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
PRDM16	63976	broad.mit.edu	37	1	3102700	3102700	+	Missense_Mutation	SNP	G	A	A			TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:3102700G>A	uc001akf.2	+	2	129	c.49G>A	c.(49-51)GTT>ATT	p.V17I	PRDM16_uc001akc.2_Missense_Mutation_p.V17I|PRDM16_uc001akd.2_Missense_Mutation_p.V17I|PRDM16_uc001ake.2_Missense_Mutation_p.V17I|PRDM16_uc009vlh.2_5'UTR	NM_022114	NP_071397	Q9HAZ2	PRD16_HUMAN	PR domain containing 16 isoform 1	17					brown fat cell differentiation|negative regulation of granulocyte differentiation|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transforming growth factor beta receptor signaling pathway|negative regulation of transforming growth factor beta receptor signaling pathway|positive regulation of transcription, DNA-dependent|positive regulation of transcription, DNA-dependent|regulation of cellular respiration|transcription, DNA-dependent	transcriptional repressor complex	protein binding|sequence-specific DNA binding|transcription coactivator activity|zinc ion binding			lung(3)|ovary(1)|breast(1)|central_nervous_system(1)|skin(1)	7	all_cancers(77;0.00208)|all_epithelial(69;0.000732)|Ovarian(185;0.0634)|Lung NSC(156;0.109)|all_lung(157;0.111)	all_epithelial(116;2.03e-21)|all_lung(118;7.55e-09)|Lung NSC(185;1.28e-06)|Breast(487;0.000792)|Renal(390;0.00137)|Hepatocellular(190;0.00515)|Myeloproliferative disorder(586;0.0267)|Ovarian(437;0.0365)|Lung SC(97;0.114)|Medulloblastoma(700;0.134)		Epithelial(90;5.59e-35)|OV - Ovarian serous cystadenocarcinoma(86;1.99e-20)|GBM - Glioblastoma multiforme(42;3.72e-11)|Colorectal(212;0.000425)|BRCA - Breast invasive adenocarcinoma(365;0.000946)|COAD - Colon adenocarcinoma(227;0.000968)|Kidney(185;0.00155)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0175)|Lung(427;0.137)		TGACGGTGACGTTGTAAATAA	0.627			T	EVI1	MDS|AML								21	95	---	---	---	---	PASS
MACF1	23499	broad.mit.edu	37	1	39934334	39934334	+	Silent	SNP	C	T	T			TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:39934334C>T	uc010oiu.1	+	61	17279	c.17148C>T	c.(17146-17148)ACC>ACT	p.T5716T	MACF1_uc010ois.1_Silent_p.T5208T|MACF1_uc001cde.1_Silent_p.T85T|MACF1_uc001cdf.1_Silent_p.T91T|MACF1_uc001cdg.2_5'UTR|MACF1_uc001cdh.2_5'UTR	NM_033044	NP_149033	Q9UPN3	MACF1_HUMAN	microfilament and actin filament cross-linker	7166	C-terminal tail (By similarity).|GAR.				cell cycle arrest|Golgi to plasma membrane protein transport|positive regulation of Wnt receptor signaling pathway|regulation of epithelial cell migration|regulation of focal adhesion assembly|regulation of microtubule-based process|Wnt receptor signaling pathway|wound healing	Golgi apparatus|microtubule|ruffle membrane	actin filament binding|ATPase activity|calcium ion binding|microtubule binding			ovary(8)|breast(3)|central_nervous_system(3)|skin(2)	16	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			TGCGCAGCACCGTGATGGTTC	0.433													8	71	---	---	---	---	PASS
MSH4	4438	broad.mit.edu	37	1	76363675	76363675	+	Missense_Mutation	SNP	A	C	C			TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:76363675A>C	uc001dhd.1	+	18	2480	c.2439A>C	c.(2437-2439)GAA>GAC	p.E813D		NM_002440	NP_002431	O15457	MSH4_HUMAN	mutS homolog 4	813					chiasma assembly|homologous chromosome segregation|mismatch repair|reciprocal meiotic recombination	synaptonemal complex	ATP binding|DNA-dependent ATPase activity|mismatched DNA binding			lung(3)|ovary(2)	5						TGCATTTTGAAGTTCAACATG	0.338								MMR					8	232	---	---	---	---	PASS
NBPF14	25832	broad.mit.edu	37	1	148004265	148004265	+	3'UTR	SNP	T	C	C			TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:148004265T>C	uc001eqq.2	-	22					LOC200030_uc010ozz.1_Intron|LOC200030_uc001eqe.2_Intron|LOC200030_uc001eqf.2_Intron|LOC200030_uc001eqg.2_Intron|FLJ39739_uc001eqo.1_Intron|NBPF14_uc010pab.1_3'UTR|NBPF14_uc010pac.1_3'UTR	NM_015383	NP_056198	Q5TI25	NBPFE_HUMAN	hypothetical protein LOC25832							cytoplasm				ovary(1)	1	all_hematologic(923;0.032)					CCCTGAGGAATTTTGTAGCTA	0.453													2	6	---	---	---	---	PASS
LCE1B	353132	broad.mit.edu	37	1	152785177	152785177	+	Silent	SNP	C	A	A			TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152785177C>A	uc001faq.2	+	1	731	c.255C>A	c.(253-255)TCC>TCA	p.S85S		NM_178349	NP_848126	Q5T7P3	LCE1B_HUMAN	late cornified envelope 1B	85	Gly-rich.				keratinization						0	Lung NSC(65;9.06e-30)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			GCCGTAGGTCCCACTGCCACA	0.687													4	103	---	---	---	---	PASS
NTRK1	4914	broad.mit.edu	37	1	156849827	156849827	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156849827C>T	uc001fqh.1	+	16	2139	c.2083C>T	c.(2083-2085)CCG>TCG	p.P695S	NTRK1_uc001fqf.1_Missense_Mutation_p.P659S|NTRK1_uc009wsi.1_Missense_Mutation_p.P394S|NTRK1_uc001fqi.1_Missense_Mutation_p.P689S|NTRK1_uc009wsk.1_Missense_Mutation_p.P692S	NM_002529	NP_002520	P04629	NTRK1_HUMAN	neurotrophic tyrosine kinase, receptor, type 1	695	Cytoplasmic (Potential).|Protein kinase.		P -> L (in CIPA).		activation of adenylate cyclase activity|activation of MAPKK activity|activation of phospholipase C activity|cell differentiation|nerve growth factor receptor signaling pathway|nervous system development|phosphatidylinositol-mediated signaling|Ras protein signal transduction	endosome|integral to plasma membrane	ATP binding|neurotrophin receptor activity|transmembrane receptor protein serine/threonine kinase activity|transmembrane receptor protein tyrosine kinase activity			lung(9)|ovary(6)|stomach(1)|central_nervous_system(1)	17	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)				Imatinib(DB00619)	TCGCTGGATGCCGCCCGAGAG	0.647			T	TPM3|TPR|TFG	papillary thyroid					TSP Lung(10;0.080)			5	129	---	---	---	---	PASS
C1orf114	57821	broad.mit.edu	37	1	169391358	169391358	+	Missense_Mutation	SNP	A	G	G			TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:169391358A>G	uc001gga.1	-	3	479	c.311T>C	c.(310-312)TTC>TCC	p.F104S	C1orf114_uc001gfz.1_Missense_Mutation_p.F104S|C1orf114_uc009wvq.1_Missense_Mutation_p.F104S|C1orf114_uc001ggb.2_Missense_Mutation_p.F104S|C1orf114_uc001ggc.1_Missense_Mutation_p.F104S	NM_021179	NP_067002	Q5TID7	CA114_HUMAN	hypothetical protein LOC57821	104											0	all_hematologic(923;0.208)					GGATTCCTGGAAAGAGTTTTC	0.393													35	179	---	---	---	---	PASS
CRB1	23418	broad.mit.edu	37	1	197390735	197390735	+	Missense_Mutation	SNP	G	A	A			TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:197390735G>A	uc001gtz.2	+	6	1912	c.1777G>A	c.(1777-1779)GCG>ACG	p.A593T	CRB1_uc010poz.1_Missense_Mutation_p.A524T|CRB1_uc010ppa.1_Intron|CRB1_uc009wza.2_Missense_Mutation_p.A481T|CRB1_uc010ppb.1_Missense_Mutation_p.A593T|CRB1_uc010ppc.1_Intron|CRB1_uc010ppd.1_Missense_Mutation_p.A74T|CRB1_uc001gub.1_Missense_Mutation_p.A242T	NM_201253	NP_957705	P82279	CRUM1_HUMAN	crumbs homolog 1 precursor	593	Extracellular (Potential).|Laminin G-like 1.				cell-cell signaling|establishment or maintenance of cell polarity	apical plasma membrane|extracellular region|integral to membrane	calcium ion binding|protein binding			ovary(5)|skin(3)|large_intestine(1)	9						GAAATGCATCGCGAAAGCTCC	0.468													36	315	---	---	---	---	PASS
ZC3H11A	9877	broad.mit.edu	37	1	203816426	203816426	+	Nonsense_Mutation	SNP	C	A	A			TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:203816426C>A	uc001hac.2	+	15	1773	c.1157C>A	c.(1156-1158)TCA>TAA	p.S386*	ZC3H11A_uc001had.2_Nonsense_Mutation_p.S386*|ZC3H11A_uc001hae.2_Nonsense_Mutation_p.S386*|ZC3H11A_uc001haf.2_Nonsense_Mutation_p.S386*|ZC3H11A_uc010pqm.1_Nonsense_Mutation_p.S332*|ZC3H11A_uc001hag.1_Nonsense_Mutation_p.S386*	NM_014827	NP_055642	O75152	ZC11A_HUMAN	zinc finger CCCH-type containing 11A	386	Potential.						nucleic acid binding|protein binding|zinc ion binding			lung(1)|central_nervous_system(1)	2	all_cancers(21;0.0904)|all_epithelial(62;0.234)		BRCA - Breast invasive adenocarcinoma(75;0.109)			GAAGGACCTTCAAAAACTGAT	0.423													18	91	---	---	---	---	PASS
EPHX1	2052	broad.mit.edu	37	1	226032237	226032237	+	Missense_Mutation	SNP	T	C	C			TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:226032237T>C	uc001hpk.2	+	8	1159	c.1079T>C	c.(1078-1080)CTC>CCC	p.L360P	EPHX1_uc001hpl.2_Missense_Mutation_p.L360P	NM_001136018	NP_001129490	P07099	HYEP_HUMAN	epoxide hydrolase 1	360					aromatic compound catabolic process|response to toxin	endoplasmic reticulum membrane|integral to membrane|microsome	cis-stilbene-oxide hydrolase activity|epoxide hydrolase activity			ovary(3)|lung(1)	4	Breast(184;0.197)					AACGTCATGCTCTACTGGACA	0.572													33	81	---	---	---	---	PASS
EFCAB2	84288	broad.mit.edu	37	1	245222709	245222709	+	Missense_Mutation	SNP	G	C	C			TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:245222709G>C	uc001ibd.2	+	4	681	c.540G>C	c.(538-540)AGG>AGC	p.R180S	EFCAB2_uc001ibc.2_Missense_Mutation_p.R44S|EFCAB2_uc010pyo.1_Missense_Mutation_p.R54S|EFCAB2_uc010pyp.1_Missense_Mutation_p.R44S|EFCAB2_uc001ibe.2_RNA	NR_026586		Q5VUJ9	EFCB2_HUMAN	RecName: Full=EF-hand calcium-binding domain-containing protein 2;	180	EF-hand 1.						calcium ion binding				0	all_cancers(71;2.93e-06)|all_epithelial(71;2.13e-05)|all_lung(81;0.0337)|Lung NSC(105;0.0472)|Ovarian(71;0.0584)|Breast(184;0.0716)|all_neural(11;0.0982)		OV - Ovarian serous cystadenocarcinoma(106;0.015)			CAATTATCAGGTCATTAGGAT	0.418													35	101	---	---	---	---	PASS
RGPD3	653489	broad.mit.edu	37	2	107021599	107021599	+	3'UTR	SNP	C	T	T			TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:107021599C>T	uc010ywi.1	-	23						NM_001144013	NP_001137485	A6NKT7	RGPD3_HUMAN	RANBP2-like and GRIP domain containing 3						intracellular transport		binding			ovary(1)	1						TTAATAAAAACATTCCTTCCA	0.323													4	78	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179659882	179659882	+	Missense_Mutation	SNP	C	A	A			TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179659882C>A	uc010zfg.1	-	7	1236	c.1012G>T	c.(1012-1014)GGT>TGT	p.G338C	TTN_uc010zfh.1_Missense_Mutation_p.G338C|TTN_uc010zfi.1_Missense_Mutation_p.G338C|TTN_uc010zfj.1_Missense_Mutation_p.G338C|TTN_uc002unb.2_Missense_Mutation_p.G338C|TTN_uc010frg.1_Missense_Mutation_p.G12C	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	338							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			ACTTCAGGACCTGTGGCCACG	0.562													4	109	---	---	---	---	PASS
KIAA2018	205717	broad.mit.edu	37	3	113379013	113379013	+	Missense_Mutation	SNP	T	C	C			TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113379013T>C	uc003eam.2	-	7	1927	c.1516A>G	c.(1516-1518)ATG>GTG	p.M506V	KIAA2018_uc003eal.2_Missense_Mutation_p.M450V	NM_001009899	NP_001009899	Q68DE3	K2018_HUMAN	hypothetical protein LOC205717	506					regulation of transcription, DNA-dependent	membrane|nucleus	calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity			skin(2)|ovary(1)	3						AGTGGCTGCATAGGTAAAGAT	0.438													38	84	---	---	---	---	PASS
ATP13A4	84239	broad.mit.edu	37	3	193177001	193177001	+	Missense_Mutation	SNP	A	G	G			TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:193177001A>G	uc003ftd.2	-	14	1651	c.1543T>C	c.(1543-1545)TTT>CTT	p.F515L	ATP13A4_uc003fte.1_Missense_Mutation_p.F515L|ATP13A4_uc011bsr.1_5'UTR|ATP13A4_uc010hzi.2_RNA|ATP13A4_uc003ftf.3_Missense_Mutation_p.F221L	NM_032279	NP_115655	Q4VNC1	AT134_HUMAN	ATPase type 13A4	515	Extracellular (Potential).				ATP biosynthetic process|cation transport	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|metal ion binding			ovary(2)	2	all_cancers(143;1.76e-08)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(49;2.72e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;0.000109)		CCTGAGGCAAAGCTGTGAACT	0.517													35	99	---	---	---	---	PASS
UGT2B10	7365	broad.mit.edu	37	4	69870669	69870669	+	Missense_Mutation	SNP	C	A	A			TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:69870669C>A	uc011cao.1	-	9	1517	c.1381G>T	c.(1381-1383)GCT>TCT	p.A461S	UGT2B10_uc011can.1_Missense_Mutation_p.A377S			P36537	UDB10_HUMAN	RecName: Full=UDP-glucuronosyltransferase 2B28;          Short=UDPGT 2B28;          EC=2.4.1.17; Flags: Precursor;	498	Helical; (Potential).				lipid metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	glucuronosyltransferase activity			skin(3)|ovary(2)	5						GCCACACAGGCCAGCAGGAAC	0.448													12	210	---	---	---	---	PASS
RASGEF1B	153020	broad.mit.edu	37	4	82355851	82355851	+	Missense_Mutation	SNP	A	G	G			TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:82355851A>G	uc003hmi.1	-	11	1286	c.1142T>C	c.(1141-1143)ATT>ACT	p.I381T	RASGEF1B_uc003hmj.1_Missense_Mutation_p.I380T|RASGEF1B_uc010ijq.1_Missense_Mutation_p.I339T	NM_152545	NP_689758	Q0VAM2	RGF1B_HUMAN	RasGEF domain family, member 1B	381	Ras-GEF.				regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	intracellular	Ras guanyl-nucleotide exchange factor activity				0						GAGGAAATAAATATCTTTGAT	0.373													17	36	---	---	---	---	PASS
FGA	2243	broad.mit.edu	37	4	155507521	155507521	+	Missense_Mutation	SNP	G	T	T			TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:155507521G>T	uc003iod.1	-	5	1118	c.1060C>A	c.(1060-1062)CCT>ACT	p.P354T	FGA_uc003ioe.1_Missense_Mutation_p.P354T|FGA_uc003iof.1_Intron	NM_000508	NP_000499	P02671	FIBA_HUMAN	fibrinogen, alpha polypeptide isoform alpha-E	354	By similarity.				platelet activation|platelet degranulation|protein polymerization|response to calcium ion|signal transduction	external side of plasma membrane|fibrinogen complex|platelet alpha granule lumen	eukaryotic cell surface binding|protein binding, bridging|receptor binding			ovary(2)|breast(1)	3	all_hematologic(180;0.215)	Renal(120;0.0458)			Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Sucralfate(DB00364)|Tenecteplase(DB00031)	GTACTACCAGGTCTAGGGCTC	0.557													57	195	---	---	---	---	PASS
GUCY1A3	2982	broad.mit.edu	37	4	156632326	156632326	+	Missense_Mutation	SNP	G	C	C			TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:156632326G>C	uc003iov.2	+	7	1545	c.1009G>C	c.(1009-1011)GGG>CGG	p.G337R	GUCY1A3_uc003iou.2_Missense_Mutation_p.G337R|GUCY1A3_uc010iqc.2_Missense_Mutation_p.G337R|GUCY1A3_uc003iow.2_Missense_Mutation_p.G337R|GUCY1A3_uc010iqd.2_Missense_Mutation_p.G336R|GUCY1A3_uc003iox.2_Missense_Mutation_p.G337R|GUCY1A3_uc003ioz.2_Missense_Mutation_p.G102R|GUCY1A3_uc003ioy.2_Missense_Mutation_p.G337R|GUCY1A3_uc010iqe.2_Missense_Mutation_p.G102R|GUCY1A3_uc003ipa.2_Intron|GUCY1A3_uc003ipb.2_Missense_Mutation_p.G337R	NM_000856	NP_000847	Q02108	GCYA3_HUMAN	guanylate cyclase 1, soluble, alpha 3 isoform A	337					blood circulation|intracellular signal transduction|nitric oxide mediated signal transduction|platelet activation	guanylate cyclase complex, soluble	GTP binding|guanylate cyclase activity|heme binding|receptor activity			central_nervous_system(2)|ovary(1)|skin(1)	4	all_hematologic(180;0.24)	Renal(120;0.0854)		COAD - Colon adenocarcinoma(41;0.17)		GACGTTTAGCGGGATCATGAC	0.383													32	123	---	---	---	---	PASS
TKTL2	84076	broad.mit.edu	37	4	164394922	164394922	+	5'UTR	SNP	G	A	A			TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:164394922G>A	uc003iqp.3	-	1						NM_032136	NP_115512	Q9H0I9	TKTL2_HUMAN	transketolase-like 2							cytoplasm	metal ion binding|transketolase activity			ovary(2)|skin(2)|pancreas(1)	5	all_hematologic(180;0.166)	Prostate(90;0.0959)|all_neural(102;0.223)				AAACGGCGCCGCAGCACCCCC	0.677													11	6	---	---	---	---	PASS
SDHA	6389	broad.mit.edu	37	5	228257	228257	+	Intron	SNP	T	G	G			TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:228257T>G	uc003jao.3	+						SDHA_uc003jan.2_Intron|SDHA_uc011clv.1_Intron|SDHA_uc011clw.1_Intron|SDHA_uc003jap.3_Intron|SDHA_uc003jaq.3_5'UTR|SDHA_uc003jar.3_5'Flank	NM_004168	NP_004159	P31040	DHSA_HUMAN	succinate dehydrogenase complex, subunit A,						nervous system development|respiratory electron transport chain|succinate metabolic process|transport|tricarboxylic acid cycle	mitochondrial respiratory chain complex II	electron carrier activity|flavin adenine dinucleotide binding|protein binding|succinate dehydrogenase (ubiquinone) activity				0			Epithelial(17;0.0159)|all cancers(22;0.0236)|OV - Ovarian serous cystadenocarcinoma(19;0.0674)|Lung(60;0.113)		Succinic acid(DB00139)	AACCTTAAAGTTTGGCTTAAC	0.398									Familial_Paragangliomas				3	95	---	---	---	---	PASS
NNT	23530	broad.mit.edu	37	5	43677827	43677827	+	Missense_Mutation	SNP	G	A	A			TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:43677827G>A	uc003joe.2	+	19	3050	c.2795G>A	c.(2794-2796)GGC>GAC	p.G932D	NNT_uc003jof.2_Missense_Mutation_p.G932D	NM_012343	NP_036475	Q13423	NNTM_HUMAN	nicotinamide nucleotide transhydrogenase	932	Mitochondrial matrix.				tricarboxylic acid cycle	integral to membrane|mitochondrial respiratory chain	NAD binding|NAD(P)+ transhydrogenase (AB-specific) activity|NAD(P)+ transhydrogenase (B-specific) activity|NADP binding			ovary(2)|central_nervous_system(1)	3	Lung NSC(6;2.58e-06)				NADH(DB00157)	TTCCTTGCAGGCTATGGTCTC	0.398													111	220	---	---	---	---	PASS
TSLP	85480	broad.mit.edu	37	5	110409195	110409195	+	Intron	SNP	C	T	T			TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:110409195C>T	uc003kpb.2	+						TSLP_uc003kpa.2_Intron|TSLP_uc010jbt.1_5'UTR	NM_033035	NP_149024	Q969D9	TSLP_HUMAN	thymic stromal lymphopoietin isoform 1							extracellular space	cytokine activity				0		all_cancers(142;2.72e-05)|all_epithelial(76;4.39e-07)|Prostate(80;0.00955)|Lung NSC(167;0.0417)|Ovarian(225;0.0443)|Colorectal(57;0.0464)|all_lung(232;0.0507)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;1.24e-08)|Epithelial(69;1.54e-07)|all cancers(49;1.73e-05)|COAD - Colon adenocarcinoma(37;0.109)		GTAAACTTTGCCGCCTATGAG	0.527													8	424	---	---	---	---	PASS
PCDHGA1	56114	broad.mit.edu	37	5	140710540	140710540	+	Missense_Mutation	SNP	G	T	T			TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140710540G>T	uc003lji.1	+	1	289	c.289G>T	c.(289-291)GCT>TCT	p.A97S	PCDHGA1_uc011dan.1_Missense_Mutation_p.A97S	NM_018912	NP_061735	Q9Y5H4	PCDG1_HUMAN	protocadherin gamma subfamily A, 1 isoform 1	97	Cadherin 1.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(1)|breast(1)|pancreas(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGAGCTCTGCGCTCAGAGCAT	0.473													10	436	---	---	---	---	PASS
DNAH11	8701	broad.mit.edu	37	7	21908580	21908580	+	Missense_Mutation	SNP	T	C	C			TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:21908580T>C	uc003svc.2	+	74	11990	c.11959T>C	c.(11959-11961)TCC>CCC	p.S3987P		NM_003777	NP_003768	Q96DT5	DYH11_HUMAN	dynein, axonemal, heavy chain 11	3987	AAA 6 (By similarity).				microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(8)|large_intestine(3)|pancreas(3)|central_nervous_system(1)	15						GGAGAAAGCTTCCAAAGGAGG	0.517									Kartagener_syndrome				21	87	---	---	---	---	PASS
DNAH11	8701	broad.mit.edu	37	7	21920474	21920474	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:21920474C>T	uc003svc.2	+	76	12402	c.12371C>T	c.(12370-12372)GCC>GTC	p.A4124V		NM_003777	NP_003768	Q96DT5	DYH11_HUMAN	dynein, axonemal, heavy chain 11	4124	AAA 6 (By similarity).				microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(8)|large_intestine(3)|pancreas(3)|central_nervous_system(1)	15						ACCATTTGTGCCAGTGTCCTC	0.498									Kartagener_syndrome				5	132	---	---	---	---	PASS
ABCA13	154664	broad.mit.edu	37	7	48556346	48556346	+	Silent	SNP	C	T	T			TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:48556346C>T	uc003toq.2	+	52	13691	c.13666C>T	c.(13666-13668)CTG>TTG	p.L4556L	ABCA13_uc010kys.1_Silent_p.L1631L|ABCA13_uc010kyt.1_RNA|ABCA13_uc010kyu.1_Silent_p.L286L	NM_152701	NP_689914	Q86UQ4	ABCAD_HUMAN	ATP binding cassette, sub-family A (ABC1),	4556	Helical; (Potential).				transport	integral to membrane	ATP binding|ATPase activity			ovary(5)|central_nervous_system(4)|skin(1)	10						ATGGATGTACCTGATGTCCAG	0.318													44	450	---	---	---	---	PASS
CLDN4	1364	broad.mit.edu	37	7	73246086	73246086	+	Missense_Mutation	SNP	T	G	G			TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73246086T>G	uc003tzi.3	+	1	894	c.555T>G	c.(553-555)TGT>TGG	p.C185W	RFC2_uc011kfa.1_Intron|CLDN4_uc003tzh.1_RNA	NM_001305	NP_001296	O14493	CLD4_HUMAN	claudin 4	185	Cytoplasmic (Potential).				calcium-independent cell-cell adhesion	integral to plasma membrane|tight junction	identical protein binding|structural molecule activity|transmembrane receptor activity				0		Lung NSC(55;0.159)				GCTGCAACTGTCCACCCCGCA	0.652													23	85	---	---	---	---	PASS
PLEC	5339	broad.mit.edu	37	8	144990746	144990746	+	Missense_Mutation	SNP	C	A	A			TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144990746C>A	uc003zaf.1	-	32	13824	c.13654G>T	c.(13654-13656)GGC>TGC	p.G4552C	PLEC_uc003zab.1_Missense_Mutation_p.G4415C|PLEC_uc003zac.1_Missense_Mutation_p.G4419C|PLEC_uc003zad.2_Missense_Mutation_p.G4415C|PLEC_uc003zae.1_Missense_Mutation_p.G4383C|PLEC_uc003zag.1_Missense_Mutation_p.G4393C|PLEC_uc003zah.2_Missense_Mutation_p.G4401C|PLEC_uc003zaj.2_Missense_Mutation_p.G4442C	NM_201380	NP_958782	Q15149	PLEC_HUMAN	plectin isoform 1	4552	Plectin 32.|Globular 2.				cellular component disassembly involved in apoptosis|hemidesmosome assembly	cytosol|focal adhesion|hemidesmosome|intermediate filament cytoskeleton|sarcolemma	actin binding|structural constituent of muscle|structural constituent of muscle			large_intestine(2)|ovary(2)|pancreas(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	9						TCCACCGTGCCGCGCTGCAGG	0.677													4	167	---	---	---	---	PASS
RCL1	10171	broad.mit.edu	37	9	4826861	4826861	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:4826861C>T	uc003zis.2	+	3	470	c.212C>T	c.(211-213)ACA>ATA	p.T71I	RCL1_uc003zit.2_Intron|RCL1_uc010mhk.1_Intron	NM_005772	NP_005763	Q9Y2P8	RCL1_HUMAN	RNA terminal phosphate cyclase-like 1	71					ribosome biogenesis|RNA processing	nucleolus	RNA-3'-phosphate cyclase activity				0	all_hematologic(13;0.137)	Acute lymphoblastic leukemia(23;0.0206)|Breast(48;0.147)		GBM - Glioblastoma multiforme(50;0.0244)		GTTTAAGGAACAACCTTATAT	0.443													11	325	---	---	---	---	PASS
HSPA5	3309	broad.mit.edu	37	9	127998975	127998975	+	Missense_Mutation	SNP	T	C	C			TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:127998975T>C	uc004bpn.2	-	8	2117	c.1861A>G	c.(1861-1863)AAG>GAG	p.K621E		NM_005347	NP_005338	P11021	GRP78_HUMAN	heat shock 70kDa protein 5	621					anti-apoptosis|cellular response to glucose starvation|ER-associated protein catabolic process|platelet activation|platelet degranulation|regulation of protein folding in endoplasmic reticulum	cell surface|endoplasmic reticulum chaperone complex|endoplasmic reticulum lumen|ER-Golgi intermediate compartment|integral to endoplasmic reticulum membrane|melanosome|midbody|nucleus|perinuclear region of cytoplasm	ATP binding|ATPase activity|calcium ion binding|caspase inhibitor activity|chaperone binding|misfolded protein binding|protein binding, bridging|protein domain specific binding|ubiquitin protein ligase binding|unfolded protein binding			ovary(3)|skin(1)	4					Antihemophilic Factor(DB00025)	TCCAGTTCCTTCTTCTTAGCT	0.423										Prostate(1;0.17)			64	163	---	---	---	---	PASS
ARID5B	84159	broad.mit.edu	37	10	63851221	63851221	+	Missense_Mutation	SNP	A	C	C			TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:63851221A>C	uc001jlt.1	+	10	2025	c.1999A>C	c.(1999-2001)AAC>CAC	p.N667H		NM_032199	NP_115575	Q14865	ARI5B_HUMAN	AT rich interactive domain 5B (MRF1-like)	667					liver development|negative regulation of transcription, DNA-dependent|positive regulation of sequence-specific DNA binding transcription factor activity|transcription, DNA-dependent		protein binding|transcription regulatory region DNA binding			ovary(2)|upper_aerodigestive_tract(1)|kidney(1)	4	Prostate(12;0.016)|all_hematologic(501;0.215)					TGGGCCCATGAACGAGAACCA	0.527													6	54	---	---	---	---	PASS
PTEN	5728	broad.mit.edu	37	10	89711891	89711891	+	Missense_Mutation	SNP	G	A	A			TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:89711891G>A	uc001kfb.2	+	7	1540	c.509G>A	c.(508-510)AGT>AAT	p.S170N		NM_000314	NP_000305	P60484	PTEN_HUMAN	phosphatase and tensin homolog	170	Phosphatase tensin-type.		S -> N (loss of phosphatase activity towards Ins(1,3,4,5)P4; retains ability to bind phospholipid membranes).|S -> R (in BZS; severely reduced protein phosphatase activity; loss of phosphatase activity towards Ins(1,3,4,5)P4).		activation of mitotic anaphase-promoting complex activity|apoptosis|canonical Wnt receptor signaling pathway|cell proliferation|central nervous system development|induction of apoptosis|inositol phosphate dephosphorylation|negative regulation of cell migration|negative regulation of cyclin-dependent protein kinase activity involved in G1/S|negative regulation of focal adhesion assembly|negative regulation of G1/S transition of mitotic cell cycle|negative regulation of protein kinase B signaling cascade|negative regulation of protein phosphorylation|nerve growth factor receptor signaling pathway|phosphatidylinositol dephosphorylation|phosphatidylinositol-mediated signaling|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|positive regulation of sequence-specific DNA binding transcription factor activity|protein stabilization|regulation of neuron projection development|T cell receptor signaling pathway	cytosol|internal side of plasma membrane|PML body	anaphase-promoting complex binding|enzyme binding|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity|lipid binding|magnesium ion binding|PDZ domain binding|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity|phosphatidylinositol-3-phosphatase activity|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity	p.R55fs*1(4)|p.V166fs*17(3)|p.?(3)|p.G165fs*9(3)|p.S170N(3)|p.S170I(3)|p.Y27fs*1(2)|p.Y27_N212>Y(2)|p.V166fs*10(1)|p.G165_K342del(1)|p.G165_*404del(1)|p.S170fs*13(1)|p.S170G(1)|p.S170fs*8(1)		endometrium(831)|central_nervous_system(657)|skin(121)|haematopoietic_and_lymphoid_tissue(101)|large_intestine(99)|prostate(97)|breast(73)|lung(65)|ovary(58)|thyroid(29)|stomach(29)|upper_aerodigestive_tract(25)|cervix(24)|liver(20)|vulva(17)|kidney(15)|NS(14)|soft_tissue(13)|urinary_tract(12)|eye(8)|pancreas(6)|salivary_gland(5)|bone(5)|biliary_tract(4)|autonomic_ganglia(2)|meninges(2)|testis(1)|oesophagus(1)	2334		all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132)	KIRC - Kidney renal clear cell carcinoma(1;0.214)	UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218)		ACTATTCCCAGTCAGAGGCGC	0.353		31	D|Mis|N|F|S		glioma| prostate|endometrial	harmartoma|glioma| prostate|endometrial			Proteus_syndrome|Cowden_syndrome|Juvenile_Polyposis|Hereditary_Mixed_Polyposis_Syndrome_type_1|Bannayan-Riley-Ruvalcaba_syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)			69	154	---	---	---	---	PASS
CYP2C9	1559	broad.mit.edu	37	10	96702177	96702177	+	Intron	SNP	G	T	T			TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:96702177G>T	uc001kka.3	+						CYP2C9_uc009xut.2_Intron|CYP2C9_uc001kjz.2_3'UTR	NM_000771	NP_000762	P11712	CP2C9_HUMAN	cytochrome P450, family 2, subfamily C,						exogenous drug catabolic process|monocarboxylic acid metabolic process|monoterpenoid metabolic process|oxidative demethylation|steroid metabolic process|urea metabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	(S)-limonene 6-monooxygenase activity|(S)-limonene 7-monooxygenase activity|4-hydroxyacetophenone monooxygenase activity|caffeine oxidase activity|drug binding|electron carrier activity|heme binding|oxygen binding|steroid hydroxylase activity			skin(4)|ovary(2)	6		Colorectal(252;0.0902)		all cancers(201;6.93e-05)	Acenocoumarol(DB01418)|Alosetron(DB00969)|Amiodarone(DB01118)|Antihemophilic Factor(DB00025)|Aprepitant(DB00673)|Bosentan(DB00559)|Carprofen(DB00821)|Carvedilol(DB01136)|Celecoxib(DB00482)|Clomipramine(DB01242)|Dapsone(DB00250)|Delavirdine(DB00705)|Desloratadine(DB00967)|Desogestrel(DB00304)|Diclofenac(DB00586)|Esomeprazole(DB00736)|Etodolac(DB00749)|Fluconazole(DB00196)|Fluoxetine(DB00472)|Flurbiprofen(DB00712)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Formoterol(DB00983)|Gemfibrozil(DB01241)|Ginkgo biloba(DB01381)|Glibenclamide(DB01016)|Glimepiride(DB00222)|Glipizide(DB01067)|Guanfacine(DB01018)|Hydromorphone(DB00327)|Ibuprofen(DB01050)|Imipramine(DB00458)|Irbesartan(DB01029)|Ketoconazole(DB01026)|Lansoprazole(DB00448)|Losartan(DB00678)|Lumiracoxib(DB01283)|Marinol(DB00470)|Mefenamic acid(DB00784)|Meloxicam(DB00814)|Mephenytoin(DB00532)|Metronidazole(DB00916)|Miconazole(DB01110)|Midazolam(DB00683)|Montelukast(DB00471)|Nateglinide(DB00731)|Nelfinavir(DB00220)|Nicardipine(DB00622)|Oxymorphone(DB01192)|Pantoprazole(DB00213)|Paramethadione(DB00617)|Phenprocoumon(DB00946)|Phenytoin(DB00252)|Pravastatin(DB00175)|Quinidine(DB00908)|Ritonavir(DB00503)|Rosiglitazone(DB00412)|Sertraline(DB01104)|Sildenafil(DB00203)|Sulfamethoxazole(DB01015)|Suprofen(DB00870)|Tamoxifen(DB00675)|Tenoxicam(DB00469)|Terfenadine(DB00342)|Tolbutamide(DB01124)|Torasemide(DB00214)|Troleandomycin(DB01361)|Valdecoxib(DB00580)|Valsartan(DB00177)|Voriconazole(DB00582)|Warfarin(DB00682)|Zafirlukast(DB00549)|Zileuton(DB00744)	CATTTCAGGGGTGGCCATATC	0.458													8	42	---	---	---	---	PASS
TUB	7275	broad.mit.edu	37	11	8060361	8060361	+	5'UTR	SNP	G	A	A			TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:8060361G>A	uc001mfy.2	+	1					TUB_uc010rbk.1_Intron	NM_003320	NP_003311	P50607	TUB_HUMAN	tubby isoform a						phagocytosis|positive regulation of phagocytosis|response to stimulus	cytoplasm|extracellular region|nucleus|plasma membrane				ovary(1)	1		all_lung(207;6.91e-20)|Lung NSC(207;3.36e-17)		Epithelial(150;1.69e-62)|BRCA - Breast invasive adenocarcinoma(625;8.54e-06)|LUSC - Lung squamous cell carcinoma(625;0.000184)		CAGGCTCCAGGTCTTACTATG	0.517													53	138	---	---	---	---	PASS
FANCF	2188	broad.mit.edu	37	11	22646829	22646829	+	Silent	SNP	C	T	T			TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:22646829C>T	uc001mql.1	-	1	559	c.528G>A	c.(526-528)GAG>GAA	p.E176E		NM_022725	NP_073562	Q9NPI8	FANCF_HUMAN	Fanconi anemia, complementation group F	176					DNA repair	nucleoplasm	protein binding			skin(1)	1						CCTTCCCCACCTCCTGCAGAC	0.597			N|F			AML|leukemia		Direct_reversal_of_damage|Involved_in_tolerance_or_repair_of_DNA_crosslinks	Fanconi_Anemia		OREG0020844	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	32	190	---	---	---	---	PASS
GLYATL1	92292	broad.mit.edu	37	11	58711084	58711084	+	5'UTR	SNP	G	C	C			TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:58711084G>C	uc001nnf.2	+	3					uc001nng.1_Intron|GLYATL1_uc001nnh.1_Missense_Mutation_p.R31S|GLYATL1_uc001nni.1_5'UTR|GLYATL1_uc001nnj.1_5'UTR			Q969I3	GLYL1_HUMAN	SubName: Full=Glycine acyltransferase family-C; SubName: Full=Glycine-N-acyltransferase-like 1, isoform CRA_a;							mitochondrion	glycine N-acyltransferase activity			ovary(1)	1					Glycine(DB00145)	aacacggaaggtacctgcagg	0.000													23	60	---	---	---	---	PASS
EML3	256364	broad.mit.edu	37	11	62375197	62375197	+	Missense_Mutation	SNP	T	C	C			TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62375197T>C	uc001ntu.1	-	11	1611	c.1303A>G	c.(1303-1305)AGT>GGT	p.S435G	EML3_uc001ntr.1_Missense_Mutation_p.S407G|EML3_uc001nts.1_Missense_Mutation_p.S407G|EML3_uc001ntt.1_Missense_Mutation_p.S319G|EML3_uc010rly.1_Missense_Mutation_p.S435G|EML3_uc009yny.1_Missense_Mutation_p.S218G	NM_153265	NP_694997	Q32P44	EMAL3_HUMAN	echinoderm microtubule associated protein like	435	WD 3.					cytoplasm|microtubule	protein binding			ovary(1)	1						ACTCCACCACTCCAATTCCAG	0.552													3	171	---	---	---	---	PASS
SPTBN2	6712	broad.mit.edu	37	11	66472256	66472256	+	Nonsense_Mutation	SNP	C	A	A			TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66472256C>A	uc001ojd.2	-	14	2563	c.2491G>T	c.(2491-2493)GAG>TAG	p.E831*		NM_006946	NP_008877	O15020	SPTN2_HUMAN	spectrin, beta, non-erythrocytic 2	831	Spectrin 5.				actin filament capping|axon guidance|cell death|vesicle-mediated transport	cytosol|spectrin	actin binding|structural constituent of cytoskeleton			large_intestine(1)|pancreas(1)|central_nervous_system(1)|skin(1)	4						TAGTGCCGCTCCAGGGTGGGC	0.731													3	25	---	---	---	---	PASS
FADD	8772	broad.mit.edu	37	11	70052642	70052642	+	3'UTR	SNP	C	T	T			TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:70052642C>T	uc001opm.2	+	2						NM_003824	NP_003815	Q13158	FADD_HUMAN	Fas-associated via death domain						activation of caspase activity|activation of pro-apoptotic gene products|cellular response to mechanical stimulus|defense response to virus|induction of apoptosis via death domain receptors|innate immune response|interspecies interaction between organisms|necrotic cell death|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interleukin-8 production|positive regulation of transcription from RNA polymerase II promoter|positive regulation of tumor necrosis factor production|positive regulation of type I interferon-mediated signaling pathway|signal transduction	cytosol	death receptor binding|identical protein binding			ovary(1)|lung(1)|pancreas(1)	3	Esophageal squamous(2;1.19e-45)		LUSC - Lung squamous cell carcinoma(11;1.46e-14)|STAD - Stomach adenocarcinoma(18;0.0513)			TGGTTCTCTCCAGGAAGGTAG	0.562													6	21	---	---	---	---	PASS
CUL5	8065	broad.mit.edu	37	11	107974931	107974931	+	Silent	SNP	A	G	G			TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:107974931A>G	uc001pjv.2	+	19	2830	c.2163A>G	c.(2161-2163)CAA>CAG	p.Q721Q	CUL5_uc001pju.2_RNA	NM_003478	NP_003469	Q93034	CUL5_HUMAN	Vasopressin-activated calcium-mobilizing	721					cell cycle arrest|cell proliferation|G1/S transition of mitotic cell cycle|induction of apoptosis by intracellular signals|interspecies interaction between organisms|negative regulation of cell proliferation|ubiquitin-dependent protein catabolic process|viral reproduction	cullin-RING ubiquitin ligase complex|cytosol	calcium channel activity|receptor activity|ubiquitin protein ligase binding			ovary(1)	1		all_cancers(61;7.09e-10)|all_epithelial(67;2.97e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|Melanoma(852;4.48e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		BRCA - Breast invasive adenocarcinoma(274;3.58e-05)|Epithelial(105;4.68e-05)|all cancers(92;0.00122)|OV - Ovarian serous cystadenocarcinoma(223;0.217)		CTATCATACAAATAATGAAAA	0.249													14	80	---	---	---	---	PASS
C12orf52	84934	broad.mit.edu	37	12	113624514	113624514	+	5'UTR	SNP	G	A	A			TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:113624514G>A	uc001tur.1	+	3					DDX54_uc001tuq.3_5'Flank|DDX54_uc001tup.2_5'Flank|C12orf52_uc009zwg.1_5'UTR|C12orf52_uc001tus.1_5'UTR|C12orf52_uc001tut.1_Missense_Mutation_p.G12D	NM_032848	NP_116237	Q96K30	RITA_HUMAN	hypothetical protein LOC84934						negative regulation of Notch signaling pathway|negative regulation of transcription from RNA polymerase II promoter|neurogenesis|Notch signaling pathway|nuclear export	centrosome|nucleus	tubulin binding				0						GGCCTGGCCGGCAGAGCACAC	0.632													3	41	---	---	---	---	PASS
RIMBP2	23504	broad.mit.edu	37	12	130926846	130926846	+	Missense_Mutation	SNP	C	T	T	rs141970284		TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:130926846C>T	uc001uil.2	-	8	1164	c.1000G>A	c.(1000-1002)GTC>ATC	p.V334I	RIMBP2_uc001uim.2_Missense_Mutation_p.V242I|RIMBP2_uc001uin.1_5'UTR	NM_015347	NP_056162	O15034	RIMB2_HUMAN	RIM-binding protein 2	334	Fibronectin type-III 1.					cell junction|synapse				upper_aerodigestive_tract(3)|ovary(3)|large_intestine(2)|central_nervous_system(2)|pancreas(1)	11	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.213)		OV - Ovarian serous cystadenocarcinoma(86;4.29e-06)|all cancers(50;4.56e-05)|Epithelial(86;5.41e-05)		TCCACCAGGACGTTGTAGCTG	0.562													60	188	---	---	---	---	PASS
ADAM6	8755	broad.mit.edu	37	14	107062359	107062359	+	RNA	SNP	G	T	T			TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:107062359G>T	uc010tyt.1	-	131		c.6236C>A								Parts of antibodies, mostly variable regions.												0						AGACAGCGCAGATGAGGGACA	0.607													5	72	---	---	---	---	PASS
MTMR10	54893	broad.mit.edu	37	15	31282988	31282988	+	Missense_Mutation	SNP	A	C	C			TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:31282988A>C	uc001zfh.1	-	2	211	c.113T>G	c.(112-114)CTT>CGT	p.L38R	MTMR10_uc010azx.1_5'UTR|MTMR10_uc001zfi.1_5'UTR|MTMR10_uc001zfj.2_5'UTR|MTMR10_uc001zfk.2_5'UTR	NM_017762	NP_060232	Q9NXD2	MTMRA_HUMAN	myotubularin related protein 10	38							phosphatase activity			ovary(1)	1		all_lung(180;2.81e-11)		all cancers(64;7.26e-15)|Epithelial(43;7.2e-11)|GBM - Glioblastoma multiforme(186;0.000158)|BRCA - Breast invasive adenocarcinoma(123;0.00426)|Lung(196;0.174)		ACCTGGCAAAAGGACTGGCTC	0.373													7	29	---	---	---	---	PASS
SPTBN5	51332	broad.mit.edu	37	15	42173407	42173407	+	Missense_Mutation	SNP	C	G	G			TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42173407C>G	uc001zos.2	-	13	2711	c.2378G>C	c.(2377-2379)GGA>GCA	p.G793A		NM_016642	NP_057726	Q9NRC6	SPTN5_HUMAN	spectrin, beta, non-erythrocytic 5	828					actin cytoskeleton organization|actin filament capping|axon guidance	cytosol|membrane|spectrin				ovary(1)|central_nervous_system(1)	2		all_cancers(109;1.84e-17)|all_epithelial(112;1.12e-15)|Lung NSC(122;7.6e-10)|all_lung(180;4.15e-09)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.173)		all cancers(2;4.33e-34)|Epithelial(2;1.72e-25)|OV - Ovarian serous cystadenocarcinoma(18;8.32e-20)|GBM - Glioblastoma multiforme(94;4.69e-07)|Colorectal(2;0.00104)|COAD - Colon adenocarcinoma(120;0.0405)|READ - Rectum adenocarcinoma(92;0.0908)		CAGGCTTTCTCCTGGAGGGCT	0.652													13	70	---	---	---	---	PASS
STRC	161497	broad.mit.edu	37	15	43902266	43902266	+	Intron	SNP	A	T	T			TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43902266A>T	uc001zsf.2	-						STRC_uc010bdl.2_Intron|STRC_uc001zse.2_5'UTR	NM_153700	NP_714544	Q7RTU9	STRC_HUMAN	stereocilin precursor						sensory perception of sound	cell surface					0		all_cancers(109;3.26e-15)|all_epithelial(112;1.48e-12)|Lung NSC(122;2.76e-08)|all_lung(180;3.1e-07)|Melanoma(134;0.027)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;3.56e-07)		catggtggtaaccacctgtcg	0.000													4	3	---	---	---	---	PASS
PRC1	9055	broad.mit.edu	37	15	91512700	91512700	+	Missense_Mutation	SNP	C	A	A			TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:91512700C>A	uc002bqm.2	-	13	1883	c.1726G>T	c.(1726-1728)GCC>TCC	p.A576S	PRC1_uc002bqn.2_Missense_Mutation_p.A576S|PRC1_uc002bqo.2_Intron|PRC1_uc010uqs.1_Intron	NM_003981	NP_003972	O43663	PRC1_HUMAN	protein regulator of cytokinesis 1 isoform 1	576	Unstructured, Arg/Lys rich.				cytokinesis|mitotic spindle elongation	cytoplasm|nucleus|spindle microtubule|spindle pole	protein binding			ovary(1)|skin(1)	2	Lung NSC(78;0.0987)|all_lung(78;0.175)					TAGGTGCTGGCAACAGAATTA	0.547													9	162	---	---	---	---	PASS
WDR90	197335	broad.mit.edu	37	16	708927	708927	+	Missense_Mutation	SNP	C	A	A			TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:708927C>A	uc002cii.1	+	24	2981	c.2927C>A	c.(2926-2928)GCT>GAT	p.A976D	WDR90_uc002cij.1_Intron|WDR90_uc002cik.1_Missense_Mutation_p.A503D|WDR90_uc002cil.1_RNA|WDR90_uc002cim.1_Missense_Mutation_p.A150D|WDR90_uc002cin.1_5'Flank	NM_145294	NP_660337	Q96KV7	WDR90_HUMAN	WD repeat domain 90	976	WD 11.									ovary(1)	1		Hepatocellular(780;0.0218)				CCCGTGCAGGCTGTGGCCTTC	0.657													7	146	---	---	---	---	PASS
GRIN2A	2903	broad.mit.edu	37	16	9857569	9857569	+	Missense_Mutation	SNP	G	T	T			TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:9857569G>T	uc002czo.3	-	13	4380	c.3832C>A	c.(3832-3834)CAA>AAA	p.Q1278K	GRIN2A_uc010uym.1_Missense_Mutation_p.Q1278K|GRIN2A_uc010uyn.1_Intron|GRIN2A_uc002czr.3_Intron	NM_001134407	NP_001127879	Q12879	NMDE1_HUMAN	N-methyl-D-aspartate receptor subunit 2A isoform	1278	Cytoplasmic (Potential).				response to ethanol	cell junction|N-methyl-D-aspartate selective glutamate receptor complex|outer membrane-bounded periplasmic space|postsynaptic membrane	N-methyl-D-aspartate selective glutamate receptor activity|zinc ion binding			skin(32)|NS(5)|ovary(4)|large_intestine(1)|lung(1)|breast(1)|kidney(1)	45					Felbamate(DB00949)|Glycine(DB00145)|L-Glutamic Acid(DB00142)|Loperamide(DB00836)|Memantine(DB01043)	TTTTGTAATTGAAGGGCATTG	0.517													20	116	---	---	---	---	PASS
TAT	6898	broad.mit.edu	37	16	71609948	71609948	+	Intron	SNP	C	A	A			TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:71609948C>A	uc002fap.2	-						TAT_uc002faq.2_Intron|TAT_uc002far.2_Missense_Mutation_p.C124F	NM_000353	NP_000344	P17735	ATTY_HUMAN	tyrosine aminotransferase						2-oxoglutarate metabolic process|glutamate metabolic process|L-phenylalanine catabolic process|tyrosine catabolic process	cytosol	1-aminocyclopropane-1-carboxylate synthase activity|L-tyrosine:2-oxoglutarate aminotransferase activity|pyridoxal phosphate binding			ovary(2)	2		Ovarian(137;0.125)		Kidney(780;0.0157)	L-Glutamic Acid(DB00142)|L-Phenylalanine(DB00120)|L-Tyrosine(DB00135)|Pyridoxal Phosphate(DB00114)	GGGAGGAAAACACAAAAGGAG	0.498													13	80	---	---	---	---	PASS
MLX	6945	broad.mit.edu	37	17	40720575	40720575	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40720575C>T	uc002iag.2	+	3	394	c.329C>T	c.(328-330)ACA>ATA	p.T110I	MLX_uc002iaf.2_Missense_Mutation_p.T56I|MLX_uc002iah.2_Intron	NM_170607	NP_733752	Q9UH92	MLX_HUMAN	transcription factor-like protein 4 isoform	110	Helix-loop-helix motif.				energy reserve metabolic process|negative regulation of transcription, DNA-dependent|positive regulation of cellular metabolic process	cytoplasm|nucleus	DNA binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|transcription factor binding				0		all_cancers(22;4.26e-05)|Breast(137;0.000153)|all_epithelial(22;0.00148)		BRCA - Breast invasive adenocarcinoma(366;0.129)		GTCCCCAACACAGGTAGGCAG	0.542													80	166	---	---	---	---	PASS
FMNL1	752	broad.mit.edu	37	17	43324263	43324263	+	3'UTR	SNP	G	C	C			TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:43324263G>C	uc002iin.2	+	27					FMNL1_uc002iiq.2_Missense_Mutation_p.D659H|FMNL1_uc010dag.2_RNA|LOC100133991_uc010dah.2_5'Flank	NM_005892	NP_005883	O95466	FMNL_HUMAN	formin-like 1						actin cytoskeleton organization		actin binding|Rho GTPase binding			pancreas(1)	1						CATCCGCGCAGACACAGGCCG	0.652											OREG0024478	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	PASS
CD300E	342510	broad.mit.edu	37	17	72610086	72610086	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:72610086C>T	uc002jlb.1	-	3	516	c.475G>A	c.(475-477)GAG>AAG	p.E159K		NM_181449	NP_852114	Q496F6	CLM2_HUMAN	CD300e molecule precursor	159	Extracellular (Potential).					integral to membrane|plasma membrane	receptor activity			skin(2)|large_intestine(1)|ovary(1)	4						GTCAACACCTCCCCGGTGCTG	0.612													12	38	---	---	---	---	PASS
SMCHD1	23347	broad.mit.edu	37	18	2722637	2722637	+	Missense_Mutation	SNP	A	G	G			TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:2722637A>G	uc002klm.3	+	20	2768	c.2579A>G	c.(2578-2580)GAT>GGT	p.D860G	SMCHD1_uc002klk.3_RNA|SMCHD1_uc002kll.3_Intron	NM_015295	NP_056110	A6NHR9	SMHD1_HUMAN	structural maintenance of chromosomes flexible	860					chromosome organization		ATP binding				0						CTAGTAACTGATATTCAGCCA	0.348													36	358	---	---	---	---	PASS
DSG1	1828	broad.mit.edu	37	18	28934518	28934518	+	Nonsense_Mutation	SNP	C	T	T			TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:28934518C>T	uc002kwp.2	+	15	2571	c.2359C>T	c.(2359-2361)CAG>TAG	p.Q787*	DSG1_uc010xbp.1_Nonsense_Mutation_p.Q146*	NM_001942	NP_001933	Q02413	DSG1_HUMAN	desmoglein 1 preproprotein	787	Cytoplasmic (Potential).				calcium-dependent cell-cell adhesion|cell-cell junction assembly|cellular component disassembly involved in apoptosis|homophilic cell adhesion|protein stabilization	cytosol|desmosome|integral to membrane|internal side of plasma membrane	calcium ion binding|gamma-catenin binding|toxin binding			skin(3)|ovary(2)|central_nervous_system(2)	7			OV - Ovarian serous cystadenocarcinoma(10;0.00559)			TTGCCTTCCTCAGGAAACAGA	0.483													22	166	---	---	---	---	PASS
DSG2	1829	broad.mit.edu	37	18	29116293	29116293	+	Missense_Mutation	SNP	G	C	C			TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:29116293G>C	uc002kwu.3	+	11	1740	c.1552G>C	c.(1552-1554)GAG>CAG	p.E518Q		NM_001943	NP_001934	Q14126	DSG2_HUMAN	desmoglein 2 preproprotein	518	Extracellular (Potential).				cellular component disassembly involved in apoptosis|homophilic cell adhesion	desmosome|integral to membrane	calcium ion binding			central_nervous_system(5)|ovary(2)|breast(1)|skin(1)	9			OV - Ovarian serous cystadenocarcinoma(10;0.0068)			TGTTACTGCAGAGGACCTGGA	0.468													15	114	---	---	---	---	PASS
HNRNPM	4670	broad.mit.edu	37	19	8532426	8532426	+	Missense_Mutation	SNP	C	A	A			TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8532426C>A	uc010dwe.2	+	8	872	c.792C>A	c.(790-792)TTC>TTA	p.F264L	HNRNPM_uc010dwc.1_Missense_Mutation_p.F264L|HNRNPM_uc010xke.1_Missense_Mutation_p.F225L|HNRNPM_uc010dwd.2_Missense_Mutation_p.F225L|HNRNPM_uc002mka.2_Missense_Mutation_p.F144L	NM_005968	NP_005959	P52272	HNRPM_HUMAN	heterogeneous nuclear ribonucleoprotein M	264	RRM 2.				alternative nuclear mRNA splicing, via spliceosome	catalytic step 2 spliceosome|integral to plasma membrane|nuclear matrix|nucleolus|paraspeckles	nucleotide binding|protein domain specific binding|RNA binding				0						CAGCTATGTTCAATGGCCAGC	0.358													4	143	---	---	---	---	PASS
CYP4F12	66002	broad.mit.edu	37	19	15794430	15794430	+	Missense_Mutation	SNP	G	A	A			TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15794430G>A	uc002nbl.2	+	7	836	c.775G>A	c.(775-777)GCC>ACC	p.A259T		NM_023944	NP_076433			cytochrome P450, family 4, subfamily F,											skin(3)|ovary(2)|central_nervous_system(2)	7	Acute lymphoblastic leukemia(2;0.0367)					CTTCCACAGGGCCTGCCGCCT	0.552													57	125	---	---	---	---	PASS
ATP4A	495	broad.mit.edu	37	19	36041444	36041444	+	3'UTR	SNP	G	T	T			TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36041444G>T	uc002oal.1	-	22					ATP4A_uc010eee.1_3'UTR	NM_000704	NP_000695	P20648	ATP4A_HUMAN	hydrogen/potassium-exchanging ATPase 4A						ATP biosynthetic process|ATP hydrolysis coupled proton transport	integral to plasma membrane	ATP binding|hydrogen:potassium-exchanging ATPase activity|magnesium ion binding			ovary(1)	1	all_lung(56;1.05e-07)|Lung NSC(56;1.63e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)		Esomeprazole(DB00736)|Lansoprazole(DB00448)|Omeprazole(DB00338)|Pantoprazole(DB00213)|Rabeprazole(DB01129)|Trifluoperazine(DB00831)	CTTGGTGGCTGTCCAGAGGGT	0.602													4	18	---	---	---	---	PASS
IGFL4	444882	broad.mit.edu	37	19	46543533	46543533	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:46543533C>T	uc002pdy.1	-	3	266	c.212G>A	c.(211-213)TGC>TAC	p.C71Y		NM_001002923	NP_001002923	Q6B9Z1	IGFL4_HUMAN	IGF-like family member 4 precursor	71						extracellular region					0		all_neural(266;0.113)|Ovarian(192;0.127)		OV - Ovarian serous cystadenocarcinoma(262;0.0036)|GBM - Glioblastoma multiforme(486;0.022)|Epithelial(262;0.208)		GTGCTGGAAGCAGGGCCAGAA	0.577													11	77	---	---	---	---	PASS
CACNG8	59283	broad.mit.edu	37	19	54483190	54483190	+	Missense_Mutation	SNP	T	G	G			TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54483190T>G	uc002qcs.1	+	3	540	c.434T>G	c.(433-435)GTG>GGG	p.V145G	MIR935_hsa-mir-935|MI0005757_5'Flank	NM_031895	NP_114101	Q8WXS5	CCG8_HUMAN	voltage-dependent calcium channel gamma-8	146	Helical; (Potential).				regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|synaptic transmission	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic density|postsynaptic membrane|voltage-gated calcium channel complex	voltage-gated calcium channel activity				0	all_cancers(19;0.0385)|all_epithelial(19;0.0207)|all_lung(19;0.145)|Lung NSC(19;0.168)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(134;0.162)		GGTGTGTGCGTGGCGGCCTCC	0.647													11	31	---	---	---	---	PASS
PEG3	5178	broad.mit.edu	37	19	57335855	57335855	+	Missense_Mutation	SNP	A	T	T			TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57335855A>T	uc002qnu.2	-	1	520	c.169T>A	c.(169-171)TTT>ATT	p.F57I	ZIM2_uc010ygq.1_Intron|ZIM2_uc010ygr.1_Intron|ZIM2_uc002qnr.2_Intron|ZIM2_uc002qnq.2_Intron|ZIM2_uc010etp.2_5'UTR|ZIM2_uc010ygs.1_Intron|PEG3_uc002qnt.2_Missense_Mutation_p.F57I|PEG3_uc002qnv.2_Missense_Mutation_p.F57I|PEG3_uc002qnw.2_Intron|PEG3_uc002qnx.2_Intron|PEG3_uc010etr.2_Missense_Mutation_p.F57I	NM_001146186	NP_001139658	Q9GZU2	PEG3_HUMAN	paternally expressed 3 isoform 1	57	SCAN box.				apoptosis|viral reproduction	cytoplasm|nucleus	nucleic acid binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(7)|skin(2)|upper_aerodigestive_tract(1)|large_intestine(1)|pancreas(1)	12		Colorectal(82;0.000256)|all_neural(62;0.103)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0269)		GGCCCAACAAATTCCACATAG	0.502													71	114	---	---	---	---	PASS
BAGE2	85319	broad.mit.edu	37	21	11039010	11039010	+	3'UTR	SNP	C	A	A			TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11039010C>A	uc002yit.1	-	6					TPTE_uc002yis.1_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)		TATGAAACATCTTTCACACAA	0.388													13	890	---	---	---	---	PASS
DOPEY2	9980	broad.mit.edu	37	21	37653892	37653892	+	Missense_Mutation	SNP	A	C	C			TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:37653892A>C	uc002yvg.2	+	32	6222	c.6143A>C	c.(6142-6144)TAC>TCC	p.Y2048S	DOPEY2_uc011aeb.1_Missense_Mutation_p.Y1997S	NM_005128	NP_005119	Q9Y3R5	DOP2_HUMAN	pad-1-like	2048					endoplasmic reticulum organization|Golgi to endosome transport|multicellular organismal development|protein transport	Golgi membrane				ovary(1)|central_nervous_system(1)	2						TACCACCTTTACCTTCCACTG	0.264													9	50	---	---	---	---	PASS
SLC19A1	6573	broad.mit.edu	37	21	46935481	46935481	+	3'UTR	SNP	C	A	A			TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:46935481C>A	uc002zhl.1	-	6					SLC19A1_uc010gpy.1_Intron|SLC19A1_uc011aft.1_3'UTR|SLC19A1_uc002zhm.1_Intron|SLC19A1_uc010gpz.1_3'UTR	NM_194255	NP_919231	P41440	S19A1_HUMAN	solute carrier family 19 member 1						folic acid metabolic process	integral to plasma membrane|membrane fraction	folic acid binding|folic acid transporter activity|methotrexate transporter activity|reduced folate carrier activity				0				Colorectal(79;0.0569)|READ - Rectum adenocarcinoma(84;0.172)		TAAGCGGAGGCCCCCATTGCT	0.682													6	65	---	---	---	---	PASS
GGT3P	2679	broad.mit.edu	37	22	18769145	18769145	+	Intron	SNP	G	A	A			TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:18769145G>A	uc010gri.1	-						GGT3P_uc011ago.1_Intron|GGT3P_uc011agp.1_RNA|GGT3P_uc002zob.1_RNA					Homo sapiens cDNA clone IMAGE:5761295, **** WARNING: chimeric clone ****.												0						TGAGGCTGCCGTTGTAGAAGG	0.612													6	27	---	---	---	---	PASS
ZNF280C	55609	broad.mit.edu	37	X	129343630	129343630	+	Missense_Mutation	SNP	A	T	T			TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:129343630A>T	uc004evm.2	-	16	2193	c.2039T>A	c.(2038-2040)CTC>CAC	p.L680H		NM_017666	NP_060136	Q8ND82	Z280C_HUMAN	zinc finger protein 280C	680					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(2)|ovary(1)	3						TGATTACCTGAGAGTTCCTGA	0.323													56	65	---	---	---	---	PASS
ZNF280C	55609	broad.mit.edu	37	X	129343631	129343631	+	Missense_Mutation	SNP	G	A	A			TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:129343631G>A	uc004evm.2	-	16	2192	c.2038C>T	c.(2038-2040)CTC>TTC	p.L680F		NM_017666	NP_060136	Q8ND82	Z280C_HUMAN	zinc finger protein 280C	680					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(2)|ovary(1)	3						GATTACCTGAGAGTTCCTGAA	0.323													59	65	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	15216	15216	+	Nonsense_Mutation	SNP	G	A	A			TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:15216G>A	uc004coy.2	+	1	456	c.381G>A	c.(379-381)TGG>TGA	p.W127*	uc004coz.1_5'Flank					Homo sapiens clone 35w unknown mRNA; mitochondrial.																		CCCATACATTGGGACAGACCT	0.453											OREG0007583	type=REGULATORY REGION|TFbs=ESR1|Dataset=Estrogen Receptor Alpha Binding Sites|EvidenceSubtype=Chromatin immunoprecipitation with tag sequencing (ChIP-TS)	41	7	---	---	---	---	PASS
ZBTB8OS	339487	broad.mit.edu	37	1	33100582	33100582	+	Intron	DEL	T	-	-			TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:33100582delT	uc001bvp.2	-						ZBTB8OS_uc001bvo.1_Intron|ZBTB8OS_uc001bvq.2_Intron	NM_178547	NP_848642	Q8IWT0	ARCH_HUMAN	zinc finger and BTB domain containing 8 opposite												0		Myeloproliferative disorder(586;0.0393)|all_neural(195;0.186)				TGTTGGAATCTTTTTTTTTTT	0.219													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	38733363	38733364	+	IGR	INS	-	CCTTCCTCCTT	CCTTCCTCCTT	rs142813208	by1000genomes	TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:38733363_38733364insCCTTCCTCCTT								POU3F1 (220913 upstream) : RRAGC (571651 downstream)																							tttcctccctcctctctcttcc	0.000													6	3	---	---	---	---	
FAM102B	284611	broad.mit.edu	37	1	109167054	109167055	+	Intron	INS	-	AA	AA	rs34112326		TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:109167054_109167055insAA	uc010ouy.1	+							NM_001010883	NP_001010883	Q5T8I3	F102B_HUMAN	hypothetical protein LOC284611											large_intestine(1)	1		all_epithelial(167;5.52e-05)|all_lung(203;0.00026)|Lung NSC(277;0.000508)		Colorectal(144;0.0217)|Lung(183;0.109)|COAD - Colon adenocarcinoma(174;0.141)|Epithelial(280;0.182)		CTTGTTATGTTAAAAAAAAAAA	0.356													4	2	---	---	---	---	
CD34	947	broad.mit.edu	37	1	208084199	208084200	+	Intron	INS	-	G	G	rs150714878	by1000genomes	TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:208084199_208084200insG	uc001hgw.1	-						CD34_uc001hgx.1_Intron|CD34_uc010psj.1_Intron	NM_001025109	NP_001020280	P28906	CD34_HUMAN	CD34 antigen isoform a						cell-cell adhesion|leukocyte migration|regulation of immune response	integral to membrane	carbohydrate binding			ovary(1)	1						GCGCTGGCCCCGGGGGGAAGCA	0.683													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	12293343	12293351	+	Intron	DEL	TTCCTTCCC	-	-	rs112549370		TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:12293343_12293351delTTCCTTCCC	uc002rbu.1	+											Homo sapiens cDNA FLJ10696 fis, clone NT2RP3000484.																		cttcattcctttccttcccttccttccct	0.000													3	4	---	---	---	---	
RBKS	64080	broad.mit.edu	37	2	28065746	28065746	+	Intron	DEL	T	-	-	rs78190424		TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:28065746delT	uc002rlo.1	-						RBKS_uc010ezi.1_Intron|RBKS_uc010ymg.1_Intron	NM_022128	NP_071411	Q9H477	RBSK_HUMAN	ribokinase						D-ribose metabolic process		ATP binding|ribokinase activity			ovary(1)|skin(1)	2	Acute lymphoblastic leukemia(172;0.155)					GCTACTCATGTTTTTTTTTTT	0.303													4	2	---	---	---	---	
BOLL	66037	broad.mit.edu	37	2	198640209	198640210	+	Intron	INS	-	A	A	rs145858712	by1000genomes	TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:198640209_198640210insA	uc002uus.2	-						BOLL_uc002uur.2_Intron|BOLL_uc002uut.2_Intron|BOLL_uc010zha.1_Intron|BOLL_uc002uuu.1_Intron	NM_033030	NP_149019	Q8N9W6	BOLL_HUMAN	boule isoform 2						cell differentiation|meiosis|multicellular organismal development|positive regulation of translational initiation|spermatogenesis	cytoplasm	nucleotide binding|protein binding|RNA binding|translation activator activity			ovary(2)	2						TTTTCCCAGCCAAAAAAATTGA	0.233													5	4	---	---	---	---	
FAM117B	150864	broad.mit.edu	37	2	203624281	203624281	+	Intron	DEL	T	-	-			TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:203624281delT	uc010zhx.1	+							NM_173511	NP_775782	Q6P1L5	F117B_HUMAN	amyotrophic lateral sclerosis 2 (juvenile)											ovary(1)	1						gcctggctaattttttttttt	0.000													4	3	---	---	---	---	
CYP20A1	57404	broad.mit.edu	37	2	204137273	204137274	+	Intron	INS	-	A	A	rs72103565		TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:204137273_204137274insA	uc002uzv.3	+						CYP20A1_uc002uzx.3_Intron|CYP20A1_uc010zif.1_Intron|CYP20A1_uc002uzy.3_Intron|CYP20A1_uc002uzw.3_Intron|CYP20A1_uc010ftw.2_Intron	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						aaccctgactcaaaaaaaaaaa	0.104													6	3	---	---	---	---	
VHL	7428	broad.mit.edu	37	3	10188296	10188296	+	Frame_Shift_Del	DEL	A	-	-			TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10188296delA	uc003bvc.2	+	2	652	c.439delA	c.(439-441)ATTfs	p.I147fs	VHL_uc003bvd.2_Intron	NM_000551	NP_000542	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor isoform 1	147	Involved in binding to CCT complex.		I -> T (in pheochromocytoma).		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.A149fs*25(4)|p.I147fs*27(2)|p.I147fs*25(1)|p.I147fs*11(1)|p.I147fs*12(1)|p.I147fs*13(1)|p.I147_F148del(1)|p.I147fs*10(1)|p.P146fs*23(1)|p.G144fs*19(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)		CGGACAGCCTATTTTTGCCAA	0.418		1	D|Mis|N|F|S		renal|hemangioma|pheochromocytoma	renal|hemangioma|pheochromocytoma			von_Hippel-Lindau_disease|Chuvash_Polycythemia_|Pheochromocytoma_(Adrenal)_Familial				243	120	---	---	---	---	
SMC4	10051	broad.mit.edu	37	3	160146393	160146393	+	Intron	DEL	T	-	-			TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:160146393delT	uc003fdh.2	+						IFT80_uc003fda.2_Intron|SMC4_uc003fdi.2_Intron|SMC4_uc003fdj.2_Intron|SMC4_uc010hwd.2_Intron|SMC4_uc003fdl.2_Intron	NM_001002800	NP_001002800	Q9NTJ3	SMC4_HUMAN	SMC4 structural maintenance of chromosomes						cell division|mitotic chromosome condensation	condensin complex|cytoplasm|nucleus	ATP binding|protein heterodimerization activity			ovary(1)|breast(1)	2			Lung(72;0.00334)|LUSC - Lung squamous cell carcinoma(72;0.00523)			CAGGATATCGTTTTTTTTTTT	0.299													5	4	---	---	---	---	
ZDHHC19	131540	broad.mit.edu	37	3	195934301	195934301	+	Frame_Shift_Del	DEL	C	-	-			TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195934301delC	uc003fwc.2	-	5	769	c.655delG	c.(655-657)GTGfs	p.V219fs	ZDHHC19_uc010hzz.2_RNA|ZDHHC19_uc010iaa.2_RNA|ZDHHC19_uc010iab.2_RNA	NM_001039617	NP_001034706	Q8WVZ1	ZDH19_HUMAN	zinc finger, DHHC domain containing 19	219						integral to membrane	acyltransferase activity|zinc ion binding			ovary(3)	3	all_cancers(143;1.68e-08)|Ovarian(172;0.0634)|Breast(254;0.206)		Epithelial(36;1.89e-25)|all cancers(36;1.46e-23)|OV - Ovarian serous cystadenocarcinoma(49;2.1e-19)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.0022)		GCCGAGCTCACGGACAGTGCC	0.706													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	10412981	10412982	+	IGR	INS	-	CT	CT	rs143148489		TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:10412981_10412982insCT								WDR1 (294408 upstream) : ZNF518B (28523 downstream)																							acagagcaagactgtctcaaaa	0.144													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	49657900	49657900	+	IGR	DEL	A	-	-			TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49657900delA								CWH43 (593807 upstream) : None (None downstream)																							aatggaatggaaaggaacgaa	0.000													4	2	---	---	---	---	
SNX25	83891	broad.mit.edu	37	4	186244502	186244502	+	Intron	DEL	T	-	-			TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:186244502delT	uc003ixh.2	+						SNX25_uc010ish.2_Intron|SNX25_uc003ixi.2_Intron	NM_031953	NP_114159	Q9H3E2	SNX25_HUMAN	sorting nexin 25						cell communication|protein transport	endosome membrane	phosphatidylinositol binding|signal transducer activity			ovary(2)|breast(2)|pancreas(1)	5		all_lung(41;1.03e-13)|Lung NSC(41;2.5e-13)|Hepatocellular(41;0.00826)|Colorectal(36;0.00886)|Renal(120;0.00988)|Prostate(90;0.0235)|all_hematologic(60;0.0592)|all_neural(102;0.243)		all cancers(43;2.13e-24)|Epithelial(43;6.15e-22)|OV - Ovarian serous cystadenocarcinoma(60;5.6e-11)|BRCA - Breast invasive adenocarcinoma(30;0.00013)|Colorectal(24;0.000165)|GBM - Glioblastoma multiforme(59;0.000357)|COAD - Colon adenocarcinoma(29;0.000887)|STAD - Stomach adenocarcinoma(60;0.00118)|LUSC - Lung squamous cell carcinoma(40;0.0129)|READ - Rectum adenocarcinoma(43;0.228)		AAAGAATTAGTTTTTTTTTTT	0.343													6	3	---	---	---	---	
MTMR12	54545	broad.mit.edu	37	5	32263539	32263539	+	Intron	DEL	T	-	-			TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32263539delT	uc003jhq.2	-						MTMR12_uc010iuk.2_Intron|MTMR12_uc010iul.2_Intron	NM_001040446	NP_001035536	Q9C0I1	MTMRC_HUMAN	myotubularin related protein 12							cytoplasm	phosphatase activity			ovary(1)	1						ACTGAGTCTCttttttttttt	0.174													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	77178944	77178945	+	IGR	INS	-	T	T	rs36111645		TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:77178944_77178945insT								TBCA (106759 upstream) : AP3B1 (119206 downstream)																							tttctttcttcttttttttttt	0.094													4	3	---	---	---	---	
ANKHD1-EIF4EBP3	404734	broad.mit.edu	37	5	139864982	139864983	+	Intron	INS	-	ACACACACAC	ACACACACAC	rs140536631	by1000genomes	TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:139864982_139864983insACACACACAC	uc003lfs.1	+						ANKHD1_uc003lfq.1_Intron|ANKHD1_uc003lfr.2_Intron|ANKHD1_uc003lft.1_Intron|ANKHD1_uc003lfu.1_Intron|ANKHD1_uc003lfv.1_5'Flank	NM_020690	NP_065741	Q8IWZ2	Q8IWZ2_HUMAN	ANKHD1-EIF4EBP3 protein							cytoplasm|nucleus	RNA binding			ovary(6)	6			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			tctctaTTAAAacacacacaca	0.035													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	161266841	161266848	+	IGR	DEL	TTCTTTCC	-	-	rs10535909	by1000genomes	TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:161266841_161266848delTTCTTTCC								GABRA6 (137243 upstream) : GABRA1 (7349 downstream)																							ctttctttctttctttccttccttcctt	0.000													6	3	---	---	---	---	
SLC35B3	51000	broad.mit.edu	37	6	8417377	8417377	+	Intron	DEL	A	-	-			TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:8417377delA	uc010joe.2	-						SLC35B3_uc003mya.2_Intron|SLC35B3_uc003myc.2_Intron|SLC35B3_uc003myb.2_Intron|SLC35B3_uc011did.1_Intron|SLC35B3_uc003myd.2_Intron	NM_001142541	NP_001136013	Q9H1N7	S35B3_HUMAN	solute carrier family 35, member B3						transmembrane transport	Golgi membrane|integral to membrane					0	Ovarian(93;0.0569)					TGATTTAATGAAAAAAAAATG	0.259													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	25261990	25261990	+	5'Flank	DEL	A	-	-	rs150117437		TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:25261990delA	uc003nex.3	-											Homo sapiens cDNA clone IMAGE:5297808.																		TGGACtatttaaaaaaaaaaa	0.179													6	3	---	---	---	---	
HLA-C	3107	broad.mit.edu	37	6	31237576	31237577	+	Intron	DEL	CA	-	-	rs72558156		TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31237576_31237577delCA	uc003nsy.2	-						HLA-C_uc011dnj.1_Intron|HLA-C_uc003nsx.2_Intron|HLA-C_uc003nsz.2_Intron|HLA-C_uc010jsl.2_Intron|HLA-C_uc003nta.2_Intron|HLA-C_uc003ntb.2_Intron|HLA-C_uc003ntc.1_Intron|HLA-B_uc010jsm.1_Intron|HLA-B_uc011dnk.1_Intron	NM_002117	NP_002108	Q9TNN7	1C05_HUMAN	major histocompatibility complex, class I, C						antigen processing and presentation of peptide antigen via MHC class I|interferon-gamma-mediated signaling pathway|interspecies interaction between organisms|regulation of immune response|type I interferon-mediated signaling pathway	integral to membrane|MHC class I protein complex					0						CCTTCATTGTCACATGTGCTTC	0.520													6	4	---	---	---	---	
GCM1	8521	broad.mit.edu	37	6	52992826	52992827	+	3'UTR	INS	-	AAAAAAAA	AAAAAAAA	rs71726666		TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:52992826_52992827insAAAAAAAA	uc003pbp.2	-	6						NM_003643	NP_003634	Q9NP62	GCM1_HUMAN	glial cells missing homolog a							transcription factor complex	DNA binding|sequence-specific DNA binding transcription factor activity|transcription factor binding			central_nervous_system(1)	1	Lung NSC(77;0.0755)					gactctgtctcaaaaaaaaaaa	0.084													4	3	---	---	---	---	
LAMA4	3910	broad.mit.edu	37	6	112475858	112475859	+	Intron	INS	-	T	T	rs149967372	by1000genomes	TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:112475858_112475859insT	uc003pvu.2	-						LAMA4_uc003pvv.2_Intron|LAMA4_uc003pvt.2_Intron	NM_001105206	NP_001098676	Q16363	LAMA4_HUMAN	laminin, alpha 4 isoform 1 precursor						cell adhesion|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	laminin-1 complex	extracellular matrix structural constituent|receptor binding			ovary(4)|breast(2)|large_intestine(1)|central_nervous_system(1)|pancreas(1)	9		all_cancers(87;0.000196)|all_hematologic(75;0.000114)|all_epithelial(87;0.00542)|Colorectal(196;0.0209)		all cancers(137;0.0335)|OV - Ovarian serous cystadenocarcinoma(136;0.0578)|Epithelial(106;0.0748)|BRCA - Breast invasive adenocarcinoma(108;0.242)		ACTACATAGCATTTTTTTTTTC	0.218													6	3	---	---	---	---	
RMND1	55005	broad.mit.edu	37	6	151744986	151744987	+	Intron	INS	-	T	T	rs72083577		TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:151744986_151744987insT	uc003qoi.2	-						RMND1_uc011eeq.1_Intron	NM_017909	NP_060379	Q9NWS8	RMND1_HUMAN	required for meiotic nuclear division 1 homolog												0		Ovarian(120;0.125)	BRCA - Breast invasive adenocarcinoma(37;0.146)	OV - Ovarian serous cystadenocarcinoma(155;6.8e-11)		tacaagaaaacttttttttttt	0.000													3	3	---	---	---	---	
CDCA7L	55536	broad.mit.edu	37	7	21956133	21956136	+	Intron	DEL	AAAA	-	-	rs72478082		TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:21956133_21956136delAAAA	uc010kuk.2	-						CDCA7L_uc003sve.3_Intron|CDCA7L_uc010kul.2_Intron|CDCA7L_uc003svf.3_Intron|CDCA7L_uc011jyk.1_Intron	NM_018719	NP_061189	Q96GN5	CDA7L_HUMAN	cell division cycle associated 7-like isoform 1						positive regulation of cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleolus					0						CCCTTTATTTaaaaaaaaaaaaaa	0.417													5	3	---	---	---	---	
KIAA0368	23392	broad.mit.edu	37	9	114206518	114206519	+	Intron	INS	-	A	A			TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:114206518_114206519insA	uc004bfe.1	-						KIAA0368_uc010muc.1_Intron	NM_001080398	NP_001073867			KIAA0368 protein												0						GTGTGTCATTTAAAAAAAAAAA	0.332													4	2	---	---	---	---	
MYOF	26509	broad.mit.edu	37	10	95066945	95066945	+	Intron	DEL	A	-	-			TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:95066945delA	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						tgccagtagcacccccccgcc	0.005													4	2	---	---	---	---	
TRPM5	29850	broad.mit.edu	37	11	2441272	2441286	+	Intron	DEL	CCCAGGCCCCCACGG	-	-			TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:2441272_2441286delCCCAGGCCCCCACGG	uc001lwm.3	-						TRPM5_uc010qxl.1_Intron|TRPM5_uc009ydn.2_Intron	NM_014555	NP_055370	Q9NZQ8	TRPM5_HUMAN	transient receptor potential cation channel,							integral to membrane|plasma membrane	receptor activity|voltage-gated ion channel activity			ovary(1)|breast(1)|central_nervous_system(1)|skin(1)	4		Medulloblastoma(188;0.0049)|Breast(177;0.00586)|all_epithelial(84;0.0075)|Ovarian(85;0.0256)|all_neural(188;0.0311)		BRCA - Breast invasive adenocarcinoma(625;0.00147)|LUSC - Lung squamous cell carcinoma(625;0.191)		AGCTCCTCCTCCCAGGCCCCCACGGCCCAGGCCCC	0.665													6	3	---	---	---	---	
RRM1	6240	broad.mit.edu	37	11	4159297	4159298	+	Intron	INS	-	G	G			TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:4159297_4159298insG	uc001lyw.3	+						RRM1_uc009yej.2_Intron|RRM1_uc009yei.2_Intron|RRM1_uc010qyc.1_Intron|RRM1_uc010qyd.1_Intron	NM_001033	NP_001024	P23921	RIR1_HUMAN	ribonucleoside-diphosphate reductase M1 chain						deoxyribonucleotide biosynthetic process|DNA replication|nucleobase, nucleoside and nucleotide interconversion	cytosol|nucleoplasm|ribonucleoside-diphosphate reductase complex	ATP binding|ribonucleoside-diphosphate reductase activity			skin(1)	1		Medulloblastoma(188;0.0025)|Breast(177;0.00502)|all_neural(188;0.0227)		BRCA - Breast invasive adenocarcinoma(625;0.0848)|LUSC - Lung squamous cell carcinoma(625;0.205)	Clofarabine(DB00631)|Fludarabine(DB01073)|Gemcitabine(DB00441)|Hydroxyurea(DB01005)	gctggccgggcgggggctgacc	0.089													5	3	---	---	---	---	
FNBP4	23360	broad.mit.edu	37	11	47788664	47788669	+	In_Frame_Del	DEL	GGTGGT	-	-	rs59413596		TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47788664_47788669delGGTGGT	uc009ylv.2	-	1	325_330	c.172_177delACCACC	c.(172-177)ACCACCdel	p.TT58del	FNBP4_uc001ngj.2_5'UTR|FNBP4_uc001ngl.2_RNA	NM_015308	NP_056123	Q8N3X1	FNBP4_HUMAN	formin binding protein 4	58_59										ovary(1)	1						CAGTCACCGCGGTGGTGGTGGTCGTC	0.748													4	2	---	---	---	---	
CAPN1	823	broad.mit.edu	37	11	64954882	64954882	+	Intron	DEL	C	-	-	rs3832790		TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64954882delC	uc009yqd.1	+						CAPN1_uc001odf.1_Intron|CAPN1_uc001odg.1_Intron|CAPN1_uc010roa.1_Intron	NM_005186	NP_005177	P07384	CAN1_HUMAN	calpain 1, large subunit						positive regulation of cell proliferation|proteolysis	cytoplasm|plasma membrane	calcium ion binding|calcium-dependent cysteine-type endopeptidase activity|protein binding			ovary(1)	1		Lung NSC(402;0.094)|Melanoma(852;0.16)		Lung(977;0.00168)|LUSC - Lung squamous cell carcinoma(976;0.00813)		CCTTTCCCCTCCTGCAGCACC	0.617													3	5	---	---	---	---	
CLEC1B	51266	broad.mit.edu	37	12	10149207	10149207	+	Intron	DEL	A	-	-	rs11285200		TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:10149207delA	uc001qwu.2	-						CLEC1B_uc009zhd.2_Intron	NM_016509	NP_057593	Q9P126	CLC1B_HUMAN	C-type lectin domain family 1, member B isoform						cell surface receptor linked signaling pathway|defense response	integral to plasma membrane	protein binding|sugar binding|transmembrane receptor activity				0						CCCACTATGTACCTGAGCTGT	0.398													4	3	---	---	---	---	
VDR	7421	broad.mit.edu	37	12	48253630	48253649	+	Intron	DEL	TTCCTTCCTTCCTTCCTTCT	-	-	rs60761635		TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:48253630_48253649delTTCCTTCCTTCCTTCCTTCT	uc001rqm.2	-						VDR_uc001rql.2_Intron|VDR_uc001rqn.2_Intron|VDR_uc010slq.1_Intron	NM_001017535	NP_001017535	P11473	VDR_HUMAN	vitamin D (1,25-dihydroxyvitamin D3) receptor						decidualization|negative regulation of cell proliferation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of vitamin D 24-hydroxylase activity|regulation of calcidiol 1-monooxygenase activity|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	retinoid X receptor binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|vitamin D3 receptor activity|zinc ion binding			ovary(1)|central_nervous_system(1)|skin(1)	3		Acute lymphoblastic leukemia(13;0.109)|all_hematologic(14;0.214)		GBM - Glioblastoma multiforme(48;0.17)	Calcidiol(DB00146)|Calcipotriol(DB02300)|Calcitriol(DB00136)|Dihydrotachysterol(DB01070)|Ergocalciferol(DB00153)|Paricalcitol(DB00910)	tttcccttccttccttccttccttccttctttccttcctt	0.036													6	4	---	---	---	---	
RACGAP1	29127	broad.mit.edu	37	12	50395874	50395874	+	Intron	DEL	G	-	-			TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:50395874delG	uc001rvt.2	-						RACGAP1_uc009zlm.1_Intron|RACGAP1_uc001rvs.2_Intron|RACGAP1_uc001rvu.2_Intron	NM_013277	NP_037409	Q9H0H5	RGAP1_HUMAN	Rac GTPase activating protein 1						blood coagulation|cytokinesis, actomyosin contractile ring assembly|cytokinesis, initiation of separation|embryo development|microtubule-based movement|neuroblast proliferation|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction|spermatogenesis|sulfate transport	acrosomal vesicle|cytosol|microtubule|midbody|nucleus|spindle	alpha-tubulin binding|beta-tubulin binding|gamma-tubulin binding|GTPase activator activity|metal ion binding			kidney(1)	1						aaaaaaaaaagaaTATCAATA	0.194													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	51590418	51590421	+	IGR	DEL	GTGT	-	-			TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:51590418_51590421delGTGT								TRIM9 (27996 upstream) : TMX1 (116465 downstream)																							cttcaagccagtgtgtgtgtgtgt	0.000													4	2	---	---	---	---	
GPR137C	283554	broad.mit.edu	37	14	53098687	53098688	+	Intron	DEL	AC	-	-	rs35962083		TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:53098687_53098688delAC	uc001wzu.3	+						GPR137C_uc001wzt.3_Intron	NM_001099652	NP_001093122	Q8N3F9	G137C_HUMAN	G protein-coupled receptor 137C							integral to membrane					0	Breast(41;0.0716)					AAAAAAAAAAACTTACACATAT	0.337													4	2	---	---	---	---	
FOXN3	1112	broad.mit.edu	37	14	89647259	89647260	+	Intron	INS	-	GCAGAGAACATGCATGGA	GCAGAGAACATGCATGGA	rs140257053	by1000genomes	TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:89647259_89647260insGCAGAGAACATGCATGGA	uc001xxo.3	-						FOXN3_uc001xxn.3_Intron|FOXN3_uc010atk.2_Intron	NM_001085471	NP_001078940	O00409	FOXN3_HUMAN	checkpoint suppressor 1 isoform 1						DNA damage checkpoint|embryo development|G2 phase of mitotic cell cycle|negative regulation of transcription, DNA-dependent|pattern specification process|regulation of sequence-specific DNA binding transcription factor activity|tissue development	transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|protein C-terminus binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding			skin(2)|ovary(1)	3						agagacagagggcagagacaga	0.173													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	83040943	83040944	+	Intron	INS	-	T	T			TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:83040943_83040944insT	uc002bhl.2	+						uc002bhm.2_Intron|uc002bic.2_Intron|uc010uoa.1_Intron					SubName: Full=Putative uncharacterized protein ENSP00000348917;																		GAACAAAAATCTTTTTTTTTTT	0.312													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	102306788	102306790	+	5'Flank	DEL	GTA	-	-			TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:102306788_102306790delGTA	uc002cbx.1	-						uc002ccc.1_5'Flank|uc002ccm.1_5'Flank					DQ582460																		TTAGTCTGTTGTAGTGGTGAGCT	0.498													4	2	---	---	---	---	
LOC283922	283922	broad.mit.edu	37	16	74378976	74378976	+	Intron	DEL	T	-	-			TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:74378976delT	uc002fcr.2	-						LOC283922_uc010vms.1_Intron					Homo sapiens cDNA FLJ39449 fis, clone PROST2008360, highly similar to Homo sapiens pyruvate dehydrogenase phosphatase regulatory subunit (PDPR), mRNA.												0						ACCTCTTGAAttttttttttt	0.179													3	3	---	---	---	---	
DNAH9	1770	broad.mit.edu	37	17	11597919	11597922	+	Intron	DEL	CTTT	-	-	rs12946299		TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:11597919_11597922delCTTT	uc002gne.2	+						DNAH9_uc010coo.2_Intron	NM_001372	NP_001363	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9 isoform 2						cell projection organization|cellular component movement|microtubule-based movement|spermatogenesis	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			skin(10)|ovary(4)|breast(3)|central_nervous_system(2)|pancreas(1)	20		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)		TACCTCGGAGctttcttgctttct	0.270													8	5	---	---	---	---	
CCDC144C	348254	broad.mit.edu	37	17	20254234	20254235	+	Intron	INS	-	T	T			TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:20254234_20254235insT	uc010cqy.1	+							NR_023380				Homo sapiens cDNA FLJ59693 complete cds, moderately similar to Ankyrin repeat domain-containing protein 26.												0						AAGAGGAATTGTTTTTTTTTTT	0.248													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	29103591	29103592	+	IGR	INS	-	T	T	rs55974169		TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:29103591_29103592insT								SUZ12P (6524 upstream) : CRLF3 (6111 downstream)																							GGTATCATTCCttttttttttt	0.163													3	4	---	---	---	---	
MSI2	124540	broad.mit.edu	37	17	55693643	55693644	+	Intron	DEL	TG	-	-			TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:55693643_55693644delTG	uc002iuz.1	+						MSI2_uc010wnm.1_Intron|MSI2_uc002iva.2_Intron	NM_138962	NP_620412	Q96DH6	MSI2H_HUMAN	musashi 2 isoform a							cytoplasm	nucleotide binding|RNA binding			central_nervous_system(1)|pancreas(1)	2	Breast(9;1.78e-08)			GBM - Glioblastoma multiforme(1;0.0025)		tgtgcatgcatgtgtgtgtgtg	0.134			T	HOXA9	CML								4	2	---	---	---	---	
DLGAP1	9229	broad.mit.edu	37	18	3581662	3581663	+	Intron	INS	-	A	A			TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:3581662_3581663insA	uc002kmf.2	-						DLGAP1_uc010wyz.1_Intron|DLGAP1_uc002kme.1_Intron|DLGAP1_uc010dkn.2_Intron|DLGAP1_uc010wyw.1_Intron|DLGAP1_uc010wyx.1_Intron|DLGAP1_uc010wyy.1_Intron|DLGAP1_uc002kmg.2_Intron	NM_004746	NP_004737	O14490	DLGP1_HUMAN	discs large homolog-associated protein 1 isoform						synaptic transmission	cell junction|postsynaptic density|postsynaptic membrane				ovary(2)|pancreas(1)|skin(1)	4		Colorectal(8;0.0257)				TTCTCACCATGaaaaaaaaaaa	0.381													5	3	---	---	---	---	
LRRC30	339291	broad.mit.edu	37	18	7232028	7232028	+	Frame_Shift_Del	DEL	A	-	-			TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:7232028delA	uc010wzk.1	+	1	892	c.892delA	c.(892-894)AAAfs	p.K298fs		NM_001105581	NP_001099051	A6NM36	LRC30_HUMAN	leucine rich repeat containing 30	298										ovary(1)|liver(1)	2						CCTGAAGGACAAAAAACACAC	0.572													294	150	---	---	---	---	
KATNAL2	83473	broad.mit.edu	37	18	44551874	44551875	+	Intron	DEL	GT	-	-	rs147121774		TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:44551874_44551875delGT	uc002lco.2	+						KATNAL2_uc010dnq.1_Intron|KATNAL2_uc002lcp.3_Intron|TCEB3C_uc010dnr.2_5'Flank	NM_031303	NP_112593	Q8IYT4	KATL2_HUMAN	katanin p60 subunit A-like 2							cytoplasm|microtubule	ATP binding|microtubule-severing ATPase activity			ovary(1)|skin(1)|central_nervous_system(1)|pancreas(1)	4						CTCTCTCTCAgtgtgtgtgtgt	0.267													4	5	---	---	---	---	
MUC16	94025	broad.mit.edu	37	19	9080284	9080295	+	Intron	DEL	AGAAAGAAAGAA	-	-	rs35032900		TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9080284_9080295delAGAAAGAAAGAA	uc002mkp.2	-							NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16						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						agaaagaaagagaaagaaagaaagaaagaaag	0.014													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	43725017	43725017	+	IGR	DEL	G	-	-			TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:43725017delG								PSG4 (15227 upstream) : PSG9 (32419 downstream)																							CATCCTCCGCGGGGTTGCTGG	0.438													4	2	---	---	---	---	
CGB	1082	broad.mit.edu	37	19	49536865	49536865	+	Intron	DEL	A	-	-			TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49536865delA	uc010yad.1	-						SNAR-G2_uc010yae.1_5'Flank	NM_033183	NP_149439	P01233	CGHB_HUMAN	chorionic gonadotropin, beta polypeptide 8						apoptosis|cell-cell signaling|cellular nitrogen compound metabolic process|female gamete generation|hormone biosynthetic process|peptide hormone processing|signal transduction	extracellular region|soluble fraction	hormone activity				0		all_epithelial(76;9.62e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		all cancers(93;0.000371)|OV - Ovarian serous cystadenocarcinoma(262;0.000503)|GBM - Glioblastoma multiforme(486;0.00518)|Epithelial(262;0.0427)	Choriogonadotropin alfa(DB00097)	actccatctcaaaaaaaaaaa	0.199													4	2	---	---	---	---	
ZIM3	114026	broad.mit.edu	37	19	57648045	57648046	+	Intron	INS	-	A	A	rs145532440	by1000genomes	TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57648045_57648046insA	uc002qnz.1	-							NM_052882	NP_443114	Q96PE6	ZIM3_HUMAN	zinc finger, imprinted 3						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			pancreas(1)|skin(1)	2		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.243)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		aaaaaaaaaagaaaaaaaaaaG	0.188													3	4	---	---	---	---	
TM9SF4	9777	broad.mit.edu	37	20	30734786	30734786	+	Intron	DEL	T	-	-			TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30734786delT	uc002wxj.2	+						TM9SF4_uc010zts.1_Intron|TM9SF4_uc002wxk.2_Intron|TM9SF4_uc010gdz.2_Intron	NM_014742	NP_055557	Q92544	TM9S4_HUMAN	transmembrane 9 superfamily protein member 4							integral to membrane				central_nervous_system(1)|pancreas(1)	2			UCEC - Uterine corpus endometrioid carcinoma (5;0.0241)			TTTAGTATACttttttttttt	0.194													4	2	---	---	---	---	
PREX1	57580	broad.mit.edu	37	20	47309117	47309117	+	Intron	DEL	A	-	-			TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:47309117delA	uc002xtw.1	-							NM_020820	NP_065871	Q8TCU6	PREX1_HUMAN	phosphatidylinositol-3,4,						actin filament polymerization|apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|neutrophil activation|small GTPase mediated signal transduction|superoxide metabolic process	cytosol|plasma membrane	enzyme binding|phospholipid binding|Rho GTPase activator activity|Rho guanyl-nucleotide exchange factor activity			lung(3)|ovary(2)|pancreas(1)	6			BRCA - Breast invasive adenocarcinoma(12;0.0135)|Colorectal(8;0.198)			atctcatgataaaagaaaaaa	0.144													8	6	---	---	---	---	
CABLES2	81928	broad.mit.edu	37	20	60973328	60973330	+	Intron	DEL	GGT	-	-			TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:60973328_60973330delGGT	uc002ycv.2	-							NM_031215	NP_112492	Q9BTV7	CABL2_HUMAN	Cdk5 and Abl enzyme substrate 2						cell cycle|cell division|regulation of cell cycle|regulation of cell division		cyclin-dependent protein kinase regulator activity			pancreas(1)	1	Breast(26;2.05e-08)		BRCA - Breast invasive adenocarcinoma(19;4.36e-06)			tggtgatggcggtggtggtggtg	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	44755961	44755961	+	IGR	DEL	C	-	-			TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:44755961delC								CRYAA (163048 upstream) : SIK1 (78437 downstream)																							accatcaccaccatcaccacc	0.000													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	48761107	48761107	+	IGR	DEL	A	-	-			TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:48761107delA								None (None upstream) : FAM19A5 (124181 downstream)																							GAaagggaggaaaagagggag	0.184													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	53785534	53785534	+	IGR	DEL	C	-	-			TCGA-A3-3316-01A-01D-0966-08	TCGA-A3-3316-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:53785534delC								HUWE1 (71861 upstream) : PHF8 (177580 downstream)																							AGCCACCTGTCCCACCTCAAG	0.473													4	2	---	---	---	---	
