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
RCC1	1104	broad.mit.edu	37	1	28858360	28858360	+	Missense_Mutation	SNP	T	A	A			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:28858360T>A	uc001bqg.1	+	3	204	c.119T>A	c.(118-120)CTA>CAA	p.L40Q	SNHG3-RCC1_uc001bqa.1_Missense_Mutation_p.L40Q|SNHG3-RCC1_uc001bqb.1_Missense_Mutation_p.L40Q|SNHG3-RCC1_uc001bqc.1_Missense_Mutation_p.L40Q|RCC1_uc001bqe.1_Missense_Mutation_p.L57Q|RCC1_uc001bqf.1_Missense_Mutation_p.L71Q	NM_001269	NP_001260	P18754	RCC1_HUMAN	regulator of chromosome condensation 1 isoform	40	RCC1 1.				cell division|chromosome segregation|G1/S transition of mitotic cell cycle|mitosis|mitotic spindle organization|regulation of mitosis|regulation of S phase of mitotic cell cycle|spindle assembly|viral reproduction	condensed nuclear chromosome|cytoplasm|nuclear chromatin|nuclear membrane|nucleoplasm	histone binding|nucleosomal DNA binding|Ran guanyl-nucleotide exchange factor activity			ovary(1)	1		Colorectal(325;3.46e-05)|Lung NSC(340;0.000318)|all_lung(284;0.000434)|Renal(390;0.00121)|Breast(348;0.00345)|all_neural(195;0.00989)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0261)|Medulloblastoma(700;0.123)		Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|STAD - Stomach adenocarcinoma(196;0.00299)|KIRC - Kidney renal clear cell carcinoma(1967;0.0101)|BRCA - Breast invasive adenocarcinoma(304;0.022)|READ - Rectum adenocarcinoma(331;0.0649)		GTGCTGACACTAGGCCAGGGC	0.572													22	103	---	---	---	---	PASS
MANEAL	149175	broad.mit.edu	37	1	38260262	38260262	+	Missense_Mutation	SNP	G	T	T			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:38260262G>T	uc001cby.2	+	1	489	c.408G>T	c.(406-408)AAG>AAT	p.K136N	MANEAL_uc001cbx.2_Missense_Mutation_p.K136N|MANEAL_uc001cbz.2_5'Flank	NM_001113482	NP_001106954	Q5VSG8	MANEL_HUMAN	mannosidase, endo-alpha-like isoform 3	136	Lumenal (Potential).					Golgi membrane|integral to membrane	hydrolase activity				0	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)				GGGACCCCAAGATCTCGGCCA	0.692													11	12	---	---	---	---	PASS
CCDC163P	126661	broad.mit.edu	37	1	45962262	45962262	+	Missense_Mutation	SNP	G	C	C			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:45962262G>C	uc001cnw.2	-	4	661	c.296C>G	c.(295-297)GCT>GGT	p.A99G	CCDC163P_uc001cnt.2_RNA|CCDC163P_uc001cnu.2_RNA|CCDC163P_uc009vxt.1_Missense_Mutation_p.A99G|CCDC163P_uc001cnv.2_RNA|CCDC163P_uc009vxu.1_RNA	NM_001102601	NP_001096071			hypothetical protein LOC126661												0						TCGTCCCTCAGCCAGCTGTTT	0.527													11	32	---	---	---	---	PASS
ORC1L	4998	broad.mit.edu	37	1	52849169	52849169	+	Missense_Mutation	SNP	G	A	A			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:52849169G>A	uc001ctt.2	-	13	2155	c.1936C>T	c.(1936-1938)CGG>TGG	p.R646W	ORC1L_uc010oni.1_Missense_Mutation_p.R641W|ORC1L_uc001ctu.2_Missense_Mutation_p.R646W|ORC1L_uc009vzd.2_Missense_Mutation_p.R400W	NM_004153	NP_004144	Q13415	ORC1_HUMAN	origin recognition complex, subunit 1	646	Necessary and sufficient for ORC complex assembly.				cell cycle checkpoint|DNA-dependent DNA replication initiation|M/G1 transition of mitotic cell cycle|regulation of transcription involved in G1/S phase of mitotic cell cycle|S phase of mitotic cell cycle	cytosol|nuclear origin of replication recognition complex|nucleolus|nucleoplasm|plasma membrane	ATP binding|DNA binding|nucleoside-triphosphatase activity|protein binding				0						ACCACAAGCCGGGCCTCCTTA	0.537													10	136	---	---	---	---	PASS
CDCP2	200008	broad.mit.edu	37	1	54610216	54610216	+	Missense_Mutation	SNP	G	A	A			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:54610216G>A	uc001cwv.1	-	2	1198	c.350C>T	c.(349-351)TCC>TTC	p.S117F		NM_201546	NP_963840	Q5VXM1	CDCP2_HUMAN	CUB domain containing protein 2 precursor	117	CUB 1.					extracellular region				ovary(1)	1						GACATGCCAGGAGGAGGTGAA	0.602													12	59	---	---	---	---	PASS
INADL	10207	broad.mit.edu	37	1	62288627	62288627	+	Missense_Mutation	SNP	T	C	C			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:62288627T>C	uc001dab.2	+	15	1808	c.1694T>C	c.(1693-1695)ATT>ACT	p.I565T	INADL_uc009waf.1_Missense_Mutation_p.I565T|INADL_uc001daa.2_Missense_Mutation_p.I565T|INADL_uc001dad.3_Missense_Mutation_p.I262T|INADL_uc001dac.2_RNA	NM_176877	NP_795352	Q8NI35	INADL_HUMAN	InaD-like	565	PDZ 4.				intracellular signal transduction|tight junction assembly	apical plasma membrane|perinuclear region of cytoplasm|tight junction	protein binding			ovary(3)|skin(1)	4						CTGCTGCCTATTCACACTCTG	0.428													69	230	---	---	---	---	PASS
RPE65	6121	broad.mit.edu	37	1	68906539	68906539	+	Missense_Mutation	SNP	C	A	A			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:68906539C>A	uc001dei.1	-	6	694	c.640G>T	c.(640-642)GCA>TCA	p.A214S		NM_000329	NP_000320	Q16518	RPE65_HUMAN	retinal pigment epithelium-specific protein	214					visual perception	cytoplasm|plasma membrane	all-trans-retinyl-palmitate hydrolase activity|metal ion binding|retinol isomerase activity			ovary(1)	1						AACTCACCTGCTTGCAGTGGT	0.348													19	98	---	---	---	---	PASS
SPAG17	200162	broad.mit.edu	37	1	118526484	118526484	+	Missense_Mutation	SNP	T	C	C			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:118526484T>C	uc001ehk.2	-	42	5890	c.5822A>G	c.(5821-5823)AAT>AGT	p.N1941S		NM_206996	NP_996879	Q6Q759	SPG17_HUMAN	sperm associated antigen 17	1941						cilium|flagellar axoneme|microtubule				upper_aerodigestive_tract(2)|ovary(2)|large_intestine(1)|skin(1)	6	Esophageal squamous(2;0.0106)	all_cancers(81;0.0204)|all_lung(203;9.46e-05)|Lung NSC(69;0.000675)|all_epithelial(167;0.01)		Lung(183;0.0858)		TGCATCTTCATTTTTCTTTGT	0.313													4	104	---	---	---	---	PASS
MRPL9	65005	broad.mit.edu	37	1	151735561	151735561	+	Missense_Mutation	SNP	C	A	A			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151735561C>A	uc001eyv.2	-	2	300	c.215G>T	c.(214-216)CGC>CTC	p.R72L	MRPL9_uc009wmz.2_RNA|MRPL9_uc010pdk.1_Missense_Mutation_p.R72L|MRPL9_uc009wna.1_Missense_Mutation_p.R72L	NM_031420	NP_113608	Q9BYD2	RM09_HUMAN	mitochondrial ribosomal protein L9 precursor	72					translation	mitochondrial ribosome	structural constituent of ribosome			ovary(1)	1	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.14)		LUSC - Lung squamous cell carcinoma(543;0.181)			CCGGTGCAGGCGCGGCTTCCG	0.632													3	85	---	---	---	---	PASS
TDRD10	126668	broad.mit.edu	37	1	154493879	154493879	+	Missense_Mutation	SNP	G	A	A			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154493879G>A	uc009wow.2	+	6	1131	c.293G>A	c.(292-294)CGA>CAA	p.R98Q	TDRD10_uc001ffd.2_Missense_Mutation_p.R98Q|TDRD10_uc001ffe.2_Missense_Mutation_p.R19Q	NM_001098475	NP_001091945	Q5VZ19	TDR10_HUMAN	tudor domain containing 10 isoform a	98	RRM.						nucleotide binding|RNA binding			ovary(1)	1	all_lung(78;1.72e-29)|Lung NSC(65;2.96e-27)|Hepatocellular(266;0.0877)|all_hematologic(923;0.088)		LUSC - Lung squamous cell carcinoma(543;0.185)			TTCCACAAGCGAAAACTGTTC	0.507													99	307	---	---	---	---	PASS
ATP1A4	480	broad.mit.edu	37	1	160143468	160143468	+	Missense_Mutation	SNP	C	G	G			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160143468C>G	uc001fve.3	+	13	2431	c.1952C>G	c.(1951-1953)GCT>GGT	p.A651G	ATP1A4_uc001fvf.3_RNA|ATP1A4_uc001fvg.2_Missense_Mutation_p.A154G	NM_144699	NP_653300	Q13733	AT1A4_HUMAN	Na+/K+ -ATPase alpha 4 subunit isoform 1	651	Cytoplasmic (Potential).				ATP biosynthetic process|ATP hydrolysis coupled proton transport|regulation of cellular pH|sperm motility	sodium:potassium-exchanging ATPase complex	ATP binding|metal ion binding|sodium:potassium-exchanging ATPase activity			ovary(2)|skin(2)	4	all_cancers(52;2.56e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			GAGGAAGTCGCTGCCCGGCTT	0.547													24	88	---	---	---	---	PASS
HMCN1	83872	broad.mit.edu	37	1	186158774	186158774	+	Missense_Mutation	SNP	A	G	G			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:186158774A>G	uc001grq.1	+	107	16901	c.16672A>G	c.(16672-16674)ACA>GCA	p.T5558A	HMCN1_uc001grs.1_Missense_Mutation_p.T1010A	NM_031935	NP_114141	Q96RW7	HMCN1_HUMAN	hemicentin 1 precursor	5558					response to stimulus|visual perception	basement membrane	calcium ion binding			ovary(22)|skin(1)	23						GGTTGCATACACACAGGATGG	0.468													16	90	---	---	---	---	PASS
ASPM	259266	broad.mit.edu	37	1	197093276	197093276	+	Missense_Mutation	SNP	A	T	T			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:197093276A>T	uc001gtu.2	-	13	3611	c.3354T>A	c.(3352-3354)GAT>GAA	p.D1118E	ASPM_uc001gtv.2_Missense_Mutation_p.D1118E|ASPM_uc001gtw.3_Intron	NM_018136	NP_060606	Q8IZT6	ASPM_HUMAN	asp (abnormal spindle)-like, microcephaly	1118	CH 2.				mitosis	cytoplasm|nucleus	calmodulin binding			ovary(4)|central_nervous_system(2)	6						CATTTACCCAATCCATCAATA	0.274													40	140	---	---	---	---	PASS
USH2A	7399	broad.mit.edu	37	1	215955404	215955404	+	Missense_Mutation	SNP	C	G	G			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:215955404C>G	uc001hku.1	-	54	11107	c.10720G>C	c.(10720-10722)GGC>CGC	p.G3574R		NM_206933	NP_996816	O75445	USH2A_HUMAN	usherin isoform B	3574	Extracellular (Potential).|Fibronectin type-III 20.				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)		GTGGCACAGCCAGCAACCGTG	0.438										HNSCC(13;0.011)			38	131	---	---	---	---	PASS
TRIM67	440730	broad.mit.edu	37	1	231298765	231298765	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:231298765C>T	uc009xfn.1	+	1	92	c.50C>T	c.(49-51)CCT>CTT	p.P17L		NM_001004342	NP_001004342	Q6ZTA4	TRI67_HUMAN	tripartite motif-containing 67	17	RING-type; degenerate.					cytoplasm|cytoskeleton	zinc ion binding			ovary(2)|breast(1)|kidney(1)	4	Breast(184;0.0871)	all_cancers(173;0.189)|Prostate(94;0.167)				TTTCGGGAGCCTATCATCCTG	0.672													3	25	---	---	---	---	PASS
OR2L2	26246	broad.mit.edu	37	1	248201987	248201987	+	Missense_Mutation	SNP	T	C	C			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248201987T>C	uc001idw.2	+	1	514	c.418T>C	c.(418-420)TGT>CGT	p.C140R	OR2L13_uc001ids.2_Intron	NM_001004686	NP_001004686	Q8NH16	OR2L2_HUMAN	olfactory receptor, family 2, subfamily L,	140	Helical; Name=4; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|central_nervous_system(1)|skin(1)	3	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0278)			CAAAAGAGTGTGTGTGATGAT	0.448													65	303	---	---	---	---	PASS
PPP1CB	5500	broad.mit.edu	37	2	29022230	29022230	+	3'UTR	SNP	G	A	A			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:29022230G>A	uc002rmg.2	+	9					PPP1CB_uc010ymj.1_3'UTR|PPP1CB_uc010yml.1_3'UTR|PPP1CB_uc002rmh.2_3'UTR|SPDYA_uc002rmi.2_Intron	NM_206876	NP_996759	P62140	PP1B_HUMAN	protein phosphatase 1, catalytic subunit, beta						cell cycle|cell division|glycogen metabolic process|triglyceride catabolic process	MLL5-L complex|nucleolus|PTW/PP1 phosphatase complex	metal ion binding|myosin phosphatase activity|myosin-light-chain-phosphatase activity|protein binding			skin(1)	1	Acute lymphoblastic leukemia(172;0.155)					TAATATATAAGTGTGCACTGT	0.368													6	22	---	---	---	---	PASS
TMEM150A	129303	broad.mit.edu	37	2	85829235	85829235	+	5'UTR	SNP	G	T	T			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:85829235G>T	uc002spw.1	-	1					USP39_uc002sqb.2_5'Flank|TMEM150A_uc002spx.1_5'UTR|TMEM150A_uc002spz.1_Intron|TMEM150A_uc002sqa.1_Intron|TMEM150A_uc002spy.1_Intron	NM_001031738	NP_001026908	Q86TG1	T150A_HUMAN	transmembrane protein 150A isoform 1							integral to membrane|plasma membrane					0						GGCCGGGAAGGGGGAGGGGAA	0.602													9	11	---	---	---	---	PASS
YSK4	80122	broad.mit.edu	37	2	135744718	135744718	+	Missense_Mutation	SNP	G	A	A			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:135744718G>A	uc002tue.1	-	7	1755	c.1724C>T	c.(1723-1725)CCG>CTG	p.P575L	YSK4_uc002tuf.1_Intron|YSK4_uc010fnc.1_Intron|YSK4_uc010fnd.1_Missense_Mutation_p.P462L|YSK4_uc010zbg.1_Intron|YSK4_uc002tuh.3_Missense_Mutation_p.P303L|YSK4_uc002tui.3_Missense_Mutation_p.P592L	NM_025052	NP_079328	Q56UN5	YSK4_HUMAN	Yeast Sps1/Ste20-related kinase 4 isoform 1	575							ATP binding|protein serine/threonine kinase activity			stomach(2)|urinary_tract(1)|ovary(1)|breast(1)	5				BRCA - Breast invasive adenocarcinoma(221;0.112)		TCCCAAAGCCGGGAAAATTTG	0.433													68	198	---	---	---	---	PASS
RIF1	55183	broad.mit.edu	37	2	152324541	152324541	+	Missense_Mutation	SNP	A	C	C			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:152324541A>C	uc002txm.2	+	31	6758	c.6628A>C	c.(6628-6630)ATA>CTA	p.I2210L	RIF1_uc002txl.2_Missense_Mutation_p.I2210L|RIF1_uc002txn.2_Missense_Mutation_p.I2210L|RIF1_uc002txo.2_Missense_Mutation_p.I2210L|RIF1_uc002txp.2_RNA	NM_018151	NP_060621	Q5UIP0	RIF1_HUMAN	RAP1 interacting factor 1	2210	Interaction with condensed chromosomes in telophase.				cell cycle|response to DNA damage stimulus	chromosome, telomeric region|cytoplasm|nucleus|spindle	binding			ovary(5)|breast(4)|skin(3)|lung(2)|kidney(1)	15				BRCA - Breast invasive adenocarcinoma(221;0.0429)		TGCAGATCCAATATACCAAGC	0.353													37	138	---	---	---	---	PASS
MYO3B	140469	broad.mit.edu	37	2	171239651	171239651	+	Silent	SNP	C	A	A			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:171239651C>A	uc002ufy.2	+	11	1280	c.1137C>A	c.(1135-1137)ATC>ATA	p.I379I	MYO3B_uc002ufv.2_Silent_p.I366I|MYO3B_uc010fqb.1_Silent_p.I366I|MYO3B_uc002ufz.2_Silent_p.I379I|MYO3B_uc002ufw.2_RNA|MYO3B_uc002ufx.2_RNA|MYO3B_uc002ugb.2_RNA	NM_138995	NP_620482	Q8WXR4	MYO3B_HUMAN	myosin IIIB isoform 2	379	Myosin head-like.				response to stimulus|visual perception	cytoplasm|myosin complex	actin binding|ATP binding|motor activity|protein serine/threonine kinase activity			lung(8)|ovary(6)|skin(4)|central_nervous_system(1)	19						TTGGAGACATCTTAATTGCCT	0.358													6	230	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179566270	179566270	+	Missense_Mutation	SNP	C	G	G			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179566270C>G	uc010zfg.1	-	107	27075	c.26851G>C	c.(26851-26853)GCA>CCA	p.A8951P	TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Missense_Mutation_p.A5612P|TTN_uc010fre.1_Missense_Mutation_p.A62P	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	9878							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity	p.I8951V(1)		ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GGTGGCACTGCTCTGATAGGC	0.433													27	84	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179584416	179584416	+	Missense_Mutation	SNP	G	A	A			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179584416G>A	uc010zfg.1	-	79	20295	c.20071C>T	c.(20071-20073)CAT>TAT	p.H6691Y	TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Missense_Mutation_p.H3352Y	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	7618							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GTAATGTGATGTTTGCTGTCT	0.403													26	253	---	---	---	---	PASS
CREB1	1385	broad.mit.edu	37	2	208461841	208461841	+	3'UTR	SNP	G	A	A			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:208461841G>A	uc002vcc.2	+	9					CREB1_uc002vcd.2_3'UTR|FAM119A_uc002vce.2_Intron	NM_134442	NP_604391	P16220	CREB1_HUMAN	cAMP responsive element binding protein 1						activation of phospholipase C activity|axon guidance|innate immune response|interspecies interaction between organisms|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|positive regulation of transcription from RNA polymerase II promoter|protein phosphorylation|stress-activated MAPK cascade|synaptic transmission|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway		protein dimerization activity|transcription cofactor activity		EWSR1/CREB1(42)	soft_tissue(42)|breast(1)|central_nervous_system(1)	44				LUSC - Lung squamous cell carcinoma(261;0.0768)|Epithelial(149;0.127)|Lung(261;0.145)	Adenosine monophosphate(DB00131)|Bromocriptine(DB01200)|Naloxone(DB01183)	GCCACAACCTGAAAGACAAAA	0.338			T	EWSR1	clear cell sarcoma|angiomatoid fibrous histiocytoma								18	64	---	---	---	---	PASS
FN1	2335	broad.mit.edu	37	2	216298131	216298131	+	Missense_Mutation	SNP	T	G	G			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:216298131T>G	uc002vfa.2	-	3	597	c.331A>C	c.(331-333)ACT>CCT	p.T111P	FN1_uc002vfb.2_Missense_Mutation_p.T111P|FN1_uc002vfc.2_Missense_Mutation_p.T111P|FN1_uc002vfd.2_Missense_Mutation_p.T111P|FN1_uc002vfe.2_Missense_Mutation_p.T111P|FN1_uc002vff.2_Missense_Mutation_p.T111P|FN1_uc002vfg.2_Missense_Mutation_p.T111P|FN1_uc002vfh.2_Missense_Mutation_p.T111P|FN1_uc002vfi.2_Missense_Mutation_p.T111P|FN1_uc002vfj.2_Missense_Mutation_p.T111P|FN1_uc002vfl.2_Missense_Mutation_p.T111P	NM_212482	NP_997647	P02751	FINC_HUMAN	fibronectin 1 isoform 1 preproprotein	111	Fibronectin type-I 2.|Fibrin- and heparin-binding 1.				acute-phase response|angiogenesis|leukocyte migration|peptide cross-linking|platelet activation|platelet degranulation|regulation of cell shape|substrate adhesion-dependent cell spreading	ER-Golgi intermediate compartment|fibrinogen complex|platelet alpha granule lumen|proteinaceous extracellular matrix	collagen binding|extracellular matrix structural constituent|heparin binding			central_nervous_system(7)|large_intestine(2)|breast(2)|ovary(1)|pancreas(1)	13		Renal(323;0.127)		Epithelial(149;9.59e-07)|all cancers(144;0.000174)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)	Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)	CGCTCATAAGTGTCACCCACT	0.498													48	116	---	---	---	---	PASS
PPP1R7	5510	broad.mit.edu	37	2	242102749	242102749	+	Missense_Mutation	SNP	G	C	C			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:242102749G>C	uc002wat.1	+	7	662	c.647G>C	c.(646-648)GGG>GCG	p.G216A	PPP1R7_uc010fzm.1_Missense_Mutation_p.G200A|PPP1R7_uc002war.2_Missense_Mutation_p.G210A|PPP1R7_uc002was.2_Missense_Mutation_p.G216A|PPP1R7_uc002wau.1_Missense_Mutation_p.G173A|PPP1R7_uc002wav.1_Missense_Mutation_p.G142A	NM_002712	NP_002703	Q15435	PP1R7_HUMAN	protein phosphatase 1, regulatory subunit 7	216	LRR 7.					cytoplasm|nucleus	protein binding|protein phosphatase type 1 regulator activity			ovary(3)	3		all_cancers(19;6.1e-33)|all_epithelial(40;1.07e-13)|Breast(86;0.000141)|Renal(207;0.00528)|all_lung(227;0.0446)|Ovarian(221;0.104)|Lung NSC(271;0.115)|Esophageal squamous(248;0.131)|all_hematologic(139;0.182)|Melanoma(123;0.238)		Epithelial(32;6.92e-32)|all cancers(36;5.35e-29)|OV - Ovarian serous cystadenocarcinoma(60;3.4e-14)|Kidney(56;4.23e-09)|KIRC - Kidney renal clear cell carcinoma(57;4.24e-08)|BRCA - Breast invasive adenocarcinoma(100;3.56e-06)|Lung(119;0.000588)|LUSC - Lung squamous cell carcinoma(224;0.0048)|Colorectal(34;0.0137)|COAD - Colon adenocarcinoma(134;0.096)		TTGTTTTTGGGGAAAAACAAA	0.493													47	419	---	---	---	---	PASS
IL17RB	55540	broad.mit.edu	37	3	53898830	53898830	+	Missense_Mutation	SNP	T	A	A			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:53898830T>A	uc003dha.2	+	11	1043	c.1004T>A	c.(1003-1005)CTT>CAT	p.L335H		NM_018725	NP_061195	Q9NRM6	I17RB_HUMAN	interleukin 17B receptor precursor	335	SEFIR.|Cytoplasmic (Potential).				defense response|regulation of cell growth	extracellular region|integral to plasma membrane	cytokine receptor activity			ovary(2)|pancreas(1)	3				BRCA - Breast invasive adenocarcinoma(193;0.000158)|KIRC - Kidney renal clear cell carcinoma(284;0.00588)|Kidney(284;0.00673)|OV - Ovarian serous cystadenocarcinoma(275;0.118)		ATTAAGGTTCTTGTGGTTTAC	0.398													69	268	---	---	---	---	PASS
OR5H2	79310	broad.mit.edu	37	3	98001737	98001737	+	Silent	SNP	G	A	A			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:98001737G>A	uc003dsj.1	+	1	6	c.6G>A	c.(4-6)TCG>TCA	p.S2S		NM_001005482	NP_001005482	Q8NGV7	OR5H2_HUMAN	olfactory receptor, family 5, subfamily H,	2	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(3)	3						CAGGGATGTCGAATGAGGACA	0.398													73	243	---	---	---	---	PASS
IMPG2	50939	broad.mit.edu	37	3	100949947	100949947	+	Silent	SNP	A	G	G			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:100949947A>G	uc003duq.1	-	16	3479	c.3276T>C	c.(3274-3276)TGT>TGC	p.C1092C	IMPG2_uc011bhe.1_Silent_p.C955C|IMPG2_uc010hpj.1_Intron	NM_016247	NP_057331	Q9BZV3	IMPG2_HUMAN	interphotoreceptor matrix proteoglycan 2	1092	Extracellular (Potential).|EGF-like 2.				visual perception	integral to membrane|proteinaceous extracellular matrix	extracellular matrix structural constituent|heparin binding|hyaluronic acid binding|receptor activity			ovary(2)|haematopoietic_and_lymphoid_tissue(1)	3						CAAATTCCTCACAGTGCTTGC	0.488													40	245	---	---	---	---	PASS
ROPN1	54763	broad.mit.edu	37	3	123687916	123687916	+	3'UTR	SNP	A	C	C			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:123687916A>C	uc003eha.2	-	7						NM_017578	NP_060048	Q9HAT0	ROP1A_HUMAN	ropporin						signal transduction		cAMP-dependent protein kinase regulator activity			ovary(1)|skin(1)	2				GBM - Glioblastoma multiforme(114;0.148)		GTACAAGAAAATTGATTTTGG	0.328													13	69	---	---	---	---	PASS
CCDC48	79825	broad.mit.edu	37	3	128757716	128757716	+	Silent	SNP	C	T	T			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:128757716C>T	uc011bkt.1	+	7	1633	c.1633C>T	c.(1633-1635)CTG>TTG	p.L545L		NM_024768	NP_079044	Q9HA90	CCD48_HUMAN	coiled-coil domain containing 48	545											0						GCTGAGCACGCTGGACGCTTT	0.547													37	152	---	---	---	---	PASS
MUC4	4585	broad.mit.edu	37	3	195511925	195511925	+	Missense_Mutation	SNP	A	G	G			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195511925A>G	uc011bto.1	-	2	6986	c.6526T>C	c.(6526-6528)TCT>CCT	p.S2176P	MUC4_uc003fvo.2_Intron|MUC4_uc003fvp.2_Intron|MUC4_uc010hzu.1_Intron	NM_018406	NP_060876	Q99102	MUC4_HUMAN	mucin 4 isoform a	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment					cell-matrix adhesion	integral to plasma membrane|proteinaceous extracellular matrix	ErbB-2 class receptor binding|extracellular matrix constituent, lubricant activity				0	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		ACAGGAAGAGAGGTGGCGTGA	0.587													2	1	---	---	---	---	PASS
TRAM1L1	133022	broad.mit.edu	37	4	118005505	118005505	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:118005505C>T	uc003ibv.3	-	1	1232	c.1045G>A	c.(1045-1047)GGA>AGA	p.G349R		NM_152402	NP_689615	Q8N609	TR1L1_HUMAN	translocation associated membrane protein 1-like	349	Cytoplasmic (Potential).				protein transport|transmembrane transport	endoplasmic reticulum membrane|integral to membrane				central_nervous_system(1)	1						ACTCCCACTCCGTTTTCTGTT	0.393													117	375	---	---	---	---	PASS
LOC285501	285501	broad.mit.edu	37	4	178911782	178911782	+	RNA	SNP	A	G	G			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:178911782A>G	uc010iru.2	+	6		c.916A>G				NR_028342				Homo sapiens cDNA clone IMAGE:4828874.												0		all_lung(41;6.03e-08)|Lung NSC(41;4.26e-07)|Breast(14;0.00066)|Melanoma(52;0.00168)|Prostate(90;0.0129)|all_hematologic(60;0.0202)|Renal(120;0.0246)|Colorectal(36;0.0508)|Hepatocellular(41;0.236)		all cancers(43;9.24e-25)|Epithelial(43;6.28e-22)|OV - Ovarian serous cystadenocarcinoma(60;5.29e-10)|LUSC - Lung squamous cell carcinoma(1;2.61e-05)|Lung(1;3.22e-05)|GBM - Glioblastoma multiforme(59;0.000185)|Colorectal(24;0.000244)|STAD - Stomach adenocarcinoma(60;0.000777)|COAD - Colon adenocarcinoma(29;0.000884)		ACCTGTCATTAGCATGTGTAA	0.413													3	27	---	---	---	---	PASS
ANKRD55	79722	broad.mit.edu	37	5	55407417	55407417	+	Silent	SNP	A	G	G			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:55407417A>G	uc003jqu.2	-	10	1310	c.1158T>C	c.(1156-1158)GAT>GAC	p.D386D	ANKRD55_uc003jqt.2_Silent_p.D98D	NM_024669	NP_078945	Q3KP44	ANR55_HUMAN	ankyrin repeat domain 55 isoform 1	385										skin(1)	1		Lung NSC(810;8.69e-05)|Prostate(74;0.00634)|Breast(144;0.0334)|Ovarian(174;0.223)				CCACGATGCTATCAAAGGTGG	0.463													153	443	---	---	---	---	PASS
HTR1A	3350	broad.mit.edu	37	5	63257288	63257288	+	Missense_Mutation	SNP	C	G	G			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:63257288C>G	uc011cqt.1	-	1	259	c.259G>C	c.(259-261)GTG>CTG	p.V87L		NM_000524	NP_000515	P08908	5HT1A_HUMAN	5-hydroxytryptamine (serotonin) receptor 1A	87	Helical; Name=2; (By similarity).				behavior|positive regulation of cell proliferation	integral to plasma membrane	serotonin receptor activity			ovary(2)|pancreas(2)	4		Lung NSC(810;3.55e-06)|Prostate(74;0.0352)|Ovarian(174;0.0545)|Breast(144;0.0575)|Colorectal(97;0.234)		Lung(70;0.105)	Alprenolol(DB00866)|Aripiprazole(DB01238)|Buspirone(DB00490)|Clozapine(DB00363)|Eletriptan(DB00216)|Ergoloid mesylate(DB01049)|Fluvoxamine(DB00176)|Lisuride(DB00589)|Methysergide(DB00247)|Mirtazapine(DB00370)|Pindolol(DB00960)|Propranolol(DB00571)|Quetiapine(DB01224)|Sertraline(DB01104)|Tegaserod(DB01079)|Trazodone(DB00656)|Venlafaxine(DB00285)|Ziprasidone(DB00246)	AGCACCAACACCGACACCATG	0.602													5	24	---	---	---	---	PASS
CWC27	10283	broad.mit.edu	37	5	64314204	64314204	+	3'UTR	SNP	A	C	C			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:64314204A>C	uc003jtn.1	+	14					CWC27_uc010iwt.1_3'UTR	NM_005869	NP_005860	Q6UX04	CWC27_HUMAN	serologically defined colon cancer antigen 10						protein folding	catalytic step 2 spliceosome	peptidyl-prolyl cis-trans isomerase activity				0						TGGCCTTGTAACAGCCATTGT	0.353													9	11	---	---	---	---	PASS
SPRY4	81848	broad.mit.edu	37	5	141694601	141694601	+	Missense_Mutation	SNP	G	A	A			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:141694601G>A	uc003lml.2	-	2	332	c.73C>T	c.(73-75)CGG>TGG	p.R25W	SPRY4_uc010jgi.1_Missense_Mutation_p.R48W	NM_001127496	NP_001120968	Q9C004	SPY4_HUMAN	sprouty homolog 4 isoform 2	25					multicellular organismal development	cytoplasm|ruffle membrane	protein binding			ovary(1)|lung(1)	2		all_hematologic(541;0.118)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGGGACATCCGGCTGTCAAGA	0.602									Testicular_Cancer_Familial_Clustering_of				16	37	---	---	---	---	PASS
GPRIN1	114787	broad.mit.edu	37	5	176025772	176025772	+	Missense_Mutation	SNP	G	T	T			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176025772G>T	uc003meo.1	-	2	1239	c.1064C>A	c.(1063-1065)CCC>CAC	p.P355H		NM_052899	NP_443131	Q7Z2K8	GRIN1_HUMAN	G protein-regulated inducer of neurite outgrowth	355						growth cone|plasma membrane				ovary(2)	2	all_cancers(89;0.00263)|Renal(175;0.000269)|Lung NSC(126;0.00902)|all_lung(126;0.0142)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CACAGATGCGGGATCTGCCAT	0.592													4	96	---	---	---	---	PASS
AGER	177	broad.mit.edu	37	6	32148926	32148926	+	Silent	SNP	C	A	A			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32148926C>A	uc003oal.1	-	11	1233	c.1209G>T	c.(1207-1209)GGG>GGT	p.G403G	AGER_uc003oak.1_Silent_p.G132G|AGER_uc003oar.2_Silent_p.G302G|AGER_uc011dpm.1_Silent_p.G293G|AGER_uc011dpn.1_3'UTR|AGER_uc010jtv.1_3'UTR|AGER_uc011dpo.1_3'UTR|AGER_uc003oam.1_RNA|AGER_uc003oan.1_3'UTR|AGER_uc003oap.1_Silent_p.G419G|AGER_uc003oat.1_3'UTR|AGER_uc003oao.1_RNA|AGER_uc003oaq.1_Silent_p.G389G|AGER_uc010jtw.1_RNA|AGER_uc003oas.1_3'UTR|AGER_uc003oau.1_3'UTR	NM_001136	NP_001127	Q15109	RAGE_HUMAN	advanced glycosylation end product-specific	403	Cytoplasmic (Potential).				cell surface receptor linked signaling pathway|inflammatory response|innate immune response|neuron projection development|positive regulation of NF-kappaB transcription factor activity	integral to plasma membrane	S100 alpha binding|transmembrane receptor activity			breast(1)	1						CCCCTCAAGGCCCTCCAGTAC	0.537													11	441	---	---	---	---	PASS
LGSN	51557	broad.mit.edu	37	6	63990712	63990712	+	Nonsense_Mutation	SNP	A	C	C			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:63990712A>C	uc003peh.2	-	4	778	c.744T>G	c.(742-744)TAT>TAG	p.Y248*	LGSN_uc003pei.2_Intron	NM_016571	NP_057655	Q5TDP6	LGSN_HUMAN	lengsin, lens protein with glutamine synthetase	248					glutamine biosynthetic process		glutamate-ammonia ligase activity			skin(2)	2					L-Glutamic Acid(DB00142)	CTCCAGTGTGATACAAGCCAT	0.403													13	72	---	---	---	---	PASS
PPIL4	85313	broad.mit.edu	37	6	149838510	149838510	+	Missense_Mutation	SNP	A	C	C			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:149838510A>C	uc003qmo.1	-	11	1089	c.1059T>G	c.(1057-1059)GAT>GAG	p.D353E	PPIL4_uc010kic.2_Intron|PPIL4_uc003qmp.1_Missense_Mutation_p.D353E	NM_139126	NP_624311	Q8WUA2	PPIL4_HUMAN	peptidylprolyl isomerase-like 4	353	Lys-rich.				protein folding	nucleus	nucleotide binding|peptidyl-prolyl cis-trans isomerase activity|RNA binding				0		Ovarian(120;0.0164)		OV - Ovarian serous cystadenocarcinoma(155;1.11e-11)|GBM - Glioblastoma multiforme(68;0.0885)		GCTTTACTTTATCTTTCAGAA	0.328													14	73	---	---	---	---	PASS
KIF25	3834	broad.mit.edu	37	6	168440859	168440859	+	Silent	SNP	G	A	A	rs147571413	byFrequency	TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:168440859G>A	uc003qwk.1	+	6	871	c.609G>A	c.(607-609)ACG>ACA	p.T203T	KIF25_uc003qwl.1_Silent_p.T203T	NM_030615	NP_085118	Q9UIL4	KIF25_HUMAN	kinesin family member 25 isoform 1	203	Kinesin-motor.				microtubule-based movement|mitotic sister chromatid segregation	cytoplasm|kinesin complex|microtubule	ATP binding|microtubule motor activity			ovary(1)|pancreas(1)	2		Breast(66;1.07e-05)|Ovarian(120;0.0728)		Epithelial(4;7.7e-30)|OV - Ovarian serous cystadenocarcinoma(33;5.82e-22)|BRCA - Breast invasive adenocarcinoma(4;1.38e-10)|GBM - Glioblastoma multiforme(31;0.000756)		TGATAATTACGGTGACTCTAA	0.512													19	46	---	---	---	---	PASS
MICALL2	79778	broad.mit.edu	37	7	1489845	1489845	+	Intron	SNP	C	T	T			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:1489845C>T	uc003skj.3	-						MICALL2_uc003skl.1_RNA	NM_182924	NP_891554	Q8IY33	MILK2_HUMAN	MICAL-like 2 isoform 1							cytoplasm|cytoskeleton	zinc ion binding			central_nervous_system(1)	1		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0178)|OV - Ovarian serous cystadenocarcinoma(56;6.01e-15)		CTGGCTAAGCCAGCTGTGAGG	0.577													15	93	---	---	---	---	PASS
INTS1	26173	broad.mit.edu	37	7	1543553	1543553	+	Missense_Mutation	SNP	G	A	A			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:1543553G>A	uc003skn.2	-	2	145	c.44C>T	c.(43-45)GCG>GTG	p.A15V	INTS1_uc003skq.2_Missense_Mutation_p.A15V	NM_001080453	NP_001073922	Q8N201	INT1_HUMAN	integrator complex subunit 1	15					snRNA processing	integral to membrane|integrator complex|nuclear membrane					0		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0181)|OV - Ovarian serous cystadenocarcinoma(56;6.99e-15)		GGGTTTGGCCGCGGCGCTGGG	0.622													3	6	---	---	---	---	PASS
LRRN3	54674	broad.mit.edu	37	7	110764578	110764578	+	Missense_Mutation	SNP	A	G	G			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:110764578A>G	uc003vft.3	+	4	2796	c.1750A>G	c.(1750-1752)AAT>GAT	p.N584D	IMMP2L_uc003vfq.1_Intron|IMMP2L_uc010ljr.1_Intron|IMMP2L_uc003vfr.2_Intron|LRRN3_uc003vfu.3_Missense_Mutation_p.N584D|LRRN3_uc003vfs.3_Missense_Mutation_p.N584D	NM_001099660	NP_001093130	Q9H3W5	LRRN3_HUMAN	leucine rich repeat neuronal 3 precursor	584	Extracellular (Potential).|Fibronectin type-III.					integral to membrane				skin(3)|ovary(2)|pancreas(2)|central_nervous_system(1)	8				UCEC - Uterine corpus endometrioid carcinoma (4;0.245)|LUSC - Lung squamous cell carcinoma(290;0.0715)|Lung(3;0.0864)|STAD - Stomach adenocarcinoma(3;0.125)		TACTCATCTGAATCCATCAAC	0.363													32	87	---	---	---	---	PASS
PTPRZ1	5803	broad.mit.edu	37	7	121668608	121668608	+	Missense_Mutation	SNP	A	T	T			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:121668608A>T	uc003vjy.2	+	14	5386	c.4991A>T	c.(4990-4992)AAA>ATA	p.K1664I	PTPRZ1_uc003vjz.2_Missense_Mutation_p.K804I|PTPRZ1_uc011knt.1_Missense_Mutation_p.K254I	NM_002851	NP_002842	P23471	PTPRZ_HUMAN	protein tyrosine phosphatase, receptor-type,	1664	Cytoplasmic (Potential).				central nervous system development	integral to plasma membrane	protein binding|protein tyrosine/threonine phosphatase activity|transmembrane receptor protein tyrosine phosphatase activity			ovary(3)|large_intestine(2)|lung(2)|central_nervous_system(1)|kidney(1)	9						ATTTCCAGGAAATGCTTCCAG	0.353													32	152	---	---	---	---	PASS
WASL	8976	broad.mit.edu	37	7	123332672	123332672	+	Missense_Mutation	SNP	G	T	T			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:123332672G>T	uc003vkz.2	-	9	1404	c.1076C>A	c.(1075-1077)CCA>CAA	p.P359Q		NM_003941	NP_003932	O00401	WASL_HUMAN	Wiskott-Aldrich syndrome gene-like protein	359	Pro-rich.				actin polymerization or depolymerization|axon guidance|cellular component movement|nitric oxide metabolic process|protein complex assembly|regulation of nitric-oxide synthase activity|regulation of transcription, DNA-dependent|transcription, DNA-dependent	actin cytoskeleton|cytosol|nucleolus|plasma membrane	actin binding|small GTPase regulator activity				0						AGGTGGTGGTGGAGGCCCTGA	0.672													70	180	---	---	---	---	PASS
ASB10	136371	broad.mit.edu	37	7	150873237	150873237	+	Missense_Mutation	SNP	G	A	A			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150873237G>A	uc003wjm.1	-	5	1627	c.1501C>T	c.(1501-1503)CGC>TGC	p.R501C	ASB10_uc003wjl.1_Missense_Mutation_p.R463C|ASB10_uc003wjn.1_Missense_Mutation_p.R441C	NM_001142459	NP_001135931	Q8WXI3	ASB10_HUMAN	ankyrin repeat and SOCS box-containing 10	456	SOCS box.				intracellular signal transduction						0			OV - Ovarian serous cystadenocarcinoma(82;0.00448)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		TGCAGGTAGCGGAGCAGGCGC	0.667													15	35	---	---	---	---	PASS
NCAPG2	54892	broad.mit.edu	37	7	158447321	158447321	+	Silent	SNP	T	C	C			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:158447321T>C	uc003wnv.1	-	22	2857	c.2712A>G	c.(2710-2712)CAA>CAG	p.Q904Q	NCAPG2_uc010lqu.1_Silent_p.Q696Q|NCAPG2_uc003wnw.1_RNA|NCAPG2_uc003wnx.1_Silent_p.Q904Q|NCAPG2_uc011kwe.1_Silent_p.Q904Q|NCAPG2_uc011kwc.1_Silent_p.Q405Q|NCAPG2_uc011kwd.1_Silent_p.Q347Q	NM_017760	NP_060230	Q86XI2	CNDG2_HUMAN	leucine zipper protein 5	904					cell division|chromosome condensation|mitosis	nucleus	methylated histone residue binding			ovary(1)|breast(1)|kidney(1)	3	Ovarian(565;0.152)	all_cancers(7;3.44e-11)|all_epithelial(9;3.05e-05)|all_hematologic(28;0.014)	OV - Ovarian serous cystadenocarcinoma(82;0.00174)	UCEC - Uterine corpus endometrioid carcinoma (81;0.187)|STAD - Stomach adenocarcinoma(7;0.18)		GCTGTAAGAGTTGCATCTGAA	0.463													69	284	---	---	---	---	PASS
MSR1	4481	broad.mit.edu	37	8	15967631	15967631	+	Nonsense_Mutation	SNP	G	T	T			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:15967631G>T	uc003wwz.2	-	10	1517	c.1319C>A	c.(1318-1320)TCA>TAA	p.S440*	MSR1_uc010lsu.2_Nonsense_Mutation_p.S458*|MSR1_uc003wxa.2_Nonsense_Mutation_p.S377*	NM_138715	NP_619729	P21757	MSRE_HUMAN	macrophage scavenger receptor 1 isoform type 1	440	SRCR.|Extracellular (Potential).				cholesterol transport|plasma lipoprotein particle clearance|positive regulation of cholesterol storage|positive regulation of macrophage derived foam cell differentiation|receptor-mediated endocytosis	collagen|integral to plasma membrane|low-density lipoprotein particle	low-density lipoprotein particle binding|protein binding|scavenger receptor activity			ovary(1)	1				Colorectal(111;0.00475)|COAD - Colon adenocarcinoma(73;0.0164)		TTCAGAATGTGAACAGGCTCT	0.378													34	187	---	---	---	---	PASS
PTK2B	2185	broad.mit.edu	37	8	27301762	27301762	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:27301762C>T	uc003xfn.1	+	28	2996	c.2188C>T	c.(2188-2190)CTC>TTC	p.L730F	PTK2B_uc003xfo.1_Missense_Mutation_p.L730F|PTK2B_uc003xfp.1_Missense_Mutation_p.L730F|PTK2B_uc003xfq.1_Missense_Mutation_p.L730F|PTK2B_uc003xfr.1_Missense_Mutation_p.L476F	NM_173174	NP_775266	Q14289	FAK2_HUMAN	PTK2B protein tyrosine kinase 2 beta isoform a	730	Pro-rich.				apoptosis|bone resorption|positive regulation of cell proliferation|signal complex assembly	cytosol	ATP binding|non-membrane spanning protein tyrosine kinase activity|signal transducer activity			lung(3)|ovary(1)|skin(1)	5		Ovarian(32;2.72e-05)		UCEC - Uterine corpus endometrioid carcinoma (27;0.023)|Epithelial(17;6.61e-10)|BRCA - Breast invasive adenocarcinoma(99;0.226)|Colorectal(74;0.229)		GCAAACCAACCTCCTGGCTCC	0.537													18	64	---	---	---	---	PASS
RAB11FIP1	80223	broad.mit.edu	37	8	37756812	37756812	+	Nonsense_Mutation	SNP	C	A	A			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:37756812C>A	uc003xkm.1	-	1	192	c.148G>T	c.(148-150)GAG>TAG	p.E50*	RAB11FIP1_uc010lvz.1_Intron|RAB11FIP1_uc003xkn.1_Nonsense_Mutation_p.E50*	NM_001002814	NP_001002814	Q6WKZ4	RFIP1_HUMAN	RAB11 family interacting protein 1 isoform 3	50	C2.				protein transport	centrosome|phagocytic vesicle membrane|recycling endosome	protein binding			ovary(1)|central_nervous_system(1)|skin(1)	3		Lung NSC(58;0.118)|all_lung(54;0.195)	LUSC - Lung squamous cell carcinoma(8;3.62e-11)			GCGTACTTCTCCTTGCCCACC	0.736													8	64	---	---	---	---	PASS
VDAC3	7419	broad.mit.edu	37	8	42260890	42260890	+	Missense_Mutation	SNP	T	C	C			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42260890T>C	uc011lct.1	+	8	756	c.613T>C	c.(613-615)TCC>CCC	p.S205P	VDAC3_uc003xpc.2_Missense_Mutation_p.S206P	NM_005662	NP_005653	Q9Y277	VDAC3_HUMAN	voltage-dependent anion channel 3 isoform b	205	Beta stranded; (By similarity).				adenine transport	mitochondrial outer membrane|pore complex	nucleotide binding|porin activity|protein binding|voltage-gated anion channel activity			upper_aerodigestive_tract(1)	1	all_cancers(6;3.86e-23)|all_lung(13;6.47e-12)|Lung NSC(13;1.08e-10)|Ovarian(28;0.00769)|Prostate(17;0.0119)|Lung SC(25;0.211)	all_lung(54;0.00671)|Lung NSC(58;0.0184)|Esophageal squamous(32;0.131)|Hepatocellular(245;0.133)|Renal(179;0.151)	BRCA - Breast invasive adenocarcinoma(8;3.48e-10)|OV - Ovarian serous cystadenocarcinoma(14;0.00266)|Lung(22;0.00849)|LUSC - Lung squamous cell carcinoma(45;0.024)		Dihydroxyaluminium(DB01375)	GATTGAAACATCCATAAACCT	0.398													16	342	---	---	---	---	PASS
ZBTB10	65986	broad.mit.edu	37	8	81399984	81399984	+	Silent	SNP	T	C	C			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:81399984T>C	uc003ybx.3	+	1	1537	c.939T>C	c.(937-939)TCT>TCC	p.S313S	ZBTB10_uc003ybv.3_Intron|ZBTB10_uc003ybw.3_Silent_p.S313S|ZBTB10_uc010lzt.2_Silent_p.S313S	NM_001105539	NP_001099009	Q96DT7	ZBT10_HUMAN	zinc finger and BTB domain containing 10 isoform	313					transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			lung(1)	1	all_cancers(3;1.68e-09)|all_epithelial(4;5.13e-11)|Lung NSC(7;1.75e-07)|all_lung(9;7.38e-07)|Breast(3;2.96e-06)		BRCA - Breast invasive adenocarcinoma(6;0.000434)|Epithelial(68;0.00486)|all cancers(69;0.0296)			ACCACGTCTCTACCGAGCACA	0.537													28	130	---	---	---	---	PASS
DCAF13	25879	broad.mit.edu	37	8	104427735	104427735	+	Missense_Mutation	SNP	T	G	G			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:104427735T>G	uc003yln.2	+	1	794	c.517T>G	c.(517-519)TTA>GTA	p.L173V	SLC25A32_uc003yll.2_5'Flank|SLC25A32_uc011lhr.1_5'Flank|DCAF13_uc003ylm.1_Silent_p.T8T|DCAF13_uc003ylo.2_5'UTR	NM_015420	NP_056235	Q9NV06	DCA13_HUMAN	WD repeats and SOF1 domain containing	21					rRNA processing	CUL4 RING ubiquitin ligase complex|nucleolus|ribonucleoprotein complex				breast(1)	1						CAAGTTGGACTTACAGAGAGG	0.567													38	28	---	---	---	---	PASS
CSMD3	114788	broad.mit.edu	37	8	113246594	113246594	+	Missense_Mutation	SNP	A	C	C			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:113246594A>C	uc003ynu.2	-	68	10899	c.10740T>G	c.(10738-10740)TTT>TTG	p.F3580L	CSMD3_uc003yns.2_Missense_Mutation_p.F2782L|CSMD3_uc003ynt.2_Missense_Mutation_p.F3540L|CSMD3_uc011lhx.1_Missense_Mutation_p.F3411L	NM_198123	NP_937756	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3 isoform 1	3580	Extracellular (Potential).					integral to membrane|plasma membrane				ovary(21)|lung(11)|skin(11)|kidney(8)|large_intestine(6)|upper_aerodigestive_tract(2)|central_nervous_system(2)|urinary_tract(1)|breast(1)	63						CTATACTTACAAAGCCATCCA	0.343										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			195	200	---	---	---	---	PASS
FOXD4	2298	broad.mit.edu	37	9	118298	118298	+	5'UTR	SNP	C	T	T	rs2492219	by1000genomes	TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:118298C>T	uc003zfz.2	-	1						NM_207305	NP_997188	Q12950	FOXD4_HUMAN	forkhead box D4						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			skin(1)	1	all_lung(41;0.218)	all_cancers(5;0.0395)|Acute lymphoblastic leukemia(5;1.91e-07)|all_hematologic(5;1.95e-06)	Kidney(42;0.112)|KIRC - Kidney renal clear cell carcinoma(5;0.157)	all cancers(5;0.000704)|Lung(218;0.00755)|GBM - Glioblastoma multiforme(5;0.0149)|Epithelial(6;0.0154)		AAGATGCCTTCGCCTTTTATA	0.493													3	12	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	9	68413569	68413569	+	RNA	SNP	C	T	T			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68413569C>T	uc004aex.2	+	1		c.124C>T								Homo sapiens mRNA; cDNA DKFZp564N0763 (from clone DKFZp564N0763).																		CCCCCAGTGGCGCCGGATCTA	0.557													3	4	---	---	---	---	PASS
PHF2	5253	broad.mit.edu	37	9	96415638	96415638	+	Silent	SNP	C	T	T			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:96415638C>T	uc004aub.2	+	6	927	c.780C>T	c.(778-780)CAC>CAT	p.H260H	PHF2_uc011lug.1_Silent_p.H143H	NM_005392	NP_005383	O75151	PHF2_HUMAN	PHD finger protein 2	260	JmjC.				liver development|negative regulation of chromatin silencing at rDNA|transcription, DNA-dependent	nucleolus	histone demethylase activity (H3-K9 specific)|iron ion binding|methylated histone residue binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|zinc ion binding			ovary(1)	1		Myeloproliferative disorder(762;0.0255)		OV - Ovarian serous cystadenocarcinoma(323;9.11e-28)		CCTGGTACCACGTGCTCAAGG	0.602													23	113	---	---	---	---	PASS
ZNF618	114991	broad.mit.edu	37	9	116779118	116779118	+	Intron	SNP	G	C	C			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:116779118G>C	uc004bid.2	+						ZNF618_uc004bib.1_Missense_Mutation_p.A268P|ZNF618_uc004bic.2_Intron|ZNF618_uc011lxi.1_Intron|ZNF618_uc011lxj.1_Intron	NM_133374	NP_588615	Q5T7W0	ZN618_HUMAN	zinc finger protein 618						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						GACAGGGTGGGCCAGCCGTTG	0.592													3	3	---	---	---	---	PASS
LCN2	3934	broad.mit.edu	37	9	130911735	130911735	+	5'UTR	SNP	C	G	G			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130911735C>G	uc004bto.1	+	1					LCN2_uc010mxq.1_5'UTR|LCN2_uc011map.1_5'UTR	NM_005564	NP_005555	P80188	NGAL_HUMAN	lipocalin 2 precursor						apoptosis|innate immune response|regulation of apoptosis|siderophore transport		iron ion binding|transporter activity				0						GCCTCTCACTCGCCACCTCCT	0.597													7	188	---	---	---	---	PASS
LRIT1	26103	broad.mit.edu	37	10	85991773	85991773	+	Silent	SNP	C	T	T			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:85991773C>T	uc001kcz.1	-	4	1804	c.1782G>A	c.(1780-1782)GAG>GAA	p.E594E		NM_015613	NP_056428	Q9P2V4	LRIT1_HUMAN	retina specific protein PAL	594	Cytoplasmic (Potential).|LRR 6.					integral to endoplasmic reticulum membrane					0						GCCTGTCAGCCTCGCTGACAC	0.562													9	39	---	---	---	---	PASS
PTEN	5728	broad.mit.edu	37	10	89712017	89712017	+	Splice_Site	SNP	G	A	A			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:89712017G>A	uc001kfb.2	+	7	1665	c.634_splice	c.e7+1	p.N212_splice		NM_000314	NP_000305	P60484	PTEN_HUMAN	phosphatase and tensin homolog						activation of mitotic anaphase-promoting complex activity|apoptosis|canonical Wnt receptor signaling pathway|cell proliferation|central nervous system development|induction of apoptosis|inositol phosphate dephosphorylation|negative regulation of cell migration|negative regulation of cyclin-dependent protein kinase activity involved in G1/S|negative regulation of focal adhesion assembly|negative regulation of G1/S transition of mitotic cell cycle|negative regulation of protein kinase B signaling cascade|negative regulation of protein phosphorylation|nerve growth factor receptor signaling pathway|phosphatidylinositol dephosphorylation|phosphatidylinositol-mediated signaling|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|positive regulation of sequence-specific DNA binding transcription factor activity|protein stabilization|regulation of neuron projection development|T cell receptor signaling pathway	cytosol|internal side of plasma membrane|PML body	anaphase-promoting complex binding|enzyme binding|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity|lipid binding|magnesium ion binding|PDZ domain binding|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity|phosphatidylinositol-3-phosphatase activity|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity	p.?(5)|p.R55fs*1(4)|p.Y27fs*1(2)|p.G165_*404del(1)		endometrium(831)|central_nervous_system(657)|skin(121)|haematopoietic_and_lymphoid_tissue(101)|large_intestine(99)|prostate(97)|breast(73)|lung(65)|ovary(58)|thyroid(29)|stomach(29)|upper_aerodigestive_tract(25)|cervix(24)|liver(20)|vulva(17)|kidney(15)|NS(14)|soft_tissue(13)|urinary_tract(12)|eye(8)|pancreas(6)|salivary_gland(5)|bone(5)|biliary_tract(4)|autonomic_ganglia(2)|meninges(2)|testis(1)|oesophagus(1)	2334		all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132)	KIRC - Kidney renal clear cell carcinoma(1;0.214)	UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218)		GGAACTTGCAGTAAGTGCTTG	0.343		31	D|Mis|N|F|S		glioma| prostate|endometrial	harmartoma|glioma| prostate|endometrial			Proteus_syndrome|Cowden_syndrome|Juvenile_Polyposis|Hereditary_Mixed_Polyposis_Syndrome_type_1|Bannayan-Riley-Ruvalcaba_syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)			68	272	---	---	---	---	PASS
INPP5F	22876	broad.mit.edu	37	10	121587100	121587100	+	Silent	SNP	T	A	A			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:121587100T>A	uc001leo.2	+	20	3373	c.3207T>A	c.(3205-3207)TCT>TCA	p.S1069S	INPP5F_uc001lep.2_Silent_p.S459S	NM_014937	NP_055752	Q9Y2H2	SAC2_HUMAN	inositol polyphosphate-5-phosphatase F	1069							phosphoric ester hydrolase activity			ovary(2)	2		Lung NSC(174;0.109)|all_lung(145;0.142)		all cancers(201;0.00205)|BRCA - Breast invasive adenocarcinoma(275;0.158)		GAGCAGTCTCTCCCTTTGCCA	0.478													50	176	---	---	---	---	PASS
SPTY2D1	144108	broad.mit.edu	37	11	18636203	18636203	+	Nonsense_Mutation	SNP	C	A	A			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:18636203C>A	uc001moy.2	-	3	1834	c.1618G>T	c.(1618-1620)GAA>TAA	p.E540*	SPTY2D1_uc010rdi.1_Nonsense_Mutation_p.E540*	NM_194285	NP_919261	Q68D10	SPT2_HUMAN	SPT2, Suppressor of Ty, domain containing 1	540	Ser-rich.									breast(1)	1						GAAATTGTTTCGGAGACAACA	0.478													4	212	---	---	---	---	PASS
PRG3	10394	broad.mit.edu	37	11	57147060	57147060	+	Silent	SNP	C	T	T			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:57147060C>T	uc001njv.1	-	3	392	c.282G>A	c.(280-282)AGG>AGA	p.R94R		NM_006093	NP_006084	Q9Y2Y8	PRG3_HUMAN	proteoglycan 3 precursor	94					basophil activation|histamine biosynthetic process|immune response|leukotriene biosynthetic process|negative regulation of translation|neutrophil activation|positive regulation of interleukin-8 biosynthetic process|superoxide anion generation		sugar binding				0						TGTCTTCTTCCCTGGGGCACT	0.517													42	170	---	---	---	---	PASS
RBM7	10179	broad.mit.edu	37	11	114271407	114271407	+	Missense_Mutation	SNP	C	A	A			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:114271407C>A	uc001pov.2	+	1	24	c.14C>A	c.(13-15)GCG>GAG	p.A5E	C11orf71_uc001pot.1_5'Flank|C11orf71_uc001pou.3_5'Flank|RBM7_uc001pow.2_Missense_Mutation_p.A5E|RBM7_uc001pox.2_5'UTR	NM_016090	NP_057174	Q9Y580	RBM7_HUMAN	RNA binding motif protein 7	5					meiosis		nucleotide binding|protein binding|RNA binding			ovary(2)	2		all_cancers(61;5.06e-12)|all_epithelial(67;5.3e-06)|all_hematologic(158;7.68e-05)|Acute lymphoblastic leukemia(157;0.000966)|Melanoma(852;0.00153)|Medulloblastoma(222;0.0523)|all_neural(223;0.0663)|Breast(348;0.0818)|Prostate(24;0.104)		BRCA - Breast invasive adenocarcinoma(274;2.56e-06)|Epithelial(105;4.17e-05)|all cancers(92;0.000348)		GGGGCGGCGGCGGCGGAAGCG	0.632													3	82	---	---	---	---	PASS
MFAP5	8076	broad.mit.edu	37	12	8802129	8802129	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:8802129C>T	uc001qut.1	-	9	590	c.377G>A	c.(376-378)CGT>CAT	p.R126H	MFAP5_uc001qus.2_Missense_Mutation_p.R116H|MFAP5_uc009zge.1_Missense_Mutation_p.R101H	NM_003480	NP_003471	Q13361	MFAP5_HUMAN	microfibrillar associated protein 5 precursor	126						microfibril	extracellular matrix structural constituent			breast(1)	1	Lung SC(5;0.184)					ACAGACAAGACGAGAGCAGAT	0.443													27	95	---	---	---	---	PASS
EPS8	2059	broad.mit.edu	37	12	15822749	15822749	+	Missense_Mutation	SNP	G	A	A			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:15822749G>A	uc009zif.2	-	5	309	c.215C>T	c.(214-216)ACC>ATC	p.T72I	EPS8_uc001rdb.2_Missense_Mutation_p.T72I|EPS8_uc009zig.2_5'UTR	NM_004447	NP_004438	Q12929	EPS8_HUMAN	epidermal growth factor receptor pathway	72	PH; first part.				cell proliferation|epidermal growth factor receptor signaling pathway		SH3/SH2 adaptor activity			ovary(2)|upper_aerodigestive_tract(1)|skin(1)	4		all_epithelial(100;1.87e-05)|Breast(259;0.000286)|Hepatocellular(102;0.244)		BRCA - Breast invasive adenocarcinoma(232;4.29e-05)|GBM - Glioblastoma multiforme(207;0.0264)		CAGGACAAAGGTAGTCAAGTG	0.348													16	90	---	---	---	---	PASS
LRMP	4033	broad.mit.edu	37	12	25232580	25232580	+	Intron	SNP	C	G	G			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:25232580C>G	uc001rgh.2	+						LRMP_uc001rgg.1_Intron|LRMP_uc010sja.1_Intron|LRMP_uc010sjb.1_5'UTR|LRMP_uc001rgi.2_Intron|LRMP_uc010sjc.1_Intron|LRMP_uc010sjd.1_Intron	NM_006152	NP_006143	Q12912	LRMP_HUMAN	lymphoid-restricted membrane protein						vesicle fusion|vesicle targeting	endoplasmic reticulum membrane|integral to plasma membrane				ovary(1)|skin(1)	2	Acute lymphoblastic leukemia(6;0.00112)|all_hematologic(7;0.00152)|Colorectal(261;0.11)					TTTGTTTCTCCTGTTGACAGA	0.363													23	93	---	---	---	---	PASS
MLL2	8085	broad.mit.edu	37	12	49442951	49442951	+	Missense_Mutation	SNP	A	T	T			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49442951A>T	uc001rta.3	-	12	3957	c.3957T>A	c.(3955-3957)CAT>CAA	p.H1319Q		NM_003482	NP_003473	O14686	MLL2_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 2	1319	Arg-rich.				chromatin silencing|histone H3-K4 methylation|oocyte growth|positive regulation of cell proliferation|positive regulation of estrogen receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|response to estrogen stimulus|transcription, DNA-dependent	histone methyltransferase complex	histone-lysine N-methyltransferase activity|protein binding|transcription regulatory region DNA binding|zinc ion binding			kidney(16)|central_nervous_system(12)|lung(4)|skin(4)|ovary(3)|pancreas(2)	41						CACGTCCTCCATGGGCTCCTC	0.572			N|F|Mis		medulloblastoma|renal					HNSCC(34;0.089)			6	24	---	---	---	---	PASS
MAP3K12	7786	broad.mit.edu	37	12	53880961	53880961	+	Intron	SNP	G	T	T			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53880961G>T	uc001sdm.1	-						MAP3K12_uc001sdn.1_Missense_Mutation_p.P72H	NM_006301	NP_006292	Q12852	M3K12_HUMAN	mitogen-activated protein kinase kinase kinase						histone phosphorylation|JNK cascade|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|protein autophosphorylation	cytosol|membrane fraction|plasma membrane	ATP binding|magnesium ion binding|MAP kinase kinase kinase activity|protein homodimerization activity|protein kinase binding			lung(2)|ovary(1)|breast(1)|skin(1)	5						AGGCTCAGGGGGCGGCTCTCC	0.647													19	81	---	---	---	---	PASS
SHMT2	6472	broad.mit.edu	37	12	57627609	57627609	+	Missense_Mutation	SNP	G	A	A			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57627609G>A	uc001snf.1	+	10	1211	c.1201G>A	c.(1201-1203)GAG>AAG	p.E401K	SHMT2_uc001sng.1_Missense_Mutation_p.E297K|SHMT2_uc001snh.1_Missense_Mutation_p.E240K|SHMT2_uc009zpk.1_Missense_Mutation_p.E391K|SHMT2_uc001sni.1_Missense_Mutation_p.E380K|SHMT2_uc010srg.1_Missense_Mutation_p.E410K|SHMT2_uc001snj.1_Missense_Mutation_p.E305K|SHMT2_uc010srh.1_Missense_Mutation_p.E380K|SHMT2_uc001snk.1_Missense_Mutation_p.E305K|SHMT2_uc010sri.1_Missense_Mutation_p.E380K|SHMT2_uc001snl.2_Missense_Mutation_p.E305K|SHMT2_uc010srj.1_Missense_Mutation_p.E56K	NM_005412	NP_005403	P34897	GLYM_HUMAN	serine hydroxymethyltransferase 2	401						microtubule cytoskeleton|mitochondrial nucleoid	glycine hydroxymethyltransferase activity|methyltransferase activity			ovary(1)|central_nervous_system(1)	2					Glycine(DB00145)|Pyridoxal Phosphate(DB00114)|Tetrahydrofolic acid(DB00116)	GCGGGTGCTAGAGCTTGTATC	0.607													27	84	---	---	---	---	PASS
CCDC59	29080	broad.mit.edu	37	12	82746875	82746875	+	3'UTR	SNP	T	A	A			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:82746875T>A	uc001szp.3	-	4						NM_014167	NP_054886	Q9P031	TAP26_HUMAN	coiled-coil domain containing 59						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	protein binding				0						GGGAGGCACATGTCACAGAAG	0.308													28	98	---	---	---	---	PASS
NOS1	4842	broad.mit.edu	37	12	117672374	117672374	+	Silent	SNP	A	T	T			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:117672374A>T	uc001twm.1	-	21	3917	c.3231T>A	c.(3229-3231)GCT>GCA	p.A1077A		NM_000620	NP_000611	P29475	NOS1_HUMAN	nitric oxide synthase 1, neuronal	1077	FAD-binding FR-type.				multicellular organismal response to stress|myoblast fusion|negative regulation of calcium ion transport into cytosol|neurotransmitter biosynthetic process|nitric oxide biosynthetic process|platelet activation|positive regulation of vasodilation|regulation of cardiac muscle contraction|response to heat|response to hypoxia	cytoskeleton|cytosol|dendritic spine|perinuclear region of cytoplasm|photoreceptor inner segment|sarcolemma|sarcoplasmic reticulum	arginine binding|cadmium ion binding|calmodulin binding|flavin adenine dinucleotide binding|FMN binding|heme binding|NADP binding|nitric-oxide synthase activity|tetrahydrobiopterin binding			ovary(3)|skin(3)|pancreas(1)	7	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.0561)	L-Citrulline(DB00155)	TGTTACCTAAAGCCGTGTTCC	0.587													10	62	---	---	---	---	PASS
CCDC60	160777	broad.mit.edu	37	12	119909965	119909965	+	Silent	SNP	T	C	C	rs139079166	byFrequency	TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:119909965T>C	uc001txe.2	+	3	802	c.337T>C	c.(337-339)TTG>CTG	p.L113L	uc001txf.2_Intron	NM_178499	NP_848594	Q8IWA6	CCD60_HUMAN	coiled-coil domain containing 60	113										ovary(2)|upper_aerodigestive_tract(1)	3	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.207)		GGACACCTTATTGAGGTAAGT	0.458													84	307	---	---	---	---	PASS
RNF17	56163	broad.mit.edu	37	13	25353868	25353868	+	Silent	SNP	T	C	C			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:25353868T>C	uc001upr.2	+	5	534	c.493T>C	c.(493-495)TTA>CTA	p.L165L	RNF17_uc010tdd.1_Silent_p.L24L|RNF17_uc010aab.2_RNA|RNF17_uc010tde.1_Silent_p.L165L|RNF17_uc001ups.2_Silent_p.L104L|RNF17_uc001upq.1_Silent_p.L165L	NM_031277	NP_112567	Q9BXT8	RNF17_HUMAN	ring finger protein 17	165					multicellular organismal development	cytoplasm|nucleus	hydrolase activity, acting on ester bonds|nucleic acid binding|zinc ion binding			ovary(1)|skin(1)	2		Lung SC(185;0.0225)|Breast(139;0.077)		all cancers(112;0.0114)|OV - Ovarian serous cystadenocarcinoma(117;0.0311)|Epithelial(112;0.0524)		TTTCGAACAGTTAAGCATTGC	0.363													31	93	---	---	---	---	PASS
BRCA2	675	broad.mit.edu	37	13	32944606	32944606	+	Missense_Mutation	SNP	C	G	G	rs80359087		TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:32944606C>G	uc001uub.1	+	19	8626	c.8399C>G	c.(8398-8400)CCT>CGT	p.P2800R		NM_000059	NP_000050	P51587	BRCA2_HUMAN	breast cancer 2, early onset	2800					cell cycle cytokinesis|centrosome duplication|double-strand break repair via homologous recombination|negative regulation of mammary gland epithelial cell proliferation|nucleotide-excision repair|positive regulation of transcription, DNA-dependent|regulation of S phase of mitotic cell cycle	BRCA2-MAGE-D1 complex|centrosome|nucleoplasm|stored secretory granule	gamma-tubulin binding|H3 histone acetyltransferase activity|H4 histone acetyltransferase activity|protease binding|single-stranded DNA binding			ovary(20)|endometrium(8)|lung(7)|breast(7)|oesophagus(5)|large_intestine(4)|central_nervous_system(3)|pancreas(3)|skin(2)|upper_aerodigestive_tract(1)|cervix(1)|salivary_gland(1)|liver(1)|kidney(1)	64		Lung SC(185;0.0262)		all cancers(112;7.13e-07)|Epithelial(112;1.59e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0291)|GBM - Glioblastoma multiforme(144;0.0704)		GACCCTAGACCTTTTCCTCTG	0.383			D|Mis|N|F|S		breast|ovarian|pancreatic	breast|ovarian|pancreatic|leukemia  (FANCB|FANCD1)		Direct_reversal_of_damage|Homologous_recombination	Fanconi_Anemia_type_D1_bi-allelic_BRCA2_mutations|Fanconi_Anemia|Pancreatic_Cancer_Familial_Clustering_of|Hereditary_Breast-Ovarian_Cancer_BRCA2_type|Hereditary_Prostate_Cancer|Li-Fraumeni_syndrome	TCGA Ovarian(8;0.087)			25	226	---	---	---	---	PASS
TPT1	7178	broad.mit.edu	37	13	45914269	45914269	+	Silent	SNP	A	G	G			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:45914269A>G	uc001uzy.1	-	3	246	c.153T>C	c.(151-153)AAT>AAC	p.N51N	TPT1_uc001uzz.1_Silent_p.N17N|SNORA31_uc001vaa.1_5'Flank|TPT1_uc010tfp.1_3'UTR|LOC100190939_uc010tfr.1_5'Flank|LOC100190939_uc001vac.2_5'Flank	NM_003295	NP_003286	P13693	TCTP_HUMAN	tumor protein, translationally-controlled 1	51					anti-apoptosis|response to virus	extracellular space|multivesicular body	calcium ion binding|protein binding				0		Lung NSC(96;0.00227)|Prostate(109;0.00578)|Breast(56;0.0192)|Lung SC(185;0.0367)|Hepatocellular(98;0.0556)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;0.000232)		CAGCGGAGGCATTTCCACCAA	0.453													39	105	---	---	---	---	PASS
LMO7	4008	broad.mit.edu	37	13	76369561	76369561	+	5'UTR	SNP	G	A	A			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:76369561G>A	uc001vjv.2	+	2					LMO7_uc010thv.1_Silent_p.V166V|LMO7_uc001vjt.1_Silent_p.V114V|LMO7_uc010thw.1_Silent_p.V75V|LMO7_uc001vju.1_RNA	NM_015842	NP_056667	Q8WWI1	LMO7_HUMAN	LIM domain only 7 isoform 2							cytoplasm|nucleus|ubiquitin ligase complex	ubiquitin-protein ligase activity|zinc ion binding			large_intestine(2)|ovary(1)|prostate(1)|skin(1)	5		Breast(118;0.0992)		GBM - Glioblastoma multiforme(99;0.0109)		ACAGGAGAGTGAAAAATGTAA	0.313													54	147	---	---	---	---	PASS
LMO7	4008	broad.mit.edu	37	13	76378569	76378569	+	Missense_Mutation	SNP	C	A	A			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:76378569C>A	uc001vjv.2	+	5	867	c.107C>A	c.(106-108)CCA>CAA	p.P36Q	LMO7_uc010thv.1_Missense_Mutation_p.P321Q|LMO7_uc001vjt.1_Missense_Mutation_p.P269Q|LMO7_uc010thw.1_Missense_Mutation_p.P230Q|LMO7_uc001vjw.1_Missense_Mutation_p.P36Q|LMO7_uc001vju.1_RNA	NM_015842	NP_056667	Q8WWI1	LMO7_HUMAN	LIM domain only 7 isoform 2	321						cytoplasm|nucleus|ubiquitin ligase complex	ubiquitin-protein ligase activity|zinc ion binding			large_intestine(2)|ovary(1)|prostate(1)|skin(1)	5		Breast(118;0.0992)		GBM - Glioblastoma multiforme(99;0.0109)		AGTAGACAGCCATCCTATGTA	0.418													6	179	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	14	19857036	19857036	+	RNA	SNP	A	G	G			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:19857036A>G	uc001vvq.1	-	5		c.494T>C								Homo sapiens cDNA FLJ12852 fis, clone NT2RP2003445.																		CTGGATAATAAAGTTCATCTC	0.373													9	130	---	---	---	---	PASS
NYNRIN	57523	broad.mit.edu	37	14	24878537	24878537	+	Missense_Mutation	SNP	G	A	A			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24878537G>A	uc001wpf.3	+	4	1855	c.1537G>A	c.(1537-1539)GCT>ACT	p.A513T		NM_025081	NP_079357	Q9P2P1	NYNRI_HUMAN	hypothetical protein LOC57523	513					DNA integration	integral to membrane	DNA binding			ovary(2)|central_nervous_system(1)	3						AGAGGGACCCGCTCCAGTGCT	0.572													11	48	---	---	---	---	PASS
ERO1L	30001	broad.mit.edu	37	14	53118958	53118958	+	Missense_Mutation	SNP	T	G	G			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:53118958T>G	uc001wzv.2	-	13	1350	c.1124A>C	c.(1123-1125)AAG>ACG	p.K375T	ERO1L_uc001wzw.2_RNA|ERO1L_uc010aof.2_RNA	NM_014584	NP_055399	Q96HE7	ERO1A_HUMAN	ERO1-like precursor	375					chaperone mediated protein folding requiring cofactor|electron transport chain|protein thiol-disulfide exchange|response to temperature stimulus|transport	endoplasmic reticulum lumen|endoplasmic reticulum membrane|microsome	disulfide oxidoreductase activity|flavin adenine dinucleotide binding|oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor				0	Breast(41;0.226)					AGTAATTACCTTTAGTTTGTG	0.303													29	117	---	---	---	---	PASS
WDHD1	11169	broad.mit.edu	37	14	55448374	55448374	+	Missense_Mutation	SNP	C	G	G			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:55448374C>G	uc001xbm.1	-	16	2025	c.1947G>C	c.(1945-1947)ATG>ATC	p.M649I	WDHD1_uc010aom.1_Missense_Mutation_p.M166I|WDHD1_uc001xbn.1_Missense_Mutation_p.M526I	NM_007086	NP_009017	O75717	WDHD1_HUMAN	WD repeat and HMG-box DNA binding protein 1	649						cytoplasm|nucleoplasm	DNA binding			skin(1)	1						CTCTGTTAAGCATTCGAACAA	0.403													46	120	---	---	---	---	PASS
MED6	10001	broad.mit.edu	37	14	71067337	71067337	+	Silent	SNP	G	A	A			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:71067337G>A	uc001xmf.2	-	1	48	c.18C>T	c.(16-18)ATC>ATT	p.I6I	MED6_uc010tth.1_Silent_p.I6I|MED6_uc010tti.1_Silent_p.I6I|MED6_uc001xmg.1_Silent_p.I6I|MED6_uc010ttj.1_Silent_p.I6I	NM_005466	NP_005457	O75586	MED6_HUMAN	mediator of RNA polymerase II transcription,	6					positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	mediator complex	transcription coactivator activity				0				all cancers(60;0.00315)|BRCA - Breast invasive adenocarcinoma(234;0.00685)|OV - Ovarian serous cystadenocarcinoma(108;0.0352)		GTATACCTCGGATATCCACCG	0.483													12	42	---	---	---	---	PASS
MAP3K9	4293	broad.mit.edu	37	14	71197381	71197381	+	Missense_Mutation	SNP	A	G	G			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:71197381A>G	uc001xmm.2	-	12	3031	c.3031T>C	c.(3031-3033)TCC>CCC	p.S1011P	MAP3K9_uc010ttk.1_Missense_Mutation_p.S739P|MAP3K9_uc001xmk.2_Missense_Mutation_p.S744P|MAP3K9_uc001xml.2_Missense_Mutation_p.S1025P	NM_033141	NP_149132	P80192	M3K9_HUMAN	mitogen-activated protein kinase kinase kinase	1011	Ser-rich.				activation of JUN kinase activity|protein autophosphorylation		ATP binding|JUN kinase kinase kinase activity|MAP kinase kinase activity|protein homodimerization activity			stomach(2)|lung(1)|central_nervous_system(1)|skin(1)	5				all cancers(60;0.00779)|BRCA - Breast invasive adenocarcinoma(234;0.00884)|OV - Ovarian serous cystadenocarcinoma(108;0.08)		TGGCTGGGGGACACAAACCAC	0.612													4	38	---	---	---	---	PASS
PTPN21	11099	broad.mit.edu	37	14	88946198	88946198	+	Missense_Mutation	SNP	T	G	G			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:88946198T>G	uc001xwv.3	-	13	1908	c.1577A>C	c.(1576-1578)TAC>TCC	p.Y526S	PTPN21_uc010twc.1_Missense_Mutation_p.Y322S	NM_007039	NP_008970	Q16825	PTN21_HUMAN	protein tyrosine phosphatase, non-receptor type	526						cytoplasm|cytoskeleton	binding|protein tyrosine phosphatase activity			ovary(3)|skin(1)	4						CTCGGCAGGGTAGGGGTAGGG	0.701													7	15	---	---	---	---	PASS
IQGAP1	8826	broad.mit.edu	37	15	91025444	91025444	+	Silent	SNP	C	T	T			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:91025444C>T	uc002bpl.1	+	28	3587	c.3486C>T	c.(3484-3486)TTC>TTT	p.F1162F		NM_003870	NP_003861	P46940	IQGA1_HUMAN	IQ motif containing GTPase activating protein 1	1162	Ras-GAP.|C1.				energy reserve metabolic process|regulation of insulin secretion|small GTPase mediated signal transduction	actin filament|cytoplasm|midbody|nucleus|plasma membrane	calmodulin binding|GTPase inhibitor activity|protein phosphatase binding|Ras GTPase activator activity			ovary(2)|lung(2)|central_nervous_system(2)|pancreas(1)|skin(1)	8	Melanoma(11;0.00551)|Lung NSC(78;0.0237)|all_lung(78;0.0488)		BRCA - Breast invasive adenocarcinoma(143;0.0745)|KIRC - Kidney renal clear cell carcinoma(17;0.138)|Kidney(142;0.194)			GGATGCGCTTCATTGCCAAAG	0.522											OREG0023473	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	30	131	---	---	---	---	PASS
CACNA1H	8912	broad.mit.edu	37	16	1254064	1254064	+	Missense_Mutation	SNP	C	T	T	rs145376050	by1000genomes	TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1254064C>T	uc002cks.2	+	10	2305	c.2057C>T	c.(2056-2058)CCC>CTC	p.P686L	CACNA1H_uc002ckt.2_Missense_Mutation_p.P686L	NM_021098	NP_066921	O95180	CAC1H_HUMAN	calcium channel, voltage-dependent, T type,	686	Cytoplasmic (Potential).				aldosterone biosynthetic process|axon guidance|cellular response to hormone stimulus|cellular response to potassium ion|cortisol biosynthetic process|muscle contraction|myoblast fusion|positive regulation of acrosome reaction|regulation of heart contraction	voltage-gated calcium channel complex	low voltage-gated calcium channel activity			breast(2)	2		Hepatocellular(780;0.00369)			Flunarizine(DB04841)|Mibefradil(DB01388)	TGCCCCCTGCCCAGCCCCCCA	0.701													4	8	---	---	---	---	PASS
TXNDC11	51061	broad.mit.edu	37	16	11773280	11773280	+	Missense_Mutation	SNP	G	T	T			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:11773280G>T	uc010buu.1	-	13	2791	c.2729C>A	c.(2728-2730)GCC>GAC	p.A910D	TXNDC11_uc002dbg.1_Missense_Mutation_p.A883D	NM_015914	NP_056998	Q6PKC3	TXD11_HUMAN	thioredoxin domain containing 11	910	Potential.				cell redox homeostasis	endoplasmic reticulum membrane|integral to membrane					0						GTTTTCTGAGGCATCGGCCAG	0.617													34	113	---	---	---	---	PASS
TP53	7157	broad.mit.edu	37	17	7577120	7577120	+	Missense_Mutation	SNP	C	T	T	rs28934576	by1000genomes	TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7577120C>T	uc002gim.2	-	8	1012	c.818G>A	c.(817-819)CGT>CAT	p.R273H	TP53_uc002gig.1_Intron|TP53_uc002gih.2_Missense_Mutation_p.R273H|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Missense_Mutation_p.R141H|TP53_uc010cng.1_Missense_Mutation_p.R141H|TP53_uc002gii.1_Missense_Mutation_p.R141H|TP53_uc010cnh.1_Missense_Mutation_p.R273H|TP53_uc010cni.1_Missense_Mutation_p.R273H|TP53_uc002gij.2_Missense_Mutation_p.R273H	NM_001126112	NP_001119584	P04637	P53_HUMAN	tumor protein p53 isoform a	273	Interaction with DNA.||Interaction with E4F1.|Interaction with HIPK1 (By similarity).|Interaction with AXIN1 (By similarity).		R -> N (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|R -> S (in a familial cancer not matching LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> L (in LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> C (in LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> G (in LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> Q (in sporadic cancers; somatic mutation).|R -> Y (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|R -> P (in sporadic cancers; somatic mutation).		activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray	cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork	ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding	p.R273H(469)|p.R273C(394)|p.R273L(83)|p.R273P(24)|p.R273S(11)|p.R273G(9)|p.0?(7)|p.R273fs*72(3)|p.?(2)|p.R273fs*33(2)|p.R273_C275delRVC(1)|p.L265_K305del41(1)|p.S269fs*21(1)|p.R273R(1)|p.E258fs*71(1)|p.R273fs*71(1)|p.F270_D281del12(1)|p.E271_R273delEVR(1)|p.V272_K292del21(1)		large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1)	22245		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)		GGCACAAACACGCACCTCAAA	0.542	R273H(NCIH1793_LUNG)|R273H(MOLT13_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273H(PANC1_PANCREAS)|R273H(NCIH508_LARGE_INTESTINE)|R273H(NCIH1975_LUNG)|R273H(U251MG_CENTRAL_NERVOUS_SYSTEM)|R273H(SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273H(PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273H(SW1783_CENTRAL_NERVOUS_SYSTEM)|R273H(NCIH2405_LUNG)|R273H(HEC59_ENDOMETRIUM)|R273H(NCIH1155_LUNG)|R273H(HT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273H(EN_ENDOMETRIUM)|R273H(SNB19_CENTRAL_NERVOUS_SYSTEM)|R273H(MDAMB468_BREAST)|R273H(SUDHL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273H(SW620_LARGE_INTESTINE)|R273H(SUIT2_PANCREAS)|R273H(SW480_LARGE_INTESTINE)|R273H(SKMEL30_SKIN)|R273H(OC314_OVARY)|R273H(HEC6_ENDOMETRIUM)|R273H(HT29_LARGE_INTESTINE)	111	Mis|N|F		breast|colorectal|lung|sarcoma|adrenocortical|glioma|multiple other tumour types	breast|sarcoma|adrenocortical carcinoma|glioma|multiple other tumour types		Other_conserved_DNA_damage_response_genes	Hereditary_Adrenocortical_Cancer|Endometrial_Cancer_Familial_Clustering_of|Hereditary_Breast-Ovarian_Cancer_non-BRCA1/2|Li-Fraumeni_syndrome|Osteosarcoma_Familial_Clustering_of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)			4	43	---	---	---	---	PASS
MYO1D	4642	broad.mit.edu	37	17	30986144	30986144	+	Silent	SNP	C	T	T			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:30986144C>T	uc002hho.1	-	17	2346	c.2334G>A	c.(2332-2334)ACG>ACA	p.T778T	MYO1D_uc002hhp.1_Silent_p.T778T	NM_015194	NP_056009	O94832	MYO1D_HUMAN	myosin ID	778						myosin complex	actin binding|ATP binding|calmodulin binding			large_intestine(1)|ovary(1)|central_nervous_system(1)	3			BRCA - Breast invasive adenocarcinoma(9;0.0362)			TATTGAAAATCGTCTGCAGGG	0.498											OREG0024311	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	22	73	---	---	---	---	PASS
WNT9B	7484	broad.mit.edu	37	17	44953652	44953652	+	Silent	SNP	C	A	A			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:44953652C>A	uc002ikw.1	+	4	679	c.642C>A	c.(640-642)GGC>GGA	p.G214G	WNT9B_uc002ikx.1_Silent_p.G214G	NM_003396	NP_003387	O14905	WNT9B_HUMAN	wingless-type MMTV integration site family,	214					anterior/posterior pattern formation|axis specification|branching involved in ureteric bud morphogenesis|canonical Wnt receptor signaling pathway|cell-cell signaling|cellular response to retinoic acid|collecting duct development|cornea development in camera-type eye|endoderm development|establishment of planar polarity involved in nephron morphogenesis|kidney rudiment formation|male genitalia development|mesonephric duct formation|metanephric tubule development|neuron differentiation|palate development|regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis|uterus morphogenesis|Wnt receptor signaling pathway, calcium modulating pathway|Wnt receptor signaling pathway, planar cell polarity pathway	extracellular space|plasma membrane|proteinaceous extracellular matrix	extracellular matrix structural constituent|G-protein-coupled receptor binding			lung(2)	2			BRCA - Breast invasive adenocarcinoma(9;0.0257)			AGTGCCATGGCGTATCAGGCT	0.642													5	73	---	---	---	---	PASS
THOC4	10189	broad.mit.edu	37	17	79845851	79845851	+	3'UTR	SNP	A	G	G			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79845851A>G	uc002kbu.2	-	6						NM_005782	NP_005773	Q86V81	THOC4_HUMAN	THO complex 4						intronless viral mRNA export from host nucleus|mRNA 3'-end processing|termination of RNA polymerase II transcription	catalytic step 2 spliceosome|cytosol|nuclear speck|transcription export complex	nucleotide binding|protein binding|RNA binding				0	all_neural(118;0.0878)|Ovarian(332;0.12)		BRCA - Breast invasive adenocarcinoma(99;0.013)|OV - Ovarian serous cystadenocarcinoma(97;0.0382)			aaaaaaaaagaaaaaaaaaaa	0.358													3	4	---	---	---	---	PASS
CCDC57	284001	broad.mit.edu	37	17	80156290	80156290	+	Missense_Mutation	SNP	T	C	C			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80156290T>C	uc002kdz.1	-	4	771	c.416A>G	c.(415-417)AAT>AGT	p.N139S	CCDC57_uc002kdx.1_Missense_Mutation_p.N139S	NM_198082	NP_932348	Q2TAC2	CCD57_HUMAN	coiled-coil domain containing 57	139	Potential.									ovary(2)	2	Breast(20;0.00285)|all_neural(118;0.0878)|all_lung(278;0.0949)|Lung NSC(278;0.128)|Ovarian(332;0.227)		BRCA - Breast invasive adenocarcinoma(99;0.0232)|OV - Ovarian serous cystadenocarcinoma(97;0.0253)			AATCTCACCATTCTTGTCACT	0.413													16	48	---	---	---	---	PASS
MYOM1	8736	broad.mit.edu	37	18	3155065	3155065	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:3155065C>T	uc002klp.2	-	11	1857	c.1523G>A	c.(1522-1524)GGA>GAA	p.G508E	MYOM1_uc002klq.2_Missense_Mutation_p.G508E	NM_003803	NP_003794	P52179	MYOM1_HUMAN	myomesin 1 isoform a	508						striated muscle myosin thick filament	structural constituent of muscle			ovary(3)|central_nervous_system(1)|pancreas(1)	5						AGCTGGGGCTCCTTCAATCTC	0.527													6	57	---	---	---	---	PASS
TGIF1	7050	broad.mit.edu	37	18	3457635	3457635	+	Silent	SNP	G	T	T			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:3457635G>T	uc002klz.2	+	3	1290	c.903G>T	c.(901-903)GTG>GTT	p.V301V	TGIF1_uc002klu.2_Silent_p.V152V|TGIF1_uc002klv.2_Silent_p.V186V|TGIF1_uc002klx.2_Silent_p.V152V|TGIF1_uc002klw.2_Silent_p.V172V|TGIF1_uc002kly.2_Silent_p.V172V|TGIF1_uc002kma.2_Silent_p.V152V|TGIF1_uc002kmb.2_Silent_p.V152V|TGIF1_uc002kmc.2_Silent_p.V152V	NM_170695	NP_733796	Q15583	TGIF1_HUMAN	TG-interacting factor isoform a	301					negative regulation of transcription from RNA polymerase II promoter	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity			ovary(1)	1	Esophageal squamous(4;0.0859)	Colorectal(8;0.0104)				GTCCATCAGTGATCTGCCATA	0.537													7	105	---	---	---	---	PASS
ARHGAP28	79822	broad.mit.edu	37	18	6898615	6898615	+	Intron	SNP	G	T	T			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:6898615G>T	uc010wzi.1	+						ARHGAP28_uc002knc.2_3'UTR|ARHGAP28_uc002knd.2_3'UTR|ARHGAP28_uc002kne.2_Intron|ARHGAP28_uc002knf.2_3'UTR			B4DXL2	B4DXL2_HUMAN	SubName: Full=Putative uncharacterized protein ARHGAP28;						signal transduction	intracellular				pancreas(1)	1		Colorectal(10;0.168)				AGGGATTTGGGTATCCAGTAG	0.363													8	161	---	---	---	---	PASS
ADAMTSL5	339366	broad.mit.edu	37	19	1508527	1508527	+	Missense_Mutation	SNP	G	A	A			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1508527G>A	uc002ltd.2	-	6	848	c.404C>T	c.(403-405)GCC>GTC	p.A135V	ADAMTSL5_uc010dsl.2_5'UTR|ADAMTSL5_uc010xgq.1_Missense_Mutation_p.A145V	NM_213604	NP_998769	Q6ZMM2	ATL5_HUMAN	ADAMTS-like 5 precursor	135						proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding				0		Acute lymphoblastic leukemia(61;5.61e-13)|all_hematologic(61;2.65e-08)		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)		GTGGTAGAAGGCGTGCCCCTC	0.701													3	9	---	---	---	---	PASS
OR1I1	126370	broad.mit.edu	37	19	15198108	15198108	+	Missense_Mutation	SNP	G	A	A	rs146090785	byFrequency	TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15198108G>A	uc010xoe.1	+	1	232	c.232G>A	c.(232-234)GTC>ATC	p.V78I		NM_001004713	NP_001004713	O60431	OR1I1_HUMAN	olfactory receptor, family 1, subfamily I,	78	Helical; Name=2; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|kidney(1)	3						CTCCACCACCGTCCCCAAGAT	0.542													10	55	---	---	---	---	PASS
ZNF761	388561	broad.mit.edu	37	19	53945909	53945909	+	Intron	SNP	T	C	C	rs28727441	by1000genomes	TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53945909T>C	uc010eqp.2	+						LOC147804_uc002qbo.2_RNA|LOC147804_uc002qbq.2_RNA|LOC147804_uc002qbp.2_RNA|ZNF761_uc002qbr.2_Intron|ZNF761_uc010ydy.1_5'Flank	NM_001008401	NP_001008401	Q86XN6	ZN761_HUMAN	zinc finger protein 761						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1				GBM - Glioblastoma multiforme(134;0.00786)		ACCCTGACTCTGCCTGAGGCC	0.562													4	60	---	---	---	---	PASS
NLRP7	199713	broad.mit.edu	37	19	55451743	55451743	+	Silent	SNP	G	A	A			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55451743G>A	uc002qih.3	-	4	520	c.444C>T	c.(442-444)GAC>GAT	p.D148D	NLRP7_uc002qig.3_Silent_p.D148D|NLRP7_uc002qii.3_Silent_p.D148D|NLRP7_uc010esk.2_Silent_p.D148D|NLRP7_uc010esl.2_Silent_p.D176D	NM_206828	NP_996611	Q8WX94	NALP7_HUMAN	NACHT, leucine rich repeat and PYD containing 7	148							ATP binding			large_intestine(1)|breast(1)|central_nervous_system(1)	3				GBM - Glioblastoma multiforme(193;0.0325)		GAGTGACGTCGTCATGGAAAT	0.493													136	500	---	---	---	---	PASS
GRIK1	2897	broad.mit.edu	37	21	30961307	30961307	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:30961307C>T	uc002yno.1	-	11	1885	c.1421G>A	c.(1420-1422)AGA>AAA	p.R474K	GRIK1_uc002ynn.2_Missense_Mutation_p.R459K|GRIK1_uc011acs.1_Missense_Mutation_p.R474K|GRIK1_uc011act.1_Intron|GRIK1_uc010glq.1_Missense_Mutation_p.R317K	NM_000830	NP_000821	P39086	GRIK1_HUMAN	glutamate receptor, ionotropic, kainate 1	474	Extracellular (Potential).				central nervous system development|synaptic transmission	cell junction|postsynaptic membrane	kainate selective glutamate receptor activity			large_intestine(1)|ovary(1)|skin(1)	3					L-Glutamic Acid(DB00142)|Topiramate(DB00273)	TCCTTCAAATCTGTCATTTCC	0.368													52	204	---	---	---	---	PASS
DERL3	91319	broad.mit.edu	37	22	24179339	24179339	+	Missense_Mutation	SNP	T	C	C			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24179339T>C	uc002zyh.2	-	6	551	c.526A>G	c.(526-528)ATT>GTT	p.I176V	DERL3_uc002zyk.3_Missense_Mutation_p.I176V|DERL3_uc002zyi.2_Missense_Mutation_p.I176V|DERL3_uc002zyj.2_Missense_Mutation_p.D132G	NM_001002862	NP_001002862	Q96Q80	DERL3_HUMAN	derlin 3 isoform 2	176	Helical; Name=4; (Potential).				endoplasmic reticulum unfolded protein response|ER-associated protein catabolic process	integral to endoplasmic reticulum membrane	protein binding			ovary(1)	1						CCCACCGCAATCCCTGTGAGA	0.632													15	46	---	---	---	---	PASS
MID1	4281	broad.mit.edu	37	X	10437719	10437719	+	Intron	SNP	A	C	C			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:10437719A>C	uc004cte.3	-						MID1_uc004ctd.3_Intron|MID1_uc004ctg.3_Intron|MID1_uc004cth.3_Intron|MID1_uc004ctk.3_Intron|MID1_uc004cti.3_Intron|MID1_uc004ctj.3_Intron|MID1_uc011mie.1_Intron|MID1_uc004ctm.1_Missense_Mutation_p.Y486D|MID1_uc004ctn.1_Missense_Mutation_p.Y435D|MID1_uc004cto.1_Missense_Mutation_p.Y397D|MID1_uc004csz.3_Intron|MID1_uc004cta.3_Intron|MID1_uc004ctb.3_Intron|MID1_uc004ctc.3_Intron|MID1_uc004ctl.1_Missense_Mutation_p.Y191D	NM_033290	NP_150632	O15344	TRI18_HUMAN	midline 1						microtubule cytoskeleton organization|pattern specification process|positive regulation of stress-activated MAPK cascade	cytoplasm|microtubule|microtubule associated complex|spindle	ligase activity|ubiquitin protein ligase binding|zinc ion binding			ovary(2)|pancreas(1)	3						AGAAATAAATAGGCCATGAGA	0.423													42	197	---	---	---	---	PASS
FAM47B	170062	broad.mit.edu	37	X	34962088	34962088	+	Silent	SNP	C	T	T			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:34962088C>T	uc004ddi.1	+	1	1158	c.1140C>T	c.(1138-1140)TAC>TAT	p.Y380Y		NM_152631	NP_689844	Q8NA70	FA47B_HUMAN	hypothetical protein LOC170062	380										ovary(3)|breast(1)	4						CTGGTAAATACCATTTTTGGG	0.552													35	69	---	---	---	---	PASS
TAF1	6872	broad.mit.edu	37	X	70643015	70643015	+	Missense_Mutation	SNP	G	T	T			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:70643015G>T	uc004dzu.3	+	30	4549	c.4498G>T	c.(4498-4500)GAT>TAT	p.D1500Y	BCYRN1_uc011mpt.1_Intron|TAF1_uc004dzt.3_Missense_Mutation_p.D1521Y|TAF1_uc004dzv.3_Missense_Mutation_p.D674Y|TAF1_uc010nld.1_RNA|TAF1_uc010nle.1_RNA|TAF1_uc010nlf.1_5'UTR|TAF1_uc004dzx.2_RNA|TAF1_uc004dzy.2_RNA|TAF1_uc004dzw.1_RNA	NM_138923	NP_620278	P21675	TAF1_HUMAN	TBP-associated factor 1 isoform 2	1500	Interaction with ASF1A and ASF1B.|Protein kinase 2.				G1 phase of mitotic cell cycle|interspecies interaction between organisms|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription initiation from RNA polymerase II promoter|protein autophosphorylation|regulation of transcription involved in G2/M-phase of mitotic cell cycle|RNA polymerase II transcriptional preinitiation complex assembly|transcription elongation from RNA polymerase II promoter|viral reproduction	MLL1 complex|transcription factor TFIID complex	ATP binding|histone acetyl-lysine binding|histone acetyltransferase activity|p53 binding|protein binding|protein serine/threonine kinase activity|sequence-specific DNA binding|TBP-class protein binding|transcription coactivator activity			ovary(7)|breast(4)|large_intestine(2)|central_nervous_system(2)|lung(1)|skin(1)	17	Renal(35;0.156)	all_lung(315;0.000321)				CCCCTTGCTGGATGATGATGA	0.423													45	161	---	---	---	---	PASS
TAF9B	51616	broad.mit.edu	37	X	77393317	77393317	+	Nonsense_Mutation	SNP	C	A	A			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:77393317C>A	uc004eda.2	-	4	405	c.334G>T	c.(334-336)GGA>TGA	p.G112*		NM_015975	NP_057059	Q9HBM6	TAF9B_HUMAN	transcription associated factor 9B	112					negative regulation of apoptosis|negative regulation of transcription from RNA polymerase II promoter|positive regulation of cell growth|transcription initiation, DNA-dependent	transcription factor TFIID complex|transcription factor TFTC complex	DNA binding|protein binding				0						AGTCTAGGTCCTGCATATGGC	0.338													5	192	---	---	---	---	PASS
CT47B1	643311	broad.mit.edu	37	X	120009353	120009353	+	Missense_Mutation	SNP	C	G	G			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:120009353C>G	uc011muc.1	-	1	427	c.172G>C	c.(172-174)GTG>CTG	p.V58L		NM_001145718	NP_001139190	P0C2W7	CT47B_HUMAN	cancer/testis antigen family 147, member B1	58											0						AGGCCTTCCACGGGCCCTGCG	0.751													20	94	---	---	---	---	PASS
AFF2	2334	broad.mit.edu	37	X	147582558	147582558	+	5'UTR	SNP	G	T	T			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:147582558G>T	uc004fcp.2	+	1					AFF2_uc004fco.2_5'UTR|AFF2_uc004fcq.2_5'UTR|AFF2_uc004fcr.2_5'UTR|AFF2_uc011mxb.1_5'UTR|AFF2_uc004fcs.2_5'UTR	NM_002025	NP_002016	P51816	AFF2_HUMAN	fragile X mental retardation 2						brain development|mRNA processing|regulation of RNA splicing|RNA splicing	nuclear speck	G-quadruplex RNA binding|protein binding			ovary(3)|pancreas(2)	5	Acute lymphoblastic leukemia(192;6.56e-05)					TGTGCCGAGAGCCGCGCCGAC	0.597													8	22	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	345	345	+	RNA	SNP	C	A	A			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:345C>A	uc004coq.3	-	1		c.22G>T			uc004cor.1_5'Flank|uc004cos.3_5'Flank					Homo sapiens cDNA: FLJ22857 fis, clone KAT01615.																		TTAAACACATCTCTGCCAAAC	0.463													26	37	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	14178	14178	+	RNA	SNP	T	C	C			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:14178T>C	uc004cox.3	+	1		c.1842T>C			uc004coy.2_5'Flank|uc004coz.1_5'Flank					Homo sapiens NADH dehydrogenase subunit 5 (MTND5) mRNA, RNA 5, complete cds; mitochondrial gene for mitochondrial product.																		CTCAATTACAATATATACACC	0.413													10	138	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	1	10177	10178	+	5'Flank	INS	-	C	C			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:10177_10178insC	uc001aaa.3	+						uc010nxq.1_5'Flank|uc010nxr.1_5'Flank					Homo sapiens mRNA for DEAD/H box polypeptide 11 like 1 (DDX11L1 gene).																		cctaaccctaacctaaccctaa	0.000													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	142823571	142823572	+	Intron	INS	-	TT	TT	rs141432767		TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:142823571_142823572insTT	uc001eiw.1	+						uc001ejb.2_Intron|uc001ejd.1_Intron|uc001ejc.2_Intron					Homo sapiens PNAS-130 mRNA, complete cds.																		GCCTATAGCAGttttttttttt	0.198													4	2	---	---	---	---	
S100A10	6281	broad.mit.edu	37	1	151955954	151955955	+	Intron	INS	-	T	T			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151955954_151955955insT	uc001ezl.2	-							NM_002966	NP_002957	P60903	S10AA_HUMAN	S100 calcium binding protein A10						signal transduction		calcium ion binding|receptor binding				0	Melanoma(130;0.0648)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.246)			ATCTAAATGTATTTTTTTTTTT	0.332													9	4	---	---	---	---	
TNN	63923	broad.mit.edu	37	1	175049103	175049104	+	Intron	INS	-	GT	GT	rs142891850	by1000genomes	TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:175049103_175049104insGT	uc001gkl.1	+						TNN_uc010pmx.1_Intron	NM_022093	NP_071376	Q9UQP3	TENN_HUMAN	tenascin N precursor						cell growth|cell migration|signal transduction	extracellular space|proteinaceous extracellular matrix				large_intestine(5)|ovary(3)|central_nervous_system(1)	9		Breast(1374;0.000962)		KIRC - Kidney renal clear cell carcinoma(1967;0.00198)		GCtgtgtgtgagtgtgtgtgtg	0.248													4	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	64603286	64603288	+	IGR	DEL	CAC	-	-	rs141929982		TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:64603286_64603288delCAC								PELI1 (231681 upstream) : HSPC159 (78039 downstream)																							ccaccaccatcaccaccatcacc	0.000													4	3	---	---	---	---	
PTCD3	55037	broad.mit.edu	37	2	86335250	86335250	+	Intron	DEL	A	-	-			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:86335250delA	uc002sqw.2	+						POLR1A_uc002sqs.2_5'Flank|POLR1A_uc002sqv.2_5'Flank|PTCD3_uc010ytc.1_Intron	NM_017952	NP_060422	Q96EY7	PTCD3_HUMAN	pentatricopeptide repeat domain 3 precursor							mitochondrion	protein binding			ovary(1)	1						ccctgtctctaaaaaaaaaaa	0.154													15	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	91797814	91797814	+	IGR	DEL	G	-	-	rs113127218		TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:91797814delG								None (None upstream) : LOC654342 (7378 downstream)																							tctgcctcccgggggtcacac	0.020													4	2	---	---	---	---	
REV1	51455	broad.mit.edu	37	2	100058707	100058708	+	Intron	INS	-	C	C			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:100058707_100058708insC	uc002tad.2	-						REV1_uc002tac.2_Intron|REV1_uc002tae.1_Intron	NM_016316	NP_057400	Q9UBZ9	REV1_HUMAN	REV1-like isoform 1						DNA replication|error-prone translesion synthesis|response to UV	nucleoplasm	damaged DNA binding|DNA-directed DNA polymerase activity|magnesium ion binding|protein binding			ovary(2)	2						agagcaaaactccatctcaaaa	0.153								DNA_polymerases_(catalytic_subunits)|Direct_reversal_of_damage					18	8	---	---	---	---	
BOLL	66037	broad.mit.edu	37	2	198643530	198643531	+	Intron	DEL	AC	-	-	rs140189200		TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:198643530_198643531delAC	uc002uus.2	-						BOLL_uc002uur.2_Intron|BOLL_uc002uut.2_Intron|BOLL_uc010zha.1_Intron|BOLL_uc002uuu.1_Intron	NM_033030	NP_149019	Q8N9W6	BOLL_HUMAN	boule isoform 2						cell differentiation|meiosis|multicellular organismal development|positive regulation of translational initiation|spermatogenesis	cytoplasm	nucleotide binding|protein binding|RNA binding|translation activator activity			ovary(2)	2						CCTCCAAAATacacacacacac	0.371													5	3	---	---	---	---	
DNER	92737	broad.mit.edu	37	2	230305880	230305882	+	Intron	DEL	CTC	-	-			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:230305880_230305882delCTC	uc002vpv.2	-							NM_139072	NP_620711	Q8NFT8	DNER_HUMAN	delta-notch-like EGF repeat-containing						central nervous system development|endocytosis|neuron migration|Notch signaling pathway|synapse assembly	dendrite|early endosome|integral to membrane|plasma membrane	calcium ion binding|clathrin binding|transmembrane receptor activity			lung(5)|ovary(2)|skin(1)	8		all_lung(227;0.00413)|Renal(207;0.0113)|Lung NSC(271;0.0211)|all_hematologic(139;0.105)|Acute lymphoblastic leukemia(138;0.175)		Epithelial(121;1.4e-11)|all cancers(144;7.7e-09)|LUSC - Lung squamous cell carcinoma(224;0.034)|Lung(119;0.0375)		CTTCTTTGAACTCCTCCCCCATG	0.424													4	2	---	---	---	---	
FANCD2	2177	broad.mit.edu	37	3	10089935	10089936	+	Intron	DEL	TC	-	-			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10089935_10089936delTC	uc003buw.2	+						FANCD2_uc003bux.1_Intron|FANCD2_uc003buy.1_Intron|FANCD2_uc010hcw.1_5'Flank	NM_033084	NP_149075	Q9BXW9	FACD2_HUMAN	Fanconi anemia complementation group D2 isoform						DNA repair|response to gamma radiation	nucleoplasm	protein binding|protein binding			central_nervous_system(2)|ovary(1)|skin(1)	4				OV - Ovarian serous cystadenocarcinoma(96;0.148)		GCTCTAAAATTCTCTGTCTGAA	0.322			D|Mis|N|F			AML|leukemia		Involved_in_tolerance_or_repair_of_DNA_crosslinks	Fanconi_Anemia				4	4	---	---	---	---	
PPM1L	151742	broad.mit.edu	37	3	160672742	160672744	+	Intron	DEL	TCC	-	-	rs72365532	by1000genomes	TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:160672742_160672744delTCC	uc003fdr.2	+						PPM1L_uc003fds.2_Intron|PPM1L_uc003fdt.2_Intron|PPM1L_uc010hwf.2_Intron	NM_139245	NP_640338	Q5SGD2	PPM1L_HUMAN	protein phosphatase 1 (formerly 2C)-like						protein dephosphorylation|sphingolipid metabolic process	endoplasmic reticulum membrane|integral to membrane|protein serine/threonine phosphatase complex	metal ion binding|protein serine/threonine phosphatase activity			breast(1)	1			Lung(72;0.00149)|LUSC - Lung squamous cell carcinoma(72;0.00216)			cttccttccttccttcctttcct	0.020													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	167606205	167606205	+	IGR	DEL	T	-	-			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:167606205delT								SERPINI1 (62849 upstream) : GOLIM4 (121449 downstream)																							GACCTGAAGGTTTTGCTATAG	0.348													20	11	---	---	---	---	
SORCS2	57537	broad.mit.edu	37	4	7726316	7726317	+	Intron	INS	-	GAG	GAG			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:7726316_7726317insGAG	uc003gkb.3	+						SORCS2_uc011bwi.1_Intron	NM_020777	NP_065828	Q96PQ0	SORC2_HUMAN	VPS10 domain receptor protein SORCS 2 precursor							integral to membrane	neuropeptide receptor activity			ovary(1)|central_nervous_system(1)	2						atggtggtggtgttggtgatgg	0.000													3	3	---	---	---	---	
CHIC2	26511	broad.mit.edu	37	4	54876132	54876132	+	3'UTR	DEL	C	-	-	rs68107873		TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:54876132delC	uc003haj.1	-	6					PDGFRA_uc003haa.2_Intron	NM_012110	NP_036242	Q9UKJ5	CHIC2_HUMAN	cysteine-rich hydrophobic domain 2							plasma membrane	protein binding			central_nervous_system(1)	1	all_cancers(7;0.0193)|all_neural(26;0.0209)|Lung NSC(11;0.0281)|Glioma(25;0.08)		LUSC - Lung squamous cell carcinoma(32;0.00216)			aaaaaaaaaacaaaaacaaaa	0.323			T	ETV6	AML								8	4	---	---	---	---	
POLR2B	5431	broad.mit.edu	37	4	57889308	57889309	+	Intron	INS	-	T	T			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:57889308_57889309insT	uc003hcl.1	+						POLR2B_uc011cae.1_Intron|POLR2B_uc011caf.1_Intron|POLR2B_uc003hcm.1_Intron	NM_000938	NP_000929	P30876	RPB2_HUMAN	DNA directed RNA polymerase II polypeptide B						mRNA capping|nuclear mRNA splicing, via spliceosome|positive regulation of viral transcription|protein phosphorylation|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair|viral reproduction	DNA-directed RNA polymerase II, core complex	DNA binding|DNA-directed RNA polymerase activity|metal ion binding|protein binding|ribonucleoside binding			ovary(2)	2	Glioma(25;0.08)|all_neural(26;0.181)					CCTTCATAGACTTTTTTTTTTG	0.366													4	2	---	---	---	---	
ADAMTS16	170690	broad.mit.edu	37	5	5305376	5305377	+	Intron	INS	-	CAC	CAC			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:5305376_5305377insCAC	uc003jdl.2	+							NM_139056	NP_620687	Q8TE57	ATS16_HUMAN	ADAM metallopeptidase with thrombospondin type 1						proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(3)|lung(2)|large_intestine(1)|breast(1)|pancreas(1)	8						ccacacacacaatcccacacca	0.000													4	2	---	---	---	---	
HMGCR	3156	broad.mit.edu	37	5	74639545	74639549	+	Intron	DEL	TTGTA	-	-	rs3064191		TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:74639545_74639549delTTGTA	uc003kdp.2	+						HMGCR_uc011cst.1_Intron|HMGCR_uc003kdq.2_Intron|HMGCR_uc010izn.1_5'Flank	NM_000859	NP_000850	P04035	HMDH_HUMAN	3-hydroxy-3-methylglutaryl-Coenzyme A reductase						cholesterol biosynthetic process|coenzyme A metabolic process|germ cell migration|gonad development|isoprenoid biosynthetic process	endoplasmic reticulum membrane|integral to membrane|peroxisomal membrane	hydroxymethylglutaryl-CoA reductase (NADPH) activity|NADP binding			ovary(1)	1		all_lung(232;0.00101)|Lung NSC(167;0.00278)|Ovarian(174;0.0129)|Prostate(461;0.174)		OV - Ovarian serous cystadenocarcinoma(47;2.24e-54)	Atorvastatin(DB01076)|Bezafibrate(DB01393)|Cerivastatin(DB00439)|Fluvastatin(DB01095)|Lovastatin(DB00227)|NADH(DB00157)|Pravastatin(DB00175)|Rosuvastatin(DB01098)|Simvastatin(DB00641)	TTTATTGGACTTGTATTGTGCTTAC	0.244													8	4	---	---	---	---	
ERAP1	51752	broad.mit.edu	37	5	96117713	96117717	+	Intron	DEL	TTTTT	-	-	rs142478570		TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:96117713_96117717delTTTTT	uc003kmm.2	-						ERAP1_uc003kml.2_Intron|ERAP1_uc010jbm.1_Intron|ERAP1_uc003kmn.2_Intron	NM_001040458	NP_001035548	Q9NZ08	ERAP1_HUMAN	type 1 tumor necrosis factor receptor shedding						angiogenesis|antigen processing and presentation of endogenous peptide antigen via MHC class I|fat cell differentiation|membrane protein ectodomain proteolysis|regulation of blood pressure|regulation of innate immune response|response to bacterium	cytosol|endoplasmic reticulum lumen|endoplasmic reticulum membrane|extracellular region|integral to membrane	aminopeptidase activity|interleukin-1, Type II receptor binding|interleukin-6 receptor binding|metalloexopeptidase activity|zinc ion binding			ovary(1)|pancreas(1)	2		all_cancers(142;1.75e-06)|all_epithelial(76;3.08e-09)|all_lung(232;0.000435)|Lung NSC(167;0.000601)|Ovarian(225;0.024)|Colorectal(57;0.0432)|Breast(839;0.244)		all cancers(79;7.26e-15)|COAD - Colon adenocarcinoma(37;0.071)		TCAGTTACAAttttttttttttttt	0.185													4	2	---	---	---	---	
DCP2	167227	broad.mit.edu	37	5	112336653	112336678	+	Intron	DEL	GTCATTTCTAGAAATAGTAAATACAA	-	-			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:112336653_112336678delGTCATTTCTAGAAATAGTAAATACAA	uc003kqh.2	+						DCP2_uc011cwa.1_Intron|DCP2_uc010jcc.2_Intron	NM_152624	NP_689837	Q8IU60	DCP2_HUMAN	DCP2 decapping enzyme						exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay|histone mRNA catabolic process|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	cytoplasmic mRNA processing body|cytosol|nucleus|RNA-induced silencing complex	exoribonuclease activity, producing 5'-phosphomonoesters|manganese ion binding|protein binding|protein binding|RNA binding				0		all_cancers(142;4.41e-05)|all_epithelial(76;3.65e-07)|Colorectal(10;0.00115)|Prostate(80;0.00133)|Ovarian(225;0.0443)		OV - Ovarian serous cystadenocarcinoma(64;6.98e-08)|Epithelial(69;7.87e-08)|all cancers(49;1.06e-05)|COAD - Colon adenocarcinoma(37;0.0123)|Colorectal(14;0.0171)		GTACCAGCCTGTCATTTCTAGAAATAGTAAATACAAGTCATGTCCC	0.336													5	4	---	---	---	---	
FBN2	2201	broad.mit.edu	37	5	127680393	127680393	+	Intron	DEL	T	-	-			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:127680393delT	uc003kuu.2	-						FBN2_uc003kuv.2_Intron	NM_001999	NP_001990	P35556	FBN2_HUMAN	fibrillin 2 precursor						bone trabecula formation|negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta|positive regulation of bone mineralization|positive regulation of osteoblast differentiation	microfibril	calcium ion binding|extracellular matrix structural constituent			ovary(8)|large_intestine(4)|pancreas(1)|kidney(1)|skin(1)	15		all_cancers(142;0.0216)|Prostate(80;0.0551)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0821)|Epithelial(69;0.146)		TCTTATAttcttttttttttt	0.164													4	2	---	---	---	---	
LSM11	134353	broad.mit.edu	37	5	157181722	157181722	+	Intron	DEL	G	-	-			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:157181722delG	uc003lxe.1	+						LSM11_uc003lxf.1_5'Flank	NM_173491	NP_775762	P83369	LSM11_HUMAN	LSM11, U7 small nuclear RNA associated						histone mRNA 3'-end processing|S phase of mitotic cell cycle|termination of RNA polymerase II transcription	histone pre-mRNA 3'end processing complex|nucleoplasm|U7 snRNP	protein binding|U7 snRNA binding				0	Renal(175;0.00488)	Medulloblastoma(196;0.0523)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			aaaaaaaaaaGATTTATTACT	0.159													4	2	---	---	---	---	
GABRB2	2561	broad.mit.edu	37	5	160921545	160921546	+	Intron	DEL	GT	-	-	rs72209597		TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:160921545_160921546delGT	uc003lys.1	-						GABRB2_uc011deh.1_Intron|GABRB2_uc003lyr.1_Intron|GABRB2_uc003lyt.1_Intron|GABRB2_uc010jiu.1_Intron|GABRB2_uc011dei.1_Intron	NM_021911	NP_068711	P47870	GBRB2_HUMAN	gamma-aminobutyric acid (GABA) A receptor, beta						gamma-aminobutyric acid signaling pathway|synaptic transmission	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	chloride channel activity|GABA-A receptor activity				0	Renal(175;0.00259)	Medulloblastoma(196;0.021)|all_neural(177;0.0463)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)		Ethchlorvynol(DB00189)|Flurazepam(DB00690)|Lorazepam(DB00186)|Midazolam(DB00683)	TTAGgtatgcgtgtgtgtgtgt	0.228													4	2	---	---	---	---	
SRPK1	6732	broad.mit.edu	37	6	35810503	35810504	+	Intron	DEL	TA	-	-	rs3213580	by1000genomes	TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:35810503_35810504delTA	uc003olj.2	-						SRPK1_uc011dtg.1_Intron|SRPK1_uc003olh.2_Intron|SRPK1_uc003oli.2_Intron	NM_003137	NP_003128	Q96SB4	SRPK1_HUMAN	SFRS protein kinase 1						cell differentiation|chromosome segregation|interspecies interaction between organisms|intracellular protein kinase cascade|mRNA processing|negative regulation of viral genome replication|positive regulation of viral genome replication|regulation of mRNA processing|RNA splicing	cytoplasm|nucleus	ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity			ovary(1)	1						ATAGATCATTTAAAAAAAAAAA	0.307													3	3	---	---	---	---	
PKHD1	5314	broad.mit.edu	37	6	51946933	51946933	+	Intron	DEL	A	-	-			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:51946933delA	uc003pah.1	-						PKHD1_uc003pai.2_Intron	NM_138694	NP_619639	P08F94	PKHD1_HUMAN	fibrocystin isoform 1						cell-cell adhesion|cilium assembly|homeostatic process|kidney development|negative regulation of cellular component movement	anchored to external side of plasma membrane|apical plasma membrane|integral to membrane|microtubule basal body	protein binding|receptor activity			lung(15)|ovary(15)|large_intestine(5)|central_nervous_system(3)|skin(3)|breast(2)|upper_aerodigestive_tract(1)	44	Lung NSC(77;0.0605)					AACTCTTTGCAAAAAAAAACA	0.368													3	6	---	---	---	---	
PPIL4	85313	broad.mit.edu	37	6	149847587	149847588	+	Intron	DEL	TG	-	-			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:149847587_149847588delTG	uc003qmo.1	-						PPIL4_uc010kic.2_Intron|PPIL4_uc003qmp.1_Intron	NM_139126	NP_624311	Q8WUA2	PPIL4_HUMAN	peptidylprolyl isomerase-like 4						protein folding	nucleus	nucleotide binding|peptidyl-prolyl cis-trans isomerase activity|RNA binding				0		Ovarian(120;0.0164)		OV - Ovarian serous cystadenocarcinoma(155;1.11e-11)|GBM - Glioblastoma multiforme(68;0.0885)		ATTATTTATCtgtgtgtgtgtg	0.262													4	3	---	---	---	---	
OPRM1	4988	broad.mit.edu	37	6	154420428	154420443	+	Intron	DEL	AAGGAAGGAAGGAAGA	-	-	rs150542233	by1000genomes	TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:154420428_154420443delAAGGAAGGAAGGAAGA	uc003qpr.2	+						OPRM1_uc011efc.1_Intron|OPRM1_uc011efd.1_Intron|OPRM1_uc011efe.1_Intron|OPRM1_uc011eff.1_Intron|OPRM1_uc011efg.1_Intron|OPRM1_uc011efh.1_Intron|OPRM1_uc003qpq.1_Intron|OPRM1_uc003qpt.1_Intron|OPRM1_uc011efi.1_Intron|OPRM1_uc003qpp.2_Intron|OPRM1_uc003qps.2_Intron|OPRM1_uc010kjg.2_Intron	NM_000914	NP_000905	P35372	OPRM_HUMAN	opioid receptor, mu 1 isoform MOR-1						behavior|negative regulation of cell proliferation|sensory perception	endoplasmic reticulum|Golgi apparatus|integral to plasma membrane	mu-opioid receptor activity|protein binding			ovary(1)	1		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;9.26e-11)|BRCA - Breast invasive adenocarcinoma(81;0.0154)	Alfentanil(DB00802)|Anileridine(DB00913)|Buprenorphine(DB00921)|Butorphanol(DB00611)|Codeine(DB00318)|Dezocine(DB01209)|Diphenoxylate(DB01081)|Fentanyl(DB00813)|Hydrocodone(DB00956)|Hydromorphone(DB00327)|Levallorphan(DB00504)|Levomethadyl Acetate(DB01227)|Levorphanol(DB00854)|Loperamide(DB00836)|Methadone(DB00333)|Methadyl Acetate(DB01433)|Morphine(DB00295)|Nalbuphine(DB00844)|Naloxone(DB01183)|Naltrexone(DB00704)|Oxycodone(DB00497)|Oxymorphone(DB01192)|Pentazocine(DB00652)|Propoxyphene(DB00647)|Remifentanil(DB00899)|Sufentanil(DB00708)|Tramadol(DB00193)	GAaaggaaggaaggaaggaaggaagaaaggaaggaa	0.023													4	3	---	---	---	---	
C7orf28A	51622	broad.mit.edu	37	7	5941115	5941116	+	Intron	INS	-	A	A	rs67969436		TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:5941115_5941116insA	uc003spf.2	+							NM_015622	NP_056437	P86791	CCZ1_HUMAN	hypothetical protein LOC51622							lysosomal membrane					0		Ovarian(82;0.0694)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0974)|OV - Ovarian serous cystadenocarcinoma(56;7.91e-15)		gactccatctcaaaaaaaaaaa	0.149													4	2	---	---	---	---	
MACC1	346389	broad.mit.edu	37	7	20229372	20229373	+	Intron	DEL	AA	-	-	rs72309121		TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:20229372_20229373delAA	uc003sus.3	-						MACC1_uc010kug.2_Intron	NM_182762	NP_877439	Q6ZN28	MACC1_HUMAN	putative binding protein 7a5						positive regulation of cell division|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus|plasma membrane	growth factor activity			ovary(2)|skin(1)	3						acaaacacataaacacacacac	0.163													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	66318329	66318330	+	IGR	INS	-	GT	GT	rs111249198		TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:66318329_66318330insGT								LOC729156 (8516 upstream) : C7orf42 (67873 downstream)																							tgggattacaggtgagcgatca	0.139													3	4	---	---	---	---	
STAG3L2	442582	broad.mit.edu	37	7	74306378	74306378	+	Intron	DEL	C	-	-			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:74306378delC	uc003ubj.3	-						PMS2L5_uc003ubl.2_5'Flank|PMS2L5_uc003ubk.2_5'Flank|PMS2L5_uc010lbw.2_5'Flank|PMS2L5_uc003ubm.3_5'Flank|STAG3L2_uc011kfj.1_5'Flank	NM_001025202	NP_001020373	P0CL84	ST3L2_HUMAN	STAG3-like							nucleus	binding				0						GGGCGGGGGGCCCCGCGCTCC	0.731													6	3	---	---	---	---	
PMS2L3	5387	broad.mit.edu	37	7	75145720	75145721	+	Intron	DEL	AT	-	-			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:75145720_75145721delAT	uc003udp.2	-						PMS2L3_uc003udn.2_Intron|PMS2L3_uc003udq.2_Intron|PMS2L3_uc003udr.1_Intron	NM_005395	NP_005386			SubName: Full=Postmeiotic segregation increased 2-like 3; SubName: Full=Postmeiotic segregation increased 2-like 3, isoform CRA_b;												0						TCCTTTGGGGatatatatatat	0.193								Direct_reversal_of_damage|MMR					5	3	---	---	---	---	
LOC100132832	100132832	broad.mit.edu	37	7	76669648	76669649	+	Intron	INS	-	ATCTC	ATCTC			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:76669648_76669649insATCTC	uc003ufy.2	+						PMS2L11_uc011kgn.1_Intron	NR_028058				Homo sapiens cDNA FLJ59034 complete cds, moderately similar to Protein deltex-2.												0						TGCACAGAAATATTTAATTTGC	0.208													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	102021199	102021199	+	Intron	DEL	A	-	-			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:102021199delA	uc003uzd.1	+						uc003uze.1_Intron|PRKRIP1_uc003uzf.2_Intron|PRKRIP1_uc003uzg.2_Intron|PRKRIP1_uc011kkq.1_Intron	NM_001003686	NP_001003686			SubName: Full=Putative uncharacterized protein PMS2L3;																		TTTTTCCCTTAAAAAAAAAAA	0.358													4	2	---	---	---	---	
LRGUK	136332	broad.mit.edu	37	7	133859563	133859563	+	Intron	DEL	T	-	-			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:133859563delT	uc003vrm.1	+							NM_144648	NP_653249	Q96M69	LRGUK_HUMAN	leucine-rich repeats and guanylate kinase domain								ATP binding|kinase activity			lung(2)|skin(2)|kidney(1)	5						AAAGTGACAATTTTTTTTTTA	0.343													5	3	---	---	---	---	
CSGALNACT1	55790	broad.mit.edu	37	8	19315383	19315383	+	Intron	DEL	A	-	-			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:19315383delA	uc011kyn.1	-						CSGALNACT1_uc011kyo.1_Intron|CSGALNACT1_uc003wzg.2_Intron|CSGALNACT1_uc011kyp.1_Intron|CSGALNACT1_uc003wzh.2_Intron	NM_001130518	NP_001123990	Q8TDX6	CGAT1_HUMAN	chondroitin sulfate						anatomical structure morphogenesis|cell proliferation|cell recognition|chondroitin sulfate biosynthetic process|chondroitin sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process|dermatan sulfate proteoglycan biosynthetic process|extracellular matrix organization|heparan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process|heparin biosynthetic process|nervous system development|UDP-glucuronate metabolic process|UDP-N-acetylgalactosamine metabolic process	Golgi cisterna membrane|integral to Golgi membrane|soluble fraction	glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity|glucuronosyltransferase activity|glucuronylgalactosylproteoglycan 4-beta-N-acetylgalactosaminyltransferase activity|metal ion binding|peptidoglycan glycosyltransferase activity			central_nervous_system(2)|ovary(1)	3				Colorectal(111;0.182)		TGTGGGCTTGAAACCTTCTTG	0.383													9	4	---	---	---	---	
ANKRD46	157567	broad.mit.edu	37	8	101535131	101535136	+	Intron	DEL	ACATAT	-	-	rs147227610	by1000genomes	TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:101535131_101535136delACATAT	uc003yjm.2	-						ANKRD46_uc003yjn.1_Intron|ANKRD46_uc003yjo.1_Intron|ANKRD46_uc003yjp.1_Intron	NM_198401	NP_940683	Q86W74	ANR46_HUMAN	ankyrin repeat domain 46							integral to membrane					0	all_cancers(14;5.07e-05)|all_epithelial(15;2.84e-07)|Lung NSC(17;0.000353)|all_lung(17;0.000998)		Epithelial(11;2.61e-11)|all cancers(13;5.03e-09)|OV - Ovarian serous cystadenocarcinoma(57;4.49e-06)|STAD - Stomach adenocarcinoma(118;0.0957)			acacacacacacatatatatatatac	0.209													4	9	---	---	---	---	
KCNQ3	3786	broad.mit.edu	37	8	133221790	133221791	+	Intron	DEL	AA	-	-	rs35349516		TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:133221790_133221791delAA	uc003ytj.2	-						KCNQ3_uc010mdt.2_Intron	NM_004519	NP_004510	O43525	KCNQ3_HUMAN	potassium voltage-gated channel KQT-like protein						axon guidance|synaptic transmission	voltage-gated potassium channel complex	voltage-gated potassium channel activity			ovary(2)|breast(1)|central_nervous_system(1)|skin(1)	5	Esophageal squamous(12;0.00507)|Ovarian(258;0.00579)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000311)			acacacacacaaacacacacac	0.005													4	2	---	---	---	---	
VLDLR	7436	broad.mit.edu	37	9	2644148	2644150	+	Intron	DEL	TTG	-	-	rs143737273		TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:2644148_2644150delTTG	uc003zhk.1	+						VLDLR_uc003zhl.1_Intron|VLDLR_uc003zhm.1_Intron|VLDLR_uc003zhn.1_Intron	NM_003383	NP_003374	P98155	VLDLR_HUMAN	very low density lipoprotein receptor isoform a						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)		GTTTTTGTttttgttgttttttt	0.153													4	2	---	---	---	---	
MOBKL2B	79817	broad.mit.edu	37	9	27444291	27444302	+	Intron	DEL	AAGGAAGGAAGA	-	-	rs67293921	by1000genomes	TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:27444291_27444302delAAGGAAGGAAGA	uc003zqn.2	-							NM_024761	NP_079037	Q86TA1	MOL2B_HUMAN	MOB1, Mps One Binder kinase activator-like 2B								metal ion binding|protein binding			ovary(1)|pleura(1)	2		all_neural(11;9.12e-11)		Lung(218;6.54e-05)|LUSC - Lung squamous cell carcinoma(38;0.000397)		ggagggaaggaaggaaggaagaaaggaaggaa	0.142													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	66461548	66461549	+	Intron	INS	-	T	T	rs149299153		TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66461548_66461549insT	uc004aec.2	+											Homo sapiens, clone IMAGE:5213378, mRNA.																		agcttaaggagttttgggtcac	0.000													5	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	68413605	68413606	+	RNA	DEL	CT	-	-			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68413605_68413606delCT	uc004aex.2	+	1		c.160_161delCT								Homo sapiens mRNA; cDNA DKFZp564N0763 (from clone DKFZp564N0763).																		TTTGCTGAAACTCTGGGGTTGA	0.609													8	4	---	---	---	---	
MAMDC2	256691	broad.mit.edu	37	9	72659303	72659308	+	Intron	DEL	GGGGTG	-	-	rs10559392		TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:72659303_72659308delGGGGTG	uc004ahm.2	+						MAMDC2_uc004ahn.2_Intron	NM_153267	NP_694999	Q7Z304	MAMC2_HUMAN	MAM domain containing 2 precursor							endoplasmic reticulum|membrane				central_nervous_system(1)|pancreas(1)	2						GGCCAAGCCTggggtgggggtggggg	0.631													6	3	---	---	---	---	
GSN	2934	broad.mit.edu	37	9	124095004	124095004	+	3'UTR	DEL	T	-	-			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:124095004delT	uc004blf.1	+	17					GSN_uc004bld.1_3'UTR|GSN_uc010mvq.1_3'UTR|GSN_uc010mvr.1_3'UTR|GSN_uc010mvu.1_3'UTR|GSN_uc010mvt.1_3'UTR|GSN_uc010mvs.1_3'UTR|GSN_uc004ble.1_3'UTR|GSN_uc010mvv.1_3'UTR|GSN_uc011lyh.1_3'UTR|GSN_uc011lyi.1_3'UTR|GSN_uc011lyj.1_3'UTR	NM_000177	NP_000168	P06396	GELS_HUMAN	gelsolin isoform a precursor						actin filament polymerization|actin filament severing|barbed-end actin filament capping|cellular component disassembly involved in apoptosis|cilium morphogenesis	actin cytoskeleton|cytosol	actin binding|calcium ion binding|protein binding			breast(2)|ovary(1)	3						gtgtTGTTTCTTTTTTTTTTT	0.348													5	3	---	---	---	---	
DENND1A	57706	broad.mit.edu	37	9	126520256	126520256	+	Intron	DEL	A	-	-			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:126520256delA	uc004bnz.1	-						DENND1A_uc004bny.1_Intron|DENND1A_uc011lzm.1_Intron|DENND1A_uc004boa.1_Intron|DENND1A_uc004bob.1_Intron|DENND1A_uc004boc.2_Intron	NM_020946	NP_065997	Q8TEH3	DEN1A_HUMAN	DENN/MADD domain containing 1A isoform 1							cell junction|clathrin coated vesicle membrane|presynaptic membrane	guanyl-nucleotide exchange factor activity			ovary(2)	2						TAAGCTAGTTaaaaaaaaaaa	0.343													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	31435689	31435694	+	IGR	DEL	CACACG	-	-	rs151268729	by1000genomes	TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:31435689_31435694delCACACG								ZNF438 (114823 upstream) : LOC220930 (169764 downstream)																							TGCGCGTacacacacgcacacacaca	0.437													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	38816815	38816815	+	IGR	DEL	T	-	-	rs138443814		TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:38816815delT								LOC399744 (75735 upstream) : None (None downstream)																							tggaatggaatcgaatggtct	0.070													4	2	---	---	---	---	
PSAP	5660	broad.mit.edu	37	10	73583573	73583574	+	Intron	INS	-	A	A	rs68178384		TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:73583573_73583574insA	uc001jsm.2	-						PSAP_uc001jsl.2_5'Flank	NM_002778	NP_002769	P07602	SAP_HUMAN	prosaposin isoform a preproprotein						glycosphingolipid metabolic process|lipid transport|platelet activation|platelet degranulation	extracellular space|Golgi apparatus|integral to membrane|lysosomal lumen	enzyme activator activity|lipid binding			ovary(1)	1						ATGCCATACCCAAAAAAAAAAA	0.470													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	357020	357021	+	IGR	INS	-	CA	CA			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:357020_357021insCA								IFITM3 (36106 upstream) : B4GALNT4 (12774 downstream)																							cacaaacacaccacacacatca	0.000													4	2	---	---	---	---	
PRR5L	79899	broad.mit.edu	37	11	36331194	36331195	+	Intron	INS	-	G	G			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:36331194_36331195insG	uc001mwo.3	+							NM_001160167	NP_001153639	Q6MZQ0	PRR5L_HUMAN	protor-2 isoform a											ovary(1)	1						gtggtggtagtggggatgatga	0.257													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	62707534	62707535	+	IGR	DEL	GT	-	-			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62707534_62707535delGT								CHRM1 (18522 upstream) : SLC22A6 (36535 downstream)																							ggaattactggtgtgtgtgtgt	0.000													4	2	---	---	---	---	
CAPN1	823	broad.mit.edu	37	11	64955442	64955442	+	Frame_Shift_Del	DEL	A	-	-			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64955442delA	uc009yqd.1	+	8	971	c.860delA	c.(859-861)CAGfs	p.Q287fs	CAPN1_uc001odf.1_Frame_Shift_Del_p.Q287fs|CAPN1_uc001odg.1_Frame_Shift_Del_p.Q287fs|CAPN1_uc010roa.1_Frame_Shift_Del_p.Q28fs	NM_005186	NP_005177	P07384	CAN1_HUMAN	calpain 1, large subunit	287	Calpain catalytic.				positive regulation of cell proliferation|proteolysis	cytoplasm|plasma membrane	calcium ion binding|calcium-dependent cysteine-type endopeptidase activity|protein binding			ovary(1)	1		Lung NSC(402;0.094)|Melanoma(852;0.16)		Lung(977;0.00168)|LUSC - Lung squamous cell carcinoma(976;0.00813)		TACCGAGGCCAGGTGGTGAGC	0.512													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	71279600	71279601	+	IGR	INS	-	T	T	rs150195971	by1000genomes	TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:71279600_71279601insT								KRTAP5-10 (1934 upstream) : KRTAP5-11 (13302 downstream)																							aaaaaaaaaaatttaagtacct	0.000													4	2	---	---	---	---	
RAB30	27314	broad.mit.edu	37	11	82703779	82703780	+	Intron	DEL	AC	-	-	rs67746307		TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:82703779_82703780delAC	uc001ozu.2	-						RAB30_uc009yve.2_Intron|RAB30_uc010rst.1_Intron|RAB30_uc001ozv.2_Intron|RAB30_uc009yvg.1_Intron	NM_014488	NP_055303	Q15771	RAB30_HUMAN	RAB30, member RAS oncogene family						protein transport|small GTPase mediated signal transduction	Golgi stack|plasma membrane	GTP binding|GTPase activity				0						tctGTCACCAacacacacacac	0.198													4	2	---	---	---	---	
NTM	50863	broad.mit.edu	37	11	131550281	131550282	+	Intron	INS	-	TG	TG			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:131550281_131550282insTG	uc010sci.1	+						NTM_uc001qgm.2_Intron|NTM_uc010sch.1_Intron	NM_001144058	NP_001137530	Q9P121	NTRI_HUMAN	neurotrimin isoform 3						cell adhesion|neuron recognition	anchored to membrane|plasma membrane				ovary(4)|central_nervous_system(1)|skin(1)	6						ctgtgagtgcctgtgtgtgtgt	0.114													5	3	---	---	---	---	
NCAPD2	9918	broad.mit.edu	37	12	6640670	6640670	+	3'UTR	DEL	T	-	-			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6640670delT	uc001qoo.2	+	32					NCAPD2_uc010sfd.1_3'UTR|GAPDH_uc001qop.1_5'Flank|GAPDH_uc009zep.1_5'Flank|GAPDH_uc001qoq.1_5'Flank|GAPDH_uc001qor.1_5'Flank	NM_014865	NP_055680	Q15021	CND1_HUMAN	non-SMC condensin I complex, subunit D2						cell division|mitotic chromosome condensation	condensin core heterodimer|cytoplasm	histone binding			ovary(2)|lung(1)|breast(1)|kidney(1)	5						TGTCTGTCTCTTTTTTTTAAA	0.229													5	4	---	---	---	---	
DIP2B	57609	broad.mit.edu	37	12	51122130	51122130	+	Intron	DEL	A	-	-			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:51122130delA	uc001rwv.2	+						DIP2B_uc009zlt.2_Intron	NM_173602	NP_775873	Q9P265	DIP2B_HUMAN	DIP2 disco-interacting protein 2 homolog B							nucleus	catalytic activity|transcription factor binding			ovary(4)|breast(1)|pancreas(1)	6						aactccatctaaaaaaaaaaa	0.124													8	4	---	---	---	---	
KRT76	51350	broad.mit.edu	37	12	53167615	53167616	+	Intron	INS	-	T	T			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53167615_53167616insT	uc001sax.2	-							NM_015848	NP_056932	Q01546	K22O_HUMAN	keratin 76						cytoskeleton organization	keratin filament	structural molecule activity			breast(1)|skin(1)	2						gacattctttcttttttttttt	0.015													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	69594093	69594102	+	IGR	DEL	AGAAAGAGAT	-	-	rs80081772		TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:69594093_69594102delAGAAAGAGAT								CPM (237073 upstream) : CPSF6 (39215 downstream)																							ataagagataagaaagagataagagataag	0.024													7	4	---	---	---	---	
SYT1	6857	broad.mit.edu	37	12	79693525	79693526	+	Intron	INS	-	AG	AG	rs148124225	by1000genomes	TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:79693525_79693526insAG	uc001sys.2	+						SYT1_uc001syt.2_Intron|SYT1_uc001syu.2_Intron|SYT1_uc001syv.2_Intron	NM_001135805	NP_001129277	P21579	SYT1_HUMAN	synaptotagmin I						detection of calcium ion|glutamate secretion|neurotransmitter secretion|protein homooligomerization	cell junction|chromaffin granule membrane|clathrin sculpted acetylcholine transport vesicle membrane|clathrin sculpted gamma-aminobutyric acid transport vesicle membrane|clathrin sculpted glutamate transport vesicle membrane|clathrin sculpted monoamine transport vesicle membrane|endocytic vesicle membrane|integral to membrane|synaptic vesicle membrane	1-phosphatidylinositol binding|low-density lipoprotein particle receptor binding|metal ion binding|syntaxin-1 binding|transporter activity			skin(3)|pancreas(2)|ovary(1)	6						TATCTGAAAGAAGAGAGACATT	0.450													4	2	---	---	---	---	
NTS	4922	broad.mit.edu	37	12	86270630	86270630	+	Intron	DEL	T	-	-			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:86270630delT	uc001tag.2	+							NM_006183	NP_006174	P30990	NEUT_HUMAN	neurotensin/neuromedin N preproprotein						regulation of blood vessel size|signal transduction	extracellular region|soluble fraction|transport vesicle	neuropeptide hormone activity				0						TTTCTTTTAGTTAAAAGAAGT	0.284													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	114889666	114889667	+	IGR	DEL	TC	-	-			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:114889666_114889667delTC								TBX5 (43419 upstream) : TBX3 (218392 downstream)																							tctccctccatctctctctccc	0.094													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	128473511	128473512	+	IGR	INS	-	GT	GT	rs148449117	by1000genomes	TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:128473511_128473512insGT								None (None upstream) : TMEM132C (425779 downstream)																							aatgtgttgtggtgtgtgtgtg	0.178													4	2	---	---	---	---	
ULK1	8408	broad.mit.edu	37	12	132403368	132403376	+	Intron	DEL	GAGTGTGTG	-	-	rs62705161		TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:132403368_132403376delGAGTGTGTG	uc001uje.2	+							NM_003565	NP_003556	O75385	ULK1_HUMAN	Unc-51-like kinase 1						autophagy|protein localization|regulation of autophagy	autophagic vacuole|cytosol|pre-autophagosomal structure|ULK1-ATG13-FIP200 complex	ATP binding|protein complex binding|protein serine/threonine kinase activity			ovary(1)|lung(1)|central_nervous_system(1)|skin(1)	4	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;2.07e-08)|Epithelial(86;2.56e-07)|all cancers(50;3.01e-07)		gtggggtgtagagtgtgtggggtgtgggg	0.010													4	2	---	---	---	---	
KATNAL1	84056	broad.mit.edu	37	13	30784788	30784790	+	Intron	DEL	AAA	-	-	rs33951005		TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:30784788_30784790delAAA	uc001uss.2	-						KATNAL1_uc001ust.2_Intron	NM_001014380	NP_001014402	Q9BW62	KATL1_HUMAN	katanin p60 subunit A-like 1							cytoplasm|microtubule	ATP binding|microtubule-severing ATPase activity				0		Lung SC(185;0.0257)		all cancers(112;0.114)|OV - Ovarian serous cystadenocarcinoma(117;0.213)		CTAAAAATTGaaaaaaaaaaaaa	0.305													4	2	---	---	---	---	
NEK5	341676	broad.mit.edu	37	13	52663229	52663230	+	Intron	INS	-	AACAACAAC	AACAACAAC	rs147701822	by1000genomes	TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:52663229_52663230insAACAACAAC	uc001vge.2	-							NM_199289	NP_954983	Q6P3R8	NEK5_HUMAN	NIMA-related kinase 5								ATP binding|metal ion binding|protein serine/threonine kinase activity			upper_aerodigestive_tract(1)	1		Breast(56;0.00173)|Lung NSC(96;0.0168)|Prostate(109;0.0412)|Hepatocellular(98;0.152)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(99;3.7e-08)		ctgtctcagaaaacaacaacaa	0.149													5	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	31931925	31931925	+	IGR	DEL	A	-	-			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:31931925delA								HEATR5A (5245 upstream) : NUBPL (98666 downstream)																							aagactgtctaaaaaaaaaaa	0.164													3	5	---	---	---	---	
HSPA2	3306	broad.mit.edu	37	14	65009534	65009535	+	3'UTR	INS	-	T	T	rs148978517	by1000genomes	TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:65009534_65009535insT	uc001xhj.2	+	2					HSPA2_uc001xhk.3_3'UTR	NM_021979	NP_068814	P54652	HSP72_HUMAN	heat shock 70kDa protein 2						response to unfolded protein|spermatid development	cell surface	ATP binding|unfolded protein binding			skin(1)	1				all cancers(60;0.00515)|OV - Ovarian serous cystadenocarcinoma(108;0.00584)|BRCA - Breast invasive adenocarcinoma(234;0.045)		CTCTCTCTCTCTTTTTTTTTGT	0.411													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	67261949	67261949	+	IGR	DEL	C	-	-			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:67261949delC								SMAD6 (187614 upstream) : SMAD3 (96246 downstream)																							tccactctaactgcttcctgc	0.000													4	2	---	---	---	---	
IDH2	3418	broad.mit.edu	37	15	90631039	90631039	+	Intron	DEL	T	-	-	rs62019176		TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:90631039delT	uc002box.2	-						IDH2_uc010uqb.1_Intron|IDH2_uc010uqc.1_Intron|IDH2_uc010bnu.2_Intron	NM_002168	NP_002159	P48735	IDHP_HUMAN	isocitrate dehydrogenase 2 (NADP+),						2-oxoglutarate metabolic process|glyoxylate cycle|isocitrate metabolic process|tricarboxylic acid cycle	mitochondrial matrix	isocitrate dehydrogenase (NADP+) activity|magnesium ion binding|NAD binding			haematopoietic_and_lymphoid_tissue(621)|central_nervous_system(80)|bone(7)|skin(3)	711	Melanoma(11;0.00551)|Lung NSC(78;0.0196)|all_lung(78;0.04)		BRCA - Breast invasive adenocarcinoma(143;0.0146)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.106)			AAACACCGCCTTTTTTTTTTT	0.318			M		GBM								6	3	---	---	---	---	
SEC14L5	9717	broad.mit.edu	37	16	5057608	5057608	+	Intron	DEL	T	-	-			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:5057608delT	uc002cye.2	+							NM_014692	NP_055507	O43304	S14L5_HUMAN	SEC14-like 5							integral to membrane|intracellular	transporter activity				0						tctttctttcttttttttttt	0.090													6	3	---	---	---	---	
KIAA0430	9665	broad.mit.edu	37	16	15696195	15696195	+	Intron	DEL	G	-	-			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:15696195delG	uc002ddr.2	-						KIAA0430_uc002ddq.2_Intron|KIAA0430_uc010uzv.1_Intron|KIAA0430_uc010uzw.1_Intron	NM_014647	NP_055462	Q9Y4F3	LKAP_HUMAN	limkain b1							peroxisome	nucleotide binding|RNA binding				0						caacgaagatgagaagatgaa	0.204													10	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	59292444	59292445	+	IGR	INS	-	GTCT	GTCT	rs139688187	by1000genomes	TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:59292444_59292445insGTCT								GOT2 (524198 upstream) : None (None downstream)																							tccttccttccttctctttctt	0.000													4	4	---	---	---	---	
GCSH	2653	broad.mit.edu	37	16	81118317	81118317	+	Intron	DEL	T	-	-	rs111388132		TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:81118317delT	uc002fgd.2	-						GCSH_uc002fge.2_Intron	NM_004483	NP_004474	P23434	GCSH_HUMAN	glycine cleavage system protein H (aminomethyl							glycine cleavage complex|mitochondrion	aminomethyltransferase activity				0					Glycine(DB00145)	TCCAAAtttcttttttttttt	0.119													6	3	---	---	---	---	
HSDL1	83693	broad.mit.edu	37	16	84165089	84165092	+	Intron	DEL	TCTA	-	-	rs36192181	by1000genomes	TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:84165089_84165092delTCTA	uc002fhk.2	-						HSDL1_uc010vnv.1_Intron	NM_031463	NP_113651	Q3SXM5	HSDL1_HUMAN	hydroxysteroid dehydrogenase like 1 isoform a							mitochondrion	oxidoreductase activity|protein binding				0						ACAGTTTCAGtctatctatctatc	0.206													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	86497959	86497964	+	IGR	DEL	TGGTGG	-	-	rs141215019	by1000genomes	TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:86497959_86497964delTGGTGG								LOC732275 (118674 upstream) : FOXF1 (46169 downstream)																							gtgatggtgatggtggtgatggtgat	0.000													3	4	---	---	---	---	
CAMTA2	23125	broad.mit.edu	37	17	4882803	4882804	+	Intron	INS	-	A	A	rs5819002		TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:4882803_4882804insA	uc002gah.1	-						CAMTA2_uc010cku.1_Intron|CAMTA2_uc002gag.1_Intron|CAMTA2_uc002gai.1_Intron|CAMTA2_uc010ckv.1_Intron	NM_015099	NP_055914	O94983	CMTA2_HUMAN	calmodulin binding transcription activator 2						cardiac muscle hypertrophy in response to stress|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nucleus	calmodulin binding|chromatin binding|histone deacetylase binding|transcription factor binding			ovary(1)	1						gaaactgtctcaaaaaaaaaaa	0.168													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	20382948	20382948	+	IGR	DEL	T	-	-	rs56272040		TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:20382948delT								LGALS9B (12100 upstream) : CCDC144NL (383762 downstream)																							tccttccttcttttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	10150773	10150773	+	IGR	DEL	T	-	-			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:10150773delT								VAPA (190756 upstream) : APCDD1 (303852 downstream)																							CTGTGTGTGCTGCATCCACGT	0.542													5	3	---	---	---	---	
C18orf16	147429	broad.mit.edu	37	18	24445878	24445880	+	Intron	DEL	TTT	-	-	rs68070007		TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:24445878_24445880delTTT	uc002kwb.2	+						C18orf16_uc010xbm.1_Intron|AQP4_uc002kwa.2_5'Flank	NR_026908				Homo sapiens cDNA FLJ30507 fis, clone BRAWH2000554.												0						ATTTACTTAATTTTTTTTTTTTT	0.300													4	2	---	---	---	---	
DSC1	1823	broad.mit.edu	37	18	28730332	28730332	+	Intron	DEL	C	-	-	rs143811853	by1000genomes	TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:28730332delC	uc002kwn.2	-						DSC1_uc002kwm.2_Intron	NM_024421	NP_077739	Q08554	DSC1_HUMAN	desmocollin 1 isoform Dsc1a preproprotein						homophilic cell adhesion	desmosome|gap junction|integral to membrane|membrane fraction	calcium ion binding			ovary(3)|skin(1)	4			OV - Ovarian serous cystadenocarcinoma(10;0.00778)			atcatcaccaccaccatcatc	0.000													4	2	---	---	---	---	
MYO5B	4645	broad.mit.edu	37	18	47501149	47501150	+	Intron	INS	-	CA	CA	rs146410387	by1000genomes	TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:47501149_47501150insCA	uc002leb.2	-						MYO5B_uc002lec.1_Intron	NM_001080467	NP_001073936	Q9ULV0	MYO5B_HUMAN	myosin VB						protein transport	myosin complex	actin binding|ATP binding|calmodulin binding|motor activity			ovary(2)|skin(2)|central_nervous_system(1)	5				READ - Rectum adenocarcinoma(32;0.103)		GCAGTCTCTCTcacacacacac	0.426													5	4	---	---	---	---	
MUM1	84939	broad.mit.edu	37	19	1376306	1376310	+	Intron	DEL	GTTTG	-	-	rs7508308		TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1376306_1376310delGTTTG	uc010xgm.1	+						MUM1_uc002lrz.2_Intron|MUM1_uc002lsb.2_Intron|MUM1_uc002lsd.2_Intron			Q2TAK8	MUM1_HUMAN	SubName: Full=MUM1 protein;						chromatin organization|DNA repair	nucleus	nucleosome binding|protein binding				0		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;3.55e-06)|all_lung(49;5.41e-06)|Breast(49;0.000172)|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)		ttttttttttgtttgtttttttttt	0.000													2	4	---	---	---	---	
MKNK2	2872	broad.mit.edu	37	19	2046580	2046581	+	Intron	INS	-	A	A			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2046580_2046581insA	uc002lus.2	-						MKNK2_uc010xgu.1_Intron|MKNK2_uc010xgv.1_Intron|MKNK2_uc002lur.2_Intron	NM_199054	NP_951009	Q9HBH9	MKNK2_HUMAN	MAP kinase-interacting serine/threonine kinase 2						cell surface receptor linked signaling pathway|intracellular protein kinase cascade|regulation of translation		ATP binding|metal ion binding|protein serine/threonine kinase activity			lung(1)|breast(1)	2		Ovarian(11;2.11e-07)|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)		GCCCTGTGCCCTCCTCCCCCTC	0.728													6	3	---	---	---	---	
ARHGEF18	23370	broad.mit.edu	37	19	7515637	7515637	+	Intron	DEL	G	-	-			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7515637delG	uc002mgi.2	+						ARHGEF18_uc010xjm.1_Intron|ARHGEF18_uc002mgh.2_Intron|ARHGEF18_uc002mgj.1_Intron	NM_001130955	NP_001124427	Q6ZSZ5	ARHGI_HUMAN	Rho/Rac guanine nucleotide exchange factor 18						actin cytoskeleton organization|apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of cell shape|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	Rho guanyl-nucleotide exchange factor activity			ovary(1)	1		Renal(5;0.0902)				ATGTTAATGCGGGATCTTGCT	0.473													3	3	---	---	---	---	
UNC13A	23025	broad.mit.edu	37	19	17750846	17750846	+	Intron	DEL	T	-	-			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17750846delT	uc002nhd.2	-							NM_001080421	NP_001073890	Q9UPW8	UN13A_HUMAN	unc-13 homolog A						exocytosis|intracellular signal transduction	cell junction|cytoplasm|presynaptic membrane	metal ion binding			ovary(3)	3						TTCTATGGCAttttttttttt	0.254													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	22778374	22778374	+	5'Flank	DEL	G	-	-			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:22778374delG	uc002nqu.3	+											Homo sapiens cDNA FLJ60031 complete cds, moderately similar to Golgin subfamily A member 2.																		AGGAGGAGCTGGGAAGCAGGA	0.637													4	5	---	---	---	---	
MIR521-2	574481	broad.mit.edu	37	19	54216854	54216855	+	5'Flank	INS	-	T	T	rs2865856	by1000genomes	TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54216854_54216855insT	hsa-mir-521-2|MI0003163	+																							0						TTTGTTTTGTGTTTTTTTTTTT	0.267													4	2	---	---	---	---	
U2AF2	11338	broad.mit.edu	37	19	56181884	56181884	+	Intron	DEL	G	-	-	rs66506071		TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56181884delG	uc002qlu.2	+						U2AF2_uc002qlt.2_Intron	NM_007279	NP_009210	P26368	U2AF2_HUMAN	U2 (RNU2) small nuclear RNA auxiliary factor 2						mRNA 3'-end processing|mRNA export from nucleus|termination of RNA polymerase II transcription	nucleoplasm|spliceosomal complex	enzyme binding|nucleotide binding|RNA binding			ovary(1)	1		Colorectal(82;0.00244)|Ovarian(87;0.133)	BRCA - Breast invasive adenocarcinoma(297;0.18)	GBM - Glioblastoma multiforme(193;0.107)		CTGCTGTCCCGTGCACCCTGC	0.532													4	2	---	---	---	---	
FRG1B	284802	broad.mit.edu	37	20	29652921	29652923	+	3'UTR	DEL	CAA	-	-	rs138423167		TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29652921_29652923delCAA	uc010ztl.1	+	4					FRG1B_uc010ztj.1_RNA|FRG1B_uc010ztk.1_3'UTR					Homo sapiens cDNA FLJ32537 fis, clone SMINT2000400, highly similar to Homo sapiens FRG1 mRNA.												0						aagcctcctccaacaagtctgga	0.000													4	2	---	---	---	---	
DSN1	79980	broad.mit.edu	37	20	35396636	35396636	+	Intron	DEL	A	-	-			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:35396636delA	uc010gfr.2	-						DSN1_uc002xfz.2_Intron|DSN1_uc002xfy.3_Intron|DSN1_uc002xga.2_Intron|DSN1_uc010zvs.1_Intron|DSN1_uc002xgc.2_Intron|DSN1_uc002xgb.2_Intron	NM_001145316	NP_001138788	Q9H410	DSN1_HUMAN	DSN1, MIND kinetochore complex component,						cell division|chromosome segregation|mitotic prometaphase	cytosol|MIS12/MIND type complex|nucleus	protein binding			ovary(2)	2		Myeloproliferative disorder(115;0.00874)				ATCTAAACTTAAAAAAAAAAA	0.194													4	2	---	---	---	---	
OSBPL2	9885	broad.mit.edu	37	20	60834808	60834826	+	Intron	DEL	GCACTGGAGCTCGCTGGGA	-	-	rs151022334		TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:60834808_60834826delGCACTGGAGCTCGCTGGGA	uc002yck.1	+						OSBPL2_uc002ycl.1_Intron|OSBPL2_uc011aah.1_Intron	NM_144498	NP_653081	Q9H1P3	OSBL2_HUMAN	oxysterol-binding protein-like protein 2 isoform						lipid transport		lipid binding			ovary(1)|central_nervous_system(1)	2	Breast(26;7.76e-09)		BRCA - Breast invasive adenocarcinoma(19;1.33e-06)			AGGAGCCTGGGCACTGGAGCTCGCTGGGAGCGCGTTCTT	0.530													2	4	---	---	---	---	
SAMD10	140700	broad.mit.edu	37	20	62608145	62608145	+	Intron	DEL	G	-	-			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62608145delG	uc002yhm.2	-						SAMD10_uc002yhn.2_Intron	NM_080621	NP_542188	Q9BYL1	SAM10_HUMAN	sterile alpha motif domain containing 10												0	all_cancers(38;2.14e-11)|all_epithelial(29;3.41e-13)|Lung NSC(23;3.41e-09)|all_lung(23;1.06e-08)					aaaaaaaaaagaaaggcagag	0.169													7	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10728541	10728541	+	IGR	DEL	T	-	-			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10728541delT								None (None upstream) : TPTE (178202 downstream)																							ctcagaatgcttctgtgtagt	0.000													8	4	---	---	---	---	
CELSR1	9620	broad.mit.edu	37	22	46839557	46839558	+	Intron	DEL	CA	-	-	rs71866651		TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:46839557_46839558delCA	uc003bhw.1	-							NM_014246	NP_055061	Q9NYQ6	CELR1_HUMAN	cadherin EGF LAG seven-pass G-type receptor 1						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)		tacacctgttcacacacacaca	0.074													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	45606320	45606323	+	5'Flank	DEL	GTGT	-	-			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:45606320_45606323delGTGT	uc011mle.1	-						MIR221_hsa-mir-221|MI0000298_5'Flank					DM004476																		gtgtgtgtgagtgtgtgtgtgtgt	0.216													5	3	---	---	---	---	
SYTL4	94121	broad.mit.edu	37	X	99930891	99930892	+	3'UTR	DEL	AT	-	-	rs67841104		TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:99930891_99930892delAT	uc004egd.3	-	19					SYTL4_uc004egc.2_3'UTR|SYTL4_uc010nnb.2_3'UTR|SYTL4_uc010nnc.2_3'UTR|SYTL4_uc004ege.3_3'UTR|SYTL4_uc004egf.3_3'UTR	NM_080737	NP_542775	Q96C24	SYTL4_HUMAN	synaptotagmin-like 4						exocytosis|intracellular protein transport	extrinsic to membrane|plasma membrane|synaptic vesicle|transport vesicle membrane	neurexin binding|phospholipid binding|Rab GTPase binding|transporter activity|zinc ion binding			ovary(2)	2					Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)	GTTTGTacacatacacacacac	0.257													4	3	---	---	---	---	
SEPT6	23157	broad.mit.edu	37	X	118768971	118768972	+	Intron	INS	-	A	A			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:118768971_118768972insA	uc004erv.2	-						SEPT6_uc010nqk.2_Intron|SEPT6_uc004ers.2_Intron|SEPT6_uc004ert.2_Intron|SEPT6_uc004eru.2_Intron|SEPT6_uc004erw.2_Intron|SEPT6_uc011mtv.1_Intron|SEPT6_uc011mtw.1_Intron	NM_015129	NP_055944	Q14141	SEPT6_HUMAN	septin 6 isoform B						cell cycle|cytokinesis|interspecies interaction between organisms	cleavage furrow|condensed chromosome kinetochore|midbody|septin complex|spindle	GTP binding|protein binding			lung(1)|ovary(1)|prostate(1)|kidney(1)	4						gactctgtctcaaaaaaaaaaa	0.168													4	2	---	---	---	---	
GRIA3	2892	broad.mit.edu	37	X	122460221	122460221	+	Intron	DEL	A	-	-	rs146181168		TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:122460221delA	uc004etq.3	+						GRIA3_uc004etr.3_Intron|GRIA3_uc004ets.3_Intron|GRIA3_uc011muf.1_Intron	NM_007325	NP_015564	P42263	GRIA3_HUMAN	glutamate receptor, ionotrophic, AMPA 3 isoform						glutamate signaling pathway|synaptic transmission	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity			ovary(3)|central_nervous_system(1)|pancreas(1)	5					L-Glutamic Acid(DB00142)	GTGGCTGCAGaaaaaaaaaaa	0.308													8	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	58988487	58988487	+	IGR	DEL	C	-	-			TCGA-A3-3308-01A-01D-0966-08	TCGA-A3-3308-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:58988487delC								None (None upstream) : None (None downstream)																							gctctgcctactggcgcatag	0.000													4	2	---	---	---	---	
