#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_AAChange	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_Codon	i_COSMIC_Gene	i_COSMIC_Gene_Freq	i_COSMIC_Site_Freq	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ChromChange	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Drug_Target	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_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Exon	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_Genome_Plus_Minus_10_Bp	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_IGV	i_Mutation_Status	i_NTotCov_SOL	i_NVaf_SOL	i_NVarCov_SOL	i_ORegAnno_bin	i_Sequence_Source	i_Sequencer	i_Sequencing_Phase	i_TTotCov_SOL	i_TVaf_SOL	i_TVarCov_SOL	i_Transcript_Id	i_Ttot_rna	i_Tvaf_rna	i_Tvar_rna	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_ccds_id	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_dbSNPPopFreq	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_type	i_germline-maf-frequency	i_havana_transcript	i_note	i_refseq_mrna_id	i_secondary_variant_classification
DDX11L1	100287102	broad.mit.edu	37	1	13411	13411	+	RNA	DEL	C	C	-			TCGA-WZ-A8D5-01A-11D-A435-10	TCGA-WZ-A8D5-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f9769d8-ba26-4ac7-91c7-7ae0494130e7	928cb9ff-09c7-4a5f-bd42-198e31335976	g.chr1:13411delC	ENST00000456328.2	+	0	659					NR_046018.2|NR_051986.1				DEAD/H (Asp-Glu-Ala-Asp/His) box helicase 11 like 1																		AGAGCCTCCACCACCCCGAGA	0.567																																					.													.	.			0			.																																											0	.			CCTCCACCACCCC	AM992871		1p36.33	2012-02-23	2012-02-23		ENSG00000223972	ENSG00000223972			37102	pseudogene	pseudogene			"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11 like 1"""			19476624	Standard	NR_046018		Approved		uc010nxq.1		OTTHUMG00000000961		1.37:g.13411delC			Somatic	16	0	0		WXS	Illumina HiSeq	Phase_I	12	0.17	2	.	6	0.00	0		RNA	DEL	ENST00000456328.2	37																																																																																						0.567	DDX11L1-002	KNOWN	basic	processed_transcript	pseudogene		OTTHUMT00000362751.1			
AGRN	375790	broad.mit.edu	37	1	955613	955613	+	Missense_Mutation	SNP	G	G	T			TCGA-WZ-A8D5-01A-11D-A435-10	TCGA-WZ-A8D5-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f9769d8-ba26-4ac7-91c7-7ae0494130e7	928cb9ff-09c7-4a5f-bd42-198e31335976	g.chr1:955613G>T	ENST00000379370.2	+	1	111	c.61G>T	c.(61-63)Gcg>Tcg	p.A21S		NM_198576.3	NP_940978.2	O00468	AGRIN_HUMAN	agrin	21					axon guidance (GO:0007411)|carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|clustering of voltage-gated sodium channels (GO:0045162)|extracellular matrix organization (GO:0030198)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|neuromuscular junction development (GO:0007528)|neurotransmitter receptor metabolic process (GO:0045213)|phototransduction, visible light (GO:0007603)|plasma membrane organization (GO:0007009)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of synaptic growth at neuromuscular junction (GO:0045887)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|receptor clustering (GO:0043113)|retinoid metabolic process (GO:0001523)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synapse organization (GO:0050808)	basal lamina (GO:0005605)|cell junction (GO:0030054)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)|synapse (GO:0045202)	acetylcholine receptor regulator activity (GO:0030548)|calcium ion binding (GO:0005509)|chondroitin sulfate binding (GO:0035374)|dystroglycan binding (GO:0002162)|heparan sulfate proteoglycan binding (GO:0043395)|laminin binding (GO:0043236)|sialic acid binding (GO:0033691)|structural constituent of cytoskeleton (GO:0005200)			breast(1)|central_nervous_system(2)|endometrium(8)|kidney(3)|large_intestine(2)|lung(20)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	42	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		UCEC - Uterine corpus endometrioid carcinoma (11;0.00462)|Epithelial(90;5.98e-38)|OV - Ovarian serous cystadenocarcinoma(86;5.43e-23)|Colorectal(212;5.97e-05)|COAD - Colon adenocarcinoma(227;0.000201)|Kidney(185;0.0024)|BRCA - Breast invasive adenocarcinoma(365;0.00246)|STAD - Stomach adenocarcinoma(132;0.00645)|KIRC - Kidney renal clear cell carcinoma(229;0.0354)|Lung(427;0.201)		TGTGGTGGCCGCGTGCGTCCT	0.791																																					p.A21S													.	AGRN	110		0			c.G61T																																									SO:0001583	missense	375790	exon1			GTGGCCGCGTGCG	XM_372195	CCDS30551.1	1p36.33	2014-09-17		2007-02-16	ENSG00000188157	ENSG00000188157		"""Proteoglycans / Extracellular Matrix : Other"""	329	protein-coding gene	gene with protein product	"""agrin proteoglycan"""	103320				1851019, 12270958	Standard	NM_198576		Approved	AGRIN	uc001ack.2	O00468	OTTHUMG00000040778	ENST00000379370.2:c.61G>T	1.37:g.955613G>T	ENSP00000368678:p.Ala21Ser		Somatic	12	0	0		WXS	Illumina HiSeq	Phase_I	5	0.40	2	NM_198576	0		0	Q5SVA1|Q5SVA2|Q60FE1|Q7KYS8|Q8N4J5|Q96IC1|Q9BTD4	Missense_Mutation	SNP	ENST00000379370.2	37	CCDS30551.1	.	.	.	.	.	.	.	.	.	.	G	9.838	1.190187	0.21954	.	.	ENSG00000188157	ENST00000379370	T	0.76968	-1.06	2.05	1.1	0.20463	.	0.772224	0.09278	U	0.824163	T	0.62575	0.2439	L	0.43152	1.355	0.09310	N	1	B	0.32160	0.358	B	0.23852	0.049	T	0.42632	-0.9440	10	0.07990	T	0.79	.	7.5176	0.27610	0.1456:0.0:0.8544:0.0	.	21	O00468	AGRIN_HUMAN	S	21	ENSP00000368678:A21S	ENSP00000368678:A21S	A	+	1	0	AGRN	945476	0.000000	0.05858	0.032000	0.17829	0.036000	0.12997	0.631000	0.24568	0.215000	0.20761	-0.383000	0.06682	GCG			0.791	AGRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000097990.2		NM_198576	
RNF186	54546	broad.mit.edu	37	1	20142036	20142036	+	5'Flank	DEL	T	T	-	rs199878028	byFrequency	TCGA-WZ-A8D5-01A-11D-A435-10	TCGA-WZ-A8D5-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f9769d8-ba26-4ac7-91c7-7ae0494130e7	928cb9ff-09c7-4a5f-bd42-198e31335976	g.chr1:20142036delT	ENST00000375121.2	-	0	0				RP11-91K11.2_ENST00000454736.1_RNA	NM_019062.1	NP_061935.1	Q9NXI6	RN186_HUMAN	ring finger protein 186							integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)			kidney(1)|lung(3)|urinary_tract(1)	5		Colorectal(325;0.000147)|Renal(390;0.000469)|all_lung(284;0.00459)|Lung NSC(340;0.00475)|Breast(348;0.00526)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0439)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|COAD - Colon adenocarcinoma(152;1.07e-05)|BRCA - Breast invasive adenocarcinoma(304;7.77e-05)|Kidney(64;0.000162)|GBM - Glioblastoma multiforme(114;0.00036)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)		tttatttaacttttttttttt	0.438													|||unknown(HR)	972	0.194089	0.1536	0.304	5008	,	,		14782	0.2401		0.1054	False		,,,				2504	0.2147				.													.	RNF186	14		0			.																																									SO:0001631	upstream_gene_variant	0	.			TTTAACTTTTTTT		CCDS199.1	1p36.13	2008-02-05			ENSG00000178828	ENSG00000178828		"""RING-type (C3HC4) zinc fingers"""	25978	protein-coding gene	gene with protein product	"""hypothetical protein FLJ20225"""					12477932	Standard	NM_019062		Approved	FLJ20225	uc001bcr.3	Q9NXI6	OTTHUMG00000002709		1.37:g.20142036delT	Exception_encountered		Somatic	5	0	0		WXS	Illumina HiSeq	Phase_I	6	0.33	2	.	0		0	Q53GE0	RNA	DEL	ENST00000375121.2	37	CCDS199.1																																																																																					0.438	RNF186-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000007694.1		NM_019062	
GPATCH3	63906	broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	1	27216507	27216507	+	IGR	SNP	C	C	T			TCGA-WZ-A8D5-01A-11D-A435-10	TCGA-WZ-A8D5-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f9769d8-ba26-4ac7-91c7-7ae0494130e7	928cb9ff-09c7-4a5f-bd42-198e31335976	g.chr1:27216507C>T	ENST00000361720.5	-	0	2123				GPN2_ENST00000374135.4_Silent_p.L27L|GPN2_ENST00000461282.1_5'Flank	NM_022078.2	NP_071361.2	Q96I76	GPTC3_HUMAN	G patch domain containing 3								nucleic acid binding (GO:0003676)			endometrium(2)|large_intestine(1)|lung(11)|skin(1)	15		all_cancers(24;1.29e-21)|all_epithelial(13;2.35e-19)|Colorectal(325;0.000147)|all_lung(284;0.00122)|Lung NSC(340;0.00128)|Breast(348;0.00131)|Renal(390;0.00211)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0707)|all_neural(195;0.0966)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Epithelial(14;3.97e-51)|OV - Ovarian serous cystadenocarcinoma(117;9.55e-30)|Colorectal(126;5.31e-09)|COAD - Colon adenocarcinoma(152;9.31e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000513)|STAD - Stomach adenocarcinoma(196;0.000595)|KIRC - Kidney renal clear cell carcinoma(1967;0.00072)|READ - Rectum adenocarcinoma(331;0.0419)		CACTCATGCCCAGGCAGTACG	0.741																																					p.L27L													GPN2,NS,carcinoma,-2,1	GPN2	18	1	0			c.G81A												13.0	16.0	15.0					1																	27216507		2185	4282	6467	SO:0001628	intergenic_variant	54707	exon1			CATGCCCAGGCAG	BC007767	CCDS290.1	1p35.3-p35.1	2013-01-28		2006-12-13	ENSG00000198746	ENSG00000198746		"""G patch domain containing"""	25720	protein-coding gene	gene with protein product				GPATC3			Standard	NM_022078		Approved	FLJ12455	uc001bne.3	Q96I76	OTTHUMG00000004229		1.37:g.27216507C>T			Somatic	21	0	0		WXS	Illumina HiSeq	Phase_I	20	0.25	5	NM_018066	16	0.19	3	Q5JYH2|Q8NDJ2|Q9H9Z3	Silent	SNP	ENST00000361720.5	37	CCDS290.1																																																																																					0.741	GPATCH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000012181.1		NM_022078	
FCRL2	79368	mdanderson.org	37	1	157716685	157716685	+	Missense_Mutation	SNP	G	G	T			TCGA-WZ-A8D5-01A-11D-A435-10	TCGA-WZ-A8D5-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f9769d8-ba26-4ac7-91c7-7ae0494130e7	928cb9ff-09c7-4a5f-bd42-198e31335976	g.chr1:157716685G>T	ENST00000361516.3	-	11	1512	c.1464C>A	c.(1462-1464)aaC>aaA	p.N488K	FCRL2_ENST00000368181.4_Missense_Mutation_p.N182K|FCRL2_ENST00000392274.3_Intron	NM_030764.3	NP_110391.2	Q96LA5	FCRL2_HUMAN	Fc receptor-like 2	488					cell-cell signaling (GO:0007267)|positive regulation of signal transduction (GO:0009967)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	SH3/SH2 adaptor activity (GO:0005070)			central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(29)|ovary(1)|pancreas(1)|prostate(3)|skin(2)	51	all_hematologic(112;0.0378)		LUSC - Lung squamous cell carcinoma(543;0.24)			GTGTCCTGATGTTTGCTGTTA	0.408																																					p.N488K													.	.			0			c.C1464A												154.0	163.0	160.0					1																	157716685		2203	4300	6503	SO:0001583	missense	79368	exon11			CCTGATGTTTGCT	AF319438	CCDS1168.1	1q23.1	2013-01-14	2002-01-14	2005-03-23	ENSG00000132704	ENSG00000132704		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	14875	protein-coding gene	gene with protein product		606509	"""SH2 domain-containing phosphatase anchor protein 1"""	SPAP1		11162587	Standard	NM_030764		Approved	FCRH2, IRTA4, CD307b	uc001fre.2	Q96LA5	OTTHUMG00000019399	ENST00000361516.3:c.1464C>A	1.37:g.157716685G>T	ENSP00000355157:p.Asn488Lys		Somatic	22	0	0		WXS	Illumina HiSeq	Phase_I	22	0.09	2	NM_030764	12	0.00	0	A0N0M5|A1L307|A6NMS0|Q6NTA1|Q9BZI4|Q9BZI5|Q9BZI6	Missense_Mutation	SNP	ENST00000361516.3	37	CCDS1168.1	.	.	.	.	.	.	.	.	.	.	G	13.73	2.325588	0.41197	.	.	ENSG00000132704	ENST00000292389;ENST00000361516;ENST00000368181	T;T	0.21191	2.02;3.32	3.44	1.52	0.23074	.	1.648920	0.04100	U	0.312667	T	0.25791	0.0628	M	0.62723	1.935	0.34914	D	0.747786	D;B;P	0.71674	0.998;0.2;0.936	D;B;P	0.66351	0.943;0.036;0.725	T	0.15321	-1.0441	10	0.66056	D	0.02	.	4.9872	0.14196	0.2819:0.0:0.7181:0.0	.	182;488;235	Q96LA5-5;Q96LA5;Q96LA5-2	.;FCRL2_HUMAN;.	K	182;488;182	ENSP00000355157:N488K;ENSP00000357163:N182K	ENSP00000292389:N182K	N	-	3	2	FCRL2	155983309	0.250000	0.23951	0.761000	0.31378	0.415000	0.31203	-0.003000	0.12901	0.759000	0.33084	0.650000	0.86243	AAC			0.408	FCRL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000051408.2		NM_030764	
ARMC4	55130	ucsc.edu	37	10	28250581	28250581	+	Missense_Mutation	SNP	T	T	A			TCGA-WZ-A8D5-01A-11D-A435-10	TCGA-WZ-A8D5-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f9769d8-ba26-4ac7-91c7-7ae0494130e7	928cb9ff-09c7-4a5f-bd42-198e31335976	g.chr10:28250581T>A	ENST00000305242.5	-	10	1394	c.1302A>T	c.(1300-1302)gaA>gaT	p.E434D	ARMC4_ENST00000537576.1_Missense_Mutation_p.E126D|ARMC4_ENST00000545014.1_De_novo_Start_OutOfFrame|ARMC4_ENST00000239715.3_Missense_Mutation_p.E291D|ARMC4_ENST00000480504.1_5'UTR	NM_018076.2	NP_060546.2	Q5T2S8	ARMC4_HUMAN	armadillo repeat containing 4	434					cell projection organization (GO:0030030)|cilium movement (GO:0003341)|left/right axis specification (GO:0070986)|outer dynein arm assembly (GO:0036158)|ventricular system development (GO:0021591)	axoneme (GO:0005930)|ciliary base (GO:0097546)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)				NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(17)|liver(1)|lung(17)|ovary(5)|prostate(3)|skin(8)|stomach(2)|urinary_tract(3)	75						CAGGTGGTTCTTCATCTTCCT	0.398																																					p.E434D													.	ARMC4	177		0			c.A1302T												72.0	68.0	69.0					10																	28250581		2202	4280	6482	SO:0001583	missense	55130	exon10			TGGTTCTTCATCT	AL136859	CCDS7157.1	10p12.1-p11.23	2014-02-03			ENSG00000169126	ENSG00000169126		"""Armadillo repeat containing"""	25583	protein-coding gene	gene with protein product		615408				11230166	Standard	XM_005252485		Approved	FLJ10817, FLJ10376, DKFZP434P1735, CILD23	uc001itz.3	Q5T2S8	OTTHUMG00000017867	ENST00000305242.5:c.1302A>T	10.37:g.28250581T>A	ENSP00000306410:p.Glu434Asp		Somatic	127	0.0393700787	5		WXS	Illumina HiSeq		153	0.09	14	NM_018076	0		0	A8K906|B7Z7I1|Q9H0C0	Missense_Mutation	SNP	ENST00000305242.5	37	CCDS7157.1	.	.	.	.	.	.	.	.	.	.	T	12.92	2.082750	0.36758	.	.	ENSG00000169126	ENST00000537576;ENST00000305242;ENST00000537573;ENST00000434029;ENST00000239715	T;T;T;T	0.60797	0.65;0.98;0.16;0.2	5.4	-1.39	0.08997	.	0.101407	0.64402	D	0.000004	T	0.44540	0.1298	L	0.58669	1.825	0.49582	D	0.999809	B	0.30542	0.284	B	0.27380	0.079	T	0.23726	-1.0180	10	0.66056	D	0.02	-33.1632	5.0207	0.14360	0.1285:0.3134:0.0:0.5582	.	434	Q5T2S8	ARMC4_HUMAN	D	126;434;126;328;291	ENSP00000443208:E126D;ENSP00000306410:E434D;ENSP00000398155:E328D;ENSP00000239715:E291D	ENSP00000239715:E291D	E	-	3	2	ARMC4	28290587	0.999000	0.42202	0.886000	0.34754	0.568000	0.35870	0.421000	0.21280	-0.097000	0.12307	0.528000	0.53228	GAA			0.398	ARMC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000047339.1		NM_018076	
PDCD11	22984	hgsc.bcm.edu;broad.mit.edu	37	10	105160253	105160253	+	Missense_Mutation	SNP	G	G	T	rs564339479		TCGA-WZ-A8D5-01A-11D-A435-10	TCGA-WZ-A8D5-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f9769d8-ba26-4ac7-91c7-7ae0494130e7	928cb9ff-09c7-4a5f-bd42-198e31335976	g.chr10:105160253G>T	ENST00000369797.3	+	3	296	c.202G>T	c.(202-204)Gca>Tca	p.A68S		NM_014976.1	NP_055791.1	Q14690	RRP5_HUMAN	programmed cell death 11	68					mRNA processing (GO:0006397)|rRNA processing (GO:0006364)	cytosol (GO:0005829)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|transcription factor binding (GO:0008134)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(10)|lung(29)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	64		Colorectal(252;0.0747)|Breast(234;0.128)		Epithelial(162;7.21e-09)|all cancers(201;1.17e-08)|BRCA - Breast invasive adenocarcinoma(275;0.208)		CAGCAAGTCCGCAAGAGAGAA	0.368																																					p.A68S													.	.			0			c.G202T												119.0	132.0	127.0					10																	105160253		2203	4300	6503	SO:0001583	missense	22984	exon3			AAGTCCGCAAGAG	D80007	CCDS31276.1	10q24.32	2010-07-06			ENSG00000148843	ENSG00000148843			13408	protein-coding gene	gene with protein product		612333				10229231	Standard	XM_005269647		Approved	KIAA0185, ALG-4, RRP5	uc001kwy.1	Q14690	OTTHUMG00000018988	ENST00000369797.3:c.202G>T	10.37:g.105160253G>T	ENSP00000358812:p.Ala68Ser		Somatic	79	0	0		WXS	Illumina HiSeq	.	74	0.05	4	NM_014976	118	0.00	0	Q2TA92|Q5W093|Q6P2J3|Q86VQ8|Q9H4P1	Missense_Mutation	SNP	ENST00000369797.3	37	CCDS31276.1	.	.	.	.	.	.	.	.	.	.	G	6.530	0.466018	0.12402	.	.	ENSG00000148843	ENST00000369797;ENST00000543503	T	0.09538	2.97	5.72	-1.61	0.08399	Nucleic acid-binding, OB-fold (1);	1.445070	0.03978	N	0.292777	T	0.03608	0.0103	N	0.03608	-0.345	0.09310	N	1	B	0.06786	0.001	B	0.08055	0.003	T	0.31668	-0.9935	10	0.09590	T	0.72	2.5432	0.6676	0.00853	0.3884:0.1233:0.238:0.2503	.	68	Q14690	RRP5_HUMAN	S	68	ENSP00000358812:A68S	ENSP00000358812:A68S	A	+	1	0	PDCD11	105150243	0.000000	0.05858	0.001000	0.08648	0.982000	0.71751	-1.029000	0.03585	-0.629000	0.05575	0.561000	0.74099	GCA			0.368	PDCD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000050151.1			
FANK1	92565	mdanderson.org	37	10	127585221	127585221	+	Nonsense_Mutation	SNP	C	C	T	rs202109621		TCGA-WZ-A8D5-01A-11D-A435-10	TCGA-WZ-A8D5-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f9769d8-ba26-4ac7-91c7-7ae0494130e7	928cb9ff-09c7-4a5f-bd42-198e31335976	g.chr10:127585221C>T	ENST00000368693.1	+	1	114	c.10C>T	c.(10-12)Cag>Tag	p.Q4*	FANK1_ENST00000449042.2_5'UTR|FANK1_ENST00000368695.1_5'UTR			Q8TC84	FANK1_HUMAN	fibronectin type III and ankyrin repeat domains 1	4						cytoplasm (GO:0005737)|nucleus (GO:0005634)				central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(6)|lung(10)|ovary(1)|urinary_tract(1)	21		all_lung(145;0.00752)|Lung NSC(174;0.0115)|Colorectal(57;0.0847)|all_neural(114;0.0936)				CATGGAGCCCCAGAGTAAGGg	0.756																																					p.Q4X													.	.			0			c.C10T												8.0	12.0	11.0					10																	127585221		2169	4258	6427	SO:0001587	stop_gained	92565	exon1			GAGCCCCAGAGTA	BC024189	CCDS31309.1	10q26.2	2013-02-11	2005-03-01		ENSG00000203780	ENSG00000203780		"""Ankyrin repeat domain containing"", ""Fibronectin type III domain containing"""	23527	protein-coding gene	gene with protein product		611640	"""fibronectin type 3 and ankyrin repeat domains 1"""			12477932	Standard	NM_145235		Approved		uc001ljh.4	Q8TC84	OTTHUMG00000019241	ENST00000368693.1:c.10C>T	10.37:g.127585221C>T	ENSP00000357682:p.Gln4*		Somatic	15	0	0		WXS	Illumina HiSeq	Phase_I	29	0.10	3	NM_145235	7	0.00	0	Q6UXY9|Q6X7T6	Nonsense_Mutation	SNP	ENST00000368693.1	37	CCDS31309.1	.	.	.	.	.	.	.	.	.	.	C	32	5.122908	0.94429	.	.	ENSG00000203780	ENST00000368693	.	.	.	2.62	1.68	0.24146	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.11485	T	0.65	.	6.8436	0.23977	0.274:0.726:0.0:0.0	.	.	.	.	X	4	.	ENSP00000357682:Q4X	Q	+	1	0	FANK1	127575211	1.000000	0.71417	0.999000	0.59377	0.552000	0.35366	1.578000	0.36525	0.621000	0.30232	0.462000	0.41574	CAG			0.756	FANK1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				NM_145235	
JAKMIP3	282973	mdanderson.org	37	10	133976881	133976881	+	Silent	SNP	C	C	A			TCGA-WZ-A8D5-01A-11D-A435-10	TCGA-WZ-A8D5-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f9769d8-ba26-4ac7-91c7-7ae0494130e7	928cb9ff-09c7-4a5f-bd42-198e31335976	g.chr10:133976881C>A	ENST00000298622.4	+	19	2521	c.2383C>A	c.(2383-2385)Cgg>Agg	p.R795R	JAKMIP3_ENST00000477275.1_3'UTR	NM_001105521.2	NP_001098991.1	Q5VZ66	JKIP3_HUMAN	Janus kinase and microtubule interacting protein 3	795			R -> G (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.			Golgi apparatus (GO:0005794)		p.R795G(1)		breast(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(10)|ovary(2)|prostate(1)|upper_aerodigestive_tract(2)	31		all_cancers(35;5.63e-09)|all_epithelial(44;9.25e-07)|Lung NSC(174;0.0108)|all_lung(145;0.0173)|Colorectal(31;0.0721)|all_neural(114;0.0726)|Breast(234;0.0949)|Glioma(114;0.172)|Melanoma(40;0.175)		OV - Ovarian serous cystadenocarcinoma(35;0.000104)|Epithelial(32;0.000142)|all cancers(32;0.000185)|BRCA - Breast invasive adenocarcinoma(275;0.224)		CCAGATCCTGCGGGAGCGCAT	0.687																																					p.R795R													JAKMIP3,NS,carcinoma,0,1	JAKMIP3	0	1	1	Substitution - Missense(1)	breast(1)	c.C2383A												33.0	27.0	29.0					10																	133976881		2200	4297	6497	SO:0001819	synonymous_variant	282973	exon19			ATCCTGCGGGAGC	AL832756	CCDS44494.1	10q26.3	2009-04-23	2009-04-23	2008-01-28	ENSG00000188385	ENSG00000188385			23523	protein-coding gene	gene with protein product	"""neuroendocrine long coiled-coil 2"""	611198	"""chromosome 10 open reading frame 39"", ""chromosome 10 open reading frame 14"""	C10orf39, C10orf14		15277531, 17572408	Standard	NM_001105521		Approved	FLJ37857, NECC2, KIAA4091, bA140A10.5	uc001lkx.4	Q5VZ66	OTTHUMG00000150167	ENST00000298622.4:c.2383C>A	10.37:g.133976881C>A			Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	12	0.17	2	NM_001105521	0		0	A6PW00|Q69YM6|Q6ZT29	Silent	SNP	ENST00000298622.4	37	CCDS44494.1																																																																																					0.687	JAKMIP3-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000051049.3		NM_194303	
MUC5B	727897	mdanderson.org	37	11	1258387	1258387	+	Missense_Mutation	SNP	G	G	A	rs202160055		TCGA-WZ-A8D5-01A-11D-A435-10	TCGA-WZ-A8D5-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f9769d8-ba26-4ac7-91c7-7ae0494130e7	928cb9ff-09c7-4a5f-bd42-198e31335976	g.chr11:1258387G>A	ENST00000529681.1	+	25	3348	c.3290G>A	c.(3289-3291)cGc>cAc	p.R1097H	MUC5B_ENST00000447027.1_Missense_Mutation_p.R1100H	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	1097	VWFD 3. {ECO:0000255|PROSITE- ProRule:PRU00580}.				cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to retinoic acid (GO:0071300)|epithelial cell differentiation (GO:0030855)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to lipopolysaccharide (GO:0032496)|response to ozone (GO:0010193)|response to sulfur dioxide (GO:0010477)|response to vitamin A (GO:0033189)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				cervix(2)|endometrium(36)|kidney(9)|lung(89)|urinary_tract(1)	137		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)		GCCGCCTGCCGCTCCCAGGTG	0.682																																					p.R1097H													MUC5B,NS,carcinoma,+1,4	MUC5B	1	4	0			c.G3290A												10.0	16.0	14.0					11																	1258387		1900	4086	5986	SO:0001583	missense	727897	exon25			CCTGCCGCTCCCA	U95031, AF086604	CCDS44515.1, CCDS44515.2	11p15.5	2007-01-19	2006-03-14			ENSG00000117983		"""Mucins"""	7516	protein-coding gene	gene with protein product		600770	"""mucin 5, subtype B, tracheobronchial"""	MUC5		9804771	Standard	NM_002458		Approved	MG1	uc001lta.3	Q9HC84		ENST00000529681.1:c.3290G>A	11.37:g.1258387G>A	ENSP00000436812:p.Arg1097His		Somatic	23	0.0434782609	1		WXS	Illumina HiSeq	Phase_I	27	0.11	3	NM_002458	0		0	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	37	CCDS44515.2	.	.	.	.	.	.	.	.	.	.	G	6.941	0.543406	0.13250	.	.	ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637;ENST00000406844	T;T	0.72505	-0.66;-0.66	4.38	-0.728	0.11162	von Willebrand factor, type D domain (1);Uncharacterised domain, cysteine-rich (2);	.	.	.	.	T	0.30198	0.0757	N	0.00135	-2.02	0.26154	N	0.980103	B;B;B	0.24132	0.004;0.098;0.098	B;B;B	0.12837	0.001;0.008;0.008	T	0.37934	-0.9684	9	0.87932	D	0	.	8.5449	0.33415	0.6733:0.0:0.3267:0.0	rs35573593	1097;1790;1100	Q9HC84;A7Y9J9;E9PBJ0	MUC5B_HUMAN;.;.	H	1097;1100;1098;1167	ENSP00000436812:R1097H;ENSP00000415793:R1100H	ENSP00000343037:R1098H	R	+	2	0	MUC5B	1214963	0.002000	0.14202	0.101000	0.21167	0.007000	0.05969	0.139000	0.16036	-0.476000	0.06842	-0.379000	0.06801	CGC			0.682	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding		OTTHUMT00000390041.2		XM_001126093	
KRTAP5-2	440021	broad.mit.edu	37	11	1619052	1619052	+	Nonsense_Mutation	SNP	G	G	T			TCGA-WZ-A8D5-01A-11D-A435-10	TCGA-WZ-A8D5-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f9769d8-ba26-4ac7-91c7-7ae0494130e7	928cb9ff-09c7-4a5f-bd42-198e31335976	g.chr11:1619052G>T	ENST00000412090.1	-	1	472	c.429C>A	c.(427-429)tgC>tgA	p.C143*	KRTAP5-AS1_ENST00000532922.1_RNA|KRTAP5-AS1_ENST00000424148.1_RNA|KRTAP5-AS1_ENST00000534077.1_RNA|KRTAP5-AS1_ENST00000524947.1_RNA	NM_001004325.1	NP_001004325.1	Q701N4	KRA52_HUMAN	keratin associated protein 5-2	143	6 X 4 AA repeats of C-C-X-P.					keratin filament (GO:0045095)				large_intestine(1)|lung(2)|skin(1)	4		all_epithelial(84;0.00018)|Ovarian(85;0.0014)|Breast(177;0.00147)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.000614)|Lung(200;0.0681)|LUSC - Lung squamous cell carcinoma(625;0.082)		AGCTGGACTGGCAGCAGCAGG	0.607																																					p.C143X													.	KRTAP5-2	38		0			c.C429A												101.0	106.0	104.0					11																	1619052		2202	4299	6501	SO:0001587	stop_gained	440021	exon1			GGACTGGCAGCAG	AB126071	CCDS31331.1	11p15.5	2008-02-05				ENSG00000205867		"""Keratin associated proteins"""	23597	protein-coding gene	gene with protein product						15144888	Standard	NM_001004325		Approved	KRTAP5.2, KRTAP5-8	uc001ltv.3	Q701N4		ENST00000412090.1:c.429C>A	11.37:g.1619052G>T	ENSP00000400041:p.Cys143*		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	68	0.04	3	NM_001004325	0		0	A9JTZ1	Nonsense_Mutation	SNP	ENST00000412090.1	37	CCDS31331.1	.	.	.	.	.	.	.	.	.	.	G	9.348	1.064734	0.20067	.	.	ENSG00000205867	ENST00000412090	.	.	.	3.63	1.65	0.23941	.	.	.	.	.	.	.	.	.	.	.	0.31893	N	0.616926	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	8.1177	0.30953	0.2179:0.0:0.7821:0.0	.	.	.	.	X	143	.	ENSP00000400041:C143X	C	-	3	2	KRTAP5-2	1575628	0.072000	0.21174	0.452000	0.26994	0.285000	0.27093	0.757000	0.26433	0.172000	0.19760	0.109000	0.15622	TGC			0.607	KRTAP5-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000384775.1		NM_001004325	
CDKN1C	1028	mdanderson.org	37	11	2906488	2906488	+	Missense_Mutation	SNP	G	G	T			TCGA-WZ-A8D5-01A-11D-A435-10	TCGA-WZ-A8D5-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f9769d8-ba26-4ac7-91c7-7ae0494130e7	928cb9ff-09c7-4a5f-bd42-198e31335976	g.chr11:2906488G>T	ENST00000414822.3	-	1	623	c.232C>A	c.(232-234)Cag>Aag	p.Q78K	CDKN1C_ENST00000440480.2_Missense_Mutation_p.Q67K|CDKN1C_ENST00000430149.2_Missense_Mutation_p.Q78K|CDKN1C_ENST00000313407.6_Missense_Mutation_p.Q67K|CDKN1C_ENST00000380725.1_Missense_Mutation_p.Q67K	NM_000076.2	NP_000067.1	P49918	CDN1C_HUMAN	cyclin-dependent kinase inhibitor 1C (p57, Kip2)	78					adrenal gland development (GO:0030325)|aging (GO:0007568)|camera-type eye development (GO:0043010)|cell cycle arrest (GO:0007050)|digestive system development (GO:0055123)|embryonic placenta morphogenesis (GO:0060669)|genetic imprinting (GO:0071514)|kidney development (GO:0001822)|multicellular organism growth (GO:0035264)|myeloid cell differentiation (GO:0030099)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of kinase activity (GO:0033673)|negative regulation of phosphorylation (GO:0042326)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron maturation (GO:0042551)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|skeletal system development (GO:0001501)|uterus development (GO:0060065)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	cyclin-dependent protein serine/threonine kinase inhibitor activity (GO:0004861)			central_nervous_system(1)|lung(1)	2		all_epithelial(84;0.000187)|Medulloblastoma(188;0.00106)|Ovarian(85;0.0014)|Breast(177;0.00328)|all_neural(188;0.00681)|all_lung(207;0.157)|Lung NSC(207;0.216)		BRCA - Breast invasive adenocarcinoma(625;0.0025)|LUSC - Lung squamous cell carcinoma(625;0.19)		TCGGTCCACTGCAGGCGTCCA	0.721																																					p.Q78K	GBM(111;59 1151 2497 5746 16112 18241 29216)												.	.			0			c.C232A												16.0	12.0	13.0					11																	2906488		2146	4249	6395	SO:0001583	missense	1028	exon1			TCCACTGCAGGCG	D64137	CCDS7738.1, CCDS44519.1	11p15.5	2014-09-17	2004-02-13		ENSG00000129757	ENSG00000129757			1786	protein-coding gene	gene with protein product		600856	"""Beckwith-Wiedemann syndrome"""	BWCR, BWS		7729684	Standard	NM_000076		Approved	P57, KIP2	uc001lws.4	P49918	OTTHUMG00000010040	ENST00000414822.3:c.232C>A	11.37:g.2906488G>T	ENSP00000413720:p.Gln78Lys		Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	34	0.09	3	NM_000076	7	0.00	0		Missense_Mutation	SNP	ENST00000414822.3	37	CCDS7738.1	.	.	.	.	.	.	.	.	.	.	g	12.29	1.893179	0.33442	.	.	ENSG00000129757	ENST00000380725;ENST00000414822;ENST00000440480;ENST00000313407;ENST00000430149	D;D;D;D;D	0.83914	-1.78;-1.78;-1.78;-1.78;-1.78	2.43	2.43	0.29744	.	.	.	.	.	T	0.71676	0.3368	N	0.25094	0.71	0.26197	N	0.97951	B;B	0.26258	0.145;0.053	B;B	0.27076	0.032;0.076	T	0.62886	-0.6759	9	0.42905	T	0.14	.	9.3629	0.38206	0.0:0.2206:0.7793:0.0	.	67;78	A6NK88;P49918	.;CDN1C_HUMAN	K	67;78;67;67;78	ENSP00000370101:Q67K;ENSP00000413720:Q78K;ENSP00000411257:Q67K;ENSP00000321019:Q67K;ENSP00000411552:Q78K	ENSP00000321019:Q67K	Q	-	1	0	CDKN1C	2863064	1.000000	0.71417	1.000000	0.80357	0.919000	0.55068	3.393000	0.52544	1.407000	0.46875	0.298000	0.19748	CAG			0.721	CDKN1C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		OTTHUMT00000027774.2		NM_000076	
ARAP1	116985	mdanderson.org	37	11	72404840	72404840	+	Silent	SNP	C	C	T			TCGA-WZ-A8D5-01A-11D-A435-10	TCGA-WZ-A8D5-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f9769d8-ba26-4ac7-91c7-7ae0494130e7	928cb9ff-09c7-4a5f-bd42-198e31335976	g.chr11:72404840C>T	ENST00000393609.3	-	28	3907	c.3705G>A	c.(3703-3705)ctG>ctA	p.L1235L	ARAP1_ENST00000359373.5_Silent_p.L1235L|ARAP1_ENST00000426523.1_Silent_p.L990L|ARAP1_ENST00000495878.1_5'UTR|ARAP1_ENST00000429686.1_Silent_p.L929L|ARAP1-AS1_ENST00000542022.1_RNA|ARAP1_ENST00000334211.8_Silent_p.L990L|ARAP1_ENST00000455638.2_Silent_p.L1235L|ARAP1_ENST00000393605.3_Silent_p.L995L	NM_001040118.2	NP_001035207.1	Q96P48	ARAP1_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 1	1235	Ras-associating. {ECO:0000255|PROSITE- ProRule:PRU00166}.				actin filament reorganization involved in cell cycle (GO:0030037)|negative regulation of stress fiber assembly (GO:0051497)|positive regulation of Cdc42 GTPase activity (GO:0043089)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of receptor recycling (GO:0001921)|regulation of ARF GTPase activity (GO:0032312)|regulation of cell shape (GO:0008360)|regulation of cellular component movement (GO:0051270)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	ARF GTPase activator activity (GO:0008060)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|Rho GTPase activator activity (GO:0005100)|zinc ion binding (GO:0008270)			cervix(2)|endometrium(2)|large_intestine(10)|lung(8)|ovary(1)|skin(3)|urinary_tract(1)	27						CCGCAAAGTGCAGGGGGCGCT	0.627																																					p.L1235L	Ovarian(102;1198 1520 13195 17913 37529)												.	.			0			c.G3705A												48.0	35.0	40.0					11																	72404840		2200	4290	6490	SO:0001819	synonymous_variant	116985	exon28			AAAGTGCAGGGGG	AF411983	CCDS8217.2, CCDS41687.1, CCDS44671.1	11q13.3	2013-01-11	2008-09-22	2008-09-22	ENSG00000186635	ENSG00000186635		"""ADP-ribosylation factor GTPase activating proteins"", ""Sterile alpha motif (SAM) domain containing"", ""Pleckstrin homology (PH) domain containing"", ""Ankyrin repeat domain containing"""	16925	protein-coding gene	gene with protein product		606646	"""centaurin, delta 2"""	CENTD2			Standard	NM_001040118		Approved		uc001osu.3	Q96P48	OTTHUMG00000157102	ENST00000393609.3:c.3705G>A	11.37:g.72404840C>T			Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	29	0.10	3	NM_001040118	112	0.00	0	A3KLL7|B2RTS2|O94879|Q4LDD5|Q59FI7|Q6PHS3|Q8WU51|Q96HP6|Q96L71	Silent	SNP	ENST00000393609.3	37	CCDS41687.1																																																																																					0.627	ARAP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		OTTHUMT00000347428.1		NM_001040118	
TMPRSS4	56649	mdanderson.org	37	11	117982461	117982461	+	Missense_Mutation	SNP	G	G	T			TCGA-WZ-A8D5-01A-11D-A435-10	TCGA-WZ-A8D5-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f9769d8-ba26-4ac7-91c7-7ae0494130e7	928cb9ff-09c7-4a5f-bd42-198e31335976	g.chr11:117982461G>T	ENST00000437212.3	+	8	803	c.589G>T	c.(589-591)Ggg>Tgg	p.G197W	TMPRSS4_ENST00000523251.1_Missense_Mutation_p.G157W|TMPRSS4_ENST00000522824.1_Missense_Mutation_p.G192W|TMPRSS4_ENST00000534111.1_Missense_Mutation_p.G195W|TMPRSS4_ENST00000522307.1_Missense_Mutation_p.G50W			Q9NRS4	TMPS4_HUMAN	transmembrane protease, serine 4	197	SRCR. {ECO:0000255|PROSITE- ProRule:PRU00196}.				proteolysis (GO:0006508)	integral component of membrane (GO:0016021)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)			breast(2)|central_nervous_system(2)|large_intestine(3)|lung(8)|ovary(1)|prostate(2)|skin(1)	19	all_hematologic(175;0.0487)	Medulloblastoma(222;0.0431)|all_hematologic(192;0.164)|Breast(348;0.183)|all_neural(223;0.238)		BRCA - Breast invasive adenocarcinoma(274;4.16e-05)|Epithelial(105;0.00204)		TCCAGCCTGTGGGAAGAGCCT	0.607																																					p.G197W													.	.			0			c.G589T												62.0	52.0	55.0					11																	117982461		2200	4296	6496	SO:0001583	missense	56649	exon8			GCCTGTGGGAAGA	AF179224	CCDS31684.1, CCDS44743.1, CCDS53716.1, CCDS53717.1	11q23.3	2010-04-13			ENSG00000137648	ENSG00000137648		"""Serine peptidases / Transmembrane"""	11878	protein-coding gene	gene with protein product	"""transmembrane serine protease 3"", ""membrane-type serine protease 2"", ""type II membrane serine protease"""	606565				10825129	Standard	NM_001083947		Approved	TMPRSS3, MT-SP2	uc021qrd.1	Q9NRS4	OTTHUMG00000164122	ENST00000437212.3:c.589G>T	11.37:g.117982461G>T	ENSP00000416037:p.Gly197Trp		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	53	0.06	3	NM_019894	0		0	A8MU84|B0YJB0|B7Z8C5|E7ERX8|Q5XKQ6|Q6UX37|Q9NZA5	Missense_Mutation	SNP	ENST00000437212.3	37	CCDS31684.1	.	.	.	.	.	.	.	.	.	.	G	19.30	3.800710	0.70567	.	.	ENSG00000137648	ENST00000534111;ENST00000522307;ENST00000523251;ENST00000437212;ENST00000522824;ENST00000522151	T;T;T;T;T;T	0.69175	-0.38;-0.28;-0.38;-0.38;-0.38;-0.38	5.06	5.06	0.68205	Peptidase cysteine/serine, trypsin-like (1);Speract/scavenger receptor-related (1);	0.000000	0.64402	D	0.000014	D	0.84197	0.5419	M	0.88105	2.93	0.80722	D	1	D;D;D;D;D	0.89917	1.0;0.998;0.999;1.0;1.0	D;D;D;D;D	0.87578	0.99;0.987;0.978;0.998;0.995	D	0.87456	0.2404	10	0.87932	D	0	.	15.3365	0.74260	0.0:0.0:1.0:0.0	.	172;157;50;197;195	B7Z900;E7ERX8;E7ESG9;Q9NRS4;Q9NRS4-3	.;.;.;TMPS4_HUMAN;.	W	195;50;157;197;192;144	ENSP00000435184:G195W;ENSP00000428814:G50W;ENSP00000429209:G157W;ENSP00000416037:G197W;ENSP00000430547:G192W;ENSP00000428407:G144W	ENSP00000416037:G197W	G	+	1	0	TMPRSS4	117487671	1.000000	0.71417	0.768000	0.31515	0.624000	0.37722	8.448000	0.90335	2.343000	0.79666	0.609000	0.83330	GGG			0.607	TMPRSS4-004	KNOWN	non_canonical_polymorphism|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		OTTHUMT00000377328.2		NM_019894	
HYOU1	10525	mdanderson.org	37	11	118925732	118925732	+	Missense_Mutation	SNP	G	G	T			TCGA-WZ-A8D5-01A-11D-A435-10	TCGA-WZ-A8D5-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f9769d8-ba26-4ac7-91c7-7ae0494130e7	928cb9ff-09c7-4a5f-bd42-198e31335976	g.chr11:118925732G>T	ENST00000404233.3	-	6	584	c.460C>A	c.(460-462)Ctc>Atc	p.L154I	HYOU1_ENST00000543287.1_Missense_Mutation_p.L67I|HYOU1_ENST00000525859.1_Missense_Mutation_p.L154I|HYOU1_ENST00000529972.1_Missense_Mutation_p.L154I	NM_001130991.1|NM_006389.3	NP_001124463.1|NP_006380.1	Q9Y4L1	HYOU1_HUMAN	hypoxia up-regulated 1	154					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|response to ischemia (GO:0002931)|response to stress (GO:0006950)	endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)	ATP binding (GO:0005524)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|lung(10)|prostate(1)|skin(2)	33	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)|all_hematologic(192;0.207)		BRCA - Breast invasive adenocarcinoma(274;7.78e-05)		GAATAATTGAGAACCATGCCC	0.532																																					p.L154I													.	.			0			c.C460A												121.0	101.0	107.0					11																	118925732		2200	4295	6495	SO:0001583	missense	10525	exon6			AATTGAGAACCAT	U65785	CCDS8408.1	11q23.1-q23.3	2011-09-02			ENSG00000149428	ENSG00000149428		"""Heat shock proteins / HSP70"""	16931	protein-coding gene	gene with protein product	"""glucose-regulated protein 170"""	601746				9020069, 10037731	Standard	XM_005271390		Approved	ORP150, HSP12A, Grp170	uc001pux.3	Q9Y4L1	OTTHUMG00000166354	ENST00000404233.3:c.460C>A	11.37:g.118925732G>T	ENSP00000384144:p.Leu154Ile		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	35	0.09	3	NM_001130991	124	0.00	0	A8C1Z0|B7Z909|Q2I204|Q53H25	Missense_Mutation	SNP	ENST00000404233.3	37	CCDS8408.1	.	.	.	.	.	.	.	.	.	.	G	26.2	4.710748	0.89112	.	.	ENSG00000149428	ENST00000404233;ENST00000353883;ENST00000529972;ENST00000536103;ENST00000535579;ENST00000525859;ENST00000544701;ENST00000543287;ENST00000530473	T;T;T;T;T	0.10960	4.59;4.59;4.59;2.82;4.59	4.96	4.96	0.65561	.	0.000000	0.85682	D	0.000000	T	0.40645	0.1125	M	0.89287	3.02	0.80722	D	1	D;D;D;D	0.89917	1.0;0.998;1.0;1.0	D;D;D;D	0.91635	0.999;0.984;0.995;0.995	T	0.47459	-0.9116	10	0.87932	D	0	-17.3501	16.5649	0.84576	0.0:0.0:1.0:0.0	.	145;198;154;154	B3KXH0;B7Z2N4;Q9Y4L1;A8C1Z0	.;.;HYOU1_HUMAN;.	I	154;145;154;154;3;154;197;67;154	ENSP00000384144:L154I;ENSP00000437313:L154I;ENSP00000433397:L154I;ENSP00000442727:L67I;ENSP00000431874:L154I	ENSP00000278752:L145I	L	-	1	0	HYOU1	118430942	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	5.649000	0.67936	2.564000	0.86499	0.561000	0.74099	CTC			0.532	HYOU1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000389353.1		NM_006389	
ERC1	23085	broad.mit.edu	37	12	1292505	1292505	+	Missense_Mutation	SNP	A	A	G			TCGA-WZ-A8D5-01A-11D-A435-10	TCGA-WZ-A8D5-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f9769d8-ba26-4ac7-91c7-7ae0494130e7	928cb9ff-09c7-4a5f-bd42-198e31335976	g.chr12:1292505A>G	ENST00000397203.2	+	11	2481	c.2075A>G	c.(2074-2076)aAg>aGg	p.K692R	ERC1_ENST00000589028.1_Missense_Mutation_p.K692R|ERC1_ENST00000355446.5_Missense_Mutation_p.K692R|ERC1_ENST00000543086.3_Missense_Mutation_p.K664R|ERC1_ENST00000546231.2_Missense_Mutation_p.K692R|ERC1_ENST00000360905.4_Missense_Mutation_p.K692R|ERC1_ENST00000536573.2_3'UTR			Q8IUD2	RB6I2_HUMAN	ELKS/RAB6-interacting/CAST family member 1	692					I-kappaB phosphorylation (GO:0007252)|multicellular organismal development (GO:0007275)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein transport (GO:0015031)|regulation of transcription, DNA-templated (GO:0006355)|retrograde transport, endosome to Golgi (GO:0042147)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|IkappaB kinase complex (GO:0008385)|presynaptic membrane (GO:0042734)	leucine zipper domain binding (GO:0043522)			NS(1)|breast(2)|cervix(2)|endometrium(2)|large_intestine(8)|lung(15)|ovary(3)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	38	all_epithelial(11;0.0698)|Ovarian(42;0.107)		OV - Ovarian serous cystadenocarcinoma(31;0.00239)|BRCA - Breast invasive adenocarcinoma(9;0.0567)			GGACTGAAAAAGGACTCACGG	0.363																																					p.K692R													.	ERC1	95		0			c.A2075G												89.0	88.0	89.0					12																	1292505		2203	4300	6503	SO:0001583	missense	23085	exon11			TGAAAAAGGACTC	AB015617	CCDS8508.1, CCDS53732.1	12p13.3	2008-02-05	2006-08-14	2006-08-14	ENSG00000082805	ENSG00000082805			17072	protein-coding gene	gene with protein product		607127	"""RAB6 interacting protein 2"""	RAB6IP2		10697956, 11929610	Standard	NM_178040		Approved	ELKS, KIAA1081, CAST2, MGC12974	uc001qjb.2	Q8IUD2	OTTHUMG00000130138	ENST00000397203.2:c.2075A>G	12.37:g.1292505A>G	ENSP00000380386:p.Lys692Arg		Somatic	428	0.0046728972	2		WXS	Illumina HiSeq	Phase_I	705	0.01	7	NM_178040	54	0.00	0	A2RU77|A7E295|D3DUP7|D3DUP8|Q6NVK2|Q8IUD3|Q8IUD4|Q8IUD5|Q8NAS1|Q9NXN5|Q9UIK7|Q9UPS1	Missense_Mutation	SNP	ENST00000397203.2	37	CCDS8508.1	.	.	.	.	.	.	.	.	.	.	A	10.81	1.455744	0.26161	.	.	ENSG00000082805	ENST00000347735;ENST00000397203;ENST00000454194;ENST00000537890;ENST00000299183;ENST00000543086;ENST00000542302;ENST00000545948;ENST00000546231;ENST00000355446;ENST00000360905;ENST00000440394;ENST00000538971;ENST00000536573	T;T;T;T;T;T;T;T	0.46063	0.88;0.88;0.88;0.88;0.88;0.88;0.88;0.88	5.37	5.37	0.77165	.	0.093551	0.64402	D	0.000001	T	0.35595	0.0937	L	0.42686	1.345	0.80722	D	1	B;B;B;B;B	0.16166	0.002;0.016;0.003;0.003;0.001	B;B;B;B;B	0.19666	0.011;0.026;0.008;0.008;0.008	T	0.16041	-1.0416	10	0.11485	T	0.65	-32.4174	15.6887	0.77434	1.0:0.0:0.0:0.0	.	440;332;664;664;692	F5H327;F5GZU8;Q8IUD2-2;Q8IUD2-3;Q8IUD2	.;.;.;.;RB6I2_HUMAN	R	664;692;664;664;392;664;664;392;692;692;692;664;440;332	ENSP00000340054:K664R;ENSP00000380386:K692R;ENSP00000438546:K664R;ENSP00000442976:K392R;ENSP00000442739:K692R;ENSP00000347621:K692R;ENSP00000354158:K692R;ENSP00000410064:K664R	ENSP00000299183:K392R	K	+	2	0	ERC1	1162766	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	6.281000	0.72632	2.170000	0.68504	0.460000	0.39030	AAG			0.363	ERC1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000398380.2		NM_015064	
KRAS	3845	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca;mdanderson.org	37	12	25380276	25380276	+	Missense_Mutation	SNP	T	T	C	rs121913240		TCGA-WZ-A8D5-01A-11D-A435-10	TCGA-WZ-A8D5-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f9769d8-ba26-4ac7-91c7-7ae0494130e7	928cb9ff-09c7-4a5f-bd42-198e31335976	g.chr12:25380276T>C	ENST00000256078.4	-	3	245	c.182A>G	c.(181-183)cAa>cGa	p.Q61R	KRAS_ENST00000311936.3_Missense_Mutation_p.Q61R|KRAS_ENST00000557334.1_Intron|AC087239.1_ENST00000594112.1_5'Flank	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	61			Q -> H (in lung carcinoma; dbSNP:rs17851045). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:16533793, ECO:0000269|Ref.7}.|Q -> R (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to glucocorticoid (GO:0051384)|response to mineralocorticoid (GO:0051385)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	focal adhesion (GO:0005925)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GMP binding (GO:0019002)|GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.Q61L(73)|p.Q61R(56)|p.Q61P(12)	UBE2L3/KRAS(2)	NS(6)|adrenal_gland(1)|autonomic_ganglia(3)|biliary_tract(532)|bone(2)|breast(32)|central_nervous_system(14)|cervix(50)|endometrium(411)|eye(4)|gastrointestinal_tract_(site_indeterminate)(7)|genital_tract(1)|haematopoietic_and_lymphoid_tissue(385)|kidney(8)|large_intestine(15267)|liver(29)|lung(3407)|oesophagus(16)|ovary(612)|pancreas(3739)|penis(1)|peritoneum(6)|prostate(96)|salivary_gland(6)|skin(45)|small_intestine(68)|soft_tissue(88)|stomach(207)|testis(17)|thymus(5)|thyroid(159)|upper_aerodigestive_tract(68)|urinary_tract(57)	25349	all_cancers(2;1e-35)|all_epithelial(2;1.97e-38)|all_lung(3;2.1e-23)|Lung NSC(3;1.16e-22)|Acute lymphoblastic leukemia(6;0.00231)|all_hematologic(7;0.00259)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12)		OV - Ovarian serous cystadenocarcinoma(3;1.23e-21)|Epithelial(3;1.31e-20)|all cancers(3;5.45e-18)|STAD - Stomach adenocarcinoma(2;2.68e-05)			GTACTCCTCTTGACCTGCTGT	0.418	Q61L(NCIH650_LUNG)|Q61L(SW948_LARGE_INTESTINE)|Q61R(PANC0213_PANCREAS)	119	Mis		"""pancreatic, colorectal, lung, thyroid, AML, others"""				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)																											p.Q61R	Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)			Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		"""L, E, M, O"""	KRAS_ENST00000256078,colon,carcinoma,+1,429	KRAS_ENST00000256078	1	429	141	Substitution - Missense(141)	large_intestine(63)|lung(27)|thyroid(14)|haematopoietic_and_lymphoid_tissue(9)|pancreas(6)|skin(5)|stomach(3)|cervix(3)|upper_aerodigestive_tract(2)|soft_tissue(1)|central_nervous_system(1)|biliary_tract(1)|endometrium(1)|urinary_tract(1)|gastrointestinal_tract_(site_indeterminate)(1)|breast(1)|prostate(1)|kidney(1)	c.A182G												109.0	97.0	101.0					12																	25380276		2203	4300	6503	SO:0001583	missense	3845	exon3	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	TCCTCTTGACCTG	BC010502	CCDS8702.1, CCDS8703.1	12p12.1	2014-09-17	2013-07-08	2005-01-24	ENSG00000133703	ENSG00000133703			6407	protein-coding gene	gene with protein product		190070	"""v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog"", ""v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog"""	KRAS2			Standard	NM_004985		Approved	KRAS1	uc001rgp.1	P01116		ENST00000256078.4:c.182A>G	12.37:g.25380276T>C	ENSP00000256078:p.Gln61Arg		Somatic	101	0	0		WXS	Illumina HiSeq	.	152	0.07	11	NM_004985	86	0.02	2	A8K8Z5|B0LPF9|P01118|Q96D10	Missense_Mutation	SNP	ENST00000256078.4	37	CCDS8703.1	.	.	.	.	.	.	.	.	.	.	T	20.6	4.022613	0.75275	.	.	ENSG00000133703	ENST00000311936;ENST00000256078	D;D	0.83673	-1.75;-1.75	5.77	5.77	0.91146	Small GTP-binding protein domain (1);	0.049057	0.85682	D	0.000000	D	0.88358	0.6415	M	0.92367	3.3	0.80722	D	1	B;B	0.26744	0.158;0.026	B;B	0.32805	0.135;0.153	D	0.87885	0.2680	10	0.66056	D	0.02	.	15.5753	0.76373	0.0:0.0:0.0:1.0	.	61;61	P01116-2;P01116	.;RASK_HUMAN	R	61	ENSP00000308495:Q61R;ENSP00000256078:Q61R	ENSP00000256078:Q61R	Q	-	2	0	KRAS	25271543	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.983000	0.88140	2.326000	0.78906	0.533000	0.62120	CAA			0.418	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		OTTHUMT00000412232.1		NM_033360	
VDR	7421	mdanderson.org	37	12	48240170	48240170	+	Missense_Mutation	SNP	G	G	T			TCGA-WZ-A8D5-01A-11D-A435-10	TCGA-WZ-A8D5-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f9769d8-ba26-4ac7-91c7-7ae0494130e7	928cb9ff-09c7-4a5f-bd42-198e31335976	g.chr12:48240170G>T	ENST00000395324.2	-	9	1240	c.972C>A	c.(970-972)aaC>aaA	p.N324K	VDR_ENST00000549336.1_Missense_Mutation_p.N324K|VDR_ENST00000535672.1_Missense_Mutation_p.N292K|VDR_ENST00000550325.1_Missense_Mutation_p.N374K|VDR_ENST00000229022.3_Missense_Mutation_p.N324K			P11473	VDR_HUMAN	vitamin D (1,25- dihydroxyvitamin D3) receptor	324	Ligand-binding.				bile acid signaling pathway (GO:0038183)|calcium ion transport (GO:0006816)|cell morphogenesis (GO:0000902)|cellular calcium ion homeostasis (GO:0006874)|decidualization (GO:0046697)|gene expression (GO:0010467)|intestinal absorption (GO:0050892)|lactation (GO:0007595)|mammary gland branching involved in pregnancy (GO:0060745)|negative regulation of cell proliferation (GO:0008285)|negative regulation of keratinocyte proliferation (GO:0010839)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|organ morphogenesis (GO:0009887)|positive regulation of apoptotic process involved in mammary gland involution (GO:0060058)|positive regulation of gene expression (GO:0010628)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of vitamin D 24-hydroxylase activity (GO:0010980)|regulation of calcidiol 1-monooxygenase activity (GO:0060558)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)|transcription initiation from RNA polymerase II promoter (GO:0006367)|vitamin D receptor signaling pathway (GO:0070561)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	calcitriol binding (GO:1902098)|calcitriol receptor activity (GO:0008434)|DNA binding (GO:0003677)|lithocholic acid binding (GO:1902121)|lithocholic acid receptor activity (GO:0038186)|retinoid X receptor binding (GO:0046965)|sequence-specific DNA binding (GO:0043565)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(10)|ovary(3)|skin(2)	22		Acute lymphoblastic leukemia(13;0.109)|all_hematologic(14;0.214)		GBM - Glioblastoma multiforme(48;0.17)	Alfacalcidol(DB01436)|Calcidiol(DB00146)|Calcipotriol(DB02300)|Calcitriol(DB00136)|Cholecalciferol(DB00169)|Dihydrotachysterol(DB01070)|Ergocalciferol(DB00153)|Paricalcitol(DB00910)	CCTCATGCAAGTTCAGCTTCT	0.612																																					p.N374K													.	.			0			c.C1122A												65.0	40.0	49.0					12																	48240170		2202	4299	6501	SO:0001583	missense	7421	exon9			ATGCAAGTTCAGC	J03258	CCDS8757.1, CCDS55820.1	12q12-q14	2014-06-13				ENSG00000111424		"""Nuclear hormone receptors"""	12679	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 163"""	601769				1662663	Standard	NM_001017536		Approved	NR1I1, PPP1R163	uc001rql.3	P11473		ENST00000395324.2:c.972C>A	12.37:g.48240170G>T	ENSP00000378734:p.Asn324Lys		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	36	0.08	3	NM_001017536	2	0.00	0	B2R5Q1|G3V1V9|Q5PSV3	Missense_Mutation	SNP	ENST00000395324.2	37	CCDS8757.1	.	.	.	.	.	.	.	.	.	.	G	15.49	2.848285	0.51164	.	.	ENSG00000111424	ENST00000395324;ENST00000229022;ENST00000549336;ENST00000550325;ENST00000535672	D;D;D;D;D	0.96459	-4.02;-4.02;-4.02;-4.02;-4.02	5.23	2.41	0.29592	Nuclear hormone receptor, ligand-binding (2);Nuclear hormone receptor, ligand-binding, core (2);	0.043026	0.85682	D	0.000000	D	0.92251	0.7542	L	0.41961	1.31	0.52501	D	0.999955	B;B;P	0.38420	0.018;0.004;0.63	B;B;B	0.38985	0.081;0.081;0.287	D	0.86558	0.1839	10	0.12103	T	0.63	.	9.6112	0.39663	0.2313:0.0:0.7687:0.0	.	292;324;374	B4DRV7;P11473;G3V1V9	.;VDR_HUMAN;.	K	324;324;324;374;292	ENSP00000378734:N324K;ENSP00000229022:N324K;ENSP00000449573:N324K;ENSP00000447173:N374K;ENSP00000442145:N292K	ENSP00000229022:N324K	N	-	3	2	VDR	46526437	1.000000	0.71417	0.998000	0.56505	0.998000	0.95712	1.887000	0.39698	0.315000	0.23110	0.655000	0.94253	AAC			0.612	VDR-001	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000406433.1			
KRT84	3890	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca;mdanderson.org	37	12	52779018	52779018	+	Missense_Mutation	SNP	C	C	T			TCGA-WZ-A8D5-01A-11D-A435-10	TCGA-WZ-A8D5-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f9769d8-ba26-4ac7-91c7-7ae0494130e7	928cb9ff-09c7-4a5f-bd42-198e31335976	g.chr12:52779018C>T	ENST00000257951.3	-	1	418	c.352G>A	c.(352-354)Ggt>Agt	p.G118S	RP3-416H24.4_ENST00000547174.1_RNA	NM_033045.3	NP_149034.2	Q9NSB2	KRT84_HUMAN	keratin 84	118	Head.				hair follicle development (GO:0001942)|nail development (GO:0035878)|regulation of keratinocyte differentiation (GO:0045616)	extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural constituent of cytoskeleton (GO:0005200)|structural constituent of epidermis (GO:0030280)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|liver(1)|lung(10)|skin(3)	27	all_hematologic(5;0.12)			BRCA - Breast invasive adenocarcinoma(357;0.189)		CCAGGGCCACCAAAGCCATAG	0.572																																					p.G118S													.	.			0			c.G352A												175.0	166.0	169.0					12																	52779018		2203	4300	6503	SO:0001583	missense	3890	exon1			GGCCACCAAAGCC	Y19209	CCDS8825.1	12q13	2013-06-25	2006-07-17	2006-07-17	ENSG00000161849	ENSG00000161849		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6461	protein-coding gene	gene with protein product	"""hard keratin type II 4"""	602766	"""keratin, hair, basic, 4"""	KRTHB4		2431943, 16831889	Standard	NM_033045		Approved	Hb-4	uc001sah.1	Q9NSB2	OTTHUMG00000169634	ENST00000257951.3:c.352G>A	12.37:g.52779018C>T	ENSP00000257951:p.Gly118Ser		Somatic	117	0	0		WXS	Illumina HiSeq	.	94	0.07	7	NM_033045	0		0	B2RA43|Q6ISB0|Q701L6	Missense_Mutation	SNP	ENST00000257951.3	37	CCDS8825.1	.	.	.	.	.	.	.	.	.	.	C	9.982	1.228490	0.22542	.	.	ENSG00000161849	ENST00000257951	D	0.97906	-4.6	5.15	0.113	0.14631	.	0.547242	0.16856	N	0.196738	D	0.95414	0.8511	M	0.84948	2.725	0.37833	D	0.928801	P	0.42735	0.788	B	0.33392	0.163	D	0.91024	0.4859	10	0.44086	T	0.13	.	5.5379	0.17021	0.2416:0.5618:0.0:0.1966	.	118	Q9NSB2	KRT84_HUMAN	S	118	ENSP00000257951:G118S	ENSP00000257951:G118S	G	-	1	0	KRT84	51065285	0.005000	0.15991	0.026000	0.17262	0.480000	0.33159	0.282000	0.18829	-0.066000	0.12998	0.609000	0.83330	GGT			0.572	KRT84-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000405187.1		NM_033045	
CEP83	51134	hgsc.bcm.edu	37	12	94796963	94796963	+	Missense_Mutation	SNP	A	A	G			TCGA-WZ-A8D5-01A-11D-A435-10	TCGA-WZ-A8D5-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f9769d8-ba26-4ac7-91c7-7ae0494130e7	928cb9ff-09c7-4a5f-bd42-198e31335976	g.chr12:94796963A>G	ENST00000397809.5	-	5	949	c.400T>C	c.(400-402)Ttt>Ctt	p.F134L	CCDC41_ENST00000547575.1_Missense_Mutation_p.F134L|CCDC41_ENST00000397807.2_Missense_Mutation_p.F101L|CCDC41_ENST00000549352.1_5'UTR|CCDC41_ENST00000339839.5_Missense_Mutation_p.F134L	NM_016122.2	NP_057206.2	Q9Y592	CEP83_HUMAN		126					cilium assembly (GO:0042384)|protein localization to centrosome (GO:0071539)|vesicle docking (GO:0048278)	centriole (GO:0005814)|ciliary transition fiber (GO:0097539)|Golgi apparatus (GO:0005794)				breast(1)|central_nervous_system(3)|kidney(3)|large_intestine(8)|lung(8)|prostate(2)|skin(2)	27						AGATTCCTAAAACGTTCTCTC	0.333																																					p.F134L													.	.			0			c.T400C												164.0	156.0	158.0					12																	94796963		1819	4080	5899	SO:0001583	missense	51134	exon5			TCCTAAAACGTTC																												ENST00000397809.5:c.400T>C	12.37:g.94796963A>G	ENSP00000380911:p.Phe134Leu		Somatic	47	0	0		WXS	Illumina HiSeq	.	65	0.06	4	NM_016122	19	0.00	0	A4FVB1|Q08AP1	Missense_Mutation	SNP	ENST00000397809.5	37	CCDS41820.1	.	.	.	.	.	.	.	.	.	.	A	11.66	1.704663	0.30232	.	.	ENSG00000173588	ENST00000339839;ENST00000397809;ENST00000397807;ENST00000547575	T;T;T;D	0.87809	0.91;0.91;0.91;-2.3	5.36	5.36	0.76844	.	.	.	.	.	D	0.83321	0.5229	L	0.60455	1.87	0.32215	N	0.575963	B;B;B	0.12013	0.002;0.005;0.001	B;B;B	0.11329	0.004;0.006;0.003	T	0.78069	-0.2348	9	0.09843	T	0.71	-3.3607	13.5815	0.61905	1.0:0.0:0.0:0.0	.	134;101;126	F8VYN8;Q9Y592-2;Q9Y592	.;.;CCD41_HUMAN	L	134;134;101;134	ENSP00000344655:F134L;ENSP00000380911:F134L;ENSP00000380909:F101L;ENSP00000448913:F134L	ENSP00000344655:F134L	F	-	1	0	CCDC41	93321094	1.000000	0.71417	0.804000	0.32291	0.847000	0.48162	5.443000	0.66581	2.036000	0.60181	0.477000	0.44152	TTT			0.333	CCDC41-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000408147.3			
TPTE2P1	646405	broad.mit.edu	37	13	25527621	25527623	+	RNA	DEL	AAC	AAC	-	rs199758569		TCGA-WZ-A8D5-01A-11D-A435-10	TCGA-WZ-A8D5-10A-01D-A438-10	AAC	AAC					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f9769d8-ba26-4ac7-91c7-7ae0494130e7	928cb9ff-09c7-4a5f-bd42-198e31335976	g.chr13:25527621_25527623delAAC	ENST00000429698.1	-	0	282							Q5T6R2	TPT2L_HUMAN	transmembrane phosphoinositide 3-phosphatase and tensin homolog 2 pseudogene 1																		TGCAATCTATAACAATACACTCA	0.276																																					.													.	.			0			.																																											0	.			ATCTATAACAATA			13q12.12-q12.13	2012-10-03			ENSG00000253771	ENSG00000253771			35196	pseudogene	pseudogene							Standard	NR_026730		Approved		uc010tdh.2	Q5T6R2	OTTHUMG00000016596		13.37:g.25527621_25527623delAAC			Somatic	8	0	0		WXS	Illumina HiSeq	Phase_I	7	0.43	3	.	0		0	B3KST4|B4DMH9	RNA	DEL	ENST00000429698.1	37																																																																																						0.276	TPTE2P1-003	KNOWN	basic	processed_transcript	pseudogene		OTTHUMT00000044206.1			
STOML3	161003	mdanderson.org	37	13	39542626	39542626	+	Silent	SNP	G	G	T	rs202188494		TCGA-WZ-A8D5-01A-11D-A435-10	TCGA-WZ-A8D5-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f9769d8-ba26-4ac7-91c7-7ae0494130e7	928cb9ff-09c7-4a5f-bd42-198e31335976	g.chr13:39542626G>T	ENST00000379631.4	-	6	906	c.562C>A	c.(562-564)Cga>Aga	p.R188R	STOML3_ENST00000423210.1_Silent_p.R179R	NM_145286.2	NP_660329.1	Q8TAV4	STML3_HUMAN	stomatin (EPB72)-like 3	188					signal transduction (GO:0007165)	cilium (GO:0005929)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)				breast(1)|large_intestine(2)|lung(5)|ovary(1)|prostate(1)|skin(1)	11		Lung NSC(96;1.42e-05)|Prostate(109;0.00851)|Breast(139;0.0199)|Lung SC(185;0.0743)		all cancers(112;2.93e-08)|Epithelial(112;3.64e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.00107)|BRCA - Breast invasive adenocarcinoma(63;0.00349)|GBM - Glioblastoma multiforme(144;0.0137)		ATTTCCACTCGGGCCACCCGG	0.502																																					p.R188R													STOML3,NS,carcinoma,+1,2	STOML3	1	2	0			c.C562A												96.0	97.0	96.0					13																	39542626		2203	4300	6503	SO:0001819	synonymous_variant	161003	exon6			CCACTCGGGCCAC	BC025760	CCDS9367.1, CCDS45040.1	13q13.2	2004-03-05			ENSG00000133115	ENSG00000133115			19420	protein-coding gene	gene with protein product		608327				12122055	Standard	NM_145286		Approved	SRO, Epb7.2l	uc001uwx.3	Q8TAV4	OTTHUMG00000016763	ENST00000379631.4:c.562C>A	13.37:g.39542626G>T			Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	47	0.06	3	NM_145286	0		0	B4E285|Q5JS35	Silent	SNP	ENST00000379631.4	37	CCDS9367.1																																																																																					0.502	STOML3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		OTTHUMT00000044604.2			
LRCH1	23143	mdanderson.org	37	13	47275277	47275277	+	Missense_Mutation	SNP	G	G	T			TCGA-WZ-A8D5-01A-11D-A435-10	TCGA-WZ-A8D5-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f9769d8-ba26-4ac7-91c7-7ae0494130e7	928cb9ff-09c7-4a5f-bd42-198e31335976	g.chr13:47275277G>T	ENST00000389798.3	+	11	1532	c.1335G>T	c.(1333-1335)caG>caT	p.Q445H	LRCH1_ENST00000389797.3_Missense_Mutation_p.Q445H|LRCH1_ENST00000311191.6_Missense_Mutation_p.Q445H	NM_015116.2	NP_055931	Q9Y2L9	LRCH1_HUMAN	leucine-rich repeats and calponin homology (CH) domain containing 1	445										breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(3)|lung(11)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	26		all_lung(13;5.61e-07)|Lung NSC(96;0.000117)|Breast(56;0.000141)|Prostate(109;0.0029)|Lung SC(185;0.0367)|Myeloproliferative disorder(33;0.0505)|Hepatocellular(98;0.0556)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;0.000123)		CCAAAGATCAGGACATGGATA	0.378																																					p.Q445H													LRCH1_ENST00000311191,NS,lymphoid_neoplasm,+1,2	LRCH1_ENST00000311191	1	2	0			c.G1335T												212.0	177.0	189.0					13																	47275277		2203	4300	6503	SO:0001583	missense	23143	exon11			AGATCAGGACATG	AB023233	CCDS31972.1, CCDS53865.1, CCDS53866.1	13q14.11	2008-02-05	2004-05-27	2004-05-28	ENSG00000136141	ENSG00000136141			20309	protein-coding gene	gene with protein product		610368	"""calponin homology (CH) domain containing 1"""	CHDC1		10231032	Standard	NM_015116		Approved	KIAA1016	uc001vbk.3	Q9Y2L9	OTTHUMG00000016877	ENST00000389798.3:c.1335G>T	13.37:g.47275277G>T	ENSP00000374448:p.Gln445His		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	41	0.07	3	NM_001164211	12	0.00	0	B7ZLL5|F8W6F0|Q17R43|Q2KHR1|Q5TBU9|Q7Z5F6|Q7Z5F7	Missense_Mutation	SNP	ENST00000389798.3	37	CCDS31972.1	.	.	.	.	.	.	.	.	.	.	G	17.65	3.442034	0.63067	.	.	ENSG00000136141	ENST00000311191;ENST00000389798;ENST00000389797	T;T;T	0.55052	0.54;0.59;0.56	6.03	3.98	0.46160	.	0.330345	0.32430	N	0.006105	T	0.62024	0.2394	M	0.67953	2.075	0.37125	D	0.900974	P;P;D;P	0.55800	0.954;0.828;0.973;0.943	P;P;P;P	0.56823	0.646;0.652;0.807;0.547	T	0.68777	-0.5319	10	0.51188	T	0.08	-9.2254	9.5703	0.39425	0.1844:0.0:0.8156:0.0	.	445;445;445;445	Q17R43;Q9Y2L9-2;F8W6F0;Q9Y2L9	.;.;.;LRCH1_HUMAN	H	445	ENSP00000308493:Q445H;ENSP00000374448:Q445H;ENSP00000374447:Q445H	ENSP00000308493:Q445H	Q	+	3	2	LRCH1	46173278	1.000000	0.71417	0.998000	0.56505	0.793000	0.44817	1.039000	0.30266	1.528000	0.49103	0.655000	0.94253	CAG			0.378	LRCH1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		OTTHUMT00000044824.2		NM_015116	
SUGT1	10910	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	13	53239790	53239791	+	Frame_Shift_Del	DEL	AG	AG	-			TCGA-WZ-A8D5-01A-11D-A435-10	TCGA-WZ-A8D5-10A-01D-A438-10	AG	AG					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f9769d8-ba26-4ac7-91c7-7ae0494130e7	928cb9ff-09c7-4a5f-bd42-198e31335976	g.chr13:53239790_53239791delAG	ENST00000343788.6	+	10	619_620	c.537_538delAG	c.(535-540)acagaafs	p.E180fs	SUGT1_ENST00000535397.1_Frame_Shift_Del_p.E92fs|SUGT1_ENST00000310528.8_Frame_Shift_Del_p.E148fs	NM_001130912.1	NP_001124384.1	Q9Y2Z0	SUGT1_HUMAN	SGT1, suppressor of G2 allele of SKP1 (S. cerevisiae)	180	CS. {ECO:0000255|PROSITE- ProRule:PRU00547}.				innate immune response (GO:0045087)|mitotic nuclear division (GO:0007067)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)				kidney(3)|large_intestine(3)|lung(2)	8		Lung NSC(96;0.00212)|Breast(56;0.00235)|Hepatocellular(98;0.065)|Prostate(109;0.0771)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;3.25e-08)		GGTATCAAACAGAATCTCAAGT	0.282																																					p.179_179del													.	SUGT1	37		0			c.536_537del																																									SO:0001589	frameshift_variant	10910	exon10			TCAAACAGAATCT	AF068289	CCDS9436.1, CCDS45050.1	13q14.3	2014-03-20			ENSG00000165416	ENSG00000165416			16987	protein-coding gene	gene with protein product		604098				10445024	Standard	NM_006704		Approved	SGT1	uc001vhc.2	Q9Y2Z0	OTTHUMG00000016977	ENST00000343788.6:c.537_538delAG	13.37:g.53239790_53239791delAG	ENSP00000367208:p.Glu180fs		Somatic	197	0	0		WXS	Illumina HiSeq	.	146	0.15	22	NM_001130912	61	0.00	0	A2A303|Q5JAK5|Q5TAM6|Q6VXY6	Frame_Shift_Del	DEL	ENST00000343788.6	37	CCDS45050.1																																																																																					0.282	SUGT1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		OTTHUMT00000045104.2			
F7	2155	mdanderson.org	37	13	113770083	113770083	+	Silent	SNP	G	G	T			TCGA-WZ-A8D5-01A-11D-A435-10	TCGA-WZ-A8D5-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f9769d8-ba26-4ac7-91c7-7ae0494130e7	928cb9ff-09c7-4a5f-bd42-198e31335976	g.chr13:113770083G>T	ENST00000375581.3	+	6	575	c.540G>T	c.(538-540)ctG>ctT	p.L180L	F7_ENST00000541084.1_Silent_p.L111L|F7_ENST00000346342.3_Silent_p.L158L	NM_000131.4	NP_000122.1	P08709	FA7_HUMAN	coagulation factor VII (serum prothrombin conversion accelerator)	180	EGF-like 2. {ECO:0000255|PROSITE- ProRule:PRU00076}.				blood coagulation (GO:0007596)|blood coagulation, extrinsic pathway (GO:0007598)|cellular protein metabolic process (GO:0044267)|circadian rhythm (GO:0007623)|organ regeneration (GO:0031100)|peptidyl-glutamic acid carboxylation (GO:0017187)|positive regulation of blood coagulation (GO:0030194)|positive regulation of cell migration (GO:0030335)|positive regulation of leukocyte chemotaxis (GO:0002690)|positive regulation of platelet-derived growth factor receptor signaling pathway (GO:0010641)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of protein kinase B signaling (GO:0051897)|post-translational protein modification (GO:0043687)|proteolysis (GO:0006508)|response to estrogen (GO:0043627)|response to growth hormone (GO:0060416)|response to vitamin K (GO:0032571)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	calcium ion binding (GO:0005509)|glycoprotein binding (GO:0001948)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			large_intestine(4)|lung(9)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	16	all_lung(23;0.000374)|Lung NSC(43;0.0107)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)	all_cancers(25;0.118)|all_lung(25;0.0364)|all_epithelial(44;0.0393)|Lung NSC(25;0.128)|Breast(118;0.188)	all cancers(43;0.0737)|Epithelial(84;0.213)|BRCA - Breast invasive adenocarcinoma(86;0.218)		Coagulation Factor IX(DB00100)|Coagulation factor VIIa(DB00036)|Menadione(DB00170)	GGTACTCTCTGCTGGCAGACG	0.597																																					p.L180L													.	.			0			c.G540T												64.0	55.0	58.0					13																	113770083		2203	4300	6503	SO:0001819	synonymous_variant	2155	exon6			CTCTCTGCTGGCA		CCDS9528.1, CCDS9529.1, CCDS73602.1	13q34	2014-02-03			ENSG00000057593	ENSG00000057593	3.4.21.21		3544	protein-coding gene	gene with protein product	"""eptacog alfa"", ""FVII coagulation protein"", ""factor VII"""	613878				3264725, 2511201	Standard	NM_000131		Approved		uc001vsv.4	P08709	OTTHUMG00000017373	ENST00000375581.3:c.540G>T	13.37:g.113770083G>T			Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	44	0.07	3	NM_000131	0		0	B0YJC8|Q14339|Q5JVF1|Q5JVF2|Q9UD52|Q9UD53|Q9UD54	Silent	SNP	ENST00000375581.3	37	CCDS9528.1																																																																																					0.597	F7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		OTTHUMT00000045838.4		NM_000131	
GPHB5	122876	broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	14	63779821	63779821	+	RNA	SNP	G	G	A			TCGA-WZ-A8D5-01A-11D-A435-10	TCGA-WZ-A8D5-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f9769d8-ba26-4ac7-91c7-7ae0494130e7	928cb9ff-09c7-4a5f-bd42-198e31335976	g.chr14:63779821G>A	ENST00000539258.1	-	0	269							Q86YW7	GPHB5_HUMAN	glycoprotein hormone beta 5						regulation of thyroid hormone mediated signaling pathway (GO:0002155)	extracellular region (GO:0005576)				breast(1)|endometrium(1)|lung(4)|urinary_tract(1)	7				OV - Ovarian serous cystadenocarcinoma(108;0.00372)|all cancers(60;0.0226)|BRCA - Breast invasive adenocarcinoma(234;0.0978)		GGGGGTTCCAGAATGGGTTTC	0.428																																					.													.	GPHB5	57		0			.												64.0	68.0	67.0					14																	63779821		1866	4119	5985			122876	.			GTTCCAGAATGGG	AF467770	CCDS73643.1	14q23.3	2006-09-25				ENSG00000179600			18055	protein-coding gene	gene with protein product		609652					Standard	NM_145171		Approved	ZLUT1, GPB5	uc021rud.1	Q86YW7			14.37:g.63779821G>A			Somatic	201	0.0049751244	1		WXS	Illumina HiSeq	Phase_I	209	0.17	36	.	0		0	Q6NTD0|Q8NFW2	RNA	SNP	ENST00000539258.1	37																																																																																						0.428	GPHB5-001	KNOWN	basic	processed_transcript	processed_transcript		OTTHUMT00000400582.1		NM_145171	
GOLGA6L1	283767	broad.mit.edu	37	15	22742718	22742718	+	Missense_Mutation	SNP	T	T	A	rs7171381		TCGA-WZ-A8D5-01A-11D-A435-10	TCGA-WZ-A8D5-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f9769d8-ba26-4ac7-91c7-7ae0494130e7	928cb9ff-09c7-4a5f-bd42-198e31335976	g.chr15:22742718T>A	ENST00000560659.2	+	8	953	c.953T>A	c.(952-954)cTg>cAg	p.L318Q	GOLGA6L1_ENST00000316397.3_Missense_Mutation_p.L368Q			Q8N7Z2	GG6L1_HUMAN	golgin A6 family-like 1	362								p.L368Q(3)		NS(1)|breast(2)|endometrium(5)|large_intestine(1)|lung(1)|skin(1)	11						ATGCGGAGGCTGGAGGAGATG	0.562																																					p.L368Q													GOLGA6L1,NS,carcinoma,0,3	GOLGA6L1	20	3	3	Substitution - Missense(3)	endometrium(2)|NS(1)	c.T1103A												2.0	1.0	2.0					15																	22742718		857	1156	2013	SO:0001583	missense	283767	exon8			GGAGGCTGGAGGA	AK097517	CCDS73699.1	15q11.2	2012-10-05	2010-02-12		ENSG00000197414	ENSG00000277865			37444	protein-coding gene	gene with protein product			"""golgi autoantigen, golgin subfamily a, 6-like 1"""				Standard	NM_001001413		Approved		uc010tzx.1	Q8N7Z2	OTTHUMG00000171883	ENST00000560659.2:c.953T>A	15.37:g.22742718T>A	ENSP00000452626:p.Leu318Gln		Somatic	99	0.0101010101	1		WXS	Illumina HiSeq	Phase_I	102	0.06	6	NM_001001413	1	0.00	0		Missense_Mutation	SNP	ENST00000560659.2	37		.	.	.	.	.	.	.	.	.	.	.	0.066	-1.212693	0.01555	.	.	ENSG00000197414	ENST00000316397;ENST00000355145	T	0.08546	3.08	.	.	.	.	.	.	.	.	T	0.02727	0.0082	N	0.13098	0.295	0.09310	N	1	.	.	.	.	.	.	T	0.44050	-0.9353	5	0.02654	T	1	.	.	.	.	rs7171381	.	.	.	Q	368	ENSP00000320207:L368Q	ENSP00000320207:L368Q	L	+	2	0	GOLGA6L1	20294082	0.004000	0.15560	0.015000	0.15790	0.015000	0.08874	-1.961000	0.01516	-1.878000	0.01128	-2.010000	0.00438	CTG			0.562	GOLGA6L1-002	KNOWN	basic|appris_candidate	protein_coding	protein_coding		OTTHUMT00000415616.2		NM_001001413	
CREBBP	1387	bcgsc.ca	37	16	3777942	3777942	+	Missense_Mutation	SNP	G	G	T			TCGA-WZ-A8D5-01A-11D-A435-10	TCGA-WZ-A8D5-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f9769d8-ba26-4ac7-91c7-7ae0494130e7	928cb9ff-09c7-4a5f-bd42-198e31335976	g.chr16:3777942G>T	ENST00000262367.5	-	31	7915	c.7106C>A	c.(7105-7107)cCc>cAc	p.P2369H	CREBBP_ENST00000382070.3_Missense_Mutation_p.P2331H	NM_004380.2	NP_004371.2	Q92793	CBP_HUMAN	CREB binding protein	2369					cellular lipid metabolic process (GO:0044255)|cellular response to hypoxia (GO:0071456)|chromatin organization (GO:0006325)|embryonic digit morphogenesis (GO:0042733)|gene expression (GO:0010467)|germ-line stem cell maintenance (GO:0030718)|histone acetylation (GO:0016573)|homeostatic process (GO:0042592)|innate immune response (GO:0045087)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein complex assembly (GO:0006461)|regulation of smoothened signaling pathway (GO:0008589)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)|response to hypoxia (GO:0001666)|rhythmic process (GO:0048511)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nuclear body (GO:0016604)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	acetyltransferase activity (GO:0016407)|chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|histone acetyltransferase activity (GO:0004402)|MRF binding (GO:0043426)|p53 binding (GO:0002039)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II transcription coactivator activity (GO:0001105)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(1)|breast(5)|central_nervous_system(4)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(125)|kidney(5)|large_intestine(32)|lung(43)|ovary(18)|pancreas(2)|prostate(6)|skin(9)|soft_tissue(1)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(21)	295		Ovarian(90;0.0266)		OV - Ovarian serous cystadenocarcinoma(1;3.54e-05)		CGAAGGCTGGGGCTGTATCCG	0.647			"""T, N, F, Mis, O"""	"""MLL, MORF, RUNXBP2"""	"""ALL, AML, DLBCL, B-NHL """		Rubinstein-Taybi syndrome																														p.P2369H				Dom/Rec	yes		16	16p13.3	1387	CREB binding protein (CBP)	yes	L	CREBBP,colon,carcinoma,+1,2	CREBBP	546	2	0			c.C7106A												99.0	96.0	97.0					16																	3777942		2197	4300	6497	SO:0001583	missense	1387	exon31			GGCTGGGGCTGTA	U85962	CCDS10509.1, CCDS45399.1	16p13.3	2011-07-01	2008-08-01		ENSG00000005339	ENSG00000005339		"""Chromatin-modifying enzymes / K-acetyltransferases"""	2348	protein-coding gene	gene with protein product		600140	"""Rubinstein-Taybi syndrome"""	RSTS		8413673	Standard	NM_001079846		Approved	RTS, CBP, KAT3A	uc002cvv.3	Q92793	OTTHUMG00000129431	ENST00000262367.5:c.7106C>A	16.37:g.3777942G>T	ENSP00000262367:p.Pro2369His		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_1	44	0.09	4	NM_004380	224	0.00	0	D3DUC9|O00147|Q16376|Q4LE28	Missense_Mutation	SNP	ENST00000262367.5	37	CCDS10509.1	.	.	.	.	.	.	.	.	.	.	g	12.73	2.025950	0.35701	.	.	ENSG00000005339	ENST00000262367;ENST00000543883;ENST00000382070;ENST00000323508	D;D	0.88896	-2.44;-2.38	5.35	5.35	0.76521	.	0.000000	0.85682	D	0.000000	D	0.91758	0.7393	L	0.32530	0.975	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.997	D	0.92661	0.6141	10	0.87932	D	0	-17.1236	18.4232	0.90598	0.0:0.0:1.0:0.0	.	2399;2369	Q4LE28;Q92793	.;CBP_HUMAN	H	2369;2399;2331;904	ENSP00000262367:P2369H;ENSP00000371502:P2331H	ENSP00000262367:P2369H	P	-	2	0	CREBBP	3717943	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.705000	0.98719	2.668000	0.90789	0.655000	0.94253	CCC			0.647	CREBBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000251591.2		NM_004380	
XYLT1	64131	mdanderson.org	37	16	17228331	17228331	+	Splice_Site	SNP	G	G	A			TCGA-WZ-A8D5-01A-11D-A435-10	TCGA-WZ-A8D5-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f9769d8-ba26-4ac7-91c7-7ae0494130e7	928cb9ff-09c7-4a5f-bd42-198e31335976	g.chr16:17228331G>A	ENST00000261381.6	-	9	2110	c.2026C>T	c.(2026-2028)Cga>Tga	p.R676*	CTD-2576D5.4_ENST00000567344.1_RNA	NM_022166.3	NP_071449.1	Q86Y38	XYLT1_HUMAN	xylosyltransferase I	676					cellular response to heat (GO:0034605)|chondroitin sulfate biosynthetic process (GO:0030206)|glycosaminoglycan biosynthetic process (GO:0006024)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)	endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	acetylglucosaminyltransferase activity (GO:0008375)|protein xylosyltransferase activity (GO:0030158)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(7)|lung(35)|ovary(4)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	67						AGGGCTCACCGGCAGCTGTTC	0.602																																					p.R676X													.	.			0			c.C2026T												52.0	49.0	50.0					16																	17228331		2196	4300	6496	SO:0001630	splice_region_variant	64131	exon9			CTCACCGGCAGCT	AJ277441	CCDS10569.1	16p12	2013-02-25			ENSG00000103489	ENSG00000103489	2.4.2.26	"""Glucosaminyl (N-acetyl) transferase and xylosyltransferase family"""	15516	protein-coding gene	gene with protein product	"""protein xylosyltransferase 1"""	608124				11099377	Standard	NM_022166		Approved	XT-I, PXYLT1	uc002dfa.3	Q86Y38	OTTHUMG00000129975	ENST00000261381.6:c.2027+1C>T	16.37:g.17228331G>A			Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	24	0.08	2	NM_022166	2	0.00	0	Q9H1B6	Nonsense_Mutation	SNP	ENST00000261381.6	37	CCDS10569.1	.	.	.	.	.	.	.	.	.	.	G	40	8.331177	0.98764	.	.	ENSG00000103489	ENST00000261381	.	.	.	5.33	-7.87	0.01183	.	0.142669	0.64402	D	0.000010	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-15.298	17.585	0.87979	0.0:0.0626:0.7505:0.1869	.	.	.	.	X	676	.	ENSP00000261381:R676X	R	-	1	2	XYLT1	17135832	0.620000	0.27068	0.934000	0.37439	0.871000	0.50021	-0.331000	0.07914	-1.119000	0.02958	0.561000	0.74099	CGA			0.602	XYLT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000252241.2		NM_022166	Nonsense_Mutation
ACD	65057	mdanderson.org	37	16	67694279	67694279	+	Missense_Mutation	SNP	C	C	T			TCGA-WZ-A8D5-01A-11D-A435-10	TCGA-WZ-A8D5-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f9769d8-ba26-4ac7-91c7-7ae0494130e7	928cb9ff-09c7-4a5f-bd42-198e31335976	g.chr16:67694279C>T	ENST00000393919.4	-	1	367	c.103G>A	c.(103-105)Gca>Aca	p.A35T	PARD6A_ENST00000602551.1_5'Flank|ACD_ENST00000219251.8_Missense_Mutation_p.A35T|PARD6A_ENST00000458121.2_5'Flank|PARD6A_ENST00000219255.3_5'Flank			Q96AP0	ACD_HUMAN	adrenocortical dysplasia homolog (mouse)	35					intracellular protein transport (GO:0006886)|negative regulation of telomere maintenance via telomerase (GO:0032211)|positive regulation of single-stranded telomeric DNA binding (GO:0060381)|positive regulation of telomerase activity (GO:0051973)|protection from non-homologous end joining at telomere (GO:0031848)|protein localization to chromosome, telomeric region (GO:0070198)|telomere assembly (GO:0032202)|telomere capping (GO:0016233)|telomere maintenance (GO:0000723)	chromosome, telomeric region (GO:0000781)|nuclear telomere cap complex (GO:0000783)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|DNA polymerase binding (GO:0070182)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	17		Acute lymphoblastic leukemia(13;3.76e-06)|all_hematologic(13;0.000303)|Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0143)|Epithelial(162;0.047)|all cancers(182;0.228)		GGGCGTCCTGCTCGGGGGCCT	0.721																																					p.A35T													.	.			0			c.G103A												11.0	14.0	13.0					16																	67694279		2167	4277	6444	SO:0001583	missense	65057	exon1			GTCCTGCTCGGGG	AF070535	CCDS10842.1, CCDS42181.1	16q22	2012-08-23			ENSG00000102977	ENSG00000102977			25070	protein-coding gene	gene with protein product	"""TIN2 interacting protein 1"", ""POT1 and TIN2 organizing protein"""	609377				15231715, 15181449	Standard	NM_001082486		Approved	Ptop, Pip1, Tpp1, Tint1	uc002etq.4	Q96AP0	OTTHUMG00000137547	ENST00000393919.4:c.103G>A	16.37:g.67694279C>T	ENSP00000377496:p.Ala35Thr		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	40	0.08	3	NM_001082487	0		0	Q562H5|Q9H8F9	Missense_Mutation	SNP	ENST00000393919.4	37	CCDS42181.1	.	.	.	.	.	.	.	.	.	.	C	14.65	2.599492	0.46318	.	.	ENSG00000102977	ENST00000219251;ENST00000393919	T;T	0.36699	1.24;1.25	2.95	-5.89	0.02282	.	1.306880	0.05671	N	0.588663	T	0.22859	0.0552	N	0.19112	0.55	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.37572	-0.9700	10	0.87932	D	0	8.8505	8.9735	0.35921	0.0:0.4847:0.3197:0.1956	.	35;35	Q96AP0;Q96AP0-2	ACD_HUMAN;.	T	35	ENSP00000219251:A35T;ENSP00000377496:A35T	ENSP00000219251:A35T	A	-	1	0	ACD	66251780	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-7.079000	0.00045	-3.560000	0.00141	-1.263000	0.01449	GCA			0.721	ACD-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		OTTHUMT00000268880.1		NM_022914	
ZCCHC14	23174	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	16	87451243	87451243	+	Silent	SNP	C	C	T			TCGA-WZ-A8D5-01A-11D-A435-10	TCGA-WZ-A8D5-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f9769d8-ba26-4ac7-91c7-7ae0494130e7	928cb9ff-09c7-4a5f-bd42-198e31335976	g.chr16:87451243C>T	ENST00000268616.4	-	8	1012	c.795G>A	c.(793-795)gcG>gcA	p.A265A		NM_015144.2	NP_055959.1	Q8WYQ9	ZCH14_HUMAN	zinc finger, CCHC domain containing 14	265							nucleic acid binding (GO:0003676)|phosphatidylinositol binding (GO:0035091)|zinc ion binding (GO:0008270)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|lung(10)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	36				BRCA - Breast invasive adenocarcinoma(80;0.0285)		CCGCGCTGCCCGCATGGGAGC	0.687																																					p.A265A													ZCCHC14,caecum,carcinoma,-1,2	ZCCHC14	-1	2	0			c.G795A												77.0	89.0	85.0					16																	87451243		2198	4300	6498	SO:0001819	synonymous_variant	23174	exon8			GCTGCCCGCATGG	AB011151	CCDS10961.1	16q24.2	2013-01-10			ENSG00000140948	ENSG00000140948		"""Zinc fingers, CCHC domain containing"", ""Sterile alpha motif (SAM) domain containing"""	24134	protein-coding gene	gene with protein product						9628581	Standard	XM_005255858		Approved	BDG29, MGC14139	uc002fjz.1	Q8WYQ9	OTTHUMG00000137655	ENST00000268616.4:c.795G>A	16.37:g.87451243C>T			Somatic	74	0	0		WXS	Illumina HiSeq	.	47	0.13	6	NM_015144	6	0.00	0	D3DUN1|O60324|Q3MJD8|Q9UFP0	Silent	SNP	ENST00000268616.4	37	CCDS10961.1																																																																																					0.687	ZCCHC14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000269107.1		NM_015144	
GLOD4	51031	mdanderson.org	37	17	686391	686391	+	5'Flank	SNP	G	G	A			TCGA-WZ-A8D5-01A-11D-A435-10	TCGA-WZ-A8D5-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f9769d8-ba26-4ac7-91c7-7ae0494130e7	928cb9ff-09c7-4a5f-bd42-198e31335976	g.chr17:686391G>A	ENST00000301328.5	-	0	0				GLOD4_ENST00000301329.6_5'Flank|GLOD4_ENST00000536578.1_5'Flank|RNMTL1_ENST00000304478.4_Missense_Mutation_p.R128H			Q9HC38	GLOD4_HUMAN	glyoxalase domain containing 4							extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)				endometrium(1)|large_intestine(1)|prostate(1)	3				UCEC - Uterine corpus endometrioid carcinoma (25;0.022)		CTGGAAGGTCGCAGGCTCATT	0.428																																					p.R128H													.	.			0			c.G383A												90.0	82.0	85.0					17																	686391		2203	4300	6503	SO:0001631	upstream_gene_variant	55178	exon2			AAGGTCGCAGGCT	AF177342	CCDS32520.1	17p13.3	2008-02-05	2007-03-14	2007-03-14		ENSG00000167699			14111	protein-coding gene	gene with protein product			"""chromosome 17 open reading frame 25"""	C17orf25		11642406, 12528892	Standard	NM_016080		Approved	CGI-150, HC71	uc002fru.3	Q9HC38			17.37:g.686391G>A	Exception_encountered		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	48	0.06	3	NM_018146	45	0.00	0	D3DTG9|D3DTH1|Q96B89|Q9H3J8|Q9HC37|Q9NVN1	Missense_Mutation	SNP	ENST00000301328.5	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	17.11|17.11	3.306596|3.306596	0.60305|0.60305	.|.	.|.	ENSG00000171861|ENSG00000167699	ENST00000304478|ENST00000397393	T|.	0.33438|.	1.41|.	5.41|5.41	3.42|3.42	0.39159|0.39159	RNA 2-O ribose methyltransferase, substrate binding (2);|.	0.111096|0.111096	0.64402|0.64402	D|D	0.000010|0.000010	T|.	0.53174|.	0.1780|.	M|M	0.74881|0.74881	2.28|2.28	0.45594|0.45594	D|D	0.998538|0.998538	P|.	0.48503|.	0.911|.	P|.	0.48552|.	0.581|.	T|.	0.52268|.	-0.8598|.	10|.	0.15952|0.02654	T|T	0.53|1	-8.4777|-8.4777	5.2126|5.2126	0.15325|0.15325	0.2251:0.0:0.6217:0.1531|0.2251:0.0:0.6217:0.1531	.|.	128|.	Q9HC36|.	RMTL1_HUMAN|.	H|X	128|39	ENSP00000306080:R128H|.	ENSP00000306080:R128H|ENSP00000380548:R39X	R|R	+|-	2|1	0|2	RNMTL1|GLOD4	633141|633141	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.974000|0.974000	0.67602|0.67602	2.417000|2.417000	0.44653|0.44653	1.287000|1.287000	0.44583|0.44583	0.650000|0.650000	0.86243|0.86243	CGC|CGA			0.428	GLOD4-005	KNOWN	basic	protein_coding	protein_coding		OTTHUMT00000437190.1		NM_016080	
SLC35G6	643664	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca;mdanderson.org	37	17	7386120	7386120	+	Missense_Mutation	SNP	G	G	C			TCGA-WZ-A8D5-01A-11D-A435-10	TCGA-WZ-A8D5-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f9769d8-ba26-4ac7-91c7-7ae0494130e7	928cb9ff-09c7-4a5f-bd42-198e31335976	g.chr17:7386120G>C	ENST00000412468.2	+	2	932	c.817G>C	c.(817-819)Gcg>Ccg	p.A273P	ZBTB4_ENST00000311403.4_Intron|POLR2A_ENST00000572844.1_5'Flank|POLR2A_ENST00000322644.6_5'Flank	NM_001102614.1	NP_001096084.1	P0C7Q6	S35G6_HUMAN	solute carrier family 35, member G6	273	EamA 2.					integral component of membrane (GO:0016021)											TGTGAGCTATGCGGTCACCAA	0.597																																					p.A273P													.	.			0			c.G817C												143.0	120.0	127.0					17																	7386120		2203	4300	6503	SO:0001583	missense	643664	exon2			AGCTATGCGGTCA		CCDS45603.1	17p13.1	2013-05-22	2011-08-03	2011-08-03		ENSG00000259224		"""Solute carriers"""	31351	protein-coding gene	gene with protein product			"""transmembrane protein 21B"", ""acyl-malonyl condensing enzyme 1-like 3"""	TMEM21B, AMAC1L3			Standard	NM_001102614		Approved		uc010cmj.1	P0C7Q6		ENST00000412468.2:c.817G>C	17.37:g.7386120G>C	ENSP00000396523:p.Ala273Pro		Somatic	157	0	0		WXS	Illumina HiSeq	.	119	0.08	9	NM_001102614	0		0		Missense_Mutation	SNP	ENST00000412468.2	37	CCDS45603.1	.	.	.	.	.	.	.	.	.	.	G	15.20	2.761628	0.49468	.	.	ENSG00000181222	ENST00000412468	T	0.77877	-1.13	4.06	3.06	0.35304	.	.	.	.	.	T	0.81064	0.4745	L	0.32530	0.975	0.52501	D	0.999952	D	0.89917	1.0	D	0.91635	0.999	T	0.81651	-0.0836	9	0.87932	D	0	-6.6496	12.1191	0.53882	0.0:0.0:0.8265:0.1735	.	273	P0C7Q6	S35G6_HUMAN	P	273	ENSP00000396523:A273P	ENSP00000396523:A273P	A	+	1	0	SLC35G6	7326844	1.000000	0.71417	0.970000	0.41538	0.083000	0.17756	5.834000	0.69361	0.806000	0.34183	0.467000	0.42956	GCG			0.597	SLC35G6-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				NM_001102614	
FLJ36000	284124	broad.mit.edu	37	17	21906822	21906822	+	lincRNA	DEL	G	G	-	rs201476839|rs436179		TCGA-WZ-A8D5-01A-11D-A435-10	TCGA-WZ-A8D5-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f9769d8-ba26-4ac7-91c7-7ae0494130e7	928cb9ff-09c7-4a5f-bd42-198e31335976	g.chr17:21906822delG	ENST00000581223.2	+	0	148					NR_027084.1																						gtgtgtgtgtgtgtgtgtgtg	0.522																																					.													.	.			0			.																																											0	.			GTGTGTGTGTGTG																													17.37:g.21906822delG			Somatic	7	0	0		WXS	Illumina HiSeq	Phase_I	6	0.33	2	.	1	0.00	0		RNA	DEL	ENST00000581223.2	37																																																																																						0.522	RP11-744K17.9-001	KNOWN	basic	lincRNA	lincRNA		OTTHUMT00000451067.1			
TMEM132E	124842	mdanderson.org	37	17	32962085	32962085	+	Missense_Mutation	SNP	G	G	T			TCGA-WZ-A8D5-01A-11D-A435-10	TCGA-WZ-A8D5-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f9769d8-ba26-4ac7-91c7-7ae0494130e7	928cb9ff-09c7-4a5f-bd42-198e31335976	g.chr17:32962085G>T	ENST00000321639.5	+	8	2014	c.1686G>T	c.(1684-1686)gaG>gaT	p.E562D		NM_207313.1	NP_997196.1	Q6IEE7	T132E_HUMAN	transmembrane protein 132E	562						integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(28)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	57				BRCA - Breast invasive adenocarcinoma(366;0.231)		CAGGACTGGAGCCAGGCACCA	0.592																																					p.E562D													.	.			0			c.G1686T												37.0	33.0	35.0					17																	32962085		2203	4300	6503	SO:0001583	missense	124842	exon8			ACTGGAGCCAGGC	BN000149	CCDS11283.1	17q12	2012-11-01			ENSG00000181291	ENSG00000181291			26991	protein-coding gene	gene with protein product							Standard	NM_207313		Approved		uc002hif.3	Q6IEE7	OTTHUMG00000132927	ENST00000321639.5:c.1686G>T	17.37:g.32962085G>T	ENSP00000316532:p.Glu562Asp		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	36	0.08	3	NM_207313	0		0	Q8WUF4|Q8WVA5	Missense_Mutation	SNP	ENST00000321639.5	37	CCDS11283.1	.	.	.	.	.	.	.	.	.	.	G	18.27	3.586166	0.66105	.	.	ENSG00000181291	ENST00000321639	T	0.52295	0.67	5.22	5.22	0.72569	.	0.047676	0.85682	D	0.000000	T	0.60996	0.2312	L	0.56280	1.765	0.58432	D	0.999997	D	0.71674	0.998	D	0.77557	0.99	T	0.58239	-0.7671	10	0.42905	T	0.14	-35.4812	11.3889	0.49802	0.0819:0.0:0.9181:0.0	.	562	Q6IEE7	T132E_HUMAN	D	562	ENSP00000316532:E562D	ENSP00000316532:E562D	E	+	3	2	TMEM132E	29986198	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	2.666000	0.46799	2.725000	0.93324	0.498000	0.49722	GAG			0.592	TMEM132E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000256440.2		NM_207313	
STARD3	10948	mdanderson.org	37	17	37817269	37817269	+	Missense_Mutation	SNP	G	G	T			TCGA-WZ-A8D5-01A-11D-A435-10	TCGA-WZ-A8D5-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f9769d8-ba26-4ac7-91c7-7ae0494130e7	928cb9ff-09c7-4a5f-bd42-198e31335976	g.chr17:37817269G>T	ENST00000336308.5	+	13	1288	c.1070G>T	c.(1069-1071)aGg>aTg	p.R357M	STARD3_ENST00000394250.4_Missense_Mutation_p.R339M|STARD3_ENST00000580611.1_Missense_Mutation_p.R331M|STARD3_ENST00000544210.2_Missense_Mutation_p.R357M	NM_001165937.1|NM_006804.3	NP_001159409.1|NP_006795.3	Q14849	STAR3_HUMAN	StAR-related lipid transfer (START) domain containing 3	357	START. {ECO:0000255|PROSITE- ProRule:PRU00197}.				cholesterol metabolic process (GO:0008203)|lipid metabolic process (GO:0006629)|lipid transport (GO:0006869)|mitochondrial transport (GO:0006839)|progesterone biosynthetic process (GO:0006701)|steroid metabolic process (GO:0008202)	cytoplasm (GO:0005737)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|mitochondrion (GO:0005739)	cholesterol binding (GO:0015485)			endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|pancreas(1)|prostate(2)|stomach(1)	14	Lung NSC(9;1.15e-09)|all_lung(9;6.24e-09)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052)		UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|BRCA - Breast invasive adenocarcinoma(8;1.04e-44)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|LUSC - Lung squamous cell carcinoma(15;0.171)			GAGCGGCGCAGGGACCGATAC	0.602																																					p.R357M													.	.			0			c.G1070T												80.0	67.0	71.0					17																	37817269		2203	4300	6503	SO:0001583	missense	10948	exon13			GGCGCAGGGACCG		CCDS11341.1, CCDS54117.1, CCDS54118.1	17q11-q12	2011-09-12	2007-08-16		ENSG00000131748	ENSG00000131748		"""StAR-related lipid transfer (START) domain containing"""	17579	protein-coding gene	gene with protein product		607048	"""START domain containing 3"""				Standard	NM_006804		Approved	es64, MLN64	uc002hsd.3	Q14849	OTTHUMG00000133213	ENST00000336308.5:c.1070G>T	17.37:g.37817269G>T	ENSP00000337446:p.Arg357Met		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	46	0.07	3	NM_006804	86	0.00	0	A8MXA4|B4DUY1|F5H0G2|Q53Y53|Q96HM9	Missense_Mutation	SNP	ENST00000336308.5	37	CCDS11341.1	.	.	.	.	.	.	.	.	.	.	G	20.4	3.979884	0.74360	.	.	ENSG00000131748	ENST00000336308;ENST00000544210;ENST00000394250	D;D;D	0.83914	-1.78;-1.78;-1.78	5.02	4.03	0.46877	Lipid-binding START (3);START-like domain (1);	0.418647	0.27126	N	0.020814	T	0.79770	0.4503	L	0.51422	1.61	0.48696	D	0.999691	D;P;P;D;P	0.57257	0.963;0.948;0.553;0.979;0.913	B;P;B;P;B	0.45639	0.446;0.488;0.359;0.473;0.353	T	0.79664	-0.1709	10	0.59425	D	0.04	.	9.9917	0.41874	0.1585:0.0:0.8415:0.0	.	357;122;357;339;357	F5H0G2;Q59EN9;B4DUY1;A8MXA4;Q14849	.;.;.;.;STAR3_HUMAN	M	357;357;339	ENSP00000337446:R357M;ENSP00000439869:R357M;ENSP00000377794:R339M	ENSP00000337446:R357M	R	+	2	0	STARD3	35070795	1.000000	0.71417	1.000000	0.80357	0.907000	0.53573	3.530000	0.53539	1.095000	0.41419	0.561000	0.74099	AGG			0.602	STARD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000256933.1			
GRB7	2886	mdanderson.org	37	17	37903113	37903113	+	Missense_Mutation	SNP	G	G	T			TCGA-WZ-A8D5-01A-11D-A435-10	TCGA-WZ-A8D5-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f9769d8-ba26-4ac7-91c7-7ae0494130e7	928cb9ff-09c7-4a5f-bd42-198e31335976	g.chr17:37903113G>T	ENST00000309156.4	+	15	1819	c.1562G>T	c.(1561-1563)tGc>tTc	p.C521F	GRB7_ENST00000445327.2_Missense_Mutation_p.C544F|GRB7_ENST00000394209.2_Missense_Mutation_p.C521F|GRB7_ENST00000394211.3_Missense_Mutation_p.C521F|GRB7_ENST00000309185.3_3'UTR|GRB7_ENST00000394204.1_3'UTR	NM_005310.3	NP_005301.2	Q14451	GRB7_HUMAN	growth factor receptor-bound protein 7	521	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				blood coagulation (GO:0007596)|epidermal growth factor receptor signaling pathway (GO:0007173)|leukocyte migration (GO:0050900)|negative regulation of translation (GO:0017148)|positive regulation of cell migration (GO:0030335)|positive regulation of signal transduction (GO:0009967)|stress granule assembly (GO:0034063)	cell projection (GO:0042995)|cytoplasmic stress granule (GO:0010494)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)|phosphatidylinositol binding (GO:0035091)|protein kinase binding (GO:0019901)|RNA binding (GO:0003723)|SH3/SH2 adaptor activity (GO:0005070)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	18	all_cancers(6;1.06e-93)|all_epithelial(6;2.33e-113)|Breast(7;9.37e-100)|Lung NSC(9;9.76e-10)|all_lung(9;5.34e-09)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052)		UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|Epithelial(3;6.86e-60)|all cancers(3;1.65e-53)|BRCA - Breast invasive adenocarcinoma(8;2.03e-43)|STAD - Stomach adenocarcinoma(3;1.43e-12)|Colorectal(5;6.23e-08)|COAD - Colon adenocarcinoma(5;8.58e-06)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|LUSC - Lung squamous cell carcinoma(15;0.171)			ATCCTGCCGTGCTTGCTGCGC	0.672																																					p.C544F													.	.			0			c.G1631T												73.0	56.0	62.0					17																	37903113		2203	4300	6503	SO:0001583	missense	2886	exon15			TGCCGTGCTTGCT	D43772	CCDS11345.1, CCDS56028.1	17q12	2013-02-14			ENSG00000141738	ENSG00000141738		"""Pleckstrin homology (PH) domain containing"", ""SH2 domain containing"""	4567	protein-coding gene	gene with protein product		601522					Standard	NM_005310		Approved		uc021twu.1	Q14451	OTTHUMG00000133253	ENST00000309156.4:c.1562G>T	17.37:g.37903113G>T	ENSP00000310771:p.Cys521Phe		Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	22	0.14	3	NM_001242442	36	0.00	0	B2RAV1|B3KNL0|B3KWP9|B7WP75|J3KQM4|Q53YD3|Q92568|Q96DF9|Q9Y220	Missense_Mutation	SNP	ENST00000309156.4	37	CCDS11345.1	.	.	.	.	.	.	.	.	.	.	G	16.20	3.056745	0.55325	.	.	ENSG00000141738	ENST00000309156;ENST00000394211;ENST00000394209;ENST00000445327	T;T;T;T	0.41758	0.99;0.99;0.99;0.99	4.89	4.89	0.63831	SH2 motif (2);	0.116521	0.64402	D	0.000018	T	0.66187	0.2764	M	0.79011	2.435	0.80722	D	1	D	0.76494	0.999	D	0.77004	0.989	T	0.70945	-0.4734	10	0.87932	D	0	-31.2092	16.9765	0.86314	0.0:0.0:1.0:0.0	.	521	Q14451	GRB7_HUMAN	F	521;521;521;544	ENSP00000310771:C521F;ENSP00000377761:C521F;ENSP00000377759:C521F;ENSP00000403459:C544F	ENSP00000310771:C521F	C	+	2	0	GRB7	35156639	1.000000	0.71417	0.229000	0.23960	0.308000	0.27856	7.559000	0.82265	2.541000	0.85698	0.655000	0.94253	TGC			0.672	GRB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000257024.2		NM_005310	
KRTAP1-1	81851	hgsc.bcm.edu;broad.mit.edu	37	17	39197304	39197304	+	Missense_Mutation	SNP	T	T	C			TCGA-WZ-A8D5-01A-11D-A435-10	TCGA-WZ-A8D5-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f9769d8-ba26-4ac7-91c7-7ae0494130e7	928cb9ff-09c7-4a5f-bd42-198e31335976	g.chr17:39197304T>C	ENST00000306271.4	-	1	409	c.346A>G	c.(346-348)Atc>Gtc	p.I116V		NM_030967.2	NP_112229.1	Q07627	KRA11_HUMAN	keratin associated protein 1-1	116						keratin filament (GO:0045095)		p.I116V(1)		NS(2)|endometrium(2)|kidney(5)|lung(4)|prostate(1)	14		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			CACCACCTGATACGGGTGCTC	0.662																																					p.I116V													KRTAP1-1,NS,malignant_melanoma,0,1	KRTAP1-1	0	1	1	Substitution - Missense(1)	NS(1)	c.A346G												22.0	27.0	25.0					17																	39197304		2019	4148	6167	SO:0001583	missense	81851	exon1			ACCTGATACGGGT	AJ406926	CCDS42324.1	17q21.2	2014-06-05			ENSG00000188581	ENSG00000188581		"""Keratin associated proteins"""	16772	protein-coding gene	gene with protein product		608819				11279113	Standard	NM_030967		Approved	KAP1.1B, HB2A, KAP1.1, KAP1.1A	uc002hvw.1	Q07627	OTTHUMG00000133592	ENST00000306271.4:c.346A>G	17.37:g.39197304T>C	ENSP00000305975:p.Ile116Val		Somatic	75	0.0133333333	1		WXS	Illumina HiSeq	.	70	0.04	3	NM_030967	0		0	A6NC32|Q96S60|Q96S67	Missense_Mutation	SNP	ENST00000306271.4	37	CCDS42324.1	.	.	.	.	.	.	.	.	.	.	T	8.173	0.792133	0.16258	.	.	ENSG00000188581	ENST00000306271;ENST00000543328	T	0.29655	1.56	4.28	-1.23	0.09465	.	.	.	.	.	T	0.12135	0.0295	N	0.03253	-0.375	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.34079	-0.9843	9	0.20046	T	0.44	.	9.4726	0.38851	0.0:0.573:0.0:0.427	.	116	Q07627	KRA11_HUMAN	V	116;106	ENSP00000305975:I116V	ENSP00000305975:I116V	I	-	1	0	KRTAP1-1	36450830	0.132000	0.22450	0.024000	0.17045	0.516000	0.34256	0.017000	0.13399	-0.199000	0.10317	0.529000	0.55759	ATC			0.662	KRTAP1-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000257696.1		NM_030967	
TMC6	11322	mdanderson.org	37	17	76120700	76120700	+	Missense_Mutation	SNP	G	G	C			TCGA-WZ-A8D5-01A-11D-A435-10	TCGA-WZ-A8D5-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f9769d8-ba26-4ac7-91c7-7ae0494130e7	928cb9ff-09c7-4a5f-bd42-198e31335976	g.chr17:76120700G>C	ENST00000590602.1	-	8	955	c.796C>G	c.(796-798)Ctg>Gtg	p.L266V	TMC6_ENST00000322914.3_Missense_Mutation_p.L266V|TMC6_ENST00000592076.1_5'Flank|TMC6_ENST00000322933.4_5'UTR|TMC6_ENST00000306591.7_Missense_Mutation_p.L266V|TMC6_ENST00000591436.1_5'Flank|TMC6_ENST00000392467.3_Missense_Mutation_p.L266V|TMC6_ENST00000589553.1_Missense_Mutation_p.L39V			Q7Z403	TMC6_HUMAN	transmembrane channel-like 6	266				L -> P (in Ref. 2; AAP69874). {ECO:0000305}.	ion transport (GO:0006811)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear membrane (GO:0031965)				NS(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(5)|upper_aerodigestive_tract(1)	14			BRCA - Breast invasive adenocarcinoma(99;0.00269)|Lung(188;0.0973)			AAGGCCACCAGCAGCAGCAGC	0.672																																					p.L266V													.	.			0			c.C796G												19.0	19.0	19.0					17																	76120700		2183	4244	6427	SO:0001583	missense	11322	exon8			CCACCAGCAGCAG	AY057379	CCDS32748.1	17q25.3	2014-09-17	2005-11-10	2005-11-10	ENSG00000141524	ENSG00000141524			18021	protein-coding gene	gene with protein product		605828	"""epidermodysplasia verruciformis 1"""	EVER1		12426567	Standard	NM_007267		Approved	LAK-4P, EVIN1	uc002juk.2	Q7Z403	OTTHUMG00000177466	ENST00000590602.1:c.796C>G	17.37:g.76120700G>C	ENSP00000465261:p.Leu266Val		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	31	0.10	3	NM_001127198	40	0.00	0	O43284|Q45VJ2|Q8IU98|Q8IUI7|Q8IWU8|Q8TEQ7|Q9HAG5	Missense_Mutation	SNP	ENST00000590602.1	37	CCDS32748.1	.	.	.	.	.	.	.	.	.	.	G	11.48	1.650996	0.29336	.	.	ENSG00000141524	ENST00000322914;ENST00000392467;ENST00000306591	T;T;T	0.54279	0.58;0.58;0.58	3.64	1.38	0.22167	.	1.022600	0.07798	N	0.955959	T	0.53498	0.1800	L	0.53249	1.67	0.33038	D	0.531028	P;D;D;D;B	0.58268	0.713;0.981;0.981;0.982;0.23	B;P;P;P;B	0.57101	0.246;0.813;0.761;0.664;0.082	T	0.56974	-0.7890	10	0.06891	T	0.86	-10.1151	4.5808	0.12257	0.211:0.184:0.605:0.0	.	103;266;39;266;266	B4E003;Q7Z403-2;Q7Z403-4;B3KTU5;Q7Z403	.;.;.;.;TMC6_HUMAN	V	266	ENSP00000313408:L266V;ENSP00000376260:L266V;ENSP00000306405:L266V	ENSP00000306405:L266V	L	-	1	2	TMC6	73632295	0.228000	0.23718	0.981000	0.43875	0.146000	0.21551	0.651000	0.24873	0.497000	0.27926	0.462000	0.41574	CTG			0.672	TMC6-007	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000437146.1			
TSPAN10	83882	broad.mit.edu;ucsc.edu;mdanderson.org	37	17	79612648	79612648	+	RNA	SNP	C	C	T			TCGA-WZ-A8D5-01A-11D-A435-10	TCGA-WZ-A8D5-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f9769d8-ba26-4ac7-91c7-7ae0494130e7	928cb9ff-09c7-4a5f-bd42-198e31335976	g.chr17:79612648C>T	ENST00000572675.1	+	0	667				TSPAN10_ENST00000328585.4_RNA			Q9H1Z9	TSN10_HUMAN	tetraspanin 10						establishment of protein localization to organelle (GO:0072594)	integral component of membrane (GO:0016021)	enzyme binding (GO:0019899)			ovary(1)	1	all_neural(118;0.0878)|all_lung(278;0.175)|Lung NSC(278;0.192)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0101)|OV - Ovarian serous cystadenocarcinoma(97;0.0739)			GGACTGGCAGCAGAACCTGTG	0.627																																					.													.	TSPAN10	21		0			.												21.0	24.0	23.0					17																	79612648		2165	4254	6419			83882	.			TGGCAGCAGAACC	BC032802		17q25.3	2013-10-02			ENSG00000182612	ENSG00000182612		"""Tetraspanins"""	29942	protein-coding gene	gene with protein product	"""oculospanin"""					12107410	Standard	NM_031945		Approved	OCSP	uc010die.3	Q9H1Z9	OTTHUMG00000178037		17.37:g.79612648C>T			Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	32	0.13	4	.	4	0.00	0	Q8N548	RNA	SNP	ENST00000572675.1	37		.	.	.	.	.	.	.	.	.	.	C	13.44	2.236791	0.39498	.	.	ENSG00000182612	ENST00000328585;ENST00000540189	.	.	.	4.15	-4.36	0.03645	.	1.915610	0.02819	N	0.125393	.	.	.	.	.	.	0.58432	D	0.999999	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-3.1148	1.4273	0.02326	0.3853:0.1496:0.2978:0.1673	.	.	.	.	X	223	.	ENSP00000331620:Q223X	Q	+	1	0	TSPAN10	77223053	0.000000	0.05858	0.290000	0.24890	0.937000	0.57800	-1.251000	0.02882	-0.571000	0.06014	0.462000	0.41574	CAG			0.627	TSPAN10-001	KNOWN	basic	polymorphic_pseudogene	polymorphic_pseudogene		OTTHUMT00000440313.1		NM_031945	
MPPE1	65258	broad.mit.edu	37	18	11911003	11911004	+	5'Flank	INS	-	-	G	rs71172029|rs200089244	byFrequency	TCGA-WZ-A8D5-01A-11D-A435-10	TCGA-WZ-A8D5-10A-01D-A438-10	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f9769d8-ba26-4ac7-91c7-7ae0494130e7	928cb9ff-09c7-4a5f-bd42-198e31335976	g.chr18:11911003_11911004insG	ENST00000588072.1	-	0	0				RP11-820I16.1_ENST00000590055.1_lincRNA|MPPE1_ENST00000344987.7_5'Flank|MPPE1_ENST00000309976.9_5'Flank|MPPE1_ENST00000399978.2_5'Flank|RP11-820I16.4_ENST00000609611.1_RNA|MPPE1_ENST00000317235.7_5'Flank	NM_023075.5	NP_075563.3	Q53F39	MPPE1_HUMAN	metallophosphoesterase 1						ER to Golgi vesicle-mediated transport (GO:0006888)|GPI anchor biosynthetic process (GO:0006506)	cis-Golgi network (GO:0005801)|endoplasmic reticulum exit site (GO:0070971)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	GPI anchor binding (GO:0034235)|manganese ion binding (GO:0030145)|phosphoric diester hydrolase activity (GO:0008081)			endometrium(1)|large_intestine(1)|lung(1)|ovary(1)|skin(1)	5						tggcctctcaaggtggaaaagg	0.569													GGG|GG|GGG|deletion	3483	0.695487	0.8865	0.719	5008	,	,		17244	0.7431		0.4712	False		,,,				2504	0.6022				.													.	.			0			.																																									SO:0001631	upstream_gene_variant	0	.			CTCTCAAGGTGGA	BC002877	CCDS11853.1, CCDS56054.1	18p11.21	2004-04-30			ENSG00000154889	ENSG00000154889			15988	protein-coding gene	gene with protein product		611900				11978971	Standard	NM_001242904		Approved		uc002kqf.3	Q53F39	OTTHUMG00000131661		18.37:g.11911005_11911005dupG	Exception_encountered		Somatic	10	0	0		WXS	Illumina HiSeq	Phase_I	9	0.89	8	.	0		0	B0YJ39|B0YJ40|B0YJ41|B5ME53|B7WNJ3|D3DUI5|D3DUI7|Q6GMP1|Q8TAD6|Q8TE26|Q8WZ32|Q9BU58|Q9H958|Q9HAI4	RNA	INS	ENST00000588072.1	37	CCDS11853.1																																																																																					0.569	MPPE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000254562.2		NM_023075	
ONECUT3	390874	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca;mdanderson.org	37	19	1775247	1775247	+	Missense_Mutation	SNP	A	A	G			TCGA-WZ-A8D5-01A-11D-A435-10	TCGA-WZ-A8D5-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f9769d8-ba26-4ac7-91c7-7ae0494130e7	928cb9ff-09c7-4a5f-bd42-198e31335976	g.chr19:1775247A>G	ENST00000382349.4	+	2	2578	c.1288A>G	c.(1288-1290)Atc>Gtc	p.I430V		NM_001080488.1	NP_001073957.1	O60422	ONEC3_HUMAN	one cut homeobox 3	430					endocrine pancreas development (GO:0031018)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)						Acute lymphoblastic leukemia(61;4.66e-11)|all_hematologic(61;4.59e-07)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		ACGCACGCTGATCGCCATCTT	0.612																																					p.I430V													ONECUT3,colon,carcinoma,-2,1	ONECUT3	-2	1	0			c.A1288G												21.0	25.0	24.0					19																	1775247		2126	4226	6352	SO:0001583	missense	390874	exon2			ACGCTGATCGCCA	AC004755	CCDS45900.1	19p13.3	2012-03-09	2007-07-16			ENSG00000205922		"""Homeoboxes / CUT class"""	13399	protein-coding gene	gene with protein product		611294	"""one cut domain, family member 3"""			9915796	Standard	NM_001080488		Approved		uc010xgr.2	O60422		ENST00000382349.4:c.1288A>G	19.37:g.1775247A>G	ENSP00000371786:p.Ile430Val		Somatic	134	0	0		WXS	Illumina HiSeq	.	131	0.27	36	NM_001080488	3	0.00	0	A8MZM7	Missense_Mutation	SNP	ENST00000382349.4	37	CCDS45900.1	.	.	.	.	.	.	.	.	.	.	a	9.182	1.023831	0.19433	.	.	ENSG00000205922	ENST00000382349	D	0.96011	-3.88	3.0	3.0	0.34707	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);	0.157646	0.39687	U	0.001290	D	0.83769	0.5326	N	0.01576	-0.805	0.45837	D	0.998708	B	0.15141	0.012	B	0.13407	0.009	T	0.76217	-0.3040	10	0.18276	T	0.48	.	9.9659	0.41723	1.0:0.0:0.0:0.0	.	430	O60422	ONEC3_HUMAN	V	430	ENSP00000371786:I430V	ENSP00000371786:I430V	I	+	1	0	ONECUT3	1726247	0.873000	0.30073	0.958000	0.39756	0.861000	0.49209	1.567000	0.36407	1.006000	0.39211	0.330000	0.21533	ATC			0.612	ONECUT3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000418499.1			
DOT1L	84444	mdanderson.org	37	19	2216567	2216567	+	Missense_Mutation	SNP	G	G	T			TCGA-WZ-A8D5-01A-11D-A435-10	TCGA-WZ-A8D5-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f9769d8-ba26-4ac7-91c7-7ae0494130e7	928cb9ff-09c7-4a5f-bd42-198e31335976	g.chr19:2216567G>T	ENST00000398665.3	+	20	2247	c.2211G>T	c.(2209-2211)caG>caT	p.Q737H	AC004490.1_ENST00000585593.1_RNA|DOT1L_ENST00000608122.1_3'UTR	NM_032482.2	NP_115871.1	Q8TEK3	DOT1L_HUMAN	DOT1-like histone H3K79 methyltransferase	737					histone lysine methylation (GO:0034968)|regulation of JAK-STAT cascade (GO:0046425)|regulation of transcription regulatory region DNA binding (GO:2000677)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription factor binding (GO:0008134)	p.Q737H(2)		NS(1)|breast(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(3)|lung(14)|ovary(2)|pancreas(2)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(9)	42		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		ACACGCCCCAGTACCTGGCCT	0.672																																					p.Q737H													DOT1L_ENST00000398665,NS,carcinoma,0,2	DOT1L_ENST00000398665	0	2	2	Substitution - Missense(2)	lung(2)	c.G2211T												39.0	46.0	44.0					19																	2216567		2061	4190	6251	SO:0001583	missense	84444	exon20			GCCCCAGTACCTG	AF509504	CCDS42460.1	19p13.3	2013-05-21	2013-05-21		ENSG00000104885	ENSG00000104885	2.1.1.43	"""Chromatin-modifying enzymes / K-methyltransferases"""	24948	protein-coding gene	gene with protein product	"""histone methyltransferase DOT1L"""	607375	"""DOT1-like, histone H3 methyltransferase (S. cerevisiae)"""			11347906, 12123582	Standard	NM_032482		Approved	KIAA1814, DOT1, KMT4	uc002lvb.4	Q8TEK3	OTTHUMG00000150431	ENST00000398665.3:c.2211G>T	19.37:g.2216567G>T	ENSP00000381657:p.Gln737His		Somatic	21	0	0		WXS	Illumina HiSeq	Phase_I	29	0.10	3	NM_032482	51	0.00	0	O60379|Q96JL1	Missense_Mutation	SNP	ENST00000398665.3	37	CCDS42460.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	14.04|14.04	2.415346|2.415346	0.42817|0.42817	.|.	.|.	ENSG00000104885|ENSG00000104885	ENST00000398665;ENST00000221482|ENST00000440640	T|.	0.26373|.	1.74|.	5.21|5.21	5.21|5.21	0.72293|0.72293	.|.	0.141125|.	0.51477|.	D|.	0.000089|.	T|T	0.58481|0.58481	0.2125|0.2125	L|L	0.50333|0.50333	1.59|1.59	0.31230|0.31230	N|N	0.696427|0.696427	P;B|.	0.35272|.	0.493;0.065|.	B;B|.	0.32864|.	0.154;0.056|.	T|T	0.61282|0.61282	-0.7094|-0.7094	10|5	0.87932|.	D|.	0|.	-32.7438|-32.7438	15.481|15.481	0.75528|0.75528	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	737;737|.	Q8TEK3;Q8TEK3-2|.	DOT1L_HUMAN;.|.	H|I	737|524	ENSP00000381657:Q737H|.	ENSP00000221482:Q737H|.	Q|S	+|+	3|2	2|0	DOT1L|DOT1L	2167567|2167567	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.901000|0.901000	0.52897|0.52897	1.788000|1.788000	0.38714|0.38714	2.437000|2.437000	0.82529|0.82529	0.655000|0.655000	0.94253|0.94253	CAG|AGT			0.672	DOT1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000318066.1		NM_032482	
DOT1L	84444	mdanderson.org	37	19	2226654	2226654	+	Silent	SNP	G	G	T			TCGA-WZ-A8D5-01A-11D-A435-10	TCGA-WZ-A8D5-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f9769d8-ba26-4ac7-91c7-7ae0494130e7	928cb9ff-09c7-4a5f-bd42-198e31335976	g.chr19:2226654G>T	ENST00000398665.3	+	27	4170	c.4134G>T	c.(4132-4134)ggG>ggT	p.G1378G		NM_032482.2	NP_115871.1	Q8TEK3	DOT1L_HUMAN	DOT1-like histone H3K79 methyltransferase	1378					histone lysine methylation (GO:0034968)|regulation of JAK-STAT cascade (GO:0046425)|regulation of transcription regulatory region DNA binding (GO:2000677)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription factor binding (GO:0008134)			NS(1)|breast(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(3)|lung(14)|ovary(2)|pancreas(2)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(9)	42		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GCCTGGCTGGGCTGAAGGGCG	0.726																																					p.G1378G													.	.			0			c.G4134T												5.0	8.0	7.0					19																	2226654		1965	4053	6018	SO:0001819	synonymous_variant	84444	exon27			GGCTGGGCTGAAG	AF509504	CCDS42460.1	19p13.3	2013-05-21	2013-05-21		ENSG00000104885	ENSG00000104885	2.1.1.43	"""Chromatin-modifying enzymes / K-methyltransferases"""	24948	protein-coding gene	gene with protein product	"""histone methyltransferase DOT1L"""	607375	"""DOT1-like, histone H3 methyltransferase (S. cerevisiae)"""			11347906, 12123582	Standard	NM_032482		Approved	KIAA1814, DOT1, KMT4	uc002lvb.4	Q8TEK3	OTTHUMG00000150431	ENST00000398665.3:c.4134G>T	19.37:g.2226654G>T			Somatic	12	0	0		WXS	Illumina HiSeq	Phase_I	15	0.20	3	NM_032482	58	0.00	0	O60379|Q96JL1	Silent	SNP	ENST00000398665.3	37	CCDS42460.1																																																																																					0.726	DOT1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000318066.1		NM_032482	
SEMA6B	10501	mdanderson.org	37	19	4555566	4555566	+	Missense_Mutation	SNP	A	A	T			TCGA-WZ-A8D5-01A-11D-A435-10	TCGA-WZ-A8D5-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f9769d8-ba26-4ac7-91c7-7ae0494130e7	928cb9ff-09c7-4a5f-bd42-198e31335976	g.chr19:4555566A>T	ENST00000586582.1	-	7	792	c.482T>A	c.(481-483)cTg>cAg	p.L161Q	SEMA6B_ENST00000586965.1_Missense_Mutation_p.L161Q|SEMA6B_ENST00000301293.3_Missense_Mutation_p.L161Q	NM_032108.3	NP_115484.2	Q9H3T3	SEM6B_HUMAN	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6B	161	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				cell differentiation (GO:0030154)|nervous system development (GO:0007399)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			breast(1)|central_nervous_system(2)|large_intestine(4)|lung(11)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0149)|STAD - Stomach adenocarcinoma(1328;0.18)		GACGGGCTGCAGGGTGTCTAT	0.637																																					p.L161Q													.	.			0			c.T482A												88.0	79.0	82.0					19																	4555566		2203	4300	6503	SO:0001583	missense	10501	exon7			GGCTGCAGGGTGT	AB022433	CCDS12131.1	19p13.3	2008-07-22				ENSG00000167680		"""Semaphorins"""	10739	protein-coding gene	gene with protein product	"""Sema VIb"", ""semaphorin Z"", ""semaphorin VIB"""	608873		SEMAN		9361278	Standard	NM_032108		Approved	semaZ, SEMA-VIB, SEM-SEMA-Y	uc010dud.2	Q9H3T3		ENST00000586582.1:c.482T>A	19.37:g.4555566A>T	ENSP00000467290:p.Leu161Gln		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	47	0.06	3	NM_032108	21	0.00	0	A5PKU4|F6IB19|Q9NRK9	Missense_Mutation	SNP	ENST00000586582.1	37	CCDS12131.1	.	.	.	.	.	.	.	.	.	.	A	15.95	2.984065	0.53827	.	.	ENSG00000167680	ENST00000301293;ENST00000301292	T	0.12147	2.71	3.06	3.06	0.35304	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.000000	0.64402	U	0.000007	T	0.40694	0.1127	M	0.92026	3.265	0.38117	D	0.937752	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	T	0.50808	-0.8784	10	0.87932	D	0	.	8.0509	0.30577	0.7953:0.2047:0.0:0.0	.	161;161	B4DT36;Q9H3T3	.;SEM6B_HUMAN	Q	161	ENSP00000301293:L161Q	ENSP00000301292:L161Q	L	-	2	0	SEMA6B	4506566	1.000000	0.71417	1.000000	0.80357	0.503000	0.33858	6.890000	0.75633	1.642000	0.50584	0.254000	0.18369	CTG			0.637	SEMA6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000458656.2		NM_032108	
KDM4B	23030	broad.mit.edu	37	19	5047517	5047517	+	Missense_Mutation	SNP	C	C	T			TCGA-WZ-A8D5-01A-11D-A435-10	TCGA-WZ-A8D5-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f9769d8-ba26-4ac7-91c7-7ae0494130e7	928cb9ff-09c7-4a5f-bd42-198e31335976	g.chr19:5047517C>T	ENST00000159111.4	+	6	681	c.463C>T	c.(463-465)Cgg>Tgg	p.R155W	KDM4B_ENST00000381759.4_Missense_Mutation_p.R155W|KDM4B_ENST00000592175.1_3'UTR|KDM4B_ENST00000536461.1_Missense_Mutation_p.R155W	NM_015015.2	NP_055830	O94953	KDM4B_HUMAN	lysine (K)-specific demethylase 4B	155	JmjC. {ECO:0000255|PROSITE- ProRule:PRU00538}.				chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(1)|liver(1)|lung(14)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	32						CGGGAGCCTCCGGACCATCCT	0.677																																					p.R155W													.	KDM4B	120		0			c.C463T												62.0	55.0	57.0					19																	5047517		2203	4300	6503	SO:0001583	missense	23030	exon6			AGCCTCCGGACCA	AB020683	CCDS12138.1	19p13.3	2013-01-23	2009-04-06	2009-04-06		ENSG00000127663		"""Chromatin-modifying enzymes / K-demethylases"", ""Tudor domain containing"""	29136	protein-coding gene	gene with protein product	"""tudor domain containing 14B"""	609765	"""jumonji domain containing 2B"""	JMJD2B		10048485, 15138608	Standard	NM_015015		Approved	KIAA0876, TDRD14B	uc002mbq.4	O94953		ENST00000159111.4:c.463C>T	19.37:g.5047517C>T	ENSP00000159111:p.Arg155Trp		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	83	0.04	3	NM_015015	12	0.00	0	B9EGN8|D6W631|O75274|Q6P3R5|Q9P1V1|Q9UF40	Missense_Mutation	SNP	ENST00000159111.4	37	CCDS12138.1	.	.	.	.	.	.	.	.	.	.	C	21.6	4.171626	0.78452	.	.	ENSG00000127663	ENST00000159111;ENST00000381759;ENST00000536461	T;T;T	0.71103	-0.54;-0.54;-0.54	4.32	-1.24	0.09435	Transcription factor jumonji/aspartyl beta-hydroxylase (2);	0.214044	0.37304	N	0.002152	T	0.66499	0.2795	L	0.27053	0.805	0.34145	D	0.666813	D;D;D	0.69078	0.983;0.997;0.99	P;P;P	0.60236	0.447;0.871;0.747	T	0.71935	-0.4442	10	0.66056	D	0.02	-28.0822	9.1808	0.37141	0.6822:0.2157:0.1021:0.0	.	155;155;155	F5GX28;O94953-2;O94953	.;.;KDM4B_HUMAN	W	155	ENSP00000159111:R155W;ENSP00000371178:R155W;ENSP00000440495:R155W	ENSP00000159111:R155W	R	+	1	2	KDM4B	4998517	1.000000	0.71417	0.770000	0.31555	0.704000	0.40688	4.475000	0.60210	0.042000	0.15717	-0.274000	0.10170	CGG			0.677	KDM4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000450558.1		NM_015015	
ZNF358	140467	mdanderson.org	37	19	7585211	7585211	+	Silent	SNP	G	G	T			TCGA-WZ-A8D5-01A-11D-A435-10	TCGA-WZ-A8D5-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f9769d8-ba26-4ac7-91c7-7ae0494130e7	928cb9ff-09c7-4a5f-bd42-198e31335976	g.chr19:7585211G>T	ENST00000597229.1	+	2	1253	c.1083G>T	c.(1081-1083)gcG>gcT	p.A361A	CTD-2207O23.11_ENST00000602083.1_RNA|MCOLN1_ENST00000264079.6_5'Flank|ZNF358_ENST00000394341.2_Silent_p.A361A	NM_018083.4	NP_060553.4	Q9NW07	ZN358_HUMAN	zinc finger protein 358	361					embryonic forelimb morphogenesis (GO:0035115)|neural tube development (GO:0021915)|regulation of transcription, DNA-templated (GO:0006355)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|kidney(1)|lung(1)|skin(2)	8						AGAGCTCAGCGCTGCTCCAGC	0.667																																					p.A361A													ZNF358,NS,carcinoma,+1,1	ZNF358	1	1	0			c.G1083T												46.0	48.0	47.0					19																	7585211		2203	4296	6499	SO:0001819	synonymous_variant	140467	exon2			CTCAGCGCTGCTC	AK001252	CCDS32890.2	19p13.2	2013-01-08			ENSG00000198816	ENSG00000198816		"""Zinc fingers, C2H2-type"""	16838	protein-coding gene	gene with protein product							Standard	NM_018083		Approved	FLJ10390, ZFEND	uc002mgn.2	Q9NW07		ENST00000597229.1:c.1083G>T	19.37:g.7585211G>T			Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	27	0.11	3	NM_018083	90	0.00	0	Q9BTM7	Silent	SNP	ENST00000597229.1	37	CCDS32890.2																																																																																					0.667	ZNF358-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000316747.1			
OLFM2	93145	bcgsc.ca	37	19	10024251	10024251	+	Intron	SNP	T	T	C			TCGA-WZ-A8D5-01A-11D-A435-10	TCGA-WZ-A8D5-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f9769d8-ba26-4ac7-91c7-7ae0494130e7	928cb9ff-09c7-4a5f-bd42-198e31335976	g.chr19:10024251T>C	ENST00000264833.4	-	1	249					NM_058164.2	NP_477512.1	O95897	NOE2_HUMAN	olfactomedin 2						protein secretion (GO:0009306)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|extracellular region (GO:0005576)|synapse (GO:0045202)				breast(1)|cervix(1)|endometrium(3)|large_intestine(8)|lung(9)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)	31						ACCATGGCCATGGTGCTCAGC	0.706																																					.													.	OLFM2	42		0			.												27.0	34.0	32.0					19																	10024251		691	1591	2282	SO:0001627	intron_variant	93145	.			TGGCCATGGTGCT	AF131839	CCDS12221.1	19p13.2	2008-07-03				ENSG00000105088			17189	protein-coding gene	gene with protein product	"""noelin 2"""						Standard	NM_058164		Approved	OlfC, NOE2	uc002mmp.3	O95897		ENST00000264833.4:c.63+22728A>G	19.37:g.10024251T>C			Somatic	22	0	0		WXS	Illumina HiSeq	Phase_1	24	0.17	4	.	5	0.60	3	Q6IMJ3|Q96FC2	Missense_Mutation	SNP	ENST00000264833.4	37	CCDS12221.1																																																																																					0.706	OLFM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000451119.1			
ANKLE1	126549	broad.mit.edu	37	19	17397500	17397501	+	3'UTR	DEL	TT	TT	-	rs71180380|rs563327402|rs534658778|rs1465582	byFrequency	TCGA-WZ-A8D5-01A-11D-A435-10	TCGA-WZ-A8D5-10A-01D-A438-10	TT	TT					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f9769d8-ba26-4ac7-91c7-7ae0494130e7	928cb9ff-09c7-4a5f-bd42-198e31335976	g.chr19:17397500_17397501delTT	ENST00000394458.3	+	0	2263_2264				ANKLE1_ENST00000598347.1_Frame_Shift_Del_p.L591fs|ANKLE1_ENST00000594072.1_3'UTR|ANKLE1_ENST00000404085.1_3'UTR	NM_152363.4	NP_689576	Q8NAG6	ANKL1_HUMAN	ankyrin repeat and LEM domain containing 1											large_intestine(1)|lung(3)|prostate(1)|skin(1)|urinary_tract(1)	7						tgtgtgtgtgtttgtgtgtgtg	0.53																																					.													.	ANKLE1	27		0			.																																									SO:0001624	3_prime_UTR_variant	126549	.			TGTGTGTTTGTGT	AK096688	CCDS12354.2, CCDS12354.3	19p13.11	2013-01-10	2008-03-25	2008-03-25	ENSG00000160117	ENSG00000160117		"""Ankyrin repeat domain containing"""	26812	protein-coding gene	gene with protein product	"""LEM domain containing 6"""		"""ankyrin repeat domain 41"""	ANKRD41			Standard	NM_152363		Approved	FLJ39369, LEMD6	uc002nga.2	Q8NAG6	OTTHUMG00000150839	ENST00000394458.3:c.*140TT>-	19.37:g.17397500_17397501delTT			Somatic	14	0	0		WXS	Illumina HiSeq	Phase_I	7	0.86	6	.	2	0.00	0	A8VU82|Q8N8J8	Frame_Shift_Del	DEL	ENST00000394458.3	37	CCDS12354.2																																																																																					0.530	ANKLE1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		OTTHUMT00000325392.2		NM_152363	
WDR87	83889	ucsc.edu	37	19	38377404	38377404	+	Missense_Mutation	SNP	C	C	T	rs201328117		TCGA-WZ-A8D5-01A-11D-A435-10	TCGA-WZ-A8D5-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f9769d8-ba26-4ac7-91c7-7ae0494130e7	928cb9ff-09c7-4a5f-bd42-198e31335976	g.chr19:38377404C>T	ENST00000303868.5	-	6	7014	c.6790G>A	c.(6790-6792)Gag>Aag	p.E2264K	WDR87_ENST00000447313.2_Missense_Mutation_p.E2303K	NM_031951.3	NP_114157.3	Q6ZQQ6	WDR87_HUMAN	WD repeat domain 87	2264	Glu-rich.									NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|lung(2)|prostate(1)|skin(3)|stomach(1)	36						tcctcctcctcccttacctcc	0.488																																					p.E2264K													.	WDR87	191		0			c.G6790A												66.0	49.0	54.0					19																	38377404		692	1591	2283	SO:0001583	missense	83889	exon6			CCTCCTCCCTTAC	AK128826	CCDS46063.1, CCDS74356.1	19q13.13	2013-01-09			ENSG00000171804	ENSG00000171804		"""WD repeat domain containing"""	29934	protein-coding gene	gene with protein product							Standard	XM_005259304		Approved	NYD-SP11	uc010efu.2	Q6ZQQ6	OTTHUMG00000048187	ENST00000303868.5:c.6790G>A	19.37:g.38377404C>T	ENSP00000368025:p.Glu2264Lys		Somatic	124	0	0		WXS	Illumina HiSeq		87	0.22	19	NM_031951	1	0.00	0	Q9BWV9	Missense_Mutation	SNP	ENST00000303868.5	37	CCDS46063.1	.	.	.	.	.	.	.	.	.	.	C	10.21	1.286996	0.23478	.	.	ENSG00000171804	ENST00000447313;ENST00000303868	T;T	0.41400	1.0;1.0	4.47	4.47	0.54385	.	.	.	.	.	T	0.39682	0.1087	L	0.29908	0.895	0.09310	N	1	D;D	0.69078	0.997;0.997	P;P	0.58577	0.841;0.841	T	0.13872	-1.0493	9	0.06099	T	0.92	.	9.1387	0.36890	0.0:0.8956:0.0:0.1044	.	2264;2303	Q6ZQQ6;E7ESW6	WDR87_HUMAN;.	K	2303;2264	ENSP00000405012:E2303K;ENSP00000368025:E2264K	ENSP00000368025:E2264K	E	-	1	0	WDR87	43069244	0.001000	0.12720	0.064000	0.19789	0.078000	0.17371	0.800000	0.27042	2.412000	0.81896	0.450000	0.29827	GAG			0.488	WDR87-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		OTTHUMT00000314628.2		XM_940478	
EMP3	2014	mdanderson.org	37	19	48833719	48833719	+	Missense_Mutation	SNP	C	C	T	rs564907309		TCGA-WZ-A8D5-01A-11D-A435-10	TCGA-WZ-A8D5-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f9769d8-ba26-4ac7-91c7-7ae0494130e7	928cb9ff-09c7-4a5f-bd42-198e31335976	g.chr19:48833719C>T	ENST00000270221.6	+	5	785	c.484C>T	c.(484-486)Cgg>Tgg	p.R162W	EMP3_ENST00000596315.1_Missense_Mutation_p.R93W|EMP3_ENST00000597279.1_Missense_Mutation_p.R162W	NM_001425.2	NP_001416.1	P54852	EMP3_HUMAN	epithelial membrane protein 3	162					cell growth (GO:0016049)|negative regulation of cell proliferation (GO:0008285)	integral component of membrane (GO:0016021)				lung(1)	1		all_epithelial(76;6.08e-07)|all_lung(116;5.76e-06)|Lung NSC(112;1.18e-05)|all_neural(266;0.00989)|Prostate(7;0.0143)|Ovarian(192;0.0261)|Breast(70;0.203)		OV - Ovarian serous cystadenocarcinoma(262;0.000138)|all cancers(93;0.00017)|Epithelial(262;0.0138)|GBM - Glioblastoma multiforme(486;0.0146)		CCTACGGAAGCGGGAGTGAGc	0.692																																					p.R162W													.	.			0			c.C484T												24.0	24.0	24.0					19																	48833719		2203	4300	6503	SO:0001583	missense	2014	exon5			CGGAAGCGGGAGT	U52101	CCDS12715.1	19q13.3	2008-07-16				ENSG00000142227			3335	protein-coding gene	gene with protein product		602335				8996089, 10331954	Standard	NM_001425		Approved	YMP	uc002piv.2	P54852		ENST00000270221.6:c.484C>T	19.37:g.48833719C>T	ENSP00000270221:p.Arg162Trp		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	45	0.07	3	NM_001425	110	0.00	0	Q6FH01	Missense_Mutation	SNP	ENST00000270221.6	37	CCDS12715.1	.	.	.	.	.	.	.	.	.	.	C	17.39	3.377978	0.61735	.	.	ENSG00000142227	ENST00000270221	D	0.96491	-4.03	4.41	4.41	0.53225	.	0.062517	0.64402	D	0.000012	D	0.95351	0.8491	M	0.63843	1.955	0.45594	D	0.998538	D	0.56287	0.975	P	0.46758	0.526	D	0.95308	0.8409	10	0.87932	D	0	.	12.0299	0.53392	0.1735:0.8265:0.0:0.0	.	162	P54852	EMP3_HUMAN	W	162	ENSP00000270221:R162W	ENSP00000270221:R162W	R	+	1	2	EMP3	53525531	1.000000	0.71417	0.999000	0.59377	0.566000	0.35808	1.081000	0.30791	2.449000	0.82847	0.561000	0.74099	CGG			0.692	EMP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000465613.1		NM_001425	
ALDH16A1	126133	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	19	49967466	49967466	+	Missense_Mutation	SNP	G	G	A			TCGA-WZ-A8D5-01A-11D-A435-10	TCGA-WZ-A8D5-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f9769d8-ba26-4ac7-91c7-7ae0494130e7	928cb9ff-09c7-4a5f-bd42-198e31335976	g.chr19:49967466G>A	ENST00000293350.4	+	10	1440	c.1277G>A	c.(1276-1278)gGc>gAc	p.G426D	ALDH16A1_ENST00000540132.1_Missense_Mutation_p.G263D|ALDH16A1_ENST00000433981.2_Missense_Mutation_p.G261D|CTD-3148I10.9_ENST00000599536.1_Intron|ALDH16A1_ENST00000455361.2_Missense_Mutation_p.G375D	NM_153329.3	NP_699160.2	Q8IZ83	A16A1_HUMAN	aldehyde dehydrogenase 16 family, member A1	426						extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor (GO:0016620)			cervix(2)|endometrium(3)|kidney(2)|large_intestine(3)|lung(5)|skin(2)|urinary_tract(3)	20		all_lung(116;5.39e-06)|Lung NSC(112;1.97e-05)|all_neural(266;0.0966)|Ovarian(192;0.15)		OV - Ovarian serous cystadenocarcinoma(262;0.00156)|GBM - Glioblastoma multiforme(486;0.0251)		CCCCGCGGGGGCAGCGCCAGT	0.701																																					p.G426D													.	.			0			c.G1277A												21.0	26.0	25.0					19																	49967466		2198	4297	6495	SO:0001583	missense	126133	exon10			GCGGGGGCAGCGC	AY007096	CCDS12766.1, CCDS46141.1	19q13.33	2014-08-12			ENSG00000161618	ENSG00000161618		"""Aldehyde dehydrogenases"""	28114	protein-coding gene	gene with protein product		613358					Standard	NM_153329		Approved	MGC10204	uc002pnt.3	Q8IZ83	OTTHUMG00000183163	ENST00000293350.4:c.1277G>A	19.37:g.49967466G>A	ENSP00000293350:p.Gly426Asp		Somatic	43	0	0		WXS	Illumina HiSeq	.	31	0.19	6	NM_153329	167	0.34	56	B4DLQ1|C9JBH6|Q86YF0|Q8IYL4|Q8TEI8	Missense_Mutation	SNP	ENST00000293350.4	37	CCDS12766.1	.	.	.	.	.	.	.	.	.	.	G	17.22	3.335252	0.60853	.	.	ENSG00000161618	ENST00000293350;ENST00000455361;ENST00000540132;ENST00000433981	T;T;T;T	0.75821	-0.97;-0.97;-0.97;-0.97	4.75	3.71	0.42584	Aldehyde dehydrogenase domain (1);Aldehyde dehydrogenase, C-terminal (1);Aldehyde/histidinol dehydrogenase (1);	0.997173	0.08130	N	0.993342	T	0.78162	0.4240	L	0.50333	1.59	0.29404	N	0.861695	P;D;P	0.61080	0.715;0.989;0.87	P;P;P	0.53360	0.448;0.724;0.66	T	0.67730	-0.5595	10	0.72032	D	0.01	-14.5768	10.4995	0.44798	0.097:0.0:0.903:0.0	.	263;375;426	F5H4B6;B4DLQ1;Q8IZ83	.;.;A16A1_HUMAN	D	426;375;263;261	ENSP00000293350:G426D;ENSP00000410142:G375D;ENSP00000445088:G263D;ENSP00000398675:G261D	ENSP00000293350:G426D	G	+	2	0	ALDH16A1	54659278	0.997000	0.39634	0.974000	0.42286	0.459000	0.32528	1.101000	0.31037	0.993000	0.38866	0.305000	0.20034	GGC			0.701	ALDH16A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000465358.1		NM_153329	
KLK11	11012	broad.mit.edu	37	19	51528037	51528037	+	Silent	SNP	T	T	C			TCGA-WZ-A8D5-01A-11D-A435-10	TCGA-WZ-A8D5-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f9769d8-ba26-4ac7-91c7-7ae0494130e7	928cb9ff-09c7-4a5f-bd42-198e31335976	g.chr19:51528037T>C	ENST00000594768.1	-	3	335	c.150A>G	c.(148-150)ggA>ggG	p.G50G	KLK11_ENST00000319720.7_Silent_p.G18G|KLK11_ENST00000391804.3_Silent_p.G18G|KLK11_ENST00000453757.3_Silent_p.G18G|KLK11_ENST00000600362.1_Intron|KLK11_ENST00000594458.1_5'UTR	NM_144947.1	NP_659196.1	Q9UBX7	KLK11_HUMAN	kallikrein-related peptidase 11	50						extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			breast(1)|endometrium(2)|large_intestine(1)|lung(2)|skin(1)	7		all_neural(266;0.026)		OV - Ovarian serous cystadenocarcinoma(262;0.00327)|GBM - Glioblastoma multiforme(134;0.00878)		TCCTGGTCTCTCCCCCTACAA	0.622																																					p.G50G													.	KLK11	28		0			c.A150G												30.0	25.0	27.0					19																	51528037		2202	4300	6502	SO:0001819	synonymous_variant	11012	exon3			GGTCTCTCCCCCT	AB012917	CCDS12818.1, CCDS12819.1, CCDS54297.1	19q13.33	2011-09-07	2006-10-27			ENSG00000167757		"""Kallikreins"", ""Serine peptidases / Serine peptidases"""	6359	protein-coding gene	gene with protein product		604434	"""kallikrein 11"""	PRSS20		9765601, 10662548, 16800724, 16800723	Standard	NM_006853		Approved	TLSP	uc002pvb.2	Q9UBX7		ENST00000594768.1:c.150A>G	19.37:g.51528037T>C			Somatic	89	0.0112359551	1		WXS	Illumina HiSeq	Phase_I	60	0.05	3	NM_144947	0		0	O75837|Q0WXX5|Q8IXD7|Q9NS65	Silent	SNP	ENST00000594768.1	37	CCDS12818.1																																																																																					0.622	KLK11-002	KNOWN	basic|CCDS	protein_coding	protein_coding		OTTHUMT00000464314.2		NM_006853	
FBXO11	80204	mdanderson.org	37	2	48132711	48132711	+	Missense_Mutation	SNP	T	T	G			TCGA-WZ-A8D5-01A-11D-A435-10	TCGA-WZ-A8D5-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f9769d8-ba26-4ac7-91c7-7ae0494130e7	928cb9ff-09c7-4a5f-bd42-198e31335976	g.chr2:48132711T>G	ENST00000403359.3	-	1	221	c.149A>C	c.(148-150)cAg>cCg	p.Q50P	AC079807.2_ENST00000417692.1_RNA|AC079807.2_ENST00000439870.1_RNA|FBXO11_ENST00000316377.4_5'UTR|AC079807.2_ENST00000432064.1_RNA|FBXO11_ENST00000378314.3_5'UTR	NM_001190274.1	NP_001177203.1	Q86XK2	FBX11_HUMAN	F-box protein 11	50					cellular protein modification process (GO:0006464)|peptidyl-arginine N-methylation (GO:0035246)|protein ubiquitination (GO:0016567)|sensory perception of sound (GO:0007605)|ubiquitin-dependent protein catabolic process (GO:0006511)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	protein-arginine N-methyltransferase activity (GO:0016274)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.0?(2)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	26		Acute lymphoblastic leukemia(82;0.0299)|all_hematologic(82;0.0358)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			ctgctgctgctgcggcggcgg	0.781			"""Mis, F, D"""		DLBCL																																p.Q50P				Rec	yes		2	2p16.3	80204	F-box protein 11		L	.	.			2	Whole gene deletion(2)	haematopoietic_and_lymphoid_tissue(2)	c.A149C																																									SO:0001583	missense	80204	exon1			TGCTGCTGCGGCG	AF174599	CCDS1837.1, CCDS54357.1	2p16.3	2014-01-29	2008-06-23	2008-06-23	ENSG00000138081	ENSG00000138081		"""Ubiquitin protein ligase E3 component n-recognins"", ""F-boxes /  ""other"""""	13590	protein-coding gene	gene with protein product	"""ubiquitin protein ligase E3 component n-recognin 6"""	607871	"""F-box only protein 11"""			10531035, 16487488, 18162545	Standard	NM_025133		Approved	FBX11, UBR6	uc002rwe.3	Q86XK2	OTTHUMG00000129130	ENST00000403359.3:c.149A>C	2.37:g.48132711T>G	ENSP00000384823:p.Gln50Pro		Somatic	8	0	0		WXS	Illumina HiSeq	Phase_I	8	0.38	3	NM_001190274	1	0.00	0	A1L491|Q52ZP1|Q53EP7|Q53RT5|Q8IXG3|Q96E90|Q9H6V8|Q9H9L1|Q9NR14|Q9UFK1|Q9UHI1|Q9UKC2	Missense_Mutation	SNP	ENST00000403359.3	37	CCDS54357.1	.	.	.	.	.	.	.	.	.	.	T	9.804	1.181361	0.21787	.	.	ENSG00000138081	ENST00000403359	T	0.41065	1.01	2.69	2.69	0.31865	.	.	.	.	.	T	0.27241	0.0668	N	0.08118	0	0.80722	D	1	.	.	.	.	.	.	T	0.12502	-1.0545	7	0.59425	D	0.04	.	8.1694	0.31245	0.0:0.0:0.0:1.0	.	.	.	.	P	50	ENSP00000384823:Q50P	ENSP00000384823:Q50P	Q	-	2	0	FBXO11	47986215	0.998000	0.40836	0.996000	0.52242	0.829000	0.46940	-0.048000	0.11944	1.078000	0.41014	0.402000	0.26972	CAG			0.781	FBXO11-001	KNOWN	basic|CCDS	protein_coding	protein_coding		OTTHUMT00000251181.3		NM_012167, NM_018693, NM_025133	
ALS2CR12	130540	mdanderson.org	37	2	202195505	202195505	+	Nonsense_Mutation	SNP	G	G	T			TCGA-WZ-A8D5-01A-11D-A435-10	TCGA-WZ-A8D5-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f9769d8-ba26-4ac7-91c7-7ae0494130e7	928cb9ff-09c7-4a5f-bd42-198e31335976	g.chr2:202195505G>T	ENST00000286190.5	-	7	622	c.576C>A	c.(574-576)taC>taA	p.Y192*	ALS2CR12_ENST00000405148.2_Nonsense_Mutation_p.Y192*|ALS2CR12_ENST00000448967.1_Intron|ALS2CR12_ENST00000439709.1_Nonsense_Mutation_p.Y192*|ALS2CR12_ENST00000392257.3_Nonsense_Mutation_p.Y192*			Q96Q35	AL2SB_HUMAN	amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 12	192					regulation of GTPase activity (GO:0043087)	outer dense fiber (GO:0001520)|sperm fibrous sheath (GO:0035686)|sperm flagellum (GO:0036126)				NS(1)|breast(5)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(6)|ovary(2)	21						AGGCTGCTTTGTAGTTGTTCT	0.517																																					p.Y192X													.	.			0			c.C576A												103.0	91.0	95.0					2																	202195505		2203	4300	6503	SO:0001587	stop_gained	130540	exon8			TGCTTTGTAGTTG	AB053314	CCDS2346.1, CCDS46488.1	2q33.1	2009-10-06			ENSG00000155749	ENSG00000155749			14439	protein-coding gene	gene with protein product							Standard	XM_006712272		Approved		uc002uya.4	Q96Q35	OTTHUMG00000132824	ENST00000286190.5:c.576C>A	2.37:g.202195505G>T	ENSP00000286190:p.Tyr192*		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	77	0.05	4	NM_139163	0		0	G5E9S3|Q53TT6|Q8N1B6	Nonsense_Mutation	SNP	ENST00000286190.5	37	CCDS2346.1	.	.	.	.	.	.	.	.	.	.	G	38	6.713106	0.97784	.	.	ENSG00000155749	ENST00000286190;ENST00000405148;ENST00000392257;ENST00000439709;ENST00000425488	.	.	.	4.19	2.37	0.29283	.	0.164448	0.29119	N	0.013090	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-4.4527	5.8134	0.18479	0.2345:0.0:0.7655:0.0	.	.	.	.	X	192;192;192;192;78	.	ENSP00000286190:Y192X	Y	-	3	2	ALS2CR12	201903750	1.000000	0.71417	0.990000	0.47175	0.768000	0.43524	0.864000	0.27926	1.127000	0.42034	0.561000	0.74099	TAC			0.517	ALS2CR12-001	KNOWN	basic|CCDS	protein_coding	protein_coding		OTTHUMT00000256286.1		NM_139163	
SPTLC3	55304	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca;mdanderson.org	37	20	13107267	13107267	+	Silent	SNP	G	G	T			TCGA-WZ-A8D5-01A-11D-A435-10	TCGA-WZ-A8D5-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f9769d8-ba26-4ac7-91c7-7ae0494130e7	928cb9ff-09c7-4a5f-bd42-198e31335976	g.chr20:13107267G>T	ENST00000399002.2	+	9	1456	c.1182G>T	c.(1180-1182)tcG>tcT	p.S394S	SPTLC3_ENST00000378194.4_Missense_Mutation_p.R321L	NM_018327.2	NP_060797.2	Q9NUV7	SPTC3_HUMAN	serine palmitoyltransferase, long chain base subunit 3	394					small molecule metabolic process (GO:0044281)|sphingoid biosynthetic process (GO:0046520)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|serine C-palmitoyltransferase complex (GO:0017059)	pyridoxal phosphate binding (GO:0030170)|serine C-palmitoyltransferase activity (GO:0004758)			breast(1)|endometrium(1)|large_intestine(7)|lung(14)|skin(1)|urinary_tract(1)	25						GGGTTCACTCGCATAGTGCTG	0.433																																					p.S394S													.	.			0			c.G1182T												275.0	254.0	260.0					20																	13107267		1913	4126	6039	SO:0001819	synonymous_variant	55304	exon9			TCACTCGCATAGT	AL109983	CCDS13115.2	20p12.1	2011-07-05	2006-12-21	2006-12-21	ENSG00000172296	ENSG00000172296	2.3.1.50		16253	protein-coding gene	gene with protein product		611120	"""chromosome 20 open reading frame 38"", ""serine palmitoyltransferase, long chain base subunit 2-like (aminotransferase 2)"""	C20orf38, SPTLC2L		17023427	Standard	NM_018327		Approved	LCB2B, FLJ11112, hLCB2b	uc002wod.1	Q9NUV7	OTTHUMG00000031899	ENST00000399002.2:c.1182G>T	20.37:g.13107267G>T			Somatic	124	0	0		WXS	Illumina HiSeq	.	106	0.05	5	NM_018327	1	0.00	0	A2A2I4|B9EK64|Q05DQ8|Q5T1U4|Q9H1L1|Q9H1Z0	Silent	SNP	ENST00000399002.2	37	CCDS13115.2	.	.	.	.	.	.	.	.	.	.	G	11.16	1.556102	0.27827	.	.	ENSG00000172296	ENST00000378194	D	0.95447	-3.71	6.17	-5.36	0.02689	.	.	.	.	.	D	0.91050	0.7184	.	.	.	0.09310	N	0.999999	.	.	.	.	.	.	D	0.83931	0.0306	6	0.72032	D	0.01	-12.236	1.7116	0.02893	0.2779:0.1784:0.3539:0.1898	.	.	.	.	L	321	ENSP00000367436:R321L	ENSP00000367436:R321L	R	+	2	0	SPTLC3	13055267	0.007000	0.16637	0.955000	0.39395	0.575000	0.36095	-1.139000	0.03213	-0.594000	0.05836	-0.781000	0.03364	CGC			0.433	SPTLC3-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000254544.1		NM_018327	
FRG1B	284802	mdanderson.org	37	20	29633902	29633902	+	Missense_Mutation	SNP	C	C	A	rs145072022		TCGA-WZ-A8D5-01A-11D-A435-10	TCGA-WZ-A8D5-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f9769d8-ba26-4ac7-91c7-7ae0494130e7	928cb9ff-09c7-4a5f-bd42-198e31335976	g.chr20:29633902C>A	ENST00000278882.3	+	9	921	c.541C>A	c.(541-543)Cca>Aca	p.P181T	FRG1B_ENST00000358464.4_Missense_Mutation_p.P181T			Q9BZ01	FRG1B_HUMAN	FSHD region gene 1 family, member B	181								p.P181T(2)		endometrium(10)|kidney(21)|lung(3)|pancreas(1)|prostate(9)|urinary_tract(9)	53						AACAAGAGAACCAAATTGAAA	0.274																																					.													.	.			2	Substitution - Missense(2)	endometrium(2)	.																																									SO:0001583	missense	284802	.			AGAGAACCAAATT			20q11.1	2013-03-18	2007-10-11	2007-10-11	ENSG00000149531	ENSG00000149531			15792	other	unknown			"""chromosome 20 open reading frame 80"""	C20orf80			Standard	NR_003579		Approved	bA348I14.2	uc010ztl.1	Q9BZ01	OTTHUMG00000032157	ENST00000278882.3:c.541C>A	20.37:g.29633902C>A	ENSP00000278882:p.Pro181Thr		Somatic	190	0.0052631579	1		WXS	Illumina HiSeq	Phase_I	173	0.05	8	.	47	0.02	1	C4AME5	RNA	SNP	ENST00000278882.3	37		.	.	.	.	.	.	.	.	.	.	c	4.973	0.180670	0.09443	.	.	ENSG00000149531	ENST00000278882;ENST00000358464	.	.	.	1.62	1.62	0.23740	.	.	.	.	.	T	0.42063	0.1186	.	.	.	0.20074	N	0.999938	.	.	.	.	.	.	T	0.34527	-0.9825	5	0.52906	T	0.07	.	9.2539	0.37571	0.0:1.0:0.0:0.0	.	.	.	.	T	181	.	ENSP00000278882:P181T	P	+	1	0	FRG1B	28247563	1.000000	0.71417	1.000000	0.80357	0.811000	0.45836	3.567000	0.53813	1.206000	0.43276	0.502000	0.49764	CCA			0.274	FRG1B-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal	protein_coding	protein_coding		OTTHUMT00000078494.2		NR_003579	
TOX2	84969	hgsc.bcm.edu	37	20	42694570	42694570	+	Silent	SNP	A	A	G			TCGA-WZ-A8D5-01A-11D-A435-10	TCGA-WZ-A8D5-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f9769d8-ba26-4ac7-91c7-7ae0494130e7	928cb9ff-09c7-4a5f-bd42-198e31335976	g.chr20:42694570A>G	ENST00000358131.5	+	6	1333	c.1125A>G	c.(1123-1125)ccA>ccG	p.P375P	TOX2_ENST00000435864.2_3'UTR|TOX2_ENST00000423191.2_Silent_p.P351P|TOX2_ENST00000341197.4_Silent_p.P393P|TOX2_ENST00000372999.1_Silent_p.P351P	NM_001098798.1	NP_001092268.1	Q96NM4	TOX2_HUMAN	TOX high mobility group box family member 2	375	Pro-rich.				female gonad development (GO:0008585)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to gonadotropin (GO:0034698)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(13)|ovary(1)|skin(2)	26		Myeloproliferative disorder(115;0.00452)	COAD - Colon adenocarcinoma(18;0.00189)			CGCCGCCGCCACCCTCCTTCC	0.716																																					p.P393P													TOX2_ENST00000348077,colon,carcinoma,0,2	TOX2_ENST00000348077	0	2	0			c.A1179G												29.0	31.0	30.0					20																	42694570		2199	4298	6497	SO:0001819	synonymous_variant	84969	exon7			GCCGCCACCCTCC	BC007636	CCDS13324.1, CCDS42875.1, CCDS46603.1	20q13.12	2007-03-20	2007-03-20	2007-03-20					16095	protein-coding gene	gene with protein product	"""granulosa cell HMG box 1"""	611163	"""chromosome 20 open reading frame 100"""	C20orf100		14764631	Standard	NM_001098796		Approved	dJ1108D11.2, GCX-1	uc010ggo.3	Q96NM4		ENST00000358131.5:c.1125A>G	20.37:g.42694570A>G			Somatic	48	0	0		WXS	Illumina HiSeq	.	53	0.06	3	NM_001098797	18	0.11	2	A8K1J1|E1P5X0|G3XAC7|Q5TE33|Q5TE34|Q5TE35|Q96IC9|Q9BQN5	Silent	SNP	ENST00000358131.5	37	CCDS42875.1																																																																																					0.716	TOX2-001	KNOWN	basic|CCDS	protein_coding	protein_coding		OTTHUMT00000079329.2			
SNAI1	6615	mdanderson.org	37	20	48600448	48600448	+	Missense_Mutation	SNP	C	C	A			TCGA-WZ-A8D5-01A-11D-A435-10	TCGA-WZ-A8D5-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f9769d8-ba26-4ac7-91c7-7ae0494130e7	928cb9ff-09c7-4a5f-bd42-198e31335976	g.chr20:48600448C>A	ENST00000244050.2	+	2	231	c.170C>A	c.(169-171)cCa>cAa	p.P57Q		NM_005985.3	NP_005976.2	O95863	SNAI1_HUMAN	snail family zinc finger 1	57					cartilage morphogenesis (GO:0060536)|cell migration (GO:0016477)|epithelial to mesenchymal transition (GO:0001837)|hair follicle morphogenesis (GO:0031069)|left/right pattern formation (GO:0060972)|mesoderm formation (GO:0001707)|negative regulation of cell differentiation involved in embryonic placenta development (GO:0060806)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902230)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of vitamin D biosynthetic process (GO:0010957)|Notch signaling involved in heart development (GO:0061314)|osteoblast differentiation (GO:0001649)|palate development (GO:0060021)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of tight junction assembly (GO:2000810)|trophoblast giant cell differentiation (GO:0060707)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	kinase binding (GO:0019900)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(10)|ovary(2)	17			BRCA - Breast invasive adenocarcinoma(9;4.03e-06)			GCCTCGCTGCCAATGCTCATC	0.642																																					p.P57Q													.	.			0			c.C170A												51.0	54.0	53.0					20																	48600448		2203	4300	6503	SO:0001583	missense	6615	exon2			CGCTGCCAATGCT	AF125377	CCDS13423.1	20q13.2	2013-05-23	2013-05-23		ENSG00000124216	ENSG00000124216		"""Snail homologs"", ""Zinc fingers, C2H2-type"""	11128	protein-coding gene	gene with protein product		604238	"""snail 1 (drosophila homolog), zinc finger protein"", ""snail homolog 1 (Drosophila)"""			10585766	Standard	NM_005985		Approved	SNA, SLUGH2, SNAH, SNAIL1, SNAIL	uc002xuz.3	O95863	OTTHUMG00000033048	ENST00000244050.2:c.170C>A	20.37:g.48600448C>A	ENSP00000244050:p.Pro57Gln		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	44	0.07	3	NM_005985	92	0.00	0	B2R842|Q9P113|Q9UBP7|Q9UHH7	Missense_Mutation	SNP	ENST00000244050.2	37	CCDS13423.1	.	.	.	.	.	.	.	.	.	.	C	20.7	4.037882	0.75617	.	.	ENSG00000124216	ENST00000244050	T	0.25414	1.8	4.94	4.94	0.65067	.	0.204155	0.44097	D	0.000497	T	0.48624	0.1510	M	0.64997	1.995	0.50039	D	0.999847	D	0.76494	0.999	D	0.66716	0.946	T	0.48080	-0.9066	10	0.52906	T	0.07	-41.0002	18.1751	0.89759	0.0:1.0:0.0:0.0	.	57	O95863	SNAI1_HUMAN	Q	57	ENSP00000244050:P57Q	ENSP00000244050:P57Q	P	+	2	0	SNAI1	48033855	0.998000	0.40836	0.994000	0.49952	0.535000	0.34838	3.883000	0.56168	2.289000	0.77006	0.557000	0.71058	CCA			0.642	SNAI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000080350.1			
CEBPB	1051	mdanderson.org	37	20	48808332	48808332	+	Silent	SNP	G	G	T			TCGA-WZ-A8D5-01A-11D-A435-10	TCGA-WZ-A8D5-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f9769d8-ba26-4ac7-91c7-7ae0494130e7	928cb9ff-09c7-4a5f-bd42-198e31335976	g.chr20:48808332G>T	ENST00000303004.3	+	1	957	c.762G>T	c.(760-762)ccG>ccT	p.P254P		NM_005194.3	NP_005185.2	P17676	CEBPB_HUMAN	CCAAT/enhancer binding protein (C/EBP), beta	254					acute-phase response (GO:0006953)|brown fat cell differentiation (GO:0050873)|cellular response to amino acid stimulus (GO:0071230)|embryonic placenta development (GO:0001892)|immune response (GO:0006955)|inflammatory response (GO:0006954)|mammary gland epithelial cell differentiation (GO:0060644)|mammary gland epithelial cell proliferation (GO:0033598)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron differentiation (GO:0030182)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of osteoblast differentiation (GO:0045669)|regulation of interleukin-6 biosynthetic process (GO:0045408)|regulation of transcription involved in cell fate commitment (GO:0060850)|regulation of transcription, DNA-templated (GO:0006355)|response to endoplasmic reticulum stress (GO:0034976)|response to lipopolysaccharide (GO:0032496)|transcription from RNA polymerase II promoter (GO:0006366)	condensed chromosome, centromeric region (GO:0000779)|cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|lung(1)	2			BRCA - Breast invasive adenocarcinoma(9;5.72e-08)|STAD - Stomach adenocarcinoma(23;0.19)			gggccgcgccggcgcccTCGC	0.716																																					p.P254P													.	.			0			c.G762T												16.0	17.0	17.0					20																	48808332		2170	4262	6432	SO:0001819	synonymous_variant	1051	exon1			CGCGCCGGCGCCC	AY193834	CCDS13429.1	20q13.1	2013-01-10			ENSG00000172216	ENSG00000172216		"""basic leucine zipper proteins"""	1834	protein-coding gene	gene with protein product	"""liver-enriched transcriptional activator protein"", ""nuclear factor of interleukin 6"", ""interleukin 6-dependent DNA-binding protein"""	189965		TCF5		1535333, 1840554	Standard	NM_005194		Approved	LAP, CRP2, NFIL6, IL6DBP, C/EBP-beta	uc002xvi.2	P17676	OTTHUMG00000032715	ENST00000303004.3:c.762G>T	20.37:g.48808332G>T			Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	28	0.11	3	NM_005194	92	0.00	0	A8K671|Q96IH2|Q9H4Z5	Silent	SNP	ENST00000303004.3	37	CCDS13429.1																																																																																					0.716	CEBPB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000079672.1		NM_005194	
ZDHHC8	29801	mdanderson.org	37	22	20128208	20128208	+	Silent	SNP	G	G	T			TCGA-WZ-A8D5-01A-11D-A435-10	TCGA-WZ-A8D5-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f9769d8-ba26-4ac7-91c7-7ae0494130e7	928cb9ff-09c7-4a5f-bd42-198e31335976	g.chr22:20128208G>T	ENST00000334554.7	+	6	870	c.729G>T	c.(727-729)gtG>gtT	p.V243V	ZDHHC8_ENST00000468112.1_3'UTR|ZDHHC8_ENST00000320602.7_Silent_p.V151V|ZDHHC8_ENST00000405930.3_Silent_p.V243V	NM_013373.3	NP_037505.1	Q9ULC8	ZDHC8_HUMAN	zinc finger, DHHC-type containing 8	243					locomotory behavior (GO:0007626)|protein palmitoylation (GO:0018345)	cytoplasmic vesicle (GO:0031410)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	palmitoyltransferase activity (GO:0016409)|protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(3)|endometrium(1)|kidney(3)|large_intestine(1)|lung(8)|ovary(1)|prostate(1)	20	Colorectal(54;0.0993)					TGGAGCACGTGCTGTGTAGCC	0.697																																					p.V243V													.	.			0			c.G729T												35.0	31.0	33.0					22																	20128208		2200	4300	6500	SO:0001819	synonymous_variant	29801	exon6			GCACGTGCTGTGT	AB033118	CCDS13776.1, CCDS54502.1	22q11.21	2009-10-06		2003-02-28	ENSG00000099904	ENSG00000099904		"""Zinc fingers, DHHC-type"""	18474	protein-coding gene	gene with protein product		608784				10574462, 15184899	Standard	NM_013373		Approved	ZNF378, KIAA1292	uc002zrr.2	Q9ULC8	OTTHUMG00000150499	ENST00000334554.7:c.729G>T	22.37:g.20128208G>T			Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	46	0.07	3	NM_001185024	14	0.00	0	Q2TGE9|Q6ICL1|Q6ZNF5|Q7Z6L9	Silent	SNP	ENST00000334554.7	37	CCDS13776.1																																																																																					0.697	ZDHHC8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000318564.1		NM_013373	
PRAME	23532	bcgsc.ca	37	22	22901775	22901775	+	5'Flank	SNP	A	A	G			TCGA-WZ-A8D5-01A-11D-A435-10	TCGA-WZ-A8D5-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f9769d8-ba26-4ac7-91c7-7ae0494130e7	928cb9ff-09c7-4a5f-bd42-198e31335976	g.chr22:22901775A>G	ENST00000398741.1	-	0	0				PRAME_ENST00000543184.1_5'Flank|PRAME_ENST00000402697.1_5'Flank|PRAME_ENST00000398743.2_5'Flank|PRAME_ENST00000405655.3_5'Flank|PRAME_ENST00000406503.1_5'Flank|LL22NC03-63E9.3_ENST00000407120.1_Start_Codon_SNP_p.M1V	NM_206955.1	NP_996838.1	P78395	PRAME_HUMAN	preferentially expressed antigen in melanoma						apoptotic process (GO:0006915)|cell differentiation (GO:0030154)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell differentiation (GO:0045596)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)|regulation of growth (GO:0040008)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|plasma membrane (GO:0005886)	retinoic acid receptor binding (GO:0042974)			autonomic_ganglia(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(17)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	36	all_hematologic(9;0.0135)|Acute lymphoblastic leukemia(84;0.17)	all_hematologic(6;1.74e-30)|Acute lymphoblastic leukemia(6;7.75e-22)|all_lung(157;4.03e-05)		READ - Rectum adenocarcinoma(21;0.0649)		CTCTAGGGGGATGGTCAGGCT	0.617											OREG0026364	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									.	Melanoma(73;1707 1838 15168 27201)												.	.			0			.																																									SO:0001631	upstream_gene_variant	0	.			AGGGGGATGGTCA	U65011	CCDS13801.1	22q11.22	2013-01-17			ENSG00000185686	ENSG00000185686		"""-"""	9336	protein-coding gene	gene with protein product	"""cancer/testis antigen 130"""	606021		MAPE		9047241, 10591208	Standard	XM_006725402		Approved	CT130	uc002zwj.3	P78395	OTTHUMG00000151172		22.37:g.22901775A>G	Exception_encountered		Somatic	49	0.0204081633	1	759	WXS	Illumina HiSeq	Phase_1	78	0.05	4	.	0		0	B2R6Y7|O43481|Q8IXN8	Translation_Start_Site	SNP	ENST00000398741.1	37	CCDS13801.1	.	.	.	.	.	.	.	.	.	.	a	3.234	-0.156731	0.06544	.	.	ENSG00000220891	ENST00000407120	.	.	.	2.0	-2.58	0.06228	.	.	.	.	.	T	0.43787	0.1263	.	.	.	.	.	.	.	.	.	.	.	.	T	0.53464	-0.8435	4	0.87932	D	0	.	5.9144	0.19048	0.5283:0.0:0.4717:0.0	.	.	.	.	V	1	.	ENSP00000383978:M1V	M	+	1	0	LL22NC03-63E9.3	21231775	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.095000	0.11077	-0.578000	0.05959	-0.269000	0.10298	ATG			0.617	PRAME-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		OTTHUMT00000321644.1		NM_206953	
HMGXB4	10042	hgsc.bcm.edu;bcgsc.ca	37	22	35661554	35661554	+	Silent	SNP	G	G	A			TCGA-WZ-A8D5-01A-11D-A435-10	TCGA-WZ-A8D5-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f9769d8-ba26-4ac7-91c7-7ae0494130e7	928cb9ff-09c7-4a5f-bd42-198e31335976	g.chr22:35661554G>A	ENST00000216106.5	+	5	1301	c.1173G>A	c.(1171-1173)aaG>aaA	p.K391K	HMGXB4_ENST00000444518.2_Silent_p.K282K	NM_001003681.2	NP_001003681.1	Q9UGU5	HMGX4_HUMAN	HMG box domain containing 4	391					endosome to lysosome transport (GO:0008333)|negative regulation of Wnt signaling pathway (GO:0030178)|Wnt signaling pathway (GO:0016055)	NURF complex (GO:0016589)	DNA binding (GO:0003677)			breast(1)|endometrium(1)|large_intestine(6)|liver(1)|lung(4)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						Aaaaaaaaaagaaaaaagaag	0.493																																					p.K391K													.	.			0			c.G1173A												24.0	27.0	26.0					22																	35661554		2191	4290	6481	SO:0001819	synonymous_variant	10042	exon5			AAAAAAGAAAAAA	AJ010069	CCDS33641.1	22q13	2011-07-01	2009-01-05	2009-01-05	ENSG00000100281	ENSG00000100281		"""High mobility group / Non-canonical"""	5003	protein-coding gene	gene with protein product		604702	"""high-mobility group protein 2-like 1"""	HMG2L1		10329004, 10591208, 20511232	Standard	NM_001003681		Approved	THC211630	uc003anl.3	Q9UGU5	OTTHUMG00000150439	ENST00000216106.5:c.1173G>A	22.37:g.35661554G>A			Somatic	104	0	0		WXS	Illumina HiSeq	.	146	0.08	12	NM_001003681	32	0.03	1	O75672|O75673|Q9UMT5	Silent	SNP	ENST00000216106.5	37	CCDS33641.1																																																																																					0.493	HMGXB4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		OTTHUMT00000318104.2		NM_005487	
CRYBG3	131544	mdanderson.org	37	3	97662072	97662072	+	Nonsense_Mutation	SNP	G	G	T	rs200227709	byFrequency	TCGA-WZ-A8D5-01A-11D-A435-10	TCGA-WZ-A8D5-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f9769d8-ba26-4ac7-91c7-7ae0494130e7	928cb9ff-09c7-4a5f-bd42-198e31335976	g.chr3:97662072G>T	ENST00000182096.4	+	19	3047	c.2983G>T	c.(2983-2985)Gga>Tga	p.G995*	MINA_ENST00000333396.7_3'UTR|CRYBG3_ENST00000389622.2_Nonsense_Mutation_p.G202*|CRYBG3_ENST00000485253.1_3'UTR	NM_153605.3	NP_705833.3	Q68DQ2	CRBG3_HUMAN	beta-gamma crystallin domain containing 3	2943							carbohydrate binding (GO:0030246)			breast(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(10)|stomach(1)|upper_aerodigestive_tract(2)	32						TATTTTAGGAGGAAATTATTG	0.373																																					p.G2943X													.	.			0			c.G8827T												80.0	78.0	79.0					3																	97662072		1816	4071	5887	SO:0001587	stop_gained	131544	exon22			TTAGGAGGAAATT			3q11.2	2008-09-30			ENSG00000080200	ENSG00000080200			34427	protein-coding gene	gene with protein product							Standard	NM_153605		Approved	DKFZp667G2110	uc021xbn.2	Q68DQ2	OTTHUMG00000159187	ENST00000182096.4:c.2983G>T	3.37:g.97662072G>T	ENSP00000182096:p.Gly995*		Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	35	0.09	3	NM_153605	18	0.00	0	B4DLE8|F6VHI2|Q4G0V8|Q7Z4R9|Q86VD0|Q8N262|Q8N7F1|Q8NDQ8	Nonsense_Mutation	SNP	ENST00000182096.4	37		.	.	.	.	.	.	.	.	.	.	G	41	8.703098	0.98920	.	.	ENSG00000080200	ENST00000182096;ENST00000389622	.	.	.	6.05	6.05	0.98169	.	0.000000	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	20.6087	0.99469	0.0:0.0:1.0:0.0	.	.	.	.	X	995;202	.	ENSP00000182096:G995X	G	+	1	0	CRYBG3	99144762	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.836000	0.69375	2.866000	0.98385	0.650000	0.86243	GGA			0.373	CRYBG3-001	KNOWN	basic|appris_principal	protein_coding	protein_coding		OTTHUMT00000353751.1		NM_153605	
RP11-190P13.2	0	broad.mit.edu	37	3	114998900	114998900	+	lincRNA	DEL	A	A	-	rs566064368		TCGA-WZ-A8D5-01A-11D-A435-10	TCGA-WZ-A8D5-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f9769d8-ba26-4ac7-91c7-7ae0494130e7	928cb9ff-09c7-4a5f-bd42-198e31335976	g.chr3:114998900delA	ENST00000459855.1	+	0	338																											TGCTAAATTTAAAAAAAAAAA	0.363																																					.													.	.			0			.																																											0	.			AAATTTAAAAAAA																													3.37:g.114998900delA			Somatic	4	0	0		WXS	Illumina HiSeq	Phase_I	8	0.50	4	.	0		0		RNA	DEL	ENST00000459855.1	37																																																																																						0.363	RP11-190P13.2-001	KNOWN	basic	lincRNA	lincRNA		OTTHUMT00000354479.1			
MUC4	4585	hgsc.bcm.edu	37	3	195505877	195505877	+	Missense_Mutation	SNP	G	G	A			TCGA-WZ-A8D5-01A-11D-A435-10	TCGA-WZ-A8D5-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f9769d8-ba26-4ac7-91c7-7ae0494130e7	928cb9ff-09c7-4a5f-bd42-198e31335976	g.chr3:195505877G>A	ENST00000463781.3	-	2	13033	c.12574C>T	c.(12574-12576)Cct>Tct	p.P4192S	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.P4192S	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		ACAGGAAGAGGGGTGGTGTCA	0.602																																					p.P4192S													MUC4_ENST00000463781,NS,carcinoma,+1,1	MUC4_ENST00000463781	1	1	0			c.C12574T																																									SO:0001583	missense	4585	exon2			GAAGAGGGGTGGT	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.12574C>T	3.37:g.195505877G>A	ENSP00000417498:p.Pro4192Ser		Somatic	74	0.027027027	2		WXS	Illumina HiSeq	.	69	0.12	8	NM_018406	3	0.00	0	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	g	0.836	-0.743674	0.03088	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.31247	1.5;1.65	.	.	.	.	.	.	.	.	T	0.32285	0.0824	N	0.19112	0.55	0.09310	N	1	D	0.63880	0.993	D	0.67725	0.953	T	0.15521	-1.0434	7	.	.	.	.	6.6097	0.22745	2.0E-4:0.0:0.9998:0.0	.	4064	E7ESK3	.	S	4192	ENSP00000417498:P4192S;ENSP00000420243:P4192S	.	P	-	1	0	MUC4	196990656	0.000000	0.05858	0.108000	0.21378	0.041000	0.13682	-0.620000	0.05565	0.452000	0.26830	0.074000	0.15403	CCT			0.602	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding		OTTHUMT00000324081.6		NM_018406	
TRMT44	152992	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	4	8470016	8470016	+	Missense_Mutation	SNP	A	A	G			TCGA-WZ-A8D5-01A-11D-A435-10	TCGA-WZ-A8D5-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f9769d8-ba26-4ac7-91c7-7ae0494130e7	928cb9ff-09c7-4a5f-bd42-198e31335976	g.chr4:8470016A>G	ENST00000389737.4	+	9	1870	c.1870A>G	c.(1870-1872)Aag>Gag	p.K624E	TRMT44_ENST00000513449.2_Missense_Mutation_p.K383E	NM_152544.2	NP_689757.2	Q8IYL2	TRM44_HUMAN	tRNA methyltransferase 44 homolog (S. cerevisiae)	624					tRNA processing (GO:0008033)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)										GTTAGGTGGAAAGCAATTAAA	0.498																																					p.K624E													.	.			0			c.A1870G												72.0	80.0	77.0					4																	8470016		2203	4300	6503	SO:0001583	missense	152992	exon9			GGTGGAAAGCAAT	AK093044	CCDS3402.1, CCDS3402.2	4p16.1	2012-06-12	2012-06-12	2012-06-12	ENSG00000155275	ENSG00000155275			26653	protein-coding gene	gene with protein product	"""tRNA methyltransferase 44 homolog (S. cerevisiae)"""	614309	"""chromosome 4 open reading frame 23"", ""methyltransferase like 19"""	C4orf23, METTL19		21658913	Standard	NM_152544		Approved	FLJ35725, TRM44	uc003glg.2	Q8IYL2	OTTHUMG00000160935	ENST00000389737.4:c.1870A>G	4.37:g.8470016A>G	ENSP00000374387:p.Lys624Glu		Somatic	79	0	0		WXS	Illumina HiSeq	.	66	0.24	16	NM_152544	10	0.30	3	Q8NA95	Missense_Mutation	SNP	ENST00000389737.4	37	CCDS3402.2	.	.	.	.	.	.	.	.	.	.	A	1.995	-0.430946	0.04669	.	.	ENSG00000155275	ENST00000513449;ENST00000389737;ENST00000285635	T;T	0.17528	2.27;2.28	3.93	-1.61	0.08399	.	1.402540	0.04992	N	0.467469	T	0.07863	0.0197	N	0.08118	0	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.08055	0.002;0.003	T	0.35325	-0.9793	10	0.05721	T	0.95	-3.8925	10.1096	0.42555	0.5389:0.0:0.4611:0.0	.	624;383	Q8IYL2;Q8IYL2-2	TRM44_HUMAN;.	E	383;624;232	ENSP00000424643:K383E;ENSP00000374387:K624E	ENSP00000285635:K232E	K	+	1	0	METTL19	8520916	0.000000	0.05858	0.000000	0.03702	0.014000	0.08584	-0.005000	0.12855	-0.349000	0.08274	0.379000	0.24179	AAG			0.498	TRMT44-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding		OTTHUMT00000359197.2		NM_152544	
SGTB	54557	mdanderson.org	37	5	65008803	65008803	+	Silent	SNP	G	G	T			TCGA-WZ-A8D5-01A-11D-A435-10	TCGA-WZ-A8D5-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f9769d8-ba26-4ac7-91c7-7ae0494130e7	928cb9ff-09c7-4a5f-bd42-198e31335976	g.chr5:65008803G>T	ENST00000381007.4	-	3	424	c.189C>A	c.(187-189)acC>acA	p.T63T		NM_019072.2	NP_061945.1	Q96EQ0	SGTB_HUMAN	small glutamine-rich tetratricopeptide repeat (TPR)-containing, beta	63										large_intestine(3)|lung(3)|skin(3)	9		Lung NSC(167;3.24e-06)|Prostate(74;0.0138)|Ovarian(174;0.0545)|Breast(144;0.174)|Colorectal(97;0.234)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0657)|Lung(70;0.00487)		AGAAGGAACTGGTAAACATTT	0.348																																					p.T63T													SGTB,NS,meningioma,0,1	SGTB	0	1	0			c.C189A												114.0	111.0	112.0					5																	65008803		2203	4300	6503	SO:0001819	synonymous_variant	54557	exon3			GGAACTGGTAAAC	AK096321	CCDS3988.1	5q12.3	2013-01-10			ENSG00000197860	ENSG00000197860		"""Tetratricopeptide (TTC) repeat domain containing"""	23567	protein-coding gene	gene with protein product						12477932	Standard	XM_005248548		Approved	Sgt2, FLJ39002	uc003jud.3	Q96EQ0	OTTHUMG00000097801	ENST00000381007.4:c.189C>A	5.37:g.65008803G>T			Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	49	0.06	3	NM_019072	22	0.00	0		Silent	SNP	ENST00000381007.4	37	CCDS3988.1																																																																																					0.348	SGTB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000215057.2		NM_019072	
PAIP2	51247	broad.mit.edu;ucsc.edu;mdanderson.org	37	5	138700433	138700433	+	Splice_Site	SNP	G	G	A			TCGA-WZ-A8D5-01A-11D-A435-10	TCGA-WZ-A8D5-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f9769d8-ba26-4ac7-91c7-7ae0494130e7	928cb9ff-09c7-4a5f-bd42-198e31335976	g.chr5:138700433G>A	ENST00000394795.2	+	3	1309		c.e3+1		CTB-43P18.1_ENST00000503553.3_RNA|PAIP2_ENST00000511706.1_Intron|PAIP2_ENST00000265192.4_Splice_Site|PAIP2_ENST00000510080.1_Splice_Site|PAIP2_ENST00000511381.1_Splice_Site			Q9BPZ3	PAIP2_HUMAN	poly(A) binding protein interacting protein 2						memory (GO:0007613)|negative regulation of translational initiation (GO:0045947)|regulation of long-term synaptic potentiation (GO:1900271)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)	mRNA binding (GO:0003729)|translation repressor activity (GO:0030371)			kidney(1)|large_intestine(2)|lung(2)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			AGATCTTGTGGTAAAAAGTTA	0.378																																					.													.	PAIP2	10		0			c.318+1G>A												78.0	70.0	73.0					5																	138700433		2203	4300	6503	SO:0001630	splice_region_variant	51247	exon3			CTTGTGGTAAAAA	AF151052	CCDS4211.1	5q32	2008-02-05			ENSG00000120727	ENSG00000120727			17970	protein-coding gene	gene with protein product		605604				11172725, 16804161	Standard	NM_016480		Approved	PAIP2A	uc003led.3	Q9BPZ3	OTTHUMG00000129227	ENST00000394795.2:c.318+1G>A	5.37:g.138700433G>A			Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	71	0.06	4	NM_016480	36	0.25	9	B2RBI1|D3DQC6|Q49A06|Q9H0Y5|Q9P0Q8	Splice_Site	SNP	ENST00000394795.2	37	CCDS4211.1	.	.	.	.	.	.	.	.	.	.	G	23.3	4.401323	0.83120	.	.	ENSG00000120727	ENST00000265192;ENST00000394795;ENST00000510080	.	.	.	5.71	5.71	0.89125	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.4627	0.94924	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	PAIP2	138728332	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	8.172000	0.89677	2.709000	0.92574	0.655000	0.94253	.			0.378	PAIP2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000373002.1		NM_016480	Intron
DIAPH1	1729	mdanderson.org	37	5	140953766	140953766	+	Missense_Mutation	SNP	G	G	T			TCGA-WZ-A8D5-01A-11D-A435-10	TCGA-WZ-A8D5-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f9769d8-ba26-4ac7-91c7-7ae0494130e7	928cb9ff-09c7-4a5f-bd42-198e31335976	g.chr5:140953766G>T	ENST00000398557.4	-	16	1791	c.1651C>A	c.(1651-1653)Ctg>Atg	p.L551M	DIAPH1_ENST00000398562.2_Missense_Mutation_p.L542M|DIAPH1_ENST00000389057.5_Missense_Mutation_p.L542M|DIAPH1_ENST00000520569.1_Missense_Mutation_p.L497M|DIAPH1_ENST00000398566.3_Missense_Mutation_p.L542M|DIAPH1_ENST00000253811.6_Missense_Mutation_p.L551M|DIAPH1_ENST00000389054.3_Missense_Mutation_p.L551M|DIAPH1_ENST00000518047.1_Missense_Mutation_p.L542M	NM_005219.4	NP_005210.3	O60610	DIAP1_HUMAN	diaphanous-related formin 1	551					actin filament polymerization (GO:0030041)|cellular response to histamine (GO:0071420)|cytoskeleton organization (GO:0007010)|positive regulation of cell migration (GO:0030335)|protein localization to microtubule (GO:0035372)|regulation of cell shape (GO:0008360)|regulation of microtubule-based process (GO:0032886)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)|mitotic spindle (GO:0072686)|ruffle membrane (GO:0032587)	ion channel binding (GO:0044325)|poly(A) RNA binding (GO:0044822)|receptor binding (GO:0005102)			breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(12)|pancreas(1)|skin(2)|stomach(2)	23			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TCCTTTGTCAGCTTGGCAACC	0.468																																					p.L551M													.	.			0			c.C1651A												75.0	74.0	74.0					5																	140953766		1986	4171	6157	SO:0001583	missense	1729	exon16			TTGTCAGCTTGGC	BC007411		5q31	2013-05-24	2013-05-24		ENSG00000131504	ENSG00000131504			2876	protein-coding gene	gene with protein product		602121	"""diaphanous (Drosophila, homolog) 1"", ""diaphanous homolog 1 (Drosophila)"""	DFNA1		9360932, 1350680	Standard	NM_005219		Approved	hDIA1, LFHL1	uc003llb.4	O60610	OTTHUMG00000149893	ENST00000398557.4:c.1651C>A	5.37:g.140953766G>T	ENSP00000381565:p.Leu551Met		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	41	0.07	3	NM_005219	73	0.00	0	A6NF18|B7ZKW2|E9PEZ2|Q17RN4|Q59FH8|Q9UC76	Missense_Mutation	SNP	ENST00000398557.4	37	CCDS43374.1	.	.	.	.	.	.	.	.	.	.	G	17.95	3.514598	0.64522	.	.	ENSG00000131504	ENST00000389054;ENST00000520569;ENST00000398562;ENST00000389057;ENST00000398566;ENST00000398557;ENST00000253811;ENST00000518047	T;T;D;T;T;T;T;T	0.90069	1.97;1.97;-2.61;1.97;1.97;1.97;1.97;1.97	5.1	4.15	0.48705	.	0.704907	0.12205	N	0.489860	D	0.92916	0.7746	M	0.71581	2.175	0.37700	D	0.924185	D;D	0.76494	0.999;0.999	D;D	0.83275	0.996;0.996	D	0.91947	0.5568	10	0.59425	D	0.04	.	8.5976	0.33725	0.1777:0.0:0.8223:0.0	.	542;551	E9PEZ2;O60610	.;DIAP1_HUMAN	M	551;497;542;542;542;551;551;542	ENSP00000373706:L551M;ENSP00000429282:L497M;ENSP00000381570:L542M;ENSP00000373709:L542M;ENSP00000381572:L542M;ENSP00000381565:L551M;ENSP00000253811:L551M;ENSP00000428268:L542M	ENSP00000253811:L551M	L	-	1	2	DIAPH1	140933950	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	1.913000	0.39956	2.656000	0.90262	0.579000	0.79373	CTG			0.468	DIAPH1-203	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding				NM_005219	
UBD	10537	hgsc.bcm.edu;broad.mit.edu	37	6	29524057	29524058	+	Frame_Shift_Ins	INS	-	-	T			TCGA-WZ-A8D5-01A-11D-A435-10	TCGA-WZ-A8D5-10A-01D-A438-10	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f9769d8-ba26-4ac7-91c7-7ae0494130e7	928cb9ff-09c7-4a5f-bd42-198e31335976	g.chr6:29524057_29524058insT	ENST00000377050.4	-	2	320_321	c.97_98insA	c.(97-99)atcfs	p.I33fs	GABBR1_ENST00000355973.3_3'UTR	NM_006398.3	NP_006389.2	O15205	UBD_HUMAN	ubiquitin D	33	Ubiquitin-like 1. {ECO:0000255|PROSITE- ProRule:PRU00214}.				aggresome assembly (GO:0070842)|myeloid dendritic cell differentiation (GO:0043011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|protein modification by small protein conjugation (GO:0032446)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)|response to interferon-gamma (GO:0034341)|response to organonitrogen compound (GO:0010243)|response to tumor necrosis factor (GO:0034612)|ubiquitin-dependent protein catabolic process (GO:0006511)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	proteasome binding (GO:0070628)			kidney(1)|lung(3)|skin(1)|upper_aerodigestive_tract(1)	6						ATGTTCTTTGATTTTTTTCACG	0.47																																					p.I33fs													.	UBD	13		0			c.98_99insA																																									SO:0001589	frameshift_variant	10537	exon2			TCTTTGATTTTTT	Y12653	CCDS4662.1	6p21.3	2008-04-11			ENSG00000213886	ENSG00000213886			18795	protein-coding gene	gene with protein product		606050				9368598, 8662070	Standard	NM_006398		Approved	FAT10	uc003nmo.3	O15205	OTTHUMG00000031289	ENST00000377050.4:c.98dupA	6.37:g.29524064_29524064dupT	ENSP00000366249:p.Ile33fs		Somatic	133	0	0		WXS	Illumina HiSeq	.	134	0.07	10	NM_006398	1253	0.00	0	B0UZT6|Q5STL2|Q5SUK2|Q96EC7	Frame_Shift_Ins	INS	ENST00000377050.4	37	CCDS4662.1																																																																																					0.470	UBD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000076628.3			
NCOA7	135112	broad.mit.edu;mdanderson.org	37	6	126249822	126249822	+	Nonsense_Mutation	SNP	G	G	T			TCGA-WZ-A8D5-01A-11D-A435-10	TCGA-WZ-A8D5-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f9769d8-ba26-4ac7-91c7-7ae0494130e7	928cb9ff-09c7-4a5f-bd42-198e31335976	g.chr6:126249822G>T	ENST00000368357.3	+	17	3086	c.2734G>T	c.(2734-2736)Gga>Tga	p.G912*	NCOA7_ENST00000229634.9_Nonsense_Mutation_p.G797*|NCOA7_ENST00000392477.2_Nonsense_Mutation_p.G912*	NM_001199619.1|NM_001199620.1	NP_001186548.1|NP_001186549.1	Q8NI08	NCOA7_HUMAN	nuclear receptor coactivator 7	912	TLD.				positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	intracellular (GO:0005622)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)			NS(1)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(6)|lung(16)|ovary(1)|skin(1)|soft_tissue(1)|urinary_tract(2)	39				UCEC - Uterine corpus endometrioid carcinoma (4;0.0803)|GBM - Glioblastoma multiforme(226;0.0193)|all cancers(137;0.237)		TTTATACCACGGACGAAGCAA	0.358																																					p.G912X													.	NCOA7	92		0			c.G2734T												116.0	121.0	120.0					6																	126249822		2203	4300	6503	SO:0001587	stop_gained	135112	exon17			TACCACGGACGAA	AJ420542	CCDS5132.1, CCDS56448.1	6q22.33	2013-03-14			ENSG00000111912	ENSG00000111912			21081	protein-coding gene	gene with protein product	"""TBC/LysM-associated domain containing 4"""	609752				11971969	Standard	NM_001199619		Approved	ERAP140, dJ187J11.3, TLDC4	uc003qai.3	Q8NI08	OTTHUMG00000015513	ENST00000368357.3:c.2734G>T	6.37:g.126249822G>T	ENSP00000357341:p.Gly912*		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	61	0.05	3	NM_001199619	33	0.00	0	B2RNS2|B7Z2C4|B9EH71|G8JL91|Q3LID6|Q4G0V1|Q5TF95|Q6IPQ4|Q6NE83|Q86T89|Q8N1W4	Nonsense_Mutation	SNP	ENST00000368357.3	37	CCDS5132.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	42|42	9.246274|9.246274	0.99113|0.99113	.|.	.|.	ENSG00000111912|ENSG00000111912	ENST00000368357;ENST00000392477;ENST00000229634|ENST00000438495	.|.	.|.	.|.	6.11|6.11	6.11|6.11	0.99139|0.99139	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	.|T	.|0.72716	.|0.3495	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.68360	.|-0.5429	.|4	0.87932|.	D|.	0|.	-20.0392|-20.0392	20.7342|20.7342	0.99715|0.99715	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|.	.|.	.|.	X|L	912;912;797|206	.|.	ENSP00000229634:G797X|.	G|R	+|+	1|2	0|0	NCOA7|NCOA7	126291515|126291515	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.961000|0.961000	0.63080|0.63080	9.869000|9.869000	0.99810|0.99810	2.906000|2.906000	0.99361|0.99361	0.655000|0.655000	0.94253|0.94253	GGA|CGG			0.358	NCOA7-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		OTTHUMT00000042083.4		XM_059748	
RP3-470B24.5	0	broad.mit.edu	37	6	168376821	168376821	+	lincRNA	SNP	T	T	C			TCGA-WZ-A8D5-01A-11D-A435-10	TCGA-WZ-A8D5-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f9769d8-ba26-4ac7-91c7-7ae0494130e7	928cb9ff-09c7-4a5f-bd42-198e31335976	g.chr6:168376821T>C	ENST00000538528.1	-	0	798																											TGGGGGTCACTCCCCCTGCAG	0.602																																					p.E171G													.	.			0			c.A512G												30.0	30.0	30.0					6																	168376821		692	1591	2283			0	exon1			GGTCACTCCCCCT																													6.37:g.168376821T>C			Somatic	222	0.0045045045	1		WXS	Illumina HiSeq	Phase_I	190	0.02	3	NM_001129895	48	0.00	0		RNA	SNP	ENST00000538528.1	37																																																																																						0.602	RP3-470B24.5-201	KNOWN	basic	lincRNA	lincRNA					
SKAP2	8935	hgsc.bcm.edu;mdanderson.org	37	7	26883702	26883702	+	Missense_Mutation	SNP	G	G	T			TCGA-WZ-A8D5-01A-11D-A435-10	TCGA-WZ-A8D5-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f9769d8-ba26-4ac7-91c7-7ae0494130e7	928cb9ff-09c7-4a5f-bd42-198e31335976	g.chr7:26883702G>T	ENST00000345317.2	-	4	567	c.254C>A	c.(253-255)aCt>aAt	p.T85N	SKAP2_ENST00000539623.1_5'UTR	NM_003930.3	NP_003921.2	O75563	SKAP2_HUMAN	src kinase associated phosphoprotein 2	85					B cell activation (GO:0042113)|negative regulation of cell proliferation (GO:0008285)|positive regulation of signal transduction (GO:0009967)|protein complex assembly (GO:0006461)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	SH3/SH2 adaptor activity (GO:0005070)			haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(7)|ovary(1)|pancreas(1)|skin(3)	17						TAATGAAATAGTGTCTGGAGG	0.403																																					p.T85N													.	.			0			c.C254A												178.0	178.0	178.0					7																	26883702		2203	4300	6503	SO:0001583	missense	8935	exon4			GAAATAGTGTCTG		CCDS5400.1	7p15.2	2013-01-10	2006-09-28	2006-09-28	ENSG00000005020	ENSG00000005020		"""Pleckstrin homology (PH) domain containing"""	15687	protein-coding gene	gene with protein product		605215	"""src family associated phosphoprotein 2"""	SCAP2		9837776, 9755858	Standard	NM_003930		Approved	RA70, SKAP-HOM, SKAP55R, SAPS	uc003syc.3	O75563	OTTHUMG00000023495	ENST00000345317.2:c.254C>A	7.37:g.26883702G>T	ENSP00000005587:p.Thr85Asn		Somatic	54	0	0		WXS	Illumina HiSeq	.	76	0.05	4	NM_003930	21	0.00	0	A4D173|Q53GP6|Q75MK6|Q75MZ4|Q9UBZ3|Q9UED8	Missense_Mutation	SNP	ENST00000345317.2	37	CCDS5400.1	.	.	.	.	.	.	.	.	.	.	G	8.639	0.895627	0.17686	.	.	ENSG00000005020	ENST00000345317;ENST00000535331;ENST00000432747	T;T	0.12879	2.64;2.64	5.57	3.64	0.41730	.	0.171766	0.51477	D	0.000085	T	0.06325	0.0163	N	0.08118	0	0.19575	N	0.999964	B;B	0.10296	0.003;0.002	B;B	0.08055	0.003;0.002	T	0.38222	-0.9671	10	0.15952	T	0.53	-16.6212	9.9099	0.41399	0.0:0.1279:0.535:0.3372	.	70;85	B7Z5N4;O75563	.;SKAP2_HUMAN	N	85;70;70	ENSP00000005587:T85N;ENSP00000408163:T70N	ENSP00000005587:T85N	T	-	2	0	SKAP2	26850227	0.531000	0.26338	0.823000	0.32752	0.947000	0.59692	0.641000	0.24720	1.337000	0.45525	0.585000	0.79938	ACT			0.403	SKAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000214128.1			
RABGEF1	27342	mdanderson.org	37	7	66273943	66273943	+	Missense_Mutation	SNP	G	G	T			TCGA-WZ-A8D5-01A-11D-A435-10	TCGA-WZ-A8D5-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f9769d8-ba26-4ac7-91c7-7ae0494130e7	928cb9ff-09c7-4a5f-bd42-198e31335976	g.chr7:66273943G>T	ENST00000284957.5	+	9	1225	c.1148G>T	c.(1147-1149)cGc>cTc	p.R383L	RABGEF1_ENST00000437078.2_Missense_Mutation_p.R397L|RABGEF1_ENST00000450873.2_Missense_Mutation_p.R383L|RABGEF1_ENST00000439720.2_Missense_Mutation_p.R396L|KCTD7_ENST00000451741.2_Missense_Mutation_p.R383L|RABGEF1_ENST00000484547.2_3'UTR|GTF2IRD1P1_ENST00000457166.1_RNA|KCTD7_ENST00000380828.2_Missense_Mutation_p.R423L|KCTD7_ENST00000510829.2_Missense_Mutation_p.R383L			Q9UJ41	RABX5_HUMAN	RAB guanine nucleotide exchange factor (GEF) 1	600					endocytosis (GO:0006897)|positive regulation of Rab GTPase activity (GO:0032851)|protein targeting to membrane (GO:0006612)	early endosome (GO:0005769)	DNA binding (GO:0003677)|Rab GTPase binding (GO:0017137)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)|zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(5)|lung(9)|ovary(1)|stomach(1)	27						GATTTTGATCGCTACATGTCT	0.463																																					p.R383L													RABGEF1,colon,carcinoma,+1,2	RABGEF1	1	2	0			c.G1148T												96.0	91.0	93.0					7																	66273943		2203	4300	6503	SO:0001583	missense	27342	exon9			TTGATCGCTACAT	AJ250042	CCDS5535.1, CCDS69308.1, CCDS75610.1	7q11.21	2010-07-09			ENSG00000154710	ENSG00000154710			17676	protein-coding gene	gene with protein product		609700				12505986, 11098082	Standard	NM_014504		Approved	rabex-5, RABEX5	uc003tvh.3	Q9UJ41	OTTHUMG00000129547	ENST00000284957.5:c.1148G>T	7.37:g.66273943G>T	ENSP00000284957:p.Arg383Leu		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	95	0.05	5	NM_014504	94	0.00	0	B4DZM7|Q3HKR2|Q3HKR3|Q53FG0	Missense_Mutation	SNP	ENST00000284957.5	37	CCDS5535.1	.	.	.	.	.	.	.	.	.	.	G	17.39	3.377489	0.61735	.	.	ENSG00000243335;ENSG00000243335;ENSG00000243335;ENSG00000243335;ENSG00000243335;ENSG00000154710;ENSG00000154710;ENSG00000154710;ENSG00000154710	ENST00000380827;ENST00000380828;ENST00000510829;ENST00000451741;ENST00000539561;ENST00000284957;ENST00000450873;ENST00000439720;ENST00000437078	T;T;T;T;T;T;T	0.32023	1.47;1.47;1.47;1.47;1.47;1.47;1.47	5.87	5.87	0.94306	Vacuolar sorting protein 9, subgroup (1);	0.047593	0.85682	D	0.000000	T	0.36690	0.0976	M	0.61703	1.905	0.80722	D	1	B;B;B	0.30664	0.032;0.027;0.289	B;B;B	0.28465	0.007;0.008;0.09	T	0.15263	-1.0443	10	0.66056	D	0.02	-8.0344	19.5705	0.95413	0.0:0.0:1.0:0.0	.	397;217;600	B4DZM7;B3KMF1;Q9UJ41	.;.;RABX5_HUMAN	L	467;423;383;383;299;383;383;396;397	ENSP00000370208:R423L;ENSP00000421124:R383L;ENSP00000398177:R383L;ENSP00000284957:R383L;ENSP00000415815:R383L;ENSP00000403429:R396L;ENSP00000390480:R397L	ENSP00000370207:R467L	R	+	2	0	RABGEF1;KCTD7	65911378	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	5.324000	0.65863	2.941000	0.99782	0.655000	0.94253	CGC			0.463	RABGEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000251737.3		NM_014504	
RP1L1	94137	ucsc.edu	37	8	10474009	10474009	+	Missense_Mutation	SNP	G	G	A			TCGA-WZ-A8D5-01A-11D-A435-10	TCGA-WZ-A8D5-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f9769d8-ba26-4ac7-91c7-7ae0494130e7	928cb9ff-09c7-4a5f-bd42-198e31335976	g.chr8:10474009G>A	ENST00000382483.3	-	3	921	c.698C>T	c.(697-699)gCc>gTc	p.A233V		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	233					cell projection organization (GO:0030030)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|visual perception (GO:0007601)	axoneme (GO:0005930)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|photoreceptor connecting cilium (GO:0032391)|photoreceptor outer segment (GO:0001750)				breast(5)|central_nervous_system(2)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(16)|lung(82)|ovary(8)|prostate(5)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(3)	148				COAD - Colon adenocarcinoma(149;0.0811)		GCTTCTCCTGGCATTTTTCAT	0.552																																					p.A233V													.	RP1L1	453		0			c.C698T												66.0	69.0	68.0					8																	10474009		1912	4135	6047	SO:0001583	missense	94137	exon3			CTCCTGGCATTTT	AY168346	CCDS43708.1	8p23.1	2011-12-06			ENSG00000183638	ENSG00000183638			15946	protein-coding gene	gene with protein product		608581				12634863	Standard	NM_178857		Approved	DCDC4B	uc003wtc.3	Q8IWN7	OTTHUMG00000163806	ENST00000382483.3:c.698C>T	8.37:g.10474009G>A	ENSP00000371923:p.Ala233Val		Somatic	42	0	0		WXS	Illumina HiSeq		43	0.09	4	NM_178857	0		0	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	Missense_Mutation	SNP	ENST00000382483.3	37	CCDS43708.1	.	.	.	.	.	.	.	.	.	.	G	1.291	-0.607710	0.03717	.	.	ENSG00000183638	ENST00000382483	D	0.86694	-2.16	4.42	0.137	0.14787	.	1.094750	0.07255	N	0.866483	T	0.71247	0.3317	N	0.19112	0.55	0.09310	N	1	B	0.26744	0.158	B	0.20767	0.031	T	0.54794	-0.8240	10	0.14656	T	0.56	-1.5712	0.5062	0.00588	0.3415:0.1761:0.3032:0.1792	.	233	A6NKC6	.	V	233	ENSP00000371923:A233V	ENSP00000371923:A233V	A	-	2	0	RP1L1	10511419	0.000000	0.05858	0.000000	0.03702	0.015000	0.08874	0.495000	0.22483	-0.172000	0.10779	0.462000	0.41574	GCC			0.552	RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000375673.1			
HR	55806	mdanderson.org	37	8	21981246	21981246	+	Missense_Mutation	SNP	G	G	T			TCGA-WZ-A8D5-01A-11D-A435-10	TCGA-WZ-A8D5-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f9769d8-ba26-4ac7-91c7-7ae0494130e7	928cb9ff-09c7-4a5f-bd42-198e31335976	g.chr8:21981246G>T	ENST00000381418.4	-	6	3311	c.1831C>A	c.(1831-1833)Cac>Aac	p.H611N	HR_ENST00000312841.8_Missense_Mutation_p.H611N	NM_005144.4	NP_005135.2	O43593	HAIR_HUMAN	hair growth associated	611					negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nuclear body (GO:0016604)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|oxidoreductase activity (GO:0016491)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(12)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	27		Breast(100;0.000162)|Acute lymphoblastic leukemia(644;0.0775)|Prostate(55;0.116)		KIRC - Kidney renal clear cell carcinoma(542;1.19e-05)|BRCA - Breast invasive adenocarcinoma(99;3.56e-05)|Colorectal(74;0.00191)|COAD - Colon adenocarcinoma(73;0.0615)|READ - Rectum adenocarcinoma(644;0.1)		CATCGCCAGTGGGTGTTGAAG	0.662																																					p.H611N													.	.			0			c.C1831A												50.0	31.0	37.0					8																	21981246		2201	4297	6498	SO:0001583	missense	55806	exon6			GCCAGTGGGTGTT	AF039196	CCDS6022.1, CCDS6023.1	8p12	2012-12-07	2012-12-07		ENSG00000168453	ENSG00000168453			5172	protein-coding gene	gene with protein product		602302	"""hairless (mouse) homolog"", ""hairless homolog (mouse)"""	ALUNC		10051399, 9463324	Standard	NM_018411		Approved	AU	uc003xas.3	O43593	OTTHUMG00000097089	ENST00000381418.4:c.1831C>A	8.37:g.21981246G>T	ENSP00000370826:p.His611Asn		Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	22	0.14	3	NM_018411	0		0	Q6GS30|Q96H33|Q9NPE1	Missense_Mutation	SNP	ENST00000381418.4	37	CCDS6022.1	.	.	.	.	.	.	.	.	.	.	G	21.9	4.222592	0.79464	.	.	ENSG00000168453	ENST00000381418;ENST00000312841	D;T	0.81821	-1.54;-1.45	5.05	5.05	0.67936	.	0.000000	0.56097	D	0.000027	D	0.88351	0.6413	M	0.72894	2.215	0.34886	D	0.74509	D;D	0.71674	0.998;0.997	D;D	0.78314	0.991;0.98	D	0.92324	0.5868	10	0.87932	D	0	-18.8092	14.2578	0.66062	0.0:0.0:1.0:0.0	.	611;611	O43593-2;O43593	.;HAIR_HUMAN	N	611	ENSP00000370826:H611N;ENSP00000326765:H611N	ENSP00000326765:H611N	H	-	1	0	HR	22037191	1.000000	0.71417	1.000000	0.80357	0.838000	0.47535	4.999000	0.63934	2.493000	0.84123	0.313000	0.20887	CAC			0.662	HR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000214213.1			
LRRCC1	85444	broad.mit.edu	37	8	86019547	86019547	+	Missense_Mutation	SNP	C	C	T			TCGA-WZ-A8D5-01A-11D-A435-10	TCGA-WZ-A8D5-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f9769d8-ba26-4ac7-91c7-7ae0494130e7	928cb9ff-09c7-4a5f-bd42-198e31335976	g.chr8:86019547C>T	ENST00000360375.3	+	1	166	c.17C>T	c.(16-18)gCg>gTg	p.A6V	LRRCC1_ENST00000414626.2_5'Flank	NM_033402.4	NP_208325.3	Q9C099	LRCC1_HUMAN	leucine rich repeat and coiled-coil centrosomal protein 1	6					mitotic nuclear division (GO:0007067)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(3)|central_nervous_system(1)|endometrium(4)|kidney(9)|large_intestine(7)|lung(16)|skin(1)|upper_aerodigestive_tract(2)	43						gcggcggcggcggtggtggcg	0.657																																					p.A6V													LRRCC1,colon,carcinoma,0,2	LRRCC1	212	2	0			c.C17T												14.0	25.0	22.0					8																	86019547		1814	4022	5836	SO:0001583	missense	85444	exon1			CGGCGGCGGTGGT	BC030701	CCDS43750.1	8q21.2	2012-04-10	2012-04-10		ENSG00000133739	ENSG00000133739			29373	protein-coding gene	gene with protein product	"""centrosomal leucine-rich repeat and coiled-coil containing protein"", ""variable number of flagella 1 homolog (Chlamydomonas)"""		"""leucine rich repeat and coiled-coil domain containing 1"""			11214970, 18728398	Standard	NM_033402		Approved	KIAA1764, CLERC, VFL1	uc003ycw.3	Q9C099	OTTHUMG00000164784	ENST00000360375.3:c.17C>T	8.37:g.86019547C>T	ENSP00000353538:p.Ala6Val		Somatic	79	0.0253164557	2		WXS	Illumina HiSeq	Phase_I	103	0.04	4	NM_033402	4	0.00	0	B4DYX6|B5RI11|Q8N768|Q96DK7|Q96N01	Missense_Mutation	SNP	ENST00000360375.3	37	CCDS43750.1	.	.	.	.	.	.	.	.	.	.	C	11.20	1.569227	0.28003	.	.	ENSG00000133739	ENST00000360375	T	0.32272	1.46	1.53	-1.48	0.08745	.	.	.	.	.	T	0.16727	0.0402	N	0.08118	0	0.09310	N	0.999995	D	0.53312	0.959	P	0.45971	0.499	T	0.18116	-1.0347	9	0.56958	D	0.05	.	6.716	0.23304	0.3338:0.6662:0.0:0.0	.	6	Q9C099	LRCC1_HUMAN	V	6	ENSP00000353538:A6V	ENSP00000353538:A6V	A	+	2	0	LRRCC1	86206799	0.117000	0.22190	0.000000	0.03702	0.473000	0.32948	0.725000	0.25970	-0.322000	0.08615	-0.410000	0.06199	GCG			0.657	LRRCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000380267.1		NM_033402	
SYBU	55638	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	8	110587804	110587804	+	Silent	SNP	C	C	T			TCGA-WZ-A8D5-01A-11D-A435-10	TCGA-WZ-A8D5-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f9769d8-ba26-4ac7-91c7-7ae0494130e7	928cb9ff-09c7-4a5f-bd42-198e31335976	g.chr8:110587804C>T	ENST00000422135.1	-	8	1838	c.1323G>A	c.(1321-1323)ttG>ttA	p.L441L	SYBU_ENST00000529690.1_Silent_p.L311L|SYBU_ENST00000527707.1_5'Flank|SYBU_ENST00000424158.2_Silent_p.L446L|SYBU_ENST00000533895.1_Silent_p.L440L|SYBU_ENST00000532779.1_Silent_p.L373L|SYBU_ENST00000533065.1_Silent_p.L322L|SYBU_ENST00000419099.1_Silent_p.L440L|SYBU_ENST00000446070.2_Silent_p.L440L|SYBU_ENST00000533171.1_Silent_p.L441L|SYBU_ENST00000529175.1_Silent_p.L235L|SYBU_ENST00000440310.1_Silent_p.L441L|SYBU_ENST00000528331.1_Silent_p.L322L|SYBU_ENST00000276646.9_Silent_p.L441L|SYBU_ENST00000528647.1_Silent_p.L440L|SYBU_ENST00000399066.3_Silent_p.L438L|SYBU_ENST00000433638.1_Silent_p.L441L|SYBU_ENST00000408908.2_Silent_p.L441L|SYBU_ENST00000408889.3_Silent_p.L322L	NM_001099744.1	NP_001093214.1	Q9NX95	SYBU_HUMAN	syntabulin (syntaxin-interacting)	441					regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)	cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|dense body (GO:0097433)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				NS(1)|breast(4)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(13)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(1)	30						TCTCATCGAACAAATCTGTGC	0.547																																					p.L441L													.	.			0			c.G1323A												149.0	151.0	150.0					8																	110587804		2066	4212	6278	SO:0001819	synonymous_variant	55638	exon8			ATCGAACAAATCT	AB040905	CCDS43763.1, CCDS43764.1, CCDS47912.1, CCDS55271.1	8q23.2	2010-08-27				ENSG00000147642			26011	protein-coding gene	gene with protein product	"""syntaphilin-like"""	611568				17611281, 16750881, 16157705, 15656992, 15459722	Standard	NM_001099743		Approved	FLJ20366, GOLSYN, KIAA1472, OCSYN, SNPHL	uc003ynj.4	Q9NX95		ENST00000422135.1:c.1323G>A	8.37:g.110587804C>T			Somatic	133	0	0		WXS	Illumina HiSeq	.	153	0.16	24	NM_001099752	1	0.00	0	A8K354|B3KQX3|B3KU61|Q5R1T1|Q5R1T2|Q5R1T3|Q5Y2M6|Q8ND49|Q8TCR6|Q96D80|Q9P256	Silent	SNP	ENST00000422135.1	37	CCDS47912.1																																																																																					0.547	SYBU-204	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		OTTHUMT00000385501.1		NM_017786	
MT-ND4	4538	broad.mit.edu;bcgsc.ca	37	M	11356	11356	+	Silent	SNP	C	C	T			TCGA-WZ-A8D5-01A-11D-A435-10	TCGA-WZ-A8D5-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f9769d8-ba26-4ac7-91c7-7ae0494130e7	928cb9ff-09c7-4a5f-bd42-198e31335976	g.chrM:11356C>T	ENST00000361381.2	+	1	597	c.597C>T	c.(595-597)taC>taT	p.Y199Y	MT-TG_ENST00000387429.1_RNA|MT-TR_ENST00000387439.1_RNA|MT-TS2_ENST00000387449.1_RNA|MT-TH_ENST00000387441.1_RNA|MT-TL2_ENST00000387456.1_RNA|MT-TK_ENST00000387421.1_RNA|MT-ND5_ENST00000361567.2_5'Flank			P03905	NU4M_HUMAN	mitochondrially encoded NADH dehydrogenase 4	199					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|prostate(1)	13						TGACTAGCTTACACAATAGCT	0.438																																					p.Y199Y													.	.			0			c.C597T																																									SO:0001819	synonymous_variant	4538	exon1			AGCTTACACAATA			mitochondria	2014-02-03	2005-02-15	2005-02-16	ENSG00000198886	ENSG00000198886	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7459	protein-coding gene	gene with protein product	"""complex I ND4 subunit"", ""NADH-ubiquinone oxidoreductase chain 4"""	516003	"""NADH dehydrogenase 4"", ""Leber optic neuropathy"""	MTND4, LHON		8103501	Standard			Approved	ND4, NAD4		P03905		ENST00000361381.2:c.597C>T	M.37:g.11356C>T			Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	19	0.26	5	ENST00000361381	0		0	Q6RL39|Q6RQN9|Q8HNR8	Missense_Mutation	SNP	ENST00000361381.2	37																																																																																						0.438	MT-ND4-201	KNOWN	basic|appris_principal	protein_coding	protein_coding				YP_003024035	
SPIN2B	474343	broad.mit.edu	37	X	57146615	57146615	+	Missense_Mutation	SNP	T	T	C			TCGA-WZ-A8D5-01A-11D-A435-10	TCGA-WZ-A8D5-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f9769d8-ba26-4ac7-91c7-7ae0494130e7	928cb9ff-09c7-4a5f-bd42-198e31335976	g.chrX:57146615T>C	ENST00000333933.3	-	2	758	c.448A>G	c.(448-450)Atg>Gtg	p.M150V	RP3-323P24.3_ENST00000439622.1_RNA|SPIN2B_ENST00000460948.1_Intron|SPIN2B_ENST00000374910.3_Intron|SPIN2B_ENST00000374912.5_Missense_Mutation_p.M150V|SPIN2B_ENST00000275988.5_Missense_Mutation_p.M150V	NM_001006681.1	NP_001006682.1	Q9BPZ2	SPI2B_HUMAN	spindlin family, member 2B	150					apoptotic process (GO:0006915)|cell cycle (GO:0007049)|gamete generation (GO:0007276)|regulation of cell cycle (GO:0051726)	nucleus (GO:0005634)				endometrium(3)|large_intestine(1)|skin(1)	5						GCTAAGACCATCCCCCTCCAT	0.408																																					p.M150V													.	SPIN2B	11		0			c.A448G												89.0	80.0	83.0					X																	57146615		2200	4294	6494	SO:0001583	missense	474343	exon2			AGACCATCCCCCT	AF356353	CCDS35311.1, CCDS65274.1	Xp11.1	2014-02-12	2006-12-05		ENSG00000186787	ENSG00000186787			33147	protein-coding gene	gene with protein product		300517				12145692	Standard	XM_005262010		Approved	SPIN-2	uc004dva.3	Q9BPZ2	OTTHUMG00000021680	ENST00000333933.3:c.448A>G	X.37:g.57146615T>C	ENSP00000335008:p.Met150Val		Somatic	376	0.0026595745	1		WXS	Illumina HiSeq	Phase_I	406	0.01	6	NM_001006683	12	0.00	0	Q7Z2M0	Missense_Mutation	SNP	ENST00000333933.3	37	CCDS35311.1	.	.	.	.	.	.	.	.	.	.	t	8.506	0.865304	0.17250	.	.	ENSG00000186787	ENST00000275988;ENST00000374912;ENST00000333933;ENST00000434397	T;T;T;T	0.45276	0.9;0.9;0.9;0.9	2.37	2.37	0.29283	.	0.000000	0.85682	D	0.000000	T	0.29684	0.0741	L	0.33753	1.03	0.40170	D	0.97716	B	0.33694	0.421	B	0.37304	0.246	T	0.05852	-1.0860	10	0.23302	T	0.38	-23.7792	7.9777	0.30164	0.0:0.0:0.0:1.0	.	150	Q9BPZ2	SPI2B_HUMAN	V	150	ENSP00000275988:M150V;ENSP00000364047:M150V;ENSP00000335008:M150V;ENSP00000404314:M150V	ENSP00000275988:M150V	M	-	1	0	SPIN2B	57163340	1.000000	0.71417	0.997000	0.53966	0.667000	0.39255	6.542000	0.73869	1.215000	0.43411	0.143000	0.16000	ATG			0.408	SPIN2B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000056912.1		NM_001006681	
AMMECR1	9949	mdanderson.org	37	X	109561071	109561071	+	Missense_Mutation	SNP	C	C	A			TCGA-WZ-A8D5-01A-11D-A435-10	TCGA-WZ-A8D5-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f9769d8-ba26-4ac7-91c7-7ae0494130e7	928cb9ff-09c7-4a5f-bd42-198e31335976	g.chrX:109561071C>A	ENST00000262844.5	-	1	396	c.229G>T	c.(229-231)Ggc>Tgc	p.G77C	AMMECR1_ENST00000372057.1_5'UTR|AMMECR1_ENST00000496695.1_5'Flank|AMMECR1_ENST00000372059.2_Missense_Mutation_p.G77C	NM_015365.2	NP_056180.1	Q9Y4X0	AMMR1_HUMAN	Alport syndrome, mental retardation, midface hypoplasia and elliptocytosis chromosomal region gene 1	77	Gly/Ser-rich.									large_intestine(1)|lung(4)|ovary(1)|stomach(1)	7						CCGCCGCCGCCGCAGCCCTGG	0.726																																					p.G77C													.	.			0			c.G229T												5.0	5.0	5.0					X																	109561071		1882	3732	5614	SO:0001583	missense	9949	exon1			CGCCGCCGCAGCC	AJ007014	CCDS14551.1, CCDS35368.1, CCDS55476.1	Xq22.3	2014-06-17	2008-09-12		ENSG00000101935	ENSG00000101935			467	protein-coding gene	gene with protein product		300195				10049589, 9480748	Standard	NM_001171689		Approved		uc004eoo.3	Q9Y4X0	OTTHUMG00000022197	ENST00000262844.5:c.229G>T	X.37:g.109561071C>A	ENSP00000262844:p.Gly77Cys		Somatic	36	0.0277777778	1		WXS	Illumina HiSeq	Phase_I	50	0.08	4	NM_015365	12	0.00	0	Q5JYV9|Q6P9D8|Q8WX22|Q9UIQ8	Missense_Mutation	SNP	ENST00000262844.5	37	CCDS14551.1	.	.	.	.	.	.	.	.	.	.	c	15.32	2.799024	0.50208	.	.	ENSG00000101935	ENST00000262844;ENST00000372059	.	.	.	4.29	3.42	0.39159	.	0.000000	0.49305	D	0.000153	T	0.48205	0.1487	L	0.29908	0.895	0.80722	D	1	P;P	0.49862	0.929;0.853	P;P	0.51777	0.679;0.599	T	0.32561	-0.9902	8	.	.	.	-0.7539	10.6389	0.45582	0.0:0.898:0.0:0.102	.	77;77	Q9Y4X0-3;Q9Y4X0	.;AMER1_HUMAN	C	77	.	.	G	-	1	0	AMMECR1	109447727	1.000000	0.71417	0.999000	0.59377	0.901000	0.52897	2.031000	0.41117	0.744000	0.32741	0.271000	0.19318	GGC			0.726	AMMECR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000057907.1			
CSAG4	100130935	broad.mit.edu	37	X	151896095	151896095	+	RNA	SNP	G	G	A			TCGA-WZ-A8D5-01A-11D-A435-10	TCGA-WZ-A8D5-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f9769d8-ba26-4ac7-91c7-7ae0494130e7	928cb9ff-09c7-4a5f-bd42-198e31335976	g.chrX:151896095G>A	ENST00000361201.4	-	0	635					NR_073432.1				CSAG family, member 4 (pseudogene)											endometrium(2)|kidney(2)|lung(1)	5						TTTTCAGGTAGCCTTGAGGTT	0.493																																					.													.	CSAG4	13		0			.																																											0	.			CAGGTAGCCTTGA	BC013171		Xq28	2014-01-21	2012-04-19		ENSG00000242599	ENSG00000242599			20923	pseudogene	pseudogene			"""CSAG family, member 4"""				Standard	NR_073432		Approved				OTTHUMG00000022646		X.37:g.151896095G>A			Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	93	0.17	16	.	1	0.00	0		RNA	SNP	ENST00000361201.4	37																																																																																						0.493	CSAG4-001	KNOWN	basic	processed_transcript	pseudogene		OTTHUMT00000058758.2			
PDZD4	57595	mdanderson.org	37	X	153069641	153069641	+	Missense_Mutation	SNP	G	G	A			TCGA-WZ-A8D5-01A-11D-A435-10	TCGA-WZ-A8D5-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f9769d8-ba26-4ac7-91c7-7ae0494130e7	928cb9ff-09c7-4a5f-bd42-198e31335976	g.chrX:153069641G>A	ENST00000164640.4	-	8	1668	c.1477C>T	c.(1477-1479)Cgg>Tgg	p.R493W	PDZD4_ENST00000544474.1_Missense_Mutation_p.R384W|PDZD4_ENST00000475140.1_5'Flank|PDZD4_ENST00000393758.2_Missense_Mutation_p.R418W	NM_032512.2	NP_115901.2	Q76G19	PDZD4_HUMAN	PDZ domain containing 4	493						cytoplasm (GO:0005737)				breast(3)|cervix(1)|endometrium(5)|lung(13)|skin(1)	23	all_lung(58;3.39e-06)|all_hematologic(71;4.25e-06)|Lung NSC(58;4.7e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					ATGGCCCGCCGCAGGGGGCTC	0.716																																					p.R493W													.	.			0			c.C1477T												8.0	9.0	9.0					X																	153069641		2155	4210	6365	SO:0001583	missense	57595	exon8			CCCGCCGCAGGGG	AK091444	CCDS14732.1	Xq28	2008-02-05		2006-01-24	ENSG00000067840	ENSG00000067840			21167	protein-coding gene	gene with protein product		300634		PDZK4		10819331, 15077175	Standard	NM_032512		Approved	KIAA1444, LU1, FLJ34125, PDZRN4L	uc004fiz.1	Q76G19	OTTHUMG00000024209	ENST00000164640.4:c.1477C>T	X.37:g.153069641G>A	ENSP00000164640:p.Arg493Trp		Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	21	0.14	3	NM_032512	8	0.00	0	B3KXB1|B7ZKY3|Q8NB75|Q9BUH9|Q9P284	Missense_Mutation	SNP	ENST00000164640.4	37	CCDS14732.1	.	.	.	.	.	.	.	.	.	.	G	13.71	2.318537	0.40996	.	.	ENSG00000067840	ENST00000164640;ENST00000393758;ENST00000537633;ENST00000544474	T;T;T	0.05139	3.49;3.49;3.7	5.15	-9.54	0.00572	.	0.355002	0.17233	U	0.181857	T	0.12008	0.0292	L	0.58810	1.83	0.23043	N	0.998384	P;P;P;P;D	0.59767	0.952;0.952;0.926;0.926;0.986	P;P;B;B;P	0.53722	0.53;0.733;0.39;0.39;0.53	T	0.28138	-1.0053	10	0.72032	D	0.01	-20.7995	19.9028	0.96995	0.0:0.0:0.1801:0.8199	.	384;499;493;418;397	B7ZKY3;Q17RL8;Q76G19;D3DWW0;B3KVR9	.;.;PDZD4_HUMAN;.;.	W	493;418;397;384	ENSP00000164640:R493W;ENSP00000377355:R418W;ENSP00000442033:R384W	ENSP00000164640:R493W	R	-	1	2	PDZD4	152722835	0.055000	0.20627	0.436000	0.26797	0.260000	0.26232	-0.087000	0.11215	-1.249000	0.02500	0.436000	0.28706	CGG			0.716	PDZD4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000061013.3		NM_032512	
