#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
RPL7P58	646346	genome.wustl.edu	37	X	26705664	26705664	+	IGR	SNP	G	G	A			TCGA-AB-2818-03B-01W-0728-08	TCGA-AB-2818-11B-01W-0728-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	84ca77c7-0799-4e5c-bed8-034e78b899f0	4bbe86bc-4b1c-43fc-a949-4599c083d8e4	g.chrX:26705664G>A								VENTXP1 (126495 upstream) : RNU1-142P (102594 downstream)																							CAGCTTCTTCGTCTTCGTCAA	0.438													G|||	1	0.000264901	0.0	0.0	3775	,	,		13224	0.0		0.0	False		,,,				2504	0.001					dbGAP											0			X																																								26615585	SO:0001628	intergenic_variant	0																															X.37:g.26705664G>A		44	0.00	0		NA	NA	NA	26615585	112	20.57	29		RNA	SNP	-	NULL		37	NULL		X																																																																																			-	-	0	0.438					LOC646346			G			26615585	+1	pseudogene	XR_017105.2	genbank	human	model	54_36p	rna	SNP	1.000	A
KLHL12	59349	genome.wustl.edu	37	1	202863740	202863740	+	Missense_Mutation	SNP	T	T	G			TCGA-AB-2818-03B-01W-0728-08	TCGA-AB-2818-11B-01W-0728-08	T	T	T	G	T	T	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	84ca77c7-0799-4e5c-bed8-034e78b899f0	4bbe86bc-4b1c-43fc-a949-4599c083d8e4	g.chr1:202863740T>G	ENST00000367261.3	-	9	1491	c.1273A>C	c.(1273-1275)Agt>Cgt	p.S425R	KLHL12_ENST00000367259.1_Missense_Mutation_p.S158R|KLHL12_ENST00000435533.3_Missense_Mutation_p.S463R	NM_021633.2	NP_067646.1	Q53G59	KLH12_HUMAN	kelch-like family member 12	425	Interaction with DVL3.				COPII vesicle coating (GO:0048208)|ER to Golgi vesicle-mediated transport (GO:0006888)|protein monoubiquitination (GO:0006513)|Wnt signaling pathway (GO:0016055)	Cul3-RING ubiquitin ligase complex (GO:0031463)|ER to Golgi transport vesicle (GO:0030134)|Golgi membrane (GO:0000139)				NS(3)|breast(2)|endometrium(1)|large_intestine(1)|lung(6)|stomach(1)	14			BRCA - Breast invasive adenocarcinoma(75;0.166)			ATCACTCCACTGGCCACTACG	0.517																																						dbGAP											0			1											138.0	138.0	138.0					1																	202863740		2203	4300	6503	201130363	SO:0001583	missense	0			AF190900	CCDS1429.1	1q32.1	2013-01-30	2013-01-30		ENSG00000117153	ENSG00000117153		"""Kelch-like"", ""BTB/POZ domain containing"""	19360	protein-coding gene	gene with protein product		614522	"""kelch-like 12 (Drosophila)"""			12477932	Standard	NM_021633		Approved	C3IP1	uc001gyo.1	Q53G59	OTTHUMG00000041385	ENST00000367261.3:c.1273A>C	1.37:g.202863740T>G	ENSP00000356230:p.Ser425Arg	27	0.00	0		3	40.00	2	201130363	56	51.30	59	A6NEN8|B7Z7B8|Q9HBX5	Missense_Mutation	SNP	HMMSmart_BTB,HMMPfam_Kelch_1,HMMSmart_Kelch,superfamily_Gal_oxid_central,superfamily_BTB/POZ_fold,HMMPfam_BACK,HMMPfam_BTB	p.S425R	ENST00000367261.3	37	c.1273	CCDS1429.1	1	.	.	.	.	.	.	.	.	.	.	T	17.06	3.293496	0.60086	.	.	ENSG00000117153	ENST00000367261;ENST00000367259;ENST00000435533	T;T;T	0.76839	-1.05;-1.05;-1.05	5.47	4.34	0.51931	Galactose oxidase, beta-propeller (1);	0.192065	0.64402	D	0.000004	T	0.60508	0.2274	N	0.10707	0.03	0.53005	D	0.999967	B;B;B	0.27166	0.07;0.17;0.028	B;B;B	0.29862	0.108;0.021;0.053	T	0.58869	-0.7560	10	0.49607	T	0.09	.	11.4956	0.50406	0.0:0.0704:0.0:0.9296	.	463;425;158	B7Z7B8;Q53G59;Q9H7R2	.;KLH12_HUMAN;.	R	425;158;463	ENSP00000356230:S425R;ENSP00000356228:S158R;ENSP00000416886:S463R	ENSP00000356228:S158R	S	-	1	0	KLHL12	201130363	1.000000	0.71417	0.998000	0.56505	0.941000	0.58515	6.178000	0.71968	1.012000	0.39366	0.455000	0.32223	AGT	-	HMMPfam_Kelch_1,HMMSmart_Kelch,superfamily_Gal_oxid_central		0.517	KLHL12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	KLHL12	protein_coding	OTTHUMT00000099151.1	T	NM_021633		201130363	-1	no_errors	NM_021633.2	genbank	human	provisional	54_36p	missense	SNP	1.000	G
DNMT3A	1788	genome.wustl.edu	37	2	25459874	25459874	+	Splice_Site	SNP	C	C	G	rs35824014		TCGA-AB-2818-03B-01W-0728-08	TCGA-AB-2818-11B-01W-0728-08	C	C	C	G	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	84ca77c7-0799-4e5c-bed8-034e78b899f0	4bbe86bc-4b1c-43fc-a949-4599c083d8e4	g.chr2:25459874C>G	ENST00000264709.3	-	21	2746	c.2409G>C	c.(2407-2409)agG>agC	p.R803S	DNMT3A_ENST00000321117.5_Splice_Site_p.R803S|DNMT3A_ENST00000474887.1_Intron|DNMT3A_ENST00000402667.1_Splice_Site_p.R580S|DNMT3A_ENST00000380746.4_Splice_Site_p.R614S	NM_175629.2	NP_783328.1	Q9Y6K1	DNM3A_HUMAN	DNA (cytosine-5-)-methyltransferase 3 alpha	803	SAM-dependent MTase C5-type. {ECO:0000255|PROSITE-ProRule:PRU01016}.				C-5 methylation of cytosine (GO:0090116)|cellular response to amino acid stimulus (GO:0071230)|DNA methylation (GO:0006306)|DNA methylation involved in embryo development (GO:0043045)|DNA methylation involved in gamete generation (GO:0043046)|DNA methylation on cytosine within a CG sequence (GO:0010424)|hypermethylation of CpG island (GO:0044027)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of gene expression by genetic imprinting (GO:0006349)|S-adenosylhomocysteine metabolic process (GO:0046498)|S-adenosylmethioninamine metabolic process (GO:0046499)|spermatogenesis (GO:0007283)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|euchromatin (GO:0000791)|nuclear heterochromatin (GO:0005720)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA (cytosine-5-)-methyltransferase activity (GO:0003886)|DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates (GO:0051718)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|unmethylated CpG binding (GO:0045322)	p.R803fs*5(3)		breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(964)|kidney(3)|large_intestine(10)|lung(29)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	1021	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					ATGCCAACGGCCTAGGAGGCA	0.582			"""Mis, F, N, S"""		AML																																	dbGAP		Rec	yes		2	2p23	1788	DNA (cytosine-5-)-methyltransferase 3 alpha		L	3	Deletion - Frameshift(3)	haematopoietic_and_lymphoid_tissue(3)	2											46.0	44.0	45.0					2																	25459874		2203	4300	6503	25313378	SO:0001630	splice_region_variant	0				CCDS1718.2, CCDS33157.1, CCDS46232.1	2p23	2014-09-17			ENSG00000119772	ENSG00000119772			2978	protein-coding gene	gene with protein product		602769				9662389, 10433969	Standard	NM_175630		Approved		uc002rgc.4	Q9Y6K1	OTTHUMG00000094777	ENST00000264709.3:c.2409-1G>C	2.37:g.25459874C>G		24	4.00	1		16	23.81	5	25313378	24	36.84	14	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.R803S	ENST00000264709.3	37	c.2409	CCDS33157.1	2	.	.	.	.	.	.	.	.	.	.	C	19.71	3.879016	0.72294	.	.	ENSG00000119772	ENST00000380746;ENST00000321117;ENST00000264709;ENST00000402667	D;D;D;D	0.96885	-4.16;-4.16;-4.16;-4.16	5.05	5.05	0.67936	.	0.000000	0.85682	D	0.000000	D	0.97794	0.9276	M	0.73962	2.25	0.80722	D	1	D;D	0.89917	0.978;1.0	P;D	0.79108	0.791;0.992	D	0.98287	1.0511	10	0.62326	D	0.03	.	16.2726	0.82628	0.0:1.0:0.0:0.0	.	803;614	Q9Y6K1;E9PEB8	DNM3A_HUMAN;.	S	614;803;803;580	ENSP00000370122:R614S;ENSP00000324375:R803S;ENSP00000264709:R803S;ENSP00000384237:R580S	ENSP00000264709:R803S	R	-	3	2	DNMT3A	25313378	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.956000	0.49129	2.510000	0.84645	0.655000	0.94253	AGG	-	superfamily_S-adenosyl-L-methionine-dependent methyltransferases		0.582	DNMT3A-001	KNOWN	basic|CCDS	protein_coding	DNMT3A	protein_coding	OTTHUMT00000211587.1	C	NM_022552	Missense_Mutation	25313378	-1	no_errors	NM_022552.3	genbank	human	reviewed	54_36p	missense	SNP	1.000	G
TRPM8	79054	genome.wustl.edu	37	2	234846004	234846004	+	Missense_Mutation	SNP	G	G	A			TCGA-AB-2818-03B-01W-0728-08	TCGA-AB-2818-11B-01W-0728-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	84ca77c7-0799-4e5c-bed8-034e78b899f0	4bbe86bc-4b1c-43fc-a949-4599c083d8e4	g.chr2:234846004G>A	ENST00000324695.4	+	4	239	c.199G>A	c.(199-201)Gtg>Atg	p.V67M	TRPM8_ENST00000433712.2_5'UTR|TRPM8_ENST00000355722.4_Missense_Mutation_p.V17M|TRPM8_ENST00000409625.1_5'UTR	NM_024080.4	NP_076985.4	Q7Z2W7	TRPM8_HUMAN	transient receptor potential cation channel, subfamily M, member 8	67					calcium ion transmembrane transport (GO:0070588)|cellular calcium ion homeostasis (GO:0006874)|detection of temperature stimulus (GO:0016048)|ion transmembrane transport (GO:0034220)|protein homotetramerization (GO:0051289)|protein homotrimerization (GO:0070207)|response to cold (GO:0009409)|thermoception (GO:0050955)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)			breast(5)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(15)|liver(2)|lung(27)|prostate(2)|skin(7)|stomach(2)	66		Breast(86;0.00205)|Renal(207;0.00694)|all_lung(227;0.0129)|Lung NSC(271;0.0408)|all_hematologic(139;0.0753)|Acute lymphoblastic leukemia(138;0.224)		Epithelial(121;1.19e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000139)|Lung(119;0.00758)|LUSC - Lung squamous cell carcinoma(224;0.0108)	Menthol(DB00825)	CAGGGAGAATGTGTGCAAGTG	0.453																																						dbGAP											0			2											112.0	97.0	102.0					2																	234846004		2203	4300	6503	234510743	SO:0001583	missense	0			AC005538	CCDS33407.1	2q37	2011-12-14			ENSG00000144481	ENSG00000144481		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	17961	protein-coding gene	gene with protein product		606678				16382100	Standard	NM_024080		Approved		uc002vvh.3	Q7Z2W7	OTTHUMG00000059129	ENST00000324695.4:c.199G>A	2.37:g.234846004G>A	ENSP00000323926:p.Val67Met	28	0.00	0		NA	NA	NA	234510743	65	49.22	63	A0AVG2|Q3YFM7|Q6QNH9|Q8TAC3|Q8TDX8|Q9BVK1	Missense_Mutation	SNP	HMMPfam_Ion_trans	p.V67M	ENST00000324695.4	37	c.199	CCDS33407.1	2	.	.	.	.	.	.	.	.	.	.	G	12.44	1.939313	0.34189	.	.	ENSG00000144481	ENST00000324695;ENST00000355722	T;T	0.60171	0.21;0.21	5.95	1.46	0.22682	.	0.785305	0.11777	N	0.530563	T	0.49729	0.1574	M	0.63843	1.955	0.80722	D	1	B;B	0.25206	0.12;0.002	B;B	0.28784	0.094;0.004	T	0.51260	-0.8728	10	0.56958	D	0.05	-7.6391	2.2238	0.03979	0.1987:0.3017:0.3709:0.1287	.	17;67	Q7Z2W7-2;Q7Z2W7	.;TRPM8_HUMAN	M	67;17	ENSP00000323926:V67M;ENSP00000347956:V17M	ENSP00000323926:V67M	V	+	1	0	TRPM8	234510743	0.005000	0.15991	0.351000	0.25721	0.914000	0.54420	0.021000	0.13489	0.370000	0.24538	0.655000	0.94253	GTG	-	NULL		0.453	TRPM8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TRPM8	protein_coding	OTTHUMT00000131005.4	G	NM_024080		234510743	+1	no_errors	NM_024080.4	genbank	human	validated	54_36p	missense	SNP	0.006	A
MAPK9	5601	genome.wustl.edu	37	5	179676061	179676061	+	Silent	SNP	C	C	T			TCGA-AB-2818-03B-01W-0728-08	TCGA-AB-2818-11B-01W-0728-08	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	84ca77c7-0799-4e5c-bed8-034e78b899f0	4bbe86bc-4b1c-43fc-a949-4599c083d8e4	g.chr5:179676061C>T	ENST00000452135.2	-	6	826	c.528G>A	c.(526-528)gcG>gcA	p.A176A	MAPK9_ENST00000393360.3_Silent_p.A176A|MAPK9_ENST00000343111.6_Silent_p.A176A|MAPK9_ENST00000425491.2_Silent_p.A176A|MAPK9_ENST00000347470.4_Silent_p.A176A|MAPK9_ENST00000524170.1_5'UTR|MAPK9_ENST00000455781.1_Silent_p.A176A|MAPK9_ENST00000539014.1_Silent_p.A176A|MAPK9_ENST00000397072.3_3'UTR			P45984	MK09_HUMAN	mitogen-activated protein kinase 9	176	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cellular response to growth factor stimulus (GO:0071363)|cellular response to interleukin-1 (GO:0071347)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to tumor necrosis factor (GO:0071356)|cellular response to UV (GO:0034644)|central nervous system development (GO:0007417)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|neuron projection development (GO:0031175)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell morphogenesis involved in differentiation (GO:0010770)|positive regulation of chemokine production (GO:0032722)|positive regulation of gene expression (GO:0010628)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of prostaglandin biosynthetic process (GO:0031394)|positive regulation of prostaglandin secretion (GO:0032308)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of transcription, DNA-templated (GO:0045893)|protein targeting to mitochondrion (GO:0006626)|regulation of JNK cascade (GO:0046328)|regulation of protein ubiquitination (GO:0031396)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|release of cytochrome c from mitochondria (GO:0001836)|response to amine (GO:0014075)|response to cadmium ion (GO:0046686)|response to drug (GO:0042493)|response to mechanical stimulus (GO:0009612)|response to stress (GO:0006950)|response to toxic substance (GO:0009636)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|JUN kinase activity (GO:0004705)|transcription factor binding (GO:0008134)			central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(5)|lung(10)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26	all_cancers(89;6.54e-05)|all_epithelial(37;1.22e-05)|Renal(175;0.000269)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.137)	all_cancers(40;0.0236)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			AGTTAGTGCACGCTGTCCGGG	0.502																																						dbGAP											0			5											150.0	150.0	150.0					5																	179676061		2203	4300	6503	179608667	SO:0001819	synonymous_variant	0			U09759	CCDS4453.1, CCDS4454.1, CCDS43409.1, CCDS43410.1, CCDS47356.1	5q35	2011-06-09			ENSG00000050748	ENSG00000050748	2.7.11.1	"""Mitogen-activated protein kinase cascade / Kinases"""	6886	protein-coding gene	gene with protein product	"""Jun kinase"""	602896		PRKM9		8001819	Standard	NM_002752		Approved	JNK2, p54a, SAPK	uc003mls.4	P45984	OTTHUMG00000130934	ENST00000452135.2:c.528G>A	5.37:g.179676061C>T		22	0.00	0		22	54.17	26	179608667	45	52.13	49	A8K0S3|B5BU66|B5M0B4|D3DWQ8|D3DWQ9|Q15708|Q15710|Q15711|Q8N5C5	Silent	SNP	HMMSmart_SM00219,HMMSmart_SM00220,PatternScan_MAPK,PatternScan_PROTEIN_KINASE_ST,superfamily_Protein kinase-like (PK-like),HMMPfam_Pkinase	p.A176	ENST00000452135.2	37	c.528	CCDS4453.1	5																																																																																			-	HMMSmart_SM00219,HMMSmart_SM00220,superfamily_Protein kinase-like (PK-like),HMMPfam_Pkinase		0.502	MAPK9-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	MAPK9	protein_coding	OTTHUMT00000253530.3	C			179608667	-1	no_errors	NM_002752.1	genbank	human	reviewed	54_36p	silent	SNP	0.606	T
MEA1	4201	genome.wustl.edu	37	6	42981063	42981063	+	Silent	SNP	G	G	A			TCGA-AB-2818-03B-01W-0728-08	TCGA-AB-2818-11B-01W-0728-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	84ca77c7-0799-4e5c-bed8-034e78b899f0	4bbe86bc-4b1c-43fc-a949-4599c083d8e4	g.chr6:42981063G>A	ENST00000244711.3	-	2	247	c.93C>T	c.(91-93)ccC>ccT	p.P31P	KLHDC3_ENST00000326974.4_5'Flank|KLHDC3_ENST00000244670.8_5'Flank	NM_014623.2	NP_055438.1	Q16626	MEA1_HUMAN	male-enhanced antigen 1	31					cell differentiation (GO:0030154)|male gonad development (GO:0008584)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)				central_nervous_system(1)|large_intestine(3)|lung(1)|skin(1)	6			Colorectal(64;0.00237)|all cancers(41;0.00411)|COAD - Colon adenocarcinoma(64;0.00473)|OV - Ovarian serous cystadenocarcinoma(102;0.0664)|KIRC - Kidney renal clear cell carcinoma(15;0.133)|Kidney(15;0.188)			CAGTCTGATTGGGGAAGATAC	0.607																																						dbGAP											0			6											97.0	96.0	97.0					6																	42981063		2203	4300	6503	43089041	SO:0001819	synonymous_variant	0				CCDS4879.1	6p21.3-p21.1	2008-08-15	2005-06-02	2005-06-02	ENSG00000124733	ENSG00000124733			6986	protein-coding gene	gene with protein product		143170	"""male-enhanced antigen"""	MEA		2813404, 12444059	Standard	NM_014623		Approved		uc003otk.3	Q16626	OTTHUMG00000014717	ENST00000244711.3:c.93C>T	6.37:g.42981063G>A		125	0.00	0		16	26.09	6	43089041	73	42.64	55	Q5TC36|Q9BV01	Silent	SNP	HMMPfam_MEA1	p.P31	ENST00000244711.3	37	c.93	CCDS4879.1	6																																																																																			-	HMMPfam_MEA1		0.607	MEA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	MEA1	protein_coding	OTTHUMT00000040574.2	G			43089041	-1	no_errors	NM_014623.2	genbank	human	validated	54_36p	silent	SNP	0.997	A
FBXO30	84085	genome.wustl.edu	37	6	146125956	146125956	+	Missense_Mutation	SNP	C	C	T			TCGA-AB-2818-03B-01W-0728-08	TCGA-AB-2818-11B-01W-0728-08	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	84ca77c7-0799-4e5c-bed8-034e78b899f0	4bbe86bc-4b1c-43fc-a949-4599c083d8e4	g.chr6:146125956C>T	ENST00000237281.4	-	2	1752	c.1586G>A	c.(1585-1587)aGg>aAg	p.R529K		NM_032145.4	NP_115521.3	Q8TB52	FBX30_HUMAN	F-box protein 30	529							ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(11)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26		Ovarian(120;0.0776)		OV - Ovarian serous cystadenocarcinoma(155;1.95e-07)|GBM - Glioblastoma multiforme(68;0.0149)		AAATTCTTTCCTTCTAAATAA	0.428																																						dbGAP											0			6											84.0	79.0	81.0					6																	146125956		2203	4300	6503	146167649	SO:0001583	missense	0			AF248640	CCDS5208.1	6q24	2008-02-05	2004-06-15		ENSG00000118496	ENSG00000118496		"""F-boxes /  ""other"""""	15600	protein-coding gene	gene with protein product		609101	"""F-box only protein, helicase, 18"""				Standard	XM_005267159		Approved	MGC21674, Fbx30	uc003qla.3	Q8TB52	OTTHUMG00000015749	ENST00000237281.4:c.1586G>A	6.37:g.146125956C>T	ENSP00000237281:p.Arg529Lys	54	1.79	1		16	27.27	6	146167649	97	45.20	80	Q9BXZ7	Missense_Mutation	SNP	HMMPfam_F-box,HMMSmart_FBOX,superfamily_Traf_like,superfamily_SSF81383	p.R529K	ENST00000237281.4	37	c.1586	CCDS5208.1	6	.	.	.	.	.	.	.	.	.	.	C	24.9	4.579035	0.86645	.	.	ENSG00000118496	ENST00000237281	T	0.59364	0.27	6.06	6.06	0.98353	.	0.000000	0.85682	D	0.000000	T	0.74779	0.3761	M	0.75615	2.305	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.75320	-0.3359	10	0.87932	D	0	-20.2415	20.6208	0.99490	0.0:1.0:0.0:0.0	.	529	Q8TB52	FBX30_HUMAN	K	529	ENSP00000237281:R529K	ENSP00000237281:R529K	R	-	2	0	FBXO30	146167649	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.818000	0.86416	2.882000	0.98803	0.655000	0.94253	AGG	-	NULL		0.428	FBXO30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	FBXO30	protein_coding	OTTHUMT00000042570.2	C			146167649	-1	no_errors	NM_032145.4	genbank	human	reviewed	54_36p	missense	SNP	1.000	T
PSD3	23362	genome.wustl.edu	37	8	18725297	18725297	+	Silent	SNP	C	C	G			TCGA-AB-2818-03B-01W-0728-08	TCGA-AB-2818-11B-01W-0728-08	C	C	C	G	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	84ca77c7-0799-4e5c-bed8-034e78b899f0	4bbe86bc-4b1c-43fc-a949-4599c083d8e4	g.chr8:18725297C>G	ENST00000327040.8	-	4	1623	c.1521G>C	c.(1519-1521)gtG>gtC	p.V507V	PSD3_ENST00000523619.1_Silent_p.V442V|PSD3_ENST00000440756.2_Silent_p.V507V	NM_015310.3	NP_056125.3	Q9NYI0	PSD3_HUMAN	pleckstrin and Sec7 domain containing 3	507					neuron differentiation (GO:0030182)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)	cell junction (GO:0030054)|postsynaptic membrane (GO:0045211)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(8)|ovary(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20				Colorectal(111;0.0281)|READ - Rectum adenocarcinoma(644;0.183)		CATCTGCAGACACACTCAGGA	0.517																																						dbGAP											0			8											196.0	195.0	196.0					8																	18725297		2135	4242	6377	18769577	SO:0001819	synonymous_variant	0			AF243495	CCDS34854.1, CCDS43720.1	8p21.3	2013-01-10			ENSG00000156011	ENSG00000156011		"""Pleckstrin homology (PH) domain containing"""	19093	protein-coding gene	gene with protein product		614440					Standard	NM_206909		Approved	KIAA0942, HCA67, EFA6R, DKFZp761K1423	uc003wza.3	Q9NYI0	OTTHUMG00000163711	ENST00000327040.8:c.1521G>C	8.37:g.18725297C>G		77	0.00	0		2	33.33	1	18769577	102	43.65	79	A6NFQ4|E9KL50|Q6B003|Q9Y2F1	Silent	SNP	HMMPfam_Sec7,HMMSmart_Sec7,superfamily_Sec7,HMMPfam_PH,HMMSmart_PH,superfamily_SSF50729	p.V507	ENST00000327040.8	37	c.1521	CCDS43720.1	8																																																																																			-	NULL		0.517	PSD3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	PSD3	protein_coding	OTTHUMT00000374867.1	C	NM_015310		18769577	-1	no_errors	NM_015310.3	genbank	human	validated	54_36p	silent	SNP	0.111	G
LINC01239	441389	genome.wustl.edu	37	9	22748240	22748240	+	lincRNA	SNP	G	G	A			TCGA-AB-2818-03B-01W-0728-08	TCGA-AB-2818-11B-01W-0728-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	84ca77c7-0799-4e5c-bed8-034e78b899f0	4bbe86bc-4b1c-43fc-a949-4599c083d8e4	g.chr9:22748240G>A	ENST00000436786.1	+	0	524					NR_038977.1																						GTAAAATCGCGTTTCTGAAAG	0.403																																						dbGAP											0			9																																								22738240			0																															9.37:g.22748240G>A		31	0.00	0		NA	NA	NA	22738240	77	48.68	74		RNA	SNP	-	NULL	ENST00000436786.1	37	NULL		9																																																																																			-	-		0.403	RP11-399D6.2-001	KNOWN	basic	lincRNA	LOC646609	lincRNA	OTTHUMT00000051938.1	G			22738240	+1	pseudogene	XR_037907.1	genbank	human	model	54_36p	rna	SNP	0.042	A
C5	727	genome.wustl.edu	37	9	123724995	123724995	+	Silent	SNP	C	C	A			TCGA-AB-2818-03B-01W-0728-08	TCGA-AB-2818-11B-01W-0728-08	C	C	C	A	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	84ca77c7-0799-4e5c-bed8-034e78b899f0	4bbe86bc-4b1c-43fc-a949-4599c083d8e4	g.chr9:123724995C>A	ENST00000223642.1	-	36	4487	c.4458G>T	c.(4456-4458)ggG>ggT	p.G1486G		NM_001735.2	NP_001726.2	P01031	CO5_HUMAN	complement component 5	1486					activation of MAPK activity (GO:0000187)|cell chemotaxis (GO:0060326)|cell surface receptor signaling pathway (GO:0007166)|cellular calcium ion homeostasis (GO:0006874)|chemotaxis (GO:0006935)|complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|cytolysis (GO:0019835)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|in utero embryonic development (GO:0001701)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|leukocyte migration involved in inflammatory response (GO:0002523)|negative regulation of dopamine secretion (GO:0033602)|negative regulation of macrophage chemotaxis (GO:0010760)|negative regulation of norepinephrine secretion (GO:0010700)|positive regulation of angiogenesis (GO:0045766)|positive regulation of chemokine secretion (GO:0090197)|positive regulation of chemotaxis (GO:0050921)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of complement activation (GO:0030449)|response to stress (GO:0006950)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane attack complex (GO:0005579)	chemokine activity (GO:0008009)|endopeptidase inhibitor activity (GO:0004866)|receptor binding (GO:0005102)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(14)|lung(5)|ovary(2)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	46				OV - Ovarian serous cystadenocarcinoma(323;4.98e-53)|GBM - Glioblastoma multiforme(294;0.0242)	Eculizumab(DB01257)|Intravenous Immunoglobulin(DB00028)	GACTGAGAAACCCAACTTCAA	0.383																																						dbGAP											0			9											113.0	118.0	116.0					9																	123724995		2203	4300	6503	122764816	SO:0001819	synonymous_variant	0			M57729	CCDS6826.1	9q33-q34	2014-09-17			ENSG00000106804	ENSG00000106804		"""Complement system"", ""Endogenous ligands"""	1331	protein-coding gene	gene with protein product	"""prepro-C5"", ""C5a anaphylatoxin"""	120900					Standard	NM_001735		Approved	CPAMD4, C5a, C5b	uc004bkv.3	P01031	OTTHUMG00000020579	ENST00000223642.1:c.4458G>T	9.37:g.123724995C>A		54	1.82	1		4	60.00	6	122764816	82	41.01	57	Q14CJ0|Q27I61	Silent	SNP	HMMPfam_ANATO,HMMSmart_ANATO,PatternScan_ANAPHYLATOXIN_1,HMMPfam_A2M,HMMPfam_A2M_N,superfamily_Terp_cyc_toroid,HMMPfam_A2M_recep,superfamily_AM_receptor_bind,HMMPfam_A2M_N_2,HMMPfam_A2M_comp,superfamily_Anaphylatoxin,HMMPfam_NTR,HMMSmart_C345C,PatternScan_ALPHA_2_MACROGLOBULIN	p.G1486	ENST00000223642.1	37	c.4458	CCDS6826.1	9																																																																																			-	HMMPfam_A2M_recep,superfamily_AM_receptor_bind		0.383	C5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	C5	protein_coding	OTTHUMT00000053844.1	C	NM_001735		122764816	-1	no_errors	NM_001735.2	genbank	human	reviewed	54_36p	silent	SNP	0.995	A
PIPSL	266971	genome.wustl.edu	37	10	95720258	95720258	+	RNA	SNP	C	C	G			TCGA-AB-2818-03B-01W-0728-08	TCGA-AB-2818-11B-01W-0728-08	C	C	C	G	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	84ca77c7-0799-4e5c-bed8-034e78b899f0	4bbe86bc-4b1c-43fc-a949-4599c083d8e4	g.chr10:95720258C>G	ENST00000480546.1	-	0	1039					NR_002319.2		A2A3N6	PIPSL_HUMAN	PIP5K1A and PSMD4-like, pseudogene							cytoplasm (GO:0005737)	phosphatidylinositol phosphate kinase activity (GO:0016307)										GGGGGCTGGTCTTCGAGTATC	0.493																																						dbGAP											0			10																																								95710248			0			BC068549		10q23.33	2010-10-27	2010-10-27	2007-07-06	ENSG00000180764	ENSG00000180764		"""Proteasome (prosome, macropain) subunits"""	23733	pseudogene	pseudogene			"""proteasome (prosome, macropain) 26S subunit, non-ATPase, 4, pseudogene 2"", ""phosphatidylinositol-4-phosphate 5-kinase, type I-like 1"", ""PIP5K1A and PSMD4-like"""	PSMD4P2, PIP5K1L1		16344562	Standard	NR_002319		Approved	PIP5K1A-PSMD4, PIP5K1P3	uc009xuj.2	A2A3N6	OTTHUMG00000137480		10.37:g.95720258C>G		31	0.00	0		34	0.00	0	95710248	59	45.95	51	Q6NUK8	Missense_Mutation	SNP	HMMSmart_VWA,HMMPfam_PIP5K,HMMPfam_UIM,HMMSmart_PIPKc,superfamily_SSF53300,superfamily_SSF56104	p.R299T	ENST00000480546.1	37	c.896		10																																																																																			-	HMMPfam_PIP5K,HMMSmart_PIPKc,superfamily_SSF56104		0.493	PIPSL-002	PUTATIVE	basic	processed_transcript	PIPSL	pseudogene	OTTHUMT00000351483.1	C	NR_002319		95710248	-1	no_errors	ENST00000340582	ensembl	human	known	54_36p	missense	SNP	0.156	G
HPS5	11234	genome.wustl.edu	37	11	18314458	18314458	+	Missense_Mutation	SNP	G	G	A			TCGA-AB-2818-03B-01W-0728-08	TCGA-AB-2818-11B-01W-0728-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	84ca77c7-0799-4e5c-bed8-034e78b899f0	4bbe86bc-4b1c-43fc-a949-4599c083d8e4	g.chr11:18314458G>A	ENST00000349215.3	-	15	2127	c.1850C>T	c.(1849-1851)aCa>aTa	p.T617I	HPS5_ENST00000352460.3_Intron|HPS5_ENST00000396253.3_Missense_Mutation_p.T503I|HPS5_ENST00000438420.2_Missense_Mutation_p.T503I	NM_181507.1	NP_852608.1	Q9UPZ3	HPS5_HUMAN	Hermansky-Pudlak syndrome 5	617					blood coagulation (GO:0007596)|organelle organization (GO:0006996)|pigmentation (GO:0043473)	BLOC-2 complex (GO:0031084)				breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(17)|ovary(1)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	30						TGCTTCTGCTGTTGCTACTTT	0.368									Hermansky-Pudlak syndrome																													dbGAP											0			11											190.0	167.0	175.0					11																	18314458		2199	4293	6492	18271034	SO:0001583	missense	0	Familial Cancer Database	HPS, HPS1-8	AB023234	CCDS7836.1, CCDS7837.1	11p14	2014-06-18			ENSG00000110756	ENSG00000110756			17022	protein-coding gene	gene with protein product		607521				10231032, 10094488	Standard	NM_181507		Approved		uc001mod.1	Q9UPZ3	OTTHUMG00000166612	ENST00000349215.3:c.1850C>T	11.37:g.18314458G>A	ENSP00000265967:p.Thr617Ile	30	0.00	0		11	42.11	8	18271034	81	44.52	65	A8K6J8|A8K8S1|D3DQX9|D3DQY0|O95942|Q8N4U0	Missense_Mutation	SNP	superfamily_WD40 repeat-like	p.T617I	ENST00000349215.3	37	c.1850	CCDS7836.1	11	.	.	.	.	.	.	.	.	.	.	G	14.60	2.585077	0.46110	.	.	ENSG00000110756	ENST00000396253;ENST00000438420;ENST00000349215	T;T;T	0.77620	-1.11;-1.11;-1.11	5.29	5.29	0.74685	.	0.105584	0.64402	D	0.000005	T	0.76601	0.4010	L	0.50333	1.59	0.80722	D	1	P	0.47604	0.898	B	0.43082	0.407	T	0.80348	-0.1420	10	0.72032	D	0.01	.	18.3031	0.90171	0.0:0.0:1.0:0.0	.	617	Q9UPZ3	HPS5_HUMAN	I	503;503;617	ENSP00000379552:T503I;ENSP00000399590:T503I;ENSP00000265967:T617I	ENSP00000265967:T617I	T	-	2	0	HPS5	18271034	1.000000	0.71417	0.998000	0.56505	0.185000	0.23345	6.713000	0.74686	2.653000	0.90120	0.655000	0.94253	ACA	-	NULL		0.368	HPS5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	HPS5	protein_coding	OTTHUMT00000390808.1	G	NM_181507		18271034	-1	no_errors	NM_181507.3	genbank	human	reviewed	54_36p	missense	SNP	1.000	A
FLT3	2322	genome.wustl.edu	37	13	28592642	28592642	+	Missense_Mutation	SNP	C	C	A	rs121913486|rs121913488		TCGA-AB-2818-03B-01W-0728-08	TCGA-AB-2818-11B-01W-0728-08	C	C	C	A	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	84ca77c7-0799-4e5c-bed8-034e78b899f0	4bbe86bc-4b1c-43fc-a949-4599c083d8e4	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	41	0.00	0		141	42.45	104	27490642	71	44.53	57	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
Unknown	0	genome.wustl.edu	37	16	33425053	33425053	+	IGR	SNP	G	G	A			TCGA-AB-2818-03B-01W-0728-08	TCGA-AB-2818-11B-01W-0728-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	84ca77c7-0799-4e5c-bed8-034e78b899f0	4bbe86bc-4b1c-43fc-a949-4599c083d8e4	g.chr16:33425053G>A								RP11-23E10.4 (58240 upstream) : BMS1P8 (72109 downstream)																							GAACATTTCCGGTGCTGACTC	0.408																																						dbGAP											0			16																																								33332554	SO:0001628	intergenic_variant	0																															16.37:g.33425053G>A		153	0.00	0		NA	NA	NA	33332554	330	12.23	46		RNA	SNP	-	NULL		37	NULL		16																																																																																			-	-	0	0.408					LOC647211			G			33332554	+1	pseudogene	XR_017499.2	genbank	human	model	54_36p	rna	SNP	0.001	A
NPM1	4869	genome.wustl.edu	37	5	170837543	170837544	+	Frame_Shift_Ins	INS	-	-	TCTG	rs17850940		TCGA-AB-2818-03B-01W-0728-08	TCGA-AB-2818-11B-01W-0728-08	-	-	-	TCTG	-	-	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	84ca77c7-0799-4e5c-bed8-034e78b899f0	4bbe86bc-4b1c-43fc-a949-4599c083d8e4	g.chr5:170837543_170837544insTCTG	ENST00000296930.5	+	11	1160_1161	c.859_860insTCTG	c.(859-861)ctcfs	p.-287fs	NPM1_ENST00000351986.6_Frame_Shift_Ins_p.-258fs|NPM1_ENST00000517671.1_Frame_Shift_Ins_p.-287fs	NM_002520.6	NP_002511.1	P06748	NPM_HUMAN	nucleophosmin (nucleolar phosphoprotein B23, numatrin)						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(7)|p.W288fs*>9(5)|p.L287fs*11(2)|p.L287F(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)			TATTCAAGATCTCTGGCAGTGG	0.317			"""T, F """	"""ALK, RARA, MLF1"""	"""NHL, APL, AML"""																																	dbGAP		Dom	yes		5	5q35	4869	"""nucleophosmin (nucleolar phosphoprotein B23, numatrin)"""		L	15	Insertion - Frameshift(14)|Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(15)	5																																								170770149	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.Leu287fs	NA	NA	NA		NA	NA	NA	170770148	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.859_860	CCDS4376.1	5																																																																																			-	NULL		0.317	NPM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NPM1	protein_coding	OTTHUMT00000252858.2	-	NM_002520		170770149	+1	no_errors	NM_002520.1	genbank	human	validated	54_36p	frame_shift_ins	INS	1.000:1.000	TCTG
RAD21	5885	genome.wustl.edu	37	8	117875497	117875498	+	Splice_Site	INS	-	-	C			TCGA-AB-2818-03B-01W-0728-08	TCGA-AB-2818-11B-01W-0728-08	-	-	-	C	-	-	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	84ca77c7-0799-4e5c-bed8-034e78b899f0	4bbe86bc-4b1c-43fc-a949-4599c083d8e4	g.chr8:117875497_117875498insC	ENST00000297338.2	-	3	432_433	c.145_146insG	c.(145-147)gtg>gGtg	p.V49fs	RAD21_ENST00000523547.1_5'UTR	NM_006265.2	NP_006256.1	O60216	RAD21_HUMAN	RAD21 homolog (S. pombe)	49					apoptotic process (GO:0006915)|chromosome segregation (GO:0007059)|DNA recombination (GO:0006310)|double-strand break repair (GO:0006302)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|protein localization to chromatin (GO:0071168)|reciprocal meiotic recombination (GO:0007131)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cohesin complex (GO:0008278)|cytosol (GO:0005829)|membrane (GO:0016020)|nuclear meiotic cohesin complex (GO:0034991)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(16)|ovary(1)|prostate(1)|skin(1)|stomach(1)	32	all_cancers(13;1.21e-21)|Lung NSC(37;0.000134)|Ovarian(258;0.0172)					TGCCATTTTCACCTATGAATAA	0.356																																						dbGAP											0			8																																								117944679	SO:0001630	splice_region_variant	0			BC050381	CCDS6321.1	8q24.11	2014-09-17	2001-11-28		ENSG00000164754	ENSG00000164754			9811	protein-coding gene	gene with protein product	"""sister chromatid cohesion 1"""	606462	"""RAD21 (S. pombe) homolog"""			8812457	Standard	NM_006265		Approved	KIAA0078, hHR21, SCC1	uc003yod.3	O60216	OTTHUMG00000164959	ENST00000297338.2:c.145-1->G	8.37:g.117875499_117875499dupC		33	0.00	0		11	0.00	0	117944678	86	47.24	77	A8K0E0|Q15001|Q99568	Frame_Shift_Ins	INS	HMMPfam_Rad21_Rec8,HMMPfam_Rad21_Rec8_N	p.V49fs	ENST00000297338.2	37	c.146_145	CCDS6321.1	8																																																																																			-	HMMPfam_Rad21_Rec8_N		0.356	RAD21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	RAD21	protein_coding	OTTHUMT00000381184.1	-	NM_006265	Frame_Shift_Ins	117944679	-1	no_errors	NM_006265.2	genbank	human	reviewed	54_36p	frame_shift_ins	INS	1.000:1.000	C
