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
C12orf71	728858	broad.mit.edu	hg19	12	27234201	27234201	+	Missense_Mutation	SNP	T	T	C			TCGA-V4-A9EF-01A-21D-A39W-08	TCGA-V4-A9EF-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4a76bb65-1241-44ac-b2ab-06e14e9cb219	abf3af68-1664-4c42-8be2-23b7e4a1e9a2	g.chr12:27234201T>C	ENST00000429849.2	-	2	746	c.716A>G	c.(715-717)aAa>aGa	p.K239R		NM_001080406.1	NP_001073875.1	A8MTZ7	CL071_HUMAN	chromosome 12 open reading frame 71	239					endometrium(2)|large_intestine(1)|lung(4)|skin(1)	8					ATGGGGACTTTTGGTGGCATT	0.527	0	89.0	87.0	88.0	12	27234201	2071	4223	6294	SO:0001583	missense		CCDS44851.1	12p11.23	2008-07-25			ENSG00000214700	ENSG00000214700		34452	protein-coding gene	gene with protein product						Standard	NM_001080406	Approved	LOC728858	uc001rhq.3	A8MTZ7	OTTHUMG00000169274	ENST00000429849.2:c.716A>G	12.37:g.27234201T>C	ENSP00000413728:p.Lys239Arg		ENST00000429849.2	37	CCDS44851.1	.	.	.	.	.	.	.	.	.	.	T	8.050	0.765710	0.15983	.	.	ENSG00000214700	ENST00000398815;ENST00000429849	T	0.47528	0.84	2.66	-1.61	0.08399	.	1.809800	0.03977	U	0.292675	T	0.26846	0.0657	N	0.19112	0.55	0.09310	N	1	B	0.32010	0.351	B	0.29077	0.098	T	0.06752	-1.0809	10	0.20519	T	0.43	1.586	2.3828	0.04358	0.4304:0.1419:0.0:0.4277	.	239	A8MTZ7	CL071_HUMAN	R	271;239	ENSP00000413728:K239R	ENSP00000381796:K271R	K	-	2	0	C12orf71	27125468	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.318000	0.08050	-0.333000	0.08476	0.334000	0.21626	AAA	C12orf71-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403258.1		90.163605	0	-9	52	0	0	1	0	NM_001080406	29	90.612309	41	0.414286
MRAS	22808	ucsc.edu	hg19	3	138116204	138116204	+	Missense_Mutation	SNP	C	C	T			TCGA-V4-A9EF-01A-21D-A39W-08	TCGA-V4-A9EF-10A-01D-A39Z-08	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	4a76bb65-1241-44ac-b2ab-06e14e9cb219	abf3af68-1664-4c42-8be2-23b7e4a1e9a2																										CAGCGCCATGCGGGAGCAATA	0.612	0	85.0	63.0	70.0	3	138116204	2203	4300	6503	SO:0001583	missense	AF022080	CCDS3100.1, CCDS58855.1	3q22.3	2014-05-09			ENSG00000158186	ENSG00000158186		7227	protein-coding gene	gene with protein product		608435			9400994, 10446149	Standard	NM_012219	Approved	M-RAs, R-RAS3, RRAS3	uc003esi.4	O14807	OTTHUMG00000159888	ENST00000289104.4:c.232C>T	3.37:g.138116204C>T	ENSP00000289104:p.Arg78Trp	B4DIK0|Q86WX8	ENST00000289104.4	37	CCDS3100.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.065591	0.76187	.	.	ENSG00000158186	ENST00000289104;ENST00000423968;ENST00000494949;ENST00000464896;ENST00000474559	T;T;T;T;T	0.79845	-1.31;-1.31;-1.31;-1.31;-1.31	5.25	3.24	0.37175	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.91513	0.7320	H	0.95294	3.65	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.92352	0.5890	10	0.87932	D	0	.	10.4369	0.44441	0.5334:0.4666:0.0:0.0	.	78	O14807	RASM_HUMAN	W	78;78;2;2;78	ENSP00000289104:R78W;ENSP00000389682:R78W;ENSP00000417685:R2W;ENSP00000419582:R2W;ENSP00000418356:R78W	ENSP00000289104:R78W	R	+	1	2	MRAS	139598894	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	2.287000	0.43505	1.189000	0.43028	-0.314000	0.08810	CGG	MRAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357990.1				-30	24						4		26	
FAM81B	153643	broad.mit.edu	hg19	5	94764367	94764367	+	Silent	SNP	G	G	A			TCGA-V4-A9EF-01A-21D-A39W-08	TCGA-V4-A9EF-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4a76bb65-1241-44ac-b2ab-06e14e9cb219	abf3af68-1664-4c42-8be2-23b7e4a1e9a2	g.chr5:94764367G>A	ENST00000283357.5	+	6	763	c.717G>A	c.(715-717)cgG>cgA	p.R239R		NM_152548.2	NP_689761	Q96LP2	FA81B_HUMAN	family with sequence similarity 81, member B	239					central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(4)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22		all_cancers(142;1.1e-06)|all_epithelial(76;1.48e-09)|all_lung(232;0.000696)|Lung NSC(167;0.000947)|Ovarian(225;0.00473)		all cancers(79;1.04e-16)	AAGAGCACCGGCAAATTGAGA	0.413	0	130.0	120.0	123.0	5	94764367	1855	4095	5950	SO:0001819	synonymous_variant		CCDS43341.1	5q15	2008-02-05			ENSG00000153347	ENSG00000153347		26335	protein-coding gene	gene with protein product						Standard	NM_152548	Approved	FLJ25333	uc003kla.1	Q96LP2	OTTHUMG00000162837	ENST00000283357.5:c.717G>A	5.37:g.94764367G>A			ENST00000283357.5	37	CCDS43341.1																																																																																			FAM81B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370690.1		-29.633566	0	-57	101	0	0	1	0	NM_152548	4	7.219918	145	0.026846
GNA11	2767	broad.mit.edu	hg19	19	3118942	3118942	+	Missense_Mutation	SNP	A	A	T			TCGA-V4-A9EF-01A-21D-A39W-08	TCGA-V4-A9EF-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4a76bb65-1241-44ac-b2ab-06e14e9cb219	abf3af68-1664-4c42-8be2-23b7e4a1e9a2	g.chr19:3118942A>T	ENST00000078429.4	+	5	868	c.626A>T	c.(625-627)cAg>cTg	p.Q209L	GNA11_ENST00000586180.1_3'UTR|AC005262.3_ENST00000587701.1_RNA	NM_002067.2	NP_002058.2	P29992	GNA11_HUMAN	guanine nucleotide binding protein (G protein), alpha 11 (Gq class)	209		activation of phospholipase C activity by dopamine receptor signaling pathway|G-protein signaling, coupled to cAMP nucleotide second messenger|platelet activation|protein ADP-ribosylation|regulation of action potential	cytoplasm|heterotrimeric G-protein complex	G-protein beta/gamma-subunit complex binding|G-protein-coupled receptor binding|GTP binding|GTPase activity|signal transducer activity	endometrium(2)|eye(132)|kidney(1)|large_intestine(2)|lung(1)|meninges(5)|ovary(1)|prostate(1)|skin(16)	161		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.79e-05)|OV - Ovarian serous cystadenocarcinoma(105;2.68e-113)|Epithelial(107;1.22e-111)|all cancers(105;5.78e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00141)|STAD - Stomach adenocarcinoma(1328;0.181)	GTGGGGGGCCAGCGGTCGGAG	0.612	82	104.0	89.0	94.0	19	3118942	2203	4300	6503	SO:0001583	missense	AF493900	CCDS12103.1	19p13.3	2014-02-04			ENSG00000088256	ENSG00000088256		4379	protein-coding gene	gene with protein product		139313	"""hypocalciuric hypercalcemia 2"""	HHC2	1302014, 23802516	Standard	NM_002067	Approved	FBH, FBH2, FHH2	uc002lxd.3	P29992	OTTHUMG00000180631	ENST00000078429.4:c.626A>T	19.37:g.3118942A>T	ENSP00000078429:p.Gln209Leu	O15109|Q14350|Q6IB00	ENST00000078429.4	37	CCDS12103.1	.	.	.	.	.	.	.	.	.	.	.	15.05	2.718086	0.48622	.	.	ENSG00000088256	ENST00000078429	D	0.91237	-2.81	3.26	3.26	0.37387	.	0.000000	0.64402	U	0.000006	D	0.96950	0.9004	H	0.99357	4.53	0.80722	D	1	D	0.59767	0.986	D	0.68483	0.958	D	0.96823	0.9605	10	0.87932	D	0	.	10.7338	0.46113	1.0:0.0:0.0:0.0	.	209	P29992	GNA11_HUMAN	L	209	ENSP00000078429:Q209L	ENSP00000078429:Q209L	Q	+	2	0	GNA11	3069942	1.000000	0.71417	0.438000	0.26821	0.027000	0.11550	9.104000	0.94239	1.256000	0.44068	0.379000	0.24179	CAG	GNA11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452261.2		80.349494	0	-26	55	0	0	1	0	NM_002067	26	80.349494	26	0.500000
BAP1	8314	broad.mit.edu	hg19	3	52440383	52440383	+	Nonsense_Mutation	SNP	G	G	C			TCGA-V4-A9EF-01A-21D-A39W-08	TCGA-V4-A9EF-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4a76bb65-1241-44ac-b2ab-06e14e9cb219	abf3af68-1664-4c42-8be2-23b7e4a1e9a2	g.chr3:52440383G>C	ENST00000460680.1	-	9	1140	c.669C>G	c.(667-669)taC>taG	p.Y223*	BAP1_ENST00000296288.5_Intron	NM_004656.2	NP_004647.1	Q92560	BAP1_HUMAN	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)	223		monoubiquitinated histone H2A deubiquitination|negative regulation of cell proliferation|protein K48-linked deubiquitination|regulation of cell cycle|regulation of cell growth|ubiquitin-dependent protein catabolic process	cytoplasm|nucleolus|PR-DUB complex	chromatin binding|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity	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)	GGATGTCGTGGTAGGGCTCCC	0.627	0	74.0	59.0	64.0	3	52440383	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.669C>G	3.37:g.52440383G>C	ENSP00000417132:p.Tyr223*	B2RBS7|B3KRH1|Q5TEN1|Q5TEN2	ENST00000460680.1	37	CCDS2853.1	.	.	.	.	.	.	.	.	.	.	G	39	7.895614	0.98548	.	.	ENSG00000163930	ENST00000460680	.	.	.	6.04	4.01	0.46588	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-8.643	8.0278	0.30446	0.3157:0.0:0.6843:0.0	.	.	.	.	X	223	.	ENSP00000417132:Y223X	Y	-	3	2	BAP1	52415423	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.222000	0.58580	1.539000	0.49286	0.650000	0.86243	TAC	BAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350895.1		103.721474	0	-17	35	0	0	1	0		29	105.598191	1	0.966667
USP25	29761	broad.mit.edu	hg19	21	17203904	17203904	+	Missense_Mutation	SNP	A	A	G			TCGA-V4-A9EF-01A-21D-A39W-08	TCGA-V4-A9EF-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4a76bb65-1241-44ac-b2ab-06e14e9cb219	abf3af68-1664-4c42-8be2-23b7e4a1e9a2	g.chr21:17203904A>G	ENST00000285681.2	+	16	2318	c.1949A>G	c.(1948-1950)tAc>tGc	p.Y650C	USP25_ENST00000285679.6_Missense_Mutation_p.Y650C|USP25_ENST00000400183.2_Missense_Mutation_p.Y650C|USP25_ENST00000351097.5_Intron	NM_001283042.1	NP_001269971.1	Q9UHP3	UBP25_HUMAN	ubiquitin specific peptidase 25	650		protein modification process|ubiquitin-dependent protein catabolic process	cytoplasm|nucleus	ubiquitin thiolesterase activity|ubiquitin-specific protease activity	breast(4)|endometrium(6)|kidney(2)|large_intestine(13)|liver(5)|lung(14)|ovary(4)|prostate(1)|skin(1)|urinary_tract(2)	52				Epithelial(23;7.55e-05)|all cancers(11;0.000429)|COAD - Colon adenocarcinoma(22;0.00543)|OV - Ovarian serous cystadenocarcinoma(11;0.00743)|Colorectal(24;0.0116)|Lung(58;0.0853)|LUSC - Lung squamous cell carcinoma(23;0.0889)	GCCAGTGCATACTGTTTAATG	0.363	0	123.0	117.0	119.0	21	17203904	2203	4300	6503	SO:0001583	missense	AF170562	CCDS33515.1, CCDS63336.1, CCDS63337.1	21q11.2	2011-02-24	2005-08-08		ENSG00000155313	ENSG00000155313	"""Ubiquitin-specific peptidases"""	12624	protein-coding gene	gene with protein product		604736	"""ubiquitin specific protease 25"""		12838346, 10612803	Standard	NM_013396	Approved	USP21	uc002yjy.1	Q9UHP3	OTTHUMG00000074343	ENST00000285679.6:c.1949A>G	21.37:g.17203904A>G	ENSP00000285679:p.Tyr650Cys	C0LSZ0|Q6DHZ9|Q9H9W1	ENST00000285679.6	37	CCDS33515.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	21.6|21.6	4.172617|4.172617	0.78452|0.78452	.|.	.|.	ENSG00000155313|ENSG00000155313	ENST00000453553|ENST00000285681;ENST00000285679;ENST00000400183	.|D;D;D	.|0.87650	.|-2.28;-2.28;-2.28	5.11|5.11	5.11|5.11	0.69529|0.69529	.|Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.94902|0.94902	0.8352|0.8352	M|M	0.93062|0.93062	3.375|3.375	0.80722|0.80722	D|D	1|1	.|D;D;D	.|0.89917	.|1.0;1.0;1.0	.|D;D;D	.|0.97110	.|1.0;1.0;0.998	D|D	0.96052|0.96052	0.9032|0.9032	5|10	.|0.87932	.|D	.|0	.|.	15.6093|15.6093	0.76704|0.76704	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|650;650;650	.|Q9UHP3-3;Q9UHP3-1;Q9UHP3	.|.;.;UBP25_HUMAN	A|C	179|650	.|ENSP00000285681:Y650C;ENSP00000285679:Y650C;ENSP00000383044:Y650C	.|ENSP00000285679:Y650C	T|Y	+|+	1|2	0|0	USP25|USP25	16125775|16125775	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.986000|0.986000	0.74619|0.74619	8.848000|8.848000	0.92172|0.92172	2.226000|2.226000	0.72624|0.72624	0.482000|0.482000	0.46254|0.46254	ACT|TAC	USP25-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157964.1		-8.332284	0	-2	39	0	0	1	0		3	6.794042	65	0.044118
GOLGB1	2804	broad.mit.edu	hg19	3	121438591	121438591	+	Silent	SNP	G	G	T			TCGA-V4-A9EF-01A-21D-A39W-08	TCGA-V4-A9EF-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4a76bb65-1241-44ac-b2ab-06e14e9cb219	abf3af68-1664-4c42-8be2-23b7e4a1e9a2	g.chr3:121438591G>T	ENST00000393667.3	-	7	783	c.673C>A	c.(673-675)Cga>Aga	p.R225R	GOLGB1_ENST00000340645.5_Silent_p.R220R	NM_001256486.1	NP_001243415.1	Q14789	GOGB1_HUMAN	golgin B1	220		Golgi organization	ER-Golgi intermediate compartment|Golgi membrane|Golgi stack|integral to membrane	protein binding	NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(2)|cervix(2)|endometrium(12)|kidney(3)|large_intestine(26)|liver(2)|lung(36)|ovary(7)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(13)	119				GBM - Glioblastoma multiforme(114;0.0989)	TCTTTCTCTCGGACCACCTGC	0.438	0	126.0	110.0	115.0	3	121438591	2203	4300	6503	SO:0001819	synonymous_variant	X75304	CCDS3004.1, CCDS58847.1, CCDS74989.1	3q13	2010-02-12	2010-02-12	2007-07-27	ENSG00000173230	ENSG00000173230		4429	protein-coding gene	gene with protein product	"""macrogolgin"", ""golgi integral membrane protein 1"""	602500	"""golgi autoantigen, golgin subfamily b, macrogolgin (with transmembrane signal), 1"", ""golgin B1, golgi integral membrane protein"""		7691276, 15004235	Standard	NM_001256486	Approved	GCP, GCP372, giantin, GOLIM1	uc010hrc.4	Q14789	OTTHUMG00000159411	ENST00000393667.3:c.673C>A	3.37:g.121438591G>T		B2ZZ91|D3DN92|E7EP74|Q14398	ENST00000393667.3	37	CCDS58847.1																																																																																			GOLGB1-002	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355160.1		-0.407011	1	-11	48	0	1	1	1	NM_004487	3	7.005743	37	0.075000
MYOF	26509	broad.mit.edu	hg19	10	95168603	95168603	+	Missense_Mutation	SNP	C	C	T			TCGA-V4-A9EF-01A-21D-A39W-08	TCGA-V4-A9EF-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4a76bb65-1241-44ac-b2ab-06e14e9cb219	abf3af68-1664-4c42-8be2-23b7e4a1e9a2	g.chr10:95168603C>T	ENST00000371501.4	-	7	792	c.670G>A	c.(670-672)Gtc>Atc	p.V224I	MYOF_ENST00000359263.4_Missense_Mutation_p.V224I|MYOF_ENST00000371489.1_Missense_Mutation_p.V224I|MYOF_ENST00000358334.5_Missense_Mutation_p.V224I|MYOF_ENST00000371502.4_Missense_Mutation_p.V224I			Q9NZM1	MYOF_HUMAN	myoferlin	224	C2 2.|Necessary for interaction with EHD2.	blood circulation|muscle contraction|plasma membrane repair	caveola|cytoplasmic vesicle membrane|integral to membrane|nuclear membrane	phospholipid binding|protein binding	NS(2)|autonomic_ganglia(1)|breast(3)|endometrium(7)|kidney(7)|large_intestine(15)|lung(14)|ovary(4)|prostate(4)|skin(6)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	67					TGGCCACAGACGTGAACTTTG	0.502	0	146.0	135.0	138.0	10	95168603	1961	4148	6109	SO:0001583	missense	AB033033	CCDS41550.1, CCDS41551.1	10q24	2014-06-27	2008-11-26	2008-11-26	ENSG00000138119	ENSG00000138119		3656	protein-coding gene	gene with protein product	"""fer-1-like family member 3"""	604603	"""fer-1 (C.elegans)-like 3 (myoferlin)"", ""fer-1-like 3, myoferlin (C. elegans)"""	FER1L3	10607832, 10995573, 17702744	Standard	NM_013451	Approved	KIAA1207	uc001kin.3	Q9NZM1	OTTHUMG00000018772	ENST00000359263.4:c.670G>A	10.37:g.95168603C>T	ENSP00000352208:p.Val224Ile	B3KQN5|Q5VWW2|Q5VWW3|Q5VWW4|Q5VWW5|Q7Z642|Q8IWH0|Q9HBU3|Q9NZM0|Q9ULL3|Q9Y4U4	ENST00000359263.4	37	CCDS41551.1	.	.	.	.	.	.	.	.	.	.	c	12.33	1.907087	0.33628	.	.	ENSG00000138119	ENST00000358334;ENST00000359263;ENST00000371501;ENST00000371502;ENST00000371489	T;T;T;T;T	0.68624	-0.34;-0.34;-0.34;-0.34;-0.34	5.55	-5.02	0.02982	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.492051	0.22153	N	0.063889	T	0.51041	0.1651	L	0.48218	1.51	0.25893	N	0.983452	B;B;B	0.21309	0.054;0.003;0.008	B;B;B	0.16722	0.012;0.016;0.013	T	0.41610	-0.9499	10	0.12430	T	0.62	-3.4163	14.3022	0.66359	0.0:0.4094:0.0:0.5906	.	206;224;224	Q9NZM1-8;Q9NZM1-6;Q9NZM1	.;.;MYOF_HUMAN	I	224	ENSP00000351094:V224I;ENSP00000352208:V224I;ENSP00000360556:V224I;ENSP00000360557:V224I;ENSP00000360544:V224I	ENSP00000351094:V224I	V	-	1	0	MYOF	95158593	0.000000	0.05858	0.232000	0.24009	0.930000	0.56654	-0.426000	0.07008	-1.225000	0.02578	0.645000	0.84053	GTC	MYOF-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000049423.2		128.475611	0	-15	65	0	0	1	0	NM_013451	41	128.478311	40	0.506173
ALOX5	240	broad.mit.edu	hg19	10	45941026	45941026	+	Missense_Mutation	SNP	G	G	A			TCGA-V4-A9EF-01A-21D-A39W-08	TCGA-V4-A9EF-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4a76bb65-1241-44ac-b2ab-06e14e9cb219	abf3af68-1664-4c42-8be2-23b7e4a1e9a2	g.chr10:45941026G>A	ENST00000374391.2	+	14	1969	c.1916G>A	c.(1915-1917)cGc>cAc	p.R639H	RP11-67C2.2_ENST00000435635.1_RNA|ALOX5_ENST00000542434.1_Missense_Mutation_p.R582H	NM_000698.3|NM_001256153.1	NP_000689.1|NP_001243082.1	P09917	LOX5_HUMAN	arachidonate 5-lipoxygenase	639	Lipoxygenase.	hormone biosynthetic process|leukotriene biosynthetic process|prostanoid metabolic process	cytosol|nuclear envelope lumen|nuclear matrix|nuclear membrane	arachidonate 5-lipoxygenase activity|iron ion binding|lipoxygenase activity|protein binding	breast(1)|cervix(2)|endometrium(3)|kidney(1)|large_intestine(6)|lung(14)|ovary(2)|pancreas(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	37		Lung SC(717;0.0257)			GCCCGATTCCGCAAGAACCTC	0.532	0	99.0	94.0	96.0	10	45941026	2203	4300	6503	SO:0001583	missense	J03571	CCDS7212.1, CCDS58078.1	10q11.2	2008-03-18			ENSG00000012779	ENSG00000012779	"""Arachidonate lipoxygenases"""	435	protein-coding gene	gene with protein product		152390			2565035	Standard	NM_001256153	Approved	5-LOX	uc001jce.4	P09917	OTTHUMG00000018081	ENST00000374391.2:c.1916G>A	10.37:g.45941026G>A	ENSP00000363512:p.Arg639His	B7ZLS0|E5FPY5|E5FPY7|E5FPY8|Q5JQ14	ENST00000374391.2	37	CCDS7212.1	.	.	.	.	.	.	.	.	.	.	G	15.92	2.976004	0.53720	.	.	ENSG00000012779	ENST00000542434;ENST00000374391	D;D	0.90444	-2.67;-2.67	5.14	4.24	0.50183	Lipoxygenase, C-terminal (3);	0.152591	0.64402	N	0.000015	D	0.89543	0.6745	M	0.81179	2.53	0.27278	N	0.958182	P;B;B	0.39862	0.692;0.068;0.043	B;B;B	0.36134	0.218;0.049;0.027	D	0.85291	0.1067	10	0.59425	D	0.04	-26.8399	11.8919	0.52635	0.085:0.0:0.915:0.0	.	582;607;639	B7ZLS0;E5FPY8;P09917	.;.;LOX5_HUMAN	H	582;639	ENSP00000437634:R582H;ENSP00000363512:R639H	ENSP00000363512:R639H	R	+	2	0	ALOX5	45261032	1.000000	0.71417	1.000000	0.80357	0.750000	0.42670	6.597000	0.74118	1.537000	0.49254	0.655000	0.94253	CGC	ALOX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047780.1		-17.088976	0	-14	75	0	0	1	0		4	7.420229	102	0.037736
C12orf50	160419	broad.mit.edu	hg19	12	88391867	88391867	+	Missense_Mutation	SNP	A	A	T			TCGA-V4-A9EF-01A-21D-A39W-08	TCGA-V4-A9EF-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4a76bb65-1241-44ac-b2ab-06e14e9cb219	abf3af68-1664-4c42-8be2-23b7e4a1e9a2	g.chr12:88391867A>T	ENST00000298699.2	-	4	414	c.234T>A	c.(232-234)caT>caA	p.H78Q	C12orf50_ENST00000550553.1_Missense_Mutation_p.H78Q	NM_152589.1	NP_689802.1	Q8NA57	CL050_HUMAN	chromosome 12 open reading frame 50	78					NS(1)|breast(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(17)|ovary(1)|skin(3)|urinary_tract(2)	34					AAACTAAAGGATGGTGGATGG	0.358	0	121.0	120.0	120.0	12	88391867	2203	4300	6503	SO:0001583	missense	AK093140	CCDS9031.1	12q21.32	2006-02-03				ENSG00000165805		26665	protein-coding gene	gene with protein product					12477932	Standard	NM_152589	Approved	FLJ35821	uc001tam.1	Q8NA57	OTTHUMG00000169869	ENST00000298699.2:c.234T>A	12.37:g.88391867A>T	ENSP00000298699:p.His78Gln	Q6P674	ENST00000298699.2	37	CCDS9031.1	.	.	.	.	.	.	.	.	.	.	A	14.58	2.577693	0.45902	.	.	ENSG00000165805	ENST00000298699;ENST00000550553;ENST00000551944;ENST00000551163	T;T	0.30448	1.53;1.54	5.72	2.0	0.26442	.	0.173757	0.40908	N	0.000982	T	0.13670	0.0331	N	0.08118	0	0.26227	N	0.979067	B;P	0.35272	0.302;0.493	B;B	0.38616	0.202;0.277	T	0.09885	-1.0654	10	0.49607	T	0.09	.	1.3176	0.02110	0.5426:0.1508:0.1613:0.1452	.	132;78	G3V208;Q8NA57	.;CL050_HUMAN	Q	78;78;132;78	ENSP00000298699:H78Q;ENSP00000448344:H78Q	ENSP00000298699:H78Q	H	-	3	2	C12orf50	86915998	1.000000	0.71417	0.999000	0.59377	0.949000	0.60115	1.013000	0.29937	0.096000	0.17463	0.482000	0.46254	CAT	C12orf50-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406328.1		35.362588	0	-6	45	0	0	1	0	NM_152589	13	36.084264	24	0.351351
DNAH1	25981	broad.mit.edu	hg19	3	52393383	52393384	+	Frame_Shift_Ins	INS	-	-	C			TCGA-V4-A9EF-01A-21D-A39W-08	TCGA-V4-A9EF-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4a76bb65-1241-44ac-b2ab-06e14e9cb219	abf3af68-1664-4c42-8be2-23b7e4a1e9a2	g.chr3:52393383_52393384insC	ENST00000420323.2	+	26	4649_4650	c.4388_4389insC	c.(4387-4392)ttccccfs	p.FP1463fs		NM_015512.4	NP_056327	Q9P2D7	DYH1_HUMAN	dynein, axonemal, heavy chain 1	1463	Stem (By similarity).	ciliary or flagellar motility|microtubule-based movement|response to mechanical stimulus	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity	cervix(2)|endometrium(18)|kidney(6)|large_intestine(3)|lung(31)|prostate(1)|urinary_tract(1)	62				BRCA - Breast invasive adenocarcinoma(193;2.02e-05)|OV - Ovarian serous cystadenocarcinoma(275;0.000207)|Kidney(197;0.0022)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)	AGCCAACTGTTCCCCCAGCTCT	0.639	0									SO:0001589	frameshift_variant	U61738	CCDS46842.1	3p21-p14	2008-02-05	2006-09-04		ENSG00000114841	ENSG00000114841	"""Axonemal dyneins"""	2940	protein-coding gene	gene with protein product		603332	"""dynein, axonemal, heavy polypeptide 1"""		8812413, 9256245	Standard	NM_015512	Approved	XLHSRF-1, DNAHC1, HDHC7, HL-11, HL11	uc011bef.2	Q9P2D7	OTTHUMG00000158378	ENST00000420323.2:c.4393dupC	3.37:g.52393388_52393388dupC	ENSP00000401514:p.Phe1463fs	B0I1R6|O00436|O15435|O95491|Q6ZU48|Q86YK7|Q8TEJ4|Q92863|Q9H8E6|Q9UFW6|Q9Y4Z7	ENST00000420323.2	37	CCDS46842.1																																																																																			DNAH1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350816.1	.	.		-8	10					NM_015512	2		4	0.33
DCPS	28960	broad.mit.edu	hg19	11	126176602	126176602	+	Frame_Shift_Del	DEL	C	C	-			TCGA-V4-A9EF-01A-21D-A39W-08	TCGA-V4-A9EF-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4a76bb65-1241-44ac-b2ab-06e14e9cb219	abf3af68-1664-4c42-8be2-23b7e4a1e9a2	g.chr11:126176602delC	ENST00000263579.4	+	2	668	c.339delC	c.(337-339)tacfs	p.Y113fs		NM_014026.3	NP_054745.1	Q96C86	DCPS_HUMAN	decapping enzyme, scavenger	113		deadenylation-dependent decapping of nuclear-transcribed mRNA|exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	cytosol|nucleus	exoribonuclease activity|protein binding	endometrium(3)|large_intestine(4)|lung(6)|ovary(1)|skin(2)|urinary_tract(1)	17	all_hematologic(175;0.145)	Breast(109;0.00156)|Lung NSC(97;0.00949)|all_lung(97;0.0101)|Medulloblastoma(222;0.0425)|all_neural(223;0.0604)		BRCA - Breast invasive adenocarcinoma(274;1.15e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.08)	ATGATATCTACAGCACCTATC	0.542	0	121.0	98.0	106.0	11	126176602	2201	4298	6499	SO:0001589	frameshift_variant	AF077201	CCDS8473.1	11q24	2008-02-05			ENSG00000110063	ENSG00000110063		29812	protein-coding gene	gene with protein product		610534			12198172, 14523240	Standard	NM_014026	Approved	HSPC015, HINT-5, HSL1	uc001qdp.3	Q96C86	OTTHUMG00000165829	ENST00000263579.4:c.339delC	11.37:g.126176602delC	ENSP00000263579:p.Tyr113fs	Q8NHL8|Q9Y2S5	ENST00000263579.4	37	CCDS8473.1																																																																																			DCPS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386455.1	.	.		-9	37					NM_014026	18		29	0.38