#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
Unknown	0	genome.wustl.edu	37	Unknown	0	0	+	IGR	SNP	G	G	A			TCGA-AB-2934-03A-01W-0755-09	TCGA-AB-2934-11A-01W-0755-09	G	G	G	A	G	G	Verified	Invalid:failed_liftOver	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	7791e140-fe03-44d0-8250-47826ea993df	c98ddb47-f34c-4646-a434-5f8e6f6b5853	g.chrUnknown:0G>A								None (None upstream) : None (None downstream)																								0.0																																						dbGAP											0			MT																																								15651	SO:0001628	intergenic_variant	0																															Unknown.37:g.0G>A		3556	2.58	95		NA	NA	NA	15651	3813	15.61	714		Missense_Mutation	SNP	HMMPfam_Cytochrom_B_N,HMMPfam_Cytochrom_B_C,superfamily_Cytochrome_b/b6_C,superfamily_Transmembr_di-haem_cytochrome	p.A302T		37	c.904		MT																																																																																			-	HMMPfam_Cytochrom_B_C,superfamily_Cytochrome_b/b6_C	0	0					MT-CYB			G			15651	+1	no_stop_codon:bad_bp_length_for_coding_region	ENST00000361789	ensembl	human	known	54_36p	missense	SNP	NULL	A
IL1RAPL2	26280	genome.wustl.edu	37	X	104650902	104650902	+	Intron	SNP	C	C	T			TCGA-AB-2934-03A-01W-0755-09	TCGA-AB-2934-11A-01W-0755-09	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	7791e140-fe03-44d0-8250-47826ea993df	c98ddb47-f34c-4646-a434-5f8e6f6b5853	g.chrX:104650902C>T	ENST00000372582.1	+	6	1453				IL1RAPL2_ENST00000344799.4_Intron	NM_017416.1	NP_059112.1	Q9NP60	IRPL2_HUMAN	interleukin 1 receptor accessory protein-like 2						central nervous system development (GO:0007417)|cytokine-mediated signaling pathway (GO:0019221)	integral component of membrane (GO:0016021)	interleukin-1 receptor activity (GO:0004908)|interleukin-1, Type II, blocking receptor activity (GO:0004910)			breast(3)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(14)|lung(23)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49						TGCTGGCCCACATGTTTAAGG	0.373																																						dbGAP											0			X																																								104537558	SO:0001627	intron_variant	0			AF181285	CCDS14517.1	Xq22	2013-01-11			ENSG00000189108	ENSG00000189108		"""Interleukins and interleukin receptors"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5997	protein-coding gene	gene with protein product		300277				10757639	Standard	NM_017416		Approved	IL-1R9, TIGIRR-1, IL1RAPL-2, IL1R9	uc004elz.1	Q9NP60	OTTHUMG00000022141	ENST00000372582.1:c.698-77403C>T	X.37:g.104650902C>T		59	9.23	6		8	0.00	0	104537558	15	87.70	107	Q2M3U3|Q9NZN0	Silent	SNP	HMMSmart_BTB,HMMPfam_K_tetra,superfamily_BTB/POZ_fold	p.H118	ENST00000372582.1	37	c.354	CCDS14517.1	X																																																																																			-	HMMSmart_BTB,HMMPfam_K_tetra,superfamily_BTB/POZ_fold		0.373	IL1RAPL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	KCTD9P2	protein_coding	OTTHUMT00000057785.1	C	NM_017416		104537558	+1	no_errors	ENST00000313275	ensembl	human	known	54_36p	silent	SNP	1.000	T
DNMT3A	1788	genome.wustl.edu	37	2	25463286	25463286	+	Missense_Mutation	SNP	C	C	T	rs139293773		TCGA-AB-2934-03A-01W-0755-09	TCGA-AB-2934-11A-01W-0755-09	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	7791e140-fe03-44d0-8250-47826ea993df	c98ddb47-f34c-4646-a434-5f8e6f6b5853	g.chr2:25463286C>T	ENST00000264709.3	-	19	2544	c.2207G>A	c.(2206-2208)cGc>cAc	p.R736H	DNMT3A_ENST00000380746.4_Missense_Mutation_p.R547H|DNMT3A_ENST00000321117.5_Missense_Mutation_p.R736H|DNMT3A_ENST00000402667.1_Missense_Mutation_p.R513H|DNMT3A_ENST00000474887.1_5'UTR	NM_175629.2	NP_783328.1	Q9Y6K1	DNM3A_HUMAN	DNA (cytosine-5-)-methyltransferase 3 alpha	736	SAM-dependent MTase C5-type. {ECO:0000255|PROSITE-ProRule:PRU01016}.				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.R736H(3)		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)					ATGCAGGAGGCGGTAGAACTC	0.587			"""Mis, F, N, S"""		AML																																	dbGAP		Rec	yes		2	2p23	1788	DNA (cytosine-5-)-methyltransferase 3 alpha		L	3	Substitution - Missense(3)	haematopoietic_and_lymphoid_tissue(3)	2						C	HIS/ARG,HIS/ARG,HIS/ARG	0,4406		0,0,2203	72.0	70.0	71.0		2207,1640,2207	4.5	1.0	2	dbSNP_134	71	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense	DNMT3A	NM_022552.3,NM_153759.2,NM_175629.1	29,29,29	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging	736/913,547/724,736/913	25463286	1,13005	2203	4300	6503	25316790	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.2207G>A	2.37:g.25463286C>T	ENSP00000264709:p.Arg736His	47	11.32	6		25	55.36	31	25316790	34	41.27	26	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.R736H	ENST00000264709.3	37	c.2207	CCDS33157.1	2	.	.	.	.	.	.	.	.	.	.	C	21.5	4.165867	0.78339	0.0	1.16E-4	ENSG00000119772	ENST00000380746;ENST00000321117;ENST00000264709;ENST00000402667	D;D;D;D	0.88431	-2.38;-2.38;-2.38;-2.38	5.38	4.5	0.54988	.	0.047243	0.85682	N	0.000000	D	0.91981	0.7460	M	0.73372	2.23	0.80722	D	1	D;P	0.69078	0.997;0.704	P;B	0.62298	0.9;0.151	D	0.89917	0.4056	10	0.22706	T	0.39	-9.1764	12.5433	0.56184	0.0:0.9186:0.0:0.0814	.	736;547	Q9Y6K1;E9PEB8	DNM3A_HUMAN;.	H	547;736;736;513	ENSP00000370122:R547H;ENSP00000324375:R736H;ENSP00000264709:R736H;ENSP00000384237:R513H	ENSP00000264709:R736H	R	-	2	0	DNMT3A	25316790	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.732000	0.47352	1.277000	0.44412	0.561000	0.74099	CGC	-	HMMPfam_DNA_methylase,superfamily_S-adenosyl-L-methionine-dependent methyltransferases		0.587	DNMT3A-001	KNOWN	basic|CCDS	protein_coding	DNMT3A	protein_coding	OTTHUMT00000211587.1	C	NM_022552		25316790	-1	no_errors	NM_022552.3	genbank	human	reviewed	54_36p	missense	SNP	1.000	T
DNMT3A	1788	genome.wustl.edu	37	2	25464576	25464576	+	Splice_Site	SNP	C	C	A			TCGA-AB-2934-03A-01W-0755-09	TCGA-AB-2934-11A-01W-0755-09	C	C	C	A	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	7791e140-fe03-44d0-8250-47826ea993df	c98ddb47-f34c-4646-a434-5f8e6f6b5853	g.chr2:25464576C>A	ENST00000264709.3	-	17	2274	c.1937G>T	c.(1936-1938)gGg>gTg	p.G646V	DNMT3A_ENST00000380746.4_Splice_Site_p.G457V|DNMT3A_ENST00000321117.5_Splice_Site_p.G646V|DNMT3A_ENST00000402667.1_Splice_Site_p.G423V|DNMT3A_ENST00000474887.1_5'UTR	NM_175629.2	NP_783328.1	Q9Y6K1	DNM3A_HUMAN	DNA (cytosine-5-)-methyltransferase 3 alpha	646	SAM-dependent MTase C5-type. {ECO:0000255|PROSITE-ProRule:PRU01016}.				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)					CACCAGGAGCCCTGCACCAGC	0.642			"""Mis, F, N, S"""		AML																																	dbGAP		Rec	yes		2	2p23	1788	DNA (cytosine-5-)-methyltransferase 3 alpha		L	0			2											98.0	56.0	70.0					2																	25464576		2203	4300	6503	25318080	SO:0001630	splice_region_variant	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.1937-1G>T	2.37:g.25464576C>A		30	3.23	1		27	34.15	14	25318080	60	37.50	36	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.G646V	ENST00000264709.3	37	c.1937	CCDS33157.1	2	.	.	.	.	.	.	.	.	.	.	C	24.4	4.528020	0.85706	.	.	ENSG00000119772	ENST00000380746;ENST00000321117;ENST00000264709;ENST00000402667	D;D;D;D	0.83673	-1.75;-1.75;-1.75;-1.75	5.18	5.18	0.71444	.	0.000000	0.85682	D	0.000000	D	0.93216	0.7839	M	0.92738	3.34	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.94755	0.7931	10	0.87932	D	0	.	17.2626	0.87075	0.0:1.0:0.0:0.0	.	646;457	Q9Y6K1;E9PEB8	DNM3A_HUMAN;.	V	457;646;646;423	ENSP00000370122:G457V;ENSP00000324375:G646V;ENSP00000264709:G646V;ENSP00000384237:G423V	ENSP00000264709:G646V	G	-	2	0	DNMT3A	25318080	1.000000	0.71417	1.000000	0.80357	0.835000	0.47333	7.818000	0.86416	2.422000	0.82143	0.561000	0.74099	GGG	-	superfamily_S-adenosyl-L-methionine-dependent methyltransferases		0.642	DNMT3A-001	KNOWN	basic|CCDS	protein_coding	DNMT3A	protein_coding	OTTHUMT00000211587.1	C	NM_022552	Missense_Mutation	25318080	-1	no_errors	NM_022552.3	genbank	human	reviewed	54_36p	missense	SNP	1.000	A
CYBRD1	79901	genome.wustl.edu	37	2	172411097	172411097	+	Silent	SNP	G	G	T			TCGA-AB-2934-03A-01W-0755-09	TCGA-AB-2934-11A-01W-0755-09	G	G	G	T	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	7791e140-fe03-44d0-8250-47826ea993df	c98ddb47-f34c-4646-a434-5f8e6f6b5853	g.chr2:172411097G>T	ENST00000321348.4	+	4	819	c.621G>T	c.(619-621)ctG>ctT	p.L207L	CYBRD1_ENST00000375252.3_Missense_Mutation_p.D138Y|CYBRD1_ENST00000409484.1_Silent_p.L149L	NM_024843.3	NP_079119.3	Q53TN4	CYBR1_HUMAN	cytochrome b reductase 1	207	Cytochrome b561. {ECO:0000255|PROSITE- ProRule:PRU00242}.				cellular iron ion homeostasis (GO:0006879)|response to iron ion (GO:0010039)|transmembrane transport (GO:0055085)	brush border membrane (GO:0031526)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ferric-chelate reductase activity (GO:0000293)|metal ion binding (GO:0046872)|oxidoreductase activity, oxidizing metal ions (GO:0016722)			endometrium(1)|kidney(1)|large_intestine(3)|liver(2)|lung(3)	10						TTGGCCTTCTGATCCTGGTGT	0.448																																						dbGAP											0			2											84.0	78.0	80.0					2																	172411097		2203	4300	6503	172119343	SO:0001819	synonymous_variant	0			AK027115	CCDS2244.1, CCDS46449.1, CCDS58736.1	2q31	2013-03-14			ENSG00000071967	ENSG00000071967		"""Cytochrome b genes"""	20797	protein-coding gene	gene with protein product	"""ferric-chelate reductase 3"", ""cytochrome b561 family, member A2"""	605745				11230685	Standard	NM_001127383		Approved	DCYTB, FLJ23462, FRRS3, CYB561A2	uc002ugy.4	Q53TN4	OTTHUMG00000132260	ENST00000321348.4:c.621G>T	2.37:g.172411097G>T		66	12.00	9		63	31.52	29	172119343	130	45.23	109	B2RE79|B4DWD7|Q6KC16|Q6KC17|Q6P147|Q6ZR51|Q9H0Q8|Q9H5G5	Missense_Mutation	SNP	HMMPfam_Cytochrom_B561,PatternScan_SPASE_I_1	p.D138Y	ENST00000321348.4	37	c.412	CCDS2244.1	2	.	.	.	.	.	.	.	.	.	.	G	17.50	3.406350	0.62288	.	.	ENSG00000071967	ENST00000375252	.	.	.	5.16	2.21	0.28008	.	.	.	.	.	T	0.29588	0.0738	.	.	.	0.27067	N	0.963407	B	0.14438	0.01	B	0.14023	0.01	T	0.25745	-1.0123	7	0.87932	D	0	-3.1487	5.347	0.16014	0.0725:0.1909:0.5328:0.2037	.	138	Q53TN4-2	.	Y	138	.	ENSP00000364401:D138Y	D	+	1	0	CYBRD1	172119343	0.992000	0.36948	0.983000	0.44433	0.892000	0.51952	0.894000	0.28350	1.178000	0.42870	-0.140000	0.14226	GAT	-	NULL		0.448	CYBRD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CYBRD1	protein_coding	OTTHUMT00000255344.2	G	NM_024843		172119343	+1	no_errors	ENST00000375252	ensembl	human	known	54_36p	missense	SNP	0.981	T
KCNH2	3757	genome.wustl.edu	37	7	150649894	150649894	+	Silent	SNP	T	T	G			TCGA-AB-2934-03A-01W-0755-09	TCGA-AB-2934-11A-01W-0755-09	T	T	T	G	T	T	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	7791e140-fe03-44d0-8250-47826ea993df	c98ddb47-f34c-4646-a434-5f8e6f6b5853	g.chr7:150649894T>G	ENST00000262186.5	-	6	1577	c.1176A>C	c.(1174-1176)gcA>gcC	p.A392A	KCNH2_ENST00000392968.2_Silent_p.A296A|KCNH2_ENST00000430723.3_Silent_p.A392A|KCNH2_ENST00000330883.4_Silent_p.A52A	NM_000238.3	NP_000229.1	Q12809	KCNH2_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 2	392					cardiac muscle contraction (GO:0060048)|cellular response to drug (GO:0035690)|membrane depolarization during action potential (GO:0086010)|membrane repolarization during action potential (GO:0086011)|membrane repolarization during cardiac muscle cell action potential (GO:0086013)|negative regulation of potassium ion export (GO:1902303)|negative regulation of potassium ion transmembrane transport (GO:1901380)|positive regulation of potassium ion transmembrane transport (GO:1901381)|potassium ion export (GO:0071435)|potassium ion homeostasis (GO:0055075)|potassium ion transmembrane transport (GO:0071805)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of heart rate by hormone (GO:0003064)|regulation of membrane potential (GO:0042391)|regulation of membrane repolarization (GO:0060306)|regulation of potassium ion transmembrane transport (GO:1901379)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|synaptic transmission (GO:0007268)|ventricular cardiac muscle cell action potential (GO:0086005)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|identical protein binding (GO:0042802)|inward rectifier potassium channel activity (GO:0005242)|phosphorelay sensor kinase activity (GO:0000155)|protein homodimerization activity (GO:0042803)|ubiquitin protein ligase binding (GO:0031625)|voltage-gated potassium channel activity (GO:0005249)|voltage-gated potassium channel activity involved in ventricular cardiac muscle cell action potential repolarization (GO:1902282)			NS(1)|cervix(1)|endometrium(10)|kidney(1)|large_intestine(5)|lung(14)|ovary(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)	42	all_neural(206;0.219)		OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)	Alfuzosin(DB00346)|Amiodarone(DB01118)|Amsacrine(DB00276)|Astemizole(DB00637)|Carvedilol(DB01136)|Chlorpromazine(DB00477)|Cisapride(DB00604)|Dofetilide(DB00204)|Doxazosin(DB00590)|Doxepin(DB01142)|Dronedarone(DB04855)|Halofantrine(DB01218)|Ibutilide(DB00308)|Imipramine(DB00458)|Miconazole(DB01110)|Pimozide(DB01100)|Prazosin(DB00457)|Propafenone(DB01182)|Quinidine(DB00908)|Sertindole(DB06144)|Sotalol(DB00489)|Terazosin(DB01162)|Thioridazine(DB00679)|Verapamil(DB00661)	GGATGCGCGGTGCCTGCAGCT	0.657																																					GBM(137;110 1844 13671 20123 45161)	dbGAP											0			7											107.0	87.0	94.0					7																	150649894		2203	4300	6503	150280827	SO:0001819	synonymous_variant	0			U04270	CCDS5910.1, CCDS5911.1	7q36.1	2014-09-17			ENSG00000055118	ENSG00000055118		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6251	protein-coding gene	gene with protein product		152427		LQT2		18616963, 7842012, 8159766, 16382104	Standard	NM_000238		Approved	Kv11.1, HERG, erg1	uc003wic.3	Q12809	OTTHUMG00000158341	ENST00000262186.5:c.1176A>C	7.37:g.150649894T>G		42	6.67	3		1	50.00	1	150280827	43	47.67	41	A5H1P7|C4PFH9|D3DX04|O75418|O75680|Q708S9|Q9BT72|Q9BUT7|Q9H3P0	Silent	SNP	HMMPfam_cNMP_binding,HMMSmart_SM00100,HMMSmart_SM00086,HMMPfam_Ion_trans,HMMPfam_PAS,superfamily_cAMP-binding domain-like,superfamily_PYP-like sensor domain (PAS domain),superfamily_Voltage-gated potassium channels	p.A392	ENST00000262186.5	37	c.1176	CCDS5910.1	7																																																																																			-	NULL		0.657	KCNH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	KCNH2	protein_coding	OTTHUMT00000350741.2	T	NM_000238		150280827	-1	no_errors	NM_000238.2	genbank	human	reviewed	54_36p	silent	SNP	0.899	G
GXYLT1P6	100132672	genome.wustl.edu	37	9	69502172	69502172	+	IGR	SNP	A	A	G	rs202052715		TCGA-AB-2934-03A-01W-0755-09	TCGA-AB-2934-11A-01W-0755-09	A	A	A	G	A	A	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	7791e140-fe03-44d0-8250-47826ea993df	c98ddb47-f34c-4646-a434-5f8e6f6b5853	g.chr9:69502172A>G								ANKRD20A4 (76612 upstream) : AL445665.2 (85205 downstream)																							TAGCAAAAACATAAGAGATCG	0.318																																						dbGAP											0			9																																								68791992	SO:0001628	intergenic_variant	0																															9.37:g.69502172A>G		24	0.00	0		NA	NA	NA	68791992	121	18.00	27		RNA	SNP	-	NULL		37	NULL		9																																																																																			-	-	0	0.318					LOC100132672			A			68791992	+1	pseudogene	XR_038504.1	genbank	human	model	54_36p	rna	SNP	0.998	G
C9orf43	257169	genome.wustl.edu	37	9	116185663	116185663	+	Missense_Mutation	SNP	A	A	G	rs140205519		TCGA-AB-2934-03A-01W-0755-09	TCGA-AB-2934-11A-01W-0755-09	A	A	A	G	A	A	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	7791e140-fe03-44d0-8250-47826ea993df	c98ddb47-f34c-4646-a434-5f8e6f6b5853	g.chr9:116185663A>G	ENST00000288462.4	+	7	987	c.541A>G	c.(541-543)Aca>Gca	p.T181A	C9orf43_ENST00000374165.1_Missense_Mutation_p.T181A	NM_152786.1	NP_689999.1	Q8TAL5	CI043_HUMAN	chromosome 9 open reading frame 43	181										breast(2)|large_intestine(6)|lung(2)|ovary(1)|pancreas(1)|prostate(3)	15						ACGAGTAGGAACACCAGGGAT	0.468																																						dbGAP											0			9						A	ALA/THR	0,4406		0,0,2203	119.0	105.0	110.0		541	-5.0	0.0	9	dbSNP_134	110	1,8599	1.2+/-3.3	0,1,4299	no	missense	C9orf43	NM_152786.1	58	0,1,6502	GG,GA,AA		0.0116,0.0,0.0077	benign	181/462	116185663	1,13005	2203	4300	6503	115225484	SO:0001583	missense	0			BC026884	CCDS6796.1	9q33.1	2012-03-15			ENSG00000157653	ENSG00000157653			23570	protein-coding gene	gene with protein product						12477932	Standard	NM_152786		Approved	MGC17358	uc004bhp.3	Q8TAL5	OTTHUMG00000020526	ENST00000288462.4:c.541A>G	9.37:g.116185663A>G	ENSP00000288462:p.Thr181Ala	101	7.34	8		NA	NA	NA	115225484	120	46.09	106		Missense_Mutation	SNP	NULL	p.T181A	ENST00000288462.4	37	c.541	CCDS6796.1	9	.	.	.	.	.	.	.	.	.	.	A	12.71	2.019573	0.35606	0.0	1.16E-4	ENSG00000157653	ENST00000374165;ENST00000288462	T;T	0.42131	0.98;0.98	4.93	-5.0	0.03001	.	1.995050	0.02200	N	0.062167	T	0.20536	0.0494	N	0.14661	0.345	0.09310	N	1	B	0.10296	0.003	B	0.08055	0.003	T	0.06481	-1.0824	10	0.21540	T	0.41	11.3622	1.9583	0.03381	0.3286:0.2778:0.286:0.1076	.	181	Q8TAL5	CI043_HUMAN	A	181	ENSP00000363280:T181A;ENSP00000288462:T181A	ENSP00000288462:T181A	T	+	1	0	C9orf43	115225484	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.254000	0.08781	-0.660000	0.05352	0.533000	0.62120	ACA	-	NULL		0.468	C9orf43-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	C9orf43	protein_coding	OTTHUMT00000053739.1	A	NM_152786		115225484	+1	no_errors	NM_152786.1	genbank	human	predicted	54_36p	missense	SNP	0.000	G
ABCG4	64137	genome.wustl.edu	37	11	119031351	119031351	+	Missense_Mutation	SNP	A	A	G			TCGA-AB-2934-03A-01W-0755-09	TCGA-AB-2934-11A-01W-0755-09	A	A	A	G	A	A	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	7791e140-fe03-44d0-8250-47826ea993df	c98ddb47-f34c-4646-a434-5f8e6f6b5853	g.chr11:119031351A>G	ENST00000449422.2	+	14	1888	c.1700A>G	c.(1699-1701)tAt>tGt	p.Y567C	ABCG4_ENST00000531739.1_Missense_Mutation_p.Y567C|ABCG4_ENST00000307417.3_Missense_Mutation_p.Y567C	NM_001142505.1	NP_001135977.1	Q9H172	ABCG4_HUMAN	ATP-binding cassette, sub-family G (WHITE), member 4	567	ABC transmembrane type-2.				cholesterol efflux (GO:0033344)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|cholesterol transporter activity (GO:0017127)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(28)|ovary(2)|prostate(1)|skin(1)	44	all_hematologic(175;0.0977)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.7e-05)		TGGAGCTCCTATCTCTCCTAT	0.577																																						dbGAP											0			11											200.0	190.0	193.0					11																	119031351		2200	4295	6495	118536561	SO:0001583	missense	0			AJ300465	CCDS8415.1	11q23	2012-03-14			ENSG00000172350	ENSG00000172350		"""ATP binding cassette transporters / subfamily G"""	13884	protein-coding gene	gene with protein product	"""putative ABC transporter"", ""ATP-binding cassette, subfamily G, member 4"""	607784				11435397	Standard	NM_022169		Approved	WHITE2	uc001pvs.3	Q9H172	OTTHUMG00000166169	ENST00000449422.2:c.1700A>G	11.37:g.119031351A>G	ENSP00000406874:p.Tyr567Cys	86	3.33	3		NA	NA	NA	118536561	135	32.84	66	A8K1B5|Q8WWH0|Q8WWH1|Q8WWH2	Missense_Mutation	SNP	HMMPfam_ABC_tran,HMMSmart_SM00382,HMMPfam_ABC2_membrane,PatternScan_ABC_TRANSPORTER_1,superfamily_P-loop containing nucleoside triphosphate hydrolases	p.Y567C	ENST00000449422.2	37	c.1700	CCDS8415.1	11	.	.	.	.	.	.	.	.	.	.	A	23.5	4.427972	0.83667	.	.	ENSG00000172350	ENST00000307417;ENST00000449422;ENST00000531739	T;T;T	0.74421	-0.84;-0.84;-0.84	5.49	5.49	0.81192	ABC-2 type transporter (1);	0.164069	0.56097	D	0.000029	D	0.88779	0.6529	M	0.92738	3.34	0.80722	D	1	D	0.71674	0.998	D	0.71870	0.975	D	0.91449	0.5180	10	0.87932	D	0	-6.8349	14.6205	0.68582	1.0:0.0:0.0:0.0	.	567	Q9H172	ABCG4_HUMAN	C	567	ENSP00000304111:Y567C;ENSP00000406874:Y567C;ENSP00000434318:Y567C	ENSP00000304111:Y567C	Y	+	2	0	ABCG4	118536561	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	9.254000	0.95512	2.105000	0.64084	0.456000	0.33151	TAT	-	HMMPfam_ABC2_membrane		0.577	ABCG4-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	ABCG4	protein_coding	OTTHUMT00000388215.1	A	NM_022169		118536561	+1	no_errors	NM_022169.1	genbank	human	reviewed	54_36p	missense	SNP	1.000	G
MGAT4C	25834	genome.wustl.edu	37	12	86373735	86373735	+	Missense_Mutation	SNP	G	G	T			TCGA-AB-2934-03A-01W-0755-09	TCGA-AB-2934-11A-01W-0755-09	G	G	G	T	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	7791e140-fe03-44d0-8250-47826ea993df	c98ddb47-f34c-4646-a434-5f8e6f6b5853	g.chr12:86373735G>T	ENST00000604798.1	-	8	1973	c.769C>A	c.(769-771)Ctt>Att	p.L257I	MGAT4C_ENST00000552435.2_Intron|MGAT4C_ENST00000548651.1_Missense_Mutation_p.L257I|MGAT4C_ENST00000393205.2_Missense_Mutation_p.L286I|MGAT4C_ENST00000549405.2_Missense_Mutation_p.L257I|MGAT4C_ENST00000552808.2_Missense_Mutation_p.L257I|MGAT4C_ENST00000332156.1_Missense_Mutation_p.L257I			Q9UBM8	MGT4C_HUMAN	MGAT4 family, member C	257					cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	alpha-1,3-mannosylglycoprotein 4-beta-N-acetylglucosaminyltransferase activity (GO:0008454)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(17)|ovary(4)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	41						ATGTAGCCAAGCTTAGAGAAT	0.363																																						dbGAP											0			12											72.0	69.0	70.0					12																	86373735		2203	4299	6502	84897866	SO:0001583	missense	0				CCDS9030.1	12q21	2014-07-14	2014-07-14		ENSG00000182050	ENSG00000182050		"""Mannosyl-glycoprotein beta N-acetylglucosaminyltransferases"""	30871	protein-coding gene	gene with protein product		607385	"""mannosyl (alpha-1,3-)-glycoprotein beta-1,4-N-acetylglucosaminyltransferase, isozyme C (putative)"""			10570912	Standard	NM_013244		Approved	HGNT-IV-H	uc001tal.4	Q9UBM8	OTTHUMG00000169846	ENST00000604798.1:c.769C>A	12.37:g.86373735G>T	ENSP00000474896:p.Leu257Ile	37	7.50	3		NA	NA	NA	84897866	72	46.76	65	B4DRH2|Q4G199|Q9UIU5	Missense_Mutation	SNP	HMMPfam_Glyco_transf_54	p.L257I	ENST00000604798.1	37	c.769	CCDS9030.1	12	.	.	.	.	.	.	.	.	.	.	G	17.43	3.387264	0.61956	.	.	ENSG00000182050	ENST00000332156;ENST00000393205;ENST00000549405;ENST00000550460;ENST00000552808;ENST00000548651;ENST00000547225	T;T;T;T;T;T	0.54279	0.58;0.58;0.58;0.58;0.58;0.58	5.79	4.9	0.64082	.	0.000000	0.85682	D	0.000000	T	0.76765	0.4033	M	0.86573	2.825	0.52501	D	0.999951	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.82065	-0.0642	10	0.72032	D	0.01	-12.8762	16.8482	0.85986	0.0:0.1286:0.8714:0.0	.	286;257	B4DRH2;Q9UBM8	.;MGT4C_HUMAN	I	257;286;257;257;257;257;257	ENSP00000331664:L257I;ENSP00000376900:L286I;ENSP00000449022:L257I;ENSP00000446647:L257I;ENSP00000447253:L257I;ENSP00000449172:L257I	ENSP00000331664:L257I	L	-	1	0	MGAT4C	84897866	1.000000	0.71417	0.998000	0.56505	0.592000	0.36648	4.878000	0.63093	1.416000	0.47057	0.655000	0.94253	CTT	-	HMMPfam_Glyco_transf_54		0.363	MGAT4C-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	MGAT4C	protein_coding	OTTHUMT00000406212.2	G	NM_013244		84897866	-1	no_errors	NM_013244.3	genbank	human	validated	54_36p	missense	SNP	1.000	T
IDH2	3418	genome.wustl.edu	37	15	90631934	90631934	+	Missense_Mutation	SNP	C	C	T	rs121913502		TCGA-AB-2934-03A-01W-0755-09	TCGA-AB-2934-11A-01W-0755-09	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	7791e140-fe03-44d0-8250-47826ea993df	c98ddb47-f34c-4646-a434-5f8e6f6b5853	g.chr15:90631934C>T	ENST00000330062.3	-	4	532	c.419G>A	c.(418-420)cGg>cAg	p.R140Q	IDH2_ENST00000540499.2_Missense_Mutation_p.R88Q|IDH2_ENST00000539790.1_Missense_Mutation_p.R10Q|IDH2_ENST00000559482.1_Intron	NM_002168.2	NP_002159.2	P48735	IDHP_HUMAN	isocitrate dehydrogenase 2 (NADP+), mitochondrial	140	Substrate binding. {ECO:0000250}.		R -> G (in D2HGA2). {ECO:0000269|PubMed:20847235}.|R -> Q (in D2HGA2). {ECO:0000269|PubMed:20847235}.		2-oxoglutarate metabolic process (GO:0006103)|carbohydrate metabolic process (GO:0005975)|cellular metabolic process (GO:0044237)|glyoxylate cycle (GO:0006097)|isocitrate metabolic process (GO:0006102)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	isocitrate dehydrogenase (NADP+) activity (GO:0004450)|magnesium ion binding (GO:0000287)|NAD binding (GO:0051287)	p.R140Q(292)|p.R140L(8)		biliary_tract(11)|bone(19)|central_nervous_system(107)|endometrium(1)|haematopoietic_and_lymphoid_tissue(953)|large_intestine(8)|lung(5)|skin(5)	1109	Melanoma(11;0.00551)|Lung NSC(78;0.0196)|all_lung(78;0.04)		BRCA - Breast invasive adenocarcinoma(143;0.0146)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.106)			CAGGATGTTCCGGATAGTTCC	0.537			M		GBM																																	dbGAP		Dom	yes		15	15q26.1	3418	"""socitrate dehydrogenase 2 (NADP+), mitochondrial """		M	300	Substitution - Missense(300)	haematopoietic_and_lymphoid_tissue(300)	15											103.0	103.0	103.0					15																	90631934		2200	4298	6498	88432938	SO:0001583	missense	0				CCDS10359.1	15q26.1	2014-09-17			ENSG00000182054	ENSG00000182054	1.1.1.42		5383	protein-coding gene	gene with protein product		147650					Standard	NM_001289910		Approved		uc002box.3	P48735	OTTHUMG00000149815	ENST00000330062.3:c.419G>A	15.37:g.90631934C>T	ENSP00000331897:p.Arg140Gln	69	2.82	2		93	46.86	82	88432938	59	46.36	51	B2R6L6|B4DFL2|Q96GT3	Missense_Mutation	SNP	HMMPfam_Iso_dh,PatternScan_IDH_IMDH,superfamily_Isocitrate/Isopropylmalate dehydrogenase-like	p.R140Q	ENST00000330062.3	37	c.419	CCDS10359.1	15	.	.	.	.	.	.	.	.	.	.	C	18.35	3.604397	0.66445	.	.	ENSG00000182054	ENST00000330062;ENST00000539790;ENST00000540499	D;D;D	0.87179	-2.22;-2.22;-2.22	5.67	4.75	0.60458	Isopropylmalate dehydrogenase-like domain (2);	0.000000	0.85682	D	0.000000	D	0.95449	0.8522	H	0.96833	3.89	0.48185	D	0.999601	D	0.89917	1.0	D	0.87578	0.998	D	0.96254	0.9185	10	0.87932	D	0	.	12.4459	0.55651	0.0:0.9189:0.0:0.0811	.	140	P48735	IDHP_HUMAN	Q	140;10;88	ENSP00000331897:R140Q;ENSP00000438457:R10Q;ENSP00000446147:R88Q	ENSP00000331897:R140Q	R	-	2	0	IDH2	88432938	1.000000	0.71417	1.000000	0.80357	0.051000	0.14879	7.797000	0.85911	1.397000	0.46682	-0.258000	0.10820	CGG	-	HMMPfam_Iso_dh,superfamily_Isocitrate/Isopropylmalate dehydrogenase-like		0.537	IDH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	IDH2	protein_coding	OTTHUMT00000313426.1	C			88432938	-1	no_errors	NM_002168.2	genbank	human	reviewed	54_36p	missense	SNP	1.000	T
USP9X	8239	genome.wustl.edu	37	X	41027390	41027391	+	Frame_Shift_Ins	INS	-	-	CG			TCGA-AB-2934-03A-01W-0755-09	TCGA-AB-2934-11A-01W-0755-09	-	-	-	CG	-	-	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	7791e140-fe03-44d0-8250-47826ea993df	c98ddb47-f34c-4646-a434-5f8e6f6b5853	g.chrX:41027390_41027391insCG	ENST00000324545.8	+	18	3188_3189	c.2555_2556insCG	c.(2554-2559)cgagtafs	p.V853fs	USP9X_ENST00000378308.2_Frame_Shift_Ins_p.V853fs	NM_001039590.2|NM_001039591.2	NP_001034679.2|NP_001034680.2	Q93008	USP9X_HUMAN	ubiquitin specific peptidase 9, X-linked	853					axon extension (GO:0048675)|BMP signaling pathway (GO:0030509)|cerebellar cortex structural organization (GO:0021698)|chromosome segregation (GO:0007059)|female gamete generation (GO:0007292)|gene expression (GO:0010467)|hippocampus development (GO:0021766)|in utero embryonic development (GO:0001701)|mitotic nuclear division (GO:0007067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron migration (GO:0001764)|post-embryonic development (GO:0009791)|protein deubiquitination (GO:0016579)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ubiquitin-dependent protein catabolic process (GO:0006511)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|growth cone (GO:0030426)|membrane (GO:0016020)	co-SMAD binding (GO:0070410)|cysteine-type endopeptidase activity (GO:0004197)|cysteine-type peptidase activity (GO:0008234)|ubiquitin thiolesterase activity (GO:0004221)			NS(3)|breast(6)|central_nervous_system(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(16)|lung(29)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	87						CGAATGGTTCGAGTATTAACTG	0.366																																					Ovarian(172;1807 2695 35459 49286)	dbGAP											0			X																																								40912335	SO:0001589	frameshift_variant	0			X98296	CCDS43930.1, CCDS55403.1	Xp11.4	2010-08-03	2006-02-14		ENSG00000124486	ENSG00000124486		"""Ubiquitin-specific peptidases"""	12632	protein-coding gene	gene with protein product		300072	"""ubiquitin specific protease 9, X chromosome (fat facets-like Drosophila)"", ""ubiquitin specific protease 9, X-linked (fat facets-like, Drosophila)"", ""ubiquitin specific peptidase 9, X-linked (fat facets-like, Drosophila)"""			8922996	Standard	NM_001039590		Approved	DFFRX, FAF	uc004dfb.3	Q93008	OTTHUMG00000021367	ENST00000324545.8:c.2554_2555dupCG	X.37:g.41027389_41027390dupCG	ENSP00000316357:p.Val853fs	85	0.00	0		9	0.00	0	40912334	217	0.00	0	O75550|Q8WWT3|Q8WX12	Frame_Shift_Ins	INS	HMMPfam_UCH,PatternScan_UCH_2_1,PatternScan_UCH_2_2,superfamily_Cysteine proteinases	p.V853fs	ENST00000324545.8	37	c.2555_2556	CCDS43930.1	X																																																																																			-	NULL		0.366	USP9X-003	KNOWN	basic|CCDS	protein_coding	USP9X	protein_coding	OTTHUMT00000056250.4	-	NM_004652		40912335	+1	no_errors	NM_001039590.2	genbank	human	reviewed	54_36p	frame_shift_ins	INS	1.000:1.000	CG
FLT3	2322	genome.wustl.edu	37	13	28608257	28608258	+	In_Frame_Ins	INS	-	-	CATATTCATATTCTCTGAAATCAACGTAGAAGTACTCATTATCTTAGGAGCCGGTCC			TCGA-AB-2934-03A-01W-0755-09	TCGA-AB-2934-11A-01W-0755-09	-	-	-	CATATTCATATTCTCTGAAATCAACGTAGAAGTACTCATTATCTTAGGAGCCGGTCC	-	-	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	7791e140-fe03-44d0-8250-47826ea993df	c98ddb47-f34c-4646-a434-5f8e6f6b5853	g.chr13:28608257_28608258insCATATTCATATTCTCTGAAATCAACGTAGAAGTACTCATTATCTTAGGAGCCGGTCC	ENST00000241453.7	-	14	1879_1880	c.1798_1799insGGACCGGCTCCTAAGATAATGAGTACTTCTACGTTGATTTCAGAGAATATGAATATG	c.(1798-1800)gat>gGGACCGGCTCCTAAGATAATGAGTACTTCTACGTTGATTTCAGAGAATATGAATATGat	p.599_600insGTGS*DNEYFYVDFREYEY	FLT3_ENST00000380982.4_In_Frame_Ins_p.599_600insGTGS*DNEYFYVDFREYEY|FLT3_ENST00000537084.1_In_Frame_Ins_p.599_600insGTGS*DNEYFYVDFREYEY	NM_004119.2	NP_004110.2	P36888	FLT3_HUMAN	fms-related tyrosine kinase 3	599					B cell differentiation (GO:0030183)|cellular response to cytokine stimulus (GO:0071345)|common myeloid progenitor cell proliferation (GO:0035726)|cytokine-mediated signaling pathway (GO:0019221)|dendritic cell differentiation (GO:0097028)|hemopoiesis (GO:0030097)|leukocyte homeostasis (GO:0001776)|lymphocyte proliferation (GO:0046651)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of B cell differentiation (GO:0045578)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of tyrosine phosphorylation of STAT protein (GO:0042531)|pro-B cell differentiation (GO:0002328)|pro-T cell differentiation (GO:0002572)|protein autophosphorylation (GO:0046777)|regulation of apoptotic process (GO:0042981)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor signaling pathway (GO:0038084)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|cytokine receptor activity (GO:0004896)|protein homodimerization activity (GO:0042803)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor-activated receptor activity (GO:0005021)	p.Y599_D600insPAPQIMSTSTLISENMNIA(2)|p.Y599_D600ins15(2)|p.Y599_D600insEYEYEYEY(2)|p.Y599_D600ins12(1)|p.D600>EPAPQINSTGSSDNEYFYVDFREYEYDLT(1)|p.D600_L601insVDFREYEY(1)		NS(1)|breast(3)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(12329)|kidney(2)|large_intestine(8)|lung(30)|ovary(4)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	12390	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0156)|Ovarian(182;0.0392)	Colorectal(13;0.000157)|READ - Rectum adenocarcinoma(15;0.105)	OV - Ovarian serous cystadenocarcinoma(117;0.00154)|all cancers(112;0.00459)|GBM - Glioblastoma multiforme(144;0.00562)|Epithelial(112;0.0959)|Lung(94;0.212)	Ponatinib(DB08901)|Sorafenib(DB00398)|Sunitinib(DB01268)	CCATTTGAGATCATATTCATAT	0.366			"""Mis, O"""		"""AML, ALL"""																																	dbGAP		Dom	yes		13	13q12	2322	fms-related tyrosine kinase 3		L	9	Insertion - In frame(8)|Complex - insertion inframe(1)	haematopoietic_and_lymphoid_tissue(9)	13																																								27506258	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.1798_1799insGGACCGGCTCCTAAGATAATGAGTACTTCTACGTTGATTTCAGAGAATATGAATATG	13.37:g.28608257_28608258insCATATTCATATTCTCTGAAATCAACGTAGAAGTACTCATTATCTTAGGAGCCGGTCC	ENSP00000241453:p.Tyr599_Asp600insGlyThrGlySer*AspAsnGluTyrPheTyrValAspPheArgGluTyrGluTyr	NA	NA	NA		NA	NA	NA	27506257	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.600in_frame_insGTGS*DNEYFYVDFREYEY	ENST00000241453.7	37	c.1799_1798	CCDS31953.1	13																																																																																			-	superfamily_Kinase_like		0.366	FLT3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	FLT3	protein_coding	OTTHUMT00000044319.2	-			27506258	-1	no_errors	NM_004119.2	genbank	human	reviewed	54_36p	in_frame_ins	INS	1.000:1.000	CATATTCATATTCTCTGAAATCAACGTAGAAGTACTCATTATCTTAGGAGCCGGTCC
