#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_AAChange	i_ACHILLES_Lineage_Results_Top_Genes	i_BAM_File	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_Codon	i_COSMIC_Gene	i_COSMIC_Gene_Freq	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ChromChange	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Drug_Target	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Exon	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_Genome_Plus_Minus_10_Bp	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_Mutation_Status	i_NTotCov_SOL	i_NVarCov_SOL	i_ORegAnno_bin	i_Sequence_Source	i_Sequencer	i_Sequencing_Phase	i_TTotCov_SOL	i_TVarCov_SOL	i_Transcript_Id	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_ccds_id	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_dbSNPPopFreq	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_type	i_havana_transcript	i_refseq_mrna_id	i_secondary_variant_classification
KMT2D	8085	hgsc.bcm.edu	37	12	49426576	49426578	+	In_Frame_Del	DEL	TGC	TGC	-			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	TGC	TGC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr12:49426576_49426578delTGC	ENST00000301067.7	-	39	11909_11911	c.11910_11912delGCA	c.(11908-11913)cagcaa>caa	p.3970_3971QQ>Q	KMT2D_ENST00000549743.1_5'Flank	NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	3970	Gln-rich.				chromatin silencing (GO:0006342)|histone H3-K4 methylation (GO:0051568)|oocyte growth (GO:0001555)|oogenesis (GO:0048477)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to estrogen (GO:0043627)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)	p.Q3701*(3)|p.Q3971*(2)									ctgctgctgttgctgctgctgtt	0.517																																					p.3971_3971del		.											.	.	.	5	Substitution - Nonsense(5)	haematopoietic_and_lymphoid_tissue(5)	c.11911_11913del						.																																			SO:0001651	inframe_deletion	8085	exon39			TGCTGTTGCTGCT	AF010403	CCDS44873.1	12q13.12	2013-05-09	2013-05-09	2013-05-09	ENSG00000167548	ENSG00000167548		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	7133	protein-coding gene	gene with protein product		602113	"""trinucleotide repeat containing 21"", ""myeloid/lymphoid or mixed-lineage leukemia 2"""	TNRC21, MLL2		9247308	Standard	NM_003482		Approved	ALR, MLL4, CAGL114		O14686	OTTHUMG00000166524	ENST00000301067.7:c.11910_11912delGCA	12.37:g.49426582_49426584delTGC	ENSP00000301067:p.Gln3974del	Somatic	24	0		WXS	Illumina HiSeq	.	49	10	NM_003482	O14687	In_Frame_Del	DEL	ENST00000301067.7	37	CCDS44873.1																																																																																			.		0.517	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2		
TP53	7157	hgsc.bcm.edu	37	17	7577579	7577580	+	Frame_Shift_Ins	INS	-	-	T	rs587780073		TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr17:7577579_7577580insT	ENST00000269305.4	-	7	890_891	c.701_702insA	c.(700-702)tacfs	p.Y234fs	TP53_ENST00000359597.4_Frame_Shift_Ins_p.Y234fs|TP53_ENST00000445888.2_Frame_Shift_Ins_p.Y234fs|TP53_ENST00000574684.1_5'UTR|TP53_ENST00000455263.2_Frame_Shift_Ins_p.Y234fs|TP53_ENST00000413465.2_Frame_Shift_Ins_p.Y234fs|TP53_ENST00000420246.2_Frame_Shift_Ins_p.Y234fs	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	234	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		Y -> C (in LFS; germline mutation and in sporadic cancers; somatic mutation).|Y -> D (in sporadic cancers; somatic mutation).|Y -> F (in a sporadic cancer; somatic mutation).|Y -> H (in sporadic cancers; somatic mutation).|Y -> K (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|Y -> N (in sporadic cancers; somatic mutation).|Y -> Q (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|Y -> S (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.Y234C(94)|p.Y234S(9)|p.Y141C(8)|p.0?(8)|p.?(5)|p.Y234*(4)|p.Y234del(3)|p.N235fs*5(2)|p.Y141S(2)|p.N235fs*6(1)|p.Y234fs*2(1)|p.V225fs*23(1)|p.Y234fs*5(1)|p.Y234fs*4(1)|p.Y234R(1)|p.Y234Y(1)|p.H233_C242del10(1)|p.D228fs*12(1)|p.Y234F(1)|p.I232_Y236delIHYNY(1)|p.T230_Y234delTTIHY(1)|p.H233fs*6(1)|p.Y234_N235insX(1)|p.I232fs*5(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	ACATGTAGTTGTAGTGGATGGT	0.574		111	"""Mis, N, F"""		"""breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"""	"""breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"""		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.Y234_N235delinsX	Pancreas(47;798 1329 9957 10801)	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"""L, E, M, O"""	TP53_ENST00000545858,colon,carcinoma,0,21	TP53_ENST00000545858	0	150	Substitution - Missense(115)|Whole gene deletion(8)|Deletion - Frameshift(7)|Deletion - In frame(6)|Unknown(5)|Substitution - Nonsense(4)|Insertion - Frameshift(3)|Insertion - In frame(1)|Substitution - coding silent(1)	lung(32)|haematopoietic_and_lymphoid_tissue(19)|breast(18)|ovary(15)|central_nervous_system(11)|urinary_tract(9)|upper_aerodigestive_tract(8)|oesophagus(8)|biliary_tract(7)|large_intestine(5)|kidney(4)|bone(4)|cervix(3)|stomach(2)|skin(2)|vulva(1)|adrenal_gland(1)|liver(1)	c.702_703insA	GRCh37	CM035576	TP53	M		.																																			SO:0001589	frameshift_variant	7157	exon7	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	GTAGTTGTAGTGG	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"""Li-Fraumeni syndrome"""	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.702dupA	17.37:g.7577580_7577580dupT	ENSP00000269305:p.Tyr234fs	Somatic	33	0		WXS	Illumina HiSeq	.	18	10	NM_001126112	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Frame_Shift_Ins	INS	ENST00000269305.4	37	CCDS11118.1																																																																																			.		0.574	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546	
FGFR2	2263	hgsc.bcm.edu	37	10	123278298	123278299	+	Intron	INS	-	-	GAA			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr10:123278298_123278299insGAA	ENST00000358487.5	-	7	1212				FGFR2_ENST00000369060.4_Intron|FGFR2_ENST00000360144.3_In_Frame_Ins_p.239_240insF|FGFR2_ENST00000478859.1_Intron|FGFR2_ENST00000369061.4_Intron|FGFR2_ENST00000457416.2_In_Frame_Ins_p.328_329insF|FGFR2_ENST00000357555.5_Intron|FGFR2_ENST00000490349.1_5'UTR|FGFR2_ENST00000346997.2_Intron|FGFR2_ENST00000356226.4_Intron|FGFR2_ENST00000369059.1_In_Frame_Ins_p.213_214insF|FGFR2_ENST00000369056.1_In_Frame_Ins_p.328_329insF|FGFR2_ENST00000351936.6_Intron	NM_000141.4	NP_000132.3	P21802	FGFR2_HUMAN	fibroblast growth factor receptor 2						angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|axonogenesis (GO:0007409)|bone development (GO:0060348)|bone mineralization (GO:0030282)|bone morphogenesis (GO:0060349)|branch elongation involved in salivary gland morphogenesis (GO:0060667)|branching involved in labyrinthine layer morphogenesis (GO:0060670)|branching involved in prostate gland morphogenesis (GO:0060442)|branching involved in salivary gland morphogenesis (GO:0060445)|branching morphogenesis of a nerve (GO:0048755)|bud elongation involved in lung branching (GO:0060449)|cell fate commitment (GO:0045165)|cell-cell signaling (GO:0007267)|coronal suture morphogenesis (GO:0060365)|digestive tract development (GO:0048565)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic organ development (GO:0048568)|embryonic organ morphogenesis (GO:0048562)|embryonic pattern specification (GO:0009880)|endodermal digestive tract morphogenesis (GO:0061031)|epidermal growth factor receptor signaling pathway (GO:0007173)|epidermis morphogenesis (GO:0048730)|epithelial cell differentiation (GO:0030855)|epithelial cell proliferation involved in salivary gland morphogenesis (GO:0060664)|epithelial to mesenchymal transition (GO:0001837)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|fibroblast growth factor receptor signaling pathway involved in hemopoiesis (GO:0035603)|fibroblast growth factor receptor signaling pathway involved in mammary gland specification (GO:0060595)|fibroblast growth factor receptor signaling pathway involved in negative regulation of apoptotic process in bone marrow (GO:0035602)|fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development (GO:0035607)|fibroblast growth factor receptor signaling pathway involved in positive regulation of cell proliferation in bone marrow (GO:0035604)|gland morphogenesis (GO:0022612)|hair follicle morphogenesis (GO:0031069)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|inner ear morphogenesis (GO:0042472)|insulin receptor signaling pathway (GO:0008286)|lacrimal gland development (GO:0032808)|lateral sprouting from an epithelium (GO:0060601)|lens fiber cell development (GO:0070307)|limb bud formation (GO:0060174)|lung alveolus development (GO:0048286)|lung development (GO:0030324)|lung lobe morphogenesis (GO:0060463)|lung-associated mesenchyme development (GO:0060484)|mammary gland bud formation (GO:0060615)|membranous septum morphogenesis (GO:0003149)|mesenchymal cell differentiation (GO:0048762)|mesenchymal cell differentiation involved in lung development (GO:0060915)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesodermal cell differentiation (GO:0048333)|midbrain development (GO:0030901)|morphogenesis of embryonic epithelium (GO:0016331)|multicellular organism growth (GO:0035264)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of mitosis (GO:0045839)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuromuscular junction development (GO:0007528)|neurotrophin TRK receptor signaling pathway (GO:0048011)|odontogenesis (GO:0042476)|orbitofrontal cortex development (GO:0021769)|organ growth (GO:0035265)|organ morphogenesis (GO:0009887)|otic vesicle formation (GO:0030916)|outflow tract septum morphogenesis (GO:0003148)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of epithelial cell proliferation involved in lung morphogenesis (GO:0060501)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of Wnt signaling pathway (GO:0030177)|post-embryonic development (GO:0009791)|prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis (GO:0060527)|prostate epithelial cord elongation (GO:0060523)|prostate gland morphogenesis (GO:0060512)|protein autophosphorylation (GO:0046777)|pyramidal neuron development (GO:0021860)|regulation of branching involved in prostate gland morphogenesis (GO:0060687)|regulation of cell fate commitment (GO:0010453)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)|regulation of morphogenesis of a branching structure (GO:0060688)|regulation of multicellular organism growth (GO:0040014)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoblast proliferation (GO:0033688)|regulation of smooth muscle cell differentiation (GO:0051150)|regulation of smoothened signaling pathway (GO:0008589)|reproductive structure development (GO:0048608)|skeletal system morphogenesis (GO:0048705)|squamous basal epithelial stem cell differentiation involved in prostate gland acinus development (GO:0060529)|synaptic vesicle transport (GO:0048489)|ureteric bud development (GO:0001657)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|ventricular zone neuroblast division (GO:0021847)	cell cortex (GO:0005938)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|excitatory synapse (GO:0060076)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|fibroblast growth factor binding (GO:0017134)|fibroblast growth factor-activated receptor activity (GO:0005007)|heparin binding (GO:0008201)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)			breast(3)|central_nervous_system(3)|cervix(2)|endometrium(98)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(7)|lung(21)|ovary(4)|skin(30)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(2)	181		Lung NSC(174;0.0841)|all_lung(145;0.106)|all_neural(114;0.107)	STAD - Stomach adenocarcinoma(1;7.52e-05)|all cancers(1;0.0722)	all cancers(201;9.73e-05)|GBM - Glioblastoma multiforme(135;0.0845)	Palifermin(DB00039)|Ponatinib(DB08901)|Regorafenib(DB08896)|Thalidomide(DB01041)	TCGGTCACATTGAACAGAGCCA	0.485		5	Mis		"""gastric. NSCLC, endometrial"""		"""Crouzon, Pfeiffer, and Apert syndromes"""		Saethre-Chotzen syndrome;Apert syndrome																												p.N329delinsFN		.		Dom	yes		10	10q26	2263	fibroblast growth factor receptor 2	yes	E	.	.	.	0			c.985_986insTTC						.																																			SO:0001627	intron_variant	2263	exon8	Familial Cancer Database	Acrocephalosyndactyly type III;Acrocephalosyndactyly type I and II, ACS1. ACS2, incl Apert-Crouzon s.	TCACATTGAACAG	AK026508	CCDS7620.2, CCDS31298.1, CCDS44485.1, CCDS44486.1, CCDS44487.1, CCDS44488.1, CCDS44489.1, CCDS53584.1, CCDS73210.1	10q25.3-q26	2013-01-11	2008-08-01		ENSG00000066468	ENSG00000066468		"""CD molecules"", ""Immunoglobulin superfamily / I-set domain containing"""	3689	protein-coding gene	gene with protein product	"""Crouzon syndrome"", ""Pfeiffer syndrome"""	176943	"""bacteria-expressed kinase"", ""keratinocyte growth factor receptor"", ""craniofacial dysostosis 1"", ""Jackson-Weiss syndrome"""	KGFR, BEK, CFD1, JWS			Standard	NM_022970		Approved	CEK3, TK14, TK25, ECT1, K-SAM, CD332	uc021pzy.1	P21802	OTTHUMG00000019175	ENST00000358487.5:c.939+1193->TTC	10.37:g.123278299_123278301dupGAA		Somatic	28	0		WXS	Illumina HiSeq	.	60	44	NM_022970	B4DFC2|E7EVR6|E9PCR0|P18443|Q01742|Q12922|Q14300|Q14301|Q14302|Q14303|Q14304|Q14305|Q14672|Q14718|Q14719|Q1KHY5|Q86YI4|Q8IXC7|Q96KL9|Q96KM0|Q96KM1|Q96KM2|Q9NZU2|Q9NZU3|Q9UD01|Q9UD02|Q9UIH3|Q9UIH4|Q9UIH5|Q9UIH6|Q9UIH7|Q9UIH8|Q9UM87|Q9UMC6|Q9UNS7|Q9UQH7|Q9UQH8|Q9UQH9|Q9UQI0	In_Frame_Ins	INS	ENST00000358487.5	37	CCDS31298.1																																																																																			.		0.485	FGFR2-001	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000050715.1	NM_022976, NM_000141	
KMT2D	8085	hgsc.bcm.edu	37	12	49426590	49426592	+	In_Frame_Del	DEL	AAA	AAA	-			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	AAA	AAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr12:49426590_49426592delAAA	ENST00000301067.7	-	39	11895_11897	c.11896_11898delTTT	c.(11896-11898)tttdel	p.F3966del	KMT2D_ENST00000549743.1_5'Flank	NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	3966	Gln-rich.				chromatin silencing (GO:0006342)|histone H3-K4 methylation (GO:0051568)|oocyte growth (GO:0001555)|oogenesis (GO:0048477)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to estrogen (GO:0043627)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)										gctgctgttgaaactgctgctgt	0.517																																					p.3966_3967del		.											.	.	.	0			c.11897_11899del						.																																			SO:0001651	inframe_deletion	8085	exon39			CTGTTGAAACTGC	AF010403	CCDS44873.1	12q13.12	2013-05-09	2013-05-09	2013-05-09	ENSG00000167548	ENSG00000167548		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	7133	protein-coding gene	gene with protein product		602113	"""trinucleotide repeat containing 21"", ""myeloid/lymphoid or mixed-lineage leukemia 2"""	TNRC21, MLL2		9247308	Standard	NM_003482		Approved	ALR, MLL4, CAGL114		O14686	OTTHUMG00000166524	ENST00000301067.7:c.11896_11898delTTT	12.37:g.49426590_49426592delAAA	ENSP00000301067:p.Phe3966del	Somatic	20	0		WXS	Illumina HiSeq	.	43	11	NM_003482	O14687	In_Frame_Del	DEL	ENST00000301067.7	37	CCDS44873.1																																																																																			.		0.517	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2		
KMT2D	8085	hgsc.bcm.edu	37	12	49426567	49426632	+	In_Frame_Del	DEL	TGCTGCTGTTGCTGCTGCTGTTGAAACTGCTGCTGTTGTTGTTGCTGTTGCTGTTGTAGCTGCTGT	TGCTGCTGTTGCTGCTGCTGTTGAAACTGCTGCTGTTGTTGTTGCTGTTGCTGTTGTAGCTGCTGT	-	rs587778473|rs375458808|rs371224852|rs180784366	byFrequency	TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	TGCTGCTGTTGCTGCTGCTGTTGAAACTGCTGCTGTTGTTGTTGCTGTTGCTGTTGTAGCTGCTGT	TGCTGCTGTTGCTGCTGCTGTTGAAACTGCTGCTGTTGTTGTTGCTGTTGCTGTTGTAGCTGCTGT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr12:49426567_49426632delTGCTGCTGTTGCTGCTGCTGTTGAAACTGCTGCTGTTGTTGTTGCTGTTGCTGTTGTAGCTGCTGT	ENST00000301067.7	-	39	11855_11920	c.11856_11921delACAGCAGCTACAACAGCAACAGCAACAACAACAGCAGCAGTTTCAACAGCAGCAGCAACAGCAGCA	c.(11854-11922)caacagcagctacaacagcaacagcaacaacaacagcagcagtttcaacagcagcagcaacagcagcag>cag	p.3952_3974QQQLQQQQQQQQQQFQQQQQQQQ>Q	KMT2D_ENST00000549743.1_5'Flank	NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	3952	Gln-rich.				chromatin silencing (GO:0006342)|histone H3-K4 methylation (GO:0051568)|oocyte growth (GO:0001555)|oogenesis (GO:0048477)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to estrogen (GO:0043627)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)	p.Q3701*(3)|p.Q3971*(2)|p.Q3704*(1)|p.Q3974*(1)|p.Q3964*(1)|p.Q3699*(1)|p.Q3694*(1)									AAGGCCCATctgctgctgttgctgctgctgttgaaactgctgctgttgttgttgctgttgctgttgtagctgctgttgctgctgtt	0.511																																					p.3953_3974del		.											.	.	.	10	Substitution - Nonsense(10)	haematopoietic_and_lymphoid_tissue(9)|upper_aerodigestive_tract(1)	c.11857_11922del						.																																			SO:0001651	inframe_deletion	8085	exon39			CCCATCTGCTGCT	AF010403	CCDS44873.1	12q13.12	2013-05-09	2013-05-09	2013-05-09	ENSG00000167548	ENSG00000167548		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	7133	protein-coding gene	gene with protein product		602113	"""trinucleotide repeat containing 21"", ""myeloid/lymphoid or mixed-lineage leukemia 2"""	TNRC21, MLL2		9247308	Standard	NM_003482		Approved	ALR, MLL4, CAGL114		O14686	OTTHUMG00000166524	ENST00000301067.7:c.11856_11921delACAGCAGCTACAACAGCAACAGCAACAACAACAGCAGCAGTTTCAACAGCAGCAGCAACAGCAGCA	12.37:g.49426567_49426632delTGCTGCTGTTGCTGCTGCTGTTGAAACTGCTGCTGTTGTTGTTGCTGTTGCTGTTGTAGCTGCTGT	ENSP00000301067:p.Gln3952_Gln3973del	Somatic	24	0		WXS	Illumina HiSeq	.	54	0	NM_003482	O14687	In_Frame_Del	DEL	ENST00000301067.7	37	CCDS44873.1																																																																																			.		0.511	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2		
ERBB4	2066	hgsc.bcm.edu	37	2	212251586	212251586	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr2:212251586G>T	ENST00000342788.4	-	27	3783	c.3473C>A	c.(3472-3474)cCc>cAc	p.P1158H	ERBB4_ENST00000436443.1_Missense_Mutation_p.P1142H|ERBB4_ENST00000402597.1_Missense_Mutation_p.P1148H	NM_005235.2	NP_005226.1	Q15303	ERBB4_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 4	1158					cardiac muscle tissue regeneration (GO:0061026)|cell fate commitment (GO:0045165)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system morphogenesis (GO:0021551)|embryonic pattern specification (GO:0009880)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|lactation (GO:0007595)|mammary gland alveolus development (GO:0060749)|mammary gland epithelial cell differentiation (GO:0060644)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neural crest cell migration (GO:0001755)|neurotrophin TRK receptor signaling pathway (GO:0048011)|olfactory bulb interneuron differentiation (GO:0021889)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of STAT protein import into nucleus (GO:2000366)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell migration (GO:0030334)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	basolateral plasma membrane (GO:0016323)|cytosol (GO:0005829)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|epidermal growth factor receptor binding (GO:0005154)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transcription regulatory region DNA binding (GO:0044212)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(1)|breast(7)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(31)|lung(71)|pancreas(1)|prostate(3)|skin(39)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	179		Renal(323;0.06)|Lung NSC(271;0.197)		UCEC - Uterine corpus endometrioid carcinoma (47;0.214)|Epithelial(149;5.86e-06)|all cancers(144;2.95e-05)|Lung(261;0.00244)|LUSC - Lung squamous cell carcinoma(224;0.00266)	Afatinib(DB08916)	ACCTTGTTTGGGTTTGTCTCG	0.473										TSP Lung(8;0.080)																											p.P1158H		.											.	.	.	0			c.C3473A						.						172.0	159.0	164.0					2																	212251586		2203	4300	6503	SO:0001583	missense	2066	exon27			TGTTTGGGTTTGT	L07868	CCDS2394.1, CCDS42811.1	2q33.3-q34	2013-10-11	2013-07-09		ENSG00000178568	ENSG00000178568			3432	protein-coding gene	gene with protein product		600543	"""v-erb-a avian erythroblastic leukemia viral oncogene homolog-like 4"""			7700649, 17018285	Standard	NM_001042599		Approved	ALS19	uc002veg.1	Q15303	OTTHUMG00000133012	ENST00000342788.4:c.3473C>A	2.37:g.212251586G>T	ENSP00000342235:p.Pro1158His	Somatic	72	0		WXS	Illumina HiSeq	.	94	4	NM_005235	B7ZLD7|B7ZLE2|B7ZLE3|Q2M1W1|Q59EW4	Missense_Mutation	SNP	ENST00000342788.4	37	CCDS2394.1	.	.	.	.	.	.	.	.	.	.	G	19.14	3.770775	0.69992	.	.	ENSG00000178568	ENST00000342788;ENST00000436443;ENST00000402597	T;T;T	0.76578	-1.03;-1.01;-1.03	5.6	4.72	0.59763	.	0.248257	0.41194	D	0.000932	T	0.73745	0.3626	L	0.42245	1.32	0.40321	D	0.978828	P;P;P;P	0.41569	0.755;0.742;0.755;0.641	B;B;B;B	0.42916	0.191;0.402;0.386;0.145	T	0.78326	-0.2247	10	0.72032	D	0.01	.	13.9096	0.63857	0.0729:0.0:0.9271:0.0	.	1132;1148;1142;1158	Q15303-4;Q15303-2;Q15303-3;Q15303	.;.;.;ERBB4_HUMAN	H	1158;1142;1148	ENSP00000342235:P1158H;ENSP00000403204:P1142H;ENSP00000385565:P1148H	ENSP00000342235:P1158H	P	-	2	0	ERBB4	211959831	1.000000	0.71417	1.000000	0.80357	0.898000	0.52572	4.007000	0.57093	2.638000	0.89438	0.462000	0.41574	CCC	.		0.473	ERBB4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256597.1	NM_001042599	
C2CD3	26005	hgsc.bcm.edu;bcgsc.ca	37	11	73805030	73805030	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr11:73805030G>T	ENST00000334126.7	-	18	3401	c.3175C>A	c.(3175-3177)Ccc>Acc	p.P1059T	C2CD3_ENST00000313663.7_Missense_Mutation_p.P1059T			Q4AC94	C2CD3_HUMAN	C2 calcium-dependent domain containing 3	1059					brain development (GO:0007420)|centriole elongation (GO:0061511)|embryonic digit morphogenesis (GO:0042733)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|neural plate axis specification (GO:0021997)|neural tube development (GO:0021915)|nonmotile primary cilium assembly (GO:0035058)|protein localization to centrosome (GO:0071539)|protein processing (GO:0016485)|regulation of proteolysis (GO:0030162)|regulation of smoothened signaling pathway (GO:0008589)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)				NS(1)|breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(26)|ovary(4)|pancreas(2)|prostate(1)|skin(3)	64	Breast(11;4.16e-06)					GTTCTGAAGGGCTTCAGAGTA	0.403																																					p.P1059T		.											.	.	.	0			c.C3175A						.						98.0	93.0	95.0					11																	73805030		2200	4293	6493	SO:0001583	missense	26005	exon18			TGAAGGGCTTCAG	BC035599	CCDS31636.1, CCDS66167.1	11q13.4	2014-02-12	2007-10-17		ENSG00000168014	ENSG00000168014			24564	protein-coding gene	gene with protein product		615944					Standard	XM_005273897		Approved	DKFZP586P0123	uc001ouu.2	Q4AC94	OTTHUMG00000168110	ENST00000334126.7:c.3175C>A	11.37:g.73805030G>T	ENSP00000334379:p.Pro1059Thr	Somatic	45	0		WXS	Illumina HiSeq	.	54	5	NM_015531	C9JR55|E2QRD1|Q2NLE1|Q3C1U9|Q6ZU92|Q8IYM4|Q8NB87|Q8NDH7|Q9Y4M2	Missense_Mutation	SNP	ENST00000334126.7	37		.	.	.	.	.	.	.	.	.	.	G	16.10	3.026783	0.54683	.	.	ENSG00000168014	ENST00000334126;ENST00000313663;ENST00000313681	T;T	0.43688	0.94;0.94	5.78	2.87	0.33458	.	0.104648	0.64402	D	0.000003	T	0.36936	0.0985	L	0.53249	1.67	0.38263	D	0.941946	B	0.25441	0.126	B	0.26864	0.074	T	0.31833	-0.9929	10	0.72032	D	0.01	-4.752	8.9636	0.35863	0.1348:0.1231:0.742:0.0	.	1059	Q4AC94-1	.	T	1059	ENSP00000334379:P1059T;ENSP00000323339:P1059T	ENSP00000323339:P1059T	P	-	1	0	C2CD3	73482678	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.976000	0.49289	0.447000	0.26695	0.655000	0.94253	CCC	.		0.403	C2CD3-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015531	
TBX1	6899	hgsc.bcm.edu	37	22	19752563	19752563	+	Missense_Mutation	SNP	C	C	T			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr22:19752563C>T	ENST00000329705.7	+	6	896	c.767C>T	c.(766-768)gCc>gTc	p.A256V	TBX1_ENST00000332710.4_Missense_Mutation_p.A256V|TBX1_ENST00000359500.3_Missense_Mutation_p.A256V	NM_080646.1	NP_542377.1	O43435	TBX1_HUMAN	T-box 1	256					angiogenesis (GO:0001525)|anterior/posterior pattern specification (GO:0009952)|aorta morphogenesis (GO:0035909)|artery morphogenesis (GO:0048844)|blood vessel development (GO:0001568)|blood vessel morphogenesis (GO:0048514)|blood vessel remodeling (GO:0001974)|cell fate specification (GO:0001708)|cell proliferation (GO:0008283)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cellular response to retinoic acid (GO:0071300)|cochlea morphogenesis (GO:0090103)|coronary artery morphogenesis (GO:0060982)|determination of left/right symmetry (GO:0007368)|ear morphogenesis (GO:0042471)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic viscerocranium morphogenesis (GO:0048703)|enamel mineralization (GO:0070166)|epithelial cell differentiation (GO:0030855)|face morphogenesis (GO:0060325)|heart development (GO:0007507)|heart morphogenesis (GO:0003007)|inner ear morphogenesis (GO:0042472)|lymph vessel development (GO:0001945)|mesenchymal cell apoptotic process (GO:0097152)|mesoderm development (GO:0007498)|middle ear morphogenesis (GO:0042474)|muscle cell fate commitment (GO:0042693)|muscle organ development (GO:0007517)|muscle organ morphogenesis (GO:0048644)|muscle tissue morphogenesis (GO:0060415)|negative regulation of cell differentiation (GO:0045596)|negative regulation of mesenchymal cell apoptotic process (GO:2001054)|neural crest cell migration (GO:0001755)|odontogenesis of dentin-containing tooth (GO:0042475)|otic vesicle morphogenesis (GO:0071600)|outer ear morphogenesis (GO:0042473)|outflow tract morphogenesis (GO:0003151)|outflow tract septum morphogenesis (GO:0003148)|parathyroid gland development (GO:0060017)|pattern specification process (GO:0007389)|pharyngeal system development (GO:0060037)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of secondary heart field cardioblast proliferation (GO:0072513)|positive regulation of tongue muscle cell differentiation (GO:2001037)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of organ morphogenesis (GO:2000027)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|retinoic acid receptor signaling pathway (GO:0048384)|semicircular canal morphogenesis (GO:0048752)|sensory perception of sound (GO:0007605)|social behavior (GO:0035176)|soft palate development (GO:0060023)|thymus development (GO:0048538)|thyroid gland development (GO:0030878)|tongue morphogenesis (GO:0043587)|transcription, DNA-templated (GO:0006351)|vagus nerve morphogenesis (GO:0021644)	nucleus (GO:0005634)	DNA binding (GO:0003677)|protein dimerization activity (GO:0046983)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding (GO:0043565)	p.A256V(3)		breast(2)|central_nervous_system(1)|lung(3)|ovary(2)	8	Colorectal(54;0.0993)	all_lung(157;3.05e-06)				GAGAAATATGCCGAGGAGAAC	0.542																																					p.A256V		.											TBX1_ENST00000359500,brain,atypical_teratoid-rhabdoid_tumour,0,3	TBX1_ENST00000359500	0	3	Substitution - Missense(3)	central_nervous_system(3)	c.C767T						.						104.0	99.0	100.0					22																	19752563		2203	4300	6503	SO:0001583	missense	6899	exon6			AATATGCCGAGGA	AF012131	CCDS13765.1, CCDS13766.1, CCDS13767.1	22q11.21	2014-09-17			ENSG00000184058	ENSG00000184058		"""T-boxes"""	11592	protein-coding gene	gene with protein product		602054	"""velocardiofacial syndrome"""	VCF		9268629, 23000736	Standard	NM_080646		Approved	CATCH22	uc002zqa.1	O43435	OTTHUMG00000150421	ENST00000329705.7:c.767C>T	22.37:g.19752563C>T	ENSP00000331176:p.Ala256Val	Somatic	30	0		WXS	Illumina HiSeq	.	52	3	NM_080647	C6G493|C6G494|O43436|Q96RJ2	Missense_Mutation	SNP	ENST00000329705.7	37	CCDS13766.1	.	.	.	.	.	.	.	.	.	.	C	13.76	2.334428	0.41297	.	.	ENSG00000184058	ENST00000332710;ENST00000329705;ENST00000359500	D;D;D	0.87650	-2.28;-2.28;-2.28	4.18	4.18	0.49190	p53-like transcription factor, DNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.81187	0.4770	L	0.43701	1.375	0.80722	D	1	B;P;B	0.38395	0.425;0.629;0.425	B;B;B	0.30646	0.052;0.118;0.11	T	0.82432	-0.0460	10	0.40728	T	0.16	.	16.2707	0.82616	0.0:1.0:0.0:0.0	.	256;256;256	Q152R5;O43435;D9ZGG0	.;TBX1_HUMAN;.	V	256	ENSP00000331791:A256V;ENSP00000331176:A256V;ENSP00000352483:A256V	ENSP00000331176:A256V	A	+	2	0	TBX1	18132563	1.000000	0.71417	0.233000	0.24025	0.164000	0.22412	5.827000	0.69300	2.174000	0.68829	0.491000	0.48974	GCC	.		0.542	TBX1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318033.1	NM_080647	
ADAMTS20	80070	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	12	43770341	43770341	+	Missense_Mutation	SNP	C	C	T			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr12:43770341C>T	ENST00000389420.3	-	33	5110	c.5111G>A	c.(5110-5112)tGt>tAt	p.C1704Y		NM_025003.3	NP_079279.3	P59510	ATS20_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 20	1704	TSP type-1 15. {ECO:0000255|PROSITE- ProRule:PRU00210}.				extracellular matrix organization (GO:0030198)|negative regulation of apoptotic process (GO:0043066)|positive regulation of melanocyte differentiation (GO:0045636)|positive regulation of signal transduction (GO:0009967)	extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(6)|endometrium(3)|kidney(4)|large_intestine(11)|liver(1)|lung(43)|ovary(4)|pancreas(3)|prostate(5)|skin(12)|upper_aerodigestive_tract(1)|urinary_tract(1)	95	all_cancers(12;2.6e-05)|Lung SC(27;0.184)	Lung NSC(34;0.0569)|all_lung(34;0.129)		GBM - Glioblastoma multiforme(48;0.0473)		ATTGGCATAACATTTCTTTTG	0.328																																					p.C1704Y		.											.	.	.	0			c.G5111A						.						76.0	76.0	76.0					12																	43770341		2202	4300	6502	SO:0001583	missense	80070	exon33			GCATAACATTTCT	AF488804	CCDS31778.2	12q12	2005-08-19	2005-08-19			ENSG00000173157		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	17178	protein-coding gene	gene with protein product		611681	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 20"""			12514189, 12562771	Standard	NM_025003		Approved	GON-1	uc010skx.2	P59510		ENST00000389420.3:c.5111G>A	12.37:g.43770341C>T	ENSP00000374071:p.Cys1704Tyr	Somatic	30	0		WXS	Illumina HiSeq	.	68	21	NM_025003	A6NNC9|J3QT00	Missense_Mutation	SNP	ENST00000389420.3	37	CCDS31778.2	.	.	.	.	.	.	.	.	.	.	C	17.49	3.402298	0.62288	.	.	ENSG00000173157	ENST00000389420	D	0.81659	-1.52	4.65	4.65	0.58169	.	0.000000	0.49305	D	0.000145	D	0.94486	0.8225	H	0.99156	4.45	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97022	0.9744	10	0.87932	D	0	.	18.4103	0.90549	0.0:1.0:0.0:0.0	.	1704	P59510	ATS20_HUMAN	Y	1704	ENSP00000374071:C1704Y	ENSP00000374071:C1704Y	C	-	2	0	ADAMTS20	42056608	1.000000	0.71417	0.963000	0.40424	0.940000	0.58332	5.121000	0.64691	2.507000	0.84556	0.557000	0.71058	TGT	.		0.328	ADAMTS20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403643.1	NM_025003	
DAW1	164781	hgsc.bcm.edu	37	2	228771962	228771962	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr2:228771962G>T	ENST00000309931.2	+	10	1050	c.967G>T	c.(967-969)Gct>Tct	p.A323S	DAW1_ENST00000373666.2_Missense_Mutation_p.A323S|DAW1_ENST00000545118.1_Missense_Mutation_p.A308S	NM_178821.1	NP_849143.1	Q8N136	DAW1_HUMAN	dynein assembly factor with WDR repeat domains 1	323						cilium (GO:0005929)											AACTGCTTCAGCTGATGGTAG	0.373																																					p.A323S		.											.	.	.	0			c.G967T						.						153.0	141.0	145.0					2																	228771962		2203	4300	6503	SO:0001583	missense	164781	exon10			GCTTCAGCTGATG		CCDS2470.1	2q36.3	2013-09-03	2013-02-19	2013-02-19	ENSG00000123977	ENSG00000123977		"""WD repeat domain containing"""	26383	protein-coding gene	gene with protein product	"""outer row dynein assembly 16 homolog (Chlamydomonas)"""		"""WD repeat domain 69"""	WDR69		20568242, 21953912	Standard	NM_178821		Approved	FLJ25955, ODA16	uc002vpn.1	Q8N136	OTTHUMG00000133190	ENST00000309931.2:c.967G>T	2.37:g.228771962G>T	ENSP00000311899:p.Ala323Ser	Somatic	56	0		WXS	Illumina HiSeq	.	90	4	NM_178821	Q6ZRY1|Q8N776	Missense_Mutation	SNP	ENST00000309931.2	37	CCDS2470.1	.	.	.	.	.	.	.	.	.	.	G	18.66	3.671153	0.67814	.	.	ENSG00000123977	ENST00000373666;ENST00000309931;ENST00000545118	T;T;T	0.60920	0.15;1.18;0.15	5.34	5.34	0.76211	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.056206	0.64402	D	0.000001	T	0.56731	0.2005	N	0.25245	0.725	0.58432	D	0.999995	P	0.45902	0.868	P	0.56216	0.794	T	0.47535	-0.9110	10	0.08599	T	0.76	.	17.6018	0.88027	0.0:0.0:1.0:0.0	.	323	Q8N136	WDR69_HUMAN	S	323;323;308	ENSP00000362770:A323S;ENSP00000311899:A323S;ENSP00000437887:A308S	ENSP00000311899:A323S	A	+	1	0	WDR69	228480206	1.000000	0.71417	0.811000	0.32455	0.818000	0.46254	8.379000	0.90146	2.477000	0.83638	0.655000	0.94253	GCT	.		0.373	DAW1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331745.1	NM_178821	
HOXB2	3212	hgsc.bcm.edu	37	17	46622342	46622342	+	5'UTR	SNP	T	T	C			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr17:46622342T>C	ENST00000330070.4	-	0	1099				HOXB-AS1_ENST00000504972.3_RNA|HOXB-AS1_ENST00000435312.1_RNA|HOXB-AS1_ENST00000508688.1_RNA|HOXB-AS1_ENST00000502764.2_RNA|HOXB2_ENST00000504772.3_5'Flank	NM_002145.3	NP_002136.1	P14652	HXB2_HUMAN	homeobox B2						anterior/posterior pattern specification (GO:0009952)|blood circulation (GO:0008015)|dorsal/ventral pattern formation (GO:0009953)|embryonic skeletal system morphogenesis (GO:0048704)|facial nerve structural organization (GO:0021612)|morphogenesis of an epithelial sheet (GO:0002011)|multicellular organismal development (GO:0007275)|neural nucleus development (GO:0048857)|rhombomere 3 development (GO:0021569)|rhombomere 4 development (GO:0021570)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(5)|prostate(1)|skin(1)	11						GGGACCCCCCTCCTGCACCCC	0.512																																					.		.											.	.	.	0			.						.																																			SO:0001623	5_prime_UTR_variant	3212	.			CCCCCCTCCTGCA		CCDS11527.1	17q21.32	2012-02-22	2005-12-22		ENSG00000173917	ENSG00000173917		"""Homeoboxes / ANTP class : HOXL subclass"""	5113	protein-coding gene	gene with protein product		142967	"""homeo box B2"""	HOX2, HOX2H		1973146, 1358459	Standard	XM_005257276		Approved		uc002inm.3	P14652	OTTHUMG00000159930	ENST00000330070.4:c.-69A>G	17.37:g.46622342T>C		Somatic	41	0		WXS	Illumina HiSeq	.	78	7	.	P10913|P17485	RNA	SNP	ENST00000330070.4	37	CCDS11527.1																																																																																			.		0.512	HOXB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358384.2		
MT-CO2	4513	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	M	7805	7805	+	Missense_Mutation	SNP	G	G	A			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chrM:7805G>A	ENST00000361739.1	+	1	220	c.220G>A	c.(220-222)Gtc>Atc	p.V74I	MT-TR_ENST00000387439.1_RNA|MT-ND4_ENST00000361381.2_5'Flank|MT-ATP8_ENST00000361851.1_5'Flank|MT-CO3_ENST00000362079.2_5'Flank|MT-TS1_ENST00000387416.2_RNA|MT-TD_ENST00000387419.1_RNA|MT-TK_ENST00000387421.1_RNA|MT-ND3_ENST00000361227.2_5'Flank|MT-ATP6_ENST00000361899.2_5'Flank|MT-TG_ENST00000387429.1_RNA|MT-TA_ENST00000387392.1_RNA|MT-TW_ENST00000387382.1_RNA|MT-ND4L_ENST00000361335.1_5'Flank|MT-TC_ENST00000387405.1_RNA|MT-TN_ENST00000387400.1_RNA|MT-TY_ENST00000387409.1_RNA			P00403	COX2_HUMAN	mitochondrially encoded cytochrome c oxidase II	74					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						CCATCATCCTAGTCCTCATCG	0.463																																					p.V74I		.											.	.	.	0			c.G220A						.																																			SO:0001583	missense	5743	exon1			ATCCTAGTCCTCA			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.220G>A	M.37:g.7805G>A	ENSP00000354876:p.Val74Ile	Somatic	355	1		WXS	Illumina HiSeq	.	2179	787	ENST00000361739	Q37526	Missense_Mutation	SNP	ENST00000361739.1	37																																																																																				.		0.463	MT-CO2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024029	
NLRP5	126206	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	19	56515295	56515295	+	Silent	SNP	C	C	T			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr19:56515295C>T	ENST00000390649.3	+	2	276	c.276C>T	c.(274-276)acC>acT	p.T92T		NM_153447.4	NP_703148.4	P59047	NALP5_HUMAN	NLR family, pyrin domain containing 5	92	DAPIN. {ECO:0000255|PROSITE- ProRule:PRU00061}.				cellular protein complex assembly (GO:0043623)|cellular protein localization (GO:0034613)|embryo implantation (GO:0007566)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|neuron death (GO:0070997)|organ morphogenesis (GO:0009887)|regulation of protein stability (GO:0031647)|regulation of RNA stability (GO:0043487)	apical cortex (GO:0045179)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|protein complex (GO:0043234)	ATP binding (GO:0005524)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|ovary(5)|skin(2)|stomach(4)|upper_aerodigestive_tract(2)	25		Colorectal(82;3.46e-05)|Ovarian(87;0.0481)|Renal(1328;0.157)		GBM - Glioblastoma multiforme(193;0.0326)		CAGAATCGACCACATGCTCTA	0.453																																					p.T92T		.											.	.	.	0			c.C276T						.						89.0	86.0	87.0					19																	56515295		1965	4165	6130	SO:0001819	synonymous_variant	126206	exon2			ATCGACCACATGC	AY154460	CCDS12938.1	19q13.43	2008-10-30	2006-12-08	2006-12-08	ENSG00000171487	ENSG00000171487		"""Nucleotide-binding domain and leucine rich repeat containing"""	21269	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 5"""	609658	"""NACHT, leucine rich repeat and PYD containing 5"""	NALP5		12563287, 11925379	Standard	NM_153447		Approved	PYPAF8, MATER, PAN11, CLR19.8	uc002qmj.3	P59047	OTTHUMG00000149887	ENST00000390649.3:c.276C>T	19.37:g.56515295C>T		Somatic	48	0		WXS	Illumina HiSeq	.	91	29	NM_153447	A8MTY4|Q86W29	Silent	SNP	ENST00000390649.3	37	CCDS12938.1																																																																																			.		0.453	NLRP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313735.1	NM_153447	
DNAJC3	5611	hgsc.bcm.edu	37	13	96412357	96412357	+	Missense_Mutation	SNP	C	C	A			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr13:96412357C>A	ENST00000602402.1	+	6	727	c.610C>A	c.(610-612)Cct>Act	p.P204T	DNAJC3_ENST00000376795.6_Missense_Mutation_p.P153T	NM_006260.4	NP_006251.1	Q13217	DNJC3_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 3	204					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|defense response to virus (GO:0051607)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of protein kinase activity (GO:0006469)|proteolysis involved in cellular protein catabolic process (GO:0051603)	cytoplasm (GO:0005737)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum Sec complex (GO:0031205)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|vesicle (GO:0031982)	protein kinase inhibitor activity (GO:0004860)			NS(1)|breast(1)|kidney(4)|large_intestine(1)|lung(4)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	15	all_neural(89;0.0878)|Breast(111;0.148)|Medulloblastoma(90;0.163)		BRCA - Breast invasive adenocarcinoma(86;0.126)			AGAAGGAGAACCTAGGAAAGC	0.358																																					p.P204T		.											DNAJC3,NS,carcinoma,0,1	DNAJC3	0	0			c.C610A						.						117.0	117.0	117.0					13																	96412357		2203	4300	6503	SO:0001583	missense	5611	exon6			GGAGAACCTAGGA	U28424	CCDS9479.1	13q32	2013-01-10			ENSG00000102580	ENSG00000102580		"""Heat shock proteins / DNAJ (HSP40)"", ""Tetratricopeptide (TTC) repeat domain containing"""	9439	protein-coding gene	gene with protein product		601184		PRKRI		7511204, 8824806	Standard	NM_006260		Approved	P58, P58IPK, HP58	uc001vmq.3	Q13217	OTTHUMG00000017227	ENST00000602402.1:c.610C>A	13.37:g.96412357C>A	ENSP00000473631:p.Pro204Thr	Somatic	55	0		WXS	Illumina HiSeq	.	46	2	NM_006260	Q86WT9|Q8N4N2	Missense_Mutation	SNP	ENST00000602402.1	37	CCDS9479.1	.	.	.	.	.	.	.	.	.	.	C	12.71	2.019308	0.35606	.	.	ENSG00000102580	ENST00000376795	.	.	.	5.56	5.56	0.83823	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.102726	0.64402	D	0.000002	T	0.58395	0.2119	L	0.40543	1.245	0.58432	D	0.999997	B;B	0.32160	0.358;0.358	B;B	0.36186	0.219;0.219	T	0.53019	-0.8497	9	0.23302	T	0.38	-14.3817	19.5168	0.95168	0.0:1.0:0.0:0.0	.	204;204	A8KA82;Q13217	.;DNJC3_HUMAN	T	204	.	ENSP00000365991:P204T	P	+	1	0	DNAJC3	95210358	1.000000	0.71417	1.000000	0.80357	0.914000	0.54420	3.513000	0.53414	2.609000	0.88269	0.561000	0.74099	CCT	.		0.358	DNAJC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045504.3		
MTSS1	9788	hgsc.bcm.edu	37	8	125568538	125568538	+	Missense_Mutation	SNP	C	C	T	rs371399134		TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr8:125568538C>T	ENST00000518547.1	-	12	1812	c.1339G>A	c.(1339-1341)Ggc>Agc	p.G447S	MTSS1_ENST00000524090.1_Missense_Mutation_p.G337S|MTSS1_ENST00000325064.5_Missense_Mutation_p.G451S|NDUFB9_ENST00000522532.1_Intron|MTSS1_ENST00000354184.4_Missense_Mutation_p.G165S|MTSS1_ENST00000378017.3_Missense_Mutation_p.G422S|MTSS1_ENST00000431961.2_Missense_Mutation_p.G165S|MTSS1_ENST00000395508.2_Missense_Mutation_p.G221S|MTSS1_ENST00000523587.1_5'UTR	NM_001282971.1|NM_014751.4	NP_001269900.1|NP_055566.3	O43312	MTSS1_HUMAN	metastasis suppressor 1	447					actin cytoskeleton organization (GO:0030036)|actin filament polymerization (GO:0030041)|adherens junction maintenance (GO:0034334)|bone mineralization (GO:0030282)|cell adhesion (GO:0007155)|cellular component movement (GO:0006928)|cellular response to fluid shear stress (GO:0071498)|epithelial cell proliferation involved in renal tubule morphogenesis (GO:2001013)|filopodium assembly (GO:0046847)|glomerulus morphogenesis (GO:0072102)|in utero embryonic development (GO:0001701)|magnesium ion homeostasis (GO:0010960)|microspike assembly (GO:0030035)|negative regulation of epithelial cell proliferation (GO:0050680)|nephron tubule epithelial cell differentiation (GO:0072160)|positive regulation of actin filament bundle assembly (GO:0032233)|renal tubule morphogenesis (GO:0061333)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	actin cytoskeleton (GO:0015629)|adherens junction (GO:0005912)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|ruffle (GO:0001726)	actin monomer binding (GO:0003785)|identical protein binding (GO:0042802)|receptor binding (GO:0005102)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(5)|lung(14)|ovary(1)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	37	Ovarian(258;0.00438)|all_neural(195;0.00459)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.00288)			GCAGGTGGGCCGCTGGCGGTA	0.632																																					p.G447S	Esophageal Squamous(160;622 1893 3862 8546 12509)	.											MTSS1,lower_third,carcinoma,0,1	MTSS1	0	0			c.G1339A						.	C	SER/GLY	0,4406		0,0,2203	80.0	67.0	72.0		1339	3.9	0.2	8		72	1,8599	1.2+/-3.3	0,1,4299	no	missense	MTSS1	NM_014751.4	56	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign	447/756	125568538	1,13005	2203	4300	6503	SO:0001583	missense	9788	exon12			GTGGGCCGCTGGC	AF086645	CCDS6353.1, CCDS64968.1, CCDS64969.1	8p22	2008-02-05			ENSG00000170873	ENSG00000170873			20443	protein-coding gene	gene with protein product		608486				12482861, 12082544	Standard	XM_005251111		Approved	KIAA0429, MIMA, MIMB, MIM	uc003yrk.2	O43312	OTTHUMG00000048189	ENST00000518547.1:c.1339G>A	8.37:g.125568538C>T	ENSP00000429064:p.Gly447Ser	Somatic	32	0		WXS	Illumina HiSeq	.	37	3	NM_014751	J3KNK6|Q8TCA2|Q96RX2	Missense_Mutation	SNP	ENST00000518547.1	37	CCDS6353.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	14.37|14.37	2.513966|2.513966	0.44763|0.44763	0.0|0.0	1.16E-4|1.16E-4	ENSG00000170873|ENSG00000170873	ENST00000378017;ENST00000518547;ENST00000354184;ENST00000395508;ENST00000325064;ENST00000431961;ENST00000524090|ENST00000519168;ENST00000523179	T;T;T;T;T;T;T|.	0.29655|.	1.58;1.57;1.57;1.57;1.57;1.57;1.56|.	4.82|4.82	3.93|3.93	0.45458|0.45458	.|.	0.226650|.	0.37906|.	N|.	0.001884|.	T|T	0.20170|0.20170	0.0485|0.0485	N|N	0.08118|0.08118	0|0	0.09310|0.09310	N|N	1|1	B;D;P;B;B;P|.	0.54047|.	0.382;0.964;0.566;0.226;0.326;0.953|.	B;B;B;B;B;B|.	0.43990|.	0.043;0.147;0.027;0.028;0.021;0.438|.	T|T	0.13282|0.13282	-1.0515|-1.0515	10|5	0.06494|.	T|.	0.89|.	-21.6492|-21.6492	9.8547|9.8547	0.41079|0.41079	0.0:0.8407:0.0:0.1593|0.0:0.8407:0.0:0.1593	.|.	337;221;422;447;422;165|.	E7EWW5;B7Z3B6;A5YM41;O43312;O43312-4;O43312-2|.	.;.;.;MTSS1_HUMAN;.;.|.	S|Q	422;447;165;221;451;165;337|234;229	ENSP00000367256:G422S;ENSP00000429064:G447S;ENSP00000346119:G165S;ENSP00000378884:G221S;ENSP00000322804:G451S;ENSP00000393606:G165S;ENSP00000428319:G337S|.	ENSP00000322804:G451S|.	G|R	-|-	1|2	0|0	MTSS1|MTSS1	125637719|125637719	0.910000|0.910000	0.30920|0.30920	0.209000|0.209000	0.23619|0.23619	0.012000|0.012000	0.07955|0.07955	3.630000|3.630000	0.54273|0.54273	2.217000|2.217000	0.71921|0.71921	0.455000|0.455000	0.32223|0.32223	GGC|CGG	.		0.632	MTSS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109625.3	NM_014751	
FBN3	84467	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	19	8191217	8191217	+	Missense_Mutation	SNP	G	G	A			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr19:8191217G>A	ENST00000600128.1	-	21	2983	c.2569C>T	c.(2569-2571)Cgg>Tgg	p.R857W	FBN3_ENST00000270509.2_Missense_Mutation_p.R857W|FBN3_ENST00000601739.1_Missense_Mutation_p.R857W			Q75N90	FBN3_HUMAN	fibrillin 3	857	TB 4.					proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(9)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(15)|lung(53)|ovary(7)|pancreas(2)|prostate(3)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	132						GCAAAGCCCCGGGCACAGGCA	0.632																																					p.R857W		.											.	.	.	0			c.C2569T						.						32.0	34.0	34.0					19																	8191217		2196	4293	6489	SO:0001583	missense	84467	exon20			AGCCCCGGGCACA		CCDS12196.1	19p13	2008-02-05							18794	protein-coding gene	gene with protein product		608529					Standard	NM_032447		Approved		uc002mjf.3	Q75N90		ENST00000600128.1:c.2569C>T	19.37:g.8191217G>A	ENSP00000470498:p.Arg857Trp	Somatic	60	0		WXS	Illumina HiSeq	.	110	44	NM_032447	Q75N91|Q75N92|Q75N93|Q86SJ5|Q96JP8	Missense_Mutation	SNP	ENST00000600128.1	37	CCDS12196.1	.	.	.	.	.	.	.	.	.	.	g	15.79	2.937938	0.52972	.	.	ENSG00000142449	ENST00000270509	D	0.87571	-2.27	2.87	2.87	0.33458	Matrix fibril-associated (2);	0.144593	0.45867	U	0.000339	D	0.91140	0.7210	M	0.77616	2.38	0.41141	D	0.985958	D	0.76494	0.999	D	0.63283	0.913	D	0.91143	0.4947	10	0.56958	D	0.05	.	10.063	0.42286	0.0:0.0:0.7984:0.2016	.	857	Q75N90	FBN3_HUMAN	W	857	ENSP00000270509:R857W	ENSP00000270509:R857W	R	-	1	2	FBN3	8097217	0.992000	0.36948	0.966000	0.40874	0.725000	0.41563	3.088000	0.50175	1.574000	0.49760	0.555000	0.69702	CGG	.		0.632	FBN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461428.2	NM_032447	
TG	7038	hgsc.bcm.edu;bcgsc.ca	37	8	133885348	133885348	+	Missense_Mutation	SNP	G	G	T	rs370188499		TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr8:133885348G>T	ENST00000220616.4	+	5	560	c.520G>T	c.(520-522)Ggg>Tgg	p.G174W	TG_ENST00000377869.1_Missense_Mutation_p.G174W	NM_003235.4	NP_003226.4	P01266	THYG_HUMAN	thyroglobulin	174	Thyroglobulin type-1 3. {ECO:0000255|PROSITE-ProRule:PRU00500}.				hormone biosynthetic process (GO:0042446)|iodide transport (GO:0015705)|regulation of myelination (GO:0031641)|signal transduction (GO:0007165)|thyroid gland development (GO:0030878)|thyroid hormone generation (GO:0006590)	extracellular region (GO:0005576)|extracellular space (GO:0005615)				NS(1)|breast(11)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(34)|liver(2)|lung(59)|ovary(9)|pancreas(2)|prostate(6)|skin(7)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(8)	168	Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)	Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0559)|Breast(495;0.0735)	BRCA - Breast invasive adenocarcinoma(115;0.000701)	KIRC - Kidney renal clear cell carcinoma(542;0.0546)		TCTTCTCCACGGGGTGGGAGA	0.423																																					p.G174W		.											.	.	.	0			c.G520T						.						104.0	93.0	97.0					8																	133885348		2203	4300	6503	SO:0001583	missense	7038	exon5			CTCCACGGGGTGG	AU141420	CCDS34944.1	8q24	2012-10-02			ENSG00000042832	ENSG00000042832			11764	protein-coding gene	gene with protein product		188450					Standard	NM_003235		Approved	TGN, AITD3	uc003ytw.3	P01266	OTTHUMG00000164649	ENST00000220616.4:c.520G>T	8.37:g.133885348G>T	ENSP00000220616:p.Gly174Trp	Somatic	29	0		WXS	Illumina HiSeq	.	46	4	NM_003235	O15274|O43899|Q15593|Q15948|Q9NYR1|Q9NYR2|Q9UMZ0|Q9UNY3	Missense_Mutation	SNP	ENST00000220616.4	37	CCDS34944.1	.	.	.	.	.	.	.	.	.	.	G	21.2	4.110526	0.77210	.	.	ENSG00000042832	ENST00000377869;ENST00000220616;ENST00000535932	D;D	0.82711	-1.64;-1.64	5.84	5.84	0.93424	Thyroglobulin type-1 (3);	0.000000	0.64402	D	0.000004	D	0.91862	0.7424	M	0.79926	2.475	0.47476	D	0.999435	D	0.89917	1.0	D	0.97110	1.0	D	0.92209	0.5774	10	0.87932	D	0	.	19.116	0.93340	0.0:0.0:1.0:0.0	.	174	P01266	THYG_HUMAN	W	174	ENSP00000367100:G174W;ENSP00000220616:G174W	ENSP00000220616:G174W	G	+	1	0	TG	133954530	1.000000	0.71417	0.854000	0.33618	0.883000	0.51084	6.433000	0.73404	2.768000	0.95171	0.561000	0.74099	GGG	.		0.423	TG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379606.1	NM_003235	
KLK14	43847	hgsc.bcm.edu;bcgsc.ca	37	19	51585890	51585890	+	Silent	SNP	G	G	T			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr19:51585890G>T	ENST00000156499.2	-	3	248	c.30C>A	c.(28-30)acC>acA	p.T10T	KLK14_ENST00000391802.1_Silent_p.T10T			Q9P0G3	KLK14_HUMAN	kallikrein-related peptidase 14	10					epidermis morphogenesis (GO:0048730)|fertilization (GO:0009566)|negative regulation of G-protein coupled receptor protein signaling pathway (GO:0045744)|positive regulation of G-protein coupled receptor protein signaling pathway (GO:0045745)|proteolysis (GO:0006508)|seminal clot liquefaction (GO:0070684)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase activity (GO:0004252)			kidney(4)|large_intestine(1)|lung(4)|skin(1)|urinary_tract(1)	11		all_neural(266;0.0199)		OV - Ovarian serous cystadenocarcinoma(262;0.00328)|GBM - Glioblastoma multiforme(134;0.00422)		CTGAGGGCCAGGTCCTGTCAA	0.547																																					p.T10T	GBM(117;2161 2172 2448 22911)	.											.	.	.	0			c.C30A						.						83.0	87.0	86.0					19																	51585890		1949	4136	6085	SO:0001819	synonymous_variant	43847	exon3			GGGCCAGGTCCTG	AF283670	CCDS12823.2	19q13.3-q13.4	2008-02-05	2006-10-27		ENSG00000129437	ENSG00000129437		"""Kallikreins"""	6362	protein-coding gene	gene with protein product		606135	"""kallikrein 14"""			16800724, 16800723	Standard	XM_006723224		Approved	KLK-L6	uc002pvs.1	Q9P0G3	OTTHUMG00000143721	ENST00000156499.2:c.30C>A	19.37:g.51585890G>T		Somatic	56	0		WXS	Illumina HiSeq	.	83	5	NM_022046	A7UNK5|Q1RMZ2|Q6B089	Silent	SNP	ENST00000156499.2	37	CCDS12823.2																																																																																			.		0.547	KLK14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000289774.2	NM_022046	
ATN1	1822	hgsc.bcm.edu	37	12	7043191	7043191	+	Splice_Site	SNP	G	G	T	rs147637415		TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr12:7043191G>T	ENST00000356654.4	+	2	264	c.27G>T	c.(25-27)tcG>tcT	p.S9S	ATN1_ENST00000396684.2_Splice_Site_p.S9S	NM_001007026.1	NP_001007027.1	P54259	ATN1_HUMAN	atrophin 1	9					cell migration (GO:0016477)|central nervous system development (GO:0007417)|maintenance of cell polarity (GO:0030011)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron apoptotic process (GO:0051402)|toxin metabolic process (GO:0009404)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	protein domain specific binding (GO:0019904)|transcription corepressor activity (GO:0003714)			breast(5)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(15)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	40						ATAAAGACTCGGTGAGTTAAA	0.483																																					p.S9S		.											.	.	.	0			c.G27T						.						39.0	39.0	39.0					12																	7043191		2203	4300	6503	SO:0001630	splice_region_variant	1822	exon2			AGACTCGGTGAGT	U23851	CCDS31734.1	12p	2007-08-01	2005-03-15	2005-03-17		ENSG00000111676			3033	protein-coding gene	gene with protein product		607462	"""dentatorubral-pallidoluysian atrophy (atrophin-1)"""	D12S755E, DRPLA		8136826	Standard	NM_001940		Approved	B37	uc001qrw.1	P54259		ENST00000356654.4:c.27+1G>T	12.37:g.7043191G>T		Somatic	47	0		WXS	Illumina HiSeq	.	69	4	NM_001007026	Q99495|Q99621|Q9UEK7	Silent	SNP	ENST00000356654.4	37	CCDS31734.1																																																																																			.		0.483	ATN1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401948.2	NM_001940	Silent
PSORS1C1	170679	hgsc.bcm.edu	37	6	31106500	31106500	+	Silent	SNP	T	T	C	rs138474986|rs9278990|rs373492377|rs375095896|rs386698869	byFrequency	TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr6:31106500T>C	ENST00000259881.9	+	5	400	c.111T>C	c.(109-111)cgT>cgC	p.R37R	PSORS1C1_ENST00000481450.2_Intron|PSORS1C1_ENST00000547221.1_5'UTR|PSORS1C2_ENST00000259845.4_Intron	NM_014068.2	NP_054787.2	Q9UIG5	PS1C1_HUMAN	psoriasis susceptibility 1 candidate 1	37			R -> H (in dbSNP:rs9263726). {ECO:0000269|PubMed:12930300}.					p.H40fs*3(1)		kidney(1)|ovary(2)|prostate(1)|skin(1)	5						AGGAAACTCGTCCCCCCCACG	0.567																																					p.R37R		.											.,2	.	11	1	Insertion - Frameshift(1)	ovary(1)	c.T111C						.						146.0	145.0	145.0					6																	31106500		1511	2709	4220	SO:0001819	synonymous_variant	170679	exon5			AACTCGTCCCCCC	AB031479	CCDS34390.1	6p21.3	2014-01-28	2003-06-12		ENSG00000204540	ENSG00000204540			17202	protein-coding gene	gene with protein product		613525	"""chromosome 6 open reading frame 16"""	C6orf16			Standard	NM_014068		Approved	SEEK1	uc003nsl.2	Q9UIG5	OTTHUMG00000031077	ENST00000259881.9:c.111T>C	6.37:g.31106500T>C		Somatic	54	0		WXS	Illumina HiSeq	.	66	4	NM_014068	B0V083|Q5ST21|Q86WJ8|Q86WJ9|Q96QC3	Silent	SNP	ENST00000259881.9	37	CCDS34390.1																																																																																			.		0.567	PSORS1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076110.3	NM_014068	
ZNF329	79673	hgsc.bcm.edu	37	19	58639391	58639391	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr19:58639391G>T	ENST00000598312.1	-	4	1713	c.1480C>A	c.(1480-1482)Cag>Aag	p.Q494K	ZNF329_ENST00000358067.4_Missense_Mutation_p.Q494K	NM_024620.3	NP_078896.3	Q86UD4	ZN329_HUMAN	zinc finger protein 329	494					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|large_intestine(10)|lung(5)|skin(3)|urinary_tract(1)	20		Colorectal(82;5.46e-05)|all_neural(62;0.0182)|Breast(46;0.029)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.017)|Lung(386;0.216)		TGAGAGTTCTGCTTGAAGGAC	0.517																																					p.Q494K		.											.	.	.	0			c.C1480A						.						152.0	144.0	147.0					19																	58639391		2203	4300	6503	SO:0001583	missense	79673	exon4			AGTTCTGCTTGAA	AK022648	CCDS12972.1	19q13.43	2013-01-08				ENSG00000181894		"""Zinc fingers, C2H2-type"""	14209	protein-coding gene	gene with protein product							Standard	XM_006723381		Approved	FLJ12586	uc002qrn.3	Q86UD4		ENST00000598312.1:c.1480C>A	19.37:g.58639391G>T	ENSP00000470008:p.Gln494Lys	Somatic	29	0		WXS	Illumina HiSeq	.	75	4	NM_024620	B3KR32|Q9H9R7	Missense_Mutation	SNP	ENST00000598312.1	37	CCDS12972.1	.	.	.	.	.	.	.	.	.	.	G	11.22	1.574462	0.28092	.	.	ENSG00000181894	ENST00000358067;ENST00000500161	T;T	0.17691	2.26;2.26	4.31	4.31	0.51392	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.39834	N	0.001258	T	0.13670	0.0331	L	0.40543	1.245	0.29384	N	0.863093	P	0.50156	0.932	B	0.41860	0.368	T	0.07520	-1.0768	10	0.48119	T	0.1	-12.4876	7.8034	0.29187	0.0:0.1744:0.6453:0.1802	.	494	Q86UD4	ZN329_HUMAN	K	494	ENSP00000350773:Q494K;ENSP00000439527:Q494K	ENSP00000350773:Q494K	Q	-	1	0	ZNF329	63331203	0.000000	0.05858	1.000000	0.80357	0.981000	0.71138	0.383000	0.20651	2.691000	0.91804	0.655000	0.94253	CAG	.		0.517	ZNF329-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466724.1	NM_024620	
OR6C3	254786	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	12	55725675	55725675	+	Missense_Mutation	SNP	C	C	A			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr12:55725675C>A	ENST00000379667.1	+	1	191	c.191C>A	c.(190-192)tCt>tAt	p.S64Y		NM_054104.1	NP_473445.1	Q9NZP0	OR6C3_HUMAN	olfactory receptor, family 6, subfamily C, member 3	64					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|kidney(2)|large_intestine(2)|lung(1)|prostate(1)|skin(2)	11						CGGAACTTCTCTTTCTTAGAA	0.413																																					p.S64Y		.											.	.	.	0			c.C191A						.						109.0	120.0	116.0					12																	55725675		2203	4300	6503	SO:0001583	missense	254786	exon1			ACTTCTCTTTCTT	AF179770	CCDS31819.1	12q13.2	2013-09-23			ENSG00000205329	ENSG00000205329		"""GPCR / Class A : Olfactory receptors"""	15437	protein-coding gene	gene with protein product							Standard	NM_054104		Approved	OST709	uc010spj.2	Q9NZP0	OTTHUMG00000169861	ENST00000379667.1:c.191C>A	12.37:g.55725675C>A	ENSP00000368989:p.Ser64Tyr	Somatic	36	0		WXS	Illumina HiSeq	.	81	33	NM_054104		Missense_Mutation	SNP	ENST00000379667.1	37	CCDS31819.1	.	.	.	.	.	.	.	.	.	.	C	17.90	3.501854	0.64298	.	.	ENSG00000205329	ENST00000379667	T	0.12361	2.69	4.82	4.82	0.62117	GPCR, rhodopsin-like superfamily (1);	0.141578	0.32769	N	0.005668	T	0.56396	0.1982	H	0.99286	4.5	0.28744	N	0.901838	D	0.63880	0.993	D	0.64042	0.921	T	0.70439	-0.4871	10	0.87932	D	0	.	18.0415	0.89320	0.0:1.0:0.0:0.0	.	64	Q9NZP0	OR6C3_HUMAN	Y	64	ENSP00000368989:S64Y	ENSP00000368989:S64Y	S	+	2	0	OR6C3	54011942	0.039000	0.19947	0.979000	0.43373	0.957000	0.61999	3.239000	0.51360	2.665000	0.90641	0.461000	0.40582	TCT	.		0.413	OR6C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406309.1		
CNTNAP2	26047	hgsc.bcm.edu	37	7	147964169	147964169	+	Silent	SNP	C	C	T			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr7:147964169C>T	ENST00000361727.3	+	21	3942	c.3426C>T	c.(3424-3426)tcC>tcT	p.S1142S	CNTNAP2_ENST00000538075.1_Silent_p.S201S	NM_014141.5	NP_054860.1	Q9UHC6	CNTP2_HUMAN	contactin associated protein-like 2	1142	Laminin G-like 4. {ECO:0000255|PROSITE- ProRule:PRU00122}.				adult behavior (GO:0030534)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cellular protein localization (GO:0034613)|cerebral cortex development (GO:0021987)|clustering of voltage-gated potassium channels (GO:0045163)|learning (GO:0007612)|limbic system development (GO:0021761)|neuron projection development (GO:0031175)|neuron recognition (GO:0008038)|protein localization to juxtaparanode region of axon (GO:0071205)|social behavior (GO:0035176)|striatum development (GO:0021756)|superior temporal gyrus development (GO:0071109)|thalamus development (GO:0021794)|transmission of nerve impulse (GO:0019226)|vocalization behavior (GO:0071625)	axolemma (GO:0030673)|axon (GO:0030424)|cell surface (GO:0009986)|dendrite (GO:0030425)|early endosome (GO:0005769)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|juxtaparanode region of axon (GO:0044224)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|perikaryon (GO:0043204)|voltage-gated potassium channel complex (GO:0008076)	enzyme binding (GO:0019899)			NS(3)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(21)|lung(105)|ovary(9)|pancreas(2)|prostate(5)|skin(7)|stomach(3)|upper_aerodigestive_tract(6)|urinary_tract(3)	188	Melanoma(164;0.153)	all_cancers(3;3.51e-10)|all_epithelial(3;1.4e-05)|Myeloproliferative disorder(3;0.00452)|Lung NSC(3;0.0067)|all_lung(3;0.00794)	OV - Ovarian serous cystadenocarcinoma(82;0.0319)			CAAGTTCATCCGACACCCTCT	0.438										HNSCC(39;0.1)																											p.S1142S		.											.	.	.	0			c.C3426T						.						212.0	184.0	194.0					7																	147964169		2203	4300	6503	SO:0001819	synonymous_variant	26047	exon21			TTCATCCGACACC	AF193613	CCDS5889.1	7q35	2008-02-04			ENSG00000174469	ENSG00000174469			13830	protein-coding gene	gene with protein product		604569				10624965, 10048485	Standard	NM_014141		Approved	Caspr2, KIAA0868, NRXN4	uc003weu.2	Q9UHC6	OTTHUMG00000152743	ENST00000361727.3:c.3426C>T	7.37:g.147964169C>T		Somatic	38	0		WXS	Illumina HiSeq	.	69	4	NM_014141	D3DWG2|Q14DG2|Q52LV1|Q5H9Q7|Q9UQ12	Silent	SNP	ENST00000361727.3	37	CCDS5889.1																																																																																			.		0.438	CNTNAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327668.1		
VAV3	10451	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	108247684	108247684	+	Splice_Site	SNP	C	C	A			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr1:108247684C>A	ENST00000370056.4	-	16	1777		c.e16-1		VAV3_ENST00000343258.4_Splice_Site|VAV3_ENST00000371846.4_Splice_Site|VAV3_ENST00000527011.1_Splice_Site	NM_006113.4	NP_006104.4	Q9UKW4	VAV3_HUMAN	vav 3 guanine nucleotide exchange factor						angiogenesis (GO:0001525)|apoptotic signaling pathway (GO:0097190)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|cellular response to DNA damage stimulus (GO:0006974)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|lamellipodium assembly (GO:0030032)|neurotrophin TRK receptor signaling pathway (GO:0048011)|neutrophil chemotaxis (GO:0030593)|platelet activation (GO:0030168)|positive regulation of apoptotic process (GO:0043065)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cell adhesion (GO:0045785)|positive regulation of GTPase activity (GO:0043547)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of signal transduction (GO:0009967)|regulation of Rac GTPase activity (GO:0032314)|regulation of small GTPase mediated signal transduction (GO:0051056)|response to drug (GO:0042493)|small GTPase mediated signal transduction (GO:0007264)|vesicle fusion (GO:0006906)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|SH3/SH2 adaptor activity (GO:0005070)			NS(2)|breast(5)|endometrium(4)|kidney(2)|large_intestine(14)|lung(20)|ovary(6)|prostate(3)|stomach(1)|urinary_tract(1)	58		all_epithelial(167;5.38e-05)|all_lung(203;0.000314)|Lung NSC(277;0.000594)		Colorectal(144;0.0331)|Lung(183;0.128)|Epithelial(280;0.204)		TATGTTAGACCTAAAAAAAGG	0.378																																					.		.											.	.	.	0			c.1503-1G>T						.						64.0	59.0	61.0					1																	108247684		2203	4300	6503	SO:0001630	splice_region_variant	10451	exon17			TTAGACCTAAAAA	AF118886	CCDS785.1, CCDS44181.1	1p13.3	2013-02-14	2007-07-25		ENSG00000134215	ENSG00000134215		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"", ""SH2 domain containing"""	12659	protein-coding gene	gene with protein product		605541	"""vav 3 oncogene"""				Standard	NM_001079874		Approved		uc001dvk.1	Q9UKW4	OTTHUMG00000010995	ENST00000370056.4:c.1503-1G>T	1.37:g.108247684C>A		Somatic	34	0		WXS	Illumina HiSeq	.	65	25	NM_006113	B1AMM0|B1APV5|B4E232|B7ZLR1|E9PQ97|O60498|O95230|Q9Y5X8	Splice_Site	SNP	ENST00000370056.4	37	CCDS785.1	.	.	.	.	.	.	.	.	.	.	C	21.4	4.143231	0.77888	.	.	ENSG00000134215	ENST00000370056;ENST00000527011;ENST00000529809;ENST00000490388;ENST00000371846	.	.	.	6.16	6.16	0.99307	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.8598	0.99761	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	VAV3	108049207	1.000000	0.71417	0.993000	0.49108	0.818000	0.46254	6.840000	0.75369	2.937000	0.99478	0.650000	0.86243	.	.		0.378	VAV3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030242.2	NM_006113	Intron
GALNT11	63917	hgsc.bcm.edu	37	7	151818669	151818669	+	Silent	SNP	C	C	T			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr7:151818669C>T	ENST00000434507.1	+	14	2171	c.1734C>T	c.(1732-1734)tgC>tgT	p.C578C	GALNT11_ENST00000452146.2_Silent_p.C497C|GALNT11_ENST00000430044.2_Silent_p.C578C|RP5-981O7.2_ENST00000424630.1_RNA|GALNT11_ENST00000320311.2_Silent_p.C578C			Q8NCW6	GLT11_HUMAN	polypeptide N-acetylgalactosaminyltransferase 11	578	Ricin B-type lectin. {ECO:0000255|PROSITE-ProRule:PRU00174}.				cellular protein metabolic process (GO:0044267)|cilium morphogenesis (GO:0060271)|determination of left/right symmetry (GO:0007368)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein O-linked glycosylation via threonine (GO:0018243)|regulation of Notch signaling pathway (GO:0008593)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|Notch binding (GO:0005112)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(7)|prostate(5)|skin(2)	27	all_neural(206;0.187)	all_hematologic(28;0.0592)|Prostate(32;0.214)	OV - Ovarian serous cystadenocarcinoma(82;0.00168)	UCEC - Uterine corpus endometrioid carcinoma (81;0.177)|BRCA - Breast invasive adenocarcinoma(188;0.0932)		TTGGACAGTGCCTGAGAGCAG	0.488																																					p.C578C		.											.	.	.	0			c.C1734T						.						117.0	100.0	106.0					7																	151818669		2203	4300	6503	SO:0001819	synonymous_variant	63917	exon12			ACAGTGCCTGAGA	AC006017	CCDS5930.1	7q36.1	2014-05-09	2014-05-09		ENSG00000178234	ENSG00000178234	2.4.1.41	"""Glycosyltransferase family 2 domain containing"""	19875	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase 11"""	615130	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 11 (GalNAc-T11)"""			11925450	Standard	NM_022087		Approved	GalNAc-T11	uc010lqg.1	Q8NCW6	OTTHUMG00000157251	ENST00000434507.1:c.1734C>T	7.37:g.151818669C>T		Somatic	20	0		WXS	Illumina HiSeq	.	64	5	NM_022087	B3KWF4|Q6PCD1|Q9H6C2|Q9H6Z5|Q9UDR8	Silent	SNP	ENST00000434507.1	37	CCDS5930.1																																																																																			.		0.488	GALNT11-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348184.1	NM_022087	
IDH1	3417	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	2	209113113	209113113	+	Missense_Mutation	SNP	G	G	A	rs121913499		TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr2:209113113G>A	ENST00000415913.1	-	4	775	c.394C>T	c.(394-396)Cgt>Tgt	p.R132C	IDH1_ENST00000446179.1_Missense_Mutation_p.R132C|IDH1_ENST00000345146.2_Missense_Mutation_p.R132C	NM_001282387.1	NP_001269316.1	O75874	IDHC_HUMAN	isocitrate dehydrogenase 1 (NADP+), soluble	132			R -> C (in colorectal cancer and glioma samples; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha- ketoglutarate but instead alpha- ketoglutarate is converted to R(-)-2- hydroxyglutarate). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:19117336}.|R -> G (in a glioma sample; glioblastoma multiforme; somatic mutation). {ECO:0000269|PubMed:19117336}.|R -> H (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:18772396}.|R -> L (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:19117336}.|R -> S (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:18772396}.		2-oxoglutarate metabolic process (GO:0006103)|cellular lipid metabolic process (GO:0044255)|female gonad development (GO:0008585)|glutathione metabolic process (GO:0006749)|glyoxylate cycle (GO:0006097)|isocitrate metabolic process (GO:0006102)|NADPH regeneration (GO:0006740)|response to oxidative stress (GO:0006979)|response to steroid hormone (GO:0048545)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	isocitrate dehydrogenase (NADP+) activity (GO:0004450)|magnesium ion binding (GO:0000287)|NAD binding (GO:0051287)|NADP binding (GO:0050661)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)	p.R132C(446)|p.R132G(125)|p.R132S(106)|p.G131_R132>VL(1)|p.R132V(1)		NS(1)|autonomic_ganglia(2)|biliary_tract(24)|bone(237)|central_nervous_system(3764)|endometrium(3)|haematopoietic_and_lymphoid_tissue(794)|kidney(2)|large_intestine(7)|lung(7)|prostate(6)|skin(5)|soft_tissue(12)|thyroid(22)|urinary_tract(1)	4887				Epithelial(149;0.0322)|LUSC - Lung squamous cell carcinoma(261;0.0711)|Lung(261;0.136)		TAAGCATGACGACCTATGATG	0.398			Mis		gliobastoma																																p.R132C	Pancreas(158;264 1958 3300 35450 36047)	.		Dom	yes		2	2q33.3	3417	"""isocitrate dehydrogenase 1 (NADP+), soluble"""		O	IDH1,NS,haematopoietic_neoplasm,0,788	IDH1	0	679	Substitution - Missense(678)|Complex - compound substitution(1)	haematopoietic_and_lymphoid_tissue(280)|central_nervous_system(181)|bone(177)|biliary_tract(21)|soft_tissue(12)|large_intestine(2)|skin(2)|autonomic_ganglia(1)|endometrium(1)|NS(1)|prostate(1)	c.C394T						.						81.0	74.0	76.0					2																	209113113		2203	4300	6503	SO:0001583	missense	3417	exon4			CATGACGACCTAT		CCDS2381.1	2q34	2014-09-17			ENSG00000138413	ENSG00000138413	1.1.1.42		5382	protein-coding gene	gene with protein product		147700					Standard	NM_005896		Approved		uc002vcu.3	O75874	OTTHUMG00000132943	ENST00000415913.1:c.394C>T	2.37:g.209113113G>A	ENSP00000390265:p.Arg132Cys	Somatic	35	0		WXS	Illumina HiSeq	.	79	41	NM_005896	Q567U4|Q6FHQ6|Q7Z3V0|Q93090|Q9NTJ9|Q9UKW8	Missense_Mutation	SNP	ENST00000415913.1	37	CCDS2381.1	.	.	.	.	.	.	.	.	.	.	G	24.6	4.550898	0.86127	.	.	ENSG00000138413	ENST00000345146;ENST00000446179;ENST00000415913;ENST00000415282	D;D;D;D	0.87029	-2.2;-2.2;-2.2;-2.2	5.57	5.57	0.84162	Isopropylmalate dehydrogenase-like domain (2);	0.000000	0.85682	D	0.000000	D	0.94049	0.8093	H	0.99379	4.54	0.80722	D	1	B	0.29862	0.259	B	0.31245	0.126	D	0.94048	0.7315	10	0.87932	D	0	-20.0399	19.5341	0.95242	0.0:0.0:1.0:0.0	.	132	O75874	IDHC_HUMAN	C	132	ENSP00000260985:R132C;ENSP00000410513:R132C;ENSP00000390265:R132C;ENSP00000391075:R132C	ENSP00000260985:R132C	R	-	1	0	IDH1	208821358	1.000000	0.71417	0.999000	0.59377	0.994000	0.84299	7.074000	0.76791	2.616000	0.88540	0.555000	0.69702	CGT	.		0.398	IDH1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336672.1		
WNT5A	7474	hgsc.bcm.edu	37	3	55504231	55504231	+	Nonsense_Mutation	SNP	G	G	T			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr3:55504231G>T	ENST00000474267.1	-	6	1553	c.1032C>A	c.(1030-1032)taC>taA	p.Y344*	WNT5A_ENST00000264634.4_Nonsense_Mutation_p.Y344*|WNT5A_ENST00000497027.1_Nonsense_Mutation_p.Y329*|WNT5A_ENST00000493406.1_5'Flank			P41221	WNT5A_HUMAN	wingless-type MMTV integration site family, member 5A	344					activation of JUN kinase activity (GO:0007257)|activation of MAPK activity (GO:0000187)|activation of protein kinase B activity (GO:0032148)|ameboidal cell migration (GO:0001667)|anterior/posterior axis specification, embryo (GO:0008595)|axon guidance (GO:0007411)|canonical Wnt signaling pathway (GO:0060070)|cartilage development (GO:0051216)|cell fate commitment (GO:0045165)|cellular protein localization (GO:0034613)|cellular response to calcium ion (GO:0071277)|cellular response to interferon-gamma (GO:0071346)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to retinoic acid (GO:0071300)|cellular response to transforming growth factor beta stimulus (GO:0071560)|cervix development (GO:0060067)|cochlea morphogenesis (GO:0090103)|convergent extension involved in organogenesis (GO:0060029)|dopaminergic neuron differentiation (GO:0071542)|embryonic digit morphogenesis (GO:0042733)|embryonic skeletal system development (GO:0048706)|epithelial cell proliferation involved in mammary gland duct elongation (GO:0060750)|epithelial to mesenchymal transition (GO:0001837)|establishment of planar polarity (GO:0001736)|face development (GO:0060324)|genitalia development (GO:0048806)|heart looping (GO:0001947)|hematopoietic stem cell proliferation (GO:0071425)|hindgut morphogenesis (GO:0007442)|hypophysis morphogenesis (GO:0048850)|keratinocyte differentiation (GO:0030216)|lateral sprouting involved in mammary gland duct morphogenesis (GO:0060599)|lens development in camera-type eye (GO:0002088)|lung development (GO:0030324)|male gonad development (GO:0008584)|mammary gland branching involved in thelarche (GO:0060744)|mesenchymal-epithelial cell signaling (GO:0060638)|midgut development (GO:0007494)|negative chemotaxis (GO:0050919)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axon extension involved in axon guidance (GO:0048843)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of mesenchymal cell proliferation (GO:0072201)|negative regulation of prostatic bud formation (GO:0060686)|negative regulation of synapse assembly (GO:0051964)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|neuron differentiation (GO:0030182)|non-canonical Wnt signaling pathway via JNK cascade (GO:0038031)|olfactory bulb interneuron development (GO:0021891)|optic cup formation involved in camera-type eye development (GO:0003408)|palate development (GO:0060021)|planar cell polarity pathway involved in cardiac muscle tissue morphogenesis (GO:0061350)|planar cell polarity pathway involved in cardiac right atrium morphogenesis (GO:0061349)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|planar cell polarity pathway involved in outflow tract morphogenesis (GO:0061347)|planar cell polarity pathway involved in pericardium morphogenesis (GO:0061354)|planar cell polarity pathway involved in ventricular septum morphogenesis (GO:0061348)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cartilage development (GO:0061036)|positive regulation of cell-cell adhesion mediated by cadherin (GO:2000049)|positive regulation of cGMP metabolic process (GO:0030825)|positive regulation of chemokine biosynthetic process (GO:0045080)|positive regulation of cytokine secretion involved in immune response (GO:0002741)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of interleukin-8 secretion (GO:2000484)|positive regulation of JNK cascade (GO:0046330)|positive regulation of macrophage activation (GO:0043032)|positive regulation of macrophage cytokine production (GO:0060907)|positive regulation of meiosis (GO:0045836)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of neuron projection development (GO:0010976)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of ossification (GO:0045778)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein kinase C signaling (GO:0090037)|positive regulation of response to cytokine stimulus (GO:0060760)|positive regulation of T cell chemotaxis (GO:0010820)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon-mediated signaling pathway (GO:0060340)|post-anal tail morphogenesis (GO:0036342)|primitive streak formation (GO:0090009)|protein phosphorylation (GO:0006468)|regulation of branching involved in mammary gland duct morphogenesis (GO:0060762)|response to organic substance (GO:0010033)|somitogenesis (GO:0001756)|type B pancreatic cell development (GO:0003323)|urinary bladder development (GO:0060157)|uterus development (GO:0060065)|vagina development (GO:0060068)|Wnt signaling pathway (GO:0016055)|Wnt signaling pathway, calcium modulating pathway (GO:0007223)|wound healing (GO:0042060)	cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	frizzled binding (GO:0005109)|receptor agonist activity (GO:0048018)|receptor tyrosine kinase-like orphan receptor binding (GO:0005115)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|endometrium(1)|large_intestine(4)|lung(3)|prostate(2)|urinary_tract(1)	13				KIRC - Kidney renal clear cell carcinoma(284;0.00377)|Kidney(284;0.00408)|OV - Ovarian serous cystadenocarcinoma(275;0.204)		TGAACTGGTCGTAGCCACGGC	0.622																																					p.Y344X		.											WNT5A,NS,carcinoma,0,1	WNT5A	0	0			c.C1032A						.						75.0	80.0	78.0					3																	55504231		2203	4300	6503	SO:0001587	stop_gained	7474	exon5			CTGGTCGTAGCCA	L20861	CCDS46850.1, CCDS58835.1	3p21-p14	2013-02-28			ENSG00000114251	ENSG00000114251		"""Wingless-type MMTV integration sites"", ""Endogenous ligands"""	12784	protein-coding gene	gene with protein product	"""WNT-5A protein"""	164975				8288227	Standard	NM_001256105		Approved	hWNT5A	uc010hmw.4	P41221	OTTHUMG00000158361	ENST00000474267.1:c.1032C>A	3.37:g.55504231G>T	ENSP00000417310:p.Tyr344*	Somatic	52	1		WXS	Illumina HiSeq	.	45	2	NM_003392	A8K4A4|Q6P278	Nonsense_Mutation	SNP	ENST00000474267.1	37	CCDS46850.1	.	.	.	.	.	.	.	.	.	.	G	39	7.332989	0.98217	.	.	ENSG00000114251	ENST00000474267;ENST00000264634;ENST00000536765;ENST00000497027	.	.	.	5.67	-4.48	0.03515	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	13.8408	0.63437	0.6388:0.0:0.3612:0.0	.	.	.	.	X	344;344;255;329	.	ENSP00000264634:Y344X	Y	-	3	2	WNT5A	55479271	0.106000	0.21978	0.962000	0.40283	0.999000	0.98932	-0.533000	0.06157	-0.877000	0.04012	0.655000	0.94253	TAC	.		0.622	WNT5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350793.3	NM_003392	
LAMC3	10319	hgsc.bcm.edu	37	9	133942411	133942411	+	Silent	SNP	C	C	A			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr9:133942411C>A	ENST00000361069.4	+	14	2545	c.2412C>A	c.(2410-2412)ccC>ccA	p.P804P	LAMC3_ENST00000480883.1_Intron	NM_006059.3	NP_006050.3	Q9Y6N6	LAMC3_HUMAN	laminin, gamma 3	804	Laminin EGF-like 7. {ECO:0000255|PROSITE- ProRule:PRU00460}.				astrocyte development (GO:0014002)|cell adhesion (GO:0007155)|cell morphogenesis involved in differentiation (GO:0000904)|extracellular matrix organization (GO:0030198)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	structural molecule activity (GO:0005198)	p.P804P(1)		endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(31)|ovary(3)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(3)	69	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;5.06e-05)|Epithelial(140;0.000551)		TTGGGCACCCCCAGCCCTGCC	0.642																																					p.P804P		.											LAMC3,NS,carcinoma,0,1	LAMC3	0	1	Substitution - coding silent(1)	lung(1)	c.C2412A						.						49.0	47.0	48.0					9																	133942411		2203	4300	6503	SO:0001819	synonymous_variant	10319	exon14			GCACCCCCAGCCC	AF041835	CCDS6938.1	9q31-q34	2013-03-01			ENSG00000050555	ENSG00000050555		"""Laminins"""	6494	protein-coding gene	gene with protein product		604349				10225960	Standard	NM_006059		Approved	DKFZp434E202	uc004caa.1	Q9Y6N6	OTTHUMG00000020819	ENST00000361069.4:c.2412C>A	9.37:g.133942411C>A		Somatic	39	0		WXS	Illumina HiSeq	.	47	3	NM_006059	B1APX9|B1APY0|Q59H72	Silent	SNP	ENST00000361069.4	37	CCDS6938.1																																																																																			.		0.642	LAMC3-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054717.3	NM_006059	
ZNRD1-AS1	80862	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	6	30025956	30025956	+	RNA	SNP	C	C	A			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr6:30025956C>A	ENST00000431012.1	-	0	112				ZNRD1-AS1_ENST00000420251.1_RNA|ZNRD1-AS1_ENST00000437417.1_RNA|ZNRD1-AS1_ENST00000452229.1_RNA|ZNRD1-AS1_ENST00000376797.3_RNA|ZNRD1-AS1_ENST00000421692.1_RNA|ZNRD1-AS1_ENST00000448093.1_RNA|ZNRD1-AS1_ENST00000425604.1_RNA|ZNRD1-AS1_ENST00000422224.1_RNA			Q2KJ03	ZRAS1_HUMAN	ZNRD1 antisense RNA 1																		AGATGATGTACCCCAGGCCAA	0.423																																					.		.											.	.	.	0			.						.																																					80862	.			GATGTACCCCAGG	AF032110		6p21.33	2014-08-14	2012-08-15	2010-11-25	ENSG00000204623	ENSG00000204623		"""Long non-coding RNAs"""	13924	non-coding RNA	RNA, long non-coding		615714	"""chromosome 6 open reading frame 12"", ""non-protein coding RNA 171"", ""ZNRD1 antisense RNA (non-protein coding)"", ""ZNRD1 antisense RNA 1 (non-protein coding)"""	C6orf12, NCRNA00171, ZNRD1AS, ZNRD1-AS		9553157, 11130983, 25110835	Standard	NR_026751		Approved	HTEX4, Em:AB023056.3	uc003rto.3	Q2KJ03	OTTHUMG00000031109		6.37:g.30025956C>A		Somatic	69	0		WXS	Illumina HiSeq	.	56	28	.		RNA	SNP	ENST00000431012.1	37																																																																																				.		0.423	ZNRD1-AS1-005	KNOWN	basic|exp_conf	antisense	antisense	OTTHUMT00000253082.1	NR_026751	
MUC16	94025	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	19	9072960	9072960	+	Missense_Mutation	SNP	T	T	C			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr19:9072960T>C	ENST00000397910.4	-	3	14689	c.14486A>G	c.(14485-14487)aAc>aGc	p.N4829S		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	4831	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						AACTACTGTGTTTATGGAAGG	0.448																																					p.N4829S		.											.	.	.	0			c.A14486G						.						157.0	148.0	151.0					19																	9072960		2084	4211	6295	SO:0001583	missense	94025	exon3			ACTGTGTTTATGG	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.14486A>G	19.37:g.9072960T>C	ENSP00000381008:p.Asn4829Ser	Somatic	20	0		WXS	Illumina HiSeq	.	110	38	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	t	3.625	-0.076784	0.07184	.	.	ENSG00000181143	ENST00000397910	T	0.24350	1.86	2.05	-0.49	0.12049	.	.	.	.	.	T	0.19366	0.0465	N	0.25647	0.755	.	.	.	P	0.39424	0.673	B	0.44278	0.445	T	0.26815	-1.0092	8	0.87932	D	0	.	4.5995	0.12347	0.5386:0.0:0.0:0.4614	.	4829	B5ME49	.	S	4829	ENSP00000381008:N4829S	ENSP00000381008:N4829S	N	-	2	0	MUC16	8933960	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.043000	0.12043	-0.187000	0.10516	0.375000	0.23000	AAC	.		0.448	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
POTEF	728378	hgsc.bcm.edu	37	2	130832762	130832762	+	Silent	SNP	T	T	C			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr2:130832762T>C	ENST00000409914.2	-	17	2682	c.2283A>G	c.(2281-2283)aaA>aaG	p.K761K	POTEF_ENST00000357462.5_Silent_p.K761K	NM_001099771.2	NP_001093241.1	A5A3E0	POTEF_HUMAN	POTE ankyrin domain family, member F	761	Actin-like.				retina homeostasis (GO:0001895)	blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)		p.K761K(1)		breast(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(4)|lung(28)|ovary(3)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	53						GGATGCCTCTTTTGCTCTGGG	0.582																																					p.K761K		.											POTEF,NS,carcinoma,0,1	POTEF	0	1	Substitution - coding silent(1)	prostate(1)	c.A2283G						.																																			SO:0001819	synonymous_variant	728378	exon17			GCCTCTTTTGCTC	EF523384	CCDS46409.1	2q21.1	2013-01-10	2008-11-26	2008-11-26	ENSG00000196604	ENSG00000196604		"""POTE ankyrin domain containing"", ""Ankyrin repeat domain containing"""	33905	protein-coding gene	gene with protein product			"""ANKRD26-like family C, member 1B"""	A26C1B		17101985	Standard	NM_001099771		Approved	POTEACTIN, POTE2alpha	uc010fmh.2	A5A3E0	OTTHUMG00000153628	ENST00000409914.2:c.2283A>G	2.37:g.130832762T>C		Somatic	51	0		WXS	Illumina HiSeq	.	98	8	NM_001099771	A6NC34	Silent	SNP	ENST00000409914.2	37	CCDS46409.1																																																																																			.		0.582	POTEF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331889.2	NM_001099771	
ZNF547	284306	hgsc.bcm.edu	37	19	57888521	57888521	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr19:57888521G>T	ENST00000282282.3	+	4	327	c.177G>T	c.(175-177)gaG>gaT	p.E59D	AC003002.4_ENST00000597658.1_Intron	NM_173631.2	NP_775902.2	Q8IVP9	ZN547_HUMAN	zinc finger protein 547	59	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(4)|ovary(1)|skin(1)	12		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0694)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		CTGAGGATGAGGAGGCACCTT	0.502																																					p.E59D		.											.	.	.	0			c.G177T						.						92.0	72.0	79.0					19																	57888521		2203	4300	6503	SO:0001583	missense	284306	exon4			GGATGAGGAGGCA	AK055662	CCDS33131.1	19q13.43	2013-01-08				ENSG00000152433		"""Zinc fingers, C2H2-type"", ""-"""	26432	protein-coding gene	gene with protein product							Standard	NM_173631		Approved	FLJ31100	uc002qol.3	Q8IVP9		ENST00000282282.3:c.177G>T	19.37:g.57888521G>T	ENSP00000282282:p.Glu59Asp	Somatic	31	0		WXS	Illumina HiSeq	.	58	4	NM_173631	A8K5Z9|Q96NC4	Missense_Mutation	SNP	ENST00000282282.3	37	CCDS33131.1	.	.	.	.	.	.	.	.	.	.	G	16.91	3.253984	0.59212	.	.	ENSG00000152433	ENST00000391704;ENST00000282282	T	0.00824	5.65	2.36	-0.784	0.10954	Krueppel-associated box (3);	.	.	.	.	T	0.00936	0.0031	L	0.52011	1.625	0.09310	N	1	P;P	0.45957	0.615;0.869	B;B	0.38106	0.122;0.265	T	0.50285	-0.8846	9	0.18710	T	0.47	.	6.176	0.20444	0.4232:0.0:0.5768:0.0	.	59;59	Q8IVP9-2;Q8IVP9	.;ZN547_HUMAN	D	59	ENSP00000282282:E59D	ENSP00000282282:E59D	E	+	3	2	ZNF547	62580333	0.012000	0.17670	0.193000	0.23327	0.611000	0.37282	0.309000	0.19332	-0.023000	0.13963	0.491000	0.48974	GAG	.		0.502	ZNF547-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465787.1	NM_173631	
VCAM1	7412	hgsc.bcm.edu;bcgsc.ca	37	1	101186235	101186235	+	Missense_Mutation	SNP	G	G	A			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr1:101186235G>A	ENST00000294728.2	+	2	369	c.268G>A	c.(268-270)Gaa>Aaa	p.E90K	VCAM1_ENST00000370119.4_Intron|VCAM1_ENST00000370115.1_Missense_Mutation_p.E90K|VCAM1_ENST00000347652.2_Missense_Mutation_p.E90K	NM_001078.3	NP_001069.1	P19320	VCAM1_HUMAN	vascular cell adhesion molecule 1	90	Ig-like C2-type 1.				acute inflammatory response (GO:0002526)|aging (GO:0007568)|amine metabolic process (GO:0009308)|B cell differentiation (GO:0030183)|cell adhesion (GO:0007155)|cell chemotaxis (GO:0060326)|cell-matrix adhesion (GO:0007160)|cellular response to glucose stimulus (GO:0071333)|cellular response to tumor necrosis factor (GO:0071356)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|chorio-allantoic fusion (GO:0060710)|chronic inflammatory response (GO:0002544)|cytokine-mediated signaling pathway (GO:0019221)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|heterophilic cell-cell adhesion (GO:0007157)|interferon-gamma-mediated signaling pathway (GO:0060333)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte tethering or rolling (GO:0050901)|membrane to membrane docking (GO:0022614)|oxidation-reduction process (GO:0055114)|positive regulation of T cell proliferation (GO:0042102)|regulation of immune response (GO:0050776)|response to ethanol (GO:0045471)|response to hypoxia (GO:0001666)|response to ionizing radiation (GO:0010212)|response to lipopolysaccharide (GO:0032496)|response to nicotine (GO:0035094)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|viral process (GO:0016032)	alpha9-beta1 integrin-vascular cell adhesion molecule-1 complex (GO:0071065)|apical part of cell (GO:0045177)|cell surface (GO:0009986)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|microvillus (GO:0005902)|plasma membrane (GO:0005886)|podosome (GO:0002102)|sarcolemma (GO:0042383)	cell adhesion molecule binding (GO:0050839)|integrin binding (GO:0005178)|primary amine oxidase activity (GO:0008131)			central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|liver(1)|lung(27)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	56		all_epithelial(167;3.83e-06)|all_lung(203;0.000485)|Lung NSC(277;0.0011)		Epithelial(280;0.0227)|all cancers(265;0.0276)|COAD - Colon adenocarcinoma(174;0.149)|Colorectal(144;0.169)|Lung(183;0.196)	Carvedilol(DB01136)	TTTTGGGAACGAACACTCTTA	0.423																																					p.E90K		.											VCAM1,NS,carcinoma,0,1	VCAM1	0	0			c.G268A						.						104.0	91.0	95.0					1																	101186235		2203	4300	6503	SO:0001583	missense	7412	exon2			GGGAACGAACACT	M60335	CCDS773.1, CCDS774.1, CCDS55617.1	1p32-p31	2014-01-30			ENSG00000162692	ENSG00000162692		"""CD molecules"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Endogenous ligands"""	12663	protein-coding gene	gene with protein product		192225					Standard	NM_080682		Approved	CD106	uc001dti.3	P19320	OTTHUMG00000010982	ENST00000294728.2:c.268G>A	1.37:g.101186235G>A	ENSP00000294728:p.Glu90Lys	Somatic	45	0		WXS	Illumina HiSeq	.	75	4	NM_001078	A8K6R7|B4DKS4|E9PDD1|Q6NUP8	Missense_Mutation	SNP	ENST00000294728.2	37	CCDS773.1	.	.	.	.	.	.	.	.	.	.	G	15.52	2.857375	0.51376	.	.	ENSG00000162692	ENST00000347652;ENST00000294728;ENST00000370115	T;T;T	0.68181	-0.31;-0.31;-0.31	5.82	5.82	0.92795	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.191742	0.56097	D	0.000038	T	0.80639	0.4661	M	0.89904	3.07	0.26401	N	0.976425	D;D	0.89917	0.997;1.0	P;D	0.79784	0.695;0.993	T	0.76992	-0.2753	9	.	.	.	-18.7626	13.9512	0.64118	0.0:0.0:0.8486:0.1514	.	90;90	P19320-2;P19320	.;VCAM1_HUMAN	K	90	ENSP00000304611:E90K;ENSP00000294728:E90K;ENSP00000359133:E90K	.	E	+	1	0	VCAM1	100958823	1.000000	0.71417	0.329000	0.25429	0.178000	0.23041	4.467000	0.60155	2.745000	0.94114	0.655000	0.94253	GAA	.		0.423	VCAM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030213.1	NM_001078	
HLA-B	3106	hgsc.bcm.edu	37	6	31322910	31322910	+	Missense_Mutation	SNP	G	G	A	rs74189305		TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr6:31322910G>A	ENST00000412585.2	-	5	1014	c.986C>T	c.(985-987)gCt>gTt	p.A329V		NM_005514.6	NP_005505.2	P30486	1B48_HUMAN	major histocompatibility complex, class I, B	329			A -> T (in dbSNP:rs1051488).		antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|immune response (GO:0006955)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|viral process (GO:0016032)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|MHC class I protein complex (GO:0042612)	peptide antigen binding (GO:0042605)	p.A329V(4)		endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(4)|lung(4)|prostate(1)|upper_aerodigestive_tract(2)	27						ACACATCACAGCAGCGACCAC	0.587									Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of																												p.A329V		.											HLA-B,NS,carcinoma,-1,4	HLA-B	-1	4	Substitution - Missense(4)	kidney(4)	c.C986T						.						102.0	101.0	101.0					6																	31322910		1511	2709	4220	SO:0001583	missense	3106	exon5	Familial Cancer Database	;Lichen Sclerosis, Familial	ATCACAGCAGCGA	M15470	CCDS34394.1	6p21.3	2013-01-11			ENSG00000234745	ENSG00000234745		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4932	protein-coding gene	gene with protein product		142830	"""ankylosing spondylitis"""	AS		3459708	Standard	NM_005514		Approved		uc011imz.2	P01889	OTTHUMG00000031153	ENST00000412585.2:c.986C>T	6.37:g.31322910G>A	ENSP00000399168:p.Ala329Val	Somatic	46	2		WXS	Illumina HiSeq	.	54	3	NM_005514	Q29764	Missense_Mutation	SNP	ENST00000412585.2	37	CCDS34394.1	.	.	.	.	.	.	.	.	.	.	N	9.051	0.992087	0.18966	.	.	ENSG00000234745	ENST00000412585;ENST00000428231	T	0.00622	6.16	3.73	-3.02	0.05446	.	.	.	.	.	T	0.00109	0.0003	N	0.00729	-1.24	0.09310	N	1	B	0.20052	0.041	B	0.29077	0.098	T	0.22906	-1.0203	9	0.49607	T	0.09	.	5.2273	0.15401	0.4363:0.3516:0.2121:0.0	.	329	P01889	1B07_HUMAN	V	329;208	ENSP00000399168:A329V	ENSP00000399168:A329V	A	-	2	0	HLA-B	31430889	0.000000	0.05858	0.128000	0.21923	0.021000	0.10359	0.033000	0.13754	-0.241000	0.09681	0.448000	0.29417	GCT	.		0.587	HLA-B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076280.4	NM_005514	
RPUSD4	84881	hgsc.bcm.edu;bcgsc.ca	37	11	126079517	126079517	+	Silent	SNP	C	C	T			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr11:126079517C>T	ENST00000298317.4	-	3	509	c.456G>A	c.(454-456)ctG>ctA	p.L152L	RPUSD4_ENST00000534393.1_5'UTR|FAM118B_ENST00000360194.4_5'Flank|FAM118B_ENST00000533050.1_5'Flank|FAM118B_ENST00000529731.1_5'Flank|RP11-50B3.4_ENST00000532866.1_RNA|RPUSD4_ENST00000533628.1_Silent_p.L152L	NM_032795.2	NP_116184.2	Q96CM3	RUSD4_HUMAN	RNA pseudouridylate synthase domain containing 4	152					pseudouridine synthesis (GO:0001522)	mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|pseudouridine synthase activity (GO:0009982)			breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(3)|lung(8)|skin(1)	17	all_hematologic(175;0.145)	Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.0919)|all_lung(97;0.0994)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.13e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0761)		TTTCCTTGTCCAGCCGGTGGC	0.532																																					p.L152L		.											.	.	.	0			c.G456A						.						238.0	220.0	226.0					11																	126079517		2201	4299	6500	SO:0001819	synonymous_variant	84881	exon3			CTTGTCCAGCCGG	BC014131	CCDS8469.1, CCDS53721.1	11q24.2	2013-02-11			ENSG00000165526	ENSG00000165526		"""RNA pseudouridylate synthase domain containing"""	25898	protein-coding gene	gene with protein product							Standard	NM_032795		Approved	FLJ14494	uc001qde.3	Q96CM3	OTTHUMG00000165815	ENST00000298317.4:c.456G>A	11.37:g.126079517C>T		Somatic	40	0		WXS	Illumina HiSeq	.	47	4	NM_001144827	E9PML2|Q96K56	Silent	SNP	ENST00000298317.4	37	CCDS8469.1																																																																																			.		0.532	RPUSD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386336.1	NM_032795	
ZMYM6	9204	hgsc.bcm.edu	37	1	35472571	35472571	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr1:35472571G>T	ENST00000357182.4	-	12	2021	c.1794C>A	c.(1792-1794)gaC>gaA	p.D598E	ZMYM6_ENST00000373340.2_Missense_Mutation_p.D598E|ZMYM6_ENST00000493328.1_5'UTR|ZMYM6_ENST00000487874.1_Missense_Mutation_p.D598E	NM_007167.3	NP_009098.3	O95789	ZMYM6_HUMAN	zinc finger, MYM-type 6	598					cytoskeleton organization (GO:0007010)|multicellular organismal development (GO:0007275)|regulation of cell morphogenesis (GO:0022604)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(10)|ovary(4)|pancreas(1)|prostate(1)|skin(1)	44		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.13)				GTGGAAGACAGTCATTCATAA	0.323																																					p.D598E		.											.	.	.	0			c.C1794A						.						87.0	83.0	84.0					1																	35472571		2202	4300	6502	SO:0001583	missense	9204	exon12			AAGACAGTCATTC	AF055470	CCDS387.2	1p34.2	2014-05-12	2005-09-12	2005-09-12	ENSG00000163867	ENSG00000163867		"""Zinc fingers, MYM type"", ""Zinc fingers, BED-type"""	13050	protein-coding gene	gene with protein product	"""zinc finger, BED-type containing 7"""	613567	"""zinc finger protein 258"", ""zinc finger, MYM-type containing 6"""	ZNF258		10486218, 23533661	Standard	NM_007167		Approved	ZNF198L4, MYM, Buster2, ZBED7	uc001byh.3	O95789	OTTHUMG00000004163	ENST00000357182.4:c.1794C>A	1.37:g.35472571G>T	ENSP00000349708:p.Asp598Glu	Somatic	104	0		WXS	Illumina HiSeq	.	94	4	NM_007167	B4DRJ6|Q32Q23|Q4G108|Q5SVZ9|Q5SW00|Q69YL4|Q96IY0|Q9NWF1|Q9P2J4	Missense_Mutation	SNP	ENST00000357182.4	37	CCDS387.2	.	.	.	.	.	.	.	.	.	.	G	15.82	2.946605	0.53186	.	.	ENSG00000163867	ENST00000373340;ENST00000357182	T;T	0.21191	2.02;3.19	5.14	-1.09	0.09904	.	0.452214	0.24377	N	0.039051	T	0.28632	0.0709	L	0.35414	1.06	0.24844	N	0.992446	D;P;B	0.76494	0.999;0.913;0.184	D;P;B	0.78314	0.991;0.688;0.124	T	0.10917	-1.0609	10	0.66056	D	0.02	-16.6125	9.3815	0.38316	0.4283:0.0:0.5717:0.0	.	501;598;598	B4DWC0;O95789;O95789-1	.;ZMYM6_HUMAN;.	E	598	ENSP00000362437:D598E;ENSP00000349708:D598E	ENSP00000349708:D598E	D	-	3	2	ZMYM6	35245158	0.965000	0.33210	0.030000	0.17652	0.867000	0.49689	-0.241000	0.08940	-0.269000	0.09298	-0.140000	0.14226	GAC	.		0.323	ZMYM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011999.1	NM_007167	
ATM	472	hgsc.bcm.edu	37	11	108205808	108205808	+	Missense_Mutation	SNP	A	A	T			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr11:108205808A>T	ENST00000452508.2	+	56	8312	c.8123A>T	c.(8122-8124)gAt>gTt	p.D2708V	C11orf65_ENST00000525729.1_Intron|ATM_ENST00000278616.4_Missense_Mutation_p.D2708V			Q13315	ATM_HUMAN	ATM serine/threonine kinase	2708					brain development (GO:0007420)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|DNA damage induced protein phosphorylation (GO:0006975)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|heart development (GO:0007507)|histone mRNA catabolic process (GO:0071044)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|lipoprotein catabolic process (GO:0042159)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of B cell proliferation (GO:0030889)|neuron apoptotic process (GO:0051402)|oocyte development (GO:0048599)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|positive regulation of neuron apoptotic process (GO:0043525)|pre-B cell allelic exclusion (GO:0002331)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reciprocal meiotic recombination (GO:0007131)|replicative senescence (GO:0090399)|response to hypoxia (GO:0001666)|response to ionizing radiation (GO:0010212)|signal transduction (GO:0007165)|signal transduction involved in mitotic G2 DNA damage checkpoint (GO:0072434)|somitogenesis (GO:0001756)|telomere maintenance (GO:0000723)	cytoplasmic vesicle (GO:0031410)|nucleoplasm (GO:0005654)|spindle (GO:0005819)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent protein kinase activity (GO:0004677)|histone serine kinase activity (GO:0035174)|protein complex binding (GO:0032403)|protein dimerization activity (GO:0046983)|protein N-terminus binding (GO:0047485)|protein serine/threonine kinase activity (GO:0004674)			NS(4)|breast(23)|central_nervous_system(11)|endometrium(10)|haematopoietic_and_lymphoid_tissue(227)|kidney(19)|large_intestine(53)|liver(5)|lung(62)|ovary(6)|pancreas(4)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	448		all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147)	Caffeine(DB00201)	GTAGGTTCCGATGGCAAGGAG	0.378			"""D, Mis, N, F, S"""		T-PLL	"""leukemia, lymphoma, medulloblastoma, glioma"""		Genes defective in diseases associated with sensitivity to DNA damaging agents	Ataxia Telangiectasia	TSP Lung(14;0.12)																											p.D2708V		.	yes	Rec	yes	Ataxia-telangiectasia	11	11q22.3	472	ataxia telangiectasia mutated		"""L, O"""	ATM_ENST00000278616,colon,carcinoma,0,2	ATM_ENST00000278616	0	0			c.A8123T						.						103.0	102.0	102.0					11																	108205808		2201	4298	6499	SO:0001583	missense	472	exon55	Familial Cancer Database	AT, Louis-Bar syndrome	GTTCCGATGGCAA	AB209133	CCDS31669.1	11q22-q23	2014-09-17	2014-06-17		ENSG00000149311	ENSG00000149311			795	protein-coding gene	gene with protein product	"""TEL1, telomere maintenance 1, homolog (S. cerevisiae)"""	607585	"""ataxia telangiectasia mutated (includes complementation groups A, C and D)"", ""ataxia telangiectasia mutated"""	ATA, ATDC, ATC, ATD			Standard	XM_005271561		Approved	TEL1, TELO1	uc001pkb.1	Q13315	OTTHUMG00000166480	ENST00000452508.2:c.8123A>T	11.37:g.108205808A>T	ENSP00000388058:p.Asp2708Val	Somatic	53	0		WXS	Illumina HiSeq	.	73	3	NM_000051	B2RNX5|O15429|Q12758|Q16551|Q93007|Q9NP02|Q9UCX7	Missense_Mutation	SNP	ENST00000452508.2	37	CCDS31669.1	.	.	.	.	.	.	.	.	.	.	A	21.6	4.177275	0.78564	.	.	ENSG00000149311	ENST00000278616;ENST00000452508	D;D	0.91180	-2.8;-2.8	5.67	5.67	0.87782	Protein kinase-like domain (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	D	0.97161	0.9072	H	0.97265	3.97	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98607	1.0661	10	0.87932	D	0	.	15.9192	0.79547	1.0:0.0:0.0:0.0	.	2708	Q13315	ATM_HUMAN	V	2708	ENSP00000278616:D2708V;ENSP00000388058:D2708V	ENSP00000278616:D2708V	D	+	2	0	ATM	107711018	1.000000	0.71417	1.000000	0.80357	0.521000	0.34408	8.624000	0.90961	2.164000	0.68074	0.533000	0.62120	GAT	.		0.378	ATM-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389938.1	NM_000051	
FRY	10129	hgsc.bcm.edu	37	13	32653148	32653148	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr13:32653148G>T	ENST00000380250.3	+	2	744	c.248G>T	c.(247-249)cGt>cTt	p.R83L		NM_023037.2	NP_075463.2	Q5TBA9	FRY_HUMAN	furry homolog (Drosophila)	83						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				NS(3)|breast(4)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(31)|lung(50)|ovary(5)|pancreas(1)|prostate(6)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	132		Lung SC(185;0.0271)		all cancers(112;4.81e-05)|Epithelial(112;0.000656)|OV - Ovarian serous cystadenocarcinoma(117;0.0123)|BRCA - Breast invasive adenocarcinoma(63;0.0295)|GBM - Glioblastoma multiforme(144;0.104)		CGCAAGATTCGTATCATTATG	0.413																																					p.R83L		.											.	.	.	0			c.G248T						.						181.0	177.0	178.0					13																	32653148		1937	4142	6079	SO:0001583	missense	10129	exon2			AGATTCGTATCAT	AL049784	CCDS41875.1	13q13.1	2008-02-05	2005-11-24	2005-11-24	ENSG00000073910	ENSG00000073910			20367	protein-coding gene	gene with protein product		614818	"""chromosome 13 open reading frame 14"""	C13orf14		14702039, 8812419	Standard	NM_023037		Approved	bA37E23.1, 13CDNA73, CG003	uc001utx.3	Q5TBA9	OTTHUMG00000016696	ENST00000380250.3:c.248G>T	13.37:g.32653148G>T	ENSP00000369600:p.Arg83Leu	Somatic	70	0		WXS	Illumina HiSeq	.	54	4	NM_023037	Q9Y3N6	Missense_Mutation	SNP	ENST00000380250.3	37	CCDS41875.1	.	.	.	.	.	.	.	.	.	.	G	27.6	4.844333	0.91197	.	.	ENSG00000073910	ENST00000380250;ENST00000436046	T	0.22945	1.93	5.83	4.96	0.65561	.	0.055722	0.85682	D	0.000000	T	0.28928	0.0718	M	0.65975	2.015	0.80722	D	1	P	0.34826	0.471	B	0.31390	0.129	T	0.08310	-1.0728	10	0.59425	D	0.04	.	14.1144	0.65144	0.0746:0.0:0.9254:0.0	.	83	Q5TBA9	FRY_HUMAN	L	83;80	ENSP00000369600:R83L	ENSP00000369600:R83L	R	+	2	0	FRY	31551148	1.000000	0.71417	0.999000	0.59377	0.987000	0.75469	7.310000	0.78947	1.412000	0.46977	0.655000	0.94253	CGT	.		0.413	FRY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044405.1	NM_023037	
TMED2	10959	hgsc.bcm.edu;bcgsc.ca	37	12	124071376	124071376	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr12:124071376G>T	ENST00000262225.3	+	2	369	c.263G>T	c.(262-264)gGa>gTa	p.G88V	TMED2_ENST00000509052.2_Missense_Mutation_p.G3V|RP11-486O12.2_ENST00000498967.2_lincRNA	NM_006815.3	NP_006806.1	Q15363	TMED2_HUMAN	transmembrane emp24 domain trafficking protein 2	88	GOLD. {ECO:0000255|PROSITE- ProRule:PRU00096}.|Interaction with F2RL1.				cargo loading into vesicle (GO:0035459)|COPI coating of Golgi vesicle (GO:0048205)|COPII vesicle coating (GO:0048208)|embryonic morphogenesis (GO:0048598)|ER to Golgi vesicle-mediated transport (GO:0006888)|Golgi organization (GO:0007030)|intracellular protein transport (GO:0006886)|maternal placenta development (GO:0001893)|negative regulation of GTPase activity (GO:0034260)|protein targeting to plasma membrane (GO:0072661)	COPI-coated vesicle (GO:0030137)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|zymogen granule membrane (GO:0042589)				kidney(1)|large_intestine(4)|lung(1)|prostate(1)	7	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000138)|Epithelial(86;0.000613)|all cancers(50;0.00745)		CACATGGATGGAACATACAAA	0.403																																					p.G88V		.											.	.	.	0			c.G263T						.						93.0	84.0	87.0					12																	124071376		2203	4300	6503	SO:0001583	missense	10959	exon2			TGGATGGAACATA	X92098	CCDS9250.1	12q24.31	2006-03-27			ENSG00000086598	ENSG00000086598			16996	protein-coding gene	gene with protein product						8663407	Standard	NM_006815		Approved	RNP24, P24A	uc001ufg.3	Q15363	OTTHUMG00000168694	ENST00000262225.3:c.263G>T	12.37:g.124071376G>T	ENSP00000262225:p.Gly88Val	Somatic	55	0		WXS	Illumina HiSeq	.	91	4	NM_006815		Missense_Mutation	SNP	ENST00000262225.3	37	CCDS9250.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.965534	0.74131	.	.	ENSG00000086598	ENST00000262225;ENST00000438031;ENST00000432022;ENST00000509052	D;D;D	0.82344	-1.6;-1.6;-1.6	4.82	4.82	0.62117	GOLD (3);	0.000000	0.85682	D	0.000000	D	0.95114	0.8417	H	0.98951	4.38	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	D	0.97434	1.0017	10	0.87932	D	0	-33.9649	18.268	0.90057	0.0:0.0:1.0:0.0	.	88	Q15363	TMED2_HUMAN	V	88;88;56;3	ENSP00000262225:G88V;ENSP00000405845:G88V;ENSP00000441161:G3V	ENSP00000262225:G88V	G	+	2	0	TMED2	122637329	1.000000	0.71417	0.978000	0.43139	0.427000	0.31564	9.860000	0.99555	2.389000	0.81357	0.555000	0.69702	GGA	.		0.403	TMED2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400606.1	NM_006815	
AL441988.1	0	hgsc.bcm.edu	37	20	29637755	29637755	+	RNA	SNP	A	A	G	rs150335122|rs138209891|rs145805990		TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr20:29637755A>G	ENST00000408392.1	+	0	139																											ATAACTATTAATATTATTGAC	0.264																																					.		.											.	.	.	0			.						.																																					140678	.			CTATTAATATTAT																													20.37:g.29637755A>G		Somatic	31	0		WXS	Illumina HiSeq	.	73	3	.		RNA	SNP	ENST00000408392.1	37																																																																																				.		0.264	AL441988.1-201	NOVEL	basic	miRNA	miRNA			
PPL	5493	hgsc.bcm.edu	37	16	4935049	4935049	+	Silent	SNP	G	G	T			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr16:4935049G>T	ENST00000345988.2	-	22	3696	c.3607C>A	c.(3607-3609)Cgg>Agg	p.R1203R	PPL_ENST00000590782.2_Silent_p.R1201R	NM_002705.4	NP_002696	O60437	PEPL_HUMAN	periplakin	1203					keratinization (GO:0031424)	cell junction (GO:0030054)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	structural constituent of cytoskeleton (GO:0005200)			breast(6)|central_nervous_system(1)|endometrium(11)|kidney(5)|large_intestine(12)|lung(12)|ovary(4)|prostate(5)|skin(3)|stomach(1)|urinary_tract(2)	62						TCGGCACCCCGGTACTTTCGC	0.632																																					p.R1203R		.											PPL,NS,carcinoma,0,2	PPL	0	0			c.C3607A						.						55.0	52.0	53.0					16																	4935049		2197	4300	6497	SO:0001819	synonymous_variant	5493	exon22			CACCCCGGTACTT	AF013717	CCDS10526.1	16p13.3	2008-02-05			ENSG00000118898	ENSG00000118898			9273	protein-coding gene	gene with protein product		602871				9570964, 9521878	Standard	NM_002705		Approved		uc002cyd.1	O60437	OTTHUMG00000129528	ENST00000345988.2:c.3607C>A	16.37:g.4935049G>T		Somatic	15	0		WXS	Illumina HiSeq	.	18	2	NM_002705	O60314|O60454|Q14C98	Silent	SNP	ENST00000345988.2	37	CCDS10526.1																																																																																			.		0.632	PPL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251715.1	NM_002705	
MRGPRX1	259249	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	11	18955600	18955600	+	Silent	SNP	C	C	T			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr11:18955600C>T	ENST00000302797.3	-	1	956	c.732G>A	c.(730-732)gtG>gtA	p.V244V	MRGPRX1_ENST00000526914.1_5'Flank|RP11-583F24.8_ENST00000528646.1_RNA	NM_147199.3	NP_671732.3	Q96LB2	MRGX1_HUMAN	MAS-related GPR, member X1	244					acute-phase response (GO:0006953)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(12)|pancreas(2)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	36						CTTCCCTGTCCACGTGGATCC	0.473																																					p.V244V		.											.	.	.	0			c.G732A						.						76.0	69.0	72.0					11																	18955600		2194	4287	6481	SO:0001819	synonymous_variant	259249	exon1			CCTGTCCACGTGG		CCDS7846.1	11p15.1	2013-10-10			ENSG00000170255	ENSG00000170255		"""GPCR / Class A : Orphans"""	17962	protein-coding gene	gene with protein product		607227				11551509	Standard	NM_147199		Approved	MRGX1	uc001mpg.3	Q96LB2	OTTHUMG00000162655	ENST00000302797.3:c.732G>A	11.37:g.18955600C>T		Somatic	55	0		WXS	Illumina HiSeq	.	92	27	NM_147199	Q4V9L2|Q8TDD8|Q8TDD9	Silent	SNP	ENST00000302797.3	37	CCDS7846.1																																																																																			.		0.473	MRGPRX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369913.1	NM_147199	
AL441988.1	0	hgsc.bcm.edu	37	20	29638070	29638070	+	RNA	SNP	T	T	G	rs77854365		TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr20:29638070T>G	ENST00000408392.1	+	0	139																											ATTGTAACATTTTGATTCAAA	0.294																																					.		.											.	.	.	0			.						.																																					140678	.			TAACATTTTGATT																													20.37:g.29638070T>G		Somatic	36	0		WXS	Illumina HiSeq	.	77	5	.		RNA	SNP	ENST00000408392.1	37																																																																																				.		0.294	AL441988.1-201	NOVEL	basic	miRNA	miRNA			
C3P1	388503	hgsc.bcm.edu	37	19	10153492	10153492	+	RNA	SNP	G	G	T			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr19:10153492G>T	ENST00000495140.1	+	0	252							Q6ZMU1	C3P1_HUMAN	complement component 3 precursor pseudogene							extracellular space (GO:0005615)	endopeptidase inhibitor activity (GO:0004866)			endometrium(4)|large_intestine(2)|lung(6)|urinary_tract(1)	13						ACACATCGAAGTAAAGACATT	0.498																																					.		.											.	.	.	0			.						.																																					388503	.			ATCGAAGTAAAGA	AK131489		19p13.2	2009-04-08			ENSG00000167798	ENSG00000167798			34414	pseudogene	pseudogene							Standard	NR_027300		Approved	CPLP	uc010dwx.2	Q6ZMU1	OTTHUMG00000158555		19.37:g.10153492G>T		Somatic	37	0		WXS	Illumina HiSeq	.	48	4	.		RNA	SNP	ENST00000495140.1	37																																																																																				.		0.498	C3P1-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000351284.1	NR_027300	
SLFN11	91607	hgsc.bcm.edu;bcgsc.ca	37	17	33690820	33690820	+	Missense_Mutation	SNP	C	C	T			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr17:33690820C>T	ENST00000394566.1	-	4	279	c.7G>A	c.(7-9)Gca>Aca	p.A3T	SLFN11_ENST00000308377.4_Missense_Mutation_p.A3T	NM_001104587.1|NM_001104588.1|NM_001104589.1|NM_001104590.1	NP_001098057.1|NP_001098058.1|NP_001098059.1|NP_001098060.1	Q7Z7L1	SLN11_HUMAN	schlafen family member 11	3					defense response to virus (GO:0051607)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|tRNA binding (GO:0000049)			autonomic_ganglia(1)|breast(1)|kidney(3)|large_intestine(14)|lung(17)|ovary(1)|prostate(4)|skin(2)|stomach(5)|upper_aerodigestive_tract(2)	50		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		CACTGATTTGCCTCCATGTTG	0.388																																					p.A3T		.											.	.	.	0			c.G7A						.						50.0	54.0	52.0					17																	33690820		2195	4296	6491	SO:0001583	missense	91607	exon2			GATTTGCCTCCAT	AK074184	CCDS11294.1	17q12	2006-04-05			ENSG00000172716	ENSG00000172716			26633	protein-coding gene	gene with protein product		614953				12477932	Standard	NM_001104587		Approved	FLJ34922	uc010ctr.3	Q7Z7L1	OTTHUMG00000132948	ENST00000394566.1:c.7G>A	17.37:g.33690820C>T	ENSP00000378067:p.Ala3Thr	Somatic	35	0		WXS	Illumina HiSeq	.	84	4	NM_152270	E1P643|Q8N3S8|Q8N762|Q8TEE0	Missense_Mutation	SNP	ENST00000394566.1	37	CCDS11294.1	.	.	.	.	.	.	.	.	.	.	C	9.689	1.151346	0.21371	.	.	ENSG00000172716	ENST00000308377;ENST00000394566;ENST00000430814;ENST00000441608;ENST00000427966	T;T;T;T;T	0.25912	4.43;4.43;1.77;2.12;1.77	3.85	-5.87	0.02297	.	2.200940	0.03079	U	0.158200	T	0.11410	0.0278	N	0.24115	0.695	0.09310	N	1	B	0.33694	0.421	B	0.26770	0.073	T	0.17228	-1.0376	10	0.07990	T	0.79	.	5.4482	0.16548	0.1356:0.4035:0.0:0.4609	.	3	Q7Z7L1	SLN11_HUMAN	T	3	ENSP00000312402:A3T;ENSP00000378067:A3T;ENSP00000397454:A3T;ENSP00000393615:A3T;ENSP00000395140:A3T	ENSP00000312402:A3T	A	-	1	0	SLFN11	30714933	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.772000	0.01787	-0.971000	0.03564	-0.140000	0.14226	GCA	.		0.388	SLFN11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256480.1	NM_152270	
AAK1	22848	hgsc.bcm.edu	37	2	69741780	69741780	+	Missense_Mutation	SNP	C	C	G			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr2:69741780C>G	ENST00000409085.4	-	13	1975	c.1599G>C	c.(1597-1599)caG>caC	p.Q533H	AAK1_ENST00000406297.3_Missense_Mutation_p.Q533H|RN7SL604P_ENST00000492589.2_RNA|AAK1_ENST00000409068.1_Missense_Mutation_p.Q533H	NM_014911.3	NP_055726	Q2M2I8	AAK1_HUMAN	AP2 associated kinase 1	533	Gln-rich.		Q -> H. {ECO:0000269|PubMed:17344846}.		endocytosis (GO:0006897)|positive regulation of Notch signaling pathway (GO:0045747)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|protein stabilization (GO:0050821)|regulation of clathrin-mediated endocytosis (GO:2000369)|regulation of protein localization (GO:0032880)	cell leading edge (GO:0031252)|clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|extrinsic component of plasma membrane (GO:0019897)|terminal bouton (GO:0043195)	AP-2 adaptor complex binding (GO:0035612)|ATP binding (GO:0005524)|Notch binding (GO:0005112)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(6)|prostate(1)	17						gctgctgctgctgGTAGAAAT	0.532																																					p.Q533H		.											AAK1_ENST00000409085,NS,carcinoma,0,2	AAK1_ENST00000409085	0	0			c.G1599C						.						38.0	40.0	39.0					2																	69741780		2200	4298	6498	SO:0001583	missense	22848	exon13			CTGCTGCTGGTAG	AB028971	CCDS1893.2	2p13.3	2012-07-10			ENSG00000115977	ENSG00000115977			19679	protein-coding gene	gene with protein product						11877461, 12471243	Standard	NM_014911		Approved	KIAA1048, DKFZp686K16132	uc002sfp.2	Q2M2I8	OTTHUMG00000129648	ENST00000409085.4:c.1599G>C	2.37:g.69741780C>G	ENSP00000386456:p.Gln533His	Somatic	47	0		WXS	Illumina HiSeq	.	72	6	NM_014911	Q4ZFZ3|Q53RX6|Q9UPV4	Missense_Mutation	SNP	ENST00000409085.4	37	CCDS1893.2	.	.	.	.	.	.	.	.	.	.	C	8.018	0.758927	0.15846	.	.	ENSG00000115977	ENST00000409068;ENST00000409085;ENST00000406297	T;T;T	0.78003	1.57;-1.13;-1.14	4.89	3.07	0.35406	.	0.854162	0.10089	N	0.717362	T	0.57725	0.2073	N	0.14661	0.345	0.25395	N	0.988498	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.0;0.001;0.0	T	0.41610	-0.9499	10	0.11794	T	0.64	0.4343	6.749	0.23477	0.0:0.7262:0.1782:0.0957	.	533;533;533	B7ZLC4;Q2M2I8-2;Q2M2I8	.;.;AAK1_HUMAN	H	533	ENSP00000386342:Q533H;ENSP00000386456:Q533H;ENSP00000385181:Q533H	ENSP00000385181:Q533H	Q	-	3	2	AAK1	69595284	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	0.245000	0.18142	0.670000	0.31165	0.447000	0.29281	CAG	.		0.532	AAK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251847.4	NM_014911	
TSNARE1	203062	hgsc.bcm.edu	37	8	143436077	143436077	+	Nonsense_Mutation	SNP	G	G	T	rs570010659		TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr8:143436077G>T	ENST00000307180.3	-	2	126	c.9C>A	c.(7-9)taC>taA	p.Y3*	TSNARE1_ENST00000524325.1_Nonsense_Mutation_p.Y3*|TSNARE1_ENST00000520166.1_Nonsense_Mutation_p.Y3*|TSNARE1_ENST00000519651.1_Nonsense_Mutation_p.Y3*	NM_145003.3	NP_659440.2	Q96NA8	TSNA1_HUMAN	t-SNARE domain containing 1	3					intracellular protein transport (GO:0006886)|synaptic vesicle exocytosis (GO:0016079)	integral component of membrane (GO:0016021)|SNARE complex (GO:0031201)	SNAP receptor activity (GO:0005484)|SNARE binding (GO:0000149)			breast(1)|endometrium(3)|kidney(4)|large_intestine(1)|lung(6)|ovary(2)|stomach(2)|urinary_tract(1)	20	all_cancers(97;7.39e-11)|all_epithelial(106;8.98e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000332)|Ovarian(258;0.0315)|Acute lymphoblastic leukemia(118;0.155)					CGATGGATCCGTATGACATCT	0.577																																					p.Y3X		.											.	.	.	0			c.C9A						.						37.0	36.0	37.0					8																	143436077		2203	4300	6503	SO:0001587	stop_gained	203062	exon2			GGATCCGTATGAC			8q24.3	2005-08-18							26437	protein-coding gene	gene with protein product						14702039	Standard	XM_005250828		Approved	FLJ31164	uc003ywk.3	Q96NA8		ENST00000307180.3:c.9C>A	8.37:g.143436077G>T	ENSP00000303437:p.Tyr3*	Somatic	47	0		WXS	Illumina HiSeq	.	61	4	NM_145003	B7ZLB0|Q14D03	Nonsense_Mutation	SNP	ENST00000307180.3	37	CCDS6384.1	.	.	.	.	.	.	.	.	.	.	G	19.13	3.767946	0.69878	.	.	ENSG00000171045	ENST00000524325;ENST00000307180;ENST00000520166;ENST00000519651;ENST00000520462;ENST00000518720	.	.	.	3.47	-6.93	0.01638	.	0.000000	0.30630	U	0.009201	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-0.2724	14.9512	0.71077	0.214:0.0:0.786:0.0	.	.	.	.	X	3;3;3;3;3;19	.	ENSP00000303437:Y3X	Y	-	3	2	TSNARE1	143433984	0.000000	0.05858	0.002000	0.10522	0.414000	0.31173	-0.743000	0.04845	-1.662000	0.01482	-0.471000	0.05019	TAC	.		0.577	TSNARE1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_145003	
PDE10A	10846	hgsc.bcm.edu	37	6	166355810	166355810	+	Intron	SNP	A	A	G	rs576889813	byFrequency	TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr6:166355810A>G	ENST00000535229.1	-	1	389				AL590482.1_ENST00000516387.1_RNA			Q9Y233	PDE10_HUMAN	phosphodiesterase 10A						blood coagulation (GO:0007596)|cAMP catabolic process (GO:0006198)|cGMP catabolic process (GO:0046069)|regulation of cAMP-mediated signaling (GO:0043949)|regulation of protein kinase A signaling (GO:0010738)|signal transduction (GO:0007165)	cytosol (GO:0005829)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|cAMP binding (GO:0030552)|cGMP binding (GO:0030553)|cGMP-stimulated cyclic-nucleotide phosphodiesterase activity (GO:0004118)|metal ion binding (GO:0046872)			breast(4)|endometrium(5)|kidney(1)|large_intestine(13)|liver(1)|lung(39)|ovary(3)|skin(4)|upper_aerodigestive_tract(1)	71		Breast(66;0.000425)|Prostate(117;0.104)|Ovarian(120;0.221)		OV - Ovarian serous cystadenocarcinoma(33;1.5e-17)|BRCA - Breast invasive adenocarcinoma(81;1.8e-06)|GBM - Glioblastoma multiforme(31;1.92e-05)	Caffeine(DB00201)|Dipyridamole(DB00975)|Papaverine(DB01113)|Tofisopam(DB08811)|Triflusal(DB08814)	atatatGCGCACACACACACA	0.353													A|||	91	0.0181709	0.0408	0.0072	5008	,	,		18560	0.0099		0.006	False		,,,				2504	0.0164				.	Esophageal Squamous(22;308 615 5753 12038 40624)	.											.	.	.	0			.						.																																			SO:0001627	intron_variant	90632	.			ATGCGCACACACA	AB020593	CCDS47513.1	6q26	2008-03-18			ENSG00000112541	ENSG00000112541	3.1.4.17	"""Phosphodiesterases"""	8772	protein-coding gene	gene with protein product		610652				10373451	Standard	NM_001130690		Approved		uc003quo.3	Q9Y233	OTTHUMG00000015986	ENST00000535229.1:c.1655+43785T>C	6.37:g.166355810A>G		Somatic	48	0		WXS	Illumina HiSeq	.	55	6	.	Q6FHX1|Q9HCP9|Q9NTV4|Q9ULW9|Q9Y5T1	RNA	SNP	ENST00000535229.1	37																																																																																				.		0.353	PDE10A-004	KNOWN	mRNA_end_NF|basic	processed_transcript	protein_coding	OTTHUMT00000470299.1		
KDF1	126695	hgsc.bcm.edu	37	1	27278443	27278443	+	Silent	SNP	G	G	T	rs535449942		TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr1:27278443G>T	ENST00000320567.5	-	2	517	c.429C>A	c.(427-429)ccC>ccA	p.P143P		NM_152365.2	NP_689578.2	Q8NAX2	KDF1_HUMAN		143					developmental growth (GO:0048589)|establishment of skin barrier (GO:0061436)|keratinocyte development (GO:0003334)|limb epidermis development (GO:0060887)|morphogenesis of embryonic epithelium (GO:0016331)|negative regulation of keratinocyte proliferation (GO:0010839)|negative regulation of stem cell proliferation (GO:2000647)|positive regulation of epidermal cell differentiation (GO:0045606)|regulation of epidermal cell division (GO:0010482)	cell cortex (GO:0005938)|cell junction (GO:0030054)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)				NS(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	17		all_cancers(24;1.29e-21)|all_epithelial(13;2.35e-19)|Colorectal(325;0.000147)|all_lung(284;0.00122)|Lung NSC(340;0.00128)|Breast(348;0.00131)|Renal(390;0.00211)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0707)|all_neural(195;0.0966)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Epithelial(14;3.37e-51)|OV - Ovarian serous cystadenocarcinoma(117;2.22e-29)|Colorectal(126;5.31e-09)|COAD - Colon adenocarcinoma(152;9.31e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000272)|STAD - Stomach adenocarcinoma(196;0.000588)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|READ - Rectum adenocarcinoma(331;0.0419)		CCCGCCGGCTGGGGGGTGCAC	0.632																																					p.P143P		.											.,1	.	38	0			c.C429A						.						24.0	27.0	26.0					1																	27278443		2203	4300	6503	SO:0001819	synonymous_variant	126695	exon2			CCGGCTGGGGGGT																												ENST00000320567.5:c.429C>A	1.37:g.27278443G>T		Somatic	24	0		WXS	Illumina HiSeq	.	17	2	NM_152365	Q5QP32|Q8N0S7	Silent	SNP	ENST00000320567.5	37	CCDS293.1	.	.	.	.	.	.	.	.	.	.	G	7.389	0.630340	0.14322	.	.	ENSG00000175707	ENST00000374109	.	.	.	4.84	-1.75	0.08031	.	0.116963	0.64402	D	0.000014	T	0.38134	0.1029	.	.	.	0.52501	D	0.999952	.	.	.	.	.	.	T	0.09185	-1.0686	6	0.24483	T	0.36	.	2.4145	0.04432	0.4097:0.1141:0.3592:0.1169	.	.	.	.	Q	104	.	ENSP00000363223:P104Q	P	-	2	0	C1orf172	27151030	0.992000	0.36948	0.578000	0.28575	0.977000	0.68977	0.403000	0.20982	-0.559000	0.06110	0.650000	0.86243	CCA	.		0.632	C1orf172-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012340.1		
MUC4	4585	hgsc.bcm.edu	37	3	195507064	195507064	+	Missense_Mutation	SNP	G	G	C			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr3:195507064G>C	ENST00000463781.3	-	2	11846	c.11387C>G	c.(11386-11388)aCc>aGc	p.T3796S	MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.T3796S	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.T3796S(1)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GGAAGTGTCGGTGACAGGAAG	0.602																																					p.T3796S		.											MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4_ENST00000463781	0	1	Substitution - Missense(1)	endometrium(1)	c.C11387G						.						7.0	7.0	7.0					3																	195507064		638	1493	2131	SO:0001583	missense	4585	exon2			GTGTCGGTGACAG	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.11387C>G	3.37:g.195507064G>C	ENSP00000417498:p.Thr3796Ser	Somatic	95	1		WXS	Illumina HiSeq	.	255	10	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	g	5.869	0.344521	0.11126	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.37752	1.26;1.18	.	.	.	.	1.826270	0.06000	U	0.647533	T	0.22475	0.0542	N	0.19112	0.55	0.19300	N	0.999973	P	0.42584	0.784	B	0.39706	0.307	T	0.19451	-1.0305	8	.	.	.	.	5.844	0.18652	9.0E-4:0.0:0.9991:0.0	.	3668	E7ESK3	.	S	3796	ENSP00000417498:T3796S;ENSP00000420243:T3796S	.	T	-	2	0	MUC4	196991843	0.000000	0.05858	0.066000	0.19879	0.066000	0.16364	-0.667000	0.05274	0.064000	0.16427	0.064000	0.15345	ACC	.		0.602	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
SLCO1B3	28234	hgsc.bcm.edu	37	12	21033923	21033923	+	Missense_Mutation	SNP	G	G	A			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr12:21033923G>A	ENST00000381545.3	+	12	1685	c.1466G>A	c.(1465-1467)tGc>tAc	p.C489Y	LST3_ENST00000381541.3_Intron|SLCO1B3_ENST00000261196.2_Missense_Mutation_p.C489Y|SLCO1B7_ENST00000554957.1_Intron|SLCO1B3_ENST00000553473.1_Missense_Mutation_p.C489Y|LST3_ENST00000540229.1_Missense_Mutation_p.C489Y	NM_019844.3	NP_062818.1	Q9NPD5	SO1B3_HUMAN	solute carrier organic anion transporter family, member 1B3	489	Kazal-like. {ECO:0000255|PROSITE- ProRule:PRU00798}.				bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|organic anion transport (GO:0015711)|small molecule metabolic process (GO:0044281)|sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	organic anion transmembrane transporter activity (GO:0008514)			breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(23)|ovary(2)|prostate(2)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(2)	63	Esophageal squamous(101;0.149)				Atorvastatin(DB01076)|Cabazitaxel(DB06772)|Caspofungin(DB00520)|Conjugated Estrogens(DB00286)|Dabrafenib(DB08912)|Digoxin(DB00390)|Docetaxel(DB01248)|Estradiol(DB00783)|Fexofenadine(DB00950)|Fluvastatin(DB01095)|Gadoxetate(DB08884)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583)|Methotrexate(DB00563)|Mycophenolate mofetil(DB00688)|Olmesartan(DB00275)|Ouabain(DB01092)|Paclitaxel(DB01229)|Pioglitazone(DB01132)|Pitavastatin(DB08860)|Pravastatin(DB00175)|Rifampicin(DB01045)|Rilpivirine(DB08864)|Rosuvastatin(DB01098)|Valsartan(DB00177)	CTAGCAGGATGCAAATCCTCA	0.358																																					p.C489Y		.											.	.	.	0			c.G1466A						.						185.0	181.0	182.0					12																	21033923		2203	4300	6503	SO:0001583	missense	28234	exon12			CAGGATGCAAATC		CCDS8684.1	12p12	2013-05-22	2003-11-25	2003-11-26		ENSG00000111700		"""Solute carriers"""	10961	protein-coding gene	gene with protein product		605495	"""solute carrier family 21 (organic anion transporter), member 8"""	SLC21A8			Standard	NM_019844		Approved	OATP8, OATP1B3	uc001rel.4	Q9NPD5	OTTHUMG00000169011	ENST00000381545.3:c.1466G>A	12.37:g.21033923G>A	ENSP00000370956:p.Cys489Tyr	Somatic	57	0		WXS	Illumina HiSeq	.	98	5	NM_019844	E7EMT8|Q5JAR4	Missense_Mutation	SNP	ENST00000381545.3	37	CCDS8684.1	.	.	.	.	.	.	.	.	.	.	.	12.60	1.987999	0.35036	.	.	ENSG00000111700;ENSG00000111700;ENSG00000111700;ENSG00000111700;ENSG00000257046	ENST00000261196;ENST00000381545;ENST00000553473;ENST00000544370;ENST00000540229	T;T;T;T;T	0.05258	3.47;3.47;3.47;3.47;3.47	3.8	3.8	0.43715	Proteinase inhibitor I1, Kazal (1);Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);Protease inhibitor, Kazal-type (1);	0.000000	0.85682	D	0.000000	T	0.38665	0.1049	H	0.98111	4.15	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	T	0.60010	-0.7346	10	0.87932	D	0	.	13.0188	0.58773	0.0:0.0:1.0:0.0	.	489;489;489	Q5JAR4;B3KP78;Q9NPD5	.;.;SO1B3_HUMAN	Y	489;489;489;313;489	ENSP00000261196:C489Y;ENSP00000370956:C489Y;ENSP00000451758:C489Y;ENSP00000443225:C313Y;ENSP00000441269:C489Y	ENSP00000441269:C489Y	C	+	2	0	SLCO1B3;RP11-545J16.1	20925190	1.000000	0.71417	0.937000	0.37676	0.100000	0.18952	7.490000	0.81461	2.115000	0.64714	0.467000	0.42956	TGC	.		0.358	SLCO1B3-001	KNOWN	upstream_ATG|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000401936.1	NM_019844	
MUSK	4593	hgsc.bcm.edu	37	9	113449410	113449410	+	Silent	SNP	C	C	A			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr9:113449410C>A	ENST00000374448.4	+	3	354	c.220C>A	c.(220-222)Cgg>Agg	p.R74R	MUSK_ENST00000416899.2_Silent_p.R74R|MUSK_ENST00000374440.3_5'UTR|MUSK_ENST00000189978.5_Silent_p.R74R|MUSK_ENST00000374439.1_5'Flank	NM_001166281.1|NM_005592.3	NP_001159753.1|NP_005583.1	O15146	MUSK_HUMAN	muscle, skeletal, receptor tyrosine kinase	74	Ig-like 1.				cell differentiation (GO:0030154)|extracellular matrix organization (GO:0030198)|memory (GO:0007613)|multicellular organismal development (GO:0007275)|neuromuscular junction development (GO:0007528)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of gene expression (GO:0010628)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of protein geranylgeranylation (GO:2000541)|positive regulation of protein phosphorylation (GO:0001934)|protein autophosphorylation (GO:0046777)|regulation of synaptic growth at neuromuscular junction (GO:0008582)|regulation of transcription, DNA-templated (GO:0006355)|skeletal muscle acetylcholine-gated channel clustering (GO:0071340)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|neuromuscular junction (GO:0031594)|postsynaptic membrane (GO:0045211)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.R74R(1)		breast(1)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(7)|lung(23)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	49						CTTTGACACCCGGTACAGCAT	0.468																																					p.R74R		.											MUSK,NS,carcinoma,0,1	MUSK	0	1	Substitution - coding silent(1)	endometrium(1)	c.C220A	GRCh37	CI043430	MUSK	I		.						135.0	136.0	136.0					9																	113449410		1957	4164	6121	SO:0001819	synonymous_variant	4593	exon3			GACACCCGGTACA	AF006464	CCDS48005.1, CCDS75874.1	9q31.3-q32	2013-01-29			ENSG00000030304	ENSG00000030304		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	7525	protein-coding gene	gene with protein product		601296				7546737	Standard	NM_005592		Approved		uc022blv.1	O15146	OTTHUMG00000020485	ENST00000374448.4:c.220C>A	9.37:g.113449410C>A		Somatic	47	0		WXS	Illumina HiSeq	.	46	2	NM_001166281	Q32MJ8|Q32MJ9|Q5VZW7|Q5VZW8	Silent	SNP	ENST00000374448.4	37	CCDS48005.1																																																																																			.		0.468	MUSK-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding			
AKNA	80709	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	9	117105995	117105995	+	Silent	SNP	C	C	T			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr9:117105995C>T	ENST00000307564.4	-	19	3911	c.3750G>A	c.(3748-3750)caG>caA	p.Q1250Q	AKNA_ENST00000223791.3_Silent_p.Q710Q|AKNA_ENST00000374079.4_Silent_p.Q195Q|AKNA_ENST00000374075.5_Silent_p.Q1169Q|AKNA_ENST00000492875.1_5'UTR|AKNA_ENST00000374088.3_Silent_p.Q1250Q	NM_030767.4	NP_110394.3	Q7Z591	AKNA_HUMAN	AT-hook transcription factor	1250					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	membrane (GO:0016020)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			breast(3)|central_nervous_system(4)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(7)|liver(2)|lung(22)|ovary(4)|stomach(2)	51						TACCCGCATCCTGGGTCCTAA	0.587																																					p.Q1250Q		.											.	.	.	0			c.G3750A						.						65.0	63.0	64.0					9																	117105995		2203	4300	6503	SO:0001819	synonymous_variant	80709	exon19			CGCATCCTGGGTC	AK024431	CCDS6805.1	9q32	2008-02-05			ENSG00000106948	ENSG00000106948			24108	protein-coding gene	gene with protein product		605729				11268217, 11853319	Standard	NM_030767		Approved	KIAA1968	uc004bis.3	Q7Z591	OTTHUMG00000020538	ENST00000307564.4:c.3750G>A	9.37:g.117105995C>T		Somatic	17	0		WXS	Illumina HiSeq	.	50	17	NM_030767	Q05BK5|Q5T535|Q5T536|Q5T537|Q64FX6|Q64FX7|Q64FX8|Q64FY2|Q6ZMK0|Q6ZNL2|Q6ZTX0|Q8TET1|Q8TF33|Q96RR9|Q9H7P7	Silent	SNP	ENST00000307564.4	37	CCDS6805.1	.	.	.	.	.	.	.	.	.	.	C	3.544	-0.093140	0.07053	.	.	ENSG00000106948	ENST00000320310	.	.	.	4.06	3.15	0.36227	.	.	.	.	.	T	0.14313	0.0346	.	.	.	0.25960	N	0.982631	.	.	.	.	.	.	T	0.18555	-1.0333	5	0.02654	T	1	-7.0768	9.4402	0.38664	0.2101:0.7899:0.0:0.0	.	.	.	.	K	261	.	ENSP00000314538:R261K	R	-	2	0	AKNA	116145816	0.050000	0.20438	0.189000	0.23252	0.045000	0.14185	0.212000	0.17497	1.278000	0.44430	0.650000	0.86243	AGG	.		0.587	AKNA-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053767.2	NM_030767	
ASPHD2	57168	hgsc.bcm.edu	37	22	26830408	26830408	+	Missense_Mutation	SNP	C	C	A			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr22:26830408C>A	ENST00000215906.5	+	2	1265	c.827C>A	c.(826-828)cCt>cAt	p.P276H		NM_020437.4	NP_065170.2	Q6ICH7	ASPH2_HUMAN	aspartate beta-hydroxylase domain containing 2	276					peptidyl-amino acid modification (GO:0018193)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	dioxygenase activity (GO:0051213)|metal ion binding (GO:0046872)			endometrium(3)|large_intestine(3)|lung(4)|ovary(1)|prostate(4)|urinary_tract(1)	16						GTGCTGAGCCCTGGGACTGTG	0.547																																					p.P276H		.											.	.	.	0			c.C827A						.						187.0	184.0	185.0					22																	26830408		2203	4300	6503	SO:0001583	missense	57168	exon2			TGAGCCCTGGGAC	AK097157	CCDS13834.2	22q12.1	2006-02-02			ENSG00000128203	ENSG00000128203			30437	protein-coding gene	gene with protein product							Standard	NM_020437		Approved	FLJ39838	uc003acg.2	Q6ICH7	OTTHUMG00000150884	ENST00000215906.5:c.827C>A	22.37:g.26830408C>A	ENSP00000215906:p.Pro276His	Somatic	54	0		WXS	Illumina HiSeq	.	78	4	NM_020437	B2RCH3|Q7L0W3|Q9NSN3	Missense_Mutation	SNP	ENST00000215906.5	37	CCDS13834.2	.	.	.	.	.	.	.	.	.	.	C	21.8	4.201774	0.79015	.	.	ENSG00000128203	ENST00000215906	T	0.53423	0.62	4.82	4.82	0.62117	.	0.000000	0.85682	D	0.000000	T	0.77651	0.4162	H	0.94345	3.525	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.84694	0.0724	10	0.87932	D	0	-16.996	17.0945	0.86631	0.0:1.0:0.0:0.0	.	276	Q6ICH7	ASPH2_HUMAN	H	276	ENSP00000215906:P276H	ENSP00000215906:P276H	P	+	2	0	ASPHD2	25160408	1.000000	0.71417	0.986000	0.45419	0.973000	0.67179	6.967000	0.76079	2.498000	0.84270	0.557000	0.71058	CCT	.		0.547	ASPHD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320422.1	NM_020437	
RMST	196475	hgsc.bcm.edu	37	12	97908556	97908556	+	RNA	SNP	G	G	T			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr12:97908556G>T	ENST00000538559.2	+	0	1523									rhabdomyosarcoma 2 associated transcript (non-protein coding)																		GACAACCTTGGGACTTATAAA	0.289																																					.		.											.	.	.	0			.						.																																					196475	.			ACCTTGGGACTTA	AK056164		12q23.1	2012-10-16	2007-11-20		ENSG00000255794	ENSG00000255794		"""Long non-coding RNAs"""	29893	non-coding RNA	RNA, long non-coding	"""non-protein coding RNA 54"", ""long intergenic non-protein coding RNA 54"""	607045				12082533, 20062813	Standard	NR_024037		Approved	NCRMS, NCRNA00054, LINC00054	uc001tey.1		OTTHUMG00000170148		12.37:g.97908556G>T		Somatic	16	0		WXS	Illumina HiSeq	.	42	4	.		RNA	SNP	ENST00000538559.2	37																																																																																				.		0.289	RMST-003	KNOWN	basic	lincRNA	processed_transcript	OTTHUMT00000407671.1	NR_024037	
NSUN2	54888	hgsc.bcm.edu	37	5	6622195	6622195	+	Missense_Mutation	SNP	C	C	T			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr5:6622195C>T	ENST00000264670.6	-	6	867	c.556G>A	c.(556-558)Gca>Aca	p.A186T	NSUN2_ENST00000506139.1_Missense_Mutation_p.A151T|NSUN2_ENST00000539938.1_Intron|NSUN2_ENST00000505264.1_Intron	NM_017755.5	NP_060225.4	Q08J23	NSUN2_HUMAN	NOP2/Sun RNA methyltransferase family, member 2	186	S-adenosyl-L-methionine binding. {ECO:0000255|PROSITE-ProRule:PRU01023}.				mitotic nuclear division (GO:0007067)|tRNA methylation (GO:0030488)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|tRNA (cytosine-5-)-methyltransferase activity (GO:0016428)|tRNA binding (GO:0000049)			breast(1)|endometrium(6)|kidney(2)|large_intestine(5)|lung(23)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	41						GAGCCAGGTGCTGCACACATA	0.343																																					p.A186T		.											.	.	.	0			c.G556A						.						163.0	139.0	147.0					5																	6622195		2203	4300	6503	SO:0001583	missense	54888	exon6			CAGGTGCTGCACA	AK000310	CCDS3869.1, CCDS54832.1	5p15.32	2014-01-31	2012-06-12		ENSG00000037474	ENSG00000037474		"""NOP2/Sun domain containing"""	25994	protein-coding gene	gene with protein product	"""tRNA methyltransferase 4 homolog (S. cerevisiae)"", ""Myc-induced SUN-domain-containing protein"""	610916	"""NOL1/NOP2/Sun domain family, member 2"", ""NOP2/Sun domain family, member 2"", ""mental retardation, non-syndromic, autosomal recessive, 5"""	MRT5		17071714, 22541559	Standard	NM_017755		Approved	FLJ20303, TRM4, Misu	uc003jdu.3	Q08J23	OTTHUMG00000090455	ENST00000264670.6:c.556G>A	5.37:g.6622195C>T	ENSP00000264670:p.Ala186Thr	Somatic	43	0		WXS	Illumina HiSeq	.	81	4	NM_017755	A8K529|B2RNR4|B3KP09|B4DQW2|G3V1R4|Q9BVN4|Q9H858|Q9NXD9	Missense_Mutation	SNP	ENST00000264670.6	37	CCDS3869.1	.	.	.	.	.	.	.	.	.	.	C	35	5.508527	0.96386	.	.	ENSG00000037474	ENST00000264670;ENST00000506139	T;T	0.71103	-0.54;-0.47	5.48	5.48	0.80851	.	0.000000	0.85682	D	0.000000	D	0.91885	0.7431	H	0.99516	4.605	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.998	D	0.95308	0.8409	10	0.87932	D	0	-29.5422	19.3709	0.94484	0.0:1.0:0.0:0.0	.	151;186	B4DQW2;Q08J23	.;NSUN2_HUMAN	T	186;151	ENSP00000264670:A186T;ENSP00000420957:A151T	ENSP00000264670:A186T	A	-	1	0	NSUN2	6675195	1.000000	0.71417	0.999000	0.59377	0.998000	0.95712	7.342000	0.79310	2.576000	0.86940	0.655000	0.94253	GCA	.		0.343	NSUN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206902.1	NM_017755	
HNRNPCL1	343069	hgsc.bcm.edu	37	1	12907275	12907275	+	Missense_Mutation	SNP	G	G	C			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr1:12907275G>C	ENST00000317869.6	-	2	1093	c.868C>G	c.(868-870)Cag>Gag	p.Q290E		NM_001013631.1|NM_001136561.2|NM_001146181.1	NP_001013653.1|NP_001130033.2|NP_001139653.1	O60812	HNRC1_HUMAN	heterogeneous nuclear ribonucleoprotein C-like 1	290						nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(15)|prostate(1)|skin(1)|stomach(2)	29						GAGTCATCCTGGCCATTGGTG	0.443																																					p.Q290E		.											HNRNPCL1,NS,neuroblastoma,0,1	HNRNPCL1	0	0			c.C868G						.						125.0	135.0	132.0					1																	12907275		2203	4299	6502	SO:0001583	missense	343069	exon2			CATCCTGGCCATT	BC002696	CCDS30591.1	1p36.21	2013-02-12		2008-04-18	ENSG00000179172	ENSG00000179172		"""RNA binding motif (RRM) containing"""	29295	protein-coding gene	gene with protein product				HNRPCL1			Standard	NM_001013631		Approved			O60812	OTTHUMG00000001931	ENST00000317869.6:c.868C>G	1.37:g.12907275G>C	ENSP00000365370:p.Gln290Glu	Somatic	60	0		WXS	Illumina HiSeq	.	75	4	NM_001013631	B2RP44	Missense_Mutation	SNP	ENST00000317869.6	37	CCDS30591.1	.	.	.	.	.	.	.	.	.	.	.	0.001	-4.135616	0.00001	.	.	ENSG00000179172	ENST00000317869	T	0.07216	3.21	1.09	-2.18	0.07037	.	0.420350	0.20880	N	0.084017	T	0.01353	0.0044	N	0.00583	-1.355	0.09310	N	0.999999	B	0.02656	0.0	B	0.01281	0.0	T	0.31971	-0.9924	10	0.02654	T	1	.	2.6632	0.05032	0.0:0.3331:0.2756:0.3913	.	290	O60812	HNRCL_HUMAN	E	290	ENSP00000365370:Q290E	ENSP00000365370:Q290E	Q	-	1	0	HNRNPCL1	12829862	0.994000	0.37717	0.016000	0.15963	0.063000	0.16089	-0.019000	0.12546	-1.068000	0.03156	-0.786000	0.03341	CAG	.		0.443	HNRNPCL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005462.1	NM_001013631	
TTN	7273	hgsc.bcm.edu	37	2	179650369	179650369	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr2:179650369G>T	ENST00000591111.1	-	15	2695	c.2471C>A	c.(2470-2472)cCt>cAt	p.P824H	TTN_ENST00000360870.5_Missense_Mutation_p.P824H|TTN_ENST00000342992.6_Missense_Mutation_p.P824H|TTN_ENST00000589042.1_Missense_Mutation_p.P824H|TTN_ENST00000460472.2_Missense_Mutation_p.P778H|TTN_ENST00000359218.5_Missense_Mutation_p.P778H|TTN_ENST00000342175.6_Missense_Mutation_p.P778H			Q8WZ42	TITIN_HUMAN	titin	33655					adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TTCTGTCTTAGGAACAGAAAT	0.393																																					p.P824H		.											.	.	.	0			c.C2471A						.						127.0	125.0	126.0					2																	179650369		2203	4300	6503	SO:0001583	missense	7273	exon15			GTCTTAGGAACAG	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.2471C>A	2.37:g.179650369G>T	ENSP00000465570:p.Pro824His	Somatic	43	0		WXS	Illumina HiSeq	.	94	4	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	G	15.68	2.906369	0.52333	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127;ENST00000360870	T;T;T;T;T	0.70164	-0.46;-0.24;-0.26;-0.27;-0.04	5.63	5.63	0.86233	Ribonuclease H-like (1);	.	.	.	.	T	0.76385	0.3980	L	0.32530	0.975	0.41880	D	0.990319	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	0.998;0.998;0.998;0.998;1.0	T	0.78163	-0.2311	9	0.87932	D	0	.	20.0499	0.97621	0.0:0.0:1.0:0.0	.	778;778;778;824;824	D3DPF9;E7EQE6;E7ET18;Q8WZ42;Q8WZ42-6	.;.;.;TITIN_HUMAN;.	H	824;778;778;778;778;824	ENSP00000343764:P824H;ENSP00000434586:P778H;ENSP00000340554:P778H;ENSP00000352154:P778H;ENSP00000354117:P824H	ENSP00000340554:P778H	P	-	2	0	TTN	179358614	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.672000	0.98629	2.798000	0.96311	0.655000	0.94253	CCT	.		0.393	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
EP300	2033	hgsc.bcm.edu	37	22	41547849	41547849	+	Missense_Mutation	SNP	G	G	A			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr22:41547849G>A	ENST00000263253.7	+	15	4049	c.2830G>A	c.(2830-2832)Gct>Act	p.A944T		NM_001429.3	NP_001420.2	Q09472	EP300_HUMAN	E1A binding protein p300	944					apoptotic process (GO:0006915)|cellular response to hypoxia (GO:0071456)|chromatin organization (GO:0006325)|circadian rhythm (GO:0007623)|G2/M transition of mitotic cell cycle (GO:0000086)|heart development (GO:0007507)|histone H2B acetylation (GO:0043969)|histone H4 acetylation (GO:0043967)|innate immune response (GO:0045087)|internal peptidyl-lysine acetylation (GO:0018393)|internal protein amino acid acetylation (GO:0006475)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|lung development (GO:0030324)|mitotic cell cycle (GO:0000278)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of protein binding (GO:0032092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|regulation of androgen receptor signaling pathway (GO:0060765)|regulation of cell cycle (GO:0051726)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)|regulation of tubulin deacetylation (GO:0090043)|response to estrogen (GO:0043627)|response to hypoxia (GO:0001666)|skeletal muscle tissue development (GO:0007519)|somitogenesis (GO:0001756)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	acetyltransferase activity (GO:0016407)|activating transcription factor binding (GO:0033613)|androgen receptor binding (GO:0050681)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|lysine N-acetyltransferase activity, acting on acetyl phosphate as donor (GO:0004468)|nuclear hormone receptor binding (GO:0035257)|pre-mRNA intronic binding (GO:0097157)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transferase activity, transferring acyl groups (GO:0016746)|zinc ion binding (GO:0008270)			NS(2)|breast(11)|central_nervous_system(7)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(31)|kidney(5)|large_intestine(31)|liver(2)|lung(33)|ovary(2)|pancreas(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(16)	171						TTCCCAGCCAGCTGTAAGCAT	0.468			"""T,  N, F, Mis, O"""	"""MLL, RUNXBP2"""	"""colorectal, breast, pancreatic, AML, ALL, DLBCL"""				Rubinstein-Taybi syndrome																												p.A944T		.		Rec	yes		22	22q13	2033	300 kd E1A-Binding protein gene		"""L, E"""	.	.	.	0			c.G2830A						.						84.0	86.0	85.0					22																	41547849		2203	4300	6503	SO:0001583	missense	2033	exon15	Familial Cancer Database	Broad Thumb-Hallux syndrome	CAGCCAGCTGTAA	U01877	CCDS14010.1	22q13.2	2011-07-01			ENSG00000100393	ENSG00000100393		"""Chromatin-modifying enzymes / K-acetyltransferases"""	3373	protein-coding gene	gene with protein product	"""histone acetyltransferase p300"""	602700				7523245	Standard	NM_001429		Approved	p300, KAT3B	uc003azl.4	Q09472	OTTHUMG00000150937	ENST00000263253.7:c.2830G>A	22.37:g.41547849G>A	ENSP00000263253:p.Ala944Thr	Somatic	29	0		WXS	Illumina HiSeq	.	73	5	NM_001429	B1AKC2	Missense_Mutation	SNP	ENST00000263253.7	37	CCDS14010.1	.	.	.	.	.	.	.	.	.	.	G	18.06	3.539985	0.65085	.	.	ENSG00000100393	ENST00000263253	D	0.83992	-1.79	5.52	4.48	0.54585	.	0.137650	0.32328	N	0.006258	T	0.77068	0.4076	L	0.46157	1.445	0.32187	N	0.57961	B	0.06786	0.001	B	0.06405	0.002	T	0.76465	-0.2949	10	0.44086	T	0.13	-4.741	11.2869	0.49226	0.0897:0.0:0.9103:0.0	.	944	Q09472	EP300_HUMAN	T	944	ENSP00000263253:A944T	ENSP00000263253:A944T	A	+	1	0	EP300	39877795	1.000000	0.71417	1.000000	0.80357	0.838000	0.47535	2.447000	0.44917	1.244000	0.43870	0.563000	0.77884	GCT	.		0.468	EP300-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320600.1	NM_001429	
LRRC37A3	374819	hgsc.bcm.edu	37	17	62856687	62856687	+	Missense_Mutation	SNP	C	C	A			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr17:62856687C>A	ENST00000584306.1	-	11	4107	c.3577G>T	c.(3577-3579)Gcc>Tcc	p.A1193S	LRRC37A3_ENST00000339474.5_Missense_Mutation_p.A311S|LRRC37A3_ENST00000319651.5_Missense_Mutation_p.A1193S|LRRC37A3_ENST00000334962.5_Missense_Mutation_p.A170S|LRRC37A3_ENST00000400877.3_Missense_Mutation_p.A231S	NM_199340.2	NP_955372.2	O60309	L37A3_HUMAN	leucine rich repeat containing 37, member A3	1193						integral component of membrane (GO:0016021)				NS(1)|breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(6)|liver(1)|lung(10)|pancreas(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	40						GATGCCTGGGCACCCTGTTCC	0.552																																					p.A1193S		.											.	.	.	0			c.G3577T						.						87.0	93.0	91.0					17																	62856687		2203	4297	6500	SO:0001583	missense	374819	exon11			CCTGGGCACCCTG	AB011135	CCDS32708.1	17q24.1	2008-10-22			ENSG00000176809	ENSG00000176809			32427	protein-coding gene	gene with protein product							Standard	NM_199340		Approved	FLJ34306, KIAA0563	uc031rbi.1	O60309	OTTHUMG00000132307	ENST00000584306.1:c.3577G>T	17.37:g.62856687C>A	ENSP00000464535:p.Ala1193Ser	Somatic	64	0		WXS	Illumina HiSeq	.	176	7	NM_199340	Q49A01|Q49A80|Q8NB33	Missense_Mutation	SNP	ENST00000584306.1	37	CCDS32708.1	.	.	.	.	.	.	.	.	.	.	.	14.88	2.668922	0.47677	.	.	ENSG00000176809	ENST00000339474;ENST00000400877;ENST00000334962;ENST00000319651	T;T;T	0.61392	1.38;1.38;0.11	2.46	2.46	0.29980	.	.	.	.	.	T	0.69205	0.3085	M	0.68593	2.085	0.09310	N	1	D;D	0.69078	0.997;0.984	P;D	0.65443	0.783;0.935	T	0.55829	-0.8079	9	0.87932	D	0	.	8.4678	0.32966	0.0:1.0:0.0:0.0	.	311;1193	B4DG20;O60309	.;L37A3_HUMAN	S	274;231;170;1193	ENSP00000383674:A231S;ENSP00000335617:A170S;ENSP00000325713:A1193S	ENSP00000325713:A1193S	A	-	1	0	LRRC37A3	60287149	0.000000	0.05858	0.001000	0.08648	0.035000	0.12851	-0.811000	0.04500	1.374000	0.46228	0.298000	0.19748	GCC	.		0.552	LRRC37A3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445377.1	NM_199340	
SQRDL	58472	hgsc.bcm.edu;broad.mit.edu	37	15	45954270	45954270	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr15:45954270G>T	ENST00000260324.7	+	3	738	c.352G>T	c.(352-354)Gtg>Ttg	p.V118L	SQRDL_ENST00000568606.1_Missense_Mutation_p.V118L|RP11-96O20.4_ENST00000564080.1_Missense_Mutation_p.V118L	NM_021199.3	NP_067022.1	Q9Y6N5	SQRD_HUMAN	sulfide quinone reductase-like (yeast)	118					cellular nitrogen compound metabolic process (GO:0034641)|small molecule metabolic process (GO:0044281)|sulfide oxidation, using sulfide:quinone oxidoreductase (GO:0070221)|sulfur amino acid catabolic process (GO:0000098)|sulfur amino acid metabolic process (GO:0000096)	mitochondrial inner membrane (GO:0005743)	sulfide:quinone oxidoreductase activity (GO:0070224)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|prostate(2)	11		Lung NSC(122;0.000117)|all_lung(180;0.000737)|Melanoma(134;0.0417)		all cancers(107;5.89e-18)|GBM - Glioblastoma multiforme(94;1.21e-06)|COAD - Colon adenocarcinoma(120;0.17)|Colorectal(133;0.188)		CAAAGCTAGAGTGACTGAGTT	0.463																																					p.V118L		.											.	.	.	0			c.G352T						.						132.0	112.0	119.0					15																	45954270		2198	4297	6495	SO:0001583	missense	58472	exon3			GCTAGAGTGACTG	AF042284	CCDS10127.1	15q21.1	2010-08-05			ENSG00000137767	ENSG00000137767			20390	protein-coding gene	gene with protein product						10810093, 10224084	Standard	NM_021199		Approved	CGI-44	uc001zvu.4	Q9Y6N5	OTTHUMG00000131476	ENST00000260324.7:c.352G>T	15.37:g.45954270G>T	ENSP00000260324:p.Val118Leu	Somatic	54	0		WXS	Illumina HiSeq	.	98	4	NM_021199	Q9UQM8	Missense_Mutation	SNP	ENST00000260324.7	37	CCDS10127.1	.	.	.	.	.	.	.	.	.	.	G	24.7	4.563683	0.86335	.	.	ENSG00000137767	ENST00000260324	T	0.44881	0.91	5.14	5.14	0.70334	Pyridine nucleotide-disulphide oxidoreductase, FAD/NAD(P)-binding domain (1);	0.056920	0.64402	D	0.000001	T	0.65291	0.2677	M	0.87328	2.875	0.80722	D	1	P	0.34522	0.455	P	0.49477	0.612	T	0.69228	-0.5200	10	0.66056	D	0.02	-11.2177	17.346	0.87309	0.0:0.0:1.0:0.0	.	118	Q9Y6N5	SQRD_HUMAN	L	118	ENSP00000260324:V118L	ENSP00000260324:V118L	V	+	1	0	SQRDL	43741562	1.000000	0.71417	0.322000	0.25334	0.824000	0.46624	7.407000	0.80029	2.665000	0.90641	0.655000	0.94253	GTG	.		0.463	SQRDL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254319.2		
EP400	57634	hgsc.bcm.edu	37	12	132547144	132547144	+	Silent	SNP	G	G	A			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr12:132547144G>A	ENST00000333577.4	+	48	8449	c.8340G>A	c.(8338-8340)caG>caA	p.Q2780Q	EP400_ENST00000389562.2_Silent_p.Q2743Q|EP400_ENST00000330386.6_Silent_p.Q2663Q|EP400_ENST00000332482.4_Silent_p.Q2707Q|EP400_ENST00000389561.2_Silent_p.Q2744Q			Q96L91	EP400_HUMAN	E1A binding protein p400	2780	Interaction with ZNF42. {ECO:0000250}.|Poly-Gln.				chromatin organization (GO:0006325)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)	NuA4 histone acetyltransferase complex (GO:0035267)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|Swr1 complex (GO:0000812)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			NS(1)|breast(6)|central_nervous_system(10)|cervix(1)|endometrium(21)|kidney(13)|large_intestine(25)|lung(56)|ovary(5)|prostate(8)|skin(6)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	161	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.198)		OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06)		agcaacagcagcagcagcaac	0.607																																					p.Q2744Q		.											EP400,NS,carcinoma,0,1	EP400	0	0			c.G8232A						.						56.0	45.0	49.0					12																	132547144		2203	4300	6503	SO:0001819	synonymous_variant	57634	exon47			ACAGCAGCAGCAG	U80743	CCDS31929.1, CCDS31929.2	12q24.33	2008-02-01	2002-02-05	2002-02-08		ENSG00000183495			11958	protein-coding gene	gene with protein product		606265	"""trinucleotide repeat containing 12"""	TNRC12		9225980, 11509179	Standard	NM_015409		Approved	CAGH32, KIAA1498, P400, KIAA1818, DKFZP434I225	uc001ujn.3	Q96L91		ENST00000333577.4:c.8340G>A	12.37:g.132547144G>A		Somatic	22	1		WXS	Illumina HiSeq	.	55	7	NM_015409	O15411|Q6P2F5|Q8N8Q7|Q8NE05|Q96JK7|Q9P230	Silent	SNP	ENST00000333577.4	37																																																																																				.		0.607	EP400-203	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015409	
PRR21	643905	hgsc.bcm.edu	37	2	240981683	240981683	+	Silent	SNP	A	A	G	rs554303020	byFrequency	TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr2:240981683A>G	ENST00000408934.1	-	1	716	c.717T>C	c.(715-717)caT>caC	p.H239H		NM_001080835.1	NP_001074304.1	Q8WXC7	PRR21_HUMAN	proline rich 21	239	Pro-rich.							p.H239H(2)		NS(1)|breast(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(3)|lung(7)|ovary(2)|prostate(5)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)	29						GTGAAGAGGCATGGACGAAGG	0.647													a|||	2075	0.414337	0.4402	0.3804	5008	,	,		9005	0.5744		0.333	False		,,,				2504	0.3221				p.H239H		.											PRR21,NS,carcinoma,0,2	PRR21	0	2	Substitution - coding silent(2)	stomach(2)	c.T717C						.						1.0	1.0	1.0					2																	240981683		180	470	650	SO:0001819	synonymous_variant	643905	exon1			AGAGGCATGGACG	AF453950	CCDS33417.1	2q37.3	2009-04-20			ENSG00000221961	ENSG00000221961			33866	protein-coding gene	gene with protein product							Standard	NM_001080835		Approved		uc010zod.2	Q8WXC7	OTTHUMG00000159174	ENST00000408934.1:c.717T>C	2.37:g.240981683A>G		Somatic	7	0		WXS	Illumina HiSeq	.	22	5	NM_001080835		Silent	SNP	ENST00000408934.1	37	CCDS33417.1																																																																																			.		0.647	PRR21-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001080835	
FAM122C	159091	hgsc.bcm.edu;bcgsc.ca	37	X	133938244	133938244	+	5'Flank	SNP	G	G	T			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chrX:133938244G>T	ENST00000370784.4	+	0	0				FAM122C_ENST00000370785.3_5'Flank|FAM122C_ENST00000414371.2_Missense_Mutation_p.G6V	NM_001170779.1	NP_001164250.1	Q6P4D5	F222C_HUMAN	family with sequence similarity 122C											endometrium(2)|kidney(1)|lung(2)	5	Acute lymphoblastic leukemia(192;0.000127)					TATTTCCCTGGAACTGGAAGG	0.413																																					p.G6V		.											.	.	.	0			c.G17T						.						268.0	210.0	227.0					X																	133938244		692	1591	2283	SO:0001631	upstream_gene_variant	159091	exon3			TCCCTGGAACTGG	BC017868	CCDS14644.1, CCDS55500.1, CCDS55501.1, CCDS76028.1	Xq26.3	2008-02-05	2006-07-11		ENSG00000156500	ENSG00000156500			25202	protein-coding gene	gene with protein product						12477932	Standard	NM_138819		Approved	RP3-473B4.1	uc004exz.2	Q6P4D5	OTTHUMG00000022716		X.37:g.133938244G>T	Exception_encountered	Somatic	38	0		WXS	Illumina HiSeq	.	52	4	NM_001170780	F5H036|Q8WVK9	Missense_Mutation	SNP	ENST00000370784.4	37	CCDS55501.1	.	.	.	.	.	.	.	.	.	.	G	11.28	1.592059	0.28357	.	.	ENSG00000156500	ENST00000414371	.	.	.	3.86	3.86	0.44501	.	.	.	.	.	T	0.49253	0.1546	N	0.08118	0	0.42493	D	0.992904	D	0.76494	0.999	D	0.70487	0.969	T	0.55661	-0.8106	8	0.59425	D	0.04	.	10.2328	0.43264	0.0:0.0:1.0:0.0	.	6	F5H036	.	V	6	.	ENSP00000402477:G6V	G	+	2	0	FAM122C	133765910	0.033000	0.19621	0.165000	0.22776	0.007000	0.05969	0.291000	0.18994	2.170000	0.68504	0.594000	0.82650	GGA	.		0.413	FAM122C-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_138819	
NRXN1	9378	hgsc.bcm.edu	37	2	50699451	50699451	+	Nonsense_Mutation	SNP	C	C	A			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr2:50699451C>A	ENST00000406316.2	-	16	4705	c.3229G>T	c.(3229-3231)Gag>Tag	p.E1077*	NRXN1_ENST00000331040.5_5'UTR|NRXN1_ENST00000406859.3_Nonsense_Mutation_p.E1077*|NRXN1_ENST00000401710.1_Nonsense_Mutation_p.E86*|NRXN1_ENST00000402717.3_Nonsense_Mutation_p.E1069*|NRXN1_ENST00000405472.3_Nonsense_Mutation_p.E1069*|NRXN1_ENST00000404971.1_Nonsense_Mutation_p.E1117*|NRXN1_ENST00000401669.2_Nonsense_Mutation_p.E1077*	NM_004801.4	NP_004792.1	Q9ULB1	NRX1A_HUMAN	neurexin 1	1077	Laminin G-like 5. {ECO:0000255|PROSITE- ProRule:PRU00122}.				adult behavior (GO:0030534)|axon guidance (GO:0007411)|calcium-dependent cell-cell adhesion (GO:0016339)|cerebellar granule cell differentiation (GO:0021707)|establishment of protein localization (GO:0045184)|extracellular matrix organization (GO:0030198)|gamma-aminobutyric acid receptor clustering (GO:0097112)|gephyrin clustering (GO:0097116)|guanylate kinase-associated protein clustering (GO:0097117)|heterophilic cell-cell adhesion (GO:0007157)|learning (GO:0007612)|N-methyl-D-aspartate receptor clustering (GO:0097114)|negative regulation of filopodium assembly (GO:0051490)|neuroligin clustering (GO:0097118)|neuromuscular process controlling balance (GO:0050885)|neuron cell-cell adhesion (GO:0007158)|neuron maturation (GO:0042551)|neurotransmitter secretion (GO:0007269)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|postsynaptic density protein 95 clustering (GO:0097119)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|receptor localization to synapse (GO:0097120)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic vesicle clustering (GO:0097091)|vocal learning (GO:0042297)|vocalization behavior (GO:0071625)	axonal growth cone (GO:0044295)|cell junction (GO:0030054)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	acetylcholine receptor binding (GO:0033130)|calcium channel regulator activity (GO:0005246)|calcium ion binding (GO:0005509)|cell adhesion molecule binding (GO:0050839)|neuroligin family protein binding (GO:0097109)|receptor activity (GO:0004872)			breast(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(33)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	58		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.192)	Lung(47;0.0813)|LUSC - Lung squamous cell carcinoma(58;0.116)			CATCCTCTCTCGATCTGTCCG	0.433																																					p.E1117X		.											NRXN1_ENST00000536085,NS,carcinoma,0,3	NRXN1_ENST00000536085	0	0			c.G3349T						.						77.0	72.0	74.0					2																	50699451		1860	4112	5972	SO:0001587	stop_gained	9378	exon17			CTCTCTCGATCTG	AB011150	CCDS1845.1, CCDS46282.1, CCDS54360.1	2p16.3	2008-05-15			ENSG00000179915	ENSG00000179915			8008	protein-coding gene	gene with protein product		600565					Standard	NM_001135659		Approved	KIAA0578, Hs.22998	uc021vhj.1	P58400	OTTHUMG00000129263	ENST00000406316.2:c.3229G>T	2.37:g.50699451C>A	ENSP00000384311:p.Glu1077*	Somatic	41	0		WXS	Illumina HiSeq	.	70	4	NM_001135659	A7KRL9|O60323|Q53TJ9|Q53TQ1|Q9C079|Q9C080|Q9C081|Q9H3M2|Q9UDM6	Nonsense_Mutation	SNP	ENST00000406316.2	37	CCDS54360.1	.	.	.	.	.	.	.	.	.	.	C	51	18.161496	0.99900	.	.	ENSG00000179915	ENST00000401710;ENST00000404971;ENST00000406316;ENST00000405472;ENST00000401669;ENST00000536085;ENST00000402717;ENST00000406859	.	.	.	5.42	5.42	0.78866	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.12103	T	0.63	.	19.6002	0.95559	0.0:1.0:0.0:0.0	.	.	.	.	X	86;1117;1077;1069;1077;1118;1069;1077	.	ENSP00000385017:E1077X	E	-	1	0	NRXN1	50552955	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	7.776000	0.85560	2.691000	0.91804	0.655000	0.94253	GAG	.		0.433	NRXN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000325291.2		
EMR3	84658	hgsc.bcm.edu	37	19	14736408	14736408	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr19:14736408G>T	ENST00000253673.5	-	15	1916	c.1816C>A	c.(1816-1818)Cag>Aag	p.Q606K	EMR3_ENST00000344373.4_Missense_Mutation_p.Q554K|EMR3_ENST00000443157.2_Missense_Mutation_p.Q480K|EMR3_ENST00000599900.1_Missense_Mutation_p.Q391K	NM_032571.3	NP_115960.2	Q9BY15	EMR3_HUMAN	egf-like module containing, mucin-like, hormone receptor-like 3	606					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(1)|autonomic_ganglia(1)|breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(12)|lung(14)|ovary(7)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	50						TATTGTTTCTGGACCTGGAAC	0.408																																					p.Q606K		.											.	.	.	0			c.C1816A						.						162.0	147.0	152.0					19																	14736408		2203	4300	6503	SO:0001583	missense	84658	exon15			GTTTCTGGACCTG	AF239764	CCDS12315.1, CCDS74296.1, CCDS74297.1	19p13.1	2014-08-08				ENSG00000131355		"""-"", ""GPCR / Class B : Orphans"""	23647	protein-coding gene	gene with protein product		606101				11279179, 12975309	Standard	XM_005260118		Approved		uc002mzi.4	Q9BY15		ENST00000253673.5:c.1816C>A	19.37:g.14736408G>T	ENSP00000253673:p.Gln606Lys	Somatic	33	0		WXS	Illumina HiSeq	.	84	4	NM_032571		Missense_Mutation	SNP	ENST00000253673.5	37	CCDS12315.1	.	.	.	.	.	.	.	.	.	.	G	12.52	1.962606	0.34659	.	.	ENSG00000131355	ENST00000443157;ENST00000253673;ENST00000344373	T;T;T	0.34275	1.37;1.37;1.37	3.79	2.75	0.32379	.	.	.	.	.	T	0.25269	0.0614	N	0.17082	0.46	0.22728	N	0.9988	B;B;B	0.28178	0.128;0.202;0.116	B;B;B	0.35550	0.101;0.205;0.146	T	0.28618	-1.0038	9	0.62326	D	0.03	.	7.1267	0.25475	0.1259:0.0:0.8741:0.0	.	480;554;606	E7EW83;Q9BY15-2;Q9BY15	.;.;EMR3_HUMAN	K	480;606;554	ENSP00000396208:Q480K;ENSP00000253673:Q606K;ENSP00000340758:Q554K	ENSP00000253673:Q606K	Q	-	1	0	EMR3	14597408	0.327000	0.24678	0.942000	0.38095	0.152000	0.21847	0.310000	0.19356	0.935000	0.37341	0.557000	0.71058	CAG	.		0.408	EMR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466488.1	NM_032571	
ZNF85	7639	hgsc.bcm.edu	37	19	21131993	21131993	+	Missense_Mutation	SNP	A	A	G			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr19:21131993A>G	ENST00000328178.8	+	4	786	c.673A>G	c.(673-675)Acg>Gcg	p.T225A	ZNF85_ENST00000601023.1_Missense_Mutation_p.T166A|ZNF85_ENST00000345030.6_Missense_Mutation_p.T192A	NM_001256173.1|NM_003429.4	NP_001243102.1|NP_003420.2	Q03923	ZNF85_HUMAN	zinc finger protein 85	225					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(1)|large_intestine(5)|lung(10)|ovary(1)|prostate(2)	20						GAGAATTCATACGGGAGAGAA	0.348																																					p.T255A		.											.	.	.	0			c.A763G						.						31.0	34.0	33.0					19																	21131993		2196	4291	6487	SO:0001583	missense	7639	exon5			ATTCATACGGGAG	U35376	CCDS32977.1, CCDS58657.1	19p12	2013-01-08	2006-05-12			ENSG00000105750		"""Zinc fingers, C2H2-type"", ""-"""	13160	protein-coding gene	gene with protein product		603899	"""zinc finger protein 85 (HPF4, HTF1)"""			2505992	Standard	NM_003429		Approved	HPF4, HTF1	uc031rjx.1	Q03923		ENST00000328178.8:c.673A>G	19.37:g.21131993A>G	ENSP00000329793:p.Thr225Ala	Somatic	51	0		WXS	Illumina HiSeq	.	78	4	NM_001256171	B9ZVP4|Q6NVI0	Missense_Mutation	SNP	ENST00000328178.8	37	CCDS32977.1	.	.	.	.	.	.	.	.	.	.	.	7.941	0.742850	0.15642	.	.	ENSG00000105750	ENST00000328178;ENST00000345030;ENST00000421385	T;T	0.26518	1.73;1.73	1.34	1.34	0.21922	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.24005	0.0581	L	0.41573	1.285	0.80722	D	1	B;B;B	0.31817	0.341;0.0;0.064	B;B;B	0.40228	0.17;0.001;0.323	T	0.10109	-1.0644	9	0.72032	D	0.01	.	7.5336	0.27697	1.0:0.0:0.0:0.0	.	192;166;225	Q03923-2;Q49A12;Q03923	.;.;ZNF85_HUMAN	A	225;192;100	ENSP00000329793:T225A;ENSP00000342340:T192A	ENSP00000329793:T225A	T	+	1	0	ZNF85	20923833	0.880000	0.30214	0.277000	0.24703	0.255000	0.26057	4.496000	0.60360	0.565000	0.29255	0.374000	0.22700	ACG	.		0.348	ZNF85-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463430.1	NM_003429	
UBAC1	10422	hgsc.bcm.edu	37	9	138836946	138836946	+	Missense_Mutation	SNP	C	C	A	rs200169387		TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr9:138836946C>A	ENST00000371756.3	-	7	1021	c.804G>T	c.(802-804)gaG>gaT	p.E268D	UBAC1_ENST00000465873.1_5'UTR	NM_016172.2	NP_057256.2	Q9BSL1	UBAC1_HUMAN	UBA domain containing 1	268					protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)				NS(1)|biliary_tract(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(2)|lung(6)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	25		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;1.1e-06)|Epithelial(140;7.79e-06)		CTCTGGCCTCCTCATCGGTGG	0.627																																					p.E268D	NSCLC(78;973 1398 27381 29552 42415)	.											UBAC1,caecum,adenoma,0,1	UBAC1	0	0			c.G804T						.						126.0	111.0	116.0					9																	138836946		2203	4300	6503	SO:0001583	missense	10422	exon7			GGCCTCCTCATCG	AF176796	CCDS35177.1	9q34.3	2008-02-05	2007-04-20	2007-04-20	ENSG00000130560	ENSG00000130560			30221	protein-coding gene	gene with protein product		608129	"""ubiquitin associated domain containing 1"""	UBADC1		10857748, 8619474	Standard	NM_016172		Approved	GBDR1	uc004cgt.3	Q9BSL1	OTTHUMG00000020920	ENST00000371756.3:c.804G>T	9.37:g.138836946C>A	ENSP00000360821:p.Glu268Asp	Somatic	14	0		WXS	Illumina HiSeq	.	31	4	NM_016172	O75500|Q9UMW7	Missense_Mutation	SNP	ENST00000371756.3	37	CCDS35177.1	.	.	.	.	.	.	.	.	.	.	C	12.29	1.894972	0.33442	.	.	ENSG00000130560	ENST00000371756	T	0.26957	1.7	5.38	-0.852	0.10713	.	0.279835	0.38272	N	0.001757	T	0.22820	0.0551	M	0.71581	2.175	0.54753	D	0.999983	B	0.15141	0.012	B	0.12156	0.007	T	0.04855	-1.0922	10	0.36615	T	0.2	-22.0358	6.9949	0.24777	0.0:0.481:0.1161:0.4029	.	268	Q9BSL1	UBAC1_HUMAN	D	268	ENSP00000360821:E268D	ENSP00000360821:E268D	E	-	3	2	UBAC1	137976767	0.042000	0.20092	0.943000	0.38184	0.438000	0.31896	-0.646000	0.05403	0.008000	0.14787	0.655000	0.94253	GAG	.		0.627	UBAC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055034.1	NM_016172	
CPNE1	8904	hgsc.bcm.edu	37	20	34218396	34218396	+	Missense_Mutation	SNP	G	G	A			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr20:34218396G>A	ENST00000317619.3	-	15	1461	c.1067C>T	c.(1066-1068)gCc>gTc	p.A356V	CPNE1_ENST00000397443.1_Missense_Mutation_p.A356V|CPNE1_ENST00000317677.5_Missense_Mutation_p.A361V|CPNE1_ENST00000397445.1_Missense_Mutation_p.A356V|CPNE1_ENST00000352393.4_Missense_Mutation_p.A356V|CPNE1_ENST00000397442.1_Missense_Mutation_p.A356V|CPNE1_ENST00000397446.1_Missense_Mutation_p.A356V			Q99829	CPNE1_HUMAN	copine I	356	VWFA.				lipid metabolic process (GO:0006629)|vesicle-mediated transport (GO:0016192)	extracellular vesicular exosome (GO:0070062)	calcium-dependent phospholipid binding (GO:0005544)|phosphatidylserine binding (GO:0001786)|transporter activity (GO:0005215)			breast(2)|kidney(2)|large_intestine(6)|lung(4)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	21	Lung NSC(9;0.0053)|all_lung(11;0.00785)		BRCA - Breast invasive adenocarcinoma(18;0.00953)			GAAATTCAAGGCAAATTCATG	0.493																																					p.A361V		.											.	.	.	0			c.C1082T						.						138.0	123.0	128.0					20																	34218396		2203	4300	6503	SO:0001583	missense	8904	exon13			TTCAAGGCAAATT	U83246	CCDS13260.1, CCDS46595.1	20q11.22	2009-06-01			ENSG00000214078	ENSG00000214078			2314	protein-coding gene	gene with protein product		604205				9430674	Standard	NM_152925		Approved	CPN1	uc002xdm.3	Q99829	OTTHUMG00000032356	ENST00000317619.3:c.1067C>T	20.37:g.34218396G>A	ENSP00000326126:p.Ala356Val	Somatic	56	0		WXS	Illumina HiSeq	.	98	4	NM_003915	E1P5Q4|Q6IBL3|Q9H243|Q9NTZ7	Missense_Mutation	SNP	ENST00000317619.3	37	CCDS13260.1	.	.	.	.	.	.	.	.	.	.	G	29.6	5.019460	0.93462	.	.	ENSG00000214078	ENST00000352393;ENST00000317677;ENST00000317619;ENST00000397446;ENST00000397445;ENST00000397443;ENST00000397442;ENST00000437340;ENST00000430570	T;T;T;T;T;T;T;T;T	0.22743	1.94;1.94;1.94;1.94;1.94;1.94;1.94;1.94;1.94	5.64	5.64	0.86602	von Willebrand factor, type A (1);Copine (1);	0.067490	0.64402	U	0.000016	T	0.56426	0.1984	M	0.93197	3.39	0.51233	D	0.999911	B;B;B;D;P	0.62365	0.08;0.445;0.43;0.991;0.794	B;P;P;D;P	0.64776	0.328;0.582;0.704;0.929;0.671	T	0.63346	-0.6658	10	0.36615	T	0.2	-16.6704	18.4717	0.90777	0.0:0.0:1.0:0.0	.	361;356;356;336;356	B0QZ18;A6PVH9;Q99829;Q59EI4;F2Z2V0	.;.;CPNE1_HUMAN;.;.	V	356;361;356;356;356;356;356;356;332	ENSP00000336945:A356V;ENSP00000317257:A361V;ENSP00000326126:A356V;ENSP00000380588:A356V;ENSP00000380587:A356V;ENSP00000380585:A356V;ENSP00000380584:A356V;ENSP00000415597:A356V;ENSP00000390626:A332V	ENSP00000326126:A356V	A	-	2	0	CPNE1	33681810	1.000000	0.71417	1.000000	0.80357	0.879000	0.50718	9.771000	0.98977	2.657000	0.90304	0.655000	0.94253	GCC	.		0.493	CPNE1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078909.3	NM_152930	
KRTDAP	388533	hgsc.bcm.edu	37	19	35978354	35978354	+	Silent	SNP	C	C	T			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr19:35978354C>T	ENST00000338897.3	-	6	364	c.276G>A	c.(274-276)agG>agA	p.R92R	KRTDAP_ENST00000479340.1_5'UTR|KRTDAP_ENST00000484218.2_Silent_p.R78R	NM_207392.2	NP_997275.1	P60985	KTDAP_HUMAN	keratinocyte differentiation-associated protein	92					cell differentiation (GO:0030154)	extracellular region (GO:0005576)				breast(1)|lung(4)|prostate(1)	6	all_lung(56;1.89e-08)|Lung NSC(56;2.9e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)			GAGTTGCGCTCCTCAGTCCTT	0.562																																					p.R92R		.											.	.	.	0			c.G276A						.						121.0	116.0	118.0					19																	35978354		2203	4300	6503	SO:0001819	synonymous_variant	388533	exon6			TGCGCTCCTCAGT	AA297512	CCDS12462.1, CCDS59377.1	19q13.12	2013-06-20			ENSG00000188508	ENSG00000188508			16313	protein-coding gene	gene with protein product						11054531	Standard	NM_207392		Approved	KDAP, UNQ467	uc002nzh.3	P60985	OTTHUMG00000155449	ENST00000338897.3:c.276G>A	19.37:g.35978354C>T		Somatic	28	0		WXS	Illumina HiSeq	.	84	4	NM_207392	A1L4D7	Silent	SNP	ENST00000338897.3	37	CCDS12462.1																																																																																			.		0.562	KRTDAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340164.1		
CA6	765	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	9027751	9027751	+	Missense_Mutation	SNP	A	A	G			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr1:9027751A>G	ENST00000377443.2	+	6	609	c.605A>G	c.(604-606)cAg>cGg	p.Q202R	CA6_ENST00000377442.2_Missense_Mutation_p.Q142R|CA6_ENST00000476083.1_3'UTR|CA6_ENST00000377436.3_Missense_Mutation_p.Q202R	NM_001215.3	NP_001206.2	P23280	CAH6_HUMAN	carbonic anhydrase VI	202					bicarbonate transport (GO:0015701)|detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|one-carbon metabolic process (GO:0006730)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	carbonate dehydratase activity (GO:0004089)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(2)|prostate(1)|skin(5)	16	Ovarian(185;0.112)|all_lung(157;0.143)	all_epithelial(116;1.02e-19)|all_lung(118;3.6e-06)|Lung NSC(185;7.94e-06)|Renal(390;0.000147)|Breast(348;0.00123)|Colorectal(325;0.00205)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.9e-07)|COAD - Colon adenocarcinoma(227;8.28e-05)|Kidney(185;0.000268)|KIRC - Kidney renal clear cell carcinoma(229;0.000971)|STAD - Stomach adenocarcinoma(132;0.00184)|BRCA - Breast invasive adenocarcinoma(304;0.00192)|READ - Rectum adenocarcinoma(331;0.0649)	Mafenide(DB06795)|Zonisamide(DB00909)	CTTGACGTTCAGGACATGCTG	0.567																																					p.Q202R		.											.	.	.	0			c.A605G						.						170.0	135.0	146.0					1																	9027751		2203	4300	6503	SO:0001583	missense	765	exon6			ACGTTCAGGACAT	M57892	CCDS30578.1, CCDS57970.1, CCDS57971.1	1p36.2	2008-02-05			ENSG00000131686	ENSG00000131686	4.2.1.1	"""Carbonic anhydrases"""	1380	protein-coding gene	gene with protein product		114780				9691177	Standard	NM_001215		Approved		uc031plc.1	P23280	OTTHUMG00000001763	ENST00000377443.2:c.605A>G	1.37:g.9027751A>G	ENSP00000366662:p.Gln202Arg	Somatic	28	0		WXS	Illumina HiSeq	.	31	25	NM_001270500	E7EMQ1|Q5FBW3|Q5FC00|Q96QX8|Q9UF03	Missense_Mutation	SNP	ENST00000377443.2	37	CCDS30578.1	.	.	.	.	.	.	.	.	.	.	A	0.107	-1.144274	0.01728	.	.	ENSG00000131686	ENST00000549778;ENST00000377443;ENST00000377436;ENST00000377442	T;T;T;T	0.66638	-0.22;-0.22;-0.22;-0.22	5.31	-6.03	0.02185	Carbonic anhydrase, alpha-class, catalytic domain (4);	0.996839	0.08138	N	0.992027	T	0.31451	0.0797	N	0.04746	-0.17	0.09310	N	0.999999	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.34104	-0.9842	10	0.02654	T	1	.	4.279	0.10824	0.3213:0.0:0.2517:0.427	.	142;202	E7EMQ1;P23280	.;CAH6_HUMAN	R	170;202;202;142	ENSP00000447108:Q170R;ENSP00000366662:Q202R;ENSP00000366654:Q202R;ENSP00000366661:Q142R	ENSP00000366654:Q202R	Q	+	2	0	CA6	8950338	0.000000	0.05858	0.001000	0.08648	0.020000	0.10135	-0.340000	0.07821	-1.504000	0.01810	-1.447000	0.01057	CAG	.		0.567	CA6-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000004911.1		
BBX	56987	hgsc.bcm.edu	37	3	107435575	107435575	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr3:107435575G>T	ENST00000325805.8	+	5	571	c.284G>T	c.(283-285)cGc>cTc	p.R95L	BBX_ENST00000402543.1_Missense_Mutation_p.R95L|BBX_ENST00000406780.1_Missense_Mutation_p.R95L|BBX_ENST00000415149.2_Missense_Mutation_p.R95L|BBX_ENST00000416476.2_Missense_Mutation_p.R95L			Q8WY36	BBX_HUMAN	bobby sox homolog (Drosophila)	95					bone development (GO:0060348)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(18)|ovary(4)|pancreas(1)|skin(2)	49			OV - Ovarian serous cystadenocarcinoma(3;0.112)			AAACGCCATCGCTCTCTTGTA	0.473																																					p.R95L		.											.	.	.	0			c.G284T						.						160.0	148.0	152.0					3																	107435575		2203	4300	6503	SO:0001583	missense	56987	exon5			GCCATCGCTCTCT	AF168718	CCDS2950.1, CCDS46881.1, CCDS63712.1	3q13.1	2008-07-18			ENSG00000114439	ENSG00000114439			14422	protein-coding gene	gene with protein product	"""x 001 protein"""					11680820	Standard	NM_001142568		Approved	MDS001, HSPC339, HBP2	uc010hpr.4	Q8WY36	OTTHUMG00000150360	ENST00000325805.8:c.284G>T	3.37:g.107435575G>T	ENSP00000319974:p.Arg95Leu	Somatic	54	0		WXS	Illumina HiSeq	.	83	4	NM_001142568	A2RRM7|Q2TAJ1|Q7L3J8|Q7LBY8|Q8NDB0|Q8WY35|Q9H0J6	Missense_Mutation	SNP	ENST00000325805.8	37	CCDS46881.1	.	.	.	.	.	.	.	.	.	.	G	32	5.113865	0.94339	.	.	ENSG00000114439	ENST00000415149;ENST00000402543;ENST00000325805;ENST00000427402;ENST00000416476;ENST00000449335;ENST00000458458;ENST00000437908;ENST00000456419;ENST00000402163;ENST00000406780;ENST00000413213;ENST00000449271;ENST00000449213;ENST00000429270	D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.98567	-5.0;-5.0;-5.0;-5.0;-5.0;-5.0;-3.58;-5.0;-5.0;-5.0;-5.0;-5.0;-5.0;-5.0	5.06	5.06	0.68205	High mobility group, superfamily (1);High mobility group, HMG1/HMG2 (4);	0.050624	0.85682	D	0.000000	D	0.99450	0.9805	H	0.98466	4.24	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;0.999	D;D;D;D	0.97110	1.0;1.0;1.0;0.997	D	0.98107	1.0418	10	0.87932	D	0	-6.4244	18.8003	0.92013	0.0:0.0:1.0:0.0	.	95;95;95;95	C9JA69;Q8WY36;A2RRM7;Q8WY36-2	.;BBX_HUMAN;.;.	L	95	ENSP00000408358:R95L;ENSP00000385317:R95L;ENSP00000319974:R95L;ENSP00000413320:R95L;ENSP00000403860:R95L;ENSP00000408297:R95L;ENSP00000404654:R95L;ENSP00000413274:R95L;ENSP00000385518:R95L;ENSP00000385530:R95L;ENSP00000403806:R95L;ENSP00000406554:R95L;ENSP00000407662:R95L;ENSP00000414673:R95L	ENSP00000319974:R95L	R	+	2	0	BBX	108918265	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	9.420000	0.97426	2.506000	0.84524	0.460000	0.39030	CGC	.		0.473	BBX-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317820.1	NM_020235	
CPXM1	56265	hgsc.bcm.edu	37	20	2776024	2776024	+	Nonsense_Mutation	SNP	C	C	A			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr20:2776024C>A	ENST00000380605.2	-	12	1823	c.1759G>T	c.(1759-1761)Gag>Tag	p.E587*		NM_001184699.1|NM_019609.4	NP_001171628.1|NP_062555.1	Q96SM3	CPXM1_HUMAN	carboxypeptidase X (M14 family), member 1	587					cell adhesion (GO:0007155)	extracellular space (GO:0005615)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)	p.E587*(1)		endometrium(5)|kidney(5)|large_intestine(8)|lung(17)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	43						ACAGTGACCTCAAAGCAGTTG	0.562																																					p.E587X		.											CPXM1,NS,carcinoma,0,1	CPXM1	0	1	Substitution - Nonsense(1)	lung(1)	c.G1759T						.						125.0	113.0	117.0					20																	2776024		2203	4300	6503	SO:0001587	stop_gained	56265	exon12			TGACCTCAAAGCA	AL035460	CCDS13033.1	20p13	2012-02-10	2006-08-24	2006-08-24	ENSG00000088882	ENSG00000088882			15771	protein-coding gene	gene with protein product	"""carboxypeptidase-like protein X1"""	609555	"""carboxypeptidase X (M14 family)"""	CPXM		14702039	Standard	NM_019609		Approved	CPX-1, CPX1	uc002wgu.3	Q96SM3	OTTHUMG00000031706	ENST00000380605.2:c.1759G>T	20.37:g.2776024C>A	ENSP00000369979:p.Glu587*	Somatic	17	0		WXS	Illumina HiSeq	.	32	2	NM_019609	Q6P4G8|Q6UW65|Q9NUB5	Nonsense_Mutation	SNP	ENST00000380605.2	37	CCDS13033.1	.	.	.	.	.	.	.	.	.	.	C	38	7.002689	0.97994	.	.	ENSG00000088882	ENST00000380605;ENST00000421947	.	.	.	5.4	5.4	0.78164	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-31.9254	16.7195	0.85406	0.0:1.0:0.0:0.0	.	.	.	.	X	587;283	.	ENSP00000369979:E587X	E	-	1	0	CPXM1	2724024	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.651000	0.83577	2.814000	0.96858	0.563000	0.77884	GAG	.		0.562	CPXM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077643.2	NM_019609	
FANCD2	2177	hgsc.bcm.edu	37	3	10108913	10108913	+	Missense_Mutation	SNP	G	G	T	rs80258959		TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr3:10108913G>T	ENST00000419585.1	+	26	2567	c.2406G>T	c.(2404-2406)caG>caT	p.Q802H	FANCD2_ENST00000383806.1_Missense_Mutation_p.Q802H|FANCD2_ENST00000383807.1_Missense_Mutation_p.Q802H|FANCD2_ENST00000287647.3_Missense_Mutation_p.Q802H			Q9BXW9	FACD2_HUMAN	Fanconi anemia, complementation group D2	802					DNA repair (GO:0006281)|gamete generation (GO:0007276)|response to gamma radiation (GO:0010332)|synapsis (GO:0007129)	condensed chromosome (GO:0000793)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA polymerase binding (GO:0070182)	p.Q802H(2)		NS(1)|breast(3)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(10)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(3)	51				OV - Ovarian serous cystadenocarcinoma(96;0.148)		CCTTCTGCCAGGAAACATCAC	0.378			"""D, Mis, N, F"""			"""AML, leukemia"""		Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																												p.Q802H		.	yes	Rec		Fanconi anaemia D2	3	3p26	2177	"""Fanconi anemia, complementation group D2"""		L	FANCD2,NS,carcinoma,0,2	FANCD2	0	2	Substitution - Missense(2)	prostate(2)	c.G2406T						.						82.0	72.0	75.0					3																	10108913		2203	4300	6503	SO:0001583	missense	2177	exon26	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	CTGCCAGGAAACA	AF340183	CCDS2595.1, CCDS33696.1	3p25.3	2014-09-17		2001-10-05	ENSG00000144554	ENSG00000144554		"""Fanconi anemia, complementation groups"""	3585	protein-coding gene	gene with protein product		613984		FACD, FANCD		7581463, 11239453, 18475298	Standard	XM_005264946		Approved	FAD, FA-D2	uc003buw.3	Q9BXW9	OTTHUMG00000128670	ENST00000419585.1:c.2406G>T	3.37:g.10108913G>T	ENSP00000398754:p.Gln802His	Somatic	45	0		WXS	Illumina HiSeq	.	38	2	NM_001018115	Q2LA86|Q69YP9|Q6PJN7|Q9BQ06|Q9H9T9	Missense_Mutation	SNP	ENST00000419585.1	37	CCDS33696.1	.	.	.	.	.	.	.	.	.	.	G	17.37	3.373535	0.61624	.	.	ENSG00000144554	ENST00000287647;ENST00000383807;ENST00000383806;ENST00000419585	T;T;T;T	0.52983	0.64;0.64;0.64;0.64	5.44	1.83	0.25207	.	0.551240	0.20789	N	0.085651	T	0.50240	0.1604	M	0.63428	1.95	0.30837	N	0.736052	P;P	0.50710	0.938;0.938	P;P	0.53988	0.739;0.739	T	0.53229	-0.8468	10	0.54805	T	0.06	.	3.6289	0.08124	0.3156:0.0:0.4962:0.1881	.	802;802	Q9BXW9-2;Q9BXW9	.;FACD2_HUMAN	H	802	ENSP00000287647:Q802H;ENSP00000373318:Q802H;ENSP00000373317:Q802H;ENSP00000398754:Q802H	ENSP00000287647:Q802H	Q	+	3	2	FANCD2	10083913	0.804000	0.28969	0.409000	0.26459	0.904000	0.53231	1.055000	0.30467	0.519000	0.28406	0.585000	0.79938	CAG	.		0.378	FANCD2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339873.1		
MUC4	4585	hgsc.bcm.edu	37	3	195513782	195513782	+	Missense_Mutation	SNP	C	C	T			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr3:195513782C>T	ENST00000463781.3	-	2	5128	c.4669G>A	c.(4669-4671)Gac>Aac	p.D1557N	MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.D1557N	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0	VWFD. {ECO:0000255|PROSITE- ProRule:PRU00580}.			V -> A (in Ref. 2; CAB81773/CAC14143/ CAC10061 and 3; AAM66747). {ECO:0000305}.	cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GAGGAAGCGTCGGTGACAGGA	0.582																																					p.D1557N		.											.	.	.	0			c.G4669A						.						10.0	8.0	9.0					3																	195513782		677	1552	2229	SO:0001583	missense	4585	exon2			AAGCGTCGGTGAC	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.4669G>A	3.37:g.195513782C>T	ENSP00000417498:p.Asp1557Asn	Somatic	66	0		WXS	Illumina HiSeq	.	242	16	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	-	8.367	0.834357	0.16820	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.30714	1.53;1.52	0.844	0.844	0.18943	.	.	.	.	.	T	0.07458	0.0188	N	0.02539	-0.55	0.09310	N	1	P	0.52463	0.953	B	0.28991	0.097	T	0.17806	-1.0357	8	.	.	.	.	5.0592	0.14548	0.0:0.6209:0.379:0.0	.	1557	E7ESK3	.	N	1557	ENSP00000417498:D1557N;ENSP00000420243:D1557N	.	D	-	1	0	MUC4	196998177	0.000000	0.05858	0.009000	0.14445	0.009000	0.06853	-0.404000	0.07205	0.088000	0.17205	0.089000	0.15464	GAC	.		0.582	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
XRCC6BP1	91419	hgsc.bcm.edu	37	12	58340779	58340779	+	Splice_Site	SNP	G	G	T			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr12:58340779G>T	ENST00000300145.3	+	3	360	c.235G>T	c.(235-237)Gct>Tct	p.A79S		NM_033276.2	NP_150592.1	Q9Y6H3	ATP23_HUMAN	XRCC6 binding protein 1	79					double-strand break repair via nonhomologous end joining (GO:0006303)|protein phosphorylation (GO:0006468)	DNA-dependent protein kinase-DNA ligase 4 complex (GO:0005958)	DNA-dependent protein kinase activity (GO:0004677)|metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			breast(2)|endometrium(1)|kidney(2)|large_intestine(2)|lung(3)|ovary(1)	11						GCCTTTTAGTGCTGTTAACAA	0.438																																					p.A79S		.											.	.	.	0			c.G235T						.						185.0	171.0	175.0					12																	58340779		1907	4127	6034	SO:0001630	splice_region_variant	91419	exon3			TTTAGTGCTGTTA	AF078164	CCDS41802.1	12q14.1	2006-01-09				ENSG00000166896			29452	protein-coding gene	gene with protein product	"""Ku70 binding protein 3"""					10219089	Standard	XM_005269223		Approved	KUB3	uc001sqp.3	Q9Y6H3	OTTHUMG00000170493	ENST00000300145.3:c.234-1G>T	12.37:g.58340779G>T		Somatic	34	0		WXS	Illumina HiSeq	.	80	4	NM_033276	Q1RLM4|Q96E81	Missense_Mutation	SNP	ENST00000300145.3	37	CCDS41802.1	.	.	.	.	.	.	.	.	.	.	G	11.12	1.545701	0.27652	.	.	ENSG00000166896	ENST00000300145	T	0.42131	0.98	5.58	4.67	0.58626	Metallopeptidase, catalytic domain (1);	0.296568	0.40554	N	0.001073	T	0.23014	0.0556	N	0.20401	0.57	0.30047	N	0.812126	B	0.22146	0.065	B	0.18561	0.022	T	0.09885	-1.0654	10	0.16420	T	0.52	-2.069	7.0194	0.24907	0.2385:0.0:0.7615:0.0	.	79	Q9Y6H3	ATP23_HUMAN	S	79	ENSP00000300145:A79S	ENSP00000300145:A79S	A	+	1	0	XRCC6BP1	56627046	1.000000	0.71417	1.000000	0.80357	0.858000	0.48976	2.227000	0.42972	2.793000	0.96121	0.655000	0.94253	GCT	.		0.438	XRCC6BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409390.1	NM_033276	Missense_Mutation
STAU2	27067	hgsc.bcm.edu	37	8	74334955	74334955	+	Intron	SNP	C	C	G			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr8:74334955C>G	ENST00000524300.1	-	14	1881				STAU2-AS1_ENST00000517604.1_lincRNA|STAU2_ENST00000521210.1_Intron|STAU2_ENST00000522695.1_Intron|STAU2_ENST00000523558.1_Intron	NM_001164380.1|NM_001164381.1	NP_001157852.1|NP_001157853.1	Q9NUL3	STAU2_HUMAN	staufen double-stranded RNA binding protein 2						transport (GO:0006810)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|microtubule (GO:0005874)|nucleus (GO:0005634)	double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(5)|liver(1)|lung(6)|ovary(1)	19	Breast(64;0.0138)		Epithelial(68;0.026)|BRCA - Breast invasive adenocarcinoma(89;0.0483)|all cancers(69;0.0972)			TGAAAACAAACAGAGAGAGCC	0.353																																					.		.											.	.	.	0			.						.						142.0	110.0	119.0					8																	74334955		692	1591	2283	SO:0001627	intron_variant	100128126	.			AACAAACAGAGAG	Y19062	CCDS6214.1, CCDS55244.1, CCDS55245.1, CCDS55246.1, CCDS55247.1, CCDS55248.1	8q21.11	2013-06-05	2013-06-05		ENSG00000040341	ENSG00000040341			11371	protein-coding gene	gene with protein product		605920	"""staufen (Drosophila, RNA-binding protein) homolog 2"", ""staufen, RNA binding protein, homolog 2 (Drosophila)"""			10585778	Standard	NM_014393		Approved	39K2	uc003xzm.3	Q9NUL3	OTTHUMG00000164499	ENST00000524300.1:c.1531-18G>C	8.37:g.74334955C>G		Somatic	40	0		WXS	Illumina HiSeq	.	36	4	.	B7Z1I6|B7Z292|B7Z8B4|E7ER74|E9PEI3|E9PF26|E9PF50|Q6AHY7|Q96HM0|Q96HM1|Q9NVI5|Q9UGG6	RNA	SNP	ENST00000524300.1	37	CCDS55247.1																																																																																			.		0.353	STAU2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379000.2	NM_001164380	
ZNF750	79755	hgsc.bcm.edu	37	17	80788577	80788577	+	Missense_Mutation	SNP	G	G	T	rs142714888		TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr17:80788577G>T	ENST00000269394.3	-	3	2446	c.1613C>A	c.(1612-1614)gCg>gAg	p.A538E	TBCD_ENST00000355528.4_Intron|ZNF750_ENST00000572562.1_Missense_Mutation_p.A139E|TBCD_ENST00000397466.2_Intron|TBCD_ENST00000539345.2_Intron	NM_024702.2	NP_078978.2	Q32MQ0	ZN750_HUMAN	zinc finger protein 750	538					cell differentiation (GO:0030154)|epidermis development (GO:0008544)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleus (GO:0005634)	core promoter sequence-specific DNA binding (GO:0001046)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			NS(3)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|large_intestine(4)|lung(12)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	31	Breast(20;0.000523)|all_neural(118;0.0779)	all_cancers(8;0.0514)|all_epithelial(8;0.0748)	OV - Ovarian serous cystadenocarcinoma(97;0.0868)|BRCA - Breast invasive adenocarcinoma(99;0.149)			GGCGGTTTCCGCCTGGGGGCT	0.627																																					p.A538E		.											.	.	.	0			c.C1613A						.						44.0	49.0	47.0					17																	80788577		2203	4295	6498	SO:0001583	missense	79755	exon3			GTTTCCGCCTGGG	AK023903	CCDS11819.1	17q25.3	2008-05-02				ENSG00000141579			25843	protein-coding gene	gene with protein product		610226				16751772	Standard	NM_024702		Approved	FLJ13841, Zfp750	uc002kga.3	Q32MQ0		ENST00000269394.3:c.1613C>A	17.37:g.80788577G>T	ENSP00000269394:p.Ala538Glu	Somatic	44	0		WXS	Illumina HiSeq	.	82	4	NM_024702	Q9H899	Missense_Mutation	SNP	ENST00000269394.3	37	CCDS11819.1	.	.	.	.	.	.	.	.	.	.	G	0.017	-1.510733	0.00984	.	.	ENSG00000141579	ENST00000269394;ENST00000543850	T	0.13538	2.58	3.43	-6.86	0.01676	.	1.961470	0.02805	U	0.123627	T	0.08313	0.0207	L	0.36672	1.1	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.25257	-1.0137	9	.	.	.	0.0575	0.9931	0.01461	0.3958:0.1137:0.2626:0.2279	.	538	Q32MQ0	ZN750_HUMAN	E	538;131	ENSP00000269394:A538E	.	A	-	2	0	ZNF750	78381866	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.543000	0.06084	-1.445000	0.01948	-0.895000	0.02911	GCG	.		0.627	ZNF750-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439074.2	NM_024702	
EIF4G2	1982	hgsc.bcm.edu	37	11	10821765	10821765	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr11:10821765G>T	ENST00000526148.1	-	18	2501	c.1991C>A	c.(1990-1992)cCa>cAa	p.P664Q	EIF4G2_ENST00000396525.2_Missense_Mutation_p.P626Q|SNORD97_ENST00000459187.1_RNA|EIF4G2_ENST00000339995.5_Missense_Mutation_p.P664Q|EIF4G2_ENST00000525681.1_Missense_Mutation_p.P664Q|RP11-685M7.5_ENST00000532365.1_RNA	NM_001172705.1	NP_001166176			eukaryotic translation initiation factor 4 gamma, 2											NS(1)|breast(2)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(14)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(6)	43				all cancers(16;2.8e-07)|Epithelial(150;4.18e-07)|BRCA - Breast invasive adenocarcinoma(625;0.111)		ACTTTCTAGTGGTTGAGCTAG	0.418																																					p.P664Q		.											.	.	.	0			c.C1991A						.						83.0	78.0	80.0					11																	10821765		2201	4294	6495	SO:0001583	missense	1982	exon18			TCTAGTGGTTGAG	U73824	CCDS31428.1, CCDS41618.1	11p15	2005-09-29			ENSG00000110321	ENSG00000110321			3297	protein-coding gene	gene with protein product		602325				9030685, 9032289	Standard	NM_001042559		Approved	DAP5, NAT1, p97	uc001mjc.3	P78344	OTTHUMG00000165823	ENST00000526148.1:c.1991C>A	11.37:g.10821765G>T	ENSP00000433664:p.Pro664Gln	Somatic	30	0		WXS	Illumina HiSeq	.	71	4	NM_001172705		Missense_Mutation	SNP	ENST00000526148.1	37	CCDS31428.1	.	.	.	.	.	.	.	.	.	.	G	15.03	2.713389	0.48517	.	.	ENSG00000110321	ENST00000526148;ENST00000525681;ENST00000339995;ENST00000396525;ENST00000429377;ENST00000528839;ENST00000379653	T;T;T;T;T	0.42131	0.98;0.98;0.98;0.98;0.98	5.76	5.76	0.90799	Initiation factor eIF-4 gamma, MA3 (1);Armadillo-type fold (1);	0.049398	0.85682	D	0.000000	T	0.38161	0.1030	L	0.39397	1.21	0.42286	D	0.992112	B;B	0.28998	0.23;0.23	B;B	0.19148	0.013;0.024	T	0.33445	-0.9868	9	0.52906	T	0.07	-5.4109	19.9731	0.97292	0.0:0.0:1.0:0.0	.	664;737	P78344;B4DZF2	IF4G2_HUMAN;.	Q	664;664;664;626;737;61;46	ENSP00000433664:P664Q;ENSP00000433371:P664Q;ENSP00000340281:P664Q;ENSP00000379778:P626Q;ENSP00000434815:P61Q	ENSP00000340281:P664Q	P	-	2	0	EIF4G2	10778341	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.506000	0.81665	2.715000	0.92844	0.563000	0.77884	CCA	.		0.418	EIF4G2-006	KNOWN	alternative_5_UTR|non_ATG_start|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000386603.1	NM_001418	
SEMA6C	10500	hgsc.bcm.edu;broad.mit.edu	37	1	151109372	151109372	+	Missense_Mutation	SNP	C	C	T			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr1:151109372C>T	ENST00000341697.3	-	11	2626	c.935G>A	c.(934-936)cGc>cAc	p.R312H				Q9H3T2	SEM6C_HUMAN	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6C	312	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(5)|lung(15)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	28	Lung SC(34;0.00471)|Ovarian(49;0.0147)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211)			GAGAGCAGAGCGGCCATGCAG	0.537																																					p.R312H		.											SEMA6C,NS,carcinoma,0,1	SEMA6C	0	0			c.G935A						.						98.0	105.0	103.0					1																	151109372		2203	4300	6503	SO:0001583	missense	10500	exon11			GCAGAGCGGCCAT	AF339154	CCDS984.1, CCDS53363.1, CCDS53364.1	1q21.2	2008-02-05			ENSG00000143434	ENSG00000143434		"""Semaphorins"""	10740	protein-coding gene	gene with protein product	"""m-Sema Y2"""	609294				12110693	Standard	NM_030913		Approved	KIAA1869	uc001ewv.3	Q9H3T2	OTTHUMG00000012261	ENST00000341697.3:c.935G>A	1.37:g.151109372C>T	ENSP00000344148:p.Arg312His	Somatic	54	0		WXS	Illumina HiSeq	.	59	4	NM_001178061	D3DV15|Q5JR71|Q5JR72|Q5JR73|Q8WXT8|Q8WXT9|Q8WXU0|Q96JF8	Missense_Mutation	SNP	ENST00000341697.3	37	CCDS984.1	.	.	.	.	.	.	.	.	.	.	C	15.40	2.821437	0.50633	.	.	ENSG00000143434	ENST00000368914;ENST00000368912;ENST00000368913;ENST00000341697;ENST00000392792	T;T;T;T	0.23147	1.92;1.92;1.92;1.92	4.69	1.83	0.25207	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.111857	0.64402	N	0.000011	T	0.14013	0.0339	M	0.85462	2.755	0.43385	D	0.995493	P;B;B;B	0.44946	0.846;0.017;0.205;0.037	B;B;B;B	0.34452	0.183;0.004;0.025;0.004	T	0.03221	-1.1059	10	0.52906	T	0.07	.	8.1793	0.31300	0.0:0.7322:0.0:0.2678	.	312;272;312;312	B4DZD4;Q9H3T2-2;Q9H3T2-3;Q9H3T2	.;.;.;SEM6C_HUMAN	H	312;272;312;312;312	ENSP00000357910:R312H;ENSP00000357908:R272H;ENSP00000357909:R312H;ENSP00000344148:R312H	ENSP00000344148:R312H	R	-	2	0	SEMA6C	149375996	0.000000	0.05858	0.993000	0.49108	0.993000	0.82548	-0.121000	0.10643	0.226000	0.20979	0.561000	0.74099	CGC	.		0.537	SEMA6C-004	KNOWN	alternative_5_UTR|mRNA_start_NF|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000034074.1	NM_030913	
DST	667	hgsc.bcm.edu	37	6	56327829	56327829	+	Intron	SNP	G	G	A			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr6:56327829G>A	ENST00000361203.3	-	96	22007				DST_ENST00000312431.6_Intron|DST_ENST00000421834.2_Intron|DST_ENST00000370769.4_Intron|DST_ENST00000370754.5_Intron|DST_ENST00000370788.2_Intron|DST_ENST00000446842.2_Intron|DST_ENST00000244364.6_Intron			Q03001	DYST_HUMAN	dystonin						axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell motility (GO:0048870)|cytoplasmic microtubule organization (GO:0031122)|cytoskeleton organization (GO:0007010)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|maintenance of cell polarity (GO:0030011)|microtubule cytoskeleton organization (GO:0000226)|regulation of microtubule polymerization or depolymerization (GO:0031110)|response to wounding (GO:0009611)|retrograde axon cargo transport (GO:0008090)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integral component of membrane (GO:0016021)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|neurofilament cytoskeleton (GO:0060053)|nucleus (GO:0005634)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|microtubule plus-end binding (GO:0051010)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)			NS(1)|breast(5)|central_nervous_system(8)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(43)|ovary(7)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	105	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			ACTGGACTCTGGGGCCTTACA	0.428																																					.		.											.	.	.	0			.						.						106.0	101.0	102.0					6																	56327829		1936	4149	6085	SO:0001627	intron_variant	100873774	.			GACTCTGGGGCCT	M22942, M69225	CCDS4959.1, CCDS47443.1, CCDS75474.1	6p12.1	2013-01-10	2004-06-25	2004-07-01	ENSG00000151914	ENSG00000151914		"""EF-hand domain containing"""	1090	protein-coding gene	gene with protein product		113810	"""bullous pemphigoid antigen 1, 230/240kDa"""	BPAG1		2461961, 2276744	Standard	NM_001144770		Approved	BP240, KIAA0728, FLJ21489, FLJ13425, FLJ32235, FLJ30627, CATX-15, BPA, MACF2	uc021zba.2	Q03001	OTTHUMG00000014913	ENST00000361203.3:c.21999+533C>T	6.37:g.56327829G>A		Somatic	43	0		WXS	Illumina HiSeq	.	49	4	.	B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	RNA	SNP	ENST00000361203.3	37																																																																																				.		0.428	DST-004	NOVEL	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000041021.3	NM_001723	
RBM47	54502	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	4	40434693	40434693	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr4:40434693G>T	ENST00000381793.2	-	5	1913	c.1517C>A	c.(1516-1518)aCt>aAt	p.T506N	RBM47_ENST00000514014.1_Missense_Mutation_p.T468N|RBM47_ENST00000381795.6_Missense_Mutation_p.T437N|RBM47_ENST00000319592.4_Missense_Mutation_p.T437N|RBM47_ENST00000515809.1_5'Flank|RBM47_ENST00000295971.7_Missense_Mutation_p.T506N			A0AV96	RBM47_HUMAN	RNA binding motif protein 47	506	Ala-rich.				hematopoietic progenitor cell differentiation (GO:0002244)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(5)|endometrium(1)|kidney(3)|large_intestine(2)|lung(9)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	29						CGTCGACACAGTGGGAATGAC	0.567																																					p.T506N		.											.	.	.	0			c.C1517A						.						51.0	56.0	55.0					4																	40434693		2203	4300	6503	SO:0001583	missense	54502	exon6			GACACAGTGGGAA	AK000280	CCDS3460.1, CCDS43223.1	4p14	2013-02-12			ENSG00000163694	ENSG00000163694		"""RNA binding motif (RRM) containing"""	30358	protein-coding gene	gene with protein product							Standard	NM_019027		Approved	FLJ20273, NET18	uc003gvc.2	A0AV96	OTTHUMG00000128598	ENST00000381793.2:c.1517C>A	4.37:g.40434693G>T	ENSP00000371212:p.Thr506Asn	Somatic	39	0		WXS	Illumina HiSeq	.	40	4	NM_001098634	A0PJK2|B5MED4|Q8NI52|Q8NI53|Q9NXG3	Missense_Mutation	SNP	ENST00000381793.2	37	CCDS43223.1	.	.	.	.	.	.	.	.	.	.	G	14.44	2.535921	0.45176	.	.	ENSG00000163694	ENST00000319592;ENST00000381793;ENST00000381795;ENST00000295971;ENST00000514014	T;T;T;T;T	0.16324	2.39;2.35;2.39;2.35;2.35	5.43	5.43	0.79202	.	0.446035	0.27023	N	0.021310	T	0.10809	0.0264	N	0.08118	0	0.34114	D	0.66334	B;B	0.26258	0.145;0.02	B;B	0.18561	0.022;0.01	T	0.14755	-1.0461	10	0.31617	T	0.26	-5.2854	18.8467	0.92210	0.0:0.0:1.0:0.0	.	437;506	A0AV96-2;A0AV96	.;RBM47_HUMAN	N	437;506;437;506;468	ENSP00000320108:T437N;ENSP00000371212:T506N;ENSP00000371214:T437N;ENSP00000295971:T506N;ENSP00000423243:T468N	ENSP00000295971:T506N	T	-	2	0	RBM47	40129450	0.998000	0.40836	0.830000	0.32933	0.020000	0.10135	9.167000	0.94773	2.553000	0.86117	0.491000	0.48974	ACT	.		0.567	RBM47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250456.2	NM_019027	
BLOC1S5	63915	hgsc.bcm.edu	37	6	8027745	8027745	+	Intron	SNP	T	T	C			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr6:8027745T>C	ENST00000397457.2	-	4	363				EEF1E1-BLOC1S5_ENST00000397456.2_Intron|BLOC1S5-TXNDC5_ENST00000439343.2_Intron|TXNDC5_ENST00000539054.1_5'Flank|BLOC1S5_ENST00000543936.1_Intron	NM_001199323.1|NM_201280.2	NP_001186252.1|NP_958437.1	Q8TDH9	BL1S5_HUMAN	biogenesis of lysosomal organelles complex-1, subunit 5, muted						anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|endosome to melanosome transport (GO:0035646)|melanosome organization (GO:0032438)|melanosome transport (GO:0032402)|neuron projection development (GO:0031175)|otolith morphogenesis (GO:0032474)|positive regulation of pigment cell differentiation (GO:0050942)	BLOC-1 complex (GO:0031083)|transport vesicle (GO:0030133)											TTAATAATGATAACCACTTAG	0.403																																					.		.											.	.	.	0			.						.																																			SO:0001627	intron_variant	100526836	.			TAATGATAACCAC	AF426434	CCDS4506.1, CCDS75394.1	6p25.1-p24.3	2012-08-01	2012-08-01	2012-08-01		ENSG00000188428		"""Biogenesis of lysosomal organelles complex-1 subunits"""	18561	protein-coding gene	gene with protein product		607289	"""muted homolog (mouse)"""	MUTED		11912185	Standard	NM_001199322		Approved	MU, dJ303A1.3		Q8TDH9	OTTHUMG00000014220	ENST00000397457.2:c.326-1087A>G	6.37:g.8027745T>C		Somatic	19	0		WXS	Illumina HiSeq	.	34	19	.	B4DVM2|Q0VDJ6|Q0VDJ7|Q5THS1|Q68D56|Q8N5F9|Q9NU16	RNA	SNP	ENST00000397457.2	37	CCDS4506.1																																																																																			.		0.403	BLOC1S5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039797.2	NM_201280	
STARD9	57519	hgsc.bcm.edu;bcgsc.ca	37	15	42981584	42981584	+	Missense_Mutation	SNP	C	C	T			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr15:42981584C>T	ENST00000290607.7	+	23	7865	c.7808C>T	c.(7807-7809)tCa>tTa	p.S2603L		NM_020759.2	NP_065810.2	Q9P2P6	STAR9_HUMAN	StAR-related lipid transfer (START) domain containing 9	2603					ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|spindle assembly (GO:0051225)	centriole (GO:0005814)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|kinesin complex (GO:0005871)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|lipid binding (GO:0008289)|microtubule binding (GO:0008017)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)			haematopoietic_and_lymphoid_tissue(1)|stomach(1)	2						GACCAGTCATCATCAGACCAG	0.483																																					p.S2603L		.											.	.	.	0			c.C7808T						.						111.0	101.0	104.0					15																	42981584		692	1590	2282	SO:0001583	missense	57519	exon23			AGTCATCATCAGA	AB037721	CCDS53935.1	15q15.2	2013-10-16	2007-08-16		ENSG00000159433	ENSG00000159433		"""StAR-related lipid transfer (START) domain containing"""	19162	protein-coding gene	gene with protein product		614642	"""START domain containing 9"""			10718198	Standard	NM_020759		Approved	KIAA1300	uc010udj.2	Q9P2P6	OTTHUMG00000175799	ENST00000290607.7:c.7808C>T	15.37:g.42981584C>T	ENSP00000290607:p.Ser2603Leu	Somatic	29	0		WXS	Illumina HiSeq	.	50	18	NM_020759	Q68DG2|Q6AI01|Q6ZWK0|Q9UF70	Missense_Mutation	SNP	ENST00000290607.7	37	CCDS53935.1	.	.	.	.	.	.	.	.	.	.	C	15.90	2.968450	0.53614	.	.	ENSG00000159433	ENST00000290607	T	0.63744	-0.06	5.55	-4.71	0.03279	.	2.128930	0.01971	N	0.044120	T	0.44286	0.1286	L	0.29908	0.895	0.09310	N	1	.	.	.	.	.	.	T	0.24048	-1.0171	8	0.34782	T	0.22	.	0.5155	0.00602	0.2517:0.2645:0.2721:0.2118	.	.	.	.	L	2603	ENSP00000290607:S2603L	ENSP00000290607:S2603L	S	+	2	0	STARD9	40768876	0.000000	0.05858	0.001000	0.08648	0.003000	0.03518	-0.395000	0.07287	-0.171000	0.10797	-0.484000	0.04775	TCA	.		0.483	STARD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000431094.1		
MARCH6	10299	hgsc.bcm.edu;bcgsc.ca	37	5	10411446	10411446	+	Splice_Site	SNP	G	G	T			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr5:10411446G>T	ENST00000274140.5	+	19	1825	c.1693G>T	c.(1693-1695)Gat>Tat	p.D565Y	MARCH6_ENST00000510792.1_Splice_Site_p.D263Y|MARCH6_ENST00000449913.2_Splice_Site_p.D517Y|MARCH6_ENST00000503788.1_Splice_Site_p.D460Y	NM_005885.3	NP_005876.2	O60337	MARH6_HUMAN	membrane-associated ring finger (C3HC4) 6, E3 ubiquitin protein ligase	565					protein K48-linked ubiquitination (GO:0070936)	integral component of endoplasmic reticulum membrane (GO:0030176)|membrane (GO:0016020)	enzyme binding (GO:0019899)|ligase activity (GO:0016874)|ubiquitin conjugating enzyme binding (GO:0031624)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(7)|lung(35)|ovary(1)|urinary_tract(3)	54						TTTGCACAGGGATCTTCATTC	0.348																																					p.D565Y		.											.	.	.	0			c.G1693T						.						74.0	73.0	73.0					5																	10411446		2203	4300	6503	SO:0001630	splice_region_variant	10299	exon19			CACAGGGATCTTC	AB011169	CCDS34135.1, CCDS59487.1, CCDS59488.1	5p15.2	2013-01-09	2012-02-23		ENSG00000145495	ENSG00000145495		"""MARCH membrane-associated ring fingers"", ""RING-type (C3HC4) zinc fingers"""	30550	protein-coding gene	gene with protein product		613297	"""membrane-associated ring finger (C3HC4) 6"""			14722266	Standard	NM_001270660		Approved	TEB4, MARCH-VI, RNF176	uc003jet.2	O60337	OTTHUMG00000162027	ENST00000274140.5:c.1692-1G>T	5.37:g.10411446G>T		Somatic	42	0		WXS	Illumina HiSeq	.	86	5	NM_005885	A5PKZ4|B4DKJ2|B4DT33|D3DTC8|O14670|Q86X77	Missense_Mutation	SNP	ENST00000274140.5	37	CCDS34135.1	.	.	.	.	.	.	.	.	.	.	G	25.1	4.598150	0.87055	.	.	ENSG00000145495	ENST00000449913;ENST00000503788;ENST00000274140;ENST00000510792	T;T;T;T	0.46451	0.87;0.87;0.87;0.87	5.49	5.49	0.81192	.	0.000000	0.85682	D	0.000000	T	0.64789	0.2630	M	0.66939	2.045	0.80722	D	1	D;D;D;P	0.89917	0.998;0.997;1.0;0.553	D;D;D;B	0.72338	0.976;0.921;0.977;0.143	T	0.63892	-0.6534	10	0.52906	T	0.07	-25.2581	19.7394	0.96219	0.0:0.0:1.0:0.0	.	460;517;145;565	B4DKJ2;B4DT33;B2RBJ1;O60337	.;.;.;MARH6_HUMAN	Y	517;460;565;263	ENSP00000414643:D517Y;ENSP00000425930:D460Y;ENSP00000274140:D565Y;ENSP00000424512:D263Y	ENSP00000274140:D565Y	D	+	1	0	MARCH6	10464446	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	9.409000	0.97331	2.745000	0.94114	0.462000	0.41574	GAT	.		0.348	MARCH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366919.2	NM_005885	Missense_Mutation
MYO15B	80022	hgsc.bcm.edu	37	17	73616212	73616212	+	Intron	SNP	G	G	T	rs3840857|rs397841632	byFrequency	TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr17:73616212G>T	ENST00000578382.2	+	45	7194					NR_003587.2		Q96JP2	MY15B_HUMAN	myosin XVB pseudogene							cytoplasm (GO:0005737)|myosin complex (GO:0016459)	ATP binding (GO:0005524)|motor activity (GO:0003774)										CCAAATCCCTGGAAGTCTGGG	0.682																																					.		.											.	.	.	0			.						.																																			SO:0001627	intron_variant	80022	.			ATCCCTGGAAGTC			17q25.1	2014-07-16			ENSG00000266714	ENSG00000266714		"""Myosins / Myosin superfamily : Class XV"""	14083	pseudogene	pseudogene						11294886	Standard	NR_003587		Approved	MYO15BP	uc002jon.1	Q96JP2	OTTHUMG00000179794	ENST00000578382.2:c.7194+112G>T	17.37:g.73616212G>T		Somatic	8	0		WXS	Illumina HiSeq	.	29	4	.		RNA	SNP	ENST00000578382.2	37																																																																																				.		0.682	MYO15B-001	KNOWN	sequence_error|basic	processed_transcript	protein_coding	OTTHUMT00000448172.2	NR_003587	
SOS1	6654	hgsc.bcm.edu	37	2	39222277	39222277	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr2:39222277G>T	ENST00000426016.1	-	21	3419	c.3333C>A	c.(3331-3333)agC>agA	p.S1111R	SOS1_ENST00000402219.2_Missense_Mutation_p.S1111R|SOS1-IT1_ENST00000594472.1_RNA|SOS1_ENST00000395038.2_Missense_Mutation_p.S1111R			Q07889	SOS1_HUMAN	son of sevenless homolog 1 (Drosophila)	1111					apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|positive regulation of apoptotic process (GO:0043065)|positive regulation of epidermal growth factor receptor signaling pathway (GO:0045742)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|Ras protein signal transduction (GO:0007265)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	DNA binding (GO:0003677)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|Rho GTPase activator activity (GO:0005100)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			autonomic_ganglia(1)|breast(6)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(9)|liver(1)|lung(29)|ovary(4)|prostate(1)|skin(4)|stomach(1)|urinary_tract(2)	75		all_hematologic(82;0.21)				AGTGAAAAGGGCTCGAATGAT	0.393									Noonan syndrome																												p.S1111R		.											.	.	.	0			c.C3333A						.						92.0	86.0	88.0					2																	39222277		2203	4300	6503	SO:0001583	missense	6654	exon20	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome	AAAAGGGCTCGAA	L13857	CCDS1802.1	2p21	2014-09-17	2002-11-05		ENSG00000115904	ENSG00000115904		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	11187	protein-coding gene	gene with protein product		182530	"""gingival fibromatosis, hereditary, 1"""	GINGF		8276400, 10995566	Standard	NM_005633		Approved	HGF, GF1	uc002rrk.4	Q07889	OTTHUMG00000102109	ENST00000426016.1:c.3333C>A	2.37:g.39222277G>T	ENSP00000387784:p.Ser1111Arg	Somatic	68	0		WXS	Illumina HiSeq	.	91	5	NM_005633	A8K2G3|B4DXG2	Missense_Mutation	SNP	ENST00000426016.1	37	CCDS1802.1	.	.	.	.	.	.	.	.	.	.	G	17.67	3.446203	0.63178	.	.	ENSG00000115904	ENST00000426016;ENST00000402219;ENST00000543698;ENST00000395038	T;T;T	0.78003	-1.04;-1.04;-1.14	5.91	5.03	0.67393	.	0.433874	0.28940	N	0.013647	T	0.69360	0.3102	L	0.59436	1.845	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.60737	-0.7204	10	0.16896	T	0.51	.	8.3608	0.32357	0.2389:0.0:0.7611:0.0	.	1111	Q07889	SOS1_HUMAN	R	1111;1111;843;1111	ENSP00000387784:S1111R;ENSP00000384675:S1111R;ENSP00000378479:S1111R	ENSP00000378479:S1111R	S	-	3	2	SOS1	39075781	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.377000	0.52425	2.813000	0.96785	0.655000	0.94253	AGC	.		0.393	SOS1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219948.3	NM_005633	
TSPEAR	54084	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	21	45938574	45938574	+	Intron	SNP	G	G	A			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr21:45938574G>A	ENST00000323084.4	-	9	1632				C21orf90_ENST00000330490.3_Silent_p.S60S|TSPEAR_ENST00000397916.1_Intron|TSPEAR-AS1_ENST00000451035.1_RNA|C21orf90_ENST00000465978.1_Intron|C21orf90_ENST00000354333.5_Missense_Mutation_p.V36I	NM_001272037.1|NM_144991.2	NP_001258966.1|NP_659428.2	Q8WU66	TSEAR_HUMAN	thrombospondin-type laminin G domain and EAR repeats						sensory perception of sound (GO:0007605)	cell surface (GO:0009986)|ciliary membrane (GO:0060170)|extracellular region (GO:0005576)|stereocilium (GO:0032420)				breast(1)|central_nervous_system(6)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(7)|ovary(1)|pancreas(1)|skin(6)|soft_tissue(1)|upper_aerodigestive_tract(2)	37						CAGCTCATTCGTTAGATGATT	0.527																																					.		.											.	.	.	0			.						.																																			SO:0001627	intron_variant	114043	.			TCATTCGTTAGAT	AJ487962	CCDS13712.1, CCDS74801.1	21q22.3	2012-10-30	2011-01-25	2011-01-25	ENSG00000175894	ENSG00000175894			1268	protein-coding gene	gene with protein product		612920	"""chromosome 21 open reading frame 29"", ""deafness, autosomal recessive 98"""	C21orf29, DFNB98		12095917, 22678063	Standard	NM_144991		Approved	MGC11251, TSP-EAR	uc002zfe.1	Q8WU66	OTTHUMG00000041215	ENST00000323084.4:c.1566+3191C>T	21.37:g.45938574G>A		Somatic	15	0		WXS	Illumina HiSeq	.	24	11	.		RNA	SNP	ENST00000323084.4	37	CCDS13712.1	.	.	.	.	.	.	.	.	.	.	G	1.393	-0.580156	0.03854	.	.	ENSG00000182912	ENST00000354333	.	.	.	0.661	-1.32	0.09201	.	.	.	.	.	T	0.33876	0.0878	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.35201	-0.9798	4	0.87932	D	0	.	.	.	.	.	.	.	.	I	36	.	ENSP00000346295:V36I	V	+	1	0	C21orf90	44763002	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-2.089000	0.01357	-1.126000	0.02929	-0.444000	0.05651	GTT	.		0.527	TSPEAR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098761.1	NM_144991	
PIK3CB	5291	hgsc.bcm.edu	37	3	138407796	138407796	+	Missense_Mutation	SNP	G	G	A			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr3:138407796G>A	ENST00000477593.1	-	15	2130	c.2057C>T	c.(2056-2058)gCt>gTt	p.A686V	PIK3CB_ENST00000544716.1_Missense_Mutation_p.A132V|PIK3CB_ENST00000289153.2_Missense_Mutation_p.A686V			P42338	PK3CB_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit beta	686	PIK helical. {ECO:0000255|PROSITE- ProRule:PRU00878}.				activation of MAPK activity (GO:0000187)|autophagy (GO:0006914)|blood coagulation (GO:0007596)|cell migration (GO:0016477)|cellular calcium ion homeostasis (GO:0006874)|chemotaxis (GO:0006935)|embryonic cleavage (GO:0040016)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|homophilic cell adhesion (GO:0007156)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|positive regulation of autophagy (GO:0010508)|regulation of cell-matrix adhesion (GO:0001952)|regulation of clathrin-mediated endocytosis (GO:2000369)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|T cell receptor signaling pathway (GO:0050852)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytosol (GO:0005829)|nucleus (GO:0005634)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)			NS(1)|breast(3)|endometrium(5)|kidney(2)|large_intestine(4)|lung(17)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(4)	41					Caffeine(DB00201)	TACTGAGACAGCAGGAATGTG	0.393																																					p.A686V		.											.	.	.	0			c.C2057T						.						87.0	77.0	80.0					3																	138407796		2203	4300	6503	SO:0001583	missense	5291	exon14			GAGACAGCAGGAA		CCDS3104.1	3q22.3	2013-09-19	2012-07-13		ENSG00000051382	ENSG00000051382	2.7.1.153		8976	protein-coding gene	gene with protein product		602925	"""phosphoinositide-3-kinase, catalytic, beta polypeptide"""	PIK3C1		8246984	Standard	NM_006219		Approved		uc011bmq.3	P42338	OTTHUMG00000159893	ENST00000477593.1:c.2057C>T	3.37:g.138407796G>A	ENSP00000418143:p.Ala686Val	Somatic	43	0		WXS	Illumina HiSeq	.	55	4	NM_006219	D3DNF0|Q24JU2	Missense_Mutation	SNP	ENST00000477593.1	37	CCDS3104.1	.	.	.	.	.	.	.	.	.	.	G	21.1	4.091123	0.76756	.	.	ENSG00000051382	ENST00000477593;ENST00000544716;ENST00000289153	T;T;T	0.64803	-0.12;-0.12;-0.12	5.24	5.24	0.73138	Phosphoinositide 3-kinase, accessory (PIK) domain (3);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.68016	0.2955	M	0.70275	2.135	0.80722	D	1	B;B;P	0.37423	0.433;0.277;0.594	B;B;B	0.41946	0.371;0.297;0.17	T	0.67624	-0.5623	10	0.36615	T	0.2	-6.8373	19.2063	0.93732	0.0:0.0:1.0:0.0	.	686;273;132	P42338;B4DZI3;Q68DL0	PK3CB_HUMAN;.;.	V	686;132;686	ENSP00000418143:A686V;ENSP00000438259:A132V;ENSP00000289153:A686V	ENSP00000289153:A686V	A	-	2	0	PIK3CB	139890486	1.000000	0.71417	0.977000	0.42913	0.818000	0.46254	9.739000	0.98837	2.592000	0.87571	0.655000	0.94253	GCT	.		0.393	PIK3CB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358019.1		
MVD	4597	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	16	88721635	88721635	+	Missense_Mutation	SNP	C	C	T			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr16:88721635C>T	ENST00000301012.3	-	7	898	c.869G>A	c.(868-870)cGc>cAc	p.R290H	MVD_ENST00000568709.1_5'Flank	NM_002461.1	NP_002452.1	P53602	MVD1_HUMAN	mevalonate (diphospho) decarboxylase	290					cellular protein metabolic process (GO:0044267)|cholesterol biosynthetic process (GO:0006695)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|dolichyl diphosphate biosynthetic process (GO:0006489)|isopentenyl diphosphate biosynthetic process, mevalonate pathway (GO:0019287)|isoprenoid biosynthetic process (GO:0008299)|positive regulation of cell proliferation (GO:0008284)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	ATP binding (GO:0005524)|diphosphomevalonate decarboxylase activity (GO:0004163)|Hsp70 protein binding (GO:0030544)|protein homodimerization activity (GO:0042803)			endometrium(3)|large_intestine(1)|lung(7)|ovary(1)	12				BRCA - Breast invasive adenocarcinoma(80;0.0478)		GGCGTTGAAGCGGTGCACCAG	0.642																																					p.R290H		.											.	.	.	0			c.G869A						.						172.0	137.0	149.0					16																	88721635		2184	4284	6468	SO:0001583	missense	4597	exon7			TTGAAGCGGTGCA	U49260	CCDS10968.1	16q24.3	2010-04-29			ENSG00000167508	ENSG00000167508	4.1.1.33		7529	protein-coding gene	gene with protein product	"""mevalonate pyrophosphate decarboxylase"""	603236				8626466	Standard	NM_002461		Approved	MPD	uc002flg.1	P53602	OTTHUMG00000137865	ENST00000301012.3:c.869G>A	16.37:g.88721635C>T	ENSP00000301012:p.Arg290His	Somatic	25	0		WXS	Illumina HiSeq	.	42	12	NM_002461	Q53Y65	Missense_Mutation	SNP	ENST00000301012.3	37	CCDS10968.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	16.33|16.33	3.092188|3.092188	0.55968|0.55968	.|.	.|.	ENSG00000167508|ENSG00000167508	ENST00000378400|ENST00000301012	.|T	.|0.29397	.|1.57	4.26|4.26	4.26|4.26	0.50523|0.50523	.|.	.|0.234802	.|0.45606	.|D	.|0.000352	T|T	0.31389|0.31389	0.0795|0.0795	M|M	0.72624|0.72624	2.21|2.21	0.45076|0.45076	D|D	0.998093|0.998093	.|B	.|0.23990	.|0.095	.|B	.|0.12837	.|0.008	T|T	0.15263|0.15263	-1.0443|-1.0443	6|10	0.87932|0.44086	D|T	0|0.13	-6.7066|-6.7066	10.7069|10.7069	0.45960|0.45960	0.0:0.9109:0.0:0.0891|0.0:0.9109:0.0:0.0891	.|.	.|290	.|P53602	.|MVD1_HUMAN	T|H	118|290	.|ENSP00000301012:R290H	ENSP00000367653:A118T|ENSP00000301012:R290H	A|R	-|-	1|2	0|0	MVD|MVD	87249136|87249136	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.802000|0.802000	0.45316|0.45316	2.637000|2.637000	0.46553|0.46553	2.092000|2.092000	0.63282|0.63282	0.491000|0.491000	0.48974|0.48974	GCT|CGC	.		0.642	MVD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269547.2	NM_002461	
NYAP2	57624	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	226447575	226447575	+	Nonsense_Mutation	SNP	C	C	A			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr2:226447575C>A	ENST00000272907.6	+	4	1855	c.1442C>A	c.(1441-1443)tCg>tAg	p.S481*	NYAP2_ENST00000409269.2_Intron	NM_020864.1	NP_065915.1	Q9P242	NYAP2_HUMAN	neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adaptor 2	481					neuron projection morphogenesis (GO:0048812)|phosphatidylinositol 3-kinase signaling (GO:0014065)												AGACCCGTGTCGCAAGATGGG	0.672																																					p.S481X		.											.	.	.	0			c.C1442A						.						36.0	40.0	39.0					2																	226447575		1993	4169	6162	SO:0001587	stop_gained	57624	exon4			CCGTGTCGCAAGA	AB040919	CCDS46529.1	2q36.3	2011-11-30	2011-11-30	2011-11-30	ENSG00000144460	ENSG00000144460			29291	protein-coding gene	gene with protein product		615478	"""KIAA1486"""	KIAA1486		10819331, 21946561	Standard	NM_020864		Approved		uc002voe.2	Q9P242	OTTHUMG00000153450	ENST00000272907.6:c.1442C>A	2.37:g.226447575C>A	ENSP00000272907:p.Ser481*	Somatic	37	0		WXS	Illumina HiSeq	.	71	24	NM_020864	A2RRN4|Q96NL2	Nonsense_Mutation	SNP	ENST00000272907.6	37	CCDS46529.1	.	.	.	.	.	.	.	.	.	.	C	41	8.657250	0.98903	.	.	ENSG00000144460	ENST00000272907	.	.	.	5.5	4.43	0.53597	.	0.739668	0.13238	N	0.403072	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-10.6316	9.8733	0.41189	0.0:0.8456:0.0:0.1544	.	.	.	.	X	481	.	ENSP00000272907:S481X	S	+	2	0	KIAA1486	226155819	0.976000	0.34144	0.997000	0.53966	0.938000	0.57974	2.024000	0.41049	2.584000	0.87258	0.563000	0.77884	TCG	.		0.672	NYAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331258.1	NM_020864	
LAMA3	3909	hgsc.bcm.edu	37	18	21513818	21513818	+	Silent	SNP	C	C	T			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr18:21513818C>T	ENST00000313654.9	+	67	9022	c.8781C>T	c.(8779-8781)tgC>tgT	p.C2927C	LAMA3_ENST00000587184.1_Silent_p.C1262C|LAMA3_ENST00000399516.3_Silent_p.C2871C|LAMA3_ENST00000588770.1_3'UTR|LAMA3_ENST00000269217.6_Silent_p.C1318C	NM_198129.1	NP_937762.1	Q16787	LAMA3_HUMAN	laminin, alpha 3	2927	Laminin G-like 3. {ECO:0000255|PROSITE- ProRule:PRU00122}.				cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-5 complex (GO:0005610)	structural molecule activity (GO:0005198)			NS(2)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(24)|lung(54)|ovary(8)|prostate(6)|skin(7)|urinary_tract(4)	128	all_cancers(21;7.81e-05)|all_epithelial(16;4.45e-07)|Lung NSC(20;0.00156)|all_lung(20;0.00508)|Colorectal(14;0.0202)|Ovarian(20;0.17)					TGGGAGGCTGCAGTTTAAACA	0.418																																					p.C2927C		.											.	.	.	0			c.C8781T						.						125.0	108.0	114.0					18																	21513818		2203	4300	6503	SO:0001819	synonymous_variant	3909	exon67			AGGCTGCAGTTTA	L34155	CCDS11880.1, CCDS42419.1, CCDS45838.1, CCDS59307.1	18q11.2	2013-03-01	2002-08-29		ENSG00000053747	ENSG00000053747		"""Laminins"""	6483	protein-coding gene	gene with protein product		600805	"""laminin, alpha 3 (nicein (150kD), kalinin (165kD), BM600 (150kD), epilegrin)"""	LAMNA		8077230	Standard	NM_000227		Approved	nicein-150kDa, kalinin-165kDa, BM600-150kDa, epiligrin	uc002kuq.3	Q16787	OTTHUMG00000131874	ENST00000313654.9:c.8781C>T	18.37:g.21513818C>T		Somatic	44	0		WXS	Illumina HiSeq	.	90	5	NM_198129	B0YJ33|Q13679|Q13680|Q6VU67|Q6VU68|Q6VU69|Q76E14|Q96TG0	Silent	SNP	ENST00000313654.9	37	CCDS42419.1																																																																																			.		0.418	LAMA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254824.3	NM_000227, NM_198129	
CSNK1A1L	122011	hgsc.bcm.edu	37	13	37678436	37678436	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr13:37678436G>T	ENST00000379800.3	-	1	1367	c.958C>A	c.(958-960)Caa>Aaa	p.Q320K		NM_145203.5	NP_660204.2	Q8N752	KC1AL_HUMAN	casein kinase 1, alpha 1-like	320					cell morphogenesis (GO:0000902)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.Q320K(1)		NS(1)|breast(3)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(10)|lung(11)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	37		Lung NSC(96;7.97e-05)|Breast(139;0.0615)|Lung SC(185;0.0743)|Prostate(109;0.109)		all cancers(112;3.58e-07)|Epithelial(112;1.29e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00695)|BRCA - Breast invasive adenocarcinoma(63;0.0117)|GBM - Glioblastoma multiforme(144;0.0407)		GTCTGGGTTTGGGCCTGCTGA	0.468																																					p.Q320K		.											CSNK1A1L,NS,carcinoma,0,1	CSNK1A1L	0	1	Substitution - Missense(1)	lung(1)	c.C958A						.						154.0	148.0	150.0					13																	37678436		2203	4300	6503	SO:0001583	missense	122011	exon1			GGGTTTGGGCCTG	BC028723	CCDS9363.1	13q13.2	2008-02-05			ENSG00000180138	ENSG00000180138			20289	protein-coding gene	gene with protein product							Standard	NM_145203		Approved	MGC33182	uc001uwm.1	Q8N752	OTTHUMG00000016748	ENST00000379800.3:c.958C>A	13.37:g.37678436G>T	ENSP00000369126:p.Gln320Lys	Somatic	30	0		WXS	Illumina HiSeq	.	43	2	NM_145203	Q5T2N2	Missense_Mutation	SNP	ENST00000379800.3	37	CCDS9363.1	.	.	.	.	.	.	.	.	.	.	G	10.04	1.242345	0.22796	.	.	ENSG00000180138	ENST00000379800	T	0.08807	3.05	1.01	0.0897	0.14460	.	.	.	.	.	T	0.04770	0.0129	N	0.19112	0.55	0.26743	N	0.970352	P	0.36392	0.551	B	0.40602	0.334	T	0.32981	-0.9886	9	0.06625	T	0.88	.	5.1036	0.14772	0.2355:0.0:0.7645:0.0	.	320	Q8N752	KC1AL_HUMAN	K	320	ENSP00000369126:Q320K	ENSP00000369126:Q320K	Q	-	1	0	CSNK1A1L	36576436	1.000000	0.71417	0.024000	0.17045	0.071000	0.16799	6.275000	0.72594	-0.013000	0.14199	0.561000	0.74099	CAA	.		0.468	CSNK1A1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044563.1	NM_145203	
MACF1	23499	hgsc.bcm.edu	37	1	39766025	39766025	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr1:39766025G>T	ENST00000372915.3	+	21	2727	c.2640G>T	c.(2638-2640)agG>agT	p.R880S	MACF1_ENST00000539005.1_Missense_Mutation_p.R880S|MACF1_ENST00000567887.1_Missense_Mutation_p.R912S|MACF1_ENST00000545844.1_Missense_Mutation_p.R880S|MACF1_ENST00000361689.2_Missense_Mutation_p.R880S|MACF1_ENST00000317713.7_Missense_Mutation_p.R880S|MACF1_ENST00000476350.1_3'UTR|MACF1_ENST00000564288.1_Missense_Mutation_p.R875S			Q9UPN3	MACF1_HUMAN	microtubule-actin crosslinking factor 1	880	SH3.				ATP catabolic process (GO:0006200)|cell cycle arrest (GO:0007050)|Golgi to plasma membrane protein transport (GO:0043001)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of epithelial cell migration (GO:0010632)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule-based process (GO:0032886)|Wnt signaling pathway (GO:0016055)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)			breast(11)|central_nervous_system(5)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(36)|lung(78)|ovary(12)|prostate(2)|skin(9)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(10)	203	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			GTGACTACAGGCAGATCGAGG	0.473																																					p.R880S		.											.	.	.	0			c.G2640T						.						87.0	71.0	77.0					1																	39766025		2203	4300	6503	SO:0001583	missense	23499	exon23			CTACAGGCAGATC	AB007934	CCDS435.1	1p32-p31	2013-01-10			ENSG00000127603	ENSG00000127603		"""EF-hand domain containing"""	13664	protein-coding gene	gene with protein product	"""actin cross-linking factor"", ""620 kDa actin binding protein"", ""macrophin 1"", ""trabeculin-alpha"", ""actin cross-linking family protein 7"""	608271				7635207, 10529403	Standard	NM_012090		Approved	KIAA0465, ACF7, ABP620, KIAA1251, MACF, FLJ45612, FLJ46776	uc031pmc.1	Q9UPN3	OTTHUMG00000007754	ENST00000372915.3:c.2640G>T	1.37:g.39766025G>T	ENSP00000362006:p.Arg880Ser	Somatic	19	0		WXS	Illumina HiSeq	.	66	5	NM_012090	B1ALC5|E9PJT0|O75053|Q5VW20|Q8WXY1|Q8WXY2|Q96PK2|Q9H540|Q9UKP0|Q9ULG9	Missense_Mutation	SNP	ENST00000372915.3	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	14.44|14.44	2.535261|2.535261	0.45176|0.45176	.|.	.|.	ENSG00000127603|ENSG00000127603	ENST00000372925|ENST00000545844;ENST00000372915;ENST00000361689;ENST00000317713;ENST00000539005;ENST00000524432;ENST00000530262;ENST00000372900	.|T;T;T;T;T;T;T	.|0.80393	.|0.16;-1.37;0.16;0.16;0.16;0.16;0.16	5.81|5.81	0.44|0.44	0.16572|0.16572	.|.	.|.	.|.	.|.	.|.	D|D	0.83294|0.83294	0.5223|0.5223	M|M	0.65320|0.65320	2|2	0.80722|0.80722	D|D	1|1	.|D;D	.|0.71674	.|0.993;0.998	.|D;D	.|0.71184	.|0.91;0.972	T|T	0.79142|0.79142	-0.1925|-0.1925	5|9	.|0.87932	.|D	.|0	.|.	2.8031|2.8031	0.05420|0.05420	0.2603:0.1115:0.5137:0.1145|0.2603:0.1115:0.5137:0.1145	.|.	.|880;845	.|F8W8Q1;Q9UPN3-3	.|.;.	S|S	14|880;880;880;880;880;838;1029;1042	.|ENSP00000439537:R880S;ENSP00000362006:R880S;ENSP00000354573:R880S;ENSP00000313438:R880S;ENSP00000444364:R880S;ENSP00000435070:R838S;ENSP00000437059:R1029S	.|ENSP00000313438:R880S	A|R	+|+	1|3	0|2	MACF1|MACF1	39538612|39538612	0.883000|0.883000	0.30277|0.30277	0.998000|0.998000	0.56505|0.56505	0.777000|0.777000	0.43975|0.43975	-0.061000|-0.061000	0.11693|0.11693	0.092000|0.092000	0.17331|0.17331	-0.140000|-0.140000	0.14226|0.14226	GCA|AGG	.		0.473	MACF1-028	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000392096.1	NM_033044	
NDST4	64579	hgsc.bcm.edu	37	4	115858480	115858480	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr4:115858480G>T	ENST00000264363.2	-	5	2079	c.1401C>A	c.(1399-1401)agC>agA	p.S467R		NM_022569.1	NP_072091.1	Q9H3R1	NDST4_HUMAN	N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 4	467	Heparan sulfate N-deacetylase 4.				heparan sulfate proteoglycan biosynthetic process (GO:0015012)|heparin biosynthetic process (GO:0030210)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	[heparan sulfate]-glucosamine N-sulfotransferase activity (GO:0015016)|deacetylase activity (GO:0019213)			NS(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(5)|lung(43)|ovary(1)|prostate(7)|skin(11)|upper_aerodigestive_tract(1)|urinary_tract(1)	81		Ovarian(17;0.156)		OV - Ovarian serous cystadenocarcinoma(123;0.000562)		TCACCATGATGCTATTGTGAA	0.443																																					p.S467R		.											.	.	.	0			c.C1401A						.						165.0	154.0	158.0					4																	115858480		2203	4300	6503	SO:0001583	missense	64579	exon5			CATGATGCTATTG	AB036429	CCDS3706.1	4q26	2008-02-05			ENSG00000138653	ENSG00000138653		"""Sulfotransferases, membrane-bound"""	20779	protein-coding gene	gene with protein product		615039				11087757	Standard	NM_022569		Approved		uc003ibu.3	Q9H3R1	OTTHUMG00000132916	ENST00000264363.2:c.1401C>A	4.37:g.115858480G>T	ENSP00000264363:p.Ser467Arg	Somatic	49	0		WXS	Illumina HiSeq	.	58	3	NM_022569	Q2KHM8	Missense_Mutation	SNP	ENST00000264363.2	37	CCDS3706.1	.	.	.	.	.	.	.	.	.	.	G	16.24	3.066727	0.55539	.	.	ENSG00000138653	ENST00000264363	T	0.35789	1.29	5.77	4.93	0.64822	.	0.479163	0.28527	N	0.015036	T	0.25827	0.0629	N	0.22421	0.69	0.38985	D	0.959037	B	0.02656	0.0	B	0.10450	0.005	T	0.08411	-1.0723	10	0.66056	D	0.02	.	10.5196	0.44912	0.1486:0.0:0.8514:0.0	.	467	Q9H3R1	NDST4_HUMAN	R	467	ENSP00000264363:S467R	ENSP00000264363:S467R	S	-	3	2	NDST4	116077929	1.000000	0.71417	0.998000	0.56505	0.974000	0.67602	4.947000	0.63583	1.424000	0.47217	0.655000	0.94253	AGC	.		0.443	NDST4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256427.1	NM_022569	
DDHD1	80821	hgsc.bcm.edu	37	14	53619480	53619480	+	Missense_Mutation	SNP	T	T	C	rs140904345|rs55671452|rs200797826	byFrequency	TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr14:53619480T>C	ENST00000323669.5	-	1	336	c.337A>G	c.(337-339)Agc>Ggc	p.S113G	RP11-547D23.1_ENST00000554235.1_RNA|DDHD1_ENST00000395606.1_Missense_Mutation_p.S113G|DDHD1_ENST00000357758.3_Missense_Mutation_p.S113G|AL356020.1_ENST00000584587.1_RNA	NM_001160148.1	NP_001153620.1	Q8NEL9	DDHD1_HUMAN	DDHD domain containing 1	113					cell death (GO:0008219)|lipid catabolic process (GO:0016042)	cytoplasm (GO:0005737)	hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			breast(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(4)|lung(11)|ovary(3)|prostate(1)	25	Breast(41;0.037)					GACAAGGAGCTGCCGCCGCCG	0.701																																					p.S113G		.											.,102	.	202	0			c.A337G						.						6.0	8.0	7.0					14																	53619480		1971	3847	5818	SO:0001583	missense	80821	exon1			AGGAGCTGCCGCC	AB051492	CCDS9714.1, CCDS53895.1, CCDS53896.1	14q21	2012-11-23			ENSG00000100523	ENSG00000100523			19714	protein-coding gene	gene with protein product	"""phosphatidic acid-preferring phospholipase A1"""	614603	"""spastic paraplegia 28 (autosomal recessive)"""	SPG28		11214970, 20359546	Standard	NM_030637		Approved	KIAA1705, PA-PLA1	uc001xai.3	Q8NEL9	OTTHUMG00000140305	ENST00000323669.5:c.337A>G	14.37:g.53619480T>C	ENSP00000327104:p.Ser113Gly	Somatic	13	0		WXS	Illumina HiSeq	.	22	0	NM_001160147	G5E9D1|Q8WVH3|Q96LL2|Q9C0F8	Missense_Mutation	SNP	ENST00000323669.5	37	CCDS53895.1	.	.	.	.	.	.	.	.	.	.	T	16.03	3.006520	0.54361	.	.	ENSG00000100523	ENST00000323669;ENST00000395606;ENST00000357758;ENST00000395610	.	.	.	3.77	2.61	0.31194	.	0.746995	0.12231	N	0.487421	T	0.35566	0.0936	N	0.22421	0.69	0.20975	N	0.999816	P;B;P	0.52577	0.954;0.0;0.954	D;B;D	0.66351	0.916;0.0;0.943	T	0.17167	-1.0378	9	0.18276	T	0.48	-5.0646	3.2899	0.06945	0.0:0.2878:0.2128:0.4994	.	113;113;113	G5E9D1;Q8NEL9;Q8NEL9-2	.;DDHD1_HUMAN;.	G	113	.	ENSP00000327104:S113G	S	-	1	0	DDHD1	52689230	.	.	0.767000	0.31495	0.958000	0.62258	.	.	0.510000	0.28216	0.374000	0.22700	AGC	.		0.701	DDHD1-003	KNOWN	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000276901.1		
MT-ND1	4535	hgsc.bcm.edu	37	M	762	762	+	5'Flank	SNP	G	G	A			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chrM:762G>A	ENST00000361390.2	+	0	0				MT-TL1_ENST00000386347.1_RNA|MT-RNR1_ENST00000389680.2_RNA|MT-RNR2_ENST00000387347.2_RNA|MT-TF_ENST00000387314.1_RNA|MT-TV_ENST00000387342.1_RNA			P03886	NU1M_HUMAN	mitochondrially encoded NADH dehydrogenase 1						cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial membrane (GO:0031966)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(1)|endometrium(13)|kidney(17)|lung(2)|prostate(1)	34					Desflurane(DB01189)|Halothane(DB01159)|Isoflurane(DB00753)|Methoxyflurane(DB01028)|Sevoflurane(DB01236)	GACAAGCATCAAGCACGCAGC	0.453																																					.		.											.	.	.	0			.						.																																			SO:0001631	upstream_gene_variant	6052	.			CATCAAGCACGCA			mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198888	ENSG00000198888	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7455	protein-coding gene	gene with protein product	"""complex I ND1 subunit"", ""NADH-ubiquinone oxidoreductase chain 1"""	516000	"""NADH dehydrogenase 1"""	MTND1			Standard			Approved	ND1, NAD1		P03886			M.37:g.762G>A	Exception_encountered	Somatic	143	0		WXS	Illumina HiSeq	.	876	117	.	C0JKH6|Q37523	RNA	SNP	ENST00000361390.2	37																																																																																				.		0.453	MT-ND1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024026	
CLGN	1047	hgsc.bcm.edu	37	4	141321605	141321605	+	Silent	SNP	G	G	T	rs138156952		TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr4:141321605G>T	ENST00000325617.5	-	7	1040	c.600C>A	c.(598-600)ccC>ccA	p.P200P	CLGN_ENST00000537281.1_Silent_p.P200P|CLGN_ENST00000414773.1_Silent_p.P200P	NM_004362.2	NP_004353.1	O14967	CLGN_HUMAN	calmegin	200					binding of sperm to zona pellucida (GO:0007339)|protein complex assembly (GO:0006461)|protein folding (GO:0006457)|single fertilization (GO:0007338)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)	calcium ion binding (GO:0005509)|unfolded protein binding (GO:0051082)	p.P200P(1)		breast(2)|endometrium(3)|kidney(1)|large_intestine(2)|liver(2)|lung(5)|ovary(2)|prostate(3)|skin(4)|urinary_tract(1)	25	all_hematologic(180;0.162)					CTCCAGTTTTGGGATGTTTAT	0.333																																					p.P200P		.											CLGN,hand,malignant_melanoma,0,1	CLGN	0	1	Substitution - coding silent(1)	skin(1)	c.C600A						.						105.0	110.0	108.0					4																	141321605		2203	4300	6503	SO:0001819	synonymous_variant	1047	exon8			AGTTTTGGGATGT	D86322	CCDS3751.1	4q28.3-q31.1	2008-02-05			ENSG00000153132	ENSG00000153132			2060	protein-coding gene	gene with protein product		601858					Standard	NM_004362		Approved		uc003iii.3	O14967	OTTHUMG00000133414	ENST00000325617.5:c.600C>A	4.37:g.141321605G>T		Somatic	31	0		WXS	Illumina HiSeq	.	45	2	NM_001130675	B3KS90|B4DXV8|D3DNY8	Silent	SNP	ENST00000325617.5	37	CCDS3751.1																																																																																			.		0.333	CLGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257272.2	NM_004362	
MT-ND6	4541	hgsc.bcm.edu	37	M	15961	15961	+	5'Flank	SNP	G	G	A			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chrM:15961G>A	ENST00000361681.2	-	0	0				MT-TP_ENST00000387461.2_RNA|MT-TE_ENST00000387459.1_RNA|MT-TT_ENST00000387460.2_RNA			P03923	NU6M_HUMAN	mitochondrially encoded NADH dehydrogenase 6						cellular metabolic process (GO:0044237)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|respiratory chain (GO:0070469)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(1)|endometrium(10)|kidney(17)|urinary_tract(1)	29						GACAAATCAGAGAAAAAGTCT	0.378																																					.		.											.	.	.	0			.						.																																			SO:0001631	upstream_gene_variant	0	.			ATCAGAGAAAAAG			mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198695	ENSG00000198695	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7462	protein-coding gene	gene with protein product	"""complex I ND6 subunit"", ""NADH-ubiquinone oxidoreductase chain 6"""	516006	"""NADH dehydrogenase 6"""	MTND6			Standard			Approved	NAD6, ND6		P03923			M.37:g.15961G>A	Exception_encountered	Somatic	7	0		WXS	Illumina HiSeq	.	35	8	.	Q34774|Q8HG30	RNA	SNP	ENST00000361681.2	37																																																																																				.		0.378	MT-ND6-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024037	
TAF1L	138474	hgsc.bcm.edu	37	9	32631851	32631851	+	Missense_Mutation	SNP	G	G	A			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr9:32631851G>A	ENST00000242310.4	-	1	3816	c.3727C>T	c.(3727-3729)Cgg>Tgg	p.R1243W	RP11-555J4.4_ENST00000430787.1_RNA	NM_153809.2	NP_722516.1	Q8IZX4	TAF1L_HUMAN	TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 210kDa-like	1243					DNA-templated transcription, initiation (GO:0006352)|histone acetylation (GO:0016573)|male meiosis (GO:0007140)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	transcription factor TFIID complex (GO:0005669)	DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|lysine-acetylated histone binding (GO:0070577)|protein serine/threonine kinase activity (GO:0004674)|TBP-class protein binding (GO:0017025)	p.R1243W(2)		breast(6)|central_nervous_system(4)|endometrium(14)|kidney(11)|large_intestine(32)|liver(2)|lung(68)|ovary(2)|pancreas(2)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)	159			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.00301)		ATCCTCCGCCGTTCTTTCCGC	0.453																																					p.R1243W		.											TAF1L,NS,carcinoma,+2,2	TAF1L	+2	2	Substitution - Missense(2)	large_intestine(1)|endometrium(1)	c.C3727T						.						98.0	96.0	96.0					9																	32631851		2203	4300	6503	SO:0001583	missense	138474	exon1			TCCGCCGTTCTTT	AF390562	CCDS35003.1	9p12	2007-07-27	2007-07-27		ENSG00000122728	ENSG00000122728			18056	protein-coding gene	gene with protein product		607798	"""TAF1-like RNA polymerase II, TATA box binding protein (TBP)-associated factor, 210kDa"""			12217962	Standard	NM_153809		Approved		uc003zrg.1	Q8IZX4	OTTHUMG00000019747	ENST00000242310.4:c.3727C>T	9.37:g.32631851G>A	ENSP00000418379:p.Arg1243Trp	Somatic	37	0		WXS	Illumina HiSeq	.	79	3	NM_153809	Q0VG57	Missense_Mutation	SNP	ENST00000242310.4	37	CCDS35003.1	.	.	.	.	.	.	.	.	.	.	G	13.53	2.265050	0.40095	.	.	ENSG00000122728	ENST00000242310	T	0.64260	-0.09	1.04	-0.675	0.11364	.	0.106321	0.64402	D	0.000005	T	0.59622	0.2207	L	0.29908	0.895	0.45528	D	0.99848	D	0.89917	1.0	D	0.71414	0.973	T	0.59369	-0.7467	10	0.87932	D	0	.	4.4056	0.11407	0.0:0.0:0.419:0.5809	.	1243	Q8IZX4	TAF1L_HUMAN	W	1243	ENSP00000418379:R1243W	ENSP00000418379:R1243W	R	-	1	2	TAF1L	32621851	1.000000	0.71417	0.784000	0.31847	0.128000	0.20619	1.695000	0.37763	0.507000	0.28148	0.195000	0.17529	CGG	.		0.453	TAF1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052012.2		
ZNF106	64397	hgsc.bcm.edu	37	15	42740764	42740764	+	Silent	SNP	G	G	T			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr15:42740764G>T	ENST00000263805.4	-	3	2898	c.2572C>A	c.(2572-2574)Cga>Aga	p.R858R	ZNF106_ENST00000565380.1_Silent_p.R86R|ZNF106_ENST00000565611.1_Silent_p.R43R	NM_001284306.1|NM_001284307.1|NM_022473.1	NP_001271235.1|NP_001271236.1|NP_071918.1	Q9H2Y7	ZN106_HUMAN	zinc finger protein 106	858					insulin receptor signaling pathway (GO:0008286)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)	p.R858*(1)									GAAAGGCTTCGCTTTCTTGCC	0.498																																					p.R858R		.											ZFP106,caecum,carcinoma,0,1	ZFP106	0	1	Substitution - Nonsense(1)	large_intestine(1)	c.C2572A						.						66.0	61.0	63.0					15																	42740764		2203	4299	6502	SO:0001819	synonymous_variant	64397	exon3			GGCTTCGCTTTCT	AF205632	CCDS32208.1, CCDS61602.1, CCDS61603.1	15q15.1	2012-11-27	2012-11-27		ENSG00000103994	ENSG00000103994		"""Zinc fingers, C2H2-type"""	12886	protein-coding gene	gene with protein product	"""SH3-domain binding protein 3"""		"""zinc finger protein 106 homolog (mouse)"""	ZFP106			Standard	XM_005254591		Approved	ZNF474, SH3BP3	uc001zpw.3	Q9H2Y7	OTTHUMG00000173244	ENST00000263805.4:c.2572C>A	15.37:g.42740764G>T		Somatic	50	0		WXS	Illumina HiSeq	.	59	4	NM_022473	B4DZ40|E9PE29|Q6NSD9|Q6PEK1|Q86T43|Q86T45|Q86T50|Q86T58|Q86TA9|Q96M37|Q9H7B8	Silent	SNP	ENST00000263805.4	37	CCDS32208.1																																																																																			.		0.498	ZNF106-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422587.1	NM_022473	
ANKRD20A5P	440482	hgsc.bcm.edu	37	18	14214318	14214318	+	IGR	SNP	G	G	T	rs76153608|rs557176001		TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr18:14214318G>T								RNU6-316P (23513 upstream) : RP11-757O6.1 (30305 downstream)																							TTAATATTAGGTTTTTTTTTT	0.308																																					.		.											.	.	.	0			.						.																																			SO:0001628	intergenic_variant	440482	.			TATTAGGTTTTTT																													18.37:g.14214318G>T		Somatic	138	0		WXS	Illumina HiSeq	.	141	6	.		RNA	SNP		37																																																																																				.	0	0.308								
PDCL	5082	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	9	125588973	125588973	+	Nonsense_Mutation	SNP	G	G	A			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr9:125588973G>A	ENST00000259467.4	-	2	259	c.94C>T	c.(94-96)Cga>Tga	p.R32*		NM_005388.4	NP_005379.3	Q13371	PHLP_HUMAN	phosducin-like	32					heterotrimeric G-protein complex assembly (GO:1902605)|intracellular signal transduction (GO:0035556)|negative regulation of protein refolding (GO:0061084)|protein folding (GO:0006457)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|signal transduction (GO:0007165)|visual perception (GO:0007601)	cytoplasm (GO:0005737)	receptor signaling protein activity (GO:0005057)			endometrium(1)|large_intestine(2)|lung(5)|skin(1)|stomach(1)	10						CATCTGCCTCGGTCCTTGTCC	0.552																																					p.R32X		.											PDCL,NS,carcinoma,0,1	PDCL	0	0			c.C94T						.						134.0	108.0	116.0					9																	125588973		2203	4300	6503	SO:0001587	stop_gained	5082	exon2			TGCCTCGGTCCTT	AF083325	CCDS6845.1	9q12-q13	2008-07-21			ENSG00000136940	ENSG00000136940			8770	protein-coding gene	gene with protein product		604421				10095058	Standard	NM_005388		Approved	PhLP, DKFZp564M1863	uc004bmz.2	Q13371	OTTHUMG00000020624	ENST00000259467.4:c.94C>T	9.37:g.125588973G>A	ENSP00000259467:p.Arg32*	Somatic	29	0		WXS	Illumina HiSeq	.	57	19	NM_005388	Q4VXB6|Q96AF1|Q9UEW7|Q9UFL0|Q9UNX1|Q9UNX2	Nonsense_Mutation	SNP	ENST00000259467.4	37	CCDS6845.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	12.18|12.18	1.861001|1.861001	0.32884|0.32884	.|.	.|.	ENSG00000136940|ENSG00000136940	ENST00000394285|ENST00000259467	.|.	.|.	.|.	5.7|5.7	-8.06|-8.06	0.01102|0.01102	.|.	.|0.785171	.|0.12689	.|N	.|0.447311	T|.	0.45716|.	0.1356|.	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.53436|.	-0.8439|.	3|.	.|.	.|.	.|.	1.0069|1.0069	14.1403|14.1403	0.65316|0.65316	0.0:0.6665:0.1209:0.2126|0.0:0.6665:0.1209:0.2126	.|.	.|.	.|.	.|.	L|X	20|32	.|.	.|.	P|R	-|-	2|1	0|2	PDCL|PDCL	124628794|124628794	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.005000|0.005000	0.04900|0.04900	-0.284000|-0.284000	0.08422|0.08422	-1.897000|-1.897000	0.01101|0.01101	-0.176000|-0.176000	0.13171|0.13171	CCG|CGA	.		0.552	PDCL-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053956.1	NM_005388	
TMPRSS11A	339967	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	4	68777188	68777188	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr4:68777188G>T	ENST00000334830.7	-	10	1884	c.1138C>A	c.(1138-1140)Ctg>Atg	p.L380M	TMPRSS11A_ENST00000508048.1_Missense_Mutation_p.L376M|TMPRSS11A_ENST00000396188.2_Missense_Mutation_p.L377M|UBA6-AS1_ENST00000500538.2_RNA			Q6ZMR5	TM11A_HUMAN	transmembrane protease, serine 11A	380	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				cell cycle (GO:0007049)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	serine-type endopeptidase activity (GO:0004252)			breast(1)|cervix(2)|kidney(1)|large_intestine(8)|lung(11)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)	29						GTATCTTTCAGATCCCTTGTG	0.358																																					p.L380M	NSCLC(26;2 894 10941 14480 22546)	.											.	.	.	0			c.C1138A						.						121.0	115.0	117.0					4																	68777188		2203	4300	6503	SO:0001583	missense	339967	exon10			CTTTCAGATCCCT	AF071882	CCDS3519.1	4q13.2	2010-04-13			ENSG00000187054	ENSG00000187054		"""Serine peptidases / Transmembrane"""	27954	protein-coding gene	gene with protein product		611704				15328353	Standard	NM_182606		Approved	ECRG1	uc003hdr.1	Q6ZMR5	OTTHUMG00000129303	ENST00000334830.7:c.1138C>A	4.37:g.68777188G>T	ENSP00000334611:p.Leu380Met	Somatic	41	0		WXS	Illumina HiSeq	.	52	5	NM_182606	J3KNQ8|Q2NKI9|Q6JE90|Q7RTY4|Q86TK8	Missense_Mutation	SNP	ENST00000334830.7	37	CCDS3519.1	.	.	.	.	.	.	.	.	.	.	G	7.190	0.591258	0.13812	.	.	ENSG00000187054	ENST00000508048;ENST00000334830;ENST00000396188;ENST00000513536	D;D;D;D	0.88741	-2.42;-2.42;-2.42;-2.42	5.66	-1.7	0.08159	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	1.210600	0.06017	N	0.650682	T	0.80138	0.4568	N	0.20685	0.6	0.09310	N	1	P;P	0.49696	0.927;0.927	P;P	0.45474	0.482;0.482	T	0.70539	-0.4844	10	0.35671	T	0.21	.	3.4072	0.07345	0.3422:0.0:0.2424:0.4154	.	377;380	B5MDI9;Q6ZMR5	.;TM11A_HUMAN	M	376;380;377;344	ENSP00000426911:L376M;ENSP00000334611:L380M;ENSP00000379491:L377M;ENSP00000427621:L344M	ENSP00000334611:L380M	L	-	1	2	TMPRSS11A	68459783	0.000000	0.05858	0.000000	0.03702	0.018000	0.09664	-0.057000	0.11768	-0.212000	0.10109	0.460000	0.39030	CTG	.		0.358	TMPRSS11A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251433.3	NM_182606	
WNK1	65125	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	12	966367	966367	+	Missense_Mutation	SNP	A	A	G			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr12:966367A>G	ENST00000315939.6	+	5	1995	c.1352A>G	c.(1351-1353)gAa>gGa	p.E451G	WNK1_ENST00000537687.1_Missense_Mutation_p.E451G|WNK1_ENST00000540360.1_3'UTR|WNK1_ENST00000535572.1_Missense_Mutation_p.E451G|WNK1_ENST00000340908.4_Missense_Mutation_p.E44G|WNK1_ENST00000530271.2_Missense_Mutation_p.E451G	NM_018979.3	NP_061852.3	Q9H4A3	WNK1_HUMAN	WNK lysine deficient protein kinase 1	451	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				intracellular signal transduction (GO:0035556)|ion transport (GO:0006811)|negative regulation of pancreatic juice secretion (GO:0090188)|negative regulation of phosphatase activity (GO:0010923)|neuron development (GO:0048666)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of systemic arterial blood pressure (GO:0003084)|protein phosphorylation (GO:0006468)|regulation of cellular process (GO:0050794)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|chloride channel inhibitor activity (GO:0019869)|phosphatase binding (GO:0019902)|protein kinase inhibitor activity (GO:0004860)|protein serine/threonine kinase activity (GO:0004674)			breast(7)|central_nervous_system(1)|endometrium(3)|kidney(6)|large_intestine(15)|lung(43)|ovary(6)|prostate(3)|skin(7)|stomach(8)|upper_aerodigestive_tract(3)|urinary_tract(2)	104	all_cancers(10;0.00611)|all_epithelial(11;0.00825)|all_lung(10;0.0331)|Ovarian(42;0.0512)|Lung NSC(10;0.0632)		Epithelial(1;1.74e-08)|all cancers(1;7.04e-08)|OV - Ovarian serous cystadenocarcinoma(31;0.000423)|BRCA - Breast invasive adenocarcinoma(9;0.0149)|Colorectal(1;0.0197)			GCAATTCCTGAAGTGAAGGAA	0.353																																					p.E451G	Colon(19;451 567 6672 12618 28860)	.											.	.	.	0			c.A1352G						.						97.0	94.0	95.0					12																	966367		2203	4300	6503	SO:0001583	missense	65125	exon5			TTCCTGAAGTGAA	AJ296290	CCDS8506.1, CCDS53731.1, CCDS73419.1	12p13.3	2014-09-17	2005-01-19	2005-01-21	ENSG00000060237	ENSG00000060237			14540	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 167"""	605232	"""protein kinase, lysine deficient 1"", ""hereditary sensory neuropathy, type II"""	PRKWNK1, HSN2			Standard	NM_001184985		Approved	HSAN2, PPP1R167	uc031qfk.1	Q9H4A3	OTTHUMG00000090321	ENST00000315939.6:c.1352A>G	12.37:g.966367A>G	ENSP00000313059:p.Glu451Gly	Somatic	100	0		WXS	Illumina HiSeq	.	131	49	NM_001184985	A1L4B0|C5HTZ5|C5HTZ6|C5HTZ7|H6WZW3|O15052|P54963|Q4VBX9|Q6IFS5|Q86WL5|Q8N673|Q96CZ6|Q9P1S9	Missense_Mutation	SNP	ENST00000315939.6	37	CCDS8506.1	.	.	.	.	.	.	.	.	.	.	A	28.9	4.959266	0.92726	.	.	ENSG00000060237	ENST00000535572;ENST00000315939;ENST00000537687;ENST00000530271;ENST00000340908	T;T;T;T;T	0.69040	-0.37;-0.37;-0.37;-0.37;1.65	5.84	5.84	0.93424	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.088534	0.48767	N	0.000164	T	0.72953	0.3525	L	0.28344	0.845	0.52099	D	0.999946	D;D	0.69078	0.996;0.997	D;D	0.75020	0.975;0.985	T	0.76688	-0.2867	10	0.87932	D	0	-18.3997	16.2233	0.82274	1.0:0.0:0.0:0.0	.	451;451	F5GWT4;Q9H4A3	.;WNK1_HUMAN	G	451;451;451;451;44	ENSP00000441972:E451G;ENSP00000313059:E451G;ENSP00000444465:E451G;ENSP00000433548:E451G;ENSP00000341292:E44G	ENSP00000313059:E451G	E	+	2	0	WNK1	836628	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	9.339000	0.96797	2.243000	0.73865	0.482000	0.46254	GAA	.		0.353	WNK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206683.1	NM_018979	
KRT1	3848	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	12	53070970	53070970	+	Splice_Site	SNP	T	T	G			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr12:53070970T>G	ENST00000252244.3	-	6	1187		c.e6-2			NM_006121.3	NP_006112.3	P04264	K2C1_HUMAN	keratin 1						complement activation, lectin pathway (GO:0001867)|establishment of skin barrier (GO:0061436)|fibrinolysis (GO:0042730)|negative regulation of inflammatory response (GO:0050728)|regulation of angiogenesis (GO:0045765)|response to oxidative stress (GO:0006979)|retina homeostasis (GO:0001895)	blood microparticle (GO:0072562)|cytoskeleton (GO:0005856)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|lung(11)|ovary(1)|prostate(7)|skin(3)	39						CTCTTCATACTAAAGATGGTA	0.428																																					.		.											.	.	.	0			c.1129-2A>C						.						130.0	124.0	126.0					12																	53070970		2203	4300	6503	SO:0001630	splice_region_variant	3848	exon7			TCATACTAAAGAT	X69725	CCDS8836.1	12q13.13	2014-06-05	2008-08-01		ENSG00000167768	ENSG00000167768		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6412	protein-coding gene	gene with protein product		139350	"""epidermolytic hyperkeratosis 1"""	EHK1		2461420, 2470667, 16831889	Standard	NM_006121		Approved	KRT1A	uc001sau.1	P04264	OTTHUMG00000169749	ENST00000252244.3:c.1129-2A>C	12.37:g.53070970T>G		Somatic	22	0		WXS	Illumina HiSeq	.	52	19	NM_006121	B2RA01|P85925|P86104|Q14720|Q6GSJ0|Q9H298	Splice_Site	SNP	ENST00000252244.3	37	CCDS8836.1	.	.	.	.	.	.	.	.	.	.	T	16.18	3.050218	0.55218	.	.	ENSG00000167768	ENST00000252244	.	.	.	4.58	4.58	0.56647	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.3995	0.67034	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	KRT1	51357237	1.000000	0.71417	0.974000	0.42286	0.734000	0.41952	5.544000	0.67231	2.062000	0.61559	0.397000	0.26171	.	.		0.428	KRT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405706.1	NM_006121	Intron
MED12L	116931	hgsc.bcm.edu;bcgsc.ca	37	3	150876586	150876586	+	Splice_Site	SNP	G	G	T			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr3:150876586G>T	ENST00000474524.1	+	6	875	c.837G>T	c.(835-837)caG>caT	p.Q279H	MED12L_ENST00000273432.4_Splice_Site_p.Q279H|MED12L_ENST00000309237.4_Splice_Site_p.Q279H|MED12L_ENST00000422248.2_Splice_Site_p.Q279H	NM_053002.4	NP_443728.3	Q86YW9	MD12L_HUMAN	mediator complex subunit 12-like	279						mediator complex (GO:0016592)	RNA polymerase II transcription cofactor activity (GO:0001104)			NS(1)|breast(3)|central_nervous_system(3)|cervix(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(27)|lung(50)|ovary(6)|prostate(3)|skin(4)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	128			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			TAATGCTGCAGGTATAGTACA	0.378																																					p.Q279H		.											.	.	.	0			c.G837T						.						76.0	67.0	70.0					3																	150876586		2203	4300	6503	SO:0001630	splice_region_variant	116931	exon6			GCTGCAGGTATAG	AB046855, AF388364	CCDS33876.1	3q25.1	2007-07-30	2007-07-30		ENSG00000144893	ENSG00000144893			16050	protein-coding gene	gene with protein product		611318	"""mediator of RNA polymerase II transcription, subunit 12 homolog (S. cerevisiae)-like"""			11524702	Standard	XM_006713487		Approved	KIAA1635, TNRC11L, TRALPUSH, TRALP	uc003eyp.3	Q86YW9	OTTHUMG00000159844	ENST00000474524.1:c.837+1G>T	3.37:g.150876586G>T		Somatic	41	0		WXS	Illumina HiSeq	.	117	5	NM_053002	Q96PC7|Q96PC8|Q9H9M5|Q9HCD7|Q9UI69	Missense_Mutation	SNP	ENST00000474524.1	37	CCDS33876.1	.	.	.	.	.	.	.	.	.	.	G	23.6	4.439014	0.83885	.	.	ENSG00000144893	ENST00000422248;ENST00000309237;ENST00000474524;ENST00000273432	T;T;T;T	0.59502	0.35;0.34;0.26;1.41	5.07	5.07	0.68467	.	0.000000	0.85682	D	0.000000	T	0.74951	0.3784	M	0.68317	2.08	0.58432	D	0.999998	P;D;D;D	0.65815	0.851;0.989;0.987;0.995	P;P;P;D	0.77004	0.492;0.795;0.878;0.989	T	0.77720	-0.2482	10	0.87932	D	0	-15.0373	17.619	0.88075	0.0:0.0:1.0:0.0	.	279;279;279;279	F8WAE6;Q86YW9;Q86YW9-2;Q86YW9-3	.;MD12L_HUMAN;.;.	H	279	ENSP00000403308:Q279H;ENSP00000310760:Q279H;ENSP00000417235:Q279H;ENSP00000273432:Q279H	ENSP00000273432:Q279H	Q	+	3	2	MED12L	152359276	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	8.111000	0.89564	2.519000	0.84933	0.467000	0.42956	CAG	.		0.378	MED12L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357707.2	NM_053002	Missense_Mutation
KCNH3	23416	hgsc.bcm.edu	37	12	49935525	49935525	+	Silent	SNP	C	C	T			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr12:49935525C>T	ENST00000257981.6	+	3	683	c.423C>T	c.(421-423)ggC>ggT	p.G141G	KCNH3_ENST00000550434.1_3'UTR	NM_012284.1	NP_036416.1	Q9ULD8	KCNH3_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 3	141	PAC. {ECO:0000255|PROSITE- ProRule:PRU00141}.				potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	phosphorelay sensor kinase activity (GO:0000155)|voltage-gated potassium channel activity (GO:0005249)	p.D143fs*65(1)		NS(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(20)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	36						ACCGAGGGGGCCCCGACAGAT	0.587																																					p.G141G		.											KCNH3,NS,carcinoma,+2,1	KCNH3	+2	1	Deletion - Frameshift(1)	lung(1)	c.C423T						.						129.0	144.0	139.0					12																	49935525		2203	4300	6503	SO:0001819	synonymous_variant	23416	exon3			AGGGGGCCCCGAC	AB022696	CCDS8786.1	12q13	2012-07-05				ENSG00000135519		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6252	protein-coding gene	gene with protein product		604527				10455180, 16382104	Standard	NM_012284		Approved	Kv12.2, BEC1, elk2	uc001ruh.1	Q9ULD8	OTTHUMG00000169517	ENST00000257981.6:c.423C>T	12.37:g.49935525C>T		Somatic	40	0		WXS	Illumina HiSeq	.	68	3	NM_012284	Q9UQ06	Silent	SNP	ENST00000257981.6	37	CCDS8786.1																																																																																			.		0.587	KCNH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404571.2	NM_012284	
C3orf52	79669	hgsc.bcm.edu	37	3	111828389	111828389	+	Splice_Site	SNP	G	G	A			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr3:111828389G>A	ENST00000264848.5	+	4	455		c.e4-1		C3orf52_ENST00000430855.1_Intron|C3orf52_ENST00000431717.2_Intron	NM_024616.2	NP_078892	Q5BVD1	TTMP_HUMAN	chromosome 3 open reading frame 52							endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(1)|lung(1)|urinary_tract(1)	4						TGTTTGTTTAGCTCACAGATG	0.408																																					.		.											.	.	.	0			c.397-1G>A						.						206.0	190.0	195.0					3																	111828389		1929	4151	6080	SO:0001630	splice_region_variant	79669	exon4			TGTTTAGCTCACA	AY830714	CCDS46887.1, CCDS54620.1	3q13.2	2006-01-30			ENSG00000114529	ENSG00000114529			26255	protein-coding gene	gene with protein product	"""TPA induced trans-membrane protein"""	611956				15737651	Standard	NM_024616		Approved	FLJ23186, TTMP	uc011bhs.2	Q5BVD1	OTTHUMG00000159230	ENST00000264848.5:c.397-1G>A	3.37:g.111828389G>A		Somatic	41	0		WXS	Illumina HiSeq	.	119	5	NM_024616	B4DNV2|B4E0Z2|Q96AJ4|Q9H5Q1	Splice_Site	SNP	ENST00000264848.5	37	CCDS46887.1	.	.	.	.	.	.	.	.	.	.	G	16.71	3.197509	0.58126	.	.	ENSG00000114529	ENST00000264848	.	.	.	4.82	4.82	0.62117	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.772	0.63032	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	C3orf52	113311079	1.000000	0.71417	0.993000	0.49108	0.746000	0.42486	5.032000	0.64140	2.377000	0.81083	0.655000	0.94253	.	.		0.408	C3orf52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353961.1	NM_024616	Intron
OR1B1	347169	hgsc.bcm.edu	37	9	125391702	125391702	+	Missense_Mutation	SNP	A	A	C			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr9:125391702A>C	ENST00000304833.3	-	1	150	c.113T>G	c.(112-114)cTg>cGg	p.L38R	RP11-64P14.7_ENST00000419604.1_RNA|RP11-64P14.7_ENST00000431442.1_RNA	NM_001004450.1	NP_001004450.1	Q8NGR6	OR1B1_HUMAN	olfactory receptor, family 1, subfamily B, member 1	38						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(6)|prostate(1)	16						TATGGTGGTCAGGTAAATAGC	0.507																																					p.L38R		.											OR1B1,NS,lymphoid_neoplasm,0,1	OR1B1	0	0			c.T113G						.						96.0	88.0	91.0					9																	125391702		2203	4300	6503	SO:0001583	missense	347169	exon1			GTGGTCAGGTAAA	AC006313	CCDS35126.1	9q33.2	2012-08-09			ENSG00000171484	ENSG00000171484		"""GPCR / Class A : Olfactory receptors"""	8181	protein-coding gene	gene with protein product							Standard	NM_001004450		Approved	OR9-B	uc011lyz.2	Q8NGR6	OTTHUMG00000020616	ENST00000304833.3:c.113T>G	9.37:g.125391702A>C	ENSP00000303151:p.Leu38Arg	Somatic	24	0		WXS	Illumina HiSeq	.	41	2	NM_001004450	Q6IFN3	Missense_Mutation	SNP	ENST00000304833.3	37	CCDS35126.1	.	.	.	.	.	.	.	.	.	.	A	12.07	1.827126	0.32329	.	.	ENSG00000171484	ENST00000304833	T	0.17691	2.26	4.59	4.59	0.56863	.	0.236164	0.21557	N	0.072636	T	0.53769	0.1817	H	0.97564	4.03	0.26816	N	0.968882	D	0.56746	0.977	P	0.62491	0.903	T	0.62329	-0.6877	10	0.87932	D	0	-6.0381	13.3902	0.60821	1.0:0.0:0.0:0.0	.	38	Q8NGR6	OR1B1_HUMAN	R	38	ENSP00000303151:L38R	ENSP00000303151:L38R	L	-	2	0	OR1B1	124431523	0.053000	0.20554	0.831000	0.32960	0.006000	0.05464	3.484000	0.53201	2.044000	0.60594	0.528000	0.53228	CTG	.		0.507	OR1B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053947.2	NM_001004450	
ALS2	57679	hgsc.bcm.edu	37	2	202593249	202593249	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr2:202593249G>T	ENST00000264276.6	-	15	3199	c.2827C>A	c.(2827-2829)Ctg>Atg	p.L943M	ALS2_ENST00000457679.2_Missense_Mutation_p.L255M	NM_020919.3	NP_065970.2	Q96Q42	ALS2_HUMAN	amyotrophic lateral sclerosis 2 (juvenile)	943	PH. {ECO:0000305}.				behavioral fear response (GO:0001662)|cell death (GO:0008219)|endosomal transport (GO:0016197)|endosome organization (GO:0007032)|locomotory behavior (GO:0007626)|neuromuscular junction development (GO:0007528)|neuron projection morphogenesis (GO:0048812)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of Rab GTPase activity (GO:0032851)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rac protein signal transduction (GO:0035022)|positive regulation of Ran GTPase activity (GO:0032853)|protein localization (GO:0008104)|receptor recycling (GO:0001881)|regulation of endosome size (GO:0051036)|response to oxidative stress (GO:0006979)|synaptic transmission, glutamatergic (GO:0035249)|vesicle organization (GO:0016050)	centrosome (GO:0005813)|cytosol (GO:0005829)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|early endosome (GO:0005769)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|postsynaptic density (GO:0014069)|protein complex (GO:0043234)|ruffle (GO:0001726)|vesicle (GO:0031982)	protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activator activity (GO:0043539)|Rab GTPase binding (GO:0017137)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|Ran guanyl-nucleotide exchange factor activity (GO:0005087)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(22)|ovary(1)|prostate(4)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)	72						GCATGGACCAGGGCATCATTA	0.468																																					p.L943M		.											.	.	.	0			c.C2827A						.						98.0	98.0	98.0					2																	202593249		1907	4117	6024	SO:0001583	missense	57679	exon15			GGACCAGGGCATC	AB053305	CCDS42800.1, CCDS46492.1	2q33-q35	2014-09-17	2004-06-23		ENSG00000003393	ENSG00000003393		"""Rho guanine nucleotide exchange factors"""	443	protein-coding gene	gene with protein product	"""alsin"""	606352	"""amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 6"""	ALS2CR6		11586298	Standard	NM_020919		Approved		uc002uyo.3	Q96Q42	OTTHUMG00000154507	ENST00000264276.6:c.2827C>A	2.37:g.202593249G>T	ENSP00000264276:p.Leu943Met	Somatic	34	0		WXS	Illumina HiSeq	.	72	3	NM_020919	Q53TT1|Q53TV2|Q8N1E0|Q96PC4|Q96Q41|Q9H973|Q9HCK9	Missense_Mutation	SNP	ENST00000264276.6	37	CCDS42800.1	.	.	.	.	.	.	.	.	.	.	G	18.68	3.675834	0.67928	.	.	ENSG00000003393	ENST00000264276;ENST00000457679	T;T	0.43294	0.95;0.95	5.82	3.75	0.43078	Pleckstrin homology-type (1);Pleckstrin homology domain (1);	0.000000	0.64402	D	0.000001	T	0.62307	0.2417	M	0.83603	2.65	0.54753	D	0.999985	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.997	T	0.65092	-0.6252	10	0.87932	D	0	.	7.0591	0.25115	0.3887:0.0:0.6113:0.0	.	943;943	Q6IQ41;Q96Q42	.;ALS2_HUMAN	M	943;255	ENSP00000264276:L943M;ENSP00000394823:L255M	ENSP00000264276:L943M	L	-	1	2	ALS2	202301494	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	1.513000	0.35823	1.368000	0.46115	0.557000	0.71058	CTG	.		0.468	ALS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335562.3	NM_020919	
DDHD2	23259	hgsc.bcm.edu	37	8	38117622	38117622	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr8:38117622G>T	ENST00000397166.2	+	17	2644	c.2119G>T	c.(2119-2121)Gat>Tat	p.D707Y	DDHD2_ENST00000529845.1_Missense_Mutation_p.D158Y|DDHD2_ENST00000520272.2_Missense_Mutation_p.D707Y|DDHD2_ENST00000517385.1_Missense_Mutation_p.D326Y	NM_015214.2	NP_056029.2	O94830	DDHD2_HUMAN	DDHD domain containing 2	707					cell death (GO:0008219)|lipid catabolic process (GO:0016042)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|microtubule organizing center (GO:0005815)	hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)	p.D707N(1)		endometrium(4)|kidney(1)|large_intestine(5)|lung(14)|ovary(1)|skin(1)|urinary_tract(2)	28	Colorectal(12;0.000442)	all_lung(54;0.0657)|Lung NSC(58;0.175)	BRCA - Breast invasive adenocarcinoma(5;3.76e-25)|COAD - Colon adenocarcinoma(9;0.0977)			TATCTTCCTTGATCAGCCTTT	0.323																																					p.D707Y		.											DDHD2,colon,carcinoma,0,2	DDHD2	0	1	Substitution - Missense(1)	large_intestine(1)	c.G2119T						.						135.0	131.0	133.0					8																	38117622		2203	4300	6503	SO:0001583	missense	23259	exon17			TTCCTTGATCAGC	AK056525	CCDS34883.1	8p11.23	2014-03-03	2004-04-05	2004-04-07				"""Sterile alpha motif (SAM) domain containing"""	29106	protein-coding gene	gene with protein product		615003	"""SAM, WWE and DDHD domain containing 1"""	SAMWD1		9872452, 11788596, 19632984, 20932832	Standard	NM_015214		Approved	KIAA0725, SPG54	uc003xlc.3	O94830		ENST00000397166.2:c.2119G>T	8.37:g.38117622G>T	ENSP00000380352:p.Asp707Tyr	Somatic	31	0		WXS	Illumina HiSeq	.	49	2	NM_001164232	B3KWV2|B3KXB5|Q9H8X7	Missense_Mutation	SNP	ENST00000397166.2	37	CCDS34883.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	27.0|27.0	4.787125|4.787125	0.90367|0.90367	.|.	.|.	ENSG00000085788|ENSG00000085788	ENST00000397166;ENST00000520272;ENST00000517385;ENST00000529845;ENST00000528613|ENST00000526144	T;T|.	0.36520|.	1.25;1.25|.	5.62|5.62	5.62|5.62	0.85841|0.85841	.|.	0.178958|.	0.49305|.	D|.	0.000160|.	T|T	0.71517|0.71517	0.3349|0.3349	M|M	0.73217|0.73217	2.22|2.22	0.80722|0.80722	D|D	1|1	D|.	0.89917|.	1.0|.	D|.	0.70935|.	0.971|.	T|T	0.65307|0.65307	-0.6200|-0.6200	10|6	0.87932|0.10636	D|T	0|0.68	-24.2941|-24.2941	18.6525|18.6525	0.91435|0.91435	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	707|.	O94830|.	DDHD2_HUMAN|.	Y|F	707;707;326;158;75|208	ENSP00000380352:D707Y;ENSP00000429932:D707Y|.	ENSP00000380352:D707Y|ENSP00000437029:L208F	D|L	+|+	1|3	0|2	DDHD2|DDHD2	38236779|38236779	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.992000|0.992000	0.81027|0.81027	9.680000|9.680000	0.98651|0.98651	2.650000|2.650000	0.89964|0.89964	0.655000|0.655000	0.94253|0.94253	GAT|TTG	.		0.323	DDHD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377251.2	XM_291291	
DNAJC28	54943	hgsc.bcm.edu	37	21	34860754	34860754	+	Nonsense_Mutation	SNP	A	A	C	rs139852262|rs3834674	byFrequency	TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr21:34860754A>C	ENST00000314399.3	-	2	1385	c.947T>G	c.(946-948)tTa>tGa	p.L316*	DNAJC28_ENST00000402202.1_Nonsense_Mutation_p.L316*|DNAJC28_ENST00000381947.3_Nonsense_Mutation_p.L316*	NM_017833.3	NP_060303.2	Q9NX36	DJC28_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 28	316				LIVPILTRQKVHFDAQKEIVRAQKIYETLIKTKEVTDRNPN NLDQGEGEKTPEIKKGFLNWMNLWKFIKIRSF -> CSHPD QAKSPF (in Ref. 2; BAA91185). {ECO:0000305}.				p.L316*(2)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(5)|skin(1)|urinary_tract(1)	18						GGGAACAATTAAATTAAAATC	0.338																																					p.L316X		.											DNAJC28,NS,carcinoma,0,2	DNAJC28	0	2	Substitution - Nonsense(2)	lung(2)	c.T947G						.						78.0	64.0	69.0					21																	34860754		2203	4291	6494	SO:0001587	stop_gained	54943	exon2			ACAATTAAATTAA	AK000468	CCDS13626.1	21q22.11	2011-09-02	2008-06-17	2008-06-17	ENSG00000177692	ENSG00000177692		"""Heat shock proteins / DNAJ (HSP40)"""	1297	protein-coding gene	gene with protein product	"""Orf28"""		"""chromosome 21 open reading frame 55"""	C21orf55			Standard	NM_017833		Approved	C21orf78	uc002yrw.3	Q9NX36	OTTHUMG00000065531	ENST00000314399.3:c.947T>G	21.37:g.34860754A>C	ENSP00000320303:p.Leu316*	Somatic	47	0		WXS	Illumina HiSeq	.	91	4	NM_001040192	D3DSF2	Nonsense_Mutation	SNP	ENST00000314399.3	37	CCDS13626.1	.	.	.	.	.	.	.	.	.	.	A	38	7.162118	0.98107	.	.	ENSG00000177692	ENST00000381947;ENST00000314399;ENST00000402202	.	.	.	5.09	5.09	0.68999	.	0.000000	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-8.8259	14.8401	0.70217	1.0:0.0:0.0:0.0	.	.	.	.	X	316	.	ENSP00000320303:L316X	L	-	2	0	DNAJC28	33782624	1.000000	0.71417	0.993000	0.49108	0.986000	0.74619	8.254000	0.89844	2.050000	0.60909	0.528000	0.53228	TTA	.		0.338	DNAJC28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140454.3		
ANKRD18DP	348840	hgsc.bcm.edu	37	3	197794345	197794345	+	RNA	SNP	C	C	A			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr3:197794345C>A	ENST00000435620.2	-	0	907					NR_003291.1				ankyrin repeat domain 18D, pseudogene																		CTAAAACTTTCGTTCTTCATG	0.408																																					.		.											.	.	.	0			.						.																																					348840	.			AACTTTCGTTCTT	BC042518		3q29	2011-11-23			ENSG00000226435	ENSG00000226435			28016	pseudogene	pseudogene							Standard	NR_003291		Approved		uc003fyx.3		OTTHUMG00000150228		3.37:g.197794345C>A		Somatic	22	0		WXS	Illumina HiSeq	.	44	4	.		RNA	SNP	ENST00000435620.2	37																																																																																				.		0.408	ANKRD18DP-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000316910.2	NR_003291	
ZNF729	100287226	hgsc.bcm.edu	37	19	22487565	22487565	+	Missense_Mutation	SNP	A	A	T			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr19:22487565A>T	ENST00000601693.1	+	3	351	c.233A>T	c.(232-234)gAg>gTg	p.E78V	ZNF729_ENST00000357491.6_Missense_Mutation_p.E78V			A6NN14	ZN729_HUMAN	zinc finger protein 729	78	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(5)|central_nervous_system(1)|lung(32)|ovary(3)	41						AAGAGACATGAGATGGTAACT	0.398																																					p.E78V		.											.	.	.	0			c.A233T						.																																			SO:0001583	missense	100287226	exon3			GACATGAGATGGT		CCDS59368.1	19p12	2014-02-14			ENSG00000196350	ENSG00000196350		"""Zinc fingers, C2H2-type"", ""-"""	32464	protein-coding gene	gene with protein product							Standard	NM_001242680		Approved		uc021urs.1	A6NN14	OTTHUMG00000182938	ENST00000601693.1:c.233A>T	19.37:g.22487565A>T	ENSP00000469582:p.Glu78Val	Somatic	73	0		WXS	Illumina HiSeq	.	57	5	NM_001242680	M0QY45	Missense_Mutation	SNP	ENST00000601693.1	37	CCDS59368.1	.	.	.	.	.	.	.	.	.	.	.	9.197	1.027521	0.19512	.	.	ENSG00000196350	ENST00000357491	T	0.07444	3.19	0.824	0.824	0.18818	.	.	.	.	.	T	0.04048	0.0113	N	0.11673	0.155	.	.	.	.	.	.	.	.	.	T	0.40213	-0.9575	6	0.29301	T	0.29	.	3.7153	0.08435	1.0:0.0:0.0:0.0	.	.	.	.	V	78	ENSP00000350085:E78V	ENSP00000350085:E78V	E	+	2	0	ZNF729	22279405	0.949000	0.32298	0.550000	0.28217	0.566000	0.35808	1.158000	0.31737	0.166000	0.19597	0.164000	0.16699	GAG	.		0.398	ZNF729-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464396.1	XM_496301	
SGOL2	151246	hgsc.bcm.edu	37	2	201407335	201407335	+	Nonsense_Mutation	SNP	A	A	T			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr2:201407335A>T	ENST00000357799.4	+	5	519	c.421A>T	c.(421-423)Aag>Tag	p.K141*	SGOL2_ENST00000469840.1_3'UTR|SGOL2_ENST00000409203.3_Nonsense_Mutation_p.K141*	NM_001160033.1|NM_001160046.1|NM_152524.5	NP_001153505.1|NP_001153518.1|NP_689737.4	Q562F6	SGOL2_HUMAN	shugoshin-like 2 (S. pombe)	141					meiotic sister chromatid cohesion, centromeric (GO:0051754)|mitotic cell cycle (GO:0000278)	chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|kinetochore (GO:0000776)|mitotic cohesin complex (GO:0030892)|nucleus (GO:0005634)				NS(2)|breast(2)|cervix(3)|endometrium(1)|kidney(2)|large_intestine(7)|lung(20)|ovary(2)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	46						GTCAGCTAGCAAGAAGAAACG	0.308																																					p.K141X		.											.	.	.	0			c.A421T						.						135.0	127.0	129.0					2																	201407335		1844	4093	5937	SO:0001587	stop_gained	151246	exon5			GCTAGCAAGAAGA	AY094614	CCDS42796.1	2q33.2	2008-02-05			ENSG00000163535	ENSG00000163535			30812	protein-coding gene	gene with protein product		612425					Standard	NM_001160046		Approved	TRIPIN, FLJ25211	uc002uvw.2	Q562F6	OTTHUMG00000154535	ENST00000357799.4:c.421A>T	2.37:g.201407335A>T	ENSP00000350447:p.Lys141*	Somatic	42	0		WXS	Illumina HiSeq	.	83	4	NM_001160046	Q53RR9|Q53T20|Q86XY4|Q8IWK2|Q8IZK1|Q8N1Q5|Q96LQ3	Nonsense_Mutation	SNP	ENST00000357799.4	37	CCDS42796.1	.	.	.	.	.	.	.	.	.	.	A	22.0	4.228448	0.79576	.	.	ENSG00000163535	ENST00000357799;ENST00000409203	.	.	.	5.2	3.01	0.34805	.	0.653568	0.14410	N	0.321370	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-3.3726	10.7268	0.46072	0.408:0.592:0.0:0.0	.	.	.	.	X	141	.	ENSP00000350447:K141X	K	+	1	0	SGOL2	201115580	0.256000	0.24012	0.992000	0.48379	0.944000	0.59088	0.735000	0.26115	0.471000	0.27319	0.402000	0.26972	AAG	.		0.308	SGOL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335834.1	NM_152524	
TIGD4	201798	hgsc.bcm.edu	37	4	153691681	153691681	+	Nonsense_Mutation	SNP	G	G	T			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr4:153691681G>T	ENST00000304337.2	-	2	1296	c.476C>A	c.(475-477)tCg>tAg	p.S159*		NM_145720.3	NP_663772.1	Q8IY51	TIGD4_HUMAN	tigger transposable element derived 4	159						nucleus (GO:0005634)	DNA binding (GO:0003677)	p.S159L(1)		breast(1)|endometrium(2)|large_intestine(9)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(2)	26	all_hematologic(180;0.093)					CCAGACAGTCGAAGGGTCTAC	0.358																																					p.S159X		.											TIGD4,colon,carcinoma,+1,3	TIGD4	+1	1	Substitution - Missense(1)	lung(1)	c.C476A						.						43.0	47.0	46.0					4																	153691681		2202	4298	6500	SO:0001587	stop_gained	201798	exon2			ACAGTCGAAGGGT	AK058054	CCDS34079.1	4q31.23	2008-02-05							18335	protein-coding gene	gene with protein product							Standard	NM_145720		Approved		uc003imy.3	Q8IY51		ENST00000304337.2:c.476C>A	4.37:g.153691681G>T	ENSP00000355162:p.Ser159*	Somatic	11	0		WXS	Illumina HiSeq	.	46	2	NM_145720	Q96LP5	Nonsense_Mutation	SNP	ENST00000304337.2	37	CCDS34079.1	.	.	.	.	.	.	.	.	.	.	G	42	9.524149	0.99195	.	.	ENSG00000169989	ENST00000304337	.	.	.	6.03	6.03	0.97812	.	0.177936	0.27460	N	0.019263	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.11794	T	0.64	-16.0731	10.5512	0.45090	0.1433:0.0:0.8567:0.0	.	.	.	.	X	159	.	ENSP00000355162:S159X	S	-	2	0	TIGD4	153911131	0.972000	0.33761	0.970000	0.41538	0.996000	0.88848	1.984000	0.40658	2.861000	0.98227	0.655000	0.94253	TCG	.		0.358	TIGD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365028.1	NM_145720	
PTTG1IP	754	hgsc.bcm.edu	37	21	46271541	46271541	+	Splice_Site	SNP	G	G	A			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr21:46271541G>A	ENST00000330938.3	-	6	718	c.498C>T	c.(496-498)ggC>ggT	p.G166G	PTTG1IP_ENST00000397886.3_Splice_Site_p.G145G|PTTG1IP_ENST00000445724.2_Splice_Site_p.A57V|PTTG1IP_ENST00000397887.3_Splice_Site_p.G93G	NM_004339.3	NP_004330.1	P53801	PTTG_HUMAN	pituitary tumor-transforming 1 interacting protein	166					multicellular organismal development (GO:0007275)|protein import into nucleus (GO:0006606)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	receptor activity (GO:0004872)			ovary(1)|prostate(1)	2				Colorectal(79;0.0659)		CTTTAAACAGGCCTGAAACAA	0.408																																					p.G166G		.											PTTG1IP_ENST00000445724,NS,carcinoma,0,2	PTTG1IP_ENST00000445724	0	0			c.C498T						.						120.0	120.0	120.0					21																	46271541		2203	4300	6503	SO:0001630	splice_region_variant	754	exon6			AAACAGGCCTGAA	AF149785	CCDS13715.1, CCDS68221.1	21q22.3	2008-07-04			ENSG00000183255	ENSG00000183255			13524	protein-coding gene	gene with protein product		603784		C21orf3, C21orf1		9570958, 10830953	Standard	NM_004339		Approved	PBF	uc002zgb.2	P53801	OTTHUMG00000090254	ENST00000330938.3:c.497-1C>T	21.37:g.46271541G>A		Somatic	48	1		WXS	Illumina HiSeq	.	74	3	NM_004339	B2RDP7|D3DSL9|Q9NS09	Silent	SNP	ENST00000330938.3	37	CCDS13715.1	.	.	.	.	.	.	.	.	.	.	G	10.87	1.471486	0.26423	.	.	ENSG00000183255	ENST00000445724	T	0.42131	0.98	5.03	-1.86	0.07760	.	.	.	.	.	T	0.25901	0.0631	.	.	.	0.20196	N	0.999928	B	0.12630	0.006	B	0.10450	0.005	T	0.32929	-0.9888	8	0.87932	D	0	.	1.9347	0.03334	0.5221:0.1255:0.2301:0.1223	.	57	B4DPZ0	.	V	57	ENSP00000395374:A57V	ENSP00000395374:A57V	A	-	2	0	PTTG1IP	45095969	1.000000	0.71417	0.941000	0.38009	0.811000	0.45836	0.708000	0.25719	0.019000	0.15079	-0.768000	0.03414	GCC	.		0.408	PTTG1IP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206553.1		Silent
SAA3P	6290	hgsc.bcm.edu	37	11	18134347	18134347	+	RNA	SNP	C	C	A			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr11:18134347C>A	ENST00000534768.1	-	0	358					NR_026576.1				serum amyloid A3 pseudogene											lung(2)	2						GGCCAGTGAGCAACAGCCCAC	0.567																																					.		.											.	.	.	0			.						.																																					6290	.			AGTGAGCAACAGC	S73444		11p15.1	2014-06-05			ENSG00000166787	ENSG00000166787			10515	pseudogene	pseudogene				SAA3		8325654, 2558975	Standard	NR_026576		Approved		uc001mnt.3		OTTHUMG00000166433		11.37:g.18134347C>A		Somatic	29	0		WXS	Illumina HiSeq	.	32	13	.		RNA	SNP	ENST00000534768.1	37																																																																																				.		0.567	SAA3P-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000389765.1		
C6orf203	51250	hgsc.bcm.edu	37	6	107361230	107361230	+	Missense_Mutation	SNP	G	G	T	rs373305216		TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr6:107361230G>T	ENST00000405204.2	+	2	873	c.266G>T	c.(265-267)aGg>aTg	p.R89M	C6orf203_ENST00000311381.5_Missense_Mutation_p.R89M|C6orf203_ENST00000443043.1_Missense_Mutation_p.R94M|C6orf203_ENST00000489790.1_3'UTR	NM_001142468.1	NP_001135940.1	Q9P0P8	CF203_HUMAN	chromosome 6 open reading frame 203	89						mitochondrion (GO:0005739)				large_intestine(4)|lung(2)|prostate(1)|urinary_tract(1)	8	Breast(9;0.00124)|all_epithelial(6;0.0729)	all_cancers(87;0.00461)|Acute lymphoblastic leukemia(125;3.07e-08)|all_hematologic(75;3.33e-06)|Colorectal(196;0.171)|all_epithelial(87;0.23)	BRCA - Breast invasive adenocarcinoma(8;0.000395)|all cancers(7;0.00065)|Epithelial(6;0.000834)|OV - Ovarian serous cystadenocarcinoma(5;0.244)	BRCA - Breast invasive adenocarcinoma(108;0.117)		AGTAATATAAGGTCTACAAAA	0.353																																					p.R94M		.											C6orf203,caecum,carcinoma,0,1	C6orf203	0	0			c.G281T						.						49.0	56.0	54.0					6																	107361230		2203	4300	6503	SO:0001583	missense	51250	exon3			ATATAAGGTCTAC	AF151064	CCDS5058.1	6q21	2012-02-22			ENSG00000130349	ENSG00000130349			17971	protein-coding gene	gene with protein product						11042152, 11707072	Standard	XM_005267008		Approved	HSPC230, PRED31	uc003prq.3	Q9P0P8	OTTHUMG00000015307	ENST00000405204.2:c.266G>T	6.37:g.107361230G>T	ENSP00000384867:p.Arg89Met	Somatic	48	0		WXS	Illumina HiSeq	.	35	2	NM_001142470	B3KRG9	Missense_Mutation	SNP	ENST00000405204.2	37	CCDS5058.1	.	.	.	.	.	.	.	.	.	.	G	14.12	2.441680	0.43326	.	.	ENSG00000130349	ENST00000443043;ENST00000405204;ENST00000311381	T;T;T	0.29917	1.55;1.55;1.55	6.08	4.31	0.51392	.	0.327603	0.37304	N	0.002156	T	0.11367	0.0277	N	0.22421	0.69	0.22226	N	0.999273	P	0.39696	0.683	B	0.40329	0.326	T	0.04090	-1.0978	10	0.62326	D	0.03	-0.5333	12.82	0.57688	0.1317:0.0:0.8683:0.0	.	89	Q9P0P8	CF203_HUMAN	M	94;89;89	ENSP00000390153:R94M;ENSP00000384867:R89M;ENSP00000310951:R89M	ENSP00000310951:R89M	R	+	2	0	C6orf203	107467923	0.998000	0.40836	0.892000	0.35008	0.775000	0.43874	2.927000	0.48900	0.904000	0.36572	0.655000	0.94253	AGG	.		0.353	C6orf203-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041684.1	NM_016487	
MGAT1	4245	hgsc.bcm.edu;bcgsc.ca	37	5	180219933	180219933	+	Silent	SNP	G	G	T			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr5:180219933G>T	ENST00000446023.2	-	3	789	c.39C>A	c.(37-39)ggC>ggA	p.G13G	MGAT1_ENST00000307826.4_Silent_p.G13G|MGAT1_ENST00000333055.3_Silent_p.G13G|MGAT1_ENST00000427865.2_Silent_p.G13G|MGAT1_ENST00000393340.3_Silent_p.G13G	NM_001114617.1|NM_001114618.1	NP_001108089.1|NP_001108090.1	P26572	MGAT1_HUMAN	mannosyl (alpha-1,3-)-glycoprotein beta-1,2-N-acetylglucosaminyltransferase	13					carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|in utero embryonic development (GO:0001701)|post-translational protein modification (GO:0043687)|protein glycosylation (GO:0006486)|protein N-linked glycosylation via asparagine (GO:0018279)|UDP-N-acetylglucosamine catabolic process (GO:0006049)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|vesicle (GO:0031982)	acetylglucosaminyltransferase activity (GO:0008375)|alpha-1,3-mannosylglycoprotein 2-beta-N-acetylglucosaminyltransferase activity (GO:0003827)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(2)|lung(7)|ovary(2)|urinary_tract(1)	13	all_cancers(89;1.11e-05)|all_epithelial(37;3.77e-06)|Renal(175;0.000159)|Lung NSC(126;0.0027)|all_lung(126;0.00351)|Breast(19;0.114)	all_cancers(40;0.00356)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_hematologic(541;0.163)|Ovarian(839;0.238)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			AGAGGATAGCGCCCCACAGCA	0.672																																					p.G13G		.											.	.	.	0			c.C39A						.						24.0	28.0	26.0					5																	180219933		2198	4293	6491	SO:0001819	synonymous_variant	4245	exon3			GATAGCGCCCCAC	M61829	CCDS4458.1	5q35.3	2013-02-25			ENSG00000131446	ENSG00000131446	2.4.1.101	"""Mannosyl-glycoprotein beta N-acetylglucosaminyltransferases"""	7044	protein-coding gene	gene with protein product		160995		MGAT, GLYT1		1827260	Standard	NM_002406		Approved	GNT-1, GLCNAC-TI	uc003mmg.4	P26572	OTTHUMG00000130937	ENST00000446023.2:c.39C>A	5.37:g.180219933G>T		Somatic	35	0		WXS	Illumina HiSeq	.	51	4	NM_001114617	A8K404|B3KRU8|D3DWR1|Q6IBE3	Silent	SNP	ENST00000446023.2	37	CCDS4458.1																																																																																			.		0.672	MGAT1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368189.1	NM_001114618	
BIRC6	57448	hgsc.bcm.edu	37	2	32757240	32757240	+	Intron	SNP	T	T	G	rs199863671		TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr2:32757240T>G	ENST00000421745.2	+	61	12425				MIR558_ENST00000384920.1_RNA	NM_016252.3	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat containing 6						apoptotic process (GO:0006915)|labyrinthine layer development (GO:0060711)|mitotic nuclear division (GO:0007067)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of cell proliferation (GO:0042127)|regulation of cytokinesis (GO:0032465)|spongiotrophoblast layer development (GO:0060712)	endosome (GO:0005768)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|spindle pole (GO:0000922)|trans-Golgi network (GO:0005802)	acid-amino acid ligase activity (GO:0016881)|cysteine-type endopeptidase inhibitor activity (GO:0004869)|ubiquitin-protein transferase activity (GO:0004842)			NS(4)|breast(8)|central_nervous_system(3)|endometrium(21)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(31)|lung(65)|ovary(7)|pancreas(1)|prostate(5)|skin(5)|stomach(1)|urinary_tract(5)	172	Acute lymphoblastic leukemia(172;0.155)					gtgtgtgtgGTTATTTTGGTA	0.368																																					.	Pancreas(94;175 1509 16028 18060 45422)	.											.	.	.	0			.						.						57.0	51.0	53.0					2																	32757240		1568	3582	5150	SO:0001627	intron_variant	693143	.			GTGTGGTTATTTT	AF265555	CCDS33175.2	2p22.3	2011-01-25	2011-01-25		ENSG00000115760	ENSG00000115760		"""Baculoviral IAP repeat containing"", ""Ubiquitin-conjugating enzymes E2"""	13516	protein-coding gene	gene with protein product	"""apollon"""	605638	"""baculoviral IAP repeat-containing 6"""			10544019	Standard	NM_016252		Approved	BRUCE	uc010ezu.3	Q9NR09	OTTHUMG00000150528	ENST00000421745.2:c.12291+622T>G	2.37:g.32757240T>G		Somatic	33	0		WXS	Illumina HiSeq	.	73	6	.	Q9ULD1	RNA	SNP	ENST00000421745.2	37	CCDS33175.2																																																																																			.		0.368	BIRC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318769.3	NM_016252	
TOP2B	7155	hgsc.bcm.edu	37	3	25675377	25675377	+	Silent	SNP	T	T	C			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr3:25675377T>C	ENST00000264331.4	-	8	980	c.981A>G	c.(979-981)aaA>aaG	p.K327K	TOP2B_ENST00000435706.2_Silent_p.K322K	NM_001068.2	NP_001059.2	Q02880	TOP2B_HUMAN	topoisomerase (DNA) II beta 180kDa	327					ATP catabolic process (GO:0006200)|axonogenesis (GO:0007409)|DNA topological change (GO:0006265)|DNA unwinding involved in DNA replication (GO:0006268)|forebrain development (GO:0030900)|mitotic DNA integrity checkpoint (GO:0044774)|mitotic recombination (GO:0006312)|neuron migration (GO:0001764)|resolution of meiotic recombination intermediates (GO:0000712)|sister chromatid segregation (GO:0000819)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|DNA topoisomerase complex (ATP-hydrolyzing) (GO:0009330)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding, bending (GO:0008301)|DNA topoisomerase type II (ATP-hydrolyzing) activity (GO:0003918)|enzyme binding (GO:0019899)|histone deacetylase binding (GO:0042826)|metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)|protein heterodimerization activity (GO:0046982)|protein kinase C binding (GO:0005080)			breast(2)|endometrium(5)|kidney(1)|large_intestine(10)|lung(14)|ovary(1)|skin(2)|stomach(1)	36					Dactinomycin(DB00970)|Daunorubicin(DB00694)|Dexrazoxane(DB00380)|Etoposide(DB00773)	GCTGGAATCCTTTTTCACTCA	0.348																																					p.K322K		.											TOP2B,right_upper_lobe,carcinoma,0,1	TOP2B	0	0			c.A966G						.						162.0	156.0	158.0					3																	25675377		1848	4087	5935	SO:0001819	synonymous_variant	7155	exon8			GAATCCTTTTTCA	X68060	CCDS46776.1	3p24.2	2012-08-30	2002-08-29		ENSG00000077097	ENSG00000077097	5.99.1.3		11990	protein-coding gene	gene with protein product		126431	"""topoisomerase (DNA) II beta (180kD)"""			1309226, 1333583	Standard	NM_001068		Approved		uc003cdj.3	Q02880	OTTHUMG00000155596	ENST00000264331.4:c.981A>G	3.37:g.25675377T>C		Somatic	63	0		WXS	Illumina HiSeq	.	49	2	NM_001068	Q13600|Q9UMG8|Q9UQP8	Silent	SNP	ENST00000264331.4	37																																																																																				.		0.348	TOP2B-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding			
ZCCHC3	85364	hgsc.bcm.edu	37	20	278688	278688	+	Missense_Mutation	SNP	C	C	A	rs11468351|rs5839847|rs6147263	byFrequency	TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr20:278688C>A	ENST00000382352.3	+	1	952	c.461C>A	c.(460-462)cCg>cAg	p.P154Q		NM_033089.6	NP_149080	Q9NUD5	ZCHC3_HUMAN	zinc finger, CCHC domain containing 3	154							poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.A159delA(3)		endometrium(2)|large_intestine(1)|lung(3)|prostate(2)	8		all_cancers(10;0.000209)|Lung NSC(37;0.0417)|all_lung(30;0.0713)|all_epithelial(17;0.0748)|Breast(17;0.231)	OV - Ovarian serous cystadenocarcinoma(29;0.149)			CAGGATGAgccggcggcggcg	0.766																																					p.P154Q		.											.,4	.	20	3	Deletion - In frame(3)	prostate(2)|large_intestine(1)	c.C461A						.						1.0	1.0	1.0					20																	278688		782	1539	2321	SO:0001583	missense	85364	exon1			ATGAGCCGGCGGC	AL034548	CCDS42844.1	20p13-p12.2	2014-04-10	2004-07-14	2004-07-14	ENSG00000177764	ENSG00000247315		"""Zinc fingers, CCHC domain containing"""	16230	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 99"""	C20orf99			Standard	NM_033089		Approved	dJ1103G7.7	uc002wdf.3	Q9NUD5	OTTHUMG00000188280	ENST00000382352.3:c.461C>A	20.37:g.278688C>A	ENSP00000371789:p.Pro154Gln	Somatic	10	0		WXS	Illumina HiSeq	.	15	2	NM_033089	Q3B7J3|Q6NT79	Missense_Mutation	SNP	ENST00000382352.3	37	CCDS42844.1	.	.	.	.	.	.	.	.	.	.	C	0.443	-0.897474	0.02472	.	.	ENSG00000177764	ENST00000382352	.	.	.	3.88	-3.04	0.05412	.	2.664870	0.01730	N	0.028791	T	0.26666	0.0652	N	0.19112	0.55	0.18873	N	0.999987	B	0.02656	0.0	B	0.01281	0.0	T	0.15263	-1.0443	9	0.34782	T	0.22	0.975	5.6625	0.17676	0.1627:0.6261:0.1076:0.1036	.	154	Q9NUD5	ZCHC3_HUMAN	Q	154	.	ENSP00000371789:P154Q	P	+	2	0	ZCCHC3	226688	0.510000	0.26171	0.018000	0.16275	0.097000	0.18754	-0.212000	0.09319	-0.309000	0.08779	0.305000	0.20034	CCG	.		0.766	ZCCHC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077447.1		
FAT1	2195	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	4	187542176	187542176	+	Missense_Mutation	SNP	G	G	A			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr4:187542176G>A	ENST00000441802.2	-	10	5773	c.5564C>T	c.(5563-5565)cCa>cTa	p.P1855L		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	1855	Cadherin 16. {ECO:0000255|PROSITE- ProRule:PRU00043}.				actin filament organization (GO:0007015)|anatomical structure morphogenesis (GO:0009653)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(38)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(33)|lung(88)|ovary(13)|pancreas(2)|prostate(16)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	228						AAATAAACGTGGGGTTCCCAT	0.403										HNSCC(5;0.00058)																											p.P1855L	Colon(197;1040 2055 4143 4984 49344)	.											.	.	.	0			c.C5564T						.						65.0	66.0	66.0					4																	187542176		1939	4128	6067	SO:0001583	missense	2195	exon10			AAACGTGGGGTTC	X87241	CCDS47177.1	4q35.2	2013-05-31	2013-05-31	2008-10-30	ENSG00000083857	ENSG00000083857		"""Cadherins / Cadherin-related"""	3595	protein-coding gene	gene with protein product	"""cadherin-related family member 8"""	600976	"""FAT tumor suppressor (Drosophila) homolog"", ""FAT tumor suppressor homolog 1 (Drosophila)"""	FAT		8586420	Standard	XM_005262834		Approved	CDHF7, CDHR8	uc003izf.3	Q14517	OTTHUMG00000160320	ENST00000441802.2:c.5564C>T	4.37:g.187542176G>A	ENSP00000406229:p.Pro1855Leu	Somatic	12	0		WXS	Illumina HiSeq	.	20	15	NM_005245		Missense_Mutation	SNP	ENST00000441802.2	37	CCDS47177.1	.	.	.	.	.	.	.	.	.	.	G	24.9	4.582377	0.86748	.	.	ENSG00000083857	ENST00000441802;ENST00000260147	T	0.57436	0.4	5.55	5.55	0.83447	Cadherin (4);Cadherin-like (1);	0.000000	0.85682	D	0.000000	T	0.79787	0.4506	M	0.91196	3.185	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.82794	-0.0281	10	0.62326	D	0.03	.	19.6941	0.96016	0.0:0.0:1.0:0.0	.	1855	Q14517	FAT1_HUMAN	L	1855;1857	ENSP00000406229:P1855L	ENSP00000260147:P1857L	P	-	2	0	FAT1	187779170	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	9.657000	0.98554	2.885000	0.99019	0.655000	0.94253	CCA	.		0.403	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245	
PRPF18	8559	hgsc.bcm.edu	37	10	13629126	13629126	+	Silent	SNP	C	C	T			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr10:13629126C>T	ENST00000378572.3	+	1	200	c.40C>T	c.(40-42)Ctg>Ttg	p.L14L		NM_003675.3	NP_003666.1	Q99633	PRP18_HUMAN	pre-mRNA processing factor 18	14					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	potassium channel inhibitor activity (GO:0019870)			central_nervous_system(1)|endometrium(5)|large_intestine(5)|lung(5)|prostate(1)	17						GAAGCGGCAGCTGGTGGAGGA	0.587																																					p.L14L		.											.	.	.	0			c.C40T						.						98.0	107.0	104.0					10																	13629126		2203	4300	6503	SO:0001819	synonymous_variant	8559	exon1			CGGCAGCTGGTGG	U51990	CCDS7100.1	10p12.33	2013-06-10	2013-06-10		ENSG00000165630	ENSG00000165630			17351	protein-coding gene	gene with protein product		604993	"""PRP18 pre-mRNA processing factor 18 homolog (yeast)"", ""PRP18 pre-mRNA processing factor 18 homolog (S. cerevisiae)"""			9000057	Standard	XM_005252634		Approved	hPrp18	uc001imp.3	Q99633	OTTHUMG00000017702	ENST00000378572.3:c.40C>T	10.37:g.13629126C>T		Somatic	66	0		WXS	Illumina HiSeq	.	95	3	NM_003675	Q5T9P9|Q9BUI9	Silent	SNP	ENST00000378572.3	37	CCDS7100.1																																																																																			.		0.587	PRPF18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046879.1		
HDGFRP2	84717	hgsc.bcm.edu	37	19	4493798	4493798	+	Silent	SNP	T	T	C	rs533672657		TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr19:4493798T>C	ENST00000301284.4	+	7	841	c.777T>C	c.(775-777)tcT>tcC	p.S259S	HDGFRP2_ENST00000586684.1_Silent_p.S259S	NM_001001520.1|NM_032631.2	NP_001001520|NP_116020.1	Q7Z4V5	HDGR2_HUMAN		259	Ser-rich.				transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)										cctcctcctcttcctcctcct	0.672													t|||	1	0.000199681	0.0	0.0	5008	,	,		13543	0.001		0.0	False		,,,				2504	0.0				p.S259S		.											.,1	.	.	0			c.T777C						.						15.0	19.0	17.0					19																	4493798		2105	4182	6287	SO:0001819	synonymous_variant	0	exon7			CTCCTCTTCCTCC																												ENST00000301284.4:c.777T>C	19.37:g.4493798T>C		Somatic	30	0		WXS	Illumina HiSeq	.	59	3	NM_032631	I3L080|K7EQZ6|Q96GI5|Q9BW08	Silent	SNP	ENST00000301284.4	37	CCDS42472.1																																																																																			.		0.672	HDGFRP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458642.1		
PKD1L1	168507	hgsc.bcm.edu	37	7	47894505	47894505	+	Missense_Mutation	SNP	C	C	T			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr7:47894505C>T	ENST00000289672.2	-	30	4884	c.4834G>A	c.(4834-4836)Gca>Aca	p.A1612T		NM_138295.3	NP_612152.1	Q8TDX9	PK1L1_HUMAN	polycystic kidney disease 1 like 1	1612					detection of mechanical stimulus (GO:0050982)|detection of nodal flow (GO:0003127)|left/right axis specification (GO:0070986)|single organismal cell-cell adhesion (GO:0016337)	calcium channel complex (GO:0034704)|cilium (GO:0005929)|membrane (GO:0016020)|nonmotile primary cilium (GO:0031513)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)		BBS9/PKD1L1(2)	NS(1)|breast(9)|central_nervous_system(1)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(27)|lung(44)|ovary(12)|prostate(5)|skin(8)|stomach(4)|upper_aerodigestive_tract(5)	142						ACGGGAAATGCCCTTGTAACA	0.393																																					p.A1612T		.											.	.	.	0			c.G4834A						.						116.0	114.0	115.0					7																	47894505		2203	4300	6503	SO:0001583	missense	168507	exon30			GAAATGCCCTTGT	AB061683	CCDS34633.1	7p12.3	2008-07-18			ENSG00000158683	ENSG00000158683			18053	protein-coding gene	gene with protein product	"""polycystin-1L1"""	609721				11863367	Standard	NM_138295		Approved	PRO19563	uc003tny.2	Q8TDX9	OTTHUMG00000155649	ENST00000289672.2:c.4834G>A	7.37:g.47894505C>T	ENSP00000289672:p.Ala1612Thr	Somatic	31	0		WXS	Illumina HiSeq	.	92	4	NM_138295	Q6UWK1	Missense_Mutation	SNP	ENST00000289672.2	37	CCDS34633.1	.	.	.	.	.	.	.	.	.	.	C	11.25	1.582317	0.28180	.	.	ENSG00000158683	ENST00000289672	T	0.22134	1.97	5.22	3.06	0.35304	.	0.436137	0.20220	N	0.096705	T	0.10723	0.0262	N	0.19112	0.55	0.09310	N	1	B	0.26876	0.162	B	0.24848	0.056	T	0.28650	-1.0037	10	0.15952	T	0.53	-9.0842	6.0706	0.19887	0.0:0.6663:0.1996:0.1341	.	1612	Q8TDX9	PK1L1_HUMAN	T	1612	ENSP00000289672:A1612T	ENSP00000289672:A1612T	A	-	1	0	PKD1L1	47861030	0.015000	0.18098	0.003000	0.11579	0.003000	0.03518	0.505000	0.22642	1.161000	0.42604	0.655000	0.94253	GCA	.		0.393	PKD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340974.1	NM_138295	
GOLPH3L	55204	hgsc.bcm.edu	37	1	150667291	150667291	+	Silent	SNP	G	G	T			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr1:150667291G>T	ENST00000271732.3	-	2	68	c.24C>A	c.(22-24)gcC>gcA	p.A8A	GOLPH3L_ENST00000479757.1_5'UTR|GOLPH3L_ENST00000540514.1_Silent_p.A8A	NM_018178.5	NP_060648.2	Q9H4A5	GLP3L_HUMAN	golgi phosphoprotein 3-like	8					Golgi organization (GO:0007030)|positive regulation of protein secretion (GO:0050714)	Golgi membrane (GO:0000139)|trans-Golgi network membrane (GO:0032588)	phosphatidylinositol-4-phosphate binding (GO:0070273)			breast(1)|endometrium(1)|large_intestine(2)|lung(3)|ovary(1)	8	all_cancers(9;3.09e-52)|all_epithelial(9;4.47e-43)|all_lung(15;1.09e-34)|Lung NSC(24;4.04e-31)|Breast(34;0.000615)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Melanoma(130;0.128)|Colorectal(459;0.171)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0241)|Epithelial(6;1.2e-23)|all cancers(9;4.81e-23)|OV - Ovarian serous cystadenocarcinoma(6;1.93e-15)|BRCA - Breast invasive adenocarcinoma(12;0.000479)|LUSC - Lung squamous cell carcinoma(543;0.171)			CAGTGCGACGGGCCCGGTGAG	0.388																																					p.A8A		.											.	.	.	0			c.C24A						.						139.0	132.0	134.0					1																	150667291		2203	4300	6503	SO:0001819	synonymous_variant	55204	exon2			GCGACGGGCCCGG	AJ296153	CCDS966.1	1q21	2008-02-05			ENSG00000143457	ENSG00000143457			24882	protein-coding gene	gene with protein product		612208					Standard	NM_018178		Approved	GPP34R	uc001evj.2	Q9H4A5	OTTHUMG00000035009	ENST00000271732.3:c.24C>A	1.37:g.150667291G>T		Somatic	47	0		WXS	Illumina HiSeq	.	76	4	NM_018178	B1AN09|B7Z6N3|Q9NVK0	Silent	SNP	ENST00000271732.3	37	CCDS966.1																																																																																			.		0.388	GOLPH3L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084734.1	NM_018178	
MYO9A	4649	hgsc.bcm.edu	37	15	72338441	72338441	+	Missense_Mutation	SNP	G	G	A			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr15:72338441G>A	ENST00000356056.5	-	2	936	c.464C>T	c.(463-465)cCt>cTt	p.P155L	MYO9A_ENST00000566885.1_Intron|RNU2-65P_ENST00000410162.1_RNA|MYO9A_ENST00000444904.1_Missense_Mutation_p.P155L|MYO9A_ENST00000563542.1_5'UTR|MYO9A_ENST00000424560.1_Missense_Mutation_p.P155L|MYO9A_ENST00000564571.1_Missense_Mutation_p.P155L	NM_006901.3	NP_008832.2	B2RTY4	MYO9A_HUMAN	myosin IXA	155	Myosin motor.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|visual perception (GO:0007601)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|unconventional myosin complex (GO:0016461)	ATP binding (GO:0005524)|GTPase activator activity (GO:0005096)|metal ion binding (GO:0046872)|motor activity (GO:0003774)			NS(4)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(29)|lung(27)|ovary(1)|pancreas(1)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	88						ATTCAAATCAGGTAAACTACA	0.378																																					p.P155L		.											.	.	.	0			c.C464T						.						79.0	81.0	80.0					15																	72338441		2199	4297	6496	SO:0001583	missense	4649	exon2			AAATCAGGTAAAC	AF117888	CCDS10239.1	15q22-q23	2011-09-27			ENSG00000066933	ENSG00000066933		"""Myosins / Myosin superfamily : Class IX"""	7608	protein-coding gene	gene with protein product		604875				10409426	Standard	NM_006901		Approved	FLJ11061, FLJ13244, MGC71859	uc002atl.5	B2RTY4	OTTHUMG00000133440	ENST00000356056.5:c.464C>T	15.37:g.72338441G>A	ENSP00000348349:p.Pro155Leu	Somatic	44	0		WXS	Illumina HiSeq	.	95	4	NM_006901	B0I1T5|C9IYB3|C9JA86|Q14787|Q3YLD7|Q3YLD8|Q6P986|Q9H8T5|Q9NTG2|Q9NUY2|Q9UEP3|Q9UNJ2	Missense_Mutation	SNP	ENST00000356056.5	37	CCDS10239.1	.	.	.	.	.	.	.	.	.	.	g	28.0	4.879978	0.91740	.	.	ENSG00000066933	ENST00000356056;ENST00000424560;ENST00000444904;ENST00000261864;ENST00000446448	D;D;D	0.87103	-2.21;-2.21;-2.21	5.79	5.79	0.91817	Myosin head, motor domain (2);	.	.	.	.	D	0.94331	0.8178	M	0.83774	2.66	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.83275	0.991;0.996;0.994	D	0.94384	0.7607	9	0.87932	D	0	.	20.1027	0.97880	0.0:0.0:1.0:0.0	.	155;155;155	B2RTY4-3;B7WP69;B2RTY4	.;.;MYO9A_HUMAN	L	155	ENSP00000348349:P155L;ENSP00000399162:P155L;ENSP00000398250:P155L	ENSP00000261864:P155L	P	-	2	0	MYO9A	70125495	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	9.768000	0.98965	2.745000	0.94114	0.644000	0.83932	CCT	.		0.378	MYO9A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257308.1	NM_006901	
SRFBP1	153443	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	5	121362644	121362644	+	Silent	SNP	A	A	T			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr5:121362644A>T	ENST00000339397.4	+	8	1185	c.1113A>T	c.(1111-1113)ccA>ccT	p.P371P	SRFBP1_ENST00000504881.1_Intron	NM_152546.2	NP_689759.2			serum response factor binding protein 1											central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(6)|skin(1)	15		all_cancers(142;0.0124)|Prostate(80;0.0322)	KIRC - Kidney renal clear cell carcinoma(527;0.206)	OV - Ovarian serous cystadenocarcinoma(64;0.000227)|Epithelial(69;0.000365)|all cancers(49;0.00517)		TAGATTTTCCACAGAATGAGC	0.318																																					p.P371P		.											.	.	.	0			c.A1113T						.						36.0	34.0	34.0					5																	121362644		1804	4063	5867	SO:0001819	synonymous_variant	153443	exon8			TTTTCCACAGAAT	AK058015	CCDS43354.1	5q23.1	2006-12-21				ENSG00000151304			26333	protein-coding gene	gene with protein product	"""BUD22 homolog (S. cerevisiae)"""	610479				15492011	Standard	NM_152546		Approved	FLJ25286, p49, STRAP, BUD22, Rlb1	uc003kst.1	Q8NEF9		ENST00000339397.4:c.1113A>T	5.37:g.121362644A>T		Somatic	34	0		WXS	Illumina HiSeq	.	61	29	NM_152546		Silent	SNP	ENST00000339397.4	37	CCDS43354.1																																																																																			.		0.318	SRFBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371200.1	NM_152546	
UHRF1BP1	54887	hgsc.bcm.edu	37	6	34803196	34803196	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr6:34803196G>T	ENST00000192788.5	+	7	966	c.795G>T	c.(793-795)gaG>gaT	p.E265D	UHRF1BP1_ENST00000452449.2_Missense_Mutation_p.E265D	NM_017754.3	NP_060224.3	Q6BDS2	URFB1_HUMAN	UHRF1 binding protein 1	265							histone deacetylase binding (GO:0042826)|identical protein binding (GO:0042802)			breast(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(11)|lung(24)|ovary(3)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)	54						AAGCCATGGAGAAGTCAGCCC	0.522																																					p.E265D		.											.	.	.	0			c.G795T						.						94.0	94.0	94.0					6																	34803196		2024	4182	6206	SO:0001583	missense	54887	exon7			CATGGAGAAGTCA	AB126777	CCDS43455.1	6p21.31	2008-10-28	2008-08-15	2007-11-27	ENSG00000065060	ENSG00000065060			21216	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 107"""	C6orf107			Standard	NM_017754		Approved	FLJ20302, dJ349A12.1, ICBP90	uc003oju.4	Q6BDS2	OTTHUMG00000014557	ENST00000192788.5:c.795G>T	6.37:g.34803196G>T	ENSP00000192788:p.Glu265Asp	Somatic	24	0		WXS	Illumina HiSeq	.	45	4	NM_017754	Q9NXE0	Missense_Mutation	SNP	ENST00000192788.5	37	CCDS43455.1	.	.	.	.	.	.	.	.	.	.	G	24.1	4.489454	0.84962	.	.	ENSG00000065060	ENST00000192788;ENST00000452449	T;T	0.10668	2.85;2.85	4.57	2.76	0.32466	.	0.000000	0.85682	D	0.000000	T	0.15998	0.0385	M	0.74881	2.28	0.58432	D	0.999999	D	0.69078	0.997	P	0.58970	0.849	T	0.01432	-1.1356	10	0.87932	D	0	-13.8301	11.2309	0.48912	0.1518:0.0:0.8482:0.0	.	265	Q6BDS2	URFB1_HUMAN	D	265	ENSP00000192788:E265D;ENSP00000400628:E265D	ENSP00000192788:E265D	E	+	3	2	UHRF1BP1	34911174	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.926000	0.56491	0.650000	0.30769	0.650000	0.86243	GAG	.		0.522	UHRF1BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040260.1	NM_017754	
HMCN1	83872	hgsc.bcm.edu	37	1	186075931	186075931	+	Intron	SNP	A	A	C			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr1:186075931A>C	ENST00000271588.4	+	70	10999				HMCN1_ENST00000367492.2_Intron	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1						response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						GTGTGGGGTTATTTACATTCA	0.313																																					.		.											.	.	.	0			.						.																																			SO:0001627	intron_variant	100302192	.			GGGGTTATTTACA	AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"""Fibulins"", ""Immunoglobulin superfamily / I-set domain containing"""	19194	protein-coding gene	gene with protein product	"""fibulin 6"""	608548	"""age-related macular degeneration 1 (senile macular degeneration)"""	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.10771-85A>C	1.37:g.186075931A>C		Somatic	14	0		WXS	Illumina HiSeq	.	24	8	.	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	RNA	SNP	ENST00000271588.4	37	CCDS30956.1																																																																																			.		0.313	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935	
AKAP11	11215	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	13	42873939	42873939	+	Missense_Mutation	SNP	A	A	C			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr13:42873939A>C	ENST00000025301.2	+	8	1232	c.1057A>C	c.(1057-1059)Agt>Cgt	p.S353R		NM_016248.3	NP_057332.1	Q9UKA4	AKA11_HUMAN	A kinase (PRKA) anchor protein 11	353					intracellular signal transduction (GO:0035556)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	protein kinase A binding (GO:0051018)|protein phosphatase 1 binding (GO:0008157)			breast(3)|central_nervous_system(4)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(10)|liver(1)|lung(22)|ovary(1)|skin(3)|stomach(2)	56		Lung NSC(96;1.86e-05)|Prostate(109;0.0165)|Lung SC(185;0.0262)|Breast(139;0.0707)|Hepatocellular(98;0.114)		OV - Ovarian serous cystadenocarcinoma(117;0.000365)|GBM - Glioblastoma multiforme(144;0.00116)|BRCA - Breast invasive adenocarcinoma(63;0.19)		CTCAGAAGTAAGTGAATTTTT	0.363																																					p.S353R		.											.	.	.	0			c.A1057C						.						37.0	38.0	38.0					13																	42873939		2202	4297	6499	SO:0001583	missense	11215	exon8			GAAGTAAGTGAAT	AB014529	CCDS9383.1	13q	2012-04-17			ENSG00000023516	ENSG00000023516		"""A-kinase anchor proteins"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	369	protein-coding gene	gene with protein product	"""AKAP 220"", ""A-kinase anchoring protein, 220kDa"", ""protein kinase A anchoring protein 11"", ""protein phosphatase 1, regulatory subunit 44"""	604696				9734811, 8621616	Standard	NM_016248		Approved	KIAA0629, AKAP220, PRKA11, FLJ11304, DKFZp781I12161, PPP1R44	uc001uys.2	Q9UKA4	OTTHUMG00000016805	ENST00000025301.2:c.1057A>C	13.37:g.42873939A>C	ENSP00000025301:p.Ser353Arg	Somatic	55	0		WXS	Illumina HiSeq	.	86	49	NM_016248	O75124|Q9NUK7	Missense_Mutation	SNP	ENST00000025301.2	37	CCDS9383.1	.	.	.	.	.	.	.	.	.	.	A	17.13	3.311757	0.60414	.	.	ENSG00000023516	ENST00000025301	T	0.26518	1.73	5.44	4.25	0.50352	.	0.000000	0.85682	D	0.000000	T	0.45617	0.1351	M	0.64997	1.995	0.58432	D	0.999993	D	0.89917	1.0	D	0.72625	0.978	T	0.44952	-0.9294	10	0.87932	D	0	.	11.9069	0.52717	0.9283:0.0:0.0717:0.0	.	353	Q9UKA4	AKA11_HUMAN	R	353	ENSP00000025301:S353R	ENSP00000025301:S353R	S	+	1	0	AKAP11	41771939	1.000000	0.71417	0.999000	0.59377	0.992000	0.81027	5.869000	0.69613	2.182000	0.69389	0.482000	0.46254	AGT	.		0.363	AKAP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044700.2	NM_016248	
ACOX1	51	hgsc.bcm.edu	37	17	73944443	73944443	+	Missense_Mutation	SNP	A	A	T			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr17:73944443A>T	ENST00000301608.4	-	13	1884	c.1824T>A	c.(1822-1824)gaT>gaA	p.D608E	ACOX1_ENST00000537812.1_Missense_Mutation_p.D570E|ACOX1_ENST00000293217.5_Missense_Mutation_p.D608E	NM_007292.5	NP_009223.2	Q15067	ACOX1_HUMAN	acyl-CoA oxidase 1, palmitoyl	608					alpha-linolenic acid metabolic process (GO:0036109)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|fatty acid oxidation (GO:0019395)|generation of precursor metabolites and energy (GO:0006091)|lipid homeostasis (GO:0055088)|lipid metabolic process (GO:0006629)|peroxisome fission (GO:0016559)|positive regulation of cholesterol homeostasis (GO:2000189)|prostaglandin metabolic process (GO:0006693)|small molecule metabolic process (GO:0044281)|spermatogenesis (GO:0007283)|unsaturated fatty acid metabolic process (GO:0033559)|very long-chain fatty acid metabolic process (GO:0000038)	membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	acyl-CoA dehydrogenase activity (GO:0003995)|acyl-CoA oxidase activity (GO:0003997)|FAD binding (GO:0071949)|fatty acid binding (GO:0005504)|flavin adenine dinucleotide binding (GO:0050660)|palmitoyl-CoA oxidase activity (GO:0016401)|PDZ domain binding (GO:0030165)|protein N-terminus binding (GO:0047485)|receptor binding (GO:0005102)			large_intestine(2)|lung(7)|ovary(2)|prostate(2)|skin(1)	14					Flavin adenine dinucleotide(DB03147)	AATCAAATGCATCAACCAAAG	0.453																																					p.D608E		.											.	.	.	0			c.T1824A						.						194.0	163.0	174.0					17																	73944443		2203	4300	6503	SO:0001583	missense	51	exon13			AAATGCATCAACC	U03254	CCDS11734.1, CCDS11735.1	17q25.1	2012-10-04	2010-04-30		ENSG00000161533	ENSG00000161533	1.3.3.6		119	protein-coding gene	gene with protein product		609751	"""acyl-Coenzyme A oxidase 1, palmitoyl"""			8159712	Standard	NM_007292		Approved	PALMCOX	uc002jqe.3	Q15067	OTTHUMG00000180027	ENST00000301608.4:c.1824T>A	17.37:g.73944443A>T	ENSP00000301608:p.Asp608Glu	Somatic	40	0		WXS	Illumina HiSeq	.	94	4	NM_007292	A8K6X8|A8KAA0|B4DK61|F5GYQ8|Q12863|Q15068|Q15101|Q16131|Q7Z3W5|Q9UD31	Missense_Mutation	SNP	ENST00000301608.4	37	CCDS11735.1	.	.	.	.	.	.	.	.	.	.	A	22.5	4.292717	0.80914	.	.	ENSG00000161533	ENST00000301608;ENST00000293217;ENST00000537812;ENST00000539791;ENST00000538781	D;D;D	0.84730	-1.89;-1.89;-1.89	5.35	2.89	0.33648	Acyl-CoA oxidase, C-terminal (1);Acyl-CoA dehydrogenase/oxidase C-terminal (2);	0.000000	0.85682	D	0.000000	D	0.91593	0.7344	M	0.84511	2.7	0.58432	D	0.99999	D;D;D;P	0.89917	1.0;1.0;0.959;0.885	D;D;P;P	0.97110	1.0;1.0;0.766;0.447	D	0.90579	0.4528	10	0.87932	D	0	-32.0135	9.3918	0.38378	0.7536:0.0:0.2464:0.0	.	540;570;608;608	F5H0M0;F5GYQ8;Q15067;Q15067-2	.;.;ACOX1_HUMAN;.	E	608;608;570;608;540	ENSP00000301608:D608E;ENSP00000293217:D608E;ENSP00000441257:D570E	ENSP00000293217:D608E	D	-	3	2	ACOX1	71456038	0.599000	0.26891	0.994000	0.49952	0.995000	0.86356	-0.055000	0.11807	0.449000	0.26747	0.533000	0.62120	GAT	.		0.453	ACOX1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439503.1		
NAV1	89796	hgsc.bcm.edu	37	1	201709171	201709171	+	Intron	SNP	C	C	A			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr1:201709171C>A	ENST00000367296.4	+	3	1646				NAV1_ENST00000367300.3_Intron|IPO9-AS1_ENST00000413035.1_RNA|NAV1_ENST00000295624.6_Intron|NAV1_ENST00000367297.4_Intron|NAV1_ENST00000367302.1_Intron|RP11-90L20.2_ENST00000429443.1_RNA|NAV1_ENST00000367295.1_Missense_Mutation_p.P7H	NM_020443.4	NP_065176.3	Q8NEY1	NAV1_HUMAN	neuron navigator 1						microtubule bundle formation (GO:0001578)|neuron migration (GO:0001764)	cytoplasm (GO:0005737)|microtubule (GO:0005874)				breast(5)|central_nervous_system(4)|endometrium(4)|haematopoietic_and_lymphoid_tissue(5)|kidney(3)|large_intestine(10)|lung(29)|ovary(4)|prostate(3)|skin(1)|stomach(2)	70						CTGCCCCTGCCCAGATCCGGA	0.701																																					p.P7H		.											.	.	.	0			c.C20A						.						28.0	40.0	36.0					1																	201709171		692	1591	2283	SO:0001627	intron_variant	89796	exon1			CCCTGCCCAGATC	AF086348	CCDS1414.1, CCDS1414.2, CCDS53456.1	1q32.3	2008-07-18			ENSG00000134369	ENSG00000134369			15989	protein-coding gene	gene with protein product	"""neuron navigator-1"", ""pore membrane and/or filament interacting like protein 3"""	611628				12079279, 12062803	Standard	NM_020443		Approved	FLJ12560, FLJ14203, KIAA1151, MGC14961, POMFIL3, steerin-1, DKFZp781D0314	uc001gwu.3	Q8NEY1	OTTHUMG00000035766	ENST00000367296.4:c.1226+21288C>A	1.37:g.201709171C>A		Somatic	106	0		WXS	Illumina HiSeq	.	93	4	NM_001167738	A8MS88|Q5SVH1|Q5SVH2|Q5SVH3|Q5SVH7|Q5VUY9|Q8IVL2|Q96II1|Q9H7V9|Q9H9S9|Q9H9T5|Q9UGI1|Q9ULK7|Q9ULR9	Missense_Mutation	SNP	ENST00000367296.4	37	CCDS1414.2	.	.	.	.	.	.	.	.	.	.	C	16.65	3.181976	0.57800	.	.	ENSG00000134369	ENST00000367295	T	0.06687	3.27	4.37	4.37	0.52481	.	.	.	.	.	T	0.13628	0.0330	.	.	.	0.80722	D	1	P	0.46457	0.878	P	0.46885	0.53	T	0.00773	-1.1572	8	0.87932	D	0	.	12.3398	0.55087	0.0:1.0:0.0:0.0	.	7	Q8NEY1-5	.	H	7	ENSP00000356264:P7H	ENSP00000356264:P7H	P	+	2	0	NAV1	199975794	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	3.172000	0.50832	2.252000	0.74401	0.586000	0.80456	CCC	.		0.701	NAV1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000087013.1	NM_020443	
BPIFB4	149954	hgsc.bcm.edu	37	20	31685468	31685468	+	Nonsense_Mutation	SNP	C	C	T			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr20:31685468C>T	ENST00000375483.3	+	11	1444	c.1444C>T	c.(1444-1446)Cag>Tag	p.Q482*		NM_182519.2	NP_872325.2	P59827	BPIB4_HUMAN	BPI fold containing family B, member 4	482						cytoplasm (GO:0005737)|extracellular region (GO:0005576)	lipid binding (GO:0008289)	p.Q443*(1)									CATCAGGATCCAGGTGCTGAA	0.592																																					p.Q482X		.											C20orf186,scalp,carcinoma,0,1	C20orf186	0	1	Substitution - Nonsense(1)	skin(1)	c.C1444T						.						161.0	137.0	145.0					20																	31685468		2203	4300	6503	SO:0001587	stop_gained	149954	exon11			AGGATCCAGGTGC	AF549190	CCDS13213.2	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000186191	ENSG00000186191		"""BPI fold containing"""	16179	protein-coding gene	gene with protein product		615718	"""chromosome 20 open reading frame 186"""	C20orf186		11971875, 21787333	Standard	NM_182519		Approved	dJ726C3.5, LPLUNC4	uc010zue.2	P59827	OTTHUMG00000032235	ENST00000375483.3:c.1444C>T	20.37:g.31685468C>T	ENSP00000364632:p.Gln482*	Somatic	7	0		WXS	Illumina HiSeq	.	38	2	NM_182519	Q5TDX6	Nonsense_Mutation	SNP	ENST00000375483.3	37	CCDS13213.2	.	.	.	.	.	.	.	.	.	.	C	37	5.987630	0.97179	.	.	ENSG00000186191	ENST00000375483	.	.	.	5.44	5.44	0.79542	.	0.354891	0.26769	N	0.022582	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.08179	T	0.78	-21.6417	15.1038	0.72303	0.0:1.0:0.0:0.0	.	.	.	.	X	482	.	ENSP00000364632:Q482X	Q	+	1	0	BPIFB4	31149129	1.000000	0.71417	1.000000	0.80357	0.813000	0.45954	1.296000	0.33389	2.711000	0.92665	0.462000	0.41574	CAG	.		0.592	BPIFB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078655.5	NM_182519	
ACO2	50	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	22	41911822	41911822	+	Missense_Mutation	SNP	G	G	A			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr22:41911822G>A	ENST00000216254.4	+	6	758	c.736G>A	c.(736-738)Gat>Aat	p.D246N	ACO2_ENST00000396512.3_Missense_Mutation_p.D246N|ACO2_ENST00000466237.1_3'UTR	NM_001098.2	NP_001089.1	Q99798	ACON_HUMAN	aconitase 2, mitochondrial	246					cell death (GO:0008219)|cellular metabolic process (GO:0044237)|citrate metabolic process (GO:0006101)|generation of precursor metabolites and energy (GO:0006091)|isocitrate metabolic process (GO:0006102)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	3 iron, 4 sulfur cluster binding (GO:0051538)|4 iron, 4 sulfur cluster binding (GO:0051539)|aconitate hydratase activity (GO:0003994)|iron ion binding (GO:0005506)			breast(3)|endometrium(5)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(2)	23						CTCACCCAAAGATGTGATCCT	0.612																																					p.D246N		.											.	.	.	0			c.G736A						.						102.0	86.0	91.0					22																	41911822		2203	4300	6503	SO:0001583	missense	50	exon6			CCCAAAGATGTGA	AH006514	CCDS14017.1	22q13.2	2013-05-21			ENSG00000100412	ENSG00000100412	4.2.1.3		118	protein-coding gene	gene with protein product	"""aconitate hydratase, mitochondrial"""	100850				10591208	Standard	NM_001098		Approved	ACONM	uc003bac.3	Q99798	OTTHUMG00000030544	ENST00000216254.4:c.736G>A	22.37:g.41911822G>A	ENSP00000216254:p.Asp246Asn	Somatic	39	0		WXS	Illumina HiSeq	.	60	14	NM_001098	O75809|Q5JZ41|Q6FHX0|Q8TAQ6	Missense_Mutation	SNP	ENST00000216254.4	37	CCDS14017.1	.	.	.	.	.	.	.	.	.	.	G	36	5.849201	0.97023	.	.	ENSG00000100412	ENST00000544234;ENST00000216254;ENST00000396512	D;D	0.97209	-4.29;-4.29	5.81	5.81	0.92471	Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha (2);Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha, subdomain 2 (1);	0.000000	0.85682	D	0.000000	D	0.99435	0.9800	H	0.99961	5.07	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.97787	1.0236	10	0.87932	D	0	.	20.0825	0.97783	0.0:0.0:1.0:0.0	.	246;246	A2A274;Q99798	.;ACON_HUMAN	N	227;246;246	ENSP00000216254:D246N;ENSP00000379769:D246N	ENSP00000216254:D246N	D	+	1	0	ACO2	40241768	1.000000	0.71417	1.000000	0.80357	0.945000	0.59286	9.192000	0.94947	2.746000	0.94184	0.655000	0.94253	GAT	.		0.612	ACO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259151.1	NM_001098	
CLCNKB	1188	broad.mit.edu	37	1	16383402	16383402	+	Silent	SNP	C	C	T	rs6698427		TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr1:16383402C>T	ENST00000375679.4	+	20	2166	c.2055C>T	c.(2053-2055)gcC>gcT	p.A685A	CLCNKB_ENST00000375667.3_Silent_p.A515A|FAM131C_ENST00000494078.1_5'Flank	NM_000085.4	NP_000076.2	P51801	CLCKB_HUMAN	chloride channel, voltage-sensitive Kb	685					excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|regulation of anion transport (GO:0044070)|transmembrane transport (GO:0055085)|transport (GO:0006810)	chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	adenyl nucleotide binding (GO:0030554)|metal ion binding (GO:0046872)|voltage-gated chloride channel activity (GO:0005247)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(2)|prostate(1)|skin(6)|stomach(2)|urinary_tract(1)	21		Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Colorectal(212;8.04e-08)|COAD - Colon adenocarcinoma(227;5.46e-06)|BRCA - Breast invasive adenocarcinoma(304;9.02e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.00655)|READ - Rectum adenocarcinoma(331;0.0649)		ATCCGCCAGCCCCAAAGTGAG	0.587																																					p.A685A													.	CLCNKB	50	0			c.C2055T						.						66.0	64.0	65.0					1																	16383402		2203	4300	6503	SO:0001819	synonymous_variant	1188	exon20			GCCAGCCCCAAAG	AK098217	CCDS168.1, CCDS57974.1	1p36	2012-09-26	2012-02-23		ENSG00000184908	ENSG00000184908		"""Ion channels / Chloride channels : Voltage-sensitive"""	2027	protein-coding gene	gene with protein product		602023	"""chloride channel Kb"""				Standard	NM_000085		Approved	hClC-Kb		P51801	OTTHUMG00000009530	ENST00000375679.4:c.2055C>T	1.37:g.16383402C>T		Somatic	102	0		WXS	Illumina GAIIx	Phase_I	111	4	NM_000085	B3KUY3|Q5T5Q7|Q5T5Q8	Silent	SNP	ENST00000375679.4	37	CCDS168.1																																																																																			.		0.587	CLCNKB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026331.1	NM_000085	
ARHGEF2	9181	broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	155952897	155952897	+	Splice_Site	SNP	C	C	T			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr1:155952897C>T	ENST00000462460.2	-	5	453		c.e5+1		ARHGEF2_ENST00000368316.1_Splice_Site|ARHGEF2_ENST00000477754.2_Intron|RP11-336K24.12_ENST00000610146.1_RNA			Q92974	ARHG2_HUMAN	Rho/Rac guanine nucleotide exchange factor (GEF) 2						actin filament organization (GO:0007015)|apoptotic signaling pathway (GO:0097190)|cell morphogenesis (GO:0000902)|cellular hyperosmotic response (GO:0071474)|cellular response to muramyl dipeptide (GO:0071225)|cellular response to tumor necrosis factor (GO:0071356)|establishment of mitotic spindle orientation (GO:0000132)|innate immune response (GO:0045087)|intracellular protein transport (GO:0006886)|mitotic nuclear division (GO:0007067)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of intrinsic apoptotic signaling pathway in response to osmotic stress (GO:1902219)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of necroptotic process (GO:0060546)|negative regulation of neurogenesis (GO:0050768)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|regulation of cell proliferation (GO:0042127)|regulation of Rho protein signal transduction (GO:0035023)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|neuronal cell body (GO:0043025)|protein complex (GO:0043234)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)|vesicle (GO:0031982)	microtubule binding (GO:0008017)|Rac GTPase binding (GO:0048365)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|Rho GTPase binding (GO:0017048)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			breast(4)|cervix(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(6)|lung(15)|ovary(1)|skin(2)	40	Hepatocellular(266;0.133)|all_hematologic(923;0.145)|all_neural(408;0.195)					CTGACTCCTACCTTGGCCTTT	0.612																																					.	Melanoma(178;35 2768 6610 28839)												.	.	.	0			.						.																																			SO:0001630	splice_region_variant	9181	.			CTCCTACCTTGGC	AB014551	CCDS1125.1, CCDS53375.1, CCDS53376.1	1q21-q22	2013-01-10	2009-06-12		ENSG00000116584	ENSG00000116584		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	682	protein-coding gene	gene with protein product		607560	"""rho/rac guanine nucleotide exchange factor (GEF) 2"""			9857026, 9734811	Standard	NM_004723		Approved	LFP40, GEF-H1, KIAA0651, P40	uc001fmt.2	Q92974	OTTHUMG00000017464	ENST00000462460.2:c.198+1G>A	1.37:g.155952897C>T		Somatic	19	0		WXS	Illumina GAIIx	Phase_I	43	17	.	D3DVA6|O75142|Q15079|Q5VY92|Q8TDA3|Q8WUG4|Q9H023	Splice_Site	SNP	ENST00000462460.2	37		.	.	.	.	.	.	.	.	.	.	C	19.25	3.791307	0.70452	.	.	ENSG00000116584	ENST00000435736	.	.	.	5.54	4.62	0.57501	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.5824	0.50900	0.1777:0.8223:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	ARHGEF2	154219521	1.000000	0.71417	1.000000	0.80357	0.908000	0.53690	3.273000	0.51623	1.558000	0.49541	0.650000	0.86243	.	.		0.612	ARHGEF2-004	PUTATIVE	NAGNAG_splice_site|basic	protein_coding	protein_coding	OTTHUMT00000046207.2	NM_004723	Intron
FAT3	120114	broad.mit.edu	37	11	92532860	92532860	+	Silent	SNP	T	T	C			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr11:92532860T>C	ENST00000298047.6	+	9	6698	c.6681T>C	c.(6679-6681)ccT>ccC	p.P2227P	FAT3_ENST00000409404.2_Silent_p.P2227P|FAT3_ENST00000525166.1_Silent_p.P2077P			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	2227	Cadherin 20. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(10)|kidney(4)|large_intestine(11)|liver(2)|lung(37)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	85		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)				ATGGGGACCCTTTTAAACAGT	0.418										TCGA Ovarian(4;0.039)																											p.P2227P													FAT3_ENST00000409404,NS,carcinoma,+1,2	FAT3	1822	0			c.T6681C						.						52.0	50.0	51.0					11																	92532860		1907	4139	6046	SO:0001819	synonymous_variant	120114	exon9			GGACCCTTTTAAA	AB076400		11q14.3	2013-05-31	2013-05-31		ENSG00000165323	ENSG00000165323		"""Cadherins / Cadherin-related"""	23112	protein-coding gene	gene with protein product	"""cadherin-related family member 10"""	612483	"""FAT tumor suppressor homolog 3 (Drosophila)"""			11811999	Standard	NM_001008781		Approved	KIAA1989, CDHF15, CDHR10	uc001pdj.4	Q8TDW7	OTTHUMG00000154468	ENST00000298047.6:c.6681T>C	11.37:g.92532860T>C		Somatic	44	0		WXS	Illumina GAIIx	Phase_I	50	4	NM_001008781	B5MDB0|Q96AU6	Silent	SNP	ENST00000298047.6	37																																																																																				.		0.418	FAT3-201	KNOWN	basic	protein_coding	protein_coding		NM_001008781	
SAP18	10284	broad.mit.edu	37	13	21714709	21714709	+	5'Flank	SNP	C	C	T	rs368287644		TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr13:21714709C>T	ENST00000607003.1	+	0	0				SAP18_ENST00000382533.4_Silent_p.V6V|SNORD27_ENST00000516319.1_RNA|RN7SL80P_ENST00000580631.1_RNA			O00422	SAP18_HUMAN	Sin3A-associated protein, 18kDa						mRNA processing (GO:0006397)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|positive regulation of apoptotic process (GO:0043065)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	ASAP complex (GO:0061574)|cytoplasm (GO:0005737)|histone deacetylase complex (GO:0000118)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|transcription corepressor activity (GO:0003714)			kidney(1)|large_intestine(1)|lung(4)	6		all_cancers(29;2.16e-20)|all_epithelial(30;2.97e-18)|all_lung(29;4.58e-16)|Lung SC(185;0.0262)|Breast(139;0.147)		all cancers(112;9.79e-05)|Epithelial(112;0.000292)|OV - Ovarian serous cystadenocarcinoma(117;0.00276)|Lung(94;0.0941)		CTGCAGGGGTCGGAGGTCAGG	0.632																																					p.V6V													.	SAP18	12	0			c.C18T						.	C		3,4399		0,3,2198	28.0	27.0	27.0		18	5.5	1.0	13		27	1,8595		0,1,4297	no	coding-synonymous	SAP18	NM_005870.4		0,4,6495	TT,TC,CC		0.0116,0.0682,0.0308		6/173	21714709	4,12994	2201	4298	6499	SO:0001631	upstream_gene_variant	10284	exon1			AGGGGTCGGAGGT	U96915	CCDS9295.2	13q12.11	2008-02-05	2006-02-02		ENSG00000150459	ENSG00000150459			10530	protein-coding gene	gene with protein product		602949	"""sin3A-associated protein, 18kDa"""			9150135	Standard	NM_005870		Approved	SAP18p, 2HOR0202, MGC27131	uc001uns.3	O00422	OTTHUMG00000016535		13.37:g.21714709C>T	Exception_encountered	Somatic	21	0		WXS	Illumina GAIIx	Phase_I	15	4	NM_005870	B2R494|Q2TTR4|Q6IAW9|Q8N606|Q9UF14	Silent	SNP	ENST00000607003.1	37																																																																																				.		0.632	SAP18-009	PUTATIVE	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000470725.1	NM_005870	
OTX2	5015	broad.mit.edu	37	14	57280005	57280005	+	5'Flank	DEL	T	T	-	rs375495685		TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr14:57280005delT	ENST00000555006.1	-	0	0				OTX2_ENST00000554559.1_5'Flank|OTX2-AS1_ENST00000554725.1_RNA|OTX2-AS1_ENST00000534909.2_RNA|OTX2-AS1_ENST00000554358.1_RNA|OTX2-AS1_ENST00000554428.1_RNA|OTX2_ENST00000339475.5_5'Flank			P32243	OTX2_HUMAN	orthodenticle homeobox 2						axon guidance (GO:0007411)|cell fate specification (GO:0001708)|diencephalon morphogenesis (GO:0048852)|dorsal/ventral pattern formation (GO:0009953)|endoderm development (GO:0007492)|eye photoreceptor cell fate commitment (GO:0042706)|forebrain development (GO:0030900)|inner ear morphogenesis (GO:0042472)|metencephalon development (GO:0022037)|midbrain development (GO:0030901)|neuron fate determination (GO:0048664)|positive regulation of embryonic development (GO:0040019)|positive regulation of gastrulation (GO:2000543)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|primitive streak formation (GO:0090009)|protein complex assembly (GO:0006461)|regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)|regulation of smoothened signaling pathway (GO:0008589)|somite rostral/caudal axis specification (GO:0032525)	cytoplasm (GO:0005737)|growth cone (GO:0030426)|nucleus (GO:0005634)|protein complex (GO:0043234)	eukaryotic initiation factor 4E binding (GO:0008190)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(7)|ovary(1)|prostate(1)|urinary_tract(1)	19	Medulloblastoma(1;0.00184)|all_neural(1;0.00414)					GGGGGGGGGGTGAAAGACTTT	0.483																																					.													.	.	.	0			.						.																																			SO:0001631	upstream_gene_variant	0	.			GGGGGGTGAAAGA	AF298117	CCDS9728.1, CCDS41960.1	14q22.3	2014-09-17	2007-02-15		ENSG00000165588	ENSG00000165588		"""Homeoboxes / PRD class"""	8522	protein-coding gene	gene with protein product		600037	"""orthodenticle homolog 2 (Drosophila)"""			7959790	Standard	NM_021728		Approved		uc031qor.1	P32243	OTTHUMG00000152338		14.37:g.57280005delT	Exception_encountered	Somatic	4	0		WXS	Illumina GAIIx	Phase_I	7	3	.	B2RAN5|Q6GTV3|Q9HAW3|Q9P2R1	RNA	DEL	ENST00000555006.1	37	CCDS41960.1																																																																																			.		0.483	OTX2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411522.1	NM_021728.	
RP11-597A11.1	0	broad.mit.edu	37	14	20098927	20098927	+	RNA	DEL	A	A	-	rs373530853|rs548019635		TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr14:20098927delA	ENST00000548261.1	+	0	245																											ATCTTGGGAGAAAAAAATAAC	0.313																																					.													.	.	.	0			.						.																																					0	.			TGGGAGAAAAAAA																													14.37:g.20098927delA		Somatic	79	3		WXS	Illumina GAIIx	Phase_I	90	5	.		RNA	DEL	ENST00000548261.1	37																																																																																				.		0.313	RP11-597A11.1-003	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000409571.1		
CDAN1	146059	broad.mit.edu	37	15	43028860	43028860	+	Frame_Shift_Del	DEL	G	G	-			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr15:43028860delG	ENST00000356231.3	-	2	232	c.209delC	c.(208-210)ccgfs	p.P70fs		NM_138477.2	NP_612486.2	Q8IWY9	CDAN1_HUMAN	codanin 1	70					chromatin assembly (GO:0031497)|chromatin organization (GO:0006325)|negative regulation of DNA replication (GO:0008156)|protein localization (GO:0008104)	cytoplasm (GO:0005737)|endomembrane system (GO:0012505)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				endometrium(2)|kidney(4)|large_intestine(3)|lung(6)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(3)	24		all_cancers(109;5.4e-16)|all_epithelial(112;2.97e-14)|Lung NSC(122;1.75e-08)|all_lung(180;5.99e-08)|Melanoma(134;0.0179)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;2.49e-07)		GGCGGGGGTCGGGGGCCCCTG	0.736																																					p.P70fs													.	CDAN1	70	0			c.209delC						.						3.0	3.0	3.0					15																	43028860		1461	3168	4629	SO:0001589	frameshift_variant	146059	exon2			GGGGTCGGGGGCC	AF525398	CCDS32209.1	15q15.2	2012-04-25	2012-04-25			ENSG00000140326			1713	protein-coding gene	gene with protein product		607465	"""congenital dyserythropoietic anemia, type I"""			8634422, 12434312	Standard	XM_005254177		Approved	CDA-I, CDAI	uc001zql.3	Q8IWY9		ENST00000356231.3:c.209delC	15.37:g.43028860delG	ENSP00000348564:p.Pro70fs	Somatic	6	0		WXS	Illumina GAIIx	Phase_I	9	3	NM_138477	Q6NYD0|Q7Z7L5|Q969N3	Frame_Shift_Del	DEL	ENST00000356231.3	37	CCDS32209.1																																																																																			.		0.736	CDAN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000431103.1	XM_085300	
TP53	7157	broad.mit.edu;bcgsc.ca	37	17	7577554	7577573	+	Frame_Shift_Del	DEL	TGCAGGAACTGTTACACATG	TGCAGGAACTGTTACACATG	-	rs375874539|rs193920789|rs397516437|rs121912655|rs587782664|rs28934573		TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr17:7577554_7577573delTGCAGGAACTGTTACACATG	ENST00000269305.4	-	7	897_916	c.708_727delCATGTGTAACAGTTCCTGCA	c.(706-729)tacatgtgtaacagttcctgcatgfs	p.MCNSSCM237fs	TP53_ENST00000359597.4_Frame_Shift_Del_p.MCNSSCM237fs|TP53_ENST00000445888.2_Frame_Shift_Del_p.MCNSSCM237fs|TP53_ENST00000574684.1_5'UTR|TP53_ENST00000455263.2_Frame_Shift_Del_p.MCNSSCM237fs|TP53_ENST00000413465.2_Frame_Shift_Del_p.MCNSSCM237fs|TP53_ENST00000420246.2_Frame_Shift_Del_p.MCNSSCM237fs	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	237	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with ZNF385A.		M -> I (in LFS; germline mutation and in sporadic cancers; somatic mutation).|M -> K (in sporadic cancers; somatic mutation).|M -> L (in sporadic cancers; somatic mutation).|M -> R (in sporadic cancers; somatic mutation).|M -> T (in sporadic cancers; somatic mutation).|M -> V (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.M237I(109)|p.S241F(85)|p.C242F(82)|p.C238Y(65)|p.C238F(46)|p.C242Y(44)|p.N239D(33)|p.N239S(28)|p.C242S(26)|p.S241C(26)|p.C238S(21)|p.C242fs*5(16)|p.N239fs*25(14)|p.C238R(14)|p.S240G(14)|p.C242R(12)|p.Y236*(12)|p.M237K(11)|p.M243L(10)|p.S241fs*6(9)|p.S241T(8)|p.S240R(8)|p.0?(8)|p.S241Y(8)|p.S241A(8)|p.N239K(7)|p.C242W(7)|p.N239Y(6)|p.M237V(6)|p.S240I(6)|p.C149F(6)|p.S241del(5)|p.C145F(5)|p.N239fs*1(5)|p.C145Y(5)|p.?(5)|p.M237L(5)|p.M144I(4)|p.N239T(4)|p.M237fs*10(4)|p.Y236del(4)|p.S148F(4)|p.M237_N239delMCN(4)|p.C238G(4)|p.C238*(4)|p.M243V(3)|p.C242*(3)|p.M237R(3)|p.N146S(3)|p.S240C(3)|p.N239_C242delNSSC(3)|p.S241S(3)|p.S241P(3)|p.Y236Y(2)|p.C242C(2)|p.C242G(2)|p.N239fs*8(2)|p.S240fs*7(2)|p.N239_S240delNS(2)|p.N239_S240insX(2)|p.S240S(2)|p.S240T(2)|p.C238W(2)|p.C149Y(2)|p.M237T(2)|p.S241fs*22(2)|p.C242fs*20(1)|p.C242fs*23(1)|p.N146fs*1(1)|p.S240>CSC(1)|p.C238_M246delCNSSCMGGM(1)|p.N239fs*26(1)|p.C242fs*98(1)|p.N235_Y236delNY(1)|p.C238fs*2(1)|p.M237_C238insX(1)|p.Y236_M237delYM(1)|p.M144K(1)|p.M144L(1)|p.C242_M246>L(1)|p.N239I(1)|p.N239N(1)|p.C145S(1)|p.M243fs*18(1)|p.H233fs*6(1)|p.S241fs*7(1)|p.S240fs*26(1)|p.N239*(1)|p.S240fs*23(1)|p.C145G(1)|p.N239_C242del(1)|p.S148T(1)|p.Y236_M243delYMCNSSCM(1)|p.N239fs*6(1)|p.S148C(1)|p.N239fs*4(1)|p.C238fs*9(1)|p.Y236_M237insXX(1)|p.M243fs*4(1)|p.M144_N146delMCN(1)|p.Y236_M237>*L(1)|p.Y143*(1)|p.I232_Y236delIHYNY(1)|p.H233_C242del10(1)|p.N239_C242>S(1)|p.S241_G245delSCMGG(1)|p.N146D(1)|p.N239_S240insN(1)|p.V225fs*23(1)|p.C238_N239insX(1)|p.S240P(1)|p.S241_C242insX(1)|p.C238del(1)|p.C238fs*21(1)|p.C238C(1)|p.M237fs*1(1)|p.N239fs*>48(1)|p.S241fs*23(1)|p.N146fs*>10(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	ATGCCGCCCATGCAGGAACTGTTACACATGTAGTTGTAGT	0.586		111	"""Mis, N, F"""		"""breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"""	"""breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"""		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.236_243del	Pancreas(47;798 1329 9957 10801)		yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"""L, E, M, O"""	TP53,NS,carcinoma,0,28	TP53	33396	920	Substitution - Missense(761)|Deletion - Frameshift(47)|Deletion - In frame(28)|Insertion - Frameshift(27)|Substitution - Nonsense(21)|Substitution - coding silent(11)|Whole gene deletion(8)|Insertion - In frame(7)|Unknown(5)|Complex - deletion inframe(2)|Complex - frameshift(1)|Complex - insertion inframe(1)|Complex - compound substitution(1)	lung(111)|breast(97)|large_intestine(90)|ovary(90)|upper_aerodigestive_tract(76)|haematopoietic_and_lymphoid_tissue(68)|oesophagus(56)|urinary_tract(52)|central_nervous_system(49)|endometrium(48)|liver(41)|stomach(26)|biliary_tract(21)|pancreas(19)|soft_tissue(18)|skin(16)|bone(11)|prostate(10)|kidney(7)|thyroid(4)|cervix(4)|eye(3)|meninges(1)|testis(1)|thymus(1)	c.708_727del	GRCh37	CD951866|CD984149|CM011014|CM025271|CM034930|CM056070|CM910618|CM920673|CM942121	TP53	D|M	rs121912655|rs28934573	.																																			SO:0001589	frameshift_variant	7157	exon7	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	CGCCCATGCAGGA	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"""Li-Fraumeni syndrome"""	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.708_727delCATGTGTAACAGTTCCTGCA	17.37:g.7577554_7577573delTGCAGGAACTGTTACACATG	ENSP00000269305:p.Met237fs	Somatic	28	0		WXS	Illumina GAIIx	Phase_I	17	7	NM_000546	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Frame_Shift_Del	DEL	ENST00000269305.4	37	CCDS11118.1																																																																																			.		0.586	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546	
Unknown	0	broad.mit.edu;ucsc.edu;bcgsc.ca	37	17	28975450	28975450	+	IGR	SNP	A	A	G			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr17:28975450A>G								LRRC37BP1 (10968 upstream) : RN7SL316P (54075 downstream)																							ggatgaacagacaaaccccac	0.542																																					.													.	.	.	0			.						.																																			SO:0001628	intergenic_variant	0	.			GAACAGACAAACC																													17.37:g.28975450A>G		Somatic	33	0		WXS	Illumina GAIIx	Phase_I	47	7	.		RNA	SNP		37																																																																																				.	0	0.542								
CTC-559E9.6	0	broad.mit.edu	37	19	19944580	19944580	+	RNA	DEL	T	T	-	rs372322378		TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr19:19944580delT	ENST00000591884.1	+	0	520																											ATGTTTAATCttttttttttt	0.378																																					.													.	.	.	0			.						.																																					0	.			TTAATCTTTTTTT																													19.37:g.19944580delT		Somatic	9	0		WXS	Illumina GAIIx	Phase_I	21	6	.		RNA	DEL	ENST00000591884.1	37																																																																																				.		0.378	CTC-559E9.6-003	KNOWN	basic	antisense	processed_transcript	OTTHUMT00000460786.1		
LOC728323	728323	broad.mit.edu	37	2	243072696	243072696	+	RNA	DEL	T	T	-	rs377762947|rs370253139		TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr2:243072696delT	ENST00000456398.1	+	0	725																											atatacaatatatattatata	0.095																																					.													.	.	.	0			.						.																																					0	.			ACAATATATATTA																													2.37:g.243072696delT		Somatic	4	0		WXS	Illumina GAIIx	Phase_I	8	3	.		RNA	DEL	ENST00000456398.1	37																																																																																				.		0.095	AC093642.5-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000322444.2		
GTF2A1L	11036	broad.mit.edu;ucsc.edu;bcgsc.ca	37	2	48896871	48896871	+	Missense_Mutation	SNP	C	C	T			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr2:48896871C>T	ENST00000403751.3	+	7	1026	c.989C>T	c.(988-990)tCt>tTt	p.S330F	STON1-GTF2A1L_ENST00000309827.2_Missense_Mutation_p.S1034F|STON1-GTF2A1L_ENST00000394751.3_Missense_Mutation_p.S987F|GTF2A1L_ENST00000430487.2_Missense_Mutation_p.S296F|STON1-GTF2A1L_ENST00000405008.1_Missense_Mutation_p.S1034F|LHCGR_ENST00000420913.3_5'Flank|STON1-GTF2A1L_ENST00000394754.1_Missense_Mutation_p.S1034F|STON1-GTF2A1L_ENST00000402114.2_Missense_Mutation_p.S1034F	NM_006872.3	NP_006863.2	Q9UNN4	TF2AY_HUMAN	general transcription factor IIA, 1-like	330					cognition (GO:0050890)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|transcription factor TFIIA complex (GO:0005672)	DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)			lung(7)	7		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			GATTCTAATTCTCAGGTGGAT	0.294																																					p.S1034F													.	STON1-GTF2A1L	180	0			c.C3101T						.						89.0	100.0	96.0					2																	48896871		2202	4299	6501	SO:0001583	missense	0	exon9			CTAATTCTCAGGT	AF106857	CCDS46281.1, CCDS54359.1	2p16.3	2007-08-02			ENSG00000242441	ENSG00000242441			30727	protein-coding gene	gene with protein product	"""TFIIA alpha/beta like factor"""	605358				10364255, 11889132, 16525715	Standard	NM_006872		Approved	ALF		Q9UNN4	OTTHUMG00000152038	ENST00000403751.3:c.989C>T	2.37:g.48896871C>T	ENSP00000384597:p.Ser330Phe	Somatic	56	1		WXS	Illumina GAIIx	Phase_I	95	42	NM_001198593	B4DY14|Q53FD9|Q5D050	Missense_Mutation	SNP	ENST00000403751.3	37	CCDS46281.1	.	.	.	.	.	.	.	.	.	.	C	0.905	-0.721100	0.03182	.	.	ENSG00000068781;ENSG00000068781;ENSG00000068781;ENSG00000068781;ENSG00000068781;ENSG00000068781;ENSG00000242441;ENSG00000242441	ENST00000405008;ENST00000402114;ENST00000394754;ENST00000309827;ENST00000394751;ENST00000394749;ENST00000430487;ENST00000403751	T;T;T;T;T;T;T	0.45668	0.89;0.89;0.89;0.89;0.89;0.89;0.89	4.94	4.07	0.47477	.	0.523804	0.19999	N	0.101379	T	0.31918	0.0812	L	0.41824	1.3	0.80722	D	1	B;B;B;B;B	0.16396	0.001;0.001;0.017;0.003;0.001	B;B;B;B;B	0.20767	0.004;0.002;0.031;0.011;0.009	T	0.15378	-1.0439	10	0.49607	T	0.09	.	6.3799	0.21529	0.1794:0.7283:0.0:0.0923	.	296;987;1034;330;1034	Q9UNN4-2;A8MXJ1;B5MCF5;Q9UNN4;Q53S48	.;.;.;TF2AY_HUMAN;.	F	1034;1034;1034;1034;987;329;296;330	ENSP00000385499:S1034F;ENSP00000385701:S1034F;ENSP00000378236:S1034F;ENSP00000311493:S1034F;ENSP00000378234:S987F;ENSP00000387896:S296F;ENSP00000384597:S330F	ENSP00000384597:S330F	S	+	2	0	STON1-GTF2A1L;GTF2A1L	48750375	0.282000	0.24268	0.891000	0.34965	0.067000	0.16453	1.091000	0.30915	1.317000	0.45149	-0.254000	0.11334	TCT	.		0.294	GTF2A1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323852.4	NM_006872	
HOXD8	3234	broad.mit.edu	37	2	176993750	176993750	+	5'Flank	SNP	T	T	C			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr2:176993750T>C	ENST00000313173.4	+	0	0				HOXD8_ENST00000429017.1_5'Flank|HOXD8_ENST00000548663.1_5'Flank|HOXD8_ENST00000450510.2_5'Flank|HOXD-AS2_ENST00000440016.2_RNA|HOXD8_ENST00000544999.1_5'Flank	NM_001199746.1|NM_019558.3	NP_001186675.1|NP_062458.1	P13378	HXD8_HUMAN	homeobox D8						anterior/posterior axis specification, embryo (GO:0008595)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|skeletal system morphogenesis (GO:0048705)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|large_intestine(2)|lung(5)|skin(1)	9			OV - Ovarian serous cystadenocarcinoma(117;0.0207)|Epithelial(96;0.195)	Colorectal(32;0.0224)|READ - Rectum adenocarcinoma(9;0.0556)		GCGCGAGCCCTTTTTCCCGCC	0.662																																					.													.	HOXD8	24	0			.						.																																			SO:0001631	upstream_gene_variant	0	.			GAGCCCTTTTTCC		CCDS2268.1, CCDS56148.1, CCDS56149.1	2q31.1	2011-06-20	2005-12-22		ENSG00000175879	ENSG00000175879		"""Homeoboxes / ANTP class : HOXL subclass"""	5139	protein-coding gene	gene with protein product		142985	"""homeo box D8"""	HOX4, HOX4E		1973146, 1358459	Standard	NM_001199747		Approved		uc002uko.3	P13378	OTTHUMG00000132513		2.37:g.176993750T>C	Exception_encountered	Somatic	41	0		WXS	Illumina GAIIx	Phase_I	52	3	.	F8WBG7|Q5BL00|Q8IXZ1	RNA	SNP	ENST00000313173.4	37	CCDS2268.1																																																																																			.		0.662	HOXD8-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255694.1		
HOXD4	3233	broad.mit.edu	37	2	177016418	177016418	+	Silent	SNP	G	G	T	rs376860683		TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr2:177016418G>T	ENST00000306324.3	+	1	469	c.57G>T	c.(55-57)ccG>ccT	p.P19P	MIR10B_ENST00000385011.1_RNA|HOXD3_ENST00000468418.3_5'UTR	NM_014621.2	NP_055436.2	P09016	HXD4_HUMAN	homeobox D4	19					multicellular organismal development (GO:0007275)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			kidney(1)|large_intestine(1)|lung(4)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	9			OV - Ovarian serous cystadenocarcinoma(117;0.00765)|Epithelial(96;0.105)	Colorectal(32;0.0224)|READ - Rectum adenocarcinoma(9;0.0556)		AGTTCCCTCCGTGCGAGGAGT	0.552																																					p.P19P													.	HOXD4	32	0			c.G57T						.						47.0	50.0	49.0					2																	177016418		2184	4230	6414	SO:0001819	synonymous_variant	3233	exon1			CCCTCCGTGCGAG		CCDS2269.1	2q31.1	2011-06-20	2005-12-22		ENSG00000170166	ENSG00000170166		"""Homeoboxes / ANTP class : HOXL subclass"""	5138	protein-coding gene	gene with protein product		142981	"""homeo box D4"""	HOX4B, HOX4		1973146, 1358459	Standard	NM_014621		Approved		uc002uks.3	P09016	OTTHUMG00000132515	ENST00000306324.3:c.57G>T	2.37:g.177016418G>T		Somatic	102	0		WXS	Illumina GAIIx	Phase_I	140	5	NM_014621	B2R9R3|Q96AU0	Silent	SNP	ENST00000306324.3	37	CCDS2269.1																																																																																			.		0.552	HOXD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255697.2		
RREB1	6239	broad.mit.edu;bcgsc.ca	37	6	7189542	7189542	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr6:7189542G>T	ENST00000349384.6	+	6	726	c.412G>T	c.(412-414)Ggg>Tgg	p.G138W	Y_RNA_ENST00000364613.1_RNA|RREB1_ENST00000379933.3_Missense_Mutation_p.G138W|RREB1_ENST00000379938.2_Missense_Mutation_p.G138W|RREB1_ENST00000334984.6_Missense_Mutation_p.G138W	NM_001003698.3	NP_001003698.1	Q92766	RREB1_HUMAN	ras responsive element binding protein 1	138					multicellular organismal development (GO:0007275)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|Ras protein signal transduction (GO:0007265)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear body (GO:0016604)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(5)|lung(18)|ovary(5)|pancreas(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	58	Ovarian(93;0.0398)	all_hematologic(90;0.0384)|Prostate(151;0.191)				TACCACCAATGGGAACATGCA	0.597																																					p.G138W													.	RREB1	242	0			c.G412T						.						65.0	51.0	56.0					6																	7189542		2203	4299	6502	SO:0001583	missense	6239	exon6			ACCAATGGGAACA	U26914	CCDS34335.1, CCDS34336.1, CCDS54963.1	6p25	2013-01-08			ENSG00000124782	ENSG00000124782		"""Zinc fingers, C2H2-type"""	10449	protein-coding gene	gene with protein product	"""hindsight homolog (drosophila)"""	602209				9367691, 18394891	Standard	NM_001003698		Approved	HNT	uc003mxb.3	Q92766	OTTHUMG00000014201	ENST00000349384.6:c.412G>T	6.37:g.7189542G>T	ENSP00000305560:p.Gly138Trp	Somatic	19	0		WXS	Illumina GAIIx	Phase_I	14	7	NM_001003700	A2RRF5|E2GM80|E2GM81|O75567|O75568|Q5VYB2|Q6BEP5|Q6BEP6|Q6BEP8|Q86SU2|Q9Y474	Missense_Mutation	SNP	ENST00000349384.6	37	CCDS34336.1	.	.	.	.	.	.	.	.	.	.	G	29.7	5.024633	0.93518	.	.	ENSG00000124782	ENST00000379933;ENST00000379938;ENST00000471433;ENST00000349384;ENST00000334984;ENST00000483150	T;T;T;T;T;T	0.10960	2.82;2.82;2.82;2.82;2.82;2.82	5.65	5.65	0.86999	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.64402	D	0.000015	T	0.27027	0.0662	M	0.66939	2.045	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	T	0.01102	-1.1451	10	0.72032	D	0.01	-52.896	19.7284	0.96174	0.0:0.0:1.0:0.0	.	138;138;138	Q92766-3;Q92766;Q92766-2	.;RREB1_HUMAN;.	W	138	ENSP00000369265:G138W;ENSP00000369270:G138W;ENSP00000420299:G138W;ENSP00000305560:G138W;ENSP00000335574:G138W;ENSP00000419511:G138W	ENSP00000335574:G138W	G	+	1	0	RREB1	7134541	1.000000	0.71417	0.997000	0.53966	0.998000	0.95712	9.162000	0.94745	2.668000	0.90789	0.591000	0.81541	GGG	.		0.597	RREB1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000352985.1		
CYP21A1P	1590	broad.mit.edu	37	6	31975463	31975463	+	5'Flank	SNP	T	T	C	rs370433041	byFrequency	TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr6:31975463T>C	ENST00000594256.1	-	0	0				CYP21A1P_ENST00000342991.6_RNA																							GCAGCGACTGTAGGAGGAGCT	0.657													C|||	271	0.0541134	0.1324	0.0303	5008	,	,		12708	0.0288		0.0268	False		,,,				2504	0.0194				.													.	CYP21A2	42	0			.						.																																			SO:0001631	upstream_gene_variant	0	.			CGACTGTAGGAGG																													6.37:g.31975463T>C	Exception_encountered	Somatic	59	0		WXS	Illumina GAIIx	Phase_I	59	4	.		RNA	SNP	ENST00000594256.1	37																																																																																				.		0.657	AL645922.1-201	NOVEL	basic|appris_principal	protein_coding	protein_coding			
DPY19L2P1	554236	broad.mit.edu	37	7	35131480	35131480	+	RNA	SNP	A	A	T			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr7:35131480A>T	ENST00000436258.1	-	0	1889							Q6NXN4	D19P1_HUMAN	DPY19L2 pseudogene 1							integral component of membrane (GO:0016021)	transferase activity, transferring glycosyl groups (GO:0016757)										ATCTTCGTAAAGTGGATGATT	0.423																																					.													.	.	.	0			.						.																																					0	.			TCGTAAAGTGGAT	BC066987		7p14.2	2014-03-18	2013-09-12		ENSG00000189212	ENSG00000189212			22305	pseudogene	pseudogene			"""dpy-19-like 2 pseudogene 1 (C. elegans)"""				Standard	NR_002833		Approved		uc031swy.1	Q6NXN4	OTTHUMG00000155026		7.37:g.35131480A>T		Somatic	60	1		WXS	Illumina GAIIx	Phase_I	156	11	.	B4E2E3	RNA	SNP	ENST00000436258.1	37																																																																																				.		0.423	DPY19L2P1-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000338113.1		
PEX1	5189	broad.mit.edu	37	7	92146721	92146721	+	Frame_Shift_Del	DEL	T	T	-			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr7:92146721delT	ENST00000248633.4	-	5	1203	c.1108delA	c.(1108-1110)attfs	p.I370fs	PEX1_ENST00000541751.1_5'UTR|PEX1_ENST00000438045.1_Intron|PEX1_ENST00000428214.1_Frame_Shift_Del_p.I370fs	NM_000466.2	NP_000457.1	O43933	PEX1_HUMAN	peroxisomal biogenesis factor 1	370					ATP catabolic process (GO:0006200)|microtubule-based peroxisome localization (GO:0060152)|peroxisome organization (GO:0007031)|protein import into peroxisome matrix (GO:0016558)|protein targeting to peroxisome (GO:0006625)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(6)|lung(17)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	41	all_cancers(62;9.35e-11)|all_epithelial(64;4.59e-10)|Breast(17;0.00201)|all_lung(186;0.0438)|Lung NSC(181;0.0592)	Breast(660;0.000932)|all_neural(109;0.00391)|Myeloproliferative disorder(862;0.0122)|Ovarian(593;0.023)|Medulloblastoma(109;0.123)	GBM - Glioblastoma multiforme(5;4.06e-06)|STAD - Stomach adenocarcinoma(4;4.51e-05)|all cancers(6;5.32e-05)|LUSC - Lung squamous cell carcinoma(200;0.225)|Lung(22;0.23)			TCTGACCTAATTTTTTTTTGA	0.353																																					p.I370fs													.	PEX1	102	0			c.1108delA						.						125.0	126.0	126.0					7																	92146721		2203	4300	6503	SO:0001589	frameshift_variant	5189	exon5			ACCTAATTTTTTT	AF026086	CCDS5627.1, CCDS64710.1	7q21.2	2010-04-21	2008-08-26		ENSG00000127980	ENSG00000127980		"""ATPases / AAA-type"""	8850	protein-coding gene	gene with protein product		602136	"""peroxisome biogenesis factor 1"", ""Zellweger syndrome 1"", ""Zellweger syndrome"""	ZWS1, ZWS		9398848	Standard	NM_001282677		Approved		uc003uly.3	O43933	OTTHUMG00000023926	ENST00000248633.4:c.1108delA	7.37:g.92146721delT	ENSP00000248633:p.Ile370fs	Somatic	41	0		WXS	Illumina GAIIx	Phase_I	136	7	NM_000466	A4D1G3|A8KA90|B4DIM7|E9PE75|Q96S71|Q96S72|Q96S73|Q99994	Frame_Shift_Del	DEL	ENST00000248633.4	37	CCDS5627.1																																																																																			.		0.353	PEX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254066.3	NM_000466	
ADCK5	203054	broad.mit.edu	37	8	145617535	145617549	+	Splice_Site	DEL	GGGGGTGCAAGGTGA	GGGGGTGCAAGGTGA	-	rs563415390|rs148509143|rs374281647	byFrequency	TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr8:145617535_145617549delGGGGGTGCAAGGTGA	ENST00000308860.6	+	12	1301_1311	c.1257_1267delGGGGGTGCAAGGTGA	c.(1255-1269)ctgggggtgcaaggt>ctgt	p.GVQG420del	CPSF1_ENST00000531727.1_5'Flank|MIR939_ENST00000401314.1_RNA	NM_174922.3	NP_777582.4	Q3MIX3	ADCK5_HUMAN	aarF domain containing kinase 5	420						integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	protein serine/threonine kinase activity (GO:0004674)	p.?(2)		endometrium(1)|lung(2)|prostate(2)|skin(1)|stomach(2)	8	all_cancers(97;6.64e-12)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;8.96e-41)|Epithelial(56;4.08e-40)|all cancers(56;4.51e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0323)|Colorectal(110;0.055)			CAGCCGCACTGGGGGTGCAAGGTGAGGGGGTGCAA	0.73														3140	0.626997	0.8109	0.562	5008	,	,		8769	0.6577		0.4205	False		,,,				2504	0.6053				p.419_423del													.	ADCK5	36	2	Unknown(2)	prostate(2)	c.1257_1267del						.			1836,894		805,226,334						4.5	0.7		dbSNP_120	4	2015,4403		639,737,1833	no	coding-near-splice	ADCK5	NM_174922.3		1444,963,2167	A1A1,A1R,RR		31.3961,32.7473,42.0966				3851,5297				SO:0001630	splice_region_variant	203054	exon12			CGCACTGGGGGTG	BC032402	CCDS34965.1, CCDS34965.2	8q24.3	2004-07-06			ENSG00000173137	ENSG00000173137			21738	protein-coding gene	gene with protein product							Standard	NM_174922		Approved	FLJ35454	uc003zch.3	Q3MIX3	OTTHUMG00000165190	ENST00000308860.6:c.1267+1GGGGGTGCAAGGTGA>-	8.37:g.145617535_145617549delGGGGGTGCAAGGTGA		Somatic	4	0		WXS	Illumina GAIIx	Phase_I	6	2	NM_174922	B3KS46|Q5U4P1|Q6P2S4|Q8N5V3	Splice_Site	DEL	ENST00000308860.6	37	CCDS34965.1																																																																																			.		0.730	ADCK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382556.2	NM_174922	In_Frame_Del
PXDNL	137902	broad.mit.edu;ucsc.edu	37	8	52321348	52321348	+	Nonsense_Mutation	SNP	G	G	A			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr8:52321348G>A	ENST00000356297.4	-	17	2936	c.2836C>T	c.(2836-2838)Cga>Tga	p.R946*	PXDNL_ENST00000543296.1_Nonsense_Mutation_p.R946*	NM_144651.4	NP_653252	A1KZ92	PXDNL_HUMAN	peroxidasin homolog (Drosophila)-like	946					hydrogen peroxide catabolic process (GO:0042744)|oxidation-reduction process (GO:0055114)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	endonuclease activity (GO:0004519)|heme binding (GO:0020037)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)			NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(6)|lung(25)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	48		all_cancers(86;0.107)|Lung NSC(129;0.00641)|all_epithelial(80;0.00716)|all_lung(136;0.015)				TGCTCCTGTCGCGCGCACTCG	0.647																																					p.R946X													PXDNL_ENST00000356297,NS,carcinoma,0,6	PXDNL	414	0			c.C2836T						.						14.0	16.0	16.0					8																	52321348		1961	4141	6102	SO:0001587	stop_gained	137902	exon17			CCTGTCGCGCGCA		CCDS47855.1	8q11.21-q11.22	2013-02-18	2007-01-12		ENSG00000147485	ENSG00000147485		"""Immunoglobulin superfamily / I-set domain containing"""	26359	protein-coding gene	gene with protein product	"""polysomal ribonuclease 1 homolog (Xenopus)"""	615904	"""peroxidasin homolog-like (Drosophila)"""			22543864	Standard	NM_144651		Approved	FLJ25471, PMR1	uc003xqu.4	A1KZ92	OTTHUMG00000164244	ENST00000356297.4:c.2836C>T	8.37:g.52321348G>A	ENSP00000348645:p.Arg946*	Somatic	10	0		WXS	Illumina GAIIx	Phase_I	18	4	NM_144651	B5ME43|B6CGZ3|H0YBM9|Q6ZMR2|Q96LH9	Nonsense_Mutation	SNP	ENST00000356297.4	37	CCDS47855.1	.	.	.	.	.	.	.	.	.	.	G	37	6.117129	0.97296	.	.	ENSG00000147485	ENST00000356297;ENST00000543296	.	.	.	3.8	-7.59	0.01308	.	1.153240	0.07191	U	0.855649	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	7.349	0.26680	0.0:0.2922:0.3431:0.3647	.	.	.	.	X	946	.	ENSP00000348645:R946X	R	-	1	2	PXDNL	52483901	0.001000	0.12720	0.000000	0.03702	0.000000	0.00434	-0.873000	0.04214	-1.741000	0.01344	-0.176000	0.13171	CGA	.		0.647	PXDNL-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377905.1	NM_144651	
KDM4C	23081	broad.mit.edu	37	9	7170012	7170012	+	Intron	SNP	G	G	T			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr9:7170012G>T	ENST00000381309.3	+	21	3559				KDM4C_ENST00000428870.2_Intron|KDM4C_ENST00000442236.2_Intron|KDM4C_ENST00000381306.3_Missense_Mutation_p.C1039F	NM_015061.3	NP_055876.2	Q9H3R0	KDM4C_HUMAN	lysine (K)-specific demethylase 4C						histone H3-K9 demethylation (GO:0033169)|positive regulation of cell proliferation (GO:0008284)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)	androgen receptor binding (GO:0050681)|dioxygenase activity (GO:0051213)|enzyme binding (GO:0019899)|histone demethylase activity (H3-K9 specific) (GO:0032454)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(8)|lung(14)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	43						AAAAGCCAATGCAACATTTTC	0.393																																					p.C1039F													.	KDM4C	186	0			c.G3116T						.						54.0	48.0	50.0					9																	7170012		692	1591	2283	SO:0001627	intron_variant	23081	exon21			GCCAATGCAACAT	AB018323	CCDS6471.1, CCDS55285.1, CCDS55286.1, CCDS55287.1	9p24-p23	2013-01-23	2009-04-06	2009-04-06	ENSG00000107077	ENSG00000107077		"""Chromatin-modifying enzymes / K-demethylases"", ""Tudor domain containing"""	17071	protein-coding gene	gene with protein product	"""tudor domain containing 14C"""	605469	"""jumonji domain containing 2C"""	JMJD2C		9872452, 15138608	Standard	NM_015061		Approved	GASC1, KIAA0780, TDRD14C	uc003zkh.3	Q9H3R0	OTTHUMG00000019536	ENST00000381309.3:c.2994+122G>T	9.37:g.7170012G>T		Somatic	58	0		WXS	Illumina GAIIx	Phase_I	104	4	NM_001146694	B4E1Y4|B7ZL46|F5H347|F5H7P0|O94877|Q2M3M0|Q5JUC9|Q5VYJ2|Q5VYJ3	Missense_Mutation	SNP	ENST00000381309.3	37	CCDS6471.1	.	.	.	.	.	.	.	.	.	.	G	8.176	0.792707	0.16327	.	.	ENSG00000107077	ENST00000381306	T	0.15487	2.42	3.88	-0.0734	0.13735	.	.	.	.	.	T	0.07908	0.0198	.	.	.	0.09310	N	1	B	0.22983	0.078	B	0.13407	0.009	T	0.38693	-0.9649	7	.	.	.	.	3.7822	0.08684	0.3185:0.1838:0.4977:0.0	.	1039	Q9H3R0-2	.	F	1039	ENSP00000370707:C1039F	.	C	+	2	0	KDM4C	7160012	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.560000	0.05964	-0.017000	0.14103	0.467000	0.42956	TGC	.		0.393	KDM4C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051692.1	NM_015061	
PLXNA3	55558	broad.mit.edu	37	X	153688565	153688565	+	Frame_Shift_Del	DEL	G	G	-	rs375310385		TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chrX:153688565delG	ENST00000369682.3	+	2	217	c.42delG	c.(40-42)gtgfs	p.V14fs		NM_017514.3	NP_059984.3	P51805	PLXA3_HUMAN	plexin A3	14					axon guidance (GO:0007411)|branchiomotor neuron axon guidance (GO:0021785)|facial nerve structural organization (GO:0021612)|hippocampus development (GO:0021766)|multicellular organismal development (GO:0007275)|negative chemotaxis (GO:0050919)|negative regulation of axon extension involved in axon guidance (GO:0048843)|positive regulation of cytoskeleton organization (GO:0051495)|pyramidal neuron development (GO:0021860)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|trigeminal nerve structural organization (GO:0021637)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|membrane (GO:0016020)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)|transmembrane signaling receptor activity (GO:0004888)	p.A17fs*39(1)		breast(2)|central_nervous_system(2)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(26)|ovary(2)|prostate(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	48	all_cancers(53;5.05e-16)|all_epithelial(53;1.87e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					TCCTTGCCGTGGGGGGGGCCC	0.682																																					p.V14fs													.	PLXNA3	156	1	Insertion - Frameshift(1)	ovary(1)	c.42delG						.			47,59,3613		1,0,29,16,2,35,20,1525,499	34.0	32.0	33.0			0.6	0.0	X		33	69,109,6290		1,0,27,40,3,50,53,2275,1663	no	codingComplex	PLXNA3	NM_017514.3		2,0,56,56,5,85,73,3800,2162	A1A1,A1A2,A1R,A1,A2A2,A2R,A2,RR,R		2.752,2.8502,2.7879			153688565	116,168,9903	2202	4292	6494	SO:0001589	frameshift_variant	55558	exon2			TGCCGTGGGGGGG	X74609	CCDS14752.1	Xq28	2008-02-05			ENSG00000130827	ENSG00000130827		"""Plexins"""	9101	protein-coding gene	gene with protein product		300022		PLXN4		8248200, 8733135	Standard	NM_017514		Approved	SEX, XAP-6, 6.3, Plxn3	uc004flm.3	P51805	OTTHUMG00000033290	ENST00000369682.3:c.42delG	X.37:g.153688565delG	ENSP00000358696:p.Val14fs	Somatic	6	0		WXS	Illumina GAIIx	Phase_I	9	3	NM_017514	Q5HY36	Frame_Shift_Del	DEL	ENST00000369682.3	37	CCDS14752.1																																																																																			.		0.682	PLXNA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000081634.1	NM_017514	
HNRNPCL1	343069	ucsc.edu;bcgsc.ca	37	1	12907358	12907358	+	Missense_Mutation	SNP	T	T	C	rs74587302|rs559905244	byFrequency	TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr1:12907358T>C	ENST00000317869.6	-	2	1010	c.785A>G	c.(784-786)cAg>cGg	p.Q262R		NM_001013631.1|NM_001136561.2|NM_001146181.1	NP_001013653.1|NP_001130033.2|NP_001139653.1	O60812	HNRC1_HUMAN	heterogeneous nuclear ribonucleoprotein C-like 1	262						nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(15)|prostate(1)|skin(1)|stomach(2)	29						GTCATCCCCCTGATCTTCATT	0.498																																					p.Q262R													HNRNPCL1,NS,neuroblastoma,0,1	HNRNPCL1	68	0			c.A785G						.						143.0	157.0	152.0					1																	12907358		2203	4300	6503	SO:0001583	missense	343069	exon2			TCCCCCTGATCTT	BC002696	CCDS30591.1	1p36.21	2013-02-12		2008-04-18	ENSG00000179172	ENSG00000179172		"""RNA binding motif (RRM) containing"""	29295	protein-coding gene	gene with protein product				HNRPCL1			Standard	NM_001013631		Approved			O60812	OTTHUMG00000001931	ENST00000317869.6:c.785A>G	1.37:g.12907358T>C	ENSP00000365370:p.Gln262Arg	Somatic	49	0		WXS	Illumina HiSeq		62	10	NM_001013631	B2RP44	Missense_Mutation	SNP	ENST00000317869.6	37	CCDS30591.1	.	.	.	.	.	.	.	.	.	.	.	0.006	-2.089806	0.00367	.	.	ENSG00000179172	ENST00000317869	T	0.09445	2.98	0.343	-0.686	0.11324	.	2.239460	0.02976	N	0.145045	T	0.04724	0.0128	N	0.02830	-0.485	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.33650	-0.9860	10	0.33940	T	0.23	.	3.9448	0.09344	0.0:0.3889:0.0:0.6111	.	262	O60812	HNRCL_HUMAN	R	262	ENSP00000365370:Q262R	ENSP00000365370:Q262R	Q	-	2	0	HNRNPCL1	12829945	0.213000	0.23551	0.005000	0.12908	0.003000	0.03518	0.096000	0.15147	-0.605000	0.05753	-0.620000	0.04034	CAG	.		0.498	HNRNPCL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005462.1	NM_001013631	
OR2T12	127064	ucsc.edu	37	1	248458419	248458419	+	Silent	SNP	G	G	C	rs142654576		TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr1:248458419G>C	ENST00000317996.1	-	1	461	c.462C>G	c.(460-462)ggC>ggG	p.G154G		NM_001004692.1	NP_001004692.1	Q8NG77	O2T12_HUMAN	olfactory receptor, family 2, subfamily T, member 12	154						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(4)|kidney(3)|large_intestine(3)|lung(25)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	43	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0201)			CCTGCAGGAGGCCGTCAGCTG	0.602																																					p.G154G													.	OR2T12	113	0			c.C462G						.						87.0	93.0	91.0					1																	248458419		2162	4286	6448	SO:0001819	synonymous_variant	127064	exon1			CAGGAGGCCGTCA	BK004485	CCDS31110.1	1q44	2012-08-09			ENSG00000177201	ENSG00000177201		"""GPCR / Class A : Olfactory receptors"""	19592	protein-coding gene	gene with protein product							Standard	NM_001004692		Approved		uc010pzj.2	Q8NG77	OTTHUMG00000040457	ENST00000317996.1:c.462C>G	1.37:g.248458419G>C		Somatic	22	0		WXS	Illumina HiSeq		39	7	NM_001004692		Silent	SNP	ENST00000317996.1	37	CCDS31110.1																																																																																			G|0.833;C|0.167		0.602	OR2T12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097353.1	NM_001004692	
ALPP	250	ucsc.edu	37	2	233246249	233246249	+	Missense_Mutation	SNP	A	A	G	rs1048994		TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr2:233246249A>G	ENST00000392027.2	+	11	1621	c.1352A>G	c.(1351-1353)gAa>gGa	p.E451G	AC068134.8_ENST00000439072.1_RNA|AC068134.8_ENST00000441266.1_RNA	NM_001632.3	NP_001623.3	P05187	PPB1_HUMAN	alkaline phosphatase, placental	451			E -> G (in dbSNP:rs1048994).		dephosphorylation (GO:0016311)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alkaline phosphatase activity (GO:0004035)|magnesium ion binding (GO:0000287)|zinc ion binding (GO:0008270)			NS(1)|biliary_tract(1)|endometrium(1)|kidney(4)|large_intestine(2)|liver(1)|lung(10)|ovary(2)	22		all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0449)|Lung NSC(271;0.132)		Epithelial(121;4.45e-22)|Kidney(3;4.42e-11)|KIRC - Kidney renal clear cell carcinoma(3;1.9e-09)|BRCA - Breast invasive adenocarcinoma(100;0.000767)|Lung(119;0.00566)|LUSC - Lung squamous cell carcinoma(224;0.00746)|STAD - Stomach adenocarcinoma(3;0.0181)|GBM - Glioblastoma multiforme(43;0.196)		CCCCTGGACGAAGAGACCCAC	0.652																																					p.E451G													.	ALPP	53	0			c.A1352G						.						29.0	32.0	31.0					2																	233246249		2202	4300	6502	SO:0001583	missense	250	exon11			TGGACGAAGAGAC	M14169	CCDS2490.1	2q37.1	2010-06-24	2010-06-24		ENSG00000163283	ENSG00000163283	3.1.3.1		439	protein-coding gene	gene with protein product	"""Regan isozyme"""	171800	"""alkaline phosphatase, placental (Regan isozyme)"""			3001717, 3461452	Standard	XM_005246439		Approved		uc002vsq.3	P05187	OTTHUMG00000133255	ENST00000392027.2:c.1352A>G	2.37:g.233246249A>G	ENSP00000375881:p.Glu451Gly	Somatic	52	2		WXS	Illumina HiSeq		65	13	NM_001632	P05188|P06861|Q53S78|Q96DB7	Missense_Mutation	SNP	ENST00000392027.2	37	CCDS2490.1	.	.	.	.	.	.	.	.	.	.	A	9.569	1.120522	0.20877	.	.	ENSG00000163283	ENST00000392027	D	0.95788	-3.81	2.35	0.169	0.15017	Alkaline phosphatase-like, alpha/beta/alpha (1);Alkaline-phosphatase-like, core domain (1);	0.915038	0.09277	N	0.824307	D	0.85204	0.5643	N	0.04297	-0.235	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.74137	-0.3762	10	0.27082	T	0.32	.	3.4287	0.07420	0.1752:0.5616:0.1571:0.1061	rs1048994;rs2678507;rs3189067;rs17416148	451	P05187	PPB1_HUMAN	G	451	ENSP00000375881:E451G	ENSP00000375881:E451G	E	+	2	0	ALPP	232954493	0.000000	0.05858	0.003000	0.11579	0.183000	0.23260	0.070000	0.14573	-0.126000	0.11682	0.254000	0.18369	GAA	A|1.000;|0.000		0.652	ALPP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257032.3	NM_001632	
DSPP	1834	ucsc.edu;bcgsc.ca	37	4	88537327	88537327	+	Silent	SNP	C	C	T			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr4:88537327C>T	ENST00000282478.7	+	4	3546	c.3513C>T	c.(3511-3513)agC>agT	p.S1171S	DSPP_ENST00000399271.1_Silent_p.S1171S|RP11-742B18.1_ENST00000506480.1_RNA			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	1171	Asp/Ser-rich.				biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|skin(3)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Hepatocellular(203;0.114)|all_hematologic(202;0.236)		OV - Ovarian serous cystadenocarcinoma(123;0.000508)		gcagcgacagcagcgatagca	0.567																																					p.S1171S													DSPP,colon,carcinoma,+1,1	DSPP	174	0			c.C3513T						.						44.0	64.0	57.0					4																	88537327		1613	2855	4468	SO:0001819	synonymous_variant	1834	exon5			CGACAGCAGCGAT	AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1		8995371, 9533027	Standard	NM_014208		Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.3513C>T	4.37:g.88537327C>T		Somatic	42	0		WXS	Illumina HiSeq		34	4	NM_014208	A8MUI0|O95815	Silent	SNP	ENST00000282478.7	37	CCDS43248.1																																																																																			.		0.567	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208	
TRAF4	9618	ucsc.edu	37	17	27075650	27075650	+	Missense_Mutation	SNP	T	T	C			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr17:27075650T>C	ENST00000262395.5	+	6	875	c.746T>C	c.(745-747)cTc>cCc	p.L249P	AC010761.10_ENST00000579468.1_RNA|TRAF4_ENST00000444415.3_Missense_Mutation_p.L249P|TRAF4_ENST00000262396.6_Intron|AC010761.9_ENST00000577325.1_RNA	NM_004295.3	NP_004286.2	Q9BUZ4	TRAF4_HUMAN	TNF receptor-associated factor 4	249					activation of NF-kappaB-inducing kinase activity (GO:0007250)|apoptotic process (GO:0006915)|positive regulation of JNK cascade (GO:0046330)|positive regulation of protein homodimerization activity (GO:0090073)|positive regulation of protein kinase activity (GO:0045860)|regulation of apoptotic process (GO:0042981)|respiratory gaseous exchange (GO:0007585)|respiratory tube development (GO:0030323)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	DNA binding (GO:0003677)|thioesterase binding (GO:0031996)|tumor necrosis factor receptor binding (GO:0005164)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|WW domain binding (GO:0050699)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(2)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	10	Lung NSC(42;0.01)		Epithelial(11;3.26e-05)|all cancers(11;0.000272)|OV - Ovarian serous cystadenocarcinoma(11;0.235)			GCCCTGGTGCTCTGCCCATTC	0.602																																					p.L249P													.	TRAF4	20	0			c.T746C						.						54.0	48.0	50.0					17																	27075650		2203	4300	6503	SO:0001583	missense	9618	exon6			TGGTGCTCTGCCC	X80200	CCDS11243.1	17q11-q21.3	2013-01-09			ENSG00000076604	ENSG00000076604		"""RING-type (C3HC4) zinc fingers"""	12034	protein-coding gene	gene with protein product		602464				7592751, 7490069	Standard	NM_004295		Approved	CART1, MLN62, RNF83	uc002hcs.3	Q9BUZ4	OTTHUMG00000132677	ENST00000262395.5:c.746T>C	17.37:g.27075650T>C	ENSP00000262395:p.Leu249Pro	Somatic	13	0		WXS	Illumina HiSeq		41	4	NM_004295	O75615|Q14848|Q2KJU4|Q2PJN8	Missense_Mutation	SNP	ENST00000262395.5	37	CCDS11243.1	.	.	.	.	.	.	.	.	.	.	T	11.63	1.695800	0.30052	.	.	ENSG00000076604	ENST00000262395;ENST00000444415	T;T	0.28454	1.61;1.61	5.65	5.65	0.86999	Zinc finger, TRAF-type (1);TRAF-like (1);	0.000000	0.85682	D	0.000000	T	0.38746	0.1052	N	0.17723	0.515	0.80722	D	1	D	0.71674	0.998	D	0.71184	0.972	T	0.16808	-1.0390	10	0.29301	T	0.29	.	14.7014	0.69160	0.0:0.0:0.0:1.0	.	249	Q9BUZ4	TRAF4_HUMAN	P	249	ENSP00000262395:L249P;ENSP00000438154:L249P	ENSP00000262395:L249P	L	+	2	0	TRAF4	24099777	1.000000	0.71417	0.997000	0.53966	0.957000	0.61999	7.377000	0.79668	2.149000	0.67028	0.533000	0.62120	CTC	.		0.602	TRAF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255944.2	NM_145751	
KRTAP9-9	81870	ucsc.edu	37	17	39412093	39412093	+	Silent	SNP	C	C	A	rs368292401		TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr17:39412093C>A	ENST00000394008.1	+	1	458	c.456C>A	c.(454-456)acC>acA	p.T152T		NM_030975.2	NP_112237.2	Q9BYP9	KRA99_HUMAN	keratin associated protein 9-9	137	14 X 5 AA repeats of C-C-[RQVGE]- [SPSTNQ]-[TASL].					keratin filament (GO:0045095)				endometrium(3)|skin(2)|upper_aerodigestive_tract(1)	6		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000397)			GCTGCAGGACCACTTGCTTCC	0.602																																					p.T152T													.	KRTAP9-9	24	0			c.C456A						.						165.0	172.0	169.0					17																	39412093		2203	4298	6501	SO:0001819	synonymous_variant	81870	exon1			CAGGACCACTTGC	AJ406951	CCDS54127.1	17q21.2	2010-06-03			ENSG00000198083	ENSG00000198083		"""Keratin associated proteins"""	16773	protein-coding gene	gene with protein product			"""keratin associated protein 9-5"""	KRTAP9-5		11279113	Standard	NM_030975		Approved	KAP9.9, KAP9.5	uc021txh.1	Q9BYP9	OTTHUMG00000133602	ENST00000394008.1:c.456C>A	17.37:g.39412093C>A		Somatic	53	2		WXS	Illumina HiSeq		147	16	NM_030975	B5MDD6|Q9BYQ1	Silent	SNP	ENST00000394008.1	37	CCDS54127.1																																																																																			.		0.602	KRTAP9-9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257710.1	NM_030975	
PLXNB1	5364	bcgsc.ca	37	3	48461494	48461494	+	Missense_Mutation	SNP	C	C	A			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	C	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr3:48461494C>A	ENST00000358536.4	-	11	2470	c.2201G>T	c.(2200-2202)aGc>aTc	p.S734I	PLXNB1_ENST00000296440.6_Missense_Mutation_p.S734I|PLXNB1_ENST00000456774.1_Intron|PLXNB1_ENST00000448774.2_Intron|PLXNB1_ENST00000358459.4_Intron	NM_002673.4	NP_002664.2	O43157	PLXB1_HUMAN	plexin B1	734	Pro-rich.				axon guidance (GO:0007411)|cell migration (GO:0016477)|intracellular signal transduction (GO:0035556)|negative regulation of cell adhesion (GO:0007162)|negative regulation of osteoblast proliferation (GO:0033689)|neuron projection morphogenesis (GO:0048812)|ossification involved in bone maturation (GO:0043931)|positive regulation of axonogenesis (GO:0050772)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell shape (GO:0008360)|regulation of cytoskeleton organization (GO:0051493)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in bone trabecula morphogenesis (GO:1900220)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	GTPase activating protein binding (GO:0032794)|receptor activity (GO:0004872)|semaphorin receptor activity (GO:0017154)|semaphorin receptor binding (GO:0030215)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(10)|ovary(3)|pancreas(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	47				BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00549)|Kidney(197;0.00619)		CCCCCAGGGGCTGAGCAGGGA	0.662																																					p.S734I													.	PLXNB1	150	0			c.G2201T						.						18.0	21.0	20.0					3																	48461494		2202	4297	6499	SO:0001583	missense	5364	exon11			CAGGGGCTGAGCA	X87904	CCDS2765.1	3p21.31	2008-07-18			ENSG00000164050	ENSG00000164050		"""Plexins"""	9103	protein-coding gene	gene with protein product		601053		PLXN5		8570614, 11035813	Standard	XM_005265234		Approved	SEP, KIAA0407	uc003csw.2	O43157	OTTHUMG00000133527	ENST00000358536.4:c.2201G>T	3.37:g.48461494C>A	ENSP00000351338:p.Ser734Ile	Somatic	42	0		WXS	Illumina HiSeq	Phase_1	43	4	NM_001130082	A6H8Y2|Q6NY20|Q9UIV7|Q9UJ92|Q9UJ93	Missense_Mutation	SNP	ENST00000358536.4	37	CCDS2765.1	.	.	.	.	.	.	.	.	.	.	C	17.22	3.335416	0.60853	.	.	ENSG00000164050	ENST00000296440;ENST00000358536	T;T	0.03181	4.02;4.02	4.48	3.61	0.41365	.	0.637901	0.14782	N	0.298752	T	0.01940	0.0061	N	0.08118	0	0.09310	N	0.999994	B	0.14438	0.01	B	0.09377	0.004	T	0.46541	-0.9184	10	0.29301	T	0.29	.	3.4708	0.07566	0.1722:0.5652:0.167:0.0956	.	734	O43157	PLXB1_HUMAN	I	734	ENSP00000296440:S734I;ENSP00000351338:S734I	ENSP00000296440:S734I	S	-	2	0	PLXNB1	48436498	0.000000	0.05858	0.991000	0.47740	0.722000	0.41435	0.262000	0.18460	0.876000	0.35872	0.561000	0.74099	AGC	.		0.662	PLXNB1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344454.1	NM_002673	
HNRNPKP4	644063	bcgsc.ca	37	3	96069164	96069164	+	IGR	SNP	C	C	T			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	C	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr3:96069164C>T								AC108739.1 (183418 upstream) : AC108697.1 (82994 downstream)																							ATTTCCCATGCGGGGAAGAGG	0.478																																					.													.	.	.	0			.						.																																			SO:0001628	intergenic_variant	644063	.			CCCATGCGGGGAA																													3.37:g.96069164C>T		Somatic	56	0		WXS	Illumina HiSeq	Phase_1	91	5	.		RNA	SNP		37																																																																																				.	0	0.478								
SEC24B	10427	bcgsc.ca	37	4	110453888	110453888	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	G	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr4:110453888G>T	ENST00000265175.5	+	21	3539	c.3484G>T	c.(3484-3486)Gac>Tac	p.D1162Y	SEC24B_ENST00000504968.2_Missense_Mutation_p.D1192Y|SEC24B_ENST00000399100.2_Missense_Mutation_p.D1127Y	NM_006323.2	NP_006314.2	O95487	SC24B_HUMAN	SEC24 family member B	1162					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|aorta morphogenesis (GO:0035909)|auditory receptor cell stereocilium organization (GO:0060088)|cellular protein metabolic process (GO:0044267)|cochlear nucleus development (GO:0021747)|COPII vesicle coating (GO:0048208)|coronary artery morphogenesis (GO:0060982)|ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)|lung lobe morphogenesis (GO:0060463)|membrane organization (GO:0061024)|neural tube closure (GO:0001843)|outflow tract morphogenesis (GO:0003151)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|pulmonary artery morphogenesis (GO:0061156)|regulation of cargo loading into COPII-coated vesicle (GO:1901301)|regulation of establishment of planar polarity involved in neural tube closure (GO:0090178)|small molecule metabolic process (GO:0044281)|vesicle-mediated transport (GO:0016192)	COPII vesicle coat (GO:0030127)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|membrane (GO:0016020)	transporter activity (GO:0005215)|zinc ion binding (GO:0008270)			breast(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(12)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	36		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;3.03e-05)		tttccttatggactgtggctc	0.438																																					p.D1162Y													.	SEC24B	186	0			c.G3484T						.						74.0	71.0	72.0					4																	110453888		1914	4121	6035	SO:0001583	missense	10427	exon21			CTTATGGACTGTG	AJ131245	CCDS43260.1, CCDS47124.1, CCDS75179.1	4q25	2013-10-21	2013-10-21		ENSG00000138802	ENSG00000138802			10704	protein-coding gene	gene with protein product		607184	"""SEC24 (S. cerevisiae) related gene family, member B"", ""SEC24 family, member B (S. cerevisiae)"""			10075675, 10329445	Standard	XM_005262688		Approved		uc003hzk.3	O95487	OTTHUMG00000161372	ENST00000265175.5:c.3484G>T	4.37:g.110453888G>T	ENSP00000265175:p.Asp1162Tyr	Somatic	38	0		WXS	Illumina HiSeq	Phase_1	24	3	NM_006323	B7ZKM8|B7ZKN4|Q0VG08	Missense_Mutation	SNP	ENST00000265175.5	37	CCDS47124.1	.	.	.	.	.	.	.	.	.	.	G	27.2	4.806449	0.90623	.	.	ENSG00000138802	ENST00000504968;ENST00000399100;ENST00000265175	T;T;T	0.65364	-0.15;-0.15;-0.15	5.75	5.75	0.90469	Gelsolin domain (1);	0.088138	0.85682	D	0.000000	D	0.84800	0.5552	M	0.94101	3.495	0.80722	D	1	P;D;P;P;D	0.71674	0.725;0.998;0.905;0.951;0.961	B;D;P;P;P	0.67548	0.324;0.952;0.609;0.531;0.661	D	0.88153	0.2852	10	0.87932	D	0	-3.9527	19.9341	0.97130	0.0:0.0:1.0:0.0	.	1076;761;1192;1127;1162	B4DTM6;B4E2E1;B7ZKM8;O95487-2;O95487	.;.;.;.;SC24B_HUMAN	Y	1192;1127;1162	ENSP00000428564:D1192Y;ENSP00000382051:D1127Y;ENSP00000265175:D1162Y	ENSP00000265175:D1162Y	D	+	1	0	SEC24B	110673337	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.244000	0.95423	2.711000	0.92665	0.563000	0.77884	GAC	.		0.438	SEC24B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000364693.2		
ZDHHC11	79844	bcgsc.ca	37	5	825293	825293	+	Missense_Mutation	SNP	C	C	T			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	C	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr5:825293C>T	ENST00000283441.8	-	8	1392	c.1009G>A	c.(1009-1011)Gat>Aat	p.D337N	ZDHHC11_ENST00000503758.2_5'UTR|ZDHHC11_ENST00000424784.2_Missense_Mutation_p.D337N	NM_024786.2	NP_079062.1	Q9H8X9	ZDH11_HUMAN	zinc finger, DHHC-type containing 11	337						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			haematopoietic_and_lymphoid_tissue(1)|liver(1)|lung(10)|pancreas(1)|prostate(5)|skin(2)|urinary_tract(1)	21			Epithelial(17;0.000445)|all cancers(22;0.00176)|OV - Ovarian serous cystadenocarcinoma(19;0.00227)|Lung(60;0.0863)			GCCGTCGAATCCCCATCCTGG	0.547																																					p.D337N													.	ZDHHC11	97	0			c.G1009A						.						188.0	135.0	153.0					5																	825293		2203	4296	6499	SO:0001583	missense	79844	exon8			TCGAATCCCCATC	AK023215	CCDS3857.1	5p15.2	2011-02-09			ENSG00000188818	ENSG00000188818		"""Zinc fingers, DHHC-type"""	19158	protein-coding gene	gene with protein product							Standard	NM_024786		Approved	ZNF399, FLJ13153	uc011cma.1	Q9H8X9	OTTHUMG00000090319	ENST00000283441.8:c.1009G>A	5.37:g.825293C>T	ENSP00000283441:p.Asp337Asn	Somatic	33	0		WXS	Illumina HiSeq	Phase_1	34	4	NM_024786	Q6UWR9	Missense_Mutation	SNP	ENST00000283441.8	37	CCDS3857.1	.	.	.	.	.	.	.	.	.	.	N	8.646	0.897104	0.17686	.	.	ENSG00000188818	ENST00000424784;ENST00000283441	T;T	0.29142	1.58;1.58	0.131	-0.261	0.12963	.	.	.	.	.	T	0.15435	0.0372	N	0.08118	0	0.09310	N	1	P	0.43392	0.805	P	0.47134	0.539	T	0.08848	-1.0702	8	0.17832	T	0.49	.	.	.	.	.	337	Q9H8X9	ZDH11_HUMAN	N	337	ENSP00000397719:D337N;ENSP00000283441:D337N	ENSP00000283441:D337N	D	-	1	0	ZDHHC11	878293	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.388000	0.00488	-1.313000	0.02303	-1.326000	0.01283	GAT	.		0.547	ZDHHC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206681.3	NM_024786	
BCLAF1P1	728366	bcgsc.ca	37	5	110283910	110283910	+	IGR	SNP	T	T	C	rs386691066|rs80293008		TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	T	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr5:110283910T>C								SLC25A46 (183053 upstream) : CTC-551A13.1 (22739 downstream)																							CCTCTTTTGGTCTAATAATCC	0.413																																					.													.	.	.	0			.						.																																			SO:0001628	intergenic_variant	0	.			TTTTGGTCTAATA																													5.37:g.110283910T>C		Somatic	26	1		WXS	Illumina HiSeq	Phase_1	37	8	.		RNA	SNP		37																																																																																				.	0	0.413								
BCLAF1P1	728366	bcgsc.ca	37	5	110283912	110283912	+	IGR	SNP	T	T	C	rs386691066|rs74826826		TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	T	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr5:110283912T>C								SLC25A46 (183055 upstream) : CTC-551A13.1 (22737 downstream)																							TCTTTTGGTCTAATAATCCAC	0.408																																					.													.	.	.	0			.						.																																			SO:0001628	intergenic_variant	0	.			TTGGTCTAATAAT																													5.37:g.110283912T>C		Somatic	23	1		WXS	Illumina HiSeq	Phase_1	38	7	.		RNA	SNP		37																																																																																				.	0	0.408								
BCLAF1P1	728366	bcgsc.ca	37	5	110283938	110283938	+	IGR	SNP	A	A	G			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	A	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr5:110283938A>G								SLC25A46 (183081 upstream) : CTC-551A13.1 (22711 downstream)																							CATCTCTGTCATGATGCAAGA	0.403																																					.													.	.	.	0			.						.																																			SO:0001628	intergenic_variant	0	.			TCTGTCATGATGC																													5.37:g.110283938A>G		Somatic	22	1		WXS	Illumina HiSeq	Phase_1	40	8	.		RNA	SNP		37																																																																																				.	0	0.403								
BCLAF1P1	728366	bcgsc.ca	37	5	110283940	110283940	+	IGR	SNP	G	G	C			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	G	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr5:110283940G>C								SLC25A46 (183083 upstream) : CTC-551A13.1 (22709 downstream)																							TCTCTGTCATGATGCAAGAAA	0.403																																					.													.	.	.	0			.						.																																			SO:0001628	intergenic_variant	0	.			TGTCATGATGCAA																													5.37:g.110283940G>C		Somatic	21	1		WXS	Illumina HiSeq	Phase_1	39	7	.		RNA	SNP		37																																																																																				.	0	0.403								
BCLAF1P1	728366	bcgsc.ca	37	5	110283944	110283944	+	IGR	SNP	C	C	A			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	C	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr5:110283944C>A								SLC25A46 (183087 upstream) : CTC-551A13.1 (22705 downstream)																							TGTCATGATGCAAGAAATACT	0.398																																					.													.	.	.	0			.						.																																			SO:0001628	intergenic_variant	0	.			ATGATGCAAGAAA																													5.37:g.110283944C>A		Somatic	19	0		WXS	Illumina HiSeq	Phase_1	37	7	.		RNA	SNP		37																																																																																				.	0	0.398								
MUC2	4583	bcgsc.ca	37	11	1092843	1092843	+	Silent	SNP	C	C	G			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	C	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr11:1092843C>G	ENST00000441003.2	+	30	4689	c.4662C>G	c.(4660-4662)ggC>ggG	p.G1554G	MUC2_ENST00000333592.6_5'Flank|MUC2_ENST00000361558.6_Intron|MUC2_ENST00000359061.5_Silent_p.G1555G	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	0	Approximate repeats.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	CACCCACCGGCACACAGACCC	0.632																																					p.G1554G													MUC2_ENST00000441003,trunk,malignant_melanoma,+1,2	MUC2	614	0			c.C4662G						.						88.0	119.0	108.0					11																	1092843		1875	3464	5339	SO:0001819	synonymous_variant	4583	exon30			CACCGGCACACAG	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"""Mucins"""	7512	protein-coding gene	gene with protein product		158370	"""mucin 2, intestinal/tracheal"""			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.4662C>G	11.37:g.1092843C>G		Somatic	238	1		WXS	Illumina HiSeq	Phase_1	375	12	NM_002457	Q14878	Silent	SNP	ENST00000441003.2	37																																																																																				.		0.632	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
MUC2	4583	bcgsc.ca	37	11	1092890	1092890	+	Missense_Mutation	SNP	C	C	T			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	C	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr11:1092890C>T	ENST00000441003.2	+	30	4736	c.4709C>T	c.(4708-4710)aCc>aTc	p.T1570I	MUC2_ENST00000333592.6_5'Flank|MUC2_ENST00000361558.6_Intron|MUC2_ENST00000359061.5_Missense_Mutation_p.T1571I	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	0	Approximate repeats.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	ACCACGGTGaccccaacccca	0.637																																					p.T1570I													MUC2_ENST00000441003,NS,carcinoma,-1,2	MUC2	614	0			c.C4709T						.						119.0	156.0	143.0					11																	1092890		1961	3652	5613	SO:0001583	missense	4583	exon30			CGGTGACCCCAAC	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"""Mucins"""	7512	protein-coding gene	gene with protein product		158370	"""mucin 2, intestinal/tracheal"""			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.4709C>T	11.37:g.1092890C>T	ENSP00000415183:p.Thr1570Ile	Somatic	405	2		WXS	Illumina HiSeq	Phase_1	589	17	NM_002457	Q14878	Missense_Mutation	SNP	ENST00000441003.2	37		.	.	.	.	.	.	.	.	.	.	C	1.561	-0.536608	0.04082	.	.	ENSG00000198788	ENST00000441003;ENST00000359061	T;T	0.15487	2.42;3.24	1.3	-2.33	0.06724	.	0.589600	0.12692	U	0.447130	T	0.07548	0.0190	.	.	.	0.09310	N	1	P	0.34699	0.464	B	0.21546	0.035	T	0.24799	-1.0150	9	0.38643	T	0.18	.	4.395	0.11358	0.3284:0.4793:0.1923:0.0	.	1570	E7EUV1	.	I	1570;1571	ENSP00000415183:T1570I;ENSP00000351956:T1571I	ENSP00000351956:T1571I	T	+	2	0	MUC2	1082890	0.002000	0.14202	0.000000	0.03702	0.033000	0.12548	0.404000	0.20999	-0.107000	0.12088	0.064000	0.15345	ACC	.		0.637	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
ME3	10873	bcgsc.ca	37	11	86157510	86157510	+	Missense_Mutation	SNP	C	C	A			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	C	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr11:86157510C>A	ENST00000393324.3	-	12	1653	c.1400G>T	c.(1399-1401)aGt>aTt	p.S467I	RP11-317J19.1_ENST00000524610.1_RNA|ME3_ENST00000359636.2_Missense_Mutation_p.S467I|ME3_ENST00000543262.1_Missense_Mutation_p.S467I	NM_001014811.1	NP_001014811.1	Q16798	MAON_HUMAN	malic enzyme 3, NADP(+)-dependent, mitochondrial	467					aerobic respiration (GO:0009060)|malate metabolic process (GO:0006108)|oxidation-reduction process (GO:0055114)|oxygen metabolic process (GO:0072592)|pyruvate metabolic process (GO:0006090)	mitochondrion (GO:0005739)	cofactor binding (GO:0048037)|malate dehydrogenase (decarboxylating) (NAD+) activity (GO:0004471)|malate dehydrogenase (decarboxylating) (NADP+) activity (GO:0004473)|malic enzyme activity (GO:0004470)|metal ion binding (GO:0046872)|NAD binding (GO:0051287)|oxaloacetate decarboxylase activity (GO:0008948)			endometrium(4)|kidney(1)|large_intestine(7)|lung(7)|ovary(2)|skin(3)|stomach(2)|urinary_tract(1)	27		Acute lymphoblastic leukemia(157;4.34e-06)|all_hematologic(158;0.00252)				AGGACTTCCACTGGCAAAAAT	0.493																																					p.S467I													.	ME3	70	0			c.G1400T						.						59.0	51.0	54.0					11																	86157510		2202	4299	6501	SO:0001583	missense	10873	exon13			CTTCCACTGGCAA	X79440	CCDS8277.1	11q14.2	2012-09-20			ENSG00000151376	ENSG00000151376	1.1.1.40		6985	protein-coding gene	gene with protein product		604626				7818469	Standard	NM_001161586		Approved		uc001pbz.3	Q16798	OTTHUMG00000167217	ENST00000393324.3:c.1400G>T	11.37:g.86157510C>A	ENSP00000376998:p.Ser467Ile	Somatic	39	0		WXS	Illumina HiSeq	Phase_1	18	3	NM_006680	B7Z6V0|Q8TBJ0	Missense_Mutation	SNP	ENST00000393324.3	37	CCDS8277.1	.	.	.	.	.	.	.	.	.	.	C	27.4	4.824305	0.90955	.	.	ENSG00000151376	ENST00000359636;ENST00000543262;ENST00000393324;ENST00000524826	T;T;T;T	0.52754	0.65;0.65;0.65;0.65	5.34	5.34	0.76211	Malic enzyme, NAD-binding (2);NAD(P)-binding domain (1);	0.000000	0.85682	D	0.000000	T	0.81069	0.4746	H	0.97682	4.055	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.88102	0.2820	9	.	.	.	-7.0653	19.0315	0.92959	0.0:1.0:0.0:0.0	.	467	Q16798	MAON_HUMAN	I	467	ENSP00000352657:S467I;ENSP00000440246:S467I;ENSP00000376998:S467I;ENSP00000431182:S467I	.	S	-	2	0	ME3	85835158	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.619000	0.83057	2.478000	0.83669	0.650000	0.86243	AGT	.		0.493	ME3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393767.2		
DGKA	1606	bcgsc.ca	37	12	56347156	56347156	+	Missense_Mutation	SNP	C	C	A			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	C	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr12:56347156C>A	ENST00000331886.5	+	23	2540	c.2086C>A	c.(2086-2088)Caa>Aaa	p.Q696K	DGKA_ENST00000549079.2_3'UTR|DGKA_ENST00000551156.1_Missense_Mutation_p.Q696K|DGKA_ENST00000394147.1_Missense_Mutation_p.Q696K	NM_001345.4	NP_001336.2	P23743	DGKA_HUMAN	diacylglycerol kinase, alpha 80kDa	696					blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|platelet activation (GO:0030168)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)	cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|diacylglycerol kinase activity (GO:0004143)|NAD+ kinase activity (GO:0003951)|phospholipid binding (GO:0005543)			breast(1)|endometrium(3)|large_intestine(1)|lung(11)|ovary(4)|pancreas(1)|skin(3)|urinary_tract(1)	25					Vitamin E(DB00163)	CCTTCCCATGCAAATTGACGG	0.468																																					p.Q696K													.	DGKA	70	0			c.C2086A						.						260.0	256.0	257.0					12																	56347156		2203	4300	6503	SO:0001583	missense	1606	exon23			CCCATGCAAATTG	AF064767	CCDS8896.1	12q13.3	2013-01-10	2002-08-29			ENSG00000065357	2.7.1.107	"""EF-hand domain containing"""	2849	protein-coding gene	gene with protein product		125855	"""diacylglycerol kinase, alpha (80kD)"""	DAGK, DAGK1		8180475, 7959783	Standard	NM_001345		Approved	DGK-alpha	uc001sim.3	P23743		ENST00000331886.5:c.2086C>A	12.37:g.56347156C>A	ENSP00000328405:p.Gln696Lys	Somatic	31	0		WXS	Illumina HiSeq	Phase_1	71	4	NM_201554	O75481|O75482|O75483|O95217|Q3ZE25|Q8IZ56|Q8N5Q2	Missense_Mutation	SNP	ENST00000331886.5	37	CCDS8896.1	.	.	.	.	.	.	.	.	.	.	C	29.8	5.035663	0.93630	.	.	ENSG00000065357	ENST00000331886;ENST00000394147;ENST00000551156	T;T;T	0.52295	0.67;0.67;0.67	4.71	4.71	0.59529	Diacylglycerol kinase, accessory domain (2);	0.000000	0.85682	D	0.000000	T	0.77532	0.4144	H	0.94503	3.545	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.84968	0.0881	10	0.87932	D	0	.	16.8197	0.85742	0.0:1.0:0.0:0.0	.	696	P23743	DGKA_HUMAN	K	696	ENSP00000328405:Q696K;ENSP00000377703:Q696K;ENSP00000450359:Q696K	ENSP00000328405:Q696K	Q	+	1	0	DGKA	54633423	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	7.380000	0.79704	2.312000	0.78011	0.561000	0.74099	CAA	.		0.468	DGKA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407291.1		
RP11-26F2.1	0	bcgsc.ca	37	15	23128413	23128413	+	RNA	SNP	G	G	T			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	G	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr15:23128413G>T	ENST00000560053.1	-	0	353																											CTTACTTTAAGAGTTCATCTC	0.333																																					.													.	.	.	0			.						.																																					0	.			CTTTAAGAGTTCA																													15.37:g.23128413G>T		Somatic	86	0		WXS	Illumina HiSeq	Phase_1	187	53	.		RNA	SNP	ENST00000560053.1	37																																																																																				.		0.333	RP11-26F2.1-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000415904.1		
DNM1P47	100216544	bcgsc.ca	37	15	102305011	102305011	+	RNA	SNP	T	T	C	rs368196195		TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	T	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr15:102305011T>C	ENST00000561463.1	+	0	13057									DNM1 pseudogene 47																		GGAGCAGGCATAGCGGCGCGA	0.587																																					.													.	.	.	0			.						.																																					0	.			CAGGCATAGCGGC	AJ576276		15q26.3	2013-04-25			ENSG00000259660	ENSG00000259660			35200	pseudogene	pseudogene				DNM1DN14@			Standard	NG_009149		Approved	DNM1DN14-3			OTTHUMG00000172265		15.37:g.102305011T>C		Somatic	34	0		WXS	Illumina HiSeq	Phase_1	55	7	.		RNA	SNP	ENST00000561463.1	37																																																																																				.		0.587	DNM1P47-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000417589.1	NG_009149	
MYH2	4620	bcgsc.ca	37	17	10436657	10436657	+	Missense_Mutation	SNP	C	C	T			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	C	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr17:10436657C>T	ENST00000245503.5	-	21	2770	c.2386G>A	c.(2386-2388)Gcc>Acc	p.A796T	MYH2_ENST00000532183.2_Intron|RP11-799N11.1_ENST00000581304.1_RNA|CTC-297N7.11_ENST00000587182.2_RNA|MYH2_ENST00000397183.2_Missense_Mutation_p.A796T|RP11-799N11.1_ENST00000399342.2_RNA	NM_017534.5	NP_060004.3	Q9UKX2	MYH2_HUMAN	myosin, heavy chain 2, skeletal muscle, adult	796	IQ. {ECO:0000255|PROSITE- ProRule:PRU00116}.				Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|membrane organization (GO:0061024)|metabolic process (GO:0008152)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|plasma membrane repair (GO:0001778)|response to activity (GO:0014823)	A band (GO:0031672)|actomyosin contractile ring (GO:0005826)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin filament (GO:0032982)|protein complex (GO:0043234)|sarcomere (GO:0030017)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			NS(1)|biliary_tract(1)|breast(9)|central_nervous_system(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|lung(99)|ovary(6)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(4)	176						CTGCACCTGGCCTGGGTTCGG	0.463																																					p.A796T													.	MYH2	390	0			c.G2386A						.						91.0	91.0	91.0					17																	10436657		2203	4300	6503	SO:0001583	missense	4620	exon21			ACCTGGCCTGGGT		CCDS11156.1	17p13.1	2014-02-04	2006-09-29		ENSG00000125414	ENSG00000125414		"""Myosins / Myosin superfamily : Class II"""	7572	protein-coding gene	gene with protein product		160740	"""myosin, heavy polypeptide 2, skeletal muscle, adult"", ""inclusion body myopathy 3, autosomal dominant"""	IBM3		7545970, 11889243	Standard	NM_001100112		Approved	MYH2A, MYHSA2, MyHC-IIa, MYHas8, MyHC-2A	uc010coi.3	Q9UKX2	OTTHUMG00000130363	ENST00000245503.5:c.2386G>A	17.37:g.10436657C>T	ENSP00000245503:p.Ala796Thr	Somatic	66	0		WXS	Illumina HiSeq	Phase_1	57	5	NM_017534	A0AVL4|Q14322|Q16229|Q567P6|Q86T56	Missense_Mutation	SNP	ENST00000245503.5	37	CCDS11156.1	.	.	.	.	.	.	.	.	.	.	C	32	5.166956	0.94768	.	.	ENSG00000125414	ENST00000245503;ENST00000397183	T;T	0.73897	-0.79;-0.79	5.17	4.2	0.49525	.	0.000000	0.39020	U	0.001488	D	0.88948	0.6576	M	0.93720	3.45	0.58432	D	0.999994	D	0.76494	0.999	D	0.87578	0.998	D	0.91206	0.4995	10	0.56958	D	0.05	.	14.0113	0.64498	0.0:0.9273:0.0:0.0727	.	796	Q9UKX2	MYH2_HUMAN	T	796	ENSP00000245503:A796T;ENSP00000380367:A796T	ENSP00000245503:A796T	A	-	1	0	MYH2	10377382	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	5.754000	0.68743	1.413000	0.46997	0.591000	0.81541	GCC	.		0.463	MYH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252726.3	NM_017534	
MKS1	54903	bcgsc.ca	37	17	56293485	56293485	+	Silent	SNP	G	G	T			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	G	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr17:56293485G>T	ENST00000393119.2	-	4	455	c.381C>A	c.(379-381)acC>acA	p.T127T	MKS1_ENST00000537529.2_Silent_p.T117T|MKS1_ENST00000313863.6_Silent_p.T127T|LPO_ENST00000582328.1_5'Flank|MKS1_ENST00000337050.7_Silent_p.T127T|MKS1_ENST00000546108.1_5'UTR	NM_017777.3	NP_060247.2	Q9NXB0	MKS1_HUMAN	Meckel syndrome, type 1	127					branching morphogenesis of an epithelial tube (GO:0048754)|cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|membrane (GO:0016020)|TCTN-B9D complex (GO:0036038)				endometrium(5)|kidney(3)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	26						AGTCAGTGTAGGTAAAGATTC	0.438																																					p.T127T													.	MKS1	100	0			c.C381A						.						197.0	184.0	188.0					17																	56293485		1903	4109	6012	SO:0001819	synonymous_variant	54903	exon4			AGTGTAGGTAAAG	DQ185029	CCDS11603.2, CCDS54148.1	17q21-q24	2014-09-17			ENSG00000011143	ENSG00000011143			7121	protein-coding gene	gene with protein product	"""POC12 centriolar protein homolog (Chlamydomonas)"""	609883		MKS		7550354, 16415886, 18327255	Standard	NM_017777		Approved	FLJ20345, POC12, BBS13	uc002ivr.2	Q9NXB0	OTTHUMG00000133714	ENST00000393119.2:c.381C>A	17.37:g.56293485G>T		Somatic	50	0		WXS	Illumina HiSeq	Phase_1	142	5	NM_017777	B7WNX4|F5H885|Q284T0|Q96G13	Silent	SNP	ENST00000393119.2	37	CCDS11603.2	.	.	.	.	.	.	.	.	.	.	G	9.922	1.212413	0.22289	.	.	ENSG00000011143	ENST00000313863	.	.	.	5.82	0.171	0.15026	.	.	.	.	.	T	0.51702	0.1690	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.39643	-0.9604	4	.	.	.	-17.8273	6.0866	0.19970	0.2942:0.1256:0.5801:0.0	.	.	.	.	H	128	.	.	P	-	2	0	MKS1	53648484	1.000000	0.71417	0.999000	0.59377	0.989000	0.77384	0.522000	0.22909	0.107000	0.17824	-0.134000	0.14843	CCT	.		0.438	MKS1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258015.2	NM_017777	
FRG1B	284802	bcgsc.ca	37	20	29628263	29628263	+	Missense_Mutation	SNP	A	A	G			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	A	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr20:29628263A>G	ENST00000278882.3	+	6	645	c.265A>G	c.(265-267)Att>Gtt	p.I89V	FRG1B_ENST00000358464.4_Missense_Mutation_p.I89V|FRG1B_ENST00000439954.2_Missense_Mutation_p.I94V			Q9BZ01	FRG1B_HUMAN	FSHD region gene 1 family, member B	89								p.I89V(4)		endometrium(10)|kidney(21)|lung(3)|pancreas(1)|prostate(9)|urinary_tract(9)	53						TAGCTGCTTTATTAGATGCAA	0.363																																					.													FRG1B,NS,carcinoma,0,20	FRG1B	181	4	Substitution - Missense(4)	prostate(2)|kidney(2)	.						.																																			SO:0001583	missense	284802	.			TGCTTTATTAGAT			20q11.1	2013-03-18	2007-10-11	2007-10-11	ENSG00000149531	ENSG00000149531			15792	other	unknown			"""chromosome 20 open reading frame 80"""	C20orf80			Standard	NR_003579		Approved	bA348I14.2	uc010ztl.1	Q9BZ01	OTTHUMG00000032157	ENST00000278882.3:c.265A>G	20.37:g.29628263A>G	ENSP00000278882:p.Ile89Val	Somatic	404	6		WXS	Illumina HiSeq	Phase_1	727	28	.	C4AME5	Missense_Mutation	SNP	ENST00000278882.3	37		.	.	.	.	.	.	.	.	.	.	a	8.196	0.797144	0.16327	.	.	ENSG00000149531	ENST00000278882;ENST00000439954;ENST00000358464	T	0.44482	0.92	2.08	2.08	0.27032	Actin cross-linking (1);	0.052017	0.85682	D	0.000000	T	0.22666	0.0547	.	.	.	0.33862	D	0.633895	B;B	0.06786	0.0;0.001	B;B	0.20767	0.018;0.031	T	0.12041	-1.0563	9	0.22706	T	0.39	.	3.8663	0.09018	0.8139:0.0:0.1861:0.0	.	94;89	F5H5R5;Q9BZ01	.;FRG1B_HUMAN	V	89;94;89	ENSP00000408863:I94V	ENSP00000278882:I89V	I	+	1	0	FRG1B	28241924	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	4.345000	0.59360	1.208000	0.43306	0.347000	0.21830	ATT	.		0.363	FRG1B-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000078494.2	NR_003579	
FRG1B	284802	bcgsc.ca	37	20	29632707	29632707	+	Silent	SNP	G	G	A	rs6057187		TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	G	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr20:29632707G>A	ENST00000278882.3	+	8	902	c.522G>A	c.(520-522)gaG>gaA	p.E174E	FRG1B_ENST00000358464.4_Silent_p.E174E			Q9BZ01	FRG1B_HUMAN	FSHD region gene 1 family, member B	174								p.E174E(10)		endometrium(10)|kidney(21)|lung(3)|pancreas(1)|prostate(9)|urinary_tract(9)	53						TTTTGCATGAGACGCTTCTGG	0.313																																					.													FRG1B,NS,malignant_melanoma,0,4	FRG1B	181	10	Substitution - coding silent(10)	endometrium(6)|kidney(4)	.						.																																			SO:0001819	synonymous_variant	284802	.			GCATGAGACGCTT			20q11.1	2013-03-18	2007-10-11	2007-10-11	ENSG00000149531	ENSG00000149531			15792	other	unknown			"""chromosome 20 open reading frame 80"""	C20orf80			Standard	NR_003579		Approved	bA348I14.2	uc010ztl.1	Q9BZ01	OTTHUMG00000032157	ENST00000278882.3:c.522G>A	20.37:g.29632707G>A		Somatic	198	6		WXS	Illumina HiSeq	Phase_1	387	19	.	C4AME5	Silent	SNP	ENST00000278882.3	37																																																																																				G|0.500;A|0.500		0.313	FRG1B-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000078494.2	NR_003579	
GART	2618	bcgsc.ca	37	21	34889332	34889332	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	G	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr21:34889332G>T	ENST00000381831.3	-	16	2334	c.2071C>A	c.(2071-2073)Ccc>Acc	p.P691T	GART_ENST00000381839.3_Missense_Mutation_p.P691T|GART_ENST00000543717.1_Missense_Mutation_p.P243T|GART_ENST00000381815.4_Missense_Mutation_p.P691T	NM_001136005.1	NP_001129477.1	P22102	PUR2_HUMAN	phosphoribosylglycinamide formyltransferase, phosphoribosylglycinamide synthetase, phosphoribosylaminoimidazole synthetase	691	AIRS.				'de novo' IMP biosynthetic process (GO:0006189)|brainstem development (GO:0003360)|cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|glycine metabolic process (GO:0006544)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase biosynthetic process (GO:0009113)|purine nucleobase metabolic process (GO:0006144)|purine ribonucleoside monophosphate biosynthetic process (GO:0009168)|response to inorganic substance (GO:0010035)|response to organic substance (GO:0010033)|small molecule metabolic process (GO:0044281)|tetrahydrofolate biosynthetic process (GO:0046654)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)|phosphoribosylamine-glycine ligase activity (GO:0004637)|phosphoribosylformylglycinamidine cyclo-ligase activity (GO:0004641)|phosphoribosylglycinamide formyltransferase activity (GO:0004644)			NS(2)|breast(1)|endometrium(3)|large_intestine(3)|lung(13)|ovary(3)|prostate(5)|urinary_tract(1)	31					Pemetrexed(DB00642)	AGGACTCTGGGGATGTTCTCT	0.438																																					p.P691T													.	GART	81	0			c.C2071A						.						110.0	107.0	108.0					21																	34889332		2203	4300	6503	SO:0001583	missense	2618	exon16			CTCTGGGGATGTT	M32082	CCDS13627.1, CCDS13628.1	21q22.11	2012-10-02			ENSG00000159131	ENSG00000159131	2.1.2.2, 6.3.3.1, 6.3.4.13		4163	protein-coding gene	gene with protein product		138440		PRGS, PGFT		2050105	Standard	NM_001136005		Approved		uc002yrx.3	P22102	OTTHUMG00000065628	ENST00000381831.3:c.2071C>A	21.37:g.34889332G>T	ENSP00000371253:p.Pro691Thr	Somatic	36	0		WXS	Illumina HiSeq	Phase_1	57	4	NM_001136005	A8K945|A8KA32|D3DSF3|D3DSF4|O14659|Q52M77	Missense_Mutation	SNP	ENST00000381831.3	37	CCDS13627.1	.	.	.	.	.	.	.	.	.	.	G	19.12	3.766201	0.69878	.	.	ENSG00000159131	ENST00000381815;ENST00000381831;ENST00000381839;ENST00000543717	T;T;T;T	0.33865	1.39;1.39;1.39;1.39	4.9	4.9	0.64082	AIR synthase-related protein, C-terminal (2);	0.000000	0.85682	D	0.000000	T	0.53465	0.1798	M	0.91510	3.215	0.80722	D	1	B	0.31752	0.338	B	0.35550	0.205	T	0.63994	-0.6511	10	0.62326	D	0.03	-14.5591	18.0987	0.89499	0.0:0.0:1.0:0.0	.	691	P22102	PUR2_HUMAN	T	691;691;691;243	ENSP00000371236:P691T;ENSP00000371253:P691T;ENSP00000371261:P691T;ENSP00000443579:P243T	ENSP00000371236:P691T	P	-	1	0	GART	33811202	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	6.282000	0.72639	2.261000	0.74972	0.462000	0.41574	CCC	.		0.438	GART-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140626.3	NM_000819	
TOP3BP1	23751	bcgsc.ca	37	22	22578444	22578444	+	IGR	SNP	G	G	C	rs28454744	byFrequency	TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	G	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr22:22578444G>C								IGLV10-54 (8784 upstream) : VPREB1 (20642 downstream)																							CTCACTCCCGGGGCAGCCTGG	0.637													-|||	2318	0.462859	0.3623	0.3458	5008	,	,		17011	0.5258		0.4185	False		,,,				2504	0.6626				.													.	.	.	0			.						.																																			SO:0001628	intergenic_variant	23751	.			CTCCCGGGGCAGC																													22.37:g.22578444G>C		Somatic	21	0		WXS	Illumina HiSeq	Phase_1	25	11	.		RNA	SNP		37																																																																																				G|0.500;C|0.500	0	0.637								
TMEM132D	121256	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	12	130184567	130184568	+	Missense_Mutation	DNP	TG	TG	CC			TCGA-W5-AA2O-01A-11D-A417-09	TCGA-W5-AA2O-10A-01D-A41A-09	TG	TG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	61057f6c-7608-4c67-8381-6df68fe11d37	3ff81ee1-202a-49fd-b64b-7ad86894fc5e	g.chr12:130184567_130184568TG>CC	ENST00000422113.2	-	2	1081_1082	c.755_756CA>GG	c.(754-756)aCA>aGG	p.T252R	RP11-174M13.2_ENST00000544036.1_lincRNA	NM_133448.2	NP_597705.2	Q14C87	T132D_HUMAN	transmembrane protein 132D	252					negative regulation of phosphatase activity (GO:0010923)	integral component of membrane (GO:0016021)				NS(1)|breast(6)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(33)|liver(1)|lung(69)|ovary(10)|pancreas(2)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(2)	152	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0934)|Breast(359;0.133)		OV - Ovarian serous cystadenocarcinoma(86;0.000288)|Epithelial(86;0.0116)|all cancers(50;0.0246)		CACTGTGGCCTGTCCGGATCCC	0.619																																					p.T252R		.											TMEM132D,right_lower_lobe,carcinoma,0,1	TMEM132D	0	0			c.C755G						.																																			SO:0001583	missense	121256	exon2			TGGCCTGTCCGGA	AB061814	CCDS9266.1	12q24.32-q24.33	2014-06-13			ENSG00000151952	ENSG00000151952			29411	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 153"""	611257				11853319, 12966072	Standard	NM_133448		Approved	KIAA1944, MOLT, PPP1R153	uc009zyl.1	Q14C87	OTTHUMG00000168400	ENST00000422113.2:c.755_756delinsCC	12.37:g.130184567_130184568delinsCC	ENSP00000408581:p.Thr252Arg	Somatic	30	0		WXS	Illumina HiSeq	.	40	13	NM_133448	Q14C96|Q76M59|Q8N1W9|Q8N3Q5|Q8TF57	Missense_Mutation	DNP	ENST00000422113.2	37	CCDS9266.1																																																																																			.		0.619	TMEM132D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399592.1	NM_133448	
