#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_ACHILLES_Lineage_Results_Top_Genes	i_BAM_File	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_Chromosome_hg18	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_End_position_hg18	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_Mutation_Status	i_NormalRefReads_WU	i_NormalVAF_WU	i_NormalVarReads_WU	i_ORegAnno_bin	i_RNARefReads_WU	i_RNAVAF_WU	i_RNAVarReads_WU	i_Sequence_Source	i_Sequencer	i_Sequencing_Phase	i_Start_position_hg18	i_TumorRefReads_WU	i_TumorVAF_WU	i_TumorVarReads_WU	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_all_domains	i_amino_acid_change	i_annotation_transcript	i_build	i_c_position	i_ccds_id	i_chromosome_name	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_deletion_substructures	i_domain	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_name	i_gene_type	i_havana_transcript	i_reference	i_refseq_mrna_id	i_secondary_variant_classification	i_stop	i_strand	i_transcript_error	i_transcript_name	i_transcript_source	i_transcript_species	i_transcript_status	i_transcript_version	i_trv_type	i_type	i_ucsc_cons	i_variant
ARSF	416	genome.wustl.edu	37	X	3021841	3021841	+	Missense_Mutation	SNP	G	G	A			TCGA-AB-2964-03A-01D-0739-09	TCGA-AB-2964-11A-01D-0739-09	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	81878b07-8cd3-47ff-86e8-75ac7e99f4a7	4f7299ec-0ee1-4eb8-88fa-1a5007bab63a	g.chrX:3021841G>A	ENST00000381127.1	+	9	1362	c.1141G>A	c.(1141-1143)Gtc>Atc	p.V381I	ARSF_ENST00000537104.1_Missense_Mutation_p.V381I|ARSF_ENST00000359361.2_Missense_Mutation_p.V381I	NM_001201538.1|NM_001201539.1	NP_001188467.1|NP_001188468.1	P54793	ARSF_HUMAN	arylsulfatase F	381					cellular protein metabolic process (GO:0044267)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)	p.V381I(1)		NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(15)|ovary(2)|prostate(3)|skin(3)|urinary_tract(2)	38		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				TGGAATCCGCGTCCCAGGAAT	0.438																																						dbGAP											1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	X											95.0	85.0	88.0					X																	3021841		2203	4300	6503	3031841	SO:0001583	missense	0			X97868	CCDS14123.1	Xp22.3	2013-02-14			ENSG00000062096	ENSG00000062096		"""Arylsulfatase family"""	721	protein-coding gene	gene with protein product		300003				7720070	Standard	NM_004042		Approved		uc022brz.1	P54793	OTTHUMG00000021081	ENST00000381127.1:c.1141G>A	X.37:g.3021841G>A	ENSP00000370519:p.Val381Ile	Somatic	726	0.27	2		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	3031841	657	38.19	406	Q8TCC5	Missense_Mutation	SNP	HMMPfam_Sulfatase,PatternScan_SULFATASE_2,PatternScan_SULFATASE_1,superfamily_Alkaline phosphatase-like	p.V381I	ENST00000381127.1	37	c.1141	CCDS14123.1	X	.	.	.	.	.	.	.	.	.	.	G	14.11	2.437101	0.43224	.	.	ENSG00000062096	ENST00000381127;ENST00000537104;ENST00000359361	D;D;D	0.95724	-3.79;-3.79;-3.79	3.53	3.53	0.40419	Alkaline phosphatase-like, alpha/beta/alpha (1);Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	0.000000	0.64402	U	0.000001	D	0.98033	0.9352	M	0.85630	2.765	0.48341	D	0.999639	B	0.32425	0.371	D	0.65443	0.935	D	0.97887	1.0295	10	0.44086	T	0.13	.	14.4629	0.67465	0.0:0.0:1.0:0.0	.	381	P54793	ARSF_HUMAN	I	381	ENSP00000370519:V381I;ENSP00000445594:V381I;ENSP00000352319:V381I	ENSP00000352319:V381I	V	+	1	0	ARSF	3031841	1.000000	0.71417	0.016000	0.15963	0.066000	0.16364	7.893000	0.87330	1.374000	0.46228	0.411000	0.27672	GTC	-	HMMPfam_Sulfatase,superfamily_Alkaline phosphatase-like		0.438	ARSF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ARSF	protein_coding	OTTHUMT00000055652.1	G			3031841	+1	no_errors	NM_004042.3	genbank	human	reviewed	54_36p	missense	SNP	1.000	A
SHROOM2	357	genome.wustl.edu	37	X	9900372	9900372	+	Nonsense_Mutation	SNP	C	C	T	rs201265738		TCGA-AB-2964-03A-01D-0739-09	TCGA-AB-2964-11A-01D-0739-09	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	81878b07-8cd3-47ff-86e8-75ac7e99f4a7	4f7299ec-0ee1-4eb8-88fa-1a5007bab63a	g.chrX:9900372C>T	ENST00000380913.3	+	6	3139	c.3049C>T	c.(3049-3051)Cga>Tga	p.R1017*	SHROOM2_ENST00000493668.1_3'UTR|SHROOM2_ENST00000418909.2_5'UTR	NM_001649.2	NP_001640.1	Q13796	SHRM2_HUMAN	shroom family member 2	1017					apical protein localization (GO:0045176)|brain development (GO:0007420)|camera-type eye development (GO:0043010)|camera-type eye morphogenesis (GO:0048593)|cell migration (GO:0016477)|cell-cell junction maintenance (GO:0045217)|cellular pigment accumulation (GO:0043482)|ear development (GO:0043583)|establishment of melanosome localization (GO:0032401)|eye pigment granule organization (GO:0008057)|lens morphogenesis in camera-type eye (GO:0002089)|melanosome organization (GO:0032438)|negative regulation of actin filament depolymerization (GO:0030835)|sodium ion transmembrane transport (GO:0035725)	apical plasma membrane (GO:0016324)|cell cortex (GO:0005938)|cell-cell adherens junction (GO:0005913)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|filamentous actin (GO:0031941)|microtubule (GO:0005874)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|beta-catenin binding (GO:0008013)|ligand-gated sodium channel activity (GO:0015280)	p.R1017*(1)		breast(4)|central_nervous_system(2)|cervix(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(13)|ovary(3)|prostate(3)|skin(6)|upper_aerodigestive_tract(2)	57		Hepatocellular(5;0.000888)				AACCCTACCTCGAGATTATAG	0.647																																						dbGAP											1	Substitution - Nonsense(1)	haematopoietic_and_lymphoid_tissue(1)	X											30.0	30.0	30.0					X																	9900372		2198	4297	6495	9860372	SO:0001587	stop_gained	0			X83543	CCDS14135.1	Xp22.3	2008-02-05	2006-07-20	2006-07-20	ENSG00000146950	ENSG00000146950			630	protein-coding gene	gene with protein product		300103	"""apical protein, Xenopus laevis-like"", ""apical protein-like (Xenopus laevis)"""	APXL		7795590, 16615870	Standard	NM_001649		Approved		uc004csu.1	Q13796	OTTHUMG00000021121	ENST00000380913.3:c.3049C>T	X.37:g.9900372C>T	ENSP00000370299:p.Arg1017*	Somatic	319	0.00	0		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	9860372	89	37.76	54	B9EIQ7	Nonsense_Mutation	SNP	HMMPfam_PDZ,HMMSmart_SM00228,superfamily_PDZ domain-like,HMMPfam_ASD2,HMMPfam_ASD1	p.R1017*	ENST00000380913.3	37	c.3049	CCDS14135.1	X	.	.	.	.	.	.	.	.	.	.	c	38	6.972123	0.97971	.	.	ENSG00000146950	ENST00000380913	.	.	.	4.26	2.17	0.27698	.	0.800436	0.11393	N	0.568569	.	.	.	.	.	.	0.18873	N	0.999983	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	5.2011	0.15264	0.4945:0.3815:0.0:0.1241	.	.	.	.	X	1017	.	ENSP00000370299:R1017X	R	+	1	2	SHROOM2	9860372	0.056000	0.20664	0.004000	0.12327	0.010000	0.07245	1.535000	0.36061	0.630000	0.30394	0.591000	0.81541	CGA	-	NULL		0.647	SHROOM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SHROOM2	protein_coding	OTTHUMT00000055721.1	C	NM_001649		9860372	+1	no_errors	NM_001649.2	genbank	human	reviewed	54_36p	nonsense	SNP	0.732	T
CAPN6	827	genome.wustl.edu	37	X	110507007	110507007	+	Missense_Mutation	SNP	C	C	T			TCGA-AB-2964-03A-01D-0739-09	TCGA-AB-2964-11A-01D-0739-09	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	81878b07-8cd3-47ff-86e8-75ac7e99f4a7	4f7299ec-0ee1-4eb8-88fa-1a5007bab63a	g.chrX:110507007C>T	ENST00000324068.1	-	2	325	c.158G>A	c.(157-159)cGt>cAt	p.R53H	CAPN6_ENST00000541758.1_5'UTR	NM_014289.3	NP_055104.2	Q9Y6Q1	CAN6_HUMAN	calpain 6	53	Calpain catalytic. {ECO:0000255|PROSITE- ProRule:PRU00239}.				microtubule bundle formation (GO:0001578)|proteolysis (GO:0006508)|regulation of cytoskeleton organization (GO:0051493)	perinuclear region of cytoplasm (GO:0048471)|spindle microtubule (GO:0005876)	calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|microtubule binding (GO:0008017)	p.R53H(1)		cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(25)|ovary(3)|skin(3)|upper_aerodigestive_tract(1)	47						TACCTGGGGACGTTTCCACAC	0.428																																						dbGAP											1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	X											136.0	120.0	125.0					X																	110507007		2203	4300	6503	110393663	SO:0001583	missense	0			AF029232	CCDS14555.1	Xq23	2008-07-29			ENSG00000077274	ENSG00000077274			1483	protein-coding gene	gene with protein product		300146				9503024, 9339374	Standard	NM_014289		Approved	CAPNX, CalpM, CANPX	uc004epc.2	Q9Y6Q1	OTTHUMG00000022203	ENST00000324068.1:c.158G>A	X.37:g.110507007C>T	ENSP00000317214:p.Arg53His	Somatic	1124	0.09	1		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	110393663	597	36.69	346	D3DUY7|Q9UEQ1|Q9UJA8	Missense_Mutation	SNP	HMMPfam_C2,HMMSmart_C2,PatternScan_THIOL_PROTEASE_CYS,PatternScan_THIOL_PROTEASE_HIS,PatternScan_THIOL_PROTEASE_ASN,HMMPfam_Peptidase_C2,HMMPfam_Calpain_III,HMMSmart_CysPc,HMMSmart_calpain_III,superfamily_Peptidase_C2,superfamily_C2_CaLB,superfamily_SSF54001	p.R53H	ENST00000324068.1	37	c.158	CCDS14555.1	X	.	.	.	.	.	.	.	.	.	.	C	24.0	4.479347	0.84747	.	.	ENSG00000077274	ENST00000324068	T	0.71461	-0.57	5.78	5.78	0.91487	Peptidase C2, calpain, catalytic domain (3);	0.000000	0.85682	D	0.000000	D	0.90463	0.7013	H	0.98466	4.24	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.93893	0.7181	10	0.87932	D	0	.	15.7781	0.78240	0.0:1.0:0.0:0.0	.	53	Q9Y6Q1	CAN6_HUMAN	H	53	ENSP00000317214:R53H	ENSP00000317214:R53H	R	-	2	0	CAPN6	110393663	0.997000	0.39634	0.998000	0.56505	0.890000	0.51754	5.046000	0.64226	2.439000	0.82584	0.544000	0.68410	CGT	-	HMMPfam_Peptidase_C2,HMMSmart_CysPc,superfamily_SSF54001		0.428	CAPN6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CAPN6	protein_coding	OTTHUMT00000057922.1	C			110393663	-1	no_errors	NM_014289.2	genbank	human	reviewed	54_36p	missense	SNP	0.998	T
STAG2	10735	genome.wustl.edu	37	X	123205041	123205041	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AB-2964-03A-01D-0739-09	TCGA-AB-2964-11A-01D-0739-09	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	81878b07-8cd3-47ff-86e8-75ac7e99f4a7	4f7299ec-0ee1-4eb8-88fa-1a5007bab63a	g.chrX:123205041C>T	ENST00000371160.1	+	25	2691	c.2401C>T	c.(2401-2403)Cag>Tag	p.Q801*	STAG2_ENST00000469481.1_Intron|STAG2_ENST00000218089.9_Nonsense_Mutation_p.Q801*|STAG2_ENST00000371157.3_Nonsense_Mutation_p.Q801*|STAG2_ENST00000371144.3_Nonsense_Mutation_p.Q801*|STAG2_ENST00000371145.3_Nonsense_Mutation_p.Q801*|STAG2_ENST00000354548.5_Nonsense_Mutation_p.Q732*	NM_001282418.1	NP_001269347.1	Q8N3U4	STAG2_HUMAN	stromal antigen 2	801					meiotic nuclear division (GO:0007126)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of DNA endoreduplication (GO:0032876)|sister chromatid cohesion (GO:0007062)|stem cell maintenance (GO:0019827)	actin cytoskeleton (GO:0015629)|chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	chromatin binding (GO:0003682)	p.Q801*(1)		breast(5)|central_nervous_system(4)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(9)|lung(21)|ovary(5)|prostate(2)|skin(5)|urinary_tract(4)	78						CTTCAGCCATCAGATTATGTC	0.373																																						dbGAP											1	Substitution - Nonsense(1)	haematopoietic_and_lymphoid_tissue(1)	X											208.0	183.0	191.0					X																	123205041		2203	4300	6503	123032722	SO:0001587	stop_gained	0			Z75331	CCDS14607.1, CCDS43990.1	Xq25	2014-09-17			ENSG00000101972	ENSG00000101972			11355	protein-coding gene	gene with protein product		300826				9305759	Standard	NM_001042750		Approved	SA-2, SCC3B	uc004eua.3	Q8N3U4	OTTHUMG00000022725	ENST00000371160.1:c.2401C>T	X.37:g.123205041C>T	ENSP00000360202:p.Gln801*	Somatic	669	0.15	1		0	100.00	7	WXS	Illumina HiSeq	Phase_IV	123032722	655	39.84	435	B1AMT5|D3DTF5|O00540|Q5JTI6|Q68DE9|Q9H1N8	Nonsense_Mutation	SNP	HMMPfam_STAG,superfamily_ARM-type_fold	p.Q801*	ENST00000371160.1	37	c.2401	CCDS14607.1	X	.	.	.	.	.	.	.	.	.	.	C	43	10.427672	0.99403	.	.	ENSG00000101972	ENST00000218089;ENST00000354548;ENST00000371160;ENST00000371157;ENST00000371145;ENST00000371144	.	.	.	5.44	5.44	0.79542	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.40728	T	0.16	-3.7593	18.3649	0.90388	0.0:1.0:0.0:0.0	.	.	.	.	X	801;732;801;801;801;801	.	ENSP00000218089:Q801X	Q	+	1	0	STAG2	123032722	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.818000	0.86416	2.278000	0.76064	0.538000	0.68166	CAG	-	superfamily_ARM-type_fold		0.373	STAG2-018	KNOWN	basic|appris_candidate|CCDS	protein_coding	STAG2	protein_coding	OTTHUMT00000156159.2	C	NM_006603		123032722	+1	no_errors	NM_001042749.1	genbank	human	validated	54_36p	nonsense	SNP	1.000	T
ZNF75D	7626	genome.wustl.edu	37	X	134428053	134428053	+	Missense_Mutation	SNP	T	T	C			TCGA-AB-2964-03A-01D-0739-09	TCGA-AB-2964-11A-01D-0739-09	T	T	T	C	T	T	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	81878b07-8cd3-47ff-86e8-75ac7e99f4a7	4f7299ec-0ee1-4eb8-88fa-1a5007bab63a	g.chrX:134428053T>C	ENST00000370766.3	-	3	2723	c.14A>G	c.(13-15)gAg>gGg	p.E5G	ZNF75D_ENST00000494295.1_Intron|ZNF75D_ENST00000370764.1_Missense_Mutation_p.E5G	NM_007131.3	NP_009062.2	P51815	ZN75D_HUMAN	zinc finger protein 75D	5					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.E5G(1)		autonomic_ganglia(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(14)|upper_aerodigestive_tract(1)|urinary_tract(2)	31						CGCGTTCAGCTCTCTCATCGC	0.493																																						dbGAP											1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	X											118.0	123.0	122.0					X																	134428053		2203	4300	6503	134255719	SO:0001583	missense	0			S43109	CCDS14648.1, CCDS55503.1	Xq26	2013-01-09	2008-06-11	2008-06-11	ENSG00000186376	ENSG00000186376		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	13145	protein-coding gene	gene with protein product		314997	"""zinc finger protein 75 (D8C6)"""	ZNF82, ZNF75		1505955	Standard	XM_005262469		Approved	ZKSCAN24, D8C6, ZSCAN28	uc004eyo.3	P51815	OTTHUMG00000022482	ENST00000370766.3:c.14A>G	X.37:g.134428053T>C	ENSP00000359802:p.Glu5Gly	Somatic	739	0.13	1		0	100.00	2	WXS	Illumina HiSeq	Phase_IV	134255719	430	41.02	299	A6NK62|B3KRI7|Q5JPG0|Q6LDE0	Missense_Mutation	SNP	HMMPfam_KRAB,HMMSmart_KRAB,superfamily_Krueppel-associated_box,HMMPfam_SCAN,HMMSmart_SCAN,HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_ZnF_C2H2,superfamily_SSF57667	p.E5G	ENST00000370766.3	37	c.14	CCDS14648.1	X	.	.	.	.	.	.	.	.	.	.	T	10.46	1.356248	0.24598	.	.	ENSG00000186376	ENST00000370766;ENST00000370764	T;T	0.07021	3.23;3.23	3.17	0.639	0.17747	.	.	.	.	.	T	0.02807	0.0084	N	0.08118	0	0.09310	N	1	B;B	0.33694	0.281;0.421	B;B	0.25291	0.057;0.059	T	0.42344	-0.9457	9	0.20046	T	0.44	.	2.2502	0.04042	0.2488:0.1459:0.0:0.6053	.	5;5	P51815;A6NK62	ZN75D_HUMAN;.	G	5	ENSP00000359802:E5G;ENSP00000359800:E5G	ENSP00000359800:E5G	E	-	2	0	ZNF75D	134255719	0.003000	0.15002	0.001000	0.08648	0.081000	0.17604	0.810000	0.27183	0.028000	0.15324	0.417000	0.27973	GAG	-	NULL		0.493	ZNF75D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	ZNF75D	protein_coding	OTTHUMT00000058415.1	T	NM_007131		134255719	-1	no_errors	NM_007131.2	genbank	human	validated	54_36p	missense	SNP	0.003	C
CAMTA1	23261	genome.wustl.edu	37	1	7721815	7721815	+	Missense_Mutation	SNP	G	G	A			TCGA-AB-2964-03A-01D-0739-09	TCGA-AB-2964-11A-01D-0739-09	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	81878b07-8cd3-47ff-86e8-75ac7e99f4a7	4f7299ec-0ee1-4eb8-88fa-1a5007bab63a	g.chr1:7721815G>A	ENST00000303635.7	+	8	901	c.694G>A	c.(694-696)Ggg>Agg	p.G232R	CAMTA1_ENST00000439411.2_Missense_Mutation_p.G232R	NM_015215.2	NP_056030.1	Q9Y6Y1	CMTA1_HUMAN	calmodulin binding transcription activator 1	232					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.G232R(1)		breast(5)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(11)|lung(29)|ovary(5)|pancreas(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	85	Ovarian(185;0.0634)	all_epithelial(116;8.38e-23)|all_lung(118;5.87e-07)|Lung NSC(185;3.43e-06)|Renal(390;0.000219)|Breast(487;0.000307)|Colorectal(325;0.000615)|Hepatocellular(190;0.0088)|Myeloproliferative disorder(586;0.0303)|Ovarian(437;0.0388)		UCEC - Uterine corpus endometrioid carcinoma (279;0.101)|Colorectal(212;1.33e-05)|COAD - Colon adenocarcinoma(227;0.000235)|BRCA - Breast invasive adenocarcinoma(304;0.000864)|Kidney(185;0.00244)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0179)|READ - Rectum adenocarcinoma(331;0.133)		CTGCAGCAATGGGAACAGCAG	0.642			T	WWTR1	epitheliod hemangioendothelioma																																	dbGAP		Dom	yes		1	1p36.31-p36.23	611501	calmodulin binding transcription activator 1		M	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	1											74.0	69.0	70.0					1																	7721815		2203	4300	6503	7644402	SO:0001583	missense	0			AB020640	CCDS30576.1, CCDS55574.1, CCDS55575.1	1p36.31-p36.23	2008-07-18			ENSG00000171735	ENSG00000171735			18806	protein-coding gene	gene with protein product		611501				11925432	Standard	NM_001195563		Approved	KIAA0833	uc001aoi.3	Q9Y6Y1	OTTHUMG00000001212	ENST00000303635.7:c.694G>A	1.37:g.7721815G>A	ENSP00000306522:p.Gly232Arg	Somatic	151	0.00	0		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	7644402	83	34.13	43	A7MBM4|G3V3Z7|Q5VUE1|Q6V701|Q8WYI3|Q96S92	Missense_Mutation	SNP	HMMPfam_IQ,HMMPfam_Ank,superfamily_Ankyrin repeat,HMMPfam_TIG,HMMPfam_CG-1,superfamily_E set domains,superfamily_P-loop containing nucleoside triphosphate hydrolases	p.G232R	ENST00000303635.7	37	c.694	CCDS30576.1	1	.	.	.	.	.	.	.	.	.	.	g	26.4	4.738696	0.89573	.	.	ENSG00000171735	ENST00000303635;ENST00000439411	T;T	0.20881	2.04;2.04	4.62	4.62	0.57501	.	0.000000	0.85682	D	0.000000	T	0.17746	0.0426	N	0.24115	0.695	0.80722	D	1	B	0.30439	0.279	B	0.33254	0.16	T	0.06789	-1.0807	10	0.30078	T	0.28	-20.2726	17.8642	0.88791	0.0:0.0:1.0:0.0	.	232	Q9Y6Y1	CMTA1_HUMAN	R	232	ENSP00000306522:G232R;ENSP00000402561:G232R	ENSP00000306522:G232R	G	+	1	0	CAMTA1	7644402	1.000000	0.71417	0.970000	0.41538	0.986000	0.74619	7.822000	0.86651	2.305000	0.77605	0.543000	0.68304	GGG	-	NULL		0.642	CAMTA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	CAMTA1	protein_coding	OTTHUMT00000003588.3	G	NM_015215		7644402	+1	no_errors	NM_015215.1	genbank	human	validated	54_36p	missense	SNP	1.000	A
AHCYL1	10768	genome.wustl.edu	37	1	110561263	110561263	+	Silent	SNP	C	C	T			TCGA-AB-2964-03A-01D-0739-09	TCGA-AB-2964-11A-01D-0739-09	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	81878b07-8cd3-47ff-86e8-75ac7e99f4a7	4f7299ec-0ee1-4eb8-88fa-1a5007bab63a	g.chr1:110561263C>T	ENST00000369799.5	+	13	1675	c.1308C>T	c.(1306-1308)ctC>ctT	p.L436L	AHCYL1_ENST00000393614.4_Silent_p.L389L|AHCYL1_ENST00000359172.3_Silent_p.L389L	NM_001242673.1|NM_001242674.1|NM_006621.5	NP_001229602.1|NP_001229603.1|NP_006612.2	O43865	SAHH2_HUMAN	adenosylhomocysteinase-like 1	436	NAD binding. {ECO:0000250}.				mRNA polyadenylation (GO:0006378)|one-carbon metabolic process (GO:0006730)|positive regulation of sodium ion transport (GO:0010765)|protein export from nucleus (GO:0006611)|regulation of anion transport (GO:0044070)|regulation of ion transmembrane transporter activity (GO:0032412)|regulation of mRNA 3'-end processing (GO:0031440)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)	adenosylhomocysteinase activity (GO:0004013)	p.L436L(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(6)|ovary(1)|prostate(2)	18		all_epithelial(167;3.58e-05)|all_lung(203;0.000116)|Lung NSC(277;0.000233)		Lung(183;0.0259)|Colorectal(144;0.123)|all cancers(265;0.134)|Epithelial(280;0.141)|LUSC - Lung squamous cell carcinoma(189;0.143)		GAGTTGTCCTCCTGGCAGAGG	0.552																																						dbGAP											1	Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(1)	1											53.0	38.0	43.0					1																	110561263		2203	4300	6503	110362786	SO:0001819	synonymous_variant	0			U82761	CCDS818.1, CCDS55620.1	1p13	2014-06-12	2009-06-12		ENSG00000168710	ENSG00000168710			344	protein-coding gene	gene with protein product	"""inositol 1,4,5-trisphosphate receptor-binding protein"", ""protein phosphatase 1, regulatory subunit 78"""	607826	"""S-adenosylhomocysteine hydrolase-like 1"""			11904675, 16754674, 12525476	Standard	NM_006621		Approved	XPVKONA, IRBIT, PPP1R78	uc001dyx.3	O43865	OTTHUMG00000011652	ENST00000369799.5:c.1308C>T	1.37:g.110561263C>T		Somatic	430	0.46	2		51	48.48	48	WXS	Illumina HiSeq	Phase_IV	110362786	403	41.85	290	B4E168|Q2TAJ6|Q502W8|Q5VSM0|Q6P171|Q96PK4|Q9UG84	Silent	SNP	HMMPfam_AdoHcyase,HMMPfam_AdoHcyase_NAD,superfamily_NAD(P)-binding Rossmann-fold domains,PatternScan_ADOHCYASE_1,PatternScan_ADOHCYASE_2,superfamily_Formate/glycerate dehydrogenase catalytic domain-like	p.L436	ENST00000369799.5	37	c.1308	CCDS818.1	1																																																																																			-	HMMPfam_AdoHcyase,HMMPfam_AdoHcyase_NAD,superfamily_NAD(P)-binding Rossmann-fold domains,superfamily_Formate/glycerate dehydrogenase catalytic domain-like		0.552	AHCYL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	AHCYL1	protein_coding	OTTHUMT00000032243.1	C			110362786	+1	no_errors	NM_006621.4	genbank	human	validated	54_36p	silent	SNP	0.942	T
CACNA1E	777	genome.wustl.edu	37	1	181689358	181689358	+	Missense_Mutation	SNP	C	C	T			TCGA-AB-2964-03A-01D-0739-09	TCGA-AB-2964-11A-01D-0739-09	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	81878b07-8cd3-47ff-86e8-75ac7e99f4a7	4f7299ec-0ee1-4eb8-88fa-1a5007bab63a	g.chr1:181689358C>T	ENST00000367573.2	+	14	1768	c.1768C>T	c.(1768-1770)Cgg>Tgg	p.R590W	CACNA1E_ENST00000526775.1_Missense_Mutation_p.R590W|CACNA1E_ENST00000357570.5_Missense_Mutation_p.R541W|CACNA1E_ENST00000360108.3_Missense_Mutation_p.R590W|CACNA1E_ENST00000367567.4_Missense_Mutation_p.R197W|CACNA1E_ENST00000358338.5_Missense_Mutation_p.R541W|CACNA1E_ENST00000367570.1_Missense_Mutation_p.R590W	NM_001205293.1	NP_001192222.1	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type, alpha 1E subunit	590					calcium ion import (GO:0070509)|energy reserve metabolic process (GO:0006112)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|voltage-gated calcium channel activity (GO:0005245)	p.R590W(2)		NS(2)|breast(9)|central_nervous_system(3)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(6)|kidney(4)|large_intestine(34)|lung(99)|ovary(6)|pancreas(1)|prostate(9)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	204						GGCTTCCCTACGGAATTTGGT	0.478																																						dbGAP											2	Substitution - Missense(2)	NS(1)|haematopoietic_and_lymphoid_tissue(1)	1											230.0	214.0	219.0					1																	181689358		2006	4164	6170	179955981	SO:0001583	missense	0			AK096563	CCDS53443.1, CCDS55664.1, CCDS55665.1	1q25.3	2013-01-10	2007-02-16		ENSG00000198216	ENSG00000198216		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"", ""EF-hand domain containing"""	1392	protein-coding gene	gene with protein product		601013		CACNL1A6		8388125, 16382099	Standard	NM_001205293		Approved	Cav2.3, BII, CACH6	uc009wxt.3	Q15878	OTTHUMG00000037301	ENST00000367573.2:c.1768C>T	1.37:g.181689358C>T	ENSP00000356545:p.Arg590Trp	Somatic	589	0.34	2		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	179955981	334	41.33	236	B1AM12|B1AM13|B1AM14|Q14580|Q14581	Missense_Mutation	SNP	HMMPfam_Ion_trans,HMMPfam_Ca_chan_IQ,superfamily_Voltage-gated potassium channels	p.R590W	ENST00000367573.2	37	c.1768	CCDS55664.1	1	.	.	.	.	.	.	.	.	.	.	C	20.5	3.995927	0.74703	.	.	ENSG00000198216	ENST00000367570;ENST00000526775;ENST00000357570;ENST00000358338;ENST00000367567;ENST00000360108;ENST00000367573	D;D;D;D;D;D;D	0.98914	-5.23;-5.23;-5.23;-5.23;-5.23;-5.23;-5.23	5.15	5.15	0.70609	.	0.097627	0.64402	D	0.000002	D	0.99453	0.9806	H	0.97852	4.09	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.996	D	0.98237	1.0486	10	0.87932	D	0	.	13.2677	0.60144	0.2005:0.7994:0.0:0.0	.	590;590	Q15878-2;Q15878-3	.;.	W	590;590;541;541;197;590;590	ENSP00000356542:R590W;ENSP00000434814:R590W;ENSP00000350183:R541W;ENSP00000351101:R541W;ENSP00000356539:R197W;ENSP00000353222:R590W;ENSP00000356545:R590W	ENSP00000350183:R541W	R	+	1	2	CACNA1E	179955981	0.988000	0.35896	0.953000	0.39169	0.962000	0.63368	2.256000	0.43231	2.391000	0.81399	0.563000	0.77884	CGG	-	HMMPfam_Ion_trans,superfamily_Voltage-gated potassium channels		0.478	CACNA1E-003	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	CACNA1E	protein_coding	OTTHUMT00000090793.2	C	NM_000721		179955981	+1	no_errors	NM_000721.2	genbank	human	reviewed	54_36p	missense	SNP	1.000	T
OR5K3	403277	genome.wustl.edu	37	3	98110321	98110321	+	Missense_Mutation	SNP	C	C	G			TCGA-AB-2964-03A-01D-0739-09	TCGA-AB-2964-11A-01D-0739-09	C	C	C	G	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	81878b07-8cd3-47ff-86e8-75ac7e99f4a7	4f7299ec-0ee1-4eb8-88fa-1a5007bab63a	g.chr3:98110321C>G	ENST00000383695.1	+	1	812	c.812C>G	c.(811-813)cCt>cGt	p.P271R	RP11-325B23.2_ENST00000508616.1_lincRNA	NM_001005516.1	NP_001005516.1	A6NET4	OR5K3_HUMAN	olfactory receptor, family 5, subfamily K, member 3	271						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.P271R(1)		NS(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(15)|prostate(1)|skin(1)|urinary_tract(1)	27						AAAGATATACCTGTTGCTATA	0.303																																						dbGAP											1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	3											90.0	87.0	88.0					3																	98110321		2203	4300	6503	99593011	SO:0001583	missense	0				CCDS33803.1	3q11.2	2013-09-23			ENSG00000206536	ENSG00000206536		"""GPCR / Class A : Olfactory receptors"""	31290	protein-coding gene	gene with protein product							Standard	NM_001005516		Approved		uc011bgw.2	A6NET4	OTTHUMG00000160077	ENST00000383695.1:c.812C>G	3.37:g.98110321C>G	ENSP00000373194:p.Pro271Arg	Somatic	559	0.36	2		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	99593011	381	47.24	342		Missense_Mutation	SNP	HMMPfam_7tm_1,PatternScan_G_PROTEIN_RECEP_F1_1,superfamily_SSF81321	p.P271R	ENST00000383695.1	37	c.812	CCDS33803.1	3	.	.	.	.	.	.	.	.	.	.	C	11.09	1.536144	0.27475	.	.	ENSG00000206536	ENST00000383695	T	0.00084	8.75	5.15	4.26	0.50523	GPCR, rhodopsin-like superfamily (1);	0.580379	0.14322	N	0.326933	T	0.00144	0.0004	L	0.27053	0.805	0.09310	N	1	P	0.48294	0.908	P	0.48488	0.579	T	0.58381	-0.7646	10	0.66056	D	0.02	-6.9004	7.2149	0.25955	0.0:0.8135:0.0:0.1865	.	271	A6NET4	OR5K3_HUMAN	R	271	ENSP00000373194:P271R	ENSP00000373194:P271R	P	+	2	0	OR5K3	99593011	0.000000	0.05858	0.172000	0.22920	0.403000	0.30841	0.459000	0.21908	2.527000	0.85204	0.603000	0.83216	CCT	-	HMMPfam_7tm_1,superfamily_SSF81321		0.303	OR5K3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	OR5K3	protein_coding	OTTHUMT00000359110.1	C			99593011	+1	no_errors	NM_001005516.1	genbank	human	provisional	54_36p	missense	SNP	0.000	G
TACR3	6870	genome.wustl.edu	37	4	104510899	104510899	+	Silent	SNP	A	A	G			TCGA-AB-2964-03A-01D-0739-09	TCGA-AB-2964-11A-01D-0739-09	A	A	A	G	A	A	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	81878b07-8cd3-47ff-86e8-75ac7e99f4a7	4f7299ec-0ee1-4eb8-88fa-1a5007bab63a	g.chr4:104510899A>G	ENST00000304883.2	-	5	1478	c.1338T>C	c.(1336-1338)tcT>tcC	p.S446S	RP11-297P16.3_ENST00000512401.1_RNA|RP11-297P16.3_ENST00000502936.1_RNA	NM_001059.2	NP_001050.1	P29371	NK3R_HUMAN	tachykinin receptor 3	446					aging (GO:0007568)|hyperosmotic salinity response (GO:0042538)|positive regulation of blood pressure (GO:0045777)|positive regulation of heart rate (GO:0010460)|positive regulation of uterine smooth muscle contraction (GO:0070474)|regulation of dopamine metabolic process (GO:0042053)|regulation of feeding behavior (GO:0060259)|response to cocaine (GO:0042220)|response to estradiol (GO:0032355)|response to morphine (GO:0043278)|tachykinin receptor signaling pathway (GO:0007217)	cytoplasm (GO:0005737)|dendrite membrane (GO:0032590)|integral component of plasma membrane (GO:0005887)|neuronal cell body membrane (GO:0032809)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	tachykinin receptor activity (GO:0004995)	p.S446S(2)		breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(19)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	51		Hepatocellular(203;0.217)		UCEC - Uterine corpus endometrioid carcinoma (10;0.22)|OV - Ovarian serous cystadenocarcinoma(123;3.4e-08)		TGGCGGAGGCAGATTTGGAAT	0.463																																						dbGAP											2	Substitution - coding silent(2)	ovary(1)|haematopoietic_and_lymphoid_tissue(1)	4											139.0	134.0	136.0					4																	104510899		2203	4300	6503	104730348	SO:0001819	synonymous_variant	0			M89473	CCDS3664.1	4q25	2012-08-08			ENSG00000169836	ENSG00000169836		"""GPCR / Class A : Tachykinin receptors"""	11528	protein-coding gene	gene with protein product	"""neurokinin beta receptor"""	162332				1374246	Standard	NM_001059		Approved	NK3R	uc003hxe.1	P29371	OTTHUMG00000131124	ENST00000304883.2:c.1338T>C	4.37:g.104510899A>G		Somatic	489	0.41	2		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	104730348	996	40.08	667	Q0P510	Silent	SNP	HMMPfam_7tm_1,PatternScan_G_PROTEIN_RECEP_F1_1,superfamily_SSF81321	p.S446	ENST00000304883.2	37	c.1338	CCDS3664.1	4																																																																																			-	NULL		0.463	TACR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TACR3	protein_coding	OTTHUMT00000253804.1	A	NM_001059		104730348	-1	no_errors	NM_001059.1	genbank	human	reviewed	54_36p	silent	SNP	0.958	G
TET2	54790	genome.wustl.edu	37	4	106157845	106157845	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AB-2964-03A-01D-0739-09	TCGA-AB-2964-11A-01D-0739-09	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	81878b07-8cd3-47ff-86e8-75ac7e99f4a7	4f7299ec-0ee1-4eb8-88fa-1a5007bab63a	g.chr4:106157845C>T	ENST00000540549.1	+	3	3606	c.2746C>T	c.(2746-2748)Cag>Tag	p.Q916*	TET2_ENST00000305737.2_Nonsense_Mutation_p.Q916*|TET2_ENST00000413648.2_Nonsense_Mutation_p.Q916*|TET2_ENST00000545826.1_Nonsense_Mutation_p.Q916*|TET2_ENST00000513237.1_Nonsense_Mutation_p.Q937*|TET2_ENST00000394764.1_Nonsense_Mutation_p.Q916*|TET2_ENST00000380013.4_Nonsense_Mutation_p.Q916*			Q6N021	TET2_HUMAN	tet methylcytosine dioxygenase 2	916	Gln-rich.				5-methylcytosine catabolic process (GO:0006211)|cell cycle (GO:0007049)|DNA demethylation (GO:0080111)|histone H3-K4 trimethylation (GO:0080182)|kidney development (GO:0001822)|myeloid cell differentiation (GO:0030099)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|protein O-linked glycosylation (GO:0006493)		DNA binding (GO:0003677)|ferrous iron binding (GO:0008198)|methylcytosine dioxygenase activity (GO:0070579)|zinc ion binding (GO:0008270)	p.Q916*(11)		NS(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1272)|kidney(3)|large_intestine(11)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	1314		Myeloproliferative disorder(5;0.0393)		OV - Ovarian serous cystadenocarcinoma(123;7.18e-08)		GCAACTTGCTCAGCAAAGGTA	0.448			"""Mis N, F"""		MDS																																	dbGAP		Rec	yes		4	4q24	54790	tet oncogene family member 2		L	11	Substitution - Nonsense(11)	haematopoietic_and_lymphoid_tissue(11)	4											58.0	52.0	54.0					4																	106157845		2203	4300	6503	106377294	SO:0001587	stop_gained	0			AB046766	CCDS3666.1, CCDS47120.1	4q24	2014-09-17	2011-09-30	2008-03-12	ENSG00000168769	ENSG00000168769			25941	protein-coding gene	gene with protein product		612839	"""KIAA1546"", ""tet oncogene family member 2"""	KIAA1546		10997877, 12646957	Standard	NM_017628		Approved	FLJ20032	uc003hxk.3	Q6N021	OTTHUMG00000131213	ENST00000540549.1:c.2746C>T	4.37:g.106157845C>T	ENSP00000442788:p.Gln916*	Somatic	675	0.00	0		19	44.12	15	WXS	Illumina HiSeq	Phase_IV	106377294	688	41.69	492	B5MDU0|Q2TB88|Q3LIB8|Q96JX5|Q9HCM6|Q9NXW0	Nonsense_Mutation	SNP	NULL	p.Q916*	ENST00000540549.1	37	c.2746	CCDS47120.1	4	.	.	.	.	.	.	.	.	.	.	C	41	8.983090	0.99025	.	.	ENSG00000168769	ENST00000305737;ENST00000540549;ENST00000545826;ENST00000513237;ENST00000380013;ENST00000394764;ENST00000413648	.	.	.	5.79	4.93	0.64822	.	0.214749	0.23461	U	0.047921	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.33141	T	0.24	.	14.9595	0.71144	0.0:0.8577:0.1423:0.0	.	.	.	.	X	916;916;916;937;916;916;916	.	ENSP00000265149:Q916X	Q	+	1	0	TET2	106377294	.	.	0.794000	0.32065	0.687000	0.40016	.	.	1.396000	0.46663	0.655000	0.94253	CAG	-	NULL		0.448	TET2-202	KNOWN	basic|appris_candidate|CCDS	protein_coding	TET2	protein_coding	OTTHUMT00000253952.2	C	NM_017628		106377294	+1	no_errors	NM_017628.1	genbank	human	validated	54_36p	nonsense	SNP	0.006	T
TET2	54790	genome.wustl.edu	37	4	106197333	106197333	+	Missense_Mutation	SNP	C	C	T			TCGA-AB-2964-03A-01D-0739-09	TCGA-AB-2964-11A-01D-0739-09	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	81878b07-8cd3-47ff-86e8-75ac7e99f4a7	4f7299ec-0ee1-4eb8-88fa-1a5007bab63a	g.chr4:106197333C>T	ENST00000540549.1	+	11	6526	c.5666C>T	c.(5665-5667)cCc>cTc	p.P1889L	TET2_ENST00000545826.1_3'UTR|TET2_ENST00000513237.1_Missense_Mutation_p.P1910L|TET2_ENST00000380013.4_Missense_Mutation_p.P1889L			Q6N021	TET2_HUMAN	tet methylcytosine dioxygenase 2	1889					5-methylcytosine catabolic process (GO:0006211)|cell cycle (GO:0007049)|DNA demethylation (GO:0080111)|histone H3-K4 trimethylation (GO:0080182)|kidney development (GO:0001822)|myeloid cell differentiation (GO:0030099)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|protein O-linked glycosylation (GO:0006493)		DNA binding (GO:0003677)|ferrous iron binding (GO:0008198)|methylcytosine dioxygenase activity (GO:0070579)|zinc ion binding (GO:0008270)	p.P1889L(1)|p.P1889R(1)|p.P1889_N1890del(1)		NS(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1272)|kidney(3)|large_intestine(11)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	1314		Myeloproliferative disorder(5;0.0393)		OV - Ovarian serous cystadenocarcinoma(123;7.18e-08)		TTAAAGAATCCCAATAGGAAT	0.502			"""Mis N, F"""		MDS																																	dbGAP		Rec	yes		4	4q24	54790	tet oncogene family member 2		L	3	Substitution - Missense(2)|Deletion - In frame(1)	haematopoietic_and_lymphoid_tissue(3)	4											61.0	53.0	55.0					4																	106197333		692	1591	2283	106416782	SO:0001583	missense	0			AB046766	CCDS3666.1, CCDS47120.1	4q24	2014-09-17	2011-09-30	2008-03-12	ENSG00000168769	ENSG00000168769			25941	protein-coding gene	gene with protein product		612839	"""KIAA1546"", ""tet oncogene family member 2"""	KIAA1546		10997877, 12646957	Standard	NM_017628		Approved	FLJ20032	uc003hxk.3	Q6N021	OTTHUMG00000131213	ENST00000540549.1:c.5666C>T	4.37:g.106197333C>T	ENSP00000442788:p.Pro1889Leu	Somatic	317	1.86	6		17	39.29	11	WXS	Illumina HiSeq	Phase_IV	106416782	781	43.50	602	B5MDU0|Q2TB88|Q3LIB8|Q96JX5|Q9HCM6|Q9NXW0	Missense_Mutation	SNP	NULL	p.P691L	ENST00000540549.1	37	c.2072	CCDS47120.1	4	.	.	.	.	.	.	.	.	.	.	C	18.21	3.573664	0.65765	.	.	ENSG00000168769	ENST00000540549;ENST00000513237;ENST00000380013	T;T;T	0.13778	2.56;2.56;2.56	5.52	4.67	0.58626	Methylcytosine dioxygenase TET, double-stranded beta helix fold domain (1);	.	.	.	.	T	0.41328	0.1154	M	0.81802	2.56	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.97110	0.964;1.0	T	0.47302	-0.9128	9	0.87932	D	0	-12.9803	16.4604	0.84033	0.0:0.8688:0.1312:0.0	.	1910;1889	E7EQS8;Q6N021	.;TET2_HUMAN	L	1889;1910;1889	ENSP00000442788:P1889L;ENSP00000425443:P1910L;ENSP00000369351:P1889L	ENSP00000369351:P1889L	P	+	2	0	TET2	106416782	1.000000	0.71417	0.089000	0.20774	0.618000	0.37518	7.284000	0.78650	1.305000	0.44909	0.655000	0.94253	CCC	-	NULL		0.502	TET2-202	KNOWN	basic|appris_candidate|CCDS	protein_coding	TET2	protein_coding	OTTHUMT00000253952.2	C	NM_017628		106416782	+1	no_start_codon	ENST00000265149	ensembl	human	known	54_36p	missense	SNP	1.000	T
STC2	8614	genome.wustl.edu	37	5	172744952	172744952	+	Silent	SNP	G	G	A			TCGA-AB-2964-03A-01D-0739-09	TCGA-AB-2964-11A-01D-0739-09	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	81878b07-8cd3-47ff-86e8-75ac7e99f4a7	4f7299ec-0ee1-4eb8-88fa-1a5007bab63a	g.chr5:172744952G>A	ENST00000265087.4	-	4	2116	c.807C>T	c.(805-807)aaC>aaT	p.N269N	STC2_ENST00000520593.1_5'Flank	NM_003714.2	NP_003705.1	O76061	STC2_HUMAN	stanniocalcin 2	269					cellular calcium ion homeostasis (GO:0006874)|cellular response to hypoxia (GO:0071456)|decidualization (GO:0046697)|embryo implantation (GO:0007566)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of gene expression (GO:0010629)|negative regulation of multicellular organism growth (GO:0040015)|regulation of hormone biosynthetic process (GO:0046885)|regulation of store-operated calcium entry (GO:2001256)|response to oxidative stress (GO:0006979)|response to peptide hormone (GO:0043434)|response to vitamin D (GO:0033280)	endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|perinuclear region of cytoplasm (GO:0048471)	enzyme binding (GO:0019899)|heme binding (GO:0020037)|protein homodimerization activity (GO:0042803)	p.N269N(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(4)|lung(10)|ovary(1)|prostate(1)|skin(3)	25	Renal(175;0.000159)|Lung NSC(126;0.00229)|all_lung(126;0.004)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)|Ovarian(839;0.223)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)			GGGCATGGGCGTTTGGGTGGC	0.637																																						dbGAP											1	Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(1)	5											78.0	80.0	79.0					5																	172744952		2203	4300	6503	172677558	SO:0001819	synonymous_variant	0			AB012664	CCDS4388.1	5q35.2	2004-05-17			ENSG00000113739	ENSG00000113739			11374	protein-coding gene	gene with protein product		603665				9723890, 9753616	Standard	NM_003714		Approved	STC-2	uc003mco.1	O76061	OTTHUMG00000130542	ENST00000265087.4:c.807C>T	5.37:g.172744952G>A		Somatic	290	1.02	3		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	172677558	55	44.44	44		Silent	SNP	HMMPfam_Stanniocalcin	p.N269	ENST00000265087.4	37	c.807	CCDS4388.1	5																																																																																			-	HMMPfam_Stanniocalcin		0.637	STC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	STC2	protein_coding	OTTHUMT00000252965.1	G	NM_003714		172677558	-1	no_errors	NM_003714.2	genbank	human	reviewed	54_36p	silent	SNP	0.153	A
ELN	2006	genome.wustl.edu	37	7	73452038	73452038	+	Splice_Site	SNP	G	G	A	rs376512299		TCGA-AB-2964-03A-01D-0739-09	TCGA-AB-2964-11A-01D-0739-09	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	81878b07-8cd3-47ff-86e8-75ac7e99f4a7	4f7299ec-0ee1-4eb8-88fa-1a5007bab63a	g.chr7:73452038G>A	ENST00000252034.7	+	4	564	c.165G>A	c.(163-165)gcG>gcA	p.A55A	ELN_ENST00000414324.1_Splice_Site_p.A45A|ELN_ENST00000380584.4_Splice_Site_p.A55A|ELN_ENST00000445912.1_Splice_Site_p.A55A|ELN_ENST00000358929.4_Splice_Site_p.A55A|ELN_ENST00000380553.4_Splice_Site_p.A55A|ELN_ENST00000380575.4_Splice_Site_p.A45A|ELN_ENST00000380562.4_Splice_Site_p.A55A|ELN_ENST00000380576.5_Splice_Site_p.A55A|ELN_ENST00000320399.6_Splice_Site_p.A55A|ELN_ENST00000320492.7_Splice_Site_p.A55A|ELN_ENST00000458204.1_Splice_Site_p.A45A|ELN_ENST00000357036.5_Splice_Site_p.A55A|ELN_ENST00000429192.1_Splice_Site_p.A55A	NM_000501.2|NM_001278915.1	NP_000492.2|NP_001265844.1	P15502	ELN_HUMAN	elastin	55					blood circulation (GO:0008015)|blood vessel remodeling (GO:0001974)|cell proliferation (GO:0008283)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|organ morphogenesis (GO:0009887)|regulation of actin filament polymerization (GO:0030833)|respiratory gaseous exchange (GO:0007585)|skeletal muscle tissue development (GO:0007519)|stress fiber assembly (GO:0043149)	elastic fiber (GO:0071953)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix binding (GO:0050840)|extracellular matrix constituent conferring elasticity (GO:0030023)|extracellular matrix structural constituent (GO:0005201)	p.A55A(1)		breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(10)|ovary(4)|pancreas(2)|prostate(1)|skin(2)|stomach(1)	32		Lung NSC(55;0.159)				CCTCTGCAGCGCTGGGGCCTG	0.587			T	PAX5	B-ALL		"""Supravalvular Aortic Stenosis, Cutis laxa , Williams-Beuren Syndrome"""																															dbGAP		Dom	yes		7	7q11.23	2006	elastin	yes	L	1	Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(1)	7						A	,,,,	3,4403	6.2+/-15.9	0,3,2200	86.0	63.0	71.0		165,135,165,165,165	-10.3	0.0	7		71	0,8600		0,0,4300	no	coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice	ELN	NM_000501.2,NM_001081752.1,NM_001081753.1,NM_001081754.1,NM_001081755.1	,,,,	0,3,6500	AA,AG,GG		0.0,0.0681,0.0231	,,,,	55/725,45/678,55/693,55/712,55/706	73452038	3,13003	2203	4300	6503	73089974	SO:0001630	splice_region_variant	0				CCDS5562.2, CCDS43598.1, CCDS43599.1, CCDS47611.1, CCDS47612.1, CCDS64673.1, CCDS64674.1, CCDS64675.1, CCDS64676.1, CCDS64677.1, CCDS64678.1, CCDS75616.1, CCDS75617.1	7q11.1-q21.1	2008-08-01	2008-08-01		ENSG00000049540	ENSG00000049540			3327	protein-coding gene	gene with protein product	"""tropoelastin"", ""supravalvular aortic stenosis"", ""Williams-Beuren syndrome"""	130160				8096434	Standard	NM_001278939		Approved	WBS, WS, SVAS	uc003tzn.3	P15502	OTTHUMG00000150229	ENST00000252034.7:c.164-1G>A	7.37:g.73452038G>A		Somatic	226	0.00	0		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	73089974	64	30.43	28	B3KTS6|O15336|O15337|Q14233|Q14234|Q14235|Q14238|Q6P0L4|Q6ZWJ6|Q75MU5|Q7Z316|Q7Z3F5|Q9UMF5	Silent	SNP	PatternScan_ENDONUCLEASE_III_2,PatternScan_HEXAPEP_TRANSFERASES	p.A55	ENST00000252034.7	37	c.165	CCDS5562.2	7																																																																																			-	NULL		0.587	ELN-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	ELN	protein_coding	OTTHUMT00000316913.1	G	NM_000501	Silent	73089974	+1	no_errors	NM_000501.2	genbank	human	reviewed	54_36p	silent	SNP	0.285	A
MUC5B	727897	genome.wustl.edu	37	11	1271786	1271786	+	Missense_Mutation	SNP	T	T	C	rs397834801		TCGA-AB-2964-03A-01D-0739-09	TCGA-AB-2964-11A-01D-0739-09	T	T	T	C	T	T	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	81878b07-8cd3-47ff-86e8-75ac7e99f4a7	4f7299ec-0ee1-4eb8-88fa-1a5007bab63a	g.chr11:1271786T>C	ENST00000529681.1	+	31	13734	c.13676T>C	c.(13675-13677)gTc>gCc	p.V4559A	MUC5B_ENST00000447027.1_Missense_Mutation_p.V4562A|RP11-532E4.2_ENST00000532061.2_RNA	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	4559	23 X approximate tandem repeats, Ser/Thr- rich.|Thr-rich.				cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to retinoic acid (GO:0071300)|epithelial cell differentiation (GO:0030855)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to lipopolysaccharide (GO:0032496)|response to ozone (GO:0010193)|response to sulfur dioxide (GO:0010477)|response to vitamin A (GO:0033189)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				cervix(2)|endometrium(36)|kidney(9)|lung(89)|urinary_tract(1)	137		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)		CCAGAGACTGTCCACACCTCC	0.657																																						dbGAP											0			11											96.0	127.0	117.0					11																	1271786		2043	4180	6223	1228362	SO:0001583	missense	0			U95031, AF086604	CCDS44515.1, CCDS44515.2	11p15.5	2007-01-19	2006-03-14			ENSG00000117983		"""Mucins"""	7516	protein-coding gene	gene with protein product		600770	"""mucin 5, subtype B, tracheobronchial"""	MUC5		9804771	Standard	NM_002458		Approved	MG1	uc001lta.3	Q9HC84		ENST00000529681.1:c.13676T>C	11.37:g.1271786T>C	ENSP00000436812:p.Val4559Ala	Somatic	5	28.57	2		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	1228362	4	20.00	1	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	HMMPfam_VWC,HMMSmart_SM00214,PatternScan_VWFC_1,HMMPfam_VWD,HMMSmart_SM00216,superfamily_Serine proterase inhibitors,HMMSmart_SM00041,PatternScan_CTCK_1,HMMPfam_Cys_knot,HMMSmart_SM00215,superfamily_PMP inhibitors,HMMPfam_C8,HMMPfam_TIL	p.V4562A	ENST00000529681.1	37	c.13685	CCDS44515.2	11	.	.	.	.	.	.	.	.	.	.	-	5.028	0.190883	0.09547	.	.	ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637;ENST00000406844;ENST00000535652	T;T	0.20332	2.08;2.27	1.66	-1.02	0.10135	.	.	.	.	.	T	0.08313	0.0207	N	0.04090	-0.28	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.27606	-1.0069	9	0.87932	D	0	.	3.2077	0.06671	0.0:0.435:0.2234:0.3416	.	5032;4562	A7Y9J9;E9PBJ0	.;.	A	4559;4562;4503;4409;336	ENSP00000436812:V4559A;ENSP00000415793:V4562A	ENSP00000343037:V4503A	V	+	2	0	MUC5B	1228362	0.002000	0.14202	0.000000	0.03702	0.017000	0.09413	0.374000	0.20501	-1.141000	0.02873	-1.160000	0.01791	GTC	-	NULL		0.657	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	MUC5B	protein_coding	OTTHUMT00000390041.2	T	XM_001126093		1228362	+1	no_errors	NM_002458.1	genbank	human	validated	54_36p	missense	SNP	0.000	C
OR6A2	8590	genome.wustl.edu	37	11	6816373	6816373	+	Silent	SNP	C	C	T			TCGA-AB-2964-03A-01D-0739-09	TCGA-AB-2964-11A-01D-0739-09	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	81878b07-8cd3-47ff-86e8-75ac7e99f4a7	4f7299ec-0ee1-4eb8-88fa-1a5007bab63a	g.chr11:6816373C>T	ENST00000332601.3	-	1	755	c.567G>A	c.(565-567)ttG>ttA	p.L189L		NM_003696.2	NP_003687.2	O95222	OR6A2_HUMAN	olfactory receptor, family 6, subfamily A, member 2	189					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L189L(1)		breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(4)|pancreas(1)|skin(1)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(2)	29		Medulloblastoma(188;0.0523)|all_neural(188;0.236)		Epithelial(150;4.78e-08)|BRCA - Breast invasive adenocarcinoma(625;0.129)		AGAGGTTGAGCAATGGAGAGA	0.463																																						dbGAP											1	Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(1)	11											127.0	131.0	130.0					11																	6816373		2201	4296	6497	6772949	SO:0001819	synonymous_variant	0			AB065822	CCDS7772.1	11p15.4	2012-08-09		2004-03-10	ENSG00000184933	ENSG00000184933		"""GPCR / Class A : Olfactory receptors"""	15301	protein-coding gene	gene with protein product		608495		OR6A2P, OR6A1			Standard	NM_003696		Approved	OR11-55	uc001mes.1	O95222	OTTHUMG00000165736	ENST00000332601.3:c.567G>A	11.37:g.6816373C>T		Somatic	1237	0.72	9		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	6772949	1422	42.82	1065	Q3MJC7|Q6IF35|Q9H206	Silent	SNP	HMMPfam_7tm_1,PatternScan_G_PROTEIN_RECEP_F1_1,superfamily_SSF81321	p.L189	ENST00000332601.3	37	c.567	CCDS7772.1	11																																																																																			-	HMMPfam_7tm_1,superfamily_SSF81321		0.463	OR6A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	OR6A2	protein_coding	OTTHUMT00000385981.1	C	NM_003696		6772949	-1	no_errors	NM_003696.2	genbank	human	provisional	54_36p	silent	SNP	0.006	T
TMTC2	160335	genome.wustl.edu	37	12	83526070	83526070	+	Missense_Mutation	SNP	G	G	A			TCGA-AB-2964-03A-01D-0739-09	TCGA-AB-2964-11A-01D-0739-09	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	81878b07-8cd3-47ff-86e8-75ac7e99f4a7	4f7299ec-0ee1-4eb8-88fa-1a5007bab63a	g.chr12:83526070G>A	ENST00000321196.3	+	12	3120	c.2413G>A	c.(2413-2415)Gcc>Acc	p.A805T	TMTC2_ENST00000549919.1_Missense_Mutation_p.A799T	NM_152588.1	NP_689801.1	Q8N394	TMTC2_HUMAN	transmembrane and tetratricopeptide repeat containing 2	805					calcium ion homeostasis (GO:0055074)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)		p.A805T(1)		breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(7)|lung(13)|ovary(2)|skin(1)|urinary_tract(1)	39						CTACCTGCGGGCCCTGCAGCT	0.512																																						dbGAP											1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	12											90.0	77.0	81.0					12																	83526070		2203	4300	6503	82050201	SO:0001583	missense	0			AK074634	CCDS9025.1	12q21.31	2014-06-09			ENSG00000179104	ENSG00000179104		"""Tetratricopeptide (TTC) repeat domain containing"""	25440	protein-coding gene	gene with protein product		615856				24764305	Standard	NM_152588		Approved	DKFZp762A217	uc001szt.3	Q8N394	OTTHUMG00000169736	ENST00000321196.3:c.2413G>A	12.37:g.83526070G>A	ENSP00000322300:p.Ala805Thr	Somatic	863	0.12	1		5	0.00	0	WXS	Illumina HiSeq	Phase_IV	82050201	407	50.66	421	B2RCU7|Q8N2K8	Missense_Mutation	SNP	HMMPfam_TPR_1,HMMPfam_TPR_2,HMMPfam_DUF1736,HMMSmart_SM00028,superfamily_TPR-like	p.A805T	ENST00000321196.3	37	c.2413	CCDS9025.1	12	.	.	.	.	.	.	.	.	.	.	G	23.1	4.377471	0.82682	.	.	ENSG00000179104	ENST00000321196;ENST00000549919;ENST00000546590	T;T	0.80214	-1.35;-1.35	5.33	5.33	0.75918	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.000000	0.85682	D	0.000000	D	0.91988	0.7462	M	0.91354	3.2	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.93487	0.6832	10	0.72032	D	0.01	-8.1757	18.0042	0.89205	0.0:0.0:1.0:0.0	.	805	Q8N394	TMTC2_HUMAN	T	805;799;560	ENSP00000322300:A805T;ENSP00000447609:A799T	ENSP00000322300:A805T	A	+	1	0	TMTC2	82050201	1.000000	0.71417	0.996000	0.52242	0.300000	0.27592	9.804000	0.99143	2.512000	0.84698	0.655000	0.94253	GCC	-	HMMPfam_TPR_1,HMMSmart_SM00028,superfamily_TPR-like		0.512	TMTC2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	TMTC2	protein_coding	OTTHUMT00000405663.1	G	NM_152588		82050201	+1	no_errors	NM_152588.1	genbank	human	provisional	54_36p	missense	SNP	1.000	A
ZFHX2	85446	genome.wustl.edu	37	14	23995221	23995221	+	Silent	SNP	G	G	T			TCGA-AB-2964-03A-01D-0739-09	TCGA-AB-2964-11A-01D-0739-09	G	G	G	T	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	81878b07-8cd3-47ff-86e8-75ac7e99f4a7	4f7299ec-0ee1-4eb8-88fa-1a5007bab63a	g.chr14:23995221G>T	ENST00000419474.3	-	9	4285	c.3930C>A	c.(3928-3930)ggC>ggA	p.G1310G	RP11-66N24.4_ENST00000556354.1_RNA|RP11-66N24.4_ENST00000554403.1_RNA|RP11-66N24.4_ENST00000553985.1_RNA	NM_033400.2	NP_207646.2	Q9C0A1	ZFHX2_HUMAN	zinc finger homeobox 2	1310					adult behavior (GO:0030534)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)	p.G1310G(1)		NS(1)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|pancreas(1)	5						TGGTGTCAGGGCCCTTCTTCT	0.597																																						dbGAP											1	Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(1)	14																																								23065061	SO:0001819	synonymous_variant	0			AB051549	CCDS55907.1	14q11.2	2012-03-09			ENSG00000136367	ENSG00000136367		"""Zinc fingers, C2H2-type"", ""Homeoboxes / ZF class"""	20152	protein-coding gene	gene with protein product			"""zinc finger protein 409"""	ZNF409		11214970, 10470851	Standard	NM_033400		Approved	KIAA1762, KIAA1056, ZFH-5	uc010tno.2	Q9C0A1	OTTHUMG00000156894	ENST00000419474.3:c.3930C>A	14.37:g.23995221G>T		Somatic	1206	0.17	2		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	23065061	483	43.21	369	Q9UPU6	Silent	SNP	HMMPfam_Homeobox,HMMSmart_SM00389,HMMSmart_SM00451,HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,superfamily_Homeodomain-like,HMMSmart_SM00355,PatternScan_HOMEOBOX_1,superfamily_C2H2 and C2HC zinc fingers	p.G1444	ENST00000419474.3	37	c.4332	CCDS55907.1	14																																																																																			-	NULL		0.597	ZFHX2-001	KNOWN	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	ZFHX2	protein_coding	OTTHUMT00000346484.3	G	NM_014894		23065061	-1	no_errors	XM_001720095.1	genbank	human	model	54_36p	silent	SNP	0.892	T
ARHGAP5	394	genome.wustl.edu	37	14	32560488	32560488	+	Missense_Mutation	SNP	G	G	A			TCGA-AB-2964-03A-01D-0739-09	TCGA-AB-2964-11A-01D-0739-09	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	81878b07-8cd3-47ff-86e8-75ac7e99f4a7	4f7299ec-0ee1-4eb8-88fa-1a5007bab63a	g.chr14:32560488G>A	ENST00000345122.3	+	2	928	c.613G>A	c.(613-615)Gtg>Atg	p.V205M	ARHGAP5_ENST00000539826.2_Missense_Mutation_p.V205M|ARHGAP5_ENST00000396582.2_Intron|ARHGAP5_ENST00000556611.1_Missense_Mutation_p.V205M|ARHGAP5_ENST00000433497.1_Intron|ARHGAP5_ENST00000432921.1_Missense_Mutation_p.V205M	NM_001030055.1	NP_001025226.1	Q13017	RHG05_HUMAN	Rho GTPase activating protein 5	205					cell adhesion (GO:0007155)|GTP catabolic process (GO:0006184)|mammary gland development (GO:0030879)|positive regulation of cell migration (GO:0030335)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell size (GO:0008361)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|Rho GTPase activator activity (GO:0005100)|SH2 domain binding (GO:0042169)	p.V205M(1)		NS(2)|breast(10)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(10)|lung(12)|ovary(4)|skin(1)|stomach(1)|urinary_tract(4)	55	Hepatocellular(127;0.0604)|Prostate(35;0.15)|Breast(36;0.186)		LUAD - Lung adenocarcinoma(48;0.00192)|Lung(238;0.00714)|BRCA - Breast invasive adenocarcinoma(188;0.0952)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.00566)		TGATGAATGCGTGGATCATTA	0.318																																					NSCLC(9;77 350 3443 29227 41353)	dbGAP											1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	14											68.0	73.0	71.0					14																	32560488		2202	4298	6500	31630239	SO:0001583	missense	0			U17032	CCDS32062.1, CCDS45095.1	14q12	2010-02-05						"""Rho GTPase activating proteins"""	675	protein-coding gene	gene with protein product		602680	"""growth factor independent 2"""	GFI2		8537347	Standard	XM_005267635		Approved	RhoGAP5, p190-B, p190BRhoGAP	uc001wrn.3	Q13017		ENST00000345122.3:c.613G>A	14.37:g.32560488G>A	ENSP00000371897:p.Val205Met	Somatic	1020	0.39	4		12	20.00	3	WXS	Illumina HiSeq	Phase_IV	31630239	371	41.94	268	A1L375|A1L376|A8KAA1|D3DS89|D3DS90|Q05BE8|Q05BU8|Q59ER0|Q6DHZ3	Missense_Mutation	SNP	HMMPfam_RhoGAP,HMMSmart_SM00324,HMMPfam_FF,HMMSmart_SM00441,superfamily_FF domain,superfamily_GTPase activation domain GAP,HMMPfam_Ras,superfamily_P-loop containing nucleoside triphosphate hydrolases	p.V205M	ENST00000345122.3	37	c.613	CCDS32062.1	14	.	.	.	.	.	.	.	.	.	.	G	14.10	2.435058	0.43224	.	.	ENSG00000100852	ENST00000556611;ENST00000539826;ENST00000345122;ENST00000432921	T;T;T;T	0.79554	-1.28;-1.28;-1.28;-1.28	5.68	5.68	0.88126	.	0.123636	0.53938	D	0.000052	D	0.89167	0.6638	M	0.73598	2.24	0.51012	D	0.999907	D;D	0.76494	0.999;0.999	D;D	0.67725	0.922;0.953	D	0.87145	0.2205	10	0.34782	T	0.22	.	19.7885	0.96447	0.0:0.0:1.0:0.0	.	205;205	Q13017-2;Q13017	.;RHG05_HUMAN	M	205	ENSP00000452222:V205M;ENSP00000441692:V205M;ENSP00000371897:V205M;ENSP00000393307:V205M	ENSP00000371897:V205M	V	+	1	0	ARHGAP5	31630239	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	6.817000	0.75252	2.660000	0.90430	0.655000	0.94253	GTG	-	HMMPfam_Ras,superfamily_P-loop containing nucleoside triphosphate hydrolases		0.318	ARHGAP5-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	ARHGAP5	protein_coding	OTTHUMT00000409735.1	G	NM_001030055		31630239	+1	no_errors	NM_001030055.1	genbank	human	reviewed	54_36p	missense	SNP	1.000	A
PRSS27	83886	genome.wustl.edu	37	16	2763665	2763665	+	Silent	SNP	G	G	C	rs140672073	byFrequency	TCGA-AB-2964-03A-01D-0739-09	TCGA-AB-2964-11A-01D-0739-09	G	G	G	C	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	81878b07-8cd3-47ff-86e8-75ac7e99f4a7	4f7299ec-0ee1-4eb8-88fa-1a5007bab63a	g.chr16:2763665G>C	ENST00000302641.3	-	5	597	c.543C>G	c.(541-543)ctC>ctG	p.L181L	AC092117.1_ENST00000410123.1_RNA	NM_031948.3	NP_114154.1	Q9BQR3	PRS27_HUMAN	protease, serine 27	181	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)	p.L181L(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)	8						TGGGCACAGCGAGTTTCTGCA	0.582																																						dbGAP											1	Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(1)	16											166.0	122.0	137.0					16																	2763665		2198	4300	6498	2703666	SO:0001819	synonymous_variant	0			AB056161	CCDS10476.1	16p13.3	2010-05-07			ENSG00000172382	ENSG00000172382		"""Serine peptidases / Serine peptidases"""	15475	protein-coding gene	gene with protein product		608018					Standard	NM_031948		Approved	MPN, pancreasin, CAPH2, marapsin	uc002crf.3	Q9BQR3	OTTHUMG00000128929	ENST00000302641.3:c.543C>G	16.37:g.2763665G>C		Somatic	294	0.00	0		3	0.00	0	WXS	Illumina HiSeq	Phase_IV	2703666	77	44.20	61		Silent	SNP	HMMPfam_Trypsin,HMMSmart_Tryp_SPc,superfamily_Pept_Ser_Cys,PatternScan_TRYPSIN_HIS,PatternScan_TRYPSIN_SER	p.L181	ENST00000302641.3	37	c.543	CCDS10476.1	16																																																																																			-	HMMPfam_Trypsin,HMMSmart_Tryp_SPc,superfamily_Pept_Ser_Cys		0.582	PRSS27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PRSS27	protein_coding	OTTHUMT00000250908.1	G	NM_031948		2703666	-1	no_errors	NM_031948.3	genbank	human	validated	54_36p	silent	SNP	0.031	C
