Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	t_alt_count	t_ref_count	validation_status	validation_method	validation_tumor_sample	validation_alt_allele	filter
UBE4B	10277	broad.mit.edu	37	1	10163061	10163061	+	Missense_Mutation	SNP	A	C	C			TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:10163061A>C	uc001aqs.3	+	5	1204	c.491A>C	c.(490-492)AAG>ACG	p.K164T	UBE4B_uc001aqr.3_Missense_Mutation_p.K164T|UBE4B_uc010oai.1_RNA|UBE4B_uc010oaj.1_5'UTR	NM_001105562	NP_001099032	O95155	UBE4B_HUMAN	ubiquitination factor E4B isoform 1	164					apoptosis|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|response to UV	cytoplasm|ubiquitin ligase complex	enzyme binding			ovary(2)|skin(2)	4		all_lung(284;1.13e-05)|Lung NSC(185;1.74e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0268)|Colorectal(212;1.42e-07)|COAD - Colon adenocarcinoma(227;2.77e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000435)|Kidney(185;0.000482)|KIRC - Kidney renal clear cell carcinoma(229;0.00164)|STAD - Stomach adenocarcinoma(132;0.0117)|READ - Rectum adenocarcinoma(331;0.046)		CTGGTCTGTAAGATCTTCCGT	0.453													17	69	---	---	---	---	PASS
LPHN2	23266	broad.mit.edu	37	1	82456349	82456349	+	Silent	SNP	T	C	C			TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:82456349T>C	uc001dit.3	+	21	3913	c.3732T>C	c.(3730-3732)GCT>GCC	p.A1244A	LPHN2_uc001dis.2_Silent_p.A224A|LPHN2_uc001diu.2_Silent_p.A1244A|LPHN2_uc001div.2_3'UTR|LPHN2_uc009wcd.2_3'UTR|LPHN2_uc001diw.2_Silent_p.A871A	NM_012302	NP_036434	O95490	LPHN2_HUMAN	latrophilin 2 precursor	1300	Cytoplasmic (Potential).				neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity|latrotoxin receptor activity|sugar binding			ovary(3)|lung(3)|breast(2)|central_nervous_system(1)	9				all cancers(265;0.00142)|Epithelial(280;0.00829)|OV - Ovarian serous cystadenocarcinoma(397;0.077)|STAD - Stomach adenocarcinoma(256;0.248)		AAGATGATGCTATTGTGGCAG	0.512													6	99	---	---	---	---	PASS
LOC728855	728855	broad.mit.edu	37	1	149648476	149648476	+	Intron	SNP	G	A	A			TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:149648476G>A	uc009wlc.2	+						LOC728855_uc009wld.2_Intron|uc001eso.1_RNA					Homo sapiens mRNA, chromosome 1 specific transcript KIAA0493.												0						ATTATCCAAAGGTACAAGACC	0.413													25	154	---	---	---	---	PASS
FLG	2312	broad.mit.edu	37	1	152282869	152282869	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152282869C>T	uc001ezu.1	-	3	4529	c.4493G>A	c.(4492-4494)GGA>GAA	p.G1498E		NM_002016	NP_002007	P20930	FILA_HUMAN	filaggrin	1498	Ser-rich.				keratinocyte differentiation	cytoplasmic membrane-bounded vesicle|intermediate filament	calcium ion binding|structural molecule activity			ovary(9)|skin(4)|upper_aerodigestive_tract(3)	16	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CTGCCTTCCTCCTCTGCTTGA	0.582									Ichthyosis				7	431	---	---	---	---	PASS
OR10J3	441911	broad.mit.edu	37	1	159283710	159283710	+	Missense_Mutation	SNP	G	C	C			TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:159283710G>C	uc010piu.1	-	1	740	c.740C>G	c.(739-741)ACA>AGA	p.T247R		NM_001004467	NP_001004467	Q5JRS4	O10J3_HUMAN	olfactory receptor, family 10, subfamily J,	247	Helical; Name=6; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)	2	all_hematologic(112;0.0429)					GATGACCACTGTGAGGTGGGA	0.517													3	99	---	---	---	---	PASS
TNR	7143	broad.mit.edu	37	1	175324685	175324685	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:175324685A>G	uc001gkp.1	-	15	3284	c.3203T>C	c.(3202-3204)ATT>ACT	p.I1068T	TNR_uc009wwu.1_Missense_Mutation_p.I1068T	NM_003285	NP_003276	Q92752	TENR_HUMAN	tenascin R precursor	1068	Fibronectin type-III 9.				axon guidance|cell adhesion|signal transduction	proteinaceous extracellular matrix				pancreas(5)|ovary(4)|central_nervous_system(1)|skin(1)	11	Renal(580;0.146)					ATAATTTTCAATCTCTGCCCT	0.512													3	81	---	---	---	---	PASS
DHX9	1660	broad.mit.edu	37	1	182812436	182812436	+	Missense_Mutation	SNP	T	G	G			TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:182812436T>G	uc001gpr.2	+	3	282	c.119T>G	c.(118-120)GTG>GGG	p.V40G	DHX9_uc001gps.2_5'UTR	NM_001357	NP_001348	Q08211	DHX9_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 9	40	DRBM 1.|Interaction with CREBBP.				CRD-mediated mRNA stabilization|nuclear mRNA splicing, via spliceosome	centrosome|CRD-mediated mRNA stability complex|nucleolus|nucleoplasm|ribonucleoprotein complex	ATP binding|ATP-dependent DNA helicase activity|ATP-dependent RNA helicase activity|DNA binding|double-stranded RNA binding|protein binding			ovary(2)	2						AAGGTTCAGGTGGAAGGTTAT	0.333													8	37	---	---	---	---	PASS
IKBKE	9641	broad.mit.edu	37	1	206649530	206649530	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:206649530G>A	uc001hdz.1	+	6	733	c.365G>A	c.(364-366)GGC>GAC	p.G122D	IKBKE_uc009xbu.1_Missense_Mutation_p.G122D|IKBKE_uc009xbv.1_Missense_Mutation_p.G122D|IKBKE_uc001hea.1_Missense_Mutation_p.G37D	NM_014002	NP_054721	Q14164	IKKE_HUMAN	IKK-related kinase epsilon	122	Protein kinase.				DNA damage response, signal transduction resulting in induction of apoptosis|innate immune response|MyD88-independent toll-like receptor signaling pathway|negative regulation of type I interferon production|positive regulation of I-kappaB kinase/NF-kappaB cascade|Toll signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|endosome membrane|plasma membrane|PML body	ATP binding|IkappaB kinase activity|NF-kappaB-inducing kinase activity|protein binding			ovary(3)|lung(3)|central_nervous_system(1)|skin(1)	8	Breast(84;0.137)					CCAGTGGCCGGCATGAACCAC	0.617													3	34	---	---	---	---	PASS
PTPN14	5784	broad.mit.edu	37	1	214656193	214656193	+	Intron	SNP	C	G	G			TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:214656193C>G	uc001hkk.1	-						PTPN14_uc010pty.1_Intron|uc010ptz.1_RNA	NM_005401	NP_005392	Q15678	PTN14_HUMAN	protein tyrosine phosphatase, non-receptor type						lymphangiogenesis	cytoplasm|cytoskeleton	protein tyrosine phosphatase activity|receptor tyrosine kinase binding			breast(2)|ovary(1)|kidney(1)|skin(1)	5				OV - Ovarian serous cystadenocarcinoma(81;0.00181)|all cancers(67;0.00194)|Epithelial(68;0.0157)|GBM - Glioblastoma multiforme(131;0.155)		ACTGATGTCACCAATGTTAAT	0.408													12	61	---	---	---	---	PASS
NUP133	55746	broad.mit.edu	37	1	229643913	229643913	+	Silent	SNP	C	G	G			TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:229643913C>G	uc001htn.2	-	1	176	c.84G>C	c.(82-84)ACG>ACC	p.T28T		NM_018230	NP_060700	Q8WUM0	NU133_HUMAN	nucleoporin 133kDa	28					carbohydrate metabolic process|glucose transport|mitotic prometaphase|mRNA export from nucleus|nuclear pore organization|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	condensed chromosome kinetochore|cytosol|Nup107-160 complex	nucleocytoplasmic transporter activity|protein binding			breast(4)|skin(2)|ovary(1)	7	Breast(184;0.104)|Ovarian(103;0.249)	Prostate(94;0.167)				CCGTCCGGGGCGTGGAGCCGG	0.726													7	8	---	---	---	---	PASS
FOSL2	2355	broad.mit.edu	37	2	28635380	28635380	+	3'UTR	SNP	C	A	A			TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:28635380C>A	uc002rma.2	+	4					FOSL2_uc010ymi.1_3'UTR	NM_005253	NP_005244	P15408	FOSL2_HUMAN	FOS-like antigen 2						cell death|regulation of transcription from RNA polymerase II promoter	nucleus	protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(2)|breast(1)	3	Acute lymphoblastic leukemia(172;0.155)					CAGGGACCAGCACCTTCAAGC	0.652													4	18	---	---	---	---	PASS
VWA3B	200403	broad.mit.edu	37	2	98804531	98804531	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:98804531A>G	uc002syo.2	+	10	1669	c.1405A>G	c.(1405-1407)AAA>GAA	p.K469E	VWA3B_uc010yvh.1_Missense_Mutation_p.K319E|VWA3B_uc002syj.2_RNA|VWA3B_uc002syk.1_Intron|VWA3B_uc002syl.1_Intron|VWA3B_uc002sym.2_Missense_Mutation_p.K469E|VWA3B_uc002syn.1_Intron|VWA3B_uc010yvi.1_Missense_Mutation_p.K126E	NM_144992	NP_659429	Q502W6	VWA3B_HUMAN	von Willebrand factor A domain containing 3B	469										ovary(3)|large_intestine(2)|skin(1)	6						CAACATTACCAAAGAGAAGTG	0.502													28	70	---	---	---	---	PASS
NCKAP5	344148	broad.mit.edu	37	2	133539879	133539879	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133539879G>T	uc002ttp.2	-	14	4879	c.4505C>A	c.(4504-4506)CCT>CAT	p.P1502H	NCKAP5_uc002ttq.2_Intron	NM_207363	NP_997246	O14513	NCKP5_HUMAN	Nck-associated protein 5 isoform 1	1502							protein binding				0						AGAAGGCCCAGGCTTCTGCTT	0.458													26	65	---	---	---	---	PASS
LRP1B	53353	broad.mit.edu	37	2	141812722	141812722	+	Silent	SNP	A	T	T			TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:141812722A>T	uc002tvj.1	-	10	2487	c.1515T>A	c.(1513-1515)ACT>ACA	p.T505T	LRP1B_uc010fnl.1_Intron	NM_018557	NP_061027	Q9NZR2	LRP1B_HUMAN	low density lipoprotein-related protein 1B	505	Extracellular (Potential).				protein transport|receptor-mediated endocytosis	integral to membrane	calcium ion binding			lung(17)|skin(12)|ovary(12)|pancreas(3)|upper_aerodigestive_tract(2)|central_nervous_system(2)|liver(1)|kidney(1)	50		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		AGTTGAAGCCAGTCCTGCAGC	0.443										TSP Lung(27;0.18)			9	68	---	---	---	---	PASS
CHRNA1	1134	broad.mit.edu	37	2	175614898	175614898	+	Splice_Site	SNP	C	T	T			TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:175614898C>T	uc002ujd.2	-	8	932	c.854_splice	c.e8-1	p.G285_splice	uc002uiw.2_Intron|CHRNA1_uc002uje.2_Splice_Site_p.G260_splice	NM_001039523	NP_001034612	P02708	ACHA_HUMAN	nicotinic cholinergic receptor alpha 1 isoform a						muscle cell homeostasis|neuromuscular junction development|neuromuscular process|neuromuscular synaptic transmission|neuron homeostasis|regulation of action potential in neuron|skeletal muscle contraction|skeletal muscle tissue growth	cell junction|cell surface|neuromuscular junction|nicotinic acetylcholine-gated receptor-channel complex|postsynaptic membrane	acetylcholine receptor activity|nicotinic acetylcholine-activated cation-selective channel activity			ovary(2)|central_nervous_system(1)|skin(1)	4						ATCTTCTCCCCTGAAAAGACC	0.348													10	26	---	---	---	---	PASS
ALPP	250	broad.mit.edu	37	2	233245025	233245025	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:233245025C>T	uc002vsq.2	+	6	952	c.787C>T	c.(787-789)CGC>TGC	p.R263C	ALPP_uc002vsr.2_5'Flank	NM_001632	NP_001623	P05187	PPB1_HUMAN	placental alkaline phosphatase preproprotein	263						anchored to membrane|cell surface|integral to membrane|plasma membrane	alkaline phosphatase activity|metal ion binding			ovary(1)	1		all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0449)|Lung NSC(271;0.132)		Epithelial(121;4.45e-22)|Kidney(3;4.42e-11)|KIRC - Kidney renal clear cell carcinoma(3;1.9e-09)|BRCA - Breast invasive adenocarcinoma(100;0.000767)|Lung(119;0.00566)|LUSC - Lung squamous cell carcinoma(224;0.00746)|STAD - Stomach adenocarcinoma(3;0.0181)|GBM - Glioblastoma multiforme(43;0.196)		GCTGGCGAAGCGCCAGGTGAT	0.667													14	104	---	---	---	---	PASS
VHL	7428	broad.mit.edu	37	3	10188290	10188290	+	Nonsense_Mutation	SNP	C	T	T			TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10188290C>T	uc003bvc.2	+	2	646	c.433C>T	c.(433-435)CAG>TAG	p.Q145*	VHL_uc003bvd.2_Intron	NM_000551	NP_000542	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor isoform 1	145	Involved in binding to CCT complex.		Q -> H (in VHLD).		anti-apoptosis|cell morphogenesis|negative regulation of cell proliferation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of cell differentiation|positive regulation of transcription, DNA-dependent|protein stabilization|protein ubiquitination|proteolysis	cytosol|endoplasmic reticulum|membrane|mitochondrion|nucleus	protein binding|transcription factor binding	p.Q145fs*12(1)|p.Q145fs*30(1)|p.G144fs*14(1)|p.Q145H(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)		TGTTGACGGACAGCCTATTTT	0.418		1	D|Mis|N|F|S		renal|hemangioma|pheochromocytoma	renal|hemangioma|pheochromocytoma			von_Hippel-Lindau_disease|Chuvash_Polycythemia_|Pheochromocytoma_(Adrenal)_Familial				40	120	---	---	---	---	PASS
FAM86D	692099	broad.mit.edu	37	3	75472015	75472015	+	3'UTR	SNP	T	G	G			TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:75472015T>G	uc003dpp.3	-	8					FAM86D_uc003dpo.3_RNA|FAM86D_uc003dps.3_RNA|FAM86D_uc003dpq.3_3'UTR|FAM86D_uc003dpr.3_RNA	NR_024241				RecName: Full=Protein FAM86B1;												0						CTCCAAACATTCCAGTACAAT	0.428													8	17	---	---	---	---	PASS
NLGN1	22871	broad.mit.edu	37	3	173998403	173998403	+	Silent	SNP	T	G	G			TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:173998403T>G	uc003fio.1	+	7	2205	c.1782T>G	c.(1780-1782)GTT>GTG	p.V594V	NLGN1_uc003fip.1_Silent_p.V594V	NM_014932	NP_055747	Q8N2Q7	NLGN1_HUMAN	neuroligin 1	611	Extracellular (Potential).				calcium-dependent cell-cell adhesion|neuron cell-cell adhesion|neuronal signal transduction|positive regulation of dendritic spine development|positive regulation of excitatory postsynaptic membrane potential|positive regulation of intracellular protein kinase cascade|positive regulation of synaptogenesis|protein targeting|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|regulation of N-methyl-D-aspartate selective glutamate receptor activity|synapse assembly|synaptic vesicle targeting	cell junction|cell surface|dendrite|integral to plasma membrane|postsynaptic density|postsynaptic membrane	cell adhesion molecule binding|neurexin binding|receptor activity			lung(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)|ovary(1)|pancreas(1)	7	Ovarian(172;0.0025)		LUSC - Lung squamous cell carcinoma(14;5.36e-13)|Lung(28;9.49e-13)			AACCAAGAGTTAAAGAACATT	0.378													24	117	---	---	---	---	PASS
MCF2L2	23101	broad.mit.edu	37	3	182897463	182897463	+	Silent	SNP	C	T	T			TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:182897463C>T	uc003fli.1	-	29	3213	c.3123G>A	c.(3121-3123)CAG>CAA	p.Q1041Q		NM_015078	NP_055893	Q86YR7	MF2L2_HUMAN	Rho family guanine-nucleotide exchange factor	1041					regulation of Rho protein signal transduction	intracellular	Rho guanyl-nucleotide exchange factor activity			ovary(2)|large_intestine(2)|breast(1)	5	all_cancers(143;1.26e-12)|Ovarian(172;0.0355)		all cancers(12;3.35e-44)|Epithelial(37;6.48e-38)|LUSC - Lung squamous cell carcinoma(7;7.12e-25)|Lung(8;6.39e-23)|OV - Ovarian serous cystadenocarcinoma(80;6.75e-21)			TGTCGTCCGACTGGAAAAGGC	0.592													11	88	---	---	---	---	PASS
PDGFRA	5156	broad.mit.edu	37	4	54265975	54265975	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:54265975T>C	uc003haa.2	+	10	970	c.784T>C	c.(784-786)TCT>CCT	p.S262P	FIP1L1_uc003gzx.3_Missense_Mutation_p.S247P|FIP1L1_uc011bzt.1_Missense_Mutation_p.S262P|FIP1L1_uc003gzy.2_Missense_Mutation_p.S262P|FIP1L1_uc011bzu.1_Missense_Mutation_p.S247P|FIP1L1_uc003gzz.2_Missense_Mutation_p.S224P|FIP1L1_uc003hab.2_Missense_Mutation_p.S227P|FIP1L1_uc003hac.2_Missense_Mutation_p.S43P|FIP1L1_uc010ign.2_RNA	NM_006206	NP_006197	P16234	PGFRA_HUMAN	platelet-derived growth factor receptor alpha	Error:Variant_position_missing_in_P16234_after_alignment					cardiac myofibril assembly|cell activation|luteinization|metanephric glomerular capillary formation|peptidyl-tyrosine phosphorylation|positive regulation of cell migration|positive regulation of DNA replication|positive regulation of fibroblast proliferation|protein autophosphorylation|retina vasculature development in camera-type eye	cytoplasm|integral to plasma membrane|nucleus	ATP binding|platelet-derived growth factor alpha-receptor activity|platelet-derived growth factor binding|platelet-derived growth factor receptor binding|protein homodimerization activity|vascular endothelial growth factor receptor activity			soft_tissue(572)|small_intestine(40)|stomach(16)|lung(16)|central_nervous_system(13)|haematopoietic_and_lymphoid_tissue(7)|skin(3)|ovary(3)|gastrointestinal_tract_(site_indeterminate)(1)|autonomic_ganglia(1)|prostate(1)|bone(1)	674	all_cancers(7;0.000425)|all_lung(4;0.000343)|Lung NSC(11;0.000467)|all_epithelial(27;0.0131)|all_neural(26;0.0209)|Glioma(25;0.08)		GBM - Glioblastoma multiforme(1;4.18e-71)|all cancers(1;4.76e-45)|LUSC - Lung squamous cell carcinoma(32;0.00256)		Becaplermin(DB00102)|Imatinib(DB00619)|Sunitinib(DB01268)	TTCTCCTCCTTCTTTGTTCAA	0.373			Mis|O|T	FIP1L1	GIST|idiopathic hypereosinophilic syndrome				Gastrointestinal_Stromal_Tumors_Sporadic_Multiple_Primary|Familial_Intestinal_Neurofibromatosis	TSP Lung(21;0.16)			25	81	---	---	---	---	PASS
TAS2R1	50834	broad.mit.edu	37	5	9629200	9629200	+	3'UTR	SNP	T	G	G			TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:9629200T>G	uc003jem.1	-	1						NM_019599	NP_062545	Q9NYW7	TA2R1_HUMAN	taste receptor T2R1						chemosensory behavior|sensory perception of taste	integral to membrane	taste receptor activity			ovary(3)	3						CAGGCATGGGTAAATCATTGA	0.433													10	56	---	---	---	---	PASS
C5orf42	65250	broad.mit.edu	37	5	37120329	37120329	+	Missense_Mutation	SNP	G	C	C			TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:37120329G>C	uc011cpa.1	-	49	9368	c.9137C>G	c.(9136-9138)CCT>CGT	p.P3046R	C5orf42_uc003jko.1_Missense_Mutation_p.P77R|C5orf42_uc003jkp.1_RNA|C5orf42_uc011coy.1_Missense_Mutation_p.P1564R|C5orf42_uc003jks.2_RNA|C5orf42_uc011coz.1_Missense_Mutation_p.P2139R	NM_023073	NP_075561	E9PH94	E9PH94_HUMAN	hypothetical protein LOC65250	3046										ovary(4)|breast(2)|skin(1)	7	all_lung(31;0.000616)		COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.177)|Colorectal(62;0.202)			ATGTGGCCAAGGTGAGCCTTG	0.363													19	73	---	---	---	---	PASS
MCCC2	64087	broad.mit.edu	37	5	70952601	70952601	+	Missense_Mutation	SNP	G	C	C			TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:70952601G>C	uc003kbs.3	+	17	1744	c.1606G>C	c.(1606-1608)GAC>CAC	p.D536H	MCCC2_uc003kbt.3_RNA	NM_022132	NP_071415	Q9HCC0	MCCB_HUMAN	methylcrotonoyl-Coenzyme A carboxylase 2 (beta)	536	Carboxyltransferase.				leucine catabolic process	mitochondrial inner membrane|mitochondrial matrix	ATP binding|methylcrotonoyl-CoA carboxylase activity			ovary(1)	1		Lung NSC(167;0.000697)|Prostate(74;0.0107)|Ovarian(174;0.0175)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;2.04e-54)	Biotin(DB00121)	TGATCCAGCAGACACCAGACT	0.423													7	268	---	---	---	---	PASS
APC	324	broad.mit.edu	37	5	112170717	112170717	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:112170717G>A	uc010jby.2	+	15	2193	c.1813G>A	c.(1813-1815)GAT>AAT	p.D605N	APC_uc011cvt.1_Missense_Mutation_p.D587N|APC_uc003kpz.3_Missense_Mutation_p.D605N|APC_uc003kpy.3_Missense_Mutation_p.D605N|APC_uc010jbz.2_Missense_Mutation_p.D322N|APC_uc010jca.2_5'UTR	NM_001127511	NP_001120983	P25054	APC_HUMAN	adenomatous polyposis coli	605	Leu-rich.|ARM 4.				canonical Wnt receptor signaling pathway|cell adhesion|cell cycle arrest|cell migration|cellular component disassembly involved in apoptosis|cytokinesis after mitosis|mitotic cell cycle spindle assembly checkpoint|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of cyclin-dependent protein kinase activity|negative regulation of microtubule depolymerization|positive regulation of apoptosis|positive regulation of cell migration|positive regulation of pseudopodium assembly|protein complex assembly|regulation of attachment of spindle microtubules to kinetochore|response to DNA damage stimulus|tight junction assembly	adherens junction|APC-Axin-1-beta-catenin complex|Axin-APC-beta-catenin-GSK3B complex|beta-catenin destruction complex|centrosome|cytosol|kinetochore|lamellipodium|lateral plasma membrane|nucleus|ruffle membrane|tight junction	beta-catenin binding|gamma-catenin binding|microtubule plus-end binding|protein kinase binding|protein kinase regulator activity	p.?(1)		large_intestine(2123)|stomach(123)|soft_tissue(55)|small_intestine(34)|breast(26)|pancreas(25)|urinary_tract(20)|lung(19)|thyroid(18)|liver(13)|central_nervous_system(10)|ovary(9)|skin(7)|upper_aerodigestive_tract(6)|adrenal_gland(6)|bone(6)|NS(5)|prostate(4)|endometrium(3)|kidney(1)|oesophagus(1)|biliary_tract(1)	2515		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		GAATAAAGCTGATATATGTGC	0.408		12	D|Mis|N|F|S		colorectal|pancreatic|desmoid|hepatoblastoma|glioma|other CNS	colorectal|pancreatic|desmoid|hepatoblastoma|glioma|other CNS			Hereditary_Desmoid_Disease|Familial_Adenomatous_Polyposis|Turcot_syndrome	TSP Lung(16;0.13)			19	110	---	---	---	---	PASS
CEP120	153241	broad.mit.edu	37	5	122722335	122722335	+	Missense_Mutation	SNP	G	C	C			TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:122722335G>C	uc003ktk.2	-	11	1539	c.1457C>G	c.(1456-1458)GCA>GGA	p.A486G	CEP120_uc011cwq.1_Missense_Mutation_p.A295G|CEP120_uc010jcz.1_Missense_Mutation_p.A460G	NM_153223	NP_694955	Q8N960	CE120_HUMAN	coiled-coil domain containing 100	486						centrosome				ovary(1)	1						AATAGGAGCTGCACTTCCAAA	0.328													12	65	---	---	---	---	PASS
CEP120	153241	broad.mit.edu	37	5	122722336	122722336	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:122722336C>A	uc003ktk.2	-	11	1538	c.1456G>T	c.(1456-1458)GCA>TCA	p.A486S	CEP120_uc011cwq.1_Missense_Mutation_p.A295S|CEP120_uc010jcz.1_Missense_Mutation_p.A460S	NM_153223	NP_694955	Q8N960	CE120_HUMAN	coiled-coil domain containing 100	486						centrosome				ovary(1)	1						ATAGGAGCTGCACTTCCAAAG	0.328													12	65	---	---	---	---	PASS
PCDHGA3	56112	broad.mit.edu	37	5	140725728	140725728	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140725728G>T	uc003ljm.1	+	1	2128	c.2128G>T	c.(2128-2130)GTG>TTG	p.V710L	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc010jfx.1_Missense_Mutation_p.V470L|PCDHGA3_uc011dap.1_Missense_Mutation_p.V710L	NM_018916	NP_061739	Q9Y5H0	PCDG3_HUMAN	protocadherin gamma subfamily A, 3 isoform 1	710	Helical; (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			breast(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTTCGTCATCGTGCTGCTGGC	0.682													4	132	---	---	---	---	PASS
TUBB2B	347733	broad.mit.edu	37	6	3227737	3227737	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:3227737T>C	uc003mvg.2	-	1	232	c.41A>G	c.(40-42)AAC>AGC	p.N14S	uc003mvi.1_5'Flank|TUBB2B_uc010jnj.2_Missense_Mutation_p.N14S|TUBB2B_uc010jnk.2_5'UTR|TUBB2B_uc003mvh.2_5'UTR	NM_178012	NP_821080	Q9BVA1	TBB2B_HUMAN	tubulin, beta 2B	14					'de novo' posttranslational protein folding|microtubule-based movement|neuron migration|protein polymerization	cytoplasm|microtubule	GTP binding|GTPase activity|structural molecule activity			large_intestine(1)	1	Ovarian(93;0.0386)	all_hematologic(90;0.108)				GCCGATCTGGTTGCCGCACTG	0.731													3	24	---	---	---	---	PASS
LRFN2	57497	broad.mit.edu	37	6	40400076	40400076	+	Missense_Mutation	SNP	G	C	C			TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:40400076G>C	uc003oph.1	-	2	1242	c.777C>G	c.(775-777)GAC>GAG	p.D259E		NM_020737	NP_065788	Q9ULH4	LRFN2_HUMAN	leucine rich repeat and fibronectin type III	259	LRRCT.|Extracellular (Potential).					cell junction|integral to membrane|postsynaptic membrane				ovary(2)|skin(1)	3	Ovarian(28;0.0418)|Colorectal(47;0.196)					CCAGGTCATCGTCCCGCTCGA	0.597													7	31	---	---	---	---	PASS
PKHD1	5314	broad.mit.edu	37	6	51656133	51656133	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:51656133T>C	uc003pah.1	-	53	8617	c.8341A>G	c.(8341-8343)AAA>GAA	p.K2781E	PKHD1_uc010jzn.1_Missense_Mutation_p.K764E|PKHD1_uc003pai.2_Missense_Mutation_p.K2781E	NM_138694	NP_619639	P08F94	PKHD1_HUMAN	fibrocystin isoform 1	2781	G8 2.|Extracellular (Potential).				cell-cell adhesion|cilium assembly|homeostatic process|kidney development|negative regulation of cellular component movement	anchored to external side of plasma membrane|apical plasma membrane|integral to membrane|microtubule basal body	protein binding|receptor activity			lung(15)|ovary(15)|large_intestine(5)|central_nervous_system(3)|skin(3)|breast(2)|upper_aerodigestive_tract(1)	44	Lung NSC(77;0.0605)					TACAGCCCTTTGAAGAATGGA	0.443													21	61	---	---	---	---	PASS
NOD1	10392	broad.mit.edu	37	7	30492639	30492639	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:30492639G>T	uc003tav.2	-	6	917	c.394C>A	c.(394-396)CAG>AAG	p.Q132K	NOD1_uc010kvs.2_Missense_Mutation_p.Q132K	NM_006092	NP_006083	Q9Y239	NOD1_HUMAN	nucleotide-binding oligomerization domain	132					activation of MAPK activity|detection of bacterium|induction of apoptosis|inflammatory response|innate immune response|interleukin-8 biosynthetic process|JNK cascade|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|positive regulation of dendritic cell antigen processing and presentation|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|protein oligomerization|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	basolateral plasma membrane|cytosol	ATP binding|CARD domain binding|caspase activator activity|peptidoglycan binding|protein homodimerization activity			ovary(1)|skin(1)	2						TGTCGCAGCTGCTGGGTATAC	0.582													3	45	---	---	---	---	PASS
MAGI2	9863	broad.mit.edu	37	7	77708312	77708312	+	Nonsense_Mutation	SNP	G	A	A			TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:77708312G>A	uc003ugx.2	-	21	3912	c.3658C>T	c.(3658-3660)CGA>TGA	p.R1220*	MAGI2_uc003ugy.2_Nonsense_Mutation_p.R1206*|MAGI2_uc010ldx.1_Nonsense_Mutation_p.R813*	NM_012301	NP_036433	Q86UL8	MAGI2_HUMAN	membrane associated guanylate kinase, WW and PDZ	1220	PDZ 6.					cell junction|synapse|synaptosome	phosphatase binding			ovary(5)|lung(4)|breast(1)|skin(1)	11		all_cancers(73;0.0064)|all_epithelial(88;0.087)|all_neural(109;0.0936)|Medulloblastoma(109;0.166)|Melanoma(862;0.236)				AGCCTCACTCGTCTTCCTCCA	0.448													13	220	---	---	---	---	PASS
ZNF3	7551	broad.mit.edu	37	7	99673136	99673136	+	Intron	SNP	G	T	T			TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99673136G>T	uc003usq.2	-						ZNF3_uc003usp.2_Intron|ZNF3_uc003usr.2_Intron|ZNF3_uc010lgj.2_Intron|ZNF3_uc003uss.2_5'UTR|ZNF3_uc003ust.3_Intron	NM_032924	NP_116313	P17036	ZNF3_HUMAN	zinc finger protein 3 isoform 2						cell differentiation|leukocyte activation|multicellular organismal development	nucleus	DNA binding|identical protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)	Ovarian(593;2.06e-05)|Myeloproliferative disorder(862;0.0122)|Breast(660;0.029)	STAD - Stomach adenocarcinoma(171;0.129)			AAAATGGAAAGGAAAAGGATA	0.527													12	28	---	---	---	---	PASS
LAMB1	3912	broad.mit.edu	37	7	107605113	107605113	+	Nonsense_Mutation	SNP	G	A	A			TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:107605113G>A	uc003vew.2	-	14	1917	c.1582C>T	c.(1582-1584)CAG>TAG	p.Q528*	LAMB1_uc003vev.2_Nonsense_Mutation_p.Q552*|LAMB1_uc003vex.2_Nonsense_Mutation_p.Q528*|LAMB1_uc010ljn.1_Nonsense_Mutation_p.Q614*	NM_002291	NP_002282	P07942	LAMB1_HUMAN	laminin, beta 1 precursor	528	Laminin EGF-like 5; truncated.				axon guidance|odontogenesis|positive regulation of cell migration|positive regulation of epithelial cell proliferation|substrate adhesion-dependent cell spreading	extracellular space|laminin-1 complex|laminin-10 complex|laminin-2 complex|laminin-8 complex|perinuclear region of cytoplasm	extracellular matrix structural constituent			ovary(4)|skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)	8					Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)	CATGAGCACTGGCCTGACTCC	0.557													7	32	---	---	---	---	PASS
ZNF425	155054	broad.mit.edu	37	7	148802462	148802462	+	Missense_Mutation	SNP	C	G	G			TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:148802462C>G	uc003wfj.2	-	4	574	c.501G>C	c.(499-501)AAG>AAC	p.K167N		NM_001001661	NP_001001661	Q6IV72	ZN425_HUMAN	zinc finger protein 425	167					negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|zinc ion binding			breast(2)|ovary(1)	3	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00463)			GCAGGTCTTTCTTGTCTGGAT	0.463													5	140	---	---	---	---	PASS
SSPO	23145	broad.mit.edu	37	7	149486279	149486279	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:149486279G>A	uc010lpk.2	+	30	4255	c.4255G>A	c.(4255-4257)GGG>AGG	p.G1419R		NM_198455	NP_940857	A2VEC9	SSPO_HUMAN	SCO-spondin precursor	1419	LDL-receptor class A 2.				cell adhesion	extracellular space	peptidase inhibitor activity				0	Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			CTGTGGGGAGGGGCAGATGAC	0.662													4	27	---	---	---	---	PASS
ERICH1	157697	broad.mit.edu	37	8	623548	623548	+	Silent	SNP	G	A	A			TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:623548G>A	uc003wph.2	-	4	869	c.804C>T	c.(802-804)GAC>GAT	p.D268D	ERICH1_uc011kwh.1_Silent_p.D268D|ERICH1_uc003wpe.1_Silent_p.D174D|ERICH1_uc003wpi.2_Silent_p.D80D	NM_207332	NP_997215	Q86X53	ERIC1_HUMAN	glutamate-rich 1	268	Glu-rich.									large_intestine(2)	2		Colorectal(14;0.158)|Ovarian(12;0.17)|Myeloproliferative disorder(644;0.185)|Hepatocellular(245;0.236)		Epithelial(5;3.29e-14)|BRCA - Breast invasive adenocarcinoma(11;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(5;3.65e-06)|READ - Rectum adenocarcinoma(1;0.0325)		CCTCCCTGGCGTCTTTAACGT	0.647													19	85	---	---	---	---	PASS
MSR1	4481	broad.mit.edu	37	8	16021600	16021600	+	Missense_Mutation	SNP	G	T	T	rs143967440		TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:16021600G>T	uc003wwz.2	-	5	989	c.791C>A	c.(790-792)ACC>AAC	p.T264N	MSR1_uc010lsu.2_Missense_Mutation_p.T282N|MSR1_uc003wxa.2_Missense_Mutation_p.T264N|MSR1_uc003wxb.2_Missense_Mutation_p.T264N|MSR1_uc011kxz.1_Missense_Mutation_p.T38N	NM_138715	NP_619729	P21757	MSRE_HUMAN	macrophage scavenger receptor 1 isoform type 1	264	Extracellular (Potential).				cholesterol transport|plasma lipoprotein particle clearance|positive regulation of cholesterol storage|positive regulation of macrophage derived foam cell differentiation|receptor-mediated endocytosis	collagen|integral to plasma membrane|low-density lipoprotein particle	low-density lipoprotein particle binding|protein binding|scavenger receptor activity			ovary(1)	1				Colorectal(111;0.00475)|COAD - Colon adenocarcinoma(73;0.0164)		ATTTCTCAAGGTCTGAGAATG	0.308													12	50	---	---	---	---	PASS
ASPH	444	broad.mit.edu	37	8	62491435	62491435	+	Intron	SNP	C	T	T			TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:62491435C>T	uc011leg.1	-						ASPH_uc003xuj.2_Intron|ASPH_uc003xuo.2_Intron|uc003xuk.2_Silent_p.D160D	NM_004318	NP_004309	Q12797	ASPH_HUMAN	aspartate beta-hydroxylase isoform a						muscle contraction	integral to endoplasmic reticulum membrane	calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle			ovary(3)	3	Lung SC(2;0.153)	Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101)			L-Aspartic Acid(DB00128)|Succinic acid(DB00139)	GGCTGACTGACGAGATCAACT	0.512													7	53	---	---	---	---	PASS
RIMS2	9699	broad.mit.edu	37	8	104709441	104709441	+	Missense_Mutation	SNP	G	C	C			TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:104709441G>C	uc003ylp.2	+	2	443	c.304G>C	c.(304-306)GAT>CAT	p.D102H		NM_001100117	NP_001093587	Q9UQ26	RIMS2_HUMAN	regulating synaptic membrane exocytosis 2	133	FYVE-type.|RabBD.				intracellular protein transport	cell junction|presynaptic membrane	metal ion binding|Rab GTPase binding			ovary(6)|lung(2)|breast(2)|skin(2)|large_intestine(1)|central_nervous_system(1)|pancreas(1)	15			OV - Ovarian serous cystadenocarcinoma(57;7.7e-07)|STAD - Stomach adenocarcinoma(118;0.229)			AAAGTTTGCTGATGGATGTGG	0.433										HNSCC(12;0.0054)			28	110	---	---	---	---	PASS
COL27A1	85301	broad.mit.edu	37	9	117052336	117052336	+	Splice_Site	SNP	A	G	G			TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:117052336A>G	uc011lxl.1	+	46	4207	c.4207_splice	c.e46-2	p.G1403_splice	COL27A1_uc004bii.2_Splice_Site	NM_032888	NP_116277	Q8IZC6	CORA1_HUMAN	collagen, type XXVII, alpha 1 precursor						cell adhesion		extracellular matrix structural constituent			ovary(3)|skin(1)	4						TTGATTTTTCAGGGACCAAAG	0.627													3	73	---	---	---	---	PASS
LAMC3	10319	broad.mit.edu	37	9	133942552	133942552	+	Silent	SNP	C	T	T			TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:133942552C>T	uc004caa.1	+	14	2651	c.2553C>T	c.(2551-2553)TAC>TAT	p.Y851Y		NM_006059	NP_006050	Q9Y6N6	LAMC3_HUMAN	laminin, gamma 3 precursor	851	Laminin EGF-like 8.				cell adhesion	basement membrane|membrane	structural molecule activity			ovary(2)|pancreas(1)	3	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;5.06e-05)|Epithelial(140;0.000551)		AAGGCTTCTACGGGAGCGCCC	0.642													18	82	---	---	---	---	PASS
C9orf140	89958	broad.mit.edu	37	9	139959180	139959180	+	Silent	SNP	A	G	G			TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:139959180A>G	uc011men.1	-	6	1232	c.1116T>C	c.(1114-1116)ATT>ATC	p.I372I		NM_178448	NP_848543	Q86UD0	CI140_HUMAN	tumor specificity and mitosis phase-dependent	372	Potential.					cytoplasm|nucleus				skin(1)	1	all_cancers(76;0.0926)	Myeloproliferative disorder(178;0.0821)	STAD - Stomach adenocarcinoma(284;0.123)	OV - Ovarian serous cystadenocarcinoma(145;3.02e-05)|Epithelial(140;0.000499)		ACAGCTGCTTAATGAGCGCCG	0.652											OREG0019628	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	6	---	---	---	---	PASS
DCLRE1C	64421	broad.mit.edu	37	10	14974910	14974910	+	Missense_Mutation	SNP	G	C	C			TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:14974910G>C	uc001inn.2	-	9	808	c.723C>G	c.(721-723)ATC>ATG	p.I241M	DCLRE1C_uc010qbx.1_Missense_Mutation_p.I241M|DCLRE1C_uc001inl.2_Missense_Mutation_p.I121M|DCLRE1C_uc009xji.2_Missense_Mutation_p.I126M|DCLRE1C_uc001inm.2_Missense_Mutation_p.I121M|DCLRE1C_uc001ino.2_Missense_Mutation_p.I126M|DCLRE1C_uc009xjh.2_RNA|DCLRE1C_uc001inp.2_Missense_Mutation_p.I121M|DCLRE1C_uc001inq.2_Missense_Mutation_p.I121M|DCLRE1C_uc001inr.2_Missense_Mutation_p.I126M|DCLRE1C_uc009xjj.1_RNA	NM_001033855	NP_001029027	Q96SD1	DCR1C_HUMAN	artemis protein isoform a	241					DNA recombination	nucleus	5'-3' exonuclease activity|single-stranded DNA specific endodeoxyribonuclease activity			ovary(1)	1						GATGATGAAGGATCTCAGGCA	0.393								Involved_in_tolerance_or_repair_of_DNA_crosslinks|NHEJ					4	151	---	---	---	---	PASS
SLC39A12	221074	broad.mit.edu	37	10	18250701	18250701	+	Silent	SNP	G	A	A			TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:18250701G>A	uc001ipo.2	+	3	726	c.453G>A	c.(451-453)AGG>AGA	p.R151R	SLC39A12_uc001ipn.2_Silent_p.R151R|SLC39A12_uc001ipp.2_Silent_p.R151R|SLC39A12_uc010qck.1_Silent_p.R17R	NM_001145195	NP_001138667	Q504Y0	S39AC_HUMAN	solute carrier family 39 (zinc transporter),	151	Extracellular (Potential).				zinc ion transport	integral to membrane	metal ion transmembrane transporter activity			ovary(1)|breast(1)	2						TGAGCCTCAGGCAGGATGAAG	0.398													13	96	---	---	---	---	PASS
HSD17B7P2	158160	broad.mit.edu	37	10	38645357	38645357	+	5'UTR	SNP	C	T	T	rs142891358	by1000genomes	TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:38645357C>T	uc010qex.1	+	1					HSD17B7P2_uc001izq.2_RNA|HSD17B7P2_uc010qew.1_5'UTR|HSD17B7P2_uc001izo.1_RNA|HSD17B7P2_uc001izp.1_5'UTR					SubName: Full=cDNA FLJ60462, highly similar to 3-keto-steroid reductase (EC 1.1.1.270);												0						GTTTGCTTCACTGCTTGGAAG	0.607													5	13	---	---	---	---	PASS
ANXA2P3	305	broad.mit.edu	37	10	66586119	66586119	+	RNA	SNP	G	T	T			TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:66586119G>T	uc009xpm.1	+	1		c.835G>T				NR_001446				Human lipocortin (LIP) 2 pseudogene mRNA, complete cds-like region.												0						TTCAGAACAAGCCCCTGTATT	0.498													7	17	---	---	---	---	PASS
GBF1	8729	broad.mit.edu	37	10	104142165	104142165	+	3'UTR	SNP	C	T	T			TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:104142165C>T	uc001kux.1	+	40					GBF1_uc001kuy.1_3'UTR|GBF1_uc001kuz.1_3'UTR	NM_004193	NP_004184	Q92538	GBF1_HUMAN	golgi-specific brefeldin A resistant guanine						COPI coating of Golgi vesicle|post-Golgi vesicle-mediated transport|regulation of ARF protein signal transduction|retrograde vesicle-mediated transport, Golgi to ER	Golgi membrane	ARF guanyl-nucleotide exchange factor activity|protein binding			ovary(1)|central_nervous_system(1)	2		Colorectal(252;0.0236)		Epithelial(162;5.16e-08)|all cancers(201;1.19e-06)		GGCTGTCCTGCGGGCCACAAG	0.552													5	22	---	---	---	---	PASS
MADD	8567	broad.mit.edu	37	11	47306055	47306055	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47306055G>A	uc001ner.1	+	12	2287	c.2096G>A	c.(2095-2097)CGC>CAC	p.R699H	MADD_uc001neq.2_Missense_Mutation_p.R699H|MADD_uc001nev.1_Missense_Mutation_p.R699H|MADD_uc001nes.1_Missense_Mutation_p.R699H|MADD_uc001net.1_Missense_Mutation_p.R699H|MADD_uc009yln.1_Missense_Mutation_p.R699H|MADD_uc001neu.1_Missense_Mutation_p.R699H|MADD_uc001nex.2_Missense_Mutation_p.R699H|MADD_uc001nez.2_Missense_Mutation_p.R699H|MADD_uc001new.2_Missense_Mutation_p.R699H	NM_003682	NP_003673	Q8WXG6	MADD_HUMAN	MAP-kinase activating death domain-containing	699					activation of MAPK activity|apoptosis|cell surface receptor linked signaling pathway|regulation of apoptosis|regulation of cell cycle	cytoplasm|integral to membrane|plasma membrane	death receptor binding|protein kinase activator activity|Rab guanyl-nucleotide exchange factor activity			ovary(5)|skin(4)|central_nervous_system(2)	11				Lung(87;0.182)		CCCCCACTGCGCTCCAGCTCT	0.592													8	48	---	---	---	---	PASS
DLG2	1740	broad.mit.edu	37	11	83243801	83243801	+	Missense_Mutation	SNP	A	T	T			TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:83243801A>T	uc001paj.2	-	16	2131	c.1828T>A	c.(1828-1830)TTG>ATG	p.L610M	DLG2_uc001pai.2_Missense_Mutation_p.L507M|DLG2_uc010rsy.1_Missense_Mutation_p.L577M|DLG2_uc010rsz.1_Missense_Mutation_p.L610M|DLG2_uc010rta.1_Missense_Mutation_p.L610M|DLG2_uc001pak.2_Missense_Mutation_p.L715M|DLG2_uc010rtb.1_Missense_Mutation_p.L577M|DLG2_uc010rsw.1_Missense_Mutation_p.L92M|DLG2_uc010rsx.1_Missense_Mutation_p.L91M	NM_001364	NP_001355	Q15700	DLG2_HUMAN	chapsyn-110 isoform 2	610						cell junction|postsynaptic density|postsynaptic membrane	guanylate kinase activity|protein binding|protein binding			ovary(3)|pancreas(2)|skin(1)	6		all_cancers(6;0.00791)|Acute lymphoblastic leukemia(157;4.44e-05)|all_hematologic(158;0.0036)				ACTGTCTTCAATCGGGCACGT	0.398													6	102	---	---	---	---	PASS
GRM5	2915	broad.mit.edu	37	11	88330476	88330476	+	Missense_Mutation	SNP	T	G	G			TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:88330476T>G	uc001pcq.2	-	5	1639	c.1439A>C	c.(1438-1440)GAT>GCT	p.D480A	GRM5_uc009yvm.2_Missense_Mutation_p.D480A	NM_001143831	NP_001137303	P41594	GRM5_HUMAN	glutamate receptor, metabotropic 5 isoform a	480	Extracellular (Potential).				activation of phospholipase C activity by metabotropic glutamate receptor signaling pathway|synaptic transmission	integral to plasma membrane	G-protein coupled receptor activity|glutamate receptor activity			central_nervous_system(4)|ovary(2)|lung(2)|breast(1)	9		Acute lymphoblastic leukemia(157;2.54e-05)|all_hematologic(158;0.00834)			Acamprosate(DB00659)	GTTGATATAATCAAAGTAATC	0.323													12	52	---	---	---	---	PASS
DDI1	414301	broad.mit.edu	37	11	103907603	103907603	+	Missense_Mutation	SNP	C	G	G			TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:103907603C>G	uc001phr.2	+	1	296	c.53C>G	c.(52-54)TCT>TGT	p.S18C	PDGFD_uc001php.2_Intron|PDGFD_uc001phq.2_Intron	NM_001001711	NP_001001711	Q8WTU0	DDI1_HUMAN	DDI1, DNA-damage inducible 1, homolog 1	18	Ubiquitin-like.				proteolysis		aspartic-type endopeptidase activity			large_intestine(3)|upper_aerodigestive_tract(1)|pancreas(1)	5		Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.00648)|Melanoma(852;0.055)|all_neural(303;0.164)		BRCA - Breast invasive adenocarcinoma(274;0.00128)|Epithelial(105;0.0631)|all cancers(92;0.169)		GTCACCTTCTCTCTCCAGGTC	0.522													6	207	---	---	---	---	PASS
RNF214	257160	broad.mit.edu	37	11	117109520	117109520	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:117109520G>A	uc001pqt.2	+	3	356	c.311G>A	c.(310-312)GGG>GAG	p.G104E	RNF214_uc001pqu.2_Missense_Mutation_p.G104E|RNF214_uc010rxf.1_Intron	NM_207343	NP_997226	Q8ND24	RN214_HUMAN	ring finger protein 214	104							zinc ion binding				0	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.88e-05)|Epithelial(105;0.000397)|all cancers(92;0.00258)		TCTGGCAGTGGGTCTCAGTCT	0.547													4	160	---	---	---	---	PASS
MLL	4297	broad.mit.edu	37	11	118376084	118376084	+	Missense_Mutation	SNP	G	C	C			TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118376084G>C	uc001pta.2	+	27	9491	c.9468G>C	c.(9466-9468)ATG>ATC	p.M3156I	MLL_uc001ptb.2_Missense_Mutation_p.M3159I	NM_005933	NP_005924	Q03164	MLL1_HUMAN	myeloid/lymphoid or mixed-lineage leukemia	3156					apoptosis|embryonic hemopoiesis|histone H4-K16 acetylation|positive regulation of transcription, DNA-dependent|protein complex assembly|transcription from RNA polymerase II promoter	MLL1 complex	AT DNA binding|histone acetyl-lysine binding|histone methyltransferase activity (H3-K4 specific)|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|unmethylated CpG binding|zinc ion binding			lung(7)|ovary(5)|kidney(5)|central_nervous_system(3)|pancreas(2)|urinary_tract(1)|breast(1)|skin(1)	25	all_hematologic(175;0.046)	all_hematologic(192;1.13e-50)|all_neural(223;3.18e-06)|Breast(348;1.07e-05)|Medulloblastoma(222;0.0425)|Hepatocellular(160;0.244)		OV - Ovarian serous cystadenocarcinoma(223;2.77e-44)|BRCA - Breast invasive adenocarcinoma(274;1.2e-11)|Lung(307;3.48e-06)|LUSC - Lung squamous cell carcinoma(976;7.92e-05)|Colorectal(284;0.144)		TGCTACCCATGTCTCATCACC	0.493			T|O	MLL|MLLT1|MLLT2|MLLT3|MLLT4|MLLT7|MLLT10|MLLT6|ELL|EPS15|AF1Q|CREBBP|SH3GL1|FNBP1|PNUTL1|MSF|GPHN|GMPS|SSH3BP1|ARHGEF12|GAS7|FOXO3A|LAF4|LCX|SEPT6|LPP|CBFA2T1|GRAF|EP300|PICALM|HEAB	AML|ALL								4	200	---	---	---	---	PASS
HYOU1	10525	broad.mit.edu	37	11	118925901	118925901	+	Missense_Mutation	SNP	T	A	A			TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118925901T>A	uc001puu.2	-	5	608	c.415A>T	c.(415-417)AGC>TGC	p.S139C	HYOU1_uc001put.2_Missense_Mutation_p.S104C|HYOU1_uc010ryu.1_Missense_Mutation_p.S159C|HYOU1_uc010ryv.1_Missense_Mutation_p.S28C|HYOU1_uc001pux.3_Missense_Mutation_p.S139C|HYOU1_uc010ryw.1_RNA|HYOU1_uc001puw.1_Missense_Mutation_p.S139C	NM_006389	NP_006380	Q9Y4L1	HYOU1_HUMAN	hypoxia up-regulated 1 precursor	139						endoplasmic reticulum lumen	ATP binding|protein binding				0	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)|all_hematologic(192;0.207)		BRCA - Breast invasive adenocarcinoma(274;7.78e-05)		ACTCACGAGCTGATCTGAAAG	0.567													24	96	---	---	---	---	PASS
KLHDC5	57542	broad.mit.edu	37	12	27950930	27950930	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:27950930G>A	uc001rij.2	+	3	1426	c.1349G>A	c.(1348-1350)GGC>GAC	p.G450D	KLHDC5_uc009zjj.2_RNA	NM_020782	NP_065833	Q9P2K6	KLDC5_HUMAN	kelch domain containing 5	450	Kelch 6.									ovary(1)|central_nervous_system(1)	2	Lung SC(9;0.0873)					CATAACGACGGCATCTACATC	0.517													3	62	---	---	---	---	PASS
ADAMTS20	80070	broad.mit.edu	37	12	43825179	43825179	+	Nonsense_Mutation	SNP	C	A	A			TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:43825179C>A	uc010skx.1	-	22	3217	c.3217G>T	c.(3217-3219)GAA>TAA	p.E1073*	ADAMTS20_uc001rno.1_Nonsense_Mutation_p.E227*|ADAMTS20_uc001rnp.1_Nonsense_Mutation_p.E227*	NM_025003	NP_079279	P59510	ATS20_HUMAN	a disintegrin-like and metalloprotease with	1073	TSP type-1 5.					proteinaceous extracellular matrix	zinc ion binding			central_nervous_system(5)|ovary(4)|lung(3)|large_intestine(2)|skin(2)|urinary_tract(1)|kidney(1)|pancreas(1)	19	all_cancers(12;2.6e-05)|Lung SC(27;0.184)	Lung NSC(34;0.0569)|all_lung(34;0.129)		GBM - Glioblastoma multiforme(48;0.0473)		GTATGAAGTTCACATGGACTC	0.418													4	112	---	---	---	---	PASS
SLC41A2	84102	broad.mit.edu	37	12	105282811	105282811	+	Missense_Mutation	SNP	C	G	G			TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:105282811C>G	uc001tla.2	-	4	1047	c.880G>C	c.(880-882)GGA>CGA	p.G294R		NM_032148	NP_115524	Q96JW4	S41A2_HUMAN	solute carrier family 41, member 2	294	Helical; (Potential).					integral to membrane|plasma membrane	magnesium ion transmembrane transporter activity			ovary(1)|skin(1)	2						ATTCACTTACCCTGCAGAAGA	0.333													31	114	---	---	---	---	PASS
MLEC	9761	broad.mit.edu	37	12	121132708	121132708	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:121132708G>A	uc001tyy.1	+	3	647	c.496G>A	c.(496-498)GAT>AAT	p.D166N		NM_014730	NP_055545	Q14165	MLEC_HUMAN	malectin precursor	166	Lumenal (Potential).				post-translational protein modification|protein folding|protein N-linked glycosylation via asparagine	endoplasmic reticulum membrane|integral to membrane	carbohydrate binding			ovary(1)	1						CACAGCTCACGATGAAATTAT	0.453													37	138	---	---	---	---	PASS
DNAH10	196385	broad.mit.edu	37	12	124379213	124379213	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124379213G>T	uc001uft.3	+	53	8894	c.8869G>T	c.(8869-8871)GAC>TAC	p.D2957Y		NM_207437	NP_997320	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	2957	AAA 4 (By similarity).				microtubule-based movement	cilium axoneme|cytoplasm|dynein complex|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(3)|skin(2)|central_nervous_system(1)	6	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)		CACTGGTATTGACTGGTTCAT	0.338													4	51	---	---	---	---	PASS
LOC374491	374491	broad.mit.edu	37	13	25168432	25168432	+	RNA	SNP	T	C	C	rs149337771	by1000genomes	TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:25168432T>C	uc001upm.2	+	10		c.1104T>C			LOC374491_uc001upn.2_RNA|LOC374491_uc001upo.2_RNA					Homo sapiens mRNA; cDNA DKFZp434J0717 (from clone DKFZp434J0717).												0						TTGAAACAGCTGGTGTATTAA	0.373													3	22	---	---	---	---	PASS
SUCLA2	8803	broad.mit.edu	37	13	48517474	48517474	+	3'UTR	SNP	T	C	C			TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:48517474T>C	uc001vbs.2	-	11					SUCLA2_uc010tgb.1_3'UTR|SUCLA2_uc010tgc.1_3'UTR|SUCLA2_uc010tgd.1_3'UTR	NM_003850	NP_003841	Q9P2R7	SUCB1_HUMAN	succinate-CoA ligase, ADP-forming, beta subunit						succinyl-CoA pathway|tricarboxylic acid cycle	mitochondrial matrix	ATP binding|metal ion binding|protein binding|succinate-CoA ligase (ADP-forming) activity			central_nervous_system(1)	1		all_cancers(8;1.13e-24)|all_epithelial(8;1.78e-13)|all_lung(13;2.85e-06)|Breast(56;0.000141)|Lung NSC(96;0.000226)|all_hematologic(8;0.000885)|Prostate(109;0.00132)|Acute lymphoblastic leukemia(8;0.0167)|Myeloproliferative disorder(33;0.039)|Hepatocellular(98;0.0556)|Lung SC(185;0.102)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(144;2.1e-06)	Succinic acid(DB00139)	ATAGCACATTTAACACCTTCA	0.368													45	127	---	---	---	---	PASS
EDNRB	1910	broad.mit.edu	37	13	78472463	78472463	+	Missense_Mutation	SNP	A	C	C			TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:78472463A>C	uc001vko.2	-	7	1459	c.1201T>G	c.(1201-1203)TTA>GTA	p.L401V	EDNRB_uc001vkq.1_Missense_Mutation_p.L401V|uc001vkn.1_Intron|EDNRB_uc010aez.1_Intron|EDNRB_uc001vkp.1_Missense_Mutation_p.L484V	NM_001122659	NP_001116131	P24530	EDNRB_HUMAN	endothelin receptor type B isoform 1 precursor	401	Cytoplasmic (Potential).				activation of phospholipase C activity by G-protein coupled receptor protein signaling pathway coupled to IP3 second messenger|enteric nervous system development|enteric smooth muscle cell differentiation|macrophage chemotaxis|negative regulation of adenylate cyclase activity|negative regulation of cellular protein metabolic process|negative regulation of neuron maturation|negative regulation of transcription from RNA polymerase II promoter|vein smooth muscle contraction	integral to plasma membrane	endothelin-B receptor activity|peptide hormone binding				0		Acute lymphoblastic leukemia(28;0.0279)|Breast(118;0.037)		GBM - Glioblastoma multiforme(99;0.0933)	Bosentan(DB00559)	CAGCAGCATAAGCATGACTGT	0.403													15	56	---	---	---	---	PASS
ARHGEF7	8874	broad.mit.edu	37	13	111932908	111932908	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:111932908G>T	uc001vrs.2	+	16	1922	c.1672G>T	c.(1672-1674)GTG>TTG	p.V558L	ARHGEF7_uc001vrr.2_Missense_Mutation_p.V537L|ARHGEF7_uc001vrt.2_Missense_Mutation_p.V508L|ARHGEF7_uc010tjn.1_RNA|ARHGEF7_uc001vru.1_Missense_Mutation_p.V380L|ARHGEF7_uc001vrv.3_Missense_Mutation_p.V380L|ARHGEF7_uc001vrw.3_Missense_Mutation_p.V380L|ARHGEF7_uc001vrx.3_Missense_Mutation_p.V380L|ARHGEF7_uc010tjo.1_Missense_Mutation_p.V455L|ARHGEF7_uc010tjp.1_Missense_Mutation_p.V302L|ARHGEF7_uc001vry.1_5'Flank	NM_001113511	NP_001106983	Q14155	ARHG7_HUMAN	PAK-interacting exchange factor beta isoform c	558	PH.				apoptosis|epidermal growth factor receptor signaling pathway|induction of apoptosis by extracellular signals|negative regulation of epidermal growth factor receptor signaling pathway|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	protein binding|Rho guanyl-nucleotide exchange factor activity			ovary(2)|skin(2)|pancreas(1)|lung(1)|kidney(1)	7	all_lung(23;3.96e-05)|Lung NSC(43;0.00156)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Medulloblastoma(90;0.163)		BRCA - Breast invasive adenocarcinoma(86;0.188)			GCGGATATTAGTGTCGTGCAA	0.507													19	120	---	---	---	---	PASS
STRN3	29966	broad.mit.edu	37	14	31388314	31388314	+	Splice_Site	SNP	T	C	C			TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:31388314T>C	uc001wqu.2	-	9	1316	c.1100_splice	c.e9-1	p.R367_splice	STRN3_uc001wqv.2_Intron|STRN3_uc010tpj.1_Intron	NM_001083893	NP_001077362	Q13033	STRN3_HUMAN	nuclear autoantigen isoform 1						negative regulation of estrogen receptor signaling pathway|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|response to estradiol stimulus	cytoplasm|dendrite|Golgi apparatus|neuronal cell body|nucleoplasm|nucleus|plasma membrane|protein complex	armadillo repeat domain binding|calmodulin binding|protein complex binding|protein phosphatase 2A binding|sequence-specific DNA binding transcription factor activity				0	Hepatocellular(127;0.0877)|Breast(36;0.148)		LUAD - Lung adenocarcinoma(48;0.00192)|Lung(238;0.0119)|BRCA - Breast invasive adenocarcinoma(188;0.0805)	GBM - Glioblastoma multiforme(265;0.0124)		TGTTGGCCCCTGTAAATTAAT	0.423													4	185	---	---	---	---	PASS
EML1	2009	broad.mit.edu	37	14	100375765	100375765	+	Nonsense_Mutation	SNP	C	A	A			TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:100375765C>A	uc001ygs.2	+	11	1257	c.1188C>A	c.(1186-1188)TAC>TAA	p.Y396*	EML1_uc010avt.1_Nonsense_Mutation_p.Y383*|EML1_uc010tww.1_Nonsense_Mutation_p.Y384*|EML1_uc001ygq.2_Nonsense_Mutation_p.Y415*|EML1_uc001ygr.2_Nonsense_Mutation_p.Y415*	NM_004434	NP_004425	O00423	EMAL1_HUMAN	echinoderm microtubule associated protein like 1	396	WD 3.					cytoplasm|microtubule|microtubule associated complex	calcium ion binding|protein binding			large_intestine(2)|pancreas(1)|ovary(1)|skin(1)	5		Melanoma(154;0.0879)|all_epithelial(191;0.216)				CACATCTCTACTTTTGGACAC	0.378													18	119	---	---	---	---	PASS
ARHGAP11B	89839	broad.mit.edu	37	15	30938316	30938316	+	Splice_Site	SNP	G	A	A	rs112615235	by1000genomes	TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:30938316G>A	uc010azv.1	+	11		c.1127_splice	c.e11-1		ARHGAP11B_uc001zeu.2_Splice_Site			Q3KRB8	RHGBB_HUMAN	Homo sapiens cDNA, FLJ17072.						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity				0		all_lung(180;2.71e-09)|Breast(32;0.00116)		all cancers(64;1.9e-15)|Epithelial(43;3.59e-12)|GBM - Glioblastoma multiforme(186;9e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00177)|Lung(196;0.153)		TTCCTTGGCAGTGGATAAGTT	0.393													4	47	---	---	---	---	PASS
ARHGAP11B	89839	broad.mit.edu	37	15	30938483	30938483	+	RNA	SNP	T	C	C	rs145453249	by1000genomes	TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:30938483T>C	uc010azv.1	+	11		c.1293T>C			ARHGAP11B_uc001zeu.2_RNA			Q3KRB8	RHGBB_HUMAN	Homo sapiens cDNA, FLJ17072.						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity				0		all_lung(180;2.71e-09)|Breast(32;0.00116)		all cancers(64;1.9e-15)|Epithelial(43;3.59e-12)|GBM - Glioblastoma multiforme(186;9e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00177)|Lung(196;0.153)		CCACCAGGCTTCTCCTTTCCC	0.463													3	28	---	---	---	---	PASS
BAHD1	22893	broad.mit.edu	37	15	40758186	40758186	+	Missense_Mutation	SNP	A	C	C			TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:40758186A>C	uc001zlu.2	+	7	2271	c.2200A>C	c.(2200-2202)AAG>CAG	p.K734Q	BAHD1_uc001zlt.2_Missense_Mutation_p.K733Q|BAHD1_uc010bbp.1_Missense_Mutation_p.K730Q|BAHD1_uc001zlv.2_Missense_Mutation_p.K731Q	NM_014952	NP_055767	Q8TBE0	BAHD1_HUMAN	bromo adjacent homology domain containing 1	734	BAH.				heterochromatin formation|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromatin silencing complex|chromosome	chromatin binding|DNA binding|protein binding				0		all_cancers(109;8.28e-19)|all_epithelial(112;2.64e-15)|Lung NSC(122;5.14e-11)|all_lung(180;1.27e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;3.46e-06)|BRCA - Breast invasive adenocarcinoma(123;0.08)		CCCCAGCCGAAAGACAGCACT	0.587													38	109	---	---	---	---	PASS
TGM5	9333	broad.mit.edu	37	15	43533161	43533161	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43533161C>A	uc001zrd.1	-	7	898	c.890G>T	c.(889-891)CGT>CTT	p.R297L	TGM5_uc001zrc.1_5'Flank|TGM5_uc001zre.1_Missense_Mutation_p.R215L	NM_201631	NP_963925	O43548	TGM5_HUMAN	transglutaminase 5 isoform 1	297					epidermis development|peptide cross-linking	cytoplasm	acyltransferase activity|metal ion binding|protein-glutamine gamma-glutamyltransferase activity			central_nervous_system(1)	1		all_cancers(109;1.37e-14)|all_epithelial(112;1.26e-12)|Lung NSC(122;2.46e-08)|all_lung(180;2.75e-07)|Melanoma(134;0.0476)|Colorectal(260;0.216)		GBM - Glioblastoma multiforme(94;4e-07)	L-Glutamine(DB00130)	GGTGATCACACGGGTAGGGAT	0.478													14	72	---	---	---	---	PASS
WDR93	56964	broad.mit.edu	37	15	90286550	90286550	+	Missense_Mutation	SNP	G	C	C			TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:90286550G>C	uc002boj.2	+	17	2090	c.1989G>C	c.(1987-1989)GAG>GAC	p.E663D	WDR93_uc010bnr.2_Missense_Mutation_p.E635D|WDR93_uc010upz.1_Missense_Mutation_p.E380D	NM_020212	NP_064597	Q6P2C0	WDR93_HUMAN	WD repeat domain 93	663					electron transport chain	mitochondrial inner membrane	oxidoreductase activity, acting on NADH or NADPH			ovary(2)	2	Lung NSC(78;0.0237)|all_lung(78;0.0478)		KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|BRCA - Breast invasive adenocarcinoma(143;0.128)			AGAACCCAGAGAAGGAGGAGG	0.587													4	91	---	---	---	---	PASS
SULT1A2	6799	broad.mit.edu	37	16	28604874	28604874	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:28604874G>T	uc002dqg.1	-	5	739	c.388C>A	c.(388-390)CGC>AGC	p.R130S	uc010vct.1_Intron|SULT1A2_uc002dqh.1_Missense_Mutation_p.R130S	NM_177528	NP_803564	P50226	ST1A2_HUMAN	sulfotransferase family, cytosolic, 1A,	130	PAPS (By similarity).				3'-phosphoadenosine 5'-phosphosulfate metabolic process|amine biosynthetic process|catecholamine metabolic process|steroid metabolic process|sulfation|xenobiotic metabolic process	cytosol	aryl sulfotransferase activity|flavonol 3-sulfotransferase activity				0						TTTGCGTTGCGGGCAACATAG	0.527													3	62	---	---	---	---	PASS
ARHGEF15	22899	broad.mit.edu	37	17	8216716	8216716	+	Intron	SNP	G	C	C			TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8216716G>C	uc002glc.2	+						ARHGEF15_uc002glb.1_3'UTR|ARHGEF15_uc002gld.2_Intron|ARHGEF15_uc010vuw.1_Intron	NM_173728	NP_776089	O94989	ARHGF_HUMAN	Rho guanine exchange factor 15						negative regulation of synapse maturation|regulation of Rho protein signal transduction	dendrite|intracellular	GTPase activator activity|Rho guanyl-nucleotide exchange factor activity			ovary(2)|skin(1)	3						GCTGAAGAGAGTTGCAGTTTT	0.547													20	38	---	---	---	---	PASS
STAC2	342667	broad.mit.edu	37	17	37369246	37369246	+	Splice_Site	SNP	A	C	C			TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:37369246A>C	uc002hrs.2	-	10	1350	c.1131_splice	c.e10+1	p.Q377_splice	STAC2_uc010cvt.2_Splice_Site_p.Q235_splice	NM_198993	NP_945344	Q6ZMT1	STAC2_HUMAN	SH3 and cysteine rich domain 2						intracellular signal transduction		metal ion binding			pancreas(1)	1						TCAGGCACTCACCTGGTTCTC	0.632													19	73	---	---	---	---	PASS
SLC16A5	9121	broad.mit.edu	37	17	73096901	73096901	+	Silent	SNP	A	T	T			TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73096901A>T	uc002jmr.2	+	5	1515	c.1143A>T	c.(1141-1143)CCA>CCT	p.P381P	SLC16A5_uc002jms.1_Silent_p.P381P|SLC16A5_uc002jmt.2_Silent_p.P381P|SLC16A5_uc002jmu.2_Silent_p.P381P|SLC16A5_uc010wrt.1_Silent_p.P421P	NM_004695	NP_004686	O15375	MOT6_HUMAN	solute carrier family 16, member 5	381	Helical; (Potential).				organic anion transport	integral to plasma membrane|membrane fraction	secondary active monocarboxylate transmembrane transporter activity|symporter activity			central_nervous_system(1)	1	all_lung(278;0.226)		LUSC - Lung squamous cell carcinoma(166;0.162)|Lung(188;0.235)		Pyruvic acid(DB00119)	TCATCTCCCCACCACTGGCCG	0.577													9	37	---	---	---	---	PASS
FLJ35220	284131	broad.mit.edu	37	17	78409975	78409975	+	3'UTR	SNP	A	G	G	rs12939348	by1000genomes	TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:78409975A>G	uc002jym.1	+	11						NM_173627	NP_775898	Q8N8Q3	ENDOV_HUMAN	hypothetical protein LOC284131 isoform 1						DNA repair		endodeoxyribonuclease activity, producing 5'-phosphomonoesters|magnesium ion binding				0	all_neural(118;0.0538)		BRCA - Breast invasive adenocarcinoma(99;0.0232)|OV - Ovarian serous cystadenocarcinoma(97;0.0487)			tcctcgtctcattcctgatcG	0.269								Direct_reversal_of_damage|Editing_and_processing_nucleases					3	40	---	---	---	---	PASS
SMARCA4	6597	broad.mit.edu	37	19	11138623	11138623	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11138623G>T	uc002mqf.3	+	24	3663	c.3379G>T	c.(3379-3381)GAT>TAT	p.D1127Y	SMARCA4_uc010dxp.2_Missense_Mutation_p.D1127Y|SMARCA4_uc010dxo.2_Missense_Mutation_p.D1127Y|SMARCA4_uc002mqg.1_Missense_Mutation_p.D1127Y|SMARCA4_uc010dxq.2_Missense_Mutation_p.D1127Y|SMARCA4_uc010dxr.2_Missense_Mutation_p.D1127Y|SMARCA4_uc002mqj.3_Missense_Mutation_p.D1127Y|SMARCA4_uc010dxs.2_Missense_Mutation_p.D1127Y|SMARCA4_uc010dxt.1_Missense_Mutation_p.D347Y|SMARCA4_uc002mqh.3_Missense_Mutation_p.D250Y|SMARCA4_uc002mqi.1_Missense_Mutation_p.D330Y	NM_003072	NP_003063	P51532	SMCA4_HUMAN	SWI/SNF-related matrix-associated	1127	Helicase C-terminal.				chromatin remodeling|negative regulation of androgen receptor signaling pathway|negative regulation of cell growth|negative regulation of S phase of mitotic cell cycle|negative regulation of transcription from RNA polymerase II promoter|nervous system development|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nBAF complex|npBAF complex|nuclear chromatin|SWI/SNF complex|WINAC complex	androgen receptor binding|ATP binding|DNA binding|DNA-dependent ATPase activity|helicase activity|histone acetyl-lysine binding|identical protein binding|p53 binding|protein N-terminus binding|transcription corepressor activity	p.?(2)		lung(29)|ovary(8)|pancreas(7)|large_intestine(5)|central_nervous_system(5)|skin(3)|prostate(3)|breast(2)|adrenal_gland(1)|stomach(1)|liver(1)|autonomic_ganglia(1)|kidney(1)	67		all_lung(6;0.0512)|Lung NSC(9;0.0568)				CCTCAGGCTTGATGGTGAGTA	0.507			F|N|Mis		NSCLC				Rhabdoid_Predisposition_syndrome				13	163	---	---	---	---	PASS
ZNF180	7733	broad.mit.edu	37	19	45001414	45001414	+	Silent	SNP	G	T	T			TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45001414G>T	uc002ozf.3	-	2	336	c.54C>A	c.(52-54)CTC>CTA	p.L18L	ZNF180_uc002ozh.3_5'UTR|ZNF180_uc002ozi.3_5'UTR|ZNF180_uc002ozg.3_Silent_p.L17L|ZNF180_uc010ejm.2_Silent_p.L18L	NM_013256	NP_037388	Q9UJW8	ZN180_HUMAN	zinc finger protein 180	18					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2		Prostate(69;0.0435)				GCAGGGTGCTGAGGTCCTGAG	0.632													3	39	---	---	---	---	PASS
GRLF1	2909	broad.mit.edu	37	19	47422608	47422608	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47422608G>A	uc010ekv.2	+	1	676	c.676G>A	c.(676-678)GTG>ATG	p.V226M		NM_004491	NP_004482	Q9NRY4	RHG35_HUMAN	glucocorticoid receptor DNA binding factor 1	226					axon guidance|negative regulation of transcription, DNA-dependent|small GTPase mediated signal transduction|transcription, DNA-dependent	cytosol	DNA binding|Rho GTPase activator activity|transcription corepressor activity			central_nervous_system(1)	1		all_cancers(25;1.51e-09)|all_epithelial(76;1.87e-07)|all_lung(116;7.86e-06)|Lung NSC(112;2.31e-05)|Ovarian(192;0.0129)|all_neural(266;0.026)|Breast(70;0.077)		all cancers(93;2.03e-05)|OV - Ovarian serous cystadenocarcinoma(262;2.57e-05)|Epithelial(262;0.00135)|GBM - Glioblastoma multiforme(486;0.0289)		CCTCCAGGTTGTGGAGACCTC	0.443													7	75	---	---	---	---	PASS
ZNF611	81856	broad.mit.edu	37	19	53208387	53208387	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53208387G>A	uc002pzz.2	-	7	2238	c.1921C>T	c.(1921-1923)CGT>TGT	p.R641C	ZNF611_uc010eqc.2_Missense_Mutation_p.R571C|ZNF611_uc010ydo.1_Missense_Mutation_p.R571C|ZNF611_uc010ydr.1_Missense_Mutation_p.R572C|ZNF611_uc010ydp.1_Missense_Mutation_p.R641C|ZNF611_uc010ydq.1_Missense_Mutation_p.R641C|ZNF611_uc002qaa.3_Missense_Mutation_p.R571C	NM_030972	NP_112234	Q8N823	ZN611_HUMAN	zinc finger protein 611 isoform a	641	C2H2-type 15.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(262;0.0233)|GBM - Glioblastoma multiforme(134;0.04)		TGAAGTCTACGATGGTATATA	0.418													8	272	---	---	---	---	PASS
ProSAPiP1	9762	broad.mit.edu	37	20	3146916	3146916	+	Missense_Mutation	SNP	T	A	A			TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3146916T>A	uc002wia.1	-	2	1948	c.550A>T	c.(550-552)AAT>TAT	p.N184Y	ProSAPiP1_uc002wib.1_Missense_Mutation_p.N184Y	NM_014731	NP_055546	O60299	PRIP1_HUMAN	ProSAPiP1 protein	184						cell junction|cytoplasm|postsynaptic density|postsynaptic membrane				pancreas(1)	1						GGAGTCCCATTGGTCTGCGGG	0.607													7	24	---	---	---	---	PASS
NCAM2	4685	broad.mit.edu	37	21	22664427	22664427	+	Missense_Mutation	SNP	G	C	C			TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:22664427G>C	uc002yld.1	+	5	734	c.485G>C	c.(484-486)CGG>CCG	p.R162P	NCAM2_uc011acb.1_Missense_Mutation_p.R20P|NCAM2_uc011acc.1_Missense_Mutation_p.R187P	NM_004540	NP_004531	O15394	NCAM2_HUMAN	neural cell adhesion molecule 2 precursor	162	Ig-like C2-type 2.|Extracellular (Potential).				neuron cell-cell adhesion	integral to membrane|plasma membrane				ovary(4)	4		Lung NSC(9;0.195)		all cancers(11;0.00102)|OV - Ovarian serous cystadenocarcinoma(11;0.00121)|Epithelial(23;0.00147)|Colorectal(24;0.174)		TTTCCAGATCGGTTCGCTATG	0.398													17	94	---	---	---	---	PASS
ADAMTS5	11096	broad.mit.edu	37	21	28296852	28296852	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:28296852G>T	uc002ymg.2	-	8	3042	c.2313C>A	c.(2311-2313)TTC>TTA	p.F771L		NM_007038	NP_008969	Q9UNA0	ATS5_HUMAN	ADAM metallopeptidase with thrombospondin type 1	771	Spacer.				proteolysis	proteinaceous extracellular matrix	integrin binding|metalloendopeptidase activity|zinc ion binding			upper_aerodigestive_tract(2)|ovary(1)|pancreas(1)	4						AATAGGCAGTGAATCTAGTCT	0.428													43	152	---	---	---	---	PASS
GGT3P	2679	broad.mit.edu	37	22	18778601	18778601	+	RNA	SNP	C	T	T			TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:18778601C>T	uc011ago.1	-	2		c.219G>A			GGT3P_uc011agp.1_RNA|GGT3P_uc002zob.1_RNA					Homo sapiens cDNA clone IMAGE:5761295, **** WARNING: chimeric clone ****.												0						GCTTGGCATCCGCGGCCACGG	0.552													5	10	---	---	---	---	PASS
LOC96610	96610	broad.mit.edu	37	22	22663086	22663086	+	RNA	SNP	T	G	G	rs1054157	by1000genomes	TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:22663086T>G	uc011aim.1	+	29		c.1859T>G			LOC96610_uc011aiq.1_RNA|LOC96610_uc011aip.1_RNA|LOC96610_uc010gto.2_RNA					Parts of antibodies, mostly variable regions.												0						AGCTGCCACATAAGTTGTCCT	0.299													4	37	---	---	---	---	PASS
ADRBK2	157	broad.mit.edu	37	22	26105967	26105967	+	Intron	SNP	C	T	T			TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:26105967C>T	uc003abx.3	+						ADRBK2_uc010gux.2_3'UTR|ADRBK2_uc003abw.2_Intron|ADRBK2_uc003aby.3_Intron	NM_005160	NP_005151	P35626	ARBK2_HUMAN	beta-adrenergic receptor kinase 2								ATP binding|beta-adrenergic receptor kinase activity|signal transducer activity			lung(3)|ovary(2)|stomach(1)|central_nervous_system(1)	7					Adenosine triphosphate(DB00171)	TACGGTACTGCCGCCCCGCCC	0.463													8	538	---	---	---	---	PASS
TCN2	6948	broad.mit.edu	37	22	31010337	31010337	+	Silent	SNP	G	A	A			TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:31010337G>A	uc003aip.1	+	4	587	c.429G>A	c.(427-429)GGG>GGA	p.G143G	TCN2_uc003aiq.1_Silent_p.G139G|TCN2_uc003air.1_Nonsense_Mutation_p.W116*	NM_000355	NP_000346	P20062	TCO2_HUMAN	transcobalamin II precursor	143					cobalamin metabolic process|cobalamin transport|cobalt ion transport	extracellular space	cobalamin binding			central_nervous_system(1)	1					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	CCCTCTCAGGGCATGATCACA	0.622													3	37	---	---	---	---	PASS
TCN2	6948	broad.mit.edu	37	22	31018990	31018990	+	Nonsense_Mutation	SNP	T	A	A			TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:31018990T>A	uc003aip.1	+	8	1300	c.1142T>A	c.(1141-1143)TTA>TAA	p.L381*	TCN2_uc003aiq.1_Nonsense_Mutation_p.L377*|TCN2_uc003air.1_Nonsense_Mutation_p.L354*	NM_000355	NP_000346	P20062	TCO2_HUMAN	transcobalamin II precursor	381					cobalamin metabolic process|cobalamin transport|cobalt ion transport	extracellular space	cobalamin binding			central_nervous_system(1)	1					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	GGCCCCTACTTAACCTCCGTG	0.562													18	64	---	---	---	---	PASS
CSNK1E	1454	broad.mit.edu	37	22	38698909	38698909	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38698909C>T	uc003avj.2	-	4	554	c.293G>A	c.(292-294)CGC>CAC	p.R98H	CSNK1E_uc003avk.2_Missense_Mutation_p.R98H|CSNK1E_uc003avl.1_RNA|CSNK1E_uc003avm.1_Missense_Mutation_p.R98H|CSNK1E_uc003avo.2_Missense_Mutation_p.R98H|CSNK1E_uc003avp.1_Missense_Mutation_p.R98H|CSNK1E_uc003avq.1_Missense_Mutation_p.R98H|LOC400927_uc010gxm.2_RNA	NM_152221	NP_689407	P49674	KC1E_HUMAN	casein kinase 1 epsilon	98	Protein kinase.				DNA repair|G2/M transition of mitotic cell cycle|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|signal transduction	cytosol|nucleus	ATP binding|protein binding|protein serine/threonine kinase activity			ovary(1)|lung(1)|central_nervous_system(1)	3	Melanoma(58;0.045)					GCTGAATTTGCGGGAACAGAA	0.612													4	101	---	---	---	---	PASS
ACE2	59272	broad.mit.edu	37	X	15609842	15609842	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:15609842C>T	uc004cxa.1	-	4	745	c.577G>A	c.(577-579)GCA>ACA	p.A193T	ACE2_uc004cxb.2_Missense_Mutation_p.A193T	NM_021804	NP_068576	Q9BYF1	ACE2_HUMAN	angiotensin I converting enzyme 2 precursor	193	Extracellular (Potential).				angiotensin-mediated drinking behavior|proteolysis|receptor biosynthetic process|regulation of cell proliferation|virion attachment, binding of host cell surface receptor	cell surface|extracellular space|integral to membrane|membrane raft|plasma membrane	carboxypeptidase activity|glycoprotein binding|metallopeptidase activity|peptidyl-dipeptidase activity|viral receptor activity|zinc ion binding			ovary(3)	3	Hepatocellular(33;0.183)				Moexipril(DB00691)	TTACGATTTGCTCTTGCCATC	0.493													4	214	---	---	---	---	PASS
PPEF1	5475	broad.mit.edu	37	X	18836175	18836175	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:18836175C>A	uc004cyq.2	+	16	1894	c.1413C>A	c.(1411-1413)AAC>AAA	p.N471K	PPEF1_uc004cyp.2_Missense_Mutation_p.N443K|PPEF1_uc004cyr.2_Missense_Mutation_p.N409K|PPEF1_uc004cys.2_Missense_Mutation_p.N471K|PPEF1_uc011mja.1_Missense_Mutation_p.N406K|PPEF1_uc011mjb.1_Missense_Mutation_p.N415K	NM_006240	NP_006231	O14829	PPE1_HUMAN	protein phosphatase with EF hand calcium-binding	471					detection of stimulus involved in sensory perception|protein dephosphorylation		calcium ion binding|iron ion binding|manganese ion binding|protein binding|protein serine/threonine phosphatase activity				0	Hepatocellular(33;0.183)					CTATGGAAAACAGCGCCATCA	0.328													5	67	---	---	---	---	PASS
IGSF1	3547	broad.mit.edu	37	X	130409627	130409627	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:130409627G>T	uc004ewd.2	-	16	3247	c.3009C>A	c.(3007-3009)CAC>CAA	p.H1003Q	IGSF1_uc004ewe.3_Missense_Mutation_p.H997Q|IGSF1_uc004ewf.2_Missense_Mutation_p.H983Q	NM_001555	NP_001546	Q8N6C5	IGSF1_HUMAN	immunoglobulin superfamily, member 1 isoform 1	1003	Extracellular (Potential).|Ig-like C2-type 10.				regulation of transcription, DNA-dependent	extracellular region|integral to membrane	inhibin beta-A binding|inhibin beta-B binding			ovary(3)|lung(1)|central_nervous_system(1)	5						CTCCTTCTTTGTGCAGAATGT	0.527													8	79	---	---	---	---	PASS
FAM131C	348487	broad.mit.edu	37	1	16386305	16386306	+	Intron	INS	-	C	C	rs143272992		TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16386305_16386306insC	uc001axz.3	-						FAM131C_uc010obz.1_Intron	NM_182623	NP_872429	Q96AQ9	F131C_HUMAN	hypothetical protein LOC348487												0		Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Colorectal(212;8.32e-08)|COAD - Colon adenocarcinoma(227;5.56e-06)|BRCA - Breast invasive adenocarcinoma(304;9.12e-05)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.00656)|READ - Rectum adenocarcinoma(331;0.0649)		AGTGATCTGGGCCCCCAAGGAC	0.599													2	9	---	---	---	---	
EXTL1	2134	broad.mit.edu	37	1	26357179	26357179	+	Intron	DEL	C	-	-			TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:26357179delC	uc001blf.2	+							NM_004455	NP_004446	Q92935	EXTL1_HUMAN	exostoses-like 1						skeletal system development	integral to membrane|intrinsic to endoplasmic reticulum membrane	glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity|protein binding			central_nervous_system(1)	1		Colorectal(325;3.46e-05)|Lung NSC(340;6.18e-05)|all_lung(284;9.43e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0155)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0298)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;6.44e-26)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|BRCA - Breast invasive adenocarcinoma(304;0.000954)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.00594)|READ - Rectum adenocarcinoma(331;0.0649)		GTTTGGGGAACCCCCCCCCCT	0.388													9	4	---	---	---	---	
FAM183A	440585	broad.mit.edu	37	1	43613850	43613851	+	Intron	INS	-	A	A	rs142077481	by1000genomes	TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:43613850_43613851insA	uc009vwo.2	+							NM_001101376	NP_001094846	A6NL82	F183A_HUMAN	hCG23177											ovary(3)	3						GCGGTCCCAGCAAAAACTCTTT	0.455													5	5	---	---	---	---	
NUP133	55746	broad.mit.edu	37	1	229631436	229631436	+	Intron	DEL	A	-	-			TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:229631436delA	uc001htn.2	-							NM_018230	NP_060700	Q8WUM0	NU133_HUMAN	nucleoporin 133kDa						carbohydrate metabolic process|glucose transport|mitotic prometaphase|mRNA export from nucleus|nuclear pore organization|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	condensed chromosome kinetochore|cytosol|Nup107-160 complex	nucleocytoplasmic transporter activity|protein binding			breast(4)|skin(2)|ovary(1)	7	Breast(184;0.104)|Ovarian(103;0.249)	Prostate(94;0.167)				TGTATACATTAAAAAAAAAAT	0.169													5	3	---	---	---	---	
RYR2	6262	broad.mit.edu	37	1	237955699	237955700	+	Intron	DEL	GT	-	-	rs112375793		TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:237955699_237955700delGT	uc001hyl.1	+						RYR2_uc010pyb.1_Intron	NM_001035	NP_001026	Q92736	RYR2_HUMAN	cardiac muscle ryanodine receptor						cardiac muscle contraction|detection of calcium ion|induction of apoptosis by ionic changes|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum|response to caffeine|response to hypoxia|response to redox state	calcium channel complex|cytosol|plasma membrane|plasma membrane enriched fraction|sarcoplasmic reticulum membrane	calcium ion binding|calmodulin binding|identical protein binding|protein kinase A catalytic subunit binding|protein kinase A regulatory subunit binding|receptor activity|ryanodine-sensitive calcium-release channel activity|suramin binding			ovary(17)|large_intestine(6)|central_nervous_system(6)|pancreas(3)|breast(1)	33	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			gtgtgtgtgcgtgtgtgtgtgt	0.104													4	2	---	---	---	---	
C2orf63	130162	broad.mit.edu	37	2	55403284	55403285	+	Intron	INS	-	TCA	TCA	rs137945910	by1000genomes	TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:55403284_55403285insTCA	uc002ryi.2	-						C2orf63_uc002ryh.2_Intron|C2orf63_uc002ryj.2_Intron	NM_152385	NP_689598	Q8NHS4	CB063_HUMAN	hypothetical protein LOC130162 isoform 1								binding			ovary(2)|central_nervous_system(1)	3			LUSC - Lung squamous cell carcinoma(58;0.179)|Lung(47;0.189)			CTCAGTCAAGCTCATGGTAAGT	0.381													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	71004413	71004414	+	IGR	INS	-	A	A	rs55926232		TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:71004413_71004414insA								ADD2 (9084 upstream) : FIGLA (28 downstream)																							aactctatctcaaaaaaaaaaa	0.163													2	4	---	---	---	---	
RGPD1	400966	broad.mit.edu	37	2	87205188	87205189	+	Intron	INS	-	T	T			TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:87205188_87205189insT	uc010fgv.2	+						RMND5A_uc002srs.3_Intron|RGPD1_uc002ssb.2_Intron|RGPD1_uc002ssc.2_Intron	NM_001024457	NP_001019628	Q68DN6	RGPD1_HUMAN	RANBP2-like and GRIP domain containing 1						intracellular transport		binding				0						ACATTTTGGTCttttttttttt	0.233													5	4	---	---	---	---	
LIMS1	3987	broad.mit.edu	37	2	109297018	109297021	+	Intron	DEL	AAAG	-	-	rs59337195		TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:109297018_109297021delAAAG	uc002teg.2	+						LIMS1_uc002tef.2_Intron|LIMS1_uc002teh.2_Intron|LIMS1_uc002tei.2_Intron|LIMS1_uc002tej.2_Intron|LIMS1_uc002tek.3_Intron	NM_004987	NP_004978	P48059	LIMS1_HUMAN	LIM and senescent cell antigen-like domains 1						cell aging|cell junction assembly|cellular response to transforming growth factor beta stimulus|negative regulation of transcription, DNA-dependent	cytosol|focal adhesion|perinuclear region of cytoplasm	protein binding|zinc ion binding				0						aaaaaaaaaaaaaGGTTCTTGAGA	0.230													3	3	---	---	---	---	
RANBP2	5903	broad.mit.edu	37	2	109369249	109369249	+	Intron	DEL	A	-	-			TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:109369249delA	uc002tem.3	+							NM_006267	NP_006258	P49792	RBP2_HUMAN	RAN binding protein 2						carbohydrate metabolic process|glucose transport|mitotic prometaphase|mRNA transport|protein folding|protein import into nucleus|regulation of glucose transport|transmembrane transport|viral reproduction	cytosol|nuclear pore	peptidyl-prolyl cis-trans isomerase activity|Ran GTPase binding|zinc ion binding		RANBP2/ALK(16)	soft_tissue(16)|lung(1)|pancreas(1)	18						actctgtctcaaaaaaaaaaa	0.144													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	161905590	161905590	+	IGR	DEL	G	-	-	rs197266	by1000genomes	TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:161905590delG								RBMS1 (555272 upstream) : TANK (87876 downstream)																							ATTGTCCCCCGACGATGAACA	0.468													4	2	---	---	---	---	
C2orf80	389073	broad.mit.edu	37	2	209047928	209047928	+	Intron	DEL	T	-	-			TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:209047928delT	uc002vcr.2	-							NM_001099334	NP_001092804	Q0P641	CB080_HUMAN	hypothetical protein LOC389073											skin(1)	1						CTCGGCCAGATTTTTTTTTTT	0.403													3	3	---	---	---	---	
C3orf17	25871	broad.mit.edu	37	3	112727000	112727000	+	Intron	DEL	T	-	-			TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:112727000delT	uc003dzr.2	-						GTPBP8_uc011bhy.1_Intron|C3orf17_uc003dzq.2_Intron|C3orf17_uc011bhz.1_Intron|C3orf17_uc010hqh.2_Intron|C3orf17_uc003dzt.2_Intron|C3orf17_uc003dzs.2_Intron|C3orf17_uc010hqg.2_Intron|C3orf17_uc011bia.1_Intron|C3orf17_uc003dzu.2_Intron|C3orf17_uc011bib.1_Intron|C3orf17_uc011bic.1_Intron|C3orf17_uc011bid.1_Intron	NM_015412	NP_056227	Q6NW34	CC017_HUMAN	hypothetical protein LOC25871							integral to membrane					0						AGTAACATAATTTTTGCAATA	0.383													60	31	---	---	---	---	
ITGB5	3693	broad.mit.edu	37	3	124484906	124484907	+	Intron	INS	-	AA	AA			TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:124484906_124484907insAA	uc003eho.2	-						ITGB5_uc010hrx.2_Intron	NM_002213	NP_002204	P18084	ITB5_HUMAN	integrin, beta 5 precursor						cell-matrix adhesion|integrin-mediated signaling pathway|multicellular organismal development|muscle contraction	integrin complex	receptor activity			skin(2)	2				GBM - Glioblastoma multiforme(114;0.163)		cagcctgtgtcaaaaaaaaaaa	0.193													8	5	---	---	---	---	
CPNE4	131034	broad.mit.edu	37	3	131256128	131256128	+	Intron	DEL	T	-	-			TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:131256128delT	uc003eok.2	-						CPNE4_uc011blq.1_Intron|CPNE4_uc003eol.2_Intron|CPNE4_uc003eom.2_Intron|CPNE4_uc003eoj.2_Intron	NM_130808	NP_570720	Q96A23	CPNE4_HUMAN	copine IV											upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	3						ttcttttctgttttttttttt	0.169													4	2	---	---	---	---	
WDR19	57728	broad.mit.edu	37	4	39216394	39216394	+	Intron	DEL	T	-	-			TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:39216394delT	uc003gtv.2	+						WDR19_uc010ifl.1_Intron|WDR19_uc003gtu.1_Intron|WDR19_uc011byi.1_Intron|WDR19_uc003gtw.1_5'Flank	NM_025132	NP_079408	Q8NEZ3	WDR19_HUMAN	WD repeat domain 19						cell projection organization	microtubule basal body|motile cilium|photoreceptor connecting cilium	binding			large_intestine(1)	1						GGAGGAATAAttttttttttt	0.169													8	4	---	---	---	---	
UGDH	7358	broad.mit.edu	37	4	39505927	39505928	+	Intron	INS	-	A	A			TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:39505927_39505928insA	uc003guk.1	-						UGDH_uc011byp.1_Intron|UGDH_uc003gul.1_Intron	NM_003359	NP_003350	O60701	UGDH_HUMAN	UDP-glucose dehydrogenase						glycosaminoglycan biosynthetic process|UDP-glucose metabolic process|UDP-glucuronate biosynthetic process|xenobiotic metabolic process	cytosol	electron carrier activity|NAD binding|UDP-glucose 6-dehydrogenase activity			large_intestine(1)|ovary(1)|central_nervous_system(1)|skin(1)	4					NADH(DB00157)	gactccatctcaaaaaaaaaaa	0.139													6	3	---	---	---	---	
MTNR1A	4543	broad.mit.edu	37	4	187455865	187455865	+	Intron	DEL	G	-	-	rs66503366		TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:187455865delG	uc003izd.1	-							NM_005958	NP_005949	P48039	MTR1A_HUMAN	melatonin receptor 1A						circadian rhythm|G-protein signaling, coupled to cyclic nucleotide second messenger|mating behavior	integral to plasma membrane	melatonin receptor activity			ovary(1)|skin(1)|breast(1)|central_nervous_system(1)|pancreas(1)	5		all_cancers(14;6.39e-56)|all_epithelial(14;1.48e-41)|all_lung(41;2.45e-15)|Lung NSC(41;7.26e-15)|Melanoma(20;1.91e-06)|Hepatocellular(41;0.00335)|Prostate(90;0.00996)|all_hematologic(60;0.014)|Colorectal(36;0.0161)|Renal(120;0.0183)|all_neural(102;0.202)		OV - Ovarian serous cystadenocarcinoma(60;7.63e-12)|BRCA - Breast invasive adenocarcinoma(30;6.68e-07)|GBM - Glioblastoma multiforme(59;3.44e-05)|LUSC - Lung squamous cell carcinoma(40;0.000106)|STAD - Stomach adenocarcinoma(60;0.000279)|READ - Rectum adenocarcinoma(43;0.159)	Melatonin(DB01065)|Ramelteon(DB00980)	TTTCCCAGGAGGGCCAGTCCA	0.552													2	5	---	---	---	---	
MDN1	23195	broad.mit.edu	37	6	90489787	90489788	+	Intron	INS	-	A	A			TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90489787_90489788insA	uc003pnn.1	-						MDN1_uc003pno.1_Intron	NM_014611	NP_055426	Q9NU22	MDN1_HUMAN	MDN1, midasin homolog						protein complex assembly|regulation of protein complex assembly	nucleus	ATP binding|ATPase activity|unfolded protein binding			ovary(8)|skin(2)	10		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)		gacttcgtctcaaaaaaaaaaa	0.129													4	2	---	---	---	---	
SMOC2	64094	broad.mit.edu	37	6	168948021	168948021	+	Intron	DEL	A	-	-	rs67307076		TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:168948021delA	uc003qws.1	+						SMOC2_uc003qwr.1_Intron	NM_022138	NP_071421	Q9H3U7	SMOC2_HUMAN	SPARC related modular calcium binding 2						signal transduction	basement membrane	calcium ion binding			ovary(1)	1		Breast(66;0.000141)|Esophageal squamous(34;0.222)|Ovarian(120;0.231)		OV - Ovarian serous cystadenocarcinoma(33;1.31e-19)|BRCA - Breast invasive adenocarcinoma(81;3.06e-06)|GBM - Glioblastoma multiforme(31;0.00109)		gaatctctttaaaaaaaacaa	0.070													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	57929445	57929445	+	IGR	DEL	A	-	-			TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57929445delA								ZNF716 (396180 upstream) : None (None downstream)																							ACAAGAGACTAGGGGGATAAG	0.403													4	3	---	---	---	---	
WDR91	29062	broad.mit.edu	37	7	134880706	134880706	+	Intron	DEL	A	-	-			TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:134880706delA	uc003vsp.2	-						WDR91_uc010lmq.2_Intron|WDR91_uc010lmr.2_Intron	NM_014149	NP_054868	A4D1P6	WDR91_HUMAN	WD repeat domain 91											breast(2)|ovary(1)|skin(1)	4						ctcaataaggaaaaaaaaaaa	0.274													4	2	---	---	---	---	
TTC26	79989	broad.mit.edu	37	7	138857969	138857969	+	Intron	DEL	A	-	-			TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:138857969delA	uc003vus.2	+						TTC26_uc011kqn.1_Intron|TTC26_uc011kqo.1_Intron|TTC26_uc011kqp.1_Intron|TTC26_uc003vut.2_Intron|TTC26_uc011kqq.1_Intron	NM_024926	NP_079202	A0AVF1	TTC26_HUMAN	tetratricopeptide repeat domain 26 isoform 1								binding			ovary(1)	1						GTACAAAGTCACCtttttttt	0.214													6	4	---	---	---	---	
CTAGE4	100128553	broad.mit.edu	37	7	143883003	143883003	+	3'UTR	DEL	G	-	-			TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:143883003delG	uc010lpc.2	+	1						NM_198495	NP_940897	Q8IX94	CTGE4_HUMAN	CTAGE family, member 4							integral to membrane					0						CAGAACCACAGCAAGAAACCT	0.408													4	2	---	---	---	---	
SMC5	23137	broad.mit.edu	37	9	72933303	72933303	+	Intron	DEL	A	-	-			TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:72933303delA	uc004ahr.2	+						uc004ahs.1_5'Flank	NM_015110	NP_055925	Q8IY18	SMC5_HUMAN	SMC5 protein						DNA recombination|DNA repair	chromosome|nucleus	ATP binding			ovary(2)|central_nervous_system(1)	3						gaccctgtctaaaaaaaaaaa	0.100													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	86535359	86535360	+	IGR	INS	-	TT	TT	rs138295367	by1000genomes	TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:86535359_86535360insTT								FAM190B (257083 upstream) : GRID1 (823952 downstream)																							cgctctttttctttttcttttt	0.000													5	5	---	---	---	---	
BTAF1	9044	broad.mit.edu	37	10	93702042	93702043	+	Intron	INS	-	A	A			TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:93702042_93702043insA	uc001khr.2	+						BTAF1_uc009xua.1_Intron	NM_003972	NP_003963	O14981	BTAF1_HUMAN	BTAF1 RNA polymerase II, B-TFIID transcription						negative regulation of transcription, DNA-dependent	nucleus	ATP binding|DNA binding|helicase activity|sequence-specific DNA binding transcription factor activity			ovary(1)|central_nervous_system(1)|skin(1)	3		Colorectal(252;0.0846)				cctcacttcttaaaaaaaaaaG	0.109													6	4	---	---	---	---	
TCTN3	26123	broad.mit.edu	37	10	97452525	97452526	+	Intron	INS	-	T	T			TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:97452525_97452526insT	uc001klb.3	-						TCTN3_uc001kla.3_Intron|TCTN3_uc010qoi.1_Intron|TCTN3_uc001kld.2_Intron|TCTN3_uc009xux.1_Intron|TCTN3_uc009xuy.1_Intron	NM_015631	NP_056446	Q6NUS6	TECT3_HUMAN	tectonic 3 isoform a precursor						apoptosis	integral to membrane					0		Colorectal(252;0.0815)		Epithelial(162;1.69e-07)|all cancers(201;5.63e-06)		attttttttgctttttttttgt	0.000													4	2	---	---	---	---	
WDR11	55717	broad.mit.edu	37	10	122619467	122619468	+	Intron	DEL	AC	-	-	rs3217470		TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:122619467_122619468delAC	uc010qtf.1	+						WDR11_uc010qte.1_Intron|WDR11_uc001lfd.1_Intron	NM_018117	NP_060587	Q9BZH6	WDR11_HUMAN	bromodomain and WD repeat domain containing 2							integral to membrane					0						GAATATTGATacacacacacac	0.238													3	7	---	---	---	---	
FNBP4	23360	broad.mit.edu	37	11	47768071	47768072	+	Intron	INS	-	T	T			TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47768071_47768072insT	uc009ylv.2	-						FNBP4_uc001ngj.2_Intron|FNBP4_uc001ngl.2_Intron	NM_015308	NP_056123	Q8N3X1	FNBP4_HUMAN	formin binding protein 4											ovary(1)	1						GTAAAAACGACttttttttttt	0.168													4	2	---	---	---	---	
ANO1	55107	broad.mit.edu	37	11	69995756	69995756	+	Intron	DEL	A	-	-	rs72410022		TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:69995756delA	uc001opj.2	+						ANO1_uc001opk.1_Intron|ANO1_uc001opl.1_Intron|ANO1_uc010rqk.1_Intron	NM_018043	NP_060513	Q5XXA6	ANO1_HUMAN	anoctamin 1, calcium activated chloride channel						multicellular organismal development	chloride channel complex|cytoplasm|plasma membrane	intracellular calcium activated chloride channel activity			ovary(1)|pancreas(1)	2						aactctgtctaaaaaaaaaaa	0.234													3	3	---	---	---	---	
DLAT	1737	broad.mit.edu	37	11	111897029	111897029	+	Intron	DEL	T	-	-	rs113392665		TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:111897029delT	uc001pmo.2	+						DLAT_uc009yyk.1_Intron|DLAT_uc010rwr.1_Intron	NM_001931	NP_001922	P10515	ODP2_HUMAN	dihydrolipoamide S-acetyltransferase precursor						glycolysis|regulation of acetyl-CoA biosynthetic process from pyruvate	mitochondrial pyruvate dehydrogenase complex	dihydrolipoyllysine-residue acetyltransferase activity|protein binding				0		all_cancers(61;4.53e-11)|all_epithelial(67;2.76e-06)|Melanoma(852;9.42e-06)|all_hematologic(158;0.000885)|Acute lymphoblastic leukemia(157;0.000966)|Breast(348;0.0512)|Medulloblastoma(222;0.0523)|all_neural(223;0.0663)		Epithelial(105;4.87e-07)|BRCA - Breast invasive adenocarcinoma(274;6.83e-07)|all cancers(92;9.63e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.0557)	NADH(DB00157)	CAGAGGTAAGttttttttttt	0.244													8	4	---	---	---	---	
IQSEC3	440073	broad.mit.edu	37	12	271387	271387	+	Intron	DEL	T	-	-	rs66703624		TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:271387delT	uc001qhw.1	+						IQSEC3_uc001qhu.1_Intron	NM_015232	NP_056047	Q9UPP2	IQEC3_HUMAN	IQ motif and Sec7 domain 3						regulation of ARF protein signal transduction	cytoplasm	ARF guanyl-nucleotide exchange factor activity			central_nervous_system(2)|large_intestine(1)|skin(1)	4	all_cancers(10;0.016)|all_lung(10;0.0222)|all_epithelial(11;0.0262)|Lung NSC(10;0.031)		OV - Ovarian serous cystadenocarcinoma(31;0.00456)	LUAD - Lung adenocarcinoma(1;0.172)|Lung(1;0.179)		actgCATCTCTTTTTTTTTTT	0.189													4	2	---	---	---	---	
SLCO1B3	28234	broad.mit.edu	37	12	20997962	20997964	+	Intron	DEL	AAA	-	-	rs36120748		TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:20997962_20997964delAAA	uc001rek.2	+						SLCO1B3_uc001rel.2_Intron|SLCO1B3_uc010sil.1_Intron|LST-3TM12_uc010sim.1_Intron	NM_019844	NP_062818	Q9NPD5	SO1B3_HUMAN	solute carrier organic anion transporter family,						bile acid metabolic process|sodium-independent organic anion transport	basolateral plasma membrane|cytoplasm|integral to plasma membrane	bile acid transmembrane transporter activity|organic anion transmembrane transporter activity			large_intestine(2)|ovary(1)|skin(1)	4	Esophageal squamous(101;0.149)					agactgtctcaaaaaaaaaaaaa	0.172													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	80632597	80632598	+	IGR	DEL	TG	-	-			TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:80632597_80632598delTG								PPP1R12A (303362 upstream) : PTPRQ (205528 downstream)																							TACACCTATTtgtgtgtgtgtg	0.302													5	3	---	---	---	---	
FSD2	123722	broad.mit.edu	37	15	83438317	83438318	+	Intron	INS	-	A	A	rs71455426		TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:83438317_83438318insA	uc002bjd.2	-						FSD2_uc010uol.1_Intron|FSD2_uc010uom.1_Intron	NM_001007122	NP_001007123	A1L4K1	FSD2_HUMAN	fibronectin type III and SPRY domain containing											central_nervous_system(1)	1						ggactcatctcaaaaaaaaaaa	0.149													5	3	---	---	---	---	
AGBL1	123624	broad.mit.edu	37	15	87089452	87089453	+	Intron	INS	-	T	T	rs66611676		TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:87089452_87089453insT	uc002blz.1	+							NM_152336	NP_689549	Q96MI9	CBPC4_HUMAN	ATP/GTP binding protein-like 1						C-terminal protein deglutamylation|protein side chain deglutamylation|proteolysis	cytosol	metallocarboxypeptidase activity|tubulin binding|zinc ion binding				0						CATTTATTTAGTTTTTTTTTTT	0.356													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	102292874	102292876	+	Intron	DEL	CTC	-	-			TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:102292874_102292876delCTC	uc010usj.1	+						uc002bxo.2_5'Flank|uc002bxp.3_5'Flank|uc002bxt.2_5'Flank|uc002bxz.3_5'Flank|uc002byd.2_5'Flank|uc002bye.2_5'Flank|uc002byf.1_5'Flank|uc002byg.2_5'Flank|uc002byi.2_5'Flank|uc002byk.2_5'Flank|uc002bym.2_5'Flank|uc002byn.2_5'Flank|uc010usm.1_5'Flank|uc002byr.2_5'Flank					RecName: Full=Uncharacterized protein C15orf51.; Flags: Fragment;																		AGTTCATCTTCTCAGAGCTGCTG	0.581													5	3	---	---	---	---	
PDIA2	64714	broad.mit.edu	37	16	332559	332559	+	Intron	DEL	G	-	-			TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:332559delG	uc002cgn.1	+						ARHGDIG_uc002cgm.1_Intron|PDIA2_uc010bqt.1_5'Flank|PDIA2_uc002cgo.1_5'Flank	NM_006849	NP_006840	Q13087	PDIA2_HUMAN	protein disulfide isomerase A2 precursor						apoptosis|cell redox homeostasis|glycerol ether metabolic process|protein folding|protein retention in ER lumen|response to hypoxia	endoplasmic reticulum lumen	electron carrier activity|protein binding|protein disulfide isomerase activity|protein disulfide oxidoreductase activity|steroid binding			central_nervous_system(1)|skin(1)	2		all_cancers(16;6.71e-07)|all_epithelial(16;1.59e-06)|Hepatocellular(16;0.000105)|Lung NSC(18;0.00769)|all_lung(18;0.0186)				GGAACGGGGCGGGGGGGGGAA	0.692													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	36398165	36398166	+	Intron	DEL	CC	-	-	rs2661195		TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:36398165_36398166delCC	uc002hpx.2	-											Homo sapiens cDNA FLJ43844 fis, clone TESTI4006308, highly  similar to Puromycin-sensitive aminopeptidase (EC 3.4.11.-).																		cacacacacacCCCCCACATAT	0.317													13	6	---	---	---	---	
KAT2A	2648	broad.mit.edu	37	17	40270120	40270123	+	Intron	DEL	GAGA	-	-	rs150172215		TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40270120_40270123delGAGA	uc002hyx.2	-							NM_021078	NP_066564	Q92830	KAT2A_HUMAN	general control of amino acid synthesis 5-like						chromatin remodeling|histone deubiquitination|interspecies interaction between organisms|regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter	Ada2/Gcn5/Ada3 transcription activator complex|STAGA complex|transcription factor TFTC complex	H3 histone acetyltransferase activity|histone deacetylase binding|protein binding|transcription coactivator activity			upper_aerodigestive_tract(1)|lung(1)	2						TGAAGCTGAGGAGAGAGAGAGTCA	0.623													6	3	---	---	---	---	
NFE2L1	4779	broad.mit.edu	37	17	46134236	46134237	+	Intron	INS	-	CT	CT	rs140826056	by1000genomes	TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:46134236_46134237insCT	uc002imz.3	+						NFE2L1_uc002ina.3_Intron|NFE2L1_uc002inb.3_Intron|NFE2L1_uc010wle.1_Intron|NFE2L1_uc010wlf.1_Intron	NM_003204	NP_003195	Q14494	NF2L1_HUMAN	nuclear factor erythroid 2-like 1						anatomical structure morphogenesis|heme biosynthetic process|inflammatory response|transcription from RNA polymerase II promoter	nucleus	protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription cofactor activity			skin(1)	1						GGACTCTTTCACTCTCTTCTGT	0.550													4	2	---	---	---	---	
TLE6	79816	broad.mit.edu	37	19	2995055	2995055	+	3'UTR	DEL	C	-	-			TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2995055delC	uc002lwu.2	+	16					TLE6_uc002lwt.2_3'UTR|TLE6_uc010dtg.2_3'UTR|TLE6_uc002lwv.2_3'UTR	NM_024760	NP_079036	Q9H808	TLE6_HUMAN	transducin-like enhancer of split 6 isoform 2						regulation of transcription, DNA-dependent	nucleus				ovary(1)	1				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CCCCCCCCTTCCCCCCCCCCA	0.627													4	3	---	---	---	---	
NANOS3	342977	broad.mit.edu	37	19	13986002	13986003	+	5'Flank	INS	-	T	T	rs77913995		TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13986002_13986003insT	uc002mxj.3	+							NM_001098622	NP_001092092	P60323	NANO3_HUMAN	nanos homolog 3						anti-apoptosis|germ cell development|multicellular organismal development|oogenesis|regulation of cell cycle|regulation of translation|spermatogenesis	cytoplasmic mRNA processing body|nucleus|stress granule	RNA binding|zinc ion binding			skin(1)	1			OV - Ovarian serous cystadenocarcinoma(19;2e-21)			CTAAAATCCCCttttttttttt	0.272													4	2	---	---	---	---	
PRDM15	63977	broad.mit.edu	37	21	43257865	43257882	+	Intron	DEL	TCCTGAGCTCCAGAACAT	-	-	rs71969131		TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:43257865_43257882delTCCTGAGCTCCAGAACAT	uc002yzq.1	-						PRDM15_uc002yzo.2_Intron|PRDM15_uc002yzp.2_Intron|PRDM15_uc002yzr.1_Intron	NM_022115	NP_071398	P57071	PRD15_HUMAN	PR domain containing 15 isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						ACCATTAAACTCCTGAGCTCCAGAACATTCCTGAGCTC	0.381													6	6	---	---	---	---	
LZTR1	8216	broad.mit.edu	37	22	21341677	21341678	+	Intron	INS	-	A	A	rs149184314		TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:21341677_21341678insA	uc002zto.2	+						LZTR1_uc002ztn.2_Intron|LZTR1_uc011ahy.1_Intron|LZTR1_uc010gsr.1_5'Flank	NM_006767	NP_006758	Q8N653	LZTR1_HUMAN	leucine-zipper-like transcription regulator 1						anatomical structure morphogenesis		sequence-specific DNA binding transcription factor activity			ovary(2)|lung(2)	4	all_cancers(11;1.83e-25)|all_epithelial(7;9.19e-23)|Lung NSC(8;3.06e-15)|all_lung(8;5.05e-14)|Melanoma(16;0.000465)|Ovarian(15;0.0028)|Colorectal(54;0.0332)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.000204)|Lung(15;0.00494)|Epithelial(17;0.195)			gactccgtctcaaaaaaaaaaa	0.257													5	3	---	---	---	---	
C22orf43	51233	broad.mit.edu	37	22	23973867	23973868	+	Intron	INS	-	C	C	rs141675360	by1000genomes	TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:23973867_23973868insC	uc002zxf.2	-							NM_016449	NP_057533	Q6PGQ1	CV043_HUMAN	hypothetical protein LOC51233											skin(1)	1						TGTCCCCCATGCCCAGACCTGG	0.535													5	4	---	---	---	---	
FAM120C	54954	broad.mit.edu	37	X	54117673	54117673	+	Intron	DEL	A	-	-			TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:54117673delA	uc004dsz.3	-						FAM120C_uc011moh.1_Intron	NM_017848	NP_060318	Q9NX05	F120C_HUMAN	hypothetical protein LOC54954											ovary(1)|central_nervous_system(1)	2						CAGCTTCAGGAAAAAAAAAAG	0.368													6	3	---	---	---	---	
MSN	4478	broad.mit.edu	37	X	64952923	64952923	+	Intron	DEL	A	-	-			TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:64952923delA	uc004dwf.2	+							NM_002444	NP_002435	P26038	MOES_HUMAN	moesin						leukocyte cell-cell adhesion|leukocyte migration|membrane to membrane docking	apical plasma membrane|cytoskeleton|extrinsic to membrane|microvillus membrane|nucleolus	cell adhesion molecule binding|receptor binding|structural constituent of cytoskeleton		MSN/ALK(6)	haematopoietic_and_lymphoid_tissue(6)|ovary(3)|lung(1)	10						tatttattttaaaaaaaaaaa	0.234			T	ALK	ALCL								4	2	---	---	---	---	
HCFC1	3054	broad.mit.edu	37	X	153222569	153222572	+	Intron	DEL	CCCT	-	-			TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:153222569_153222572delCCCT	uc004fjp.2	-							NM_005334	NP_005325	P51610	HCFC1_HUMAN	host cell factor 1						cell cycle|interspecies interaction between organisms|positive regulation of cell cycle|positive regulation of gene expression|protein stabilization|reactivation of latent virus|regulation of protein complex assembly|transcription from RNA polymerase II promoter	mitochondrion|MLL1 complex|MLL5-L complex|Set1C/COMPASS complex	chromatin binding|identical protein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity			ovary(2)	2	all_cancers(53;6.23e-16)|all_epithelial(53;5.61e-10)|all_lung(58;3.99e-07)|Lung NSC(58;5.02e-07)|all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					CCCCTGCTGCCCCTAGACTATAAT	0.549													21	19	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	13601466	13601467	+	IGR	INS	-	T	T	rs112972965		TCGA-B0-5812-01A-11D-1669-08	TCGA-B0-5812-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:13601466_13601467insT								None (None upstream) : None (None downstream)																							AGAGCAGGCTCTTGCCCACATC	0.490													7	4	---	---	---	---	
