#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_ORegAnno_bin	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
ACADVL	37	hgsc.bcm.edu	37	17	7127350	7127350	+	Missense_Mutation	SNP	G	G	A			TCGA-57-1584-01	TCGA-57-1584-11	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	TCGA-57-1584-01	TCGA-57-1584-11	g.chr17:7127350G>A	ENST00000356839.5	+	14	1575	c.1396G>A	c.(1396-1398)Gac>Aac	p.D466N	MIR324_ENST00000362183.1_RNA|ACADVL_ENST00000543245.2_Missense_Mutation_p.D489N|ACADVL_ENST00000350303.5_Missense_Mutation_p.D444N	NM_000018.3|NM_001270448.1	NP_000009.1|NP_001257377.1	P49748	ACADV_HUMAN	acyl-CoA dehydrogenase, very long chain	466	Catalytic.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular lipid metabolic process (GO:0044255)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|energy derivation by oxidation of organic compounds (GO:0015980)|epithelial cell differentiation (GO:0030855)|fatty acid beta-oxidation (GO:0006635)|fatty acid beta-oxidation using acyl-CoA dehydrogenase (GO:0033539)|negative regulation of fatty acid biosynthetic process (GO:0045717)|negative regulation of fatty acid oxidation (GO:0046322)|regulation of cholesterol metabolic process (GO:0090181)|small molecule metabolic process (GO:0044281)|temperature homeostasis (GO:0001659)	cytoplasm (GO:0005737)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	acyl-CoA dehydrogenase activity (GO:0003995)|flavin adenine dinucleotide binding (GO:0050660)|long-chain-acyl-CoA dehydrogenase activity (GO:0004466)	p.D466N(1)		breast(2)|cervix(2)|endometrium(6)|kidney(1)|large_intestine(2)|liver(2)|lung(1)|ovary(4)|skin(1)	21						GGGGACAAATGACATTCTTCG	0.542																																																1	Substitution - Missense(1)	ovary(1)	17											94.0	87.0	89.0					17																	7127350		2203	4300	6503	7068074	SO:0001583	missense	37			BC012912	CCDS11090.1, CCDS42249.1, CCDS58509.1	17p13.1	2010-04-30	2010-04-30		ENSG00000072778	ENSG00000072778			92	protein-coding gene	gene with protein product		609575	"""acyl-Coenzyme A dehydrogenase, very long chain"""			8921384	Standard	NM_000018		Approved	VLCAD, LCACD, ACAD6	uc002gev.4	P49748	OTTHUMG00000102157	ENST00000356839.5:c.1396G>A	17.37:g.7127350G>A	ENSP00000349297:p.Asp466Asn		7068074	B4DEB6|F5H2A9|O76056|Q8WUL0	Missense_Mutation	SNP	ENST00000356839.5	37	CCDS11090.1	SNP	45	Baylor	.	.	.	.	.	.	.	.	.	.	G	12.97	2.097862	0.37048	.	.	ENSG00000072778	ENST00000543245;ENST00000356839;ENST00000350303;ENST00000322910;ENST00000542255	D;D	0.95788	-3.81;-3.81	5.74	5.74	0.90152	Acyl-CoA dehydrogenase/oxidase C-terminal (2);Acyl-CoA oxidase/dehydrogenase, type 1 (1);	0.000000	0.85682	D	0.000000	D	0.96571	0.8881	L	0.46157	1.445	0.80722	D	1	D;D;D	0.89917	0.994;0.994;1.0	D;D;D	0.79784	0.967;0.976;0.993	D	0.96807	0.9594	10	0.87932	D	0	.	15.4119	0.74933	0.0:0.0:1.0:0.0	.	489;444;466	F5H2A9;P49748-2;P49748	.;.;ACADV_HUMAN	N	489;512;444;466;512	ENSP00000438689:D489N;ENSP00000344152:D444N	ENSP00000325395:D466N	D	+	1	0	ACADVL	7068074	1.000000	0.71417	0.988000	0.46212	0.335000	0.28730	8.460000	0.90369	2.719000	0.93026	0.655000	0.94253	GAC		0.542	ACADVL-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000220001.5	NM_000018		Missense_Mutation
AHNAK	79026	hgsc.bcm.edu	37	11	62298437	62298437	+	Missense_Mutation	SNP	G	G	C			TCGA-57-1584-01	TCGA-57-1584-11	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	TCGA-57-1584-01	TCGA-57-1584-11	g.chr11:62298437G>C	ENST00000378024.4	-	5	3726	c.3452C>G	c.(3451-3453)cCt>cGt	p.P1151R	AHNAK_ENST00000530124.1_Intron|AHNAK_ENST00000257247.7_Intron	NM_001620.1	NP_001611.1	Q09666	AHNK_HUMAN	AHNAK nucleoprotein	1151					protein oligomerization (GO:0051259)|regulation of RNA splicing (GO:0043484)|regulation of voltage-gated calcium channel activity (GO:1901385)	actin cytoskeleton (GO:0015629)|cell-cell contact zone (GO:0044291)|costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|vesicle (GO:0031982)	poly(A) RNA binding (GO:0044822)|S100 protein binding (GO:0044548)|structural molecule activity conferring elasticity (GO:0097493)	p.P1151R(1)		NS(3)|autonomic_ganglia(1)|breast(10)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(33)|large_intestine(40)|liver(1)|lung(108)|ovary(13)|pancreas(4)|prostate(5)|skin(16)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	268		Melanoma(852;0.155)				GTCAGCCTTAGGCAAGTTCAC	0.542																																																1	Substitution - Missense(1)	ovary(1)	11											158.0	153.0	155.0					11																	62298437		2202	4299	6501	62055013	SO:0001583	missense	79026			M80899	CCDS31584.1, CCDS44625.1	11q12-q13	2008-02-05	2007-03-30		ENSG00000124942	ENSG00000124942			347	protein-coding gene	gene with protein product	"""desmoyokin"""	103390	"""AHNAK nucleoprotein (desmoyokin)"""			7987395, 12153988	Standard	NM_024060		Approved	MGC5395	uc001ntl.3	Q09666	OTTHUMG00000167558	ENST00000378024.4:c.3452C>G	11.37:g.62298437G>C	ENSP00000367263:p.Pro1151Arg		62055013	A1A586	Missense_Mutation	SNP	ENST00000378024.4	37	CCDS31584.1	SNP	35	Baylor	.	.	.	.	.	.	.	.	.	.	g	9.720	1.159394	0.21454	.	.	ENSG00000124942	ENST00000378024	T	0.05717	3.4	4.88	3.97	0.46021	.	0.403463	0.18250	N	0.146973	T	0.36276	0.0961	H	0.97340	3.985	0.29346	N	0.865702	D	0.58970	0.984	D	0.63033	0.91	T	0.54583	-0.8272	10	0.72032	D	0.01	-7.5358	13.4047	0.60906	0.0:0.1577:0.8423:0.0	.	1151	Q09666	AHNK_HUMAN	R	1151	ENSP00000367263:P1151R	ENSP00000367263:P1151R	P	-	2	0	AHNAK	62055013	1.000000	0.71417	0.136000	0.22124	0.010000	0.07245	6.851000	0.75425	1.075000	0.40932	-0.132000	0.14878	CCT		0.542	AHNAK-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395572.1	NM_024060		Missense_Mutation
AKAP12	9590	hgsc.bcm.edu	37	6	151627040	151627040	+	Splice_Site	SNP	T	T	G			TCGA-57-1584-01	TCGA-57-1584-11	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	TCGA-57-1584-01	TCGA-57-1584-11	g.chr6:151627040T>G	ENST00000253332.1	+	2	508		c.e2+2		AKAP12_ENST00000402676.2_Splice_Site			Q02952	AKA12_HUMAN	A kinase (PRKA) anchor protein 12						G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of protein kinase A signaling (GO:0010739)|protein targeting (GO:0006605)|regulation of protein kinase C signaling (GO:0090036)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)	adenylate cyclase binding (GO:0008179)|protein kinase A binding (GO:0051018)	p.?(1)		breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(22)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	68		Ovarian(120;0.125)	BRCA - Breast invasive adenocarcinoma(37;0.175)	OV - Ovarian serous cystadenocarcinoma(155;2.98e-11)		TCACAGAGGGTAAGCCGCCCC	0.527																																					Melanoma(141;1616 1805 10049 24534 51979)											1	Unknown(1)	ovary(1)	6											34.0	28.0	30.0					6																	151627040		2202	4300	6502	151668733	SO:0001630	splice_region_variant	9590			U81607	CCDS5229.1, CCDS5230.1	6q24-q25	2011-07-01	2008-08-29		ENSG00000131016	ENSG00000131016		"""A-kinase anchor proteins"""	370	protein-coding gene	gene with protein product	"""gravin"", ""Src-Suppressed C Kinase Substrate"""	604698	"""A kinase (PRKA) anchor protein (gravin) 12"""			9000000	Standard	NM_144497		Approved	AKAP250, SSeCKS	uc011eep.2	Q02952	OTTHUMG00000015833	ENST00000253332.1:c.319+2T>G	6.37:g.151627040T>G			151668733	O00310|O00498|Q4LE68|Q5SZ80|Q5TGN1|Q68D82|Q99970	Splice_Site_SNP	SNP	ENST00000253332.1	37	CCDS5229.1	SNP	57	Baylor	.	.	.	.	.	.	.	.	.	.	T	9.953	1.220758	0.22457	.	.	ENSG00000131016	ENST00000402676;ENST00000253332	.	.	.	4.56	4.56	0.56223	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.613	0.45434	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	AKAP12	151668733	1.000000	0.71417	0.999000	0.59377	0.024000	0.10985	1.894000	0.39768	1.835000	0.53391	0.454000	0.30748	.		0.527	AKAP12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042712.1		Intron	Splice_Site_SNP
AKR1B1	231	hgsc.bcm.edu	37	7	134135631	134135631	+	Silent	SNP	C	C	T			TCGA-57-1584-01	TCGA-57-1584-11	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	TCGA-57-1584-01	TCGA-57-1584-11	g.chr7:134135631C>T	ENST00000285930.4	-	3	337	c.258G>A	c.(256-258)aaG>aaA	p.K86K	AKR1B1_ENST00000489022.1_5'UTR	NM_001628.2	NP_001619.1	P15121	ALDR_HUMAN	aldo-keto reductase family 1, member B1 (aldose reductase)	86					C21-steroid hormone biosynthetic process (GO:0006700)|carbohydrate metabolic process (GO:0005975)|daunorubicin metabolic process (GO:0044597)|doxorubicin metabolic process (GO:0044598)|response to stress (GO:0006950)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	alditol:NADP+ 1-oxidoreductase activity (GO:0004032)|aldo-keto reductase (NADP) activity (GO:0004033)|electron carrier activity (GO:0009055)|glyceraldehyde oxidoreductase activity (GO:0043795)	p.K86K(1)		kidney(1)|large_intestine(5)|lung(2)|ovary(3)|prostate(1)|skin(2)	14					Sulindac(DB00605)	TCACCAGGCCCTTCTCATGGT	0.562																																																1	Substitution - coding silent(1)	ovary(1)	7											89.0	67.0	75.0					7																	134135631		2203	4300	6503	133786171	SO:0001819	synonymous_variant	231			J04795	CCDS5831.1	7q35	2010-04-08			ENSG00000085662	ENSG00000085662	1.1.1.21	"""Aldo-keto reductases"""	381	protein-coding gene	gene with protein product		103880		ALDR1		1901827	Standard	NM_001628		Approved	AR	uc003vrp.1	P15121	OTTHUMG00000155322	ENST00000285930.4:c.258G>A	7.37:g.134135631C>T			133786171	B2R8N3|Q5U031|Q6FGA4|Q6ICP2|Q9BS21|Q9UCI9	Silent	SNP	ENST00000285930.4	37	CCDS5831.1	SNP	24	Baylor																																																																																				0.562	AKR1B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339448.2	NM_001628		Silent
ARFGAP1	55738	hgsc.bcm.edu	37	20	61907471	61907471	+	Missense_Mutation	SNP	C	C	G			TCGA-57-1584-01	TCGA-57-1584-11	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	TCGA-57-1584-01	TCGA-57-1584-11	g.chr20:61907471C>G	ENST00000370283.4	+	3	229	c.89C>G	c.(88-90)cCt>cGt	p.P30R	ARFGAP1_ENST00000519273.2_5'UTR|ARFGAP1_ENST00000547204.1_Intron|ARFGAP1_ENST00000353546.3_Missense_Mutation_p.P30R|ARFGAP1_ENST00000519604.1_Intron|ARFGAP1_ENST00000370275.4_Missense_Mutation_p.P30R	NM_018209.2	NP_060679.1	Q8N6T3	ARFG1_HUMAN	ADP-ribosylation factor GTPase activating protein 1	30	Arf-GAP. {ECO:0000255|PROSITE- ProRule:PRU00288}.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|COPI coating of Golgi vesicle (GO:0048205)|endoplasmic reticulum unfolded protein response (GO:0030968)|membrane organization (GO:0061024)|positive regulation of GTPase activity (GO:0043547)|protein transport (GO:0015031)|regulation of ARF GTPase activity (GO:0032312)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	cytosol (GO:0005829)|Golgi-associated vesicle membrane (GO:0030660)|synapse (GO:0045202)	ARF GTPase activator activity (GO:0008060)|GTPase activator activity (GO:0005096)|zinc ion binding (GO:0008270)	p.P30R(1)		endometrium(2)|kidney(2)|large_intestine(1)|lung(6)|ovary(1)|pancreas(1)	13	all_cancers(38;1.59e-09)					GCGTTCAATCCTCAGTGGGTC	0.612																																																1	Substitution - Missense(1)	ovary(1)	20											150.0	137.0	141.0					20																	61907471		2203	4300	6503	61377916	SO:0001583	missense	55738			AK001629	CCDS13515.1, CCDS13516.1, CCDS63326.1, CCDS63327.1, CCDS63328.1	20q13.33	2009-11-30	2002-08-20	2002-08-23	ENSG00000101199	ENSG00000101199		"""ADP-ribosylation factor GTPase activating proteins"""	15852	protein-coding gene	gene with protein product		608377	"""ADP-ribosylation factor 1 GTPase activating protein"""	ARF1GAP		11210549	Standard	NM_018209		Approved	FLJ10767, bA261N11.3	uc002yel.3	Q8N6T3	OTTHUMG00000032965	ENST00000370283.4:c.89C>G	20.37:g.61907471C>G	ENSP00000359306:p.Pro30Arg		61377916	B7Z3U0|B7Z8H8|B7ZBI3|E1P5I9|E7EV62|Q6PK71|Q96KC4|Q96T02|Q9NSU3|Q9NVF6|Q9UIL0	Missense_Mutation	SNP	ENST00000370283.4	37	CCDS13515.1	SNP	24	Baylor	.	.	.	.	.	.	.	.	.	.	C	23.7	4.447626	0.84101	.	.	ENSG00000101199	ENST00000370283;ENST00000523114;ENST00000370275;ENST00000353546;ENST00000522403;ENST00000550188	T;T;T;T;T;T	0.69685	-0.42;-0.42;-0.42;-0.42;-0.42;-0.42	4.68	4.68	0.58851	.	0.000000	0.85682	D	0.000000	D	0.90789	0.7108	H	0.99825	4.815	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.95443	0.8527	10	0.87932	D	0	0.3405	17.9471	0.89042	0.0:1.0:0.0:0.0	.	30;30;30	B7ZBI2;Q8N6T3;Q8N6T3-2	.;ARFG1_HUMAN;.	R	30	ENSP00000359306:P30R;ENSP00000428355:P30R;ENSP00000359298:P30R;ENSP00000314615:P30R;ENSP00000430929:P30R;ENSP00000449515:P30R	ENSP00000314615:P30R	P	+	2	0	ARFGAP1	61377916	1.000000	0.71417	0.968000	0.41197	0.945000	0.59286	7.555000	0.82223	2.310000	0.77875	0.462000	0.41574	CCT		0.612	ARFGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080134.3	NM_018209		Missense_Mutation
ARIH2	10425	hgsc.bcm.edu	37	3	49012255	49012255	+	Silent	SNP	C	C	T			TCGA-57-1584-01	TCGA-57-1584-11	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	TCGA-57-1584-01	TCGA-57-1584-11	g.chr3:49012255C>T	ENST00000356401.4	+	10	1233	c.894C>T	c.(892-894)ccC>ccT	p.P298P	ARIH2_ENST00000449376.1_Silent_p.P298P|ARIH2_ENST00000490095.1_3'UTR	NM_006321.2	NP_006312.1	O95376	ARI2_HUMAN	ariadne RBR E3 ubiquitin protein ligase 2	298					developmental cell growth (GO:0048588)|hematopoietic stem cell proliferation (GO:0071425)|multicellular organismal development (GO:0007275)|protein K48-linked ubiquitination (GO:0070936)|protein K63-linked ubiquitination (GO:0070534)|protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|nucleic acid binding (GO:0003676)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.P298P(1)		cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(3)|ovary(1)|skin(1)	13				BRCA - Breast invasive adenocarcinoma(193;9.42e-05)|Kidney(197;0.00258)|KIRC - Kidney renal clear cell carcinoma(197;0.00269)		CTCAGTGTCCCAAGTGCAACA	0.502																																																1	Substitution - coding silent(1)	ovary(1)	3											184.0	159.0	168.0					3																	49012255		2203	4300	6503	48987259	SO:0001819	synonymous_variant	10425			AF099149	CCDS2780.1	3p21	2013-10-03	2013-10-03		ENSG00000177479	ENSG00000177479			690	protein-coding gene	gene with protein product	"""all-trans retinoic acid inducible RING finger"""	605615	"""ariadne (Drosophila) homolog 2"", ""ariadne homolog 2 (Drosophila)"""			10422847, 24058416	Standard	XM_005264798		Approved	TRIAD1	uc003cvb.3	O95376	OTTHUMG00000133547	ENST00000356401.4:c.894C>T	3.37:g.49012255C>T			48987259	Q9HBZ6|Q9UEM9	Silent	SNP	ENST00000356401.4	37	CCDS2780.1	SNP	21	Baylor																																																																																				0.502	ARIH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257525.1	NM_006321		Silent
CAMTA1	23261	hgsc.bcm.edu	37	1	7737695	7737695	+	Missense_Mutation	SNP	T	T	A			TCGA-57-1584-01	TCGA-57-1584-11	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	TCGA-57-1584-01	TCGA-57-1584-11	g.chr1:7737695T>A	ENST00000303635.7	+	11	3023	c.2816T>A	c.(2815-2817)tTc>tAc	p.F939Y	CAMTA1_ENST00000439411.2_Missense_Mutation_p.F939Y	NM_015215.2	NP_056030.1	Q9Y6Y1	CMTA1_HUMAN	calmodulin binding transcription activator 1	939	IPT/TIG.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.F939Y(1)		breast(5)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(11)|lung(29)|ovary(5)|pancreas(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	85	Ovarian(185;0.0634)	all_epithelial(116;8.38e-23)|all_lung(118;5.87e-07)|Lung NSC(185;3.43e-06)|Renal(390;0.000219)|Breast(487;0.000307)|Colorectal(325;0.000615)|Hepatocellular(190;0.0088)|Myeloproliferative disorder(586;0.0303)|Ovarian(437;0.0388)		UCEC - Uterine corpus endometrioid carcinoma (279;0.101)|Colorectal(212;1.33e-05)|COAD - Colon adenocarcinoma(227;0.000235)|BRCA - Breast invasive adenocarcinoma(304;0.000864)|Kidney(185;0.00244)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0179)|READ - Rectum adenocarcinoma(331;0.133)		CAAGTTGCCTTCAACAACCAG	0.557			T	WWTR1	epitheliod hemangioendothelioma																																		Dom	yes		1	1p36.31-p36.23	611501	calmodulin binding transcription activator 1		M	1	Substitution - Missense(1)	ovary(1)	1											198.0	176.0	183.0					1																	7737695		2203	4300	6503	7660282	SO:0001583	missense	23261			AB020640	CCDS30576.1, CCDS55574.1, CCDS55575.1	1p36.31-p36.23	2008-07-18			ENSG00000171735	ENSG00000171735			18806	protein-coding gene	gene with protein product		611501				11925432	Standard	NM_001195563		Approved	KIAA0833	uc001aoi.3	Q9Y6Y1	OTTHUMG00000001212	ENST00000303635.7:c.2816T>A	1.37:g.7737695T>A	ENSP00000306522:p.Phe939Tyr		7660282	A7MBM4|G3V3Z7|Q5VUE1|Q6V701|Q8WYI3|Q96S92	Missense_Mutation	SNP	ENST00000303635.7	37	CCDS30576.1	SNP	62	Baylor	.	.	.	.	.	.	.	.	.	.	t	7.033	0.560966	0.13498	.	.	ENSG00000171735	ENST00000303635;ENST00000439411;ENST00000414738	T;T	0.75821	-0.97;-0.97	5.19	5.19	0.71726	Cell surface receptor IPT/TIG (1);Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.122271	0.56097	D	0.000026	T	0.56232	0.1971	N	0.14661	0.345	0.36214	D	0.851535	B;B	0.06786	0.001;0.001	B;B	0.10450	0.005;0.005	T	0.58526	-0.7621	10	0.27785	T	0.31	-20.9059	10.356	0.43964	0.1464:0.0:0.0:0.8536	.	939;939	Q9Y6Y1-2;Q9Y6Y1	.;CMTA1_HUMAN	Y	939;939;26	ENSP00000306522:F939Y;ENSP00000402561:F939Y	ENSP00000306522:F939Y	F	+	2	0	CAMTA1	7660282	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.984000	0.56923	1.976000	0.57569	0.454000	0.30748	TTC		0.557	CAMTA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000003588.3	NM_015215		Missense_Mutation
CFHR2	3080	hgsc.bcm.edu	37	1	196918732	196918732	+	Missense_Mutation	SNP	G	G	A	rs144596551		TCGA-57-1584-01	TCGA-57-1584-11	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	TCGA-57-1584-01	TCGA-57-1584-11	g.chr1:196918732G>A	ENST00000367415.5	+	2	306	c.206G>A	c.(205-207)cGc>cAc	p.R69H	CFHR2_ENST00000496448.1_Intron|CFHR2_ENST00000367421.3_Missense_Mutation_p.R69H|CFHR2_ENST00000476712.2_Missense_Mutation_p.R69H	NM_005666.2	NP_005657.1	P36980	FHR2_HUMAN	complement factor H-related 2	69	Sushi 1. {ECO:0000255|PROSITE- ProRule:PRU00302}.					extracellular region (GO:0005576)		p.R69H(1)		large_intestine(2)|ovary(1)|skin(3)	6						TTTTGGACTCGCATAACGTGC	0.393																																																1	Substitution - Missense(1)	ovary(1)	1											97.0	87.0	90.0					1																	196918732		2203	4300	6503	195185355	SO:0001583	missense	3080			X64877	CCDS30959.1	1q31.3	2008-02-05	2004-08-09	2006-02-28	ENSG00000080910	ENSG00000080910		"""Complement system"""	4890	protein-coding gene	gene with protein product		600889	"""H factor (complement)-like 3"""	HFL3, CFHL2		1533657, 7672821	Standard	NM_005666		Approved	FHR2	uc001gtq.1	P36980	OTTHUMG00000036518	ENST00000367415.5:c.206G>A	1.37:g.196918732G>A	ENSP00000356385:p.Arg69His		195185355	Q14310|Q5T9T1	Missense_Mutation	SNP	ENST00000367415.5	37	CCDS30959.1	SNP	38	Baylor	.	.	.	.	.	.	.	.	.	.	.	11.75	1.733228	0.30684	.	.	ENSG00000080910	ENST00000367421;ENST00000367415	T;T	0.64803	-0.12;-0.12	3.15	-6.29	0.02013	Complement control module (2);Sushi/SCR/CCP (2);	1.243780	0.06385	N	0.715952	T	0.63873	0.2548	L	0.44542	1.39	0.09310	N	1	D	0.89917	1.0	D	0.66847	0.947	T	0.61540	-0.7042	10	0.42905	T	0.14	.	5.3275	0.15915	0.3221:0.4369:0.241:0.0	.	69	P36980	FHR2_HUMAN	H	69	ENSP00000356391:R69H;ENSP00000356385:R69H	ENSP00000356385:R69H	R	+	2	0	CFHR2	195185355	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-3.088000	0.00610	-1.636000	0.01533	-0.357000	0.07601	CGC		0.393	CFHR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088815.2	NM_005666		Missense_Mutation
CHRNA6	8973	hgsc.bcm.edu	37	8	42611054	42611054	+	Nonsense_Mutation	SNP	C	C	A			TCGA-57-1584-01	TCGA-57-1584-11	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	TCGA-57-1584-01	TCGA-57-1584-11	g.chr8:42611054C>A	ENST00000276410.2	-	5	1643	c.1288G>T	c.(1288-1290)Gaa>Taa	p.E430*	CHRNA6_ENST00000534622.1_Nonsense_Mutation_p.E415*|CHRNA6_ENST00000530869.1_5'Flank	NM_004198.3	NP_004189.1	Q15825	ACHA6_HUMAN	cholinergic receptor, nicotinic, alpha 6 (neuronal)	430					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|membrane depolarization (GO:0051899)|regulation of dopamine secretion (GO:0014059)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transport (GO:0006810)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)	p.E430*(1)		endometrium(2)|large_intestine(3)|liver(1)|lung(15)|ovary(1)	22	all_lung(13;3.33e-12)|Lung NSC(13;9.17e-11)|Ovarian(28;0.01)|Prostate(17;0.0119)|Lung SC(25;0.184)	all_lung(54;0.00439)|Lung NSC(58;0.0124)|Esophageal squamous(32;0.131)|Hepatocellular(245;0.133)|Renal(179;0.151)	Lung(22;0.0252)|LUSC - Lung squamous cell carcinoma(45;0.0869)		Galantamine(DB00674)|Nicotine(DB00184)|Varenicline(DB01273)	ATCACATCTTCAACTTCAGGC	0.448																																																1	Substitution - Nonsense(1)	ovary(1)	8											236.0	206.0	216.0					8																	42611054		2203	4300	6503	42730211	SO:0001587	stop_gained	8973			U62435	CCDS6135.1, CCDS56536.1	8p22	2012-02-11	2012-02-07					"""Cholinergic receptors"", ""Ligand-gated ion channels / Acetylcholine receptors, nicotinic"""	15963	protein-coding gene	gene with protein product	"""acetylcholine receptor, nicotinic, alpha 6 (neuronal)"""	606888	"""cholinergic receptor, nicotinic, alpha polypeptide 6"""			8906617	Standard	NM_004198		Approved		uc003xpj.3	Q15825		ENST00000276410.2:c.1288G>T	8.37:g.42611054C>A	ENSP00000276410:p.Glu430*		42730211	B2R8V4|B4DQH1	Nonsense_Mutation	SNP	ENST00000276410.2	37	CCDS6135.1	SNP	29	Baylor	.	.	.	.	.	.	.	.	.	.	C	33	5.229428	0.95173	.	.	ENSG00000147434	ENST00000276410;ENST00000534622	.	.	.	5.93	4.95	0.65309	.	0.276047	0.42053	D	0.000768	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.10377	T	0.69	.	3.9365	0.09309	0.0:0.6839:0.0:0.3161	.	.	.	.	X	430;415	.	ENSP00000276410:E430X	E	-	1	0	CHRNA6	42730211	0.537000	0.26386	0.964000	0.40570	0.222000	0.24845	3.299000	0.51826	2.815000	0.96918	0.561000	0.74099	GAA		0.448	CHRNA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383156.1			Nonsense_Mutation
CIZ1	25792	hgsc.bcm.edu	37	9	130941075	130941075	+	Missense_Mutation	SNP	C	C	T			TCGA-57-1584-01	TCGA-57-1584-11	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	TCGA-57-1584-01	TCGA-57-1584-11	g.chr9:130941075C>T	ENST00000393608.1	-	8	1613	c.1411G>A	c.(1411-1413)Gtg>Atg	p.V471M	CIZ1_ENST00000277465.4_Missense_Mutation_p.V443M|CIZ1_ENST00000325721.8_Missense_Mutation_p.V442M|CIZ1_ENST00000476727.2_Intron|CIZ1_ENST00000372938.5_Missense_Mutation_p.V471M|CIZ1_ENST00000357558.5_Missense_Mutation_p.V443M|CIZ1_ENST00000372948.3_Missense_Mutation_p.V415M|CIZ1_ENST00000372954.1_Missense_Mutation_p.V391M|CIZ1_ENST00000541172.1_Missense_Mutation_p.V370M|CIZ1_ENST00000538431.1_Missense_Mutation_p.V471M	NM_012127.2	NP_036259.2	Q9ULV3	CIZ1_HUMAN	CDKN1A interacting zinc finger protein 1	471					maintenance of protein location in nucleus (GO:0051457)|positive regulation of DNA-dependent DNA replication initiation (GO:0032298)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)	p.V471M(1)		NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(8)|liver(1)|lung(9)|ovary(3)|prostate(2)|urinary_tract(2)	35						AGCAACGACACCTGCGGCTGG	0.597																																																1	Substitution - Missense(1)	ovary(1)	9											113.0	98.0	103.0					9																	130941075		2203	4300	6503	129980896	SO:0001583	missense	25792			AB030835	CCDS6894.1, CCDS48033.1, CCDS48034.1, CCDS75910.1	9q34.1	2012-10-05			ENSG00000148337	ENSG00000148337			16744	protein-coding gene	gene with protein product		611420				10529385	Standard	NM_001131015		Approved	LSFR1, ZNF356	uc011mas.2	Q9ULV3	OTTHUMG00000020735	ENST00000393608.1:c.1411G>A	9.37:g.130941075C>T	ENSP00000377232:p.Val471Met		129980896	A8K9J8|B4E131|B7ZAS8|Q5SYW3|Q5SYW5|Q8WU72|Q9H868|Q9NYM8|Q9UHK4|Q9Y3F9|Q9Y3G0	Missense_Mutation	SNP	ENST00000393608.1	37	CCDS6894.1	SNP	18	Baylor	.	.	.	.	.	.	.	.	.	.	C	13.21	2.170111	0.38315	.	.	ENSG00000148337	ENST00000372954;ENST00000393608;ENST00000538431;ENST00000357558;ENST00000325721;ENST00000537314;ENST00000541172;ENST00000277465;ENST00000372948;ENST00000372938;ENST00000415526	T;T;T;T;T;T;T;T;T;T	0.38077	1.16;1.31;1.27;1.33;1.31;1.73;1.33;1.16;1.31;1.89	4.29	3.39	0.38822	.	0.805612	0.10784	N	0.634536	T	0.45397	0.1340	L	0.42245	1.32	0.09310	N	1	D;D;D;D;D;D;D;D	0.71674	0.997;0.993;0.998;0.989;0.989;0.997;0.998;0.993	P;P;D;P;P;P;P;P	0.64776	0.85;0.656;0.929;0.814;0.87;0.897;0.904;0.836	T	0.19549	-1.0302	10	0.35671	T	0.21	-2.5245	6.4642	0.21973	0.0:0.7906:0.0:0.2094	.	471;410;471;415;391;471;442;443	B7Z3U7;B4E0A3;F5H2X7;Q9ULV3-4;Q9ULV3-3;Q9ULV3;Q9ULV3-2;Q5SYW2	.;.;.;.;.;CIZ1_HUMAN;.;.	M	391;471;471;443;442;410;370;443;415;471;393	ENSP00000362045:V391M;ENSP00000377232:V471M;ENSP00000439244:V471M;ENSP00000350169:V443M;ENSP00000320374:V442M;ENSP00000445057:V370M;ENSP00000277465:V443M;ENSP00000362039:V415M;ENSP00000362029:V471M;ENSP00000398011:V393M	ENSP00000277465:V443M	V	-	1	0	CIZ1	129980896	0.000000	0.05858	0.267000	0.24556	0.065000	0.16274	0.317000	0.19487	1.395000	0.46643	0.561000	0.74099	GTG		0.597	CIZ1-203	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054399.1	NM_012127		Missense_Mutation
COX4I2	84701	hgsc.bcm.edu	37	20	30226830	30226830	+	Silent	SNP	A	A	C			TCGA-57-1584-01	TCGA-57-1584-11	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	TCGA-57-1584-01	TCGA-57-1584-11	g.chr20:30226830A>C	ENST00000376075.3	+	2	85	c.10A>C	c.(10-12)Aga>Cga	p.R4R	COX4I2_ENST00000490030.1_3'UTR	NM_032609.2	NP_115998.2	Q96KJ9	COX42_HUMAN	cytochrome c oxidase subunit IV isoform 2 (lung)	4					cellular respiration (GO:0045333)|generation of precursor metabolites and energy (GO:0006091)|hydrogen ion transmembrane transport (GO:1902600)|oxidation-reduction process (GO:0055114)	mitochondrial respiratory chain complex IV (GO:0005751)	cytochrome-c oxidase activity (GO:0004129)	p.R4R(1)		breast(1)|endometrium(1)|large_intestine(4)|liver(1)|lung(3)|ovary(1)	11	all_cancers(5;7.12e-06)|Lung NSC(7;3.95e-06)|all_epithelial(3;4.36e-06)|all_lung(7;6.68e-06)|all_hematologic(12;0.158)|Ovarian(7;0.198)		Epithelial(4;1.01e-05)|all cancers(5;9.46e-05)|OV - Ovarian serous cystadenocarcinoma(3;0.00121)|Colorectal(19;0.0055)|COAD - Colon adenocarcinoma(19;0.0264)			GATGCTCCCCAGAGCTGCCTG	0.592																																																1	Substitution - coding silent(1)	ovary(1)	20											87.0	71.0	76.0					20																	30226830		2203	4300	6503	29690491	SO:0001819	synonymous_variant	84701			AF257180	CCDS13187.1	20q11.21	2011-07-04	2004-08-11		ENSG00000131055	ENSG00000131055		"""Mitochondrial respiratory chain complex / Complex IV"""	16232	protein-coding gene	gene with protein product	"""cytochrome c oxidase subunit IV-like 2"""	607976	"""cytochrome c oxidase subunit IV isoform 2"""	COX4L2		11311561, 17937768	Standard	NM_032609		Approved	COXIV-2, COX4B, dJ857M17.2, COX4-2	uc002wwj.1	Q96KJ9	OTTHUMG00000032180	ENST00000376075.3:c.10A>C	20.37:g.30226830A>C			29690491	Q6GTF4|Q9H0Z4	Silent	SNP	ENST00000376075.3	37	CCDS13187.1	SNP	7	Baylor																																																																																				0.592	COX4I2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078548.1	NM_032609		Silent
CRB1	23418	hgsc.bcm.edu	37	1	197411330	197411330	+	Missense_Mutation	SNP	C	C	G			TCGA-57-1584-01	TCGA-57-1584-11	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	TCGA-57-1584-01	TCGA-57-1584-11	g.chr1:197411330C>G	ENST00000367400.3	+	11	4048	c.3913C>G	c.(3913-3915)Ccg>Gcg	p.P1305A	CRB1_ENST00000544212.1_Missense_Mutation_p.P786A|CRB1_ENST00000367399.2_Missense_Mutation_p.P1193A|CRB1_ENST00000367397.1_3'UTR|CRB1_ENST00000538660.1_Missense_Mutation_p.P769A|RP11-75C23.1_ENST00000422250.1_RNA|CRB1_ENST00000535699.1_Missense_Mutation_p.P1281A	NM_201253.2	NP_957705.1	P82279	CRUM1_HUMAN	crumbs family member 1, photoreceptor morphogenesis associated	1305	EGF-like 19; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.		P -> L (in RP12). {ECO:0000269|PubMed:22128245}.		cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|eye photoreceptor cell development (GO:0042462)|plasma membrane organization (GO:0007009)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|microvillus (GO:0005902)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.P1305A(1)		NS(1)|breast(4)|central_nervous_system(2)|cervix(3)|endometrium(13)|kidney(4)|large_intestine(21)|lung(58)|ovary(7)|prostate(3)|skin(10)|upper_aerodigestive_tract(4)|urinary_tract(2)	132						TGCCTCTGATCCGTGTGTCAA	0.488																																																1	Substitution - Missense(1)	ovary(1)	1											299.0	282.0	288.0					1																	197411330		2203	4300	6503	195677953	SO:0001583	missense	23418				CCDS1390.1, CCDS53454.1, CCDS58052.1, CCDS58053.1	1q31-q32.1	2014-02-06	2014-02-06		ENSG00000134376	ENSG00000134376			2343	protein-coding gene	gene with protein product		604210	"""crumbs (Drosophila) homolog 1"", ""crumbs homolog 1 (Drosophila)"""	RP12		10373321, 10508521	Standard	NM_201253		Approved	LCA8	uc001gtz.3	P82279	OTTHUMG00000035663	ENST00000367400.3:c.3913C>G	1.37:g.197411330C>G	ENSP00000356370:p.Pro1305Ala		195677953	A2A308|B7Z5T2|B9EG71|Q5K3A6|Q5TC28|Q5VUT1|Q6N027|Q8WWY0|Q8WWY1	Missense_Mutation	SNP	ENST00000367400.3	37	CCDS1390.1	SNP	30	Baylor	.	.	.	.	.	.	.	.	.	.	C	24.6	4.552221	0.86127	.	.	ENSG00000134376	ENST00000535699;ENST00000538660;ENST00000367400;ENST00000367399;ENST00000544212;ENST00000448952	D;D;D;D;D;D	0.99732	-3.88;-3.88;-3.88;-3.88;-3.88;-6.57	5.36	5.36	0.76844	EGF-like calcium-binding, conserved site (1);EGF (1);EGF-like calcium-binding (1);Epidermal growth factor-like, type 3 (1);	.	.	.	.	D	0.99778	0.9908	M	0.91300	3.195	0.80722	D	1	D;D;D;D	0.89917	0.999;1.0;1.0;1.0	D;D;D;D	0.91635	0.946;0.998;0.997;0.999	D	0.97368	0.9974	9	0.62326	D	0.03	.	19.0906	0.93225	0.0:1.0:0.0:0.0	.	769;1281;1193;1305	B7Z5T2;F5H0L2;P82279-3;P82279	.;.;.;CRUM1_HUMAN	A	1281;769;1305;1193;786;11	ENSP00000438786:P1281A;ENSP00000438091:P769A;ENSP00000356370:P1305A;ENSP00000356369:P1193A;ENSP00000444556:P786A;ENSP00000395407:P11A	ENSP00000356369:P1193A	P	+	1	0	CRB1	195677953	1.000000	0.71417	0.037000	0.18230	0.815000	0.46073	7.736000	0.84948	2.513000	0.84729	0.591000	0.81541	CCG		0.488	CRB1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086565.2	NM_201253		Missense_Mutation
DBF4B	80174	hgsc.bcm.edu	37	17	42818777	42818777	+	Missense_Mutation	SNP	C	C	G			TCGA-57-1584-01	TCGA-57-1584-11	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	TCGA-57-1584-01	TCGA-57-1584-11	g.chr17:42818777C>G	ENST00000315005.3	+	10	925	c.787C>G	c.(787-789)Ccc>Gcc	p.P263A	DBF4B_ENST00000398338.3_3'UTR|DBF4B_ENST00000393547.2_Missense_Mutation_p.P263A	NM_145663.2	NP_663696.1	Q8NFT6	DBF4B_HUMAN	DBF4 zinc finger B	263					cell cycle (GO:0007049)|positive regulation of cell proliferation (GO:0008284)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|positive regulation of nuclear cell cycle DNA replication (GO:0010571)|positive regulation of protein kinase activity (GO:0045860)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|protein kinase activator activity (GO:0030295)|protein kinase binding (GO:0019901)|zinc ion binding (GO:0008270)	p.P263A(1)		kidney(1)|large_intestine(1)|lung(5)	7		Prostate(33;0.0322)				AGATGCAAGTCCCTTTGAGGC	0.493																																																1	Substitution - Missense(1)	ovary(1)	17											103.0	97.0	99.0					17																	42818777		2203	4300	6503	40174303	SO:0001583	missense	80174			AF465820	CCDS11485.1, CCDS45706.1, CCDS45706.2	17q21.31	2014-02-17	2014-02-17		ENSG00000161692	ENSG00000161692		"""Zinc fingers, DBF-type"""	17883	protein-coding gene	gene with protein product	"""chiffon homolog B (Drosophila)"", ""zinc finger, DBF-type containing 1B"""	611661	"""DBF4 homolog B (S. cerevisiae)"""			15668232	Standard	NM_145663		Approved	FLJ13087, DRF1, ASKL1, chifb, ZDBF1B	uc002ihf.3	Q8NFT6	OTTHUMG00000165717	ENST00000315005.3:c.787C>G	17.37:g.42818777C>G	ENSP00000323663:p.Pro263Ala		40174303	D3DX56|Q8TEX0|Q96B19|Q9H912	Missense_Mutation	SNP	ENST00000315005.3	37	CCDS11485.1	SNP	30	Baylor	.	.	.	.	.	.	.	.	.	.	C	18.29	3.592380	0.66219	.	.	ENSG00000161692	ENST00000393547;ENST00000315005	T;T	0.13901	2.55;2.55	5.49	5.49	0.81192	.	0.000000	0.64402	D	0.000003	T	0.39200	0.1069	M	0.76838	2.35	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.998;0.999	T	0.15235	-1.0444	10	0.62326	D	0.03	-21.5851	14.8798	0.70522	0.0:1.0:0.0:0.0	.	263;263;77	Q8NFT6-2;Q8NFT6;Q8NFT6-3	.;DBF4B_HUMAN;.	A	263	ENSP00000377178:P263A;ENSP00000323663:P263A	ENSP00000323663:P263A	P	+	1	0	DBF4B	40174303	0.998000	0.40836	0.984000	0.44739	0.640000	0.38277	3.695000	0.54749	2.572000	0.86782	0.655000	0.94253	CCC		0.493	DBF4B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000385930.1	NM_025104		Missense_Mutation
GABRQ	55879	hgsc.bcm.edu	37	X	151815600	151815600	+	Missense_Mutation	SNP	C	C	G			TCGA-57-1584-01	TCGA-57-1584-11	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	TCGA-57-1584-01	TCGA-57-1584-11	g.chrX:151815600C>G	ENST00000370306.2	+	4	518	c.498C>G	c.(496-498)caC>caG	p.H166Q		NM_018558.2	NP_061028.3	Q9UN88	GBRT_HUMAN	gamma-aminobutyric acid (GABA) A receptor, theta	166					neurotransmitter transport (GO:0006836)|signal transduction (GO:0007165)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|postsynaptic membrane (GO:0045211)|receptor complex (GO:0043235)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)|neurotransmitter transporter activity (GO:0005326)|transmembrane signaling receptor activity (GO:0004888)	p.H166Q(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(9)|lung(25)|ovary(3)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	52	Acute lymphoblastic leukemia(192;6.56e-05)				Acamprosate(DB00659)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Flumazenil(DB01205)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	TTCAGCTTCACCCAGATGGAA	0.522																																																1	Substitution - Missense(1)	ovary(1)	X											208.0	146.0	167.0					X																	151815600		2203	4300	6503	151566256	SO:0001583	missense	55879			U47334	CCDS14707.1	Xq28	2012-06-22	2012-02-03		ENSG00000147402	ENSG00000268089		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	14454	protein-coding gene	gene with protein product	"""GABA(A) receptor, theta"""	300349	"""gamma-aminobutyric acid (GABA) receptor, theta"""			10804200, 10449790	Standard	NM_018558		Approved	THETA	uc004ffp.1	Q9UN88	OTTHUMG00000022649	ENST00000370306.2:c.498C>G	X.37:g.151815600C>G	ENSP00000359329:p.His166Gln		151566256	A6NFN1|Q32MB4|Q9NZK8	Missense_Mutation	SNP	ENST00000370306.2	37	CCDS14707.1	SNP	18	Baylor	.	.	.	.	.	.	.	.	.	.	C	6.663	0.490933	0.12702	.	.	ENSG00000147402	ENST00000370306	T	0.79033	-1.23	5.19	-0.868	0.10652	Neurotransmitter-gated ion-channel ligand-binding (3);	0.155258	0.30639	N	0.009196	T	0.63367	0.2505	L	0.35723	1.085	0.30526	N	0.76796	B	0.27166	0.17	B	0.30716	0.119	T	0.55724	-0.8096	10	0.42905	T	0.14	.	6.136	0.20233	0.0:0.3638:0.4188:0.2174	.	166	Q9UN88	GBRT_HUMAN	Q	166	ENSP00000359329:H166Q	ENSP00000359329:H166Q	H	+	3	2	GABRQ	151566256	0.311000	0.24536	0.928000	0.36995	0.137000	0.21094	-0.330000	0.07925	-0.174000	0.10743	0.544000	0.68410	CAC		0.522	GABRQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058763.2	NM_018558		Missense_Mutation
GGA3	23163	hgsc.bcm.edu	37	17	73236436	73236436	+	Nonsense_Mutation	SNP	C	C	T			TCGA-57-1584-01	TCGA-57-1584-11	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	TCGA-57-1584-01	TCGA-57-1584-11	g.chr17:73236436C>T	ENST00000245541.6	-	12	1466	c.1250G>A	c.(1249-1251)tGg>tAg	p.W417*	GGA3_ENST00000538886.1_Nonsense_Mutation_p.W295*|GGA3_ENST00000578348.1_Nonsense_Mutation_p.W295*|GGA3_ENST00000582717.1_Nonsense_Mutation_p.W345*|GGA3_ENST00000582486.1_Nonsense_Mutation_p.W345*|GGA3_ENST00000351904.7_Nonsense_Mutation_p.W384*	NM_138619.2	NP_619525.1	Q9NZ52	GGA3_HUMAN	golgi-associated, gamma adaptin ear containing, ARF binding protein 3	417	Unstructured hinge.				intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	clathrin adaptor complex (GO:0030131)|endosome (GO:0005768)|trans-Golgi network (GO:0005802)	ADP-ribosylation factor binding (GO:0030306)	p.W417*(1)		breast(2)|endometrium(3)|large_intestine(4)|liver(1)|lung(4)|ovary(2)|prostate(2)|skin(1)|urinary_tract(1)	20			all cancers(21;2.39e-06)|Epithelial(20;2.38e-05)			GAGCAGGTGCCACTGGCTGTT	0.572																																																1	Substitution - Nonsense(1)	ovary(1)	17											45.0	39.0	41.0					17																	73236436		2202	4300	6502	70748031	SO:0001587	stop_gained	23163			AF190864	CCDS11716.1, CCDS11717.1, CCDS54164.1, CCDS58597.1	17q25	2010-02-12	2010-02-12			ENSG00000125447			17079	protein-coding gene	gene with protein product		606006				10747089, 10749927	Standard	NR_033345		Approved	KIAA0154	uc002jni.2	Q9NZ52		ENST00000245541.6:c.1250G>A	17.37:g.73236436C>T	ENSP00000245541:p.Trp417*		70748031	B7Z7E2|B7Z7M9|J3KRN0|Q15017|Q6IS16|Q9UJY3	Nonsense_Mutation	SNP	ENST00000245541.6	37	CCDS11717.1	SNP	21	Baylor	.	.	.	.	.	.	.	.	.	.	C	40	7.917952	0.98560	.	.	ENSG00000125447	ENST00000245541;ENST00000351904;ENST00000537584;ENST00000538886	.	.	.	5.19	5.19	0.71726	.	0.000000	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.22706	T	0.39	-28.2999	17.2923	0.87160	0.0:1.0:0.0:0.0	.	.	.	.	X	417;384;345;295	.	ENSP00000245541:W417X	W	-	2	0	GGA3	70748031	1.000000	0.71417	1.000000	0.80357	0.869000	0.49853	3.741000	0.55090	2.422000	0.82143	0.655000	0.94253	TGG		0.572	GGA3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446645.1	NM_138619		Nonsense_Mutation
GRIA1	2890	hgsc.bcm.edu	37	5	153190663	153190663	+	Missense_Mutation	SNP	G	G	T	rs139474308		TCGA-57-1584-01	TCGA-57-1584-11	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	TCGA-57-1584-01	TCGA-57-1584-11	g.chr5:153190663G>T	ENST00000285900.5	+	16	2942	c.2599G>T	c.(2599-2601)Gcc>Tcc	p.A867S	GRIA1_ENST00000521843.2_Missense_Mutation_p.A798S|GRIA1_ENST00000448073.4_Missense_Mutation_p.A877S|GRIA1_ENST00000518783.1_Missense_Mutation_p.A877S|GRIA1_ENST00000340592.5_Missense_Mutation_p.A867S|GRIA1_ENST00000518142.1_Missense_Mutation_p.A787S	NM_000827.3|NM_001258019.1	NP_000818.2|NP_001244948.1	P42261	GRIA1_HUMAN	glutamate receptor, ionotropic, AMPA 1	867				AGA -> TAP (in Ref. 1; AAA58613). {ECO:0000305}.	ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|long-term memory (GO:0007616)|receptor internalization (GO:0031623)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|axonal spine (GO:0044308)|cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|dendrite membrane (GO:0032590)|dendritic spine (GO:0043197)|endocytic vesicle membrane (GO:0030666)|endoplasmic reticulum (GO:0005783)|neuron spine (GO:0044309)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|synaptic vesicle (GO:0008021)	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:0004971)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glutamate receptor activity (GO:0008066)|PDZ domain binding (GO:0030165)	p.A867S(1)		NS(1)|breast(4)|endometrium(7)|kidney(3)|large_intestine(24)|liver(2)|lung(23)|ovary(4)|pancreas(1)|prostate(5)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	81		Medulloblastoma(196;0.0391)|all_neural(177;0.16)|all_hematologic(541;0.21)	Kidney(363;0.000173)|KIRC - Kidney renal clear cell carcinoma(527;0.000785)		Desflurane(DB01189)|Enflurane(DB00228)|Isoflurane(DB00753)|Methoxyflurane(DB01028)|Perampanel(DB08883)|Sevoflurane(DB01236)	CGGGGCAGGAGCCAGCAGCGG	0.582																																																1	Substitution - Missense(1)	ovary(1)	5											45.0	49.0	48.0					5																	153190663		2203	4300	6503	153170856	SO:0001583	missense	2890				CCDS4322.1, CCDS47318.1, CCDS58986.1, CCDS58987.1, CCDS58988.1, CCDS58989.1	5q33	2012-08-29			ENSG00000155511	ENSG00000155511		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4571	protein-coding gene	gene with protein product		138248		GLUR1		1652753, 1319477	Standard	NM_000827		Approved	GluA1, GLURA	uc011dcy.2	P42261	OTTHUMG00000130148	ENST00000285900.5:c.2599G>T	5.37:g.153190663G>T	ENSP00000285900:p.Ala867Ser		153170856	B7Z2S0|B7Z2W8|B7Z3F6|B7Z9G9|D3DQI4|E7ESV8|Q2NKM6	Missense_Mutation	SNP	ENST00000285900.5	37	CCDS4322.1	SNP	34	Baylor	.	.	.	.	.	.	.	.	.	.	G	4.440	0.081503	0.08533	.	.	ENSG00000155511	ENST00000285900;ENST00000544403;ENST00000518142;ENST00000340592;ENST00000521843;ENST00000544794;ENST00000518783;ENST00000448073	T;T;T;T;T;T;T	0.11169	2.85;2.8;2.85;2.8;2.8;2.85;2.85	5.16	3.32	0.38043	.	0.513949	0.21490	N	0.073699	T	0.02083	0.0065	N	0.00268	-1.735	0.40172	D	0.977182	B;B;B;B;B	0.19331	0.0;0.001;0.035;0.0;0.027	B;B;B;B;B	0.15052	0.001;0.001;0.012;0.001;0.005	T	0.40997	-0.9533	10	0.02654	T	1	.	9.9252	0.41487	0.1713:0.0:0.8287:0.0	.	877;877;787;867;867	E7ESV8;B7Z9G9;B7Z3F6;P42261-2;P42261	.;.;.;.;GRIA1_HUMAN	S	867;867;787;867;800;798;877;877	ENSP00000285900:A867S;ENSP00000427920:A787S;ENSP00000339343:A867S;ENSP00000427864:A800S;ENSP00000442108:A798S;ENSP00000428994:A877S;ENSP00000415569:A877S	ENSP00000285900:A867S	A	+	1	0	GRIA1	153170856	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	0.955000	0.29188	0.516000	0.28340	0.655000	0.94253	GCC		0.582	GRIA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252456.3			Missense_Mutation
HIPK3	10114	hgsc.bcm.edu	37	11	33374958	33374958	+	Silent	SNP	C	C	T			TCGA-57-1584-01	TCGA-57-1584-11	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	TCGA-57-1584-01	TCGA-57-1584-11	g.chr11:33374958C>T	ENST00000303296.4	+	17	3797	c.3492C>T	c.(3490-3492)gtC>gtT	p.V1164V	HIPK3_ENST00000456517.1_Silent_p.V1143V|HIPK3_ENST00000379016.3_Silent_p.V1143V|AL122015.1_ENST00000411202.1_RNA|HIPK3_ENST00000525975.1_Silent_p.V1143V	NM_005734.3	NP_005725.3	Q9H422	HIPK3_HUMAN	homeodomain interacting protein kinase 3	1164					apoptotic process (GO:0006915)|mRNA transcription (GO:0009299)|negative regulation of apoptotic process (GO:0043066)|negative regulation of JUN kinase activity (GO:0043508)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|protein phosphorylation (GO:0006468)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|PML body (GO:0016605)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.V1164V(1)		endometrium(3)|kidney(3)|large_intestine(9)|liver(4)|lung(10)|ovary(2)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	39						TTCACCAAGTCCCAGTGGGCT	0.488																																																1	Substitution - coding silent(1)	ovary(1)	11											173.0	148.0	156.0					11																	33374958		2202	4298	6500	33331534	SO:0001819	synonymous_variant	10114			AF004849	CCDS7884.1, CCDS41634.1	11p13	2008-07-18	2001-11-29		ENSG00000110422	ENSG00000110422			4915	protein-coding gene	gene with protein product		604424	"""homeodomain-interacting protein kinase 3"""			9373137, 9748262	Standard	NM_005734		Approved	PKY, DYRK6, YAK1, FIST3	uc031pzm.1	Q9H422	OTTHUMG00000132269	ENST00000303296.4:c.3492C>T	11.37:g.33374958C>T			33331534	O14632|Q2PBG4|Q2PBG5|Q92632|Q9HAS2	Silent	SNP	ENST00000303296.4	37	CCDS7884.1	SNP	30	Baylor																																																																																				0.488	HIPK3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255358.1	NM_005734		Silent
KBTBD4	55709	hgsc.bcm.edu	37	11	47594667	47594667	+	Missense_Mutation	SNP	C	C	G			TCGA-57-1584-01	TCGA-57-1584-11	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	TCGA-57-1584-01	TCGA-57-1584-11	g.chr11:47594667C>G	ENST00000526005.1	-	4	1525	c.1372G>C	c.(1372-1374)Gag>Cag	p.E458Q	KBTBD4_ENST00000395288.2_Missense_Mutation_p.E458Q|NDUFS3_ENST00000533507.1_Intron|KBTBD4_ENST00000430070.2_Missense_Mutation_p.E474Q|PTPMT1_ENST00000527079.2_3'UTR|KBTBD4_ENST00000533290.1_Missense_Mutation_p.E483Q			Q9NVX7	KBTB4_HUMAN	kelch repeat and BTB (POZ) domain containing 4	458								p.E458Q(1)		NS(1)|breast(1)|central_nervous_system(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(5)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	24						CTCCAGGCCTCAGGAAGGCAA	0.552																																																1	Substitution - Missense(1)	ovary(1)	11											54.0	53.0	53.0					11																	47594667		2201	4298	6499	47551243	SO:0001583	missense	55709			AF151086	CCDS7940.1, CCDS44594.1	11p11.2	2013-01-08	2003-12-12	2003-12-17	ENSG00000123444	ENSG00000123444		"""BTB/POZ domain containing"""	23761	protein-coding gene	gene with protein product			"""BTB and kelch domain containing 4"""	BKLHD4		11042152	Standard	NM_018095		Approved	FLJ10450, HSPC252	uc001nfz.3	Q9NVX7	OTTHUMG00000166894	ENST00000526005.1:c.1372G>C	11.37:g.47594667C>G	ENSP00000433340:p.Glu458Gln		47551243	D3DQS1|D3DQS2|Q6IA85|Q9BUC3|Q9NV76	Missense_Mutation	SNP	ENST00000526005.1	37	CCDS7940.1	SNP	29	Baylor	.	.	.	.	.	.	.	.	.	.	C	18.39	3.612974	0.66672	.	.	ENSG00000123444	ENST00000526005;ENST00000533290;ENST00000395288;ENST00000430070	T;T;T;T	0.66815	-0.23;-0.23;-0.23;-0.23	5.95	5.95	0.96441	Kelch-type beta propeller (1);	0.047454	0.85682	D	0.000000	T	0.57286	0.2043	N	0.19112	0.55	0.80722	D	1	P;B;B	0.39480	0.675;0.321;0.361	B;B;B	0.37888	0.26;0.133;0.1	T	0.62086	-0.6928	10	0.66056	D	0.02	-23.6497	20.3748	0.98911	0.0:1.0:0.0:0.0	.	474;458;483	Q9NVX7-2;Q9NVX7;B3KRH9	.;KBTB4_HUMAN;.	Q	458;483;458;474	ENSP00000433340:E458Q;ENSP00000436713:E483Q;ENSP00000378703:E458Q;ENSP00000415106:E474Q	ENSP00000378703:E458Q	E	-	1	0	KBTBD4	47551243	1.000000	0.71417	0.993000	0.49108	0.994000	0.84299	7.487000	0.81328	2.817000	0.96982	0.563000	0.77884	GAG		0.552	KBTBD4-003	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000391763.1	NM_016506		Missense_Mutation
KCNA6	3742	hgsc.bcm.edu	37	12	4920006	4920006	+	Missense_Mutation	SNP	G	G	C			TCGA-57-1584-01	TCGA-57-1584-11	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	TCGA-57-1584-01	TCGA-57-1584-11	g.chr12:4920006G>C	ENST00000280684.3	+	1	1665	c.799G>C	c.(799-801)Gag>Cag	p.E267Q	KCNA6_ENST00000433855.1_Missense_Mutation_p.E267Q|RP11-234B24.4_ENST00000542988.1_lincRNA			P17658	KCNA6_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 6	267					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|voltage-gated potassium channel activity (GO:0005249)	p.E267Q(1)		NS(1)|breast(3)|endometrium(5)|large_intestine(6)|lung(17)|ovary(3)|pancreas(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(5)	49					Dalfampridine(DB06637)	CTTTCTGGTGGAGACGCTGTG	0.552										HNSCC(72;0.22)																																						1	Substitution - Missense(1)	ovary(1)	12											86.0	87.0	86.0					12																	4920006		2203	4300	6503	4790267	SO:0001583	missense	3742			X17622	CCDS8534.1	12p13	2014-06-12						"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6225	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 96"""	176257				16382104	Standard	NM_002235		Approved	Kv1.6, HBK2, PPP1R96	uc001qng.3	P17658		ENST00000280684.3:c.799G>C	12.37:g.4920006G>C	ENSP00000280684:p.Glu267Gln		4790267		Missense_Mutation	SNP	ENST00000280684.3	37	CCDS8534.1	SNP	41	Baylor	.	.	.	.	.	.	.	.	.	.	G	23.4	4.411417	0.83340	.	.	ENSG00000151079	ENST00000433855;ENST00000280684	D;D	0.97976	-4.64;-4.64	5.18	5.18	0.71444	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.99221	0.9729	H	0.96720	3.87	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.98936	1.0789	10	0.87932	D	0	.	17.8587	0.88775	0.0:0.0:1.0:0.0	.	267	P17658	KCNA6_HUMAN	Q	267	ENSP00000408321:E267Q;ENSP00000280684:E267Q	ENSP00000280684:E267Q	E	+	1	0	KCNA6	4790267	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.580000	0.98207	2.688000	0.91661	0.655000	0.94253	GAG		0.552	KCNA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398909.1	NM_002235		Missense_Mutation
KLHL20	27252	hgsc.bcm.edu	37	1	173743507	173743507	+	Silent	SNP	G	G	C			TCGA-57-1584-01	TCGA-57-1584-11	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	TCGA-57-1584-01	TCGA-57-1584-11	g.chr1:173743507G>C	ENST00000209884.4	+	9	1495	c.1359G>C	c.(1357-1359)gtG>gtC	p.V453V	KLHL20_ENST00000546011.1_Silent_p.V264V	NM_014458.3	NP_055273.2	Q9Y2M5	KLH20_HUMAN	kelch-like family member 20	453					cytoskeleton organization (GO:0007010)|Golgi to endosome transport (GO:0006895)|negative regulation of apoptotic process (GO:0043066)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein K33-linked ubiquitination (GO:1990390)|protein transport (GO:0015031)|protein ubiquitination (GO:0016567)|response to interferon-alpha (GO:0035455)	actin cytoskeleton (GO:0015629)|cell projection (GO:0042995)|Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|PML body (GO:0016605)|trans-Golgi network (GO:0005802)	interferon-gamma binding (GO:0019964)|ubiquitin-protein transferase activity (GO:0004842)	p.V453V(1)		breast(3)|endometrium(6)|kidney(1)|large_intestine(8)|lung(14)|ovary(1)|upper_aerodigestive_tract(1)	34						GACTAGGTGTGGCTGTGGCTG	0.502																																					GBM(159;862 2695 6559 23041)											1	Substitution - coding silent(1)	ovary(1)	1											251.0	219.0	229.0					1																	173743507		2203	4300	6503	172010130	SO:0001819	synonymous_variant	27252			AB026190	CCDS1310.1	1q25.1	2013-01-30	2013-01-30		ENSG00000076321	ENSG00000076321		"""Kelch-like"", ""BTB/POZ domain containing"""	25056	protein-coding gene	gene with protein product			"""kelch-like 20 (Drosophila)"""			14668487, 20389280	Standard	NM_014458		Approved	KLEIP, KHLHX	uc001gjc.3	Q9Y2M5	OTTHUMG00000040548	ENST00000209884.4:c.1359G>C	1.37:g.173743507G>C			172010130	B3KMA0|B4DUR0|Q5TZF2|Q5ZF45|Q9H457	Silent	SNP	ENST00000209884.4	37	CCDS1310.1	SNP	47	Baylor																																																																																				0.502	KLHL20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097582.1	NM_014458		Silent
LAMA2	3908	hgsc.bcm.edu	37	6	129748970	129748970	+	Missense_Mutation	SNP	A	A	T			TCGA-57-1584-01	TCGA-57-1584-11	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	TCGA-57-1584-01	TCGA-57-1584-11	g.chr6:129748970A>T	ENST00000421865.2	+	41	5988	c.5939A>T	c.(5938-5940)gAa>gTa	p.E1980V		NM_000426.3|NM_001079823.1	NP_000417|NP_001073291.1	P24043	LAMA2_HUMAN	laminin, alpha 2	1980	Domain II and I.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|myelination in peripheral nervous system (GO:0022011)|positive regulation of synaptic transmission, cholinergic (GO:0032224)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|sarcolemma (GO:0042383)	structural molecule activity (GO:0005198)	p.E1980V(1)		NS(2)|biliary_tract(2)|breast(10)|central_nervous_system(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(35)|lung(84)|ovary(10)|prostate(4)|skin(9)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(2)	194				OV - Ovarian serous cystadenocarcinoma(136;0.178)|all cancers(137;0.245)		ATTCTTAACGAAGCCAAGAAG	0.383																																																1	Substitution - Missense(1)	ovary(1)	6											113.0	111.0	112.0					6																	129748970		2203	4300	6503	129790663	SO:0001583	missense	3908			Z26653	CCDS5138.1	6q22-q23	2014-09-17	2008-08-01		ENSG00000196569	ENSG00000196569		"""Laminins"""	6482	protein-coding gene	gene with protein product	"""merosin"", ""congenital muscular dystrophy"""	156225		LAMM		2185464, 8294519	Standard	NM_000426		Approved		uc003qbn.3	P24043	OTTHUMG00000015545	ENST00000421865.2:c.5939A>T	6.37:g.129748970A>T	ENSP00000400365:p.Glu1980Val		129790663	Q14736|Q5VUM2|Q93022	Missense_Mutation	SNP	ENST00000421865.2	37	CCDS5138.1	SNP	9	Baylor	.	.	.	.	.	.	.	.	.	.	A	21.2	4.114594	0.77210	.	.	ENSG00000196569	ENST00000358023;ENST00000354729;ENST00000421865	T	0.24723	1.84	5.92	5.92	0.95590	.	0.163736	0.53938	D	0.000052	T	0.16385	0.0394	M	0.62723	1.935	0.34008	D	0.651115	P;P	0.39665	0.682;0.682	B;B	0.38378	0.272;0.272	T	0.16394	-1.0404	10	0.87932	D	0	.	10.8699	0.46877	0.9273:0.0:0.0727:0.0	.	1980;1980	A6NF00;P24043	.;LAMA2_HUMAN	V	1980	ENSP00000400365:E1980V	ENSP00000346769:E1980V	E	+	2	0	LAMA2	129790663	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	2.882000	0.48546	2.267000	0.75376	0.477000	0.44152	GAA		0.383	LAMA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042180.1			Missense_Mutation
LAMB4	22798	hgsc.bcm.edu	37	7	107748113	107748113	+	Missense_Mutation	SNP	G	G	T			TCGA-57-1584-01	TCGA-57-1584-11	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	TCGA-57-1584-01	TCGA-57-1584-11	g.chr7:107748113G>T	ENST00000388781.3	-	6	637	c.554C>A	c.(553-555)tCc>tAc	p.S185Y	LAMB4_ENST00000205386.4_Missense_Mutation_p.S185Y|LAMB4_ENST00000414450.2_Missense_Mutation_p.S185Y|LAMB4_ENST00000388780.3_Missense_Mutation_p.S185Y|LAMB4_ENST00000418464.1_Missense_Mutation_p.S185Y	NM_007356.2	NP_031382.2	A4D0S4	LAMB4_HUMAN	laminin, beta 4	185	Laminin N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00466}.				cell adhesion (GO:0007155)	basement membrane (GO:0005604)		p.S185Y(1)		NS(1)|breast(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(22)|lung(40)|ovary(4)|prostate(5)|skin(4)	97						CGAGTATTTGGAGTCACAAAC	0.373																																																1	Substitution - Missense(1)	ovary(1)	7											105.0	103.0	104.0					7																	107748113		2203	4300	6503	107535349	SO:0001583	missense	22798			AF028816	CCDS34732.1	7q31	2013-03-01			ENSG00000091128	ENSG00000091128		"""Laminins"""	6491	protein-coding gene	gene with protein product							Standard	NM_007356		Approved		uc010ljo.1	A4D0S4	OTTHUMG00000154874	ENST00000388781.3:c.554C>A	7.37:g.107748113G>T	ENSP00000373433:p.Ser185Tyr		107535349	A5PKU6|B2RTT3|B5MEB9|Q86TP7|Q86XN2|Q8NBX5	Missense_Mutation	SNP	ENST00000388781.3	37	CCDS34732.1	SNP	41	Baylor	.	.	.	.	.	.	.	.	.	.	G	16.91	3.252347	0.59212	.	.	ENSG00000091128	ENST00000205386;ENST00000388781;ENST00000388780;ENST00000418464;ENST00000414450	T;T;T;T;T	0.80123	-1.34;-1.34;-1.34;-1.34;-1.34	5.86	4.96	0.65561	Laminin, N-terminal (3);	0.130434	0.35378	N	0.003258	D	0.89262	0.6665	M	0.75447	2.3	0.52501	D	0.999958	D	0.89917	1.0	D	0.72982	0.979	D	0.90673	0.4599	10	0.87932	D	0	.	16.7991	0.85609	0.0:0.1289:0.8711:0.0	.	185	A4D0S4	LAMB4_HUMAN	Y	185	ENSP00000205386:S185Y;ENSP00000373433:S185Y;ENSP00000373432:S185Y;ENSP00000402353:S185Y;ENSP00000402265:S185Y	ENSP00000205386:S185Y	S	-	2	0	LAMB4	107535349	0.982000	0.34865	0.978000	0.43139	0.656000	0.38851	2.611000	0.46334	1.434000	0.47414	0.655000	0.94253	TCC		0.373	LAMB4-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337442.1	XM_209857		Missense_Mutation
PPWD1	23398	hgsc.bcm.edu	37	5	64872833	64872833	+	Missense_Mutation	SNP	C	C	G			TCGA-57-1584-01	TCGA-57-1584-11	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	TCGA-57-1584-01	TCGA-57-1584-11	g.chr5:64872833C>G	ENST00000261308.5	+	6	1169	c.1097C>G	c.(1096-1098)aCt>aGt	p.T366S	PPWD1_ENST00000535264.1_Missense_Mutation_p.T336S|PPWD1_ENST00000538977.1_Missense_Mutation_p.T210S	NM_015342.3	NP_056157.1	Q96BP3	PPWD1_HUMAN	peptidylprolyl isomerase domain and WD repeat containing 1	366					mRNA splicing, via spliceosome (GO:0000398)|protein folding (GO:0006457)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)	peptidyl-prolyl cis-trans isomerase activity (GO:0003755)	p.T366S(1)		breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)	19		Lung NSC(167;7.21e-05)|Prostate(74;0.0174)|Ovarian(174;0.186)		Lung(70;0.00451)		TTTGATGAAACTGGACACTTC	0.368																																																1	Substitution - Missense(1)	ovary(1)	5											126.0	135.0	132.0					5																	64872833		2203	4300	6503	64908589	SO:0001583	missense	23398			AK025679	CCDS3985.1, CCDS64161.1, CCDS64162.1	5q12.3	2013-01-09			ENSG00000113593	ENSG00000113593		"""WD repeat domain containing"""	28954	protein-coding gene	gene with protein product						7584044	Standard	NM_015342		Approved	KIAA0073	uc003jtv.5	Q96BP3	OTTHUMG00000131226	ENST00000261308.5:c.1097C>G	5.37:g.64872833C>G	ENSP00000261308:p.Thr366Ser		64908589	B4DWR9|Q15002|Q7KZ89	Missense_Mutation	SNP	ENST00000261308.5	37	CCDS3985.1	SNP	20	Baylor	.	.	.	.	.	.	.	.	.	.	C	8.147	0.786415	0.16189	.	.	ENSG00000113593	ENST00000261308;ENST00000535264;ENST00000538977	T;T;T	0.61980	0.06;0.06;5.11	5.24	5.24	0.73138	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.36963	0.0986	N	0.02391	-0.57	0.80722	D	1	B;B	0.21309	0.054;0.032	B;B	0.26094	0.066;0.03	T	0.42766	-0.9432	10	0.02654	T	1	.	18.8273	0.92123	0.0:1.0:0.0:0.0	.	336;366	F5H7P7;Q96BP3	.;PPWD1_HUMAN	S	366;336;210	ENSP00000261308:T366S;ENSP00000442371:T336S;ENSP00000444496:T210S	ENSP00000261308:T366S	T	+	2	0	PPWD1	64908589	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.818000	0.86416	2.463000	0.83235	0.455000	0.32223	ACT		0.368	PPWD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253970.2	NM_015342		Missense_Mutation
PIK3R1	5295	hgsc.bcm.edu	37	5	67588086	67588086	+	Splice_Site	SNP	G	G	C			TCGA-57-1584-01	TCGA-57-1584-11	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	TCGA-57-1584-01	TCGA-57-1584-11	g.chr5:67588086G>C	ENST00000521381.1	+	8	1532		c.e8-1		PIK3R1_ENST00000274335.5_Splice_Site|PIK3R1_ENST00000521657.1_Splice_Site|PIK3R1_ENST00000320694.8_Splice_Site|PIK3R1_ENST00000523872.1_5'Flank|PIK3R1_ENST00000336483.5_Splice_Site|PIK3R1_ENST00000396611.1_Splice_Site	NM_181523.2	NP_852664.1	P27986	P85A_HUMAN	phosphoinositide-3-kinase, regulatory subunit 1 (alpha)						B cell differentiation (GO:0030183)|blood coagulation (GO:0007596)|cellular response to UV (GO:0034644)|epidermal growth factor receptor signaling pathway (GO:0007173)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|growth hormone receptor signaling pathway (GO:0060396)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|leukocyte migration (GO:0050900)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of osteoclast differentiation (GO:0045671)|neurotrophin TRK receptor signaling pathway (GO:0048011)|NFAT protein import into nucleus (GO:0051531)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of cell migration (GO:0030335)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of glucose import (GO:0046326)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|protein phosphorylation (GO:0006468)|regulation of phosphatidylinositol 3-kinase activity (GO:0043551)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|membrane (GO:0016020)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	ErbB-3 class receptor binding (GO:0043125)|insulin binding (GO:0043559)|insulin receptor binding (GO:0005158)|insulin receptor substrate binding (GO:0043560)|insulin-like growth factor receptor binding (GO:0005159)|neurotrophin TRKA receptor binding (GO:0005168)|phosphatidylinositol 3-kinase binding (GO:0043548)|phosphatidylinositol 3-kinase regulator activity (GO:0035014)|protein phosphatase binding (GO:0019903)|transmembrane receptor protein tyrosine kinase adaptor activity (GO:0005068)	p.?(2)|p.0?(1)		breast(12)|central_nervous_system(31)|cervix(1)|endometrium(68)|haematopoietic_and_lymphoid_tissue(5)|kidney(1)|large_intestine(32)|lung(10)|ovary(9)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	178		Lung NSC(167;1.99e-05)|Prostate(74;0.00308)|Ovarian(174;0.00473)|Colorectal(97;0.0176)		OV - Ovarian serous cystadenocarcinoma(47;3.76e-51)|Lung(70;0.0211)	Isoprenaline(DB01064)	TTCATCTGCAGCACTGCCTCC	0.343			"""Mis, F, O"""		"""gliobastoma, ovarian, colorectal"""					TCGA GBM(4;<1E-08)																													Rec	yes		5	5q13.1	5295	"""phosphoinositide-3-kinase, regulatory subunit 1 (alpha)"""		"""E, O"""	3	Unknown(2)|Whole gene deletion(1)	large_intestine(1)|lung(1)|ovary(1)	5											141.0	130.0	134.0					5																	67588086		2203	4300	6503	67623842	SO:0001630	splice_region_variant	5295			M61906	CCDS3993.1, CCDS3994.1, CCDS3995.1, CCDS56374.1	5q13.1	2014-09-17	2008-02-04		ENSG00000145675	ENSG00000145675		"""SH2 domain containing"""	8979	protein-coding gene	gene with protein product		171833				1314371, 18387942	Standard	NM_181524		Approved	GRB1, p85-ALPHA, p85	uc003jva.3	P27986	OTTHUMG00000131251	ENST00000521381.1:c.917-1G>C	5.37:g.67588086G>C			67623842	B3KT19|D3DWA0|E7EX19|Q15747|Q4VBZ7|Q53EM6|Q8IXA2|Q8N1C5	Splice_Site_SNP	SNP	ENST00000521381.1	37	CCDS3993.1	SNP	34	Baylor	.	.	.	.	.	.	.	.	.	.	G	18.80	3.701571	0.68501	.	.	ENSG00000145675	ENST00000521381;ENST00000521657;ENST00000396611;ENST00000274335;ENST00000523807;ENST00000522084;ENST00000320694;ENST00000336483	.	.	.	5.13	5.13	0.70059	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.115	0.93334	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	PIK3R1	67623842	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	9.601000	0.98297	2.822000	0.97130	0.563000	0.77884	.		0.343	PIK3R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254013.2	NM_181504	Intron	Splice_Site_SNP
RORB	6096	hgsc.bcm.edu	37	9	77286722	77286722	+	Nonsense_Mutation	SNP	G	G	T			TCGA-57-1584-01	TCGA-57-1584-11	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	TCGA-57-1584-01	TCGA-57-1584-11	g.chr9:77286722G>T	ENST00000396204.2	+	9	1162	c.1162G>T	c.(1162-1164)Gaa>Taa	p.E388*	RORB_ENST00000376896.3_Nonsense_Mutation_p.E377*			Q92753	RORB_HUMAN	RAR-related orphan receptor B	388	Ligand-binding. {ECO:0000255}.				amacrine cell differentiation (GO:0035881)|cellular response to retinoic acid (GO:0071300)|eye photoreceptor cell development (GO:0042462)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of circadian rhythm (GO:0042752)|regulation of transcription, DNA-templated (GO:0006355)|retina development in camera-type eye (GO:0060041)|retinal cone cell development (GO:0046549)|retinal rod cell development (GO:0046548)|rhythmic process (GO:0048511)|transcription initiation from RNA polymerase II promoter (GO:0006367)|visual perception (GO:0007601)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)	p.E377Q(2)|p.E377*(1)		breast(2)|large_intestine(4)|lung(1)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	12					Melatonin(DB01065)	CTGGCTTATAGAACCAAGGAA	0.428																																																3	Substitution - Missense(2)|Substitution - Nonsense(1)	breast(2)|ovary(1)	9											73.0	69.0	70.0					9																	77286722		2203	4300	6503	76476542	SO:0001587	stop_gained	6096			Y08639	CCDS6646.1	9q22	2013-01-16			ENSG00000198963	ENSG00000198963		"""Nuclear hormone receptors"""	10259	protein-coding gene	gene with protein product		601972				7926749	Standard	NM_006914		Approved	RZRB, NR1F2, ROR-BETA	uc004ajh.3	Q92753	OTTHUMG00000020026	ENST00000396204.2:c.1162G>T	9.37:g.77286722G>T	ENSP00000379507:p.Glu388*		76476542	Q8WX73	Nonsense_Mutation	SNP	ENST00000396204.2	37		SNP	33	Baylor	.	.	.	.	.	.	.	.	.	.	G	38	6.700148	0.97772	.	.	ENSG00000198963	ENST00000376896;ENST00000396204	.	.	.	5.73	5.73	0.89815	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.52906	T	0.07	.	20.2602	0.98440	0.0:0.0:1.0:0.0	.	.	.	.	X	377;388	.	ENSP00000366093:E377X	E	+	1	0	RORB	76476542	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.807000	0.99171	2.861000	0.98227	0.655000	0.94253	GAA		0.428	RORB-201	KNOWN	basic	protein_coding	protein_coding				Nonsense_Mutation
SCRIB	23513	hgsc.bcm.edu	37	8	144890926	144890926	+	Silent	SNP	C	C	T			TCGA-57-1584-01	TCGA-57-1584-11	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	TCGA-57-1584-01	TCGA-57-1584-11	g.chr8:144890926C>T	ENST00000320476.3	-	15	1974	c.1968G>A	c.(1966-1968)cgG>cgA	p.R656R	SCRIB_ENST00000356994.2_Silent_p.R656R|SCRIB_ENST00000377533.3_Silent_p.R575R	NM_015356.4	NP_056171	Q14160	SCRIB_HUMAN	scribbled planar cell polarity protein	656	Sufficient for targeting to adherens junction and to inhibit cell proliferation.				activation of Rac GTPase activity (GO:0032863)|apoptotic process involved in morphogenesis (GO:0060561)|astrocyte cell migration (GO:0043615)|asymmetric protein localization (GO:0008105)|auditory receptor cell stereocilium organization (GO:0060088)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cochlear nucleus development (GO:0021747)|establishment of apical/basal cell polarity (GO:0035089)|mammary gland duct morphogenesis (GO:0060603)|negative regulation of mitotic cell cycle (GO:0045930)|neural tube closure (GO:0001843)|positive chemotaxis (GO:0050918)|positive regulation of apoptotic process (GO:0043065)|positive regulation of receptor recycling (GO:0001921)|protein localization to adherens junction (GO:0071896)|single organismal cell-cell adhesion (GO:0016337)|synaptic vesicle endocytosis (GO:0048488)|synaptic vesicle targeting (GO:0016080)|viral process (GO:0016032)|wound healing (GO:0042060)	basolateral plasma membrane (GO:0016323)|cell projection (GO:0042995)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|myelin sheath abaxonal region (GO:0035748)|plasma membrane (GO:0005886)|Scrib-APC-beta-catenin complex (GO:0034750)				NS(1)|autonomic_ganglia(1)|central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(3)|lung(20)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	42	all_cancers(97;2.31e-11)|all_epithelial(106;1.58e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;1.23e-39)|all cancers(56;1.12e-34)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.18)			ccttctGGGCCCGAGGAGCCC	0.662																																					Pancreas(51;966 1133 10533 14576 29674)											0			8											45.0	50.0	49.0					8																	144890926		2203	4300	6503	144962914	SO:0001819	synonymous_variant	23513			AY062238	CCDS6411.1, CCDS6412.1	8q24.3	2013-03-05	2013-03-05		ENSG00000180900	ENSG00000180900			30377	protein-coding gene	gene with protein product		607733	"""scribbled homolog (Drosophila)"""			11027293, 14681682	Standard	NM_182706		Approved	KIAA0147, SCRB1, Vartul	uc003yzo.1	Q14160	OTTHUMG00000165154	ENST00000320476.3:c.1968G>A	8.37:g.144890926C>T			144962914	Q6P496|Q7Z5D1|Q8WWV8|Q96C69|Q96GG1	Silent	SNP	ENST00000320476.3	37	CCDS6411.1	SNP	22	Baylor																																																																																				0.662	SCRIB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000382215.1	NM_015356		Silent
TAS2R42	353164	hgsc.bcm.edu	37	12	11338781	11338781	+	Missense_Mutation	SNP	C	C	A	rs1669413	byFrequency	TCGA-57-1584-01	TCGA-57-1584-11	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	TCGA-57-1584-01	TCGA-57-1584-11	g.chr12:11338781C>A	ENST00000334266.1	-	1	762	c.763G>T	c.(763-765)Ggg>Tgg	p.G255W		NM_181429.1	NP_852094.1	Q7RTR8	T2R42_HUMAN	taste receptor, type 2, member 42	255			G -> W (in dbSNP:rs1669413). {ECO:0000269|PubMed:16541075}.		sensory perception of taste (GO:0050909)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(1)|kidney(2)|lung(4)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	11			OV - Ovarian serous cystadenocarcinoma(49;0.0455)			AAAAATATCCCATTGGCCACT	0.398													A|||	3810	0.760783	0.407	0.8473	5008	,	,		18737	0.9514		0.8688	False		,,,				2504	0.8701				Melanoma(15;352 722 10077 19546 48810)											0			12						A	TRP/GLY	2061,2345	606.7+/-390.8	491,1079,633	75.0	72.0	73.0		763	2.3	0.0	12	dbSNP_89	73	7221,1379	266.8+/-286.9	3052,1117,131	yes	missense	TAS2R42	NM_181429.1	184	3543,2196,764	AA,AC,CC		16.0349,46.7771,28.6329	benign	255/315	11338781	9282,3724	2203	4300	6503	11230048	SO:0001583	missense	353164			AX097739, AB199241	CCDS31747.1	12p13	2012-08-22			ENSG00000186136	ENSG00000186136		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	18888	protein-coding gene	gene with protein product		613966				12679530	Standard	NM_181429		Approved	T2R24, T2R55, hT2R55, TAS2R55	uc001qzr.1	Q7RTR8	OTTHUMG00000168567	ENST00000334266.1:c.763G>T	12.37:g.11338781C>A	ENSP00000334050:p.Gly255Trp		11230048	A2RRP4|Q645X0	Missense_Mutation	SNP	ENST00000334266.1	37	CCDS31747.1	SNP	21	Baylor	1725	0.7898351648351648	205	0.4166666666666667	307	0.8480662983425414	547	0.9562937062937062	666	0.8786279683377308	A	4.947	0.176020	0.09443	0.467771	0.839651	ENSG00000186136	ENST00000334266	T	0.37235	1.21	3.59	2.32	0.28847	GPCR, rhodopsin-like superfamily (1);	0.292022	0.19342	N	0.116621	T	0.00012	0.0000	N	0.00019	-2.79	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.35001	-0.9806	9	0.15066	T	0.55	.	3.9363	0.09307	0.5624:0.2228:0.0:0.2148	rs1669413	255	Q7RTR8	T2R42_HUMAN	W	255	ENSP00000334050:G255W	ENSP00000334050:G255W	G	-	1	0	TAS2R42	11230048	0.003000	0.15002	0.006000	0.13384	0.000000	0.00434	1.221000	0.32503	0.588000	0.29660	-0.264000	0.10439	GGG		0.398	TAS2R42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400243.1	NM_181429		Missense_Mutation
TMEM176A	55365	hgsc.bcm.edu	37	7	150500785	150500785	+	Missense_Mutation	SNP	C	C	A			TCGA-57-1584-01	TCGA-57-1584-11	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	TCGA-57-1584-01	TCGA-57-1584-11	g.chr7:150500785C>A	ENST00000484928.1	+	5	1001	c.420C>A	c.(418-420)ttC>ttA	p.F140L	TMEM176A_ENST00000461345.1_Missense_Mutation_p.F81L|TMEM176B_ENST00000447204.2_5'Flank|TMEM176A_ENST00000004103.3_Missense_Mutation_p.F140L			Q96HP8	T176A_HUMAN	transmembrane protein 176A	140					negative regulation of dendritic cell differentiation (GO:2001199)	integral component of membrane (GO:0016021)		p.F140L(1)		breast(1)|endometrium(1)|lung(7)|ovary(2)|stomach(1)	12			OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		ATGAAGATTTCCGATATGGCT	0.557																																																1	Substitution - Missense(1)	ovary(1)	7											76.0	81.0	79.0					7																	150500785		2203	4300	6503	150131718	SO:0001583	missense	55365			AF258340	CCDS5909.1	7q36.1	2006-09-04			ENSG00000002933	ENSG00000002933			24930	protein-coding gene	gene with protein product		610334				12097419, 8889548	Standard	NM_018487		Approved	HCA112	uc003whx.1	Q96HP8	OTTHUMG00000158114	ENST00000484928.1:c.420C>A	7.37:g.150500785C>A	ENSP00000417626:p.Phe140Leu		150131718	D3DX00|Q9NYC7	Missense_Mutation	SNP	ENST00000484928.1	37	CCDS5909.1	SNP	30	Baylor	.	.	.	.	.	.	.	.	.	.	C	5.731	0.319294	0.10845	.	.	ENSG00000002933	ENST00000484928;ENST00000004103;ENST00000461345;ENST00000475536;ENST00000468689	T;T;T;T;T	0.01685	4.69;4.69;4.69;4.69;4.69	3.56	-3.26	0.05064	.	0.800176	0.11357	N	0.572313	T	0.00906	0.0030	N	0.11560	0.145	0.09310	N	1	B	0.16603	0.018	B	0.15484	0.013	T	0.46428	-0.9192	10	0.23891	T	0.37	-16.5997	2.5444	0.04734	0.1412:0.2655:0.4162:0.1771	.	140	Q96HP8	T176A_HUMAN	L	140;140;81;92;81	ENSP00000417626:F140L;ENSP00000004103:F140L;ENSP00000420818:F81L;ENSP00000417834:F92L;ENSP00000420081:F81L	ENSP00000004103:F140L	F	+	3	2	TMEM176A	150131718	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.344000	0.07780	-0.762000	0.04664	-1.325000	0.01285	TTC		0.557	TMEM176A-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350222.1	NM_018487		Missense_Mutation
TP53	7157	hgsc.bcm.edu	37	17	7578403	7578403	+	Missense_Mutation	SNP	C	C	T			TCGA-57-1584-01	TCGA-57-1584-11	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	TCGA-57-1584-01	TCGA-57-1584-11	g.chr17:7578403C>T	ENST00000269305.4	-	5	716	c.527G>A	c.(526-528)tGc>tAc	p.C176Y	TP53_ENST00000445888.2_Missense_Mutation_p.C176Y|TP53_ENST00000574684.1_5'UTR|TP53_ENST00000359597.4_Missense_Mutation_p.C176Y|TP53_ENST00000413465.2_Missense_Mutation_p.C176Y|TP53_ENST00000455263.2_Missense_Mutation_p.C176Y|TP53_ENST00000420246.2_Missense_Mutation_p.C176Y	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	176	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		C -> F (in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:1394225, ECO:0000269|PubMed:1868473, ECO:0000269|PubMed:8829627, ECO:0000269|PubMed:9450901}.|C -> G (in sporadic cancers; somatic mutation).|C -> R (in sporadic cancers; somatic mutation).|C -> S (in sporadic cancers; somatic mutation).|C -> W (in sporadic cancers; somatic mutation).|C -> Y (in sporadic cancers; somatic mutation).|CP -> FS (in a sporadic cancer; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.C176F(129)|p.C176Y(63)|p.C83F(9)|p.C44F(9)|p.C176S(8)|p.0?(8)|p.C176_R181delCPHHER(3)|p.R174fs*24(3)|p.C44Y(3)|p.C83Y(3)|p.R175_E180delRCPHHE(3)|p.V173fs*59(2)|p.R174fs*1(2)|p.V157_C176del20(1)|p.C176fs*65(1)|p.C176_P177delCP(1)|p.V173fs*69(1)|p.C176fs*68(1)|p.E171fs*61(1)|p.V173fs*23(1)|p.R174_H178>S(1)|p.V172_E180delVVRRCPHHE(1)|p.R174_H179delRRCPHH(1)|p.E171fs*1(1)|p.R175_H178>X(1)|p.R42fs*24(1)|p.R174_C176delRRC(1)|p.H168fs*69(1)|p.R174fs*70(1)|p.C176del(1)|p.E171_H179delEVVRRCPHH(1)|p.R81fs*24(1)|p.R174_E180>K(1)|p.H178fs*3(1)|p.R174fs*3(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	ATGGTGGGGGCAGCGCCTCAC	0.652		111	"""Mis, N, F"""		"""breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"""	"""breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"""		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"""L, E, M, O"""	267	Substitution - Missense(224)|Deletion - Frameshift(18)|Deletion - In frame(13)|Whole gene deletion(8)|Complex - deletion inframe(3)|Insertion - Frameshift(1)	lung(42)|large_intestine(38)|upper_aerodigestive_tract(36)|oesophagus(26)|breast(26)|liver(20)|ovary(19)|haematopoietic_and_lymphoid_tissue(13)|stomach(10)|central_nervous_system(9)|bone(9)|urinary_tract(7)|genital_tract(2)|skin(2)|pancreas(2)|prostate(2)|adrenal_gland(1)|vulva(1)|biliary_tract(1)|endometrium(1)	17											49.0	49.0	49.0					17																	7578403		2203	4300	6503	7519128	SO:0001583	missense	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"""Li-Fraumeni syndrome"""	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.527G>A	17.37:g.7578403C>T	ENSP00000269305:p.Cys176Tyr		7519128	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	SNP	25	Baylor	.	.	.	.	.	.	.	.	.	.	C	24.1	4.497871	0.85069	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944;ENST00000414315	D;D;D;D;D;D;D;D	0.99982	-10.62;-10.62;-10.62;-10.62;-10.62;-10.62;-10.62;-10.62	5.59	4.61	0.57282	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.092184	0.85682	D	0.000000	D	0.99981	0.9994	M	0.92923	3.36	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	0.999;0.996;0.997;0.998;0.998;0.997;0.997	D	0.96187	0.9135	10	0.87932	D	0	-18.1821	13.8336	0.63395	0.1543:0.8457:0.0:0.0	.	137;176;176;83;176;176;176	B4E095;P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;.;P53_HUMAN;.;.	Y	176;176;176;176;176;176;165;83;44;83;44	ENSP00000410739:C176Y;ENSP00000352610:C176Y;ENSP00000269305:C176Y;ENSP00000398846:C176Y;ENSP00000391127:C176Y;ENSP00000391478:C176Y;ENSP00000425104:C44Y;ENSP00000423862:C83Y	ENSP00000269305:C176Y	C	-	2	0	TP53	7519128	1.000000	0.71417	0.999000	0.59377	0.851000	0.48451	7.775000	0.85489	1.472000	0.48140	0.655000	0.94253	TGC		0.652	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		Missense_Mutation
TRIM23	373	hgsc.bcm.edu	37	5	64905203	64905203	+	Missense_Mutation	SNP	T	T	C			TCGA-57-1584-01	TCGA-57-1584-11	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	TCGA-57-1584-01	TCGA-57-1584-11	g.chr5:64905203T>C	ENST00000231524.9	-	6	1282	c.911A>G	c.(910-912)gAa>gGa	p.E304G	TRIM23_ENST00000381018.3_Missense_Mutation_p.E304G|TRIM23_ENST00000274327.7_Missense_Mutation_p.E304G|TRIM23_ENST00000508808.1_5'UTR	NM_001656.3	NP_001647.1	P36406	TRI23_HUMAN	tripartite motif containing 23	304					GTP catabolic process (GO:0006184)|positive regulation of catalytic activity (GO:0043085)|protein ubiquitination (GO:0016567)|small GTPase mediated signal transduction (GO:0007264)|viral process (GO:0016032)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|lysosomal membrane (GO:0005765)|nucleus (GO:0005634)	enzyme activator activity (GO:0008047)|GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.E304G(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(9)|lung(5)|ovary(4)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	28		Lung NSC(167;3.24e-06)|Prostate(74;0.0138)|Breast(144;0.0433)|Ovarian(174;0.0545)|Colorectal(97;0.234)		Lung(70;0.00473)		TAGAGCCATTTCTTCTTGACG	0.388																																																1	Substitution - Missense(1)	ovary(1)	5											110.0	101.0	104.0					5																	64905203		2203	4300	6503	64940959	SO:0001583	missense	373			L04510	CCDS3986.1, CCDS3987.1, CCDS43322.1	5q12.3	2013-01-09	2011-01-25	2004-06-04	ENSG00000113595	ENSG00000113595		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	660	protein-coding gene	gene with protein product		601747	"""ADP-ribosylation factor domain protein 1, 64kDa"", ""tripartite motif-containing 23"""	ARFD1		8473324	Standard	NM_001656		Approved	ARD1, RNF46	uc003jty.3	P36406	OTTHUMG00000097802	ENST00000231524.9:c.911A>G	5.37:g.64905203T>C	ENSP00000231524:p.Glu304Gly		64940959	Q9BZY4|Q9BZY5	Missense_Mutation	SNP	ENST00000231524.9	37	CCDS3987.1	SNP	62	Baylor	.	.	.	.	.	.	.	.	.	.	T	21.1	4.101537	0.76983	.	.	ENSG00000113595	ENST00000231524;ENST00000381018;ENST00000274327	T;T;T	0.74526	-0.79;-0.78;-0.85	5.39	5.39	0.77823	B-box, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.70570	0.3239	L	0.50333	1.59	0.80722	D	1	P;P;P	0.47910	0.816;0.902;0.884	B;B;B	0.40940	0.115;0.269;0.344	T	0.75883	-0.3160	10	0.72032	D	0.01	.	15.7009	0.77541	0.0:0.0:0.0:1.0	.	304;304;304	P36406;P36406-2;P36406-3	TRI23_HUMAN;.;.	G	304	ENSP00000231524:E304G;ENSP00000370406:E304G;ENSP00000274327:E304G	ENSP00000231524:E304G	E	-	2	0	TRIM23	64940959	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.655000	0.83696	2.169000	0.68431	0.533000	0.62120	GAA		0.388	TRIM23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215058.2	NM_001656		Missense_Mutation
WDR78	79819	hgsc.bcm.edu	37	1	67292619	67292619	+	Missense_Mutation	SNP	C	C	A	rs373263656		TCGA-57-1584-01	TCGA-57-1584-11	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	TCGA-57-1584-01	TCGA-57-1584-11	g.chr1:67292619C>A	ENST00000371026.3	-	15	2278	c.2223G>T	c.(2221-2223)ttG>ttT	p.L741F	WDR78_ENST00000431318.1_Missense_Mutation_p.L454F|RP11-342H21.2_ENST00000456389.1_RNA	NM_024763.4	NP_079039.4	Q5VTH9	WDR78_HUMAN	WD repeat domain 78	741					hematopoietic progenitor cell differentiation (GO:0002244)			p.L741F(1)		NS(1)|endometrium(3)|kidney(6)|large_intestine(6)|lung(10)|ovary(3)|skin(3)	32						GATAAAAACTCAAAGATGGCT	0.393																																																1	Substitution - Missense(1)	ovary(1)	1											136.0	137.0	137.0					1																	67292619		2203	4300	6503	67065207	SO:0001583	missense	79819			BX648840	CCDS635.1, CCDS44157.1	1p31.2	2014-02-21	2013-02-19	2013-02-19	ENSG00000152763	ENSG00000152763		"""WD repeat domain containing"""	26252	protein-coding gene	gene with protein product						21953912	Standard	NM_207014		Approved	DIC4, FLJ23129	uc001dcx.3	Q5VTH9	OTTHUMG00000009165	ENST00000371026.3:c.2223G>T	1.37:g.67292619C>A	ENSP00000360065:p.Leu741Phe		67065207	A8K9W5|B5MDT3|H7BY80|Q5VTI0|Q8N5G5|Q9H5R9|Q9UF44	Missense_Mutation	SNP	ENST00000371026.3	37	CCDS635.1	SNP	29	Baylor	.	.	.	.	.	.	.	.	.	.	C	10.24	1.296362	0.23650	.	.	ENSG00000152763	ENST00000371026;ENST00000431318;ENST00000464352	T;T;T	0.65732	1.6;-0.17;-0.17	5.16	3.26	0.37387	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.294073	0.33591	N	0.004757	T	0.26521	0.0648	L	0.28694	0.88	0.36534	D	0.870897	B;B	0.24092	0.036;0.097	B;B	0.30105	0.059;0.111	T	0.08932	-1.0698	10	0.39692	T	0.17	-5.4098	2.3514	0.04284	0.1372:0.5129:0.133:0.2169	.	454;741	Q5VTH9-3;Q5VTH9	.;WDR78_HUMAN	F	741;454;474	ENSP00000360065:L741F;ENSP00000393182:L454F;ENSP00000433682:L474F	ENSP00000360065:L741F	L	-	3	2	WDR78	67065207	0.997000	0.39634	1.000000	0.80357	0.512000	0.34134	0.417000	0.21214	0.538000	0.28769	0.555000	0.69702	TTG		0.393	WDR78-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025404.1	NM_024763		Missense_Mutation
ZNF615	284370	hgsc.bcm.edu	37	19	52496212	52496212	+	Missense_Mutation	SNP	C	C	T			TCGA-57-1584-01	TCGA-57-1584-11	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	TCGA-57-1584-01	TCGA-57-1584-11	g.chr19:52496212C>T	ENST00000602063.1	-	6	2466	c.2117G>A	c.(2116-2118)aGg>aAg	p.R706K	ZNF615_ENST00000391795.3_Missense_Mutation_p.R711K|ZNF615_ENST00000594083.1_Missense_Mutation_p.R717K|ZNF615_ENST00000376716.5_Missense_Mutation_p.R706K|ZNF615_ENST00000598071.1_Missense_Mutation_p.R717K			Q8N8J6	ZN615_HUMAN	zinc finger protein 615	706					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)	p.R717K(1)|p.R706K(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(12)|ovary(5)|prostate(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(2)	42		all_neural(266;0.117)		GBM - Glioblastoma multiforme(134;0.00142)|OV - Ovarian serous cystadenocarcinoma(262;0.019)		TCCATAGGGCCTCTCTCCTGT	0.438																																																2	Substitution - Missense(2)	ovary(2)	19											169.0	169.0	169.0					19																	52496212		2203	4300	6503	57188024	SO:0001583	missense	284370			AK096691	CCDS12846.1, CCDS59418.1	19q13.41	2013-01-08						"""Zinc fingers, C2H2-type"", ""-"""	24740	protein-coding gene	gene with protein product						12477932	Standard	NM_001199324		Approved	FLJ33710	uc002pyf.2	Q8N8J6		ENST00000602063.1:c.2117G>A	19.37:g.52496212C>T	ENSP00000473089:p.Arg706Lys		57188024	B7ZKW9|Q2M2Y6|Q5CZB0|Q6ZMT7|Q6ZRB3	Missense_Mutation	SNP	ENST00000602063.1	37	CCDS12846.1	SNP	24	Baylor	.	.	.	.	.	.	.	.	.	.	C	3.626	-0.076512	0.07184	.	.	ENSG00000197619	ENST00000376716;ENST00000354939;ENST00000391795;ENST00000391793	T;T	0.12361	2.69;2.69	3.21	1.05	0.20165	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.02888	0.0086	N	0.00754	-1.215	0.23468	N	0.997618	B;B;B;B	0.11235	0.004;0.003;0.003;0.004	B;B;B;B	0.12837	0.008;0.007;0.007;0.008	T	0.45056	-0.9287	9	0.02654	T	1	.	4.5302	0.12001	0.0:0.4996:0.0:0.5004	.	711;713;717;706	B4DH87;Q8N8J6-3;Q8N8J6-2;Q8N8J6	.;.;.;ZN615_HUMAN	K	706;716;711;660	ENSP00000365906:R706K;ENSP00000375672:R711K	ENSP00000347019:R716K	R	-	2	0	ZNF615	57188024	0.000000	0.05858	0.367000	0.25926	0.990000	0.78478	-1.036000	0.03560	0.670000	0.31165	0.655000	0.94253	AGG		0.438	ZNF615-009	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462391.1	NM_198480		Missense_Mutation
