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
CPSF3L	54973	broad.mit.edu	37	1	1250912	1250912	+	Silent	SNP	A	C	C			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1250912A>C	uc001aee.1	-	5	574	c.516T>G	c.(514-516)TCT>TCG	p.S172S	CPSF3L_uc009vjy.1_RNA|CPSF3L_uc001aef.1_Silent_p.S178S|CPSF3L_uc009vjz.1_Silent_p.S150S|CPSF3L_uc010nyj.1_Silent_p.S143S|CPSF3L_uc001aeg.1_Silent_p.S48S|CPSF3L_uc001aeh.1_Silent_p.S71S|CPSF3L_uc001aei.1_Silent_p.S74S|CPSF3L_uc001aej.1_Intron|CPSF3L_uc001aek.1_5'UTR	NM_017871	NP_060341	Q5TA45	INT11_HUMAN	cleavage and polyadenylation specific factor	172						Golgi apparatus|nucleus	hydrolase activity				0	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		Epithelial(90;6.71e-35)|OV - Ovarian serous cystadenocarcinoma(86;4.35e-21)|Colorectal(212;0.000166)|COAD - Colon adenocarcinoma(227;0.000196)|Kidney(185;0.00235)|BRCA - Breast invasive adenocarcinoma(365;0.00255)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0349)|Lung(427;0.201)		TGTAGACCACAGACTCTGAGC	0.582													19	43	---	---	---	---	PASS
NBPF1	55672	broad.mit.edu	37	1	16892549	16892549	+	Intron	SNP	G	A	A			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16892549G>A	uc009vos.1	-						uc001ayw.2_5'Flank	NM_017940	NP_060410	Q3BBV0	NBPF1_HUMAN	hypothetical protein LOC55672							cytoplasm					0				UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.52e-06)|COAD - Colon adenocarcinoma(227;1.05e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.179)		AATTGGCCGGGTGACACACTG	0.363													4	15	---	---	---	---	PASS
ESPNP	284729	broad.mit.edu	37	1	17030504	17030504	+	Missense_Mutation	SNP	T	G	G	rs601031	by1000genomes	TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17030504T>G	uc001azn.1	-	5	832	c.718A>C	c.(718-720)ACC>CCC	p.T240P		NR_026567				RecName: Full=Espin; AltName: Full=Ectoplasmic specialization protein; AltName: Full=Autosomal recessive deafness type 36 protein;												0						TTGGAGAGGGTGCTGGTGGGC	0.632													4	93	---	---	---	---	PASS
ARID1A	8289	broad.mit.edu	37	1	27094308	27094308	+	Nonsense_Mutation	SNP	G	T	T			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:27094308G>T	uc001bmv.1	+	11	3389	c.3016G>T	c.(3016-3018)GAG>TAG	p.E1006*	ARID1A_uc001bmt.1_Nonsense_Mutation_p.E1006*|ARID1A_uc001bmu.1_Nonsense_Mutation_p.E1006*|ARID1A_uc001bmw.1_Nonsense_Mutation_p.E623*	NM_006015	NP_006006	O14497	ARI1A_HUMAN	AT rich interactive domain 1A isoform a	1006					androgen receptor signaling pathway|chromatin-mediated maintenance of transcription|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|nervous system development|nucleosome mobilization|transcription, DNA-dependent	nBAF complex|npBAF complex|SWI/SNF complex	DNA binding|protein binding			ovary(124)|pancreas(5)|central_nervous_system(3)|endometrium(3)|kidney(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1)	142		all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242)		TACAACCAATGAGAAGATCAC	0.483			Mis|N|F|S|D		clear cell ovarian carcinoma|RCC								21	62	---	---	---	---	PASS
MATN1	4146	broad.mit.edu	37	1	31188992	31188992	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:31188992C>T	uc001brz.2	-	5	1005	c.971G>A	c.(970-972)CGC>CAC	p.R324H	uc001bsb.1_5'Flank|MATN1_uc001bsa.1_Missense_Mutation_p.R242H	NM_002379	NP_002370	P21941	MATN1_HUMAN	matrilin 1, cartilage matrix protein precursor	324	VWFA 2.				protein complex assembly	proteinaceous extracellular matrix	extracellular matrix structural constituent|protein binding			central_nervous_system(1)	1		Colorectal(325;0.00792)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)|Ovarian(437;0.0563)|Breast(348;0.0848)|Medulloblastoma(700;0.123)		Colorectal(126;1.29e-05)|COAD - Colon adenocarcinoma(152;0.000726)|STAD - Stomach adenocarcinoma(196;0.0183)|READ - Rectum adenocarcinoma(331;0.0649)		GAACTCCTGGCGCACAGAGCT	0.567													26	62	---	---	---	---	PASS
PHC2	1912	broad.mit.edu	37	1	33820614	33820614	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:33820614G>T	uc001bxg.1	-	7	1271	c.1217C>A	c.(1216-1218)CCA>CAA	p.P406Q	PHC2_uc001bxh.1_Missense_Mutation_p.P377Q|PHC2_uc009vuh.1_Missense_Mutation_p.P406Q	NM_198040	NP_932157	Q8IXK0	PHC2_HUMAN	polyhomeotic-like 2 isoform a	406					multicellular organismal development	PcG protein complex	DNA binding|identical protein binding|zinc ion binding			ovary(1)	1		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.211)				ACACTGGAGTGGCAGGGCGGG	0.557													13	22	---	---	---	---	PASS
KIAA0319L	79932	broad.mit.edu	37	1	35909816	35909816	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:35909816G>A	uc001byx.2	-	17	2860	c.2602C>T	c.(2602-2604)CGG>TGG	p.R868W	KIAA0319L_uc001byw.2_Missense_Mutation_p.R310W|KIAA0319L_uc010ohv.1_Missense_Mutation_p.R510W	NM_024874	NP_079150	Q8IZA0	K319L_HUMAN	dyslexia susceptibility 2-like	868	Extracellular (Potential).					cytoplasmic vesicle part|integral to membrane	protein binding			skin(2)	2		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				TTTTGCTTCCGCAGCTCACTC	0.478													18	47	---	---	---	---	PASS
SMAP2	64744	broad.mit.edu	37	1	40872508	40872508	+	Silent	SNP	T	A	A			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:40872508T>A	uc001cfj.2	+	2	269	c.204T>A	c.(202-204)GTT>GTA	p.V68V	SMAP2_uc010ojh.1_Silent_p.V68V|SMAP2_uc001cfk.2_Silent_p.V38V|SMAP2_uc010oji.1_5'UTR	NM_022733	NP_073570	Q8WU79	SMAP2_HUMAN	small ArfGAP2	68	Arf-GAP.				regulation of ARF GTPase activity	cytoplasm|nucleus	ARF GTPase activator activity|zinc ion binding				0	Lung NSC(20;1.56e-05)|Ovarian(52;0.00769)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)	OV - Ovarian serous cystadenocarcinoma(33;1.04e-17)			TAAAGTCAGTTAACCTCGACC	0.473													31	53	---	---	---	---	PASS
IGSF3	3321	broad.mit.edu	37	1	117156509	117156509	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:117156509T>C	uc001egr.1	-	4	1415	c.710A>G	c.(709-711)CAG>CGG	p.Q237R	IGSF3_uc001egq.1_Missense_Mutation_p.Q237R	NM_001007237	NP_001007238	O75054	IGSF3_HUMAN	immunoglobulin superfamily, member 3 isoform 2	237	Ig-like C2-type 2.|Extracellular (Potential).					integral to membrane				ovary(2)	2	Lung SC(450;0.225)	all_cancers(81;1.24e-06)|all_epithelial(167;4.85e-07)|all_lung(203;1.66e-06)|Lung NSC(69;1.11e-05)		Lung(183;0.0142)|Colorectal(144;0.0929)|LUSC - Lung squamous cell carcinoma(189;0.108)|COAD - Colon adenocarcinoma(174;0.139)|all cancers(265;0.159)|Epithelial(280;0.166)		GTCAGAAGGCTGCAGGTGGAA	0.627													8	32	---	---	---	---	PASS
PPIAL4G	644591	broad.mit.edu	37	1	143767782	143767782	+	Nonsense_Mutation	SNP	T	A	A			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:143767782T>A	uc001ejt.2	-	1	100	c.67A>T	c.(67-69)AAA>TAA	p.K23*		NM_001123068	NP_001116540	A2BFH1	PAL4G_HUMAN	peptidylprolyl isomerase A (cyclophilin A)-like	23	PPIase cyclophilin-type.				protein folding	cytoplasm	peptidyl-prolyl cis-trans isomerase activity				0						GCAAACTGTTTGATGGAGATG	0.498													14	270	---	---	---	---	PASS
ITGA10	8515	broad.mit.edu	37	1	145530386	145530386	+	Nonsense_Mutation	SNP	C	T	T			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145530386C>T	uc001eoa.2	+	6	677	c.601C>T	c.(601-603)CAG>TAG	p.Q201*	NBPF10_uc001emp.3_Intron|ITGA10_uc010oyv.1_Nonsense_Mutation_p.Q70*|ITGA10_uc009wiw.2_Nonsense_Mutation_p.Q58*|ITGA10_uc010oyw.1_Nonsense_Mutation_p.Q146*	NM_003637	NP_003628	O75578	ITA10_HUMAN	integrin, alpha 10 precursor	201	VWFA.|Extracellular (Potential).				cell-matrix adhesion|integrin-mediated signaling pathway	integrin complex	collagen binding|receptor activity			lung(2)|ovary(2)|kidney(2)|large_intestine(1)|skin(1)	8	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					TGACCCAGAACAGATACAGGT	0.373													27	74	---	---	---	---	PASS
APOB	338	broad.mit.edu	37	2	21229236	21229236	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:21229236C>A	uc002red.2	-	26	10632	c.10504G>T	c.(10504-10506)GGT>TGT	p.G3502C		NM_000384	NP_000375	P04114	APOB_HUMAN	apolipoprotein B precursor	3502	Heparin-binding.				cholesterol homeostasis|cholesterol metabolic process|leukocyte migration|low-density lipoprotein particle clearance|low-density lipoprotein particle remodeling|platelet activation|positive regulation of cholesterol storage|positive regulation of macrophage derived foam cell differentiation|receptor-mediated endocytosis|response to virus	chylomicron remnant|clathrin-coated endocytic vesicle membrane|endoplasmic reticulum lumen|endoplasmic reticulum membrane|endosome lumen|endosome membrane|intermediate-density lipoprotein particle|low-density lipoprotein particle|mature chylomicron|microsome|plasma membrane|very-low-density lipoprotein particle	cholesterol transporter activity|enzyme binding|heparin binding|low-density lipoprotein particle receptor binding|phospholipid binding|protein heterodimerization activity			ovary(11)|skin(9)|central_nervous_system(3)|large_intestine(2)|upper_aerodigestive_tract(1)|pancreas(1)	27	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)				Atorvastatin(DB01076)	AGAACCGAACCCTTGACATCT	0.473													76	97	---	---	---	---	PASS
BUB1	699	broad.mit.edu	37	2	111395597	111395597	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:111395597C>T	uc002tgc.2	-	25	3314	c.3202G>A	c.(3202-3204)GCC>ACC	p.A1068T	BUB1_uc010yxh.1_Missense_Mutation_p.A1048T|BUB1_uc010fkb.2_Missense_Mutation_p.A1011T	NM_004336	NP_004327	O43683	BUB1_HUMAN	budding uninhibited by benzimidazoles 1	1068	Protein kinase.				apoptosis|cell division|chromosome segregation|interspecies interaction between organisms|mitotic cell cycle spindle assembly checkpoint|mitotic prometaphase|regulation of sister chromatid cohesion	condensed chromosome kinetochore|cytosol	ATP binding|protein binding|protein serine/threonine kinase activity			lung(2)|breast(2)|stomach(1)|ovary(1)|kidney(1)	7		Ovarian(717;0.0822)		BRCA - Breast invasive adenocarcinoma(221;0.0556)		TTACGTAGGGCCCTAATCTTG	0.328													4	121	---	---	---	---	PASS
LOC440905	440905	broad.mit.edu	37	2	130786055	130786055	+	RNA	SNP	A	T	T			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:130786055A>T	uc002tpz.2	-	11		c.2813T>A			LOC440905_uc002tpy.1_RNA	NR_026758				Homo sapiens cDNA FLJ43933 fis, clone TESTI4013685.												0						AGACCTGGAAACCTGGGGGAA	0.428													6	9	---	---	---	---	PASS
LOC440905	440905	broad.mit.edu	37	2	130786063	130786063	+	Intron	SNP	G	A	A			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:130786063G>A	uc002tpz.2	-						LOC440905_uc002tpy.1_RNA	NR_026758				Homo sapiens cDNA FLJ43933 fis, clone TESTI4013685.												0						AAACCTGGGGGAAAAAAGAGA	0.423													6	8	---	---	---	---	PASS
ILKAP	80895	broad.mit.edu	37	2	239093850	239093850	+	Silent	SNP	A	G	G			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:239093850A>G	uc002vxv.2	-	6	634	c.504T>C	c.(502-504)CAT>CAC	p.H168H	ILKAP_uc010zns.1_Silent_p.H100H|ILKAP_uc002vxw.2_Silent_p.H48H|ILKAP_uc010znt.1_Silent_p.H48H	NM_030768	NP_110395	Q9H0C8	ILKAP_HUMAN	integrin-linked kinase-associated protein	168	PP2C-like.					cytoplasm|protein serine/threonine phosphatase complex	metal ion binding|protein binding			ovary(3)	3		Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0481)|all_lung(227;0.152)|all_hematologic(139;0.158)|Melanoma(123;0.203)|Hepatocellular(293;0.244)		Epithelial(121;5.49e-24)|OV - Ovarian serous cystadenocarcinoma(60;3.93e-12)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;6.82e-08)|BRCA - Breast invasive adenocarcinoma(100;0.00012)|Lung(119;0.00942)|LUSC - Lung squamous cell carcinoma(224;0.0163)		TTAAGTTTTGATGCAAATTCT	0.373													3	65	---	---	---	---	PASS
VHL	7428	broad.mit.edu	37	3	10188308	10188308	+	Missense_Mutation	SNP	A	T	T	rs5030624		TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10188308A>T	uc003bvc.2	+	2	664	c.451A>T	c.(451-453)ATC>TTC	p.I151F	VHL_uc003bvd.2_Intron	NM_000551	NP_000542	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor isoform 1	151	Involved in binding to CCT complex.				anti-apoptosis|cell morphogenesis|negative regulation of cell proliferation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of cell differentiation|positive regulation of transcription, DNA-dependent|protein stabilization|protein ubiquitination|proteolysis	cytosol|endoplasmic reticulum|membrane|mitochondrion|nucleus	protein binding|transcription factor binding	p.I151S(6)|p.I151T(3)|p.I151M(2)|p.I151N(2)|p.I151F(1)|p.?(1)|p.N150fs*7(1)|p.N150fs*23(1)|p.I151_T152del(1)|p.I151fs*8(1)|p.G144fs*19(1)		kidney(1273)|soft_tissue(24)|adrenal_gland(15)|large_intestine(13)|pancreas(5)|endometrium(4)|thyroid(3)|upper_aerodigestive_tract(3)|central_nervous_system(2)|lung(2)|pleura(1)|paratesticular_tissues(1)	1346				Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569)		TTTTGCCAATATCACACTGCC	0.403		1	D|Mis|N|F|S		renal|hemangioma|pheochromocytoma	renal|hemangioma|pheochromocytoma			von_Hippel-Lindau_disease|Chuvash_Polycythemia_|Pheochromocytoma_(Adrenal)_Familial				58	84	---	---	---	---	PASS
VHL	7428	broad.mit.edu	37	3	10188309	10188309	+	Missense_Mutation	SNP	T	A	A			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10188309T>A	uc003bvc.2	+	2	665	c.452T>A	c.(451-453)ATC>AAC	p.I151N	VHL_uc003bvd.2_Intron	NM_000551	NP_000542	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor isoform 1	151	Involved in binding to CCT complex.				anti-apoptosis|cell morphogenesis|negative regulation of cell proliferation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of cell differentiation|positive regulation of transcription, DNA-dependent|protein stabilization|protein ubiquitination|proteolysis	cytosol|endoplasmic reticulum|membrane|mitochondrion|nucleus	protein binding|transcription factor binding	p.I151S(6)|p.I151T(3)|p.I151M(2)|p.I151N(2)|p.I151F(1)|p.?(1)|p.N150fs*7(1)|p.I151_T152del(1)|p.I151fs*8(1)|p.G144fs*19(1)		kidney(1273)|soft_tissue(24)|adrenal_gland(15)|large_intestine(13)|pancreas(5)|endometrium(4)|thyroid(3)|upper_aerodigestive_tract(3)|central_nervous_system(2)|lung(2)|pleura(1)|paratesticular_tissues(1)	1346				Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569)		TTTGCCAATATCACACTGCCA	0.398		1	D|Mis|N|F|S		renal|hemangioma|pheochromocytoma	renal|hemangioma|pheochromocytoma			von_Hippel-Lindau_disease|Chuvash_Polycythemia_|Pheochromocytoma_(Adrenal)_Familial				56	84	---	---	---	---	PASS
ECE2	9718	broad.mit.edu	37	3	184001749	184001749	+	Silent	SNP	T	A	A			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184001749T>A	uc003fni.3	+	8	1385	c.1347T>A	c.(1345-1347)ATT>ATA	p.I449I	ECE2_uc011brh.1_Silent_p.I302I|ECE2_uc003fnl.3_Silent_p.I377I|ECE2_uc003fnm.3_Silent_p.I331I|ECE2_uc003fnk.3_Silent_p.I302I|ECE2_uc011bri.1_Silent_p.I364I|ECE2_uc010hxv.2_Silent_p.I93I	NM_014693	NP_055508	O60344	ECE2_HUMAN	endothelin converting enzyme 2 isoform A	449	Lumenal (Potential).|Endothelin-converting enzyme 2 region.				brain development|cardioblast differentiation|cell-cell signaling|peptide hormone processing	cytoplasmic vesicle membrane|Golgi membrane|integral to membrane	metal ion binding|metalloendopeptidase activity|methyltransferase activity			ovary(2)|skin(2)	4	all_cancers(143;1.39e-10)|Ovarian(172;0.0339)		Epithelial(37;8.28e-34)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			AGATGAGCATTTCGGAGCTGC	0.617													23	42	---	---	---	---	PASS
TBCCD1	55171	broad.mit.edu	37	3	186276258	186276258	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:186276258C>A	uc003fqg.2	-	3	569	c.440G>T	c.(439-441)AGA>ATA	p.R147I	TBCCD1_uc011bry.1_Missense_Mutation_p.R147I|TBCCD1_uc003fqh.2_Missense_Mutation_p.R51I	NM_018138	NP_060608	Q9NVR7	TBCC1_HUMAN	TBCC domain containing 1	147					cell morphogenesis|maintenance of centrosome location|maintenance of Golgi location|regulation of cell migration|regulation of cell shape	spindle pole centrosome	binding			large_intestine(1)|ovary(1)	2	all_cancers(143;3.75e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;4.3e-21)	GBM - Glioblastoma multiforme(93;0.0474)		AGATTTGTTTCTGGGACTGGG	0.408													54	140	---	---	---	---	PASS
MTTP	4547	broad.mit.edu	37	4	100515934	100515934	+	Missense_Mutation	SNP	T	C	C	rs146513720		TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:100515934T>C	uc003hvc.3	+	8	1059	c.803T>C	c.(802-804)ATG>ACG	p.M268T	MTTP_uc011cej.1_Missense_Mutation_p.M295T	NM_000253	NP_000244	P55157	MTP_HUMAN	microsomal triglyceride transfer protein large	268	Vitellogenin.				lipid metabolic process|lipoprotein metabolic process	endoplasmic reticulum lumen	lipid binding|lipid transporter activity			ovary(3)|central_nervous_system(1)	4				OV - Ovarian serous cystadenocarcinoma(123;6.04e-09)	Hesperetin(DB01094)	CCAAGATTGATGTCTGGAAAG	0.438													26	99	---	---	---	---	PASS
HTR1A	3350	broad.mit.edu	37	5	63256620	63256620	+	Missense_Mutation	SNP	G	T	T	rs140681943		TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:63256620G>T	uc011cqt.1	-	1	927	c.927C>A	c.(925-927)AGC>AGA	p.S309R		NM_000524	NP_000515	P08908	5HT1A_HUMAN	5-hydroxytryptamine (serotonin) receptor 1A	309	Cytoplasmic (By similarity).				behavior|positive regulation of cell proliferation	integral to plasma membrane	serotonin receptor activity			ovary(2)|pancreas(2)	4		Lung NSC(810;3.55e-06)|Prostate(74;0.0352)|Ovarian(174;0.0545)|Breast(144;0.0575)|Colorectal(97;0.234)		Lung(70;0.105)	Alprenolol(DB00866)|Aripiprazole(DB01238)|Buspirone(DB00490)|Clozapine(DB00363)|Eletriptan(DB00216)|Ergoloid mesylate(DB01049)|Fluvoxamine(DB00176)|Lisuride(DB00589)|Methysergide(DB00247)|Mirtazapine(DB00370)|Pindolol(DB00960)|Propranolol(DB00571)|Quetiapine(DB01224)|Sertraline(DB01104)|Tegaserod(DB01079)|Trazodone(DB00656)|Venlafaxine(DB00285)|Ziprasidone(DB00246)	GACCAGCCTCGCTGGGCAGAG	0.647													13	37	---	---	---	---	PASS
G3BP1	10146	broad.mit.edu	37	5	151166157	151166157	+	5'UTR	SNP	C	T	T			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:151166157C>T	uc003lun.2	+	2					G3BP1_uc010jhy.1_5'UTR|G3BP1_uc003lum.2_Intron|G3BP1_uc011dcu.1_5'UTR|G3BP1_uc010jhz.2_5'UTR|uc003luo.1_5'Flank|uc003lup.1_5'Flank	NM_005754	NP_005745	Q13283	G3BP1_HUMAN	Ras-GTPase-activating protein SH3-domain-binding						Ras protein signal transduction|transport	cytosol|nucleus|plasma membrane	ATP binding|ATP-dependent DNA helicase activity|ATP-dependent RNA helicase activity|DNA binding|endonuclease activity|protein binding|RNA binding			skin(3)|ovary(1)	4		all_hematologic(541;0.0338)|Medulloblastoma(196;0.091)	Kidney(363;0.000171)|KIRC - Kidney renal clear cell carcinoma(527;0.000785)			GACTCTTTTCCCCCCAGGTTG	0.468													33	94	---	---	---	---	PASS
ODZ2	57451	broad.mit.edu	37	5	167645829	167645829	+	Missense_Mutation	SNP	A	T	T			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:167645829A>T	uc010jjd.2	+	23	4906	c.4906A>T	c.(4906-4908)ATG>TTG	p.M1636L	ODZ2_uc003lzr.3_Missense_Mutation_p.M1406L|ODZ2_uc003lzt.3_Missense_Mutation_p.M1009L|ODZ2_uc010jje.2_Missense_Mutation_p.M900L	NM_001122679	NP_001116151			odz, odd Oz/ten-m homolog 2											ovary(6)|central_nervous_system(4)	10	Renal(175;0.00124)|Lung NSC(126;0.136)|all_lung(126;0.242)	Medulloblastoma(196;0.0241)|all_neural(177;0.026)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0444)|OV - Ovarian serous cystadenocarcinoma(192;0.0694)|Epithelial(171;0.124)		CAGCAGTGGCATGCCCCGTCA	0.502													37	164	---	---	---	---	PASS
LTA	4049	broad.mit.edu	37	6	31541279	31541279	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31541279C>G	uc011dnu.1	+	4	640	c.427C>G	c.(427-429)CCC>GCC	p.P143A	LTA_uc003nue.1_Missense_Mutation_p.P143A|LTA_uc003nuf.2_Intron|LTA_uc003nuh.2_Intron|LTA_uc003nug.2_Intron|LTA_uc010jsr.2_Intron|TNF_uc003nui.2_5'Flank	NM_001159740	NP_001153212	P01374	TNFB_HUMAN	lymphotoxin alpha precursor	143					cell-cell signaling|induction of apoptosis|signal transduction	extracellular space|membrane	cytokine activity|tumor necrosis factor receptor binding				0					Etanercept(DB00005)	CTCCCAGTACCCCTTCCATGT	0.607													34	107	---	---	---	---	PASS
RXRB	6257	broad.mit.edu	37	6	33163381	33163381	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33163381C>T	uc003odb.2	-	7	1401	c.1222G>A	c.(1222-1224)GCC>ACC	p.A408T	RXRB_uc003odc.2_Missense_Mutation_p.A408T|RXRB_uc003odd.2_Missense_Mutation_p.A312T|RXRB_uc011dqr.1_Missense_Mutation_p.A218T	NM_021976	NP_068811	P28702	RXRB_HUMAN	retinoid X receptor, beta	408	Ligand-binding (By similarity).				regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	ligand-regulated transcription factor activity|retinoid-X receptor activity|sequence-specific DNA binding transcription factor activity|steroid binding|steroid hormone receptor activity|zinc ion binding			ovary(3)	3					Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Bexarotene(DB00307)|Etretinate(DB00926)|Tazarotene(DB00799)|Tretinoin(DB00755)	GCTGAATGGGCTGAGTTGCGG	0.567													13	31	---	---	---	---	PASS
ITPR3	3710	broad.mit.edu	37	6	33661519	33661519	+	Intron	SNP	A	C	C			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33661519A>C	uc011drk.1	+						ITPR3_uc003oey.2_3'UTR	NM_002224	NP_002215	Q14573	ITPR3_HUMAN	inositol 1,4,5-triphosphate receptor, type 3						activation of phospholipase C activity|calcium ion transport into cytosol|energy reserve metabolic process|G-protein coupled receptor protein signaling pathway|nerve growth factor receptor signaling pathway|platelet activation|protein heterooligomerization|protein homooligomerization|regulation of insulin secretion|response to calcium ion	apical part of cell|brush border|endoplasmic reticulum membrane|integral to plasma membrane|myelin sheath|neuronal cell body|nuclear outer membrane|platelet dense tubular network membrane	inositol 1,3,4,5 tetrakisphosphate binding|inositol 1,4,5 trisphosphate binding|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity|inositol hexakisphosphate binding|intracellular ligand-gated calcium channel activity|protein binding			ovary(6)|lung(5)|central_nervous_system(5)|breast(2)|kidney(1)	19						GTGGGCCCAAACCAGCCATTC	0.592													4	12	---	---	---	---	PASS
KCNK17	89822	broad.mit.edu	37	6	39267378	39267378	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:39267378G>A	uc003ooo.2	-	5	964	c.824C>T	c.(823-825)TCC>TTC	p.S275F	KCNK17_uc003oop.2_3'UTR	NM_031460	NP_113648	Q96T54	KCNKH_HUMAN	potassium channel, subfamily K, member 17	275	Cytoplasmic (Potential).					integral to membrane	potassium channel activity|voltage-gated ion channel activity			skin(2)	2						GTGGCAGCAGGAACATACCCT	0.562													31	98	---	---	---	---	PASS
CUL9	23113	broad.mit.edu	37	6	43173114	43173114	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43173114G>A	uc003ouk.2	+	24	4821	c.4746G>A	c.(4744-4746)ATG>ATA	p.M1582I	CUL9_uc003oul.2_Missense_Mutation_p.M1582I|CUL9_uc010jyk.2_Missense_Mutation_p.M734I	NM_015089	NP_055904	Q8IWT3	CUL9_HUMAN	p53-associated parkin-like cytoplasmic protein	1582					ubiquitin-dependent protein catabolic process	cullin-RING ubiquitin ligase complex|cytoplasm	ATP binding|ubiquitin protein ligase binding|zinc ion binding			ovary(5)|lung(3)|skin(2)|breast(1)|central_nervous_system(1)	12						AACCCATTATGGTCCTTTCTG	0.552													77	209	---	---	---	---	PASS
FAM46A	55603	broad.mit.edu	37	6	82459345	82459345	+	3'UTR	SNP	C	T	T			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:82459345C>T	uc003pjg.2	-	3					FAM46A_uc003pjf.2_3'UTR	NM_017633	NP_060103	Q96IP4	FA46A_HUMAN	hypothetical protein LOC55603												0		all_cancers(76;6.74e-06)|Acute lymphoblastic leukemia(125;3.41e-06)|all_hematologic(105;0.000282)|all_epithelial(107;0.0104)		BRCA - Breast invasive adenocarcinoma(397;0.0428)		ttttttttttctttttttttt	0.353													4	4	---	---	---	---	PASS
MLLT4	4301	broad.mit.edu	37	6	168344080	168344080	+	Splice_Site	SNP	A	G	G			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:168344080A>G	uc003qwd.2	+	24	3284	c.3142_splice	c.e24-2	p.D1048_splice	MLLT4_uc003qwb.1_Splice_Site_p.D1033_splice|MLLT4_uc003qwc.1_Splice_Site_p.D1049_splice|MLLT4_uc003qwg.1_Splice_Site_p.D358_splice	NM_001040001	NP_001035090	P55196	AFAD_HUMAN	myeloid/lymphoid or mixed-lineage leukemia						adherens junction organization|cell adhesion|cell junction assembly|cell-cell signaling|signal transduction	adherens junction|cell-cell junction|cytosol|nucleus	protein C-terminus binding			ovary(2)|lung(1)|kidney(1)|central_nervous_system(1)	5		Breast(66;1.07e-05)|Ovarian(120;0.024)		Epithelial(4;2.38e-32)|OV - Ovarian serous cystadenocarcinoma(33;9.99e-23)|BRCA - Breast invasive adenocarcinoma(4;1.2e-11)|GBM - Glioblastoma multiforme(31;0.00117)		GGATTTGCCTAGGATGGACGT	0.458			T	MLL	AL								24	56	---	---	---	---	PASS
MAGI2	9863	broad.mit.edu	37	7	77885771	77885771	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:77885771C>A	uc003ugx.2	-	10	1790	c.1536G>T	c.(1534-1536)TTG>TTT	p.L512F	MAGI2_uc003ugy.2_Missense_Mutation_p.L512F|MAGI2_uc010ldx.1_Missense_Mutation_p.L121F|MAGI2_uc010ldy.1_Missense_Mutation_p.L121F|MAGI2_uc011kgr.1_Missense_Mutation_p.L344F|MAGI2_uc011kgs.1_Missense_Mutation_p.L349F	NM_012301	NP_036433	Q86UL8	MAGI2_HUMAN	membrane associated guanylate kinase, WW and PDZ	512						cell junction|synapse|synaptosome	phosphatase binding			ovary(5)|lung(4)|breast(1)|skin(1)	11		all_cancers(73;0.0064)|all_epithelial(88;0.087)|all_neural(109;0.0936)|Medulloblastoma(109;0.166)|Melanoma(862;0.236)				GATCAAAGGGCAAAGGGTAGC	0.483													13	33	---	---	---	---	PASS
PTPRZ1	5803	broad.mit.edu	37	7	121650583	121650583	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:121650583G>A	uc003vjy.2	+	12	1878	c.1483G>A	c.(1483-1485)GTT>ATT	p.V495I	PTPRZ1_uc003vjz.2_Missense_Mutation_p.V495I|PTPRZ1_uc011knt.1_5'UTR	NM_002851	NP_002842	P23471	PTPRZ_HUMAN	protein tyrosine phosphatase, receptor-type,	495	Extracellular (Potential).				central nervous system development	integral to plasma membrane	protein binding|protein tyrosine/threonine phosphatase activity|transmembrane receptor protein tyrosine phosphatase activity			ovary(3)|large_intestine(2)|lung(2)|central_nervous_system(1)|kidney(1)	9						AAAGGGTGATGTTCCCAATAC	0.423													6	103	---	---	---	---	PASS
PTPRN2	5799	broad.mit.edu	37	7	157414088	157414088	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:157414088G>C	uc003wno.2	-	15	2431	c.2310C>G	c.(2308-2310)AAC>AAG	p.N770K	PTPRN2_uc003wnp.2_Missense_Mutation_p.N753K|PTPRN2_uc003wnq.2_Missense_Mutation_p.N741K|PTPRN2_uc003wnr.2_Missense_Mutation_p.N732K|PTPRN2_uc011kwa.1_Missense_Mutation_p.N793K	NM_002847	NP_002838	Q92932	PTPR2_HUMAN	protein tyrosine phosphatase, receptor type, N	770	Cytoplasmic (Potential).|Tyrosine-protein phosphatase.					integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			ovary(4)|large_intestine(1)|pleura(1)|skin(1)	7	all_neural(206;0.181)	all_cancers(7;8.99e-13)|all_epithelial(9;2.4e-06)|all_hematologic(28;0.0155)|Breast(660;0.132)	OV - Ovarian serous cystadenocarcinoma(82;0.00463)	STAD - Stomach adenocarcinoma(7;0.0875)		TCTTGGGCACGTTCTCCTCCC	0.652													6	335	---	---	---	---	PASS
EPPK1	83481	broad.mit.edu	37	8	144943012	144943012	+	Nonsense_Mutation	SNP	C	T	T			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144943012C>T	uc003zaa.1	-	1	4423	c.4410G>A	c.(4408-4410)TGG>TGA	p.W1470*		NM_031308	NP_112598	P58107	EPIPL_HUMAN	epiplakin 1	1470						cytoplasm|cytoskeleton	protein binding|structural molecule activity			pancreas(1)|skin(1)	2	all_cancers(97;1.42e-10)|all_epithelial(106;1.99e-09)|Lung NSC(106;0.000126)|all_lung(105;0.000354)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;2.88e-40)|all cancers(56;1.82e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			GCAGCAGGTCCCAGAGTGACA	0.652													10	14	---	---	---	---	PASS
NDUFB6	4712	broad.mit.edu	37	9	32571039	32571039	+	Silent	SNP	T	C	C	rs146518353	by1000genomes	TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:32571039T>C	uc003zre.1	-	2	316	c.192A>G	c.(190-192)GTA>GTG	p.V64V	NDUFB6_uc003zrf.1_Silent_p.V64V	NM_002493	NP_002484	O95139	NDUB6_HUMAN	NADH dehydrogenase (ubiquinone) 1 beta	64					mitochondrial electron transport, NADH to ubiquinone|transport	integral to membrane|mitochondrial respiratory chain complex I	NADH dehydrogenase (ubiquinone) activity				0			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.00199)	NADH(DB00157)	TCTTTTTGTATACCCCATGGA	0.338													10	32	---	---	---	---	PASS
FKBP15	23307	broad.mit.edu	37	9	115928291	115928291	+	3'UTR	SNP	G	A	A			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:115928291G>A	uc004bgs.2	-	28					FKBP15_uc004bgr.2_3'UTR|FKBP15_uc011lxc.1_3'UTR	NM_015258	NP_056073	Q5T1M5	FKB15_HUMAN	FK506 binding protein 15, 133kDa						endocytosis|protein folding	axon|early endosome	actin binding			ovary(3)	3						TAGACCCAGGGTTGGCTGTGC	0.542													2	1	---	---	---	---	PASS
OR1L1	26737	broad.mit.edu	37	9	125424692	125424692	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:125424692G>C	uc011lza.1	+	1	848	c.848G>C	c.(847-849)GGA>GCA	p.G283A		NM_001005236	NP_001005236	Q8NH94	OR1L1_HUMAN	olfactory receptor, family 1, subfamily L,	283	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(3)|ovary(1)	4						TCAGCTGCTGGAAAGCGTAAA	0.428													59	164	---	---	---	---	PASS
C10orf4	118924	broad.mit.edu	37	10	95459948	95459948	+	Intron	SNP	A	C	C			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:95459948A>C	uc001kiz.1	-						C10orf4_uc001kiv.1_Intron|C10orf4_uc001kja.1_Intron|C10orf4_uc001kjb.1_5'UTR|C10orf4_uc009xuh.1_Intron	NM_145246	NP_660289	Q70Z53	F10C1_HUMAN	FRA10AC1 protein							nucleus	protein binding				0		Colorectal(252;0.122)				gttatcttaaacagccacaat	0.149													8	11	---	---	---	---	PASS
OPALIN	93377	broad.mit.edu	37	10	98113209	98113209	+	Intron	SNP	G	A	A			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:98113209G>A	uc001kmj.2	-						OPALIN_uc010qor.1_Missense_Mutation_p.R2W|OPALIN_uc001kmi.2_Missense_Mutation_p.R2W|OPALIN_uc001kmk.2_Intron|OPALIN_uc010qos.1_Intron	NM_033207	NP_149984	Q96PE5	OPALI_HUMAN	transmembrane protein 10 isoform a							Golgi apparatus|integral to membrane|plasma membrane					0						cctaccatccgcattgtccag	0.289													4	115	---	---	---	---	PASS
IGF2	3481	broad.mit.edu	37	11	2154084	2154084	+	3'UTR	SNP	G	A	A			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:2154084G>A	uc009yde.2	-	4					IGF2_uc001lvf.2_RNA|IGF2_uc001lvg.2_3'UTR|IGF2_uc009ydf.2_3'UTR|IGF2_uc001lvh.2_3'UTR|INS-IGF2_uc001lvi.2_RNA	NM_001007139	NP_001007140	P01344	IGF2_HUMAN	insulin-like growth factor 2 isoform 1						glucose metabolic process|ossification|phosphatidylinositol 3-kinase cascade involved in insulin receptor signaling|positive regulation of activated T cell proliferation|positive regulation of cell division|positive regulation of glycogen (starch) synthase activity|positive regulation of glycogen biosynthetic process|positive regulation of insulin receptor signaling pathway|positive regulation of MAPKKK cascade|positive regulation of mitosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of protein kinase B signaling cascade|regulation of gene expression by genetic imprinting|regulation of transcription, DNA-dependent|skeletal system development	extracellular space	growth factor activity|hormone activity|insulin receptor binding|insulin-like growth factor receptor binding|protein serine/threonine kinase activator activity|receptor activator activity			central_nervous_system(1)	1		all_epithelial(84;5.04e-06)|Breast(177;0.000777)|Ovarian(85;0.0014)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)|all_lung(207;0.24)	Colorectal(5;0.0179)|COAD - Colon adenocarcinoma(6;0.029)	BRCA - Breast invasive adenocarcinoma(625;1.09e-05)|LUSC - Lung squamous cell carcinoma(625;0.082)|Lung(200;0.153)		CGGGGCACGGGGACTGGGTCA	0.597													7	122	---	---	---	---	PASS
QSER1	79832	broad.mit.edu	37	11	32953804	32953804	+	Silent	SNP	C	T	T			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:32953804C>T	uc001mty.2	+	4	880	c.613C>T	c.(613-615)CTG>TTG	p.L205L	QSER1_uc001mtz.1_Silent_p.L205L|QSER1_uc001mua.2_5'Flank	NM_001076786	NP_001070254	Q2KHR3	QSER1_HUMAN	glutamine and serine rich 1	205	Ser-rich.									ovary(3)|central_nervous_system(2)|skin(1)	6	Breast(20;0.158)					TCAGGCACAACTGACTGGTTC	0.408													19	52	---	---	---	---	PASS
MS4A6A	64231	broad.mit.edu	37	11	59949129	59949129	+	Silent	SNP	T	C	C			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:59949129T>C	uc001nor.2	-	2	310	c.72A>G	c.(70-72)GCA>GCG	p.A24A	MS4A6A_uc001noq.2_Silent_p.A24A|MS4A6A_uc001nos.3_Silent_p.A52A|MS4A6A_uc009ymv.2_Silent_p.A24A|MS4A6A_uc001not.2_Silent_p.A24A|MS4A6A_uc010rla.1_Silent_p.A52A|MS4A6A_uc010rlb.1_Silent_p.A24A	NM_152852	NP_690591	Q9H2W1	M4A6A_HUMAN	membrane-spanning 4-domains, subfamily A, member	24	Cytoplasmic (Potential).					integral to membrane	receptor activity				0						CGGGTTTCTCTGCTTGGGAGA	0.438													64	159	---	---	---	---	PASS
NARS2	79731	broad.mit.edu	37	11	78176964	78176964	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:78176964C>G	uc001ozi.2	-	11	1498	c.1122G>C	c.(1120-1122)AAG>AAC	p.K374N	NARS2_uc010rsq.1_Missense_Mutation_p.K147N	NM_024678	NP_078954	Q96I59	SYNM_HUMAN	asparaginyl-tRNA synthetase 2, mitochondrial	374					asparaginyl-tRNA aminoacylation	mitochondrial matrix	asparagine-tRNA ligase activity|ATP binding|nucleic acid binding			ovary(2)	2	all_cancers(14;2.63e-17)|all_epithelial(13;1.85e-19)				L-Asparagine(DB00174)	TGTAGAAAGGCTTGAGTGTTA	0.418													4	105	---	---	---	---	PASS
DPAGT1	1798	broad.mit.edu	37	11	118968574	118968574	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118968574C>T	uc001pvi.2	-	6	1328	c.908G>A	c.(907-909)CGC>CAC	p.R303H	H2AFX_uc001pvg.2_5'Flank|H2AFX_uc001pvh.1_5'Flank|DPAGT1_uc001pvj.2_Missense_Mutation_p.R196H|DPAGT1_uc009zaq.2_Intron|DPAGT1_uc001pvk.2_Missense_Mutation_p.R131H|DPAGT1_uc010ryz.1_Missense_Mutation_p.R303H|DPAGT1_uc001pvm.1_3'UTR|DPAGT1_uc010rza.1_Missense_Mutation_p.R196H	NM_001382	NP_001373	Q9H3H5	GPT_HUMAN	UDP-N-acetylglucosamine-dolichyl-phosphate	303	Cytoplasmic (Potential).				dolichol biosynthetic process|dolichol-linked oligosaccharide biosynthetic process|post-translational protein modification|protein N-linked glycosylation via asparagine|protein oligomerization	integral to endoplasmic reticulum membrane|microsome	phospho-N-acetylmuramoyl-pentapeptide-transferase activity|transferase activity, transferring glycosyl groups|UDP-N-acetylglucosamine-dolichyl-phosphate N-acetylglucosaminephosphotransferase activity			breast(2)|ovary(1)	3	all_hematologic(175;0.0977)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.55e-05)		CCTGGGTATGCGGTGGCGAGG	0.502													5	187	---	---	---	---	PASS
PVRL1	5818	broad.mit.edu	37	11	119510667	119510667	+	Silent	SNP	G	T	T			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:119510667G>T	uc001pwu.1	-	6	1231	c.1059C>A	c.(1057-1059)ACC>ACA	p.T353T		NM_203285	NP_976030	Q15223	PVRL1_HUMAN	poliovirus receptor-related 1 isoform 2	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment					adherens junction organization|cell junction assembly|entry of virus into host cell|heterophilic cell-cell adhesion|homophilic cell adhesion|immune response	cell-cell adherens junction|extracellular region|integral to membrane	cell adhesion molecule binding|coreceptor activity|protein homodimerization activity				0		Breast(348;0.037)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.29e-05)		ACACGGCCACGGTGCCCGCCA	0.597													3	33	---	---	---	---	PASS
ABCC9	10060	broad.mit.edu	37	12	21991035	21991035	+	Silent	SNP	T	A	A			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:21991035T>A	uc001rfi.1	-	28	3563	c.3543A>T	c.(3541-3543)GGA>GGT	p.G1181G	ABCC9_uc001rfh.2_Silent_p.G1181G|ABCC9_uc001rfj.1_Silent_p.G1145G	NM_005691	NP_005682	O60706	ABCC9_HUMAN	ATP-binding cassette, sub-family C, member 9	1181	Extracellular (Potential).|ABC transmembrane type-1 2.				defense response to virus|potassium ion import	ATP-sensitive potassium channel complex	ATP binding|ATPase activity, coupled to transmembrane movement of substances|potassium channel regulator activity|sulfonylurea receptor activity			ovary(4)|skin(2)	6					Adenosine triphosphate(DB00171)|Glibenclamide(DB01016)	TGGTGGTGAGTCCTTCTGCTG	0.413													35	57	---	---	---	---	PASS
FGD4	121512	broad.mit.edu	37	12	32786521	32786521	+	Silent	SNP	T	G	G			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:32786521T>G	uc001rkz.2	+	15	2277	c.1800T>G	c.(1798-1800)CTT>CTG	p.L600L	FGD4_uc001rlc.2_Silent_p.L685L|FGD4_uc001rky.2_Silent_p.L352L|FGD4_uc001rla.2_Silent_p.L256L|FGD4_uc010ske.1_Silent_p.L712L|FGD4_uc001rlb.1_RNA	NM_139241	NP_640334	Q96M96	FGD4_HUMAN	FYVE, RhoGEF and PH domain containing 4	600	FYVE-type.				actin cytoskeleton organization|apoptosis|filopodium assembly|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Cdc42 GTPase activity|regulation of cell shape|small GTPase mediated signal transduction	cytoskeleton|cytosol|filopodium|Golgi apparatus|lamellipodium|ruffle	metal ion binding|Rho guanyl-nucleotide exchange factor activity|small GTPase binding			ovary(2)|central_nervous_system(1)	3	Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.204)					AAGCTCAACTTGAATATGATG	0.303													16	50	---	---	---	---	PASS
C12orf40	283461	broad.mit.edu	37	12	40041619	40041619	+	Missense_Mutation	SNP	T	A	A			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:40041619T>A	uc001rmc.2	+	6	577	c.410T>A	c.(409-411)ATG>AAG	p.M137K	C12orf40_uc009zjv.1_RNA	NM_001031748	NP_001026918	Q86WS4	CL040_HUMAN	hypothetical protein LOC283461	137										ovary(6)	6						TCATATAGTATGCTTCACCCT	0.328													15	42	---	---	---	---	PASS
CNTN1	1272	broad.mit.edu	37	12	41422971	41422971	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:41422971G>A	uc001rmm.1	+	23	3043	c.2930G>A	c.(2929-2931)CGC>CAC	p.R977H	CNTN1_uc001rmn.1_Missense_Mutation_p.R966H	NM_001843	NP_001834	Q12860	CNTN1_HUMAN	contactin 1 isoform 1 precursor	977	Fibronectin type-III 4.				axon guidance|cell adhesion|Notch signaling pathway	anchored to membrane|membrane fraction|plasma membrane				lung(4)|ovary(3)|large_intestine(1)|skin(1)	9	all_cancers(12;2.07e-06)|all_epithelial(1;4.26e-06)|Breast(8;0.0716)	Lung NSC(34;0.0211)|all_lung(34;0.0294)				GTGGAGGTTCGCGCGCACAGT	0.448													66	181	---	---	---	---	PASS
TRIAP1	51499	broad.mit.edu	37	12	120882569	120882569	+	3'UTR	SNP	C	A	A			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120882569C>A	uc001tyg.2	-	2					GATC_uc010szi.1_5'Flank	NM_016399	NP_057483	O43715	TRIA1_HUMAN	p53-inducible cell-survival factor						anti-apoptosis|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest	mitochondrion|perinuclear region of cytoplasm	caspase inhibitor activity|protein binding				0	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					CTCCTCTCTCCTAAGTTCCTC	0.408													17	34	---	---	---	---	PASS
TRPC4	7223	broad.mit.edu	37	13	38357212	38357212	+	Missense_Mutation	SNP	C	T	T	rs140628205		TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:38357212C>T	uc001uws.2	-	2	494	c.259G>A	c.(259-261)GAA>AAA	p.E87K	TRPC4_uc010abv.2_5'UTR|TRPC4_uc001uwt.2_Missense_Mutation_p.E87K|TRPC4_uc010tey.1_Missense_Mutation_p.E87K|TRPC4_uc010abw.2_Missense_Mutation_p.E87K|TRPC4_uc010abx.2_Missense_Mutation_p.E87K|TRPC4_uc010aby.2_Missense_Mutation_p.E87K	NM_016179	NP_057263	Q9UBN4	TRPC4_HUMAN	transient receptor potential cation channel,	87	ANK 2.|Cytoplasmic (Potential).|Multimerization domain (By similarity).				axon guidance|calcium ion import	basolateral plasma membrane|calcium channel complex|cell surface|cortical cytoskeleton	beta-catenin binding|cadherin binding|store-operated calcium channel activity			ovary(3)|skin(2)|breast(1)	6				all cancers(112;1.92e-08)|Epithelial(112;5.04e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000677)|GBM - Glioblastoma multiforme(144;0.00623)|BRCA - Breast invasive adenocarcinoma(63;0.0126)		AAGAGTAGTTCgatgagctcc	0.209													27	58	---	---	---	---	PASS
TMEM55B	90809	broad.mit.edu	37	14	20928822	20928822	+	Nonsense_Mutation	SNP	C	A	A			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:20928822C>A	uc001vxl.2	-	2	478	c.325G>T	c.(325-327)GAA>TAA	p.E109*	TMEM55B_uc001vxk.2_Nonsense_Mutation_p.E116*	NM_144568	NP_653169	Q86T03	TM55B_HUMAN	transmembrane protein 55B isoform 2	109						integral to membrane|late endosome membrane|lysosomal membrane	hydrolase activity				0	all_cancers(95;0.00123)	all_lung(585;0.235)	Epithelial(56;1.09e-07)|all cancers(55;1.19e-06)	GBM - Glioblastoma multiforme(265;0.0224)|READ - Rectum adenocarcinoma(17;0.193)		ACGGTGGCTTCATTGCAGACA	0.498													4	98	---	---	---	---	PASS
AKAP6	9472	broad.mit.edu	37	14	33243070	33243070	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:33243070C>T	uc001wrq.2	+	12	3729	c.3559C>T	c.(3559-3561)CGT>TGT	p.R1187C	uc001wrr.2_5'Flank	NM_004274	NP_004265	Q13023	AKAP6_HUMAN	A-kinase anchor protein 6	1187					protein targeting	calcium channel complex|nuclear membrane|sarcoplasmic reticulum	protein kinase A binding|receptor binding			breast(6)|ovary(5)|lung(4)|skin(3)|large_intestine(2)|pancreas(1)	21	Breast(36;0.0388)|Prostate(35;0.15)		LUAD - Lung adenocarcinoma(48;0.00107)|Lung(238;0.00677)|STAD - Stomach adenocarcinoma(7;0.116)	GBM - Glioblastoma multiforme(265;0.019)		GTGGCAAACACGTCTACAAAA	0.413													6	28	---	---	---	---	PASS
PSMA6	5687	broad.mit.edu	37	14	35761756	35761756	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:35761756T>C	uc001wtd.2	+	1	183	c.74T>C	c.(73-75)GTA>GCA	p.V25A	KIAA0391_uc001wta.2_Intron|PSMA6_uc010tpt.1_5'UTR|PSMA6_uc010tpu.1_5'UTR	NM_002791	NP_002782	P60900	PSA6_HUMAN	proteasome alpha 6 subunit	25					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of NF-kappaB transcription factor activity|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|viral reproduction	mitochondrion|nuclear matrix|polysome|proteasome core complex, alpha-subunit complex|sarcomere	NF-kappaB binding|purine ribonucleoside triphosphate binding|RNA binding|threonine-type endopeptidase activity				0	Breast(36;0.0519)|Hepatocellular(127;0.158)		Lung(238;3.81e-05)|LUAD - Lung adenocarcinoma(48;5.59e-05)|Epithelial(34;0.00342)|all cancers(34;0.00973)	GBM - Glioblastoma multiforme(112;0.0234)		CTCTACCAAGTAGGTGAGTGA	0.567													23	62	---	---	---	---	PASS
FAM96A	84191	broad.mit.edu	37	15	64380992	64380992	+	Silent	SNP	C	A	A			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:64380992C>A	uc002amt.1	-	2	423	c.183G>T	c.(181-183)GTG>GTT	p.V61V	FAM96A_uc002amu.1_Silent_p.V61V|FAM96A_uc010uin.1_Silent_p.V61V	NM_032231	NP_115607	Q9H5X1	FA96A_HUMAN	family with sequence similarity 96, member A	61					chromosome segregation						0						TTTCCGAGACCACTTCCAGTT	0.388													18	47	---	---	---	---	PASS
ABHD2	11057	broad.mit.edu	37	15	89731484	89731484	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:89731484C>G	uc002bnj.2	+	13	1793	c.876C>G	c.(874-876)AGC>AGG	p.S292R	ABHD2_uc002bnk.2_Missense_Mutation_p.S292R	NM_007011	NP_008942	P08910	ABHD2_HUMAN	alpha/beta hydrolase domain containing protein	292						integral to membrane	carboxylesterase activity			ovary(1)|lung(1)	2	Lung NSC(78;0.0472)|all_lung(78;0.089)					CGGACTTGAGCCGGCTCTACA	0.532													14	50	---	---	---	---	PASS
ABHD2	11057	broad.mit.edu	37	15	89744352	89744352	+	3'UTR	SNP	T	A	A			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:89744352T>A	uc002bnj.2	+	16					ABHD2_uc002bnk.2_3'UTR	NM_007011	NP_008942	P08910	ABHD2_HUMAN	alpha/beta hydrolase domain containing protein							integral to membrane	carboxylesterase activity			ovary(1)|lung(1)	2	Lung NSC(78;0.0472)|all_lung(78;0.089)					TGGCTGCAATTACAACAAGAA	0.269													10	20	---	---	---	---	PASS
CACNA1H	8912	broad.mit.edu	37	16	1260841	1260841	+	Missense_Mutation	SNP	A	T	T			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1260841A>T	uc002cks.2	+	21	4341	c.4093A>T	c.(4093-4095)AAC>TAC	p.N1365Y	CACNA1H_uc002ckt.2_Missense_Mutation_p.N1365Y|CACNA1H_uc002cku.2_Missense_Mutation_p.N71Y|CACNA1H_uc010brj.2_Missense_Mutation_p.N71Y|CACNA1H_uc002ckv.2_Missense_Mutation_p.N71Y	NM_021098	NP_066921	O95180	CAC1H_HUMAN	calcium channel, voltage-dependent, T type,	1365	Helical; Name=S3 of repeat III; (Potential).|III.				aldosterone biosynthetic process|axon guidance|cellular response to hormone stimulus|cellular response to potassium ion|cortisol biosynthetic process|muscle contraction|myoblast fusion|positive regulation of acrosome reaction|regulation of heart contraction	voltage-gated calcium channel complex	low voltage-gated calcium channel activity			breast(2)	2		Hepatocellular(780;0.00369)			Flunarizine(DB04841)|Mibefradil(DB01388)	GAGCAGCTGGAACCTGCTGGA	0.677													12	65	---	---	---	---	PASS
TUSC5	286753	broad.mit.edu	37	17	1198811	1198811	+	Silent	SNP	C	T	T			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1198811C>T	uc002fsi.1	+	2	753	c.414C>T	c.(412-414)AAC>AAT	p.N138N		NM_172367	NP_758955	Q8IXB3	TUSC5_HUMAN	LOST1	138					response to biotic stimulus	integral to membrane				skin(2)	2				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)		AACAGGGCAACGTGGACGGCG	0.632													60	153	---	---	---	---	PASS
ZNF594	84622	broad.mit.edu	37	17	5086060	5086060	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:5086060T>C	uc010cla.1	-	2	1648	c.1492A>G	c.(1492-1494)AGG>GGG	p.R498G		NM_032530	NP_115919	Q96JF6	ZN594_HUMAN	zinc finger protein 594	498	C2H2-type 14.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)|skin(1)	3						GAACGCCGCCTGAAGGCTTTC	0.468													3	61	---	---	---	---	PASS
ALKBH5	54890	broad.mit.edu	37	17	18111566	18111566	+	Silent	SNP	C	T	T			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:18111566C>T	uc010cpw.2	+	4	1732	c.1041C>T	c.(1039-1041)AAC>AAT	p.N347N	ALKBH5_uc010cpx.2_RNA	NM_017758	NP_060228	Q6P6C2	ALKB5_HUMAN	alkB, alkylation repair homolog 5	347						integral to membrane	metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen				0	all_neural(463;0.228)					AGGAAGAGAACCGGCGCTCGG	0.602													35	90	---	---	---	---	PASS
KRTAP1-3	81850	broad.mit.edu	37	17	39191063	39191063	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39191063C>G	uc002hvv.2	-	1	45	c.11G>C	c.(10-12)TGC>TCC	p.C4S		NM_030966	NP_112228	Q8IUG1	KRA13_HUMAN	keratin associated protein 1-3	4						extracellular region|keratin filament	structural constituent of epidermis				0		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			GCTGGTCTGGCAGCAGGTCAT	0.572													8	36	---	---	---	---	PASS
NT5C3L	115024	broad.mit.edu	37	17	39988684	39988684	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39988684G>C	uc002hyc.3	-	5	385	c.376C>G	c.(376-378)CAC>GAC	p.H126D	NT5C3L_uc002hxx.3_5'UTR|NT5C3L_uc010wfu.1_5'UTR|NT5C3L_uc002hyb.3_Missense_Mutation_p.H49D|NT5C3L_uc002hyd.3_Missense_Mutation_p.H49D|NT5C3L_uc002hxy.3_Missense_Mutation_p.H84D|NT5C3L_uc002hxz.3_Missense_Mutation_p.H49D|NT5C3L_uc002hya.3_Missense_Mutation_p.H84D	NM_052935	NP_443167	C9JKC4	C9JKC4_HUMAN	5'-nucleotidase, cytosolic III-like	92						cytoplasm	5'-nucleotidase activity|magnesium ion binding				0		Breast(137;0.000162)		BRCA - Breast invasive adenocarcinoma(366;0.15)		ACGGTCCGGTGTGGGTCGATC	0.527													4	79	---	---	---	---	PASS
MTMR4	9110	broad.mit.edu	37	17	56588730	56588730	+	Intron	SNP	G	A	A			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:56588730G>A	uc002iwj.2	-						MTMR4_uc010dcx.1_3'UTR	NM_004687	NP_004678	Q9NYA4	MTMR4_HUMAN	myotubularin related protein 4							cytoplasm|membrane	metal ion binding|protein tyrosine phosphatase activity			skin(1)	1	Medulloblastoma(34;0.127)|all_neural(34;0.237)					AAACCCTGCAGCACAGAGAAC	0.483													3	63	---	---	---	---	PASS
AFG3L2	10939	broad.mit.edu	37	18	12353075	12353075	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:12353075C>A	uc002kqz.1	-	10	1360	c.1247G>T	c.(1246-1248)AGA>ATA	p.R416I		NM_006796	NP_006787	Q9Y4W6	AFG32_HUMAN	AFG3 ATPase family gene 3-like 2	416					cell death|protein catabolic process|proteolysis	integral to membrane	ATP binding|metalloendopeptidase activity|nucleoside-triphosphatase activity|unfolded protein binding|zinc ion binding				0					Adenosine triphosphate(DB00171)	GCCTCTTCCTCTCTTCCTTCC	0.498													4	112	---	---	---	---	PASS
DOT1L	84444	broad.mit.edu	37	19	2229711	2229711	+	Intron	SNP	C	A	A			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2229711C>A	uc002lvb.3	+						DOT1L_uc002lvc.1_3'UTR	NM_032482	NP_115871	Q8TEK3	DOT1L_HUMAN	DOT1-like, histone H3 methyltransferase							nucleus	DNA binding|histone-lysine N-methyltransferase activity|protein binding			pancreas(2)|upper_aerodigestive_tract(1)|lung(1)	4		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CGGTCCCCAGCCTGGGTGAGT	0.637													16	75	---	---	---	---	PASS
FEM1A	55527	broad.mit.edu	37	19	4792504	4792504	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4792504G>A	uc002mbf.2	+	1	777	c.638G>A	c.(637-639)GGC>GAC	p.G213D	uc002mbg.1_RNA	NM_018708	NP_061178	Q9BSK4	FEM1A_HUMAN	fem-1 homolog a	213					regulation of ubiquitin-protein ligase activity	cytoplasm	binding|ubiquitin-protein ligase activity				0		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0139)		GAACGTGACGGCTACGGCATG	0.687													3	38	---	---	---	---	PASS
KIAA1543	57662	broad.mit.edu	37	19	7670197	7670197	+	Silent	SNP	G	T	T			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7670197G>T	uc002mgv.3	+	2	335	c.234G>T	c.(232-234)CTG>CTT	p.L78L	KIAA1543_uc002mgu.3_Silent_p.L78L	NM_020902	NP_065953	Q9P1Y5	CAMP3_HUMAN	NEZHA isoform 2	78					epithelial cell-cell adhesion|microtubule anchoring|regulation of microtubule cytoskeleton organization|zonula adherens maintenance	cytoplasm|microtubule|zonula adherens	microtubule minus-end binding			pancreas(1)	1						CACGGCTGCTGCTCTCAGCCG	0.667													7	141	---	---	---	---	PASS
LIPE	3991	broad.mit.edu	37	19	42907058	42907058	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42907058C>T	uc002otr.2	-	9	2945	c.2668G>A	c.(2668-2670)GAC>AAC	p.D890N	uc010eif.1_Intron	NM_005357	NP_005348	Q05469	LIPS_HUMAN	hormone-sensitive lipase	890					cholesterol metabolic process|protein phosphorylation|triglyceride catabolic process	caveola|cytosol	hormone-sensitive lipase activity|protein binding			ovary(1)|breast(1)	2		Prostate(69;0.00682)				TCGGGGGTGTCCGACGACGTC	0.607													26	60	---	---	---	---	PASS
ASPDH	554235	broad.mit.edu	37	19	51017905	51017905	+	5'Flank	SNP	C	G	G			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51017905C>G	uc010enz.2	-						ASPDH_uc002psr.3_5'UTR	NM_001114598	NP_001108070	A6ND91	ASPD_HUMAN	aspartate dehydrogenase isoform 1						NAD biosynthetic process|NADP catabolic process		aspartate dehydrogenase activity|NADP binding				0						GCCTCTGTGCCTTGAGGGTGC	0.677													8	11	---	---	---	---	PASS
ZNF528	84436	broad.mit.edu	37	19	52918551	52918551	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:52918551A>G	uc002pzh.2	+	7	872	c.446A>G	c.(445-447)GAA>GGA	p.E149G	ZNF528_uc002pzi.2_5'UTR	NM_032423	NP_115799	Q3MIS6	ZN528_HUMAN	zinc finger protein 528	149					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)|skin(1)	2				GBM - Glioblastoma multiforme(134;0.00249)|OV - Ovarian serous cystadenocarcinoma(262;0.00817)		TCACCGCTTGAAAAAATTTCT	0.358													24	45	---	---	---	---	PASS
NAPB	63908	broad.mit.edu	37	20	23377799	23377799	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:23377799C>G	uc002wta.2	-	3	322	c.205G>C	c.(205-207)GCC>CCC	p.A69P	NAPB_uc002wtc.2_5'UTR|NAPB_uc002wtb.2_Missense_Mutation_p.A73P|NAPB_uc002wtd.3_RNA|NAPB_uc010zss.1_5'Flank|NAPB_uc010zst.1_Intron	NM_022080	NP_071363	Q9H115	SNAB_HUMAN	N-ethylmaleimide-sensitive factor attachment	69					intracellular protein transport|vesicle-mediated transport	membrane				ovary(1)	1	Lung NSC(19;0.0646)|Colorectal(13;0.0993)|all_lung(19;0.143)					TGGAGCTTGGCTGCCTGACAA	0.502													7	50	---	---	---	---	PASS
FRG1B	284802	broad.mit.edu	37	20	29625961	29625961	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29625961C>A	uc010ztl.1	+	2	147	c.115C>A	c.(115-117)CAA>AAA	p.Q39K	FRG1B_uc002wvm.1_RNA|FRG1B_uc010ztj.1_RNA|FRG1B_uc010gdr.1_RNA|FRG1B_uc010ztk.1_Intron					Homo sapiens cDNA FLJ32537 fis, clone SMINT2000400, highly similar to Homo sapiens FRG1 mRNA.												0						ACCAAGAGAACAATGGGAACC	0.333													5	82	---	---	---	---	PASS
GGT3P	2679	broad.mit.edu	37	22	18778601	18778601	+	RNA	SNP	C	T	T			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:18778601C>T	uc011ago.1	-	2		c.219G>A			GGT3P_uc011agp.1_RNA|GGT3P_uc002zob.1_RNA					Homo sapiens cDNA clone IMAGE:5761295, **** WARNING: chimeric clone ****.												0						GCTTGGCATCCGCGGCCACGG	0.552													3	21	---	---	---	---	PASS
LOC96610	96610	broad.mit.edu	37	22	22664721	22664721	+	RNA	SNP	T	C	C			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:22664721T>C	uc011aim.1	+	31		c.2236T>C			LOC96610_uc011aiq.1_RNA					Parts of antibodies, mostly variable regions.												0						AACTCAGGCTTGCCCATGGTG	0.512													3	32	---	---	---	---	PASS
FAM118A	55007	broad.mit.edu	37	22	45724290	45724290	+	Intron	SNP	G	A	A			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:45724290G>A	uc003bfz.3	+						FAM118A_uc003bga.3_Intron|FAM118A_uc011aqr.1_5'Flank	NM_001104595	NP_001098065	Q9NWS6	F118A_HUMAN	hypothetical protein LOC55007							integral to membrane					0		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0178)		CTGGGGCTGCGGGCAGCCTGC	0.527													18	26	---	---	---	---	PASS
CXorf23	256643	broad.mit.edu	37	X	19988376	19988376	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:19988376G>A	uc004czp.2	-	1	7	c.7C>T	c.(7-9)CGG>TGG	p.R3W		NM_198279	NP_938020	A2AJT9	CX023_HUMAN	hypothetical protein LOC256643	3						mitochondrion				lung(1)|skin(1)	2						GATCGTGACCGTGCCATCCTT	0.443													4	121	---	---	---	---	PASS
KLHL34	257240	broad.mit.edu	37	X	21674907	21674907	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:21674907G>T	uc004czz.1	-	1	1542	c.1000C>A	c.(1000-1002)CAG>AAG	p.Q334K		NM_153270	NP_695002	Q8N239	KLH34_HUMAN	kelch-like 34	334	Kelch 1.									ovary(1)	1						ACCACGTTCTGGGTGAGCTCC	0.522													6	12	---	---	---	---	PASS
CYSLTR1	10800	broad.mit.edu	37	X	77528390	77528390	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:77528390G>T	uc004edb.2	-	3	1254	c.854C>A	c.(853-855)GCA>GAA	p.A285E	CYSLTR1_uc010nma.2_Missense_Mutation_p.A285E|CYSLTR1_uc010nmb.2_Missense_Mutation_p.A285E	NM_006639	NP_006630	Q9Y271	CLTR1_HUMAN	cysteinyl leukotriene receptor 1	285	Helical; Name=7; (Potential).				elevation of cytosolic calcium ion concentration|respiratory gaseous exchange	integral to plasma membrane|membrane fraction	leukotriene receptor activity			ovary(1)	1					Amlexanox(DB01025)|Cinalukast(DB00587)|Montelukast(DB00471)|Nedocromil(DB00716)|Pranlukast(DB01411)|Zafirlukast(DB00549)	ACAATTGGATGCAGCCAGAGA	0.418													22	67	---	---	---	---	PASS
TKTL1	8277	broad.mit.edu	37	X	153524232	153524232	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:153524232G>C	uc004fkg.2	+	1	206	c.20G>C	c.(19-21)AGG>ACG	p.R7T	TEX28_uc004fke.2_5'Flank|TEX28_uc004fkf.2_5'Flank|TEX28_uc010nut.1_5'Flank|TKTL1_uc011mzl.1_Missense_Mutation_p.R7T|TKTL1_uc011mzm.1_Missense_Mutation_p.R7T	NM_012253	NP_036385	P51854	TKTL1_HUMAN	transketolase-like 1 isoform a	7					glucose catabolic process|thiamine metabolic process	cytoplasm|nucleus	metal ion binding|transketolase activity			ovary(3)|skin(1)	4	all_cancers(53;5.05e-16)|all_epithelial(53;1.82e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					GCTGAGGCGAGGGCTGAGTTC	0.612													45	94	---	---	---	---	PASS
ACP6	51205	broad.mit.edu	37	1	147124557	147124557	+	Intron	DEL	A	-	-			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:147124557delA	uc001epr.2	-						ACP6_uc009wjj.1_Intron	NM_016361	NP_057445	Q9NPH0	PPA6_HUMAN	acid phosphatase 6, lysophosphatidic precursor						lipid metabolic process	extracellular region|mitochondrion	acid phosphatase activity|protein binding			ovary(4)	4	all_hematologic(923;0.0276)					GAAGGCCAGGAAAAAAAAAAA	0.328													9	5	---	---	---	---	
SLC4A1AP	22950	broad.mit.edu	37	2	27908052	27908052	+	Frame_Shift_Del	DEL	G	-	-			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27908052delG	uc002rlk.3	+	10	2306	c.2024delG	c.(2023-2025)AGTfs	p.S675fs		NM_018158	NP_060628	Q9BWU0	NADAP_HUMAN	solute carrier family 4 (anion exchanger),	675	Glu-rich.					cytoplasm|nucleus	double-stranded RNA binding|protein binding				0	Acute lymphoblastic leukemia(172;0.155)					GGAAGCCTCAGTAGGCCACAG	0.348													97	71	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	201967197	201967197	+	IGR	DEL	A	-	-	rs77338628		TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:201967197delA								NDUFB3 (16726 upstream) : CFLAR (13619 downstream)																							actctgtctcaaaaaaaaaaa	0.174													4	2	---	---	---	---	
USP37	57695	broad.mit.edu	37	2	219352921	219352921	+	Intron	DEL	G	-	-			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:219352921delG	uc002vie.2	-						USP37_uc010fvs.1_Intron|USP37_uc010zkf.1_Intron|USP37_uc002vif.2_Intron|USP37_uc002vig.2_Intron	NM_020935	NP_065986	Q86T82	UBP37_HUMAN	ubiquitin specific peptidase 37						ubiquitin-dependent protein catabolic process	nucleus	cysteine-type peptidase activity|ubiquitin thiolesterase activity			skin(3)|ovary(1)|prostate(1)	5		Renal(207;0.0915)		Epithelial(149;1.08e-06)|all cancers(144;0.000197)|LUSC - Lung squamous cell carcinoma(224;0.00375)|Lung(261;0.00487)		aaaaaaaaaagaaaagaaAAG	0.104													9	6	---	---	---	---	
ZFAND2B	130617	broad.mit.edu	37	2	220071889	220071889	+	Intron	DEL	T	-	-			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:220071889delT	uc002vka.2	+						ZFAND2B_uc010zkt.1_Intron|ZFAND2B_uc010fwd.1_Intron|ZFAND2B_uc002vjy.1_Intron|ZFAND2B_uc002vjz.1_Intron|ZFAND2B_uc002vkb.1_5'Flank	NM_138802	NP_620157	Q8WV99	ZFN2B_HUMAN	zinc finger, AN1-type domain 2B							endoplasmic reticulum	protein binding|zinc ion binding				0		Renal(207;0.0915)		Epithelial(149;1.16e-06)|all cancers(144;0.000191)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		TGGGGGGGGGTGGTCAGCGGC	0.627													6	3	---	---	---	---	
KIF1A	547	broad.mit.edu	37	2	241724234	241724234	+	Intron	DEL	G	-	-	rs113212728		TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:241724234delG	uc002vzy.2	-						KIF1A_uc010fzk.2_Intron|KIF1A_uc002vzz.1_Intron	NM_004321	NP_004312	Q12756	KIF1A_HUMAN	axonal transport of synaptic vesicles						anterograde axon cargo transport	cytoplasm|microtubule|nucleus	ATP binding|microtubule motor activity			lung(1)	1		all_epithelial(40;1.35e-15)|Breast(86;2.14e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0295)|all_neural(83;0.0459)|Lung NSC(271;0.0942)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;6.12e-30)|all cancers(36;3.46e-27)|OV - Ovarian serous cystadenocarcinoma(60;1.38e-14)|Kidney(56;5e-09)|KIRC - Kidney renal clear cell carcinoma(57;5e-08)|BRCA - Breast invasive adenocarcinoma(100;5.87e-06)|Lung(119;0.00209)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Colorectal(34;0.0282)|COAD - Colon adenocarcinoma(134;0.176)		CCTCTGGGGCGGGGGGGGGGA	0.657													3	5	---	---	---	---	
C3orf63	23272	broad.mit.edu	37	3	56661910	56661912	+	Intron	DEL	AAT	-	-	rs145293853		TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:56661910_56661912delAAT	uc003did.3	-						C3orf63_uc003dib.3_Intron|C3orf63_uc003dic.3_Intron|C3orf63_uc003die.3_Intron	NM_015224	NP_056039	Q9UK61	CC063_HUMAN	retinoblastoma-associated protein 140 isoform b											ovary(3)|kidney(1)|central_nervous_system(1)	5				KIRC - Kidney renal clear cell carcinoma(284;0.0126)|Kidney(284;0.0147)		AAGCCACACAAATAATATTCCCA	0.369													4	7	---	---	---	---	
DNAJC13	23317	broad.mit.edu	37	3	132193689	132193689	+	Intron	DEL	G	-	-			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:132193689delG	uc003eor.2	+							NM_015268	NP_056083	O75165	DJC13_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 13								heat shock protein binding			ovary(1)|breast(1)	2						TTTTTTTTTTGCTTATTATAA	0.254													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	194711825	194711827	+	IGR	DEL	TCC	-	-			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:194711825_194711827delTCC								FAM43A (302061 upstream) : C3orf21 (77188 downstream)																							ctcctcctcttcctcctcctctt	0.000													4	3	---	---	---	---	
WDR19	57728	broad.mit.edu	37	4	39226486	39226487	+	Intron	INS	-	T	T			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:39226486_39226487insT	uc003gtv.2	+						WDR19_uc003gtu.1_Intron|WDR19_uc011byi.1_Intron|WDR19_uc003gtw.1_Intron	NM_025132	NP_079408	Q8NEZ3	WDR19_HUMAN	WD repeat domain 19						cell projection organization	microtubule basal body|motile cilium|photoreceptor connecting cilium	binding			large_intestine(1)	1						TCATGGCTGGATTTTTTTTTTT	0.282													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	110475293	110475294	+	IGR	INS	-	CTTCAGGAAG	CTTCAGGAAG	rs148787567	by1000genomes	TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:110475293_110475294insCTTCAGGAAG								SEC24B (13679 upstream) : CCDC109B (6061 downstream)																							GTCTCCTTGCTCAGGCAGAAAA	0.460													4	3	---	---	---	---	
NR3C2	4306	broad.mit.edu	37	4	149035136	149035137	+	Intron	INS	-	A	A			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:149035136_149035137insA	uc003ilj.3	-						NR3C2_uc003ilk.3_Intron|NR3C2_uc010iph.2_Intron	NM_000901	NP_000892	P08235	MCR_HUMAN	nuclear receptor subfamily 3, group C, member 2						regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	endoplasmic reticulum membrane|nucleoplasm	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid binding|steroid hormone receptor activity|zinc ion binding			large_intestine(1)	1	all_hematologic(180;0.151)			GBM - Glioblastoma multiforme(119;0.0614)	Desoxycorticosterone Pivalate(DB01134)|Eplerenone(DB00700)|Fludrocortisone(DB00687)|Spironolactone(DB00421)	tatccttaatggagtcaacaga	0.173													2	4	---	---	---	---	
DAP	1611	broad.mit.edu	37	5	10748142	10748142	+	Intron	DEL	C	-	-	rs3217459		TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:10748142delC	uc003jez.3	-						DAP_uc011cmw.1_Intron	NM_004394	NP_004385	P51397	DAP1_HUMAN	death-associated protein						activation of caspase activity|cellular response to amino acid starvation|induction of apoptosis by extracellular signals|negative regulation of autophagy|negative regulation of NF-kappaB transcription factor activity|negative regulation of transcription, DNA-dependent		death domain binding				0		Ovarian(839;1.34e-05)|Breast(839;0.0634)|Lung NSC(810;0.0804)				GCCCCCTCCTCCCTGATTAGG	0.502													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	159674905	159674905	+	IGR	DEL	A	-	-	rs10568222		TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:159674905delA								FABP6 (9176 upstream) : CCNJL (3766 downstream)																							actctggctcaaaaaaaaaaa	0.229													3	4	---	---	---	---	
C1QTNF2	114898	broad.mit.edu	37	5	159797454	159797456	+	Intron	DEL	TCC	-	-			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:159797454_159797456delTCC	uc003lyd.2	-							NM_031908	NP_114114	Q9BXJ5	C1QT2_HUMAN	C1q and tumor necrosis factor related protein 2							collagen				skin(1)	1	Renal(175;0.00196)	Medulloblastoma(196;0.0354)|all_neural(177;0.116)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			GCAGTGCGAGTCCTCCTCCTCCT	0.734													4	2	---	---	---	---	
FAM8A1	51439	broad.mit.edu	37	6	17603123	17603123	+	Intron	DEL	A	-	-			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:17603123delA	uc003ncc.2	+							NM_016255	NP_057339	Q9UBU6	FA8A1_HUMAN	family with sequence similarity 8, member A1							integral to membrane					0	Breast(50;0.0259)|Ovarian(93;0.0584)	all_hematologic(90;0.143)	all cancers(50;0.176)|Epithelial(50;0.204)			ACTAGAAAGGAAAAAAAATAG	0.303													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	26055865	26055866	+	IGR	INS	-	TC	TC	rs144566523	by1000genomes	TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26055865_26055866insTC								HIST1H3C (9769 upstream) : HIST1H1C (103 downstream)																							CACCCAATTCGTCTGATACCTC	0.465													4	5	---	---	---	---	
RAPGEF5	9771	broad.mit.edu	37	7	22330863	22330863	+	Intron	DEL	A	-	-			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:22330863delA	uc003svg.2	-							NM_012294	NP_036426	Q92565	RPGF5_HUMAN	Rap guanine nucleotide exchange factor (GEF) 5						nervous system development|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	nucleus	GTP-dependent protein binding|Rap guanyl-nucleotide exchange factor activity			ovary(1)	1						GATGAGACCTAAAAAAAAAAA	0.333													6	3	---	---	---	---	
WBSCR17	64409	broad.mit.edu	37	7	71142502	71142502	+	Intron	DEL	T	-	-			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:71142502delT	uc003tvy.2	+						WBSCR17_uc003tvz.2_Intron	NM_022479	NP_071924	Q6IS24	GLTL3_HUMAN	UDP-GalNAc:polypeptide							Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			skin(3)|upper_aerodigestive_tract(1)|ovary(1)|pancreas(1)|central_nervous_system(1)	7		all_cancers(73;0.2)|Lung NSC(55;0.094)|all_lung(88;0.125)				AGCATGCAGAttttttttttt	0.169													3	4	---	---	---	---	
BRAF	673	broad.mit.edu	37	7	140434620	140434621	+	Intron	INS	-	AAAG	AAAG	rs145368076	by1000genomes	TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:140434620_140434621insAAAG	uc003vwc.3	-							NM_004333	NP_004324	P15056	BRAF_HUMAN	B-Raf						activation of MAPKK activity|anti-apoptosis|nerve growth factor receptor signaling pathway|organ morphogenesis|positive regulation of peptidyl-serine phosphorylation|small GTPase mediated signal transduction|synaptic transmission	cytosol|nucleus|plasma membrane	ATP binding|metal ion binding		KIAA1549/BRAF(229)|AKAP9_ENST00000356239/BRAF(10)|AGTRAP/BRAF(2)|FCHSD1/BRAF(2)|SLC45A3/BRAF(2)	thyroid(8166)|large_intestine(5052)|skin(3798)|NS(368)|central_nervous_system(284)|ovary(236)|lung(78)|eye(53)|prostate(44)|endometrium(30)|biliary_tract(28)|soft_tissue(27)|haematopoietic_and_lymphoid_tissue(22)|breast(18)|upper_aerodigestive_tract(13)|stomach(13)|pancreas(10)|small_intestine(10)|testis(7)|bone(6)|cervix(5)|genital_tract(4)|oesophagus(3)|urinary_tract(3)|adrenal_gland(3)|gastrointestinal_tract_(site_indeterminate)(2)|liver(2)|meninges(1)|kidney(1)|autonomic_ganglia(1)|pituitary(1)|salivary_gland(1)	18290	Melanoma(164;0.00956)				Sorafenib(DB00398)	aaaagaaaaaaaaagaaagaaa	0.262		61	Mis|T|O	AKAP9|KIAA1549	melanoma|colorectal|papillary thyroid|borderline ov|Non small-cell lung cancer (NSCLC)|cholangiocarcinoma|pilocytic astrocytoma		Cardio-facio-cutaneous syndrome		Cardiofaciocutaneous_syndrome				4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	7679341	7679342	+	IGR	INS	-	A	A			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:7679341_7679342insA								FAM90A7 (262107 upstream) : SPAG11A (26060 downstream)																							gactccttctcaaaaaaaaaaa	0.074													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	47511973	47511976	+	IGR	DEL	CTCT	-	-			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:47511973_47511976delCTCT								None (None upstream) : BEYLA (240532 downstream)																							TTCTGGATTGCTCTCTAAGAGATT	0.284													4	3	---	---	---	---	
RGS22	26166	broad.mit.edu	37	8	101011387	101011387	+	Intron	DEL	A	-	-	rs35746502		TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:101011387delA	uc003yjb.1	-						RGS22_uc003yja.1_Intron|RGS22_uc003yjc.1_Intron	NM_015668	NP_056483	Q8NE09	RGS22_HUMAN	regulator of G-protein signaling 22						negative regulation of signal transduction	cytoplasm|plasma membrane	GTPase activator activity|signal transducer activity			ovary(3)|skin(2)|breast(1)|central_nervous_system(1)	7			Epithelial(11;6.71e-08)|all cancers(13;4.19e-06)|OV - Ovarian serous cystadenocarcinoma(57;0.000469)|STAD - Stomach adenocarcinoma(118;0.169)			cccattccttaaaaaaaaaaa	0.015													5	3	---	---	---	---	
CSMD3	114788	broad.mit.edu	37	8	113353593	113353593	+	Intron	DEL	T	-	-			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:113353593delT	uc003ynu.2	-						CSMD3_uc003yns.2_Intron|CSMD3_uc003ynt.2_Intron|CSMD3_uc011lhx.1_Intron	NM_198123	NP_937756	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3 isoform 1							integral to membrane|plasma membrane				ovary(21)|lung(11)|skin(11)|kidney(8)|large_intestine(6)|upper_aerodigestive_tract(2)|central_nervous_system(2)|urinary_tract(1)|breast(1)	63						TTGGCTTAAGTTTTTTTTTTT	0.289										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			4	2	---	---	---	---	
C9orf24	84688	broad.mit.edu	37	9	34382581	34382582	+	Intron	INS	-	A	A	rs35997251		TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:34382581_34382582insA	uc003zuh.1	-						C9orf24_uc003zug.1_5'Flank|C9orf24_uc003zuf.1_5'Flank|C9orf24_uc003zui.1_5'Flank	NM_032596	NP_115985	Q8NCR6	CI024_HUMAN	testes development-related NYD-SP22 isoform 1											ovary(1)	1			LUSC - Lung squamous cell carcinoma(29;0.0107)	GBM - Glioblastoma multiforme(74;0.123)		agactctatctaaaaaaaaaaa	0.183													3	3	---	---	---	---	
VAX1	11023	broad.mit.edu	37	10	118897631	118897632	+	5'UTR	DEL	GC	-	-	rs71677026		TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:118897631_118897632delGC	uc009xyx.2	-	1					VAX1_uc001ldb.1_5'UTR	NM_001112704	NP_001106175	Q5SQQ9	VAX1_HUMAN	ventral anterior homeobox 1 isoform a							nucleus	sequence-specific DNA binding			ovary(2)	2				all cancers(201;0.0108)		AGGGGGGGGGGCGGAGAAGGAA	0.441													3	7	---	---	---	---	
C11orf46	120534	broad.mit.edu	37	11	30358034	30358034	+	Intron	DEL	T	-	-			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:30358034delT	uc001mso.1	+						C11orf46_uc001msp.2_5'Flank	NM_152316	NP_689529	Q8N8R7	CK046_HUMAN	hypothetical protein LOC120534												0						TTTTATCTCCTTTTTTTTTTT	0.284													4	2	---	---	---	---	
CD44	960	broad.mit.edu	37	11	35223423	35223423	+	Intron	DEL	G	-	-	rs140631691	by1000genomes	TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:35223423delG	uc001mvu.2	+						CD44_uc001mvv.2_Intron|CD44_uc001mvw.2_Intron|CD44_uc001mvx.2_Intron|CD44_uc001mvy.2_Intron|CD44_uc001mwc.3_Intron|CD44_uc010rer.1_Intron|CD44_uc009ykh.2_Intron|CD44_uc010res.1_Intron|CD44_uc010ret.1_Intron|CD44_uc010reu.1_Intron	NM_000610	NP_000601	P16070	CD44_HUMAN	CD44 antigen isoform 1 precursor						cell-cell adhesion|cell-matrix adhesion|interferon-gamma-mediated signaling pathway|negative regulation of apoptosis|negative regulation of DNA damage response, signal transduction by p53 class mediator|positive regulation of ERK1 and ERK2 cascade|positive regulation of peptidyl-serine phosphorylation|positive regulation of peptidyl-tyrosine phosphorylation	cell surface|Golgi apparatus|integral to plasma membrane	collagen binding|hyaluronic acid binding|receptor activity			pancreas(1)	1	all_cancers(35;0.212)|all_lung(20;0.0874)|all_epithelial(35;0.112)	all_hematologic(20;0.107)	STAD - Stomach adenocarcinoma(6;0.00731)		Hyaluronidase(DB00070)	GAAATTGGCCGCATCTTCTAT	0.383													8	5	---	---	---	---	
GRIP1	23426	broad.mit.edu	37	12	66957859	66957860	+	Intron	INS	-	TT	TT	rs146009716	by1000genomes	TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:66957859_66957860insTT	uc001stk.2	-						GRIP1_uc010sta.1_Intron|GRIP1_uc001stl.1_Intron|GRIP1_uc001stm.2_Intron	NM_021150	NP_066973	Q9Y3R0	GRIP1_HUMAN	glutamate receptor interacting protein 1						androgen receptor signaling pathway|intracellular signal transduction|positive regulation of transcription, DNA-dependent|synaptic transmission	cell junction|cytoplasmic membrane-bounded vesicle|cytosol|endoplasmic reticulum|postsynaptic membrane	androgen receptor binding|beta-catenin binding|protein C-terminus binding|receptor signaling complex scaffold activity|transcription coactivator activity			ovary(2)	2			GBM - Glioblastoma multiforme(2;0.00069)	GBM - Glioblastoma multiforme(28;0.0933)		GGTTTCTTCTCTGTCTTTTTCA	0.277													4	3	---	---	---	---	
KPNA3	3839	broad.mit.edu	37	13	50299782	50299783	+	Intron	INS	-	T	T	rs35089210		TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:50299782_50299783insT	uc001vdj.2	-							NM_002267	NP_002258	O00505	IMA3_HUMAN	karyopherin alpha 3						interspecies interaction between organisms|NLS-bearing substrate import into nucleus|protein complex assembly	cytoplasm|nuclear pore	nuclear localization sequence binding|protein transporter activity				0		Lung NSC(96;2.46e-05)|Breast(56;9.7e-05)|Prostate(109;0.00174)|Hepatocellular(98;0.0207)|Myeloproliferative disorder(33;0.163)|Lung SC(185;0.187)|all_neural(104;0.19)		GBM - Glioblastoma multiforme(99;1.42e-09)		GCCAACCCTACttttttttttt	0.178													4	2	---	---	---	---	
TEP1	7011	broad.mit.edu	37	14	20851195	20851197	+	Intron	DEL	AAC	-	-			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:20851195_20851197delAAC	uc001vxe.2	-						TEP1_uc010ahk.2_Intron|TEP1_uc010tlf.1_Intron|TEP1_uc010tlg.1_Intron|TEP1_uc010tlh.1_5'Flank	NM_007110	NP_009041	Q99973	TEP1_HUMAN	telomerase-associated protein 1						telomere maintenance via recombination	chromosome, telomeric region|cytoplasm|nuclear matrix|soluble fraction|telomerase holoenzyme complex	ATP binding|RNA binding			ovary(5)	5	all_cancers(95;0.00123)	all_lung(585;0.235)	Epithelial(56;7.42e-08)|all cancers(55;6.46e-07)	GBM - Glioblastoma multiforme(265;0.028)|READ - Rectum adenocarcinoma(17;0.233)		TTTTCTTATTAACAACTTCCCAT	0.532													1	5	---	---	---	---	
EIF5	1983	broad.mit.edu	37	14	103803003	103803003	+	Intron	DEL	C	-	-			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:103803003delC	uc001ymq.2	+						EIF5_uc001ymr.2_Intron|EIF5_uc001yms.2_Intron|EIF5_uc001ymt.2_Intron|EIF5_uc001ymu.2_Intron|SNORA28_uc001ymv.1_5'Flank	NM_001969	NP_001960	P55010	IF5_HUMAN	eukaryotic translation initiation factor 5						regulation of translational initiation|RNA metabolic process	cytosol	GTP binding|GTPase activity|translation initiation factor activity			pancreas(1)|breast(1)|skin(1)	3		Melanoma(154;0.155)	Epithelial(46;0.182)			ACTCCTTTTTCATTCAAATAG	0.348													44	28	---	---	---	---	
PACS2	23241	broad.mit.edu	37	14	105861116	105861116	+	3'UTR	DEL	A	-	-			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:105861116delA	uc001yqt.2	+	24					PACS2_uc001yqs.2_3'UTR|PACS2_uc001yqv.2_3'UTR|PACS2_uc001yqu.2_3'UTR	NM_015197	NP_056012	Q86VP3	PACS2_HUMAN	phosphofurin acidic cluster sorting protein 2						apoptosis|interspecies interaction between organisms	endoplasmic reticulum lumen|mitochondrion				pancreas(1)	1		all_cancers(154;0.0351)|all_epithelial(191;0.153)|Melanoma(154;0.155)	OV - Ovarian serous cystadenocarcinoma(23;0.0145)|Epithelial(46;0.036)	Epithelial(152;0.138)		AAACACAAAGAGAAACAGTCT	0.507													11	9	---	---	---	---	
ADAM6	8755	broad.mit.edu	37	14	106234031	106234032	+	Intron	INS	-	G	G			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106234031_106234032insG	uc010tyt.1	-						uc001yrs.2_Intron|uc001yrt.2_Intron|uc001yrw.1_Intron|uc001yrx.1_Intron|uc001yrz.1_Intron|uc001yse.2_Intron|uc001ysf.2_Intron|uc001ysh.1_Intron|uc001ysi.1_Intron					Parts of antibodies, mostly variable regions.												0						GGACAGTTTGTGAGAGCGTGGG	0.505													4	3	---	---	---	---	
ADAM6	8755	broad.mit.edu	37	14	106405448	106405448	+	RNA	DEL	C	-	-	rs77404616		TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106405448delC	uc010tyt.1	-	2359		c.42471delG								Parts of antibodies, mostly variable regions.												0						aaaaaaaaaacaacaaCAGTT	0.259													8	4	---	---	---	---	
TJP1	7082	broad.mit.edu	37	15	30020389	30020390	+	Intron	INS	-	T	T			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:30020389_30020390insT	uc001zcr.2	-						TJP1_uc010azl.2_Intron|TJP1_uc001zcq.2_Intron|TJP1_uc001zcs.2_Intron	NM_003257	NP_003248	Q07157	ZO1_HUMAN	tight junction protein 1 isoform a						cell-cell junction assembly|cellular component disassembly involved in apoptosis	basolateral plasma membrane|cell-cell adherens junction|Golgi apparatus|tight junction				ovary(4)|central_nervous_system(1)|pancreas(1)	6		all_lung(180;7.48e-11)|Breast(32;0.000153)		all cancers(64;3.29e-10)|Epithelial(43;5.34e-09)|BRCA - Breast invasive adenocarcinoma(123;0.0034)|GBM - Glioblastoma multiforme(186;0.0139)|Lung(196;0.186)		GCATACTTCCCTTTTTTTTTTT	0.163													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	102292874	102292876	+	Intron	DEL	CTC	-	-			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:102292874_102292876delCTC	uc010usj.1	+						uc002bxo.2_5'Flank|uc002bxp.3_5'Flank|uc002bxt.2_5'Flank|uc002bxz.3_5'Flank|uc002byd.2_5'Flank|uc002bye.2_5'Flank|uc002byf.1_5'Flank|uc002byg.2_5'Flank|uc002byi.2_5'Flank|uc002byk.2_5'Flank|uc002bym.2_5'Flank|uc002byn.2_5'Flank|uc010usm.1_5'Flank|uc002byr.2_5'Flank					RecName: Full=Uncharacterized protein C15orf51.; Flags: Fragment;																		AGTTCATCTTCTCAGAGCTGCTG	0.581													5	3	---	---	---	---	
LOC283922	283922	broad.mit.edu	37	16	74394379	74394380	+	Intron	INS	-	A	A	rs142790741	by1000genomes	TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:74394379_74394380insA	uc002fcr.2	-						LOC283922_uc010vms.1_Intron					Homo sapiens cDNA FLJ39449 fis, clone PROST2008360, highly similar to Homo sapiens pyruvate dehydrogenase phosphatase regulatory subunit (PDPR), mRNA.												0						TAGTCATCCTTAAACAAAATTC	0.327													4	2	---	---	---	---	
UTP6	55813	broad.mit.edu	37	17	30207445	30207445	+	Intron	DEL	A	-	-			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:30207445delA	uc002hgr.2	-						UTP6_uc002hgq.2_Intron|UTP6_uc010cst.2_Intron|UTP6_uc010wbw.1_3'UTR	NM_018428	NP_060898	Q9NYH9	UTP6_HUMAN	hepatocellular carcinoma-associated antigen 66						rRNA processing	nucleolus	binding			ovary(1)	1		all_hematologic(16;0.0149)|Ovarian(249;0.021)|Myeloproliferative disorder(56;0.0255)|Acute lymphoblastic leukemia(14;0.0257)|Breast(31;0.231)				gcctcccaataaaaaaaaaaa	0.179													5	3	---	---	---	---	
C20orf117	140710	broad.mit.edu	37	20	35445891	35445891	+	Intron	DEL	A	-	-			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:35445891delA	uc002xgd.1	-						C20orf117_uc002xge.1_5'Flank	NM_199181	NP_954650	O94964	K0889_HUMAN	hypothetical protein LOC140710 isoform 2												0		Myeloproliferative disorder(115;0.00874)				AGatttaattaaaaaaaaaaa	0.507													6	3	---	---	---	---	
GGT1	2678	broad.mit.edu	37	22	25016169	25016170	+	Intron	INS	-	AT	AT	rs28418841	by1000genomes	TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:25016169_25016170insAT	uc003aan.1	+						GGT1_uc003aas.1_Intron|GGT1_uc003aat.1_Intron|GGT1_uc003aau.1_Intron|GGT1_uc003aav.1_Intron|GGT1_uc003aaw.1_Intron|GGT1_uc003aax.1_Intron	NM_013430	NP_038347	P19440	GGT1_HUMAN	gamma-glutamyltransferase 1 precursor						glutathione biosynthetic process	integral to membrane	acyltransferase activity|gamma-glutamyltransferase activity|protein binding				0					Glutathione(DB00143)	aaaaaaaaaaaaTCTTTCCTCC	0.277													4	2	---	---	---	---	
MYO18B	84700	broad.mit.edu	37	22	26400979	26400979	+	Intron	DEL	A	-	-			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:26400979delA	uc003abz.1	+						MYO18B_uc003aca.1_Intron|MYO18B_uc010guy.1_Intron|MYO18B_uc010guz.1_Intron|MYO18B_uc011aka.1_Intron|MYO18B_uc011akb.1_Intron|MYO18B_uc010gva.1_Intron	NM_032608	NP_115997	Q8IUG5	MY18B_HUMAN	myosin XVIIIB							nucleus|sarcomere|unconventional myosin complex	actin binding|ATP binding|motor activity			ovary(5)|central_nervous_system(3)|large_intestine(2)|breast(2)	12						tagctgtgtgactttaggcag	0.114													4	3	---	---	---	---	
ARSE	415	broad.mit.edu	37	X	2856421	2856422	+	Intron	INS	-	TC	TC	rs142734776		TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:2856421_2856422insTC	uc004crc.3	-						ARSE_uc011mhi.1_Intron|ARSE_uc011mhh.1_Intron	NM_000047	NP_000038	P51690	ARSE_HUMAN	arylsulfatase E precursor						skeletal system development	Golgi stack	arylsulfatase activity|metal ion binding			ovary(1)|central_nervous_system(1)	2		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)				gtctctcaatttctctctctct	0.248													4	2	---	---	---	---	
MORC4	79710	broad.mit.edu	37	X	106199946	106199947	+	Intron	DEL	AG	-	-			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:106199946_106199947delAG	uc004emu.3	-						MORC4_uc004emp.3_Intron|MORC4_uc004emv.3_Intron|MORC4_uc004emw.3_Intron	NM_024657	NP_078933	Q8TE76	MORC4_HUMAN	zinc finger, CW type with coiled-coil domain 2								ATP binding|zinc ion binding			ovary(1)	1						GTGCCCCACCagagagagagag	0.356													6	3	---	---	---	---	
