#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_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
OR2D2	120776	hgsc.bcm.edu	37	11	6913264	6913264	+	Silent	SNP	A	A	C			TCGA-09-1666-01A-01W-0615-10	TCGA-09-1666-10A-01W-0616-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_III	WXS	none			SOLID	89624b91-5fc5-4a15-9793-588d7b033703	6a789747-4a8c-4678-ae32-37789b17855d	g.chr11:6913264A>C	ENST00000299459.2	-	1	566	c.468T>G	c.(466-468)tcT>tcG	p.S156S		NM_003700.1	NP_003691.1	Q9H210	OR2D2_HUMAN	olfactory receptor, family 2, subfamily D, member 2	156					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.S156S(1)		breast(1)|central_nervous_system(1)|cervix(1)|large_intestine(3)|lung(9)|ovary(1)|skin(2)	18		Medulloblastoma(188;0.0523)|all_neural(188;0.236)		Epithelial(150;4.68e-08)|BRCA - Breast invasive adenocarcinoma(625;0.129)		TGTCTACCACAGACACCAGAA	0.493																																																1	Substitution - coding silent(1)	ovary(1)	11											125.0	94.0	105.0					11																	6913264		2201	4296	6497	6869840	SO:0001819	synonymous_variant	120776			AB065824	CCDS31416.1	11p15.4	2012-08-09			ENSG00000166368	ENSG00000166368		"""GPCR / Class A : Olfactory receptors"""	8244	protein-coding gene	gene with protein product		608494		OR2D1		9787077	Standard	NM_003700		Approved	OR11-610, hg27	uc010rau.2	Q9H210	OTTHUMG00000165741	ENST00000299459.2:c.468T>G	11.37:g.6913264A>C			6869840	B9EIL5|O95224|Q6IF28|Q8NGH4|Q96R52	Silent	SNP	ENST00000299459.2	37	CCDS31416.1																																																																																				0.493	OR2D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385986.1	NM_003700	
RYR1	6261	hgsc.bcm.edu	37	19	38980821	38980821	+	Missense_Mutation	SNP	C	C	T			TCGA-09-1666-01A-01W-0615-10	TCGA-09-1666-10A-01W-0616-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_III	WXS	none			SOLID	89624b91-5fc5-4a15-9793-588d7b033703	6a789747-4a8c-4678-ae32-37789b17855d	g.chr19:38980821C>T	ENST00000359596.3	+	36	5920	c.5920C>T	c.(5920-5922)Cgg>Tgg	p.R1974W	RYR1_ENST00000355481.4_Missense_Mutation_p.R1974W|RYR1_ENST00000360985.3_Missense_Mutation_p.R1974W			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	1974	6 X approximate repeats.				calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)	p.R1974W(1)		NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	GGCCAACCAGCGGAGCCGCTA	0.602																																																1	Substitution - Missense(1)	ovary(1)	19											60.0	53.0	55.0					19																	38980821		2203	4300	6503	43672661	SO:0001583	missense	6261			J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218		"""Ion channels / Ryanodine receptors"""	10483	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 137"""	180901	"""central core disease of muscle"""	MHS, MHS1, CCO		1862346, 16621918	Standard	NM_000540		Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.5920C>T	19.37:g.38980821C>T	ENSP00000352608:p.Arg1974Trp		43672661	Q16314|Q16368|Q9NPK1|Q9P1U4	Missense_Mutation	SNP	ENST00000359596.3	37	CCDS33011.1	.	.	.	.	.	.	.	.	.	.	C	12.18	1.859942	0.32884	.	.	ENSG00000196218	ENST00000359596;ENST00000355481;ENST00000360985	T;T;T	0.73897	-0.79;-0.79;-0.79	4.61	-0.288	0.12855	.	0.000000	0.64402	U	0.000014	D	0.84620	0.5512	M	0.83483	2.645	0.30899	N	0.729433	D;D	0.89917	1.0;1.0	D;P	0.66084	0.941;0.874	D	0.85554	0.1223	10	0.66056	D	0.02	.	15.5957	0.76578	0.7178:0.2821:0.0:0.0	.	1974;1974	P21817-2;P21817	.;RYR1_HUMAN	W	1974	ENSP00000352608:R1974W;ENSP00000347667:R1974W;ENSP00000354254:R1974W	ENSP00000347667:R1974W	R	+	1	2	RYR1	43672661	0.978000	0.34361	0.953000	0.39169	0.498000	0.33706	0.101000	0.15251	-0.104000	0.12154	-0.270000	0.10280	CGG		0.602	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1		
ATG3	64422	hgsc.bcm.edu	37	3	112280341	112280341	+	Missense_Mutation	SNP	G	G	A			TCGA-09-1666-01A-01W-0615-10	TCGA-09-1666-10A-01W-0616-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_III	WXS	454_PCR_WGA			SOLID	89624b91-5fc5-4a15-9793-588d7b033703	6a789747-4a8c-4678-ae32-37789b17855d	g.chr3:112280341G>A	ENST00000283290.5	-	1	469	c.35C>T	c.(34-36)gCa>gTa	p.A12V	ATG3_ENST00000495756.1_5'UTR|ATG3_ENST00000402314.2_Missense_Mutation_p.A12V|SLC35A5_ENST00000492406.1_5'Flank	NM_022488.3	NP_071933.2	Q9NT62	ATG3_HUMAN	autophagy related 3	12					autophagic vacuole assembly (GO:0000045)|cellular protein modification process (GO:0006464)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|mitochondrion degradation (GO:0000422)|nucleophagy (GO:0044804)|protein targeting to membrane (GO:0006612)|protein ubiquitination (GO:0016567)|regulation of cilium assembly (GO:1902017)	cytoplasmic ubiquitin ligase complex (GO:0000153)|cytosol (GO:0005829)	Atg12 ligase activity (GO:0019777)|Atg8 ligase activity (GO:0019776)|enzyme binding (GO:0019899)|small conjugating protein ligase activity (GO:0019787)	p.A12V(1)		breast(1)|kidney(1)|large_intestine(1)|lung(3)|ovary(3)	9						CACTTCCAGTGCCTTTCCCTT	0.627																																																1	Substitution - Missense(1)	ovary(1)	3											83.0	72.0	76.0					3																	112280341		2203	4300	6503	113763031	SO:0001583	missense	64422				CCDS2966.1, CCDS63721.1	3q13.2	2014-02-12	2012-06-06	2005-09-11	ENSG00000144848	ENSG00000144848			20962	protein-coding gene	gene with protein product		609606	"""APG3 autophagy 3-like (S. cerevisiae)"", ""ATG3 autophagy related 3 homolog (S. cerevisiae)"""	APG3L		11825910	Standard	NM_022488		Approved	PC3-96, FLJ22125, MGC15201, DKFZp564M1178	uc003dzd.3	Q9NT62	OTTHUMG00000159260	ENST00000283290.5:c.35C>T	3.37:g.112280341G>A	ENSP00000283290:p.Ala12Val		113763031	Q6PKC5|Q9H6L9	Missense_Mutation	SNP	ENST00000283290.5	37	CCDS2966.1	.	.	.	.	.	.	.	.	.	.	G	35	5.530372	0.96446	.	.	ENSG00000144848	ENST00000283290;ENST00000402314	.	.	.	4.96	4.96	0.65561	Autophagy-related protein 3, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.71929	0.3398	L	0.54863	1.705	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.65389	-0.6180	9	0.06757	T	0.87	-2.0396	17.1368	0.86742	0.0:0.0:1.0:0.0	.	12;12	Q9NT62;Q9NT62-2	ATG3_HUMAN;.	V	12	.	ENSP00000283290:A12V	A	-	2	0	ATG3	113763031	1.000000	0.71417	0.997000	0.53966	0.998000	0.95712	6.897000	0.75671	2.567000	0.86603	0.563000	0.77884	GCA		0.627	ATG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354147.1	NM_022488	
BRWD3	254065	hgsc.bcm.edu	37	X	79988966	79988966	+	Silent	SNP	G	G	A			TCGA-09-1666-01A-01W-0615-10	TCGA-09-1666-10A-01W-0616-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_III	WXS	454_PCR_WGA			SOLID	89624b91-5fc5-4a15-9793-588d7b033703	6a789747-4a8c-4678-ae32-37789b17855d	g.chrX:79988966G>A	ENST00000373275.4	-	12	1332	c.1116C>T	c.(1114-1116)aaC>aaT	p.N372N		NM_153252.4	NP_694984	Q6RI45	BRWD3_HUMAN	bromodomain and WD repeat domain containing 3	372					cytoskeleton organization (GO:0007010)|regulation of cell shape (GO:0008360)			p.N372N(1)		breast(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|lung(39)|ovary(4)|prostate(2)|skin(3)	87						TGTCTCCATTGTTACAGAACT	0.308																																																1	Substitution - coding silent(1)	ovary(1)	X											99.0	89.0	92.0					X																	79988966		2203	4296	6499	79875622	SO:0001819	synonymous_variant	254065				CCDS14447.1	Xq21.1	2013-01-09			ENSG00000165288	ENSG00000165288		"""WD repeat domain containing"""	17342	protein-coding gene	gene with protein product		300553				15543602, 16094372	Standard	NM_153252		Approved	FLJ38568, MRX93	uc004edt.3	Q6RI45	OTTHUMG00000021908	ENST00000373275.4:c.1116C>T	X.37:g.79988966G>A			79875622	C9IZ39|C9J3F3|Q2T9J6|Q5JRN1|Q6RI37|Q6RI42|Q6RI44|Q8N916	Silent	SNP	ENST00000373275.4	37	CCDS14447.1																																																																																				0.308	BRWD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057344.1	NM_153252	
GPATCH2L	55668	hgsc.bcm.edu	37	14	76638272	76638272	+	Missense_Mutation	SNP	G	G	C			TCGA-09-1666-01A-01W-0615-10	TCGA-09-1666-10A-01W-0616-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_III	WXS	454_PCR_WGA			SOLID	89624b91-5fc5-4a15-9793-588d7b033703	6a789747-4a8c-4678-ae32-37789b17855d	g.chr14:76638272G>C	ENST00000261530.7	+	4	880	c.814G>C	c.(814-816)Gat>Cat	p.D272H	GPATCH2L_ENST00000557263.1_Missense_Mutation_p.D272H|GPATCH2L_ENST00000556663.1_Missense_Mutation_p.D272H|GPATCH2L_ENST00000312858.5_Missense_Mutation_p.D272H	NM_017926.2	NP_060396.2	Q9NWQ4	GPT2L_HUMAN	G patch domain containing 2-like	272								p.D272H(1)									GTGGGCTCCTGATCATTGTTC	0.428																																																1	Substitution - Missense(1)	ovary(1)	14											157.0	150.0	153.0					14																	76638272		2203	4300	6503	75708025	SO:0001583	missense	55668			AK000696	CCDS9848.1, CCDS9849.1	14q24.3	2012-09-25	2012-09-25	2012-09-25	ENSG00000089916	ENSG00000089916			20210	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 118"""	C14orf118		10574461	Standard	NM_017926		Approved	FLJ20689, FLJ10033	uc001xsh.3	Q9NWQ4	OTTHUMG00000171490	ENST00000261530.7:c.814G>C	14.37:g.76638272G>C	ENSP00000261530:p.Asp272His		75708025	B3KN42|Q6PEJ7|Q9H3M3|Q9NWH0|Q9ULR8	Missense_Mutation	SNP	ENST00000261530.7	37	CCDS9848.1	.	.	.	.	.	.	.	.	.	.	G	22.3	4.272337	0.80580	.	.	ENSG00000089916	ENST00000336993;ENST00000557263;ENST00000312858;ENST00000261530;ENST00000556663	T;T;T;T	0.54479	0.57;0.57;0.58;0.57	5.43	5.43	0.79202	.	0.059640	0.64402	D	0.000005	T	0.70211	0.3198	L	0.60455	1.87	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.997;0.997;0.999	T	0.71570	-0.4553	10	0.87932	D	0	-18.0466	17.5969	0.88014	0.0:0.0:1.0:0.0	.	272;272;272	Q9NWQ4-1;Q9NWQ4-4;Q9NWQ4	.;.;CN118_HUMAN	H	272	ENSP00000451587:D272H;ENSP00000323775:D272H;ENSP00000261530:D272H;ENSP00000450657:D272H	ENSP00000261530:D272H	D	+	1	0	C14orf118	75708025	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.745000	0.74860	2.824000	0.97209	0.655000	0.94253	GAT		0.428	GPATCH2L-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000413698.2	NM_017926	
C3orf20	84077	hgsc.bcm.edu	37	3	14768465	14768465	+	Missense_Mutation	SNP	G	G	T			TCGA-09-1666-01A-01W-0615-10	TCGA-09-1666-10A-01W-0616-10	G	G	T	T	G	G	Unknown	Valid	Somatic	Phase_III	WXS	454_PCR_WGA			SOLID	89624b91-5fc5-4a15-9793-588d7b033703	6a789747-4a8c-4678-ae32-37789b17855d	g.chr3:14768465G>T	ENST00000253697.3	+	11	2076	c.1624G>T	c.(1624-1626)Gct>Tct	p.A542S	C3orf20_ENST00000435614.1_Missense_Mutation_p.A420S|C3orf20_ENST00000412910.1_Missense_Mutation_p.A420S	NM_032137.4	NP_115513.4	Q8ND61	CC020_HUMAN	chromosome 3 open reading frame 20	542						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)		p.A542S(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(13)|lung(11)|ovary(4)|skin(2)	40						CCGAGCCCTGGCTGAGATCAA	0.542																																																1	Substitution - Missense(1)	ovary(1)	3											122.0	111.0	115.0					3																	14768465		2203	4300	6503	14743469	SO:0001583	missense	84077			AL136781	CCDS33706.1, CCDS54555.1	3p25.1	2011-01-25			ENSG00000131379	ENSG00000131379			25320	protein-coding gene	gene with protein product						11230166	Standard	NM_032137		Approved	DKFZP434N1817	uc003byy.3	Q8ND61	OTTHUMG00000155545	ENST00000253697.3:c.1624G>T	3.37:g.14768465G>T	ENSP00000253697:p.Ala542Ser		14743469	Q7L0U6|Q8NCP2|Q9H0I7	Missense_Mutation	SNP	ENST00000253697.3	37	CCDS33706.1	.	.	.	.	.	.	.	.	.	.	G	15.26	2.781505	0.49891	.	.	ENSG00000131379	ENST00000253697;ENST00000435614;ENST00000412910	T;T;T	0.11495	2.77;2.77;2.77	5.05	3.2	0.36748	.	0.604547	0.14832	N	0.295786	T	0.14527	0.0351	M	0.63428	1.95	0.23089	N	0.998317	P;P	0.50156	0.872;0.932	P;P	0.45856	0.495;0.495	T	0.12863	-1.0531	10	0.66056	D	0.02	-5.3936	6.4788	0.22051	0.0976:0.1839:0.7184:0.0	.	420;542	Q8ND61-2;Q8ND61	.;CC020_HUMAN	S	542;420;420	ENSP00000253697:A542S;ENSP00000402933:A420S;ENSP00000396081:A420S	ENSP00000253697:A542S	A	+	1	0	C3orf20	14743469	0.896000	0.30565	0.356000	0.25785	0.874000	0.50279	1.423000	0.34837	0.677000	0.31305	0.491000	0.48974	GCT		0.542	C3orf20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340586.1	NM_032137	
CD3E	916	hgsc.bcm.edu	37	11	118186243	118186243	+	Missense_Mutation	SNP	C	C	G			TCGA-09-1666-01A-01W-0615-10	TCGA-09-1666-10A-01W-0616-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_III	WXS	454_PCR_WGA			SOLID	89624b91-5fc5-4a15-9793-588d7b033703	6a789747-4a8c-4678-ae32-37789b17855d	g.chr11:118186243C>G	ENST00000361763.4	+	9	901	c.610C>G	c.(610-612)Cag>Gag	p.Q204E	CD3E_ENST00000528600.1_Missense_Mutation_p.Q198E	NM_000733.3	NP_000724.1	P07766	CD3E_HUMAN	CD3e molecule, epsilon (CD3-TCR complex)	204	ITAM. {ECO:0000255|PROSITE- ProRule:PRU00379}.				apoptotic signaling pathway (GO:0097190)|cell surface receptor signaling pathway (GO:0007166)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|negative regulation of smoothened signaling pathway (GO:0045879)|negative thymic T cell selection (GO:0045060)|positive regulation of alpha-beta T cell proliferation (GO:0046641)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of interleukin-4 production (GO:0032753)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of T cell anergy (GO:0002669)|positive regulation of T cell proliferation (GO:0042102)|protein complex assembly (GO:0006461)|regulation of apoptotic process (GO:0042981)|regulation of immune response (GO:0050776)|response to nutrient (GO:0007584)|signal complex assembly (GO:0007172)|T cell activation (GO:0042110)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	alpha-beta T cell receptor complex (GO:0042105)|cell-cell junction (GO:0005911)|external side of plasma membrane (GO:0009897)|immunological synapse (GO:0001772)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|T cell receptor complex (GO:0042101)	protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|receptor signaling complex scaffold activity (GO:0030159)|receptor signaling protein activity (GO:0005057)|SH3 domain binding (GO:0017124)|T cell receptor binding (GO:0042608)|transmembrane signaling receptor activity (GO:0004888)	p.Q204E(1)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|ovary(2)|stomach(1)	8	all_hematologic(175;0.046)	Medulloblastoma(222;0.0425)|Breast(348;0.181)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;3.09e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0251)	Muromonab(DB00075)	TGGCCTGAATCAGAGACGCAT	0.612																																																1	Substitution - Missense(1)	ovary(1)	11											59.0	53.0	55.0					11																	118186243		2200	4296	6496	117691453	SO:0001583	missense	916			X03884	CCDS31685.1	11q23	2014-09-17	2006-03-28		ENSG00000198851	ENSG00000198851		"""CD molecules"""	1674	protein-coding gene	gene with protein product		186830	"""CD3e antigen, epsilon polypeptide (TiT3 complex)"""				Standard	NM_000733		Approved		uc001psq.4	P07766	OTTHUMG00000166968	ENST00000361763.4:c.610C>G	11.37:g.118186243C>G	ENSP00000354566:p.Gln204Glu		117691453	A8K997	Missense_Mutation	SNP	ENST00000361763.4	37	CCDS31685.1	.	.	.	.	.	.	.	.	.	.	C	20.3	3.972495	0.74246	.	.	ENSG00000198851	ENST00000361763;ENST00000528600	T;T	0.44482	0.92;0.92	4.96	4.96	0.65561	.	0.287009	0.28482	N	0.015184	T	0.58991	0.2161	L	0.57536	1.79	0.34604	D	0.716854	D	0.76494	0.999	D	0.87578	0.998	T	0.66468	-0.5916	10	0.39692	T	0.17	-1.7631	13.5817	0.61907	0.0:1.0:0.0:0.0	.	204	P07766	CD3E_HUMAN	E	204;198	ENSP00000354566:Q204E;ENSP00000433975:Q198E	ENSP00000354566:Q204E	Q	+	1	0	CD3E	117691453	0.998000	0.40836	1.000000	0.80357	0.841000	0.47740	1.662000	0.37418	2.556000	0.86216	0.655000	0.94253	CAG		0.612	CD3E-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000392120.1	NM_000733	
GABRE	2564	hgsc.bcm.edu	37	X	151129761	151129761	+	Missense_Mutation	SNP	A	A	G			TCGA-09-1666-01A-01W-0615-10	TCGA-09-1666-10A-01W-0616-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_III	WXS	454_PCR_WGA			SOLID	89624b91-5fc5-4a15-9793-588d7b033703	6a789747-4a8c-4678-ae32-37789b17855d	g.chrX:151129761A>G	ENST00000370328.3	-	5	693	c.640T>C	c.(640-642)Tct>Cct	p.S214P	MIR452_ENST00000385020.1_RNA|GABRE_ENST00000393914.3_Intron|GABRE_ENST00000370325.1_Missense_Mutation_p.S214P|MIR224_ENST00000384889.1_RNA	NM_004961.3	NP_004952.2	P78334	GBRE_HUMAN	gamma-aminobutyric acid (GABA) A receptor, epsilon	214					gamma-aminobutyric acid signaling pathway (GO:0007214)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)	p.S101P(1)		breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(9)|ovary(2)|skin(1)	27	Acute lymphoblastic leukemia(192;6.56e-05)				Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Ketazolam(DB01587)|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)	TCACAGCTAGAGAAAGATAGA	0.468																																																1	Substitution - Missense(1)	ovary(1)	X											119.0	110.0	113.0					X																	151129761		2203	4300	6503	150880417	SO:0001583	missense	2564			Y09765	CCDS14703.1	Xq28	2012-06-22			ENSG00000102287	ENSG00000102287		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4085	protein-coding gene	gene with protein product	"""GABA(A) receptor, epsilon"""	300093				9039914, 9084408	Standard	NM_004961		Approved		uc004ffi.3	P78334	OTTHUMG00000024176	ENST00000370328.3:c.640T>C	X.37:g.151129761A>G	ENSP00000359353:p.Ser214Pro		150880417	E7ET93|O15345|O15346|Q6PCD2|Q99520	Missense_Mutation	SNP	ENST00000370328.3	37	CCDS14703.1	.	.	.	.	.	.	.	.	.	.	A	25.3	4.620304	0.87460	.	.	ENSG00000102287	ENST00000370328;ENST00000370325	T;T	0.79940	-1.32;-1.32	5.75	5.75	0.90469	Neurotransmitter-gated ion-channel ligand-binding (3);	0.252575	0.28219	N	0.016154	D	0.86657	0.5985	L	0.58583	1.82	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.85075	0.0942	10	0.31617	T	0.26	.	12.79	0.57528	1.0:0.0:0.0:0.0	.	214	P78334	GBRE_HUMAN	P	214	ENSP00000359353:S214P;ENSP00000359350:S214P	ENSP00000359350:S214P	S	-	1	0	GABRE	150880417	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.379000	0.66196	1.928000	0.55862	0.486000	0.48141	TCT		0.468	GABRE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060903.1	NM_004961, NM_021990, NM_021984	
OLFM1	10439	hgsc.bcm.edu	37	9	138011971	138011971	+	Missense_Mutation	SNP	C	C	A			TCGA-09-1666-01A-01W-0615-10	TCGA-09-1666-10A-01W-0616-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_III	WXS	454_PCR_WGA			SOLID	89624b91-5fc5-4a15-9793-588d7b033703	6a789747-4a8c-4678-ae32-37789b17855d	g.chr9:138011971C>A	ENST00000371793.3	+	6	1656	c.1405C>A	c.(1405-1407)Cag>Aag	p.Q469K	OLFM1_ENST00000252854.4_Missense_Mutation_p.Q451K|OLFM1_ENST00000371796.3_Missense_Mutation_p.Q442K	NM_001282611.1	NP_001269540.1	Q99784	NOE1_HUMAN	olfactomedin 1	469	Olfactomedin-like. {ECO:0000255|PROSITE- ProRule:PRU00446}.				negative regulation of beta-amyloid formation (GO:1902430)|negative regulation of neuron migration (GO:2001223)|nervous system development (GO:0007399)|protein oligomerization (GO:0051259)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|extracellular space (GO:0005615)|synapse (GO:0045202)	beta-amyloid binding (GO:0001540)	p.Q451K(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(6)|ovary(1)|prostate(1)|skin(2)	21		Myeloproliferative disorder(178;0.0333)		Epithelial(140;5.49e-08)|OV - Ovarian serous cystadenocarcinoma(145;9.68e-08)|all cancers(34;1.88e-07)		CAACGGCCACCAGATCCTCTA	0.562																																																1	Substitution - Missense(1)	ovary(1)	9											119.0	104.0	109.0					9																	138011971		2203	4300	6503	137151792	SO:0001583	missense	10439			AF035301	CCDS6986.1, CCDS6987.1, CCDS65183.1, CCDS65184.1	9q34.3	2014-01-20			ENSG00000130558	ENSG00000130558			17187	protein-coding gene	gene with protein product	"""pancortin"""	605366				9039501	Standard	NM_006334		Approved	NOE1, OlfA, AMY, NOELIN	uc004cfl.4	Q99784	OTTHUMG00000020897	ENST00000371793.3:c.1405C>A	9.37:g.138011971C>A	ENSP00000360858:p.Gln469Lys		137151792	Q53XZ8|Q6IMJ4|Q6IMJ5|Q8N8R0|Q969S7|Q99452	Missense_Mutation	SNP	ENST00000371793.3	37		.	.	.	.	.	.	.	.	.	.	C	24.0	4.486040	0.84854	.	.	ENSG00000130558	ENST00000252854;ENST00000371796;ENST00000371793	D;D;D	0.89617	-2.54;-2.54;-2.54	4.94	4.94	0.65067	Olfactomedin-like (3);Quinonprotein alcohol dehydrogenase-like (1);	0.000000	0.85682	D	0.000000	D	0.95582	0.8564	M	0.91406	3.205	0.80722	D	1	P;D	0.65815	0.826;0.995	P;D	0.70487	0.551;0.969	D	0.96283	0.9208	10	0.59425	D	0.04	.	18.1661	0.89727	0.0:1.0:0.0:0.0	.	469;451	Q99784;Q6IMJ8	NOE1_HUMAN;.	K	451;442;469	ENSP00000252854:Q451K;ENSP00000360861:Q442K;ENSP00000360858:Q469K	ENSP00000252854:Q451K	Q	+	1	0	OLFM1	137151792	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.563000	0.82314	2.296000	0.77279	0.561000	0.74099	CAG		0.562	OLFM1-004	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000054974.1	NM_014279	
PLB1	151056	hgsc.bcm.edu	37	2	28849343	28849343	+	Missense_Mutation	SNP	G	G	T			TCGA-09-1666-01A-01W-0615-10	TCGA-09-1666-10A-01W-0616-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_III	WXS	454_PCR_WGA			SOLID	89624b91-5fc5-4a15-9793-588d7b033703	6a789747-4a8c-4678-ae32-37789b17855d	g.chr2:28849343G>T	ENST00000327757.5	+	51	3672	c.3628G>T	c.(3628-3630)Gtc>Ttc	p.V1210F	PLB1_ENST00000541605.1_Missense_Mutation_p.V175F|PLB1_ENST00000422425.2_Missense_Mutation_p.V1199F	NM_153021.4	NP_694566.4	Q6P1J6	PLB1_HUMAN	phospholipase B1	1210	4 X 308-326 AA approximate repeats.				glycerophospholipid biosynthetic process (GO:0046474)|lipid catabolic process (GO:0016042)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phospholipid metabolic process (GO:0006644)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	lysophospholipase activity (GO:0004622)|phospholipase A2 activity (GO:0004623)	p.V1210F(1)		NS(2)|breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(10)|lung(31)|ovary(6)|prostate(1)|skin(7)|stomach(2)	69	Acute lymphoblastic leukemia(172;0.155)					CTTCATTGGGGTCAACGACTT	0.542																																																1	Substitution - Missense(1)	ovary(1)	2											156.0	135.0	142.0					2																	28849343		2203	4300	6503	28702847	SO:0001583	missense	151056				CCDS33168.1, CCDS54340.1	2p23.3	2014-03-14			ENSG00000163803	ENSG00000163803	3.1.1.4, 3.1.1.5		30041	protein-coding gene	gene with protein product		610179				12150957	Standard	NM_153021		Approved	PLB, FLJ30866	uc002rmb.2	Q6P1J6	OTTHUMG00000152014	ENST00000327757.5:c.3628G>T	2.37:g.28849343G>T	ENSP00000330442:p.Val1210Phe		28702847	A8KAX2|Q53S03|Q8IUP7|Q96DP9	Missense_Mutation	SNP	ENST00000327757.5	37	CCDS33168.1	.	.	.	.	.	.	.	.	.	.	G	11.48	1.650247	0.29336	.	.	ENSG00000163803	ENST00000327757;ENST00000422425;ENST00000541605	T;T;T	0.14144	2.53;2.53;2.53	5.41	-1.81	0.07882	Esterase, SGNH hydrolase-type (1);Esterase, SGNH hydrolase-type, subgroup (1);Lipase, GDSL (1);	0.866114	0.10428	N	0.675828	T	0.09862	0.0242	N	0.08118	0	0.09310	N	1	P;P	0.52316	0.941;0.952	P;P	0.51229	0.532;0.663	T	0.38499	-0.9658	10	0.23891	T	0.37	-0.0134	10.8265	0.46635	0.7507:0.0:0.2493:0.0	.	1199;1210	Q6P1J6-3;Q6P1J6	.;PLB1_HUMAN	F	1210;1199;175	ENSP00000330442:V1210F;ENSP00000416440:V1199F;ENSP00000437426:V175F	ENSP00000330442:V1210F	V	+	1	0	PLB1	28702847	0.988000	0.35896	0.032000	0.17829	0.166000	0.22503	0.413000	0.21148	-0.206000	0.10203	-0.350000	0.07774	GTC		0.542	PLB1-012	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000353348.2		
PMEL	6490	hgsc.bcm.edu	37	12	56355196	56355196	+	Missense_Mutation	SNP	G	G	C			TCGA-09-1666-01A-01W-0615-10	TCGA-09-1666-10A-01W-0616-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_III	WXS	454_PCR_WGA			SOLID	89624b91-5fc5-4a15-9793-588d7b033703	6a789747-4a8c-4678-ae32-37789b17855d	g.chr12:56355196G>C	ENST00000548747.1	-	3	901	c.239C>G	c.(238-240)gCa>gGa	p.A80G	PMEL_ENST00000550464.1_Intron|PMEL_ENST00000360714.4_Missense_Mutation_p.A80G|PMEL_ENST00000449260.2_Missense_Mutation_p.A80G|PMEL_ENST00000548689.1_5'UTR|PMEL_ENST00000548493.1_Missense_Mutation_p.A80G|PMEL_ENST00000539511.1_Intron|PMEL_ENST00000536427.1_Missense_Mutation_p.A80G|PMEL_ENST00000552882.1_Missense_Mutation_p.A80G|PMEL_ENST00000550447.1_Missense_Mutation_p.A43G			P40967	PMEL_HUMAN	premelanosome protein	80					melanin biosynthetic process (GO:0042438)|melanosome organization (GO:0032438)	endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|melanosome (GO:0042470)|multivesicular body membrane (GO:0032585)|plasma membrane (GO:0005886)		p.A80G(1)		NS(1)|breast(2)|endometrium(2)|large_intestine(4)|lung(4)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						GGAGGCATTTGCACCAATCAG	0.507																																																1	Substitution - Missense(1)	ovary(1)	12											174.0	153.0	160.0					12																	56355196		2203	4300	6503	54641463	SO:0001583	missense	6490			AK092881	CCDS8897.1, CCDS55833.1, CCDS55834.1	12q13-q14	2010-12-17	2010-12-17	2010-12-17	ENSG00000185664	ENSG00000185664			10880	protein-coding gene	gene with protein product		155550	"""silver (mouse homolog) like"", ""silver homolog (mouse)"""	SIL, SILV		8739560	Standard	NM_001200053		Approved	D12S53E, SI, Pmel17, gp100	uc001siq.3	P40967		ENST00000548747.1:c.239C>G	12.37:g.56355196G>C	ENSP00000448828:p.Ala80Gly		54641463	B3KS57|B7Z6D7|Q12763|Q14448|Q14817|Q16565	Missense_Mutation	SNP	ENST00000548747.1	37	CCDS8897.1	.	.	.	.	.	.	.	.	.	.	g	21.5	4.165315	0.78339	.	.	ENSG00000185664	ENST00000449260;ENST00000552882;ENST00000548747;ENST00000548493;ENST00000360714;ENST00000536427;ENST00000550447;ENST00000548803;ENST00000547137;ENST00000549418;ENST00000549233	T;T;T;T;T;T;T;T	0.37411	2.65;2.69;2.69;2.69;2.65;2.4;1.2;2.17	5.15	5.15	0.70609	.	0.000000	0.50627	D	0.000105	T	0.61135	0.2323	M	0.71581	2.175	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.83275	0.996;0.991	T	0.64305	-0.6439	10	0.72032	D	0.01	-7.7768	17.783	0.88529	0.0:0.0:1.0:0.0	.	80;80	P40967-2;P40967	.;PMEL_HUMAN	G	80;80;80;80;80;80;43;80;80;80;83	ENSP00000402758:A80G;ENSP00000449690:A80G;ENSP00000448828:A80G;ENSP00000447374:A80G;ENSP00000353940:A80G;ENSP00000438695:A80G;ENSP00000447732:A80G;ENSP00000448849:A80G	ENSP00000353940:A80G	A	-	2	0	PMEL	54641463	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.315000	0.89983	2.560000	0.86352	0.643000	0.83706	GCA		0.507	PMEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409626.1	NM_006928	
TP53	7157	hgsc.bcm.edu	37	17	7578555	7578555	+	Splice_Site	SNP	C	C	A			TCGA-09-1666-01A-01W-0615-10	TCGA-09-1666-10A-01W-0616-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_III	WXS	454_PCR_WGA			SOLID	89624b91-5fc5-4a15-9793-588d7b033703	6a789747-4a8c-4678-ae32-37789b17855d	g.chr17:7578555C>A	ENST00000269305.4	-	5	565		c.e5-1		TP53_ENST00000574684.1_5'Flank|TP53_ENST00000445888.2_Splice_Site|TP53_ENST00000455263.2_Splice_Site|TP53_ENST00000413465.2_Splice_Site|TP53_ENST00000420246.2_Splice_Site|TP53_ENST00000359597.4_Splice_Site	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						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.?(39)|p.0?(8)|p.V73fs*9(1)|p.Y126fs*11(1)|p.P13fs*18(1)|p.T125_Y126insX(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)	CAGGGGAGTACTGTAGGAAGA	0.552		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"""	51	Unknown(39)|Whole gene deletion(8)|Deletion - Frameshift(3)|Insertion - In frame(1)	ovary(9)|pancreas(6)|bone(5)|upper_aerodigestive_tract(4)|liver(4)|lung(4)|breast(4)|large_intestine(3)|central_nervous_system(3)|oesophagus(3)|haematopoietic_and_lymphoid_tissue(2)|stomach(1)|endometrium(1)|urinary_tract(1)|autonomic_ganglia(1)	17											42.0	42.0	42.0					17																	7578555		2203	4300	6503	7519280	SO:0001630	splice_region_variant	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.376-1G>T	17.37:g.7578555C>A			7519280	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	Splice_Site	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	C	17.36	3.370877	0.61624	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000514944;ENST00000508793;ENST00000503591	.	.	.	4.87	3.9	0.45041	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.4246	0.50003	0.0:0.9094:0.0:0.0906	.	.	.	.	.	-1	.	.	.	-	.	.	TP53	7519280	1.000000	0.71417	0.999000	0.59377	0.918000	0.54935	7.639000	0.83342	1.359000	0.45940	0.655000	0.94253	.		0.552	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546	Intron
UQCRB	7381	hgsc.bcm.edu	37	8	97247742	97247742	+	Missense_Mutation	SNP	G	G	C	rs200758329		TCGA-09-1666-01A-01W-0615-10	TCGA-09-1666-10A-01W-0616-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_III	WXS	454_PCR_WGA			SOLID	89624b91-5fc5-4a15-9793-588d7b033703	6a789747-4a8c-4678-ae32-37789b17855d	g.chr8:97247742G>C	ENST00000287022.5	-	1	120	c.17C>G	c.(16-18)gCc>gGc	p.A6G	UQCRB_ENST00000517523.1_5'Flank|UQCRB_ENST00000518406.1_Missense_Mutation_p.A6G|UQCRB_ENST00000523920.1_Missense_Mutation_p.A6G|KB-1043D8.6_ENST00000520575.1_RNA	NM_001199975.2|NM_006294.4	NP_001186904.1|NP_006285.1	P14927	QCR7_HUMAN	ubiquinol-cytochrome c reductase binding protein	6				A -> G (in Ref. 2; AAA60236). {ECO:0000305}.	aerobic respiration (GO:0009060)|cellular metabolic process (GO:0044237)|mitochondrial electron transport, ubiquinol to cytochrome c (GO:0006122)|oxidation-reduction process (GO:0055114)|oxidative phosphorylation (GO:0006119)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain (GO:0005746)|mitochondrial respiratory chain complex III (GO:0005750)		p.A6G(1)		kidney(1)|large_intestine(3)|lung(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	10	Breast(36;5.16e-05)					TTACTTACCGGCCTGCTTACC	0.532																																																1	Substitution - Missense(1)	ovary(1)	8											118.0	109.0	112.0					8																	97247742		2203	4300	6503	97316918	SO:0001583	missense	7381			X13585	CCDS6269.1, CCDS59107.1	8q22	2011-07-04			ENSG00000156467	ENSG00000156467		"""Mitochondrial respiratory chain complex / Complex III"""	12582	protein-coding gene	gene with protein product	"""ubiquinol-cytochrome c reductase, complex III subunit VI"", ""cytochrome b-c1 complex subunit 7"""	191330		UQBP		2167087, 2543413, 3056408	Standard	NM_006294		Approved	QP-C, QCR7, UQCR6	uc022ayx.1	P14927	OTTHUMG00000164711	ENST00000287022.5:c.17C>G	8.37:g.97247742G>C	ENSP00000287022:p.Ala6Gly		97316918	E5RJU0|Q6FGD1	Missense_Mutation	SNP	ENST00000287022.5	37	CCDS6269.1	.	.	.	.	.	.	.	.	.	.	G	19.16	3.774663	0.70107	.	.	ENSG00000156467	ENST00000287022;ENST00000518406;ENST00000523920	T;T;T	0.44482	0.92;0.92;0.92	4.2	4.2	0.49525	.	0.544734	0.19684	N	0.108435	T	0.41511	0.1162	M	0.62723	1.935	0.09310	N	1	B	0.24823	0.112	B	0.24701	0.055	T	0.41215	-0.9521	10	0.59425	D	0.04	-11.7994	12.2323	0.54495	0.0:0.0:1.0:0.0	.	6	P14927	QCR7_HUMAN	G	6	ENSP00000287022:A6G;ENSP00000430494:A6G;ENSP00000430560:A6G	ENSP00000287022:A6G	A	-	2	0	UQCRB	97316918	0.018000	0.18449	0.005000	0.12908	0.023000	0.10783	2.217000	0.42880	2.323000	0.78572	0.655000	0.94253	GCC		0.532	UQCRB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379863.1	NM_006294	
ABCA12	26154	hgsc.bcm.edu	37	2	215914348	215914348	+	Splice_Site	SNP	A	A	T			TCGA-09-1666-01A-01W-0615-10	TCGA-09-1666-10A-01W-0616-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_III	WXS	Sanger_PCR_WGA			SOLID	89624b91-5fc5-4a15-9793-588d7b033703	6a789747-4a8c-4678-ae32-37789b17855d	g.chr2:215914348A>T	ENST00000272895.7	-	6	913		c.e6+1			NM_173076.2	NP_775099.2	Q86UK0	ABCAC_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 12						cellular homeostasis (GO:0019725)|ceramide transport (GO:0035627)|establishment of skin barrier (GO:0061436)|keratinization (GO:0031424)|lipid homeostasis (GO:0055088)|lipid transport (GO:0006869)|lung alveolus development (GO:0048286)|phospholipid efflux (GO:0033700)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of protein localization to cell surface (GO:2000010)|protein localization to plasma membrane (GO:0072659)|regulated secretory pathway (GO:0045055)|secretion by cell (GO:0032940)|surfactant homeostasis (GO:0043129)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|epidermal lamellar body (GO:0097209)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)	apolipoprotein A-I receptor binding (GO:0034191)|ATP binding (GO:0005524)|lipid transporter activity (GO:0005319)|lipid-transporting ATPase activity (GO:0034040)|receptor binding (GO:0005102)	p.?(1)		NS(3)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(45)|lung(44)|ovary(8)|pancreas(2)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	139		Renal(323;0.127)		Epithelial(149;1.01e-05)|all cancers(144;0.00112)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.011)		ATCTACACTCACCTGGGAGAA	0.383																																					Ovarian(66;664 1488 5121 34295)											1	Unknown(1)	ovary(1)	2											70.0	68.0	69.0					2																	215914348		2203	4300	6503	215622593	SO:0001630	splice_region_variant	26154			AF418105	CCDS33372.1, CCDS33373.1	2q34	2012-03-14			ENSG00000144452	ENSG00000144452		"""ATP binding cassette transporters / subfamily A"""	14637	protein-coding gene	gene with protein product		607800	"""ichthyosis congenita II, lamellar ichthyosis B"""	ICR2B		11435397, 12915478, 8845852, 10094194	Standard	NM_015657		Approved	DKFZP434G232, LI2	uc002vew.3	Q86UK0	OTTHUMG00000154801	ENST00000272895.7:c.693+1T>A	2.37:g.215914348A>T			215622593	Q53QE2|Q53S55|Q8IZW6|Q96JT3|Q9Y4M5	Splice_Site	SNP	ENST00000272895.7	37	CCDS33372.1	.	.	.	.	.	.	.	.	.	.	A	20.7	4.035200	0.75617	.	.	ENSG00000144452	ENST00000272895	.	.	.	5.75	5.75	0.90469	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.874	0.63643	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	ABCA12	215622593	1.000000	0.71417	1.000000	0.80357	0.847000	0.48162	4.964000	0.63701	2.323000	0.78572	0.533000	0.62120	.		0.383	ABCA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337111.1	NM_173076	Intron
APEH	327	hgsc.bcm.edu	37	3	49712671	49712671	+	Nonsense_Mutation	SNP	C	C	A			TCGA-09-1666-01A-01W-0615-10	TCGA-09-1666-10A-01W-0616-10	C	C	A	A	C	C	Unknown	Valid	Somatic	Phase_III	WXS	Sanger_PCR_WGA			SOLID	89624b91-5fc5-4a15-9793-588d7b033703	6a789747-4a8c-4678-ae32-37789b17855d	g.chr3:49712671C>A	ENST00000296456.5	+	3	601	c.201C>A	c.(199-201)taC>taA	p.Y67*	APEH_ENST00000438011.1_Nonsense_Mutation_p.Y67*	NM_001640.3	NP_001631.3	P13798	ACPH_HUMAN	acylaminoacyl-peptide hydrolase	67					beta-amyloid metabolic process (GO:0050435)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear membrane (GO:0031965)	omega peptidase activity (GO:0008242)|poly(A) RNA binding (GO:0044822)|serine-type endopeptidase activity (GO:0004252)	p.Y67*(1)		endometrium(3)|large_intestine(1)|lung(6)|ovary(1)|skin(1)|stomach(2)|urinary_tract(1)	15				BRCA - Breast invasive adenocarcinoma(193;4.53e-05)|Kidney(197;0.00218)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)		GCCGCCAATACCTGGTGTTCC	0.577																																																1	Substitution - Nonsense(1)	ovary(1)	3											111.0	96.0	101.0					3																	49712671		2203	4300	6503	49687675	SO:0001587	stop_gained	327			D38441	CCDS2801.1	3p21	2013-05-29	2013-05-29		ENSG00000164062	ENSG00000164062	3.4.19.1		586	protein-coding gene	gene with protein product	"""acylaminoacyl-peptidase"""	102645	"""N-acylaminoacyl-peptide hydrolase"""	D3F15S2, DNF15S2, D3S48E		2392324	Standard	NM_001640		Approved		uc003cxf.3	P13798	OTTHUMG00000156882	ENST00000296456.5:c.201C>A	3.37:g.49712671C>A	ENSP00000296456:p.Tyr67*		49687675	Q9BQ33|Q9P0Y2	Nonsense_Mutation	SNP	ENST00000296456.5	37	CCDS2801.1	.	.	.	.	.	.	.	.	.	.	C	38	6.926449	0.97940	.	.	ENSG00000164062	ENST00000296456;ENST00000438011;ENST00000457042	.	.	.	4.63	1.67	0.24075	.	0.125794	0.56097	D	0.000034	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-27.1109	9.8844	0.41253	0.0:0.7496:0.0:0.2504	.	.	.	.	X	67;67;64	.	ENSP00000296456:Y67X	Y	+	3	2	APEH	49687675	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	2.431000	0.44775	0.450000	0.26774	0.655000	0.94253	TAC		0.577	APEH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346415.2		
DNMT1	1786	hgsc.bcm.edu	37	19	10248608	10248608	+	Missense_Mutation	SNP	G	G	A	rs375225009		TCGA-09-1666-01A-01W-0615-10	TCGA-09-1666-10A-01W-0616-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_III	WXS	Sanger_PCR_WGA			SOLID	89624b91-5fc5-4a15-9793-588d7b033703	6a789747-4a8c-4678-ae32-37789b17855d	g.chr19:10248608G>A	ENST00000340748.4	-	35	4380	c.4145C>T	c.(4144-4146)tCg>tTg	p.S1382L	DNMT1_ENST00000540357.1_Missense_Mutation_p.S1382L|DNMT1_ENST00000359526.4_Missense_Mutation_p.S1398L|DNMT1_ENST00000589538.1_5'Flank			P26358	DNMT1_HUMAN	DNA (cytosine-5-)-methyltransferase 1	1382	Catalytic.|Interaction with the PRC2/EED-EZH2 complex. {ECO:0000250}.|SAM-dependent MTase C5-type. {ECO:0000255|PROSITE-ProRule:PRU01016}.				cellular response to amino acid stimulus (GO:0071230)|chromatin modification (GO:0016568)|DNA methylation (GO:0006306)|gene silencing (GO:0016458)|maintenance of DNA methylation (GO:0010216)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of gene expression (GO:0010628)|positive regulation of histone H3-K4 methylation (GO:0051571)|regulation of cell proliferation (GO:0042127)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|pericentric heterochromatin (GO:0005721)|replication fork (GO:0005657)	chromatin binding (GO:0003682)|DNA (cytosine-5-)-methyltransferase activity (GO:0003886)|DNA binding (GO:0003677)|DNA-methyltransferase activity (GO:0009008)|methyl-CpG binding (GO:0008327)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)	p.S1382L(1)		breast(5)|endometrium(8)|kidney(5)|large_intestine(21)|lung(11)|ovary(2)|pancreas(1)|prostate(10)|skin(5)|stomach(1)|urinary_tract(1)	70			OV - Ovarian serous cystadenocarcinoma(20;1.59e-09)|Epithelial(33;2.86e-06)|all cancers(31;6.68e-06)		Azacitidine(DB00928)|Decitabine(DB01262)|Flucytosine(DB01099)|Procainamide(DB01035)	CTCCAGTGCCGAGGCTCCATT	0.622																																																1	Substitution - Missense(1)	ovary(1)	19						G	LEU/SER,LEU/SER	0,4406		0,0,2203	65.0	49.0	54.0		4193,4145	4.3	0.0	19		54	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	DNMT1	NM_001130823.1,NM_001379.2	145,145	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	possibly-damaging,possibly-damaging	1398/1633,1382/1617	10248608	1,13005	2203	4300	6503	10109608	SO:0001583	missense	1786			X63692	CCDS12228.1, CCDS45958.1	19p13.2	2014-09-17				ENSG00000130816	2.1.1.37		2976	protein-coding gene	gene with protein product		126375		DNMT		1594447	Standard	NM_001379		Approved	MCMT, CXXC9	uc010xlc.2	P26358		ENST00000340748.4:c.4145C>T	19.37:g.10248608G>A	ENSP00000345739:p.Ser1382Leu		10109608	A0AV63|B7ZLW6|Q9UHG5|Q9ULA2|Q9UMZ6	Missense_Mutation	SNP	ENST00000340748.4	37	CCDS12228.1	.	.	.	.	.	.	.	.	.	.	G	17.50	3.405251	0.62288	0.0	1.16E-4	ENSG00000130816	ENST00000359526;ENST00000540357;ENST00000340748;ENST00000541266	D;D;D	0.84223	-1.82;-1.82;-1.82	5.38	4.34	0.51931	.	0.121936	0.56097	D	0.000027	D	0.86703	0.5996	M	0.64630	1.985	0.48185	D	0.999608	P;P;D	0.53619	0.952;0.952;0.961	P;P;P	0.50537	0.51;0.51;0.643	D	0.87259	0.2278	10	0.59425	D	0.04	.	13.1521	0.59494	0.0795:0.0:0.9205:0.0	.	1382;1398;1382	F5GX68;P26358-2;P26358	.;.;DNMT1_HUMAN	L	1398;1382;1382;1250	ENSP00000352516:S1398L;ENSP00000440457:S1382L;ENSP00000345739:S1382L	ENSP00000345739:S1382L	S	-	2	0	DNMT1	10109608	1.000000	0.71417	0.015000	0.15790	0.008000	0.06430	9.416000	0.97383	1.255000	0.44051	0.655000	0.94253	TCG		0.622	DNMT1-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451166.1	NM_001379	
OCA2	4948	hgsc.bcm.edu	37	15	28196959	28196959	+	Missense_Mutation	SNP	G	G	C			TCGA-09-1666-01A-01W-0615-10	TCGA-09-1666-10A-01W-0616-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_III	WXS	Sanger_PCR_WGA			SOLID	89624b91-5fc5-4a15-9793-588d7b033703	6a789747-4a8c-4678-ae32-37789b17855d	g.chr15:28196959G>C	ENST00000354638.3	-	18	2077	c.1922C>G	c.(1921-1923)tCg>tGg	p.S641W	OCA2_ENST00000353809.5_Missense_Mutation_p.S617W|OCA2_ENST00000382996.2_Missense_Mutation_p.S641W	NM_000275.2	NP_000266.2	Q04671	P_HUMAN	oculocutaneous albinism II	641					cell proliferation (GO:0008283)|eye pigment biosynthetic process (GO:0006726)|melanin biosynthetic process (GO:0042438)|melanocyte differentiation (GO:0030318)|spermatid development (GO:0007286)|tyrosine transport (GO:0015828)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|melanosome membrane (GO:0033162)	L-tyrosine transmembrane transporter activity (GO:0005302)|transporter activity (GO:0005215)	p.S641W(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(11)|lung(48)|ovary(4)|pancreas(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	85		all_lung(180;2.93e-12)|Breast(32;0.000315)|Colorectal(260;0.234)		all cancers(64;5.03e-07)|Epithelial(43;2.13e-06)|BRCA - Breast invasive adenocarcinoma(123;0.045)		AGGGACAAACGAATTGAGGAA	0.443									Oculocutaneous Albinism																																							1	Substitution - Missense(1)	ovary(1)	15											177.0	137.0	151.0					15																	28196959		2203	4300	6503	25870554	SO:0001583	missense	4948	Familial Cancer Database			CCDS10020.1, CCDS73701.1	15q12	2013-01-08	2008-01-30		ENSG00000104044	ENSG00000104044			8101	protein-coding gene	gene with protein product	"""melanocyte-specific transporter protein"""	611409	"""oculocutaneous albinism II (pink-eye dilution (murine) homolog)"", ""eye color 3 (brown)"", ""eye color 2 (central brown)"", ""oculocutaneous albinism II (pink-eye dilution homolog, mouse)"""	D15S12, P, EYCL3, EYCL2			Standard	NM_000275		Approved	BEY2, EYCL, BEY, BEY1	uc001zbh.4	Q04671	OTTHUMG00000128871	ENST00000354638.3:c.1922C>G	15.37:g.28196959G>C	ENSP00000346659:p.Ser641Trp		25870554	Q15211|Q15212|Q96EN1|Q9UMI5	Missense_Mutation	SNP	ENST00000354638.3	37	CCDS10020.1	.	.	.	.	.	.	.	.	.	.	G	21.3	4.125294	0.77436	.	.	ENSG00000104044	ENST00000354638;ENST00000353809;ENST00000382996	D;D;D	0.91843	-1.5;-1.5;-2.92	5.37	5.37	0.77165	Divalent ion symporter (1);	0.066681	0.64402	D	0.000006	D	0.96993	0.9018	M	0.92555	3.32	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.997;0.999	D	0.97835	1.0265	10	0.87932	D	0	-13.1334	16.6066	0.84831	0.0:0.0:1.0:0.0	.	617;641	Q04671-2;Q04671	.;P_HUMAN	W	641;617;641	ENSP00000346659:S641W;ENSP00000261276:S617W;ENSP00000372457:S641W	ENSP00000261276:S617W	S	-	2	0	OCA2	25870554	1.000000	0.71417	0.850000	0.33497	0.831000	0.47069	8.681000	0.91228	2.516000	0.84829	0.655000	0.94253	TCG		0.443	OCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250823.1	NM_000275	
TNS1	7145	hgsc.bcm.edu	37	2	218712478	218712478	+	Missense_Mutation	SNP	T	T	C			TCGA-09-1666-01A-01W-0615-10	TCGA-09-1666-10A-01W-0616-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_III	WXS	Sanger_PCR_WGA			SOLID	89624b91-5fc5-4a15-9793-588d7b033703	6a789747-4a8c-4678-ae32-37789b17855d	g.chr2:218712478T>C	ENST00000171887.4	-	17	2839	c.2387A>G	c.(2386-2388)tAt>tGt	p.Y796C	TNS1_ENST00000419504.1_Missense_Mutation_p.Y796C|TNS1_ENST00000480665.1_5'Flank|TNS1_ENST00000430930.1_Missense_Mutation_p.Y796C	NM_022648.4	NP_072174.3	Q9HBL0	TENS1_HUMAN	tensin 1	796					cell-substrate junction assembly (GO:0007044)|fibroblast migration (GO:0010761)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)	poly(A) RNA binding (GO:0044822)	p.Y796C(1)		breast(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(23)|liver(1)|lung(24)|ovary(3)|pancreas(1)|prostate(3)|skin(5)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	79		Renal(207;0.0483)|Lung NSC(271;0.213)		Epithelial(149;4.43e-06)|all cancers(144;0.000653)|LUSC - Lung squamous cell carcinoma(224;0.0091)|Lung(261;0.013)		CTGATAGTCATAAGGTGAGTA	0.577																																																1	Substitution - Missense(1)	ovary(1)	2											70.0	57.0	62.0					2																	218712478		2203	4300	6503	218420723	SO:0001583	missense	7145			AB209238	CCDS2407.1	2q35-q36	2014-06-13	2005-05-13	2005-05-13	ENSG00000079308	ENSG00000079308		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"", ""SH2 domain containing"""	11973	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 155"""	600076	"""tensin"", ""matrix-remodelling associated 6"""	TNS, MXRA6			Standard	NM_022648		Approved	DKFZp586K0617, PPP1R155	uc002vgt.2	Q9HBL0	OTTHUMG00000133056	ENST00000171887.4:c.2387A>G	2.37:g.218712478T>C	ENSP00000171887:p.Tyr796Cys		218420723	Q4ZG71|Q6IPI5	Missense_Mutation	SNP	ENST00000171887.4	37	CCDS2407.1	.	.	.	.	.	.	.	.	.	.	T	12.31	1.899790	0.33535	.	.	ENSG00000079308	ENST00000171887;ENST00000419504;ENST00000430930	D;D;D	0.91521	-2.85;-2.86;-2.85	4.11	4.11	0.48088	.	0.170785	0.22544	U	0.058699	D	0.90058	0.6895	N	0.24115	0.695	0.80722	D	1	D;D;D;D;D	0.76494	0.997;0.998;0.998;0.999;0.998	P;P;P;P;P	0.61592	0.891;0.818;0.818;0.887;0.818	D	0.90623	0.4561	10	0.54805	T	0.06	.	13.2705	0.60157	0.0:0.0:0.0:1.0	.	796;850;796;796;796	B2RU35;A1L0S7;Q9HBL0;E9PGF5;E9PF55	.;.;TENS1_HUMAN;.;.	C	796	ENSP00000171887:Y796C;ENSP00000408724:Y796C;ENSP00000406016:Y796C	ENSP00000171887:Y796C	Y	-	2	0	TNS1	218420723	1.000000	0.71417	1.000000	0.80357	0.364000	0.29643	4.220000	0.58567	1.705000	0.51264	0.379000	0.24179	TAT		0.577	TNS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256672.2	NM_022648	
