#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
ELAVL4	1996	genome.wustl.edu	37	1	50575630	50575630	+	Intron	SNP	G	G	A			TCGA-AB-2928-03A-01W-0745-08	TCGA-AB-2928-11A-01W-0745-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	39402967-4dad-4a46-b8d0-5fcb824bc2c2	233dc863-8cfb-4b4d-ad97-ee0685247f3a	g.chr1:50575630G>A	ENST00000371823.4	+	1	233				ELAVL4_ENST00000371821.1_Silent_p.L6L|ELAVL4_ENST00000371827.1_Intron|ELAVL4_ENST00000357083.4_Intron|ELAVL4_ENST00000371819.1_Silent_p.L6L|ELAVL4_ENST00000371824.1_Intron|ELAVL4_ENST00000448907.2_Intron	NM_001144774.1|NM_021952.3	NP_001138246.1|NP_068771.2	P26378	ELAV4_HUMAN	ELAV like neuron-specific RNA binding protein 4						mRNA processing (GO:0006397)|RNA processing (GO:0006396)		AU-rich element binding (GO:0017091)|mRNA 3'-UTR binding (GO:0003730)|nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			NS(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|liver(2)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	32						GGAATGGCTTGAAGATGGTAA	0.473																																						dbGAP											0			1											59.0	54.0	55.0					1																	50575630		876	1991	2867	50348217	SO:0001627	intron_variant	0			AY033998	CCDS553.1, CCDS44138.1, CCDS44139.1, CCDS44140.1, CCDS53315.1, CCDS72788.1	1p34	2013-10-03	2013-10-03		ENSG00000162374	ENSG00000162374		"""RNA binding motif (RRM) containing"""	3315	protein-coding gene	gene with protein product	"""Hu antigen D"""	168360	"""ELAV (embryonic lethal, abnormal vision, Drosophila)-like 4 (Hu antigen D)"", ""ELAV (embryonic lethal, abnormal vision, Drosophila)-like 4"""	HUD		8222755	Standard	XM_005270581		Approved	PNEM	uc001csb.2	P26378	OTTHUMG00000007877	ENST00000371823.4:c.9+760G>A	1.37:g.50575630G>A		262	12.00	36		NA	NA	NA	50348217	121	50.20	126	B1APY6|B1APY7|B7Z4G7|Q8IYD4|Q96J74|Q96J75|Q9UD24	Silent	SNP	HMMPfam_RRM_1,HMMSmart_RRM,superfamily_SSF54928	p.L6	ENST00000371823.4	37	c.18	CCDS553.1	1																																																																																			-	NULL		0.473	ELAVL4-004	KNOWN	basic|CCDS	protein_coding	ELAVL4	protein_coding	OTTHUMT00000021712.1	G	NM_021952		50348217	+1	no_errors	ENST00000371821	ensembl	human	known	54_36p	silent	SNP	1.000	A
DNMT3A	1788	genome.wustl.edu	37	2	25462065	25462065	+	Missense_Mutation	SNP	T	T	C			TCGA-AB-2928-03A-01W-0745-08	TCGA-AB-2928-11A-01W-0745-08	T	T	T	C	T	T	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	39402967-4dad-4a46-b8d0-5fcb824bc2c2	233dc863-8cfb-4b4d-ad97-ee0685247f3a	g.chr2:25462065T>C	ENST00000264709.3	-	20	2679	c.2342A>G	c.(2341-2343)gAt>gGt	p.D781G	DNMT3A_ENST00000474887.1_5'UTR|DNMT3A_ENST00000321117.5_Missense_Mutation_p.D781G|DNMT3A_ENST00000380746.4_Missense_Mutation_p.D592G|DNMT3A_ENST00000402667.1_Missense_Mutation_p.D558G	NM_175629.2	NP_783328.1	Q9Y6K1	DNM3A_HUMAN	DNA (cytosine-5-)-methyltransferase 3 alpha	781	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)					TTCTTTGGCATCAATCATCAC	0.562			"""Mis, F, N, S"""		AML																																	dbGAP		Rec	yes		2	2p23	1788	DNA (cytosine-5-)-methyltransferase 3 alpha		L	0			2											65.0	59.0	61.0					2																	25462065		2203	4300	6503	25315569	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.2342A>G	2.37:g.25462065T>C	ENSP00000264709:p.Asp781Gly	59	9.23	6		29	65.06	54	25315569	57	40.62	39	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.D781G	ENST00000264709.3	37	c.2342	CCDS33157.1	2	.	.	.	.	.	.	.	.	.	.	T	23.1	4.378201	0.82682	.	.	ENSG00000119772	ENST00000380746;ENST00000321117;ENST00000264709;ENST00000402667	D;D;D;D	0.96940	-4.18;-4.18;-4.18;-4.18	5.46	4.3	0.51218	.	0.000000	0.85682	D	0.000000	D	0.97860	0.9297	M	0.87456	2.885	0.80722	D	1	D;D	0.89917	1.0;0.988	D;B	0.73708	0.981;0.423	D	0.97629	1.0141	10	0.72032	D	0.01	-8.5836	9.6545	0.39917	0.0:0.083:0.0:0.917	.	781;592	Q9Y6K1;E9PEB8	DNM3A_HUMAN;.	G	592;781;781;558	ENSP00000370122:D592G;ENSP00000324375:D781G;ENSP00000264709:D781G;ENSP00000384237:D558G	ENSP00000264709:D781G	D	-	2	0	DNMT3A	25315569	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.040000	0.89188	0.909000	0.36697	0.459000	0.35465	GAT	-	superfamily_S-adenosyl-L-methionine-dependent methyltransferases		0.562	DNMT3A-001	KNOWN	basic|CCDS	protein_coding	DNMT3A	protein_coding	OTTHUMT00000211587.1	T	NM_022552		25315569	-1	no_errors	NM_022552.3	genbank	human	reviewed	54_36p	missense	SNP	1.000	C
DNMT3A	1788	genome.wustl.edu	37	2	25470516	25470516	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AB-2928-03A-01W-0745-08	TCGA-AB-2928-11A-01W-0745-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	39402967-4dad-4a46-b8d0-5fcb824bc2c2	233dc863-8cfb-4b4d-ad97-ee0685247f3a	g.chr2:25470516G>A	ENST00000264709.3	-	8	1295	c.958C>T	c.(958-960)Cga>Tga	p.R320*	DNMT3A_ENST00000321117.5_Nonsense_Mutation_p.R320*|DNMT3A_ENST00000380746.4_Nonsense_Mutation_p.R131*|DNMT3A_ENST00000402667.1_Nonsense_Mutation_p.R97*	NM_175629.2	NP_783328.1	Q9Y6K1	DNM3A_HUMAN	DNA (cytosine-5-)-methyltransferase 3 alpha	320	Interaction with DNMT1 and DNMT3B.|PWWP. {ECO:0000255|PROSITE- ProRule:PRU00162}.				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.R320*(2)		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)					TCAGCTGCTCGGCTCCGGCCC	0.637			"""Mis, F, N, S"""		AML																																	dbGAP		Rec	yes		2	2p23	1788	DNA (cytosine-5-)-methyltransferase 3 alpha		L	2	Substitution - Nonsense(2)	haematopoietic_and_lymphoid_tissue(2)	2											111.0	116.0	114.0					2																	25470516		2203	4300	6503	25324020	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.958C>T	2.37:g.25470516G>A	ENSP00000264709:p.Arg320*	88	13.46	14		40	28.57	16	25324020	73	44.36	59	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.R320*	ENST00000264709.3	37	c.958	CCDS33157.1	2	.	.	.	.	.	.	.	.	.	.	G	40	8.102727	0.98654	.	.	ENSG00000119772	ENST00000380746;ENST00000321117;ENST00000264709;ENST00000402667	.	.	.	4.97	4.97	0.65823	.	0.063127	0.64402	D	0.000005	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-1.8665	16.9479	0.86235	0.0:0.0:1.0:0.0	.	.	.	.	X	131;320;320;97	.	ENSP00000264709:R320X	R	-	1	2	DNMT3A	25324020	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.044000	0.64214	2.584000	0.87258	0.462000	0.41574	CGA	-	HMMPfam_PWWP,HMMSmart_SM00293,superfamily_Tudor/PWWP/MBT		0.637	DNMT3A-001	KNOWN	basic|CCDS	protein_coding	DNMT3A	protein_coding	OTTHUMT00000211587.1	G	NM_022552		25324020	-1	no_errors	NM_022552.3	genbank	human	reviewed	54_36p	nonsense	SNP	1.000	A
IDH1	3417	genome.wustl.edu	37	2	209113113	209113113	+	Missense_Mutation	SNP	G	G	A	rs121913499		TCGA-AB-2928-03A-01W-0745-08	TCGA-AB-2928-11A-01W-0745-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	39402967-4dad-4a46-b8d0-5fcb824bc2c2	233dc863-8cfb-4b4d-ad97-ee0685247f3a	g.chr2:209113113G>A	ENST00000415913.1	-	4	775	c.394C>T	c.(394-396)Cgt>Tgt	p.R132C	IDH1_ENST00000446179.1_Missense_Mutation_p.R132C|IDH1_ENST00000345146.2_Missense_Mutation_p.R132C	NM_001282387.1	NP_001269316.1	O75874	IDHC_HUMAN	isocitrate dehydrogenase 1 (NADP+), soluble	132			R -> C (in colorectal cancer and glioma samples; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha- ketoglutarate but instead alpha- ketoglutarate is converted to R(-)-2- hydroxyglutarate). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:19117336}.|R -> G (in a glioma sample; glioblastoma multiforme; somatic mutation). {ECO:0000269|PubMed:19117336}.|R -> H (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:18772396}.|R -> L (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:19117336}.|R -> S (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:18772396}.		2-oxoglutarate metabolic process (GO:0006103)|cellular lipid metabolic process (GO:0044255)|female gonad development (GO:0008585)|glutathione metabolic process (GO:0006749)|glyoxylate cycle (GO:0006097)|isocitrate metabolic process (GO:0006102)|NADPH regeneration (GO:0006740)|response to oxidative stress (GO:0006979)|response to steroid hormone (GO:0048545)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	isocitrate dehydrogenase (NADP+) activity (GO:0004450)|magnesium ion binding (GO:0000287)|NAD binding (GO:0051287)|NADP binding (GO:0050661)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)	p.R132C(446)|p.R132G(125)|p.R132S(106)|p.G131_R132>VL(1)|p.R132V(1)		NS(1)|autonomic_ganglia(2)|biliary_tract(24)|bone(237)|central_nervous_system(3764)|endometrium(3)|haematopoietic_and_lymphoid_tissue(794)|kidney(2)|large_intestine(7)|lung(7)|prostate(6)|skin(5)|soft_tissue(12)|thyroid(22)|urinary_tract(1)	4887				Epithelial(149;0.0322)|LUSC - Lung squamous cell carcinoma(261;0.0711)|Lung(261;0.136)		TAAGCATGACGACCTATGATG	0.398			Mis		gliobastoma																																Pancreas(158;264 1958 3300 35450 36047)	dbGAP		Dom	yes		2	2q33.3	3417	"""isocitrate dehydrogenase 1 (NADP+), soluble"""		O	679	Substitution - Missense(678)|Complex - compound substitution(1)	haematopoietic_and_lymphoid_tissue(280)|central_nervous_system(181)|bone(177)|biliary_tract(21)|soft_tissue(12)|large_intestine(2)|skin(2)|autonomic_ganglia(1)|endometrium(1)|NS(1)|prostate(1)	2											81.0	74.0	76.0					2																	209113113		2203	4300	6503	208821358	SO:0001583	missense	0				CCDS2381.1	2q34	2014-09-17			ENSG00000138413	ENSG00000138413	1.1.1.42		5382	protein-coding gene	gene with protein product		147700					Standard	NM_005896		Approved		uc002vcu.3	O75874	OTTHUMG00000132943	ENST00000415913.1:c.394C>T	2.37:g.209113113G>A	ENSP00000390265:p.Arg132Cys	94	10.48	11		26	59.38	38	208821358	102	37.72	63	Q567U4|Q6FHQ6|Q7Z3V0|Q93090|Q9NTJ9|Q9UKW8	Missense_Mutation	SNP	HMMPfam_Iso_dh,PatternScan_IDH_IMDH,superfamily_Isocitrate/Isopropylmalate dehydrogenase-like	p.R132C	ENST00000415913.1	37	c.394	CCDS2381.1	2	.	.	.	.	.	.	.	.	.	.	G	24.6	4.550898	0.86127	.	.	ENSG00000138413	ENST00000345146;ENST00000446179;ENST00000415913;ENST00000415282	D;D;D;D	0.87029	-2.2;-2.2;-2.2;-2.2	5.57	5.57	0.84162	Isopropylmalate dehydrogenase-like domain (2);	0.000000	0.85682	D	0.000000	D	0.94049	0.8093	H	0.99379	4.54	0.80722	D	1	B	0.29862	0.259	B	0.31245	0.126	D	0.94048	0.7315	10	0.87932	D	0	-20.0399	19.5341	0.95242	0.0:0.0:1.0:0.0	.	132	O75874	IDHC_HUMAN	C	132	ENSP00000260985:R132C;ENSP00000410513:R132C;ENSP00000390265:R132C;ENSP00000391075:R132C	ENSP00000260985:R132C	R	-	1	0	IDH1	208821358	1.000000	0.71417	0.999000	0.59377	0.994000	0.84299	7.074000	0.76791	2.616000	0.88540	0.555000	0.69702	CGT	-	HMMPfam_Iso_dh,superfamily_Isocitrate/Isopropylmalate dehydrogenase-like		0.398	IDH1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	IDH1	protein_coding	OTTHUMT00000336672.1	G			208821358	-1	no_errors	NM_005896.2	genbank	human	reviewed	54_36p	missense	SNP	1.000	A
TET2	54790	genome.wustl.edu	37	4	106190777	106190777	+	Missense_Mutation	SNP	A	A	T			TCGA-AB-2928-03A-01W-0745-08	TCGA-AB-2928-11A-01W-0745-08	A	A	A	T	A	A	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	39402967-4dad-4a46-b8d0-5fcb824bc2c2	233dc863-8cfb-4b4d-ad97-ee0685247f3a	g.chr4:106190777A>T	ENST00000540549.1	+	9	4915	c.4055A>T	c.(4054-4056)gAa>gTa	p.E1352V	TET2_ENST00000545826.1_3'UTR|TET2_ENST00000513237.1_Missense_Mutation_p.E1373V|TET2_ENST00000380013.4_Missense_Mutation_p.E1352V			Q6N021	TET2_HUMAN	tet methylcytosine dioxygenase 2	1352					5-methylcytosine catabolic process (GO:0006211)|cell cycle (GO:0007049)|DNA demethylation (GO:0080111)|histone H3-K4 trimethylation (GO:0080182)|kidney development (GO:0001822)|myeloid cell differentiation (GO:0030099)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|protein O-linked glycosylation (GO:0006493)		DNA binding (GO:0003677)|ferrous iron binding (GO:0008198)|methylcytosine dioxygenase activity (GO:0070579)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1272)|kidney(3)|large_intestine(11)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	1314		Myeloproliferative disorder(5;0.0393)		OV - Ovarian serous cystadenocarcinoma(123;7.18e-08)		ATTGAATATGAACACAGAGCA	0.428			"""Mis N, F"""		MDS																																	dbGAP		Rec	yes		4	4q24	54790	tet oncogene family member 2		L	0			4											101.0	86.0	90.0					4																	106190777		692	1591	2283	106410226	SO:0001583	missense	0			AB046766	CCDS3666.1, CCDS47120.1	4q24	2014-09-17	2011-09-30	2008-03-12	ENSG00000168769	ENSG00000168769			25941	protein-coding gene	gene with protein product		612839	"""KIAA1546"", ""tet oncogene family member 2"""	KIAA1546		10997877, 12646957	Standard	NM_017628		Approved	FLJ20032	uc003hxk.3	Q6N021	OTTHUMG00000131213	ENST00000540549.1:c.4055A>T	4.37:g.106190777A>T	ENSP00000442788:p.Glu1352Val	152	11.86	21		19	50.00	19	106410226	181	39.46	118	B5MDU0|Q2TB88|Q3LIB8|Q96JX5|Q9HCM6|Q9NXW0	Missense_Mutation	SNP	NULL	p.E154V	ENST00000540549.1	37	c.461	CCDS47120.1	4	.	.	.	.	.	.	.	.	.	.	A	32	5.180554	0.94846	.	.	ENSG00000168769	ENST00000540549;ENST00000513237;ENST00000380013	T;T;T	0.14266	2.52;2.52;2.52	5.87	5.87	0.94306	.	.	.	.	.	T	0.43787	0.1263	M	0.86028	2.79	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.48364	-0.9042	9	0.87932	D	0	-13.1879	16.2742	0.82636	1.0:0.0:0.0:0.0	.	1373;1352	E7EQS8;Q6N021	.;TET2_HUMAN	V	1352;1373;1352	ENSP00000442788:E1352V;ENSP00000425443:E1373V;ENSP00000369351:E1352V	ENSP00000369351:E1352V	E	+	2	0	TET2	106410226	1.000000	0.71417	0.991000	0.47740	0.993000	0.82548	9.163000	0.94750	2.253000	0.74438	0.533000	0.62120	GAA	-	NULL		0.428	TET2-202	KNOWN	basic|appris_candidate|CCDS	protein_coding	TET2	protein_coding	OTTHUMT00000253952.2	A	NM_017628		106410226	+1	no_start_codon	ENST00000265149	ensembl	human	known	54_36p	missense	SNP	1.000	T
SEMA3A	10371	genome.wustl.edu	37	7	83592543	83592543	+	Missense_Mutation	SNP	C	C	T			TCGA-AB-2928-03A-01W-0745-08	TCGA-AB-2928-11A-01W-0745-08	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	39402967-4dad-4a46-b8d0-5fcb824bc2c2	233dc863-8cfb-4b4d-ad97-ee0685247f3a	g.chr7:83592543C>T	ENST00000265362.4	-	16	2152	c.1838G>A	c.(1837-1839)cGa>cAa	p.R613Q	SEMA3A_ENST00000436949.1_Missense_Mutation_p.R613Q	NM_006080.2	NP_006071.1	Q14563	SEM3A_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3A	613	Ig-like C2-type.				apoptotic process (GO:0006915)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|axonogenesis involved in innervation (GO:0060385)|branchiomotor neuron axon guidance (GO:0021785)|dendrite morphogenesis (GO:0048813)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|facial nerve structural organization (GO:0021612)|gonadotrophin-releasing hormone neuronal migration to the hypothalamus (GO:0021828)|negative regulation of axon extension involved in axon guidance (GO:0048843)|negative regulation of epithelial cell migration (GO:0010633)|nerve development (GO:0021675)|neural crest cell migration involved in autonomic nervous system development (GO:1901166)|neural crest cell migration involved in sympathetic nervous system development (GO:1903045)|neuron migration (GO:0001764)|olfactory bulb development (GO:0021772)|positive regulation of male gonad development (GO:2000020)|positive regulation of neuron migration (GO:2001224)|regulation of axon extension involved in axon guidance (GO:0048841)|regulation of heart rate (GO:0002027)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|semaphorin-plexin signaling pathway involved in neuron projection guidance (GO:1902285)|sensory system development (GO:0048880)|sympathetic ganglion development (GO:0061549)|sympathetic nervous system development (GO:0048485)|sympathetic neuron projection extension (GO:0097490)|sympathetic neuron projection guidance (GO:0097491)|trigeminal nerve structural organization (GO:0021637)	axon (GO:0030424)|dendrite (GO:0030425)|extracellular region (GO:0005576)|membrane (GO:0016020)	chemorepellent activity (GO:0045499)|neuropilin binding (GO:0038191)|receptor activity (GO:0004872)	p.R613Q(1)		breast(3)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|liver(1)|lung(22)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	53						CTCTTCATTTCGCCTCTGGAA	0.403																																						dbGAP											1	Substitution - Missense(1)	large_intestine(1)	7											187.0	187.0	187.0					7																	83592543		2203	4300	6503	83430479	SO:0001583	missense	0			L26081	CCDS5599.1	7p12.1	2013-01-11			ENSG00000075213	ENSG00000075213		"""Semaphorins"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	10723	protein-coding gene	gene with protein product	"""sema III"""	603961		SEMAD		8269517, 7748561	Standard	NM_006080		Approved	SEMA1, SemD, coll-1, Hsema-I	uc003uhz.3	Q14563	OTTHUMG00000023443	ENST00000265362.4:c.1838G>A	7.37:g.83592543C>T	ENSP00000265362:p.Arg613Gln	190	4.98	10		NA	NA	NA	83430479	138	19.65	34		Missense_Mutation	SNP	HMMPfam_Sema,HMMSmart_Sema,superfamily_Sema,HMMSmart_IG,HMMSmart_PSI,HMMPfam_ig,superfamily_Plexin-like_fold,superfamily_SSF48726	p.R613Q	ENST00000265362.4	37	c.1838	CCDS5599.1	7	.	.	.	.	.	.	.	.	.	.	C	11.78	1.740001	0.30865	.	.	ENSG00000075213	ENST00000265362;ENST00000436949	T;T	0.01527	4.8;4.8	5.9	4.91	0.64330	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.355176	0.32624	N	0.005858	T	0.00724	0.0024	N	0.01705	-0.755	0.31357	N	0.681812	B	0.02656	0.0	B	0.01281	0.0	T	0.43877	-0.9364	10	0.14252	T	0.57	.	3.4603	0.07531	0.0:0.5419:0.2844:0.1737	.	613	Q14563	SEM3A_HUMAN	Q	613	ENSP00000265362:R613Q;ENSP00000415260:R613Q	ENSP00000265362:R613Q	R	-	2	0	SEMA3A	83430479	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.637000	0.46553	2.802000	0.96397	0.650000	0.86243	CGA	-	HMMSmart_IG,HMMPfam_ig,superfamily_SSF48726		0.403	SEMA3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SEMA3A	protein_coding	OTTHUMT00000253355.2	C	NM_006080		83430479	-1	no_errors	NM_006080.2	genbank	human	reviewed	54_36p	missense	SNP	0.991	T
FLT3	2322	genome.wustl.edu	37	13	28592629	28592629	+	Missense_Mutation	SNP	T	T	C			TCGA-AB-2928-03A-01W-0745-08	TCGA-AB-2928-11A-01W-0745-08	T	T	T	C	T	T	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	39402967-4dad-4a46-b8d0-5fcb824bc2c2	233dc863-8cfb-4b4d-ad97-ee0685247f3a	g.chr13:28592629T>C	ENST00000241453.7	-	20	2597	c.2516A>G	c.(2515-2517)gAt>gGt	p.D839G	FLT3_ENST00000380982.4_Missense_Mutation_p.D839G|FLT3_ENST00000537084.1_Intron	NM_004119.2	NP_004110.2	P36888	FLT3_HUMAN	fms-related tyrosine kinase 3	839	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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)	ATAGTTGGAATCACTCATGAT	0.453			"""Mis, O"""		"""AML, ALL"""																																	dbGAP		Dom	yes		13	13q12	2322	fms-related tyrosine kinase 3		L	0			13											190.0	144.0	160.0					13																	28592629		2203	4300	6503	27490629	SO:0001583	missense	0			U02687	CCDS31953.1	13q12	2014-09-17			ENSG00000122025	ENSG00000122025	2.7.10.1	"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	3765	protein-coding gene	gene with protein product		136351				8394751	Standard	NM_004119		Approved	STK1, FLK2, CD135	uc001urw.3	P36888	OTTHUMG00000016646	ENST00000241453.7:c.2516A>G	13.37:g.28592629T>C	ENSP00000241453:p.Asp839Gly	171	5.98	11		171	25.65	59	27490629	130	24.02	43	A0AVG9|B7ZLT7|B7ZLT8|F5H0A0|Q13414	Missense_Mutation	SNP	HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,PatternScan_RECEPTOR_TYR_KIN_III,PatternScan_PROTEIN_KINASE_TYR,superfamily_Kinase_like,HMMPfam_ig,PatternScan_PROTEIN_KINASE_ATP,superfamily_SSF48726	p.D839G	ENST00000241453.7	37	c.2516	CCDS31953.1	13	.	.	.	.	.	.	.	.	.	.	T	27.0	4.791463	0.90367	.	.	ENSG00000122025	ENST00000241453;ENST00000380982	D;D	0.83837	-1.77;-1.77	5.84	5.84	0.93424	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.64402	D	0.000001	D	0.83917	0.5358	N	0.20401	0.57	0.80722	D	1	P	0.44139	0.827	P	0.58331	0.837	D	0.85839	0.1396	10	0.59425	D	0.04	.	16.2826	0.82703	0.0:0.0:0.0:1.0	.	839	P36888	FLT3_HUMAN	G	839	ENSP00000241453:D839G;ENSP00000370369:D839G	ENSP00000241453:D839G	D	-	2	0	FLT3	27490629	1.000000	0.71417	0.856000	0.33681	0.928000	0.56348	8.037000	0.88933	2.253000	0.74438	0.454000	0.30748	GAT	-	HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,superfamily_Kinase_like		0.453	FLT3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	FLT3	protein_coding	OTTHUMT00000044319.2	T			27490629	-1	no_errors	NM_004119.2	genbank	human	reviewed	54_36p	missense	SNP	1.000	C
PKD1L2	114780	genome.wustl.edu	37	16	81180903	81180903	+	RNA	SNP	C	C	T			TCGA-AB-2928-03A-01W-0745-08	TCGA-AB-2928-11A-01W-0745-08	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	39402967-4dad-4a46-b8d0-5fcb824bc2c2	233dc863-8cfb-4b4d-ad97-ee0685247f3a	g.chr16:81180903C>T	ENST00000525539.1	-	0	5187				PKD1L2_ENST00000533478.1_RNA	NM_052892.3	NP_443124.3	Q7Z442	PK1L2_HUMAN	polycystic kidney disease 1-like 2						ion transport (GO:0006811)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(20)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44						CAGGGCTTACCTTTCATTTCT	0.512																																						dbGAP											0			16											134.0	136.0	135.0					16																	81180903		1943	4128	6071	79738404			0			AY164483	CCDS61998.1, CCDS61999.1	16q23.2	2014-09-11			ENSG00000166473	ENSG00000166473			21715	protein-coding gene	gene with protein product		607894				12782129	Standard	NM_052892		Approved	KIAA1879	uc002fgf.1	Q7Z442	OTTHUMG00000166126		16.37:g.81180903C>T		248	13.15	38		NA	NA	NA	79738404	78	44.29	62	Q6UEE1|Q6ZN46|Q6ZSP2|Q8N1H9|Q96CL2|Q96Q08	Missense_Mutation	SNP	HMMPfam_GPS,HMMSmart_SM00303,PatternScan_CHANNEL_COLICIN,HMMPfam_PLAT,HMMSmart_SM00308,HMMPfam_Lectin_C,HMMSmart_SM00034,superfamily_Lipase/lipooxygenase domain (PLAT/LH2 domain),HMMPfam_PKD_channel,superfamily_C-type lectin-like	p.R1731K	ENST00000525539.1	37	c.5192		16																																																																																			-	NULL		0.512	PKD1L2-001	KNOWN	non_canonical_polymorphism|basic	polymorphic_pseudogene	PKD1L2	polymorphic_pseudogene	OTTHUMT00000387972.2	C			79738404	-1	no_errors	ENST00000299598	ensembl	human	known	54_36p	missense	SNP	1.000	T
CCBE1	147372	genome.wustl.edu	37	18	57103289	57103289	+	Missense_Mutation	SNP	C	C	T			TCGA-AB-2928-03A-01W-0745-08	TCGA-AB-2928-11A-01W-0745-08	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	39402967-4dad-4a46-b8d0-5fcb824bc2c2	233dc863-8cfb-4b4d-ad97-ee0685247f3a	g.chr18:57103289C>T	ENST00000439986.4	-	11	1109	c.1072G>A	c.(1072-1074)Ggg>Agg	p.G358R	CCBE1_ENST00000398179.2_Missense_Mutation_p.G87R	NM_133459.3	NP_597716.1	Q6UXH8	CCBE1_HUMAN	collagen and calcium binding EGF domains 1	358					lymphangiogenesis (GO:0001946)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of lymphangiogenesis (GO:1901492)|positive regulation of protein processing (GO:0010954)|positive regulation of vascular endothelial growth factor signaling pathway (GO:1900748)|positive regulation vascular endothelial growth factor production (GO:0010575)|sprouting angiogenesis (GO:0002040)|venous blood vessel morphogenesis (GO:0048845)	collagen trimer (GO:0005581)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|protease binding (GO:0002020)			NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|liver(1)|lung(6)|ovary(1)|prostate(1)|skin(3)	24		Colorectal(73;0.175)				GTCCGGTGCCCGAACACCTTT	0.547																																					NSCLC(137;1340 1860 15773 39604 51087)|Esophageal Squamous(139;339 1777 2926 19691 38524)	dbGAP											0			18											141.0	145.0	144.0					18																	57103289		2203	4300	6503	55254269	SO:0001583	missense	0			AB075863	CCDS32838.1	18q21.32	2005-01-18				ENSG00000183287			29426	protein-coding gene	gene with protein product		612753				11853319, 12975309	Standard	NM_133459		Approved	FLJ30681, KIAA1983	uc002lib.3	Q6UXH8		ENST00000439986.4:c.1072G>A	18.37:g.57103289C>T	ENSP00000404464:p.Gly358Arg	116	15.22	21		NA	NA	NA	55254269	118	41.38	84	Q6MZX5|Q86SS2|Q8TF19	Missense_Mutation	SNP	PatternScan_ASX_HYDROXYL,HMMSmart_SM00179,HMMSmart_SM00181,HMMPfam_Collagen,PatternScan_EGF_2,HMMPfam_EGF_CA,PatternScan_EGF_CA,superfamily_EGF/Laminin	p.G358R	ENST00000439986.4	37	c.1072	CCDS32838.1	18	.	.	.	.	.	.	.	.	.	.	C	22.0	4.233200	0.79688	.	.	ENSG00000183287	ENST00000439986;ENST00000398179	D;T	0.85088	-1.94;1.6	5.8	4.0	0.46444	.	0.048365	0.85682	D	0.000000	T	0.81997	0.4941	M	0.63843	1.955	0.53005	D	0.999965	P;P;P	0.47841	0.901;0.84;0.564	B;B;B	0.39152	0.292;0.116;0.119	T	0.79115	-0.1936	10	0.27082	T	0.32	-24.9056	15.6345	0.76941	0.0:0.7396:0.2604:0.0	.	87;358;167	Q6UXH8-2;Q6UXH8;Q6UXH8-3	.;CCBE1_HUMAN;.	R	358;87	ENSP00000404464:G358R;ENSP00000381241:G87R	ENSP00000381241:G87R	G	-	1	0	CCBE1	55254269	1.000000	0.71417	0.998000	0.56505	0.987000	0.75469	3.519000	0.53458	0.772000	0.33382	-0.150000	0.13652	GGG	-	NULL		0.547	CCBE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CCBE1	protein_coding	OTTHUMT00000449685.2	C	NM_133459		55254269	-1	no_errors	NM_133459.1	genbank	human	provisional	54_36p	missense	SNP	1.000	T
ZNF99	7652	genome.wustl.edu	37	19	22952090	22952090	+	Missense_Mutation	SNP	C	C	T	rs201519928	byFrequency	TCGA-AB-2928-03A-01W-0745-08	TCGA-AB-2928-11A-01W-0745-08	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	39402967-4dad-4a46-b8d0-5fcb824bc2c2	233dc863-8cfb-4b4d-ad97-ee0685247f3a	g.chr19:22952090C>T	ENST00000596209.1	-	2	130	c.40G>A	c.(40-42)Gct>Act	p.A14T	ZNF99_ENST00000397104.3_Missense_Mutation_p.A35T	NM_001080409.2	NP_001073878.2	A8MXY4	ZNF99_HUMAN	zinc finger protein 99	14	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)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(20)|lung(55)|ovary(2)|prostate(10)|skin(5)|stomach(9)|upper_aerodigestive_tract(2)|urinary_tract(3)	124		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.102)				TCCTCCAGAGCGAATTCTATG	0.408													A|||	9	0.00179712	0.0061	0.0014	5008	,	,		15476	0.0		0.0	False		,,,				2504	0.0					dbGAP											0			19						A	THR/ALA	32,4364		0,32,2166	76.0	82.0	80.0		103	-2.1	0.0	19		80	0,8600		0,0,4300	no	missense	ZNF99	NM_001080409.2	58	0,32,6466	TT,TC,CC		0.0,0.7279,0.2462	benign	35/912	22952090	32,12964	2198	4300	6498	22743930	SO:0001583	missense	0			BC021822	CCDS59369.1	19p12	2013-01-08	2006-01-17		ENSG00000213973	ENSG00000213973		"""Zinc fingers, C2H2-type"", ""-"""	13175	protein-coding gene	gene with protein product		603981	"""zinc finger protein 99 (F8281)"", ""chromosome 19 open reading frame 9"""	C19orf9			Standard	NM_001080409		Approved	MGC24986	uc021urt.1	A8MXY4		ENST00000596209.1:c.40G>A	19.37:g.22952090C>T	ENSP00000472969:p.Ala14Thr	87	15.24	16		0	0.00	0	22743930	85	44.59	70	M0R335	Missense_Mutation	SNP	HMMPfam_KRAB,HMMSmart_KRAB,superfamily_Krueppel-associated_box,HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_ZnF_C2H2,superfamily_SSF57667	p.A35T	ENST00000596209.1	37	c.103	CCDS59369.1	19	.	.	.	.	.	.	.	.	.	.	a	2.370	-0.344467	0.05208	0.007279	0.0	ENSG00000213973	ENST00000397104	T	0.01051	5.4	1.04	-2.08	0.07254	Krueppel-associated box (4);	.	.	.	.	T	0.00178	0.0005	N	0.00028	-2.64	0.09310	N	1	B	0.31227	0.314	B	0.29942	0.109	T	0.30707	-0.9969	9	0.06891	T	0.86	.	1.8418	0.03151	0.2931:0.2542:0.0:0.4528	.	35	A8MXY4	ZNF99_HUMAN	T	35	ENSP00000380293:A35T	ENSP00000380293:A35T	A	-	1	0	ZNF99	22743930	0.449000	0.25689	0.003000	0.11579	0.002000	0.02628	-0.456000	0.06754	-1.794000	0.01256	-1.953000	0.00484	GCT	-	HMMPfam_KRAB,HMMSmart_KRAB,superfamily_Krueppel-associated_box		0.408	ZNF99-001	NOVEL	not_best_in_genome_evidence|basic|CCDS	protein_coding	ZNF99	protein_coding	OTTHUMT00000464591.1	C	XM_065124		22743930	-1	no_errors	NM_001080409.1	genbank	human	provisional	54_36p	missense	SNP	0.002	T
TET2	54790	genome.wustl.edu	37	4	106158442	106158442	+	Frame_Shift_Del	DEL	C	C	-			TCGA-AB-2928-03A-01W-0745-08	TCGA-AB-2928-11A-01W-0745-08	C	C	C	-	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	39402967-4dad-4a46-b8d0-5fcb824bc2c2	233dc863-8cfb-4b4d-ad97-ee0685247f3a	g.chr4:106158442delC	ENST00000540549.1	+	3	4203	c.3343delC	c.(3343-3345)cctfs	p.P1115fs	TET2_ENST00000545826.1_Frame_Shift_Del_p.P1115fs|TET2_ENST00000513237.1_Frame_Shift_Del_p.P1136fs|TET2_ENST00000305737.2_Frame_Shift_Del_p.P1115fs|TET2_ENST00000380013.4_Frame_Shift_Del_p.P1115fs|TET2_ENST00000394764.1_Frame_Shift_Del_p.P1115fs|TET2_ENST00000413648.2_Frame_Shift_Del_p.P1115fs			Q6N021	TET2_HUMAN	tet methylcytosine dioxygenase 2	1115					5-methylcytosine catabolic process (GO:0006211)|cell cycle (GO:0007049)|DNA demethylation (GO:0080111)|histone H3-K4 trimethylation (GO:0080182)|kidney development (GO:0001822)|myeloid cell differentiation (GO:0030099)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|protein O-linked glycosylation (GO:0006493)		DNA binding (GO:0003677)|ferrous iron binding (GO:0008198)|methylcytosine dioxygenase activity (GO:0070579)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1272)|kidney(3)|large_intestine(11)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	1314		Myeloproliferative disorder(5;0.0393)		OV - Ovarian serous cystadenocarcinoma(123;7.18e-08)		ACTAGATACTCCTATAAAAAA	0.373			"""Mis N, F"""		MDS																																	dbGAP		Rec	yes		4	4q24	54790	tet oncogene family member 2		L	0			4							,	10,4254		5,0,2127	51.0	57.0	55.0		,	-11.6	0.1	4		55	21,8233		10,1,4116	no	frameshift,frameshift	TET2	NM_017628.4,NM_001127208.2	,	15,1,6243	A1A1,A1R,RR		0.2544,0.2345,0.2476	,	,	106158442	31,12487	2203	4300	6503	106377891	SO:0001589	frameshift_variant	0			AB046766	CCDS3666.1, CCDS47120.1	4q24	2014-09-17	2011-09-30	2008-03-12	ENSG00000168769	ENSG00000168769			25941	protein-coding gene	gene with protein product		612839	"""KIAA1546"", ""tet oncogene family member 2"""	KIAA1546		10997877, 12646957	Standard	NM_017628		Approved	FLJ20032	uc003hxk.3	Q6N021	OTTHUMG00000131213	ENST00000540549.1:c.3343delC	4.37:g.106158442delC	ENSP00000442788:p.Pro1115fs	72	10.84	9		15	37.50	9	106377891	74	39.84	51	B5MDU0|Q2TB88|Q3LIB8|Q96JX5|Q9HCM6|Q9NXW0	Frame_Shift_Del	DEL	NULL	p.P1115fs	ENST00000540549.1	37	c.3343	CCDS47120.1	4																																																																																			-	NULL		0.373	TET2-202	KNOWN	basic|appris_candidate|CCDS	protein_coding	TET2	protein_coding	OTTHUMT00000253952.2	C	NM_017628		106377891	+1	no_errors	NM_017628.1	genbank	human	validated	54_36p	frame_shift_del	DEL	0.996	-
