#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_ACHILLES_Lineage_Results_Top_Genes	i_BAM_File	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_ORegAnno_bin	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_ccds_id	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_type	i_havana_transcript	i_refseq_mrna_id	i_secondary_variant_classification
CUBN	8029	broad.mit.edu;hgsc.bcm.edu;ucsc.edu;mdanderson.org	37	10	16967262	16967262	+	Silent	SNP	G	G	A			TCGA-KL-8323-01A-21D-2310-10	TCGA-KL-8323-11A-01D-2310-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fae88d21-171c-4df4-b258-3c5948a1034b	f5c7fb67-5906-4db0-ad0d-129df8e065cb	g.chr10:16967262G>A	ENST00000377833.4	-	43	6689	c.6624C>T	c.(6622-6624)atC>atT	p.I2208I		NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	2208	CUB 15. {ECO:0000255|PROSITE- ProRule:PRU00059}.				cholesterol metabolic process (GO:0008203)|cobalamin metabolic process (GO:0009235)|cobalamin transport (GO:0015889)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|tissue homeostasis (GO:0001894)|vitamin D metabolic process (GO:0042359)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|Golgi apparatus (GO:0005794)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|cobalamin binding (GO:0031419)|protein homodimerization activity (GO:0042803)|receptor activity (GO:0004872)|transporter activity (GO:0005215)			breast(8)|central_nervous_system(4)|cervix(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(42)|liver(1)|lung(107)|ovary(9)|pancreas(2)|prostate(3)|skin(9)|stomach(3)|upper_aerodigestive_tract(11)|urinary_tract(8)	241					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	CCTCATATTTGATTTTAAATC	0.328																																						.											0													60.0	61.0	60.0					10																	16967262		2203	4300	6503	SO:0001819	synonymous_variant	8029			AF034611	CCDS7113.1	10p12	2014-09-17			ENSG00000107611	ENSG00000107611			2548	protein-coding gene	gene with protein product		602997		MGA1		9572993, 9478979	Standard	NM_001081		Approved	IFCR, gp280	uc001ioo.3	O60494	OTTHUMG00000017741	ENST00000377833.4:c.6624C>T	10.37:g.16967262G>A			B0YIZ4|Q5VTA6|Q96RU9	Silent	SNP	ENST00000377833.4	37	CCDS7113.1																																																																																				0.328	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	NM_001081	
PTEN	5728	broad.mit.edu;hgsc.bcm.edu;mdanderson.org;bcgsc.ca	37	10	89711966	89711966	+	Missense_Mutation	SNP	T	T	C			TCGA-KL-8323-01A-21D-2310-10	TCGA-KL-8323-11A-01D-2310-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fae88d21-171c-4df4-b258-3c5948a1034b	f5c7fb67-5906-4db0-ad0d-129df8e065cb	g.chr10:89711966T>C	ENST00000371953.3	+	6	1941	c.584T>C	c.(583-585)tTt>tCt	p.F195S	PTEN_ENST00000472832.1_3'UTR	NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog	195	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.R55fs*1(5)|p.?(4)|p.G165fs*9(3)|p.Y27fs*1(2)|p.G165_*404del(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)		GCACTGTTGTTTCACAAGATG	0.398		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)																												.	yes	Rec	yes	"""Cowden Syndrome, Bannayan-Riley-Ruvalcaba syndrome"""	10	10q23.3	5728	phosphatase and tensin homolog gene		"""L, E, M, O"""	52	Whole gene deletion(37)|Deletion - Frameshift(10)|Unknown(4)|Deletion - In frame(1)	prostate(16)|central_nervous_system(13)|skin(8)|lung(4)|haematopoietic_and_lymphoid_tissue(3)|breast(3)|ovary(3)|soft_tissue(1)|urinary_tract(1)											154.0	152.0	153.0					10																	89711966		2203	4300	6503	SO:0001583	missense	5728	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.	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.584T>C	10.37:g.89711966T>C	ENSP00000361021:p.Phe195Ser		B2R904|F2YHV0|O00633|O02679|Q6ICT7	Missense_Mutation	SNP	ENST00000371953.3	37	CCDS31238.1	.	.	.	.	.	.	.	.	.	.	T	32	5.149283	0.94645	.	.	ENSG00000171862	ENST00000371953	D	0.85411	-1.98	5.85	5.85	0.93711	Tensin phosphatase, C2 domain (2);C2 calcium/lipid-binding domain, CaLB (1);	0.092703	0.85682	D	0.000000	D	0.90366	0.6985	L	0.60455	1.87	0.80722	D	1	D	0.76494	0.999	D	0.68483	0.958	D	0.89873	0.4024	9	.	.	.	-4.4487	16.2416	0.82411	0.0:0.0:0.0:1.0	.	195	P60484	PTEN_HUMAN	S	195	ENSP00000361021:F195S	.	F	+	2	0	PTEN	89701946	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.615000	0.83006	2.241000	0.73720	0.477000	0.44152	TTT		0.398	PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049241.1	NM_000314	
RASAL2	9462	hgsc.bcm.edu	37	1	178421771	178421771	+	Silent	SNP	C	C	T			TCGA-KL-8323-01A-21D-2310-10	TCGA-KL-8323-11A-01D-2310-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fae88d21-171c-4df4-b258-3c5948a1034b	f5c7fb67-5906-4db0-ad0d-129df8e065cb	g.chr1:178421771C>T	ENST00000462775.1	+	9	1674	c.1549C>T	c.(1549-1551)Ctg>Ttg	p.L517L	RASAL2_ENST00000367649.3_Silent_p.L665L|RASAL2_ENST00000448150.3_Silent_p.L647L	NM_004841.3	NP_004832.1	Q9UJF2	NGAP_HUMAN	RAS protein activator like 2	517	Ras-GAP. {ECO:0000255|PROSITE- ProRule:PRU00167}.				negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of Ras GTPase activity (GO:0032320)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)	Ras GTPase activator activity (GO:0005099)			biliary_tract(1)|breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(2)|lung(25)|ovary(2)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	54						CATTCAGAACCTGGCCAACTT	0.433																																						.											0													117.0	107.0	110.0					1																	178421771		2203	4299	6502	SO:0001819	synonymous_variant	9462			AF047711	CCDS1321.1, CCDS1322.1, CCDS1321.2	1q25	2013-01-10			ENSG00000075391	ENSG00000075391		"""Pleckstrin homology (PH) domain containing"""	9874	protein-coding gene	gene with protein product	"""Ras GTPase activating protein-like"", ""Ras protein activator like 1"""	606136				9877179	Standard	NM_004841		Approved	nGAP	uc001glq.3	Q9UJF2	OTTHUMG00000035022	ENST00000462775.1:c.1549C>T	1.37:g.178421771C>T			F8W755|O95174|Q2TB22|Q5TFU9	Silent	SNP	ENST00000462775.1	37	CCDS1322.1	.	.	.	.	.	.	.	.	.	.	C	8.494	0.862639	0.17178	.	.	ENSG00000075391	ENST00000433130	.	.	.	5.15	3.29	0.37713	.	.	.	.	.	T	0.59293	0.2183	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.53351	-0.8451	4	.	.	.	.	9.6673	0.39992	0.0:0.7753:0.0:0.2247	.	.	.	.	L	67	.	.	P	+	2	0	RASAL2	176688394	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.876000	0.63079	0.567000	0.29293	0.557000	0.71058	CCT		0.433	RASAL2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000084758.3	NM_170692	
OBSCN	84033	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	1	228548164	228548164	+	Intron	SNP	G	G	A			TCGA-KL-8323-01A-21D-2310-10	TCGA-KL-8323-11A-01D-2310-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fae88d21-171c-4df4-b258-3c5948a1034b	f5c7fb67-5906-4db0-ad0d-129df8e065cb	g.chr1:228548164G>A	ENST00000422127.1	+	80	18705				OBSCN_ENST00000366709.4_Missense_Mutation_p.R3643Q|OBSCN_ENST00000284548.11_Missense_Mutation_p.R6524Q|OBSCN_ENST00000366707.4_Intron|OBSCN_ENST00000570156.2_Intron	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF						apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				CTGGGTCCCCGAGGCCCTCTC	0.692																																						.											0													16.0	20.0	19.0					1																	228548164		1950	4134	6084	SO:0001627	intron_variant	84033			AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.18662-2113G>A	1.37:g.228548164G>A			Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Missense_Mutation	SNP	ENST00000422127.1	37	CCDS58065.1	.	.	.	.	.	.	.	.	.	.	G	17.77	3.471288	0.63625	.	.	ENSG00000154358	ENST00000284548;ENST00000366709	T;T	0.55760	0.5;0.65	4.06	0.729	0.18266	.	.	.	.	.	T	0.33990	0.0882	L	0.56769	1.78	0.09310	N	1	P	0.43633	0.813	B	0.31101	0.124	T	0.18967	-1.0320	9	0.19147	T	0.46	.	2.2287	0.03991	0.2401:0.0:0.2551:0.5048	.	6524	Q5VST9-3	.	Q	6524;3643	ENSP00000284548:R6524Q;ENSP00000355670:R3643Q	ENSP00000284548:R6524Q	R	+	2	0	OBSCN	226614787	0.001000	0.12720	0.000000	0.03702	0.021000	0.10359	1.314000	0.33597	0.340000	0.23745	-0.293000	0.09583	CGA		0.692	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
MESDC1	59274	broad.mit.edu;hgsc.bcm.edu;ucsc.edu;mdanderson.org	37	15	81295653	81295653	+	Silent	SNP	G	G	A	rs527572667		TCGA-KL-8323-01A-21D-2310-10	TCGA-KL-8323-11A-01D-2310-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fae88d21-171c-4df4-b258-3c5948a1034b	f5c7fb67-5906-4db0-ad0d-129df8e065cb	g.chr15:81295653G>A	ENST00000267984.2	+	1	2359	c.1041G>A	c.(1039-1041)agG>agA	p.R347R		NM_022566.2	NP_072088.1	Q9H1K6	MESD1_HUMAN	mesoderm development candidate 1	347										endometrium(1)|lung(2)	3						TAAGGGAGAGGTCTTCGCCCA	0.567																																						.											0													17.0	23.0	21.0					15																	81295653		2136	4266	6402	SO:0001819	synonymous_variant	59274			AY007810	CCDS10316.1	15q13	2008-07-18			ENSG00000140406	ENSG00000140406			13519	protein-coding gene	gene with protein product		615466				11247670	Standard	NM_022566		Approved	MGC99595	uc002bfz.3	Q9H1K6	OTTHUMG00000144185	ENST00000267984.2:c.1041G>A	15.37:g.81295653G>A				Silent	SNP	ENST00000267984.2	37	CCDS10316.1																																																																																				0.567	MESDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000291390.1	NM_022566	
NTRK3	4916	broad.mit.edu;hgsc.bcm.edu;ucsc.edu;mdanderson.org	37	15	88727494	88727494	+	Silent	SNP	G	G	A	rs536176882		TCGA-KL-8323-01A-21D-2310-10	TCGA-KL-8323-11A-01D-2310-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fae88d21-171c-4df4-b258-3c5948a1034b	f5c7fb67-5906-4db0-ad0d-129df8e065cb	g.chr15:88727494G>A	ENST00000360948.2	-	3	446	c.285C>T	c.(283-285)aaC>aaT	p.N95N	NTRK3_ENST00000357724.2_Silent_p.N95N|NTRK3_ENST00000394480.2_Silent_p.N95N|NTRK3_ENST00000540489.2_Silent_p.N95N|NTRK3_ENST00000558676.1_Silent_p.N95N|NTRK3_ENST00000542733.2_De_novo_Start_OutOfFrame|NTRK3_ENST00000557856.1_Silent_p.N95N|NTRK3_ENST00000355254.2_Silent_p.N95N|NTRK3_ENST00000317501.3_Silent_p.N95N	NM_001012338.2	NP_001012338.1	Q16288	NTRK3_HUMAN	neurotrophic tyrosine kinase, receptor, type 3	95					activation of MAPK activity (GO:0000187)|activation of protein kinase B activity (GO:0032148)|activation of Ras GTPase activity (GO:0032856)|cellular response to retinoic acid (GO:0071300)|circadian rhythm (GO:0007623)|cochlea development (GO:0090102)|lens fiber cell differentiation (GO:0070306)|mechanoreceptor differentiation (GO:0042490)|modulation by virus of host transcription (GO:0019056)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of cell death (GO:0060548)|negative regulation of protein phosphorylation (GO:0001933)|neuron fate specification (GO:0048665)|neuron migration (GO:0001764)|neurotrophin signaling pathway (GO:0038179)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of axon extension involved in regeneration (GO:0048691)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of positive chemotaxis (GO:0050927)|protein autophosphorylation (GO:0046777)|response to axon injury (GO:0048678)|response to corticosterone (GO:0051412)|response to ethanol (GO:0045471)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|neurotrophin binding (GO:0043121)|neurotrophin receptor activity (GO:0005030)|p53 binding (GO:0002039)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)		ETV6/NTRK3(238)	breast(3)|central_nervous_system(3)|endometrium(6)|kidney(1)|large_intestine(22)|lung(63)|ovary(6)|pancreas(3)|prostate(1)|skin(4)|stomach(5)|upper_aerodigestive_tract(2)	119			BRCA - Breast invasive adenocarcinoma(143;0.211)			TGTCCACGGCGTTGAGCGTGT	0.577			T	ETV6	"""congenital fibrosarcoma, Secretory breast """					TSP Lung(13;0.10)			G|||	1	0.000199681	0.0	0.0	5008	,	,		14678	0.0		0.0	False		,,,				2504	0.001					.		Dom	yes		15	15q25	4916	"""neurotrophic tyrosine kinase, receptor, type 3"""		"""E, M"""	0													106.0	78.0	87.0					15																	88727494		2201	4299	6500	SO:0001819	synonymous_variant	4916			U05012	CCDS10340.1, CCDS32322.1, CCDS32323.1, CCDS58399.1	15q24-q25	2013-01-11			ENSG00000140538	ENSG00000140538	2.7.10.1	"""Immunoglobulin superfamily / I-set domain containing"""	8033	protein-coding gene	gene with protein product		191316				7806211	Standard	NM_001012338		Approved	TRKC	uc002bme.2	Q16288	OTTHUMG00000148677	ENST00000360948.2:c.285C>T	15.37:g.88727494G>A			B7Z4C5|E9PG56|H0YND1|O75682|Q12827|Q16289	Silent	SNP	ENST00000360948.2	37	CCDS32322.1																																																																																				0.577	NTRK3-204	KNOWN	basic|CCDS	protein_coding	protein_coding			
ZNF469	84627	broad.mit.edu;hgsc.bcm.edu;ucsc.edu;mdanderson.org;bcgsc.ca	37	16	88499219	88499219	+	Missense_Mutation	SNP	G	G	A	rs555047442		TCGA-KL-8323-01A-21D-2310-10	TCGA-KL-8323-11A-01D-2310-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fae88d21-171c-4df4-b258-3c5948a1034b	f5c7fb67-5906-4db0-ad0d-129df8e065cb	g.chr16:88499219G>A	ENST00000437464.1	+	2	5257	c.5257G>A	c.(5257-5259)Ggc>Agc	p.G1753S	ZNF469_ENST00000565624.1_Missense_Mutation_p.G1781S	NM_001127464.1	NP_001120936.1	Q96JG9	ZN469_HUMAN	zinc finger protein 469	1753					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(4)|endometrium(6)|kidney(3)|large_intestine(1)|skin(6)	20						CCCAGAGCCCGGCACAGCAGA	0.607													g|||	1	0.000199681	0.0	0.0	5008	,	,		15399	0.001		0.0	False		,,,				2504	0.0					.											0													25.0	23.0	24.0					16																	88499219		692	1591	2283	SO:0001583	missense	84627			AB058761	CCDS45544.1	16q24	2010-08-04				ENSG00000225614		"""Zinc fingers, C2H2-type"""	23216	protein-coding gene	gene with protein product		612078				11347906	Standard	NM_001127464		Approved	KIAA1858	uc002fku.2	Q96JG9		ENST00000437464.1:c.5257G>A	16.37:g.88499219G>A	ENSP00000402343:p.Gly1753Ser			Missense_Mutation	SNP	ENST00000437464.1	37	CCDS45544.1	.	.	.	.	.	.	.	.	.	.	g	12.11	1.840354	0.32513	.	.	ENSG00000225614	ENST00000437464	T	0.05580	3.42	3.9	-6.73	0.01749	.	.	.	.	.	T	0.01976	0.0062	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.45116	-0.9283	9	0.12430	T	0.62	.	0.3706	0.00379	0.3478:0.1867:0.2467:0.2188	.	1753	Q96JG9	ZN469_HUMAN	S	1753	ENSP00000402343:G1753S	ENSP00000402343:G1753S	G	+	1	0	ZNF469	87026720	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.043000	0.03535	-2.050000	0.00905	-2.017000	0.00434	GGC		0.607	ZNF469-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NG_012236	
TNFSF13	8741	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	17	7462433	7462433	+	Missense_Mutation	SNP	C	C	T			TCGA-KL-8323-01A-21D-2310-10	TCGA-KL-8323-11A-01D-2310-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fae88d21-171c-4df4-b258-3c5948a1034b	f5c7fb67-5906-4db0-ad0d-129df8e065cb	g.chr17:7462433C>T	ENST00000338784.4	+	1	520	c.77C>T	c.(76-78)gCa>gTa	p.A26V	TNFSF13_ENST00000483039.1_Intron|TNFSF13_ENST00000349228.4_Missense_Mutation_p.A26V|TNFSF12-TNFSF13_ENST00000293826.4_Intron|TNFSF13_ENST00000380535.4_Missense_Mutation_p.A26V|SENP3_ENST00000321337.7_5'Flank|TNFSF13_ENST00000396545.4_Missense_Mutation_p.A26V|TNFSF12_ENST00000557233.1_Intron|TNFSF13_ENST00000396542.1_Missense_Mutation_p.A9V	NM_003808.3	NP_003799.1	O75888	TNF13_HUMAN	tumor necrosis factor (ligand) superfamily, member 13	26					gene expression (GO:0010467)|immunoglobulin production in mucosal tissue (GO:0002426)|mRNA metabolic process (GO:0016071)|positive regulation of cell proliferation (GO:0008284)|positive regulation of germinal center formation (GO:0002636)|positive regulation of isotype switching to IgA isotypes (GO:0048298)|RNA metabolic process (GO:0016070)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)	receptor binding (GO:0005102)			large_intestine(2)|lung(2)|skin(1)	5		Prostate(122;0.157)				AGAGAGCCGGCACTCTCAGTT	0.632																																						.											0													25.0	29.0	28.0					17																	7462433		2195	4289	6484	SO:0001583	missense	8741			AF046888	CCDS11111.1, CCDS11112.1, CCDS42256.1, CCDS56019.1, CCDS73957.1	17p13.1	2007-07-23			ENSG00000161955	ENSG00000161955		"""Tumor necrosis factor (ligand) superfamily"", ""CD molecules"""	11928	protein-coding gene	gene with protein product		604472				9743536	Standard	NM_172088		Approved	APRIL, CD256		O75888	OTTHUMG00000108145	ENST00000338784.4:c.77C>T	17.37:g.7462433C>T	ENSP00000343505:p.Ala26Val		A8MYD5|B4DVT2|Q541E1|Q5U0G8|Q96HV6|Q9P1M8|Q9P1M9	Missense_Mutation	SNP	ENST00000338784.4	37	CCDS11111.1	.	.	.	.	.	.	.	.	.	.	C	19.07	3.756550	0.69648	.	.	ENSG00000161955	ENST00000396542;ENST00000438470;ENST00000436057;ENST00000349228;ENST00000338784;ENST00000380535;ENST00000396545	D;T;T;D;D;D;D	0.98914	-5.18;0.9;0.9;-4.48;-4.29;-5.23;-4.3	5.17	4.18	0.49190	.	.	.	.	.	D	0.98738	0.9576	M	0.66939	2.045	0.33660	D	0.609558	D;D;D;D;D	0.71674	0.997;0.997;0.996;0.997;0.998	D;D;D;D;D	0.80764	0.985;0.985;0.99;0.985;0.994	D	0.99954	1.1603	9	0.72032	D	0.01	.	11.951	0.52954	0.0:0.8246:0.1754:0.0	.	26;26;26;26;26	B4DVT2;Q2QBA2;O75888-2;O75888;O75888-3	.;.;.;TNF13_HUMAN;.	V	9;9;9;26;26;26;26	ENSP00000379792:A9V;ENSP00000390771:A9V;ENSP00000410094:A9V;ENSP00000314455:A26V;ENSP00000343505:A26V;ENSP00000369908:A26V;ENSP00000379794:A26V	ENSP00000343505:A26V	A	+	2	0	TNFSF13	7403157	0.961000	0.32948	1.000000	0.80357	0.960000	0.62799	3.662000	0.54510	1.272000	0.44329	0.655000	0.94253	GCA		0.632	TNFSF13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000226948.2	NM_003808	
CACNA1A	773	broad.mit.edu;hgsc.bcm.edu;mdanderson.org;bcgsc.ca	37	19	13476272	13476272	+	Missense_Mutation	SNP	C	C	T			TCGA-KL-8323-01A-21D-2310-10	TCGA-KL-8323-11A-01D-2310-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fae88d21-171c-4df4-b258-3c5948a1034b	f5c7fb67-5906-4db0-ad0d-129df8e065cb	g.chr19:13476272C>T	ENST00000360228.5	-	5	642	c.643G>A	c.(643-645)Gtc>Atc	p.V215I	CACNA1A_ENST00000573710.2_Missense_Mutation_p.V215I	NM_000068.3|NM_001127222.1|NM_001174080.1|NM_023035.2	NP_000059.3|NP_001120694.1|NP_001167551.1|NP_075461.2	O00555	CAC1A_HUMAN	calcium channel, voltage-dependent, P/Q type, alpha 1A subunit	215					adult walking behavior (GO:0007628)|behavioral response to pain (GO:0048266)|calcium ion import (GO:0070509)|calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|cell death (GO:0008219)|cell growth (GO:0016049)|cellular chloride ion homeostasis (GO:0030644)|cerebellar molecular layer development (GO:0021679)|cerebellar Purkinje cell differentiation (GO:0021702)|cerebellum maturation (GO:0021590)|dendrite morphogenesis (GO:0048813)|energy reserve metabolic process (GO:0006112)|gamma-aminobutyric acid secretion (GO:0014051)|gamma-aminobutyric acid signaling pathway (GO:0007214)|glucose metabolic process (GO:0006006)|hormone metabolic process (GO:0042445)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|musculoskeletal movement, spinal reflex action (GO:0050883)|negative regulation of hormone biosynthetic process (GO:0032353)|negative regulation of neuron apoptotic process (GO:0043524)|neuromuscular process controlling balance (GO:0050885)|neuromuscular synaptic transmission (GO:0007274)|neurotransmitter metabolic process (GO:0042133)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|receptor clustering (GO:0043113)|regulation of acetylcholine secretion, neurotransmission (GO:0014056)|regulation of axonogenesis (GO:0050770)|regulation of calcium ion-dependent exocytosis (GO:0017158)|regulation of insulin secretion (GO:0050796)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|spinal cord motor neuron differentiation (GO:0021522)|sulfur amino acid metabolic process (GO:0000096)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transmission of nerve impulse (GO:0019226)|vestibular nucleus development (GO:0021750)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|syntaxin binding (GO:0019905)|voltage-gated calcium channel activity (GO:0005245)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(25)|prostate(2)|urinary_tract(1)	42			OV - Ovarian serous cystadenocarcinoma(19;5.07e-21)		Bepridil(DB01244)|Loperamide(DB00836)|Pregabalin(DB00230)|Spironolactone(DB00421)|Verapamil(DB00661)	GACTTCAGGACGACTTGTAAA	0.502																																						.											0													47.0	47.0	47.0					19																	13476272		1920	4135	6055	SO:0001583	missense	773			U79666	CCDS45998.1, CCDS45999.1	19p13	2014-09-17			ENSG00000141837	ENSG00000141837		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1388	protein-coding gene	gene with protein product		601011		CACNL1A4, SCA6, MHP1, MHP		8825650, 16382099, 23827678	Standard	NM_000068		Approved	Cav2.1, EA2, APCA, HPCA, FHM	uc010xne.2	O00555	OTTHUMG00000044590	ENST00000360228.5:c.643G>A	19.37:g.13476272C>T	ENSP00000353362:p.Val215Ile		J3KP41|P78510|P78511|Q16290|Q92690|Q99790|Q99791|Q99792|Q99793|Q9NS88|Q9UDC4	Missense_Mutation	SNP	ENST00000360228.5	37	CCDS45998.1	.	.	.	.	.	.	.	.	.	.	C	18.49	3.636162	0.67130	.	.	ENSG00000141837	ENST00000360228;ENST00000418012;ENST00000357018;ENST00000325084	D	0.98381	-4.9	5.55	4.52	0.55395	Ion transport (1);	0.000000	0.64402	D	0.000001	D	0.97303	0.9118	L	0.57536	1.79	0.46356	D	0.999	P;D	0.58268	0.951;0.982	B;P	0.47941	0.32;0.562	D	0.96952	0.9695	10	0.72032	D	0.01	.	13.3098	0.60374	0.0:0.9229:0.0:0.0771	.	215;215	O00555;Q9NS88	CAC1A_HUMAN;.	I	215	ENSP00000353362:V215I	ENSP00000317661:V215I	V	-	1	0	CACNA1A	13337272	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.585000	0.82584	1.347000	0.45714	-0.136000	0.14681	GTC		0.502	CACNA1A-001	KNOWN	non_canonical_U12|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000104062.2	NM_000068	
WDR62	284403	broad.mit.edu;hgsc.bcm.edu	37	19	36558850	36558851	+	Frame_Shift_Ins	INS	-	-	AC			TCGA-KL-8323-01A-21D-2310-10	TCGA-KL-8323-11A-01D-2310-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fae88d21-171c-4df4-b258-3c5948a1034b	f5c7fb67-5906-4db0-ad0d-129df8e065cb	g.chr19:36558850_36558851insAC	ENST00000270301.7	+	7	820_821	c.820_821insAC	c.(820-822)tacfs	p.Y274fs	WDR62_ENST00000401500.2_Frame_Shift_Ins_p.Y274fs|WDR62_ENST00000388999.3_Frame_Shift_Ins_p.Y274fs|WDR62_ENST00000378860.4_3'UTR			O43379	WDR62_HUMAN	WD repeat domain 62	274					cerebral cortex development (GO:0021987)|neurogenesis (GO:0022008)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|spindle pole (GO:0000922)				cervix(1)|endometrium(8)|kidney(2)|large_intestine(8)|lung(15)|prostate(4)|stomach(2)|urinary_tract(3)	43	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.06)			CTGTGTGTCCTACTCGGGCCTC	0.599																																						.											0																																										SO:0001589	frameshift_variant	284403			BX647726	CCDS33001.1, CCDS46059.1	19q13.12	2013-01-09	2005-05-09	2005-05-09	ENSG00000075702	ENSG00000075702		"""WD repeat domain containing"""	24502	protein-coding gene	gene with protein product		613583	"""chromosome 19 open reading frame 14"", ""microcephaly, primary autosomal recessive 2"""	C19orf14, MCPH2		19910486, 20729831, 20890278, 21496009	Standard	NM_001083961		Approved	DKFZP434J046, FLJ33298	uc002odd.2	O43379	OTTHUMG00000048139	ENST00000270301.7:c.821_822dupAC	19.37:g.36558851_36558852dupAC	ENSP00000270301:p.Tyr274fs		Q63HP9|Q659D7|Q8NBF7|Q96AD9	Frame_Shift_Ins	INS	ENST00000270301.7	37	CCDS33001.1																																																																																				0.599	WDR62-006	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000457436.1	NM_015671	
GPR27	2850	broad.mit.edu;hgsc.bcm.edu;mdanderson.org;bcgsc.ca	37	3	71804279	71804279	+	Missense_Mutation	SNP	G	G	A			TCGA-KL-8323-01A-21D-2310-10	TCGA-KL-8323-11A-01D-2310-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fae88d21-171c-4df4-b258-3c5948a1034b	f5c7fb67-5906-4db0-ad0d-129df8e065cb	g.chr3:71804279G>A	ENST00000304411.2	+	1	1079	c.1079G>A	c.(1078-1080)cGg>cAg	p.R360Q	EIF4E3_ENST00000421769.2_5'Flank|EIF4E3_ENST00000448225.1_5'Flank|EIF4E3_ENST00000295612.3_5'Flank	NM_018971.1	NP_061844.1	Q9NS67	GPR27_HUMAN	G protein-coupled receptor 27	360					signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			kidney(1)|lung(2)|ovary(1)|prostate(1)	5		Prostate(10;0.00899)		BRCA - Breast invasive adenocarcinoma(55;1.78e-05)|Epithelial(33;5.75e-05)|Lung(16;0.0012)|LUSC - Lung squamous cell carcinoma(21;0.00156)		CAGAGCCCCCGGACCACCCAG	0.642																																						.											0													12.0	12.0	12.0					3																	71804279		2103	4141	6244	SO:0001583	missense	2850			AB040799	CCDS2915.1	3p21-p14	2012-08-21			ENSG00000170837	ENSG00000170837		"""GPCR / Class A : Orphans"""	4482	protein-coding gene	gene with protein product		605187				10833454	Standard	NM_018971		Approved	SREB1	uc011bge.2	Q9NS67	OTTHUMG00000158810	ENST00000304411.2:c.1079G>A	3.37:g.71804279G>A	ENSP00000303149:p.Arg360Gln			Missense_Mutation	SNP	ENST00000304411.2	37	CCDS2915.1	.	.	.	.	.	.	.	.	.	.	G	5.821	0.335788	0.11013	.	.	ENSG00000170837	ENST00000304411	T	0.38077	1.16	4.71	-0.255	0.12988	.	0.263235	0.31167	N	0.008121	T	0.12475	0.0303	N	0.04508	-0.205	0.22975	N	0.998484	B	0.06786	0.001	B	0.04013	0.001	T	0.33317	-0.9873	10	0.07482	T	0.82	-4.752	8.3324	0.32195	0.6664:0.0:0.3336:0.0	.	360	Q9NS67	GPR27_HUMAN	Q	360	ENSP00000303149:R360Q	ENSP00000303149:R360Q	R	+	2	0	GPR27	71886969	.	.	0.985000	0.45067	0.974000	0.67602	.	.	-0.052000	0.13311	-0.384000	0.06662	CGG		0.642	GPR27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352303.1	NM_018971	
POU5F2	134187	broad.mit.edu;hgsc.bcm.edu;mdanderson.org;bcgsc.ca	37	5	93076393	93076393	+	Missense_Mutation	SNP	G	G	C			TCGA-KL-8323-01A-21D-2310-10	TCGA-KL-8323-11A-01D-2310-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fae88d21-171c-4df4-b258-3c5948a1034b	f5c7fb67-5906-4db0-ad0d-129df8e065cb	g.chr5:93076393G>C	ENST00000510627.4	-	1	950	c.877C>G	c.(877-879)Cac>Gac	p.H293D	FAM172A_ENST00000395965.3_Intron|FAM172A_ENST00000509163.1_Intron|FAM172A_ENST00000509739.1_Intron|FAM172A_ENST00000505869.1_Intron|RP11-185E12.2_ENST00000606528.1_RNA|POU5F2_ENST00000606183.1_5'UTR	NM_153216.1	NP_694948.1	Q8N7G0	PO5F2_HUMAN	POU domain class 5, transcription factor 2	293					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)						all_cancers(142;3.87e-05)|all_epithelial(76;4.59e-07)|all_lung(232;0.0126)|Lung NSC(167;0.0155)|Ovarian(174;0.0218)|Prostate(281;0.173)|Colorectal(57;0.19)		UCEC - Uterine corpus endometrioid carcinoma (5;0.0415)|all cancers(79;2.03e-19)		AGTCCCAGGTGAAAGCACACT	0.617																																						.											0													35.0	39.0	38.0					5																	93076393		1920	4110	6030	SO:0001583	missense	134187				CCDS59489.1	5q15	2011-06-20				ENSG00000248483		"""Homeoboxes / POU class"""	26367	protein-coding gene	gene with protein product						7908264	Standard	NM_153216		Approved	SPRM-1, FLJ25680	uc003kkl.1	Q8N7G0		ENST00000510627.4:c.877C>G	5.37:g.93076393G>C	ENSP00000464890:p.His293Asp		Q15169|Q6MZL7|Q8N748	Missense_Mutation	SNP	ENST00000510627.4	37	CCDS59489.1																																																																																				0.617	POU5F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369873.5	NM_153216	
ASIC3	9311	broad.mit.edu;hgsc.bcm.edu	37	7	150746017	150746017	+	Silent	SNP	G	G	A	rs369122567		TCGA-KL-8323-01A-21D-2310-10	TCGA-KL-8323-11A-01D-2310-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fae88d21-171c-4df4-b258-3c5948a1034b	f5c7fb67-5906-4db0-ad0d-129df8e065cb	g.chr7:150746017G>A	ENST00000349064.5	+	1	243	c.45G>A	c.(43-45)tcG>tcA	p.S15S	ASIC3_ENST00000357922.4_Silent_p.S15S|ASIC3_ENST00000297512.8_Silent_p.S15S	NM_004769.3|NM_020321.3	NP_004760.1|NP_064717.1	Q9UHC3	ASIC3_HUMAN	acid-sensing (proton-gated) ion channel 3	15					cation transmembrane transport (GO:0098655)|detection of chemical stimulus involved in sensory perception of pain (GO:0050968)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|detection of temperature stimulus involved in sensory perception of pain (GO:0050965)|ion transmembrane transport (GO:0034220)|response to acid chemical (GO:0001101)|response to acidic pH (GO:0010447)|response to heat (GO:0009408)|sensory perception (GO:0007600)|sensory perception of sour taste (GO:0050915)|signal transduction (GO:0007165)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cation channel activity (GO:0005261)|enterobactin transporter activity (GO:0042931)|ligand-gated sodium channel activity (GO:0015280)|sodium channel activity (GO:0005272)										GGCCAGCCTCGGACATCCGCG	0.687																																						.											0								G	,,	0,4404		0,0,2202	33.0	42.0	39.0		45,45,45	-5.2	0.7	7		39	1,8589		0,1,4294	no	coding-synonymous,coding-synonymous,coding-synonymous	ACCN3	NM_004769.2,NM_020321.2,NM_020322.2	,,	0,1,6496	AA,AG,GG		0.0116,0.0,0.0077	,,	15/532,15/550,15/544	150746017	1,12993	2202	4295	6497	SO:0001819	synonymous_variant	9311			AB010575	CCDS5914.1, CCDS5915.1, CCDS5916.1	7q35	2012-02-23	2012-02-22	2012-02-22	ENSG00000213199	ENSG00000213199		"""Ion channels / Acid-sensing (proton-gated) ion channels"""	101	protein-coding gene	gene with protein product	"""testis sodium channel 1"""	611741	"""amiloride-sensitive cation channel 3, testis"", ""amiloride-sensitive cation channel 3"""	ACCN3		9571199, 9744806	Standard	NM_004769		Approved	TNaC1, DRASIC	uc003wio.3	Q9UHC3	OTTHUMG00000158685	ENST00000349064.5:c.45G>A	7.37:g.150746017G>A			B2R9V0|O60263|O75906|Q59FN9|Q9UER8|Q9UHC4	Silent	SNP	ENST00000349064.5	37	CCDS5916.1																																																																																				0.687	ASIC3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351725.1	NM_004769	
PTPRN2	5799	broad.mit.edu;hgsc.bcm.edu;ucsc.edu;mdanderson.org;bcgsc.ca	37	7	157931202	157931202	+	Missense_Mutation	SNP	G	G	A	rs370624864		TCGA-KL-8323-01A-21D-2310-10	TCGA-KL-8323-11A-01D-2310-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fae88d21-171c-4df4-b258-3c5948a1034b	f5c7fb67-5906-4db0-ad0d-129df8e065cb	g.chr7:157931202G>A	ENST00000389418.4	-	7	925	c.916C>T	c.(916-918)Cgg>Tgg	p.R306W	PTPRN2_ENST00000389413.3_Missense_Mutation_p.R306W|PTPRN2_ENST00000409483.1_Missense_Mutation_p.R268W|PTPRN2_ENST00000389416.4_Missense_Mutation_p.R289W|PTPRN2_ENST00000404321.2_Missense_Mutation_p.R329W	NM_002847.3	NP_002838.2	Q92932	PTPR2_HUMAN	protein tyrosine phosphatase, receptor type, N polypeptide 2	306					negative regulation of GTPase activity (GO:0034260)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	endoplasmic reticulum lumen (GO:0005788)|integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)|secretory granule (GO:0030141)|terminal bouton (GO:0043195)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|liver(1)|lung(42)|ovary(4)|pleura(1)|prostate(2)|skin(10)|upper_aerodigestive_tract(1)	86	all_neural(206;0.181)	all_cancers(7;8.99e-13)|all_epithelial(9;2.4e-06)|all_hematologic(28;0.0155)|Breast(660;0.132)	OV - Ovarian serous cystadenocarcinoma(82;0.00463)	STAD - Stomach adenocarcinoma(7;0.0875)		GTATGAATCCGTGCTCCTAGG	0.632																																						.											0									TRP/ARG,TRP/ARG,TRP/ARG	1,4405	2.1+/-5.4	0,1,2202	48.0	51.0	50.0		916,865,916	1.8	0.0	7		50	0,8600		0,0,4300	no	missense,missense,missense	PTPRN2	NM_002847.3,NM_130842.2,NM_130843.2	101,101,101	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging,probably-damaging,probably-damaging	306/1016,289/999,306/987	157931202	1,13005	2203	4300	6503	SO:0001583	missense	5799			AB002385	CCDS5947.1, CCDS5948.1, CCDS5949.1	7q36	2011-06-09			ENSG00000155093	ENSG00000155093		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"""	9677	protein-coding gene	gene with protein product	"""IAR PTPRP"""	601698				8954911, 9220540	Standard	NM_130842		Approved	KIAA0387, phogrin, ICAAR, IA-2beta	uc003wno.3	Q92932	OTTHUMG00000152646	ENST00000389418.4:c.916C>T	7.37:g.157931202G>A	ENSP00000374069:p.Arg306Trp		E9PC57|Q8N4I5|Q92662|Q9Y4F8|Q9Y4I6	Missense_Mutation	SNP	ENST00000389418.4	37	CCDS5947.1	.	.	.	.	.	.	.	.	.	.	G	11.60	1.688479	0.29962	2.27E-4	0.0	ENSG00000155093	ENST00000409483;ENST00000389413;ENST00000389416;ENST00000389418;ENST00000404321	T;T;T;T;T	0.02944	4.12;4.1;4.11;4.11;4.1	4.11	1.83	0.25207	.	.	.	.	.	T	0.02380	0.0073	N	0.24115	0.695	0.09310	N	1	D;D;D;D;D	0.59767	0.986;0.975;0.986;0.975;0.975	B;B;B;B;B	0.43783	0.431;0.248;0.431;0.248;0.248	T	0.49753	-0.8906	9	0.39692	T	0.17	.	5.0987	0.14747	0.4449:0.0:0.5551:0.0	.	329;268;306;289;306	Q92932-3;E7EM83;Q92932-2;E9PC57;Q92932	.;.;.;.;PTPR2_HUMAN	W	268;306;289;306;329	ENSP00000387114:R268W;ENSP00000374064:R306W;ENSP00000374067:R289W;ENSP00000374069:R306W;ENSP00000385464:R329W	ENSP00000374064:R306W	R	-	1	2	PTPRN2	157623963	0.000000	0.05858	0.000000	0.03702	0.015000	0.08874	0.615000	0.24329	0.267000	0.21916	0.650000	0.86243	CGG		0.632	PTPRN2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000353214.1		
NMRK1	54981	broad.mit.edu;hgsc.bcm.edu;ucsc.edu;mdanderson.org;bcgsc.ca	37	9	77681741	77681741	+	Missense_Mutation	SNP	G	G	T			TCGA-KL-8323-01A-21D-2310-10	TCGA-KL-8323-11A-01D-2310-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fae88d21-171c-4df4-b258-3c5948a1034b	f5c7fb67-5906-4db0-ad0d-129df8e065cb	g.chr9:77681741G>T	ENST00000361092.4	-	8	748	c.512C>A	c.(511-513)aCa>aAa	p.T171K	NMRK1_ENST00000482537.1_5'UTR|NMRK1_ENST00000376811.1_Missense_Mutation_p.T175K|NMRK1_ENST00000376808.4_Missense_Mutation_p.T147K	NM_017881.2	NP_060351.1	Q9NWW6	NRK1_HUMAN	nicotinamide riboside kinase 1	171					NAD biosynthetic process (GO:0009435)		ATP binding (GO:0005524)|metal ion binding (GO:0046872)|ribosylnicotinamide kinase activity (GO:0050262)										TTCAGATTTTGTTCCATCCAG	0.363																																						.											0													132.0	126.0	128.0					9																	77681741		2203	4300	6503	SO:0001583	missense	54981			AK097144	CCDS6650.1, CCDS47981.1	9q21.31	2012-03-30	2012-03-30	2012-03-30	ENSG00000106733	ENSG00000106733			26057	protein-coding gene	gene with protein product		608704	"""chromosome 9 open reading frame 95"""	C9orf95		15137942	Standard	NM_017881		Approved	FLJ20559, NRK1, bA235O14.2	uc004ajr.4	Q9NWW6	OTTHUMG00000020034	ENST00000361092.4:c.512C>A	9.37:g.77681741G>T	ENSP00000354387:p.Thr171Lys		Q5W124|Q8N430	Missense_Mutation	SNP	ENST00000361092.4	37	CCDS6650.1	.	.	.	.	.	.	.	.	.	.	G	13.90	2.375440	0.42105	.	.	ENSG00000106733	ENST00000376811;ENST00000376794;ENST00000361092;ENST00000376808	T;T;T	0.36340	1.26;1.26;1.26	5.45	3.61	0.41365	.	0.360554	0.29159	N	0.012968	T	0.44726	0.1307	M	0.83953	2.67	0.43637	D	0.996032	D;P;D	0.59357	0.985;0.884;0.971	P;B;P	0.51999	0.687;0.106;0.614	T	0.54735	-0.8249	10	0.07030	T	0.85	-14.6147	8.1753	0.31278	0.2484:0.0:0.7516:0.0	.	147;175;171	Q9NWW6-2;Q5W125;Q9NWW6	.;.;NRK1_HUMAN	K	175;175;171;147	ENSP00000366007:T175K;ENSP00000354387:T171K;ENSP00000366004:T147K	ENSP00000354387:T171K	T	-	2	0	C9orf95	76871561	1.000000	0.71417	0.994000	0.49952	0.383000	0.30230	2.942000	0.49018	0.680000	0.31366	0.650000	0.86243	ACA		0.363	NMRK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052705.1	NM_017881	
ENTPD8	377841	broad.mit.edu;hgsc.bcm.edu;ucsc.edu;mdanderson.org;bcgsc.ca	37	9	140327707	140327707	+	IGR	SNP	G	G	A			TCGA-KL-8323-01A-21D-2310-10	TCGA-KL-8323-11A-01D-2310-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fae88d21-171c-4df4-b258-3c5948a1034b	f5c7fb67-5906-4db0-ad0d-129df8e065cb	g.chr9:140327707G>A	ENST00000472938.1	-	0	1749				NOXA1_ENST00000392815.2_Missense_Mutation_p.G245S|NOXA1_ENST00000341349.2_Missense_Mutation_p.G301S			Q5MY95	ENTP8_HUMAN	ectonucleoside triphosphate diphosphohydrolase 8						nucleoside diphosphate biosynthetic process (GO:0009133)|nucleoside monophosphate biosynthetic process (GO:0009124)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|nucleoside-diphosphatase activity (GO:0017110)|nucleoside-triphosphatase activity (GO:0017111)	p.G301C(1)		biliary_tract(1)|lung(4)|prostate(1)|skin(1)	7	all_cancers(76;0.0926)			OV - Ovarian serous cystadenocarcinoma(145;0.000224)|Epithelial(140;0.000898)		GGACCCCGCGGGTGCTGGGGT	0.652																																						.											1	Substitution - Missense(1)	cervix(1)											10.0	12.0	11.0					9																	140327707		2171	4281	6452	SO:0001628	intergenic_variant	10811			AY359088	CCDS7043.1, CCDS43913.1	9q34.3	2013-09-20			ENSG00000188833	ENSG00000188833			24860	protein-coding gene	gene with protein product	"""GLSR2492"""					12975309	Standard	NM_198585		Approved	UNQ2492, NTPDase-8	uc004cmw.3	Q5MY95	OTTHUMG00000131831		9.37:g.140327707G>A			A2BG17|Q6UVZ0	Missense_Mutation	SNP	ENST00000472938.1	37	CCDS43913.1	.	.	.	.	.	.	.	.	.	.	G	4.715	0.132877	0.09032	.	.	ENSG00000188747	ENST00000341349;ENST00000392815	D;D	0.87029	-1.99;-2.2	2.27	-2.21	0.06973	.	1.949590	0.02659	N	0.107253	T	0.69333	0.3099	N	0.08118	0	0.09310	N	1	B;B;B	0.33318	0.408;0.01;0.007	B;B;B	0.31751	0.135;0.006;0.02	T	0.62959	-0.6743	10	0.09590	T	0.72	.	3.4659	0.07549	0.4195:0.2046:0.3759:0.0	.	245;301;301	Q86UR1-3;Q86UR1;Q86UR1-2	.;NOXA1_HUMAN;.	S	301;245	ENSP00000342848:G301S;ENSP00000376562:G245S	ENSP00000342848:G301S	G	+	1	0	NOXA1	139447528	0.000000	0.05858	0.000000	0.03702	0.111000	0.19643	-0.315000	0.08081	-0.611000	0.05709	0.561000	0.74099	GGT		0.652	ENTPD8-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355991.1	NM_198585	
CHDC2	286464	broad.mit.edu;hgsc.bcm.edu;mdanderson.org;bcgsc.ca	37	X	36117961	36117961	+	Missense_Mutation	SNP	C	C	T			TCGA-KL-8323-01A-21D-2310-10	TCGA-KL-8323-11A-01D-2310-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fae88d21-171c-4df4-b258-3c5948a1034b	f5c7fb67-5906-4db0-ad0d-129df8e065cb	g.chrX:36117961C>T	ENST00000313548.4	+	7	1003	c.817C>T	c.(817-819)Cgg>Tgg	p.R273W		NM_173695.2	NP_775966.1	Q8N9S7	CHDC2_HUMAN	calponin homology domain containing 2	273						integral component of membrane (GO:0016021)											CTGGAGTAAACGGGCATGGAC	0.333																																						.											0													101.0	111.0	108.0					X																	36117961		2202	4299	6501	SO:0001583	missense	286464			AK093920	CCDS14238.1	Xp21.1	2014-08-07	2012-11-28	2012-11-28	ENSG00000176034	ENSG00000176034			26708	protein-coding gene	gene with protein product			"""chromosome X open reading frame 59"""	CXorf59			Standard	NM_173695		Approved	FLJ36601, RP13-11B7.1	uc004ddk.1	Q8N9S7	OTTHUMG00000021351	ENST00000313548.4:c.817C>T	X.37:g.36117961C>T	ENSP00000324767:p.Arg273Trp			Missense_Mutation	SNP	ENST00000313548.4	37	CCDS14238.1	.	.	.	.	.	.	.	.	.	.	C	14.43	2.532042	0.45073	.	.	ENSG00000176034	ENST00000378660;ENST00000313548	.	.	.	5.73	1.91	0.25777	.	0.000000	0.52532	D	0.000062	T	0.24661	0.0598	L	0.59436	1.845	0.23862	N	0.996633	P	0.47962	0.903	B	0.34722	0.188	T	0.33574	-0.9863	9	0.87932	D	0	-5.3905	3.2514	0.06815	0.1409:0.5656:0.1339:0.1596	.	273	Q8N9S7	CX059_HUMAN	W	273	.	ENSP00000324767:R273W	R	+	1	2	CXorf59	36027882	1.000000	0.71417	0.997000	0.53966	0.868000	0.49771	0.524000	0.22940	-0.049000	0.13379	0.506000	0.49869	CGG		0.333	CHDC2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_173695	
USP9X	8239	broad.mit.edu;hgsc.bcm.edu;mdanderson.org;bcgsc.ca	37	X	41002593	41002593	+	Missense_Mutation	SNP	T	T	G			TCGA-KL-8323-01A-21D-2310-10	TCGA-KL-8323-11A-01D-2310-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fae88d21-171c-4df4-b258-3c5948a1034b	f5c7fb67-5906-4db0-ad0d-129df8e065cb	g.chrX:41002593T>G	ENST00000324545.8	+	10	1844	c.1211T>G	c.(1210-1212)cTt>cGt	p.L404R	USP9X_ENST00000378308.2_Missense_Mutation_p.L404R	NM_001039590.2|NM_001039591.2	NP_001034679.2|NP_001034680.2	Q93008	USP9X_HUMAN	ubiquitin specific peptidase 9, X-linked	404					axon extension (GO:0048675)|BMP signaling pathway (GO:0030509)|cerebellar cortex structural organization (GO:0021698)|chromosome segregation (GO:0007059)|female gamete generation (GO:0007292)|gene expression (GO:0010467)|hippocampus development (GO:0021766)|in utero embryonic development (GO:0001701)|mitotic nuclear division (GO:0007067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron migration (GO:0001764)|post-embryonic development (GO:0009791)|protein deubiquitination (GO:0016579)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ubiquitin-dependent protein catabolic process (GO:0006511)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|growth cone (GO:0030426)|membrane (GO:0016020)	co-SMAD binding (GO:0070410)|cysteine-type endopeptidase activity (GO:0004197)|cysteine-type peptidase activity (GO:0008234)|ubiquitin thiolesterase activity (GO:0004221)			NS(3)|breast(6)|central_nervous_system(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(16)|lung(29)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	87						CGAGATAGTCTTCATCAGCCA	0.338																																					Ovarian(172;1807 2695 35459 49286)	.											0													62.0	56.0	58.0					X																	41002593		2004	4199	6203	SO:0001583	missense	8239			X98296	CCDS43930.1, CCDS55403.1	Xp11.4	2010-08-03	2006-02-14		ENSG00000124486	ENSG00000124486		"""Ubiquitin-specific peptidases"""	12632	protein-coding gene	gene with protein product		300072	"""ubiquitin specific protease 9, X chromosome (fat facets-like Drosophila)"", ""ubiquitin specific protease 9, X-linked (fat facets-like, Drosophila)"", ""ubiquitin specific peptidase 9, X-linked (fat facets-like, Drosophila)"""			8922996	Standard	NM_001039590		Approved	DFFRX, FAF	uc004dfb.3	Q93008	OTTHUMG00000021367	ENST00000324545.8:c.1211T>G	X.37:g.41002593T>G	ENSP00000316357:p.Leu404Arg		O75550|Q8WWT3|Q8WX12	Missense_Mutation	SNP	ENST00000324545.8	37	CCDS43930.1	.	.	.	.	.	.	.	.	.	.	T	20.7	4.041996	0.75732	.	.	ENSG00000124486	ENST00000378308;ENST00000324545	T;T	0.76709	-1.04;-1.04	5.22	5.22	0.72569	.	0.000000	0.85682	D	0.000000	D	0.86851	0.6032	M	0.81341	2.54	0.80722	D	1	D;D	0.58620	0.964;0.983	P;P	0.61201	0.885;0.771	D	0.88730	0.3236	10	0.72032	D	0.01	.	14.3718	0.66846	0.0:0.0:0.0:1.0	.	404;404	Q93008-1;Q93008	.;USP9X_HUMAN	R	404	ENSP00000367558:L404R;ENSP00000316357:L404R	ENSP00000316357:L404R	L	+	2	0	USP9X	40887537	1.000000	0.71417	1.000000	0.80357	0.936000	0.57629	7.651000	0.83577	1.843000	0.53566	0.339000	0.21740	CTT		0.338	USP9X-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000056250.4	NM_004652	
UBR4	23352	broad.mit.edu;hgsc.bcm.edu;ucsc.edu;mdanderson.org	37	1	19480348	19480349	+	Missense_Mutation	DNP	GC	GC	TA			TCGA-KL-8323-01A-21D-2310-10	TCGA-KL-8323-11A-01D-2310-10	GC	GC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fae88d21-171c-4df4-b258-3c5948a1034b	f5c7fb67-5906-4db0-ad0d-129df8e065cb	g.chr1:19480348_19480349GC>TA	ENST00000375254.3	-	45	6570_6571	c.6543_6544GC>TA	c.(6541-6546)caGCaa>caTAaa	p.2181_2182QQ>HK	UBR4_ENST00000375226.2_Missense_Mutation_p.2181_2182QQ>HK|UBR4_ENST00000375217.2_Missense_Mutation_p.2181_2182QQ>HK|UBR4_ENST00000375267.2_Missense_Mutation_p.2181_2182QQ>HK	NM_020765.2	NP_065816.2	Q5T4S7	UBR4_HUMAN	ubiquitin protein ligase E3 component n-recognin 4	2181					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|viral process (GO:0016032)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(7)|central_nervous_system(1)|cervix(2)|endometrium(23)|kidney(25)|large_intestine(25)|liver(2)|lung(47)|ovary(10)|pancreas(2)|prostate(7)|skin(5)|stomach(5)|upper_aerodigestive_tract(4)|urinary_tract(6)	171		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000328)|Lung NSC(340;0.000406)|Breast(348;0.000814)|Ovarian(437;0.00774)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00674)|BRCA - Breast invasive adenocarcinoma(304;5.43e-05)|Kidney(64;0.000337)|KIRC - Kidney renal clear cell carcinoma(64;0.00426)|STAD - Stomach adenocarcinoma(196;0.00715)|READ - Rectum adenocarcinoma(331;0.0816)		CCTGTAGTTTGCTGGACACAGC	0.495																																						.											0																																										SO:0001583	missense	23352			AF348492	CCDS189.1	1p36.13	2008-06-23	2007-06-19	2007-06-19	ENSG00000127481	ENSG00000127481		"""Ubiquitin protein ligase E3 component n-recognins"""	30313	protein-coding gene	gene with protein product		609890	"""zinc finger, UBR1 type 1"""	ZUBR1		14702039, 10718198, 16055722	Standard	XM_005245802		Approved	KIAA1307, KIAA0462, RBAF600	uc001bbi.3	Q5T4S7	OTTHUMG00000002498	ENST00000375254.3:c.6543_6544delinsTA	1.37:g.19480348_19480349delinsTA	ENSP00000364403:p.Q2181_Q2182delinsHK		A8MPT2|A8MQ33|A8MQB1|O60646|O75050|Q4QRK5|Q5T4S8|Q5T4S9|Q5TBN8|Q5TBP2|Q6DKH8|Q6P4A4|Q7L8P7|Q8IXJ4|Q8TDN5|Q8WV67|Q9HA46|Q9P2N9|Q9UG82	Missense_Mutation	DNP	ENST00000375254.3	37	CCDS189.1																																																																																				0.495	UBR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007085.1	NM_020765	
DLX2	1746	hgsc.bcm.edu	37	2	172966928	172966928	+	Silent	SNP	G	G	T	rs143444914		TCGA-KL-8323-01A-21D-2310-10	TCGA-KL-8323-11A-01D-2310-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fae88d21-171c-4df4-b258-3c5948a1034b	f5c7fb67-5906-4db0-ad0d-129df8e065cb	g.chr2:172966928G>T	ENST00000234198.4	-	1	700	c.339C>A	c.(337-339)acC>acA	p.T113T	DLX2_ENST00000466293.2_Silent_p.T113T|AC104801.1_ENST00000448117.1_lincRNA	NM_004405.3	NP_004396.1	Q07687	DLX2_HUMAN	distal-less homeobox 2	113					brain development (GO:0007420)|branching morphogenesis of a nerve (GO:0048755)|cartilage development (GO:0051216)|cerebral cortex GABAergic interneuron fate commitment (GO:0021893)|embryonic cranial skeleton morphogenesis (GO:0048701)|hippocampus development (GO:0021766)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|odontogenesis of dentin-containing tooth (GO:0042475)|olfactory bulb development (GO:0021772)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|proximal/distal pattern formation (GO:0009954)|regulation of transcription from RNA polymerase II promoter involved in forebrain neuron fate commitment (GO:0021882)|subpallium development (GO:0021544)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded RNA binding (GO:0003727)			endometrium(1)|large_intestine(1)|lung(6)|ovary(2)|urinary_tract(1)	11			OV - Ovarian serous cystadenocarcinoma(117;0.216)			TGTAGGCGGCGGTGTAGCCCA	0.602													G|||	1	0.000199681	0.0008	0.0	5008	,	,		15923	0.0		0.0	False		,,,				2504	0.0				GBM(188;775 2993 11256 23072)	.											0								G		1,4405	2.1+/-5.4	0,1,2202	139.0	132.0	134.0		339	0.3	1.0	2	dbSNP_134	134	0,8600		0,0,4300	no	coding-synonymous	DLX2	NM_004405.3		0,1,6502	TT,TG,GG		0.0,0.0227,0.0077		113/329	172966928	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	1746			U51003	CCDS2248.1	2q31.1	2011-06-20	2005-12-22		ENSG00000115844	ENSG00000115844		"""Homeoboxes / ANTP class : NKL subclass"""	2915	protein-coding gene	gene with protein product		126255	"""distal-less homeo box 2"""			1354641	Standard	NM_004405		Approved	TES-1	uc002uhn.3	Q07687	OTTHUMG00000132276	ENST00000234198.4:c.339C>A	2.37:g.172966928G>T			B4DMK4|B7ZA14	Silent	SNP	ENST00000234198.4	37	CCDS2248.1																																																																																				0.602	DLX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255368.3		
PHF8	23133	hgsc.bcm.edu	37	X	54049206	54049206	+	Missense_Mutation	SNP	G	G	T			TCGA-KL-8323-01A-21D-2310-10	TCGA-KL-8323-11A-01D-2310-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fae88d21-171c-4df4-b258-3c5948a1034b	f5c7fb67-5906-4db0-ad0d-129df8e065cb	g.chrX:54049206G>T	ENST00000357988.5	-	3	635	c.277C>A	c.(277-279)Cat>Aat	p.H93N	PHF8_ENST00000322659.8_Missense_Mutation_p.H57N|PHF8_ENST00000338946.6_Missense_Mutation_p.H57N|PHF8_ENST00000338154.6_Missense_Mutation_p.H57N	NM_001184896.1	NP_001171825.1	Q9UPP1	PHF8_HUMAN	PHD finger protein 8	93					brain development (GO:0007420)|G1/S transition of mitotic cell cycle (GO:0000082)|histone H3-K27 demethylation (GO:0071557)|histone H3-K36 demethylation (GO:0070544)|histone H3-K9 demethylation (GO:0033169)|histone H4-K20 demethylation (GO:0035574)|mitotic cell cycle (GO:0000278)|negative regulation of chromatin silencing at rDNA (GO:0061188)|positive regulation of transcription from RNA polymerase I promoter (GO:0045943)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|histone demethylase activity (GO:0032452)|histone demethylase activity (H3-K27 specific) (GO:0071558)|histone demethylase activity (H3-K36 specific) (GO:0051864)|histone demethylase activity (H3-K9 specific) (GO:0032454)|histone demethylase activity (H4-K20 specific) (GO:0035575)|iron ion binding (GO:0005506)|methylated histone binding (GO:0035064)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)|zinc ion binding (GO:0008270)			endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(7)|lung(10)|ovary(4)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	40						GAGGGCCCATGCAAGACTTCA	0.453																																						.											0													58.0	44.0	49.0					X																	54049206		2203	4300	6503	SO:0001583	missense	23133			AB029034	CCDS14355.1, CCDS55418.1, CCDS55419.1, CCDS55420.1	Xp11.22	2013-01-28			ENSG00000172943	ENSG00000172943		"""Chromatin-modifying enzymes / K-demethylases"", ""Zinc fingers, PHD-type"""	20672	protein-coding gene	gene with protein product	"""jumonji C domain-containing histone demethylase 1F"""	300560				10470851, 20023638, 20644565	Standard	NM_015107		Approved	ZNF422, KIAA1111, JHDM1F	uc004dsu.3	Q9UPP1	OTTHUMG00000021622	ENST00000357988.5:c.277C>A	X.37:g.54049206G>T	ENSP00000350676:p.His93Asn		B3KMV4|B7Z911|Q5H9U5|Q5JPR9|Q5JPS0|Q5JPS2|Q5JPS3|Q5VUJ4|Q7Z6D4|Q9HAH2	Missense_Mutation	SNP	ENST00000357988.5	37	CCDS55420.1	.	.	.	.	.	.	.	.	.	.	G	21.3	4.134979	0.77662	.	.	ENSG00000172943	ENST00000357988;ENST00000338154;ENST00000338946;ENST00000396277;ENST00000322659;ENST00000425862;ENST00000437224;ENST00000415025;ENST00000453905;ENST00000445025;ENST00000433120	T;T;T;T;T;T;T;T;T;T	0.62498	0.02;0.02;0.02;0.02;0.02;0.02;0.02;0.02;0.02;0.02	5.59	5.59	0.84812	Zinc finger, FYVE/PHD-type (1);	0.000000	0.85682	D	0.000000	T	0.66703	0.2816	M	0.82630	2.6	0.58432	D	0.999999	P;P	0.48407	0.91;0.861	B;B	0.39590	0.274;0.304	T	0.75039	-0.3458	10	0.62326	D	0.03	-5.8121	17.3188	0.87231	0.0:0.0:1.0:0.0	.	57;93	B7Z911;Q9UPP1	.;PHF8_HUMAN	N	93;57;57;87;57;57;57;57;93;57;57	ENSP00000350676:H93N;ENSP00000338868:H57N;ENSP00000340051:H57N;ENSP00000319473:H57N;ENSP00000408113:H57N;ENSP00000398995:H57N;ENSP00000404117:H57N;ENSP00000405897:H93N;ENSP00000416546:H57N;ENSP00000410100:H57N	ENSP00000319473:H57N	H	-	1	0	PHF8	54065931	1.000000	0.71417	1.000000	0.80357	0.743000	0.42351	9.802000	0.99131	2.357000	0.79964	0.538000	0.68166	CAT		0.453	PHF8-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000056784.2	NM_015107	
RC3H1	149041	broad.mit.edu	37	1	173912597	173912597	+	Missense_Mutation	SNP	T	T	C			TCGA-KL-8323-01A-21D-2310-10	TCGA-KL-8323-11A-01D-2310-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fae88d21-171c-4df4-b258-3c5948a1034b	f5c7fb67-5906-4db0-ad0d-129df8e065cb	g.chr1:173912597T>C	ENST00000367696.2	-	18	3469	c.3118A>G	c.(3118-3120)Aca>Gca	p.T1040A	RC3H1_ENST00000367694.2_Missense_Mutation_p.T1031A|RC3H1_ENST00000258349.4_Missense_Mutation_p.T1040A			Q5TC82	RC3H1_HUMAN	ring finger and CCCH-type domains 1	1040					B cell homeostasis (GO:0001782)|cytoplasmic mRNA processing body assembly (GO:0033962)|lymph node development (GO:0048535)|negative regulation of activated T cell proliferation (GO:0046007)|negative regulation of B cell proliferation (GO:0030889)|negative regulation of germinal center formation (GO:0002635)|negative regulation of T-helper cell differentiation (GO:0045623)|nuclear-transcribed mRNA catabolic process (GO:0000956)|positive regulation of NIK/NF-kappaB signaling (GO:1901224)|posttranscriptional regulation of gene expression (GO:0010608)|protein ubiquitination (GO:0016567)|regulation of germinal center formation (GO:0002634)|regulation of mRNA stability (GO:0043488)|regulation of T cell receptor signaling pathway (GO:0050856)|spleen development (GO:0048536)|T cell homeostasis (GO:0043029)|T cell proliferation (GO:0042098)|T follicular helper cell differentiation (GO:0061470)	cytoplasmic mRNA processing body (GO:0000932)|cytoplasmic stress granule (GO:0010494)	mRNA 3'-UTR binding (GO:0003730)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(7)|lung(20)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	50						AGTTCCCGTGTTCTCTTCCCG	0.498																																						.											0													230.0	214.0	219.0					1																	173912597		2203	4300	6503	SO:0001583	missense	149041			AK093501	CCDS30940.1, CCDS72987.1	1q25.1	2013-01-18	2010-09-15		ENSG00000135870	ENSG00000135870		"""RING-type (C3HC4) zinc fingers"", ""Zinc fingers, CCCH-type domain containing"""	29434	protein-coding gene	gene with protein product	"""KIAA2025 protein"""	609424	"""ring finger and CCCH-type zinc finger domains 1"""			15917799	Standard	XM_005244918		Approved	KIAA2025, roquin, RP5-1198E17.5, RNF198	uc001gju.4	Q5TC82	OTTHUMG00000037275	ENST00000367696.2:c.3118A>G	1.37:g.173912597T>C	ENSP00000356669:p.Thr1040Ala		B3KVK1|Q5W180|Q5W181|Q8IVE6|Q8N9V1	Missense_Mutation	SNP	ENST00000367696.2	37	CCDS30940.1	.	.	.	.	.	.	.	.	.	.	T	16.61	3.172503	0.57584	.	.	ENSG00000135870	ENST00000367696;ENST00000258349;ENST00000367694	T;T;T	0.47869	0.89;0.89;0.83	5.24	5.24	0.73138	.	0.157302	0.56097	D	0.000030	T	0.40595	0.1123	L	0.50333	1.59	0.51767	D	0.999934	P;P;P;P	0.45126	0.767;0.767;0.851;0.767	B;B;P;B	0.47402	0.344;0.344;0.546;0.344	T	0.41734	-0.9492	10	0.56958	D	0.05	-11.204	15.1378	0.72583	0.0:0.0:0.0:1.0	.	1040;1031;1031;1040	B9EGU6;B7ZMB3;Q5TC82-2;Q5TC82	.;.;.;RC3H1_HUMAN	A	1040;1040;1031	ENSP00000356669:T1040A;ENSP00000258349:T1040A;ENSP00000356667:T1031A	ENSP00000258349:T1040A	T	-	1	0	RC3H1	172179220	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	5.837000	0.69381	1.978000	0.57642	0.533000	0.62120	ACA		0.498	RC3H1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090733.2	NM_172071	
OR2T8	343172	broad.mit.edu	37	1	248084369	248084369	+	Missense_Mutation	SNP	A	A	G			TCGA-KL-8323-01A-21D-2310-10	TCGA-KL-8323-11A-01D-2310-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fae88d21-171c-4df4-b258-3c5948a1034b	f5c7fb67-5906-4db0-ad0d-129df8e065cb	g.chr1:248084369A>G	ENST00000319968.4	+	1	50	c.50A>G	c.(49-51)aAc>aGc	p.N17S		NM_001005522.1	NP_001005522.1	A6NH00	OR2T8_HUMAN	olfactory receptor, family 2, subfamily T, member 8	17						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(20)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	34	all_cancers(71;0.000139)|all_epithelial(71;1.58e-05)|Breast(184;0.0117)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)	all_cancers(173;0.0211)	OV - Ovarian serous cystadenocarcinoma(106;0.0319)			GGACTCTTTAACCACACCAGA	0.428																																						.											0													104.0	101.0	102.0					1																	248084369		2203	4300	6503	SO:0001583	missense	343172				CCDS31100.1	1q44	2012-08-09		2004-03-10	ENSG00000177462	ENSG00000177462		"""GPCR / Class A : Olfactory receptors"""	15020	protein-coding gene	gene with protein product				OR2T8P			Standard	XM_005273117		Approved		uc010pzc.2	A6NH00	OTTHUMG00000040205	ENST00000319968.4:c.50A>G	1.37:g.248084369A>G	ENSP00000326225:p.Asn17Ser			Missense_Mutation	SNP	ENST00000319968.4	37	CCDS31100.1	.	.	.	.	.	.	.	.	.	.	A	0.010	-1.744473	0.00675	.	.	ENSG00000177462	ENST00000319968	T	0.00316	8.13	3.51	-0.677	0.11357	.	1.231280	0.06234	U	0.689141	T	0.00144	0.0004	L	0.34521	1.04	0.09310	N	1	B	0.16396	0.017	B	0.15484	0.013	T	0.40175	-0.9577	10	0.02654	T	1	.	4.6608	0.12641	0.6428:0.1616:0.1956:0.0	.	17	A6NH00	OR2T8_HUMAN	S	17	ENSP00000326225:N17S	ENSP00000326225:N17S	N	+	2	0	OR2T8	246150992	0.000000	0.05858	0.037000	0.18230	0.018000	0.09664	0.097000	0.15168	0.027000	0.15297	-0.323000	0.08544	AAC		0.428	OR2T8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096862.1	NM_001005522	
RN7SL453P	106481046	broad.mit.edu	37	10	47379799	47379799	+	RNA	SNP	G	G	A			TCGA-KL-8323-01A-21D-2310-10	TCGA-KL-8323-11A-01D-2310-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fae88d21-171c-4df4-b258-3c5948a1034b	f5c7fb67-5906-4db0-ad0d-129df8e065cb	g.chr10:47379799G>A	ENST00000582987.1	-	0	284									RNA, 7SL, cytoplasmic 453, pseudogene																		AGTATCAGAAGACACAGCTTC	0.363																																						.											0																																												439965					10q11.22	2013-04-02			ENSG00000264710			"""ncRNAs / Small cytoplasmic RNAs"""	46469	pseudogene	RNA, pseudogene							Standard			Approved						10.37:g.47379799G>A				RNA	SNP	ENST00000582987.1	37																																																																																					0.363	RN7SL453P-201	KNOWN	basic	misc_RNA	misc_RNA			
CFAP46	54777	broad.mit.edu	37	10	134664800	134664800	+	Missense_Mutation	SNP	C	C	T			TCGA-KL-8323-01A-21D-2310-10	TCGA-KL-8323-11A-01D-2310-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fae88d21-171c-4df4-b258-3c5948a1034b	f5c7fb67-5906-4db0-ad0d-129df8e065cb	g.chr10:134664800C>T	ENST00000368586.5	-	40	5684	c.5584G>A	c.(5584-5586)Gtc>Atc	p.V1862I	TTC40_ENST00000263170.5_Missense_Mutation_p.V23I	NM_001200049.2	NP_001186978.2														breast(1)|endometrium(5)|lung(19)|urinary_tract(3)	28						GGCGTGTTGACGTTCTGCAAC	0.577																																						.											0													46.0	40.0	42.0					10																	134664800		2201	4300	6501	SO:0001583	missense	54777																														ENST00000368586.5:c.5584G>A	10.37:g.134664800C>T	ENSP00000357575:p.Val1862Ile			Missense_Mutation	SNP	ENST00000368586.5	37	CCDS58101.1	.	.	.	.	.	.	.	.	.	.	C	0.019	-1.457552	0.01071	.	.	ENSG00000171811	ENST00000368586;ENST00000263170	T;T	0.12361	2.94;2.69	4.66	-0.355	0.12587	.	0.702248	0.11048	N	0.605408	T	0.05456	0.0144	N	0.16790	0.44	0.09310	N	0.999999	B	0.27951	0.195	B	0.16722	0.016	T	0.41556	-0.9502	10	0.12430	T	0.62	.	2.8339	0.05508	0.2131:0.2868:0.0:0.5001	.	23	Q8IYW2	CJ092_HUMAN	I	1862;23	ENSP00000357575:V1862I;ENSP00000263170:V23I	ENSP00000263170:V23I	V	-	1	0	C10orf93	134514790	0.011000	0.17503	0.042000	0.18584	0.403000	0.30841	-0.656000	0.05342	0.037000	0.15575	0.563000	0.77884	GTC		0.577	TTC40-001	PUTATIVE	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000051095.3		
PHRF1	57661	broad.mit.edu;ucsc.edu;mdanderson.org;bcgsc.ca	37	11	605169	605169	+	Missense_Mutation	SNP	G	G	T			TCGA-KL-8323-01A-21D-2310-10	TCGA-KL-8323-11A-01D-2310-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fae88d21-171c-4df4-b258-3c5948a1034b	f5c7fb67-5906-4db0-ad0d-129df8e065cb	g.chr11:605169G>T	ENST00000264555.5	+	11	1331	c.1203G>T	c.(1201-1203)agG>agT	p.R401S	PHRF1_ENST00000416188.2_Missense_Mutation_p.R401S|PHRF1_ENST00000533464.1_Missense_Mutation_p.R397S|PHRF1_ENST00000413872.2_Missense_Mutation_p.R400S	NM_020901.2	NP_065952.2	Q9P1Y6	PHRF1_HUMAN	PHD and ring finger domains 1	401	Arg-rich.				mRNA processing (GO:0006397)|transcription from RNA polymerase II promoter (GO:0006366)	membrane (GO:0016020)	RNA polymerase binding (GO:0070063)|zinc ion binding (GO:0008270)			breast(1)|cervix(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(13)|urinary_tract(2)	28						GCCTGCGCAGGCCTGTTCACA	0.567																																						.											0													46.0	49.0	48.0					11																	605169		2071	4212	6283	SO:0001583	missense	57661			BC004950	CCDS44507.1, CCDS65987.1, CCDS65988.1, CCDS65989.1	11p15.5	2014-06-13			ENSG00000070047	ENSG00000070047		"""RING-type (C3HC4) zinc fingers"", ""Zinc fingers, PHD-type"""	24351	protein-coding gene	gene with protein product	"""CTD binding SR like protein rA9"", ""protein phosphatase 1, regulatory subunit 125"""	611780		RNF221			Standard	XM_005253027		Approved	KIAA1542, PPP1R125	uc010qwc.2	Q9P1Y6	OTTHUMG00000165141	ENST00000264555.5:c.1203G>T	11.37:g.605169G>T	ENSP00000264555:p.Arg401Ser		A6H8W1|B7ZM64|B9EGP0|C9JS82|Q6PJP2|Q8IVY2|Q8N2Y7|Q9BSM2	Missense_Mutation	SNP	ENST00000264555.5	37		.	.	.	.	.	.	.	.	.	.	G	7.714	0.695759	0.15106	.	.	ENSG00000070047	ENST00000264555;ENST00000413872;ENST00000416188;ENST00000533464	D;D;D;D	0.92199	-2.99;-2.99;-2.99;-2.99	4.65	1.63	0.23807	.	0.620308	0.13443	N	0.387560	T	0.81545	0.4845	N	0.24115	0.695	0.28574	N	0.910468	B;B;B;B	0.24823	0.068;0.112;0.112;0.068	B;B;B;B	0.20955	0.014;0.032;0.032;0.014	T	0.69339	-0.5171	10	0.33141	T	0.24	-17.2271	1.0008	0.01476	0.2743:0.1627:0.397:0.166	.	397;400;401;401	E9PJ24;F8WEF5;Q9P1Y6-3;Q9P1Y6	.;.;.;PHRF1_HUMAN	S	401;400;401;397	ENSP00000264555:R401S;ENSP00000388589:R400S;ENSP00000410626:R401S;ENSP00000431870:R397S	ENSP00000264555:R401S	R	+	3	2	PHRF1	595169	1.000000	0.71417	0.260000	0.24451	0.024000	0.10985	1.285000	0.33261	0.551000	0.29008	0.563000	0.77884	AGG		0.567	PHRF1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000382133.1	NM_020901	
MUC5B	727897	broad.mit.edu	37	11	1270385	1270385	+	Missense_Mutation	SNP	C	C	G			TCGA-KL-8323-01A-21D-2310-10	TCGA-KL-8323-11A-01D-2310-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fae88d21-171c-4df4-b258-3c5948a1034b	f5c7fb67-5906-4db0-ad0d-129df8e065cb	g.chr11:1270385C>G	ENST00000529681.1	+	31	12333	c.12275C>G	c.(12274-12276)gCc>gGc	p.A4092G	MUC5B_ENST00000447027.1_Missense_Mutation_p.A4095G|RP11-532E4.2_ENST00000532061.2_RNA	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	4092	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)		CACACCACGGCCACCTCCAGG	0.701																																						.											0													89.0	122.0	111.0					11																	1270385		2095	4203	6298	SO:0001583	missense	727897			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.12275C>G	11.37:g.1270385C>G	ENSP00000436812:p.Ala4092Gly		O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	37	CCDS44515.2	.	.	.	.	.	.	.	.	.	.	c	5.394	0.257910	0.10239	.	.	ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637;ENST00000406844	T;T	0.17528	2.27;2.46	1.88	-0.722	0.11184	.	.	.	.	.	T	0.17023	0.0409	M	0.67953	2.075	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.29305	-1.0016	9	0.87932	D	0	.	5.417	0.16380	0.0:0.4252:0.3955:0.1793	.	4565;4095	A7Y9J9;E9PBJ0	.;.	G	4092;4095;4036;3942	ENSP00000436812:A4092G;ENSP00000415793:A4095G	ENSP00000343037:A4036G	A	+	2	0	MUC5B	1226961	0.005000	0.15991	0.002000	0.10522	0.162000	0.22319	1.701000	0.37825	-0.378000	0.07918	0.393000	0.25936	GCC		0.701	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
MED17	9440	broad.mit.edu;ucsc.edu;mdanderson.org;bcgsc.ca	37	11	93517753	93517753	+	Missense_Mutation	SNP	A	A	G			TCGA-KL-8323-01A-21D-2310-10	TCGA-KL-8323-11A-01D-2310-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fae88d21-171c-4df4-b258-3c5948a1034b	f5c7fb67-5906-4db0-ad0d-129df8e065cb	g.chr11:93517753A>G	ENST00000251871.3	+	1	361	c.74A>G	c.(73-75)gAt>gGt	p.D25G	MED17_ENST00000530819.1_Missense_Mutation_p.D25G	NM_004268.4	NP_004259.3	Q9NVC6	MED17_HUMAN	mediator complex subunit 17	25					androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|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)			large_intestine(2)|lung(11)|ovary(1)	14		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				GTGGGCCTGGATGGCACCGAG	0.672																																						.											0													43.0	33.0	36.0					11																	93517753		2199	4298	6497	SO:0001583	missense	9440			AF104254	CCDS8295.1	11q21	2007-07-30	2007-07-30	2007-07-30	ENSG00000042429	ENSG00000042429			2375	protein-coding gene	gene with protein product		603810	"""cofactor required for Sp1 transcriptional activation, subunit 6 (77kD)"", ""cofactor required for Sp1 transcriptional activation, subunit 6, 77kDa"""	CRSP6		9989412, 10198638	Standard	NM_004268		Approved	CRSP77, TRAP80, DRIP80	uc001pem.4	Q9NVC6	OTTHUMG00000167497	ENST00000251871.3:c.74A>G	11.37:g.93517753A>G	ENSP00000251871:p.Asp25Gly		B3KN07|Q9HA81|Q9UNP7|Q9Y2W0|Q9Y660	Missense_Mutation	SNP	ENST00000251871.3	37	CCDS8295.1	.	.	.	.	.	.	.	.	.	.	A	34	5.386599	0.95967	.	.	ENSG00000042429	ENST00000251871;ENST00000530819;ENST00000427225;ENST00000533359	T;T;T	0.66995	-0.24;0.2;0.26	5.76	5.76	0.90799	.	0.102946	0.64402	D	0.000002	T	0.80798	0.4692	M	0.72118	2.19	0.80722	D	1	D;D	0.71674	0.998;0.974	D;P	0.71870	0.975;0.772	T	0.82839	-0.0259	10	0.72032	D	0.01	-26.298	16.0699	0.80919	1.0:0.0:0.0:0.0	.	25;25	Q9NVC6;Q9NVC6-2	MED17_HUMAN;.	G	25	ENSP00000251871:D25G;ENSP00000434459:D25G;ENSP00000431524:D25G	ENSP00000251871:D25G	D	+	2	0	MED17	93157401	1.000000	0.71417	1.000000	0.80357	0.874000	0.50279	8.563000	0.90723	2.200000	0.70718	0.459000	0.35465	GAT		0.672	MED17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394800.2	NM_004268	
LIMA1	51474	broad.mit.edu	37	12	50575718	50575718	+	Missense_Mutation	SNP	A	A	G			TCGA-KL-8323-01A-21D-2310-10	TCGA-KL-8323-11A-01D-2310-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fae88d21-171c-4df4-b258-3c5948a1034b	f5c7fb67-5906-4db0-ad0d-129df8e065cb	g.chr12:50575718A>G	ENST00000341247.4	-	10	1392	c.1243T>C	c.(1243-1245)Ttc>Ctc	p.F415L	LIMA1_ENST00000547825.1_Missense_Mutation_p.F113L|LIMA1_ENST00000552783.1_Missense_Mutation_p.F256L|LIMA1_ENST00000394943.3_Missense_Mutation_p.F416L|LIMA1_ENST00000552491.1_Missense_Mutation_p.F112L|LIMA1_ENST00000552909.1_Missense_Mutation_p.F254L|LIMA1_ENST00000552823.1_Missense_Mutation_p.F255L	NM_001113546.1|NM_016357.4	NP_001107018.1|NP_057441.1	Q9UHB6	LIMA1_HUMAN	LIM domain and actin binding 1	415	LIM zinc-binding. {ECO:0000255|PROSITE- ProRule:PRU00125}.			F -> L (in Ref. 8; AAG17267). {ECO:0000305}.	actin filament bundle assembly (GO:0051017)|negative regulation of actin filament depolymerization (GO:0030835)|ruffle organization (GO:0031529)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|stress fiber (GO:0001725)	actin filament binding (GO:0051015)|actin monomer binding (GO:0003785)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(17)|ovary(1)|prostate(2)|skin(2)	44						GAGCAACGGAAGCAGCTGATG	0.488																																						.											0													110.0	99.0	103.0					12																	50575718		2203	4300	6503	SO:0001583	missense	51474			AF198454	CCDS8802.1, CCDS44877.1, CCDS55826.1, CCDS58230.1	12q13.12	2006-04-12				ENSG00000050405			24636	protein-coding gene	gene with protein product	"""epithelial protein lost in neoplasm beta"""	608364				10806352, 10618726, 12566430	Standard	NM_016357		Approved	EPLIN	uc001rwk.4	Q9UHB6		ENST00000341247.4:c.1243T>C	12.37:g.50575718A>G	ENSP00000340184:p.Phe415Leu		B2RB09|Q2TAN7|Q59FE8|Q9BVF2|Q9H8J1|Q9HBN5|Q9NX96|Q9NXC3|Q9NXU6|Q9P0H8|Q9UHB5	Missense_Mutation	SNP	ENST00000341247.4	37	CCDS8802.1	.	.	.	.	.	.	.	.	.	.	A	36	5.631391	0.96682	.	.	ENSG00000050405	ENST00000552491;ENST00000547825;ENST00000552823;ENST00000394943;ENST00000341247;ENST00000552783;ENST00000552909;ENST00000420992	D;D;D;D;D;D;D	0.92199	-2.99;-2.99;-2.99;-2.99;-2.99;-2.99;-2.99	5.49	5.49	0.81192	Zinc finger, LIM-type (5);	0.000000	0.85682	D	0.000000	D	0.95887	0.8661	M	0.77616	2.38	0.80722	D	1	D;D;D	0.89917	1.0;0.997;0.964	D;D;D	0.97110	1.0;0.991;0.978	D	0.96323	0.9238	10	0.72032	D	0.01	.	15.8844	0.79232	1.0:0.0:0.0:0.0	.	425;415;254	Q59FE8;Q9UHB6;F8VQE1	.;LIMA1_HUMAN;.	L	112;113;255;416;415;256;254;334	ENSP00000448463:F112L;ENSP00000448706:F113L;ENSP00000450266:F255L;ENSP00000378400:F416L;ENSP00000340184:F415L;ENSP00000448779:F256L;ENSP00000450087:F254L	ENSP00000340184:F415L	F	-	1	0	LIMA1	48861985	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.910000	0.92685	2.218000	0.71995	0.533000	0.62120	TTC		0.488	LIMA1-003	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000406235.2	NM_016357	
ALKBH2	121642	broad.mit.edu;ucsc.edu	37	12	109526037	109526037	+	Missense_Mutation	SNP	G	G	A	rs373220366		TCGA-KL-8323-01A-21D-2310-10	TCGA-KL-8323-11A-01D-2310-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fae88d21-171c-4df4-b258-3c5948a1034b	f5c7fb67-5906-4db0-ad0d-129df8e065cb	g.chr12:109526037G>A	ENST00000429722.2	-	4	1123	c.760C>T	c.(760-762)Cgt>Tgt	p.R254C	ALKBH2_ENST00000343075.3_Missense_Mutation_p.R254C|ALKBH2_ENST00000440112.2_3'UTR	NM_001145374.1	NP_001138846.1	Q6NS38	ALKB2_HUMAN	alkB, alkylation repair homolog 2 (E. coli)	254	Alpha-ketoglutarate binding.|Fe2OG dioxygenase. {ECO:0000255|PROSITE- ProRule:PRU00805}.				DNA dealkylation involved in DNA repair (GO:0006307)|DNA demethylation (GO:0080111)|DNA repair (GO:0006281)|oxidative demethylation (GO:0070989)|oxidative DNA demethylation (GO:0035511)	nucleoplasm (GO:0005654)	cytosine C-5 DNA demethylase activity (GO:0051747)|DNA-N1-methyladenine dioxygenase activity (GO:0043734)|ferrous iron binding (GO:0008198)			endometrium(1)|kidney(3)|large_intestine(1)|lung(3)	8					Vitamin C(DB00126)	AAAATTTTACGAAAAGTCAGA	0.428								Direct reversal of damage																														.											0								G	CYS/ARG,CYS/ARG,CYS/ARG,,	0,4406		0,0,2203	72.0	77.0	75.0		760,760,760,,	3.7	0.1	12		75	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense,utr-3,utr-3	ALKBH2	NM_001001655.2,NM_001145374.1,NM_001145375.1,NM_001205179.1,NM_001205180.1	180,180,180,,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging,,	254/262,254/262,254/262,,	109526037	1,13005	2203	4300	6503	SO:0001583	missense	121642			AY754389	CCDS31897.1, CCDS55883.1	12q24.11	2008-04-24			ENSG00000189046	ENSG00000189046		"""Alkylation repair homologs"""	32487	protein-coding gene	gene with protein product		610602					Standard	NM_001145374		Approved	MGC90512, ABH2	uc010sxj.1	Q6NS38	OTTHUMG00000169246	ENST00000429722.2:c.760C>T	12.37:g.109526037G>A	ENSP00000398181:p.Arg254Cys		A4PET2|Q5XLE3	Missense_Mutation	SNP	ENST00000429722.2	37	CCDS31897.1	.	.	.	.	.	.	.	.	.	.	G	15.24	2.774679	0.49786	0.0	1.16E-4	ENSG00000189046	ENST00000429722;ENST00000343075;ENST00000435370	T;T	0.75260	-0.92;-0.92	5.62	3.74	0.42951	Oxoglutarate/iron-dependent oxygenase (2);	0.000000	0.85682	D	0.000000	D	0.91415	0.7291	H	0.98701	4.305	0.80722	D	1	D	0.89917	1.0	D	0.79784	0.993	D	0.93711	0.7024	10	0.87932	D	0	-10.7766	14.1155	0.65151	0.0:0.0:0.6126:0.3874	.	254	Q6NS38	ALKB2_HUMAN	C	254	ENSP00000398181:R254C;ENSP00000343021:R254C	ENSP00000343021:R254C	R	-	1	0	ALKBH2	108010420	1.000000	0.71417	0.126000	0.21872	0.478000	0.33099	3.442000	0.52900	0.670000	0.31165	0.655000	0.94253	CGT		0.428	ALKBH2-007	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403063.2	NM_001001655	
HERC2	8924	broad.mit.edu	37	15	28447318	28447318	+	Missense_Mutation	SNP	A	A	G			TCGA-KL-8323-01A-21D-2310-10	TCGA-KL-8323-11A-01D-2310-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fae88d21-171c-4df4-b258-3c5948a1034b	f5c7fb67-5906-4db0-ad0d-129df8e065cb	g.chr15:28447318A>G	ENST00000261609.7	-	47	7666	c.7558T>C	c.(7558-7560)Tcc>Ccc	p.S2520P		NM_004667.5	NP_004658.3			HECT and RLD domain containing E3 ubiquitin protein ligase 2											NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(3)|cervix(3)|endometrium(20)|kidney(11)|large_intestine(33)|lung(95)|ovary(7)|prostate(8)|skin(7)|upper_aerodigestive_tract(8)|urinary_tract(4)	204		all_lung(180;1.3e-11)|Breast(32;0.000194)|Colorectal(260;0.227)		all cancers(64;3.93e-09)|Epithelial(43;9.99e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0271)|GBM - Glioblastoma multiforme(186;0.0497)|Lung(196;0.199)		TACTCGTCGGACACCGTGTCT	0.612																																						.											0													12.0	12.0	12.0					15																	28447318		2183	4260	6443	SO:0001583	missense	8924			AF071172	CCDS10021.1	15q13	2012-02-23	2012-02-23		ENSG00000128731	ENSG00000128731			4868	protein-coding gene	gene with protein product		605837	"""hect domain and RLD 2"""			9949213	Standard	NM_004667		Approved	jdf2, p528, D15F37S1	uc001zbj.4	O95714	OTTHUMG00000129251	ENST00000261609.7:c.7558T>C	15.37:g.28447318A>G	ENSP00000261609:p.Ser2520Pro			Missense_Mutation	SNP	ENST00000261609.7	37	CCDS10021.1	.	.	.	.	.	.	.	.	.	.	A	14.58	2.576880	0.45902	.	.	ENSG00000128731	ENST00000261609	T	0.41758	0.99	4.49	4.49	0.54785	.	0.121312	0.56097	D	0.000023	T	0.53546	0.1803	L	0.44542	1.39	0.80722	D	1	D	0.54601	0.967	D	0.65874	0.939	T	0.50617	-0.8807	10	0.37606	T	0.19	.	14.2901	0.66270	1.0:0.0:0.0:0.0	.	2520	O95714	HERC2_HUMAN	P	2520	ENSP00000261609:S2520P	ENSP00000261609:S2520P	S	-	1	0	HERC2	26120913	1.000000	0.71417	0.982000	0.44146	0.091000	0.18340	9.120000	0.94369	2.026000	0.59711	0.374000	0.22700	TCC		0.612	HERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251358.2	NM_004667	
MAPK7	5598	broad.mit.edu;mdanderson.org	37	17	19284374	19284374	+	Silent	SNP	C	C	T	rs145605078		TCGA-KL-8323-01A-21D-2310-10	TCGA-KL-8323-11A-01D-2310-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fae88d21-171c-4df4-b258-3c5948a1034b	f5c7fb67-5906-4db0-ad0d-129df8e065cb	g.chr17:19284374C>T	ENST00000308406.5	+	4	1238	c.852C>T	c.(850-852)gcC>gcT	p.A284A	MAPK7_ENST00000395602.4_Silent_p.A284A|B9D1_ENST00000477478.2_5'Flank|MAPK7_ENST00000571657.1_Intron|MAPK7_ENST00000299612.7_Silent_p.A145A|MFAP4_ENST00000574313.2_5'Flank|B9D1_ENST00000575403.1_5'Flank|MAPK7_ENST00000395604.3_Silent_p.A284A	NM_139033.2	NP_620602.2	Q13164	MK07_HUMAN	mitogen-activated protein kinase 7	284	Necessary for oligomerization. {ECO:0000250}.|Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cAMP-mediated signaling (GO:0019933)|cell cycle (GO:0007049)|cell differentiation (GO:0030154)|cellular response to growth factor stimulus (GO:0071363)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to laminar fluid shear stress (GO:0071499)|cellular response to transforming growth factor beta stimulus (GO:0071560)|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 cAMP catabolic process (GO:0030821)|negative regulation of cyclic-nucleotide phosphodiesterase activity (GO:0051344)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of heterotypic cell-cell adhesion (GO:0034115)|negative regulation of inflammatory response (GO:0050728)|negative regulation of NFAT protein import into nucleus (GO:0051534)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|negative regulation of response to cytokine stimulus (GO:0060761)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of protein metabolic process (GO:0051247)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to stress (GO:0036003)|regulation of angiogenesis (GO:0045765)|signal transduction (GO:0007165)|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)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)	ATP binding (GO:0005524)|MAP kinase activity (GO:0004707)|mitogen-activated protein kinase binding (GO:0051019)			autonomic_ganglia(1)|central_nervous_system(4)|endometrium(5)|kidney(2)|large_intestine(4)|lung(9)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	30	all_cancers(12;2.87e-05)|all_epithelial(12;0.00114)|Hepatocellular(7;0.00345)|Breast(13;0.206)					CATCACCAGCCGTGATTCAGG	0.607																																						.											0								C	,,,	1,4405	2.1+/-5.4	0,1,2202	36.0	39.0	38.0		852,435,852,852	-5.6	0.4	17	dbSNP_134	38	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	MAPK7	NM_002749.3,NM_139032.2,NM_139033.2,NM_139034.2	,,,	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	,,,	284/817,145/678,284/817,284/817	19284374	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	5598			U25278	CCDS11206.1, CCDS11207.1	17p11.2	2011-06-09			ENSG00000166484	ENSG00000166484	2.7.11.24	"""Mitogen-activated protein kinase cascade / Kinases"""	6880	protein-coding gene	gene with protein product	"""BMK1 kinase"", ""extracellular-signal-regulated kinase 5"""	602521		PRKM7		10072598, 7759517	Standard	NM_139032		Approved	BMK1, ERK5	uc002gvp.3	Q13164	OTTHUMG00000059587	ENST00000308406.5:c.852C>T	17.37:g.19284374C>T			Q16634|Q59F50|Q6QLU7|Q7L4P4|Q969G1|Q96G51	Silent	SNP	ENST00000308406.5	37	CCDS11206.1																																																																																				0.607	MAPK7-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132506.1	NM_139033	
SPAG5	10615	broad.mit.edu	37	17	26910630	26910630	+	Missense_Mutation	SNP	G	G	T			TCGA-KL-8323-01A-21D-2310-10	TCGA-KL-8323-11A-01D-2310-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fae88d21-171c-4df4-b258-3c5948a1034b	f5c7fb67-5906-4db0-ad0d-129df8e065cb	g.chr17:26910630G>T	ENST00000321765.5	-	15	2916	c.2584C>A	c.(2584-2586)Caa>Aaa	p.Q862K		NM_006461.3	NP_006452.3	Q96R06	SPAG5_HUMAN	sperm associated antigen 5	862					chromosome segregation (GO:0007059)|mitotic sister chromatid segregation (GO:0000070)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|spindle organization (GO:0007051)	cytoplasm (GO:0005737)|kinetochore (GO:0000776)|microtubule plus-end (GO:0035371)|mitotic spindle (GO:0072686)				NS(1)|breast(3)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(8)|lung(17)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	43	Lung NSC(42;0.00431)					TCCAGATCTTGCTCCTGGTTA	0.463																																						.											0													166.0	145.0	152.0					17																	26910630		2203	4300	6503	SO:0001583	missense	10615			AF063308	CCDS32594.1	17q11.2	2008-07-18			ENSG00000076382	ENSG00000076382			13452	protein-coding gene	gene with protein product	"""mitotic spindle coiled-coil related protein"", ""astrin"", ""mitotic spindle associated protein p126"""	615562				11549262	Standard	NM_006461		Approved	DEEPEST, MAP126, hMAP126	uc002hbq.3	Q96R06	OTTHUMG00000166586	ENST00000321765.5:c.2584C>A	17.37:g.26910630G>T	ENSP00000323300:p.Gln862Lys		O95213|Q9BWE8|Q9NT17|Q9UFE6	Missense_Mutation	SNP	ENST00000321765.5	37	CCDS32594.1	.	.	.	.	.	.	.	.	.	.	G	12.42	1.933531	0.34096	.	.	ENSG00000076382;ENSG00000258472	ENST00000321765;ENST00000531839	T;T	0.32515	1.45;1.45	5.17	3.07	0.35406	.	0.687189	0.13323	N	0.396492	T	0.24774	0.0601	L	0.32530	0.975	0.21290	N	0.999732	B;B	0.11235	0.004;0.0	B;B	0.08055	0.003;0.001	T	0.22977	-1.0201	10	0.87932	D	0	0.2695	11.0107	0.47661	0.0:0.0:0.627:0.373	.	267;862	E9PMD0;Q96R06	.;SPAG5_HUMAN	K	862;267	ENSP00000323300:Q862K;ENSP00000431165:Q267K	ENSP00000431165:Q267K	Q	-	1	0	SPAG5;RP11-192H23.4	23934757	0.966000	0.33281	0.403000	0.26384	0.941000	0.58515	1.752000	0.38349	0.740000	0.32651	0.650000	0.86243	CAA		0.463	SPAG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390564.2	NM_006461	
SOCS7	30837	broad.mit.edu	37	17	36520640	36520640	+	Missense_Mutation	SNP	A	A	G			TCGA-KL-8323-01A-21D-2310-10	TCGA-KL-8323-11A-01D-2310-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fae88d21-171c-4df4-b258-3c5948a1034b	f5c7fb67-5906-4db0-ad0d-129df8e065cb	g.chr17:36520640A>G	ENST00000577233.1	+	3	859	c.859A>G	c.(859-861)Act>Gct	p.T287A	SOCS7_ENST00000331159.5_Missense_Mutation_p.T287A	NM_014598.2	NP_055413.1	O14512	SOCS7_HUMAN	suppressor of cytokine signaling 7	287	Mediates interaction with SORBS3.				fat cell differentiation (GO:0045444)|insulin receptor signaling pathway (GO:0008286)|intracellular signal transduction (GO:0035556)|negative regulation of signal transduction (GO:0009968)|protein ubiquitination (GO:0016567)|regulation of growth (GO:0040008)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	SH3 domain binding (GO:0017124)			central_nervous_system(1)|endometrium(1)|kidney(1)|prostate(1)|skin(5)	9	Breast(7;3.47e-17)					CTCAGGTGAAACTGTGTCGCT	0.572																																						.											0													145.0	123.0	130.0					17																	36520640		2203	4300	6503	SO:0001583	missense	30837			AB005216	CCDS32637.1	17q12	2014-08-12			ENSG00000274211	ENSG00000274211		"""Suppressors of cytokine signaling"", ""SH2 domain containing"""	29846	protein-coding gene	gene with protein product	"""Nck, Ash and phospholipase C binding protein"", ""NCK-associated protein 4"""	608788				9344857, 12076535	Standard	XM_005257264		Approved	NAP4, NCKAP4	uc002hqa.3	O14512	OTTHUMG00000188546	ENST00000577233.1:c.859A>G	17.37:g.36520640A>G	ENSP00000464034:p.Thr287Ala		A2VCU2|Q0IJ63	Missense_Mutation	SNP	ENST00000577233.1	37	CCDS32637.1	.	.	.	.	.	.	.	.	.	.	A	11.29	1.594183	0.28445	.	.	ENSG00000174111	ENST00000331159	T	0.66815	-0.23	6.06	4.96	0.65561	.	1.199420	0.05838	N	0.618771	T	0.67748	0.2926	L	0.58101	1.795	0.51233	D	0.999913	P;P	0.41393	0.748;0.748	B;B	0.38842	0.283;0.283	T	0.55617	-0.8113	10	0.54805	T	0.06	-6.8465	13.1442	0.59452	0.8664:0.1336:0.0:0.0	.	37;287	B5MDS8;O14512	.;SOCS7_HUMAN	A	287	ENSP00000330659:T287A	ENSP00000330659:T287A	T	+	1	0	SOCS7	33774166	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	8.858000	0.92256	1.077000	0.40990	0.533000	0.62120	ACT		0.572	SOCS7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440486.4	XM_371052	
KRT20	54474	broad.mit.edu;mdanderson.org;bcgsc.ca	37	17	39041356	39041356	+	Missense_Mutation	SNP	G	G	A			TCGA-KL-8323-01A-21D-2310-10	TCGA-KL-8323-11A-01D-2310-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fae88d21-171c-4df4-b258-3c5948a1034b	f5c7fb67-5906-4db0-ad0d-129df8e065cb	g.chr17:39041356G>A	ENST00000167588.3	-	1	123	c.82C>T	c.(82-84)Cgc>Tgc	p.R28C		NM_019010.2	NP_061883.1	P35900	K1C20_HUMAN	keratin 20	28	Head.				apoptotic process (GO:0006915)|cellular response to stress (GO:0033554)|intermediate filament organization (GO:0045109)|regulation of protein secretion (GO:0050708)	cytoplasm (GO:0005737)|intermediate filament (GO:0005882)	structural constituent of cytoskeleton (GO:0005200)			NS(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|skin(1)	14		Breast(137;0.000301)|Ovarian(249;0.15)				GTCCCGAGGCGCTGCATGCCC	0.597																																						.											0													36.0	36.0	36.0					17																	39041356		2203	4300	6503	SO:0001583	missense	54474			BC031559	CCDS11379.1	17q21.2	2013-01-16			ENSG00000171431	ENSG00000171431		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	20412	protein-coding gene	gene with protein product		608218				8359595, 12515621, 16831889	Standard	NM_019010		Approved	CK20, K20, MGC35423	uc002hvl.3	P35900	OTTHUMG00000133366	ENST00000167588.3:c.82C>T	17.37:g.39041356G>A	ENSP00000167588:p.Arg28Cys		B2R6W7	Missense_Mutation	SNP	ENST00000167588.3	37	CCDS11379.1	.	.	.	.	.	.	.	.	.	.	G	16.28	3.077922	0.55753	.	.	ENSG00000171431	ENST00000167588	D	0.84070	-1.8	5.17	1.94	0.25998	.	1.630110	0.03448	N	0.210284	T	0.69842	0.3156	N	0.14661	0.345	0.09310	N	0.99999	B	0.10296	0.003	B	0.04013	0.001	T	0.58323	-0.7656	10	0.38643	T	0.18	.	4.8168	0.13371	0.0849:0.1149:0.5878:0.2124	.	28	P35900	K1C20_HUMAN	C	28	ENSP00000167588:R28C	ENSP00000167588:R28C	R	-	1	0	KRT20	36294882	0.999000	0.42202	0.609000	0.28983	0.014000	0.08584	1.653000	0.37323	1.332000	0.45431	0.655000	0.94253	CGC		0.597	KRT20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257202.2		
GAA	2548	broad.mit.edu	37	17	78082576	78082576	+	Silent	SNP	G	G	A			TCGA-KL-8323-01A-21D-2310-10	TCGA-KL-8323-11A-01D-2310-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fae88d21-171c-4df4-b258-3c5948a1034b	f5c7fb67-5906-4db0-ad0d-129df8e065cb	g.chr17:78082576G>A	ENST00000302262.3	+	8	1494	c.1275G>A	c.(1273-1275)ccG>ccA	p.P425P	GAA_ENST00000390015.3_Silent_p.P425P	NM_000152.3	NP_000143.2	P10253	LYAG_HUMAN	glucosidase, alpha; acid	425					cardiac muscle contraction (GO:0060048)|diaphragm contraction (GO:0002086)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|heart morphogenesis (GO:0003007)|locomotory behavior (GO:0007626)|lysosome organization (GO:0007040)|maltose metabolic process (GO:0000023)|muscle cell cellular homeostasis (GO:0046716)|neuromuscular process controlling balance (GO:0050885)|neuromuscular process controlling posture (GO:0050884)|regulation of the force of heart contraction (GO:0002026)|sucrose metabolic process (GO:0005985)|tissue development (GO:0009888)|vacuolar sequestering (GO:0043181)	extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)	alpha-1,4-glucosidase activity (GO:0004558)|carbohydrate binding (GO:0030246)|maltose alpha-glucosidase activity (GO:0032450)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|lung(6)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	21	all_neural(118;0.117)		OV - Ovarian serous cystadenocarcinoma(97;0.0292)|BRCA - Breast invasive adenocarcinoma(99;0.139)		Acarbose(DB00284)|Miglitol(DB00491)	GGGACTTCCCGGCCATGGTGC	0.647																																						.											0													25.0	21.0	23.0					17																	78082576		2198	4298	6496	SO:0001819	synonymous_variant	2548				CCDS32760.1	17q25.2-q25.3	2014-09-17	2008-08-01				3.2.1.20		4065	protein-coding gene	gene with protein product	"""Pompe disease"", ""glycogen storage disease type II"""	606800					Standard	NM_000152		Approved		uc002jxq.3	P10253		ENST00000302262.3:c.1275G>A	17.37:g.78082576G>A			Q09GN4|Q14351|Q16302|Q8IWE7	Silent	SNP	ENST00000302262.3	37	CCDS32760.1																																																																																				0.647	GAA-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437441.1		
LMAN1	3998	broad.mit.edu	37	18	57022610	57022610	+	Missense_Mutation	SNP	A	A	G			TCGA-KL-8323-01A-21D-2310-10	TCGA-KL-8323-11A-01D-2310-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fae88d21-171c-4df4-b258-3c5948a1034b	f5c7fb67-5906-4db0-ad0d-129df8e065cb	g.chr18:57022610A>G	ENST00000251047.5	-	3	1129	c.412T>C	c.(412-414)Ttt>Ctt	p.F138L		NM_005570.3	NP_005561.1	P49257	LMAN1_HUMAN	lectin, mannose-binding, 1	138	L-type lectin-like. {ECO:0000255|PROSITE- ProRule:PRU00658}.				blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum organization (GO:0007029)|ER to Golgi vesicle-mediated transport (GO:0006888)|Golgi organization (GO:0007030)|positive regulation of organelle organization (GO:0010638)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)|protein transport (GO:0015031)	endoplasmic reticulum membrane (GO:0005789)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|ER to Golgi transport vesicle membrane (GO:0012507)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|sarcomere (GO:0030017)	mannose binding (GO:0005537)|metal ion binding (GO:0046872)|unfolded protein binding (GO:0051082)			breast(2)|endometrium(1)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|skin(1)	16		Colorectal(73;0.0946)			Antihemophilic Factor(DB00025)	GCTGATCCAAACACAGGGCCC	0.368																																						.											0													86.0	78.0	80.0					18																	57022610		2203	4300	6503	SO:0001583	missense	3998			X71661	CCDS11974.1	18q21.3-q22	2014-09-17	2002-08-30		ENSG00000074695	ENSG00000074695			6631	protein-coding gene	gene with protein product	"""endoplasmic reticulum-golgi intermediate compartment protein 53"""	601567	"""coagulation factor V-factor VIII combined deficiency"""	F5F8D		9546392, 8854877	Standard	NM_005570		Approved	MR60, ERGIC-53, ERGIC53, gp58, MCFD1, FMFD1	uc002lhz.3	P49257	OTTHUMG00000132758	ENST00000251047.5:c.412T>C	18.37:g.57022610A>G	ENSP00000251047:p.Phe138Leu		Q12895|Q8N5I7|Q9UQG1|Q9UQG2|Q9UQG3|Q9UQG4|Q9UQG5|Q9UQG6|Q9UQG7|Q9UQG8|Q9UQG9|Q9UQH0|Q9UQH1|Q9UQH2	Missense_Mutation	SNP	ENST00000251047.5	37	CCDS11974.1	.	.	.	.	.	.	.	.	.	.	A	28.4	4.918353	0.92249	.	.	ENSG00000074695	ENST00000251047	T	0.75589	-0.95	5.52	5.52	0.82312	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);	0.060560	0.64402	D	0.000001	D	0.85331	0.5672	M	0.78344	2.41	0.58432	D	0.999999	P;B	0.36753	0.568;0.197	P;B	0.55871	0.786;0.413	D	0.85384	0.1121	10	0.49607	T	0.09	-15.3839	15.338	0.74273	1.0:0.0:0.0:0.0	.	138;138	B4DVV0;P49257	.;LMAN1_HUMAN	L	138	ENSP00000251047:F138L	ENSP00000251047:F138L	F	-	1	0	LMAN1	55173590	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.691000	0.91279	2.099000	0.63709	0.533000	0.62120	TTT		0.368	LMAN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256129.2	NM_005570	
HMHA1	23526	broad.mit.edu;mdanderson.org	37	19	1084344	1084344	+	Splice_Site	SNP	A	A	G			TCGA-KL-8323-01A-21D-2310-10	TCGA-KL-8323-11A-01D-2310-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fae88d21-171c-4df4-b258-3c5948a1034b	f5c7fb67-5906-4db0-ad0d-129df8e065cb	g.chr19:1084344A>G	ENST00000313093.2	+	22	3294	c.3063A>G	c.(3061-3063)agA>agG	p.R1021R	HMHA1_ENST00000590577.1_Splice_Site_p.R656R|HMHA1_ENST00000543365.1_Splice_Site_p.R904R|HMHA1_ENST00000536472.1_Splice_Site_p.R889R|HMHA1_ENST00000539243.2_Splice_Site_p.R1037R|HMHA1_ENST00000591169.1_3'UTR|HMHA1_ENST00000586866.1_Splice_Site_p.R1025R|HMHA1_ENST00000590214.1_Splice_Site_p.R1048R	NM_012292.3	NP_036424.2	Q92619	HMHA1_HUMAN	histocompatibility (minor) HA-1	1021					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|lung(7)|ovary(1)|prostate(2)	16		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|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)		ACGGGTGCAGAGGTGAGTGTG	0.682																																						.											0													36.0	39.0	38.0					19																	1084344		2200	4299	6499	SO:0001630	splice_region_variant	23526			D86976	CCDS32863.1, CCDS58637.1, CCDS74242.1, CCDS74243.1	19p13.3	2011-09-07				ENSG00000180448		"""Rho GTPase activating proteins"""	17102	protein-coding gene	gene with protein product		601155				9820596, 9039502	Standard	NM_012292		Approved	KIAA0223, HA-1, ARHGAP45	uc010xgd.2	Q92619		ENST00000313093.2:c.3064+1A>G	19.37:g.1084344A>G			B4DTS4|F6QP70|Q6P189|Q7LE26|Q86WS1|Q8HX84|Q9GJN9|Q9GJP0|Q9GJP1|Q9MY24	Silent	SNP	ENST00000313093.2	37	CCDS32863.1																																																																																				0.682	HMHA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458026.1		Silent
ZNF257	113835	broad.mit.edu	37	19	22256335	22256335	+	Missense_Mutation	SNP	G	G	A			TCGA-KL-8323-01A-21D-2310-10	TCGA-KL-8323-11A-01D-2310-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fae88d21-171c-4df4-b258-3c5948a1034b	f5c7fb67-5906-4db0-ad0d-129df8e065cb	g.chr19:22256335G>A	ENST00000594947.1	+	3	339	c.195G>A	c.(193-195)atG>atA	p.M65I	ZNF257_ENST00000600162.1_Missense_Mutation_p.M65I	NM_033468.2	NP_258429.2	Q9Y2Q1	ZN257_HUMAN	zinc finger protein 257	65	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)|zinc ion binding (GO:0008270)			haematopoietic_and_lymphoid_tissue(2)|lung(4)	6		all_lung(12;0.0961)|Lung NSC(12;0.103)				CCTGTAATATGAAGAGACATG	0.448																																						.											0													139.0	151.0	147.0					19																	22256335		2203	4300	6503	SO:0001583	missense	113835			AF070651	CCDS46030.1	19p12	2014-02-14			ENSG00000197134	ENSG00000197134		"""Zinc fingers, C2H2-type"", ""-"""	13498	protein-coding gene	gene with protein product		606957				10585455	Standard	NM_033468		Approved	BMZF-4	uc010ecx.3	Q9Y2Q1	OTTHUMG00000182927	ENST00000594947.1:c.195G>A	19.37:g.22256335G>A	ENSP00000470209:p.Met65Ile		B3KPS4|E9PG34|Q8NE34	Missense_Mutation	SNP	ENST00000594947.1	37	CCDS46030.1	.	.	.	.	.	.	.	.	.	.	G	0.570	-0.841484	0.02692	.	.	ENSG00000197134	ENST00000435820;ENST00000397123	.	.	.	0.195	-0.39	0.12450	Krueppel-associated box (1);	.	.	.	.	T	0.14184	0.0343	N	0.04387	-0.21	0.09310	N	1	B	0.16396	0.017	B	0.13407	0.009	T	0.19224	-1.0312	7	0.35671	T	0.21	.	.	.	.	.	65	Q9Y2Q1	ZN257_HUMAN	I	65	.	ENSP00000380312:M65I	M	+	3	0	ZNF257	22048175	0.005000	0.15991	0.022000	0.16811	0.022000	0.10575	0.268000	0.18571	-0.697000	0.05092	-0.683000	0.03753	ATG		0.448	ZNF257-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464382.1		
FFAR1	2864	broad.mit.edu	37	19	35842701	35842701	+	Missense_Mutation	SNP	G	G	A			TCGA-KL-8323-01A-21D-2310-10	TCGA-KL-8323-11A-01D-2310-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fae88d21-171c-4df4-b258-3c5948a1034b	f5c7fb67-5906-4db0-ad0d-129df8e065cb	g.chr19:35842701G>A	ENST00000246553.2	+	1	257	c.247G>A	c.(247-249)Gcg>Acg	p.A83T		NM_005303.2	NP_005294.1	O14842	FFAR1_HUMAN	free fatty acid receptor 1	83					energy reserve metabolic process (GO:0006112)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|insulin secretion (GO:0030073)|positive regulation of GTPase activity (GO:0043547)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|guanyl-nucleotide exchange factor activity (GO:0005085)|lipid binding (GO:0008289)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(1)|lung(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	10	all_lung(56;9.78e-09)|Lung NSC(56;1.46e-08)|Esophageal squamous(110;0.162)		Epithelial(14;4.58e-20)|OV - Ovarian serous cystadenocarcinoma(14;6.67e-19)|all cancers(14;2.01e-17)|LUSC - Lung squamous cell carcinoma(66;0.0417)		Icosapent(DB00159)	CCCCGTCTTCGCGGTGGCCCA	0.701																																						.											0													13.0	13.0	13.0					19																	35842701		2192	4282	6474	SO:0001583	missense	2864			AF024687	CCDS12458.1	19q13.1	2012-08-08	2006-02-15	2006-02-15	ENSG00000126266	ENSG00000126266		"""GPCR / Class A : Fatty acid receptors"""	4498	protein-coding gene	gene with protein product		603820	"""G protein-coupled receptor 40"""	GPR40		15684720	Standard	NM_005303		Approved	FFA1R	uc002nzc.2	O14842		ENST00000246553.2:c.247G>A	19.37:g.35842701G>A	ENSP00000246553:p.Ala83Thr		Q0VAS2|Q4VBL4	Missense_Mutation	SNP	ENST00000246553.2	37	CCDS12458.1	.	.	.	.	.	.	.	.	.	.	G	9.563	1.119086	0.20877	.	.	ENSG00000126266	ENST00000246553	T	0.37411	1.2	4.6	4.6	0.57074	GPCR, rhodopsin-like superfamily (1);	0.409722	0.23997	U	0.042504	T	0.15435	0.0372	N	0.12569	0.235	0.09310	N	1	P	0.48162	0.906	B	0.37650	0.255	T	0.10753	-1.0616	10	0.09338	T	0.73	-4.6107	8.5191	0.33264	0.1038:0.0:0.8962:0.0	.	83	O14842	FFAR1_HUMAN	T	83	ENSP00000246553:A83T	ENSP00000246553:A83T	A	+	1	0	FFAR1	40534541	0.005000	0.15991	0.012000	0.15200	0.003000	0.03518	1.884000	0.39668	2.375000	0.81037	0.555000	0.69702	GCG		0.701	FFAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466112.2	NM_005303	
THADA	63892	broad.mit.edu;ucsc.edu;bcgsc.ca	37	2	43507026	43507026	+	Missense_Mutation	SNP	T	T	C			TCGA-KL-8323-01A-21D-2310-10	TCGA-KL-8323-11A-01D-2310-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fae88d21-171c-4df4-b258-3c5948a1034b	f5c7fb67-5906-4db0-ad0d-129df8e065cb	g.chr2:43507026T>C	ENST00000405006.4	-	36	5525	c.5174A>G	c.(5173-5175)gAt>gGt	p.D1725G	THADA_ENST00000330266.7_Intron|THADA_ENST00000415080.2_Missense_Mutation_p.D1406G|THADA_ENST00000405975.2_Missense_Mutation_p.D1725G	NM_001083953.1|NM_001271643.1	NP_001077422.1|NP_001258572.1	Q6YHU6	THADA_HUMAN	thyroid adenoma associated	1725										breast(1)|endometrium(9)|kidney(5)|large_intestine(9)|liver(1)|lung(28)|ovary(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	66		Acute lymphoblastic leukemia(82;0.00361)|all_hematologic(82;0.00837)				AGCAAGTGTATCCTGCAACTC	0.473																																						.											0													52.0	50.0	51.0					2																	43507026		1941	4148	6089	SO:0001583	missense	63892			AY149629	CCDS46268.1, CCDS62901.1, CCDS62902.1	2p21	2008-02-05			ENSG00000115970	ENSG00000115970			19217	protein-coding gene	gene with protein product		611800				12063398, 11214970	Standard	NM_022065		Approved	FLJ21877, KIAA1767, GITA	uc002rsx.4	Q6YHU6	OTTHUMG00000152398	ENST00000405006.4:c.5174A>G	2.37:g.43507026T>C	ENSP00000385995:p.Asp1725Gly		A8K1V8|B7WNS6|Q3KR04|Q53RC6|Q53TB2|Q6YHU2|Q6ZU38|Q8IY32|Q8TAU8|Q96I88|Q9BZF7|Q9C096|Q9H6U0|Q9H6W7	Missense_Mutation	SNP	ENST00000405006.4	37	CCDS46268.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	13.26|13.26	2.182988|2.182988	0.38511|0.38511	.|.	.|.	ENSG00000115970|ENSG00000115970	ENST00000405975;ENST00000356975;ENST00000415080;ENST00000405006|ENST00000407351	T;T;T|.	0.12879|.	2.89;2.64;2.89|.	5.14|5.14	2.51|2.51	0.30379|0.30379	.|.	0.302295|.	0.30547|.	N|.	0.009382|.	T|T	0.34337|0.34337	0.0894|0.0894	L|L	0.41824|0.41824	1.3|1.3	0.25115|0.25115	N|N	0.990682|0.990682	B;B|.	0.26483|.	0.15;0.125|.	B;B|.	0.22601|.	0.04;0.026|.	T|T	0.22347|0.22347	-1.0219|-1.0219	10|5	0.22706|.	T|.	0.39|.	-25.4555|-25.4555	4.9913|4.9913	0.14216|0.14216	0.0:0.0963:0.1842:0.7195|0.0:0.0963:0.1842:0.7195	.|.	1652;1725|.	B6ZDQ0;Q6YHU6|.	.;THADA_HUMAN|.	G|V	1725;1652;1406;1725|965	ENSP00000386088:D1725G;ENSP00000416048:D1406G;ENSP00000385995:D1725G|.	ENSP00000349464:D1652G|.	D|I	-|-	2|1	0|0	THADA|THADA	43360530|43360530	0.992000|0.992000	0.36948|0.36948	0.997000|0.997000	0.53966|0.53966	0.998000|0.998000	0.95712|0.95712	0.517000|0.517000	0.22832|0.22832	0.761000|0.761000	0.33130|0.33130	0.533000|0.533000	0.62120|0.62120	GAT|ATA		0.473	THADA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326070.3	NM_022065	
SMYD1	150572	broad.mit.edu	37	2	88387571	88387571	+	Missense_Mutation	SNP	T	T	C			TCGA-KL-8323-01A-21D-2310-10	TCGA-KL-8323-11A-01D-2310-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fae88d21-171c-4df4-b258-3c5948a1034b	f5c7fb67-5906-4db0-ad0d-129df8e065cb	g.chr2:88387571T>C	ENST00000419482.2	+	3	590	c.505T>C	c.(505-507)Tac>Cac	p.Y169H	SMYD1_ENST00000444564.2_Missense_Mutation_p.Y169H|SMYD1_ENST00000438570.1_Intron|SMYD1_ENST00000468008.1_3'UTR	NM_198274.3	NP_938015.1	Q8NB12	SMYD1_HUMAN	SET and MYND domain containing 1	169	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				chromatin remodeling (GO:0006338)|heart development (GO:0007507)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of myoblast differentiation (GO:0045663)|positive regulation of myotube differentiation (GO:0010831)|skeletal muscle cell differentiation (GO:0035914)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|metal ion binding (GO:0046872)|transcription corepressor activity (GO:0003714)			NS(1)|breast(4)|central_nervous_system(1)|large_intestine(6)|lung(19)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	41						CAGCATGCAGTACATCTCGCA	0.612																																						.											0													113.0	74.0	87.0					2																	88387571		2203	4300	6503	SO:0001583	missense	150572			AF086123	CCDS33240.1	2p11.1	2011-07-01			ENSG00000115593	ENSG00000115593		"""Zinc fingers, MYND-type"", ""Chromatin-modifying enzymes / K-methyltransferases"""	20986	protein-coding gene	gene with protein product		606846				11923873	Standard	NM_198274		Approved	BOP, ZMYND22, KMT3D	uc002ssr.3	Q8NB12	OTTHUMG00000155045	ENST00000419482.2:c.505T>C	2.37:g.88387571T>C	ENSP00000393453:p.Tyr169His		A0AV30|A6NE13	Missense_Mutation	SNP	ENST00000419482.2	37	CCDS33240.1	.	.	.	.	.	.	.	.	.	.	T	17.71	3.457883	0.63401	.	.	ENSG00000115593	ENST00000419482;ENST00000444564;ENST00000295833	T;T	0.81415	-1.49;-1.49	5.04	5.04	0.67666	SET domain (2);	0.228496	0.46442	D	0.000286	D	0.82770	0.5109	L	0.36672	1.1	0.80722	D	1	D	0.60575	0.988	D	0.67103	0.949	T	0.83212	-0.0073	10	0.52906	T	0.07	-25.3302	10.3599	0.43987	0.0:0.0804:0.0:0.9196	.	169	Q8NB12	SMYD1_HUMAN	H	169;169;3	ENSP00000393453:Y169H;ENSP00000407888:Y169H	ENSP00000295833:Y3H	Y	+	1	0	SMYD1	88168686	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	3.230000	0.51286	2.007000	0.58848	0.459000	0.35465	TAC		0.612	SMYD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338229.2	XM_097915	
LOC150776	150776	broad.mit.edu	37	2	132273252	132273252	+	RNA	SNP	C	C	T			TCGA-KL-8323-01A-21D-2310-10	TCGA-KL-8323-11A-01D-2310-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fae88d21-171c-4df4-b258-3c5948a1034b	f5c7fb67-5906-4db0-ad0d-129df8e065cb	g.chr2:132273252C>T	ENST00000438378.2	+	0	1312					NR_026922.1																						TTGCCAACAGCCTGAAGCCAG	0.652																																						.											0																																												0																															2.37:g.132273252C>T				RNA	SNP	ENST00000438378.2	37																																																																																					0.652	AC093838.4-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000331819.7		
CCDC74A	90557	broad.mit.edu;mdanderson.org	37	2	132290278	132290278	+	Missense_Mutation	SNP	G	G	A	rs138310081	byFrequency	TCGA-KL-8323-01A-21D-2310-10	TCGA-KL-8323-11A-01D-2310-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fae88d21-171c-4df4-b258-3c5948a1034b	f5c7fb67-5906-4db0-ad0d-129df8e065cb	g.chr2:132290278G>A	ENST00000295171.6	+	5	938	c.800G>A	c.(799-801)cGa>cAa	p.R267Q	CCDC74A_ENST00000409856.3_Missense_Mutation_p.R201Q|CCDC74A_ENST00000467992.2_3'UTR	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	267										endometrium(4)|large_intestine(3)|lung(9)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19						CTTCCCCTGCGAAAGCCCACC	0.642													g|||	15	0.00299521	0.0106	0.0	5008	,	,		18428	0.0		0.0	False		,,,				2504	0.001					.											0								G	GLN/ARG	34,4372		0,34,2169	76.0	79.0	78.0		800	1.7	1.0	2	dbSNP_134	78	0,8600		0,0,4300	no	missense	CCDC74A	NM_138770.1	43	0,34,6469	AA,AG,GG		0.0,0.7717,0.2614	probably-damaging	267/379	132290278	34,12972	2203	4300	6503	SO:0001583	missense	90557				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.800G>A	2.37:g.132290278G>A	ENSP00000295171:p.Arg267Gln		Q6P4I5	Missense_Mutation	SNP	ENST00000295171.6	37	CCDS2167.1	.	.	.	.	.	.	.	.	.	.	.	10.85	1.465782	0.26335	0.007717	0.0	ENSG00000163040	ENST00000295171;ENST00000409856	T;T	0.55052	0.54;0.54	2.66	1.72	0.24424	.	0.235784	0.21781	U	0.069216	T	0.50154	0.1599	L	0.46741	1.465	0.80722	D	1	D;P	0.89917	1.0;0.727	D;B	0.79108	0.992;0.035	T	0.56318	-0.7999	10	0.72032	D	0.01	.	4.841	0.13491	0.1891:0.0:0.8109:0.0	.	201;267	Q96AQ1-2;Q96AQ1	.;CC74A_HUMAN	Q	267;201	ENSP00000295171:R267Q;ENSP00000387009:R201Q	ENSP00000295171:R267Q	R	+	2	0	CCDC74A	132006748	1.000000	0.71417	0.991000	0.47740	0.057000	0.15508	1.217000	0.32455	1.192000	0.43071	0.194000	0.17425	CGA		0.642	CCDC74A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254570.2	NM_138770	
CCDC74A	90557	broad.mit.edu;mdanderson.org	37	2	132290352	132290352	+	Missense_Mutation	SNP	G	G	C	rs376130814		TCGA-KL-8323-01A-21D-2310-10	TCGA-KL-8323-11A-01D-2310-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fae88d21-171c-4df4-b258-3c5948a1034b	f5c7fb67-5906-4db0-ad0d-129df8e065cb	g.chr2:132290352G>C	ENST00000295171.6	+	5	1012	c.874G>C	c.(874-876)Gag>Cag	p.E292Q	CCDC74A_ENST00000409856.3_Missense_Mutation_p.E226Q|CCDC74A_ENST00000467992.2_3'UTR	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	292										endometrium(4)|large_intestine(3)|lung(9)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19						GCAGACCCAAGAGGTGAGGCC	0.652																																						.											0								G	GLN/GLU	0,4404		0,0,2202	32.0	35.0	34.0		874	2.7	1.0	2		34	2,8588		0,2,4293	no	missense	CCDC74A	NM_138770.1	29	0,2,6495	CC,CG,GG		0.0233,0.0,0.0154	probably-damaging	292/379	132290352	2,12992	2202	4295	6497	SO:0001583	missense	90557				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.874G>C	2.37:g.132290352G>C	ENSP00000295171:p.Glu292Gln		Q6P4I5	Missense_Mutation	SNP	ENST00000295171.6	37	CCDS2167.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	14.21|14.21	2.466460|2.466460	0.43839|0.43839	0.0|0.0	2.33E-4|2.33E-4	ENSG00000163040|ENSG00000163040	ENST00000295171;ENST00000409856|ENST00000434330	T;T|T	0.53206|0.55930	0.63;0.63|0.49	2.66|2.66	2.66|2.66	0.31614|0.31614	.|.	0.000000|.	0.36854|.	U|.	0.002376|.	T|T	0.60818|0.60818	0.2298|0.2298	M|M	0.72894|0.72894	2.215|2.215	0.80722|0.80722	D|D	1|1	D;D|.	0.76494|.	0.999;0.968|.	D;D|.	0.80764|.	0.994;0.969|.	T|T	0.61710|0.61710	-0.7007|-0.7007	10|7	0.87932|0.51188	D|T	0|0.08	.|.	9.0698|9.0698	0.36486|0.36486	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	226;292|.	Q96AQ1-2;Q96AQ1|.	.;CC74A_HUMAN|.	Q|N	292;226|180	ENSP00000295171:E292Q;ENSP00000387009:E226Q|ENSP00000406839:K180N	ENSP00000295171:E292Q|ENSP00000406839:K180N	E|K	+|+	1|3	0|2	CCDC74A|CCDC74A	132006822|132006822	1.000000|1.000000	0.71417|0.71417	0.993000|0.993000	0.49108|0.49108	0.289000|0.289000	0.27227|0.27227	4.189000|4.189000	0.58358|0.58358	1.192000|1.192000	0.43071|0.43071	0.194000|0.194000	0.17425|0.17425	GAG|AAG		0.652	CCDC74A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254570.2	NM_138770	
NEB	4703	broad.mit.edu	37	2	152350685	152350685	+	Missense_Mutation	SNP	T	T	C	rs200544122		TCGA-KL-8323-01A-21D-2310-10	TCGA-KL-8323-11A-01D-2310-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fae88d21-171c-4df4-b258-3c5948a1034b	f5c7fb67-5906-4db0-ad0d-129df8e065cb	g.chr2:152350685T>C	ENST00000172853.10	-	141	19148	c.19001A>G	c.(19000-19002)aAc>aGc	p.N6334S	NEB_ENST00000498015.2_Intron|NEB_ENST00000509223.2_Missense_Mutation_p.N134S|NEB_ENST00000427231.2_Missense_Mutation_p.N8190S|NEB_ENST00000603639.1_Missense_Mutation_p.N8190S|NEB_ENST00000397345.3_Missense_Mutation_p.N8190S|RIF1_ENST00000457745.1_Intron|NEB_ENST00000409198.1_Missense_Mutation_p.N6334S|NEB_ENST00000397336.2_Missense_Mutation_p.N165S|NEB_ENST00000604864.1_Missense_Mutation_p.N8190S			P20929	NEBU_HUMAN	nebulin	6334					muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|regulation of actin filament length (GO:0030832)|somatic muscle development (GO:0007525)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Z disc (GO:0030018)	structural constituent of muscle (GO:0008307)			NS(5)|autonomic_ganglia(3)|breast(9)|central_nervous_system(5)|cervix(3)|endometrium(35)|kidney(16)|large_intestine(77)|liver(1)|lung(99)|ovary(9)|pancreas(3)|prostate(13)|skin(7)|stomach(8)|upper_aerodigestive_tract(6)|urinary_tract(2)	301				BRCA - Breast invasive adenocarcinoma(221;0.219)		CGAGCTAATGTTTTCTTGATT	0.428																																						.											0													109.0	90.0	96.0					2																	152350685		1881	4117	5998	SO:0001583	missense	4703			X83957	CCDS46424.1, CCDS54407.1, CCDS54408.1, CCDS74588.1	2q22	2014-09-17			ENSG00000183091	ENSG00000183091			7720	protein-coding gene	gene with protein product	"""nemaline myopathy type 2"""	161650		NEM2		10051637, 9359044	Standard	NM_001164507		Approved	NEB177D	uc010fnx.3	P20929	OTTHUMG00000153784	ENST00000172853.10:c.19001A>G	2.37:g.152350685T>C	ENSP00000172853:p.Asn6334Ser		F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Missense_Mutation	SNP	ENST00000172853.10	37		0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	T|T	15.08|15.08	2.728603|2.728603	0.48833|0.48833	.|.	.|.	ENSG00000183091|ENSG00000183091	ENST00000409198;ENST00000397345;ENST00000427231;ENST00000397342;ENST00000413693;ENST00000172853;ENST00000397336;ENST00000509223|ENST00000397337;ENST00000434685	T;T;T;T;T;T;T|.	0.51325|.	0.71;0.71;0.71;0.71;0.71;0.71;0.71|.	5.82|5.82	5.82|5.82	0.92795|0.92795	.|.	0.092478|.	0.46758|.	D|.	0.000265|.	D|D	0.83275|0.83275	0.5219|0.5219	M|M	0.88979|0.88979	2.995|2.995	0.50171|0.50171	D|D	0.999852|0.999852	B;B;B;P;P;D|.	0.69078|.	0.445;0.087;0.019;0.938;0.932;0.997|.	P;B;B;P;D;D|.	0.67103|.	0.497;0.232;0.05;0.785;0.949;0.93|.	D|D	0.86179|0.86179	0.1605|0.1605	10|5	0.29301|.	T|.	0.29|.	.|.	15.8312|15.8312	0.78752|0.78752	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	134;165;134;6334;2734;8190|.	B7Z6B9;B7Z6P9;B7Z6N8;P20929;Q14215;F8WCL5|.	.;.;.;NEBU_HUMAN;.;.|.	S|A	6334;8190;8190;2352;2734;6334;165;134|324;493	ENSP00000386259:N6334S;ENSP00000380505:N8190S;ENSP00000416578:N8190S;ENSP00000410961:N2734S;ENSP00000172853:N6334S;ENSP00000380497:N165S;ENSP00000427083:N134S|.	ENSP00000172853:N6334S|.	N|T	-|-	2|1	0|0	NEB|NEB	152058931|152058931	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	4.356000|4.356000	0.59430|0.59430	2.207000|2.207000	0.71202|0.71202	0.533000|0.533000	0.62120|0.62120	AAC|ACA		0.428	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543	
GAL3ST2	64090	broad.mit.edu;ucsc.edu	37	2	242741375	242741375	+	Missense_Mutation	SNP	C	C	T	rs376256085		TCGA-KL-8323-01A-21D-2310-10	TCGA-KL-8323-11A-01D-2310-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fae88d21-171c-4df4-b258-3c5948a1034b	f5c7fb67-5906-4db0-ad0d-129df8e065cb	g.chr2:242741375C>T	ENST00000192314.6	+	3	430	c.299C>T	c.(298-300)gCg>gTg	p.A100V	AC114730.5_ENST00000437438.1_RNA	NM_022134.2	NP_071417.2	Q9H3Q3	G3ST2_HUMAN	galactose-3-O-sulfotransferase 2	100					biosynthetic process (GO:0009058)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	galactosylceramide sulfotransferase activity (GO:0001733)|sulfotransferase activity (GO:0008146)			endometrium(1)|kidney(1)|large_intestine(1)|lung(9)|prostate(1)|skin(1)	14		all_cancers(19;1.09e-40)|all_epithelial(40;2.03e-18)|Breast(86;1.53e-05)|all_lung(227;0.00338)|Renal(207;0.00502)|Ovarian(221;0.00716)|Lung NSC(271;0.012)|Esophageal squamous(248;0.129)|Melanoma(123;0.144)|all_hematologic(139;0.158)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;4.59e-33)|all cancers(36;9.89e-31)|OV - Ovarian serous cystadenocarcinoma(60;7.89e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.63e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0833)		CTCTTCCTGGCGCGCTACGTG	0.662																																						.											0													46.0	44.0	44.0					2																	242741375		2201	4300	6501	SO:0001583	missense	64090			AB040610	CCDS33427.1	2q37.2	2014-05-19			ENSG00000154252	ENSG00000154252		"""Sulfotransferases, membrane-bound"""	24869	protein-coding gene	gene with protein product		608237				11029462	Standard	NM_022134		Approved	GP3ST	uc002wcj.1	Q9H3Q3	OTTHUMG00000151473	ENST00000192314.6:c.299C>T	2.37:g.242741375C>T	ENSP00000192314:p.Ala100Val		Q17RK0|Q57Z52	Missense_Mutation	SNP	ENST00000192314.6	37	CCDS33427.1	.	.	.	.	.	.	.	.	.	.	C	15.32	2.797667	0.50208	.	.	ENSG00000154252	ENST00000192314	T	0.16897	2.31	3.8	3.8	0.43715	.	0.293227	0.29451	N	0.012115	T	0.16811	0.0404	L	0.31157	0.91	0.30871	N	0.732501	D	0.54207	0.965	P	0.47891	0.56	T	0.03514	-1.1029	10	0.25106	T	0.35	-12.4576	14.3673	0.66815	0.0:1.0:0.0:0.0	.	100	Q9H3Q3	G3ST2_HUMAN	V	100	ENSP00000192314:A100V	ENSP00000192314:A100V	A	+	2	0	GAL3ST2	242390048	0.290000	0.24343	0.957000	0.39632	0.024000	0.10985	3.739000	0.55075	2.118000	0.64928	0.306000	0.20318	GCG		0.662	GAL3ST2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322792.1	NM_022134	
PATZ1	23598	broad.mit.edu	37	22	31741114	31741114	+	Missense_Mutation	SNP	A	A	G			TCGA-KL-8323-01A-21D-2310-10	TCGA-KL-8323-11A-01D-2310-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fae88d21-171c-4df4-b258-3c5948a1034b	f5c7fb67-5906-4db0-ad0d-129df8e065cb	g.chr22:31741114A>G	ENST00000266269.5	-	1	1104	c.475T>C	c.(475-477)Tcc>Ccc	p.S159P	AC005003.1_ENST00000504184.2_5'Flank|PATZ1_ENST00000215919.3_Missense_Mutation_p.S159P|PATZ1_ENST00000405309.3_Missense_Mutation_p.S159P|PATZ1_ENST00000351933.4_Missense_Mutation_p.S159P	NM_014323.2	NP_055138.2	Q9HBE1	PATZ1_HUMAN	POZ (BTB) and AT hook containing zinc finger 1	159					male gonad development (GO:0008584)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|T cell differentiation (GO:0030217)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)		EWSR1/PATZ1(2)	NS(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|skin(2)	12						TGTACGTTGGACTGTTTGATG	0.577																																						.											0													142.0	150.0	147.0					22																	31741114		2203	4300	6503	SO:0001583	missense	23598			AL096880	CCDS13894.1, CCDS13895.1, CCDS13896.1, CCDS46691.1	22q12.2	2013-01-09	2006-09-19	2006-09-19	ENSG00000100105	ENSG00000100105		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	13071	protein-coding gene	gene with protein product		605165	"""zinc finger protein 278"""	ZNF278		10591208, 18241078, 18401526	Standard	NM_014323		Approved	MAZR, dJ400N23, ZBTB19, ZSG, RIAZ, PATZ	uc003akq.3	Q9HBE1	OTTHUMG00000151254	ENST00000266269.5:c.475T>C	22.37:g.31741114A>G	ENSP00000266269:p.Ser159Pro		Q9HBE2|Q9HBE3|Q9P1A9|Q9UDU0|Q9Y529	Missense_Mutation	SNP	ENST00000266269.5	37	CCDS13894.1	.	.	.	.	.	.	.	.	.	.	A	18.72	3.683389	0.68157	.	.	ENSG00000100105	ENST00000266269;ENST00000405309;ENST00000351933;ENST00000215919	T;T;T;T	0.70045	-0.45;-0.45;-0.45;-0.45	4.1	4.1	0.47936	BTB/POZ-like (1);BTB/POZ (1);BTB/POZ fold (1);	0.117336	0.64402	D	0.000013	T	0.78130	0.4235	M	0.62723	1.935	0.58432	D	0.999998	D;D;D;D	0.76494	0.994;0.994;0.999;0.994	P;P;D;P	0.83275	0.81;0.81;0.996;0.81	T	0.80190	-0.1485	10	0.66056	D	0.02	-16.0422	12.5937	0.56456	1.0:0.0:0.0:0.0	.	159;159;159;159	Q9HBE1-4;Q9HBE1-3;Q9HBE1;Q9HBE1-2	.;.;PATZ1_HUMAN;.	P	159	ENSP00000266269:S159P;ENSP00000384173:S159P;ENSP00000337520:S159P;ENSP00000215919:S159P	ENSP00000215919:S159P	S	-	1	0	PATZ1	30071114	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	5.863000	0.69568	1.635000	0.50512	0.459000	0.35465	TCC		0.577	PATZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321932.1	NM_032052	
SFI1	9814	broad.mit.edu;ucsc.edu	37	22	32000342	32000342	+	Silent	SNP	C	C	T			TCGA-KL-8323-01A-21D-2310-10	TCGA-KL-8323-11A-01D-2310-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fae88d21-171c-4df4-b258-3c5948a1034b	f5c7fb67-5906-4db0-ad0d-129df8e065cb	g.chr22:32000342C>T	ENST00000400288.2	+	19	2034	c.1929C>T	c.(1927-1929)gaC>gaT	p.D643D	SFI1_ENST00000400289.1_Silent_p.D561D|SFI1_ENST00000443011.1_Silent_p.D490D|SFI1_ENST00000414585.1_Silent_p.D490D|SFI1_ENST00000540643.1_Silent_p.D588D|SFI1_ENST00000443326.1_Silent_p.D561D|SFI1_ENST00000432498.1_Silent_p.D612D	NM_001007467.2	NP_001007468.1	A8K8P3	SFI1_HUMAN	Sfi1 homolog, spindle assembly associated (yeast)	643	Interaction with CETN2.				G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|negative regulation of phosphatase activity (GO:0010923)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)	phosphatase binding (GO:0019902)			NS(2)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|large_intestine(7)|liver(1)|lung(11)|ovary(1)|prostate(3)|upper_aerodigestive_tract(3)	38						TGCGAGCAGACCTGCACCACC	0.647											OREG0003526	type=REGULATORY REGION|Gene=SFI1|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																										.											0													13.0	18.0	16.0					22																	32000342		2085	4216	6301	SO:0001819	synonymous_variant	9814			AB011114	CCDS43004.1, CCDS43005.1, CCDS58803.1, CCDS58804.1	22q12.2	2014-06-13			ENSG00000198089	ENSG00000198089			29064	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 139"""	612765				14504268	Standard	NM_001007467		Approved	KIAA0542, PISD, PPP1R139	uc003ale.4	A8K8P3	OTTHUMG00000030249	ENST00000400288.2:c.1929C>T	22.37:g.32000342C>T		829	A1L373|A1L387|A2A2L2|B1AKL9|B5MDB7|B7Z1V6|B7Z8G3|B7ZBE2|B7ZBE3|O60289|Q2TAN8|Q5W1B5|Q86TK0|Q8N4U8|Q8N8C1|Q8WU14	Silent	SNP	ENST00000400288.2	37	CCDS43004.1																																																																																				0.647	SFI1-023	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337180.3	NM_014775	
VILL	50853	broad.mit.edu	37	3	38040855	38040855	+	Silent	SNP	C	C	T			TCGA-KL-8323-01A-21D-2310-10	TCGA-KL-8323-11A-01D-2310-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fae88d21-171c-4df4-b258-3c5948a1034b	f5c7fb67-5906-4db0-ad0d-129df8e065cb	g.chr3:38040855C>T	ENST00000283713.6	+	11	1373	c.1107C>T	c.(1105-1107)gaC>gaT	p.D369D	VILL_ENST00000465644.1_Silent_p.D87D|VILL_ENST00000383759.2_Silent_p.D369D			O15195	VILL_HUMAN	villin-like	369					actin filament capping (GO:0051693)|cytoskeleton organization (GO:0007010)	actin cytoskeleton (GO:0015629)	structural constituent of cytoskeleton (GO:0005200)			cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(5)|liver(1)|lung(7)|ovary(1)|pancreas(1)|prostate(3)|stomach(3)|urinary_tract(2)	28				KIRC - Kidney renal clear cell carcinoma(284;0.0525)|Kidney(284;0.0661)		TAAAGCTGGACGTGGGCAAGC	0.627																																						.											0													98.0	83.0	88.0					3																	38040855		2203	4300	6503	SO:0001819	synonymous_variant	50853				CCDS2670.2	3p21	2004-07-28			ENSG00000136059	ENSG00000136059			30906	protein-coding gene	gene with protein product						9179494	Standard	XM_005265191		Approved		uc003chl.3	O15195	OTTHUMG00000130814	ENST00000283713.6:c.1107C>T	3.37:g.38040855C>T			A8MZP1|Q9BT80|Q9BWH7	Silent	SNP	ENST00000283713.6	37	CCDS2670.2																																																																																				0.627	VILL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253360.3	NM_015873	
VEPH1	79674	broad.mit.edu	37	3	157082297	157082297	+	Missense_Mutation	SNP	T	T	C			TCGA-KL-8323-01A-21D-2310-10	TCGA-KL-8323-11A-01D-2310-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fae88d21-171c-4df4-b258-3c5948a1034b	f5c7fb67-5906-4db0-ad0d-129df8e065cb	g.chr3:157082297T>C	ENST00000362010.2	-	8	1439	c.1132A>G	c.(1132-1134)Aaa>Gaa	p.K378E	RP11-550I24.2_ENST00000487238.1_RNA|VEPH1_ENST00000543418.1_Missense_Mutation_p.K378E|VEPH1_ENST00000392833.2_Missense_Mutation_p.K378E|VEPH1_ENST00000392832.2_Missense_Mutation_p.K378E	NM_001167912.1	NP_001161384.1	Q14D04	MELT_HUMAN	ventricular zone expressed PH domain-containing 1	378						plasma membrane (GO:0005886)				autonomic_ganglia(1)|breast(5)|cervix(1)|kidney(3)|large_intestine(9)|lung(22)|ovary(1)|pancreas(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	48			Lung(72;0.0272)|LUSC - Lung squamous cell carcinoma(72;0.0461)			GTGCTGATTTTTCTCCTAAAG	0.353																																						.											0													95.0	91.0	92.0					3																	157082297		2203	4300	6503	SO:0001583	missense	79674			AL713656	CCDS3179.1, CCDS54661.1, CCDS54662.1, CCDS54663.1	3q24-q25	2013-01-10	2012-12-10		ENSG00000197415	ENSG00000197415		"""Pleckstrin homology (PH) domain containing"""	25735	protein-coding gene	gene with protein product		609594	"""ventricular zone expressed PH domain homolog 1 (zebrafish)"""			11214970, 15388229	Standard	NM_024621		Approved	FLJ12604, KIAA1692	uc003fbk.2	Q14D04	OTTHUMG00000158711	ENST00000362010.2:c.1132A>G	3.37:g.157082297T>C	ENSP00000354919:p.Lys378Glu		D3DNL0|F5GZ91|Q2TAA9|Q3MIX2|Q6PEL3|Q86TL5|Q8TCR3|Q96SP7|Q9C0H1|Q9H9Q7	Missense_Mutation	SNP	ENST00000362010.2	37	CCDS3179.1	.	.	.	.	.	.	.	.	.	.	T	9.139	1.013384	0.19277	.	.	ENSG00000197415	ENST00000392833;ENST00000362010;ENST00000543418;ENST00000392832	T;T;T;T	0.08896	3.04;3.05;3.04;3.05	5.61	1.96	0.26148	.	0.275741	0.39341	N	0.001393	T	0.03390	0.0098	N	0.14661	0.345	0.58432	D	0.999997	B;B	0.06786	0.0;0.001	B;B	0.08055	0.003;0.002	T	0.40270	-0.9572	10	0.02654	T	1	0.0063	5.7345	0.18059	0.0:0.506:0.0:0.494	.	378;378	Q14D04-2;Q14D04	.;MELT_HUMAN	E	378	ENSP00000376578:K378E;ENSP00000354919:K378E;ENSP00000446258:K378E;ENSP00000376577:K378E	ENSP00000354919:K378E	K	-	1	0	VEPH1	158564991	1.000000	0.71417	0.716000	0.30569	0.861000	0.49209	3.419000	0.52728	0.420000	0.25954	0.528000	0.53228	AAA		0.353	VEPH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351845.3	NM_024621	
AADAT	51166	broad.mit.edu	37	4	171009684	171009684	+	Missense_Mutation	SNP	C	C	T			TCGA-KL-8323-01A-21D-2310-10	TCGA-KL-8323-11A-01D-2310-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fae88d21-171c-4df4-b258-3c5948a1034b	f5c7fb67-5906-4db0-ad0d-129df8e065cb	g.chr4:171009684C>T	ENST00000337664.4	-	2	375	c.99G>A	c.(97-99)atG>atA	p.M33I	AADAT_ENST00000353187.2_Missense_Mutation_p.M33I|AADAT_ENST00000509167.1_Missense_Mutation_p.M37I|AADAT_ENST00000515480.1_Missense_Mutation_p.M33I	NM_016228.3	NP_057312.1	Q8N5Z0	AADAT_HUMAN	aminoadipate aminotransferase	33					2-oxoglutarate metabolic process (GO:0006103)|biosynthetic process (GO:0009058)|cellular nitrogen compound metabolic process (GO:0034641)|glutamate metabolic process (GO:0006536)|kynurenine metabolic process (GO:0070189)|L-kynurenine metabolic process (GO:0097052)|L-lysine catabolic process to acetyl-CoA via saccharopine (GO:0033512)|lysine catabolic process (GO:0006554)|small molecule metabolic process (GO:0044281)|tryptophan catabolic process (GO:0006569)|tryptophan catabolic process to kynurenine (GO:0019441)	mitochondrial matrix (GO:0005759)	2-aminoadipate transaminase activity (GO:0047536)|kynurenine-oxoglutarate transaminase activity (GO:0016212)|protein homodimerization activity (GO:0042803)|pyridoxal phosphate binding (GO:0030170)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|pancreas(1)|stomach(1)	11		Prostate(90;0.00601)|Renal(120;0.0183)|all_neural(102;0.122)|Melanoma(52;0.17)		GBM - Glioblastoma multiforme(119;0.0355)|LUSC - Lung squamous cell carcinoma(193;0.118)		CCAAGGAGATCATCGATTTTG	0.388																																						.											0													152.0	133.0	139.0					4																	171009684		2203	4300	6503	SO:0001583	missense	51166			AF097994	CCDS3814.1, CCDS75209.1	4q33	2010-12-09			ENSG00000109576	ENSG00000109576	2.6.1.39		17929	protein-coding gene	gene with protein product	"""kynurenine aminotransferase II"", ""L kynurenine/alpha aminoadipate aminotransferase"""	611754				12126930, 10441733	Standard	NM_182662		Approved	KATII, KAT2	uc003isr.3	Q8N5Z0	OTTHUMG00000160912	ENST00000337664.4:c.99G>A	4.37:g.171009684C>T	ENSP00000336808:p.Met33Ile		B3KP84|Q9UL02	Missense_Mutation	SNP	ENST00000337664.4	37	CCDS3814.1	.	.	.	.	.	.	.	.	.	.	C	0.137	-1.107192	0.01813	.	.	ENSG00000109576	ENST00000337664;ENST00000515480;ENST00000509167;ENST00000353187;ENST00000510340;ENST00000507375;ENST00000502392	T;T;T;T;T;T;T	0.38077	1.16;1.16;1.16;1.16;2.2;2.2;2.2	5.19	3.43	0.39272	Pyridoxal phosphate-dependent transferase, major domain (1);	0.671285	0.15651	N	0.251382	T	0.18002	0.0432	N	0.05510	-0.035	0.23425	N	0.9977	B;B	0.09022	0.002;0.001	B;B	0.09377	0.004;0.003	T	0.20042	-1.0287	10	0.29301	T	0.29	0.8926	8.1753	0.31278	0.0:0.2958:0.4236:0.2806	.	37;33	Q8N5Z0-2;Q8N5Z0	.;AADAT_HUMAN	I	33;33;37;33;24;33;33	ENSP00000336808:M33I;ENSP00000423341:M33I;ENSP00000423190:M37I;ENSP00000226840:M33I;ENSP00000425067:M24I;ENSP00000421389:M33I;ENSP00000423843:M33I	ENSP00000336808:M33I	M	-	3	0	AADAT	171246259	1.000000	0.71417	0.606000	0.28943	0.002000	0.02628	1.159000	0.31749	0.543000	0.28864	-0.165000	0.13383	ATG		0.388	AADAT-004	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000362952.1	NM_016228	
FAM153B	202134	broad.mit.edu	37	5	175530235	175530235	+	Missense_Mutation	SNP	A	A	C			TCGA-KL-8323-01A-21D-2310-10	TCGA-KL-8323-11A-01D-2310-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fae88d21-171c-4df4-b258-3c5948a1034b	f5c7fb67-5906-4db0-ad0d-129df8e065cb	g.chr5:175530235A>C	ENST00000253490.4	+	13	727	c.670A>C	c.(670-672)Atc>Ctc	p.I224L	FAM153B_ENST00000510151.1_Missense_Mutation_p.I147L|FAM153B_ENST00000512862.1_Intron|FAM153B_ENST00000515817.1_Missense_Mutation_p.I147L			P0C7A2	F153B_HUMAN	family with sequence similarity 153, member B	224										endometrium(3)|kidney(2)|large_intestine(1)|lung(8)|ovary(1)|prostate(1)	16	all_cancers(89;0.00406)|Renal(175;0.000269)|Lung NSC(126;0.0103)|all_lung(126;0.0164)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)|all_hematologic(541;0.214)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)	Kidney(146;0.0965)		CCTAGTTCTGATCAGGGATGT	0.507																																						.											0													165.0	174.0	171.0					5																	175530235		2203	4300	6503	SO:0001583	missense	202134			AK055006	CCDS43401.1, CCDS43401.2	5q35.2	2010-05-12			ENSG00000182230	ENSG00000182230			27323	protein-coding gene	gene with protein product							Standard	NM_001265615		Approved		uc031smb.1	P0C7A2	OTTHUMG00000163181	ENST00000253490.4:c.670A>C	5.37:g.175530235A>C	ENSP00000253490:p.Ile224Leu		A8MTI1	Missense_Mutation	SNP	ENST00000253490.4	37		.	.	.	.	.	.	.	.	.	.	A	1.491	-0.554597	0.03996	.	.	ENSG00000182230	ENST00000515817;ENST00000253490	.	.	.	1.26	-2.53	0.06326	.	.	.	.	.	T	0.16557	0.0398	N	0.08118	0	0.09310	N	1	B	0.15141	0.012	B	0.08055	0.003	T	0.19614	-1.0300	8	0.87932	D	0	.	5.9593	0.19291	0.3919:0.6081:0.0:0.0	.	224	P0C7A2	F153B_HUMAN	L	147;224	.	ENSP00000253490:I224L	I	+	1	0	FAM153B	175462841	0.002000	0.14202	0.000000	0.03702	0.005000	0.04900	0.742000	0.26216	-0.649000	0.05430	0.145000	0.16022	ATC		0.507	FAM153B-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_001079529	
ZC4H2	55906	broad.mit.edu;bcgsc.ca	37	X	64137684	64137684	+	Silent	SNP	C	C	T	rs149235340	byFrequency	TCGA-KL-8323-01A-21D-2310-10	TCGA-KL-8323-11A-01D-2310-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fae88d21-171c-4df4-b258-3c5948a1034b	f5c7fb67-5906-4db0-ad0d-129df8e065cb	g.chrX:64137684C>T	ENST00000374839.3	-	5	760	c.654G>A	c.(652-654)ccG>ccA	p.P218P	ZC4H2_ENST00000488608.1_5'UTR|ZC4H2_ENST00000337990.2_Silent_p.P195P|ZC4H2_ENST00000545618.1_Silent_p.P213P|ZC4H2_ENST00000447788.2_Missense_Mutation_p.R164Q	NM_018684.3	NP_061154.1	Q9NQZ6	ZC4H2_HUMAN	zinc finger, C4H2 domain containing	218					nervous system development (GO:0007399)|neuromuscular junction development (GO:0007528)|spinal cord motor neuron differentiation (GO:0021522)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)	metal ion binding (GO:0046872)			endometrium(2)|large_intestine(4)|lung(13)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	24						GCTTCCGTTTCGGCTTTTTGG	0.488																																						.											0								C	,GLN/ARG,	1,3834		0,1,1631,571	167.0	104.0	126.0		585,491,654	-10.8	0.5	X	dbSNP_134	126	1,6727		0,1,2427,1872	no	coding-synonymous,missense,coding-synonymous	ZC4H2	NM_001178032.2,NM_001178033.2,NM_018684.3	,43,	0,2,4058,2443	TT,TC,CC,C		0.0149,0.0261,0.0189	,,	195/202,164/177,218/225	64137684	2,10561	2203	4300	6503	SO:0001819	synonymous_variant	55906			AF270491	CCDS14380.1, CCDS55431.1, CCDS55432.1	Xq11.1	2013-07-23	2008-10-01	2008-10-01	ENSG00000126970	ENSG00000126970		"""Zinc fingers"""	24931	protein-coding gene	gene with protein product		300897	"""KIAA1166"", ""Wieacker-Wolff syndrome"""	KIAA1166, WWS		10574461, 12097419, 23623388	Standard	NM_018684		Approved	HCA127	uc004dvu.3	Q9NQZ6	OTTHUMG00000021712	ENST00000374839.3:c.654G>A	X.37:g.64137684C>T			B2RDC2|B3KVZ5|B4DED0|E7EM74|G3V1L3|Q53H73|Q5JTF9|Q9H9C3|Q9H9H7|Q9ULQ4	Missense_Mutation	SNP	ENST00000374839.3	37	CCDS14380.1	.	.	.	.	.	.	.	.	.	.	C	14.06	2.421866	0.43020	2.61E-4	1.49E-4	ENSG00000126970	ENST00000447788	.	.	.	5.42	-10.8	0.00216	.	.	.	.	.	T	0.34658	0.0905	.	.	.	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.16867	-1.0388	7	0.66056	D	0.02	.	3.2734	0.06889	0.0948:0.27:0.3669:0.2684	.	164	B4DED0	.	Q	164	.	ENSP00000399126:R164Q	R	-	2	0	ZC4H2	64054409	0.997000	0.39634	0.497000	0.27552	0.994000	0.84299	0.219000	0.17641	-2.224000	0.00725	-0.365000	0.07479	CGA		0.488	ZC4H2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056958.1	NM_018684	
ATP11C	286410	broad.mit.edu	37	X	138823233	138823233	+	Missense_Mutation	SNP	G	G	C			TCGA-KL-8323-01A-21D-2310-10	TCGA-KL-8323-11A-01D-2310-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fae88d21-171c-4df4-b258-3c5948a1034b	f5c7fb67-5906-4db0-ad0d-129df8e065cb	g.chrX:138823233G>C	ENST00000327569.3	-	27	3158	c.3060C>G	c.(3058-3060)ttC>ttG	p.F1020L	ATP11C_ENST00000359686.2_Missense_Mutation_p.F1020L|ATP11C_ENST00000370543.1_Missense_Mutation_p.F1020L|ATP11C_ENST00000361648.2_Missense_Mutation_p.F1020L|ATP11C_ENST00000370557.1_Missense_Mutation_p.F1014L|ATP11C_ENST00000460773.1_5'UTR	NM_173694.4	NP_775965	Q8NB49	AT11C_HUMAN	ATPase, class VI, type 11C	1020					ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|positive regulation of B cell differentiation (GO:0045579)|pre-B cell differentiation (GO:0002329)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			breast(2)|central_nervous_system(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(15)|lung(31)|ovary(5)|prostate(1)|skin(3)	75	Acute lymphoblastic leukemia(192;0.000127)					TCCACGTCCAGAATCGGGTAT	0.388																																						.											0													69.0	61.0	64.0					X																	138823233		2203	4300	6503	SO:0001583	missense	286410			AJ580094	CCDS14668.1, CCDS35410.1	Xq27.1	2011-06-09	2007-09-19		ENSG00000101974	ENSG00000101974		"""ATPases / P-type"""	13554	protein-coding gene	gene with protein product		300516	"""ATPase, Class VI, type 11C"""			11015572	Standard	NM_173694		Approved	ATPIG, ATPIQ	uc004faz.3	Q8NB49	OTTHUMG00000022538	ENST00000327569.3:c.3060C>G	X.37:g.138823233G>C	ENSP00000332756:p.Phe1020Leu		Q5JT69|Q5JT70|Q5JT71|Q5JT72|Q5JT73|Q6ZND5|Q6ZU50|Q6ZUP7|Q70IJ9|Q70IK0|Q8WX24	Missense_Mutation	SNP	ENST00000327569.3	37	CCDS14668.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	21.9|21.9	4.220727|4.220727	0.79464|0.79464	.|.	.|.	ENSG00000101974|ENSG00000101974	ENST00000370557;ENST00000361648;ENST00000327569;ENST00000450801;ENST00000370543;ENST00000359686|ENST00000433868	T;T;T;T;T;T|.	0.59083|.	0.29;0.29;0.29;0.29;0.29;0.29|.	5.51|5.51	5.51|5.51	0.81932|0.81932	.|.	0.102643|.	0.64402|.	D|.	0.000002|.	T|T	0.57184|0.57184	0.2036|0.2036	L|L	0.28504|0.28504	0.86|0.86	0.58432|0.58432	D|D	0.999994|0.999994	B;B;B|.	0.31383|.	0.321;0.215;0.321|.	B;B;B|.	0.35550|.	0.205;0.101;0.205|.	T|T	0.52764|0.52764	-0.8532|-0.8532	10|5	0.49607|.	T|.	0.09|.	.|.	17.4019|17.4019	0.87463|0.87463	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	1020;1020;1020|.	Q8NB49-3;Q8NB49;Q8NB49-2|.	.;AT11C_HUMAN;.|.	L|V	1014;1020;1020;84;1020;1020|53	ENSP00000359588:F1014L;ENSP00000355165:F1020L;ENSP00000332756:F1020L;ENSP00000391259:F84L;ENSP00000359574:F1020L;ENSP00000352715:F1020L|.	ENSP00000332756:F1020L|.	F|L	-|-	3|1	2|2	ATP11C|ATP11C	138650899|138650899	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.982000|0.982000	0.71751|0.71751	7.578000|7.578000	0.82498|0.82498	2.323000|2.323000	0.78572|0.78572	0.600000|0.600000	0.82982|0.82982	TTC|CTG		0.388	ATP11C-008	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000354945.1	NM_173694	
ADAM32	203102	ucsc.edu	37	8	38965348	38965348	+	Silent	SNP	A	A	G			TCGA-KL-8323-01A-21D-2310-10	TCGA-KL-8323-11A-01D-2310-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fae88d21-171c-4df4-b258-3c5948a1034b	f5c7fb67-5906-4db0-ad0d-129df8e065cb	g.chr8:38965348A>G	ENST00000379907.4	+	1	181	c.54A>G	c.(52-54)agA>agG	p.R18R	ADAM32_ENST00000519315.1_Silent_p.R18R|ADAM32_ENST00000437682.2_Missense_Mutation_p.D52G	NM_145004.5	NP_659441	Q8TC27	ADA32_HUMAN	ADAM metallopeptidase domain 32	18						integral component of membrane (GO:0016021)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(14)|ovary(1)|skin(2)	31		all_cancers(7;3e-05)|all_lung(54;0.00187)|Hepatocellular(245;0.00745)|Lung NSC(58;0.00771)|Breast(189;0.0503)	LUSC - Lung squamous cell carcinoma(45;6.2e-07)|Colorectal(1;0.00699)|READ - Rectum adenocarcinoma(1;0.146)			TGGCGTCAAGACCCGGTGAGC	0.692																																						.											0													8.0	10.0	10.0					8																	38965348		1652	3666	5318	SO:0001819	synonymous_variant	203102			BC026085	CCDS47846.1	8p11.22	2005-08-18	2005-08-18		ENSG00000197140	ENSG00000197140		"""ADAM metallopeptidase domain containing"""	15479	protein-coding gene	gene with protein product			"""a disintegrin and metalloproteinase domain 32"""			12568724	Standard	NM_145004		Approved		uc003xmt.4	Q8TC27	OTTHUMG00000164071	ENST00000379907.4:c.54A>G	8.37:g.38965348A>G			Q8TC42	Silent	SNP	ENST00000379907.4	37	CCDS47846.1	.	.	.	.	.	.	.	.	.	.	A	10.02	1.235989	0.22626	.	.	ENSG00000197140	ENST00000437682	T	0.05717	3.4	2.78	-3.24	0.05094	.	.	.	.	.	T	0.03434	0.0099	.	.	.	0.20403	N	0.999902	B	0.21688	0.059	B	0.26416	0.069	T	0.45848	-0.9233	8	0.31617	T	0.26	.	0.3329	0.00321	0.3506:0.1976:0.2584:0.1934	.	52	E7EPX8	.	G	52	ENSP00000405978:D52G	ENSP00000405978:D52G	D	+	2	0	ADAM32	39084505	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	0.152000	0.16302	-0.696000	0.05098	-0.466000	0.05196	GAC		0.692	ADAM32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377089.1	NM_145004	
AIM1L	55057	ucsc.edu	37	1	26664510	26664510	+	Missense_Mutation	SNP	T	T	C			TCGA-KL-8323-01A-21D-2310-10	TCGA-KL-8323-11A-01D-2310-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fae88d21-171c-4df4-b258-3c5948a1034b	f5c7fb67-5906-4db0-ad0d-129df8e065cb	g.chr1:26664510T>C	ENST00000308182.5	-	7	794	c.365A>G	c.(364-366)gAg>gGg	p.E122G	AIM1L_ENST00000527815.1_Missense_Mutation_p.E293G|AIM1L_ENST00000522993.1_5'UTR			Q8N1P7	AIM1L_HUMAN	absent in melanoma 1-like	122							carbohydrate binding (GO:0030246)			endometrium(2)|kidney(2)|large_intestine(1)|lung(4)|pancreas(1)|skin(2)	12		all_cancers(24;4.67e-25)|Colorectal(325;3.46e-05)|all_lung(284;5.94e-05)|Lung NSC(340;7.26e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.00637)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;1.51e-27)|Colorectal(126;1.61e-08)|COAD - Colon adenocarcinoma(152;9.32e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.000792)|BRCA - Breast invasive adenocarcinoma(304;0.00104)|STAD - Stomach adenocarcinoma(196;0.00154)|GBM - Glioblastoma multiforme(114;0.00858)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.165)|LUSC - Lung squamous cell carcinoma(448;0.239)		TACCCTGGGCTCCCCTGGCTT	0.577																																						.											0													48.0	39.0	42.0					1																	26664510		2203	4300	6503	SO:0001583	missense	55057					1p35	2010-07-14			ENSG00000176092	ENSG00000176092			17295	protein-coding gene	gene with protein product	"""beta-gamma crystallin domain containing 2"""						Standard	NM_001039775		Approved	CRYBG2, FLJ38020	uc001bmd.4	Q8N1P7	OTTHUMG00000003490	ENST00000308182.5:c.365A>G	1.37:g.26664510T>C	ENSP00000310435:p.Glu122Gly		B2RNG3|Q5T137|Q5T150	Missense_Mutation	SNP	ENST00000308182.5	37		.	.	.	.	.	.	.	.	.	.	T	26.8	4.768605	0.90020	.	.	ENSG00000176092	ENST00000527815;ENST00000308182	T;T	0.76709	-1.04;-1.01	5.13	3.98	0.46160	Beta/gamma crystallin (1);Gamma-crystallin-related (1);	0.303860	0.35040	N	0.003481	D	0.84037	0.5384	M	0.76727	2.345	0.80722	D	1	D;D	0.63880	0.984;0.993	P;P	0.61328	0.829;0.887	T	0.83285	-0.0036	10	0.49607	T	0.09	.	9.4283	0.38595	0.159:0.0:0.0:0.841	.	39;122	Q9NTH7;Q8N1P7	.;AIM1L_HUMAN	G	293;122	ENSP00000433931:E293G;ENSP00000310435:E122G	ENSP00000310435:E122G	E	-	2	0	AIM1L	26537097	0.988000	0.35896	0.997000	0.53966	0.978000	0.69477	2.987000	0.49378	0.939000	0.37446	0.533000	0.62120	GAG		0.577	AIM1L-201	KNOWN	basic	protein_coding	protein_coding		NM_001039775.2	
ATF6	22926	ucsc.edu	37	1	161790871	161790871	+	Silent	SNP	T	T	C			TCGA-KL-8323-01A-21D-2310-10	TCGA-KL-8323-11A-01D-2310-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fae88d21-171c-4df4-b258-3c5948a1034b	f5c7fb67-5906-4db0-ad0d-129df8e065cb	g.chr1:161790871T>C	ENST00000367942.3	+	9	1174	c.1107T>C	c.(1105-1107)ctT>ctC	p.L369L		NM_007348.3	NP_031374.2	P18850	ATF6A_HUMAN	activating transcription factor 6	369	bZIP. {ECO:0000255|PROSITE- ProRule:PRU00978}.			NQRL -> LRNS (in Ref. 5; no nucleotide entry). {ECO:0000305}.	activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|positive regulation of transcription from RNA polymerase II promoter involved in unfolded protein response (GO:0006990)|protein folding (GO:0006457)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to stress (GO:0006950)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	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)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			breast(2)|endometrium(3)|kidney(2)|large_intestine(8)|lung(14)|ovary(3)|skin(1)|stomach(1)	34	all_hematologic(112;0.156)		BRCA - Breast invasive adenocarcinoma(70;0.00953)		Pseudoephedrine(DB00852)	ACCAGAGGCTTAAAGTCCCTA	0.343																																						.											0													148.0	151.0	150.0					1																	161790871		2203	4300	6503	SO:0001819	synonymous_variant	22926			AB015856	CCDS1235.1	1q22-q23	2013-01-10			ENSG00000118217	ENSG00000118217		"""basic leucine zipper proteins"""	791	protein-coding gene	gene with protein product	"""activating transcription factor 6 alpha"""	605537				9837962, 9271374, 11256944	Standard	NM_007348		Approved	ATF6A	uc001gbs.3	P18850	OTTHUMG00000023961	ENST00000367942.3:c.1107T>C	1.37:g.161790871T>C			O15139|Q5VW62|Q6IPB5|Q9UEC9	Silent	SNP	ENST00000367942.3	37	CCDS1235.1																																																																																				0.343	ATF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060304.2	NM_007348	
HDAC4	9759	ucsc.edu	37	2	240033259	240033259	+	Silent	SNP	A	A	G			TCGA-KL-8323-01A-21D-2310-10	TCGA-KL-8323-11A-01D-2310-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fae88d21-171c-4df4-b258-3c5948a1034b	f5c7fb67-5906-4db0-ad0d-129df8e065cb	g.chr2:240033259A>G	ENST00000345617.3	-	14	2717	c.1926T>C	c.(1924-1926)tcT>tcC	p.S642S	HDAC4_ENST00000543185.1_Silent_p.S226S|HDAC4_ENST00000541256.1_Silent_p.S616S	NM_006037.3	NP_006028.2	P56524	HDAC4_HUMAN	histone deacetylase 4	642					B cell activation (GO:0042113)|B cell differentiation (GO:0030183)|cardiac muscle hypertrophy in response to stress (GO:0014898)|chromatin remodeling (GO:0006338)|histone deacetylation (GO:0016575)|histone H3 deacetylation (GO:0070932)|histone H4 deacetylation (GO:0070933)|inflammatory response (GO:0006954)|negative regulation of cell proliferation (GO:0008285)|negative regulation of glycolytic process (GO:0045820)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of osteoblast differentiation (GO:0045668)|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)|nervous system development (GO:0007399)|osteoblast development (GO:0002076)|peptidyl-lysine deacetylation (GO:0034983)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein sumoylation (GO:0033235)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of gene expression, epigenetic (GO:0040029)|regulation of protein binding (GO:0043393)|regulation of skeletal muscle fiber development (GO:0048742)|response to denervation involved in regulation of muscle adaptation (GO:0014894)|response to drug (GO:0042493)|response to interleukin-1 (GO:0070555)|skeletal system development (GO:0001501)|transcription, DNA-templated (GO:0006351)	A band (GO:0031672)|actomyosin (GO:0042641)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|histone deacetylase complex (GO:0000118)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)|Z disc (GO:0030018)	activating transcription factor binding (GO:0033613)|core promoter binding (GO:0001047)|histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|potassium ion binding (GO:0030955)|protein deacetylase activity (GO:0033558)|repressing transcription factor binding (GO:0070491)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(1)|biliary_tract(1)|breast(4)|endometrium(5)|kidney(2)|large_intestine(7)|lung(27)|ovary(3)|pancreas(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(5)	62		all_epithelial(40;1.45e-17)|Breast(86;1.53e-05)|Renal(207;0.000355)|all_lung(227;0.0121)|Ovarian(221;0.0183)|Lung NSC(271;0.0413)|Melanoma(123;0.0749)|all_hematologic(139;0.159)		Epithelial(121;6.38e-25)|OV - Ovarian serous cystadenocarcinoma(60;2.48e-12)|Kidney(56;6.04e-08)|KIRC - Kidney renal clear cell carcinoma(57;1.18e-06)|BRCA - Breast invasive adenocarcinoma(100;3.99e-05)|Lung(119;0.00942)|LUSC - Lung squamous cell carcinoma(224;0.04)		GCTCCTGCACAGACACGGGGA	0.701																																						.											0													26.0	23.0	24.0					2																	240033259		2199	4299	6498	SO:0001819	synonymous_variant	9759			AB006626	CCDS2529.1	2q37.3	2014-02-12			ENSG00000068024	ENSG00000068024			14063	protein-coding gene	gene with protein product		605314	"""brachydactyly-mental retardation syndrome"""	BDMR		10206986, 10220385, 20691407	Standard	NM_006037		Approved	KIAA0288, HDAC-A, HDACA, HD4, HA6116, HDAC-4	uc002vyk.4	P56524	OTTHUMG00000133344	ENST00000345617.3:c.1926T>C	2.37:g.240033259A>G			Q9UND6	Silent	SNP	ENST00000345617.3	37	CCDS2529.1																																																																																				0.701	HDAC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257174.2	NM_006037	
KATNB1	10300	ucsc.edu	37	16	57788846	57788846	+	Silent	SNP	A	A	G			TCGA-KL-8323-01A-21D-2310-10	TCGA-KL-8323-11A-01D-2310-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fae88d21-171c-4df4-b258-3c5948a1034b	f5c7fb67-5906-4db0-ad0d-129df8e065cb	g.chr16:57788846A>G	ENST00000379661.3	+	14	1625	c.1233A>G	c.(1231-1233)gcA>gcG	p.A411A		NM_005886.2	NP_005877.2			katanin p80 (WD repeat containing) subunit B 1											cervix(1)|endometrium(3)|kidney(2)|large_intestine(1)|lung(6)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	16		all_neural(199;0.223)				CTCCAGACGCAGCCACAGCAA	0.612																																						.											0													123.0	128.0	126.0					16																	57788846		2198	4300	6498	SO:0001819	synonymous_variant	10300			AF052432	CCDS10788.1	16q12.2	2013-01-09	2003-03-13		ENSG00000140854	ENSG00000140854		"""WD repeat domain containing"""	6217	protein-coding gene	gene with protein product		602703	"""katanin p80 (WD40-containing) subunit B 1"""			9568719	Standard	XM_006721121		Approved		uc002eml.1	Q9BVA0	OTTHUMG00000133467	ENST00000379661.3:c.1233A>G	16.37:g.57788846A>G				Silent	SNP	ENST00000379661.3	37	CCDS10788.1																																																																																				0.612	KATNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257343.3		
MEGF10	84466	ucsc.edu	37	5	126755867	126755867	+	Missense_Mutation	SNP	T	T	C			TCGA-KL-8323-01A-21D-2310-10	TCGA-KL-8323-11A-01D-2310-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fae88d21-171c-4df4-b258-3c5948a1034b	f5c7fb67-5906-4db0-ad0d-129df8e065cb	g.chr5:126755867T>C	ENST00000274473.6	+	13	1825	c.1558T>C	c.(1558-1560)Tgg>Cgg	p.W520R	MEGF10_ENST00000418761.2_Missense_Mutation_p.W520R|MEGF10_ENST00000508365.1_Missense_Mutation_p.W520R|MEGF10_ENST00000503335.2_Missense_Mutation_p.W520R	NM_032446.2	NP_115822.1	Q96KG7	MEG10_HUMAN	multiple EGF-like-domains 10	520	EGF-like 9. {ECO:0000255|PROSITE- ProRule:PRU00076}.|Necessary for interaction with AP2M1, self-assembly and formation of the irregular, mosaic-like adhesion pattern.				homotypic cell-cell adhesion (GO:0034109)|muscle cell development (GO:0055001)|recognition of apoptotic cell (GO:0043654)|regulation of muscle cell differentiation (GO:0051147)|regulation of skeletal muscle tissue development (GO:0048641)|skeletal muscle satellite cell activation (GO:0014719)|skeletal muscle satellite cell differentiation (GO:0014816)|skeletal muscle satellite cell proliferation (GO:0014841)	cell projection (GO:0042995)|integral component of membrane (GO:0016021)|phagocytic cup (GO:0001891)				breast(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(28)|ovary(4)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	68		Prostate(80;0.165)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0657)|Epithelial(69;0.123)		TGCACCTGGATGGCGCGGGGA	0.562																																						.											0													84.0	72.0	76.0					5																	126755867		2203	4300	6503	SO:0001583	missense	84466			AK021631	CCDS4142.1	5q33	2008-02-05			ENSG00000145794	ENSG00000145794			29634	protein-coding gene	gene with protein product		612453				11347906	Standard	NM_032446		Approved	KIAA1780	uc003kui.4	Q96KG7	OTTHUMG00000128984	ENST00000274473.6:c.1558T>C	5.37:g.126755867T>C	ENSP00000274473:p.Trp520Arg		Q68DE5|Q8WUL3	Missense_Mutation	SNP	ENST00000274473.6	37	CCDS4142.1	.	.	.	.	.	.	.	.	.	.	T	25.2	4.614955	0.87359	.	.	ENSG00000145794	ENST00000503335;ENST00000508365;ENST00000418761;ENST00000274473	T;T;T;T	0.55052	0.54;0.54;0.54;0.54	5.72	5.72	0.89469	Epidermal growth factor-like (1);EGF-like region, conserved site (2);Epidermal growth factor-like, type 3 (1);	0.000000	0.64402	D	0.000001	T	0.71409	0.3336	M	0.86097	2.795	0.80722	D	1	P;P	0.47034	0.55;0.889	B;P	0.54815	0.412;0.761	T	0.76255	-0.3026	10	0.66056	D	0.02	-22.1087	16.2962	0.82776	0.0:0.0:0.0:1.0	.	520;520	Q96KG7-2;Q96KG7	.;MEG10_HUMAN	R	520	ENSP00000423354:W520R;ENSP00000423195:W520R;ENSP00000416284:W520R;ENSP00000274473:W520R	ENSP00000274473:W520R	W	+	1	0	MEGF10	126783766	1.000000	0.71417	1.000000	0.80357	0.851000	0.48451	7.957000	0.87870	2.304000	0.77564	0.528000	0.53228	TGG		0.562	MEGF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250973.2	NM_032446	
DNM1	1759	ucsc.edu;mdanderson.org	37	9	131007047	131007047	+	Intron	SNP	C	C	G			TCGA-KL-8323-01A-21D-2310-10	TCGA-KL-8323-11A-01D-2310-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fae88d21-171c-4df4-b258-3c5948a1034b	f5c7fb67-5906-4db0-ad0d-129df8e065cb	g.chr9:131007047C>G	ENST00000372923.3	+	16	1763				MIR199B_ENST00000384849.1_RNA|DNM1_ENST00000393594.3_Intron|MIR3154_ENST00000577829.1_RNA|DNM1_ENST00000341179.7_Intron|DNM1_ENST00000475805.1_Intron|DNM1_ENST00000486160.1_Intron|DNM1_ENST00000493925.1_Intron	NM_004408.2	NP_004399.2	Q05193	DYN1_HUMAN	dynamin 1						endocytosis (GO:0006897)|endosome organization (GO:0007032)|GTP catabolic process (GO:0006184)|receptor internalization (GO:0031623)|receptor-mediated endocytosis (GO:0006898)	extracellular vesicular exosome (GO:0070062)|membrane coat (GO:0030117)|microtubule (GO:0005874)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(15)|lung(6)|ovary(2)|urinary_tract(2)	32						GACTACTGTACAATTTGGGAG	0.602																																					GBM(113;146 1575 2722 28670 29921)	.											0													71.0	73.0	72.0					9																	131007047		1568	3582	5150	SO:0001627	intron_variant	406978			L07807	CCDS6895.1, CCDS43882.1, CCDS75911.1, CCDS75912.1	9q34	2013-01-10			ENSG00000106976	ENSG00000106976		"""Pleckstrin homology (PH) domain containing"""	2972	protein-coding gene	gene with protein product		602377		DNM		2144893, 9143509	Standard	XM_005251763		Approved		uc022bob.1	Q05193	OTTHUMG00000020733	ENST00000372923.3:c.1672-1626C>G	9.37:g.131007047C>G			A6NLM6|Q5SYX0|Q5SYX2|Q6P3T6|Q86VD2	RNA	SNP	ENST00000372923.3	37	CCDS6895.1																																																																																				0.602	DNM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054367.1	NM_004408	
PRMT7	54496	ucsc.edu	37	16	68373380	68373380	+	Silent	SNP	T	T	C			TCGA-KL-8323-01A-21D-2310-10	TCGA-KL-8323-11A-01D-2310-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fae88d21-171c-4df4-b258-3c5948a1034b	f5c7fb67-5906-4db0-ad0d-129df8e065cb	g.chr16:68373380T>C	ENST00000339507.5	+	8	1490	c.660T>C	c.(658-660)ccT>ccC	p.P220P	PRMT7_ENST00000348497.4_Silent_p.P146P|PRMT7_ENST00000441236.1_Silent_p.P170P|PRMT7_ENST00000564441.1_3'UTR|PRMT7_ENST00000449359.3_Silent_p.P170P			Q9NVM4	ANM7_HUMAN	protein arginine methyltransferase 7	220	SAM-dependent MTase PRMT-type 1. {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)		AGAGCTGCCCTGGCGCACCCT	0.592																																						.											0													113.0	88.0	96.0					16																	68373380		2198	4300	6498	SO:0001819	synonymous_variant	54496			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.660T>C	16.37:g.68373380T>C			B3KPR0|B3KUG9|B4E379|Q96PV5|Q9H9L0	Silent	SNP	ENST00000339507.5	37	CCDS10866.1																																																																																				0.592	PRMT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268892.3	NM_019023	
R3HCC1L	27291	ucsc.edu;bcgsc.ca	37	10	99991273	99991273	+	Missense_Mutation	SNP	C	C	T			TCGA-KL-8323-01A-21D-2310-10	TCGA-KL-8323-11A-01D-2310-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fae88d21-171c-4df4-b258-3c5948a1034b	f5c7fb67-5906-4db0-ad0d-129df8e065cb	g.chr10:99991273C>T	ENST00000298999.3	+	6	2093	c.1790C>T	c.(1789-1791)tCa>tTa	p.S597L	R3HCC1L_ENST00000370584.3_Missense_Mutation_p.S597L|R3HCC1L_ENST00000314594.5_Missense_Mutation_p.S13L|R3HCC1L_ENST00000370586.2_Missense_Mutation_p.S3L	NM_014472.4	NP_055287	Q7Z5L2	R3HCL_HUMAN	R3H domain and coiled-coil containing 1-like	611							nucleotide binding (GO:0000166)										TTCTAGTTATCAGGGAATACC	0.383																																						.											0													99.0	90.0	93.0					10																	99991273		2203	4300	6503	SO:0001583	missense	27291			AF525304	CCDS31267.1, CCDS58093.1, CCDS73178.1	10q24.2	2012-05-23	2012-05-23	2012-05-23	ENSG00000166024	ENSG00000166024			23512	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 28"""	C10orf28			Standard	NM_014472		Approved	GIDRP86, PSORT	uc001kox.4	Q7Z5L2	OTTHUMG00000018873	ENST00000298999.3:c.1790C>T	10.37:g.99991273C>T	ENSP00000298999:p.Ser597Leu		O60598|Q5W0B4|Q5W0B5|Q86VT9|Q8N9H0	Missense_Mutation	SNP	ENST00000298999.3	37	CCDS31267.1	.	.	.	.	.	.	.	.	.	.	C	24.0	4.486925	0.84854	.	.	ENSG00000166024	ENST00000370584;ENST00000298999;ENST00000370586;ENST00000314594;ENST00000544834	T;T;T;T	0.32515	1.45;1.45;1.45;1.45	5.83	5.83	0.93111	.	0.351150	0.27971	N	0.017111	T	0.40619	0.1124	L	0.60455	1.87	0.39744	D	0.971786	B;P;P	0.52842	0.103;0.956;0.843	B;P;P	0.51016	0.058;0.656;0.487	T	0.18967	-1.0320	9	.	.	.	-8.6307	12.9136	0.58192	0.0:0.9218:0.0:0.0782	.	3;611;597	Q7Z5L2-3;Q7Z5L2;Q7Z5L2-2	.;GIDRP_HUMAN;.	L	597;597;3;13;4	ENSP00000359616:S597L;ENSP00000298999:S597L;ENSP00000359618:S3L;ENSP00000314018:S13L	.	S	+	2	0	C10orf28	99981263	0.994000	0.37717	1.000000	0.80357	0.845000	0.48019	1.536000	0.36072	2.744000	0.94065	0.655000	0.94253	TCA		0.383	R3HCC1L-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049764.1	NM_014472	
RGPD4	285190	ucsc.edu	37	2	108487266	108487266	+	Missense_Mutation	SNP	G	G	A			TCGA-KL-8323-01A-21D-2310-10	TCGA-KL-8323-11A-01D-2310-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fae88d21-171c-4df4-b258-3c5948a1034b	f5c7fb67-5906-4db0-ad0d-129df8e065cb	g.chr2:108487266G>A	ENST00000408999.3	+	20	2883	c.2806G>A	c.(2806-2808)Gaa>Aaa	p.E936K	RGPD4_ENST00000354986.4_Missense_Mutation_p.E936K	NM_182588.2	NP_872394.2	Q7Z3J3	RGPD4_HUMAN	RANBP2-like and GRIP domain containing 4	936					protein targeting to Golgi (GO:0000042)					breast(1)|endometrium(7)|kidney(4)|lung(23)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(3)	43						TCAAGAAAAGGAAAGTGAAAA	0.408																																						.											0													198.0	153.0	167.0					2																	108487266		692	1586	2278	SO:0001583	missense	285190			BX537861	CCDS46381.1	2q12.3	2013-01-10			ENSG00000196862	ENSG00000196862		"""Tetratricopeptide (TTC) repeat domain containing"""	32417	protein-coding gene	gene with protein product		612707				15710750, 15815621	Standard	NM_182588		Approved	RGP4, DKFZp686P0288	uc010ywk.2	Q7Z3J3	OTTHUMG00000153208	ENST00000408999.3:c.2806G>A	2.37:g.108487266G>A	ENSP00000386810:p.Glu936Lys		B9A029	Missense_Mutation	SNP	ENST00000408999.3	37	CCDS46381.1	.	.	.	.	.	.	.	.	.	.	-	0.001	-3.008718	0.00043	.	.	ENSG00000196862	ENST00000354986;ENST00000408999;ENST00000439322	T;T	0.36878	1.23;1.23	2.33	1.17	0.20885	.	.	.	.	.	T	0.06872	0.0175	N	0.00197	-1.87	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.37244	-0.9714	9	0.02654	T	1	-1.0096	6.0551	0.19807	0.5942:0.0:0.4058:0.0	.	936	Q7Z3J3	RGPD4_HUMAN	K	936;936;694	ENSP00000347081:E936K;ENSP00000386810:E936K	ENSP00000347081:E936K	E	+	1	0	RGPD4	107853698	0.375000	0.25089	0.383000	0.26132	0.198000	0.23893	1.757000	0.38400	0.141000	0.18875	-1.867000	0.00556	GAA		0.408	RGPD4-001	NOVEL	not_best_in_genome_evidence|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330096.2	XM_496581	
RMND1	55005	ucsc.edu	37	6	151744763	151744763	+	Silent	SNP	T	T	C			TCGA-KL-8323-01A-21D-2310-10	TCGA-KL-8323-11A-01D-2310-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fae88d21-171c-4df4-b258-3c5948a1034b	f5c7fb67-5906-4db0-ad0d-129df8e065cb	g.chr6:151744763T>C	ENST00000367303.4	-	7	956	c.834A>G	c.(832-834)ggA>ggG	p.G278G	RMND1_ENST00000336451.3_Silent_p.G67G	NM_017909.2	NP_060379.2	Q9NWS8	RMND1_HUMAN	required for meiotic nuclear division 1 homolog (S. cerevisiae)	278					translation (GO:0006412)	mitochondrion (GO:0005739)				central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	12		Ovarian(120;0.125)	BRCA - Breast invasive adenocarcinoma(37;0.146)	OV - Ovarian serous cystadenocarcinoma(155;6.8e-11)		GTTTTGACTGTCCCCTGTGAA	0.358																																						.											0													103.0	104.0	104.0					6																	151744763		2203	4300	6503	SO:0001819	synonymous_variant	55005			AK000634	CCDS5232.1, CCDS75539.1	6q25.1	2008-02-05	2006-11-24	2006-11-24	ENSG00000155906	ENSG00000155906			21176	protein-coding gene	gene with protein product		614917	"""chromosome 6 open reading frame 96"""	C6orf96			Standard	NM_001271937		Approved	bA351K16.3, FLJ20627, RMD1	uc003qoi.3	Q9NWS8	OTTHUMG00000015837	ENST00000367303.4:c.834A>G	6.37:g.151744763T>C			A8K8H4|Q0VDG6|Q5SZ48|Q5SZ83|Q6NSC5|Q96EN7	Silent	SNP	ENST00000367303.4	37	CCDS5232.1																																																																																				0.358	RMND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042718.2	NM_017909	
STRN	6801	ucsc.edu	37	2	37094995	37094995	+	Silent	SNP	A	A	G			TCGA-KL-8323-01A-21D-2310-10	TCGA-KL-8323-11A-01D-2310-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fae88d21-171c-4df4-b258-3c5948a1034b	f5c7fb67-5906-4db0-ad0d-129df8e065cb	g.chr2:37094995A>G	ENST00000263918.4	-	12	1517	c.1509T>C	c.(1507-1509)tcT>tcC	p.S503S	RNU6-577P_ENST00000516947.1_RNA|STRN_ENST00000379213.2_Silent_p.S454S	NM_003162.3	NP_003153.2	O43815	STRN_HUMAN	striatin, calmodulin binding protein	503					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)				CTACATCAAGAGAAGTGCTCC	0.299																																						.											0													110.0	115.0	113.0					2																	37094995		2203	4292	6495	SO:0001819	synonymous_variant	6801			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.1509T>C	2.37:g.37094995A>G			Q3KP65|Q53TQ8|Q9NP38	Silent	SNP	ENST00000263918.4	37	CCDS1784.1																																																																																				0.299	STRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218568.1		
ZBBX	79740	ucsc.edu	37	3	166960302	166960302	+	Missense_Mutation	SNP	T	T	C			TCGA-KL-8323-01A-21D-2310-10	TCGA-KL-8323-11A-01D-2310-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fae88d21-171c-4df4-b258-3c5948a1034b	f5c7fb67-5906-4db0-ad0d-129df8e065cb	g.chr3:166960302T>C	ENST00000392766.2	-	20	2607	c.2267A>G	c.(2266-2268)gAg>gGg	p.E756G	ZBBX_ENST00000307529.5_Missense_Mutation_p.E795G|ZBBX_ENST00000455345.2_Missense_Mutation_p.E795G|ZBBX_ENST00000392767.2_Missense_Mutation_p.E756G|ZBBX_ENST00000392764.1_Missense_Mutation_p.E727G	NM_001199201.1|NM_024687.3	NP_001186130.1|NP_078963.2	A8MT70	ZBBX_HUMAN	zinc finger, B-box domain containing	756						intracellular (GO:0005622)	zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(5)|kidney(5)|large_intestine(9)|liver(1)|lung(38)|ovary(2)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)	70						CCTCAATTCCTCAACTCCACA	0.353																																						.											0													86.0	81.0	82.0					3																	166960302		1810	4064	5874	SO:0001583	missense	79740			AK026702	CCDS3199.2, CCDS56295.1, CCDS56296.1	3q26.1	2010-03-23			ENSG00000169064	ENSG00000169064			26245	protein-coding gene	gene with protein product						12477932	Standard	NM_024687		Approved	FLJ23049	uc011bpc.2	A8MT70	OTTHUMG00000133560	ENST00000392766.2:c.2267A>G	3.37:g.166960302T>C	ENSP00000376519:p.Glu756Gly		A8MV69|B3KSC1|B5MDJ6|F2Z370|Q9H5T8	Missense_Mutation	SNP	ENST00000392766.2	37	CCDS3199.2	.	.	.	.	.	.	.	.	.	.	T	11.65	1.702067	0.30232	.	.	ENSG00000169064	ENST00000392766;ENST00000392767;ENST00000455345;ENST00000307529;ENST00000392764	T;T;T;T;T	0.57107	0.42;0.42;0.42;0.42;0.42	5.01	2.62	0.31277	.	0.308843	0.27336	N	0.019836	T	0.41096	0.1144	L	0.44542	1.39	0.09310	N	1	B;B	0.13594	0.008;0.005	B;B	0.13407	0.009;0.004	T	0.38693	-0.9649	10	0.87932	D	0	-2.0389	6.6105	0.22749	0.0:0.1936:0.0:0.8064	.	795;756	A8MT70-2;A8MT70	.;ZBBX_HUMAN	G	756;756;795;795;727	ENSP00000376519:E756G;ENSP00000376520:E756G;ENSP00000390232:E795G;ENSP00000305065:E795G;ENSP00000376517:E727G	ENSP00000305065:E795G	E	-	2	0	ZBBX	168442996	0.098000	0.21812	0.067000	0.19924	0.024000	0.10985	1.233000	0.32648	0.268000	0.21939	0.482000	0.46254	GAG		0.353	ZBBX-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000257657.3	NM_024687	
PABPC3	5042	mdanderson.org	37	13	25670907	25670907	+	Missense_Mutation	SNP	C	C	A	rs76264750	byFrequency	TCGA-KL-8323-01A-21D-2310-10	TCGA-KL-8323-11A-01D-2310-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fae88d21-171c-4df4-b258-3c5948a1034b	f5c7fb67-5906-4db0-ad0d-129df8e065cb	g.chr13:25670907C>A	ENST00000281589.3	+	1	608	c.571C>A	c.(571-573)Ccc>Acc	p.P191T		NM_030979.2	NP_112241.2	Q9H361	PABP3_HUMAN	poly(A) binding protein, cytoplasmic 3	191	RRM 3. {ECO:0000255|PROSITE- ProRule:PRU00176}.				mRNA metabolic process (GO:0016071)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	nucleotide binding (GO:0000166)|poly(A) binding (GO:0008143)			breast(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(21)|ovary(4)|pancreas(1)|skin(3)	47		Lung SC(185;0.0225)|Breast(139;0.0602)		all cancers(112;0.0071)|Epithelial(112;0.0398)|OV - Ovarian serous cystadenocarcinoma(117;0.151)|GBM - Glioblastoma multiforme(144;0.222)|Lung(94;0.241)		AAAAGAGTTCCCCAATGTTTA	0.428																																						.											0													100.0	93.0	95.0					13																	25670907		2203	4300	6503	SO:0001583	missense	5042			AF132026	CCDS9311.1	13q12-q13	2013-02-12	2001-11-28		ENSG00000151846	ENSG00000151846		"""RNA binding motif (RRM) containing"""	8556	protein-coding gene	gene with protein product	"""testis PABP"""	604680	"""poly(A)-binding protein, cytoplasmic 3"""	PABPL3		8432538, 10543404	Standard	NM_030979		Approved	PABP3, tPABP	uc001upy.3	Q9H361	OTTHUMG00000016601	ENST00000281589.3:c.571C>A	13.37:g.25670907C>A	ENSP00000281589:p.Pro191Thr		Q8NHV0|Q9H086	Missense_Mutation	SNP	ENST00000281589.3	37	CCDS9311.1	.	.	.	.	.	.	.	.	.	.	C	0.011	-1.725491	0.00694	.	.	ENSG00000151846	ENST00000281589	D	0.85411	-1.98	1.27	-2.55	0.06288	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (1);	0.127499	0.32769	N	0.005664	T	0.42245	0.1194	N	0.00170	-1.935	0.25196	N	0.99009	B	0.02656	0.0	B	0.01281	0.0	T	0.58896	-0.7555	10	0.02654	T	1	.	6.4602	0.21952	0.5046:0.4954:0.0:0.0	.	191	Q9H361	PABP3_HUMAN	T	191	ENSP00000281589:P191T	ENSP00000281589:P191T	P	+	1	0	PABPC3	24568907	1.000000	0.71417	0.927000	0.36925	0.792000	0.44763	4.521000	0.60532	-0.661000	0.05345	-0.738000	0.03535	CCC		0.428	PABPC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044220.2	NM_030979	
PRDM9	56979	mdanderson.org	37	5	23527637	23527637	+	Missense_Mutation	SNP	A	A	C	rs61051796		TCGA-KL-8323-01A-21D-2310-10	TCGA-KL-8323-11A-01D-2310-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fae88d21-171c-4df4-b258-3c5948a1034b	f5c7fb67-5906-4db0-ad0d-129df8e065cb	g.chr5:23527637A>C	ENST00000296682.3	+	11	2622	c.2440A>C	c.(2440-2442)Agc>Cgc	p.S814R		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)	p.S814R(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						GCGGGGCTTTAGCAATAAGTC	0.567										HNSCC(3;0.000094)																												.											1	Substitution - Missense(1)	skin(1)						A	ARG/SER	17,4251		0,17,2117	35.0	47.0	43.0		2440	3.0	0.7	5	dbSNP_129	43	3,8531		0,3,4264	no	missense	PRDM9	NM_020227.2	110	0,20,6381	CC,CA,AA		0.0352,0.3983,0.1562	possibly-damaging	814/895	23527637	20,12782	2134	4267	6401	SO:0001583	missense	56979			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.2440A>C	5.37:g.23527637A>C	ENSP00000296682:p.Ser814Arg		B4DX22|Q27Q50	Missense_Mutation	SNP	ENST00000296682.3	37	CCDS43307.1	.	.	.	.	.	.	.	.	.	.	A	1.621	-0.521388	0.04171	0.003983	3.52E-4	ENSG00000164256	ENST00000296682	T	0.37411	1.2	3.02	3.02	0.34903	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.22282	0.0537	L	0.28504	0.86	0.09310	N	0.999998	P	0.42908	0.793	B	0.37304	0.246	T	0.06110	-1.0845	9	0.33940	T	0.23	.	5.6652	0.17690	0.7579:0.0:0.0:0.2421	rs61051796	814	Q9NQV7	PRDM9_HUMAN	R	814	ENSP00000296682:S814R	ENSP00000296682:S814R	S	+	1	0	PRDM9	23563394	0.000000	0.05858	0.690000	0.30148	0.013000	0.08279	-0.284000	0.08422	1.653000	0.50694	0.386000	0.25728	AGC		0.567	PRDM9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366375.1	NM_020227	
UBR4	23352	bcgsc.ca	37	1	19480348	19480349	+	Missense_Mutation	DNP	GC	GC	TA			TCGA-KL-8323-01A-21D-2310-10	TCGA-KL-8323-11A-01D-2310-10	G|C	G|C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fae88d21-171c-4df4-b258-3c5948a1034b	f5c7fb67-5906-4db0-ad0d-129df8e065cb	g.chr1:19480348_19480349GC>TA	ENST00000375254.3	-	45	6570_6571	c.6543_6544GC>TA	c.(6541-6546)caGCaa>caTAaa	p.2181_2182QQ>HK	UBR4_ENST00000375226.2_Missense_Mutation_p.2181_2182QQ>HK|UBR4_ENST00000375217.2_Missense_Mutation_p.2181_2182QQ>HK|UBR4_ENST00000375267.2_Missense_Mutation_p.2181_2182QQ>HK	NM_020765.2	NP_065816.2	Q5T4S7	UBR4_HUMAN	ubiquitin protein ligase E3 component n-recognin 4	2181					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|viral process (GO:0016032)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(7)|central_nervous_system(1)|cervix(2)|endometrium(23)|kidney(25)|large_intestine(25)|liver(2)|lung(47)|ovary(10)|pancreas(2)|prostate(7)|skin(5)|stomach(5)|upper_aerodigestive_tract(4)|urinary_tract(6)	171		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000328)|Lung NSC(340;0.000406)|Breast(348;0.000814)|Ovarian(437;0.00774)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00674)|BRCA - Breast invasive adenocarcinoma(304;5.43e-05)|Kidney(64;0.000337)|KIRC - Kidney renal clear cell carcinoma(64;0.00426)|STAD - Stomach adenocarcinoma(196;0.00715)|READ - Rectum adenocarcinoma(331;0.0816)		CCTGTAGTTTGCTGGACACAGC	0.495																																						.											0																																										SO:0001583	missense	23352			AF348492	CCDS189.1	1p36.13	2008-06-23	2007-06-19	2007-06-19	ENSG00000127481	ENSG00000127481		"""Ubiquitin protein ligase E3 component n-recognins"""	30313	protein-coding gene	gene with protein product		609890	"""zinc finger, UBR1 type 1"""	ZUBR1		14702039, 10718198, 16055722	Standard	XM_005245802		Approved	KIAA1307, KIAA0462, RBAF600	uc001bbi.3	Q5T4S7	OTTHUMG00000002498	ENST00000375254.3:c.6543_6544delinsTA	1.37:g.19480348_19480349delinsTA	ENSP00000364403:p.Q2181_Q2182delinsHK		A8MPT2|A8MQ33|A8MQB1|O60646|O75050|Q4QRK5|Q5T4S8|Q5T4S9|Q5TBN8|Q5TBP2|Q6DKH8|Q6P4A4|Q7L8P7|Q8IXJ4|Q8TDN5|Q8WV67|Q9HA46|Q9P2N9|Q9UG82	Missense_Mutation	SNP	ENST00000375254.3	37	CCDS189.1																																																																																				0.495	UBR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007085.1	NM_020765	
ITGA3	3675	bcgsc.ca	37	17	48165656	48165656	+	Missense_Mutation	SNP	A	A	G			TCGA-KL-8323-01A-21D-2310-10	TCGA-KL-8323-11A-01D-2310-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fae88d21-171c-4df4-b258-3c5948a1034b	f5c7fb67-5906-4db0-ad0d-129df8e065cb	g.chr17:48165656A>G	ENST00000320031.8	+	25	3443	c.3113A>G	c.(3112-3114)aAg>aGg	p.K1038R	ITGA3_ENST00000007722.7_Intron	NM_002204.2|NM_005501.2	NP_002195.1|NP_005492.1	P26006	ITA3_HUMAN	integrin, alpha 3 (antigen CD49C, alpha 3 subunit of VLA-3 receptor)	1038					blood coagulation (GO:0007596)|cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|lung development (GO:0030324)|maternal process involved in female pregnancy (GO:0060135)|memory (GO:0007613)|mesodermal cell differentiation (GO:0048333)|negative regulation of cell projection organization (GO:0031345)|nephron development (GO:0072006)|neuron migration (GO:0001764)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of gene expression (GO:0010628)|positive regulation of neuron projection development (GO:0010976)|regulation of BMP signaling pathway (GO:0030510)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|regulation of Wnt signaling pathway (GO:0030111)|renal filtration (GO:0097205)|response to drug (GO:0042493)|response to gonadotropin (GO:0034698)|skin development (GO:0043588)	basolateral plasma membrane (GO:0016323)|cell periphery (GO:0071944)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|integrin alpha3-beta1 complex (GO:0034667)|integrin complex (GO:0008305)|invadopodium membrane (GO:0071438)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|synapse (GO:0045202)	glycoprotein binding (GO:0001948)|metal ion binding (GO:0046872)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)			endometrium(3)|kidney(2)|large_intestine(7)|lung(11)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(2)	31						GCGGAGATGAAGAGCCAGCCG	0.682																																						.											0													14.0	16.0	15.0					17																	48165656		2183	4271	6454	SO:0001583	missense	3675			M59911	CCDS11557.1, CCDS11558.1	17q21.33	2010-03-23	2003-10-13		ENSG00000005884	ENSG00000005884		"""CD molecules"", ""Integrins"""	6139	protein-coding gene	gene with protein product		605025	"""antigen identified by monoclonal antibody J143"""	MSK18		1655803, 9704023	Standard	NM_005501		Approved	CD49c, VLA3a, VCA-2, GAP-B3	uc010dbm.3	P26006	OTTHUMG00000161890	ENST00000320031.8:c.3113A>G	17.37:g.48165656A>G	ENSP00000315190:p.Lys1038Arg		A7E246|B7ZM80|B9EGQ1|D3DTX4|D3DTX5	Missense_Mutation	SNP	ENST00000320031.8	37	CCDS11558.1	.	.	.	.	.	.	.	.	.	.	A	7.011	0.556719	0.13436	.	.	ENSG00000005884	ENST00000538917;ENST00000320031	T	0.23348	1.91	5.1	1.61	0.23674	.	.	.	.	.	T	0.06462	0.0166	N	0.01352	-0.895	0.80722	D	1	B	0.18461	0.028	B	0.13407	0.009	T	0.36480	-0.9746	9	0.02654	T	1	.	7.2659	0.26229	0.7307:0.0:0.2693:0.0	.	1038	P26006	ITA3_HUMAN	R	1024;1038	ENSP00000315190:K1038R	ENSP00000315190:K1038R	K	+	2	0	ITGA3	45520655	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	3.238000	0.51352	0.264000	0.21851	0.379000	0.24179	AAG		0.682	ITGA3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000366298.1	NM_005501	
SMURF2	64750	bcgsc.ca	37	17	62579654	62579654	+	Missense_Mutation	SNP	T	T	C			TCGA-KL-8323-01A-21D-2310-10	TCGA-KL-8323-11A-01D-2310-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fae88d21-171c-4df4-b258-3c5948a1034b	f5c7fb67-5906-4db0-ad0d-129df8e065cb	g.chr17:62579654T>C	ENST00000262435.9	-	7	681	c.494A>G	c.(493-495)gAa>gGa	p.E165G	SMURF2_ENST00000578200.1_Intron	NM_022739.3	NP_073576.1	Q9HAU4	SMUF2_HUMAN	SMAD specific E3 ubiquitin protein ligase 2	165	WW 1. {ECO:0000255|PROSITE- ProRule:PRU00224}.				BMP signaling pathway (GO:0030509)|gene expression (GO:0010467)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ubiquitin-dependent protein catabolic process (GO:0006511)|ubiquitin-dependent SMAD protein catabolic process (GO:0030579)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ubiquitin ligase complex (GO:0000151)	identical protein binding (GO:0042802)|ligase activity (GO:0016874)|SMAD binding (GO:0046332)|ubiquitin-protein transferase activity (GO:0004842)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(2)|lung(6)|prostate(1)|skin(4)	22	Breast(5;1.32e-14)		BRCA - Breast invasive adenocarcinoma(8;9.88e-12)			GGTTCTCCTTTCTTCCCAGCT	0.398																																						.											0													113.0	98.0	103.0					17																	62579654		2203	4300	6503	SO:0001583	missense	64750			AF301463	CCDS32707.1	17q22-q23	2012-10-05			ENSG00000108854	ENSG00000108854			16809	protein-coding gene	gene with protein product		605532				11016919	Standard	XM_005257585		Approved		uc002jep.1	Q9HAU4	OTTHUMG00000179189	ENST00000262435.9:c.494A>G	17.37:g.62579654T>C	ENSP00000262435:p.Glu165Gly		Q52LL1|Q9H260	Missense_Mutation	SNP	ENST00000262435.9	37	CCDS32707.1	.	.	.	.	.	.	.	.	.	.	T	14.60	2.585245	0.46110	.	.	ENSG00000108854	ENST00000262435	D	0.85171	-1.95	5.06	5.06	0.68205	WW/Rsp5/WWP (5);	0.093513	0.64402	D	0.000001	D	0.88941	0.6574	M	0.93720	3.45	0.80722	D	1	B	0.22983	0.078	B	0.22880	0.042	D	0.87742	0.2586	10	0.44086	T	0.13	.	15.1061	0.72322	0.0:0.0:0.0:1.0	.	165	Q9HAU4	SMUF2_HUMAN	G	165	ENSP00000262435:E165G	ENSP00000262435:E165G	E	-	2	0	SMURF2	60010116	1.000000	0.71417	1.000000	0.80357	0.931000	0.56810	7.359000	0.79477	2.024000	0.59613	0.477000	0.44152	GAA		0.398	SMURF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445227.1	NM_022739	
HM13	81502	bcgsc.ca	37	20	30149459	30149459	+	Missense_Mutation	SNP	T	T	C			TCGA-KL-8323-01A-21D-2310-10	TCGA-KL-8323-11A-01D-2310-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fae88d21-171c-4df4-b258-3c5948a1034b	f5c7fb67-5906-4db0-ad0d-129df8e065cb	g.chr20:30149459T>C	ENST00000340852.5	+	10	992	c.868T>C	c.(868-870)Tac>Cac	p.Y290H	HM13-IT1_ENST00000421894.1_RNA|HM13_ENST00000492709.1_3'UTR|HM13_ENST00000335574.5_Missense_Mutation_p.Y290H|HM13_ENST00000376127.3_Missense_Mutation_p.Y248H|HM13_ENST00000398174.3_Missense_Mutation_p.Y290H	NM_030789.2	NP_110416.1	Q8TCT9	HM13_HUMAN	histocompatibility (minor) 13	290					membrane protein proteolysis (GO:0033619)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|integral component of cytoplasmic side of endoplasmic reticulum membrane (GO:0071458)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|membrane (GO:0016020)|plasma membrane (GO:0005886)|rough endoplasmic reticulum (GO:0005791)	aspartic endopeptidase activity, intramembrane cleaving (GO:0042500)|peptidase activity (GO:0008233)|protein homodimerization activity (GO:0042803)			breast(1)|endometrium(2)|large_intestine(2)|lung(4)|prostate(1)|skin(1)|urinary_tract(1)	12	all_cancers(5;3.44e-05)|Lung NSC(7;4.38e-06)|all_lung(7;7.65e-06)|all_hematologic(12;0.158)|Ovarian(7;0.198)		all cancers(5;0.000479)|Colorectal(19;0.00202)|COAD - Colon adenocarcinoma(19;0.0264)			TACCCACACCTACTTCTACAC	0.502																																						.											0													240.0	168.0	192.0					20																	30149459		2203	4300	6503	SO:0001583	missense	81502			AL110115	CCDS13182.1, CCDS13183.1, CCDS42861.1	20q11.21	2012-02-21			ENSG00000101294	ENSG00000101294			16435	protein-coding gene	gene with protein product	"""signal peptide peptidase beta"", ""presenilin-like protein 3"", ""intramembrane protease"", ""signal peptide peptidase like 1"""	607106				12077416, 14704149	Standard	NM_030789		Approved	H13, dJ324O17.1, SPP, PSL3, IMP1, IMPAS, PSENL3, SPPL1	uc002wwc.3	Q8TCT9	OTTHUMG00000032175	ENST00000340852.5:c.868T>C	20.37:g.30149459T>C	ENSP00000343032:p.Tyr290His		B2RAY5|E1P5L3|Q15K36|Q540H8|Q5JWP2|Q5JWP3|Q5JWP4|Q5JWP5|Q7Z4F2|Q86Y35|Q95H87|Q9H110|Q9H111	Missense_Mutation	SNP	ENST00000340852.5	37	CCDS13182.1	.	.	.	.	.	.	.	.	.	.	T	28.5	4.926434	0.92319	.	.	ENSG00000101294	ENST00000335574;ENST00000340852;ENST00000398174;ENST00000376127;ENST00000344042	T;T;T;T;T	0.51071	0.72;0.72;0.72;0.72;0.72	5.84	5.84	0.93424	.	0.000000	0.85682	D	0.000000	T	0.81158	0.4764	H	0.98314	4.2	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.97110	1.0;1.0;0.988	D	0.88395	0.3011	10	0.72032	D	0.01	-23.9758	15.4114	0.74923	0.0:0.0:0.0:1.0	.	290;290;290	Q8TCT9;Q8TCT9-4;Q8TCT9-2	HM13_HUMAN;.;.	H	290;290;290;248;248	ENSP00000335294:Y290H;ENSP00000343032:Y290H;ENSP00000381237:Y290H;ENSP00000365296:Y248H;ENSP00000341347:Y248H	ENSP00000335294:Y290H	Y	+	1	0	HM13	29613120	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.387000	0.79785	2.228000	0.72767	0.533000	0.62120	TAC		0.502	HM13-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078527.2	NM_178580	
MT-CO2	4513	bcgsc.ca	37	M	7887	7887	+	Missense_Mutation	SNP	G	G	A			TCGA-KL-8323-01A-21D-2310-10	TCGA-KL-8323-11A-01D-2310-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fae88d21-171c-4df4-b258-3c5948a1034b	f5c7fb67-5906-4db0-ad0d-129df8e065cb	g.chrM:7887G>A	ENST00000361739.1	+	1	302	c.302G>A	c.(301-303)gGc>gAc	p.G101D	MT-TR_ENST00000387439.1_RNA|MT-TA_ENST00000387392.1_RNA|MT-TN_ENST00000387400.1_RNA|MT-TS1_ENST00000387416.2_RNA|MT-ND4_ENST00000361381.2_5'Flank|MT-CO3_ENST00000362079.2_5'Flank|MT-TY_ENST00000387409.1_RNA|MT-ATP6_ENST00000361899.2_5'Flank|MT-TC_ENST00000387405.1_RNA|MT-ND4L_ENST00000361335.1_5'Flank|MT-ATP8_ENST00000361851.1_5'Flank|MT-TK_ENST00000387421.1_RNA|MT-TG_ENST00000387429.1_RNA|MT-TD_ENST00000387419.1_RNA|MT-TW_ENST00000387382.1_RNA|MT-ND3_ENST00000361227.2_5'Flank			P00403	COX2_HUMAN	mitochondrially encoded cytochrome c oxidase II	101					cellular metabolic process (GO:0044237)|hydrogen ion transmembrane transport (GO:1902600)|mitochondrial electron transport, cytochrome c to oxygen (GO:0006123)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|respiratory chain complex IV (GO:0045277)	copper ion binding (GO:0005507)|cytochrome-c oxidase activity (GO:0004129)			endometrium(5)|kidney(8)|lung(2)|pancreas(3)|prostate(1)	19						CAAATCAATTGGCCACCAATG	0.522																																						.											0																																										SO:0001583	missense	5743					mitochondria	2012-11-16	2005-02-15	2005-02-16	ENSG00000198712	ENSG00000198712		"""Mitochondrial respiratory chain complex / Complex IV"""	7421	protein-coding gene	gene with protein product		516040	"""cytochrome c oxidase II"""	MTCO2		1712754, 1989603	Standard			Approved	COX2, CO2		P00403		ENST00000361739.1:c.302G>A	M.37:g.7887G>A	ENSP00000354876:p.Gly101Asp		Q37526	Missense_Mutation	SNP	ENST00000361739.1	37																																																																																					0.522	MT-CO2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024029	
WDR62	284403	bcgsc.ca	37	19	36558851	36558852	+	Frame_Shift_Ins	INS	-	-	AC			TCGA-KL-8323-01A-21D-2310-10	TCGA-KL-8323-11A-01D-2310-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fae88d21-171c-4df4-b258-3c5948a1034b	f5c7fb67-5906-4db0-ad0d-129df8e065cb	g.chr19:36558851_36558852insAC	ENST00000270301.7	+	7	821_822	c.821_822insAC	c.(820-825)tactcgfs	p.YS274fs	WDR62_ENST00000401500.2_Frame_Shift_Ins_p.YS274fs|WDR62_ENST00000388999.3_Frame_Shift_Ins_p.YS274fs|WDR62_ENST00000378860.4_3'UTR			O43379	WDR62_HUMAN	WD repeat domain 62	274					cerebral cortex development (GO:0021987)|neurogenesis (GO:0022008)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|spindle pole (GO:0000922)				cervix(1)|endometrium(8)|kidney(2)|large_intestine(8)|lung(15)|prostate(4)|stomach(2)|urinary_tract(3)	43	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.06)			TGTGTGTCCTACTCGGGCCTCC	0.599																																						.											0																																										SO:0001589	frameshift_variant	284403			BX647726	CCDS33001.1, CCDS46059.1	19q13.12	2013-01-09	2005-05-09	2005-05-09	ENSG00000075702	ENSG00000075702		"""WD repeat domain containing"""	24502	protein-coding gene	gene with protein product		613583	"""chromosome 19 open reading frame 14"", ""microcephaly, primary autosomal recessive 2"""	C19orf14, MCPH2		19910486, 20729831, 20890278, 21496009	Standard	NM_001083961		Approved	DKFZP434J046, FLJ33298	uc002odd.2	O43379	OTTHUMG00000048139	Exception_encountered	19.37:g.36558851_36558852insAC	ENSP00000270301:p.Tyr274fs		Q63HP9|Q659D7|Q8NBF7|Q96AD9	Nonsense_Mutation	INS	ENST00000270301.7	37	CCDS33001.1																																																																																				0.599	WDR62-006	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000457436.1	NM_015671	
