#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
KDM6A	7403	genome.wustl.edu	37	X	44923000	44923000	+	Missense_Mutation	SNP	C	C	T	rs139486036		TCGA-AB-2867-03B-01W-0728-08	TCGA-AB-2867-11B-01W-0729-08	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	b3f3ba24-dfbe-4b4b-8502-83ec6ecd7df3	4e18dd6e-74b8-41c3-9665-900c92d39bee	g.chrX:44923000C>T	ENST00000377967.4	+	16	1902	c.1861C>T	c.(1861-1863)Cgc>Tgc	p.R621C	KDM6A_ENST00000536777.1_Missense_Mutation_p.R576C|KDM6A_ENST00000382899.4_Missense_Mutation_p.R628C|KDM6A_ENST00000543216.1_Missense_Mutation_p.R542C	NM_021140.2	NP_066963.2	O15550	KDM6A_HUMAN	lysine (K)-specific demethylase 6A	621	Interaction with SUPT6H. {ECO:0000250}.				canonical Wnt signaling pathway (GO:0060070)|heart morphogenesis (GO:0003007)|histone H3-K4 methylation (GO:0051568)|in utero embryonic development (GO:0001701)|mesodermal cell differentiation (GO:0048333)|multicellular organism growth (GO:0035264)|neural tube closure (GO:0001843)|notochord morphogenesis (GO:0048570)|regulation of gene expression (GO:0010468)|respiratory system process (GO:0003016)|somite rostral/caudal axis specification (GO:0032525)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|histone demethylase activity (H3-K27 specific) (GO:0071558)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)	p.0?(6)|p.0(2)		NS(1)|breast(7)|central_nervous_system(27)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(24)|kidney(24)|large_intestine(9)|liver(1)|lung(21)|oesophagus(11)|pancreas(2)|prostate(5)|skin(1)|soft_tissue(1)|urinary_tract(29)	170						ACCTCATAACCGCACAAACCT	0.453			"""D, N, F, S"""		"""renal, oesophageal SCC, MM"""																																Colon(129;1273 1667 15230 27352 52914)	dbGAP		Rec	yes		X	Xp11.2	7403	"""lysine (K)-specific demethylase 6A, UTX"""		"""E, L"""	8	Whole gene deletion(6)|No detectable mRNA/protein(2)	haematopoietic_and_lymphoid_tissue(2)|oesophagus(2)|breast(2)|pancreas(2)	X						C	CYS/ARG	1,3834		0,0,1,1632,570	57.0	45.0	49.0		1861	5.3	1.0	X	dbSNP_134	49	1,6727		0,1,0,2427,1872	yes	missense	KDM6A	NM_021140.2	180	0,1,1,4059,2442	TT,TC,T,CC,C		0.0149,0.0261,0.0189	benign	621/1402	44923000	2,10561	2203	4300	6503	44807944	SO:0001583	missense	0			AF000992	CCDS14265.1	Xp11.2	2014-09-17	2009-04-17	2009-04-17	ENSG00000147050	ENSG00000147050		"""Chromatin-modifying enzymes / K-demethylases"", ""Tetratricopeptide (TTC) repeat domain containing"""	12637	protein-coding gene	gene with protein product		300128	"""ubiquitously transcribed tetratricopeptide repeat, X chromosome"""	UTX		9499428, 9381176	Standard	XM_005272655		Approved		uc004dge.4	O15550	OTTHUMG00000021402	ENST00000377967.4:c.1861C>T	X.37:g.44923000C>T	ENSP00000367203:p.Arg621Cys	Somatic	116	5.65	7		26	25.71	9	WXS	Illumina HiSeq	Phase_IV	44807944	73	34.82	39	Q52LL9|Q5JVQ7	Missense_Mutation	SNP	HMMPfam_TPR_1,HMMSmart_JmjC,HMMPfam_JmjC,HMMSmart_TPR,superfamily_SSF48452	p.R621C	ENST00000377967.4	37	c.1861	CCDS14265.1	X	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	14.93|14.93	2.682956|2.682956	0.47991|0.47991	2.61E-4|2.61E-4	1.49E-4|1.49E-4	ENSG00000147050|ENSG00000147050	ENST00000414389;ENST00000433797|ENST00000334516;ENST00000377967;ENST00000536777;ENST00000382899;ENST00000543216	.|T;T;T;T	.|0.16597	.|2.42;2.41;2.39;2.33	5.28|5.28	5.28|5.28	0.74379|0.74379	.|.	.|0.045909	.|0.85682	.|D	.|0.000000	T|T	0.21022|0.21022	0.0506|0.0506	N|N	0.03115|0.03115	-0.41|-0.41	0.80722|0.80722	D|D	1|1	.|B;D;B;B;B;B	.|0.89917	.|0.005;1.0;0.002;0.0;0.005;0.001	.|B;D;B;B;B;B	.|0.81914	.|0.001;0.995;0.002;0.002;0.001;0.001	T|T	0.45498|0.45498	-0.9257|-0.9257	5|10	.|0.31617	.|T	.|0.26	-2.2948|-2.2948	18.2207|18.2207	0.89901|0.89901	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|260;628;576;673;587;621	.|B4E0L8;F8W8R6;F5H6S1;B7ZKN5;B4E253;O15550	.|.;.;.;.;.;KDM6A_HUMAN	L|C	218;263|318;621;576;628;542	.|ENSP00000367203:R621C;ENSP00000437405:R576C;ENSP00000372355:R628C;ENSP00000443078:R542C	.|ENSP00000334340:R318C	P|R	+|+	2|1	0|0	KDM6A|KDM6A	44807944|44807944	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	4.443000|4.443000	0.59994|0.59994	2.327000|2.327000	0.79052|0.79052	0.513000|0.513000	0.50165|0.50165	CCG|CGC	-	NULL		0.453	KDM6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	UTX	protein_coding	OTTHUMT00000056324.1	C	NM_021140		44807944	+1	no_errors	NM_021140.2	genbank	human	validated	54_36p	missense	SNP	1.000	T
SPATA21	374955	genome.wustl.edu	37	1	16736345	16736345	+	Missense_Mutation	SNP	G	G	A			TCGA-AB-2867-03B-01W-0728-08	TCGA-AB-2867-11B-01W-0729-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	b3f3ba24-dfbe-4b4b-8502-83ec6ecd7df3	4e18dd6e-74b8-41c3-9665-900c92d39bee	g.chr1:16736345G>A	ENST00000335496.1	-	6	820	c.338C>T	c.(337-339)tCg>tTg	p.S113L	SPATA21_ENST00000466212.1_5'UTR|SPATA21_ENST00000540400.1_Missense_Mutation_p.S90L	NM_198546.1	NP_940948.1	Q7Z572	SPT21_HUMAN	spermatogenesis associated 21	113							calcium ion binding (GO:0005509)			breast(1)|endometrium(2)|lung(8)|ovary(2)|pancreas(3)|stomach(1)|urinary_tract(2)	19		Colorectal(325;0.000147)|Renal(390;0.00145)|Lung NSC(340;0.00215)|Breast(348;0.00224)|all_lung(284;0.00351)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|COAD - Colon adenocarcinoma(227;1.15e-05)|BRCA - Breast invasive adenocarcinoma(304;4.2e-05)|Kidney(64;0.000183)|KIRC - Kidney renal clear cell carcinoma(64;0.00269)|STAD - Stomach adenocarcinoma(313;0.0122)|READ - Rectum adenocarcinoma(331;0.0651)		GGTCCTGGGCGACTTCTGGGC	0.672																																						dbGAP											0			1											32.0	39.0	37.0					1																	16736345		2203	4299	6502	16608932	SO:0001583	missense	0				CCDS172.1	1p36.13	2013-01-10			ENSG00000187144	ENSG00000187144		"""EF-hand domain containing"""	28026	protein-coding gene	gene with protein product							Standard	NM_198546		Approved	spergen-2, spergen2	uc001ayn.3	Q7Z572	OTTHUMG00000002312	ENST00000335496.1:c.338C>T	1.37:g.16736345G>A	ENSP00000335612:p.Ser113Leu	Somatic	390	2.24	9		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	16608932	183	30.42	80	B9EK40|F5GXP5	Missense_Mutation	SNP	PatternScan_EF_HAND_1,HMMPfam_efhand,superfamily_SSF47473	p.S113L	ENST00000335496.1	37	c.338	CCDS172.1	1	.	.	.	.	.	.	.	.	.	.	G	12.40	1.926902	0.34002	.	.	ENSG00000187144	ENST00000335496;ENST00000540400	T;T	0.71103	-0.54;-0.52	4.07	0.876	0.19138	.	0.882556	0.09648	N	0.774056	T	0.53142	0.1778	L	0.34521	1.04	0.09310	N	1	B;B	0.21688	0.045;0.059	B;B	0.13407	0.009;0.009	T	0.34104	-0.9842	10	0.27785	T	0.31	-6.4679	3.638	0.08157	0.259:0.2062:0.5348:0.0	.	90;113	F5GXP5;Q7Z572	.;SPT21_HUMAN	L	113;90	ENSP00000335612:S113L;ENSP00000440046:S90L	ENSP00000335612:S113L	S	-	2	0	SPATA21	16608932	0.303000	0.24463	0.001000	0.08648	0.071000	0.16799	0.444000	0.21661	0.075000	0.16796	0.442000	0.29010	TCG	-	NULL		0.672	SPATA21-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	SPATA21	protein_coding	OTTHUMT00000006677.2	G	NM_198546		16608932	-1	no_errors	NM_198546.1	genbank	human	provisional	54_36p	missense	SNP	0.005	A
OR2M3	127062	genome.wustl.edu	37	1	248367136	248367136	+	Nonsense_Mutation	SNP	T	T	A			TCGA-AB-2867-03B-01W-0728-08	TCGA-AB-2867-11B-01W-0729-08	T	T	T	A	T	T	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	b3f3ba24-dfbe-4b4b-8502-83ec6ecd7df3	4e18dd6e-74b8-41c3-9665-900c92d39bee	g.chr1:248367136T>A	ENST00000456743.1	+	1	805	c.767T>A	c.(766-768)tTg>tAg	p.L256*		NM_001004689.1	NP_001004689.1	Q8NG83	OR2M3_HUMAN	olfactory receptor, family 2, subfamily M, member 3	256						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(6)|large_intestine(4)|lung(33)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	50	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0245)			GGAGCAGCTTTGTTCATGTAC	0.498																																						dbGAP											0			1											215.0	198.0	204.0					1																	248367136		2203	4300	6503	246433759	SO:0001587	stop_gained	0				CCDS31107.1	1q44	2012-08-09		2004-03-10	ENSG00000228198	ENSG00000228198		"""GPCR / Class A : Olfactory receptors"""	8269	protein-coding gene	gene with protein product				OR2M6, OR2M3P			Standard	NM_001004689		Approved	OST003	uc010pzg.2	Q8NG83	OTTHUMG00000040459	ENST00000456743.1:c.767T>A	1.37:g.248367136T>A	ENSP00000389625:p.Leu256*	Somatic	136	2.13	3		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	246433759	143	32.86	70	B9EH06|Q6IEY0	Nonsense_Mutation	SNP	HMMPfam_7tm_1,PatternScan_G_PROTEIN_RECEP_F1_1,superfamily_Family A G protein-coupled receptor-like	p.L256*	ENST00000456743.1	37	c.767	CCDS31107.1	1	.	.	.	.	.	.	.	.	.	.	T	14.07	2.426255	0.43020	.	.	ENSG00000228198	ENST00000456743	.	.	.	2.54	1.37	0.22104	.	0.686149	0.10987	U	0.612049	.	.	.	.	.	.	0.49389	D	0.999787	.	.	.	.	.	.	.	.	.	.	0.27785	T	0.31	.	6.1949	0.20544	0.0:0.2429:0.0:0.7571	.	.	.	.	X	256	.	ENSP00000389625:L256X	L	+	2	0	OR2M3	246433759	0.000000	0.05858	0.001000	0.08648	0.006000	0.05464	0.206000	0.17375	0.225000	0.20959	0.327000	0.21459	TTG	-	HMMPfam_7tm_1,superfamily_Family A G protein-coupled receptor-like		0.498	OR2M3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	OR2M3	protein_coding	OTTHUMT00000097355.1	T	NM_001004689		246433759	+1	no_errors	NM_001004689.1	genbank	human	provisional	54_36p	nonsense	SNP	0.000	A
DNMT3A	1788	genome.wustl.edu	37	2	25458687	25458687	+	Missense_Mutation	SNP	T	T	C			TCGA-AB-2867-03B-01W-0728-08	TCGA-AB-2867-11B-01W-0729-08	T	T	T	C	T	T	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	b3f3ba24-dfbe-4b4b-8502-83ec6ecd7df3	4e18dd6e-74b8-41c3-9665-900c92d39bee	g.chr2:25458687T>C	ENST00000264709.3	-	22	2823	c.2486A>G	c.(2485-2487)aAa>aGa	p.K829R	DNMT3A_ENST00000321117.5_Missense_Mutation_p.K829R|DNMT3A_ENST00000402667.1_Missense_Mutation_p.K606R|DNMT3A_ENST00000380746.4_Missense_Mutation_p.K640R|DNMT3A_ENST00000474887.1_5'UTR	NM_175629.2	NP_783328.1	Q9Y6K1	DNM3A_HUMAN	DNA (cytosine-5-)-methyltransferase 3 alpha	829	SAM-dependent MTase C5-type. {ECO:0000255|PROSITE-ProRule:PRU01016}.				C-5 methylation of cytosine (GO:0090116)|cellular response to amino acid stimulus (GO:0071230)|DNA methylation (GO:0006306)|DNA methylation involved in embryo development (GO:0043045)|DNA methylation involved in gamete generation (GO:0043046)|DNA methylation on cytosine within a CG sequence (GO:0010424)|hypermethylation of CpG island (GO:0044027)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of gene expression by genetic imprinting (GO:0006349)|S-adenosylhomocysteine metabolic process (GO:0046498)|S-adenosylmethioninamine metabolic process (GO:0046499)|spermatogenesis (GO:0007283)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|euchromatin (GO:0000791)|nuclear heterochromatin (GO:0005720)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA (cytosine-5-)-methyltransferase activity (GO:0003886)|DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates (GO:0051718)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|unmethylated CpG binding (GO:0045322)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(964)|kidney(3)|large_intestine(10)|lung(29)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	1021	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GGTCCTCACTTTGCTGAACTA	0.443			"""Mis, F, N, S"""		AML																																	dbGAP		Rec	yes		2	2p23	1788	DNA (cytosine-5-)-methyltransferase 3 alpha		L	0			2											156.0	142.0	146.0					2																	25458687		2203	4300	6503	25312191	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.2486A>G	2.37:g.25458687T>C	ENSP00000264709:p.Lys829Arg	Somatic	208	4.55	10		9	70.00	21	WXS	Illumina HiSeq	Phase_IV	25312191	45	38.67	29	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.K829R	ENST00000264709.3	37	c.2486	CCDS33157.1	2	.	.	.	.	.	.	.	.	.	.	T	31	5.093519	0.94149	.	.	ENSG00000119772	ENST00000380746;ENST00000321117;ENST00000264709;ENST00000402667	D;D;D;D	0.96830	-4.14;-4.14;-4.14;-4.14	5.72	5.72	0.89469	.	0.000000	0.85682	D	0.000000	D	0.97607	0.9216	M	0.67700	2.07	0.80722	D	1	D;D	0.89917	1.0;0.998	D;D	0.79784	0.993;0.987	D	0.98348	1.0542	10	0.87932	D	0	-5.6822	14.8303	0.70142	0.0:0.0:0.0:1.0	.	829;640	Q9Y6K1;E9PEB8	DNM3A_HUMAN;.	R	640;829;829;606	ENSP00000370122:K640R;ENSP00000324375:K829R;ENSP00000264709:K829R;ENSP00000384237:K606R	ENSP00000264709:K829R	K	-	2	0	DNMT3A	25312191	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.949000	0.87791	2.194000	0.70268	0.528000	0.53228	AAA	-	superfamily_S-adenosyl-L-methionine-dependent methyltransferases		0.443	DNMT3A-001	KNOWN	basic|CCDS	protein_coding	DNMT3A	protein_coding	OTTHUMT00000211587.1	T	NM_022552		25312191	-1	no_errors	NM_022552.3	genbank	human	reviewed	54_36p	missense	SNP	1.000	C
DNMT3A	1788	genome.wustl.edu	37	2	25469055	25469055	+	Missense_Mutation	SNP	T	T	C			TCGA-AB-2867-03B-01W-0728-08	TCGA-AB-2867-11B-01W-0729-08	T	T	T	C	T	T	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	b3f3ba24-dfbe-4b4b-8502-83ec6ecd7df3	4e18dd6e-74b8-41c3-9665-900c92d39bee	g.chr2:25469055T>C	ENST00000264709.3	-	11	1740	c.1403A>G	c.(1402-1404)aAg>aGg	p.K468R	DNMT3A_ENST00000321117.5_Missense_Mutation_p.K468R|DNMT3A_ENST00000402667.1_Missense_Mutation_p.K245R|DNMT3A_ENST00000380746.4_Missense_Mutation_p.K279R|DNMT3A_ENST00000474887.1_5'Flank	NM_175629.2	NP_783328.1	Q9Y6K1	DNM3A_HUMAN	DNA (cytosine-5-)-methyltransferase 3 alpha	468					C-5 methylation of cytosine (GO:0090116)|cellular response to amino acid stimulus (GO:0071230)|DNA methylation (GO:0006306)|DNA methylation involved in embryo development (GO:0043045)|DNA methylation involved in gamete generation (GO:0043046)|DNA methylation on cytosine within a CG sequence (GO:0010424)|hypermethylation of CpG island (GO:0044027)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of gene expression by genetic imprinting (GO:0006349)|S-adenosylhomocysteine metabolic process (GO:0046498)|S-adenosylmethioninamine metabolic process (GO:0046499)|spermatogenesis (GO:0007283)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|euchromatin (GO:0000791)|nuclear heterochromatin (GO:0005720)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA (cytosine-5-)-methyltransferase activity (GO:0003886)|DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates (GO:0051718)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|unmethylated CpG binding (GO:0045322)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(964)|kidney(3)|large_intestine(10)|lung(29)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	1021	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					AATAATCTCCTTGACCTTGGG	0.612			"""Mis, F, N, S"""		AML																																	dbGAP		Rec	yes		2	2p23	1788	DNA (cytosine-5-)-methyltransferase 3 alpha		L	0			2											143.0	140.0	141.0					2																	25469055		2203	4300	6503	25322559	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.1403A>G	2.37:g.25469055T>C	ENSP00000264709:p.Lys468Arg	Somatic	84	1.16	1		27	10.00	3	WXS	Illumina HiSeq	Phase_IV	25322559	22	31.25	10	E9PEB8|Q86TE8|Q86XF5|Q8IZV0|Q8WXU9	Missense_Mutation	SNP	HMMPfam_PWWP,HMMSmart_SM00293,HMMPfam_DNA_methylase,superfamily_FYVE/PHD zinc finger,PatternScan_C5_MTASE_1,superfamily_S-adenosyl-L-methionine-dependent methyltransferases,superfamily_Tudor/PWWP/MBT	p.K468R	ENST00000264709.3	37	c.1403	CCDS33157.1	2	.	.	.	.	.	.	.	.	.	.	T	16.57	3.159426	0.57368	.	.	ENSG00000119772	ENST00000380746;ENST00000321117;ENST00000264709;ENST00000402667	T;T;T;T	0.33438	1.41;1.41;1.41;1.41	5.74	5.74	0.90152	.	0.050007	0.85682	D	0.000000	T	0.24699	0.0599	N	0.25890	0.77	0.80722	D	1	B;B	0.15141	0.012;0.001	B;B	0.16289	0.015;0.002	T	0.03202	-1.1061	10	0.62326	D	0.03	-14.0597	13.9916	0.64369	0.0:0.0:0.0:1.0	.	468;279	Q9Y6K1;E9PEB8	DNM3A_HUMAN;.	R	279;468;468;245	ENSP00000370122:K279R;ENSP00000324375:K468R;ENSP00000264709:K468R;ENSP00000384237:K245R	ENSP00000264709:K468R	K	-	2	0	DNMT3A	25322559	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.833000	0.69349	2.188000	0.69820	0.533000	0.62120	AAG	-	NULL		0.612	DNMT3A-001	KNOWN	basic|CCDS	protein_coding	DNMT3A	protein_coding	OTTHUMT00000211587.1	T	NM_022552		25322559	-1	no_errors	NM_022552.3	genbank	human	reviewed	54_36p	missense	SNP	1.000	C
IDH1	3417	genome.wustl.edu	37	2	209113113	209113113	+	Missense_Mutation	SNP	G	G	A	rs121913499		TCGA-AB-2867-03B-01W-0728-08	TCGA-AB-2867-11B-01W-0729-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	b3f3ba24-dfbe-4b4b-8502-83ec6ecd7df3	4e18dd6e-74b8-41c3-9665-900c92d39bee	g.chr2:209113113G>A	ENST00000415913.1	-	4	775	c.394C>T	c.(394-396)Cgt>Tgt	p.R132C	IDH1_ENST00000446179.1_Missense_Mutation_p.R132C|IDH1_ENST00000345146.2_Missense_Mutation_p.R132C	NM_001282387.1	NP_001269316.1	O75874	IDHC_HUMAN	isocitrate dehydrogenase 1 (NADP+), soluble	132			R -> C (in colorectal cancer and glioma samples; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha- ketoglutarate but instead alpha- ketoglutarate is converted to R(-)-2- hydroxyglutarate). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:19117336}.|R -> G (in a glioma sample; glioblastoma multiforme; somatic mutation). {ECO:0000269|PubMed:19117336}.|R -> H (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:18772396}.|R -> L (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:19117336}.|R -> S (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:18772396}.		2-oxoglutarate metabolic process (GO:0006103)|cellular lipid metabolic process (GO:0044255)|female gonad development (GO:0008585)|glutathione metabolic process (GO:0006749)|glyoxylate cycle (GO:0006097)|isocitrate metabolic process (GO:0006102)|NADPH regeneration (GO:0006740)|response to oxidative stress (GO:0006979)|response to steroid hormone (GO:0048545)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	isocitrate dehydrogenase (NADP+) activity (GO:0004450)|magnesium ion binding (GO:0000287)|NAD binding (GO:0051287)|NADP binding (GO:0050661)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)	p.R132C(446)|p.R132G(125)|p.R132S(106)|p.G131_R132>VL(1)|p.R132V(1)		NS(1)|autonomic_ganglia(2)|biliary_tract(24)|bone(237)|central_nervous_system(3764)|endometrium(3)|haematopoietic_and_lymphoid_tissue(794)|kidney(2)|large_intestine(7)|lung(7)|prostate(6)|skin(5)|soft_tissue(12)|thyroid(22)|urinary_tract(1)	4887				Epithelial(149;0.0322)|LUSC - Lung squamous cell carcinoma(261;0.0711)|Lung(261;0.136)		TAAGCATGACGACCTATGATG	0.398			Mis		gliobastoma																																Pancreas(158;264 1958 3300 35450 36047)	dbGAP		Dom	yes		2	2q33.3	3417	"""isocitrate dehydrogenase 1 (NADP+), soluble"""		O	679	Substitution - Missense(678)|Complex - compound substitution(1)	haematopoietic_and_lymphoid_tissue(280)|central_nervous_system(181)|bone(177)|biliary_tract(21)|soft_tissue(12)|large_intestine(2)|skin(2)|autonomic_ganglia(1)|endometrium(1)|NS(1)|prostate(1)	2											81.0	74.0	76.0					2																	209113113		2203	4300	6503	208821358	SO:0001583	missense	0				CCDS2381.1	2q34	2014-09-17			ENSG00000138413	ENSG00000138413	1.1.1.42		5382	protein-coding gene	gene with protein product		147700					Standard	NM_005896		Approved		uc002vcu.3	O75874	OTTHUMG00000132943	ENST00000415913.1:c.394C>T	2.37:g.209113113G>A	ENSP00000390265:p.Arg132Cys	Somatic	115	3.31	4		17	56.41	22	WXS	Illumina HiSeq	Phase_IV	208821358	48	37.66	29	Q567U4|Q6FHQ6|Q7Z3V0|Q93090|Q9NTJ9|Q9UKW8	Missense_Mutation	SNP	HMMPfam_Iso_dh,PatternScan_IDH_IMDH,superfamily_Isocitrate/Isopropylmalate dehydrogenase-like	p.R132C	ENST00000415913.1	37	c.394	CCDS2381.1	2	.	.	.	.	.	.	.	.	.	.	G	24.6	4.550898	0.86127	.	.	ENSG00000138413	ENST00000345146;ENST00000446179;ENST00000415913;ENST00000415282	D;D;D;D	0.87029	-2.2;-2.2;-2.2;-2.2	5.57	5.57	0.84162	Isopropylmalate dehydrogenase-like domain (2);	0.000000	0.85682	D	0.000000	D	0.94049	0.8093	H	0.99379	4.54	0.80722	D	1	B	0.29862	0.259	B	0.31245	0.126	D	0.94048	0.7315	10	0.87932	D	0	-20.0399	19.5341	0.95242	0.0:0.0:1.0:0.0	.	132	O75874	IDHC_HUMAN	C	132	ENSP00000260985:R132C;ENSP00000410513:R132C;ENSP00000390265:R132C;ENSP00000391075:R132C	ENSP00000260985:R132C	R	-	1	0	IDH1	208821358	1.000000	0.71417	0.999000	0.59377	0.994000	0.84299	7.074000	0.76791	2.616000	0.88540	0.555000	0.69702	CGT	-	HMMPfam_Iso_dh,superfamily_Isocitrate/Isopropylmalate dehydrogenase-like		0.398	IDH1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	IDH1	protein_coding	OTTHUMT00000336672.1	G			208821358	-1	no_errors	NM_005896.2	genbank	human	reviewed	54_36p	missense	SNP	1.000	A
KALRN	8997	genome.wustl.edu	37	3	124223788	124223788	+	Silent	SNP	C	C	T			TCGA-AB-2867-03B-01W-0728-08	TCGA-AB-2867-11B-01W-0729-08	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	b3f3ba24-dfbe-4b4b-8502-83ec6ecd7df3	4e18dd6e-74b8-41c3-9665-900c92d39bee	g.chr3:124223788C>T	ENST00000393496.1	+	1	203	c.39C>T	c.(37-39)aaC>aaT	p.N13N	KALRN_ENST00000360013.3_Intron|KALRN_ENST00000460856.1_Intron|KALRN_ENST00000240874.3_Intron			O60229	KALRN_HUMAN	kalirin, RhoGEF kinase	1640					apoptotic signaling pathway (GO:0097190)|intracellular signal transduction (GO:0035556)|nervous system development (GO:0007399)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|protein phosphorylation (GO:0006468)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|vesicle-mediated transport (GO:0016192)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(21)|lung(28)|ovary(4)|prostate(5)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	83						CCAAGGCAAACAAGGCTCAAG	0.483																																						dbGAP											0			3											22.0	17.0	19.0					3																	124223788		876	1989	2865	125706478	SO:0001819	synonymous_variant	0			U94190	CCDS3027.1, CCDS3028.1	3q21.2	2013-02-11	2005-03-11	2005-03-12	ENSG00000160145	ENSG00000160145		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	4814	protein-coding gene	gene with protein product	"""serine/threonine kinase with Dbl and pleckstrin homology domains"""	604605	"""huntingtin-associated protein interacting protein (duo)"""	HAPIP		9285789, 10023074	Standard	NM_001024660		Approved	duo, Hs.8004, TRAD, DUET, Kalirin, ARHGEF24	uc003ehd.3	O60229	OTTHUMG00000125545	ENST00000393496.1:c.39C>T	3.37:g.124223788C>T		Somatic	260	2.61	7		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	125706478	123	31.69	58	A8MSI4|C9JQ37|Q6ZN45|Q8TBQ5|Q9NSZ4|Q9Y2A5	Silent	SNP	HMMPfam_RhoGEF,HMMSmart_RhoGEF,superfamily_DH-domain,HMMPfam_SH3_1,HMMSmart_SH3,superfamily_SH3,HMMPfam_PH,HMMSmart_PH,HMMPfam_SH3_2,superfamily_SSF50729	p.N13	ENST00000393496.1	37	c.39		3																																																																																			-	superfamily_SH3		0.483	KALRN-002	NOVEL	basic	protein_coding	KALRN	protein_coding	OTTHUMT00000258840.2	C	NM_003947		125706478	+1	no_errors	ENST00000393496	ensembl	human	known	54_36p	silent	SNP	1.000	T
TUBA3C	7278	genome.wustl.edu	37	13	19751388	19751388	+	Silent	SNP	G	G	A			TCGA-AB-2867-03B-01W-0728-08	TCGA-AB-2867-11B-01W-0729-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	b3f3ba24-dfbe-4b4b-8502-83ec6ecd7df3	4e18dd6e-74b8-41c3-9665-900c92d39bee	g.chr13:19751388G>A	ENST00000400113.3	-	4	839	c.735C>T	c.(733-735)gaC>gaT	p.D245D		NM_006001.2	NP_005992.1	Q13748	TBA3C_HUMAN	tubulin, alpha 3c	245					'de novo' posttranslational protein folding (GO:0051084)|cellular protein metabolic process (GO:0044267)|microtubule-based process (GO:0007017)|protein folding (GO:0006457)|protein polymerization (GO:0051258)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|biliary_tract(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(33)|ovary(4)|prostate(7)|skin(7)|urinary_tract(1)	72		all_cancers(29;1.31e-20)|all_epithelial(30;1.59e-20)|all_lung(29;6.91e-20)|Lung NSC(5;9.25e-17)|Hepatocellular(1;0.0207)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;6.78e-06)|Epithelial(112;3.79e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00172)|Lung(94;0.0186)|LUSC - Lung squamous cell carcinoma(192;0.108)		TCAGGGCCCCGTCAAATCGCA	0.612																																						dbGAP											0			13											160.0	139.0	146.0					13																	19751388		2203	4300	6503	18649388	SO:0001819	synonymous_variant	0			AF005392	CCDS9284.1	13q12.11	2007-06-20	2007-02-12	2007-02-12	ENSG00000198033	ENSG00000198033		"""Tubulins"""	12408	protein-coding gene	gene with protein product		602528	"""tubulin, alpha 2"""	TUBA2		9465305	Standard	NM_006001		Approved	bA408E5.3	uc009zzj.3	Q13748	OTTHUMG00000016481	ENST00000400113.3:c.735C>T	13.37:g.19751388G>A		Somatic	123	2.36	3		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	18649388	37	37.29	22	A6NJQ0|Q5W099|Q6PEY3|Q96F18	Silent	SNP	HMMPfam_Tubulin,superfamily_Tubulin C-terminal domain-like,PatternScan_TUBULIN,HMMPfam_Tubulin_C,superfamily_Tubulin nucleotide-binding domain-like	p.D245	ENST00000400113.3	37	c.735	CCDS9284.1	13																																																																																			-	HMMPfam_Tubulin,superfamily_Tubulin nucleotide-binding domain-like		0.612	TUBA3C-002	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	TUBA3C	protein_coding	OTTHUMT00000044007.2	G	NM_006001		18649388	-1	no_errors	NM_006001.1	genbank	human	reviewed	54_36p	silent	SNP	0.999	A
NALCN	259232	genome.wustl.edu	37	13	101712314	101712314	+	Silent	SNP	C	C	T			TCGA-AB-2867-03B-01W-0728-08	TCGA-AB-2867-11B-01W-0729-08	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	b3f3ba24-dfbe-4b4b-8502-83ec6ecd7df3	4e18dd6e-74b8-41c3-9665-900c92d39bee	g.chr13:101712314C>T	ENST00000251127.6	-	42	4842	c.4761G>A	c.(4759-4761)caG>caA	p.Q1587Q	NALCN-AS1_ENST00000457843.1_RNA	NM_052867.2	NP_443099.1	Q8IZF0	NALCN_HUMAN	sodium leak channel, non-selective	1587					calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|cell death (GO:0008219)|ion transmembrane transport (GO:0034220)|membrane depolarization during action potential (GO:0086010)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sodium channel activity (GO:0005272)|voltage-gated calcium channel activity (GO:0005245)			NS(1)|autonomic_ganglia(2)|breast(6)|central_nervous_system(2)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(33)|liver(2)|lung(81)|ovary(8)|pancreas(3)|prostate(5)|skin(6)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	177	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					ACGACTGCTGCTGTTTCTATG	0.527																																						dbGAP											0			13											94.0	79.0	84.0					13																	101712314		2203	4300	6503	100510315	SO:0001819	synonymous_variant	0			AY141972	CCDS9498.1	13q32.3	2012-02-21	2007-04-26	2007-04-26	ENSG00000102452	ENSG00000102452		"""Ion channels / Sodium leak channels, non-selective"""	19082	protein-coding gene	gene with protein product		611549	"""voltage gated channel like 1"""	VGCNL1		17448995	Standard	XM_006719943		Approved	bA430M15.1, CanIon	uc001vox.1	Q8IZF0	OTTHUMG00000017295	ENST00000251127.6:c.4761G>A	13.37:g.101712314C>T		Somatic	220	4.35	10		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	100510315	99	35.71	55	Q6P2S6|Q6ZMI7|Q8IZZ1|Q8TAH1	Silent	SNP	HMMPfam_Ion_trans,superfamily_Voltage-gated potassium channels	p.Q1587	ENST00000251127.6	37	c.4761	CCDS9498.1	13																																																																																			-	NULL		0.527	NALCN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NALCN	protein_coding	OTTHUMT00000045663.2	C	NM_052867		100510315	-1	no_errors	NM_052867.2	genbank	human	validated	54_36p	silent	SNP	1.000	T
OXA1L	5018	genome.wustl.edu	37	14	23236556	23236556	+	Missense_Mutation	SNP	T	T	G			TCGA-AB-2867-03B-01W-0728-08	TCGA-AB-2867-11B-01W-0729-08	T	T	T	G	T	T	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	b3f3ba24-dfbe-4b4b-8502-83ec6ecd7df3	4e18dd6e-74b8-41c3-9665-900c92d39bee	g.chr14:23236556T>G	ENST00000604262.1	+	2	186	c.163T>G	c.(163-165)Ttc>Gtc	p.F55V	CTD-2555K7.2_ENST00000554730.1_RNA|OXA1L_ENST00000412791.1_Missense_Mutation_p.F55V|CTD-2555K7.2_ENST00000554857.1_RNA|OXA1L_ENST00000285848.5_Missense_Mutation_p.F115V|CTD-2555K7.2_ENST00000553792.1_RNA|OXA1L_ENST00000358043.5_Missense_Mutation_p.F39V			Q15070	OXA1L_HUMAN	oxidase (cytochrome c) assembly 1-like	55					aerobic respiration (GO:0009060)|mitochondrial proton-transporting ATP synthase complex assembly (GO:0033615)|mitochondrial respiratory chain complex I assembly (GO:0032981)|mitochondrial respiratory chain complex I biogenesis (GO:0097031)|negative regulation of ATPase activity (GO:0032780)|negative regulation of oxidoreductase activity (GO:0051354)|oxidation-reduction process (GO:0055114)|protein complex assembly (GO:0006461)|protein insertion into membrane (GO:0051205)|protein tetramerization (GO:0051262)	integral component of mitochondrial membrane (GO:0032592)|mitochondrial membrane (GO:0031966)|mitochondrial respiratory chain (GO:0005746)|mitochondrion (GO:0005739)|protein complex (GO:0043234)	mitochondrial ribosome binding (GO:0097177)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(5)|skin(2)	19	all_cancers(95;8.44e-05)			GBM - Glioblastoma multiforme(265;0.0096)		ACACTACCTCTTCCTTGCGGC	0.602																																						dbGAP											0			14											46.0	45.0	45.0					14																	23236556		2203	4300	6503	22306396	SO:0001583	missense	0				CCDS9573.1	14q11.2	2009-05-26			ENSG00000155463	ENSG00000155463			8526	protein-coding gene	gene with protein product		601066				8586451, 19349278	Standard	NM_005015		Approved	MGC133129, OXA1	uc001wgn.2	Q15070	OTTHUMG00000028691	ENST00000604262.1:c.163T>G	14.37:g.23236556T>G	ENSP00000474623:p.Phe55Val	Somatic	107	1.83	2		65	36.27	37	WXS	Illumina HiSeq	Phase_IV	22306396	43	30.65	19	B4DPA2	Missense_Mutation	SNP	HMMPfam_60KD_IMP	p.F115V	ENST00000604262.1	37	c.343		14	.	.	.	.	.	.	.	.	.	.	T	13.68	2.309944	0.40895	.	.	ENSG00000155463	ENST00000285848;ENST00000412791;ENST00000358043	T;T;T	0.28666	1.6;1.63;1.63	5.1	2.22	0.28083	.	0.706306	0.13187	N	0.407049	T	0.17109	0.0411	N	0.22421	0.69	0.22424	N	0.999118	B;B;B;B	0.09022	0.002;0.001;0.001;0.001	B;B;B;B	0.06405	0.002;0.002;0.002;0.002	T	0.17899	-1.0354	10	0.30854	T	0.27	-14.2613	4.31	0.10965	0.0:0.6039:0.1905:0.2056	.	55;55;55;115	B4DGZ2;E7EVY0;Q15070;Q2M1J6	.;.;OXA1L_HUMAN;.	V	115;55;39	ENSP00000285848:F115V;ENSP00000387601:F55V;ENSP00000350740:F39V	ENSP00000285848:F115V	F	+	1	0	OXA1L	22306396	0.000000	0.05858	0.634000	0.29324	0.137000	0.21094	-0.250000	0.08830	0.795000	0.33922	-0.242000	0.12053	TTC	-	NULL		0.602	OXA1L-012	NOVEL	basic|appris_principal	protein_coding	OXA1L	protein_coding	OTTHUMT00000468876.1	T	NM_005015		22306396	+1	no_errors	NM_005015.3	genbank	human	validated	54_36p	missense	SNP	0.001	G
NID2	22795	genome.wustl.edu	37	14	52520434	52520434	+	Missense_Mutation	SNP	G	G	A	rs142884639		TCGA-AB-2867-03B-01W-0728-08	TCGA-AB-2867-11B-01W-0729-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	b3f3ba24-dfbe-4b4b-8502-83ec6ecd7df3	4e18dd6e-74b8-41c3-9665-900c92d39bee	g.chr14:52520434G>A	ENST00000216286.5	-	5	1291	c.1292C>T	c.(1291-1293)tCg>tTg	p.S431L	NID2_ENST00000541773.1_Missense_Mutation_p.S378L	NM_007361.3	NP_031387.3	Q14112	NID2_HUMAN	nidogen 2 (osteonidogen)	431					basement membrane organization (GO:0071711)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|cell surface (GO:0009986)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)			NS(1)|breast(5)|endometrium(9)|kidney(4)|large_intestine(11)|liver(1)|lung(40)|ovary(2)|pancreas(2)|prostate(2)|skin(3)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	87	Breast(41;0.0639)|all_epithelial(31;0.123)					ATCCATTTCCGAAGGCACTGG	0.537													G|||	1	0.000199681	0.0	0.0	5008	,	,		20204	0.0		0.001	False		,,,				2504	0.0					dbGAP											0			14						G	LEU/SER	2,4404	4.2+/-10.8	0,2,2201	87.0	84.0	85.0		1292	4.9	0.3	14	dbSNP_134	85	1,8599	1.2+/-3.3	0,1,4299	yes	missense	NID2	NM_007361.3	145	0,3,6500	AA,AG,GG		0.0116,0.0454,0.0231	benign	431/1376	52520434	3,13003	2203	4300	6503	51590184	SO:0001583	missense	0			AB009799	CCDS9706.1	14q22.1	2008-05-14			ENSG00000087303	ENSG00000087303			13389	protein-coding gene	gene with protein product		605399				9733643	Standard	NM_007361		Approved		uc001wzo.3	Q14112	OTTHUMG00000140298	ENST00000216286.5:c.1292C>T	14.37:g.52520434G>A	ENSP00000216286:p.Ser431Leu	Somatic	206	1.43	3		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	51590184	190	23.20	58	A8K6I7|B4DU19|O43710	Missense_Mutation	SNP	HMMPfam_Ldl_recept_b,HMMSmart_SM00135,PatternScan_ASX_HYDROXYL,HMMPfam_Thyroglobulin_1,HMMSmart_SM00211,PatternScan_THYROGLOBULIN_1_1,superfamily_Thyroglobulin type-1 domain,HMMSmart_SM00179,HMMPfam_NIDO,HMMSmart_SM00539,HMMPfam_EGF,HMMSmart_SM00181,HMMPfam_G2F,HMMSmart_SM00682,superfamily_GFP-like,PatternScan_EGF_2,HMMPfam_EGF_CA,PatternScan_EGF_CA,superfamily_EGF/Laminin,superfamily_YWTD domain	p.S431L	ENST00000216286.5	37	c.1292	CCDS9706.1	14	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	15.31	2.795561	0.50208	4.54E-4	1.16E-4	ENSG00000087303	ENST00000216286;ENST00000541773;ENST00000395707	D;D	0.83673	-1.75;-1.65	4.91	4.91	0.64330	.	1.049410	0.07390	N	0.888912	T	0.73442	0.3587	L	0.27053	0.805	0.31807	N	0.627637	P;P;B	0.44659	0.789;0.84;0.188	B;B;B	0.28465	0.09;0.06;0.006	T	0.73886	-0.3841	10	0.51188	T	0.08	.	17.037	0.86479	0.0:0.0:1.0:0.0	.	378;433;431	Q14112-2;Q5CZI2;Q14112	.;.;NID2_HUMAN	L	431;378;433	ENSP00000216286:S431L;ENSP00000443730:S378L	ENSP00000216286:S431L	S	-	2	0	NID2	51590184	0.367000	0.25023	0.252000	0.24328	0.056000	0.15407	4.095000	0.57728	2.530000	0.85305	0.655000	0.94253	TCG	-	NULL		0.537	NID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NID2	protein_coding	OTTHUMT00000276888.1	G			51590184	-1	no_errors	NM_007361.3	genbank	human	validated	54_36p	missense	SNP	0.063	A
CENPN	55839	genome.wustl.edu	37	16	81056223	81056223	+	Missense_Mutation	SNP	C	C	T			TCGA-AB-2867-03B-01W-0728-08	TCGA-AB-2867-11B-01W-0729-08	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	b3f3ba24-dfbe-4b4b-8502-83ec6ecd7df3	4e18dd6e-74b8-41c3-9665-900c92d39bee	g.chr16:81056223C>T	ENST00000305850.5	+	7	1343	c.553C>T	c.(553-555)Cac>Tac	p.H185Y	CENPN_ENST00000439957.3_Missense_Mutation_p.H165Y|CENPN_ENST00000299572.5_Intron|RP11-303E16.3_ENST00000562315.1_RNA|CENPN_ENST00000393335.3_Missense_Mutation_p.H185Y|CENPN_ENST00000428963.2_Intron|CMC2_ENST00000565914.1_5'Flank|RP11-303E16.3_ENST00000561808.1_RNA|RP11-303E16.3_ENST00000566390.1_RNA	NM_001100624.2|NM_001270474.1	NP_001094094.2|NP_001257403.1	Q96H22	CENPN_HUMAN	centromere protein N	185					CENP-A containing nucleosome assembly (GO:0034080)|chromosome segregation (GO:0007059)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|nucleosome assembly (GO:0006334)	cytosol (GO:0005829)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				breast(1)|large_intestine(5)|lung(4)	10						TGCTAGCAAACACCATCAGAT	0.368																																						dbGAP											0			16											92.0	92.0	92.0					16																	81056223		2012	4203	6215	79613724	SO:0001583	missense	0			AK026313	CCDS10931.1, CCDS42199.1, CCDS42200.1, CCDS58482.1, CCDS58483.1	16q23.2	2013-11-05	2006-06-15	2006-06-15	ENSG00000166451	ENSG00000166451			30873	protein-coding gene	gene with protein product		611509	"""chromosome 16 open reading frame 60"""	C16orf60		16622419	Standard	NM_001100625		Approved	FLJ13607, FLJ22660, BM039	uc002ffy.4	Q96H22	OTTHUMG00000137628	ENST00000305850.5:c.553C>T	16.37:g.81056223C>T	ENSP00000305608:p.His185Tyr	Somatic	160	3.01	5		0	0.00	0	WXS	Illumina HiSeq	Phase_IV	79613724	74	34.51	39	A8MZE6|B3KN53|B4DJD1|B4DPY7|C9JJM5|D3DUK8|E7ES30|E7ETS3|Q9NZ83	Missense_Mutation	SNP	HMMPfam_CHL4	p.H185Y	ENST00000305850.5	37	c.553	CCDS42200.1	16	.	.	.	.	.	.	.	.	.	.	C	5.815	0.334607	0.11013	.	.	ENSG00000166451	ENST00000305850;ENST00000439957;ENST00000393335	T;T;T	0.22539	1.95;1.95;1.95	5.95	3.78	0.43462	.	0.210963	0.51477	D	0.000098	T	0.10937	0.0267	L	0.34521	1.04	0.80722	D	1	B;B;B	0.21225	0.005;0.053;0.006	B;B;B	0.21708	0.007;0.036;0.017	T	0.13124	-1.0521	10	0.07325	T	0.83	-17.1624	2.0023	0.03470	0.3024:0.4489:0.0:0.2487	.	165;185;185	E7ETS3;A8MZE6;Q96H22	.;.;CENPN_HUMAN	Y	185;165;185	ENSP00000305608:H185Y;ENSP00000395235:H165Y;ENSP00000377007:H185Y	ENSP00000305608:H185Y	H	+	1	0	CENPN	79613724	0.998000	0.40836	1.000000	0.80357	0.914000	0.54420	1.508000	0.35769	1.483000	0.48342	0.655000	0.94253	CAC	-	HMMPfam_CHL4		0.368	CENPN-001	NOVEL	basic|appris_principal|CCDS	protein_coding	CENPN	protein_coding	OTTHUMT00000269051.1	C	NM_018455		79613724	+1	no_errors	NM_001100625.1	genbank	human	validated	54_36p	missense	SNP	0.998	T
RIBC2	26150	genome.wustl.edu	37	22	45813582	45813582	+	Silent	SNP	G	G	A	rs141584704		TCGA-AB-2867-03B-01W-0728-08	TCGA-AB-2867-11B-01W-0729-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	b3f3ba24-dfbe-4b4b-8502-83ec6ecd7df3	4e18dd6e-74b8-41c3-9665-900c92d39bee	g.chr22:45813582G>A	ENST00000342894.3	+	3	507	c.93G>A	c.(91-93)caG>caA	p.Q31Q	RIBC2_ENST00000538017.1_Silent_p.Q99Q			Q9H4K1	RIBC2_HUMAN	RIB43A domain with coiled-coils 2	31						nucleus (GO:0005634)				NS(1)|endometrium(1)|kidney(2)|large_intestine(3)|skin(2)|urinary_tract(1)	10		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0178)		ACTTCCAACAGAGCTTTCAGA	0.448																																						dbGAP											0			22											55.0	52.0	53.0					22																	45813582		2203	4300	6503	44192246	SO:0001819	synonymous_variant	0			AK098586		22q13.3	2004-08-18	2004-08-18	2004-08-18	ENSG00000128408	ENSG00000128408			13241	protein-coding gene	gene with protein product			"""chromosome 22 open reading frame 11"""	C22orf11		12477932	Standard	NM_015653		Approved	DKFZp566F0546, FLJ25720	uc011aqs.3	Q9H4K1	OTTHUMG00000151332	ENST00000342894.3:c.93G>A	22.37:g.45813582G>A		Somatic	232	4.08	10		0	100.00	3	WXS	Illumina HiSeq	Phase_IV	44192246	120	41.46	85	Q6ICD0|Q9Y413	Silent	SNP	HMMPfam_RIB43A	p.Q31	ENST00000342894.3	37	c.93		22																																																																																			-	HMMPfam_RIB43A		0.448	RIBC2-001	KNOWN	basic	protein_coding	RIBC2	protein_coding	OTTHUMT00000322250.1	G	NM_015653		44192246	+1	no_errors	NM_015653.2	genbank	human	validated	54_36p	silent	SNP	0.149	A
