#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_ACHILLES_Lineage_Results_Top_Genes	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_Chromosome_hg18	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_End_position_hg18	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_Mutation_Status	i_ORegAnno_bin	i_Sequence_Source	i_Sequencer	i_Sequencing_Phase	i_Start_position_hg18	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_ccds_id	i_classification	i_context	i_dataset	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_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_havana_transcript	i_refseq_mrna_id	i_secondary_variant_classification	i_type
ARID1A	8289	hgsc.bcm.edu	37	1	27089611	27089611	+	Missense_Mutation	SNP	G	G	T			TCGA-10-0927-01	TCGA-10-0927-11	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-10-0927-01	TCGA-10-0927-11	g.chr1:27089611G>T	ENST00000324856.7	+	8	2938	c.2567G>T	c.(2566-2568)gGg>gTg	p.G856V	ARID1A_ENST00000457599.2_Missense_Mutation_p.G856V|RN7SL501P_ENST00000578818.1_RNA|ARID1A_ENST00000374152.2_Missense_Mutation_p.G473V	NM_006015.4	NP_006006.3	O14497	ARI1A_HUMAN	AT rich interactive domain 1A (SWI-like)	856					androgen receptor signaling pathway (GO:0030521)|ATP-dependent chromatin remodeling (GO:0043044)|cardiac chamber development (GO:0003205)|chromatin remodeling (GO:0006338)|chromatin-mediated maintenance of transcription (GO:0048096)|forebrain development (GO:0030900)|glucocorticoid receptor signaling pathway (GO:0042921)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|nucleosome disassembly (GO:0006337)|nucleosome mobilization (GO:0042766)|optic cup formation involved in camera-type eye development (GO:0003408)|placenta blood vessel development (GO:0060674)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|transcription coactivator activity (GO:0003713)	p.G856V(1)	ARID1A/MAST2_ENST00000361297(2)	NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(13)|central_nervous_system(6)|cervix(2)|endometrium(56)|haematopoietic_and_lymphoid_tissue(8)|kidney(10)|large_intestine(41)|liver(31)|lung(34)|ovary(130)|pancreas(18)|prostate(8)|skin(9)|stomach(14)|upper_aerodigestive_tract(4)|urinary_tract(24)	411		all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242)		CTCCCTCCAGGGAGGATGAGT	0.612			"""Mis, N, F, S, D"""		"""clear cell ovarian carcinoma, RCC"""																																		Rec	yes		1	1p35.3	8289	AT rich interactive domain 1A (SWI-like)		E	1	Substitution - Missense(1)	ovary(1)	1											88.0	71.0	77.0					1																	27089611		2203	4300	6503	26962198	SO:0001583	missense	8289			AB001895	CCDS285.1, CCDS44091.1	1p36.1-p35	2014-09-17	2006-11-08	2004-01-30	ENSG00000117713	ENSG00000117713		"""-"""	11110	protein-coding gene	gene with protein product		603024	"""SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily f, member 1"", ""AT rich interactive domain 1A (SWI- like)"""	C1orf4, SMARCF1		9630625, 9434167	Standard	NM_139135		Approved	B120, P270, C10rf4, BAF250, BAF250a	uc001bmv.1	O14497	OTTHUMG00000004004	ENST00000324856.7:c.2567G>T	1.37:g.27089611G>T	ENSP00000320485:p.Gly856Val	Somatic		Capture	SOLID	Phase_IV	26962198	D3DPL1|Q53FK9|Q5T0W1|Q5T0W2|Q5T0W3|Q8NFD6|Q96T89|Q9BY33|Q9HBJ5|Q9UPZ1	Missense_Mutation	SNP	ENST00000324856.7	37	CCDS285.1	SNP	43	Baylor	.	.	.	.	.	.	.	.	.	.	G	20.7	4.037789	0.75617	.	.	ENSG00000117713	ENST00000324856;ENST00000457599;ENST00000374152	T;T;T	0.03152	4.09;4.08;4.03	5.65	5.65	0.86999	.	0.000000	0.85682	D	0.000000	T	0.14013	0.0339	L	0.54323	1.7	0.80722	D	1	D;D;D	0.69078	0.995;0.997;0.995	P;P;P	0.60949	0.763;0.881;0.763	T	0.00039	-1.2240	10	0.51188	T	0.08	-9.0643	19.9142	0.97043	0.0:0.0:1.0:0.0	.	856;856;510	O14497;O14497-2;Q4LE49	ARI1A_HUMAN;.;.	V	856;856;473	ENSP00000320485:G856V;ENSP00000387636:G856V;ENSP00000363267:G473V	ENSP00000320485:G856V	G	+	2	0	ARID1A	26962198	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.028000	0.76470	2.941000	0.99782	0.655000	0.94253	GGG		0.612	ARID1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011437.2	NM_139135		Missense_Mutation
BRPF1	7862	hgsc.bcm.edu	37	3	9781506	9781506	+	Missense_Mutation	SNP	G	G	C			TCGA-10-0927-01	TCGA-10-0927-11	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-10-0927-01	TCGA-10-0927-11	g.chr3:9781506G>C	ENST00000457855.1	+	2	1434	c.1423G>C	c.(1423-1425)Ggt>Cgt	p.G475R	BRPF1_ENST00000433861.2_Missense_Mutation_p.G475R|BRPF1_ENST00000302054.3_Missense_Mutation_p.G475R|BRPF1_ENST00000383829.2_Missense_Mutation_p.G475R|BRPF1_ENST00000424362.1_Missense_Mutation_p.G475R			P55201	BRPF1_HUMAN	bromodomain and PHD finger containing, 1	475					chromatin organization (GO:0006325)|histone H3 acetylation (GO:0043966)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.G475R(1)		central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(8)|lung(15)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	49	Medulloblastoma(99;0.227)					ggaggatgaggGTAAGGGCTG	0.592																																																1	Substitution - Missense(1)	ovary(1)	3											62.0	60.0	61.0					3																	9781506		2203	4299	6502	9756506	SO:0001583	missense	7862			M91585	CCDS2575.1, CCDS33692.1	3p26-p25	2008-07-18			ENSG00000156983	ENSG00000156983			14255	protein-coding gene	gene with protein product	"""peregrin"", ""bromodomain-containing protein, 140kD"""	602410				8946209, 7906940	Standard	NM_001003694		Approved	BR140	uc003bsf.3	P55201	OTTHUMG00000097033	ENST00000457855.1:c.1423G>C	3.37:g.9781506G>C	ENSP00000410210:p.Gly475Arg	Somatic		Capture	SOLID	Phase_IV	9756506	B4DEZ6|Q7Z6E0|Q8TCM6|Q9UHI0	Missense_Mutation	SNP	ENST00000457855.1	37	CCDS2575.1	SNP	43	Baylor	.	.	.	.	.	.	.	.	.	.	G	19.11	3.763475	0.69763	.	.	ENSG00000156983	ENST00000433861;ENST00000424362;ENST00000383829;ENST00000302054;ENST00000457855	T;T;T;T;T	0.18502	2.22;2.21;3.61;2.21;2.21	6.04	6.04	0.98038	.	0.111328	0.64402	D	0.000013	T	0.19327	0.0464	L	0.48642	1.525	0.80722	D	1	B;B;B;B	0.34103	0.13;0.008;0.05;0.437	B;B;B;B	0.31495	0.039;0.012;0.022;0.131	T	0.01762	-1.1279	10	0.27082	T	0.32	.	20.5792	0.99380	0.0:0.0:1.0:0.0	.	475;475;475;475	P55201-4;P55201-3;P55201-2;P55201	.;.;.;BRPF1_HUMAN	R	475	ENSP00000402485:G475R;ENSP00000398863:G475R;ENSP00000373340:G475R;ENSP00000306297:G475R;ENSP00000410210:G475R	ENSP00000306297:G475R	G	+	1	0	BRPF1	9756506	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.166000	0.77553	2.873000	0.98535	0.561000	0.74099	GGT		0.592	BRPF1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000338485.1	NM_001003694		Missense_Mutation
CHD6	84181	hgsc.bcm.edu	37	20	40112056	40112056	+	Silent	SNP	C	C	T			TCGA-10-0927-01	TCGA-10-0927-11	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-10-0927-01	TCGA-10-0927-11	g.chr20:40112056C>T	ENST00000373233.3	-	16	2538	c.2361G>A	c.(2359-2361)ttG>ttA	p.L787L	CHD6_ENST00000309279.7_Intron	NM_032221.3	NP_115597.3	Q8TD26	CHD6_HUMAN	chromodomain helicase DNA binding protein 6	787	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				ATP catabolic process (GO:0006200)|chromatin modification (GO:0016568)|positive regulation of transcription from RNA polymerase II promoter in response to oxidative stress (GO:0036091)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|transcription cofactor binding (GO:0001221)	p.L787L(1)		breast(8)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(24)|lung(53)|ovary(8)|prostate(5)|skin(8)|stomach(1)|urinary_tract(9)	129		Myeloproliferative disorder(115;0.00425)				GTTTATCAATCAACACAAGCT	0.488																																																1	Substitution - coding silent(1)	ovary(1)	20											111.0	103.0	106.0					20																	40112056		2203	4300	6503	39545470	SO:0001819	synonymous_variant	84181			AF525085	CCDS13317.1	20q12	2003-03-07			ENSG00000124177	ENSG00000124177			19057	protein-coding gene	gene with protein product						11889561	Standard	NM_032221		Approved	KIAA1335, FLJ22369, dJ620E11.1, CHD5, RIGB	uc002xka.1	Q8TD26	OTTHUMG00000032487	ENST00000373233.3:c.2361G>A	20.37:g.40112056C>T		Somatic		Capture	SOLID	Phase_IV	39545470	Q5JYQ0|Q5TGZ9|Q5TH00|Q5TH01|Q8IZR2|Q8WTY0|Q9H4H6|Q9H6D4|Q9NTT7|Q9P2L1	Silent	SNP	ENST00000373233.3	37	CCDS13317.1	SNP	29	Baylor																																																																																				0.488	CHD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079270.1			Silent
DYX1C1	161582	hgsc.bcm.edu	37	15	55759242	55759242	+	Frame_Shift_Del	DEL	T	T	-			TCGA-10-0927-01	TCGA-10-0927-11	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-10-0927-01	TCGA-10-0927-11	g.chr15:55759242delT	ENST00000321149.3	-	5	890	c.523delA	c.(523-525)attfs	p.I175fs	DYX1C1-CCPG1_ENST00000565113.1_RNA|DYX1C1_ENST00000348518.3_Frame_Shift_Del_p.I175fs|DYX1C1_ENST00000380679.1_Frame_Shift_Del_p.I175fs|DYX1C1_ENST00000457155.2_Frame_Shift_Del_p.I175fs|DYX1C1_ENST00000448430.2_Frame_Shift_Del_p.I175fs	NM_130810.3	NP_570722.2	Q8WXU2	DYXC1_HUMAN	dyslexia susceptibility 1 candidate 1	175					cilium movement (GO:0003341)|determination of left/right symmetry (GO:0007368)|inner dynein arm assembly (GO:0036159)|neuron migration (GO:0001764)|outer dynein arm assembly (GO:0036158)|regulation of intracellular estrogen receptor signaling pathway (GO:0033146)|regulation of proteasomal protein catabolic process (GO:0061136)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	estrogen receptor binding (GO:0030331)	p.I175fs*21(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(7)|ovary(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	18				all cancers(107;0.0118)|GBM - Glioblastoma multiforme(80;0.171)		tctctctgaatttttttttgc	0.279																																																1	Deletion - Frameshift(1)	ovary(1)	15							,,	58,4074		8,42,2016	49.0	42.0	45.0		,,	1.2	0.0	15		44	114,7900		12,90,3905	no	frameshift,frameshift,frameshift	DYX1C1	NM_130810.3,NM_001033560.1,NM_001033559.2	,,	20,132,5921	A1A1,A1R,RR		1.4225,1.4037,1.4161	,,	,,	55759242	172,11974	2140	4191	6331	53546534	SO:0001589	frameshift_variant	161582				CCDS10154.1, CCDS32243.1, CCDS32244.1	15q21.3	2014-09-11			ENSG00000256061	ENSG00000256061		"""Tetratricopeptide (TTC) repeat domain containing"""	21493	protein-coding gene	gene with protein product		608706				12954984	Standard	NM_130810		Approved	EKN1, FLJ37882, CILD25	uc002adc.3	Q8WXU2	OTTHUMG00000132008	ENST00000321149.3:c.523delA	15.37:g.55759242delT	ENSP00000323275:p.Ile175fs	Somatic		Capture	SOLID	Phase_IV	53546534	Q6P5Y9|Q8N1S6	Frame_Shift_Del	DEL	ENST00000321149.3	37	CCDS10154.1	DEL	52	Baylor																																																																																				0.279	DYX1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254976.1	NM_130810		Frame_Shift_Del
FASTKD2	22868	hgsc.bcm.edu	37	2	207652688	207652688	+	Missense_Mutation	SNP	A	A	G			TCGA-10-0927-01	TCGA-10-0927-11	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-10-0927-01	TCGA-10-0927-11	g.chr2:207652688A>G	ENST00000236980.6	+	9	1970	c.1622A>G	c.(1621-1623)cAt>cGt	p.H541R	FASTKD2_ENST00000403094.3_Missense_Mutation_p.H541R|FASTKD2_ENST00000402774.3_Missense_Mutation_p.H541R	NM_014929.3	NP_055744.2	Q9NYY8	FAKD2_HUMAN	FAST kinase domains 2	541					cellular respiration (GO:0045333)	mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)	p.H541R(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(7)|ovary(3)|prostate(1)|skin(2)	21				LUSC - Lung squamous cell carcinoma(261;0.0718)|Epithelial(149;0.119)|Lung(261;0.138)		TACAAGCTGCATACTTTGGAT	0.363																																																1	Substitution - Missense(1)	ovary(1)	2											75.0	75.0	75.0					2																	207652688		2203	4300	6503	207360933	SO:0001583	missense	22868			BC001544	CCDS2371.1	2q33.3	2008-02-05	2006-07-07	2006-07-07	ENSG00000118246	ENSG00000118246			29160	protein-coding gene	gene with protein product		612322	"""KIAA0971"""	KIAA0971			Standard	NM_014929		Approved		uc002vbx.3	Q9NYY8	OTTHUMG00000132917	ENST00000236980.6:c.1622A>G	2.37:g.207652688A>G	ENSP00000236980:p.His541Arg	Somatic		Capture	SOLID	Phase_IV	207360933	Q9NVX6|Q9Y2H7	Missense_Mutation	SNP	ENST00000236980.6	37	CCDS2371.1	SNP	8	Baylor	.	.	.	.	.	.	.	.	.	.	a	9.783	1.175777	0.21704	.	.	ENSG00000118246	ENST00000236980;ENST00000402774;ENST00000403094	T;T;T	0.43294	0.95;0.95;0.95	5.67	-1.08	0.09936	FAST kinase-like protein, subdomain 2 (1);	0.392297	0.28895	N	0.013797	T	0.24431	0.0592	L	0.39020	1.185	0.20563	N	0.999888	B;B	0.22746	0.023;0.074	B;B	0.24006	0.021;0.05	T	0.16129	-1.0413	10	0.18710	T	0.47	-1.6201	4.7283	0.12952	0.5565:0.0:0.3104:0.1332	.	541;541	Q9NYY8-2;Q9NYY8	.;FAKD2_HUMAN	R	541	ENSP00000236980:H541R;ENSP00000385990:H541R;ENSP00000384929:H541R	ENSP00000236980:H541R	H	+	2	0	FASTKD2	207360933	0.079000	0.21365	0.024000	0.17045	0.014000	0.08584	0.554000	0.23407	-0.330000	0.08514	-0.255000	0.11280	CAT		0.363	FASTKD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256428.2	NM_014929		Missense_Mutation
FAM124B	79843	hgsc.bcm.edu	37	2	225266248	225266248	+	Missense_Mutation	SNP	C	C	A			TCGA-10-0927-01	TCGA-10-0927-11	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-10-0927-01	TCGA-10-0927-11	g.chr2:225266248C>A	ENST00000409685.3	-	1	503	c.238G>T	c.(238-240)Gat>Tat	p.D80Y	FAM124B_ENST00000243806.2_Missense_Mutation_p.D80Y|FAM124B_ENST00000389874.3_Missense_Mutation_p.D80Y	NM_001122779.1	NP_001116251.1	Q9H5Z6	F124B_HUMAN	family with sequence similarity 124B	80								p.D80Y(1)		endometrium(2)|large_intestine(2)|lung(7)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)	16		Renal(207;0.0112)|all_lung(227;0.0126)|Lung NSC(271;0.0161)|all_hematologic(139;0.138)		Epithelial(121;4.4e-10)|all cancers(144;2.02e-07)|Lung(261;0.00766)|LUSC - Lung squamous cell carcinoma(224;0.00825)		AATAGCCTATCCTCTCCCGGG	0.567																																																1	Substitution - Missense(1)	ovary(1)	2											60.0	57.0	58.0					2																	225266248		2203	4300	6503	224974492	SO:0001583	missense	79843			AK075126	CCDS2461.1, CCDS46527.1	2q36.2	2008-02-05			ENSG00000124019	ENSG00000124019			26224	protein-coding gene	gene with protein product						12477932	Standard	NM_001122779		Approved	FLJ22746	uc002vnx.3	Q9H5Z6	OTTHUMG00000133168	ENST00000409685.3:c.238G>T	2.37:g.225266248C>A	ENSP00000386895:p.Asp80Tyr	Somatic		Capture	SOLID	Phase_IV	224974492	A6NNC7|Q8NBZ4|Q8TAV7	Missense_Mutation	SNP	ENST00000409685.3	37	CCDS46527.1	SNP	30	Baylor	.	.	.	.	.	.	.	.	.	.	C	14.11	2.437143	0.43224	.	.	ENSG00000124019	ENST00000389874;ENST00000409685;ENST00000243806	T;T;T	0.46451	0.87;0.87;0.87	5.69	2.86	0.33363	.	0.196143	0.52532	D	0.000064	T	0.43389	0.1245	L	0.29908	0.895	0.38865	D	0.956566	D;B	0.54964	0.969;0.432	P;B	0.50970	0.655;0.116	T	0.50642	-0.8804	10	0.87932	D	0	-13.044	16.8892	0.86082	0.0:0.6386:0.3614:0.0	.	80;80	Q9H5Z6;Q9H5Z6-2	F124B_HUMAN;.	Y	80	ENSP00000374524:D80Y;ENSP00000386895:D80Y;ENSP00000243806:D80Y	ENSP00000243806:D80Y	D	-	1	0	FAM124B	224974492	1.000000	0.71417	0.048000	0.18961	0.002000	0.02628	3.099000	0.50267	0.317000	0.23160	-0.818000	0.03119	GAT		0.567	FAM124B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330873.1	NM_024785		Missense_Mutation
GLT8D2	83468	hgsc.bcm.edu	37	12	104397084	104397084	+	Splice_Site	SNP	T	T	G			TCGA-10-0927-01	TCGA-10-0927-11	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-10-0927-01	TCGA-10-0927-11	g.chr12:104397084T>G	ENST00000360814.4	-	5	518	c.113A>C	c.(112-114)gAt>gCt	p.D38A	GLT8D2_ENST00000548660.1_Splice_Site_p.D38A|GLT8D2_ENST00000546436.1_Splice_Site_p.D38A	NM_031302.3	NP_112592.1	Q9H1C3	GL8D2_HUMAN	glycosyltransferase 8 domain containing 2	38						integral component of membrane (GO:0016021)	transferase activity, transferring glycosyl groups (GO:0016757)	p.D38A(1)		kidney(3)|large_intestine(5)|lung(5)|ovary(1)|prostate(1)|skin(1)	16						GGATTCATCATCTGGAAACAT	0.463																																																1	Substitution - Missense(1)	ovary(1)	12											128.0	113.0	118.0					12																	104397084		2203	4300	6503	102921214	SO:0001630	splice_region_variant	83468			BC022343	CCDS9096.1	12q23.3	2013-02-22			ENSG00000120820	ENSG00000120820		"""Glycosyltransferase family 8 domain containing"""	24890	protein-coding gene	gene with protein product							Standard	NM_031302		Approved	FLJ31494	uc001tkh.1	Q9H1C3	OTTHUMG00000170120	ENST00000360814.4:c.113-1A>C	12.37:g.104397084T>G		Somatic		Capture	SOLID	Phase_IV	102921214	Q96KA2	Missense_Mutation	SNP	ENST00000360814.4	37	CCDS9096.1	SNP	50	Baylor	.	.	.	.	.	.	.	.	.	.	T	11.46	1.644012	0.29246	.	.	ENSG00000120820	ENST00000360814;ENST00000546436;ENST00000548660	T;T;T	0.29917	1.55;1.55;1.55	5.73	3.38	0.38709	.	0.225757	0.43919	D	0.000512	T	0.18964	0.0455	L	0.32530	0.975	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.08411	-1.0723	10	0.31617	T	0.26	.	4.1186	0.10094	0.1844:0.1598:0.0:0.6558	.	38	Q9H1C3	GL8D2_HUMAN	A	38	ENSP00000354053:D38A;ENSP00000449750:D38A;ENSP00000447450:D38A	ENSP00000354053:D38A	D	-	2	0	GLT8D2	102921214	0.677000	0.27577	0.667000	0.29798	0.719000	0.41307	0.614000	0.24314	0.451000	0.26802	0.460000	0.39030	GAT		0.463	GLT8D2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407371.1	NM_031302	Missense_Mutation	Missense_Mutation
GRM1	2911	hgsc.bcm.edu	37	6	146350692	146350692	+	Silent	SNP	T	T	C			TCGA-10-0927-01	TCGA-10-0927-11	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-10-0927-01	TCGA-10-0927-11	g.chr6:146350692T>C	ENST00000282753.1	+	1	274	c.39T>C	c.(37-39)ttT>ttC	p.F13F	GRM1_ENST00000392299.2_Silent_p.F13F|GRM1_ENST00000492807.2_Silent_p.F13F|GRM1_ENST00000355289.4_Silent_p.F13F|GRM1_ENST00000507907.1_Silent_p.F13F|GRM1_ENST00000361719.2_Silent_p.F13F			Q13255	GRM1_HUMAN	glutamate receptor, metabotropic 1	13					activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|cell death (GO:0008219)|cellular response to electrical stimulus (GO:0071257)|dimeric G-protein coupled receptor signaling pathway (GO:0038042)|G-protein coupled glutamate receptor signaling pathway (GO:0007216)|G-protein coupled receptor signaling pathway (GO:0007186)|locomotory behavior (GO:0007626)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of sensory perception of pain (GO:0051930)|regulation of synaptic transmission, glutamatergic (GO:0051966)|sensory perception of pain (GO:0019233)|synaptic transmission (GO:0007268)	dendrite (GO:0030425)|G-protein coupled receptor dimeric complex (GO:0038037)|G-protein coupled receptor homodimeric complex (GO:0038038)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)	p.F13F(1)		NS(2)|breast(5)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(54)|ovary(7)|pancreas(2)|prostate(5)|skin(7)|upper_aerodigestive_tract(4)|urinary_tract(1)	126		Ovarian(120;0.0387)		OV - Ovarian serous cystadenocarcinoma(155;5.35e-08)|GBM - Glioblastoma multiforme(68;0.00762)		CAGCGATCTTTTTGGAGGTGT	0.607																																																1	Substitution - coding silent(1)	ovary(1)	6											109.0	127.0	121.0					6																	146350692		2202	4300	6502	146392385	SO:0001819	synonymous_variant	2911			U31215	CCDS5209.1, CCDS47497.1, CCDS64548.1	6q24	2014-06-12			ENSG00000152822	ENSG00000152822		"""GPCR / Class C : Glutamate receptors, metabotropic"", ""Glutamate receptors"""	4593	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 85"""	604473				9076744, 9376535	Standard	NM_001278064		Approved	GPRC1A, mGlu1, MGLUR1, PPP1R85	uc010khw.2	Q13255	OTTHUMG00000015752	ENST00000282753.1:c.39T>C	6.37:g.146350692T>C		Somatic		Capture	SOLID	Phase_IV	146392385	B9EG79|F8W805|Q13256|Q14757|Q14758|Q5VTF7|Q5VTF8|Q9NU10|Q9UGS9|Q9UGT0	Silent	SNP	ENST00000282753.1	37	CCDS5209.1	SNP	64	Baylor																																																																																				0.607	GRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042574.1	NM_000838		Silent
GTF2IRD1	9569	hgsc.bcm.edu	37	7	73944105	73944105	+	Missense_Mutation	SNP	C	C	T			TCGA-10-0927-01	TCGA-10-0927-11	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-10-0927-01	TCGA-10-0927-11	g.chr7:73944105C>T	ENST00000265755.3	+	9	1525	c.1132C>T	c.(1132-1134)Cgg>Tgg	p.R378W	GTF2IRD1_ENST00000476977.1_Missense_Mutation_p.R378W|GTF2IRD1_ENST00000455841.2_Missense_Mutation_p.R410W|GTF2IRD1_ENST00000424337.2_Missense_Mutation_p.R378W|GTF2IRD1_ENST00000489094.1_3'UTR	NM_005685.3|NM_016328.2	NP_005676.3|NP_057412.1	Q9UHL9	GT2D1_HUMAN	GTF2I repeat domain containing 1	378				R -> Q (in Ref. 5; AAF21796). {ECO:0000305}.	multicellular organismal development (GO:0007275)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)|transition between slow and fast fiber (GO:0014886)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R378W(1)		NS(1)|breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(9)|lung(19)|ovary(6)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49						CGTGCCCTACCGGAAGATTGC	0.607																																																1	Substitution - Missense(1)	ovary(1)	7											69.0	59.0	62.0					7																	73944105		2203	4300	6503	73582041	SO:0001583	missense	9569			AF151354	CCDS5571.1, CCDS47613.1, CCDS56492.1	7q11.23	2008-04-18	2002-01-14		ENSG00000006704	ENSG00000006704			4661	protein-coding gene	gene with protein product	"""binding factor for early enhancer"""	604318	"""GTF2I repeat domain-containing 1"""	WBSCR11		9774679, 10198167	Standard	NM_016328		Approved	MusTRD1, RBAP2, GTF3, WBSCR12, BEN, Cream1	uc010lbq.3	Q9UHL9	OTTHUMG00000023782	ENST00000265755.3:c.1132C>T	7.37:g.73944105C>T	ENSP00000265755:p.Arg378Trp	Somatic		Capture	SOLID	Phase_IV	73582041	O95444|Q6DSU6|Q75MX7|Q86UM3|Q8WVC4|Q9UHK8|Q9UI91	Missense_Mutation	SNP	ENST00000265755.3	37	CCDS5571.1	SNP	23	Baylor	.	.	.	.	.	.	.	.	.	.	c	19.69	3.873889	0.72180	.	.	ENSG00000006704	ENST00000265755;ENST00000455841;ENST00000424337;ENST00000476977	T;T;T;T	0.46063	0.88;0.88;0.88;0.88	4.46	-2.05	0.07321	.	0.000000	0.85682	D	0.000000	T	0.46927	0.1418	N	0.19112	0.55	0.52501	D	0.999952	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.83275	0.993;0.957;0.996;0.974	T	0.52245	-0.8601	10	0.87932	D	0	-25.9307	17.2233	0.86963	0.259:0.7409:0.0:0.0	.	410;378;378;378	Q6DSU6;E9PFE2;Q9UHL9;Q9UHL9-2	.;.;GT2D1_HUMAN;.	W	378;410;378;378	ENSP00000265755:R378W;ENSP00000397566:R410W;ENSP00000408477:R378W;ENSP00000418383:R378W	ENSP00000265755:R378W	R	+	1	2	GTF2IRD1	73582041	1.000000	0.71417	0.996000	0.52242	0.862000	0.49288	2.453000	0.44970	-0.142000	0.11354	-0.535000	0.04281	CGG		0.607	GTF2IRD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252654.2	NM_016328		Missense_Mutation
MYBPC3	4607	hgsc.bcm.edu	37	11	47350684	47350684	+	IGR	SNP	C	C	T			TCGA-10-0927-01	TCGA-10-0927-11	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-10-0927-01	TCGA-10-0927-11	g.chr11:47350684C>T	ENST00000545968.1	-	0	4217				MADD_ENST00000402192.2_Missense_Mutation_p.R1583W|MADD_ENST00000407859.3_Missense_Mutation_p.R1561W|MADD_ENST00000349238.3_Missense_Mutation_p.R1604W|MADD_ENST00000311027.5_Missense_Mutation_p.R1643W|MADD_ENST00000395336.3_3'UTR|MADD_ENST00000395344.3_Missense_Mutation_p.R1537W|MADD_ENST00000402799.1_Missense_Mutation_p.R1541W|MADD_ENST00000406482.1_3'UTR|MADD_ENST00000342922.4_Missense_Mutation_p.R1584W	NM_000256.3	NP_000247.2	Q14896	MYPC3_HUMAN	myosin binding protein C, cardiac						cardiac muscle contraction (GO:0060048)|cell adhesion (GO:0007155)|heart morphogenesis (GO:0003007)|muscle filament sliding (GO:0030049)|myosin filament assembly (GO:0031034)|positive regulation of ATPase activity (GO:0032781)|regulation of heart rate (GO:0002027)|regulation of muscle filament sliding (GO:0032971)|regulation of striated muscle contraction (GO:0006942)|sarcomere organization (GO:0045214)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	A band (GO:0031672)|C zone (GO:0014705)|cytosol (GO:0005829)|sarcomere (GO:0030017)|striated muscle myosin thick filament (GO:0005863)	ATPase activator activity (GO:0001671)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|myosin binding (GO:0017022)|myosin heavy chain binding (GO:0032036)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)	p.R1643W(1)|p.R1643R(1)		breast(2)|central_nervous_system(2)|endometrium(9)|kidney(1)|large_intestine(4)|lung(16)|ovary(3)|prostate(3)|urinary_tract(2)	42				Lung(87;0.176)		AACCCCGCCCCGGCCTGTCTC	0.592																																																2	Substitution - Missense(1)|Substitution - coding silent(1)	ovary(1)|lung(1)	11											103.0	103.0	103.0					11																	47350684		2201	4298	6499	47307260	SO:0001628	intergenic_variant	8567			X84075	CCDS53621.1	11p11.2	2014-09-17	2001-11-28			ENSG00000134571		"""Myosin binding proteins"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	7551	protein-coding gene	gene with protein product		600958	"""myosin-binding protein C, cardiac"""	CMH4		7744002, 8358441	Standard	NM_000256		Approved	MYBP-C, FHC	uc021qis.1	Q14896			11.37:g.47350684C>T		Somatic		Capture	SOLID	Phase_IV	47307260	A5PL00|Q16410|Q6R2F7|Q9UE27|Q9UM53	Missense_Mutation	SNP	ENST00000545968.1	37	CCDS53621.1	SNP	23	Baylor	.	.	.	.	.	.	.	.	.	.	C	27.2	4.811847	0.90707	.	.	ENSG00000110514	ENST00000342922;ENST00000402799;ENST00000349238;ENST00000311027;ENST00000407859;ENST00000395344;ENST00000402192	T;T;T;T;T;T;T	0.08634	3.2;3.07;3.2;3.11;3.07;3.07;3.2	5.78	5.78	0.91487	.	0.000000	0.85682	D	0.000000	T	0.25232	0.0613	L	0.44542	1.39	0.80722	D	1	D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D	0.91635	0.993;0.993;0.997;0.999;0.998;0.997;0.999	T	0.00128	-1.2017	10	0.87932	D	0	-17.409	20.0016	0.97412	0.0:1.0:0.0:0.0	.	1537;1537;1541;1604;1561;1643;1584	B5MEE5;A8K8S7;Q8WXG6-5;Q8WXG6-2;Q8WXG6-4;Q8WXG6;Q8WXG6-3	.;.;.;.;.;MADD_HUMAN;.	W	1584;1541;1604;1643;1561;1537;1583	ENSP00000343902:R1584W;ENSP00000385585:R1541W;ENSP00000304505:R1604W;ENSP00000310933:R1643W;ENSP00000384204:R1561W;ENSP00000378753:R1537W;ENSP00000384287:R1583W	ENSP00000310933:R1643W	R	+	1	2	MADD	47307260	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	3.003000	0.49505	2.731000	0.93534	0.555000	0.69702	CGG		0.592	MYBPC3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000392271.3			Missense_Mutation
MEN1	4221	hgsc.bcm.edu	37	11	64573219	64573219	+	Missense_Mutation	SNP	T	T	C			TCGA-10-0927-01	TCGA-10-0927-11	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-10-0927-01	TCGA-10-0927-11	g.chr11:64573219T>C	ENST00000337652.1	-	8	1591	c.1088A>G	c.(1087-1089)gAg>gGg	p.E363G	MEN1_ENST00000443283.1_Missense_Mutation_p.E363G|MAP4K2_ENST00000294066.2_5'Flank|MEN1_ENST00000315422.4_Missense_Mutation_p.E358G|MAP4K2_ENST00000377350.3_5'Flank|MEN1_ENST00000377321.1_Missense_Mutation_p.E323G|MEN1_ENST00000312049.6_Missense_Mutation_p.E358G|MEN1_ENST00000377316.2_Missense_Mutation_p.E358G|MEN1_ENST00000394376.1_Missense_Mutation_p.E363G|MEN1_ENST00000478548.1_5'UTR|MEN1_ENST00000377313.1_Missense_Mutation_p.E363G|MAP4K2_ENST00000468062.1_5'Flank|MEN1_ENST00000377326.3_Missense_Mutation_p.E358G|MEN1_ENST00000394374.2_Missense_Mutation_p.E363G	NM_130803.2	NP_570715	O00255	MEN1_HUMAN	multiple endocrine neoplasia I	363	Interaction with FANCD2.				brain development (GO:0007420)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|chromatin remodeling (GO:0006338)|DNA repair (GO:0006281)|embryonic skeletal system morphogenesis (GO:0048704)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|histone lysine methylation (GO:0034968)|leukocyte homeostasis (GO:0001776)|MAPK cascade (GO:0000165)|maternal process involved in female pregnancy (GO:0060135)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of JNK cascade (GO:0046329)|negative regulation of organ growth (GO:0046621)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of telomerase activity (GO:0051974)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|osteoblast development (GO:0002076)|osteoblast fate commitment (GO:0002051)|palate development (GO:0060021)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell division (GO:0051781)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of histone methylation (GO:0031062)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of protein binding (GO:0032092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of activin receptor signaling pathway (GO:0032925)|response to gamma radiation (GO:0010332)|response to UV (GO:0009411)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	chromatin (GO:0000785)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|histone methyltransferase complex (GO:0035097)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|four-way junction DNA binding (GO:0000400)|protein binding, bridging (GO:0030674)|protein N-terminus binding (GO:0047485)|R-SMAD binding (GO:0070412)|sequence-specific DNA binding (GO:0043565)|transcription regulatory region DNA binding (GO:0044212)|Y-form DNA binding (GO:0000403)	p.E358G(1)		NS(7)|adrenal_gland(5)|breast(2)|central_nervous_system(5)|endometrium(1)|gastrointestinal_tract_(site_indeterminate)(15)|large_intestine(2)|lung(21)|ovary(1)|pancreas(64)|parathyroid(181)|pituitary(7)|prostate(4)|retroperitoneum(1)|skin(1)|small_intestine(13)|soft_tissue(4)|stomach(1)|thymus(2)	337						GTAGATCTCCTCGTCTTCCCG	0.617			"""D, Mis, N, F, S"""		"""parathyroid tumors, Pancreatic neuroendocrine tumors"""	"""parathyroid adenoma, pituitary adenoma, pancreatic islet cell, carcinoid"""			Multiple Endocrine Neoplasia, type 1;Hyperparathyroidism, Familial Isolated																												Esophageal Squamous(1;83 158 15500 18603 18803 29295)	yes	Rec	yes	Multiple Endocrine Neoplasia Type 1	11	11q13	4221	multiple endocrine neoplasia type 1 gene		E	1	Substitution - Missense(1)	ovary(1)	11											117.0	116.0	117.0					11																	64573219		2201	4297	6498	64329795	SO:0001583	missense	4221	Familial Cancer Database	MEN1, Wermer disease;FIHP, FIHPT, HRPT1, Familial Isolated Primary Hyperparathyroidism	U93236	CCDS8083.1, CCDS31600.1	11q13	2014-09-17			ENSG00000133895	ENSG00000133895			7010	protein-coding gene	gene with protein product	"""menin"""	613733					Standard	NM_130799		Approved		uc001obn.3	O00255	OTTHUMG00000045366	ENST00000337652.1:c.1088A>G	11.37:g.64573219T>C	ENSP00000337088:p.Glu363Gly	Somatic		Capture	SOLID	Phase_IV	64329795	A5HBC6|A5HBC7|A5HBC8|A5HBC9|A5HBD0|A5HBD1|A5HBD2|O00632|Q9BUF0|Q9BUK2	Missense_Mutation	SNP	ENST00000337652.1	37	CCDS8083.1	SNP	54	Baylor	.	.	.	.	.	.	.	.	.	.	T	18.59	3.657644	0.67586	.	.	ENSG00000133895	ENST00000377316;ENST00000377321;ENST00000377326;ENST00000312049;ENST00000315422;ENST00000337652;ENST00000394376;ENST00000394374;ENST00000443283;ENST00000377313	D;D;D;D;D;D;D;D;D;D	0.99667	-6.34;-6.34;-6.34;-6.34;-6.34;-6.34;-6.34;-6.34;-6.34;-6.34	3.72	3.72	0.42706	.	0.000000	0.85682	D	0.000000	D	0.99245	0.9737	L	0.52126	1.63	0.80722	D	1	B;D;B	0.69078	0.137;0.997;0.165	B;D;B	0.75484	0.178;0.986;0.272	D	0.98468	1.0599	10	0.49607	T	0.09	-23.2955	10.7627	0.46274	0.0:0.0:0.0:1.0	.	358;323;363	O00255-2;O00255-3;O00255	.;.;MEN1_HUMAN	G	358;323;358;358;358;363;363;363;363;363	ENSP00000366533:E358G;ENSP00000366538:E323G;ENSP00000366543:E358G;ENSP00000308975:E358G;ENSP00000323747:E358G;ENSP00000337088:E363G;ENSP00000377901:E363G;ENSP00000377899:E363G;ENSP00000396940:E363G;ENSP00000366530:E363G	ENSP00000308975:E358G	E	-	2	0	MEN1	64329795	1.000000	0.71417	0.997000	0.53966	0.987000	0.75469	6.951000	0.75983	1.725000	0.51514	0.374000	0.22700	GAG		0.617	MEN1-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000143881.1			Missense_Mutation
NANS	54187	hgsc.bcm.edu	37	9	100845218	100845218	+	Frame_Shift_Del	DEL	G	G	-			TCGA-10-0927-01	TCGA-10-0927-11	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-10-0927-01	TCGA-10-0927-11	g.chr9:100845218delG	ENST00000210444.5	+	6	1031	c.961delG	c.(961-963)ggcfs	p.G321fs	TRIM14_ENST00000375098.3_Intron|NANS_ENST00000461452.1_3'UTR|TRIM14_ENST00000478530.1_Intron	NM_018946.3	NP_061819.2	Q9NR45	SIAS_HUMAN	N-acetylneuraminic acid synthase	321	AFP-like. {ECO:0000255|PROSITE- ProRule:PRU00021}.			G -> A (in Ref. 1; AAF75261). {ECO:0000305}.	lipopolysaccharide biosynthetic process (GO:0009103)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	N-acetylneuraminate synthase activity (GO:0050462)|N-acylneuraminate cytidylyltransferase activity (GO:0008781)|N-acylneuraminate-9-phosphate synthase activity (GO:0047444)	p.G321fs*10(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)|prostate(1)|skin(1)	11		Acute lymphoblastic leukemia(62;0.0559)				TGAGCCCAAAGGCTATCCTCC	0.483																																																1	Deletion - Frameshift(1)	ovary(1)	9											100.0	91.0	94.0					9																	100845218		2203	4300	6503	99885039	SO:0001589	frameshift_variant	54187			AF161387	CCDS6733.1	9p24.1-p23	2008-07-31	2008-07-31		ENSG00000095380	ENSG00000095380			19237	protein-coding gene	gene with protein product	"""sialic acid synthase"""	605202				10749855	Standard	NM_018946		Approved	SAS	uc004ayc.3	Q9NR45	OTTHUMG00000020341	ENST00000210444.5:c.961delG	9.37:g.100845218delG	ENSP00000210444:p.Gly321fs	Somatic		Capture	SOLID	Phase_IV	99885039	B2RE98|Q8WUV9|Q9BWS6|Q9NVD4	Frame_Shift_Del	DEL	ENST00000210444.5	37	CCDS6733.1	DEL	35	Baylor																																																																																				0.483	NANS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053359.1	NM_018946		Frame_Shift_Del
OLR1	4973	hgsc.bcm.edu	37	12	10319539	10319539	+	Missense_Mutation	SNP	G	G	A			TCGA-10-0927-01	TCGA-10-0927-11	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-10-0927-01	TCGA-10-0927-11	g.chr12:10319539G>A	ENST00000309539.3	-	3	256	c.196C>T	c.(196-198)Ctc>Ttc	p.L66F	OLR1_ENST00000543993.1_5'UTR|OLR1_ENST00000545927.1_Missense_Mutation_p.L66F|OLR1_ENST00000432556.2_Missense_Mutation_p.L66F|OLR1_ENST00000544577.1_Missense_Mutation_p.L66F	NM_002543.3	NP_002534.1	P78380	OLR1_HUMAN	oxidized low density lipoprotein (lectin-like) receptor 1	66	Neck.				blood circulation (GO:0008015)|blood coagulation (GO:0007596)|cell death (GO:0008219)|inflammatory response (GO:0006954)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|lipoprotein metabolic process (GO:0042157)|proteolysis (GO:0006508)|response to hydrogen peroxide (GO:0042542)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	carbohydrate binding (GO:0030246)|low-density lipoprotein receptor activity (GO:0005041)	p.L66F(1)		breast(1)|endometrium(1)|large_intestine(2)|lung(3)|ovary(1)|pancreas(1)|skin(1)	10						TGTGTTAGGAGGTCAGACACC	0.433																																																1	Substitution - Missense(1)	ovary(1)	12											121.0	114.0	116.0					12																	10319539		2203	4300	6503	10210806	SO:0001583	missense	4973			D89050	CCDS8618.1, CCDS53745.1, CCDS53746.1	12p13.1-p12.3	2011-08-30	2006-12-07		ENSG00000173391	ENSG00000173391		"""C-type lectin domain containing"""	8133	protein-coding gene	gene with protein product		602601	"""oxidised low density lipoprotein (lectin-like) receptor 1"""			9763655	Standard	NM_002543		Approved	LOX-1, SCARE1, CLEC8A	uc001qxo.1	P78380	OTTHUMG00000168527	ENST00000309539.3:c.196C>T	12.37:g.10319539G>A	ENSP00000309124:p.Leu66Phe	Somatic		Capture	SOLID	Phase_IV	10210806	A8K7V9|B4DI48|G3V1I4|Q2PP00|Q7Z484	Missense_Mutation	SNP	ENST00000309539.3	37	CCDS8618.1	SNP	35	Baylor	.	.	.	.	.	.	.	.	.	.	G	9.358	1.067353	0.20067	.	.	ENSG00000173391	ENST00000309539;ENST00000544577;ENST00000545927;ENST00000432556;ENST00000539518;ENST00000543414	T;T;T;T;T	0.42513	4.9;1.45;0.97;1.45;4.85	4.89	3.99	0.46301	.	0.356051	0.20649	N	0.088251	T	0.54208	0.1844	L	0.58101	1.795	0.09310	N	1	D;P	0.69078	0.997;0.952	D;P	0.66497	0.944;0.523	T	0.45205	-0.9277	10	0.19590	T	0.45	.	11.8357	0.52323	0.0:0.1777:0.8223:0.0	.	66;66	B4DI48;P78380	.;OLR1_HUMAN	F	66;66;66;66;13;13	ENSP00000309124:L66F;ENSP00000444457:L66F;ENSP00000439251:L66F;ENSP00000405116:L66F;ENSP00000442389:L13F	ENSP00000309124:L66F	L	-	1	0	OLR1	10210806	0.587000	0.26791	0.007000	0.13788	0.007000	0.05969	1.248000	0.32827	1.358000	0.45922	0.591000	0.81541	CTC		0.433	OLR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400091.1	NM_002543		Missense_Mutation
PGBD1	84547	hgsc.bcm.edu	37	6	28269965	28269965	+	Silent	SNP	C	C	T			TCGA-10-0927-01	TCGA-10-0927-11	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-10-0927-01	TCGA-10-0927-11	g.chr6:28269965C>T	ENST00000405948.2	+	7	2754	c.2334C>T	c.(2332-2334)caC>caT	p.H778H	PGBD1_ENST00000259883.3_Silent_p.H778H	NM_001184743.1|NM_032507.3	NP_001171672.1|NP_115896.1	Q96JS3	PGBD1_HUMAN	piggyBac transposable element derived 1	778						membrane (GO:0016020)|nucleus (GO:0005634)	scavenger receptor activity (GO:0005044)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.H778H(1)		endometrium(2)|kidney(2)|large_intestine(7)|lung(16)|ovary(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)	41						GGCAACTACACAGAGCCTGTA	0.418																																																1	Substitution - coding silent(1)	ovary(1)	6											83.0	80.0	81.0					6																	28269965		2203	4300	6503	28377944	SO:0001819	synonymous_variant	84547			D88259	CCDS4648.1	6p22.1	2013-01-09			ENSG00000137338	ENSG00000137338		"""-"""	19398	protein-coding gene	gene with protein product							Standard	NM_001184743		Approved	HUCEP-4, dJ874C20.4, SCAND4	uc003nkz.3	Q96JS3	OTTHUMG00000014520	ENST00000405948.2:c.2334C>T	6.37:g.28269965C>T		Somatic		Capture	SOLID	Phase_IV	28377944	Q53F43|Q6NTF5|Q8WWS4	Silent	SNP	ENST00000405948.2	37	CCDS4648.1	SNP	17	Baylor																																																																																				0.418	PGBD1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040188.2			Silent
PPIL2	23759	hgsc.bcm.edu	37	22	22036752	22036752	+	Silent	SNP	C	C	T			TCGA-10-0927-01	TCGA-10-0927-11	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-10-0927-01	TCGA-10-0927-11	g.chr22:22036752C>T	ENST00000335025.8	+	8	505	c.414C>T	c.(412-414)gcC>gcT	p.A138A	PPIL2_ENST00000406385.1_Silent_p.A138A|PPIL2_ENST00000412327.1_Silent_p.A138A|PPIL2_ENST00000492445.2_Silent_p.A138A|PPIL2_ENST00000398831.3_Silent_p.A138A|PPIL2_ENST00000456792.2_Silent_p.A117A					peptidylprolyl isomerase (cyclophilin)-like 2									p.A138A(1)		endometrium(4)|kidney(2)|large_intestine(4)|lung(3)|ovary(2)|skin(2)	17	Colorectal(54;0.105)					ATATCAAGGCCAAGAACTTCC	0.602																																																1	Substitution - coding silent(1)	ovary(1)	22											126.0	100.0	109.0					22																	22036752		2203	4300	6503	20366752	SO:0001819	synonymous_variant	23759				CCDS13793.1	22q11.21	2013-01-29			ENSG00000100023	ENSG00000100023		"""U-box domain containing"""	9261	protein-coding gene	gene with protein product	"""U-box domain containing 7"""	607588				10591208	Standard	NM_014337		Approved	UBOX7, CYC4, Cyp-60	uc002zvh.4	Q13356	OTTHUMG00000030174	ENST00000335025.8:c.414C>T	22.37:g.22036752C>T		Somatic		Capture	SOLID	Phase_IV	20366752		Silent	SNP	ENST00000335025.8	37	CCDS13793.1	SNP	21	Baylor																																																																																				0.602	PPIL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075028.4			Silent
PRKCQ	5588	hgsc.bcm.edu	37	10	6533664	6533664	+	Silent	SNP	C	C	A			TCGA-10-0927-01	TCGA-10-0927-11	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-10-0927-01	TCGA-10-0927-11	g.chr10:6533664C>A	ENST00000263125.5	-	8	870	c.771G>T	c.(769-771)cgG>cgT	p.R257R	PRKCQ_ENST00000397176.2_Silent_p.R257R|PRKCQ_ENST00000539722.1_Silent_p.R132R	NM_001282644.1|NM_006257.3	NP_001269573.1|NP_006248.1	Q04759	KPCT_HUMAN	protein kinase C, theta	257					apoptotic process (GO:0006915)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|Fc-epsilon receptor signaling pathway (GO:0038095)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|membrane protein ectodomain proteolysis (GO:0006509)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of T cell apoptotic process (GO:0070233)|phototransduction, visible light (GO:0007603)|platelet activation (GO:0030168)|positive regulation of interleukin-17 production (GO:0032740)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of interleukin-4 production (GO:0032753)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of T-helper 17 type immune response (GO:2000318)|positive regulation of T-helper 2 cell activation (GO:2000570)|protein ubiquitination (GO:0016567)|regulation of cell growth (GO:0001558)|regulation of platelet aggregation (GO:0090330)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|regulation of transcription, DNA-templated (GO:0006355)|rhodopsin mediated signaling pathway (GO:0016056)|T cell receptor signaling pathway (GO:0050852)	cytosol (GO:0005829)|immunological synapse (GO:0001772)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)|ubiquitin-protein transferase activity (GO:0004842)	p.R257R(1)		NS(1)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|liver(1)|lung(13)|ovary(4)|prostate(1)|skin(4)|stomach(2)	45					Tamoxifen(DB00675)	TGAGTCCTTGCCGTGCCAGTC	0.547																																					Ovarian(50;572 1126 10530 25349 30594)											1	Substitution - coding silent(1)	ovary(1)	10											114.0	102.0	106.0					10																	6533664		2203	4300	6503	6573670	SO:0001819	synonymous_variant	5588			L07032	CCDS7079.1, CCDS55701.1, CCDS60482.1	10p15	2009-07-10			ENSG00000065675	ENSG00000065675	2.7.11.1		9410	protein-coding gene	gene with protein product		600448				8444877	Standard	NM_001282645		Approved		uc001ijj.2	Q04759	OTTHUMG00000017623	ENST00000263125.5:c.771G>T	10.37:g.6533664C>A		Somatic		Capture	SOLID	Phase_IV	6573670	B4DF52|Q14DH6|Q3MJF1|Q64FY5|Q9H508|Q9H549	Silent	SNP	ENST00000263125.5	37	CCDS7079.1	SNP	26	Baylor																																																																																				0.547	PRKCQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046665.1	NM_006257		Silent
RREB1	6239	hgsc.bcm.edu	37	6	7226816	7226816	+	Missense_Mutation	SNP	C	C	A			TCGA-10-0927-01	TCGA-10-0927-11	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-10-0927-01	TCGA-10-0927-11	g.chr6:7226816C>A	ENST00000349384.6	+	9	1138	c.824C>A	c.(823-825)cCt>cAt	p.P275H	RREB1_ENST00000379938.2_Missense_Mutation_p.P275H|RREB1_ENST00000379933.3_Missense_Mutation_p.P275H|RREB1_ENST00000334984.6_Missense_Mutation_p.P275H	NM_001003698.3	NP_001003698.1	Q92766	RREB1_HUMAN	ras responsive element binding protein 1	275					multicellular organismal development (GO:0007275)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|Ras protein signal transduction (GO:0007265)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear body (GO:0016604)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.P275H(1)		breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(5)|lung(18)|ovary(5)|pancreas(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	58	Ovarian(93;0.0398)	all_hematologic(90;0.0384)|Prostate(151;0.191)				CAGAACAACCCTTCAATTCCT	0.502																																																1	Substitution - Missense(1)	ovary(1)	6											212.0	186.0	195.0					6																	7226816		2203	4300	6503	7171815	SO:0001583	missense	6239			U26914	CCDS34335.1, CCDS34336.1, CCDS54963.1	6p25	2013-01-08			ENSG00000124782	ENSG00000124782		"""Zinc fingers, C2H2-type"""	10449	protein-coding gene	gene with protein product	"""hindsight homolog (drosophila)"""	602209				9367691, 18394891	Standard	NM_001003698		Approved	HNT	uc003mxb.3	Q92766	OTTHUMG00000014201	ENST00000349384.6:c.824C>A	6.37:g.7226816C>A	ENSP00000305560:p.Pro275His	Somatic		Capture	SOLID	Phase_IV	7171815	A2RRF5|E2GM80|E2GM81|O75567|O75568|Q5VYB2|Q6BEP5|Q6BEP6|Q6BEP8|Q86SU2|Q9Y474	Missense_Mutation	SNP	ENST00000349384.6	37	CCDS34336.1	SNP	24	Baylor	.	.	.	.	.	.	.	.	.	.	C	27.2	4.806364	0.90623	.	.	ENSG00000124782	ENST00000379933;ENST00000379938;ENST00000349384;ENST00000334984;ENST00000483150	T;T;T;T;T	0.12774	2.83;2.75;2.83;2.65;2.83	4.99	4.99	0.66335	.	0.000000	0.64402	D	0.000016	T	0.11110	0.0271	N	0.13043	0.29	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.998;0.995;1.0	T	0.19516	-1.0303	10	0.09084	T	0.74	-17.4617	18.2888	0.90122	0.0:1.0:0.0:0.0	.	275;275;275	Q92766-3;Q92766;Q92766-2	.;RREB1_HUMAN;.	H	275	ENSP00000369265:P275H;ENSP00000369270:P275H;ENSP00000305560:P275H;ENSP00000335574:P275H;ENSP00000419511:P275H	ENSP00000335574:P275H	P	+	2	0	RREB1	7171815	1.000000	0.71417	0.975000	0.42487	0.967000	0.64934	5.350000	0.66016	2.311000	0.77944	0.655000	0.94253	CCT		0.502	RREB1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000352985.1			Missense_Mutation
SAMD9L	219285	hgsc.bcm.edu	37	7	92765125	92765125	+	Missense_Mutation	SNP	C	C	T			TCGA-10-0927-01	TCGA-10-0927-11	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-10-0927-01	TCGA-10-0927-11	g.chr7:92765125C>T	ENST00000318238.4	-	5	1376	c.160G>A	c.(160-162)Gac>Aac	p.D54N	SAMD9L_ENST00000411955.1_Missense_Mutation_p.D54N|SAMD9L_ENST00000437805.1_Missense_Mutation_p.D54N	NM_152703.2	NP_689916.2	Q8IVG5	SAM9L_HUMAN	sterile alpha motif domain containing 9-like	54	SAM. {ECO:0000255|PROSITE- ProRule:PRU00184}.				common myeloid progenitor cell proliferation (GO:0035726)|endosomal vesicle fusion (GO:0034058)|hematopoietic progenitor cell differentiation (GO:0002244)|regulation of protein catabolic process (GO:0042176)|spleen development (GO:0048536)|stem cell division (GO:0017145)	early endosome (GO:0005769)		p.D54N(1)		central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(23)|liver(2)|lung(31)|ovary(5)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	88	all_cancers(62;4.15e-11)|all_epithelial(64;2.29e-10)|Breast(17;0.000675)|Lung NSC(181;0.0755)|all_lung(186;0.0989)		STAD - Stomach adenocarcinoma(171;0.000302)			TCTACAAGGTCCTTCTCAGTT	0.398																																																1	Substitution - Missense(1)	ovary(1)	7											120.0	121.0	120.0					7																	92765125		2203	4300	6503	92603061	SO:0001583	missense	219285			AB095926	CCDS34681.1	7q21.2	2013-01-10		2005-04-26	ENSG00000177409	ENSG00000177409		"""Sterile alpha motif (SAM) domain containing"""	1349	protein-coding gene	gene with protein product		611170	"""chromosome 7 open reading frame 6"""	C7orf6			Standard	NM_152703		Approved	KIAA2005, FLJ39885	uc003umh.1	Q8IVG5	OTTHUMG00000155807	ENST00000318238.4:c.160G>A	7.37:g.92765125C>T	ENSP00000326247:p.Asp54Asn	Somatic		Capture	SOLID	Phase_IV	92603061	A0JP23|A0JP24|A0PJG8|A4D1G8|D6W5Q6|Q2TV71|Q2TV75|Q2UZV8|Q8IWI4|Q8N3L9|Q8N875	Missense_Mutation	SNP	ENST00000318238.4	37	CCDS34681.1	SNP	30	Baylor	.	.	.	.	.	.	.	.	.	.	C	19.35	3.811711	0.70797	.	.	ENSG00000177409	ENST00000318238;ENST00000411955;ENST00000437805;ENST00000394472;ENST00000446959;ENST00000439952;ENST00000414791;ENST00000446033	T;T;T;D;D;D;D	0.87179	1.67;1.67;1.67;-2.22;-2.22;-2.22;-2.22	4.73	3.83	0.44106	Sterile alpha motif domain (1);Sterile alpha motif/pointed domain (2);	0.000000	0.56097	D	0.000038	D	0.89532	0.6742	L	0.43152	1.355	0.42380	D	0.992487	D;D	0.89917	1.0;0.998	D;D	0.87578	0.998;0.948	D	0.86489	0.1796	10	0.17832	T	0.49	-17.8106	14.4864	0.67619	0.0:0.8517:0.1483:0.0	.	54;54	Q8IVG5-2;Q8IVG5	.;SAM9L_HUMAN	N	54	ENSP00000326247:D54N;ENSP00000405760:D54N;ENSP00000408796:D54N;ENSP00000391699:D54N;ENSP00000391387:D54N;ENSP00000396137:D54N;ENSP00000410062:D54N	ENSP00000326247:D54N	D	-	1	0	SAMD9L	92603061	0.030000	0.19436	0.718000	0.30602	0.930000	0.56654	0.448000	0.21726	1.196000	0.43129	0.460000	0.39030	GAC		0.398	SAMD9L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341730.1	NM_152703		Missense_Mutation
SQRDL	58472	hgsc.bcm.edu	37	15	45954156	45954156	+	Missense_Mutation	SNP	C	C	T			TCGA-10-0927-01	TCGA-10-0927-11	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-10-0927-01	TCGA-10-0927-11	g.chr15:45954156C>T	ENST00000260324.7	+	3	624	c.238C>T	c.(238-240)Cat>Tat	p.H80Y	RP11-96O20.4_ENST00000564080.1_Missense_Mutation_p.H80Y|SQRDL_ENST00000568606.1_Missense_Mutation_p.H80Y	NM_021199.3	NP_067022.1	Q9Y6N5	SQRD_HUMAN	sulfide quinone reductase-like (yeast)	80					cellular nitrogen compound metabolic process (GO:0034641)|small molecule metabolic process (GO:0044281)|sulfide oxidation, using sulfide:quinone oxidoreductase (GO:0070221)|sulfur amino acid catabolic process (GO:0000098)|sulfur amino acid metabolic process (GO:0000096)	mitochondrial inner membrane (GO:0005743)	sulfide:quinone oxidoreductase activity (GO:0070224)	p.H80Y(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|prostate(2)	11		Lung NSC(122;0.000117)|all_lung(180;0.000737)|Melanoma(134;0.0417)		all cancers(107;5.89e-18)|GBM - Glioblastoma multiforme(94;1.21e-06)|COAD - Colon adenocarcinoma(120;0.17)|Colorectal(133;0.188)		TTCTCAGAGACATTTCTACCA	0.443																																																1	Substitution - Missense(1)	ovary(1)	15											69.0	60.0	63.0					15																	45954156		2198	4297	6495	43741448	SO:0001583	missense	58472			AF042284	CCDS10127.1	15q21.1	2010-08-05			ENSG00000137767	ENSG00000137767			20390	protein-coding gene	gene with protein product						10810093, 10224084	Standard	NM_021199		Approved	CGI-44	uc001zvu.4	Q9Y6N5	OTTHUMG00000131476	ENST00000260324.7:c.238C>T	15.37:g.45954156C>T	ENSP00000260324:p.His80Tyr	Somatic		Capture	SOLID	Phase_IV	43741448	Q9UQM8	Missense_Mutation	SNP	ENST00000260324.7	37	CCDS10127.1	SNP	17	Baylor	.	.	.	.	.	.	.	.	.	.	C	27.1	4.801805	0.90538	.	.	ENSG00000137767	ENST00000260324	T	0.39406	1.08	5.52	5.52	0.82312	Pyridine nucleotide-disulphide oxidoreductase, FAD/NAD(P)-binding domain (1);	0.000000	0.85682	D	0.000000	T	0.78071	0.4226	H	0.97516	4.02	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.86084	0.1546	10	0.87932	D	0	.	18.0115	0.89225	0.0:1.0:0.0:0.0	.	80	Q9Y6N5	SQRD_HUMAN	Y	80	ENSP00000260324:H80Y	ENSP00000260324:H80Y	H	+	1	0	SQRDL	43741448	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	7.461000	0.80834	2.585000	0.87301	0.655000	0.94253	CAT		0.443	SQRDL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254319.2			Missense_Mutation
TIGD6	81789	hgsc.bcm.edu	37	5	149374880	149374880	+	Silent	SNP	T	T	C	rs397756704|rs3832324|rs201139146	byFrequency	TCGA-10-0927-01	TCGA-10-0927-11	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-10-0927-01	TCGA-10-0927-11	g.chr5:149374880T>C	ENST00000296736.3	-	2	1806	c.1032A>G	c.(1030-1032)caA>caG	p.Q344Q	TIGD6_ENST00000515406.2_Silent_p.Q344Q	NM_030953.3	NP_112215.1	Q17RP2	TIGD6_HUMAN	tigger transposable element derived 6	344	DDE.					nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|ovary(2)|prostate(1)|stomach(1)	10			KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)			CCACCTCTTCTTGATCCTCAC	0.502																																																0			5											98.0	51.0	67.0					5																	149374880		2168	4015	6183	149355073	SO:0001819	synonymous_variant	81789			AK056604	CCDS4301.1	5q33.1	2008-02-05			ENSG00000164296	ENSG00000164296			18332	protein-coding gene	gene with protein product						11230166	Standard	NM_030953		Approved	DKFZp761E2110	uc003lrj.3	Q17RP2	OTTHUMG00000130045	ENST00000296736.3:c.1032A>G	5.37:g.149374880T>C		Somatic		Capture	SOLID	Phase_IV	149355073	B3KTZ8|Q96MQ4|Q9H0X7	Silent	SNP	ENST00000296736.3	37	CCDS4301.1	SNP	56	Baylor																																																																																				0.502	TIGD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252324.1	NM_030953		Silent
TIMD4	91937	hgsc.bcm.edu	37	5	156353323	156353323	+	Splice_Site	SNP	G	G	T			TCGA-10-0927-01	TCGA-10-0927-11	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-10-0927-01	TCGA-10-0927-11	g.chr5:156353323G>T	ENST00000274532.2	-	6	901	c.845C>A	c.(844-846)gCa>gAa	p.A282E	TIMD4_ENST00000406964.1_5'UTR|TIMD4_ENST00000407087.3_Splice_Site_p.A254E	NM_138379.2	NP_612388.2	Q96H15	TIMD4_HUMAN	T-cell immunoglobulin and mucin domain containing 4	282						integral component of membrane (GO:0016021)		p.A282E(1)		NS(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(23)|ovary(2)|skin(2)	37	Renal(175;0.00488)	Medulloblastoma(196;0.0523)|all_neural(177;0.21)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			TGTATCAGATGCTGGGAAGGA	0.363																																																1	Substitution - Missense(1)	ovary(1)	5											157.0	143.0	148.0					5																	156353323		2203	4300	6503	156285901	SO:0001630	splice_region_variant	91937			BC008988	CCDS4332.1, CCDS54943.1	5q33.3	2013-01-11			ENSG00000145850	ENSG00000145850		"""Immunoglobulin superfamily / V-set domain containing"""	25132	protein-coding gene	gene with protein product		610096				12477932	Standard	NM_001146726		Approved		uc003lwh.2	Q96H15	OTTHUMG00000130244	ENST00000274532.2:c.845-1C>A	5.37:g.156353323G>T		Somatic		Capture	SOLID	Phase_IV	156285901	B5MCL9	Missense_Mutation	SNP	ENST00000274532.2	37	CCDS4332.1	SNP	46	Baylor	.	.	.	.	.	.	.	.	.	.	g	0.482	-0.879479	0.02530	.	.	ENSG00000145850	ENST00000274532;ENST00000407087	T;T	0.18502	2.21;2.24	4.3	-5.53	0.02552	.	2.124380	0.02595	N	0.100386	T	0.06416	0.0165	N	0.14661	0.345	0.09310	N	1	B;B	0.21452	0.056;0.056	B;B	0.15484	0.013;0.008	T	0.23691	-1.0181	10	0.06625	T	0.88	.	0.6551	0.00833	0.2025:0.2536:0.1594:0.3844	.	254;282	B5MCL9;Q96H15	.;TIMD4_HUMAN	E	282;254	ENSP00000274532:A282E;ENSP00000385973:A254E	ENSP00000274532:A282E	A	-	2	0	TIMD4	156285901	0.000000	0.05858	0.005000	0.12908	0.156000	0.22039	-1.603000	0.02077	-0.810000	0.04375	-0.833000	0.03075	GCA		0.363	TIMD4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252568.1	NM_138379	Missense_Mutation	Missense_Mutation
TTC29	83894	hgsc.bcm.edu	37	4	147724801	147724801	+	Frame_Shift_Del	DEL	C	C	-			TCGA-10-0927-01	TCGA-10-0927-11	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-10-0927-01	TCGA-10-0927-11	g.chr4:147724801delC	ENST00000325106.4	-	11	1364	c.1138delG	c.(1138-1140)gctfs	p.A380fs	TTC29_ENST00000506019.1_5'UTR|TTC29_ENST00000398886.4_Frame_Shift_Del_p.A406fs|TTC29_ENST00000513335.1_Frame_Shift_Del_p.A406fs	NM_031956.2	NP_114162.2	Q8NA56	TTC29_HUMAN	tetratricopeptide repeat domain 29	380								p.A380fs*6(1)		breast(2)|cervix(2)|endometrium(3)|kidney(4)|large_intestine(6)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	26	all_hematologic(180;0.151)					GTGTCAAAAGCTTGCTGAAAG	0.353																																																1	Deletion - Frameshift(1)	ovary(1)	4											58.0	56.0	57.0					4																	147724801		1879	4111	5990	147944251	SO:0001589	frameshift_variant	83894			AF345910	CCDS47141.1, CCDS75200.1	4q31.23	2013-01-11				ENSG00000137473		"""Tetratricopeptide (TTC) repeat domain containing"""	29936	protein-coding gene	gene with protein product						12477932	Standard	NM_031956		Approved	NYD-SP14	uc003ikw.4	Q8NA56		ENST00000325106.4:c.1138delG	4.37:g.147724801delC	ENSP00000316740:p.Ala380fs	Somatic		Capture	SOLID	Phase_IV	147944251	A4GU95|Q9BXB6	Frame_Shift_Del	DEL	ENST00000325106.4	37	CCDS47141.1	DEL	28	Baylor																																																																																				0.353	TTC29-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_031956		Frame_Shift_Del
UBR5	51366	hgsc.bcm.edu	37	8	103354864	103354864	+	Missense_Mutation	SNP	T	T	G			TCGA-10-0927-01	TCGA-10-0927-11	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	454_PCR_WGA	.	.	Illumina GAIIx	TCGA-10-0927-01	TCGA-10-0927-11	g.chr8:103354864T>G	ENST00000520539.1	-	9	1541	c.935A>C	c.(934-936)gAa>gCa	p.E312A	UBR5_ENST00000521922.1_Missense_Mutation_p.E306A|UBR5_ENST00000220959.4_Missense_Mutation_p.E312A	NM_001282873.1|NM_015902.5	NP_001269802.1|NP_056986.2	O95071	UBR5_HUMAN	ubiquitin protein ligase E3 component n-recognin 5	312					cell proliferation (GO:0008283)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|negative regulation of double-strand break repair (GO:2000780)|negative regulation of histone H2A K63-linked ubiquitination (GO:1901315)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of protein import into nucleus, translocation (GO:0033160)|progesterone receptor signaling pathway (GO:0050847)|protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ligase activity (GO:0016874)|RNA binding (GO:0003723)|ubiquitin-protein transferase activity (GO:0004842)|ubiquitin-ubiquitin ligase activity (GO:0034450)|zinc ion binding (GO:0008270)	p.E312A(1)		NS(1)|breast(13)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(8)|large_intestine(19)|liver(1)|lung(51)|ovary(6)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	124	all_cancers(14;8e-07)|all_epithelial(15;2.18e-08)|Lung NSC(17;2.55e-05)|all_lung(17;8.85e-05)		OV - Ovarian serous cystadenocarcinoma(57;0.000442)			TAAAACGGATTCACGTTCACG	0.463																																					Ovarian(131;96 1741 5634 7352 27489)											1	Substitution - Missense(1)	ovary(1)	8											112.0	97.0	102.0					8																	103354864		2203	4300	6503	103424040	SO:0001583	missense	51366			AF006010	CCDS34933.1, CCDS64946.1	8q22	2008-06-23	2007-06-19	2007-06-19	ENSG00000104517	ENSG00000104517		"""Ubiquitin protein ligase E3 component n-recognins"""	16806	protein-coding gene	gene with protein product		608413	"""E3 ubiquitin protein ligase, HECT domain containing, 1"""	EDD1		10030672, 16055722	Standard	NM_015902		Approved	DD5, HYD, EDD, KIAA0896	uc003ykr.2	O95071	OTTHUMG00000164755	ENST00000520539.1:c.935A>C	8.37:g.103354864T>G	ENSP00000429084:p.Glu312Ala	Somatic		Capture	SOLID	Phase_IV	103424040	B2RP24|J3KMW7|O94970|Q9NPL3	Missense_Mutation	SNP	ENST00000520539.1	37	CCDS34933.1	SNP	62	Baylor	.	.	.	.	.	.	.	.	.	.	T	24.4	4.525326	0.85600	.	.	ENSG00000104517	ENST00000520539;ENST00000220959;ENST00000521922	T;T;T	0.48836	0.8;0.8;0.8	5.12	5.12	0.69794	.	0.000000	0.85682	D	0.000000	T	0.61073	0.2318	L	0.52011	1.625	0.80722	D	1	P;P	0.52842	0.956;0.956	P;P	0.62184	0.899;0.899	T	0.64351	-0.6428	10	0.72032	D	0.01	.	15.2225	0.73324	0.0:0.0:0.0:1.0	.	306;312	E7EMW7;O95071	.;UBR5_HUMAN	A	312;312;306	ENSP00000429084:E312A;ENSP00000220959:E312A;ENSP00000427819:E306A	ENSP00000220959:E312A	E	-	2	0	UBR5	103424040	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.993000	0.88291	2.050000	0.60909	0.528000	0.53228	GAA		0.463	UBR5-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000380075.2	NM_015902		Missense_Mutation
USH2A	7399	hgsc.bcm.edu	37	1	216062067	216062067	+	Missense_Mutation	SNP	T	T	A	rs143523460		TCGA-10-0927-01	TCGA-10-0927-11	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-10-0927-01	TCGA-10-0927-11	g.chr1:216062067T>A	ENST00000307340.3	-	41	8310	c.7924A>T	c.(7924-7926)Ata>Tta	p.I2642L	RP5-1111A8.3_ENST00000414995.1_RNA|USH2A_ENST00000366943.2_Missense_Mutation_p.I2642L	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	2642	Fibronectin type-III 13. {ECO:0000255|PROSITE-ProRule:PRU00316}.				hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)	p.I2642L(1)		NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		TGCCAAGATATAATCACAGAT	0.498										HNSCC(13;0.011)																																						1	Substitution - Missense(1)	ovary(1)	1											80.0	87.0	84.0					1																	216062067		2203	4300	6503	214128690	SO:0001583	missense	7399			AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"""Fibronectin type III domain containing"""	12601	protein-coding gene	gene with protein product	"""usherin"""	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.7924A>T	1.37:g.216062067T>A	ENSP00000305941:p.Ile2642Leu	Somatic		Capture	SOLID	Phase_IV	214128690	Q5VVM9|Q6S362|Q9NS27	Missense_Mutation	SNP	ENST00000307340.3	37	CCDS31025.1	SNP	49	Baylor	.	.	.	.	.	.	.	.	.	.	T	10.28	1.306578	0.23736	.	.	ENSG00000042781	ENST00000307340;ENST00000366943	T;T	0.38401	1.14;1.14	5.58	-4.48	0.03515	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.299519	0.22699	N	0.056714	T	0.15825	0.0381	L	0.41824	1.3	0.20196	N	0.999928	B	0.14805	0.011	B	0.14023	0.01	T	0.40776	-0.9545	10	0.02654	T	1	.	2.1942	0.03906	0.1068:0.188:0.3318:0.3734	.	2642	O75445	USH2A_HUMAN	L	2642	ENSP00000305941:I2642L;ENSP00000355910:I2642L	ENSP00000305941:I2642L	I	-	1	0	USH2A	214128690	0.020000	0.18652	0.073000	0.20177	0.951000	0.60555	0.182000	0.16900	-0.888000	0.03956	-0.290000	0.09829	ATA		0.498	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123		Missense_Mutation
WDR60	55112	hgsc.bcm.edu	37	7	158704350	158704350	+	Missense_Mutation	SNP	G	G	C			TCGA-10-0927-01	TCGA-10-0927-11	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-10-0927-01	TCGA-10-0927-11	g.chr7:158704350G>C	ENST00000407559.3	+	12	1728	c.1570G>C	c.(1570-1572)Ggg>Cgg	p.G524R		NM_018051.4	NP_060521.4	Q8WVS4	WDR60_HUMAN	WD repeat domain 60	524					cell projection organization (GO:0030030)	cilium (GO:0005929)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)		p.G524R(1)		NS(3)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(3)|kidney(1)|large_intestine(2)|liver(4)|lung(16)|ovary(2)	35	Ovarian(565;0.152)	all_cancers(7;1.25e-09)|all_epithelial(9;0.000894)|all_hematologic(28;0.00603)	OV - Ovarian serous cystadenocarcinoma(82;0.00174)	UCEC - Uterine corpus endometrioid carcinoma (81;0.19)|STAD - Stomach adenocarcinoma(7;0.18)		CAGAAACTTTGGGAAAAAAAA	0.328																																																1	Substitution - Missense(1)	ovary(1)	7											93.0	90.0	91.0					7																	158704350		1818	4075	5893	158397111	SO:0001583	missense	55112				CCDS47757.1	7q36.3	2013-11-15			ENSG00000126870	ENSG00000126870		"""WD repeat domain containing"""	21862	protein-coding gene	gene with protein product		615462				23910462	Standard	NM_018051		Approved	FLJ10300, FAP163	uc003woe.4	Q8WVS4	OTTHUMG00000151443	ENST00000407559.3:c.1570G>C	7.37:g.158704350G>C	ENSP00000384290:p.Gly524Arg	Somatic		Capture	SOLID	Phase_IV	158397111	Q9NW58	Missense_Mutation	SNP	ENST00000407559.3	37	CCDS47757.1	SNP	47	Baylor	.	.	.	.	.	.	.	.	.	.	G	23.2	4.388451	0.82902	.	.	ENSG00000126870	ENST00000407559	D	0.89196	-2.48	5.03	5.03	0.67393	.	0.000000	0.85682	D	0.000000	D	0.94618	0.8265	M	0.84326	2.69	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.97110	1.0;0.986	D	0.95339	0.8436	10	0.87932	D	0	-32.876	15.8944	0.79323	0.0:0.0:1.0:0.0	.	7;524	A4D230;Q8WVS4	.;WDR60_HUMAN	R	524	ENSP00000384290:G524R	ENSP00000384290:G524R	G	+	1	0	WDR60	158397111	1.000000	0.71417	0.995000	0.50966	0.889000	0.51656	8.425000	0.90270	2.330000	0.79161	0.462000	0.41574	GGG		0.328	WDR60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322668.1	NM_018051		Missense_Mutation
XIRP2	129446	hgsc.bcm.edu	37	2	167992543	167992543	+	Missense_Mutation	SNP	C	C	A			TCGA-10-0927-01	TCGA-10-0927-11	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-10-0927-01	TCGA-10-0927-11	g.chr2:167992543C>A	ENST00000409728.1	+	3	622	c.533C>A	c.(532-534)cCt>cAt	p.P178H	XIRP2_ENST00000420519.1_Missense_Mutation_p.P178H|XIRP2_ENST00000409195.1_Missense_Mutation_p.P178H|XIRP2-AS1_ENST00000525330.1_RNA|XIRP2_ENST00000295237.9_Missense_Mutation_p.P178H|XIRP2_ENST00000409043.1_Missense_Mutation_p.P178H|XIRP2_ENST00000409756.2_Missense_Mutation_p.P178H	NM_001199143.1	NP_001186072.1	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	3					actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)		p.P178H(2)		NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						AAGATGTCACCTGAAAGTGGT	0.408																																																2	Substitution - Missense(2)	ovary(2)	2											87.0	87.0	87.0					2																	167992543		1896	4118	6014	167700789	SO:0001583	missense	129446			AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"""myomaxin"""	609778	"""cardiomyopathy associated 3"""	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409728.1:c.533C>A	2.37:g.167992543C>A	ENSP00000386619:p.Pro178His	Somatic		Capture	SOLID	Phase_IV	167700789	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Missense_Mutation	SNP	ENST00000409728.1	37	CCDS56143.1	SNP	24	Baylor	.	.	.	.	.	.	.	.	.	.	C	18.67	3.674051	0.67928	.	.	ENSG00000163092	ENST00000409043;ENST00000409728;ENST00000409195;ENST00000409756;ENST00000420519;ENST00000295237	T;T;T;T;T;T	0.80123	-1.22;-1.34;4.13;-1.22;-1.34;4.13	5.51	5.51	0.81932	.	0.732373	0.11232	U	0.585502	T	0.82148	0.4974	N	0.14661	0.345	0.28718	N	0.903185	D;D;D	0.71674	0.998;0.998;0.998	D;D;P	0.63113	0.911;0.911;0.847	T	0.78237	-0.2282	10	0.62326	D	0.03	-0.0586	17.6029	0.88030	0.0:1.0:0.0:0.0	.	178;178;3	A4UGR9-4;A4UGR9-6;A4UGR9-3	.;.;.	H	178	ENSP00000386454:P178H;ENSP00000386619:P178H;ENSP00000386840:P178H;ENSP00000386724:P178H;ENSP00000415541:P178H;ENSP00000295237:P178H	ENSP00000295237:P178H	P	+	2	0	XIRP2	167700789	1.000000	0.71417	1.000000	0.80357	0.719000	0.41307	4.911000	0.63328	2.597000	0.87782	0.591000	0.81541	CCT		0.408	XIRP2-006	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333552.1	NM_152381		Missense_Mutation
ZBTB16	7704	hgsc.bcm.edu	37	11	113934217	113934217	+	Silent	SNP	C	C	T			TCGA-10-0927-01	TCGA-10-0927-11	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	454_PCR_WGA	.	.	Illumina GAIIx	TCGA-10-0927-01	TCGA-10-0927-11	g.chr11:113934217C>T	ENST00000335953.4	+	2	575	c.195C>T	c.(193-195)cgC>cgT	p.R65R	ZBTB16_ENST00000392996.2_Silent_p.R65R	NM_006006.4	NP_005997.2	Q05516	ZBT16_HUMAN	zinc finger and BTB domain containing 16	65	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|cartilage development (GO:0051216)|central nervous system development (GO:0007417)|embryonic digit morphogenesis (GO:0042733)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic pattern specification (GO:0009880)|forelimb morphogenesis (GO:0035136)|hemopoiesis (GO:0030097)|male germ-line stem cell asymmetric division (GO:0048133)|mesonephros development (GO:0001823)|myeloid cell differentiation (GO:0030099)|negative regulation of cell proliferation (GO:0008285)|negative regulation of myeloid cell differentiation (GO:0045638)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cartilage development (GO:0061036)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of NK T cell differentiation (GO:0051138)|positive regulation of ossification (GO:0045778)|positive regulation of transcription, DNA-templated (GO:0045893)|protein localization to nucleus (GO:0034504)|protein ubiquitination (GO:0016567)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|nuclear body (GO:0016604)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)|transcriptional repressor complex (GO:0017053)	DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R65R(1)		central_nervous_system(1)|large_intestine(2)|skin(1)|upper_aerodigestive_tract(2)	6		all_cancers(61;3.79e-18)|all_epithelial(67;2.32e-10)|all_hematologic(158;2.96e-05)|Melanoma(852;0.000362)|Acute lymphoblastic leukemia(157;0.00108)|Breast(348;0.0104)|all_neural(223;0.0294)|Prostate(24;0.0318)|Medulloblastoma(222;0.0438)		BRCA - Breast invasive adenocarcinoma(274;6.75e-06)|Epithelial(105;0.000181)|all cancers(92;0.0018)		TCTTCCACCGCAATAGTCAAC	0.547																																																1	Substitution - coding silent(1)	ovary(1)	11											105.0	85.0	92.0					11																	113934217		2201	4296	6497	113439427	SO:0001819	synonymous_variant	7704			Z19002	CCDS8367.1	11q23	2013-10-17	2004-07-16	2004-07-16	ENSG00000109906	ENSG00000109906		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	12930	protein-coding gene	gene with protein product	"""promyelocytic leukaemia zinc finger"""	176797	"""zinc finger protein 145 (Kruppel-like, expressed in promyelocytic leukemia)"""	ZNF145			Standard	XM_006718899		Approved	PLZF	uc001poq.3	Q05516	OTTHUMG00000168243	ENST00000335953.4:c.195C>T	11.37:g.113934217C>T		Somatic		Capture	SOLID	Phase_IV	113439427	Q8TAL4	Silent	SNP	ENST00000335953.4	37	CCDS8367.1	SNP	25	Baylor																																																																																				0.547	ZBTB16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398940.1	NM_006006		Silent
ZNF155	7711	hgsc.bcm.edu	37	19	44501456	44501456	+	Missense_Mutation	SNP	C	C	A	rs142327702		TCGA-10-0927-01	TCGA-10-0927-11	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	454_PCR_WGA	.	.	Illumina GAIIx	TCGA-10-0927-01	TCGA-10-0927-11	g.chr19:44501456C>A	ENST00000270014.2	+	5	1575	c.1447C>A	c.(1447-1449)Cca>Aca	p.P483T	RP11-15A1.7_ENST00000589021.1_RNA|RP11-15A1.7_ENST00000586860.1_RNA|ZNF155_ENST00000590615.1_Missense_Mutation_p.P483T|ZNF155_ENST00000407951.2_Missense_Mutation_p.P494T	NM_001260487.1|NM_198089.2	NP_001247416|NP_932355	Q12901	ZN155_HUMAN	zinc finger protein 155	483					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)	p.P483T(1)		endometrium(3)|kidney(2)|large_intestine(1)|lung(6)|ovary(1)|upper_aerodigestive_tract(2)	15		Prostate(69;0.0352)				CCAGAAAAAACCATTCAAATG	0.453													C|||	1	0.000199681	0.0	0.0	5008	,	,		17003	0.001		0.0	False		,,,				2504	0.0				NSCLC(61;554 1277 20909 42067 42312)											1	Substitution - Missense(1)	ovary(1)	19						C	THR/PRO,THR/PRO	0,4406		0,0,2203	94.0	99.0	97.0		1447,1447	-0.8	0.0	19	dbSNP_134	97	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	ZNF155	NM_003445.2,NM_198089.1	38,38	0,1,6502	AA,AC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging	483/539,483/539	44501456	1,13005	2203	4300	6503	49193296	SO:0001583	missense	7711			U09852	CCDS12634.1, CCDS58668.1	19q13.2-q13.32	2013-01-08	2006-08-22			ENSG00000204920		"""Zinc fingers, C2H2-type"", ""-"""	12940	protein-coding gene	gene with protein product		604086	"""zinc finger protein 155 (pHZ-96)"""			7557990	Standard	NM_001260486		Approved	pHZ-96	uc010xwt.2	Q12901		ENST00000270014.2:c.1447C>A	19.37:g.44501456C>A	ENSP00000270014:p.Pro483Thr	Somatic		Capture	SOLID	Phase_IV	49193296	A2BDE6|B2RB63|B4DM95|J3KQ08|Q6AZZ8|Q9UIE1|Q9UK14	Missense_Mutation	SNP	ENST00000270014.2	37	CCDS12634.1	SNP	18	Baylor	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	C	13.37	2.218054	0.39201	0.0	1.16E-4	ENSG00000204920	ENST00000407951;ENST00000270014	T;T	0.07021	3.23;3.23	2.83	-0.751	0.11076	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.17534	0.0421	M	0.65320	2	0.09310	N	1	D;D	0.64830	0.99;0.994	D;D	0.71870	0.918;0.975	T	0.16394	-1.0404	9	0.66056	D	0.02	.	1.5214	0.02516	0.1667:0.4434:0.164:0.2259	.	494;483	B4DM95;Q12901	.;ZN155_HUMAN	T	494;483	ENSP00000385163:P494T;ENSP00000270014:P483T	ENSP00000270014:P483T	P	+	1	0	ZNF155	49193296	0.660000	0.27420	0.006000	0.13384	0.199000	0.23934	2.278000	0.43426	0.057000	0.16193	-0.304000	0.09214	CCA		0.453	ZNF155-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000460074.1	NM_003445		Missense_Mutation
