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
C1orf122	127687	broad.mit.edu	37	1	38272663	38272663	+	5'UTR	SNP	G	A	A			TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:38272663G>A	uc001ccb.1	+	1					YRDC_uc001cca.1_Intron			Q6ZSJ8	CA122_HUMAN	SubName: Full=Chromosome 1 open reading frame 122;												0	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0393)				AAGGCAAGGGGAAAGGGATCA	0.483													14	49	---	---	---	---	PASS
POMGNT1	55624	broad.mit.edu	37	1	46656513	46656513	+	Intron	SNP	T	C	C			TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:46656513T>C	uc001cpe.2	-						POMGNT1_uc010olx.1_Intron|POMGNT1_uc010oly.1_Intron|POMGNT1_uc010olz.1_Intron|POMGNT1_uc001cpg.2_Intron|POMGNT1_uc001cpf.2_Intron|POMGNT1_uc001cph.1_3'UTR|POMGNT1_uc001cpi.1_3'UTR	NM_017739	NP_060209	Q8WZA1	PMGT1_HUMAN	O-linked mannose						protein N-linked glycosylation|protein O-linked glycosylation	Golgi membrane|integral to membrane|microsome	alpha-1,3-mannosylglycoprotein 2-beta-N-acetylglucosaminyltransferase activity|beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,3-N-acetylglucosaminyltransferase activity			ovary(1)	1	Acute lymphoblastic leukemia(166;0.155)					CCACACCCACTTGCTGACCAG	0.493													4	24	---	---	---	---	PASS
CHIA	27159	broad.mit.edu	37	1	111857933	111857933	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:111857933T>C	uc001eas.2	+	6	459	c.356T>C	c.(355-357)TTC>TCC	p.F119S	CHIA_uc001ear.2_Missense_Mutation_p.F11S|CHIA_uc001eaq.2_Missense_Mutation_p.F11S|CHIA_uc009wgc.2_Missense_Mutation_p.F11S|CHIA_uc001eat.2_Intron|CHIA_uc001eav.2_5'UTR|CHIA_uc001eau.2_Intron|CHIA_uc009wgd.2_Intron	NM_201653	NP_970615	Q9BZP6	CHIA_HUMAN	acidic chitinase isoform c	119					apoptosis|cell wall chitin metabolic process|chitin catabolic process|digestion|immune response|positive regulation of chemokine secretion|production of molecular mediator involved in inflammatory response|response to acid|response to fungus	cytoplasm|extracellular space	cation binding|chitin binding|chitinase activity|kinase binding|lysozyme activity|sugar binding			ovary(1)	1		all_cancers(81;3.23e-05)|all_epithelial(167;1.2e-05)|all_lung(203;0.000154)|Lung NSC(277;0.000304)		Colorectal(144;0.0115)|Lung(183;0.0292)|COAD - Colon adenocarcinoma(174;0.0314)|all cancers(265;0.0477)|Epithelial(280;0.0918)|LUSC - Lung squamous cell carcinoma(189;0.154)		CGCCAGACTTTCATCACCTCA	0.542													9	134	---	---	---	---	PASS
ST7L	54879	broad.mit.edu	37	1	113124710	113124710	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:113124710G>A	uc001ecd.2	-	9	1278	c.973C>T	c.(973-975)CCT>TCT	p.P325S	ST7L_uc009wgh.2_Intron|ST7L_uc001ecc.2_Missense_Mutation_p.P142S|ST7L_uc010owg.1_Missense_Mutation_p.P260S|ST7L_uc010owh.1_Intron|ST7L_uc001ece.2_Missense_Mutation_p.P325S|ST7L_uc001ecf.2_Missense_Mutation_p.P308S|ST7L_uc001ecg.2_RNA|ST7L_uc010owi.1_Missense_Mutation_p.P260S|ST7L_uc001ech.2_Missense_Mutation_p.P308S|ST7L_uc001eci.2_Missense_Mutation_p.P325S|ST7L_uc009wgi.1_RNA|ST7L_uc010owj.1_Missense_Mutation_p.P308S	NM_017744	NP_060214	Q8TDW4	ST7L_HUMAN	suppression of tumorigenicity 7-like isoform 1	325					negative regulation of cell growth	integral to membrane	binding				0	Lung SC(450;0.246)	all_cancers(81;1.44e-07)|all_epithelial(167;7.64e-07)|all_lung(203;2.16e-05)|Lung NSC(69;3.86e-05)		Lung(183;0.0234)|all cancers(265;0.0246)|Epithelial(280;0.0342)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		ATGGTAAGAGGAGGAAATTCT	0.333													9	61	---	---	---	---	PASS
ST7L	54879	broad.mit.edu	37	1	113124711	113124711	+	Silent	SNP	A	T	T			TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:113124711A>T	uc001ecd.2	-	9	1277	c.972T>A	c.(970-972)CCT>CCA	p.P324P	ST7L_uc009wgh.2_Intron|ST7L_uc001ecc.2_Silent_p.P141P|ST7L_uc010owg.1_Silent_p.P259P|ST7L_uc010owh.1_Intron|ST7L_uc001ece.2_Silent_p.P324P|ST7L_uc001ecf.2_Silent_p.P307P|ST7L_uc001ecg.2_RNA|ST7L_uc010owi.1_Silent_p.P259P|ST7L_uc001ech.2_Silent_p.P307P|ST7L_uc001eci.2_Silent_p.P324P|ST7L_uc009wgi.1_RNA|ST7L_uc010owj.1_Silent_p.P307P	NM_017744	NP_060214	Q8TDW4	ST7L_HUMAN	suppression of tumorigenicity 7-like isoform 1	324					negative regulation of cell growth	integral to membrane	binding				0	Lung SC(450;0.246)	all_cancers(81;1.44e-07)|all_epithelial(167;7.64e-07)|all_lung(203;2.16e-05)|Lung NSC(69;3.86e-05)		Lung(183;0.0234)|all cancers(265;0.0246)|Epithelial(280;0.0342)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		TGGTAAGAGGAGGAAATTCTT	0.338													8	60	---	---	---	---	PASS
DCLRE1B	64858	broad.mit.edu	37	1	114454408	114454408	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:114454408G>C	uc001eeg.2	+	4	1365	c.1194G>C	c.(1192-1194)AAG>AAC	p.K398N	DCLRE1B_uc001eeh.2_Missense_Mutation_p.K272N|DCLRE1B_uc001eei.2_Missense_Mutation_p.K272N	NM_022836	NP_073747	Q9H816	DCR1B_HUMAN	DNA cross-link repair 1B (PSO2 homolog, S.	398					cell cycle checkpoint|DNA repair|protection from non-homologous end joining at telomere|telomeric 3' overhang formation|telomeric loop formation	centrosome|chromosome, telomeric region|nucleus	5'-3' exonuclease activity|protein binding				0	Lung SC(450;0.184)	all_cancers(81;1.46e-05)|all_epithelial(167;2.42e-05)|all_lung(203;0.000353)|Lung NSC(69;0.000518)		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)		GGATCAAGAAGCAGTTGTTCC	0.488								Direct_reversal_of_damage|Other_identified_genes_with_known_or_suspected_DNA_repair_function					50	167	---	---	---	---	PASS
FCRL1	115350	broad.mit.edu	37	1	157789883	157789883	+	Translation_Start_Site	SNP	C	T	T			TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:157789883C>T	uc001frg.2	-	1	58	c.-55G>A	c.(-57--53)AGGTG>AGATG		FCRL1_uc001frh.2_Translation_Start_Site|FCRL1_uc001fri.2_Translation_Start_Site|FCRL1_uc001frj.2_RNA	NM_052938	NP_443170	Q96LA6	FCRL1_HUMAN	Fc receptor-like 1 isoform 1 precursor							integral to membrane|plasma membrane	receptor activity			skin(4)|ovary(3)	7	all_hematologic(112;0.0378)		LUSC - Lung squamous cell carcinoma(543;0.24)			AAAGAATGCACCTCAGAGTCG	0.502													3	33	---	---	---	---	PASS
OR10K2	391107	broad.mit.edu	37	1	158390417	158390417	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158390417C>A	uc010pii.1	-	1	240	c.240G>T	c.(238-240)AAG>AAT	p.K80N		NM_001004476	NP_001004476	Q6IF99	O10K2_HUMAN	olfactory receptor, family 10, subfamily K,	80	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			pancreas(1)	1	all_hematologic(112;0.0378)					CAACCAGCATCTTGGGTACAA	0.498													17	154	---	---	---	---	PASS
FAM5C	339479	broad.mit.edu	37	1	190068174	190068174	+	Silent	SNP	C	T	T			TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:190068174C>T	uc001gse.1	-	8	1507	c.1275G>A	c.(1273-1275)TCG>TCA	p.S425S	FAM5C_uc010pot.1_Silent_p.S323S	NM_199051	NP_950252	Q76B58	FAM5C_HUMAN	family with sequence similarity 5, member C	425						extracellular region				lung(2)|ovary(1)|kidney(1)|skin(1)	5	Prostate(682;0.198)					GACACGTGCACGAGTGCGTCT	0.567													14	46	---	---	---	---	PASS
OPTC	26254	broad.mit.edu	37	1	203465310	203465310	+	Silent	SNP	C	T	T			TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:203465310C>T	uc001gzu.1	+	2	293	c.177C>T	c.(175-177)GTC>GTT	p.V59V		NM_014359	NP_055174	Q9UBM4	OPT_HUMAN	opticin precursor	59						proteinaceous extracellular matrix	extracellular matrix structural constituent|protein binding				0			BRCA - Breast invasive adenocarcinoma(75;0.109)			ATGGTGAAGTCATTGACCTGA	0.527													4	58	---	---	---	---	PASS
IARS2	55699	broad.mit.edu	37	1	220318982	220318982	+	Silent	SNP	C	T	T			TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:220318982C>T	uc001hmc.2	+	22	2987	c.2883C>T	c.(2881-2883)CTC>CTT	p.L961L	IARS2_uc001hmd.2_Silent_p.L297L	NM_018060	NP_060530	Q9NSE4	SYIM_HUMAN	mitochondrial isoleucine tRNA synthetase	961					isoleucyl-tRNA aminoacylation	mitochondrial matrix	ATP binding|isoleucine-tRNA ligase activity			ovary(2)|skin(2)	4				GBM - Glioblastoma multiforme(131;0.0554)	L-Isoleucine(DB00167)	GGAAATTCCTCATCAACTTAG	0.388													7	36	---	---	---	---	PASS
PRSS38	339501	broad.mit.edu	37	1	228004909	228004909	+	Splice_Site	SNP	G	T	T			TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:228004909G>T	uc001hrh.2	+	3	312	c.312_splice	c.e3-1	p.R104_splice		NM_183062	NP_898885	A1L453	PRS38_HUMAN	marapsin 2 precursor						proteolysis	extracellular region	serine-type endopeptidase activity			ovary(1)|pancreas(1)	2						CACCCCCACAGGGACAAGAAT	0.582													9	91	---	---	---	---	PASS
ASB3	51130	broad.mit.edu	37	2	53941688	53941688	+	Silent	SNP	G	A	A			TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:53941688G>A	uc002rxg.1	-	7	948	c.813C>T	c.(811-813)AAC>AAT	p.N271N	ASB3_uc002rxh.1_Silent_p.N198N|ASB3_uc002rxi.3_Silent_p.N309N|ASB3_uc010yoo.1_Silent_p.N188N	NM_016115	NP_057199	Q9Y575	ASB3_HUMAN	ankyrin repeat and SOCS box-containing protein 3	271	ANK 8.				intracellular signal transduction					ovary(1)|kidney(1)	2			Lung(47;0.125)|LUSC - Lung squamous cell carcinoma(58;0.181)			CACAGGCCCGGTTAGTAAGTG	0.388													8	161	---	---	---	---	PASS
MTHFD2	10797	broad.mit.edu	37	2	74438783	74438783	+	Intron	SNP	G	A	A			TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:74438783G>A	uc002skk.2	+						SLC4A5_uc002skl.2_RNA|MTHFD2_uc002skj.2_Intron|MTHFD2_uc010yro.1_Intron|MTHFD2_uc010ffb.2_Intron|MTHFD2_uc010yrp.1_Intron	NM_006636	NP_006627	P13995	MTDC_HUMAN	methylenetetrahydrofolate dehydrogenase 2						folic acid-containing compound biosynthetic process|one-carbon metabolic process|tetrahydrofolate metabolic process	mitochondrion	magnesium ion binding|methenyltetrahydrofolate cyclohydrolase activity|methylenetetrahydrofolate dehydrogenase (NAD+) activity|methylenetetrahydrofolate dehydrogenase (NADP+) activity|phosphate binding|protein binding				0					NADH(DB00157)|Tetrahydrofolic acid(DB00116)	AGTTCTTCAGGGTCTCTTGAA	0.303													4	33	---	---	---	---	PASS
CTNNA2	1496	broad.mit.edu	37	2	80782891	80782891	+	Silent	SNP	G	T	T			TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:80782891G>T	uc010ysh.1	+	11	1619	c.1614G>T	c.(1612-1614)CGG>CGT	p.R538R	CTNNA2_uc010yse.1_Silent_p.R538R|CTNNA2_uc010ysf.1_Silent_p.R538R|CTNNA2_uc010ysg.1_Silent_p.R538R|CTNNA2_uc010ysi.1_Silent_p.R170R	NM_004389	NP_004380	P26232	CTNA2_HUMAN	catenin, alpha 2 isoform 1	538					axonogenesis|brain morphogenesis|cell-cell adhesion|dendrite morphogenesis|muscle cell differentiation|positive regulation of muscle cell differentiation|prepulse inhibition|radial glia guided migration of Purkinje cell|regulation of synapse structural plasticity	actin cytoskeleton|axon|cytosol	cadherin binding|structural constituent of cytoskeleton			pancreas(4)|lung(3)|breast(1)|skin(1)	9						CTCTGGACCGGACTGCAGGGG	0.507													13	105	---	---	---	---	PASS
DNAH6	1768	broad.mit.edu	37	2	84780110	84780110	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:84780110G>C	uc010fgb.2	+	10	1691	c.1554G>C	c.(1552-1554)ATG>ATC	p.M518I	DNAH6_uc002soo.2_Missense_Mutation_p.M97I|DNAH6_uc002sop.2_Missense_Mutation_p.M97I	NM_001370	NP_001361	Q9C0G6	DYH6_HUMAN	dynein, axonemal, heavy polypeptide 6	518	Stem (By similarity).				microtubule-based movement	cilium axoneme|cytoplasm|dynein complex|microtubule	ATP binding|ATPase activity|microtubule motor activity			central_nervous_system(1)	1						CAGAACTAATGTTGACAGTCC	0.393													26	131	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	2	89161488	89161488	+	RNA	SNP	G	A	A			TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:89161488G>A	uc010ytr.1	-	198		c.9002C>T			uc002sti.1_5'Flank|uc002stj.1_RNA					Parts of antibodies, mostly variable regions.																		CTCACCAAAGGGGAACAGAGT	0.493													8	45	---	---	---	---	PASS
PROC	5624	broad.mit.edu	37	2	128185973	128185973	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:128185973C>A	uc002tok.2	+	9	910	c.837C>A	c.(835-837)GAC>GAA	p.D279E	PROC_uc002tol.2_Missense_Mutation_p.D300E|PROC_uc010yzi.1_Missense_Mutation_p.D335E|PROC_uc010yzj.1_Missense_Mutation_p.D174E|PROC_uc010yzk.1_Missense_Mutation_p.D334E|PROC_uc002tom.2_Missense_Mutation_p.D313E	NM_000312	NP_000303	P04070	PROC_HUMAN	protein C	279	Peptidase S1.				blood coagulation|leukocyte migration|negative regulation of apoptosis|negative regulation of blood coagulation|peptidyl-glutamic acid carboxylation|post-translational protein modification|proteolysis	endoplasmic reticulum lumen|Golgi lumen|plasma membrane	calcium ion binding|protein binding|serine-type endopeptidase activity				0	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0673)	Antihemophilic Factor(DB00025)|Drotrecogin alfa(DB00055)|Menadione(DB00170)|Sodium Tetradecyl Sulfate(DB00464)	GGGAGCTGGACCTGGACATCA	0.637													13	33	---	---	---	---	PASS
SPEG	10290	broad.mit.edu	37	2	220338227	220338227	+	Silent	SNP	C	A	A			TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:220338227C>A	uc010fwg.2	+	17	4149	c.4149C>A	c.(4147-4149)GGC>GGA	p.G1383G		NM_005876	NP_005867	Q15772	SPEG_HUMAN	SPEG complex locus	1383					muscle organ development|negative regulation of cell proliferation	nucleus	ATP binding|protein serine/threonine kinase activity			stomach(9)|ovary(4)|central_nervous_system(1)	14		Renal(207;0.0183)		Epithelial(149;4.5e-10)|all cancers(144;7.93e-08)|Lung(261;0.00639)|LUSC - Lung squamous cell carcinoma(224;0.00829)|READ - Rectum adenocarcinoma(5;0.163)		TCCTCCCAGGCCCAACCCTGG	0.348													13	78	---	---	---	---	PASS
ITPR1	3708	broad.mit.edu	37	3	4821290	4821290	+	Silent	SNP	C	T	T			TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:4821290C>T	uc003bqa.2	+	46	6552	c.6204C>T	c.(6202-6204)AAC>AAT	p.N2068N	ITPR1_uc010hca.1_Silent_p.N2053N|ITPR1_uc011asu.1_Intron|ITPR1_uc003bqc.2_Silent_p.N1038N	NM_001099952	NP_001093422	Q14643	ITPR1_HUMAN	inositol 1,4,5-triphosphate receptor, type 1	2116	Cytoplasmic (Potential).				activation of phospholipase C activity|cell death|energy reserve metabolic process|nerve growth factor receptor signaling pathway|platelet activation|regulation of insulin secretion|response to hypoxia	endoplasmic reticulum membrane|integral to membrane|platelet dense granule membrane|platelet dense tubular network membrane	calcium ion transmembrane transporter activity|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity|intracellular ligand-gated calcium channel activity|phosphatidylinositol binding|protein binding			lung(7)|breast(5)|ovary(4)|large_intestine(1)|liver(1)|skin(1)|kidney(1)|pancreas(1)	21				Epithelial(13;0.0199)|OV - Ovarian serous cystadenocarcinoma(96;0.0361)|all cancers(10;0.0982)		ACAGTGAAAACGCAGAGAGGA	0.502													5	72	---	---	---	---	PASS
PLXNA1	5361	broad.mit.edu	37	3	126708047	126708047	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:126708047G>A	uc003ejg.2	+	1	546	c.542G>A	c.(541-543)CGT>CAT	p.R181H		NM_032242	NP_115618	Q9UIW2	PLXA1_HUMAN	plexin A1	204	Sema.|Extracellular (Potential).				axon guidance	integral to membrane|intracellular|plasma membrane	semaphorin receptor activity			ovary(1)|pancreas(1)|skin(1)	3				GBM - Glioblastoma multiforme(114;0.155)		CTGTCCAGCCGTCGGCTCATG	0.617													9	50	---	---	---	---	PASS
TMEM128	85013	broad.mit.edu	37	4	4239697	4239697	+	Intron	SNP	C	A	A	rs116836858	by1000genomes	TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:4239697C>A	uc003ghr.1	-						TMEM128_uc003ghq.1_Intron|TMEM128_uc003ghs.2_3'UTR|TMEM128_uc011bvv.1_Intron|TMEM128_uc011bvw.1_Intron	NM_032927	NP_116316	Q5BJH2	TM128_HUMAN	transmembrane protein 128							integral to membrane					0				UCEC - Uterine corpus endometrioid carcinoma (64;0.166)		TTGACAACTCCAATATGCATC	0.323													10	17	---	---	---	---	PASS
C4orf35	85438	broad.mit.edu	37	4	71201085	71201085	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:71201085C>A	uc003hff.2	+	1	415	c.329C>A	c.(328-330)TCT>TAT	p.S110Y		NM_033122	NP_149113	Q96KC9	CABS1_HUMAN	testis development protein NYD-SP26	110						flagellum	calcium ion binding				0		all_hematologic(202;0.196)				ACAAGAGACTCTATTACCGAA	0.363													4	73	---	---	---	---	PASS
PCDH10	57575	broad.mit.edu	37	4	134071474	134071474	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:134071474G>A	uc003iha.2	+	1	1005	c.179G>A	c.(178-180)AGG>AAG	p.R60K	uc003igy.2_5'Flank|PCDH10_uc003igz.2_Missense_Mutation_p.R60K	NM_032961	NP_116586	Q9P2E7	PCD10_HUMAN	protocadherin 10 isoform 1 precursor	60	Cadherin 1.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(2)	2				LUSC - Lung squamous cell carcinoma(193;0.227)		CCCAACTCAAGGACCCCTTAC	0.527													17	92	---	---	---	---	PASS
KIF2A	3796	broad.mit.edu	37	5	61649100	61649100	+	Splice_Site	SNP	A	G	G			TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:61649100A>G	uc003jsy.3	+	6	769	c.458_splice	c.e6-2	p.S153_splice	KIF2A_uc003jsz.3_Splice_Site_p.S153_splice|KIF2A_uc010iwp.2_Splice_Site_p.A134_splice|KIF2A_uc003jsx.3_Splice_Site_p.S133_splice|KIF2A_uc010iwq.2_5'UTR	NM_004520	NP_004511	O00139	KIF2A_HUMAN	kinesin heavy chain member 2 isoform 1						blood coagulation|cell differentiation|cell division|microtubule-based movement|mitotic prometaphase|mitotic spindle organization|nervous system development	centrosome|cytosol|microtubule|spindle pole	ATP binding|microtubule motor activity|protein binding				0		Lung NSC(810;8.94e-06)|Prostate(74;0.0132)|Ovarian(174;0.051)|Breast(144;0.077)		Lung(70;0.14)		TTTTCTTTTCAGCACGTAGAA	0.318													3	10	---	---	---	---	PASS
RAPGEF6	51735	broad.mit.edu	37	5	130834154	130834154	+	Silent	SNP	G	T	T			TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:130834154G>T	uc003kvn.1	-	12	1607	c.1401C>A	c.(1399-1401)ATC>ATA	p.I467I	RAPGEF6_uc003kvp.1_Silent_p.I517I|RAPGEF6_uc003kvo.1_Silent_p.I467I|RAPGEF6_uc010jdi.1_Silent_p.I467I|RAPGEF6_uc010jdj.1_Silent_p.I467I|RAPGEF6_uc003kvq.2_Silent_p.I184I|RAPGEF6_uc003kvr.2_Silent_p.I467I|RAPGEF6_uc011cxe.1_RNA|RAPGEF6_uc010jdk.2_Silent_p.I467I	NM_016340	NP_057424	Q8TEU7	RPGF6_HUMAN	PDZ domain-containing guanine nucleotide	467	N-terminal Ras-GEF.				Ras protein signal transduction|regulation of GTPase activity|regulation of small GTPase mediated signal transduction	cytoplasm|plasma membrane	GTP-dependent protein binding|guanyl-nucleotide exchange factor activity|Ras GTPase binding			ovary(1)|lung(1)|central_nervous_system(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Lung(113;0.0721)		TTAAGCTGTCGATCTTAAACC	0.318													6	132	---	---	---	---	PASS
PCDHGC4	56098	broad.mit.edu	37	5	140865503	140865503	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140865503G>T	uc003lky.1	+	1	763	c.763G>T	c.(763-765)GCA>TCA	p.A255S	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc003ljm.1_Intron|PCDHGA3_uc010jfx.1_Intron|PCDHGB1_uc003ljo.1_Intron|PCDHGA4_uc003ljq.1_Intron|PCDHGB2_uc003ljs.1_Intron|PCDHGA5_uc003lju.1_Intron|PCDHGB3_uc003ljw.1_Intron|PCDHGA6_uc003ljy.1_Intron|PCDHGA7_uc003lka.1_Intron|PCDHGB4_uc003lkc.1_Intron|PCDHGA8_uc003lkd.1_Intron|PCDHGB5_uc003lkf.1_Intron|PCDHGA9_uc003lkh.1_Intron|PCDHGB6_uc003lkj.1_Intron|PCDHGA10_uc003lkl.1_Intron|PCDHGB7_uc003lkn.1_Intron|PCDHGA11_uc003lkp.1_Intron|PCDHGA11_uc003lkq.1_Intron|PCDHGA12_uc003lkt.1_Intron|PCDHGC3_uc003lkv.1_Intron|PCDHGC3_uc003lkw.1_Intron|PCDHGC4_uc011dbb.1_Missense_Mutation_p.A255S	NM_018928	NP_061751	Q9Y5F7	PCDGL_HUMAN	protocadherin gamma subfamily C, 4 isoform 1	255	Cadherin 3.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(4)	4			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GTTGGAGAGCGCACCAGCGGG	0.577													8	81	---	---	---	---	PASS
ITK	3702	broad.mit.edu	37	5	156671410	156671410	+	Silent	SNP	G	A	A			TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:156671410G>A	uc003lwo.1	+	13	1453	c.1371G>A	c.(1369-1371)GAG>GAA	p.E457E		NM_005546	NP_005537	Q08881	ITK_HUMAN	IL2-inducible T-cell kinase	457	Protein kinase.				cellular defense response|intracellular signal transduction|T cell receptor signaling pathway	cytosol|plasma membrane	ATP binding|metal ion binding|non-membrane spanning protein tyrosine kinase activity|protein binding			lung(12)|ovary(8)|skin(4)|stomach(1)|central_nervous_system(1)	26	Renal(175;0.00212)	Medulloblastoma(196;0.0354)|all_neural(177;0.1)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			TTGCTGCAGAGACCCTGCTGG	0.567			T	SYK	peripheral T-cell lymphoma								5	94	---	---	---	---	PASS
SLIT3	6586	broad.mit.edu	37	5	168093623	168093623	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:168093623C>G	uc003mab.2	-	36	4828	c.4408G>C	c.(4408-4410)GCC>CCC	p.A1470P	SLIT3_uc010jjg.2_Missense_Mutation_p.A1477P	NM_003062	NP_003053	O75094	SLIT3_HUMAN	slit homolog 3 precursor	1470	CTCK.				apoptosis involved in luteolysis|axon extension involved in axon guidance|cellular response to hormone stimulus|negative chemotaxis|negative regulation of cell growth|negative regulation of chemokine-mediated signaling pathway|response to cortisol stimulus|Roundabout signaling pathway	extracellular space|mitochondrion	calcium ion binding|Roundabout binding			ovary(3)|skin(1)	4	Renal(175;0.000159)|Lung NSC(126;0.0174)|all_lung(126;0.0392)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			ACCTTGGAGGCTGTGGCACAT	0.602													12	57	---	---	---	---	PASS
GFPT2	9945	broad.mit.edu	37	5	179745870	179745870	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179745870C>T	uc003mlw.1	-	10	979	c.881G>A	c.(880-882)CGG>CAG	p.R294Q		NM_005110	NP_005101	O94808	GFPT2_HUMAN	glutamine-fructose-6-phosphate transaminase 2	294					dolichol-linked oligosaccharide biosynthetic process|energy reserve metabolic process|fructose 6-phosphate metabolic process|glutamine metabolic process|post-translational protein modification|protein N-linked glycosylation via asparagine|UDP-N-acetylglucosamine biosynthetic process	cytosol	glutamine-fructose-6-phosphate transaminase (isomerizing) activity|sugar binding			ovary(1)|skin(1)	2	all_cancers(89;4.97e-05)|all_epithelial(37;1.22e-05)|Renal(175;0.000269)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.137)	Medulloblastoma(196;0.0392)|all_neural(177;0.0529)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)		L-Glutamine(DB00130)	GCGCTTGACCCGGTGAATGGA	0.572													16	49	---	---	---	---	PASS
NUP153	9972	broad.mit.edu	37	6	17626234	17626234	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:17626234T>C	uc003ncd.1	-	19	3906	c.3706A>G	c.(3706-3708)AGC>GGC	p.S1236G	NUP153_uc011dje.1_Missense_Mutation_p.S1267G|NUP153_uc010jpl.1_Missense_Mutation_p.S1194G	NM_005124	NP_005115	P49790	NU153_HUMAN	nucleoporin 153kDa	1236					carbohydrate metabolic process|glucose transport|interspecies interaction between organisms|mRNA transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	cytoplasm|nuclear membrane|nuclear pore|nucleolus|nucleoplasm	DNA binding|protein binding|transporter activity|zinc ion binding			lung(4)|ovary(2)|breast(2)|skin(1)	9	Breast(50;0.0259)|Ovarian(93;0.0584)	all_hematologic(90;0.125)	all cancers(50;0.0981)|Epithelial(50;0.112)			GCAGAGCTGCTCACAGGATTG	0.498													3	36	---	---	---	---	PASS
PI16	221476	broad.mit.edu	37	6	36922579	36922579	+	Silent	SNP	C	T	T			TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:36922579C>T	uc003ona.2	+	1	371	c.43C>T	c.(43-45)CTG>TTG	p.L15L	PI16_uc003omz.1_Silent_p.L15L|PI16_uc003onb.2_Silent_p.L15L	NM_153370	NP_699201	Q6UXB8	PI16_HUMAN	protease inhibitor 16 precursor	15						extracellular region|integral to membrane	peptidase inhibitor activity				0						gctgccgctactgctactgct	0.498													5	29	---	---	---	---	PASS
KCNQ5	56479	broad.mit.edu	37	6	73830249	73830249	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:73830249T>C	uc003pgk.2	+	8	1516	c.1169T>C	c.(1168-1170)ATT>ACT	p.I390T	KCNQ5_uc003pgj.3_Missense_Mutation_p.I390T|KCNQ5_uc011dyh.1_Missense_Mutation_p.I390T|KCNQ5_uc011dyi.1_Missense_Mutation_p.I390T|KCNQ5_uc010kat.2_Missense_Mutation_p.I390T|KCNQ5_uc011dyj.1_Missense_Mutation_p.I390T|KCNQ5_uc011dyk.1_Missense_Mutation_p.I149T	NM_019842	NP_062816	Q9NR82	KCNQ5_HUMAN	potassium voltage-gated channel, KQT-like	390					protein complex assembly|synaptic transmission	voltage-gated potassium channel complex	inward rectifier potassium channel activity			ovary(4)|large_intestine(2)|skin(1)	7		all_epithelial(107;0.116)|Lung NSC(302;0.219)		COAD - Colon adenocarcinoma(1;0.0107)|Colorectal(1;0.0583)		TCTGTTTCCATTGCAACCTGG	0.458													3	51	---	---	---	---	PASS
SLC35A1	10559	broad.mit.edu	37	6	88218885	88218885	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:88218885T>C	uc011dzj.1	+	7	957	c.878T>C	c.(877-879)TTA>TCA	p.L293S	SLC35A1_uc003plx.2_RNA|SLC35A1_uc010kbw.2_Missense_Mutation_p.L141S|SLC35A1_uc003plz.2_RNA|SLC35A1_uc011dzi.1_Missense_Mutation_p.L159S|SLC35A1_uc003ply.2_RNA|SLC35A1_uc010kbx.2_Missense_Mutation_p.L234S|SLC35A1_uc010kby.2_RNA	NM_006416	NP_006407	P78382	S35A1_HUMAN	solute carrier family 35 (CMP-sialic acid	293	Lumenal (Potential).				carbohydrate metabolic process|protein modification process	Golgi membrane|integral to plasma membrane	CMP-N-acetylneuraminate transmembrane transporter activity|sugar:hydrogen symporter activity				0		all_cancers(76;3.93e-06)|Acute lymphoblastic leukemia(125;3.55e-10)|Prostate(29;3.51e-09)|all_hematologic(105;3.29e-06)|all_epithelial(107;0.00575)		BRCA - Breast invasive adenocarcinoma(108;0.0429)		CTGTTTGGATTACAGATAAGT	0.393													23	159	---	---	---	---	PASS
MANEA	79694	broad.mit.edu	37	6	96053676	96053676	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:96053676C>G	uc003poo.1	+	5	924	c.784C>G	c.(784-786)CTT>GTT	p.L262V		NM_024641	NP_078917	Q5SRI9	MANEA_HUMAN	mannosidase, endo-alpha	262	Catalytic (Probable).|Lumenal (Potential).				post-translational protein modification|protein N-linked glycosylation via asparagine	Golgi membrane|integral to membrane	glycoprotein endo-alpha-1,2-mannosidase activity			ovary(2)|breast(1)	3		all_cancers(76;1.01e-06)|Acute lymphoblastic leukemia(125;3.58e-09)|all_hematologic(75;1.22e-06)|all_epithelial(107;0.00433)|Colorectal(196;0.0341)		BRCA - Breast invasive adenocarcinoma(108;0.148)		TGGCAATGCTCTTCCTATGTT	0.368													18	68	---	---	---	---	PASS
PPIL4	85313	broad.mit.edu	37	6	149855873	149855873	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:149855873C>T	uc003qmo.1	-	6	532	c.502G>A	c.(502-504)GAC>AAC	p.D168N	PPIL4_uc010kic.2_Intron|PPIL4_uc003qmp.1_Missense_Mutation_p.D168N	NM_139126	NP_624311	Q8WUA2	PPIL4_HUMAN	peptidylprolyl isomerase-like 4	168					protein folding	nucleus	nucleotide binding|peptidyl-prolyl cis-trans isomerase activity|RNA binding				0		Ovarian(120;0.0164)		OV - Ovarian serous cystadenocarcinoma(155;1.11e-11)|GBM - Glioblastoma multiforme(68;0.0885)		TCAGGAGGGTCATCAAATGGA	0.299													8	79	---	---	---	---	PASS
SOD2	6648	broad.mit.edu	37	6	160113748	160113748	+	Silent	SNP	G	T	T			TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:160113748G>T	uc003qsg.2	-	2	325	c.171C>A	c.(169-171)GCC>GCA	p.A57A	SOD2_uc003qsh.2_Silent_p.A57A|SOD2_uc003qsi.1_Silent_p.A57A|SOD2_uc011efu.1_Silent_p.A57A|SOD2_uc011efv.1_Silent_p.A57A|SOD2_uc003qsj.2_Silent_p.A57A	NM_001024465	NP_001019636	P04179	SODM_HUMAN	manganese superoxide dismutase isoform A	57					age-dependent response to reactive oxygen species|negative regulation of neuron apoptosis|oxygen homeostasis|protein homotetramerization|regulation of transcription from RNA polymerase II promoter|release of cytochrome c from mitochondria|removal of superoxide radicals|vasodilation by acetylcholine involved in regulation of systemic arterial blood pressure		manganese ion binding|superoxide dismutase activity				0		Breast(66;0.000776)|Ovarian(120;0.0303)|Prostate(117;0.103)		OV - Ovarian serous cystadenocarcinoma(65;1.4e-18)|BRCA - Breast invasive adenocarcinoma(81;5.77e-06)		TGTTCACGTAGGCCGCGTGGT	0.642													12	63	---	---	---	---	PASS
STK31	56164	broad.mit.edu	37	7	23826468	23826468	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:23826468G>A	uc003sws.3	+	20	2479	c.2412G>A	c.(2410-2412)ATG>ATA	p.M804I	STK31_uc003swt.3_Missense_Mutation_p.M781I|STK31_uc011jze.1_Missense_Mutation_p.M804I|STK31_uc010kuq.2_Missense_Mutation_p.M781I|STK31_uc003swv.1_5'Flank	NM_031414	NP_113602	Q9BXU1	STK31_HUMAN	serine/threonine kinase 31 isoform a	804	Protein kinase.						ATP binding|nucleic acid binding|protein serine/threonine kinase activity			skin(3)|lung(2)|ovary(2)|stomach(2)	9						CTGATCCTATGGCTTATCTGA	0.348													35	100	---	---	---	---	PASS
ZMIZ2	83637	broad.mit.edu	37	7	44796728	44796728	+	Silent	SNP	G	A	A			TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:44796728G>A	uc003tlr.2	+	4	471	c.348G>A	c.(346-348)GGG>GGA	p.G116G	ZMIZ2_uc003tlq.2_Silent_p.G84G|ZMIZ2_uc003tls.2_Silent_p.G116G|ZMIZ2_uc003tlt.2_5'Flank|ZMIZ2_uc010kyj.2_5'Flank	NM_031449	NP_113637	Q8NF64	ZMIZ2_HUMAN	zinc finger, MIZ-type containing 2 isoform 1	116	Gly-rich.				positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nuclear replication fork	ligand-dependent nuclear receptor transcription coactivator activity|protein binding|zinc ion binding			ovary(2)|large_intestine(2)|breast(1)	5						GCTACCCTGGGGCCCCCGGCT	0.642													9	28	---	---	---	---	PASS
SERPINE1	5054	broad.mit.edu	37	7	100780229	100780229	+	Intron	SNP	T	G	G			TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100780229T>G	uc003uxt.2	+						SERPINE1_uc011kkj.1_Intron|SERPINE1_uc003uxu.1_3'UTR	NM_000602	NP_000593	P05121	PAI1_HUMAN	plasminogen activator inhibitor-1 isoform 1						angiogenesis|cellular response to chemical stimulus|cellular response to lipopolysaccharide|chronological cell aging|defense response to Gram-negative bacterium|fibrinolysis|negative regulation of apoptosis|negative regulation of cell adhesion mediated by integrin|negative regulation of fibrinolysis|negative regulation of plasminogen activation|negative regulation of smooth muscle cell migration|negative regulation of smooth muscle cell-matrix adhesion|negative regulation of vascular wound healing|platelet activation|platelet degranulation|positive regulation of angiogenesis|positive regulation of interleukin-8 production|positive regulation of leukotriene production involved in inflammatory response|positive regulation of monocyte chemotaxis|positive regulation of receptor-mediated endocytosis|regulation of receptor activity	extracellular matrix|extracellular space|plasma membrane|platelet alpha granule lumen	protease binding|serine-type endopeptidase inhibitor activity			ovary(1)|lung(1)|central_nervous_system(1)	3	Lung NSC(181;0.136)|all_lung(186;0.182)				Atorvastatin(DB01076)|Dimethyl sulfoxide(DB01093)|Drotrecogin alfa(DB00055)|Simvastatin(DB00641)|Tenecteplase(DB00031)|Troglitazone(DB00197)|Urokinase(DB00013)	GGGGTGGGGGTGGTGCCAGTG	0.348													9	27	---	---	---	---	PASS
C7orf66	154907	broad.mit.edu	37	7	108524125	108524125	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:108524125C>T	uc003vfo.2	-	2	335	c.287G>A	c.(286-288)CGG>CAG	p.R96Q		NM_001024607	NP_001019778	A4D0T2	CG066_HUMAN	hypothetical protein LOC154907	96						integral to membrane				ovary(2)	2						GTGGACAATCCGTAGATATGC	0.348													3	116	---	---	---	---	PASS
SGK3	23678	broad.mit.edu	37	8	67748071	67748071	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:67748071A>G	uc003xwr.2	+	9	898	c.599A>G	c.(598-600)AAC>AGC	p.N200S	SGK3_uc003xwp.2_Missense_Mutation_p.N194S|SGK3_uc003xwt.2_Missense_Mutation_p.N200S|SGK3_uc003xwu.2_Missense_Mutation_p.N200S	NM_001033578	NP_001028750	Q96BR1	SGK3_HUMAN	serum/glucocorticoid regulated kinase 3 isoform	200	Protein kinase.|Nuclear localization signal (By similarity).				cell communication|response to stress	cytoplasmic membrane-bounded vesicle|early endosome	ATP binding|phosphatidylinositol binding|protein serine/threonine kinase activity			ovary(1)|large_intestine(1)|lung(1)|breast(1)	4	Breast(64;0.186)	Lung NSC(129;0.0908)|all_lung(136;0.152)	Epithelial(68;0.0046)|OV - Ovarian serous cystadenocarcinoma(28;0.0112)|all cancers(69;0.0141)|BRCA - Breast invasive adenocarcinoma(89;0.206)			ATAGTTCTCAACAGAAAAGAG	0.303													4	75	---	---	---	---	PASS
MTERFD1	51001	broad.mit.edu	37	8	97258647	97258647	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:97258647G>A	uc003yhs.1	-	5	791	c.713C>T	c.(712-714)GCA>GTA	p.A238V	MTERFD1_uc003yhr.1_Missense_Mutation_p.A117V|MTERFD1_uc010mbd.1_Missense_Mutation_p.A238V	NM_015942	NP_057026	Q96E29	MTER1_HUMAN	MTERF domain containing 1 precursor	238					negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	mitochondrion	transcription regulatory region DNA binding			ovary(1)	1	Breast(36;5.16e-05)					TGCAACATCTGCTTTACTGAA	0.348													5	51	---	---	---	---	PASS
ZC3H3	23144	broad.mit.edu	37	8	144550433	144550433	+	Silent	SNP	G	C	C			TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144550433G>C	uc003yyd.2	-	8	2150	c.2121C>G	c.(2119-2121)ACC>ACG	p.T707T		NM_015117	NP_055932	Q8IXZ2	ZC3H3_HUMAN	zinc finger CCCH-type containing 3	707	C3H1-type 2.				mRNA polyadenylation|poly(A)+ mRNA export from nucleus|regulation of mRNA export from nucleus	nucleus	nucleic acid binding|zinc ion binding			skin(1)	1	all_cancers(97;8.64e-11)|all_epithelial(106;6.43e-09)|Lung NSC(106;0.000202)|all_lung(105;0.000548)|Ovarian(258;0.0212)|Acute lymphoblastic leukemia(118;0.155)		Colorectal(110;0.107)|BRCA - Breast invasive adenocarcinoma(115;0.107)			TTTTCTTGCAGGTGCCCCGGA	0.652													11	39	---	---	---	---	PASS
NRBP2	340371	broad.mit.edu	37	8	144920929	144920929	+	Nonsense_Mutation	SNP	G	A	A			TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144920929G>A	uc011lkt.1	-	10	903	c.763C>T	c.(763-765)CAG>TAG	p.Q255*	NRBP2_uc003yzv.2_Nonsense_Mutation_p.Q12*|NRBP2_uc003yzz.1_5'Flank|NRBP2_uc003yzw.2_5'Flank|NRBP2_uc010mfl.2_5'Flank|NRBP2_uc010mfm.2_Nonsense_Mutation_p.Q12*|NRBP2_uc011lks.1_Nonsense_Mutation_p.Q12*|NRBP2_uc003yzy.2_Nonsense_Mutation_p.Q12*	NM_178564	NP_848659	Q9NSY0	NRBP2_HUMAN	nuclear receptor binding protein 2	255	Protein kinase.				negative regulation of neuron apoptosis|neuron differentiation	cytoplasm	ATP binding|protein kinase activity			central_nervous_system(2)	2	all_cancers(97;2.31e-11)|all_epithelial(106;1.58e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;1.23e-39)|all cancers(56;6.82e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.18)			CCATTGGTCTGGATTTCCAGT	0.637													5	26	---	---	---	---	PASS
IFNA16	3449	broad.mit.edu	37	9	21217253	21217253	+	Missense_Mutation	SNP	A	C	C			TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:21217253A>C	uc003zor.1	-	1	58	c.52T>G	c.(52-54)TCC>GCC	p.S18A	IFNA14_uc003zoo.1_Intron	NM_002173	NP_002164	P05015	IFN16_HUMAN	interferon, alpha 16 precursor	18					blood coagulation|regulation of type I interferon-mediated signaling pathway|response to virus|type I interferon-mediated signaling pathway	extracellular space	cytokine activity|interferon-alpha/beta receptor binding			skin(1)	1				Lung(24;2.12e-22)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)|OV - Ovarian serous cystadenocarcinoma(39;0.116)		GAACAGATGGATTTGTAGCTG	0.488													10	75	---	---	---	---	PASS
FRMPD1	22844	broad.mit.edu	37	9	37733482	37733482	+	Silent	SNP	A	G	G			TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:37733482A>G	uc004aag.1	+	11	1052	c.1008A>G	c.(1006-1008)GGA>GGG	p.G336G	FRMPD1_uc004aah.1_Silent_p.G336G|FRMPD1_uc011lqm.1_Silent_p.G158G|FRMPD1_uc011lqn.1_Silent_p.G205G	NM_014907	NP_055722	Q5SYB0	FRPD1_HUMAN	FERM and PDZ domain containing 1	336	FERM.					cytoskeleton|cytosol|plasma membrane				ovary(4)|central_nervous_system(2)|skin(2)|breast(1)	9				GBM - Glioblastoma multiforme(29;0.00655)		AAGACTGGGGAATAGAGAACT	0.413													14	72	---	---	---	---	PASS
GDA	9615	broad.mit.edu	37	9	74863196	74863196	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:74863196C>G	uc004aiq.2	+	14	1486	c.1303C>G	c.(1303-1305)CGA>GGA	p.R435G	GDA_uc011lse.1_Missense_Mutation_p.R361G|GDA_uc011lsf.1_Missense_Mutation_p.R361G|GDA_uc004air.2_Missense_Mutation_p.R435G|GDA_uc010mow.1_RNA|GDA_uc004ais.2_Missense_Mutation_p.R357G	NM_004293	NP_004284	Q9Y2T3	GUAD_HUMAN	guanine deaminase	435					nervous system development|purine base metabolic process|purine nucleotide catabolic process	cytosol	guanine deaminase activity|zinc ion binding			ovary(2)|central_nervous_system(2)|skin(1)	5		Myeloproliferative disorder(762;0.0122)		Lung(182;0.0583)		AGGAGATGATCGAAATATTGA	0.403													12	95	---	---	---	---	PASS
DIP2C	22982	broad.mit.edu	37	10	332271	332271	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:332271C>T	uc001ifp.2	-	34	4151	c.4061G>A	c.(4060-4062)CGG>CAG	p.R1354Q		NM_014974	NP_055789	Q9Y2E4	DIP2C_HUMAN	DIP2 disco-interacting protein 2 homolog C	1354						nucleus	catalytic activity|transcription factor binding			breast(4)|ovary(2)|large_intestine(1)	7		all_cancers(4;0.00336)|all_lung(4;0.00732)|Lung NSC(4;0.00785)|all_epithelial(10;0.0159)|Colorectal(49;0.235)	OV - Ovarian serous cystadenocarcinoma(33;0.136)	Epithelial(11;0.0123)|all cancers(11;0.0467)|Lung(33;0.0864)|OV - Ovarian serous cystadenocarcinoma(14;0.106)		AATTATAATCCGAACCCCTGG	0.463													25	150	---	---	---	---	PASS
CRTAC1	55118	broad.mit.edu	37	10	99640010	99640010	+	Silent	SNP	G	A	A			TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:99640010G>A	uc001kou.1	-	14	2171	c.1815C>T	c.(1813-1815)TGC>TGT	p.C605C	CRTAC1_uc001kov.2_Silent_p.C594C|CRTAC1_uc001kot.1_Missense_Mutation_p.A381V	NM_018058	NP_060528	Q9NQ79	CRAC1_HUMAN	cartilage acidic protein 1 precursor	605	EGF-like.					proteinaceous extracellular matrix	calcium ion binding			ovary(4)|pancreas(1)	5		Colorectal(252;0.24)		Epithelial(162;2.18e-10)|all cancers(201;3.27e-09)		ACTCACCCACGCAGGCTGTGC	0.602													10	82	---	---	---	---	PASS
LOC650368	650368	broad.mit.edu	37	11	3424847	3424847	+	Intron	SNP	G	T	T			TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:3424847G>T	uc001lxy.2	+						LOC650368_uc010qxs.1_RNA|LOC650368_uc001lxx.2_RNA					Homo sapiens cDNA FLJ41654 fis, clone FEBRA2025463, weakly  similar to Homo sapiens HMT-1 mRNA for beta-1,4 mannosyltransferase.												0						ACTCTTGATGGACACAACCTT	0.413													7	90	---	---	---	---	PASS
NAV2	89797	broad.mit.edu	37	11	20139938	20139938	+	3'UTR	SNP	C	A	A	rs141058022		TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:20139938C>A	uc001mpr.3	+	38					NAV2_uc001mpp.2_3'UTR|NAV2_uc009yhx.2_3'UTR|NAV2_uc009yhz.2_3'UTR|NAV2_uc001mpu.2_3'UTR|NAV2_uc001mpv.2_3'UTR	NM_182964	NP_892009	Q8IVL1	NAV2_HUMAN	neuron navigator 2 isoform 1							nucleus	ATP binding|helicase activity			skin(4)|ovary(1)|pancreas(1)	6						CGAGACCCCCCGTCCTTCAGC	0.612													15	13	---	---	---	---	PASS
QSER1	79832	broad.mit.edu	37	11	32953488	32953488	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:32953488G>C	uc001mty.2	+	4	564	c.297G>C	c.(295-297)TTG>TTC	p.L99F	QSER1_uc001mtz.1_Missense_Mutation_p.L99F|QSER1_uc001mua.2_5'Flank	NM_001076786	NP_001070254	Q2KHR3	QSER1_HUMAN	glutamine and serine rich 1	99										ovary(3)|central_nervous_system(2)|skin(1)	6	Breast(20;0.158)					ATGACCCTTTGCTACAAATCA	0.418													16	148	---	---	---	---	PASS
OR5L1	219437	broad.mit.edu	37	11	55579228	55579228	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55579228G>A	uc001nhw.1	+	1	286	c.286G>A	c.(286-288)GGG>AGG	p.G96R		NM_001004738	NP_001004738	Q8NGL2	OR5L1_HUMAN	olfactory receptor, family 5, subfamily L,	96	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(3)|ovary(2)	5		all_epithelial(135;0.208)				CTCCTTCCTAGGGTGCATGGT	0.473													21	174	---	---	---	---	PASS
OR5W2	390148	broad.mit.edu	37	11	55681565	55681565	+	Missense_Mutation	SNP	C	T	T	rs148084259		TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55681565C>T	uc010rir.1	-	1	494	c.494G>A	c.(493-495)CGC>CAC	p.R165H		NM_001001960	NP_001001960	Q8NH69	OR5W2_HUMAN	olfactory receptor, family 5, subfamily W,	165	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|skin(1)	2						GAAGCATAGGCGGAAGGCCAG	0.428													21	98	---	---	---	---	PASS
INTS4	92105	broad.mit.edu	37	11	77672068	77672068	+	Silent	SNP	G	C	C			TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:77672068G>C	uc001oys.2	-	5	616	c.588C>G	c.(586-588)GTC>GTG	p.V196V	INTS4_uc001oyt.2_RNA|INTS4_uc001oyu.1_Silent_p.V196V	NM_033547	NP_291025	Q96HW7	INT4_HUMAN	integrator complex subunit 4	196	HEAT 3.				snRNA processing	integrator complex	protein binding			ovary(2)	2	all_cancers(14;4.53e-19)|all_epithelial(13;1.73e-21)|Breast(9;2.71e-16)|Ovarian(111;0.152)		Epithelial(5;1.13e-46)|all cancers(3;8.92e-44)|BRCA - Breast invasive adenocarcinoma(5;8.4e-26)|OV - Ovarian serous cystadenocarcinoma(8;1.05e-23)			TAATCTTCTGGACATCTCTGG	0.443													4	236	---	---	---	---	PASS
OR10G7	390265	broad.mit.edu	37	11	123908892	123908892	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:123908892C>T	uc001pzq.1	-	1	817	c.817G>A	c.(817-819)GTT>ATT	p.V273I		NM_001004463	NP_001004463	Q8NGN6	O10G7_HUMAN	olfactory receptor, family 10, subfamily G,	273	Helical; Name=7; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)	2		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0521)		GTGTAGAAAACGGCCACAACC	0.512													20	39	---	---	---	---	PASS
PZP	5858	broad.mit.edu	37	12	9345314	9345314	+	Missense_Mutation	SNP	A	C	C			TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:9345314A>C	uc001qvl.2	-	12	1305	c.1276T>G	c.(1276-1278)TTG>GTG	p.L426V	PZP_uc009zgl.2_Missense_Mutation_p.L295V	NM_002864	NP_002855			pregnancy-zone protein precursor											ovary(3)|upper_aerodigestive_tract(1)|large_intestine(1)	5						TGAAAACACAAGTTGGGATGC	0.413													4	62	---	---	---	---	PASS
ADAMTS20	80070	broad.mit.edu	37	12	43822466	43822466	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:43822466C>A	uc010skx.1	-	25	3626	c.3626G>T	c.(3625-3627)GGA>GTA	p.G1209V	ADAMTS20_uc001rno.1_Missense_Mutation_p.G327V|ADAMTS20_uc001rnp.1_Missense_Mutation_p.G363V	NM_025003	NP_079279	P59510	ATS20_HUMAN	a disintegrin-like and metalloprotease with	1209	TSP type-1 8.					proteinaceous extracellular matrix	zinc ion binding			central_nervous_system(5)|ovary(4)|lung(3)|large_intestine(2)|skin(2)|urinary_tract(1)|kidney(1)|pancreas(1)	19	all_cancers(12;2.6e-05)|Lung SC(27;0.184)	Lung NSC(34;0.0569)|all_lung(34;0.129)		GBM - Glioblastoma multiforme(48;0.0473)		TTGCCACTCTCCACAAGGGGT	0.348													6	49	---	---	---	---	PASS
UBC	7316	broad.mit.edu	37	12	125396407	125396407	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:125396407C>G	uc001ugs.3	-	2	2359	c.1911G>C	c.(1909-1911)AAG>AAC	p.K637N	UBC_uc001ugr.2_RNA|UBC_uc001ugu.1_Missense_Mutation_p.K561N|UBC_uc001ugt.2_Missense_Mutation_p.K485N|UBC_uc001ugv.2_Missense_Mutation_p.K105N	NM_021009	NP_066289	P0CG48	UBC_HUMAN	ubiquitin C	637	Ubiquitin-like 9.				activation of MAPK activity|anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|anti-apoptosis|apoptosis|cellular membrane organization|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA repair|endosome transport|epidermal growth factor receptor signaling pathway|G1/S transition of mitotic cell cycle|I-kappaB kinase/NF-kappaB cascade|induction of apoptosis by extracellular signals|innate immune response|JNK cascade|M/G1 transition of mitotic cell cycle|mRNA metabolic process|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of epidermal growth factor receptor signaling pathway|negative regulation of type I interferon production|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|nerve growth factor receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|S phase of mitotic cell cycle|stress-activated MAPK cascade|T cell receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway|viral reproduction	cytosol|endocytic vesicle membrane|endosome membrane|nucleoplasm|plasma membrane	protein binding			ovary(2)	2	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;6.17e-05)|Epithelial(86;0.000207)|all cancers(50;0.00308)		TATCTTGGATCTTTGCCTTGA	0.517													8	205	---	---	---	---	PASS
ATP11A	23250	broad.mit.edu	37	13	113485756	113485756	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:113485756G>A	uc001vsi.3	+	13	1377	c.1289G>A	c.(1288-1290)TGC>TAC	p.C430Y	ATP11A_uc001vsj.3_Missense_Mutation_p.C430Y|ATP11A_uc001vsm.1_Missense_Mutation_p.C306Y	NM_015205	NP_056020	P98196	AT11A_HUMAN	ATPase, class VI, type 11A isoform a	430	Cytoplasmic (Potential).				ATP biosynthetic process	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			large_intestine(2)|ovary(2)	4	all_lung(23;0.000374)|Lung NSC(43;0.0107)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)	all_lung(25;0.134)|all_epithelial(44;0.141)				AAGGAGTGCTGCATCGAAGGC	0.582													9	41	---	---	---	---	PASS
OR4K2	390431	broad.mit.edu	37	14	20345133	20345133	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:20345133C>A	uc001vwh.1	+	1	707	c.707C>A	c.(706-708)GCC>GAC	p.A236D		NM_001005501	NP_001005501	Q8NGD2	OR4K2_HUMAN	olfactory receptor, family 4, subfamily K,	236	Helical; Name=6; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|skin(2)	4	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)		TCATCTAAGGCCCTTTCTACT	0.393													12	314	---	---	---	---	PASS
PARP2	10038	broad.mit.edu	37	14	20822982	20822982	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:20822982G>A	uc001vxc.2	+	9	845	c.817G>A	c.(817-819)GCA>ACA	p.A273T	PARP2_uc001vxd.2_Missense_Mutation_p.A260T|PARP2_uc001vxb.1_Missense_Mutation_p.A273T|PARP2_uc010tle.1_Missense_Mutation_p.A23T	NM_005484	NP_005475	Q9UGN5	PARP2_HUMAN	poly (ADP-ribose) polymerase family, member 2	273	PARP alpha-helical.				protein ADP-ribosylation	nucleolus|nucleoplasm	DNA binding|NAD+ ADP-ribosyltransferase activity			ovary(1)|pancreas(1)	2	all_cancers(95;0.00092)	all_lung(585;0.235)	Epithelial(56;5.34e-07)|all cancers(55;3.7e-06)	GBM - Glioblastoma multiforme(265;0.00888)|READ - Rectum adenocarcinoma(17;0.0649)		GCTGACAGTGGCACAAATCAA	0.468								Direct_reversal_of_damage|PARP_enzymes_that_bind_to_DNA					5	161	---	---	---	---	PASS
MMP14	4323	broad.mit.edu	37	14	23310798	23310798	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23310798G>T	uc001whc.2	+	2	441	c.207G>T	c.(205-207)CAG>CAT	p.Q69H		NM_004995	NP_004986	P50281	MMP14_HUMAN	matrix metalloproteinase 14 preproprotein	69						extracellular matrix|integral to plasma membrane|melanosome	calcium ion binding|metalloendopeptidase activity|zinc ion binding				0	all_cancers(95;9.47e-05)			GBM - Glioblastoma multiforme(265;0.00551)		CTGCCATGCAGAAGTTTTACG	0.562													4	28	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	15	28929547	28929547	+	RNA	SNP	T	C	C	rs140867295	by1000genomes	TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:28929547T>C	uc010azc.2	+	14		c.2252T>C								Homo sapiens I.M.A.G.E. clone 321824, mRNA sequence.																		GGAGAAGCATTAGGGTGTCCG	0.562													2	10	---	---	---	---	PASS
CAPN3	825	broad.mit.edu	37	15	42652148	42652148	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42652148C>T	uc001zpn.1	+	1	451	c.145C>T	c.(145-147)CGC>TGC	p.R49C	CAPN3_uc001zpk.1_Intron|CAPN3_uc001zpl.1_Intron|CAPN3_uc010udf.1_Intron|CAPN3_uc010udg.1_Intron|CAPN3_uc001zpo.1_Missense_Mutation_p.R49C|CAPN3_uc001zpp.1_Missense_Mutation_p.R49C	NM_000070	NP_000061	P20807	CAN3_HUMAN	calpain 3 isoform a	49					muscle organ development|proteolysis	cytoplasm	calcium ion binding|calcium-dependent cysteine-type endopeptidase activity|signal transducer activity			central_nervous_system(1)	1		all_cancers(109;1.65e-16)|all_epithelial(112;8.34e-15)|Lung NSC(122;3.56e-09)|all_lung(180;1.68e-08)|Melanoma(134;0.0574)|Colorectal(260;0.152)		GBM - Glioblastoma multiforme(94;7.36e-07)		CATCATCAGCCGCAATTTTCC	0.522													42	198	---	---	---	---	PASS
COPS2	9318	broad.mit.edu	37	15	49420221	49420221	+	Nonsense_Mutation	SNP	G	A	A			TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:49420221G>A	uc001zxf.2	-	13	1337	c.1258C>T	c.(1258-1260)CGA>TGA	p.R420*	COPS2_uc001zxh.2_Nonsense_Mutation_p.R427*|COPS2_uc010ufa.1_Nonsense_Mutation_p.R356*	NM_004236	NP_004227	P61201	CSN2_HUMAN	COP9 constitutive photomorphogenic homolog	420					cullin deneddylation|transcription from RNA polymerase II promoter	cytoplasm|signalosome	protein binding|signal transducer activity			lung(1)	1		all_lung(180;0.0428)		all cancers(107;1.34e-07)|GBM - Glioblastoma multiforme(94;3.02e-05)		GCAGTATATCGTGCACCACCC	0.413													7	86	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	15	82620400	82620400	+	RNA	SNP	T	C	C			TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:82620400T>C	uc010bls.1	+	1		c.493T>C								Homo sapiens mRNA for FLJ00317 protein.																		GACCCAAGGGTCAGCCTGAGT	0.672													2	7	---	---	---	---	PASS
TEKT5	146279	broad.mit.edu	37	16	10788652	10788652	+	Missense_Mutation	SNP	C	A	A	rs61731533	byFrequency	TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:10788652C>A	uc002czz.1	-	1	151	c.79G>T	c.(79-81)GTA>TTA	p.V27L		NM_144674	NP_653275	Q96M29	TEKT5_HUMAN	tektin 5	27					microtubule cytoskeleton organization	cilium axoneme|flagellar axoneme|microtubule				ovary(2)	2						GGCGCCTGTACAGCTGGCAGT	0.552													6	64	---	---	---	---	PASS
PDXDC1	23042	broad.mit.edu	37	16	15129348	15129348	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:15129348A>G	uc002dda.3	+	22	2269	c.2045A>G	c.(2044-2046)CAA>CGA	p.Q682R	PDXDC1_uc010uzl.1_Missense_Mutation_p.Q667R|PDXDC1_uc010uzm.1_Missense_Mutation_p.Q591R|PDXDC1_uc002ddb.3_Missense_Mutation_p.Q655R|PDXDC1_uc010uzn.1_Missense_Mutation_p.Q654R|PDXDC1_uc002ddc.2_Intron	NM_015027	NP_055842	Q6P996	PDXD1_HUMAN	pyridoxal-dependent decarboxylase domain	682					carboxylic acid metabolic process		carboxy-lyase activity|protein binding|pyridoxal phosphate binding			skin(1)	1					Pyridoxal Phosphate(DB00114)	TACAAAGCACAAGGTGCAGGA	0.582													5	26	---	---	---	---	PASS
GPR139	124274	broad.mit.edu	37	16	20043222	20043222	+	Silent	SNP	C	T	T			TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:20043222C>T	uc002dgu.1	-	2	1059	c.897G>A	c.(895-897)ACG>ACA	p.T299T	GPR139_uc010vaw.1_Silent_p.T206T	NM_001002911	NP_001002911	Q6DWJ6	GP139_HUMAN	G protein-coupled receptor 139	299	Cytoplasmic (Potential).					integral to membrane|plasma membrane				ovary(2)	2						AAGCCTTGAGCGTGGCGGCTG	0.512													5	138	---	---	---	---	PASS
ACD	65057	broad.mit.edu	37	16	67692130	67692130	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67692130G>A	uc002etq.3	-	10	1560	c.1223C>T	c.(1222-1224)GCC>GTC	p.A408V	ACD_uc002etp.3_Missense_Mutation_p.A405V|ACD_uc002etr.3_Missense_Mutation_p.A405V|ACD_uc010vjt.1_3'UTR|PARD6A_uc002ets.2_5'Flank|PARD6A_uc002ett.2_5'Flank	NM_001082486	NP_001075955	Q96AP0	ACD_HUMAN	adrenocortical dysplasia homolog isoform 1	408	Ser-rich.				intracellular protein transport|negative regulation of telomere maintenance via telomerase|positive regulation of single-stranded telomeric DNA binding|positive regulation of telomerase activity|protection from non-homologous end joining at telomere|protein localization to chromosome, telomeric region|telomere assembly	nuclear telomere cap complex|nucleoplasm	DNA binding|DNA polymerase binding			pancreas(1)	1		Acute lymphoblastic leukemia(13;3.76e-06)|all_hematologic(13;0.000303)|Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0143)|Epithelial(162;0.047)|all cancers(182;0.228)		GGTGGCAGGGGCTGAGCAGAT	0.662													15	72	---	---	---	---	PASS
NFE2L1	4779	broad.mit.edu	37	17	46128663	46128663	+	Silent	SNP	C	A	A			TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:46128663C>A	uc002imz.3	+	2	834	c.183C>A	c.(181-183)ACC>ACA	p.T61T	NFE2L1_uc002ina.3_Silent_p.T61T|NFE2L1_uc002inb.3_Silent_p.T61T|NFE2L1_uc002inc.1_Silent_p.T61T	NM_003204	NP_003195	Q14494	NF2L1_HUMAN	nuclear factor erythroid 2-like 1	61					anatomical structure morphogenesis|heme biosynthetic process|inflammatory response|transcription from RNA polymerase II promoter	nucleus	protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription cofactor activity			skin(1)	1						TGAGGAATACCTTGGATGGCT	0.567													17	100	---	---	---	---	PASS
CYP4F2	8529	broad.mit.edu	37	19	16006353	16006353	+	Silent	SNP	G	A	A			TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:16006353G>A	uc002nbs.1	-	3	356	c.306C>T	c.(304-306)TGC>TGT	p.C102C	CYP4F2_uc010xot.1_5'UTR|CYP4F2_uc010xou.1_Intron	NM_001082	NP_001073	P78329	CP4F2_HUMAN	cytochrome P450, family 4, subfamily F,	102					leukotriene metabolic process|long-chain fatty acid metabolic process|very long-chain fatty acid metabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	alkane 1-monooxygenase activity|electron carrier activity|heme binding|leukotriene-B4 20-monooxygenase activity|oxygen binding|protein binding			ovary(1)|skin(1)	2						TGTCGGGGTGGCACAAACTGA	0.597													5	273	---	---	---	---	PASS
CATSPERG	57828	broad.mit.edu	37	19	38858204	38858204	+	Silent	SNP	C	T	T			TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:38858204C>T	uc002oih.3	+	24	2913	c.2826C>T	c.(2824-2826)TTC>TTT	p.F942F	CATSPERG_uc002oig.3_Silent_p.F902F|CATSPERG_uc002oif.3_Silent_p.F582F|CATSPERG_uc010efw.2_RNA	NM_021185	NP_067008	Q6ZRH7	CTSRG_HUMAN	cation channel, sperm-associated, gamma	942	Extracellular (Potential).				cell differentiation|multicellular organismal development|spermatogenesis	integral to membrane				ovary(1)|skin(1)	2						CCGGCAGTTTCCAGGGCAGGT	0.547													10	614	---	---	---	---	PASS
FCGBP	8857	broad.mit.edu	37	19	40367841	40367841	+	Silent	SNP	T	G	G			TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:40367841T>G	uc002omp.3	-	29	13127	c.13119A>C	c.(13117-13119)GCA>GCC	p.A4373A		NM_003890	NP_003881	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein precursor	4373	TIL 10.					extracellular region	protein binding			ovary(4)|skin(4)|central_nervous_system(1)	9	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			TCGTAAGGGGTGCAGGGGACG	0.627													6	15	---	---	---	---	PASS
MAP3K10	4294	broad.mit.edu	37	19	40720964	40720964	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:40720964G>T	uc002ona.2	+	10	2918	c.2630G>T	c.(2629-2631)CGC>CTC	p.R877L	MAP3K10_uc002onb.2_Missense_Mutation_p.R266L	NM_002446	NP_002437	Q02779	M3K10_HUMAN	mitogen-activated protein kinase kinase kinase	877					activation of JUN kinase activity|induction of apoptosis|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription, DNA-dependent|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|positive regulation of JNK cascade|protein autophosphorylation|smoothened signaling pathway	cytoplasm	ATP binding|bHLH transcription factor binding|JUN kinase kinase kinase activity|protein homodimerization activity|transcription corepressor activity			ovary(2)|lung(2)|skin(1)|pancreas(1)	6						TTCCCAGGCCGCCCCACCACC	0.711													3	13	---	---	---	---	PASS
PLAUR	5329	broad.mit.edu	37	19	44160640	44160640	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44160640C>T	uc002oxf.1	-	4	693	c.463G>A	c.(463-465)GGT>AGT	p.G155S	PLAUR_uc002oxd.1_Missense_Mutation_p.G155S|PLAUR_uc002oxe.1_Missense_Mutation_p.G150S|PLAUR_uc002oxg.1_Missense_Mutation_p.G155S	NM_002659	NP_002650	Q03405	UPAR_HUMAN	plasminogen activator, urokinase receptor	155	UPAR/Ly6 2.				attachment of GPI anchor to protein|blood coagulation|C-terminal protein lipidation|cellular component movement|chemotaxis|fibrinolysis|regulation of proteolysis	anchored to membrane|cell surface|endoplasmic reticulum lumen|endoplasmic reticulum membrane|extracellular region|extrinsic to membrane|integral to membrane|plasma membrane	enzyme binding|U-plasminogen activator receptor activity			ovary(1)	1		Prostate(69;0.0153)			Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Streptokinase(DB00086)|Tenecteplase(DB00031)|Urokinase(DB00013)	CCTTCTTCACCTTCCTGGATC	0.488													20	198	---	---	---	---	PASS
EPN1	29924	broad.mit.edu	37	19	56204133	56204133	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56204133C>G	uc002qlw.2	+	8	1490	c.1148C>G	c.(1147-1149)CCT>CGT	p.P383R	EPN1_uc002qlv.2_Missense_Mutation_p.P358R|EPN1_uc010etd.2_Missense_Mutation_p.P383R|EPN1_uc002qlx.2_Missense_Mutation_p.P469R	NM_001130072	NP_001123544	Q9Y6I3	EPN1_HUMAN	epsin 1 isoform b	383	Ala/Gly/Pro-rich.				endocytosis|epidermal growth factor receptor signaling pathway|negative regulation of epidermal growth factor receptor signaling pathway	coated pit|cytoplasm|nucleus|plasma membrane	lipid binding				0		Colorectal(82;0.00244)|Ovarian(87;0.133)		GBM - Glioblastoma multiforme(193;0.112)		GGAGGGTCACCTGCCAAGCCC	0.632													3	7	---	---	---	---	PASS
HMOX1	3162	broad.mit.edu	37	22	35785885	35785885	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:35785885C>A	uc003ant.1	+	4	745	c.665C>A	c.(664-666)ACC>AAC	p.T222N		NM_002133	NP_002124	P09601	HMOX1_HUMAN	heme oxygenase (decyclizing) 1	222					angiogenesis|anti-apoptosis|cell death|cellular iron ion homeostasis|endothelial cell proliferation|erythrocyte homeostasis|heme catabolic process|heme oxidation|intracellular protein kinase cascade|low-density lipoprotein particle clearance|negative regulation of leukocyte migration|negative regulation of smooth muscle cell proliferation|positive regulation of chemokine biosynthetic process|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of smooth muscle cell proliferation|protein homooligomerization|regulation of transcription from RNA polymerase II promoter in response to oxidative stress|response to hydrogen peroxide|response to nicotine|smooth muscle hyperplasia|transmembrane transport|wound healing involved in inflammatory response	endoplasmic reticulum membrane|extracellular space|microsome	enzyme binding|heme binding|heme oxygenase (decyclizing) activity|protein homodimerization activity|signal transducer activity			ovary(1)	1					NADH(DB00157)	GAGCTGCTGACCCATGACACC	0.562													3	21	---	---	---	---	PASS
DCAF8L1	139425	broad.mit.edu	37	X	27997690	27997690	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:27997690C>T	uc004dbx.1	-	1	1877	c.1762G>A	c.(1762-1764)GAG>AAG	p.E588K		NM_001017930	NP_001017930	A6NGE4	DC8L1_HUMAN	DDB1 and CUL4 associated factor 8-like 1	588										ovary(3)|skin(1)	4						CCCTCCTCCTCGGATGTATCT	0.502													14	47	---	---	---	---	PASS
MIR1298	100302153	broad.mit.edu	37	X	113949683	113949683	+	RNA	SNP	G	T	T			TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:113949683G>T	hsa-mir-1298|MI0003938	+			c.34G>T			HTR2C_uc004epu.1_Intron|HTR2C_uc010nqc.1_Intron|HTR2C_uc004epv.1_Intron																	0						CGGCTGTCCAGATGTATCCAA	0.433													9	47	---	---	---	---	PASS
BRS3	680	broad.mit.edu	37	X	135570317	135570317	+	Nonsense_Mutation	SNP	C	A	A			TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:135570317C>A	uc004ezv.1	+	1	193	c.44C>A	c.(43-45)TCA>TAA	p.S15*		NM_001727	NP_001718	P32247	BRS3_HUMAN	bombesin-like receptor 3	15	Extracellular (Potential).				adult feeding behavior|glucose metabolic process|regulation of blood pressure	integral to membrane|plasma membrane	bombesin receptor activity			ovary(1)	1	Acute lymphoblastic leukemia(192;0.000127)					ACTTTAATTTCAATCACAAAT	0.388													8	50	---	---	---	---	PASS
USP24	23358	broad.mit.edu	37	1	55557859	55557860	+	Intron	INS	-	TT	TT	rs144000884	by1000genomes	TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:55557859_55557860insTT	uc001cyg.3	-							NM_015306	NP_056121	Q9UPU5	UBP24_HUMAN	ubiquitin specific protease 24						ubiquitin-dependent protein catabolic process		binding|cysteine-type peptidase activity|ubiquitin thiolesterase activity			ovary(6)|kidney(6)|breast(1)	13						ATTATTACACAGTTACGAACTA	0.282													7	5	---	---	---	---	
TAF13	6884	broad.mit.edu	37	1	109617401	109617402	+	Intron	INS	-	A	A	rs35227534		TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:109617401_109617402insA	uc001dwm.1	-							NM_005645	NP_005636	Q15543	TAF13_HUMAN	TBP-associated factor 13						transcription elongation from RNA polymerase II promoter|viral reproduction	transcription factor TFIID complex	protein C-terminus binding|sequence-specific DNA binding transcription factor activity				0		all_epithelial(167;0.000102)|all_lung(203;0.000321)|Lung NSC(277;0.000626)		Colorectal(144;0.0138)|Lung(183;0.0425)|COAD - Colon adenocarcinoma(174;0.113)|Epithelial(280;0.166)|all cancers(265;0.191)|LUSC - Lung squamous cell carcinoma(189;0.228)		gactccgtctcaaaaaaaaaaa	0.153													4	3	---	---	---	---	
NBPF10	100132406	broad.mit.edu	37	1	145209324	145209332	+	5'UTR	DEL	GGCGGCGGC	-	-	rs72083240	by1000genomes	TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145209324_145209332delGGCGGCGGC	uc001emp.3	+	1					NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|NOTCH2NL_uc001emn.3_5'UTR|NOTCH2NL_uc001emm.3_5'UTR|NOTCH2NL_uc001emo.2_5'UTR|NOTCH2NL_uc010oyh.1_RNA	NM_017940	NP_060410	A6NDV3	A6NDV3_HUMAN	hypothetical protein LOC55672												0	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		GATCTGCCCAggcggcggcggcggcggcg	0.589													4	2	---	---	---	---	
UGGT1	56886	broad.mit.edu	37	2	128941484	128941485	+	Intron	DEL	GT	-	-	rs67237920		TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:128941484_128941485delGT	uc002tps.2	+						UGGT1_uc002tpr.2_Intron	NM_020120	NP_064505	Q9NYU2	UGGG1_HUMAN	UDP-glucose ceramide glucosyltransferase-like 1						'de novo' posttranslational protein folding|post-translational protein modification|protein N-linked glycosylation via asparagine	endoplasmic reticulum lumen|ER-Golgi intermediate compartment	UDP-glucose:glycoprotein glucosyltransferase activity|unfolded protein binding			ovary(1)	1						TTTTTTCATGgtgtgtgtgtgt	0.292													4	2	---	---	---	---	
FASTKD1	79675	broad.mit.edu	37	2	170425526	170425526	+	Intron	DEL	C	-	-			TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:170425526delC	uc002uev.3	-						FASTKD1_uc002uew.3_Intron|FASTKD1_uc002uex.3_Intron|FASTKD1_uc002uey.2_Intron	NM_024622	NP_078898	Q53R41	FAKD1_HUMAN	FAST kinase domains 1						apoptosis|cellular respiration	mitochondrion	ATP binding|protein kinase activity			ovary(4)	4						aaaaaaaaaaCAACAACACAT	0.164													4	2	---	---	---	---	
DFNB59	494513	broad.mit.edu	37	2	179322311	179322312	+	Intron	INS	-	GGTCCCTCCCACC	GGTCCCTCCCACC	rs143243913	by1000genomes	TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179322311_179322312insGGTCCCTCCCACC	uc002umi.3	+						DFNB59_uc002umj.3_Intron	NM_001042702	NP_001036167	Q0ZLH3	PJVK_HUMAN	deafness, autosomal recessive 59						sensory perception of sound						0			OV - Ovarian serous cystadenocarcinoma(117;0.00406)|Epithelial(96;0.0159)|all cancers(119;0.0564)			TGAAAAGCCGTGCTTTTGTGCT	0.436													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	27162863	27162863	+	IGR	DEL	T	-	-			TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:27162863delT								STIM2 (137055 upstream) : None (None downstream)																							TCATGTTCTATTTTTTTTTGG	0.378													4	2	---	---	---	---	
NHEDC1	150159	broad.mit.edu	37	4	103870262	103870263	+	Intron	INS	-	AT	AT			TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:103870262_103870263insAT	uc003hww.2	-						NHEDC1_uc003hwu.2_Intron|NHEDC1_uc010ilm.2_Intron|NHEDC1_uc003hwv.2_Intron|NHEDC1_uc011cev.1_Intron	NM_139173	NP_631912	Q4ZJI4	NHDC1_HUMAN	Na+/H+ exchanger domain containing 1 isoform 1							integral to membrane	solute:hydrogen antiporter activity			ovary(1)|skin(1)	2		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;1.5e-08)		GAGCTGTACACACACACACACA	0.238													4	2	---	---	---	---	
OOEP	441161	broad.mit.edu	37	6	74082632	74082632	+	Intron	DEL	T	-	-			TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:74082632delT	uc003pgv.3	-							NM_001080507	NP_001073976	A6NGQ2	OOEP_HUMAN	oocyte expressed protein homolog							cytoplasm					0						ttttctttccttttttttttt	0.378													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	65160100	65160100	+	Intron	DEL	C	-	-			TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:65160100delC	uc003tud.1	-						INTS4L2_uc003tue.2_RNA					Homo sapiens hypothetical LOC441242, mRNA (cDNA clone MGC:87648 IMAGE:5267764), complete cds.																		AGCACTTGGACCCTCAGGGAG	0.507													36	16	---	---	---	---	
LOC729156	729156	broad.mit.edu	37	7	66304731	66304731	+	Intron	DEL	T	-	-			TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:66304731delT	uc003tvj.1	-							NR_003934				Homo sapiens cDNA FLJ36054 fis, clone TESTI2018290.												0						TTTCTTTCCCttttttttttt	0.438													4	3	---	---	---	---	
SBDS	51119	broad.mit.edu	37	7	66456423	66456424	+	Intron	INS	-	A	A			TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:66456423_66456424insA	uc003tvm.1	-							NM_016038	NP_057122	Q9Y3A5	SBDS_HUMAN	Shwachman-Bodian-Diamond syndrome protein						bone marrow development|bone mineralization|leukocyte chemotaxis|mature ribosome assembly|mitotic spindle stabilization|positive regulation of translation|ribosomal large subunit biogenesis|rRNA processing	cytoplasm|nucleolus|nucleoplasm|spindle pole	microtubule binding|ribosome binding|rRNA binding			ovary(1)	1						aagtgaccgttaaaaaaaaaat	0.059			Gene Conversion			AML|MDS			Shwachman-Diamond_syndrome				4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	117523462	117523464	+	IGR	DEL	AAA	-	-	rs112456636		TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:117523462_117523464delAAA								CTTNBP2 (9901 upstream) : NAA38 (300622 downstream)																							CTGTCAAATGaaaaaaaaaaaaa	0.241													5	3	---	---	---	---	
KLHDC10	23008	broad.mit.edu	37	7	129760949	129760950	+	Intron	INS	-	T	T	rs145009695	by1000genomes	TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:129760949_129760950insT	uc003vpj.1	+						KLHDC10_uc003vpk.1_Intron|KLHDC10_uc010lmb.1_Intron	NM_014997	NP_055812	Q6PID8	KLD10_HUMAN	kelch domain containing 10												0						cctttcttttctttttttttcA	0.287													4	2	---	---	---	---	
AKR1D1	6718	broad.mit.edu	37	7	137707868	137707868	+	Intron	DEL	G	-	-			TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:137707868delG	uc011kqb.1	+						AKR1D1_uc011kqc.1_Intron|AKR1D1_uc011kqd.1_Intron	NM_005989	NP_005980	P51857	AK1D1_HUMAN	aldo-keto reductase family 1, member D1						androgen metabolic process|bile acid biosynthetic process|bile acid catabolic process|C21-steroid hormone metabolic process|cholesterol catabolic process|digestion	cytosol	aldo-keto reductase (NADP) activity|delta4-3-oxosteroid 5beta-reductase activity|steroid binding			skin(1)	1						aaaaaaaaaaGATTTTTAGAG	0.169													4	2	---	---	---	---	
IARS	3376	broad.mit.edu	37	9	95055581	95055585	+	Intron	DEL	AATAA	-	-			TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:95055581_95055585delAATAA	uc004art.1	-						IARS_uc004aru.3_Intron|IARS_uc010mqr.2_Intron|IARS_uc010mqt.2_Intron|SNORA84_uc010mqv.2_5'Flank	NM_013417	NP_038203	P41252	SYIC_HUMAN	isoleucine tRNA synthetase						isoleucyl-tRNA aminoacylation	cytosol|nucleus|soluble fraction	ATP binding|isoleucine-tRNA ligase activity|protein binding			ovary(1)|skin(1)	2					L-Isoleucine(DB00167)	acggtacatcaataaaataagtatc	0.078													3	4	---	---	---	---	
VWA2	340706	broad.mit.edu	37	10	116014989	116014989	+	Intron	DEL	T	-	-			TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:116014989delT	uc001lbl.1	+						VWA2_uc001lbk.1_Intron|VWA2_uc009xyf.1_Intron	NM_198496	NP_940898	Q5GFL6	VWA2_HUMAN	von Willebrand factor A domain containing 2							extracellular region				ovary(2)|large_intestine(1)|central_nervous_system(1)|skin(1)	5				Epithelial(162;0.036)|all cancers(201;0.0793)		catctttttcttttttttttt	0.000													3	3	---	---	---	---	
NCAPD3	23310	broad.mit.edu	37	11	134029714	134029717	+	Intron	DEL	CAGA	-	-	rs151072505		TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:134029714_134029717delCAGA	uc001qhd.1	-						NCAPD3_uc010scm.1_Intron|NCAPD3_uc009zda.1_Intron|NCAPD3_uc001qhc.1_Intron	NM_015261	NP_056076	P42695	CNDD3_HUMAN	non-SMC condensin II complex, subunit D3						cell division|mitotic chromosome condensation	nuclear centromeric heterochromatin|nuclear condensin complex	methylated histone residue binding			ovary(2)|upper_aerodigestive_tract(1)|lung(1)|kidney(1)	5	all_hematologic(175;0.127)	all_cancers(12;1.68e-21)|all_epithelial(12;5.86e-16)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000182)|Medulloblastoma(222;0.0245)|all_neural(223;0.0505)|Esophageal squamous(93;0.0559)		Epithelial(10;8.74e-10)|BRCA - Breast invasive adenocarcinoma(10;1e-08)|all cancers(11;1.46e-08)|OV - Ovarian serous cystadenocarcinoma(99;0.00345)|Lung(977;0.227)		TGAGAGGTGCCAGACAAACGACAG	0.578													7	5	---	---	---	---	
ACSM4	341392	broad.mit.edu	37	12	7476752	7476752	+	Intron	DEL	A	-	-			TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:7476752delA	uc001qsx.1	+							NM_001080454	NP_001073923	P0C7M7	ACSM4_HUMAN	acyl-CoA synthetase medium-chain family member 4						fatty acid metabolic process	mitochondrial matrix	ATP binding|butyrate-CoA ligase activity|metal ion binding				0						actctgtctcaaaaaaaaaaa	0.169													4	2	---	---	---	---	
SLC2A3	6515	broad.mit.edu	37	12	8082586	8082586	+	Intron	DEL	T	-	-			TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:8082586delT	uc001qtr.2	-						SLC2A3_uc001qts.2_3'UTR	NM_006931	NP_008862	P11169	GTR3_HUMAN	solute carrier family 2 (facilitated glucose						carbohydrate metabolic process|water-soluble vitamin metabolic process	integral to membrane|plasma membrane	D-glucose transmembrane transporter activity|dehydroascorbic acid transporter activity			ovary(3)|pancreas(1)	4				Kidney(36;0.0866)		CATCCATTCCttttttttttt	0.254													6	4	---	---	---	---	
DENND5B	160518	broad.mit.edu	37	12	31562360	31562360	+	Intron	DEL	A	-	-	rs111670680		TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:31562360delA	uc001rki.1	-						DENND5B_uc001rkh.1_Intron|DENND5B_uc009zjq.1_Intron	NM_144973	NP_659410	Q6ZUT9	DEN5B_HUMAN	DENN/MADD domain containing 5B							integral to membrane				ovary(1)|central_nervous_system(1)	2						AGTATCAAAGAAAAAAAAAAA	0.254													5	3	---	---	---	---	
PPFIA2	8499	broad.mit.edu	37	12	81655692	81655693	+	Intron	INS	-	T	T			TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:81655692_81655693insT	uc001szo.1	-						PPFIA2_uc010sue.1_Intron|PPFIA2_uc010sug.1_Intron|PPFIA2_uc010suh.1_Intron|PPFIA2_uc010suf.1_Intron|PPFIA2_uc009zsh.2_Intron	NM_003625	NP_003616	B7Z663	B7Z663_HUMAN	PTPRF interacting protein alpha 2											ovary(3)|lung(2)|pancreas(1)	6						ATTTTTTTGTCTTTTTTTTTTT	0.406													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	21835723	21835728	+	IGR	DEL	GGCGAG	-	-			TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:21835723_21835728delGGCGAG								MRP63 (82505 upstream) : ZDHHC20 (114782 downstream)																							GATGGACTGAGGCGAGGGGTGGGACT	0.646													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	48340720	48340720	+	IGR	DEL	T	-	-	rs112736233		TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:48340720delT								HTR2A (869670 upstream) : SUCLA2 (176072 downstream)																							GTTTTTGTTGTTTTTTTTTTT	0.234													4	2	---	---	---	---	
C14orf37	145407	broad.mit.edu	37	14	58737826	58737826	+	Intron	DEL	A	-	-			TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:58737826delA	uc010tro.1	-						PSMA3_uc001xdj.1_Intron|PSMA3_uc001xdk.1_Intron|uc001xdl.2_Intron	NM_001001872	NP_001001872	Q86TY3	CN037_HUMAN	hypothetical protein LOC145407 precursor							integral to membrane	binding				0						tccctaatttaaaaaaaaaaa	0.209													4	2	---	---	---	---	
UBR1	197131	broad.mit.edu	37	15	43262925	43262925	+	Intron	DEL	T	-	-			TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43262925delT	uc001zqq.2	-							NM_174916	NP_777576	Q8IWV7	UBR1_HUMAN	ubiquitin protein ligase E3 component n-recognin						cellular response to leucine|negative regulation of TOR signaling cascade	cytosol	leucine binding|zinc ion binding			lung(1)	1		all_cancers(109;4.32e-15)|all_epithelial(112;4.05e-13)|Lung NSC(122;1.75e-08)|all_lung(180;2e-07)|Melanoma(134;0.0179)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;4.08e-07)|COAD - Colon adenocarcinoma(120;0.185)|Colorectal(105;0.214)		GGttctttccttttttttttt	0.129													4	2	---	---	---	---	
FLYWCH1	84256	broad.mit.edu	37	16	2988609	2988609	+	Intron	DEL	T	-	-			TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2988609delT	uc002csd.2	+						FLYWCH1_uc002csb.2_Intron|FLYWCH1_uc002csc.2_Intron|FLYWCH1_uc010bsv.2_Intron|FLYWCH1_uc002cse.2_Intron	NM_032296	NP_115672	Q4VC44	FWCH1_HUMAN	FLYWCH-type zinc finger 1 isoform a							nucleus	DNA binding|metal ion binding				0						CCAGtctttgttttttttttt	0.224													4	3	---	---	---	---	
CHRNB1	1140	broad.mit.edu	37	17	7359369	7359380	+	Intron	DEL	TTTTTTTTTTTT	-	-	rs67180661		TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7359369_7359380delTTTTTTTTTTTT	uc002ghb.2	+						CHRNB1_uc010vty.1_Intron	NM_000747	NP_000738	P11230	ACHB_HUMAN	nicotinic acetylcholine receptor beta 1 subunit						behavioral response to nicotine|muscle contraction|muscle fiber development|neuromuscular synaptic transmission|postsynaptic membrane organization|regulation of membrane potential|synaptic transmission, cholinergic	cell junction|nicotinic acetylcholine-gated receptor-channel complex|postsynaptic membrane	acetylcholine binding|receptor activity			ovary(2)	2		Prostate(122;0.157)				tttttttggctttttttttttttttttttttt	0.241													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	7858583	7858584	+	IGR	INS	-	A	A	rs78611358		TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7858583_7858584insA								CNTROB (5688 upstream) : GUCY2D (47404 downstream)																							cctgtctcaagaaaaaaaaaaa	0.168													5	3	---	---	---	---	
USP32	84669	broad.mit.edu	37	17	58332410	58332410	+	Intron	DEL	T	-	-	rs35284371		TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:58332410delT	uc002iyo.1	-						USP32_uc002iyn.1_Intron|USP32_uc010wov.1_Intron	NM_032582	NP_115971	Q8NFA0	UBP32_HUMAN	ubiquitin specific protease 32						protein deubiquitination|ubiquitin-dependent protein catabolic process	Golgi apparatus|membrane	calcium ion binding|cysteine-type peptidase activity|ubiquitin thiolesterase activity			lung(2)|breast(2)|large_intestine(1)	5	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;2.02e-11)|all cancers(12;5.23e-10)|Colorectal(3;0.198)			AATGTAGTTCttttttttttt	0.353													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	2056544	2056545	+	IGR	DEL	AC	-	-	rs72165579		TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:2056544_2056545delAC								PDYN (81841 upstream) : STK35 (25983 downstream)																							AAAAAAAAATacacacacacac	0.178													3	3	---	---	---	---	
PLCB1	23236	broad.mit.edu	37	20	8665965	8665966	+	Intron	DEL	CA	-	-	rs75405686		TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:8665965_8665966delCA	uc002wnb.2	+						PLCB1_uc010zrb.1_Intron|PLCB1_uc002wna.2_Intron|PLCB1_uc002wnc.1_Intron	NM_015192	NP_056007	Q9NQ66	PLCB1_HUMAN	phosphoinositide-specific phospholipase C beta 1						activation of meiosis involved in egg activation|CD24 biosynthetic process|cerebral cortex development|G1 phase|G2/M transition of mitotic cell cycle|glutamate signaling pathway|insulin-like growth factor receptor signaling pathway|interleukin-1-mediated signaling pathway|interleukin-12-mediated signaling pathway|interleukin-15-mediated signaling pathway|intracellular signal transduction|lipid catabolic process|memory|muscarinic acetylcholine receptor signaling pathway|negative regulation of monocyte extravasation|negative regulation of transcription, DNA-dependent|phosphatidylinositol metabolic process|positive regulation of acrosome reaction|positive regulation of developmental growth|positive regulation of embryonic development|positive regulation of interleukin-12 production|positive regulation of JNK cascade|positive regulation of myoblast differentiation|positive regulation of transcription, DNA-dependent|regulation of fertilization|regulation of G-protein coupled receptor protein signaling pathway|synaptic transmission	cytosol|nuclear chromatin|nuclear speck	calcium ion binding|calmodulin binding|enzyme binding|GTPase activator activity|phosphatidylinositol phospholipase C activity|phosphatidylinositol-4,5-bisphosphate binding|protein homodimerization activity|signal transducer activity			ovary(4)|breast(3)|upper_aerodigestive_tract(2)|skin(2)|lung(1)	12						AAAATGCAACCACGGCTGACAT	0.441													6	3	---	---	---	---	
C20orf12	55184	broad.mit.edu	37	20	18429510	18429511	+	Intron	INS	-	A	A	rs78222530		TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:18429510_18429511insA	uc010zsa.1	-						C20orf12_uc002wqr.3_Intron|C20orf12_uc002wqs.3_Intron|C20orf12_uc002wqq.3_Intron|C20orf12_uc002wqu.1_Intron|C20orf12_uc010gct.1_Intron	NM_001099407	NP_001092877	Q9NVP4	CT012_HUMAN	hypothetical protein LOC55184							intracellular	zinc ion binding			ovary(1)	1		Myeloproliferative disorder(85;0.0122)				gactccgtctcaaaaaaaaaaa	0.149													6	3	---	---	---	---	
OSBPL2	9885	broad.mit.edu	37	20	60859431	60859431	+	Intron	DEL	T	-	-	rs112769454		TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:60859431delT	uc002yck.1	+						OSBPL2_uc002ycl.1_Intron|OSBPL2_uc011aah.1_Intron|OSBPL2_uc002ycm.1_3'UTR	NM_144498	NP_653081	Q9H1P3	OSBL2_HUMAN	oxysterol-binding protein-like protein 2 isoform						lipid transport		lipid binding			ovary(1)|central_nervous_system(1)	2	Breast(26;7.76e-09)		BRCA - Breast invasive adenocarcinoma(19;1.33e-06)			tttctttccattttttttttt	0.204													5	3	---	---	---	---	
DIP2A	23181	broad.mit.edu	37	21	47976820	47976820	+	Intron	DEL	T	-	-			TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:47976820delT	uc002zjo.2	+						DIP2A_uc011afz.1_Intron|DIP2A_uc002zjr.2_Intron	NM_015151	NP_055966	Q14689	DIP2A_HUMAN	disco-interacting protein 2A isoform a						multicellular organismal development	nucleus	catalytic activity|transcription factor binding			ovary(2)	2	Breast(49;0.0933)			Epithelial(3;3.12e-06)|OV - Ovarian serous cystadenocarcinoma(3;5.68e-06)|all cancers(3;4.08e-05)|Colorectal(79;0.0129)|COAD - Colon adenocarcinoma(84;0.0824)		TTCATTTCACTTTTTTTTTTT	0.468													3	3	---	---	---	---	
TTLL1	25809	broad.mit.edu	37	22	43435575	43435576	+	3'UTR	INS	-	A	A	rs143546633	by1000genomes	TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:43435575_43435576insA	uc003bdi.2	-	11					TTLL1_uc010gzh.2_3'UTR|TTLL1_uc003bdj.2_3'UTR|TTLL1_uc003bdh.2_3'UTR	NM_012263	NP_036395	O95922	TTLL1_HUMAN	tubulin tyrosine ligase-like family, member 1						protein polyglutamylation	cytoplasm|microtubule	ATP binding|tubulin-glutamic acid ligase activity|tubulin-tyrosine ligase activity			skin(1)	1		Ovarian(80;0.0694)		BRCA - Breast invasive adenocarcinoma(115;0.00461)		GGTTAAAAATTAAAAAAAAAAG	0.312													3	4	---	---	---	---	
SMC1B	27127	broad.mit.edu	37	22	45749773	45749774	+	Intron	INS	-	A	A			TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:45749773_45749774insA	uc003bgc.2	-						SMC1B_uc003bgd.2_Intron	NM_148674	NP_683515	Q8NDV3	SMC1B_HUMAN	SMC1 structural maintenance of chromosomes						chromosome organization|meiosis	chromosome, centromeric region|cytoplasm|meiotic cohesin complex|nucleus	ATP binding			ovary(2)	2		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0182)		TATTTCCCACCaaaaaaaaaaa	0.327													14	7	---	---	---	---	
SHROOM4	57477	broad.mit.edu	37	X	50378792	50378792	+	Intron	DEL	G	-	-	rs5915290	by1000genomes	TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:50378792delG	uc004dpe.2	-						SHROOM4_uc004dpd.3_Intron|SHROOM4_uc004dpf.1_Intron	NM_020717	NP_065768	Q9ULL8	SHRM4_HUMAN	shroom family member 4						actin filament organization|brain development|cell morphogenesis|cognition	apical plasma membrane|basal plasma membrane|internal side of plasma membrane|nucleus	actin filament binding			upper_aerodigestive_tract(1)	1	Ovarian(276;0.236)					AAAAAAAAAAGGGGGAAGAAA	0.483													2	4	---	---	---	---	
LONRF3	79836	broad.mit.edu	37	X	118140361	118140361	+	Intron	DEL	C	-	-			TCGA-CJ-6028-01A-11D-1669-08	TCGA-CJ-6028-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:118140361delC	uc004eqw.2	+						LONRF3_uc004eqx.2_Intron|LONRF3_uc004eqy.2_Intron|LONRF3_uc004eqz.2_Intron	NM_001031855	NP_001027026	Q496Y0	LONF3_HUMAN	LON peptidase N-terminal domain and ring finger						proteolysis		ATP-dependent peptidase activity|protein binding|zinc ion binding			breast(1)|central_nervous_system(1)	2						CTCCTGTCttctttttttttt	0.244													7	5	---	---	---	---	
