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
CROCCL2	114819	broad.mit.edu	37	1	16812970	16812970	+	Intron	SNP	C	A	A	rs150878633	by1000genomes	TCGA-CH-5739-01	TCGA-CH-5739-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16812970C>A	uc001ays.2	-						CROCCL2_uc001ayt.2_RNA					Homo sapiens mRNA for KIAA1922 protein, partial cds.												0						TGCTGCTGGGCCAGGTCCTTC	0.647													3	3	---	---	---	---	PASS
HNRNPR	10236	broad.mit.edu	37	1	23650124	23650124	+	Silent	SNP	T	C	C			TCGA-CH-5739-01	TCGA-CH-5739-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:23650124T>C	uc001bgr.3	-	6	759	c.600A>G	c.(598-600)CCA>CCG	p.P200P	HNRNPR_uc001bgp.3_Silent_p.P200P|HNRNPR_uc009vqk.2_Silent_p.P99P|HNRNPR_uc001bgs.3_Silent_p.P99P|HNRNPR_uc010odw.1_Silent_p.P162P|HNRNPR_uc010odx.1_Intron|HNRNPR_uc009vql.2_Silent_p.P61P	NM_005826	NP_005817	O43390	HNRPR_HUMAN	heterogeneous nuclear ribonucleoprotein R	200	RRM 1.					catalytic step 2 spliceosome|cytoplasm|heterogeneous nuclear ribonucleoprotein complex|nucleoplasm	nucleotide binding|protein binding|RNA binding			upper_aerodigestive_tract(1)|skin(1)	2		Colorectal(325;3.46e-05)|Lung NSC(340;4.15e-05)|all_lung(284;6.64e-05)|Renal(390;0.000219)|Breast(348;0.00394)|Ovarian(437;0.00539)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;6.83e-27)|Colorectal(126;6.01e-08)|COAD - Colon adenocarcinoma(152;3.32e-06)|GBM - Glioblastoma multiforme(114;6.69e-05)|BRCA - Breast invasive adenocarcinoma(304;0.00101)|KIRC - Kidney renal clear cell carcinoma(1967;0.00357)|STAD - Stomach adenocarcinoma(196;0.0131)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.0875)|LUSC - Lung squamous cell carcinoma(448;0.19)		GACCGGACAGTGGATCCATCA	0.443													10	197	---	---	---	---	PASS
CC2D1B	200014	broad.mit.edu	37	1	52823499	52823499	+	Silent	SNP	C	A	A	rs62000427	byFrequency	TCGA-CH-5739-01	TCGA-CH-5739-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:52823499C>A	uc001ctq.1	-	14	1689	c.1551G>T	c.(1549-1551)CTG>CTT	p.L517L	CC2D1B_uc001ctr.2_Silent_p.L57L|CC2D1B_uc001cts.2_Silent_p.L202L	NM_032449	NP_115825	Q5T0F9	C2D1B_HUMAN	coiled-coil and C2 domain containing 1B	517										ovary(2)	2						TGGGCTCAGGCAGGCGCTGGG	0.632													4	76	---	---	---	---	PASS
INADL	10207	broad.mit.edu	37	1	62261168	62261168	+	Missense_Mutation	SNP	A	G	G	rs7516332	byFrequency	TCGA-CH-5739-01	TCGA-CH-5739-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:62261168A>G	uc001dab.2	+	10	1312	c.1198A>G	c.(1198-1200)ATA>GTA	p.I400V	INADL_uc009waf.1_Missense_Mutation_p.I400V|INADL_uc001daa.2_Missense_Mutation_p.I400V|INADL_uc001dad.3_Missense_Mutation_p.I97V	NM_176877	NP_795352	Q8NI35	INADL_HUMAN	InaD-like	400	PDZ 3.				intracellular signal transduction|tight junction assembly	apical plasma membrane|perinuclear region of cytoplasm|tight junction	protein binding			ovary(3)|skin(1)	4						TGTGAAAAGTATAATACCTGG	0.383													4	165	---	---	---	---	PASS
RPE65	6121	broad.mit.edu	37	1	68906685	68906685	+	Splice_Site	SNP	T	C	C			TCGA-CH-5739-01	TCGA-CH-5739-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:68906685T>C	uc001dei.1	-	6	550	c.496_splice	c.e6-1	p.V166_splice		NM_000329	NP_000320	Q16518	RPE65_HUMAN	retinal pigment epithelium-specific protein						visual perception	cytoplasm|plasma membrane	all-trans-retinyl-palmitate hydrolase activity|metal ion binding|retinol isomerase activity			ovary(1)	1						AAGATCAACCTACGGAAGTAA	0.428													4	79	---	---	---	---	PASS
ABCA4	24	broad.mit.edu	37	1	94514475	94514475	+	Missense_Mutation	SNP	C	T	T	rs61749441	byFrequency	TCGA-CH-5739-01	TCGA-CH-5739-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:94514475C>T	uc001dqh.2	-	18	2796	c.2692G>A	c.(2692-2694)GAG>AAG	p.E898K	ABCA4_uc010otn.1_Missense_Mutation_p.E824K	NM_000350	NP_000341	P78363	ABCA4_HUMAN	ATP-binding cassette, sub-family A member 4	898	Cytoplasmic.				phototransduction, visible light|visual perception	integral to plasma membrane|membrane fraction	ATP binding|ATPase activity, coupled to transmembrane movement of substances			ovary(4)|skin(4)|central_nervous_system(2)|upper_aerodigestive_tract(1)|breast(1)	12		all_lung(203;0.000757)|Lung NSC(277;0.00335)		all cancers(265;0.00432)|GBM - Glioblastoma multiforme(16;0.00715)|Epithelial(280;0.171)		GTTAGGGGCTCGGTCTTTTCC	0.517													14	171	---	---	---	---	PASS
SLC16A4	9122	broad.mit.edu	37	1	110925493	110925493	+	Missense_Mutation	SNP	C	G	G			TCGA-CH-5739-01	TCGA-CH-5739-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:110925493C>G	uc001dzo.1	-	3	365	c.183G>C	c.(181-183)TGG>TGC	p.W61C	SLC16A4_uc009wfs.1_Missense_Mutation_p.W61C|SLC16A4_uc001dzp.1_Missense_Mutation_p.W61C|SLC16A4_uc010ovy.1_Intron|SLC16A4_uc001dzq.1_Intron|SLC16A4_uc010ovz.1_Intron	NM_004696	NP_004687	O15374	MOT5_HUMAN	solute carrier family 16, member 4	61	Helical; (Potential).					integral to plasma membrane|membrane fraction	monocarboxylic acid transmembrane transporter activity|symporter activity			ovary(3)	3		all_cancers(81;0.000476)|all_epithelial(167;0.000401)|all_lung(203;0.00277)|Lung NSC(277;0.0043)		Lung(183;0.0251)|all cancers(265;0.0766)|Epithelial(280;0.0807)|Colorectal(144;0.112)|LUSC - Lung squamous cell carcinoma(189;0.14)	Pyruvic acid(DB00119)	TGGATCCAATCCAACCAATTT	0.408													62	156	---	---	---	---	PASS
PTGFRN	5738	broad.mit.edu	37	1	117529548	117529548	+	Missense_Mutation	SNP	C	T	T	rs140355100		TCGA-CH-5739-01	TCGA-CH-5739-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:117529548C>T	uc001egv.1	+	9	2736	c.2599C>T	c.(2599-2601)CGG>TGG	p.R867W		NM_020440	NP_065173	Q9P2B2	FPRP_HUMAN	prostaglandin F2 receptor negative regulator	867	Cytoplasmic (Potential).					endoplasmic reticulum membrane|Golgi apparatus|integral to membrane	protein binding			liver(1)	1	Lung SC(450;0.225)	all_cancers(81;0.00104)|all_lung(203;8.97e-05)|all_epithelial(167;0.000139)|Lung NSC(69;0.000446)		Lung(183;0.0704)|LUSC - Lung squamous cell carcinoma(189;0.227)|Colorectal(144;0.248)		TCAGGAGACACGGCGCGAGCG	0.617													56	108	---	---	---	---	PASS
PDE4DIP	9659	broad.mit.edu	37	1	144879542	144879542	+	Missense_Mutation	SNP	A	G	G			TCGA-CH-5739-01	TCGA-CH-5739-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144879542A>G	uc001elw.3	-	27	4199	c.3908T>C	c.(3907-3909)CTC>CCC	p.L1303P	NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Missense_Mutation_p.L1259P|PDE4DIP_uc001elv.3_Missense_Mutation_p.L310P	NM_014644	NP_055459	Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein isoform	1303					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)		CATTTCCTTGAGGCTGTTGTG	0.522			T	PDGFRB	MPD								5	224	---	---	---	---	PASS
GJA5	2702	broad.mit.edu	37	1	147230995	147230995	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5739-01	TCGA-CH-5739-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:147230995G>A	uc001eps.1	-	2	493	c.352C>T	c.(352-354)CGG>TGG	p.R118W	GJA5_uc001ept.1_Missense_Mutation_p.R118W	NM_181703	NP_859054	P36382	CXA5_HUMAN	connexin 40	118	Cytoplasmic (Potential).				angiogenesis|cell-cell junction assembly|muscle contraction	integral to membrane				ovary(1)	1	all_hematologic(923;0.0276)		LUSC - Lung squamous cell carcinoma(543;0.202)			CCAGAGCCCCGGACCTCTTTG	0.622													53	149	---	---	---	---	PASS
CRNN	49860	broad.mit.edu	37	1	152382359	152382359	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5739-01	TCGA-CH-5739-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152382359G>A	uc001ezx.2	-	3	1273	c.1199C>T	c.(1198-1200)CCG>CTG	p.P400L		NM_016190	NP_057274	Q9UBG3	CRNN_HUMAN	cornulin	400					cell-cell adhesion|response to heat	cytoplasm|membrane	calcium ion binding			ovary(2)|skin(1)	3	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)			CTGTCCTCCCGGTACTGTCTC	0.612													50	105	---	---	---	---	PASS
LCE1C	353133	broad.mit.edu	37	1	152777624	152777624	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5739-01	TCGA-CH-5739-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152777624C>T	uc001fap.1	-	2	382	c.331G>A	c.(331-333)GGC>AGC	p.G111S		NM_178351	NP_848128	Q5T751	LCE1C_HUMAN	late cornified envelope 1C	111	Gly-rich.				keratinization						0	Lung NSC(65;9.06e-30)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			GAGTGCTGGCCACTCCCCCCG	0.657													14	39	---	---	---	---	PASS
LCE1A	353131	broad.mit.edu	37	1	152800255	152800255	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5739-01	TCGA-CH-5739-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152800255G>A	uc010pdw.1	+	1	307	c.307G>A	c.(307-309)GGC>AGC	p.G103S		NM_178348	NP_848125	Q5T7P2	LCE1A_HUMAN	late cornified envelope 1A	103	Cys-rich.				keratinization					ovary(1)|skin(1)	2	Lung NSC(65;9.06e-30)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			AGGGGACAGCGGCCAGCACTC	0.622													4	14	---	---	---	---	PASS
TPR	7175	broad.mit.edu	37	1	186289546	186289546	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5739-01	TCGA-CH-5739-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:186289546G>A	uc001grv.2	-	46	6763	c.6466C>T	c.(6466-6468)CCG>TCG	p.P2156S		NM_003292	NP_003283	P12270	TPR_HUMAN	nuclear pore complex-associated protein TPR	2156					carbohydrate metabolic process|glucose transport|mitotic cell cycle spindle assembly checkpoint|mRNA transport|protein import into nucleus|regulation of glucose transport|seryl-tRNA aminoacylation|transmembrane transport|viral reproduction	condensed chromosome kinetochore|cytoplasm|nuclear membrane|nuclear pore|nucleoplasm	ATP binding|protein binding|serine-tRNA ligase activity			ovary(2)|lung(2)|urinary_tract(1)|central_nervous_system(1)|skin(1)	7		Breast(1374;0.000659)|Lung SC(1967;0.0262)|Prostate(1639;0.157)		Colorectal(1306;1.12e-05)|KIRC - Kidney renal clear cell carcinoma(1967;0.00553)		GCAACCTGCGGCGAACTAAAT	0.398			T	NTRK1	papillary thyroid								14	63	---	---	---	---	PASS
CR1	1378	broad.mit.edu	37	1	207787796	207787796	+	Missense_Mutation	SNP	T	C	C	rs61822976		TCGA-CH-5739-01	TCGA-CH-5739-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:207787796T>C	uc001hfy.2	+	32	5413	c.5273T>C	c.(5272-5274)ATG>ACG	p.M1758T	CR1_uc001hfx.2_Missense_Mutation_p.M2208T	NM_000573	NP_000564	P17927	CR1_HUMAN	complement receptor 1 isoform F precursor	1758	Extracellular (Potential).|Sushi 27.				complement activation, classical pathway|innate immune response	integral to plasma membrane	complement receptor activity			ovary(3)	3						TTGGCTGGAATGAAAGCCCTT	0.408													5	74	---	---	---	---	PASS
CPSF3	51692	broad.mit.edu	37	2	9595849	9595849	+	Silent	SNP	C	G	G			TCGA-CH-5739-01	TCGA-CH-5739-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:9595849C>G	uc002qzo.1	+	13	1601	c.1566C>G	c.(1564-1566)CCC>CCG	p.P522P	CPSF3_uc010ewx.1_Silent_p.P473P|CPSF3_uc002qzp.1_Silent_p.P485P|CPSF3_uc002qzq.1_Silent_p.P99P	NM_016207	NP_057291	Q9UKF6	CPSF3_HUMAN	cleavage and polyadenylation specific factor 3,	522					histone mRNA 3'-end processing|mRNA cleavage|mRNA export from nucleus|mRNA polyadenylation|nuclear mRNA splicing, via spliceosome|termination of RNA polymerase II transcription	mRNA cleavage and polyadenylation specificity factor complex|ribonucleoprotein complex	5'-3' exonuclease activity|endoribonuclease activity|metal ion binding|protein binding|RNA binding			breast(2)	2	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)	all_cancers(51;2.39e-25)|all_epithelial(98;8.75e-19)|Lung NSC(108;2.38e-06)|Ovarian(717;0.0308)		all cancers(51;2.2e-40)|Epithelial(75;6.71e-35)|OV - Ovarian serous cystadenocarcinoma(76;4.35e-21)|STAD - Stomach adenocarcinoma(1183;0.00644)		ATACTGGTCCCTTTAATTTGC	0.383													14	121	---	---	---	---	PASS
MSH6	2956	broad.mit.edu	37	2	48018072	48018072	+	Missense_Mutation	SNP	C	A	A			TCGA-CH-5739-01	TCGA-CH-5739-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:48018072C>A	uc002rwd.3	+	2	419	c.267C>A	c.(265-267)GAC>GAA	p.D89E	MSH6_uc002rwc.2_Missense_Mutation_p.D89E|MSH6_uc010fbj.2_5'UTR|MSH6_uc010yoi.1_Intron|MSH6_uc010yoj.1_5'UTR	NM_000179	NP_000170	P52701	MSH6_HUMAN	mutS homolog 6	89					determination of adult lifespan|DNA damage response, signal transduction resulting in induction of apoptosis|isotype switching|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|response to UV|somatic hypermutation of immunoglobulin genes	MutSalpha complex	ATP binding|DNA-dependent ATPase activity|protein binding			large_intestine(53)|central_nervous_system(28)|endometrium(28)|stomach(22)|haematopoietic_and_lymphoid_tissue(9)|lung(7)|skin(6)|urinary_tract(5)|breast(5)|ovary(3)|thyroid(1)|upper_aerodigestive_tract(1)	168		Acute lymphoblastic leukemia(82;0.0299)|all_hematologic(82;0.0358)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			ACAGTTGTGACTTCTCACCAG	0.433			Mis|N|F|S		colorectal	colorectal|endometrial|ovarian		MMR	Lynch_syndrome|Muir-Torre_syndrome|Turcot_syndrome|Constitutional_Mismatch_Repair_Deficiency_Syndrome				5	201	---	---	---	---	PASS
PROKR1	10887	broad.mit.edu	37	2	68882252	68882252	+	Silent	SNP	G	T	T			TCGA-CH-5739-01	TCGA-CH-5739-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:68882252G>T	uc010yqj.1	+	2	726	c.726G>T	c.(724-726)GTG>GTT	p.V242V	PROKR1_uc002ses.2_RNA	NM_138964	NP_620414	Q8TCW9	PKR1_HUMAN	G protein-coupled receptor 73	242	Helical; Name=5; (Potential).					integral to membrane|plasma membrane	neuropeptide Y receptor activity			ovary(1)	1						TAGAATTCGTGGGCCCCGTGG	0.557													32	86	---	---	---	---	PASS
ANKRD36	375248	broad.mit.edu	37	2	97869931	97869931	+	Missense_Mutation	SNP	A	T	T	rs76309140		TCGA-CH-5739-01	TCGA-CH-5739-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:97869931A>T	uc010yva.1	+	50	3236	c.2992A>T	c.(2992-2994)ACA>TCA	p.T998S	ANKRD36_uc002sxp.3_RNA	NM_001164315	NP_001157787	A6QL64	AN36A_HUMAN	ankyrin repeat domain 36	998											0						CATTCAGGCTACAAGTGATGA	0.289													5	33	---	---	---	---	PASS
GPR17	2840	broad.mit.edu	37	2	128408804	128408804	+	Silent	SNP	G	A	A			TCGA-CH-5739-01	TCGA-CH-5739-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:128408804G>A	uc010yzn.1	+	4	1190	c.579G>A	c.(577-579)CCG>CCA	p.P193P	LIMS2_uc002tox.2_Intron|LIMS2_uc010fmb.2_Intron|LIMS2_uc002toy.2_Intron|LIMS2_uc010yzm.1_Intron|LIMS2_uc002tpa.2_Intron|LIMS2_uc002toz.2_Intron|LIMS2_uc002tpb.2_Intron|GPR17_uc002tpc.2_Silent_p.P193P|GPR17_uc010yzo.1_Silent_p.P165P|GPR17_uc002tpd.2_Silent_p.P165P	NM_001161415	NP_001154887	Q13304	GPR17_HUMAN	G protein-coupled receptor 17 isoform a	193	Helical; Name=4; (Potential).					integral to plasma membrane	chemokine receptor activity|purinergic nucleotide receptor activity, G-protein coupled				0	Colorectal(110;0.1)	Ovarian(717;0.15)		BRCA - Breast invasive adenocarcinoma(221;0.0677)		CCATGGCCCCGCTGCTGGTGA	0.667													45	106	---	---	---	---	PASS
FAM126B	285172	broad.mit.edu	37	2	201846109	201846109	+	Nonsense_Mutation	SNP	G	A	A			TCGA-CH-5739-01	TCGA-CH-5739-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:201846109G>A	uc002uws.3	-	12	1665	c.1477C>T	c.(1477-1479)CAG>TAG	p.Q493*	FAM126B_uc002uwu.2_Nonsense_Mutation_p.Q467*|FAM126B_uc002uwv.2_Nonsense_Mutation_p.Q493*	NM_173822	NP_776183	Q8IXS8	F126B_HUMAN	hypothetical protein LOC285172	493						intracellular				ovary(1)	1						CGGTCTTCCTGCAGACTGACA	0.512													33	60	---	---	---	---	PASS
ATRIP	84126	broad.mit.edu	37	3	48506045	48506045	+	Missense_Mutation	SNP	G	T	T			TCGA-CH-5739-01	TCGA-CH-5739-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:48506045G>T	uc003ctf.1	+	11	2071	c.2039G>T	c.(2038-2040)TGC>TTC	p.C680F	ATRIP_uc011bbj.1_Missense_Mutation_p.C553F|ATRIP_uc003ctg.1_Intron|TREX1_uc010hjy.2_5'UTR|TREX1_uc003ctj.2_5'Flank|TREX1_uc003ctk.2_5'Flank|TREX1_uc010hjz.2_5'Flank|TREX1_uc010hka.2_5'Flank	NM_130384	NP_569055	Q8WXE1	ATRIP_HUMAN	ATR interacting protein isoform 1	680					DNA damage checkpoint|DNA repair|DNA replication	nucleoplasm	protein binding|protein serine/threonine kinase activity			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;0.000293)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		GGCTCCAACTGCCAGTGTAAT	0.607								Other_conserved_DNA_damage_response_genes					5	158	---	---	---	---	PASS
APEH	327	broad.mit.edu	37	3	49720848	49720848	+	3'UTR	SNP	G	A	A			TCGA-CH-5739-01	TCGA-CH-5739-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49720848G>A	uc003cxf.2	+	22						NM_001640	NP_001631	P13798	ACPH_HUMAN	N-acylaminoacyl-peptide hydrolase						proteolysis	cytoplasm|nuclear membrane	serine-type endopeptidase activity			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;4.53e-05)|Kidney(197;0.00218)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)		GGTCTGGCAGGGCAGCAGGAG	0.567													3	66	---	---	---	---	PASS
ACTR8	93973	broad.mit.edu	37	3	53905310	53905310	+	Nonsense_Mutation	SNP	C	A	A			TCGA-CH-5739-01	TCGA-CH-5739-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:53905310C>A	uc003dhd.2	-	11	1575	c.1516G>T	c.(1516-1518)GGA>TGA	p.G506*	ACTR8_uc003dhb.2_Nonsense_Mutation_p.G211*|ACTR8_uc003dhc.2_Nonsense_Mutation_p.G395*	NM_022899	NP_075050	Q9H981	ARP8_HUMAN	actin-related protein 8	506					cell division|DNA recombination|DNA repair|mitosis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	Ino80 complex	protein binding			ovary(1)|central_nervous_system(1)	2				BRCA - Breast invasive adenocarcinoma(193;0.000143)|KIRC - Kidney renal clear cell carcinoma(284;0.00544)|Kidney(284;0.00607)|OV - Ovarian serous cystadenocarcinoma(275;0.111)		AGGGCTTTTCCTTCAAACAGC	0.547													6	234	---	---	---	---	PASS
MYH15	22989	broad.mit.edu	37	3	108117984	108117984	+	Missense_Mutation	SNP	A	T	T			TCGA-CH-5739-01	TCGA-CH-5739-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:108117984A>T	uc003dxa.1	-	35	4984	c.4927T>A	c.(4927-4929)TGT>AGT	p.C1643S		NM_014981	NP_055796	Q9Y2K3	MYH15_HUMAN	myosin, heavy polypeptide 15	1643	Potential.					myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|motor activity			ovary(5)|central_nervous_system(2)	7						CGGTTGGCACAGCTAAGCTGG	0.488													66	96	---	---	---	---	PASS
COPG	22820	broad.mit.edu	37	3	128996296	128996296	+	3'UTR	SNP	C	T	T			TCGA-CH-5739-01	TCGA-CH-5739-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:128996296C>T	uc003els.2	+	24					COPG_uc010htb.2_3'UTR|C3orf37_uc003elt.2_5'Flank|C3orf37_uc003elu.2_5'Flank|C3orf37_uc003elv.2_5'Flank|C3orf37_uc003elw.2_5'Flank	NM_016128	NP_057212	Q9Y678	COPG_HUMAN	coatomer protein complex, subunit gamma 1						COPI coating of Golgi vesicle|intracellular protein transport|retrograde vesicle-mediated transport, Golgi to ER	COPI vesicle coat|cytosol	protein binding|structural molecule activity			ovary(3)|breast(1)	4						ACCTCATACCCTTCCCCAACA	0.483													10	18	---	---	---	---	PASS
SRPRB	58477	broad.mit.edu	37	3	133525537	133525537	+	Missense_Mutation	SNP	T	G	G			TCGA-CH-5739-01	TCGA-CH-5739-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:133525537T>G	uc003epx.1	+	2	255	c.239T>G	c.(238-240)CTC>CGC	p.L80R		NM_021203	NP_067026	Q9Y5M8	SRPRB_HUMAN	signal recognition particle receptor, beta	80						endoplasmic reticulum membrane|integral to membrane	GTP binding|protein binding|receptor activity			ovary(1)	1						AAAACGTTGCTCTTTGTCAGG	0.403													21	165	---	---	---	---	PASS
MUC4	4585	broad.mit.edu	37	3	195481125	195481125	+	Missense_Mutation	SNP	G	T	T			TCGA-CH-5739-01	TCGA-CH-5739-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195481125G>T	uc011bto.1	-	20	15363	c.14903C>A	c.(14902-14904)GCC>GAC	p.A4968D	MUC4_uc010hzq.2_5'Flank|MUC4_uc003fuz.2_Missense_Mutation_p.A694D|MUC4_uc003fva.2_Missense_Mutation_p.A576D|MUC4_uc003fvb.2_Missense_Mutation_p.A612D|MUC4_uc003fvc.2_Intron|MUC4_uc003fvd.2_Intron|MUC4_uc003fve.2_Missense_Mutation_p.A612D|MUC4_uc010hzr.2_Intron|MUC4_uc011btf.1_Missense_Mutation_p.A576D|MUC4_uc011btg.1_Intron|MUC4_uc011bth.1_Missense_Mutation_p.A660D|MUC4_uc011bti.1_Missense_Mutation_p.A660D|MUC4_uc011btj.1_Missense_Mutation_p.A837D|MUC4_uc011btk.1_Missense_Mutation_p.A576D|MUC4_uc011btl.1_Missense_Mutation_p.A605D|MUC4_uc011btm.1_Missense_Mutation_p.A785D|MUC4_uc011btn.1_Missense_Mutation_p.A576D|MUC4_uc003fvo.2_Missense_Mutation_p.A860D|MUC4_uc003fvp.2_Missense_Mutation_p.A809D	NM_018406	NP_060876	Q99102	MUC4_HUMAN	mucin 4 isoform a	1853					cell-matrix adhesion	integral to plasma membrane|proteinaceous extracellular matrix	ErbB-2 class receptor binding|extracellular matrix constituent, lubricant activity				0	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		TGGAGGGCAGGCCTCGCAGCC	0.677													9	145	---	---	---	---	PASS
SEPSECS	51091	broad.mit.edu	37	4	25160704	25160704	+	Missense_Mutation	SNP	T	C	C			TCGA-CH-5739-01	TCGA-CH-5739-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:25160704T>C	uc003grg.2	-	2	353	c.140A>G	c.(139-141)GAT>GGT	p.D47G	uc003grj.2_5'Flank|PI4K2B_uc011bxs.1_5'Flank|SEPSECS_uc003gri.2_Missense_Mutation_p.D46G|SEPSECS_uc003grh.2_Intron	NM_153825	NP_722547	Q9HD40	SPCS_HUMAN	Sep (O-phosphoserine) tRNA:Sec (selenocysteine)	47					selenocysteine incorporation	cytoplasm|nucleus	pyridoxal phosphate binding|transferase activity, transferring selenium-containing groups|tRNA binding				0		Breast(46;0.173)			Pyridoxal Phosphate(DB00114)	TGTACTTTCATCCCAGCCATT	0.353													9	44	---	---	---	---	PASS
RASGEF1B	153020	broad.mit.edu	37	4	82377759	82377759	+	Intron	SNP	C	A	A			TCGA-CH-5739-01	TCGA-CH-5739-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:82377759C>A	uc003hmi.1	-						RASGEF1B_uc003hmj.1_Intron|RASGEF1B_uc010ijq.1_Intron|RASGEF1B_uc003hmk.2_Missense_Mutation_p.A162S	NM_152545	NP_689758	Q0VAM2	RGF1B_HUMAN	RasGEF domain family, member 1B						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	intracellular	Ras guanyl-nucleotide exchange factor activity				0						CCCACCCAGGCTCTGCCTGGG	0.483													10	94	---	---	---	---	PASS
ZNF608	57507	broad.mit.edu	37	5	123973554	123973554	+	3'UTR	SNP	T	A	A			TCGA-CH-5739-01	TCGA-CH-5739-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:123973554T>A	uc003ktq.1	-	9					ZNF608_uc003ktr.1_RNA|ZNF608_uc003ktp.1_3'UTR	NM_020747	NP_065798	Q9ULD9	ZN608_HUMAN	zinc finger protein 608							intracellular	zinc ion binding			skin(3)|ovary(2)|lung(1)	6		all_cancers(142;0.186)|Prostate(80;0.081)	KIRC - Kidney renal clear cell carcinoma(527;0.159)|Kidney(363;0.221)	OV - Ovarian serous cystadenocarcinoma(64;0.00126)|Epithelial(69;0.00238)|all cancers(49;0.00783)		CGCTTCCCCATGTGATCCAGT	0.348													42	121	---	---	---	---	PASS
ARHGEF37	389337	broad.mit.edu	37	5	149011707	149011707	+	Missense_Mutation	SNP	G	C	C			TCGA-CH-5739-01	TCGA-CH-5739-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:149011707G>C	uc003lra.1	+	13	2045	c.1981G>C	c.(1981-1983)GCC>CCC	p.A661P		NM_001001669	NP_001001669	A1IGU5	ARH37_HUMAN	hypothetical protein LOC389337	661	SH3 2.				regulation of Rho protein signal transduction	cytoplasm	Rho guanyl-nucleotide exchange factor activity				0						TGGCTTCTTGGCCAGGGCTCG	0.592													3	93	---	---	---	---	PASS
HLA-DMB	3109	broad.mit.edu	37	6	32905075	32905075	+	Missense_Mutation	SNP	C	A	A			TCGA-CH-5739-01	TCGA-CH-5739-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32905075C>A	uc003ocl.1	-	3	729	c.496G>T	c.(496-498)GCC>TCC	p.A166S	HLA-DMB_uc003ocj.1_3'UTR|HLA-DMB_uc003ock.1_5'Flank|HLA-DMB_uc010jud.1_Missense_Mutation_p.A35S|HLA-DMB_uc010jue.1_Missense_Mutation_p.A35S|HLA-DMB_uc010juf.1_Missense_Mutation_p.A35S|HLA-DMB_uc011dql.1_Missense_Mutation_p.A166S	NM_002118	NP_002109	P28068	DMB_HUMAN	major histocompatibility complex, class II, DM	166	Lumenal (Potential).|Ig-like C1-type.|Beta-2.				antigen processing and presentation of peptide or polysaccharide antigen via MHC class II|interferon-gamma-mediated signaling pathway|T cell costimulation|T cell receptor signaling pathway	integral to membrane|late endosome membrane|lysosomal membrane|MHC class II protein complex					0						TTGGGCTGGGCAGTCTTGTGC	0.562													5	200	---	---	---	---	PASS
NUDT1	4521	broad.mit.edu	37	7	2290680	2290680	+	3'UTR	SNP	A	C	C			TCGA-CH-5739-01	TCGA-CH-5739-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:2290680A>C	uc003slp.1	+	5					NUDT1_uc003slq.1_3'UTR|NUDT1_uc003slr.1_3'UTR|NUDT1_uc003sls.1_3'UTR|NUDT1_uc003slt.1_3'UTR|NUDT1_uc003slu.1_3'UTR|NUDT1_uc003slv.1_3'UTR	NM_198949	NP_945187	P36639	8ODP_HUMAN	nudix-type motif 1 isoform p22						DNA protection|DNA repair|response to oxidative stress	cytoplasm	8-oxo-7,8-dihydrodeoxyguanosine triphosphate pyrophosphatase activity|8-oxo-7,8-dihydroguanosine triphosphate pyrophosphatase activity|GTPase activity|metal ion binding|protein binding				0		Ovarian(82;0.0253)|Melanoma(862;0.155)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0822)|OV - Ovarian serous cystadenocarcinoma(56;2.8e-14)|BRCA - Breast invasive adenocarcinoma(126;0.15)		TGGCTGCTGAACAGCCGCAAA	0.587								Direct_reversal_of_damage|Modulation_of_nucleotide_pools					11	27	---	---	---	---	PASS
SDK1	221935	broad.mit.edu	37	7	3990604	3990604	+	Silent	SNP	G	A	A			TCGA-CH-5739-01	TCGA-CH-5739-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:3990604G>A	uc003smx.2	+	6	1036	c.897G>A	c.(895-897)CCG>CCA	p.P299P		NM_152744	NP_689957	Q7Z5N4	SDK1_HUMAN	sidekick 1 precursor	299	Ig-like C2-type 3.				cell adhesion	integral to membrane				large_intestine(3)|ovary(2)|skin(1)	6		all_cancers(1;0.127)|Ovarian(82;0.0177)|Myeloproliferative disorder(862;0.194)		UCEC - Uterine corpus endometrioid carcinoma (126;0.121)|OV - Ovarian serous cystadenocarcinoma(56;9.65e-15)		TGGTTCCCCCGGGCAACAGAA	0.512													36	68	---	---	---	---	PASS
CLEC5A	23601	broad.mit.edu	37	7	141635653	141635653	+	Silent	SNP	T	C	C			TCGA-CH-5739-01	TCGA-CH-5739-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:141635653T>C	uc003vwv.1	-	5	503	c.306A>G	c.(304-306)AAA>AAG	p.K102K	CLEC5A_uc011krm.1_Silent_p.K79K|CLEC5A_uc003vww.1_Silent_p.K102K|CLEC5A_uc010lnq.1_Silent_p.K79K|CLEC5A_uc010lnr.1_Intron	NM_013252	NP_037384	Q9NY25	CLC5A_HUMAN	C-type lectin, superfamily member 5	102	C-type lectin.|Extracellular (Potential).				anti-apoptosis|cellular defense response|innate immune response|interspecies interaction between organisms|osteoblast development	cell surface|integral to plasma membrane	sugar binding|viral receptor activity				0	Melanoma(164;0.0171)					ATGTGGATCCTTTTCCTTTGC	0.448													43	168	---	---	---	---	PASS
NCAPG2	54892	broad.mit.edu	37	7	158451099	158451099	+	Missense_Mutation	SNP	T	A	A			TCGA-CH-5739-01	TCGA-CH-5739-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:158451099T>A	uc003wnv.1	-	17	2136	c.1991A>T	c.(1990-1992)GAT>GTT	p.D664V	NCAPG2_uc010lqu.1_Missense_Mutation_p.D456V|NCAPG2_uc003wnw.1_RNA|NCAPG2_uc003wnx.1_Missense_Mutation_p.D664V|NCAPG2_uc011kwe.1_Missense_Mutation_p.D664V|NCAPG2_uc011kwc.1_Missense_Mutation_p.D165V|NCAPG2_uc011kwd.1_Missense_Mutation_p.D107V	NM_017760	NP_060230	Q86XI2	CNDG2_HUMAN	leucine zipper protein 5	664					cell division|chromosome condensation|mitosis	nucleus	methylated histone residue binding			ovary(1)|breast(1)|kidney(1)	3	Ovarian(565;0.152)	all_cancers(7;3.44e-11)|all_epithelial(9;3.05e-05)|all_hematologic(28;0.014)	OV - Ovarian serous cystadenocarcinoma(82;0.00174)	UCEC - Uterine corpus endometrioid carcinoma (81;0.187)|STAD - Stomach adenocarcinoma(7;0.18)		GCAGCGATCATCCTAAAAGCG	0.383													14	31	---	---	---	---	PASS
ZHX2	22882	broad.mit.edu	37	8	123964946	123964946	+	Missense_Mutation	SNP	G	T	T			TCGA-CH-5739-01	TCGA-CH-5739-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:123964946G>T	uc003ypk.1	+	3	1763	c.1196G>T	c.(1195-1197)GGA>GTA	p.G399V		NM_014943	NP_055758	Q9Y6X8	ZHX2_HUMAN	zinc fingers and homeoboxes 2	399	Required for interaction with NFYA.|Required for repressor activity.|Required for nuclear localization.					cytoplasm|nucleus|plasma membrane	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|skin(1)	2	Lung NSC(37;2e-09)|Ovarian(258;0.0205)|Hepatocellular(40;0.105)		STAD - Stomach adenocarcinoma(47;0.00527)			GCCGTGGCAGGAGTCACCAAC	0.627													25	57	---	---	---	---	PASS
FER1L6	654463	broad.mit.edu	37	8	125072891	125072891	+	Missense_Mutation	SNP	G	A	A	rs138376786	byFrequency	TCGA-CH-5739-01	TCGA-CH-5739-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:125072891G>A	uc003yqw.2	+	24	3294	c.3088G>A	c.(3088-3090)GTG>ATG	p.V1030M	uc003yqy.1_RNA	NM_001039112	NP_001034201	Q2WGJ9	FR1L6_HUMAN	fer-1-like 6	1030	Cytoplasmic (Potential).					integral to membrane				ovary(5)|skin(5)|central_nervous_system(1)	11	Lung NSC(37;4.1e-12)|Ovarian(258;0.00438)|all_neural(195;0.0741)		STAD - Stomach adenocarcinoma(47;0.00186)			GAAGTCCTGCGTGATCCAGAG	0.547													8	137	---	---	---	---	PASS
FLJ43859	389761	broad.mit.edu	37	9	84547870	84547870	+	3'UTR	SNP	T	C	C	rs138226188	by1000genomes	TCGA-CH-5739-01	TCGA-CH-5739-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:84547870T>C	uc004amh.2	+	4					uc004ami.1_Intron|uc004amj.1_5'Flank	NM_001145197	NP_001138669	Q6ZUB0	YI020_HUMAN	hypothetical protein LOC389761							integral to membrane					0						CGTGAACCCATAGAAATCTTC	0.428													4	17	---	---	---	---	PASS
NCBP1	4686	broad.mit.edu	37	9	100396133	100396133	+	5'UTR	SNP	C	T	T			TCGA-CH-5739-01	TCGA-CH-5739-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:100396133C>T	uc004axq.2	+	1					TSTD2_uc004axn.2_5'Flank|TSTD2_uc004axo.2_5'Flank	NM_002486	NP_002477	Q09161	NCBP1_HUMAN	nuclear cap binding protein subunit 1, 80kDa						gene silencing by RNA|histone mRNA metabolic process|mRNA 3'-end processing|mRNA capping|mRNA cleavage|mRNA export from nucleus|ncRNA metabolic process|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|positive regulation of mRNA 3'-end processing|positive regulation of viral transcription|regulation of translational initiation|spliceosomal snRNP assembly|termination of RNA polymerase II transcription|transcription elongation from RNA polymerase II promoter|viral reproduction	cytosol|mRNA cap binding complex|nucleoplasm|ribonucleoprotein complex	protein binding|RNA cap binding			central_nervous_system(1)	1		Acute lymphoblastic leukemia(62;0.158)				ACCGCCTGGCCTCTCGGTTCC	0.741													2	2	---	---	---	---	PASS
TGFBR1	7046	broad.mit.edu	37	9	101900330	101900330	+	Missense_Mutation	SNP	G	T	T			TCGA-CH-5739-01	TCGA-CH-5739-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:101900330G>T	uc004azc.2	+	4	840	c.764G>T	c.(763-765)CGT>CTT	p.R255L	TGFBR1_uc004azd.2_Missense_Mutation_p.R178L|TGFBR1_uc011lvc.1_Missense_Mutation_p.R186L	NM_004612	NP_004603	P36897	TGFR1_HUMAN	transforming growth factor, beta receptor I	255	Protein kinase.|Cytoplasmic (Potential).				activation of MAPKK activity|anterior/posterior pattern formation|artery morphogenesis|collagen fibril organization|embryonic cranial skeleton morphogenesis|germ cell migration|heart development|kidney development|neuron fate commitment|palate development|parathyroid gland development|pathway-restricted SMAD protein phosphorylation|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|pharyngeal system development|positive regulation of cell growth|positive regulation of cell proliferation|positive regulation of cellular component movement|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of protein kinase B signaling cascade|positive regulation of SMAD protein import into nucleus|positive regulation of survival gene product expression|positive regulation of transcription, DNA-dependent|response to cholesterol|thymus development|transforming growth factor beta receptor signaling pathway		ATP binding|I-SMAD binding|metal ion binding|transforming growth factor beta binding|transforming growth factor beta receptor activity, type I|type II transforming growth factor beta receptor binding			lung(2)|ovary(1)	3		Acute lymphoblastic leukemia(62;0.0559)				GTAATGTTACGTCATGAAAAC	0.378													55	132	---	---	---	---	PASS
ACTL7B	10880	broad.mit.edu	37	9	111617062	111617062	+	Silent	SNP	G	T	T			TCGA-CH-5739-01	TCGA-CH-5739-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:111617062G>T	uc004bdi.2	-	1	1214	c.1149C>A	c.(1147-1149)GGC>GGA	p.G383G		NM_006686	NP_006677	Q9Y614	ACL7B_HUMAN	actin-like 7B	383						actin cytoskeleton|cytoplasm	structural constituent of cytoskeleton			pancreas(1)	1						GGATGGAACCGCCGGTCCACA	0.657													3	28	---	---	---	---	PASS
LRIT2	340745	broad.mit.edu	37	10	85981837	85981837	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5739-01	TCGA-CH-5739-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:85981837G>A	uc001kcy.2	-	3	1500	c.1492C>T	c.(1492-1494)CGC>TGC	p.R498C	LRIT2_uc010qmc.1_Missense_Mutation_p.R508C	NM_001017924	NP_001017924	A6NDA9	LRIT2_HUMAN	leucine rich repeat containing 22 precursor	498						integral to membrane				ovary(2)	2						AGACAGCCGCGCAGGACCCAC	0.637													38	87	---	---	---	---	PASS
MRGPRX3	117195	broad.mit.edu	37	11	18159642	18159642	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5739-01	TCGA-CH-5739-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:18159642C>T	uc001mnu.2	+	3	1254	c.893C>T	c.(892-894)ACG>ATG	p.T298M		NM_054031	NP_473372	Q96LB0	MRGX3_HUMAN	MAS-related GPR, member X3	298	Cytoplasmic (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(1)|pancreas(1)	2						CTGCAGGACACGCCTGAGGTG	0.562													10	80	---	---	---	---	PASS
SCGB2A2	4250	broad.mit.edu	37	11	62038408	62038408	+	Silent	SNP	G	C	C			TCGA-CH-5739-01	TCGA-CH-5739-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62038408G>C	uc001ntc.2	+	2	170	c.111G>C	c.(109-111)GTG>GTC	p.V37V	SCGB2A2_uc009ynx.2_Silent_p.V37V	NM_002411	NP_002402	Q13296	SG2A2_HUMAN	secretoglobin, family 2A, member 2 precursor	37						extracellular region	steroid binding			ovary(1)	1						ATCCACAAGTGTCTAAGACTG	0.418													55	128	---	---	---	---	PASS
TRIM49	57093	broad.mit.edu	37	11	89531568	89531568	+	Silent	SNP	T	C	C	rs139075721	by1000genomes	TCGA-CH-5739-01	TCGA-CH-5739-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:89531568T>C	uc001pdb.2	-	8	1418	c.1089A>G	c.(1087-1089)AAA>AAG	p.K363K		NM_020358	NP_065091	P0CI25	TRI49_HUMAN	ring finger protein 18	363	B30.2/SPRY.					intracellular	zinc ion binding				0		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00556)				GATTCTTCTCTTTCCGATACA	0.458													6	225	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	12	92000	92000	+	Missense_Mutation	SNP	A	T	T			TCGA-CH-5739-01	TCGA-CH-5739-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:92000A>T	uc010sdi.1	-	2	338	c.310T>A	c.(310-312)TTG>ATG	p.L104M	uc010sdj.1_RNA					SubName: Full=DEAD/H box polypeptide 11 like 11;																		GGTCCTGGCAACACTCTGGAC	0.572													3	4	---	---	---	---	PASS
HSN2	378465	broad.mit.edu	37	12	977305	977305	+	Missense_Mutation	SNP	A	C	C			TCGA-CH-5739-01	TCGA-CH-5739-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:977305A>C	uc001qiq.2	+	1	436	c.310A>C	c.(310-312)ACA>CCA	p.T104P	WNK1_uc001qio.3_Intron|WNK1_uc001qip.3_Intron|WNK1_uc001qir.3_Intron	NM_213655	NP_998820			hereditary sensory neuropathy, type II												0	all_cancers(10;0.0107)|all_epithelial(11;0.0151)|Ovarian(42;0.0512)|all_lung(10;0.0521)|Lung NSC(10;0.0987)		OV - Ovarian serous cystadenocarcinoma(31;0.000967)|BRCA - Breast invasive adenocarcinoma(9;0.0178)			GTTGGGTACTACAGCCAGTAG	0.493													10	36	---	---	---	---	PASS
RNF17	56163	broad.mit.edu	37	13	25416253	25416253	+	Missense_Mutation	SNP	A	G	G			TCGA-CH-5739-01	TCGA-CH-5739-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:25416253A>G	uc001upr.2	+	19	2598	c.2557A>G	c.(2557-2559)ATT>GTT	p.I853V	RNF17_uc010tdd.1_Missense_Mutation_p.I712V|RNF17_uc010aab.2_RNA|RNF17_uc010tde.1_Missense_Mutation_p.I853V|RNF17_uc001ups.2_Missense_Mutation_p.I792V|RNF17_uc010aac.2_Missense_Mutation_p.I51V|RNF17_uc010aad.2_5'Flank	NM_031277	NP_112567	Q9BXT8	RNF17_HUMAN	ring finger protein 17	853					multicellular organismal development	cytoplasm|nucleus	hydrolase activity, acting on ester bonds|nucleic acid binding|zinc ion binding			ovary(1)|skin(1)	2		Lung SC(185;0.0225)|Breast(139;0.077)		all cancers(112;0.0114)|OV - Ovarian serous cystadenocarcinoma(117;0.0311)|Epithelial(112;0.0524)		TACTACTAGTATTAATGACCA	0.343													55	127	---	---	---	---	PASS
NUFIP1	26747	broad.mit.edu	37	13	45523879	45523879	+	Silent	SNP	T	C	C			TCGA-CH-5739-01	TCGA-CH-5739-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:45523879T>C	uc001uzp.2	-	8	1158	c.1116A>G	c.(1114-1116)TCA>TCG	p.S372S		NM_012345	NP_036477	Q9UHK0	NUFP1_HUMAN	nuclear fragile X mental retardation protein	372					box C/D snoRNP assembly|positive regulation of transcription from RNA polymerase II promoter|RNA processing	actin cytoskeleton|cytosolic ribosome|nuclear matrix|nucleolus|perichromatin fibrils|pre-snoRNP complex|presynaptic active zone|transcription elongation factor complex	DNA binding|identical protein binding|protein binding, bridging|RNA binding|zinc ion binding				0		Lung NSC(96;8.23e-05)|Breast(139;0.00378)|Prostate(109;0.0107)|all_hematologic(4;0.014)|Lung SC(185;0.0262)|Hepatocellular(98;0.0524)|Acute lymphoblastic leukemia(4;0.143)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;0.000306)|BRCA - Breast invasive adenocarcinoma(63;0.125)		TCTCTGACCCTGAAAGACTGC	0.443													6	127	---	---	---	---	PASS
LRCH1	23143	broad.mit.edu	37	13	47269054	47269054	+	Nonsense_Mutation	SNP	G	T	T			TCGA-CH-5739-01	TCGA-CH-5739-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:47269054G>T	uc001vbj.2	+	9	1383	c.1147G>T	c.(1147-1149)GAG>TAG	p.E383*	LRCH1_uc010acp.2_Nonsense_Mutation_p.E383*|LRCH1_uc001vbk.2_Nonsense_Mutation_p.E383*|LRCH1_uc001vbl.3_Nonsense_Mutation_p.E383*	NM_015116	NP_055931	Q9Y2L9	LRCH1_HUMAN	leucine-rich repeats and calponin homology (CH)	383										ovary(1)|central_nervous_system(1)	2		all_lung(13;5.61e-07)|Lung NSC(96;0.000117)|Breast(56;0.000141)|Prostate(109;0.0029)|Lung SC(185;0.0367)|Myeloproliferative disorder(33;0.0505)|Hepatocellular(98;0.0556)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;0.000123)		ATTTCAACCGGAGCCTTCCCT	0.408													84	82	---	---	---	---	PASS
SLITRK5	26050	broad.mit.edu	37	13	88328403	88328403	+	Missense_Mutation	SNP	T	C	C			TCGA-CH-5739-01	TCGA-CH-5739-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:88328403T>C	uc001vln.2	+	2	979	c.760T>C	c.(760-762)TCC>CCC	p.S254P	SLITRK5_uc010tic.1_Intron	NM_015567	NP_056382	O94991	SLIK5_HUMAN	SLIT and NTRK-like family, member 5 precursor	254	LRRCT 1.|Extracellular (Potential).					integral to membrane				ovary(2)|pancreas(2)|central_nervous_system(1)	5	all_neural(89;0.101)|Medulloblastoma(90;0.163)					GGACAGCATCTCCTATTCAGC	0.507													75	242	---	---	---	---	PASS
PAPLN	89932	broad.mit.edu	37	14	73731013	73731013	+	Missense_Mutation	SNP	G	A	A	rs145618706		TCGA-CH-5739-01	TCGA-CH-5739-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:73731013G>A	uc010ttx.1	+	20	3119	c.2956G>A	c.(2956-2958)GAC>AAC	p.D986N	PAPLN_uc001xnw.3_Missense_Mutation_p.D959N|PAPLN_uc010arl.2_RNA|PAPLN_uc010ttw.1_RNA|PAPLN_uc010tty.1_Missense_Mutation_p.D970N|PAPLN_uc010arm.2_Missense_Mutation_p.D185N|PAPLN_uc010arn.2_Missense_Mutation_p.D186N	NM_173462	NP_775733	O95428	PPN_HUMAN	papilin	986	Ig-like C2-type 1.					proteinaceous extracellular matrix	metalloendopeptidase activity|serine-type endopeptidase inhibitor activity|zinc ion binding			ovary(1)|central_nervous_system(1)|skin(1)	3				BRCA - Breast invasive adenocarcinoma(234;0.00394)|OV - Ovarian serous cystadenocarcinoma(108;0.0468)		GCCAGGCCGCGACTCCCAGAA	0.647													16	38	---	---	---	---	PASS
ADAM6	8755	broad.mit.edu	37	14	107035020	107035020	+	RNA	SNP	C	T	T	rs75660488	by1000genomes	TCGA-CH-5739-01	TCGA-CH-5739-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:107035020C>T	uc010tyt.1	-	154		c.7213G>A			uc001ysz.2_Silent_p.E20E					Parts of antibodies, mostly variable regions.												0						CCAGCTGCACCTCGGCACAGA	0.557													3	15	---	---	---	---	PASS
IGDCC4	57722	broad.mit.edu	37	15	65685846	65685846	+	Nonsense_Mutation	SNP	G	A	A	rs138576438		TCGA-CH-5739-01	TCGA-CH-5739-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:65685846G>A	uc002aou.1	-	10	1948	c.1738C>T	c.(1738-1740)CGA>TGA	p.R580*	IGDCC4_uc002aot.1_Nonsense_Mutation_p.R168*	NM_020962	NP_066013	Q8TDY8	IGDC4_HUMAN	immunoglobulin superfamily, DCC subclass, member	580	Fibronectin type-III 2.|Extracellular (Potential).					integral to membrane|plasma membrane				ovary(1)|pancreas(1)|skin(1)	3						TCATTTCCTCGCACCTCAGTA	0.552													32	83	---	---	---	---	PASS
LCTL	197021	broad.mit.edu	37	15	66853375	66853375	+	Missense_Mutation	SNP	C	A	A			TCGA-CH-5739-01	TCGA-CH-5739-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:66853375C>A	uc002aqc.2	-	6	806	c.674G>T	c.(673-675)GGC>GTC	p.G225V	LCTL_uc002aqd.3_Missense_Mutation_p.G52V|LCTL_uc010bhw.2_Intron	NM_207338	NP_997221	Q6UWM7	LCTL_HUMAN	lactase-like precursor	225	Extracellular (Potential).				carbohydrate metabolic process	endoplasmic reticulum membrane|integral to membrane	cation binding|hydrolase activity, hydrolyzing O-glycosyl compounds			ovary(2)	2						CTTGTACAGGCCGGTGCCGCG	0.602													9	99	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	16	62983	62983	+	Intron	SNP	G	T	T			TCGA-CH-5739-01	TCGA-CH-5739-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:62983G>T	uc010utx.1	+						uc010bqm.2_RNA					Homo sapiens mRNA for DEAD/H box polypeptide 11 like 10 (DDX11L10 gene).																		GTCCTGGACAGGCTGTTGGCC	0.562													3	3	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	16	62996	62996	+	Intron	SNP	A	G	G			TCGA-CH-5739-01	TCGA-CH-5739-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:62996A>G	uc010utx.1	+						uc010bqm.2_RNA					Homo sapiens mRNA for DEAD/H box polypeptide 11 like 10 (DDX11L10 gene).																		TGTTGGCCTGAATCTGAGCCC	0.567													3	3	---	---	---	---	PASS
NTN3	4917	broad.mit.edu	37	16	2521965	2521965	+	Missense_Mutation	SNP	C	A	A			TCGA-CH-5739-01	TCGA-CH-5739-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2521965C>A	uc002cqj.2	+	1	466	c.263C>A	c.(262-264)GCC>GAC	p.A88D		NM_006181	NP_006172	O00634	NET3_HUMAN	netrin 3 precursor	88	Laminin N-terminal.				axon guidance|muscle cell differentiation|positive regulation of muscle cell differentiation	proteinaceous extracellular matrix				central_nervous_system(1)	1						GGGGGCACGGCCAGCCCTCTG	0.721													5	25	---	---	---	---	PASS
NAGPA	51172	broad.mit.edu	37	16	5075311	5075311	+	3'UTR	SNP	G	A	A			TCGA-CH-5739-01	TCGA-CH-5739-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:5075311G>A	uc002cyg.2	-	10					NAGPA_uc010buc.2_3'UTR|NAGPA_uc002cyf.2_3'UTR|NAGPA_uc002cyh.2_RNA|NAGPA_uc002cyi.2_3'UTR	NM_016256	NP_057340	Q9UK23	NAGPA_HUMAN	N-acetylglucosamine-1-phosphodiester						carbohydrate metabolic process|lysosome organization|protein modification process|protein targeting to lysosome	Golgi cisterna membrane|integral to membrane	N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase activity				0					N-Acetyl-D-glucosamine(DB00141)	GCCCTGGCAGGTGGCCAGGTG	0.627													10	21	---	---	---	---	PASS
STAT3	6774	broad.mit.edu	37	17	40474448	40474448	+	Silent	SNP	A	G	G			TCGA-CH-5739-01	TCGA-CH-5739-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40474448A>G	uc002hzl.1	-	21	2193	c.1953T>C	c.(1951-1953)GCT>GCC	p.A651A	STAT3_uc002hzk.1_Silent_p.A651A|STAT3_uc002hzm.1_Silent_p.A651A|STAT3_uc010wgh.1_Silent_p.A553A|STAT3_uc002hzn.1_Silent_p.A651A	NM_139276	NP_644805	P40763	STAT3_HUMAN	signal transducer and activator of transcription	651	SH2.				cellular component movement|eating behavior|eye photoreceptor cell differentiation|glucose homeostasis|interleukin-6-mediated signaling pathway|interspecies interaction between organisms|JAK-STAT cascade involved in growth hormone signaling pathway|negative regulation of transcription from RNA polymerase II promoter|nerve growth factor receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|protein import into nucleus|response to estradiol stimulus|sexual reproduction|temperature homeostasis	cytosol|nucleus|plasma membrane	calcium ion binding|ligand-regulated transcription factor activity|protein dimerization activity|protein kinase binding|sequence-specific DNA binding transcription factor activity|signal transducer activity|transcription factor binding|transcription regulatory region DNA binding			ovary(1)|lung(1)|breast(1)|central_nervous_system(1)	4		all_cancers(22;1.39e-06)|all_epithelial(22;2.95e-05)|Breast(137;0.000135)		BRCA - Breast invasive adenocarcinoma(366;0.139)		TGATGATTTCAGCAAATGACA	0.473									Hyperimmunoglobulin_E_Recurrent_Infection_Syndrome				98	239	---	---	---	---	PASS
LRRC37A2	474170	broad.mit.edu	37	17	44630768	44630768	+	Missense_Mutation	SNP	A	G	G			TCGA-CH-5739-01	TCGA-CH-5739-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:44630768A>G	uc002ikn.1	+	11	4815	c.4812A>G	c.(4810-4812)ATA>ATG	p.I1604M	ARL17A_uc002iko.3_Intron|LRRC37A2_uc002ikq.1_Missense_Mutation_p.I565M|ARL17A_uc002iks.2_3'UTR	NM_001006607	NP_001006608	A6NM11	L37A2_HUMAN	c114 SLIT-like testicular protein precursor	1604	Cytoplasmic (Potential).					integral to membrane					0		Melanoma(429;0.211)		BRCA - Breast invasive adenocarcinoma(366;0.232)		TAAAACAGATATGTTGTCACC	0.284													4	167	---	---	---	---	PASS
ARL17A	51326	broad.mit.edu	37	17	44630848	44630848	+	3'UTR	SNP	C	T	T	rs139733485	by1000genomes	TCGA-CH-5739-01	TCGA-CH-5739-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:44630848C>T	uc002iks.2	-	4					LRRC37A2_uc002ikn.1_Intron|ARL17A_uc002iko.3_Intron|LRRC37A2_uc002ikq.1_Intron	NM_001113738	NP_001107210	Q8IVW1	ARL17_HUMAN	hypothetical protein LOC51326 isoform a						protein transport|vesicle-mediated transport	Golgi apparatus	GTP binding				0						tttttttcttctcttttgaga	0.154													6	123	---	---	---	---	PASS
ARL17A	51326	broad.mit.edu	37	17	44630855	44630855	+	3'UTR	SNP	G	C	C	rs144516284	by1000genomes	TCGA-CH-5739-01	TCGA-CH-5739-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:44630855G>C	uc002iks.2	-	4					LRRC37A2_uc002ikn.1_Intron|ARL17A_uc002iko.3_Intron|LRRC37A2_uc002ikq.1_Intron	NM_001113738	NP_001107210	Q8IVW1	ARL17_HUMAN	hypothetical protein LOC51326 isoform a						protein transport|vesicle-mediated transport	Golgi apparatus	GTP binding				0						cttctcttttgagacggagtt	0.139													4	120	---	---	---	---	PASS
CDC27	996	broad.mit.edu	37	17	45234386	45234386	+	Silent	SNP	G	T	T			TCGA-CH-5739-01	TCGA-CH-5739-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:45234386G>T	uc002ild.3	-	7	862	c.735C>A	c.(733-735)GTC>GTA	p.V245V	CDC27_uc002ile.3_Silent_p.V245V|CDC27_uc002ilf.3_Silent_p.V245V|CDC27_uc010wkp.1_Silent_p.V184V|CDC27_uc010wkq.1_RNA	NM_001256	NP_001247	P30260	CDC27_HUMAN	cell division cycle protein 27 isoform 2	245					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell proliferation|mitotic cell cycle spindle assembly checkpoint|mitotic metaphase/anaphase transition|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein K11-linked ubiquitination	anaphase-promoting complex|centrosome|cytosol|nucleoplasm|spindle microtubule	protein phosphatase binding			lung(2)|breast(2)|ovary(1)	5						TTCCCAGTGGGACAGTATCAG	0.358													8	131	---	---	---	---	PASS
COL1A1	1277	broad.mit.edu	37	17	48264184	48264184	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5739-01	TCGA-CH-5739-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48264184C>T	uc002iqm.2	-	48	3757	c.3631G>A	c.(3631-3633)GAT>AAT	p.D1211N		NM_000088	NP_000079	P02452	CO1A1_HUMAN	alpha 1 type I collagen preproprotein	1211	Nonhelical region (C-terminal).				axon guidance|blood vessel development|collagen biosynthetic process|collagen fibril organization|embryonic skeletal system development|leukocyte migration|platelet activation|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of cell migration|positive regulation of epithelial to mesenchymal transition|positive regulation of transcription, DNA-dependent|protein localization to nucleus|sensory perception of sound|skin morphogenesis|tooth mineralization|visual perception	collagen type I|extracellular space|plasma membrane	identical protein binding|platelet-derived growth factor binding		COL1A1/PDGFB(372)	soft_tissue(372)|central_nervous_system(7)|skin(1)|breast(1)|pancreas(1)	382					Collagenase(DB00048)|Palifermin(DB00039)	CGGCCACCATCGTGAGCCTTC	0.637			T	PDGFB|USP6	dermatofibrosarcoma protuberans|aneurysmal bone cyst 		Osteogenesis imperfecta						45	122	---	---	---	---	PASS
GAA	2548	broad.mit.edu	37	17	78079689	78079689	+	Missense_Mutation	SNP	G	T	T	rs145866792	byFrequency	TCGA-CH-5739-01	TCGA-CH-5739-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:78079689G>T	uc002jxo.2	+	4	870	c.688G>T	c.(688-690)GTG>TTG	p.V230L	GAA_uc002jxp.2_Missense_Mutation_p.V230L|GAA_uc002jxq.2_Missense_Mutation_p.V230L	NM_001079803	NP_001073271	P10253	LYAG_HUMAN	acid alpha-glucosidase preproprotein	230					cardiac muscle contraction|diaphragm contraction|glycogen catabolic process|lysosome organization|tongue morphogenesis|vacuolar sequestering|ventricular cardiac muscle tissue morphogenesis	lysosomal membrane	carbohydrate binding|maltose alpha-glucosidase activity			ovary(1)	1	all_neural(118;0.117)		OV - Ovarian serous cystadenocarcinoma(97;0.0292)|BRCA - Breast invasive adenocarcinoma(99;0.139)		Acarbose(DB00284)	GGACGGCCGCGTGCTGTGAGT	0.662													22	36	---	---	---	---	PASS
SKA1	220134	broad.mit.edu	37	18	47906549	47906549	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5739-01	TCGA-CH-5739-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:47906549G>A	uc002let.2	+	3	326	c.142G>A	c.(142-144)GTA>ATA	p.V48I	SKA1_uc002leu.2_Missense_Mutation_p.V48I|SKA1_uc010xdl.1_Missense_Mutation_p.V48I	NM_145060	NP_659497	Q96BD8	SKA1_HUMAN	spindle and KT associated 1	48					cell division|chromosome segregation|mitotic anaphase|mitotic prometaphase|regulation of microtubule polymerization or depolymerization	condensed chromosome outer kinetochore|cytosol|spindle microtubule	microtubule binding				0						TGAGATCATTGTAATAAATGA	0.289													79	151	---	---	---	---	PASS
MUC16	94025	broad.mit.edu	37	19	8959691	8959691	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5739-01	TCGA-CH-5739-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8959691G>A	uc002mkp.2	-	84	43645	c.43441C>T	c.(43441-43443)CGG>TGG	p.R14481W	MUC16_uc010dwi.2_RNA|MUC16_uc010dwj.2_Missense_Mutation_p.R1281W|MUC16_uc010xki.1_RNA	NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	22126	Cytoplasmic (Potential).				cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			lung(30)|ovary(15)|breast(8)|large_intestine(1)|skin(1)|prostate(1)|pancreas(1)	57						TCCTTCTTCCGCCGGCGGGTG	0.582													8	17	---	---	---	---	PASS
ZNF283	284349	broad.mit.edu	37	19	44352689	44352689	+	Missense_Mutation	SNP	A	G	G			TCGA-CH-5739-01	TCGA-CH-5739-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44352689A>G	uc002oxr.3	+	7	2204	c.1936A>G	c.(1936-1938)AGA>GGA	p.R646G	ZNF283_uc002oxp.3_Missense_Mutation_p.R507G	NM_181845	NP_862828	Q8N7M2	ZN283_HUMAN	zinc finger protein 283	646					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Prostate(69;0.0352)				TGTTCATGAGAGAACTCATAG	0.368													5	132	---	---	---	---	PASS
PRKD2	25865	broad.mit.edu	37	19	47193933	47193933	+	Missense_Mutation	SNP	G	T	T			TCGA-CH-5739-01	TCGA-CH-5739-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47193933G>T	uc002pfh.2	-	14	2075	c.1733C>A	c.(1732-1734)GCA>GAA	p.A578E	PRKD2_uc002pfd.2_5'Flank|PRKD2_uc010eks.2_5'UTR|PRKD2_uc010ekt.2_5'UTR|PRKD2_uc002pfe.2_Missense_Mutation_p.A98E|PRKD2_uc002pff.2_Missense_Mutation_p.A98E|PRKD2_uc002pfg.2_Missense_Mutation_p.A421E|PRKD2_uc002pfi.2_Missense_Mutation_p.A578E|PRKD2_uc002pfj.2_Missense_Mutation_p.A578E|PRKD2_uc010xye.1_Missense_Mutation_p.A578E|PRKD2_uc002pfk.2_Missense_Mutation_p.A421E	NM_001079881	NP_001073350	Q9BZL6	KPCD2_HUMAN	protein kinase D2 isoform A	578	Protein kinase.				cell death|intracellular signal transduction|positive regulation of transcription from RNA polymerase II promoter|protein autophosphorylation|T cell receptor signaling pathway	cytoplasm|membrane|nucleus	ATP binding|metal ion binding|protein kinase C activity			ovary(2)|central_nervous_system(2)|stomach(1)|large_intestine(1)|lung(1)	7		Ovarian(192;0.0129)|all_neural(266;0.0459)|Breast(70;0.212)		OV - Ovarian serous cystadenocarcinoma(262;0.000189)|all cancers(93;0.000545)|Epithelial(262;0.0219)|GBM - Glioblastoma multiforme(486;0.0353)		GACCTTAACTGCCACGTCCCG	0.572													7	122	---	---	---	---	PASS
KRTAP10-1	386677	broad.mit.edu	37	21	45959776	45959776	+	Missense_Mutation	SNP	C	A	A			TCGA-CH-5739-01	TCGA-CH-5739-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:45959776C>A	uc002zfh.1	-	1	303	c.258G>T	c.(256-258)CAG>CAT	p.Q86H	C21orf29_uc002zfe.1_Intron|C21orf29_uc010gpv.1_Intron	NM_198691	NP_941964	P60331	KR101_HUMAN	keratin associated protein 10-1	86	24 X 5 AA repeats of C-C-X(3).					keratin filament				skin(1)	1						agcaagccggctggcagctag	0.333													5	60	---	---	---	---	PASS
PI4KAP2	375133	broad.mit.edu	37	22	21829507	21829507	+	Missense_Mutation	SNP	G	A	A	rs140118179	by1000genomes	TCGA-CH-5739-01	TCGA-CH-5739-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:21829507G>A	uc002zuv.3	-	14	3895	c.1636C>T	c.(1636-1638)CTC>TTC	p.L546F	PI4KAP2_uc002zuw.2_Intron|PI4KAP2_uc011aid.1_Intron					SubName: Full=Putative uncharacterized protein PI4KA;												0						TACTTCAAGAGCTTGATTGTC	0.542													5	10	---	---	---	---	PASS
FAM47B	170062	broad.mit.edu	37	X	34962549	34962549	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5739-01	TCGA-CH-5739-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:34962549C>T	uc004ddi.1	+	1	1619	c.1601C>T	c.(1600-1602)GCG>GTG	p.A534V		NM_152631	NP_689844	Q8NA70	FA47B_HUMAN	hypothetical protein LOC170062	534										ovary(3)|breast(1)	4						AGACGCCGGGCGGCACCGCAT	0.502													16	57	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	1	27307015	27307015	+	IGR	DEL	T	-	-			TCGA-CH-5739-01	TCGA-CH-5739-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:27307015delT								C1orf172 (20118 upstream) : TRNP1 (13180 downstream)																							AGCACCAAtcttttttttttt	0.169													4	2	---	---	---	---	
PPT1	5538	broad.mit.edu	37	1	40557538	40557538	+	Intron	DEL	A	-	-	rs11308805		TCGA-CH-5739-01	TCGA-CH-5739-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:40557538delA	uc001cfb.2	-						PPT1_uc010ojf.1_Intron|PPT1_uc010ojg.1_Intron|PPT1_uc009vwa.2_Intron	NM_000310	NP_000301	P50897	PPT1_HUMAN	palmitoyl-protein thioesterase 1 isoform 1						brain development|cofactor metabolic process|cofactor transport|DNA fragmentation involved in apoptotic nuclear change|lysosomal lumen acidification|membrane raft organization|negative regulation of cell growth|negative regulation of neuron apoptosis|neuron development|pinocytosis|positive regulation of pinocytosis|positive regulation of receptor-mediated endocytosis|protein depalmitoylation|protein transport|receptor-mediated endocytosis|regulation of synapse structure and activity|sphingolipid catabolic process|visual perception	axon|cytosol|Golgi apparatus|lysosome|membrane fraction|membrane raft|nucleus|synaptic vesicle	palmitoyl-(protein) hydrolase activity|palmitoyl-CoA hydrolase activity			ovary(1)	1	Lung NSC(20;3.43e-06)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;1e-18)|Epithelial(16;3.6e-17)|all cancers(16;1.1e-15)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			attctgtctcaaaaaaaaaaa	0.129													4	2	---	---	---	---	
CEBPZ	10153	broad.mit.edu	37	2	37443095	37443095	+	Intron	DEL	A	-	-			TCGA-CH-5739-01	TCGA-CH-5739-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:37443095delA	uc002rpz.2	-							NM_005760	NP_005751	Q03701	CEBPZ_HUMAN	CCAAT/enhancer binding protein zeta						regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	nucleus	DNA binding			pancreas(1)	1		all_hematologic(82;0.21)				taataaagttaaaaaaaaaaa	0.149													5	4	---	---	---	---	
CHIC2	26511	broad.mit.edu	37	4	54876132	54876132	+	3'UTR	DEL	C	-	-	rs68107873		TCGA-CH-5739-01	TCGA-CH-5739-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:54876132delC	uc003haj.1	-	6					PDGFRA_uc003haa.2_Intron	NM_012110	NP_036242	Q9UKJ5	CHIC2_HUMAN	cysteine-rich hydrophobic domain 2							plasma membrane	protein binding			central_nervous_system(1)	1	all_cancers(7;0.0193)|all_neural(26;0.0209)|Lung NSC(11;0.0281)|Glioma(25;0.08)		LUSC - Lung squamous cell carcinoma(32;0.00216)			aaaaaaaaaacaaaaacaaaa	0.323			T	ETV6	AML								13	8	---	---	---	---	
SHROOM3	57619	broad.mit.edu	37	4	77669968	77669968	+	Intron	DEL	T	-	-			TCGA-CH-5739-01	TCGA-CH-5739-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:77669968delT	uc011cbx.1	+						SHROOM3_uc003hkg.2_Intron	NM_020859	NP_065910	Q8TF72	SHRM3_HUMAN	shroom family member 3 protein						apical protein localization|cell morphogenesis|cellular pigment accumulation|pattern specification process|regulation of cell shape	adherens junction|apical junction complex|apical plasma membrane|cytoplasm|microtubule	actin binding			skin(2)|ovary(1)	3			Lung(101;0.0903)			ctgactctgcttttttttttt	0.328													7	4	---	---	---	---	
UFSP2	55325	broad.mit.edu	37	4	186334625	186334625	+	Intron	DEL	A	-	-			TCGA-CH-5739-01	TCGA-CH-5739-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:186334625delA	uc003ixo.2	-						UFSP2_uc003ixn.2_Intron|UFSP2_uc003ixq.2_Intron|UFSP2_uc003ixp.2_Intron	NM_018359	NP_060829	Q9NUQ7	UFSP2_HUMAN	UFM1-specific peptidase 2							endoplasmic reticulum|nucleus	small conjugating protein-specific protease activity				0		all_lung(41;1.3e-11)|Lung NSC(41;2.25e-11)|Melanoma(20;0.00109)|Colorectal(36;0.0215)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|Prostate(90;0.0283)|all_hematologic(60;0.0749)		all cancers(43;3.4e-25)|Epithelial(43;2.23e-22)|OV - Ovarian serous cystadenocarcinoma(60;1.54e-11)|BRCA - Breast invasive adenocarcinoma(30;8.1e-05)|GBM - Glioblastoma multiforme(59;0.000148)|STAD - Stomach adenocarcinoma(60;0.000782)|LUSC - Lung squamous cell carcinoma(40;0.00939)|COAD - Colon adenocarcinoma(29;0.0108)|READ - Rectum adenocarcinoma(43;0.166)		GTTCAGAATGAAAAAAAATGG	0.259													4	2	---	---	---	---	
DNAH5	1767	broad.mit.edu	37	5	13842160	13842160	+	Intron	DEL	A	-	-	rs34885898		TCGA-CH-5739-01	TCGA-CH-5739-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:13842160delA	uc003jfd.2	-							NM_001369	NP_001360	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5						microtubule-based movement	cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(14)|skin(13)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1)|pancreas(1)	31	Lung NSC(4;0.00476)					TCAAAACAATAAAAAAAAAAG	0.184									Kartagener_syndrome				3	3	---	---	---	---	
CRHBP	1393	broad.mit.edu	37	5	76264841	76264842	+	3'UTR	DEL	CA	-	-			TCGA-CH-5739-01	TCGA-CH-5739-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:76264841_76264842delCA	uc003ker.2	+	7						NM_001882	NP_001873	P24387	CRHBP_HUMAN	corticotropin releasing hormone binding protein						female pregnancy|learning or memory|signal transduction	soluble fraction					0		all_lung(232;0.000414)|Lung NSC(167;0.0011)|Ovarian(174;0.0129)|Prostate(461;0.11)		OV - Ovarian serous cystadenocarcinoma(54;2.17e-51)|Epithelial(54;8.79e-46)|all cancers(79;2.49e-41)		CGcacgcgcgcacacacacaca	0.292													6	3	---	---	---	---	
GPR98	84059	broad.mit.edu	37	5	89947720	89947720	+	Intron	DEL	A	-	-			TCGA-CH-5739-01	TCGA-CH-5739-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:89947720delA	uc003kju.2	+						GPR98_uc003kjt.2_Intron	NM_032119	NP_115495	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98 precursor						cell communication|cell-cell adhesion|maintenance of organ identity|neuropeptide signaling pathway|photoreceptor cell maintenance	cell surface|cytoplasm|integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity			ovary(11)|central_nervous_system(3)|pancreas(2)	16		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		ACTTATCTTCAAAAAAAAAAA	0.328													4	2	---	---	---	---	
HSPA9	3313	broad.mit.edu	37	5	137909330	137909331	+	Intron	INS	-	AAA	AAA	rs55663873		TCGA-CH-5739-01	TCGA-CH-5739-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137909330_137909331insAAA	uc003ldf.2	-						HSPA9_uc011cyw.1_Intron	NM_004134	NP_004125	P38646	GRP75_HUMAN	heat shock 70kDa protein 9 precursor						anti-apoptosis|protein folding	cell surface|mitochondrial nucleoid	ATP binding|unfolded protein binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			agactgtctccaaaaaaaaaaa	0.149													9	4	---	---	---	---	
SKIV2L	6499	broad.mit.edu	37	6	31933879	31933880	+	Intron	INS	-	T	T			TCGA-CH-5739-01	TCGA-CH-5739-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31933879_31933880insT	uc003nyn.1	+						SKIV2L_uc011dou.1_Intron|SKIV2L_uc011dov.1_Intron	NM_006929	NP_008860	Q15477	SKIV2_HUMAN	superkiller viralicidic activity 2-like homolog							nucleus	ATP binding|ATP-dependent RNA helicase activity|protein binding|RNA binding			ovary(1)|large_intestine(1)|breast(1)|central_nervous_system(1)	4						tttcttcttccttttttttttg	0.252													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	62701951	62701952	+	IGR	INS	-	A	A			TCGA-CH-5739-01	TCGA-CH-5739-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:62701951_62701952insA								None (None upstream) : LOC643955 (49720 downstream)																							CTTTTTTGGAGAAAAAATATAT	0.337													9	5	---	---	---	---	
FLJ44082	389762	broad.mit.edu	37	9	84564423	84564423	+	3'UTR	DEL	T	-	-			TCGA-CH-5739-01	TCGA-CH-5739-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:84564423delT	uc010mpt.2	+	4					uc004ami.1_Intron|uc004amm.1_5'Flank	NM_207416	NP_997299	P0C874	YI039_HUMAN	hypothetical protein LOC389762							integral to membrane					0						ACTGGGACTATTGAAGCTCAG	0.438													4	2	---	---	---	---	
CEP110	11064	broad.mit.edu	37	9	123939699	123939699	+	3'UTR	DEL	T	-	-	rs75910820		TCGA-CH-5739-01	TCGA-CH-5739-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:123939699delT	uc004bkx.1	+	42					CEP110_uc004blb.1_3'UTR|CEP110_uc010mvp.1_3'UTR	NM_007018	NP_008949	Q7Z7A1	CNTRL_HUMAN	centrosomal protein 110kDa						cell division|G2/M transition of mitotic cell cycle	centrosome|cytosol	protein binding				0						TGGCTGAGCCTTTTTTTTTTT	0.289													4	2	---	---	---	---	
GSN	2934	broad.mit.edu	37	9	124095004	124095004	+	3'UTR	DEL	T	-	-			TCGA-CH-5739-01	TCGA-CH-5739-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:124095004delT	uc004blf.1	+	17					GSN_uc004bld.1_3'UTR|GSN_uc010mvq.1_3'UTR|GSN_uc010mvr.1_3'UTR|GSN_uc010mvu.1_3'UTR|GSN_uc010mvt.1_3'UTR|GSN_uc010mvs.1_3'UTR|GSN_uc004ble.1_3'UTR|GSN_uc010mvv.1_3'UTR|GSN_uc011lyh.1_3'UTR|GSN_uc011lyi.1_3'UTR|GSN_uc011lyj.1_3'UTR	NM_000177	NP_000168	P06396	GELS_HUMAN	gelsolin isoform a precursor						actin filament polymerization|actin filament severing|barbed-end actin filament capping|cellular component disassembly involved in apoptosis|cilium morphogenesis	actin cytoskeleton|cytosol	actin binding|calcium ion binding|protein binding			breast(2)|ovary(1)	3						gtgtTGTTTCTTTTTTTTTTT	0.348													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	133834273	133834275	+	IGR	DEL	CAC	-	-			TCGA-CH-5739-01	TCGA-CH-5739-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:133834273_133834275delCAC								FIBCD1 (19818 upstream) : LAMC3 (50229 downstream)																							ccaccaccatcaccaccatcacc	0.000													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	42010455	42010462	+	IGR	DEL	AAAAGAAA	-	-	rs72331687		TCGA-CH-5739-01	TCGA-CH-5739-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:42010455_42010462delAAAAGAAA								LRRC4C (529132 upstream) : None (None downstream)																							agaaagaaagaaaagaaagaaagaaaga	0.130													4	2	---	---	---	---	
FMNL3	91010	broad.mit.edu	37	12	50048641	50048642	+	Intron	DEL	AC	-	-			TCGA-CH-5739-01	TCGA-CH-5739-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:50048641_50048642delAC	uc001ruv.1	-						FMNL3_uc001ruw.1_Intron|FMNL3_uc001rut.1_5'Flank|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						TTGTCAAGGAACACACACACAG	0.505													224	7	---	---	---	---	
TBC1D15	64786	broad.mit.edu	37	12	72286900	72286901	+	Intron	INS	-	T	T			TCGA-CH-5739-01	TCGA-CH-5739-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:72286900_72286901insT	uc001swu.2	+						TBC1D15_uc009zrv.2_Intron|TBC1D15_uc010stt.1_Intron|TBC1D15_uc001swv.2_Intron|TBC1D15_uc001sww.2_Intron	NM_022771	NP_073608	Q8TC07	TBC15_HUMAN	TBC1 domain family, member 15 isoform 1								protein binding|Rab GTPase activator activity				0						AATATTTTGGGTTTTTTTTTTT	0.228													11	5	---	---	---	---	
GLIPR1	11010	broad.mit.edu	37	12	75884364	75884364	+	Intron	DEL	A	-	-	rs146756328		TCGA-CH-5739-01	TCGA-CH-5739-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:75884364delA	uc001sxs.2	+						GLIPR1_uc009zsb.1_Intron	NM_006851	NP_006842	P48060	GLIP1_HUMAN	GLI pathogenesis-related 1 precursor						cellular lipid metabolic process	extracellular region|integral to membrane				large_intestine(1)|ovary(1)|skin(1)	3						AAACAACAACAAAAAAAAACA	0.274													7	5	---	---	---	---	
BTBD11	121551	broad.mit.edu	37	12	108008872	108008879	+	Frame_Shift_Del	DEL	ACCCCGAG	-	-	rs76689600		TCGA-CH-5739-01	TCGA-CH-5739-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:108008872_108008879delACCCCGAG	uc001tmk.1	+	7	2455_2462	c.1934_1941delACCCCGAG	c.(1933-1941)CACCCCGAGfs	p.H645fs	BTBD11_uc009zut.1_Frame_Shift_Del_p.H645fs|BTBD11_uc001tmj.2_Frame_Shift_Del_p.H645fs|BTBD11_uc001tml.1_Frame_Shift_Del_p.H182fs	NM_001018072	NP_001018082	A6QL63	BTBDB_HUMAN	BTB (POZ) domain containing 11 isoform a	645_647						integral to membrane	DNA binding			skin(2)|ovary(1)	3						CCATCCGTCCACCCCGAGACCCGCCATT	0.404													78	11	---	---	---	---	
FLT3	2322	broad.mit.edu	37	13	28642186	28642187	+	Intron	INS	-	TGTTTTGTTT	TGTTTTGTTT	rs150868508	by1000genomes	TCGA-CH-5739-01	TCGA-CH-5739-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:28642186_28642187insTGTTTTGTTT	uc001urw.2	-						FLT3_uc010aao.2_Intron|FLT3_uc010tdn.1_Intron	NM_004119	NP_004110	P36888	FLT3_HUMAN	fms-related tyrosine kinase 3 precursor						positive regulation of cell proliferation	integral to plasma membrane	ATP binding|vascular endothelial growth factor receptor activity			haematopoietic_and_lymphoid_tissue(8536)|lung(7)|ovary(3)|stomach(1)|central_nervous_system(1)|skin(1)	8549	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0156)|Ovarian(182;0.0392)	Colorectal(13;0.000157)|READ - Rectum adenocarcinoma(15;0.105)	OV - Ovarian serous cystadenocarcinoma(117;0.00154)|all cancers(112;0.00459)|GBM - Glioblastoma multiforme(144;0.00562)|Epithelial(112;0.0959)|Lung(94;0.212)	Sorafenib(DB00398)|Sunitinib(DB01268)	tgtttttattatgttttgtttt	0.332			Mis|O		AML|ALL								4	2	---	---	---	---	
FLT1	2321	broad.mit.edu	37	13	28932006	28932006	+	Intron	DEL	T	-	-	rs71816101		TCGA-CH-5739-01	TCGA-CH-5739-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:28932006delT	uc001usb.3	-							NM_002019	NP_002010	P17948	VGFR1_HUMAN	fms-related tyrosine kinase 1 isoform 1						cell differentiation|female pregnancy|positive regulation of vascular endothelial growth factor receptor signaling pathway	extracellular space|Golgi apparatus|integral to plasma membrane|nucleus	ATP binding|growth factor binding|vascular endothelial growth factor receptor activity			lung(10)|central_nervous_system(5)|ovary(3)|stomach(2)|skin(2)|urinary_tract(1)|breast(1)	24	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0262)|Breast(139;0.188)	Colorectal(13;0.000674)	all cancers(112;0.0301)|Epithelial(112;0.155)|GBM - Glioblastoma multiforme(144;0.184)|OV - Ovarian serous cystadenocarcinoma(117;0.205)|Lung(94;0.207)	Sunitinib(DB01268)	ttttctttccttttttttttt	0.418													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	106713233	106713234	+	IGR	INS	-	ACAC	ACAC	rs144847152	by1000genomes	TCGA-CH-5739-01	TCGA-CH-5739-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:106713233_106713234insACAC								DAOA (569851 upstream) : EFNB2 (428864 downstream)																							ATTCCACCCCAacacacacaca	0.361													4	2	---	---	---	---	
HAUS4	54930	broad.mit.edu	37	14	23419353	23419354	+	Intron	INS	-	A	A			TCGA-CH-5739-01	TCGA-CH-5739-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23419353_23419354insA	uc001whp.2	-						HAUS4_uc001who.2_Intron|HAUS4_uc001whq.2_Intron|HAUS4_uc001whr.2_Intron|HAUS4_uc001whs.2_Intron|HAUS4_uc001wht.2_Intron|HAUS4_uc001whu.2_Intron|HAUS4_uc001whv.2_Intron|HAUS4_uc001whw.2_Intron|HAUS4_uc001whx.2_Intron	NM_017815	NP_060285	Q9H6D7	HAUS4_HUMAN	HAUS augmin-like complex, subunit 4						cell division|centrosome organization|mitosis|spindle assembly	centrosome|HAUS complex|microtubule|spindle				ovary(1)	1						aaaaaaaaaacaaaaaaacaaa	0.139													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	88226836	88226838	+	IGR	DEL	GGG	-	-			TCGA-CH-5739-01	TCGA-CH-5739-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:88226836_88226838delGGG								BANP (115913 upstream) : ZNF469 (267041 downstream)																							tggtggtggtggggatggtggtg	0.000													4	2	---	---	---	---	
HMHA1	23526	broad.mit.edu	37	19	1079503	1079503	+	Intron	DEL	A	-	-			TCGA-CH-5739-01	TCGA-CH-5739-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1079503delA	uc002lqz.1	+						HMHA1_uc010xgd.1_Intron|HMHA1_uc010xge.1_Intron|HMHA1_uc002lra.1_Intron|HMHA1_uc002lrb.1_Intron|HMHA1_uc002lrc.1_Intron	NM_012292	NP_036424	Q92619	HMHA1_HUMAN	minor histocompatibility antigen HA-1						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity|metal ion binding			lung(1)	1		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		actccatctcaaaaaaaaaaa	0.000													5	3	---	---	---	---	
COL5A3	50509	broad.mit.edu	37	19	10094530	10094531	+	Intron	INS	-	A	A	rs141118767	by1000genomes	TCGA-CH-5739-01	TCGA-CH-5739-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10094530_10094531insA	uc002mmq.1	-							NM_015719	NP_056534	P25940	CO5A3_HUMAN	collagen, type V, alpha 3 preproprotein						collagen fibril organization|skin development	collagen type V	collagen binding|extracellular matrix structural constituent			ovary(7)|lung(1)|central_nervous_system(1)|skin(1)	10			Epithelial(33;7.11e-05)			TCGTTAAAAAGAAAAAAaaatc	0.079													2	4	---	---	---	---	
ZNF333	84449	broad.mit.edu	37	19	14810278	14810278	+	Intron	DEL	T	-	-			TCGA-CH-5739-01	TCGA-CH-5739-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14810278delT	uc002mzn.2	+						ZNF333_uc010dzq.2_Intron|ZNF333_uc002mzk.3_Intron|ZNF333_uc002mzl.3_Intron|ZNF333_uc002mzm.2_Intron|ZNF333_uc010dzr.1_Intron	NM_032433	NP_115809	Q96JL9	ZN333_HUMAN	zinc finger protein 333						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)|central_nervous_system(1)|pancreas(1)	3						TGCTCAAGACttttttttttt	0.254													4	3	---	---	---	---	
PPFIA3	8541	broad.mit.edu	37	19	49641825	49641826	+	Intron	DEL	AA	-	-	rs3032696		TCGA-CH-5739-01	TCGA-CH-5739-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49641825_49641826delAA	uc002pmr.2	+						PPFIA3_uc010yai.1_Intron|PPFIA3_uc010yaj.1_Intron|PPFIA3_uc002pms.2_Intron	NM_003660	NP_003651	O75145	LIPA3_HUMAN	PTPRF interacting protein alpha 3							cell surface|cytoplasm	protein binding			lung(1)	1		all_lung(116;3.16e-06)|Lung NSC(112;6.25e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392)		all cancers(93;2.36e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.000203)|GBM - Glioblastoma multiforme(486;0.00307)|Epithelial(262;0.00677)		GTTCAAACTCAAAGGGCAAAGG	0.475													6	4	---	---	---	---	
POLD1	5424	broad.mit.edu	37	19	50916604	50916605	+	Intron	INS	-	G	G	rs55804623		TCGA-CH-5739-01	TCGA-CH-5739-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50916604_50916605insG	uc002psb.3	+						POLD1_uc002psc.3_Intron|POLD1_uc010enx.2_Intron|POLD1_uc010eny.2_Intron	NM_002691	NP_002682	P28340	DPOD1_HUMAN	DNA-directed DNA polymerase delta 1						base-excision repair, gap-filling|DNA replication proofreading|DNA replication, removal of RNA primer|DNA synthesis involved in DNA repair|nucleotide-excision repair, DNA gap filling|regulation of mitotic cell cycle|response to UV|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|transcription-coupled nucleotide-excision repair	delta DNA polymerase complex|nucleoplasm|nucleotide-excision repair complex	3'-5'-exodeoxyribonuclease activity|chromatin binding|DNA binding|DNA-directed DNA polymerase activity|metal ion binding|nucleotide binding|protein binding			upper_aerodigestive_tract(1)|central_nervous_system(1)	2		all_neural(266;0.0571)		OV - Ovarian serous cystadenocarcinoma(262;0.00794)|GBM - Glioblastoma multiforme(134;0.0195)		atggcagaggcgggacccCTCC	0.351								DNA_polymerases_(catalytic_subunits)					4	2	---	---	---	---	
CXADR	1525	broad.mit.edu	37	21	18931675	18931675	+	Intron	DEL	A	-	-	rs147134822		TCGA-CH-5739-01	TCGA-CH-5739-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:18931675delA	uc002yki.2	+						CXADR_uc002ykh.1_Intron|CXADR_uc010gld.1_Intron|CXADR_uc010gle.1_Intron|CXADR_uc002ykj.1_Intron	NM_001338	NP_001329	P78310	CXAR_HUMAN	coxsackie virus and adenovirus receptor						blood coagulation|cell adhesion|interspecies interaction between organisms|leukocyte migration|regulation of immune response	adherens junction|basolateral plasma membrane|extracellular region|integral to plasma membrane|nucleus|tight junction	receptor activity			ovary(1)	1				Epithelial(23;0.000206)|all cancers(11;0.000302)|OV - Ovarian serous cystadenocarcinoma(11;0.0194)|Lung(58;0.0233)|COAD - Colon adenocarcinoma(22;0.0389)|Colorectal(24;0.0483)|LUSC - Lung squamous cell carcinoma(23;0.0782)		ttttttttttaaaaaatgtgt	0.000													2	4	---	---	---	---	
ITSN1	6453	broad.mit.edu	37	21	35191386	35191387	+	Intron	INS	-	A	A	rs150009763	by1000genomes	TCGA-CH-5739-01	TCGA-CH-5739-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:35191386_35191387insA	uc002yta.1	+						DONSON_uc002ysn.1_Intron|ITSN1_uc002yth.3_Intron|ITSN1_uc002ysz.2_Intron|ITSN1_uc010gmg.2_Intron|ITSN1_uc010gmh.2_Intron|ITSN1_uc002ysw.2_Intron|ITSN1_uc010gmi.2_Intron|ITSN1_uc010gmj.2_Intron|ITSN1_uc002ysy.2_Intron|ITSN1_uc002ysx.2_Intron|ITSN1_uc002ytb.1_Intron|ITSN1_uc002ytd.2_Intron|ITSN1_uc010gmk.2_Intron|ITSN1_uc010gml.2_Intron|ITSN1_uc002ytj.2_Intron|ITSN1_uc010gmm.1_Intron|ITSN1_uc002yte.2_Intron|ITSN1_uc002ytg.1_Intron	NM_003024	NP_003015	Q15811	ITSN1_HUMAN	intersectin 1 isoform ITSN-l						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|synaptic vesicle endocytosis	cell junction|coated pit|cytosol|lamellipodium|synapse|synaptosome	calcium ion binding|proline-rich region binding|protein complex scaffold|Rho guanyl-nucleotide exchange factor activity			ovary(3)|skin(1)	4						GCCTCTGTAGTACCTTATTATG	0.351													4	4	---	---	---	---	
FAM3A	60343	broad.mit.edu	37	X	153735498	153735499	+	Intron	INS	-	G	G			TCGA-CH-5739-01	TCGA-CH-5739-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:153735498_153735499insG	uc004fls.1	-						FAM3A_uc004flt.1_Intron|FAM3A_uc011mzp.1_Intron|FAM3A_uc004flu.1_Intron|FAM3A_uc011mzq.1_Intron|FAM3A_uc004flw.1_Intron	NM_021806	NP_068578	P98173	FAM3A_HUMAN	family 3, member A protein precursor							extracellular region				large_intestine(1)	1	all_cancers(53;5.05e-16)|all_epithelial(53;1.87e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					GGCGACAGGCTGCCCCGGTGGG	0.678													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	28582961	28582962	+	IGR	INS	-	AT	AT	rs4008413		TCGA-CH-5739-01	TCGA-CH-5739-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:28582961_28582962insAT								None (None upstream) : None (None downstream)																							AAGTATAAAACAAAAACCTAAA	0.322													3	3	---	---	---	---	
