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
KLHL17	339451	broad.mit.edu	37	1	897302	897302	+	Missense_Mutation	SNP	G	T	T			TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:897302G>T	uc001aca.1	+	4	693	c.586G>T	c.(586-588)GGT>TGT	p.G196C	NOC2L_uc001abz.3_5'Flank|NOC2L_uc009vjq.2_5'Flank|NOC2L_uc009vjr.1_5'Flank|KLHL17_uc001acb.1_Missense_Mutation_p.G72C|KLHL17_uc010nya.1_Missense_Mutation_p.G72C|KLHL17_uc001acc.1_5'Flank|KLHL17_uc010nyb.1_5'Flank	NM_198317	NP_938073	Q6TDP4	KLH17_HUMAN	kelch-like 17	196	BACK.				actin cytoskeleton organization	actin cytoskeleton|cell junction|postsynaptic density|postsynaptic membrane	protein complex scaffold				0	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;9.48e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)		UCEC - Uterine corpus endometrioid carcinoma (11;0.00459)|Epithelial(90;1.52e-38)|OV - Ovarian serous cystadenocarcinoma(86;5.59e-23)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|BRCA - Breast invasive adenocarcinoma(365;0.000469)|Kidney(185;0.00227)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.199)		CAACTGCCTGGGTATCCGGGG	0.627													5	101	---	---	---	---	PASS
CSMD2	114784	broad.mit.edu	37	1	34033301	34033301	+	Missense_Mutation	SNP	G	A	A			TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:34033301G>A	uc001bxn.1	-	54	8232	c.8203C>T	c.(8203-8205)CGG>TGG	p.R2735W	CSMD2_uc001bxm.1_Missense_Mutation_p.R2758W	NM_052896	NP_443128	Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2	2735	Sushi 18.|Extracellular (Potential).					integral to membrane|plasma membrane	protein binding			ovary(6)|skin(5)|pancreas(1)	12		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)				ACACTGCCCCGGTAGCTGTAG	0.562													6	45	---	---	---	---	PASS
ZMYM4	9202	broad.mit.edu	37	1	35870746	35870746	+	Nonsense_Mutation	SNP	G	A	A			TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:35870746G>A	uc001byt.2	+	24	3731	c.3651G>A	c.(3649-3651)TGG>TGA	p.W1217*	ZMYM4_uc009vuu.2_Nonsense_Mutation_p.W1185*|ZMYM4_uc001byu.2_Nonsense_Mutation_p.W893*|ZMYM4_uc009vuv.2_Nonsense_Mutation_p.W956*	NM_005095	NP_005086	Q5VZL5	ZMYM4_HUMAN	zinc finger protein 262	1217					multicellular organismal development		DNA binding|zinc ion binding			large_intestine(2)|ovary(1)|kidney(1)|skin(1)	5		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				GGAAGAACTGGGTTCAGTGGA	0.458													11	139	---	---	---	---	PASS
EIF2C3	192669	broad.mit.edu	37	1	36509078	36509078	+	Missense_Mutation	SNP	A	G	G			TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:36509078A>G	uc001bzp.2	+	17	2459	c.2203A>G	c.(2203-2205)ACA>GCA	p.T735A	EIF2C3_uc001bzq.2_Missense_Mutation_p.T501A	NM_024852	NP_079128	Q9H9G7	AGO3_HUMAN	eukaryotic translation initiation factor 2C, 3	735	Piwi.				mRNA catabolic process|negative regulation of translation involved in gene silencing by miRNA	cytoplasmic mRNA processing body|cytosol	protein binding|RNA binding				0		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				CCCAGCTGGAACAACAGTTGA	0.343													13	74	---	---	---	---	PASS
ATPAF1	64756	broad.mit.edu	37	1	47101285	47101285	+	3'UTR	SNP	C	A	A			TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:47101285C>A	uc001cqh.2	-	9					ATPAF1_uc001cqg.2_3'UTR|ATPAF1_uc009vyk.2_3'UTR|ATPAF1_uc010omg.1_3'UTR|ATPAF1_uc001cqi.2_3'UTR	NM_022745	NP_073582	Q5TC12	ATPF1_HUMAN	ATP synthase mitochondrial F1 complex assembly						protein complex assembly	mitochondrion	protein binding				0	Acute lymphoblastic leukemia(166;0.155)					TCCTGAATATCAAGTAATAGG	0.408													3	14	---	---	---	---	PASS
PDE4DIP	9659	broad.mit.edu	37	1	145074882	145074882	+	3'UTR	SNP	G	T	T	rs3845334		TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145074882G>T	uc001emk.2	-	2					NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001emh.2_Intron			Q5VU43	MYOME_HUMAN	SubName: Full=Phosphodiesterase 4D interacting protein;						cellular protein complex assembly	centrosome|Golgi apparatus|myofibril|nucleus	enzyme binding			ovary(4)|haematopoietic_and_lymphoid_tissue(1)	5				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		TAAAAAGCCTGCAGCACAATC	0.303			T	PDGFRB	MPD								7	23	---	---	---	---	PASS
PLA2G4A	5321	broad.mit.edu	37	1	186839572	186839572	+	Silent	SNP	G	A	A			TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:186839572G>A	uc001gsc.2	+	3	244	c.39G>A	c.(37-39)GAG>GAA	p.E13E	PLA2G4A_uc010pos.1_Silent_p.E13E	NM_024420	NP_077734	P47712	PA24A_HUMAN	cytosolic phospholipase A2, group IVA	13	C2.|Phospholipid binding (Probable).				phospholipid catabolic process|platelet activating factor biosynthetic process|platelet activation	cytosol|endoplasmic reticulum membrane	calcium ion binding|calcium-dependent phospholipid binding|lysophospholipase activity			lung(2)|breast(1)	3					Flunisolide(DB00180)|Fluocinolone Acetonide(DB00591)|Fluocinonide(DB01047)|Fluorometholone(DB00324)|Flurandrenolide(DB00846)|Fluticasone Propionate(DB00588)|Medrysone(DB00253)|Quinacrine(DB01103)	TCCAGGTGGAGCACCAGTATT	0.368													16	85	---	---	---	---	PASS
CR1L	1379	broad.mit.edu	37	1	207867951	207867951	+	Missense_Mutation	SNP	A	G	G			TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:207867951A>G	uc001hga.3	+	5	838	c.717A>G	c.(715-717)ATA>ATG	p.I239M	CR1L_uc001hfz.2_RNA|CR1L_uc001hgb.1_RNA	NM_175710	NP_783641	Q2VPA4	CR1L_HUMAN	complement component (3b/4b) receptor 1-like	239	Sushi 4.					cytoplasm|extracellular region|membrane					0						AAAATGGAATATTGGTATCTG	0.473													20	441	---	---	---	---	PASS
NID1	4811	broad.mit.edu	37	1	236192916	236192916	+	Missense_Mutation	SNP	G	T	T			TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:236192916G>T	uc001hxo.2	-	7	1774	c.1672C>A	c.(1672-1674)CAG>AAG	p.Q558K	NID1_uc009xgd.2_Missense_Mutation_p.Q558K	NM_002508	NP_002499	P14543	NID1_HUMAN	nidogen 1 precursor	558	Nidogen G2 beta-barrel.				cell-matrix adhesion	basement membrane	calcium ion binding			large_intestine(1)|pancreas(1)	2	Ovarian(103;0.0544)|Breast(184;0.23)	all_cancers(173;0.00491)|Prostate(94;0.184)|Acute lymphoblastic leukemia(190;0.229)	OV - Ovarian serous cystadenocarcinoma(106;0.00162)		Becaplermin(DB00102)|Urokinase(DB00013)	AACGGAATCTGCGGCACGCGG	0.647													3	24	---	---	---	---	PASS
STON1-GTF2A1L	286749	broad.mit.edu	37	2	48809480	48809480	+	Missense_Mutation	SNP	A	G	G			TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:48809480A>G	uc010yol.1	+	1	1755	c.1708A>G	c.(1708-1710)ATA>GTA	p.I570V	STON1_uc002rwo.3_Missense_Mutation_p.I570V|STON1_uc010fbm.2_Missense_Mutation_p.I570V|STON1-GTF2A1L_uc002rwp.1_Missense_Mutation_p.I570V|STON1_uc002rwr.2_RNA|STON1_uc002rwq.2_Missense_Mutation_p.I570V	NM_006873	NP_006864	B7ZL16	B7ZL16_HUMAN	stonin 1	570					endocytosis|intracellular protein transport|transcription initiation from RNA polymerase II promoter	clathrin adaptor complex|transcription factor TFIIA complex				ovary(3)|pancreas(1)|skin(1)	5		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.176)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			CAATATAAGGATACACTTTCC	0.502													10	160	---	---	---	---	PASS
MARCH7	64844	broad.mit.edu	37	2	160585646	160585646	+	Missense_Mutation	SNP	A	G	G			TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:160585646A>G	uc002uax.2	+	2	235	c.113A>G	c.(112-114)CAC>CGC	p.H38R	MARCH7_uc010foq.2_Missense_Mutation_p.H38R|MARCH7_uc010zcn.1_Missense_Mutation_p.H38R	NM_022826	NP_073737	Q9H992	MARH7_HUMAN	axotrophin	38	Ser-rich.						ligase activity|zinc ion binding				0						GATACCTATCACTCAAGAGAC	0.373													27	117	---	---	---	---	PASS
VHL	7428	broad.mit.edu	37	3	10188322	10188322	+	Splice_Site	SNP	T	C	C	rs5030815		TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10188322T>C	uc003bvc.2	+	2	676	c.463_splice	c.e2+2	p.V155_splice	VHL_uc003bvd.2_Intron	NM_000551	NP_000542	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor isoform 1						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.?(11)		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)		CACTGCCAGGTACTGACGTTT	0.403		1	D|Mis|N|F|S		renal|hemangioma|pheochromocytoma	renal|hemangioma|pheochromocytoma			von_Hippel-Lindau_disease|Chuvash_Polycythemia_|Pheochromocytoma_(Adrenal)_Familial				43	174	---	---	---	---	PASS
FGD5	152273	broad.mit.edu	37	3	14964587	14964587	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:14964587C>T	uc003bzc.2	+	16	3952	c.3842C>T	c.(3841-3843)CCG>CTG	p.P1281L	FGD5_uc011avk.1_Missense_Mutation_p.P1281L|FGD5_uc003bzd.2_Missense_Mutation_p.P359L	NM_152536	NP_689749	Q6ZNL6	FGD5_HUMAN	FYVE, RhoGEF and PH domain containing 5	1281	FYVE-type.				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(3)|kidney(1)|pancreas(1)	5						AACAAGTACCCGCTGAAGTAC	0.617													18	63	---	---	---	---	PASS
EPHA6	285220	broad.mit.edu	37	3	96706398	96706398	+	Silent	SNP	A	G	G			TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:96706398A>G	uc010how.1	+	3	718	c.675A>G	c.(673-675)GAA>GAG	p.E225E	EPHA6_uc003drp.1_Silent_p.E225E	NM_001080448	NP_001073917	Q9UF33	EPHA6_HUMAN	EPH receptor A6 isoform a	130	Ephrin-binding.|Extracellular (Potential).					integral to plasma membrane	ATP binding|ephrin receptor activity			stomach(5)|lung(4)|central_nervous_system(3)|breast(1)|skin(1)|ovary(1)|kidney(1)	16						TTTATATGGAATCAGATGAGT	0.383													8	268	---	---	---	---	PASS
CLSTN2	64084	broad.mit.edu	37	3	140122558	140122558	+	Missense_Mutation	SNP	G	A	A	rs145666342		TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:140122558G>A	uc003etn.2	+	3	510	c.320G>A	c.(319-321)CGT>CAT	p.R107H	CLSTN2_uc003etm.2_Missense_Mutation_p.R107H	NM_022131	NP_071414	Q9H4D0	CSTN2_HUMAN	calsyntenin 2 precursor	107	Extracellular (Potential).|Cadherin 1.				homophilic cell adhesion	endoplasmic reticulum membrane|Golgi membrane|integral to membrane|plasma membrane	calcium ion binding			skin(3)|large_intestine(2)|pancreas(1)|central_nervous_system(1)	7						GGCCGGCTCCGTGCCAAGAGC	0.562										HNSCC(16;0.037)			11	202	---	---	---	---	PASS
FNDC3B	64778	broad.mit.edu	37	3	172096213	172096213	+	Silent	SNP	C	T	T			TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:172096213C>T	uc003fhy.2	+	24	3334	c.3162C>T	c.(3160-3162)CCC>CCT	p.P1054P	FNDC3B_uc003fhz.3_Silent_p.P1054P	NM_022763	NP_073600	Q53EP0	FND3B_HUMAN	fibronectin type III domain containing 3B	1054	Fibronectin type-III 9.					endoplasmic reticulum|integral to membrane				ovary(2)|breast(1)	3	all_cancers(22;1.01e-18)|Ovarian(172;0.00167)|Breast(254;0.165)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)	GBM - Glioblastoma multiforme(1;0.0494)		AAAGTGTCCCCCCCACCATCA	0.463													7	77	---	---	---	---	PASS
ACAP2	23527	broad.mit.edu	37	3	195009916	195009916	+	Missense_Mutation	SNP	G	A	A			TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195009916G>A	uc003fun.3	-	21	2349	c.2108C>T	c.(2107-2109)ACT>ATT	p.T703I		NM_012287	NP_036419	Q15057	ACAP2_HUMAN	centaurin, beta 2	703					regulation of ARF GTPase activity		ARF GTPase activator activity|zinc ion binding			large_intestine(1)|ovary(1)	2						TTCTTCATCAGTGGCATGTTG	0.368													18	109	---	---	---	---	PASS
PDE6B	5158	broad.mit.edu	37	4	654278	654278	+	Missense_Mutation	SNP	C	G	G			TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:654278C>G	uc003gap.2	+	12	1543	c.1490C>G	c.(1489-1491)ACC>AGC	p.T497S	PDE6B_uc003gao.3_Missense_Mutation_p.T497S|PDE6B_uc011buy.1_Missense_Mutation_p.T218S	NM_000283	NP_000274	P35913	PDE6B_HUMAN	phosphodiesterase 6B isoform 1	497					cytosolic calcium ion homeostasis|GMP metabolic process|phototransduction, visible light|platelet activation|visual perception	cytosol|membrane	3',5'-cyclic-GMP phosphodiesterase activity|metal ion binding				0						CCAGGGCCCACCACATTTGAC	0.567													18	58	---	---	---	---	PASS
PRKG2	5593	broad.mit.edu	37	4	82126123	82126123	+	Missense_Mutation	SNP	G	A	A			TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:82126123G>A	uc003hmh.2	-	1	93	c.79C>T	c.(79-81)CGG>TGG	p.R27W	PRKG2_uc011cch.1_Missense_Mutation_p.R27W	NM_006259	NP_006250	Q13237	KGP2_HUMAN	protein kinase, cGMP-dependent, type II	27					platelet activation|signal transduction	cytosol	ATP binding|cGMP binding|cGMP-dependent protein kinase activity			breast(3)|central_nervous_system(2)|ovary(1)|large_intestine(1)	7						ACCTTGTTCCGCAGAGCATCA	0.527													16	74	---	---	---	---	PASS
F11	2160	broad.mit.edu	37	4	187201213	187201213	+	Missense_Mutation	SNP	G	A	A			TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:187201213G>A	uc003iza.1	+	8	1136	c.803G>A	c.(802-804)CGC>CAC	p.R268H		NM_000128	NP_000119	P03951	FA11_HUMAN	coagulation factor XI precursor	268	Apple 3.				blood coagulation, intrinsic pathway|plasminogen activation|positive regulation of fibrinolysis	extracellular space|plasma membrane	heparin binding|serine-type endopeptidase activity				0		all_cancers(14;6.2e-52)|all_epithelial(14;1.62e-38)|all_lung(41;1.34e-13)|Lung NSC(41;3.58e-13)|Melanoma(20;1.91e-06)|Hepatocellular(41;0.00886)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|Colorectal(36;0.0161)|all_neural(102;0.202)		OV - Ovarian serous cystadenocarcinoma(60;2.13e-11)|BRCA - Breast invasive adenocarcinoma(30;4.59e-06)|GBM - Glioblastoma multiforme(59;0.000149)|STAD - Stomach adenocarcinoma(60;0.000314)|LUSC - Lung squamous cell carcinoma(40;0.00112)|READ - Rectum adenocarcinoma(43;0.176)	Coagulation Factor IX(DB00100)	CCCAGTACACGCATTAAAAAG	0.393													8	94	---	---	---	---	PASS
FSTL4	23105	broad.mit.edu	37	5	132736492	132736492	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:132736492C>T	uc003kyn.1	-	4	565	c.347G>A	c.(346-348)CGT>CAT	p.R116H		NM_015082	NP_055897	Q6MZW2	FSTL4_HUMAN	follistatin-like 4 precursor	116	Kazal-like.					extracellular region	calcium ion binding			central_nervous_system(1)|skin(1)	2		all_cancers(142;0.244)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			GCAAGCAGCACGGTGGAGCTT	0.572													24	93	---	---	---	---	PASS
PCDHGB3	56102	broad.mit.edu	37	5	140750994	140750994	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140750994C>T	uc003ljw.1	+	1	1033	c.1033C>T	c.(1033-1035)CCG>TCG	p.P345S	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc003ljm.1_Intron|PCDHGA3_uc010jfx.1_Intron|PCDHGB1_uc003ljo.1_Intron|PCDHGA4_uc003ljq.1_Intron|PCDHGB2_uc003ljs.1_Intron|PCDHGA5_uc003lju.1_Intron|PCDHGA6_uc003ljy.1_5'Flank|PCDHGB3_uc011dat.1_Missense_Mutation_p.P345S|PCDHGA6_uc011dau.1_5'Flank	NM_018924	NP_061747	Q9Y5G1	PCDGF_HUMAN	protocadherin gamma subfamily B, 3 isoform 1	345	Extracellular (Potential).|Cadherin 3.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGACAATGCCCCGGAGATAAC	0.438													9	60	---	---	---	---	PASS
ANXA6	309	broad.mit.edu	37	5	150519791	150519791	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:150519791C>T	uc003ltl.1	-	3	184	c.32G>A	c.(31-33)CGG>CAG	p.R11Q	ANXA6_uc011dcp.1_5'UTR|ANXA6_uc003ltm.1_Missense_Mutation_p.R11Q|ANXA6_uc003ltn.1_Missense_Mutation_p.R11Q|ANXA6_uc003lto.1_5'UTR	NM_001155	NP_001146	P08133	ANXA6_HUMAN	annexin VI isoform 1	11						melanosome	calcium ion binding|calcium-dependent phospholipid binding|protein binding				0		Medulloblastoma(196;0.0912)|all_hematologic(541;0.208)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			GATGGAGCCCCGGTACTTGGC	0.597													10	56	---	---	---	---	PASS
C5orf54	63920	broad.mit.edu	37	5	159821039	159821039	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:159821039C>T	uc003lye.1	-	2	1923	c.1459G>A	c.(1459-1461)GAT>AAT	p.D487N	C5orf54_uc003lyf.1_Missense_Mutation_p.D487N	NM_022090	NP_071373	Q8IZ13	CE054_HUMAN	transposon-derived Buster3 transposase-like	487										pancreas(1)	1						aaataactatcatcaacaaaa	0.000													10	170	---	---	---	---	PASS
F13A1	2162	broad.mit.edu	37	6	6145785	6145785	+	3'UTR	SNP	G	A	A			TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:6145785G>A	uc003mwv.2	-	15					F13A1_uc011dib.1_3'UTR	NM_000129	NP_000120	P00488	F13A_HUMAN	coagulation factor XIII A1 subunit precursor						peptide cross-linking|platelet activation|platelet degranulation	extracellular region|platelet alpha granule lumen	acyltransferase activity|metal ion binding|protein-glutamine gamma-glutamyltransferase activity			ovary(2)|haematopoietic_and_lymphoid_tissue(1)|central_nervous_system(1)|pancreas(1)|skin(1)	6	Ovarian(93;0.0816)	all_hematologic(90;0.152)			L-Glutamine(DB00130)	CTATTTTTGCGTTAGAATTTC	0.468													5	60	---	---	---	---	PASS
HIVEP1	3096	broad.mit.edu	37	6	12120167	12120167	+	Missense_Mutation	SNP	G	A	A			TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:12120167G>A	uc003nac.2	+	4	318	c.139G>A	c.(139-141)GGT>AGT	p.G47S	HIVEP1_uc011diq.1_RNA	NM_002114	NP_002105	P15822	ZEP1_HUMAN	human immunodeficiency virus type I enhancer	47					transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|protein binding|zinc ion binding			ovary(3)|large_intestine(1)|central_nervous_system(1)|skin(1)	6	Breast(50;0.0639)|Ovarian(93;0.0816)	all_hematologic(90;0.117)				ATCCCTTAAAGGTGTGAAACG	0.363													63	230	---	---	---	---	PASS
SLC44A4	80736	broad.mit.edu	37	6	31846720	31846720	+	Missense_Mutation	SNP	T	C	C			TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31846720T>C	uc010jti.2	-	1	104	c.38A>G	c.(37-39)TAC>TGC	p.Y13C	SLC44A4_uc011dol.1_5'Flank|SLC44A4_uc011dom.1_Missense_Mutation_p.Y13C	NM_025257	NP_079533	Q53GD3	CTL4_HUMAN	choline transporter-like protein 4	13	Cytoplasmic (Potential).					integral to membrane|plasma membrane	choline transmembrane transporter activity			large_intestine(2)|ovary(1)|central_nervous_system(1)	4					Choline(DB00122)	AGTCTCACCGTAGGCCTCGTC	0.667													10	158	---	---	---	---	PASS
BRPF3	27154	broad.mit.edu	37	6	36185716	36185716	+	Silent	SNP	A	G	G			TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:36185716A>G	uc003olv.3	+	9	3236	c.3012A>G	c.(3010-3012)AAA>AAG	p.K1004K	BRPF3_uc010jwb.2_Silent_p.K734K|BRPF3_uc011dtj.1_RNA|BRPF3_uc010jwc.2_RNA|BRPF3_uc011dtk.1_Intron|BRPF3_uc010jwd.2_5'UTR	NM_015695	NP_056510	Q9ULD4	BRPF3_HUMAN	bromodomain and PHD finger containing, 3	1004					histone H3 acetylation|platelet activation|platelet degranulation	cytosol|extracellular region|MOZ/MORF histone acetyltransferase complex	protein binding|zinc ion binding			ovary(1)|skin(1)	2						GCTTTGGAAAACACACCGAAA	0.517													21	94	---	---	---	---	PASS
BMP5	653	broad.mit.edu	37	6	55620404	55620404	+	Missense_Mutation	SNP	T	A	A			TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:55620404T>A	uc003pcq.2	-	7	2004	c.1292A>T	c.(1291-1293)TAC>TTC	p.Y431F	BMP5_uc011dxf.1_Missense_Mutation_p.Y394F	NM_021073	NP_066551	P22003	BMP5_HUMAN	bone morphogenetic protein 5 preproprotein	431					cartilage development|cell differentiation|growth|ossification	extracellular space	BMP receptor binding|cytokine activity|growth factor activity			ovary(2)	2	Lung NSC(77;0.0462)		LUSC - Lung squamous cell carcinoma(124;0.181)			GTCATCAAAGTACAGAACAGA	0.348													31	136	---	---	---	---	PASS
DST	667	broad.mit.edu	37	6	56357198	56357198	+	Nonsense_Mutation	SNP	G	A	A			TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:56357198G>A	uc003pdf.2	-	79	14255	c.14227C>T	c.(14227-14229)CAG>TAG	p.Q4743*	DST_uc003pcz.3_Nonsense_Mutation_p.Q4565*|DST_uc011dxj.1_Nonsense_Mutation_p.Q4594*|DST_uc011dxk.1_Nonsense_Mutation_p.Q4605*|DST_uc003pcy.3_Nonsense_Mutation_p.Q4239*|DST_uc003pda.3_5'UTR	NM_001144769	NP_001138241	Q03001	DYST_HUMAN	dystonin isoform 2	6651	Spectrin 17.				cell adhesion|cell cycle arrest|cell motility|hemidesmosome assembly|integrin-mediated signaling pathway|intermediate filament cytoskeleton organization|maintenance of cell polarity|microtubule cytoskeleton organization|response to wounding	actin cytoskeleton|axon|axon part|basement membrane|cell cortex|cell leading edge|cytoplasmic membrane-bounded vesicle|endoplasmic reticulum membrane|hemidesmosome|hemidesmosome|integral to membrane|intermediate filament|intermediate filament cytoskeleton|microtubule cytoskeleton|microtubule plus end|nuclear envelope|sarcomere|Z disc	actin binding|calcium ion binding|integrin binding|microtubule plus-end binding|protein binding|protein C-terminus binding|protein homodimerization activity			ovary(7)|central_nervous_system(6)|upper_aerodigestive_tract(1)	14	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			TCTATTATCTGCTCACGATGA	0.328													33	124	---	---	---	---	PASS
SLC17A5	26503	broad.mit.edu	37	6	74354149	74354149	+	Missense_Mutation	SNP	T	G	G			TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:74354149T>G	uc003phn.3	-	2	400	c.272A>C	c.(271-273)AAA>ACA	p.K91T	SLC17A5_uc010kay.2_RNA|SLC17A5_uc011dyo.1_5'UTR	NM_012434	NP_036566	Q9NRA2	S17A5_HUMAN	sialin	91					anion transport	integral to plasma membrane|lysosomal membrane|membrane fraction	sialic acid:hydrogen symporter activity			skin(5)|central_nervous_system(1)	6						ATGATGAACTTTTATGGGAGC	0.323													26	100	---	---	---	---	PASS
IRAK1BP1	134728	broad.mit.edu	37	6	79607842	79607842	+	Missense_Mutation	SNP	C	A	A			TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:79607842C>A	uc003pim.2	+	4	679	c.574C>A	c.(574-576)CTT>ATT	p.L192I	IRAK1BP1_uc010kbg.1_Intron|IRAK1BP1_uc003pin.2_Missense_Mutation_p.L105I	NM_001010844	NP_001010844	Q5VVH5	IKBP1_HUMAN	interleukin-1 receptor-associated kinase 1	192					I-kappaB kinase/NF-kappaB cascade|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus					0		all_cancers(76;0.0398)|Acute lymphoblastic leukemia(125;1.24e-05)|all_hematologic(105;0.00223)		BRCA - Breast invasive adenocarcinoma(397;0.21)		AGTCTGTAACCTTGTTGGCCA	0.408													18	100	---	---	---	---	PASS
WDR27	253769	broad.mit.edu	37	6	170070745	170070745	+	Missense_Mutation	SNP	C	A	A			TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:170070745C>A	uc003qwx.2	-	4	896	c.376G>T	c.(376-378)GTG>TTG	p.V126L	WDR27_uc010kkw.1_Missense_Mutation_p.V126L|WDR27_uc003qwy.2_Intron|WDR27_uc011egw.1_RNA|WDR27_uc010kkx.2_3'UTR			A2RRH5	WDR27_HUMAN	RecName: Full=WD repeat-containing protein 27;	126										pancreas(1)	1		Breast(66;1.53e-05)|Ovarian(120;0.216)		OV - Ovarian serous cystadenocarcinoma(33;6.48e-20)|BRCA - Breast invasive adenocarcinoma(81;3.56e-07)|GBM - Glioblastoma multiforme(31;0.00168)		AAACACAGCACCTTTCCCAAA	0.448													10	165	---	---	---	---	PASS
ABCB5	340273	broad.mit.edu	37	7	20685734	20685734	+	5'Flank	SNP	T	A	A			TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:20685734T>A	uc003suw.3	+						ABCB5_uc010kuh.2_Silent_p.P318P|ABCB5_uc003suv.3_5'Flank|ABCB5_uc011jyi.1_5'Flank	NM_178559	NP_848654	Q2M3G0	ABCB5_HUMAN	ATP-binding cassette, sub-family B, member 5						regulation of membrane potential	apical plasma membrane|Golgi membrane|integral to plasma membrane|intercellular canaliculus	ATP binding|ATPase activity, coupled to transmembrane movement of substances|efflux transmembrane transporter activity			skin(2)|large_intestine(1)|haematopoietic_and_lymphoid_tissue(1)|ovary(1)|pancreas(1)	6						ATGGAGAACCTGGATATACCA	0.408													4	84	---	---	---	---	PASS
PODXL	5420	broad.mit.edu	37	7	131194125	131194125	+	Nonsense_Mutation	SNP	C	T	T			TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:131194125C>T	uc003vqw.3	-	4	1280	c.1022G>A	c.(1021-1023)TGG>TAG	p.W341*	PODXL_uc003vqx.3_Nonsense_Mutation_p.W309*	NM_001018111	NP_001018121	O00592	PODXL_HUMAN	podocalyxin-like isoform 1 precursor	341	Extracellular (Potential).				cell adhesion|epithelial tube formation|negative regulation of cell-cell adhesion|positive regulation of cell migration|positive regulation of cell-cell adhesion mediated by integrin|regulation of microvillus assembly	actin cytoskeleton|apical plasma membrane|centrosome|filopodium|integral to plasma membrane|lamellipodium|membrane raft|microvillus membrane|nucleolus|ruffle				breast(2)|pancreas(1)	3	Melanoma(18;0.162)					TGGAGTTACCCAGTTACTCTC	0.557													32	105	---	---	---	---	PASS
EXT1	2131	broad.mit.edu	37	8	118825167	118825167	+	Missense_Mutation	SNP	T	A	A			TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:118825167T>A	uc003yok.1	-	8	2439	c.1666A>T	c.(1666-1668)ATC>TTC	p.I556F		NM_000127	NP_000118	Q16394	EXT1_HUMAN	exostosin 1	556	Lumenal (Potential).				glycosaminoglycan biosynthetic process|heparan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process|ossification|signal transduction|skeletal system development	Golgi membrane|integral to endoplasmic reticulum membrane	glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity|heparan sulfate N-acetylglucosaminyltransferase activity|N-acetylglucosaminyl-proteoglycan 4-beta-glucuronosyltransferase activity|protein heterodimerization activity|protein homodimerization activity			ovary(2)|lung(2)	4	all_cancers(13;2.36e-26)|Lung NSC(37;5.02e-07)|Ovarian(258;0.0173)		STAD - Stomach adenocarcinoma(47;0.012)			TCTGTGATGATGTTGTCGTAG	0.532			Mis|N|F|S			exostoses|osteosarcoma			Hereditary_Multiple_Exostoses|Langer-Giedion_syndrome				3	40	---	---	---	---	PASS
EIF2C2	27161	broad.mit.edu	37	8	141559213	141559213	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:141559213C>T	uc003yvn.2	-	12	1628	c.1588G>A	c.(1588-1590)GCC>ACC	p.A530T	EIF2C2_uc010men.2_Missense_Mutation_p.A453T|EIF2C2_uc010meo.2_Missense_Mutation_p.A530T	NM_012154	NP_036286	Q9UKV8	AGO2_HUMAN	argonaute 2 isoform 1	530	Piwi.				mRNA cleavage involved in gene silencing by miRNA|negative regulation of translation involved in gene silencing by miRNA|negative regulation of translational initiation|pre-miRNA processing|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasmic mRNA processing body|cytosol|micro-ribonucleoprotein complex|mRNA cap binding complex|nucleus|polysome|RNA-induced silencing complex	endoribonuclease activity, cleaving siRNA-paired mRNA|metal ion binding|protein binding|RNA 7-methylguanosine cap binding|siRNA binding|translation initiation factor activity				0	all_cancers(97;2.54e-14)|all_epithelial(106;5.99e-13)|Lung NSC(106;1.45e-05)|all_lung(105;2.07e-05)|Ovarian(258;0.0154)|Acute lymphoblastic leukemia(118;0.155)	Breast(495;0.159)	BRCA - Breast invasive adenocarcinoma(115;0.158)			CCACACCTACCGTACACGGGC	0.647													4	27	---	---	---	---	PASS
LY6E	4061	broad.mit.edu	37	8	144103076	144103076	+	Missense_Mutation	SNP	G	C	C			TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144103076G>C	uc003yxn.2	+	4	420	c.266G>C	c.(265-267)GGC>GCC	p.G89A	LY6E_uc003yxm.2_Missense_Mutation_p.G89A|LY6E_uc003yxo.2_RNA	NM_001127213	NP_001120685	Q16553	LY6E_HUMAN	lymphocyte antigen 6 complex, locus E precursor	89	UPAR/Ly6.				cell surface receptor linked signaling pathway	anchored to membrane|integral to plasma membrane					0	all_cancers(97;1.94e-10)|all_epithelial(106;1.22e-08)|Lung NSC(106;0.000228)|all_lung(105;0.000633)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)					GCTTCCATGGGCATCAGCTGC	0.627													20	85	---	---	---	---	PASS
LY6E	4061	broad.mit.edu	37	8	144103077	144103077	+	Silent	SNP	C	T	T			TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144103077C>T	uc003yxn.2	+	4	421	c.267C>T	c.(265-267)GGC>GGT	p.G89G	LY6E_uc003yxm.2_Silent_p.G89G|LY6E_uc003yxo.2_RNA	NM_001127213	NP_001120685	Q16553	LY6E_HUMAN	lymphocyte antigen 6 complex, locus E precursor	89	UPAR/Ly6.				cell surface receptor linked signaling pathway	anchored to membrane|integral to plasma membrane					0	all_cancers(97;1.94e-10)|all_epithelial(106;1.22e-08)|Lung NSC(106;0.000228)|all_lung(105;0.000633)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)					CTTCCATGGGCATCAGCTGCT	0.627													20	84	---	---	---	---	PASS
C9orf131	138724	broad.mit.edu	37	9	35044086	35044086	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35044086C>T	uc003zvw.2	+	2	1489	c.1460C>T	c.(1459-1461)CCC>CTC	p.P487L	C9orf131_uc003zvu.2_Missense_Mutation_p.P439L|C9orf131_uc003zvv.2_Missense_Mutation_p.P414L|C9orf131_uc003zvx.2_Missense_Mutation_p.P452L	NM_203299	NP_976044	Q5VYM1	CI131_HUMAN	hypothetical protein LOC138724 isoform A	487											0	all_epithelial(49;0.22)		LUSC - Lung squamous cell carcinoma(32;0.00117)|Lung(28;0.00309)			GTAATGGGCCCCCAGGGAGTC	0.537													36	162	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	10	30986357	30986357	+	5'UTR	SNP	T	C	C	rs117915096	by1000genomes	TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:30986357T>C	uc010qdx.1	+	3										SubName: Full=cDNA FLJ59642, highly similar to Supervillin;																		CGGCGCTCAATAGTGGGGACT	0.552													3	40	---	---	---	---	PASS
ADAM8	101	broad.mit.edu	37	10	135076555	135076555	+	3'UTR	SNP	G	T	T			TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:135076555G>T	uc010qva.1	-	20					ADAM8_uc010quz.1_3'UTR|ADAM8_uc009ybi.2_3'UTR			P78325	ADAM8_HUMAN	SubName: Full=cDNA FLJ50704, highly similar to ADAM 8 (EC 3.4.24.-) (A disintegrinand metalloproteinase domain 8);						integrin-mediated signaling pathway|proteolysis		metalloendopeptidase activity			large_intestine(2)|central_nervous_system(1)	3		all_cancers(35;1.14e-09)|all_epithelial(44;5.79e-08)|Lung NSC(174;0.00263)|all_lung(145;0.0039)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.172)|Glioma(114;0.203)		all cancers(32;7.72e-06)|OV - Ovarian serous cystadenocarcinoma(35;8.23e-06)|Epithelial(32;1.02e-05)		AGCCTGCAAAGTCAGGGTCTA	0.587													9	159	---	---	---	---	PASS
OR5P2	120065	broad.mit.edu	37	11	7818120	7818120	+	Missense_Mutation	SNP	T	A	A			TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:7818120T>A	uc001mfp.1	-	1	370	c.370A>T	c.(370-372)AGT>TGT	p.S124C		NM_153444	NP_703145	Q8WZ92	OR5P2_HUMAN	olfactory receptor, family 5, subfamily P,	124	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|skin(2)|central_nervous_system(1)	5				Epithelial(150;8.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)		AGCAGTGGACTGCAAATTGCC	0.473													12	136	---	---	---	---	PASS
C11orf46	120534	broad.mit.edu	37	11	30358133	30358133	+	Missense_Mutation	SNP	A	T	T			TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:30358133A>T	uc001mso.1	+	4	738	c.574A>T	c.(574-576)AGT>TGT	p.S192C	C11orf46_uc001msp.2_5'Flank	NM_152316	NP_689529	Q8N8R7	CK046_HUMAN	hypothetical protein LOC120534	192											0						ACCAGCAAAGAGTAAGGTCTA	0.348													43	172	---	---	---	---	PASS
AMICA1	120425	broad.mit.edu	37	11	118083800	118083800	+	Intron	SNP	G	T	T			TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118083800G>T	uc001psk.2	-						AMICA1_uc001psh.2_5'Flank|AMICA1_uc009yzw.1_5'Flank|AMICA1_uc001psi.2_5'UTR|AMICA1_uc001psj.2_Intron|AMICA1_uc010rxw.1_Intron|AMICA1_uc010rxx.1_Intron|AMICA1_uc001psl.1_5'Flank	NM_001098526	NP_001091996	Q86YT9	JAML1_HUMAN	adhesion molecule, interacts with CXADR antigen						blood coagulation|cell adhesion|leukocyte migration|regulation of immune response	cell junction|integral to membrane				ovary(1)	1	all_hematologic(175;0.046)	Medulloblastoma(222;0.0425)|Breast(348;0.181)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;3.4e-05)		CCACCACAGAGCACAGCTTTC	0.493													3	16	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	11	124120764	124120764	+	IGR	SNP	G	A	A			TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:124120764G>A								OR8G2 (24454 upstream) : OR8D1 (58973 downstream)																							AGTGTCACATGTTGGCTGCAA	0.458													8	221	---	---	---	---	PASS
GPRC5A	9052	broad.mit.edu	37	12	13061472	13061472	+	Missense_Mutation	SNP	C	G	G			TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:13061472C>G	uc001rba.2	+	2	939	c.289C>G	c.(289-291)CGC>GGC	p.R97G	GPRC5A_uc001raz.2_Missense_Mutation_p.R97G	NM_003979	NP_003970	Q8NFJ5	RAI3_HUMAN	G protein-coupled receptor, family C, group 5,	97	Extracellular (Potential).					cytoplasmic vesicle membrane|Golgi apparatus|integral to plasma membrane	G-protein coupled receptor activity				0		Prostate(47;0.141)		BRCA - Breast invasive adenocarcinoma(232;0.0708)	Tretinoin(DB00755)	AGGGCCCACACGCTTCTTCCT	0.572													55	348	---	---	---	---	PASS
GRIN2B	2904	broad.mit.edu	37	12	13717155	13717155	+	Missense_Mutation	SNP	C	G	G			TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:13717155C>G	uc001rbt.2	-	13	3196	c.3017G>C	c.(3016-3018)TGT>TCT	p.C1006S		NM_000834	NP_000825	Q13224	NMDE2_HUMAN	N-methyl-D-aspartate receptor subunit 2B	1006	Cytoplasmic (Potential).				response to ethanol	cell junction|N-methyl-D-aspartate selective glutamate receptor complex|outer membrane-bounded periplasmic space|postsynaptic membrane	glycine binding|N-methyl-D-aspartate selective glutamate receptor activity|zinc ion binding			central_nervous_system(4)|ovary(3)|skin(3)|lung(2)	12					Felbamate(DB00949)|Haloperidol(DB00502)|L-Glutamic Acid(DB00142)|Loperamide(DB00836)|Memantine(DB01043)	TGGGTTGTCACAGTCGTAGAG	0.587													5	99	---	---	---	---	PASS
KIF21A	55605	broad.mit.edu	37	12	39763950	39763950	+	Missense_Mutation	SNP	T	C	C			TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:39763950T>C	uc001rly.2	-	2	304	c.158A>G	c.(157-159)TAT>TGT	p.Y53C	KIF21A_uc001rlx.2_Missense_Mutation_p.Y53C|KIF21A_uc001rlz.2_Missense_Mutation_p.Y53C|KIF21A_uc010skl.1_Missense_Mutation_p.Y53C|KIF21A_uc001rma.1_Missense_Mutation_p.Y53C	NM_017641	NP_060111	Q7Z4S6	KI21A_HUMAN	kinesin family member 21A	53	Kinesin-motor.				microtubule-based movement	cytoplasm|microtubule	ATP binding|microtubule motor activity			ovary(4)|pancreas(1)|lung(1)|skin(1)	7		Lung NSC(34;0.179)|all_lung(34;0.213)				GTCAAATACATAGTCAAAAGT	0.388													8	264	---	---	---	---	PASS
APPL2	55198	broad.mit.edu	37	12	105567935	105567935	+	3'UTR	SNP	C	A	A			TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:105567935C>A	uc001tlf.1	-	21					APPL2_uc010swt.1_3'UTR|APPL2_uc001tlg.1_3'UTR|APPL2_uc010swu.1_3'UTR	NM_018171	NP_060641	Q8NEU8	DP13B_HUMAN	adaptor protein, phosphotyrosine interaction, PH						cell cycle|cell proliferation|signal transduction	early endosome membrane|nucleus	protein binding			upper_aerodigestive_tract(1)	1						TTCTTAGTTTCCCTCCCAAGT	0.403													5	12	---	---	---	---	PASS
C14orf106	55320	broad.mit.edu	37	14	45673409	45673409	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:45673409C>T	uc001wwf.2	-	17	3761	c.3302G>A	c.(3301-3303)GGA>GAA	p.G1101E		NM_018353	NP_060823	Q6P0N0	M18BP_HUMAN	chromosome 14 open reading frame 106	1101					cell division|CenH3-containing nucleosome assembly at centromere|mitosis	chromosome, centromeric region|nucleoplasm	DNA binding				0						AGAGTTTTCTCCTAAGTCTGT	0.274													14	112	---	---	---	---	PASS
MUDENG	55745	broad.mit.edu	37	14	57748924	57748924	+	Missense_Mutation	SNP	G	A	A			TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:57748924G>A	uc001xcv.2	+	4	1493	c.1066G>A	c.(1066-1068)GCC>ACC	p.A356T	MUDENG_uc010tri.1_Missense_Mutation_p.A110T|MUDENG_uc010trj.1_Missense_Mutation_p.A253T	NM_018229	NP_060699	Q9H0R1	MUDEN_HUMAN	Mu-2 related death-inducing protein	356	MHD.				intracellular protein transport|vesicle-mediated transport	clathrin adaptor complex				ovary(1)	1						ATTCTGTGAAGCCCATATACC	0.299													14	93	---	---	---	---	PASS
C14orf149	112849	broad.mit.edu	37	14	59951040	59951040	+	5'UTR	SNP	G	A	A			TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:59951040G>A	uc001xee.1	-	1					C14orf149_uc010trx.1_5'UTR|JKAMP_uc001xef.3_5'Flank|JKAMP_uc001xeh.3_5'Flank|JKAMP_uc001xeg.3_5'Flank|JKAMP_uc010try.1_5'Flank|JKAMP_uc001xei.3_5'Flank|JKAMP_uc001xej.3_5'Flank	NM_144581	NP_653182	Q96EM0	PRCM_HUMAN	proline racemase-like								proline racemase activity			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(108;0.14)	L-Proline(DB00172)	TCCATGGTCTGCGTCGGGGGA	0.706													7	35	---	---	---	---	PASS
RPAP1	26015	broad.mit.edu	37	15	41822090	41822090	+	Missense_Mutation	SNP	G	A	A			TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41822090G>A	uc001zod.2	-	8	1155	c.1031C>T	c.(1030-1032)CCC>CTC	p.P344L		NM_015540	NP_056355	Q9BWH6	RPAP1_HUMAN	RNA polymerase II associated protein 1	344						nucleus	DNA binding|DNA-directed RNA polymerase activity			large_intestine(1)	1		all_cancers(109;6.59e-20)|all_epithelial(112;7.67e-17)|Lung NSC(122;5.34e-11)|all_lung(180;4.17e-10)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.173)		OV - Ovarian serous cystadenocarcinoma(18;2.84e-17)|GBM - Glioblastoma multiforme(113;1.68e-06)|Colorectal(105;0.0163)|BRCA - Breast invasive adenocarcinoma(123;0.117)		CCGGACAGGGGGCAAGTCCTG	0.622													11	46	---	---	---	---	PASS
TP53BP1	7158	broad.mit.edu	37	15	43748344	43748344	+	Missense_Mutation	SNP	A	C	C			TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43748344A>C	uc001zrs.2	-	12	2595	c.2447T>G	c.(2446-2448)CTG>CGG	p.L816R	TP53BP1_uc010udp.1_Missense_Mutation_p.L816R|TP53BP1_uc001zrq.3_Missense_Mutation_p.L821R|TP53BP1_uc001zrr.3_Missense_Mutation_p.L821R|TP53BP1_uc010udq.1_Missense_Mutation_p.L821R	NM_005657	NP_005648	Q12888	TP53B_HUMAN	tumor protein p53 binding protein 1 isoform 3	816					double-strand break repair via homologous recombination|positive regulation of transcription from RNA polymerase II promoter	condensed chromosome kinetochore|cytoplasm|nucleoplasm	p53 binding|RNA polymerase II activating transcription factor binding|RNA polymerase II transcription cofactor activity			ovary(2)|skin(2)|large_intestine(1)|pancreas(1)|kidney(1)	7		all_cancers(109;6.94e-11)|all_epithelial(112;2.69e-09)|Lung NSC(122;7.86e-07)|all_lung(180;7.84e-06)|Melanoma(134;0.0728)		GBM - Glioblastoma multiforme(94;1.59e-06)		CCCTGATTTCAGATCTCCTTC	0.428								Direct_reversal_of_damage|Other_conserved_DNA_damage_response_genes					8	252	---	---	---	---	PASS
APH1B	83464	broad.mit.edu	37	15	63569840	63569840	+	Silent	SNP	C	T	T			TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:63569840C>T	uc002ama.2	+	1	92	c.18C>T	c.(16-18)TTC>TTT	p.F6F	APH1B_uc002amb.2_Silent_p.F6F|APH1B_uc010bgq.2_5'UTR|APH1B_uc010bgr.2_5'Flank	NM_031301	NP_112591	Q8WW43	APH1B_HUMAN	presenilin stabilization factor-like isoform 1	6	Helical; Name=1; (Potential).				apoptosis|induction of apoptosis by extracellular signals|membrane protein intracellular domain proteolysis|nerve growth factor receptor signaling pathway|Notch receptor processing|Notch signaling pathway|positive regulation of catalytic activity|protein processing	integral to membrane|plasma membrane|transport vesicle	peptidase activity|protein binding				0						CGGCCGTGTTCTTCGGCTGCG	0.687													10	57	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	15	102294771	102294771	+	5'Flank	SNP	A	C	C			TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:102294771A>C	uc002bxo.2	-						uc002bxq.2_5'Flank|uc002bxr.2_5'Flank|uc010usk.1_5'Flank|uc002bxs.2_5'Flank|uc002bxu.1_5'Flank|uc002bxv.1_5'Flank|uc002bxw.1_5'Flank|uc002bxy.1_5'Flank|uc002byb.1_5'Flank|uc002byd.2_RNA|uc002byc.2_5'Flank|uc002bye.2_5'Flank|uc002byf.1_5'Flank|uc002byg.2_5'Flank|uc002byi.2_5'Flank|uc002byk.2_5'Flank|uc002bym.2_5'Flank|uc002byn.2_5'Flank|uc010usm.1_5'Flank|uc002byr.2_5'Flank|uc002bys.2_5'Flank|uc002byv.2_5'Flank|uc002byx.3_5'Flank|uc002bza.2_5'Flank|uc002bzb.2_5'Flank|uc002bzc.1_5'Flank|uc002bzd.2_5'Flank|uc002bze.2_5'Flank|uc002bzg.2_5'Flank|uc002bzi.1_5'Flank|uc002bzj.2_5'Flank|uc002bzl.2_5'Flank|uc002bzm.2_5'Flank|uc002bzo.2_5'Flank|uc002bzp.2_5'Flank|uc002bzq.2_5'Flank|uc002bzr.2_5'Flank					DQ593630																		TGGGAACGAGAAGACACTCGT	0.577													8	14	---	---	---	---	PASS
ATP2A1	487	broad.mit.edu	37	16	28909648	28909648	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:28909648C>T	uc002dro.1	+	14	1824	c.1640C>T	c.(1639-1641)GCG>GTG	p.A547V	uc010vct.1_Intron|ATP2A1_uc002drn.1_Missense_Mutation_p.A547V|ATP2A1_uc002drp.1_Missense_Mutation_p.A422V	NM_173201	NP_775293	O14983	AT2A1_HUMAN	ATPase, Ca++ transporting, fast twitch 1 isoform	547	Cytoplasmic (By similarity).				apoptosis in response to endoplasmic reticulum stress|apoptotic mitochondrial changes|ATP biosynthetic process|calcium ion import|elevation of endoplasmic reticulum calcium ion concentration|elevation of mitochondrial calcium ion concentration|maintenance of mitochondrion location|negative regulation of striated muscle contraction|platelet activation|positive regulation of fast-twitch skeletal muscle fiber contraction|reduction of endoplasmic reticulum calcium ion concentration|relaxation of skeletal muscle|response to endoplasmic reticulum stress	endoplasmic reticulum membrane|ER-Golgi intermediate compartment|H zone|I band|microsome|perinuclear region of cytoplasm|platelet dense tubular network membrane|sarcoplasmic reticulum|sarcoplasmic reticulum membrane	ATP binding|ATP binding|calcium ion binding|calcium ion binding|calcium-transporting ATPase activity|protein homodimerization activity	p.A547A(1)		ovary(2)|central_nervous_system(1)|pancreas(1)	4						AAGATCATGGCGGTGATCAAG	0.652													21	111	---	---	---	---	PASS
RSPRY1	89970	broad.mit.edu	37	16	57265168	57265168	+	Missense_Mutation	SNP	T	C	C			TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57265168T>C	uc002elb.2	+	13	1744	c.1466T>C	c.(1465-1467)ATG>ACG	p.M489T	RSPRY1_uc002elc.2_Missense_Mutation_p.M489T|RSPRY1_uc002eld.2_Missense_Mutation_p.M489T	NM_133368	NP_588609	Q96DX4	RSPRY_HUMAN	ring finger and SPRY domain containing 1	489						extracellular region	zinc ion binding			ovary(1)	1						CCACCATCTATGAAATTTAGC	0.368													30	145	---	---	---	---	PASS
ABR	29	broad.mit.edu	37	17	915255	915255	+	Intron	SNP	G	C	C	rs113364180		TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:915255G>C	uc002fsd.2	-						ABR_uc002fse.2_Intron|ABR_uc010vqf.1_Intron|ABR_uc010vqg.1_Intron|ABR_uc002fsg.2_Intron|ABR_uc002fsh.1_Intron|ABR_uc002fsf.2_Missense_Mutation_p.C181W	NM_021962	NP_068781	Q12979	ABR_HUMAN	active breakpoint cluster region-related						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity|protein binding|Rho guanyl-nucleotide exchange factor activity			upper_aerodigestive_tract(1)	1				UCEC - Uterine corpus endometrioid carcinoma (25;0.0228)		TGGGTGGAGGGCAGCCCCCAC	0.662													8	39	---	---	---	---	PASS
ZNF594	84622	broad.mit.edu	37	17	5086703	5086703	+	Silent	SNP	G	T	T			TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:5086703G>T	uc010cla.1	-	2	1005	c.849C>A	c.(847-849)GTC>GTA	p.V283V		NM_032530	NP_115919	Q96JF6	ZN594_HUMAN	zinc finger protein 594	283	C2H2-type 6.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)|skin(1)	3						TCTGATGTGGGACAAGGTGTG	0.418													32	145	---	---	---	---	PASS
SLC13A5	284111	broad.mit.edu	37	17	6594203	6594203	+	Silent	SNP	G	A	A			TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:6594203G>A	uc002gdj.2	-	10	1420	c.1332C>T	c.(1330-1332)CCC>CCT	p.P444P	SLC13A5_uc010vtf.1_Silent_p.P444P|SLC13A5_uc010clq.2_Silent_p.P401P|SLC13A5_uc002gdk.2_Silent_p.P427P	NM_177550	NP_808218	Q86YT5	S13A5_HUMAN	solute carrier family 13, member 5 isoform a	444	Helical; (Potential).					integral to membrane	citrate transmembrane transporter activity				0						TGGCTGCCGGGGGCACTGCGT	0.552													35	127	---	---	---	---	PASS
DNAH9	1770	broad.mit.edu	37	17	11593688	11593688	+	Nonsense_Mutation	SNP	C	T	T	rs144649934		TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:11593688C>T	uc002gne.2	+	20	4617	c.4549C>T	c.(4549-4551)CGA>TGA	p.R1517*	DNAH9_uc010coo.2_Nonsense_Mutation_p.R811*	NM_001372	NP_001363	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9 isoform 2	1517	Stem (By similarity).				cell projection organization|cellular component movement|microtubule-based movement|spermatogenesis	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			skin(10)|ovary(4)|breast(3)|central_nervous_system(2)|pancreas(1)	20		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)		TGAAGTGCAGCGAACATGGAC	0.483													22	114	---	---	---	---	PASS
AMAC1	146861	broad.mit.edu	37	17	33521121	33521121	+	Missense_Mutation	SNP	G	A	A	rs149963193		TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:33521121G>A	uc002hjd.2	-	1	292	c.206C>T	c.(205-207)TCG>TTG	p.S69L		NM_152462	NP_689675	Q8N808	AMAC1_HUMAN	acyl-malonyl condensing enzyme 1	69	DUF6 1.|Helical; (Potential).					integral to membrane					0				BRCA - Breast invasive adenocarcinoma(366;0.0917)		CAGCTCCAGCGAGGGCAGGTT	0.637													49	164	---	---	---	---	PASS
TAF15	8148	broad.mit.edu	37	17	34161584	34161584	+	Missense_Mutation	SNP	G	A	A			TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:34161584G>A	uc002hkd.2	+	9	741	c.655G>A	c.(655-657)GGA>AGA	p.G219R	TAF15_uc010ctw.1_RNA|TAF15_uc002hkc.2_Missense_Mutation_p.G216R	NM_139215	NP_631961	Q92804	RBP56_HUMAN	TBP-associated factor 15 isoform 1	219					positive regulation of transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|nucleotide binding|protein binding|RNA binding|zinc ion binding		TAF15/NR4A3(33)	bone(33)|lung(1)|skin(1)	35		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0193)		CAGGGATTATGGACCCAGAAC	0.333			T	TEC|CHN1|ZNF384	extraskeletal myxoid chondrosarcomas|ALL								14	172	---	---	---	---	PASS
COIL	8161	broad.mit.edu	37	17	55028280	55028280	+	Missense_Mutation	SNP	T	A	A			TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:55028280T>A	uc002iuu.2	-	2	354	c.323A>T	c.(322-324)AAA>ATA	p.K108I		NM_004645	NP_004636	P38432	COIL_HUMAN	coilin	108						Cajal body|nucleolus	protein C-terminus binding			ovary(1)	1	Breast(9;6.15e-08)					CTTCTTTGCTTTTCTAAGAGA	0.363													17	252	---	---	---	---	PASS
SETBP1	26040	broad.mit.edu	37	18	42618593	42618593	+	Missense_Mutation	SNP	G	A	A			TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:42618593G>A	uc010dni.2	+	5	4440	c.4144G>A	c.(4144-4146)GCT>ACT	p.A1382T		NM_015559	NP_056374	Q9Y6X0	SETBP_HUMAN	SET binding protein 1 isoform a	1382						nucleus	DNA binding			upper_aerodigestive_tract(2)|large_intestine(1)	3				Colorectal(1;0.0622)|COAD - Colon adenocarcinoma(74;0.201)		ATCTCTCCTTGCTGCATCTGC	0.517									Schinzel-Giedion_syndrome				20	66	---	---	---	---	PASS
MOBKL2A	126308	broad.mit.edu	37	19	2078599	2078599	+	5'UTR	SNP	C	G	G			TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2078599C>G	uc002luu.2	-	1					MOBKL2A_uc002luv.2_5'UTR	NM_130807	NP_570719	Q96BX8	MOL2A_HUMAN	MOB-LAK							intracellular	metal ion binding			lung(1)	1		Ovarian(11;1.78e-06)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GTAGAGGGGTCCTGGGCCAGC	0.592													10	39	---	---	---	---	PASS
LYL1	4066	broad.mit.edu	37	19	13211728	13211728	+	Silent	SNP	C	T	T			TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13211728C>T	uc002mwi.2	-	2	619	c.258G>A	c.(256-258)CCG>CCA	p.P86P		NM_005583	NP_005574	P12980	LYL1_HUMAN	lymphoblastic leukemia derived sequence 1	86					B cell differentiation|blood vessel maturation|definitive hemopoiesis|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding				0			OV - Ovarian serous cystadenocarcinoma(19;6.08e-22)			GTTGCAGCAGCGGGGGCCGCA	0.682			T	TRB@	T-ALL								5	2	---	---	---	---	PASS
CIC	23152	broad.mit.edu	37	19	42797181	42797181	+	Missense_Mutation	SNP	G	C	C			TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42797181G>C	uc002otf.1	+	15	3583	c.3543G>C	c.(3541-3543)AAG>AAC	p.K1181N		NM_015125	NP_055940	Q96RK0	CIC_HUMAN	capicua homolog	1181	Pro-rich.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding			ovary(4)|breast(4)|lung(1)|central_nervous_system(1)|skin(1)	11		Prostate(69;0.00682)				AGAAAGTGAAGGCAGCCATCG	0.657			T	DUX4	soft tissue sarcoma								14	49	---	---	---	---	PASS
ZNF749	388567	broad.mit.edu	37	19	57954668	57954668	+	Missense_Mutation	SNP	A	C	C			TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57954668A>C	uc002qoq.2	+	3	406	c.152A>C	c.(151-153)CAT>CCT	p.H51P	ZNF547_uc002qpm.3_Intron	NM_001023561	NP_001018855	O43361	ZN749_HUMAN	zinc finger protein 749	51	KRAB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.221)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0264)|Lung(386;0.177)		GGTTGTTGGCATGGAGCCAAG	0.507													12	33	---	---	---	---	PASS
COMMD7	149951	broad.mit.edu	37	20	31291079	31291079	+	3'UTR	SNP	C	T	T			TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31291079C>T	uc002wya.3	-	9					COMMD7_uc010ged.2_3'UTR|COMMD7_uc002wyb.2_3'UTR	NM_053041	NP_444269	Q86VX2	COMD7_HUMAN	COMM domain containing 7 isoform 1						negative regulation of NF-kappaB transcription factor activity|negative regulation of transcription, DNA-dependent|tumor necrosis factor-mediated signaling pathway		NF-kappaB binding			breast(1)	1						CAGCAGGGCCCCATGGAGCAT	0.577													4	21	---	---	---	---	PASS
PTPRT	11122	broad.mit.edu	37	20	40944543	40944543	+	Silent	SNP	C	A	A			TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:40944543C>A	uc002xkg.2	-	12	2143	c.1959G>T	c.(1957-1959)CGG>CGT	p.R653R	PTPRT_uc010ggj.2_Silent_p.R653R	NM_007050	NP_008981	O14522	PTPRT_HUMAN	protein tyrosine phosphatase, receptor type, T	653	Extracellular (Potential).|Fibronectin type-III 4.				homophilic cell adhesion|transmembrane receptor protein tyrosine kinase signaling pathway	cell surface|integral to membrane|plasma membrane	alpha-catenin binding|beta-catenin binding|cadherin binding|delta-catenin binding|gamma-catenin binding|protein tyrosine phosphatase activity|receptor activity			skin(8)|ovary(7)|lung(5)	20		Myeloproliferative disorder(115;0.00452)|Lung NSC(126;0.0573)|all_lung(126;0.0783)				TGGAGGCATTCCGATAGCTCA	0.512													40	124	---	---	---	---	PASS
PTPRT	11122	broad.mit.edu	37	20	40944544	40944544	+	Missense_Mutation	SNP	C	A	A			TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:40944544C>A	uc002xkg.2	-	12	2142	c.1958G>T	c.(1957-1959)CGG>CTG	p.R653L	PTPRT_uc010ggj.2_Missense_Mutation_p.R653L	NM_007050	NP_008981	O14522	PTPRT_HUMAN	protein tyrosine phosphatase, receptor type, T	653	Extracellular (Potential).|Fibronectin type-III 4.				homophilic cell adhesion|transmembrane receptor protein tyrosine kinase signaling pathway	cell surface|integral to membrane|plasma membrane	alpha-catenin binding|beta-catenin binding|cadherin binding|delta-catenin binding|gamma-catenin binding|protein tyrosine phosphatase activity|receptor activity			skin(8)|ovary(7)|lung(5)	20		Myeloproliferative disorder(115;0.00452)|Lung NSC(126;0.0573)|all_lung(126;0.0783)				GGAGGCATTCCGATAGCTCAC	0.517													40	126	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	22	18842438	18842438	+	Intron	SNP	G	A	A	rs9604886		TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:18842438G>A	uc010grj.1	+						uc002zoe.2_RNA					Homo sapiens mRNA; cDNA DKFZp434K191 (from clone DKFZp434K191).																		TGGGGAAGAGGAGAGTGGCTC	0.627													8	20	---	---	---	---	PASS
GGT5	2687	broad.mit.edu	37	22	24621029	24621029	+	Missense_Mutation	SNP	T	C	C			TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24621029T>C	uc002zzo.3	-	11	1966	c.1549A>G	c.(1549-1551)ATT>GTT	p.I517V	GGT5_uc002zzp.3_Missense_Mutation_p.I518V|GGT5_uc002zzr.3_Missense_Mutation_p.I485V|GGT5_uc002zzq.3_Missense_Mutation_p.I485V|GGT5_uc011ajm.1_Missense_Mutation_p.I441V	NM_004121	NP_004112	P36269	GGT5_HUMAN	gamma-glutamyltransferase 5 isoform b	517	Extracellular (Potential).				glutathione biosynthetic process|hormone biosynthetic process|leukotriene biosynthetic process|prostanoid metabolic process	integral to membrane|plasma membrane	acyltransferase activity|gamma-glutamyltransferase activity			ovary(2)|skin(1)	3						GGGGCTGCAATGGCCGCTCTC	0.602													3	18	---	---	---	---	PASS
OSBP2	23762	broad.mit.edu	37	22	31302447	31302447	+	3'UTR	SNP	T	C	C			TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:31302447T>C	uc003aiy.1	+	14					OSBP2_uc011ala.1_3'UTR|OSBP2_uc010gwc.1_3'UTR|OSBP2_uc011alb.1_3'UTR|OSBP2_uc003aiz.1_3'UTR|OSBP2_uc003aja.1_3'UTR|OSBP2_uc011alc.1_3'UTR|OSBP2_uc003ajb.2_3'UTR|OSBP2_uc011ald.1_3'UTR|OSBP2_uc010gwd.1_3'UTR	NM_030758	NP_110385	Q969R2	OSBP2_HUMAN	oxysterol binding protein 2 isoform a						lipid transport	membrane	lipid binding			breast(1)|skin(1)	2						CTATTTCCTTTCCTATTTTTT	0.542													5	8	---	---	---	---	PASS
ARMCX5	64860	broad.mit.edu	37	X	101858509	101858509	+	Silent	SNP	A	T	T			TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:101858509A>T	uc004ejg.2	+	6	2321	c.1440A>T	c.(1438-1440)GCA>GCT	p.A480A	ARMCX5_uc004ejh.2_Silent_p.A480A	NM_022838	NP_073749	Q6P1M9	ARMX5_HUMAN	armadillo repeat containing, X-linked 5	480	ARM 3.						binding			ovary(1)	1						CATTGGTTGCACCCTTTAACA	0.303													15	170	---	---	---	---	PASS
GPRASP2	114928	broad.mit.edu	37	X	101971084	101971084	+	Silent	SNP	C	A	A			TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:101971084C>A	uc004ejk.2	+	4	2621	c.1287C>A	c.(1285-1287)TCC>TCA	p.S429S	GPRASP2_uc004ejl.2_Silent_p.S429S|GPRASP2_uc004ejm.2_Silent_p.S429S|GPRASP2_uc011mrp.1_5'Flank	NM_138437	NP_612446	Q96D09	GASP2_HUMAN	G protein-coupled receptor associated sorting	429						cytoplasm	protein binding			ovary(1)	1						AGGAAAAGTCCAGTTTGGGGG	0.577													56	188	---	---	---	---	PASS
GPR112	139378	broad.mit.edu	37	X	135482053	135482053	+	Missense_Mutation	SNP	A	G	G			TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:135482053A>G	uc004ezu.1	+	21	8644	c.8353A>G	c.(8353-8355)ACA>GCA	p.T2785A	GPR112_uc010nsb.1_Missense_Mutation_p.T2580A	NM_153834	NP_722576	Q8IZF6	GP112_HUMAN	G-protein coupled receptor 112	2785	Helical; Name=2; (Potential).				neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(5)|large_intestine(2)|skin(2)|lung(1)|breast(1)|pancreas(1)	12	Acute lymphoblastic leukemia(192;0.000127)					CAACCTGTGCACAGCACTACT	0.348													7	176	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	3320	3320	+	5'Flank	SNP	A	G	G			TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:3320A>G	uc004coq.3	-						uc004cos.3_RNA|uc011mfh.1_5'Flank					Homo sapiens cDNA: FLJ22857 fis, clone KAT01615.																		ACCCATGGCCAACCTCCTACT	0.274													2	0	---	---	---	---	PASS
FAM167B	84734	broad.mit.edu	37	1	32711939	32711940	+	5'Flank	DEL	TC	-	-			TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:32711939_32711940delTC	uc001buw.2	+							NM_032648	NP_116037	Q9BTA0	F167B_HUMAN	hypothetical protein LOC84734											ovary(1)	1						ctccctcccttcTCTCTCTCtc	0.030													4	2	---	---	---	---	
STXBP3	6814	broad.mit.edu	37	1	109301020	109301020	+	Intron	DEL	C	-	-	rs3841723		TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:109301020delC	uc001dvy.2	+						STXBP3_uc001dvz.2_Intron	NM_007269	NP_009200	O00186	STXB3_HUMAN	syntaxin binding protein 3						negative regulation of calcium ion-dependent exocytosis|neutrophil degranulation|platelet aggregation|protein transport|vesicle docking involved in exocytosis	cytosol|nucleus|platelet alpha granule|specific granule|tertiary granule	syntaxin-2 binding			ovary(3)|central_nervous_system(1)	4		all_epithelial(167;0.000154)|all_lung(203;0.00026)|Lung NSC(277;0.000508)		Colorectal(144;0.0386)|Lung(183;0.104)|COAD - Colon adenocarcinoma(174;0.137)|Epithelial(280;0.231)		AAACTTTTAGCCAGTAAAGTT	0.234													2	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	242995203	242995204	+	IGR	INS	-	GAAA	GAAA	rs10926878	by1000genomes	TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:242995203_242995204insGAAA								PLD5 (307205 upstream) : CEP170 (292527 downstream)																							aaggaaggaaggaaggaaggag	0.000													6	3	---	---	---	---	
MTA3	57504	broad.mit.edu	37	2	42760223	42760223	+	Intron	DEL	C	-	-			TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:42760223delC	uc002rso.1	+							NM_020744	NP_065795	Q9BTC8	MTA3_HUMAN	metastasis associated 1 family, member 3							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)	2						GTGGGGCAttctttttttttt	0.239													4	2	---	---	---	---	
NBEAL1	65065	broad.mit.edu	37	2	204002714	204002714	+	Intron	DEL	A	-	-	rs112429768		TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:204002714delA	uc002uzt.3	+						NBEAL1_uc002uzs.3_Intron	NM_001114132	NP_001107604	Q6ZS30	NBEL1_HUMAN	neurobeachin-like 1 isoform 3								binding			ovary(1)|skin(1)	2						actccgtctcaaaaaaaaaaa	0.154													3	4	---	---	---	---	
ING5	84289	broad.mit.edu	37	2	242657739	242657742	+	Intron	DEL	CCTC	-	-	rs112407089		TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:242657739_242657742delCCTC	uc002wcd.2	+						ING5_uc002wcc.1_Intron	NM_032329	NP_115705	Q8WYH8	ING5_HUMAN	inhibitor of growth family, member 5						DNA replication|histone H3 acetylation|negative regulation of cell proliferation|negative regulation of growth|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	MOZ/MORF histone acetyltransferase complex	protein binding|zinc ion binding				0		all_cancers(19;1.09e-40)|all_epithelial(40;2.03e-18)|Breast(86;1.53e-05)|all_lung(227;0.00338)|Renal(207;0.00502)|Ovarian(221;0.00716)|Lung NSC(271;0.012)|Esophageal squamous(248;0.129)|Melanoma(123;0.144)|all_hematologic(139;0.158)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;2.16e-33)|all cancers(36;4.99e-31)|OV - Ovarian serous cystadenocarcinoma(60;3.6e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.65e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0839)		ttcctcccttcctccctccctccc	0.000													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	13246237	13246240	+	IGR	DEL	CTTA	-	-			TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:13246237_13246240delCTTA								IQSEC1 (131620 upstream) : NUP210 (111497 downstream)																							ttctttctatcttactttctttcc	0.255													10	6	---	---	---	---	
SLIT2	9353	broad.mit.edu	37	4	20619357	20619357	+	Intron	DEL	A	-	-	rs71653889		TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:20619357delA	uc003gpr.1	+						SLIT2_uc003gps.1_Intron	NM_004787	NP_004778	O94813	SLIT2_HUMAN	slit homolog 2 precursor						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						agaaaaagtgaaaaaaaaaaa	0.303													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	53661678	53661679	+	IGR	INS	-	G	G			TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:53661678_53661679insG								KIAA0114 (81373 upstream) : RASL11B (66816 downstream)																							gaaggaaggaagaagaagaaga	0.000													3	4	---	---	---	---	
C4orf37	285555	broad.mit.edu	37	4	99055730	99055731	+	Intron	INS	-	TAA	TAA	rs143595982	by1000genomes	TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:99055730_99055731insTAA	uc003htt.1	-							NM_174952	NP_777612	Q8N412	CD037_HUMAN	hypothetical protein LOC285555												0				OV - Ovarian serous cystadenocarcinoma(123;2.27e-08)		ATTTTCAGAACTGTCTAGTCAG	0.262													9	6	---	---	---	---	
ANK2	287	broad.mit.edu	37	4	114135124	114135125	+	Intron	INS	-	T	T	rs140341344	by1000genomes	TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:114135124_114135125insT	uc003ibe.3	+						ANK2_uc003ibd.3_Intron|ANK2_uc003ibf.3_Intron|ANK2_uc003ibc.2_Intron|ANK2_uc011cgb.1_Intron	NM_001148	NP_001139	Q01484	ANK2_HUMAN	ankyrin 2 isoform 1						axon guidance|signal transduction	apical plasma membrane|basolateral plasma membrane|cytoskeleton|cytosol|sarcomere	protein binding|protein binding			central_nervous_system(7)|ovary(3)|large_intestine(2)|breast(1)|skin(1)	14		Ovarian(17;0.0448)|Hepatocellular(203;0.218)		OV - Ovarian serous cystadenocarcinoma(123;4.92e-05)		ttttttttttattttttttttA	0.218													4	2	---	---	---	---	
FABP2	2169	broad.mit.edu	37	4	120243419	120243420	+	5'Flank	INS	-	TT	TT	rs151066719	by1000genomes	TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:120243419_120243420insTT	uc003icw.2	-							NM_000134	NP_000125	P12104	FABPI_HUMAN	intestinal fatty acid binding protein 2								fatty acid binding			ovary(1)	1						AATTCTTATTAATTAATTCTTA	0.287													4	5	---	---	---	---	
SMAD1	4086	broad.mit.edu	37	4	146449213	146449214	+	Intron	DEL	AC	-	-			TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:146449213_146449214delAC	uc003ikc.2	+						SMAD1_uc003ikd.2_Intron|SMAD1_uc010iov.2_Intron|SMAD1_uc011cic.1_Intron	NM_005900	NP_005891	Q15797	SMAD1_HUMAN	Sma- and Mad-related protein 1						BMP signaling pathway|embryonic pattern specification|primary miRNA processing|SMAD protein complex assembly|transforming growth factor beta receptor signaling pathway	cytosol|integral to membrane|nuclear inner membrane	co-SMAD binding|I-SMAD binding|identical protein binding|protein kinase binding|sequence-specific DNA binding transcription factor activity|transforming growth factor beta receptor, pathway-specific cytoplasmic mediator activity			ovary(1)	1	all_hematologic(180;0.151)					ttttgtttgtacacacacacac	0.000													4	2	---	---	---	---	
CYP4V2	285440	broad.mit.edu	37	4	187118942	187118945	+	Intron	DEL	TATG	-	-	rs144489932		TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:187118942_187118945delTATG	uc003iyw.3	+							NM_207352	NP_997235	Q6ZWL3	CP4V2_HUMAN	cytochrome P450, family 4, subfamily v,						response to stimulus|visual perception	endoplasmic reticulum membrane|integral to membrane	electron carrier activity|heme binding|monooxygenase activity|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen				0		all_cancers(14;4.27e-52)|all_epithelial(14;7.69e-39)|all_lung(41;1.34e-13)|Lung NSC(41;3.58e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.0066)|Hepatocellular(41;0.00886)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|all_neural(102;0.243)		OV - Ovarian serous cystadenocarcinoma(60;1.33e-10)|BRCA - Breast invasive adenocarcinoma(30;3.84e-05)|GBM - Glioblastoma multiforme(59;0.000132)|STAD - Stomach adenocarcinoma(60;0.000293)|LUSC - Lung squamous cell carcinoma(40;0.00242)|READ - Rectum adenocarcinoma(43;0.17)		acatctagattatgtagtaattta	0.093													2	4	---	---	---	---	
RGNEF	64283	broad.mit.edu	37	5	73153410	73153413	+	Intron	DEL	ACAT	-	-	rs72397069		TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:73153410_73153413delACAT	uc011csq.1	+						RGNEF_uc003kcx.2_Intron|RGNEF_uc010izf.2_Intron|RGNEF_uc011csr.1_Intron	NM_001080479	NP_001073948	Q8N1W1	RGNEF_HUMAN	Rho-guanine nucleotide exchange factor						cell differentiation|intracellular signal transduction|regulation of Rho protein signal transduction	cytoplasm|plasma membrane	metal ion binding|Rho guanyl-nucleotide exchange factor activity|RNA binding				0		Lung NSC(167;0.0378)|all_lung(232;0.04)|Ovarian(174;0.0798)		OV - Ovarian serous cystadenocarcinoma(47;1.25e-51)		acacacacacacatacacacacac	0.221													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	81655269	81655270	+	IGR	DEL	AT	-	-	rs148541786	by1000genomes	TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:81655269_81655270delAT								ATP6AP1L (41123 upstream) : TMEM167A (693397 downstream)																							acacacacacatacacacacac	0.342													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	90717601	90717606	+	IGR	DEL	ACACAC	-	-	rs72414317		TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:90717601_90717606delACACAC								LOC100129716 (1070 upstream) : None (None downstream)																							acatacacatacacacacacacacac	0.175													4	2	---	---	---	---	
ANKHD1-EIF4EBP3	404734	broad.mit.edu	37	5	139865024	139865025	+	Intron	DEL	TA	-	-	rs150399423		TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:139865024_139865025delTA	uc003lfs.1	+						ANKHD1_uc003lfq.1_Intron|ANKHD1_uc003lfr.2_Intron|ANKHD1_uc003lft.1_Intron|ANKHD1_uc003lfu.1_Intron|ANKHD1_uc003lfv.1_5'Flank	NM_020690	NP_065741	Q8IWZ2	Q8IWZ2_HUMAN	ANKHD1-EIF4EBP3 protein							cytoplasm|nucleus	RNA binding			ovary(6)	6			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			tatgtatgtgtatatatatata	0.074													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	26322645	26322646	+	5'Flank	INS	-	T	T	rs151208857		TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26322645_26322646insT	uc003nhn.2	-											full-length cDNA clone CS0DF024YI14 of Fetal brain of Homo sapiens (human).																		CAATTGCAGTAttttttttttt	0.332													4	2	---	---	---	---	
GSTA3	2940	broad.mit.edu	37	6	52765063	52765063	+	Intron	DEL	T	-	-			TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:52765063delT	uc003pbb.2	-						GSTA3_uc010jzq.2_Intron	NM_000847	NP_000838	Q16772	GSTA3_HUMAN	glutathione S-transferase alpha 3						glutathione metabolic process|xenobiotic metabolic process	cytosol	glutathione transferase activity				0	Lung NSC(77;0.0912)				Glutathione(DB00143)	tttctttttcttttttttttt	0.045													5	3	---	---	---	---	
CDCA7L	55536	broad.mit.edu	37	7	21942183	21942184	+	Intron	INS	-	GATTCAGAGTTTATTA	GATTCAGAGTTTATTA	rs141458032	by1000genomes	TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:21942183_21942184insGATTCAGAGTTTATTA	uc010kuk.2	-						CDCA7L_uc003sve.3_Intron|CDCA7L_uc010kul.2_Intron|CDCA7L_uc003svf.3_Intron	NM_018719	NP_061189	Q96GN5	CDA7L_HUMAN	cell division cycle associated 7-like isoform 1						positive regulation of cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleolus					0						TCCAGAACCACGATTCAGAGTT	0.436													4	2	---	---	---	---	
RABGEF1	27342	broad.mit.edu	37	7	66098581	66098581	+	Intron	DEL	T	-	-			TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:66098581delT	uc003tvf.2	+						KCTD7_uc003tvd.3_Intron|KCTD7_uc003tve.2_Intron	NM_014504	NP_055319	Q9UJ41	RABX5_HUMAN	RAB guanine nucleotide exchange factor (GEF) 1						endocytosis|protein transport	early endosome|recycling endosome	DNA binding|protein binding|zinc ion binding			ovary(1)	1						AAGAGATCAATTTTTTTTTTT	0.333													4	3	---	---	---	---	
GTF2I	2969	broad.mit.edu	37	7	74129040	74129040	+	Intron	DEL	T	-	-			TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:74129040delT	uc003uau.2	+						GTF2I_uc003uat.2_Intron|GTF2I_uc003uav.2_Intron|GTF2I_uc003uaw.2_Intron|GTF2I_uc003uay.2_Intron|GTF2I_uc003uax.2_Intron|uc003uaz.2_Intron	NM_032999	NP_127492	P78347	GTF2I_HUMAN	general transcription factor IIi isoform 1						negative regulation of angiogenesis|signal transduction|transcription initiation from RNA polymerase II promoter	cytoplasm|nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity				0						CTTGTCAGTCttttttttttt	0.294													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	101967482	101967482	+	IGR	DEL	A	-	-			TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:101967482delA								SH2B2 (5305 upstream) : SPDYE6 (18711 downstream)																							ACTCTGTCTCAAAAAAAAAAA	0.189													4	2	---	---	---	---	
FAM71F2	346653	broad.mit.edu	37	7	128317558	128317559	+	Intron	INS	-	AAA	AAA	rs10659136		TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:128317558_128317559insAAA	uc003vnk.3	+						FAM71F2_uc010llm.1_Intron|FAM71F2_uc003vnl.2_Intron|FAM71F2_uc010lln.1_Intron	NM_001012454	NP_001012457	Q6NXP2	F71F2_HUMAN	hypothetical protein LOC346653 isoform a												0						gactccgtctcaaaaaaaaaaa	0.223													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	30181786	30181789	+	IGR	DEL	AAGA	-	-			TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:30181786_30181789delAAGA								DCTN6 (140727 upstream) : RBPMS (60155 downstream)																							ggaaggaaggaagaaagaaagaaa	0.083													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	73144053	73144054	+	Intron	INS	-	TGTGTGTG	TGTGTGTG	rs151064569	by1000genomes	TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:73144053_73144054insTGTGTGTG	uc010lzg.2	-											Homo sapiens cDNA, FLJ99767.																		GGCTTACTACCtgtgtgtgtgt	0.228													4	2	---	---	---	---	
LY96	23643	broad.mit.edu	37	8	74914329	74914334	+	Intron	DEL	TCTCTC	-	-			TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:74914329_74914334delTCTCTC	uc003yad.2	+							NM_015364	NP_056179	Q9Y6Y9	LY96_HUMAN	MD-2 protein precursor						cellular defense response|detection of lipopolysaccharide|I-kappaB kinase/NF-kappaB cascade|inflammatory response|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway	extracellular space|lipopolysaccharide receptor complex|plasma membrane	coreceptor activity|lipopolysaccharide receptor activity|protein binding				0	Breast(64;0.0311)		Epithelial(68;0.0208)|BRCA - Breast invasive adenocarcinoma(89;0.0499)|all cancers(69;0.0619)			tttctttctttctctctctctctctc	0.000													5	3	---	---	---	---	
CA2	760	broad.mit.edu	37	8	86389130	86389131	+	Intron	INS	-	T	T	rs111230295		TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:86389130_86389131insT	uc003ydk.2	+							NM_000067	NP_000058	P00918	CAH2_HUMAN	carbonic anhydrase II						one-carbon metabolic process	apical part of cell	carbonate dehydratase activity|zinc ion binding			central_nervous_system(1)	1					Acetazolamide(DB00819)|Bendroflumethiazide(DB00436)|Benzthiazide(DB00562)|Brinzolamide(DB01194)|Chlorothiazide(DB00880)|Cyclothiazide(DB00606)|Diazoxide(DB01119)|Dorzolamide(DB00869)|Ethinamate(DB01031)|Hydrochlorothiazide(DB00999)|Hydroflumethiazide(DB00774)|Methyclothiazide(DB00232)|Quinethazone(DB01325)|Topiramate(DB00273)|Trichlormethiazide(DB01021)	TGTGAAAATAGTTTTTTTTTTT	0.252													4	2	---	---	---	---	
TG	7038	broad.mit.edu	37	8	134129131	134129131	+	Intron	DEL	A	-	-			TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:134129131delA	uc003ytw.2	+						TG_uc010mdw.2_Intron|TG_uc011ljb.1_Intron|TG_uc011ljc.1_Intron	NM_003235	NP_003226	P01266	THYG_HUMAN	thyroglobulin precursor						hormone biosynthetic process|signal transduction|thyroid gland development|thyroid hormone generation	extracellular space	hormone activity			ovary(8)|breast(4)|pancreas(1)|central_nervous_system(1)|skin(1)	15	Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)	Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0559)|Breast(495;0.0735)	BRCA - Breast invasive adenocarcinoma(115;0.000701)	KIRC - Kidney renal clear cell carcinoma(542;0.0546)		ggggaaagttaaaaaaaaaaa	0.055													4	2	---	---	---	---	
AQP7	364	broad.mit.edu	37	9	33386733	33386734	+	Intron	INS	-	A	A	rs144694820	by1000genomes	TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:33386733_33386734insA	uc003zst.2	-						SUGT1P1_uc010mjq.1_Intron|AQP7_uc003zsu.1_Intron|AQP7_uc010mjs.2_Intron|AQP7_uc010mjt.2_Intron|AQP7_uc011lnx.1_Intron|AQP7_uc011lny.1_Intron|AQP7_uc003zss.3_Intron|AQP7_uc011lnz.1_Intron|AQP7_uc011loa.1_Intron	NM_001170	NP_001161	O14520	AQP7_HUMAN	aquaporin 7						excretion|generation of precursor metabolites and energy	cell-cell junction|cytoplasm|integral to plasma membrane	glycerol channel activity|water channel activity				0			LUSC - Lung squamous cell carcinoma(29;0.00788)	GBM - Glioblastoma multiforme(74;0.191)		gaggaacacagaggcgatggct	0.158													4	2	---	---	---	---	
UBQLN1	29979	broad.mit.edu	37	9	86276533	86276533	+	3'UTR	DEL	T	-	-	rs33950155		TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:86276533delT	uc004amv.2	-	11					UBQLN1_uc004amw.2_3'UTR	NM_013438	NP_038466	Q9UMX0	UBQL1_HUMAN	ubiquilin 1 isoform 1						apoptosis|regulation of protein ubiquitination|response to hypoxia	endoplasmic reticulum|nucleus|perinuclear region of cytoplasm|proteasome complex	kinase binding				0						AAAAGAAAAATACAGAAAAAC	0.338													1	5	---	---	---	---	
PTGR1	22949	broad.mit.edu	37	9	114354959	114354959	+	Intron	DEL	T	-	-			TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:114354959delT	uc004bfh.2	-						PTGR1_uc011lwr.1_Intron|PTGR1_uc004bfi.3_Intron|PTGR1_uc004bfj.3_Intron|PTGR1_uc010mue.2_Intron	NM_012212	NP_036344	Q14914	PTGR1_HUMAN	prostaglandin reductase 1 isoform 1						leukotriene metabolic process	cytoplasm	15-oxoprostaglandin 13-oxidase activity|2-alkenal reductase activity|alcohol dehydrogenase (NAD) activity|zinc ion binding				0						GGACAAATACTTTTTTTTTTT	0.209													4	3	---	---	---	---	
PLXDC2	84898	broad.mit.edu	37	10	20303118	20303126	+	Intron	DEL	CTCCCTTGT	-	-	rs71388888		TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:20303118_20303126delCTCCCTTGT	uc001iqg.1	+						PLXDC2_uc001iqh.1_Intron	NM_032812	NP_116201	Q6UX71	PXDC2_HUMAN	plexin domain containing 2 precursor							integral to membrane				ovary(2)|central_nervous_system(1)|skin(1)	4						ccctccctccctcccttgtttccttcctt	0.110													4	2	---	---	---	---	
CD151	977	broad.mit.edu	37	11	836540	836540	+	Intron	DEL	G	-	-	rs56063221		TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:836540delG	uc001lry.2	+						CD151_uc001lrx.2_Intron|CD151_uc001lrz.2_Intron|CD151_uc001lsa.2_Intron|CD151_uc001lsb.2_Intron	NM_004357	NP_004348	P48509	CD151_HUMAN	CD151 antigen						cell adhesion|hemidesmosome assembly	cytosol|integral to plasma membrane|membrane fraction	protein binding				0		all_cancers(49;2.31e-08)|all_epithelial(84;3.72e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.179)|all_lung(207;0.227)		all cancers(45;1.54e-25)|Epithelial(43;1.22e-24)|OV - Ovarian serous cystadenocarcinoma(40;6.91e-19)|BRCA - Breast invasive adenocarcinoma(625;4.23e-05)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		GTGCTCACCTGGGGGGGGGGT	0.652													0	6	---	---	---	---	
BBS1	582	broad.mit.edu	37	11	66282290	66282291	+	Intron	INS	-	T	T	rs72050815		TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66282290_66282291insT	uc001oij.1	+						BBS1_uc001oii.1_Intron|BBS1_uc010rpf.1_Intron|BBS1_uc010rpg.1_Intron|BBS1_uc001oik.1_Intron|BBS1_uc001oil.1_Intron	NM_024649	NP_078925	Q8NFJ9	BBS1_HUMAN	Bardet-Biedl syndrome 1						nonmotile primary cilium assembly|photoreceptor cell maintenance|response to stimulus|retina homeostasis	BBSome|cilium membrane|cytoplasm	protein binding			ovary(1)	1						AGTGATGGCACttttttttttt	0.302									Bardet-Biedl_syndrome				4	2	---	---	---	---	
PARP11	57097	broad.mit.edu	37	12	3950020	3950020	+	Intron	DEL	A	-	-			TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:3950020delA	uc001qml.2	-						PARP11_uc009zef.2_Intron|PARP11_uc001qmm.2_Intron|PARP11_uc001qmn.2_Intron	NM_020367	NP_065100	Q9NR21	PAR11_HUMAN	poly (ADP-ribose) polymerase family, member 11								NAD+ ADP-ribosyltransferase activity			ovary(1)|central_nervous_system(1)	2			all cancers(3;1.58e-07)|OV - Ovarian serous cystadenocarcinoma(31;0.00287)|GBM - Glioblastoma multiforme(3;0.0141)|COAD - Colon adenocarcinoma(12;0.0264)			CCTGCAGAACAAAAGCCAGCA	0.438													124	77	---	---	---	---	
VWF	7450	broad.mit.edu	37	12	6089343	6089344	+	Intron	INS	-	GGAA	GGAA			TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6089343_6089344insGGAA	uc001qnn.1	-						VWF_uc010set.1_Intron	NM_000552	NP_000543	P04275	VWF_HUMAN	von Willebrand factor preproprotein						blood coagulation, intrinsic pathway|cell-substrate adhesion|platelet activation|platelet degranulation|protein homooligomerization	endoplasmic reticulum|platelet alpha granule lumen|proteinaceous extracellular matrix|Weibel-Palade body	chaperone binding|collagen binding|glycoprotein binding|immunoglobulin binding|integrin binding|protease binding|protein homodimerization activity|protein N-terminus binding			skin(4)|ovary(3)|pancreas(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|breast(1)	12					Antihemophilic Factor(DB00025)	gagggagggagggagggaggga	0.015													4	2	---	---	---	---	
A2ML1	144568	broad.mit.edu	37	12	8993575	8993578	+	Intron	DEL	GAAG	-	-			TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:8993575_8993578delGAAG	uc001quz.3	+						A2ML1_uc001qva.1_5'Flank	NM_144670	NP_653271	A8K2U0	A2ML1_HUMAN	alpha-2-macroglobulin-like 1 precursor							extracellular space	endopeptidase inhibitor activity			ovary(2)|skin(1)	3						aggaaggaaagaaggaaggaagga	0.000													11	5	---	---	---	---	
ABCC9	10060	broad.mit.edu	37	12	22041045	22041056	+	Intron	DEL	GACAGAGGGGTT	-	-	rs145112683		TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:22041045_22041056delGACAGAGGGGTT	uc001rfi.1	-						ABCC9_uc001rfh.2_Intron|ABCC9_uc001rfj.1_Intron	NM_005691	NP_005682	O60706	ABCC9_HUMAN	ATP-binding cassette, sub-family C, member 9						defense response to virus|potassium ion import	ATP-sensitive potassium channel complex	ATP binding|ATPase activity, coupled to transmembrane movement of substances|potassium channel regulator activity|sulfonylurea receptor activity			ovary(4)|skin(2)	6					Adenosine triphosphate(DB00171)|Glibenclamide(DB01016)	aattgctgaggacagaggggtttccaggacat	0.175													3	4	---	---	---	---	
OVCH1	341350	broad.mit.edu	37	12	29592104	29592105	+	Intron	INS	-	A	A	rs145743678	by1000genomes	TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:29592104_29592105insA	uc001rix.1	-							NM_183378	NP_899234	Q7RTY7	OVCH1_HUMAN	ovochymase 1 precursor						proteolysis	extracellular region	metal ion binding|serine-type endopeptidase activity			ovary(3)|central_nervous_system(3)|pancreas(3)|large_intestine(1)	10	Lung NSC(12;1.84e-09)|Acute lymphoblastic leukemia(23;0.00885)|all_hematologic(23;0.0155)					ccaatatattcaccttcctaca	0.000													7	6	---	---	---	---	
DENND5B	160518	broad.mit.edu	37	12	31562360	31562360	+	Intron	DEL	A	-	-	rs111670680		TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:31562360delA	uc001rki.1	-						DENND5B_uc001rkh.1_Intron|DENND5B_uc009zjq.1_Intron	NM_144973	NP_659410	Q6ZUT9	DEN5B_HUMAN	DENN/MADD domain containing 5B							integral to membrane				ovary(1)|central_nervous_system(1)	2						AGTATCAAAGAAAAAAAAAAA	0.254													4	2	---	---	---	---	
FMNL3	91010	broad.mit.edu	37	12	50045327	50045327	+	Intron	DEL	A	-	-			TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:50045327delA	uc001ruv.1	-						FMNL3_uc001ruw.1_Intron|FMNL3_uc001rut.1_Intron|FMNL3_uc001ruu.1_Intron	NM_175736	NP_783863	Q8IVF7	FMNL3_HUMAN	formin-like 3 isoform 1						actin cytoskeleton organization		actin binding|Rho GTPase binding			breast(2)|pancreas(2)	4						TCTGAGAGTTAAAAAAAAAaa	0.269													6	3	---	---	---	---	
TIMELESS	8914	broad.mit.edu	37	12	56824949	56824949	+	Intron	DEL	C	-	-	rs79733408		TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56824949delC	uc001slf.2	-						TIMELESS_uc001slg.2_Intron	NM_003920	NP_003911	Q9UNS1	TIM_HUMAN	timeless homolog						cell division|circadian rhythm|detection of abiotic stimulus|mitosis|morphogenesis of an epithelium|negative regulation of transcription, DNA-dependent|regulation of S phase|response to DNA damage stimulus|transcription, DNA-dependent	nuclear chromatin				ovary(5)|breast(2)|pancreas(1)	8						accagcctggccaacatggtg	0.005													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	82642192	82642193	+	IGR	DEL	CA	-	-	rs145530676		TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:82642192_82642193delCA								PPFIA2 (489083 upstream) : CCDC59 (103897 downstream)																							CTTGATTCATcacacacacaca	0.074													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	93553462	93553462	+	IGR	DEL	A	-	-	rs146337263		TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:93553462delA								EEA1 (230355 upstream) : NUDT4 (218239 downstream)																							tctctggaagaaaaaaaaggt	0.000													4	2	---	---	---	---	
UHRF1BP1L	23074	broad.mit.edu	37	12	100464068	100464069	+	Intron	INS	-	TT	TT			TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:100464068_100464069insTT	uc001tgq.2	-						UHRF1BP1L_uc001tgr.2_Intron|UHRF1BP1L_uc001tgp.2_Intron	NM_015054	NP_055869	A0JNW5	UH1BL_HUMAN	UHRF1 (ICBP90) binding protein 1-like isoform a											ovary(2)	2						taattaattaattttttttttt	0.124													4	2	---	---	---	---	
SLC17A8	246213	broad.mit.edu	37	12	100806371	100806371	+	Intron	DEL	A	-	-			TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:100806371delA	uc010svi.1	+						SLC17A8_uc009ztx.2_Intron	NM_139319	NP_647480	Q8NDX2	VGLU3_HUMAN	solute carrier family 17 (sodium-dependent						neurotransmitter transport|sensory perception of sound|sodium ion transport	cell junction|integral to membrane|synaptic vesicle membrane|synaptosome	L-glutamate transmembrane transporter activity|symporter activity			ovary(3)	3						aagtaaagttaaaaaaaaaaa	0.109													5	3	---	---	---	---	
GPR81	27198	broad.mit.edu	37	12	123150129	123150130	+	Intron	INS	-	TCTTT	TCTTT	rs148758720	by1000genomes	TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123150129_123150130insTCTTT	uc001ucw.1	-							NM_032554		Q9BXC0	HCAR1_HUMAN	G protein-coupled receptor 81						response to estradiol stimulus	integral to membrane|plasma membrane	G-protein coupled receptor activity				0	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;2.14e-05)|Epithelial(86;3.25e-05)|BRCA - Breast invasive adenocarcinoma(302;0.197)		tttttcttttctcttttctttt	0.050													6	3	---	---	---	---	
TPTE2P1	646405	broad.mit.edu	37	13	25525716	25525716	+	Intron	DEL	A	-	-			TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:25525716delA	uc010tdh.1	-						TPTE2P1_uc001upx.3_Intron	NR_026730				RecName: Full=C2 tensin-type domain-containing protein ENSP00000371290;												0						TGGAAGAAACAAAAAAAAGAA	0.383													3	4	---	---	---	---	
COG6	57511	broad.mit.edu	37	13	40325364	40325365	+	3'UTR	INS	-	T	T			TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:40325364_40325365insT	uc001uxh.2	+	19					COG6_uc001uxi.2_3'UTR|COG6_uc010acb.2_Intron	NM_020751	NP_065802	Q9Y2V7	COG6_HUMAN	component of oligomeric golgi complex 6 isoform						protein transport	Golgi membrane|Golgi transport complex				kidney(1)|skin(1)	2		Lung NSC(96;0.000124)|Breast(139;0.0199)|Prostate(109;0.0233)|Lung SC(185;0.0367)		all cancers(112;6.03e-09)|Epithelial(112;7e-07)|OV - Ovarian serous cystadenocarcinoma(117;0.00015)|BRCA - Breast invasive adenocarcinoma(63;0.00438)|GBM - Glioblastoma multiforme(144;0.0168)		AGTCCCGATAATTTTTTTTTTT	0.297													6	3	---	---	---	---	
COG3	83548	broad.mit.edu	37	13	46060468	46060475	+	Intron	DEL	GGGAGACG	-	-	rs150878511	by1000genomes	TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:46060468_46060475delGGGAGACG	uc001vak.2	+						COG3_uc010tfu.1_Intron|COG3_uc001vai.2_Intron|COG3_uc001vaj.1_Intron|COG3_uc010tfv.1_Intron|COG3_uc010aci.2_Intron	NM_031431	NP_113619	Q96JB2	COG3_HUMAN	component of golgi transport complex 3						ER to Golgi vesicle-mediated transport|intra-Golgi vesicle-mediated transport|intracellular protein transport|protein glycosylation|protein localization to organelle|protein stabilization|retrograde vesicle-mediated transport, Golgi to ER	cis-Golgi network|Golgi cisterna membrane|Golgi transport complex	protein binding|protein transporter activity			breast(1)|skin(1)	2		Lung NSC(96;0.000145)|Breast(56;0.000596)|Prostate(109;0.00438)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;0.000124)		gacgggagacgggagacgggagagggag	0.159													4	2	---	---	---	---	
RORA	6095	broad.mit.edu	37	15	60806630	60806632	+	Intron	DEL	GAG	-	-			TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:60806630_60806632delGAG	uc002agv.2	-						uc002ags.1_Intron|RORA_uc002agt.3_Intron|RORA_uc002agw.2_Intron|RORA_uc002agx.2_Intron	NM_134260	NP_599022	P35398	RORA_HUMAN	RAR-related orphan receptor A isoform b						positive regulation of transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			large_intestine(1)|ovary(1)	2						CTCTGAGGATGAGGAGGAGGAGG	0.567													4	2	---	---	---	---	
CILP	8483	broad.mit.edu	37	15	65494067	65494069	+	Intron	DEL	AAA	-	-			TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:65494067_65494069delAAA	uc002aon.2	-							NM_003613	NP_003604	O75339	CILP1_HUMAN	cartilage intermediate layer protein						negative regulation of insulin-like growth factor receptor signaling pathway	extracellular matrix part|extracellular space|proteinaceous extracellular matrix				ovary(4)|pancreas(2)|skin(1)	7						actccatctcaaaaaaaaaaaaa	0.133													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	79026913	79026913	+	IGR	DEL	T	-	-			TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:79026913delT								CHRNB4 (74039 upstream) : ADAMTS7 (24633 downstream)																							AAGAGGAGGGTTTTTTTTTGT	0.577													4	2	---	---	---	---	
ACAN	176	broad.mit.edu	37	15	89403776	89403777	+	Intron	INS	-	CTCAGGCTT	CTCAGGCTT	rs147084610	by1000genomes	TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:89403776_89403777insCTCAGGCTT	uc010upo.1	+						ACAN_uc010upp.1_Intron|ACAN_uc002bna.2_Intron	NM_013227	NP_037359	E7EX88	E7EX88_HUMAN	aggrecan isoform 2 precursor						cell adhesion		hyaluronic acid binding|sugar binding			ovary(2)|central_nervous_system(1)	3	Lung NSC(78;0.0392)|all_lung(78;0.077)		BRCA - Breast invasive adenocarcinoma(143;0.146)			GTCCACTGAGGCTCAGGCTGGG	0.416													5	3	---	---	---	---	
PPL	5493	broad.mit.edu	37	16	4952694	4952694	+	Intron	DEL	T	-	-			TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:4952694delT	uc002cyd.1	-							NM_002705	NP_002696	O60437	PEPL_HUMAN	periplakin						keratinization	cytoskeleton|desmosome|mitochondrion|nucleus	protein binding|structural constituent of cytoskeleton			ovary(4)|central_nervous_system(1)|skin(1)	6						TCCCATGCACttttttttttt	0.299													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	10612763	10612766	+	IGR	DEL	TCCC	-	-	rs36095074		TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:10612763_10612766delTCCC								ATF7IP2 (35269 upstream) : EMP2 (9514 downstream)																							catccctccttccctccctccctc	0.000													3	3	---	---	---	---	
PRKCB	5579	broad.mit.edu	37	16	24032510	24032517	+	Intron	DEL	TCTTTCTT	-	-			TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:24032510_24032517delTCTTTCTT	uc002dmd.2	+						PRKCB_uc002dme.2_Intron	NM_212535	NP_997700	P05771	KPCB_HUMAN	protein kinase C, beta isoform 1						apoptosis|B cell activation|B cell receptor signaling pathway|intracellular signal transduction|lipoprotein transport|platelet activation|positive regulation of I-kappaB kinase/NF-kappaB cascade|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|synaptic transmission|transcription, DNA-dependent	cytosol|nucleus|plasma membrane	androgen receptor binding|ATP binding|chromatin binding|histone binding|histone kinase activity (H3-T6 specific)|ligand-dependent nuclear receptor transcription coactivator activity|protein kinase C activity|protein kinase C binding|zinc ion binding			ovary(3)|central_nervous_system(3)|lung(2)|large_intestine(1)	9					Vitamin E(DB00163)	ccttccttcctctttctttctttctttc	0.000													4	2	---	---	---	---	
CLN3	1201	broad.mit.edu	37	16	28493308	28493308	+	Intron	DEL	A	-	-	rs2520416		TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:28493308delA	uc002dpo.2	-						uc010vct.1_Intron|CLN3_uc002dpl.2_Intron|CLN3_uc010vcu.1_Intron|CLN3_uc002dpn.2_Intron|CLN3_uc002dpm.2_Intron|CLN3_uc010vcv.1_Intron|CLN3_uc010byd.2_Intron|CLN3_uc002dpp.2_Intron|CLN3_uc002dpt.1_Intron|CLN3_uc002dpq.1_Intron|CLN3_uc010bye.1_Intron|CLN3_uc002dpr.1_Intron|CLN3_uc010byf.1_Intron|CLN3_uc002dps.1_Intron|CLN3_uc002dpu.1_Intron	NM_000086	NP_000077	Q13286	CLN3_HUMAN	ceroid-lipofuscinosis, neuronal 3						amyloid precursor protein catabolic process|arginine transport|associative learning|autophagic vacuole fusion|cell death|cellular amino acid metabolic process|cytosolic calcium ion homeostasis|galactosylceramide metabolic process|globoside metabolic process|glucosylceramide metabolic process|ionotropic glutamate receptor signaling pathway|lysosomal lumen acidification|lysosomal lumen pH elevation|negative regulation of catalytic activity|negative regulation of macroautophagy|negative regulation of neuron apoptosis|negative regulation of proteolysis|neuromuscular process controlling balance|neurotransmitter metabolic process|protein catabolic process|protein folding|protein processing|receptor-mediated endocytosis|regulation of action potential|sphingomyelin metabolic process|vacuolar transport	autophagic vacuole|caveola|cytosol|early endosome|Golgi membrane|Golgi stack|integral to endoplasmic reticulum membrane|late endosome|lysosomal membrane|membrane fraction|mitochondrion|neuron projection|nucleus|synaptic vesicle|trans-Golgi network	unfolded protein binding				0						actctgtctcaaaaaaaaaaa	0.129													4	2	---	---	---	---	
C16orf70	80262	broad.mit.edu	37	16	67165083	67165084	+	Intron	INS	-	T	T			TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67165083_67165084insT	uc002erc.2	+						C16orf70_uc002erd.2_Intron|C16orf70_uc002ere.1_Intron	NM_025187	NP_079463	Q9BSU1	CP070_HUMAN	lin-10											ovary(2)	2		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0017)|Epithelial(162;0.00655)|all cancers(182;0.0579)		ATTGGTAATAGttttttttttt	0.173													7	4	---	---	---	---	
MYH3	4621	broad.mit.edu	37	17	10547483	10547486	+	Intron	DEL	AAAC	-	-	rs147605554		TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10547483_10547486delAAAC	uc002gmq.1	-							NM_002470	NP_002461	P11055	MYH3_HUMAN	myosin, heavy chain 3, skeletal muscle,						muscle filament sliding|muscle organ development	cytosol|myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|microfilament motor activity			ovary(4)|central_nervous_system(2)|pancreas(1)	7						caaaaaaaaaaaacaaacaaaaaa	0.201													3	3	---	---	---	---	
POLDIP2	26073	broad.mit.edu	37	17	26681591	26681591	+	Frame_Shift_Del	DEL	A	-	-			TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26681591delA	uc002haz.2	-	6	396	c.264delT	c.(262-264)TTTfs	p.F88fs	POLDIP2_uc010wag.1_Intron	NM_015584	NP_056399	Q9Y2S7	PDIP2_HUMAN	DNA polymerase delta interacting protein 2	88						mitochondrial nucleoid|nucleus					0	all_lung(13;0.000354)|Lung NSC(42;0.00115)			UCEC - Uterine corpus endometrioid carcinoma (53;0.154)		CTCGGTAGCCAAAAATGCTAT	0.542													4	2	---	---	---	---	
C17orf98	388381	broad.mit.edu	37	17	36993201	36993202	+	Intron	INS	-	A	A	rs113691927		TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:36993201_36993202insA	uc002hqv.2	-							NM_001080465	NP_001073934	A8MV24	CQ098_HUMAN	hypothetical protein LOC388381												0						gaccacgtctcaaaaaaaaaaa	0.223													4	2	---	---	---	---	
RECQL5	9400	broad.mit.edu	37	17	73626922	73626923	+	Intron	INS	-	T	T	rs56158987		TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73626922_73626923insT	uc010dgl.2	-						RECQL5_uc010dgk.2_Intron|RECQL5_uc002jot.3_5'Flank|LOC643008_uc002jow.2_5'Flank	NM_004259	NP_004250	O94762	RECQ5_HUMAN	RecQ protein-like 5 isoform 1						DNA recombination|DNA repair	cytoplasm|nuclear membrane|nucleolus|nucleoplasm	ATP binding|ATP-dependent helicase activity|DNA helicase activity|nucleic acid binding			kidney(3)	3	all_cancers(13;2.73e-08)|Breast(9;6.04e-09)|all_epithelial(9;6.79e-09)		all cancers(21;1.15e-06)|Epithelial(20;2.19e-06)|Lung(188;0.101)|LUSC - Lung squamous cell carcinoma(166;0.112)			TCTCATCTGTGGGGGGGGGGGG	0.649								Other_identified_genes_with_known_or_suspected_DNA_repair_function					4	2	---	---	---	---	
MARCH2	51257	broad.mit.edu	37	19	8495418	8495419	+	Intron	INS	-	A	A	rs74326673		TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8495418_8495419insA	uc002mjv.2	+						MARCH2_uc002mjw.2_Intron|MARCH2_uc002mjx.2_Intron	NM_016496	NP_057580	Q9P0N8	MARH2_HUMAN	membrane-associated ring finger (C3HC4) 2						endocytosis	cytoplasmic vesicle|endoplasmic reticulum membrane|endosome membrane|integral to membrane|lysosomal membrane	ubiquitin-protein ligase activity|zinc ion binding			ovary(2)	2						gaatctgtctcaaaaaaaaaaa	0.248													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	32668613	32668614	+	IGR	INS	-	GAAA	GAAA	rs78373305	by1000genomes	TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:32668613_32668614insGAAA								TSHZ3 (828423 upstream) : ZNF507 (167900 downstream)																							aaggaaggaaggaaAATGATCT	0.104													4	2	---	---	---	---	
CACNG8	59283	broad.mit.edu	37	19	54483335	54483336	+	Intron	INS	-	GC	GC	rs140673589	by1000genomes	TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54483335_54483336insGC	uc002qcs.1	+						MIR935_hsa-mir-935|MI0005757_5'Flank	NM_031895	NP_114101	Q8WXS5	CCG8_HUMAN	voltage-dependent calcium channel gamma-8						regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|synaptic transmission	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic density|postsynaptic membrane|voltage-gated calcium channel complex	voltage-gated calcium channel activity				0	all_cancers(19;0.0385)|all_epithelial(19;0.0207)|all_lung(19;0.145)|Lung NSC(19;0.168)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(134;0.162)		tgtgtgtgtgtgtgtgcgcgcg	0.559													6	4	---	---	---	---	
C20orf117	140710	broad.mit.edu	37	20	35423173	35423173	+	Intron	DEL	T	-	-	rs79620367		TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:35423173delT	uc002xgd.1	-						C20orf117_uc002xge.1_Intron	NM_199181	NP_954650	O94964	K0889_HUMAN	hypothetical protein LOC140710 isoform 2												0		Myeloproliferative disorder(115;0.00874)				CTGCAttttcttttttttttt	0.104													4	2	---	---	---	---	
COL6A1	1291	broad.mit.edu	37	21	47419706	47419707	+	Intron	INS	-	G	G	rs149102148	by1000genomes	TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:47419706_47419707insG	uc002zhu.1	+						COL6A1_uc010gqd.1_Intron|COL6A1_uc002zhv.1_5'Flank|COL6A1_uc002zhw.1_5'Flank	NM_001848	NP_001839	P12109	CO6A1_HUMAN	collagen, type VI, alpha 1 precursor						axon guidance|cell adhesion|protein heterotrimerization	collagen type VI|protein complex	platelet-derived growth factor binding			ovary(1)	1	all_hematologic(128;0.24)			Colorectal(79;0.0265)|READ - Rectum adenocarcinoma(84;0.0649)	Palifermin(DB00039)	ACGCTGCTCACGGGGGGGTGGG	0.624													6	5	---	---	---	---	
CTPS2	56474	broad.mit.edu	37	X	16716680	16716682	+	Intron	DEL	TTT	-	-	rs72307111		TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:16716680_16716682delTTT	uc004cxk.2	-						CTPS2_uc004cxl.2_Intron|CTPS2_uc004cxm.2_Intron	NM_001144002	NP_001137474	Q9NRF8	PYRG2_HUMAN	cytidine triphosphate synthase II						glutamine metabolic process|nucleobase, nucleoside and nucleotide interconversion|pyrimidine nucleotide biosynthetic process	cytosol	ATP binding|CTP synthase activity			ovary(1)	1	Hepatocellular(33;0.0997)					ctttgttttgtttttttttttta	0.138													3	4	---	---	---	---	
MORC4	79710	broad.mit.edu	37	X	106184602	106184609	+	3'UTR	DEL	GAGAGAGA	-	-			TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:106184602_106184609delGAGAGAGA	uc004emu.3	-	17					MORC4_uc004emp.3_Intron|MORC4_uc004emv.3_3'UTR|MORC4_uc004emw.3_3'UTR	NM_024657	NP_078933	Q8TE76	MORC4_HUMAN	zinc finger, CW type with coiled-coil domain 2								ATP binding|zinc ion binding			ovary(1)	1						AGGTGAGGGTgagagagagagagagaga	0.284													4	2	---	---	---	---	
DOCK11	139818	broad.mit.edu	37	X	117676483	117676484	+	Intron	INS	-	TA	TA	rs149027952		TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:117676483_117676484insTA	uc004eqp.2	+							NM_144658	NP_653259	Q5JSL3	DOC11_HUMAN	dedicator of cytokinesis 11						blood coagulation	cytosol	GTP binding			ovary(3)	3						gtgtgtgtgtttgtgtgtgtgt	0.124													8	4	---	---	---	---	
IGSF1	3547	broad.mit.edu	37	X	130579277	130579277	+	Intron	DEL	T	-	-			TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:130579277delT	uc004ewf.2	-							NM_001555	NP_001546	Q8N6C5	IGSF1_HUMAN	immunoglobulin superfamily, member 1 isoform 1						regulation of transcription, DNA-dependent	extracellular region|integral to membrane	inhibin beta-A binding|inhibin beta-B binding			ovary(3)|lung(1)|central_nervous_system(1)	5						ATAAATTTTCTTTTTCCTTtt	0.095													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	133301110	133301110	+	IGR	DEL	A	-	-			TCGA-CZ-4856-01A-02D-1429-08	TCGA-CZ-4856-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:133301110delA								GPC3 (181444 upstream) : MIR363 (2298 downstream)																							TGAAATGTTCAAAAAAAAAAA	0.269													4	2	---	---	---	---	
