#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_ACHILLES_Lineage_Results_Top_Genes	i_BAM_File	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_Chromosome_hg18	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_End_position_hg18	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_Mutation_Status	i_NormalRefReads_WU	i_NormalVAF_WU	i_NormalVarReads_WU	i_ORegAnno_bin	i_RNARefReads_WU	i_RNAVAF_WU	i_RNAVarReads_WU	i_Sequence_Source	i_Sequencer	i_Sequencing_Phase	i_Start_position_hg18	i_TumorRefReads_WU	i_TumorVAF_WU	i_TumorVarReads_WU	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_all_domains	i_amino_acid_change	i_annotation_transcript	i_build	i_c_position	i_ccds_id	i_chromosome_name	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_deletion_substructures	i_domain	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_name	i_gene_type	i_havana_transcript	i_reference	i_refseq_mrna_id	i_secondary_variant_classification	i_stop	i_strand	i_transcript_error	i_transcript_name	i_transcript_source	i_transcript_species	i_transcript_status	i_transcript_version	i_trv_type	i_type	i_ucsc_cons	i_variant
Unknown	0	genome.wustl.edu	37	Unknown	0	0	+	IGR	SNP	G	G	A			TCGA-AB-2811-03B-01W-0728-08	TCGA-AB-2811-11B-01W-0728-08	G	G	G	A	G	G	Verified	Invalid:failed_liftOver	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	7e9b79b7-d6b7-4365-8597-dad296c4b3f5	9602849c-4204-47bd-9c80-7af80031f25c	g.chrUnknown:0G>A								None (None upstream) : None (None downstream)																								0.0																																						dbGAP											0			MT																																								2779	SO:0001628	intergenic_variant	0																															Unknown.37:g.0G>A		Somatic	1745	4.52	83		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	2779	3832	26.70	1399		RNA	SNP	-	NULL		37	NULL		MT																																																																																			-	-	0	0					ENSG00000210082			G			2779	+1	no_errors	ENST00000387347	ensembl	human	known	54_36p	rna	SNP	NULL	A
SMC1A	8243	genome.wustl.edu	37	X	53432579	53432579	+	Missense_Mutation	SNP	C	C	T			TCGA-AB-2811-03B-01W-0728-08	TCGA-AB-2811-11B-01W-0728-08	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	7e9b79b7-d6b7-4365-8597-dad296c4b3f5	9602849c-4204-47bd-9c80-7af80031f25c	g.chrX:53432579C>T	ENST00000322213.4	-	11	1884	c.1757G>A	c.(1756-1758)cGg>cAg	p.R586Q	SMC1A_ENST00000375340.6_Missense_Mutation_p.R352Q	NM_006306.2	NP_006297.2	Q14683	SMC1A_HUMAN	structural maintenance of chromosomes 1A	586	Flexible hinge.				DNA repair (GO:0006281)|gene expression (GO:0010467)|meiotic nuclear division (GO:0007126)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic sister chromatid cohesion (GO:0007064)|mitotic sister chromatid segregation (GO:0000070)|mitotic spindle organization (GO:0007052)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of DNA endoreduplication (GO:0032876)|response to radiation (GO:0009314)|RNA splicing (GO:0008380)|signal transduction in response to DNA damage (GO:0042770)|sister chromatid cohesion (GO:0007062)|stem cell maintenance (GO:0019827)	chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cohesin core heterodimer (GO:0008280)|condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|meiotic cohesin complex (GO:0030893)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|microtubule motor activity (GO:0003777)|poly(A) RNA binding (GO:0044822)|protein heterodimerization activity (GO:0046982)			NS(1)|breast(3)|central_nervous_system(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(8)|ovary(5)|upper_aerodigestive_tract(2)	49						CTTCAGCTCCCGGAGTTTCTC	0.532																																						dbGAP											0			X											56.0	45.0	49.0					X																	53432579		2203	4300	6503	53449304	SO:0001583	missense	0			S78271	CCDS14352.1, CCDS75985.1	Xp11.22-p11.21	2014-09-17	2006-07-06	2006-07-06	ENSG00000072501	ENSG00000072501		"""Structural maintenance of chromosomes proteins"""	11111	protein-coding gene	gene with protein product		300040	"""SMC1 (structural maintenance of chromosomes 1, yeast)-like 1"", ""SMC1 structural maintenance of chromosomes 1-like 1 (yeast)"""	SMC1L1		7757074	Standard	NM_006306		Approved	DXS423E, KIAA0178, SB1.8, Smcb	uc004dsg.3	Q14683	OTTHUMG00000021614	ENST00000322213.4:c.1757G>A	X.37:g.53432579C>T	ENSP00000323421:p.Arg586Gln	Somatic	22	4.35	1		5	70.59	12	WXS	Illumina HiSeq	Phase_IV	53449304	8	92.38	97	O14995|Q16351|Q2M228	Missense_Mutation	SNP	HMMPfam_SMC_N,HMMPfam_SMC_hinge,superfamily_SMC_hinge,superfamily_SSF52540	p.R586Q	ENST00000322213.4	37	c.1757	CCDS14352.1	X	.	.	.	.	.	.	.	.	.	.	C	23.9	4.472433	0.84640	.	.	ENSG00000072501	ENST00000322213;ENST00000375340	D;D	0.86097	-2.07;-2.07	5.15	5.15	0.70609	SMCs flexible hinge (3);RecF/RecN/SMC (1);	0.000000	0.85682	D	0.000000	D	0.92051	0.7481	M	0.75884	2.315	0.80722	D	1	D;D;D	0.89917	0.996;0.998;1.0	P;D;D	0.91635	0.893;0.924;0.999	D	0.92912	0.6348	10	0.87932	D	0	.	16.9916	0.86355	0.0:1.0:0.0:0.0	.	352;564;586	B7Z709;Q6MZR8;Q14683	.;.;SMC1A_HUMAN	Q	586;352	ENSP00000323421:R586Q;ENSP00000364489:R352Q	ENSP00000323421:R586Q	R	-	2	0	SMC1A	53449304	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.589000	0.82641	2.476000	0.83614	0.600000	0.82982	CGG	-	HMMPfam_SMC_N,HMMPfam_SMC_hinge,superfamily_SMC_hinge,superfamily_SSF52540		0.532	SMC1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SMC1A	protein_coding	OTTHUMT00000056756.2	C	NM_006306		53449304	-1	no_errors	NM_006306.2	genbank	human	reviewed	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-2811-03B-01W-0728-08	TCGA-AB-2811-11B-01W-0728-08	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	7e9b79b7-d6b7-4365-8597-dad296c4b3f5	9602849c-4204-47bd-9c80-7af80031f25c	g.chr2:25457242C>T	ENST00000264709.3	-	23	2982	c.2645G>A	c.(2644-2646)cGc>cAc	p.R882H	DNMT3A_ENST00000402667.1_Missense_Mutation_p.R659H|DNMT3A_ENST00000474887.1_5'Flank|DNMT3A_ENST00000380746.4_Missense_Mutation_p.R693H|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	Somatic	73	7.50	6		23	53.06	26	WXS	Illumina HiSeq	Phase_IV	25310746	91	48.00	84	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
TEKT4	150483	genome.wustl.edu	37	2	95542461	95542461	+	Missense_Mutation	SNP	A	A	G			TCGA-AB-2811-03B-01W-0728-08	TCGA-AB-2811-11B-01W-0728-08	A	A	A	G	A	A	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	7e9b79b7-d6b7-4365-8597-dad296c4b3f5	9602849c-4204-47bd-9c80-7af80031f25c	g.chr2:95542461A>G	ENST00000295201.4	+	6	1392	c.1255A>G	c.(1255-1257)Atg>Gtg	p.M419V	AC097374.2_ENST00000568768.1_RNA	NM_144705.2	NP_653306.1	Q8WW24	TEKT4_HUMAN	tektin 4	419					cell projection organization (GO:0030030)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|motile cilium (GO:0031514)|nucleus (GO:0005634)				NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(15)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	28						CCAGAAGTGCATGGCCCATCG	0.607																																						dbGAP											0			2											82.0	57.0	66.0					2																	95542461		2203	4300	6503	94906188	SO:0001583	missense	0			AK097438	CCDS2005.1	2q11.2	2008-02-05			ENSG00000163060	ENSG00000163060			31012	protein-coding gene	gene with protein product							Standard	XM_005263876		Approved	MGC27019	uc002stw.1	Q8WW24	OTTHUMG00000130396	ENST00000295201.4:c.1255A>G	2.37:g.95542461A>G	ENSP00000295201:p.Met419Val	Somatic	41	2.38	1		3	0.00	0	WXS	Illumina HiSeq	Phase_IV	94906188	60	46.90	53		Missense_Mutation	SNP	HMMPfam_Tektin	p.M419V	ENST00000295201.4	37	c.1255	CCDS2005.1	2	.	.	.	.	.	.	.	.	.	.	.	16.91	3.253973	0.59212	.	.	ENSG00000163060	ENST00000295201	T	0.02837	4.14	2.43	-1.48	0.08745	.	0.088193	0.85682	D	0.000000	T	0.07863	0.0197	M	0.86805	2.84	0.80722	D	1	P	0.45531	0.86	P	0.52309	0.695	T	0.10520	-1.0626	10	0.54805	T	0.06	-23.8065	3.4079	0.07348	0.5506:0.2268:0.0:0.2226	.	419	Q8WW24	TEKT4_HUMAN	V	419	ENSP00000295201:M419V	ENSP00000295201:M419V	M	+	1	0	TEKT4	94906188	1.000000	0.71417	0.992000	0.48379	0.874000	0.50279	2.693000	0.47027	-0.030000	0.13804	0.234000	0.17832	ATG	-	HMMPfam_Tektin		0.607	TEKT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TEKT4	protein_coding	OTTHUMT00000252777.1	A	NM_144705		94906188	+1	no_errors	NM_144705.2	genbank	human	provisional	54_36p	missense	SNP	1.000	G
OR2Y1	134083	genome.wustl.edu	37	5	180167000	180167000	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AB-2811-03B-01W-0728-08	TCGA-AB-2811-11B-01W-0728-08	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	7e9b79b7-d6b7-4365-8597-dad296c4b3f5	9602849c-4204-47bd-9c80-7af80031f25c	g.chr5:180167000C>T	ENST00000307832.2	-	1	99	c.59G>A	c.(58-60)tGg>tAg	p.W20*		NM_001001657.1	NP_001001657.1	Q8NGV0	OR2Y1_HUMAN	olfactory receptor, family 2, subfamily Y, member 1	20						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(9)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	20	all_cancers(89;1.25e-05)|all_epithelial(37;4.36e-06)|Renal(175;0.000159)|Lung NSC(126;0.00317)|all_lung(126;0.0041)|Breast(19;0.114)	all_cancers(40;0.0834)|Medulloblastoma(196;0.0392)|all_neural(177;0.0529)|all_hematologic(541;0.191)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CAGTTGCGGCCAATCTGAGAA	0.458																																						dbGAP											0			5											50.0	54.0	53.0					5																	180167000		2203	4300	6503	180099606	SO:0001587	stop_gained	0			AB065676	CCDS34323.1	5q35	2012-08-09			ENSG00000174339	ENSG00000174339		"""GPCR / Class A : Olfactory receptors"""	14837	protein-coding gene	gene with protein product							Standard	NM_001001657		Approved		uc003mmf.1	Q8NGV0	OTTHUMG00000162237	ENST00000307832.2:c.59G>A	5.37:g.180167000C>T	ENSP00000312403:p.Trp20*	Somatic	183	11.17	23		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	180099606	307	45.57	257	B9EIP1|Q6IFB1|Q96R16	Nonsense_Mutation	SNP	HMMPfam_7tm_1,PatternScan_G_PROTEIN_RECEP_F1_1,superfamily_SSF81321	p.W20*	ENST00000307832.2	37	c.59	CCDS34323.1	5	.	.	.	.	.	.	.	.	.	.	c	11.08	1.534740	0.27475	.	.	ENSG00000174339	ENST00000307832	.	.	.	4.41	1.58	0.23477	.	0.154798	0.30999	N	0.008455	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.23891	T	0.37	.	3.7676	0.08629	0.1691:0.5523:0.0:0.2787	.	.	.	.	X	20	.	ENSP00000312403:W20X	W	-	2	0	OR2Y1	180099606	0.000000	0.05858	0.024000	0.17045	0.000000	0.00434	-1.333000	0.02667	0.197000	0.20387	-0.409000	0.06214	TGG	-	superfamily_SSF81321		0.458	OR2Y1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	OR2Y1	protein_coding	OTTHUMT00000368059.2	C	XM_068682		180099606	-1	no_errors	NM_001001657.1	genbank	human	provisional	54_36p	nonsense	SNP	0.001	T
DOCK4	9732	genome.wustl.edu	37	7	111381644	111381644	+	Missense_Mutation	SNP	G	G	T			TCGA-AB-2811-03B-01W-0728-08	TCGA-AB-2811-11B-01W-0728-08	G	G	G	T	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	7e9b79b7-d6b7-4365-8597-dad296c4b3f5	9602849c-4204-47bd-9c80-7af80031f25c	g.chr7:111381644G>T	ENST00000437633.1	-	45	5100	c.4844C>A	c.(4843-4845)gCa>gAa	p.A1615E	DOCK4_ENST00000494651.2_Missense_Mutation_p.A498E|DOCK4_ENST00000428084.1_Missense_Mutation_p.A1624E	NM_014705.3	NP_055520.3	Q8N1I0	DOCK4_HUMAN	dedicator of cytokinesis 4	1615					cell chemotaxis (GO:0060326)|positive regulation of Rac GTPase activity (GO:0032855)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)|stereocilium (GO:0032420)|stereocilium bundle (GO:0032421)	guanyl-nucleotide exchange factor activity (GO:0005085)|PDZ domain binding (GO:0030165)|Rac GTPase activator activity (GO:0030675)|Rac GTPase binding (GO:0048365)|receptor tyrosine kinase binding (GO:0030971)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(13)|lung(31)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(4)	72		Acute lymphoblastic leukemia(1;0.0441)				AGAAGCAGGTGCTGAGTTTCT	0.453																																						dbGAP											0			7											70.0	68.0	68.0					7																	111381644		1896	4133	6029	111168880	SO:0001583	missense	0				CCDS47688.1	7q31.1	2007-08-07			ENSG00000128512	ENSG00000128512			19192	protein-coding gene	gene with protein product		607679				12432077, 12628187	Standard	XM_006716188		Approved	FLJ34238, KIAA0716	uc003vfx.3	Q8N1I0	OTTHUMG00000155077	ENST00000437633.1:c.4844C>A	7.37:g.111381644G>T	ENSP00000404179:p.Ala1615Glu	Somatic	50	1.96	1		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	111168880	126	46.84	111	O14584|O94824|Q8NB45	Missense_Mutation	SNP	HMMSmart_SM00326,superfamily_SH3-domain,HMMPfam_SH3_2	p.A1615E	ENST00000437633.1	37	c.4844	CCDS47688.1	7	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	4.547|4.547	0.101619|0.101619	0.08731|0.08731	.|.	.|.	ENSG00000128512|ENSG00000128512	ENST00000352877;ENST00000428084;ENST00000494651;ENST00000437633;ENST00000342288|ENST00000423057;ENST00000445943	T;T;T|.	0.05649|.	4.14;3.41;4.14|.	5.24|5.24	4.36|4.36	0.52297|0.52297	.|.	0.294275|.	0.36854|.	N|.	0.002362|.	T|T	0.41558|0.41558	0.1164|0.1164	N|N	0.22421|0.22421	0.69|0.69	0.38483|0.38483	D|D	0.947767|0.947767	B;B;B;B;B|.	0.28933|.	0.01;0.228;0.034;0.005;0.008|.	B;B;B;B;B|.	0.33846|.	0.017;0.171;0.039;0.017;0.038|.	T|T	0.34601|0.34601	-0.9822|-0.9822	10|5	0.02654|.	T|.	1|.	.|.	8.4241|8.4241	0.32718|0.32718	0.2181:0.0:0.7819:0.0|0.2181:0.0:0.7819:0.0	.|.	522;498;1660;1615;1624|.	B7Z2K9;F5GXW1;Q149N5;Q8N1I0;Q8N1I0-2|.	.;.;.;DOCK4_HUMAN;.|.	E|N	1603;1624;498;1615;1612|1076;1648	ENSP00000410746:A1624E;ENSP00000440944:A498E;ENSP00000404179:A1615E|.	ENSP00000345432:A1612E|.	A|H	-|-	2|1	0|0	DOCK4|DOCK4	111168880|111168880	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.996000|0.996000	0.88848|0.88848	2.943000|2.943000	0.49026|0.49026	1.431000|1.431000	0.47355|0.47355	0.655000|0.655000	0.94253|0.94253	GCA|CAC	-	NULL		0.453	DOCK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	DOCK4	protein_coding	OTTHUMT00000338369.4	G	NM_014705		111168880	-1	no_errors	NM_014705.3	genbank	human	reviewed	54_36p	missense	SNP	0.994	T
PTCH1	5727	genome.wustl.edu	37	9	98220525	98220525	+	Missense_Mutation	SNP	C	C	T			TCGA-AB-2811-03B-01W-0728-08	TCGA-AB-2811-11B-01W-0728-08	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	7e9b79b7-d6b7-4365-8597-dad296c4b3f5	9602849c-4204-47bd-9c80-7af80031f25c	g.chr9:98220525C>T	ENST00000331920.6	-	18	3237	c.2938G>A	c.(2938-2940)Ggc>Agc	p.G980S	PTCH1_ENST00000437951.1_Missense_Mutation_p.G914S|PTCH1_ENST00000421141.1_Missense_Mutation_p.G829S|PTCH1_ENST00000418258.1_Missense_Mutation_p.G829S|PTCH1_ENST00000430669.2_Missense_Mutation_p.G914S|PTCH1_ENST00000429896.2_Missense_Mutation_p.G829S|PTCH1_ENST00000375274.2_Missense_Mutation_p.G979S	NM_000264.3	NP_000255.2	Q13635	PTC1_HUMAN	patched 1	980					brain development (GO:0007420)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation involved in kidney development (GO:0061005)|cell proliferation involved in metanephros development (GO:0072203)|cellular response to cholesterol (GO:0071397)|dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|embryonic organ development (GO:0048568)|epidermis development (GO:0008544)|glucose homeostasis (GO:0042593)|heart morphogenesis (GO:0003007)|hindlimb morphogenesis (GO:0035137)|in utero embryonic development (GO:0001701)|keratinocyte proliferation (GO:0043616)|limb morphogenesis (GO:0035108)|mammary gland duct morphogenesis (GO:0060603)|mammary gland epithelial cell differentiation (GO:0060644)|negative regulation of cell division (GO:0051782)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural plate axis specification (GO:0021997)|neural tube closure (GO:0001843)|neural tube patterning (GO:0021532)|organ morphogenesis (GO:0009887)|pharyngeal system development (GO:0060037)|positive regulation of cholesterol efflux (GO:0010875)|protein processing (GO:0016485)|protein targeting to plasma membrane (GO:0072661)|regulation of mitotic cell cycle (GO:0007346)|regulation of protein localization (GO:0032880)|regulation of smoothened signaling pathway (GO:0008589)|renal system development (GO:0072001)|response to chlorate (GO:0010157)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to mechanical stimulus (GO:0009612)|response to retinoic acid (GO:0032526)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)|somite development (GO:0061053)|spinal cord motor neuron differentiation (GO:0021522)	axonal growth cone (GO:0044295)|caveola (GO:0005901)|dendritic growth cone (GO:0044294)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|midbody (GO:0030496)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|primary cilium (GO:0072372)	cholesterol binding (GO:0015485)|cyclin binding (GO:0030332)|hedgehog family protein binding (GO:0097108)|hedgehog receptor activity (GO:0008158)|heparin binding (GO:0008201)|smoothened binding (GO:0005119)	p.I963fs*2(1)		NS(8)|bone(33)|breast(10)|central_nervous_system(95)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(8)|kidney(2)|large_intestine(18)|lung(22)|meninges(1)|oesophagus(3)|ovary(6)|prostate(2)|skin(262)|upper_aerodigestive_tract(11)|urinary_tract(2)|vulva(1)	490		Medulloblastoma(1;7.87e-06)|all_neural(1;0.000555)|Acute lymphoblastic leukemia(62;0.136)				TCCCGCAAGCCGTTGAGGTAG	0.557																																						dbGAP											1	Deletion - Frameshift(1)	central_nervous_system(1)	9											42.0	38.0	39.0					9																	98220525		2203	4300	6503	97260346	SO:0001583	missense	0			AI494442	CCDS6714.1, CCDS43851.1, CCDS47995.1, CCDS47996.1	9q22.1-q31	2014-09-17	2010-06-24	2006-09-26	ENSG00000185920	ENSG00000185920			9585	protein-coding gene	gene with protein product		601309	"""patched (Drosophila) homolog"", ""patched homolog (Drosophila)"", ""patched homolog 1 (Drosophila)"""	NBCCS, PTCH		8658145	Standard	NM_001083603		Approved	BCNS	uc004avk.4	Q13635	OTTHUMG00000020280	ENST00000331920.6:c.2938G>A	9.37:g.98220525C>T	ENSP00000332353:p.Gly980Ser	Somatic	172	11.56	23		1	0.00	0	WXS	Illumina HiSeq	Phase_IV	97260346	132	44.77	107	A3KBI9|E9PEJ8|Q13463|Q5R1U7|Q5R1U9|Q5R1V0|Q5VZC0|Q5VZC2|Q86XG7	Missense_Mutation	SNP	HMMPfam_Patched,superfamily_SSF82866	p.G980S	ENST00000331920.6	37	c.2938	CCDS6714.1	9	.	.	.	.	.	.	.	.	.	.	C	33	5.205698	0.95033	.	.	ENSG00000185920	ENST00000331920;ENST00000437951;ENST00000421141;ENST00000418258;ENST00000375275;ENST00000430669;ENST00000429896;ENST00000375274	D;D;D;D;D;D;D	0.85411	-1.98;-1.98;-1.98;-1.98;-1.98;-1.98;-1.98	5.21	5.21	0.72293	.	0.000000	0.85682	D	0.000000	D	0.90096	0.6906	M	0.64404	1.975	0.80722	D	1	D;D;D	0.89917	0.999;1.0;1.0	D;D;D	0.72982	0.964;0.978;0.979	D	0.84974	0.0884	10	0.08837	T	0.75	-32.7445	19.314	0.94204	0.0:1.0:0.0:0.0	.	914;979;980	Q13635-3;Q13635-2;Q13635	.;.;PTC1_HUMAN	S	980;914;829;829;416;914;829;979	ENSP00000332353:G980S;ENSP00000389744:G914S;ENSP00000399981:G829S;ENSP00000396135:G829S;ENSP00000410287:G914S;ENSP00000414823:G829S;ENSP00000364423:G979S	ENSP00000332353:G980S	G	-	1	0	PTCH1	97260346	1.000000	0.71417	0.998000	0.56505	0.947000	0.59692	5.574000	0.67424	2.873000	0.98535	0.561000	0.74099	GGC	-	HMMPfam_Patched		0.557	PTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PTCH1	protein_coding	OTTHUMT00000053229.2	C	NM_000264		97260346	-1	no_errors	NM_000264.3	genbank	human	reviewed	54_36p	missense	SNP	1.000	T
CSRNP2	81566	genome.wustl.edu	37	12	51457701	51457701	+	Missense_Mutation	SNP	T	T	C			TCGA-AB-2811-03B-01W-0728-08	TCGA-AB-2811-11B-01W-0728-08	T	T	T	C	T	T	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	7e9b79b7-d6b7-4365-8597-dad296c4b3f5	9602849c-4204-47bd-9c80-7af80031f25c	g.chr12:51457701T>C	ENST00000228515.1	-	5	1757	c.1460A>G	c.(1459-1461)gAa>gGa	p.E487G		NM_030809.2	NP_110436.1	Q9H175	CSRN2_HUMAN	cysteine-serine-rich nuclear protein 2	487					apoptotic process (GO:0006915)|negative regulation of phosphatase activity (GO:0010923)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleus (GO:0005634)	phosphatase binding (GO:0019902)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(5)|urinary_tract(1)	14						GTTACAATCTTCGGGCAATAG	0.557																																						dbGAP											0			12											100.0	109.0	106.0					12																	51457701		2203	4300	6503	49743968	SO:0001583	missense	0			AJ298133	CCDS8807.1	12q13.11-q13.12	2012-04-17	2009-01-07	2009-01-07				"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	16006	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 72"""		"""chromosome 12 open reading frame 22"", ""family with sequence similarity 130, member A1"""	C12orf22, FAM130A1		17726538	Standard	NM_030809		Approved	C12ORF2, TAIP-12, PPP1R72	uc001rxu.2	Q9H175		ENST00000228515.1:c.1460A>G	12.37:g.51457701T>C	ENSP00000228515:p.Glu487Gly	Somatic	73	3.95	3		8	27.27	3	WXS	Illumina HiSeq	Phase_IV	49743968	161	45.05	132		Missense_Mutation	SNP	NULL	p.E487G	ENST00000228515.1	37	c.1460	CCDS8807.1	12	.	.	.	.	.	.	.	.	.	.	T	14.58	2.576973	0.45902	.	.	ENSG00000110925	ENST00000228515	T	0.50277	0.75	4.91	4.91	0.64330	.	0.115379	0.39834	N	0.001241	T	0.26268	0.0641	N	0.08118	0	0.36819	D	0.886285	B	0.29301	0.241	B	0.26969	0.075	T	0.27020	-1.0086	10	0.22109	T	0.4	-7.9018	12.447	0.55657	0.0:0.0:0.0:1.0	.	487	Q9H175	CSRN2_HUMAN	G	487	ENSP00000228515:E487G	ENSP00000228515:E487G	E	-	2	0	CSRNP2	49743968	0.998000	0.40836	1.000000	0.80357	0.899000	0.52679	1.975000	0.40569	2.202000	0.70862	0.454000	0.30748	GAA	-	NULL		0.557	CSRNP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CSRNP2	protein_coding	OTTHUMT00000404893.1	T			49743968	-1	no_errors	NM_030809.1	genbank	human	provisional	54_36p	missense	SNP	0.750	C
FLT3	2322	genome.wustl.edu	37	13	28592642	28592642	+	Missense_Mutation	SNP	C	C	A	rs121913486|rs121913488		TCGA-AB-2811-03B-01W-0728-08	TCGA-AB-2811-11B-01W-0728-08	C	C	C	A	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	7e9b79b7-d6b7-4365-8597-dad296c4b3f5	9602849c-4204-47bd-9c80-7af80031f25c	g.chr13:28592642C>A	ENST00000241453.7	-	20	2584	c.2503G>T	c.(2503-2505)Gat>Tat	p.D835Y	FLT3_ENST00000537084.1_Intron|FLT3_ENST00000380982.4_Missense_Mutation_p.D835Y	NM_004119.2	NP_004110.2	P36888	FLT3_HUMAN	fms-related tyrosine kinase 3	835	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		D -> E (in acute lymphoblastic leukemia patients and in acute myelogenous leukemia patients; somatic mutation; constitutively activated). {ECO:0000269|PubMed:11290608, ECO:0000269|PubMed:14504097}.|D -> H (in acute lymphoblastic leukemia patients and in acute myelogenous leukemia patients; somatic mutation; constitutively activated). {ECO:0000269|PubMed:11290608, ECO:0000269|PubMed:11442493, ECO:0000269|PubMed:14504097}.|D -> N (in acute lymphoblastic leukemia patients and in acute myelogenous leukemia patients; somatic mutation; constitutively activated). {ECO:0000269|PubMed:11290608}.|D -> V (in acute lymphoblastic leukemia patients and in acute myelogenous leukemia patients; somatic mutation; constitutively activated). {ECO:0000269|PubMed:11290608}.|D -> Y (in acute lymphoblastic leukemia patients and in acute myelogenous leukemia patients; somatic mutation; constitutively activated). {ECO:0000269|PubMed:11290608, ECO:0000269|PubMed:11442493, ECO:0000269|PubMed:14504097}.		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.D835Y(190)|p.D835H(30)|p.?(23)|p.D835N(6)|p.D835del(1)|p.R834_D835del(1)|p.D835F(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)	CTCATGATATCTCGAGCCAAT	0.453			"""Mis, O"""		"""AML, ALL"""																																	dbGAP		Dom	yes		13	13q12	2322	fms-related tyrosine kinase 3		L	252	Substitution - Missense(227)|Unknown(23)|Deletion - In frame(2)	haematopoietic_and_lymphoid_tissue(252)	13											187.0	141.0	156.0					13																	28592642		2203	4300	6503	27490642	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.2503G>T	13.37:g.28592642C>A	ENSP00000241453:p.Asp835Tyr	Somatic	69	2.82	2		235	33.24	117	WXS	Illumina HiSeq	Phase_IV	27490642	118	49.14	114	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.D835Y	ENST00000241453.7	37	c.2503	CCDS31953.1	13	.	.	.	.	.	.	.	.	.	.	C	28.8	4.949190	0.92660	.	.	ENSG00000122025	ENST00000241453;ENST00000380982	D;D	0.83755	-1.76;-1.76	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);	0.074843	0.56097	D	0.000030	D	0.87981	0.6315	L	0.34521	1.04	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.88564	0.3125	10	0.87932	D	0	.	20.221	0.98325	0.0:1.0:0.0:0.0	.	835	P36888	FLT3_HUMAN	Y	835	ENSP00000241453:D835Y;ENSP00000370369:D835Y	ENSP00000241453:D835Y	D	-	1	0	FLT3	27490642	1.000000	0.71417	0.960000	0.40013	0.940000	0.58332	7.815000	0.86186	2.792000	0.96026	0.556000	0.70494	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	C			27490642	-1	no_errors	NM_004119.2	genbank	human	reviewed	54_36p	missense	SNP	1.000	A
NPM1	4869	genome.wustl.edu	37	5	170837547	170837548	+	Frame_Shift_Ins	INS	-	-	TCTG			TCGA-AB-2811-03B-01W-0728-08	TCGA-AB-2811-11B-01W-0728-08	-	-	-	TCTG	-	-	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	7e9b79b7-d6b7-4365-8597-dad296c4b3f5	9602849c-4204-47bd-9c80-7af80031f25c	g.chr5:170837547_170837548insTCTG	ENST00000296930.5	+	11	1164_1165	c.863_864insTCTG	c.(862-867)tggcagfs	p.WQ288fs	NPM1_ENST00000517671.1_Frame_Shift_Ins_p.WQ288fs|NPM1_ENST00000351986.6_Frame_Shift_Ins_p.WQ259fs	NM_002520.6	NP_002511.1	P06748	NPM_HUMAN	nucleophosmin (nucleolar phosphoprotein B23, numatrin)	288	Required for nucleolar localization.			WQWRKSL -> CLAVEEVSLRK (in Ref. 6; AAW67752/AAW67755). {ECO:0000305}.|WQWRKSL -> CMAVEEVSLRK (in Ref. 6; AAW67753 and 7; ABC40399). {ECO:0000305}.|WQWRKSL -> CVAVEEVSLRK (in Ref. 6; AAW67754). {ECO:0000305}.	cell aging (GO:0007569)|CENP-A containing nucleosome assembly (GO:0034080)|centrosome cycle (GO:0007098)|DNA repair (GO:0006281)|intracellular protein transport (GO:0006886)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of centrosome duplication (GO:0010826)|negative regulation of protein kinase activity by regulation of protein phosphorylation (GO:0044387)|nucleocytoplasmic transport (GO:0006913)|nucleosome assembly (GO:0006334)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of translation (GO:0045727)|protein localization (GO:0008104)|protein oligomerization (GO:0051259)|regulation of centriole replication (GO:0046599)|regulation of eIF2 alpha phosphorylation by dsRNA (GO:0060735)|regulation of endodeoxyribonuclease activity (GO:0032071)|regulation of endoribonuclease activity (GO:0060699)|response to stress (GO:0006950)|ribosome assembly (GO:0042255)|signal transduction (GO:0007165)|viral process (GO:0016032)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|spindle pole centrosome (GO:0031616)	histone binding (GO:0042393)|NF-kappaB binding (GO:0051059)|poly(A) RNA binding (GO:0044822)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|protein kinase inhibitor activity (GO:0004860)|ribosomal large subunit binding (GO:0043023)|ribosomal small subunit binding (GO:0043024)|RNA binding (GO:0003723)|Tat protein binding (GO:0030957)|transcription coactivator activity (GO:0003713)|unfolded protein binding (GO:0051082)	p.W288fs*12(2114)|p.W288fs*10(9)|p.Q289fs*11(3)|p.W288*(1)	NPM1/ALK(632)	central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(4261)|kidney(1)|large_intestine(1)|lung(4)|skin(1)	4269	Renal(175;0.000159)|Lung NSC(126;0.00576)|all_lung(126;0.00963)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			CAAGATCTCTGGCAGTGGAGGA	0.312			"""T, F """	"""ALK, RARA, MLF1"""	"""NHL, APL, AML"""																																	dbGAP		Dom	yes		5	5q35	4869	"""nucleophosmin (nucleolar phosphoprotein B23, numatrin)"""		L	2127	Insertion - Frameshift(2118)|Complex - frameshift(8)|Substitution - Nonsense(1)	haematopoietic_and_lymphoid_tissue(2127)	5																																								170770153	SO:0001589	frameshift_variant	0			M26697	CCDS4376.1, CCDS4377.1, CCDS43399.1	5q35.1	2014-09-17			ENSG00000181163	ENSG00000181163			7910	protein-coding gene	gene with protein product	"""nucleolar phosphoprotein B23"", ""numatrin"", ""nucleophosmin/nucleoplasmin family, member 1"""	164040				8471164, 8122112	Standard	NM_002520		Approved	B23, NPM	uc003mbi.3	P06748	OTTHUMG00000130465	ENST00000296930.5:c.860_863dupTCTG	5.37:g.170837544_170837547dupTCTG	ENSP00000296930:p.Trp288fs	Somatic	NA	NA	NA		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	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
