#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_NTotCov_SOL	i_NVaf_SOL	i_NVarCov_SOL	i_ORegAnno_bin	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
AGBL4	84871	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	1	50163073	50163073	+	Missense_Mutation	SNP	T	T	C			TCGA-ZM-AA0D-01A-11D-A435-10	TCGA-ZM-AA0D-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	cbb77b02-9739-4272-bf41-30251840590b	7ac40e81-4d59-492f-a5cf-f3b25df9905c	g.chr1:50163073T>C	ENST00000371839.1	-	3	310	c.194A>G	c.(193-195)gAg>gGg	p.E65G	AGBL4_ENST00000497451.1_5'UTR|AGBL4_ENST00000371836.1_Missense_Mutation_p.E65G|AGBL4_ENST00000371838.1_Missense_Mutation_p.E65G	NM_032785.3	NP_116174.3	Q5VU57	CBPC6_HUMAN	ATP/GTP binding protein-like 4	65					C-terminal protein deglutamylation (GO:0035609)|protein side chain deglutamylation (GO:0035610)	cytosol (GO:0005829)	metallocarboxypeptidase activity (GO:0004181)|tubulin binding (GO:0015631)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|ovary(1)|stomach(1)	15				Colorectal(2;0.00349)|COAD - Colon adenocarcinoma(2;0.0037)		CAGATCATACTCAAACTCAGA	0.423																																					p.E65G													.	.			0			c.A194G												133.0	116.0	121.0					1																	50163073		692	1590	2282	SO:0001583	missense	84871	exon3			TCATACTCAAACT	AK027348	CCDS44137.1	1p33	2014-06-23			ENSG00000186094	ENSG00000186094			25892	protein-coding gene	gene with protein product	"""cytosolic carboxypeptidase 6"""					21074048	Standard	NM_032785		Approved	FLJ14442, CCP6	uc001cru.2	Q5VU57	OTTHUMG00000007793	ENST00000371839.1:c.194A>G	1.37:g.50163073T>C	ENSP00000360905:p.Glu65Gly		262	0	0		347	0.10	33	NM_032785	1	0.00	0	B3KT26|B4DG37	Missense_Mutation	SNP	ENST00000371839.1	37	CCDS44137.1	.	.	.	.	.	.	.	.	.	.	T	28.3	4.910585	0.92107	.	.	ENSG00000186094	ENST00000371839;ENST00000411952;ENST00000371838;ENST00000371836	T;T;T	0.34275	1.37;1.37;1.37	5.84	5.84	0.93424	.	0.104310	0.41823	D	0.000803	T	0.73575	0.3604	H	0.96720	3.87	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.994;1.0	D	0.83427	0.0036	9	.	.	.	-13.766	16.2231	0.82269	0.0:0.0:0.0:1.0	.	65;65	Q5VU57-2;Q5VU57	.;CBPC6_HUMAN	G	65;59;65;65	ENSP00000360905:E65G;ENSP00000360904:E65G;ENSP00000360902:E65G	.	E	-	2	0	AGBL4	49935660	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.412000	0.80091	2.235000	0.73313	0.377000	0.23210	GAG			0.423	AGBL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000021346.4		NM_032785	
VASH2	79805	mdanderson.org	37	1	213125107	213125107	+	Missense_Mutation	SNP	C	C	A			TCGA-ZM-AA0D-01A-11D-A435-10	TCGA-ZM-AA0D-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	cbb77b02-9739-4272-bf41-30251840590b	7ac40e81-4d59-492f-a5cf-f3b25df9905c	g.chr1:213125107C>A	ENST00000517399.1	+	1	223	c.223C>A	c.(223-225)Cct>Act	p.P75T	VASH2_ENST00000366968.4_Missense_Mutation_p.P10T|VASH2_ENST00000366965.2_Missense_Mutation_p.P75T|VASH2_ENST00000271776.4_Intron|VASH2_ENST00000366964.3_5'UTR|VASH2_ENST00000366966.2_Missense_Mutation_p.P10T|VASH2_ENST00000366967.2_Intron			Q86V25	VASH2_HUMAN	vasohibin 2	75					positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell proliferation (GO:0001938)	cytoplasm (GO:0005737)				endometrium(2)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	7				OV - Ovarian serous cystadenocarcinoma(81;0.00479)|all cancers(67;0.00844)|GBM - Glioblastoma multiforme(131;0.0496)|Epithelial(68;0.0986)		CAAGGTGCACCCTAAGGGGGG	0.637																																					p.P75T													.	.			0			c.C223A												39.0	34.0	36.0					1																	213125107		2203	4299	6502	SO:0001583	missense	79805	exon2			GTGCACCCTAAGG	AK022567	CCDS1511.1, CCDS44315.1, CCDS44316.1, CCDS73026.1	1q23	2008-02-05			ENSG00000143494	ENSG00000143494			25723	protein-coding gene	gene with protein product		610471				16528006	Standard	XR_247041		Approved	FLJ12505	uc001hjw.3	Q86V25	OTTHUMG00000036925	ENST00000517399.1:c.223C>A	1.37:g.213125107C>A	ENSP00000428324:p.Pro75Thr		57	0	0		35	0.09	3	NM_024749	0		0	B4DYZ5|Q2VT46|Q5VTE7|Q5VTE9|Q7Z6E3|Q8IZ24|Q9H9W5	Missense_Mutation	SNP	ENST00000517399.1	37	CCDS1511.1	.	.	.	.	.	.	.	.	.	.	C	32	5.162616	0.94727	.	.	ENSG00000143494	ENST00000366966;ENST00000366968;ENST00000490792;ENST00000366965;ENST00000517399	.	.	.	4.81	4.81	0.61882	.	0.000000	0.85682	D	0.000000	T	0.78259	0.4255	M	0.67397	2.05	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.998;0.998	T	0.81138	-0.1069	9	0.87932	D	0	-6.8405	17.8368	0.88700	0.0:1.0:0.0:0.0	.	75;75;75	Q86V25;Q86V25-5;Q86V25-4	VASH2_HUMAN;.;.	T	10;10;10;75;75	.	ENSP00000355932:P75T	P	+	1	0	VASH2	211191730	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	6.940000	0.75917	2.363000	0.80096	0.563000	0.77884	CCT			0.637	VASH2-013	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000381686.1		NM_024749	
GNPAT	8443	mdanderson.org	37	1	231396280	231396280	+	Missense_Mutation	SNP	G	G	T			TCGA-ZM-AA0D-01A-11D-A435-10	TCGA-ZM-AA0D-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	cbb77b02-9739-4272-bf41-30251840590b	7ac40e81-4d59-492f-a5cf-f3b25df9905c	g.chr1:231396280G>T	ENST00000366647.4	+	3	458	c.289G>T	c.(289-291)Gat>Tat	p.D97Y	GNPAT_ENST00000366646.3_Missense_Mutation_p.D36Y	NM_014236.3	NP_055051.1	O15228	GNPAT_HUMAN	glyceronephosphate O-acyltransferase	97					cellular lipid metabolic process (GO:0044255)|cerebellum morphogenesis (GO:0021587)|ether lipid biosynthetic process (GO:0008611)|glycerophospholipid biosynthetic process (GO:0046474)|membrane organization (GO:0061024)|paranodal junction assembly (GO:0030913)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid metabolic process (GO:0006644)|response to drug (GO:0042493)|response to fatty acid (GO:0070542)|response to nutrient (GO:0007584)|response to starvation (GO:0042594)|small molecule metabolic process (GO:0044281)|synapse assembly (GO:0007416)	membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	glycerone-phosphate O-acyltransferase activity (GO:0016287)|palmitoyl-CoA hydrolase activity (GO:0016290)|receptor binding (GO:0005102)			breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(9)|ovary(3)|prostate(1)|skin(1)	23	Breast(184;0.0871)	all_cancers(173;0.2)|Prostate(94;0.183)				TCAATCTGTGGATGTCCTCCG	0.408																																					p.D97Y													.	.			0			c.G289T												184.0	190.0	188.0					1																	231396280		2203	4300	6503	SO:0001583	missense	8443	exon3			TCTGTGGATGTCC	AF043937	CCDS1592.1	1q42	2008-02-05			ENSG00000116906	ENSG00000116906	2.3.1.42		4416	protein-coding gene	gene with protein product		602744				9459311, 9536089	Standard	NM_014236		Approved	DHAPAT, DAPAT, DAP-AT	uc001hup.4	O15228	OTTHUMG00000038024	ENST00000366647.4:c.289G>T	1.37:g.231396280G>T	ENSP00000355607:p.Asp97Tyr		33	0	0		42	0.07	3	NM_014236	3	0.00	0	B4DNM9|Q5TBH7|Q9BWC2	Missense_Mutation	SNP	ENST00000366647.4	37	CCDS1592.1	.	.	.	.	.	.	.	.	.	.	G	19.74	3.884231	0.72410	.	.	ENSG00000116906	ENST00000436239;ENST00000366647;ENST00000366646;ENST00000416000	D;T;T;T	0.86956	-2.19;-0.2;-0.21;-0.18	5.98	2.9	0.33743	.	0.154925	0.56097	D	0.000026	D	0.88168	0.6364	L	0.53249	1.67	0.50632	D	0.999884	D;P	0.56521	0.976;0.773	P;P	0.54706	0.759;0.664	D	0.87903	0.2692	10	0.87932	D	0	.	10.8048	0.46512	0.0664:0.2469:0.6867:0.0	.	36;97	B4DNM9;O15228	.;GNPAT_HUMAN	Y	36;97;36;97	ENSP00000402811:D36Y;ENSP00000355607:D97Y;ENSP00000355606:D36Y;ENSP00000411640:D97Y	ENSP00000355606:D36Y	D	+	1	0	GNPAT	229462903	1.000000	0.71417	0.716000	0.30569	0.828000	0.46876	7.593000	0.82686	0.836000	0.34901	0.563000	0.77884	GAT			0.408	GNPAT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		OTTHUMT00000092871.1			
PDLIM1	9124	mdanderson.org	37	10	97006973	97006973	+	Splice_Site	SNP	T	T	C			TCGA-ZM-AA0D-01A-11D-A435-10	TCGA-ZM-AA0D-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	cbb77b02-9739-4272-bf41-30251840590b	7ac40e81-4d59-492f-a5cf-f3b25df9905c	g.chr10:97006973T>C	ENST00000329399.6	-	5	792	c.684A>G	c.(682-684)aaA>aaG	p.K228K	PDLIM1_ENST00000477757.1_5'UTR	NM_020992.2	NP_066272.1	O00151	PDLI1_HUMAN	PDZ and LIM domain 1	228					regulation of transcription, DNA-templated (GO:0006355)|response to hypoxia (GO:0001666)|response to oxidative stress (GO:0006979)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)|transcription factor complex (GO:0005667)	transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(5)|lung(1)|ovary(1)|skin(2)	10		Colorectal(252;0.083)		Epithelial(162;1.64e-06)|all cancers(201;3.71e-05)		GCTGATTACCTTTTTCTTCAG	0.468											OREG0020387	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.K228K													.	.			0			c.A684G												145.0	143.0	144.0					10																	97006973		2203	4300	6503	SO:0001630	splice_region_variant	9124	exon5			ATTACCTTTTTCT	U90878	CCDS7441.1	10q23.1	2008-07-29	2008-07-29		ENSG00000107438	ENSG00000107438			2067	protein-coding gene	gene with protein product	"""carboxyl terminal LIM domain protein 1"", ""elfin"""	605900	"""PDZ and LIM domain 1 (elfin)"""	CLIM1		10861853	Standard	NM_020992		Approved	CLP-36, hCLIM1, CLP36	uc001kkh.4	O00151	OTTHUMG00000018810	ENST00000329399.6:c.685+1A>G	10.37:g.97006973T>C			59	0	0	1325	42	0.07	3	NM_020992	172	0.00	0	B2RBS6|Q5VZH5|Q9BPZ9	Silent	SNP	ENST00000329399.6	37	CCDS7441.1																																																																																					0.468	PDLIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000049508.1			Silent
SFXN2	118980	mdanderson.org	37	10	104503811	104503811	+	IGR	SNP	A	A	G			TCGA-ZM-AA0D-01A-11D-A435-10	TCGA-ZM-AA0D-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	cbb77b02-9739-4272-bf41-30251840590b	7ac40e81-4d59-492f-a5cf-f3b25df9905c	g.chr10:104503811A>G	ENST00000369893.5	+	0	6866				WBP1L_ENST00000448841.1_Start_Codon_SNP_p.M1V	NM_178858.4	NP_849189.1	Q96NB2	SFXN2_HUMAN	sideroflexin 2						iron ion homeostasis (GO:0055072)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)	cation transmembrane transporter activity (GO:0008324)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|liver(2)|lung(3)|prostate(1)	13		Colorectal(252;0.207)		Epithelial(162;4.53e-09)|all cancers(201;1.2e-07)|BRCA - Breast invasive adenocarcinoma(275;0.218)		caggagggggatggagaggag	0.667																																					p.M1V													.	.			0			c.A1G												15.0	22.0	20.0					10																	104503811		2024	4144	6168	SO:0001628	intergenic_variant	54838	exon1			AGGGGGATGGAGA	AF462052	CCDS7539.1	10q24.32	2006-03-13			ENSG00000156398	ENSG00000156398		"""Sideroflexins"""	16086	protein-coding gene	gene with protein product		615570					Standard	NM_178858		Approved		uc001kwb.2	Q96NB2	OTTHUMG00000018967		10.37:g.104503811A>G			32	0.03125	1		29	0.14	4	NM_001083913	1	0.00	0	Q5JSM6	Missense_Mutation	SNP	ENST00000369893.5	37	CCDS7539.1	.	.	.	.	.	.	.	.	.	.	A	16.11	3.030772	0.54790	.	.	ENSG00000166272	ENST00000448841	T	0.28895	1.59	4.4	4.4	0.53042	.	.	.	.	.	T	0.47930	0.1472	.	.	.	0.23010	N	0.998439	P	0.43578	0.811	P	0.57846	0.828	T	0.32903	-0.9889	8	0.87932	D	0	-2.4281	10.1756	0.42937	1.0:0.0:0.0:0.0	.	1	Q9NX94-2	.	V	1	ENSP00000414721:M1V	ENSP00000414721:M1V	M	+	1	0	C10orf26	104493801	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.124000	0.57924	1.966000	0.57179	0.379000	0.24179	ATG			0.667	SFXN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000050096.2		XM_058359	
MTCH2	23788	mdanderson.org	37	11	47653218	47653218	+	Missense_Mutation	SNP	G	G	T			TCGA-ZM-AA0D-01A-11D-A435-10	TCGA-ZM-AA0D-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	cbb77b02-9739-4272-bf41-30251840590b	7ac40e81-4d59-492f-a5cf-f3b25df9905c	g.chr11:47653218G>T	ENST00000302503.3	-	6	572	c.415C>A	c.(415-417)Cat>Aat	p.H139N	MTCH2_ENST00000534074.1_5'Flank|MTCH2_ENST00000542981.1_Intron	NM_014342.3	NP_055157.1	Q9Y6C9	MTCH2_HUMAN	mitochondrial carrier 2	139					protein localization to mitochondrion (GO:0070585)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|nucleus (GO:0005634)				endometrium(1)|kidney(2)|large_intestine(2)|lung(3)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	11						TGGAAGGGATGTGTGATGAGG	0.418																																					p.H139N													.	.			0			c.C415A												165.0	133.0	144.0					11																	47653218		2201	4298	6499	SO:0001583	missense	23788	exon6			AGGGATGTGTGAT	AF085361	CCDS7943.1	11p11.2	2013-05-22	2011-05-19		ENSG00000109919	ENSG00000109919		"""Solute carriers"""	17587	protein-coding gene	gene with protein product	"""solute carrier family 25, member 50"""	613221	"""mitochondrial carrier homolog 2 (C. elegans)"""				Standard	NM_014342		Approved	SLC25A50	uc010rho.2	Q9Y6C9	OTTHUMG00000166926	ENST00000302503.3:c.415C>A	11.37:g.47653218G>T	ENSP00000303222:p.His139Asn		63	0	0		48	0.06	3	NM_014342	71	0.00	0	B2R7L8	Missense_Mutation	SNP	ENST00000302503.3	37	CCDS7943.1	.	.	.	.	.	.	.	.	.	.	G	26.0	4.698608	0.88830	.	.	ENSG00000109919	ENST00000302503;ENST00000530428;ENST00000530558	T;T	0.41065	1.01;1.01	5.71	5.71	0.89125	Mitochondrial carrier domain (2);	0.000000	0.85682	D	0.000000	T	0.49029	0.1533	L	0.28504	0.86	0.80722	D	1	D	0.71674	0.998	D	0.72625	0.978	T	0.24297	-1.0164	10	0.02654	T	1	.	18.6391	0.91389	0.0:0.0:1.0:0.0	.	139	Q9Y6C9	MTCH2_HUMAN	N	139;130;118	ENSP00000303222:H139N;ENSP00000432043:H130N	ENSP00000303222:H139N	H	-	1	0	MTCH2	47609794	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.028000	0.70889	2.709000	0.92574	0.655000	0.94253	CAT			0.418	MTCH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000391921.2		NM_014342	
OR5D18	219438	mdanderson.org	37	11	55587808	55587808	+	Missense_Mutation	SNP	C	C	T	rs149397041		TCGA-ZM-AA0D-01A-11D-A435-10	TCGA-ZM-AA0D-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	cbb77b02-9739-4272-bf41-30251840590b	7ac40e81-4d59-492f-a5cf-f3b25df9905c	g.chr11:55587808C>T	ENST00000333976.4	+	1	723	c.703C>T	c.(703-705)Cgc>Tgc	p.R235C		NM_001001952.1	NP_001001952.1	Q8NGL1	OR5DI_HUMAN	olfactory receptor, family 5, subfamily D, member 18	235						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(2)|breast(1)|endometrium(3)|large_intestine(6)|lung(33)|ovary(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	55		all_epithelial(135;0.208)				AGTCAGTGGGCGCCGCAAAGC	0.493																																					p.R235C													OR5D18,NS,adenocarcinoma,0,7	OR5D18	0	7	0			c.C703T												141.0	119.0	126.0					11																	55587808		2200	4296	6496	SO:0001583	missense	219438	exon1			AGTGGGCGCCGCA	AB065781	CCDS31510.1	11q11	2012-08-09			ENSG00000186119	ENSG00000186119		"""GPCR / Class A : Olfactory receptors"""	15285	protein-coding gene	gene with protein product							Standard	NM_001001952		Approved		uc010rin.2	Q8NGL1	OTTHUMG00000166811	ENST00000333976.4:c.703C>T	11.37:g.55587808C>T	ENSP00000335025:p.Arg235Cys		118	0	0		115	0.04	5	NM_001001952	0		0	Q6IF67|Q6IFD3|Q96RB3	Missense_Mutation	SNP	ENST00000333976.4	37	CCDS31510.1	.	.	.	.	.	.	.	.	.	.	.	7.344	0.621417	0.14193	.	.	ENSG00000186119	ENST00000333976	T	0.00337	8.05	4.9	1.31	0.21738	GPCR, rhodopsin-like superfamily (1);	0.599517	0.14038	N	0.345621	T	0.00412	0.0013	M	0.91561	3.22	0.09310	N	1	B	0.18741	0.03	B	0.20384	0.029	T	0.37361	-0.9709	10	0.72032	D	0.01	-0.2535	6.401	0.21638	0.5194:0.3857:0.0:0.0948	.	235	Q8NGL1	OR5DI_HUMAN	C	235	ENSP00000335025:R235C	ENSP00000335025:R235C	R	+	1	0	OR5D18	55344384	0.000000	0.05858	0.000000	0.03702	0.258000	0.26162	-1.358000	0.02604	0.579000	0.29504	0.573000	0.79308	CGC			0.493	OR5D18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000391515.1		NM_001001952	
SORL1	6653	broad.mit.edu;mdanderson.org	37	11	121466453	121466453	+	Nonsense_Mutation	SNP	C	C	A			TCGA-ZM-AA0D-01A-11D-A435-10	TCGA-ZM-AA0D-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	cbb77b02-9739-4272-bf41-30251840590b	7ac40e81-4d59-492f-a5cf-f3b25df9905c	g.chr11:121466453C>A	ENST00000260197.7	+	32	4620	c.4491C>A	c.(4489-4491)tgC>tgA	p.C1497*	SORL1_ENST00000525532.1_Nonsense_Mutation_p.C441*|SORL1_ENST00000532694.1_Nonsense_Mutation_p.C343*|SORL1_ENST00000534286.1_Nonsense_Mutation_p.C407*|SORL1_ENST00000527934.1_Nonsense_Mutation_p.C112*	NM_003105.5	NP_003096	Q92673	SORL_HUMAN	sortilin-related receptor, L(DLR class) A repeats containing	1497	LDL-receptor class A 10. {ECO:0000255|PROSITE-ProRule:PRU00124}.				cell death (GO:0008219)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cholesterol metabolic process (GO:0008203)|lipid transport (GO:0006869)|negative regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process (GO:1902960)|negative regulation of beta-amyloid formation (GO:1902430)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of metalloendopeptidase activity involved in amyloid precursor protein catabolic process (GO:1902963)|negative regulation of neurofibrillary tangle assembly (GO:1902997)|negative regulation of neurogenesis (GO:0050768)|negative regulation of neuron death (GO:1901215)|negative regulation of protein binding (GO:0032091)|negative regulation of protein oligomerization (GO:0032460)|negative regulation of tau-protein kinase activity (GO:1902948)|positive regulation of choline O-acetyltransferase activity (GO:1902771)|positive regulation of early endosome to recycling endosome transport (GO:1902955)|positive regulation of endocytic recycling (GO:2001137)|positive regulation of ER to Golgi vesicle-mediated transport (GO:1902953)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein exit from endoplasmic reticulum (GO:0070863)|positive regulation of protein localization to early endosome (GO:1902966)|post-Golgi vesicle-mediated transport (GO:0006892)|protein maturation (GO:0051604)|protein retention in Golgi apparatus (GO:0045053)|protein targeting (GO:0006605)|protein targeting to Golgi (GO:0000042)|protein targeting to lysosome (GO:0006622)|receptor-mediated endocytosis (GO:0006898)|regulation of smooth muscle cell migration (GO:0014910)|signal transduction (GO:0007165)	early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi cisterna (GO:0031985)|integral component of plasma membrane (GO:0005887)|low-density lipoprotein particle (GO:0034362)|membrane (GO:0016020)|multivesicular body (GO:0005771)|neuronal cell body (GO:0043025)|nuclear envelope lumen (GO:0005641)|recycling endosome (GO:0055037)|trans-Golgi network (GO:0005802)	ADP-ribosylation factor binding (GO:0030306)|beta-amyloid binding (GO:0001540)|low-density lipoprotein particle binding (GO:0030169)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|liver(2)|lung(34)|ovary(5)|pancreas(1)|skin(12)|stomach(2)|upper_aerodigestive_tract(2)	91		Breast(109;0.00119)|Medulloblastoma(222;0.0429)|all_neural(223;0.113)		BRCA - Breast invasive adenocarcinoma(274;3.34e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.108)		ACCAAGATTGCCAGGATGGCC	0.577																																					p.C1497X													.	SORL1	218		0			c.C4491A												67.0	54.0	58.0					11																	121466453		2203	4299	6502	SO:0001587	stop_gained	6653	exon32			AGATTGCCAGGAT	Y08110	CCDS8436.1	11q23.2-q24.4	2014-06-05	2011-01-25		ENSG00000137642	ENSG00000137642		"""Fibronectin type III domain containing"""	11185	protein-coding gene	gene with protein product	"""LDLR relative with 11 ligand-binding repeats"""	602005	"""chromosome 11 open reading frame 32"", ""sortilin-related receptor, L(DLR class) A repeats-containing"""	C11orf32		9157966, 8940146	Standard	NM_003105		Approved	gp250, LR11, LRP9, SorLA, SorLA-1	uc001pxx.3	Q92673	OTTHUMG00000166057	ENST00000260197.7:c.4491C>A	11.37:g.121466453C>A	ENSP00000260197:p.Cys1497*		46	0	0		42	0.12	5	NM_003105	0		0	B2RNX7|Q92856	Nonsense_Mutation	SNP	ENST00000260197.7	37	CCDS8436.1	.	.	.	.	.	.	.	.	.	.	C	38	6.907295	0.97924	.	.	ENSG00000137642	ENST00000260197;ENST00000525532;ENST00000532694;ENST00000534286;ENST00000527934	.	.	.	5.38	2.48	0.30137	.	0.056442	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	10.5559	0.45117	0.0:0.7846:0.0:0.2154	.	.	.	.	X	1497;441;343;407;112	.	ENSP00000260197:C1497X	C	+	3	2	SORL1	120971663	1.000000	0.71417	0.995000	0.50966	0.992000	0.81027	1.064000	0.30579	0.650000	0.30769	-0.136000	0.14681	TGC			0.577	SORL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000387626.2		NM_003105	
USP5	8078	mdanderson.org	37	12	6970675	6970675	+	Missense_Mutation	SNP	G	G	T	rs199632125		TCGA-ZM-AA0D-01A-11D-A435-10	TCGA-ZM-AA0D-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	cbb77b02-9739-4272-bf41-30251840590b	7ac40e81-4d59-492f-a5cf-f3b25df9905c	g.chr12:6970675G>T	ENST00000229268.8	+	13	1619	c.1567G>T	c.(1567-1569)Gtt>Ttt	p.V523F	USP5_ENST00000389231.5_Missense_Mutation_p.V523F|USP5_ENST00000541969.1_3'UTR	NM_001098536.1	NP_001092006.1	P45974	UBP5_HUMAN	ubiquitin specific peptidase 5 (isopeptidase T)	523	USP.				positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|protein K48-linked deubiquitination (GO:0071108)|ubiquitin-dependent protein catabolic process (GO:0006511)	lysosome (GO:0005764)	cysteine-type endopeptidase activity (GO:0004197)|omega peptidase activity (GO:0008242)|ubiquitin thiolesterase activity (GO:0004221)|zinc ion binding (GO:0008270)			breast(6)|endometrium(4)|kidney(2)|large_intestine(6)|lung(14)|skin(2)|urinary_tract(2)	36						GCCAGAACTGGTTCGGGCCCA	0.612													g|||	1	0.000199681	0.0	0.0014	5008	,	,		-128	0.0		0.0	False		,,,				2504	0.0				p.V523F													.	.			0			c.G1567T												70.0	69.0	70.0					12																	6970675		2203	4300	6503	SO:0001583	missense	8078	exon13			GAACTGGTTCGGG	U35116	CCDS31733.1, CCDS41743.1	12p13	2007-03-02	2005-08-08		ENSG00000111667	ENSG00000111667		"""Ubiquitin-specific peptidases"""	12628	protein-coding gene	gene with protein product		601447	"""ubiquitin specific protease 5 (isopeptidase T)"""			12838346, 8723724	Standard	NM_003481		Approved	IsoT	uc001qri.4	P45974	OTTHUMG00000169233	ENST00000229268.8:c.1567G>T	12.37:g.6970675G>T	ENSP00000229268:p.Val523Phe		33	0	0		46	0.07	3	NM_003481	27	0.00	0	D3DUS7|D3DUS8|Q96J22	Missense_Mutation	SNP	ENST00000229268.8	37	CCDS41743.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	g	26.5	4.744335	0.89663	.	.	ENSG00000111667	ENST00000229268;ENST00000389231	T;T	0.26223	1.76;1.75	5.18	5.18	0.71444	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.120057	0.56097	D	0.000028	T	0.53546	0.1803	M	0.76002	2.32	0.58432	D	0.999996	D;D	0.89917	0.996;1.0	D;D	0.78314	0.982;0.991	T	0.56135	-0.8029	10	0.72032	D	0.01	.	18.885	0.92372	0.0:0.0:1.0:0.0	.	523;523	P45974;P45974-2	UBP5_HUMAN;.	F	523	ENSP00000229268:V523F;ENSP00000373883:V523F	ENSP00000229268:V523F	V	+	1	0	USP5	6840936	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.018000	0.76406	2.696000	0.92011	0.556000	0.70494	GTT	0		0.612	USP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000402982.1			
MTIF3	219402	ucsc.edu	37	13	28014392	28014392	+	Missense_Mutation	SNP	C	C	T			TCGA-ZM-AA0D-01A-11D-A435-10	TCGA-ZM-AA0D-10A-01D-A438-10	C	C					Unknown	Untested	Somatic		RNA-Seq	none			Illumina HiSeq	cbb77b02-9739-4272-bf41-30251840590b	7ac40e81-4d59-492f-a5cf-f3b25df9905c	g.chr13:28014392C>T	ENST00000381116.1	-	5	428	c.194G>A	c.(193-195)gGa>gAa	p.G65E	MTIF3_ENST00000431572.2_Missense_Mutation_p.G65E|MTIF3_ENST00000461838.1_5'UTR|MTIF3_ENST00000405591.2_Missense_Mutation_p.G65E|MTIF3_ENST00000381120.3_Missense_Mutation_p.G65E			Q9H2K0	IF3M_HUMAN	mitochondrial translational initiation factor 3	65					formation of translation initiation complex (GO:0001732)|regulation of translational initiation (GO:0006446)|ribosome disassembly (GO:0032790)	mitochondrion (GO:0005739)	ribosomal small subunit binding (GO:0043024)|translation factor activity, nucleic acid binding (GO:0008135)|translation initiation factor activity (GO:0003743)			endometrium(1)|large_intestine(1)|lung(2)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	7		Lung SC(185;0.0161)	Colorectal(13;0.00042)|READ - Rectum adenocarcinoma(15;0.105)	all cancers(112;0.108)|OV - Ovarian serous cystadenocarcinoma(117;0.157)		TGTCTTTTTTCCTTCATTCTG	0.403																																					p.G65E													.	MTIF3	21		0			c.G194A												106.0	109.0	108.0					13																	28014392		2203	4300	6503	SO:0001583	missense	219402	exon4			TTTTTTCCTTCAT	BC046166	CCDS9322.1	13q12.2	2007-05-03			ENSG00000122033	ENSG00000122033			29788	protein-coding gene	gene with protein product						12095986	Standard	NM_152912		Approved	IF-3mt, IF3(mt)	uc001uri.3	Q9H2K0	OTTHUMG00000016633	ENST00000381116.1:c.194G>A	13.37:g.28014392C>T	ENSP00000370508:p.Gly65Glu		150	0	0		123	0.02	2	NM_001166263	133	0.11	14	Q05BL8|Q5W0V0|Q86X68	Missense_Mutation	SNP	ENST00000381116.1	37	CCDS9322.1	.	.	.	.	.	.	.	.	.	.	C	3.884	-0.025346	0.07589	.	.	ENSG00000122033	ENST00000431572;ENST00000405591;ENST00000381116;ENST00000381120	T;T;T;T	0.29917	1.55;1.55;1.55;1.55	5.82	-0.823	0.10815	.	0.504141	0.21766	N	0.069438	T	0.15912	0.0383	L	0.36672	1.1	0.09310	N	1	B	0.23806	0.091	B	0.19148	0.024	T	0.09357	-1.0678	10	0.32370	T	0.25	-6.0618	0.9703	0.01414	0.2413:0.3473:0.1435:0.2679	.	65	Q9H2K0	IF3M_HUMAN	E	65	ENSP00000400084:G65E;ENSP00000384659:G65E;ENSP00000370508:G65E;ENSP00000370512:G65E	ENSP00000370508:G65E	G	-	2	0	MTIF3	26912392	0.000000	0.05858	0.000000	0.03702	0.034000	0.12701	-2.094000	0.01351	0.048000	0.15891	0.655000	0.94253	GGA			0.403	MTIF3-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000044300.1	rescued with RNA-seq	NM_152912	
IRS2	8660	mdanderson.org	37	13	110434970	110434970	+	Missense_Mutation	SNP	C	C	T			TCGA-ZM-AA0D-01A-11D-A435-10	TCGA-ZM-AA0D-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	cbb77b02-9739-4272-bf41-30251840590b	7ac40e81-4d59-492f-a5cf-f3b25df9905c	g.chr13:110434970C>T	ENST00000375856.3	-	1	3945	c.3431G>A	c.(3430-3432)cGc>cAc	p.R1144H		NM_003749.2	NP_003740.2	Q9Y4H2	IRS2_HUMAN	insulin receptor substrate 2	1144					brain development (GO:0007420)|cell proliferation (GO:0008283)|cellular response to glucose stimulus (GO:0071333)|cellular response to insulin stimulus (GO:0032869)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|lipid homeostasis (GO:0055088)|mammary gland development (GO:0030879)|negative regulation of B cell apoptotic process (GO:0002903)|negative regulation of kinase activity (GO:0033673)|negative regulation of plasma membrane long-chain fatty acid transport (GO:0010748)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of fatty acid beta-oxidation (GO:0032000)|positive regulation of glucose import (GO:0046326)|positive regulation of glucose metabolic process (GO:0010907)|positive regulation of glycogen biosynthetic process (GO:0045725)|positive regulation of insulin secretion (GO:0032024)|positive regulation of mesenchymal cell proliferation (GO:0002053)|regulation of lipid metabolic process (GO:0019216)|response to glucose (GO:0009749)|signal transduction (GO:0007165)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	signal transducer activity (GO:0004871)			kidney(2)|large_intestine(2)|lung(8)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)	19	all_cancers(4;7.57e-15)|all_epithelial(4;5.91e-09)|all_lung(23;7.64e-07)|Lung NSC(43;0.000183)|Colorectal(4;0.00159)|all_neural(89;0.00294)|Medulloblastoma(90;0.00596)|Lung SC(71;0.0155)	Breast(118;0.159)	all cancers(43;0.00815)|BRCA - Breast invasive adenocarcinoma(86;0.11)|Epithelial(84;0.127)|GBM - Glioblastoma multiforme(44;0.147)			GTGGCGGCGGCGGCCCCCCTG	0.721																																					p.R1144H	Melanoma(100;613 2409 40847)												.	.			0			c.G3431A												3.0	4.0	4.0					13																	110434970		1716	3511	5227	SO:0001583	missense	8660	exon1			CGGCGGCGGCCCC	AB000732	CCDS9510.1	13q34	2013-01-10			ENSG00000185950	ENSG00000185950		"""Pleckstrin homology (PH) domain containing"""	6126	protein-coding gene	gene with protein product		600797				9312143	Standard	NM_003749		Approved		uc001vqv.3	Q9Y4H2	OTTHUMG00000017338	ENST00000375856.3:c.3431G>A	13.37:g.110434970C>T	ENSP00000365016:p.Arg1144His		53	0	0		33	0.09	3	NM_003749	0		0	Q96RR2|Q9BZG0|Q9Y6I5	Missense_Mutation	SNP	ENST00000375856.3	37	CCDS9510.1	.	.	.	.	.	.	.	.	.	.	C	15.61	2.885518	0.51908	.	.	ENSG00000185950	ENST00000375856	T	0.32272	1.46	3.92	3.92	0.45320	.	0.000000	0.85682	U	0.000000	T	0.52964	0.1767	M	0.70595	2.14	0.40397	D	0.979605	D	0.89917	1.0	D	0.80764	0.994	T	0.60005	-0.7347	10	0.72032	D	0.01	-18.8912	13.5507	0.61730	0.0:1.0:0.0:0.0	.	1144	Q9Y4H2	IRS2_HUMAN	H	1144	ENSP00000365016:R1144H	ENSP00000365016:R1144H	R	-	2	0	IRS2	109232971	1.000000	0.71417	0.998000	0.56505	0.240000	0.25518	5.852000	0.69488	2.039000	0.60335	0.644000	0.83932	CGC			0.721	IRS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000045755.1		NM_003749	
NID2	22795	mdanderson.org	37	14	52535528	52535528	+	Missense_Mutation	SNP	G	G	T			TCGA-ZM-AA0D-01A-11D-A435-10	TCGA-ZM-AA0D-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	cbb77b02-9739-4272-bf41-30251840590b	7ac40e81-4d59-492f-a5cf-f3b25df9905c	g.chr14:52535528G>T	ENST00000216286.5	-	1	184	c.185C>A	c.(184-186)gCg>gAg	p.A62E	NID2_ENST00000541773.1_Missense_Mutation_p.A9E	NM_007361.3	NP_031387.3	Q14112	NID2_HUMAN	nidogen 2 (osteonidogen)	62					basement membrane organization (GO:0071711)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|cell surface (GO:0009986)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)			NS(1)|breast(5)|endometrium(9)|kidney(4)|large_intestine(11)|liver(1)|lung(40)|ovary(2)|pancreas(2)|prostate(2)|skin(3)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	87	Breast(41;0.0639)|all_epithelial(31;0.123)					CAGGGGATTCGCCAGCTTCAC	0.632																																					p.A62E													.	.			0			c.C185A												104.0	89.0	94.0					14																	52535528		2203	4300	6503	SO:0001583	missense	22795	exon1			GGATTCGCCAGCT	AB009799	CCDS9706.1	14q22.1	2008-05-14			ENSG00000087303	ENSG00000087303			13389	protein-coding gene	gene with protein product		605399				9733643	Standard	NM_007361		Approved		uc001wzo.3	Q14112	OTTHUMG00000140298	ENST00000216286.5:c.185C>A	14.37:g.52535528G>T	ENSP00000216286:p.Ala62Glu		48	0	0		46	0.07	3	NM_007361	0		0	A8K6I7|B4DU19|O43710	Missense_Mutation	SNP	ENST00000216286.5	37	CCDS9706.1	.	.	.	.	.	.	.	.	.	.	G	10.49	1.365830	0.24684	.	.	ENSG00000087303	ENST00000216286;ENST00000316204;ENST00000541773;ENST00000395707	T;T	0.23754	1.89;1.89	4.81	-1.3	0.09259	.	0.902895	0.09679	N	0.770020	T	0.14270	0.0345	L	0.33293	1	0.09310	N	1	P;B;B	0.41748	0.761;0.008;0.002	B;B;B	0.38655	0.278;0.003;0.002	T	0.12426	-1.0548	10	0.05525	T	0.97	.	8.4514	0.32873	0.0:0.348:0.3948:0.2571	.	9;64;62	Q14112-2;Q5CZI2;Q14112	.;.;NID2_HUMAN	E	62;62;9;64	ENSP00000216286:A62E;ENSP00000443730:A9E	ENSP00000216286:A62E	A	-	2	0	NID2	51605278	0.000000	0.05858	0.142000	0.22268	0.525000	0.34531	0.011000	0.13264	0.065000	0.16485	0.455000	0.32223	GCG			0.632	NID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000276888.1			
SYNE2	23224	mdanderson.org	37	14	64626069	64626069	+	Nonsense_Mutation	SNP	G	G	T			TCGA-ZM-AA0D-01A-11D-A435-10	TCGA-ZM-AA0D-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	cbb77b02-9739-4272-bf41-30251840590b	7ac40e81-4d59-492f-a5cf-f3b25df9905c	g.chr14:64626069G>T	ENST00000344113.4	+	87	16215	c.16003G>T	c.(16003-16005)Gag>Tag	p.E5335*	ESR2_ENST00000542956.1_Intron|SYNE2_ENST00000394768.2_Nonsense_Mutation_p.E1720*|SYNE2_ENST00000357395.3_Nonsense_Mutation_p.E1720*|SYNE2_ENST00000554584.1_Nonsense_Mutation_p.E5252*|SYNE2_ENST00000555002.1_Nonsense_Mutation_p.E1969*|SYNE2_ENST00000358025.3_Nonsense_Mutation_p.E5335*	NM_015180.4	NP_055995.4	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	5335					centrosome localization (GO:0051642)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment or maintenance of cell polarity (GO:0007163)|fibroblast migration (GO:0010761)|nuclear envelope organization (GO:0006998)|nuclear migration (GO:0007097)|nuclear migration along microfilament (GO:0031022)|positive regulation of cell migration (GO:0030335)|protein localization to nucleus (GO:0034504)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intermediate filament cytoskeleton (GO:0045111)|lamellipodium membrane (GO:0031258)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nuclear lumen (GO:0031981)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)|SUN-KASH complex (GO:0034993)|Z disc (GO:0030018)	actin binding (GO:0003779)			NS(5)|breast(17)|central_nervous_system(3)|cervix(8)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(21)|large_intestine(34)|lung(75)|ovary(10)|pancreas(2)|prostate(8)|skin(8)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(4)	224				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)		AGGGAGTTGGGAGAAACTCCA	0.428																																					p.E5335X													.	.			0			c.G16003T												82.0	85.0	84.0					14																	64626069		2203	4300	6503	SO:0001587	stop_gained	23224	exon87			AGTTGGGAGAAAC	AB023228	CCDS9761.2, CCDS41963.1, CCDS45124.1, CCDS45125.1	14q22.1-q22.3	2014-09-17			ENSG00000054654	ENSG00000054654			17084	protein-coding gene	gene with protein product	"""nuclear envelope spectrin repeat-2"", ""nucleus and actin connecting element"""	608442				10231032, 10878022	Standard	NM_182910		Approved	SYNE-2, DKFZP434H2235, Nesprin-2, NUANCE, NUA, KIAA1011, Nesp2	uc001xgl.3	Q8WXH0	OTTHUMG00000140349	ENST00000344113.4:c.16003G>T	14.37:g.64626069G>T	ENSP00000341781:p.Glu5335*		46	0	0		45	0.07	3	NM_015180	9	0.00	0	Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	Nonsense_Mutation	SNP	ENST00000344113.4	37	CCDS41963.1	.	.	.	.	.	.	.	.	.	.	G	34	5.407754	0.96051	.	.	ENSG00000054654	ENST00000358025;ENST00000357395;ENST00000344113;ENST00000554584;ENST00000261678;ENST00000555002;ENST00000394768	.	.	.	5.98	-0.0102	0.13998	.	0.831368	0.10264	N	0.695599	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.36615	T	0.2	.	8.3859	0.32499	0.1264:0.1239:0.7497:0.0	.	.	.	.	X	5335;1720;5335;5252;5258;1969;1720	.	ENSP00000261678:E5258X	E	+	1	0	SYNE2	63695822	1.000000	0.71417	0.996000	0.52242	0.843000	0.47879	1.064000	0.30579	0.060000	0.16281	0.655000	0.94253	GAG			0.428	SYNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000276994.2		NM_182914	
RRN3P2	653390	broad.mit.edu	37	16	29102416	29102416	+	RNA	DEL	A	A	-			TCGA-ZM-AA0D-01A-11D-A435-10	TCGA-ZM-AA0D-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	cbb77b02-9739-4272-bf41-30251840590b	7ac40e81-4d59-492f-a5cf-f3b25df9905c	g.chr16:29102416delA	ENST00000564580.1	+	0	750							A6NIE6	RN3P2_HUMAN	RNA polymerase I transcription factor homolog (S. cerevisiae) pseudogene 2																		tataaaaaataaaaaaaaaaa	0.507																																					.													.	.			0			.																																											0	.			AAAAATAAAAAAA			16p11.2	2011-12-02			ENSG00000103472	ENSG00000103472			37619	pseudogene	pseudogene							Standard	NR_003369		Approved		uc002dsf.4	A6NIE6			16.37:g.29102416delA			6	0	0		7	0.29	2	.	0		0		RNA	DEL	ENST00000564580.1	37																																																																																						0.507	RRN3P2-001	KNOWN	basic	processed_transcript	pseudogene		OTTHUMT00000433243.1		NR_003369	
MYLK3	91807	mdanderson.org	37	16	46762966	46762966	+	Missense_Mutation	SNP	C	C	T			TCGA-ZM-AA0D-01A-11D-A435-10	TCGA-ZM-AA0D-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	cbb77b02-9739-4272-bf41-30251840590b	7ac40e81-4d59-492f-a5cf-f3b25df9905c	g.chr16:46762966C>T	ENST00000394809.4	-	7	1857	c.1742G>A	c.(1741-1743)aGc>aAc	p.S581N	MYLK3_ENST00000536476.1_Missense_Mutation_p.S240N	NM_182493.2	NP_872299.2	Q32MK0	MYLK3_HUMAN	myosin light chain kinase 3	581	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cardiac myofibril assembly (GO:0055003)|cellular response to interleukin-1 (GO:0071347)|positive regulation of sarcomere organization (GO:0060298)|protein phosphorylation (GO:0006468)|regulation of vascular permeability involved in acute inflammatory response (GO:0002528)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)|myosin light chain kinase activity (GO:0004687)			central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(7)|lung(11)|ovary(3)|prostate(3)|skin(5)|stomach(3)	37		all_cancers(37;0.00023)|all_epithelial(9;0.000543)|all_lung(18;0.00585)|Lung NSC(13;0.0496)|Breast(268;0.116)				GCTGTGCTTGCTCTCGAAGGC	0.582																																					p.S581N													.	.			0			c.G1742A												241.0	199.0	213.0					16																	46762966		2203	4300	6503	SO:0001583	missense	91807	exon7			TGCTTGCTCTCGA	AJ247087	CCDS10723.2	16q11.2	2008-10-23			ENSG00000140795	ENSG00000140795			29826	protein-coding gene	gene with protein product	"""MLC kinase"""	612147				17885681	Standard	NM_182493		Approved	caMLCK, MLCK	uc002eei.4	Q32MK0	OTTHUMG00000132543	ENST00000394809.4:c.1742G>A	16.37:g.46762966C>T	ENSP00000378288:p.Ser581Asn		48	0	0		43	0.07	3	NM_182493	0		0	B5BUL9|B7Z5U8|Q32MK1|Q96DV1	Missense_Mutation	SNP	ENST00000394809.4	37	CCDS10723.2	.	.	.	.	.	.	.	.	.	.	C	16.57	3.161360	0.57368	.	.	ENSG00000140795	ENST00000394809;ENST00000536476	T;T	0.64991	-0.13;-0.13	5.39	5.39	0.77823	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.42682	D	0.000674	T	0.49830	0.1580	N	0.25094	0.71	0.39796	D	0.972507	B;B	0.21452	0.056;0.047	B;B	0.20767	0.017;0.031	T	0.52079	-0.8623	10	0.66056	D	0.02	.	14.2343	0.65916	0.0:0.8496:0.1504:0.0	.	581;581	B5BUL9;Q32MK0	.;MYLK3_HUMAN	N	581;240	ENSP00000378288:S581N;ENSP00000439297:S240N	ENSP00000378288:S581N	S	-	2	0	MYLK3	45320467	1.000000	0.71417	1.000000	0.80357	0.758000	0.43043	2.883000	0.48554	2.534000	0.85438	0.491000	0.48974	AGC			0.582	MYLK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000255743.2		NM_182493	
CES4A	283848	hgsc.bcm.edu;broad.mit.edu;mdanderson.org	37	16	67036993	67036993	+	Silent	SNP	G	G	T	rs181709052		TCGA-ZM-AA0D-01A-11D-A435-10	TCGA-ZM-AA0D-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	cbb77b02-9739-4272-bf41-30251840590b	7ac40e81-4d59-492f-a5cf-f3b25df9905c	g.chr16:67036993G>T	ENST00000326686.5	+	6	711	c.711G>T	c.(709-711)tcG>tcT	p.S237S	CES4A_ENST00000540947.2_Silent_p.S237S|CES4A_ENST00000338718.4_Silent_p.S260S|CES4A_ENST00000535696.1_Silent_p.S143S|CES4A_ENST00000540579.1_Silent_p.S139S|CES4A_ENST00000398354.1_Silent_p.S237S|CES4A_ENST00000541479.1_Silent_p.S260S			Q5XG92	EST4A_HUMAN	carboxylesterase 4A	237						extracellular region (GO:0005576)	carboxylic ester hydrolase activity (GO:0052689)			large_intestine(2)|liver(2)|lung(4)|ovary(1)	9						CCCTAGCCTCGGGTCTCTTCC	0.542																																					p.S237S													.	.			0			c.G711T												112.0	110.0	111.0					16																	67036993		1973	4153	6126	SO:0001819	synonymous_variant	283848	exon6			AGCCTCGGGTCTC	AK094783	CCDS42174.1, CCDS42174.2, CCDS54024.1, CCDS54025.1, CCDS42174.3	16q22.1	2011-10-25	2010-10-12	2010-10-12	ENSG00000172824	ENSG00000172824		"""Carboxylesterases"""	26741	protein-coding gene	gene with protein product			"""carboxylesterase 8 (putative)"""	CES8		12975309, 17364878, 20931200	Standard	NM_001190201		Approved	FLJ37464	uc010vix.2	Q5XG92		ENST00000326686.5:c.711G>T	16.37:g.67036993G>T			152	0	0		82	0.05	4	NM_173815	2	0.00	0	A8KAJ6|B7Z349|B7Z3L2|B7Z6R3|Q6UX55|Q8N9F4	Silent	SNP	ENST00000326686.5	37																																																																																						0.542	CES4A-201	KNOWN	basic|appris_principal	protein_coding	protein_coding				NM_173815	
ZNF469	84627	mdanderson.org	37	16	88502519	88502519	+	Missense_Mutation	SNP	C	C	A	rs529243785		TCGA-ZM-AA0D-01A-11D-A435-10	TCGA-ZM-AA0D-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	cbb77b02-9739-4272-bf41-30251840590b	7ac40e81-4d59-492f-a5cf-f3b25df9905c	g.chr16:88502519C>A	ENST00000437464.1	+	2	8557	c.8557C>A	c.(8557-8559)Cgc>Agc	p.R2853S	ZNF469_ENST00000565624.1_Missense_Mutation_p.R2881S	NM_001127464.1	NP_001120936.1	Q96JG9	ZN469_HUMAN	zinc finger protein 469	2853					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(4)|endometrium(6)|kidney(3)|large_intestine(1)|skin(6)	20						CTACGGGAAGCGCTGTGAGAA	0.632																																					p.R2853S													ZNF469,NS,carcinoma,-1,2	ZNF469	-1	2	0			c.C8557A												12.0	17.0	16.0					16																	88502519		691	1587	2278	SO:0001583	missense	84627	exon2			GGGAAGCGCTGTG	AB058761	CCDS45544.1	16q24	2010-08-04				ENSG00000225614		"""Zinc fingers, C2H2-type"""	23216	protein-coding gene	gene with protein product		612078				11347906	Standard	NM_001127464		Approved	KIAA1858	uc002fku.2	Q96JG9		ENST00000437464.1:c.8557C>A	16.37:g.88502519C>A	ENSP00000402343:p.Arg2853Ser		52	0	0		52	0.06	3	NM_001127464	0		0		Missense_Mutation	SNP	ENST00000437464.1	37	CCDS45544.1	.	.	.	.	.	.	.	.	.	.	C	10.15	1.272159	0.23221	.	.	ENSG00000225614	ENST00000437464	T	0.48522	0.81	5.28	0.628	0.17681	.	.	.	.	.	T	0.46580	0.1400	L	0.27053	0.805	0.09310	N	1	D	0.76494	0.999	D	0.65010	0.931	T	0.28713	-1.0035	9	0.87932	D	0	.	3.492	0.07641	0.1126:0.536:0.1231:0.2283	.	2853	Q96JG9	ZN469_HUMAN	S	2853	ENSP00000402343:R2853S	ENSP00000402343:R2853S	R	+	1	0	ZNF469	87030020	0.968000	0.33430	0.003000	0.11579	0.018000	0.09664	0.521000	0.22893	0.232000	0.21100	0.561000	0.74099	CGC			0.632	ZNF469-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				NG_012236	
RASD1	51655	bcgsc.ca	37	17	17398600	17398600	+	Missense_Mutation	SNP	G	G	A			TCGA-ZM-AA0D-01A-11D-A435-10	TCGA-ZM-AA0D-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	cbb77b02-9739-4272-bf41-30251840590b	7ac40e81-4d59-492f-a5cf-f3b25df9905c	g.chr17:17398600G>A	ENST00000225688.3	-	2	896	c.685C>T	c.(685-687)Cgg>Tgg	p.R229W	RASD1_ENST00000579152.1_3'UTR	NM_001199989.1|NM_016084.4	NP_001186918.1|NP_057168.1	Q9Y272	RASD1_HUMAN	RAS, dexamethasone-induced 1	229					G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of transcription, DNA-templated (GO:0045892)|nitric oxide mediated signal transduction (GO:0007263)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			endometrium(1)|lung(2)|upper_aerodigestive_tract(1)	4						ctgccgGCCCGCAGCAGCTTC	0.687																																					p.R229W													.	RASD1	8		0			c.C685T												5.0	6.0	5.0					17																	17398600		1933	3789	5722	SO:0001583	missense	51655	exon2			CGGCCCGCAGCAG	AF069506	CCDS11185.1, CCDS58519.1	17p11.2	2014-05-09			ENSG00000108551	ENSG00000108551			15828	protein-coding gene	gene with protein product	"""ras-related protein"", ""dexamethasone-induced ras-related protein 1"", ""activator of G protein signaling"""	605550				10947988	Standard	NM_001199989		Approved	DEXRAS1, AGS1	uc002gri.3	Q9Y272	OTTHUMG00000059292	ENST00000225688.3:c.685C>T	17.37:g.17398600G>A	ENSP00000225688:p.Arg229Trp		73	0	0		45	0.09	4	NM_016084	42	0.00	0	B2R709|B4DFF4|Q9NYB4	Missense_Mutation	SNP	ENST00000225688.3	37	CCDS11185.1	.	.	.	.	.	.	.	.	.	.	G	20.6	4.013815	0.75161	.	.	ENSG00000108551	ENST00000225688	T	0.73575	-0.76	5.0	3.97	0.46021	.	0.138702	0.33610	N	0.004735	T	0.65144	0.2663	N	0.22421	0.69	0.80722	D	1	D	0.56287	0.975	P	0.48571	0.582	T	0.68880	-0.5292	10	0.72032	D	0.01	.	9.431	0.38610	0.0:0.0:0.671:0.329	.	229	Q9Y272	RASD1_HUMAN	W	229	ENSP00000225688:R229W	ENSP00000225688:R229W	R	-	1	2	RASD1	17339325	0.998000	0.40836	0.998000	0.56505	0.983000	0.72400	1.669000	0.37492	2.299000	0.77371	0.561000	0.74099	CGG			0.687	RASD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000131668.1		NM_016084	
LRRC37BP1	147172	broad.mit.edu	37	17	28960993	28960994	+	RNA	INS	-	-	TTTTC	rs57752761		TCGA-ZM-AA0D-01A-11D-A435-10	TCGA-ZM-AA0D-10A-01D-A438-10	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	cbb77b02-9739-4272-bf41-30251840590b	7ac40e81-4d59-492f-a5cf-f3b25df9905c	g.chr17:28960993_28960994insTTTTC	ENST00000417404.1	+	0	1269									leucine rich repeat containing 37B pseudogene 1																		tcttttttcttttttttttttt	0.302																																					.													.	.			0			.																																											0	.			TTTTCTTTTTTTT	BC118647		17q11.2	2012-10-05	2010-08-16	2010-08-16	ENSG00000250462	ENSG00000250462			25390	pseudogene	pseudogene			"""leucine rich repeat containing 37, member B2"""	LRRC37B2			Standard	NR_015341		Approved	DKFZp667M2411	uc010csj.3		OTTHUMG00000132795		17.37:g.28960993_28960994insTTTTC			74	0	0		75	0.31	23	.	0		0		RNA	INS	ENST00000417404.1	37																																																																																						0.302	LRRC37BP1-003	KNOWN	basic	processed_transcript	pseudogene		OTTHUMT00000256203.1		NR_015341	
SYNRG	11276	mdanderson.org	37	17	35889886	35889886	+	Intron	SNP	T	T	C			TCGA-ZM-AA0D-01A-11D-A435-10	TCGA-ZM-AA0D-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	cbb77b02-9739-4272-bf41-30251840590b	7ac40e81-4d59-492f-a5cf-f3b25df9905c	g.chr17:35889886T>C	ENST00000339208.6	-	19	3807				SYNRG_ENST00000346661.4_Intron|SYNRG_ENST00000345615.4_Intron|SYNRG_ENST00000591288.1_Intron|SYNRG_ENST00000585472.1_Intron|SYNRG_ENST00000502449.2_Intron|SYNRG_ENST00000394378.2_Splice_Site_p.K1167R	NM_001163544.1|NM_001163545.1|NM_007247.4	NP_001157016.1|NP_001157017.1|NP_009178.3	Q9UMZ2	SYNRG_HUMAN	synergin, gamma						endocytosis (GO:0006897)|intracellular protein transport (GO:0006886)	AP-1 adaptor complex (GO:0030121)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)	calcium ion binding (GO:0005509)			breast(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(14)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	36						CTGTGATACCTTTTCTTCTAA	0.483																																					p.K1167R													.	.			0			c.A3500G												110.0	93.0	98.0					17																	35889886		692	1591	2283	SO:0001627	intron_variant	11276	exon19			GATACCTTTTCTT	AF169548	CCDS11321.1, CCDS11322.1, CCDS11322.2, CCDS54113.1, CCDS54114.1, CCDS59284.1, CCDS59285.1	17q12	2014-04-16	2009-07-20	2009-07-20	ENSG00000006114	ENSG00000275066			557	protein-coding gene	gene with protein product	"""gamma-synergin"", ""adaptor-related protein complex 1 gamma subunit-binding protein 1"""	607291	"""AP1 gamma subunit binding protein 1"""	AP1GBP1		10477754	Standard	XM_005256980		Approved	SYNG, MGC104959	uc010wdf.2	Q9UMZ2	OTTHUMG00000188473	ENST00000339208.6:c.3666+6194A>G	17.37:g.35889886T>C			44	0	0		44	0.07	3	NM_198882	9	0.00	0	A8MWU4|B7ZKZ2|B7ZKZ3|Q17RI2|Q5BKU5|Q6ZT17	Missense_Mutation	SNP	ENST00000339208.6	37	CCDS11321.1	.	.	.	.	.	.	.	.	.	.	T	7.939	0.742338	0.15642	.	.	ENSG00000006114	ENST00000394378	T	0.44083	0.93	2.52	2.52	0.30459	.	.	.	.	.	T	0.39226	0.1070	N	0.08118	0	0.25794	N	0.984583	P	0.49696	0.927	D	0.67725	0.953	T	0.14811	-1.0459	9	0.62326	D	0.03	.	7.021	0.24914	0.0:0.0:0.0:1.0	.	1167	A8MWU4	.	R	1167	ENSP00000377903:K1167R	ENSP00000377903:K1167R	K	-	2	0	SYNRG	32963999	0.026000	0.19158	0.081000	0.20488	0.236000	0.25371	0.351000	0.20096	1.421000	0.47157	0.374000	0.22700	AAG			0.483	SYNRG-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		OTTHUMT00000256811.2		NM_007247	
KANSL1	284058	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca;mdanderson.org	37	17	44248976	44248976	+	Silent	SNP	C	C	T			TCGA-ZM-AA0D-01A-11D-A435-10	TCGA-ZM-AA0D-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	cbb77b02-9739-4272-bf41-30251840590b	7ac40e81-4d59-492f-a5cf-f3b25df9905c	g.chr17:44248976C>T	ENST00000262419.6	-	2	1004	c.534G>A	c.(532-534)ggG>ggA	p.G178G	KANSL1_ENST00000432791.1_Silent_p.G178G|KANSL1_ENST00000393476.3_5'UTR|KANSL1_ENST00000574590.1_Silent_p.G178G|KANSL1_ENST00000576248.1_5'Flank|KANSL1_ENST00000572904.1_Silent_p.G178G|KANSL1_ENST00000575318.1_Silent_p.G178G	NM_001193466.1	NP_001180395	Q7Z3B3	KANL1_HUMAN	KAT8 regulatory NSL complex subunit 1	178					chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)	histone acetyltransferase complex (GO:0000123)|MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)											CCCGTTTTCCCCCATTGAGGG	0.478																																					p.G178G													.	.			0			c.G534A												105.0	139.0	128.0					17																	44248976		2203	4300	6503	SO:0001819	synonymous_variant	284058	exon2			TTTTCCCCCATTG	BX538006	CCDS11503.1, CCDS11503.2, CCDS74084.1	17q21.31	2012-02-20	2012-02-20	2012-02-20	ENSG00000120071	ENSG00000120071			24565	protein-coding gene	gene with protein product	"""centromere protein 36"""	612452	"""KIAA1267"""	KIAA1267		10574462	Standard	NM_015443		Approved	DKFZP727C091, MSL1v1, CENP-36, NSL1	uc002ikd.3	Q7Z3B3		ENST00000262419.6:c.534G>A	17.37:g.44248976C>T			99	0	0		91	0.05	5	NM_001193466	10	0.20	2	A8K5E4|Q6AW85|Q8IYH1|Q9BRH0|Q9NTE7|Q9UFT0|Q9ULF3	Silent	SNP	ENST00000262419.6	37	CCDS11503.1																																																																																					0.478	KANSL1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000440274.1		NM_015443	
TGIF1	7050	mdanderson.org	37	18	3457889	3457889	+	Missense_Mutation	SNP	C	C	T			TCGA-ZM-AA0D-01A-11D-A435-10	TCGA-ZM-AA0D-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	cbb77b02-9739-4272-bf41-30251840590b	7ac40e81-4d59-492f-a5cf-f3b25df9905c	g.chr18:3457889C>T	ENST00000330513.5	+	3	1460	c.1157C>T	c.(1156-1158)gCa>gTa	p.A386V	TGIF1_ENST00000407501.2_Missense_Mutation_p.A257V|TGIF1_ENST00000551541.1_Missense_Mutation_p.A237V|TGIF1_ENST00000401449.1_Missense_Mutation_p.A237V|TGIF1_ENST00000405385.3_Missense_Mutation_p.A237V|TGIF1_ENST00000472042.1_Missense_Mutation_p.A237V|TGIF1_ENST00000548489.2_Missense_Mutation_p.A271V|TGIF1_ENST00000343820.5_Missense_Mutation_p.A257V|TGIF1_ENST00000400167.2_Missense_Mutation_p.A237V|TGIF1_ENST00000345133.5_Missense_Mutation_p.A237V	NM_170695.2	NP_733796.2	Q15583	TGIF1_HUMAN	TGFB-induced factor homeobox 1	386					determination of left/right symmetry (GO:0007368)|dorsal/ventral pattern formation (GO:0009953)|gene expression (GO:0010467)|multicellular organismal development (GO:0007275)|negative regulation of cell proliferation (GO:0008285)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|nodal signaling pathway (GO:0038092)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of neuron differentiation (GO:0045666)|regulation of gastrulation (GO:0010470)|response to drug (GO:0042493)|retina development in camera-type eye (GO:0060041)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	nucleoplasm (GO:0005654)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			cervix(1)|endometrium(3)|large_intestine(4)|lung(2)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	13	Esophageal squamous(4;0.0859)	Colorectal(8;0.0104)				GTGGATGTTGCACTCAAACGG	0.478																																					p.A386V													.	.			0			c.C1157T												64.0	64.0	64.0					18																	3457889		2203	4300	6503	SO:0001583	missense	7050	exon3			ATGTTGCACTCAA	X89750	CCDS11832.1, CCDS11833.1, CCDS11834.1, CCDS11835.1	18p11.31	2011-06-20	2007-01-30	2007-01-30	ENSG00000177426	ENSG00000177426		"""Homeoboxes / TALE class"""	11776	protein-coding gene	gene with protein product		602630	"""TGFB-induced factor (TALE family homeobox)"""	HPE4, TGIF		8537382, 10835638	Standard	NM_173211		Approved		uc002klz.3	Q15583	OTTHUMG00000131511	ENST00000330513.5:c.1157C>T	18.37:g.3457889C>T	ENSP00000327959:p.Ala386Val		16	0	0		16	0.13	2	NM_170695	190	0.00	0	A6NE42|A6NLU7|F8VZB6|Q6ICR0|Q8N5X9|Q9NRS0	Missense_Mutation	SNP	ENST00000330513.5	37	CCDS11834.1	.	.	.	.	.	.	.	.	.	.	C	22.6	4.311428	0.81358	.	.	ENSG00000177426	ENST00000401449;ENST00000548489;ENST00000405385;ENST00000343820;ENST00000407501;ENST00000551541;ENST00000345133;ENST00000330513;ENST00000549546;ENST00000400167;ENST00000472042	T;T;T;T;T;T;T;T;T;T;T	0.73897	-0.53;-0.55;-0.53;-0.61;-0.61;-0.53;-0.53;-0.79;-0.43;-0.53;-0.53	5.26	5.26	0.73747	.	0.000000	0.85682	D	0.000000	D	0.87581	0.6213	M	0.84082	2.675	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;1.0;1.0	D	0.88188	0.2875	9	.	.	.	-26.2341	18.869	0.92305	0.0:1.0:0.0:0.0	.	386;257;271	Q15583;Q15583-2;F8VZB6	TGIF1_HUMAN;.;.	V	237;271;237;257;257;237;237;386;237;237;237	ENSP00000385206:A237V;ENSP00000447747:A271V;ENSP00000384970:A237V;ENSP00000339631:A257V;ENSP00000384133:A257V;ENSP00000450025:A237V;ENSP00000343969:A237V;ENSP00000327959:A386V;ENSP00000449580:A237V;ENSP00000383031:A237V;ENSP00000449501:A237V	.	A	+	2	0	TGIF1	3447889	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.442000	0.80503	2.474000	0.83562	0.563000	0.77884	GCA			0.478	TGIF1-003	KNOWN	basic|CCDS	protein_coding	protein_coding		OTTHUMT00000254368.4		NM_170695	
EPB41L3	23136	mdanderson.org	37	18	5445201	5445201	+	Missense_Mutation	SNP	G	G	T			TCGA-ZM-AA0D-01A-11D-A435-10	TCGA-ZM-AA0D-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	cbb77b02-9739-4272-bf41-30251840590b	7ac40e81-4d59-492f-a5cf-f3b25df9905c	g.chr18:5445201G>T	ENST00000341928.2	-	4	764	c.424C>A	c.(424-426)Cac>Aac	p.H142N	EPB41L3_ENST00000400111.3_Missense_Mutation_p.H142N|EPB41L3_ENST00000342933.3_Missense_Mutation_p.H142N|EPB41L3_ENST00000540638.2_Missense_Mutation_p.H142N|EPB41L3_ENST00000544123.1_Missense_Mutation_p.H142N|EPB41L3_ENST00000542652.2_5'UTR	NM_012307.2	NP_036439.2	Q9Y2J2	E41L3_HUMAN	erythrocyte membrane protein band 4.1-like 3	142	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				apoptotic process (GO:0006915)|cortical actin cytoskeleton organization (GO:0030866)|cortical cytoskeleton organization (GO:0030865)|cytoskeletal anchoring at plasma membrane (GO:0007016)|myelin maintenance (GO:0043217)|neuron projection morphogenesis (GO:0048812)|paranodal junction assembly (GO:0030913)|protein localization to juxtaparanode region of axon (GO:0071205)|protein localization to paranode region of axon (GO:0002175)|protein localization to plasma membrane (GO:0072659)|regulation of cell shape (GO:0008360)	axolemma (GO:0030673)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)|juxtaparanode region of axon (GO:0044224)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)	structural constituent of cytoskeleton (GO:0005200)			breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(24)|lung(52)|ovary(5)|prostate(4)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	105						AAGTTCAAGTGTTCACACACT	0.393																																					p.H142N													.	.			0			c.C424A												191.0	151.0	164.0					18																	5445201		2203	4300	6503	SO:0001583	missense	23136	exon4			TCAAGTGTTCACA	AB023204	CCDS11838.1, CCDS62381.1, CCDS62382.1	18p11.32	2006-06-28			ENSG00000082397	ENSG00000082397			3380	protein-coding gene	gene with protein product		605331				9828140, 9892180	Standard	NM_012307		Approved	DAL1, KIAA0987, 4.1B	uc002kmt.1	Q9Y2J2	OTTHUMG00000131562	ENST00000341928.2:c.424C>A	18.37:g.5445201G>T	ENSP00000343158:p.His142Asn		57	0.0175438596	1		38	0.08	3	NM_012307	0		0	B7Z4I5|F5GX05|O95713|Q9BRP5	Missense_Mutation	SNP	ENST00000341928.2	37	CCDS11838.1	.	.	.	.	.	.	.	.	.	.	G	35	5.490986	0.96339	.	.	ENSG00000082397	ENST00000341928;ENST00000540638;ENST00000544123;ENST00000545076;ENST00000342933;ENST00000400111;ENST00000542652	T;T;T;T	0.77098	-1.07;-1.07;-1.07;-1.07	5.82	5.82	0.92795	FERM, N-terminal (1);Band 4.1 domain (1);FERM domain (1);	0.000000	0.85682	D	0.000000	D	0.90065	0.6897	M	0.87456	2.885	0.80722	D	1	D;P;D;D;B	0.71674	0.981;0.662;0.998;0.998;0.341	D;B;D;D;P	0.83275	0.978;0.356;0.996;0.992;0.483	D	0.90925	0.4786	10	0.72032	D	0.01	.	18.8665	0.92294	0.0:0.0:1.0:0.0	.	142;142;33;142;142	F5GX05;Q9Y2J2-3;A8K968;Q9Y2J2-2;Q9Y2J2	.;.;.;.;E41L3_HUMAN	N	142;33;142;33;142;142;223	ENSP00000343158:H142N;ENSP00000441174:H142N;ENSP00000341138:H142N;ENSP00000382981:H142N	ENSP00000343158:H142N	H	-	1	0	EPB41L3	5435201	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.527000	0.81931	2.753000	0.94483	0.467000	0.42956	CAC			0.393	EPB41L3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		OTTHUMT00000254424.1		NM_012307	
TTC39C	125488	mdanderson.org	37	18	21698092	21698092	+	Missense_Mutation	SNP	G	G	T			TCGA-ZM-AA0D-01A-11D-A435-10	TCGA-ZM-AA0D-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	cbb77b02-9739-4272-bf41-30251840590b	7ac40e81-4d59-492f-a5cf-f3b25df9905c	g.chr18:21698092G>T	ENST00000317571.3	+	8	1318	c.1082G>T	c.(1081-1083)tGg>tTg	p.W361L	RP11-799B12.2_ENST00000583782.1_RNA|TTC39C_ENST00000540918.2_Missense_Mutation_p.W54L|TTC39C_ENST00000304621.6_Missense_Mutation_p.W300L	NM_001135993.1	NP_001129465.1	Q8N584	TT39C_HUMAN	tetratricopeptide repeat domain 39C	361										breast(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|skin(1)	19						TTCATAGGTTGGTGCAGCATG	0.418																																					p.W361L													.	.			0			c.G1082T												123.0	113.0	116.0					18																	21698092		2203	4300	6503	SO:0001583	missense	125488	exon8			TAGGTTGGTGCAG	AK091080	CCDS32804.1, CCDS45839.1, CCDS58616.1	18q11.2	2014-02-07	2008-06-23	2008-06-23	ENSG00000168234	ENSG00000168234		"""Tetratricopeptide (TTC) repeat domain containing"""	26595	protein-coding gene	gene with protein product			"""chromosome 18 open reading frame 17"""	C18orf17		14702039	Standard	NM_153211		Approved	FLJ33761, HsT2697	uc002kuw.3	Q8N584	OTTHUMG00000179403	ENST00000317571.3:c.1082G>T	18.37:g.21698092G>T	ENSP00000323645:p.Trp361Leu		52	0	0		42	0.07	3	NM_001135993	6	0.00	0	B7WP63|J3QRR1|Q0VAJ2|Q8N284	Missense_Mutation	SNP	ENST00000317571.3	37	CCDS45839.1	.	.	.	.	.	.	.	.	.	.	G	28.1	4.892826	0.91889	.	.	ENSG00000168234	ENST00000304621;ENST00000317571;ENST00000540918	T;T;T	0.40476	1.03;1.03;1.03	5.45	5.45	0.79879	Tetratricopeptide-like helical (1);	0.000000	0.85682	D	0.000000	T	0.63803	0.2542	M	0.69185	2.1	0.80722	D	1	D	0.63880	0.993	D	0.68192	0.956	T	0.66444	-0.5922	10	0.87932	D	0	-16.9013	18.0387	0.89313	0.0:0.0:1.0:0.0	.	361	Q8N584	TT39C_HUMAN	L	300;361;54	ENSP00000306598:W300L;ENSP00000323645:W361L;ENSP00000443016:W54L	ENSP00000306598:W300L	W	+	2	0	TTC39C	19952090	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	9.227000	0.95236	2.544000	0.85801	0.655000	0.94253	TGG			0.418	TTC39C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000446107.1		NM_153211	
SLC25A23	79085	mdanderson.org	37	19	6444206	6444206	+	Missense_Mutation	SNP	G	G	T			TCGA-ZM-AA0D-01A-11D-A435-10	TCGA-ZM-AA0D-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	cbb77b02-9739-4272-bf41-30251840590b	7ac40e81-4d59-492f-a5cf-f3b25df9905c	g.chr19:6444206G>T	ENST00000301454.4	-	9	1284	c.1178C>A	c.(1177-1179)gCc>gAc	p.A393D	SLC25A23_ENST00000334510.5_Missense_Mutation_p.A393D|SLC25A23_ENST00000414491.2_Missense_Mutation_p.A154D|SLC25A23_ENST00000601760.1_5'UTR	NM_024103.2	NP_077008.2	Q9BV35	SCMC3_HUMAN	solute carrier family 25 (mitochondrial carrier; phosphate carrier), member 23	393					adenine nucleotide transport (GO:0051503)|cellular response to calcium ion (GO:0071277)|regulation of cellular respiration (GO:0043457)|regulation of oxidative phosphorylation (GO:0002082)|regulation of sequestering of calcium ion (GO:0051282)|transmembrane transport (GO:0055085)|urea homeostasis (GO:0097274)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)	calcium ion binding (GO:0005509)			endometrium(3)|kidney(1)|large_intestine(6)|lung(3)|ovary(2)|pancreas(1)|skin(1)	17						CGGGTAACTGGCTATCTGGCC	0.657																																					p.A393D													.	.			0			c.C1178A												31.0	28.0	29.0					19																	6444206		2203	4300	6503	SO:0001583	missense	79085	exon9			TAACTGGCTATCT	AJ619962	CCDS32882.1	19p13.1	2014-02-06			ENSG00000125648	ENSG00000125648		"""Solute carriers"", ""EF-hand domain containing"""	19375	protein-coding gene	gene with protein product		608746				15123600	Standard	NM_024103		Approved	FLJ30339, MGC2615, APC2	uc002mex.1	Q9BV35	OTTHUMG00000180852	ENST00000301454.4:c.1178C>A	19.37:g.6444206G>T	ENSP00000301454:p.Ala393Asp		54	0	0		32	0.09	3	NM_024103	15	0.00	0	B4DGB6|Q4LBC2|Q705K3|Q86Y43|Q8N2N4|Q96NQ4	Missense_Mutation	SNP	ENST00000301454.4	37	CCDS32882.1	.	.	.	.	.	.	.	.	.	.	G	33	5.205636	0.95033	.	.	ENSG00000125648	ENST00000264088;ENST00000422102;ENST00000301454;ENST00000414491;ENST00000334510	T;T;T;T	0.80480	-1.29;-1.38;-1.38;-1.29	5.04	5.04	0.67666	Mitochondrial carrier domain (2);	0.000000	0.85682	D	0.000000	D	0.94009	0.8081	H	0.98738	4.315	0.80722	D	1	P;D	0.63880	0.908;0.993	P;D	0.70716	0.835;0.97	D	0.96484	0.9358	10	0.72032	D	0.01	-26.5945	17.1508	0.86777	0.0:0.0:1.0:0.0	.	154;393	E7ESZ5;Q9BV35	.;SCMC3_HUMAN	D	440;94;393;154;393	ENSP00000264088:A440D;ENSP00000301454:A393D;ENSP00000408814:A154D;ENSP00000334537:A393D	ENSP00000264088:A440D	A	-	2	0	SLC25A23	6395206	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.345000	0.97053	2.345000	0.79718	0.462000	0.41574	GCC			0.657	SLC25A23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000453325.1		NM_024103	
GPATCH1	55094	mdanderson.org	37	19	33610018	33610018	+	Missense_Mutation	SNP	G	G	T			TCGA-ZM-AA0D-01A-11D-A435-10	TCGA-ZM-AA0D-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	cbb77b02-9739-4272-bf41-30251840590b	7ac40e81-4d59-492f-a5cf-f3b25df9905c	g.chr19:33610018G>T	ENST00000170564.2	+	17	2830	c.2516G>T	c.(2515-2517)tGc>tTc	p.C839F		NM_018025.2	NP_060495.2	Q9BRR8	GPTC1_HUMAN	G patch domain containing 1	839					mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)	nucleic acid binding (GO:0003676)			breast(4)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(15)|prostate(4)|skin(4)	40	Esophageal squamous(110;0.137)					CCCGTCTTCTGCCCCAGTGAG	0.557											OREG0025409	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.C839F	Pancreas(67;88 1713 4567 18227)												.	.			0			c.G2516T												33.0	31.0	32.0					19																	33610018		2203	4300	6503	SO:0001583	missense	55094	exon17			TCTTCTGCCCCAG	AF434677	CCDS12428.1	19q13.12	2013-01-28		2006-12-13		ENSG00000076650		"""G patch domain containing"""	24658	protein-coding gene	gene with protein product	"""evolutionarily conserved G patch domain containing"""			GPATC1		12477932	Standard	NM_018025		Approved	ECGP, FLJ10206, FLJ38686	uc002nug.1	Q9BRR8		ENST00000170564.2:c.2516G>T	19.37:g.33610018G>T	ENSP00000170564:p.Cys839Phe		35	0	0	841	45	0.07	3	NM_018025	66	0.00	0	Q8IZV6|Q8N3B7|Q9NW94	Missense_Mutation	SNP	ENST00000170564.2	37	CCDS12428.1	.	.	.	.	.	.	.	.	.	.	G	16.54	3.152009	0.57151	.	.	ENSG00000076650	ENST00000170564	T	0.11277	2.79	4.79	4.79	0.61399	.	0.329050	0.31936	N	0.006828	T	0.19327	0.0464	L	0.57536	1.79	0.30422	N	0.778014	D;D	0.57899	0.981;0.981	P;P	0.51999	0.491;0.687	T	0.02983	-1.1086	10	0.54805	T	0.06	-10.5665	11.5995	0.50995	0.0:0.1801:0.8198:0.0	.	839;839	B2RDX4;Q9BRR8	.;GPTC1_HUMAN	F	839	ENSP00000170564:C839F	ENSP00000170564:C839F	C	+	2	0	GPATCH1	38301858	1.000000	0.71417	1.000000	0.80357	0.873000	0.50193	1.873000	0.39558	2.358000	0.79984	0.655000	0.94253	TGC			0.557	GPATCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000450834.1		NM_018025	
ZNF135	7694	broad.mit.edu	37	19	58578438	58578438	+	Missense_Mutation	SNP	A	A	G			TCGA-ZM-AA0D-01A-11D-A435-10	TCGA-ZM-AA0D-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	cbb77b02-9739-4272-bf41-30251840590b	7ac40e81-4d59-492f-a5cf-f3b25df9905c	g.chr19:58578438A>G	ENST00000313434.5	+	5	687	c.586A>G	c.(586-588)Agg>Ggg	p.R196G	RN7SL526P_ENST00000469492.2_RNA|ZNF135_ENST00000439855.2_Missense_Mutation_p.R196G|ZNF135_ENST00000511556.1_Missense_Mutation_p.R208G|ZNF135_ENST00000401053.4_Missense_Mutation_p.R220G|ZNF135_ENST00000359978.6_Missense_Mutation_p.R208G|ZNF135_ENST00000506786.1_Missense_Mutation_p.R154G	NM_003436.3	NP_003427.3	P52742	ZN135_HUMAN	zinc finger protein 135	196					cytoskeleton organization (GO:0007010)|regulation of cell morphogenesis (GO:0022604)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(3)|large_intestine(6)|liver(2)|lung(26)|ovary(1)|skin(1)|urinary_tract(1)	41		Colorectal(82;0.000256)|all_neural(62;0.0412)|Breast(46;0.147)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0161)		ACGTGGAAAAAGGGAGAAGCC	0.458																																					p.R220G													ZNF135_ENST00000401053,right_upper_lobe,carcinoma,0,2	ZNF135	159	2	0			c.A658G												65.0	64.0	65.0					19																	58578438		2203	4300	6503	SO:0001583	missense	7694	exon4			GGAAAAAGGGAGA	U09413	CCDS12970.1, CCDS12970.2, CCDS54329.1, CCDS54330.1, CCDS74471.1, CCDS74472.1	19q13.4	2013-01-08	2006-05-12			ENSG00000176293		"""Zinc fingers, C2H2-type"", ""-"""	12919	protein-coding gene	gene with protein product		604077	"""zinc finger protein 61"", ""zinc finger protein 135 (clone pHZ-17)"""	ZNF61, ZNF78L1		7557990, 1505991	Standard	NM_003436		Approved	pHZ-17	uc002qrg.3	P52742		ENST00000313434.5:c.586A>G	19.37:g.58578438A>G	ENSP00000321406:p.Arg196Gly		71	0	0		65	0.05	3	NM_007134	17	0.00	0	B4DHH9|E9PEV2|F5GYY9|I3L0B3|Q5U5L3|Q8N1I7	Missense_Mutation	SNP	ENST00000313434.5	37		.	.	.	.	.	.	.	.	.	.	A	8.387	0.838946	0.16891	.	.	ENSG00000176293	ENST00000504540;ENST00000401053;ENST00000359978;ENST00000439855;ENST00000313434;ENST00000511556;ENST00000506786	T;T;T;T;T;T	0.06294	3.42;3.49;3.43;3.43;3.43;3.32	2.94	2.94	0.34122	.	.	.	.	.	T	0.05960	0.0155	L	0.42245	1.32	0.09310	N	0.999991	B;B;B	0.23185	0.004;0.081;0.01	B;B;B	0.18263	0.003;0.021;0.004	T	0.28038	-1.0056	9	0.44086	T	0.13	.	4.798	0.13282	0.8599:0.0:0.1401:0.0	.	208;196;208	E9PEV2;P52742;Q8N1I7	.;ZN135_HUMAN;.	G	208;220;208;196;196;208;154	ENSP00000441410:R220G;ENSP00000369437:R208G;ENSP00000444828:R196G;ENSP00000321406:R196G;ENSP00000422074:R208G;ENSP00000427691:R154G	ENSP00000321406:R196G	R	+	1	2	ZNF135	63270250	.	.	0.003000	0.11579	0.052000	0.14988	.	.	1.609000	0.50190	0.374000	0.22700	AGG			0.458	ZNF135-003	KNOWN	basic|appris_candidate	protein_coding	protein_coding		OTTHUMT00000361899.2		NM_003436	
ALK	238	mdanderson.org	37	2	30143262	30143262	+	Silent	SNP	G	G	T			TCGA-ZM-AA0D-01A-11D-A435-10	TCGA-ZM-AA0D-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	cbb77b02-9739-4272-bf41-30251840590b	7ac40e81-4d59-492f-a5cf-f3b25df9905c	g.chr2:30143262G>T	ENST00000389048.3	-	1	1170	c.264C>A	c.(262-264)cgC>cgA	p.R88R	ALK_ENST00000431873.1_Silent_p.R88R	NM_004304.4	NP_004295.2	Q9UM73	ALK_HUMAN	anaplastic lymphoma receptor tyrosine kinase	88					activation of MAPK activity (GO:0000187)|cell proliferation (GO:0008283)|neuron development (GO:0048666)|NIK/NF-kappaB signaling (GO:0038061)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphorylation (GO:0016310)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein autophosphorylation (GO:0046777)|regulation of apoptotic process (GO:0042981)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|protein complex (GO:0043234)	ATP binding (GO:0005524)|NF-kappaB-inducing kinase activity (GO:0004704)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)		ATIC/ALK(24)|FN1/ALK(2)|C2orf44/ALK(2)|TPM3/ALK(33)|KLC1/ALK(2)|VCL/ALK(4)|TPM4/ALK(12)|KIF5B/ALK(8)|RANBP2/ALK(34)|SQSTM1/ALK(2)|EML4/ALK(543)|PPFIBP1/ALK(3)|SEC31A/ALK(3)|NPM1/ALK(632)|CLTC/ALK(44)|CARS/ALK(5)|MSN/ALK(6)|TFG/ALK(9)	NS(2)|autonomic_ganglia(198)|breast(8)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(7)|kidney(4)|large_intestine(25)|lung(61)|ovary(6)|pancreas(1)|prostate(2)|skin(5)|soft_tissue(3)|stomach(2)|thyroid(2)	340	Acute lymphoblastic leukemia(172;0.155)				Adenosine triphosphate(DB00171)|Crizotinib(DB08865)	CTAGCGAGCCGCGGGCCTCGG	0.716			"""T, Mis, A"""	"""NPM1, TPM3, TFG, TPM4, ATIC, CLTC, MSN, ALO17, CARS, EML4, KIF5B, C2orf22"""	"""ALCL, NSCLC, Neuroblastoma"""	neuroblastoma			Neuroblastoma, Familial Clustering of;Congenital Central Hypoventilation Syndrome																												p.R88R			yes	Dom	yes	Familial neuroblastoma	2	2p23	238	anaplastic lymphoma kinase (Ki-1)		"""L, E, M"""	.	.			0			c.C264A												12.0	14.0	13.0					2																	30143262		2177	4244	6421	SO:0001819	synonymous_variant	238	exon1	Familial Cancer Database	Familial Neuroblastoma;CCHS, Ondine Curse, incl. Ondine-Hirschsprung Disease	CGAGCCGCGGGCC	D45915	CCDS33172.1	2p23	2014-09-17	2008-01-23		ENSG00000171094	ENSG00000171094		"""CD molecules"""	427	protein-coding gene	gene with protein product		105590	"""anaplastic lymphoma kinase (Ki-1)"""			8122112	Standard	NM_004304		Approved	CD246	uc002rmy.3	Q9UM73	OTTHUMG00000152034	ENST00000389048.3:c.264C>A	2.37:g.30143262G>T			33	0	0		37	0.08	3	NM_004304	0		0	Q4ZFX9|Q53QQ6|Q53RZ4|Q59FI3|Q9Y4K6	Silent	SNP	ENST00000389048.3	37	CCDS33172.1																																																																																					0.716	ALK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000324994.1		NM_004304	
RANBP2	5903	broad.mit.edu;bcgsc.ca;mdanderson.org	37	2	109382856	109382856	+	Missense_Mutation	SNP	C	C	T			TCGA-ZM-AA0D-01A-11D-A435-10	TCGA-ZM-AA0D-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	cbb77b02-9739-4272-bf41-30251840590b	7ac40e81-4d59-492f-a5cf-f3b25df9905c	g.chr2:109382856C>T	ENST00000283195.6	+	20	5987	c.5861C>T	c.(5860-5862)aCt>aTt	p.T1954I		NM_006267.4	NP_006258.3	P49792	RBP2_HUMAN	RAN binding protein 2	1954					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|negative regulation of glucokinase activity (GO:0033132)|protein folding (GO:0006457)|protein import into nucleus (GO:0006606)|protein sumoylation (GO:0016925)|regulation of gluconeogenesis involved in cellular glucose homeostasis (GO:0090526)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)	ligase activity (GO:0016874)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|Ran GTPase binding (GO:0008536)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)		RANBP2/ALK(34)	NS(1)|biliary_tract(1)|breast(3)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(21)|large_intestine(19)|lung(51)|pancreas(1)|prostate(8)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1)	129						GCAAAATCAACTTCAGGAGAA	0.418																																					p.T1954I													.	RANBP2	488		0			c.C5861T												106.0	115.0	112.0					2																	109382856		2188	4284	6472	SO:0001583	missense	5903	exon20			AATCAACTTCAGG	D42063	CCDS2079.1	2q13	2013-11-14			ENSG00000153201	ENSG00000153201		"""Tetratricopeptide (TTC) repeat domain containing"""	9848	protein-coding gene	gene with protein product		601181	"""acute necrotizing encephalopathy 1 (autosomal dominant)"""	ANE1		7724562, 19118815	Standard	NM_006267		Approved	NUP358, ADANE	uc002tem.4	P49792	OTTHUMG00000130981	ENST00000283195.6:c.5861C>T	2.37:g.109382856C>T	ENSP00000283195:p.Thr1954Ile		872	0	0		1062	0.07	79	NM_006267	4	0.00	0	Q13074|Q15280|Q53TE2|Q59FH7	Missense_Mutation	SNP	ENST00000283195.6	37	CCDS2079.1	.	.	.	.	.	.	.	.	.	.	C	9.563	1.118997	0.20877	.	.	ENSG00000153201	ENST00000409491;ENST00000283195	T	0.27890	1.64	5.34	3.49	0.39957	.	.	.	.	.	T	0.26304	0.0642	L	0.44542	1.39	0.22500	N	0.999044	B	0.10296	0.003	B	0.08055	0.003	T	0.18713	-1.0328	9	0.49607	T	0.09	-4.7021	9.1494	0.36953	0.2735:0.6558:0.0:0.0707	.	1954	P49792	RBP2_HUMAN	I	978;1954	ENSP00000283195:T1954I	ENSP00000283195:T1954I	T	+	2	0	RANBP2	108749288	1.000000	0.71417	0.978000	0.43139	0.979000	0.70002	3.789000	0.55454	0.674000	0.31244	0.557000	0.71058	ACT			0.418	RANBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000253594.1		NM_006267	
SMOX	54498	hgsc.bcm.edu;broad.mit.edu	37	20	4162476	4162476	+	Frame_Shift_Del	DEL	C	C	-			TCGA-ZM-AA0D-01A-11D-A435-10	TCGA-ZM-AA0D-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	cbb77b02-9739-4272-bf41-30251840590b	7ac40e81-4d59-492f-a5cf-f3b25df9905c	g.chr20:4162476delC	ENST00000305958.4	+	4	687	c.462delC	c.(460-462)ttcfs	p.F154fs	SMOX_ENST00000346595.2_Intron|SMOX_ENST00000339123.6_Frame_Shift_Del_p.F154fs|SMOX_ENST00000278795.3_Frame_Shift_Del_p.F154fs|SMOX_ENST00000484515.1_3'UTR|SMOX_ENST00000379460.2_Frame_Shift_Del_p.F154fs	NM_175839.2	NP_787033.1	Q9NWM0	SMOX_HUMAN	spermine oxidase	154					cellular nitrogen compound metabolic process (GO:0034641)|oxidation-reduction process (GO:0055114)|polyamine biosynthetic process (GO:0006596)|polyamine catabolic process (GO:0006598)|polyamine metabolic process (GO:0006595)|small molecule metabolic process (GO:0044281)|spermine catabolic process (GO:0046208)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	N1-acetylspermine:oxygen oxidoreductase (N1-acetylspermidine-forming) activity (GO:0052895)|norspermine:oxygen oxidoreductase activity (GO:0052894)|polyamine oxidase activity (GO:0046592)|spermine:oxygen oxidoreductase (spermidine-forming) activity (GO:0052901)			breast(1)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(7)|lung(5)|skin(2)|urinary_tract(1)	26					Spermine(DB00127)	AGGAGTTCTTCCGGCACGATA	0.527																																					p.F154fs													.	SMOX	119		0			c.461delT												93.0	91.0	92.0					20																	4162476		2203	4300	6503	SO:0001589	frameshift_variant	54498	exon4			GTTCTTCCGGCAC	AK000753	CCDS13075.1, CCDS13076.1, CCDS13077.1, CCDS13078.1, CCDS74702.1	20p13	2003-10-15	2003-10-15	2003-10-15	ENSG00000088826	ENSG00000088826			15862	protein-coding gene	gene with protein product		615854	"""chromosome 20 open reading frame 16"""	C20orf16		11454677, 12398765	Standard	NM_175839		Approved	FLJ20746, dJ779E11.1, PAO, PAOh1, MGC1010, SMO	uc002wkp.3	Q9NWM0	OTTHUMG00000031777	ENST00000305958.4:c.462delC	20.37:g.4162476delC	ENSP00000307252:p.Phe154fs		116	0	0		114	0.10	11	NM_175839	9	0.00	0	A2A2P5|A2A2P6|A8BE87|D3DVZ4|Q5TE26|Q5TE27|Q6UY28|Q8IX00|Q96LC3|Q96LC4|Q96QT3|Q9BW38|Q9H6H1|Q9NP51|Q9NPY1|Q9NPY2	Frame_Shift_Del	DEL	ENST00000305958.4	37	CCDS13075.1																																																																																					0.527	SMOX-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000077806.1		NM_175842	
TTLL9	164395	mdanderson.org	37	20	30486361	30486361	+	Missense_Mutation	SNP	G	G	T			TCGA-ZM-AA0D-01A-11D-A435-10	TCGA-ZM-AA0D-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	cbb77b02-9739-4272-bf41-30251840590b	7ac40e81-4d59-492f-a5cf-f3b25df9905c	g.chr20:30486361G>T	ENST00000375938.4	+	4	452	c.199G>T	c.(199-201)Gtg>Ttg	p.V67L	TTLL9_ENST00000375922.4_Missense_Mutation_p.V17L|TTLL9_ENST00000310998.4_Missense_Mutation_p.V17L|TTLL9_ENST00000535842.1_Missense_Mutation_p.V67L|TTLL9_ENST00000375934.4_Missense_Mutation_p.V49L|TTLL9_ENST00000375921.2_Missense_Mutation_p.V17L|RNU1-94P_ENST00000362627.1_RNA			Q3SXZ7	TTLL9_HUMAN	tubulin tyrosine ligase-like family, member 9	67	TTL. {ECO:0000255|PROSITE- ProRule:PRU00568}.				cellular protein modification process (GO:0006464)	cilium (GO:0005929)|cytoplasm (GO:0005737)|microtubule (GO:0005874)	ligase activity (GO:0016874)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	26			Colorectal(19;0.00306)|COAD - Colon adenocarcinoma(19;0.0347)			ATGGGTGGAAGTGAAGGAGTA	0.562																																					p.V67L													.	.			0			c.G199T												84.0	86.0	86.0					20																	30486361		2042	4192	6234	SO:0001583	missense	164395	exon4			GTGGAAGTGAAGG	AL031658	CCDS42863.1	20q11	2013-02-14	2005-07-28	2005-07-28		ENSG00000131044		"""Tubulin tyrosine ligase-like family"""	16118	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 125"""	C20orf125		15890843	Standard	NM_001008409		Approved	dJ310O13.1	uc010gdx.1	Q3SXZ7		ENST00000375938.4:c.199G>T	20.37:g.30486361G>T	ENSP00000365105:p.Val67Leu		147	0	0		106	0.05	5	NM_001008409	0		0	A6NH06|A6NIS5|B3KSG8|Q3SXZ8|Q5JYS3|Q5JYS4	Missense_Mutation	SNP	ENST00000375938.4	37	CCDS42863.1	.	.	.	.	.	.	.	.	.	.	G	17.38	3.374997	0.61735	.	.	ENSG00000131044	ENST00000375938;ENST00000535842;ENST00000310998;ENST00000375921;ENST00000375935;ENST00000375934;ENST00000375922	T;T;T;T;T;T	0.11277	3.73;3.73;3.71;3.01;2.79;3.72	5.48	5.48	0.80851	.	0.152261	0.24693	U	0.036379	T	0.13756	0.0333	M	0.64080	1.96	0.43152	D	0.994923	P	0.35124	0.485	B	0.29598	0.104	T	0.01604	-1.1314	10	0.66056	D	0.02	.	14.8474	0.70270	0.0:0.0:1.0:0.0	.	67	Q3SXZ7	TTLL9_HUMAN	L	67;67;17;17;49;49;17	ENSP00000365105:V67L;ENSP00000442515:V67L;ENSP00000308980:V17L;ENSP00000365086:V17L;ENSP00000365100:V49L;ENSP00000365088:V17L	ENSP00000308980:V17L	V	+	1	0	TTLL9	29950022	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	5.431000	0.66507	2.582000	0.87167	0.563000	0.77884	GTG			0.562	TTLL9-205	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				NM_001008409	
SALL4	57167	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	20	50408195	50408195	+	Missense_Mutation	SNP	C	C	T			TCGA-ZM-AA0D-01A-11D-A435-10	TCGA-ZM-AA0D-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	cbb77b02-9739-4272-bf41-30251840590b	7ac40e81-4d59-492f-a5cf-f3b25df9905c	g.chr20:50408195C>T	ENST00000217086.4	-	2	938	c.827G>A	c.(826-828)aGc>aAc	p.S276N	SALL4_ENST00000395997.3_Missense_Mutation_p.S276N|SALL4_ENST00000483130.1_5'Flank|SALL4_ENST00000371539.3_Intron	NM_020436.3	NP_065169.1	Q9UJQ4	SALL4_HUMAN	spalt-like transcription factor 4	276					embryonic limb morphogenesis (GO:0030326)|inner cell mass cell proliferation (GO:0001833)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)|ventricular septum development (GO:0003281)	cytoplasm (GO:0005737)|heterochromatin (GO:0000792)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(27)|ovary(5)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						AGCTTTCTGGCTGAGCAAAGC	0.607																																					p.S276N													.	.			0			c.G827A												53.0	44.0	47.0					20																	50408195		2203	4300	6503	SO:0001583	missense	57167	exon2			TTCTGGCTGAGCA	AK001666	CCDS13438.1	20q13.2	2014-09-17	2013-10-17		ENSG00000101115	ENSG00000101115		"""Zinc fingers, C2H2-type"""	15924	protein-coding gene	gene with protein product		607343	"""sal (Drosophila)-like 4"", ""sal-like 4 (Drosophila)"""				Standard	NM_020436		Approved	dJ1112F19.1, ZNF797	uc002xwh.4	Q9UJQ4	OTTHUMG00000032752	ENST00000217086.4:c.827G>A	20.37:g.50408195C>T	ENSP00000217086:p.Ser276Asn		45	0	0		47	0.11	5	NM_020436	12	0.17	2	A2A2D8|Q540H3|Q6Y8G6	Missense_Mutation	SNP	ENST00000217086.4	37	CCDS13438.1	.	.	.	.	.	.	.	.	.	.	C	12.95	2.091002	0.36855	.	.	ENSG00000101115	ENST00000217086;ENST00000395997	T;T	0.70749	-0.51;-0.51	5.29	4.35	0.52113	.	0.116249	0.39759	N	0.001276	T	0.71863	0.3390	M	0.80028	2.48	0.80722	D	1	B;B	0.18863	0.031;0.003	B;B	0.10450	0.005;0.003	T	0.72004	-0.4421	10	0.87932	D	0	-37.3797	13.21	0.59819	0.0:0.9227:0.0:0.0773	.	276;276	A2A2D8;Q9UJQ4	.;SALL4_HUMAN	N	276	ENSP00000217086:S276N;ENSP00000379319:S276N	ENSP00000217086:S276N	S	-	2	0	SALL4	49841602	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.836000	0.62789	1.225000	0.43566	0.655000	0.94253	AGC			0.607	SALL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000079738.3			
CDC42EP1	11135	mdanderson.org	37	22	37964167	37964167	+	Silent	SNP	G	G	A			TCGA-ZM-AA0D-01A-11D-A435-10	TCGA-ZM-AA0D-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	cbb77b02-9739-4272-bf41-30251840590b	7ac40e81-4d59-492f-a5cf-f3b25df9905c	g.chr22:37964167G>A	ENST00000249014.4	+	3	936	c.516G>A	c.(514-516)ccG>ccA	p.P172P		NM_152243.2	NP_689449.1	Q00587	BORG5_HUMAN	CDC42 effector protein (Rho GTPase binding) 1	172					positive regulation of pseudopodium assembly (GO:0031274)|regulation of cell shape (GO:0008360)|Rho protein signal transduction (GO:0007266)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)				endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(2)|lung(4)|prostate(5)	15	Melanoma(58;0.0574)					CGGAAAAGCCGCATGACCGAG	0.647																																					p.P172P													.	.			0			c.G516A												85.0	95.0	92.0					22																	37964167		2203	4300	6503	SO:0001819	synonymous_variant	11135	exon3			AAAGCCGCATGAC	M88338	CCDS13949.1	22q13.1	2008-06-11			ENSG00000128283	ENSG00000128283			17014	protein-coding gene	gene with protein product	"""55 kDa bone marrow stromal/endothelial cell protein"", ""serum constituent protein"""	606084				1629197, 10430899	Standard	NM_152243		Approved	MSE55, CEP1, Borg5	uc003asz.4	Q00587	OTTHUMG00000150591	ENST00000249014.4:c.516G>A	22.37:g.37964167G>A			70	0	0		46	0.07	3	NM_152243	45	0.00	0	A8K825|Q96GN1	Silent	SNP	ENST00000249014.4	37	CCDS13949.1																																																																																					0.647	CDC42EP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000318993.1		NM_152243	
ATP2B2	491	mdanderson.org	37	3	10426999	10426999	+	Missense_Mutation	SNP	G	G	A			TCGA-ZM-AA0D-01A-11D-A435-10	TCGA-ZM-AA0D-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	cbb77b02-9739-4272-bf41-30251840590b	7ac40e81-4d59-492f-a5cf-f3b25df9905c	g.chr3:10426999G>A	ENST00000352432.4	-	7	1022	c.953C>T	c.(952-954)gCg>gTg	p.A318V	ATP2B2_ENST00000397077.1_Intron|ATP2B2_ENST00000383800.4_Intron|ATP2B2_ENST00000360273.2_Missense_Mutation_p.A318V|ATP2B2_ENST00000343816.4_Missense_Mutation_p.A318V			Q01814	AT2B2_HUMAN	ATPase, Ca++ transporting, plasma membrane 2	318					auditory receptor cell stereocilium organization (GO:0060088)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cerebellar granule cell differentiation (GO:0021707)|cerebellar Purkinje cell differentiation (GO:0021702)|cGMP metabolic process (GO:0046068)|cochlea development (GO:0090102)|cytosolic calcium ion homeostasis (GO:0051480)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|ion transmembrane transport (GO:0034220)|lactation (GO:0007595)|locomotion (GO:0040011)|locomotory behavior (GO:0007626)|neuromuscular process controlling balance (GO:0050885)|neuron differentiation (GO:0030182)|organelle organization (GO:0006996)|otolith mineralization (GO:0045299)|positive regulation of calcium ion transport (GO:0051928)|regulation of cell size (GO:0008361)|regulation of synaptic plasticity (GO:0048167)|sensory perception of sound (GO:0007605)|serotonin metabolic process (GO:0042428)|synapse organization (GO:0050808)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|cilium (GO:0005929)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calcium-dependent ATPase activity (GO:0030899)|calcium-transporting ATPase activity (GO:0005388)|calmodulin binding (GO:0005516)|metal ion binding (GO:0046872)|PDZ domain binding (GO:0030165)|protein C-terminus binding (GO:0008022)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(7)|large_intestine(19)|lung(29)|ovary(5)|prostate(2)|skin(4)|stomach(2)|urinary_tract(2)	74						TGAAGCTGCCGCACCGTCTGC	0.547																																					p.A318V	Ovarian(125;1619 1709 15675 19819 38835)												.	.			0			c.C953T												54.0	47.0	50.0					3																	10426999		2203	4300	6503	SO:0001583	missense	491	exon8			GCTGCCGCACCGT	X63575	CCDS2601.1, CCDS33701.1	3p25.3	2010-04-20	2001-12-04		ENSG00000157087	ENSG00000157087	3.6.3.8	"""ATPases / P-type"""	815	protein-coding gene	gene with protein product	"""plasma membrane Ca2+ pump 2"", ""plasma membrane calcium-transporting ATPase 2"""	108733				1313367	Standard	NM_001001331		Approved	PMCA2	uc003bvt.3	Q01814	OTTHUMG00000128679	ENST00000352432.4:c.953C>T	3.37:g.10426999G>A	ENSP00000324172:p.Ala318Val		38	0.0263157895	1		46	0.07	3	NM_001001331	0		0	O00766|Q12994|Q16818	Missense_Mutation	SNP	ENST00000352432.4	37	CCDS33701.1	.	.	.	.	.	.	.	.	.	.	G	13.67	2.305935	0.40795	.	.	ENSG00000157087	ENST00000352432;ENST00000360273;ENST00000343816;ENST00000342354	D;D;D	0.92149	-2.94;-2.94;-2.98	5.34	3.52	0.40303	ATPase, P-type, ATPase-associated domain (1);	0.820878	0.10281	N	0.693572	D	0.84334	0.5449	N	0.08118	0	0.45464	D	0.998431	P	0.44260	0.83	B	0.43155	0.41	T	0.75105	-0.3435	10	0.28530	T	0.3	-13.2372	10.8322	0.46667	0.0714:0.1312:0.7974:0.0	.	318	Q01814	AT2B2_HUMAN	V	318	ENSP00000324172:A318V;ENSP00000353414:A318V;ENSP00000344677:A318V	ENSP00000342954:A318V	A	-	2	0	ATP2B2	10401999	1.000000	0.71417	0.975000	0.42487	0.708000	0.40852	4.972000	0.63756	0.610000	0.30035	-0.379000	0.06801	GCG			0.547	ATP2B2-001	KNOWN	basic|CCDS	protein_coding	protein_coding		OTTHUMT00000250576.2		NM_001683	
STT3B	201595	mdanderson.org	37	3	31641852	31641852	+	Splice_Site	SNP	G	G	T			TCGA-ZM-AA0D-01A-11D-A435-10	TCGA-ZM-AA0D-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	cbb77b02-9739-4272-bf41-30251840590b	7ac40e81-4d59-492f-a5cf-f3b25df9905c	g.chr3:31641852G>T	ENST00000295770.2	+	5	987	c.778G>T	c.(778-780)Gtc>Ttc	p.V260F	STT3B_ENST00000453168.1_3'UTR	NM_178862.1	NP_849193.1	Q8TCJ2	STT3B_HUMAN	STT3B, subunit of the oligosaccharyltransferase complex (catalytic)	260					co-translational protein modification (GO:0043686)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|glycoprotein catabolic process (GO:0006516)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|response to unfolded protein (GO:0006986)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|oligosaccharyltransferase complex (GO:0008250)	dolichyl-diphosphooligosaccharide-protein glycotransferase activity (GO:0004579)			autonomic_ganglia(1)|biliary_tract(1)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	19						TTTCCTATAGGTCTCTGCTTG	0.294																																					p.V260F													.	.			0			c.G778T												151.0	136.0	141.0					3																	31641852		2203	4298	6501	SO:0001630	splice_region_variant	201595	exon5			CTATAGGTCTCTG	AK027789	CCDS2650.1	3p24.1	2013-03-06	2013-03-06		ENSG00000163527	ENSG00000163527	2.4.99.18		30611	protein-coding gene	gene with protein product	"""source of immunodominant MHC associated peptides"", ""dolichyl-diphosphooligosaccharide protein glycotransferase"""	608605	"""STT3, subunit of the oligosaccharyltransferase complex, homolog B (S. cerevisiae)"""			12887896, 12439619	Standard	XM_006713017		Approved	SIMP, FLJ90106, STT3-B	uc011axe.2	Q8TCJ2	OTTHUMG00000130673	ENST00000295770.2:c.778-1G>T	3.37:g.31641852G>T			40	0	0		37	0.08	3	NM_178862	9	0.00	0	Q96JZ4|Q96KY7	Missense_Mutation	SNP	ENST00000295770.2	37	CCDS2650.1	.	.	.	.	.	.	.	.	.	.	G	27.5	4.836656	0.91117	.	.	ENSG00000163527	ENST00000295770	.	.	.	5.78	5.78	0.91487	.	0.000000	0.85682	D	0.000000	D	0.84275	0.5436	M	0.93328	3.405	0.80722	D	1	P	0.50617	0.937	P	0.55345	0.774	D	0.87723	0.2574	8	.	.	.	-4.7059	18.7792	0.91925	0.0:0.0:1.0:0.0	.	260	Q8TCJ2	STT3B_HUMAN	F	260	.	.	V	+	1	0	STT3B	31616856	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	9.187000	0.94912	2.703000	0.92315	0.650000	0.86243	GTC			0.294	STT3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000253166.2		NM_178862	Missense_Mutation
PTPN23	25930	mdanderson.org	37	3	47446253	47446253	+	Missense_Mutation	SNP	G	G	A			TCGA-ZM-AA0D-01A-11D-A435-10	TCGA-ZM-AA0D-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	cbb77b02-9739-4272-bf41-30251840590b	7ac40e81-4d59-492f-a5cf-f3b25df9905c	g.chr3:47446253G>A	ENST00000265562.4	+	3	348	c.271G>A	c.(271-273)Gct>Act	p.A91T	PTPN23_ENST00000431726.1_Intron	NM_015466.2	NP_056281.1	Q9H3S7	PTN23_HUMAN	protein tyrosine phosphatase, non-receptor type 23	91	BRO1. {ECO:0000255|PROSITE- ProRule:PRU00526}.				cilium morphogenesis (GO:0060271)|negative regulation of epithelial cell migration (GO:0010633)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of adherens junction organization (GO:1903393)|positive regulation of early endosome to late endosome transport (GO:2000643)|positive regulation of homophilic cell adhesion (GO:1903387)|protein transport (GO:0015031)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)	ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)			breast(3)|central_nervous_system(1)|large_intestine(5)|lung(7)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	23				BRCA - Breast invasive adenocarcinoma(193;0.000271)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		CCAGGAGGCCGCTGTCCCTGT	0.657																																					p.A91T													PTPN23,NS,carcinoma,0,1	PTPN23	0	1	0			c.G271A												28.0	29.0	29.0					3																	47446253		2203	4300	6503	SO:0001583	missense	25930	exon3			GAGGCCGCTGTCC	AB025194	CCDS2754.1	3p21.3	2011-06-09			ENSG00000076201	ENSG00000076201		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"""	14406	protein-coding gene	gene with protein product		606584				11095967	Standard	NM_015466		Approved	DKFZP564F0923, KIAA1471, HD-PTP	uc003crf.1	Q9H3S7	OTTHUMG00000133520	ENST00000265562.4:c.271G>A	3.37:g.47446253G>A	ENSP00000265562:p.Ala91Thr		81	0	0		64	0.08	5	NM_015466	9	0.00	0	A8K0D7|Q7KZF8|Q8N6Z5|Q9BSR5|Q9P257|Q9UG03|Q9UMZ4	Missense_Mutation	SNP	ENST00000265562.4	37	CCDS2754.1	.	.	.	.	.	.	.	.	.	.	G	19.40	3.820887	0.71028	.	.	ENSG00000076201	ENST00000456221;ENST00000456408;ENST00000265562	T;T	0.16897	2.31;2.31	5.95	5.06	0.68205	BRO1 domain (3);	0.178984	0.48286	D	0.000196	T	0.20780	0.0500	L	0.39397	1.21	0.53688	D	0.999974	D	0.60575	0.988	P	0.48770	0.589	T	0.00986	-1.1490	10	0.42905	T	0.14	-14.6282	13.1175	0.59307	0.0:0.0:0.709:0.291	.	91	Q9H3S7	PTN23_HUMAN	T	66;66;91	ENSP00000396328:A66T;ENSP00000265562:A91T	ENSP00000265562:A91T	A	+	1	0	PTPN23	47421257	1.000000	0.71417	0.470000	0.27216	0.804000	0.45430	4.680000	0.61656	1.483000	0.48342	0.655000	0.94253	GCT			0.657	PTPN23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000257492.2		NM_015466	
FAM86EP	348926	broad.mit.edu	37	4	3955156	3955156	+	RNA	DEL	C	C	-			TCGA-ZM-AA0D-01A-11D-A435-10	TCGA-ZM-AA0D-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	cbb77b02-9739-4272-bf41-30251840590b	7ac40e81-4d59-492f-a5cf-f3b25df9905c	g.chr4:3955156delC	ENST00000313946.8	-	0	92				AC226119.5_ENST00000281228.8_RNA					family with sequence similarity 86, member E, pseudogene																		AGGTCATGGGCCAGCTCCCTG	0.552																																					.													.	.			0			.																																											0	.			CATGGGCCAGCTC			4p16.3	2011-07-01			ENSG00000251669	ENSG00000251669			28017	pseudogene	pseudogene						12477932	Standard	NR_024253		Approved		uc011bvu.2		OTTHUMG00000159867		4.37:g.3955156delC			7	0	0		6	0.33	2	.	0		0		RNA	DEL	ENST00000313946.8	37																																																																																						0.552	FAM86EP-002	KNOWN	basic	processed_transcript	pseudogene		OTTHUMT00000357822.1			
CCDC96	257236	broad.mit.edu;mdanderson.org	37	4	7044591	7044591	+	Silent	SNP	C	C	T	rs372279731		TCGA-ZM-AA0D-01A-11D-A435-10	TCGA-ZM-AA0D-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	cbb77b02-9739-4272-bf41-30251840590b	7ac40e81-4d59-492f-a5cf-f3b25df9905c	g.chr4:7044591C>T	ENST00000310085.4	-	1	137	c.75G>A	c.(73-75)ccG>ccA	p.P25P	RP11-367J11.2_ENST00000500031.1_RNA|TADA2B_ENST00000512388.1_5'Flank|TADA2B_ENST00000310074.7_5'Flank	NM_153376.2	NP_699207.1	Q2M329	CCD96_HUMAN	coiled-coil domain containing 96	25										endometrium(3)|kidney(1)|large_intestine(3)|lung(2)|skin(1)|urinary_tract(1)	11						TGATCTTGGACGGCCGCGCGG	0.706																																					p.P25P													.	CCDC96	34		0			c.G75A							C		0,4328		0,0,2164	11.0	13.0	12.0		75	3.5	0.0	4		12	2,8550		0,2,4274	no	coding-synonymous	CCDC96	NM_153376.2		0,2,6438	TT,TC,CC		0.0234,0.0,0.0155		25/556	7044591	2,12878	2164	4276	6440	SO:0001819	synonymous_variant	257236	exon1			CTTGGACGGCCGC	AK075056	CCDS3395.1	4p16.1	2008-02-05			ENSG00000173013	ENSG00000173013			26900	protein-coding gene	gene with protein product							Standard	NM_153376		Approved	FLJ90575	uc003gjv.2	Q2M329	OTTHUMG00000125511	ENST00000310085.4:c.75G>A	4.37:g.7044591C>T			19	0	0		27	0.11	3	NM_153376	1	0.00	0	Q8N2I7	Silent	SNP	ENST00000310085.4	37	CCDS3395.1																																																																																					0.706	CCDC96-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000246838.1		NM_153376	
KIT	3815	broad.mit.edu;bcgsc.ca;mdanderson.org	37	4	55599320	55599320	+	Missense_Mutation	SNP	G	G	T	rs121913506		TCGA-ZM-AA0D-01A-11D-A435-10	TCGA-ZM-AA0D-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	cbb77b02-9739-4272-bf41-30251840590b	7ac40e81-4d59-492f-a5cf-f3b25df9905c	g.chr4:55599320G>T	ENST00000288135.5	+	17	2543	c.2446G>T	c.(2446-2448)Gac>Tac	p.D816Y		NM_000222.2|NM_001093772.1	NP_000213.1|NP_001087241.1	P10721	KIT_HUMAN	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	816	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		D -> F (in mastocytosis; requires 2 nucleotide substitutions; somatic mutation; constitutively activated and is much more rapidly autophosphorylated than wild type). {ECO:0000269|PubMed:9990072}.|D -> H (in a testicular tumor; seminoma; somatic mutation; constitutively activated; dbSNP:rs28933969). {ECO:0000269|PubMed:10362788}.|D -> V (in mast cell leukemia and mastocytosis; somatic mutation; constitutively activated; loss of interaction with MPDZ). {ECO:0000269|PubMed:7691885, ECO:0000269|PubMed:9990072}.|D -> Y (in acute myeloid leukemia, mastocytosis and a germ cell tumor of the testis; somatic mutation; constitutively activated). {ECO:0000269|PubMed:16175573, ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:9657776, ECO:0000269|PubMed:9990072}.		actin cytoskeleton reorganization (GO:0031532)|activation of MAPK activity (GO:0000187)|cell chemotaxis (GO:0060326)|cellular response to thyroid hormone stimulus (GO:0097067)|cytokine-mediated signaling pathway (GO:0019221)|dendritic cell cytokine production (GO:0002371)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|digestive tract development (GO:0048565)|ectopic germ cell programmed cell death (GO:0035234)|embryonic hemopoiesis (GO:0035162)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell proliferation (GO:0050673)|erythrocyte differentiation (GO:0030218)|erythropoietin-mediated signaling pathway (GO:0038162)|Fc receptor signaling pathway (GO:0038093)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell migration (GO:0008354)|glycosphingolipid metabolic process (GO:0006687)|hemopoiesis (GO:0030097)|immature B cell differentiation (GO:0002327)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|Kit signaling pathway (GO:0038109)|lamellipodium assembly (GO:0030032)|lymphoid progenitor cell differentiation (GO:0002320)|male gonad development (GO:0008584)|mast cell chemotaxis (GO:0002551)|mast cell cytokine production (GO:0032762)|mast cell degranulation (GO:0043303)|mast cell differentiation (GO:0060374)|mast cell proliferation (GO:0070662)|megakaryocyte development (GO:0035855)|melanocyte adhesion (GO:0097326)|melanocyte differentiation (GO:0030318)|melanocyte migration (GO:0097324)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of programmed cell death (GO:0043069)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ovarian follicle development (GO:0001541)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|pigmentation (GO:0043473)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of pseudopodium assembly (GO:0031274)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell proliferation (GO:0042127)|regulation of cell shape (GO:0008360)|regulation of developmental pigmentation (GO:0048070)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|somatic stem cell division (GO:0048103)|somatic stem cell maintenance (GO:0035019)|spermatid development (GO:0007286)|spermatogenesis (GO:0007283)|stem cell differentiation (GO:0048863)|stem cell maintenance (GO:0019827)|T cell differentiation (GO:0030217)|visual learning (GO:0008542)	acrosomal vesicle (GO:0001669)|cell-cell junction (GO:0005911)|cytoplasmic side of plasma membrane (GO:0009898)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|mast cell granule (GO:0042629)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cytokine binding (GO:0019955)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|stem cell factor receptor activity (GO:0005020)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.D816Y(46)|p.D816H(42)|p.D816F(6)|p.D816I(2)|p.D816N(1)|p.R815_D816insVI(1)		NS(8)|autonomic_ganglia(1)|bone(21)|breast(2)|central_nervous_system(4)|endometrium(10)|eye(12)|genital_tract(18)|haematopoietic_and_lymphoid_tissue(1820)|kidney(17)|large_intestine(17)|lung(27)|ovary(23)|pancreas(4)|prostate(1)|salivary_gland(15)|skin(228)|soft_tissue(4117)|stomach(3)|testis(55)|thymus(7)|upper_aerodigestive_tract(1)	6411	all_cancers(7;0.00453)|all_lung(4;0.000565)|Lung NSC(11;0.00129)|all_epithelial(27;0.0104)|Glioma(25;0.08)|all_neural(26;0.101)		LUSC - Lung squamous cell carcinoma(32;0.000276)|Epithelial(7;0.209)	Colorectal(1;0.0276)|COAD - Colon adenocarcinoma(1;0.171)	Dasatinib(DB01254)|Imatinib(DB00619)|Nilotinib(DB04868)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	TCTAGCCAGAGACATCAAGAA	0.393		1	"""Mis, O"""		"""GIST, AML, TGCT, mastocytosis, mucosal melanoma"""	"""GIST, epithelioma"""	Piebald trait		Piebaldism;Mast Cell disease, Familial Clustering of;Gastrointestinal Stromal Tumors, Sporadic Multiple Primary;Familial Gastrointestinal Stromal Tumors																												p.D816Y			yes	Dom	yes	Familial gastrointestinal stromal tumour	4	4q12	3815	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	yes	"""L, M, O, E"""	KIT,colon,carcinoma,0,932	KIT	7396	932	98	Substitution - Missense(97)|Insertion - In frame(1)	haematopoietic_and_lymphoid_tissue(68)|testis(15)|ovary(10)|soft_tissue(3)|genital_tract(1)|skin(1)	c.G2446T												144.0	146.0	145.0					4																	55599320		2203	4300	6503	SO:0001583	missense	3815	exon17	Familial Cancer Database	Piebald trait;incl.: Familial Cutaneous Mastocytosis (Urticaria Pigmentosum);Sporadic Multiple GIST;Familial GIST, incl. Multiple Familial Gastrointestinal Autonomic Nerve Tumors (GANT)	GCCAGAGACATCA	S67773	CCDS3496.1, CCDS47058.1	4q12	2014-09-17			ENSG00000157404	ENSG00000157404		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6342	protein-coding gene	gene with protein product		164920	"""piebald trait"""	PBT		9027509	Standard	NM_001093772		Approved	CD117, SCFR, C-Kit	uc010igr.3	P10721	OTTHUMG00000128713	ENST00000288135.5:c.2446G>T	4.37:g.55599320G>T	ENSP00000288135:p.Asp816Tyr		54	0	0		82	0.10	8	NM_000222	26	0.31	8	B5A956|D5LXN2|D5M931|F5H8F8|Q6IQ28|Q99662|Q9UM99	Missense_Mutation	SNP	ENST00000288135.5	37	CCDS3496.1	.	.	.	.	.	.	.	.	.	.	G	29.1	4.976091	0.92982	.	.	ENSG00000157404	ENST00000288135;ENST00000412167	D;D	0.83755	-1.76;-1.76	5.62	5.62	0.85841	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.64402	D	0.000011	D	0.87869	0.6286	L	0.39692	1.235	0.80722	D	1	D;D	0.89917	1.0;0.997	D;D	0.65684	0.937;0.919	D	0.88642	0.3176	10	0.87932	D	0	.	19.6484	0.95791	0.0:0.0:1.0:0.0	.	812;816	P10721-2;P10721	.;KIT_HUMAN	Y	816;812	ENSP00000288135:D816Y;ENSP00000390987:D812Y	ENSP00000288135:D816Y	D	+	1	0	KIT	55294077	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.700000	0.98707	2.659000	0.90383	0.585000	0.79938	GAC			0.393	KIT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		OTTHUMT00000250618.1			
ADH1B	125	hgsc.bcm.edu;mdanderson.org	37	4	100232749	100232749	+	Missense_Mutation	SNP	G	G	T			TCGA-ZM-AA0D-01A-11D-A435-10	TCGA-ZM-AA0D-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	cbb77b02-9739-4272-bf41-30251840590b	7ac40e81-4d59-492f-a5cf-f3b25df9905c	g.chr4:100232749G>T	ENST00000305046.8	-	7	960	c.893C>A	c.(892-894)gCt>gAt	p.A298D	ADH1B_ENST00000394887.3_Missense_Mutation_p.A258D			P00325	ADH1B_HUMAN	alcohol dehydrogenase 1B (class I), beta polypeptide	298					ethanol oxidation (GO:0006069)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	alcohol dehydrogenase activity, zinc-dependent (GO:0004024)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(12)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	33				OV - Ovarian serous cystadenocarcinoma(123;1.02e-07)	Ethanol(DB00898)|Fomepizole(DB01213)	GTTCTGGGAAGCAGGAGGTAC	0.488																																					p.A298D													ADH1B,NS,carcinoma,-1,1	ADH1B	-1	1	0			c.C893A												223.0	211.0	215.0					4																	100232749		2203	4300	6503	SO:0001583	missense	125	exon7			TGGGAAGCAGGAG	AF153821	CCDS34033.1, CCDS68761.1	4q23	2008-02-05	2007-11-06		ENSG00000196616	ENSG00000196616	1.1.1.1	"""Alcohol dehydrogenases"""	250	protein-coding gene	gene with protein product		103720		ADH2		3006456	Standard	NM_000668		Approved		uc003hus.4	P00325	OTTHUMG00000161413	ENST00000305046.8:c.893C>A	4.37:g.100232749G>T	ENSP00000306606:p.Ala298Asp		114	0	0		113	0.04	5	NM_000668	3	0.00	0	A8MYN5|B4DRS9|B4DVC3|Q13711|Q4ZGI9|Q96KI7	Missense_Mutation	SNP	ENST00000305046.8	37	CCDS34033.1	.	.	.	.	.	.	.	.	.	.	G	9.308	1.054895	0.19907	.	.	ENSG00000196616	ENST00000305046;ENST00000394887;ENST00000412614	T;T	0.28255	1.62;1.62	3.66	-2.55	0.06288	Alcohol dehydrogenase, C-terminal (1);NAD(P)-binding domain (1);	1.925610	0.02588	N	0.099593	T	0.29749	0.0743	L	0.49699	1.58	0.09310	N	0.999998	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.001;0.001	T	0.34601	-0.9822	10	0.54805	T	0.06	0.4754	8.8493	0.35190	0.0:0.2936:0.5593:0.1471	.	285;258;298	F5HB16;A8MYN5;P00325	.;.;ADH1B_HUMAN	D	298;258;285	ENSP00000306606:A298D;ENSP00000378351:A258D	ENSP00000306606:A298D	A	-	2	0	ADH1B	100451772	0.000000	0.05858	0.000000	0.03702	0.066000	0.16364	-0.114000	0.10757	-0.919000	0.03803	-0.364000	0.07487	GCT			0.488	ADH1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000364853.1		NM_000668	
RXFP1	59350	mdanderson.org	37	4	159573048	159573048	+	Missense_Mutation	SNP	G	G	T			TCGA-ZM-AA0D-01A-11D-A435-10	TCGA-ZM-AA0D-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	cbb77b02-9739-4272-bf41-30251840590b	7ac40e81-4d59-492f-a5cf-f3b25df9905c	g.chr4:159573048G>T	ENST00000307765.5	+	18	2366	c.2115G>T	c.(2113-2115)atG>atT	p.M705I	RXFP1_ENST00000470033.1_Missense_Mutation_p.M672I|RXFP1_ENST00000460056.2_Missense_Mutation_p.M624I|RXFP1_ENST00000448688.2_Missense_Mutation_p.M600I|RXFP1_ENST00000343542.5_Missense_Mutation_p.M657I	NM_001253727.1|NM_001253728.1|NM_001253730.1|NM_001253732.1|NM_001253733.1|NM_021634.3	NP_001240656.1|NP_001240657.1|NP_001240659.1|NP_001240661.1|NP_001240662.1|NP_067647.2	Q9HBX9	RXFP1_HUMAN	relaxin/insulin-like family peptide receptor 1	705					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|cell differentiation (GO:0030154)|extracellular matrix organization (GO:0030198)|lung connective tissue development (GO:0060427)|nipple morphogenesis (GO:0060658)|parturition (GO:0007567)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|hormone binding (GO:0042562)|metal ion binding (GO:0046872)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|liver(2)|lung(22)|prostate(1)|skin(10)	49	all_hematologic(180;0.24)	Renal(120;0.0854)		COAD - Colon adenocarcinoma(41;0.0219)		GAAAATCTATGGACAGCAAAG	0.408																																					p.M732I													.	.			0			c.G2196T												116.0	108.0	110.0					4																	159573048		1894	4107	6001	SO:0001583	missense	59350	exon18			ATCTATGGACAGC	AF190500	CCDS43276.1, CCDS58929.1, CCDS58930.1, CCDS75204.1, CCDS75205.1, CCDS75206.1	4q31.3	2012-08-08	2006-05-09	2006-05-09	ENSG00000171509	ENSG00000171509		"""GPCR / Class A : Relaxin family peptide receptors"""	19718	protein-coding gene	gene with protein product		606654	"""leucine-rich repeat-containing G protein-coupled receptor 7"""	LGR7		15956688, 16507880	Standard	NM_021634		Approved	RXFPR1	uc003ipz.3	Q9HBX9	OTTHUMG00000149973	ENST00000307765.5:c.2115G>T	4.37:g.159573048G>T	ENSP00000303248:p.Met705Ile		62	0	0		54	0.06	3	NM_001253727	0		0	B4DHD1|B4DTV2|Q2M215|Q3KU24|Q3KU25|Q3KU26	Missense_Mutation	SNP	ENST00000307765.5	37	CCDS43276.1	.	.	.	.	.	.	.	.	.	.	G	0.012	-1.691603	0.00731	.	.	ENSG00000171509	ENST00000460056;ENST00000307765;ENST00000448688;ENST00000343542;ENST00000470033;ENST00000440678	T;T;T;T;T	0.36340	1.26;1.26;1.26;1.26;1.26	5.75	-4.09	0.03951	.	0.669254	0.16076	N	0.230760	T	0.05823	0.0152	N	0.00308	-1.67	0.09310	N	1	B;B;B;B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0;0.0;0.0;0.0	B;B;B;B;B;B;B;B	0.01281	0.0;0.0;0.0;0.0;0.0;0.0;0.0;0.0	T	0.36261	-0.9755	10	0.15066	T	0.55	.	1.0079	0.01491	0.1703:0.2196:0.2741:0.336	.	716;732;600;657;672;624;575;705	B3KV27;B4DGP2;B4DHD1;Q9HBX9-4;Q9HBX9-2;E9PCA3;Q59H16;Q9HBX9	.;.;.;.;.;.;.;RXFP1_HUMAN	I	624;705;600;657;672;575	ENSP00000423306:M624I;ENSP00000303248:M705I;ENSP00000414885:M600I;ENSP00000345889:M657I;ENSP00000420712:M672I	ENSP00000303248:M705I	M	+	3	0	RXFP1	159792498	0.001000	0.12720	0.078000	0.20375	0.303000	0.27691	-0.030000	0.12308	-0.424000	0.07382	-1.193000	0.01689	ATG			0.408	RXFP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000314865.1		NM_021634	
DIAPH1	1729	hgsc.bcm.edu	37	5	140953563	140953563	+	Silent	SNP	T	T	A	rs374236039|rs3075570		TCGA-ZM-AA0D-01A-11D-A435-10	TCGA-ZM-AA0D-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	cbb77b02-9739-4272-bf41-30251840590b	7ac40e81-4d59-492f-a5cf-f3b25df9905c	g.chr5:140953563T>A	ENST00000398557.4	-	16	1994	c.1854A>T	c.(1852-1854)ccA>ccT	p.P618P	DIAPH1_ENST00000389057.5_Silent_p.P609P|DIAPH1_ENST00000398562.2_Silent_p.P609P|DIAPH1_ENST00000398566.3_Silent_p.P609P|DIAPH1_ENST00000518047.1_Silent_p.P609P|DIAPH1_ENST00000389054.3_Silent_p.P618P|DIAPH1_ENST00000520569.1_Silent_p.P564P|DIAPH1_ENST00000253811.6_Silent_p.P618P	NM_005219.4	NP_005210.3	O60610	DIAP1_HUMAN	diaphanous-related formin 1	618	FH1.				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)			GCAAaggaggtggaggaggag	0.577																																					p.P618P													DIAPH1,NS,carcinoma,0,1	DIAPH1	0	1	0			c.A1854T												21.0	21.0	21.0					5																	140953563		1987	4116	6103	SO:0001819	synonymous_variant	1729	exon16			AGGAGGTGGAGGA	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.1854A>T	5.37:g.140953563T>A			26	0	0		24	0.17	4	NM_005219	1	0.00	0	A6NF18|B7ZKW2|E9PEZ2|Q17RN4|Q59FH8|Q9UC76	Silent	SNP	ENST00000398557.4	37	CCDS43374.1																																																																																					0.577	DIAPH1-203	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding				NM_005219	
EEF1A1	1915	hgsc.bcm.edu	37	6	74228474	74228474	+	Missense_Mutation	SNP	C	C	T			TCGA-ZM-AA0D-01A-11D-A435-10	TCGA-ZM-AA0D-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	cbb77b02-9739-4272-bf41-30251840590b	7ac40e81-4d59-492f-a5cf-f3b25df9905c	g.chr6:74228474C>T	ENST00000316292.9	-	4	1710	c.719G>A	c.(718-720)cGt>cAt	p.R240H	EEF1A1_ENST00000331523.2_Missense_Mutation_p.R240H|EEF1A1_ENST00000309268.6_Missense_Mutation_p.R240H|EEF1A1_ENST00000491404.1_Intron	NM_001402.5	NP_001393.1	P68104	EF1A1_HUMAN	eukaryotic translation elongation factor 1 alpha 1	240	tr-type G.				cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|translation (GO:0006412)|translational elongation (GO:0006414)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|eukaryotic translation elongation factor 1 complex (GO:0005853)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|translation elongation factor activity (GO:0003746)	p.R240H(2)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(6)|prostate(2)|skin(3)	18						GTCAGTTGGACGAGTTGGTGG	0.498											OREG0003891|OREG0003895	type=REGULATORY REGION|Gene=D16891|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay|type=REGULATORY REGION|Gene=EEF1A1|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																									p.R240H													EEF1A1,NS,carcinoma,0,2	EEF1A1	0	2	2	Substitution - Missense(2)	prostate(1)|skin(1)	c.G719A												120.0	117.0	118.0					6																	74228474		2203	4297	6500	SO:0001583	missense	1915	exon5			GTTGGACGAGTTG	BC019669	CCDS4980.1	6q14.1	2010-06-30	2004-11-19		ENSG00000156508	ENSG00000156508			3189	protein-coding gene	gene with protein product		130590	"""leukocyte receptor cluster (LRC) member 7"""	EF1A, EEF1A, LENG7		8812466, 10941842	Standard	NM_001402		Approved	EE1A1	uc003phj.3	P68104	OTTHUMG00000015031	ENST00000316292.9:c.719G>A	6.37:g.74228474C>T	ENSP00000339063:p.Arg240His		110	0	0	1151	113	0.04	5	NM_001402	5033	0.00	0	P04719|P04720|Q6IQ15	Missense_Mutation	SNP	ENST00000316292.9	37	CCDS4980.1	.	.	.	.	.	.	.	.	.	.	C	16.68	3.190760	0.58017	.	.	ENSG00000156508	ENST00000316292;ENST00000358190;ENST00000309268;ENST00000331523;ENST00000391977	T;T;T	0.47869	0.83;0.83;0.83	4.59	4.59	0.56863	.	0.062472	0.64402	U	0.000008	T	0.50786	0.1636	M	0.93328	3.405	0.80722	D	1	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.62905	-0.6755	10	0.62326	D	0.03	.	17.8137	0.88624	0.0:1.0:0.0:0.0	.	240;240;240;240	P68104;Q53HR5;Q6IPS9;Q5VTE0	EF1A1_HUMAN;.;.;EF1A3_HUMAN	H	240;240;240;240;219	ENSP00000339063:R240H;ENSP00000339053:R240H;ENSP00000330054:R240H	ENSP00000339053:R240H	R	-	2	0	EEF1A1	74285195	1.000000	0.71417	0.995000	0.50966	0.994000	0.84299	7.442000	0.80503	2.259000	0.74868	0.549000	0.68633	CGT			0.498	EEF1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000041210.2		NM_001402	
TBP	6908	hgsc.bcm.edu	37	6	170871004	170871004	+	Silent	SNP	G	G	A			TCGA-ZM-AA0D-01A-11D-A435-10	TCGA-ZM-AA0D-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	cbb77b02-9739-4272-bf41-30251840590b	7ac40e81-4d59-492f-a5cf-f3b25df9905c	g.chr6:170871004G>A	ENST00000392092.2	+	3	459	c.180G>A	c.(178-180)caG>caA	p.Q60Q	TBP_ENST00000540980.1_Silent_p.Q40Q|TBP_ENST00000230354.6_Silent_p.Q60Q	NM_003194.4	NP_003185.1	P20226	TBP_HUMAN	TATA box binding protein	60	Poly-Gln.				cell death (GO:0008219)|gene expression (GO:0010467)|positive regulation of transcription, DNA-templated (GO:0045893)|spermatogenesis (GO:0007283)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription from RNA polymerase III promoter (GO:0006383)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	cytoplasm (GO:0005737)|female pronucleus (GO:0001939)|male pronucleus (GO:0001940)|nuclear euchromatin (GO:0005719)|nucleoplasm (GO:0005654)|transcription factor TFIIA complex (GO:0005672)|transcription factor TFIID complex (GO:0005669)	repressing transcription factor binding (GO:0070491)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(9)|ovary(1)|prostate(4)|urinary_tract(1)	26		Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246)		OV - Ovarian serous cystadenocarcinoma(33;1.07e-22)|BRCA - Breast invasive adenocarcinoma(81;5.01e-06)|GBM - Glioblastoma multiforme(31;0.00591)		Ggcagcagcagcaacaacaac	0.542																																					p.Q60Q													.	.			0			c.G180A												43.0	45.0	44.0					6																	170871004		2203	4300	6503	SO:0001819	synonymous_variant	6908	exon3			GCAGCAGCAACAA	M55654	CCDS5315.1, CCDS55077.1	6q27	2014-04-02			ENSG00000112592	ENSG00000112592		"""General transcription factors"""	11588	protein-coding gene	gene with protein product		600075		GTF2D1, SCA17		2194289, 11448935	Standard	NM_003194		Approved	TFIID	uc003qxu.3	P20226	OTTHUMG00000016084	ENST00000392092.2:c.180G>A	6.37:g.170871004G>A			54	0	0		67	0.15	10	NM_003194	12	0.08	1	B4E3B3|F5H869|Q16845|Q6IBM6|Q9UC02	Silent	SNP	ENST00000392092.2	37	CCDS5315.1																																																																																					0.542	TBP-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		OTTHUMT00000043271.2		NM_003194	
GNA12	2768	mdanderson.org	37	7	2883564	2883564	+	Missense_Mutation	SNP	G	G	T			TCGA-ZM-AA0D-01A-11D-A435-10	TCGA-ZM-AA0D-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	cbb77b02-9739-4272-bf41-30251840590b	7ac40e81-4d59-492f-a5cf-f3b25df9905c	g.chr7:2883564G>T	ENST00000275364.3	-	1	394	c.232C>A	c.(232-234)Cgc>Agc	p.R78S	GNA12_ENST00000544127.1_Missense_Mutation_p.R2S	NM_007353.2	NP_031379.2	Q03113	GNA12_HUMAN	guanine nucleotide binding protein (G protein) alpha 12	78					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|embryonic digit morphogenesis (GO:0042733)|G-protein coupled receptor signaling pathway (GO:0007186)|in utero embryonic development (GO:0001701)|platelet activation (GO:0030168)|regulation of cell shape (GO:0008360)|regulation of fibroblast migration (GO:0010762)|regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032434)|regulation of TOR signaling (GO:0032006)|response to drug (GO:0042493)|Rho protein signal transduction (GO:0007266)	brush border membrane (GO:0031526)|focal adhesion (GO:0005925)|heterotrimeric G-protein complex (GO:0005834)|plasma membrane (GO:0005886)	D5 dopamine receptor binding (GO:0031752)|G-protein beta/gamma-subunit complex binding (GO:0031683)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)			endometrium(1)|large_intestine(5)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	13		Ovarian(82;0.0112)		OV - Ovarian serous cystadenocarcinoma(56;1.02e-13)		TGGATGATGCGCATCTGCTTG	0.697																																					p.R78S													.	.			0			c.C232A												33.0	27.0	29.0					7																	2883564		2202	4300	6502	SO:0001583	missense	2768	exon1			TGATGCGCATCTG	L01694	CCDS5335.1, CCDS64584.1, CCDS64583.1	7p22.3	2006-07-08			ENSG00000146535	ENSG00000146535			4380	protein-coding gene	gene with protein product		604394				8423800, 16247467	Standard	NM_007353		Approved	gep	uc003smu.3	Q03113	OTTHUMG00000023064	ENST00000275364.3:c.232C>A	7.37:g.2883564G>T	ENSP00000275364:p.Arg78Ser		61	0	0		52	0.06	3	NM_007353	3	0.00	0	A4D204|B3KXS2|B7Z3F7|Q2T9L1|Q5PPR5|Q86UM8|Q8TD71|Q9UDU9	Missense_Mutation	SNP	ENST00000275364.3	37	CCDS5335.1	.	.	.	.	.	.	.	.	.	.	G	15.26	2.781846	0.49891	.	.	ENSG00000146535	ENST00000275364;ENST00000544127	D;D	0.89681	-2.55;-2.55	2.81	0.938	0.19500	G protein alpha subunit, helical insertion (1);	0.218384	0.37761	N	0.001952	D	0.94994	0.8380	H	0.95574	3.69	0.80722	D	1	B;D	0.89917	0.075;1.0	B;D	0.85130	0.007;0.997	D	0.93115	0.6520	10	0.87932	D	0	.	8.2714	0.31846	0.2017:0.0:0.7983:0.0	.	78;78	Q5PPR5;Q03113	.;GNA12_HUMAN	S	78;2	ENSP00000275364:R78S;ENSP00000437469:R2S	ENSP00000275364:R78S	R	-	1	0	GNA12	2850090	1.000000	0.71417	0.951000	0.38953	0.795000	0.44927	2.519000	0.45546	0.097000	0.17492	0.558000	0.71614	CGC			0.697	GNA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000241608.1		NM_007353	
CHN2	1124	mdanderson.org	37	7	29438103	29438103	+	Splice_Site	SNP	G	G	T			TCGA-ZM-AA0D-01A-11D-A435-10	TCGA-ZM-AA0D-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	cbb77b02-9739-4272-bf41-30251840590b	7ac40e81-4d59-492f-a5cf-f3b25df9905c	g.chr7:29438103G>T	ENST00000222792.6	+	5	820		c.e5+1		CHN2_ENST00000435288.2_Splice_Site|CHN2_ENST00000546235.1_Splice_Site|CHN2_ENST00000495789.2_Splice_Site|CHN2_ENST00000539406.1_Splice_Site|CHN2_ENST00000539389.1_Intron	NM_004067.2	NP_004058.1	P52757	CHIO_HUMAN	chimerin 2						positive regulation of GTPase activity (GO:0043547)|positive regulation of signal transduction (GO:0009967)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)|metal ion binding (GO:0046872)|SH3/SH2 adaptor activity (GO:0005070)			breast(2)|endometrium(3)|large_intestine(2)|lung(12)|ovary(2)|urinary_tract(2)	23						TGGCTCTCAGGTGAGGCGCAT	0.483																																					.	Ovarian(1;44 48 13232 18918 31480)												.	.			0			c.290+1G>T												93.0	77.0	83.0					7																	29438103		2203	4300	6503	SO:0001630	splice_region_variant	1124	exon5			TCTCAGGTGAGGC	L29126	CCDS5420.1	7p15.3	2013-02-14	2012-10-17		ENSG00000106069	ENSG00000106069		"""Rho GTPase activating proteins"", ""SH2 domain containing"""	1944	protein-coding gene	gene with protein product	"""beta chimerin"", ""chimaerin 2"""	602857	"""chimerin (chimaerin) 2"""			8175705	Standard	XM_005249602		Approved	ARHGAP3, RhoGAP3	uc003szz.3	P52757	OTTHUMG00000023063	ENST00000222792.6:c.290+1G>T	7.37:g.29438103G>T			40	0	0		49	0.06	3	NM_004067	1	0.00	0	A4D1A2|B3VCF1|B3VCF2|B3VCF3|B3VCF7|B3VCG1|C9J7B0|E9PGE0|F8QPL9|Q2M203|Q75MM2	Splice_Site	SNP	ENST00000222792.6	37	CCDS5420.1	.	.	.	.	.	.	.	.	.	.	G	17.28	3.350324	0.61183	.	.	ENSG00000106069	ENST00000439384;ENST00000539406;ENST00000222792;ENST00000435288;ENST00000409350;ENST00000495789;ENST00000546235	.	.	.	5.14	5.14	0.70334	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.1999	0.89834	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	CHN2	29404628	1.000000	0.71417	0.991000	0.47740	0.593000	0.36681	9.166000	0.94766	2.402000	0.81655	0.467000	0.42956	.			0.483	CHN2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		OTTHUMT00000214228.2		NM_004067	Intron
WNK2	65268	broad.mit.edu;bcgsc.ca;mdanderson.org	37	9	96024344	96024344	+	Silent	SNP	C	C	T			TCGA-ZM-AA0D-01A-11D-A435-10	TCGA-ZM-AA0D-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	cbb77b02-9739-4272-bf41-30251840590b	7ac40e81-4d59-492f-a5cf-f3b25df9905c	g.chr9:96024344C>T	ENST00000297954.4	+	12	3315	c.3315C>T	c.(3313-3315)gcC>gcT	p.A1105A	WNK2_ENST00000356055.3_5'UTR|WNK2_ENST00000395475.2_3'UTR|WNK2_ENST00000349097.3_Silent_p.A717A|WNK2_ENST00000395477.2_Silent_p.A1105A|WNK2_ENST00000427277.2_Silent_p.A717A	NM_001282394.1	NP_001269323.1	Q9Y3S1	WNK2_HUMAN	WNK lysine deficient protein kinase 2	1105					intracellular signal transduction (GO:0035556)|negative regulation of cell proliferation (GO:0008285)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of ion homeostasis (GO:2000021)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(1)|endometrium(11)|kidney(4)|large_intestine(5)|lung(17)|ovary(2)|prostate(3)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)	54						CCGGGATCGCCAGCCCTTGCC	0.682																																					p.A1105A													.	WNK2	277		0			c.C3315T												20.0	18.0	19.0					9																	96024344		2195	4286	6481	SO:0001819	synonymous_variant	65268	exon12			GATCGCCAGCCCT	AJ242724	CCDS75858.1	9q22.3	2008-02-05	2003-06-23	2005-01-22	ENSG00000165238	ENSG00000165238			14542	protein-coding gene	gene with protein product		606249	"""serologically defined colon cancer antigen 43"""	SDCCAG43, PRKWNK2		9610721, 11571656	Standard	NM_006648		Approved	NY-CO-43, KIAA1760	uc004atj.3	Q9Y3S1	OTTHUMG00000020247	ENST00000297954.4:c.3315C>T	9.37:g.96024344C>T			111	0.009009009	1		103	0.07	7	NM_006648	0		0	Q5VWF1|Q5VWF2|Q8IY36|Q9C0A3|Q9H3P4	Silent	SNP	ENST00000297954.4	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	2.171|2.171	-0.389965|-0.389965	0.04932|0.04932	.|.	.|.	ENSG00000165238|ENSG00000165238	ENST00000432730|ENST00000411624	.|.	.|.	.|.	5.3|5.3	-4.6|-4.6	0.03390|0.03390	.|.	.|.	.|.	.|.	.|.	T|.	0.47764|.	0.1463|.	.|.	.|.	.|.	0.39890|0.39890	D|D	0.973759|0.973759	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.46205|.	-0.9208|.	4|.	.|.	.|.	.|.	.|.	6.5117|6.5117	0.22226|0.22226	0.1216:0.3341:0.0:0.5443|0.1216:0.3341:0.0:0.5443	.|.	.|.	.|.	.|.	L|X	1101|709	.|.	.|.	P|Q	+|+	2|1	0|0	WNK2|WNK2	95064165|95064165	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.234000|0.234000	0.25298|0.25298	-1.365000|-1.365000	0.02587|0.02587	-0.941000|-0.941000	0.03700|0.03700	0.467000|0.467000	0.42956|0.42956	CCA|CAG			0.682	WNK2-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		OTTHUMT00000317359.1		NM_006648	
FBXW5	54461	mdanderson.org	37	9	139835404	139835404	+	Silent	SNP	G	G	T			TCGA-ZM-AA0D-01A-11D-A435-10	TCGA-ZM-AA0D-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	cbb77b02-9739-4272-bf41-30251840590b	7ac40e81-4d59-492f-a5cf-f3b25df9905c	g.chr9:139835404G>T	ENST00000325285.3	-	9	1756	c.1677C>A	c.(1675-1677)tcC>tcA	p.S559S	FBXW5_ENST00000483559.1_5'UTR|RP11-229P13.25_ENST00000569497.1_RNA	NM_018998.3	NP_061871.1	Q969U6	FBXW5_HUMAN	F-box and WD repeat domain containing 5	559					centrosome duplication (GO:0051298)|mitotic nuclear division (GO:0007067)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)|cytoplasm (GO:0005737)|SCF ubiquitin ligase complex (GO:0019005)	protein kinase binding (GO:0019901)			breast(1)|endometrium(2)|large_intestine(2)|lung(3)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	12	all_cancers(76;0.11)	Myeloproliferative disorder(178;0.0511)	STAD - Stomach adenocarcinoma(284;0.19)	OV - Ovarian serous cystadenocarcinoma(145;7.8e-06)|Epithelial(140;0.000106)		TGGCAAGCCAGGAGAAGAAGG	0.677																																					p.S559S													.	.			0			c.C1677A												27.0	27.0	27.0					9																	139835404		2170	4284	6454	SO:0001819	synonymous_variant	54461	exon9			AAGCCAGGAGAAG	BC014130	CCDS7014.1	9q34.3	2013-01-09	2007-02-08		ENSG00000159069	ENSG00000159069		"""F-boxes / WD-40 domains"", ""WD repeat domain containing"""	13613	protein-coding gene	gene with protein product		609072	"""F-box and WD-40 domain protein 5"""				Standard	NM_018998		Approved	DKFZP434B205, MGC20962, Fbw5	uc004cjx.3	Q969U6	OTTHUMG00000020967	ENST00000325285.3:c.1677C>A	9.37:g.139835404G>T			44	0	0		36	0.08	3	NM_018998	202	0.00	0	B2RDZ6|Q59ET5|Q5SPZ8|Q5SPZ9|Q5SQ00|Q5SQ02|Q5SQ03|Q5SQ04|Q8WY79|Q96GJ6|Q9BSU8|Q9H6A8|Q9HBQ6|Q9NSZ3	Silent	SNP	ENST00000325285.3	37	CCDS7014.1																																																																																					0.677	FBXW5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000055227.1		NM_018998	
ARHGAP6	395	hgsc.bcm.edu	37	X	11197553	11197553	+	Missense_Mutation	SNP	C	C	A			TCGA-ZM-AA0D-01A-11D-A435-10	TCGA-ZM-AA0D-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	cbb77b02-9739-4272-bf41-30251840590b	7ac40e81-4d59-492f-a5cf-f3b25df9905c	g.chrX:11197553C>A	ENST00000337414.4	-	7	2221	c.1349G>T	c.(1348-1350)cGt>cTt	p.R450L	ARHGAP6_ENST00000413512.3_Missense_Mutation_p.R259L|ARHGAP6_ENST00000380732.3_Missense_Mutation_p.R482L|ARHGAP6_ENST00000380736.1_Missense_Mutation_p.R247L|ARHGAP6_ENST00000380718.1_Missense_Mutation_p.R450L|ARHGAP6_ENST00000303025.6_Missense_Mutation_p.R247L|ARHGAP6_ENST00000534860.1_Missense_Mutation_p.R275L|ARHGAP6_ENST00000491514.1_5'UTR	NM_013427.2	NP_038286.2	O43182	RHG06_HUMAN	Rho GTPase activating protein 6	450	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				actin filament polymerization (GO:0030041)|activation of phospholipase C activity (GO:0007202)|focal adhesion assembly (GO:0048041)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of stress fiber assembly (GO:0051497)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of signal transduction (GO:0009967)|regulation of GTPase activity (GO:0043087)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|actin filament (GO:0005884)|cytoplasm (GO:0005737)|cytosol (GO:0005829)	phospholipase activator activity (GO:0016004)|phospholipase binding (GO:0043274)|Rho GTPase activator activity (GO:0005100)|SH3/SH2 adaptor activity (GO:0005070)			cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(19)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	38						ATCAATCCCACGGTCAAATTC	0.522																																					p.R450L													.	.			0			c.G1349T												148.0	103.0	119.0					X																	11197553		2203	4300	6503	SO:0001583	missense	395	exon7			ATCCCACGGTCAA	AF012272	CCDS14140.1, CCDS14141.1, CCDS14142.1	Xp22.3	2008-02-05			ENSG00000047648	ENSG00000047648		"""Rho GTPase activating proteins"""	676	protein-coding gene	gene with protein product		300118				9417914	Standard	XM_005274507		Approved	rhoGAPX-1	uc004cup.1	O43182	OTTHUMG00000021134	ENST00000337414.4:c.1349G>T	X.37:g.11197553C>A	ENSP00000338967:p.Arg450Leu		52	0	0		68	0.06	4	NM_006125	0		0	B2RWQ0|O43437|Q9P1B3|Q9UK81|Q9UK82	Missense_Mutation	SNP	ENST00000337414.4	37	CCDS14140.1	.	.	.	.	.	.	.	.	.	.	C	23.8	4.463909	0.84425	.	.	ENSG00000047648	ENST00000534860;ENST00000380736;ENST00000303025;ENST00000337414;ENST00000380717;ENST00000380718;ENST00000413512;ENST00000380732	T;T;T;T;T;T;T;T	0.20332	2.08;2.08;2.08;2.08;2.08;2.08;2.08;2.08	5.61	5.61	0.85477	Rho GTPase-activating protein domain (4);Rho GTPase activation protein (1);	0.000000	0.53938	D	0.000044	T	0.39036	0.1063	L	0.58302	1.8	0.80722	D	1	P;P;P;P;P	0.52061	0.485;0.518;0.847;0.897;0.95	B;B;P;P;P	0.54590	0.147;0.235;0.457;0.627;0.756	T	0.11227	-1.0596	10	0.62326	D	0.03	.	18.7948	0.91990	0.0:1.0:0.0:0.0	.	259;247;450;450;450	B7Z8H7;O43182-5;O43182-2;O43182;A8KAL3	.;.;.;RHG06_HUMAN;.	L	275;247;247;450;286;450;259;482	ENSP00000438135:R275L;ENSP00000370112:R247L;ENSP00000302312:R247L;ENSP00000338967:R450L;ENSP00000370093:R286L;ENSP00000370094:R450L;ENSP00000389394:R259L;ENSP00000370108:R482L	ENSP00000302312:R247L	R	-	2	0	ARHGAP6	11107474	0.996000	0.38824	1.000000	0.80357	0.997000	0.91878	2.924000	0.48876	2.385000	0.81259	0.523000	0.50628	CGT			0.522	ARHGAP6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		OTTHUMT00000055760.2		NM_013427	
NUDT10	170685	mdanderson.org	37	X	51075901	51075901	+	Silent	SNP	G	G	A	rs2801627		TCGA-ZM-AA0D-01A-11D-A435-10	TCGA-ZM-AA0D-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	cbb77b02-9739-4272-bf41-30251840590b	7ac40e81-4d59-492f-a5cf-f3b25df9905c	g.chrX:51075901G>A	ENST00000376006.3	+	2	304	c.84G>A	c.(82-84)gaG>gaA	p.E28E	NUDT10_ENST00000356450.2_Silent_p.E28E	NM_153183.2	NP_694853.1	Q9BW91	NUDT9_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 10	0					ADP catabolic process (GO:0046032)|IDP catabolic process (GO:0046709)|nucleobase-containing small molecule catabolic process (GO:0034656)|nucleobase-containing small molecule metabolic process (GO:0055086)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|mitochondrial matrix (GO:0005759)	adenosine-diphosphatase activity (GO:0043262)|ADP-ribose diphosphatase activity (GO:0047631)|ADP-sugar diphosphatase activity (GO:0019144)	p.E28E(2)		cervix(1)|endometrium(8)|kidney(1)|large_intestine(1)|lung(1)|prostate(3)|upper_aerodigestive_tract(1)	16	Ovarian(276;0.236)					TCCGGAGCGAGCGCGAGGACG	0.687																																					p.E28E	NSCLC(90;1817 2035 37909 38249)												.	.			2	Substitution - coding silent(2)	upper_aerodigestive_tract(1)|prostate(1)	c.G84A												41.0	35.0	37.0					X																	51075901		2203	4300	6503	SO:0001819	synonymous_variant	170685	exon2			GAGCGAGCGCGAG	AF469196	CCDS35278.1	Xp11.22-p11.1	2014-05-20			ENSG00000122824	ENSG00000122824		"""Nudix motif containing"""	17621	protein-coding gene	gene with protein product		300527				12105228	Standard	NM_153183		Approved	DIPP3a, hDIPP3alpha	uc004dph.3	Q8NFP7	OTTHUMG00000021530	ENST00000376006.3:c.84G>A	X.37:g.51075901G>A			198	0.0050505051	1		202	0.04	9	NM_153183	0		0	Q8NBN1|Q8NCB9|Q8NG25	Silent	SNP	ENST00000376006.3	37	CCDS35278.1																																																																																					0.687	NUDT10-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000056578.1		NM_153183	
AMER1	139285	mdanderson.org	37	X	63410103	63410103	+	Missense_Mutation	SNP	G	G	T			TCGA-ZM-AA0D-01A-11D-A435-10	TCGA-ZM-AA0D-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	cbb77b02-9739-4272-bf41-30251840590b	7ac40e81-4d59-492f-a5cf-f3b25df9905c	g.chrX:63410103G>T	ENST00000330258.3	-	2	3336	c.3064C>A	c.(3064-3066)Cgt>Agt	p.R1022S	AMER1_ENST00000403336.1_Intron|AMER1_ENST00000374869.3_Intron	NM_152424.3	NP_689637.3	Q5JTC6	AMER1_HUMAN	APC membrane recruitment protein 1	1022	Pro-rich.				adipose tissue development (GO:0060612)|bone development (GO:0060348)|mesenchymal cell differentiation involved in kidney development (GO:0072161)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|regulation of canonical Wnt signaling pathway (GO:0060828)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)	p.0?(67)									TGTGAGGGACGAGCTAGTTGA	0.567																																					p.R1022S													.	.			67	Whole gene deletion(67)	kidney(65)|ovary(1)|large_intestine(1)	c.C3064A												52.0	59.0	57.0					X																	63410103		2117	4216	6333	SO:0001583	missense	139285	exon2			AGGGACGAGCTAG	AK097146	CCDS14377.2	Xq11.1	2012-12-03	2012-12-03	2012-12-03	ENSG00000184675	ENSG00000184675		"""-"""	26837	protein-coding gene	gene with protein product	"""Wilms Tumor on the X"", ""adenomatous polyposis coli membrane recruitment 1"""	300647	"""family with sequence similarity 123B"""	FAM123B		21304492, 21498506, 20843316	Standard	NM_152424		Approved	RP11-403E24.2, FLJ39827, WTX	uc004dvo.3	Q5JTC6	OTTHUMG00000021703	ENST00000330258.3:c.3064C>A	X.37:g.63410103G>T	ENSP00000329117:p.Arg1022Ser		45	0	0		49	0.06	3	NM_152424	0		0	A2IB86|Q8N885	Missense_Mutation	SNP	ENST00000330258.3	37	CCDS14377.2	.	.	.	.	.	.	.	.	.	.	G	13.05	2.121431	0.37436	.	.	ENSG00000184675	ENST00000330258	T	0.59364	0.27	4.93	4.07	0.47477	.	.	.	.	.	T	0.48537	0.1505	L	0.27053	0.805	0.80722	D	1	P	0.49961	0.93	P	0.48488	0.579	T	0.37753	-0.9692	8	.	.	.	-6.5728	9.7959	0.40735	0.0988:0.0:0.9012:0.0	.	1022	Q5JTC6	F123B_HUMAN	S	1022	ENSP00000329117:R1022S	.	R	-	1	0	FAM123B	63326828	0.026000	0.19158	0.949000	0.38748	0.183000	0.23260	0.693000	0.25497	1.221000	0.43506	-0.297000	0.09499	CGT			0.567	AMER1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000316584.1		NM_152424	
SMARCA1	6594	broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	X	128625996	128625996	+	Silent	SNP	G	G	A			TCGA-ZM-AA0D-01A-11D-A435-10	TCGA-ZM-AA0D-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	cbb77b02-9739-4272-bf41-30251840590b	7ac40e81-4d59-492f-a5cf-f3b25df9905c	g.chrX:128625996G>A	ENST00000371122.4	-	14	1866	c.1737C>T	c.(1735-1737)ctC>ctT	p.L579L	SMARCA1_ENST00000371121.3_Silent_p.L567L|SMARCA1_ENST00000371123.1_Silent_p.L567L	NM_003069.3	NP_003060.2	P28370	SMCA1_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 1	579	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|brain development (GO:0007420)|chromatin remodeling (GO:0006338)|DNA strand renaturation (GO:0000733)|neuron differentiation (GO:0030182)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of neural precursor cell proliferation (GO:2000177)|transcription, DNA-templated (GO:0006351)	CERF complex (GO:0090537)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|NURF complex (GO:0016589)	annealing helicase activity (GO:0036310)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			biliary_tract(1)|breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|liver(1)|lung(13)|ovary(5)|prostate(1)|skin(1)	45						GGTTAATTCCGAGACCTCCAG	0.378																																					p.L579L													.	SMARCA1	126		0			c.C1737T												152.0	145.0	148.0					X																	128625996		2203	4300	6503	SO:0001819	synonymous_variant	6594	exon14			AATTCCGAGACCT	M88163	CCDS14612.1, CCDS76018.1, CCDS76019.1	Xq25	2008-02-05			ENSG00000102038	ENSG00000102038			11097	protein-coding gene	gene with protein product		300012		SNF2L1, SNF2L		1408766, 14609955	Standard	XM_005262461		Approved	SNF2LB, NURF140, ISWI, SWI	uc004eun.4	P28370	OTTHUMG00000022370	ENST00000371122.4:c.1737C>T	X.37:g.128625996G>A			189	0	0		209	0.13	27	NM_003069	3	0.00	0	Q5JV41|Q5JV42	Silent	SNP	ENST00000371122.4	37	CCDS14612.1																																																																																					0.378	SMARCA1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		OTTHUMT00000058206.1		NM_003069	
