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
PGD	5226	broad.mit.edu	37	1	10477169	10477169	+	Silent	SNP	C	A	A			TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:10477169C>A	uc001arc.2	+	9	1060	c.970C>A	c.(970-972)CGG>AGG	p.R324R	PGD_uc001ard.2_Silent_p.R244R|PGD_uc010oak.1_Silent_p.R302R|PGD_uc010oal.1_Silent_p.R311R	NM_002631	NP_002622	P52209	6PGD_HUMAN	phosphogluconate dehydrogenase	324					pentose-phosphate shunt, oxidative branch	cytosol	NADP binding|phosphogluconate dehydrogenase (decarboxylating) activity|protein binding			ovary(1)	1	Ovarian(185;0.203)	all_lung(284;1.31e-05)|Lung NSC(185;2.19e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.14e-07)|COAD - Colon adenocarcinoma(227;7.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000294)|Kidney(185;0.000728)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(132;0.00832)|READ - Rectum adenocarcinoma(331;0.0487)		GGAGGACATTCGGAAGGTGGG	0.527													25	79	---	---	---	---	PASS
MTOR	2475	broad.mit.edu	37	1	11188164	11188164	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11188164G>C	uc001asd.2	-	43	6051	c.5930C>G	c.(5929-5931)ACA>AGA	p.T1977R	MTOR_uc001asc.2_Missense_Mutation_p.T182R	NM_004958	NP_004949	P42345	MTOR_HUMAN	FK506 binding protein 12-rapamycin associated	1977	FAT.				cell growth|cellular response to hypoxia|insulin receptor signaling pathway|nerve growth factor receptor signaling pathway|peptidyl-serine phosphorylation|phosphatidylinositol-mediated signaling|protein autophosphorylation|protein catabolic process|response to amino acid stimulus|response to nutrient|T cell costimulation|TOR signaling cascade	endoplasmic reticulum membrane|Golgi membrane|lysosome|mitochondrial outer membrane|phosphatidylinositol 3-kinase complex|PML body|TORC1 complex|TORC2 complex	ATP binding|phosphoprotein binding|protein serine/threonine kinase activity			central_nervous_system(7)|lung(6)|ovary(6)|skin(3)|kidney(3)|large_intestine(2)|breast(2)	29						AGAAGCCACTGTCAGTGGGTA	0.478													5	96	---	---	---	---	PASS
ESPNP	284729	broad.mit.edu	37	1	17033858	17033858	+	Silent	SNP	C	T	T			TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17033858C>T	uc001azn.1	-	4	621	c.507G>A	c.(505-507)GGG>GGA	p.G169G	ESPNP_uc010ocj.1_3'UTR	NR_026567				RecName: Full=Espin; AltName: Full=Ectoplasmic specialization protein; AltName: Full=Autosomal recessive deafness type 36 protein;												0						CGGCCGCGTACCCGTCGCGGT	0.687													5	16	---	---	---	---	PASS
CELA3B	23436	broad.mit.edu	37	1	22310726	22310726	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22310726G>A	uc001bfk.2	+	6	659	c.544G>A	c.(544-546)GTG>ATG	p.V182M	CELA3B_uc009vqf.2_Intron	NM_007352	NP_031378	P08861	CEL3B_HUMAN	elastase 3B, pancreatic preproprotein	182	Peptidase S1.				cholesterol metabolic process|proteolysis	extracellular region	serine-type endopeptidase activity			ovary(1)	1						CCTGCTGCCGGTGGTGGACTA	0.627													5	54	---	---	---	---	PASS
WDR78	79819	broad.mit.edu	37	1	67292538	67292538	+	Silent	SNP	C	T	T			TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:67292538C>T	uc001dcx.2	-	15	2360	c.2304G>A	c.(2302-2304)GAG>GAA	p.E768E	WDR78_uc009waw.2_Silent_p.E481E|WDR78_uc009wax.2_RNA	NM_024763	NP_079039	Q5VTH9	WDR78_HUMAN	WD repeat domain 78 isoform 1	768	WD 5.									ovary(2)	2						CCACCCTGTTCTCATTTGCAG	0.378													8	96	---	---	---	---	PASS
SLC44A5	204962	broad.mit.edu	37	1	75708659	75708659	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:75708659T>C	uc001dgu.2	-	8	527	c.383A>G	c.(382-384)TAT>TGT	p.Y128C	SLC44A5_uc001dgt.2_Missense_Mutation_p.Y128C|SLC44A5_uc001dgs.2_Missense_Mutation_p.Y86C|SLC44A5_uc001dgr.2_Missense_Mutation_p.Y86C|SLC44A5_uc010oqz.1_Missense_Mutation_p.Y167C|SLC44A5_uc010ora.1_Missense_Mutation_p.Y122C|SLC44A5_uc010orb.1_5'UTR	NM_152697	NP_689910	Q8NCS7	CTL5_HUMAN	solute carrier family 44, member 5 isoform A	128	Extracellular (Potential).					integral to membrane|plasma membrane	choline transmembrane transporter activity			ovary(2)|skin(2)	4						CATTTCCACATAGGTTAAAAA	0.403													9	64	---	---	---	---	PASS
TAF5L	27097	broad.mit.edu	37	1	229730773	229730773	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:229730773G>C	uc001htq.2	-	5	1207	c.1041C>G	c.(1039-1041)AGC>AGG	p.S347R		NM_014409	NP_055224	O75529	TAF5L_HUMAN	PCAF associated factor 65 beta isoform a	347	WD 2.				histone H3 acetylation|transcription from RNA polymerase II promoter	STAGA complex|transcription factor TFTC complex	sequence-specific DNA binding transcription factor activity|transcription coactivator activity			ovary(1)	1	Breast(184;0.193)|Ovarian(103;0.249)	Prostate(94;0.167)				GGAACCTCGTGCTGTACACTG	0.537													15	63	---	---	---	---	PASS
LPIN1	23175	broad.mit.edu	37	2	11911528	11911528	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:11911528C>T	uc010yjn.1	+	5	593	c.319C>T	c.(319-321)CCC>TCC	p.P107S	LPIN1_uc010yjm.1_Missense_Mutation_p.P156S|LPIN1_uc002rbt.2_Missense_Mutation_p.P107S|LPIN1_uc002rbs.2_Missense_Mutation_p.P107S	NM_145693	NP_663731	Q14693	LPIN1_HUMAN	lipin 1	107	N-LIP.				fatty acid catabolic process|transcription, DNA-dependent|triglyceride biosynthetic process|triglyceride mobilization	cytosol|endoplasmic reticulum membrane	phosphatidate phosphatase activity			ovary(2)|large_intestine(1)|skin(1)	4	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.11)|OV - Ovarian serous cystadenocarcinoma(76;0.173)		GGCCACCTCCCCCATCCTGTC	0.517													5	47	---	---	---	---	PASS
ALK	238	broad.mit.edu	37	2	29416082	29416082	+	3'UTR	SNP	G	T	T			TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:29416082G>T	uc002rmy.2	-	29					ALK_uc010ymo.1_3'UTR	NM_004304	NP_004295	Q9UM73	ALK_HUMAN	anaplastic lymphoma kinase precursor						protein autophosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|protein binding|transmembrane receptor protein tyrosine kinase activity		NPM1/ALK(632)|EML4/ALK(246)|CLTC/ALK(44)|TPM3/ALK(33)|ATIC/ALK(24)|RANBP2/ALK(16)|TPM4/ALK(12)|TFG/ALK(7)|MSN/ALK(6)|CARS/ALK(5)|VCL/ALK(4)|KIF5B/ALK(4)|PPFIBP1/ALK(3)|SEC31A/ALK(3)|SQSTM1/ALK(2)	haematopoietic_and_lymphoid_tissue(726)|lung(262)|autonomic_ganglia(148)|soft_tissue(61)|breast(4)|kidney(4)|large_intestine(3)|skin(3)|ovary(3)|thyroid(2)|central_nervous_system(1)|pancreas(1)	1218	Acute lymphoblastic leukemia(172;0.155)				Adenosine triphosphate(DB00171)	GTGAGTGTGCGACCGAGCTCA	0.517			T|Mis|A	NPM1|TPM3|TFG|TPM4|ATIC|CLTC|MSN|ALO17|CARS|EML4	ALCL|NSCLC|Neuroblastoma	neuroblastoma			Neuroblastoma_Familial_Clustering_of|Congenital_Central_Hypoventilation_Syndrome				10	27	---	---	---	---	PASS
MRPS5	64969	broad.mit.edu	37	2	95780928	95780928	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:95780928T>C	uc002sub.2	-	3	378	c.160A>G	c.(160-162)ACC>GCC	p.T54A	MRPS5_uc002suc.2_RNA|MRPS5_uc010yud.1_Missense_Mutation_p.T54A	NM_031902	NP_114108	P82675	RT05_HUMAN	mitochondrial ribosomal protein S5	54					translation	mitochondrion|ribosome	protein binding|RNA binding|structural constituent of ribosome			ovary(2)|central_nervous_system(1)	3						GTGTCTCTGGTTCCCAGTGAT	0.463											OREG0014795	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	9	81	---	---	---	---	PASS
RNPEPL1	57140	broad.mit.edu	37	2	241516160	241516160	+	Silent	SNP	G	A	A			TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:241516160G>A	uc002vzi.2	+	9	1619	c.1026G>A	c.(1024-1026)CTG>CTA	p.L342L	RNPEPL1_uc010fzf.2_Silent_p.L248L|RNPEPL1_uc002vzj.2_5'UTR	NM_018226	NP_060696	Q9HAU8	RNPL1_HUMAN	arginyl aminopeptidase (aminopeptidase B)-like	342					leukotriene biosynthetic process|proteolysis		aminopeptidase activity|metallopeptidase activity|zinc ion binding			large_intestine(1)|skin(1)	2		all_epithelial(40;1.13e-11)|Breast(86;0.000169)|Renal(207;0.00571)|Ovarian(221;0.104)|all_hematologic(139;0.182)|all_lung(227;0.204)|Melanoma(123;0.238)		Epithelial(32;3.05e-31)|all cancers(36;8.2e-29)|OV - Ovarian serous cystadenocarcinoma(60;8.55e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;5.12e-06)|Lung(119;0.00168)|Colorectal(34;0.005)|LUSC - Lung squamous cell carcinoma(224;0.00813)|COAD - Colon adenocarcinoma(134;0.0322)		ACCGGCTCCTGGATGGGTCCC	0.692													24	60	---	---	---	---	PASS
COL7A1	1294	broad.mit.edu	37	3	48612153	48612153	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:48612153C>A	uc003ctz.2	-	77	6351	c.6350G>T	c.(6349-6351)GGG>GTG	p.G2117V		NM_000094	NP_000085	Q02388	CO7A1_HUMAN	alpha 1 type VII collagen precursor	2117	Triple-helical region.				cell adhesion|epidermis development	basement membrane|collagen type VII	protein binding|serine-type endopeptidase inhibitor activity			ovary(4)|breast(3)|skin(3)|central_nervous_system(1)	11				BRCA - Breast invasive adenocarcinoma(193;0.000293)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		GCCCGGCTCCCCCTGTGGGGA	0.607													4	43	---	---	---	---	PASS
PBRM1	55193	broad.mit.edu	37	3	52621446	52621446	+	Nonsense_Mutation	SNP	C	A	A			TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52621446C>A	uc003des.2	-	19	3058	c.3046G>T	c.(3046-3048)GAA>TAA	p.E1016*	PBRM1_uc003dex.2_RNA|PBRM1_uc003deq.2_Nonsense_Mutation_p.E1016*|PBRM1_uc003der.2_Nonsense_Mutation_p.E984*|PBRM1_uc003det.2_Nonsense_Mutation_p.E1031*|PBRM1_uc003deu.2_Nonsense_Mutation_p.E1031*|PBRM1_uc003dev.2_RNA|PBRM1_uc003dew.2_Nonsense_Mutation_p.E1016*|PBRM1_uc010hmk.1_Nonsense_Mutation_p.E991*|PBRM1_uc003dey.2_Nonsense_Mutation_p.E991*|PBRM1_uc003dez.1_Nonsense_Mutation_p.E1015*|PBRM1_uc003dfb.1_Nonsense_Mutation_p.E928*|PBRM1_uc003dfa.1_Nonsense_Mutation_p.E362*	NM_181042	NP_060635	Q86U86	PB1_HUMAN	polybromo 1 isoform 4	1016	BAH 1.				chromatin remodeling|mitosis|negative regulation of cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear chromosome	chromatin binding|DNA binding|protein binding			kidney(136)|breast(4)	140				BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)		TTAAAAACTTCTTTTTCTAGA	0.378			Mis|N|F|S|D|O		clear cell renal carcinoma|breast								9	36	---	---	---	---	PASS
GAP43	2596	broad.mit.edu	37	3	115439677	115439677	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:115439677G>C	uc003ebq.2	+	3	1051	c.665G>C	c.(664-666)CGG>CCG	p.R222P	GAP43_uc003ebr.2_Missense_Mutation_p.R258P	NM_002045	NP_002036	P17677	NEUM_HUMAN	growth associated protein 43 isoform 2	222					activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|cell differentiation|nervous system development|regulation of filopodium assembly|regulation of growth|response to wounding	cell junction|filopodium membrane|growth cone membrane|synapse	calmodulin binding			ovary(1)	1				GBM - Glioblastoma multiforme(114;0.164)		GAAAGTGCCCGGCAGGACGAG	0.478													8	195	---	---	---	---	PASS
TFDP2	7029	broad.mit.edu	37	3	141692908	141692908	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:141692908C>G	uc003eun.3	-	8	1024	c.645G>C	c.(643-645)CAG>CAC	p.Q215H	TFDP2_uc003euk.3_Missense_Mutation_p.Q128H|TFDP2_uc010hur.2_Missense_Mutation_p.Q155H|TFDP2_uc003eul.3_Missense_Mutation_p.Q155H|TFDP2_uc011bnf.1_Missense_Mutation_p.Q118H|TFDP2_uc011bng.1_Missense_Mutation_p.Q79H|TFDP2_uc003eum.3_Missense_Mutation_p.Q155H	NM_006286	NP_006277	Q14188	TFDP2_HUMAN	transcription factor Dp-2 (E2F dimerization	215					cell cycle	transcription factor complex	DNA binding|protein domain specific binding|sequence-specific DNA binding transcription factor activity|transcription cofactor activity|transcription factor binding			kidney(1)	1						TCTGACATTCCTGAGCAGAAT	0.308													18	44	---	---	---	---	PASS
D4S234E	27065	broad.mit.edu	37	4	4389419	4389419	+	Silent	SNP	C	G	G			TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:4389419C>G	uc011bvz.1	+	5	1344	c.63C>G	c.(61-63)GGC>GGG	p.G21G	D4S234E_uc011bwa.1_Silent_p.G21G|D4S234E_uc003ghz.2_Silent_p.G21G|D4S234E_uc003gia.2_Silent_p.G21G|D4S234E_uc003gib.2_Silent_p.G21G	NM_014392	NP_055207	P42857	NSG1_HUMAN	brain neuron cytoplasmic protein 1	21	Cytoplasmic (Potential).				dopamine receptor signaling pathway	Golgi membrane|integral to membrane|nucleus	dopamine receptor binding			ovary(1)	1				UCEC - Uterine corpus endometrioid carcinoma (64;0.166)		TGGAGGATGGCTTCGACACCA	0.642													8	42	---	---	---	---	PASS
FER	2241	broad.mit.edu	37	5	108521914	108521914	+	Silent	SNP	A	G	G			TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:108521914A>G	uc003kop.1	+	19	2601	c.2217A>G	c.(2215-2217)TCA>TCG	p.S739S	FER_uc011cvg.1_Silent_p.S564S	NM_005246	NP_005237	P16591	FER_HUMAN	fer (fps/fes related) tyrosine kinase	739	Protein kinase.				intracellular signal transduction|peptidyl-tyrosine phosphorylation	cytoplasm|nucleus	ATP binding|non-membrane spanning protein tyrosine kinase activity			lung(2)|stomach(1)|ovary(1)|kidney(1)	5		all_cancers(142;2.86e-06)|all_epithelial(76;9.81e-08)|Prostate(80;0.00972)|Lung NSC(167;0.039)|Ovarian(225;0.0448)|all_lung(232;0.0496)|Colorectal(57;0.0986)|Breast(839;0.152)		OV - Ovarian serous cystadenocarcinoma(64;6.77e-10)|Epithelial(69;4.13e-08)|COAD - Colon adenocarcinoma(37;0.0174)		GATACAGTTCAGAGAGTGACG	0.473													10	132	---	---	---	---	PASS
FBXO38	81545	broad.mit.edu	37	5	147778625	147778625	+	Silent	SNP	G	A	A			TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:147778625G>A	uc003lpf.1	+	3	312	c.192G>A	c.(190-192)GTG>GTA	p.V64V	FBXO38_uc003lpg.1_Silent_p.V64V|FBXO38_uc003lph.2_Silent_p.V64V	NM_205836	NP_995308	Q6PIJ6	FBX38_HUMAN	F-box protein 38 isoform b	64	Interaction with KLF7 (By similarity).|F-box.					cytoplasm|nucleus				ovary(4)|skin(2)	6			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AGGAAGCAGTGACCCTATATC	0.453													14	72	---	---	---	---	PASS
ZNF184	7738	broad.mit.edu	37	6	27420021	27420021	+	Silent	SNP	A	G	G			TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:27420021A>G	uc003njj.2	-	5	2128	c.1317T>C	c.(1315-1317)ACT>ACC	p.T439T	ZNF184_uc010jqv.2_Silent_p.T439T|ZNF184_uc003nji.2_Silent_p.T439T	NM_007149	NP_009080	Q99676	ZN184_HUMAN	zinc finger protein 184	439	C2H2-type 8.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1						CCCCAGTATGAGTTTTTTGAT	0.413													5	85	---	---	---	---	PASS
OR5V1	81696	broad.mit.edu	37	6	29323588	29323588	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:29323588G>A	uc011dlo.1	-	1	467	c.385C>T	c.(385-387)CCT>TCT	p.P129S		NM_030876	NP_110503	Q9UGF6	OR5V1_HUMAN	olfactory receptor, family 5, subfamily V,	129	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(3)|kidney(1)	4						TACCTTAAAGGATTGCAGATT	0.428													6	62	---	---	---	---	PASS
LY6G6C	80740	broad.mit.edu	37	6	31686821	31686821	+	3'UTR	SNP	G	A	A			TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31686821G>A	uc003nwh.2	-	3					LY6G6C_uc010jtd.2_RNA	NM_025261	NP_079537	O95867	LY66C_HUMAN	lymphocyte antigen 6 complex G6C precursor							anchored to membrane|plasma membrane					0						GACACAGGGAGAGAGGCTCAG	0.542													7	29	---	---	---	---	PASS
DAXX	1616	broad.mit.edu	37	6	33289504	33289504	+	Missense_Mutation	SNP	A	T	T			TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33289504A>T	uc003oec.2	-	2	403	c.199T>A	c.(199-201)TTC>ATC	p.F67I	DAXX_uc011drd.1_Intron|DAXX_uc011dre.1_Missense_Mutation_p.F79I|DAXX_uc003oed.2_Missense_Mutation_p.F67I|DAXX_uc010juw.2_5'UTR	NM_001350	NP_001341	Q9UER7	DAXX_HUMAN	death-domain associated protein isoform a	67	Necessary for interaction with USP7.				activation of JUN kinase activity|androgen receptor signaling pathway|apoptosis|induction of apoptosis via death domain receptors|interspecies interaction between organisms|negative regulation of transcription, DNA-dependent|regulation of protein ubiquitination|transcription, DNA-dependent	chromosome, centromeric region|cytosol|nucleolus|PML body	androgen receptor binding|heat shock protein binding|p53 binding|protein homodimerization activity|protein N-terminus binding|receptor signaling protein activity|transcription factor binding|ubiquitin protein ligase binding			pancreas(18)|ovary(2)|skin(2)|prostate(1)	23						ACCTCTTCGAACAGCTTCTCA	0.468			Mis|F|N		Pancreatic neuroendocrine tumors								50	245	---	---	---	---	PASS
BACH2	60468	broad.mit.edu	37	6	90647879	90647879	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90647879C>T	uc011eab.1	-	8	2836	c.2027G>A	c.(2026-2028)TGT>TAT	p.C676Y	BACH2_uc003pnw.2_Missense_Mutation_p.C676Y	NM_021813	NP_068585	Q9BYV9	BACH2_HUMAN	BTB and CNC homology 1, basic leucine zipper	676	Leucine-zipper.					nucleus	protein dimerization activity|sequence-specific DNA binding			ovary(3)|pancreas(1)|lung(1)|skin(1)	6		all_cancers(76;7.37e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.0063)		BRCA - Breast invasive adenocarcinoma(108;0.0799)		GCGGATTTCACATTCTAAATT	0.458													8	89	---	---	---	---	PASS
LOC402644	402644	broad.mit.edu	37	7	28319099	28319099	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:28319099C>T	uc010kuz.1	-	1	220	c.220G>A	c.(220-222)GGT>AGT	p.G74S		NM_001126493	NP_001119965			hypothetical protein LOC402644												0						GACTTGCCACCAGTGCCATTA	0.453													8	44	---	---	---	---	PASS
CASD1	64921	broad.mit.edu	37	7	94164833	94164833	+	Missense_Mutation	SNP	A	C	C			TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:94164833A>C	uc003uni.3	+	8	1068	c.841A>C	c.(841-843)ACT>CCT	p.T281P	CASD1_uc003unh.2_Intron|CASD1_uc003unj.3_Missense_Mutation_p.T281P	NM_022900	NP_075051	Q96PB1	CASD1_HUMAN	CAS1 domain containing 1 precursor	281						integral to membrane				ovary(2)	2	all_cancers(62;6.71e-10)|all_epithelial(64;5e-09)|Lung NSC(181;0.188)|all_lung(186;0.215)		STAD - Stomach adenocarcinoma(171;0.0031)			GAGCAGAGAAACTGTGAGAAA	0.299													4	56	---	---	---	---	PASS
ZAN	7455	broad.mit.edu	37	7	100395076	100395076	+	Silent	SNP	G	A	A			TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100395076G>A	uc003uwj.2	+	47	8520	c.8355G>A	c.(8353-8355)ACG>ACA	p.T2785T	ZAN_uc003uwk.2_Silent_p.T2694T|ZAN_uc003uwl.2_RNA|ZAN_uc010lhh.2_RNA|ZAN_uc010lhi.2_RNA|ZAN_uc011kke.1_Silent_p.T734T	NM_003386	NP_003377	Q9Y493	ZAN_HUMAN	zonadhesin isoform 3	2785	VWFC 5.|Cytoplasmic (Potential).				binding of sperm to zona pellucida|cell-cell adhesion	integral to membrane|plasma membrane				ovary(4)|large_intestine(3)|central_nervous_system(2)|pancreas(2)	11	Lung NSC(181;0.041)|all_lung(186;0.0581)		STAD - Stomach adenocarcinoma(171;0.19)			TTTACAGAACGAGGAGGAAGA	0.617													3	28	---	---	---	---	PASS
SERPINE1	5054	broad.mit.edu	37	7	100778823	100778823	+	Silent	SNP	G	A	A			TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100778823G>A	uc003uxt.2	+	6	1096	c.948G>A	c.(946-948)CTG>CTA	p.L316L	SERPINE1_uc011kkj.1_Silent_p.L301L|SERPINE1_uc003uxu.1_3'UTR	NM_000602	NP_000593	P05121	PAI1_HUMAN	plasminogen activator inhibitor-1 isoform 1	316					angiogenesis|cellular response to chemical stimulus|cellular response to lipopolysaccharide|chronological cell aging|defense response to Gram-negative bacterium|fibrinolysis|negative regulation of apoptosis|negative regulation of cell adhesion mediated by integrin|negative regulation of fibrinolysis|negative regulation of plasminogen activation|negative regulation of smooth muscle cell migration|negative regulation of smooth muscle cell-matrix adhesion|negative regulation of vascular wound healing|platelet activation|platelet degranulation|positive regulation of angiogenesis|positive regulation of interleukin-8 production|positive regulation of leukotriene production involved in inflammatory response|positive regulation of monocyte chemotaxis|positive regulation of receptor-mediated endocytosis|regulation of receptor activity	extracellular matrix|extracellular space|plasma membrane|platelet alpha granule lumen	protease binding|serine-type endopeptidase inhibitor activity			ovary(1)|lung(1)|central_nervous_system(1)	3	Lung NSC(181;0.136)|all_lung(186;0.182)				Atorvastatin(DB01076)|Dimethyl sulfoxide(DB01093)|Drotrecogin alfa(DB00055)|Simvastatin(DB00641)|Tenecteplase(DB00031)|Troglitazone(DB00197)|Urokinase(DB00013)	TAGAGAACCTGGGAATGACCG	0.557													8	104	---	---	---	---	PASS
PTPRZ1	5803	broad.mit.edu	37	7	121651006	121651006	+	Missense_Mutation	SNP	T	A	A			TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:121651006T>A	uc003vjy.2	+	12	2301	c.1906T>A	c.(1906-1908)TCA>ACA	p.S636T	PTPRZ1_uc003vjz.2_Missense_Mutation_p.S636T|PTPRZ1_uc011knt.1_Missense_Mutation_p.S86T	NM_002851	NP_002842	P23471	PTPRZ_HUMAN	protein tyrosine phosphatase, receptor-type,	636	Extracellular (Potential).				central nervous system development	integral to plasma membrane	protein binding|protein tyrosine/threonine phosphatase activity|transmembrane receptor protein tyrosine phosphatase activity			ovary(3)|large_intestine(2)|lung(2)|central_nervous_system(1)|kidney(1)	9						AGATTCAACTTCATCAGGTTC	0.418													15	37	---	---	---	---	PASS
PTPRZ1	5803	broad.mit.edu	37	7	121651023	121651023	+	Missense_Mutation	SNP	A	T	T			TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:121651023A>T	uc003vjy.2	+	12	2318	c.1923A>T	c.(1921-1923)GAA>GAT	p.E641D	PTPRZ1_uc003vjz.2_Missense_Mutation_p.E641D|PTPRZ1_uc011knt.1_Missense_Mutation_p.E91D	NM_002851	NP_002842	P23471	PTPRZ_HUMAN	protein tyrosine phosphatase, receptor-type,	641	Extracellular (Potential).				central nervous system development	integral to plasma membrane	protein binding|protein tyrosine/threonine phosphatase activity|transmembrane receptor protein tyrosine phosphatase activity			ovary(3)|large_intestine(2)|lung(2)|central_nervous_system(1)|kidney(1)	9						GTTCAGAAGAATCACTAAAGG	0.428													15	37	---	---	---	---	PASS
CASP2	835	broad.mit.edu	37	7	143000899	143000899	+	Missense_Mutation	SNP	C	A	A	rs145619760		TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:143000899C>A	uc003wco.2	+	9	1137	c.990C>A	c.(988-990)GAC>GAA	p.D330E	CASP2_uc003wcp.2_3'UTR|CASP2_uc011kta.1_Missense_Mutation_p.D214E|CASP2_uc003wcq.2_RNA|CASP2_uc011ktb.1_Missense_Mutation_p.D80E	NM_032982	NP_116764	P42575	CASP2_HUMAN	caspase 2 isoform 1 preproprotein	330					apoptosis|cellular response to mechanical stimulus|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|protein maturation by peptide bond cleavage	cytosol	cysteine-type endopeptidase activity|enzyme binding|protein binding|protein domain specific binding			lung(2)|ovary(1)	3	Melanoma(164;0.059)					GTGGGGTTGACCAACAAGATG	0.522													3	15	---	---	---	---	PASS
AGPAT5	55326	broad.mit.edu	37	8	6612685	6612685	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:6612685A>G	uc003wqo.2	+	7	1171	c.859A>G	c.(859-861)ATC>GTC	p.I287V	AGPAT5_uc011kwm.1_3'UTR	NM_018361	NP_060831	Q9NUQ2	PLCE_HUMAN	1-acylglycerol-3-phosphate O-acyltransferase 5	287					phospholipid biosynthetic process	integral to membrane|mitochondrion	1-acylglycerol-3-phosphate O-acyltransferase activity				0			STAD - Stomach adenocarcinoma(24;0.0578)	READ - Rectum adenocarcinoma(644;0.156)|COAD - Colon adenocarcinoma(149;0.191)		ACGTTTCGAAATCAAAGATAA	0.353													4	34	---	---	---	---	PASS
ZNF395	55893	broad.mit.edu	37	8	28209116	28209116	+	Missense_Mutation	SNP	A	T	T			TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:28209116A>T	uc003xgq.2	-	7	1217	c.1129T>A	c.(1129-1131)TCC>ACC	p.S377T	ZNF395_uc003xgt.2_Missense_Mutation_p.S377T|ZNF395_uc003xgr.2_Missense_Mutation_p.S377T|ZNF395_uc003xgs.2_Missense_Mutation_p.S377T	NM_018660	NP_061130	Q9H8N7	ZN395_HUMAN	zinc finger protein 395	377					transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|zinc ion binding				0		Ovarian(32;2.06e-05)		KIRC - Kidney renal clear cell carcinoma(542;0.102)|Kidney(114;0.123)|Colorectal(74;0.142)		TCTGGGCCGGAGGACTGGGCT	0.637													40	123	---	---	---	---	PASS
EBAG9	9166	broad.mit.edu	37	8	110576864	110576864	+	3'UTR	SNP	G	C	C			TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:110576864G>C	uc003ynf.2	+	7					EBAG9_uc003yng.2_3'UTR	NM_198120	NP_936056	O00559	RCAS1_HUMAN	estrogen receptor binding site associated						apoptosis|regulation of cell growth	focal adhesion|Golgi membrane|integral to membrane|soluble fraction	apoptotic protease activator activity				0			OV - Ovarian serous cystadenocarcinoma(57;1.39e-14)			ATGGATTTAAGAGTATTTTAA	0.368													4	52	---	---	---	---	PASS
SEC16A	9919	broad.mit.edu	37	9	139369367	139369367	+	Missense_Mutation	SNP	T	A	A			TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:139369367T>A	uc004chx.2	-	3	3010	c.2701A>T	c.(2701-2703)AGT>TGT	p.S901C	SEC16A_uc004chv.3_Intron|SEC16A_uc004chw.2_Missense_Mutation_p.S901C|SEC16A_uc010nbn.2_Missense_Mutation_p.S901C|SEC16A_uc010nbo.1_Missense_Mutation_p.S901C	NM_014866	NP_055681	O15027	SC16A_HUMAN	SEC16 homolog A	723					protein transport|vesicle-mediated transport	endoplasmic reticulum membrane|Golgi membrane					0		Myeloproliferative disorder(178;0.0511)		Epithelial(140;2.9e-06)|OV - Ovarian serous cystadenocarcinoma(145;5.88e-06)		TGGGCAACACTGCTAGGCAGA	0.502													6	30	---	---	---	---	PASS
EPC1	80314	broad.mit.edu	37	10	32635831	32635831	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:32635831A>G	uc001iwg.1	-	1	283	c.13T>C	c.(13-15)TCG>CCG	p.S5P	EPC1_uc001iwi.3_Intron|EPC1_uc009xlt.2_Intron|EPC1_uc001iwh.1_Missense_Mutation_p.S5P	NM_025209	NP_079485	Q9H2F5	EPC1_HUMAN	enhancer of polycomb 1	5					histone H2A acetylation|histone H4 acetylation|negative regulation of gene expression, epigenetic|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|regulation of growth|transcription, DNA-dependent	NuA4 histone acetyltransferase complex|nuclear membrane|Piccolo NuA4 histone acetyltransferase complex				ovary(3)|central_nervous_system(1)	4		Prostate(175;0.0199)				GCCCGAAACGACAGTTTACTC	0.647													4	48	---	---	---	---	PASS
PLAU	5328	broad.mit.edu	37	10	75675037	75675037	+	Missense_Mutation	SNP	A	T	T			TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:75675037A>T	uc001jwa.2	+	10	1145	c.999A>T	c.(997-999)AAA>AAT	p.K333N	C10orf55_uc001jvz.1_Intron|PLAU_uc010qkw.1_Missense_Mutation_p.K316N|PLAU_uc010qkx.1_Missense_Mutation_p.K247N|PLAU_uc001jwb.2_RNA|PLAU_uc001jwc.2_Missense_Mutation_p.K333N|PLAU_uc009xrq.1_Missense_Mutation_p.K297N	NM_002658	NP_002649	P00749	UROK_HUMAN	plasminogen activator, urokinase isoform 1	333	Peptidase S1.				blood coagulation|chemotaxis|fibrinolysis|proteolysis|regulation of cell adhesion mediated by integrin|regulation of receptor activity|regulation of smooth muscle cell migration|regulation of smooth muscle cell-matrix adhesion|signal transduction	cell surface|extracellular space|plasma membrane	serine-type endopeptidase activity			ovary(2)|kidney(1)	3	Prostate(51;0.0112)				Amiloride(DB00594)|Urokinase(DB00013)	AGCAGCTGAAAATGACTGTTG	0.527													9	71	---	---	---	---	PASS
C10orf91	170393	broad.mit.edu	37	10	134261287	134261287	+	Silent	SNP	C	T	T			TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:134261287C>T	uc001llm.2	+	3	200	c.160C>T	c.(160-162)CTG>TTG	p.L54L		NM_173541	NP_775812	Q5T1B1	CJ091_HUMAN	hypothetical protein LOC170393	54										ovary(1)	1		all_cancers(35;6.69e-12)|all_epithelial(44;1.55e-08)|Lung NSC(174;0.000845)|all_lung(145;0.00144)|all_neural(114;0.0299)|Breast(234;0.106)|Colorectal(31;0.109)|Melanoma(40;0.123)|Glioma(114;0.203)|all_hematologic(284;0.224)		OV - Ovarian serous cystadenocarcinoma(35;6.95e-05)|Epithelial(32;0.000142)|all cancers(32;0.000162)		TCTCAGCTTCCTGTTCACAGA	0.537													16	129	---	---	---	---	PASS
LSP1	4046	broad.mit.edu	37	11	1908746	1908746	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1908746C>T	uc001lui.2	+	10	1148	c.973C>T	c.(973-975)CAT>TAT	p.H325Y	LSP1_uc001luj.2_Missense_Mutation_p.H453Y|LSP1_uc001luk.2_Missense_Mutation_p.H263Y|LSP1_uc001lul.2_Missense_Mutation_p.H263Y|LSP1_uc001lum.2_Missense_Mutation_p.H263Y	NM_002339	NP_002330	P33241	LSP1_HUMAN	lymphocyte-specific protein 1 isoform 1	325					cellular component movement|cellular defense response	actin cytoskeleton|Golgi apparatus|plasma membrane	actin binding|signal transducer activity			large_intestine(1)	1		all_epithelial(84;0.000138)|Breast(177;0.000962)|Ovarian(85;0.0014)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00147)|Lung(200;0.0729)|LUSC - Lung squamous cell carcinoma(625;0.0856)		GGCCACCGGGCATGGGAAGTA	0.572													12	45	---	---	---	---	PASS
IGSF22	283284	broad.mit.edu	37	11	18738373	18738373	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:18738373G>A	uc009yht.2	-	10	1338	c.1148C>T	c.(1147-1149)ACG>ATG	p.T383M	IGSF22_uc001mpa.2_RNA	NM_173588	NP_775859	Q8N9C0	IGS22_HUMAN	immunoglobulin superfamily, member 22	383										ovary(4)|large_intestine(2)|kidney(1)	7						AAGCGTGTGCGTCAGACCATC	0.527													10	132	---	---	---	---	PASS
OR10AG1	282770	broad.mit.edu	37	11	55735328	55735328	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55735328C>A	uc010rit.1	-	1	612	c.612G>T	c.(610-612)TTG>TTT	p.L204F		NM_001005491	NP_001005491	Q8NH19	O10AG_HUMAN	olfactory receptor, family 10, subfamily AG,	204	Helical; Name=5; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(2)	2	Esophageal squamous(21;0.0137)					AGACAACAATCAACAGAAATG	0.418													8	34	---	---	---	---	PASS
OR4D6	219983	broad.mit.edu	37	11	59224931	59224931	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:59224931C>A	uc010rku.1	+	1	498	c.498C>A	c.(496-498)TTC>TTA	p.F166L		NM_001004708	NP_001004708	Q8NGJ1	OR4D6_HUMAN	olfactory receptor, family 4, subfamily D,	166	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1						TGCTTCCATTCCCCTTCTGTG	0.502													8	126	---	---	---	---	PASS
C11orf84	144097	broad.mit.edu	37	11	63594357	63594357	+	Intron	SNP	G	C	C			TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:63594357G>C	uc001nxt.2	+						C11orf84_uc001nxu.1_RNA	NM_138471	NP_612480	Q9BUA3	CK084_HUMAN	hypothetical protein LOC144097												0						GTGGTGGGGTGTCTGGGGGGC	0.632													3	11	---	---	---	---	PASS
KAT5	10524	broad.mit.edu	37	11	65484261	65484261	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65484261G>T	uc001ofi.2	+	10	1304	c.1054G>T	c.(1054-1056)GTG>TTG	p.V352L	KAT5_uc001ofj.2_Missense_Mutation_p.V300L|KAT5_uc001ofk.2_Missense_Mutation_p.V385L|KAT5_uc010roo.1_Missense_Mutation_p.V333L|KAT5_uc001ofl.2_Missense_Mutation_p.V141L	NM_006388	NP_006379	Q92993	KAT5_HUMAN	K(lysine) acetyltransferase 5 isoform 2	352					androgen receptor signaling pathway|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|double-strand break repair|interspecies interaction between organisms|negative regulation of interleukin-2 production|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|regulation of growth|transcription, DNA-dependent	NuA4 histone acetyltransferase complex|nucleolus|perinuclear region of cytoplasm|Piccolo NuA4 histone acetyltransferase complex	androgen receptor binding|histone acetyltransferase activity|metal ion binding|repressing transcription factor binding|transcription coactivator activity				0						CTTCCACATCGTGGGCTACTT	0.532													6	133	---	---	---	---	PASS
TEX12	56158	broad.mit.edu	37	11	112039968	112039968	+	Intron	SNP	C	T	T			TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:112039968C>T	uc001pnc.2	+						TEX12_uc001pnd.2_5'UTR	NM_031275	NP_112565	Q9BXU0	TEX12_HUMAN	testis expressed sequence 12												0		all_cancers(61;5.7e-14)|all_epithelial(67;3.4e-08)|Melanoma(852;8.81e-06)|all_hematologic(158;0.000405)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0112)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		Epithelial(105;1.2e-06)|BRCA - Breast invasive adenocarcinoma(274;1.4e-06)|all cancers(92;1.97e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0512)		TTGTTCTAAGCTTTGTAGCTG	0.433													15	92	---	---	---	---	PASS
AEBP2	121536	broad.mit.edu	37	12	19593226	19593226	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:19593226C>A	uc001ref.2	+	1	619	c.593C>A	c.(592-594)GCG>GAG	p.A198E	AEBP2_uc001ree.2_Missense_Mutation_p.A198E|AEBP2_uc001reg.1_5'Flank	NM_001114176	NP_001107648	Q6ZN18	AEBP2_HUMAN	AE binding protein 2 isoform b	198	Ser-rich.|Gly-rich.				chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	ESC/E(Z) complex	DNA binding|zinc ion binding			ovary(1)	1	Acute lymphoblastic leukemia(4;0.000455)|all_hematologic(4;0.00804)|Esophageal squamous(101;0.143)					ggaagcagcgCGACCTCCGGG	0.338													4	8	---	---	---	---	PASS
SLCO1B1	10599	broad.mit.edu	37	12	21331930	21331930	+	Missense_Mutation	SNP	G	A	A	rs147421160		TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:21331930G>A	uc001req.3	+	7	807	c.703G>A	c.(703-705)GTG>ATG	p.V235M		NM_006446	NP_006437	Q9Y6L6	SO1B1_HUMAN	solute carrier organic anion transporter family,	235	Helical; Name=5; (Potential).				bile acid metabolic process|sodium-independent organic anion transport	basolateral plasma membrane|integral to plasma membrane|membrane fraction	bile acid transmembrane transporter activity|sodium-independent organic anion transmembrane transporter activity|thyroid hormone transmembrane transporter activity			ovary(3)|skin(3)|pancreas(1)|central_nervous_system(1)	8					Digoxin(DB00390)|Gemfibrozil(DB01241)|Pravastatin(DB00175)	TAAAATGTACGTGGATATTGG	0.328													19	82	---	---	---	---	PASS
BAZ2A	11176	broad.mit.edu	37	12	57007904	57007904	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57007904T>C	uc001slq.1	-	4	949	c.755A>G	c.(754-756)TAC>TGC	p.Y252C	BAZ2A_uc001slp.1_Missense_Mutation_p.Y250C|BAZ2A_uc009zow.1_Missense_Mutation_p.Y220C	NM_013449	NP_038477	Q9UIF9	BAZ2A_HUMAN	bromodomain adjacent to zinc finger domain, 2A	252					chromatin silencing at rDNA|DNA methylation|transcription, DNA-dependent	chromatin silencing complex|nucleolus|rDNA heterochromatin	DNA binding|histone acetyl-lysine binding|ligand-dependent nuclear receptor binding|RNA binding|zinc ion binding				0						AGAGCCATTGTAGCCACACAT	0.453													4	27	---	---	---	---	PASS
AVPR1A	552	broad.mit.edu	37	12	63543859	63543859	+	Nonsense_Mutation	SNP	G	T	T			TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:63543859G>T	uc001sro.1	-	1	2732	c.758C>A	c.(757-759)TCG>TAG	p.S253*		NM_000706	NP_000697	P37288	V1AR_HUMAN	arginine vasopressin receptor 1A	253	Cytoplasmic (Potential).				activation of phospholipase C activity|elevation of cytosolic calcium ion concentration|generation of precursor metabolites and energy	endosome|integral to plasma membrane	protein kinase C binding|vasopressin receptor activity				0			BRCA - Breast invasive adenocarcinoma(9;0.193)	GBM - Glioblastoma multiforme(28;0.0569)	Conivaptan(DB00872)|Desmopressin(DB00035)|Felypressin(DB00093)|Terlipressin(DB02638)|Vasopressin(DB00067)	GCTCTGGCGCGACGCCGTCTT	0.617													34	150	---	---	---	---	PASS
COQ5	84274	broad.mit.edu	37	12	120966769	120966769	+	Missense_Mutation	SNP	A	T	T			TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120966769A>T	uc001tyn.2	-	1	196	c.176T>A	c.(175-177)GTG>GAG	p.V59E	COQ5_uc001tyo.2_5'UTR|COQ5_uc010szj.1_Missense_Mutation_p.V59E	NM_032314	NP_115690	Q5HYK3	COQ5_HUMAN	coenzyme Q5 homolog, methyltransferase	59					ubiquinone biosynthetic process	mitochondrion	methyltransferase activity			ovary(1)	1	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					CTCTTCCGACACAGTCTCAAA	0.597													16	81	---	---	---	---	PASS
FAM123A	219287	broad.mit.edu	37	13	25744223	25744223	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:25744223T>C	uc001uqb.2	-	1	1635	c.1535A>G	c.(1534-1536)GAG>GGG	p.E512G	FAM123A_uc001uqa.2_Missense_Mutation_p.E393G|FAM123A_uc001uqc.2_Missense_Mutation_p.E393G	NM_152704	NP_689917	Q8N7J2	F123A_HUMAN	hypothetical protein LOC219287 isoform 1	512										ovary(2)|large_intestine(1)|lung(1)	4		Lung SC(185;0.0225)|Breast(139;0.0602)		all cancers(112;0.0071)|Epithelial(112;0.0398)|OV - Ovarian serous cystadenocarcinoma(117;0.151)|GBM - Glioblastoma multiforme(144;0.222)|Lung(94;0.241)		TTCCTGCTGCTCCTTCTCCGG	0.657													13	58	---	---	---	---	PASS
FOXO1	2308	broad.mit.edu	37	13	41134652	41134652	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:41134652C>G	uc001uxl.3	-	2	1361	c.976G>C	c.(976-978)GGG>CGG	p.G326R	FOXO1_uc010acc.1_Missense_Mutation_p.G141R	NM_002015	NP_002006	Q12778	FOXO1_HUMAN	forkhead box O1	326					anti-apoptosis|blood vessel development|embryo development|endocrine pancreas development|insulin receptor signaling pathway|negative regulation of stress-activated MAPK cascade|nerve growth factor receptor signaling pathway|pattern specification process|phosphatidylinositol-mediated signaling|positive regulation of transcription from RNA polymerase II promoter|regulation of cell proliferation|regulation of sequence-specific DNA binding transcription factor activity|response to DNA damage stimulus|tissue development	cytosol|transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|protein kinase binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription factor binding		PAX3/FOXO1(749)|PAX7/FOXO1(197)	soft_tissue(946)|lung(1)|central_nervous_system(1)	948		Lung NSC(96;1.18e-05)|Breast(139;0.00394)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(188;0.194)		all cancers(112;7.32e-09)|Epithelial(112;2.87e-06)|OV - Ovarian serous cystadenocarcinoma(117;6.98e-05)|GBM - Glioblastoma multiforme(144;0.00394)|BRCA - Breast invasive adenocarcinoma(63;0.0815)		GAGAGTCTCCCACTAATAGTA	0.483													7	78	---	---	---	---	PASS
AP1G2	8906	broad.mit.edu	37	14	24035666	24035666	+	Intron	SNP	G	C	C			TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24035666G>C	uc001wkl.2	-						AP1G2_uc001wkj.2_Intron|AP1G2_uc001wkk.3_Intron|AP1G2_uc001wkn.2_Intron|uc001wko.1_RNA|AP1G2_uc001wkp.1_5'Flank|AP1G2_uc010tnp.1_Intron|AP1G2_uc010aks.2_Intron|AP1G2_uc010akt.2_Intron|AP1G2_uc010tnq.1_Intron	NM_003917	NP_003908	O75843	AP1G2_HUMAN	adaptor-related protein complex 1, gamma 2						interspecies interaction between organisms|intracellular protein transport|vesicle-mediated transport	AP-1 adaptor complex|endosome membrane	protein binding|protein transporter activity			ovary(1)	1	all_cancers(95;0.000251)			GBM - Glioblastoma multiforme(265;0.00672)		AAACCTCTGAGAAAATCAGTC	0.542													13	111	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	14	28734092	28734092	+	Silent	SNP	G	A	A			TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:28734092G>A	uc001wqd.2	+	1	473	c.333G>A	c.(331-333)AAG>AAA	p.K111K						SubName: Full=cDNA FLJ60537, highly similar to BCL2/adenovirus E1B 19 kDa protein-interacting protein 3;																		GCATCTTGAAGAAAAACTCAG	0.463													3	50	---	---	---	---	PASS
MAX	4149	broad.mit.edu	37	14	65569055	65569055	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:65569055C>A	uc001xif.1	-	1	173	c.3G>T	c.(1-3)ATG>ATT	p.M1I	MAX_uc001xic.1_Missense_Mutation_p.M1I|MAX_uc001xie.1_Missense_Mutation_p.M1I|MAX_uc010aql.1_Missense_Mutation_p.M1I|MAX_uc001xig.1_Missense_Mutation_p.M1I|MAX_uc001xih.1_RNA|MAX_uc001xii.1_Missense_Mutation_p.M1I|MAX_uc001xij.1_Missense_Mutation_p.M1I|MAX_uc001xik.2_Missense_Mutation_p.M1I	NM_002382	NP_002373	P61244	MAX_HUMAN	MAX protein isoform a	1					transcription from RNA polymerase II promoter	cytoplasm|MLL1 complex	sequence-specific DNA binding transcription factor activity|transcription coactivator activity			lung(1)	1				all cancers(60;0.000776)|OV - Ovarian serous cystadenocarcinoma(108;0.00359)|BRCA - Breast invasive adenocarcinoma(234;0.00999)		CGTTATCGCTCATTTCCTACG	0.552													4	19	---	---	---	---	PASS
KIAA1409	57578	broad.mit.edu	37	14	94088412	94088412	+	Silent	SNP	C	A	A			TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:94088412C>A	uc001ybv.1	+	28	4451	c.4368C>A	c.(4366-4368)TCC>TCA	p.S1456S	KIAA1409_uc001ybs.1_Silent_p.S1434S	NM_020818	NP_065869	Q9P2D8	UNC79_HUMAN	hypothetical protein LOC57578	1611						integral to membrane				ovary(10)|skin(4)|large_intestine(3)	17		all_cancers(154;0.0354)|all_epithelial(191;0.216)		Epithelial(152;0.188)		TAGATCTATCCTCAGATTCAA	0.463													12	51	---	---	---	---	PASS
SERPINA12	145264	broad.mit.edu	37	14	94964360	94964360	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:94964360C>A	uc001ydj.2	-	3	1171	c.375G>T	c.(373-375)CAG>CAT	p.Q125H		NM_173850	NP_776249	Q8IW75	SPA12_HUMAN	serine (or cysteine) proteinase inhibitor, clade	125					regulation of proteolysis	extracellular region	serine-type endopeptidase inhibitor activity			central_nervous_system(2)|ovary(1)|lung(1)	4				COAD - Colon adenocarcinoma(157;0.235)		CCTGGGTCTTCTGGGTCAGCT	0.488													26	63	---	---	---	---	PASS
LOC646214	646214	broad.mit.edu	37	15	21937594	21937594	+	RNA	SNP	G	C	C			TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:21937594G>C	uc010tzj.1	-	1		c.3146C>G				NR_027053				Homo sapiens mRNA for p21-activated kinase 2 variant protein.												0						GGCAATAATGGGAGGGGCAGT	0.502													5	85	---	---	---	---	PASS
MTMR15	22909	broad.mit.edu	37	15	31220813	31220813	+	Missense_Mutation	SNP	T	G	G			TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:31220813T>G	uc001zff.2	+	11	2837	c.2546T>G	c.(2545-2547)ATC>AGC	p.I849S	MTMR15_uc001zfe.2_Missense_Mutation_p.I454S	NM_014967	NP_055782	Q9Y2M0	FAN1_HUMAN	myotubularin related protein 15 isoform a	849					double-strand break repair via homologous recombination|nucleotide-excision repair, DNA incision	nucleus	5'-3' exonuclease activity|5'-flap endonuclease activity|DNA binding|magnesium ion binding|phosphodiesterase I activity|ubiquitin binding				0		all_lung(180;2.23e-09)		all cancers(64;4.72e-15)|Epithelial(43;5.4e-11)|GBM - Glioblastoma multiforme(186;0.000136)|BRCA - Breast invasive adenocarcinoma(123;0.00402)|Lung(196;0.168)		CTGTGGGACATCATCTTCATG	0.478								Direct_reversal_of_damage|Editing_and_processing_nucleases					11	166	---	---	---	---	PASS
JMJD7-PLA2G4B	8681	broad.mit.edu	37	15	42136439	42136439	+	Intron	SNP	A	G	G			TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42136439A>G	uc010bco.2	+						JMJD7-PLA2G4B_uc001zoo.3_Intron|JMJD7-PLA2G4B_uc010bcn.2_Intron|JMJD7-PLA2G4B_uc001zoq.3_Intron|JMJD7-PLA2G4B_uc001zor.1_5'UTR	NM_001114633	NP_001108105	P0C869	PA24B_HUMAN	phospholipase A2, group IVB						arachidonic acid metabolic process|calcium-mediated signaling|glycerophospholipid catabolic process|inflammatory response|parturition	cytosol|early endosome membrane|extracellular region|mitochondrial membrane	calcium ion binding|calcium-dependent phospholipase A2 activity|calcium-dependent phospholipid binding|lysophospholipase activity			large_intestine(1)	1						CAAGGAGATGAGGCTCAGAAC	0.592													3	11	---	---	---	---	PASS
UBR1	197131	broad.mit.edu	37	15	43281101	43281101	+	Nonsense_Mutation	SNP	C	A	A			TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43281101C>A	uc001zqq.2	-	35	3979	c.3913G>T	c.(3913-3915)GGA>TGA	p.G1305*		NM_174916	NP_777576	Q8IWV7	UBR1_HUMAN	ubiquitin protein ligase E3 component n-recognin	1305					cellular response to leucine|negative regulation of TOR signaling cascade	cytosol	leucine binding|zinc ion binding			lung(1)	1		all_cancers(109;4.32e-15)|all_epithelial(112;4.05e-13)|Lung NSC(122;1.75e-08)|all_lung(180;2e-07)|Melanoma(134;0.0179)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;4.08e-07)|COAD - Colon adenocarcinoma(120;0.185)|Colorectal(105;0.214)		ACTTTCAATCCAATTCTATAA	0.368													13	62	---	---	---	---	PASS
MYO5C	55930	broad.mit.edu	37	15	52539694	52539694	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:52539694C>G	uc010bff.2	-	15	1979	c.1842G>C	c.(1840-1842)AAG>AAC	p.K614N	MYO5C_uc010uga.1_RNA|MYO5C_uc010ugb.1_RNA	NM_018728	NP_061198	Q9NQX4	MYO5C_HUMAN	myosin VC	614	Myosin head-like.					myosin complex	actin binding|ATP binding|calmodulin binding|motor activity			ovary(7)|central_nervous_system(3)|large_intestine(2)|skin(2)	14				all cancers(107;0.0137)		TGCTGTTTGGCTTGATGACTT	0.478													23	57	---	---	---	---	PASS
IREB2	3658	broad.mit.edu	37	15	78778167	78778167	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:78778167A>G	uc002bdr.2	+	13	1856	c.1694A>G	c.(1693-1695)TAT>TGT	p.Y565C	IREB2_uc010unb.1_Missense_Mutation_p.Y315C	NM_004136	NP_004127	P48200	IREB2_HUMAN	iron-responsive element binding protein 2	565							4 iron, 4 sulfur cluster binding|metal ion binding|protein binding				0				UCEC - Uterine corpus endometrioid carcinoma (272;0.232)		GTATTACCATATCTAAGTAAG	0.393													8	101	---	---	---	---	PASS
KLHL25	64410	broad.mit.edu	37	15	86311567	86311567	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:86311567C>A	uc002bly.2	-	2	1678	c.1475G>T	c.(1474-1476)AGC>ATC	p.S492I		NM_022480	NP_071925	Q9H0H3	ENC2_HUMAN	BTB/POZ KELCH domain protein	492	Kelch 4.					cytoplasm				ovary(2)	2						GAAGATCTGGCTGCCCAGGAC	0.612													11	83	---	---	---	---	PASS
SPNS1	83985	broad.mit.edu	37	16	28993800	28993800	+	Silent	SNP	C	T	T			TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:28993800C>T	uc010vdi.1	+	9	1229	c.1089C>T	c.(1087-1089)CTC>CTT	p.L363L	uc010vct.1_Intron|SPNS1_uc002drx.2_Silent_p.L290L|SPNS1_uc002dsa.2_Silent_p.L363L|SPNS1_uc002drz.2_Silent_p.L311L|SPNS1_uc010byp.2_Silent_p.L289L|SPNS1_uc010byq.1_Silent_p.L295L|LAT_uc010vdj.1_5'Flank|LAT_uc002dsb.2_5'Flank|LAT_uc002dsd.2_5'Flank|LAT_uc002dsc.2_5'Flank|LAT_uc010vdk.1_5'Flank|LAT_uc010vdl.1_5'Flank	NM_001142448	NP_001135920	Q9H2V7	SPNS1_HUMAN	spinster homolog 1 isoform 1	363	Helical; (Potential).				lipid transport|transmembrane transport	integral to membrane|mitochondrial inner membrane	protein binding				0						CCACTGGCCTCCTGGGCTCTG	0.577													38	71	---	---	---	---	PASS
RNF40	9810	broad.mit.edu	37	16	30774777	30774777	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30774777G>T	uc002dzq.2	+	4	462	c.339G>T	c.(337-339)GAG>GAT	p.E113D	C16orf93_uc002dzm.2_5'Flank|C16orf93_uc002dzn.2_5'Flank|C16orf93_uc002dzo.2_5'Flank|C16orf93_uc002dzp.2_5'Flank|RNF40_uc010caa.2_Missense_Mutation_p.E113D|RNF40_uc010cab.2_Missense_Mutation_p.E113D|RNF40_uc010vfa.1_Intron|RNF40_uc002dzr.2_Missense_Mutation_p.E113D|RNF40_uc010vfb.1_Intron	NM_014771	NP_055586	O75150	BRE1B_HUMAN	ring finger protein 40	113				E->Q: Abolishes interaction with RB1.	histone H2B ubiquitination|histone monoubiquitination|ubiquitin-dependent protein catabolic process	nucleus|synaptosome|ubiquitin ligase complex	protein homodimerization activity|ubiquitin protein ligase binding|zinc ion binding			central_nervous_system(1)	1			Colorectal(24;0.198)			GATGCCATGAGAGCCAGGGGG	0.542													16	84	---	---	---	---	PASS
PKD1L2	114780	broad.mit.edu	37	16	81183400	81183400	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:81183400C>A	uc002fgh.1	-	28	4648	c.4648G>T	c.(4648-4650)GTC>TTC	p.V1550F	PKD1L2_uc002fgg.1_RNA	NM_052892	NP_443124	Q7Z442	PK1L2_HUMAN	polycystin 1-like 2 isoform a	1550	Cytoplasmic (Potential).				neuropeptide signaling pathway	integral to membrane	calcium ion binding|ion channel activity|sugar binding			ovary(1)|central_nervous_system(1)|pancreas(1)	3						ACCCTCTGGACGCGGGTGAAG	0.587													3	28	---	---	---	---	PASS
CD300E	342510	broad.mit.edu	37	17	72613272	72613272	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:72613272C>T	uc002jlb.1	-	2	414	c.373G>A	c.(373-375)GTG>ATG	p.V125M		NM_181449	NP_852114	Q496F6	CLM2_HUMAN	CD300e molecule precursor	125	Extracellular (Potential).					integral to membrane|plasma membrane	receptor activity			skin(2)|large_intestine(1)|ovary(1)	4						GAAACATACACCCTAACCAGG	0.547													6	62	---	---	---	---	PASS
BAIAP2	10458	broad.mit.edu	37	17	79027521	79027521	+	Silent	SNP	G	A	A			TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79027521G>A	uc002jzg.2	+	2	216	c.108G>A	c.(106-108)AAG>AAA	p.K36K	BAIAP2_uc002jyz.3_Silent_p.K36K|BAIAP2_uc002jza.2_Silent_p.K36K|BAIAP2_uc002jzc.2_Silent_p.K36K|BAIAP2_uc002jzb.2_5'UTR|BAIAP2_uc002jzd.2_Silent_p.K36K|BAIAP2_uc002jzf.2_Silent_p.K36K|BAIAP2_uc002jze.2_Silent_p.K69K|BAIAP2_uc010wuh.1_Intron	NM_017451	NP_059345	Q9UQB8	BAIP2_HUMAN	BAI1-associated protein 2 isoform 2	36	IMD.				axonogenesis|filopodium assembly|insulin receptor signaling pathway|regulation of actin cytoskeleton organization|response to bacterium	cell junction|cytoskeleton|cytosol|filopodium|nucleus|ruffle	cytoskeletal adaptor activity|proline-rich region binding|protein C-terminus binding|SH3 domain binding				0	all_neural(118;0.101)		BRCA - Breast invasive adenocarcinoma(99;0.0228)|OV - Ovarian serous cystadenocarcinoma(97;0.0524)			CCATGGGGAAGAATTACGAGA	0.612													8	83	---	---	---	---	PASS
PHLPP1	23239	broad.mit.edu	37	18	60646514	60646514	+	Silent	SNP	G	A	A			TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:60646514G>A	uc002lis.2	+	18	3646	c.3468G>A	c.(3466-3468)CCG>CCA	p.P1156P		NM_194449	NP_919431	O60346	PHLP1_HUMAN	PH domain and leucine rich repeat protein	1668					apoptosis|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling	cytosol|membrane|nucleus	metal ion binding|protein serine/threonine phosphatase activity				0						TCATACCCCCGGAGCTGGAAG	0.343													2	7	---	---	---	---	PASS
ABCA7	10347	broad.mit.edu	37	19	1054031	1054031	+	Missense_Mutation	SNP	A	T	T			TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1054031A>T	uc002lqw.3	+	26	3730	c.3499A>T	c.(3499-3501)ACA>TCA	p.T1167S	ABCA7_uc010dsb.1_Missense_Mutation_p.T1029S|ABCA7_uc002lqy.2_5'Flank	NM_019112	NP_061985	Q8IZY2	ABCA7_HUMAN	ATP-binding cassette, sub-family A, member 7	1167					phagocytosis|transmembrane transport	ATP-binding cassette (ABC) transporter complex|endosome membrane|Golgi membrane|integral to membrane|plasma membrane	ATP binding|ATPase activity|transporter activity			pancreas(7)|ovary(1)|central_nervous_system(1)	9		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)		GCACCTATGCACAGGCATTGC	0.592													20	68	---	---	---	---	PASS
TMIGD2	126259	broad.mit.edu	37	19	4294619	4294619	+	Silent	SNP	A	C	C			TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4294619A>C	uc002lzx.1	-	4	553	c.507T>G	c.(505-507)GGT>GGG	p.G169G	TMIGD2_uc010dtv.1_Silent_p.G169G	NM_144615	NP_653216	Q96BF3	TMIG2_HUMAN	transmembrane and immunoglobulin domain	169	Helical; (Potential).					integral to membrane					0				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0339)|STAD - Stomach adenocarcinoma(1328;0.18)		AGAACCAGGCACCCCACACGA	0.627													12	93	---	---	---	---	PASS
TIMM44	10469	broad.mit.edu	37	19	7997527	7997527	+	Silent	SNP	G	A	A			TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7997527G>A	uc002miz.2	-	9	974	c.972C>T	c.(970-972)ATC>ATT	p.I324I	TIMM44_uc002mja.2_Silent_p.I64I|TIMM44_uc010dvx.1_RNA	NM_006351	NP_006342	O43615	TIM44_HUMAN	translocase of inner mitochondrial membrane 44	324					protein targeting to mitochondrion	mitochondrial inner membrane presequence translocase complex|mitochondrial matrix	ATP binding|P-P-bond-hydrolysis-driven protein transmembrane transporter activity			ovary(1)	1						GGACATTGGGGATGATGTCGT	0.652													6	99	---	---	---	---	PASS
POLD1	5424	broad.mit.edu	37	19	50918766	50918766	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50918766C>A	uc002psb.3	+	21	2692	c.2636C>A	c.(2635-2637)TCC>TAC	p.S879Y	POLD1_uc002psc.3_Missense_Mutation_p.S879Y|POLD1_uc010enx.2_RNA|POLD1_uc010eny.2_Missense_Mutation_p.S905Y	NM_002691	NP_002682	P28340	DPOD1_HUMAN	DNA-directed DNA polymerase delta 1	879					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)		ATCGATATCTCCCAGCTGGTC	0.682								DNA_polymerases_(catalytic_subunits)					13	21	---	---	---	---	PASS
PEG3	5178	broad.mit.edu	37	19	57325907	57325907	+	Silent	SNP	T	G	G			TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57325907T>G	uc002qnu.2	-	7	4254	c.3903A>C	c.(3901-3903)GTA>GTC	p.V1301V	ZIM2_uc010ygq.1_Intron|ZIM2_uc010ygr.1_Intron|ZIM2_uc002qnr.2_Intron|ZIM2_uc002qnq.2_Intron|ZIM2_uc010etp.2_Intron|ZIM2_uc010ygs.1_Intron|PEG3_uc002qnt.2_Silent_p.V1272V|PEG3_uc002qnv.2_Silent_p.V1301V|PEG3_uc002qnw.2_Silent_p.V1177V|PEG3_uc002qnx.2_Silent_p.V1175V|PEG3_uc010etr.2_Silent_p.V1301V	NM_001146186	NP_001139658	Q9GZU2	PEG3_HUMAN	paternally expressed 3 isoform 1	1301	C2H2-type 9.				apoptosis|viral reproduction	cytoplasm|nucleus	nucleic acid binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(7)|skin(2)|upper_aerodigestive_tract(1)|large_intestine(1)|pancreas(1)	12		Colorectal(82;0.000256)|all_neural(62;0.103)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0269)		TATGAACAGTTACGTGATCTG	0.458													18	40	---	---	---	---	PASS
ZNF154	7710	broad.mit.edu	37	19	58213740	58213740	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58213740C>G	uc010euf.2	-	3	817	c.577G>C	c.(577-579)GAG>CAG	p.E193Q	ZNF776_uc002qpx.2_Intron|ZNF154_uc002qpy.2_RNA	NM_001085384	NP_001078853	Q13106	ZN154_HUMAN	zinc finger protein 154	193	C2H2-type 4.					nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0257)		TTCCCACACTCTCGACATTCA	0.423													8	130	---	---	---	---	PASS
CHMP2A	27243	broad.mit.edu	37	19	59065512	59065512	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:59065512T>C	uc002qti.2	-	1	494	c.68A>G	c.(67-69)AAC>AGC	p.N23S	CHMP2A_uc002qtj.2_Missense_Mutation_p.N23S|CHMP2A_uc002qtk.2_Missense_Mutation_p.N23S	NM_198426	NP_940818	O43633	CHM2A_HUMAN	chromatin modifying protein 2A	23	Potential.				cellular membrane organization|endosome transport|protein transport	cytosol|late endosome membrane	protein domain specific binding				0		all_cancers(17;4.4e-22)|all_epithelial(17;2.15e-16)|Lung NSC(17;1.24e-06)|all_lung(17;5.41e-06)|Colorectal(82;3.46e-05)|Renal(17;0.00179)|all_neural(62;0.00607)|Ovarian(87;0.0443)|Breast(46;0.0928)|Medulloblastoma(540;0.184)		UCEC - Uterine corpus endometrioid carcinoma (67;0.0434)|all cancers(4;1.39e-13)|Epithelial(4;1.01e-10)|OV - Ovarian serous cystadenocarcinoma(4;2.34e-09)|GBM - Glioblastoma multiforme(193;0.0102)|Lung(386;0.179)		CATGGCACGGTTCAGGGCCCT	0.572													6	140	---	---	---	---	PASS
PAK7	57144	broad.mit.edu	37	20	9520102	9520102	+	3'UTR	SNP	C	T	T			TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:9520102C>T	uc002wnl.2	-	11					PAK7_uc002wnk.2_3'UTR|PAK7_uc002wnj.2_3'UTR|PAK7_uc010gby.1_3'UTR	NM_020341	NP_065074	Q9P286	PAK7_HUMAN	p21-activated kinase 7								ATP binding|protein binding|protein serine/threonine kinase activity			lung(11)|skin(5)|central_nervous_system(3)|ovary(2)|large_intestine(1)|stomach(1)	23			COAD - Colon adenocarcinoma(9;0.194)			CTACACGAATCCTCTGCTCAG	0.483													16	172	---	---	---	---	PASS
CSF2RB	1439	broad.mit.edu	37	22	37326825	37326825	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:37326825C>G	uc003aqa.3	+	8	1182	c.965C>G	c.(964-966)TCT>TGT	p.S322C	CSF2RB_uc003aqc.3_Missense_Mutation_p.S328C	NM_000395	NP_000386	P32927	IL3RB_HUMAN	colony stimulating factor 2 receptor, beta	322	Extracellular (Potential).				respiratory gaseous exchange	granulocyte macrophage colony-stimulating factor receptor complex	cytokine receptor activity			skin(2)|pancreas(1)	3					Sargramostim(DB00020)	TACATCGTCTCTGTTCAGCCA	0.617													3	61	---	---	---	---	PASS
FOXR2	139628	broad.mit.edu	37	X	55650703	55650703	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:55650703G>C	uc004duo.2	+	1	871	c.559G>C	c.(559-561)GAG>CAG	p.E187Q		NM_198451	NP_940853	Q6PJQ5	FOXR2_HUMAN	forkhead box R2	187					embryo development|organ development|pattern specification process|regulation of sequence-specific DNA binding transcription factor activity|tissue development	transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding			lung(2)|central_nervous_system(1)	3						CAACAACCAAGAGAAGTCCTG	0.502													10	52	---	---	---	---	PASS
POF1B	79983	broad.mit.edu	37	X	84634493	84634493	+	5'UTR	SNP	T	A	A			TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:84634493T>A	uc004eer.2	-	2					POF1B_uc004ees.2_5'UTR	NM_024921	NP_079197	Q8WVV4	POF1B_HUMAN	premature ovarian failure, 1B								actin binding				0						ACCTCCCAGATGTTCTACCTA	0.413													7	26	---	---	---	---	PASS
ZDHHC9	51114	broad.mit.edu	37	X	128962964	128962964	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:128962964C>T	uc004euv.2	-	3	690	c.321G>A	c.(319-321)ATG>ATA	p.M107I	ZDHHC9_uc004euw.2_Missense_Mutation_p.M107I|ZDHHC9_uc004eux.1_Missense_Mutation_p.M107I|ZDHHC9_uc004euy.1_Missense_Mutation_p.M34I	NM_001008222	NP_001008223	Q9Y397	ZDHC9_HUMAN	zinc finger, DHHC domain containing 9	107	Cytoplasmic (Potential).					endoplasmic reticulum membrane|Golgi membrane|integral to membrane	acyltransferase activity|zinc ion binding			ovary(1)	1						CACCTATCTCCATTTCTATGA	0.468													19	107	---	---	---	---	PASS
TFDP3	51270	broad.mit.edu	37	X	132352095	132352095	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:132352095G>A	uc004exb.1	-	1	282	c.193C>T	c.(193-195)CCA>TCA	p.P65S		NM_016521	NP_057605	Q5H9I0	TFDP3_HUMAN	transcription factor Dp family, member 3	65						transcription factor complex	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1	Acute lymphoblastic leukemia(192;0.000127)					GATGCTGCTGGTCTCTGAGGC	0.552													7	57	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	11403	11403	+	RNA	SNP	G	A	A			TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:11403G>A	uc004cov.3	+	1		c.826G>A			uc004cow.1_5'Flank|uc004cox.3_5'Flank					Homo sapiens potential LAG1 interactor mRNA, partial cds.																		ACTCCACTTATGACTCCCTAA	0.443													6	19	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	13063	13063	+	RNA	SNP	G	A	A			TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:13063G>A	uc004cox.3	+	1		c.727G>A			uc004coy.2_5'Flank|uc004coz.1_5'Flank					Homo sapiens NADH dehydrogenase subunit 5 (MTND5) mRNA, RNA 5, complete cds; mitochondrial gene for mitochondrial product.																		GCCCCACCCCAGTCTCAGCCC	0.547													3	44	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	2	91801335	91801336	+	IGR	INS	-	CAATG	CAATG	rs56326147		TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:91801335_91801336insCAATG								None (None upstream) : LOC654342 (3856 downstream)																							tcatgactaccattagctccca	0.000													5	3	---	---	---	---	
PLEKHB2	55041	broad.mit.edu	37	2	131975813	131975814	+	Intron	INS	-	TGGGC	TGGGC			TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:131975813_131975814insTGGGC	uc002tsh.2	+						POTEE_uc002tsn.2_5'Flank|POTEE_uc002tsk.2_5'Flank|POTEE_uc002tsl.2_5'Flank			Q96CS7	PKHB2_HUMAN	SubName: Full=Putative uncharacterized protein PLEKHB2;							membrane	protein binding			ovary(2)	2				BRCA - Breast invasive adenocarcinoma(221;0.0828)		CCTGGGTGGGGTGGGCTGGGCT	0.619													3	6	---	---	---	---	
UGT2B4	7363	broad.mit.edu	37	4	70361791	70361792	+	5'Flank	INS	-	T	T	rs41299972		TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:70361791_70361792insT	uc003hek.3	-						UGT2B4_uc011cap.1_Intron|UGT2B4_uc003hel.3_5'Flank	NM_021139	NP_066962	P06133	UD2B4_HUMAN	UDP glucuronosyltransferase 2B4 precursor						estrogen catabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	glucuronosyltransferase activity			skin(2)	2						TTCTTTTTGGATTTTTTTTTTT	0.173													4	2	---	---	---	---	
CXCL9	4283	broad.mit.edu	37	4	76926198	76926198	+	Intron	DEL	T	-	-			TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:76926198delT	uc003hjh.1	-							NM_002416	NP_002407	Q07325	CXCL9_HUMAN	small inducible cytokine B9 precursor						cell-cell signaling|cellular defense response|chemotaxis|G-protein coupled receptor protein signaling pathway|immune response|inflammatory response	extracellular space	chemokine activity			ovary(1)	1			Lung(101;0.0809)|LUSC - Lung squamous cell carcinoma(112;0.0934)			ACTGGTTGAAttttttttttt	0.149													4	2	---	---	---	---	
NSUN2	54888	broad.mit.edu	37	5	6605703	6605703	+	Intron	DEL	G	-	-			TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:6605703delG	uc003jdu.2	-						NSUN2_uc003jds.2_5'Flank|NSUN2_uc003jdt.2_Intron|NSUN2_uc011cmk.1_Intron|NSUN2_uc003jdv.2_Intron	NM_017755	NP_060225	Q08J23	NSUN2_HUMAN	NOL1/NOP2/Sun domain family, member 2							cytoplasm|nucleolus	tRNA (cytosine-5-)-methyltransferase activity|tRNA binding			ovary(1)	1						AAACCTCCACGTAACATTTAT	0.463													6	4	---	---	---	---	
FAM151B	167555	broad.mit.edu	37	5	79796999	79797000	+	Intron	INS	-	T	T	rs76066273		TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:79796999_79797000insT	uc003kgv.1	+						FAM151B_uc010jal.1_Intron	NM_205548	NP_991111	Q6UXP7	F151B_HUMAN	hypothetical protein LOC167555												0		Lung NSC(167;0.0427)|all_lung(232;0.0464)|Ovarian(174;0.113)		OV - Ovarian serous cystadenocarcinoma(54;8.21e-47)|Epithelial(54;8.3e-42)|all cancers(79;1.97e-36)		cacctggctaattttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	170261080	170261082	+	IGR	DEL	CAT	-	-	rs111380690		TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:170261080_170261082delCAT								GABRP (20032 upstream) : RANBP17 (27940 downstream)																							ccaccatcaccatcaccaccacc	0.118													6	3	---	---	---	---	
TFR2	7036	broad.mit.edu	37	7	100230357	100230357	+	Intron	DEL	G	-	-			TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100230357delG	uc003uvv.1	-						TFR2_uc010lhc.1_Intron|TFR2_uc003uvu.1_Intron	NM_003227	NP_003218	Q9UP52	TFR2_HUMAN	transferrin receptor 2						cellular iron ion homeostasis|iron ion transport|proteolysis	cytoplasm|integral to plasma membrane	peptidase activity|transferrin receptor activity			ovary(1)|pancreas(1)	2	Lung NSC(181;0.0261)|all_lung(186;0.0392)|Esophageal squamous(72;0.0439)					aaaaaaaaaagaacctttttt	0.000													4	3	---	---	---	---	
RASA4	10156	broad.mit.edu	37	7	102246649	102246649	+	Intron	DEL	C	-	-			TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:102246649delC	uc003vae.2	-						UPK3BL_uc003uzy.2_Intron|RASA4_uc011kla.1_Intron|RASA4_uc010lig.2_Intron|RASA4_uc003vaf.2_Intron|RASA4_uc011klb.1_Intron|RASA4_uc010lih.2_Intron|RASA4_uc011kld.1_Intron	NM_006989	NP_008920	O43374	RASL2_HUMAN	RAS p21 protein activator 4 isoform 1						intracellular signal transduction|negative regulation of Ras protein signal transduction	cytosol|intrinsic to internal side of plasma membrane	metal ion binding|Ras GTPase activator activity				0						aagtcagtgacctggggcctg	0.090													3	3	---	---	---	---	
IFRD1	3475	broad.mit.edu	37	7	112113100	112113123	+	Intron	DEL	TGTGTGTGTGTGTGTGTGTGTGTA	-	-	rs141635606	by1000genomes	TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:112113100_112113123delTGTGTGTGTGTGTGTGTGTGTGTA	uc003vgh.2	+						IFRD1_uc011kmn.1_Intron|IFRD1_uc003vgj.2_Intron|IFRD1_uc011kmo.1_Intron|IFRD1_uc011kmp.1_Intron|IFRD1_uc003vgk.2_Intron	NM_001007245	NP_001007246	O00458	IFRD1_HUMAN	interferon-related developmental regulator 1						multicellular organismal development|myoblast cell fate determination		binding			kidney(1)|central_nervous_system(1)	2						tgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtatatatgtgtc	0.210													4	2	---	---	---	---	
ST7	7982	broad.mit.edu	37	7	116778443	116778444	+	Intron	INS	-	T	T			TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:116778443_116778444insT	uc003vin.2	+						ST7_uc011knl.1_Intron|ST7_uc003vio.2_Intron|ST7_uc003viq.2_Intron|ST7_uc011knm.1_Intron|ST7_uc003vir.2_Intron|ST7OT2_uc003viu.2_Intron|ST7_uc011knn.1_Intron|ST7OT2_uc003viw.2_Intron|ST7_uc003vix.1_Intron	NM_021908	NP_068708	Q9NRC1	ST7_HUMAN	suppression of tumorigenicity 7 isoform b							integral to membrane	binding			central_nervous_system(1)|skin(1)	2	all_cancers(3;3.88e-07)|all_epithelial(6;3.42e-07)|Lung NSC(10;0.00072)|all_lung(10;0.000847)		STAD - Stomach adenocarcinoma(10;0.000512)	LUSC - Lung squamous cell carcinoma(290;0.133)		GGGCCTCTGTATTTTTTTTTTT	0.366													4	2	---	---	---	---	
ASZ1	136991	broad.mit.edu	37	7	117020837	117020838	+	Intron	INS	-	AAAAAC	AAAAAC	rs147516910	by1000genomes	TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:117020837_117020838insAAAAAC	uc003vjb.2	-						ASZ1_uc011kno.1_Intron|ASZ1_uc011knp.1_Intron	NM_130768	NP_570124	Q8WWH4	ASZ1_HUMAN	ankyrin repeat, SAM and basic leucine zipper						cell differentiation|DNA methylation involved in gamete generation|gene silencing by RNA|male meiosis|multicellular organismal development|piRNA metabolic process|spermatogenesis	pi-body	signal transducer activity			central_nervous_system(2)|ovary(1)	3	Lung NSC(10;0.00156)|all_lung(10;0.00175)		STAD - Stomach adenocarcinoma(10;0.000512)			GACAATCTGAAAAAAACAAAAA	0.282													9	6	---	---	---	---	
AGK	55750	broad.mit.edu	37	7	141321396	141321397	+	Intron	DEL	GA	-	-			TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:141321396_141321397delGA	uc003vwi.2	+						AGK_uc011krg.1_Intron	NM_018238	NP_060708	Q53H12	AGK_HUMAN	acylglycerol kinase precursor						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway	mitochondrial membrane	acylglycerol kinase activity|ATP binding|diacylglycerol kinase activity|NAD+ kinase activity			ovary(1)|breast(1)	2	Melanoma(164;0.0171)					gaaggagggggagagagagaga	0.228													4	2	---	---	---	---	
DPP6	1804	broad.mit.edu	37	7	154681143	154681143	+	Intron	DEL	T	-	-			TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:154681143delT	uc003wlk.2	+						DPP6_uc003wli.2_Intron|DPP6_uc003wlm.2_Intron|DPP6_uc011kvq.1_Intron	NM_130797	NP_570629	P42658	DPP6_HUMAN	dipeptidyl-peptidase 6 isoform 1						cell death|proteolysis	integral to membrane	dipeptidyl-peptidase activity|serine-type peptidase activity			pancreas(3)|breast(1)	4	all_neural(206;0.181)	all_hematologic(28;0.0044)|all_lung(21;0.0176)|Lung NSC(21;0.0204)	OV - Ovarian serous cystadenocarcinoma(82;0.0562)			TCTTCCTCTCTTTTTTTTTTT	0.383													6	3	---	---	---	---	
FAM135B	51059	broad.mit.edu	37	8	139207744	139207748	+	Intron	DEL	TGGAC	-	-	rs71956584		TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139207744_139207748delTGGAC	uc003yuy.2	-						FAM135B_uc003yux.2_Intron|FAM135B_uc003yuz.2_Intron	NM_015912	NP_056996	Q49AJ0	F135B_HUMAN	hypothetical protein LOC51059											ovary(7)|skin(2)	9	all_epithelial(106;8.29e-14)|Lung NSC(106;6.88e-06)|all_lung(105;1.44e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0805)			ATTGGAGCCATGGACTGGACTGAGC	0.444										HNSCC(54;0.14)			4	3	---	---	---	---	
ZNF462	58499	broad.mit.edu	37	9	109692789	109692798	+	Intron	DEL	CCACTGTATT	-	-			TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:109692789_109692798delCCACTGTATT	uc004bcz.2	+						ZNF462_uc010mto.2_Intron|ZNF462_uc004bda.2_Intron|ZNF462_uc011lvz.1_5'Flank	NM_021224	NP_067047	Q96JM2	ZN462_HUMAN	zinc finger protein 462						transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(5)	5						CTGATGGCTACCACTGTATTTTACCAGCCT	0.419													10	5	---	---	---	---	
WAC	51322	broad.mit.edu	37	10	28824816	28824817	+	Intron	INS	-	T	T	rs144095892	by1000genomes	TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:28824816_28824817insT	uc001iuf.2	+						WAC_uc001iud.2_Intron|WAC_uc001iue.2_Intron|WAC_uc009xlb.2_Intron|WAC_uc001iug.2_Intron|WAC_uc001iuh.2_Intron	NM_016628	NP_057712	Q9BTA9	WAC_HUMAN	WW domain-containing adapter with a coiled-coil						cell cycle checkpoint|histone H2B conserved C-terminal lysine ubiquitination|histone monoubiquitination|positive regulation of transcription, DNA-dependent|response to DNA damage stimulus|transcription, DNA-dependent	nuclear speck	chromatin binding|RNA polymerase II core binding			large_intestine(1)|ovary(1)	2						TAATCCTATCATTTTTTTTTTA	0.257													4	2	---	---	---	---	
DDX21	9188	broad.mit.edu	37	10	70730242	70730242	+	Intron	DEL	T	-	-			TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70730242delT	uc001jov.1	+						DDX21_uc001jow.1_Intron	NM_004728	NP_004719	Q9NR30	DDX21_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 21							nucleolus	ATP binding|ATP-dependent RNA helicase activity|protein binding|RNA binding			ovary(2)|kidney(1)	3						AGGAAGCTACttttttttttt	0.179													4	2	---	---	---	---	
CPN1	1369	broad.mit.edu	37	10	101816475	101816475	+	Intron	DEL	T	-	-			TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:101816475delT	uc001kql.2	-							NM_001308	NP_001299	P15169	CBPN_HUMAN	carboxypeptidase N, polypeptide 1 precursor						proteolysis	extracellular space	metallocarboxypeptidase activity|zinc ion binding			central_nervous_system(3)|pancreas(1)	4		Colorectal(252;0.234)		Epithelial(162;4.77e-10)|all cancers(201;3.82e-08)		cttggctatcttttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	122860416	122860417	+	IGR	INS	-	ATT	ATT			TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:122860416_122860417insATT								BSX (8037 upstream) : LOC341056 (27857 downstream)																							tggtggtggtgatggtgatggt	0.054													4	2	---	---	---	---	
KDM5A	5927	broad.mit.edu	37	12	415910	415910	+	Intron	DEL	A	-	-			TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:415910delA	uc001qif.1	-						KDM5A_uc001qie.1_Intron	NM_001042603	NP_001036068	P29375	KDM5A_HUMAN	retinoblastoma binding protein 2 isoform 1						chromatin modification|multicellular organismal development|positive regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	cytoplasm|nucleolus	DNA binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(2)|ovary(1)	3						ctccatctccaaaaaaaaaaa	0.124			T 	NUP98	AML								4	3	---	---	---	---	
SOAT2	8435	broad.mit.edu	37	12	53514402	53514403	+	Intron	INS	-	A	A	rs35658019		TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53514402_53514403insA	uc001sbv.2	+						SOAT2_uc009zms.2_Intron	NM_003578	NP_003569	O75908	SOAT2_HUMAN	acyl-CoA:cholesterol acyltransferase 2						cholesterol efflux|cholesterol esterification|cholesterol homeostasis|cholesterol metabolic process|macrophage derived foam cell differentiation|very-low-density lipoprotein particle assembly	brush border|endoplasmic reticulum membrane|integral to membrane|microsome	cholesterol binding|cholesterol O-acyltransferase activity|fatty-acyl-CoA binding			ovary(1)	1						cagcctgtctcaaaaaaaaaaa	0.193													6	3	---	---	---	---	
RXFP2	122042	broad.mit.edu	37	13	32360924	32360927	+	Intron	DEL	AAAT	-	-	rs3051238		TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:32360924_32360927delAAAT	uc001utt.2	+						RXFP2_uc010aba.2_Intron	NM_130806	NP_570718	Q8WXD0	RXFP2_HUMAN	relaxin/insulin-like family peptide receptor 2							integral to membrane|plasma membrane					0		Lung SC(185;0.0262)		all cancers(112;0.000559)|Epithelial(112;0.0017)|OV - Ovarian serous cystadenocarcinoma(117;0.0145)|BRCA - Breast invasive adenocarcinoma(63;0.0535)		ACTGAATGACAAATAAGCCTCATT	0.368													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	45168861	45168862	+	IGR	INS	-	T	T			TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:45168861_45168862insT								TSC22D1 (18160 upstream) : NUFIP1 (344522 downstream)																							TTTGTATTACCTTTTTTTTTTT	0.347													4	2	---	---	---	---	
GCHFR	2644	broad.mit.edu	37	15	41056072	41056072	+	5'Flank	DEL	C	-	-			TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41056072delC	uc001zmr.1	+						GCHFR_uc010ucr.1_5'Flank	NM_005258	NP_005249	P30047	GFRP_HUMAN	GTP cyclohydrolase I feedback regulatory						negative regulation of biosynthetic process|neurotransmitter metabolic process|nitric oxide biosynthetic process	cytosol|dendrite|melanosome|nuclear membrane				ovary(1)	1		all_cancers(109;3.3e-18)|all_epithelial(112;2.33e-15)|Lung NSC(122;5.34e-11)|all_lung(180;1.33e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)		GBM - Glioblastoma multiforme(113;2.58e-05)|COAD - Colon adenocarcinoma(120;0.149)|BRCA - Breast invasive adenocarcinoma(123;0.163)		GCCCCCTCCTCCCCGCACTCC	0.522													3	3	---	---	---	---	
CCDC78	124093	broad.mit.edu	37	16	773292	773292	+	Intron	DEL	C	-	-	rs67977308		TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:773292delC	uc002cjg.2	-						CCDC78_uc002cjf.2_Intron|CCDC78_uc002cji.3_3'UTR|CCDC78_uc002cjj.3_3'UTR|CCDC78_uc002cjh.2_Intron	NM_001031737	NP_001026907	A2IDD5	CCD78_HUMAN	coiled-coil domain containing 78											central_nervous_system(1)	1		Hepatocellular(780;0.0218)				GAGGCATGGGCCCCCCCCGTG	0.687													2	5	---	---	---	---	
LOC81691	81691	broad.mit.edu	37	16	20856634	20856634	+	Intron	DEL	T	-	-			TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:20856634delT	uc002dhv.2	+						ERI2_uc002dht.3_Intron|LOC81691_uc002dhx.2_Intron|LOC81691_uc002dhw.2_Intron|LOC81691_uc002dhy.3_Intron	NM_030941	NP_112203	Q96IC2	REXON_HUMAN	exonuclease NEF-sp isoform 1							nucleolus	exonuclease activity|nucleotide binding|RNA binding			ovary(1)|kidney(1)	2						TCCTTTAATCTTTTTTTTTTT	0.493													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	32437251	32437252	+	IGR	INS	-	C	C			TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32437251_32437252insC								HERC2P4 (273377 upstream) : TP53TG3B (247589 downstream)																							GACATTTTTTTCAAAATATTAA	0.282													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	74419892	74419892	+	Intron	DEL	T	-	-			TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:74419892delT	uc010vmt.1	+											RecName: Full=Nuclear pore complex-interacting protein-like 2; Flags: Precursor;																		cctttctctcttttttttttt	0.169													4	3	---	---	---	---	
RHBDF2	79651	broad.mit.edu	37	17	74476089	74476090	+	Intron	INS	-	TG	TG	rs138608987	by1000genomes	TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74476089_74476090insTG	uc002jrq.1	-						RHBDF2_uc002jrp.1_Intron|RHBDF2_uc002jrr.1_Intron|RHBDF2_uc010wtf.1_Intron|RHBDF2_uc002jrs.1_Intron	NM_024599	NP_078875	Q6PJF5	RHDF2_HUMAN	rhomboid, veinlet-like 6 isoform 1						negative regulation of protein secretion|protein transport|proteolysis	endoplasmic reticulum membrane|integral to membrane	growth factor binding|serine-type endopeptidase activity				0						tatatatataatgtgtgtgtgt	0.178													3	3	---	---	---	---	
NCLN	56926	broad.mit.edu	37	19	3192359	3192364	+	Intron	DEL	GGGCTG	-	-	rs11278022		TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3192359_3192364delGGGCTG	uc002lxi.2	+						NCLN_uc002lxh.1_Intron	NM_020170	NP_064555	Q969V3	NCLN_HUMAN	nicalin precursor						proteolysis|regulation of signal transduction	endoplasmic reticulum membrane|integral to membrane|nucleus	peptidase activity|protein binding				0		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.83e-113)|Epithelial(107;1.65e-111)|all cancers(105;1.53e-103)|BRCA - Breast invasive adenocarcinoma(158;0.00139)|STAD - Stomach adenocarcinoma(1328;0.18)		TCCAGGTTGTgggctggggctggggc	0.612													2	4	---	---	---	---	
C19orf10	56005	broad.mit.edu	37	19	4668862	4668862	+	Intron	DEL	T	-	-			TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4668862delT	uc002may.2	-							NM_019107	NP_061980	Q969H8	CS010_HUMAN	hypothetical protein LOC56005 precursor							ER-Golgi intermediate compartment|extracellular region					0		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.015)		acccgactaattttttttttt	0.000													4	2	---	---	---	---	
CALR3	125972	broad.mit.edu	37	19	16590240	16590241	+	Intron	INS	-	A	A	rs150170208		TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:16590240_16590241insA	uc002ned.2	-						MED26_uc002nee.2_Intron	NM_145046	NP_659483	Q96L12	CALR3_HUMAN	calreticulin 3 precursor						protein folding	endoplasmic reticulum lumen	calcium ion binding|sugar binding|unfolded protein binding				0						accaaaaatacaaaaaaaaaaa	0.000													5	3	---	---	---	---	
AKT2	208	broad.mit.edu	37	19	40761345	40761346	+	Intron	INS	-	GT	GT	rs138053162	by1000genomes	TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:40761345_40761346insGT	uc002onf.2	-						AKT2_uc010egs.2_Intron|AKT2_uc010egt.2_Intron|AKT2_uc010xvj.1_Intron|AKT2_uc010egu.1_Intron|AKT2_uc010xvk.1_Intron	NM_001626	NP_001617	P31751	AKT2_HUMAN	AKT2 kinase						insulin receptor signaling pathway|negative regulation of plasma membrane long-chain fatty acid transport|positive regulation of fatty acid beta-oxidation|positive regulation of glucose import|positive regulation of glycogen biosynthetic process	cytosol|nucleus	ATP binding|protein binding|protein serine/threonine kinase activity			lung(2)	2			Lung(22;0.000499)			ctcagggtctagtgtgtgtgtg	0.000			A		ovarian|pancreatic 								6	3	---	---	---	---	
COL9A3	1299	broad.mit.edu	37	20	61471746	61471747	+	Intron	INS	-	CT	CT	rs140852150	by1000genomes	TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:61471746_61471747insCT	uc002ydm.2	+						COL9A3_uc002ydn.2_Intron	NM_001853	NP_001844	Q14050	CO9A3_HUMAN	alpha 3 type IX collagen precursor						axon guidance	collagen type IX					0	Breast(26;5.68e-08)					CTTTGTGTGCCGTTCCCTCGGC	0.688													6	7	---	---	---	---	
IFNGR2	3460	broad.mit.edu	37	21	34793638	34793639	+	Intron	INS	-	A	A			TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:34793638_34793639insA	uc002yrp.3	+						IFNGR2_uc002yrq.3_Intron|IFNGR2_uc010gma.2_Intron|IFNGR2_uc002yrr.3_Intron	NM_005534	NP_005525	P38484	INGR2_HUMAN	interferon gamma receptor 2 precursor						regulation of interferon-gamma-mediated signaling pathway|response to virus	endoplasmic reticulum|integral to plasma membrane	interferon-gamma receptor activity				0					Interferon gamma-1b(DB00033)	aactccatctcaaaaaaaaaaa	0.163													6	4	---	---	---	---	
NF2	4771	broad.mit.edu	37	22	30073959	30073960	+	Intron	INS	-	TGAGGGA	TGAGGGA	rs150466339	by1000genomes	TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:30073959_30073960insTGAGGGA	uc003age.3	+						NF2_uc003afy.3_Intron|NF2_uc003afz.3_Intron|NF2_uc003agf.3_Intron|NF2_uc003agb.3_Intron|NF2_uc003agc.3_Intron|NF2_uc003agd.3_Intron|NF2_uc003agg.3_Intron|NF2_uc003aga.3_Intron|NF2_uc003agh.3_Intron|NF2_uc003agi.3_Intron|NF2_uc003agj.3_Intron|NF2_uc003agk.3_Intron|NF2_uc010gvp.2_Intron|NF2_uc011akq.1_Intron	NM_000268	NP_000259	P35240	MERL_HUMAN	neurofibromin 2 isoform 1						actin cytoskeleton organization|negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of cell-cell adhesion|negative regulation of cell-matrix adhesion|negative regulation of DNA replication|negative regulation of tyrosine phosphorylation of Stat3 protein|negative regulation of tyrosine phosphorylation of Stat5 protein|positive regulation of stress fiber assembly|regulation of hippo signaling cascade|Schwann cell proliferation	cytoskeleton|early endosome|extrinsic to membrane|filopodium membrane|nucleolus|perinuclear region of cytoplasm|ruffle membrane	cytoskeletal protein binding|protein binding	p.?(1)		meninges(372)|soft_tissue(284)|central_nervous_system(20)|kidney(10)|pleura(9)|skin(7)|large_intestine(5)|breast(5)|urinary_tract(3)|thyroid(2)|endometrium(2)|ovary(2)|lung(2)|stomach(2)|bone(2)|pituitary(1)	728						GGTTAGAGATTTGAGGGATGAT	0.361			D|Mis|N|F|S|O		meningioma|acoustic neuroma|renal 	meningioma|acoustic neuroma			Neurofibromatosis_type_2				6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	13483364	13483364	+	IGR	DEL	T	-	-			TCGA-CJ-4913-01A-01D-1429-08	TCGA-CJ-4913-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:13483364delT								None (None upstream) : None (None downstream)																							tctgtcacaattcccctttag	0.000													6	6	---	---	---	---	
