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
UBE4B	10277	broad.mit.edu	37	1	10163026	10163026	+	Missense_Mutation	SNP	A	T	T			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:10163026A>T	uc001aqs.3	+	5	1169	c.456A>T	c.(454-456)GAA>GAT	p.E152D	UBE4B_uc001aqr.3_Missense_Mutation_p.E152D|UBE4B_uc010oai.1_RNA|UBE4B_uc010oaj.1_Translation_Start_Site	NM_001105562	NP_001099032	O95155	UBE4B_HUMAN	ubiquitination factor E4B isoform 1	152					apoptosis|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|response to UV	cytoplasm|ubiquitin ligase complex	enzyme binding			ovary(2)|skin(2)	4		all_lung(284;1.13e-05)|Lung NSC(185;1.74e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0268)|Colorectal(212;1.42e-07)|COAD - Colon adenocarcinoma(227;2.77e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000435)|Kidney(185;0.000482)|KIRC - Kidney renal clear cell carcinoma(229;0.00164)|STAD - Stomach adenocarcinoma(132;0.0117)|READ - Rectum adenocarcinoma(331;0.046)		CGGGCCCTGAAGTGTCTGAAG	0.448													31	105	---	---	---	---	PASS
PRAMEF4	400735	broad.mit.edu	37	1	12943139	12943139	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12943139G>A	uc001aun.2	-	2	148	c.77C>T	c.(76-78)GCC>GTC	p.A26V		NM_001009611	NP_001009611	O60810	PRAM4_HUMAN	PRAME family member 4	26										ovary(1)	1	Ovarian(185;0.249)	Lung NSC(185;3.67e-05)|all_lung(284;4.03e-05)|Renal(390;0.000147)|Breast(348;0.000278)|Colorectal(325;0.00058)|Ovarian(437;0.00965)|Hepatocellular(190;0.0245)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Colorectal(212;4.88e-06)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|COAD - Colon adenocarcinoma(227;0.000241)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		GGTGGACATGGCCAAAGCTTG	0.577													71	107	---	---	---	---	PASS
COL16A1	1307	broad.mit.edu	37	1	32149718	32149718	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:32149718C>T	uc001btk.1	-	32	2640	c.2275G>A	c.(2275-2277)GGT>AGT	p.G759S	COL16A1_uc001btj.1_Missense_Mutation_p.G588S|COL16A1_uc001btl.3_Missense_Mutation_p.G759S	NM_001856	NP_001847	Q07092	COGA1_HUMAN	alpha 1 type XVI collagen precursor	759	Triple-helical region 5 (COL5) with 3 imperfections.				cell adhesion|female pregnancy|integrin-mediated signaling pathway	collagen type XVI	integrin binding|structural molecule activity			ovary(8)	8		Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0423)|all_neural(195;0.0837)|Breast(348;0.116)		STAD - Stomach adenocarcinoma(196;0.059)		ACGGGTTTACCAGGTCGGCCC	0.692													6	10	---	---	---	---	PASS
PARS2	25973	broad.mit.edu	37	1	55224207	55224207	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:55224207A>G	uc001cxy.2	-	2	711	c.628T>C	c.(628-630)TAC>CAC	p.Y210H		NM_152268	NP_689481	Q7L3T8	SYPM_HUMAN	prolyl-tRNA synthetase (mitochondrial)(putative)	210					prolyl-tRNA aminoacylation	mitochondrial matrix	ATP binding|proline-tRNA ligase activity			ovary(2)	2					L-Proline(DB00172)	TCAAAGGTGTACATATCCTTC	0.547													35	82	---	---	---	---	PASS
ANGPTL3	27329	broad.mit.edu	37	1	63063407	63063407	+	Missense_Mutation	SNP	T	A	A			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:63063407T>A	uc001das.1	+	1	221	c.170T>A	c.(169-171)CTT>CAT	p.L57H	DOCK7_uc001dan.2_Intron|DOCK7_uc001dao.2_Intron|DOCK7_uc001dap.2_Intron|DOCK7_uc001daq.2_Intron|DOCK7_uc009wah.1_Intron	NM_014495	NP_055310	Q9Y5C1	ANGL3_HUMAN	angiopoietin-like 3 precursor	57					acylglycerol homeostasis|artery morphogenesis|cell-matrix adhesion|cholesterol homeostasis|cholesterol metabolic process|fatty acid metabolic process|glycerol metabolic process|integrin-mediated signaling pathway|lipid storage|negative regulation of lipoprotein lipase activity|negative regulation of phospholipase activity|phospholipid catabolic process|phospholipid homeostasis|positive regulation of angiogenesis|positive regulation of cell migration|positive regulation of lipid catabolic process|triglyceride homeostasis	extracellular space	cell surface binding|growth factor activity|integrin binding|phospholipase inhibitor activity				0						GGACATGGTCTTAAAGACTTT	0.358													39	121	---	---	---	---	PASS
LMO4	8543	broad.mit.edu	37	1	87805218	87805218	+	Splice_Site	SNP	G	C	C			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:87805218G>C	uc001dmi.2	+	3	1017	c.237_splice	c.e3-1	p.R79_splice	LMO4_uc001dmj.2_Splice_Site_p.R79_splice	NM_006769	NP_006760	P61968	LMO4_HUMAN	LIM domain only 4						neural tube closure|transcription from RNA polymerase II promoter	transcription factor complex	sequence-specific DNA binding transcription factor activity|transcription factor binding|zinc ion binding				0		Lung NSC(277;0.179)		all cancers(265;0.00456)|Epithelial(280;0.0148)|BRCA - Breast invasive adenocarcinoma(282;0.153)		CTTTGTTTCAGGTTATTTGGA	0.448													19	48	---	---	---	---	PASS
LPPR4	9890	broad.mit.edu	37	1	99771434	99771434	+	Missense_Mutation	SNP	C	G	G			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:99771434C>G	uc001dse.2	+	7	1266	c.1160C>G	c.(1159-1161)ACA>AGA	p.T387R	LPPR4_uc010oue.1_Missense_Mutation_p.T329R	NM_014839	NP_055654	Q7Z2D5	LPPR4_HUMAN	plasticity related gene 1	387							phosphatidate phosphatase activity			ovary(3)	3		all_epithelial(167;3.54e-06)|all_lung(203;0.00139)|Lung NSC(277;0.00202)		Epithelial(280;0.0736)|all cancers(265;0.0975)|COAD - Colon adenocarcinoma(174;0.142)|Lung(183;0.201)|Colorectal(170;0.22)		AGCTCTCTGACAAATCTCAAA	0.478													32	84	---	---	---	---	PASS
THBS3	7059	broad.mit.edu	37	1	155170785	155170785	+	Missense_Mutation	SNP	A	T	T			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155170785A>T	uc001fix.2	-	13	1474	c.1451T>A	c.(1450-1452)CTT>CAT	p.L484H	RAG1AP1_uc010pey.1_Intron|THBS3_uc009wqi.2_Missense_Mutation_p.L475H|THBS3_uc001fiz.2_Missense_Mutation_p.L447H|THBS3_uc001fiy.2_Missense_Mutation_p.L13H|THBS3_uc010pfu.1_Missense_Mutation_p.L364H|THBS3_uc010pfv.1_RNA|THBS3_uc001fja.2_RNA	NM_007112	NP_009043	P49746	TSP3_HUMAN	thrombospondin 3 precursor	484	TSP type-3 1.				cell-matrix adhesion	extracellular region|perinuclear region of cytoplasm	calcium ion binding|heparin binding|structural molecule activity			breast(3)|ovary(2)	5	all_epithelial(22;5.72e-28)|all_lung(78;2.07e-24)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		Epithelial(20;3.72e-10)|all cancers(21;1.19e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193)			GGGTGTCAAAAGGCAGTTGTC	0.562													87	262	---	---	---	---	PASS
LAMC2	3918	broad.mit.edu	37	1	183197726	183197726	+	Silent	SNP	G	A	A			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:183197726G>A	uc001gqa.2	+	11	2000	c.1686G>A	c.(1684-1686)TTG>TTA	p.L562L	LAMC2_uc001gpz.3_Silent_p.L562L|LAMC2_uc010poa.1_Silent_p.L262L	NM_005562	NP_005553	Q13753	LAMC2_HUMAN	laminin, gamma 2 isoform a precursor	562	Laminin EGF-like 7.				cell adhesion|epidermis development|hemidesmosome assembly		heparin binding			skin(2)|ovary(1)	3						GGGACCCATTGGCTCCCAACC	0.567											OREG0014041	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	47	130	---	---	---	---	PASS
NBAS	51594	broad.mit.edu	37	2	15607839	15607839	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:15607839T>C	uc002rcc.1	-	18	1993	c.1967A>G	c.(1966-1968)GAA>GGA	p.E656G	NBAS_uc002rcd.1_RNA	NM_015909	NP_056993	A2RRP1	NBAS_HUMAN	neuroblastoma-amplified protein	656										ovary(2)|liver(1)|skin(1)	4						GAGCTCCTTTTCCTTTTTATT	0.338													43	43	---	---	---	---	PASS
CYP20A1	57404	broad.mit.edu	37	2	204161733	204161733	+	3'UTR	SNP	A	G	G			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:204161733A>G	uc002uzv.3	+	13					CYP20A1_uc002uzx.3_3'UTR|CYP20A1_uc010zif.1_3'UTR|CYP20A1_uc002uzy.3_3'UTR|CYP20A1_uc002uzw.3_RNA|CYP20A1_uc010ftw.2_3'UTR	NM_177538	NP_803882	Q6UW02	CP20A_HUMAN	cytochrome P450, family 20, subfamily A,							integral to membrane	electron carrier activity|heme binding|monooxygenase activity|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen				0						ACTTTGTAATATAAACACCTA	0.219													6	0	---	---	---	---	PASS
TBC1D5	9779	broad.mit.edu	37	3	17279709	17279709	+	Nonsense_Mutation	SNP	G	A	A			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:17279709G>A	uc003cbf.2	-	17	3199	c.1534C>T	c.(1534-1536)CAG>TAG	p.Q512*	TBC1D5_uc010heu.2_Nonsense_Mutation_p.Q99*|TBC1D5_uc010hev.2_Nonsense_Mutation_p.Q512*|TBC1D5_uc003cbe.2_Nonsense_Mutation_p.Q512*|TBC1D5_uc010hew.1_Nonsense_Mutation_p.Q464*	NM_014744	NP_055559	Q92609	TBCD5_HUMAN	TBC1 domain family, member 5 isoform b	512						intracellular	protein binding|Rab GTPase activator activity			ovary(1)	1						TGCTGCTGCTGTTGCTGTTGC	0.473													28	50	---	---	---	---	PASS
OXSR1	9943	broad.mit.edu	37	3	38294372	38294372	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:38294372G>A	uc003chy.2	+	18	1916	c.1574G>A	c.(1573-1575)AGC>AAC	p.S525N	OXSR1_uc010hhb.2_Missense_Mutation_p.S459N	NM_005109	NP_005100	O95747	OXSR1_HUMAN	oxidative-stress responsive 1	525					intracellular protein kinase cascade|response to oxidative stress		ATP binding|identical protein binding|magnesium ion binding|protein serine/threonine kinase activity			skin(1)	1				KIRC - Kidney renal clear cell carcinoma(284;0.0588)|Kidney(284;0.0738)		GCCCAGCTCAGCATCAGCTAA	0.448													22	57	---	---	---	---	PASS
GPR15	2838	broad.mit.edu	37	3	98251516	98251516	+	Silent	SNP	C	T	T			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:98251516C>T	uc011bgy.1	+	1	639	c.639C>T	c.(637-639)ACC>ACT	p.T213T		NM_005290	NP_005281	P49685	GPR15_HUMAN	G protein-coupled receptor 15	213	Helical; Name=5; (Potential).					integral to plasma membrane	purinergic nucleotide receptor activity, G-protein coupled			ovary(1)	1		Lung NSC(201;7.93e-06)|all_neural(597;0.00172)|Hepatocellular(537;0.00825)|Myeloproliferative disorder(1037;0.0255)		Lung(72;0.246)		GCATTGTGACCTGCTACTGTT	0.413													9	235	---	---	---	---	PASS
COL8A1	1295	broad.mit.edu	37	3	99513362	99513362	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:99513362G>A	uc003dtg.1	+	5	862	c.617G>A	c.(616-618)GGC>GAC	p.G206D	COL8A1_uc003dth.1_Missense_Mutation_p.G206D|COL8A1_uc003dti.1_Missense_Mutation_p.G207D	NM_001850	NP_001841	P27658	CO8A1_HUMAN	alpha 1 type VIII collagen precursor	206	Triple-helical region (COL1).				angiogenesis|cell adhesion	basement membrane|collagen type VIII					0						GGACTTCCTGGCATTGGGAAG	0.592													22	59	---	---	---	---	PASS
KIAA2018	205717	broad.mit.edu	37	3	113377055	113377055	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113377055C>A	uc003eam.2	-	7	3885	c.3474G>T	c.(3472-3474)AGG>AGT	p.R1158S	KIAA2018_uc003eal.2_Missense_Mutation_p.R1102S	NM_001009899	NP_001009899	Q68DE3	K2018_HUMAN	hypothetical protein LOC205717	1158					regulation of transcription, DNA-dependent	membrane|nucleus	calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity			skin(2)|ovary(1)	3						AAGCAACTTCCCTTATATCAG	0.468													29	114	---	---	---	---	PASS
UBA5	79876	broad.mit.edu	37	3	132387698	132387698	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:132387698A>G	uc003epa.3	+	4	576	c.334A>G	c.(334-336)AAT>GAT	p.N112D	NPHP3_uc003eoz.1_Intron|UBA5_uc010htr.2_Missense_Mutation_p.N56D|UBA5_uc010htt.2_Missense_Mutation_p.N112D|UBA5_uc003epb.3_Missense_Mutation_p.N56D	NM_024818	NP_079094	Q9GZZ9	UBA5_HUMAN	ubiquitin-activating enzyme 5 isoform 1	112					protein ufmylation	aggresome|cytoplasm|cytoplasm|nucleus	ATP binding|cofactor binding|metal ion binding|oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor|protein binding|UFM1 activating enzyme activity			kidney(1)	1						GGAACTAGCCAATATGAATAG	0.323													35	124	---	---	---	---	PASS
FETUB	26998	broad.mit.edu	37	3	186364117	186364117	+	Silent	SNP	A	T	T			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:186364117A>T	uc010hyq.2	+	6	936	c.675A>T	c.(673-675)TCA>TCT	p.S225S	FETUB_uc011brz.1_Silent_p.S77S|FETUB_uc003fqn.2_Silent_p.S225S|FETUB_uc003fqo.2_Silent_p.S120S|FETUB_uc010hyr.2_Silent_p.S188S|FETUB_uc010hys.2_Silent_p.S77S|FETUB_uc003fqp.3_Silent_p.S160S	NM_014375	NP_055190	Q9UGM5	FETUB_HUMAN	fetuin B precursor	225	Cystatin fetuin-B-type 2.					extracellular space	cysteine-type endopeptidase inhibitor activity			ovary(1)|lung(1)	2	all_cancers(143;6.64e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;5.73e-20)	GBM - Glioblastoma multiforme(93;0.0479)		GCAGCTGTTCACTTCAGTCCT	0.413													72	188	---	---	---	---	PASS
IDUA	3425	broad.mit.edu	37	4	980873	980873	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:980873A>G	uc003gby.2	+	1	89	c.1A>G	c.(1-3)ATG>GTG	p.M1V	SLC26A1_uc003gbx.2_Intron|IDUA_uc003gbz.2_RNA|IDUA_uc003gca.2_Missense_Mutation_p.M1V	NM_000203	NP_000194	P35475	IDUA_HUMAN	alpha-L-iduronidase precursor	1					disaccharide metabolic process	lysosome	cation binding|L-iduronidase activity				0			OV - Ovarian serous cystadenocarcinoma(23;0.0158)		Laronidase(DB00090)	ACGCGTGGCCATGCGTCCCCT	0.567													2	3	---	---	---	---	PASS
DCAF16	54876	broad.mit.edu	37	4	17805767	17805767	+	5'UTR	SNP	G	A	A			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:17805767G>A	uc003gpn.2	-	3					DCAF16_uc003gpo.2_RNA	NM_017741	NP_060211	Q9NXF7	DCA16_HUMAN	DDB1 and CUL4 associated factor 16							CUL4 RING ubiquitin ligase complex				ovary(1)	1						GGACCCATCAGAATAAAACAC	0.383													21	60	---	---	---	---	PASS
N4BP2	55728	broad.mit.edu	37	4	40122527	40122527	+	Silent	SNP	C	T	T			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:40122527C>T	uc003guy.3	+	9	3134	c.2796C>T	c.(2794-2796)GGC>GGT	p.G932G	N4BP2_uc010ifq.2_Silent_p.G852G|N4BP2_uc010ifr.2_Silent_p.G852G	NM_018177	NP_060647	Q86UW6	N4BP2_HUMAN	Nedd4 binding protein 2	932						cytoplasm	ATP binding|ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity|endonuclease activity|protein binding			lung(3)|breast(2)|kidney(2)|ovary(1)	8						CCTGTTGGGGCACAAGCTCTC	0.413													21	63	---	---	---	---	PASS
HERC5	51191	broad.mit.edu	37	4	89385020	89385020	+	Missense_Mutation	SNP	T	G	G			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:89385020T>G	uc003hrt.2	+	6	948	c.795T>G	c.(793-795)TTT>TTG	p.F265L		NM_016323	NP_057407	Q9UII4	HERC5_HUMAN	hect domain and RLD 5	265	RCC1 4.				innate immune response|ISG15-protein conjugation|negative regulation of type I interferon production|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|regulation of cyclin-dependent protein kinase activity|regulation of defense response to virus|response to virus	cytosol|perinuclear region of cytoplasm	ISG15 ligase activity|protein binding|ubiquitin-protein ligase activity			ovary(4)|lung(3)|skin(2)	9		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000209)		GGCTGCTGTTTACTTTCGGTG	0.388													37	103	---	---	---	---	PASS
LARP1B	55132	broad.mit.edu	37	4	129043237	129043237	+	Missense_Mutation	SNP	G	C	C	rs142360155		TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:129043237G>C	uc003iga.2	+	11	1549	c.1418G>C	c.(1417-1419)CGG>CCG	p.R473P	LARP1B_uc003igc.2_5'UTR|LARP1B_uc003ifz.1_Missense_Mutation_p.R473P|LARP1B_uc003igb.1_Missense_Mutation_p.R188P	NM_018078	NP_060548	Q659C4	LAR1B_HUMAN	La ribonucleoprotein domain family member 2	473				R -> Q (in Ref. 1; BAC03970).			RNA binding				0						CACATGTCTCGGGCAAAAATC	0.388													38	137	---	---	---	---	PASS
GPX3	2878	broad.mit.edu	37	5	150407548	150407548	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:150407548C>A	uc011dcm.1	+	6	755	c.538C>A	c.(538-540)CGC>AGC	p.R180S	GPX3_uc003ltc.2_RNA|GPX3_uc003ltd.2_RNA	NM_002084	NP_002075	P22352	GPX3_HUMAN	glutathione peroxidase 3 precursor	180					hydrogen peroxide catabolic process|protein homotetramerization|response to lipid hydroperoxide	extracellular space	glutathione peroxidase activity|selenium binding|transcription factor binding				0		Medulloblastoma(196;0.091)|all_hematologic(541;0.207)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		Glutathione(DB00143)	TCACGACATCCGCTGGAACTT	0.567													23	65	---	---	---	---	PASS
ABCF1	23	broad.mit.edu	37	6	30548295	30548295	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:30548295A>G	uc003nql.2	+	8	772	c.677A>G	c.(676-678)CAG>CGG	p.Q226R	ABCF1_uc003nqk.2_Missense_Mutation_p.Q227R|ABCF1_uc003nqm.2_Missense_Mutation_p.Q226R|ABCF1_uc010jsb.2_Intron	NM_001025091	NP_001020262	Q8NE71	ABCF1_HUMAN	ATP-binding cassette, sub-family F, member 1	226	Glu-rich.				inflammatory response|translational initiation	nuclear envelope|nuclear envelope|nucleoplasm|nucleoplasm|polysomal ribosome	ATP binding|ATP binding|ATPase activity|protein binding|ribosome binding|translation activator activity|translation factor activity, nucleic acid binding			ovary(2)	2						AAGGCAGAGCAGGTGTGTATT	0.473													4	19	---	---	---	---	PASS
ZNF76	7629	broad.mit.edu	37	6	35258122	35258122	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:35258122G>T	uc003oki.1	+	6	717	c.512G>T	c.(511-513)GGC>GTC	p.G171V	ZNF76_uc011dsy.1_Missense_Mutation_p.G171V|ZNF76_uc011dsz.1_Missense_Mutation_p.G171V|ZNF76_uc003okj.1_Missense_Mutation_p.G171V	NM_003427	NP_003418	P36508	ZNF76_HUMAN	zinc finger protein 76 (expressed in testis)	171	C2H2-type 1.				regulation of transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase III promoter|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						GGCTACAAGGGCTGTGGGCGT	0.532													74	199	---	---	---	---	PASS
C6orf64	55776	broad.mit.edu	37	6	39073238	39073238	+	Missense_Mutation	SNP	C	G	G			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:39073238C>G	uc003ook.1	-	2	522	c.522G>C	c.(520-522)GAG>GAC	p.E174D	C6orf64_uc011dty.1_RNA|C6orf64_uc003oom.1_RNA	NM_018322	NP_060792	Q9NPB0	CF064_HUMAN	hypothetical protein LOC55776	174						integral to membrane					0						TCAACTGTAACTCGCGCTCCA	0.532													42	133	---	---	---	---	PASS
ABCC10	89845	broad.mit.edu	37	6	43402438	43402438	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43402438C>T	uc003ouy.1	+	4	1675	c.1460C>T	c.(1459-1461)GCC>GTC	p.A487V	ABCC10_uc003ouz.1_Missense_Mutation_p.A444V|ABCC10_uc010jyo.1_5'Flank	NM_033450	NP_258261	Q5T3U5	MRP7_HUMAN	ATP-binding cassette, sub-family C, member 10	487	ABC transmembrane type-1 1.					integral to membrane|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances			ovary(6)|central_nervous_system(1)	7	all_lung(25;0.00536)		Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0152)|OV - Ovarian serous cystadenocarcinoma(102;0.0804)			CGAGTAGAGGCCTGCCGGGCT	0.602													55	181	---	---	---	---	PASS
EPHA7	2045	broad.mit.edu	37	6	93964470	93964470	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:93964470C>A	uc003poe.2	-	14	2668	c.2427G>T	c.(2425-2427)CAG>CAT	p.Q809H	EPHA7_uc003pof.2_Missense_Mutation_p.Q804H|EPHA7_uc011eac.1_Missense_Mutation_p.Q805H	NM_004440	NP_004431	Q15375	EPHA7_HUMAN	ephrin receptor EphA7 precursor	809	Cytoplasmic (Potential).|Protein kinase.					integral to plasma membrane	ATP binding|ephrin receptor activity			lung(8)|ovary(7)|upper_aerodigestive_tract(3)|central_nervous_system(3)|skin(3)|large_intestine(2)|stomach(1)|pancreas(1)	28		all_cancers(76;7.47e-10)|Acute lymphoblastic leukemia(125;1.88e-09)|all_hematologic(75;1.75e-07)|all_epithelial(107;3.6e-05)|Lung NSC(302;0.0368)|all_lung(197;0.0509)|Colorectal(196;0.142)		BRCA - Breast invasive adenocarcinoma(108;0.0847)		ATTTCCGGTACTGGATGGCTT	0.363													28	58	---	---	---	---	PASS
TIAM2	26230	broad.mit.edu	37	6	155498049	155498049	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:155498049G>A	uc003qqb.2	+	12	3734	c.2461G>A	c.(2461-2463)GGA>AGA	p.G821R	TIAM2_uc003qqe.2_Missense_Mutation_p.G821R|TIAM2_uc010kjj.2_Missense_Mutation_p.G354R|TIAM2_uc003qqf.2_Missense_Mutation_p.G197R|TIAM2_uc011efl.1_Missense_Mutation_p.G157R|TIAM2_uc003qqg.2_Missense_Mutation_p.G133R	NM_012454	NP_036586	Q8IVF5	TIAM2_HUMAN	T-cell lymphoma invasion and metastasis 2	821	RBD.				apoptosis|cellular lipid metabolic process|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|filopodium|growth cone|lamellipodium	receptor signaling protein activity|Rho guanyl-nucleotide exchange factor activity			ovary(3)|breast(1)	4		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;8.1e-13)|BRCA - Breast invasive adenocarcinoma(81;0.0053)		GGACAATCACGGAGTTACTGT	0.423													58	133	---	---	---	---	PASS
FBXL18	80028	broad.mit.edu	37	7	5541300	5541300	+	Silent	SNP	G	A	A			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:5541300G>A	uc003soo.2	-	3	694	c.600C>T	c.(598-600)TAC>TAT	p.Y200Y	FBXL18_uc003son.3_Silent_p.Y200Y	NM_024963	NP_079239	Q96ME1	FXL18_HUMAN	F-box and leucine-rich repeat protein 18	200	LRR 4.									central_nervous_system(2)|ovary(1)	3		Ovarian(82;0.0607)		UCEC - Uterine corpus endometrioid carcinoma (126;0.181)|OV - Ovarian serous cystadenocarcinoma(56;3.64e-13)		GAATCTCGAAGTAGAGCAGCA	0.647													4	11	---	---	---	---	PASS
POU6F2	11281	broad.mit.edu	37	7	39247075	39247075	+	Missense_Mutation	SNP	A	T	T			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:39247075A>T	uc003thb.1	+	4	409	c.367A>T	c.(367-369)ATT>TTT	p.I123F	POU6F2_uc010kxo.2_Missense_Mutation_p.I115F	NM_007252	NP_009183	P78424	PO6F2_HUMAN	POU class 6 homeobox 2 isoform 1	123					central nervous system development|ganglion mother cell fate determination|transcription from RNA polymerase II promoter|visual perception		sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(1)	1						GCCAATCCTCATTCCCTTCAA	0.597													42	124	---	---	---	---	PASS
CASD1	64921	broad.mit.edu	37	7	94185226	94185226	+	3'UTR	SNP	A	C	C			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:94185226A>C	uc003uni.3	+	18					CASD1_uc003unj.3_3'UTR	NM_022900	NP_075051	Q96PB1	CASD1_HUMAN	CAS1 domain containing 1 precursor							integral to membrane				ovary(2)	2	all_cancers(62;6.71e-10)|all_epithelial(64;5e-09)|Lung NSC(181;0.188)|all_lung(186;0.215)		STAD - Stomach adenocarcinoma(171;0.0031)			ATGTGGTTGTATATATTGGAA	0.313													5	10	---	---	---	---	PASS
PIK3CG	5294	broad.mit.edu	37	7	106509619	106509619	+	Missense_Mutation	SNP	C	T	T	rs142822484	byFrequency	TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:106509619C>T	uc003vdv.3	+	2	1698	c.1613C>T	c.(1612-1614)CCG>CTG	p.P538L	PIK3CG_uc003vdu.2_Missense_Mutation_p.P538L|PIK3CG_uc003vdw.2_Missense_Mutation_p.P538L	NM_002649	NP_002640	P48736	PK3CG_HUMAN	phosphoinositide-3-kinase, catalytic, gamma	538					G-protein coupled receptor protein signaling pathway|phosphatidylinositol-mediated signaling|platelet activation	phosphatidylinositol 3-kinase complex	1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol-4,5-bisphosphate 3-kinase activity|protein binding			lung(16)|central_nervous_system(8)|breast(5)|pancreas(3)|stomach(2)|ovary(2)|upper_aerodigestive_tract(1)|skin(1)	38						ACCCCTGACCCGGAAGGGGAC	0.547													32	112	---	---	---	---	PASS
AMAC1L2	83650	broad.mit.edu	37	8	11188632	11188632	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:11188632C>A	uc003wtp.1	+	1	138	c.17C>A	c.(16-18)CCC>CAC	p.P6H		NM_054028	NP_473369	Q96KT7	AMCL2_HUMAN	acyl-malonyl condensing enzyme	6						integral to membrane					0			STAD - Stomach adenocarcinoma(15;0.00676)	COAD - Colon adenocarcinoma(149;0.0563)		GGCAGTCACCCCTACTTCAAC	0.642													21	36	---	---	---	---	PASS
MTUS1	57509	broad.mit.edu	37	8	17612616	17612616	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:17612616G>T	uc003wxv.2	-	2	1175	c.701C>A	c.(700-702)ACA>AAA	p.T234K	MTUS1_uc010lsy.2_RNA|MTUS1_uc003wxw.2_Missense_Mutation_p.T234K|MTUS1_uc010lsz.2_Missense_Mutation_p.T234K	NM_001001924	NP_001001924	Q9ULD2	MTUS1_HUMAN	mitochondrial tumor suppressor 1 isoform 1	234						Golgi apparatus|microtubule|microtubule organizing center|mitochondrion|nucleus|plasma membrane|spindle				ovary(1)|skin(1)	2				Colorectal(111;0.0778)		TTCTGATGGTGTGACTTGAGG	0.393													59	147	---	---	---	---	PASS
XPO7	23039	broad.mit.edu	37	8	21840307	21840307	+	Missense_Mutation	SNP	G	C	C			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:21840307G>C	uc003xaa.3	+	11	1363	c.1261G>C	c.(1261-1263)GTG>CTG	p.V421L	XPO7_uc010lti.2_Missense_Mutation_p.V430L|XPO7_uc010ltk.2_Missense_Mutation_p.V422L	NM_015024	NP_055839	Q9UIA9	XPO7_HUMAN	exportin 7 isoform b	421				Missing (in Ref. 3; BAA34465).	mRNA transport|protein export from nucleus|transmembrane transport	cytoplasm|nuclear pore	nuclear export signal receptor activity|protein transporter activity			ovary(1)|kidney(1)|breast(1)|central_nervous_system(1)|pancreas(1)	5				Colorectal(74;0.0187)|COAD - Colon adenocarcinoma(73;0.0724)		GTTGGAATCTGTGCACATCAT	0.517													29	106	---	---	---	---	PASS
PCMTD1	115294	broad.mit.edu	37	8	52732871	52732871	+	3'UTR	SNP	T	C	C	rs77261625	by1000genomes	TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:52732871T>C	uc003xqx.3	-	6					PCMTD1_uc011ldm.1_3'UTR|PCMTD1_uc003xqw.3_3'UTR|PCMTD1_uc011ldn.1_3'UTR|PCMTD1_uc010lya.2_3'UTR	NM_052937	NP_443169	Q96MG8	PCMD1_HUMAN	protein-L-isoaspartate (D-aspartate)							cytoplasm	protein-L-isoaspartate (D-aspartate) O-methyltransferase activity				0		Lung NSC(129;0.0795)|all_lung(136;0.144)				TTTTCAAGACTAAAGGAATTA	0.313													5	35	---	---	---	---	PASS
UQCRB	7381	broad.mit.edu	37	8	97244062	97244062	+	Silent	SNP	T	A	A			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:97244062T>A	uc003yhq.3	-	3	302	c.198A>T	c.(196-198)GCA>GCT	p.A66A	UQCRB_uc011lgt.1_RNA|UQCRB_uc010mbc.2_RNA	NM_006294	NP_006285	P14927	QCR7_HUMAN	ubiquinol-cytochrome c reductase binding	66					aerobic respiration|mitochondrial electron transport, ubiquinol to cytochrome c	mitochondrial respiratory chain	ubiquinol-cytochrome-c reductase activity			ovary(1)	1	Breast(36;5.16e-05)					TCAGGTCCAGTGCCCTCTTAA	0.413													60	138	---	---	---	---	PASS
UBR5	51366	broad.mit.edu	37	8	103341598	103341598	+	Silent	SNP	A	G	G			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:103341598A>G	uc003ykr.1	-	10	1161	c.1128T>C	c.(1126-1128)GCT>GCC	p.A376A	UBR5_uc003yks.1_Silent_p.A376A	NM_015902	NP_056986	O95071	UBR5_HUMAN	ubiquitin protein ligase E3 component n-recognin	376					cell proliferation|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of catenin import into nucleus|positive regulation of protein import into nucleus, translocation|progesterone receptor signaling pathway|protein polyubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|response to DNA damage stimulus	nucleus|soluble fraction	protein binding|RNA binding|ubiquitin-ubiquitin ligase activity|zinc ion binding			lung(16)|ovary(4)|large_intestine(3)|breast(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|kidney(1)	28	all_cancers(14;8e-07)|all_epithelial(15;2.18e-08)|Lung NSC(17;2.55e-05)|all_lung(17;8.85e-05)		OV - Ovarian serous cystadenocarcinoma(57;0.000442)			CAGAATACAGAGCCCCAATAC	0.333													61	261	---	---	---	---	PASS
DENND3	22898	broad.mit.edu	37	8	142178354	142178354	+	Silent	SNP	C	A	A			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:142178354C>A	uc003yvy.2	+	13	2043	c.1765C>A	c.(1765-1767)CGG>AGG	p.R589R	DENND3_uc010mep.2_Silent_p.R550R|DENND3_uc003yvz.1_Silent_p.R273R	NM_014957	NP_055772	A2RUS2	DEND3_HUMAN	DENN/MADD domain containing 3	589										ovary(1)	1	all_cancers(97;7.36e-15)|all_epithelial(106;2.33e-13)|Lung NSC(106;1.23e-05)|all_lung(105;1.75e-05)|Ovarian(258;0.01)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.105)			AACAGACATACGGATCTTTCC	0.557													38	138	---	---	---	---	PASS
SPATC1	375686	broad.mit.edu	37	8	145096167	145096167	+	Silent	SNP	T	G	G			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145096167T>G	uc011lkw.1	+	4	1443	c.1341T>G	c.(1339-1341)GGT>GGG	p.G447G	SPATC1_uc011lkx.1_Intron	NM_198572	NP_940974	Q76KD6	SPERI_HUMAN	spermatogenesis and centriole associated 1	447										ovary(1)|central_nervous_system(1)	2	all_cancers(97;8.2e-11)|all_epithelial(106;1.1e-09)|Lung NSC(106;5.89e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;6.79e-41)|Epithelial(56;1.02e-39)|all cancers(56;3.67e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			GGCTGGTGGGTGAGATTGCCT	0.622													5	18	---	---	---	---	PASS
TXN	7295	broad.mit.edu	37	9	113007067	113007067	+	Missense_Mutation	SNP	C	G	G			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:113007067C>G	uc004bep.1	-	4	309	c.246G>C	c.(244-246)AAG>AAC	p.K82N	TXN_uc004beq.1_Missense_Mutation_p.K62N	NM_003329	NP_003320	P10599	THIO_HUMAN	thioredoxin	82	Thioredoxin.				cell proliferation|cell-cell signaling|cellular component movement|electron transport chain|glycerol ether metabolic process|nucleobase, nucleoside and nucleotide interconversion|positive regulation of DNA binding|regulation of protein import into nucleus, translocation|response to radiation|signal transduction|transcription, DNA-dependent|transport	cytosol|extracellular region|nucleoplasm	electron carrier activity|protein binding|protein disulfide oxidoreductase activity				0				OV - Ovarian serous cystadenocarcinoma(323;7.36e-07)		CCTTTTGTCCCTTCTTAAAAA	0.393													44	222	---	---	---	---	PASS
AKNA	80709	broad.mit.edu	37	9	117106062	117106062	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:117106062G>T	uc004biq.3	-	18	3818	c.3683C>A	c.(3682-3684)TCC>TAC	p.S1228Y	AKNA_uc004bin.3_Missense_Mutation_p.S475Y|AKNA_uc004bio.3_Missense_Mutation_p.S688Y|AKNA_uc004bip.3_Missense_Mutation_p.S1147Y|AKNA_uc004bir.3_Missense_Mutation_p.S1228Y|AKNA_uc004bis.3_Missense_Mutation_p.S1228Y|AKNA_uc010mve.2_Missense_Mutation_p.S1109Y	NM_030767	NP_110394	Q7Z591	AKNA_HUMAN	AT-hook transcription factor	1228					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			ovary(4)|central_nervous_system(2)	6						CGCCTTAGGGGACAGAACATG	0.522													17	74	---	---	---	---	PASS
DEC1	50514	broad.mit.edu	37	9	118163493	118163493	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:118163493A>G	uc004bjk.1	+	7	628	c.109A>G	c.(109-111)AGA>GGA	p.R37G	DEC1_uc004bjl.1_RNA	NM_017418	NP_059114	Q9P2X7	DEC1_HUMAN	deleted in esophageal cancer 1	37					negative regulation of cell proliferation					ovary(1)	1						TGCCCTGCACAGAGAGAGGTC	0.473													8	72	---	---	---	---	PASS
GRID1	2894	broad.mit.edu	37	10	87407078	87407078	+	Silent	SNP	G	T	T			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:87407078G>T	uc001kdl.1	-	13	2175	c.2074C>A	c.(2074-2076)CGA>AGA	p.R692R	GRID1_uc009xsu.1_RNA|GRID1_uc010qmf.1_Silent_p.R263R|uc001kdm.1_RNA	NM_017551	NP_060021	Q9ULK0	GRID1_HUMAN	glutamate receptor, ionotropic, delta 1	692	Extracellular (Potential).					cell junction|integral to membrane|outer membrane-bounded periplasmic space|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|ionotropic glutamate receptor activity			ovary(5)|upper_aerodigestive_tract(2)|large_intestine(2)|central_nervous_system(1)	10					L-Glutamic Acid(DB00142)	CCCTTGGCTCGGAAGTACTCA	0.552										Multiple Myeloma(13;0.14)			111	324	---	---	---	---	PASS
MMRN2	79812	broad.mit.edu	37	10	88702115	88702115	+	Missense_Mutation	SNP	C	G	G			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:88702115C>G	uc001kea.2	-	6	2553	c.2426G>C	c.(2425-2427)GGG>GCG	p.G809A	MMRN2_uc010qmn.1_Missense_Mutation_p.G452A|MMRN2_uc009xtb.2_Missense_Mutation_p.G766A	NM_024756	NP_079032	Q9H8L6	MMRN2_HUMAN	multimerin 2 precursor	809						extracellular space				large_intestine(1)	1						TGGCACAGGCCCTGTGACCCG	0.647													19	75	---	---	---	---	PASS
TLL2	7093	broad.mit.edu	37	10	98273269	98273269	+	Silent	SNP	G	A	A			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:98273269G>A	uc001kml.1	-	1	400	c.174C>T	c.(172-174)GCC>GCT	p.A58A	TLL2_uc009xvf.1_Silent_p.A58A	NM_012465	NP_036597	Q9Y6L7	TLL2_HUMAN	tolloid-like 2 precursor	58					cell differentiation|multicellular organismal development|proteolysis	extracellular region	calcium ion binding|metalloendopeptidase activity|zinc ion binding			ovary(1)|pancreas(1)|skin(1)	3		Colorectal(252;0.0846)		Epithelial(162;1.51e-07)|all cancers(201;7.59e-06)		GGCACCTACCGGCTTTGCAAG	0.642													15	33	---	---	---	---	PASS
PNLIPRP1	5407	broad.mit.edu	37	10	118352110	118352110	+	Intron	SNP	T	C	C			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:118352110T>C	uc001lco.1	+						PNLIPRP1_uc001lcp.2_Intron|PNLIPRP1_uc001lcn.2_Silent_p.S129S|PNLIPRP1_uc009xys.1_Intron	NM_006229	NP_006220	P54315	LIPR1_HUMAN	pancreatic lipase-related protein 1 precursor						lipid metabolic process		calcium ion binding|triglyceride lipase activity			ovary(1)|breast(1)	2				all cancers(201;0.0161)		TGCTAACATCTCTGCATCACT	0.413													18	51	---	---	---	---	PASS
PDZD8	118987	broad.mit.edu	37	10	119044256	119044256	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:119044256G>A	uc001lde.1	-	5	2187	c.1988C>T	c.(1987-1989)TCA>TTA	p.S663L		NM_173791	NP_776152	Q8NEN9	PDZD8_HUMAN	PDZ domain containing 8	663					intracellular signal transduction		metal ion binding				0		Colorectal(252;0.19)		all cancers(201;0.0121)		GGAAGTTTCTGAAGTGACATC	0.418													9	174	---	---	---	---	PASS
SFXN4	119559	broad.mit.edu	37	10	120917388	120917388	+	Missense_Mutation	SNP	T	G	G			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:120917388T>G	uc001leb.2	-	8	511	c.466A>C	c.(466-468)AGT>CGT	p.S156R	SFXN4_uc001ldy.2_Missense_Mutation_p.S40R|SFXN4_uc001ldz.2_Missense_Mutation_p.S40R|SFXN4_uc001lea.2_RNA	NM_213649	NP_998814	Q6P4A7	SFXN4_HUMAN	sideroflexin 4	156					iron ion homeostasis	integral to membrane|mitochondrial membrane	cation transmembrane transporter activity			ovary(1)	1		Lung NSC(174;0.094)|all_lung(145;0.123)		all cancers(201;0.0261)		CTCACGTAACTTCTGTTTCCA	0.408													37	84	---	---	---	---	PASS
WDR11	55717	broad.mit.edu	37	10	122663626	122663626	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:122663626G>A	uc010qtf.1	+	24	3237	c.2999G>A	c.(2998-3000)TGT>TAT	p.C1000Y	WDR11_uc010qte.1_Missense_Mutation_p.C602Y|WDR11_uc001lfd.1_Missense_Mutation_p.C518Y|WDR11_uc009xzn.2_Missense_Mutation_p.C291Y	NM_018117	NP_060587	Q9BZH6	WDR11_HUMAN	bromodomain and WD repeat domain containing 2	1000						integral to membrane					0						ACAAGGAAATGTACAGACCAG	0.338													42	106	---	---	---	---	PASS
MUC2	4583	broad.mit.edu	37	11	1086012	1086012	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1086012C>T	uc001lsx.1	+	22	2879	c.2852C>T	c.(2851-2853)ACG>ATG	p.T951M		NM_002457	NP_002448	Q02817	MUC2_HUMAN	mucin 2 precursor	951	VWFD 3.					inner mucus layer|outer mucus layer	protein binding			lung(1)|breast(1)	2		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	GCCTACACCACGCGGGAGGTG	0.617													15	34	---	---	---	---	PASS
MUC2	4583	broad.mit.edu	37	11	1090371	1090371	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1090371C>A	uc001lsx.1	+	27	3694	c.3667C>A	c.(3667-3669)CCG>ACG	p.P1223T		NM_002457	NP_002448	Q02817	MUC2_HUMAN	mucin 2 precursor	1223						inner mucus layer|outer mucus layer	protein binding			lung(1)|breast(1)	2		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	CGTCTGCAGGCCGGAGGAAGG	0.657													5	11	---	---	---	---	PASS
PSMA1	5682	broad.mit.edu	37	11	14535543	14535543	+	Intron	SNP	T	G	G			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:14535543T>G	uc001mlk.2	-						PSMA1_uc001mll.2_Intron|PSMA1_uc010rcp.1_Intron|PSMA1_uc001mlj.2_Intron|PSMA1_uc010rcq.1_3'UTR	NM_002786	NP_002777	P25786	PSA1_HUMAN	proteasome alpha 1 subunit isoform 2						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|viral reproduction	cytoplasm|nucleus|polysome|proteasome core complex, alpha-subunit complex	protein binding|RNA binding|threonine-type endopeptidase activity			upper_aerodigestive_tract(1)|skin(1)	2						TGTTGCATAATCCACCAGAGA	0.313													3	4	---	---	---	---	PASS
SPRYD5	84767	broad.mit.edu	37	11	55653128	55653128	+	Missense_Mutation	SNP	T	A	A	rs150592372	by1000genomes	TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55653128T>A	uc010rip.1	+	2	316	c.224T>A	c.(223-225)TTC>TAC	p.F75Y	SPRYD5_uc010riq.1_5'Flank	NM_032681	NP_116070	Q9BSJ1	SPRY5_HUMAN	SPRY domain containing 5	75						intracellular	zinc ion binding				0		all_epithelial(135;0.226)				AACATGGCTTTCATTGCCAGA	0.473													7	27	---	---	---	---	PASS
SLC22A9	114571	broad.mit.edu	37	11	63175588	63175588	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:63175588G>A	uc001nww.2	+	8	1561	c.1293G>A	c.(1291-1293)ATG>ATA	p.M431I	SLC22A9_uc001nwx.2_Intron	NM_080866	NP_543142	Q8IVM8	S22A9_HUMAN	solute carrier family 22 (organic anion/cation	431	Extracellular (Potential).				transmembrane transport	integral to membrane				breast(2)|large_intestine(1)	3						CTCCAGAAATGCAGACGCTGC	0.478													9	37	---	---	---	---	PASS
MALAT1	378938	broad.mit.edu	37	11	65273403	65273403	+	RNA	SNP	C	A	A			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65273403C>A	uc010roh.1	+	1		c.8171C>A			uc001ody.2_5'Flank	NR_002819				Homo sapiens clone alpha1 mRNA sequence.												0						TGCAAAAATTCTCTGCTAAGA	0.443													42	86	---	---	---	---	PASS
AASDHPPT	60496	broad.mit.edu	37	11	105962108	105962108	+	Missense_Mutation	SNP	A	T	T			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:105962108A>T	uc001pjc.1	+	4	743	c.597A>T	c.(595-597)GAA>GAT	p.E199D	AASDHPPT_uc010rvn.1_RNA|AASDHPPT_uc001pjd.1_Missense_Mutation_p.E52D	NM_015423	NP_056238	Q9NRN7	ADPPT_HUMAN	aminoadipate-semialdehyde	199					macromolecule biosynthetic process|pantothenate metabolic process	cytosol	holo-[acyl-carrier-protein] synthase activity|magnesium ion binding|protein binding				0		Melanoma(852;0.000878)|Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Breast(348;0.0321)		BRCA - Breast invasive adenocarcinoma(274;5.78e-05)|Epithelial(105;0.00622)|all cancers(92;0.041)		AGCGGCTTGAATTTGATCTAT	0.363													48	121	---	---	---	---	PASS
C12orf11	55726	broad.mit.edu	37	12	27059272	27059272	+	Nonsense_Mutation	SNP	T	A	A			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:27059272T>A	uc001rhk.3	-	16	2581	c.2044A>T	c.(2044-2046)AGA>TGA	p.R682*	C12orf11_uc001rhj.3_Nonsense_Mutation_p.R250*|C12orf11_uc010sjk.1_Nonsense_Mutation_p.R581*	NM_018164	NP_060634	Q9NVM9	M89BB_HUMAN	hypothetical protein LOC55726	682					cell division|mitosis|regulation of mitotic cell cycle		protein binding			large_intestine(1)|ovary(1)|central_nervous_system(1)	3	Colorectal(261;0.0847)					AGTTCAGCTCTGTTATTAACA	0.353													132	179	---	---	---	---	PASS
GNS	2799	broad.mit.edu	37	12	65136922	65136922	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:65136922G>A	uc001ssg.3	-	6	961	c.791C>T	c.(790-792)ACG>ATG	p.T264M	GNS_uc001ssf.2_Missense_Mutation_p.T208M|GNS_uc010ssq.1_Missense_Mutation_p.T296M|GNS_uc010ssr.1_Missense_Mutation_p.T244M	NM_002076	NP_002067	P15586	GNS_HUMAN	glucosamine (N-acetyl)-6-sulfatase precursor	264						lysosome	metal ion binding|N-acetylglucosamine-6-sulfatase activity|protein binding			central_nervous_system(1)	1	Lung NSC(1;7.25e-14)|all_lung(1;1.25e-12)		LUAD - Lung adenocarcinoma(6;0.115)	GBM - Glioblastoma multiforme(28;0.0435)		GGAAGCTACCGTTCCATGGAT	0.458													64	297	---	---	---	---	PASS
CAND1	55832	broad.mit.edu	37	12	67696132	67696132	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:67696132G>T	uc001stn.2	+	8	1467	c.1030G>T	c.(1030-1032)GAC>TAC	p.D344Y	CAND1_uc001sto.2_Missense_Mutation_p.D22Y	NM_018448	NP_060918	Q86VP6	CAND1_HUMAN	TIP120 protein	344	Asp-rich.|HEAT 8.				cell differentiation|negative regulation of catalytic activity|protein ubiquitination|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus|ubiquitin ligase complex	protein binding			central_nervous_system(1)|skin(1)	2			GBM - Glioblastoma multiforme(1;1.13e-10)|Lung(24;0.000342)|LUSC - Lung squamous cell carcinoma(43;0.196)	GBM - Glioblastoma multiforme(28;0.0279)		TGATGATGATGACATGAGTTG	0.393													84	275	---	---	---	---	PASS
ANKS1B	56899	broad.mit.edu	37	12	99793525	99793525	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:99793525T>C	uc001tge.1	-	12	2057	c.1640A>G	c.(1639-1641)TAT>TGT	p.Y547C	ANKS1B_uc001tgf.1_Missense_Mutation_p.Y127C|ANKS1B_uc009ztt.1_Missense_Mutation_p.Y513C	NM_152788	NP_690001	Q7Z6G8	ANS1B_HUMAN	cajalin 2 isoform a	547						Cajal body|cell junction|cytoplasm|dendritic spine|postsynaptic density|postsynaptic membrane					0		all_cancers(3;0.0197)|all_epithelial(3;0.0101)|Esophageal squamous(3;0.0559)|Breast(359;0.209)		OV - Ovarian serous cystadenocarcinoma(2;2.89e-08)|Epithelial(2;6.12e-08)|all cancers(2;4.07e-06)		GATTTCAAAATATTCTTGGTT	0.418													45	124	---	---	---	---	PASS
TRPV4	59341	broad.mit.edu	37	12	110240804	110240804	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110240804T>C	uc001tpj.1	-	3	799	c.704A>G	c.(703-705)TAC>TGC	p.Y235C	TRPV4_uc001tpg.1_Missense_Mutation_p.Y201C|TRPV4_uc001tph.1_Missense_Mutation_p.Y235C|TRPV4_uc001tpi.1_Missense_Mutation_p.Y235C|TRPV4_uc001tpk.1_Missense_Mutation_p.Y235C|TRPV4_uc001tpl.1_Missense_Mutation_p.Y235C	NM_021625	NP_067638	Q9HBA0	TRPV4_HUMAN	transient receptor potential cation channel,	235	Cytoplasmic (Potential).				actin cytoskeleton reorganization|actin filament organization|calcium ion import|cell death|cell volume homeostasis|cell-cell junction assembly|cellular hypotonic response|cortical microtubule organization|elevation of cytosolic calcium ion concentration|microtubule polymerization|negative regulation of neuron projection development|osmosensory signaling pathway|positive regulation of microtubule depolymerization|response to mechanical stimulus	cortical actin cytoskeleton|filopodium|focal adhesion|growth cone|integral to membrane|lamellipodium|ruffle membrane	actin filament binding|alpha-tubulin binding|beta-tubulin binding|calcium channel activity|calmodulin binding|microtubule binding|protein binding|protein kinase C binding|SH2 domain binding			ovary(2)|haematopoietic_and_lymphoid_tissue(1)|skin(1)	4						ACCTCGATAGTAGATGTCACG	0.607													38	33	---	---	---	---	PASS
C12orf65	91574	broad.mit.edu	37	12	123741655	123741655	+	3'UTR	SNP	G	C	C			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123741655G>C	uc001uen.2	+	3					C12orf65_uc001ueo.2_RNA|C12orf65_uc010tan.1_3'UTR	NM_152269	NP_689482	Q9H3J6	CL065_HUMAN	hypothetical protein LOC91574							mitochondrion	translation release factor activity				0	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000595)|Epithelial(86;0.00199)		TCCATCACCAGCATTATTATA	0.373													25	28	---	---	---	---	PASS
EBPL	84650	broad.mit.edu	37	13	50243946	50243946	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:50243946C>T	uc001vdg.2	-	2	271	c.208G>A	c.(208-210)GTT>ATT	p.V70I	EBPL_uc001vdh.2_RNA|EBPL_uc001vdi.2_Missense_Mutation_p.V70I	NM_032565	NP_115954	Q9BY08	EBPL_HUMAN	emopamil binding related protein, delta8-delta7	70					sterol metabolic process	endoplasmic reticulum membrane|integral to membrane	cholestenol delta-isomerase activity				0		Lung NSC(96;0.000468)|Breast(56;0.0011)|Prostate(109;0.00243)|Hepatocellular(98;0.0556)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(99;2.06e-09)		GAATTTGCAACGTTTCCTACT	0.398											OREG0022412	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	23	66	---	---	---	---	PASS
EBPL	84650	broad.mit.edu	37	13	50243947	50243947	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:50243947G>T	uc001vdg.2	-	2	270	c.207C>A	c.(205-207)AAC>AAA	p.N69K	EBPL_uc001vdh.2_RNA|EBPL_uc001vdi.2_Missense_Mutation_p.N69K	NM_032565	NP_115954	Q9BY08	EBPL_HUMAN	emopamil binding related protein, delta8-delta7	69					sterol metabolic process	endoplasmic reticulum membrane|integral to membrane	cholestenol delta-isomerase activity				0		Lung NSC(96;0.000468)|Breast(56;0.0011)|Prostate(109;0.00243)|Hepatocellular(98;0.0556)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(99;2.06e-09)		AATTTGCAACGTTTCCTACTA	0.398											OREG0022412	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	23	66	---	---	---	---	PASS
RNF219	79596	broad.mit.edu	37	13	79190711	79190711	+	Silent	SNP	A	G	G			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:79190711A>G	uc001vkw.1	-	6	1244	c.1185T>C	c.(1183-1185)CTT>CTC	p.L395L	uc001vku.1_RNA|RNF219_uc010afb.1_Silent_p.L205L|RNF219_uc010afc.2_Intron	NM_024546	NP_078822	Q5W0B1	RN219_HUMAN	ring finger protein 219	395							zinc ion binding			large_intestine(2)	2		Acute lymphoblastic leukemia(28;0.0279)|Breast(118;0.0848)		GBM - Glioblastoma multiforme(99;0.0414)		GAAGGCAACTAAGGGACAAAG	0.428													10	211	---	---	---	---	PASS
SEC23A	10484	broad.mit.edu	37	14	39511999	39511999	+	Nonsense_Mutation	SNP	A	C	C			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:39511999A>C	uc001wup.1	-	17	2200	c.1977T>G	c.(1975-1977)TAT>TAG	p.Y659*	SEC23A_uc010tqa.1_Nonsense_Mutation_p.Y545*|SEC23A_uc010tqb.1_Nonsense_Mutation_p.Y630*	NM_006364	NP_006355	Q15436	SC23A_HUMAN	SEC23-related protein A	659					COPII vesicle coating|intracellular protein transport|post-translational protein modification|protein N-linked glycosylation via asparagine	COPII vesicle coat|cytosol|Golgi membrane|smooth endoplasmic reticulum membrane	protein binding|zinc ion binding			ovary(4)|upper_aerodigestive_tract(1)	5	Hepatocellular(127;0.213)		Lung(238;0.00047)|LUAD - Lung adenocarcinoma(48;0.000565)	GBM - Glioblastoma multiforme(112;0.0151)		CCTCACCATGATAAATCAAAA	0.338													35	66	---	---	---	---	PASS
JMJD7-PLA2G4B	8681	broad.mit.edu	37	15	42127085	42127085	+	Missense_Mutation	SNP	A	G	G	rs148006565		TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42127085A>G	uc001zoo.3	+	2	252	c.212A>G	c.(211-213)TAT>TGT	p.Y71C	JMJD7-PLA2G4B_uc010bcm.1_RNA|JMJD7-PLA2G4B_uc001zom.2_Intron|JMJD7-PLA2G4B_uc001zon.2_Missense_Mutation_p.Y71C|JMJD7-PLA2G4B_uc010bcn.2_Missense_Mutation_p.Y71C|JMJD7-PLA2G4B_uc001zop.1_5'UTR|JMJD7-PLA2G4B_uc001zoq.3_5'Flank	NM_005090	NP_005081	P0C869	PA24B_HUMAN	JMJD7-PLA2G4B protein	Error:Variant_position_missing_in_P0C869_after_alignment					arachidonic acid metabolic process|calcium-mediated signaling|glycerophospholipid catabolic process|inflammatory response|parturition	cytosol|early endosome membrane|extracellular region|mitochondrial membrane	calcium ion binding|calcium-dependent phospholipase A2 activity|calcium-dependent phospholipid binding|lysophospholipase activity			large_intestine(1)	1						TCCCTCCCCTATTTCAGGTGG	0.622													27	79	---	---	---	---	PASS
THAP10	56906	broad.mit.edu	37	15	71174954	71174954	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:71174954G>T	uc002asv.2	-	3	755	c.613C>A	c.(613-615)CTG>ATG	p.L205M	LRRC49_uc002asu.2_Intron	NM_020147	NP_064532	Q9P2Z0	THA10_HUMAN	THAP domain containing 10	205							DNA binding|metal ion binding			ovary(1)|skin(1)	2						GCATTACACAGTCTTTTTCCA	0.363													31	125	---	---	---	---	PASS
CCDC33	80125	broad.mit.edu	37	15	74622668	74622668	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:74622668G>A	uc002axo.2	+	12	1823	c.1429G>A	c.(1429-1431)GGC>AGC	p.G477S	CCDC33_uc002axp.2_Missense_Mutation_p.G299S|CCDC33_uc002axq.2_Missense_Mutation_p.G70S|CCDC33_uc002axr.2_Missense_Mutation_p.G70S	NM_025055	NP_079331	Q8N5R6	CCD33_HUMAN	coiled-coil domain containing 33 isoform 1	680	Potential.						protein binding			ovary(3)|skin(2)	5						AGAGGGGCAGGGCAAAGCCAG	0.642													4	14	---	---	---	---	PASS
IL16	3603	broad.mit.edu	37	15	81601012	81601012	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:81601012C>T	uc002bgh.3	+	19	4248	c.3872C>T	c.(3871-3873)GCC>GTC	p.A1291V	IL16_uc002bge.3_RNA|IL16_uc010unp.1_Missense_Mutation_p.A1332V|IL16_uc002bgg.2_Missense_Mutation_p.A1290V|IL16_uc002bgj.2_Missense_Mutation_p.A784V|IL16_uc002bgk.2_Missense_Mutation_p.A590V	NM_172217	NP_757366	Q14005	IL16_HUMAN	interleukin 16 isoform 2	1291	PDZ 4.				immune response|interspecies interaction between organisms|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|extracellular space|nucleus|plasma membrane	cytokine activity			ovary(2)|lung(1)|skin(1)	4						GGTGGCACTGCCATGCAGGGC	0.522													36	99	---	---	---	---	PASS
RCCD1	91433	broad.mit.edu	37	15	91504264	91504264	+	Missense_Mutation	SNP	A	C	C			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:91504264A>C	uc002bqj.2	+	8	1239	c.959A>C	c.(958-960)GAG>GCG	p.E320A	RCCD1_uc002bqk.2_Missense_Mutation_p.E320A|RCCD1_uc002bql.2_Missense_Mutation_p.E318A|RCCD1_uc010bob.2_Missense_Mutation_p.E109A	NM_033544	NP_291022	A6NED2	RCCD1_HUMAN	RCC1 domain containing 1	320	RCC1 4.										0	Lung NSC(78;0.0987)|all_lung(78;0.175)		Lung(145;0.189)			GGAACAGGGGAGCTCTACACC	0.507													24	71	---	---	---	---	PASS
RHOT2	89941	broad.mit.edu	37	16	720301	720301	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:720301A>G	uc002cip.2	+	7	449	c.382A>G	c.(382-384)ATG>GTG	p.M128V	RHOT2_uc002ciq.2_Missense_Mutation_p.M21V|RHOT2_uc010bqy.2_5'Flank	NM_138769	NP_620124	Q8IXI1	MIRO2_HUMAN	ras homolog gene family, member T2	128	Miro 1.|Mitochondrial intermembrane (Potential).				apoptosis|cellular homeostasis|mitochondrion transport along microtubule|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|integral to mitochondrial outer membrane|plasma membrane	calcium ion binding|GTP binding|GTPase activity|protein binding			pancreas(1)	1		Hepatocellular(780;0.0218)				GGGGAGCTCCATGGAGGCCGT	0.632													41	73	---	---	---	---	PASS
ATXN2L	11273	broad.mit.edu	37	16	28841977	28841977	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:28841977G>T	uc002drc.2	+	9	1244	c.1076G>T	c.(1075-1077)GGT>GTT	p.G359V	uc010vct.1_Intron|ATXN2L_uc010byl.1_Missense_Mutation_p.G359V|ATXN2L_uc002drb.2_Missense_Mutation_p.G359V|ATXN2L_uc002dqy.2_Missense_Mutation_p.G359V|ATXN2L_uc002dra.2_Missense_Mutation_p.G359V|ATXN2L_uc002dqz.2_Missense_Mutation_p.G359V|ATXN2L_uc010vdb.1_Missense_Mutation_p.G359V|ATXN2L_uc002dre.2_Missense_Mutation_p.G359V|ATXN2L_uc002drf.2_5'UTR	NM_007245	NP_009176	Q8WWM7	ATX2L_HUMAN	ataxin 2 related protein isoform A	359						membrane				upper_aerodigestive_tract(1)|ovary(1)	2						GTCCGGGAAGGTCCCCGGGGA	0.582													17	70	---	---	---	---	PASS
DCTPP1	79077	broad.mit.edu	37	16	30435760	30435760	+	Silent	SNP	G	A	A			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30435760G>A	uc002dyf.2	-	3	379	c.307C>T	c.(307-309)CTG>TTG	p.L103L	ZNF771_uc010bzx.2_Intron	NM_024096	NP_077001	Q9H773	DCTP1_HUMAN	dCTP pyrophosphatase 1	103					nucleoside triphosphate catabolic process	cytosol	dCTP diphosphatase activity|identical protein binding|magnesium ion binding				0						AATGCCACCAGGTAGATGAGG	0.622													20	46	---	---	---	---	PASS
CYB5B	80777	broad.mit.edu	37	16	69481136	69481136	+	Missense_Mutation	SNP	T	A	A			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:69481136T>A	uc002exg.1	+	2	347	c.258T>A	c.(256-258)GAT>GAA	p.D86E	CYB5B_uc002exf.2_Missense_Mutation_p.D86E|CYB5B_uc010cfl.1_Missense_Mutation_p.D86E	NM_030579	NP_085056	O43169	CYB5B_HUMAN	cytochrome b5 outer mitochondrial membrane	82	Cytochrome b5 heme-binding.				electron transport chain|transport	integral to membrane|mitochondrial outer membrane	heme binding				0		Ovarian(137;0.101)				ACTCTTCTGATGCCAGAGAAA	0.443													8	96	---	---	---	---	PASS
CYB5B	80777	broad.mit.edu	37	16	69481137	69481137	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:69481137G>A	uc002exg.1	+	2	348	c.259G>A	c.(259-261)GCC>ACC	p.A87T	CYB5B_uc002exf.2_Missense_Mutation_p.A87T|CYB5B_uc010cfl.1_Missense_Mutation_p.A87T	NM_030579	NP_085056	O43169	CYB5B_HUMAN	cytochrome b5 outer mitochondrial membrane	83	Cytochrome b5 heme-binding.				electron transport chain|transport	integral to membrane|mitochondrial outer membrane	heme binding				0		Ovarian(137;0.101)				CTCTTCTGATGCCAGAGAAAT	0.443													7	97	---	---	---	---	PASS
CYB5B	80777	broad.mit.edu	37	16	69481138	69481138	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:69481138C>T	uc002exg.1	+	2	349	c.260C>T	c.(259-261)GCC>GTC	p.A87V	CYB5B_uc002exf.2_Missense_Mutation_p.A87V|CYB5B_uc010cfl.1_Missense_Mutation_p.A87V	NM_030579	NP_085056	O43169	CYB5B_HUMAN	cytochrome b5 outer mitochondrial membrane	83	Cytochrome b5 heme-binding.				electron transport chain|transport	integral to membrane|mitochondrial outer membrane	heme binding				0		Ovarian(137;0.101)				TCTTCTGATGCCAGAGAAATG	0.448													7	97	---	---	---	---	PASS
ZC3H18	124245	broad.mit.edu	37	16	88696911	88696911	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:88696911C>T	uc002fky.2	+	17	2785	c.2585C>T	c.(2584-2586)TCA>TTA	p.S862L	ZC3H18_uc010voz.1_Missense_Mutation_p.S886L|ZC3H18_uc010chw.2_RNA|ZC3H18_uc002fkz.2_Missense_Mutation_p.S132L	NM_144604	NP_653205	Q86VM9	ZCH18_HUMAN	zinc finger CCCH-type containing 18	862						nucleus	nucleic acid binding|zinc ion binding			skin(1)	1				BRCA - Breast invasive adenocarcinoma(80;0.0542)		GACCGGAAGTCAGGTGGGAGA	0.632													5	17	---	---	---	---	PASS
ZNF276	92822	broad.mit.edu	37	16	89789515	89789515	+	Intron	SNP	C	G	G			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89789515C>G	uc002fos.3	+						C16orf7_uc002fom.1_5'Flank|ZNF276_uc010ciq.2_Intron|ZNF276_uc002fop.2_Intron|ZNF276_uc002foq.3_Intron|ZNF276_uc010cir.2_Intron|ZNF276_uc002for.3_Intron|ZNF276_uc010cis.2_Intron|ZNF276_uc002fot.3_Intron|ZNF276_uc010vpm.1_5'UTR|ZNF276_uc010cit.1_5'Flank	NM_001113525	NP_001106997	Q8N554	ZN276_HUMAN	zinc finger protein 276 isoform a						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Lung NSC(15;2.19e-05)|all_lung(18;3.07e-05)|all_hematologic(23;0.0256)		BRCA - Breast invasive adenocarcinoma(80;0.0278)		GCCTGCTTGTCCTGCTCATGG	0.637													14	53	---	---	---	---	PASS
COX10	1352	broad.mit.edu	37	17	13972886	13972886	+	5'UTR	SNP	A	T	T			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:13972886A>T	uc002gof.3	+	1					COX10_uc010vvs.1_5'UTR|COX10_uc010vvt.1_5'UTR|uc002goe.1_5'Flank	NM_001303	NP_001294	Q12887	COX10_HUMAN	heme A:farnesyltransferase precursor						heme a biosynthetic process|heme O biosynthetic process|respiratory chain complex IV assembly	integral to membrane|mitochondrial membrane	protoheme IX farnesyltransferase activity				0		all_lung(20;0.06)|Lung SC(565;0.168)		UCEC - Uterine corpus endometrioid carcinoma (92;0.106)		GAGAGAGGACACAGGGATCCC	0.672													7	16	---	---	---	---	PASS
EFCAB5	374786	broad.mit.edu	37	17	28384816	28384816	+	Missense_Mutation	SNP	G	C	C			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:28384816G>C	uc002het.2	+	13	2680	c.2488G>C	c.(2488-2490)GAC>CAC	p.D830H	EFCAB5_uc010wbj.1_Missense_Mutation_p.D774H|EFCAB5_uc010wbk.1_Missense_Mutation_p.D487H|EFCAB5_uc010csd.2_RNA|EFCAB5_uc010cse.2_Intron|EFCAB5_uc010csf.2_Missense_Mutation_p.D709H	NM_198529	NP_940931	A4FU69	EFCB5_HUMAN	EF-hand calcium binding domain 5 isoform a	830							calcium ion binding			ovary(1)|skin(1)	2						TGTTGGTGAAGACGCTCCCTT	0.443													57	134	---	---	---	---	PASS
VAT1	10493	broad.mit.edu	37	17	41168133	41168133	+	Missense_Mutation	SNP	T	G	G			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:41168133T>G	uc002icm.1	-	6	1247	c.1127A>C	c.(1126-1128)GAG>GCG	p.E376A	VAT1_uc010cyw.1_Missense_Mutation_p.E242A|VAT1_uc010whk.1_Missense_Mutation_p.E308A	NM_006373	NP_006364	Q99536	VAT1_HUMAN	vesicle amine transport protein 1	376						cytoplasm|integral to membrane	oxidoreductase activity|zinc ion binding				0		Breast(137;0.000717)		BRCA - Breast invasive adenocarcinoma(366;0.156)		ATTCTTCTTCTCCTGCATCTG	0.557													104	335	---	---	---	---	PASS
LRRC37A4	55073	broad.mit.edu	37	17	43587569	43587569	+	Intron	SNP	G	C	C	rs149697015	by1000genomes	TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:43587569G>C	uc002ije.2	-						uc010wjp.1_RNA					Homo sapiens cDNA FLJ34414 fis, clone HEART2003168, highly similar to Homo sapiens c114 SLIT-like testicular protein (LOC474170), mRNA.												0						aactccgtctgaaaagaaaag	0.144													4	49	---	---	---	---	PASS
LRRC37A4	55073	broad.mit.edu	37	17	43587576	43587576	+	Intron	SNP	A	G	G	rs2684618		TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:43587576A>G	uc002ije.2	-						uc010wjp.1_RNA					Homo sapiens cDNA FLJ34414 fis, clone HEART2003168, highly similar to Homo sapiens c114 SLIT-like testicular protein (LOC474170), mRNA.												0						tctgaaaagaaaagaaaaaaa	0.154													4	60	---	---	---	---	PASS
AXIN2	8313	broad.mit.edu	37	17	63532473	63532473	+	Silent	SNP	G	T	T			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:63532473G>T	uc002jfi.2	-	8	2395	c.2106C>A	c.(2104-2106)CGC>CGA	p.R702R	AXIN2_uc002jfh.2_Silent_p.R637R	NM_004655	NP_004646	Q9Y2T1	AXIN2_HUMAN	axin 2	702					cellular protein localization|cellular response to organic cyclic compound|dorsal/ventral axis specification|intramembranous ossification|maintenance of DNA repeat elements|mRNA stabilization|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of catenin import into nucleus|negative regulation of cell proliferation|negative regulation of osteoblast differentiation|odontogenesis|positive regulation of cell death|positive regulation of epithelial to mesenchymal transition|positive regulation of protein phosphorylation|regulation of centromeric sister chromatid cohesion|regulation of mismatch repair|Wnt receptor signaling pathway involved in somitogenesis	Axin-APC-beta-catenin-GSK3B complex|cell cortex|centrosome|cytoplasmic membrane-bounded vesicle|cytoplasmic microtubule|nucleus|plasma membrane|postsynaptic density	armadillo repeat domain binding|beta-catenin binding|GTPase activator activity|protein kinase binding|signal transducer activity|ubiquitin protein ligase binding			central_nervous_system(1)|skin(1)	2						CAGCTAGCCTGCGACAGGCCT	0.652									Oligodontia_Ectodermal_Dysplasia_and_Colorectal_Polyp_syndrome				4	14	---	---	---	---	PASS
ABCA8	10351	broad.mit.edu	37	17	66878106	66878106	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:66878106C>A	uc002jhp.2	-	29	3903	c.3724G>T	c.(3724-3726)GCC>TCC	p.A1242S	ABCA8_uc002jhq.2_Missense_Mutation_p.A1282S|ABCA8_uc010wqq.1_Missense_Mutation_p.A1277S	NM_007168	NP_009099	O94911	ABCA8_HUMAN	ATP-binding cassette, sub-family A member 8	1242						integral to membrane|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances			ovary(2)|skin(1)	3	Breast(10;4.56e-13)					AGACAGCTGGCAATGATGACT	0.413													35	114	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	17	76497744	76497744	+	RNA	SNP	T	G	G			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:76497744T>G	uc002jvt.1	+	2		c.3203T>G								Homo sapiens cDNA FLJ45552 fis, clone BRTHA2038279.																		AGTGGCAGGGTCTGAAGTCCC	0.627													9	11	---	---	---	---	PASS
TTC39C	125488	broad.mit.edu	37	18	21694593	21694593	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:21694593G>A	uc002kuw.2	+	7	1512	c.1060G>A	c.(1060-1062)GTC>ATC	p.V354I	TTC39C_uc002kuu.2_Missense_Mutation_p.V293I	NM_001135993	NP_001129465	Q8N584	TT39C_HUMAN	tetratricopeptide repeat domain 39C isoform 1	354	TPR 2.						binding			ovary(1)	1						AATTCAACATGTCTGTCTGTA	0.378													33	105	---	---	---	---	PASS
CDH2	1000	broad.mit.edu	37	18	25591824	25591824	+	Nonsense_Mutation	SNP	G	A	A			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:25591824G>A	uc002kwg.2	-	4	991	c.532C>T	c.(532-534)CAA>TAA	p.Q178*	CDH2_uc010xbn.1_Nonsense_Mutation_p.Q147*	NM_001792	NP_001783	P19022	CADH2_HUMAN	cadherin 2, type 1 preproprotein	178	Cadherin 1.|Extracellular (Potential).				adherens junction organization|cell junction assembly|positive regulation of muscle cell differentiation	catenin complex|integral to membrane	alpha-catenin binding|beta-catenin binding|calcium ion binding|gamma-catenin binding			ovary(3)|lung(1)	4						ACAAGCTCTTGAGGAAAAGGT	0.398													52	141	---	---	---	---	PASS
ABCA7	10347	broad.mit.edu	37	19	1043790	1043790	+	Missense_Mutation	SNP	C	G	G			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1043790C>G	uc002lqw.3	+	10	1228	c.997C>G	c.(997-999)CCC>GCC	p.P333A	ABCA7_uc010dsb.1_Missense_Mutation_p.P195A	NM_019112	NP_061985	Q8IZY2	ABCA7_HUMAN	ATP-binding cassette, sub-family A, member 7	333	Extracellular (By similarity).				phagocytosis|transmembrane transport	ATP-binding cassette (ABC) transporter complex|endosome membrane|Golgi membrane|integral to membrane|plasma membrane	ATP binding|ATPase activity|transporter activity			pancreas(7)|ovary(1)|central_nervous_system(1)	9		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|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)		GATGCTGGGACCCCGGATCTT	0.632													71	231	---	---	---	---	PASS
PRAM1	84106	broad.mit.edu	37	19	8564330	8564330	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8564330T>C	uc002mkd.2	-	2	382	c.362A>G	c.(361-363)AAA>AGA	p.K121R	PRAM1_uc002mkc.2_Missense_Mutation_p.K121R	NM_032152	NP_115528	Q96QH2	PRAM_HUMAN	PML-RARA regulated adaptor molecule 1	169	Pro-rich.						lipid binding|protein binding				0						CAACTCCAGTTTGGACGGCTT	0.632													6	154	---	---	---	---	PASS
MUC16	94025	broad.mit.edu	37	19	9067241	9067241	+	Silent	SNP	G	T	T			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9067241G>T	uc002mkp.2	-	3	20409	c.20205C>A	c.(20203-20205)ATC>ATA	p.I6735I		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	6737	Thr-rich.|Extracellular (Potential).				cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			lung(30)|ovary(15)|breast(8)|large_intestine(1)|skin(1)|prostate(1)|pancreas(1)	57						TTCGAGTGATGATGGTCATAT	0.512													90	254	---	---	---	---	PASS
MUC16	94025	broad.mit.edu	37	19	9067242	9067242	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9067242A>G	uc002mkp.2	-	3	20408	c.20204T>C	c.(20203-20205)ATC>ACC	p.I6735T		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	6737	Thr-rich.|Extracellular (Potential).				cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			lung(30)|ovary(15)|breast(8)|large_intestine(1)|skin(1)|prostate(1)|pancreas(1)	57						TCGAGTGATGATGGTCATATT	0.517													94	251	---	---	---	---	PASS
PDE4A	5141	broad.mit.edu	37	19	10568586	10568586	+	Silent	SNP	C	T	T			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10568586C>T	uc002moj.2	+	8	1017	c.909C>T	c.(907-909)CCC>CCT	p.P303P	PDE4A_uc002mok.2_Silent_p.P277P|PDE4A_uc002mol.2_Silent_p.P242P|PDE4A_uc002mom.2_Silent_p.P64P|PDE4A_uc002mon.2_Intron|PDE4A_uc002moo.2_5'Flank	NM_001111307	NP_001104777	P27815	PDE4A_HUMAN	phosphodiesterase 4A isoform 1	303					signal transduction	cytosol|membrane fraction|perinuclear region of cytoplasm|ruffle membrane|soluble fraction	3',5'-cyclic-AMP phosphodiesterase activity|metal ion binding|protein binding			ovary(1)|breast(1)|central_nervous_system(1)	3			OV - Ovarian serous cystadenocarcinoma(20;5.8e-10)|Epithelial(33;7.58e-07)|all cancers(31;3.91e-06)		Cilostazol(DB01166)|Dipyridamole(DB00975)|Dyphylline(DB00651)|Enprofylline(DB00824)|Iloprost(DB01088)|Milrinone(DB00235)|Pentoxifylline(DB00806)|Phentolamine(DB00692)|Tadalafil(DB00820)|Theophylline(DB00277)	TCCCATCACCCACGATGAAGG	0.557													13	51	---	---	---	---	PASS
TNPO2	30000	broad.mit.edu	37	19	12825697	12825697	+	Silent	SNP	C	T	T			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12825697C>T	uc002muo.2	-	9	1013	c.828G>A	c.(826-828)GAG>GAA	p.E276E	TNPO2_uc002mup.2_Silent_p.E368E|TNPO2_uc002muq.2_Silent_p.E276E|TNPO2_uc002mur.2_Silent_p.E276E	NM_001136196	NP_001129668	O14787	TNPO2_HUMAN	transportin 2 (importin 3, karyopherin beta 2b)	276	HEAT 4.				intracellular protein transport	cytoplasm|nucleus	nuclear localization sequence binding|protein binding|protein transporter activity			ovary(1)	1						TCAGCCAGAACTCACAGGCCT	0.627													27	119	---	---	---	---	PASS
NR2C2AP	126382	broad.mit.edu	37	19	19313200	19313200	+	Silent	SNP	C	T	T			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:19313200C>T	uc002nlx.2	-	4	612	c.243G>A	c.(241-243)CAG>CAA	p.Q81Q	NR2C2AP_uc010xqq.1_5'Flank|NR2C2AP_uc002nly.2_Missense_Mutation_p.R105K	NM_176880	NP_795361	Q86WQ0	NR2CA_HUMAN	TR4 orphan receptor associated protein TRA16	81					cell adhesion|gene expression|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm				ovary(1)	1			Epithelial(12;0.00235)			CCTGAGTGCCCTGTGAACCTT	0.582													77	209	---	---	---	---	PASS
GRAMD1A	57655	broad.mit.edu	37	19	35501023	35501023	+	Missense_Mutation	SNP	T	G	G			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:35501023T>G	uc010xse.1	+	5	490	c.353T>G	c.(352-354)ATC>AGC	p.I118S	GRAMD1A_uc002nxi.1_Missense_Mutation_p.I205S|GRAMD1A_uc002nxk.2_Missense_Mutation_p.I111S|GRAMD1A_uc002nxl.2_5'UTR|GRAMD1A_uc010xsf.1_Missense_Mutation_p.I123S	NM_020895	NP_065946	Q96CP6	GRM1A_HUMAN	GRAM domain containing 1A isoform 1	118	GRAM.					integral to membrane					0	all_lung(56;2.66e-08)|Lung NSC(56;4.13e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0849)			CAGCGTGAGATCCTGCTCCAG	0.657													36	109	---	---	---	---	PASS
FCGBP	8857	broad.mit.edu	37	19	40376319	40376319	+	Silent	SNP	G	A	A			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:40376319G>A	uc002omp.3	-	25	11993	c.11985C>T	c.(11983-11985)TAC>TAT	p.Y3995Y		NM_003890	NP_003881	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein precursor	3995	Cys-rich.					extracellular region	protein binding			ovary(4)|skin(4)|central_nervous_system(1)	9	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			CTACCTCATAGTAGACACCAT	0.542													19	54	---	---	---	---	PASS
CEACAM5	1048	broad.mit.edu	37	19	42221409	42221409	+	Missense_Mutation	SNP	T	G	G			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42221409T>G	uc002ork.2	+	5	1115	c.994T>G	c.(994-996)TCC>GCC	p.S332A	CEACAM5_uc002orj.1_Missense_Mutation_p.S331A|CEACAM5_uc002orl.2_Missense_Mutation_p.S332A	NM_004363	NP_004354	P06731	CEAM5_HUMAN	carcinoembryonic antigen-related cell adhesion	332	Ig-like 4.					anchored to membrane|basolateral plasma membrane|integral to plasma membrane				skin(2)	2				OV - Ovarian serous cystadenocarcinoma(3;0.00278)|all cancers(3;0.00625)|Epithelial(262;0.0379)|GBM - Glioblastoma multiforme(1328;0.142)		CAGCAACAACTCCAACCCCGT	0.522													35	111	---	---	---	---	PASS
PLEKHA4	57664	broad.mit.edu	37	19	49362923	49362923	+	Silent	SNP	A	C	C			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49362923A>C	uc002pkx.2	-	7	1046	c.495T>G	c.(493-495)CCT>CCG	p.P165P	PLEKHA4_uc002pkw.1_5'Flank|PLEKHA4_uc010eml.2_Silent_p.P165P	NM_020904	NP_065955	Q9H4M7	PKHA4_HUMAN	pleckstrin homology domain containing family A	165	Pro-rich.					cytoplasm|membrane	1-phosphatidylinositol binding			ovary(1)|central_nervous_system(1)|skin(1)	3		all_lung(116;4.89e-05)|Lung NSC(112;8.3e-05)|all_epithelial(76;0.000108)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.00027)|all cancers(93;0.00084)|GBM - Glioblastoma multiforme(486;0.0244)|Epithelial(262;0.0364)		GGGGTCGTGCAGGTGACCTGG	0.607													8	29	---	---	---	---	PASS
ZNF534	147658	broad.mit.edu	37	19	52942411	52942411	+	Silent	SNP	G	A	A	rs113700997		TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:52942411G>A	uc002pzk.2	+	4	1798	c.1737G>A	c.(1735-1737)GCG>GCA	p.A579A	ZNF534_uc002pzj.1_Intron|ZNF534_uc010epo.1_Intron|ZNF534_uc002pzl.2_Silent_p.A566A	NM_001143939	NP_001137411	Q76KX8	ZN534_HUMAN	zinc finger protein 534 isoform 2	579	C2H2-type 14.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						CACACCTTGCGCGACATAGGA	0.443													3	21	---	---	---	---	PASS
PIGU	128869	broad.mit.edu	37	20	33245016	33245016	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:33245016C>A	uc002xas.2	-	2	363	c.163G>T	c.(163-165)GTA>TTA	p.V55L	PIGU_uc010zul.1_Missense_Mutation_p.V55L|PIGU_uc002xat.2_Missense_Mutation_p.V55L|PIGU_uc010gev.1_RNA	NM_080476	NP_536724	Q9H490	PIGU_HUMAN	phosphatidylinositol glycan anchor biosynthesis,	55					attachment of GPI anchor to protein|C-terminal protein lipidation|regulation of JAK-STAT cascade	GPI-anchor transamidase complex|plasma membrane					0						TACGGAGATACTCCCAAGTCC	0.403													28	68	---	---	---	---	PASS
ZNF831	128611	broad.mit.edu	37	20	57766296	57766296	+	Silent	SNP	C	T	T			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:57766296C>T	uc002yan.2	+	1	222	c.222C>T	c.(220-222)CGC>CGT	p.R74R		NM_178457	NP_848552	Q5JPB2	ZN831_HUMAN	zinc finger protein 831	74	Pro-rich.					intracellular	nucleic acid binding|zinc ion binding			skin(13)|ovary(1)	14	all_lung(29;0.0085)					TCCAGCCCCGCGCCCCGCTAG	0.701													6	15	---	---	---	---	PASS
BAGE2	85319	broad.mit.edu	37	21	11098733	11098733	+	5'UTR	SNP	G	A	A			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11098733G>A	uc002yit.1	-	1					BAGE_uc002yix.2_RNA	NM_182482	NP_872288			B melanoma antigen family, member 2 precursor												0			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		tgctccggccgccatcttact	0.000													12	94	---	---	---	---	PASS
NF2	4771	broad.mit.edu	37	22	30079118	30079118	+	Intron	SNP	A	G	G			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:30079118A>G	uc003age.3	+						NF2_uc003afy.3_3'UTR|NF2_uc003afz.3_Intron|NF2_uc003agf.3_Intron|NF2_uc003agb.3_Intron|NF2_uc003agc.3_Intron|NF2_uc003agd.3_Intron|NF2_uc003agg.3_Intron|NF2_uc003aga.3_Intron|NF2_uc003agh.3_Intron|NF2_uc003agi.3_Intron|NF2_uc003agj.3_Intron|NF2_uc003agk.3_Intron|NF2_uc010gvp.2_Intron|NF2_uc011akq.1_Intron	NM_000268	NP_000259	P35240	MERL_HUMAN	neurofibromin 2 isoform 1						actin cytoskeleton organization|negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of cell-cell adhesion|negative regulation of cell-matrix adhesion|negative regulation of DNA replication|negative regulation of tyrosine phosphorylation of Stat3 protein|negative regulation of tyrosine phosphorylation of Stat5 protein|positive regulation of stress fiber assembly|regulation of hippo signaling cascade|Schwann cell proliferation	cytoskeleton|early endosome|extrinsic to membrane|filopodium membrane|nucleolus|perinuclear region of cytoplasm|ruffle membrane	cytoskeletal protein binding|protein binding	p.?(1)		meninges(372)|soft_tissue(284)|central_nervous_system(20)|kidney(10)|pleura(9)|skin(7)|large_intestine(5)|breast(5)|urinary_tract(3)|thyroid(2)|endometrium(2)|ovary(2)|lung(2)|stomach(2)|bone(2)|pituitary(1)	728						TAACCCGTGCATGAGCTTGCC	0.547			D|Mis|N|F|S|O		meningioma|acoustic neuroma|renal 	meningioma|acoustic neuroma			Neurofibromatosis_type_2				29	87	---	---	---	---	PASS
MORC2	22880	broad.mit.edu	37	22	31322760	31322760	+	3'UTR	SNP	T	G	G			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:31322760T>G	uc003aje.1	-	27						NM_014941	NP_055756	Q9Y6X9	MORC2_HUMAN	MORC family CW-type zinc finger 2								ATP binding|zinc ion binding			ovary(1)|pancreas(1)	2						GAGGGGCAGGTGGGCAGGGGA	0.552													9	23	---	---	---	---	PASS
CYP2D7P1	1564	broad.mit.edu	37	22	42538870	42538870	+	Missense_Mutation	SNP	A	C	C	rs2982057	by1000genomes	TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:42538870A>C	uc003bci.2	-	3	475	c.94T>G	c.(94-96)TCG>GCG	p.S32A	CYP2D7P1_uc003bcg.2_5'Flank|CYP2D7P1_uc003bch.2_5'Flank|CYP2D7P1_uc010gyv.2_Intron|CYP2D7P1_uc010gyw.2_RNA|CYP2D7P1_uc010gyx.1_Missense_Mutation_p.S32A	NR_002570				SubName: Full=Cytochrome P450 2D6;          EC=1.14.14.1;												0						CCATAGCGCGACAGGAACACC	0.687													3	25	---	---	---	---	PASS
ADM2	79924	broad.mit.edu	37	22	50921276	50921276	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50921276G>A	uc003blj.2	+	2	656	c.391G>A	c.(391-393)GCC>ACC	p.A131T	ADM2_uc011ary.1_Missense_Mutation_p.A131T	NM_024866	NP_079142	Q7Z4H4	ADM2_HUMAN	adrenomedullin 2 precursor	131					positive regulation of angiogenesis	extracellular region	hormone activity				0		all_cancers(38;4.58e-14)|all_epithelial(38;1.12e-12)|all_lung(38;3.07e-05)|Breast(42;6.27e-05)|Lung NSC(38;0.000813)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)		CATGGGACCGGCCGGCCGGCA	0.706													3	19	---	---	---	---	PASS
CAPN6	827	broad.mit.edu	37	X	110491970	110491970	+	Silent	SNP	G	A	A			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:110491970G>A	uc004epc.1	-	10	1479	c.1311C>T	c.(1309-1311)CAC>CAT	p.H437H	CAPN6_uc011msu.1_Silent_p.H182H	NM_014289	NP_055104	Q9Y6Q1	CAN6_HUMAN	calpain 6	437	Domain III.				microtubule bundle formation|proteolysis|regulation of cytoskeleton organization	perinuclear region of cytoplasm|spindle microtubule	calcium-dependent cysteine-type endopeptidase activity|microtubule binding			ovary(2)|upper_aerodigestive_tract(1)|large_intestine(1)|lung(1)|skin(1)	6						TGTAGAGGTGGTGGAGGCGGA	0.448													38	126	---	---	---	---	PASS
HPRT1	3251	broad.mit.edu	37	X	133609298	133609298	+	Missense_Mutation	SNP	C	A	A	rs137852481		TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:133609298C>A	uc004exl.3	+	3	389	c.222C>A	c.(220-222)TTC>TTA	p.F74L	HPRT1_uc010nrs.2_RNA	NM_000194	NP_000185	P00492	HPRT_HUMAN	hypoxanthine phosphoribosyltransferase 1	74			F -> L (in LNS; Flint/RJK 892/DW/Perth/ 1522).		adenine salvage|central nervous system neuron development|cerebral cortex neuron differentiation|cytolysis|dendrite morphogenesis|GMP catabolic process|GMP salvage|grooming behavior|guanine salvage|hypoxanthine salvage|IMP salvage|lymphocyte proliferation|positive regulation of dopamine metabolic process|protein homotetramerization|purine ribonucleoside salvage|response to amphetamine|striatum development	cytosol	guanine phosphoribosyltransferase activity|hypoxanthine phosphoribosyltransferase activity|magnesium ion binding|nucleotide binding|protein homodimerization activity				0	Acute lymphoblastic leukemia(192;0.000127)				Mercaptopurine(DB01033)|Thioguanine(DB00352)	GCTATAAATTCTTTGCTGACC	0.423													44	115	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	1	5050112	5050113	+	IGR	DEL	TC	-	-			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:5050112_5050113delTC								AJAP1 (206262 upstream) : NPHP4 (872757 downstream)																							aggccttctgtctctctctctc	0.000													2	4	---	---	---	---	
NOTCH2	4853	broad.mit.edu	37	1	120612224	120612226	+	5'UTR	DEL	GCC	-	-			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:120612224_120612226delGCC	uc001eik.2	-	1					NOTCH2_uc001eil.2_5'UTR|NOTCH2_uc001eim.3_5'UTR	NM_024408	NP_077719	Q04721	NOTC2_HUMAN	notch 2 preproprotein						anti-apoptosis|bone remodeling|cell cycle arrest|cell fate determination|cell growth|hemopoiesis|induction of apoptosis|negative regulation of cell proliferation|nervous system development|Notch receptor processing|Notch signaling pathway|organ morphogenesis|positive regulation of Ras protein signal transduction|regulation of transcription, DNA-dependent|stem cell maintenance|transcription, DNA-dependent	cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm	calcium ion binding|ligand-regulated transcription factor activity|protein binding|receptor activity			lung(8)|haematopoietic_and_lymphoid_tissue(7)|ovary(4)|central_nervous_system(2)|skin(2)|kidney(2)|breast(1)|prostate(1)	27	all_neural(166;0.153)	all_lung(203;1.96e-06)|Lung NSC(69;1.47e-05)|all_epithelial(167;0.000809)		Lung(183;0.0242)|LUSC - Lung squamous cell carcinoma(189;0.133)		CGCCGCCTCAGCCGCCGCCCGAA	0.695			N|F|Mis		marginal zone lymphoma|DLBCL				Alagille_Syndrome				4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	149090330	149090331	+	IGR	DEL	AG	-	-			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:149090330_149090331delAG								LOC645166 (137276 upstream) : LOC388692 (189145 downstream)																							acagacagacagagagagagag	0.277													6	3	---	---	---	---	
TUFT1	7286	broad.mit.edu	37	1	151518484	151518485	+	Intron	INS	-	TC	TC	rs145600399		TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151518484_151518485insTC	uc001eyl.2	+						TUFT1_uc001eym.2_Intron|TUFT1_uc010pdf.1_Intron|TUFT1_uc010pdg.1_Intron	NM_020127	NP_064512	Q9NNX1	TUFT1_HUMAN	tuftelin 1 isoform 1						bone mineralization|odontogenesis	cytoplasm|extracellular region	structural constituent of tooth enamel				0	Ovarian(49;0.0273)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		LUSC - Lung squamous cell carcinoma(543;0.181)			tttttcttttttttttttttct	0.139													3	3	---	---	---	---	
LOC400794	400794	broad.mit.edu	37	1	165450998	165450999	+	Intron	INS	-	AGAA	AGAA	rs143219054	by1000genomes	TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:165450998_165450999insAGAA	uc001gdc.2	-						LOC400794_uc001gdd.2_Intron	NR_026744				Homo sapiens cDNA FLJ35813 fis, clone TESTI2006067.												0						aggaaagagagagaaagaaaga	0.000													3	5	---	---	---	---	
TBX19	9095	broad.mit.edu	37	1	168262597	168262598	+	Intron	INS	-	G	G	rs145449033	by1000genomes	TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:168262597_168262598insG	uc001gfl.2	+						TBX19_uc001gfj.3_Intron	NM_005149	NP_005140	O60806	TBX19_HUMAN	T-box 19						anatomical structure morphogenesis	nucleus	DNA binding				0	all_hematologic(923;0.215)					GCAGGATGGGCGGGGGGGGTCC	0.396													6	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	189767973	189767974	+	IGR	INS	-	GGAA	GGAA			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:189767973_189767974insGGAA								None (None upstream) : FAM5C (298823 downstream)																							aagaaagaaagggaaggaagga	0.000													5	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	203723077	203723084	+	IGR	DEL	GAAGGAAG	-	-			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:203723077_203723084delGAAGGAAG								ATP2B4 (9870 upstream) : LAX1 (11200 downstream)																							agaaaagaaagaaggaaggaaggaagga	0.000													4	2	---	---	---	---	
OBSCN	84033	broad.mit.edu	37	1	228404669	228404677	+	Intron	DEL	GTGCTCAGG	-	-			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:228404669_228404677delGTGCTCAGG	uc009xez.1	+						OBSCN_uc001hsn.2_Intron	NM_001098623	NP_001092093	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and						apoptosis|cell differentiation|induction of apoptosis by extracellular signals|multicellular organismal development|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|M band|Z disc	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity|Rho guanyl-nucleotide exchange factor activity|structural constituent of muscle|titin binding			stomach(8)|large_intestine(7)|breast(5)|ovary(4)|skin(2)|central_nervous_system(1)|pancreas(1)	28		Prostate(94;0.0405)				GGCCAAGTTTGTGCTCAGGGCCTCTGCAG	0.656													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	16866916	16866917	+	IGR	INS	-	CCTTCCTT	CCTTCCTT	rs3085836		TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:16866916_16866917insCCTTCCTT								FAM49A (19820 upstream) : RAD51AP2 (825069 downstream)																							ctacataattcccttccttcct	0.000													3	3	---	---	---	---	
SLC4A5	57835	broad.mit.edu	37	2	74491617	74491618	+	Intron	DEL	GT	-	-	rs71940211		TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:74491617_74491618delGT	uc002sko.1	-						SLC4A5_uc002skl.2_Intron|SLC4A5_uc002skn.2_Intron|SLC4A5_uc010ffc.1_Intron|SLC4A5_uc002skp.1_Intron|SLC4A5_uc002sks.1_Intron	NM_021196	NP_067019	Q9BY07	S4A5_HUMAN	sodium bicarbonate transporter 4 isoform a							apical plasma membrane|integral to membrane	inorganic anion exchanger activity|sodium:bicarbonate symporter activity			ovary(5)|skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)	9						tcaagggcacgtgtgtgtgtgt	0.119													4	3	---	---	---	---	
MAP4K4	9448	broad.mit.edu	37	2	102503487	102503487	+	Intron	DEL	A	-	-			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:102503487delA	uc002tbg.2	+						MAP4K4_uc002tbc.2_Intron|MAP4K4_uc002tbd.2_Intron|MAP4K4_uc002tbe.2_Intron|MAP4K4_uc002tbf.2_Intron|MAP4K4_uc010yvy.1_Intron|MAP4K4_uc002tbh.2_Intron|MAP4K4_uc002tbi.2_Intron|MAP4K4_uc010yvz.1_Intron|MAP4K4_uc002tbk.2_Intron|MAP4K4_uc002tbl.2_Intron	NM_145687	NP_663720	O95819	M4K4_HUMAN	mitogen-activated protein kinase kinase kinase						intracellular protein kinase cascade|regulation of JNK cascade|response to stress	cytoplasm	ATP binding|protein binding|protein serine/threonine kinase activity|small GTPase regulator activity			stomach(1)|lung(1)|central_nervous_system(1)|skin(1)	4						actccgtctcaaaaaaaaaaa	0.164													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	106219070	106219077	+	Intron	DEL	GGAAAGAA	-	-	rs10178590		TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:106219070_106219077delGGAAAGAA	uc002tdf.2	-											Homo sapiens hypothetical protein LOC285000, mRNA (cDNA clone IMAGE:3925223), partial cds.																		aaggaaagatggaaagaaggaaagaagg	0.000													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	108353515	108353524	+	IGR	DEL	GTGTGTGTGT	-	-	rs67571119		TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:108353515_108353524delGTGTGTGTGT								ST6GAL2 (849952 upstream) : LOC729121 (85996 downstream)																							TACAAGAGGGgtgtgtgtgtgtgtgtgtgt	0.305													4	2	---	---	---	---	
PAX8	7849	broad.mit.edu	37	2	114012660	114012666	+	Intron	DEL	GAAGGAA	-	-			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:114012660_114012666delGAAGGAA	uc010yxt.1	-						PAX8_uc010yxu.1_Intron|PAX8_uc010yxv.1_Intron|PAX8_uc002tjm.2_Intron|PAX8_uc002tjn.2_Intron|PAX8_uc010fku.1_Intron|LOC654433_uc002tjq.3_Intron|LOC654433_uc010fks.2_Intron|LOC654433_uc010fkt.2_Intron|LOC654433_uc002tjr.3_Intron|LOC654433_uc002tjs.3_Intron	NM_003466	NP_003457	Q06710	PAX8_HUMAN	paired box 8 isoform PAX8A						branching involved in ureteric bud morphogenesis|cellular response to gonadotropin stimulus|central nervous system development|mesenchymal to epithelial transition involved in metanephros morphogenesis|mesonephros development|metanephric collecting duct development|metanephric comma-shaped body morphogenesis|metanephric distal convoluted tubule development|metanephric nephron tubule formation|metanephric S-shaped body morphogenesis|negative regulation of mesenchymal stem cell apoptosis involved in metanephric nephron morphogenesis|otic vesicle development|positive regulation of branching involved in ureteric bud morphogenesis|positive regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis|positive regulation of metanephric DCT cell differentiation|positive regulation of thyroid hormone generation|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|pronephric field specification|regulation of metanephric nephron tubule epithelial cell differentiation|regulation of thyroid-stimulating hormone secretion|thyroid gland development|transcription, DNA-dependent	nucleoplasm	protein binding|RNA polymerase II core promoter sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|thyroid-stimulating hormone receptor activity			ovary(1)|lung(1)	2						aagaaggaaggaaggaaaaaagaagga	0.097			T	PPARG	follicular thyroid		Thyroid dysgenesis 						4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	128824754	128824754	+	IGR	DEL	A	-	-	rs113610724		TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:128824754delA								SAP130 (39121 upstream) : UGGT1 (24000 downstream)																							gactccatctaaaaaaaaaaa	0.174													3	8	---	---	---	---	
RBMS1	5937	broad.mit.edu	37	2	161157245	161157245	+	Intron	DEL	T	-	-			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:161157245delT	uc002ubo.2	-						RBMS1_uc002ubj.2_Intron|RBMS1_uc002ubk.2_Intron|RBMS1_uc002ubl.2_Intron|RBMS1_uc002ubn.2_Intron|RBMS1_uc002ubi.3_Intron|RBMS1_uc002ubm.2_Intron|RBMS1_uc002ubp.2_Intron|RBMS1_uc010fox.2_Intron	NM_016836	NP_058520	P29558	RBMS1_HUMAN	RNA binding motif, single stranded interacting						DNA replication|RNA processing	nucleus	double-stranded DNA binding|nucleotide binding|protein binding|RNA binding|single-stranded DNA binding				0						TTCCATCCtatttataataaa	0.274													47	38	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	162364000	162364000	+	IGR	DEL	G	-	-			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:162364000delG								TBR1 (82427 upstream) : SLC4A10 (116845 downstream)																							GCAGACAATCGCTCTCCTGTT	0.433													32	47	---	---	---	---	
FN1	2335	broad.mit.edu	37	2	216235277	216235278	+	Intron	INS	-	A	A	rs1250207		TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:216235277_216235278insA	uc002vfa.2	-						FN1_uc002vfb.2_Intron|FN1_uc002vfc.2_Intron|FN1_uc002vfd.2_Intron|FN1_uc002vfe.2_Intron|FN1_uc002vff.2_Intron|FN1_uc002vfg.2_Intron|FN1_uc002vfh.2_Intron|FN1_uc002vfi.2_Intron|FN1_uc002vfj.2_Intron|FN1_uc002vez.2_Intron|FN1_uc010zjp.1_Intron|FN1_uc002vfk.1_Intron|FN1_uc010fva.1_Intron|FN1_uc010fvb.1_Intron|FN1_uc010fvc.1_Intron|FN1_uc010fvd.1_Intron	NM_212482	NP_997647	P02751	FINC_HUMAN	fibronectin 1 isoform 1 preproprotein						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)	aaacaaaaaacaaaaaaaaaaa	0.411													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	226807037	226807038	+	IGR	INS	-	AGGA	AGGA	rs10660054		TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:226807037_226807038insAGGA								KIAA1486 (211566 upstream) : IRS1 (788996 downstream)																							ggaaggaacggaggaaggaagg	0.045													7	6	---	---	---	---	
COL4A3	1285	broad.mit.edu	37	2	228058652	228058654	+	Intron	DEL	AAG	-	-	rs71036161		TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:228058652_228058654delAAG	uc002vom.1	+						COL4A3_uc002von.1_Intron|COL4A3_uc002voo.1_Intron|COL4A3_uc002vop.1_Intron	NM_000091	NP_000082	Q01955	CO4A3_HUMAN	alpha 3 type IV collagen isoform 1 precursor						activation of caspase activity|axon guidance|blood circulation|cell adhesion|cell proliferation|cell surface receptor linked signaling pathway|glomerular basement membrane development|induction of apoptosis|negative regulation of angiogenesis|negative regulation of cell proliferation|sensory perception of sound	collagen type IV	extracellular matrix structural constituent|integrin binding|metalloendopeptidase inhibitor activity			skin(2)|ovary(1)	3		all_lung(227;0.00101)|Lung NSC(271;0.00278)|Renal(207;0.0112)|Ovarian(221;0.0129)|all_hematologic(139;0.211)|Esophageal squamous(248;0.247)		Epithelial(121;1.17e-46)|all cancers(144;6.87e-42)|Lung(261;0.0137)|LUSC - Lung squamous cell carcinoma(224;0.0187)		gaagggaaataaggagagaggga	0.000													6	4	---	---	---	---	
VHL	7428	broad.mit.edu	37	3	10183864	10183865	+	Frame_Shift_Ins	INS	-	A	A	rs104893824		TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10183864_10183865insA	uc003bvc.2	+	1	546_547	c.333_334insA	c.(331-336)AGCTACfs	p.S111fs	VHL_uc003bvd.2_Frame_Shift_Ins_p.S111fs	NM_000551	NP_000542	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor isoform 1	111_112	Involved in binding to CCT complex.		Y -> H (in VHLD; type IIA).|Y -> N (in VHLD).		anti-apoptosis|cell morphogenesis|negative regulation of cell proliferation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of cell differentiation|positive regulation of transcription, DNA-dependent|protein stabilization|protein ubiquitination|proteolysis	cytosol|endoplasmic reticulum|membrane|mitochondrion|nucleus	protein binding|transcription factor binding	p.S111N(3)|p.S111S(2)|p.S111R(2)|p.S111G(2)|p.S111fs*48(1)|p.S111fs*49(1)|p.?(1)|p.Y112D(1)|p.I109_R113del(1)|p.S111fs*22(1)|p.S111fs*45(1)|p.H110_S111del(1)|p.S111I(1)|p.S111_Y112del(1)|p.Y112fs*47(1)		kidney(1273)|soft_tissue(24)|adrenal_gland(15)|large_intestine(13)|pancreas(5)|endometrium(4)|thyroid(3)|upper_aerodigestive_tract(3)|central_nervous_system(2)|lung(2)|pleura(1)|paratesticular_tissues(1)	1346				Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569)		GCATCCACAGCTACCGAGGTAC	0.639		1	D|Mis|N|F|S		renal|hemangioma|pheochromocytoma	renal|hemangioma|pheochromocytoma			von_Hippel-Lindau_disease|Chuvash_Polycythemia_|Pheochromocytoma_(Adrenal)_Familial				6	4	---	---	---	---	
LTF	4057	broad.mit.edu	37	3	46524213	46524214	+	Intron	INS	-	AAGG	AAGG	rs71615448		TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:46524213_46524214insAAGG	uc003cpr.2	-							NM_002343	NP_002334	P02788	TRFL_HUMAN	lactotransferrin precursor						cellular iron ion homeostasis|defense response to bacterium|humoral immune response|iron ion transport	extracellular region|stored secretory granule	ferric iron binding|heparin binding|protein binding|serine-type endopeptidase activity			central_nervous_system(2)|ovary(1)|lung(1)	4				all cancers(1;7.55e-14)|GBM - Glioblastoma multiforme(1;2.1e-09)|Epithelial(1;9.25e-07)|Colorectal(1;3.81e-05)|BRCA - Breast invasive adenocarcinoma(193;0.00129)|COAD - Colon adenocarcinoma(1;0.00308)|KIRC - Kidney renal clear cell carcinoma(197;0.0205)|Kidney(197;0.0242)|OV - Ovarian serous cystadenocarcinoma(275;0.089)	Pefloxacin(DB00487)	aaagagaaagaaaggaaggaag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	87543497	87543498	+	IGR	DEL	AG	-	-	rs146116458		TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:87543497_87543498delAG								POU1F1 (217760 upstream) : HTR1F (488228 downstream)																							aaagagaaaaagaaagaagaag	0.000													9	4	---	---	---	---	
ARL13B	200894	broad.mit.edu	37	3	93699571	93699574	+	Intron	DEL	GTGT	-	-			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:93699571_93699574delGTGT	uc003drc.2	+						ARL13B_uc010hop.2_Intron|ARL13B_uc003drd.2_Intron|ARL13B_uc003dre.2_Intron|ARL13B_uc003drf.2_Intron|ARL13B_uc003drg.2_Intron	NM_182896	NP_878899	Q3SXY8	AR13B_HUMAN	ADP-ribosylation factor-like 2-like 1 isoform 1								GTP binding				0						TTGTTAAAAAgtgtgtgtgtgtgt	0.275													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	186204359	186204360	+	Intron	INS	-	G	G	rs111354223		TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:186204359_186204360insG	uc003fqd.1	-											Homo sapiens cDNA FLJ32735 fis, clone TESTI2001229.																		gaaggaaggaaggacagactac	0.000													5	4	---	---	---	---	
ZNF876P	642280	broad.mit.edu	37	4	247254	247255	+	Intron	DEL	TA	-	-	rs34738994		TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:247254_247255delTA	uc010iba.2	+							NR_027481				Homo sapiens cDNA clone IMAGE:4828836.												0						TTTGTATAAGTATATATATATT	0.134													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	49512654	49512654	+	IGR	DEL	T	-	-	rs113012804		TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49512654delT								CWH43 (448561 upstream) : None (None downstream)																							ACATTCTGCGTTTTTTTGGGG	0.368													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	69242367	69242368	+	IGR	INS	-	A	A	rs35810847		TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:69242367_69242368insA								YTHDC1 (26543 upstream) : UGT2B15 (269948 downstream)																							GCTTTGACTTGAAAAAAAAAAA	0.238													5	3	---	---	---	---	
SCARB2	950	broad.mit.edu	37	4	77097814	77097815	+	Intron	INS	-	A	A			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:77097814_77097815insA	uc003hju.1	-						SCARB2_uc011cbu.1_Intron	NM_005506	NP_005497	Q14108	SCRB2_HUMAN	scavenger receptor class B, member 2						cell adhesion|protein targeting to lysosome	integral to plasma membrane|lysosomal lumen|lysosomal membrane|membrane fraction	enzyme binding|receptor activity				0			Lung(101;0.196)			taggtgtgattaatatctacaa	0.005													9	4	---	---	---	---	
DMP1	1758	broad.mit.edu	37	4	88578286	88578286	+	Intron	DEL	A	-	-			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:88578286delA	uc003hqv.2	+						DMP1_uc003hqw.2_Intron	NM_004407	NP_004398	Q13316	DMP1_HUMAN	dentin matrix acidic phosphoprotein 1 isoform 1						biomineral tissue development|ossification	cytoplasm|nucleus|proteinaceous extracellular matrix	calcium ion binding|integrin binding			pancreas(1)|skin(1)	2		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.227)		OV - Ovarian serous cystadenocarcinoma(123;0.000516)		ttatGAGTATAACCAAATTGA	0.274													17	13	---	---	---	---	
RGS7BP	401190	broad.mit.edu	37	5	63799450	63799453	+	5'Flank	DEL	AAAA	-	-			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:63799450_63799453delAAAA	uc003jtj.2	+							NM_001029875	NP_001025046	Q6MZT1	R7BP_HUMAN	regulator of G-protein signaling 7 binding						negative regulation of signal transduction	cytoplasm|nucleus|plasma membrane					0		Lung NSC(810;0.000518)|Prostate(74;0.0435)|Ovarian(174;0.186)		Lung(70;0.147)		ggaaggaaggaaaaaaggaaggaa	0.074													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	67107698	67107699	+	IGR	INS	-	T	T			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:67107698_67107699insT								CD180 (615081 upstream) : PIK3R1 (403905 downstream)																							tctttcttctcttttttttctt	0.005													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	90475765	90475772	+	IGR	DEL	GAAGGAAG	-	-			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:90475765_90475772delGAAGGAAG								GPR98 (15733 upstream) : ARRDC3 (188769 downstream)																							aaggaaggaagaaggaaggaaggaagga	0.029													12	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	3222231	3222232	+	5'Flank	INS	-	T	T			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:3222231_3222232insT	uc011dhu.1	+											Synthetic construct Homo sapiens gateway clone IMAGE:100018300 3' read TUBB2A mRNA.																		accaccaccacactaccaccac	0.134													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	44969476	44969477	+	IGR	INS	-	TC	TC	rs144170109	by1000genomes	TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:44969476_44969477insTC								PURB (44516 upstream) : MYO1G (32783 downstream)																							ctttctttctttttctttcttt	0.010													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	64975077	64975078	+	IGR	INS	-	AGAC	AGAC			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:64975077_64975078insAGAC								ZNF92 (109080 upstream) : INTS4L2 (137699 downstream)																							AGTGCACCCGAAAACAAAGATG	0.455													7	4	---	---	---	---	
NUP205	23165	broad.mit.edu	37	7	135287859	135287860	+	Intron	DEL	AC	-	-			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:135287859_135287860delAC	uc003vsw.2	+							NM_015135	NP_055950	Q92621	NU205_HUMAN	nucleoporin 205kDa						carbohydrate metabolic process|glucose transport|mRNA transport|protein import into nucleus, docking|regulation of glucose transport|transmembrane transport|viral reproduction	nuclear pore	protein binding			ovary(3)|breast(1)|central_nervous_system(1)|skin(1)	6						GCCTCAttttactttttttttt	0.153													6	6	---	---	---	---	
TUSC3	7991	broad.mit.edu	37	8	15546921	15546923	+	Intron	DEL	TTG	-	-			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:15546921_15546923delTTG	uc003wwt.2	+						TUSC3_uc003wwr.2_Intron|TUSC3_uc003wws.2_Intron|TUSC3_uc003wwu.2_Intron|TUSC3_uc003wwv.2_Intron|TUSC3_uc003www.2_Intron|TUSC3_uc003wwx.2_Intron|TUSC3_uc003wwy.2_Intron	NM_006765	NP_006756	Q13454	TUSC3_HUMAN	tumor suppressor candidate 3 isoform a						cell redox homeostasis|post-translational protein modification|protein N-linked glycosylation via asparagine	integral to membrane|oligosaccharyltransferase complex				ovary(2)|central_nervous_system(1)	3				Colorectal(111;0.113)		GAAGGCGACCTTGTTGTTCTTGA	0.571													5	3	---	---	---	---	
SULF1	23213	broad.mit.edu	37	8	70552844	70552844	+	Intron	DEL	A	-	-			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:70552844delA	uc010lza.1	+						SULF1_uc003xyd.2_Intron|SULF1_uc003xye.2_Intron|SULF1_uc003xyf.2_Intron|SULF1_uc003xyg.2_Intron|SULF1_uc003xyh.1_Intron|SULF1_uc003xyi.1_Intron|SULF1_uc003xyj.1_Intron	NM_015170	NP_055985	Q8IWU6	SULF1_HUMAN	sulfatase 1 precursor						apoptosis|bone development|heparan sulfate proteoglycan metabolic process|kidney development|negative regulation of fibroblast growth factor receptor signaling pathway	cell surface|endoplasmic reticulum|extracellular space|Golgi stack	arylsulfatase activity|calcium ion binding			central_nervous_system(3)|ovary(2)|pancreas(1)|skin(1)	7	Breast(64;0.0654)		Epithelial(68;0.0124)|OV - Ovarian serous cystadenocarcinoma(28;0.0265)|all cancers(69;0.0534)			TTTTTTTTTTATCTTAAACCT	0.363													4	2	---	---	---	---	
MTAP	4507	broad.mit.edu	37	9	22028213	22028214	+	Intron	DEL	AT	-	-	rs142048183		TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:22028213_22028214delAT	uc003zpi.1	+						CDKN2BAS_uc010miw.1_Intron|CDKN2BAS_uc010mix.1_Intron|CDKN2BAS_uc003zpm.2_Intron	NM_002451	NP_002442	Q13126	MTAP_HUMAN	5'-methylthioadenosine phosphorylase						nucleoside metabolic process	cytoplasm	phosphorylase activity|S-methyl-5-thioadenosine phosphorylase activity			central_nervous_system(1)	1		all_cancers(5;0)|Hepatocellular(5;0.00162)|Colorectal(97;0.173)		GBM - Glioblastoma multiforme(3;0)|Lung(24;2.24e-57)|LUSC - Lung squamous cell carcinoma(38;1.97e-36)|STAD - Stomach adenocarcinoma(4;3.26e-05)|OV - Ovarian serous cystadenocarcinoma(39;0.00931)|COAD - Colon adenocarcinoma(8;0.15)	Adenine(DB00173)	catataaaacatataaaaatat	0.248													5	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	90460010	90460015	+	IGR	DEL	TGTGTG	-	-	rs36046714		TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:90460010_90460015delTGTGTG								CTSL3 (58211 upstream) : C9orf79 (37726 downstream)																							AGTCTTGCTCtgtgtgtgtgtgtgtg	0.301													3	3	---	---	---	---	
EXD3	54932	broad.mit.edu	37	9	140249951	140249952	+	Intron	INS	-	G	G	rs143208480		TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140249951_140249952insG	uc004cmp.2	-						C9orf167_uc011mew.1_Intron|EXD3_uc010ncf.1_Intron|EXD3_uc004cmq.1_Intron|EXD3_uc010ncg.1_Intron	NM_017820	NP_060290	Q8N9H8	MUT7_HUMAN	exonuclease 3'-5' domain containing 3						nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	intracellular	3'-5' exonuclease activity|nucleic acid binding				0						ggatggaggaaggaggaaggag	0.030													4	2	---	---	---	---	
MYOF	26509	broad.mit.edu	37	10	95066953	95066953	+	Intron	DEL	G	-	-	rs60442844		TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:95066953delG	uc001kin.2	-						MYOF_uc001kio.2_Intron|MYOF_uc009xue.2_Intron	NM_013451	NP_038479	Q9NZM1	MYOF_HUMAN	myoferlin isoform a						blood circulation|muscle contraction|plasma membrane repair	caveola|cytoplasmic vesicle membrane|integral to membrane|nuclear membrane	phospholipid binding|protein binding			ovary(3)|breast(1)	4						gcacccccccgccaagttgtt	0.005													4	2	---	---	---	---	
PLEKHA1	59338	broad.mit.edu	37	10	124175273	124175277	+	Intron	DEL	GACTA	-	-	rs4751892	by1000genomes	TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:124175273_124175277delGACTA	uc001lge.1	+						PLEKHA1_uc001lgf.1_Intron|PLEKHA1_uc001lgg.1_Intron|PLEKHA1_uc001lgh.2_Intron	NM_001001974	NP_001001974	Q9HB21	PKHA1_HUMAN	pleckstrin homology domain containing, family A						B cell receptor signaling pathway|cellular response to hydrogen peroxide|establishment of protein localization|negative regulation of protein kinase B signaling cascade|phosphatidylinositol 3-kinase cascade|ruffle organization	cytoplasm|nucleus|ruffle membrane	PDZ domain binding|phosphatidylinositol-3,4-bisphosphate binding			kidney(1)	1		all_neural(114;0.0765)|Lung NSC(174;0.132)|all_lung(145;0.163)|Breast(234;0.238)				ATCTGTTTCTGACTAATCTAAGGTG	0.268													6	5	---	---	---	---	
MUC5B	727897	broad.mit.edu	37	11	1248193	1248193	+	Intron	DEL	G	-	-			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1248193delG	uc009ycr.1	+						MUC5B_uc009yct.1_Intron|MUC5B_uc001ltb.2_Intron|MUC5B_uc001lta.2_5'Flank	NM_017511	NP_059981	Q9HC84	MUC5B_HUMAN	SubName: Full=Mucin 5AC, oligomeric mucus/gel-forming;						cell adhesion	extracellular region	extracellular matrix structural constituent|protein binding				0		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)		GGCCAGGGCTGGGGGGGGGTT	0.721													5	3	---	---	---	---	
LDHC	3948	broad.mit.edu	37	11	18460186	18460186	+	Frame_Shift_Del	DEL	T	-	-			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:18460186delT	uc001mon.3	+	6	816	c.704delT	c.(703-705)ATTfs	p.I235fs	LDHC_uc001mom.3_Frame_Shift_Del_p.I235fs|LDHC_uc009yhp.2_Frame_Shift_Del_p.I235fs|LDHC_uc001moo.3_Frame_Shift_Del_p.I119fs|LDHC_uc009yhq.2_RNA|LDHC_uc009yhr.2_Intron	NM_017448	NP_059144	P07864	LDHC_HUMAN	L-lactate dehydrogenase C	235					glycolysis	cytoplasm	binding|L-lactate dehydrogenase activity				0					NADH(DB00157)	AAACAAGTTATTCAAAGGTAA	0.358													44	27	---	---	---	---	
LOC646813	646813	broad.mit.edu	37	11	50368905	50368905	+	Intron	DEL	T	-	-			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:50368905delT	uc001nhe.2	+						LOC646813_uc001nhf.1_Intron|LOC646813_uc001nhg.1_Intron	NR_024504				Homo sapiens mRNA for hypothetical protein, partial sequence, clone:Hsa11-digit09-11-09-R.												0						TTGTTTTCCCTTTCCCCTGTT	0.279													7	7	---	---	---	---	
TM7SF2	7108	broad.mit.edu	37	11	64879505	64879505	+	Frame_Shift_Del	DEL	C	-	-			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64879505delC	uc001oct.2	+	1	165	c.18delC	c.(16-18)GGCfs	p.G6fs	TM7SF2_uc010rny.1_5'UTR|TM7SF2_uc001ocu.2_Frame_Shift_Del_p.G6fs|TM7SF2_uc001ocv.2_5'UTR	NM_003273	NP_003264	O76062	ERG24_HUMAN	transmembrane 7 superfamily member 2	6					cholesterol biosynthetic process	endoplasmic reticulum membrane|integral to plasma membrane	delta14-sterol reductase activity			ovary(1)	1						CCACTCAGGGCCCCCGGGCCC	0.642													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	100517160	100517175	+	IGR	DEL	GAAGGAAGGAAGGAAA	-	-	rs145916362	by1000genomes	TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:100517160_100517175delGAAGGAAGGAAGGAAA								CNTN5 (289688 upstream) : ARHGAP42 (41232 downstream)																							aggaaggaaggaaggaaggaaggaaagaaggaagga	0.009													4	2	---	---	---	---	
PLEKHA5	54477	broad.mit.edu	37	12	19498709	19498710	+	Intron	INS	-	AATTG	AATTG			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:19498709_19498710insAATTG	uc001reb.2	+						PLEKHA5_uc010sie.1_Intron|PLEKHA5_uc001rea.2_Intron|PLEKHA5_uc009zin.2_Intron|PLEKHA5_uc010sif.1_Intron|PLEKHA5_uc010sig.1_Intron|PLEKHA5_uc010sih.1_Intron|PLEKHA5_uc001rec.1_Intron|PLEKHA5_uc009zio.2_Intron	NM_019012	NP_061885	Q9HAU0	PKHA5_HUMAN	pleckstrin homology domain containing, family A								1-phosphatidylinositol binding|protein binding			ovary(1)|kidney(1)|skin(1)	3	Acute lymphoblastic leukemia(4;0.000455)|all_hematologic(4;0.00804)					aaaacaaaagaaaTTGTTCTTT	0.134													31	28	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	77054710	77054710	+	IGR	DEL	A	-	-	rs35714759		TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:77054710delA								OSBPL8 (101121 upstream) : ZDHHC17 (103144 downstream)																							TCTGGGCTATaaaaaaaaaaa	0.299													7	4	---	---	---	---	
PLXNC1	10154	broad.mit.edu	37	12	94690824	94690824	+	Intron	DEL	T	-	-			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:94690824delT	uc001tdc.2	+						PLXNC1_uc010sut.1_Intron|PLXNC1_uc009zsv.2_Intron	NM_005761	NP_005752	O60486	PLXC1_HUMAN	plexin C1 precursor						axon guidance|cell adhesion	integral to membrane|intracellular|plasma membrane	receptor activity|receptor binding			ovary(2)|central_nervous_system(1)	3						GGGGGAAAAATGTAGCTATGG	0.453													15	8	---	---	---	---	
PITPNM2	57605	broad.mit.edu	37	12	123477012	123477012	+	Intron	DEL	C	-	-			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123477012delC	uc001uej.1	-						PITPNM2_uc001uek.1_Intron	NM_020845	NP_065896	Q9BZ72	PITM2_HUMAN	phosphatidylinositol transfer protein,						metabolic process|transport	endomembrane system|integral to membrane|intracellular membrane-bounded organelle	calcium ion binding|lipid binding			ovary(1)|central_nervous_system(1)|skin(1)	3	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;2.55e-05)|Epithelial(86;8.43e-05)|BRCA - Breast invasive adenocarcinoma(302;0.123)		ACCCCACCTTCCCCCAGAGGA	0.642													42	22	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	22300055	22300058	+	IGR	DEL	ACCA	-	-	rs144195875		TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:22300055_22300058delACCA								FGF9 (21415 upstream) : None (None downstream)																							caccaccaccaccaaccatcacca	0.034													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	22300217	22300218	+	IGR	INS	-	AT	AT			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:22300217_22300218insAT								FGF9 (21577 upstream) : None (None downstream)																							tcaccatcaccaccaccatcac	0.015													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	75588839	75588840	+	IGR	INS	-	CTTCCTTC	CTTCCTTC	rs9543833		TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:75588839_75588840insCTTCCTTC								KLF12 (880445 upstream) : LOC647288 (223050 downstream)																							tttctttctttcttccttcctt	0.139													11	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	97538090	97538090	+	IGR	DEL	C	-	-			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:97538090delC								HS6ST3 (46279 upstream) : OXGR1 (99883 downstream)																							AAAAGAAAAGCCTTACAAGTA	0.443													12	6	---	---	---	---	
KTN1	3895	broad.mit.edu	37	14	56106778	56106778	+	Intron	DEL	T	-	-			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:56106778delT	uc001xcb.2	+						KTN1_uc001xce.2_Intron|KTN1_uc001xcc.2_Intron|KTN1_uc001xcd.2_Intron|KTN1_uc010trb.1_Intron|KTN1_uc001xcf.1_Intron	NM_182926	NP_891556	Q86UP2	KTN1_HUMAN	kinectin 1 isoform a						microtubule-based movement	endoplasmic reticulum membrane|integral to plasma membrane|membrane fraction				breast(3)|ovary(2)|lung(1)|central_nervous_system(1)	7						TTTAAATTACTTTGATGCACA	0.279			T	RET	papillary thryoid								51	30	---	---	---	---	
KLC1	3831	broad.mit.edu	37	14	104053846	104053846	+	Intron	DEL	T	-	-			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:104053846delT	uc010tyd.1	+						C14orf153_uc001ynl.3_Intron|C14orf153_uc010tyc.1_Intron	NM_005552	NP_005543	Q07866	KLC1_HUMAN	kinesin light chain 1 isoform 1						blood coagulation|microtubule-based movement|stress granule disassembly	cytosol|kinesin complex|microtubule	microtubule motor activity|protein binding				0		Melanoma(154;0.155)|all_epithelial(191;0.19)				tctttttttcttttttttttt	0.129													4	2	---	---	---	---	
SLC28A1	9154	broad.mit.edu	37	15	85443229	85443232	+	Intron	DEL	AGGC	-	-			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:85443229_85443232delAGGC	uc002blg.2	+						SLC28A1_uc010upd.1_Intron|SLC28A1_uc010bnb.2_Intron|SLC28A1_uc010upe.1_Intron|SLC28A1_uc010upf.1_Intron|SLC28A1_uc010upg.1_Intron	NM_004213	NP_004204	O00337	S28A1_HUMAN	solute carrier family 28, member 1 isoform 1						nucleobase, nucleoside and nucleotide metabolic process	integral to plasma membrane|membrane fraction	nucleoside binding			skin(2)|ovary(1)	3			BRCA - Breast invasive adenocarcinoma(143;0.0587)			gaaAAGAAAAaggcaggcaggcag	0.025													4	6	---	---	---	---	
C16orf71	146562	broad.mit.edu	37	16	4788056	4788056	+	Intron	DEL	T	-	-			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:4788056delT	uc002cxn.2	+							NM_139170	NP_631909	Q8IYS4	CP071_HUMAN	hypothetical protein LOC146562											central_nervous_system(1)	1						AACATGGTCCTTTTTTTTTTC	0.498													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	13356528	13356535	+	IGR	DEL	AGGGAGGG	-	-	rs7500959	by1000genomes	TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:13356528_13356535delAGGGAGGG								SHISA9 (22256 upstream) : ERCC4 (657479 downstream)																							gaaggaaggaagggagggaggaaggaag	0.154													5	3	---	---	---	---	
TMC5	79838	broad.mit.edu	37	16	19476434	19476445	+	Intron	DEL	CCTCCCTCCCTC	-	-	rs71812351		TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:19476434_19476445delCCTCCCTCCCTC	uc002dgc.3	+						TMC5_uc010vaq.1_Intron|TMC5_uc002dgb.3_Intron|TMC5_uc010var.1_Intron|TMC5_uc002dgd.1_Intron|TMC5_uc002dge.3_Intron|TMC5_uc002dgf.3_Intron|TMC5_uc002dgg.3_Intron	NM_001105248	NP_001098718	Q6UXY8	TMC5_HUMAN	transmembrane channel-like 5 isoform a							integral to membrane				skin(1)	1						ttccttccttcctccctccctccctccctccc	0.014													1	8	---	---	---	---	
GPRC5B	51704	broad.mit.edu	37	16	19884264	19884264	+	Intron	DEL	T	-	-			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:19884264delT	uc002dgt.2	-						GPRC5B_uc010vav.1_Intron	NM_016235	NP_057319	Q9NZH0	GPC5B_HUMAN	G protein-coupled receptor, family C, group 5,											lung(1)|breast(1)|skin(1)	3						ACTCGCCTCATTTCAAACctg	0.348													15	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	25031511	25031512	+	IGR	INS	-	GGAAGGAA	GGAAGGAA	rs7498498	by1000genomes	TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:25031511_25031512insGGAAGGAA								ARHGAP17 (4836 upstream) : LCMT1 (91535 downstream)																							gaaggaaggacggaaggaagga	0.144													3	3	---	---	---	---	
SEZ6L2	26470	broad.mit.edu	37	16	29898789	29898789	+	Intron	DEL	T	-	-	rs34805858		TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:29898789delT	uc002duq.3	-						uc002dtf.2_Intron|BOLA2_uc010bzb.1_Intron|SEZ6L2_uc002dup.3_Intron|SEZ6L2_uc002dur.3_Intron|SEZ6L2_uc002dus.3_Intron|SEZ6L2_uc010vec.1_Intron|SEZ6L2_uc010ved.1_Intron	NM_201575	NP_963869	Q6UXD5	SE6L2_HUMAN	seizure related 6 homolog (mouse)-like 2 isoform							endoplasmic reticulum membrane|integral to membrane|plasma membrane				ovary(1)|skin(1)	2						gcccggctaattttttttttt	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	86055052	86055052	+	IGR	DEL	T	-	-	rs149616291		TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:86055052delT								IRF8 (98843 upstream) : LOC732275 (310404 downstream)																							ttcctttctCttttttttttt	0.114													4	3	---	---	---	---	
FLJ36000	284124	broad.mit.edu	37	17	21904445	21904446	+	Intron	DEL	TG	-	-	rs111648393		TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21904445_21904446delTG	uc002gza.2	+							NR_027084				Homo sapiens cDNA FLJ36000 fis, clone TESTI2015180.												0						TCTTTCCCTCtgtgtgtgtgtg	0.455													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	12303771	12303771	+	IGR	DEL	A	-	-			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:12303771delA								CIDEA (26179 upstream) : TUBB6 (4469 downstream)																							AATGCATCTCaaaaaaaaaaa	0.209													5	3	---	---	---	---	
SMARCA4	6597	broad.mit.edu	37	19	11098744	11098744	+	Intron	DEL	C	-	-			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11098744delC	uc002mqf.3	+						SMARCA4_uc010dxp.2_Intron|SMARCA4_uc010dxo.2_Intron|SMARCA4_uc002mqg.1_Intron|SMARCA4_uc010dxq.2_Intron|SMARCA4_uc010dxr.2_Intron|SMARCA4_uc002mqj.3_Intron|SMARCA4_uc010dxs.2_Intron|SMARCA4_uc002mqe.2_Intron	NM_003072	NP_003063	P51532	SMCA4_HUMAN	SWI/SNF-related matrix-associated						chromatin remodeling|negative regulation of androgen receptor signaling pathway|negative regulation of cell growth|negative regulation of S phase of mitotic cell cycle|negative regulation of transcription from RNA polymerase II promoter|nervous system development|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nBAF complex|npBAF complex|nuclear chromatin|SWI/SNF complex|WINAC complex	androgen receptor binding|ATP binding|DNA binding|DNA-dependent ATPase activity|helicase activity|histone acetyl-lysine binding|identical protein binding|p53 binding|protein N-terminus binding|transcription corepressor activity	p.?(1)		lung(29)|ovary(8)|pancreas(7)|large_intestine(5)|central_nervous_system(5)|skin(3)|prostate(3)|breast(2)|adrenal_gland(1)|stomach(1)|liver(1)|autonomic_ganglia(1)|kidney(1)	67		all_lung(6;0.0512)|Lung NSC(9;0.0568)				ttcctcacctccctgctccca	0.254			F|N|Mis		NSCLC				Rhabdoid_Predisposition_syndrome				4	2	---	---	---	---	
MAN2B1	4125	broad.mit.edu	37	19	12767170	12767171	+	Intron	INS	-	A	A			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12767170_12767171insA	uc002mub.2	-						MAN2B1_uc010dyv.1_Intron	NM_000528	NP_000519	O00754	MA2B1_HUMAN	mannosidase, alpha, class 2B, member 1						protein deglycosylation	lysosome	alpha-mannosidase activity|zinc ion binding			ovary(4)|central_nervous_system(2)	6						gactccgtctcaaaaaaaaaaa	0.292													4	2	---	---	---	---	
PAK4	10298	broad.mit.edu	37	19	39614528	39614541	+	5'Flank	DEL	AAAGAAAGAAAGAA	-	-	rs112512175		TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39614528_39614541delAAAGAAAGAAAGAA	uc002okj.1	+						PAK4_uc002okl.1_5'Flank|PAK4_uc002okn.1_5'Flank|PAK4_uc002okm.1_5'Flank|PAK4_uc002oko.1_5'Flank|PAK4_uc002okp.1_5'Flank	NM_001014831	NP_001014831	O96013	PAK4_HUMAN	p21-activated kinase 4 isoform 1						cellular component movement|signal transduction	Golgi apparatus	ATP binding|protein binding|protein serine/threonine kinase activity			lung(3)|ovary(1)	4	all_cancers(60;1.03e-07)|all_epithelial(25;9.66e-08)|all_lung(34;1.58e-07)|Lung NSC(34;1.88e-07)|Ovarian(47;0.0454)		Epithelial(26;4.82e-25)|all cancers(26;2.94e-22)|Lung(45;0.000797)|LUSC - Lung squamous cell carcinoma(53;0.00113)			aaagaaagagaaagaaagaaagaaaaagaaagaa	0.000													5	3	---	---	---	---	
CKM	1158	broad.mit.edu	37	19	45822685	45822685	+	Intron	DEL	C	-	-	rs68016783		TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45822685delC	uc002pbd.2	-							NM_001824	NP_001815	P06732	KCRM_HUMAN	muscle creatine kinase						creatine metabolic process	cytosol	ATP binding|creatine kinase activity			skin(1)	1		Ovarian(192;0.0336)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;2.29e-44)|Epithelial(262;1.05e-38)|GBM - Glioblastoma multiforme(486;3.56e-07)	Creatine(DB00148)	aaaactgaggcCCCCCCCCCT	0.338													4	2	---	---	---	---	
ZNF880	400713	broad.mit.edu	37	19	52877717	52877717	+	Intron	DEL	T	-	-	rs77187934		TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:52877717delT	uc002pzc.2	+						ZNF880_uc002pzb.3_Intron	NM_001145434	NP_001138906	Q6PDB4	ZN880_HUMAN	zinc finger protein LOC400713						regulation of transcription, DNA-dependent	intracellular	nucleic acid binding|zinc ion binding				0						GGCCCCATAAttttttttttt	0.254													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	16113002	16113013	+	IGR	DEL	AGGAAGGAAGGA	-	-	rs34362040		TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:16113002_16113013delAGGAAGGAAGGA								MACROD2 (79163 upstream) : KIF16B (139736 downstream)																							cactAAACACaggaaggaaggaaggaaggaag	0.009													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	32823673	32823676	+	IGR	DEL	AAGG	-	-	rs71337945		TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:32823673_32823676delAAGG								EIF2S2 (123588 upstream) : ASIP (24495 downstream)																							gaaggaaggaaaggaaggaaggaa	0.000													11	5	---	---	---	---	
SON	6651	broad.mit.edu	37	21	34948508	34948509	+	Intron	INS	-	T	T	rs111372529		TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:34948508_34948509insT	uc002yse.1	+						SON_uc002ysd.2_Intron|SON_uc002ysf.1_Intron|SON_uc002ysh.2_Intron|DONSON_uc002ysi.1_Intron	NM_138927	NP_620305	P18583	SON_HUMAN	SON DNA-binding protein isoform F						anti-apoptosis|cytokinesis|mRNA processing|regulation of cell cycle|regulation of RNA splicing|RNA splicing|spindle pole body separation	nuclear speck	DNA binding|double-stranded RNA binding			ovary(4)|skin(2)	6						TTTGCAGTCCCTTTCCCAAATG	0.287													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	44755923	44755925	+	IGR	DEL	CAT	-	-	rs66544012		TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:44755923_44755925delCAT								CRYAA (163010 upstream) : SIK1 (78473 downstream)																							tcaccatcaccatcaccaccacc	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	44756517	44756517	+	IGR	DEL	C	-	-			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:44756517delC								CRYAA (163604 upstream) : SIK1 (77881 downstream)																							tcaccaccatcaccaccacca	0.000													4	2	---	---	---	---	
CECR2	27443	broad.mit.edu	37	22	17898573	17898578	+	Intron	DEL	GAAGAG	-	-			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:17898573_17898578delGAAGAG	uc010gqv.1	+							NM_031413	NP_113601	Q9BXF3	CECR2_HUMAN	cat eye syndrome chromosome region, candidate 2						chromatin modification|cytokinesis|cytoskeleton organization|DNA fragmentation involved in apoptotic nuclear change|vesicle-mediated transport		protein binding			ovary(1)|skin(1)	2		all_epithelial(15;0.139)		Lung(27;0.146)		agaagaagaagaagaggaagaggaag	0.257													10	7	---	---	---	---	
MYO18B	84700	broad.mit.edu	37	22	26413051	26413054	+	Intron	DEL	CTCC	-	-	rs144669857		TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:26413051_26413054delCTCC	uc003abz.1	+						MYO18B_uc003aca.1_Intron|MYO18B_uc010guy.1_Intron|MYO18B_uc010guz.1_Intron|MYO18B_uc011aka.1_Intron|MYO18B_uc011akb.1_Intron|MYO18B_uc010gva.1_Intron	NM_032608	NP_115997	Q8IUG5	MY18B_HUMAN	myosin XVIIIB							nucleus|sarcomere|unconventional myosin complex	actin binding|ATP binding|motor activity			ovary(5)|central_nervous_system(3)|large_intestine(2)|breast(2)	12						ctctgtgcctctccctccctccct	0.078													5	4	---	---	---	---	
DRG1	4733	broad.mit.edu	37	22	31806803	31806803	+	Intron	DEL	A	-	-			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:31806803delA	uc003aku.2	+							NM_004147	NP_004138	Q9Y295	DRG1_HUMAN	developmentally regulated GTP binding protein 1						multicellular organismal development|transcription, DNA-dependent	cytoplasm|intermediate filament cytoskeleton|nucleus	GTP binding|transcription factor binding			central_nervous_system(1)	1						ctccatctccaaaaaaaaaaa	0.154													3	3	---	---	---	---	
CACNA1I	8911	broad.mit.edu	37	22	39966252	39966259	+	5'Flank	DEL	CCTTCCTT	-	-	rs10528897		TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:39966252_39966259delCCTTCCTT	uc003ayc.2	+						CACNA1I_uc003ayd.2_5'Flank	NM_021096	NP_066919	Q9P0X4	CAC1I_HUMAN	calcium channel, voltage-dependent, T type,						axon guidance|signal transduction	voltage-gated calcium channel complex	low voltage-gated calcium channel activity|protein binding			breast(1)|central_nervous_system(1)	2	Melanoma(58;0.0749)				Flunarizine(DB04841)|Paramethadione(DB00617)|Verapamil(DB00661)	AGTTAAGATCccttccttccttccttcc	0.144													4	2	---	---	---	---	
MED14	9282	broad.mit.edu	37	X	40541809	40541809	+	Intron	DEL	T	-	-			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:40541809delT	uc004dex.3	-							NM_004229	NP_004220	O60244	MED14_HUMAN	mediator complex subunit 14						androgen receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	mediator complex	ligand-dependent nuclear receptor transcription coactivator activity|receptor activity|RNA polymerase II transcription cofactor activity|thyroid hormone receptor binding|vitamin D receptor binding			breast(2)|kidney(1)|skin(1)	4						GGGTGAGGGCttttttttttt	0.323													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	44509049	44509049	+	IGR	DEL	A	-	-			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:44509049delA								FUNDC1 (106828 upstream) : DUSP21 (194200 downstream)																							ATCTGCCTGGAAAAAAAAAAA	0.199													5	3	---	---	---	---	
KLF8	11279	broad.mit.edu	37	X	56296860	56296861	+	Intron	DEL	AG	-	-			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:56296860_56296861delAG	uc004dur.2	+						KLF8_uc011mop.1_Intron|KLF8_uc010nkh.2_Intron	NM_007250	NP_009181	O95600	KLF8_HUMAN	Kruppel-like factor 8 isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1						agagaggggcagagagagagag	0.233													5	3	---	---	---	---	
ATP7A	538	broad.mit.edu	37	X	77270019	77270019	+	Intron	DEL	C	-	-			TCGA-B0-5075-01A-01D-1462-08	TCGA-B0-5075-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:77270019delC	uc004ecx.3	+							NM_000052	NP_000043	Q04656	ATP7A_HUMAN	ATPase, Cu++ transporting, alpha polypeptide						ATP biosynthetic process|blood vessel development|blood vessel remodeling|cartilage development|cellular copper ion homeostasis|cerebellar Purkinje cell differentiation|collagen fibril organization|copper ion import|detoxification of copper ion|dopamine metabolic process|elastic fiber assembly|elastin biosynthetic process|epinephrine metabolic process|hair follicle morphogenesis|locomotory behavior|lung alveolus development|negative regulation of metalloenzyme activity|neuroprotection|peptidyl-lysine modification|pigmentation|positive regulation of metalloenzyme activity|positive regulation of oxidoreductase activity|pyramidal neuron development|regulation of oxidative phosphorylation|removal of superoxide radicals|serotonin metabolic process|skin development|T-helper cell differentiation|tryptophan metabolic process	basolateral plasma membrane|cytosol|endoplasmic reticulum|endoplasmic reticulum|integral to membrane|late endosome|neuron projection|neuronal cell body|perinuclear region of cytoplasm|trans-Golgi network|trans-Golgi network transport vesicle	ATP binding|copper-dependent protein binding|copper-exporting ATPase activity|superoxide dismutase copper chaperone activity				0						TGAAGTGAAACATTTTCATAT	0.229													13	7	---	---	---	---	
