#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
Unknown	0	genome.wustl.edu	37	Unknown	0	0	+	IGR	SNP	T	T	C			TCGA-AB-2814-03D-01W-0755-09	TCGA-AB-2814-11D-01W-0755-09	T	T	T	C	T	T	Verified	Invalid:failed_liftOver	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	604f0c72-efc7-4868-bc54-79d8f3f3507b	8fb40399-ec65-44a3-9ca3-700a7728c333	g.chrUnknown:0T>C								None (None upstream) : None (None downstream)																								0.0																																						dbGAP											0			MT																																								7962	SO:0001628	intergenic_variant	0																															Unknown.37:g.0T>C		Somatic	2573	1.26	33		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	7962	227	82.09	1109		Silent	SNP	PatternScan_COX2,HMMPfam_COX2,superfamily_Cupredoxins,HMMPfam_COX2_TM,superfamily_Cytochrome^^_^^c^^_^^oxidase^^_^^subunit^^_^^II-like^^_^^transmembrane^^_^^region	p.L126		37	c.376		MT																																																																																			-	HMMPfam_COX2,superfamily_Cupredoxins	0	0					MT-CO2			T			7962	+1	no_errors	ENST00000361739	ensembl	human	known	54_36p	silent	SNP	NULL	C
SHROOM2	357	genome.wustl.edu	37	X	9862449	9862449	+	Silent	SNP	C	C	A			TCGA-AB-2814-03D-01W-0755-09	TCGA-AB-2814-11D-01W-0755-09	C	C	C	A	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	604f0c72-efc7-4868-bc54-79d8f3f3507b	8fb40399-ec65-44a3-9ca3-700a7728c333	g.chrX:9862449C>A	ENST00000380913.3	+	4	591	c.501C>A	c.(499-501)cgC>cgA	p.R167R		NM_001649.2	NP_001640.1	Q13796	SHRM2_HUMAN	shroom family member 2	167					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)			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)				ACCTACAGCGCACCTTAGATC	0.572																																						dbGAP											0			X											90.0	72.0	78.0					X																	9862449		2203	4300	6503	9822449	SO:0001819	synonymous_variant	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.501C>A	X.37:g.9862449C>A		Somatic	31	0.00	0		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	9822449	81	30.17	35	B9EIQ7	Silent	SNP	HMMPfam_PDZ,HMMSmart_SM00228,superfamily_PDZ domain-like,HMMPfam_ASD2,HMMPfam_ASD1	p.R167	ENST00000380913.3	37	c.501	CCDS14135.1	X																																																																																			-	NULL		0.572	SHROOM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SHROOM2	protein_coding	OTTHUMT00000055721.1	C	NM_001649		9822449	+1	no_errors	NM_001649.2	genbank	human	reviewed	54_36p	silent	SNP	0.890	A
HSD3B1	3283	genome.wustl.edu	37	1	120054278	120054278	+	Missense_Mutation	SNP	G	G	A			TCGA-AB-2814-03D-01W-0755-09	TCGA-AB-2814-11D-01W-0755-09	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	604f0c72-efc7-4868-bc54-79d8f3f3507b	8fb40399-ec65-44a3-9ca3-700a7728c333	g.chr1:120054278G>A	ENST00000369413.3	+	3	443	c.298G>A	c.(298-300)Gtc>Atc	p.V100I	HSD3B1_ENST00000235547.6_Missense_Mutation_p.V102I|HSD3B1_ENST00000528909.1_Missense_Mutation_p.V100I			P14060	3BHS1_HUMAN	hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 1	100					androgen biosynthetic process (GO:0006702)|estrogen biosynthetic process (GO:0006703)|glucocorticoid biosynthetic process (GO:0006704)|mineralocorticoid biosynthetic process (GO:0006705)|small molecule metabolic process (GO:0044281)|steroid biosynthetic process (GO:0006694)|steroid metabolic process (GO:0008202)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|smooth endoplasmic reticulum membrane (GO:0030868)	3-beta-hydroxy-delta5-steroid dehydrogenase activity (GO:0003854)|steroid delta-isomerase activity (GO:0004769)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(18)|ovary(2)|prostate(1)|skin(1)	32	all_neural(166;0.219)	all_lung(203;3.16e-06)|Lung NSC(69;2.19e-05)|all_epithelial(167;0.000624)		Lung(183;0.0106)|LUSC - Lung squamous cell carcinoma(189;0.0554)	Trilostane(DB01108)	TATCATGAATGTCAATGTGAA	0.512																																						dbGAP											0			1											111.0	103.0	106.0					1																	120054278		2203	4300	6503	119855801	SO:0001583	missense	0			S45679	CCDS903.1	1p12	2014-06-03			ENSG00000203857	ENSG00000203857	1.1.1.145, 5.3.3.1	"""Short chain dehydrogenase/reductase superfamily / Extended SDR fold"""	5217	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 11E, member 1"""	109715		HSDB3, HSD3B		2779585, 19027726	Standard	NM_000862		Approved	SDR11E1	uc001ehv.1	P14060	OTTHUMG00000012525	ENST00000369413.3:c.298G>A	1.37:g.120054278G>A	ENSP00000358421:p.Val100Ile	Somatic	170	0.00	0		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	119855801	288	22.40	84	A8K691|Q14545|Q8IV65	Missense_Mutation	SNP	HMMPfam_3Beta_HSD,superfamily_NAD(P)-bd	p.V100I	ENST00000369413.3	37	c.298	CCDS903.1	1	.	.	.	.	.	.	.	.	.	.	G	10.60	1.394750	0.25205	.	.	ENSG00000203857	ENST00000369413;ENST00000235547;ENST00000528909	D;D;D	0.89123	-2.47;-2.47;-2.47	3.11	2.18	0.27775	3-beta hydroxysteroid dehydrogenase/isomerase (1);NAD(P)-binding domain (1);	0.131467	0.50627	D	0.000107	T	0.72061	0.3414	L	0.44542	1.39	0.34549	D	0.711118	B;B	0.21753	0.06;0.059	B;B	0.32289	0.116;0.143	T	0.58567	-0.7614	9	.	.	.	0.1042	4.9615	0.14068	0.2868:0.0:0.7132:0.0	.	102;100	Q5TDG2;P14060	.;3BHS1_HUMAN	I	100;102;100	ENSP00000358421:V100I;ENSP00000235547:V102I;ENSP00000432268:V100I	.	V	+	1	0	HSD3B1	119855801	0.834000	0.29399	0.290000	0.24890	0.027000	0.11550	1.109000	0.31135	0.499000	0.27970	0.313000	0.20887	GTC	-	HMMPfam_3Beta_HSD,superfamily_NAD(P)-bd		0.512	HSD3B1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	HSD3B1	protein_coding	OTTHUMT00000034993.3	G	NM_000862		119855801	+1	no_errors	NM_000862.2	genbank	human	validated	54_36p	missense	SNP	0.976	A
PAPPA2	60676	genome.wustl.edu	37	1	176585451	176585451	+	Intron	SNP	G	G	A			TCGA-AB-2814-03D-01W-0755-09	TCGA-AB-2814-11D-01W-0755-09	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	604f0c72-efc7-4868-bc54-79d8f3f3507b	8fb40399-ec65-44a3-9ca3-700a7728c333	g.chr1:176585451G>A	ENST00000367662.3	+	3	3155				PAPPA2_ENST00000367661.3_Intron	NM_020318.2	NP_064714.2	Q9BXP8	PAPP2_HUMAN	pappalysin 2						bone morphogenesis (GO:0060349)|cell differentiation (GO:0030154)|cellular protein metabolic process (GO:0044267)|proteolysis (GO:0006508)|regulation of cell growth (GO:0001558)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|membrane (GO:0016020)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(3)|breast(3)|central_nervous_system(7)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(19)|lung(136)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|upper_aerodigestive_tract(8)|urinary_tract(1)	226						TCTTTGAAGCGCAGCCGCATT	0.383																																						dbGAP											0			1																																								174852074	SO:0001627	intron_variant	0			BG354569	CCDS41438.1, CCDS41439.1	1q23-q25	2008-05-23	2004-07-07	2004-07-09	ENSG00000116183	ENSG00000116183			14615	protein-coding gene	gene with protein product			"""placenta-specific 3"""	PLAC3		11018262, 11264294	Standard	NM_021936		Approved	PAPPE, PAPP-A2	uc001gkz.3	Q9BXP8	OTTHUMG00000035025	ENST00000367662.3:c.1991+20720G>A	1.37:g.176585451G>A		Somatic	154	0.65	1		1	0.00	0	WXS	Illumina HiSeq	Phase_IV	174852074	212	39.03	137	A9Z1Y8|Q96PH7|Q96PH8|Q9H4C9	Missense_Mutation	SNP	superfamily_(Phosphotyrosine protein) phosphatases II	p.R156C	ENST00000367662.3	37	c.466	CCDS41438.1	1																																																																																			-	superfamily_(Phosphotyrosine protein) phosphatases II		0.383	PAPPA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	LOC730167	protein_coding	OTTHUMT00000084763.1	G			174852074	-1	no_errors	XM_001134386.1	genbank	human	model	54_36p	missense	SNP	1.000	A
ATP11B	23200	genome.wustl.edu	37	3	182583253	182583253	+	Missense_Mutation	SNP	G	G	A	rs200423302		TCGA-AB-2814-03D-01W-0755-09	TCGA-AB-2814-11D-01W-0755-09	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	604f0c72-efc7-4868-bc54-79d8f3f3507b	8fb40399-ec65-44a3-9ca3-700a7728c333	g.chr3:182583253G>A	ENST00000323116.5	+	13	1470	c.1210G>A	c.(1210-1212)Gtg>Atg	p.V404M		NM_014616.2	NP_055431.1	Q9Y2G3	AT11B_HUMAN	ATPase, class VI, type 11B	404					aminophospholipid transport (GO:0015917)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|phospholipid translocation (GO:0045332)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear inner membrane (GO:0005637)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|ion transmembrane transporter activity (GO:0015075)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			breast(3)|cervix(2)|endometrium(2)|kidney(4)|large_intestine(6)|liver(2)|lung(14)|ovary(2)|pancreas(2)|prostate(1)|skin(2)|urinary_tract(1)	41	all_cancers(143;9.04e-15)|Ovarian(172;0.0355)		all cancers(12;1.2e-42)|Epithelial(37;2.77e-36)|LUSC - Lung squamous cell carcinoma(7;7.58e-24)|Lung(8;4.66e-22)|OV - Ovarian serous cystadenocarcinoma(80;2.35e-20)			GGTAGAGTACGTGTTTACAGA	0.348																																						dbGAP											0			3											95.0	94.0	95.0					3																	182583253		2203	4300	6503	184065947	SO:0001583	missense	0			AF156548	CCDS33896.1	3q27	2010-04-20	2007-09-19		ENSG00000058063	ENSG00000058063		"""ATPases / P-type"""	13553	protein-coding gene	gene with protein product		605869	"""ATPase, Class VI, type 11B"""			10231032, 11015572	Standard	NM_014616		Approved	ATPIF, ATPIR, KIAA0956	uc003flb.3	Q9Y2G3	OTTHUMG00000158295	ENST00000323116.5:c.1210G>A	3.37:g.182583253G>A	ENSP00000321195:p.Val404Met	Somatic	50	0.00	0		53	41.76	38	WXS	Illumina HiSeq	Phase_IV	184065947	94	31.16	43	Q96FN1|Q9UKK7	Missense_Mutation	SNP	HMMPfam_Hydrolase,HMMPfam_E1-E2_ATPase,PatternScan_ATPASE_E1_E2,superfamily_SSF56784,superfamily_SSF81653,superfamily_SSF81660	p.V404M	ENST00000323116.5	37	c.1210	CCDS33896.1	3	.	.	.	.	.	.	.	.	.	.	G	20.2	3.950745	0.73787	.	.	ENSG00000058063	ENST00000323116	T	0.63744	-0.06	5.58	4.71	0.59529	HAD-like domain (1);ATPase, P-type, cytoplasmic domain N (1);	0.118725	0.56097	D	0.000030	T	0.77356	0.4118	M	0.88640	2.97	0.80722	D	1	P	0.46784	0.884	P	0.50970	0.655	T	0.83037	-0.0159	10	0.87932	D	0	.	16.6731	0.85271	0.0:0.1298:0.8702:0.0	.	404	Q9Y2G3	AT11B_HUMAN	M	404	ENSP00000321195:V404M	ENSP00000321195:V404M	V	+	1	0	ATP11B	184065947	1.000000	0.71417	1.000000	0.80357	0.808000	0.45660	6.690000	0.74567	1.355000	0.45865	-0.162000	0.13425	GTG	-	HMMPfam_Hydrolase,superfamily_SSF56784		0.348	ATP11B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ATP11B	protein_coding	OTTHUMT00000350598.1	G	NM_014616		184065947	+1	no_errors	NM_014616.1	genbank	human	validated	54_36p	missense	SNP	1.000	A
Unknown	0	genome.wustl.edu	37	4	27774	27774	+	IGR	SNP	G	G	A			TCGA-AB-2814-03D-01W-0755-09	TCGA-AB-2814-11D-01W-0755-09	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	604f0c72-efc7-4868-bc54-79d8f3f3507b	8fb40399-ec65-44a3-9ca3-700a7728c333	g.chr4:27774G>A								None (None upstream) : Z95704.4 (21216 downstream)																							ACTCTTTGGGGGACACAGGCA	0.547																																						dbGAP											0			4																																								17774	SO:0001628	intergenic_variant	0																															4.37:g.27774G>A		Somatic	377	8.05	33		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	17774	1078	10.81	132		Missense_Mutation	SNP	NULL	p.P30S		37	c.88		4																																																																																			-	NULL	0	0.547					LOC100133718			G			17774	-1	no_start_codon:pseudogene:no_stop_codon	XM_001713866.1	genbank	human	model	54_36p	missense	SNP	0.000	A
Unknown	0	genome.wustl.edu	37	5	84845268	84845268	+	IGR	SNP	C	C	T			TCGA-AB-2814-03D-01W-0755-09	TCGA-AB-2814-11D-01W-0755-09	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	604f0c72-efc7-4868-bc54-79d8f3f3507b	8fb40399-ec65-44a3-9ca3-700a7728c333	g.chr5:84845268C>T								AC026700.1 (21316 upstream) : AC010595.1 (84961 downstream)																							AAAGGCCAGGCGAGGCAGTAT	0.547																																						dbGAP											0			5																																								84881024	SO:0001628	intergenic_variant	0																															5.37:g.84845268C>T		Somatic	33	2.86	1		8	0.00	0	WXS	Illumina HiSeq	Phase_IV	84881024	71	39.50	47		RNA	SNP	-	NULL		37	NULL		5																																																																																			-	-	0	0.547					LOC645181			C			84881024	+1	pseudogene	XR_017382.2	genbank	human	model	54_36p	rna	SNP	0.618	T
PMPCB	9512	genome.wustl.edu	37	7	102939894	102939894	+	Missense_Mutation	SNP	G	G	T			TCGA-AB-2814-03D-01W-0755-09	TCGA-AB-2814-11D-01W-0755-09	G	G	G	T	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	604f0c72-efc7-4868-bc54-79d8f3f3507b	8fb40399-ec65-44a3-9ca3-700a7728c333	g.chr7:102939894G>T	ENST00000249269.4	+	3	283	c.245G>T	c.(244-246)gGa>gTa	p.G82V	PMPCB_ENST00000428154.1_Missense_Mutation_p.G82V|PMPCB_ENST00000420236.2_5'UTR	NM_004279.2	NP_004270.2	O75439	MPPB_HUMAN	peptidase (mitochondrial processing) beta	82					cellular protein metabolic process (GO:0044267)|protein targeting to mitochondrion (GO:0006626)	mitochondrial inner membrane (GO:0005743)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|liver(1)|lung(9)|ovary(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						ATTAAGGTTGGACTCTGGATT	0.368																																						dbGAP											0			7											110.0	104.0	107.0					7																	102939894		2203	4300	6503	102727130	SO:0001583	missense	0			AF054182	CCDS5730.1	7q22.1	2007-07-30			ENSG00000105819	ENSG00000105819			9119	protein-coding gene	gene with protein product		603131				9653160	Standard	XM_005250717		Approved	MPPB, MPPP52	uc003vbl.3	O75439	OTTHUMG00000157205	ENST00000249269.4:c.245G>T	7.37:g.102939894G>T	ENSP00000249269:p.Gly82Val	Somatic	94	1.05	1		57	56.82	75	WXS	Illumina HiSeq	Phase_IV	102727130	130	32.47	63	O60416|Q96FV4	Missense_Mutation	SNP	PatternScan_INSULINASE,HMMPfam_Peptidase_M16_C,superfamily_Metalloenz_metal-bd,HMMPfam_Peptidase_M16	p.G82V	ENST00000249269.4	37	c.245	CCDS5730.1	7	.	.	.	.	.	.	.	.	.	.	G	25.7	4.666631	0.88251	.	.	ENSG00000105819	ENST00000249269;ENST00000428154	T;T	0.20738	2.05;2.05	5.12	5.12	0.69794	Peptidase M16, core (1);Metalloenzyme, LuxS/M16 peptidase-like, metal-binding (1);Peptidase M16, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.67739	0.2925	H	0.99238	4.48	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;0.999;1.0	T	0.83239	-0.0059	10	0.87932	D	0	.	18.9858	0.92769	0.0:0.0:1.0:0.0	.	82;82;82	B3KM34;O75439;G3V0E4	.;MPPB_HUMAN;.	V	82	ENSP00000249269:G82V;ENSP00000390035:G82V	ENSP00000249269:G82V	G	+	2	0	PMPCB	102727130	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	9.813000	0.99286	2.551000	0.86045	0.650000	0.86243	GGA	-	superfamily_Metalloenz_metal-bd,HMMPfam_Peptidase_M16		0.368	PMPCB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PMPCB	protein_coding	OTTHUMT00000347913.1	G	NM_004279		102727130	+1	no_errors	NM_004279.2	genbank	human	reviewed	54_36p	missense	SNP	1.000	T
CACNA1B	774	genome.wustl.edu	37	9	140943767	140943767	+	Splice_Site	SNP	C	C	T			TCGA-AB-2814-03D-01W-0755-09	TCGA-AB-2814-11D-01W-0755-09	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	604f0c72-efc7-4868-bc54-79d8f3f3507b	8fb40399-ec65-44a3-9ca3-700a7728c333	g.chr9:140943767C>T	ENST00000371372.1	+	24	3855	c.3710C>T	c.(3709-3711)tCa>tTa	p.S1237L	CACNA1B_ENST00000371363.1_Splice_Site_p.S1237L|CACNA1B_ENST00000371355.4_Splice_Site_p.S1238L|CACNA1B_ENST00000371357.1_Splice_Site_p.S1238L|CACNA1B_ENST00000277549.5_Splice_Site_p.S429L|CACNA1B_ENST00000277551.2_Splice_Site_p.S1237L	NM_000718.3|NM_001243812.1	NP_000709.1|NP_001230741.1	Q00975	CAC1B_HUMAN	calcium channel, voltage-dependent, N type, alpha 1B subunit	1237					calcium ion import (GO:0070509)|locomotory behavior (GO:0007626)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|neurotransmitter secretion (GO:0007269)|regulation of blood pressure (GO:0008217)|regulation of calcium ion transport (GO:0051924)|regulation of heart contraction (GO:0008016)|response to pain (GO:0048265)|synaptic transmission (GO:0007268)|transport (GO:0006810)	dendrite (GO:0030425)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|protein C-terminus binding (GO:0008022)|voltage-gated calcium channel activity (GO:0005245)			NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(17)|lung(31)|ovary(1)|prostate(1)|skin(2)|stomach(2)|urinary_tract(2)	80	all_cancers(76;0.166)			OV - Ovarian serous cystadenocarcinoma(145;1.16e-05)|Epithelial(140;0.000476)	Amlodipine(DB00381)|Gabapentin(DB00996)|Levetiracetam(DB01202)|Spironolactone(DB00421)|Verapamil(DB00661)	TTTGCTTTCTCGTAAGTAACG	0.567																																						dbGAP											0			9											125.0	121.0	122.0					9																	140943767		2070	4206	6276	140063588	SO:0001630	splice_region_variant	0			AB209467	CCDS59522.1, CCDS59523.1	9q34	2013-01-10	2007-02-16		ENSG00000148408	ENSG00000148408		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"", ""EF-hand domain containing"""	1389	protein-coding gene	gene with protein product		601012		CACNL1A5		8825650, 16382099	Standard	NM_000718		Approved	Cav2.2, CACNN	uc004cog.3	Q00975	OTTHUMG00000021002	ENST00000371372.1:c.3710+1C>T	9.37:g.140943767C>T		Somatic	265	0.38	1		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	140063588	236	36.80	138	B1AQK5	Missense_Mutation	SNP	HMMPfam_Ion_trans,HMMPfam_Ca_chan_IQ,superfamily_Voltage-gated potassium channels	p.S1237L	ENST00000371372.1	37	c.3710	CCDS59522.1	9	.	.	.	.	.	.	.	.	.	.	C	36	5.927202	0.97110	.	.	ENSG00000148408	ENST00000371372;ENST00000277551;ENST00000277549;ENST00000371363;ENST00000371357;ENST00000371355	D;D;D;D;D;D	0.98617	-5.03;-5.03;-5.03;-5.03;-5.03;-5.03	5.13	5.13	0.70059	.	1.141480	0.06318	N	0.703971	D	0.98764	0.9584	L	0.42245	1.32	0.80722	D	1	B;D;D	0.71674	0.174;0.998;0.998	B;D;D	0.63283	0.049;0.913;0.913	D	0.95258	0.8366	10	0.87932	D	0	.	18.1658	0.89724	0.0:1.0:0.0:0.0	.	1237;1238;1237	B1AQK4;B1AQK7;B1AQK6	.;.;.	L	1237;1237;429;1237;1238;1238	ENSP00000360423:S1237L;ENSP00000277551:S1237L;ENSP00000277549:S429L;ENSP00000360414:S1237L;ENSP00000360408:S1238L;ENSP00000360406:S1238L	ENSP00000277549:S429L	S	+	2	0	CACNA1B	140063588	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	7.698000	0.84413	2.386000	0.81285	0.491000	0.48974	TCA;TCA;TCG;TCA;TCA;TCA	-	HMMPfam_Ion_trans,superfamily_Voltage-gated potassium channels		0.567	CACNA1B-001	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	CACNA1B	protein_coding	OTTHUMT00000055380.1	C	NM_000718	Missense_Mutation	140063588	+1	no_errors	NM_000718.2	genbank	human	validated	54_36p	missense	SNP	1.000	T
FLT3	2322	genome.wustl.edu	37	13	28592640	28592640	+	Missense_Mutation	SNP	A	A	C	rs121913487|rs121913486		TCGA-AB-2814-03D-01W-0755-09	TCGA-AB-2814-11D-01W-0755-09	A	A	A	C	A	A	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	604f0c72-efc7-4868-bc54-79d8f3f3507b	8fb40399-ec65-44a3-9ca3-700a7728c333	g.chr13:28592640A>C	ENST00000241453.7	-	20	2586	c.2505T>G	c.(2503-2505)gaT>gaG	p.D835E	FLT3_ENST00000537084.1_Intron|FLT3_ENST00000380982.4_Missense_Mutation_p.D835E	NM_004119.2	NP_004110.2	P36888	FLT3_HUMAN	fms-related tyrosine kinase 3	835	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		D -> E (in acute lymphoblastic leukemia patients and in acute myelogenous leukemia patients; somatic mutation; constitutively activated). {ECO:0000269|PubMed:11290608, ECO:0000269|PubMed:14504097}.|D -> H (in acute lymphoblastic leukemia patients and in acute myelogenous leukemia patients; somatic mutation; constitutively activated). {ECO:0000269|PubMed:11290608, ECO:0000269|PubMed:11442493, ECO:0000269|PubMed:14504097}.|D -> N (in acute lymphoblastic leukemia patients and in acute myelogenous leukemia patients; somatic mutation; constitutively activated). {ECO:0000269|PubMed:11290608}.|D -> V (in acute lymphoblastic leukemia patients and in acute myelogenous leukemia patients; somatic mutation; constitutively activated). {ECO:0000269|PubMed:11290608}.|D -> Y (in acute lymphoblastic leukemia patients and in acute myelogenous leukemia patients; somatic mutation; constitutively activated). {ECO:0000269|PubMed:11290608, ECO:0000269|PubMed:11442493, ECO:0000269|PubMed:14504097}.		B cell differentiation (GO:0030183)|cellular response to cytokine stimulus (GO:0071345)|common myeloid progenitor cell proliferation (GO:0035726)|cytokine-mediated signaling pathway (GO:0019221)|dendritic cell differentiation (GO:0097028)|hemopoiesis (GO:0030097)|leukocyte homeostasis (GO:0001776)|lymphocyte proliferation (GO:0046651)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of B cell differentiation (GO:0045578)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of tyrosine phosphorylation of STAT protein (GO:0042531)|pro-B cell differentiation (GO:0002328)|pro-T cell differentiation (GO:0002572)|protein autophosphorylation (GO:0046777)|regulation of apoptotic process (GO:0042981)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor signaling pathway (GO:0038084)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|cytokine receptor activity (GO:0004896)|protein homodimerization activity (GO:0042803)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor-activated receptor activity (GO:0005021)	p.?(23)|p.D835E(11)|p.D835_I836>V(1)|p.D835del(1)|p.R834_D835del(1)		NS(1)|breast(3)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(12329)|kidney(2)|large_intestine(8)|lung(30)|ovary(4)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	12390	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0156)|Ovarian(182;0.0392)	Colorectal(13;0.000157)|READ - Rectum adenocarcinoma(15;0.105)	OV - Ovarian serous cystadenocarcinoma(117;0.00154)|all cancers(112;0.00459)|GBM - Glioblastoma multiforme(144;0.00562)|Epithelial(112;0.0959)|Lung(94;0.212)	Ponatinib(DB08901)|Sorafenib(DB00398)|Sunitinib(DB01268)	CACTCATGATATCTCGAGCCA	0.448			"""Mis, O"""		"""AML, ALL"""																																	dbGAP		Dom	yes		13	13q12	2322	fms-related tyrosine kinase 3		L	37	Unknown(23)|Substitution - Missense(11)|Deletion - In frame(2)|Complex - deletion inframe(1)	haematopoietic_and_lymphoid_tissue(37)	13											190.0	142.0	158.0					13																	28592640		2203	4300	6503	27490640	SO:0001583	missense	0			U02687	CCDS31953.1	13q12	2014-09-17			ENSG00000122025	ENSG00000122025	2.7.10.1	"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	3765	protein-coding gene	gene with protein product		136351				8394751	Standard	NM_004119		Approved	STK1, FLK2, CD135	uc001urw.3	P36888	OTTHUMG00000016646	ENST00000241453.7:c.2505T>G	13.37:g.28592640A>C	ENSP00000241453:p.Asp835Glu	Somatic	48	0.00	0		309	32.24	147	WXS	Illumina HiSeq	Phase_IV	27490640	93	19.83	24	A0AVG9|B7ZLT7|B7ZLT8|F5H0A0|Q13414	Missense_Mutation	SNP	HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,PatternScan_RECEPTOR_TYR_KIN_III,PatternScan_PROTEIN_KINASE_TYR,superfamily_Kinase_like,HMMPfam_ig,PatternScan_PROTEIN_KINASE_ATP,superfamily_SSF48726	p.D835E	ENST00000241453.7	37	c.2505	CCDS31953.1	13	.	.	.	.	.	.	.	.	.	.	A	22.3	4.273327	0.80580	.	.	ENSG00000122025	ENST00000241453;ENST00000380982	D;D	0.82893	-1.66;-1.66	5.84	-4.76	0.03229	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.074843	0.56097	N	0.000030	T	0.81650	0.4867	N	0.17922	0.545	0.80722	D	1	D	0.56521	0.976	D	0.67382	0.951	T	0.79933	-0.1594	10	0.87932	D	0	.	16.6884	0.85315	0.3945:0.0:0.6055:0.0	.	835	P36888	FLT3_HUMAN	E	835	ENSP00000241453:D835E;ENSP00000370369:D835E	ENSP00000241453:D835E	D	-	3	2	FLT3	27490640	0.998000	0.40836	0.408000	0.26446	0.936000	0.57629	0.485000	0.22324	-1.493000	0.01835	-0.424000	0.05967	GAT	-	HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,superfamily_Kinase_like		0.448	FLT3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	FLT3	protein_coding	OTTHUMT00000044319.2	A			27490640	-1	no_errors	NM_004119.2	genbank	human	reviewed	54_36p	missense	SNP	0.991	C
FAM65A	79567	genome.wustl.edu	37	16	67578879	67578879	+	Missense_Mutation	SNP	C	C	T	rs557085966		TCGA-AB-2814-03D-01W-0755-09	TCGA-AB-2814-11D-01W-0755-09	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	604f0c72-efc7-4868-bc54-79d8f3f3507b	8fb40399-ec65-44a3-9ca3-700a7728c333	g.chr16:67578879C>T	ENST00000379312.3	+	17	3023	c.2902C>T	c.(2902-2904)Cgg>Tgg	p.R968W	FAM65A_ENST00000428437.2_Missense_Mutation_p.R978W|FAM65A_ENST00000540839.3_Missense_Mutation_p.R983W|FAM65A_ENST00000042381.4_Missense_Mutation_p.R964W|CTD-2012K14.3_ENST00000563083.1_RNA|CTD-2012K14.4_ENST00000564717.1_RNA|FAM65A_ENST00000422602.2_Missense_Mutation_p.R984W	NM_001193522.1|NM_024519.3	NP_001180451.1|NP_078795.2	Q6ZS17	FA65A_HUMAN	family with sequence similarity 65, member A	968						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)				central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(12)|lung(12)|ovary(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	39		Acute lymphoblastic leukemia(13;3.76e-06)|all_hematologic(13;0.000303)|Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0474)|Epithelial(162;0.117)		CTCGGCCTCTCGGCCTGGCTT	0.602																																						dbGAP											0			16											148.0	149.0	149.0					16																	67578879		2198	4300	6498	66136380	SO:0001583	missense	0			AK127792	CCDS10840.1, CCDS54026.1, CCDS54027.1, CCDS54028.1	16q22.1	2008-02-05			ENSG00000039523	ENSG00000039523			25836	protein-coding gene	gene with protein product						11572484	Standard	NM_001193522		Approved	FLJ13725	uc010vjp.2	Q6ZS17	OTTHUMG00000137536	ENST00000379312.3:c.2902C>T	16.37:g.67578879C>T	ENSP00000368614:p.Arg968Trp	Somatic	48	0.00	0		16	56.76	21	WXS	Illumina HiSeq	Phase_IV	66136380	30	51.61	32	B4DEQ9|B4DIM2|E9PBS3|Q4G0A4|Q7Z5R7|Q8NDA4|Q96J39|Q96PV8|Q9H8D9	Missense_Mutation	SNP	superfamily_ARM-type_fold	p.R964W	ENST00000379312.3	37	c.2890	CCDS54028.1	16	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	15.20|15.20	2.764039|2.764039	0.49574|0.49574	.|.	.|.	ENSG00000039523|ENSG00000039523	ENST00000379312;ENST00000042381;ENST00000422602;ENST00000540839|ENST00000428437	T;T;T|.	0.80566|.	-1.39;-1.39;-1.39|.	5.44|5.44	2.14|2.14	0.27477|0.27477	.|.	0.205916|.	0.45867|.	D|.	0.000325|.	T|T	0.50837|0.50837	0.1639|0.1639	L|L	0.58101|0.58101	1.795|1.795	0.25985|0.25985	N|N	0.982324|0.982324	D;D;D|.	0.89917|.	1.0;1.0;1.0|.	D;D;D|.	0.66979|.	0.948;0.948;0.948|.	T|T	0.41998|0.41998	-0.9477|-0.9477	10|6	0.87932|0.32370	D|T	0|0.25	-10.8097|-10.8097	12.4485|12.4485	0.55666|0.55666	0.5903:0.4097:0.0:0.0|0.5903:0.4097:0.0:0.0	.|.	978;984;968|.	B4DIM2;E9PBS3;Q6ZS17|.	.;.;FA65A_HUMAN|.	W|L	968;964;984;978|957	ENSP00000368614:R968W;ENSP00000042381:R964W;ENSP00000400099:R984W|.	ENSP00000042381:R964W|ENSP00000389456:S957L	R|S	+|+	1|2	2|0	FAM65A|FAM65A	66136380|66136380	0.106000|0.106000	0.21978|0.21978	0.999000|0.999000	0.59377|0.59377	0.653000|0.653000	0.38743|0.38743	1.204000|1.204000	0.32296|0.32296	0.625000|0.625000	0.30304|0.30304	0.655000|0.655000	0.94253|0.94253	CGG|TCG	-	NULL		0.602	FAM65A-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	FAM65A	protein_coding	OTTHUMT00000268866.3	C	NM_024519		66136380	+1	no_errors	NM_024519.2	genbank	human	validated	54_36p	missense	SNP	0.018	T
UPF1	5976	genome.wustl.edu	37	19	18963815	18963815	+	Missense_Mutation	SNP	T	T	A			TCGA-AB-2814-03D-01W-0755-09	TCGA-AB-2814-11D-01W-0755-09	T	T	T	A	T	T	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	604f0c72-efc7-4868-bc54-79d8f3f3507b	8fb40399-ec65-44a3-9ca3-700a7728c333	g.chr19:18963815T>A	ENST00000599848.1	+	7	1201	c.992T>A	c.(991-993)gTc>gAc	p.V331D	UPF1_ENST00000262803.5_Missense_Mutation_p.V331D			Q92900	RENT1_HUMAN	UPF1 regulator of nonsense transcripts homolog (yeast)	331	Sufficient for interaction with RENT2.				ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|dosage compensation by inactivation of X chromosome (GO:0009048)|gene expression (GO:0010467)|histone mRNA catabolic process (GO:0071044)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process (GO:0000956)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of translational termination (GO:0006449)|RNA metabolic process (GO:0016070)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|exon-exon junction complex (GO:0035145)|nucleus (GO:0005634)|supraspliceosomal complex (GO:0044530)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(11)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	40						AACATCACTGTCAGGTGGGAC	0.517																																						dbGAP											0			19											130.0	114.0	120.0					19																	18963815		2203	4300	6503	18824815	SO:0001583	missense	0			AF074016	CCDS12386.1, CCDS74315.1	19p13.2-p13.11	2012-02-29	2006-02-07	2006-02-07	ENSG00000005007	ENSG00000005007			9962	protein-coding gene	gene with protein product	"""UP Frameshift 1"", ""smg-2 homolog, nonsense mediated mRNA decay factor (C. elegans)"""	601430	"""regulator of nonsense transcripts 1"""	RENT1		8855285, 9064659	Standard	XM_005260015		Approved	HUPF1, KIAA0221, NORF1, pNORF1, smg-2	uc002nkf.3	Q92900		ENST00000599848.1:c.992T>A	19.37:g.18963815T>A	ENSP00000470142:p.Val331Asp	Somatic	40	0.00	0		55	43.30	42	WXS	Illumina HiSeq	Phase_IV	18824815	51	37.80	31	O00239|O43343|Q86Z25|Q92842	Missense_Mutation	SNP	HMMPfam_ResIII,HMMPfam_UPF1_Zn_bind,superfamily_SSF52540	p.V331D	ENST00000599848.1	37	c.992		19	.	.	.	.	.	.	.	.	.	.	T	22.3	4.269480	0.80469	.	.	ENSG00000005007	ENST00000262803	D	0.92965	-3.14	4.44	4.44	0.53790	.	0.000000	0.85682	D	0.000000	D	0.96405	0.8827	M	0.90369	3.11	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.997;0.999	D	0.97005	0.9732	10	0.87932	D	0	-49.2431	12.8733	0.57977	0.0:0.0:0.0:1.0	.	331;331	Q92900;Q92900-2	RENT1_HUMAN;.	D	331	ENSP00000262803:V331D	ENSP00000262803:V331D	V	+	2	0	UPF1	18824815	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.687000	0.84139	1.648000	0.50643	0.438000	0.28831	GTC	-	NULL		0.517	UPF1-002	KNOWN	basic	protein_coding	UPF1	protein_coding	OTTHUMT00000464684.1	T	NM_002911		18824815	+1	no_errors	NM_002911.3	genbank	human	reviewed	54_36p	missense	SNP	1.000	A
TMPRSS15	5651	genome.wustl.edu	37	21	19666640	19666640	+	Silent	SNP	G	G	A	rs377055842		TCGA-AB-2814-03D-01W-0755-09	TCGA-AB-2814-11D-01W-0755-09	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	604f0c72-efc7-4868-bc54-79d8f3f3507b	8fb40399-ec65-44a3-9ca3-700a7728c333	g.chr21:19666640G>A	ENST00000284885.3	-	21	2466	c.2433C>T	c.(2431-2433)ggC>ggT	p.G811G		NM_002772.2	NP_002763	P98073	ENTK_HUMAN	transmembrane protease, serine 15	811	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					brush border (GO:0005903)|integral component of membrane (GO:0016021)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(2)|cervix(1)|endometrium(4)|kidney(7)|large_intestine(19)|lung(36)|ovary(6)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)	85						CGAGAGATGCGCCGCAGAGCA	0.567																																						dbGAP											0			21						G		0,4406		0,0,2203	76.0	79.0	78.0		2433	-9.3	0.7	21		78	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	TMPRSS15	NM_002772.2		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		811/1020	19666640	1,13005	2203	4300	6503	18588511	SO:0001819	synonymous_variant	0				CCDS13571.1	21q21	2010-12-09	2010-04-21	2010-04-21	ENSG00000154646	ENSG00000154646		"""Serine peptidases / Transmembrane"""	9490	protein-coding gene	gene with protein product	"""proenterokinase"", ""enteropeptidase"""	606635	"""protease, serine, 7 (enterokinase)"""	PRSS7		8052624	Standard	NM_002772		Approved	ENTK, MGC133046	uc002ykw.3	P98073	OTTHUMG00000074518	ENST00000284885.3:c.2433C>T	21.37:g.19666640G>A		Somatic	21	0.00	0		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	18588511	45	40.00	30	Q2NKL7	Silent	SNP	HMMPfam_SEA,HMMSmart_SM00200,HMMPfam_CUB,HMMSmart_SM00042,superfamily_Spermadhesin CUB domain,HMMPfam_MAM,HMMSmart_SM00137,PatternScan_MAM_1,HMMPfam_SRCR,HMMPfam_Trypsin,HMMSmart_SM00020,HMMPfam_Ldl_recept_a,HMMSmart_SM00192,PatternScan_LDLRA_1,superfamily_LDL receptor-like module,superfamily_Trypsin-like serine proteases,HMMSmart_SM00202,superfamily_SRCR-like,PatternScan_TRYPSIN_HIS,PatternScan_TRYPSIN_SER,superfamily_SEA domain	p.G811	ENST00000284885.3	37	c.2433	CCDS13571.1	21																																																																																			-	HMMPfam_Trypsin,HMMSmart_SM00020,superfamily_Trypsin-like serine proteases		0.567	TMPRSS15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PRSS7	protein_coding	OTTHUMT00000158231.2	G	NM_002772		18588511	-1	no_errors	NM_002772.2	genbank	human	reviewed	54_36p	silent	SNP	0.930	A
BCORL1	63035	genome.wustl.edu	37	X	129148536	129148537	+	Frame_Shift_Ins	INS	-	-	A			TCGA-AB-2814-03D-01W-0755-09	TCGA-AB-2814-11D-01W-0755-09	-	-	-	A	-	-	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	604f0c72-efc7-4868-bc54-79d8f3f3507b	8fb40399-ec65-44a3-9ca3-700a7728c333	g.chrX:129148536_129148537insA	ENST00000218147.7	+	4	1985_1986	c.1788_1789insA	c.(1789-1791)accfs	p.T597fs	BCORL1_ENST00000540052.1_Frame_Shift_Ins_p.T597fs|BCORL1_ENST00000359304.2_Frame_Shift_Ins_p.T597fs|BCORL1_ENST00000303743.5_Frame_Shift_Ins_p.T597fs			Q5H9F3	BCORL_HUMAN	BCL6 corepressor-like 1	597	Pro-rich.				chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(9)|liver(3)|lung(30)|ovary(7)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	75						GGACTTCCGTTACCTTCTCTCC	0.619																																						dbGAP											0			X																																								128976218	SO:0001589	frameshift_variant	0			AL136450	CCDS14616.1	Xq25-q26.1	2014-09-17	2010-06-10		ENSG00000085185	ENSG00000085185		"""Ankyrin repeat domain containing"""	25657	protein-coding gene	gene with protein product		300688	"""chromosome X open reading frame 10"", ""BCL6 co-repressor-like 1"""	CXorf10			Standard	NM_021946		Approved	FLJ11362	uc022cdu.1	Q5H9F3	OTTHUMG00000022379	ENST00000218147.7:c.1789dupA	X.37:g.129148537_129148537dupA	ENSP00000218147:p.Thr597fs	Somatic	20	0.00	0		17	67.31	35	WXS	Illumina HiSeq	Phase_IV	128976217	48	40.00	32	B5MDQ8|Q5H9F2|Q5H9F4|Q6ZVE0|Q8TEN3|Q9Y528	Frame_Shift_Ins	INS	HMMPfam_Ank,HMMSmart_SM00248,superfamily_Ankyrin repeat	p.T596fs	ENST00000218147.7	37	c.1788_1789	CCDS14616.1	X																																																																																			-	NULL		0.619	BCORL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	BCORL1	protein_coding	OTTHUMT00000058223.1	-	NM_021946		128976218	+1	no_errors	NM_021946.2	genbank	human	validated	54_36p	frame_shift_ins	INS	0.002:0.198	A
