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	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	t_alt_count	t_ref_count	validation_status	validation_method	validation_tumor_sample	validation_alt_allele	filter
VPS13D	55187	broad.mit.edu	37	1	12321995	12321995	+	Silent	SNP	G	T	T			TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12321995G>T	uc001atv.2	+	13	1593	c.1452G>T	c.(1450-1452)TCG>TCT	p.S484S	VPS13D_uc001atw.2_Silent_p.S484S	NM_015378	NP_056193	Q5THJ4	VP13D_HUMAN	vacuolar protein sorting 13D isoform 1	484					protein localization					ovary(4)|pancreas(1)	5	Ovarian(185;0.249)	Lung NSC(185;4.08e-05)|all_lung(284;4.55e-05)|Renal(390;0.000147)|Colorectal(325;0.00058)|Breast(348;0.00093)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0327)|Colorectal(212;4.63e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000289)|COAD - Colon adenocarcinoma(227;0.000801)|Kidney(185;0.00216)|KIRC - Kidney renal clear cell carcinoma(229;0.00544)|STAD - Stomach adenocarcinoma(313;0.012)|READ - Rectum adenocarcinoma(331;0.0476)|Lung(427;0.209)		CAGATGCCTCGTGTATGAACA	0.438													13	157	---	---	---	---	PASS
MST1P9	11223	broad.mit.edu	37	1	17084263	17084263	+	Nonsense_Mutation	SNP	C	T	T			TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17084263C>T	uc010ock.1	-	13	1754	c.1754G>A	c.(1753-1755)TGG>TAG	p.W585*	CROCC_uc009voy.1_Intron|MST1P9_uc001azp.3_Nonsense_Mutation_p.W185*	NR_002729				SubName: Full=Hepatocyte growth factor-like protein homolog;												0						GGTCTCACCCCAGCCTGCAAT	0.587													15	506	---	---	---	---	PASS
RPS6KA1	6195	broad.mit.edu	37	1	26898427	26898427	+	Intron	SNP	C	A	A			TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:26898427C>A	uc001bmr.1	+						RPS6KA1_uc010ofe.1_Intron|RPS6KA1_uc010off.1_3'UTR|RPS6KA1_uc001bms.1_Intron|RPS6KA1_uc009vsl.1_Intron	NM_002953	NP_002944	Q15418	KS6A1_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide						axon guidance|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|stress-activated MAPK cascade|synaptic transmission|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|nucleoplasm	ATP binding|caspase inhibitor activity|magnesium ion binding|protein binding|protein serine/threonine kinase activity			lung(1)	1		all_cancers(24;2.49e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.00571)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Epithelial(14;1.12e-50)|OV - Ovarian serous cystadenocarcinoma(117;2.89e-29)|Colorectal(126;1.4e-08)|COAD - Colon adenocarcinoma(152;9.31e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000537)|KIRC - Kidney renal clear cell carcinoma(1967;0.000759)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.0361)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.161)|LUSC - Lung squamous cell carcinoma(448;0.234)		GTGAGTGCCCCTGGCCTGGAC	0.637													3	27	---	---	---	---	PASS
HECTD3	79654	broad.mit.edu	37	1	45473182	45473182	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:45473182C>A	uc009vxk.2	-	10	1504	c.1406G>T	c.(1405-1407)AGC>ATC	p.S469I	HECTD3_uc001cmx.3_5'Flank|HECTD3_uc001cmy.3_Missense_Mutation_p.S79I|HECTD3_uc010olh.1_Missense_Mutation_p.S185I	NM_024602	NP_078878	Q5T447	HECD3_HUMAN	HECT domain containing 3	469					proteasomal ubiquitin-dependent protein catabolic process|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	perinuclear region of cytoplasm	ubiquitin-protein ligase activity				0	Acute lymphoblastic leukemia(166;0.155)					TGGCATGAAGCTGGGCTTGCT	0.607													21	67	---	---	---	---	PASS
POGZ	23126	broad.mit.edu	37	1	151378051	151378051	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151378051C>T	uc001eyd.1	-	19	3766	c.3460G>A	c.(3460-3462)GAA>AAA	p.E1154K	POGZ_uc001eye.1_Missense_Mutation_p.E1101K|POGZ_uc010pdb.1_Missense_Mutation_p.E1145K|POGZ_uc001eyf.1_Missense_Mutation_p.E1110K|POGZ_uc010pdc.1_Missense_Mutation_p.E1092K|POGZ_uc009wmv.1_Missense_Mutation_p.E1059K|POGZ_uc010pdd.1_Missense_Mutation_p.E645K	NM_015100	NP_055915	Q7Z3K3	POGZ_HUMAN	pogo transposable element with ZNF domain	1154	DDE.				cell division|kinetochore assembly|mitotic sister chromatid cohesion|regulation of transcription, DNA-dependent	cytoplasm|nuclear chromatin	DNA binding|protein binding|zinc ion binding			ovary(3)	3	Lung SC(34;0.00471)|Ovarian(49;0.00672)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.112)|LUSC - Lung squamous cell carcinoma(543;0.181)			CACCAAGGTTCCCCTGTGCCC	0.512													5	114	---	---	---	---	PASS
CENPF	1063	broad.mit.edu	37	1	214818891	214818891	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:214818891C>G	uc001hkm.2	+	13	6152	c.5978C>G	c.(5977-5979)TCT>TGT	p.S1993C		NM_016343	NP_057427	P49454	CENPF_HUMAN	centromere protein F	2089	Potential.				cell differentiation|cell division|cell proliferation|DNA replication|G2 phase of mitotic cell cycle|kinetochore assembly|metaphase plate congression|mitotic cell cycle spindle assembly checkpoint|mitotic prometaphase|muscle organ development|negative regulation of transcription, DNA-dependent|protein transport|regulation of G2/M transition of mitotic cell cycle|regulation of striated muscle tissue development|response to drug	condensed chromosome outer kinetochore|cytosol|midbody|nuclear envelope|nuclear matrix|perinuclear region of cytoplasm|spindle pole	chromatin binding|dynein binding|protein C-terminus binding|protein homodimerization activity|transcription factor binding			ovary(6)|central_nervous_system(4)|large_intestine(2)|skin(1)	13				all cancers(67;0.00836)|OV - Ovarian serous cystadenocarcinoma(81;0.00855)|GBM - Glioblastoma multiforme(131;0.0694)|Epithelial(68;0.0833)		GAGCTTGAGTCTCATCAAAGT	0.443													16	55	---	---	---	---	PASS
ASAP2	8853	broad.mit.edu	37	2	9531296	9531296	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:9531296C>T	uc002qzh.2	+	23	2829	c.2489C>T	c.(2488-2490)CCG>CTG	p.P830L	ASAP2_uc002qzi.2_Intron	NM_003887	NP_003878	O43150	ASAP2_HUMAN	ArfGAP with SH3 domain, ankyrin repeat and PH	830	Pro-rich.				regulation of ARF GTPase activity	Golgi cisterna membrane|plasma membrane	ARF GTPase activator activity|protein binding|zinc ion binding				0						GTCCATCCACCGCTGCCCCCT	0.562													27	130	---	---	---	---	PASS
EMILIN1	11117	broad.mit.edu	37	2	27306232	27306232	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27306232G>C	uc002rii.3	+	4	2221	c.1793G>C	c.(1792-1794)GGT>GCT	p.G598A	EMILIN1_uc002rik.3_5'Flank	NM_007046	NP_008977	Q9Y6C2	EMIL1_HUMAN	elastin microfibril interfacer 1 precursor	598	Potential.				cell adhesion	collagen				pancreas(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CTTCGGGATGGTGTGGAGCGC	0.706													19	66	---	---	---	---	PASS
GPR45	11250	broad.mit.edu	37	2	105859391	105859391	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:105859391C>A	uc002tco.1	+	1	1192	c.1076C>A	c.(1075-1077)CCA>CAA	p.P359Q		NM_007227	NP_009158	Q9Y5Y3	GPR45_HUMAN	G protein-coupled receptor 45	359	Cytoplasmic (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity|protein binding			ovary(1)|breast(1)|central_nervous_system(1)	3						AGAATCCAGCCAAGCACAGTC	0.567													19	114	---	---	---	---	PASS
RGPD4	285190	broad.mit.edu	37	2	108489172	108489172	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:108489172G>C	uc010ywk.1	+	20	4794	c.4712G>C	c.(4711-4713)GGA>GCA	p.G1571A	RGPD4_uc002tdu.2_Missense_Mutation_p.G758A|RGPD4_uc010ywl.1_Intron	NM_182588	NP_872394	Q7Z3J3	RGPD4_HUMAN	RANBP2-like and GRIP domain containing 4	1571					intracellular transport		binding			skin(2)	2						TCTTTGTTTGGATTTAGTTTT	0.348													81	337	---	---	---	---	PASS
OSBPL6	114880	broad.mit.edu	37	2	179203777	179203777	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179203777A>G	uc002ulx.2	+	10	1228	c.850A>G	c.(850-852)ATA>GTA	p.I284V	OSBPL6_uc002ulw.2_Missense_Mutation_p.I284V|OSBPL6_uc002uly.2_Missense_Mutation_p.I284V|OSBPL6_uc010zfe.1_Missense_Mutation_p.I284V|OSBPL6_uc002ulz.2_Missense_Mutation_p.I284V|OSBPL6_uc002uma.2_Missense_Mutation_p.I263V	NM_032523	NP_115912	Q9BZF3	OSBL6_HUMAN	oxysterol-binding protein-like protein 6 isoform	284					lipid transport		lipid binding			pancreas(1)	1			OV - Ovarian serous cystadenocarcinoma(117;0.00578)|Epithelial(96;0.00847)|all cancers(119;0.0335)			AAATTTGGAAATACTTCAGAG	0.353													16	65	---	---	---	---	PASS
CDK15	65061	broad.mit.edu	37	2	202700487	202700487	+	Splice_Site	SNP	G	T	T			TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:202700487G>T	uc002uyt.2	+	8	900	c.851_splice	c.e8+1	p.W284_splice	CDK15_uc010ftm.2_Splice_Site_p.W149_splice|CDK15_uc002uys.2_Splice_Site_p.W233_splice|CDK15_uc010ftn.1_Splice_Site_p.W233_splice|CDK15_uc010fto.1_Splice_Site_p.W263_splice	NM_139158	NP_631897	Q96Q40	CDK15_HUMAN	PFTAIRE protein kinase 2								ATP binding|cyclin-dependent protein kinase activity|metal ion binding|protein binding			breast(2)|ovary(1)|lung(1)|kidney(1)	5					Adenosine triphosphate(DB00171)	TGGACATATGGTAAGAGTGGT	0.438													9	41	---	---	---	---	PASS
PTH2R	5746	broad.mit.edu	37	2	209271710	209271710	+	5'UTR	SNP	G	C	C			TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:209271710G>C	uc002vdb.2	+	1					PTH2R_uc010zjb.1_Intron	NM_005048	NP_005039	P49190	PTH2R_HUMAN	parathyroid hormone 2 receptor precursor							integral to plasma membrane	parathyroid hormone receptor activity			ovary(1)|breast(1)|skin(1)	3				Epithelial(149;0.0684)|Lung(261;0.0785)|LUSC - Lung squamous cell carcinoma(261;0.0836)		TTGGCAACTTGGAAGCTTCTC	0.677													6	95	---	---	---	---	PASS
SPHKAP	80309	broad.mit.edu	37	2	228882779	228882779	+	Nonsense_Mutation	SNP	C	A	A			TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:228882779C>A	uc002vpq.2	-	7	2838	c.2791G>T	c.(2791-2793)GAA>TAA	p.E931*	SPHKAP_uc002vpp.2_Nonsense_Mutation_p.E931*|SPHKAP_uc010zlx.1_Nonsense_Mutation_p.E931*	NM_001142644	NP_001136116	Q2M3C7	SPKAP_HUMAN	sphingosine kinase type 1-interacting protein	931	PKA-RII subunit binding domain (By similarity).					cytoplasm	protein binding			skin(5)|ovary(4)|lung(1)	10		Renal(207;0.025)|all_hematologic(139;0.15)|all_lung(227;0.204)|Acute lymphoblastic leukemia(138;0.205)|Esophageal squamous(248;0.23)		Epithelial(121;8.17e-11)|all cancers(144;7.92e-08)|Lung(261;0.0168)|LUSC - Lung squamous cell carcinoma(224;0.0232)		GCTAATTCTTCCGCAAAGTCT	0.473													43	173	---	---	---	---	PASS
ATG7	10533	broad.mit.edu	37	3	11354777	11354777	+	Splice_Site	SNP	G	T	T			TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:11354777G>T	uc003bwc.2	+	6	529	c.412_splice	c.e6-1	p.D138_splice	ATG7_uc003bwd.2_Splice_Site_p.D138_splice|ATG7_uc011aum.1_Intron	NM_006395	NP_006386	O95352	ATG7_HUMAN	APG7 autophagy 7-like isoform a						autophagy|cellular membrane fusion|positive regulation of protein modification process|protein lipidation|protein transport	cytoplasm	APG12 activating enzyme activity|protein homodimerization activity|ubiquitin activating enzyme activity			central_nervous_system(1)	1						TTTTTTTCTAGGATCTAAAGA	0.368													10	44	---	---	---	---	PASS
KBTBD5	131377	broad.mit.edu	37	3	42728136	42728136	+	Silent	SNP	C	A	A			TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:42728136C>A	uc003clv.1	+	1	1126	c.1026C>A	c.(1024-1026)TCC>TCA	p.S342S		NM_152393	NP_689606	Q2TBA0	KBTB5_HUMAN	kelch repeat and BTB (POZ) domain containing 5	342										ovary(1)	1				KIRC - Kidney renal clear cell carcinoma(284;0.214)		ACTGTGCTTCCCTCTCCAACC	0.567													4	77	---	---	---	---	PASS
C3orf58	205428	broad.mit.edu	37	3	143691275	143691275	+	Nonsense_Mutation	SNP	C	A	A			TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:143691275C>A	uc003evo.2	+	1	636	c.101C>A	c.(100-102)TCG>TAG	p.S34*	C3orf58_uc011bnl.1_5'Flank	NM_173552	NP_775823	Q8NDZ4	CC058_HUMAN	hypothetical protein LOC205428 isoform a	34						COPI vesicle coat|extracellular region				ovary(1)	1						CACTCGCCGTCGCTGCTCGCC	0.692													4	13	---	---	---	---	PASS
IGSF10	285313	broad.mit.edu	37	3	151154637	151154637	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:151154637G>A	uc011bod.1	-	6	7712	c.7712C>T	c.(7711-7713)TCA>TTA	p.S2571L	IGSF10_uc011bob.1_Missense_Mutation_p.S598L|IGSF10_uc011boc.1_Missense_Mutation_p.S550L	NM_178822	NP_849144	Q6WRI0	IGS10_HUMAN	immunoglobulin superfamily, member 10 precursor	2571	Ig-like C2-type 12.				cell differentiation|multicellular organismal development|ossification	extracellular region				skin(7)|ovary(5)|central_nervous_system(1)	13			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			ACTTGCCGTTGAGAGAAGGGA	0.507													13	86	---	---	---	---	PASS
KIAA1530	57654	broad.mit.edu	37	4	1348531	1348531	+	Missense_Mutation	SNP	A	C	C			TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:1348531A>C	uc003gde.3	+	6	1390	c.943A>C	c.(943-945)AAG>CAG	p.K315Q		NM_020894	NP_065945	Q2YD98	K1530_HUMAN	hypothetical protein LOC57654	315											0			OV - Ovarian serous cystadenocarcinoma(23;0.0138)			AGAGGGCCTGAAGGTGCAGGA	0.622													5	29	---	---	---	---	PASS
GRSF1	2926	broad.mit.edu	37	4	71690078	71690078	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:71690078C>G	uc010iia.1	-	9	1484	c.1401G>C	c.(1399-1401)AGG>AGC	p.R467S	GRSF1_uc011caz.1_Missense_Mutation_p.R349S|GRSF1_uc003hfs.2_Missense_Mutation_p.R305S	NM_002092	NP_002083	Q12849	GRSF1_HUMAN	G-rich RNA sequence binding factor 1 isoform 1	467	RRM 3.				mRNA polyadenylation		mRNA binding|nucleotide binding				0		all_hematologic(202;0.21)	Lung(101;0.235)			GTTCAATATACCTATGATCTG	0.318													2	10	---	---	---	---	PASS
UGT3A2	167127	broad.mit.edu	37	5	36035666	36035666	+	3'UTR	SNP	C	T	T			TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:36035666C>T	uc003jjz.1	-	7					UGT3A2_uc011cos.1_3'UTR|UGT3A2_uc011cot.1_3'UTR	NM_174914	NP_777574	Q3SY77	UD3A2_HUMAN	UDP glycosyltransferase 3 family, polypeptide A2							integral to membrane	glucuronosyltransferase activity			ovary(2)|skin(2)|large_intestine(1)|pancreas(1)	6	all_lung(31;0.000179)		Lung(74;0.111)|Epithelial(62;0.113)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			GATTTTTGGCCATTTTTCCTG	0.443													4	2	---	---	---	---	PASS
HEXB	3074	broad.mit.edu	37	5	74014627	74014627	+	Silent	SNP	G	T	T	rs137915238	byFrequency	TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:74014627G>T	uc003kdf.3	+	11	1365	c.1248G>T	c.(1246-1248)GCG>GCT	p.A416A	HEXB_uc003kdd.2_Silent_p.A191A|HEXB_uc010izh.2_RNA|HEXB_uc003kdg.1_Intron|HEXB_uc010izi.1_Intron	NM_000521	NP_000512	P07686	HEXB_HUMAN	hexosaminidase B preproprotein	416					cell death	lysosome	cation binding|protein heterodimerization activity|protein homodimerization activity			ovary(1)	1		all_lung(232;0.00101)|Lung NSC(167;0.00278)|Ovarian(174;0.0129)|Breast(144;0.231)		OV - Ovarian serous cystadenocarcinoma(47;1.72e-57)		AATAGCTTGCGCCGGGCACAA	0.393													3	115	---	---	---	---	PASS
ACSL6	23305	broad.mit.edu	37	5	131323811	131323811	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:131323811G>A	uc010jdo.1	-	7	769	c.686C>T	c.(685-687)CCA>CTA	p.P229L	ACSL6_uc003kvv.1_RNA|ACSL6_uc003kvx.1_Missense_Mutation_p.P254L|ACSL6_uc003kvy.1_Missense_Mutation_p.P254L|ACSL6_uc003kwb.2_Missense_Mutation_p.P219L|ACSL6_uc003kvz.1_Missense_Mutation_p.P194L|ACSL6_uc003kwa.1_Missense_Mutation_p.P240L|ACSL6_uc010jdn.1_Missense_Mutation_p.P244L|ACSL6_uc010jdp.1_5'Flank	NM_015256	NP_056071	Q9UKU0	ACSL6_HUMAN	acyl-CoA synthetase long-chain family member 6	229	Cytoplasmic (Potential).				fatty acid metabolic process|long-chain fatty-acyl-CoA biosynthetic process|triglyceride biosynthetic process	endoplasmic reticulum membrane|integral to membrane|microsome|mitochondrial outer membrane|peroxisomal membrane|plasma membrane	ATP binding|long-chain fatty acid-CoA ligase activity			upper_aerodigestive_tract(1)|ovary(1)|skin(1)	3		all_cancers(142;0.107)|Breast(839;0.198)|Lung NSC(810;0.216)|all_lung(232;0.248)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			TTCTTCGAATGGGTCCATGAG	0.562													9	481	---	---	---	---	PASS
DBN1	1627	broad.mit.edu	37	5	176894482	176894482	+	Silent	SNP	C	G	G			TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176894482C>G	uc003mgy.2	-	5	649	c.477G>C	c.(475-477)GTG>GTC	p.V159V	DBN1_uc003mgx.2_Silent_p.V161V|DBN1_uc010jkn.1_Silent_p.V109V|DBN1_uc003mgz.1_Silent_p.V96V	NM_004395	NP_004386	Q16643	DREB_HUMAN	drebrin 1 isoform a	159					actin filament organization|regulation of dendrite development|regulation of neuronal synaptic plasticity	actomyosin|cytoplasm|dendrite	actin binding|profilin binding			breast(3)|ovary(1)|lung(1)|skin(1)	6	all_cancers(89;2.17e-05)|Renal(175;0.000269)|Lung NSC(126;0.0014)|all_lung(126;0.0025)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			ACACACTAACCACGGGCTCTG	0.672													5	11	---	---	---	---	PASS
DOM3Z	1797	broad.mit.edu	37	6	31938297	31938297	+	Intron	SNP	C	A	A			TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31938297C>A	uc003nyo.1	-						DOM3Z_uc003nyp.1_Intron|DOM3Z_uc003nyq.1_Intron|DOM3Z_uc003nyr.1_Intron|DOM3Z_uc003nys.1_3'UTR|DOM3Z_uc010jtl.1_3'UTR|STK19_uc003nyt.2_5'Flank|STK19_uc011dow.1_5'Flank|STK19_uc011dox.1_5'Flank|STK19_uc003nyv.2_5'Flank|STK19_uc003nyw.2_5'Flank|STK19_uc010jtn.1_5'Flank	NM_005510	NP_005501	O77932	DOM3Z_HUMAN	DOM-3 homolog Z								identical protein binding|metal ion binding|nucleotide binding				0						CCTCGTGCACCCTCCATTCTG	0.577													4	86	---	---	---	---	PASS
TAP2	6891	broad.mit.edu	37	6	32805899	32805899	+	Silent	SNP	G	A	A			TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32805899G>A	uc003occ.2	-	1	143	c.112C>T	c.(112-114)CTA>TTA	p.L38L	TAP2_uc011dqf.1_Silent_p.L38L|TAP2_uc003ocb.1_Silent_p.L38L|TAP2_uc003ocd.2_Silent_p.L38L	NM_018833	NP_061313	Q03519	TAP2_HUMAN	transporter 2, ATP-binding cassette, sub-family	38	Cytoplasmic (Potential).				antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent|antigen processing and presentation of endogenous peptide antigen via MHC class Ib via ER pathway, TAP-dependent|antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent|cytosol to ER transport|intracellular transport of viral proteins in host cell|peptide antigen transport|positive regulation of antigen processing and presentation of peptide antigen via MHC class I|positive regulation of T cell mediated cytotoxicity	nucleus|plasma membrane|TAP complex	ATP binding|MHC class I protein binding|oligopeptide-transporting ATPase activity|peptide antigen binding|peptide antigen-transporting ATPase activity|TAP1 binding|TAP2 binding|tapasin binding				0						TCCAGCCATAGTCCTGGCAGC	0.637													16	61	---	---	---	---	PASS
DNAH8	1769	broad.mit.edu	37	6	38952015	38952015	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:38952015G>A	uc003ooe.1	+	85	12934	c.12334G>A	c.(12334-12336)GGA>AGA	p.G4112R	DNAH8_uc003oog.1_Missense_Mutation_p.G561R	NM_001371	NP_001362			dynein, axonemal, heavy polypeptide 8											skin(8)|ovary(7)|lung(2)|large_intestine(1)|central_nervous_system(1)|kidney(1)|pancreas(1)	21						GTACATGATCGGAGAAGTACA	0.348													17	75	---	---	---	---	PASS
TDRD6	221400	broad.mit.edu	37	6	46657639	46657639	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:46657639C>G	uc003oyj.2	+	1	1774	c.1774C>G	c.(1774-1776)CAG>GAG	p.Q592E	TDRD6_uc010jze.2_Missense_Mutation_p.Q586E	NM_001010870	NP_001010870	O60522	TDRD6_HUMAN	tudor domain containing 6	592	Tudor 3.				cell differentiation|multicellular organismal development|spermatogenesis	chromatoid body	nucleic acid binding			breast(3)|ovary(2)|skin(1)	6			Lung(136;0.192)			TCAGTTTAGGCAGCTACCAAT	0.448													34	110	---	---	---	---	PASS
RAB23	51715	broad.mit.edu	37	6	57075110	57075110	+	Silent	SNP	T	A	A			TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57075110T>A	uc003pds.2	-	2	275	c.69A>T	c.(67-69)TCA>TCT	p.S23S	RAB23_uc003pdt.2_Silent_p.S23S|RAB23_uc010kac.2_Silent_p.S23S|RAB23_uc010kad.2_RNA	NM_183227	NP_899050	Q9ULC3	RAB23_HUMAN	Ras-related protein Rab-23	23	GTP (By similarity).				protein transport|small GTPase mediated signal transduction	plasma membrane	GTP binding			skin(1)	1	Lung NSC(77;0.121)		LUSC - Lung squamous cell carcinoma(124;0.0785)|Lung(124;0.13)			GAATCATACTTGATTTTCCAA	0.393													31	181	---	---	---	---	PASS
EEF1A1	1915	broad.mit.edu	37	6	74228230	74228230	+	Silent	SNP	G	T	T			TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:74228230G>T	uc003phi.2	-	5	913	c.876C>A	c.(874-876)GTC>GTA	p.V292V	EEF1A1_uc003phd.2_Silent_p.V17V|EEF1A1_uc003phe.2_Silent_p.V282V|EEF1A1_uc003phf.2_Silent_p.V292V|EEF1A1_uc003phg.2_Silent_p.V292V|EEF1A1_uc003phh.2_Silent_p.V138V|EEF1A1_uc003phj.2_Silent_p.V292V|EEF1A1_uc003phk.2_Silent_p.V292V|EEF1A1_uc003phl.2_Intron|EEF1A1_uc003phm.1_Intron	NM_001402	NP_001393	P68104	EF1A1_HUMAN	eukaryotic translation elongation factor 1 alpha	292						cytosol|eukaryotic translation elongation factor 1 complex	GTP binding|GTPase activity|protein binding|translation elongation factor activity				0						GGTGCATTTCGACAGATTTTA	0.488											OREG0003895	type=REGULATORY REGION|Gene=D16891|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	11	42	---	---	---	---	PASS
SLC35A1	10559	broad.mit.edu	37	6	88210341	88210341	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:88210341A>G	uc011dzj.1	+	3	389	c.310A>G	c.(310-312)ATG>GTG	p.M104V	SLC35A1_uc003plx.2_RNA|SLC35A1_uc010kbw.2_5'UTR|SLC35A1_uc003plz.2_Intron|SLC35A1_uc011dzi.1_Intron|SLC35A1_uc003ply.2_RNA|SLC35A1_uc010kbx.2_Missense_Mutation_p.M104V|SLC35A1_uc010kby.2_RNA	NM_006416	NP_006407	P78382	S35A1_HUMAN	solute carrier family 35 (CMP-sialic acid	104	Helical; (Potential).				carbohydrate metabolic process|protein modification process	Golgi membrane|integral to plasma membrane	CMP-N-acetylneuraminate transmembrane transporter activity|sugar:hydrogen symporter activity				0		all_cancers(76;3.93e-06)|Acute lymphoblastic leukemia(125;3.55e-10)|Prostate(29;3.51e-09)|all_hematologic(105;3.29e-06)|all_epithelial(107;0.00575)		BRCA - Breast invasive adenocarcinoma(108;0.0429)		TCAGAACAACATGGCTTTCCT	0.403													14	76	---	---	---	---	PASS
GPER	2852	broad.mit.edu	37	7	1131562	1131562	+	Silent	SNP	C	A	A			TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:1131562C>A	uc010ksd.1	+	2	587	c.198C>A	c.(196-198)ACC>ACA	p.T66T	C7orf50_uc003sju.2_Intron|C7orf50_uc011jvt.1_Intron|C7orf50_uc011jvu.1_Intron|GPER_uc003sjz.1_Silent_p.T66T|GPER_uc003ska.1_Silent_p.T66T|GPER_uc003skb.2_Silent_p.T66T	NM_001098201	NP_001091671	Q99527	GPER_HUMAN	G protein-coupled receptor 30	66	Helical; Name=1; (Potential).					endoplasmic reticulum membrane|Golgi membrane|integral to plasma membrane	G-protein coupled receptor activity			ovary(1)	1		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0178)|OV - Ovarian serous cystadenocarcinoma(56;2.32e-16)		GCCTCTACACCATCTTCCTCT	0.592													3	67	---	---	---	---	PASS
ANKMY2	57037	broad.mit.edu	37	7	16655424	16655424	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:16655424T>C	uc003sti.2	-	5	676	c.476A>G	c.(475-477)AAG>AGG	p.K159R	ANKMY2_uc010ktz.2_RNA	NM_020319	NP_064715	Q8IV38	ANKY2_HUMAN	ankyrin repeat and MYND domain containing 2	159	ANK 3.					cilium	zinc ion binding			central_nervous_system(1)	1	Lung NSC(10;0.103)|all_lung(11;0.204)			UCEC - Uterine corpus endometrioid carcinoma (126;0.195)		GCCTGCCAACTTTGGGGGCAG	0.428													12	57	---	---	---	---	PASS
MACC1	346389	broad.mit.edu	37	7	20180449	20180449	+	3'UTR	SNP	G	C	C	rs113534252		TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:20180449G>C	uc003sus.3	-	7					MACC1_uc010kug.2_3'UTR	NM_182762	NP_877439	Q6ZN28	MACC1_HUMAN	putative binding protein 7a5						positive regulation of cell division|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus|plasma membrane	growth factor activity			ovary(2)|skin(1)	3						cacacacacagacacacacac	0.164													3	35	---	---	---	---	PASS
HERPUD2	64224	broad.mit.edu	37	7	35673462	35673462	+	Intron	SNP	C	T	T			TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:35673462C>T	uc003tet.2	-						HERPUD2_uc003tes.3_Intron	NM_022373	NP_071768	Q9BSE4	HERP2_HUMAN	HERPUD family member 2						response to unfolded protein	integral to membrane				ovary(3)	3						TAAGACGCTCCTTTCAAGCAA	0.403													33	114	---	---	---	---	PASS
INHBA	3624	broad.mit.edu	37	7	41729694	41729694	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:41729694C>A	uc003thq.2	-	2	1070	c.835G>T	c.(835-837)GCA>TCA	p.A279S	INHBA_uc003thr.2_Missense_Mutation_p.A279S	NM_002192	NP_002183	P08476	INHBA_HUMAN	inhibin beta A precursor	279					cell cycle arrest|cell surface receptor linked signaling pathway|defense response|erythrocyte differentiation|eyelid development in camera-type eye|G1/S transition of mitotic cell cycle|growth|hair follicle development|hemoglobin biosynthetic process|hemopoietic progenitor cell differentiation|induction of apoptosis|male gonad development|negative regulation of B cell differentiation|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of follicle-stimulating hormone secretion|negative regulation of interferon-gamma biosynthetic process|negative regulation of macrophage differentiation|negative regulation of phosphorylation|nervous system development|odontogenesis|ovarian follicle development|palate development|positive regulation of erythrocyte differentiation|positive regulation of follicle-stimulating hormone secretion|positive regulation of ovulation|positive regulation of transcription from RNA polymerase II promoter|progesterone secretion|regulation of activin receptor signaling pathway	activin A complex|inhibin A complex	cytokine activity|follistatin binding|growth factor activity|hormone activity|identical protein binding|signal transducer activity			lung(5)|ovary(1)	6						tctgctcctgccccaccttca	0.378										TSP Lung(11;0.080)			16	55	---	---	---	---	PASS
PILRB	29990	broad.mit.edu	37	7	99956460	99956460	+	Nonsense_Mutation	SNP	G	A	A			TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99956460G>A	uc003uuk.2	+	16	2708	c.212G>A	c.(211-213)TGG>TAG	p.W71*	PILRB_uc003uul.2_Intron|PILRB_uc003uum.1_RNA|PILRB_uc003uun.2_Nonsense_Mutation_p.W71*	NM_013440	NP_038468	Q9UKJ0	PILRB_HUMAN	paired immunoglobulin-like type 2 receptor beta	71	Extracellular (Potential).|Ig-like V-type.				activation of transmembrane receptor protein tyrosine kinase activity	integral to plasma membrane	protein binding|receptor activity				0	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					AGAATATCCTGGAGACGGGGC	0.537													27	99	---	---	---	---	PASS
RHEB	6009	broad.mit.edu	37	7	151181869	151181869	+	Missense_Mutation	SNP	A	T	T			TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151181869A>T	uc003wkh.1	-	3	559	c.146T>A	c.(145-147)GTA>GAA	p.V49E		NM_005614	NP_005605	Q15382	RHEB_HUMAN	Ras homolog enriched in brain precursor	49				V->A: Causes slightly reduced phosphorylation of EIF4EBP1.	cell cycle arrest|insulin receptor signaling pathway|positive regulation of TOR signaling cascade|small GTPase mediated signal transduction	cytosol|plasma membrane	GTP binding|GTPase activity|metal ion binding|protein binding			large_intestine(1)|lung(1)	2			OV - Ovarian serous cystadenocarcinoma(82;0.00306)	UCEC - Uterine corpus endometrioid carcinoma (81;0.174)		TTGTCCATTTACTGTGATCAA	0.358													11	53	---	---	---	---	PASS
BMP1	649	broad.mit.edu	37	8	22034151	22034151	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:22034151A>G	uc003xbg.2	+	4	783	c.539A>G	c.(538-540)TAT>TGT	p.Y180C	BMP1_uc011kzb.1_RNA|BMP1_uc003xba.2_Missense_Mutation_p.Y180C|BMP1_uc003xbb.2_Missense_Mutation_p.Y180C|BMP1_uc003xbe.2_RNA|BMP1_uc003xbc.2_5'UTR|BMP1_uc003xbd.2_RNA|BMP1_uc003xbf.2_5'UTR|BMP1_uc011kzc.1_5'UTR|BMP1_uc003xbh.2_RNA|BMP1_uc003xbi.2_RNA	NM_006129	NP_006120	P13497	BMP1_HUMAN	bone morphogenetic protein 1 isoform 3	180	Metalloprotease.				cartilage condensation|cell differentiation|lipid metabolic process|lipoprotein metabolic process|ossification|positive regulation of cartilage development|proteolysis	extracellular space	calcium ion binding|cytokine activity|growth factor activity|metalloendopeptidase activity|zinc ion binding			ovary(2)|breast(1)	3				Colorectal(74;0.00229)|COAD - Colon adenocarcinoma(73;0.0661)|READ - Rectum adenocarcinoma(644;0.11)		GTGTTCACCTATCGACCTTGC	0.627													21	77	---	---	---	---	PASS
EXTL3	2137	broad.mit.edu	37	8	28574199	28574199	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:28574199G>A	uc003xgz.1	+	3	1216	c.623G>A	c.(622-624)AGC>AAC	p.S208N		NM_001440	NP_001431	O43909	EXTL3_HUMAN	exostoses-like 3	208	Lumenal (Potential).					integral to membrane|intrinsic to endoplasmic reticulum membrane	glucuronyl-galactosyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity|metal ion binding|protein binding			skin(2)	2		Ovarian(32;0.069)		KIRC - Kidney renal clear cell carcinoma(542;0.107)|Kidney(114;0.129)|Colorectal(74;0.228)		GTCTTTGGCAGCTACCTGGAT	0.512													20	87	---	---	---	---	PASS
TMEM68	137695	broad.mit.edu	37	8	56652730	56652730	+	Silent	SNP	T	C	C			TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:56652730T>C	uc003xsg.1	-	6	1005	c.936A>G	c.(934-936)CCA>CCG	p.P312P	TMEM68_uc003xsh.1_Silent_p.P245P	NM_152417	NP_689630	Q96MH6	TMM68_HUMAN	transmembrane protein 68	312						integral to membrane	acyltransferase activity			skin(1)	1			Epithelial(17;0.000361)|all cancers(17;0.00326)			TAATGTTTCCTGGTATTCTTT	0.299													18	62	---	---	---	---	PASS
C8orf34	116328	broad.mit.edu	37	8	69621309	69621309	+	Nonsense_Mutation	SNP	C	G	G			TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:69621309C>G	uc010lyz.2	+	9	1113	c.1064C>G	c.(1063-1065)TCA>TGA	p.S355*	C8orf34_uc003xyb.2_Nonsense_Mutation_p.S330*	NM_052958	NP_443190	Q49A92	CH034_HUMAN	hypothetical protein LOC116328	355					signal transduction		cAMP-dependent protein kinase regulator activity			large_intestine(1)	1			Epithelial(68;0.0117)|OV - Ovarian serous cystadenocarcinoma(28;0.0227)|all cancers(69;0.0502)			ATCCCAGATTCATTCGGTAAG	0.343													7	46	---	---	---	---	PASS
ZFPM2	23414	broad.mit.edu	37	8	106810965	106810965	+	Silent	SNP	T	C	C			TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:106810965T>C	uc003ymd.2	+	7	776	c.753T>C	c.(751-753)CCT>CCC	p.P251P	ZFPM2_uc011lhs.1_5'UTR|uc003yme.1_5'Flank	NM_012082	NP_036214	Q8WW38	FOG2_HUMAN	zinc finger protein, multitype 2	251	C2HC-type 1.				blood coagulation|negative regulation of fat cell differentiation|outflow tract septum morphogenesis|right ventricular cardiac muscle tissue morphogenesis|ventricular septum morphogenesis	nucleoplasm	DNA binding|RNA polymerase II transcription coactivator activity|transcription corepressor activity|transcription factor binding|zinc ion binding			ovary(4)|large_intestine(1)	5			OV - Ovarian serous cystadenocarcinoma(57;8.28e-08)			ATATATTCCCTTGCAAGTCCT	0.468													8	34	---	---	---	---	PASS
MLLT3	4300	broad.mit.edu	37	9	20414343	20414343	+	Silent	SNP	A	G	G			TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:20414343A>G	uc003zoe.2	-	5	760	c.501T>C	c.(499-501)AGT>AGC	p.S167S	MLLT3_uc011lne.1_Silent_p.S135S|MLLT3_uc011lnf.1_Silent_p.S164S|MLLT3_uc003zof.2_5'UTR|MLLT3_uc011lng.1_Missense_Mutation_p.V129A	NM_004529	NP_004520	P42568	AF9_HUMAN	myeloid/lymphoid or mixed-lineage leukemia	167	Poly-Ser.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	protein binding			lung(2)|ovary(1)	3				GBM - Glioblastoma multiforme(3;4.35e-105)|Lung(42;3.48e-06)|LUSC - Lung squamous cell carcinoma(42;7.92e-05)		tgctgctgctactgctgctgc	0.139			T	MLL	ALL								4	40	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	9	21278188	21278188	+	RNA	SNP	C	G	G			TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:21278188C>G	uc003zou.1	-	1		c.375G>C								Messenger RNA for human leukocyte (alpha) interferon.																		AAAGTATTTTCTCACAGCCAG	0.453													26	179	---	---	---	---	PASS
LOC442421	442421	broad.mit.edu	37	9	66500810	66500810	+	RNA	SNP	G	A	A	rs142815546	by1000genomes	TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66500810G>A	uc004aed.1	+	3		c.903G>A								Homo sapiens similar to prostaglandin E receptor 4, subtype EP4; PGE receptor, EP4 subtype; prostaglandin E2 receptor, mRNA (cDNA clone IMAGE:5288780).												0						ACCTACGGTCGGTTGTGTGCA	0.637													9	19	---	---	---	---	PASS
C9orf84	158401	broad.mit.edu	37	9	114484858	114484858	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:114484858C>A	uc004bfr.2	-	13	1905	c.1770G>T	c.(1768-1770)CAG>CAT	p.Q590H	C9orf84_uc011lwt.1_RNA|C9orf84_uc004bfq.2_Missense_Mutation_p.Q551H|C9orf84_uc010mug.2_Missense_Mutation_p.Q536H	NM_173521	NP_775792	Q5VXU9	CI084_HUMAN	hypothetical protein LOC158401 isoform 1	590										ovary(2)	2						ATGCTTGGCACTGGCTATCTG	0.388													19	67	---	---	---	---	PASS
SLC25A25	114789	broad.mit.edu	37	9	130865982	130865982	+	Missense_Mutation	SNP	T	A	A			TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130865982T>A	uc004bte.2	+	5	538	c.509T>A	c.(508-510)CTA>CAA	p.L170Q	SLC25A25_uc004btb.2_Missense_Mutation_p.L204Q|SLC25A25_uc004btc.2_Missense_Mutation_p.L190Q|SLC25A25_uc004btd.2_Missense_Mutation_p.L202Q|SLC25A25_uc004btf.2_Missense_Mutation_p.L67Q	NM_052901	NP_443133	Q6KCM7	SCMC2_HUMAN	solute carrier family 25, member 25 isoform a	170	Mitochondrial intermembrane (Potential).				transmembrane transport	integral to membrane|mitochondrial inner membrane	calcium ion binding				0						GGTGAGAATCTAACGGTCCCG	0.597													12	58	---	---	---	---	PASS
DDX31	64794	broad.mit.edu	37	9	135470291	135470291	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:135470291C>G	uc004cbq.1	-	20	2670	c.2518G>C	c.(2518-2520)GGT>CGT	p.G840R	DDX31_uc010mzu.1_Missense_Mutation_p.G767R	NM_022779	NP_073616	Q9H8H2	DDX31_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 31	840						nucleolus	ATP binding|ATP-dependent helicase activity|RNA binding			central_nervous_system(1)	1				OV - Ovarian serous cystadenocarcinoma(145;2.67e-06)|Epithelial(140;7.61e-05)		CGCTGTACACCTTTTTGGGTT	0.552													49	200	---	---	---	---	PASS
SSNA1	8636	broad.mit.edu	37	9	140083619	140083619	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140083619G>A	uc004cls.2	+	2	279	c.154G>A	c.(154-156)GAG>AAG	p.E52K	ANAPC2_uc004clq.1_5'Flank|ANAPC2_uc004clr.1_5'Flank|ANAPC2_uc011mer.1_5'Flank	NM_003731	NP_003722	O43805	SSNA1_HUMAN	nuclear autoantigen of 14 kDa	52	Potential.				G2/M transition of mitotic cell cycle	centrosome|cytosol|nucleus				breast(1)	1	all_cancers(76;0.0926)		STAD - Stomach adenocarcinoma(284;0.0698)	OV - Ovarian serous cystadenocarcinoma(145;6.43e-05)|Epithelial(140;0.00087)		GCAGCTGACAGAGAAGCTGGC	0.627													8	21	---	---	---	---	PASS
CSRP3	8048	broad.mit.edu	37	11	19213960	19213960	+	Silent	SNP	G	A	A			TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:19213960G>A	uc001mpk.2	-	2	153	c.36C>T	c.(34-36)GCC>GCT	p.A12A		NM_003476	NP_003467	P50461	CSRP3_HUMAN	cysteine and glycine-rich protein 3	12	LIM zinc-binding 1.				cell differentiation|skeletal muscle tissue development	cytoskeleton|nucleus	protein binding|zinc ion binding				0						TCTTTTCACAGGCTCCACATT	0.498													17	60	---	---	---	---	PASS
CSRP3	8048	broad.mit.edu	37	11	19213973	19213973	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:19213973G>T	uc001mpk.2	-	2	140	c.23C>A	c.(22-24)GCA>GAA	p.A8E		NM_003476	NP_003467	P50461	CSRP3_HUMAN	cysteine and glycine-rich protein 3	8					cell differentiation|skeletal muscle tissue development	cytoskeleton|nucleus	protein binding|zinc ion binding				0						TCCACATTTTGCGCCTCCGCC	0.493													16	56	---	---	---	---	PASS
LRRN4CL	221091	broad.mit.edu	37	11	62455461	62455461	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62455461C>G	uc001nun.2	-	2	827	c.520G>C	c.(520-522)GGG>CGG	p.G174R		NM_203422	NP_981967	Q8ND94	LRN4L_HUMAN	LRRN4 C-terminal like precursor	174	Extracellular (Potential).					integral to membrane					0						ATGTCGGCCCCCTCGAGGCCC	0.721													5	12	---	---	---	---	PASS
CCDC82	79780	broad.mit.edu	37	11	96098194	96098194	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:96098194A>G	uc009ywp.2	-	5	1573	c.1330T>C	c.(1330-1332)TAT>CAT	p.Y444H	CCDC82_uc009ywq.2_Missense_Mutation_p.Y444H|CCDC82_uc001pfx.3_Missense_Mutation_p.Y444H|CCDC82_uc009ywr.2_Missense_Mutation_p.Y444H	NM_024725	NP_079001	Q8N4S0	CCD82_HUMAN	coiled-coil domain containing 82	444							protein binding			ovary(1)	1		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)		BRCA - Breast invasive adenocarcinoma(274;0.154)		CTGGTGTTATACAACTCTCCT	0.328													13	72	---	---	---	---	PASS
ATM	472	broad.mit.edu	37	11	108199913	108199913	+	Nonsense_Mutation	SNP	A	T	T			TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:108199913A>T	uc001pkb.1	+	49	7640	c.7255A>T	c.(7255-7257)AGA>TGA	p.R2419*	ATM_uc009yxr.1_Nonsense_Mutation_p.R2419*|C11orf65_uc010rvx.1_Intron|ATM_uc001pke.1_Nonsense_Mutation_p.R1071*|ATM_uc001pkg.1_Nonsense_Mutation_p.R776*	NM_000051	NP_000042	Q13315	ATM_HUMAN	ataxia telangiectasia mutated isoform 1	2419	FAT.				cell cycle arrest|cellular response to gamma radiation|DNA damage induced protein phosphorylation|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|double-strand break repair via homologous recombination|G2/M transition DNA damage checkpoint|histone mRNA catabolic process|mitotic cell cycle spindle assembly checkpoint|negative regulation of B cell proliferation|peptidyl-serine phosphorylation|positive regulation of DNA damage response, signal transduction by p53 class mediator|pre-B cell allelic exclusion|protein autophosphorylation|reciprocal meiotic recombination|replicative senescence	cytoplasmic membrane-bounded vesicle|nucleoplasm	1-phosphatidylinositol-3-kinase activity|ATP binding|DNA binding|DNA-dependent protein kinase activity|identical protein binding|protein complex binding|protein dimerization activity|protein N-terminus binding	p.K2418_R2419insK(1)		haematopoietic_and_lymphoid_tissue(174)|lung(25)|breast(15)|large_intestine(9)|ovary(5)|kidney(5)|central_nervous_system(4)|upper_aerodigestive_tract(1)|stomach(1)|NS(1)	240		all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147)		TCTCCTGAAAAGAGCCAAAGA	0.373			D|Mis|N|F|S		T-PLL	leukemia|lymphoma|medulloblastoma|glioma		Genes_defective_in_diseases_associated_with_sensitivity_to_DNA_damaging_agents	Ataxia_Telangiectasia	TSP Lung(14;0.12)			19	45	---	---	---	---	PASS
RAPGEF3	10411	broad.mit.edu	37	12	48143587	48143587	+	Silent	SNP	C	T	T			TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:48143587C>T	uc009zkp.2	-	8	1145	c.705G>A	c.(703-705)GGG>GGA	p.G235G	RAPGEF3_uc010sln.1_5'Flank|RAPGEF3_uc001rpy.2_5'Flank|RAPGEF3_uc009zkq.2_Silent_p.G235G|RAPGEF3_uc001rpz.3_Silent_p.G277G|RAPGEF3_uc001rqa.2_5'Flank|RAPGEF3_uc009zkr.2_RNA|RAPGEF3_uc009zks.2_Silent_p.G289G|RAPGEF3_uc001rqb.3_Silent_p.G277G	NM_001098532	NP_001092002	A8K2G5	A8K2G5_HUMAN	Rap guanine nucleotide exchange factor 3 isoform	235					regulation of protein phosphorylation|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cAMP-dependent protein kinase complex	cAMP-dependent protein kinase regulator activity|guanyl-nucleotide exchange factor activity			lung(2)|skin(1)|pancreas(1)	4	Lung SC(27;0.192)			GBM - Glioblastoma multiforme(48;0.0375)		TGCCCTTGTCCCCCTGGCTGA	0.602													24	113	---	---	---	---	PASS
AAAS	8086	broad.mit.edu	37	12	53702266	53702266	+	Silent	SNP	C	A	A			TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53702266C>A	uc001scr.3	-	12	1297	c.1134G>T	c.(1132-1134)GTG>GTT	p.V378V	AAAS_uc001scs.3_Silent_p.V345V	NM_015665	NP_056480	Q9NRG9	AAAS_HUMAN	achalasia, adrenocortical insufficiency,	378					carbohydrate metabolic process|glucose transport|nucleocytoplasmic transport|regulation of glucose transport|regulation of nucleocytoplasmic transport|transmembrane transport|viral reproduction	nuclear pore				ovary(1)	1						ACAGATCTGCCACAATCGTTG	0.527													20	126	---	---	---	---	PASS
FZD10	11211	broad.mit.edu	37	12	130648324	130648324	+	Silent	SNP	C	T	T			TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:130648324C>T	uc001uii.2	+	1	1293	c.837C>T	c.(835-837)ATC>ATT	p.I279I	uc001uig.1_5'Flank|uc001uih.1_5'Flank	NM_007197	NP_009128	Q9ULW2	FZD10_HUMAN	frizzled 10 precursor	279	Helical; Name=2; (Potential).				brain development|canonical Wnt receptor signaling pathway|cellular response to retinoic acid|embryo development|gonad development|negative regulation of Rho GTPase activity|neuron differentiation|non-canonical Wnt receptor signaling pathway|positive regulation of JUN kinase activity|positive regulation of Rac GTPase activity|regulation of actin cytoskeleton organization|vasculature development	cell projection|cell surface|cytoplasm|integral to plasma membrane	G-protein coupled receptor activity|PDZ domain binding|Wnt receptor activity|Wnt-protein binding			lung(3)|breast(1)|central_nervous_system(1)	5	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.3e-06)|Epithelial(86;1.66e-05)|all cancers(50;5.18e-05)		GCTACCTCATCCGCCTCTTCG	0.657													30	98	---	---	---	---	PASS
SACS	26278	broad.mit.edu	37	13	23904812	23904812	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:23904812C>A	uc001uon.2	-	10	13792	c.13203G>T	c.(13201-13203)TGG>TGT	p.W4401C	SACS_uc001uoo.2_Missense_Mutation_p.W4254C|SACS_uc001uop.1_Intron|SACS_uc001uoq.1_Intron	NM_014363	NP_055178	Q9NZJ4	SACS_HUMAN	sacsin	4401					cell death|negative regulation of inclusion body assembly|protein folding	axon|cell body fiber|dendrite|mitochondrion|nucleus	ATP binding|chaperone binding|Hsp70 protein binding|proteasome binding			ovary(7)|skin(2)|upper_aerodigestive_tract(1)|large_intestine(1)|pancreas(1)	12		all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189)		CTTCTTGATTCCATGAAGTAT	0.423													25	106	---	---	---	---	PASS
AKAP11	11215	broad.mit.edu	37	13	42872846	42872846	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:42872846A>G	uc001uys.1	+	7	704	c.529A>G	c.(529-531)AAC>GAC	p.N177D		NM_016248	NP_057332	Q9UKA4	AKA11_HUMAN	A-kinase anchor protein 11	177					intracellular protein kinase cascade	microtubule organizing center	protein kinase A binding|protein phosphatase 1 binding			ovary(1)|central_nervous_system(1)	2		Lung NSC(96;1.86e-05)|Prostate(109;0.0165)|Lung SC(185;0.0262)|Breast(139;0.0707)|Hepatocellular(98;0.114)		OV - Ovarian serous cystadenocarcinoma(117;0.000365)|GBM - Glioblastoma multiforme(144;0.00116)|BRCA - Breast invasive adenocarcinoma(63;0.19)		TGATGATACTAACCAGTCTGT	0.398													4	115	---	---	---	---	PASS
FGF14	2259	broad.mit.edu	37	13	103053874	103053874	+	Missense_Mutation	SNP	T	A	A			TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:103053874T>A	uc001vpf.2	-	1	251	c.155A>T	c.(154-156)CAT>CTT	p.H52L		NM_175929	NP_787125	Q92915	FGF14_HUMAN	fibroblast growth factor 14 isoform 1B	Error:Variant_position_missing_in_Q92915_after_alignment					cell death|cell-cell signaling|JNK cascade|nervous system development|signal transduction	nucleus	growth factor activity|heparin binding			ovary(2)|lung(1)|large_intestine(1)	4	all_neural(89;0.0239)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					CTGCAGCATATGCGTTCCTTT	0.408													25	97	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	14	19856989	19856989	+	RNA	SNP	C	G	G			TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:19856989C>G	uc001vvq.1	-	5		c.541G>C								Homo sapiens cDNA FLJ12852 fis, clone NT2RP2003445.																		TCACAGTGCTCTAAAAGCTCT	0.398													3	79	---	---	---	---	PASS
FERMT2	10979	broad.mit.edu	37	14	53385908	53385908	+	Silent	SNP	A	G	G			TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:53385908A>G	uc001xad.2	-	3	379	c.324T>C	c.(322-324)TAT>TAC	p.Y108Y	FERMT2_uc001xac.2_Silent_p.Y108Y|FERMT2_uc001xae.2_Silent_p.Y108Y|FERMT2_uc001xaf.2_Silent_p.Y108Y	NM_006832	NP_006823	Q96AC1	FERM2_HUMAN	fermitin family homolog 2 isoform 1	108					actin cytoskeleton organization|cell adhesion|cell junction assembly|regulation of cell shape	cell cortex|cytosol|focal adhesion|stress fiber	binding				0	Breast(41;0.0342)					TCACCTTCACATACTTCATGT	0.393													38	103	---	---	---	---	PASS
TBPL2	387332	broad.mit.edu	37	14	55895569	55895569	+	Silent	SNP	G	A	A			TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:55895569G>A	uc001xby.2	-	5	912	c.912C>T	c.(910-912)CCC>CCT	p.P304P		NM_199047	NP_950248	Q6SJ96	TBPL2_HUMAN	TATA box binding protein like 2	304					multicellular organismal development|transcription initiation from RNA polymerase II promoter	cytoplasm|nucleus	DNA binding				0						CCAGCCTGATGGGAAATCTCA	0.408													32	81	---	---	---	---	PASS
KIAA0284	283638	broad.mit.edu	37	14	105361169	105361169	+	Silent	SNP	A	C	C			TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:105361169A>C	uc010axb.2	+	19	4763	c.4539A>C	c.(4537-4539)TCA>TCC	p.S1513S	INF2_uc010tyi.1_Intron|KIAA0284_uc001ypr.2_Silent_p.S1443S|KIAA0284_uc001yps.2_Silent_p.S1454S|KIAA0284_uc001ypt.2_Silent_p.S181S	NM_001112726	NP_001106197	Q9Y4F5	K0284_HUMAN	hypothetical protein LOC283638 isoform 1	1548						cytoplasm|microtubule				breast(1)	1		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000472)|OV - Ovarian serous cystadenocarcinoma(23;0.00596)|Epithelial(46;0.0149)|GBM - Glioblastoma multiforme(11;0.116)	Epithelial(152;0.178)		GCCCACCCTCACCCGCCTCAG	0.711													3	15	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	15	22440773	22440773	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:22440773C>T	uc001yug.2	-	1	93	c.74G>A	c.(73-75)CGG>CAG	p.R25Q						full-length cDNA clone CS0DI014YE21 of Placenta Cot 25-normalized of Homo sapiens (human).																		CTCATACTTCCGCTTCTTGTG	0.577													4	12	---	---	---	---	PASS
SCAMP5	192683	broad.mit.edu	37	15	75311376	75311376	+	3'UTR	SNP	C	A	A			TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:75311376C>A	uc002azk.1	+	7					SCAMP5_uc002azl.1_3'UTR|SCAMP5_uc002azm.1_3'UTR|SCAMP5_uc002azn.1_3'UTR|SCAMP5_uc010uly.1_3'UTR	NM_138967	NP_620417	Q8TAC9	SCAM5_HUMAN	secretory carrier membrane protein 5						exocytosis|negative regulation of endocytosis|positive regulation of calcium ion-dependent exocytosis|positive regulation of cytokine secretion|protein transport|response to endoplasmic reticulum stress	cell junction|integral to membrane|recycling endosome membrane|synaptic vesicle membrane|trans-Golgi network membrane	protein binding			ovary(1)	1						ACAGGGGGCTCAAGCCACATC	0.498													7	11	---	---	---	---	PASS
PCSK6	5046	broad.mit.edu	37	15	101971643	101971643	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:101971643C>A	uc002bwy.2	-	5	853	c.539G>T	c.(538-540)TGC>TTC	p.C180F	PCSK6_uc010bpd.2_Missense_Mutation_p.C50F|PCSK6_uc010bpe.2_Missense_Mutation_p.C180F|PCSK6_uc002bxa.2_Missense_Mutation_p.C180F|PCSK6_uc002bxb.2_Missense_Mutation_p.C180F|PCSK6_uc002bxc.1_Missense_Mutation_p.C180F|PCSK6_uc002bxd.1_Missense_Mutation_p.C180F|PCSK6_uc002bxe.2_Missense_Mutation_p.C180F|PCSK6_uc002bxg.1_Missense_Mutation_p.C180F	NM_002570	NP_002561	P29122	PCSK6_HUMAN	paired basic amino acid cleaving system 4	180	Catalytic.				glycoprotein metabolic process|nerve growth factor processing|nerve growth factor production|nerve growth factor receptor signaling pathway|regulation of BMP signaling pathway|secretion by cell	cell surface|endomembrane system|endoplasmic reticulum|extracellular matrix|extracellular space|Golgi lumen|membrane|soluble fraction	eukaryotic cell surface binding|heparin binding|nerve growth factor binding|serine-type endopeptidase activity			pancreas(2)	2	Lung NSC(78;0.00102)|all_lung(78;0.00128)|Melanoma(26;0.00505)		OV - Ovarian serous cystadenocarcinoma(32;0.000803)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)			TTCCGACCGGCAGCGACTGTT	0.532													4	18	---	---	---	---	PASS
PDIA2	64714	broad.mit.edu	37	16	337078	337078	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:337078G>A	uc002cgn.1	+	16	2651	c.1543G>A	c.(1543-1545)GCC>ACC	p.A515T	PDIA2_uc010bqt.1_Missense_Mutation_p.A360T|PDIA2_uc002cgo.1_Missense_Mutation_p.A515T	NM_006849	NP_006840	Q13087	PDIA2_HUMAN	protein disulfide isomerase A2 precursor	515					apoptosis|cell redox homeostasis|glycerol ether metabolic process|protein folding|protein retention in ER lumen|response to hypoxia	endoplasmic reticulum lumen	electron carrier activity|protein binding|protein disulfide isomerase activity|protein disulfide oxidoreductase activity|steroid binding			central_nervous_system(1)|skin(1)	2		all_cancers(16;6.71e-07)|all_epithelial(16;1.59e-06)|Hepatocellular(16;0.000105)|Lung NSC(18;0.00769)|all_lung(18;0.0186)				GGAGCCACCGGCCAACTCCAC	0.632													3	62	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	16	16418712	16418712	+	3'UTR	SNP	G	A	A			TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:16418712G>A	uc010vab.1	+	12					uc002der.3_RNA|uc010vac.1_5'UTR					SubName: Full=cDNA FLJ59085, highly similar to Polycystin-1;																		CCAACCGCCCGCCGCTGGGGG	0.687													5	11	---	---	---	---	PASS
PDXDC2	283970	broad.mit.edu	37	16	70010646	70010646	+	3'UTR	SNP	G	A	A	rs149870591	by1000genomes	TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70010646G>A	uc010vlq.1	-	6					CLEC18C_uc002exy.2_Intron|PDXDC2_uc002eyb.2_Intron|PDXDC2_uc002eyc.2_Intron					SubName: Full=Putative uncharacterized protein;												0						CTGTAGGGCCGAAGAAGGGAA	0.478													4	64	---	---	---	---	PASS
PDXDC2	283970	broad.mit.edu	37	16	70010650	70010650	+	3'UTR	SNP	A	G	G	rs144900726	by1000genomes	TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70010650A>G	uc010vlq.1	-	6					CLEC18C_uc002exy.2_Intron|PDXDC2_uc002eyb.2_Intron|PDXDC2_uc002eyc.2_Intron					SubName: Full=Putative uncharacterized protein;												0						AGGGCCGAAGAAGGGAATGTT	0.468													4	59	---	---	---	---	PASS
PITPNM3	83394	broad.mit.edu	37	17	6386893	6386893	+	Silent	SNP	G	A	A			TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:6386893G>A	uc002gdd.3	-	6	682	c.531C>T	c.(529-531)CTC>CTT	p.L177L	PITPNM3_uc010cln.2_Silent_p.L141L|PITPNM3_uc002gdc.3_5'Flank	NM_031220	NP_112497	Q9BZ71	PITM3_HUMAN	PITPNM family member 3 isoform 1	177					phosphatidylinositol metabolic process	endomembrane system|integral to membrane	calcium ion binding|lipid binding|phosphatidylinositol transporter activity|receptor tyrosine kinase binding			ovary(2)|central_nervous_system(2)	4				Colorectal(2;0.000372)|READ - Rectum adenocarcinoma(2;0.0276)|LUAD - Lung adenocarcinoma(2;0.0836)|COAD - Colon adenocarcinoma(228;0.185)		CGAACTTGATGAGGATGTGGC	0.592													11	45	---	---	---	---	PASS
FLJ36000	284124	broad.mit.edu	37	17	21904083	21904083	+	RNA	SNP	C	A	A			TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21904083C>A	uc002gza.2	+	1		c.22C>A				NR_027084				Homo sapiens cDNA FLJ36000 fis, clone TESTI2015180.												0						ctgacctctccacggggtcca	0.000													3	22	---	---	---	---	PASS
CDK3	1018	broad.mit.edu	37	17	73998205	73998205	+	Silent	SNP	C	A	A			TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73998205C>A	uc010dgt.2	+	4	373	c.297C>A	c.(295-297)CTC>CTA	p.L99L	CDK3_uc002jqg.3_Silent_p.L127L	NM_001258	NP_001249	Q00526	CDK3_HUMAN	cyclin-dependent kinase 3	99	Protein kinase.				cell division|cell proliferation|mitosis		ATP binding|cyclin-dependent protein kinase activity			central_nervous_system(1)	1						GCTCAGAGCTCCCCCTGCACC	0.597													7	70	---	---	---	---	PASS
ALPK2	115701	broad.mit.edu	37	18	56205356	56205356	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:56205356G>A	uc002lhj.3	-	5	2277	c.2063C>T	c.(2062-2064)ACA>ATA	p.T688I	ALPK2_uc002lhk.1_Missense_Mutation_p.T19I	NM_052947	NP_443179	Q86TB3	ALPK2_HUMAN	heart alpha-kinase	688							ATP binding|protein serine/threonine kinase activity			ovary(7)|skin(5)|lung(1)|central_nervous_system(1)	14						GAAGGAAATTGTTGTGGTCCC	0.498													21	61	---	---	---	---	PASS
VPS4B	9525	broad.mit.edu	37	18	61064237	61064237	+	Intron	SNP	G	A	A	rs71995228		TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:61064237G>A	uc002lix.2	-						VPS4B_uc010dpx.2_Silent_p.I374I|VPS4B_uc010dpy.2_Silent_p.I256I	NM_004869	NP_004860	O75351	VPS4B_HUMAN	vacuolar protein sorting factor 4B						cell cycle|cell division|cellular membrane organization|endosome to lysosome transport via multivesicular body sorting pathway|intracellular cholesterol transport|protein transport|response to lipid	cytosol|early endosome|late endosome membrane|lysosome|nucleus|vacuolar membrane	ATP binding|ATPase activity, coupled|protein C-terminus binding			ovary(1)	1						aaaaaaaaaaGATAGGAAAGG	0.179													7	36	---	---	---	---	PASS
FBXW9	84261	broad.mit.edu	37	19	12807200	12807200	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12807200G>A	uc010dyx.2	-	1	196	c.196C>T	c.(196-198)CGG>TGG	p.R66W	FBXW9_uc010xmp.1_RNA|FBXW9_uc002mum.1_Missense_Mutation_p.R66W|FBXW9_uc002mun.1_5'UTR	NM_032301	NP_115677	Q5XUX1	FBXW9_HUMAN	F-box and WD-40 domain protein 9	66							protein binding			ovary(1)	1						GACGCGGCCCGAGGCTCCGAA	0.697													4	14	---	---	---	---	PASS
HAUS8	93323	broad.mit.edu	37	19	17169444	17169444	+	Missense_Mutation	SNP	T	G	G			TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17169444T>G	uc002nfe.2	-	8	671	c.560A>C	c.(559-561)AAG>ACG	p.K187T	HAUS8_uc002nff.2_Missense_Mutation_p.K186T|HAUS8_uc002nfg.1_Missense_Mutation_p.K126T|HAUS8_uc002nfh.1_Missense_Mutation_p.K187T	NM_033417	NP_219485	Q9BT25	HAUS8_HUMAN	sarcoma antigen NY-SAR-48 isoform a	187	Potential.				cell division|centrosome organization|mitosis|spindle assembly	centrosome|HAUS complex|microtubule|spindle pole					0						TTTCTGTAGCTTCTCCTTCTC	0.453													16	58	---	---	---	---	PASS
SFRS14	10147	broad.mit.edu	37	19	19129981	19129981	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:19129981C>T	uc002nkx.2	-	4	1933	c.1787G>A	c.(1786-1788)CGT>CAT	p.R596H	SFRS14_uc002nkz.1_Missense_Mutation_p.R610H|SFRS14_uc002nla.1_Missense_Mutation_p.R596H|SFRS14_uc002nlb.2_Missense_Mutation_p.R596H|SFRS14_uc010xqk.1_Missense_Mutation_p.R365H	NM_014884	NP_055699	Q8IX01	SUGP2_HUMAN	splicing factor, arginine/serine-rich 14	596	SURP motif 1.				mRNA processing|RNA splicing	nucleus	RNA binding				0			OV - Ovarian serous cystadenocarcinoma(5;3.05e-05)|Epithelial(12;0.00161)			TTCGATGACACGTTTCACAAG	0.507													10	46	---	---	---	---	PASS
RYR1	6261	broad.mit.edu	37	19	39008078	39008078	+	Silent	SNP	G	T	T			TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39008078G>T	uc002oit.2	+	66	9895	c.9765G>T	c.(9763-9765)GGG>GGT	p.G3255G	RYR1_uc002oiu.2_Silent_p.G3255G|RYR1_uc002oiv.1_Silent_p.G175G|RYR1_uc010xuf.1_Silent_p.G175G	NM_000540	NP_000531	P21817	RYR1_HUMAN	skeletal muscle ryanodine receptor isoform 1	3255					muscle contraction|release of sequestered calcium ion into cytosol|response to caffeine|response to hypoxia	cell cortex|cytosol|I band|integral to plasma membrane|junctional sarcoplasmic reticulum membrane|smooth endoplasmic reticulum|terminal cisterna	calcium ion binding|calmodulin binding|receptor activity|ryanodine-sensitive calcium-release channel activity			ovary(7)|pancreas(2)|breast(1)|central_nervous_system(1)|skin(1)	12	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Dantrolene(DB01219)	ACATTGGGGGGCTGGCCGAGT	0.662													9	44	---	---	---	---	PASS
AKT2	208	broad.mit.edu	37	19	40739535	40739535	+	3'UTR	SNP	A	G	G			TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:40739535A>G	uc002onf.2	-	14					AKT2_uc010egs.2_3'UTR|AKT2_uc010egt.2_3'UTR|AKT2_uc010xvj.1_3'UTR|AKT2_uc002one.2_3'UTR	NM_001626	NP_001617	P31751	AKT2_HUMAN	AKT2 kinase						insulin receptor signaling pathway|negative regulation of plasma membrane long-chain fatty acid transport|positive regulation of fatty acid beta-oxidation|positive regulation of glucose import|positive regulation of glycogen biosynthetic process	cytosol|nucleus	ATP binding|protein binding|protein serine/threonine kinase activity			lung(2)	2			Lung(22;0.000499)			CCAACAGCCCAGGCCTGGGCG	0.647			A		ovarian|pancreatic 								11	43	---	---	---	---	PASS
ETFB	2109	broad.mit.edu	37	19	51857941	51857941	+	Intron	SNP	A	T	T			TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51857941A>T	uc002pwh.2	-						ETFB_uc002pwg.2_5'UTR	NM_001985	NP_001976	P38117	ETFB_HUMAN	electron-transfer-flavoprotein, beta polypeptide						respiratory electron transport chain|transport	mitochondrial matrix	electron carrier activity				0		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000226)|OV - Ovarian serous cystadenocarcinoma(262;0.00661)		CTGATACATAAATACAAATga	0.159													9	27	---	---	---	---	PASS
ZNF808	388558	broad.mit.edu	37	19	53058493	53058493	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53058493G>T	uc010epq.1	+	5	2501	c.2324G>T	c.(2323-2325)TGG>TTG	p.W775L	ZNF808_uc002pzq.2_RNA|ZNF808_uc010epr.1_5'Flank	NM_001039886	NP_001034975	Q8N4W9	ZN808_HUMAN	zinc finger protein 808	775	C2H2-type 20.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0				OV - Ovarian serous cystadenocarcinoma(262;0.00501)|GBM - Glioblastoma multiforme(134;0.0213)		TTCCGTCACTGGTCATCCCTT	0.443													52	223	---	---	---	---	PASS
ZNF761	388561	broad.mit.edu	37	19	53945909	53945909	+	Intron	SNP	T	C	C	rs28727441	by1000genomes	TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53945909T>C	uc010eqp.2	+						LOC147804_uc002qbo.2_RNA|LOC147804_uc002qbq.2_RNA|LOC147804_uc002qbp.2_RNA|ZNF761_uc002qbr.2_Intron|ZNF761_uc010ydy.1_5'Flank	NM_001008401	NP_001008401	Q86XN6	ZN761_HUMAN	zinc finger protein 761						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1				GBM - Glioblastoma multiforme(134;0.00786)		ACCCTGACTCTGCCTGAGGCC	0.562													3	68	---	---	---	---	PASS
LILRB1	10859	broad.mit.edu	37	19	55147170	55147170	+	Intron	SNP	C	T	T			TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55147170C>T	uc002qgj.2	+						LILRB1_uc010erp.1_Missense_Mutation_p.P202L|LILRB1_uc002qgl.2_Intron|LILRB1_uc002qgk.2_Intron|LILRB1_uc002qgm.2_Intron|LILRB1_uc010erq.2_Intron|LILRB1_uc010err.2_Intron	NM_006669	NP_006660	Q8NHL6	LIRB1_HUMAN	leukocyte immunoglobulin-like receptor,						regulation of immune response|response to virus	integral to membrane|plasma membrane	protein phosphatase 1 binding|receptor activity			large_intestine(1)|ovary(1)|skin(1)	3				GBM - Glioblastoma multiforme(193;0.0188)		CACGGTGGACCCCTCCTTGTC	0.652										HNSCC(37;0.09)			6	50	---	---	---	---	PASS
CDC45	8318	broad.mit.edu	37	22	19467681	19467681	+	Missense_Mutation	SNP	A	T	T			TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:19467681A>T	uc002zpr.2	+	2	128	c.52A>T	c.(52-54)AGG>TGG	p.R18W	UFD1L_uc002zpm.2_5'Flank|UFD1L_uc002zpo.2_5'Flank|UFD1L_uc011agy.1_5'Flank|UFD1L_uc002zpp.2_5'Flank|UFD1L_uc010grq.2_5'Flank|CDC45_uc011agz.1_Missense_Mutation_p.R13W|CDC45_uc011aha.1_Missense_Mutation_p.R18W|CDC45_uc002zps.2_Missense_Mutation_p.R18W|CDC45_uc002zpt.2_Missense_Mutation_p.R18W	NM_003504	NP_003495	O75419	CDC45_HUMAN	CDC45-like	18					DNA replication checkpoint|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|M/G1 transition of mitotic cell cycle|regulation of transcription involved in G1/S phase of mitotic cell cycle|S phase of mitotic cell cycle	centrosome|nucleoplasm	protein binding			lung(1)	1						TCCCCGATAGAGGGTCCTTCT	0.682													18	76	---	---	---	---	PASS
PI4KAP1	728233	broad.mit.edu	37	22	20385733	20385733	+	RNA	SNP	A	G	G			TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:20385733A>G	uc010gse.1	-	12		c.1968T>C			PI4KAP1_uc010gsf.1_RNA|PI4KAP1_uc010gsg.1_RNA|PI4KAP1_uc010gsh.1_RNA|PI4KAP1_uc002zsc.3_RNA					Homo sapiens cDNA FLJ11279 fis, clone PLACE1009444, highly similar to PHOSPHATIDYLINOSITOL 4-KINASE ALPHA (EC 2.7.1.67).												0						TACTTCAAGAACTTGATTGTC	0.537													3	7	---	---	---	---	PASS
GTSE1	51512	broad.mit.edu	37	22	46708174	46708174	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:46708174G>T	uc011aqy.1	+	5	1111	c.899G>T	c.(898-900)GGC>GTC	p.G300V	GTSE1_uc011aqz.1_Missense_Mutation_p.G147V	NM_016426	NP_057510	Q9NYZ3	GTSE1_HUMAN	G-2 and S-phase expressed 1	281					DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G2 phase of mitotic cell cycle|microtubule-based process	cytoplasmic microtubule				ovary(1)	1		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00462)		TTGGGCCAGGGCAAGCGGGCG	0.592													7	39	---	---	---	---	PASS
HDAC10	83933	broad.mit.edu	37	22	50686660	50686660	+	Nonsense_Mutation	SNP	G	A	A			TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50686660G>A	uc003bkg.2	-	12	1448	c.1075C>T	c.(1075-1077)CAG>TAG	p.Q359*	HDAC10_uc003bke.2_Nonsense_Mutation_p.Q85*|HDAC10_uc003bkf.2_Nonsense_Mutation_p.Q85*|HDAC10_uc010hav.2_Nonsense_Mutation_p.Q339*|HDAC10_uc003bkh.2_Nonsense_Mutation_p.Q152*|HDAC10_uc003bki.2_Nonsense_Mutation_p.Q309*|HDAC10_uc003bkj.2_RNA|HDAC10_uc003bkk.1_5'UTR	NM_032019	NP_114408	Q969S8	HDA10_HUMAN	histone deacetylase 10 isoform 1	359					negative regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	cytoplasm|histone deacetylase complex|nucleus	histone deacetylase activity|histone deacetylase activity (H3-K16 specific)|histone deacetylase binding|NAD-dependent histone deacetylase activity (H3-K14 specific)|NAD-dependent histone deacetylase activity (H3-K9 specific)|NAD-dependent histone deacetylase activity (H4-K16 specific)				0		all_cancers(38;5.78e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)		TGACCTTGCTGCTGGAGGCTC	0.627													4	71	---	---	---	---	PASS
TAF1	6872	broad.mit.edu	37	X	70602417	70602417	+	Silent	SNP	T	C	C			TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:70602417T>C	uc004dzu.3	+	10	1617	c.1566T>C	c.(1564-1566)TCT>TCC	p.S522S	BCYRN1_uc011mpt.1_Intron|TAF1_uc004dzt.3_Silent_p.S543S	NM_138923	NP_620278	P21675	TAF1_HUMAN	TBP-associated factor 1 isoform 2	522					G1 phase of mitotic cell cycle|interspecies interaction between organisms|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription initiation from RNA polymerase II promoter|protein autophosphorylation|regulation of transcription involved in G2/M-phase of mitotic cell cycle|RNA polymerase II transcriptional preinitiation complex assembly|transcription elongation from RNA polymerase II promoter|viral reproduction	MLL1 complex|transcription factor TFIID complex	ATP binding|histone acetyl-lysine binding|histone acetyltransferase activity|p53 binding|protein binding|protein serine/threonine kinase activity|sequence-specific DNA binding|TBP-class protein binding|transcription coactivator activity			ovary(7)|breast(4)|large_intestine(2)|central_nervous_system(2)|lung(1)|skin(1)	17	Renal(35;0.156)	all_lung(315;0.000321)				AGGCCACCTCTAACTCCCCCT	0.443													24	88	---	---	---	---	PASS
BRWD3	254065	broad.mit.edu	37	X	79991541	79991541	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:79991541C>G	uc004edt.2	-	9	1123	c.860G>C	c.(859-861)GGT>GCT	p.G287A	BRWD3_uc004edo.2_5'UTR|BRWD3_uc004edp.2_Missense_Mutation_p.G116A|BRWD3_uc004edq.2_Intron|BRWD3_uc010nmj.1_Intron|BRWD3_uc004edr.2_Intron|BRWD3_uc004eds.2_Intron|BRWD3_uc004edu.2_Intron|BRWD3_uc004edv.2_5'UTR|BRWD3_uc004edw.2_Intron|BRWD3_uc004edx.2_5'UTR|BRWD3_uc004edy.2_Intron|BRWD3_uc004edz.2_Intron|BRWD3_uc004eea.2_Intron|BRWD3_uc004eeb.2_5'UTR	NM_153252	NP_694984	Q6RI45	BRWD3_HUMAN	bromodomain and WD repeat domain containing 3	287	WD 4.									ovary(4)	4						TCCATCAGCACCAGTAGAAGT	0.294													11	50	---	---	---	---	PASS
HCFC1	3054	broad.mit.edu	37	X	153214721	153214721	+	3'UTR	SNP	T	G	G			TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:153214721T>G	uc004fjp.2	-	26						NM_005334	NP_005325	P51610	HCFC1_HUMAN	host cell factor 1						cell cycle|interspecies interaction between organisms|positive regulation of cell cycle|positive regulation of gene expression|protein stabilization|reactivation of latent virus|regulation of protein complex assembly|transcription from RNA polymerase II promoter	mitochondrion|MLL1 complex|MLL5-L complex|Set1C/COMPASS complex	chromatin binding|identical protein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity			ovary(2)	2	all_cancers(53;6.23e-16)|all_epithelial(53;5.61e-10)|all_lung(58;3.99e-07)|Lung NSC(58;5.02e-07)|all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					TGGGACGGGGTGGGAGGGGTG	0.542													11	63	---	---	---	---	PASS
KIAA0090	23065	broad.mit.edu	37	1	19563461	19563462	+	Intron	INS	-	A	A	rs71577881		TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:19563461_19563462insA	uc001bbo.2	-						KIAA0090_uc001bbp.2_Intron|KIAA0090_uc001bbq.2_Intron|KIAA0090_uc001bbr.2_Intron	NM_015047	NP_055862	Q8N766	K0090_HUMAN	hypothetical protein LOC23065 precursor							integral to membrane	protein binding			ovary(1)	1		Colorectal(325;0.000147)|Renal(390;0.000469)|Breast(348;0.00366)|all_lung(284;0.00519)|Lung NSC(340;0.00544)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0707)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00492)|BRCA - Breast invasive adenocarcinoma(304;3.84e-05)|Kidney(64;0.000191)|KIRC - Kidney renal clear cell carcinoma(64;0.00274)|GBM - Glioblastoma multiforme(114;0.005)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0656)		gactctatctcaaaaaaaaaaa	0.198													4	2	---	---	---	---	
C1orf177	163747	broad.mit.edu	37	1	55279346	55279352	+	Intron	DEL	CCGGCCT	-	-	rs67384270		TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:55279346_55279352delCCGGCCT	uc001cyb.3	+						C1orf177_uc001cya.3_Intron	NM_001110533	NP_001104003	Q3ZCV2	CA177_HUMAN	hypothetical protein LOC163747 isoform 2												0						TGAGGCTGGCCCGGCCTCCGGCCTCCG	0.604													3	3	---	---	---	---	
LIN9	286826	broad.mit.edu	37	1	226475683	226475683	+	Intron	DEL	T	-	-			TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:226475683delT	uc001hqa.2	-						LIN9_uc001hqb.2_Intron|LIN9_uc001hqc.2_Intron|LIN9_uc009xel.1_Intron	NM_173083	NP_775106	Q5TKA1	LIN9_HUMAN	lin-9 homolog						cell cycle|DNA replication	nucleoplasm					0	Breast(184;0.158)			GBM - Glioblastoma multiforme(131;0.131)		GATTATTGCCttttttttttt	0.139													4	2	---	---	---	---	
COG2	22796	broad.mit.edu	37	1	230778244	230778244	+	5'UTR	DEL	C	-	-			TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:230778244delC	uc001htw.2	+	1					COG2_uc001htx.2_5'UTR|COG2_uc010pwc.1_5'UTR	NM_007357	NP_031383	Q14746	COG2_HUMAN	component of oligomeric golgi complex 2 isoform						Golgi organization|intra-Golgi vesicle-mediated transport|intracellular protein transport|oligosaccharide biosynthetic process|protein glycosylation	Golgi membrane|Golgi stack|Golgi transport complex	protein binding|protein transporter activity				0	Breast(184;0.0871)|Ovarian(103;0.183)	Prostate(94;0.178)				CGGAAGCGGACCCCCCTGTGC	0.726													4	2	---	---	---	---	
ASXL2	55252	broad.mit.edu	37	2	26079232	26079233	+	Intron	INS	-	TTTTTT	TTTTTT	rs143352675		TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:26079232_26079233insTTTTTT	uc002rgs.2	-							NM_018263	NP_060733	Q76L83	ASXL2_HUMAN	additional sex combs like 2						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	metal ion binding|protein binding			pancreas(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					ctggccTATACttttttttttt	0.218													6	3	---	---	---	---	
PSME4	23198	broad.mit.edu	37	2	54131004	54131005	+	Intron	INS	-	T	T			TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:54131004_54131005insT	uc002rxp.2	-						PSME4_uc010yop.1_Intron|PSME4_uc010yoq.1_Intron|PSME4_uc010fbu.1_Intron|PSME4_uc010fbv.1_Intron	NM_014614	NP_055429	Q14997	PSME4_HUMAN	proteasome (prosome, macropain) activator						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|cell differentiation|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|M/G1 transition of mitotic cell cycle|mRNA metabolic process|multicellular organismal development|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|spermatogenesis|viral reproduction	nuclear speck|proteasome complex	binding			ovary(2)|breast(2)|pancreas(1)	5			Lung(47;0.125)|LUSC - Lung squamous cell carcinoma(58;0.181)			tttgaaatacattaaaaaaaag	0.074													6	3	---	---	---	---	
HAT1	8520	broad.mit.edu	37	2	172809273	172809273	+	Intron	DEL	T	-	-			TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:172809273delT	uc002uhi.2	+						HAT1_uc010fqi.2_Intron|HAT1_uc002uhj.2_Intron	NM_003642	NP_003633	O14929	HAT1_HUMAN	histone acetyltransferase 1						chromatin silencing at telomere|DNA packaging	cytoplasm|nuclear matrix|nucleoplasm	histone acetyltransferase activity|protein binding			large_intestine(1)|ovary(1)	2			OV - Ovarian serous cystadenocarcinoma(117;0.216)			TTATTGTAGATTTTTTTTTTA	0.129													4	2	---	---	---	---	
C2orf80	389073	broad.mit.edu	37	2	209047927	209047928	+	Intron	INS	-	T	T			TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:209047927_209047928insT	uc002vcr.2	-							NM_001099334	NP_001092804	Q0P641	CB080_HUMAN	hypothetical protein LOC389073											skin(1)	1						GCTCGGCCAGATTTTTTTTTTT	0.406													6	4	---	---	---	---	
TMEM207	131920	broad.mit.edu	37	3	190147704	190147704	+	Intron	DEL	A	-	-	rs67899321		TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:190147704delA	uc003fsj.2	-							NM_207316	NP_997199	Q6UWW9	TM207_HUMAN	transmembrane protein 207 precursor							integral to membrane					0	all_cancers(143;3.61e-10)|Ovarian(172;0.0991)		Lung(62;2.23e-05)|LUSC - Lung squamous cell carcinoma(58;3.15e-05)	GBM - Glioblastoma multiforme(93;0.0176)		CACAGGGGGGAAAAAAAAAAT	0.353													4	2	---	---	---	---	
RGS12	6002	broad.mit.edu	37	4	3314643	3314644	+	5'Flank	INS	-	A	A	rs10647468		TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3314643_3314644insA	uc003ggw.2	+						RGS12_uc003ggu.2_Intron|RGS12_uc010ics.1_Intron|RGS12_uc011bvr.1_Intron|RGS12_uc003ggv.2_5'Flank	NM_198229	NP_937872	O14924	RGS12_HUMAN	regulator of G-protein signalling 12 isoform 1							condensed nuclear chromosome|cytoplasm|plasma membrane	GTPase activator activity|receptor signaling protein activity			skin(1)	1				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)		CAGTTTTCTCCAAAAAAAAAAA	0.272													4	2	---	---	---	---	
DAPP1	27071	broad.mit.edu	37	4	100784875	100784876	+	Intron	INS	-	T	T	rs71913814		TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:100784875_100784876insT	uc003hvf.3	+						DAPP1_uc011cek.1_Intron|DAPP1_uc010ilh.2_Intron	NM_014395	NP_055210	Q9UN19	DAPP1_HUMAN	dual adaptor of phosphotyrosine and						signal transduction	cytoplasm|plasma membrane	phosphatidylinositol-3,4,5-trisphosphate binding|phosphatidylinositol-3,4-bisphosphate binding|protein tyrosine phosphatase activity				0				OV - Ovarian serous cystadenocarcinoma(123;7.04e-09)		AGATTTGTCTGTTTTTTTTTTT	0.356													4	3	---	---	---	---	
NHEDC1	150159	broad.mit.edu	37	4	103826510	103826511	+	Intron	DEL	CA	-	-			TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:103826510_103826511delCA	uc003hww.2	-						NHEDC1_uc003hwu.2_Intron|NHEDC1_uc010ilm.2_Intron|NHEDC1_uc003hwv.2_Intron|NHEDC1_uc011cev.1_Intron	NM_139173	NP_631912	Q4ZJI4	NHDC1_HUMAN	Na+/H+ exchanger domain containing 1 isoform 1							integral to membrane	solute:hydrogen antiporter activity			ovary(1)|skin(1)	2		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;1.5e-08)		cctgagtagccaggaCTGGTTA	0.119													11	5	---	---	---	---	
CHD1	1105	broad.mit.edu	37	5	98199049	98199049	+	Intron	DEL	A	-	-			TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:98199049delA	uc003knf.2	-						CHD1_uc010jbn.2_Intron	NM_001270	NP_001261	O14646	CHD1_HUMAN	chromodomain helicase DNA binding protein 1						regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	cytoplasm|nucleus	ATP binding|ATP-dependent DNA helicase activity|DNA binding|methylated histone residue binding			lung(2)|ovary(1)|breast(1)|pancreas(1)	5		all_cancers(142;5.36e-08)|all_epithelial(76;6.97e-11)|Lung NSC(167;0.000693)|Prostate(80;0.000986)|all_lung(232;0.00119)|Ovarian(225;0.024)|Colorectal(57;0.117)		COAD - Colon adenocarcinoma(37;0.0717)	Epirubicin(DB00445)	GAAAGAAAACAAAAAAAAAAA	0.254													9	5	---	---	---	---	
C5orf48	389320	broad.mit.edu	37	5	125971528	125971528	+	Intron	DEL	A	-	-	rs71573967		TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:125971528delA	uc003kub.1	+							NM_207408	NP_997291	Q6ZNM6	CE048_HUMAN	hypothetical protein LOC389320											ovary(1)	1						ctaattttttattttttgtat	0.000													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	30665317	30665317	+	IGR	DEL	T	-	-	rs137943555		TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:30665317delT								NRM (6259 upstream) : MDC1 (2268 downstream)																							tttctctctcttttttttttt	0.194													5	4	---	---	---	---	
KCTD20	222658	broad.mit.edu	37	6	36452323	36452323	+	Intron	DEL	A	-	-			TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:36452323delA	uc003ome.2	+						KCTD20_uc011dtm.1_Intron|KCTD20_uc011dtn.1_Intron|KCTD20_uc010jwk.2_Intron|KCTD20_uc011dto.1_Intron	NM_173562	NP_775833	Q7Z5Y7	KCD20_HUMAN	potassium channel tetramerisation domain							voltage-gated potassium channel complex	voltage-gated potassium channel activity			ovary(2)	2						ctgagactataaaaatttctc	0.065													7	4	---	---	---	---	
RNGTT	8732	broad.mit.edu	37	6	89614281	89614282	+	Intron	INS	-	A	A	rs113231405		TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:89614281_89614282insA	uc003pmr.2	-						RNGTT_uc003pms.2_Intron|RNGTT_uc011dzu.1_Intron|RNGTT_uc003pmt.2_Intron	NM_003800	NP_003791	O60942	MCE1_HUMAN	RNA guanylyltransferase and 5'-phosphatase						interspecies interaction between organisms|mRNA capping|transcription from RNA polymerase II promoter|viral reproduction	nucleoplasm	GTP binding|mRNA guanylyltransferase activity|polynucleotide 5'-phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			upper_aerodigestive_tract(1)	1		all_cancers(76;4.07e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.49e-10)|all_hematologic(105;7.79e-07)|all_epithelial(107;6.86e-05)		BRCA - Breast invasive adenocarcinoma(108;0.151)		actttctctccaaaaaaaaaaa	0.129													4	2	---	---	---	---	
SASH1	23328	broad.mit.edu	37	6	148869296	148869297	+	Intron	INS	-	CACT	CACT	rs150196011	by1000genomes	TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:148869296_148869297insCACT	uc003qme.1	+						SASH1_uc003qmf.1_Intron	NM_015278	NP_056093	O94885	SASH1_HUMAN	SAM and SH3 domain containing 1								protein binding			central_nervous_system(1)	1		Ovarian(120;0.0169)		OV - Ovarian serous cystadenocarcinoma(155;5.63e-11)|GBM - Glioblastoma multiforme(68;0.0701)		TTGATCTCTGACACTCATTGCA	0.401													3	6	---	---	---	---	
NUP205	23165	broad.mit.edu	37	7	135287861	135287862	+	Intron	DEL	TT	-	-	rs145569473		TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:135287861_135287862delTT	uc003vsw.2	+							NM_015135	NP_055950	Q92621	NU205_HUMAN	nucleoporin 205kDa						carbohydrate metabolic process|glucose transport|mRNA transport|protein import into nucleus, docking|regulation of glucose transport|transmembrane transport|viral reproduction	nuclear pore	protein binding			ovary(3)|breast(1)|central_nervous_system(1)|skin(1)	6						CTCAttttactttttttttttt	0.144													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	142045168	142045169	+	Intron	INS	-	AATTCAAA	AATTCAAA			TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142045168_142045169insAATTCAAA	uc011kro.1	+						uc011krp.1_Intron|uc011krr.1_Intron|uc003vxp.3_5'Flank|uc011krt.1_5'Flank					SubName: Full=V_segment translation product; Flags: Fragment;																		CCAGCCCAGACAATTCAAATCT	0.520													5	3	---	---	---	---	
GALNT12	79695	broad.mit.edu	37	9	101602544	101602545	+	Intron	INS	-	C	C	rs145380479	by1000genomes	TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:101602544_101602545insC	uc004ayz.2	+							NM_024642	NP_078918	Q8IXK2	GLT12_HUMAN	N-acetylgalactosaminyltransferase 12							Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			upper_aerodigestive_tract(1)|ovary(1)	2		Acute lymphoblastic leukemia(62;0.0559)				CCGCCTGCCCACCCCCCACCAC	0.510													8	6	---	---	---	---	
CUBN	8029	broad.mit.edu	37	10	17109903	17109903	+	Intron	DEL	A	-	-	rs63451761		TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:17109903delA	uc001ioo.2	-							NM_001081	NP_001072	O60494	CUBN_HUMAN	cubilin precursor						cholesterol metabolic process|cobalamin transport|hormone biosynthetic process|lipoprotein metabolic process|receptor-mediated endocytosis|tissue homeostasis|vitamin D metabolic process	brush border membrane|cytosol|endosome membrane|extrinsic to external side of plasma membrane|lysosomal lumen|lysosomal membrane	calcium ion binding|cobalamin binding|protein homodimerization activity|receptor activity|transporter activity			ovary(9)|breast(4)|pancreas(2)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)|kidney(1)	19					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	taATGCCTACAAGGCCACAAC	0.214													2	6	---	---	---	---	
ECD	11319	broad.mit.edu	37	10	74913882	74913883	+	Intron	INS	-	T	T			TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:74913882_74913883insT	uc001jtn.2	-						ECD_uc009xqx.2_Intron|ECD_uc009xqy.2_Intron|ECD_uc001jto.2_Intron	NM_007265	NP_009196	O95905	SGT1_HUMAN	suppressor of S. cerevisiae gcr2 isoform 1						regulation of glycolysis|regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	cytoplasm|nucleus	transcription coactivator activity			pancreas(1)	1	Prostate(51;0.0119)					AGAATATTTCCTTTTTTTTCTA	0.173													4	2	---	---	---	---	
MYOF	26509	broad.mit.edu	37	10	95095461	95095462	+	Intron	INS	-	TTTCC	TTTCC	rs148769270	by1000genomes	TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:95095461_95095462insTTTCC	uc001kin.2	-						MYOF_uc001kio.2_Intron|MYOF_uc009xue.2_Intron	NM_013451	NP_038479	Q9NZM1	MYOF_HUMAN	myoferlin isoform a						blood circulation|muscle contraction|plasma membrane repair	caveola|cytoplasmic vesicle membrane|integral to membrane|nuclear membrane	phospholipid binding|protein binding			ovary(3)|breast(1)	4						CCCCTCCCCCTTTTCCTTTCTG	0.574													6	3	---	---	---	---	
IFITM2	10581	broad.mit.edu	37	11	307939	307940	+	5'Flank	INS	-	T	T	rs150923440	by1000genomes	TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:307939_307940insT	uc001lox.3	+							NM_006435	NP_006426	Q01629	IFM2_HUMAN	interferon induced transmembrane protein 2						response to virus|type I interferon-mediated signaling pathway	integral to membrane|plasma membrane	protein binding				0		all_cancers(49;2e-09)|all_epithelial(84;3.36e-06)|Breast(177;0.000162)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.0538)|all_lung(207;0.0713)		all cancers(45;5.73e-28)|Epithelial(43;3.42e-27)|OV - Ovarian serous cystadenocarcinoma(40;1.14e-20)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0328)|LUSC - Lung squamous cell carcinoma(625;0.122)		TCTCCAGGACCCCACACCACTA	0.589													5	4	---	---	---	---	
GAL	51083	broad.mit.edu	37	11	68458593	68458593	+	3'UTR	DEL	T	-	-	rs75147512		TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:68458593delT	uc001oob.2	+	6						NM_015973	NP_057057	P22466	GALA_HUMAN	galanin preproprotein						growth hormone secretion|insulin secretion|neuropeptide signaling pathway|smooth muscle contraction	extracellular region	neuropeptide hormone activity				0	Esophageal squamous(3;7.33e-10)	Melanoma(852;0.0749)	LUAD - Lung adenocarcinoma(13;0.0514)	Kidney(183;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(183;3.23e-08)|Lung(977;0.000152)|LUSC - Lung squamous cell carcinoma(976;0.00154)		TCATTTAAGATTTTTTTTTTT	0.358													4	2	---	---	---	---	
DNAJB13	374407	broad.mit.edu	37	11	73680791	73680794	+	Intron	DEL	AAAC	-	-	rs34820619		TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:73680791_73680794delAAAC	uc001ouo.2	+							NM_153614	NP_705842	P59910	DJB13_HUMAN	testis spermatogenesis apoptosis-related protein						apoptosis|protein folding|spermatogenesis		heat shock protein binding|unfolded protein binding				0	Breast(11;7.42e-05)					CCCATGTCTTAAACAAAGTTTCTG	0.529													3	5	---	---	---	---	
XRRA1	143570	broad.mit.edu	37	11	74645032	74645033	+	Intron	INS	-	TTCA	TTCA	rs140602440	by1000genomes	TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:74645032_74645033insTTCA	uc009yub.2	-						XRRA1_uc001ovm.2_Intron|XRRA1_uc001ovo.2_Intron|XRRA1_uc001ovq.3_Intron|XRRA1_uc001ovp.3_Intron|XRRA1_uc001ovr.2_Intron	NM_182969	NP_892014	Q6P2D8	XRRA1_HUMAN	X-ray radiation resistance associated 1						response to X-ray	cytoplasm|nucleus				central_nervous_system(1)	1						TTGTTTGCTTGttcattcattc	0.193													4	2	---	---	---	---	
DLAT	1737	broad.mit.edu	37	11	111897029	111897029	+	Intron	DEL	T	-	-	rs113392665		TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:111897029delT	uc001pmo.2	+						DLAT_uc009yyk.1_Intron|DLAT_uc010rwr.1_Intron	NM_001931	NP_001922	P10515	ODP2_HUMAN	dihydrolipoamide S-acetyltransferase precursor						glycolysis|regulation of acetyl-CoA biosynthetic process from pyruvate	mitochondrial pyruvate dehydrogenase complex	dihydrolipoyllysine-residue acetyltransferase activity|protein binding				0		all_cancers(61;4.53e-11)|all_epithelial(67;2.76e-06)|Melanoma(852;9.42e-06)|all_hematologic(158;0.000885)|Acute lymphoblastic leukemia(157;0.000966)|Breast(348;0.0512)|Medulloblastoma(222;0.0523)|all_neural(223;0.0663)		Epithelial(105;4.87e-07)|BRCA - Breast invasive adenocarcinoma(274;6.83e-07)|all cancers(92;9.63e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.0557)	NADH(DB00157)	CAGAGGTAAGttttttttttt	0.244													8	4	---	---	---	---	
MLL	4297	broad.mit.edu	37	11	118309874	118309874	+	Intron	DEL	A	-	-	rs67536668		TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118309874delA	uc001pta.2	+						MLL_uc001ptb.2_Intron|MLL_uc001psz.1_Intron	NM_005933	NP_005924	Q03164	MLL1_HUMAN	myeloid/lymphoid or mixed-lineage leukemia						apoptosis|embryonic hemopoiesis|histone H4-K16 acetylation|positive regulation of transcription, DNA-dependent|protein complex assembly|transcription from RNA polymerase II promoter	MLL1 complex	AT DNA binding|histone acetyl-lysine binding|histone methyltransferase activity (H3-K4 specific)|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|unmethylated CpG binding|zinc ion binding			lung(7)|ovary(5)|kidney(5)|central_nervous_system(3)|pancreas(2)|urinary_tract(1)|breast(1)|skin(1)	25	all_hematologic(175;0.046)	all_hematologic(192;1.13e-50)|all_neural(223;3.18e-06)|Breast(348;1.07e-05)|Medulloblastoma(222;0.0425)|Hepatocellular(160;0.244)		OV - Ovarian serous cystadenocarcinoma(223;2.77e-44)|BRCA - Breast invasive adenocarcinoma(274;1.2e-11)|Lung(307;3.48e-06)|LUSC - Lung squamous cell carcinoma(976;7.92e-05)|Colorectal(284;0.144)		ATACAGCAGCaaaaaaaaaaa	0.318			T|O	MLL|MLLT1|MLLT2|MLLT3|MLLT4|MLLT7|MLLT10|MLLT6|ELL|EPS15|AF1Q|CREBBP|SH3GL1|FNBP1|PNUTL1|MSF|GPHN|GMPS|SSH3BP1|ARHGEF12|GAS7|FOXO3A|LAF4|LCX|SEPT6|LPP|CBFA2T1|GRAF|EP300|PICALM|HEAB	AML|ALL								6	3	---	---	---	---	
PLXNC1	10154	broad.mit.edu	37	12	94620767	94620767	+	Intron	DEL	C	-	-	rs63735761		TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:94620767delC	uc001tdc.2	+							NM_005761	NP_005752	O60486	PLXC1_HUMAN	plexin C1 precursor						axon guidance|cell adhesion	integral to membrane|intracellular|plasma membrane	receptor activity|receptor binding			ovary(2)|central_nervous_system(1)	3						ccactgcactcccagcctggg	0.104													3	8	---	---	---	---	
RIMBP2	23504	broad.mit.edu	37	12	130919596	130919596	+	Intron	DEL	T	-	-			TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:130919596delT	uc001uil.2	-						RIMBP2_uc001uim.2_Intron|RIMBP2_uc001uin.1_Intron	NM_015347	NP_056162	O15034	RIMB2_HUMAN	RIM-binding protein 2							cell junction|synapse				upper_aerodigestive_tract(3)|ovary(3)|large_intestine(2)|central_nervous_system(2)|pancreas(1)	11	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.213)		OV - Ovarian serous cystadenocarcinoma(86;4.29e-06)|all cancers(50;4.56e-05)|Epithelial(86;5.41e-05)		CACCAGAAtcttttttttttt	0.328													5	3	---	---	---	---	
GOLGA3	2802	broad.mit.edu	37	12	133374766	133374766	+	Intron	DEL	G	-	-	rs33920278		TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:133374766delG	uc001ukz.1	-						GOLGA3_uc001ula.1_Intron|GOLGA3_uc001ulb.2_Intron	NM_005895	NP_005886	Q08378	GOGA3_HUMAN	Golgi autoantigen, golgin subfamily a, 3						intra-Golgi vesicle-mediated transport	Golgi cisterna membrane|Golgi transport complex	protein binding|transporter activity			ovary(3)|central_nervous_system(2)|pancreas(1)	6	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0176)|Lung NSC(355;0.204)		OV - Ovarian serous cystadenocarcinoma(86;2.27e-08)|Epithelial(86;3.34e-07)|all cancers(50;9.4e-06)		GATGAGGGGTGGGGGGGGGGT	0.567													8	4	---	---	---	---	
ABCC6	368	broad.mit.edu	37	16	16306170	16306170	+	Intron	DEL	T	-	-			TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:16306170delT	uc002den.3	-						ABCC6_uc010bvo.2_Intron|ABCC6_uc010uzz.1_Intron	NM_001171	NP_001162	O95255	MRP6_HUMAN	ATP-binding cassette, sub-family C, member 6						response to drug|visual perception	integral to membrane|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances			skin(2)|ovary(1)	3				UCEC - Uterine corpus endometrioid carcinoma (3;0.123)		GAACTGTGTAttttttttttt	0.264													9	4	---	---	---	---	
SLC13A5	284111	broad.mit.edu	37	17	6607061	6607062	+	Intron	INS	-	T	T			TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:6607061_6607062insT	uc002gdj.2	-						SLC13A5_uc010vtf.1_Intron|SLC13A5_uc010clq.2_Intron|SLC13A5_uc002gdk.2_Intron|SLC13A5_uc002gdl.1_Intron	NM_177550	NP_808218	Q86YT5	S13A5_HUMAN	solute carrier family 13, member 5 isoform a							integral to membrane	citrate transmembrane transporter activity				0						AGTATTTTCTATTTTTTTTTCT	0.460													4	2	---	---	---	---	
UBTF	7343	broad.mit.edu	37	17	42284469	42284469	+	3'UTR	DEL	T	-	-			TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42284469delT	uc002igb.2	-	20					UBTF_uc002igc.2_3'UTR|UBTF_uc010czs.2_3'UTR|UBTF_uc002igd.2_3'UTR|UBTF_uc010czt.2_3'UTR	NM_014233	NP_055048	P17480	UBF1_HUMAN	upstream binding transcription factor, RNA						positive regulation of transcription from RNA polymerase I promoter|termination of RNA polymerase I transcription|transcription elongation from RNA polymerase I promoter|transcription initiation from RNA polymerase I promoter	nucleolus|nucleoplasm	DNA binding|protein binding				0		Breast(137;0.00765)|Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.114)		CCCCACCGTATTTTTTTTTTT	0.562													4	2	---	---	---	---	
DHX40P1	653645	broad.mit.edu	37	17	58066608	58066608	+	Intron	DEL	T	-	-			TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:58066608delT	uc002iyf.2	-						uc002iye.1_Intron	NR_002924				Homo sapiens DEAH (Asp-Glu-Ala-His) box polypeptide 40 pseudogene, mRNA (cDNA clone IMAGE:5170263).												0						TTGATTGTGATTTTTTTTTTT	0.313													9	6	---	---	---	---	
CCDC46	201134	broad.mit.edu	37	17	64025826	64025829	+	Intron	DEL	AAAC	-	-	rs67867456		TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:64025826_64025829delAAAC	uc002jfl.2	-						CCDC46_uc010deo.2_Intron|CCDC46_uc002jfm.2_Intron|CCDC46_uc010dep.2_Intron	NM_145036	NP_659473	Q8N8E3	CE112_HUMAN	coiled-coil domain containing 46 isoform a							centrosome					0			BRCA - Breast invasive adenocarcinoma(6;1.53e-06)			gtctctaaataaacaaacaaacaa	0.123													3	3	---	---	---	---	
AZI1	22994	broad.mit.edu	37	17	79166473	79166473	+	Intron	DEL	C	-	-	rs3744149	by1000genomes	TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79166473delC	uc002jzp.1	-						AZI1_uc002jzm.1_Intron|AZI1_uc002jzn.1_Intron|AZI1_uc002jzo.1_Intron|AZI1_uc010wum.1_Intron|AZI1_uc002jzq.2_Intron	NM_014984	NP_055799	Q9UPN4	AZI1_HUMAN	5-azacytidine induced 1 isoform a						cell differentiation|G2/M transition of mitotic cell cycle|multicellular organismal development|spermatogenesis	centrosome|cytosol|intracellular membrane-bounded organelle				central_nervous_system(2)|large_intestine(1)|ovary(1)	4	all_neural(118;0.0804)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0272)|OV - Ovarian serous cystadenocarcinoma(97;0.117)			GGTGAGGGGGCGGGGGGGAGG	0.726													7	4	---	---	---	---	
KATNAL2	83473	broad.mit.edu	37	18	44626462	44626469	+	Intron	DEL	TCTCTTCC	-	-	rs3217429		TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:44626462_44626469delTCTCTTCC	uc002lco.2	+						KATNAL2_uc002lcp.3_Intron	NM_031303	NP_112593	Q8IYT4	KATL2_HUMAN	katanin p60 subunit A-like 2							cytoplasm|microtubule	ATP binding|microtubule-severing ATPase activity			ovary(1)|skin(1)|central_nervous_system(1)|pancreas(1)	4						GCTAGCAGGGTCTCTTCCTCAAGCACTG	0.457											OREG0024959	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	50005692	50005692	+	5'Flank	DEL	G	-	-			TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50005692delG	uc010yaw.1	-						MIR150_hsa-mir-150|MI0000479_5'Flank					DM004425																		aaaaaaaaaagaTACCAGCCT	0.189													4	2	---	---	---	---	
ZNF813	126017	broad.mit.edu	37	19	53983619	53983620	+	Intron	DEL	AA	-	-	rs35502614		TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53983619_53983620delAA	uc002qbu.2	+							NM_001004301	NP_001004301	Q6ZN06	ZN813_HUMAN	zinc finger protein 813						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			large_intestine(1)	1				GBM - Glioblastoma multiforme(134;0.00619)		GTTGTGATGTAAAAAAAAAAAA	0.361													4	5	---	---	---	---	
WFDC5	149708	broad.mit.edu	37	20	43743529	43743534	+	Intron	DEL	CACGCG	-	-	rs137896112	by1000genomes	TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:43743529_43743534delCACGCG	uc002xne.1	-							NM_145652	NP_663627	Q8TCV5	WFDC5_HUMAN	WAP four-disulfide core domain 5 precursor							extracellular region	serine-type endopeptidase inhibitor activity			ovary(1)	1		Myeloproliferative disorder(115;0.0122)				cgcacacacacacgcgcacacacacC	0.398													4	4	---	---	---	---	
ITSN1	6453	broad.mit.edu	37	21	35260248	35260248	+	Intron	DEL	T	-	-	rs11343877		TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:35260248delT	uc002yta.1	+						DONSON_uc002ysn.1_Intron|ITSN1_uc002ytb.1_Intron|ITSN1_uc002ytj.2_Intron|ITSN1_uc010gmm.1_Intron	NM_003024	NP_003015	Q15811	ITSN1_HUMAN	intersectin 1 isoform ITSN-l						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|synaptic vesicle endocytosis	cell junction|coated pit|cytosol|lamellipodium|synapse|synaptosome	calcium ion binding|proline-rich region binding|protein complex scaffold|Rho guanyl-nucleotide exchange factor activity			ovary(3)|skin(1)	4						TGGGGTTGGGTTTTTTTTTTT	0.279													6	5	---	---	---	---	
IL3RA	3563	broad.mit.edu	37	X	1467572	1467573	+	Intron	DEL	TT	-	-			TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:1467572_1467573delTT	uc004cps.2	+						IL3RA_uc011mhd.1_Intron	NM_002183	NP_002174	P26951	IL3RA_HUMAN	interleukin 3 receptor, alpha precursor							integral to membrane|plasma membrane	interleukin-3 receptor activity			skin(2)|lung(1)	3		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)			Sargramostim(DB00020)	tctttctttctttctttctttc	0.045													9	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	53043948	53043948	+	IGR	DEL	A	-	-			TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:53043948delA								FAM156A (106365 upstream) : GPR173 (34558 downstream)																							agaccttgccaaaaaaaaaaa	0.000													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	53142508	53142509	+	Intron	INS	-	A	A	rs146094031		TCGA-CJ-5686-01A-11D-1669-08	TCGA-CJ-5686-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:53142508_53142509insA	uc004dry.2	+											full-length cDNA clone CS0DC007YA11 of Neuroblastoma Cot 25-normalized of Homo sapiens (human).																		AACACACACACAAAAAAAAACC	0.262													5	4	---	---	---	---	
