89I	L	-	1	0	CLDN1	191513478	0.644000	0.27277	1.000000	0.80357	0.730000	0.41778	0.142000	0.16096	0.812000	0.34326	0.655000	0.94253	CTC	.		0.463	CLDN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343516.2	NM_021101	
ATP5LP3	53409	bcgsc.ca	37	4	24659835	24659835	+	lincRNA	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr4:24659835T>G	ENST00000569621.1	+	0	0																											TGACTATTGTTTTCAGGCTCT	0.483																																					.													.	.	.	0			.						.																																					53409	.			TATTGTTTTCAGG																													4.37:g.24659835T>G		Somatic	31	0		WXS	Illumina HiSeq	Phase_1	28	8	.		RNA	SNP	ENST00000569621.1	37																																																																																				.		0.483	RP11-496D24.2-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000431526.1		
Unknown	0	bcgsc.ca	37	4	70013196	70013196	+	IGR	SNP	T	T	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr4:70013196T>C								UGT2B7 (34491 upstream) : RP11-704M14.1 (34621 downstream)																							AGCAGTTTTCTGGATCGAGTT	0.458																																					.													.	.	.	0			.						.																																			SO:0001628	intergenic_variant	0	.			GTTTTCTGGATCG																													4.37:g.70013196T>C		Somatic	64	0		WXS	Illumina HiSeq	Phase_1	16	12	.		RNA	SNP		37																																																																																				.	0	0.458								
STOX2	56977	bcgsc.ca	37	4	184931986	184931986	+	Silent	SNP	C	C	T	rs559919334		TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr4:184931986C>T	ENST00000308497.4	+	3	3430	c.1995C>T	c.(1993-1995)ccC>ccT	p.P665P	STOX2_ENST00000438269.1_Silent_p.P665P	NM_020225.1	NP_064610.1	Q9P2F5	STOX2_HUMAN	storkhead box 2	665					embryo development (GO:0009790)|maternal placenta development (GO:0001893)					breast(1)|endometrium(7)|lung(6)	14		all_lung(41;1.89e-12)|Lung NSC(41;3.48e-12)|Colorectal(36;0.00435)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|all_hematologic(60;0.027)|Prostate(90;0.0283)		all cancers(43;2.85e-26)|Epithelial(43;2.27e-22)|OV - Ovarian serous cystadenocarcinoma(60;3.4e-10)|Colorectal(24;8.23e-06)|GBM - Glioblastoma multiforme(59;1.64e-05)|STAD - Stomach adenocarcinoma(60;3.6e-05)|COAD - Colon adenocarcinoma(29;4.37e-05)|LUSC - Lung squamous cell carcinoma(40;0.008)|READ - Rectum adenocarcinoma(43;0.227)		GTGGGGGCCCCGCTGCTTCGG	0.622																																					p.P665P													.	STOX2	142	0			c.C1995T						.																																			SO:0001819	synonymous_variant	56977	exon3			GGGCCCCGCTGCT	AB037813	CCDS47167.1	4q35.1	2014-09-11			ENSG00000173320	ENSG00000173320			25450	protein-coding gene	gene with protein product							Standard	XM_005263142		Approved	DKFZp762K222	uc003ivz.1	Q9P2F5	OTTHUMG00000160618	ENST00000308497.4:c.1995C>T	4.37:g.184931986C>T		Somatic	59	0		WXS	Illumina HiSeq	Phase_1	18	3	NM_020225	A6H8U4|Q9NPS8	Silent	SNP	ENST00000308497.4	37	CCDS47167.1																																																																																			.		0.622	STOX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361433.3	NM_020225	
GUSBP1	728411	bcgsc.ca	37	5	21483021	21483021	+	RNA	SNP	C	C	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr5:21483021C>T	ENST00000607545.1	+	0	179					NR_027026.1		Q15486	GUSP1_HUMAN	glucuronidase, beta pseudogene 1						carbohydrate metabolic process (GO:0005975)|nervous system development (GO:0007399)|skeletal system development (GO:0001501)		hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)										CCTCTGGGCACGTGCTGCAGC	0.592																																					.													.	.	.	0			.						.																																					0	.			TGGGCACGTGCTG	BC064850, X75940		5p14.3	2012-10-04			ENSG00000183666	ENSG00000183666			13670	pseudogene	pseudogene						8565635	Standard	NR_027026		Approved		uc010iub.3	Q15486	OTTHUMG00000162474		5.37:g.21483021C>T		Somatic	463	0		WXS	Illumina HiSeq	Phase_1	556	88	.	A6NLY8|A8K1B7|Q969T8|Q9BUH2	RNA	SNP	ENST00000607545.1	37																																																																																				.		0.592	GUSBP1-006	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000470546.1	NG_008324	
RP11-1023L17.1	0	bcgsc.ca	37	5	34192504	34192504	+	RNA	SNP	G	G	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr5:34192504G>A	ENST00000514048.1	-	0	0																											TTGAGGACAAGGCCACCTCGG	0.627																																					.													.	.	.	0			.						.																																					0	.			GGACAAGGCCACC																													5.37:g.34192504G>A		Somatic	1156	0		WXS	Illumina HiSeq	Phase_1	955	24	.		RNA	SNP	ENST00000514048.1	37																																																																																				.		0.627	RP11-1023L17.1-003	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000367775.1		
INTS6P1	285634	bcgsc.ca	37	5	39720610	39720610	+	IGR	SNP	A	A	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr5:39720610A>G								CTD-2078B5.2 (195800 upstream) : LINC00603 (331782 downstream)																							AAATACATTGACACAGTTCAG	0.423																																					.													.	.	.	0			.						.																																			SO:0001628	intergenic_variant	285634	.			ACATTGACACAGT																													5.37:g.39720610A>G		Somatic	43	0		WXS	Illumina HiSeq	Phase_1	57	11	.		RNA	SNP		37																																																																																				.	0	0.423								
GPR98	84059	bcgsc.ca	37	5	89948370	89948370	+	Silent	SNP	A	A	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr5:89948370A>G	ENST00000405460.2	+	19	3720	c.3624A>G	c.(3622-3624)gtA>gtG	p.V1208V		NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	1208	Calx-beta 9. {ECO:0000305|PubMed:11606593}.				detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|G-protein coupled receptor signaling pathway (GO:0007186)|inner ear receptor stereocilium organization (GO:0060122)|maintenance of organ identity (GO:0048496)|nervous system development (GO:0007399)|neurological system process (GO:0050877)|neuropeptide signaling pathway (GO:0007218)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|stereocilia ankle link complex (GO:0002142)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(4)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(18)|large_intestine(46)|liver(2)|lung(80)|ovary(12)|pancreas(5)|prostate(1)|skin(50)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(6)	269		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		TAAAACTTGTAAACATTTCAG	0.279																																					p.V1208V													GPR98,NS,carcinoma,+2,1	GPR98	605	0			c.A3624G						.						43.0	39.0	40.0					5																	89948370		1818	4070	5888	SO:0001819	synonymous_variant	84059	exon19			ACTTGTAAACATT	AB014586	CCDS47246.1	5q13	2014-08-08	2006-05-26	2006-05-26	ENSG00000164199	ENSG00000164199		"""-"", ""GPCR / Class B : Orphans"""	17416	protein-coding gene	gene with protein product		602851	"""monogenic, audiogenic seizure susceptibility 1 homolog (mouse)"""	USH2C, MASS1		10976914, 14740321	Standard	NM_032119		Approved	DKFZp761P0710, KIAA0686, FEB4, VLGR1b	uc003kju.3	Q8WXG9	OTTHUMG00000162668	ENST00000405460.2:c.3624A>G	5.37:g.89948370A>G		Somatic	42	0		WXS	Illumina HiSeq	Phase_1	38	13	NM_032119	O75171|Q8TF58|Q9H0X5|Q9UL61	Silent	SNP	ENST00000405460.2	37	CCDS47246.1	.	.	.	.	.	.	.	.	.	.	A	2.577	-0.298276	0.05532	.	.	ENSG00000164199	ENST00000504142	.	.	.	6.07	-12.1	0.00011	.	.	.	.	.	T	0.46132	0.1377	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.59236	-0.7492	4	.	.	.	.	9.5378	0.39233	0.0964:0.3362:0.484:0.0834	.	.	.	.	E	797	.	.	K	+	1	0	GPR98	89984126	0.204000	0.23447	0.142000	0.22268	0.443000	0.32047	-0.433000	0.06948	-1.909000	0.01085	-0.334000	0.08254	AAA	.		0.279	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119	
Unknown	0	bcgsc.ca	37	5	143902542	143902542	+	IGR	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr5:143902542A>C								KCTD16 (37293 upstream) : RN7SKP246 (12374 downstream)																							CAGTTCAGCAAGCTGAGTAAG	0.358																																					.													.	.	.	0			.						.																																			SO:0001628	intergenic_variant	0	.			TCAGCAAGCTGAG																													5.37:g.143902542A>C		Somatic	37	0		WXS	Illumina HiSeq	Phase_1	32	23	.		RNA	SNP		37																																																																																				.	0	0.358								
GLRX3P2	728344	bcgsc.ca	37	6	3978522	3978522	+	IGR	SNP	C	C	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr6:3978522C>T								RP1-140K8.5 (66309 upstream) : C6ORF50 (4386 downstream)																							GCTCTGTTCCCACTTTTCTGT	0.403											OREG0017157	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									.													.	.	.	0			.						.																																			SO:0001628	intergenic_variant	0	.			TGTTCCCACTTTT																													6.37:g.3978522C>T		Somatic	35	0	615	WXS	Illumina HiSeq	Phase_1	26	14	.		RNA	SNP		37																																																																																				.	0	0.403								
Unknown	0	bcgsc.ca	37	6	27704914	27704914	+	IGR	SNP	C	C	T	rs371851152		TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr6:27704914C>T								TRNAI6 (105603 upstream) : HIST1H2BL (70342 downstream)																							CCAAGGACTTCGGTAATTATG	0.418																																					.													.	.	.	0			.						.																																			SO:0001628	intergenic_variant	0	.			GGACTTCGGTAAT																													6.37:g.27704914C>T		Somatic	89	0		WXS	Illumina HiSeq	Phase_1	71	44	.		RNA	SNP		37																																																																																				.	0	0.418								
Z97352.1	0	bcgsc.ca	37	6	130068934	130068934	+	RNA	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr6:130068934A>C	ENST00000390707.1	+	0	53																											tcaatggcaaaaaccgcaatt	0.373																																					.													.	.	.	0			.						.																																					0	.			TGGCAAAAACCGC																													6.37:g.130068934A>C		Somatic	17	0		WXS	Illumina HiSeq	Phase_1	4	4	.		RNA	SNP	ENST00000390707.1	37																																																																																				.		0.373	Z97352.1-201	NOVEL	basic	miRNA	miRNA			
Unknown	0	bcgsc.ca	37	6	135219170	135219170	+	IGR	SNP	G	G	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr6:135219170G>A								RP1-287H17.1 (190683 upstream) : ALDH8A1 (19357 downstream)																							CAGGATATACGTACTGTGGGT	0.473																																					.													.	.	.	0			.						.																																			SO:0001628	intergenic_variant	0	.			ATATACGTACTGT																													6.37:g.135219170G>A		Somatic	45	0		WXS	Illumina HiSeq	Phase_1	42	4	.		RNA	SNP		37																																																																																				.	0	0.473								
Unknown	0	bcgsc.ca	37	6	139982567	139982567	+	IGR	SNP	G	G	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr6:139982567G>T								RP11-12A2.3 (188375 upstream) : RP5-899B16.1 (193488 downstream)																							TCCTATTAAAGGAAATAAAAA	0.363																																					.													.	.	.	0			.						.																																			SO:0001628	intergenic_variant	0	.			ATTAAAGGAAATA																													6.37:g.139982567G>T		Somatic	18	0		WXS	Illumina HiSeq	Phase_1	10	3	.		RNA	SNP		37																																																																																				.	0	0.363								
Unknown	0	bcgsc.ca	37	7	55005715	55005715	+	IGR	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr7:55005715T>G								SNORA73 (71998 upstream) : EGFR (80998 downstream)																							AGTTTTTCTTTTACAATGGAG	0.408																																					.													.	.	.	0			.						.																																			SO:0001628	intergenic_variant	0	.			TTTCTTTTACAAT																													7.37:g.55005715T>G		Somatic	81	0		WXS	Illumina HiSeq	Phase_1	63	6	.		RNA	SNP		37																																																																																				.	0	0.408								
SNORA67	26781	bcgsc.ca	37	7	88078165	88078165	+	RNA	SNP	C	C	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr7:88078165C>A	ENST00000384366.1	-	0	140									small nucleolar RNA, H/ACA box 67																		TGTAGAAAATCTCTATGTCTT	0.493																																					.													.	.	.	0			.						.																																					100462826	.			GAAAATCTCTATG	Y11161		17p13.1	2013-09-05	2006-04-05	2006-04-05	ENSG00000207152			"""ncRNAs / Small nucleolar RNAs : H/ACA box containing"""	10224	non-coding RNA	RNA, small nucleolar			"""RNA, U67 small nucleolar"""	RNU67		15199136, 16381836	Standard	NR_002912		Approved	U67	uc010cml.1				7.37:g.88078165C>A		Somatic	18	0		WXS	Illumina HiSeq	Phase_1	13	6	.		RNA	SNP	ENST00000384366.1	37																																																																																				.		0.493	SNORA67.3-201	NOVEL	basic	snoRNA	snoRNA		NR_002912	
Unknown	0	bcgsc.ca	37	7	150447077	150447077	+	IGR	SNP	T	T	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr7:150447077T>C								GIMAP5 (5926 upstream) : TMEM176B (41295 downstream)																							ATGGGCAAACTGGAGATTTTA	0.328																																					.													.	.	.	0			.						.						100.0	81.0	87.0					7																	150447077		692	1591	2283	SO:0001628	intergenic_variant	55340	.			GCAAACTGGAGAT																													7.37:g.150447077T>C		Somatic	113	0		WXS	Illumina HiSeq	Phase_1	71	40	.		RNA	SNP		37																																																																																				.	0	0.328								
AC104133.1	0	bcgsc.ca	37	7	155664620	155664620	+	RNA	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr7:155664620T>G	ENST00000408186.1	+	0	36																											gtaagtgcggtttttgccatt	0.373																																					.													.	.	.	0			.						.																																					0	.			GTGCGGTTTTTGC																													7.37:g.155664620T>G		Somatic	40	0		WXS	Illumina HiSeq	Phase_1	30	13	.		RNA	SNP	ENST00000408186.1	37																																																																																				.		0.373	AC104133.1-201	NOVEL	basic	miRNA	miRNA			
RPL29P19	389655	bcgsc.ca	37	8	49297445	49297445	+	IGR	SNP	G	G	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr8:49297445G>T								RNU6-295P (76855 upstream) : RP11-567J20.3 (130966 downstream)																							TGCCTACGTTGCCCACTCCAA	0.577																																					.													.	.	.	0			.						.																																			SO:0001628	intergenic_variant	389655	.			TACGTTGCCCACT																													8.37:g.49297445G>T		Somatic	44	0		WXS	Illumina HiSeq	Phase_1	37	4	.		RNA	SNP		37																																																																																				.	0	0.577								
TTC39B	158219	bcgsc.ca	37	9	15307282	15307282	+	Missense_Mutation	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr9:15307282T>G	ENST00000512701.2	-	1	76	c.40A>C	c.(40-42)Aat>Cat	p.N14H	TTC39B_ENST00000380850.4_Missense_Mutation_p.N14H|TTC39B_ENST00000297615.5_Missense_Mutation_p.N14H|TTC39B_ENST00000541445.1_5'Flank|TTC39B_ENST00000355694.2_5'UTR			Q5VTQ0	TT39B_HUMAN	tetratricopeptide repeat domain 39B	14										NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(7)|ovary(2)|prostate(1)	21						GCTACTCGATTTCCCCGCCCC	0.751																																					p.N14H													.	TTC39B	83	0			c.A40C						.						6.0	9.0	8.0					9																	15307282		687	1578	2265	SO:0001583	missense	158219	exon1			CTCGATTTCCCCG	AK091187	CCDS6477.1, CCDS6477.2, CCDS55294.1, CCDS55295.1, CCDS55296.1	9p22.2	2013-01-11	2008-06-23	2008-06-23	ENSG00000155158	ENSG00000155158		"""Tetratricopeptide (TTC) repeat domain containing"""	23704	protein-coding gene	gene with protein product		613574	"""chromosome 9 open reading frame 52"""	C9orf52			Standard	NM_001168339		Approved	FLJ33868	uc003zlr.2	Q5VTQ0	OTTHUMG00000019581	ENST00000512701.2:c.40A>C	9.37:g.15307282T>G	ENSP00000422496:p.Asn14His	Somatic	20	0		WXS	Illumina HiSeq	Phase_1	14	8	NM_001168340	A5PLN1|B4DQ10|B4DQX4|B4DW93|Q8IVR7|Q8IXZ6|Q8N267	Missense_Mutation	SNP	ENST00000512701.2	37	CCDS6477.2	.	.	.	.	.	.	.	.	.	.	T	18.15	3.560474	0.65538	.	.	ENSG00000155158	ENST00000380850;ENST00000297615;ENST00000512701	T;T;T	0.54279	1.38;0.58;1.38	3.96	-0.361	0.12564	.	.	.	.	.	T	0.29491	0.0735	N	0.08118	0	0.31448	N	0.671179	.	.	.	.	.	.	T	0.33828	-0.9853	7	0.66056	D	0.02	.	3.7437	0.08540	0.0:0.2639:0.2865:0.4496	.	.	.	.	H	14	ENSP00000370231:N14H;ENSP00000297615:N14H;ENSP00000422496:N14H	ENSP00000297615:N14H	N	-	1	0	TTC39B	15297282	0.475000	0.25894	0.457000	0.27056	0.161000	0.22273	-0.233000	0.09041	-0.153000	0.11137	0.260000	0.18958	AAT	.		0.751	TTC39B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051758.3	NM_152574	
AL157884.1	0	bcgsc.ca	37	9	32764313	32764313	+	RNA	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr9:32764313A>C	ENST00000408769.1	+	0	20																											gttggtgcaaaagtaattgcg	0.299																																					.													.	.	.	0			.						.																																					0	.			GTGCAAAAGTAAT																													9.37:g.32764313A>C		Somatic	86	0		WXS	Illumina HiSeq	Phase_1	59	26	.		RNA	SNP	ENST00000408769.1	37																																																																																				.		0.299	AL157884.1-201	NOVEL	basic	miRNA	miRNA			
KRT8P11	347265	bcgsc.ca	37	9	102068170	102068170	+	IGR	SNP	T	T	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr9:102068170T>C								RN7SKP225 (21515 upstream) : NAMA (49521 downstream)																							CCGACATGTCTATGGTGCTGT	0.567																																					.													.	.	.	0			.						.																																			SO:0001628	intergenic_variant	347265	.			CATGTCTATGGTG																													9.37:g.102068170T>C		Somatic	21	0		WXS	Illumina HiSeq	Phase_1	13	4	.		Silent	SNP		37																																																																																				.	0	0.567								
GAPVD1	26130	bcgsc.ca	37	9	128094335	128094335	+	Silent	SNP	G	G	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr9:128094335G>T	ENST00000495955.1	+	14	2594	c.2304G>T	c.(2302-2304)gtG>gtT	p.V768V	GAPVD1_ENST00000394105.2_Silent_p.V768V|GAPVD1_ENST00000297933.6_Silent_p.V768V|GAPVD1_ENST00000470056.1_Silent_p.V768V|GAPVD1_ENST00000394083.2_Silent_p.V747V|GAPVD1_ENST00000394104.2_Silent_p.V768V|GAPVD1_ENST00000312123.9_Silent_p.V747V|GAPVD1_ENST00000265956.4_Silent_p.V768V			Q14C86	GAPD1_HUMAN	GTPase activating protein and VPS9 domains 1	768					endocytosis (GO:0006897)|positive regulation of GTPase activity (GO:0043547)|regulation of protein transport (GO:0051223)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)	cytosol (GO:0005829)|endosome (GO:0005768)|membrane (GO:0016020)	GTPase activating protein binding (GO:0032794)|GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)			central_nervous_system(2)|endometrium(7)|kidney(4)|large_intestine(10)|lung(11)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	44						TCAGTGTTGTGTCCGGTATGT	0.468																																					p.V768V													.	GAPVD1	124	0			c.G2304T						.						99.0	77.0	84.0					9																	128094335		2203	4300	6503	SO:0001819	synonymous_variant	26130	exon12			TGTTGTGTCCGGT		CCDS65130.1, CCDS65131.1, CCDS65132.1	9q34.11	2008-02-05			ENSG00000165219	ENSG00000165219			23375	protein-coding gene	gene with protein product		611714					Standard	XM_005251901		Approved	DKFZP434C212, KIAA1521	uc004bpr.3	Q14C86	OTTHUMG00000020678	ENST00000495955.1:c.2304G>T	9.37:g.128094335G>T		Somatic	63	0		WXS	Illumina HiSeq	Phase_1	55	4	NM_015635	A8MYK3|B0QZ62|B0QZ63|B0QZ64|Q14C76|Q2Q1W1|Q8ND92|Q8WU86|Q96CZ4|Q9NXQ1|Q9P207|Q9Y4N0	Silent	SNP	ENST00000495955.1	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	9.689|9.689	1.151328|1.151328	0.21371|0.21371	.|.	.|.	ENSG00000165219|ENSG00000165219	ENST00000431329|ENST00000436712	.|T	.|0.13901	.|2.55	5.98|5.98	5.04|5.04	0.67666|0.67666	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.24198|0.24198	0.0586|0.0586	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.00087|0.00087	-1.2093|-1.2093	4|6	.|.	.|.	.|.	.|.	13.2037|13.2037	0.59782|0.59782	0.0709:0.1257:0.8034:0.0|0.0709:0.1257:0.8034:0.0	.|.	.|.	.|.	.|.	F|F	631|605	.|ENSP00000391251:V605F	.|.	C|V	+|+	2|1	0|0	GAPVD1|GAPVD1	127134156|127134156	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	2.394000|2.394000	0.44450|0.44450	2.837000|2.837000	0.97791|0.97791	0.637000|0.637000	0.83480|0.83480	TGT|GTC	.		0.468	GAPVD1-014	KNOWN	alternative_5_UTR|basic	protein_coding	protein_coding	OTTHUMT00000355644.1		
RNMTL1P1	100420295	bcgsc.ca	37	10	21683402	21683402	+	IGR	SNP	C	C	A	rs374279881		TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr10:21683402C>A								RP11-275N1.1 (21523 upstream) : Y_RNA (87242 downstream)																							CTTCTTTAGCCGTCTAGAATA	0.478													C|||	0	0.0	0.0	0.0	5008	,	,		18341	0.0		0.0	False		,,,				2504	0.0				.													.	.	.	0			.						.																																			SO:0001628	intergenic_variant	0	.			TTTAGCCGTCTAG																													10.37:g.21683402C>A		Somatic	39	0		WXS	Illumina HiSeq	Phase_1	20	8	.		RNA	SNP		37																																																																																				.	0	0.478								
LINC00842	643650	bcgsc.ca	37	10	47151591	47151591	+	lincRNA	SNP	A	A	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr10:47151591A>T	ENST00000422732.2	-	0	0					NR_033957.2				long intergenic non-protein coding RNA 842																		GCTGGTCACGAGGGGGGACGC	0.667											OREG0020158	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									.													.	.	.	0			.						.																																					0	.			GTCACGAGGGGGG			10q11.22	2013-01-04			ENSG00000223477	ENSG00000274909		"""Long non-coding RNAs"""	44989	non-coding RNA	RNA, long non-coding							Standard	NR_033957		Approved		uc001jef.3		OTTHUMG00000018109		10.37:g.47151591A>T		Somatic	152	0	944	WXS	Illumina HiSeq	Phase_1	98	19	.		Silent	SNP	ENST00000422732.2	37																																																																																				.		0.667	LINC00842-002	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000047838.2	NR_033957	
AC074323.1	0	bcgsc.ca	37	10	80510412	80510412	+	RNA	SNP	T	T	G	rs542070792	byFrequency	TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr10:80510412T>G	ENST00000411311.1	+	0	54																											tgccattacttttaatggcaa	0.353																																					.													.	.	.	0			.						.																																					0	.			ATTACTTTTAATG																													10.37:g.80510412T>G		Somatic	58	0		WXS	Illumina HiSeq	Phase_1	42	19	.		RNA	SNP	ENST00000411311.1	37																																																																																				.		0.353	AC074323.1-201	NOVEL	basic	miRNA	miRNA			
MMRN2	79812	bcgsc.ca	37	10	88703690	88703690	+	Missense_Mutation	SNP	G	G	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr10:88703690G>A	ENST00000372027.5	-	6	1172	c.851C>T	c.(850-852)gCt>gTt	p.A284V	MMRN2_ENST00000488950.1_5'UTR	NM_024756.2	NP_079032.2	Q9H8L6	MMRN2_HUMAN	multimerin 2	284					angiogenesis (GO:0001525)|negative regulation of cell migration involved in sprouting angiogenesis (GO:0090051)|negative regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030948)	basement membrane (GO:0005604)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				breast(1)|kidney(1)|large_intestine(6)|lung(7)|prostate(2)|skin(1)|stomach(1)	19						CTGGAAGTCAGCCCTGGCCAC	0.612																																					p.A284V													.	MMRN2	49	0			c.C851T						.						61.0	57.0	59.0					10																	88703690		2203	4300	6503	SO:0001583	missense	79812	exon6			AAGTCAGCCCTGG	AK023527	CCDS7379.1	10q23.31	2004-03-10	2004-03-02	2004-03-02	ENSG00000173269	ENSG00000173269		"""EMI domain containing"""	19888	protein-coding gene	gene with protein product		608925	"""elastin microfibril interfacer 3"""	EMILIN3		11559704	Standard	NM_024756		Approved	EndoGlyx-1, FLJ13465	uc001kea.3	Q9H8L6	OTTHUMG00000018663	ENST00000372027.5:c.851C>T	10.37:g.88703690G>A	ENSP00000361097:p.Ala284Val	Somatic	21	0		WXS	Illumina HiSeq	Phase_1	10	3	NM_024756	Q504V7|Q6P2N2	Missense_Mutation	SNP	ENST00000372027.5	37	CCDS7379.1	.	.	.	.	.	.	.	.	.	.	G	12.26	1.884345	0.33255	.	.	ENSG00000173269	ENST00000372027	T	0.15017	2.46	5.19	-0.422	0.12329	.	0.987031	0.08259	N	0.973281	T	0.13200	0.0320	M	0.64997	1.995	0.09310	N	1	P;B	0.35077	0.483;0.031	B;B	0.24974	0.057;0.01	T	0.27536	-1.0071	10	0.33940	T	0.23	1.0E-4	3.1426	0.06461	0.1452:0.0986:0.4187:0.3375	.	223;284	B4E3H8;Q9H8L6	.;MMRN2_HUMAN	V	284	ENSP00000361097:A284V	ENSP00000361097:A284V	A	-	2	0	MMRN2	88693670	0.000000	0.05858	0.006000	0.13384	0.758000	0.43043	0.012000	0.13287	0.171000	0.19730	0.561000	0.74099	GCT	.		0.612	MMRN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049179.2	NM_024756	
SORBS1	10580	bcgsc.ca	37	10	97116445	97116445	+	Missense_Mutation	SNP	T	T	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr10:97116445T>C	ENST00000607232.1	-	18	2013	c.1847A>G	c.(1846-1848)aAg>aGg	p.K616R	SORBS1_ENST00000371241.1_Intron|SORBS1_ENST00000371246.2_Intron|SORBS1_ENST00000353505.5_Intron|SORBS1_ENST00000277982.5_Intron|SORBS1_ENST00000306402.6_Intron|SORBS1_ENST00000474353.2_Intron|SORBS1_ENST00000354106.3_Intron|SORBS1_ENST00000371227.4_Intron|SORBS1_ENST00000347291.4_Intron|SORBS1_ENST00000393949.1_Intron|SORBS1_ENST00000371239.1_Intron|SORBS1_ENST00000371247.2_Intron|SORBS1_ENST00000371249.2_Intron|SORBS1_ENST00000371245.3_Intron|SORBS1_ENST00000361941.3_Intron					sorbin and SH3 domain containing 1											NS(1)|breast(3)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(19)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	42		Colorectal(252;0.0429)		Epithelial(162;1.7e-06)|all cancers(201;6.52e-05)		CATCCCAGCCTTTCTTGAGAG	0.582																																					.													.	SORBS1	185	0			.						.																																			SO:0001583	missense	0	.			CCAGCCTTTCTTG	AF136381	CCDS7442.1, CCDS31252.1, CCDS31253.1, CCDS31254.1, CCDS31255.1, CCDS31256.1, CCDS73169.1	10q23.33	2011-07-25	2002-05-08		ENSG00000095637	ENSG00000095637			14565	protein-coding gene	gene with protein product	"""c-Cbl-associated protein"""	605264	"""SH3-domain protein 5 (ponsin)"""	SH3D5		10085297, 11001060	Standard	XM_005269405		Approved	FLJ12406, CAP, sh3p12, ponsin, KIAA1296	uc001kkp.3	Q9BX66	OTTHUMG00000018812	ENST00000607232.1:c.1847A>G	10.37:g.97116445T>C	ENSP00000475901:p.Lys616Arg	Somatic	26	0		WXS	Illumina HiSeq	Phase_1	14	4	.		Missense_Mutation	SNP	ENST00000607232.1	37		.	.	.	.	.	.	.	.	.	.	T	11.18	1.562815	0.27915	.	.	ENSG00000212950	ENST00000371228	.	.	.	5.98	4.86	0.63082	.	.	.	.	.	T	0.49677	0.1571	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.37033	-0.9723	5	0.12430	T	0.62	.	11.542	0.50672	0.0:0.0692:0.0:0.9307	.	.	.	.	R	131	.	ENSP00000360272:K131R	K	-	2	0	RP11-476E15.3	97106435	1.000000	0.71417	0.933000	0.37362	0.986000	0.74619	2.189000	0.42621	2.289000	0.77006	0.482000	0.46254	AAG	.		0.582	SORBS1-017	KNOWN	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000468280.1		
OR4A1P	8596	bcgsc.ca	37	11	49920193	49920193	+	IGR	SNP	T	T	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr11:49920193T>C								RP11-707M1.1 (88222 upstream) : OR4C13 (53749 downstream)																							CCAGTTCCAATAATGGGTACA	0.408																																					.													.	.	.	0			.						.																																			SO:0001628	intergenic_variant	8596	.			TTCCAATAATGGG																													11.37:g.49920193T>C		Somatic	26	0		WXS	Illumina HiSeq	Phase_1	14	5	.		RNA	SNP		37																																																																																				.	0	0.408								
OR7E126P	81176	bcgsc.ca	37	11	71614820	71614820	+	Intron	SNP	C	C	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr11:71614820C>A	ENST00000528511.2	-	4	624				AP000719.1_ENST00000583110.1_RNA																							GACACCTTCACCAGGAACATC	0.433																																					.													.	.	.	0			.						.																																			SO:0001627	intron_variant	0	.			CCTTCACCAGGAA																												ENST00000528511.2:c.615+12299G>T	11.37:g.71614820C>A		Somatic	29	0		WXS	Illumina HiSeq	Phase_1	20	4	.		RNA	SNP	ENST00000528511.2	37																																																																																				.		0.433	RP11-849H4.2-003	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000394950.2		
OR5BS1P	390313	bcgsc.ca	37	12	48953837	48953837	+	IGR	SNP	C	C	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr12:48953837C>T								OR8S1 (30157 upstream) : LALBA (7629 downstream)																							CTCTGCACCCCTATGTACTTC	0.473																																					.													.	.	.	0			.						.																																			SO:0001628	intergenic_variant	0	.			GCACCCCTATGTA																													12.37:g.48953837C>T		Somatic	36	0		WXS	Illumina HiSeq	Phase_1	20	5	.		RNA	SNP		37																																																																																				.	0	0.473								
APAF1	317	bcgsc.ca	37	12	99080607	99080607	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr12:99080607G>T	ENST00000551964.1	+	16	2996	c.2260G>T	c.(2260-2262)Gat>Tat	p.D754Y	APAF1_ENST00000549007.1_Missense_Mutation_p.D754Y|APAF1_ENST00000547045.1_Missense_Mutation_p.D754Y|APAF1_ENST00000359972.2_Missense_Mutation_p.D743Y|APAF1_ENST00000333991.1_Intron|APAF1_ENST00000550527.1_Missense_Mutation_p.D743Y|APAF1_ENST00000357310.1_Missense_Mutation_p.D754Y|APAF1_ENST00000552268.1_Intron|APAF1_ENST00000339433.3_Missense_Mutation_p.D754Y	NM_181861.1	NP_863651.1	O14727	APAF_HUMAN	apoptotic peptidase activating factor 1	754					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c (GO:0008635)|apoptotic process (GO:0006915)|forebrain development (GO:0030900)|intrinsic apoptotic signaling pathway (GO:0097193)|nervous system development (GO:0007399)|neural tube closure (GO:0001843)|neuron apoptotic process (GO:0051402)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|regulation of apoptotic DNA fragmentation (GO:1902510)|regulation of apoptotic process (GO:0042981)|response to G1 DNA damage checkpoint signaling (GO:0072432)	apoptosome (GO:0043293)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|nucleotide binding (GO:0000166)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(13)|liver(1)|lung(15)|ovary(2)|prostate(2)|skin(1)	42					Adenosine triphosphate(DB00171)	ATTTTCACCAGATGATAAGCT	0.318																																					p.D754Y													.	APAF1	111	0			c.G2260T						.						154.0	145.0	148.0					12																	99080607		2202	4300	6502	SO:0001583	missense	317	exon16			TCACCAGATGATA	AF013263	CCDS9069.1, CCDS9070.1, CCDS9071.1, CCDS55862.1, CCDS55863.1	12q23	2013-01-10	2006-10-23			ENSG00000120868		"""WD repeat domain containing"""	576	protein-coding gene	gene with protein product		602233	"""apoptotic protease activating factor"", ""apoptotic peptidase activating factor"""			9267021, 10702682	Standard	NM_181861		Approved	CED4, APAF-1	uc001tfz.3	O14727	OTTHUMG00000170214	ENST00000551964.1:c.2260G>T	12.37:g.99080607G>T	ENSP00000448165:p.Asp754Tyr	Somatic	61	0		WXS	Illumina HiSeq	Phase_1	45	4	NM_181868	B2RMX8|O43297|Q7Z438|Q9BXZ6|Q9UBZ5|Q9UGN8|Q9UGN9|Q9UGP0|Q9UJ58|Q9UJ59|Q9UJ60|Q9UJ61|Q9UJ62|Q9UJ63|Q9UJ64|Q9UJ65|Q9UJ66|Q9UJ67|Q9UNC9	Missense_Mutation	SNP	ENST00000551964.1	37	CCDS9069.1	.	.	.	.	.	.	.	.	.	.	G	18.15	3.560399	0.65538	.	.	ENSG00000120868	ENST00000551964;ENST00000359972;ENST00000357310;ENST00000339433;ENST00000550527;ENST00000547045;ENST00000549007	T;T;T;T;T;T;T	0.64438	1.23;1.76;4.56;-0.1;1.23;4.56;-0.1	5.54	5.54	0.83059	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.187600	0.56097	D	0.000026	T	0.79028	0.4377	M	0.82193	2.58	0.80722	D	1	D;D;D;D;D	0.89917	1.0;0.999;0.999;1.0;1.0	D;D;D;D;D	0.91635	0.992;0.978;0.978;0.985;0.999	T	0.81504	-0.0903	10	0.87932	D	0	-3.236	10.946	0.47301	0.1188:0.0:0.8811:0.0	.	754;754;743;754;743	C9JLV4;O14727-4;O14727-3;O14727;O14727-2	.;.;.;APAF_HUMAN;.	Y	754;743;754;754;743;754;754	ENSP00000448165:D754Y;ENSP00000353059:D743Y;ENSP00000349862:D754Y;ENSP00000341830:D754Y;ENSP00000448449:D743Y;ENSP00000449791:D754Y;ENSP00000448161:D754Y	ENSP00000341830:D754Y	D	+	1	0	APAF1	97604738	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.740000	0.55082	2.601000	0.87937	0.655000	0.94253	GAT	.		0.318	APAF1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408006.1	NM_181861.1	
DNAH10OS	642797	bcgsc.ca	37	12	124418997	124418997	+	Missense_Mutation	SNP	A	A	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr12:124418997A>T	ENST00000514254.2	-	1	534	c.134T>A	c.(133-135)cTc>cAc	p.L45H	DNAH10_ENST00000409039.3_Intron|CCDC92_ENST00000544798.1_Intron|RP11-380L11.3_ENST00000602292.1_RNA			P0CZ25	D10OS_HUMAN	dynein, axonemal, heavy chain 10 opposite strand	45	Pro-rich.																TCCTCCACAGAGGGAAGGTGG	0.657																																					.													.	DNAH10	888	0			.						.																																			SO:0001583	missense	642797	.			CCACAGAGGGAAG	AK127211		12q24.31	2013-01-23	2010-02-09		ENSG00000250091	ENSG00000250091			37121	protein-coding gene	gene with protein product			"""dynein, axonemal, heavy chain 10 opposite strand"", ""dynein, axonemal, heavy chain 10 opposite strand (non-protein coding)"""			19726446	Standard			Approved	FLJ45278		P0CZ25	OTTHUMG00000162010	ENST00000514254.2:c.134T>A	12.37:g.124418997A>T	ENSP00000422769:p.Leu45His	Somatic	51	0		WXS	Illumina HiSeq	Phase_1	37	10	.		Missense_Mutation	SNP	ENST00000514254.2	37		.	.	.	.	.	.	.	.	.	.	A	5.002	0.186067	0.09495	.	.	ENSG00000250091	ENST00000514254	.	.	.	2.3	-1.78	0.07957	.	.	.	.	.	T	0.38241	0.1033	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.43426	-0.9392	5	0.87932	D	0	.	6.3617	0.21433	0.398:0.0:0.602:0.0	.	.	.	.	H	45	.	ENSP00000422769:L45H	L	-	2	0	DNAH10OS	122984950	0.000000	0.05858	0.000000	0.03702	0.076000	0.17211	-0.012000	0.12699	-0.410000	0.07542	0.459000	0.35465	CTC	.		0.657	DNAH10OS-001	NOVEL	basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000366728.3		
ZNF839	55778	bcgsc.ca	37	14	102800980	102800980	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr14:102800980G>T	ENST00000558850.1	+	4	1508	c.1158G>T	c.(1156-1158)atG>atT	p.M386I	ZNF839_ENST00000262236.5_Missense_Mutation_p.M386I|ZNF839_ENST00000559185.1_Missense_Mutation_p.M386I|ZNF839_ENST00000442396.2_Missense_Mutation_p.M502I	NM_001267827.1	NP_001254756.1	A8K0R7	ZN839_HUMAN	zinc finger protein 839	386							metal ion binding (GO:0046872)			breast(2)|central_nervous_system(1)|endometrium(5)|large_intestine(2)|lung(5)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	19						TTCTTCTGATGAAGGTGAGTA	0.398																																					p.M502I													.	ZNF839	41	0			c.G1506T						.						126.0	116.0	119.0					14																	102800980		1917	4134	6051	SO:0001583	missense	55778	exon4			TCTGATGAAGGTG	AK093342	CCDS45164.1, CCDS58336.1	14q32.32	2010-05-06	2008-06-23	2008-06-23	ENSG00000022976	ENSG00000022976			20345	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 131"""	C14orf131			Standard	NM_018335		Approved		uc010awk.2	A8K0R7		ENST00000558850.1:c.1158G>T	14.37:g.102800980G>T	ENSP00000453363:p.Met386Ile	Somatic	80	0		WXS	Illumina HiSeq	Phase_1	56	4	NM_018335	B3KSD2|Q53FH5|Q6GPI5|Q86TU1|Q9BQ86|Q9NUU3	Translation_Start_Site	SNP	ENST00000558850.1	37	CCDS58336.1	.	.	.	.	.	.	.	.	.	.	G	14.98	2.698077	0.48307	.	.	ENSG00000022976	ENST00000442396;ENST00000262236;ENST00000398436	T;T	0.20332	2.08;2.08	4.89	4.89	0.63831	.	0.984707	0.08295	N	0.967803	T	0.29684	0.0741	L	0.55990	1.75	0.28940	N	0.891059	P;P;P;P	0.47962	0.903;0.903;0.903;0.903	P;P;B;P	0.46275	0.51;0.51;0.31;0.51	T	0.13176	-1.0519	10	0.56958	D	0.05	.	11.8788	0.52562	0.0804:0.0:0.9196:0.0	.	502;386;265;386	A8K0R7-5;A8K0R7-2;Q9NT83;A8K0R7	.;.;.;ZN839_HUMAN	I	502;386;54	ENSP00000399863:M502I;ENSP00000262236:M386I	ENSP00000262236:M386I	M	+	3	0	ZNF839	101870733	1.000000	0.71417	1.000000	0.80357	0.934000	0.57294	4.188000	0.58351	2.428000	0.82296	0.561000	0.74099	ATG	.		0.398	ZNF839-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000415492.2	NM_018335	
ADAMTS7P3	400406	bcgsc.ca	37	15	78280865	78280865	+	RNA	SNP	G	G	T			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr15:78280865G>T	ENST00000568041.1	+	0	136																											GGATACACGGGACCTCTGGAC	0.662																																					.													.	.	.	0			.						.																																					0	.			ACACGGGACCTCT																													15.37:g.78280865G>T		Somatic	59	0		WXS	Illumina HiSeq	Phase_1	30	12	.		RNA	SNP	ENST00000568041.1	37																																																																																				.		0.662	RP11-114H24.5-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000421592.1		
CRAMP1L	57585	bcgsc.ca	37	16	1675956	1675956	+	Intron	SNP	C	C	T	rs533859710		TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr16:1675956C>T	ENST00000397412.3	+	3	445				CRAMP1L_ENST00000293925.5_Intron|CRAMP1L_ENST00000436138.3_Intron|LA16c-395F10.1_ENST00000415176.1_RNA			Q96RY5	CRML_HUMAN	Crm, cramped-like (Drosophila)							nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(3)|lung(6)|pancreas(1)	22						GATCACTGTACGGTGCTTTCT	0.637													C|||	1	0.000199681	0.0	0.0	5008	,	,		18524	0.0		0.0	False		,,,				2504	0.001				.													.	CRAMP1L	60	0			.						.						35.0	34.0	34.0					16																	1675956		692	1591	2283	SO:0001627	intron_variant	0	.			ACTGTACGGTGCT	AB037847	CCDS10440.2	16p13.3	2008-07-30	2001-11-28		ENSG00000007545	ENSG00000007545			14122	protein-coding gene	gene with protein product			"""Crm (Cramped Drosophila)-like"""				Standard	NM_020825		Approved	KIAA1426	uc010uvh.2	Q96RY5	OTTHUMG00000074087	ENST00000397412.3:c.347-18C>T	16.37:g.1675956C>T		Somatic	20	0		WXS	Illumina HiSeq	Phase_1	18	3	.	A8MZL1|B1AJY1|Q8NDN1|Q9P2C1	Splice_Site	SNP	ENST00000397412.3	37	CCDS10440.2																																																																																			.		0.637	CRAMP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157297.4		
PAPD5	64282	bcgsc.ca	37	16	50248133	50248133	+	Splice_Site	SNP	T	T	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr16:50248133T>A	ENST00000561678.1	+	3	592	c.518T>A	c.(517-519)gTc>gAc	p.V173D	PAPD5_ENST00000357464.3_Splice_Site_p.V161D|PAPD5_ENST00000436909.3_Splice_Site_p.V240D			Q8NDF8	PAPD5_HUMAN	PAP associated domain containing 5	161					histone mRNA catabolic process (GO:0071044)|mitotic nuclear division (GO:0007067)|mRNA processing (GO:0006397)|rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|polynucleotide adenylyltransferase activity (GO:0004652)			endometrium(1)|kidney(1)|lung(2)	4		all_cancers(37;0.0452)		BRCA - Breast invasive adenocarcinoma(181;0.0843)|GBM - Glioblastoma multiforme(240;0.231)		CTGTTTCAGGTCCAGATATTT	0.323																																					p.V240D													.	PAPD5	57	0			c.T719A						.						68.0	63.0	65.0					16																	50248133		1805	4080	5885	SO:0001630	splice_region_variant	64282	exon4			TTCAGGTCCAGAT	AF089897	CCDS54006.1	16q12.1	2010-11-18				ENSG00000121274			30758	protein-coding gene	gene with protein product	"""TUTase3"""	605540				10066793	Standard	NM_001040284		Approved	TRF4-2	uc010vgo.2	Q8NDF8		ENST00000561678.1:c.517-1T>A	16.37:g.50248133T>A		Somatic	60	0		WXS	Illumina HiSeq	Phase_1	55	4	NM_001040284	B4DV38|Q9NW67|Q9Y6C0	Missense_Mutation	SNP	ENST00000561678.1	37		.	.	.	.	.	.	.	.	.	.	T	22.4	4.283448	0.80803	.	.	ENSG00000121274	ENST00000436909;ENST00000357464	T;T	0.59364	0.27;0.28	5.36	5.36	0.76844	Nucleotidyl transferase domain (1);	0.000000	0.85682	D	0.000000	D	0.85401	0.5688	H	0.98507	4.25	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	D	0.91234	0.5016	10	0.87932	D	0	.	15.6571	0.77150	0.0:0.0:0.0:1.0	.	240;161	B4DV38;Q8NDF8	.;PAPD5_HUMAN	D	240;161	ENSP00000396995:V240D;ENSP00000350054:V161D	ENSP00000350054:V161D	V	+	2	0	PAPD5	48805634	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	7.278000	0.78587	2.147000	0.66899	0.533000	0.62120	GTC	.		0.323	PAPD5-002	PUTATIVE	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000423150.1	NM_022447	Missense_Mutation
RP11-142G1.1	0	bcgsc.ca	37	16	52289409	52289409	+	lincRNA	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr16:52289409T>G	ENST00000568286.1	+	0	317				AC007333.1_ENST00000408588.1_RNA																							attgcggtttttgccattgtt	0.313																																					.													.	.	.	0			.						.																																					0	.			CGGTTTTTGCCAT																													16.37:g.52289409T>G		Somatic	135	0		WXS	Illumina HiSeq	Phase_1	139	73	.		RNA	SNP	ENST00000568286.1	37																																																																																				.		0.313	RP11-142G1.1-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000422568.1		
RP11-142G1.1	0	bcgsc.ca	37	16	52289431	52289431	+	lincRNA	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr16:52289431A>C	ENST00000568286.1	+	0	317				AC007333.1_ENST00000408588.1_RNA																							ttaatggcaaaaaccgcaatt	0.328																																					.													.	.	.	0			.						.																																					0	.			TGGCAAAAACCGC																													16.37:g.52289431A>C		Somatic	88	0		WXS	Illumina HiSeq	Phase_1	102	28	.		RNA	SNP	ENST00000568286.1	37																																																																																				.		0.328	RP11-142G1.1-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000422568.1		
RP11-142G1.1	0	bcgsc.ca	37	16	52289444	52289444	+	lincRNA	SNP	T	T	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr16:52289444T>G	ENST00000568286.1	+	0	317				AC007333.1_ENST00000408588.1_RNA																							ccgcaattacttttgcaccac	0.323																																					.													.	.	.	0			.						.																																					0	.			AATTACTTTTGCA																													16.37:g.52289444T>G		Somatic	123	0		WXS	Illumina HiSeq	Phase_1	97	52	.		RNA	SNP	ENST00000568286.1	37																																																																																				.		0.323	RP11-142G1.1-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000422568.1		
CTC1	80169	bcgsc.ca	37	17	8140835	8140835	+	Missense_Mutation	SNP	T	T	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr17:8140835T>A	ENST00000315684.8	-	5	657	c.650A>T	c.(649-651)aAc>aTc	p.N217I	CTC1_ENST00000581671.1_5'UTR	NM_025099.5	NP_079375.3	Q2NKJ3	CTC1_HUMAN	CTS telomere maintenance complex component 1	217					bone marrow development (GO:0048539)|cellular response to DNA damage stimulus (GO:0006974)|hematopoietic stem cell proliferation (GO:0071425)|multicellular organism growth (GO:0035264)|positive regulation of DNA replication (GO:0045740)|positive regulation of fibroblast proliferation (GO:0048146)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|replicative senescence (GO:0090399)|spleen development (GO:0048536)|telomere maintenance (GO:0000723)|telomere maintenance via telomere lengthening (GO:0010833)|thymus development (GO:0048538)	nuclear chromosome, telomeric region (GO:0000784)|nucleus (GO:0005634)|Stn1-Ten1 complex (GO:0070188)	single-stranded DNA binding (GO:0003697)			NS(1)|endometrium(6)|kidney(3)|large_intestine(6)|lung(8)|ovary(1)|skin(4)	29						TCTGAGCTTGTTTCTAAGAAG	0.478																																					p.N217I													.	CTC1	75	0			c.A650T						.						58.0	57.0	57.0					17																	8140835		1919	4127	6046	SO:0001583	missense	80169	exon5			AGCTTGTTTCTAA	AL831955	CCDS42259.1	17p13.1	2011-02-21	2011-02-21	2011-02-21	ENSG00000178971	ENSG00000178971			26169	protein-coding gene	gene with protein product	"""conserved telomere maintenance component 1"", ""alpha accessory factor 132"", ""conserved telomere capping protein 1"""	613129	"""tmp494178"", ""chromosome 17 open reading frame 68"""	C17orf68		19854130, 19854131	Standard	NM_025099		Approved	FLJ22170, AAF132	uc002gkq.4	Q2NKJ3		ENST00000315684.8:c.650A>T	17.37:g.8140835T>A	ENSP00000313759:p.Asn217Ile	Somatic	39	0		WXS	Illumina HiSeq	Phase_1	17	7	NM_025099	B3KR66|C9JEX5|Q1PCD1|Q2TBE3|Q8N3S6|Q9H6L0	Missense_Mutation	SNP	ENST00000315684.8	37	CCDS42259.1	.	.	.	.	.	.	.	.	.	.	T	15.58	2.874775	0.51695	.	.	ENSG00000178971	ENST00000315684	D	0.82619	-1.63	3.61	-0.788	0.10939	.	0.882627	0.09876	N	0.744260	T	0.61110	0.2321	N	0.08118	0	0.21386	N	0.999707	B	0.06786	0.001	B	0.04013	0.001	T	0.46721	-0.9171	10	0.36615	T	0.2	0.1642	2.7011	0.05149	0.2083:0.4162:0.0:0.3755	.	217	Q2NKJ3	CTC1_HUMAN	I	217	ENSP00000313759:N217I	ENSP00000313759:N217I	N	-	2	0	CTC1	8081560	0.800000	0.28916	0.648000	0.29521	0.921000	0.55340	0.016000	0.13377	-0.084000	0.12595	-0.903000	0.02851	AAC	.		0.478	CTC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000442012.1	NM_025099	
CEACAM1	634	bcgsc.ca	37	19	43031434	43031434	+	Missense_Mutation	SNP	T	T	A	rs140316654		TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr19:43031434T>A	ENST00000161559.6	-	2	317	c.183A>T	c.(181-183)caA>caT	p.Q61H	CEACAM1_ENST00000403444.3_Missense_Mutation_p.Q61H|CEACAM1_ENST00000403461.1_Missense_Mutation_p.Q61H|LIPE-AS1_ENST00000594624.2_RNA|CEACAM1_ENST00000358394.3_Missense_Mutation_p.Q61H|CEACAM1_ENST00000599389.1_Missense_Mutation_p.Q61H|CEACAM1_ENST00000308072.4_Missense_Mutation_p.Q21H|LIPE-AS1_ENST00000457234.2_RNA|LIPE-AS1_ENST00000594688.1_RNA|CEACAM1_ENST00000352591.5_Missense_Mutation_p.Q61H|CEACAM1_ENST00000351134.3_Missense_Mutation_p.Q61H	NM_001712.4	NP_001703.2	P13688	CEAM1_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 1 (biliary glycoprotein)	61	Ig-like V-type.				angiogenesis (GO:0001525)|cell migration (GO:0016477)|homophilic cell adhesion (GO:0007156)|integrin-mediated signaling pathway (GO:0007229)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(3)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(1)	17		Prostate(69;0.00682)		GBM - Glioblastoma multiforme(486;0.00148)	Arcitumomab(DB00113)	AGCCAAAAAGTTGCTGGGGCA	0.522																																					p.Q61H													.	CEACAM1	43	0			c.A183T						.						205.0	169.0	181.0					19																	43031434		2203	4300	6503	SO:0001583	missense	634	exon2			AAAAAGTTGCTGG	M72238	CCDS12609.1, CCDS46089.1, CCDS54272.1, CCDS54273.1, CCDS54274.1	19q13.2	2014-05-16			ENSG00000079385	ENSG00000079385		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	1814	protein-coding gene	gene with protein product		109770		BGP		2457922, 2025273	Standard	NM_001712		Approved	BGP1, CD66a	uc002otv.3	P13688	OTTHUMG00000151078	ENST00000161559.6:c.183A>T	19.37:g.43031434T>A	ENSP00000161559:p.Gln61His	Somatic	121	2		WXS	Illumina HiSeq	Phase_1	85	5	NM_001184816	A6NE38|A8MY49|O60430|Q069I7|Q13854|Q13857|Q13858|Q13859|Q13860|Q15600|Q15601|Q16170|Q5UB49|Q7KYP5|Q96CA7|Q9UQV9	Missense_Mutation	SNP	ENST00000161559.6	37	CCDS12609.1	.	.	.	.	.	.	.	.	.	.	a	9.737	1.163731	0.21538	.	.	ENSG00000079385	ENST00000161559;ENST00000358394;ENST00000351134;ENST00000446434;ENST00000378065;ENST00000352591;ENST00000403444;ENST00000403461;ENST00000308072;ENST00000377806;ENST00000344391;ENST00000403136	T;T;T;T;T;T;T	0.01527	4.8;4.8;4.8;4.8;4.8;4.8;4.8	3.6	-2.71	0.05986	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00637	0.0021	N	0.01048	-1.04	0.09310	N	1	B;B;B;B;B;B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0;0.0;0.0;0.0;0.0;0.0	B;B;B;B;B;B;B;B;B;B	0.08055	0.003;0.0;0.0;0.0;0.0;0.0;0.0;0.0;0.0;0.0	T	0.45804	-0.9236	9	0.41790	T	0.15	.	1.0812	0.01643	0.3:0.1745:0.3535:0.172	.	61;61;61;61;61;61;61;61;61;61	P13688-7;P13688-10;P13688-3;P13688-4;P13688-2;P13688-11;P13688-6;P13688-5;P13688-8;P13688	.;.;.;.;.;.;.;.;.;CEAM1_HUMAN	H	61;61;61;88;21;61;61;61;21;61;61;61	ENSP00000161559:Q61H;ENSP00000351165:Q61H;ENSP00000325946:Q61H;ENSP00000244291:Q61H;ENSP00000384709:Q61H;ENSP00000384083:Q61H;ENSP00000312184:Q21H	ENSP00000161559:Q61H	Q	-	3	2	CEACAM1	47723274	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.340000	0.02650	-0.660000	0.05352	-0.508000	0.04489	CAA	.		0.522	CEACAM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000321190.2	NM_001712	
MLLT10P1	140678	bcgsc.ca	37	20	29637850	29637850	+	RNA	SNP	T	T	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr20:29637850T>C	ENST00000408392.1	+	0	139																											TTCTTGGATTTCTTTCAACAC	0.368																																					.													.	.	.	0			.						.																																					140678	.			TGGATTTCTTTCA																													20.37:g.29637850T>C		Somatic	151	4		WXS	Illumina HiSeq	Phase_1	68	8	.		RNA	SNP	ENST00000408392.1	37																																																																																				.		0.368	AL441988.1-201	NOVEL	basic	miRNA	miRNA			
RPSAP1	170529	bcgsc.ca	37	20	49748142	49748142	+	IGR	SNP	T	T	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr20:49748142T>C								KCNG1 (108476 upstream) : AL035457.1 (45899 downstream)																							AGTGGGTTCCTGCTGCAAGGA	0.458																																					.													.	.	.	0			.						.																																			SO:0001628	intergenic_variant	170529	.			GGTTCCTGCTGCA																													20.37:g.49748142T>C		Somatic	20	0		WXS	Illumina HiSeq	Phase_1	19	9	.		RNA	SNP		37																																																																																				.	0	0.458								
IGKV2OR22-3	3529	bcgsc.ca	37	22	17402464	17402464	+	IGR	SNP	C	C	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr22:17402464C>G								AC007064.24 (50448 upstream) : GAB4 (40361 downstream)																							AGGCCCGGTTCAAAACCAAAT	0.527																																					.													.	.	.	0			.						.																																			SO:0001628	intergenic_variant	3529	.			CCGGTTCAAAACC																													22.37:g.17402464C>G		Somatic	55	0		WXS	Illumina HiSeq	Phase_1	45	25	.		RNA	SNP		37																																																																																				.	0	0.527								
GGT2	728441	bcgsc.ca	37	22	21563355	21563355	+	Silent	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr22:21563355A>C	ENST00000401924.1	-	12	1760	c.1269T>G	c.(1267-1269)acT>acG	p.T423T	GGT2_ENST00000424627.1_Silent_p.T423T|GGT2_ENST00000405188.4_Silent_p.T413T			P36268	GGT2_HUMAN	gamma-glutamyltransferase 2	423					glutathione biosynthetic process (GO:0006750)|glutathione derivative biosynthetic process (GO:1901687)|glutathione metabolic process (GO:0006749)|leukotriene biosynthetic process (GO:0019370)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	anchored component of external side of plasma membrane (GO:0031362)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	gamma-glutamyltransferase activity (GO:0003840)										GGAGAGCTGAAGTCGTCCATT	0.602																																					.													.	.	.	0			.						.																																			SO:0001819	synonymous_variant	728441	.			AGCTGAAGTCGTC	M30474		22q11.21	2012-04-19			ENSG00000133475	ENSG00000133475	2.3.2.2	"""Gamma-glutamyltransferases"""	4251	protein-coding gene	gene with protein product		137181		GGT		8104871, 18357469	Standard	XM_006724392		Approved		uc011aic.1	P36268	OTTHUMG00000150617	ENST00000401924.1:c.1269T>G	22.37:g.21563355A>C		Somatic	220	0		WXS	Illumina HiSeq	Phase_1	135	42	.		Silent	SNP	ENST00000401924.1	37																																																																																				.		0.602	GGT2-002	KNOWN	non_canonical_other|not_best_in_genome_evidence|basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000320092.2	XM_001129377	
Unknown	0	bcgsc.ca	37	X	9147497	9147497	+	IGR	SNP	A	A	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chrX:9147497A>G								FAM9B (16255 upstream) : GS1-519E5.1 (70462 downstream)																							ACATTGAGATAATCACCAGCA	0.448																																					.													.	.	.	0			.						.																																			SO:0001628	intergenic_variant	0	.			TGAGATAATCACC																													X.37:g.9147497A>G		Somatic	19	0		WXS	Illumina HiSeq	Phase_1	14	14	.		RNA	SNP		37																																																																																				.	0	0.448								
AC112778.1	0	bcgsc.ca	37	X	25224509	25224509	+	RNA	SNP	A	A	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	A	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chrX:25224509A>C	ENST00000390786.1	-	0	68																											gtgcaaaagtaattgcggttt	0.294																																					.													.	.	.	0			.						.																																					0	.			AAAAGTAATTGCG																													X.37:g.25224509A>C		Somatic	147	0		WXS	Illumina HiSeq	Phase_1	85	40	.		RNA	SNP	ENST00000390786.1	37																																																																																				.		0.294	AC112778.1-201	NOVEL	basic	miRNA	miRNA			
Unknown	0	bcgsc.ca	37	X	52613599	52613599	+	IGR	SNP	G	G	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chrX:52613599G>A								XAGE1E (67402 upstream) : SSX7 (59540 downstream)																							CAGTGTGCCAGAGCCTTAACA	0.458																																					.													.	.	.	0			.						.																																			SO:0001628	intergenic_variant	0	.			GTGCCAGAGCCTT																													X.37:g.52613599G>A		Somatic	13	0		WXS	Illumina HiSeq	Phase_1	5	5	.		RNA	SNP		37																																																																																				.	0	0.458								
COL4A5	1287	bcgsc.ca	37	X	107909789	107909789	+	Missense_Mutation	SNP	G	G	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chrX:107909789G>A	ENST00000361603.2	+	39	3762	c.3518G>A	c.(3517-3519)gGt>gAt	p.G1173D	COL4A5_ENST00000328300.6_Missense_Mutation_p.G1173D	NM_000495.4	NP_000486.1	P29400	CO4A5_HUMAN	collagen, type IV, alpha 5	1173	Triple-helical region.				axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|neuromuscular junction development (GO:0007528)	basal lamina (GO:0005605)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|neuromuscular junction (GO:0031594)	extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(25)|lung(32)|ovary(4)|prostate(2)|skin(8)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	99						GGTCAAGATGGTATTCCTGGA	0.448									Alport syndrome with Diffuse Leiomyomatosis																												p.G1173D													.	COL4A5	262	0			c.G3518A						.						69.0	60.0	63.0					X																	107909789		2203	4300	6503	SO:0001583	missense	1287	exon39	Familial Cancer Database		AAGATGGTATTCC	M90464	CCDS14543.1, CCDS35366.1	Xq22	2014-09-17	2008-07-28		ENSG00000188153	ENSG00000188153		"""Collagens"""	2207	protein-coding gene	gene with protein product		303630	"""Alport syndrome"""	ASLN, ATS			Standard	NM_000495		Approved		uc004enz.2	P29400	OTTHUMG00000022182	ENST00000361603.2:c.3518G>A	X.37:g.107909789G>A	ENSP00000354505:p.Gly1173Asp	Somatic	55	0		WXS	Illumina HiSeq	Phase_1	25	4	NM_000495	Q16006|Q16126|Q6LD84|Q7Z700|Q9NUB7	Missense_Mutation	SNP	ENST00000361603.2	37	CCDS14543.1	.	.	.	.	.	.	.	.	.	.	G	19.32	3.805021	0.70682	.	.	ENSG00000188153	ENST00000328300;ENST00000361603;ENST00000508186	D;D	0.99353	-5.77;-5.77	5.49	5.49	0.81192	.	0.000000	0.85682	D	0.000000	D	0.99729	0.9894	H	0.98965	4.385	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.96983	0.9716	10	0.87932	D	0	.	18.4199	0.90587	0.0:0.0:1.0:0.0	.	1173;1173	E7EVY4;P29400	.;CO4A5_HUMAN	D	1173	ENSP00000331902:G1173D;ENSP00000354505:G1173D	ENSP00000331902:G1173D	G	+	2	0	COL4A5	107796445	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.265000	0.89869	2.290000	0.77057	0.600000	0.82982	GGT	.		0.448	COL4A5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000057880.2		
MPDZ	8777	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	9	13190162	13190162	+	Missense_Mutation	SNP	T	T	C	rs4740548	byFrequency	TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr9:13190162T>C	ENST00000319217.7	-	16	2352	c.2105A>G	c.(2104-2106)gAg>gGg	p.E702G	MPDZ_ENST00000541718.1_Missense_Mutation_p.E702G|MPDZ_ENST00000536827.1_Missense_Mutation_p.E702G|MPDZ_ENST00000381022.2_Missense_Mutation_p.E702G|MPDZ_ENST00000381015.4_Missense_Mutation_p.E702G|MPDZ_ENST00000447879.1_Missense_Mutation_p.E702G|MPDZ_ENST00000546205.1_Missense_Mutation_p.E702G	NM_001261406.1	NP_001248335.1	O75970	MPDZ_HUMAN	multiple PDZ domain protein	702	PDZ 5. {ECO:0000255|PROSITE- ProRule:PRU00143}.		E -> K (in dbSNP:rs4741289).|E -> V (in dbSNP:rs4740548).		cell adhesion (GO:0007155)|myelination (GO:0042552)|viral process (GO:0016032)	apical plasma membrane (GO:0016324)|apicolateral plasma membrane (GO:0016327)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|neuron projection (GO:0043005)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)|tight junction (GO:0005923)	protein C-terminus binding (GO:0008022)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(14)|lung(15)|ovary(5)|prostate(7)|stomach(1)|urinary_tract(2)	61				GBM - Glioblastoma multiforme(50;2.03e-06)		TTTCTCCAGCTCTATGTGCTG	0.438																																					p.E702G		.											.	.	.	0			c.A2105G						.						72.0	69.0	70.0					9																	13190162		2002	4182	6184	SO:0001583	missense	8777	exon16			TCCAGCTCTATGT	AF093419	CCDS47951.1, CCDS59119.1, CCDS59120.1	9p23	2008-05-15			ENSG00000107186	ENSG00000107186			7208	protein-coding gene	gene with protein product		603785					Standard	NM_003829		Approved	MUPP1	uc003zlb.4	O75970	OTTHUMG00000021031	ENST00000319217.7:c.2105A>G	9.37:g.13190162T>C	ENSP00000320006:p.Glu702Gly	Somatic	50	0		WXS	Illumina HiSeq	.	31	20	NM_003829	A6NLC2|B2RTS3|B7ZMI4|O43798|Q4LE30|Q5CZ80|Q5JTX3|Q5JTX6|Q5JTX7|Q5JUC3|Q5JUC4|Q5VZ62|Q8N790	Missense_Mutation	SNP	ENST00000319217.7	37		.	.	.	.	.	.	.	.	.	.	T	21.6	4.172316	0.78452	.	.	ENSG00000107186	ENST00000319217;ENST00000541718;ENST00000381022;ENST00000536827;ENST00000447879;ENST00000381015;ENST00000399902;ENST00000546205	T;T;T;T;T;T;T	0.28454	1.61;1.61;1.61;1.61;1.61;1.61;1.61	5.83	4.68	0.58851	.	0.000000	0.44285	D	0.000475	T	0.53706	0.1813	M	0.90252	3.1	0.80722	D	1	D;D;D	0.69078	0.986;0.982;0.997	P;P;P	0.58172	0.834;0.744;0.804	T	0.59783	-0.7389	10	0.72032	D	0.01	.	8.1209	0.30971	0.1341:0.0:0.1404:0.7255	.	702;702;702	B7ZMI4;O75970-3;O75970-2	.;.;.	G	702;702;702;702;702;702;652;702	ENSP00000320006:E702G;ENSP00000439807:E702G;ENSP00000370410:E702G;ENSP00000444151:E702G;ENSP00000415208:E702G;ENSP00000370403:E702G;ENSP00000446358:E702G	ENSP00000320006:E702G	E	-	2	0	MPDZ	13180162	1.000000	0.71417	0.998000	0.56505	0.958000	0.62258	5.808000	0.69165	1.016000	0.39470	0.533000	0.62120	GAG	.		0.438	MPDZ-001	KNOWN	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000055485.2	NM_003829	
JADE2	23338	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	5	133887780	133887780	+	Silent	SNP	G	G	T	rs12163993	byFrequency	TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr5:133887780G>T	ENST00000402835.1	+	4	447	c.192G>T	c.(190-192)ccG>ccT	p.P64P	PHF15_ENST00000282605.4_Silent_p.P64P|PHF15_ENST00000395003.1_Silent_p.P64P|PHF15_ENST00000361895.2_Silent_p.P64P																NS(1)|breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(6)|prostate(1)|skin(1)	22			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			TGAAGATCCCGGACTCATACC	0.592																																					p.P64P		.											.	.	.	0			c.G192T						.						96.0	92.0	93.0					5																	133887780		2203	4300	6503	SO:0001819	synonymous_variant	23338	exon4			GATCCCGGACTCA																												ENST00000402835.1:c.192G>T	5.37:g.133887780G>T		Somatic	40	0		WXS	Illumina HiSeq	.	39	11	NM_015288		Silent	SNP	ENST00000402835.1	37																																																																																				.		0.592	PHF15-007	PUTATIVE	alternative_5_UTR|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000318543.1		
ZNF355P	100505852	hgsc.bcm.edu;bcgsc.ca	37	21	14469494	14469495	+	IGR	DNP	GC	GC	TT	rs80211083	byFrequency	TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	GC	GC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr21:14469494_14469495GC>TT								RNU6-614P (49484 upstream) : AL050302.1 (272435 downstream)																							CCACTTAAAAGCTTTGCCACAT	0.366																																					.		.											.	.	.	0			.						.																																			SO:0001628	intergenic_variant	149992	.			TAAAAGCTTTGCC																													21.37:g.14469494_14469495delinsTT		Somatic	191	1		WXS	Illumina HiSeq	.	70	45	.		RNA	DNP		37																																																																																				.	0	0.366								
PCF11	51585	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	11	82877706	82877707	+	Missense_Mutation	DNP	AA	AA	CC			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	AA	AA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr11:82877706_82877707AA>CC	ENST00000298281.4	+	5	2219_2220	c.1767_1768AA>CC	c.(1765-1770)caAAgt>caCCgt	p.589_590QS>HR		NM_015885.3	NP_056969.2	O94913	PCF11_HUMAN	PCF11 cleavage and polyadenylation factor subunit	589					gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA cleavage (GO:0006379)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	mRNA cleavage factor complex (GO:0005849)|nucleoplasm (GO:0005654)				cervix(1)|endometrium(3)|kidney(4)|large_intestine(1)|lung(22)|ovary(1)|urinary_tract(1)	33						AAAACTGGCAAAGTTCCAAGTC	0.376																																					p.QS589HR		.											PCF11_ENST00000298281,NS,carcinoma,0,2	PCF11_ENST00000298281	0	0			c.A1768C						.																																			SO:0001583	missense	51585	exon5			TGGCAAAGTTCCA	AB020631	CCDS44689.1	11q13	2013-07-02	2013-07-02		ENSG00000165494	ENSG00000165494			30097	protein-coding gene	gene with protein product		608876	"""PCF11, cleavage and polyadenylation factor II subunit, homolog (S. cerevisiae)"", ""PCF11, cleavage and polyadenylation factor subunit, homolog (S. cerevisiae)"""			11060040	Standard	NM_015885		Approved	KIAA0824	uc001ozx.4	O94913	OTTHUMG00000167031	Exception_encountered	11.37:g.82877706_82877707delinsCC	ENSP00000298281:p.Q589_S590delinsHR	Somatic	130	0		WXS	Illumina HiSeq	.	94	37	NM_015885	A6H8W7|O43671|Q6P0X8	Missense_Mutation	DNP	ENST00000298281.4	37	CCDS44689.1																																																																																			.		0.376	PCF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392548.2	NM_015885	
CREM	1390	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	10	35500212	35500213	+	Intron	DNP	GA	GA	CT			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	GA	GA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr10:35500212_35500213GA>CT	ENST00000395895.2	+	10	1100				CREM_ENST00000429130.3_Intron|CREM_ENST00000474362.1_Intron|CREM_ENST00000439705.1_Nonsense_Mutation_p.248_249KK>N*|CREM_ENST00000484283.1_Intron|CREM_ENST00000463314.1_Intron|CREM_ENST00000337656.4_Nonsense_Mutation_p.262_263KK>N*|CREM_ENST00000374728.3_Intron|CREM_ENST00000395887.3_Intron|CREM_ENST00000488741.1_Nonsense_Mutation_p.65_66KK>N*|CREM_ENST00000488328.1_Intron|CREM_ENST00000342105.3_Intron|CREM_ENST00000487763.1_Intron|CREM_ENST00000479070.1_Intron|CREM_ENST00000474931.1_Nonsense_Mutation_p.75_76KK>N*|CREM_ENST00000374734.3_Nonsense_Mutation_p.199_200KK>N*|CREM_ENST00000473940.1_Nonsense_Mutation_p.83_84KK>N*|CREM_ENST00000345491.3_Intron|CREM_ENST00000344351.5_Nonsense_Mutation_p.58_59KK>N*|CREM_ENST00000356917.5_Nonsense_Mutation_p.71_72KK>N*|CREM_ENST00000354759.3_Nonsense_Mutation_p.211_212KK>N*|CREM_ENST00000468236.1_Intron|CREM_ENST00000463960.1_Intron|CREM_ENST00000460270.1_Nonsense_Mutation_p.58_59KK>N*|CREM_ENST00000333809.8_Nonsense_Mutation_p.311_312KK>N*|RP11-324I22.3_ENST00000602435.1_RNA|CREM_ENST00000374721.3_Nonsense_Mutation_p.232_233KK>N*|CREM_ENST00000490511.1_Intron|CREM_ENST00000348787.2_Intron|CREM_ENST00000361599.4_Intron			Q03060	CREM_HUMAN	cAMP responsive element modulator						cell differentiation (GO:0030154)|glycosphingolipid metabolic process (GO:0006687)|multicellular organismal development (GO:0007275)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|rhythmic process (GO:0048511)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	cAMP response element binding protein binding (GO:0008140)|DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(7)|prostate(1)	14						GCAGGAAGAAGAAAGAATATGT	0.465																																					p.KK311N*		.											.	.	.	0			c.A787T						.																																			SO:0001627	intron_variant	1390	exon7			AAGAAGAAAGAAT		CCDS7180.1, CCDS7181.1, CCDS7182.1, CCDS7183.1, CCDS7184.1, CCDS7185.1, CCDS7186.1, CCDS7187.1, CCDS7188.1, CCDS31181.1, CCDS53519.1, CCDS53520.1, CCDS53517.1, CCDS53518.1, CCDS53521.1, CCDS58074.1, CCDS58075.1, CCDS58076.1	10p12.1-p11.1	2013-01-10			ENSG00000095794	ENSG00000095794		"""basic leucine zipper proteins"""	2352	protein-coding gene	gene with protein product		123812				1461747, 7916662	Standard	NM_182717		Approved	hCREM-2	uc001iyb.3	Q03060	OTTHUMG00000017953	Exception_encountered	10.37:g.35500212_35500213delinsCT		Somatic	84	0		WXS	Illumina HiSeq	.	38	11	NM_183011	A8K014|A8K3J7|A8K6A1|A8MPQ2|B4DXC1|C9J785|C9JZ10|E9PAR4|E9PHM1|O75519|Q14501|Q14503|Q14504|Q14505|Q14506|Q15731|Q16114|Q16116|Q5T9H7|Q5W1A6|Q5W1A7|Q5W1A8|Q5W1A9|Q5W1B0|Q5W1B2|Q7Z2Q6|Q8IVD4|Q96AG7|Q9NZ98|Q9NZ99|Q9NZB9	Nonsense_Mutation	DNP	ENST00000395895.2	37																																																																																				.		0.465	CREM-203	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001881	
SDR16C5	195814	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	8	57228891	57228892	+	Nonsense_Mutation	DNP	GC	GC	AA			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	GC	GC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr8:57228891_57228892GC>AA	ENST00000303749.3	-	2	652_653	c.15_16GC>TT	c.(13-18)ctGCaa>ctTTaa	p.Q6*	SDR16C5_ENST00000396721.2_Nonsense_Mutation_p.Q6*|SDR16C5_ENST00000522671.1_Nonsense_Mutation_p.Q6*	NM_138969.2	NP_620419.2	Q8N3Y7	RDHE2_HUMAN	short chain dehydrogenase/reductase family 16C, member 5	6					detection of light stimulus involved in visual perception (GO:0050908)|keratinocyte proliferation (GO:0043616)|retinal metabolic process (GO:0042574)|retinol metabolic process (GO:0042572)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	retinol dehydrogenase activity (GO:0004745)			breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(3)|ovary(1)|prostate(1)|skin(1)	16						TTTGATGATTGCAGGTTGAAAG	0.416																																					p.Q6*		.											.	.	.	0			c.G15T						.																																			SO:0001587	stop_gained	195814	exon2			TGATTGCAGGTTG		CCDS6167.1	8q12.1	2011-09-20			ENSG00000170786	ENSG00000170786	1.1.1.-	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 3"""	30311	protein-coding gene	gene with protein product		608989				12372410	Standard	NM_138969		Approved	RDHE2, RDH-E2	uc003xsy.1	Q8N3Y7	OTTHUMG00000164311	ENST00000303749.3:c.15_16delinsAA	8.37:g.57228891_57228892delinsAA	ENSP00000307607:p.Gln6*	Somatic	27	0		WXS	Illumina HiSeq	.	15	7	NM_138969	B4DGK2|Q330K3|Q8TDV9|Q96LX1	Nonsense_Mutation	DNP	ENST00000303749.3	37	CCDS6167.1																																																																																			.		0.416	SDR16C5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378235.1	NM_138969	
MGAT5B	146664	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	17	74936851	74936852	+	Missense_Mutation	DNP	GC	GC	TT			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	GC	GC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr17:74936851_74936852GC>TT	ENST00000569840.2	+	15	2343_2344	c.1769_1770GC>TT	c.(1768-1770)gGC>gTT	p.G590V	MGAT5B_ENST00000428789.2_Missense_Mutation_p.G599V|MGAT5B_ENST00000301618.4_Missense_Mutation_p.G588V	NM_001199172.1	NP_001186101.1	Q3V5L5	MGT5B_HUMAN	mannosyl (alpha-1,6-)-glycoprotein beta-1,6-N-acetyl-glucosaminyltransferase, isozyme B	590					protein N-linked glycosylation (GO:0006487)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase activity (GO:0030144)|metal ion binding (GO:0046872)			breast(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(15)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						AACTTCATCGGCAAGCCCCACG	0.545																																					p.G599V		.											.	.	.	0			c.C1797T						.																																			SO:0001583	missense	146664	exon13			CATCGGCAAGCCC	AB109185	CCDS11751.1, CCDS45788.1, CCDS59299.1	17q25.3	2013-02-25	2005-11-16		ENSG00000167889	ENSG00000167889		"""Mannosyl-glycoprotein beta N-acetylglucosaminyltransferases"""	24140	protein-coding gene	gene with protein product		612441	"""mannosyl (alpha-1,6-)-glycoprotein beta-1,6-N-acetyl-glucosaminyltransferase, isoenzyme B"""			14617637, 14623122	Standard	NM_001199172		Approved	GnT-IX, FLJ25132, GnT-VB	uc002jth.3	Q3V5L5	OTTHUMG00000177278	Exception_encountered	17.37:g.74936851_74936852delinsTT	ENSP00000456037:p.Gly590Val	Somatic	33	0		WXS	Illumina HiSeq	.	23	4	NM_198955	Q6P3S8|Q6P6B3|Q766X5|Q76D04|Q96LS2	Missense_Mutation	DNP	ENST00000569840.2	37	CCDS59299.1																																																																																			.		0.545	MGAT5B-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460624.2	NM_144677	
EIF3H	8667	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	8	117767993	117767994	+	Missense_Mutation	DNP	GA	GA	TT			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	GA	GA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr8:117767993_117767994GA>TT	ENST00000276682.4	-	3	851_852	c.85_86TC>AA	c.(85-87)TCc>AAc	p.S29N	EIF3H_ENST00000521861.1_Missense_Mutation_p.S15N					eukaryotic translation initiation factor 3, subunit H											large_intestine(2)|lung(10)|skin(1)	13	all_cancers(13;3.98e-22)|Lung NSC(37;0.000183)|Ovarian(258;0.0172)					GGTGGAGCTGGAAGAGGTGGCA	0.564																																					p.S29N		.											.	.	.	0			c.T43A						.																																			SO:0001583	missense	8667	exon1			AGCTGGAAGAGGT	U54559	CCDS6319.1	8q24.11	2007-07-27	2007-07-27	2007-07-27	ENSG00000147677	ENSG00000147677			3273	protein-coding gene	gene with protein product		603912	"""eukaryotic translation initiation factor 3, subunit 3 gamma, 40kDa"""	EIF3S3		9341143	Standard	NM_003756		Approved	eIF3-gamma, eIF3-p40, eIF3h	uc003yoa.3	O15372	OTTHUMG00000164919	ENST00000276682.4:c.85_86delinsTT	8.37:g.117767993_117767994delinsTT	ENSP00000276682:p.Ser29Asn	Somatic	52	0		WXS	Illumina HiSeq	.	32	11	NM_003756		Missense_Mutation	DNP	ENST00000276682.4	37																																																																																				.		0.564	EIF3H-003	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000380913.1	NM_003756	
ELN	2006	hgsc.bcm.edu	37	7	73474781	73474782	+	Missense_Mutation	DNP	CT	CT	TC	rs138876104	byFrequency	TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	CT	CT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr7:73474781_73474782CT>TC	ENST00000252034.7	+	25	2096_2097	c.1697_1698CT>TC	c.(1696-1698)gCT>gTC	p.A566V	ELN_ENST00000380584.4_Missense_Mutation_p.A518V|ELN_ENST00000380575.4_Missense_Mutation_p.A537V|ELN_ENST00000458204.1_Missense_Mutation_p.A556V|ELN_ENST00000414324.1_Missense_Mutation_p.A542V|ELN_ENST00000320492.7_Missense_Mutation_p.A485V|ELN_ENST00000429192.1_Missense_Mutation_p.A552V|ELN_ENST00000357036.5_Missense_Mutation_p.A571V|ELN_ENST00000380553.4_Missense_Mutation_p.A430V|ELN_ENST00000380562.4_Missense_Mutation_p.A572V|ELN_ENST00000358929.4_Missense_Mutation_p.A601V|ELN_ENST00000320399.6_Missense_Mutation_p.A566V|ELN_ENST00000445912.1_Missense_Mutation_p.A566V|CTB-51J22.1_ENST00000435932.1_RNA|ELN_ENST00000380576.5_Missense_Mutation_p.A547V	NM_000501.2|NM_001278915.1	NP_000492.2|NP_001265844.1	P15502	ELN_HUMAN	elastin	0	Ala-rich.				blood circulation (GO:0008015)|blood vessel remodeling (GO:0001974)|cell proliferation (GO:0008283)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|organ morphogenesis (GO:0009887)|regulation of actin filament polymerization (GO:0030833)|respiratory gaseous exchange (GO:0007585)|skeletal muscle tissue development (GO:0007519)|stress fiber assembly (GO:0043149)	elastic fiber (GO:0071953)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix binding (GO:0050840)|extracellular matrix constituent conferring elasticity (GO:0030023)|extracellular matrix structural constituent (GO:0005201)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(10)|ovary(4)|pancreas(2)|prostate(1)|skin(2)|stomach(1)	32		Lung NSC(55;0.159)				GGAGTTGGTGCTGGTGTTCCTG	0.629			T	PAX5	B-ALL		"""Supravalvular Aortic Stenosis, Cutis laxa , Williams-Beuren Syndrome"""																														p.A601V		.		Dom	yes		7	7q11.23	2006	elastin	yes	L	.	.	.	0			c.T1713C						.																																			SO:0001583	missense	2006	exon25			TGGTGCTGGTGTT		CCDS5562.2, CCDS43598.1, CCDS43599.1, CCDS47611.1, CCDS47612.1, CCDS64673.1, CCDS64674.1, CCDS64675.1, CCDS64676.1, CCDS64677.1, CCDS64678.1, CCDS75616.1, CCDS75617.1	7q11.1-q21.1	2008-08-01	2008-08-01		ENSG00000049540	ENSG00000049540			3327	protein-coding gene	gene with protein product	"""tropoelastin"", ""supravalvular aortic stenosis"", ""Williams-Beuren syndrome"""	130160				8096434	Standard	NM_001278939		Approved	WBS, WS, SVAS	uc003tzn.3	P15502	OTTHUMG00000150229	Exception_encountered	7.37:g.73474781_73474782delinsTC	ENSP00000252034:p.Ala566Val	Somatic	31	0		WXS	Illumina HiSeq	.	16	4	NM_001081754	B3KTS6|O15336|O15337|Q14233|Q14234|Q14235|Q14238|Q6P0L4|Q6ZWJ6|Q75MU5|Q7Z316|Q7Z3F5|Q9UMF5	Missense_Mutation	DNP	ENST00000252034.7	37	CCDS5562.2																																																																																			.		0.629	ELN-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000316913.1	NM_000501	
DICER1	23405	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	14	95569702	95569703	+	Missense_Mutation	DNP	GA	GA	AT			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	GA	GA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr14:95569702_95569703GA>AT	ENST00000526495.1	-	23	4321_4322	c.4030_4031TC>AT	c.(4030-4032)TCa>ATa	p.S1344I	DICER1_ENST00000343455.3_Missense_Mutation_p.S1344I|DICER1_ENST00000556045.1_Missense_Mutation_p.S242I|DICER1_ENST00000393063.1_Missense_Mutation_p.S1344I|DICER1_ENST00000527414.1_Missense_Mutation_p.S1344I|DICER1_ENST00000541352.1_Missense_Mutation_p.S1344I			Q9UPY3	DICER_HUMAN	dicer 1, ribonuclease type III	1344	RNase III 1. {ECO:0000255|PROSITE- ProRule:PRU00177}.				angiogenesis (GO:0001525)|branching morphogenesis of an epithelial tube (GO:0048754)|cardiac muscle cell development (GO:0055013)|cerebral cortex development (GO:0021987)|defense response to virus (GO:0051607)|embryonic hindlimb morphogenesis (GO:0035116)|gene expression (GO:0010467)|hair follicle cell proliferation (GO:0071335)|hair follicle morphogenesis (GO:0031069)|inner ear receptor cell development (GO:0060119)|intestinal epithelial cell development (GO:0060576)|lung development (GO:0030324)|mRNA stabilization (GO:0048255)|multicellular organism growth (GO:0035264)|negative regulation of Schwann cell proliferation (GO:0010626)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nerve development (GO:0021675)|neuron projection morphogenesis (GO:0048812)|olfactory bulb interneuron differentiation (GO:0021889)|peripheral nervous system myelin formation (GO:0032290)|positive regulation of gene expression (GO:0010628)|positive regulation of miRNA metabolic process (GO:2000630)|positive regulation of myelination (GO:0031643)|positive regulation of Schwann cell differentiation (GO:0014040)|post-embryonic development (GO:0009791)|pre-miRNA processing (GO:0031054)|production of miRNAs involved in gene silencing by miRNA (GO:0035196)|production of siRNA involved in RNA interference (GO:0030422)|regulation of cell cycle (GO:0051726)|regulation of enamel mineralization (GO:0070173)|regulation of neuron differentiation (GO:0045664)|regulation of oligodendrocyte differentiation (GO:0048713)|regulation of viral genome replication (GO:0045069)|reproductive structure development (GO:0048608)|RNA phosphodiester bond hydrolysis (GO:0090501)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|spinal cord motor neuron differentiation (GO:0021522)|spindle assembly (GO:0051225)|spleen development (GO:0048536)|stem cell maintenance (GO:0019827)|targeting of mRNA for destruction involved in RNA interference (GO:0030423)|zygote asymmetric cell division (GO:0010070)	axon (GO:0030424)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|growth cone (GO:0030426)|RISC complex (GO:0016442)	ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|miRNA binding (GO:0035198)|ribonuclease III activity (GO:0004525)	p.S1344L(1)		NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(1)|central_nervous_system(1)|endometrium(13)|kidney(3)|large_intestine(10)|lung(33)|ovary(1)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(3)	75		all_cancers(154;0.0621)|all_epithelial(191;0.223)		Epithelial(152;0.211)|COAD - Colon adenocarcinoma(157;0.215)		TCTCATATATGAAAGGCGGCCC	0.411			"""Mis F, N"""		"""sex cord-stromal tumour, TGCT, embryonal rhadomyosarcoma"""	pleuropulmonary blastoma			Familial Multinodular Goiter ;DICER 1 syndrome																												p.S1344I		.	yes	Rec	yes	Familial Pleuropulmonary Blastoma	14	14q32.13	23405	"""dicer 1, ribonuclease type III """		"""E, M, O"""	.	.	.	1	Substitution - Missense(1)	endometrium(1)	c.T4030A						.																																			SO:0001583	missense	23405	exon22	Familial Cancer Database	Adolescent Multinodular Goiter, incl. Multinodular Euthyroid Goiter & Non-Medullary Thyroid Cancer;incl. Pleuropulmonary Blastoma, Familial ; Cystic Nephroma, Familial	TATATGAAAGGCG	AB028449	CCDS9931.1, CCDS55941.1	14q32.13	2014-09-17	2008-02-20		ENSG00000100697	ENSG00000100697			17098	protein-coding gene	gene with protein product	"""dicer 1, double-stranded RNA-specific endoribonuclease"""	606241	"""Dicer1, Dcr-1 homolog (Drosophila)"", ""multinodular goitre 1"""	MNG1		10051563, 10786632, 21205968	Standard	NM_177438		Approved	Dicer, KIAA0928, K12H4.8-LIKE, HERNA	uc001ydw.2	Q9UPY3	OTTHUMG00000166134	ENST00000526495.1:c.4030_4031delinsAT	14.37:g.95569702_95569703delinsAT	ENSP00000437256:p.Ser1344Ile	Somatic	35	0		WXS	Illumina HiSeq	.	27	13	NM_030621	A7E2D3|B3KRG4|E0AD28|O95943|Q9UQ02	Missense_Mutation	DNP	ENST00000526495.1	37	CCDS9931.1																																																																																			.		0.411	DICER1-004	KNOWN	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000387997.1		
KRT85	3891	bcgsc.ca	37	12	52757179	52757180	+	Missense_Mutation	DNP	GG	GG	TT			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	GG	GG	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr12:52757179_52757180GG>TT	ENST00000257901.3	-	5	876_877	c.801_802CC>AA	c.(799-804)ctCCaa>ctAAaa	p.Q268K	KRT85_ENST00000544265.1_Missense_Mutation_p.Q56K	NM_002283.3	NP_002274.1	P78386	KRT85_HUMAN	keratin 85	268	Coil 1B.|Rod.				epidermis development (GO:0008544)	extracellular space (GO:0005615)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|endometrium(6)|kidney(1)|large_intestine(7)|liver(1)|lung(15)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	36	Myeloproliferative disorder(4;0.0484)|all_hematologic(5;0.088)			BRCA - Breast invasive adenocarcinoma(357;0.189)		ATGTGGGCTTGGAGAACGCGGA	0.554																																					p.Q268K													KRT85,NS,carcinoma,-2,1	KRT85	78	0			c.C801A						.																																			SO:0001583	missense	3891	exon5			GGCTTGGAGAACG	X99140	CCDS8824.1, CCDS73472.1	12q13.13	2013-06-20	2006-07-17	2006-07-17	ENSG00000135443	ENSG00000135443		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6462	protein-coding gene	gene with protein product	"""hard keratin type II"""	602767	"""keratin, hair, basic, 5"""	KRTHB5		9084137, 16831889	Standard	NM_002283		Approved	Hb-5	uc001sag.3	P78386	OTTHUMG00000169633	ENST00000257901.3:c.801_802delinsTT	12.37:g.52757179_52757180delinsTT	ENSP00000257901:p.Gln268Lys	Somatic	35	1		WXS	Illumina HiSeq	Phase_1	20	12	NM_002283	Q9NSB1	Missense_Mutation	DNP	ENST00000257901.3	37	CCDS8824.1																																																																																			.		0.554	KRT85-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405184.1	NM_002283	
BTBD18	643376	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	11	57509283	57509283	+	IGR	SNP	C	C	G			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr11:57509283C>G	ENST00000436147.3	-	0	2947				TMX2-CTNND1_ENST00000528395.1_Intron|RP11-691N7.6_ENST00000531074.1_5'Flank|C11orf31_ENST00000534355.1_Missense_Mutation_p.T42S|C11orf31_ENST00000388857.4_Missense_Mutation_p.T42S			B2RXH4	BTBDI_HUMAN	BTB (POZ) domain containing 18											endometrium(3)|kidney(1)	4						CTCCCTAGCACTAGCTGACGC	0.677																																					.		.											.	.	.	0			.						.						10.0	13.0	12.0					11																	57509283		1807	4044	5851	SO:0001628	intergenic_variant	280636	p.T42S			CTAGCACTAGCTG		CCDS44603.1	11q12.1	2013-01-08			ENSG00000233436	ENSG00000233436		"""BTB/POZ domain containing"""	37214	protein-coding gene	gene with protein product							Standard	NM_001145101		Approved		uc010rjy.2	B2RXH4	OTTHUMG00000167203		11.37:g.57509283C>G		Somatic	79	0		WXS	Illumina HiSeq	Phase_I	45	6	.		Missense_Mutation	SNP	ENST00000436147.3	37	CCDS44603.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	10.17|10.17	1.276302|1.276302	0.23307|0.23307	.|.	.|.	ENSG00000211450|ENSG00000211450	ENST00000528798|ENST00000534355;ENST00000388857	.|T;T	.|0.46063	.|0.88;0.88	5.43|5.43	2.47|2.47	0.30058|0.30058	.|Thioredoxin-like fold (2);	.|.	.|.	.|.	.|.	T|T	0.29556|0.29556	0.0737|0.0737	L|L	0.49126|0.49126	1.545|1.545	0.22034|0.22034	N|N	0.999408|0.999408	.|B	.|0.26975	.|0.165	.|B	.|0.28385	.|0.089	T|T	0.26360|0.26360	-1.0105|-1.0105	5|9	.|0.09084	.|T	.|0.74	-9.2637|-9.2637	3.4709|3.4709	0.07567|0.07567	0.2486:0.5228:0.1425:0.086|0.2486:0.5228:0.1425:0.086	.|.	.|42	.|Q8IZQ5	.|SELH_HUMAN	Q|S	13|42	.|ENSP00000434511:T42S;ENSP00000373509:T42S	.|ENSP00000373509:T42S	H|T	+|+	3|2	2|0	C11orf31|C11orf31	57265859|57265859	0.707000|0.707000	0.27866|0.27866	0.976000|0.976000	0.42696|0.42696	0.909000|0.909000	0.53808|0.53808	0.882000|0.882000	0.28186|0.28186	1.530000|1.530000	0.49136|0.49136	0.655000|0.655000	0.94253|0.94253	CAC|ACT	.		0.677	BTBD18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393718.2	NM_001145101	
GPX2	2877	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	14	65406264	65406264	+	Missense_Mutation	SNP	G	G	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr14:65406264G>C	ENST00000389614.5	-	2	601	c.515C>G	c.(514-516)aCc>aGc	p.T172S	CHURC1-FNTB_ENST00000549987.1_Intron|FNTB_ENST00000542227.1_Intron|FNTB_ENST00000447296.2_Intron	NM_002083.3	NP_002074.2	P18283	GPX2_HUMAN	glutathione peroxidase 2 (gastrointestinal)	172					interaction with symbiont (GO:0051702)|negative regulation of inflammatory response to antigenic stimulus (GO:0002862)|response to oxidative stress (GO:0006979)|response to symbiotic bacterium (GO:0009609)|temperature homeostasis (GO:0001659)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	electron carrier activity (GO:0009055)|glutathione peroxidase activity (GO:0004602)			large_intestine(2)|ovary(1)|skin(1)	4				all cancers(60;0.00117)|OV - Ovarian serous cystadenocarcinoma(108;0.00557)|BRCA - Breast invasive adenocarcinoma(234;0.00971)	Glutathione(DB00143)	GGTTGGGAAGGTGCGGCTGTA	0.537																																					.		.											.	.	.	0			.						.						161.0	156.0	158.0					14																	65406264		2002	4170	6172	SO:0001583	missense	2877	p.T172S			GGGAAGGTGCGGC		CCDS41964.1	14q23.3	2012-05-22			ENSG00000176153	ENSG00000176153	1.11.1.9		4554	protein-coding gene	gene with protein product		138319				8428933, 8287691	Standard	NM_002083		Approved	GSHPX-GI	uc021ruq.2	P18283	OTTHUMG00000171677	ENST00000389614.5:c.515C>G	14.37:g.65406264G>C	ENSP00000374265:p.Thr172Ser	Somatic	42	0		WXS	Illumina HiSeq	Phase_I	31	15	.	Q6PJ52|Q8WWI7|Q9NRP9	Missense_Mutation	SNP	ENST00000389614.5	37	CCDS41964.1	.	.	.	.	.	.	.	.	.	.	G	12.99	2.104798	0.37145	.	.	ENSG00000176153	ENST00000389614;ENST00000557049	T;T	0.22336	1.96;3.76	6.05	5.15	0.70609	Thioredoxin-like fold (2);	0.427480	0.22936	N	0.053850	T	0.14960	0.0361	N	0.25992	0.78	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.06092	-1.0846	10	0.32370	T	0.25	-0.9409	10.4834	0.44706	0.0:0.2684:0.5929:0.1387	.	172	P18283	GPX2_HUMAN	S	172;116	ENSP00000374265:T172S;ENSP00000451721:T116S	ENSP00000374265:T172S	T	-	2	0	GPX2	64476017	0.870000	0.30015	1.000000	0.80357	0.998000	0.95712	1.000000	0.29770	1.546000	0.49388	0.650000	0.86243	ACC	.		0.537	GPX2-001	KNOWN	basic|appris_principal|CCDS|seleno	protein_coding	protein_coding	OTTHUMT00000414708.1		
ZNF274	10782	hgsc.bcm.edu	37	19	58718365	58718365	+	Splice_Site	SNP	T	T	C			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr19:58718365T>C	ENST00000326804.4	+	6	992	c.533T>C	c.(532-534)cTg>cCg	p.L178P	ZNF274_ENST00000345813.3_Splice_Site_p.L146P|ZNF274_ENST00000424679.2_Splice_Site_p.L73P|ZNF274_ENST00000597818.1_3'UTR	NM_001278734.1|NM_133502.1	NP_001265663.1|NP_598009.1	Q96GC6	ZN274_HUMAN	zinc finger protein 274	179	SCAN box. {ECO:0000255|PROSITE- ProRule:PRU00187}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(13)|ovary(1)|prostate(1)|skin(1)	21		Colorectal(82;5.46e-05)|all_neural(62;0.0182)|Ovarian(87;0.0443)|Breast(46;0.0889)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0168)|Lung(386;0.215)		CCGGGAGCCCTGGACCAGCTC	0.627																																					.		.											ZNF274,NS,carcinoma,0,1	ZNF274	0	0			.						.						16.0	19.0	18.0					19																	58718365		2203	4298	6501	SO:0001630	splice_region_variant	10782	p.L178P			GAGCCCTGGACCA	AB029149	CCDS74473.1, CCDS74474.1, CCDS74475.1, CCDS74476.1	19q13.43	2013-01-09				ENSG00000171606		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	13068	protein-coding gene	gene with protein product		605467				10777669	Standard	NM_133502		Approved	ZKSCAN19, ZSCAN51	uc002qrs.1	Q96GC6		ENST00000326804.4:c.532-1T>C	19.37:g.58718365T>C		Somatic	103	1		WXS	Illumina HiSeq	Phase_I	53	4	.	Q53XU4|Q6MZG1|Q8WY37|Q8WY38|Q92969|Q9UII0|Q9UII1	Missense_Mutation	SNP	ENST00000326804.4	37		.	.	.	.	.	.	.	.	.	.	T	11.85	1.763061	0.31228	.	.	ENSG00000171606	ENST00000326804;ENST00000345813;ENST00000424679	T;T;T	0.09350	2.99;2.99;2.99	4.46	3.42	0.39159	Retrovirus capsid, C-terminal (1);Transcription regulator SCAN (3);	0.267012	0.20042	N	0.100495	T	0.25568	0.0622	.	.	.	0.49213	D	0.999762	D;D;D	0.69078	0.997;0.997;0.995	P;P;D	0.63192	0.899;0.899;0.912	T	0.00862	-1.1536	9	0.87932	D	0	-6.0561	7.6585	0.28389	0.1888:0.0:0.0:0.8112	.	74;147;179	Q96GC6-3;Q96GC6-2;Q96GC6	.;.;ZN274_HUMAN	P	178;146;73	ENSP00000321209:L178P;ENSP00000321187:L146P;ENSP00000409872:L73P	ENSP00000321209:L178P	L	+	2	0	ZNF274	63410177	0.001000	0.12720	0.663000	0.29738	0.077000	0.17291	0.637000	0.24659	0.787000	0.33731	0.533000	0.62120	CTG	.		0.627	ZNF274-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_133502	Missense_Mutation
SELT	51714	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	3	150340940	150340940	+	Nonsense_Mutation	SNP	G	G	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr3:150340940G>A	ENST00000485923.1	+	3	573	c.185G>A	c.(184-186)tGg>tAg	p.W62*	SELT_ENST00000477889.1_Nonsense_Mutation_p.W62*|SELT_ENST00000480740.1_Nonsense_Mutation_p.W62*|SELT_ENST00000471696.1_Nonsense_Mutation_p.W120*			P62341	SELT_HUMAN		120					cell redox homeostasis (GO:0045454)|insulin secretion involved in cellular response to glucose stimulus (GO:0035773)|pancreas development (GO:0031016)|selenocysteine incorporation (GO:0001514)	endoplasmic reticulum (GO:0005783)	selenium binding (GO:0008430)							LUSC - Lung squamous cell carcinoma(72;0.0538)|Lung(72;0.066)			ATCTGGCAGTGGGGCCAAGAA	0.343																																					.		.											.	.	.	0			.						.						69.0	61.0	63.0					3																	150340940		1831	4078	5909	SO:0001587	stop_gained	0	p.W120*			GGCAGTGGGGCCA																												ENST00000485923.1:c.185G>A	3.37:g.150340940G>A	ENSP00000420390:p.Trp62*	Somatic	101	0		WXS	Illumina HiSeq	Phase_I	93	53	.	O95904|Q8IY80|Q9CZ45|Q9NZJ3	Nonsense_Mutation	SNP	ENST00000485923.1	37		.	.	.	.	.	.	.	.	.	.	G	37	6.044850	0.97231	.	.	ENSG00000198843	ENST00000480740;ENST00000471696;ENST00000477889;ENST00000485923	.	.	.	5.55	5.55	0.83447	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-7.6132	19.5145	0.95157	0.0:0.0:1.0:0.0	.	.	.	.	X	62;120;62;62	.	ENSP00000418910:W120X	W	+	2	0	RP11-392O18.1	151823630	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.117000	0.94347	2.608000	0.88229	0.650000	0.86243	TGG	.		0.343	SELT-005	PUTATIVE	alternative_5_UTR|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000357629.1		
DNAH11	8701	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	7	21630880	21630880	+	Silent	SNP	G	G	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr7:21630880G>A	ENST00000409508.3	+	14	2383	c.2352G>A	c.(2350-2352)ctG>ctA	p.L784L	DNAH11_ENST00000328843.6_Silent_p.L784L	NM_001277115.1	NP_001264044.1	Q96DT5	DYH11_HUMAN	dynein, axonemal, heavy chain 11	784	Stem. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(1)|autonomic_ganglia(1)|breast(13)|central_nervous_system(3)|cervix(4)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(50)|lung(101)|ovary(10)|pancreas(4)|prostate(7)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	230						AATACCCTCTGATTGAAGATG	0.493									Kartagener syndrome																												.		.											.	.	.	0			.						.						51.0	52.0	52.0					7																	21630880		1929	4131	6060	SO:0001819	synonymous_variant	8701	p.L784L	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	CCCTCTGATTGAA	U83569	CCDS64602.1	7p21	2008-07-18	2006-09-04					"""Axonemal dyneins"""	2942	protein-coding gene	gene with protein product	"""dynein, ciliary, heavy chain 11"", ""dynein, heavy chain beta-like"""	603339	"""dynein, axonemal, heavy polypeptide 11"""			9256245	Standard	NM_001277115		Approved	Dnahc11, DPL11, CILD7, DNAHC11, DNAHBL, DNHBL	uc031swp.1	Q96DT5		ENST00000409508.3:c.2352G>A	7.37:g.21630880G>A		Somatic	71	0		WXS	Illumina HiSeq	Phase_I	31	16	.	Q9UJ82	Silent	SNP	ENST00000409508.3	37																																																																																				.		0.493	DNAH11-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000326582.6	NM_003777	
MEST	4232	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	7	130147634	130147634	+	IGR	SNP	G	G	A			TCGA-W5-AA39-01A-11D-A417-09	TCGA-W5-AA39-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad952427-a9f6-4d9e-9f93-1145909c4a7a	6aa737b3-0e89-415b-b64f-2a66b3a847fc	g.chr7:130147634G>A	ENST00000223215.4	+	0	2465				RP11-2E11.9_ENST00000604965.1_RNA	NM_001253900.1|NM_002402.3	NP_001240829.1|NP_002393.2	Q5EB52	MEST_HUMAN	mesoderm specific transcript						mesoderm development (GO:0007498)|regulation of lipid storage (GO:0010883)|response to retinoic acid (GO:0032526)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	hydrolase activity (GO:0016787)			breast(1)|endometrium(2)|large_intestine(3)|lung(4)|ovary(2)	12	Melanoma(18;0.0435)					TTCTGAATATGGTCAGACACA	0.428																																					.	Colon(126;2182 2305 6517 35181)	.											.	.	.	0			.						.						116.0	110.0	112.0					7																	130147634		1906	4125	6031	SO:0001628	intergenic_variant	26958	p.H44Y			GAATATGGTCAGA		CCDS5822.1, CCDS5823.1, CCDS59081.1	7q32	2014-08-22	2012-12-07		ENSG00000106484	ENSG00000106484			7028	protein-coding gene	gene with protein product	"""Paternally-expressed gene 1"""	601029	"""mesoderm specific transcript (mouse) homolog"", ""mesoderm specific transcript homolog (mouse)"""			8884280	Standard	NM_002402		Approved	PEG1	uc003vqg.3	Q5EB52	OTTHUMG00000156661		7.37:g.130147634G>A		Somatic	29	0		WXS	Illumina HiSeq	Phase_I	16	6	.	B2R6S1|O14973|O15007|Q6AI49|Q92571	Missense_Mutation	SNP	ENST00000223215.4	37	CCDS5822.1																																																																																			.		0.428	MEST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345183.2	NM_002402	
