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
TMEM51	55092	broad.mit.edu	37	1	15541519	15541519	+	5'UTR	SNP	T	C	C			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:15541519T>C	uc001avw.3	+	3					TMEM51_uc010obk.1_5'UTR|TMEM51_uc001avz.2_5'UTR|TMEM51_uc001avy.2_5'UTR|TMEM51_uc001avx.2_5'UTR	NM_001136216	NP_001129688	Q9NW97	TMM51_HUMAN	transmembrane protein 51							integral to membrane					0		Renal(390;0.00145)|Breast(348;0.00186)|Colorectal(325;0.00215)|all_lung(284;0.00459)|Lung NSC(340;0.0104)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0798)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0265)|Colorectal(212;2.07e-06)|COAD - Colon adenocarcinoma(227;7.14e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000175)|KIRC - Kidney renal clear cell carcinoma(229;0.00141)|STAD - Stomach adenocarcinoma(313;0.00644)|READ - Rectum adenocarcinoma(331;0.0751)		GTTTTTGTTGTGACTGCTGCC	0.512													3	44	---	---	---	---	PASS
RCC2	55920	broad.mit.edu	37	1	17748729	17748729	+	Silent	SNP	G	A	A			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17748729G>A	uc001bal.2	-	5	761	c.714C>T	c.(712-714)AAC>AAT	p.N238N	RCC2_uc001bam.2_Silent_p.N238N	NM_001136204	NP_001129676	Q9P258	RCC2_HUMAN	regulator of chromosome condensation 2	238	RCC1 3.				cell division|mitotic prometaphase	chromosome, centromeric region|cytosol|microtubule|nucleolus|spindle					0		Colorectal(325;0.000147)|Breast(348;0.00122)|Renal(390;0.00145)|all_lung(284;0.0054)|Lung NSC(340;0.00566)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0439)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00492)|BRCA - Breast invasive adenocarcinoma(304;7.69e-06)|COAD - Colon adenocarcinoma(227;1.19e-05)|Kidney(64;0.000189)|KIRC - Kidney renal clear cell carcinoma(64;0.00273)|STAD - Stomach adenocarcinoma(196;0.0135)|READ - Rectum adenocarcinoma(331;0.0656)|Lung(427;0.19)		CGTCTGTCTGGTTGCCAAGGC	0.502													60	85	---	---	---	---	PASS
PTPRU	10076	broad.mit.edu	37	1	29585159	29585159	+	Silent	SNP	C	T	T			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:29585159C>T	uc001bru.2	+	3	458	c.348C>T	c.(346-348)ACC>ACT	p.T116T	PTPRU_uc001brv.2_Silent_p.T116T|PTPRU_uc001brw.2_Silent_p.T116T|PTPRU_uc009vtq.2_Silent_p.T116T|PTPRU_uc009vtr.2_Silent_p.T116T	NM_005704	NP_005695	Q92729	PTPRU_HUMAN	protein tyrosine phosphatase, receptor type, U	116	Extracellular (Potential).|MAM.				canonical Wnt receptor signaling pathway|cell differentiation|negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of transcription, DNA-dependent|protein localization at cell surface|transmembrane receptor protein tyrosine phosphatase signaling pathway	cell-cell junction|integral to plasma membrane	beta-catenin binding|transmembrane receptor protein tyrosine phosphatase activity			large_intestine(3)|ovary(1)|kidney(1)|central_nervous_system(1)|skin(1)	7		Colorectal(325;0.000399)|Lung NSC(340;0.00953)|all_lung(284;0.0112)|Breast(348;0.0126)|all_neural(195;0.0199)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0563)|Medulloblastoma(700;0.123)		Colorectal(126;6.99e-07)|COAD - Colon adenocarcinoma(152;3.18e-05)|STAD - Stomach adenocarcinoma(196;0.0234)|READ - Rectum adenocarcinoma(331;0.0686)|BRCA - Breast invasive adenocarcinoma(304;0.0871)		GCCCGGGCACCCTGGGCGTCT	0.627													49	177	---	---	---	---	PASS
GJB3	2707	broad.mit.edu	37	1	35250435	35250435	+	Nonsense_Mutation	SNP	G	A	A			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:35250435G>A	uc001bxx.2	+	2	687	c.72G>A	c.(70-72)TGG>TGA	p.W24*	GJB3_uc001bxy.2_Nonsense_Mutation_p.W24*|GJB3_uc001bxz.3_Nonsense_Mutation_p.W24*|uc010ohs.1_RNA	NM_024009	NP_076872	O75712	CXB3_HUMAN	connexin 31	24	Helical; (Potential).				cell communication	connexon complex|integral to membrane	gap junction channel activity				0		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.234)				GGCGCATCTGGCTGTCCGTGG	0.617													9	34	---	---	---	---	PASS
EIF2C4	192670	broad.mit.edu	37	1	36319144	36319144	+	Nonsense_Mutation	SNP	C	T	T			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:36319144C>T	uc001bzj.1	+	18	2714	c.2524C>T	c.(2524-2526)CAG>TAG	p.Q842*		NM_017629	NP_060099	Q9HCK5	AGO4_HUMAN	eukaryotic translation initiation factor 2C, 4	842					mRNA catabolic process|negative regulation of translation involved in gene silencing by miRNA	cytoplasmic mRNA processing body|cytosol	protein binding|RNA binding			ovary(1)	1		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				CCGGGATCCTCAGGCCTTGGC	0.403													32	56	---	---	---	---	PASS
ZSWIM5	57643	broad.mit.edu	37	1	45500121	45500121	+	Nonsense_Mutation	SNP	G	C	C			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:45500121G>C	uc001cnd.2	-	11	2540	c.2312C>G	c.(2311-2313)TCA>TGA	p.S771*		NM_020883	NP_065934	Q9P217	ZSWM5_HUMAN	zinc finger, SWIM domain containing 5	771							zinc ion binding				0	Acute lymphoblastic leukemia(166;0.155)					TGCAGAAGCTGAGTTTTCTAA	0.537													4	147	---	---	---	---	PASS
CYP4A11	1579	broad.mit.edu	37	1	47401310	47401310	+	Missense_Mutation	SNP	C	T	T			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:47401310C>T	uc001cqp.3	-	5	571	c.520G>A	c.(520-522)GAA>AAA	p.E174K	CYP4A11_uc001cqq.2_Missense_Mutation_p.E174K|CYP4A11_uc010omm.1_RNA	NM_000778	NP_000769	Q02928	CP4AB_HUMAN	cytochrome P450, family 4, subfamily A,	174					long-chain fatty acid metabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	alkane 1-monooxygenase activity|electron carrier activity|heme binding|oxygen binding			ovary(2)|skin(2)	4					NADH(DB00157)	AGGAGCTCTTCCCATTTGTCC	0.522													6	44	---	---	---	---	PASS
CLCA4	22802	broad.mit.edu	37	1	87031612	87031612	+	Missense_Mutation	SNP	T	C	C			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:87031612T>C	uc009wcs.2	+	6	907	c.863T>C	c.(862-864)ATG>ACG	p.M288T	CLCA4_uc009wct.2_Missense_Mutation_p.M51T|CLCA4_uc009wcu.2_Missense_Mutation_p.M108T	NM_012128	NP_036260	Q14CN2	CLCA4_HUMAN	chloride channel accessory 4	288						apical plasma membrane|extracellular region|integral to plasma membrane	chloride channel activity			ovary(2)	2		Lung NSC(277;0.238)		all cancers(265;0.0202)|Epithelial(280;0.0404)		ACCATACCCATGGTGACACCA	0.408													48	74	---	---	---	---	PASS
LMO4	8543	broad.mit.edu	37	1	87805280	87805280	+	Missense_Mutation	SNP	G	A	A			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:87805280G>A	uc001dmi.2	+	3	1078	c.298G>A	c.(298-300)GTC>ATC	p.V100I	LMO4_uc001dmj.2_Missense_Mutation_p.V100I	NM_006769	NP_006760	P61968	LMO4_HUMAN	LIM domain only 4	100	LIM zinc-binding 2.				neural tube closure|transcription from RNA polymerase II promoter	transcription factor complex	sequence-specific DNA binding transcription factor activity|transcription factor binding|zinc ion binding				0		Lung NSC(277;0.179)		all cancers(265;0.00456)|Epithelial(280;0.0148)|BRCA - Breast invasive adenocarcinoma(282;0.153)		GAGTGAACTCGTCATGAGGGC	0.423													16	45	---	---	---	---	PASS
HSP90B3P	343477	broad.mit.edu	37	1	92108377	92108377	+	Missense_Mutation	SNP	A	C	C			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:92108377A>C	uc010osx.1	+	3	404	c.404A>C	c.(403-405)GAA>GCA	p.E135A		NR_003130				SubName: Full=cDNA FLJ58812, highly similar to Endoplasmin (Heat shock protein 90kDa beta member 1);												0						ACTGAAGGGGAAGTTACCTTC	0.328													15	21	---	---	---	---	PASS
RBM8A	9939	broad.mit.edu	37	1	145507665	145507665	+	5'UTR	SNP	A	T	T			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145507665A>T	uc001ent.1	+	1					NBPF10_uc001emp.3_Intron|RBM8A_uc001enu.1_5'UTR|RBM8A_uc001enw.1_5'Flank	NM_005105	NP_005096	Q9Y5S9	RBM8A_HUMAN	RNA binding motif protein 8A						mRNA 3'-end processing|mRNA export from nucleus|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|regulation of translation|termination of RNA polymerase II transcription	catalytic step 2 spliceosome|cytosol|exon-exon junction complex|nuclear speck	mRNA binding|nucleotide binding|protein binding				0	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					ATCGAAGGCGAGATGGCGGAC	0.592											OREG0013748	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	21	8	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	1	151740639	151740639	+	IGR	SNP	G	T	T			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151740639G>T								OAZ3 (-3166 upstream) : OAZ3 (-5194 downstream)																							CCATTGGCACGGCCTTCTCTG	0.567													13	45	---	---	---	---	PASS
LCE1B	353132	broad.mit.edu	37	1	152785104	152785104	+	Missense_Mutation	SNP	G	C	C			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152785104G>C	uc001faq.2	+	1	658	c.182G>C	c.(181-183)GGC>GCC	p.G61A		NM_178349	NP_848126	Q5T7P3	LCE1B_HUMAN	late cornified envelope 1B	61	Gly-rich.				keratinization						0	Lung NSC(65;9.06e-30)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			GGAAGCTGTGGCTCCAGCTCT	0.652													104	66	---	---	---	---	PASS
OR10T2	128360	broad.mit.edu	37	1	158368416	158368416	+	Missense_Mutation	SNP	C	G	G			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158368416C>G	uc010pih.1	-	1	841	c.841G>C	c.(841-843)GTT>CTT	p.V281L		NM_001004475	NP_001004475	Q8NGX3	O10T2_HUMAN	olfactory receptor, family 10, subfamily T,	281	Helical; Name=7; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|central_nervous_system(1)	3	all_hematologic(112;0.0378)					AAGGGAGTAACCACTGTGTAG	0.473													34	24	---	---	---	---	PASS
IGSF9	57549	broad.mit.edu	37	1	159901558	159901558	+	Intron	SNP	T	G	G			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:159901558T>G	uc001fur.2	-						IGSF9_uc001fuq.2_Intron|IGSF9_uc001fup.2_5'UTR	NM_001135050	NP_001128522	Q9P2J2	TUTLA_HUMAN	immunoglobulin superfamily, member 9 isoform a							cell junction|integral to membrane|synapse				ovary(2)|central_nervous_system(2)|large_intestine(1)	5	all_hematologic(112;0.0597)	Breast(1374;0.000126)	BRCA - Breast invasive adenocarcinoma(70;0.111)			GAGGCAGGGGTGTAGTGGGCG	0.642													7	33	---	---	---	---	PASS
NPHS2	7827	broad.mit.edu	37	1	179520276	179520276	+	3'UTR	SNP	C	G	G			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:179520276C>G	uc001gmq.3	-	8					C1orf125_uc009wxg.2_Intron|C1orf125_uc001gmo.2_Intron|C1orf125_uc001gmp.2_Intron|C1orf125_uc009wxh.2_Intron|NPHS2_uc009wxi.2_3'UTR|C1orf125_uc001gmr.2_RNA	NM_014625	NP_055440	Q9NP85	PODO_HUMAN	podocin						excretion	integral to plasma membrane	protein binding				0						CTATGGCAGGCCCCTTTACAG	0.488													7	52	---	---	---	---	PASS
FAM5C	339479	broad.mit.edu	37	1	190067888	190067888	+	Missense_Mutation	SNP	G	T	T			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:190067888G>T	uc001gse.1	-	8	1793	c.1561C>A	c.(1561-1563)CTC>ATC	p.L521I	FAM5C_uc010pot.1_Missense_Mutation_p.L419I	NM_199051	NP_950252	Q76B58	FAM5C_HUMAN	family with sequence similarity 5, member C	521						extracellular region				lung(2)|ovary(1)|kidney(1)|skin(1)	5	Prostate(682;0.198)					CAGCTATTGAGGCGCATGTCA	0.453													4	194	---	---	---	---	PASS
F13B	2165	broad.mit.edu	37	1	197024881	197024881	+	Missense_Mutation	SNP	C	T	T			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:197024881C>T	uc001gtt.1	-	8	1362	c.1318G>A	c.(1318-1320)GAA>AAA	p.E440K		NM_001994	NP_001985	P05160	F13B_HUMAN	coagulation factor XIII B subunit precursor	440	Sushi 7.				blood coagulation	extracellular region				upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	3						TTTCCTTGTTCGCAACGAGAT	0.393													23	148	---	---	---	---	PASS
USH2A	7399	broad.mit.edu	37	1	215990344	215990344	+	Missense_Mutation	SNP	C	T	T			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:215990344C>T	uc001hku.1	-	48	9952	c.9565G>A	c.(9565-9567)GCT>ACT	p.A3189T		NM_206933	NP_996816	O75445	USH2A_HUMAN	usherin isoform B	3189	Extracellular (Potential).|Fibronectin type-III 18.				maintenance of organ identity|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	basement membrane|cytoplasm|integral to membrane|stereocilium membrane	collagen binding			ovary(20)|upper_aerodigestive_tract(2)|skin(2)|kidney(1)|central_nervous_system(1)	26				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		CTTACCTTAGCTTCAGAAGAA	0.383										HNSCC(13;0.011)			119	67	---	---	---	---	PASS
RSAD2	91543	broad.mit.edu	37	2	7023569	7023569	+	Silent	SNP	G	A	A			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:7023569G>A	uc002qyp.1	+	2	550	c.414G>A	c.(412-414)AAG>AAA	p.K138K		NM_080657	NP_542388	Q8WXG1	RSAD2_HUMAN	radical S-adenosyl methionine domain containing	138					defense response to virus	endoplasmic reticulum membrane|Golgi apparatus	catalytic activity|iron-sulfur cluster binding|metal ion binding				0	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			OV - Ovarian serous cystadenocarcinoma(76;0.191)		ACCTGGGCAAGTTGGTGAGGT	0.502													34	52	---	---	---	---	PASS
PELI1	57162	broad.mit.edu	37	2	64321981	64321981	+	Missense_Mutation	SNP	C	A	A			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:64321981C>A	uc002scs.3	-	6	5151	c.1112G>T	c.(1111-1113)TGT>TTT	p.C371F	PELI1_uc002sct.3_Missense_Mutation_p.C371F|PELI1_uc002scr.3_Missense_Mutation_p.C192F	NM_020651	NP_065702	Q96FA3	PELI1_HUMAN	pellino protein	371					innate immune response|MyD88-dependent toll-like receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway	cytosol				ovary(1)	1						CTTTTCTGAACACACATGCCC	0.512													4	117	---	---	---	---	PASS
NAGK	55577	broad.mit.edu	37	2	71299849	71299849	+	Missense_Mutation	SNP	G	C	C			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:71299849G>C	uc002shp.3	+	5	840	c.434G>C	c.(433-435)GGC>GCC	p.G145A	NAGK_uc010fea.2_RNA|NAGK_uc002shq.3_5'UTR|NAGK_uc002shr.2_Missense_Mutation_p.G94A	NM_017567	NP_060037	Q9UJ70	NAGK_HUMAN	N-Acetylglucosamine kinase	145	Substrate binding.				N-acetylglucosamine metabolic process|N-acetylmannosamine metabolic process		ATP binding|N-acetylglucosamine kinase activity|protein binding				0					N-Acetyl-D-glucosamine(DB00141)	GGCTGCGGCGGCTGGGGCCAT	0.582													10	22	---	---	---	---	PASS
C2orf29	55571	broad.mit.edu	37	2	101883240	101883240	+	Missense_Mutation	SNP	A	G	G			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:101883240A>G	uc002taw.3	+	5	1219	c.1137A>G	c.(1135-1137)ATA>ATG	p.I379M		NM_017546	NP_060016	Q9UKZ1	CB029_HUMAN	hypothetical protein LOC55571	379					cell proliferation|nuclear-transcribed mRNA poly(A) tail shortening	cytosol				ovary(2)|pancreas(1)|central_nervous_system(1)|skin(1)	5						TAGTCGCTATAGAAATGTTGC	0.413													75	130	---	---	---	---	PASS
NPHP1	4867	broad.mit.edu	37	2	110922222	110922222	+	Missense_Mutation	SNP	G	T	T			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:110922222G>T	uc002tfn.3	-	8	908	c.814C>A	c.(814-816)CTA>ATA	p.L272I	NPHP1_uc002tfm.3_Intron|NPHP1_uc002tfl.3_Missense_Mutation_p.L272I|NPHP1_uc002tfo.3_Intron|NPHP1_uc010ywx.1_Intron|NPHP1_uc010fjv.1_Intron	NM_207181	NP_997064	O15259	NPHP1_HUMAN	nephrocystin 1 isoform 2	272					actin cytoskeleton organization|cell projection organization|cell-cell adhesion|excretion|retina development in camera-type eye|signal transduction|spermatid differentiation|visual behavior	adherens junction|cell-cell junction|cilium axoneme|cytoplasm|cytoskeleton|motile cilium|photoreceptor connecting cilium	protein binding|structural molecule activity			ovary(2)	2						AGAACTATTAGGTAGCAAAAC	0.458													89	196	---	---	---	---	PASS
ACVR1	90	broad.mit.edu	37	2	158595006	158595006	+	Silent	SNP	T	C	C			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:158595006T>C	uc002tzm.3	-	11	1680	c.1341A>G	c.(1339-1341)GTA>GTG	p.V447V	ACVR1_uc002tzn.3_Silent_p.V447V|ACVR1_uc010fog.2_Silent_p.V447V	NM_001111067	NP_001104537	Q04771	ACVR1_HUMAN	activin A receptor, type I precursor	447	Cytoplasmic (Potential).|Protein kinase.				BMP signaling pathway|G1/S transition of mitotic cell cycle|negative regulation of activin receptor signaling pathway|negative regulation of apoptosis|positive regulation of bone mineralization|positive regulation of osteoblast differentiation|positive regulation of transcription, DNA-dependent|transforming growth factor beta receptor signaling pathway	activin receptor complex	activin binding|ATP binding|follistatin binding|metal ion binding|protein homodimerization activity|SMAD binding|transforming growth factor beta binding			ovary(2)|skin(1)	3				BRCA - Breast invasive adenocarcinoma(221;0.104)	Adenosine triphosphate(DB00171)	CCACACAGACTACCTTCCTCA	0.443													69	164	---	---	---	---	PASS
SETD5	55209	broad.mit.edu	37	3	9495474	9495474	+	Missense_Mutation	SNP	C	A	A			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:9495474C>A	uc003brt.2	+	17	2833	c.2398C>A	c.(2398-2400)CCC>ACC	p.P800T	SETD5_uc003brs.1_Missense_Mutation_p.P781T|SETD5_uc003bru.2_Missense_Mutation_p.P702T|SETD5_uc003brv.2_Missense_Mutation_p.P689T|SETD5_uc010hck.2_Missense_Mutation_p.P282T|SETD5_uc003brx.2_Missense_Mutation_p.P469T	NM_001080517	NP_001073986	Q9C0A6	SETD5_HUMAN	SET domain containing 5	800										ovary(2)	2	Medulloblastoma(99;0.227)			OV - Ovarian serous cystadenocarcinoma(96;0.112)		ATCATCTGTACCCCAAGAGAC	0.363													25	27	---	---	---	---	PASS
ZMYND10	51364	broad.mit.edu	37	3	50380356	50380356	+	Silent	SNP	C	T	T			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:50380356C>T	uc003dag.1	-	7	839	c.693G>A	c.(691-693)CGG>CGA	p.R231R	RASSF1_uc003dad.1_5'Flank|RASSF1_uc003dae.1_5'Flank|RASSF1_uc010hlk.1_5'Flank|RASSF1_uc003daf.1_5'Flank|RASSF1_uc011bdq.1_5'Flank|ZMYND10_uc010hll.1_Intron|ZMYND10_uc003dah.1_Silent_p.R152R	NM_015896	NP_056980	O75800	ZMY10_HUMAN	zinc finger, MYND domain-containing 10	231						cytoplasm	protein binding|zinc ion binding			lung(4)|ovary(1)	5				BRCA - Breast invasive adenocarcinoma(193;0.000272)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00607)		TACCTCCTTCCCGCCGGCTCC	0.597										TSP Lung(30;0.18)			19	16	---	---	---	---	PASS
FAM3D	131177	broad.mit.edu	37	3	58619924	58619924	+	3'UTR	SNP	T	G	G			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:58619924T>G	uc003dkq.2	-	10						NM_138805	NP_620160	Q96BQ1	FAM3D_HUMAN	family with sequence similarity 3, member D						negative regulation of insulin secretion	extracellular region	cytokine activity				0				BRCA - Breast invasive adenocarcinoma(55;0.000225)|Kidney(10;0.000667)|KIRC - Kidney renal clear cell carcinoma(10;0.000802)|OV - Ovarian serous cystadenocarcinoma(275;0.169)		CTGCTCCTCCTCCTCAGCCCC	0.637													20	13	---	---	---	---	PASS
POPDC2	64091	broad.mit.edu	37	3	119367299	119367299	+	Missense_Mutation	SNP	G	A	A			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:119367299G>A	uc003ecx.1	-	3	951	c.817C>T	c.(817-819)CCC>TCC	p.P273S	POPDC2_uc010hqw.1_Missense_Mutation_p.P273S|POPDC2_uc003ecy.1_Missense_Mutation_p.P91S	NM_022135	NP_071418	Q9HBU9	POPD2_HUMAN	popeye protein 2	273						integral to membrane				central_nervous_system(1)	1				GBM - Glioblastoma multiforme(114;0.242)		GCAGCAGTGGGACCCAGGACA	0.562													40	40	---	---	---	---	PASS
TRH	7200	broad.mit.edu	37	3	129696118	129696118	+	3'UTR	SNP	C	T	T			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:129696118C>T	uc003enc.2	+	3						NM_007117	NP_009048	P20396	TRH_HUMAN	thyrotropin-releasing hormone						cell-cell signaling|hormone-mediated signaling pathway	extracellular region|soluble fraction	neuropeptide hormone activity|thyrotropin-releasing hormone activity			ovary(1)	1						CCTGTGTGCCCCACCATTCAT	0.577													6	12	---	---	---	---	PASS
CP	1356	broad.mit.edu	37	3	148928072	148928072	+	Silent	SNP	T	C	C			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:148928072T>C	uc003ewy.3	-	3	742	c.489A>G	c.(487-489)GAA>GAG	p.E163E	CP_uc011bnr.1_RNA|CP_uc003ewx.3_5'Flank|CP_uc003ewz.2_Silent_p.E163E|CP_uc010hvf.1_5'Flank	NM_000096	NP_000087	P00450	CERU_HUMAN	ceruloplasmin precursor	163	F5/8 type A 1.|Plastocyanin-like 1.				cellular iron ion homeostasis|copper ion transport|transmembrane transport	extracellular space	chaperone binding|ferroxidase activity			ovary(1)	1		Prostate(884;0.00217)|Hepatocellular(537;0.00826)|Myeloproliferative disorder(1037;0.0122)|all_neural(597;0.0189)|Melanoma(1037;0.152)	LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)		Drotrecogin alfa(DB00055)	GACTTTGTTCTTCAGTGGCAA	0.448													32	113	---	---	---	---	PASS
QDPR	5860	broad.mit.edu	37	4	17506031	17506031	+	Missense_Mutation	SNP	C	T	T			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:17506031C>T	uc003gpd.2	-	3	446	c.266G>A	c.(265-267)GGA>GAA	p.G89E	QDPR_uc003gpe.2_Missense_Mutation_p.G58E|QDPR_uc003gpf.2_RNA	NM_000320	NP_000311	P09417	DHPR_HUMAN	quinoid dihydropteridine reductase	89					dihydrobiopterin metabolic process|L-phenylalanine catabolic process|tetrahydrobiopterin biosynthetic process	cytosol	6,7-dihydropteridine reductase activity|binding|electron carrier activity			ovary(1)	1					NADH(DB00157)	CCCGGCCCATCCTCCAGCAAC	0.468													27	41	---	---	---	---	PASS
SEL1L3	23231	broad.mit.edu	37	4	25834685	25834685	+	Missense_Mutation	SNP	C	T	T			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:25834685C>T	uc003gru.3	-	5	1182	c.1030G>A	c.(1030-1032)GTA>ATA	p.V344I		NM_015187	NP_056002	Q68CR1	SE1L3_HUMAN	sel-1 suppressor of lin-12-like 3	344						integral to membrane	binding				0						TTAGTTTTTACAGCAAGGTCT	0.388													15	75	---	---	---	---	PASS
CXCL10	3627	broad.mit.edu	37	4	76942991	76942991	+	3'UTR	SNP	G	T	T			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:76942991G>T	uc003hjl.3	-	4					ART3_uc003hji.2_Intron|ART3_uc003hjj.2_Intron|ART3_uc003hjk.2_Intron	NM_001565	NP_001556	P02778	CXL10_HUMAN	small inducible cytokine B10 precursor						blood circulation|cell surface receptor linked signaling pathway|cell-cell signaling|chemotaxis|inflammatory response|muscle organ development|positive regulation of cell proliferation	extracellular space	cAMP-dependent protein kinase regulator activity|chemokine activity				0			Lung(101;0.0809)|LUSC - Lung squamous cell carcinoma(112;0.0934)			ATTATGGCTTGACATATACTC	0.448													7	41	---	---	---	---	PASS
LARP1B	55132	broad.mit.edu	37	4	129012653	129012653	+	Silent	SNP	T	C	C			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:129012653T>C	uc003iga.2	+	7	785	c.654T>C	c.(652-654)TAT>TAC	p.Y218Y	LARP1B_uc003ifw.1_Silent_p.Y171Y|LARP1B_uc003ifx.2_Silent_p.Y218Y|LARP1B_uc003ify.2_Silent_p.Y218Y|LARP1B_uc003ifz.1_Silent_p.Y218Y	NM_018078	NP_060548	Q659C4	LAR1B_HUMAN	La ribonucleoprotein domain family member 2	218	HTH La-type RNA-binding.						RNA binding				0						TTAAAGAGTATATTAAGCGTC	0.338													56	80	---	---	---	---	PASS
KIAA0922	23240	broad.mit.edu	37	4	154504367	154504367	+	Missense_Mutation	SNP	A	G	G			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:154504367A>G	uc003inm.3	+	10	970	c.918A>G	c.(916-918)ATA>ATG	p.I306M	KIAA0922_uc010ipp.2_Missense_Mutation_p.I306M|KIAA0922_uc010ipq.2_Missense_Mutation_p.I158M|KIAA0922_uc010ips.1_5'Flank	NM_015196	NP_056011	A2VDJ0	T131L_HUMAN	hypothetical protein LOC23240 isoform 2	306	Extracellular (Potential).					integral to membrane				upper_aerodigestive_tract(1)|ovary(1)	2	all_hematologic(180;0.093)	Renal(120;0.118)				ATATGTATATATTACATTCAG	0.308													63	85	---	---	---	---	PASS
ANXA10	11199	broad.mit.edu	37	4	169100409	169100409	+	Missense_Mutation	SNP	G	T	T			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:169100409G>T	uc003irm.2	+	9	815	c.670G>T	c.(670-672)GAT>TAT	p.D224Y	ANXA10_uc003irn.2_Missense_Mutation_p.D96Y	NM_007193	NP_009124	Q9UJ72	ANX10_HUMAN	annexin A10	224	Annexin 3.						calcium ion binding|calcium-dependent phospholipid binding				0		Prostate(90;0.00876)|Renal(120;0.0183)|all_neural(102;0.0837)|Melanoma(52;0.132)		GBM - Glioblastoma multiforme(119;0.0325)		AGATATGGTAGATGCCATTAA	0.284													17	19	---	---	---	---	PASS
MAP1B	4131	broad.mit.edu	37	5	71494891	71494891	+	Silent	SNP	C	A	A			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:71494891C>A	uc003kbw.3	+	5	5950	c.5709C>A	c.(5707-5709)GGC>GGA	p.G1903G	MAP1B_uc010iyw.1_Silent_p.G1920G|MAP1B_uc010iyx.1_Silent_p.G1777G|MAP1B_uc010iyy.1_Silent_p.G1777G	NM_005909	NP_005900	P46821	MAP1B_HUMAN	microtubule-associated protein 1B	1903	MAP1B 2.					microtubule|microtubule associated complex	structural molecule activity			large_intestine(2)|ovary(1)|central_nervous_system(1)|pancreas(1)	5		Lung NSC(167;0.00202)|Ovarian(174;0.0175)|Prostate(461;0.142)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;7.99e-54)		ATGTGGGTGGCTATTACTATG	0.458													31	65	---	---	---	---	PASS
MCC	4163	broad.mit.edu	37	5	112437520	112437520	+	Missense_Mutation	SNP	C	T	T			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:112437520C>T	uc003kqj.3	-	6	1274	c.744G>A	c.(742-744)ATG>ATA	p.M248I	MCC_uc003kqk.3_RNA|MCC_uc003kql.3_Missense_Mutation_p.M438I|MCC_uc011cwb.1_Missense_Mutation_p.M248I|MCC_uc010jcd.1_Missense_Mutation_p.M210I	NM_002387	NP_002378	P23508	CRCM_HUMAN	mutated in colorectal cancers isoform 2	248					negative regulation of canonical Wnt receptor signaling pathway|negative regulation of epithelial cell migration|negative regulation of epithelial cell proliferation|Wnt receptor signaling pathway	cytoplasm|nucleus|plasma membrane	protein binding|receptor activity			ovary(1)	1		all_cancers(142;5.89e-08)|all_epithelial(76;3.57e-11)|all_lung(232;0.000605)|Lung NSC(810;0.000697)|Colorectal(10;0.00146)|Prostate(80;0.00174)|Ovarian(225;0.0175)|Breast(839;0.198)		OV - Ovarian serous cystadenocarcinoma(64;2.04e-54)|Epithelial(69;9.69e-49)|all cancers(49;6.25e-44)|COAD - Colon adenocarcinoma(37;0.0432)|Colorectal(14;0.0766)		TGCTGCACAGCATGGCAGTCA	0.602													61	99	---	---	---	---	PASS
PPP2R2B	5521	broad.mit.edu	37	5	145969638	145969638	+	Missense_Mutation	SNP	C	A	A			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:145969638C>A	uc003loe.2	-	9	1729	c.1204G>T	c.(1204-1206)GAC>TAC	p.D402Y	PPP2R2B_uc010jgm.2_Missense_Mutation_p.D391Y|PPP2R2B_uc003log.3_Missense_Mutation_p.D402Y|PPP2R2B_uc003lof.3_Missense_Mutation_p.D402Y|PPP2R2B_uc003loi.3_Missense_Mutation_p.D405Y|PPP2R2B_uc003loh.3_Missense_Mutation_p.D402Y|PPP2R2B_uc003loj.3_Missense_Mutation_p.D382Y|PPP2R2B_uc003lok.3_Missense_Mutation_p.D391Y|PPP2R2B_uc011dbu.1_Missense_Mutation_p.D408Y|PPP2R2B_uc011dbv.1_Missense_Mutation_p.D460Y	NM_004576	NP_004567	Q00005	2ABB_HUMAN	beta isoform of regulatory subunit B55, protein	402					apoptosis|signal transduction	cytoskeleton|mitochondrial outer membrane|protein phosphatase type 2A complex	protein binding|protein phosphatase type 2A regulator activity			ovary(1)|prostate(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			CTGATCTCGTCTTTTCTCCGC	0.498													72	149	---	---	---	---	PASS
ABLIM3	22885	broad.mit.edu	37	5	148590289	148590289	+	Missense_Mutation	SNP	G	T	T			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:148590289G>T	uc003lpy.2	+	7	827	c.576G>T	c.(574-576)AAG>AAT	p.K192N	ABLIM3_uc003lpz.1_Missense_Mutation_p.K192N|ABLIM3_uc003lqa.1_Missense_Mutation_p.K200N|ABLIM3_uc003lqb.2_Missense_Mutation_p.K192N|ABLIM3_uc003lqc.1_Missense_Mutation_p.K192N|ABLIM3_uc003lqd.1_Missense_Mutation_p.K192N|ABLIM3_uc003lqf.2_Missense_Mutation_p.K192N|ABLIM3_uc003lqe.1_Missense_Mutation_p.K192N	NM_014945	NP_055760	O94929	ABLM3_HUMAN	actin binding LIM protein family, member 3	192	LIM zinc-binding 3.				axon guidance|cytoskeleton organization	cytoplasm	actin binding|zinc ion binding			ovary(2)|skin(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTTCTTGCAGGGATGGTGTTC	0.493													36	74	---	---	---	---	PASS
BTNL3	10917	broad.mit.edu	37	5	180424374	180424374	+	Missense_Mutation	SNP	A	C	C			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:180424374A>C	uc003mmr.2	+	3	687	c.559A>C	c.(559-561)AGC>CGC	p.S187R		NM_197975	NP_932079	Q6UXE8	BTNL3_HUMAN	butyrophilin-like 3 precursor	187	Ig-like V-type.|Extracellular (Potential).				lipid metabolic process	integral to membrane					0	all_cancers(89;3.37e-05)|all_epithelial(37;3.77e-06)|Renal(175;0.000159)|Lung NSC(126;0.00211)|all_lung(126;0.00371)|Breast(19;0.114)	all_cancers(40;0.00336)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_hematologic(541;0.163)|Ovarian(839;0.238)|all_lung(500;0.248)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000272)			AGATGGGTACAGCCTGTATGA	0.512													13	59	---	---	---	---	PASS
RREB1	6239	broad.mit.edu	37	6	7229380	7229380	+	Missense_Mutation	SNP	G	A	A			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:7229380G>A	uc003mxc.2	+	10	1438	c.1048G>A	c.(1048-1050)GCC>ACC	p.A350T	RREB1_uc003mxb.2_Missense_Mutation_p.A350T|RREB1_uc010jnx.2_Missense_Mutation_p.A350T	NM_001003698	NP_001003698	Q92766	RREB1_HUMAN	ras responsive element binding protein 1 isoform	350					multicellular organismal development|positive regulation of transcription, DNA-dependent|Ras protein signal transduction|transcription from RNA polymerase II promoter	cytoplasm|nuclear speck	DNA binding|zinc ion binding			ovary(4)|large_intestine(2)|pancreas(2)|skin(2)|breast(1)	11	Ovarian(93;0.0398)	all_hematologic(90;0.0384)|Prostate(151;0.191)				AAAGCCGCAGGCCACGCCCCT	0.652													6	33	---	---	---	---	PASS
SOX4	6659	broad.mit.edu	37	6	21594792	21594792	+	Missense_Mutation	SNP	G	C	C			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:21594792G>C	uc003ndi.2	+	1	821	c.27G>C	c.(25-27)GAG>GAC	p.E9D		NM_003107	NP_003098	Q06945	SOX4_HUMAN	SRY (sex determining region Y)-box 4	9					canonical Wnt receptor signaling pathway|cardiac ventricle formation|cellular response to glucose stimulus|DNA damage response, detection of DNA damage|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|glial cell development|glial cell proliferation|limb bud formation|negative regulation of apoptosis|negative regulation of cell proliferation|negative regulation of protein export from nucleus|negative regulation of protein ubiquitination|neural tube formation|neuroepithelial cell differentiation|noradrenergic neuron differentiation|positive regulation of apoptosis|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of cell proliferation|positive regulation of insulin secretion|positive regulation of N-terminal peptidyl-lysine acetylation|positive regulation of translation|pro-B cell differentiation|protein stabilization|skeletal system development|spinal cord motor neuron differentiation|sympathetic nervous system development|T cell differentiation	mitochondrion|nucleus	core promoter sequence-specific DNA binding|protein binding|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription|RNA polymerase II transcription coactivator activity				0	Ovarian(93;0.163)		all cancers(50;0.0751)|Epithelial(50;0.155)			ACAATGCCGAGAACACGGAAG	0.761													7	13	---	---	---	---	PASS
SLC26A8	116369	broad.mit.edu	37	6	35927246	35927246	+	Silent	SNP	C	T	T			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:35927246C>T	uc003olm.2	-	16	1965	c.1854G>A	c.(1852-1854)CCG>CCA	p.P618P	SLC26A8_uc010jwa.2_RNA|SLC26A8_uc003olk.2_Silent_p.P200P|SLC26A8_uc003oln.2_Silent_p.P618P|SLC26A8_uc003oll.2_Silent_p.P513P	NM_052961	NP_443193	Q96RN1	S26A8_HUMAN	solute carrier family 26, member 8 isoform a	618	STAS.|Cytoplasmic (Potential).				cell differentiation|meiosis|multicellular organismal development|spermatogenesis	integral to membrane|plasma membrane	anion:anion antiporter activity|chloride channel activity|oxalate transmembrane transporter activity|protein binding|sulfate transmembrane transporter activity			ovary(2)	2						CCCTGGGCAGCGGCTCCAGAT	0.343													4	148	---	---	---	---	PASS
TDRD6	221400	broad.mit.edu	37	6	46660119	46660119	+	Silent	SNP	C	T	T			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:46660119C>T	uc003oyj.2	+	1	4254	c.4254C>T	c.(4252-4254)TGC>TGT	p.C1418C	TDRD6_uc010jze.2_Silent_p.C1412C	NM_001010870	NP_001010870	O60522	TDRD6_HUMAN	tudor domain containing 6	1418					cell differentiation|multicellular organismal development|spermatogenesis	chromatoid body	nucleic acid binding			breast(3)|ovary(2)|skin(1)	6			Lung(136;0.192)			GCATTCATTGCTCCTTGCAGG	0.393													80	367	---	---	---	---	PASS
GPR116	221395	broad.mit.edu	37	6	46830726	46830726	+	Missense_Mutation	SNP	T	G	G			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:46830726T>G	uc003oyo.3	-	15	2387	c.2098A>C	c.(2098-2100)ATT>CTT	p.I700L	GPR116_uc011dwj.1_Missense_Mutation_p.I255L|GPR116_uc011dwk.1_Missense_Mutation_p.I129L|GPR116_uc003oyp.3_Missense_Mutation_p.I558L|GPR116_uc003oyq.3_Missense_Mutation_p.I700L|GPR116_uc010jzi.1_Missense_Mutation_p.I372L	NM_001098518	NP_001091988	Q8IZF2	GP116_HUMAN	G-protein coupled receptor 116 precursor	700	Extracellular (Potential).				neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			central_nervous_system(1)|skin(1)	2			Lung(136;0.192)			GTCCCGCCAATGGGACTCTCA	0.532													67	101	---	---	---	---	PASS
PRDM1	639	broad.mit.edu	37	6	106553602	106553602	+	Missense_Mutation	SNP	G	A	A			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:106553602G>A	uc003prd.2	+	5	1801	c.1567G>A	c.(1567-1569)GCC>ACC	p.A523T	PRDM1_uc003pre.2_Missense_Mutation_p.A389T	NM_001198	NP_001189	O75626	PRDM1_HUMAN	PR domain containing 1, with ZNF domain isoform	523					negative regulation of transcription from RNA polymerase II promoter	cytoplasm|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			haematopoietic_and_lymphoid_tissue(54)|ovary(1)|skin(1)	56	Breast(9;0.022)	all_cancers(87;2.2e-31)|all_epithelial(87;2.03e-21)|Acute lymphoblastic leukemia(125;4.99e-11)|all_lung(197;7.55e-09)|all_hematologic(75;5.82e-08)|Lung NSC(302;1.28e-06)|Colorectal(196;0.0112)|Ovarian(999;0.0365)		all cancers(137;1.83e-46)|Epithelial(106;5.59e-35)|OV - Ovarian serous cystadenocarcinoma(136;1.99e-20)|GBM - Glioblastoma multiforme(226;3.72e-11)|BRCA - Breast invasive adenocarcinoma(108;1.38e-05)		GGGAACAGCCGCCACGGCAGA	0.612			D|N|Mis|F|S		DLBCL								24	36	---	---	---	---	PASS
RPS12	6206	broad.mit.edu	37	6	133137575	133137575	+	Intron	SNP	A	G	G			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:133137575A>G	uc003qdx.2	+						RPS12_uc003qdy.1_3'UTR	NM_001016	NP_001007	P25398	RS12_HUMAN	ribosomal protein S12						endocrine pancreas development|translational elongation|translational termination|viral transcription	cytosolic small ribosomal subunit	structural constituent of ribosome				0	Breast(56;0.214)			OV - Ovarian serous cystadenocarcinoma(155;0.00284)|GBM - Glioblastoma multiforme(226;0.0256)		TTTTAGCTCCATTTTCATTGT	0.423													23	31	---	---	---	---	PASS
TNRC18	84629	broad.mit.edu	37	7	5391571	5391571	+	Silent	SNP	C	T	T			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:5391571C>T	uc003soi.3	-	17	5698	c.5349G>A	c.(5347-5349)GCG>GCA	p.A1783A	TNRC18_uc003soj.2_Silent_p.A165A	NM_001080495	NP_001073964	O15417	TNC18_HUMAN	trinucleotide repeat containing 18	1783							DNA binding				0		Ovarian(82;0.142)		UCEC - Uterine corpus endometrioid carcinoma (126;0.195)|OV - Ovarian serous cystadenocarcinoma(56;5.32e-15)		TCCGGGGGGCCGCCAGGCCCC	0.637													14	23	---	---	---	---	PASS
BBS9	27241	broad.mit.edu	37	7	33376135	33376135	+	Missense_Mutation	SNP	C	G	G			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:33376135C>G	uc003tdn.1	+	10	1612	c.1099C>G	c.(1099-1101)CAA>GAA	p.Q367E	BBS9_uc003tdo.1_Missense_Mutation_p.Q367E|BBS9_uc003tdp.1_Missense_Mutation_p.Q367E|BBS9_uc003tdq.1_Missense_Mutation_p.Q367E|BBS9_uc010kwn.1_RNA|BBS9_uc011kao.1_Missense_Mutation_p.Q245E	NM_198428	NP_940820	Q3SYG4	PTHB1_HUMAN	parathyroid hormone-responsive B1 isoform 2	367					fat cell differentiation|response to stimulus|visual perception	BBSome|cilium membrane|microtubule organizing center|nucleus	protein binding			ovary(3)|upper_aerodigestive_tract(1)|skin(1)	5			GBM - Glioblastoma multiforme(11;0.0894)			TTCTCTGTTCCAAGCTCCAAA	0.383									Bardet-Biedl_syndrome				29	38	---	---	---	---	PASS
SEPT14	346288	broad.mit.edu	37	7	55886846	55886846	+	Missense_Mutation	SNP	C	T	T			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:55886846C>T	uc003tqz.2	-	7	908	c.791G>A	c.(790-792)CGT>CAT	p.R264H		NM_207366	NP_997249	Q6ZU15	SEP14_HUMAN	septin 14	264		GTP (By similarity).			cell cycle|cell division	septin complex	GTP binding|protein binding				0	Breast(14;0.214)		Lung(13;0.00024)|LUSC - Lung squamous cell carcinoma(13;0.00099)			AGGGTAGTGACGGCCTCTGAC	0.403													10	4	---	---	---	---	PASS
LOC643955	643955	broad.mit.edu	37	7	62752443	62752443	+	3'UTR	SNP	G	C	C			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:62752443G>C	uc011kdj.1	-	3						NR_003952				Homo sapiens cDNA clone IMAGE:30377995, containing frame-shift errors.												0						CTTATGTCTAGTAAGGTTTGA	0.438													3	21	---	---	---	---	PASS
RPL23AP53	644128	broad.mit.edu	37	8	163325	163325	+	RNA	SNP	C	T	T			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:163325C>T	uc010lra.2	-	4		c.808G>A			RPL23AP53_uc003woq.3_RNA|RPL23AP53_uc010lrb.2_RNA	NR_003572				Homo sapiens cDNA FLJ45055 fis, clone BRAWH3022900.												0						TTCTCTTTATCAGGAAAAATC	0.443													17	39	---	---	---	---	PASS
CDCA2	157313	broad.mit.edu	37	8	25327450	25327450	+	Silent	SNP	A	G	G			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:25327450A>G	uc003xep.1	+	7	1253	c.774A>G	c.(772-774)TTA>TTG	p.L258L	PPP2R2A_uc003xek.2_Intron|CDCA2_uc011lae.1_Silent_p.L258L|CDCA2_uc003xeq.1_Silent_p.L243L|CDCA2_uc003xer.1_5'UTR	NM_152562	NP_689775	Q69YH5	CDCA2_HUMAN	cell division cycle associated 2	258					cell division|mitosis	cytoplasm|nucleus					0		all_cancers(63;0.0378)|Ovarian(32;0.000878)|all_epithelial(46;0.0162)|Breast(100;0.0164)|Prostate(55;0.191)		UCEC - Uterine corpus endometrioid carcinoma (27;0.022)|Epithelial(17;1.37e-11)|Colorectal(74;0.0129)|COAD - Colon adenocarcinoma(73;0.0443)		CTGGATTTTTAGTTGAAGAGT	0.348													3	135	---	---	---	---	PASS
FGFR1	2260	broad.mit.edu	37	8	38272389	38272389	+	Missense_Mutation	SNP	C	G	G			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38272389C>G	uc003xlp.2	-	15	2827	c.1885G>C	c.(1885-1887)GTC>CTC	p.V629L	FGFR1_uc010lwf.2_RNA|FGFR1_uc011lbo.1_Missense_Mutation_p.V627L|FGFR1_uc011lbp.1_Missense_Mutation_p.V540L|FGFR1_uc011lbq.1_Missense_Mutation_p.V538L|FGFR1_uc010lwk.2_Missense_Mutation_p.V619L	NM_023110	NP_075598	P11362	FGFR1_HUMAN	fibroblast growth factor receptor 1 isoform 1	629	Cytoplasmic (Potential).|Protein kinase.				axon guidance|cell growth|insulin receptor signaling pathway|MAPKKK cascade|positive regulation of cell proliferation|skeletal system development	extracellular region|integral to plasma membrane|membrane fraction	ATP binding|fibroblast growth factor receptor activity|heparin binding|protein homodimerization activity			lung(5)|central_nervous_system(5)|stomach(2)|breast(2)|ovary(1)	15	all_cancers(2;9.05e-47)|all_epithelial(2;2.64e-50)|all_lung(3;1.71e-23)|Lung NSC(2;3.61e-23)|Colorectal(12;0.000442)	Breast(189;1.48e-05)|all_lung(54;0.00354)|Lung NSC(58;0.0138)|Hepatocellular(245;0.065)	Epithelial(3;3.96e-34)|all cancers(3;3.06e-30)|BRCA - Breast invasive adenocarcinoma(5;2.28e-21)|COAD - Colon adenocarcinoma(9;0.24)		Palifermin(DB00039)	GTCACCAGGACATTCCTGGCT	0.433		1	T	BCR|FOP|ZNF198|CEP1	MPD|NHL		Pfeiffer syndrome|Kallman syndrome						20	52	---	---	---	---	PASS
RP1	6101	broad.mit.edu	37	8	55542521	55542521	+	Missense_Mutation	SNP	G	A	A			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:55542521G>A	uc003xsd.1	+	4	6227	c.6079G>A	c.(6079-6081)GAT>AAT	p.D2027N	RP1_uc011ldy.1_Intron	NM_006269	NP_006260	P56715	RP1_HUMAN	retinitis pigmentosa RP1 protein	2027					axoneme assembly|intracellular signal transduction|photoreceptor cell maintenance|photoreceptor cell outer segment organization|phototransduction, visible light|retinal cone cell development|retinal rod cell development	cilium axoneme|cytoplasm|microtubule|microtubule associated complex|photoreceptor connecting cilium|photoreceptor inner segment|photoreceptor outer segment	microtubule binding			skin(7)|ovary(4)|pancreas(1)	12		all_lung(136;0.0831)|Lung NSC(129;0.109)|all_epithelial(80;0.123)	OV - Ovarian serous cystadenocarcinoma(7;4.4e-07)|Epithelial(17;3.37e-05)|all cancers(17;0.000285)			ATTTCAACCAGATTTGAAGGA	0.338													26	104	---	---	---	---	PASS
ASPH	444	broad.mit.edu	37	8	62492264	62492264	+	Intron	SNP	C	G	G			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:62492264C>G	uc011leg.1	-						ASPH_uc003xuj.2_Intron|ASPH_uc003xuo.2_Intron|uc003xuk.2_3'UTR	NM_004318	NP_004309	Q12797	ASPH_HUMAN	aspartate beta-hydroxylase isoform a						muscle contraction	integral to endoplasmic reticulum membrane	calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle			ovary(3)	3	Lung SC(2;0.153)	Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101)			L-Aspartic Acid(DB00128)|Succinic acid(DB00139)	CCTACCCCTCCTGCGCTGCCC	0.617													3	23	---	---	---	---	PASS
CNGB3	54714	broad.mit.edu	37	8	87591035	87591035	+	Missense_Mutation	SNP	A	T	T			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:87591035A>T	uc003ydx.2	-	17	2031	c.1985T>A	c.(1984-1986)CTT>CAT	p.L662H	CNGB3_uc010maj.2_Missense_Mutation_p.L519H	NM_019098	NP_061971	Q9NQW8	CNGB3_HUMAN	cyclic nucleotide gated channel beta 3	662	Cytoplasmic (Potential).|cGMP (By similarity).				signal transduction|visual perception	integral to membrane	cGMP binding			ovary(2)|pancreas(1)	3						GAGGAGGGCAAGATCTTTTCT	0.453													37	52	---	---	---	---	PASS
VLDLR	7436	broad.mit.edu	37	9	2652826	2652826	+	Missense_Mutation	SNP	T	A	A	rs140801553	by1000genomes	TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:2652826T>A	uc003zhk.1	+	18	2860	c.2463T>A	c.(2461-2463)AAT>AAA	p.N821K	VLDLR_uc003zhl.1_Missense_Mutation_p.N793K|VLDLR_uc003zhm.1_RNA|VLDLR_uc003zhn.1_Missense_Mutation_p.N752K	NM_003383	NP_003374	P98155	VLDLR_HUMAN	very low density lipoprotein receptor isoform a	821	Cytoplasmic (Potential).				cholesterol metabolic process|endocytosis|lipid transport|memory|very-low-density lipoprotein particle clearance	coated pit|integral to membrane|membrane fraction|plasma membrane|very-low-density lipoprotein particle	apolipoprotein binding|calcium ion binding|low-density lipoprotein receptor activity|very-low-density lipoprotein particle receptor activity			ovary(1)|central_nervous_system(1)|pancreas(1)	3				GBM - Glioblastoma multiforme(50;0.0668)|Lung(218;0.123)		TGTGGCGGAATTGGCAACACA	0.428													26	72	---	---	---	---	PASS
FOXD4L6	653404	broad.mit.edu	37	9	69200146	69200146	+	3'UTR	SNP	C	A	A			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:69200146C>A	uc004afi.2	-	1						NM_001085476	NP_001078945	Q3SYB3	FX4L6_HUMAN	forkhead box D4-like 6						axon extension involved in axon guidance|cartilage development|dichotomous subdivision of terminal units involved in ureteric bud branching|embryo development|enteric nervous system development|iridophore differentiation|lateral line nerve glial cell development|melanocyte differentiation|neural crest cell migration|pattern specification process|peripheral nervous system development|positive regulation of BMP signaling pathway|positive regulation of kidney development|positive regulation of transcription from RNA polymerase II promoter|regulation of sequence-specific DNA binding transcription factor activity|sympathetic nervous system development	transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding				0						TGCTCTCCAGCGGGATTCAGA	0.567													6	27	---	---	---	---	PASS
FLJ43950	347127	broad.mit.edu	37	9	84532047	84532047	+	3'UTR	SNP	G	T	T			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:84532047G>T	uc011lst.1	+	4					uc004ame.2_5'Flank	NR_026851				SubName: Full=cDNA FLJ43950 fis, clone TESTI4015293, moderately similar to FAM75-like protein;												0						CATTCCTGGAGATTTTCCACT	0.488													14	43	---	---	---	---	PASS
DNAJC25-GNG10	552891	broad.mit.edu	37	9	114429212	114429212	+	Silent	SNP	T	C	C			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:114429212T>C	uc004bfn.2	+	2	476	c.454T>C	c.(454-456)TTA>CTA	p.L152L	GNG10_uc011lws.1_RNA|GNG10_uc004bfp.2_Silent_p.L67L	NM_004125	NP_004116	Q9H1X3	DJC25_HUMAN	DNAJC25-GNG10 protein	Error:Variant_position_missing_in_Q9H1X3_after_alignment					protein folding	integral to membrane	heat shock protein binding|unfolded protein binding				0						ATCCTGTGCTTTACTCTGAAG	0.493													9	38	---	---	---	---	PASS
SCAI	286205	broad.mit.edu	37	9	127733961	127733961	+	Missense_Mutation	SNP	G	A	A			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:127733961G>A	uc004bpe.2	-	16	1643	c.1562C>T	c.(1561-1563)TCA>TTA	p.S521L	SCAI_uc004bpd.2_Missense_Mutation_p.S544L|SCAI_uc010mwu.2_RNA	NM_001144877	NP_001138349	Q8N9R8	SCAI_HUMAN	suppressor of cancer cell invasion isoform 2	521					negative regulation of cell migration|negative regulation of Rho protein signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|integral to membrane|nucleus	protein binding|transcription corepressor activity			ovary(2)|breast(2)|central_nervous_system(1)	5						TATTGAACGTGAATGAGTCAG	0.363													119	89	---	---	---	---	PASS
SPTAN1	6709	broad.mit.edu	37	9	131331096	131331096	+	Missense_Mutation	SNP	A	T	T			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131331096A>T	uc004bvl.3	+	3	396	c.283A>T	c.(283-285)AAC>TAC	p.N95Y	SPTAN1_uc011mbg.1_Missense_Mutation_p.N95Y|SPTAN1_uc011mbh.1_Missense_Mutation_p.N107Y|SPTAN1_uc004bvm.3_Missense_Mutation_p.N95Y|SPTAN1_uc004bvn.3_Missense_Mutation_p.N95Y	NM_003127	NP_003118	Q13813	SPTA2_HUMAN	spectrin, alpha, non-erythrocytic 1	95	Spectrin 2.				actin filament capping|axon guidance|cellular component disassembly involved in apoptosis	cytosol|intracellular membrane-bounded organelle|membrane fraction|microtubule cytoskeleton|spectrin	actin binding|calcium ion binding|calmodulin binding|structural constituent of cytoskeleton			breast(5)|ovary(4)|pancreas(1)	10						AGTGCAGGCCAACTCAGGAGC	0.483													22	24	---	---	---	---	PASS
NTNG2	84628	broad.mit.edu	37	9	135102354	135102354	+	Silent	SNP	C	A	A			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:135102354C>A	uc004cbh.2	+	4	1752	c.976C>A	c.(976-978)CGG>AGG	p.R326R		NM_032536	NP_115925	Q96CW9	NTNG2_HUMAN	netrin G2 precursor	326	Laminin EGF-like 1.				axonogenesis	anchored to plasma membrane					0				OV - Ovarian serous cystadenocarcinoma(145;1.23e-05)|Epithelial(140;0.000173)		TTTCCGCACCCGGTCCTGGCG	0.667													9	22	---	---	---	---	PASS
TUBBP5	643224	broad.mit.edu	37	9	141070909	141070909	+	Silent	SNP	A	G	G			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:141070909A>G	uc004com.2	+	4	573	c.312A>G	c.(310-312)TCA>TCG	p.S104S	TUBBP5_uc010ncq.2_3'UTR					RecName: Full=Putative tubulin beta-4q chain;												0						CCAAGGTGTCAGACACCGTGG	0.537													4	64	---	---	---	---	PASS
KIAA1462	57608	broad.mit.edu	37	10	30316647	30316647	+	Missense_Mutation	SNP	G	C	C			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:30316647G>C	uc001iux.2	-	2	2489	c.2430C>G	c.(2428-2430)TGC>TGG	p.C810W	KIAA1462_uc001iuy.2_Intron|KIAA1462_uc001iuz.2_Missense_Mutation_p.C672W|KIAA1462_uc009xle.1_Missense_Mutation_p.C810W	NM_020848	NP_065899	Q9P266	K1462_HUMAN	hypothetical protein LOC57608	810										ovary(4)	4						GTTTACTGTTGCAAGGGCCCG	0.577													36	128	---	---	---	---	PASS
LOC100133308	100133308	broad.mit.edu	37	10	45644312	45644312	+	Intron	SNP	A	C	C			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:45644312A>C	uc009xmq.1	-						LOC100133308_uc001jbz.2_5'Flank|uc001jca.3_RNA	NR_024472				Homo sapiens cDNA FLJ32851 fis, clone TESTI2003432.												0						ATTTTTACCTAGAAAGTCACC	0.343													22	27	---	---	---	---	PASS
C10orf137	26098	broad.mit.edu	37	10	127442319	127442319	+	Missense_Mutation	SNP	A	C	C			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:127442319A>C	uc001liq.1	+	24	3743	c.3450A>C	c.(3448-3450)GAA>GAC	p.E1150D	C10orf137_uc001lio.1_Missense_Mutation_p.E1116D|C10orf137_uc001lip.1_Missense_Mutation_p.E854D|C10orf137_uc001lis.1_Missense_Mutation_p.E476D|C10orf137_uc001lit.1_Missense_Mutation_p.E60D	NM_015608	NP_056423	Q3B7T1	EDRF1_HUMAN	erythroid differentiation-related factor 1	1150					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	binding			ovary(5)|large_intestine(3)|lung(2)	10		all_lung(145;0.0096)|Lung NSC(174;0.0145)|Colorectal(57;0.0846)|all_neural(114;0.0936)				TCAATCGAGAAGAAGTGATGA	0.393													46	100	---	---	---	---	PASS
C11orf17	56672	broad.mit.edu	37	11	8940960	8940960	+	Nonsense_Mutation	SNP	T	G	G			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:8940960T>G	uc001mgx.2	+	6	642	c.566T>G	c.(565-567)TTA>TGA	p.L189*	C11orf17_uc001mgz.2_Nonsense_Mutation_p.L162*|C11orf17_uc001mgy.2_Nonsense_Mutation_p.L162*|C11orf17_uc001mha.2_Nonsense_Mutation_p.L189*	NM_020642	NP_065693	Q9NQ31	AKIP1_HUMAN	chromosome 11 open reading frame 17	189						nucleus	protein binding				0				Epithelial(150;5.08e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0243)		TCAAATGACTTAACCAAGAAG	0.448													86	162	---	---	---	---	PASS
SLC17A6	57084	broad.mit.edu	37	11	22397594	22397594	+	Nonsense_Mutation	SNP	C	A	A			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:22397594C>A	uc001mqk.2	+	10	1654	c.1241C>A	c.(1240-1242)TCA>TAA	p.S414*		NM_020346	NP_065079	Q9P2U8	VGLU2_HUMAN	solute carrier family 17 (sodium-dependent	414	Helical; (Potential).				sodium ion transport	cell junction|integral to membrane|synaptic vesicle membrane|synaptosome	L-glutamate transmembrane transporter activity|symporter activity			ovary(3)|breast(1)	4						GTAGCAATCTCATTCTTGGTA	0.393													74	126	---	---	---	---	PASS
MAPK8IP1	9479	broad.mit.edu	37	11	45925699	45925699	+	Silent	SNP	C	T	T			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:45925699C>T	uc001nbr.2	+	7	1823	c.1653C>T	c.(1651-1653)CCC>CCT	p.P551P		NM_005456	NP_005447	Q9UQF2	JIP1_HUMAN	mitogen-activated protein kinase 8 interacting	551					vesicle-mediated transport	nucleus|perinuclear region of cytoplasm	kinesin binding|MAP-kinase scaffold activity|protein kinase inhibitor activity			ovary(2)|breast(1)|skin(1)	4				GBM - Glioblastoma multiforme(35;0.231)		CCAAGGAGCCCGAGCACATGG	0.592													10	21	---	---	---	---	PASS
MS4A14	84689	broad.mit.edu	37	11	60183976	60183976	+	Missense_Mutation	SNP	C	A	A			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:60183976C>A	uc001npj.2	+	5	2100	c.1535C>A	c.(1534-1536)TCC>TAC	p.S512Y	MS4A14_uc001npi.2_Missense_Mutation_p.S400Y|MS4A14_uc001npn.2_Missense_Mutation_p.S250Y|MS4A14_uc001npk.2_Missense_Mutation_p.S495Y|MS4A14_uc001npl.2_Missense_Mutation_p.S250Y|MS4A14_uc001npm.2_Missense_Mutation_p.S250Y	NM_032597	NP_115986	Q96JA4	M4A14_HUMAN	membrane-spanning 4-domains, subfamily A, member	512	Gln-rich.					integral to membrane	receptor activity			breast(1)	1						GGCCAGAAATCCTCAAAGAGG	0.443													38	64	---	---	---	---	PASS
C11orf9	745	broad.mit.edu	37	11	61539075	61539075	+	Missense_Mutation	SNP	G	A	A			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:61539075G>A	uc001nsc.1	+	6	940	c.844G>A	c.(844-846)GTG>ATG	p.V282M	C11orf9_uc001nse.1_Missense_Mutation_p.V273M	NM_001127392	NP_001120864	Q9Y2G1	MRF_HUMAN	myelin gene regulatory factor isoform 2	282	NDT80.|Pro-rich.				central nervous system myelination|positive regulation of myelination|positive regulation of transcription, DNA-dependent	integral to membrane|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			breast(1)	1						GCCTGGGACCGTGACAGCCCT	0.637													66	140	---	---	---	---	PASS
CLPB	81570	broad.mit.edu	37	11	72005414	72005414	+	Silent	SNP	C	T	T			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:72005414C>T	uc001osj.2	-	15	1775	c.1725G>A	c.(1723-1725)GAG>GAA	p.E575E	CLPB_uc010rqx.1_Silent_p.E530E|CLPB_uc010rqy.1_Silent_p.E516E|CLPB_uc001osk.2_Silent_p.E545E|CLPB_uc009ytg.2_RNA|CLPB_uc010rqz.1_Silent_p.E374E|CLPB_uc001osi.2_Silent_p.E183E	NM_030813	NP_110440	Q9H078	CLPB_HUMAN	caseinolytic peptidase B	575					cellular response to heat		ATP binding|nucleoside-triphosphatase activity|protein binding			pancreas(1)	1						GTTGGATGAGCTCCGAGTGGC	0.562													23	68	---	---	---	---	PASS
MTNR1B	4544	broad.mit.edu	37	11	92702959	92702959	+	Nonsense_Mutation	SNP	C	A	A			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:92702959C>A	uc001pdk.1	+	1	171	c.68C>A	c.(67-69)TCG>TAG	p.S23*		NM_005959	NP_005950	P49286	MTR1B_HUMAN	melatonin receptor 1B	23	Extracellular (Potential).				G-protein signaling, coupled to cyclic nucleotide second messenger|glucose homeostasis|regulation of insulin secretion|synaptic transmission	integral to plasma membrane	melatonin receptor activity			ovary(1)|central_nervous_system(1)	2		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)			Ramelteon(DB00980)	CCGGGCTGGTCGGGGGCTGGC	0.726													14	12	---	---	---	---	PASS
PHB2	11331	broad.mit.edu	37	12	7079388	7079388	+	Silent	SNP	G	A	A			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:7079388G>A	uc001qsd.2	-	2	393	c.183C>T	c.(181-183)GAC>GAT	p.D61D	PHB2_uc010sft.1_Silent_p.D61D|PHB2_uc010sfu.1_Silent_p.D61D|EMG1_uc009zfo.2_5'Flank|EMG1_uc001qsh.3_5'Flank|EMG1_uc010sfv.1_5'Flank	NM_001144831	NP_001138303	Q99623	PHB2_HUMAN	prohibitin 2 isoform 1	61					negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	mitochondrial inner membrane|nucleus	estrogen receptor binding|receptor activity			ovary(2)|pancreas(1)	3						CCAGGATAGTGTCCTGCTGCA	0.617													52	107	---	---	---	---	PASS
GRIN2B	2904	broad.mit.edu	37	12	13761631	13761631	+	Missense_Mutation	SNP	G	A	A			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:13761631G>A	uc001rbt.2	-	9	2095	c.1916C>T	c.(1915-1917)GCT>GTT	p.A639V		NM_000834	NP_000825	Q13224	NMDE2_HUMAN	N-methyl-D-aspartate receptor subunit 2B	639	Helical; (Potential).				response to ethanol	cell junction|N-methyl-D-aspartate selective glutamate receptor complex|outer membrane-bounded periplasmic space|postsynaptic membrane	glycine binding|N-methyl-D-aspartate selective glutamate receptor activity|zinc ion binding			central_nervous_system(4)|ovary(3)|skin(3)|lung(2)	12					Felbamate(DB00949)|Haloperidol(DB00502)|L-Glutamic Acid(DB00142)|Loperamide(DB00836)|Memantine(DB01043)	GAAGATGACAGCAAAGAAGGC	0.507													3	59	---	---	---	---	PASS
ARHGDIB	397	broad.mit.edu	37	12	15103538	15103538	+	Missense_Mutation	SNP	C	T	T			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:15103538C>T	uc001rcq.1	-	2	213	c.109G>A	c.(109-111)GAA>AAA	p.E37K	ARHGDIB_uc001rcp.1_5'Flank	NM_001175	NP_001166	P52566	GDIR2_HUMAN	Rho GDP dissociation inhibitor (GDI) beta	37					actin cytoskeleton organization|cellular component movement|immune response|multicellular organismal development|negative regulation of cell adhesion|regulation of small GTPase mediated signal transduction|Rho protein signal transduction	cytoplasmic membrane-bounded vesicle|cytoskeleton|cytosol	GTPase activator activity|Rho GDP-dissociation inhibitor activity				0						TTGTCCATTTCCTGCAGCTCT	0.483													66	116	---	---	---	---	PASS
SLC38A2	54407	broad.mit.edu	37	12	46760917	46760917	+	Silent	SNP	T	C	C			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:46760917T>C	uc001rpg.2	-	6	863	c.423A>G	c.(421-423)GCA>GCG	p.A141A	SLC38A2_uc010sli.1_5'Flank|SLC38A2_uc001rph.2_Silent_p.A41A	NM_018976	NP_061849	Q96QD8	S38A2_HUMAN	solute carrier family 38, member 2	141	Cytoplasmic (Potential).				cellular nitrogen compound metabolic process|glutamate secretion|neurotransmitter secretion|sodium ion transport	integral to membrane|plasma membrane	amino acid transmembrane transporter activity|symporter activity			urinary_tract(1)|skin(1)	2	Lung SC(27;0.192)|Renal(347;0.236)		OV - Ovarian serous cystadenocarcinoma(5;0.0048)|Epithelial(2;0.0374)	GBM - Glioblastoma multiforme(48;0.226)		CTAATCCAAATGCCTTATATC	0.328													60	116	---	---	---	---	PASS
PIP4K2C	79837	broad.mit.edu	37	12	57995122	57995122	+	Silent	SNP	C	G	G			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57995122C>G	uc001sou.2	+	9	1307	c.1176C>G	c.(1174-1176)GTC>GTG	p.V392V	PIP4K2C_uc001sot.2_Silent_p.V392V|PIP4K2C_uc010srs.1_Silent_p.V374V|PIP4K2C_uc010srt.1_Silent_p.V344V	NM_001146258	NP_001139730	Q8TBX8	PI42C_HUMAN	phosphatidylinositol-5-phosphate 4-kinase, type	392	PIPK.					cytoplasm|membrane	1-phosphatidylinositol-5-phosphate 4-kinase activity|ATP binding|identical protein binding			central_nervous_system(2)|lung(1)	3	Melanoma(17;0.122)					CCAAAACTGTCAAGCATGGGG	0.478													22	49	---	---	---	---	PASS
THAP2	83591	broad.mit.edu	37	12	72068028	72068028	+	Silent	SNP	T	G	G			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:72068028T>G	uc001swq.2	+	2	623	c.117T>G	c.(115-117)GTT>GTG	p.V39V		NM_031435	NP_113623	Q9H0W7	THAP2_HUMAN	THAP domain containing, apoptosis associated	39	THAP-type.					nucleolus	DNA binding|metal ion binding			ovary(1)	1						TTCGCCTGGTTAGGCGCAAAA	0.378													36	74	---	---	---	---	PASS
TMTC3	160418	broad.mit.edu	37	12	88588684	88588684	+	Missense_Mutation	SNP	C	G	G			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:88588684C>G	uc001tau.2	+	14	2223	c.2003C>G	c.(2002-2004)GCT>GGT	p.A668G		NM_181783	NP_861448	Q6ZXV5	TMTC3_HUMAN	transmembrane and tetratricopeptide repeat	669	TPR 7.					integral to membrane	binding			skin(1)	1						CCACTAGATGCTAATGGGTAT	0.343													30	64	---	---	---	---	PASS
METAP2	10988	broad.mit.edu	37	12	95867897	95867897	+	5'UTR	SNP	T	G	G			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:95867897T>G	uc001tec.2	+	1					METAP2_uc010suv.1_5'UTR|METAP2_uc009ztd.2_5'UTR|METAP2_uc001ted.2_5'UTR|METAP2_uc001tef.2_5'UTR|METAP2_uc001tee.2_RNA	NM_006838	NP_006829	P50579	AMPM2_HUMAN	methionyl aminopeptidase 2						N-terminal protein amino acid modification|peptidyl-methionine modification|protein processing|proteolysis	cytoplasm	aminopeptidase activity|metal ion binding|metalloexopeptidase activity				0					L-Methionine(DB00134)	TGTAGGCGGGTGGAGAAGGAT	0.677													7	18	---	---	---	---	PASS
NCOR2	9612	broad.mit.edu	37	12	124839984	124839984	+	Silent	SNP	G	A	A			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124839984G>A	uc010tba.1	-	24	3516	c.3399C>T	c.(3397-3399)ATC>ATT	p.I1133I	NCOR2_uc010tay.1_Silent_p.I1132I|NCOR2_uc010taz.1_Silent_p.I1116I|NCOR2_uc010tbb.1_Silent_p.I1125I|NCOR2_uc010tbc.1_Silent_p.I1115I|NCOR2_uc001ugj.1_Silent_p.I1133I	NM_001077261	NP_001070729	Q9Y618	NCOR2_HUMAN	nuclear receptor co-repressor 2 isoform 2	1133					cellular lipid metabolic process|negative regulation of transcription from RNA polymerase II promoter|regulation of cellular ketone metabolic process by negative regulation of transcription from an RNA polymerase II promoter|transcription, DNA-dependent	nuclear body|nucleus|transcriptional repressor complex	DNA binding|histone deacetylase binding|Notch binding|protein N-terminus binding|transcription corepressor activity			skin(3)|ovary(1)	4	all_neural(191;0.0804)|Medulloblastoma(191;0.163)			Epithelial(86;3.99e-05)|OV - Ovarian serous cystadenocarcinoma(86;9.14e-05)|all cancers(50;0.000402)|BRCA - Breast invasive adenocarcinoma(302;0.0764)		TCACTTGGGAGATGGCACCTA	0.453													15	42	---	---	---	---	PASS
SLITRK5	26050	broad.mit.edu	37	13	88329649	88329649	+	Missense_Mutation	SNP	G	A	A			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:88329649G>A	uc001vln.2	+	2	2225	c.2006G>A	c.(2005-2007)AGC>AAC	p.S669N	SLITRK5_uc010tic.1_Missense_Mutation_p.S428N	NM_015567	NP_056382	O94991	SLIK5_HUMAN	SLIT and NTRK-like family, member 5 precursor	669	Helical; (Potential).					integral to membrane				ovary(2)|pancreas(2)|central_nervous_system(1)	5	all_neural(89;0.101)|Medulloblastoma(90;0.163)					TTAATTCTCAGCCTCCTGCTG	0.637													10	43	---	---	---	---	PASS
MYO16	23026	broad.mit.edu	37	13	109779862	109779862	+	Missense_Mutation	SNP	G	A	A			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:109779862G>A	uc001vqt.1	+	31	4075	c.3949G>A	c.(3949-3951)GCC>ACC	p.A1317T	MYO16_uc010agk.1_Missense_Mutation_p.A1339T|MYO16_uc010tjh.1_Missense_Mutation_p.A829T	NM_015011	NP_055826	Q9Y6X6	MYO16_HUMAN	myosin heavy chain Myr 8	1317					cerebellum development|negative regulation of cell proliferation|negative regulation of S phase of mitotic cell cycle	myosin complex|nucleoplasm|perinuclear region of cytoplasm|plasma membrane	actin filament binding|ATP binding|motor activity			ovary(6)|large_intestine(1)|kidney(1)|breast(1)|central_nervous_system(1)	10	all_lung(23;0.000332)|all_neural(89;0.00294)|Medulloblastoma(90;0.00596)|Lung NSC(43;0.00751)|Lung SC(71;0.104)		BRCA - Breast invasive adenocarcinoma(86;0.19)|all cancers(43;0.201)			GGCTGTGAGCGCCTGCCTCTC	0.672													9	14	---	---	---	---	PASS
CGRRF1	10668	broad.mit.edu	37	14	54997025	54997025	+	Intron	SNP	C	T	T			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:54997025C>T	uc001xay.2	+						CGRRF1_uc010tra.1_Intron|CGRRF1_uc001xaz.2_RNA	NM_006568	NP_006559	Q99675	CGRF1_HUMAN	cell growth regulator with ring finger domain 1						cell cycle arrest|negative regulation of cell proliferation|response to stress		zinc ion binding			ovary(1)	1						ATTGATCATTCTTGGTATACT	0.353													3	33	---	---	---	---	PASS
GPHN	10243	broad.mit.edu	37	14	67147886	67147886	+	Silent	SNP	C	T	T			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:67147886C>T	uc001xiy.2	+	2	1247	c.126C>T	c.(124-126)CTC>CTT	p.L42L	GPHN_uc001xiw.2_Silent_p.L42L|GPHN_uc001xix.2_Silent_p.L42L|GPHN_uc010tss.1_Silent_p.L42L|GPHN_uc010tst.1_Silent_p.L42L	NM_001024218	NP_001019389	Q9NQX3	GEPH_HUMAN	gephyrin isoform 2	42	MPT Mo-transferase.				Mo-molybdopterin cofactor biosynthetic process|water-soluble vitamin metabolic process	cell junction|cytoplasm|cytoskeleton|postsynaptic membrane	ATP binding|metal ion binding|nucleotidyltransferase activity			ovary(2)	2		all_cancers(7;0.0476)|all_hematologic(31;0.0116)		Epithelial(1;1.73e-08)|all cancers(60;3.15e-07)|OV - Ovarian serous cystadenocarcinoma(108;0.000275)|BRCA - Breast invasive adenocarcinoma(234;0.00323)|Colorectal(3;0.0938)|KIRC - Kidney renal clear cell carcinoma(182;0.184)		TCAAAGATCTCGTACAAGATC	0.299			T	MLL	AL								15	17	---	---	---	---	PASS
SNRPN	6638	broad.mit.edu	37	15	25220568	25220568	+	Missense_Mutation	SNP	G	T	T			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:25220568G>T	uc001ywp.1	+	8	957	c.67G>T	c.(67-69)GAT>TAT	p.D23Y	SNRPN_uc001ywq.1_Missense_Mutation_p.D23Y|SNRPN_uc001ywr.1_Missense_Mutation_p.D23Y|SNRPN_uc001yws.1_Missense_Mutation_p.D23Y|SNRPN_uc001ywt.1_Missense_Mutation_p.D23Y|SNRPN_uc001ywv.1_Missense_Mutation_p.D26Y|SNRPN_uc001yww.1_Missense_Mutation_p.D23Y|SNRPN_uc001ywx.1_Missense_Mutation_p.D23Y|SNRPN_uc001ywz.1_Intron|PAR-SN_uc001yxa.1_Intron|SNRPN_uc001ywy.1_3'UTR	NM_022807	NP_073718	P63162	RSMN_HUMAN	small nuclear ribonucleoprotein polypeptide N	23					RNA splicing	small nuclear ribonucleoprotein complex|spliceosomal complex	identical protein binding|RNA binding			ovary(1)	1		all_cancers(20;9.33e-22)|Breast(32;0.000625)		all cancers(64;3.38e-08)|Epithelial(43;3.45e-07)|BRCA - Breast invasive adenocarcinoma(123;0.000207)|GBM - Glioblastoma multiforme(186;0.125)		TATCCTGCAAGATGGCCGAAT	0.418									Prader-Willi_syndrome				51	110	---	---	---	---	PASS
COPS2	9318	broad.mit.edu	37	15	49423011	49423011	+	Missense_Mutation	SNP	G	T	T			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:49423011G>T	uc001zxf.2	-	10	1029	c.950C>A	c.(949-951)GCC>GAC	p.A317D	COPS2_uc001zxh.2_Missense_Mutation_p.A324D|COPS2_uc010ufa.1_Missense_Mutation_p.A253D	NM_004236	NP_004227	P61201	CSN2_HUMAN	COP9 constitutive photomorphogenic homolog	317	PCI.				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)		ATTCTGATAGGCACTAATAGA	0.308													28	46	---	---	---	---	PASS
MYO5C	55930	broad.mit.edu	37	15	52571772	52571772	+	Nonsense_Mutation	SNP	C	A	A			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:52571772C>A	uc010bff.2	-	3	375	c.238G>T	c.(238-240)GAG>TAG	p.E80*	MYO5C_uc010uga.1_RNA|MYO5C_uc010ugb.1_RNA|MYO5C_uc010ugc.1_Nonsense_Mutation_p.E43*|MIR1266_hsa-mir-1266|MI0006403_5'Flank	NM_018728	NP_061198	Q9NQX4	MYO5C_HUMAN	myosin VC	80	Myosin head-like.					myosin complex	actin binding|ATP binding|calmodulin binding|motor activity			ovary(7)|central_nervous_system(3)|large_intestine(2)|skin(2)	14				all cancers(107;0.0137)		ACCGCGGGCTCGTGAAGATAG	0.507													30	50	---	---	---	---	PASS
CILP	8483	broad.mit.edu	37	15	65499201	65499201	+	Missense_Mutation	SNP	C	T	T			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:65499201C>T	uc002aon.2	-	4	524	c.343G>A	c.(343-345)GAG>AAG	p.E115K		NM_003613	NP_003604	O75339	CILP1_HUMAN	cartilage intermediate layer protein	115					negative regulation of insulin-like growth factor receptor signaling pathway	extracellular matrix part|extracellular space|proteinaceous extracellular matrix				ovary(4)|pancreas(2)|skin(1)	7						CAGAAACCCTCACGGGGACTA	0.637													13	59	---	---	---	---	PASS
FAM108C1	58489	broad.mit.edu	37	15	81046666	81046666	+	Silent	SNP	A	G	G			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:81046666A>G	uc002bfu.2	+	3	1064	c.945A>G	c.(943-945)CTA>CTG	p.L315L	FAM108C1_uc002bft.2_Silent_p.L274L	NM_021214	NP_067037	Q6PCB6	F108C_HUMAN	hypothetical protein LOC58489	315							hydrolase activity				0						CACAATACCTAGAAAGACTAA	0.468													11	22	---	---	---	---	PASS
DET1	55070	broad.mit.edu	37	15	89056233	89056233	+	Silent	SNP	C	T	T			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:89056233C>T	uc002bmr.2	-	5	1754	c.1602G>A	c.(1600-1602)AGG>AGA	p.R534R	DET1_uc002bmp.3_RNA|DET1_uc010bnk.2_RNA|DET1_uc002bmq.2_Silent_p.R545R	NM_001144074	NP_001137546	Q7L5Y6	DET1_HUMAN	de-etiolated 1 isoform 2	534						nucleus				lung(1)|pancreas(1)	2	Lung NSC(78;0.105)|all_lung(78;0.182)		BRCA - Breast invasive adenocarcinoma(143;0.188)			CAGCATTAGTCCTCTGCACAG	0.522													41	60	---	---	---	---	PASS
RHCG	51458	broad.mit.edu	37	15	90022631	90022631	+	Silent	SNP	G	A	A			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:90022631G>A	uc002bnz.2	-	5	783	c.759C>T	c.(757-759)ACC>ACT	p.T253T	RHCG_uc002bny.2_Silent_p.T24T|RHCG_uc002boa.2_RNA|RHCG_uc010bnq.1_Silent_p.T137T	NM_016321	NP_057405	Q9UBD6	RHCG_HUMAN	Rh family, C glycoprotein	253	Helical; (Potential).				amine transport|cellular ion homeostasis|epithelial cell differentiation|transepithelial ammonium transport	apical plasma membrane|basolateral plasma membrane|cytoplasmic vesicle|integral to plasma membrane	ammonia transmembrane transporter activity|ammonium transmembrane transporter activity|ankyrin binding			kidney(1)	1	Lung NSC(78;0.0237)|all_lung(78;0.0478)					AGGAGCAGTAGGTGTTGATGG	0.597													21	27	---	---	---	---	PASS
SPSB3	90864	broad.mit.edu	37	16	1827748	1827748	+	Missense_Mutation	SNP	C	G	G	rs147512809		TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1827748C>G	uc002cmr.2	-	5	754	c.721G>C	c.(721-723)GGT>CGT	p.G241R	SPSB3_uc002cms.2_Missense_Mutation_p.G113R|SPSB3_uc002cmt.2_Missense_Mutation_p.G113R|SPSB3_uc002cmu.2_Missense_Mutation_p.G241R|SPSB3_uc002cmv.2_Missense_Mutation_p.G113R	NM_080861	NP_543137	Q6PJ21	SPSB3_HUMAN	splA/ryanodine receptor domain and SOCS box	241	B30.2/SPRY.				intracellular signal transduction						0						ACGGCCTCACCTATACACTTC	0.602													21	43	---	---	---	---	PASS
CIITA	4261	broad.mit.edu	37	16	10997656	10997656	+	Missense_Mutation	SNP	C	G	G			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:10997656C>G	uc002dai.3	+	9	974	c.841C>G	c.(841-843)CCA>GCA	p.P281A	CIITA_uc002daj.3_Missense_Mutation_p.P282A|CIITA_uc002dak.3_Missense_Mutation_p.P232A|CIITA_uc002dag.2_Missense_Mutation_p.P281A|CIITA_uc002dah.2_Missense_Mutation_p.P233A|CIITA_uc010bup.1_Missense_Mutation_p.P281A	NM_000246	NP_000237	P33076	C2TA_HUMAN	class II transactivator	281					interferon-gamma-mediated signaling pathway|negative regulation of transcription from RNA polymerase II promoter|positive regulation of MHC class I biosynthetic process|positive regulation of transcription from RNA polymerase II promoter|response to antibiotic|transcription, DNA-dependent	nucleus	activating transcription factor binding|ATP binding|protein C-terminus binding|protein complex binding|transcription coactivator activity|transcription regulatory region DNA binding			central_nervous_system(1)	1						CCCAACATCTCCAGACCGGCC	0.612			T	FLJ27352|CD274|CD273|RALGDS|RUNDC2A|C16orf75	PMBL|Hodgkin Lymphona|								48	77	---	---	---	---	PASS
PDXDC1	23042	broad.mit.edu	37	16	15225426	15225426	+	Intron	SNP	C	G	G			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:15225426C>G	uc002ddc.2	+						uc010uzs.1_RNA|uc002ddh.2_5'UTR|uc002ddi.2_5'Flank|uc010uzt.1_5'UTR	NM_015027	NP_055842	Q6P996	PDXD1_HUMAN	pyridoxal-dependent decarboxylase domain						carboxylic acid metabolic process		carboxy-lyase activity|protein binding|pyridoxal phosphate binding			skin(1)	1					Pyridoxal Phosphate(DB00114)	GTTGAGCACGCGGGAGCGCGT	0.697													3	45	---	---	---	---	PASS
CIRH1A	84916	broad.mit.edu	37	16	69199288	69199288	+	Silent	SNP	C	T	T			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:69199288C>T	uc002ews.3	+	15	1788	c.1692C>T	c.(1690-1692)AGC>AGT	p.S564S	CIRH1A_uc002ewr.2_Silent_p.S564S|CIRH1A_uc002ewt.3_Silent_p.S481S|CIRH1A_uc010cfi.2_Silent_p.S366S	NM_032830	NP_116219	Q969X6	CIR1A_HUMAN	cirhin	564						nucleolus	protein binding				0				OV - Ovarian serous cystadenocarcinoma(108;0.125)		CAGATTGGAGCCGGACTGTCC	0.488													28	46	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	16	70268080	70268080	+	RNA	SNP	T	C	C	rs149244259	by1000genomes	TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70268080T>C	uc010cfp.1	-	3		c.335A>G								Homo sapiens cDNA, FLJ98908.																		GTCTTACTGTTGGCTAAAAGG	0.373													3	13	---	---	---	---	PASS
GCSH	2653	broad.mit.edu	37	16	81118200	81118200	+	Splice_Site	SNP	C	A	A			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:81118200C>A	uc002fgd.2	-	4	390	c.293_splice	c.e4-1	p.D98_splice	GCSH_uc002fge.2_Splice_Site	NM_004483	NP_004474	P23434	GCSH_HUMAN	glycine cleavage system protein H (aminomethyl							glycine cleavage complex|mitochondrion	aminomethyltransferase activity				0					Glycine(DB00145)	CCAAACTCATCTAAGTGGAAA	0.318													13	33	---	---	---	---	PASS
ZC3H18	124245	broad.mit.edu	37	16	88694152	88694152	+	Missense_Mutation	SNP	C	T	T			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:88694152C>T	uc002fky.2	+	14	2431	c.2231C>T	c.(2230-2232)TCT>TTT	p.S744F	ZC3H18_uc010voz.1_Missense_Mutation_p.S768F|ZC3H18_uc010chw.2_Intron|ZC3H18_uc002fkz.2_Missense_Mutation_p.S14F	NM_144604	NP_653205	Q86VM9	ZCH18_HUMAN	zinc finger CCCH-type containing 18	744	Ser-rich.					nucleus	nucleic acid binding|zinc ion binding			skin(1)	1				BRCA - Breast invasive adenocarcinoma(80;0.0542)		TCAGCCAGCTCTCGGTCCCCG	0.652													13	38	---	---	---	---	PASS
ZNF276	92822	broad.mit.edu	37	16	89804478	89804478	+	Missense_Mutation	SNP	G	C	C			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89804478G>C	uc002fos.3	+	11	1766	c.1669G>C	c.(1669-1671)GAC>CAC	p.D557H	ZNF276_uc010ciq.2_Missense_Mutation_p.D343H|ZNF276_uc002fop.2_3'UTR|ZNF276_uc002foq.3_Missense_Mutation_p.D482H|ZNF276_uc010cir.2_RNA|ZNF276_uc002for.3_Missense_Mutation_p.D343H|ZNF276_uc010cis.2_Missense_Mutation_p.D316H|ZNF276_uc002fot.3_RNA|ZNF276_uc010vpm.1_Missense_Mutation_p.D395H|ZNF276_uc010cit.1_3'UTR|FANCA_uc002fou.1_3'UTR|FANCA_uc010vpn.1_3'UTR	NM_001113525	NP_001106997	Q8N554	ZN276_HUMAN	zinc finger protein 276 isoform a	557	C2H2-type 5.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Lung NSC(15;2.19e-05)|all_lung(18;3.07e-05)|all_hematologic(23;0.0256)		BRCA - Breast invasive adenocarcinoma(80;0.0278)		CTTTGCCTGTGACCAGTGTGG	0.597													14	45	---	---	---	---	PASS
ITGAE	3682	broad.mit.edu	37	17	3657179	3657179	+	Silent	SNP	G	C	C			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:3657179G>C	uc002fwo.3	-	13	1524	c.1425C>G	c.(1423-1425)TCC>TCG	p.S475S		NM_002208	NP_002199	P38570	ITAE_HUMAN	integrin, alpha E precursor	475	FG-GAP 4.|Extracellular (Potential).				cell adhesion|integrin-mediated signaling pathway	integrin complex	receptor activity			large_intestine(2)|breast(1)|pancreas(1)	4				UCEC - Uterine corpus endometrioid carcinoma (3;0.0813)		CCGCGATGTAGGAGAGGCTGC	0.627													20	32	---	---	---	---	PASS
KIAA0100	9703	broad.mit.edu	37	17	26965110	26965110	+	Silent	SNP	A	G	G			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26965110A>G	uc002hbu.2	-	14	1614	c.1515T>C	c.(1513-1515)GGT>GGC	p.G505G		NM_014680	NP_055495	Q14667	K0100_HUMAN	hypothetical protein LOC9703 precursor	505						extracellular region				ovary(2)|breast(1)|skin(1)	4	Lung NSC(42;0.00431)					GGTTATAGCTACCCTAGAGAA	0.493													14	56	---	---	---	---	PASS
AMZ2P1	201283	broad.mit.edu	37	17	62964436	62964436	+	RNA	SNP	G	T	T			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:62964436G>T	uc002jez.3	-	5		c.743C>A			AMZ2P1_uc002jfa.3_RNA|AMZ2P1_uc002jfb.3_RNA|AMZ2P1_uc010del.2_RNA					Homo sapiens cDNA FLJ32065 fis, clone OCBBF1000086, weakly similar to Archeobacterial metalloproteinase-like protein 2 (EC 3.-.-.-).												0						TTATCCTCACGACTGTGTTCT	0.443													27	44	---	---	---	---	PASS
ST6GALNAC1	55808	broad.mit.edu	37	17	74625522	74625522	+	Missense_Mutation	SNP	T	C	C			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74625522T>C	uc002jsh.2	-	2	577	c.403A>G	c.(403-405)AAC>GAC	p.N135D	ST6GALNAC1_uc002jsi.2_Missense_Mutation_p.N3D|ST6GALNAC1_uc002jsj.2_RNA	NM_018414	NP_060884	Q9NSC7	SIA7A_HUMAN	sialyltransferase 7A	135	Lumenal (Potential).				protein glycosylation	integral to Golgi membrane	alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase activity				0						GACAGTGTGTTCACCATGGTT	0.572													76	128	---	---	---	---	PASS
SLC26A11	284129	broad.mit.edu	37	17	78215586	78215586	+	Silent	SNP	C	T	T			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:78215586C>T	uc002jyb.1	+	10	1271	c.1002C>T	c.(1000-1002)TAC>TAT	p.Y334Y	SLC26A11_uc002jyc.1_Silent_p.Y334Y|SLC26A11_uc002jyd.1_Silent_p.Y334Y|SLC26A11_uc010dhv.1_Silent_p.Y334Y	NM_173626	NP_775897	Q86WA9	S2611_HUMAN	solute carrier family 26, member 11	334	Extracellular (Potential).					endoplasmic reticulum|Golgi apparatus|integral to membrane|lysosomal membrane|plasma membrane	anion:anion antiporter activity|secondary active sulfate transmembrane transporter activity				0	all_neural(118;0.0538)		OV - Ovarian serous cystadenocarcinoma(97;0.0344)|BRCA - Breast invasive adenocarcinoma(99;0.0908)			AGAATAATTACCGCATCGATG	0.512													43	119	---	---	---	---	PASS
COLEC12	81035	broad.mit.edu	37	18	346953	346953	+	Silent	SNP	C	A	A			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:346953C>A	uc002kkm.2	-	5	884	c.669G>T	c.(667-669)CTG>CTT	p.L223L		NM_130386	NP_569057	Q5KU26	COL12_HUMAN	collectin sub-family member 12	223	Potential.|Extracellular (Potential).				carbohydrate mediated signaling|innate immune response|phagocytosis, recognition|protein homooligomerization	collagen|integral to membrane	galactose binding|low-density lipoprotein particle binding|metal ion binding|pattern recognition receptor activity|scavenger receptor activity			ovary(1)|pancreas(1)	2		all_cancers(4;0.0442)|Myeloproliferative disorder(11;0.0426)				CAGACCGCTGCAGATTCGTGA	0.473													67	102	---	---	---	---	PASS
HRH4	59340	broad.mit.edu	37	18	22056745	22056745	+	Missense_Mutation	SNP	A	G	G			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:22056745A>G	uc002kvi.2	+	3	492	c.392A>G	c.(391-393)AAG>AGG	p.K131R	HRH4_uc010xbd.1_3'UTR|HRH4_uc010dlx.2_Intron	NM_021624	NP_067637	Q9H3N8	HRH4_HUMAN	histamine H4 receptor isoform 1	131	Cytoplasmic (Potential).					integral to membrane|plasma membrane	histamine receptor activity			ovary(2)	2	all_cancers(21;0.000545)|all_epithelial(16;6.56e-06)|Lung NSC(20;0.0027)|all_lung(20;0.0085)|Colorectal(14;0.0361)|Ovarian(20;0.0991)				Clozapine(DB00363)	GGGGTCTTGAAGATTGTTACT	0.383													55	117	---	---	---	---	PASS
FAM59A	64762	broad.mit.edu	37	18	29867421	29867421	+	Missense_Mutation	SNP	G	A	A			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:29867421G>A	uc002kxl.2	-	4	1195	c.1139C>T	c.(1138-1140)ACC>ATC	p.T380I	FAM59A_uc002kxk.1_Missense_Mutation_p.T380I	NM_022751	NP_073588	Q9H706	FA59A_HUMAN	family with sequence similarity 59, member A	380										ovary(1)|skin(1)	2						GAAGGACTGGGTGAGCTCATC	0.567													38	47	---	---	---	---	PASS
SHC2	25759	broad.mit.edu	37	19	422337	422337	+	Missense_Mutation	SNP	G	T	T			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:422337G>T	uc002loq.3	-	11	1429	c.1429C>A	c.(1429-1431)CCC>ACC	p.P477T	SHC2_uc002lop.3_Missense_Mutation_p.P218T	NM_012435	NP_036567	P98077	SHC2_HUMAN	SHC (Src homology 2 domain containing)	477	CH1.				insulin receptor signaling pathway|nerve growth factor receptor signaling pathway|Ras protein signal transduction	cytosol					0		all_cancers(10;1.13e-36)|all_epithelial(18;1.46e-23)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.1e-06)|all_lung(49;1.55e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		TCCTCCGTGGGGGCCACAGGG	0.692													7	16	---	---	---	---	PASS
DOT1L	84444	broad.mit.edu	37	19	2211150	2211150	+	Silent	SNP	G	A	A			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2211150G>A	uc002lvb.3	+	15	1440	c.1404G>A	c.(1402-1404)CAG>CAA	p.Q468Q	DOT1L_uc002lvc.1_5'UTR	NM_032482	NP_115871	Q8TEK3	DOT1L_HUMAN	DOT1-like, histone H3 methyltransferase	468						nucleus	DNA binding|histone-lysine N-methyltransferase activity|protein binding			pancreas(2)|upper_aerodigestive_tract(1)|lung(1)	4		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CGAGCGTGCAGCGGCACTCCC	0.697													18	114	---	---	---	---	PASS
MUC16	94025	broad.mit.edu	37	19	8976796	8976796	+	Silent	SNP	T	C	C			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8976796T>C	uc002mkp.2	-	73	42474	c.42270A>G	c.(42268-42270)CCA>CCG	p.P14090P	MUC16_uc010dwi.2_RNA|MUC16_uc010dwj.2_Silent_p.P890P|MUC16_uc010xki.1_Intron	NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment					cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			lung(30)|ovary(15)|breast(8)|large_intestine(1)|skin(1)|prostate(1)|pancreas(1)	57						TGCCCATATCTGGTGAATACT	0.567													16	52	---	---	---	---	PASS
PDE4A	5141	broad.mit.edu	37	19	10574570	10574570	+	Missense_Mutation	SNP	G	C	C			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10574570G>C	uc002moj.2	+	14	1953	c.1845G>C	c.(1843-1845)CAG>CAC	p.Q615H	PDE4A_uc002mok.2_Missense_Mutation_p.Q589H|PDE4A_uc002mol.2_Missense_Mutation_p.Q554H|PDE4A_uc002mom.2_Missense_Mutation_p.Q376H|PDE4A_uc002mon.2_Missense_Mutation_p.Q70H|PDE4A_uc002moo.2_Missense_Mutation_p.Q281H	NM_001111307	NP_001104777	P27815	PDE4A_HUMAN	phosphodiesterase 4A isoform 1	615	Catalytic.				signal transduction	cytosol|membrane fraction|perinuclear region of cytoplasm|ruffle membrane|soluble fraction	3',5'-cyclic-AMP phosphodiesterase activity|metal ion binding|protein binding			ovary(1)|breast(1)|central_nervous_system(1)	3			OV - Ovarian serous cystadenocarcinoma(20;5.8e-10)|Epithelial(33;7.58e-07)|all cancers(31;3.91e-06)		Cilostazol(DB01166)|Dipyridamole(DB00975)|Dyphylline(DB00651)|Enprofylline(DB00824)|Iloprost(DB01088)|Milrinone(DB00235)|Pentoxifylline(DB00806)|Phentolamine(DB00692)|Tadalafil(DB00820)|Theophylline(DB00277)	AGTTCTTCCAGCAGGGTGACC	0.617													18	68	---	---	---	---	PASS
RYR1	6261	broad.mit.edu	37	19	39038896	39038896	+	Missense_Mutation	SNP	G	A	A			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39038896G>A	uc002oit.2	+	89	12248	c.12118G>A	c.(12118-12120)GCC>ACC	p.A4040T	RYR1_uc002oiu.2_Missense_Mutation_p.A4035T|RYR1_uc002oiv.1_Missense_Mutation_p.A949T	NM_000540	NP_000531	P21817	RYR1_HUMAN	skeletal muscle ryanodine receptor isoform 1	4040	Helical; Name=M2; (Potential).				muscle contraction|release of sequestered calcium ion into cytosol|response to caffeine|response to hypoxia	cell cortex|cytosol|I band|integral to plasma membrane|junctional sarcoplasmic reticulum membrane|smooth endoplasmic reticulum|terminal cisterna	calcium ion binding|calmodulin binding|receptor activity|ryanodine-sensitive calcium-release channel activity			ovary(7)|pancreas(2)|breast(1)|central_nervous_system(1)|skin(1)	12	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Dantrolene(DB01219)	CGGCATGATCGCCCGGCAGAT	0.577													29	49	---	---	---	---	PASS
ZNF546	339327	broad.mit.edu	37	19	40520538	40520538	+	Missense_Mutation	SNP	C	T	T			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:40520538C>T	uc002oms.2	+	7	1617	c.1361C>T	c.(1360-1362)ACG>ATG	p.T454M	ZNF546_uc002omt.2_Missense_Mutation_p.T428M	NM_178544	NP_848639	Q86UE3	ZN546_HUMAN	zinc finger protein 546	454	C2H2-type 9.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)|breast(1)|skin(1)	3	all_cancers(60;9.55e-06)|all_lung(34;1.17e-07)|Lung NSC(34;1.41e-07)|Ovarian(47;0.0925)					CGTCTTCAAACGGAACTTACT	0.393													32	73	---	---	---	---	PASS
EML2	24139	broad.mit.edu	37	19	46119737	46119737	+	Silent	SNP	G	A	A			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:46119737G>A	uc002pcn.2	-	15	1526	c.1491C>T	c.(1489-1491)AGC>AGT	p.S497S	EML2_uc002pco.2_Intron|EML2_uc002pcp.2_Silent_p.S381S|EML2_uc010xxl.1_Silent_p.S644S|EML2_uc010xxm.1_Silent_p.S698S|EML2_uc010xxn.1_RNA	NM_012155	NP_036287	O95834	EMAL2_HUMAN	echinoderm microtubule associated protein like	497	WD 8.				sensory perception of sound|visual perception	cytoplasm|intracellular membrane-bounded organelle|microtubule|microtubule associated complex	catalytic activity|protein binding			large_intestine(1)|ovary(1)	2		Ovarian(192;0.179)|all_neural(266;0.224)		OV - Ovarian serous cystadenocarcinoma(262;0.00553)|GBM - Glioblastoma multiforme(486;0.131)|Epithelial(262;0.197)		TGCCCAGGCGGCTGACCTTGC	0.687													24	57	---	---	---	---	PASS
RUVBL2	10856	broad.mit.edu	37	19	49510383	49510383	+	Missense_Mutation	SNP	G	C	C			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49510383G>C	uc002plr.1	+	5	387	c.374G>C	c.(373-375)CGG>CCG	p.R125P	RUVBL2_uc002plq.1_Missense_Mutation_p.R80P|RUVBL2_uc010yab.1_Missense_Mutation_p.R125P|RUVBL2_uc002pls.1_RNA|RUVBL2_uc010emn.1_Missense_Mutation_p.R80P|RUVBL2_uc010yac.1_Missense_Mutation_p.R80P	NM_006666	NP_006657	Q9Y230	RUVB2_HUMAN	RuvB-like 2	125					cellular response to UV|DNA recombination|DNA repair|histone H2A acetylation|histone H4 acetylation|protein folding|regulation of growth|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|Ino80 complex|membrane|MLL1 complex|NuA4 histone acetyltransferase complex|nuclear matrix	ATP binding|ATP-dependent DNA helicase activity|damaged DNA binding|identical protein binding|unfolded protein binding				0		all_epithelial(76;5.29e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		all cancers(93;0.000449)|OV - Ovarian serous cystadenocarcinoma(262;0.000555)|GBM - Glioblastoma multiforme(486;0.00585)|Epithelial(262;0.047)		GCCTTCCGGCGGTCCATCGGC	0.677													35	87	---	---	---	---	PASS
SHANK1	50944	broad.mit.edu	37	19	51215207	51215207	+	Silent	SNP	G	A	A			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51215207G>A	uc002psx.1	-	6	976	c.957C>T	c.(955-957)CAC>CAT	p.H319H		NM_016148	NP_057232	Q9Y566	SHAN1_HUMAN	SH3 and multiple ankyrin repeat domains 1	319	ANK 4.				cytoskeletal anchoring at plasma membrane	cell junction|cytoplasm|dendrite|membrane fraction|postsynaptic density|postsynaptic membrane	ionotropic glutamate receptor binding			large_intestine(2)	2		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00493)|GBM - Glioblastoma multiforme(134;0.0199)		GGAGCACCTGGTGGATTTCCT	0.642													51	101	---	---	---	---	PASS
C19orf48	84798	broad.mit.edu	37	19	51305662	51305662	+	Intron	SNP	C	T	T			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51305662C>T	uc002ptf.2	-						C19orf48_uc002pte.2_Intron|C19orf48_uc002ptg.2_Intron|SNORD88A_uc002pth.1_5'Flank|SNORD88C_uc002pti.1_RNA	NM_199249	NP_954857	Q6RUI8	CS048_HUMAN	multidrug resistance-related protein											ovary(1)	1		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00531)|GBM - Glioblastoma multiforme(134;0.0145)		CAGTGCTGGACATCATGGGAG	0.567													6	8	---	---	---	---	PASS
C20orf79	140856	broad.mit.edu	37	20	18794406	18794406	+	5'UTR	SNP	G	A	A			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:18794406G>A	uc002wrk.2	+	1					uc002wrj.1_Intron	NM_178483	NP_848578	Q9UJQ7	CT079_HUMAN	hypothetical protein LOC140856								sterol binding			skin(3)	3						GTATTAATCTGGTCACAGCTG	0.483													21	33	---	---	---	---	PASS
SYNJ1	8867	broad.mit.edu	37	21	34053921	34053921	+	Missense_Mutation	SNP	T	G	G	rs36101417		TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:34053921T>G	uc002yqh.2	-	11	1355	c.1355A>C	c.(1354-1356)GAA>GCA	p.E452A	SYNJ1_uc011ads.1_Missense_Mutation_p.E413A|SYNJ1_uc002yqf.2_Missense_Mutation_p.E413A|SYNJ1_uc002yqg.2_Missense_Mutation_p.E413A|SYNJ1_uc002yqi.2_Missense_Mutation_p.E452A	NM_003895	NP_003886	O43426	SYNJ1_HUMAN	synaptojanin 1 isoform a	413	SAC.						inositol-polyphosphate 5-phosphatase activity|nucleotide binding|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity|RNA binding			ovary(4)|skin(1)	5						CTGAGGCTTTTCAGCTAAACC	0.348													59	102	---	---	---	---	PASS
UFD1L	7353	broad.mit.edu	37	22	19438137	19438137	+	3'UTR	SNP	G	A	A			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:19438137G>A	uc002zpm.2	-	12					HIRA_uc010gro.1_5'Flank|HIRA_uc010grp.2_5'Flank|C22orf39_uc002zpi.2_5'Flank|C22orf39_uc002zpk.1_5'Flank|UFD1L_uc002zpo.2_3'UTR	NM_005659	NP_005650	Q92890	UFD1_HUMAN	ubiquitin fusion degradation 1-like isoform A						skeletal system development|ubiquitin-dependent protein catabolic process	cytosol|nucleus	protein binding|ubiquitin-specific protease activity				0	Colorectal(54;0.0993)					GTAACTAAAAGCCAAGATGTT	0.378													9	72	---	---	---	---	PASS
SYNGR1	9145	broad.mit.edu	37	22	39777742	39777742	+	Silent	SNP	C	G	G			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:39777742C>G	uc003axq.3	+	4	587	c.525C>G	c.(523-525)GGC>GGG	p.G175G	TAB1_uc003axr.2_Intron	NM_004711	NP_004702	O43759	SNG1_HUMAN	synaptogyrin 1 isoform 1a	175					regulation of long-term neuronal synaptic plasticity|regulation of short-term neuronal synaptic plasticity	cell junction|integral to plasma membrane|melanosome					0	Melanoma(58;0.04)					ACCAGATTGGCGCCGACTCGG	0.687													19	50	---	---	---	---	PASS
CELSR1	9620	broad.mit.edu	37	22	46792566	46792566	+	Missense_Mutation	SNP	C	T	T			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:46792566C>T	uc003bhw.1	-	13	5779	c.5779G>A	c.(5779-5781)GGC>AGC	p.G1927S	CELSR1_uc011arc.1_Missense_Mutation_p.G248S	NM_014246	NP_055061	Q9NYQ6	CELR1_HUMAN	cadherin EGF LAG seven-pass G-type receptor 1	1927	Extracellular (Potential).|EGF-like 6; calcium-binding.				central nervous system development|homophilic cell adhesion|neural tube closure|neuropeptide signaling pathway	integral to plasma membrane	calcium ion binding|G-protein coupled receptor activity|protein dimerization activity			lung(4)|breast(4)|pancreas(2)|skin(1)	11		Ovarian(80;0.00142)|Breast(42;0.00296)|all_neural(38;0.0416)|Colorectal(5;0.0766)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00643)|BRCA - Breast invasive adenocarcinoma(115;0.171)		TGCGGGGAGCCGGGGGAGCGC	0.617													7	16	---	---	---	---	PASS
DDX3X	1654	broad.mit.edu	37	X	41203656	41203656	+	Intron	SNP	T	A	A			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:41203656T>A	uc004dfe.2	+						DDX3X_uc010nhf.1_Nonsense_Mutation_p.Y327*|DDX3X_uc004dff.2_Intron|DDX3X_uc011mkq.1_Intron|DDX3X_uc011mkr.1_Intron|DDX3X_uc011mks.1_Intron|DDX3X_uc004dfg.2_Intron|DDX3X_uc011mkt.1_Intron	NM_001356	NP_001347	O00571	DDX3X_HUMAN	DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 3						interspecies interaction between organisms	cytoplasm|nuclear speck	ATP binding|ATP-dependent RNA helicase activity|DNA binding|protein binding|RNA binding			ovary(2)|breast(2)|central_nervous_system(1)|skin(1)	6						TTTGCAAGTAtgttttatttt	0.214										HNSCC(61;0.18)			4	76	---	---	---	---	PASS
MAGED2	10916	broad.mit.edu	37	X	54841822	54841822	+	Missense_Mutation	SNP	G	C	C			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:54841822G>C	uc004dtk.1	+	12	1622	c.1528G>C	c.(1528-1530)GAG>CAG	p.E510Q	MAGED2_uc004dtl.1_Missense_Mutation_p.E510Q|MAGED2_uc004dtm.1_Missense_Mutation_p.E425Q|MAGED2_uc010nkc.1_Intron|MAGED2_uc004dtn.1_Missense_Mutation_p.E510Q|MAGED2_uc004dto.1_Missense_Mutation_p.E484Q	NM_177433	NP_803182	Q9UNF1	MAGD2_HUMAN	melanoma antigen family D, 2	510										ovary(2)|breast(1)	3						GCTCGGCTCGGAGAATGCTGC	0.527													17	4	---	---	---	---	PASS
MAGEE1	57692	broad.mit.edu	37	X	75648791	75648791	+	Silent	SNP	C	T	T			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:75648791C>T	uc004ecm.1	+	1	675	c.468C>T	c.(466-468)GCC>GCT	p.A156A		NM_020932	NP_065983	Q9HCI5	MAGE1_HUMAN	melanoma antigen family E, 1	156	Pro-rich.					dendrite|nucleus|perinuclear region of cytoplasm|postsynaptic membrane				breast(3)|ovary(1)|pancreas(1)|skin(1)	6						CGCCCACCGCCTCTGAGGTAC	0.687													29	13	---	---	---	---	PASS
HNRNPH2	3188	broad.mit.edu	37	X	100668362	100668362	+	3'UTR	SNP	A	C	C			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:100668362A>C	uc004ehm.2	+	2					HNRNPH2_uc004ehn.2_3'UTR	NM_019597	NP_062543	P55795	HNRH2_HUMAN	heterogeneous nuclear ribonucleoprotein H2						nuclear mRNA splicing, via spliceosome	actin cytoskeleton|cytoplasm|heterogeneous nuclear ribonucleoprotein complex|nucleoplasm	nucleotide binding|protein binding|RNA binding				0						CTCCAGATATAAAAGCTGTAC	0.383													54	27	---	---	---	---	PASS
CROCC	9696	broad.mit.edu	37	1	17278378	17278378	+	Intron	DEL	T	-	-	rs35956886		TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17278378delT	uc001azt.2	+						CROCC_uc009voz.1_Intron|CROCC_uc001azu.2_Intron	NM_014675	NP_055490	Q5TZA2	CROCC_HUMAN	ciliary rootlet coiled-coil						cell cycle|cell projection organization|centrosome organization|protein localization	actin cytoskeleton|centriole|ciliary rootlet|plasma membrane	kinesin binding|structural molecule activity			ovary(2)|breast(2)|central_nervous_system(1)	5		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000174)|all_lung(284;0.000234)|Renal(390;0.000518)|Ovarian(437;0.00669)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.63e-06)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.181)		ggtaaagctcttttttttttt	0.000													4	2	---	---	---	---	
EIF3I	8668	broad.mit.edu	37	1	32691628	32691629	+	Intron	INS	-	A	A	rs74686229		TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:32691628_32691629insA	uc001bur.3	+						EIF3I_uc009vuc.2_Intron|EIF3I_uc001bus.2_Intron	NM_003757	NP_003748	Q13347	EIF3I_HUMAN	eukaryotic translation initiation factor 3,							cytosol|eukaryotic translation initiation factor 3 complex	protein binding|translation initiation factor activity			ovary(1)	1		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Ovarian(437;0.101)|Breast(348;0.212)				tctcaaaaaagaaaaaaaaaaa	0.173													5	3	---	---	---	---	
MYCL1	4610	broad.mit.edu	37	1	40362835	40362835	+	3'UTR	DEL	C	-	-			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:40362835delC	uc001cer.1	-	3					MYCL1_uc001ces.1_3'UTR	NM_001033082	NP_001028254	P12524	MYCL1_HUMAN	l-myc-1 proto-oncogene isoform 1							nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			lung(1)|liver(1)	2	all_cancers(7;1.73e-14)|all_lung(5;2.77e-17)|all_epithelial(6;6.81e-17)|Lung SC(1;2.85e-13)|Lung NSC(20;7.03e-07)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;1.51e-19)|Epithelial(16;3.36e-18)|all cancers(16;8.43e-17)|LUSC - Lung squamous cell carcinoma(16;0.000261)|Lung(16;0.000457)			ATACAGCACTCCCATGAGTCA	0.532			A		small cell lung 								5	4	---	---	---	---	
ATP2B4	493	broad.mit.edu	37	1	203676048	203676048	+	Intron	DEL	A	-	-			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:203676048delA	uc001gzw.2	+						ATP2B4_uc001gzv.2_Intron|ATP2B4_uc009xaq.2_Intron	NM_001684	NP_001675	P23634	AT2B4_HUMAN	plasma membrane calcium ATPase 4 isoform 4b						ATP biosynthetic process|platelet activation	integral to plasma membrane	ATP binding|calcium-transporting ATPase activity|calmodulin binding|metal ion binding|protein binding			ovary(2)|skin(1)	3	all_cancers(21;0.071)|all_epithelial(62;0.228)		BRCA - Breast invasive adenocarcinoma(75;0.109)			AATTGGCAACAAAGGCTACAA	0.408													12	13	---	---	---	---	
FMN2	56776	broad.mit.edu	37	1	240255569	240255571	+	In_Frame_Del	DEL	GGC	-	-	rs35817759		TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:240255569_240255571delGGC	uc010pyd.1	+	1	385_387	c.160_162delGGC	c.(160-162)GGCdel	p.G59del	FMN2_uc010pye.1_In_Frame_Del_p.G59del	NM_020066	NP_064450	Q9NZ56	FMN2_HUMAN	formin 2	59					actin cytoskeleton organization|establishment of meiotic spindle localization|intracellular signal transduction|meiotic chromosome movement towards spindle pole|meiotic metaphase I|multicellular organismal development|oogenesis|polar body extrusion after meiotic divisions		actin binding			ovary(4)|pancreas(3)|skin(3)|large_intestine(1)|central_nervous_system(1)	12	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)			GGGGGGAgggggcggcggcggcg	0.557													4	5	---	---	---	---	
MATN3	4148	broad.mit.edu	37	2	20201952	20201953	+	Intron	INS	-	ACAG	ACAG	rs147407955	by1000genomes	TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:20201952_20201953insACAG	uc002rdl.2	-						MATN3_uc010exu.1_Intron	NM_002381	NP_002372	O15232	MATN3_HUMAN	matrilin 3 precursor						skeletal system development	proteinaceous extracellular matrix	extracellular matrix structural constituent|protein binding				0	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					cacacacacacaGAGCTAATGA	0.173													5	5	---	---	---	---	
PREPL	9581	broad.mit.edu	37	2	44555958	44555958	+	Intron	DEL	A	-	-			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:44555958delA	uc002ruf.2	-						PREPL_uc002rug.2_Intron|PREPL_uc002ruh.2_Intron|PREPL_uc010fax.2_Intron|PREPL_uc002rui.3_Intron|PREPL_uc002ruj.1_Intron|PREPL_uc002ruk.1_Intron	NM_006036	NP_006027	Q4J6C6	PPCEL_HUMAN	prolyl endopeptidase-like isoform C						proteolysis	cytosol	serine-type endopeptidase activity			ovary(1)	1		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)				TTAGGAATACAAAAATTGAAT	0.323													17	12	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	64602820	64602821	+	IGR	INS	-	CAT	CAT	rs145819064		TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:64602820_64602821insCAT								PELI1 (231215 upstream) : HSPC159 (78506 downstream)																							accaccaccaccaccatcacca	0.000													6	3	---	---	---	---	
RGPD4	285190	broad.mit.edu	37	2	108487034	108487035	+	Intron	INS	-	ATC	ATC			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:108487034_108487035insATC	uc010ywk.1	+						RGPD4_uc002tdu.2_Intron|RGPD4_uc010ywl.1_Intron	NM_182588	NP_872394	Q7Z3J3	RGPD4_HUMAN	RANBP2-like and GRIP domain containing 4						intracellular transport		binding			skin(2)	2						caataaatgttatcatcatcat	0.099													12	6	---	---	---	---	
TMEFF2	23671	broad.mit.edu	37	2	192820810	192820811	+	Intron	INS	-	TGTGTGAATGCT	TGTGTGAATGCT	rs149857491	by1000genomes	TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:192820810_192820811insTGTGTGAATGCT	uc002utc.2	-							NM_016192	NP_057276	Q9UIK5	TEFF2_HUMAN	transmembrane protein with EGF-like and two							extracellular region|integral to membrane				lung(2)|pancreas(1)|breast(1)|skin(1)	5			OV - Ovarian serous cystadenocarcinoma(117;0.0835)			TTTTTTTTTAgtgtgtgagtat	0.257													4	3	---	---	---	---	
FARSB	10056	broad.mit.edu	37	2	223512162	223512163	+	Intron	INS	-	A	A	rs147059558	by1000genomes	TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:223512162_223512163insA	uc002vne.1	-						FARSB_uc010zlq.1_Intron|FARSB_uc002vnf.1_Intron|FARSB_uc002vng.1_Intron	NM_005687	NP_005678	Q9NSD9	SYFB_HUMAN	phenylalanyl-tRNA synthetase, beta subunit						phenylalanyl-tRNA aminoacylation	cytosol|soluble fraction	ATP binding|magnesium ion binding|phenylalanine-tRNA ligase activity|RNA binding			ovary(1)	1		Renal(207;0.0183)		Epithelial(121;3.47e-10)|all cancers(144;1.86e-07)|LUSC - Lung squamous cell carcinoma(224;0.00871)|Lung(261;0.011)	L-Phenylalanine(DB00120)	GACCAGCTTTCAGTTTTACTGA	0.450													4	2	---	---	---	---	
VHL	7428	broad.mit.edu	37	3	10191540	10191541	+	Frame_Shift_Ins	INS	-	G	G	rs5030822		TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10191540_10191541insG	uc003bvc.2	+	3	746_747	c.533_534insG	c.(532-534)CTGfs	p.L178fs	VHL_uc003bvd.2_Frame_Shift_Ins_p.L137fs	NM_000551	NP_000542	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor isoform 1	178			L -> P (in VHLD; type I-II; common mutation).		anti-apoptosis|cell morphogenesis|negative regulation of cell proliferation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of cell differentiation|positive regulation of transcription, DNA-dependent|protein stabilization|protein ubiquitination|proteolysis	cytosol|endoplasmic reticulum|membrane|mitochondrion|nucleus	protein binding|transcription factor binding	p.L178R(1)|p.R177fs*37(1)|p.L178_V181del(1)|p.?fs(1)|p.L178fs*24(1)|p.L178fs*36(1)|p.D179fs*36(1)		kidney(1273)|soft_tissue(24)|adrenal_gland(15)|large_intestine(13)|pancreas(5)|endometrium(4)|thyroid(3)|upper_aerodigestive_tract(3)|central_nervous_system(2)|lung(2)|pleura(1)|paratesticular_tissues(1)	1346				Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569)		TACAGGAGACTGGACATCGTCA	0.530		1	D|Mis|N|F|S		renal|hemangioma|pheochromocytoma	renal|hemangioma|pheochromocytoma			von_Hippel-Lindau_disease|Chuvash_Polycythemia_|Pheochromocytoma_(Adrenal)_Familial				21	17	---	---	---	---	
MST1	4485	broad.mit.edu	37	3	49723726	49723727	+	Intron	INS	-	CC	CC	rs10662055		TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49723726_49723727insCC	uc003cxg.2	-						MST1_uc011bcs.1_Frame_Shift_Ins_p.G344fs|MST1_uc010hkx.2_3'UTR|MST1_uc011bct.1_3'UTR	NM_020998	NP_066278	P26927	HGFL_HUMAN	macrophage stimulating 1 (hepatocyte growth						proteolysis	extracellular region	serine-type endopeptidase activity			lung(1)	1				BRCA - Breast invasive adenocarcinoma(193;4.47e-05)|Kidney(197;0.00216)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)		CCCAACGCCCGCCCCCCCCCCC	0.658													4	2	---	---	---	---	
GAK	2580	broad.mit.edu	37	4	891773	891773	+	Intron	DEL	A	-	-			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:891773delA	uc003gbm.3	-						GAK_uc003gbn.3_Intron|GAK_uc010ibk.1_Intron|GAK_uc003gbl.3_Intron	NM_005255	NP_005246	O14976	GAK_HUMAN	cyclin G associated kinase						cell cycle	focal adhesion|Golgi apparatus|perinuclear region of cytoplasm	ATP binding|heat shock protein binding|protein serine/threonine kinase activity			lung(2)|central_nervous_system(1)|skin(1)	4				Colorectal(103;0.219)		CAGGGCGTGGAATGTGGGAAG	0.458													11	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	49098900	49098904	+	IGR	DEL	ATTCG	-	-	rs6856382		TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49098900_49098904delATTCG								CWH43 (34807 upstream) : None (None downstream)																							attccattccattcgattccatttc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	160415816	160415816	+	IGR	DEL	A	-	-			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:160415816delA								RAPGEF2 (134517 upstream) : None (None downstream)																							ttgtctctttaaaaaaaaaaa	0.214													6	3	---	---	---	---	
MTRR	4552	broad.mit.edu	37	5	7869456	7869456	+	Intron	DEL	C	-	-	rs34828626		TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:7869456delC	uc003jed.2	+						FASTKD3_uc011cmp.1_5'Flank|FASTKD3_uc003jeb.2_5'Flank|FASTKD3_uc003jec.2_5'Flank|MTRR_uc010itn.1_Intron|MTRR_uc003jee.3_Intron|MTRR_uc003jef.3_Intron|MTRR_uc003jeg.3_Intron|MTRR_uc010ito.2_Intron	NM_024010	NP_076915	Q9UBK8	MTRR_HUMAN	methionine synthase reductase isoform 2						methionine biosynthetic process	cytosol	[methionine synthase] reductase activity|flavin adenine dinucleotide binding|FMN binding|iron ion binding|NADP binding			ovary(1)	1					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)|L-Methionine(DB00134)	CCTTCGGCCTCCGGGGGTCGC	0.746													4	4	---	---	---	---	
FER	2241	broad.mit.edu	37	5	108133721	108133721	+	Intron	DEL	T	-	-			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:108133721delT	uc003kop.1	+						FER_uc011cve.1_Intron|FER_uc011cvf.1_Intron|FER_uc003koq.2_Intron|FER_uc011cvg.1_Intron	NM_005246	NP_005237	P16591	FER_HUMAN	fer (fps/fes related) tyrosine kinase						intracellular signal transduction|peptidyl-tyrosine phosphorylation	cytoplasm|nucleus	ATP binding|non-membrane spanning protein tyrosine kinase activity			lung(2)|stomach(1)|ovary(1)|kidney(1)	5		all_cancers(142;2.86e-06)|all_epithelial(76;9.81e-08)|Prostate(80;0.00972)|Lung NSC(167;0.039)|Ovarian(225;0.0448)|all_lung(232;0.0496)|Colorectal(57;0.0986)|Breast(839;0.152)		OV - Ovarian serous cystadenocarcinoma(64;6.77e-10)|Epithelial(69;4.13e-08)|COAD - Colon adenocarcinoma(37;0.0174)		ttcagtTGTGTTTTTTTTTTT	0.114													5	3	---	---	---	---	
PCDHGA10	56106	broad.mit.edu	37	5	140812926	140812929	+	Intron	DEL	CTAT	-	-	rs72463976		TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140812926_140812929delCTAT	uc003lkl.1	+						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|PCDHGB7_uc003lkn.1_Intron|PCDHGA11_uc003lkp.1_Intron|PCDHGA11_uc003lkq.1_Intron|PCDHGA12_uc003lkt.1_Intron	NM_018913	NP_061736	Q9Y5H3	PCDGA_HUMAN	protocadherin gamma subfamily A, 10 isoform 1						homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			tactgtctgcctatctatctatct	0.000													4	2	---	---	---	---	
HK3	3101	broad.mit.edu	37	5	176314899	176314899	+	Intron	DEL	T	-	-	rs113393288		TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176314899delT	uc003mfa.2	-						HK3_uc003mez.2_Intron	NM_002115	NP_002106	P52790	HXK3_HUMAN	hexokinase 3						glucose transport|glycolysis|transmembrane transport	cytosol|membrane	ATP binding|glucokinase activity			ovary(3)|large_intestine(1)|haematopoietic_and_lymphoid_tissue(1)|breast(1)|skin(1)	7	all_cancers(89;0.000104)|Renal(175;0.000269)|Lung NSC(126;0.00696)|all_lung(126;0.0115)	Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			GCCCCATCACTtttttttttt	0.323													6	3	---	---	---	---	
GCNT2	2651	broad.mit.edu	37	6	10586869	10586869	+	Intron	DEL	C	-	-			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:10586869delC	uc010joo.2	+						GCNT2_uc010jol.2_Intron|GCNT2_uc010jom.2_Intron|GCNT2_uc010jop.2_Intron|GCNT2_uc003mza.2_Intron|GCNT2_uc003mzc.3_Intron|GCNT2_uc003mzd.2_Intron|GCNT2_uc003mze.2_Frame_Shift_Del_p.T216fs	NM_145649	NP_663624	Q8N0V5	GNT2A_HUMAN	glucosaminyl (N-acetyl) transferase 2,							Golgi membrane|integral to membrane	N-acetyllactosaminide beta-1,6-N-acetylglucosaminyltransferase activity			ovary(2)	2	Ovarian(93;0.107)|Breast(50;0.148)	all_hematologic(90;0.107)		KIRC - Kidney renal clear cell carcinoma(1;0.099)|Kidney(1;0.119)		AAAAATATCACCCCAGGGGTG	0.433													72	49	---	---	---	---	
GMPR	2766	broad.mit.edu	37	6	16247054	16247055	+	Intron	INS	-	T	T			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:16247054_16247055insT	uc003nbs.2	+							NM_006877	NP_006868	P36959	GMPR1_HUMAN	guanosine monophosphate reductase						nucleotide metabolic process|purine base metabolic process|purine-containing compound salvage|response to cold	cytosol	GMP reductase activity|metal ion binding			ovary(1)	1	Breast(50;0.0427)|Ovarian(93;0.103)	all_hematologic(90;0.0895)				CTTTTTCTTTCTTTTTTTTTGG	0.441													130	56	---	---	---	---	
TMEM63B	55362	broad.mit.edu	37	6	44114668	44114669	+	Intron	DEL	AG	-	-			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:44114668_44114669delAG	uc003owr.2	+						TMEM63B_uc003owq.1_Intron|TMEM63B_uc003ows.2_Intron|TMEM63B_uc010jyz.2_Intron	NM_018426	NP_060896	Q5T3F8	TM63B_HUMAN	transmembrane protein 63B							integral to membrane	nucleotide binding|protein binding			pancreas(2)|central_nervous_system(1)	3	all_cancers(18;1.66e-06)|Lung NSC(15;0.00108)|all_lung(25;0.00278)|Hepatocellular(11;0.00309)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0215)			CAGAGAGGTAAGGGACTGGGGG	0.564													45	21	---	---	---	---	
LRRC1	55227	broad.mit.edu	37	6	53784275	53784276	+	Intron	INS	-	TAA	TAA	rs59246960	byFrequency	TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:53784275_53784276insTAA	uc003pcd.1	+							NM_018214	NP_060684	Q9BTT6	LRRC1_HUMAN	leucine rich repeat containing 1							cytoplasm|membrane				ovary(1)	1	Lung NSC(77;0.0147)			BRCA - Breast invasive adenocarcinoma(397;0.0745)		TCTCtttttttaaaaaaaaaaa	0.371													6	7	---	---	---	---	
FAM135A	57579	broad.mit.edu	37	6	71236468	71236469	+	Intron	DEL	AT	-	-	rs111717563		TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:71236468_71236469delAT	uc003pfj.2	+						FAM135A_uc003pfi.2_Intron|FAM135A_uc003pfh.2_Intron|FAM135A_uc003pfl.2_Intron|FAM135A_uc003pfn.2_Intron|FAM135A_uc003pfo.1_Intron|FAM135A_uc010kan.1_5'Flank	NM_001162529	NP_001156001	Q9P2D6	F135A_HUMAN	hypothetical protein LOC57579 isoform c											central_nervous_system(1)	1						acacacacacatacacacacac	0.218													9	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	73308509	73308510	+	IGR	INS	-	G	G			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:73308509_73308510insG								RIMS1 (196002 upstream) : KCNQ5 (23061 downstream)																							CAGAAAATCGAGGGTTTTTTTT	0.366													7	5	---	---	---	---	
THSD7A	221981	broad.mit.edu	37	7	11452108	11452108	+	Intron	DEL	A	-	-			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:11452108delA	uc003ssf.3	-							NM_015204	NP_056019	Q9UPZ6	THS7A_HUMAN	thrombospondin, type I, domain containing 7A							integral to membrane				ovary(3)	3				UCEC - Uterine corpus endometrioid carcinoma (126;0.163)		AGTGTTTACTAAAAAAAAAAC	0.323										HNSCC(18;0.044)			4	2	---	---	---	---	
SP8	221833	broad.mit.edu	37	7	20824858	20824858	+	Frame_Shift_Del	DEL	A	-	-			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:20824858delA	uc003suy.2	-	3	765	c.524delT	c.(523-525)ATCfs	p.I175fs	SP8_uc003suz.2_Frame_Shift_Del_p.I193fs	NM_198956	NP_945194	Q8IXZ3	SP8_HUMAN	Sp8 transcription factor isoform 2	175					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			pancreas(1)	1						CCGCGGGTAGATGCCCTGCAG	0.647													10	5	---	---	---	---	
AKR1B1	231	broad.mit.edu	37	7	134134487	134134487	+	Frame_Shift_Del	DEL	A	-	-			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:134134487delA	uc003vrp.1	-	4	488	c.414delT	c.(412-414)ATTfs	p.I138fs	AKR1B1_uc003vrq.1_RNA	NM_001628	NP_001619	P15121	ALDR_HUMAN	aldo-keto reductase family 1, member B1	138					C21-steroid hormone biosynthetic process|carbohydrate metabolic process|response to stress	cytosol|extracellular space|nucleus	alditol:NADP+ 1-oxidoreductase activity|electron carrier activity|protein binding			ovary(3)	3					NADH(DB00157)|Sulindac(DB00605)	ACGTGTCCAGAATGTTGGTGT	0.458													207	116	---	---	---	---	
LUC7L2	51631	broad.mit.edu	37	7	139087001	139087001	+	Intron	DEL	T	-	-			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:139087001delT	uc003vux.2	+						LUC7L2_uc011kqs.1_Intron|LUC7L2_uc011kqt.1_Intron|LUC7L2_uc003vuy.2_Intron|LUC7L2_uc003vuz.1_Intron|LUC7L2_uc003vva.2_Intron	NM_016019	NP_057103	Q9Y383	LC7L2_HUMAN	LUC7-like 2								enzyme binding|metal ion binding				0	Melanoma(164;0.242)					AAGGTAAGAATTTTAATCATT	0.249													20	16	---	---	---	---	
ADAM28	10863	broad.mit.edu	37	8	24192864	24192864	+	Intron	DEL	A	-	-			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:24192864delA	uc003xdy.2	+						ADAM28_uc003xdx.2_Intron|ADAM28_uc011kzz.1_Intron|ADAM28_uc011laa.1_Intron|ADAM28_uc010lua.2_Intron	NM_014265	NP_055080	Q9UKQ2	ADA28_HUMAN	ADAM metallopeptidase domain 28 isoform 1						proteolysis|spermatogenesis	extracellular region|integral to membrane|plasma membrane	metalloendopeptidase activity|zinc ion binding			skin(3)|lung(1)|central_nervous_system(1)	5		Prostate(55;0.0959)		Colorectal(74;0.0129)|COAD - Colon adenocarcinoma(73;0.0434)|BRCA - Breast invasive adenocarcinoma(99;0.175)		TACTATGCCCAAAAAGTCCAA	0.318													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	31644562	31644563	+	IGR	INS	-	T	T			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:31644562_31644563insT								None (None upstream) : ACO1 (740038 downstream)																							CACAAGGAGAGTTTTTTTTTTT	0.371													4	2	---	---	---	---	
FXN	2395	broad.mit.edu	37	9	71668387	71668388	+	Intron	INS	-	GATGGATG	GATGGATG	rs73647061	by1000genomes	TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:71668387_71668388insGATGGATG	uc004aha.2	+						FXN_uc011lrr.1_Intron|FXN_uc004agz.2_Intron	NM_000144	NP_000135	Q16595	FRDA_HUMAN	frataxin isoform 1 preproprotein						cellular iron ion homeostasis|cellular response to hydrogen peroxide|heme biosynthetic process|ion transport|iron incorporation into metallo-sulfur cluster|negative regulation of apoptosis|negative regulation of release of cytochrome c from mitochondria|positive regulation of cell growth|positive regulation of cell proliferation|positive regulation of lyase activity|positive regulation of metalloenzyme activity|positive regulation of oxidoreductase activity|positive regulation of transferase activity|protein autoprocessing|regulation of ferrochelatase activity|response to iron ion	cytosol|mitochondrial matrix	2 iron, 2 sulfur cluster binding|ferric iron binding|ferrous iron binding|ferroxidase activity|iron chaperone activity|protein binding				0						actctgtcatagatggatggat	0.069													4	2	---	---	---	---	
SLC27A4	10999	broad.mit.edu	37	9	131117233	131117234	+	Intron	DEL	AA	-	-	rs151315045		TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131117233_131117234delAA	uc004but.2	+						SLC27A4_uc004buu.2_Intron	NM_005094	NP_005085	Q6P1M0	S27A4_HUMAN	solute carrier family 27 (fatty acid						long-chain fatty acid transport|transmembrane transport	integral to membrane	fatty acid transporter activity|nucleotide binding|protein binding				0						actccgtctcaaaaaaaaaaaa	0.262													4	2	---	---	---	---	
WDR34	89891	broad.mit.edu	37	9	131397627	131397627	+	Intron	DEL	A	-	-			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131397627delA	uc004bvq.1	-						WDR34_uc004bvs.1_Intron|WDR34_uc004bvr.1_Intron	NM_052844	NP_443076	Q96EX3	WDR34_HUMAN	WD repeat domain 34							cytoplasm				central_nervous_system(2)|skin(1)	3						CTCTTCCAGGAAAAAAAAAAA	0.622											OREG0019522	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	42392302	42392302	+	IGR	DEL	G	-	-	rs72505279		TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42392302delG								None (None upstream) : LOC441666 (435013 downstream)																							aacatcgaatggaatcgaatg	0.000													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	81270425	81270426	+	Intron	INS	-	G	G			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:81270425_81270426insG	uc010qls.1	-						EIF5AL1_uc009xrx.2_5'Flank					SubName: Full=cDNA FLJ60964, weakly similar to Homo sapiens dentin sialophosphoprotein (DSPP), mRNA;																		CCAGTTGTTGAGGCCTTTCTTG	0.465													7	4	---	---	---	---	
KIF20B	9585	broad.mit.edu	37	10	91469973	91469973	+	Intron	DEL	T	-	-			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:91469973delT	uc001kgs.1	+						KIF20B_uc001kgr.1_Intron	NM_016195	NP_057279	Q96Q89	KI20B_HUMAN	M-phase phosphoprotein 1						cell cycle arrest|cell division|microtubule-based movement|mitosis|regulation of mitosis	centrosome|microtubule|nucleolus|nucleoplasm|spindle	ATP binding|ATPase activity|microtubule motor activity|WW domain binding			ovary(1)|pancreas(1)|skin(1)	3						CGTATTGCTGttttttttttt	0.144													13	7	---	---	---	---	
FAM45A	404636	broad.mit.edu	37	10	120879759	120879760	+	Intron	INS	-	A	A			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:120879759_120879760insA	uc001ldw.2	+						FAM45A_uc010qsv.1_Intron|FAM45A_uc010qsw.1_Intron|FAM45A_uc010qsx.1_Intron|FAM45A_uc010qsy.1_Intron|FAM45A_uc010qsz.1_Intron	NM_207009	NP_996892	Q8TCE6	FA45A_HUMAN	hypothetical protein LOC404636											ovary(1)	1		Lung NSC(174;0.094)|all_lung(145;0.123)		all cancers(201;0.0293)		gactcggtctcaaaaaaaaaag	0.089													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	1824515	1824516	+	IGR	DEL	GC	-	-	rs10839721	by1000genomes	TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1824515_1824516delGC								CTSD (39293 upstream) : SYT8 (24193 downstream)																							TGTGGGCAGGGCCAGGAGGGGG	0.644													18	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	49327167	49327167	+	IGR	DEL	A	-	-			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:49327167delA								FOLH1 (96945 upstream) : LOC440040 (252913 downstream)																							TAAAGTTAGcaaaaaaaaaaa	0.204													6	3	---	---	---	---	
TMX2	51075	broad.mit.edu	37	11	57505890	57505890	+	Frame_Shift_Del	DEL	T	-	-			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:57505890delT	uc001nlc.1	+	4	478	c.429delT	c.(427-429)GATfs	p.D143fs	CTNND1_uc001nlf.1_Intron|TMX2_uc001nld.1_Frame_Shift_Del_p.D49fs|TMX2_uc001nle.1_Frame_Shift_Del_p.D105fs|C11orf31_uc010rjx.1_5'Flank	NM_015959	NP_057043	Q9Y320	TMX2_HUMAN	thioredoxin domain containing 14 isoform 1	143	Cytoplasmic (Potential).|Thioredoxin.				cell redox homeostasis	integral to membrane					0						ACTTCAATGATAAAACCATTG	0.423													174	86	---	---	---	---	
HTR7P1	93164	broad.mit.edu	37	12	13174141	13174142	+	Intron	INS	-	AAC	AAC	rs112328257	by1000genomes	TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:13174141_13174142insAAC	uc001rbh.2	+											Homo sapiens cDNA FLJ43688 fis, clone TBAES2003492.												0						tctgtctcaaaaacaacaacaa	0.168													5	4	---	---	---	---	
PITPNM2	57605	broad.mit.edu	37	12	123497230	123497232	+	In_Frame_Del	DEL	ATA	-	-			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123497230_123497232delATA	uc001uej.1	-	4	482_484	c.343_345delTAT	c.(343-345)TATdel	p.Y115del	PITPNM2_uc001uek.1_In_Frame_Del_p.Y115del|PITPNM2_uc009zxu.1_In_Frame_Del_p.Y115del|hsa-mir-4304|MI0015832_5'Flank	NM_020845	NP_065896	Q9BZ72	PITM2_HUMAN	phosphatidylinositol transfer protein,	115					metabolic process|transport	endomembrane system|integral to membrane|intracellular membrane-bounded organelle	calcium ion binding|lipid binding			ovary(1)|central_nervous_system(1)|skin(1)	3	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;2.55e-05)|Epithelial(86;8.43e-05)|BRCA - Breast invasive adenocarcinoma(302;0.123)		CATCAGTTTTATAAAAGGTTTCA	0.512													265	152	---	---	---	---	
DOCK9	23348	broad.mit.edu	37	13	99537420	99537420	+	Intron	DEL	T	-	-			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:99537420delT	uc001vnt.2	-						DOCK9_uc001vnw.2_Intron|DOCK9_uc001vnv.1_Intron|DOCK9_uc010tir.1_Intron|DOCK9_uc010tis.1_Intron|DOCK9_uc010tit.1_Intron|DOCK9_uc010afu.1_Intron	NM_015296	NP_056111	Q9BZ29	DOCK9_HUMAN	dedicator of cytokinesis 9 isoform a						blood coagulation	cytosol|endomembrane system|membrane	GTP binding|GTPase binding|guanyl-nucleotide exchange factor activity			central_nervous_system(1)	1	all_neural(89;0.101)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)					CAAGCCAATGTAAAACCGTCT	0.353													14	7	---	---	---	---	
SNX6	58533	broad.mit.edu	37	14	35037351	35037351	+	Intron	DEL	T	-	-			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:35037351delT	uc001wsf.1	-						SNX6_uc001wse.1_Intron|SNX6_uc010tpm.1_Intron|SNX6_uc010amm.1_Intron	NM_152233	NP_689419	Q9UNH7	SNX6_HUMAN	sorting nexin 6 isoform b						cell communication|intracellular protein transport|negative regulation of epidermal growth factor receptor activity|negative regulation of transcription, DNA-dependent|negative regulation of transforming growth factor beta receptor signaling pathway|retrograde transport, endosome to Golgi	cytoplasmic vesicle membrane|early endosome membrane|nucleus	phosphatidylinositol binding|protein homodimerization activity				0	Breast(36;0.0473)|Hepatocellular(127;0.158)		LUAD - Lung adenocarcinoma(48;0.00169)|Lung(238;0.00199)|Epithelial(34;0.187)	GBM - Glioblastoma multiforme(112;0.0245)		GTTACTCCAAttttttttttt	0.234													4	2	---	---	---	---	
PTGR2	145482	broad.mit.edu	37	14	74327307	74327307	+	Frame_Shift_Del	DEL	A	-	-			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:74327307delA	uc001xow.2	+	3	263	c.103delA	c.(103-105)AATfs	p.N35fs	PTGR2_uc010tue.1_Frame_Shift_Del_p.N35fs|PTGR2_uc001xox.2_Frame_Shift_Del_p.N35fs|ZNF410_uc001xoy.1_RNA	NM_001146154	NP_001139626	Q8N8N7	PTGR2_HUMAN	prostaglandin reductase 2	35					prostaglandin metabolic process		15-oxoprostaglandin 13-oxidase activity|zinc ion binding				0						AGATAATATTAATGAAGGACA	0.284													53	33	---	---	---	---	
TUBGCP5	114791	broad.mit.edu	37	15	22845637	22845638	+	Intron	INS	-	TATTTTTAAA	TATTTTTAAA	rs144200387	by1000genomes	TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:22845637_22845638insTATTTTTAAA	uc001yur.3	+						TUBGCP5_uc001yuq.2_Intron	NM_052903	NP_443135	Q96RT8	GCP5_HUMAN	tubulin, gamma complex associated protein 5						G2/M transition of mitotic cell cycle|microtubule nucleation	centrosome|cytosol|gamma-tubulin ring complex|microtubule|spindle pole	microtubule binding			skin(1)	1		all_cancers(20;2.26e-25)|all_epithelial(15;2.1e-22)|Lung NSC(15;3.36e-17)|all_lung(15;1.04e-16)|Breast(32;0.000776)|Colorectal(260;0.0488)		all cancers(64;2.86e-06)|Epithelial(43;2.63e-05)|BRCA - Breast invasive adenocarcinoma(123;0.000949)		TACATAAATGTTAGGTAGCTGT	0.203													5	3	---	---	---	---	
TMOD3	29766	broad.mit.edu	37	15	52218859	52218859	+	Intron	DEL	A	-	-			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:52218859delA	uc010bfc.1	+							NM_014547		Q9NYL9	TMOD3_HUMAN	tropomodulin 3 (ubiquitous)							cytoplasm|cytoskeleton	actin binding|tropomyosin binding			ovary(1)	1				all cancers(107;0.00194)		agtctgtctcaaaaaaaaaaa	0.164													4	3	---	---	---	---	
RSL1D1	26156	broad.mit.edu	37	16	11940251	11940252	+	Intron	INS	-	A	A			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:11940251_11940252insA	uc002dbp.1	-						RSL1D1_uc010buv.1_Intron|RSL1D1_uc010uyw.1_Intron|RSL1D1_uc010buw.2_Intron	NM_015659	NP_056474	O76021	RL1D1_HUMAN	ribosomal L1 domain containing 1						regulation of protein localization|translation	large ribosomal subunit|nucleolus	protein binding|RNA binding|structural constituent of ribosome				0						gactccatctcaaaaaaaaaaa	0.094													8	6	---	---	---	---	
SMG1	23049	broad.mit.edu	37	16	18897123	18897123	+	Intron	DEL	A	-	-			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:18897123delA	uc002dfm.2	-						SMG1_uc010bwb.2_Intron	NM_015092	NP_055907	Q96Q15	SMG1_HUMAN	PI-3-kinase-related kinase SMG-1						DNA repair|mRNA export from nucleus|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|peptidyl-serine phosphorylation|phosphatidylinositol phosphorylation|protein autophosphorylation	cytoplasm|nucleus	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity			breast(5)|stomach(4)|lung(4)|kidney(2)|ovary(1)	16						AGTTTTAGTTAAAAAAAAAAA	0.149													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	21513145	21513150	+	Intron	DEL	GCCGCC	-	-			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21513145_21513150delGCCGCC	uc002diq.3	+						LOC100271836_uc002dja.2_Intron|LOC100271836_uc002djb.2_Intron					Homo sapiens cDNA FLJ59829 complete cds.																		TGCCGTTGGTgccgccgccgccgccg	0.592													4	3	---	---	---	---	
CPNE7	27132	broad.mit.edu	37	16	89650390	89650404	+	Intron	DEL	CAGGCCCCACCTGGC	-	-			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89650390_89650404delCAGGCCCCACCTGGC	uc002fnp.2	+						CPNE7_uc002fnq.2_Intron	NM_014427	NP_055242	Q9UBL6	CPNE7_HUMAN	copine 7 isoform b						lipid metabolic process		transporter activity				0		all_hematologic(23;0.0748)		all cancers(4;3.63e-08)|OV - Ovarian serous cystadenocarcinoma(4;1.7e-06)|BRCA - Breast invasive adenocarcinoma(80;0.0147)		ACGGTGGGGTCAGGCCCCACCTGGCCAAGCCTGGA	0.712													26	12	---	---	---	---	
SRCIN1	80725	broad.mit.edu	37	17	36717995	36717996	+	Frame_Shift_Ins	INS	-	A	A			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:36717995_36717996insA	uc002hqd.2	-	7	1628_1629	c.1403_1404insT	c.(1402-1404)TTCfs	p.F468fs	SRCIN1_uc002hqf.1_Frame_Shift_Ins_p.F340fs|SRCIN1_uc002hqe.2_Frame_Shift_Ins_p.F322fs|SRCIN1_uc002hqg.2_5'Flank|SRCIN1_uc002hqh.1_Frame_Shift_Ins_p.F528fs	NM_025248	NP_079524	Q9C0H9	SRCN1_HUMAN	SNAP25-interacting protein	340					exocytosis|negative regulation of protein tyrosine kinase activity|positive regulation of protein tyrosine kinase activity|regulation of cell migration|regulation of dendritic spine morphogenesis|substrate adhesion-dependent cell spreading	actin cytoskeleton|axon|cell junction|cytoplasm|dendrite|postsynaptic density|postsynaptic membrane	protein kinase binding				0						GCGGCAGGCGGAAGCCGTAGCC	0.639													4	2	---	---	---	---	
TOM1L1	10040	broad.mit.edu	37	17	53027110	53027110	+	Intron	DEL	G	-	-			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:53027110delG	uc002iud.2	+						TOM1L1_uc010dca.1_Intron|TOM1L1_uc010wnb.1_Intron|TOM1L1_uc010wnc.1_Intron|TOM1L1_uc010dbz.2_Intron|TOM1L1_uc010wnd.1_Intron	NM_005486	NP_005477	O75674	TM1L1_HUMAN	target of myb1-like 1						intracellular protein transport|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway	cytosol|endosome membrane|Golgi stack|lysosome	SH3 domain binding|ubiquitin binding			ovary(1)	1						TTAAGCTAATGAAACAAATTC	0.313													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	76521380	76521381	+	IGR	INS	-	C	C	rs137895113	by1000genomes	TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:76521380_76521381insC								DNAH17 (52524 upstream) : CYTH1 (148750 downstream)																							TACAACGGTGTCCCACCTGGAG	0.663													4	2	---	---	---	---	
MYOM1	8736	broad.mit.edu	37	18	3085192	3085192	+	Intron	DEL	T	-	-	rs148266515		TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:3085192delT	uc002klp.2	-						MYOM1_uc002klq.2_Intron	NM_003803	NP_003794	P52179	MYOM1_HUMAN	myomesin 1 isoform a							striated muscle myosin thick filament	structural constituent of muscle			ovary(3)|central_nervous_system(1)|pancreas(1)	5						GTATCTGTGATTTTTTTTTTT	0.294													5	3	---	---	---	---	
KIAA1328	57536	broad.mit.edu	37	18	34465512	34465513	+	Intron	INS	-	A	A	rs137989513	by1000genomes	TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:34465512_34465513insA	uc002kzz.2	+							NM_020776	NP_065827	Q86T90	K1328_HUMAN	hypothetical protein LOC57536											central_nervous_system(1)	1				COAD - Colon adenocarcinoma(74;0.195)		TTTTTTTTTTTATTTCAGAGTA	0.361													6	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	77393978	77393989	+	IGR	DEL	TGGTGATGGTGA	-	-			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:77393978_77393989delTGGTGATGGTGA								NFATC1 (104656 upstream) : CTDP1 (45812 downstream)																							gtgatggtggtggtgatggtgatgatggtggt	0.000													4	3	---	---	---	---	
ANKRD24	170961	broad.mit.edu	37	19	4199809	4199810	+	Intron	INS	-	A	A	rs140961038	by1000genomes	TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4199809_4199810insA	uc010dtt.1	+						ANKRD24_uc002lzs.2_Intron|ANKRD24_uc002lzt.2_Intron	NM_133475	NP_597732	Q8TF21	ANR24_HUMAN	ankyrin repeat domain 24												0				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0233)|STAD - Stomach adenocarcinoma(1328;0.181)		GAGCCCCTGTCGGGGGCGTGGG	0.708													1	5	---	---	---	---	
TMEM146	257062	broad.mit.edu	37	19	5766300	5766301	+	Intron	INS	-	AA	AA	rs10645590		TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:5766300_5766301insAA	uc002mda.2	+						TMEM146_uc010duj.1_Intron	NM_152784	NP_689997	Q86XM0	TM146_HUMAN	transmembrane protein 146 precursor							integral to membrane				ovary(1)|central_nervous_system(1)|pancreas(1)	3						cgtctctactgaaaaaaaaaaa	0.000													4	3	---	---	---	---	
RGL3	57139	broad.mit.edu	37	19	11526892	11526893	+	Intron	INS	-	T	T	rs60951384		TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11526892_11526893insT	uc002mrp.2	-						RGL3_uc002mrn.2_Intron|RGL3_uc002mrm.2_Intron|RGL3_uc002mro.2_Intron	NM_001035223	NP_001030300	Q3MIN7	RGL3_HUMAN	ral guanine nucleotide dissociation						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	intracellular				ovary(1)	1						CTCCTGGTACCttttttttttt	0.307													7	4	---	---	---	---	
CACNG8	59283	broad.mit.edu	37	19	54483312	54483315	+	Intron	DEL	GTGT	-	-	rs71949256		TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54483312_54483315delGTGT	uc002qcs.1	+						MIR935_hsa-mir-935|MI0005757_5'Flank	NM_031895	NP_114101	Q8WXS5	CCG8_HUMAN	voltage-dependent calcium channel gamma-8						regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|synaptic transmission	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic density|postsynaptic membrane|voltage-gated calcium channel complex	voltage-gated calcium channel activity				0	all_cancers(19;0.0385)|all_epithelial(19;0.0207)|all_lung(19;0.145)|Lung NSC(19;0.168)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(134;0.162)		GGGCGCGCACgtgtgtgtgtgtgt	0.534													8	4	---	---	---	---	
KREMEN1	83999	broad.mit.edu	37	22	29490561	29490566	+	Intron	DEL	ACACAC	-	-			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:29490561_29490566delACACAC	uc011akm.1	+						KREMEN1_uc003ael.2_Intron|KREMEN1_uc011akn.1_Intron	NM_032045	NP_114434	Q96MU8	KREM1_HUMAN	kringle-containing transmembrane protein 1						cell communication|regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway	integral to membrane|membrane fraction	protein binding			ovary(3)|lung(2)	5						TTCACACCTTacacacacacacacac	0.209													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	48647252	48647252	+	IGR	DEL	C	-	-			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:48647252delC								None (None upstream) : FAM19A5 (238036 downstream)																							ctcatacacacagctgaacac	0.000													5	6	---	---	---	---	
DIAPH2	1730	broad.mit.edu	37	X	96194492	96194515	+	Intron	DEL	TATATATGTATATATATATGTATG	-	-	rs72476044		TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:96194492_96194515delTATATATGTATATATATATGTATG	uc004efu.3	+						DIAPH2_uc004eft.3_Intron	NM_006729	NP_006720	O60879	DIAP2_HUMAN	diaphanous 2 isoform 156						cell differentiation|cytokinesis|multicellular organismal development|oogenesis	cytosol|early endosome|Golgi apparatus|mitochondrion|nucleolus	receptor binding|Rho GTPase binding			ovary(3)|lung(1)	4						tgtatgtatatatatatgtatatatatatgtatgtatatatata	0.107													8	6	---	---	---	---	
NXF5	55998	broad.mit.edu	37	X	101093049	101093049	+	Intron	DEL	A	-	-	rs66689050		TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:101093049delA	uc011mrk.1	-						NXF5_uc004eih.1_Intron|NXF5_uc004eii.1_Intron|NXF5_uc004eij.1_Intron|NXF5_uc004eik.1_Intron|NXF5_uc004eil.1_Intron	NM_032946	NP_116564	Q9H1B4	NXF5_HUMAN	nuclear RNA export factor 5						mRNA export from nucleus|multicellular organismal development	actin cytoskeleton|cytoplasm|nucleus	nucleocytoplasmic transporter activity|nucleotide binding|protein binding|RNA binding			central_nervous_system(1)	1						ACCTGTGGGGAAAGCAGTGAG	0.577													1	5	---	---	---	---	
PAK3	5063	broad.mit.edu	37	X	110416193	110416194	+	Intron	INS	-	C	C			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:110416193_110416194insC	uc004epa.2	+						PAK3_uc010npt.1_Intron|PAK3_uc010npu.1_Intron|PAK3_uc004eoy.1_Intron|PAK3_uc004eoz.2_Intron|PAK3_uc011mst.1_Intron|PAK3_uc010npv.1_Intron|PAK3_uc010npw.1_Intron	NM_001128173	NP_001121645	O75914	PAK3_HUMAN	p21-activated kinase 3 isoform d						multicellular organismal development		ATP binding|metal ion binding|protein serine/threonine kinase activity|SH3 domain binding			lung(6)|ovary(3)|large_intestine(1)	10						tctctctctctctctctctctT	0.317										TSP Lung(19;0.15)			5	6	---	---	---	---	
MTMR1	8776	broad.mit.edu	37	X	149898765	149898766	+	Intron	INS	-	T	T			TCGA-CW-6090-01A-11D-1669-08	TCGA-CW-6090-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:149898765_149898766insT	uc004fei.2	+						MTMR1_uc011mya.1_Intron|MTMR1_uc004feg.1_Intron|MTMR1_uc004feh.1_Intron|MTMR1_uc004fej.2_Intron|MTMR1_uc010ntf.2_Intron	NM_003828	NP_003819	Q13613	MTMR1_HUMAN	myotubularin-related protein 1							plasma membrane	protein tyrosine phosphatase activity			ovary(1)	1	Acute lymphoblastic leukemia(192;6.56e-05)					TTTTCCAGAGGTTTTTTTTTTT	0.347													6	3	---	---	---	---	
