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	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	ref_context	gc_content	COSMIC_n_overlapping_mutations	ESP_AvgAAsampleReadDepth	ESP_AvgEAsampleReadDepth	ESP_AvgSampleReadDepth	ESP_Chromosome	ESP_Position	ESP_TotalAAsamplesCovered	ESP_TotalEAsamplesCovered	ESP_TotalSamplesCovered	Ensembl_so_accession	Ensembl_so_term	HGNC_AccessionNumbers	HGNC_CCDSIDs	HGNC_Chromosome	HGNC_DateModified	HGNC_DateNameChanged	HGNC_DateSymbolChanged	HGNC_EnsemblGeneID	HGNC_EnsemblIDsuppliedbyEnsembl	HGNC_Genefamilydescription	HGNC_HGNCID	HGNC_LocusGroup	HGNC_LocusType	HGNC_NameSynonyms	HGNC_OMIMIDsuppliedbyNCBI	HGNC_PreviousNames	HGNC_PreviousSymbols	HGNC_PubmedIDs	HGNC_RecordType	HGNC_RefSeqsuppliedbyNCBI	HGNC_Status	HGNC_Synonyms	HGNC_UCSCIDsuppliedbyUCSC	HGNC_UniProtIDsuppliedbyUniProt	HGNC_VEGAIDs	HGVS_coding_DNA_change	HGVS_genomic_change	HGVS_protein_change	UniProt_alt_uniprot_accessions	annotation_transcript	build	ccds_id	dbNSFP_1000Gp1_AC	dbNSFP_1000Gp1_AF	dbNSFP_1000Gp1_AFR_AC	dbNSFP_1000Gp1_AFR_AF	dbNSFP_1000Gp1_AMR_AC	dbNSFP_1000Gp1_AMR_AF	dbNSFP_1000Gp1_ASN_AC	dbNSFP_1000Gp1_ASN_AF	dbNSFP_1000Gp1_EUR_AC	dbNSFP_1000Gp1_EUR_AF	dbNSFP_Ancestral_allele	dbNSFP_CADD_phred	dbNSFP_CADD_raw	dbNSFP_CADD_raw_rankscore	dbNSFP_ESP6500_AA_AF	dbNSFP_ESP6500_EA_AF	dbNSFP_Ensembl_geneid	dbNSFP_Ensembl_transcriptid	dbNSFP_FATHMM_pred	dbNSFP_FATHMM_rankscore	dbNSFP_FATHMM_score	dbNSFP_GERP_NR	dbNSFP_GERP_RS	dbNSFP_GERP_RS_rankscore	dbNSFP_Interpro_domain	dbNSFP_LRT_Omega	dbNSFP_LRT_converted_rankscore	dbNSFP_LRT_pred	dbNSFP_LRT_score	dbNSFP_LR_pred	dbNSFP_LR_rankscore	dbNSFP_LR_score	dbNSFP_MutationAssessor_pred	dbNSFP_MutationAssessor_rankscore	dbNSFP_MutationAssessor_score	dbNSFP_MutationTaster_converted_rankscore	dbNSFP_MutationTaster_pred	dbNSFP_MutationTaster_score	dbNSFP_Polyphen2_HDIV_pred	dbNSFP_Polyphen2_HDIV_rankscore	dbNSFP_Polyphen2_HDIV_score	dbNSFP_Polyphen2_HVAR_pred	dbNSFP_Polyphen2_HVAR_rankscore	dbNSFP_Polyphen2_HVAR_score	dbNSFP_RadialSVM_pred	dbNSFP_RadialSVM_rankscore	dbNSFP_RadialSVM_score	dbNSFP_Reliability_index	dbNSFP_SIFT_converted_rankscore	dbNSFP_SIFT_pred	dbNSFP_SIFT_score	dbNSFP_SLR_test_statistic	dbNSFP_SiPhy_29way_logOdds	dbNSFP_SiPhy_29way_logOdds_rankscore	dbNSFP_SiPhy_29way_pi	dbNSFP_UniSNP_ids	dbNSFP_Uniprot_aapos	dbNSFP_Uniprot_acc	dbNSFP_Uniprot_id	dbNSFP_aaalt	dbNSFP_aapos	dbNSFP_aapos_FATHMM	dbNSFP_aapos_SIFT	dbNSFP_aaref	dbNSFP_cds_strand	dbNSFP_codonpos	dbNSFP_folddegenerate	dbNSFP_genename	dbNSFP_hg18_pos1coor	dbNSFP_phastCons100way_vertebrate	dbNSFP_phastCons100way_vertebrate_rankscore	dbNSFP_phastCons46way_placental	dbNSFP_phastCons46way_placental_rankscore	dbNSFP_phastCons46way_primate	dbNSFP_phastCons46way_primate_rankscore	dbNSFP_phyloP100way_vertebrate	dbNSFP_phyloP100way_vertebrate_rankscore	dbNSFP_phyloP46way_placental	dbNSFP_phyloP46way_placental_rankscore	dbNSFP_phyloP46way_primate	dbNSFP_phyloP46way_primate_rankscore	dbNSFP_refcodon	gencode_transcript_name	gencode_transcript_status	gencode_transcript_tags	gencode_transcript_type	gene_type	havana_transcript	init_n_lod	init_t_lod	isArtifactMode	n_alt_count	n_ref_count	oxoGCut	pox	pox_cutoff	qox	refseq_mrna_id	t_alt_count	t_lod_fstar	t_ref_count	tumor_f
LRP1B	53353	broad.mit.edu	hg19	2	141201962	141201962	+	Missense_Mutation	SNP	G	G	A			TCGA-V4-A9EL-01A-11D-A39W-08	TCGA-V4-A9EL-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6bf15a15-4a35-4e55-9c10-770fdff09fad	9dc7146a-1ee2-431a-a6b8-b8e9f16417c7	g.chr2:141201962G>A	ENST00000389484.3	-	65	11202	c.10231C>T	c.(10231-10233)Cca>Tca	p.P3411S		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	3411	LDL-receptor class A 23.	protein transport|receptor-mediated endocytosis	integral to membrane	calcium ion binding	NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)	AAGTTTACTGGGATACATTTC	0.393	0	203.0	189.0	194.0	2	141201962	2203	4300	6503	SO:0001583	missense	AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702	"""Low density lipoprotein receptors"""	6693	protein-coding gene	gene with protein product	"""LRP-deleted in tumors"""	608766			10766186	Standard	NM_018557	Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.10231C>T	2.37:g.141201962G>A	ENSP00000374135:p.Pro3411Ser	Q8WY29|Q8WY30|Q8WY31	ENST00000389484.3	37	CCDS2182.1	.	.	.	.	.	.	.	.	.	.	G	27.8	4.866382	0.91511	.	.	ENSG00000168702	ENST00000389484;ENST00000544579	D	0.95554	-3.74	5.42	5.42	0.78866	Low-density lipoprotein (LDL) receptor class A, conserved site (1);	0.000000	0.85682	U	0.000000	D	0.96231	0.8771	L	0.37800	1.135	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.94538	0.7742	10	0.25751	T	0.34	.	19.4095	0.94665	0.0:0.0:1.0:0.0	.	3411	Q9NZR2	LRP1B_HUMAN	S	3411;3349	ENSP00000374135:P3411S	ENSP00000374135:P3411S	P	-	1	0	LRP1B	140918432	1.000000	0.71417	0.998000	0.56505	0.873000	0.50193	9.601000	0.98297	2.817000	0.96982	0.563000	0.77884	CCA	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2		183.430693	0	7	109	0	0	1	0	NM_018557	58	184.132170	79	0.423358
CSNK1A1P1	0	broad.mit.edu	hg19	15	37109490	37109490	+	RNA	SNP	C	C	T			TCGA-V4-A9EL-01A-11D-A39W-08	TCGA-V4-A9EL-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6bf15a15-4a35-4e55-9c10-770fdff09fad	9dc7146a-1ee2-431a-a6b8-b8e9f16417c7	g.chr15:37109490C>T	ENST00000430593.3	-	0	733					NR_027320.1																GATCAGGGTCCTGAAAAGAAT	0.473	0											BC028192		15q13.3	2010-09-21	2010-07-20	2010-07-20		ENSG00000223518		30446	pseudogene	pseudogene			"""casein kinase 1, alpha 1 pseudogene"""	CSNK1A1P		Standard	NR_027320	Approved		uc001zjg.4				15.37:g.37109490C>T			ENST00000430593.3	37																																																																																				CSNK1A1P1-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000419759.1		22.389637	0	-2	49	0	0	1	0	NR_027320	8	23.391509	19	0.296296
RTTN	25914	ucsc.edu	hg19	18	67776945	67776945	+	Missense_Mutation	SNP	G	G	A			TCGA-V4-A9EL-01A-11D-A39W-08	TCGA-V4-A9EL-10A-01D-A39Z-08	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	6bf15a15-4a35-4e55-9c10-770fdff09fad	9dc7146a-1ee2-431a-a6b8-b8e9f16417c7																										AAGAAGTTCCGAGCATTTCCT	0.438	0	43.0	43.0	43.0	18	67776945	1872	4104	5976	SO:0001583	missense	AL117635	CCDS42443.1	18q22.1	2008-08-01				ENSG00000176225		18654	protein-coding gene	gene with protein product		610436			11900971	Standard	NM_173630	Approved	DKFZP434G145	uc002lkp.2	Q86VV8		ENST00000255674.6:c.3692C>T	18.37:g.67776945G>A	ENSP00000255674:p.Ser1231Leu	Q68CS9|Q6ZRL8|Q6ZTK3|Q86TG4|Q8N8N8|Q8TBQ4|Q96IN9|Q9UFJ4	ENST00000255674.6	37	CCDS42443.1	.	.	.	.	.	.	.	.	.	.	G	2.235	-0.375116	0.05034	2.67E-4	0.0	ENSG00000176225	ENST00000255674;ENST00000437017	T;T	0.68479	-0.33;-0.33	5.08	-0.495	0.12030	.	0.291643	0.29362	N	0.012375	T	0.17534	0.0421	N	0.00128	-2.045	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.40421	-0.9564	10	0.02654	T	1	.	5.6031	0.17365	0.6496:0.133:0.2174:0.0	.	1231	Q86VV8	RTTN_HUMAN	L	1231	ENSP00000255674:S1231L;ENSP00000399520:S1231L	ENSP00000255674:S1231L	S	-	2	0	RTTN	65927925	0.872000	0.30054	0.700000	0.30305	0.943000	0.58893	1.381000	0.34362	-0.264000	0.09365	-0.440000	0.05779	TCG	RTTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442988.1				-17	28					NM_173630	4		32	
LMLN	89782	broad.mit.edu	hg19	3	197710814	197710814	+	Splice_Site	SNP	G	G	A			TCGA-V4-A9EL-01A-11D-A39W-08	TCGA-V4-A9EL-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6bf15a15-4a35-4e55-9c10-770fdff09fad	9dc7146a-1ee2-431a-a6b8-b8e9f16417c7	g.chr3:197710814G>A	ENST00000330198.4	+	7	751	c.729G>A	c.(727-729)agG>agA	p.R243R	LMLN_ENST00000482695.1_Splice_Site_p.R191R|LMLN_ENST00000420910.2_Splice_Site_p.R243R|LMLN_ENST00000332636.5_Splice_Site_p.R191R	NM_033029.3	NP_149018.2	Q96KR4	LMLN_HUMAN	leishmanolysin-like (metallopeptidase M8 family)	243		cell adhesion|cell division|mitosis|proteolysis	cytoplasm|membrane	metalloendopeptidase activity|zinc ion binding	endometrium(3)|kidney(2)|large_intestine(4)|lung(12)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	25	all_cancers(143;1.15e-09)|Ovarian(172;0.0418)|Breast(254;0.0976)	Lung NSC(153;0.132)	Epithelial(36;9.84e-24)|all cancers(36;3.18e-22)|OV - Ovarian serous cystadenocarcinoma(49;5.35e-19)|LUSC - Lung squamous cell carcinoma(58;6.94e-07)|Lung(62;9.92e-07)	GBM - Glioblastoma multiforme(93;0.111)	GTTTTGACAGGCCAATAGCAG	0.368	0	127.0	113.0	118.0	3	197710814	2203	4300	6503	SO:0001630	splice_region_variant	AJ312398	CCDS3332.1, CCDS46988.1	3q29	2008-02-04			ENSG00000185621	ENSG00000185621		15991	protein-coding gene	gene with protein product		609380				Standard	NM_033029	Approved	Gp63, Msp	uc010iar.3	Q96KR4	OTTHUMG00000155375	ENST00000420910.2:c.729-1G>A	3.37:g.197710814G>A		B3LDG9|B3LDH0|C9J796|F8WB28|Q96KR5	ENST00000420910.2	37	CCDS46988.1																																																																																			LMLN-004	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000339704.1		-6.125926	0	11	77	0	0	1	0	NM_033029	3	6.483899	56	0.050847
EWSR1	2130	broad.mit.edu	hg19	22	29674050	29674050	+	Nonsense_Mutation	SNP	C	C	G			TCGA-V4-A9EL-01A-11D-A39W-08	TCGA-V4-A9EL-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6bf15a15-4a35-4e55-9c10-770fdff09fad	9dc7146a-1ee2-431a-a6b8-b8e9f16417c7	g.chr22:29674050C>G	ENST00000397938.2	+	5	577	c.258C>G	c.(256-258)taC>taG	p.Y86*	EWSR1_ENST00000414183.2_Nonsense_Mutation_p.Y92*|EWSR1_ENST00000331029.7_Nonsense_Mutation_p.Y86*|EWSR1_ENST00000332050.6_Nonsense_Mutation_p.Y86*|EWSR1_ENST00000406548.1_Nonsense_Mutation_p.Y86*|EWSR1_ENST00000332035.6_Nonsense_Mutation_p.Y86*|EWSR1_ENST00000333395.6_Nonsense_Mutation_p.Y86*	NM_001163285.1|NM_001163286.1|NM_005243.3|NM_013986.3	NP_001156757.1|NP_001156758.1|NP_005234.1|NP_053733.2	Q01844	EWS_HUMAN	EWS RNA-binding protein 1	86	31 X approximate tandem repeats.|EAD (Gln/Pro/Thr-rich).	regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus|plasma membrane	calmodulin binding|nucleotide binding|RNA binding|zinc ion binding	breast(2)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|liver(1)|lung(6)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	26					CCCAGGCATACAGCCAGCCTG	0.527	0	35.0	36.0	35.0	22	29674050	2203	4300	6503	SO:0001587	stop_gained		CCDS13851.1, CCDS13852.1, CCDS13852.2, CCDS54512.1, CCDS54513.1, CCDS54514.1	22q12.2	2013-05-24	2013-05-24		ENSG00000182944	ENSG00000182944	"""RNA binding motif (RRM) containing"""	3508	protein-coding gene	gene with protein product		133450	"""Ewing sarcoma breakpoint region 1"""		1522903	Standard	NM_005243	Approved	EWS	uc003aev.3	Q01844	OTTHUMG00000151107	ENST00000414183.2:c.276C>G	22.37:g.29674050C>G	ENSP00000400142:p.Tyr92*	B0QYK1|Q5THL0|Q92635|Q96FE8|Q96MN4|Q96MX4|Q9BWA2	ENST00000414183.2	37	CCDS13852.2	.	.	.	.	.	.	.	.	.	.	C	17.75	3.466621	0.63625	.	.	ENSG00000182944	ENST00000332050;ENST00000397938;ENST00000436425;ENST00000447973;ENST00000406548;ENST00000437155;ENST00000331029;ENST00000414183;ENST00000333395;ENST00000455726;ENST00000332035	.	.	.	5.31	2.09	0.27110	.	0.000000	0.64402	U	0.000002	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	8.3611	0.32359	0.0:0.6285:0.0:0.3715	.	.	.	.	X	86;86;93;92;86;87;86;92;86;86;86	.	ENSP00000330516:Y86X	Y	+	3	2	EWSR1	28004050	0.968000	0.33430	0.998000	0.56505	0.992000	0.81027	0.039000	0.13884	0.325000	0.23359	-0.142000	0.14014	TAC	EWSR1-021	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000358290.1		38.527190	0	17	42	0	0	1	0	NM_005243	11	38.570690	9	0.550000
GNAQ	2776	broad.mit.edu	hg19	9	80409488	80409488	+	Missense_Mutation	SNP	T	T	A	rs121913492		TCGA-V4-A9EL-01A-11D-A39W-08	TCGA-V4-A9EL-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6bf15a15-4a35-4e55-9c10-770fdff09fad	9dc7146a-1ee2-431a-a6b8-b8e9f16417c7	g.chr9:80409488T>A	ENST00000286548.4	-	5	848	c.626A>T	c.(625-627)cAa>cTa	p.Q209L	GNAQ_ENST00000397476.3_Missense_Mutation_p.Q7L	NM_002072.3	NP_002063.2	P50148	GNAQ_HUMAN	guanine nucleotide binding protein (G protein), q polypeptide	209		activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity by dopamine receptor signaling pathway|glutamate signaling pathway|negative regulation of protein kinase activity|platelet activation|protein ADP-ribosylation|protein stabilization|regulation of action potential|regulation of catenin import into nucleus	cytoplasm|heterotrimeric G-protein complex	G-protein beta/gamma-subunit complex binding|G-protein-coupled receptor binding|GTP binding|GTPase activator activity|GTPase activity|signal transducer activity	NS(1)|endometrium(3)|eye(229)|kidney(1)|large_intestine(4)|lung(6)|meninges(11)|ovary(1)|prostate(1)|skin(44)|upper_aerodigestive_tract(1)	302					CTCTGACCTTTGGCCCCCTAC	0.348	153	108.0	105.0	106.0	9	80409488	2203	4300	6503	SO:0001583	missense		CCDS6658.1	9q21	2010-03-17			ENSG00000156052	ENSG00000156052		4390	protein-coding gene	gene with protein product		600998			8825633	Standard	NM_002072	Approved	G-ALPHA-q, GAQ	uc004akw.3	P50148	OTTHUMG00000020059	ENST00000286548.4:c.626A>T	9.37:g.80409488T>A	ENSP00000286548:p.Gln209Leu	O15108|Q13462|Q6NT27|Q92471|Q9BZB9	ENST00000286548.4	37	CCDS6658.1	.	.	.	.	.	.	.	.	.	.	T	29.2	4.985495	0.93044	.	.	ENSG00000156052	ENST00000286548;ENST00000397476	D;D	0.91237	-2.81;-2.81	5.69	5.69	0.88448	.	0.000000	0.85682	D	0.000000	D	0.97573	0.9205	H	0.99347	4.525	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.99402	1.0928	10	0.87932	D	0	.	15.9502	0.79827	0.0:0.0:0.0:1.0	.	209	P50148	GNAQ_HUMAN	L	209;7	ENSP00000286548:Q209L;ENSP00000443197:Q7L	ENSP00000286548:Q209L	Q	-	2	0	GNAQ	79599308	1.000000	0.71417	0.999000	0.59377	0.995000	0.86356	8.040000	0.89188	2.167000	0.68274	0.460000	0.39030	CAA	GNAQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052761.1		145.834004	0	-7	105	0	0	1	0	NM_002072	46	146.411989	63	0.422018
SYTL3	94120	broad.mit.edu	hg19	6	159181693	159181693	+	Missense_Mutation	SNP	G	G	A			TCGA-V4-A9EL-01A-11D-A39W-08	TCGA-V4-A9EL-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6bf15a15-4a35-4e55-9c10-770fdff09fad	9dc7146a-1ee2-431a-a6b8-b8e9f16417c7	g.chr6:159181693G>A	ENST00000297239.9	+	14	1524	c.1330G>A	c.(1330-1332)Gtt>Att	p.V444I	SYTL3_ENST00000360448.3_Missense_Mutation_p.V376I|SYTL3_ENST00000367081.3_Missense_Mutation_p.V170I			Q4VX76	SYTL3_HUMAN	synaptotagmin-like 3	444		intracellular protein transport	endomembrane system|membrane	Rab GTPase binding	endometrium(2)|kidney(3)|large_intestine(5)|lung(7)|ovary(1)|pancreas(1)|urinary_tract(1)	20		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;1.54e-17)|BRCA - Breast invasive adenocarcinoma(81;8.24e-06)	CGAAGACAGCGTTCCTCAGAG	0.557	0	123.0	114.0	117.0	6	159181693	2203	4300	6503	SO:0001583	missense	AK055750	CCDS34563.1, CCDS56458.1	6q25.3	2008-07-04			ENSG00000164674	ENSG00000164674		15587	protein-coding gene	gene with protein product					11773082	Standard	NM_001242384	Approved	SLP3, exophilin-6	uc003qrp.3	Q4VX76	OTTHUMG00000015916	ENST00000297239.9:c.1330G>A	6.37:g.159181693G>A	ENSP00000297239:p.Val444Ile	Q496J4|Q496J6|Q5U3B9	ENST00000297239.9	37	CCDS56458.1	.	.	.	.	.	.	.	.	.	.	G	7.930	0.740384	0.15642	.	.	ENSG00000164674	ENST00000360448;ENST00000543689;ENST00000297239;ENST00000367081	T;T;T	0.63096	2.15;2.14;-0.02	4.3	-8.0	0.01126	.	2.784810	0.01180	N	0.007074	T	0.11452	0.0279	N	0.08118	0	0.09310	N	1	B;B;B	0.12630	0.006;0.0;0.005	B;B;B	0.09377	0.003;0.001;0.004	T	0.06144	-1.0843	10	0.15066	T	0.55	.	3.4759	0.07585	0.3914:0.3776:0.1257:0.1053	.	170;444;376	F8W7H4;Q4VX76;Q4VX76-2	.;SYTL3_HUMAN;.	I	376;444;444;170	ENSP00000353631:V376I;ENSP00000297239:V444I;ENSP00000356048:V170I	ENSP00000297239:V444I	V	+	1	0	SYTL3	159101681	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-2.851000	0.00732	-1.958000	0.01019	-0.119000	0.15052	GTT	SYTL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042876.1		137.898842	0	-24	90	0	0	1	0		41	140.364280	16	0.719298
PITRM1	10531	broad.mit.edu	hg19	10	3191920	3191920	+	Silent	SNP	G	G	A			TCGA-V4-A9EL-01A-11D-A39W-08	TCGA-V4-A9EL-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6bf15a15-4a35-4e55-9c10-770fdff09fad	9dc7146a-1ee2-431a-a6b8-b8e9f16417c7	g.chr10:3191920G>A	ENST00000380989.2	-	16	1802	c.1764C>T	c.(1762-1764)tgC>tgT	p.C588C	PITRM1-AS1_ENST00000598280.1_RNA|PITRM1_ENST00000451104.2_Silent_p.C556C|PITRM1-AS1_ENST00000601046.1_RNA|PITRM1_ENST00000380994.1_Silent_p.C146C|PITRM1_ENST00000224949.4_Silent_p.C588C	NM_001242307.1|NM_014889.3	NP_001229236.1|NP_055704.2	E7ES23	E7ES23_HUMAN	pitrilysin metallopeptidase 1	556		proteolysis		metalloendopeptidase activity|zinc ion binding	breast(2)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(5)|liver(1)|lung(5)|ovary(1)|pancreas(1)|prostate(4)|skin(1)|stomach(2)|urinary_tract(3)	33					TGGGCTGGGCGCAGTACTGAA	0.473	0	110.0	113.0	112.0	10	3191920	1889	4123	6012	SO:0001819	synonymous_variant	AB029027	CCDS55699.1, CCDS55700.1, CCDS59208.1	10p15.2	2008-07-30	2005-08-17		ENSG00000107959	ENSG00000107959		17663	protein-coding gene	gene with protein product	"""PreP peptidasome"""		"""pitrilysin metalloproteinase 1"""		1036083, 10470851, 16849325	Standard	NM_014889	Approved	MP1, KIAA1104, hMP1, PreP	uc009xhv.2	Q5JRX3	OTTHUMG00000017557	ENST00000224949.4:c.1764C>T	10.37:g.3191920G>A		B3KMJ6|B4E0J8|C9JSL2|E7ES23|O95204|Q2M2G6|Q4VBR1|Q5JRW7|Q7L5Z7|Q9BSI6|Q9BVJ5|Q9UPP8	ENST00000224949.4	37	CCDS59208.1																																																																																			PITRM1-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000046469.2		-18.695429	0	-9	103	0	0	1	0		4	7.805297	109	0.035398
NUP188	23511	broad.mit.edu	hg19	9	131760467	131760467	+	Missense_Mutation	SNP	G	G	A			TCGA-V4-A9EL-01A-11D-A39W-08	TCGA-V4-A9EL-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6bf15a15-4a35-4e55-9c10-770fdff09fad	9dc7146a-1ee2-431a-a6b8-b8e9f16417c7	g.chr9:131760467G>A	ENST00000372577.2	+	31	3410	c.3389G>A	c.(3388-3390)cGc>cAc	p.R1130H		NM_015354.1	NP_056169.1	Q5SRE5	NU188_HUMAN	nucleoporin 188kDa	1130		carbohydrate metabolic process|glucose transport|mRNA transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	nuclear pore	protein binding	breast(2)|central_nervous_system(3)|endometrium(6)|kidney(4)|large_intestine(9)|lung(20)|ovary(6)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	60					GTGGTGCGTCGCCAGCTCTTT	0.438	0	203.0	205.0	204.0	9	131760467	2203	4300	6503	SO:0001583	missense	D79991	CCDS35156.1	9q34.13	2014-01-28	2004-03-19	2004-03-24	ENSG00000095319	ENSG00000095319		17859	protein-coding gene	gene with protein product		615587	"""KIAA0169"""	KIAA0169	11029043	Standard	NM_015354	Approved		uc004bws.2	Q5SRE5	OTTHUMG00000020768	ENST00000372577.2:c.3389G>A	9.37:g.131760467G>A	ENSP00000361658:p.Arg1130His	Q14675|Q2TA87|Q7Z3K8|Q8IWF1	ENST00000372577.2	37	CCDS35156.1	.	.	.	.	.	.	.	.	.	.	G	9.043	0.990052	0.18966	.	.	ENSG00000095319	ENST00000356693;ENST00000372577	T	0.31510	1.49	5.67	2.86	0.33363	.	0.257998	0.39544	N	0.001326	T	0.20740	0.0499	L	0.36672	1.1	0.30026	N	0.813911	B;B	0.06786	0.001;0.0	B;B	0.01281	0.0;0.0	T	0.22347	-1.0219	10	0.15499	T	0.54	-2.5035	9.5606	0.39366	0.3138:0.0:0.6862:0.0	.	463;1130	E9PET9;Q5SRE5	.;NU188_HUMAN	H	1019;1130	ENSP00000361658:R1130H	ENSP00000349125:R1019H	R	+	2	0	NUP188	130800288	0.998000	0.40836	1.000000	0.80357	0.579000	0.36224	0.717000	0.25851	0.349000	0.23975	-1.149000	0.01842	CGC	NUP188-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054529.2		-84.332469	0	-94	278	0	0	1	0		5	7.001185	336	0.014663
ACVRL1	94	broad.mit.edu	hg19	12	52309036	52309036	+	Missense_Mutation	SNP	G	G	A			TCGA-V4-A9EL-01A-11D-A39W-08	TCGA-V4-A9EL-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6bf15a15-4a35-4e55-9c10-770fdff09fad	9dc7146a-1ee2-431a-a6b8-b8e9f16417c7	g.chr12:52309036G>A	ENST00000550683.1	+	6	943	c.842G>A	c.(841-843)cGc>cAc	p.R281H	ACVRL1_ENST00000419526.2_Missense_Mutation_p.R93H|ACVRL1_ENST00000388922.4_Missense_Mutation_p.R267H	NM_001077401.1	NP_001070869.1	P37023	ACVL1_HUMAN	activin A receptor type II-like 1	267	Protein kinase.	blood vessel endothelial cell proliferation involved in sprouting angiogenesis|blood vessel maturation|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of endothelial cell migration|negative regulation of focal adhesion assembly|positive regulation of BMP signaling pathway|positive regulation of transcription, DNA-dependent|regulation of blood pressure|regulation of blood vessel endothelial cell migration|regulation of DNA replication|regulation of endothelial cell proliferation|transforming growth factor beta receptor signaling pathway|wound healing, spreading of epidermal cells	cell surface|integral to plasma membrane	activin binding|activin receptor activity, type I|ATP binding|metal ion binding|receptor signaling protein serine/threonine kinase activity|SMAD binding|transforming growth factor beta binding|transforming growth factor beta receptor activity	breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(9)|prostate(1)|skin(1)|urinary_tract(1)	20				BRCA - Breast invasive adenocarcinoma(357;0.0991)	ATGACCTCCCGCAACTCGAGC	0.617	0	64.0	55.0	58.0	12	52309036	2203	4300	6503	SO:0001583	missense	L17075	CCDS31804.1	12q13.13	2014-09-17			ENSG00000139567	ENSG00000139567		175	protein-coding gene	gene with protein product		601284		ACVRLK1, ORW2	8397373, 8640225	Standard	NM_000020	Approved	HHT2, ALK1, HHT	uc001rzk.3	P37023	OTTHUMG00000169507	ENST00000419526.2:c.278G>A	12.37:g.52309036G>A	ENSP00000392492:p.Arg93His	A6NGA8	ENST00000419526.2	37		.	.	.	.	.	.	.	.	.	.	G	19.63	3.863696	0.71949	2.27E-4	0.0	ENSG00000139567	ENST00000388922;ENST00000267008;ENST00000550683;ENST00000548659;ENST00000419526	D;D;D	0.93426	-3.22;-3.22;-3.22	5.44	5.44	0.79542	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.45126	D	0.000385	D	0.94935	0.8362	L	0.36672	1.1	0.54753	D	0.999988	B;D	0.89917	0.212;1.0	B;D	0.74674	0.024;0.984	D	0.94983	0.8127	10	0.59425	D	0.04	.	19.055	0.93059	0.0:0.0:1.0:0.0	.	93;267	E7EN07;P37023	.;ACVL1_HUMAN	H	267;267;281;93;93	ENSP00000373574:R267H;ENSP00000447884:R281H;ENSP00000392492:R93H	ENSP00000267008:R267H	R	+	2	0	ACVRL1	50595303	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.461000	0.53035	2.824000	0.97209	0.655000	0.94253	CGC	ACVRL1-003	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000404524.1		3.715687	0	-4	45	0	0	1	0		3	7.250615	22	0.120000
SERPINB4	6318	broad.mit.edu	hg19	18	61305232	61305232	+	Silent	SNP	C	C	T			TCGA-V4-A9EL-01A-11D-A39W-08	TCGA-V4-A9EL-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6bf15a15-4a35-4e55-9c10-770fdff09fad	9dc7146a-1ee2-431a-a6b8-b8e9f16417c7	g.chr18:61305232C>T	ENST00000341074.5	-	8	1009	c.894G>A	c.(892-894)acG>acA	p.T298T	SERPINB4_ENST00000356424.6_Silent_p.T246T	NM_002974.2	NP_002965.1			serpin peptidase inhibitor, clade B (ovalbumin), member 4						breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(22)|ovary(3)|skin(4)|upper_aerodigestive_tract(1)	42					TGGTTCTCAACGTGTCCTTGA	0.453	0	185.0	160.0	168.0	18	61305232	2203	4300	6503	SO:0001819	synonymous_variant	X89015	CCDS11986.1	18q21.33	2014-02-18	2005-08-18		ENSG00000206073	ENSG00000206073	"""Serine (or cysteine) peptidase inhibitors"""	10570	protein-coding gene	gene with protein product	"""squamous cell carcinoma antigen 2"""	600518	"""serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 4"""	SCCA2	7724531, 14630915, 24172014	Standard	NM_175041	Approved	PI11, LEUPIN, SCCA-2, SCCA1		P48594	OTTHUMG00000060405	ENST00000341074.5:c.894G>A	18.37:g.61305232C>T		A8K847	ENST00000341074.5	37	CCDS11986.1	.	.	.	.	.	.	.	.	.	.	C	5.939	0.357213	0.11239	.	.	ENSG00000206073	ENST00000413673	.	.	.	4.51	-9.03	0.00737	.	.	.	.	.	T	0.16514	0.0397	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.14699	-1.0463	4	.	.	.	.	3.1776	0.06573	0.1342:0.1224:0.239:0.5045	.	.	.	.	H	279	.	.	R	-	2	0	SERPINB4	59456212	0.000000	0.05858	0.000000	0.03702	0.222000	0.24845	-4.287000	0.00259	-2.264000	0.00689	-0.192000	0.12808	CGT	SERPINB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133794.2		66.299786	0	-11	71	0	0	1	0	NM_175041	23	68.520153	50	0.315068
WDR47	22911	broad.mit.edu	hg19	1	109553777	109553777	+	Silent	SNP	G	G	C			TCGA-V4-A9EL-01A-11D-A39W-08	TCGA-V4-A9EL-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6bf15a15-4a35-4e55-9c10-770fdff09fad	9dc7146a-1ee2-431a-a6b8-b8e9f16417c7	g.chr1:109553777G>C	ENST00000357672.3	-	4	1182	c.807C>G	c.(805-807)tcC>tcG	p.S269S	WDR47_ENST00000400794.3_Silent_p.S304S|WDR47_ENST00000369965.4_Silent_p.S297S|WDR47_ENST00000361054.3_Silent_p.S269S|WDR47_ENST00000369962.3_Silent_p.S297S			O94967	WDR47_HUMAN	WD repeat domain 47	297					breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	20		all_lung(203;0.00519)|all_epithelial(167;0.00611)|Lung NSC(277;0.00822)		Colorectal(144;0.0165)|Lung(183;0.0484)|COAD - Colon adenocarcinoma(174;0.128)|Epithelial(280;0.168)|all cancers(265;0.201)|LUSC - Lung squamous cell carcinoma(189;0.244)	TTCTCATTGGGGATGATGGAT	0.428	0	267.0	284.0	278.0	1	109553777	2203	4296	6499	SO:0001819	synonymous_variant	AB020700	CCDS30787.1, CCDS44186.1, CCDS44187.1	1p13.3	2013-01-09			ENSG00000085433	ENSG00000085433	"""WD repeat domain containing"""	29141	protein-coding gene	gene with protein product		615734			10048485	Standard	NM_014969	Approved	KIAA0893	uc001dwl.3	O94967	OTTHUMG00000011734	ENST00000369965.4:c.891C>G	1.37:g.109553777G>C		A8MX09|Q5TYV7|Q5TYV8|Q5TYV9|Q8IXT7|Q8IYU9	ENST00000369965.4	37	CCDS30787.1																																																																																			WDR47-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000032413.2		375.126026	0	-32	277	0	0	1	0	NM_014969	127	379.091558	204	0.383686
PAMR1	25891	broad.mit.edu	hg19	11	35513670	35513670	+	Frame_Shift_Del	DEL	C	C	-			TCGA-V4-A9EL-01A-11D-A39W-08	TCGA-V4-A9EL-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6bf15a15-4a35-4e55-9c10-770fdff09fad	9dc7146a-1ee2-431a-a6b8-b8e9f16417c7	g.chr11:35513670delC	ENST00000378880.2	-	3	747	c.302delG	c.(301-303)ggtfs	p.G101fs	PAMR1_ENST00000532848.1_Frame_Shift_Del_p.G61fs|PAMR1_ENST00000534803.1_5'UTR|PAMR1_ENST00000278360.3_Frame_Shift_Del_p.G101fs|PAMR1_ENST00000378878.3_Frame_Shift_Del_p.G101fs	NM_001001991.1	NP_001001991.1	Q6UXH9	PAMR1_HUMAN	peptidase domain containing associated with muscle regeneration 1	101		proteolysis	extracellular region	serine-type endopeptidase activity	breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(8)|ovary(3)|upper_aerodigestive_tract(1)	26					ATCCAAGGTACCCCCCCATGA	0.517	0	201.0	193.0	196.0	11	35513670	2202	4298	6500	SO:0001589	frameshift_variant		CCDS7898.1, CCDS31460.1, CCDS60759.1, CCDS60760.1	11p13	2009-09-30			ENSG00000149090	ENSG00000149090		24554	protein-coding gene	gene with protein product	"""regeneration-associated muscle protease"""				15111323	Standard	NM_001282675	Approved	RAMP, DKFZP586H2123	uc001mwf.3	Q6UXH9	OTTHUMG00000166328	ENST00000378880.2:c.302delG	11.37:g.35513670delC	ENSP00000368158:p.Gly101fs	A8MQ58|B7ZA73|Q5EBL7|Q5JPI4|Q6N062|Q71RE9|Q96JW2|Q9Y432	ENST00000378880.2	37	CCDS31460.1																																																																																			PAMR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389177.1	.	.		-43	191					NM_015430	7		286	0.02
ZNF473	25888	broad.mit.edu	hg19	19	50549632	50549632	+	Frame_Shift_Del	DEL	C	C	-			TCGA-V4-A9EL-01A-11D-A39W-08	TCGA-V4-A9EL-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6bf15a15-4a35-4e55-9c10-770fdff09fad	9dc7146a-1ee2-431a-a6b8-b8e9f16417c7	g.chr19:50549632delC	ENST00000595661.1	+	6	2427	c.1932delC	c.(1930-1932)cacfs	p.H644fs	ZNF473_ENST00000601364.1_Intron|CTD-2126E3.3_ENST00000599914.1_RNA|ZNF473_ENST00000391821.2_Frame_Shift_Del_p.H644fs|ZNF473_ENST00000270617.3_Frame_Shift_Del_p.H644fs|CTD-2126E3.3_ENST00000599410.1_RNA|ZNF473_ENST00000445728.3_Frame_Shift_Del_p.H632fs			Q8WTR7	ZN473_HUMAN	zinc finger protein 473	644		histone mRNA 3'-end processing|regulation of transcription, DNA-dependent|termination of RNA polymerase II transcription	Cajal body	DNA binding|protein binding|zinc ion binding	NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(9)|liver(2)|lung(12)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	37		all_neural(266;0.0459)|Ovarian(192;0.0728)		GBM - Glioblastoma multiforme(134;0.00111)|OV - Ovarian serous cystadenocarcinoma(262;0.0058)	CAAAGGAGCACCCTTTTAAAT	0.453	0	78.0	73.0	75.0	19	50549632	2203	4300	6503	SO:0001589	frameshift_variant	AB032967	CCDS33077.1	19q13.33	2013-01-08					"""Zinc fingers, C2H2-type"", ""-"""	23239	protein-coding gene	gene with protein product					11782445	Standard	NM_015428	Approved	KIAA1141, DKFZP434N043, HZFP100	uc002prn.3	Q8WTR7		ENST00000595661.1:c.1932delC	19.37:g.50549632delC	ENSP00000472808:p.His644fs	A8K8T7|Q9ULS9|Q9Y4Q7	ENST00000595661.1	37	CCDS33077.1																																																																																			ZNF473-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464833.1	.	.		-10	46					XM_046390	25		47	0.35
BAP1	8314	broad.mit.edu	hg19	3	52438542	52438542	+	Nonsense_Mutation	SNP	G	G	A			TCGA-V4-A9EL-01A-11D-A39W-08	TCGA-V4-A9EL-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6bf15a15-4a35-4e55-9c10-770fdff09fad	9dc7146a-1ee2-431a-a6b8-b8e9f16417c7	g.chr3:52438542G>A	ENST00000460680.1	-	12	1648	c.1177C>T	c.(1177-1179)Cag>Tag	p.Q393*	BAP1_ENST00000296288.5_Nonsense_Mutation_p.Q375*	NM_004656.2	NP_004647.1	Q99496	RING2_HUMAN	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)	0		anterior/posterior axis specification (GO:0009948)|gastrulation with mouth forming second (GO:0001702)|histone H2A monoubiquitination (GO:0035518)|histone H2A-K119 monoubiquitination (GO:0036353)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	euchromatin (GO:0000791)|MLL1 complex (GO:0071339)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)|sex chromatin (GO:0001739)|ubiquitin ligase complex (GO:0000151)	chromatin binding (GO:0003682)|ligase activity (GO:0016874)|RING-like zinc finger domain binding (GO:0071535)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	NS(1)|breast(4)|endometrium(3)|eye(42)|kidney(60)|large_intestine(3)|lung(9)|ovary(4)|pleura(39)|prostate(4)|skin(9)|urinary_tract(2)	180				BRCA - Breast invasive adenocarcinoma(193;1.72e-05)|Kidney(197;0.0018)|KIRC - Kidney renal clear cell carcinoma(197;0.00203)|OV - Ovarian serous cystadenocarcinoma(275;0.0277)	TCTGAGTACTGCTGGGGTGGG	0.572	0	117.0	89.0	99.0	3	52438542	2203	4300	6503	SO:0001587	stop_gained	AF045581	CCDS2853.1	3p21.31-p21.2	2014-09-17			ENSG00000163930	ENSG00000163930		950	protein-coding gene	gene with protein product		603089			9528852	Standard	NM_004656	Approved	hucep-6, KIAA0272, UCHL2	uc003ddx.4	Q92560	OTTHUMG00000158392	ENST00000460680.1:c.1177C>T	3:g.52438542G>A	ENSP00000417132:p.Gln393*	B2RBS7|B3KRH1|Q5TEN1|Q5TEN2	ENST00000460680.1		CCDS2853.1	.	.	.	.	.	.	.	.	.	.	G	38	6.723555	0.97788	.	.	ENSG00000163930	ENST00000460680;ENST00000296288	.	.	.	5.54	5.54	0.83059	.	0.124915	0.56097	D	0.000039	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.46703	T	0.11	.	17.6638	0.88198	0.0:0.0:1.0:0.0	.	.	.	.	X	393;375	.	ENSP00000296288:Q375X	Q	-	1	0	BAP1	52413582	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.512000	0.81728	2.603000	0.88011	0.655000	0.94253	CAG	BAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350895.1	8.120000e+00	1.635000e+01		2	28						4		2	6.670000e-01
BAP1	8314	broad.mit.edu	hg19	3	52438543	52438548	+	In_Frame_Del	DEL	CTGGGG	CTGGGG	-			TCGA-V4-A9EL-01A-11D-A39W-08	TCGA-V4-A9EL-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6bf15a15-4a35-4e55-9c10-770fdff09fad	9dc7146a-1ee2-431a-a6b8-b8e9f16417c7	g.chr3:52438543_52438548delCTGGGG	ENST00000460680.1	-	12	1642_1647	c.1171_1176delCCCCAG	c.(1171-1176)ccccagdel	p.PQ391del	BAP1_ENST00000296288.5_In_Frame_Del_p.PQ373del	NM_004656.2	NP_004647.1	Q99496	RING2_HUMAN	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)	0		anterior/posterior axis specification (GO:0009948)|gastrulation with mouth forming second (GO:0001702)|histone H2A monoubiquitination (GO:0035518)|histone H2A-K119 monoubiquitination (GO:0036353)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	euchromatin (GO:0000791)|MLL1 complex (GO:0071339)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)|sex chromatin (GO:0001739)|ubiquitin ligase complex (GO:0000151)	chromatin binding (GO:0003682)|ligase activity (GO:0016874)|RING-like zinc finger domain binding (GO:0071535)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	NS(1)|breast(4)|endometrium(3)|eye(42)|kidney(60)|large_intestine(3)|lung(9)|ovary(4)|pleura(39)|prostate(4)|skin(9)|urinary_tract(2)	180				BRCA - Breast invasive adenocarcinoma(193;1.72e-05)|Kidney(197;0.0018)|KIRC - Kidney renal clear cell carcinoma(197;0.00203)|OV - Ovarian serous cystadenocarcinoma(275;0.0277)	CTGAGTACTGCTGGGGTGGGCGGACT	0.578	0									SO:0001651	inframe_deletion	AF045581	CCDS2853.1	3p21.31-p21.2	2014-09-17			ENSG00000163930	ENSG00000163930		950	protein-coding gene	gene with protein product		603089			9528852	Standard	NM_004656	Approved	hucep-6, KIAA0272, UCHL2	uc003ddx.4	Q92560	OTTHUMG00000158392	ENST00000460680.1:c.1171_1176delCCCCAG	3:g.52438543_52438548delCTGGGG	ENSP00000417132:p.Pro391_Gln392del	B2RBS7|B3KRH1|Q5TEN1|Q5TEN2	ENST00000460680.1		CCDS2853.1																																																																																			BAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350895.1	8.110000e+00	1.634000e+01		1	27						4		2	6.670000e-01