#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_NormalRefReads_WU	i_NormalVAF_WU	i_NormalVarReads_WU	i_ORegAnno_bin	i_RNARefReads_WU	i_RNAVAF_WU	i_RNAVarReads_WU	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
DNMT3A	1788	genome.wustl.edu	37	2	25457243	25457243	+	Missense_Mutation	SNP	G	G	A	rs377577594		TCGA-AB-2981-03A-01D-0739-09	TCGA-AB-2981-11A-01D-0739-09	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	7212ba7b-f637-4f9f-b616-94109bfb8898	25cb572c-99a3-4fe6-8e7f-87ed37ab2d17	g.chr2:25457243G>A	ENST00000264709.3	-	23	2981	c.2644C>T	c.(2644-2646)Cgc>Tgc	p.R882C	DNMT3A_ENST00000402667.1_Missense_Mutation_p.R659C|DNMT3A_ENST00000321117.5_Missense_Mutation_p.R882C|DNMT3A_ENST00000380746.4_Missense_Mutation_p.R693C|DNMT3A_ENST00000474887.1_5'Flank	NM_175629.2	NP_783328.1	Q9Y6K1	DNM3A_HUMAN	DNA (cytosine-5-)-methyltransferase 3 alpha	882	SAM-dependent MTase C5-type. {ECO:0000255|PROSITE-ProRule:PRU01016}.		R -> C (in a patient with chronic myelomonocytic leukemia; somatic mutation). {ECO:0000269|PubMed:21828135}.|R -> H (in a patient with chronic myelomonocytic leukemia; somatic mutation). {ECO:0000269|PubMed:21828135}.|R -> P (in a patient with chronic myelomonocytic leukemia; somatic mutation). {ECO:0000269|PubMed:21828135}.		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)	p.R882C(93)|p.R882S(8)		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)					CTCGCCAAGCGGCTCATGTTG	0.597			"""Mis, F, N, S"""		AML																																	dbGAP		Rec	yes		2	2p23	1788	DNA (cytosine-5-)-methyltransferase 3 alpha		L	101	Substitution - Missense(101)	haematopoietic_and_lymphoid_tissue(101)	2						G	CYS/ARG,CYS/ARG,CYS/ARG	0,4406		0,0,2203	55.0	50.0	52.0		2644,2077,2644	5.7	1.0	2		52	4,8596		0,4,4296	no	missense,missense,missense	DNMT3A	NM_022552.3,NM_153759.2,NM_175629.1	180,180,180	0,4,6499	AA,AG,GG		0.0465,0.0,0.0308	probably-damaging,probably-damaging,probably-damaging	882/913,693/724,882/913	25457243	4,13002	2203	4300	6503	25310747	SO:0001583	missense	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.2644C>T	2.37:g.25457243G>A	ENSP00000264709:p.Arg882Cys	731	20.07	185		10	52.38	11	25310747	257	50.48	263	E9PEB8|Q86TE8|Q86XF5|Q8IZV0|Q8WXU9	Missense_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.R882C	ENST00000264709.3	37	c.2644	CCDS33157.1	2	.	.	.	.	.	.	.	.	.	.	G	22.0	4.224411	0.79576	0.0	4.65E-4	ENSG00000119772	ENST00000380746;ENST00000321117;ENST00000264709;ENST00000402667	D;D;D;D	0.97186	-4.28;-4.28;-4.28;-4.28	5.72	5.72	0.89469	.	0.000000	0.85682	D	0.000000	D	0.98538	0.9512	M	0.87180	2.865	0.80722	D	1	D;D	0.89917	1.0;1.0	D;P	0.65573	0.936;0.685	D	0.99425	1.0934	10	0.87932	D	0	-8.768	18.4404	0.90665	0.0:0.0:1.0:0.0	.	882;693	Q9Y6K1;E9PEB8	DNM3A_HUMAN;.	C	693;882;882;659	ENSP00000370122:R693C;ENSP00000324375:R882C;ENSP00000264709:R882C;ENSP00000384237:R659C	ENSP00000264709:R882C	R	-	1	0	DNMT3A	25310747	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.864000	0.99589	2.698000	0.92095	0.561000	0.74099	CGC	-	superfamily_S-adenosyl-L-methionine-dependent methyltransferases		0.597	DNMT3A-001	KNOWN	basic|CCDS	protein_coding	DNMT3A	protein_coding	OTTHUMT00000211587.1	G	NM_022552		25310747	-1	no_errors	NM_022552.3	genbank	human	reviewed	54_36p	missense	SNP	1.000	A
BBS7	55212	genome.wustl.edu	37	4	122791466	122791466	+	Start_Codon_SNP	SNP	C	C	A			TCGA-AB-2981-03A-01D-0739-09	TCGA-AB-2981-11A-01D-0739-09	C	C	C	A	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	7212ba7b-f637-4f9f-b616-94109bfb8898	25cb572c-99a3-4fe6-8e7f-87ed37ab2d17	g.chr4:122791466C>A	ENST00000264499.4	-	1	186	c.3G>T	c.(1-3)atG>atT	p.M1I	BBS7_ENST00000506636.1_Start_Codon_SNP_p.M1I|RP11-63B13.1_ENST00000567769.1_lincRNA	NM_176824.2	NP_789794.1	Q8IWZ6	BBS7_HUMAN	Bardet-Biedl syndrome 7	1					brain development (GO:0007420)|cilium morphogenesis (GO:0060271)|determination of left/right symmetry (GO:0007368)|digestive tract morphogenesis (GO:0048546)|eye development (GO:0001654)|fat cell differentiation (GO:0045444)|heart looping (GO:0001947)|limb development (GO:0060173)|melanosome transport (GO:0032402)|nonmotile primary cilium assembly (GO:0035058)|palate development (GO:0060021)|pigment granule aggregation in cell center (GO:0051877)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|protein transport (GO:0015031)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|smoothened signaling pathway (GO:0007224)|visual perception (GO:0007601)	axoneme (GO:0005930)|BBSome (GO:0034464)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	RNA polymerase II repressing transcription factor binding (GO:0001103)	p.M1I(1)		central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(11)|ovary(2)|prostate(1)|skin(2)	30						AAATCAGATCCATGATGACTA	0.617									Bardet-Biedl syndrome																													dbGAP											1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	4											57.0	57.0	57.0					4																	122791466		2203	4300	6503	123010916	SO:0001582	initiator_codon_variant	0	Familial Cancer Database	BBS, Bardet-Biedl syndrome, type 1-12: BBS1-12,Laurence-Moon-Biedl syndrome	AF521644	CCDS3724.1, CCDS54799.1	4q27	2013-01-08			ENSG00000138686	ENSG00000138686			18758	protein-coding gene	gene with protein product		607590					Standard	NM_176824		Approved	FLJ10715, BBS2L1	uc003ied.3	Q8IWZ6	OTTHUMG00000133076	ENST00000264499.4:c.3G>T	4.37:g.122791466C>A	ENSP00000264499:p.Met1Ile	677	15.54	126		7	46.15	6	123010916	297	47.44	269	Q4W5P8|Q8N581|Q9NVI4	Missense_Mutation	SNP	NULL	p.M1I	ENST00000264499.4	37	c.3	CCDS3724.1	4	.	.	.	.	.	.	.	.	.	.	C	21.4	4.146385	0.77888	.	.	ENSG00000138686	ENST00000264499;ENST00000506636	D;D	0.92299	-3.01;-3.01	4.52	4.52	0.55395	.	0.040901	0.85682	D	0.000000	D	0.95686	0.8597	.	.	.	0.53688	D	0.999974	D	0.67145	0.996	D	0.64776	0.929	D	0.96293	0.9215	9	0.87932	D	0	-7.0406	16.8837	0.86070	0.0:1.0:0.0:0.0	.	1	Q8IWZ6	BBS7_HUMAN	I	1	ENSP00000264499:M1I;ENSP00000423626:M1I	ENSP00000264499:M1I	M	-	3	0	BBS7	123010916	1.000000	0.71417	1.000000	0.80357	0.200000	0.23975	4.836000	0.62789	2.456000	0.83038	0.491000	0.48974	ATG	-	NULL		0.617	BBS7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	BBS7	protein_coding	OTTHUMT00000256716.1	C		Missense_Mutation	123010916	-1	no_errors	NM_176824.2	genbank	human	reviewed	54_36p	missense	SNP	1.000	A
ZDHHC11	79844	genome.wustl.edu	37	5	850655	850655	+	Silent	SNP	C	C	T			TCGA-AB-2981-03A-01D-0739-09	TCGA-AB-2981-11A-01D-0739-09	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	7212ba7b-f637-4f9f-b616-94109bfb8898	25cb572c-99a3-4fe6-8e7f-87ed37ab2d17	g.chr5:850655C>T	ENST00000283441.8	-	1	446	c.63G>A	c.(61-63)aaG>aaA	p.K21K	ZDHHC11_ENST00000424784.2_Silent_p.K21K	NM_024786.2	NP_079062.1	Q9H8X9	ZDH11_HUMAN	zinc finger, DHHC-type containing 11	21						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)	p.K21K(2)		haematopoietic_and_lymphoid_tissue(1)|liver(1)|lung(10)|pancreas(1)|prostate(5)|skin(2)|urinary_tract(1)	21			Epithelial(17;0.000445)|all cancers(22;0.00176)|OV - Ovarian serous cystadenocarcinoma(19;0.00227)|Lung(60;0.0863)			GCAAGACCAGCTTTTCATTAT	0.602																																						dbGAP											2	Substitution - coding silent(2)	haematopoietic_and_lymphoid_tissue(2)	5											94.0	95.0	94.0					5																	850655		2203	4300	6503	903655	SO:0001819	synonymous_variant	0			AK023215	CCDS3857.1	5p15.2	2011-02-09			ENSG00000188818	ENSG00000188818		"""Zinc fingers, DHHC-type"""	19158	protein-coding gene	gene with protein product							Standard	NM_024786		Approved	ZNF399, FLJ13153	uc011cma.1	Q9H8X9	OTTHUMG00000090319	ENST00000283441.8:c.63G>A	5.37:g.850655C>T		134	17.07	28		NA	NA	NA	903655	92	52.33	101	Q6UWR9	Silent	SNP	HMMPfam_zf-DHHC	p.K21	ENST00000283441.8	37	c.63	CCDS3857.1	5																																																																																			-	NULL		0.602	ZDHHC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ZDHHC11	protein_coding	OTTHUMT00000206681.3	C	NM_024786		903655	-1	no_errors	NM_024786.2	genbank	human	validated	54_36p	silent	SNP	0.002	T
NEMF	9147	genome.wustl.edu	37	14	50262635	50262635	+	Silent	SNP	A	A	G			TCGA-AB-2981-03A-01D-0739-09	TCGA-AB-2981-11A-01D-0739-09	A	A	A	G	A	A	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	7212ba7b-f637-4f9f-b616-94109bfb8898	25cb572c-99a3-4fe6-8e7f-87ed37ab2d17	g.chr14:50262635A>G	ENST00000298310.5	-	26	2942	c.2493T>C	c.(2491-2493)agT>agC	p.S831S	NEMF_ENST00000556925.1_5'UTR|NEMF_ENST00000382135.2_Silent_p.S31S|NEMF_ENST00000546046.1_Silent_p.S810S|NEMF_ENST00000545773.1_Silent_p.S789S			O60524	NEMF_HUMAN	nuclear export mediator factor	831					nuclear export (GO:0051168)	nucleus (GO:0005634)		p.S831S(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(13)|liver(1)|lung(9)|prostate(1)|skin(1)|urinary_tract(1)	36						CTCCTGAGTCACTTGGAAGTT	0.338																																						dbGAP											1	Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(1)	14											133.0	125.0	128.0					14																	50262635		2202	4300	6502	49332385	SO:0001819	synonymous_variant	0			AF039687	CCDS9694.1	14q21.3	2012-11-19	2011-01-31	2011-01-31	ENSG00000165525	ENSG00000165525			10663	protein-coding gene	gene with protein product		608378	"""serologically defined colon cancer antigen 1"""	SDCCAG1		9610721, 10575219	Standard	XR_429334		Approved	NY-CO-1, FLJ10051	uc001wxc.3	O60524	OTTHUMG00000170857	ENST00000298310.5:c.2493T>C	14.37:g.50262635A>G		394	12.94	59		37	47.14	33	49332385	136	43.10	103	A0JLQ3|B3KSK1|B4DDL3|B4DHA9|B4E3F3|Q32Q66|Q8WW70|Q9NWG1	Silent	SNP	HMMPfam_DUF814,HMMPfam_FbpA	p.S831	ENST00000298310.5	37	c.2493	CCDS9694.1	14																																																																																			-	NULL		0.338	NEMF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SDCCAG1	protein_coding	OTTHUMT00000410798.1	A	NM_004713		49332385	-1	no_errors	NM_004713.3	genbank	human	validated	54_36p	silent	SNP	0.789	G
PTPN9	5780	genome.wustl.edu	37	15	75836563	75836563	+	Intron	SNP	C	C	T	rs540917851		TCGA-AB-2981-03A-01D-0739-09	TCGA-AB-2981-11A-01D-0739-09	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	7212ba7b-f637-4f9f-b616-94109bfb8898	25cb572c-99a3-4fe6-8e7f-87ed37ab2d17	g.chr15:75836563C>T	ENST00000306726.2	-	2	576				CTD-2323K18.1_ENST00000568707.1_RNA	NM_002833.2	NP_002824.1	P43378	PTN9_HUMAN	protein tyrosine phosphatase, non-receptor type 9						peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)	non-membrane spanning protein tyrosine phosphatase activity (GO:0004726)|protein tyrosine phosphatase activity (GO:0004725)			central_nervous_system(1)|endometrium(4)|large_intestine(4)|lung(9)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						CGGAAAAAAACGAAACCTGCC	0.463																																						dbGAP											0			15																																								73623618	SO:0001627	intron_variant	0				CCDS10280.1	15q23	2011-06-09			ENSG00000169410	ENSG00000169410		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"""	9661	protein-coding gene	gene with protein product		600768				1557404	Standard	NM_002833		Approved	MEG2	uc002bal.3	P43378	OTTHUMG00000142838	ENST00000306726.2:c.64-16961G>A	15.37:g.75836563C>T		546	14.51	93		7	30.00	3	73623618	161	44.29	128	Q53XR9	Silent	SNP	PatternScan_LECTIN_LEGUME_BETA	p.S130	ENST00000306726.2	37	c.390	CCDS10280.1	15																																																																																			-	NULL		0.463	PTPN9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	LOC100128562	protein_coding	OTTHUMT00000286474.1	C			73623618	-1	no_errors	XM_001726845.1	genbank	human	model	54_36p	silent	SNP	0.000	T
FAM57B	83723	genome.wustl.edu	37	16	30036568	30036568	+	Missense_Mutation	SNP	C	C	T	rs367744777		TCGA-AB-2981-03A-01D-0739-09	TCGA-AB-2981-11A-01D-0739-09	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	7212ba7b-f637-4f9f-b616-94109bfb8898	25cb572c-99a3-4fe6-8e7f-87ed37ab2d17	g.chr16:30036568C>T	ENST00000380495.4	-	5	1492	c.761G>A	c.(760-762)cGt>cAt	p.R254H	FAM57B_ENST00000564806.1_3'UTR|FAM57B_ENST00000279389.4_Missense_Mutation_p.R204H	NM_031478.4	NP_113666.2	Q71RH2	FA57B_HUMAN	family with sequence similarity 57, member B	254	TLC. {ECO:0000255|PROSITE- ProRule:PRU00205}.				ceramide biosynthetic process (GO:0046513)|negative regulation of fat cell differentiation (GO:0045599)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	sphingosine N-acyltransferase activity (GO:0050291)	p.R254H(1)		central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(4)|lung(5)|upper_aerodigestive_tract(1)	14						GCAGGCCCCACGGCAGATGAG	0.756																																						dbGAP											1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	16						C	HIS/ARG	0,3878		0,0,1939	14.0	14.0	14.0		761	4.9	1.0	16		14	1,7615		0,1,3807	no	missense	FAM57B	NM_031478.4	29	0,1,5746	TT,TC,CC		0.0131,0.0,0.0087	probably-damaging	254/275	30036568	1,11493	1939	3808	5747	29944069	SO:0001583	missense	0			AF370365	CCDS10667.2	16p11.2	2013-02-19			ENSG00000149926	ENSG00000149926			25295	protein-coding gene	gene with protein product		615175				11230166, 23275342	Standard	NM_031478		Approved	DKFZP434I2117	uc002dvt.3	Q71RH2	OTTHUMG00000132105	ENST00000380495.4:c.761G>A	16.37:g.30036568C>T	ENSP00000369863:p.Arg254His	91	22.22	26		NA	NA	NA	29944069	31	48.33	29	Q9H0J1	Missense_Mutation	SNP	HMMPfam_TRAM_LAG1_CLN8,HMMSmart_SM00724	p.R254H	ENST00000380495.4	37	c.761	CCDS10667.2	16	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	24.7|24.7	4.556900|4.556900	0.86231|0.86231	0.0|0.0	1.31E-4|1.31E-4	ENSG00000149926|ENSG00000149926	ENST00000380495|ENST00000279389	D|.	0.87103|.	-2.21|.	4.92|4.92	4.92|4.92	0.64577|0.64577	TRAM/LAG1/CLN8 homology domain (3);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.73659|0.73659	0.3615|0.3615	M|M	0.80982|0.80982	2.52|2.52	0.80722|0.80722	D|D	1|1	D|.	0.89917|.	1.0|.	D|.	0.81914|.	0.995|.	T|T	0.75439|0.75439	-0.3317|-0.3317	10|5	0.87932|.	D|.	0|.	-9.1085|-9.1085	10.5465|10.5465	0.45062|0.45062	0.0:0.9088:0.0:0.0912|0.0:0.9088:0.0:0.0912	.|.	254|.	Q71RH2|.	FA57B_HUMAN|.	H|M	254|221	ENSP00000369863:R254H|.	ENSP00000369863:R254H|.	R|V	-|-	2|1	0|0	FAM57B|FAM57B	29944069|29944069	0.905000|0.905000	0.30787|0.30787	0.998000|0.998000	0.56505|0.56505	0.977000|0.977000	0.68977|0.68977	1.884000|1.884000	0.39668|0.39668	2.255000|2.255000	0.74692|0.74692	0.655000|0.655000	0.94253|0.94253	CGT|GTG	-	HMMPfam_TRAM_LAG1_CLN8,HMMSmart_SM00724		0.756	FAM57B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	FAM57B	protein_coding	OTTHUMT00000255142.2	C	NM_031478		29944069	-1	no_errors	NM_031478.4	genbank	human	validated	54_36p	missense	SNP	0.997	T
NPM1	4869	genome.wustl.edu	37	5	170837547	170837548	+	Frame_Shift_Ins	INS	-	-	TCTG			TCGA-AB-2981-03A-01D-0739-09	TCGA-AB-2981-11A-01D-0739-09	-	-	-	TCTG	-	-	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	7212ba7b-f637-4f9f-b616-94109bfb8898	25cb572c-99a3-4fe6-8e7f-87ed37ab2d17	g.chr5:170837547_170837548insTCTG	ENST00000296930.5	+	11	1164_1165	c.863_864insTCTG	c.(862-867)tggcagfs	p.WQ288fs	NPM1_ENST00000517671.1_Frame_Shift_Ins_p.WQ288fs|NPM1_ENST00000351986.6_Frame_Shift_Ins_p.WQ259fs	NM_002520.6	NP_002511.1	P06748	NPM_HUMAN	nucleophosmin (nucleolar phosphoprotein B23, numatrin)	288	Required for nucleolar localization.			WQWRKSL -> CLAVEEVSLRK (in Ref. 6; AAW67752/AAW67755). {ECO:0000305}.|WQWRKSL -> CMAVEEVSLRK (in Ref. 6; AAW67753 and 7; ABC40399). {ECO:0000305}.|WQWRKSL -> CVAVEEVSLRK (in Ref. 6; AAW67754). {ECO:0000305}.	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(2114)|p.W288fs*10(9)|p.Q289fs*11(3)|p.W288*(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)			CAAGATCTCTGGCAGTGGAGGA	0.312			"""T, F """	"""ALK, RARA, MLF1"""	"""NHL, APL, AML"""																																	dbGAP		Dom	yes		5	5q35	4869	"""nucleophosmin (nucleolar phosphoprotein B23, numatrin)"""		L	2127	Insertion - Frameshift(2118)|Complex - frameshift(8)|Substitution - Nonsense(1)	haematopoietic_and_lymphoid_tissue(2127)	5																																								170770153	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.Trp288fs	NA	NA	NA		NA	NA	NA	170770152	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.863_864	CCDS4376.1	5																																																																																			-	NULL		0.312	NPM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NPM1	protein_coding	OTTHUMT00000252858.2	-	NM_002520		170770153	+1	no_errors	NM_002520.1	genbank	human	validated	54_36p	frame_shift_ins	INS	1.000:1.000	TCTG
FLT3	2322	genome.wustl.edu	37	13	28608311	28608312	+	In_Frame_Ins	INS	-	-	ATTCATATTCTCTGAAATCAACGTAGAAGTACTCATTATCTGAGGAGCCGGCCA			TCGA-AB-2981-03A-01D-0739-09	TCGA-AB-2981-11A-01D-0739-09	-	-	-	ATTCATATTCTCTGAAATCAACGTAGAAGTACTCATTATCTGAGGAGCCGGCCA	-	-	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	7212ba7b-f637-4f9f-b616-94109bfb8898	25cb572c-99a3-4fe6-8e7f-87ed37ab2d17	g.chr13:28608311_28608312insATTCATATTCTCTGAAATCAACGTAGAAGTACTCATTATCTGAGGAGCCGGCCA	ENST00000241453.7	-	14	1825_1826	c.1744_1745insTGGCCGGCTCCTCAGATAATGAGTACTTCTACGTTGATTTCAGAGAATATGAAT	c.(1744-1746)acc>aTGGCCGGCTCCTCAGATAATGAGTACTTCTACGTTGATTTCAGAGAATATGAATcc	p.582_582T>MAGSSDNEYFYVDFREYES	FLT3_ENST00000380982.4_In_Frame_Ins_p.582_582T>MAGSSDNEYFYVDFREYES|FLT3_ENST00000537084.1_In_Frame_Ins_p.582_582T>MAGSSDNEYFYVDFREYES	NM_004119.2	NP_004110.2	P36888	FLT3_HUMAN	fms-related tyrosine kinase 3	582					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)			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)	TGAGGAGCCGGTCACCTGTACC	0.381			"""Mis, O"""		"""AML, ALL"""																																	dbGAP		Dom	yes		13	13q12	2322	fms-related tyrosine kinase 3		L	0			13																																								27506312	SO:0001652	inframe_insertion	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.1744_1745insTGGCCGGCTCCTCAGATAATGAGTACTTCTACGTTGATTTCAGAGAATATGAAT	13.37:g.28608311_28608312insATTCATATTCTCTGAAATCAACGTAGAAGTACTCATTATCTGAGGAGCCGGCCA	ENSP00000241453:p.Thr582delinsMetAlaGlySerSerAspAsnGluTyrPheTyrValAspPheArgGluTyrGluSer	NA	NA	NA		NA	NA	NA	27506311	NA	NA	NA	A0AVG9|B7ZLT7|B7ZLT8|F5H0A0|Q13414	In_Frame_Ins	INS	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.T582in_frame_insMAGSSDNEYFYVDFREYES	ENST00000241453.7	37	c.1745_1744	CCDS31953.1	13																																																																																			-	superfamily_Kinase_like		0.381	FLT3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	FLT3	protein_coding	OTTHUMT00000044319.2	-			27506312	-1	no_errors	NM_004119.2	genbank	human	reviewed	54_36p	in_frame_ins	INS	0.986:0.998	ATTCATATTCTCTGAAATCAACGTAGAAGTACTCATTATCTGAGGAGCCGGCCA
