#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
BRINP3	339479	genome.wustl.edu	37	1	190067990	190067990	+	Missense_Mutation	SNP	C	C	T			TCGA-AB-2965-03A-01D-0739-09	TCGA-AB-2965-11A-01D-0739-09	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	3467d556-ea36-46aa-b48f-29896f5b56f3	882146d8-0b40-490b-b405-7ba28bf8aaa0	g.chr1:190067990C>T	ENST00000367462.3	-	8	1690	c.1459G>A	c.(1459-1461)Ggc>Agc	p.G487S	BRINP3_ENST00000534846.1_Missense_Mutation_p.G385S	NM_199051.1	NP_950252.1	Q76B58	BRNP3_HUMAN	bone morphogenetic protein/retinoic acid inducible neural-specific 3	487					cell cycle arrest (GO:0007050)|cellular response to retinoic acid (GO:0071300)|negative regulation of mitotic cell cycle (GO:0045930)|positive regulation of neuron differentiation (GO:0045666)	dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)		p.G487S(1)									GTTTCAAAGCCAATATAGTGA	0.522																																						dbGAP											1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	1											155.0	155.0	155.0					1																	190067990		2203	4300	6503	188334613	SO:0001583	missense	0			AB111893	CCDS1373.1	1q31.1	2013-09-18	2013-09-18	2013-09-18	ENSG00000162670	ENSG00000162670			22393	protein-coding gene	gene with protein product			"""family with sequence similarity 5, member C"""	FAM5C		16018821, 15193423	Standard	NM_199051		Approved	DBCCR1L, DBCCR1L1	uc001gse.1	Q76B58	OTTHUMG00000035533	ENST00000367462.3:c.1459G>A	1.37:g.190067990C>T	ENSP00000356432:p.Gly487Ser	382	13.18	58		NA	NA	NA	188334613	308	47.09	275	B3KVP1|B7Z260|O95726|Q2M330	Missense_Mutation	SNP	HMMPfam_MACPF,HMMSmart_SM00457	p.G487S	ENST00000367462.3	37	c.1459	CCDS1373.1	1	.	.	.	.	.	.	.	.	.	.	C	15.89	2.965152	0.53507	.	.	ENSG00000162670	ENST00000367462;ENST00000534846	T;T	0.33216	1.42;1.42	5.75	5.75	0.90469	.	0.000000	0.85682	D	0.000000	T	0.37544	0.1007	L	0.45137	1.4	0.80722	D	1	P;P	0.46142	0.873;0.633	P;B	0.49561	0.615;0.255	T	0.01528	-1.1332	10	0.25751	T	0.34	.	17.4417	0.87566	0.0:1.0:0.0:0.0	.	385;487	B7Z260;Q76B58	.;FAM5C_HUMAN	S	487;385	ENSP00000356432:G487S;ENSP00000438022:G385S	ENSP00000356432:G487S	G	-	1	0	FAM5C	188334613	1.000000	0.71417	0.997000	0.53966	0.928000	0.56348	6.010000	0.70753	2.712000	0.92718	0.591000	0.81541	GGC	-	NULL		0.522	BRINP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	FAM5C	protein_coding	OTTHUMT00000086278.1	C	NM_199051		188334613	-1	no_errors	NM_199051.1	genbank	human	provisional	54_36p	missense	SNP	1.000	T
DNMT3A	1788	genome.wustl.edu	37	2	25457242	25457242	+	Missense_Mutation	SNP	C	C	T	rs147001633	byFrequency	TCGA-AB-2965-03A-01D-0739-09	TCGA-AB-2965-11A-01D-0739-09	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	3467d556-ea36-46aa-b48f-29896f5b56f3	882146d8-0b40-490b-b405-7ba28bf8aaa0	g.chr2:25457242C>T	ENST00000264709.3	-	23	2982	c.2645G>A	c.(2644-2646)cGc>cAc	p.R882H	DNMT3A_ENST00000380746.4_Missense_Mutation_p.R693H|DNMT3A_ENST00000474887.1_5'Flank|DNMT3A_ENST00000402667.1_Missense_Mutation_p.R659H|DNMT3A_ENST00000321117.5_Missense_Mutation_p.R882H	NM_175629.2	NP_783328.1	Q9Y6K1	DNM3A_HUMAN	DNA (cytosine-5-)-methyltransferase 3 alpha	882	SAM-dependent MTase C5-type. {ECO:0000255|PROSITE-ProRule:PRU01016}.		R -> C (in a patient with chronic myelomonocytic leukemia; somatic mutation). {ECO:0000269|PubMed:21828135}.|R -> H (in a patient with chronic myelomonocytic leukemia; somatic mutation). {ECO:0000269|PubMed:21828135}.|R -> P (in a patient with chronic myelomonocytic leukemia; somatic mutation). {ECO:0000269|PubMed:21828135}.		C-5 methylation of cytosine (GO:0090116)|cellular response to amino acid stimulus (GO:0071230)|DNA methylation (GO:0006306)|DNA methylation involved in embryo development (GO:0043045)|DNA methylation involved in gamete generation (GO:0043046)|DNA methylation on cytosine within a CG sequence (GO:0010424)|hypermethylation of CpG island (GO:0044027)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of gene expression by genetic imprinting (GO:0006349)|S-adenosylhomocysteine metabolic process (GO:0046498)|S-adenosylmethioninamine metabolic process (GO:0046499)|spermatogenesis (GO:0007283)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|euchromatin (GO:0000791)|nuclear heterochromatin (GO:0005720)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA (cytosine-5-)-methyltransferase activity (GO:0003886)|DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates (GO:0051718)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|unmethylated CpG binding (GO:0045322)	p.R882H(209)|p.R882P(5)		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)					CCTCGCCAAGCGGCTCATGTT	0.592			"""Mis, F, N, S"""		AML																																	dbGAP		Rec	yes		2	2p23	1788	DNA (cytosine-5-)-methyltransferase 3 alpha		L	214	Substitution - Missense(214)	haematopoietic_and_lymphoid_tissue(214)	2						C	HIS/ARG,HIS/ARG,HIS/ARG	4,4402	6.2+/-15.9	0,4,2199	56.0	51.0	53.0		2645,2078,2645	5.7	1.0	2	dbSNP_134	53	5,8595	3.0+/-9.4	0,5,4295	yes	missense,missense,missense	DNMT3A	NM_022552.3,NM_153759.2,NM_175629.1	29,29,29	0,9,6494	TT,TC,CC		0.0581,0.0908,0.0692	possibly-damaging,possibly-damaging,possibly-damaging	882/913,693/724,882/913	25457242	9,12997	2203	4300	6503	25310746	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.2645G>A	2.37:g.25457242C>T	ENSP00000264709:p.Arg882His	21	16.00	4		16	48.39	15	25310746	12	45.45	10	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.R882H	ENST00000264709.3	37	c.2645	CCDS33157.1	2	.	.	.	.	.	.	.	.	.	.	C	23.1	4.380427	0.82682	9.08E-4	5.81E-4	ENSG00000119772	ENST00000380746;ENST00000321117;ENST00000264709;ENST00000402667	D;D;D;D	0.97186	-4.28;-4.28;-4.28;-4.28	5.72	5.72	0.89469	.	0.000000	0.85682	D	0.000000	D	0.95843	0.8647	M	0.80982	2.52	0.80722	D	1	P;B	0.38922	0.651;0.11	B;B	0.23018	0.043;0.003	D	0.95939	0.8945	10	0.62326	D	0.03	-8.768	18.4404	0.90665	0.0:1.0:0.0:0.0	.	882;693	Q9Y6K1;E9PEB8	DNM3A_HUMAN;.	H	693;882;882;659	ENSP00000370122:R693H;ENSP00000324375:R882H;ENSP00000264709:R882H;ENSP00000384237:R659H	ENSP00000264709:R882H	R	-	2	0	DNMT3A	25310746	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.814000	0.86154	2.698000	0.92095	0.561000	0.74099	CGC	-	superfamily_S-adenosyl-L-methionine-dependent methyltransferases		0.592	DNMT3A-001	KNOWN	basic|CCDS	protein_coding	DNMT3A	protein_coding	OTTHUMT00000211587.1	C	NM_022552		25310746	-1	no_errors	NM_022552.3	genbank	human	reviewed	54_36p	missense	SNP	1.000	T
ARHGEF4	50649	genome.wustl.edu	37	2	131674718	131674718	+	Intron	SNP	G	G	A			TCGA-AB-2965-03A-01D-0739-09	TCGA-AB-2965-11A-01D-0739-09	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	3467d556-ea36-46aa-b48f-29896f5b56f3	882146d8-0b40-490b-b405-7ba28bf8aaa0	g.chr2:131674718G>A	ENST00000326016.5	+	1	411				ARHGEF4_ENST00000409359.1_Missense_Mutation_p.A737T|ARHGEF4_ENST00000428230.2_5'UTR|ARHGEF4_ENST00000392953.3_Intron|ARHGEF4_ENST00000525839.1_5'Flank	NM_015320.2	NP_056135.2	Q9NR80	ARHG4_HUMAN	Rho guanine nucleotide exchange factor (GEF) 4						apoptotic signaling pathway (GO:0097190)|filopodium assembly (GO:0046847)|lamellipodium assembly (GO:0030032)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Rac GTPase activity (GO:0032855)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell projection (GO:0042995)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)|protein domain specific binding (GO:0019904)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)			NS(1)|breast(4)|cervix(1)|endometrium(2)|large_intestine(5)|lung(7)|ovary(3)|pancreas(1)|prostate(1)|skin(4)	29		Prostate(154;0.055)		BRCA - Breast invasive adenocarcinoma(221;0.097)		GGCTGGAATCGCACACACCCT	0.652																																						dbGAP											0			2																																								131391188	SO:0001627	intron_variant	0			AL137289	CCDS2165.1, CCDS42754.1	2q22	2013-01-10			ENSG00000136002	ENSG00000136002		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	684	protein-coding gene	gene with protein product	"""APC-stimulated guanine nucleotide exchange factor"""	605216				10873612	Standard	NM_015320		Approved	STM6, KIAA1112, ASEF	uc002tsa.1	Q9NR80	OTTHUMG00000131657	ENST00000326016.5:c.-109+84G>A	2.37:g.131674718G>A		93	13.08	14		NA	NA	NA	131391188	99	52.63	110	Q9HDC6|Q9UPP0	Missense_Mutation	SNP	NULL	p.A1067T	ENST00000326016.5	37	c.3199	CCDS2165.1	2	.	.	.	.	.	.	.	.	.	.	G	14.10	2.434117	0.43224	.	.	ENSG00000136002	ENST00000409359;ENST00000438985	T;T	0.46451	0.87;0.9	5.09	-2.44	0.06502	.	.	.	.	.	T	0.19327	0.0464	.	.	.	0.09310	N	1	P	0.38863	0.65	B	0.29524	0.103	T	0.13656	-1.0501	8	0.30078	T	0.28	.	5.1993	0.15254	0.4127:0.2997:0.2876:0.0	.	737	E7EV07	.	T	737;61	ENSP00000386794:A737T;ENSP00000389661:A61T	ENSP00000386794:A737T	A	+	1	0	ARHGEF4	131391188	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.816000	0.27267	-0.229000	0.09854	-0.479000	0.04858	GCA	-	NULL		0.652	ARHGEF4-001	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	LOC730032	protein_coding	OTTHUMT00000254554.4	G			131391188	+1	no_errors	XM_001132160.2	genbank	human	model	54_36p	missense	SNP	0.000	A
VIPR1	7433	genome.wustl.edu	37	3	42555253	42555253	+	Missense_Mutation	SNP	G	G	A			TCGA-AB-2965-03A-01D-0739-09	TCGA-AB-2965-11A-01D-0739-09	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	3467d556-ea36-46aa-b48f-29896f5b56f3	882146d8-0b40-490b-b405-7ba28bf8aaa0	g.chr3:42555253G>A	ENST00000325123.4	+	2	204	c.91G>A	c.(91-93)Gcc>Acc	p.A31T	VIPR1_ENST00000433647.1_5'UTR|VIPR1_ENST00000438259.2_Intron|VIPR1-AS1_ENST00000596630.1_RNA|VIPR1-AS1_ENST00000601312.1_RNA|VIPR1-AS1_ENST00000598837.1_RNA|VIPR1-AS1_ENST00000600342.1_RNA|VIPR1-AS1_ENST00000593611.1_RNA|VIPR1-AS1_ENST00000602176.1_RNA|VIPR1-AS1_ENST00000593621.1_RNA|VIPR1_ENST00000543411.1_Intron|VIPR1-AS1_ENST00000452639.3_RNA	NM_001251885.1|NM_004624.3	NP_001238814.1|NP_004615.2	P32241	VIPR1_HUMAN	vasoactive intestinal peptide receptor 1	31					digestion (GO:0007586)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|immune response (GO:0006955)|muscle contraction (GO:0006936)|positive regulation of cell proliferation (GO:0008284)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	vasoactive intestinal polypeptide receptor activity (GO:0004999)	p.A31T(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|ovary(2)|skin(1)|urinary_tract(3)	18				KIRC - Kidney renal clear cell carcinoma(284;0.241)		CGGCCAGGCGGCCAGGCTGCA	0.617																																						dbGAP											1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	3											38.0	31.0	34.0					3																	42555253		2073	4002	6075	42530257	SO:0001583	missense	0			AH005329	CCDS2698.1, CCDS58827.1, CCDS58828.1, CCDS58829.1	3p22	2012-08-10			ENSG00000114812	ENSG00000114812		"""GPCR / Class B : VIP and PACAP (ADCYAP1) receptors"""	12694	protein-coding gene	gene with protein product	"""VIP and PACAP receptor 1"""	192321				7708752	Standard	NM_004624		Approved	VPAC1, RDC1, HVR1, VPAC1R	uc003clf.2	P32241	OTTHUMG00000131792	ENST00000325123.4:c.91G>A	3.37:g.42555253G>A	ENSP00000327246:p.Ala31Thr	342	12.24	48		NA	NA	NA	42530257	87	56.93	115	A5JUT9|B3KPV1|B4DEB5|B4DGI4|F5H1F5|G3V0I1|Q15871|Q6P2M6	Missense_Mutation	SNP	HMMPfam_7tm_2,HMMPfam_HRM,HMMSmart_SM00008,PatternScan_G_PROTEIN_RECEP_F2_1,PatternScan_G_PROTEIN_RECEP_F2_2,superfamily_Hormone receptor domain (HRM Pfam 02793),superfamily_Family A G protein-coupled receptor-like	p.A31T	ENST00000325123.4	37	c.91	CCDS2698.1	3	.	.	.	.	.	.	.	.	.	.	G	10.67	1.416693	0.25552	.	.	ENSG00000114812	ENST00000439731;ENST00000325123	T;T	0.54479	0.57;0.57	4.15	-2.59	0.06209	.	1.163900	0.06692	N	0.769873	T	0.28067	0.0692	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.22836	-1.0205	10	0.12766	T	0.61	.	9.4098	0.38485	0.6617:0.0:0.3383:0.0	.	31	P32241	VIPR1_HUMAN	T	31	ENSP00000403478:A31T;ENSP00000327246:A31T	ENSP00000327246:A31T	A	+	1	0	VIPR1	42530257	0.000000	0.05858	0.000000	0.03702	0.021000	0.10359	-0.838000	0.04372	-0.581000	0.05937	0.561000	0.74099	GCC	-	superfamily_Hormone receptor domain (HRM Pfam 02793)		0.617	VIPR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	VIPR1	protein_coding	OTTHUMT00000254728.4	G	NM_004624		42530257	+1	no_errors	NM_004624.3	genbank	human	validated	54_36p	missense	SNP	0.000	A
HK1	3098	genome.wustl.edu	37	10	71158533	71158533	+	Missense_Mutation	SNP	G	G	A	rs538768945		TCGA-AB-2965-03A-01D-0739-09	TCGA-AB-2965-11A-01D-0739-09	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	3467d556-ea36-46aa-b48f-29896f5b56f3	882146d8-0b40-490b-b405-7ba28bf8aaa0	g.chr10:71158533G>A	ENST00000359426.6	+	17	2662	c.2558G>A	c.(2557-2559)cGt>cAt	p.R853H	HK1_ENST00000448642.2_Missense_Mutation_p.R888H|HK1_ENST00000404387.2_Missense_Mutation_p.R857H|HK1_ENST00000298649.3_Missense_Mutation_p.R852H|HK1_ENST00000360289.2_Missense_Mutation_p.R841H	NM_000188.2	NP_000179.2	P19367	HXK1_HUMAN	hexokinase 1	853	Catalytic.|Hexokinase type-2 2.				carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|cell death (GO:0008219)|cellular glucose homeostasis (GO:0001678)|glucose 6-phosphate metabolic process (GO:0051156)|glucose transport (GO:0015758)|glycolytic process (GO:0006096)|hexose metabolic process (GO:0019318)|hexose transport (GO:0008645)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|fructokinase activity (GO:0008865)|glucokinase activity (GO:0004340)|hexokinase activity (GO:0004396)|mannokinase activity (GO:0019158)	p.R857H(1)		breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|liver(1)|lung(14)|ovary(1)|urinary_tract(2)	35						GGACTGGACCGTCTGAATGTG	0.592													G|||	1	0.000199681	0.0	0.0	5008	,	,		20130	0.001		0.0	False		,,,				2504	0.0					dbGAP											1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	10											106.0	96.0	99.0					10																	71158533		2203	4300	6503	70828539	SO:0001583	missense	0			M75126	CCDS7289.1, CCDS7290.1, CCDS7291.1, CCDS7292.1	10q22	2014-09-17			ENSG00000156515	ENSG00000156515	2.7.1.1		4922	protein-coding gene	gene with protein product		142600					Standard	NM_033496		Approved		uc001jpi.4	P19367	OTTHUMG00000018380	ENST00000359426.6:c.2558G>A	10.37:g.71158533G>A	ENSP00000352398:p.Arg853His	557	17.47	119		32	45.76	27	70828539	190	48.93	183	E9PCK0|O43443|O43444|O75574|Q5VTC3|Q96HC8|Q9NNZ4|Q9NNZ5	Missense_Mutation	SNP	HMMPfam_Hexokinase_1,HMMPfam_Hexokinase_2,PatternScan_HEXOKINASES,superfamily_SSF53067	p.R857H	ENST00000359426.6	37	c.2570	CCDS7292.1	10	.	.	.	.	.	.	.	.	.	.	G	8.227	0.803801	0.16467	.	.	ENSG00000156515	ENST00000360289;ENST00000448642;ENST00000404387;ENST00000298649;ENST00000359426;ENST00000405407	D;D;D;D;D	0.96334	-3.98;-3.98;-3.98;-3.98;-3.98	5.49	-6.87	0.01671	Hexokinase, C-terminal (1);	0.244803	0.47455	N	0.000234	T	0.80154	0.4571	N	0.04260	-0.245	0.09310	N	1	B;B;B;B;B	0.34399	0.0;0.0;0.0;0.0;0.452	B;B;B;B;B	0.13407	0.0;0.0;0.001;0.0;0.009	T	0.82450	-0.0451	10	0.17832	T	0.49	-2.7662	2.7801	0.05358	0.4238:0.1886:0.2953:0.0922	.	853;852;888;857;841	P19367;P19367-2;E7ENR4;P19367-3;P19367-4	HXK1_HUMAN;.;.;.;.	H	841;888;857;852;853;853	ENSP00000353433:R841H;ENSP00000402103:R888H;ENSP00000384774:R857H;ENSP00000298649:R852H;ENSP00000352398:R853H	ENSP00000298649:R852H	R	+	2	0	HK1	70828539	0.000000	0.05858	0.020000	0.16555	0.982000	0.71751	-0.067000	0.11579	-0.792000	0.04480	-0.251000	0.11542	CGT	-	HMMPfam_Hexokinase_2,superfamily_SSF53067		0.592	HK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	HK1	protein_coding	OTTHUMT00000048429.2	G	NM_000188		70828539	+1	no_errors	NM_033497.2	genbank	human	reviewed	54_36p	missense	SNP	0.888	A
RASSF7	8045	genome.wustl.edu	37	11	562159	562159	+	Missense_Mutation	SNP	G	G	T	rs371463729	byFrequency	TCGA-AB-2965-03A-01D-0739-09	TCGA-AB-2965-11A-01D-0739-09	G	G	G	T	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	3467d556-ea36-46aa-b48f-29896f5b56f3	882146d8-0b40-490b-b405-7ba28bf8aaa0	g.chr11:562159G>T	ENST00000397583.3	+	3	638	c.205G>T	c.(205-207)Gcc>Tcc	p.A69S	RASSF7_ENST00000454668.2_Missense_Mutation_p.A69S|C11orf35_ENST00000329451.3_5'Flank|RASSF7_ENST00000524468.1_3'UTR|RP11-496I9.1_ENST00000527620.1_RNA|RASSF7_ENST00000397582.3_Missense_Mutation_p.A69S|RASSF7_ENST00000431809.1_Missense_Mutation_p.A69S|RP11-496I9.1_ENST00000527113.1_RNA|RASSF7_ENST00000344375.4_Missense_Mutation_p.A69S	NM_003475.3	NP_003466.1	Q02833	RASF7_HUMAN	Ras association (RalGDS/AF-6) domain family (N-terminal) member 7	69	Ras-associating. {ECO:0000255|PROSITE- ProRule:PRU00166}.				apoptotic process (GO:0006915)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)		p.A69S(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|skin(3)	8		all_cancers(49;2.16e-06)|all_epithelial(84;0.000256)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;7.18e-28)|Epithelial(43;6.93e-27)|OV - Ovarian serous cystadenocarcinoma(40;6.97e-21)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0375)|LUSC - Lung squamous cell carcinoma(625;0.0703)		TCCAGTGGGCGCCCAGGCCAC	0.642																																					Pancreas(184;1170 3913 7268)	dbGAP											1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	11											27.0	26.0	26.0					11																	562159		2201	4299	6500	552159	SO:0001583	missense	0			M91083	CCDS7702.1, CCDS44505.1, CCDS44506.1	11p15.5	2008-02-22	2008-02-22	2005-09-14	ENSG00000099849	ENSG00000099849			1166	protein-coding gene	gene with protein product		143023	"""chromosome 11 open reading frame 13"""	C11orf13		1339391	Standard	NM_001143993		Approved	HRC1, HRAS1	uc001lqc.3	Q02833	OTTHUMG00000132004	ENST00000397583.3:c.205G>T	11.37:g.562159G>T	ENSP00000380713:p.Ala69Ser	59	9.23	6		3	62.50	5	552159	28	41.67	20	G5E9N9|Q3KP41|Q3KP42	Missense_Mutation	SNP	HMMPfam_RA,HMMSmart_SM00314	p.A69S	ENST00000397583.3	37	c.205	CCDS7702.1	11	.	.	.	.	.	.	.	.	.	.	G	8.630	0.893483	0.17613	.	.	ENSG00000099849	ENST00000431809;ENST00000397582;ENST00000344375;ENST00000397583;ENST00000454668;ENST00000528736	T;T;T;T;T;T	0.19394	2.15;2.15;2.15;2.15;2.15;2.15	3.8	3.8	0.43715	Ras-association (3);	0.285386	0.34628	N	0.003818	T	0.08802	0.0218	N	0.00801	-1.175	0.33377	D	0.574342	P;P;P	0.39443	0.623;0.674;0.623	B;P;B	0.46685	0.389;0.524;0.389	T	0.22800	-1.0206	10	0.13853	T	0.58	-0.1349	10.7102	0.45980	0.0:0.0:0.6841:0.3159	.	69;69;69	G5E9N9;Q02833;Q02833-2	.;RASF7_HUMAN;.	S	69	ENSP00000403068:A69S;ENSP00000380712:A69S;ENSP00000344226:A69S;ENSP00000380713:A69S;ENSP00000405606:A69S;ENSP00000433165:A69S	ENSP00000344226:A69S	A	+	1	0	RASSF7	552159	0.984000	0.35163	1.000000	0.80357	0.965000	0.64279	2.860000	0.48372	1.970000	0.57323	0.555000	0.69702	GCC	-	HMMPfam_RA,HMMSmart_SM00314		0.642	RASSF7-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	RASSF7	protein_coding	OTTHUMT00000254972.2	G	NM_003475		552159	+1	no_errors	NM_003475.1	genbank	human	validated	54_36p	missense	SNP	0.996	T
EFTUD1	79631	genome.wustl.edu	37	15	82530687	82530687	+	Missense_Mutation	SNP	T	T	C			TCGA-AB-2965-03A-01D-0739-09	TCGA-AB-2965-11A-01D-0739-09	T	T	T	C	T	T	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	3467d556-ea36-46aa-b48f-29896f5b56f3	882146d8-0b40-490b-b405-7ba28bf8aaa0	g.chr15:82530687T>C	ENST00000268206.7	-	7	860	c.692A>G	c.(691-693)aAt>aGt	p.N231S	EFTUD1_ENST00000359445.3_Missense_Mutation_p.N180S	NM_024580.5	NP_078856.4	Q7Z2Z2	ETUD1_HUMAN	elongation factor Tu GTP binding domain containing 1	231	tr-type G. {ECO:0000255|PROSITE- ProRule:PRU01059}.				GTP catabolic process (GO:0006184)|mature ribosome assembly (GO:0042256)		GTP binding (GO:0005525)|GTPase activity (GO:0003924)|ribosome binding (GO:0043022)|translation elongation factor activity (GO:0003746)	p.N231S(1)		cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(14)|ovary(1)|pancreas(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	32						AAACACCACATTTCCCTGTTC	0.413																																						dbGAP											1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	15											88.0	86.0	87.0					15																	82530687		1887	4123	6010	80317742	SO:0001583	missense	0			AK056656	CCDS42070.1, CCDS42071.1	15q25.2	2012-07-04			ENSG00000140598	ENSG00000140598			25789	protein-coding gene	gene with protein product	"""ribosome assembly 1 homolog (yeast)"""					14702039	Standard	NM_024580		Approved	FLJ13119, FAM42A, HsT19294, RIA1	uc002bgt.1	Q7Z2Z2	OTTHUMG00000172573	ENST00000268206.7:c.692A>G	15.37:g.82530687T>C	ENSP00000268206:p.Asn231Ser	376	13.56	59		8	57.89	11	80317742	191	50.77	197	A6NKY5|B7Z6I0|Q9H8Z6	Missense_Mutation	SNP	HMMPfam_EFG_C,HMMPfam_GTP_EFTU,HMMPfam_EFG_IV,superfamily_Translation proteins,superfamily_EF-G C-terminal domain-like,superfamily_Ribosomal protein S5 domain 2-like,superfamily_P-loop containing nucleoside triphosphate hydrolases	p.N231S	ENST00000268206.7	37	c.692	CCDS42071.1	15	.	.	.	.	.	.	.	.	.	.	T	15.80	2.939852	0.52972	.	.	ENSG00000140598	ENST00000268206;ENST00000359445	T;T	0.77358	-1.09;-1.09	4.34	3.21	0.36854	Protein synthesis factor, GTP-binding (1);	0.317365	0.24873	U	0.034909	D	0.83298	0.5224	M	0.64567	1.98	0.58432	D	0.999998	D;P	0.64830	0.994;0.774	D;P	0.63877	0.919;0.53	T	0.83318	-0.0019	10	0.87932	D	0	.	10.0983	0.42488	0.0:0.0807:0.0:0.9193	.	180;231	Q7Z2Z2-2;Q7Z2Z2	.;ETUD1_HUMAN	S	231;180	ENSP00000268206:N231S;ENSP00000352418:N180S	ENSP00000268206:N231S	N	-	2	0	EFTUD1	80317742	1.000000	0.71417	0.818000	0.32626	0.989000	0.77384	5.865000	0.69583	0.808000	0.34231	0.333000	0.21579	AAT	-	HMMPfam_GTP_EFTU,superfamily_P-loop containing nucleoside triphosphate hydrolases		0.413	EFTUD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	EFTUD1	protein_coding	OTTHUMT00000419252.1	T	NM_024580		80317742	-1	no_errors	NM_024580.2	genbank	human	validated	54_36p	missense	SNP	0.997	C
ZNF689	115509	genome.wustl.edu	37	16	30616519	30616519	+	Missense_Mutation	SNP	G	G	C			TCGA-AB-2965-03A-01D-0739-09	TCGA-AB-2965-11A-01D-0739-09	G	G	G	C	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	3467d556-ea36-46aa-b48f-29896f5b56f3	882146d8-0b40-490b-b405-7ba28bf8aaa0	g.chr16:30616519G>C	ENST00000287461.3	-	3	906	c.569C>G	c.(568-570)tCc>tGc	p.S190C	RP11-146F11.5_ENST00000563540.1_RNA|ZNF689_ENST00000566673.1_5'UTR	NM_138447.1	NP_612456.1	Q96CS4	ZN689_HUMAN	zinc finger protein 689	190					regulation of transcription, DNA-templated (GO:0006355)|skeletal muscle cell differentiation (GO:0035914)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.S190C(1)		NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(4)|prostate(1)|urinary_tract(1)	14			Colorectal(24;0.198)			GACCAGCAGGGATGGATAGGA	0.587																																						dbGAP											1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	16											71.0	74.0	73.0					16																	30616519		2197	4300	6497	30524020	SO:0001583	missense	0			BC014000	CCDS10686.1	16p11.2	2013-01-08			ENSG00000156853	ENSG00000156853		"""Zinc fingers, C2H2-type"", ""-"""	25173	protein-coding gene	gene with protein product							Standard	NM_138447		Approved	FLJ90415	uc031qvq.1	Q96CS4	OTTHUMG00000132415	ENST00000287461.3:c.569C>G	16.37:g.30616519G>C	ENSP00000287461:p.Ser190Cys	386	13.62	61		2	75.00	6	30524020	126	43.24	96	Q658J5	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.S190C	ENST00000287461.3	37	c.569	CCDS10686.1	16	.	.	.	.	.	.	.	.	.	.	g	5.714	0.316195	0.10789	.	.	ENSG00000156853	ENST00000287461;ENST00000443190	T	0.58940	0.3	5.13	5.13	0.70059	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.40554	N	0.001074	T	0.63616	0.2526	M	0.82433	2.59	0.09310	N	1	B	0.26195	0.144	B	0.27715	0.082	T	0.61608	-0.7028	10	0.66056	D	0.02	-24.2342	16.1202	0.81346	0.0:0.0:1.0:0.0	.	190	Q96CS4	ZN689_HUMAN	C	190	ENSP00000287461:S190C	ENSP00000287461:S190C	S	-	2	0	ZNF689	30524020	0.022000	0.18835	1.000000	0.80357	0.006000	0.05464	1.773000	0.38563	2.666000	0.90696	0.557000	0.71058	TCC	-	HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_ZnF_C2H2,superfamily_SSF57667		0.587	ZNF689-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ZNF689	protein_coding	OTTHUMT00000255552.1	G	NM_138447		30524020	-1	no_errors	NM_138447.1	genbank	human	provisional	54_36p	missense	SNP	0.705	C
TET2	54790	genome.wustl.edu	37	4	106180919	106180919	+	Frame_Shift_Del	DEL	C	C	-			TCGA-AB-2965-03A-01D-0739-09	TCGA-AB-2965-11A-01D-0739-09	C	C	C	-	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	3467d556-ea36-46aa-b48f-29896f5b56f3	882146d8-0b40-490b-b405-7ba28bf8aaa0	g.chr4:106180919delC	ENST00000540549.1	+	7	4807	c.3947delC	c.(3946-3948)ccafs	p.P1316fs	TET2_ENST00000380013.4_Frame_Shift_Del_p.P1316fs|TET2_ENST00000513237.1_Frame_Shift_Del_p.P1337fs|TET2_ENST00000545826.1_3'UTR			Q6N021	TET2_HUMAN	tet methylcytosine dioxygenase 2	1316					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)	p.P1316fs*47(1)		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)		GGGGATGACCCAAAAGAGGTT	0.383			"""Mis N, F"""		MDS																																	dbGAP		Rec	yes		4	4q24	54790	tet oncogene family member 2		L	1	Deletion - Frameshift(1)	haematopoietic_and_lymphoid_tissue(1)	4											88.0	75.0	79.0					4																	106180919		692	1591	2283	106400368	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.3947delC	4.37:g.106180919delC	ENSP00000442788:p.Pro1316fs	213	0.00	0		11	0.00	0	106400368	202	0.00	0	B5MDU0|Q2TB88|Q3LIB8|Q96JX5|Q9HCM6|Q9NXW0	Frame_Shift_Del	DEL	NULL	p.P118fs	ENST00000540549.1	37	c.353	CCDS47120.1	4																																																																																			-	NULL		0.383	TET2-202	KNOWN	basic|appris_candidate|CCDS	protein_coding	TET2	protein_coding	OTTHUMT00000253952.2	C	NM_017628		106400368	+1	no_start_codon	ENST00000265149	ensembl	human	known	54_36p	frame_shift_del	DEL	1.000	-
NPM1	4869	genome.wustl.edu	37	5	170837547	170837548	+	Frame_Shift_Ins	INS	-	-	TCTG			TCGA-AB-2965-03A-01D-0739-09	TCGA-AB-2965-11A-01D-0739-09	-	-	-	TCTG	-	-	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	3467d556-ea36-46aa-b48f-29896f5b56f3	882146d8-0b40-490b-b405-7ba28bf8aaa0	g.chr5:170837547_170837548insTCTG	ENST00000296930.5	+	11	1164_1165	c.863_864insTCTG	c.(862-867)tggcagfs	p.WQ288fs	NPM1_ENST00000351986.6_Frame_Shift_Ins_p.WQ259fs|NPM1_ENST00000517671.1_Frame_Shift_Ins_p.WQ288fs	NM_002520.6	NP_002511.1	P06748	NPM_HUMAN	nucleophosmin (nucleolar phosphoprotein B23, numatrin)	288	Required for nucleolar localization.			WQWRKSL -> CLAVEEVSLRK (in Ref. 6; AAW67752/AAW67755). {ECO:0000305}.|WQWRKSL -> CMAVEEVSLRK (in Ref. 6; AAW67753 and 7; ABC40399). {ECO:0000305}.|WQWRKSL -> CVAVEEVSLRK (in Ref. 6; AAW67754). {ECO:0000305}.	cell aging (GO:0007569)|CENP-A containing nucleosome assembly (GO:0034080)|centrosome cycle (GO:0007098)|DNA repair (GO:0006281)|intracellular protein transport (GO:0006886)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of centrosome duplication (GO:0010826)|negative regulation of protein kinase activity by regulation of protein phosphorylation (GO:0044387)|nucleocytoplasmic transport (GO:0006913)|nucleosome assembly (GO:0006334)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of translation (GO:0045727)|protein localization (GO:0008104)|protein oligomerization (GO:0051259)|regulation of centriole replication (GO:0046599)|regulation of eIF2 alpha phosphorylation by dsRNA (GO:0060735)|regulation of endodeoxyribonuclease activity (GO:0032071)|regulation of endoribonuclease activity (GO:0060699)|response to stress (GO:0006950)|ribosome assembly (GO:0042255)|signal transduction (GO:0007165)|viral process (GO:0016032)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|spindle pole centrosome (GO:0031616)	histone binding (GO:0042393)|NF-kappaB binding (GO:0051059)|poly(A) RNA binding (GO:0044822)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|protein kinase inhibitor activity (GO:0004860)|ribosomal large subunit binding (GO:0043023)|ribosomal small subunit binding (GO:0043024)|RNA binding (GO:0003723)|Tat protein binding (GO:0030957)|transcription coactivator activity (GO:0003713)|unfolded protein binding (GO:0051082)	p.W288fs*12(2114)|p.W288fs*10(9)|p.Q289fs*11(3)|p.W288*(1)	NPM1/ALK(632)	central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(4261)|kidney(1)|large_intestine(1)|lung(4)|skin(1)	4269	Renal(175;0.000159)|Lung NSC(126;0.00576)|all_lung(126;0.00963)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			CAAGATCTCTGGCAGTGGAGGA	0.312			"""T, F """	"""ALK, RARA, MLF1"""	"""NHL, APL, AML"""																																	dbGAP		Dom	yes		5	5q35	4869	"""nucleophosmin (nucleolar phosphoprotein B23, numatrin)"""		L	2127	Insertion - Frameshift(2118)|Complex - frameshift(8)|Substitution - Nonsense(1)	haematopoietic_and_lymphoid_tissue(2127)	5																																								170770153	SO:0001589	frameshift_variant	0			M26697	CCDS4376.1, CCDS4377.1, CCDS43399.1	5q35.1	2014-09-17			ENSG00000181163	ENSG00000181163			7910	protein-coding gene	gene with protein product	"""nucleolar phosphoprotein B23"", ""numatrin"", ""nucleophosmin/nucleoplasmin family, member 1"""	164040				8471164, 8122112	Standard	NM_002520		Approved	B23, NPM	uc003mbi.3	P06748	OTTHUMG00000130465	ENST00000296930.5:c.860_863dupTCTG	5.37:g.170837544_170837547dupTCTG	ENSP00000296930:p.Trp288fs	NA	NA	NA		NA	NA	NA	170770152	NA	NA	NA	A8K3N7|B5BU00|D3DQL6|P08693|Q12826|Q13440|Q13441|Q14115|Q5EU94|Q5EU95|Q5EU96|Q5EU97|Q5EU98|Q5EU99|Q6V962|Q8WTW5|Q96AT6|Q96DC4|Q96EA5|Q9BYG9|Q9UDJ7	Frame_Shift_Ins	INS	HMMPfam_Nucleoplasmin,superfamily_Nucleoplasmin-like core domain	p.W288fs	ENST00000296930.5	37	c.863_864	CCDS4376.1	5																																																																																			-	NULL		0.312	NPM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NPM1	protein_coding	OTTHUMT00000252858.2	-	NM_002520		170770153	+1	no_errors	NM_002520.1	genbank	human	validated	54_36p	frame_shift_ins	INS	1.000:1.000	TCTG
FLT3	2322	genome.wustl.edu	37	13	28608338	28608339	+	In_Frame_Ins	INS	-	-	TTCTCTGAAATCAACGTAGAAGTACTCATTATCTGAGGAGCCGGTCACCTGTACCATCTGTAGCTGGCTTTT			TCGA-AB-2965-03A-01D-0739-09	TCGA-AB-2965-11A-01D-0739-09	-	-	-	TTCTCTGAAATCAACGTAGAAGTACTCATTATCTGAGGAGCCGGTCACCTGTACCATCTGTAGCTGGCTTTT	-	-	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	3467d556-ea36-46aa-b48f-29896f5b56f3	882146d8-0b40-490b-b405-7ba28bf8aaa0	g.chr13:28608338_28608339insTTCTCTGAAATCAACGTAGAAGTACTCATTATCTGAGGAGCCGGTCACCTGTACCATCTGTAGCTGGCTTTT	ENST00000241453.7	-	14	1798_1799	c.1717_1718insAAAAGCCAGCTACAGATGGTACAGGTGACCGGCTCCTCAGATAATGAGTACTTCTACGTTGATTTCAGAGAA	c.(1717-1719)gaa>gAAAAGCCAGCTACAGATGGTACAGGTGACCGGCTCCTCAGATAATGAGTACTTCTACGTTGATTTCAGAGAAaa	p.573_574insKPATDGTGDRLLR**VLLR*FQRK	FLT3_ENST00000537084.1_In_Frame_Ins_p.573_574insKPATDGTGDRLLR**VLLR*FQRK|FLT3_ENST00000380982.4_In_Frame_Ins_p.573_574insKPATDGTGDRLLR**VLLR*FQRK	NM_004119.2	NP_004110.2	P36888	FLT3_HUMAN	fms-related tyrosine kinase 3	573					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.Q569_Q580del(1)|p.Y572_E573ins32(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)	TAGCTGGCTTTCATACCTAAAT	0.381			"""Mis, O"""		"""AML, ALL"""																																	dbGAP		Dom	yes		13	13q12	2322	fms-related tyrosine kinase 3		L	2	Insertion - In frame(1)|Deletion - In frame(1)	haematopoietic_and_lymphoid_tissue(2)	13																																								27506339	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.1717_1718insAAAAGCCAGCTACAGATGGTACAGGTGACCGGCTCCTCAGATAATGAGTACTTCTACGTTGATTTCAGAGAA	13.37:g.28608338_28608339insTTCTCTGAAATCAACGTAGAAGTACTCATTATCTGAGGAGCCGGTCACCTGTACCATCTGTAGCTGGCTTTT	ENSP00000241453:p.Glu573_Ser574insLysProAlaThrAspGlyThrGlyAspArgLeuLeuArg**ValLeuLeuArg*PheGlnArgLys	NA	NA	NA		NA	NA	NA	27506338	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.574in_frame_insKPATDGTGDRLLR**VLLR*FQRK	ENST00000241453.7	37	c.1718_1717	CCDS31953.1	13																																																																																			-	superfamily_Kinase_like		0.381	FLT3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	FLT3	protein_coding	OTTHUMT00000044319.2	-			27506339	-1	no_errors	NM_004119.2	genbank	human	reviewed	54_36p	in_frame_ins	INS	1.000:1.000	TTCTCTGAAATCAACGTAGAAGTACTCATTATCTGAGGAGCCGGTCACCTGTACCATCTGTAGCTGGCTTTT
