#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
B4GALT3	8703	genome.wustl.edu	37	1	161143511	161143511	+	Silent	SNP	C	C	T	rs200680049		TCGA-AB-2861-03B-01W-0728-08	TCGA-AB-2861-11B-01W-0729-08	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	6f4de42a-16ce-4536-b5a7-a9380540dda4	c2a59421-c7d4-4b57-a82d-ee675481ba9b	g.chr1:161143511C>T	ENST00000319769.5	-	6	909	c.687G>A	c.(685-687)ccG>ccA	p.P229P	B4GALT3_ENST00000470882.1_5'UTR|PPOX_ENST00000535223.1_Intron|B4GALT3_ENST00000367998.1_Silent_p.P229P|PPOX_ENST00000495483.1_Intron|PPOX_ENST00000432542.2_Intron	NM_001199873.1|NM_003779.3	NP_001186802.1|NP_003770.1	O60512	B4GT3_HUMAN	UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 3	229					carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity (GO:0003831)|galactosyltransferase activity (GO:0008378)|metal ion binding (GO:0046872)|N-acetyllactosamine synthase activity (GO:0003945)			cervix(1)|endometrium(5)|large_intestine(6)|lung(6)	18	all_cancers(52;3.73e-19)|Breast(13;0.000577)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00275)		N-Acetyl-D-glucosamine(DB00141)	ACTGGGGGTACGGGAGGCTAG	0.552																																						dbGAP											0			1											125.0	115.0	118.0					1																	161143511		2203	4300	6503	159410135	SO:0001819	synonymous_variant	0			BC006099	CCDS1222.1	1q21-q23	2013-02-19			ENSG00000158850	ENSG00000158850		"""Beta 4-glycosyltransferases"""	926	protein-coding gene	gene with protein product		604014				9405390, 9597550	Standard	NM_001199873		Approved	beta4Gal-T3	uc001fys.2	O60512	OTTHUMG00000034348	ENST00000319769.5:c.687G>A	1.37:g.161143511C>T		Somatic	611	2.70	17		35	55.56	45	WXS	Illumina HiSeq	Phase_IV	159410135	109	40.86	76	D3DVG3|O60910|Q9BPZ4|Q9H8T2	Silent	SNP	HMMPfam_Galactosyl_T_2,superfamily_Nucleotide-diphospho-sugar transferases	p.P229	ENST00000319769.5	37	c.687	CCDS1222.1	1																																																																																			-	HMMPfam_Galactosyl_T_2,superfamily_Nucleotide-diphospho-sugar transferases		0.552	B4GALT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	B4GALT3	protein_coding	OTTHUMT00000083054.1	C	NM_003779		159410135	-1	no_errors	NM_003779.2	genbank	human	reviewed	54_36p	silent	SNP	0.701	T
DNMT3A	1788	genome.wustl.edu	37	2	25467032	25467032	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AB-2861-03B-01W-0728-08	TCGA-AB-2861-11B-01W-0729-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	6f4de42a-16ce-4536-b5a7-a9380540dda4	c2a59421-c7d4-4b57-a82d-ee675481ba9b	g.chr2:25467032G>A	ENST00000264709.3	-	15	2180	c.1843C>T	c.(1843-1845)Cag>Tag	p.Q615*	DNMT3A_ENST00000321117.5_Nonsense_Mutation_p.Q615*|DNMT3A_ENST00000380746.4_Nonsense_Mutation_p.Q426*|DNMT3A_ENST00000402667.1_Nonsense_Mutation_p.Q392*|DNMT3A_ENST00000474887.1_5'UTR	NM_175629.2	NP_783328.1	Q9Y6K1	DNM3A_HUMAN	DNA (cytosine-5-)-methyltransferase 3 alpha	615					C-5 methylation of cytosine (GO:0090116)|cellular response to amino acid stimulus (GO:0071230)|DNA methylation (GO:0006306)|DNA methylation involved in embryo development (GO:0043045)|DNA methylation involved in gamete generation (GO:0043046)|DNA methylation on cytosine within a CG sequence (GO:0010424)|hypermethylation of CpG island (GO:0044027)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of gene expression by genetic imprinting (GO:0006349)|S-adenosylhomocysteine metabolic process (GO:0046498)|S-adenosylmethioninamine metabolic process (GO:0046499)|spermatogenesis (GO:0007283)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|euchromatin (GO:0000791)|nuclear heterochromatin (GO:0005720)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA (cytosine-5-)-methyltransferase activity (GO:0003886)|DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates (GO:0051718)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|unmethylated CpG binding (GO:0045322)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(964)|kidney(3)|large_intestine(10)|lung(29)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	1021	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					ACAAATTCCTGGTCGTGGTTA	0.632			"""Mis, F, N, S"""		AML																																	dbGAP		Rec	yes		2	2p23	1788	DNA (cytosine-5-)-methyltransferase 3 alpha		L	0			2											32.0	38.0	36.0					2																	25467032		2203	4300	6503	25320536	SO:0001587	stop_gained	0				CCDS1718.2, CCDS33157.1, CCDS46232.1	2p23	2014-09-17			ENSG00000119772	ENSG00000119772			2978	protein-coding gene	gene with protein product		602769				9662389, 10433969	Standard	NM_175630		Approved		uc002rgc.4	Q9Y6K1	OTTHUMG00000094777	ENST00000264709.3:c.1843C>T	2.37:g.25467032G>A	ENSP00000264709:p.Gln615*	Somatic	46	0.00	0		10	28.57	4	WXS	Illumina HiSeq	Phase_IV	25320536	5	61.54	8	E9PEB8|Q86TE8|Q86XF5|Q8IZV0|Q8WXU9	Nonsense_Mutation	SNP	HMMPfam_PWWP,HMMSmart_SM00293,HMMPfam_DNA_methylase,superfamily_FYVE/PHD zinc finger,PatternScan_C5_MTASE_1,superfamily_S-adenosyl-L-methionine-dependent methyltransferases,superfamily_Tudor/PWWP/MBT	p.Q615*	ENST00000264709.3	37	c.1843	CCDS33157.1	2	.	.	.	.	.	.	.	.	.	.	G	43	9.929607	0.99298	.	.	ENSG00000119772	ENST00000380746;ENST00000321117;ENST00000264709;ENST00000402667	.	.	.	5.08	5.08	0.68730	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.10377	T	0.69	-9.0995	17.0371	0.86479	0.0:0.0:1.0:0.0	.	.	.	.	X	426;615;615;392	.	ENSP00000264709:Q615X	Q	-	1	0	DNMT3A	25320536	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.883000	0.87264	2.354000	0.79902	0.655000	0.94253	CAG	-	NULL		0.632	DNMT3A-001	KNOWN	basic|CCDS	protein_coding	DNMT3A	protein_coding	OTTHUMT00000211587.1	G	NM_022552		25320536	-1	no_errors	NM_022552.3	genbank	human	reviewed	54_36p	nonsense	SNP	1.000	A
WIPF1	7456	genome.wustl.edu	37	2	175432735	175432735	+	Missense_Mutation	SNP	G	G	C			TCGA-AB-2861-03B-01W-0728-08	TCGA-AB-2861-11B-01W-0729-08	G	G	G	C	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	6f4de42a-16ce-4536-b5a7-a9380540dda4	c2a59421-c7d4-4b57-a82d-ee675481ba9b	g.chr2:175432735G>C	ENST00000392547.2	-	6	1295	c.1196C>G	c.(1195-1197)cCt>cGt	p.P399R	WIPF1_ENST00000392546.2_Missense_Mutation_p.P399R|WIPF1_ENST00000272746.5_Missense_Mutation_p.P399R|AC018890.6_ENST00000412835.1_RNA|WIPF1_ENST00000359761.3_Missense_Mutation_p.P399R|WIPF1_ENST00000467149.1_5'UTR|AC018890.6_ENST00000442996.1_RNA|WIPF1_ENST00000409891.1_Missense_Mutation_p.P399R	NM_003387.4	NP_003378.3	O43516	WIPF1_HUMAN	WAS/WASL interacting protein family, member 1	399	Pro-rich.				actin filament-based movement (GO:0030048)|actin polymerization or depolymerization (GO:0008154)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|protein complex assembly (GO:0006461)|response to other organism (GO:0051707)	actin cytoskeleton (GO:0015629)|actin filament (GO:0005884)|cell projection (GO:0042995)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)	actin binding (GO:0003779)|profilin binding (GO:0005522)			NS(1)|breast(1)|endometrium(5)|large_intestine(7)|lung(15)|ovary(2)|skin(1)	32						TGGCAACTGAGGGGTAGCAGG	0.612																																						dbGAP											0			2											53.0	50.0	51.0					2																	175432735		2203	4300	6503	175140981	SO:0001583	missense	0			AF031588	CCDS2260.1	2q31.2	2014-09-17	2006-10-12	2006-10-12	ENSG00000115935	ENSG00000115935			12736	protein-coding gene	gene with protein product		602357	"""Wiskott-Aldrich syndrome protein interacting protein"""	WASPIP		9405671	Standard	NM_001077269		Approved	WIP	uc002uiz.3	O43516	OTTHUMG00000132334	ENST00000392547.2:c.1196C>G	2.37:g.175432735G>C	ENSP00000376330:p.Pro399Arg	Somatic	182	1.09	2		37	47.14	33	WXS	Illumina HiSeq	Phase_IV	175140981	37	46.38	32	B8ZZM1|D3DPE4|Q15220|Q53TA9|Q6MZU9|Q9BU37|Q9UNP1	Missense_Mutation	SNP	HMMPfam_WH2,HMMSmart_SM00246	p.P399R	ENST00000392547.2	37	c.1196	CCDS2260.1	2	.	.	.	.	.	.	.	.	.	.	G	18.86	3.712722	0.68730	.	.	ENSG00000115935	ENST00000392547;ENST00000392548;ENST00000272746;ENST00000359761;ENST00000392546;ENST00000409891	T;T;T;T;D	0.89050	0.25;-1.19;0.25;0.25;-2.46	5.49	5.49	0.81192	.	0.116881	0.64402	D	0.000010	D	0.94574	0.8252	M	0.81802	2.56	0.80722	D	1	D;D;D	0.69078	0.997;0.997;0.995	D;D;P	0.65773	0.938;0.938;0.868	D	0.94767	0.7941	10	0.87932	D	0	.	19.7433	0.96241	0.0:0.0:1.0:0.0	.	399;399;399	O43516-3;O43516-2;O43516	.;.;WIPF1_HUMAN	R	399;255;399;399;399;399	ENSP00000376330:P399R;ENSP00000272746:P399R;ENSP00000352802:P399R;ENSP00000376329:P399R;ENSP00000386431:P399R	ENSP00000272746:P399R	P	-	2	0	WIPF1	175140981	1.000000	0.71417	1.000000	0.80357	0.767000	0.43475	7.381000	0.79718	2.733000	0.93635	0.655000	0.94253	CCT	-	NULL		0.612	WIPF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	WIPF1	protein_coding	OTTHUMT00000255453.1	G	NM_003387		175140981	-1	no_errors	NM_001077269.1	genbank	human	reviewed	54_36p	missense	SNP	1.000	C
ZNF197	10168	genome.wustl.edu	37	3	44674061	44674061	+	Silent	SNP	C	C	T			TCGA-AB-2861-03B-01W-0728-08	TCGA-AB-2861-11B-01W-0729-08	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	6f4de42a-16ce-4536-b5a7-a9380540dda4	c2a59421-c7d4-4b57-a82d-ee675481ba9b	g.chr3:44674061C>T	ENST00000396058.1	+	4	906	c.739C>T	c.(739-741)Ctg>Ttg	p.L247L	ZNF197_ENST00000383744.4_Silent_p.L247L|ZNF197_ENST00000344387.4_Silent_p.L247L|ZNF197_ENST00000383745.2_Silent_p.L247L|RP11-944L7.4_ENST00000457331.1_RNA			O14709	ZN197_HUMAN	zinc finger protein 197	247	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(9)|ovary(3)|prostate(1)|skin(1)	25				KIRC - Kidney renal clear cell carcinoma(197;0.0478)|Kidney(197;0.0598)		GGATGTGATGCTGGAGAATTA	0.438																																						dbGAP											0			3											218.0	200.0	206.0					3																	44674061		2203	4300	6503	44649065	SO:0001819	synonymous_variant	0			AF011573	CCDS2717.1, CCDS33743.1	3p21	2013-01-09	2003-10-07		ENSG00000186448	ENSG00000186448		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	12988	protein-coding gene	gene with protein product			"""zinc finger protein 166"""	ZNF166		9380504, 8353497	Standard	XM_005264783		Approved	P18, D3S1363E, ZKSCAN9, ZSCAN41	uc003cnm.3	O14709	OTTHUMG00000133089	ENST00000396058.1:c.739C>T	3.37:g.44674061C>T		Somatic	232	6.07	15		4	42.86	3	WXS	Illumina HiSeq	Phase_IV	44649065	129	42.48	96	B2RAH8|Q86VG0	Silent	SNP	HMMPfam_KRAB,HMMSmart_SM00349,superfamily_KRAB domain (Kruppel-associated box Pfam 01352),HMMPfam_SCAN,HMMSmart_SM00431,HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_SM00355,superfamily_C2H2 and C2HC zinc fingers	p.L247	ENST00000396058.1	37	c.739	CCDS2717.1	3																																																																																			-	HMMPfam_KRAB,HMMSmart_SM00349,superfamily_KRAB domain (Kruppel-associated box Pfam 01352)		0.438	ZNF197-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ZNF197	protein_coding	OTTHUMT00000256747.4	C	NM_006991		44649065	+1	no_errors	NM_006991.1	genbank	human	reviewed	54_36p	silent	SNP	0.997	T
MEPE	56955	genome.wustl.edu	37	4	88767387	88767387	+	Missense_Mutation	SNP	G	G	A			TCGA-AB-2861-03B-01W-0728-08	TCGA-AB-2861-11B-01W-0729-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	6f4de42a-16ce-4536-b5a7-a9380540dda4	c2a59421-c7d4-4b57-a82d-ee675481ba9b	g.chr4:88767387G>A	ENST00000424957.3	+	4	1440	c.1367G>A	c.(1366-1368)gGc>gAc	p.G456D	MEPE_ENST00000361056.3_Missense_Mutation_p.G456D|MEPE_ENST00000395102.4_Missense_Mutation_p.G487D|MEPE_ENST00000540395.1_Missense_Mutation_p.G343D|MEPE_ENST00000508016.1_3'UTR|MEPE_ENST00000560249.1_Missense_Mutation_p.G343D|MEPE_ENST00000497649.2_Missense_Mutation_p.G432D	NM_001184694.1	NP_001171623.1	Q9NQ76	MEPE_HUMAN	matrix extracellular phosphoglycoprotein	456					biomineral tissue development (GO:0031214)|negative regulation of bone mineralization (GO:0030502)|regulation of bone remodeling (GO:0046850)|skeletal system development (GO:0001501)	proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)			cervix(1)|endometrium(1)|kidney(3)|large_intestine(5)|lung(19)|ovary(1)|skin(5)|upper_aerodigestive_tract(1)	36		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000432)		TCCTTTAATGGCCCCAGTCAT	0.393																																						dbGAP											0			4											61.0	60.0	60.0					4																	88767387		2203	4300	6503	88986411	SO:0001583	missense	0			AJ276396	CCDS3625.1, CCDS54776.1	4q21.1	2008-08-29	2008-08-29		ENSG00000152595	ENSG00000152595			13361	protein-coding gene	gene with protein product		605912	"""matrix, extracellular phosphoglycoprotein with ASARM motif (bone)"""			10945470	Standard	NM_020203		Approved		uc003hqy.3	Q9NQ76	OTTHUMG00000130592	ENST00000424957.3:c.1367G>A	4.37:g.88767387G>A	ENSP00000416984:p.Gly456Asp	Somatic	282	2.76	8		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	88986411	50	35.06	27	A1A4X9|A8MTA3|D2CFR4|F5H5C5	Missense_Mutation	SNP	HMMPfam_Osteoregulin	p.G456D	ENST00000424957.3	37	c.1367	CCDS3625.1	4	.	.	.	.	.	.	.	.	.	.	G	11.36	1.614641	0.28712	.	.	ENSG00000152595	ENST00000424957;ENST00000395102;ENST00000497649;ENST00000540395;ENST00000361056	T;T;T;T;T	0.48522	0.81;0.82;0.81;0.81;0.81	4.89	-1.04	0.10068	.	1.344650	0.05077	N	0.482659	T	0.36717	0.0977	L	0.48935	1.535	0.09310	N	1	B	0.30664	0.289	B	0.28784	0.094	T	0.17018	-1.0383	10	0.39692	T	0.17	-0.0867	3.1492	0.06481	0.3499:0.0:0.3497:0.3005	.	456	Q9NQ76	MEPE_HUMAN	D	456;487;432;343;456	ENSP00000416984:G456D;ENSP00000378534:G487D;ENSP00000422747:G432D;ENSP00000443491:G343D;ENSP00000354341:G456D	ENSP00000354341:G456D	G	+	2	0	MEPE	88986411	0.000000	0.05858	0.000000	0.03702	0.310000	0.27922	-0.346000	0.07760	-0.508000	0.06540	0.563000	0.77884	GGC	-	NULL		0.393	MEPE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	MEPE	protein_coding	OTTHUMT00000253038.1	G			88986411	+1	no_errors	NM_020203.2	genbank	human	validated	54_36p	missense	SNP	0.000	A
VARS	7407	genome.wustl.edu	37	6	31752211	31752211	+	Silent	SNP	G	G	A	rs369896276		TCGA-AB-2861-03B-01W-0728-08	TCGA-AB-2861-11B-01W-0729-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	6f4de42a-16ce-4536-b5a7-a9380540dda4	c2a59421-c7d4-4b57-a82d-ee675481ba9b	g.chr6:31752211G>A	ENST00000375663.3	-	12	1976	c.1536C>T	c.(1534-1536)ttC>ttT	p.F512F	VARS_ENST00000444930.2_Silent_p.F217F|VARS_ENST00000482996.1_5'Flank	NM_006295.2	NP_006286.1	P26640	SYVC_HUMAN	valyl-tRNA synthetase	512					gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)|valyl-tRNA aminoacylation (GO:0006438)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	aminoacyl-tRNA editing activity (GO:0002161)|ATP binding (GO:0005524)|valine-tRNA ligase activity (GO:0004832)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(18)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	30					L-Valine(DB00161)	CGAGGACCCCGAACTCCACCT	0.597																																						dbGAP											0			6						G		0,4406		0,0,2203	79.0	82.0	81.0		1536	1.9	1.0	6		81	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	VARS	NM_006295.2		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		512/1265	31752211	1,13005	2203	4300	6503	31860190	SO:0001819	synonymous_variant	0			BC012808	CCDS34412.1	6p21.3	2011-07-01		2005-07-05	ENSG00000204394	ENSG00000204394	6.1.1.9	"""Aminoacyl tRNA synthetases / Class I"""	12651	protein-coding gene	gene with protein product	"""valine tRNA ligase 1, cytoplasmic"""	192150	"""valyl-tRNA synthetase 2"""	VARS2		15779907	Standard	XM_005249362		Approved		uc003nxe.3	P26640	OTTHUMG00000031286	ENST00000375663.3:c.1536C>T	6.37:g.31752211G>A		Somatic	110	2.63	3		65	56.67	85	WXS	Illumina HiSeq	Phase_IV	31860190	15	44.44	12	B0V1N1|B4DZ61|Q5JQ90|Q96E77|Q9UQM2	Silent	SNP	PatternScan_AA_TRNA_LIGASE_I,HMMPfam_tRNA-synt_1,HMMPfam_GST_N,HMMPfam_GST_C,superfamily_ValRS/IleRS/LeuRS editing domain,superfamily_Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases,superfamily_Glutathione S-transferase (GST) C-terminal domain,HMMPfam_Anticodon_1,superfamily_Nucleotidylyl transferase	p.F512	ENST00000375663.3	37	c.1536	CCDS34412.1	6																																																																																			-	HMMPfam_tRNA-synt_1,superfamily_ValRS/IleRS/LeuRS editing domain,superfamily_Nucleotidylyl transferase		0.597	VARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	VARS	protein_coding	OTTHUMT00000076619.2	G	NM_006295		31860190	-1	no_errors	NM_006295.2	genbank	human	reviewed	54_36p	silent	SNP	1.000	A
PGM3	5238	genome.wustl.edu	37	6	83881683	83881683	+	Missense_Mutation	SNP	A	A	T			TCGA-AB-2861-03B-01W-0728-08	TCGA-AB-2861-11B-01W-0729-08	A	A	A	T	A	A	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	6f4de42a-16ce-4536-b5a7-a9380540dda4	c2a59421-c7d4-4b57-a82d-ee675481ba9b	g.chr6:83881683A>T	ENST00000283977.4	-	10	1221	c.1095T>A	c.(1093-1095)gaT>gaA	p.D365E	PGM3_ENST00000512866.1_Missense_Mutation_p.D446E|PGM3_ENST00000506587.1_Missense_Mutation_p.D474E|PGM3_ENST00000513973.1_Missense_Mutation_p.D446E					phosphoglucomutase 3											NS(1)|breast(1)|endometrium(2)|large_intestine(4)|lung(6)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	18		all_cancers(76;0.000504)|Acute lymphoblastic leukemia(125;3.85e-06)|all_hematologic(105;0.0017)|all_epithelial(107;0.068)		BRCA - Breast invasive adenocarcinoma(397;0.0478)		TGTTTGGAAGATCTGTATAGA	0.383																																						dbGAP											0			6											122.0	112.0	116.0					6																	83881683		2203	4300	6503	83938402	SO:0001583	missense	0			BC001258	CCDS4997.1, CCDS56435.1, CCDS56436.1, CCDS75487.1	6q14.1-q15	2012-10-02			ENSG00000013375	ENSG00000013375	5.4.2.3		8907	protein-coding gene	gene with protein product	"""acetylglucosamine phosphomutase"""	172100				12174217, 10721701	Standard	NM_001199917		Approved	AGM1, DKFZP434B187, PAGM	uc011dyz.2	O95394	OTTHUMG00000015110	ENST00000283977.4:c.1095T>A	6.37:g.83881683A>T	ENSP00000283977:p.Asp365Glu	Somatic	219	2.65	6		6	40.00	4	WXS	Illumina HiSeq	Phase_IV	83938402	96	44.51	77		Missense_Mutation	SNP	HMMPfam_PGM_PMM_IV,HMMPfam_PGM_PMM_I,superfamily_Phosphoglucomutase first 3 domains,PatternScan_PGM_PMM,superfamily_Phosphoglucomutase C-terminal domain	p.D446E	ENST00000283977.4	37	c.1338		6	.	.	.	.	.	.	.	.	.	.	A	13.77	2.337034	0.41398	.	.	ENSG00000013375	ENST00000513973;ENST00000512866;ENST00000283977;ENST00000506587;ENST00000509219	T;T;T;T;T	0.43294	0.95;0.95;0.95;0.95;0.95	5.79	-5.46	0.02608	.	0.000000	0.85682	D	0.000000	T	0.44993	0.1320	M	0.67953	2.075	0.58432	D	0.999991	P;B;D	0.89917	0.735;0.395;1.0	P;P;D	0.77004	0.779;0.646;0.989	T	0.60915	-0.7168	10	0.37606	T	0.19	-38.4187	16.472	0.84114	0.4227:0.0:0.5773:0.0	.	474;474;446	E9PF86;B4DX94;O95394	.;.;AGM1_HUMAN	E	446;446;365;474;77	ENSP00000424874:D446E;ENSP00000421565:D446E;ENSP00000283977:D365E;ENSP00000425809:D474E;ENSP00000423389:D77E	ENSP00000283977:D365E	D	-	3	2	PGM3	83938402	0.984000	0.35163	0.490000	0.27465	0.480000	0.33159	0.259000	0.18405	-1.070000	0.03149	-0.899000	0.02877	GAT	-	superfamily_Phosphoglucomutase C-terminal domain		0.383	PGM3-003	PUTATIVE	basic|exp_conf	protein_coding	PGM3	protein_coding	OTTHUMT00000366385.2	A	NM_015599		83938402	-1	no_errors	NM_015599.1	genbank	human	provisional	54_36p	missense	SNP	0.937	T
HDAC2	3066	genome.wustl.edu	37	6	114274557	114274557	+	Missense_Mutation	SNP	C	C	T			TCGA-AB-2861-03B-01W-0728-08	TCGA-AB-2861-11B-01W-0729-08	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	6f4de42a-16ce-4536-b5a7-a9380540dda4	c2a59421-c7d4-4b57-a82d-ee675481ba9b	g.chr6:114274557C>T	ENST00000519065.1	-	6	899	c.523G>A	c.(523-525)Gat>Aat	p.D175N	HDAC2_ENST00000368632.2_Missense_Mutation_p.D145N|HDAC2_ENST00000398283.2_Missense_Mutation_p.D269N|HDAC2_ENST00000519108.1_Missense_Mutation_p.D145N			Q92769	HDAC2_HUMAN	histone deacetylase 2	175	Histone deacetylase.				ATP-dependent chromatin remodeling (GO:0043044)|blood coagulation (GO:0007596)|cardiac muscle cell development (GO:0055013)|chromatin remodeling (GO:0006338)|circadian regulation of gene expression (GO:0032922)|dendrite development (GO:0016358)|embryonic digit morphogenesis (GO:0042733)|epidermal cell differentiation (GO:0009913)|eyelid development in camera-type eye (GO:0061029)|fungiform papilla formation (GO:0061198)|hair follicle placode formation (GO:0060789)|hippocampus development (GO:0021766)|histone deacetylation (GO:0016575)|histone H3 deacetylation (GO:0070932)|histone H4 deacetylation (GO:0070933)|maintenance of chromatin silencing (GO:0006344)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cardiac muscle cell proliferation (GO:0060044)|negative regulation of cell cycle (GO:0045786)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|negative regulation of MHC class II biosynthetic process (GO:0045347)|negative regulation of neuron projection development (GO:0010977)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotrophin TRK receptor signaling pathway (GO:0048011)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of cell proliferation (GO:0008284)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of oligodendrocyte differentiation (GO:0048714)|positive regulation of proteolysis (GO:0045862)|positive regulation of receptor biosynthetic process (GO:0010870)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of protein deacetylation (GO:0090311)|regulation of protein kinase B signaling (GO:0051896)|regulation of sarcomere organization (GO:0060297)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|ESC/E(Z) complex (GO:0035098)|heterochromatin (GO:0000792)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|NuRD complex (GO:0016581)|protein complex (GO:0043234)|replication fork (GO:0005657)|Sin3 complex (GO:0016580)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|chromatin DNA binding (GO:0031490)|deacetylase activity (GO:0019213)|enzyme binding (GO:0019899)|histone deacetylase activity (GO:0004407)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|poly(A) RNA binding (GO:0044822)|protein deacetylase activity (GO:0033558)|RNA polymerase II repressing transcription factor binding (GO:0001103)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			biliary_tract(1)|central_nervous_system(5)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(11)|ovary(1)|prostate(1)|skin(2)	27		all_cancers(87;0.000629)|all_epithelial(87;0.00274)|Colorectal(196;0.0317)|all_lung(197;0.24)		all cancers(137;0.00318)|OV - Ovarian serous cystadenocarcinoma(136;0.00569)|Epithelial(106;0.0112)|GBM - Glioblastoma multiforme(226;0.0832)	Aminophylline(DB01223)|Lovastatin(DB00227)|Oxtriphylline(DB01303)|Theophylline(DB00277)|Valproic Acid(DB00313)|Vorinostat(DB02546)	ATATCTATATCAATATATAAG	0.343																																						dbGAP											0			6											106.0	101.0	103.0					6																	114274557		1828	4073	5901	114381250	SO:0001583	missense	0			U31814	CCDS43493.1, CCDS43493.2	6q21	2008-08-29			ENSG00000196591	ENSG00000196591			4853	protein-coding gene	gene with protein product		605164				9782097	Standard	NM_001527		Approved	RPD3, YAF1	uc003pwd.2	Q92769	OTTHUMG00000015411	ENST00000519065.1:c.523G>A	6.37:g.114274557C>T	ENSP00000430432:p.Asp175Asn	Somatic	90	0.00	0		58	40.82	40	WXS	Illumina HiSeq	Phase_IV	114381250	80	34.15	42	B3KRS5|B4DL58|E1P561|Q5SRI8|Q5SZ86|Q8NEH4	Missense_Mutation	SNP	HMMPfam_Hist_deacetyl,superfamily_SSF52768	p.D269N	ENST00000519065.1	37	c.805	CCDS43493.2	6	.	.	.	.	.	.	.	.	.	.	C	36	5.755796	0.96898	.	.	ENSG00000196591	ENST00000519065;ENST00000398283;ENST00000519108;ENST00000368632	D;D;D;D	0.95001	-3.58;-3.58;-3.58;-3.58	5.76	5.76	0.90799	Histone deacetylase domain (2);	0.073664	0.56097	D	0.000037	D	0.98902	0.9628	H	0.99770	4.765	0.80722	D	1	D;D	0.76494	0.999;0.992	D;D	0.81914	0.995;0.933	D	0.99167	1.0863	10	0.87932	D	0	-41.1835	20.3431	0.98773	0.0:1.0:0.0:0.0	.	145;175	B3KRS5;Q92769	.;HDAC2_HUMAN	N	175;269;145;145	ENSP00000430432:D175N;ENSP00000381331:D269N;ENSP00000430008:D145N;ENSP00000357621:D145N	ENSP00000357621:D145N	D	-	1	0	HDAC2	114381250	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	7.776000	0.85560	2.880000	0.98712	0.650000	0.86243	GAT	-	HMMPfam_Hist_deacetyl,superfamily_SSF52768		0.343	HDAC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	HDAC2	protein_coding	OTTHUMT00000041909.2	C			114381250	-1	no_errors	NM_001527.2	genbank	human	reviewed	54_36p	missense	SNP	1.000	T
ARHGEF5	7984	genome.wustl.edu	37	7	144062359	144062359	+	Missense_Mutation	SNP	G	G	A			TCGA-AB-2861-03B-01W-0728-08	TCGA-AB-2861-11B-01W-0729-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	6f4de42a-16ce-4536-b5a7-a9380540dda4	c2a59421-c7d4-4b57-a82d-ee675481ba9b	g.chr7:144062359G>A	ENST00000056217.5	+	2	2771	c.2597G>A	c.(2596-2598)cGg>cAg	p.R866Q	ARHGEF5_ENST00000471847.2_5'Flank	NM_005435.3	NP_005426.2	Q12774	ARHG5_HUMAN	Rho guanine nucleotide exchange factor (GEF) 5	866					actin cytoskeleton organization (GO:0030036)|intracellular signal transduction (GO:0035556)|myeloid dendritic cell chemotaxis (GO:0002408)|positive regulation of podosome assembly (GO:0071803)|regulation of Rho GTPase activity (GO:0032319)		GTP binding (GO:0005525)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|endometrium(6)|kidney(8)|large_intestine(9)|liver(1)|lung(8)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	40	Melanoma(164;0.14)					AGGAGCACTCGGGGAGGACAT	0.607																																						dbGAP											0			7											79.0	91.0	87.0					7																	144062359		2202	4298	6500	143693292	SO:0001583	missense	0			U02082	CCDS34771.1	7q35	2012-09-20			ENSG00000050327	ENSG00000050327		"""Rho guanine nucleotide exchange factors"""	13209	protein-coding gene	gene with protein product	"""transforming immortalized mammary oncogene"", ""guanine nucleotide regulatory protein TIM"""	600888				8134109, 7656213	Standard	NM_005435		Approved	TIM, TIM1, GEF5, P60	uc003wel.3	Q12774	OTTHUMG00000158004	ENST00000056217.5:c.2597G>A	7.37:g.144062359G>A	ENSP00000056217:p.Arg866Gln	Somatic	573	0.00	0		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	143693292	475	12.04	65	A6NNJ2|Q6ZML7	Missense_Mutation	SNP	HMMPfam_RhoGEF,HMMSmart_SM00325,superfamily_DBL homology domain (DH-domain),PatternScan_DH_1,HMMSmart_SM00326,superfamily_SH3-domain,HMMPfam_PH,HMMSmart_SM00233,HMMPfam_SH3_2,superfamily_PH domain-like	p.R866Q	ENST00000056217.5	37	c.2597	CCDS34771.1	7	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	0.005|0.005	-2.178615|-2.178615	0.00308|0.00308	.|.	.|.	ENSG00000050327|ENSG00000050327	ENST00000474817|ENST00000056217	.|T	.|0.70164	.|-0.46	4.27|4.27	1.55|1.55	0.23275|0.23275	.|.	.|0.846688	.|0.09883	.|N	.|0.743423	T|T	0.27349|0.27349	0.0671|0.0671	N|N	0.00926|0.00926	-1.1|-1.1	0.26965|0.26965	N|N	0.965715|0.965715	.|B	.|0.06786	.|0.001	.|B	.|0.01281	.|0.0	T|T	0.33777|0.33777	-0.9855|-0.9855	5|10	.|0.02654	.|T	.|1	-2.6284|-2.6284	3.2822|3.2822	0.06920|0.06920	0.6848:0.0:0.1135:0.2017|0.6848:0.0:0.1135:0.2017	.|.	.|866	.|Q12774	.|ARHG5_HUMAN	R|Q	120|866	.|ENSP00000056217:R866Q	.|ENSP00000056217:R866Q	G|R	+|+	1|2	0|0	ARHGEF5|ARHGEF5	143693292|143693292	0.360000|0.360000	0.24964|0.24964	0.245000|0.245000	0.24217|0.24217	0.018000|0.018000	0.09664|0.09664	2.614000|2.614000	0.46359|0.46359	0.172000|0.172000	0.19760|0.19760	-0.474000|-0.474000	0.04947|0.04947	GGG|CGG	-	NULL		0.607	ARHGEF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ARHGEF5	protein_coding	OTTHUMT00000349981.1	G	NM_005435		143693292	+1	no_errors	NM_005435.3	genbank	human	reviewed	54_36p	missense	SNP	0.023	A
TUSC3	7991	genome.wustl.edu	37	8	15480637	15480637	+	Missense_Mutation	SNP	C	C	T			TCGA-AB-2861-03B-01W-0728-08	TCGA-AB-2861-11B-01W-0729-08	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	6f4de42a-16ce-4536-b5a7-a9380540dda4	c2a59421-c7d4-4b57-a82d-ee675481ba9b	g.chr8:15480637C>T	ENST00000503731.1	+	2	335	c.187C>T	c.(187-189)Cgc>Tgc	p.R63C	TUSC3_ENST00000503191.1_3'UTR|TUSC3_ENST00000509380.1_Missense_Mutation_p.R63C|TUSC3_ENST00000506802.1_Missense_Mutation_p.R63C|TUSC3_ENST00000382020.4_Missense_Mutation_p.R63C	NM_006765.3	NP_006756.2	Q13454	TUSC3_HUMAN	tumor suppressor candidate 3	63	Thioredoxin.				cell redox homeostasis (GO:0045454)|cellular protein metabolic process (GO:0044267)|cognition (GO:0050890)|magnesium ion transport (GO:0015693)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|mitochondrion (GO:0005739)|oligosaccharyltransferase complex (GO:0008250)	magnesium ion transmembrane transporter activity (GO:0015095)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(10)|lung(10)|ovary(2)	28				Colorectal(111;0.113)		GAGTTCCAGACGCTCAATCTT	0.368																																						dbGAP											0			8											70.0	71.0	70.0					8																	15480637		2203	4300	6503	15525008	SO:0001583	missense	0			AK026149	CCDS5993.1, CCDS5994.1	8p22	2010-10-22			ENSG00000104723	ENSG00000104723			30242	protein-coding gene	gene with protein product	"""oligosaccharyltransferase 3 homolog A (S. cerevisiae)"""	601385				8661104, 10097140	Standard	NM_178234		Approved	MGC13453, N33, OST3A, MRT7	uc003wwt.3	Q13454	OTTHUMG00000094803	ENST00000503731.1:c.187C>T	8.37:g.15480637C>T	ENSP00000424544:p.Arg63Cys	Somatic	86	0.00	0		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	15525008	108	29.87	46	A8MSM0|D3DSP2|Q14911|Q14912|Q96FW0	Missense_Mutation	SNP	HMMPfam_OST3_OST6,superfamily_Thioredoxin-like	p.R63C	ENST00000503731.1	37	c.187	CCDS5994.1	8	.	.	.	.	.	.	.	.	.	.	C	24.7	4.556328	0.86231	.	.	ENSG00000104723	ENST00000382020;ENST00000506802;ENST00000509380;ENST00000503731	T;T;T;T	0.48522	0.83;0.81;0.83;0.83	5.59	5.59	0.84812	Thioredoxin-like fold (2);	0.045721	0.85682	D	0.000000	T	0.58524	0.2128	L	0.38175	1.15	0.80722	D	1	D;D;D;D;D;D	0.89917	0.997;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.79784	0.962;0.972;0.992;0.943;0.978;0.993	T	0.58555	-0.7616	10	0.62326	D	0.03	-12.9411	13.8712	0.63619	0.1524:0.8476:0.0:0.0	.	63;63;63;63;63;63	D6RDV0;D6RIY7;Q13454-2;Q13454;D6RA37;A8MSM0	.;.;.;TUSC3_HUMAN;.;.	C	63	ENSP00000371450:R63C;ENSP00000425777:R63C;ENSP00000423426:R63C;ENSP00000424544:R63C	ENSP00000221167:R63C	R	+	1	0	TUSC3	15525008	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.487000	0.81328	2.804000	0.96469	0.650000	0.86243	CGC	-	HMMPfam_OST3_OST6,superfamily_Thioredoxin-like		0.368	TUSC3-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	TUSC3	protein_coding	OTTHUMT00000365367.1	C	NM_006765		15525008	+1	no_errors	NM_006765.2	genbank	human	reviewed	54_36p	missense	SNP	1.000	T
BNC2	54796	genome.wustl.edu	37	9	16436735	16436735	+	Missense_Mutation	SNP	C	C	T			TCGA-AB-2861-03B-01W-0728-08	TCGA-AB-2861-11B-01W-0729-08	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	6f4de42a-16ce-4536-b5a7-a9380540dda4	c2a59421-c7d4-4b57-a82d-ee675481ba9b	g.chr9:16436735C>T	ENST00000380672.4	-	6	1514	c.1457G>A	c.(1456-1458)cGt>cAt	p.R486H	BNC2_ENST00000545497.1_Missense_Mutation_p.R391H|BNC2_ENST00000380667.2_Missense_Mutation_p.R419H|BNC2_ENST00000380666.2_Missense_Mutation_p.R486H	NM_017637.5	NP_060107.3			basonuclin 2											NS(2)|breast(3)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(16)|liver(1)|lung(22)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	60				GBM - Glioblastoma multiforme(50;9.01e-08)		GTGGCGATTACGACTTCGGAG	0.463																																						dbGAP											0			9											143.0	133.0	137.0					9																	16436735		2203	4300	6503	16426735	SO:0001583	missense	0			AK092247	CCDS6482.2	9p22.2	2013-05-20			ENSG00000173068	ENSG00000173068		"""Zinc fingers, C2H2-type"""	30988	protein-coding gene	gene with protein product		608669				14702039	Standard	XM_006716784		Approved	BSN2, FLJ20043	uc003zml.3	Q6ZN30	OTTHUMG00000019593	ENST00000380672.4:c.1457G>A	9.37:g.16436735C>T	ENSP00000370047:p.Arg486His	Somatic	648	0.46	3		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	16426735	127	26.16	45		Missense_Mutation	SNP	HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_SM00355,superfamily_C2H2 and C2HC zinc fingers	p.R486H	ENST00000380672.4	37	c.1457	CCDS6482.2	9	.	.	.	.	.	.	.	.	.	.	C	20.3	3.973250	0.74246	.	.	ENSG00000173068	ENST00000380672;ENST00000418777;ENST00000380667;ENST00000545497;ENST00000544198;ENST00000380666;ENST00000540340	T;T;T;T;T	0.28454	1.61;1.61;1.61;1.61;1.61	5.88	5.88	0.94601	Zinc finger, C2H2-like (1);	0.000000	0.85682	D	0.000000	T	0.59742	0.2216	M	0.74467	2.265	0.80722	D	1	D;D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;0.999;1.0;1.0;1.0	D;D;D;D;D;D;D;D;D	0.97110	1.0;0.997;0.996;1.0;0.996;0.98;0.998;0.994;0.998	T	0.60188	-0.7312	10	0.72032	D	0.01	-12.1064	20.2422	0.98381	0.0:1.0:0.0:0.0	.	391;419;486;312;486;443;486;391;251	F5H586;B1APH0;Q6ZN30-2;B4E3J2;F5H8G9;Q5H9S4;Q6ZN30;B4DR27;D3DRJ1	.;.;.;.;.;.;BNC2_HUMAN;.;.	H	486;443;419;391;312;486;486	ENSP00000370047:R486H;ENSP00000408370:R443H;ENSP00000370042:R419H;ENSP00000444640:R391H;ENSP00000370041:R486H	ENSP00000370041:R486H	R	-	2	0	BNC2	16426735	1.000000	0.71417	0.969000	0.41365	0.986000	0.74619	7.818000	0.86416	2.782000	0.95742	0.655000	0.94253	CGT	-	HMMSmart_SM00355,superfamily_C2H2 and C2HC zinc fingers		0.463	BNC2-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	BNC2	protein_coding	OTTHUMT00000216901.5	C	NM_017637		16426735	-1	no_errors	NM_017637.5	genbank	human	validated	54_36p	missense	SNP	1.000	T
BTBD16	118663	genome.wustl.edu	37	10	124034613	124034613	+	Splice_Site	SNP	C	C	T	rs202065129		TCGA-AB-2861-03B-01W-0728-08	TCGA-AB-2861-11B-01W-0729-08	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	6f4de42a-16ce-4536-b5a7-a9380540dda4	c2a59421-c7d4-4b57-a82d-ee675481ba9b	g.chr10:124034613C>T	ENST00000260723.4	+	2	268	c.17C>T	c.(16-18)aCg>aTg	p.T6M	BTBD16_ENST00000368994.2_Splice_Site_p.T6M	NM_144587.2	NP_653188.2	Q32M84	BTBDG_HUMAN	BTB (POZ) domain containing 16	6										breast(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(5)|lung(3)|skin(2)|stomach(1)|urinary_tract(1)	15		all_neural(114;0.107)|Lung NSC(174;0.175)|all_lung(145;0.222)|Breast(234;0.238)				ATGTCGAACACGGTGAGTAGA	0.408																																						dbGAP											0			10						T	MET/THR	0,4406		0,0,2203	199.0	180.0	186.0		17	-2.9	0.0	10		186	1,8599	1.2+/-3.3	0,1,4299	yes	missense-near-splice	BTBD16	NM_144587.2	81	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging	6/507	124034613	1,13005	2203	4300	6503	124024603	SO:0001630	splice_region_variant	0			AK058088	CCDS31301.1	10q26.13	2013-01-24	2006-07-04	2006-07-04	ENSG00000138152	ENSG00000138152		"""BTB/POZ domain containing"""	26340	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 87"""	C10orf87			Standard	NM_144587		Approved	FLJ25359, Em:AC061711.1	uc001lgc.1	Q32M84	OTTHUMG00000019182	ENST00000260723.4:c.18+1C>T	10.37:g.124034613C>T		Somatic	353	0.28	1		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	124024603	102	41.71	73	A6NM63|Q4VXL1|Q96LN0	Missense_Mutation	SNP	superfamily_POZ domain,HMMPfam_BTB	p.T6M	ENST00000260723.4	37	c.17	CCDS31301.1	10	.	.	.	.	.	.	.	.	.	.	c	6.082	0.383367	0.11524	0.0	1.16E-4	ENSG00000138152	ENST00000260723;ENST00000368994	T;T	0.18338	2.24;2.22	3.74	-2.88	0.05682	.	2.739860	0.01330	N	0.011223	T	0.07683	0.0193	N	0.08118	0	0.09310	N	1	B;B	0.19583	0.016;0.037	B;B	0.12156	0.001;0.007	T	0.20571	-1.0271	10	0.46703	T	0.11	0.321	0.2086	0.00153	0.2967:0.2708:0.1455:0.287	.	6;6	Q32M84-2;Q32M84	.;BTBDG_HUMAN	M	6	ENSP00000260723:T6M;ENSP00000357990:T6M	ENSP00000260723:T6M	T	+	2	0	BTBD16	124024603	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.104000	0.03326	-0.648000	0.05437	-0.735000	0.03563	ACG	-	NULL		0.408	BTBD16-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	BTBD16	protein_coding	OTTHUMT00000050780.3	C	NM_144587	Missense_Mutation	124024603	+1	no_errors	NM_144587.2	genbank	human	validated	54_36p	missense	SNP	0.000	T
KRAS	3845	genome.wustl.edu	37	12	25398284	25398284	+	Missense_Mutation	SNP	C	C	A	rs121913529		TCGA-AB-2861-03B-01W-0728-08	TCGA-AB-2861-11B-01W-0729-08	C	C	C	A	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	6f4de42a-16ce-4536-b5a7-a9380540dda4	c2a59421-c7d4-4b57-a82d-ee675481ba9b	g.chr12:25398284C>A	ENST00000256078.4	-	2	98	c.35G>T	c.(34-36)gGt>gTt	p.G12V	KRAS_ENST00000311936.3_Missense_Mutation_p.G12V|KRAS_ENST00000557334.1_Missense_Mutation_p.G12V|KRAS_ENST00000556131.1_Missense_Mutation_p.G12V	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	12			G -> A (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.|G -> C (in lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:6320174}.|G -> D (in pancreatic carcinoma, GASC and lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929, ECO:0000269|PubMed:8439212}.|G -> R (in lung cancer and bladder cancer; somatic mutation). {ECO:0000269|PubMed:6695174}.|G -> S (in lung carcinoma and GASC; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929}.|G -> V (in lung carcinoma, pancreatic carcinoma, colon cancer and GASC; somatic mutation, constitutively activated). {ECO:0000269|PubMed:14534542, ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:22711838, ECO:0000269|PubMed:3034404, ECO:0000269|PubMed:6092920, ECO:0000269|PubMed:8439212}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to glucocorticoid (GO:0051384)|response to mineralocorticoid (GO:0051385)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	focal adhesion (GO:0005925)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GMP binding (GO:0019002)|GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.G12D(8562)|p.G12V(5775)|p.G12A(1407)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12E(3)|p.G12W(3)|p.G12Y(2)|p.G12fs*3(1)|p.G12C(1)|p.G12N(1)	UBE2L3/KRAS(2)	NS(6)|adrenal_gland(1)|autonomic_ganglia(3)|biliary_tract(532)|bone(2)|breast(32)|central_nervous_system(14)|cervix(50)|endometrium(411)|eye(4)|gastrointestinal_tract_(site_indeterminate)(7)|genital_tract(1)|haematopoietic_and_lymphoid_tissue(385)|kidney(8)|large_intestine(15267)|liver(29)|lung(3407)|oesophagus(16)|ovary(612)|pancreas(3739)|penis(1)|peritoneum(6)|prostate(96)|salivary_gland(6)|skin(45)|small_intestine(68)|soft_tissue(88)|stomach(207)|testis(17)|thymus(5)|thyroid(159)|upper_aerodigestive_tract(68)|urinary_tract(57)	25349	all_cancers(2;1e-35)|all_epithelial(2;1.97e-38)|all_lung(3;2.1e-23)|Lung NSC(3;1.16e-22)|Acute lymphoblastic leukemia(6;0.00231)|all_hematologic(7;0.00259)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12)		OV - Ovarian serous cystadenocarcinoma(3;1.23e-21)|Epithelial(3;1.31e-20)|all cancers(3;5.45e-18)|STAD - Stomach adenocarcinoma(2;2.68e-05)			GCCTACGCCACCAGCTCCAAC	0.348	G12A(KMS28BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(KPNSI9S_AUTONOMIC_GANGLIA)|G12A(MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(NCIH1573_LUNG)|G12A(NCIH2009_LUNG)|G12A(RERFLCAD1_LUNG)|G12A(RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(SW1116_LARGE_INTESTINE)|G12D(AGS_STOMACH)|G12D(ASPC1_PANCREAS)|G12D(COLO678_LARGE_INTESTINE)|G12D(HEC1A_ENDOMETRIUM)|G12D(HEC50B_ENDOMETRIUM)|G12D(HEYA8_OVARY)|G12D(HPAC_PANCREAS)|G12D(HPAFII_PANCREAS)|G12D(KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KP4_PANCREAS)|G12D(L33_PANCREAS)|G12D(LS180_LARGE_INTESTINE)|G12D(LS513_LARGE_INTESTINE)|G12D(MCAS_OVARY)|G12D(PANC0203_PANCREAS)|G12D(PANC0403_PANCREAS)|G12D(PANC0504_PANCREAS)|G12D(PANC0813_PANCREAS)|G12D(PANC1_PANCREAS)|G12D(PK1_PANCREAS)|G12D(PK59_PANCREAS)|G12D(SKLU1_LUNG)|G12D(SNUC2A_LARGE_INTESTINE)|G12D(SU8686_PANCREAS)|G12D(SUIT2_PANCREAS)|G12D(SW1990_PANCREAS)|G12V(A498_KIDNEY)|G12V(CAPAN2_PANCREAS)|G12V(CFPAC1_PANCREAS)|G12V(COLO668_LUNG)|G12V(CORL23_LUNG)|G12V(DANG_PANCREAS)|G12V(HCC56_LARGE_INTESTINE)|G12V(HUPT4_PANCREAS)|G12V(KP3_PANCREAS)|G12V(LCLC97TM1_LUNG)|G12V(NCIH2444_LUNG)|G12V(NCIH441_LUNG)|G12V(NCIH727_LUNG)|G12V(PANC0327_PANCREAS)|G12V(PATU8902_PANCREAS)|G12V(PATU8988S_PANCREAS)|G12V(QGP1_PANCREAS)|G12V(RCM1_LARGE_INTESTINE)|G12V(RERFLCAD2_LUNG)|G12V(RKN_OVARY)|G12V(SH10TC_STOMACH)|G12V(SHP77_LUNG)|G12V(SNGM_ENDOMETRIUM)|G12V(SW403_LARGE_INTESTINE)|G12V(SW480_LARGE_INTESTINE)|G12V(SW620_LARGE_INTESTINE)|G12V(SW900_LUNG)|G12V(YAPC_PANCREAS)	119	Mis		"""pancreatic, colorectal, lung, thyroid, AML, others"""				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)																											Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)	dbGAP		Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		"""L, E, M, O"""	15813	Substitution - Missense(15812)|Deletion - Frameshift(1)	large_intestine(9453)|pancreas(3002)|lung(1512)|ovary(500)|biliary_tract(369)|endometrium(319)|haematopoietic_and_lymphoid_tissue(163)|stomach(124)|prostate(59)|thyroid(55)|small_intestine(43)|upper_aerodigestive_tract(30)|urinary_tract(30)|soft_tissue(28)|skin(27)|cervix(22)|liver(16)|breast(11)|testis(9)|oesophagus(8)|central_nervous_system(7)|peritoneum(5)|kidney(4)|eye(4)|gastrointestinal_tract_(site_indeterminate)(3)|NS(3)|thymus(3)|autonomic_ganglia(2)|salivary_gland(1)|bone(1)	12											91.0	81.0	85.0					12																	25398284		2203	4300	6503	25289551	SO:0001583	missense	0	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	BC010502	CCDS8702.1, CCDS8703.1	12p12.1	2014-09-17	2013-07-08	2005-01-24	ENSG00000133703	ENSG00000133703			6407	protein-coding gene	gene with protein product		190070	"""v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog"", ""v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog"""	KRAS2			Standard	NM_004985		Approved	KRAS1	uc001rgp.1	P01116		ENST00000256078.4:c.35G>T	12.37:g.25398284C>A	ENSP00000256078:p.Gly12Val	Somatic	30	3.23	1		18	33.33	9	WXS	Illumina HiSeq	Phase_IV	25289551	35	30.00	15	A8K8Z5|B0LPF9|P01118|Q96D10	Missense_Mutation	SNP	HMMSmart_SM00176,HMMSmart_SM00173,HMMSmart_SM00174,HMMSmart_SM00175,HMMPfam_Ras,superfamily_P-loop containing nucleoside triphosphate hydrolases	p.G12V	ENST00000256078.4	37	c.35	CCDS8703.1	12	.	.	.	.	.	.	.	.	.	.	C	27.2	4.808637	0.90707	.	.	ENSG00000133703	ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131	T;T;T;T	0.78707	-1.2;-1.2;-1.2;-1.2	5.68	5.68	0.88126	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.90373	0.6987	M	0.90650	3.135	0.80722	D	1	D;D	0.76494	0.997;0.999	D;D	0.72625	0.969;0.978	D	0.91773	0.5429	10	0.72032	D	0.01	.	18.3719	0.90409	0.0:1.0:0.0:0.0	.	12;12	P01116-2;P01116	.;RASK_HUMAN	V	12	ENSP00000308495:G12V;ENSP00000452512:G12V;ENSP00000256078:G12V;ENSP00000451856:G12V	ENSP00000256078:G12V	G	-	2	0	KRAS	25289551	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.743000	0.85020	2.668000	0.90789	0.563000	0.77884	GGT	-	HMMSmart_SM00176,HMMSmart_SM00173,HMMSmart_SM00174,HMMSmart_SM00175,HMMPfam_Ras,superfamily_P-loop containing nucleoside triphosphate hydrolases		0.348	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	KRAS	protein_coding	OTTHUMT00000412232.1	C	NM_033360		25289551	-1	no_errors	NM_033360.3	genbank	human	reviewed	54_36p	missense	SNP	1.000	A
Unknown	0	genome.wustl.edu	37	14	19476106	19476106	+	IGR	SNP	G	G	A	rs572491546		TCGA-AB-2861-03B-01W-0728-08	TCGA-AB-2861-11B-01W-0729-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	6f4de42a-16ce-4536-b5a7-a9380540dda4	c2a59421-c7d4-4b57-a82d-ee675481ba9b	g.chr14:19476106G>A								RP11-536C10.16 (62208 upstream) : MED15P1 (23739 downstream)																							CAACTGAGTCGTCACTCGAAG	0.453																																						dbGAP											0			14																																								18546106	SO:0001628	intergenic_variant	0																															14.37:g.19476106G>A		Somatic	156	1.27	2		0	100.00	1	WXS	Illumina HiSeq	Phase_IV	18546106	162	12.43	23		RNA	SNP	-	NULL		37	NULL		14																																																																																			-	-	0	0.453					LOC642458			G			18546106	-1	pseudogene	XR_016116.2	genbank	human	model	54_36p	rna	SNP	0.986	A
MEFV	4210	genome.wustl.edu	37	16	3294587	3294587	+	Splice_Site	SNP	C	C	T			TCGA-AB-2861-03B-01W-0728-08	TCGA-AB-2861-11B-01W-0729-08	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	6f4de42a-16ce-4536-b5a7-a9380540dda4	c2a59421-c7d4-4b57-a82d-ee675481ba9b	g.chr16:3294587C>T	ENST00000219596.1	-	7	1651	c.1612G>A	c.(1612-1614)Gct>Act	p.A538T	MEFV_ENST00000536379.1_Splice_Site_p.A327T|MEFV_ENST00000541159.1_Splice_Site_p.A327T|MEFV_ENST00000339854.4_Splice_Site_p.A358T	NM_000243.2	NP_000234.1	O15553	MEFV_HUMAN	Mediterranean fever	538	Required for homotrimerization and induction of pyroptosomes.				inflammatory response (GO:0006954)|innate immune response (GO:0045087)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-1 beta production (GO:0032691)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of macrophage inflammatory protein 1 alpha production (GO:0071641)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of cysteine-type endopeptidase activity (GO:2001056)	cell projection (GO:0042995)|cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|nucleus (GO:0005634)	actin binding (GO:0003779)|zinc ion binding (GO:0008270)			NS(2)|biliary_tract(1)|breast(5)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(6)|lung(19)|ovary(3)|prostate(1)|skin(6)	50						ACTGTCTTAGCCCTAGAGACA	0.517																																						dbGAP											0			16											99.0	94.0	95.0					16																	3294587		2197	4300	6497	3234588	SO:0001630	splice_region_variant	0			AF018080	CCDS10498.1, CCDS55981.1	16p13.3	2014-09-17			ENSG00000103313	ENSG00000103313		"""Tripartite motif containing / Tripartite motif containing"""	6998	protein-coding gene	gene with protein product	"""pyrin"""	608107		MEF		9288094	Standard	NM_000243		Approved	FMF, TRIM20	uc002cun.1	O15553	OTTHUMG00000129324	ENST00000219596.1:c.1611-1G>A	16.37:g.3294587C>T		Somatic	205	6.82	15		10	33.33	5	WXS	Illumina HiSeq	Phase_IV	3234588	22	58.49	31	D3DUC0|F5H0Q3|Q3MJ84|Q96PN4|Q96PN5	Missense_Mutation	SNP	HMMPfam_zf-B_box,HMMSmart_SM00336,HMMPfam_SPRY,HMMPfam_PAAD_DAPIN,HMMSmart_SM00589,superfamily_DEATH domain,HMMSmart_SM00449,superfamily_B-box zinc-binding domain	p.A538T	ENST00000219596.1	37	c.1612	CCDS10498.1	16	.	.	.	.	.	.	.	.	.	.	C	11.54	1.669846	0.29693	.	.	ENSG00000103313	ENST00000545159;ENST00000219596;ENST00000339854;ENST00000541159;ENST00000536379;ENST00000534868	T;T;T;T	0.64260	-0.09;0.33;0.27;0.34	5.07	4.12	0.48240	.	0.407506	0.20986	N	0.082122	T	0.56717	0.2004	M	0.72118	2.19	0.80722	D	1	B	0.29909	0.261	B	0.22880	0.042	T	0.57347	-0.7827	10	0.42905	T	0.14	-13.5867	9.1166	0.36762	0.0:0.9021:0.0:0.0979	.	538	O15553	MEFV_HUMAN	T	538;538;358;327;327;327	ENSP00000219596:A538T;ENSP00000339639:A358T;ENSP00000438711:A327T;ENSP00000445079:A327T	ENSP00000219596:A538T	A	-	1	0	MEFV	3234588	1.000000	0.71417	0.993000	0.49108	0.565000	0.35776	1.350000	0.34010	1.376000	0.46267	0.563000	0.77884	GCT	-	NULL		0.517	MEFV-001	KNOWN	basic|appris_principal|CCDS	protein_coding	MEFV	protein_coding	OTTHUMT00000251464.1	C	NM_000243	Missense_Mutation	3234588	-1	no_errors	NM_000243.2	genbank	human	reviewed	54_36p	missense	SNP	0.911	T
NOMO2	283820	genome.wustl.edu	37	16	18532148	18532148	+	Missense_Mutation	SNP	C	C	T			TCGA-AB-2861-03B-01W-0728-08	TCGA-AB-2861-11B-01W-0729-08	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	6f4de42a-16ce-4536-b5a7-a9380540dda4	c2a59421-c7d4-4b57-a82d-ee675481ba9b	g.chr16:18532148C>T	ENST00000381474.3	-	19	2277	c.2212G>A	c.(2212-2214)Gtg>Atg	p.V738M	NOMO2_ENST00000543392.1_Missense_Mutation_p.V571M|NOMO2_ENST00000330537.6_Missense_Mutation_p.V738M	NM_001004060.1	NP_001004060.1	Q5JPE7	NOMO2_HUMAN	NODAL modulator 2	738						endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)	p.V738M(1)		endometrium(4)|kidney(1)|large_intestine(2)|liver(3)|lung(5)|ovary(3)|prostate(1)|skin(1)	20						ATCTCCTGCACGGGAGGCTTG	0.552																																						dbGAP											1	Substitution - Missense(1)	endometrium(1)	16											274.0	277.0	276.0					16																	18532148		2196	4297	6493	18439649	SO:0001583	missense	0			AL512687	CCDS10570.1, CCDS32394.1	16p12.3	2008-02-05			ENSG00000185164	ENSG00000185164			22652	protein-coding gene	gene with protein product		609158				15257293	Standard	NM_001004060		Approved	NOMO, PM5	uc002dfe.3	Q5JPE7	OTTHUMG00000131366	ENST00000381474.3:c.2212G>A	16.37:g.18532148C>T	ENSP00000370883:p.Val738Met	Somatic	517	4.42	24		65	42.48	48	WXS	Illumina HiSeq	Phase_IV	18439649	97	26.52	35	Q4G177	Missense_Mutation	SNP	HMMPfam_Cna_B,superfamily_Carboxypeptidase regulatory domain,superfamily_Starch-binding domain-like	p.V738M	ENST00000381474.3	37	c.2212	CCDS32394.1	16	.	.	.	.	.	.	.	.	.	.	.	9.246	1.039509	0.19669	.	.	ENSG00000185164	ENST00000330537;ENST00000381474;ENST00000543392	T;T;T	0.04917	3.56;3.53;3.53	3.37	2.41	0.29592	.	0.523027	0.20259	N	0.095907	T	0.03608	0.0103	N	0.08118	0	0.40773	D	0.983102	P;P	0.48998	0.903;0.918	B;B	0.41646	0.362;0.212	T	0.56390	-0.7987	10	0.41790	T	0.15	-2.7384	9.9589	0.41684	0.0:0.8966:0.0:0.1034	.	571;738	Q4G177;Q5JPE7	.;NOMO2_HUMAN	M	738;738;571	ENSP00000331851:V738M;ENSP00000370883:V738M;ENSP00000439970:V571M	ENSP00000331851:V738M	V	-	1	0	NOMO2	18439649	0.956000	0.32656	0.267000	0.24556	0.218000	0.24690	2.603000	0.46266	0.724000	0.32296	0.455000	0.32223	GTG	-	NULL		0.552	NOMO2-002	KNOWN	basic|CCDS	protein_coding	NOMO2	protein_coding	OTTHUMT00000435858.1	C	NM_001004060		18439649	-1	no_errors	NM_001004060.1	genbank	human	reviewed	54_36p	missense	SNP	0.986	T
CACNG1	786	genome.wustl.edu	37	17	65040806	65040806	+	Silent	SNP	C	C	T			TCGA-AB-2861-03B-01W-0728-08	TCGA-AB-2861-11B-01W-0729-08	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	6f4de42a-16ce-4536-b5a7-a9380540dda4	c2a59421-c7d4-4b57-a82d-ee675481ba9b	g.chr17:65040806C>T	ENST00000226021.3	+	1	101	c.30C>T	c.(28-30)cgC>cgT	p.R10R		NM_000727.3	NP_000718.1	Q06432	CCG1_HUMAN	calcium channel, voltage-dependent, gamma subunit 1	10					muscle contraction (GO:0006936)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transport (GO:0006810)	voltage-gated calcium channel complex (GO:0005891)	voltage-gated calcium channel activity (GO:0005245)			breast(1)|large_intestine(2)|lung(2)|prostate(1)|skin(2)	8	all_cancers(12;1.04e-10)|Breast(2;1.45e-16)|all_epithelial(3;4.81e-12)				Diltiazem(DB00343)|Fluspirilene(DB04842)|Ibutilide(DB00308)|Lercanidipine(DB00528)|Magnesium Sulfate(DB00653)|Nitrendipine(DB01054)|Spironolactone(DB00421)	TGAAGGTCCGCGTGACCCTCT	0.652																																						dbGAP											0			17											90.0	76.0	80.0					17																	65040806		2203	4300	6503	62471268	SO:0001819	synonymous_variant	0			L07738	CCDS11668.1	17q24	2008-05-02				ENSG00000108878		"""Calcium channel subunits"""	1405	protein-coding gene	gene with protein product		114209		CACNLG		8395940	Standard	NM_000727		Approved		uc002jfu.3	Q06432		ENST00000226021.3:c.30C>T	17.37:g.65040806C>T		Somatic	118	6.35	8		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	62471268	8	50.00	8	B2R9N3|Q14D59	Silent	SNP	HMMPfam_PMP22_Claudin	p.R10	ENST00000226021.3	37	c.30	CCDS11668.1	17																																																																																			-	HMMPfam_PMP22_Claudin		0.652	CACNG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CACNG1	protein_coding	OTTHUMT00000447039.1	C			62471268	+1	no_errors	NM_000727.2	genbank	human	reviewed	54_36p	silent	SNP	0.962	T
KATNAL2	83473	genome.wustl.edu	37	18	44625704	44625704	+	Missense_Mutation	SNP	C	C	A			TCGA-AB-2861-03B-01W-0728-08	TCGA-AB-2861-11B-01W-0729-08	C	C	C	A	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	6f4de42a-16ce-4536-b5a7-a9380540dda4	c2a59421-c7d4-4b57-a82d-ee675481ba9b	g.chr18:44625704C>A	ENST00000245121.5	+	13	1280	c.1086C>A	c.(1084-1086)caC>caA	p.H362Q	KATNAL2_ENST00000356157.7_Missense_Mutation_p.H434Q	NM_031303.2	NP_112593.2			katanin p60 subunit A-like 2											central_nervous_system(2)|endometrium(3)|large_intestine(8)|lung(8)|ovary(1)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(2)	27						TGATCTACCACTGGCTGCCTC	0.612																																						dbGAP											0			18											54.0	50.0	52.0					18																	44625704		2203	4300	6503	42879702	SO:0001583	missense	0			BC034999	CCDS32828.1	18q21.1	2010-04-21			ENSG00000167216	ENSG00000167216		"""ATPases / AAA-type"""	25387	protein-coding gene	gene with protein product		614697				12477932	Standard	NM_031303		Approved	MGC33211, DKFZP667C165	uc002lco.3	Q8IYT4		ENST00000245121.5:c.1086C>A	18.37:g.44625704C>A	ENSP00000245121:p.His362Gln	Somatic	223	0.89	2		3	0.00	0	WXS	Illumina HiSeq	Phase_IV	42879702	39	46.58	34		Missense_Mutation	SNP	HMMSmart_AAA,HMMPfam_AAA,superfamily_SSF52540	p.H362Q	ENST00000245121.5	37	c.1086	CCDS32828.1	18	.	.	.	.	.	.	.	.	.	.	C	11.52	1.664023	0.29604	.	.	ENSG00000167216	ENST00000356157;ENST00000245121	D;D	0.94650	-3.48;-3.48	4.75	1.89	0.25635	.	0.000000	0.85682	D	0.000000	D	0.89962	0.6867	L	0.43152	1.355	0.48087	D	0.999589	B	0.15930	0.015	B	0.12156	0.007	T	0.83208	-0.0075	10	0.27082	T	0.32	.	11.0751	0.48027	0.0:0.7189:0.0:0.2811	.	434	Q8IYT4	KATL2_HUMAN	Q	434;362	ENSP00000348478:H434Q;ENSP00000245121:H362Q	ENSP00000245121:H362Q	H	+	3	2	KATNAL2	42879702	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	0.780000	0.26760	0.531000	0.28639	0.555000	0.69702	CAC	-	HMMPfam_AAA,superfamily_SSF52540		0.612	KATNAL2-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	KATNAL2	protein_coding	OTTHUMT00000446138.2	C	NM_031303		42879702	+1	no_errors	NM_031303.1	genbank	human	provisional	54_36p	missense	SNP	0.999	A
WDR87	83889	genome.wustl.edu	37	19	38384123	38384123	+	Silent	SNP	A	A	T			TCGA-AB-2861-03B-01W-0728-08	TCGA-AB-2861-11B-01W-0729-08	A	A	A	T	A	A	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	6f4de42a-16ce-4536-b5a7-a9380540dda4	c2a59421-c7d4-4b57-a82d-ee675481ba9b	g.chr19:38384123A>T	ENST00000303868.5	-	4	2327	c.2103T>A	c.(2101-2103)atT>atA	p.I701I	WDR87_ENST00000447313.2_Silent_p.I740I	NM_031951.3	NP_114157.3	Q6ZQQ6	WDR87_HUMAN	WD repeat domain 87	701										NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|lung(2)|prostate(1)|skin(3)|stomach(1)	36						GGTCAAAGGCAATGGCCCGGT	0.478																																						dbGAP											0			19											60.0	51.0	54.0					19																	38384123		692	1591	2283	43075963	SO:0001819	synonymous_variant	0			AK128826	CCDS46063.1, CCDS74356.1	19q13.13	2013-01-09			ENSG00000171804	ENSG00000171804		"""WD repeat domain containing"""	29934	protein-coding gene	gene with protein product							Standard	XM_005259304		Approved	NYD-SP11	uc010efu.2	Q6ZQQ6	OTTHUMG00000048187	ENST00000303868.5:c.2103T>A	19.37:g.38384123A>T		Somatic	535	3.07	17		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	43075963	75	45.26	62	Q9BWV9	Silent	SNP	HMMSmart_SM00320,superfamily_WD40 repeat-like,PatternScan_C_TYPE_LECTIN_1,HMMPfam_WD40	p.I701	ENST00000303868.5	37	c.2103	CCDS46063.1	19																																																																																			-	NULL		0.478	WDR87-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	WDR87	protein_coding	OTTHUMT00000314628.2	A	XM_940478		43075963	-1	no_stop_codon	ENST00000303868	ensembl	human	known	54_36p	silent	SNP	1.000	T
GRWD1	83743	genome.wustl.edu	37	19	48954396	48954396	+	Missense_Mutation	SNP	G	G	A			TCGA-AB-2861-03B-01W-0728-08	TCGA-AB-2861-11B-01W-0729-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	6f4de42a-16ce-4536-b5a7-a9380540dda4	c2a59421-c7d4-4b57-a82d-ee675481ba9b	g.chr19:48954396G>A	ENST00000253237.5	+	6	1164	c.931G>A	c.(931-933)Gtc>Atc	p.V311I		NM_031485.3	NP_113673.3	Q9BQ67	GRWD1_HUMAN	glutamate-rich WD repeat containing 1	311						cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|stomach(1)	19		all_lung(116;0.000147)|Lung NSC(112;0.000251)|all_epithelial(76;0.000326)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000206)|all cancers(93;0.000207)|Epithelial(262;0.0125)|GBM - Glioblastoma multiforme(486;0.0222)		TGATGGGGACGTCAATGTCAT	0.632																																						dbGAP											0			19											48.0	51.0	50.0					19																	48954396		2203	4300	6503	53646208	SO:0001583	missense	0			AF337808	CCDS12720.1	19q13.33	2013-05-21				ENSG00000105447		"""WD repeat domain containing"""	21270	protein-coding gene	gene with protein product	regulator of ribosome biogenesis 1 homolog (S. cerevisiae)	610597				15885502	Standard	NM_031485		Approved	WDR28, GRWD, RRB1	uc002pjd.2	Q9BQ67		ENST00000253237.5:c.931G>A	19.37:g.48954396G>A	ENSP00000253237:p.Val311Ile	Somatic	122	0.00	0		48	31.43	22	WXS	Illumina HiSeq	Phase_IV	53646208	21	25.00	7	Q8TF59	Missense_Mutation	SNP	HMMSmart_SM00320,superfamily_WD40 repeat-like,PatternScan_WD_REPEATS_1,HMMPfam_WD40	p.V311I	ENST00000253237.5	37	c.931	CCDS12720.1	19	.	.	.	.	.	.	.	.	.	.	G	13.63	2.293376	0.40594	.	.	ENSG00000105447	ENST00000253237	T	0.67171	-0.25	3.84	2.8	0.32819	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.236850	0.35870	N	0.002930	T	0.55970	0.1954	L	0.35593	1.075	0.58432	D	0.999999	P	0.46952	0.887	P	0.44860	0.462	T	0.52675	-0.8544	10	0.33141	T	0.24	-32.8188	10.875	0.46906	0.0961:0.0:0.9039:0.0	.	311	Q9BQ67	GRWD1_HUMAN	I	311	ENSP00000253237:V311I	ENSP00000253237:V311I	V	+	1	0	GRWD1	53646208	0.998000	0.40836	0.822000	0.32727	0.309000	0.27889	2.836000	0.48183	0.989000	0.38761	-0.224000	0.12420	GTC	-	HMMSmart_SM00320,superfamily_WD40 repeat-like,HMMPfam_WD40		0.632	GRWD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	GRWD1	protein_coding	OTTHUMT00000466122.1	G	NM_031485		53646208	+1	no_errors	NM_031485.2	genbank	human	provisional	54_36p	missense	SNP	0.990	A
U2AF1	7307	genome.wustl.edu	37	21	44524456	44524456	+	Missense_Mutation	SNP	G	G	T	rs371769427		TCGA-AB-2861-03B-01W-0728-08	TCGA-AB-2861-11B-01W-0729-08	G	G	G	T	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	6f4de42a-16ce-4536-b5a7-a9380540dda4	c2a59421-c7d4-4b57-a82d-ee675481ba9b	g.chr21:44524456G>T	ENST00000291552.4	-	2	193	c.101C>A	c.(100-102)tCt>tAt	p.S34Y	U2AF1_ENST00000486519.1_5'UTR|U2AF1_ENST00000398137.1_5'UTR|U2AF1_ENST00000459639.1_5'UTR|U2AF1_ENST00000380276.2_Missense_Mutation_p.S34Y	NM_006758.2	NP_006749.1	Q01081	U2AF1_HUMAN	U2 small nuclear RNA auxiliary factor 1	34					gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	Cajal body (GO:0015030)|catalytic step 2 spliceosome (GO:0071013)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.S34F(45)|p.S34Y(12)		breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(111)|large_intestine(2)|lung(7)|prostate(2)|skin(1)	126						GTGCAACCGAGAGCACCTGTC	0.358			Mis		"""CLL, MDS"""																																	dbGAP		Dom	yes		21	21q22.3	7307	U2 small nuclear RNA auxiliary factor 1		L	57	Substitution - Missense(57)	haematopoietic_and_lymphoid_tissue(43)|lung(12)|endometrium(2)	21											67.0	64.0	65.0					21																	44524456		2203	4300	6503	43397525	SO:0001583	missense	0			BC001177	CCDS13694.1, CCDS33574.1, CCDS42948.1	21q22.3	2014-09-17	2006-04-11		ENSG00000160201	ENSG00000160201		"""RNA binding motif (RRM) containing"""	12453	protein-coding gene	gene with protein product		191317	"""U2(RNU2) small nuclear RNA auxiliary factor binding protein"", ""U2(RNU2) small nuclear RNA auxiliary factor 1"""	U2AFBP		8660980, 7956352	Standard	NM_006758		Approved	U2AF35, RNU2AF1, RN	uc002zdb.1	Q01081	OTTHUMG00000086836	ENST00000291552.4:c.101C>A	21.37:g.44524456G>T	ENSP00000291552:p.Ser34Tyr	Somatic	175	2.76	5		103	52.31	113	WXS	Illumina HiSeq	Phase_IV	43397525	15	33.33	8	Q701P4|Q71RF1	Missense_Mutation	SNP	HMMPfam_RRM_1,HMMSmart_RRM,HMMPfam_zf-CCCH,HMMSmart_ZnF_C3H1,superfamily_SSF54928	p.S34Y	ENST00000291552.4	37	c.101	CCDS13694.1	21	.	.	.	.	.	.	.	.	.	.	G	28.9	4.962845	0.92791	.	.	ENSG00000160201	ENST00000380276;ENST00000291552	T;T	0.46063	0.88;0.88	5.47	5.47	0.80525	Zinc finger, CCCH-type (3);	0.000000	0.85682	D	0.000000	T	0.77239	0.4101	H	0.96430	3.82	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.997;0.997	D	0.84864	0.0821	10	0.87932	D	0	-15.7954	19.3169	0.94218	0.0:0.0:1.0:0.0	.	34;34;34	Q69YM7;Q01081;Q701P4	.;U2AF1_HUMAN;.	Y	34	ENSP00000369629:S34Y;ENSP00000291552:S34Y	ENSP00000291552:S34Y	S	-	2	0	U2AF1	43397525	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.864000	0.92294	2.560000	0.86352	0.563000	0.77884	TCT	-	HMMPfam_zf-CCCH,HMMSmart_ZnF_C3H1		0.358	U2AF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	U2AF1	protein_coding	OTTHUMT00000195541.1	G	NM_006758		43397525	-1	no_errors	NM_001025203.1	genbank	human	reviewed	54_36p	missense	SNP	1.000	T
NPM1	4869	genome.wustl.edu	37	5	170837543	170837544	+	Frame_Shift_Ins	INS	-	-	TCTG	rs17850940		TCGA-AB-2861-03B-01W-0728-08	TCGA-AB-2861-11B-01W-0729-08	-	-	-	TCTG	-	-	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	6f4de42a-16ce-4536-b5a7-a9380540dda4	c2a59421-c7d4-4b57-a82d-ee675481ba9b	g.chr5:170837543_170837544insTCTG	ENST00000296930.5	+	11	1160_1161	c.859_860insTCTG	c.(859-861)ctcfs	p.-287fs	NPM1_ENST00000351986.6_Frame_Shift_Ins_p.-258fs|NPM1_ENST00000517671.1_Frame_Shift_Ins_p.-287fs	NM_002520.6	NP_002511.1	P06748	NPM_HUMAN	nucleophosmin (nucleolar phosphoprotein B23, numatrin)						cell aging (GO:0007569)|CENP-A containing nucleosome assembly (GO:0034080)|centrosome cycle (GO:0007098)|DNA repair (GO:0006281)|intracellular protein transport (GO:0006886)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of centrosome duplication (GO:0010826)|negative regulation of protein kinase activity by regulation of protein phosphorylation (GO:0044387)|nucleocytoplasmic transport (GO:0006913)|nucleosome assembly (GO:0006334)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of translation (GO:0045727)|protein localization (GO:0008104)|protein oligomerization (GO:0051259)|regulation of centriole replication (GO:0046599)|regulation of eIF2 alpha phosphorylation by dsRNA (GO:0060735)|regulation of endodeoxyribonuclease activity (GO:0032071)|regulation of endoribonuclease activity (GO:0060699)|response to stress (GO:0006950)|ribosome assembly (GO:0042255)|signal transduction (GO:0007165)|viral process (GO:0016032)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|spindle pole centrosome (GO:0031616)	histone binding (GO:0042393)|NF-kappaB binding (GO:0051059)|poly(A) RNA binding (GO:0044822)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|protein kinase inhibitor activity (GO:0004860)|ribosomal large subunit binding (GO:0043023)|ribosomal small subunit binding (GO:0043024)|RNA binding (GO:0003723)|Tat protein binding (GO:0030957)|transcription coactivator activity (GO:0003713)|unfolded protein binding (GO:0051082)	p.W288fs*12(7)|p.W288fs*>9(5)|p.L287fs*11(2)|p.L287F(1)	NPM1/ALK(632)	central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(4261)|kidney(1)|large_intestine(1)|lung(4)|skin(1)	4269	Renal(175;0.000159)|Lung NSC(126;0.00576)|all_lung(126;0.00963)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			TATTCAAGATCTCTGGCAGTGG	0.317			"""T, F """	"""ALK, RARA, MLF1"""	"""NHL, APL, AML"""																																	dbGAP		Dom	yes		5	5q35	4869	"""nucleophosmin (nucleolar phosphoprotein B23, numatrin)"""		L	15	Insertion - Frameshift(14)|Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(15)	5																																								170770149	SO:0001589	frameshift_variant	0			M26697	CCDS4376.1, CCDS4377.1, CCDS43399.1	5q35.1	2014-09-17			ENSG00000181163	ENSG00000181163			7910	protein-coding gene	gene with protein product	"""nucleolar phosphoprotein B23"", ""numatrin"", ""nucleophosmin/nucleoplasmin family, member 1"""	164040				8471164, 8122112	Standard	NM_002520		Approved	B23, NPM	uc003mbi.3	P06748	OTTHUMG00000130465	ENST00000296930.5:c.860_863dupTCTG	5.37:g.170837544_170837547dupTCTG	ENSP00000296930:p.Leu287fs	Somatic	NA	NA	NA		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	170770148	NA	NA	NA	A8K3N7|B5BU00|D3DQL6|P08693|Q12826|Q13440|Q13441|Q14115|Q5EU94|Q5EU95|Q5EU96|Q5EU97|Q5EU98|Q5EU99|Q6V962|Q8WTW5|Q96AT6|Q96DC4|Q96EA5|Q9BYG9|Q9UDJ7	Frame_Shift_Ins	INS	HMMPfam_Nucleoplasmin,superfamily_Nucleoplasmin-like core domain	p.W288fs	ENST00000296930.5	37	c.859_860	CCDS4376.1	5																																																																																			-	NULL		0.317	NPM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NPM1	protein_coding	OTTHUMT00000252858.2	-	NM_002520		170770149	+1	no_errors	NM_002520.1	genbank	human	validated	54_36p	frame_shift_ins	INS	1.000:1.000	TCTG
