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
MYOM3	127294	broad.mit.edu	37	1	24432548	24432548	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:24432548T>C	uc001bin.3	-	5	585	c.422A>G	c.(421-423)GAG>GGG	p.E141G	MYOM3_uc001bio.2_Missense_Mutation_p.E141G|MYOM3_uc001bip.1_5'UTR	NM_152372	NP_689585	Q5VTT5	MYOM3_HUMAN	myomesin family, member 3	141	Potential.									skin(2)|ovary(1)	3		Colorectal(325;3.55e-05)|Renal(390;0.000703)|Lung NSC(340;0.001)|all_lung(284;0.0014)|Ovarian(437;0.00351)|Breast(348;0.0126)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;5.31e-24)|Colorectal(126;7.52e-08)|COAD - Colon adenocarcinoma(152;4.01e-06)|GBM - Glioblastoma multiforme(114;4.36e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00108)|KIRC - Kidney renal clear cell carcinoma(1967;0.00404)|STAD - Stomach adenocarcinoma(196;0.00966)|READ - Rectum adenocarcinoma(331;0.0678)|Lung(427;0.153)		CTCCTTGGCCTCCTGGACCTT	0.637													6	28	---	---	---	---	PASS
GNL2	29889	broad.mit.edu	37	1	38059398	38059398	+	Silent	SNP	G	A	A			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:38059398G>A	uc001cbk.2	-	2	277	c.114C>T	c.(112-114)ATC>ATT	p.I38I	GNL2_uc010oif.1_5'UTR|GNL2_uc009vve.2_Silent_p.I38I	NM_013285	NP_037417	Q13823	NOG2_HUMAN	guanine nucleotide binding protein-like 2	38					ribosome biogenesis	nucleolus	GTP binding|GTPase activity|protein binding			ovary(1)|central_nervous_system(1)	2		Myeloproliferative disorder(586;0.0393)				TCAGGCGCCGGATGGTGGCCC	0.507													24	121	---	---	---	---	PASS
AKNAD1	254268	broad.mit.edu	37	1	109366227	109366227	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:109366227G>A	uc001dwa.2	-	12	2289	c.2020C>T	c.(2020-2022)CCT>TCT	p.P674S	AKNAD1_uc010ovb.1_Missense_Mutation_p.P381S|AKNAD1_uc001dwb.2_RNA	NM_152763	NP_689976	Q5T1N1	AKND1_HUMAN	hypothetical protein LOC254268	674										ovary(3)	3						CGGGAGGTAGGAATCTTAGTG	0.483													14	121	---	---	---	---	PASS
RNF115	27246	broad.mit.edu	37	1	145684643	145684643	+	Missense_Mutation	SNP	C	G	G			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145684643C>G	uc001eoj.2	+	7	836	c.632C>G	c.(631-633)TCT>TGT	p.S211C	NBPF10_uc001emp.3_Intron|RNF115_uc001eok.2_Missense_Mutation_p.S178C|RNF115_uc009wiy.2_Missense_Mutation_p.S130C	NM_014455	NP_055270	Q9Y4L5	RN115_HUMAN	Rabring 7	211					protein autoubiquitination	cytosol	protein binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)	1						AAGATCACATCTCTTCCAACA	0.418													4	67	---	---	---	---	PASS
METTL13	51603	broad.mit.edu	37	1	171756920	171756920	+	Missense_Mutation	SNP	C	G	G			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:171756920C>G	uc001ghz.2	+	4	1506	c.1159C>G	c.(1159-1161)CAG>GAG	p.Q387E	METTL13_uc001gia.2_Missense_Mutation_p.Q301E|METTL13_uc001gib.2_Missense_Mutation_p.Q231E|METTL13_uc010pml.1_Missense_Mutation_p.Q386E	NM_015935	NP_057019	Q8N6R0	MTL13_HUMAN	CGI-01 protein isoform 1	387							methyltransferase activity|protein binding			kidney(1)	1						CCGGACCGTTCAGCACCAAGA	0.517													13	48	---	---	---	---	PASS
KDM5B	10765	broad.mit.edu	37	1	202777266	202777266	+	Silent	SNP	G	C	C	rs150129345	byFrequency	TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:202777266G>C	uc001gyf.2	-	1	284	c.168C>G	c.(166-168)GCC>GCG	p.A56A	KDM5B_uc009xag.2_Silent_p.A56A|KDM5B_uc001gyg.1_5'Flank	NM_006618	NP_006609	Q9UGL1	KDM5B_HUMAN	jumonji, AT rich interactive domain 1B	56	JmjN.				negative regulation of transcription, DNA-dependent	nucleolus	DNA binding|histone demethylase activity (H3-dimethyl-K4 specific)|histone demethylase activity (H3-trimethyl-K4 specific)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|protein binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity|zinc ion binding			ovary(2)|breast(2)|urinary_tract(1)	5						CAGTCTGCTCGGCTATGGGCC	0.637													4	42	---	---	---	---	PASS
LYST	1130	broad.mit.edu	37	1	235894212	235894212	+	Missense_Mutation	SNP	A	C	C			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:235894212A>C	uc001hxj.2	-	36	9154	c.8979T>G	c.(8977-8979)TTT>TTG	p.F2993L	LYST_uc001hxi.2_Missense_Mutation_p.F217L	NM_000081	NP_000072	Q99698	LYST_HUMAN	lysosomal trafficking regulator	2993					defense response to bacterium|defense response to protozoan|defense response to virus|endosome to lysosome transport via multivesicular body sorting pathway|leukocyte chemotaxis|mast cell secretory granule organization|melanosome organization|natural killer cell mediated cytotoxicity|protein transport	cytoplasm|microtubule cytoskeleton	protein binding			ovary(6)|breast(4)|central_nervous_system(2)	12	Ovarian(103;0.0634)|Breast(184;0.23)	all_cancers(173;0.00246)|Prostate(94;0.0771)|Acute lymphoblastic leukemia(190;0.228)	OV - Ovarian serous cystadenocarcinoma(106;0.000674)			TTTTGTCTTCAAACAGGTAAG	0.333									Chediak-Higashi_syndrome				11	141	---	---	---	---	PASS
FMN2	56776	broad.mit.edu	37	1	240370625	240370625	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:240370625A>G	uc010pyd.1	+	5	2738	c.2513A>G	c.(2512-2514)CAA>CGA	p.Q838R	FMN2_uc010pye.1_Missense_Mutation_p.Q842R	NM_020066	NP_064450	Q9NZ56	FMN2_HUMAN	formin 2	838	Pro-rich.|FH1.				actin cytoskeleton organization|establishment of meiotic spindle localization|intracellular signal transduction|meiotic chromosome movement towards spindle pole|meiotic metaphase I|multicellular organismal development|oogenesis|polar body extrusion after meiotic divisions		actin binding			ovary(4)|pancreas(3)|skin(3)|large_intestine(1)|central_nervous_system(1)	12	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)			ACCGAGTTTCAAACCAGCCAC	0.547													10	84	---	---	---	---	PASS
KIAA1841	84542	broad.mit.edu	37	2	61336340	61336340	+	Missense_Mutation	SNP	G	C	C			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61336340G>C	uc002saw.3	+	16	1956	c.1653G>C	c.(1651-1653)CAG>CAC	p.Q551H	KIAA1841_uc002sax.3_Missense_Mutation_p.Q405H|KIAA1841_uc002say.2_Missense_Mutation_p.Q551H	NM_001129993	NP_001123465	Q6NSI8	K1841_HUMAN	KIAA1841 protein isoform a	551											0			Epithelial(17;0.193)			AGAAACAACAGTCACTGTTTT	0.254													11	116	---	---	---	---	PASS
NAGK	55577	broad.mit.edu	37	2	71299785	71299785	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:71299785A>G	uc002shp.3	+	5	776	c.370A>G	c.(370-372)ATA>GTA	p.I124V	NAGK_uc010fea.2_RNA|NAGK_uc002shq.3_5'UTR|NAGK_uc002shr.2_Missense_Mutation_p.I73V	NM_017567	NP_060037	Q9UJ70	NAGK_HUMAN	N-Acetylglucosamine kinase	124					N-acetylglucosamine metabolic process|N-acetylmannosamine metabolic process		ATP binding|N-acetylglucosamine kinase activity|protein binding				0					N-Acetyl-D-glucosamine(DB00141)	AGTTGTGCTCATATCTGGAAC	0.577													6	34	---	---	---	---	PASS
CCNT2	905	broad.mit.edu	37	2	135711411	135711411	+	Silent	SNP	A	G	G			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:135711411A>G	uc002tuc.1	+	9	1418	c.1386A>G	c.(1384-1386)GAA>GAG	p.E462E	CCNT2_uc002tub.1_Silent_p.E462E|CCNT2_uc010zbf.1_Silent_p.E287E|CCNT2_uc002tud.1_Silent_p.E125E	NM_058241	NP_490595	O60583	CCNT2_HUMAN	cyclin T2 isoform b	462					cell cycle|cell division|interspecies interaction between organisms|regulation of cyclin-dependent protein kinase activity|regulation of transcription, DNA-dependent|transcription elongation from RNA polymerase II promoter|viral reproduction	nucleoplasm	protein kinase binding			ovary(2)|lung(1)	3				BRCA - Breast invasive adenocarcinoma(221;0.107)		CCCAGGTAGAACAGCAGCACA	0.383													13	64	---	---	---	---	PASS
LRP1B	53353	broad.mit.edu	37	2	141773379	141773379	+	Silent	SNP	T	G	G			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:141773379T>G	uc002tvj.1	-	13	3048	c.2076A>C	c.(2074-2076)TCA>TCC	p.S692S	LRP1B_uc010fnl.1_Intron	NM_018557	NP_061027	Q9NZR2	LRP1B_HUMAN	low density lipoprotein-related protein 1B	692	Extracellular (Potential).|LDL-receptor class B 7.				protein transport|receptor-mediated endocytosis	integral to membrane	calcium ion binding			lung(17)|skin(12)|ovary(12)|pancreas(3)|upper_aerodigestive_tract(2)|central_nervous_system(2)|liver(1)|kidney(1)	50		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		ACAGCATCTTTGAAGTCACAA	0.413										TSP Lung(27;0.18)			12	126	---	---	---	---	PASS
KBTBD10	10324	broad.mit.edu	37	2	170371427	170371427	+	Silent	SNP	A	T	T			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:170371427A>T	uc002ueu.1	+	3	1409	c.1332A>T	c.(1330-1332)TCA>TCT	p.S444S	KBTBD10_uc010zdh.1_Silent_p.S382S	NM_006063	NP_006054	O60662	KBTBA_HUMAN	kelch repeat and BTB (POZ) domain containing 10	444	Kelch 2.				striated muscle contraction	centrosome|nucleolus|plasma membrane|pseudopodium|ruffle					0						ATGTGATTTCACATAAAGGGA	0.338													14	88	---	---	---	---	PASS
OSBPL6	114880	broad.mit.edu	37	2	179253841	179253841	+	Silent	SNP	C	G	G			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179253841C>G	uc002ulx.2	+	21	2640	c.2262C>G	c.(2260-2262)ACC>ACG	p.T754T	OSBPL6_uc002uly.2_Silent_p.T779T|OSBPL6_uc010zfe.1_Silent_p.T723T|OSBPL6_uc002ulz.2_Silent_p.T718T|OSBPL6_uc002uma.2_Silent_p.T758T	NM_032523	NP_115912	Q9BZF3	OSBL6_HUMAN	oxysterol-binding protein-like protein 6 isoform	754					lipid transport		lipid binding			pancreas(1)	1			OV - Ovarian serous cystadenocarcinoma(117;0.00578)|Epithelial(96;0.00847)|all cancers(119;0.0335)			TCAGAAATACCAAAAGCAGTG	0.343													18	72	---	---	---	---	PASS
VIL1	7429	broad.mit.edu	37	2	219296898	219296898	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:219296898G>A	uc002via.2	+	12	1398	c.1333G>A	c.(1333-1335)GTT>ATT	p.V445I	VIL1_uc010zke.1_Missense_Mutation_p.V134I|VIL1_uc002vib.2_Missense_Mutation_p.V445I	NM_007127	NP_009058	P09327	VILI_HUMAN	villin 1	445	Gelsolin-like 4.|Core.				actin filament capping|actin filament depolymerization|actin filament polymerization|actin filament severing|apoptosis|cellular response to epidermal growth factor stimulus|cytoplasmic actin-based contraction involved in cell motility|epidermal growth factor receptor signaling pathway|positive regulation of actin filament bundle assembly|positive regulation of epithelial cell migration|regulation of actin nucleation|regulation of cell shape|regulation of lamellipodium morphogenesis|regulation of wound healing|response to bacterium	actin filament bundle|cytoplasm|filopodium tip|intracellular membrane-bounded organelle|lamellipodium|microvillus|ruffle	actin filament binding|calcium ion binding|caspase inhibitor activity|lysophosphatidic acid binding|phosphatidylinositol-4,5-bisphosphate binding|protein homodimerization activity			ovary(1)	1		Renal(207;0.0474)		Epithelial(149;6.88e-07)|all cancers(144;0.00013)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		CCTGCTCTACGTTTGGCAGGT	0.463													5	34	---	---	---	---	PASS
CHL1	10752	broad.mit.edu	37	3	391066	391066	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:391066C>A	uc003bou.2	+	9	1096	c.825C>A	c.(823-825)AAC>AAA	p.N275K	CHL1_uc003bot.2_Missense_Mutation_p.N291K|CHL1_uc003bow.1_Missense_Mutation_p.N275K|CHL1_uc011asi.1_Missense_Mutation_p.N291K	NM_006614	NP_006605	O00533	CHL1_HUMAN	cell adhesion molecule with homology to L1CAM	275	Ig-like C2-type 3.|Extracellular (Potential).				axon guidance|cell adhesion|signal transduction	integral to membrane|plasma membrane|proteinaceous extracellular matrix				skin(5)|central_nervous_system(4)|large_intestine(2)|ovary(1)	12		all_cancers(2;1.14e-06)|all_epithelial(2;0.00367)|all_lung(1;0.061)|Lung NSC(2;0.201)		Epithelial(13;5.36e-06)|all cancers(10;1.4e-05)|OV - Ovarian serous cystadenocarcinoma(96;0.00323)|COAD - Colon adenocarcinoma(1;0.00925)|Colorectal(20;0.0198)		TTGATTGGAACAAAATTGGTG	0.328													18	38	---	---	---	---	PASS
VHL	7428	broad.mit.edu	37	3	10188240	10188240	+	Missense_Mutation	SNP	T	A	A			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10188240T>A	uc003bvc.2	+	2	596	c.383T>A	c.(382-384)CTT>CAT	p.L128H	VHL_uc003bvd.2_Intron	NM_000551	NP_000542	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor isoform 1	128	Involved in binding to CCT complex.		L -> F (in VHLD; type II).		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.L128fs*31(5)|p.L128P(3)|p.L128fs*4(2)|p.L128R(2)|p.L128H(1)|p.L128I(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)		CACGATGGGCTTCTGGTTAAC	0.413		1	D|Mis|N|F|S		renal|hemangioma|pheochromocytoma	renal|hemangioma|pheochromocytoma			von_Hippel-Lindau_disease|Chuvash_Polycythemia_|Pheochromocytoma_(Adrenal)_Familial				64	118	---	---	---	---	PASS
BAP1	8314	broad.mit.edu	37	3	52443866	52443866	+	Missense_Mutation	SNP	C	G	G			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52443866C>G	uc003ddx.2	-	1	144	c.29G>C	c.(28-30)AGC>ACC	p.S10T	PHF7_uc003ddy.2_5'Flank|PHF7_uc003ddz.2_5'Flank	NM_004656	NP_004647	Q92560	BAP1_HUMAN	BRCA1 associated protein-1	10					monoubiquitinated histone H2A deubiquitination|negative regulation of cell proliferation|protein K48-linked deubiquitination|regulation of cell cycle|regulation of cell growth|ubiquitin-dependent protein catabolic process	cytoplasm|nucleolus|PR-DUB complex	chromatin binding|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			pleura(32)|eye(28)|lung(2)|ovary(2)|breast(1)	65				BRCA - Breast invasive adenocarcinoma(193;1.72e-05)|Kidney(197;0.0018)|KIRC - Kidney renal clear cell carcinoma(197;0.00203)|OV - Ovarian serous cystadenocarcinoma(275;0.0277)		ACCTGGGTCGCTCTCCAGCTC	0.746			N|Mis|F|S|O		uveal melanoma|breast|NSCLC								5	23	---	---	---	---	PASS
OR5H15	403274	broad.mit.edu	37	3	97887843	97887843	+	Silent	SNP	A	G	G			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:97887843A>G	uc011bgu.1	+	1	300	c.300A>G	c.(298-300)CAA>CAG	p.Q100Q		NM_001005515	NP_001005515	A6NDH6	O5H15_HUMAN	olfactory receptor, family 5, subfamily H,	100	Helical; Name=3; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|skin(1)	2						GCAAGATACAATTTTTTTCCA	0.383													52	225	---	---	---	---	PASS
EEFSEC	60678	broad.mit.edu	37	3	128060617	128060617	+	Missense_Mutation	SNP	G	C	C			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:128060617G>C	uc003eki.2	+	5	1366	c.1328G>C	c.(1327-1329)CGG>CCG	p.R443P	EEFSEC_uc003ekj.2_Missense_Mutation_p.R388P	NM_021937	NP_068756	P57772	SELB_HUMAN	eukaryotic elongation factor,	443						cytoplasm|nucleus	GTP binding|GTPase activity|translation elongation factor activity			ovary(1)	1						AACACGTGCCGGCTAGCCTTC	0.602													23	66	---	---	---	---	PASS
EEFSEC	60678	broad.mit.edu	37	3	128060618	128060618	+	Silent	SNP	G	T	T			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:128060618G>T	uc003eki.2	+	5	1367	c.1329G>T	c.(1327-1329)CGG>CGT	p.R443R	EEFSEC_uc003ekj.2_Silent_p.R388R	NM_021937	NP_068756	P57772	SELB_HUMAN	eukaryotic elongation factor,	443						cytoplasm|nucleus	GTP binding|GTPase activity|translation elongation factor activity			ovary(1)	1						ACACGTGCCGGCTAGCCTTCC	0.602													23	65	---	---	---	---	PASS
FAIM	55179	broad.mit.edu	37	3	138348071	138348071	+	Intron	SNP	T	G	G			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:138348071T>G	uc003esr.2	+						FAIM_uc003eso.1_3'UTR|FAIM_uc003esp.2_Intron|FAIM_uc003esq.2_Intron|FAIM_uc003ess.2_Intron	NM_001033032	NP_001028204	Q9NVQ4	FAIM1_HUMAN	Fas apoptotic inhibitory molecule isoform c						apoptosis	cytoplasm					0						CATTTCCTAATTATAGAGATC	0.378													4	35	---	---	---	---	PASS
SLITRK3	22865	broad.mit.edu	37	3	164907318	164907318	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:164907318A>G	uc003fej.3	-	2	1745	c.1301T>C	c.(1300-1302)TTG>TCG	p.L434S	SLITRK3_uc003fek.2_Missense_Mutation_p.L434S	NM_014926	NP_055741	O94933	SLIK3_HUMAN	slit and trk like 3 protein precursor	434	LRR 8.|Extracellular (Potential).					integral to membrane				ovary(6)|skin(3)|pancreas(1)	10						CAAGAGATCCAAGGAAGAAAA	0.408										HNSCC(40;0.11)			7	66	---	---	---	---	PASS
IGF2BP2	10644	broad.mit.edu	37	3	185393190	185393190	+	Missense_Mutation	SNP	T	A	A			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:185393190T>A	uc003fpo.2	-	9	1044	c.965A>T	c.(964-966)GAA>GTA	p.E322V	IGF2BP2_uc010hyi.2_Missense_Mutation_p.E265V|IGF2BP2_uc010hyj.2_Missense_Mutation_p.E259V|IGF2BP2_uc010hyk.2_Missense_Mutation_p.E186V|IGF2BP2_uc010hyl.2_Missense_Mutation_p.E259V|IGF2BP2_uc003fpp.2_Missense_Mutation_p.E322V|IGF2BP2_uc003fpq.2_Missense_Mutation_p.E327V	NM_006548	NP_006539	Q9Y6M1	IF2B2_HUMAN	insulin-like growth factor 2 mRNA binding	322	KH 2.				anatomical structure morphogenesis|negative regulation of translation	cytoskeletal part|cytosol|nucleus	mRNA 3'-UTR binding|mRNA 5'-UTR binding|nucleotide binding|protein binding|translation regulator activity				0	all_cancers(143;5.84e-11)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(80;7.41e-21)			GATGGTTCTTTCCGGGTTGTA	0.403													31	112	---	---	---	---	PASS
SLIT2	9353	broad.mit.edu	37	4	20490577	20490577	+	Silent	SNP	G	A	A			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:20490577G>A	uc003gpr.1	+	8	951	c.747G>A	c.(745-747)GAG>GAA	p.E249E	SLIT2_uc003gps.1_Silent_p.E249E	NM_004787	NP_004778	O94813	SLIT2_HUMAN	slit homolog 2 precursor	249	LRRCT 1.				apoptosis involved in luteolysis|axon extension involved in axon guidance|branching morphogenesis of a tube|cell migration involved in sprouting angiogenesis|cellular response to heparin|cellular response to hormone stimulus|chemorepulsion involved in postnatal olfactory bulb interneuron migration|corticospinal neuron axon guidance through spinal cord|induction of negative chemotaxis|motor axon guidance|negative regulation of actin filament polymerization|negative regulation of cell growth|negative regulation of cellular response to growth factor stimulus|negative regulation of chemokine-mediated signaling pathway|negative regulation of endothelial cell migration|negative regulation of lamellipodium assembly|negative regulation of mononuclear cell migration|negative regulation of neutrophil chemotaxis|negative regulation of protein phosphorylation|negative regulation of retinal ganglion cell axon guidance|negative regulation of small GTPase mediated signal transduction|negative regulation of smooth muscle cell chemotaxis|negative regulation of vascular permeability|positive regulation of apoptosis|positive regulation of axonogenesis|response to cortisol stimulus|retinal ganglion cell axon guidance|Roundabout signaling pathway|ureteric bud development	cell surface|cytoplasm|extracellular space|plasma membrane	calcium ion binding|GTPase inhibitor activity|heparin binding|laminin-1 binding|protein homodimerization activity|proteoglycan binding|Roundabout binding			central_nervous_system(4)|skin(4)|ovary(3)	11						ATGTAGCCGAGGTTCAAAAAC	0.502													14	141	---	---	---	---	PASS
FRYL	285527	broad.mit.edu	37	4	48507685	48507685	+	Intron	SNP	A	C	C			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:48507685A>C	uc003gyh.1	-						FRYL_uc003gye.1_5'UTR|FRYL_uc003gyf.1_Intron|FRYL_uc003gyg.1_Intron	NM_015030	NP_055845	O94915	FRYL_HUMAN	furry-like						regulation of transcription, DNA-dependent|transcription, DNA-dependent		protein binding			skin(1)	1						GGGTAGTGTAACAGCCTGTCC	0.348													9	30	---	---	---	---	PASS
PCDHA11	56138	broad.mit.edu	37	5	140248769	140248769	+	Silent	SNP	G	A	A			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140248769G>A	uc003lia.2	+	1	939	c.81G>A	c.(79-81)GGG>GGA	p.G27G	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhi.2_Intron|PCDHA4_uc003lhh.1_Intron|PCDHA5_uc003lhk.1_Intron|PCDHA5_uc003lhl.2_Intron|PCDHA6_uc003lhn.2_Intron|PCDHA6_uc003lho.2_Intron|PCDHA7_uc003lhq.2_Intron|PCDHA8_uc003lhs.2_Intron|PCDHA9_uc003lhu.2_Intron|PCDHA10_uc003lhw.2_Intron|PCDHA10_uc003lhx.2_Intron|PCDHA11_uc011dae.1_Silent_p.G27G	NM_018902	NP_061725	Q9Y5I1	PCDAB_HUMAN	protocadherin alpha 11 isoform 1 precursor	27					homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding|protein binding			breast(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGGAGGTGGGGAGCGGCCAGC	0.622													56	110	---	---	---	---	PASS
KCNMB1	3779	broad.mit.edu	37	5	169810630	169810630	+	Intron	SNP	T	C	C			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:169810630T>C	uc003maq.1	-						KCNIP1_uc003map.2_Intron|KCNMB1_uc003mar.2_Missense_Mutation_p.E120G	NM_004137	NP_004128	Q16558	KCMB1_HUMAN	potassium large conductance calcium-activated						platelet activation|synaptic transmission		calcium-activated potassium channel activity|potassium channel regulator activity			ovary(2)	2	Renal(175;0.000159)|Lung NSC(126;0.0165)|all_lung(126;0.026)	Medulloblastoma(196;0.0109)|all_neural(177;0.0146)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.175)		AGGAACAGGCTCACACACCTG	0.398													5	26	---	---	---	---	PASS
CRISP3	10321	broad.mit.edu	37	6	49700907	49700907	+	Splice_Site	SNP	C	T	T			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:49700907C>T	uc003ozs.2	-	6	536	c.521_splice	c.e6+1	p.A174_splice		NM_006061	NP_006052	P54108	CRIS3_HUMAN	cysteine-rich secretory protein 3 precursor						innate immune response	proteinaceous extracellular matrix|specific granule				skin(2)	2	Lung NSC(77;0.0161)		KIRC - Kidney renal clear cell carcinoma(2;0.106)|Kidney(12;0.156)			TATATACTTACGCAGGACAAT	0.299													14	176	---	---	---	---	PASS
C6orf142	90523	broad.mit.edu	37	6	54095578	54095578	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:54095578G>T	uc003pcg.3	+	11	1293	c.1180G>T	c.(1180-1182)GCT>TCT	p.A394S	C6orf142_uc003pch.3_Intron|C6orf142_uc011dxa.1_Missense_Mutation_p.A929S	NM_138569	NP_612636	Q5VWP3	MLIP_HUMAN	hypothetical protein LOC90523	394						nuclear envelope|PML body	protein binding				0	Lung NSC(77;0.0317)					CTATCCTCCTGCTAAGTCACT	0.498													76	341	---	---	---	---	PASS
GFRAL	389400	broad.mit.edu	37	6	55214903	55214903	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:55214903G>T	uc003pcm.1	+	4	416	c.330G>T	c.(328-330)GAG>GAT	p.E110D		NM_207410	NP_997293	Q6UXV0	GFRAL_HUMAN	GDNF family receptor alpha like precursor	110	Extracellular (Potential).					integral to membrane	receptor activity			ovary(1)|breast(1)	2	Lung NSC(77;0.0875)|Renal(3;0.122)		LUSC - Lung squamous cell carcinoma(124;0.23)			ACGTGAAAGAGGATAAATTCA	0.289													14	89	---	---	---	---	PASS
DST	667	broad.mit.edu	37	6	56399926	56399926	+	Silent	SNP	T	C	C			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:56399926T>C	uc003pdf.2	-	57	10606	c.10578A>G	c.(10576-10578)GAA>GAG	p.E3526E	DST_uc003pcz.3_Silent_p.E3348E|DST_uc011dxj.1_Silent_p.E3377E|DST_uc011dxk.1_Silent_p.E3388E|DST_uc003pcy.3_Silent_p.E3022E	NM_001144769	NP_001138241	Q03001	DYST_HUMAN	dystonin isoform 2	5434	Spectrin 8.				cell adhesion|cell cycle arrest|cell motility|hemidesmosome assembly|integrin-mediated signaling pathway|intermediate filament cytoskeleton organization|maintenance of cell polarity|microtubule cytoskeleton organization|response to wounding	actin cytoskeleton|axon|axon part|basement membrane|cell cortex|cell leading edge|cytoplasmic membrane-bounded vesicle|endoplasmic reticulum membrane|hemidesmosome|hemidesmosome|integral to membrane|intermediate filament|intermediate filament cytoskeleton|microtubule cytoskeleton|microtubule plus end|nuclear envelope|sarcomere|Z disc	actin binding|calcium ion binding|integrin binding|microtubule plus-end binding|protein binding|protein C-terminus binding|protein homodimerization activity			ovary(7)|central_nervous_system(6)|upper_aerodigestive_tract(1)	14	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			TTACCTTTTGTTCTTGTATCT	0.408													67	198	---	---	---	---	PASS
SLC22A16	85413	broad.mit.edu	37	6	110763747	110763747	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:110763747G>T	uc003puf.2	-	4	950	c.883C>A	c.(883-885)CTT>ATT	p.L295I	SLC22A16_uc003pue.2_Missense_Mutation_p.L276I	NM_033125	NP_149116	Q86VW1	S22AG_HUMAN	solute carrier family 22, member 16	295					acid secretion|cell differentiation|multicellular organismal development|single fertilization|sperm motility|spermatogenesis	integral to membrane	carnitine transporter activity			ovary(1)	1		all_cancers(87;0.00221)|Acute lymphoblastic leukemia(125;2.27e-07)|all_hematologic(75;1.38e-05)|all_epithelial(87;0.0485)|Colorectal(196;0.101)		OV - Ovarian serous cystadenocarcinoma(136;0.0513)|Epithelial(106;0.0921)|all cancers(137;0.115)		TCTGAGAGAAGCCAAAAAGGT	0.473													21	98	---	---	---	---	PASS
REV3L	5980	broad.mit.edu	37	6	111694714	111694714	+	Missense_Mutation	SNP	G	C	C			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:111694714G>C	uc003puy.3	-	13	5167	c.4844C>G	c.(4843-4845)TCT>TGT	p.S1615C	REV3L_uc003pux.3_Missense_Mutation_p.S1537C|REV3L_uc003puz.3_Missense_Mutation_p.S1537C	NM_002912	NP_002903	O60673	DPOLZ_HUMAN	DNA polymerase zeta	1615					DNA-dependent DNA replication|translesion synthesis	nucleus|zeta DNA polymerase complex	DNA binding|DNA-directed DNA polymerase activity|metal ion binding|nucleotide binding			large_intestine(2)|ovary(2)|skin(2)	6		all_cancers(87;7.57e-06)|Acute lymphoblastic leukemia(125;2.46e-08)|all_hematologic(75;1.08e-06)|all_epithelial(87;0.00138)|Colorectal(196;0.021)		OV - Ovarian serous cystadenocarcinoma(136;0.0314)|Epithelial(106;0.057)|all cancers(137;0.0663)		ATCTGATACAGAGTTATCCAA	0.328								DNA_polymerases_(catalytic_subunits)|Direct_reversal_of_damage					13	188	---	---	---	---	PASS
MAD1L1	8379	broad.mit.edu	37	7	2260622	2260622	+	Intron	SNP	G	C	C			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:2260622G>C	uc003slh.1	-						MAD1L1_uc003slf.1_Intron|MAD1L1_uc003slg.1_Intron|MAD1L1_uc010ksh.1_Intron|MAD1L1_uc003sli.1_Missense_Mutation_p.S31C|MAD1L1_uc010ksi.1_Intron|MAD1L1_uc010ksj.2_Intron	NM_001013836	NP_001013858	Q9Y6D9	MD1L1_HUMAN	MAD1-like 1 protein						cell division|mitotic anaphase|mitotic cell cycle spindle assembly checkpoint|mitotic metaphase|mitotic prometaphase|mitotic telophase	actin cytoskeleton|centrosome|condensed chromosome kinetochore|cytosol|mitochondrion|nucleus|spindle	protein binding			lung(1)|central_nervous_system(1)	2		Ovarian(82;0.0272)		UCEC - Uterine corpus endometrioid carcinoma (27;0.134)|OV - Ovarian serous cystadenocarcinoma(56;3.63e-14)		AGGCGCATAAGATAATTCCAG	0.622													5	18	---	---	---	---	PASS
ZNF789	285989	broad.mit.edu	37	7	99084910	99084910	+	Silent	SNP	T	C	C			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99084910T>C	uc003uqq.1	+	5	1296	c.1077T>C	c.(1075-1077)CAT>CAC	p.H359H	ZNF789_uc010lfw.1_Silent_p.H264H|ZNF789_uc003uqr.1_Silent_p.H301H	NM_213603	NP_998768	Q5FWF6	ZN789_HUMAN	zinc finger protein 789 isoform 1	359	C2H2-type 6.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	all_cancers(62;2.54e-08)|all_epithelial(64;2.55e-09)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0166)					TCATTCAGCATCAAAGAATCC	0.398													23	123	---	---	---	---	PASS
STAG3	10734	broad.mit.edu	37	7	99811404	99811404	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99811404T>C	uc003utx.1	+	33	3799	c.3644T>C	c.(3643-3645)TTA>TCA	p.L1215S	STAG3_uc011kjk.1_Missense_Mutation_p.L1157S|GATS_uc003uty.3_Intron|GATS_uc003utz.3_Intron|GATS_uc003uua.3_Intron|GATS_uc010lgt.2_Intron|STAG3_uc003uub.1_Missense_Mutation_p.L440S|GATS_uc011kjl.1_Intron|GATS_uc010lgu.2_Intron	NM_012447	NP_036579	Q9UJ98	STAG3_HUMAN	stromal antigen 3	1215					chromosome segregation|synaptonemal complex assembly	chromosome, centromeric region|meiotic cohesin complex|synaptonemal complex	binding			ovary(4)|skin(2)|lung(1)|kidney(1)	8	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					CTGGACCTCTTAGATTCTACA	0.488													9	106	---	---	---	---	PASS
FLNC	2318	broad.mit.edu	37	7	128494133	128494133	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:128494133G>A	uc003vnz.3	+	40	6799	c.6590G>A	c.(6589-6591)CGG>CAG	p.R2197Q	FLNC_uc003voa.3_Missense_Mutation_p.R2164Q	NM_001458	NP_001449	Q14315	FLNC_HUMAN	gamma filamin isoform a	2197	Intradomain insert.				cell junction assembly	cytoskeleton|cytosol|plasma membrane|sarcomere	actin binding			breast(5)|large_intestine(3)|ovary(2)|central_nervous_system(1)|skin(1)	12						AGCAAGACGCGGGGCGGGGAG	0.682													6	24	---	---	---	---	PASS
TACC1	6867	broad.mit.edu	37	8	38684968	38684968	+	Intron	SNP	G	A	A			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38684968G>A	uc010lwp.2	+						TACC1_uc011lby.1_Intron|TACC1_uc003xma.2_Intron|TACC1_uc003xlz.2_Intron|TACC1_uc003xmc.3_Intron|TACC1_uc011lbz.1_Intron|TACC1_uc003xmb.3_Intron|TACC1_uc003xme.1_Intron|TACC1_uc003xmd.1_Intron|TACC1_uc010lwo.1_Intron|TACC1_uc003xmf.3_Intron|TACC1_uc011lca.1_Intron|TACC1_uc011lcb.1_Intron|TACC1_uc011lcc.1_3'UTR|TACC1_uc011lcd.1_Intron|TACC1_uc003xmh.3_Intron|TACC1_uc010lwq.2_Intron	NM_006283	NP_006274	O75410	TACC1_HUMAN	transforming, acidic coiled-coil containing						cell cycle|cell division	intermediate filament cytoskeleton|microtubule organizing center|nucleus	protein binding			ovary(1)	1		all_lung(54;0.00292)|Lung NSC(58;0.0115)|Hepatocellular(245;0.065)	LUSC - Lung squamous cell carcinoma(45;1.7e-09)|COAD - Colon adenocarcinoma(9;0.235)			AGCAGGAGGAGCCTTACAGAG	0.398													5	11	---	---	---	---	PASS
KLHL38	340359	broad.mit.edu	37	8	124658127	124658127	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:124658127G>A	uc003yqs.1	-	3	1622	c.1598C>T	c.(1597-1599)ACG>ATG	p.T533M		NM_001081675	NP_001075144	Q2WGJ6	KLH38_HUMAN	kelch-like 38	533	Kelch 6.										0						GTTGCAGTCCGTGGTCAGCCG	0.577													7	99	---	---	---	---	PASS
GPR172A	79581	broad.mit.edu	37	8	145584463	145584463	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145584463G>A	uc003zcc.1	+	5	1283	c.1126G>A	c.(1126-1128)GTG>ATG	p.V376M	FBXL6_uc003zbz.2_5'Flank|FBXL6_uc003zca.2_5'Flank|FBXL6_uc003zcb.2_5'Flank|FBXL6_uc010mfx.2_5'Flank|GPR172A_uc003zcd.1_Missense_Mutation_p.V376M|GPR172A_uc003zce.1_Missense_Mutation_p.V376M|GPR172A_uc010mfy.1_Missense_Mutation_p.V376M|GPR172A_uc003zcf.1_Missense_Mutation_p.V376M|GPR172A_uc011llc.1_Missense_Mutation_p.V288M	NM_024531	NP_078807	Q9HAB3	RFT3_HUMAN	G protein-coupled receptor 172A precursor	376	Helical; (Potential).					integral to plasma membrane	receptor activity|riboflavin transporter activity				0	all_cancers(97;6.64e-12)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;4.43e-40)|Epithelial(56;1.48e-39)|all cancers(56;1.49e-34)|BRCA - Breast invasive adenocarcinoma(115;0.0441)|Colorectal(110;0.055)			TCCCCCTCAGGTGCTGTCGTG	0.672													16	45	---	---	---	---	PASS
PPP1R16A	84988	broad.mit.edu	37	8	145722670	145722670	+	Silent	SNP	C	T	T			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145722670C>T	uc003zdd.2	+	2	1006	c.93C>T	c.(91-93)GCC>GCT	p.A31A	uc003zde.1_Nonsense_Mutation_p.W148*|PPP1R16A_uc003zdf.2_Silent_p.A31A	NM_032902	NP_116291	Q96I34	PP16A_HUMAN	protein phosphatase 1, regulatory (inhibitor)	31	Potential.					plasma membrane	protein binding				0	all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055)			AGCGGCGCGCCCAGCAGGTGA	0.682													4	18	---	---	---	---	PASS
KCNV2	169522	broad.mit.edu	37	9	2718197	2718197	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:2718197G>A	uc003zho.1	+	1	672	c.458G>A	c.(457-459)CGC>CAC	p.R153H		NM_133497	NP_598004	Q8TDN2	KCNV2_HUMAN	potassium channel, subfamily V, member 2	153	Cytoplasmic (Potential).					voltage-gated potassium channel complex	voltage-gated potassium channel activity			ovary(1)|central_nervous_system(1)	2				GBM - Glioblastoma multiforme(50;0.0257)		TTCTTCGACCGCGACCCGGCC	0.652													6	29	---	---	---	---	PASS
ABCA1	19	broad.mit.edu	37	9	107618219	107618219	+	Intron	SNP	C	G	G			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:107618219C>G	uc004bcl.2	-							NM_005502	NP_005493	O95477	ABCA1_HUMAN	ATP-binding cassette, sub-family A member 1						Cdc42 protein signal transduction|cellular lipid metabolic process|cholesterol efflux|cholesterol homeostasis|cholesterol metabolic process|endosome transport|G-protein coupled receptor protein signaling pathway|high-density lipoprotein particle assembly|interleukin-1 beta secretion|intracellular cholesterol transport|lysosome organization|negative regulation of cholesterol storage|negative regulation of macrophage derived foam cell differentiation|phospholipid efflux|phospholipid homeostasis|platelet dense granule organization|positive regulation of cAMP biosynthetic process|reverse cholesterol transport	integral to plasma membrane|membrane fraction|membrane raft|phagocytic vesicle	anion transmembrane transporter activity|apolipoprotein A-I receptor activity|ATP binding|ATPase activity|cholesterol transporter activity|phospholipid transporter activity|small GTPase binding|syntaxin-13 binding			large_intestine(4)|lung(4)|ovary(4)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1)|skin(1)|pancreas(1)	17				OV - Ovarian serous cystadenocarcinoma(323;0.023)	Adenosine triphosphate(DB00171)|Glibenclamide(DB01016)	ATATGTCTCTCGTGAAATTCC	0.448													14	83	---	---	---	---	PASS
MEGF9	1955	broad.mit.edu	37	9	123384993	123384993	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:123384993T>C	uc004bkj.1	-	5	955	c.955A>G	c.(955-957)ATA>GTA	p.I319V	MEGF9_uc011lyb.1_Missense_Mutation_p.I274V	NM_001080497	NP_001073966	Q9H1U4	MEGF9_HUMAN	multiple EGF-like-domains 9	282	Laminin EGF-like 2.|Extracellular (Potential).					integral to membrane	calcium ion binding				0						CGGTCACATATAGAGCCAATG	0.413													21	53	---	---	---	---	PASS
C9orf114	51490	broad.mit.edu	37	9	131586388	131586388	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131586388C>A	uc004bwd.2	-	10	903	c.877G>T	c.(877-879)GGC>TGC	p.G293C	C9orf114_uc004bwe.2_Missense_Mutation_p.G293C|C9orf114_uc010mym.2_RNA	NM_016390	NP_057474	Q5T280	CI114_HUMAN	hypothetical protein LOC51490	293											0						ACATCTGAGCCGCGCTCTGAC	0.647													5	36	---	---	---	---	PASS
YME1L1	10730	broad.mit.edu	37	10	27437878	27437878	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:27437878T>C	uc001iti.2	-	2	307	c.125A>G	c.(124-126)CAG>CGG	p.Q42R	YME1L1_uc001itj.2_Missense_Mutation_p.Q42R|YME1L1_uc010qdl.1_Missense_Mutation_p.Q42R|YME1L1_uc009xkv.2_RNA|YME1L1_uc001itk.1_Missense_Mutation_p.Q42R	NM_139312	NP_647473	Q96TA2	YMEL1_HUMAN	YME1-like 1 isoform 1	42					protein catabolic process|proteolysis	membrane|mitochondrion	ATP binding|metal ion binding|metalloendopeptidase activity|nucleoside-triphosphatase activity			ovary(1)	1						ATCTCGATGCTGGTTTTGAGA	0.393													67	192	---	---	---	---	PASS
PAPSS2	9060	broad.mit.edu	37	10	89473886	89473886	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:89473886A>G	uc001kex.2	+	4	730	c.467A>G	c.(466-468)GAA>GGA	p.E156G	PAPSS2_uc001kew.2_Missense_Mutation_p.E156G|PAPSS2_uc009xtg.1_RNA	NM_004670	NP_004661	O95340	PAPS2_HUMAN	3'-phosphoadenosine 5'-phosphosulfate synthase 2	156	Adenylyl-sulfate kinase.				3'-phosphoadenosine 5'-phosphosulfate biosynthetic process|skeletal system development|sulfate assimilation|xenobiotic metabolic process	cytosol	adenylylsulfate kinase activity|ATP binding|protein binding|sulfate adenylyltransferase (ATP) activity			central_nervous_system(1)|skin(1)	2		Melanoma(5;0.019)|Colorectal(252;0.123)		UCEC - Uterine corpus endometrioid carcinoma (6;0.00164)|Colorectal(12;0.000323)|COAD - Colon adenocarcinoma(12;0.00124)		AATATTTGTGAAAGCAGAGAC	0.423													38	122	---	---	---	---	PASS
TM9SF3	56889	broad.mit.edu	37	10	98282079	98282079	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:98282079C>A	uc001kmm.3	-	15	1928	c.1711G>T	c.(1711-1713)GGT>TGT	p.G571C	TM9SF3_uc010qot.1_Missense_Mutation_p.G571C	NM_020123	NP_064508	Q9HD45	TM9S3_HUMAN	transmembrane 9 superfamily member 3 precursor	571	Helical; (Potential).					integral to membrane	binding				0		Colorectal(252;0.158)		Epithelial(162;1.84e-09)|all cancers(201;2.84e-08)		CCCATGTAACCAATCGCTCCT	0.338													9	119	---	---	---	---	PASS
CTBP2	1488	broad.mit.edu	37	10	126683133	126683133	+	Silent	SNP	G	A	A			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:126683133G>A	uc009yak.2	-	7	972	c.685C>T	c.(685-687)CTG>TTG	p.L229L	CTBP2_uc009yal.2_Silent_p.L229L|CTBP2_uc001lif.3_Silent_p.L229L|CTBP2_uc001lih.3_Silent_p.L229L|CTBP2_uc001lid.3_Silent_p.L297L|CTBP2_uc001lie.3_Silent_p.L769L	NM_001329	NP_001320	P56545	CTBP2_HUMAN	C-terminal binding protein 2 isoform 1	229					negative regulation of cell proliferation|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent|viral genome replication|white fat cell differentiation	cell junction|synapse|transcriptional repressor complex	NAD binding|oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor|protein binding				0		all_lung(145;0.0132)|Lung NSC(174;0.0193)|all_neural(114;0.116)|Colorectal(57;0.173)		Colorectal(40;0.00572)|COAD - Colon adenocarcinoma(40;0.0127)|GBM - Glioblastoma multiforme(135;0.147)		AAATCCTGCAGGGTGTAGACC	0.507													14	62	---	---	---	---	PASS
F2	2147	broad.mit.edu	37	11	46742358	46742358	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:46742358C>T	uc001ndf.3	+	4	327	c.284C>T	c.(283-285)ACG>ATG	p.T95M	F2_uc001ndg.3_RNA	NM_000506	NP_000497	P00734	THRB_HUMAN	coagulation factor II preproprotein	95					activation of caspase activity|acute-phase response|blood coagulation, intrinsic pathway|cell surface receptor linked signaling pathway|cytosolic calcium ion homeostasis|fibrinolysis|leukocyte migration|negative regulation of astrocyte differentiation|negative regulation of fibrinolysis|negative regulation of platelet activation|negative regulation of proteolysis|peptidyl-glutamic acid carboxylation|platelet activation|positive regulation of collagen biosynthetic process|positive regulation of protein phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of release of sequestered calcium ion into cytosol|post-translational protein modification|proteolysis|STAT protein import into nucleus|tyrosine phosphorylation of STAT protein	cytosol|endoplasmic reticulum lumen|extracellular space|Golgi lumen|plasma membrane|soluble fraction	calcium ion binding|growth factor activity|serine-type endopeptidase activity|thrombospondin receptor activity			ovary(3)	3		all_lung(304;0.000414)|Lung NSC(402;0.0011)		BRCA - Breast invasive adenocarcinoma(625;0.146)	Antihemophilic Factor(DB00025)|Argatroban(DB00278)|Bivalirudin(DB00006)|Coagulation Factor IX(DB00100)|Drotrecogin alfa(DB00055)|Enoxaparin(DB01225)|Heparin(DB01109)|Lepirudin(DB00001)|Menadione(DB00170)|Proflavine(DB01123)|Simvastatin(DB00641)|Suramin(DB04786)|Warfarin(DB00682)|Ximelagatran(DB04898)	ACAGCGAGGACGCCTCGAGAT	0.572													19	233	---	---	---	---	PASS
SPRYD5	84767	broad.mit.edu	37	11	55653066	55653066	+	Missense_Mutation	SNP	A	T	T			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55653066A>T	uc010rip.1	+	2	254	c.162A>T	c.(160-162)GAA>GAT	p.E54D	SPRYD5_uc010riq.1_5'Flank	NM_032681	NP_116070	Q9BSJ1	SPRY5_HUMAN	SPRY domain containing 5	54	RING-type.					intracellular	zinc ion binding				0		all_epithelial(135;0.226)				AGTGCTCTGAATGCAAGAAGA	0.502													9	37	---	---	---	---	PASS
TTC9C	283237	broad.mit.edu	37	11	62496235	62496235	+	5'UTR	SNP	T	A	A			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62496235T>A	uc001nuy.2	+	1					HNRNPUL2_uc001nuu.1_5'Flank|HNRNPUL2_uc001nuw.2_5'Flank|TTC9C_uc001nux.2_Intron	NM_173810	NP_776171	Q8N5M4	TTC9C_HUMAN	tetratricopeptide repeat domain 9C								binding			ovary(1)|pancreas(1)	2						TTAAATTGGCTGCTACTGTCA	0.527													4	10	---	---	---	---	PASS
SNHG1	23642	broad.mit.edu	37	11	62621378	62621378	+	Intron	SNP	T	G	G			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62621378T>G	uc001nvp.2	-						SLC3A2_uc001nwb.2_5'Flank|SLC3A2_uc001nwc.2_5'Flank|SLC3A2_uc001nwd.2_5'Flank|SLC3A2_uc001nwe.2_5'Flank|SLC3A2_uc001nwf.2_5'Flank|SNHG1_uc001nvo.2_Intron|SNHG1_uc001nvq.2_Intron|SNHG1_uc001nvs.2_Intron|SNHG1_uc001nvr.2_Intron|SNHG1_uc001nvt.2_RNA|SNHG1_uc001nvu.2_Intron|SNORD22_uc001nvv.2_5'Flank|SNORD31_uc009yoj.1_5'Flank|SNORD30_uc001nvw.1_5'Flank|SNORD29_uc001nvx.2_RNA					Homo sapiens cDNA FLJ38530 fis, clone HCHON2001039.												0						GTTCTCCAGTTTCTCAGGTGT	0.433													23	139	---	---	---	---	PASS
EXPH5	23086	broad.mit.edu	37	11	108382192	108382192	+	Missense_Mutation	SNP	C	G	G			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:108382192C>G	uc001pkk.2	-	6	4153	c.4042G>C	c.(4042-4044)GCT>CCT	p.A1348P	EXPH5_uc010rvy.1_Missense_Mutation_p.A1160P|EXPH5_uc010rvz.1_Missense_Mutation_p.A1192P|EXPH5_uc010rwa.1_Missense_Mutation_p.A1272P	NM_015065	NP_055880	Q8NEV8	EXPH5_HUMAN	exophilin 5 isoform a	1348					intracellular protein transport		Rab GTPase binding			skin(3)|ovary(2)	5		all_cancers(61;3.99e-08)|Acute lymphoblastic leukemia(157;3.97e-05)|Melanoma(852;4.04e-05)|all_epithelial(67;0.000116)|all_hematologic(158;0.000315)|Breast(348;0.104)|all_neural(303;0.16)		Epithelial(105;8.1e-06)|BRCA - Breast invasive adenocarcinoma(274;1.22e-05)|all cancers(92;0.000129)|OV - Ovarian serous cystadenocarcinoma(223;0.11)|Colorectal(284;0.184)		TCAACAGAAGCCATTTCCTGT	0.418													18	50	---	---	---	---	PASS
ABCC9	10060	broad.mit.edu	37	12	21960403	21960403	+	Silent	SNP	G	A	A			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:21960403G>A	uc001rfi.1	-	36	4346	c.4326C>T	c.(4324-4326)GTC>GTT	p.V1442V	ABCC9_uc001rfh.2_Silent_p.V1442V|ABCC9_uc001rfj.1_Silent_p.V1406V|ABCC9_uc001rfg.2_5'UTR	NM_005691	NP_005682	O60706	ABCC9_HUMAN	ATP-binding cassette, sub-family C, member 9	1442	Cytoplasmic (Potential).|ABC transporter 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)	CACCTTCAGTGACAACCGCAT	0.398													11	111	---	---	---	---	PASS
TBC1D15	64786	broad.mit.edu	37	12	72274276	72274276	+	Missense_Mutation	SNP	C	G	G			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:72274276C>G	uc001swu.2	+	4	307	c.298C>G	c.(298-300)CAG>GAG	p.Q100E	TBC1D15_uc009zrv.2_5'UTR|TBC1D15_uc010stt.1_Missense_Mutation_p.Q86E|TBC1D15_uc001swv.2_Missense_Mutation_p.Q100E|TBC1D15_uc001sww.2_5'UTR	NM_022771	NP_073608	Q8TC07	TBC15_HUMAN	TBC1 domain family, member 15 isoform 1	78							protein binding|Rab GTPase activator activity				0						AGAATGGACTCAGGCCCCAAA	0.323													10	23	---	---	---	---	PASS
NAV3	89795	broad.mit.edu	37	12	78531145	78531145	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:78531145G>A	uc001syp.2	+	19	4803	c.4630G>A	c.(4630-4632)GTT>ATT	p.V1544I	NAV3_uc001syo.2_Missense_Mutation_p.V1544I|NAV3_uc010sub.1_Missense_Mutation_p.V1030I|NAV3_uc009zsf.2_Missense_Mutation_p.V375I	NM_014903	NP_055718	Q8IVL0	NAV3_HUMAN	neuron navigator 3	1544	Ser-rich.					nuclear outer membrane	ATP binding|nucleoside-triphosphatase activity			large_intestine(6)|ovary(5)|lung(2)|breast(1)|skin(1)|kidney(1)|pancreas(1)	17						CATGGAAGAAGGTAAGCGTTG	0.458										HNSCC(70;0.22)			8	108	---	---	---	---	PASS
NAV3	89795	broad.mit.edu	37	12	78531146	78531146	+	Splice_Site	SNP	G	T	T			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:78531146G>T	uc001syp.2	+	19	4803	c.4630_splice	c.e19+1	p.V1544_splice	NAV3_uc001syo.2_Splice_Site_p.V1544_splice|NAV3_uc010sub.1_Splice_Site_p.V1030_splice|NAV3_uc009zsf.2_Splice_Site_p.V375_splice	NM_014903	NP_055718	Q8IVL0	NAV3_HUMAN	neuron navigator 3							nuclear outer membrane	ATP binding|nucleoside-triphosphatase activity			large_intestine(6)|ovary(5)|lung(2)|breast(1)|skin(1)|kidney(1)|pancreas(1)	17						ATGGAAGAAGGTAAGCGTTGA	0.458										HNSCC(70;0.22)			8	110	---	---	---	---	PASS
NOS1	4842	broad.mit.edu	37	12	117768660	117768660	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:117768660A>G	uc001twm.1	-	2	901	c.215T>C	c.(214-216)TTG>TCG	p.L72S		NM_000620	NP_000611	P29475	NOS1_HUMAN	nitric oxide synthase 1, neuronal	72	Interaction with NOSIP (By similarity).|PDZ.				multicellular organismal response to stress|myoblast fusion|negative regulation of calcium ion transport into cytosol|neurotransmitter biosynthetic process|nitric oxide biosynthetic process|platelet activation|positive regulation of vasodilation|regulation of cardiac muscle contraction|response to heat|response to hypoxia	cytoskeleton|cytosol|dendritic spine|perinuclear region of cytoplasm|photoreceptor inner segment|sarcolemma|sarcoplasmic reticulum	arginine binding|cadmium ion binding|calmodulin binding|flavin adenine dinucleotide binding|FMN binding|heme binding|NADP binding|nitric-oxide synthase activity|tetrahydrobiopterin binding			ovary(3)|skin(3)|pancreas(1)	7	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.0561)	L-Citrulline(DB00155)	CAGGTCCACCAAGGGCCGGCC	0.622													17	69	---	---	---	---	PASS
KIAA0564	23078	broad.mit.edu	37	13	42361642	42361642	+	Missense_Mutation	SNP	T	G	G			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:42361642T>G	uc001uyj.2	-	18	2171	c.2101A>C	c.(2101-2103)AAT>CAT	p.N701H	KIAA0564_uc001uyk.2_Missense_Mutation_p.N701H	NM_015058	NP_055873	A3KMH1	K0564_HUMAN	hypothetical protein LOC23078 isoform a	701						extracellular region	ATP binding|ATPase activity			ovary(3)|upper_aerodigestive_tract(1)|kidney(1)|skin(1)	6		Lung NSC(96;4.61e-06)|Prostate(109;0.0167)|Lung SC(185;0.0262)|Breast(139;0.0854)|Hepatocellular(98;0.114)		OV - Ovarian serous cystadenocarcinoma(117;0.000368)|GBM - Glioblastoma multiforme(144;0.0033)|BRCA - Breast invasive adenocarcinoma(63;0.0969)		TCTGCCAGATTTTTTTCTAAT	0.373													28	77	---	---	---	---	PASS
MIR1297	100302187	broad.mit.edu	37	13	54886172	54886172	+	RNA	SNP	T	A	A			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:54886172T>A	hsa-mir-1297|MI0006358	-			c.12T>A																				0						AGATCAACCCTAGAGATAAAC	0.323													10	65	---	---	---	---	PASS
POTEG	404785	broad.mit.edu	37	14	19566062	19566062	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:19566062C>A	uc001vuz.1	+	6	1158	c.1106C>A	c.(1105-1107)TCT>TAT	p.S369Y	POTEG_uc001vva.1_RNA|POTEG_uc010ahc.1_RNA|uc001vvb.2_Intron	NM_001005356	NP_001005356	Q6S5H5	POTEG_HUMAN	POTE ankyrin domain family, member G	369										ovary(1)	1						CTAAAAGTCTCTTCTGAAAAC	0.214													10	236	---	---	---	---	PASS
DACT1	51339	broad.mit.edu	37	14	59113096	59113096	+	Silent	SNP	G	A	A			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:59113096G>A	uc001xdw.2	+	4	1919	c.1755G>A	c.(1753-1755)AAG>AAA	p.K585K	DACT1_uc010trv.1_Silent_p.K304K|DACT1_uc001xdx.2_Silent_p.K548K|DACT1_uc010trw.1_Silent_p.K304K	NM_016651	NP_057735	Q9NYF0	DACT1_HUMAN	dapper 1 isoform 1	585					multicellular organismal development|Wnt receptor signaling pathway	cytoplasm|nucleus				large_intestine(2)|lung(2)|ovary(1)	5						CCAGCCTGAAGCACCGCGGCC	0.657													4	26	---	---	---	---	PASS
HEATR4	399671	broad.mit.edu	37	14	73945690	73945690	+	Intron	SNP	C	G	G			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:73945690C>G	uc010tua.1	-						uc001xoi.1_RNA	NM_203309	NP_976054			HEAT repeat containing 4											ovary(1)	1				BRCA - Breast invasive adenocarcinoma(234;0.00386)|OV - Ovarian serous cystadenocarcinoma(108;0.0719)		gtcgcccaggctggagttcag	0.154													5	8	---	---	---	---	PASS
SNORD115-20	100033460	broad.mit.edu	37	15	25463960	25463960	+	Intron	SNP	C	G	G	rs140817292	by1000genomes	TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:25463960C>G	uc001yzq.1	+						uc001yzt.1_Intron|SNORD115-26_uc001yzw.1_RNA|HBII-52-27_uc010ayq.1_5'Flank	NR_003313				Homo sapiens small nucleolar RNA, C/D box 115-15 (SNORD115-15), non-coding RNA.												0						GTGGCCCAACCTGTCTCTGCA	0.582													6	51	---	---	---	---	PASS
CCNB2	9133	broad.mit.edu	37	15	59406998	59406998	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:59406998G>A	uc002afz.2	+	5	668	c.520G>A	c.(520-522)GTA>ATA	p.V174I	CCNB2_uc010bge.2_Missense_Mutation_p.V93I	NM_004701	NP_004692	O95067	CCNB2_HUMAN	cyclin B2	174					cell cycle checkpoint|cell division|G2/M transition of mitotic cell cycle|mitosis|regulation of cyclin-dependent protein kinase activity|regulation of G2/M transition of mitotic cell cycle	centrosome|cytosol|nucleus	protein kinase binding				0						GGATTGGCTGGTACAAGTCCA	0.458													43	145	---	---	---	---	PASS
ARIH1	25820	broad.mit.edu	37	15	72848195	72848195	+	Silent	SNP	T	C	C			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:72848195T>C	uc002aut.3	+	5	998	c.684T>C	c.(682-684)ACT>ACC	p.T228T		NM_005744	NP_005735	Q9Y4X5	ARI1_HUMAN	ariadne ubiquitin-conjugating enzyme E2 binding	228	Interaction with UBE2L3.|RING-type 1; atypical.				ubiquitin-dependent protein catabolic process	cytoplasm|ubiquitin ligase complex	ubiquitin protein ligase binding|ubiquitin-protein ligase activity|zinc ion binding				0						TTTTTCAGACTATTTCGTGTC	0.219													18	73	---	---	---	---	PASS
UBL7	84993	broad.mit.edu	37	15	74748922	74748922	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:74748922T>C	uc002axw.1	-	3	437	c.275A>G	c.(274-276)AAG>AGG	p.K92R	UBL7_uc002axx.1_Missense_Mutation_p.K132R|UBL7_uc010bjr.1_Intron|UBL7_uc002axy.1_Missense_Mutation_p.K92R|UBL7_uc002axz.1_Missense_Mutation_p.K92R	NM_032907	NP_116296	Q96S82	UBL7_HUMAN	ubiquitin-like 7	92	Ubiquitin-like.						protein binding			ovary(1)	1						AGGCCAGGACTTTCGCAGAAC	0.488													5	123	---	---	---	---	PASS
SIN3A	25942	broad.mit.edu	37	15	75682103	75682103	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:75682103C>A	uc002bai.2	-	16	3170	c.2911G>T	c.(2911-2913)GAT>TAT	p.D971Y	SIN3A_uc002baj.2_Missense_Mutation_p.D971Y|SIN3A_uc010uml.1_Missense_Mutation_p.D971Y	NM_015477	NP_056292	Q96ST3	SIN3A_HUMAN	transcriptional co-repressor Sin3A	971					blood coagulation|cellular lipid metabolic process|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleolus|Sin3 complex	protein binding			skin(3)|ovary(1)|lung(1)	5						ATGTTGCCATCCAGCAGGCTC	0.468													59	129	---	---	---	---	PASS
ADAMTS7	11173	broad.mit.edu	37	15	79059040	79059040	+	Silent	SNP	A	G	G	rs144043775	by1000genomes	TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:79059040A>G	uc002bej.3	-	19	3424	c.3213T>C	c.(3211-3213)AAT>AAC	p.N1071N	ADAMTS7_uc010und.1_3'UTR	NM_014272	NP_055087	Q9UKP4	ATS7_HUMAN	ADAM metallopeptidase with thrombospondin type 1	1071					proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding				0						CCTCGTGGAAATTGATGAAAT	0.617													3	40	---	---	---	---	PASS
ADAMTS7	11173	broad.mit.edu	37	15	79059041	79059041	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:79059041T>C	uc002bej.3	-	19	3423	c.3212A>G	c.(3211-3213)AAT>AGT	p.N1071S	ADAMTS7_uc010und.1_3'UTR	NM_014272	NP_055087	Q9UKP4	ATS7_HUMAN	ADAM metallopeptidase with thrombospondin type 1	1071					proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding				0						CTCGTGGAAATTGATGAAATT	0.617													3	40	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	16	31212808	31212808	+	IGR	SNP	T	C	C			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31212808T>C								FUS (9711 upstream) : PYCARD (1 downstream)																							ACACACAAGTTCAAGCTGGCT	0.522													34	78	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	16	70268158	70268158	+	RNA	SNP	A	C	C			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70268158A>C	uc010cfp.1	-	3		c.257T>G								Homo sapiens cDNA, FLJ98908.																		TTCTTCATTAAAACAGCTACT	0.333													3	9	---	---	---	---	PASS
CLEC18B	497190	broad.mit.edu	37	16	74445808	74445808	+	Intron	SNP	T	C	C	rs146209466	by1000genomes	TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:74445808T>C	uc002fct.2	-						CLEC18B_uc002fcu.2_Intron|CLEC18B_uc010vmu.1_3'UTR|CLEC18B_uc010vmv.1_Intron	NM_001011880	NP_001011880	Q6UXF7	CL18B_HUMAN	C-type lectin domain family 18, member B							extracellular region	sugar binding				0						GGGTcaggagtgagctggtca	0.294													5	27	---	---	---	---	PASS
CNTNAP1	8506	broad.mit.edu	37	17	40848118	40848118	+	Missense_Mutation	SNP	G	C	C			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40848118G>C	uc002iay.2	+	20	3638	c.3422G>C	c.(3421-3423)GGC>GCC	p.G1141A	CNTNAP1_uc010wgs.1_RNA	NM_003632	NP_003623	P78357	CNTP1_HUMAN	contactin associated protein 1 precursor	1141	Laminin G-like 4.|Extracellular (Potential).				axon guidance|cell adhesion	paranode region of axon	receptor activity|receptor binding|SH3 domain binding|SH3/SH2 adaptor activity			ovary(3)|breast(3)|upper_aerodigestive_tract(1)|lung(1)	8		Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.143)		GTGACCGATGGCCAGCCCCAT	0.537													15	59	---	---	---	---	PASS
COL1A1	1277	broad.mit.edu	37	17	48272628	48272628	+	Missense_Mutation	SNP	C	T	T	rs72648328		TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48272628C>T	uc002iqm.2	-	19	1390	c.1264G>A	c.(1264-1266)GGC>AGC	p.G422S		NM_000088	NP_000079	P02452	CO1A1_HUMAN	alpha 1 type I collagen preproprotein	422	Triple-helical region.		G -> C (in OI2A).		axon guidance|blood vessel development|collagen biosynthetic process|collagen fibril organization|embryonic skeletal system development|leukocyte migration|platelet activation|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of cell migration|positive regulation of epithelial to mesenchymal transition|positive regulation of transcription, DNA-dependent|protein localization to nucleus|sensory perception of sound|skin morphogenesis|tooth mineralization|visual perception	collagen type I|extracellular space|plasma membrane	identical protein binding|platelet-derived growth factor binding		COL1A1/PDGFB(372)	soft_tissue(372)|central_nervous_system(7)|skin(1)|breast(1)|pancreas(1)	382					Collagenase(DB00048)|Palifermin(DB00039)	CCGCCGGGGCCCTGGGGTCCA	0.672			T	PDGFB|USP6	dermatofibrosarcoma protuberans|aneurysmal bone cyst 		Osteogenesis imperfecta						10	25	---	---	---	---	PASS
CACNG5	27091	broad.mit.edu	37	17	64875148	64875148	+	Silent	SNP	G	A	A			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:64875148G>A	uc010wqi.1	+	3	492	c.255G>A	c.(253-255)CTG>CTA	p.L85L	CACNG5_uc002jfr.2_Silent_p.L85L|CACNG5_uc010wqj.1_Silent_p.L85L	NM_145811	NP_665810	Q9UF02	CCG5_HUMAN	voltage-dependent calcium channel gamma-5	85					regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|postsynaptic density|postsynaptic membrane	voltage-gated calcium channel activity			pancreas(1)|skin(1)	2			BRCA - Breast invasive adenocarcinoma(6;1.61e-08)			ACACCCAGCTGACATCCGAGT	0.532													25	75	---	---	---	---	PASS
LAMA1	284217	broad.mit.edu	37	18	7009293	7009293	+	Missense_Mutation	SNP	C	T	T	rs149753863	byFrequency	TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:7009293C>T	uc002knm.2	-	27	4040	c.3946G>A	c.(3946-3948)GAT>AAT	p.D1316N	LAMA1_uc010wzj.1_Missense_Mutation_p.D792N	NM_005559	NP_005550	P25391	LAMA1_HUMAN	laminin, alpha 1 precursor	1316	Laminin IV type A 2.				axon guidance|cell adhesion|cell surface receptor linked signaling pathway|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	extracellular space|laminin-1 complex|laminin-3 complex	extracellular matrix structural constituent|receptor binding			ovary(8)|large_intestine(4)|upper_aerodigestive_tract(2)|breast(2)|skin(2)|pancreas(2)|central_nervous_system(1)	21		Colorectal(10;0.172)			Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)	TACTCAATATCGCTGAGGACA	0.363													29	150	---	---	---	---	PASS
MAPK4	5596	broad.mit.edu	37	18	48190332	48190332	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:48190332G>A	uc002lev.2	+	2	1004	c.4G>A	c.(4-6)GCT>ACT	p.A2T	MAPK4_uc010xdm.1_Intron|MAPK4_uc010doz.2_Missense_Mutation_p.A2T	NM_002747	NP_002738	P31152	MK04_HUMAN	mitogen-activated protein kinase 4	2					cell cycle		ATP binding|MAP kinase activity			lung(4)|skin(2)	6		Colorectal(6;0.0297)		Colorectal(21;0.156)		GCCCACAATGGCTGAGAAGGG	0.587													20	76	---	---	---	---	PASS
ZNF833	401898	broad.mit.edu	37	19	11762663	11762663	+	RNA	SNP	G	A	A			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11762663G>A	uc002msl.3	+	6		c.675G>A								Homo sapiens cDNA FLJ44800 fis, clone BRACE3041162, moderately similar to Homo sapiens zinc finger protein 14 (KOX 6) (ZNF14).												0						GACACAAACCGTATGAGTGTC	0.458													8	40	---	---	---	---	PASS
USHBP1	83878	broad.mit.edu	37	19	17370531	17370531	+	Missense_Mutation	SNP	G	T	T	rs150046287	byFrequency	TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17370531G>T	uc002nfs.1	-	6	892	c.779C>A	c.(778-780)TCC>TAC	p.S260Y	USHBP1_uc002nfr.1_5'Flank|USHBP1_uc002nft.1_RNA|USHBP1_uc010xpk.1_Missense_Mutation_p.S196Y|USHBP1_uc010eam.1_Missense_Mutation_p.S188Y	NM_031941	NP_114147	Q8N6Y0	USBP1_HUMAN	Usher syndrome 1C binding protein 1	260							PDZ domain binding			ovary(1)	1						GTGAGCCAGGGAGAAGGAGTC	0.557													10	90	---	---	---	---	PASS
U2AF1L4	199746	broad.mit.edu	37	19	36235124	36235124	+	Intron	SNP	C	T	T			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36235124C>T	uc002obg.2	-						TMEM149_uc002obb.2_5'Flank|TMEM149_uc002obc.2_5'Flank|TMEM149_uc002obd.3_5'Flank|TMEM149_uc010xsy.1_5'Flank|TMEM149_uc010eej.2_Intron|U2AF1L4_uc002obh.1_5'UTR|U2AF1L4_uc002obe.2_Intron|U2AF1L4_uc002obf.2_Intron|PSENEN_uc002obi.1_5'Flank|PSENEN_uc002obj.1_5'Flank|PSENEN_uc002obk.1_5'Flank			Q8WU68	U2AF4_HUMAN	Homo sapiens cDNA FLJ35525 fis, clone SPLEN2001650.						mRNA processing|RNA splicing	nuclear speck|spliceosomal complex	nucleotide binding|RNA binding|zinc ion binding				0	all_lung(56;3.33e-07)|Lung NSC(56;5.02e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			TGGGGCTGGACTGGATTTAGT	0.562													3	21	---	---	---	---	PASS
ATP1A3	478	broad.mit.edu	37	19	42482093	42482093	+	Missense_Mutation	SNP	G	C	C			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42482093G>C	uc002osg.2	-	14	2092	c.1938C>G	c.(1936-1938)AAC>AAG	p.N646K	ATP1A3_uc010xwf.1_Missense_Mutation_p.N657K|ATP1A3_uc010xwg.1_Missense_Mutation_p.N616K|ATP1A3_uc010xwh.1_Missense_Mutation_p.N659K|ATP1A3_uc002osh.2_Missense_Mutation_p.N646K	NM_152296	NP_689509	P13637	AT1A3_HUMAN	Na+/K+ -ATPase alpha 3 subunit	646	Cytoplasmic (Potential).				ATP biosynthetic process	endoplasmic reticulum|Golgi apparatus	ATP binding|metal ion binding|sodium:potassium-exchanging ATPase activity			ovary(1)|pancreas(1)	2						CTCACCGGGGGTTAACCTGGC	0.647													22	80	---	---	---	---	PASS
KLK13	26085	broad.mit.edu	37	19	51559929	51559929	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51559929C>T	uc002pvn.2	-	5	792	c.749G>A	c.(748-750)CGT>CAT	p.R250H	KLK13_uc002pvl.2_RNA|KLK13_uc002pvm.2_RNA|KLK13_uc002pvo.2_RNA|KLK13_uc002pvp.2_RNA|KLK13_uc010eon.2_Missense_Mutation_p.R177H|KLK13_uc002pvq.2_RNA|KLK13_uc010eoo.2_Missense_Mutation_p.R98H	NM_015596	NP_056411	Q9UKR3	KLK13_HUMAN	kallikrein 13 precursor	250	Peptidase S1.				proteolysis		protein binding|serine-type endopeptidase activity				0		all_neural(266;0.026)		OV - Ovarian serous cystadenocarcinoma(262;0.00224)|GBM - Glioblastoma multiforme(134;0.00432)		TCTTGAGACACGGGTGTAGAC	0.512													69	174	---	---	---	---	PASS
FAM83D	81610	broad.mit.edu	37	20	37580732	37580732	+	Nonsense_Mutation	SNP	C	T	T			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:37580732C>T	uc002xjg.2	+	4	1458	c.1417C>T	c.(1417-1419)CAG>TAG	p.Q473*		NM_030919	NP_112181	Q9H4H8	FA83D_HUMAN	hypothetical protein LOC81610	443					cell division|mitosis	cytoplasm|spindle pole				ovary(3)	3		Myeloproliferative disorder(115;0.00878)				GACCACTACTCAGACTGACAT	0.468													21	80	---	---	---	---	PASS
CHD6	84181	broad.mit.edu	37	20	40049199	40049199	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:40049199C>A	uc002xka.1	-	31	6254	c.6076G>T	c.(6076-6078)GAT>TAT	p.D2026Y		NM_032221	NP_115597	Q8TD26	CHD6_HUMAN	chromodomain helicase DNA binding protein 6	2026					chromatin remodeling|nervous system development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	ATP binding|ATP-dependent helicase activity|chromatin binding|DNA binding			ovary(6)|skin(5)|lung(2)|central_nervous_system(1)	14		Myeloproliferative disorder(115;0.00425)				TTCTCAAAATCCATGTCTTCT	0.398													7	138	---	---	---	---	PASS
NRIP1	8204	broad.mit.edu	37	21	16338035	16338035	+	Nonsense_Mutation	SNP	G	A	A			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:16338035G>A	uc002yjx.2	-	4	3077	c.2479C>T	c.(2479-2481)CAA>TAA	p.Q827*		NM_003489	NP_003480	P48552	NRIP1_HUMAN	nuclear receptor interacting protein 1	827	Repression domain 3.				androgen receptor signaling pathway|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent		androgen receptor binding|estrogen receptor binding|glucocorticoid receptor binding|transcription coactivator activity|transcription corepressor activity				0				Epithelial(23;1.19e-05)|all cancers(11;4.64e-05)|COAD - Colon adenocarcinoma(22;0.000232)|Colorectal(24;0.0006)|OV - Ovarian serous cystadenocarcinoma(11;0.00418)|Lung(58;0.199)|LUSC - Lung squamous cell carcinoma(23;0.24)		TAACTATCTTGATTTTGTCTT	0.403													19	174	---	---	---	---	PASS
SYNJ1	8867	broad.mit.edu	37	21	34066598	34066598	+	Silent	SNP	A	T	T			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:34066598A>T	uc002yqh.2	-	6	846	c.846T>A	c.(844-846)GTT>GTA	p.V282V	SYNJ1_uc011ads.1_Silent_p.V243V|SYNJ1_uc002yqf.2_Silent_p.V243V|SYNJ1_uc002yqg.2_Silent_p.V243V|SYNJ1_uc002yqi.2_Silent_p.V282V	NM_003895	NP_003886	O43426	SYNJ1_HUMAN	synaptojanin 1 isoform a	243	SAC.						inositol-polyphosphate 5-phosphatase activity|nucleotide binding|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity|RNA binding			ovary(4)|skin(1)	5						TGAAGGAAGAAACTGAGTCAT	0.318													5	53	---	---	---	---	PASS
ITGB2	3689	broad.mit.edu	37	21	46321408	46321408	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:46321408G>A	uc002zgd.2	-	5	784	c.740C>T	c.(739-741)CCG>CTG	p.P247L	ITGB2_uc002zge.2_Missense_Mutation_p.P247L|ITGB2_uc002zgf.3_Missense_Mutation_p.P247L|ITGB2_uc011afl.1_Missense_Mutation_p.P169L|ITGB2_uc010gpw.2_Missense_Mutation_p.P190L|ITGB2_uc002zgg.2_Missense_Mutation_p.P247L	NM_001127491	NP_001120963	P05107	ITB2_HUMAN	integrin, beta 2 precursor	247	Extracellular (Potential).|VWFA.				apoptosis|blood coagulation|cell-cell signaling|cell-matrix adhesion|inflammatory response|integrin-mediated signaling pathway|leukocyte cell-cell adhesion|multicellular organismal development|neutrophil chemotaxis|regulation of cell shape|regulation of immune response|regulation of peptidyl-tyrosine phosphorylation	integrin complex	glycoprotein binding|protein kinase binding|receptor activity			ovary(4)|central_nervous_system(3)|breast(2)	9				Colorectal(79;0.0669)	Simvastatin(DB00641)	CGGCCTCACCGGGCAGGCGGC	0.687													5	30	---	---	---	---	PASS
SCML1	6322	broad.mit.edu	37	X	17768309	17768309	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:17768309G>T	uc004cyb.2	+	6	924	c.599G>T	c.(598-600)GGT>GTT	p.G200V	SCML1_uc004cyc.2_Missense_Mutation_p.G173V|SCML1_uc004cyd.2_Missense_Mutation_p.G79V|SCML1_uc004cye.2_Missense_Mutation_p.G79V	NM_001037540	NP_001032629	Q9UN30	SCML1_HUMAN	sex comb on midleg-like 1 isoform a	200					anatomical structure morphogenesis	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			breast(2)|ovary(1)	3	Hepatocellular(33;0.183)					GCATCTGATGGTGCAACGTAT	0.542													16	62	---	---	---	---	PASS
RPGR	6103	broad.mit.edu	37	X	38182653	38182653	+	Silent	SNP	G	A	A			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:38182653G>A	uc004ded.1	-	2	321	c.153C>T	c.(151-153)ACC>ACT	p.T51T	RPGR_uc004deb.2_Silent_p.T51T|RPGR_uc004dea.2_RNA|RPGR_uc004dec.2_RNA	NM_001034853	NP_001030025	Q92834	RPGR_HUMAN	retinitis pigmentosa GTPase regulator isoform C	51					intracellular protein transport|response to stimulus|visual perception	Golgi apparatus|photoreceptor outer segment	guanyl-nucleotide exchange factor activity|protein binding			ovary(1)	1						AATACTAACCGGTAACAACAG	0.303													4	24	---	---	---	---	PASS
ZNF711	7552	broad.mit.edu	37	X	84510342	84510342	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:84510342G>A	uc004eeo.2	+	4	504	c.157G>A	c.(157-159)GAT>AAT	p.D53N	ZNF711_uc004eep.2_Missense_Mutation_p.D53N|ZNF711_uc004eeq.2_Missense_Mutation_p.D53N	NM_021998	NP_068838	Q9Y462	ZN711_HUMAN	zinc finger protein 711	53					positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	protein binding|sequence-specific DNA binding|zinc ion binding			ovary(3)|skin(1)	4						TTTAGTTTCTGATGTTGTCAC	0.413													14	99	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	14568	14568	+	RNA	SNP	C	A	A			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:14568C>A	uc004cox.3	+	1		c.2232C>A			uc004coy.2_5'Flank|uc004coz.1_5'Flank					Homo sapiens NADH dehydrogenase subunit 5 (MTND5) mRNA, RNA 5, complete cds; mitochondrial gene for mitochondrial product.																		CCCGACCACACCGCTAACAAT	0.378													24	56	---	---	---	---	PASS
C1orf109	54955	broad.mit.edu	37	1	38155688	38155688	+	Intron	DEL	T	-	-			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:38155688delT	uc001cbp.2	-						C1orf109_uc010oig.1_Intron|C1orf109_uc001cbo.2_Intron|C1orf109_uc001cbq.1_Intron|CDCA8_uc001cbr.2_5'Flank|CDCA8_uc001cbs.2_5'Flank|CDCA8_uc010oih.1_5'Flank	NM_017850	NP_060320	Q9NX04	CA109_HUMAN	hypothetical protein LOC54955												0		Myeloproliferative disorder(586;0.0393)				AGAAGCAGGGttttttttttg	0.299													4	2	---	---	---	---	
C1orf177	163747	broad.mit.edu	37	1	55279346	55279352	+	Intron	DEL	CCGGCCT	-	-	rs67384270		TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:55279346_55279352delCCGGCCT	uc001cyb.3	+						C1orf177_uc001cya.3_Intron	NM_001110533	NP_001104003	Q3ZCV2	CA177_HUMAN	hypothetical protein LOC163747 isoform 2												0						TGAGGCTGGCCCGGCCTCCGGCCTCCG	0.604													3	3	---	---	---	---	
MAGI3	260425	broad.mit.edu	37	1	113992210	113992210	+	Intron	DEL	T	-	-	rs34091729		TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:113992210delT	uc001edk.2	+						MAGI3_uc001edh.3_Intron|MAGI3_uc001edi.3_Intron|MAGI3_uc010owm.1_Intron	NM_001142782	NP_001136254	Q5TCQ9	MAGI3_HUMAN	membrane-associated guanylate kinase-related  3						apoptosis|interspecies interaction between organisms|intracellular signal transduction	nucleus|tight junction	ATP binding|guanylate kinase activity|protein binding			lung(3)|ovary(2)|central_nervous_system(1)	6	Lung SC(450;0.184)	all_cancers(81;2.34e-09)|all_epithelial(167;7.41e-09)|all_lung(203;7.13e-06)|Lung NSC(69;1.2e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		TGCAAGTGCATTTTTTTTTCC	0.353													3	4	---	---	---	---	
SDCCAG8	10806	broad.mit.edu	37	1	243434124	243434124	+	Intron	DEL	T	-	-			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:243434124delT	uc001hzw.2	+						SDCCAG8_uc010pyk.1_Intron|SDCCAG8_uc010pyl.1_Intron	NM_006642	NP_006633	Q86SQ7	SDCG8_HUMAN	serologically defined colon cancer antigen 8						establishment of cell polarity|G2/M transition of mitotic cell cycle|tube formation	cell-cell junction|centriole|cytosol	protein binding				0	all_cancers(71;0.000545)|all_epithelial(71;0.000509)|all_lung(81;0.0821)|Ovarian(71;0.0919)|all_neural(11;0.101)|Breast(184;0.218)	all_cancers(173;0.00395)	all cancers(7;1.58e-07)|GBM - Glioblastoma multiforme(7;5.12e-06)|OV - Ovarian serous cystadenocarcinoma(106;0.00392)	COAD - Colon adenocarcinoma(196;0.145)		gtagaaattcttttttttttt	0.025													4	2	---	---	---	---	
AHCTF1	25909	broad.mit.edu	37	1	247031193	247031193	+	Intron	DEL	A	-	-			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247031193delA	uc001ibu.1	-						AHCTF1_uc001ibv.1_Intron|AHCTF1_uc009xgs.1_Intron|AHCTF1_uc001ibw.1_Intron	NM_015446	NP_056261	Q8WYP5	ELYS_HUMAN	transcription factor ELYS						cytokinesis|mitotic prometaphase|mRNA transport|nuclear pore complex assembly|protein transport|transmembrane transport	condensed chromosome kinetochore|cytosol|nuclear matrix|nuclear membrane|nuclear pore|nucleoplasm	DNA binding			ovary(5)|skin(2)	7	all_cancers(71;3.05e-05)|all_epithelial(71;6.72e-06)|Ovarian(71;0.0173)|Breast(184;0.0318)|all_lung(81;0.0458)|Lung NSC(105;0.0518)	all_cancers(173;0.0266)	OV - Ovarian serous cystadenocarcinoma(106;0.00271)			GAATGATTACACCCCCCCCCC	0.244													4	2	---	---	---	---	
RAD51AP2	729475	broad.mit.edu	37	2	17696274	17696275	+	Intron	INS	-	A	A	rs34060092		TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:17696274_17696275insA	uc002rcl.1	-						RAD51AP2_uc010exn.1_Intron	NM_001099218	NP_001092688	Q09MP3	R51A2_HUMAN	RAD51 associated protein 2											ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)					CTTCTTGCTGGAAAAAAAAAAA	0.307													5	3	---	---	---	---	
NCOA1	8648	broad.mit.edu	37	2	24949704	24949704	+	Intron	DEL	A	-	-	rs71960773		TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:24949704delA	uc002rfk.2	+						NCOA1_uc010eye.2_Intron|NCOA1_uc002rfi.2_Intron|NCOA1_uc002rfj.2_Intron|NCOA1_uc002rfl.2_Intron	NM_003743	NP_003734	Q15788	NCOA1_HUMAN	nuclear receptor coactivator 1 isoform 1										PAX3/NCOA1(8)	soft_tissue(8)|ovary(1)|lung(1)|skin(1)	11	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					AATACTTACTAAAAAAAAAAA	0.154			T	PAX3	alveolar rhadomyosarcoma								9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	64602905	64602906	+	IGR	INS	-	CAT	CAT			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:64602905_64602906insCAT								PELI1 (231300 upstream) : HSPC159 (78421 downstream)																							accaccatcaccaccatcacca	0.000													6	5	---	---	---	---	
TEX261	113419	broad.mit.edu	37	2	71219277	71219277	+	Intron	DEL	T	-	-	rs112462352		TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:71219277delT	uc002shn.2	-						TEX261_uc010fdy.2_Intron	NM_144582	NP_653183	Q6UWH6	TX261_HUMAN	testis expressed sequence 261							integral to membrane					0						AAAGGCAACAttttttttttt	0.284													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	134405284	134405285	+	IGR	INS	-	AAGGAAGG	AAGGAAGG			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:134405284_134405285insAAGGAAGG								NCKAP5 (79253 upstream) : MGAT5 (606545 downstream)																							aaagaaaaagaaaggaaggaag	0.000													4	2	---	---	---	---	
NEB	4703	broad.mit.edu	37	2	152417311	152417312	+	Intron	INS	-	C	C	rs150437657	by1000genomes	TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:152417311_152417312insC	uc010fnx.2	-						NEB_uc002txr.2_Intron	NM_004543	NP_004534	P20929	NEBU_HUMAN	nebulin isoform 3						muscle filament sliding|muscle organ development|regulation of actin filament length|somatic muscle development	actin cytoskeleton|cytosol|Z disc	actin binding|structural constituent of muscle			ovary(8)|large_intestine(5)|breast(3)|central_nervous_system(2)|skin(1)|pancreas(1)	20				BRCA - Breast invasive adenocarcinoma(221;0.219)		TCTCACACACTCCCTACTAACT	0.411													3	3	---	---	---	---	
UBE2E3	10477	broad.mit.edu	37	2	181886340	181886359	+	Intron	DEL	TCCCTCTCTCCCTCCCTTTT	-	-	rs79152755		TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:181886340_181886359delTCCCTCTCTCCCTCCCTTTT	uc002unq.1	+						UBE2E3_uc002unr.1_Intron|UBE2E3_uc010fri.1_Intron	NM_182678	NP_872619	Q969T4	UB2E3_HUMAN	ubiquitin-conjugating enzyme E2E 3						protein K11-linked ubiquitination|protein K48-linked ubiquitination|protein K63-linked ubiquitination|regulation of growth	cytoplasm|nucleolus	ATP binding|protein binding|ubiquitin-protein ligase activity			ovary(1)	1						ccttccttcctccctctctccctcccttttttccttcctt	0.082													5	3	---	---	---	---	
MYLK	4638	broad.mit.edu	37	3	123539447	123539447	+	Intron	DEL	C	-	-			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:123539447delC	uc003ego.2	-						MYLK_uc003egp.2_Intron|MYLK_uc003egq.2_Intron|MYLK_uc003egr.2_Intron|MYLK_uc003egs.2_Intron|MYLK_uc003egu.1_Intron	NM_053025	NP_444253	Q15746	MYLK_HUMAN	myosin light chain kinase isoform 1						aorta smooth muscle tissue morphogenesis|muscle contraction	cytosol	actin binding|ATP binding|calmodulin binding|metal ion binding|myosin light chain kinase activity			ovary(6)|skin(2)|stomach(1)	9		Lung NSC(201;0.0496)		GBM - Glioblastoma multiforme(114;0.0736)		AGCTAAGCTACCAGTGATTGA	0.239													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	125391768	125391771	+	IGR	DEL	TCTT	-	-			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:125391768_125391771delTCTT								LOC285419 (540250 upstream) : ANKRD50 (193697 downstream)																							tctccctttctctttctttctttc	0.049													4	2	---	---	---	---	
HSPA4L	22824	broad.mit.edu	37	4	128744877	128744880	+	Intron	DEL	TTAA	-	-			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:128744877_128744880delTTAA	uc003ifm.2	+						HSPA4L_uc011cgr.1_Intron	NM_014278	NP_055093	O95757	HS74L_HUMAN	heat shock 70kDa protein 4-like						protein folding|response to unfolded protein	cytoplasm|nucleus	ATP binding|protein binding			ovary(2)|central_nervous_system(1)|skin(1)	4						TTTTAAttttttaattgagaggaa	0.118													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	165331871	165331872	+	IGR	INS	-	TCCTTCCTTCTTTCCTTCCTTCCTTCTT	TCCTTCCTTCTTTCCTTCCTTCCTTCTT	rs35349836		TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:165331871_165331872insTCCTTCCTTCTTTCCTTCCTTCCTTCTT								MARCH1 (26669 upstream) : TRIM61 (543728 downstream)																							ctctccctccctccttccttct	0.119													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	131368633	131368636	+	IGR	DEL	GGAG	-	-	rs59143826		TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:131368633_131368636delGGAG								ACSL6 (20763 upstream) : IL3 (27711 downstream)																							agagagagaaggagggagggaggg	0.000													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	18046050	18046053	+	IGR	DEL	CCTC	-	-	rs34935394		TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:18046050_18046053delCCTC								KIF13A (58251 upstream) : NHLRC1 (74665 downstream)																							ttccttccttcctccctccctccc	0.113													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	29785715	29785715	+	IGR	DEL	G	-	-			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:29785715delG								HCG4 (24865 upstream) : HLA-G (9041 downstream)																							aggaggtcctggtttccaaag	0.000													4	2	---	---	---	---	
LY6G6C	80740	broad.mit.edu	37	6	31687694	31687694	+	Intron	DEL	A	-	-			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31687694delA	uc003nwh.2	-						LY6G6C_uc010jtd.2_Intron	NM_025261	NP_079537	O95867	LY66C_HUMAN	lymphocyte antigen 6 complex G6C precursor							anchored to membrane|plasma membrane					0						acattaattgaaaaaaaggca	0.070													4	2	---	---	---	---	
RSPH9	221421	broad.mit.edu	37	6	43623774	43623782	+	Intron	DEL	CCCTTCTTT	-	-	rs70993404		TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43623774_43623782delCCCTTCTTT	uc003ovw.1	+						RSPH9_uc003ovx.1_Intron	NM_152732	NP_689945	Q9H1X1	RSPH9_HUMAN	radial spoke head 9 homolog						cilium axoneme assembly|cilium movement	cytoplasm|cytoskeleton				upper_aerodigestive_tract(1)|skin(1)	2						tccttccttccccttctttcccttctttc	0.129									Kartagener_syndrome				4	2	---	---	---	---	
C6orf142	90523	broad.mit.edu	37	6	54119533	54119534	+	Intron	INS	-	CCTCC	CCTCC	rs75266768		TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:54119533_54119534insCCTCC	uc003pcg.3	+						C6orf142_uc003pch.3_Intron|C6orf142_uc011dxa.1_Intron	NM_138569	NP_612636	Q5VWP3	MLIP_HUMAN	hypothetical protein LOC90523							nuclear envelope|PML body	protein binding				0	Lung NSC(77;0.0317)					TCTTTTTTtttctccctccctt	0.282													6	3	---	---	---	---	
COL12A1	1303	broad.mit.edu	37	6	75798722	75798722	+	Intron	DEL	C	-	-	rs672648		TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:75798722delC	uc003phs.2	-						COL12A1_uc003pht.2_Intron	NM_004370	NP_004361	Q99715	COCA1_HUMAN	collagen, type XII, alpha 1 long isoform						cell adhesion|collagen fibril organization|skeletal system development	collagen type XII|extracellular space	extracellular matrix structural constituent conferring tensile strength			ovary(6)|large_intestine(1)|breast(1)|skin(1)	9						gtctcaaaaacaaaaaaaaga	0.184													9	5	---	---	---	---	
RARS2	57038	broad.mit.edu	37	6	88228193	88228194	+	Intron	INS	-	T	T	rs71554727		TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:88228193_88228194insT	uc003pme.2	-						RARS2_uc003pmb.2_Intron|RARS2_uc003pmc.2_Intron|RARS2_uc003pmd.2_Intron|RARS2_uc003pmf.2_Intron	NM_020320	NP_064716	Q5T160	SYRM_HUMAN	arginyl-tRNA synthetase 2, mitochondrial						arginyl-tRNA aminoacylation	mitochondrial matrix	arginine-tRNA ligase activity|ATP binding|protein binding			ovary(2)|central_nervous_system(1)	3		all_cancers(76;3.93e-06)|Acute lymphoblastic leukemia(125;3.55e-10)|Prostate(29;3.51e-09)|all_hematologic(105;3.29e-06)|all_epithelial(107;0.00575)		BRCA - Breast invasive adenocarcinoma(108;0.0456)		tgctcaataaatTTTTTTTTTT	0.208													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	91183095	91183098	+	IGR	DEL	TGTG	-	-			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:91183095_91183098delTGTG								BACH2 (176533 upstream) : MAP3K7 (42255 downstream)																							tgagcttctttgtgtgtgtgtgtg	0.000													3	3	---	---	---	---	
ARMC2	84071	broad.mit.edu	37	6	109232029	109232030	+	Intron	INS	-	TGTT	TGTT	rs147647034	by1000genomes	TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:109232029_109232030insTGTT	uc003pss.3	+						ARMC2_uc011eao.1_Intron	NM_032131	NP_115507	Q8NEN0	ARMC2_HUMAN	armadillo repeat containing 2								binding				0		all_cancers(87;1.14e-07)|Acute lymphoblastic leukemia(125;2.3e-10)|all_hematologic(75;3.3e-08)|all_epithelial(87;0.000111)|Colorectal(196;0.03)|all_lung(197;0.11)		Epithelial(106;0.000197)|BRCA - Breast invasive adenocarcinoma(108;0.000236)|all cancers(137;0.000279)|OV - Ovarian serous cystadenocarcinoma(136;0.00434)		TTAAAAATAGATGTGGTTTATT	0.282													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	137428490	137428491	+	IGR	DEL	TC	-	-			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:137428490_137428491delTC								IL20RA (62192 upstream) : IL22RA2 (36467 downstream)																							cctccttcTGtctctctctctc	0.104													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	166319503	166319503	+	Intron	DEL	C	-	-			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:166319503delC	uc003qup.1	-											Homo sapiens cDNA FLJ33369 fis, clone BRACE2005904.																		ttccttccttccctccctccc	0.040													4	2	---	---	---	---	
BMPER	168667	broad.mit.edu	37	7	33977125	33977126	+	Intron	INS	-	GTGT	GTGT			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:33977125_33977126insGTGT	uc011kap.1	+							NM_133468	NP_597725	Q8N8U9	BMPER_HUMAN	BMP-binding endothelial regulator precursor						blood vessel endothelial cell proliferation involved in sprouting angiogenesis|endothelial cell activation|negative regulation of BMP signaling pathway|positive regulation of ERK1 and ERK2 cascade|regulation of endothelial cell migration|regulation of pathway-restricted SMAD protein phosphorylation	extracellular space				ovary(2)|central_nervous_system(1)	3						GGAGAAGTAGGgtgtgtgtgtg	0.391													4	2	---	---	---	---	
C8orf41	80185	broad.mit.edu	37	8	33373121	33373121	+	5'Flank	DEL	C	-	-			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:33373121delC	uc003xjl.3	-						C8orf41_uc003xjk.3_5'Flank|C8orf41_uc010lvv.2_5'Flank|C8orf41_uc003xjm.3_5'Flank|C8orf41_uc003xjn.1_5'Flank	NM_025115	NP_079391	Q6NXR4	CH041_HUMAN	hypothetical protein LOC80185								binding				0				KIRC - Kidney renal clear cell carcinoma(67;0.0923)|Kidney(114;0.111)		ttccttccttccttccttctt	0.055													4	2	---	---	---	---	
TSNARE1	203062	broad.mit.edu	37	8	143337326	143337326	+	Intron	DEL	C	-	-			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:143337326delC	uc003ywk.2	-						TSNARE1_uc011lju.1_Intron|TSNARE1_uc003ywj.2_Intron	NM_145003	NP_659440	Q96NA8	TSNA1_HUMAN	t-SNARE domain containing 1						vesicle-mediated transport	integral to membrane					0	all_cancers(97;7.39e-11)|all_epithelial(106;8.98e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000332)|Ovarian(258;0.0315)|Acute lymphoblastic leukemia(118;0.155)					atcaccaccaccatcaccatc	0.000													4	2	---	---	---	---	
RCL1	10171	broad.mit.edu	37	9	4850493	4850494	+	Intron	INS	-	TT	TT	rs10974811		TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:4850493_4850494insTT	uc003zis.2	+						RCL1_uc003zit.2_Intron|RCL1_uc010mhk.1_Intron|RCL1_uc010mhl.1_Intron	NM_005772	NP_005763	Q9Y2P8	RCL1_HUMAN	RNA terminal phosphate cyclase-like 1						ribosome biogenesis|RNA processing	nucleolus	RNA-3'-phosphate cyclase activity				0	all_hematologic(13;0.137)	Acute lymphoblastic leukemia(23;0.0206)|Breast(48;0.147)		GBM - Glioblastoma multiforme(50;0.0244)		ttttttttttcttttttttttt	0.416													7	5	---	---	---	---	
HIATL2	84278	broad.mit.edu	37	9	99734982	99734982	+	Intron	DEL	A	-	-			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:99734982delA	uc004aws.2	-						HIATL2_uc004awr.1_Intron	NR_002894				RecName: Full=Hippocampus abundant transcript-like protein 2;												0						ACCACAATGGaaaaaaaaaaa	0.358													8	4	---	---	---	---	
C9orf5	23731	broad.mit.edu	37	9	111813111	111813112	+	Intron	INS	-	A	A			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:111813111_111813112insA	uc004bdt.3	-						C9orf5_uc004bds.3_Intron|C9orf5_uc004bdr.3_Intron	NM_032012	NP_114401	Q9H330	CI005_HUMAN	hypothetical protein LOC23731							integral to membrane				central_nervous_system(1)	1		Myeloproliferative disorder(63;0.204)		OV - Ovarian serous cystadenocarcinoma(323;3.08e-05)|STAD - Stomach adenocarcinoma(157;0.0823)		AAATGAAAATTAAAAAAAAAAA	0.272													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	130209778	130209778	+	IGR	DEL	A	-	-			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130209778delA								ZNF79 (2128 upstream) : RPL12 (177 downstream)																							actctgtctcaaaaaaaaaaa	0.209													8	5	---	---	---	---	
EXD3	54932	broad.mit.edu	37	9	140268130	140268132	+	Intron	DEL	TTT	-	-	rs66959515		TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140268130_140268132delTTT	uc004cmp.2	-						C9orf167_uc011mew.1_Intron|EXD3_uc010ncg.1_Intron|EXD3_uc004cmr.2_Intron|EXD3_uc004cms.2_Intron	NM_017820	NP_060290	Q8N9H8	MUT7_HUMAN	exonuclease 3'-5' domain containing 3						nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	intracellular	3'-5' exonuclease activity|nucleic acid binding				0						CGCAGAGAGGTTTTTTAAAATTT	0.571													5	3	---	---	---	---	
MLLT10	8028	broad.mit.edu	37	10	22006567	22006569	+	Intron	DEL	CTT	-	-			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:22006567_22006569delCTT	uc001iqs.2	+						MLLT10_uc001iqt.2_Intron|MLLT10_uc001iqv.2_Intron|MLLT10_uc001iqy.2_Intron|MLLT10_uc001ira.2_Intron|MLLT10_uc001irb.2_Intron	NM_004641	NP_004632	P55197	AF10_HUMAN	myeloid/lymphoid or mixed-lineage leukemia						positive regulation of transcription from RNA polymerase II promoter	cytoplasm|nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			lung(1)|skin(1)	2						cctcctcctccttttcctcctcc	0.000			T	MLL|PICALM|CDK6	AL								4	2	---	---	---	---	
YME1L1	10730	broad.mit.edu	37	10	27434230	27434231	+	Intron	INS	-	A	A	rs117799729		TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:27434230_27434231insA	uc001iti.2	-						YME1L1_uc001itj.2_Intron|YME1L1_uc010qdl.1_Intron|YME1L1_uc009xkv.2_Intron	NM_139312	NP_647473	Q96TA2	YMEL1_HUMAN	YME1-like 1 isoform 1						protein catabolic process|proteolysis	membrane|mitochondrion	ATP binding|metal ion binding|metalloendopeptidase activity|nucleoside-triphosphatase activity			ovary(1)	1						AAAAAAAAAACAAAAAAAAAAC	0.158													4	2	---	---	---	---	
FAR1	84188	broad.mit.edu	37	11	13749908	13749908	+	Intron	DEL	A	-	-			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:13749908delA	uc001mld.2	+							NM_032228	NP_115604	Q8WVX9	FACR1_HUMAN	fatty acyl CoA reductase 1						ether lipid biosynthetic process	integral to membrane|peroxisomal matrix|peroxisomal membrane	protein binding			ovary(1)|skin(1)	2						TAAAGATGTCAAAAAAAAAGT	0.358													4	4	---	---	---	---	
GDPD5	81544	broad.mit.edu	37	11	75152589	75152590	+	Intron	DEL	GT	-	-	rs34643232		TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:75152589_75152590delGT	uc001owo.3	-						GDPD5_uc001owp.3_Intron|GDPD5_uc001own.3_Intron|GDPD5_uc009yuc.2_Intron|GDPD5_uc009yud.2_Intron	NM_030792	NP_110419	Q8WTR4	GDPD5_HUMAN	glycerophosphodiester phosphodiesterase domain						glycerol metabolic process|lipid metabolic process|nervous system development	endomembrane system|growth cone|integral to membrane|perinuclear region of cytoplasm	glycerophosphodiester phosphodiesterase activity			ovary(1)	1						CTGCCCGACCgtgtgtgtgtgt	0.569													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	98001221	98001222	+	IGR	INS	-	A	A	rs140908201	by1000genomes	TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:98001221_98001222insA								None (None upstream) : CNTN5 (890649 downstream)																							GGCTTTCCTACAAAAAACATAG	0.381													4	3	---	---	---	---	
CNTN5	53942	broad.mit.edu	37	11	99072131	99072133	+	Intron	DEL	CTT	-	-			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:99072131_99072133delCTT	uc001pga.2	+						CNTN5_uc009ywv.1_Intron|CNTN5_uc001pfz.2_Intron|CNTN5_uc001pgb.2_Intron	NM_014361	NP_055176	O94779	CNTN5_HUMAN	contactin 5 isoform long						cell adhesion	anchored to membrane|plasma membrane	protein binding			skin(3)|ovary(2)|pancreas(2)|breast(1)	8		all_hematologic(158;1.22e-05)|Acute lymphoblastic leukemia(157;3.81e-05)|Melanoma(852;0.219)		BRCA - Breast invasive adenocarcinoma(274;0.00146)|KIRC - Kidney renal clear cell carcinoma(183;0.156)|Kidney(183;0.196)		ccttccttcccttctttcttcct	0.059													6	4	---	---	---	---	
CNTN5	53942	broad.mit.edu	37	11	99200993	99200996	+	Intron	DEL	AGAC	-	-			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:99200993_99200996delAGAC	uc001pga.2	+						CNTN5_uc009ywv.1_Intron|CNTN5_uc001pfz.2_Intron|CNTN5_uc001pgb.2_Intron	NM_014361	NP_055176	O94779	CNTN5_HUMAN	contactin 5 isoform long						cell adhesion	anchored to membrane|plasma membrane	protein binding			skin(3)|ovary(2)|pancreas(2)|breast(1)	8		all_hematologic(158;1.22e-05)|Acute lymphoblastic leukemia(157;3.81e-05)|Melanoma(852;0.219)		BRCA - Breast invasive adenocarcinoma(274;0.00146)|KIRC - Kidney renal clear cell carcinoma(183;0.156)|Kidney(183;0.196)		ggaaggagagagacagagtaaggg	0.132													7	4	---	---	---	---	
NTM	50863	broad.mit.edu	37	11	131982613	131982614	+	Intron	DEL	AC	-	-	rs113888941		TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:131982613_131982614delAC	uc001qgp.2	+						NTM_uc001qgm.2_Intron|NTM_uc010sch.1_Intron|NTM_uc010sci.1_Intron|NTM_uc010scj.1_Intron|NTM_uc001qgo.2_Intron|NTM_uc001qgq.2_Intron	NM_016522	NP_057606	Q9P121	NTRI_HUMAN	neurotrimin isoform 1						cell adhesion|neuron recognition	anchored to membrane|plasma membrane				ovary(4)|central_nervous_system(1)|skin(1)	6						CTGcacacttacacacacacac	0.396													4	2	---	---	---	---	
JAM3	83700	broad.mit.edu	37	11	134018851	134018852	+	Intron	DEL	AC	-	-	rs111255782		TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:134018851_134018852delAC	uc001qhb.1	+						JAM3_uc009zcz.1_Intron	NM_032801	NP_116190	Q9BX67	JAM3_HUMAN	junctional adhesion molecule 3 precursor						angiogenesis|blood coagulation|regulation of neutrophil chemotaxis	cell-cell contact zone|desmosome|extracellular space|integral to membrane	integrin binding			ovary(1)	1	all_hematologic(175;0.127)	all_cancers(12;1.06e-21)|all_epithelial(12;3.37e-16)|all_lung(97;7.03e-06)|Lung NSC(97;1.67e-05)|Breast(109;0.000182)|Medulloblastoma(222;0.0245)|all_neural(223;0.0506)|Esophageal squamous(93;0.0566)		Epithelial(10;1.55e-09)|BRCA - Breast invasive adenocarcinoma(10;1.35e-08)|all cancers(11;2.81e-08)|OV - Ovarian serous cystadenocarcinoma(99;0.00402)|Lung(977;0.245)		CTTCACAGTAacacacacacac	0.371													3	4	---	---	---	---	
C12orf59	120939	broad.mit.edu	37	12	10341149	10341150	+	Intron	INS	-	GAAAAC	GAAAAC	rs138907777	by1000genomes	TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:10341149_10341150insGAAAAC	uc001qxr.2	+						C12orf59_uc001qxq.2_Intron			Q4KMG9	CL059_HUMAN	RecName: Full=Uncharacterized protein C12orf59; Flags: Precursor;							integral to membrane				ovary(1)	1						aagaagaaaaagaaaaagaaaa	0.020													4	2	---	---	---	---	
PLXNC1	10154	broad.mit.edu	37	12	94653675	94653676	+	Intron	INS	-	A	A	rs67260160		TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:94653675_94653676insA	uc001tdc.2	+						PLXNC1_uc010sut.1_Intron|PLXNC1_uc009zsv.2_5'Flank	NM_005761	NP_005752	O60486	PLXC1_HUMAN	plexin C1 precursor						axon guidance|cell adhesion	integral to membrane|intracellular|plasma membrane	receptor activity|receptor binding			ovary(2)|central_nervous_system(1)	3						cttgtctctacaaaaaaaaaaa	0.158													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	98614903	98614904	+	IGR	INS	-	ACAA	ACAA	rs146367999	by1000genomes	TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:98614903_98614904insACAA								RMST (656110 upstream) : LOC100128191 (291849 downstream)																							cacacacacacacacacacaca	0.302													4	2	---	---	---	---	
SLC7A7	9056	broad.mit.edu	37	14	23244438	23244442	+	Intron	DEL	CTTAT	-	-	rs71421155		TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23244438_23244442delCTTAT	uc001wgr.3	-						SLC7A7_uc001wgs.3_Intron|SLC7A7_uc001wgt.3_Intron|SLC7A7_uc001wgu.3_Intron|SLC7A7_uc001wgv.3_Intron	NM_003982	NP_003973	Q9UM01	YLAT1_HUMAN	solute carrier family 7 member 7						blood coagulation|cellular amino acid metabolic process|ion transport|leukocyte migration|protein complex assembly	basolateral plasma membrane|integral to plasma membrane	amino acid transmembrane transporter activity			ovary(1)|breast(1)	2	all_cancers(95;8.44e-05)			GBM - Glioblastoma multiforme(265;0.00741)		TACTTTTTGCCTTATCTTAGAGCAG	0.429													3	3	---	---	---	---	
MDGA2	161357	broad.mit.edu	37	14	47314874	47314874	+	Intron	DEL	T	-	-			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:47314874delT	uc001wwj.3	-						MDGA2_uc001wwh.3_Intron|MDGA2_uc001wwi.3_Intron	NM_001113498	NP_001106970	Q7Z553	MDGA2_HUMAN	MAM domain containing 1 isoform 1						spinal cord motor neuron differentiation	anchored to membrane|plasma membrane				ovary(4)|large_intestine(1)|pancreas(1)	6						CAACTAAAAATAACTCCGttt	0.219													3	4	---	---	---	---	
C14orf102	55051	broad.mit.edu	37	14	90784177	90784178	+	Intron	INS	-	A	A	rs148485591	by1000genomes	TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:90784177_90784178insA	uc001xyi.1	-						C14orf102_uc001xyj.1_Intron	NM_017970	NP_060440	Q9H7Z3	CN102_HUMAN	hypothetical protein LOC55051 isoform 1								protein binding			ovary(2)|lung(1)	3		all_cancers(154;0.118)		COAD - Colon adenocarcinoma(157;0.218)		GCAAAGCAAAGAAAAAAAAAAG	0.351													3	3	---	---	---	---	
WARS	7453	broad.mit.edu	37	14	100833386	100833386	+	Intron	DEL	A	-	-			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:100833386delA	uc001yhf.1	-						WARS_uc001yhg.1_Intron|WARS_uc001yhh.1_Intron|WARS_uc001yhi.1_Intron|WARS_uc001yhj.1_Intron|WARS_uc001yhk.1_Intron|WARS_uc001yhl.1_Intron|WARS_uc010twz.1_Intron	NM_173701	NP_776049	P23381	SYWC_HUMAN	tryptophanyl-tRNA synthetase isoform a						angiogenesis|negative regulation of cell proliferation|regulation of angiogenesis|tryptophanyl-tRNA aminoacylation	cytosol|soluble fraction	ATP binding|protein binding|tryptophan-tRNA ligase activity			breast(1)	1		all_cancers(154;0.00223)|all_lung(585;2.48e-06)|all_epithelial(191;0.000564)|Melanoma(154;0.152)			L-Tryptophan(DB00150)	AAATAAGAttaaaaaaaaaaa	0.055													4	2	---	---	---	---	
FAM189A1	23359	broad.mit.edu	37	15	29846519	29846519	+	Intron	DEL	A	-	-			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:29846519delA	uc010azk.1	-							NM_015307	NP_056122	O60320	F1891_HUMAN	hypothetical protein LOC23359							integral to membrane					0						actccgtctcaaaaaaaaaaa	0.000													4	2	---	---	---	---	
BNIP2	663	broad.mit.edu	37	15	59972354	59972354	+	Intron	DEL	T	-	-			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:59972354delT	uc010uhc.1	-						BNIP2_uc010uhb.1_Intron	NM_004330	NP_004321	Q12982	BNIP2_HUMAN	BCL2/adenovirus E1B 19kD interacting protein 2						anti-apoptosis|apoptosis|positive regulation of muscle cell differentiation	nuclear envelope|perinuclear region of cytoplasm	calcium ion binding|GTPase activator activity|protein binding			ovary(1)	1						AAAACTCAAGTTTTTTTTTTT	0.299													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	15021948	15021948	+	Intron	DEL	C	-	-			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:15021948delC	uc010uzk.1	+						NPIP_uc002dcx.3_Intron					SubName: Full=cDNA FLJ57488, highly similar to Polycystin-1;																		cctctcctctccccccttttc	0.134													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	87255723	87255725	+	Intron	DEL	CAC	-	-			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:87255723_87255725delCAC	uc002fjt.1	-											Homo sapiens cDNA FLJ43761 fis, clone TESTI2048109.																		ccaccaccatcaccaccaccacc	0.000													4	3	---	---	---	---	
SERPINF2	5345	broad.mit.edu	37	17	1657979	1657979	+	3'UTR	DEL	T	-	-	rs147557405	by1000genomes	TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1657979delT	uc002ftk.1	+	10					SERPINF2_uc010vqr.1_3'UTR	NM_000934	NP_000925	P08697	A2AP_HUMAN	alpha-2-antiplasmin isoform a precursor						acute-phase response|fibrinolysis|platelet activation|platelet degranulation|regulation of proteolysis	extracellular space|platelet alpha granule lumen	protease binding|serine-type endopeptidase inhibitor activity				0				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)	Streptokinase(DB00086)	GAGTTTAGGGTGGGGGGGGGG	0.647													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	5620718	5620724	+	IGR	DEL	TCTTTCC	-	-	rs60705446	by1000genomes	TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:5620718_5620724delTCTTTCC								NLRP1 (132886 upstream) : WSCD1 (351713 downstream)																							cttccttccttctttcctccttccttc	0.000													3	4	---	---	---	---	
TBC1D3	729873	broad.mit.edu	37	17	36361540	36361541	+	Intron	INS	-	A	A			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:36361540_36361541insA	uc010wdn.1	-									Q8IZP1	TBC3A_HUMAN	Homo sapiens TBC1D3 mRNA for TBC1 domain family, member 3, complete cds.							intracellular	Rab GTPase activator activity				0	Breast(7;2.97e-12)	Breast(25;0.102)|Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		aaaaAAGAAAGAAAAAGAGGCT	0.035													5	3	---	---	---	---	
RPTOR	57521	broad.mit.edu	37	17	78674482	78674483	+	Intron	INS	-	TGA	TGA			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:78674482_78674483insTGA	uc002jyt.1	+						RPTOR_uc002jys.2_Intron|RPTOR_uc010wuf.1_Intron|RPTOR_uc010wug.1_Intron	NM_020761	NP_065812	Q8N122	RPTOR_HUMAN	raptor isoform 1						cell cycle arrest|cell growth|cellular response to amino acid stimulus|cellular response to nutrient levels|insulin receptor signaling pathway|positive regulation of protein serine/threonine kinase activity|positive regulation of TOR signaling cascade|TOR signaling cascade	cytosol|lysosome|TORC1 complex	protein complex binding			lung(4)|urinary_tract(1)|ovary(1)	6						gatgatggaggtggtggtgatg	0.000													6	5	---	---	---	---	
CCDC57	284001	broad.mit.edu	37	17	80141902	80141911	+	Intron	DEL	CGCGCGCACA	-	-	rs72278140	by1000genomes	TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80141902_80141911delCGCGCGCACA	uc002kdz.1	-						CCDC57_uc002kdx.1_Intron|CCDC57_uc010dik.1_Intron	NM_198082	NP_932348	Q2TAC2	CCD57_HUMAN	coiled-coil domain containing 57											ovary(2)	2	Breast(20;0.00285)|all_neural(118;0.0878)|all_lung(278;0.0949)|Lung NSC(278;0.128)|Ovarian(332;0.227)		BRCA - Breast invasive adenocarcinoma(99;0.0232)|OV - Ovarian serous cystadenocarcinoma(97;0.0253)			TGCGCGCGCGCGCGCGcacacacacacaca	0.386													9	6	---	---	---	---	
DLGAP1	9229	broad.mit.edu	37	18	3740991	3740991	+	Intron	DEL	C	-	-			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:3740991delC	uc002kmf.2	-						DLGAP1_uc010wyz.1_Intron|DLGAP1_uc002kme.1_Intron|DLGAP1_uc010dkn.2_Intron|DLGAP1_uc010wyw.1_Intron|DLGAP1_uc010wyx.1_Intron|DLGAP1_uc010wyy.1_Intron|DLGAP1_uc002kmg.2_Intron|DLGAP1_uc002kmk.2_Intron	NM_004746	NP_004737	O14490	DLGP1_HUMAN	discs large homolog-associated protein 1 isoform						synaptic transmission	cell junction|postsynaptic density|postsynaptic membrane				ovary(2)|pancreas(1)|skin(1)	4		Colorectal(8;0.0257)				accaccaccaccatcacctca	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	23569461	23569462	+	IGR	INS	-	AAGG	AAGG	rs72480940		TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:23569461_23569462insAAGG								ZNF521 (637247 upstream) : SS18 (26757 downstream)																							GTGAGACTCgaaaggaaggaag	0.129													4	5	---	---	---	---	
EMR3	84658	broad.mit.edu	37	19	14762192	14762192	+	Intron	DEL	A	-	-			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14762192delA	uc002mzi.3	-						EMR3_uc010dzp.2_Intron|EMR3_uc010xnv.1_Intron	NM_032571	NP_115960	Q9BY15	EMR3_HUMAN	egf-like module-containing mucin-like receptor						neuropeptide signaling pathway	extracellular space|integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity			ovary(5)|skin(1)	6						tgctgcctctaaaaaaaaaaT	0.025													5	3	---	---	---	---	
MLL4	9757	broad.mit.edu	37	19	36224005	36224006	+	Frame_Shift_Ins	INS	-	C	C	rs147972814	by1000genomes	TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36224005_36224006insC	uc010eei.2	+	29	6555_6556	c.6555_6556insC	c.(6553-6558)AAACCCfs	p.K2185fs		NM_014727	NP_055542	Q9UMN6	MLL4_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 4	2185_2186					chromatin-mediated maintenance of transcription		DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			central_nervous_system(6)|breast(2)|ovary(1)|kidney(1)|skin(1)	11	all_lung(56;3.33e-07)|Lung NSC(56;5.02e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			AGCCCCCCAAACCCGCCACATC	0.629													7	4	---	---	---	---	
RNF24	11237	broad.mit.edu	37	20	3928693	3928694	+	Intron	INS	-	A	A			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3928693_3928694insA	uc002wkh.2	-						RNF24_uc002wki.2_Intron|RNF24_uc002wkj.2_Intron	NM_007219	NP_009150	Q9Y225	RNF24_HUMAN	ring finger protein 24 isoform 1							Golgi membrane|integral to membrane	zinc ion binding				0						aactccgtctcaaaaaaaaaaa	0.109													4	2	---	---	---	---	
SLC9A8	23315	broad.mit.edu	37	20	48494743	48494743	+	Intron	DEL	A	-	-			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:48494743delA	uc002xuv.1	+						SLC9A8_uc010zym.1_Intron|SLC9A8_uc010gic.2_Intron|SLC9A8_uc010gid.2_Intron	NM_015266	NP_056081	Q9Y2E8	SL9A8_HUMAN	sodium/hydrogen exchanger 8							Golgi membrane|integral to membrane	sodium:hydrogen antiporter activity			ovary(1)	1			BRCA - Breast invasive adenocarcinoma(9;3.91e-07)			TTCTTTTGTTAAAAAAAAAAA	0.303													4	2	---	---	---	---	
TPTE	7179	broad.mit.edu	37	21	10996309	10996310	+	Intron	INS	-	AAA	AAA	rs114636497		TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10996309_10996310insAAA	uc002yis.1	-									P56180	TPTE_HUMAN	Homo sapiens putative tyrosine phosphatase mRNA, complete cds.						signal transduction	integral to membrane	ion channel activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			ovary(2)|lung(1)|breast(1)|skin(1)	5			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		TAAAAACAACCAAAAAAAAAAA	0.302													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	20150779	20150781	+	IGR	DEL	ACC	-	-			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:20150779_20150781delACC								ZDHHC8 (15250 upstream) : LOC150197 (43074 downstream)																							caccatcactaccaccaccacca	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	20151841	20151842	+	IGR	INS	-	CAC	CAC	rs10627070		TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:20151841_20151842insCAC								ZDHHC8 (16312 upstream) : LOC150197 (42013 downstream)																							accaccaccatcaccaccacca	0.025													4	2	---	---	---	---	
GGT1	2678	broad.mit.edu	37	22	25016158	25016159	+	Intron	INS	-	AA	AA	rs9612679		TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:25016158_25016159insAA	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)	actcaaaaaagaaaaaaaaaaa	0.248													4	2	---	---	---	---	
NUP50	10762	broad.mit.edu	37	22	45577017	45577019	+	Intron	DEL	CCC	-	-	rs66468525		TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:45577017_45577019delCCC	uc003bfr.2	+						NUP50_uc003bfs.2_Intron|NUP50_uc011aqn.1_Intron|NUP50_uc003bft.2_Intron|NUP50_uc011aqo.1_Intron	NM_007172	NP_009103	Q9UKX7	NUP50_HUMAN	nucleoporin 50kDa isoform b						carbohydrate metabolic process|glucose transport|intracellular transport|mRNA transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	nuclear membrane|nuclear pore|nucleoplasm	protein binding				0		Ovarian(80;0.00965)|all_neural(38;0.0244)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0178)		CTTCTGGCATCCCCCCCCCCCCC	0.404													3	3	---	---	---	---	
IL3RA	3563	broad.mit.edu	37	X	1467599	1467600	+	Intron	INS	-	TTTC	TTTC			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:1467599_1467600insTTTC	uc004cps.2	+						IL3RA_uc011mhd.1_Intron	NM_002183	NP_002174	P26951	IL3RA_HUMAN	interleukin 3 receptor, alpha precursor							integral to membrane|plasma membrane	interleukin-3 receptor activity			skin(2)|lung(1)	3		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)			Sargramostim(DB00020)	ctttctttctgtttctgtttct	0.045													4	2	---	---	---	---	
WWC3	55841	broad.mit.edu	37	X	10109659	10109659	+	3'UTR	DEL	A	-	-			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:10109659delA	uc004csx.3	+	23					WWC3_uc010nds.2_3'UTR|WWC3_uc010ndt.2_RNA	NM_015691	NP_056506	Q9ULE0	WWC3_HUMAN	WWC family member 3											ovary(4)	4						CACATTTTGTAAAAAAAAAAA	0.279													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	9368302	9368303	+	IGR	DEL	TG	-	-			TCGA-B0-5088-01A-01D-1462-08	TCGA-B0-5088-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:9368302_9368303delTG								TSPY1 (20913 upstream) : RBMY3AP (80027 downstream)																							ACTCtgtgtctgtgtgtgtgtg	0.262													4	3	---	---	---	---	
