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
SPEN	23013	broad.mit.edu	37	1	16256217	16256217	+	Missense_Mutation	SNP	T	C	C			TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16256217T>C	uc001axk.1	+	11	3686	c.3482T>C	c.(3481-3483)ATT>ACT	p.I1161T	SPEN_uc010obp.1_Missense_Mutation_p.I1120T	NM_015001	NP_055816	Q96T58	MINT_HUMAN	spen homolog, transcriptional regulator	1161					interspecies interaction between organisms|negative regulation of transcription, DNA-dependent|Notch signaling pathway	nucleus	nucleotide binding|protein binding|RNA binding			ovary(6)|breast(3)|lung(2)|skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)	15		Colorectal(325;0.000258)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(313;0.013)|READ - Rectum adenocarcinoma(331;0.0681)		AAAATTGGCATTGACATCGAT	0.403													31	7	---	---	---	---	PASS
AK2	204	broad.mit.edu	37	1	33476353	33476353	+	3'UTR	SNP	C	T	T	rs66599471		TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:33476353C>T	uc001bwo.1	-	7					uc001bwn.2_Intron|AK2_uc010ohq.1_3'UTR|AK2_uc009vud.1_3'UTR	NM_013411	NP_037543	P54819	KAD2_HUMAN	adenylate kinase 2 isoform b						nucleobase, nucleoside and nucleotide interconversion	mitochondrial intermembrane space	adenylate kinase activity|ATP binding				0		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)				CACCCTTCCCCTCTGCCCAGC	0.552													5	18	---	---	---	---	PASS
ATG4C	84938	broad.mit.edu	37	1	63269471	63269471	+	Missense_Mutation	SNP	G	C	C			TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:63269471G>C	uc001dat.2	+	2	176	c.14G>C	c.(13-15)GGA>GCA	p.G5A	ATG4C_uc001dau.2_Missense_Mutation_p.G5A	NM_178221	NP_835739	Q96DT6	ATG4C_HUMAN	APG4 autophagy 4 homolog C isoform 8	5					autophagic vacuole assembly|protein targeting to membrane|proteolysis	cytosol|extracellular region	cysteine-type endopeptidase activity			ovary(1)	1						GAGGCTACAGGAACAGATGAA	0.284													28	10	---	---	---	---	PASS
TXNIP	10628	broad.mit.edu	37	1	145439572	145439572	+	Intron	SNP	C	A	A			TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145439572C>A	uc001enn.3	+						NBPF10_uc001emp.3_Intron|TXNIP_uc001enm.1_Intron|TXNIP_uc010oys.1_Missense_Mutation_p.T22N	NM_006472	NP_006463	Q9H3M7	TXNIP_HUMAN	thioredoxin interacting protein						cell cycle|keratinocyte differentiation|transcription, DNA-dependent		ubiquitin protein ligase binding			ovary(2)	2	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					CTAATGGCTACTCGATTTTCT	0.423													8	112	---	---	---	---	PASS
PI4KB	5298	broad.mit.edu	37	1	151280208	151280208	+	Missense_Mutation	SNP	G	C	C			TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151280208G>C	uc001ext.2	-	4	1439	c.1024C>G	c.(1024-1026)CTC>GTC	p.L342V	PI4KB_uc001exr.2_Missense_Mutation_p.L354V|PI4KB_uc001exs.2_Missense_Mutation_p.L327V|PI4KB_uc001exu.2_Missense_Mutation_p.L327V|PI4KB_uc010pcw.1_Missense_Mutation_p.L10V	NM_002651	NP_002642	Q9UBF8	PI4KB_HUMAN	catalytic phosphatidylinositol 4-kinase beta	342					phosphatidylinositol biosynthetic process|phosphatidylinositol-mediated signaling|receptor-mediated endocytosis	endosome|Golgi apparatus|mitochondrial outer membrane|perinuclear region of cytoplasm|rough endoplasmic reticulum membrane	1-phosphatidylinositol 4-kinase activity|ATP binding|protein binding			ovary(2)|skin(2)	4	Lung SC(34;0.00471)|Ovarian(49;0.0147)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.112)|LUSC - Lung squamous cell carcinoma(543;0.181)			TTGGTGGGGAGCGTGGCCAGC	0.567													49	88	---	---	---	---	PASS
BRE	9577	broad.mit.edu	37	2	28531159	28531159	+	Intron	SNP	A	C	C			TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:28531159A>C	uc002rlr.2	+						BRE_uc002rlp.1_Intron|BRE_uc002rlq.2_Intron|BRE_uc002rls.2_Intron|BRE_uc002rlt.2_Intron|BRE_uc002rlu.2_Intron|BRE_uc002rlv.2_Intron|BRE_uc002rlx.2_Intron|uc002rly.2_RNA	NM_199194	NP_954664	Q9NXR7	BRE_HUMAN	brain and reproductive organ-expressed (TNFRSF1A						apoptosis|chromatin modification|double-strand break repair|G2/M transition DNA damage checkpoint|positive regulation of anti-apoptosis|positive regulation of DNA repair|response to ionizing radiation|signal transduction	BRCA1-A complex|BRISC complex|cytoplasm|nuclear ubiquitin ligase complex	peroxisome targeting sequence binding|polyubiquitin binding|tumor necrosis factor receptor binding			lung(1)|kidney(1)|skin(1)	3	Acute lymphoblastic leukemia(172;0.155)					CACATCACCCACCTGCCAGTG	0.502													8	27	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	2	96568655	96568655	+	Intron	SNP	A	T	T			TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:96568655A>T	uc002sva.1	-						uc002suz.1_5'UTR|uc002svb.1_Intron					Homo sapiens cDNA FLJ41632 fis, clone FCBBF1000297, highly  similar to Human protein immuno-reactive with anti-PTH polyclonal antibodies mRNA.																		TTTTCTCCATACTTTTTTCCT	0.279													3	17	---	---	---	---	PASS
SLC35F5	80255	broad.mit.edu	37	2	114487054	114487054	+	Missense_Mutation	SNP	C	A	A			TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:114487054C>A	uc002tku.1	-	11	1438	c.1014G>T	c.(1012-1014)ATG>ATT	p.M338I	SLC35F5_uc002tkt.2_RNA	NM_025181	NP_079457	Q8WV83	S35F5_HUMAN	solute carrier family 35, member F5	338	Helical; (Potential).				transport	integral to membrane					0						CAGCATAGAGCATGGCTCCAG	0.338													3	48	---	---	---	---	PASS
DDX18	8886	broad.mit.edu	37	2	118577223	118577223	+	Splice_Site	SNP	A	G	G			TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:118577223A>G	uc002tlh.1	+	3	470	c.371_splice	c.e3-2	p.D124_splice		NM_006773	NP_006764	Q9NVP1	DDX18_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 18								ATP binding|ATP-dependent RNA helicase activity|RNA binding			breast(2)|ovary(1)|lung(1)	4						TTAAAACCAAAGATACGAAAA	0.303											OREG0003814	type=REGULATORY REGION|Gene=DDX18|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	13	15	---	---	---	---	PASS
THSD7B	80731	broad.mit.edu	37	2	138414637	138414637	+	Missense_Mutation	SNP	G	A	A			TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:138414637G>A	uc002tva.1	+	23	4195	c.4195G>A	c.(4195-4197)GGC>AGC	p.G1399S	THSD7B_uc010zbj.1_Intron	NM_001080427	NP_001073896			thrombospondin, type I, domain containing 7B											ovary(4)|central_nervous_system(2)|pancreas(1)	7				BRCA - Breast invasive adenocarcinoma(221;0.19)		ACTTACAGGAGGCAAATGTTA	0.393													15	104	---	---	---	---	PASS
COL6A3	1293	broad.mit.edu	37	2	238249156	238249156	+	Silent	SNP	G	C	C			TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:238249156G>C	uc002vwl.2	-	38	8688	c.8403C>G	c.(8401-8403)TCC>TCG	p.S2801S	COL6A3_uc002vwo.2_Silent_p.S2595S|COL6A3_uc010znj.1_Silent_p.S2194S|COL6A3_uc002vwj.2_Silent_p.S182S	NM_004369	NP_004360	P12111	CO6A3_HUMAN	alpha 3 type VI collagen isoform 1 precursor	2801	VWFA 12.|Nonhelical region.				axon guidance|cell adhesion|muscle organ development	collagen type VI|extracellular space	serine-type endopeptidase inhibitor activity			ovary(8)|central_nervous_system(6)|skin(2)|upper_aerodigestive_tract(1)|pancreas(1)	18		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)		TGAGCTCGGTGGACTTGTCCA	0.557													31	35	---	---	---	---	PASS
PRSS42	339906	broad.mit.edu	37	3	46874543	46874543	+	Silent	SNP	A	T	T			TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:46874543A>T	uc011bap.1	-	3	525	c.525T>A	c.(523-525)CCT>CCA	p.P175P	PRSS42_uc003cqj.2_Silent_p.P71P	NM_182702	NP_874361	Q7Z5A4	PRS42_HUMAN	testis serine protease 2 precursor	175	Peptidase S1.				proteolysis	extracellular region	serine-type endopeptidase activity			pancreas(1)	1						TAAAATTCACAGGATGTTGGA	0.498													3	50	---	---	---	---	PASS
NBEAL2	23218	broad.mit.edu	37	3	47047316	47047316	+	Silent	SNP	C	A	A			TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:47047316C>A	uc003cqp.2	+	42	6959	c.6780C>A	c.(6778-6780)ATC>ATA	p.I2260I	NBEAL2_uc010hjm.1_Silent_p.I1637I|NBEAL2_uc010hjn.1_Silent_p.I656I|NBEAL2_uc010hjo.1_5'UTR	NM_015175	NP_055990	Q6ZNJ1	NBEL2_HUMAN	neurobeachin-like 2	2260	BEACH.						binding			ovary(1)	1		Acute lymphoblastic leukemia(5;0.0534)		BRCA - Breast invasive adenocarcinoma(193;0.0012)|KIRC - Kidney renal clear cell carcinoma(197;0.00575)|Kidney(197;0.00656)		AGGACTTCATCCAGCAGCACC	0.612													3	40	---	---	---	---	PASS
USP19	10869	broad.mit.edu	37	3	49154237	49154237	+	Missense_Mutation	SNP	C	A	A			TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49154237C>A	uc003cwd.1	-	6	907	c.746G>T	c.(745-747)CGG>CTG	p.R249L	USP19_uc003cwa.2_Missense_Mutation_p.R55L|USP19_uc003cvz.3_Missense_Mutation_p.R350L|USP19_uc011bcg.1_Missense_Mutation_p.R340L|USP19_uc003cwb.2_Missense_Mutation_p.R335L|USP19_uc003cwc.1_Missense_Mutation_p.R3L|USP19_uc011bch.1_Missense_Mutation_p.R350L|USP19_uc011bci.1_Missense_Mutation_p.R335L	NM_006677	NP_006668	O94966	UBP19_HUMAN	ubiquitin thioesterase 19	249	Cytoplasmic (Potential).				ER-associated protein catabolic process|positive regulation of cell cycle process|protein deubiquitination|regulation of protein stability|response to endoplasmic reticulum stress|skeletal muscle atrophy	endoplasmic reticulum membrane|integral to membrane	ubiquitin thiolesterase activity|ubiquitin-specific protease activity|zinc ion binding			ovary(4)|breast(2)|lung(1)	7				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00219)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		GTTTCTGCTCCGGACCATGGC	0.587													3	43	---	---	---	---	PASS
PBRM1	55193	broad.mit.edu	37	3	52661325	52661325	+	Nonsense_Mutation	SNP	G	C	C			TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52661325G>C	uc003des.2	-	13	1517	c.1505C>G	c.(1504-1506)TCA>TGA	p.S502*	PBRM1_uc003dex.2_RNA|PBRM1_uc003deq.2_Nonsense_Mutation_p.S502*|PBRM1_uc003der.2_Nonsense_Mutation_p.S470*|PBRM1_uc003det.2_Nonsense_Mutation_p.S502*|PBRM1_uc003deu.2_Nonsense_Mutation_p.S502*|PBRM1_uc003dev.2_RNA|PBRM1_uc003dew.2_Nonsense_Mutation_p.S502*|PBRM1_uc010hmk.1_Nonsense_Mutation_p.S502*|PBRM1_uc003dey.2_Nonsense_Mutation_p.S502*|PBRM1_uc003dez.1_Nonsense_Mutation_p.S502*|PBRM1_uc003dfb.1_Nonsense_Mutation_p.S400*	NM_181042	NP_060635	Q86U86	PB1_HUMAN	polybromo 1 isoform 4	502					chromatin remodeling|mitosis|negative regulation of cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear chromosome	chromatin binding|DNA binding|protein binding			kidney(136)|breast(4)	140				BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)		AGAGGTGGCTGAAGAGATCAT	0.433			Mis|N|F|S|D|O		clear cell renal carcinoma|breast								47	9	---	---	---	---	PASS
SLIT2	9353	broad.mit.edu	37	4	20541152	20541152	+	Missense_Mutation	SNP	C	A	A			TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:20541152C>A	uc003gpr.1	+	19	2125	c.1921C>A	c.(1921-1923)CAA>AAA	p.Q641K	SLIT2_uc003gps.1_Missense_Mutation_p.Q633K	NM_004787	NP_004778	O94813	SLIT2_HUMAN	slit homolog 2 precursor	641	LRR 16.				apoptosis involved in luteolysis|axon extension involved in axon guidance|branching morphogenesis of a tube|cell migration involved in sprouting angiogenesis|cellular response to heparin|cellular response to hormone stimulus|chemorepulsion involved in postnatal olfactory bulb interneuron migration|corticospinal neuron axon guidance through spinal cord|induction of negative chemotaxis|motor axon guidance|negative regulation of actin filament polymerization|negative regulation of cell growth|negative regulation of cellular response to growth factor stimulus|negative regulation of chemokine-mediated signaling pathway|negative regulation of endothelial cell migration|negative regulation of lamellipodium assembly|negative regulation of mononuclear cell migration|negative regulation of neutrophil chemotaxis|negative regulation of protein phosphorylation|negative regulation of retinal ganglion cell axon guidance|negative regulation of small GTPase mediated signal transduction|negative regulation of smooth muscle cell chemotaxis|negative regulation of vascular permeability|positive regulation of apoptosis|positive regulation of axonogenesis|response to cortisol stimulus|retinal ganglion cell axon guidance|Roundabout signaling pathway|ureteric bud development	cell surface|cytoplasm|extracellular space|plasma membrane	calcium ion binding|GTPase inhibitor activity|heparin binding|laminin-1 binding|protein homodimerization activity|proteoglycan binding|Roundabout binding			central_nervous_system(4)|skin(4)|ovary(3)	11						GTATGATAATCAAATTACTAC	0.378													37	20	---	---	---	---	PASS
MTTP	4547	broad.mit.edu	37	4	100532310	100532310	+	Missense_Mutation	SNP	C	T	T			TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:100532310C>T	uc003hvc.3	+	14	2036	c.1780C>T	c.(1780-1782)CGT>TGT	p.R594C	MTTP_uc011cej.1_Missense_Mutation_p.R621C	NM_000253	NP_000244	P55157	MTP_HUMAN	microsomal triglyceride transfer protein large	594	Vitellogenin.				lipid metabolic process|lipoprotein metabolic process	endoplasmic reticulum lumen	lipid binding|lipid transporter activity			ovary(3)|central_nervous_system(1)	4				OV - Ovarian serous cystadenocarcinoma(123;6.04e-09)	Hesperetin(DB01094)	CAAAATTGTCCGTCGAGTTCT	0.398													10	59	---	---	---	---	PASS
GOLPH3	64083	broad.mit.edu	37	5	32126321	32126321	+	Silent	SNP	C	T	T			TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32126321C>T	uc003jhp.1	-	4	1179	c.894G>A	c.(892-894)AAG>AAA	p.K298K		NM_022130	NP_071413	Q9H4A6	GOLP3_HUMAN	golgi phosphoprotein 3	298					cell proliferation|positive regulation of TOR signaling cascade|regulation of mitochondrion organization	cytosol|endosome|Golgi cisterna membrane|mitochondrial intermembrane space|plasma membrane|trans-Golgi network	protein binding			ovary(1)	1						AGCAGAGTTACTTGGTGAACG	0.488													74	237	---	---	---	---	PASS
FOXD1	2297	broad.mit.edu	37	5	72743654	72743654	+	Silent	SNP	C	T	T	rs1052207		TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:72743654C>T	uc003kcp.2	-	1	699	c.534G>A	c.(532-534)TCG>TCA	p.S178S		NM_004472	NP_004463	Q16676	FOXD1_HUMAN	forkhead box D1	178	Fork-head.				axon extension involved in axon guidance|cartilage development|dichotomous subdivision of terminal units involved in ureteric bud branching|embryo development|enteric nervous system development|iridophore differentiation|lateral line nerve glial cell development|melanocyte differentiation|metanephric capsule specification|negative regulation of transcription, DNA-dependent|neural crest cell migration|peripheral nervous system development|positive regulation of BMP signaling pathway|positive regulation of kidney development|positive regulation of transcription from RNA polymerase II promoter|regulation of sequence-specific DNA binding transcription factor activity|sympathetic nervous system development	transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding				0		Lung NSC(167;0.00327)|Ovarian(174;0.0175)|Prostate(461;0.151)		OV - Ovarian serous cystadenocarcinoma(47;1.07e-54)		AGTCGTTGAGCGAGAGGTTGT	0.637													48	70	---	---	---	---	PASS
UNC5A	90249	broad.mit.edu	37	5	176305475	176305475	+	Splice_Site	SNP	G	A	A			TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176305475G>A	uc003mey.2	+	13	2212	c.2020_splice	c.e13-1	p.E674_splice		NM_133369	NP_588610	Q6ZN44	UNC5A_HUMAN	netrin receptor Unc5h1 precursor						apoptosis|axon guidance|regulation of apoptosis	integral to membrane|plasma membrane				skin(1)	1	all_cancers(89;0.000119)|Renal(175;0.000269)|Lung NSC(126;0.00696)|all_lung(126;0.0115)	Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			ATCCCCATCAGGAGATCCCCT	0.612													35	79	---	---	---	---	PASS
HLA-J	3137	broad.mit.edu	37	6	29976859	29976859	+	Missense_Mutation	SNP	T	A	A			TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:29976859T>A	uc003rtl.3	+	3	549	c.187T>A	c.(187-189)TCC>ACC	p.S63T	HLA-G_uc011dmb.1_Intron|NCRNA00171_uc011dme.1_Intron|HLA-J_uc003nou.3_RNA|HLA-J_uc003nov.3_RNA					Homo sapiens major histocompatibility complex, class I, J (pseudogene), mRNA (cDNA clone IMAGE:4694038).												0						ACTAGGAGGTTCCTCTAGGAC	0.512													36	9	---	---	---	---	PASS
MRPL2	51069	broad.mit.edu	37	6	43024130	43024130	+	Missense_Mutation	SNP	T	G	G			TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43024130T>G	uc003ots.1	-	3	442	c.319A>C	c.(319-321)ATT>CTT	p.I107L	CUL7_uc011dvb.1_5'Flank|CUL7_uc003otq.2_5'Flank|CUL7_uc010jyh.2_5'Flank|KLC4_uc003otr.1_Intron|MRPL2_uc011dvc.1_Missense_Mutation_p.I107L	NM_015950	NP_057034	Q5T653	RM02_HUMAN	mitochondrial ribosomal protein L2 precursor	107					translation	mitochondrion|ribosome	structural constituent of ribosome				0		Ovarian(999;0.0014)	Colorectal(64;0.00237)|COAD - Colon adenocarcinoma(64;0.00473)|all cancers(41;0.00708)|OV - Ovarian serous cystadenocarcinoma(102;0.0442)	BRCA - Breast invasive adenocarcinoma(397;0.0026)		AGAAAGTCAATCATTCGATAA	0.512													32	7	---	---	---	---	PASS
NFE2L3	9603	broad.mit.edu	37	7	26225102	26225102	+	Missense_Mutation	SNP	G	A	A			TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:26225102G>A	uc003sxq.2	+	4	2056	c.1784G>A	c.(1783-1785)TGT>TAT	p.C595Y		NM_004289	NP_004280	Q9Y4A8	NF2L3_HUMAN	nuclear factor erythroid 2-like 3	595	Basic motif.				transcription from RNA polymerase II promoter	nucleus	protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity			skin(3)|ovary(1)	4						GCGCAGAACTGTCGTAAACGC	0.368													5	105	---	---	---	---	PASS
MET	4233	broad.mit.edu	37	7	116380121	116380121	+	Missense_Mutation	SNP	G	C	C			TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:116380121G>C	uc003vij.2	+	4	1697	c.1510G>C	c.(1510-1512)GTT>CTT	p.V504L	MET_uc010lkh.2_Missense_Mutation_p.V504L|MET_uc011knc.1_Missense_Mutation_p.V504L|MET_uc011knd.1_Missense_Mutation_p.V504L|MET_uc011kne.1_Missense_Mutation_p.V504L|MET_uc011knf.1_Missense_Mutation_p.V504L|MET_uc011kng.1_Missense_Mutation_p.V504L|MET_uc011knh.1_Missense_Mutation_p.V504L|MET_uc011kni.1_Missense_Mutation_p.V504L|MET_uc011knj.1_Missense_Mutation_p.V74L|MET_uc011kna.1_Missense_Mutation_p.V504L|MET_uc011knb.1_Missense_Mutation_p.V504L	NM_000245	NP_000236	P08581	MET_HUMAN	met proto-oncogene isoform b precursor	504	Extracellular (Potential).|Sema.				axon guidance|cell proliferation	basal plasma membrane|integral to plasma membrane	ATP binding|hepatocyte growth factor receptor activity|protein binding			upper_aerodigestive_tract(63)|lung(41)|kidney(18)|NS(10)|ovary(5)|thyroid(4)|central_nervous_system(4)|stomach(3)|liver(3)|pleura(2)|large_intestine(2)|breast(2)|testis(1)|skin(1)	159	all_cancers(3;1.25e-07)|all_epithelial(6;4.07e-08)|Lung NSC(10;0.00108)|all_lung(10;0.00125)	Ovarian(593;0.133)	GBM - Glioblastoma multiforme(2;2.31e-07)|all cancers(2;0.000419)|STAD - Stomach adenocarcinoma(10;0.000512)			CTACACACTGGTTATCACTGG	0.443			Mis		papillary renal|head-neck squamous cell 	papillary renal			Hereditary_Papillary_Renal_Carcinoma_(type_1)				78	103	---	---	---	---	PASS
ATP6V1B2	526	broad.mit.edu	37	8	20075680	20075680	+	Missense_Mutation	SNP	T	C	C			TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:20075680T>C	uc003wzp.2	+	13	1497	c.1283T>C	c.(1282-1284)ATT>ACT	p.I428T	ATP6V1B2_uc003wzq.1_5'Flank	NM_001693	NP_001684	P21281	VATB2_HUMAN	vacuolar H+ATPase B2	428					ATP hydrolysis coupled proton transport|cellular iron ion homeostasis|insulin receptor signaling pathway|transferrin transport	cytosol|endomembrane system|Golgi apparatus|melanosome|plasma membrane|proton-transporting V-type ATPase, V1 domain	ATP binding|hydrogen ion transporting ATP synthase activity, rotational mechanism|proton-transporting ATPase activity, rotational mechanism				0				Colorectal(74;0.0535)|COAD - Colon adenocarcinoma(73;0.211)		TGCTATGCTATTGGAAAGGAT	0.438													59	92	---	---	---	---	PASS
ENTPD4	9583	broad.mit.edu	37	8	23306332	23306332	+	Silent	SNP	A	G	G			TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:23306332A>G	uc003xdl.2	-	3	293	c.129T>C	c.(127-129)GCT>GCC	p.A43A	ENTPD4_uc011kzu.1_Silent_p.A43A|ENTPD4_uc003xdm.2_Silent_p.A43A|ENTPD4_uc011kzv.1_Silent_p.A43A|ENTPD4_uc011kzw.1_Silent_p.A9A	NM_004901	NP_004892	Q9Y227	ENTP4_HUMAN	ectonucleoside triphosphate diphosphohydrolase 4	43	Helical; (Potential).			A -> AA (in Ref. 1; AAC17217).	UDP catabolic process	autophagic vacuole membrane|cytoplasmic vesicle|integral to Golgi membrane	uridine-diphosphatase activity			ovary(1)|kidney(1)	2		Prostate(55;0.114)		Colorectal(74;0.0161)|COAD - Colon adenocarcinoma(73;0.0649)		AAAGTGAAACAGCAGCAGCCA	0.373													12	176	---	---	---	---	PASS
PCMTD1	115294	broad.mit.edu	37	8	52732871	52732871	+	3'UTR	SNP	T	C	C	rs77261625	by1000genomes	TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:52732871T>C	uc003xqx.3	-	6					PCMTD1_uc011ldm.1_3'UTR|PCMTD1_uc003xqw.3_3'UTR|PCMTD1_uc011ldn.1_3'UTR|PCMTD1_uc010lya.2_3'UTR	NM_052937	NP_443169	Q96MG8	PCMD1_HUMAN	protein-L-isoaspartate (D-aspartate)							cytoplasm	protein-L-isoaspartate (D-aspartate) O-methyltransferase activity				0		Lung NSC(129;0.0795)|all_lung(136;0.144)				TTTTCAAGACTAAAGGAATTA	0.313													3	26	---	---	---	---	PASS
PKHD1L1	93035	broad.mit.edu	37	8	110477389	110477389	+	Silent	SNP	C	T	T			TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:110477389C>T	uc003yne.2	+	49	8432	c.8328C>T	c.(8326-8328)GAC>GAT	p.D2776D		NM_177531	NP_803875	Q86WI1	PKHL1_HUMAN	fibrocystin L precursor	2776	Extracellular (Potential).				immune response	cytosol|extracellular space|integral to membrane	receptor activity			ovary(9)|central_nervous_system(2)|large_intestine(1)|breast(1)|pancreas(1)	14			OV - Ovarian serous cystadenocarcinoma(57;9.88e-13)			AGTTTGTTGACGTCCAGTATT	0.433										HNSCC(38;0.096)			40	54	---	---	---	---	PASS
HAS2	3037	broad.mit.edu	37	8	122641328	122641328	+	Missense_Mutation	SNP	C	A	A			TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:122641328C>A	uc003yph.2	-	2	791	c.253G>T	c.(253-255)GTT>TTT	p.V85F		NM_005328	NP_005319	Q92819	HAS2_HUMAN	hyaluronan synthase 2	85	Cytoplasmic (Potential).					integral to plasma membrane	hyaluronan synthase activity		HAS2/PLAG1(10)	soft_tissue(10)|ovary(5)	15	Lung NSC(37;3.12e-08)|Ovarian(258;0.0254)|Hepatocellular(40;0.0997)|all_neural(195;0.142)		STAD - Stomach adenocarcinoma(47;0.00503)			CAAAGGGCAACTGTTTTGTTC	0.413													8	543	---	---	---	---	PASS
NDRG1	10397	broad.mit.edu	37	8	134276801	134276801	+	Missense_Mutation	SNP	A	C	C			TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:134276801A>C	uc003yuh.2	-	4	780	c.194T>G	c.(193-195)ATC>AGC	p.I65S	NDRG1_uc003yug.2_Missense_Mutation_p.I65S|NDRG1_uc010mee.2_Intron|NDRG1_uc010mef.2_5'UTR|NDRG1_uc011ljh.1_5'UTR|NDRG1_uc011lji.1_Intron	NM_001135242	NP_001128714	Q92597	NDRG1_HUMAN	N-myc downstream regulated 1	65					cellular response to hypoxia|response to metal ion	cytoplasm|microtubule cytoskeleton|nucleus|plasma membrane	protein binding			ovary(4)	4	all_epithelial(106;4.26e-24)|Lung NSC(106;7.26e-07)|all_lung(105;2.77e-06)|Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0107)			GTTCATGCCGATGTCATGGTA	0.577													3	87	---	---	---	---	PASS
UBAP1	51271	broad.mit.edu	37	9	34241601	34241601	+	Missense_Mutation	SNP	C	T	T			TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:34241601C>T	uc003ztx.2	+	4	813	c.578C>T	c.(577-579)GCT>GTT	p.A193V	UBAP1_uc010mka.1_Missense_Mutation_p.A229V|UBAP1_uc003zty.2_Missense_Mutation_p.A193V|UBAP1_uc011loi.1_Missense_Mutation_p.A229V|UBAP1_uc011loj.1_Missense_Mutation_p.A257V|KIF24_uc010mkb.2_Intron|UBAP1_uc003ztz.2_Missense_Mutation_p.A193V	NM_016525	NP_057609	Q9NZ09	UBAP1_HUMAN	ubiquitin associated protein 1	193						cytoplasm					0			LUSC - Lung squamous cell carcinoma(29;0.00272)			CCCATTATGGCTCAGTTATTG	0.463													3	61	---	---	---	---	PASS
FLJ46321	389763	broad.mit.edu	37	9	84605805	84605805	+	Silent	SNP	C	A	A			TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:84605805C>A	uc004amn.2	+	4	467	c.420C>A	c.(418-420)ATC>ATA	p.I140I		NM_001001670	NP_001001670	Q6ZQQ2	F75D1_HUMAN	hypothetical protein LOC389763	140						integral to membrane					0						CTGCTGATATCCAGCAACTGC	0.552													26	26	---	---	---	---	PASS
MYO3A	53904	broad.mit.edu	37	10	26463158	26463158	+	Missense_Mutation	SNP	G	T	T			TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:26463158G>T	uc001isn.2	+	30	4325	c.3965G>T	c.(3964-3966)GGC>GTC	p.G1322V	MYO3A_uc009xkp.1_Intron|MYO3A_uc009xkq.1_Intron	NM_017433	NP_059129	Q8NEV4	MYO3A_HUMAN	myosin IIIA	1322					protein autophosphorylation|response to stimulus|sensory perception of sound|visual perception	cytoplasm|filamentous actin|filopodium|myosin complex	actin binding|actin-dependent ATPase activity|ADP binding|ATP binding|calmodulin binding|plus-end directed microfilament motor activity|protein serine/threonine kinase activity			ovary(6)|stomach(3)|lung(3)|central_nervous_system(2)|breast(1)|skin(1)|kidney(1)|pancreas(1)	18						CAGGAGGAAGGCAGAGGCCGT	0.478													16	160	---	---	---	---	PASS
RBP3	5949	broad.mit.edu	37	10	48388012	48388012	+	Missense_Mutation	SNP	C	T	T			TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:48388012C>T	uc001jez.2	-	1	2980	c.2866G>A	c.(2866-2868)GAG>AAG	p.E956K		NM_002900	NP_002891	P10745	RET3_HUMAN	retinol-binding protein 3 precursor	956	4 X approximate tandem repeats.|4.				lipid metabolic process|proteolysis|transport|visual perception	interphotoreceptor matrix	retinal binding|serine-type peptidase activity			large_intestine(1)|central_nervous_system(1)	2					Vitamin A(DB00162)	GCCCCCAGCTCGGCAGAGGCA	0.632													4	74	---	---	---	---	PASS
ZMIZ1	57178	broad.mit.edu	37	10	81065919	81065919	+	Missense_Mutation	SNP	C	T	T			TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:81065919C>T	uc001kaf.2	+	22	3058	c.2486C>T	c.(2485-2487)TCG>TTG	p.S829L	ZMIZ1_uc001kag.2_Missense_Mutation_p.S705L|ZMIZ1_uc010qlq.1_5'UTR	NM_020338	NP_065071	Q9ULJ6	ZMIZ1_HUMAN	retinoic acid induced 17	829					transcription, DNA-dependent	cytoplasm|nuclear speck	zinc ion binding			ovary(2)|breast(1)|skin(1)	4	all_cancers(46;0.0292)|Breast(12;8.52e-05)|all_epithelial(25;0.000854)|Prostate(51;0.00985)		Epithelial(14;0.00256)|all cancers(16;0.00726)|Colorectal(32;0.229)			CCCATCAAGTCGGACTTACAC	0.592													43	5	---	---	---	---	PASS
EIF3A	8661	broad.mit.edu	37	10	120832959	120832959	+	Missense_Mutation	SNP	G	A	A			TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:120832959G>A	uc001ldu.2	-	3	517	c.371C>T	c.(370-372)CCT>CTT	p.P124L	EIF3A_uc010qsu.1_Missense_Mutation_p.P90L	NM_003750	NP_003741	Q14152	EIF3A_HUMAN	eukaryotic translation initiation factor 3,	124					formation of translation initiation complex	cytosol|eukaryotic translation initiation factor 3 complex	protein binding|structural molecule activity|translation initiation factor activity				0		Lung NSC(174;0.094)|all_lung(145;0.123)		all cancers(201;0.0236)		ATACCTCTCAGGAGTTTGAAT	0.353													50	14	---	---	---	---	PASS
HPS5	11234	broad.mit.edu	37	11	18303659	18303659	+	Missense_Mutation	SNP	C	G	G			TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:18303659C>G	uc001mod.1	-	22	3445	c.3167G>C	c.(3166-3168)GGG>GCG	p.G1056A	HPS5_uc001moe.1_Missense_Mutation_p.G942A|HPS5_uc001mof.1_Missense_Mutation_p.G942A	NM_181507	NP_852608	Q9UPZ3	HPS5_HUMAN	Hermansky-Pudlak syndrome 5 isoform a	1056						cytosol				ovary(1)|pancreas(1)|skin(1)	3						GGGGGAAGGCCCATCACTGAG	0.562									Hermansky-Pudlak_syndrome				35	54	---	---	---	---	PASS
OR4P4	81300	broad.mit.edu	37	11	55406625	55406625	+	Silent	SNP	A	G	G			TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55406625A>G	uc010rij.1	+	1	792	c.792A>G	c.(790-792)TCA>TCG	p.S264S		NM_001004124	NP_001004124	Q8NGL7	OR4P4_HUMAN	olfactory receptor, family 4, subfamily P,	264	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			central_nervous_system(1)	1						CAACATTCTCAGAAGATAAAG	0.418													5	213	---	---	---	---	PASS
TMEM123	114908	broad.mit.edu	37	11	102272803	102272803	+	Missense_Mutation	SNP	T	C	C			TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:102272803T>C	uc001pha.2	-	3	713	c.292A>G	c.(292-294)ACA>GCA	p.T98A	TMEM123_uc009yxc.2_Missense_Mutation_p.T79A	NM_052932	NP_443164	Q8N131	PORIM_HUMAN	transmembrane protein 123 precursor	98	Thr-rich.|Extracellular (Potential).				oncosis	external side of plasma membrane|integral to membrane	receptor activity			breast(2)	2	all_cancers(8;0.00027)|all_epithelial(12;0.0021)|Lung NSC(15;0.227)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0033)	Epithelial(9;0.0314)|Lung(13;0.109)|all cancers(10;0.12)|LUSC - Lung squamous cell carcinoma(19;0.151)	BRCA - Breast invasive adenocarcinoma(274;0.0149)		CCTGGTGTTGTTGTATTAGAT	0.423													126	170	---	---	---	---	PASS
SPSB2	84727	broad.mit.edu	37	12	6981774	6981774	+	Nonsense_Mutation	SNP	C	A	A			TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6981774C>A	uc001qrl.2	-	2	448	c.292G>T	c.(292-294)GAG>TAG	p.E98*	SPSB2_uc001qrm.2_Nonsense_Mutation_p.E98*|SPSB2_uc010sfp.1_Nonsense_Mutation_p.E98*|LRRC23_uc001qrn.1_5'Flank	NM_001146316	NP_001139788	Q99619	SPSB2_HUMAN	splA/ryanodine receptor domain and SOCS box	98	B30.2/SPRY.				intracellular signal transduction	cytoplasm	protein binding			kidney(1)	1						CCCCTCTGCTCTAGGGGCCAG	0.697											OREG0021639	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	34	55	---	---	---	---	PASS
PLEKHG7	440107	broad.mit.edu	37	12	93134670	93134670	+	Silent	SNP	T	C	C			TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:93134670T>C	uc001tcj.2	+	3	275	c.45T>C	c.(43-45)TAT>TAC	p.Y15Y		NM_001004330	NP_001004330	Q6ZR37	PKHG7_HUMAN	pleckstrin homology domain containing, family G	15	DH.				regulation of Rho protein signal transduction	intracellular	Rho guanyl-nucleotide exchange factor activity			ovary(1)	1						CTCATGAATATCTCCTAGATG	0.323													7	78	---	---	---	---	PASS
C13orf30	144809	broad.mit.edu	37	13	43362794	43362794	+	Silent	SNP	A	C	C			TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:43362794A>C	uc010tfk.1	+	4	411	c.288A>C	c.(286-288)TCA>TCC	p.S96S	C13orf30_uc010tfl.1_Silent_p.S96S	NM_182508	NP_872314	Q8N7L0	CM030_HUMAN	hypothetical protein LOC144809	96											0		Lung NSC(96;0.000369)|Prostate(109;0.0305)|Lung SC(185;0.0367)|Breast(139;0.0406)		GBM - Glioblastoma multiforme(144;0.000512)|OV - Ovarian serous cystadenocarcinoma(117;0.000563)|BRCA - Breast invasive adenocarcinoma(63;0.0677)		AGAGAGCCTCAGCCAAGGTAG	0.453													71	93	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	14	22788632	22788632	+	Intron	SNP	C	T	T			TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:22788632C>T	uc001wbw.2	+						uc010aja.1_Intron|uc010tmk.1_Intron|uc010tmo.1_Intron|uc001wco.2_Intron|uc010aje.1_Intron|uc001wcp.2_Intron|uc001wcr.1_Intron|uc001wcs.1_Intron|uc010ajf.1_Intron|uc010ajg.1_Intron|uc001wcx.3_Intron|uc001wdd.2_Intron|uc010ajj.1_Intron|uc001wde.1_Intron|uc001wdf.2_Intron|uc010ajk.1_Intron|uc001wdg.1_Intron|uc010ajl.1_Intron|uc001wdj.2_Intron|uc010ajo.1_Intron|uc010ajp.1_Intron|uc001wdr.2_Missense_Mutation_p.R5W					SubName: Full=Alpha-chain C region; Flags: Fragment;																		GGTGAAGATCCGGCAATTTTT	0.418													89	180	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	14	22788633	22788633	+	Intron	SNP	G	C	C			TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:22788633G>C	uc001wbw.2	+						uc010aja.1_Intron|uc010tmk.1_Intron|uc010tmo.1_Intron|uc001wco.2_Intron|uc010aje.1_Intron|uc001wcp.2_Intron|uc001wcr.1_Intron|uc001wcs.1_Intron|uc010ajf.1_Intron|uc010ajg.1_Intron|uc001wcx.3_Intron|uc001wdd.2_Intron|uc010ajj.1_Intron|uc001wde.1_Intron|uc001wdf.2_Intron|uc010ajk.1_Intron|uc001wdg.1_Intron|uc010ajl.1_Intron|uc001wdj.2_Intron|uc010ajo.1_Intron|uc010ajp.1_Intron|uc001wdr.2_Missense_Mutation_p.R5P					SubName: Full=Alpha-chain C region; Flags: Fragment;																		GTGAAGATCCGGCAATTTTTG	0.418													89	180	---	---	---	---	PASS
RABGGTA	5875	broad.mit.edu	37	14	24737807	24737807	+	Missense_Mutation	SNP	C	G	G			TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24737807C>G	uc001wof.2	-	9	1341	c.919G>C	c.(919-921)GCC>CCC	p.A307P	RABGGTA_uc001woe.2_RNA|RABGGTA_uc001wog.2_Missense_Mutation_p.A307P|RABGGTA_uc001woh.2_RNA|RABGGTA_uc001woi.2_RNA	NM_004581	NP_004572	Q92696	PGTA_HUMAN	Rab geranylgeranyltransferase alpha	307					visual perception		Rab geranylgeranyltransferase activity|zinc ion binding				0				GBM - Glioblastoma multiforme(265;0.0184)		TTGAGGGAGGCAGCAGGCAGG	0.542													45	68	---	---	---	---	PASS
NYNRIN	57523	broad.mit.edu	37	14	24885001	24885001	+	Missense_Mutation	SNP	C	T	T			TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24885001C>T	uc001wpf.3	+	9	4364	c.4046C>T	c.(4045-4047)ACG>ATG	p.T1349M		NM_025081	NP_079357	Q9P2P1	NYNRI_HUMAN	hypothetical protein LOC57523	1349					DNA integration	integral to membrane	DNA binding			ovary(2)|central_nervous_system(1)	3						TCCCCTTACACGCCAACCTAT	0.597													76	81	---	---	---	---	PASS
PHF23	79142	broad.mit.edu	37	17	7139291	7139291	+	Missense_Mutation	SNP	C	G	G			TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7139291C>G	uc002gfa.2	-	4	1182	c.955G>C	c.(955-957)GGC>CGC	p.G319R	DVL2_uc002gez.1_5'Flank|DVL2_uc010vtr.1_5'Flank|DVL2_uc010clz.1_5'Flank|PHF23_uc010vtt.1_Missense_Mutation_p.G252R|PHF23_uc010cma.2_Missense_Mutation_p.G189R	NM_024297	NP_077273	Q9BUL5	PHF23_HUMAN	PHD finger protein 23	319							zinc ion binding				0						CGCATCTCGCCTTCACTGGAG	0.577													230	347	---	---	---	---	PASS
MYH4	4622	broad.mit.edu	37	17	10366258	10366258	+	Missense_Mutation	SNP	T	A	A			TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10366258T>A	uc002gmn.2	-	11	1043	c.932A>T	c.(931-933)TAT>TTT	p.Y311F	uc002gml.1_Intron	NM_017533	NP_060003	Q9Y623	MYH4_HUMAN	myosin, heavy polypeptide 4, skeletal muscle	311	Myosin head-like.				muscle filament sliding	muscle myosin complex|myosin filament|sarcomere	actin binding|ATP binding|calmodulin binding|microfilament motor activity|structural constituent of muscle			ovary(10)|skin(2)|central_nervous_system(1)	13						TGCGAAGTCATATGGGTTGGT	0.418													40	38	---	---	---	---	PASS
MYH4	4622	broad.mit.edu	37	17	10366705	10366705	+	Missense_Mutation	SNP	C	G	G			TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10366705C>G	uc002gmn.2	-	9	866	c.755G>C	c.(754-756)AGG>ACG	p.R252T	uc002gml.1_Intron	NM_017533	NP_060003	Q9Y623	MYH4_HUMAN	myosin, heavy polypeptide 4, skeletal muscle	252	Myosin head-like.				muscle filament sliding	muscle myosin complex|myosin filament|sarcomere	actin binding|ATP binding|calmodulin binding|microfilament motor activity|structural constituent of muscle			ovary(10)|skin(2)|central_nervous_system(1)	13						AAAATGGATCCTGATGAATTT	0.323													48	62	---	---	---	---	PASS
MYH4	4622	broad.mit.edu	37	17	10366884	10366884	+	Missense_Mutation	SNP	T	A	A			TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10366884T>A	uc002gmn.2	-	8	836	c.725A>T	c.(724-726)GAC>GTC	p.D242V	uc002gml.1_Intron	NM_017533	NP_060003	Q9Y623	MYH4_HUMAN	myosin, heavy polypeptide 4, skeletal muscle	242	Myosin head-like.				muscle filament sliding	muscle myosin complex|myosin filament|sarcomere	actin binding|ATP binding|calmodulin binding|microfilament motor activity|structural constituent of muscle			ovary(10)|skin(2)|central_nervous_system(1)	13						AGAGGAGTTGTCATTCCTCAC	0.438													45	90	---	---	---	---	PASS
THRA	7067	broad.mit.edu	37	17	38240101	38240101	+	Missense_Mutation	SNP	G	A	A			TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:38240101G>A	uc002htw.2	+	5	719	c.236G>A	c.(235-237)CGC>CAC	p.R79H	THRA_uc010cwp.1_Missense_Mutation_p.R79H|THRA_uc002htv.2_Missense_Mutation_p.R79H|THRA_uc002htx.2_Missense_Mutation_p.R79H	NM_003250	NP_003241	P10827	THA_HUMAN	thyroid hormone receptor, alpha isoform 2	79	Nuclear receptor.				negative regulation of RNA polymerase II transcriptional preinitiation complex assembly|negative regulation of transcription initiation, DNA-dependent|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|transcription from RNA polymerase II promoter	cytosol|nucleoplasm	protein domain specific binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|TBP-class protein binding|thyroid hormone binding|thyroid hormone receptor activity|transcription regulatory region DNA binding|zinc ion binding				0	Colorectal(19;0.000442)	Myeloproliferative disorder(1115;0.0255)			Levothyroxine(DB00451)|Liothyronine(DB00279)	TTCTTTCGCCGCACAATCCAG	0.547													4	126	---	---	---	---	PASS
KRT23	25984	broad.mit.edu	37	17	39086293	39086293	+	Nonsense_Mutation	SNP	G	A	A			TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39086293G>A	uc002hvm.1	-	4	1124	c.535C>T	c.(535-537)CGA>TGA	p.R179*	KRT23_uc010wfl.1_Nonsense_Mutation_p.R42*|KRT23_uc010cxf.1_Intron|KRT23_uc010cxg.2_Nonsense_Mutation_p.R179*|KRT23_uc002hvn.1_Nonsense_Mutation_p.R179*	NM_015515	NP_056330	Q9C075	K1C23_HUMAN	keratin 23	179	Rod.|Coil 1B.					intermediate filament	structural molecule activity			ovary(1)	1		Breast(137;0.000301)|Ovarian(249;0.15)				AAGGTCCTTCGGAGGCCCTCG	0.458													62	74	---	---	---	---	PASS
CNP	1267	broad.mit.edu	37	17	40120690	40120690	+	Missense_Mutation	SNP	G	A	A			TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40120690G>A	uc002hyl.1	+	2	752	c.608G>A	c.(607-609)CGC>CAC	p.R203H	CNP_uc002hyk.1_Missense_Mutation_p.R203H|CNP_uc010wfz.1_Intron|CNP_uc002hym.1_Missense_Mutation_p.R183H|CNP_uc010wga.1_Intron	NM_033133	NP_149124	P09543	CN37_HUMAN	2',3'-cyclic nucleotide 3' phosphodiesterase	203					cell killing|cyclic nucleotide catabolic process|RNA metabolic process|synaptic transmission	extracellular space|melanosome	2',3'-cyclic-nucleotide 3'-phosphodiesterase activity|ATP binding|protein binding				0		all_cancers(22;2.38e-06)|all_epithelial(22;6.79e-05)|Breast(137;0.000143)		UCEC - Uterine corpus endometrioid carcinoma (308;0.171)		GAGACCCTCCGCAAAGCCGGC	0.582													3	46	---	---	---	---	PASS
NGFR	4804	broad.mit.edu	37	17	47587945	47587945	+	Missense_Mutation	SNP	C	A	A			TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:47587945C>A	uc002ioz.3	+	4	865	c.740C>A	c.(739-741)ACC>AAC	p.T247N		NM_002507	NP_002498	P08138	TNR16_HUMAN	nerve growth factor receptor precursor	247	Ser/Thr-rich.|Extracellular (Potential).				anti-apoptosis|apoptosis|induction of apoptosis by extracellular signals|membrane protein intracellular domain proteolysis|negative regulation of axonogenesis|negative regulation of cell cycle|nerve growth factor receptor signaling pathway|positive regulation of axonogenesis	cell surface|cytosol|endosome|extracellular region|integral to plasma membrane|nucleoplasm				ovary(1)|lung(1)	2	all_cancers(4;1.45e-13)|Breast(4;6.34e-28)|all_epithelial(4;4.95e-17)					ACCCGAGGCACCACCGACAAC	0.607													48	53	---	---	---	---	PASS
ABCA5	23461	broad.mit.edu	37	17	67280186	67280186	+	Nonsense_Mutation	SNP	G	C	C			TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:67280186G>C	uc002jif.2	-	17	3518	c.2300C>G	c.(2299-2301)TCA>TGA	p.S767*	ABCA5_uc002jic.2_5'UTR|ABCA5_uc002jid.2_5'UTR|ABCA5_uc002jie.2_RNA|ABCA5_uc002jig.2_Nonsense_Mutation_p.S767*|ABCA5_uc002jih.2_Nonsense_Mutation_p.S767*|ABCA5_uc010dfe.2_Nonsense_Mutation_p.S767*	NM_018672	NP_061142	Q8WWZ7	ABCA5_HUMAN	ATP-binding cassette, sub-family A , member 5	767					cholesterol efflux|high-density lipoprotein particle remodeling|negative regulation of macrophage derived foam cell differentiation	Golgi membrane|integral to membrane|late endosome membrane|lysosomal membrane	ATP binding|ATPase activity			ovary(2)|central_nervous_system(1)|skin(1)	4	Breast(10;3.72e-11)					ACCCAAATTTGAATGACTGTC	0.299													7	61	---	---	---	---	PASS
TMC8	147138	broad.mit.edu	37	17	76137117	76137117	+	Missense_Mutation	SNP	G	A	A			TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:76137117G>A	uc002jup.2	+	16	2487	c.2105G>A	c.(2104-2106)CGT>CAT	p.R702H	TMC8_uc002juq.2_Missense_Mutation_p.R479H	NM_152468	NP_689681	Q8IU68	TMC8_HUMAN	transmembrane channel-like 8	702	Cytoplasmic (Potential).					endoplasmic reticulum membrane|integral to membrane					0			BRCA - Breast invasive adenocarcinoma(99;0.00269)|Lung(188;0.0973)|OV - Ovarian serous cystadenocarcinoma(97;0.192)			GCGGGACTGCGTTCCCCTTGC	0.756									Epidermodysplasia_Verruciformis_Familial_Clustering_of				7	5	---	---	---	---	PASS
TMPRSS9	360200	broad.mit.edu	37	19	2415831	2415831	+	Silent	SNP	C	T	T			TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2415831C>T	uc010xgx.1	+	10	1635	c.1635C>T	c.(1633-1635)TGC>TGT	p.C545C		NM_182973	NP_892018	Q7Z410	TMPS9_HUMAN	transmembrane protease, serine 9	545	Extracellular (Potential).|Peptidase S1 2.				proteolysis	integral to plasma membrane	serine-type endopeptidase activity			ovary(1)|central_nervous_system(1)	2				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)		CCGCCCACTGCTTCAACCAGT	0.677													5	70	---	---	---	---	PASS
IL12RB1	3594	broad.mit.edu	37	19	18191685	18191685	+	Silent	SNP	C	T	T			TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:18191685C>T	uc002nhw.1	-	4	430	c.366G>A	c.(364-366)CAG>CAA	p.Q122Q	IL12RB1_uc010xqb.1_Silent_p.Q122Q|IL12RB1_uc002nhx.1_Silent_p.Q162Q|IL12RB1_uc002nhy.2_Silent_p.Q122Q	NM_005535	NP_005526	P42701	I12R1_HUMAN	interleukin 12 receptor, beta 1 isoform 1	122	Extracellular (Potential).|Fibronectin type-III 1.				cellular response to interferon-gamma|interleukin-12-mediated signaling pathway|positive regulation of activated T cell proliferation|positive regulation of defense response to virus by host|positive regulation of interferon-gamma production|positive regulation of memory T cell differentiation|positive regulation of T cell mediated cytotoxicity|positive regulation of T-helper 1 type immune response|positive regulation of T-helper 17 cell lineage commitment|positive regulation of T-helper 17 type immune response	interleukin-12 receptor complex|interleukin-23 receptor complex	cytokine receptor activity			pancreas(1)	1						ACTTCTCTGTCTGGTTCCTGG	0.597													37	59	---	---	---	---	PASS
PRX	57716	broad.mit.edu	37	19	40901528	40901528	+	Missense_Mutation	SNP	C	T	T			TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:40901528C>T	uc002onr.2	-	7	3000	c.2731G>A	c.(2731-2733)GTG>ATG	p.V911M	PRX_uc002onq.2_Missense_Mutation_p.V772M|PRX_uc002ons.2_3'UTR	NM_181882	NP_870998	Q9BXM0	PRAX_HUMAN	periaxin isoform 2	911					axon ensheathment	cytoplasm|nucleus|plasma membrane	protein binding			ovary(2)	2			Lung(22;6.24e-05)|LUSC - Lung squamous cell carcinoma(20;0.000384)			TCAATTTCCACGGCGGGCAGC	0.587													59	80	---	---	---	---	PASS
SLC8A2	6543	broad.mit.edu	37	19	47969097	47969097	+	Missense_Mutation	SNP	C	G	G			TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47969097C>G	uc002pgx.2	-	2	842	c.564G>C	c.(562-564)GAG>GAC	p.E188D	SLC8A2_uc010xyq.1_Intron|SLC8A2_uc010xyr.1_Intron|SLC8A2_uc010ele.2_Missense_Mutation_p.E188D	NM_015063	NP_055878	Q9UPR5	NAC2_HUMAN	solute carrier family 8 member 2 precursor	188	Cytoplasmic (Potential).				cell communication|platelet activation	integral to membrane|plasma membrane	calcium:sodium antiporter activity|calmodulin binding			skin(3)|ovary(1)	4		all_cancers(25;3.05e-07)|all_lung(116;4.19e-06)|Lung NSC(112;7.16e-06)|all_epithelial(76;7.65e-06)|all_neural(266;0.0652)|Ovarian(192;0.086)|Breast(70;0.173)		OV - Ovarian serous cystadenocarcinoma(262;0.000501)|all cancers(93;0.00058)|Epithelial(262;0.0181)|GBM - Glioblastoma multiforme(486;0.0457)		TCTTGCGGCTCTCGCCGGCTG	0.572													15	23	---	---	---	---	PASS
LILRB4	11006	broad.mit.edu	37	19	55174440	55174440	+	5'UTR	SNP	G	A	A			TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55174440G>A	uc002qgp.2	+	1					LILRB4_uc002qgo.1_Silent_p.L26L|LILRB4_uc002qgq.2_5'UTR|LILRB4_uc010ers.1_5'UTR|LILRB4_uc002qgr.2_Silent_p.L26L|LILRB4_uc010ert.2_Silent_p.L26L|LILRB4_uc010eru.2_Silent_p.L26L	NM_006847	NP_006838	Q8NHJ6	LIRB4_HUMAN	leukocyte immunoglobulin-like receptor,							integral to membrane|plasma membrane	antigen binding|receptor activity			ovary(3)	3				GBM - Glioblastoma multiforme(193;0.035)		TGCCGGCACTGAGGACTCATC	0.607											OREG0003670	type=REGULATORY REGION|Gene=LILRB4|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	52	56	---	---	---	---	PASS
SPTLC3	55304	broad.mit.edu	37	20	12989763	12989763	+	5'UTR	SNP	G	A	A			TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:12989763G>A	uc002wod.1	+	1					SPTLC3_uc002wob.1_RNA|SPTLC3_uc002woc.2_5'UTR	NM_018327	NP_060797	Q9NUV7	SPTC3_HUMAN	serine palmitoyltransferase, long chain base						sphingoid biosynthetic process	integral to membrane|serine C-palmitoyltransferase complex	pyridoxal phosphate binding|serine C-palmitoyltransferase activity|transferase activity, transferring nitrogenous groups				0					Pyridoxal Phosphate(DB00114)	AAAAAGATAGGCTGTTGCTCT	0.433													3	19	---	---	---	---	PASS
EPB41L1	2036	broad.mit.edu	37	20	34776292	34776292	+	Missense_Mutation	SNP	G	T	T			TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34776292G>T	uc002xfb.2	+	9	1068	c.897G>T	c.(895-897)ATG>ATT	p.M299I	EPB41L1_uc002xeu.2_Missense_Mutation_p.M237I|EPB41L1_uc010zvo.1_Missense_Mutation_p.M299I|EPB41L1_uc002xev.2_Missense_Mutation_p.M299I|EPB41L1_uc002xew.2_Missense_Mutation_p.M202I|EPB41L1_uc002xex.2_Missense_Mutation_p.M268I|EPB41L1_uc002xey.2_Missense_Mutation_p.M226I|EPB41L1_uc002xez.2_Missense_Mutation_p.M237I	NM_012156	NP_036288	Q9H4G0	E41L1_HUMAN	erythrocyte membrane protein band 4.1-like 1	299	FERM.				cortical actin cytoskeleton organization|synaptic transmission	cytoskeleton|cytosol|extrinsic to membrane|plasma membrane	actin binding|structural molecule activity			ovary(2)|pancreas(1)	3	Breast(12;0.0239)					TCGACATCATGTTAGGCGTTT	0.572													65	100	---	---	---	---	PASS
PIGT	51604	broad.mit.edu	37	20	44045233	44045233	+	Silent	SNP	A	G	G			TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44045233A>G	uc002xoh.1	+	2	337	c.264A>G	c.(262-264)TCA>TCG	p.S88S	PIGT_uc010ghb.1_Silent_p.S88S|PIGT_uc010zwt.1_RNA|PIGT_uc010ghd.1_Intron|PIGT_uc010ghc.1_RNA|PIGT_uc010ghe.1_Silent_p.S88S|PIGT_uc010ghf.1_Silent_p.S88S|PIGT_uc002xoj.1_Silent_p.S88S|PIGT_uc002xok.1_Silent_p.S88S|PIGT_uc010zwu.1_5'UTR|PIGT_uc002xoi.1_RNA|PIGT_uc010zwv.1_Intron|PIGT_uc010zww.1_Silent_p.S88S|PIGT_uc010zwx.1_5'UTR|PIGT_uc010zwy.1_Intron|PIGT_uc010zwz.1_Intron|PIGT_uc010zxa.1_5'UTR|PIGT_uc002xol.1_5'Flank	NM_015937	NP_057021	Q969N2	PIGT_HUMAN	phosphatidylinositol glycan anchor biosynthesis,	88	Lumenal (Potential).				attachment of GPI anchor to protein|C-terminal protein lipidation	GPI-anchor transamidase complex	protein binding			pancreas(1)	1		Myeloproliferative disorder(115;0.0122)				TGCACCTGTCATTCACACAAG	0.577													17	22	---	---	---	---	PASS
PIGT	51604	broad.mit.edu	37	20	44045300	44045300	+	Missense_Mutation	SNP	G	A	A			TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44045300G>A	uc002xoh.1	+	2	404	c.331G>A	c.(331-333)GAG>AAG	p.E111K	PIGT_uc010ghb.1_Missense_Mutation_p.E111K|PIGT_uc010zwt.1_RNA|PIGT_uc010ghd.1_Intron|PIGT_uc010ghc.1_RNA|PIGT_uc010ghe.1_Missense_Mutation_p.E111K|PIGT_uc010ghf.1_Intron|PIGT_uc002xoj.1_Missense_Mutation_p.E111K|PIGT_uc002xok.1_Missense_Mutation_p.E111K|PIGT_uc010zwu.1_Intron|PIGT_uc002xoi.1_RNA|PIGT_uc010zwv.1_Intron|PIGT_uc010zww.1_Intron|PIGT_uc010zwx.1_5'UTR|PIGT_uc010zwy.1_Intron|PIGT_uc010zwz.1_Intron|PIGT_uc010zxa.1_5'UTR|PIGT_uc002xol.1_5'Flank	NM_015937	NP_057021	Q969N2	PIGT_HUMAN	phosphatidylinositol glycan anchor biosynthesis,	111	Lumenal (Potential).				attachment of GPI anchor to protein|C-terminal protein lipidation	GPI-anchor transamidase complex	protein binding			pancreas(1)	1		Myeloproliferative disorder(115;0.0122)				ATCAGGTGCAGAGCTGTGGGT	0.577													18	22	---	---	---	---	PASS
B4GALT5	9334	broad.mit.edu	37	20	48330184	48330184	+	Missense_Mutation	SNP	A	T	T			TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:48330184A>T	uc002xuu.3	-	1	238	c.44T>A	c.(43-45)CTG>CAG	p.L15Q		NM_004776	NP_004767	O43286	B4GT5_HUMAN	UDP-Gal:betaGlcNAc beta 1,4-	15	Helical; Signal-anchor for type II membrane protein; (Potential).				post-translational protein modification|protein N-linked glycosylation via asparagine	Golgi cisterna membrane|integral to membrane	galactosyltransferase activity|metal ion binding			ovary(1)	1			BRCA - Breast invasive adenocarcinoma(9;2.51e-06)			CGCGGCGAGCAGCGAGCGGCG	0.721													3	2	---	---	---	---	PASS
LOC100132288	100132288	broad.mit.edu	37	21	9907198	9907198	+	3'UTR	SNP	C	T	T			TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:9907198C>T	uc002zka.1	-	4					LOC100132288_uc010gqn.1_RNA	NM_001033515	NP_001028687			hypothetical protein LOC100132288												0						GTGCAGAAAGCTAACGCACTG	0.592													3	17	---	---	---	---	PASS
EIF3L	51386	broad.mit.edu	37	22	38274117	38274117	+	Missense_Mutation	SNP	G	T	T			TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38274117G>T	uc003auf.2	+	11	1601	c.1514G>T	c.(1513-1515)GGT>GTT	p.G505V	EIF3L_uc003aue.1_Missense_Mutation_p.G505V|EIF3L_uc011ann.1_Missense_Mutation_p.G457V|EIF3L_uc003aug.2_Missense_Mutation_p.G397V|EIF3L_uc003auh.2_Missense_Mutation_p.G238V	NM_016091	NP_057175	Q9Y262	EIF3L_HUMAN	eukaryotic translation initiation factor 3	505						eukaryotic translation initiation factor 3 complex	protein binding|translation initiation factor activity			ovary(1)	1						TGGACCAGCGGTATCTCAGCC	0.512													62	66	---	---	---	---	PASS
ARSF	416	broad.mit.edu	37	X	2990145	2990145	+	Silent	SNP	T	C	C			TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:2990145T>C	uc004cre.1	+	3	311	c.90T>C	c.(88-90)CCT>CCC	p.P30P	ARSF_uc004crf.1_Silent_p.P30P	NM_004042	NP_004033	P54793	ARSF_HUMAN	arylsulfatase F precursor	30						extracellular region	arylsulfatase activity|metal ion binding			ovary(2)	2		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				ACGACAAGCCTAATATTGTCC	0.498													3	97	---	---	---	---	PASS
RAP1GAP	5909	broad.mit.edu	37	1	21924516	21924516	+	Frame_Shift_Del	DEL	C	-	-			TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:21924516delC	uc001bex.2	-	23	2179	c.1921delG	c.(1921-1923)GACfs	p.D641fs	RAP1GAP_uc001bev.2_Frame_Shift_Del_p.D726fs|RAP1GAP_uc001bew.2_Frame_Shift_Del_p.D705fs|RAP1GAP_uc001bey.2_Frame_Shift_Del_p.D659fs	NM_002885	NP_002876	P47736	RPGP1_HUMAN	RAP1 GTPase activating protein isoform c	641					regulation of Ras GTPase activity|signal transduction	cytosol|Golgi membrane|membrane fraction	GTPase activator activity|GTPase activity|protein homodimerization activity|Ras GTPase binding			breast(2)|ovary(1)	3		Colorectal(325;0.000147)|Renal(390;0.000734)|Lung NSC(340;0.000861)|all_lung(284;0.000901)|Breast(348;0.012)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0427)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0192)|OV - Ovarian serous cystadenocarcinoma(117;2.3e-26)|COAD - Colon adenocarcinoma(152;1.59e-05)|GBM - Glioblastoma multiforme(114;2.7e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000354)|STAD - Stomach adenocarcinoma(196;0.00645)|KIRC - Kidney renal clear cell carcinoma(1967;0.00862)|READ - Rectum adenocarcinoma(331;0.0625)|Lung(427;0.146)		CACGCAGGGTCCCCCAACTTG	0.692													4	2	---	---	---	---	
ROCK2	9475	broad.mit.edu	37	2	11355800	11355804	+	Intron	DEL	AAAAG	-	-			TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:11355800_11355804delAAAAG	uc002rbd.1	-							NM_004850	NP_004841	O75116	ROCK2_HUMAN	Rho-associated, coiled-coil containing protein						axon guidance|cytokinesis|intracellular signal transduction	cytosol|plasma membrane	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|structural molecule activity			stomach(2)|skin(2)	4	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.137)|OV - Ovarian serous cystadenocarcinoma(76;0.162)		TTATTATCAAAAAAGTATGTATAAA	0.288													16	16	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	64602820	64602821	+	IGR	INS	-	CAT	CAT	rs145819064		TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:64602820_64602821insCAT								PELI1 (231215 upstream) : HSPC159 (78506 downstream)																							accaccaccaccaccatcacca	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	133020743	133020744	+	IGR	INS	-	T	T	rs137914230		TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133020743_133020744insT								NCRNA00164 (5201 upstream) : GPR39 (153403 downstream)																							TTAGATAGCTCTTTATTGTCAT	0.327													7	8	---	---	---	---	
VHL	7428	broad.mit.edu	37	3	10183787	10183787	+	Frame_Shift_Del	DEL	C	-	-			TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10183787delC	uc003bvc.2	+	1	469	c.256delC	c.(256-258)CCCfs	p.P86fs	VHL_uc003bvd.2_Frame_Shift_Del_p.P86fs	NM_000551	NP_000542	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor isoform 1	86			P -> R (in VHLD; type I).|P -> S (in VHLD).|P -> L (in VHLD; type I).|P -> H (in VHLD).|P -> A (in VHLD; type I).		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.P86H(3)|p.P86L(2)|p.P86fs*72(2)|p.P86S(2)|p.S72_V87>L(1)|p.R60fs*35(1)|p.P86A(1)|p.V84_E94>E(1)|p.P86R(1)|p.L85fs*46(1)|p.V84fs*72(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)		CGTCGTGCTGCCCGTATGGCT	0.721		1	D|Mis|N|F|S		renal|hemangioma|pheochromocytoma	renal|hemangioma|pheochromocytoma			von_Hippel-Lindau_disease|Chuvash_Polycythemia_|Pheochromocytoma_(Adrenal)_Familial				4	9	---	---	---	---	
SMARCAD1	56916	broad.mit.edu	37	4	95186071	95186071	+	Intron	DEL	A	-	-			TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:95186071delA	uc003htc.3	+						SMARCAD1_uc003htb.3_Intron|SMARCAD1_uc003htd.3_Intron|SMARCAD1_uc010ila.2_Intron|SMARCAD1_uc011cdw.1_Intron	NM_020159	NP_064544	Q9H4L7	SMRCD_HUMAN	SWI/SNF-related, matrix-associated						chromatin modification|nucleotide metabolic process|positive regulation of transcription, DNA-dependent|protein homooligomerization|regulation of DNA recombination	nuclear matrix	ATP binding|DNA binding|helicase activity			skin(2)|ovary(1)|breast(1)	4				OV - Ovarian serous cystadenocarcinoma(123;4.33e-08)		ATCTTTGTTGAATATATTTAT	0.328													13	20	---	---	---	---	
MARCH6	10299	broad.mit.edu	37	5	10423809	10423811	+	Intron	DEL	AAC	-	-			TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:10423809_10423811delAAC	uc003jet.1	+						MARCH6_uc011cmu.1_Intron|MARCH6_uc003jeu.1_Intron|MARCH6_uc011cmv.1_Intron	NM_005885	NP_005876	O60337	MARH6_HUMAN	membrane-associated ring finger (C3HC4) 6						protein K48-linked ubiquitination	integral to endoplasmic reticulum membrane	ubiquitin conjugating enzyme binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)|breast(1)	2						ATTGTTAAAAAACAACAGAAATA	0.345													31	40	---	---	---	---	
PPWD1	23398	broad.mit.edu	37	5	64880705	64880706	+	Intron	INS	-	AA	AA	rs10682457		TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:64880705_64880706insAA	uc003jtv.3	+						PPWD1_uc011cqv.1_Intron|PPWD1_uc011cqw.1_Intron	NM_015342	NP_056157	Q96BP3	PPWD1_HUMAN	peptidylprolyl isomerase domain and WD repeat						protein folding	catalytic step 2 spliceosome	peptidyl-prolyl cis-trans isomerase activity			ovary(1)	1		Lung NSC(167;7.21e-05)|Prostate(74;0.0174)|Ovarian(174;0.186)		Lung(70;0.00451)		TAGAGATTATGAAAAAAAAAAA	0.332													5	3	---	---	---	---	
NSD1	64324	broad.mit.edu	37	5	176709782	176709783	+	Intron	INS	-	TTA	TTA			TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176709782_176709783insTTA	uc003mfr.3	+						NSD1_uc003mft.3_Intron|NSD1_uc011dfx.1_Intron	NM_022455	NP_071900	Q96L73	NSD1_HUMAN	nuclear receptor binding SET domain protein 1						negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|nucleus	androgen receptor binding|chromatin binding|estrogen receptor binding|histone methyltransferase activity (H3-K36 specific)|histone methyltransferase activity (H4-K20 specific)|ligand-dependent nuclear receptor binding|retinoid X receptor binding|thyroid hormone receptor binding|transcription corepressor activity|zinc ion binding			ovary(2)|kidney(1)	3	all_cancers(89;1.57e-05)|Renal(175;0.000269)|Lung NSC(126;0.00111)|all_lung(126;0.002)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)|Epithelial(233;0.198)	Kidney(146;0.235)		TACAGCAGCTTTTAGCATTGTT	0.376			T	NUP98	AML		Sotos Syndrome		Beckwith-Wiedemann_syndrome|Sotos_syndrome|Weaver_syndrome	HNSCC(47;0.14)			9	6	---	---	---	---	
BTN3A1	11119	broad.mit.edu	37	6	26410419	26410420	+	Intron	INS	-	A	A			TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26410419_26410420insA	uc003nhv.2	+						BTN3A1_uc011dkj.1_Intron|BTN3A1_uc011dkk.1_Intron|BTN3A1_uc010jqj.2_Intron	NM_007048	NP_008979	O00481	BT3A1_HUMAN	butyrophilin, subfamily 3, member A1 isoform a						lipid metabolic process	integral to membrane				upper_aerodigestive_tract(1)|ovary(1)	2						TTGCCaaaaagaaaaaaaaaaa	0.342													6	3	---	---	---	---	
HCG4	54435	broad.mit.edu	37	6	29761770	29761770	+	5'Flank	DEL	G	-	-			TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:29761770delG	uc003nns.2	-						uc003nnt.2_Intron|uc011dma.1_RNA	NR_002139				Homo sapiens clone HCG IV.9 unknown mRNA.												0						gacatcctcagcaggattggt	0.005													4	2	---	---	---	---	
CGA	1081	broad.mit.edu	37	6	87797955	87797956	+	Intron	DEL	AC	-	-	rs71944433		TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:87797955_87797956delAC	uc003plj.1	-							NM_000735	NP_000726	P01215	GLHA_HUMAN	glycoprotein hormones, alpha polypeptide						hormone biosynthetic process|peptide hormone processing|signal transduction	extracellular region|soluble fraction	hormone activity			ovary(1)	1		all_cancers(76;5.98e-09)|Acute lymphoblastic leukemia(125;2.15e-10)|Prostate(29;5.29e-10)|all_hematologic(105;1.08e-06)|all_epithelial(107;0.000102)		BRCA - Breast invasive adenocarcinoma(108;0.0484)		AAAAAAAAAAACAAAAAACAGT	0.371													3	6	---	---	---	---	
MANEA	79694	broad.mit.edu	37	6	96034896	96034897	+	Intron	DEL	TG	-	-			TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:96034896_96034897delTG	uc003poo.1	+						MANEA_uc003pon.2_Frame_Shift_Del_p.L194fs	NM_024641	NP_078917	Q5SRI9	MANEA_HUMAN	mannosidase, endo-alpha						post-translational protein modification|protein N-linked glycosylation via asparagine	Golgi membrane|integral to membrane	glycoprotein endo-alpha-1,2-mannosidase activity			ovary(2)|breast(1)	3		all_cancers(76;1.01e-06)|Acute lymphoblastic leukemia(125;3.58e-09)|all_hematologic(75;1.22e-06)|all_epithelial(107;0.00433)|Colorectal(196;0.0341)		BRCA - Breast invasive adenocarcinoma(108;0.148)		tgtttgtgtctgtatatatgca	0.233													8	7	---	---	---	---	
PTPRK	5796	broad.mit.edu	37	6	128561077	128561078	+	Intron	DEL	CA	-	-			TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:128561077_128561078delCA	uc003qbk.2	-						PTPRK_uc003qbj.2_Intron|PTPRK_uc010kfc.2_Intron|PTPRK_uc011ebu.1_Intron|PTPRK_uc003qbl.1_Intron|PTPRK_uc011ebv.1_Intron	NM_002844	NP_002835	Q15262	PTPRK_HUMAN	protein tyrosine phosphatase, receptor type, K						cell migration|cellular response to reactive oxygen species|cellular response to UV|focal adhesion assembly|negative regulation of cell cycle|negative regulation of cell migration|negative regulation of keratinocyte proliferation|negative regulation of transcription, DNA-dependent|protein localization at cell surface|transforming growth factor beta receptor signaling pathway	adherens junction|cell surface|cell-cell junction|integral to plasma membrane|leading edge membrane	beta-catenin binding|gamma-catenin binding|protein kinase binding|transmembrane receptor protein tyrosine phosphatase activity			ovary(3)|skin(2)|pancreas(1)|kidney(1)|central_nervous_system(1)	8				all cancers(137;0.0118)|GBM - Glioblastoma multiforme(226;0.0372)|OV - Ovarian serous cystadenocarcinoma(136;0.24)		TGTGCACACGCACACACACACA	0.396													4	2	---	---	---	---	
AMPH	273	broad.mit.edu	37	7	38543103	38543103	+	Intron	DEL	T	-	-	rs10225047		TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:38543103delT	uc003tgu.2	-						AMPH_uc003tgv.2_Intron	NM_001635	NP_001626	P49418	AMPH_HUMAN	amphiphysin isoform 1						endocytosis|synaptic transmission	actin cytoskeleton|cell junction|synaptic vesicle membrane				ovary(3)|liver(1)|skin(1)	5						GGCGGGGGGGTGGGTGGTGGA	0.423													6	6	---	---	---	---	
SLC26A5	375611	broad.mit.edu	37	7	103017133	103017135	+	Intron	DEL	AGA	-	-	rs66928926	byFrequency	TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:103017133_103017135delAGA	uc003vbz.2	-						SLC26A5_uc003vbt.1_Intron|SLC26A5_uc003vbu.1_Intron|SLC26A5_uc003vbv.1_Intron|SLC26A5_uc003vbw.2_Intron|SLC26A5_uc003vbx.2_Intron|SLC26A5_uc003vby.2_Intron|SLC26A5_uc010liy.2_Intron	NM_198999	NP_945350	P58743	S26A5_HUMAN	prestin isoform a						regulation of cell shape|sensory perception of sound	integral to membrane	secondary active sulfate transmembrane transporter activity			ovary(1)	1						GTGATTTTTCAGAAGAACAATTT	0.320													8	9	---	---	---	---	
AASS	10157	broad.mit.edu	37	7	121717991	121717991	+	Frame_Shift_Del	DEL	T	-	-			TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:121717991delT	uc003vka.2	-	22	2659	c.2563delA	c.(2563-2565)ACGfs	p.T855fs	AASS_uc011knu.1_RNA|AASS_uc011knv.1_RNA|AASS_uc003vkb.2_Frame_Shift_Del_p.T855fs|AASS_uc011knw.1_Frame_Shift_Del_p.T343fs	NM_005763	NP_005754	Q9UDR5	AASS_HUMAN	aminoadipate-semialdehyde synthase precursor	855	Saccharopine dehydrogenase.				protein tetramerization	mitochondrial matrix	binding|saccharopine dehydrogenase (NAD+, L-glutamate-forming) activity|saccharopine dehydrogenase (NADP+, L-lysine-forming) activity			upper_aerodigestive_tract(1)|ovary(1)	2					L-Glutamic Acid(DB00142)|NADH(DB00157)	AGATCAATCGTTTTATGTTCT	0.413													393	258	---	---	---	---	
UBE3C	9690	broad.mit.edu	37	7	156962829	156962829	+	Intron	DEL	C	-	-	rs66735407		TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:156962829delC	uc010lqs.2	+						UBE3C_uc003wnf.2_Intron|UBE3C_uc003wng.2_Intron	NM_014671	NP_055486	Q15386	UBE3C_HUMAN	ubiquitin protein ligase E3C						protein polyubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	nucleus|proteasome complex	protein binding|ubiquitin-protein ligase activity			ovary(2)|lung(2)|large_intestine(1)	5		all_hematologic(28;0.0185)|all_epithelial(9;0.0664)	OV - Ovarian serous cystadenocarcinoma(82;0.00448)	UCEC - Uterine corpus endometrioid carcinoma (81;0.19)		ttttttttttctttttAACCA	0.174													8	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	10335889	10335903	+	IGR	DEL	GGCTGCAGTGGTTGT	-	-			TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:10335889_10335903delGGCTGCAGTGGTTGT								MSRA (49490 upstream) : PRSS55 (47178 downstream)																							GTGGTTGTCAGGCTGCAGTGGTTGTGGCTGCAGTG	0.586													2	5	---	---	---	---	
C8orf34	116328	broad.mit.edu	37	8	69728341	69728342	+	Intron	DEL	GT	-	-	rs111246993		TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:69728341_69728342delGT	uc010lyz.2	+						C8orf34_uc003xyb.2_Intron	NM_052958	NP_443190	Q49A92	CH034_HUMAN	hypothetical protein LOC116328						signal transduction		cAMP-dependent protein kinase regulator activity			large_intestine(1)	1			Epithelial(68;0.0117)|OV - Ovarian serous cystadenocarcinoma(28;0.0227)|all cancers(69;0.0502)			TTTCCTAAGAgtgtgtgtgtgt	0.252													9	4	---	---	---	---	
FER1L6	654463	broad.mit.edu	37	8	125034095	125034096	+	Intron	INS	-	T	T	rs138450142	by1000genomes	TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:125034095_125034096insT	uc003yqw.2	+						uc003yqx.1_Intron	NM_001039112	NP_001034201	Q2WGJ9	FR1L6_HUMAN	fer-1-like 6							integral to membrane				ovary(5)|skin(5)|central_nervous_system(1)	11	Lung NSC(37;4.1e-12)|Ovarian(258;0.00438)|all_neural(195;0.0741)		STAD - Stomach adenocarcinoma(47;0.00186)			AGCTTTATTCATTTTTTTTTCA	0.386													3	3	---	---	---	---	
WDR34	89891	broad.mit.edu	37	9	131396796	131396797	+	Intron	DEL	CT	-	-			TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131396796_131396797delCT	uc004bvq.1	-						WDR34_uc004bvs.1_Intron|WDR34_uc004bvr.1_Intron	NM_052844	NP_443076	Q96EX3	WDR34_HUMAN	WD repeat domain 34							cytoplasm				central_nervous_system(2)|skin(1)	3						GGAGTTGGTCCTCTCATTAGAG	0.614													3	6	---	---	---	---	
EGFL7	51162	broad.mit.edu	37	9	139565480	139565480	+	Intron	DEL	G	-	-	rs71988346		TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:139565480delG	uc004cid.2	+						EGFL7_uc004cif.2_Intron|EGFL7_uc004cig.2_Intron|EGFL7_uc010nbp.2_Intron|EGFL7_uc004cie.2_Intron|EGFL7_uc004cih.2_Intron	NM_201446	NP_958854	Q9UHF1	EGFL7_HUMAN	EGF-like-domain, multiple 7						angiogenesis|vasculogenesis		calcium ion binding			ovary(1)	1	all_cancers(76;0.109)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;9.87e-06)|Epithelial(140;0.000123)		AGGCATTGGTGGGGGGGGGGG	0.667													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	81632947	81632948	+	IGR	INS	-	T	T			TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:81632947_81632948insT								LOC650623 (184299 upstream) : MBL1P (31706 downstream)																							CTCTTCAtttcttttttttttt	0.218													6	3	---	---	---	---	
PTEN	5728	broad.mit.edu	37	10	89692880	89692893	+	Frame_Shift_Del	DEL	ATTCACTGTAAAGC	-	-	rs121909222		TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:89692880_89692893delATTCACTGTAAAGC	uc001kfb.2	+	6	1395_1408	c.364_377delATTCACTGTAAAGC	c.(364-378)ATTCACTGTAAAGCTfs	p.I122fs		NM_000314	NP_000305	P60484	PTEN_HUMAN	phosphatase and tensin homolog	122_126	Phosphatase tensin-type.				activation of mitotic anaphase-promoting complex activity|apoptosis|canonical Wnt receptor signaling pathway|cell proliferation|central nervous system development|induction of apoptosis|inositol phosphate dephosphorylation|negative regulation of cell migration|negative regulation of cyclin-dependent protein kinase activity involved in G1/S|negative regulation of focal adhesion assembly|negative regulation of G1/S transition of mitotic cell cycle|negative regulation of protein kinase B signaling cascade|negative regulation of protein phosphorylation|nerve growth factor receptor signaling pathway|phosphatidylinositol dephosphorylation|phosphatidylinositol-mediated signaling|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|positive regulation of sequence-specific DNA binding transcription factor activity|protein stabilization|regulation of neuron projection development|T cell receptor signaling pathway	cytosol|internal side of plasma membrane|PML body	anaphase-promoting complex binding|enzyme binding|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity|lipid binding|magnesium ion binding|PDZ domain binding|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity|phosphatidylinositol-3-phosphatase activity|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity	p.C124S(7)|p.A126T(5)|p.R55fs*1(4)|p.H123Y(4)|p.C124fs*10(3)|p.I122fs*2(3)|p.A126D(3)|p.K125N(2)|p.K125E(2)|p.Y27_N212>Y(2)|p.?(2)|p.Y27fs*1(2)|p.A126P(2)|p.C124F(1)|p.I122N(1)|p.I122S(1)|p.A121_F145del(1)|p.F56fs*2(1)|p.C124Y(1)|p.A126V(1)|p.A126S(1)|p.K125*(1)		endometrium(831)|central_nervous_system(657)|skin(121)|haematopoietic_and_lymphoid_tissue(101)|large_intestine(99)|prostate(97)|breast(73)|lung(65)|ovary(58)|thyroid(29)|stomach(29)|upper_aerodigestive_tract(25)|cervix(24)|liver(20)|vulva(17)|kidney(15)|NS(14)|soft_tissue(13)|urinary_tract(12)|eye(8)|pancreas(6)|salivary_gland(5)|bone(5)|biliary_tract(4)|autonomic_ganglia(2)|meninges(2)|testis(1)|oesophagus(1)	2334		all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132)	KIRC - Kidney renal clear cell carcinoma(1;0.214)	UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218)		TGTTGCAGCAATTCACTGTAAAGCTGGAAAGGGA	0.407		31	D|Mis|N|F|S		glioma| prostate|endometrial	harmartoma|glioma| prostate|endometrial			Proteus_syndrome|Cowden_syndrome|Juvenile_Polyposis|Hereditary_Mixed_Polyposis_Syndrome_type_1|Bannayan-Riley-Ruvalcaba_syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)			30	42	---	---	---	---	
C11orf46	120534	broad.mit.edu	37	11	30358033	30358034	+	Intron	DEL	CT	-	-	rs77082221		TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:30358033_30358034delCT	uc001mso.1	+						C11orf46_uc001msp.2_5'Flank	NM_152316	NP_689529	Q8N8R7	CK046_HUMAN	hypothetical protein LOC120534												0						ATTTTATCTCCTTTTTTTTTTT	0.282													10	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	55647218	55647219	+	IGR	INS	-	TTACTTCC	TTACTTCC			TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55647218_55647219insTTACTTCC								OR5D16 (40006 upstream) : SPRYD5 (3554 downstream)																							TATCAGATATTTTACTTCCTTA	0.337													4	3	---	---	---	---	
MMP27	64066	broad.mit.edu	37	11	102576586	102576586	+	5'Flank	DEL	T	-	-	rs150085097		TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:102576586delT	uc001phd.1	-							NM_022122	NP_071405	Q9H306	MMP27_HUMAN	matrix metalloproteinase 27 precursor						collagen catabolic process|proteolysis	proteinaceous extracellular matrix	calcium ion binding|metalloendopeptidase activity|zinc ion binding			ovary(2)|skin(1)	3	all_cancers(8;0.000843)|all_epithelial(12;0.00362)|Lung NSC(15;0.21)	all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)	Epithelial(9;0.0509)|Lung(13;0.0696)|LUSC - Lung squamous cell carcinoma(19;0.13)|all cancers(10;0.176)	BRCA - Breast invasive adenocarcinoma(274;0.0151)		CATGATTTGCttttttttttt	0.308													4	2	---	---	---	---	
CD63	967	broad.mit.edu	37	12	56120118	56120118	+	Intron	DEL	C	-	-	rs114172797		TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56120118delC	uc001shm.2	-						CD63_uc009znz.2_Intron|CD63_uc001shn.2_Intron|CD63_uc001sho.2_Intron|CD63_uc001shp.2_Intron	NM_001780	NP_001771	P08962	CD63_HUMAN	CD63 antigen isoform A						platelet activation|platelet degranulation	integral to plasma membrane|late endosome membrane|lysosomal membrane|platelet dense granule membrane					0						GATGAGAAttctttttttttt	0.214													13	10	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	77054675	77054676	+	IGR	INS	-	A	A	rs34680604		TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:77054675_77054676insA								OSBPL8 (101086 upstream) : ZDHHC17 (103178 downstream)																							TAATAGGTGttaaaaaaaaaaa	0.386													6	3	---	---	---	---	
CEP290	80184	broad.mit.edu	37	12	88525006	88525006	+	Intron	DEL	A	-	-			TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:88525006delA	uc001tar.2	-						CEP290_uc001tat.2_5'Flank|CEP290_uc009zsl.1_Intron	NM_025114	NP_079390	O15078	CE290_HUMAN	centrosomal protein 290kDa						cilium assembly|eye photoreceptor cell development|G2/M transition of mitotic cell cycle|hindbrain development|otic vesicle formation|positive regulation of transcription, DNA-dependent|pronephros development|protein transport	cell surface|centrosome|cytosol|nucleus|photoreceptor connecting cilium	protein binding			ovary(5)|breast(1)|pancreas(1)	7						Ctaaaatagtaaaaaaaaaaa	0.199													4	2	---	---	---	---	
FGD6	55785	broad.mit.edu	37	12	95500974	95500975	+	Intron	INS	-	T	T	rs148392232	by1000genomes	TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:95500974_95500975insT	uc001tdp.3	-						FGD6_uc009zsx.2_Intron|FGD6_uc001tdq.1_Intron	NM_018351	NP_060821	Q6ZV73	FGD6_HUMAN	FYVE, RhoGEF and PH domain containing 6						actin cytoskeleton organization|filopodium assembly|regulation of Cdc42 GTPase activity|regulation of cell shape	cytoskeleton|Golgi apparatus|lamellipodium|ruffle	metal ion binding|Rho guanyl-nucleotide exchange factor activity|small GTPase binding			ovary(2)|breast(1)	3						TACCCAGAATGTTTATTAGAAT	0.287													6	4	---	---	---	---	
CHST11	50515	broad.mit.edu	37	12	104851282	104851282	+	Frame_Shift_Del	DEL	C	-	-			TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:104851282delC	uc001tkx.1	+	2	384	c.93delC	c.(91-93)TTCfs	p.F31fs	CHST11_uc001tky.2_Frame_Shift_Del_p.F31fs	NM_018413	NP_060883	Q9NPF2	CHSTB_HUMAN	carbohydrate sulfotransferase 11	31	Helical; Signal-anchor for type II membrane protein; (Potential).				chondroitin sulfate biosynthetic process	Golgi membrane|integral to membrane	chondroitin 4-sulfotransferase activity|N-acetylgalactosamine 4-O-sulfotransferase activity				0						TGGTCATCTTCTATTTCCAAA	0.512													95	77	---	---	---	---	
RPGRIP1	57096	broad.mit.edu	37	14	21756340	21756340	+	Intron	DEL	T	-	-	rs11335332		TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:21756340delT	uc001wag.2	+							NM_020366	NP_065099	Q96KN7	RPGR1_HUMAN	retinitis pigmentosa GTPase regulator						response to stimulus|visual perception	cilium				ovary(4)|breast(2)|pancreas(1)	7	all_cancers(95;0.0017)	all_cancers(140;0.0973)	Epithelial(56;6.24e-07)|all cancers(55;6.56e-06)	GBM - Glioblastoma multiforme(265;0.00888)		GTCTTCTCACttttttttttt	0.199													9	4	---	---	---	---	
JPH4	84502	broad.mit.edu	37	14	24046212	24046213	+	Intron	INS	-	G	G			TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24046212_24046213insG	uc001wkq.2	-						JPH4_uc001wkr.2_Intron|JPH4_uc001wks.2_Intron	NM_032452	NP_115828	Q96JJ6	JPH4_HUMAN	junctophilin 4						calcium ion transport into cytosol|regulation of ryanodine-sensitive calcium-release channel activity	integral to membrane|junctional sarcoplasmic reticulum membrane				ovary(1)|pancreas(1)	2	all_cancers(95;0.000251)			GBM - Glioblastoma multiforme(265;0.00654)		GCGCAAATGGCGGGCGAAGGCC	0.653													4	2	---	---	---	---	
MIPOL1	145282	broad.mit.edu	37	14	37739846	37739847	+	Intron	INS	-	T	T			TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:37739846_37739847insT	uc001wuc.2	+						MIPOL1_uc010amr.2_Intron|MIPOL1_uc001wub.3_Intron|MIPOL1_uc001wud.2_Intron|MIPOL1_uc010ams.2_Intron|MIPOL1_uc001wue.2_Intron|MIPOL1_uc010amt.2_Intron	NM_138731	NP_620059	Q8TD10	MIPO1_HUMAN	mirror-image polydactyly 1											ovary(1)|central_nervous_system(1)	2	Breast(36;0.119)|Esophageal squamous(585;0.164)|Hepatocellular(127;0.213)		Lung(238;6.03e-07)|LUAD - Lung adenocarcinoma(48;2.48e-05)|Epithelial(34;0.047)|all cancers(34;0.0953)|LUSC - Lung squamous cell carcinoma(13;0.0975)|BRCA - Breast invasive adenocarcinoma(188;0.196)	GBM - Glioblastoma multiforme(112;0.0358)		GGAAGCTCTCCTTTTTTTTTTT	0.366													6	3	---	---	---	---	
FERMT2	10979	broad.mit.edu	37	14	53326539	53326539	+	Intron	DEL	T	-	-			TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:53326539delT	uc001xad.2	-						FERMT2_uc001xac.2_Intron|FERMT2_uc001xae.2_Intron|FERMT2_uc001xaf.2_Intron	NM_006832	NP_006823	Q96AC1	FERM2_HUMAN	fermitin family homolog 2 isoform 1						actin cytoskeleton organization|cell adhesion|cell junction assembly|regulation of cell shape	cell cortex|cytosol|focal adhesion|stress fiber	binding				0	Breast(41;0.0342)					AGTACTAttcttttttttttt	0.174													4	2	---	---	---	---	
DLST	1743	broad.mit.edu	37	14	75359600	75359601	+	Frame_Shift_Ins	INS	-	A	A			TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:75359600_75359601insA	uc001xqv.2	+	8	569_570	c.506_507insA	c.(505-507)ACAfs	p.T169fs	DLST_uc001xqu.2_Frame_Shift_Ins_p.T81fs|DLST_uc001xqt.2_Frame_Shift_Ins_p.T85fs|DLST_uc010tuw.1_Frame_Shift_Ins_p.T83fs|DLST_uc001xqs.2_RNA|DLST_uc010tuv.1_Frame_Shift_Ins_p.T169fs	NM_001933	NP_001924	P36957	ODO2_HUMAN	dihydrolipoamide S-succinyltransferase (E2	169					lysine catabolic process|tricarboxylic acid cycle	mitochondrial matrix|nucleus	dihydrolipoyllysine-residue succinyltransferase activity			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(234;0.00698)		GCAGAACCTACAGCAGCGGCAG	0.584													58	35	---	---	---	---	
CASC5	57082	broad.mit.edu	37	15	40921686	40921688	+	Intron	DEL	GCC	-	-			TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:40921686_40921688delGCC	uc010bbs.1	+						CASC5_uc010bbt.1_Intron	NM_170589	NP_733468	Q8NG31	CASC5_HUMAN	cancer susceptibility candidate 5 isoform 1						acrosome assembly|attachment of spindle microtubules to kinetochore|cell division|CenH3-containing nucleosome assembly at centromere|mitotic prometaphase|spindle assembly checkpoint	acrosomal vesicle|condensed chromosome kinetochore|cytosol|nucleoplasm	protein binding			breast(3)|central_nervous_system(1)|skin(1)	5		all_cancers(109;2.03e-18)|all_epithelial(112;4.26e-15)|Lung NSC(122;1.12e-10)|all_lung(180;2.59e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)		GBM - Glioblastoma multiforme(113;4.99e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0861)|COAD - Colon adenocarcinoma(120;0.211)		ttttttttttgccttttcttttt	0.123													6	5	---	---	---	---	
SEMA6D	80031	broad.mit.edu	37	15	48054097	48054099	+	Intron	DEL	AAG	-	-	rs149404019		TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:48054097_48054099delAAG	uc010bek.2	+						SEMA6D_uc001zvw.2_Intron|SEMA6D_uc001zvx.1_Intron|SEMA6D_uc001zvy.2_Intron|SEMA6D_uc001zvz.2_Intron|SEMA6D_uc001zwa.2_Intron|SEMA6D_uc001zwb.2_Intron|SEMA6D_uc001zwc.2_Intron	NM_153618	NP_705871	Q8NFY4	SEM6D_HUMAN	semaphorin 6D isoform 4 precursor						axon guidance	cytoplasm|integral to membrane|plasma membrane	receptor activity			skin(3)|breast(1)	4		all_lung(180;0.000635)|Myeloproliferative disorder(241;0.116)|Melanoma(134;0.18)		all cancers(107;1.2e-11)|GBM - Glioblastoma multiforme(94;1.2e-06)		TTTCCAAAAAAAGAAGAAATTAA	0.291													7	5	---	---	---	---	
PRC1	9055	broad.mit.edu	37	15	91523763	91523764	+	Intron	INS	-	G	G	rs28584391		TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:91523763_91523764insG	uc002bqm.2	-						PRC1_uc002bqn.2_Intron|PRC1_uc002bqo.2_Intron|PRC1_uc010uqs.1_Intron	NM_003981	NP_003972	O43663	PRC1_HUMAN	protein regulator of cytokinesis 1 isoform 1						cytokinesis|mitotic spindle elongation	cytoplasm|nucleus|spindle microtubule|spindle pole	protein binding			ovary(1)|skin(1)	2	Lung NSC(78;0.0987)|all_lung(78;0.175)					ttttttttttttttgagacagg	0.134													0	6	---	---	---	---	
SLC9A3R2	9351	broad.mit.edu	37	16	2087452	2087453	+	Intron	INS	-	G	G			TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2087452_2087453insG	uc002coi.2	+						SLC9A3R2_uc002coj.2_Intron|SLC9A3R2_uc002cok.2_Intron	NM_001130012	NP_001123484	Q15599	NHRF2_HUMAN	solute carrier family 9 isoform 3 regulator 2						protein complex assembly	apical plasma membrane|endomembrane system|nucleus	beta-catenin binding|phosphatase binding|protein C-terminus binding|receptor binding			central_nervous_system(1)	1						GAGCACACACTGGGGGGGGGTG	0.649													3	3	---	---	---	---	
HYDIN	54768	broad.mit.edu	37	16	71061896	71061896	+	Intron	DEL	T	-	-	rs142337199		TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:71061896delT	uc002ezr.2	-						HYDIN_uc010cfz.1_Intron|HYDIN_uc002ezv.2_Intron	NM_032821	NP_116210	Q4G0P3	HYDIN_HUMAN	hydrocephalus inducing isoform a											ovary(1)|skin(1)	2		Ovarian(137;0.0654)				AATATAAGACTTTTTTTTTTT	0.408													4	3	---	---	---	---	
C17orf50	146853	broad.mit.edu	37	17	34088119	34088119	+	Intron	DEL	T	-	-			TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:34088119delT	uc002hjx.2	+						MMP28_uc002hjw.1_Intron	NM_145272	NP_660315	Q8WW18	CQ050_HUMAN	hypothetical protein LOC146853												0		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		CCTTCCTGAAttttttttttt	0.254													4	2	---	---	---	---	
GRIN2C	2905	broad.mit.edu	37	17	72858493	72858494	+	5'Flank	INS	-	C	C	rs150874217	by1000genomes	TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:72858493_72858494insC	uc002jlt.1	-						GRIN2C_uc010wrh.1_5'Flank|GRIN2C_uc002jlu.1_5'Flank|GRIN2C_uc002jlv.1_5'Flank	NM_000835	NP_000826	Q14957	NMDE3_HUMAN	N-methyl-D-aspartate receptor subunit 2C						glutamate signaling pathway	cell junction|outer membrane-bounded periplasmic space|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|N-methyl-D-aspartate selective glutamate receptor activity			ovary(2)|breast(2)	4	all_lung(278;0.172)|Lung NSC(278;0.207)				Glycine(DB00145)|L-Glutamic Acid(DB00142)|Loperamide(DB00836)	GCCCCATCAAGCCCCAATGAGG	0.658											OREG0024719	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	3	5	---	---	---	---	
TK1	7083	broad.mit.edu	37	17	76170949	76170960	+	In_Frame_Del	DEL	CCGGCAGGCTGG	-	-	rs1065767	byFrequency	TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:76170949_76170960delCCGGCAGGCTGG	uc002juw.2	-	7	795_806	c.585_596delCCAGCCTGCCGG	c.(583-597)GGCCAGCCTGCCGGG>GGG	p.195_199GQPAG>G	TK1_uc002jux.2_In_Frame_Del_p.270_274GQPAG>G	NM_003258	NP_003249	P04183	KITH_HUMAN	thymidine kinase 1	195_199					DNA replication|protein homotetramerization|pyrimidine base metabolic process|pyrimidine nucleoside salvage	cytosol	ATP binding|thymidine kinase activity|zinc ion binding				0			BRCA - Breast invasive adenocarcinoma(99;0.00269)|OV - Ovarian serous cystadenocarcinoma(97;0.0804)|Lung(188;0.23)			GTTGTCCGGCCCGGCAGGCTGGCCTGAGGCCT	0.618													27	13	---	---	---	---	
ACAA2	10449	broad.mit.edu	37	18	47320868	47320871	+	Intron	DEL	TAAA	-	-			TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:47320868_47320871delTAAA	uc002ldw.3	-						ACAA2_uc002ldx.3_Intron	NM_006111	NP_006102	P42765	THIM_HUMAN	acetyl-coenzyme A acyltransferase 2						anti-apoptosis|cholesterol biosynthetic process		acetyl-CoA C-acyltransferase activity|protein binding			ovary(1)	1						ATAATTTCTTTAAATAATCAACAC	0.240													11	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	63778855	63778858	+	IGR	DEL	GAAG	-	-			TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:63778855_63778858delGAAG								CDH7 (230681 upstream) : CDH19 (392463 downstream)																							aaggaagaaagaaggaaggaagga	0.000													5	3	---	---	---	---	
PLIN4	729359	broad.mit.edu	37	19	4510389	4510389	+	Intron	DEL	C	-	-	rs56906779		TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4510389delC	uc002mar.1	-						PLIN4_uc010dub.1_Intron	NM_001080400	NP_001073869	Q96Q06	PLIN4_HUMAN	plasma membrane associated protein, S3-12							lipid particle|plasma membrane					0						aaaaaaaaaacaaaaCAGTCA	0.294													5	6	---	---	---	---	
RGL3	57139	broad.mit.edu	37	19	11526892	11526893	+	Intron	INS	-	T	T	rs60951384		TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11526892_11526893insT	uc002mrp.2	-						RGL3_uc002mrn.2_Intron|RGL3_uc002mrm.2_Intron|RGL3_uc002mro.2_Intron	NM_001035223	NP_001030300	Q3MIN7	RGL3_HUMAN	ral guanine nucleotide dissociation						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	intracellular				ovary(1)	1						CTCCTGGTACCttttttttttt	0.307													4	2	---	---	---	---	
HKR1	284459	broad.mit.edu	37	19	37852828	37852828	+	Intron	DEL	A	-	-	rs67608963		TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:37852828delA	uc002ogb.2	+						HKR1_uc002ofx.2_Intron|HKR1_uc002ofy.2_Intron|HKR1_uc002oga.2_Intron|HKR1_uc010xto.1_Intron|HKR1_uc002ogc.2_Intron|HKR1_uc010xtp.1_Intron|HKR1_uc002ogd.2_Intron	NM_181786	NP_861451	P10072	HKR1_HUMAN	GLI-Kruppel family member HKR1						multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			aaaaaaaaacaaaaaaacaaa	0.144													4	3	---	---	---	---	
SUV420H2	84787	broad.mit.edu	37	19	55854541	55854542	+	Intron	INS	-	GCCCCTGCCCCT	GCCCCTGCCCCT	rs139540072	by1000genomes	TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55854541_55854542insGCCCCTGCCCCT	uc002qkj.3	+						SUV420H2_uc010esx.1_3'UTR|SUV420H2_uc002qkk.1_3'UTR|SUV420H2_uc002qkl.2_Intron	NM_032701	NP_116090	Q86Y97	SV422_HUMAN	suppressor of variegation 4-20 homolog 2						regulation of transcription, DNA-dependent|transcription, DNA-dependent		protein binding				0	Breast(117;0.191)		BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.044)		TGCAATGAGGAGCCCCTGCCCC	0.599													4	2	---	---	---	---	
SLC12A5	57468	broad.mit.edu	37	20	44685640	44685642	+	Intron	DEL	ACG	-	-			TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44685640_44685642delACG	uc010zxl.1	+						SLC12A5_uc002xrb.2_Intron	NM_001134771	NP_001128243	Q9H2X9	S12A5_HUMAN	solute carrier family 12 (potassium-chloride						potassium ion transport|sodium ion transport	integral to membrane	potassium:chloride symporter activity			ovary(2)|large_intestine(1)|central_nervous_system(1)|skin(1)	5		Myeloproliferative disorder(115;0.0122)			Bumetanide(DB00887)|Potassium Chloride(DB00761)	AATTGGTGCCACGACCTCTGGGA	0.532													18	12	---	---	---	---	
psiTPTE22	387590	broad.mit.edu	37	22	17131536	17131537	+	Intron	INS	-	CTG	CTG	rs34452519		TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:17131536_17131537insCTG	uc002zls.1	+						psiTPTE22_uc002zlt.2_Intron					Homo sapiens cDNA FLJ10437 fis, clone NT2RP1000581.												0						TGCCCACTCTTCTGGTCTCATG	0.470													4	2	---	---	---	---	
CABIN1	23523	broad.mit.edu	37	22	24480374	24480374	+	Intron	DEL	T	-	-			TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24480374delT	uc002zzi.1	+						CABIN1_uc002zzj.1_Intron|CABIN1_uc002zzl.1_Intron	NM_012295	NP_036427	Q9Y6J0	CABIN_HUMAN	calcineurin binding protein 1						cell surface receptor linked signaling pathway|chromatin modification	nucleus	protein phosphatase inhibitor activity			ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|pancreas(1)	5						gtaGTGCAGATTTTTTTTTTT	0.184													10	5	---	---	---	---	
TRMU	55687	broad.mit.edu	37	22	46745993	46745994	+	Intron	INS	-	T	T	rs72489274		TCGA-EU-5907-01A-11D-1669-08	TCGA-EU-5907-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:46745993_46745994insT	uc003bhp.2	+						TRMU_uc011arb.1_Intron|TRMU_uc003bhq.2_Intron|TRMU_uc003bhs.2_Intron|TRMU_uc003bhr.2_Intron|TRMU_uc003bht.2_Intron|TRMU_uc003bhu.2_Intron|TRMU_uc003bhv.2_Intron	NM_018006	NP_060476	O75648	MTU1_HUMAN	tRNA 5-methylaminomethyl-2-thiouridylate							mitochondrion	ATP binding|sulfurtransferase activity|tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase activity|tRNA binding			ovary(1)	1		Ovarian(80;0.00965)|Breast(42;0.0194)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00449)|LUAD - Lung adenocarcinoma(64;0.248)		TAAAATCCTTGTTTTTTTTTTT	0.347													4	2	---	---	---	---	
