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
ATAD3A	55210	broad.mit.edu	37	1	1458925	1458925	+	Missense_Mutation	SNP	C	T	T	rs142299242	byFrequency	TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1458925C>T	uc001afz.1	+	9	1179	c.1085C>T	c.(1084-1086)GCG>GTG	p.A362V	ATAD3A_uc001aga.1_Missense_Mutation_p.A314V|ATAD3A_uc001agb.1_Missense_Mutation_p.A235V	NM_018188	NP_060658	Q9NVI7	ATD3A_HUMAN	ATPase family, AAA domain containing 3A	362							ATP binding|nucleoside-triphosphatase activity|protein binding			skin(1)	1	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;9.48e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)		Epithelial(90;1.12e-36)|OV - Ovarian serous cystadenocarcinoma(86;2.18e-22)|Colorectal(212;0.000164)|COAD - Colon adenocarcinoma(227;0.000195)|Kidney(185;0.00233)|BRCA - Breast invasive adenocarcinoma(365;0.00469)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0347)|Lung(427;0.147)		CCCCAGGACGCGCTGGAGGGT	0.711													4	58	---	---	---	---	PASS
TNFRSF14	8764	broad.mit.edu	37	1	2490091	2490091	+	Intron	SNP	C	G	G			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:2490091C>G	uc001ajr.2	+						TNFRSF14_uc010nzc.1_Intron|TNFRSF14_uc009vlf.1_Intron|TNFRSF14_uc001ajt.1_5'UTR|TNFRSF14_uc001ajs.2_Intron|LOC115110_uc010nzb.1_5'Flank	NM_003820	NP_003811	Q92956	TNR14_HUMAN	tumor necrosis factor receptor superfamily,						immune response|interspecies interaction between organisms|T cell costimulation		tumor necrosis factor receptor activity			kidney(1)	1	all_cancers(77;0.000158)|all_epithelial(69;8.01e-05)|all_lung(157;0.0212)|Lung NSC(156;0.0376)|Ovarian(185;0.0634)	all_epithelial(116;3.18e-20)|all_lung(118;1.67e-08)|Lung NSC(185;2.69e-06)|Breast(487;0.00147)|Renal(390;0.00183)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.0847)|Medulloblastoma(700;0.123)		Epithelial(90;1.1e-37)|OV - Ovarian serous cystadenocarcinoma(86;6.02e-23)|GBM - Glioblastoma multiforme(42;1.11e-08)|Colorectal(212;3.94e-05)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.000326)|BRCA - Breast invasive adenocarcinoma(365;0.00435)|KIRC - Kidney renal clear cell carcinoma(229;0.00544)|STAD - Stomach adenocarcinoma(132;0.00644)|Lung(427;0.199)		CGGCCCCCGTCCACCTCTGTC	0.677			Mis|N|F		follicular lymphoma								5	15	---	---	---	---	PASS
H6PD	9563	broad.mit.edu	37	1	9324048	9324048	+	Missense_Mutation	SNP	G	T	T	rs141034012		TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:9324048G>T	uc001apt.2	+	5	1769	c.1496G>T	c.(1495-1497)CGC>CTC	p.R499L		NM_004285	NP_004276	O95479	G6PE_HUMAN	hexose-6-phosphate dehydrogenase precursor	499	Glucose 1-dehydrogenase.					endoplasmic reticulum lumen	6-phosphogluconolactonase activity|glucose 1-dehydrogenase|glucose-6-phosphate dehydrogenase activity|NADP binding				0	all_lung(157;0.23)	all_epithelial(116;1.28e-19)|all_lung(118;5.22e-06)|Lung NSC(185;1.98e-05)|Renal(390;0.000147)|Breast(348;0.00109)|Colorectal(325;0.00205)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;1.88e-07)|COAD - Colon adenocarcinoma(227;7.47e-05)|Kidney(185;0.000244)|KIRC - Kidney renal clear cell carcinoma(229;0.000905)|STAD - Stomach adenocarcinoma(132;0.00176)|BRCA - Breast invasive adenocarcinoma(304;0.00183)|READ - Rectum adenocarcinoma(331;0.0419)	NADH(DB00157)	AAGGCCCCACGCCTCTACCCT	0.582													11	432	---	---	---	---	PASS
CLCN6	1185	broad.mit.edu	37	1	11876723	11876723	+	Missense_Mutation	SNP	G	A	A			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11876723G>A	uc001ate.3	+	4	378	c.265G>A	c.(265-267)GTC>ATC	p.V89I	CLCN6_uc009vne.1_3'UTR|CLCN6_uc009vnf.1_Missense_Mutation_p.V89I|CLCN6_uc009vng.1_Missense_Mutation_p.V89I|CLCN6_uc009vnh.1_Missense_Mutation_p.V89I|CLCN6_uc010oat.1_5'UTR|CLCN6_uc010oau.1_Missense_Mutation_p.V67I	NM_001286	NP_001277	P51797	CLCN6_HUMAN	chloride channel 6 isoform ClC-6a	89	Helical; (By similarity).				cell volume homeostasis|signal transduction	endosome membrane|integral to membrane	antiporter activity|ATP binding|voltage-gated chloride channel activity				0	Ovarian(185;0.249)	Lung NSC(185;8.69e-05)|all_lung(284;9.87e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.13e-06)|COAD - Colon adenocarcinoma(227;0.000274)|BRCA - Breast invasive adenocarcinoma(304;0.000311)|Kidney(185;0.000816)|KIRC - Kidney renal clear cell carcinoma(229;0.00268)|STAD - Stomach adenocarcinoma(313;0.00743)|READ - Rectum adenocarcinoma(331;0.0649)		TGCCATTGGAGTCTGCACTGG	0.542													10	23	---	---	---	---	PASS
CLCN6	1185	broad.mit.edu	37	1	11876724	11876724	+	Missense_Mutation	SNP	T	C	C			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11876724T>C	uc001ate.3	+	4	379	c.266T>C	c.(265-267)GTC>GCC	p.V89A	CLCN6_uc009vne.1_3'UTR|CLCN6_uc009vnf.1_Missense_Mutation_p.V89A|CLCN6_uc009vng.1_Missense_Mutation_p.V89A|CLCN6_uc009vnh.1_Missense_Mutation_p.V89A|CLCN6_uc010oat.1_5'UTR|CLCN6_uc010oau.1_Missense_Mutation_p.V67A	NM_001286	NP_001277	P51797	CLCN6_HUMAN	chloride channel 6 isoform ClC-6a	89	Helical; (By similarity).				cell volume homeostasis|signal transduction	endosome membrane|integral to membrane	antiporter activity|ATP binding|voltage-gated chloride channel activity				0	Ovarian(185;0.249)	Lung NSC(185;8.69e-05)|all_lung(284;9.87e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.13e-06)|COAD - Colon adenocarcinoma(227;0.000274)|BRCA - Breast invasive adenocarcinoma(304;0.000311)|Kidney(185;0.000816)|KIRC - Kidney renal clear cell carcinoma(229;0.00268)|STAD - Stomach adenocarcinoma(313;0.00743)|READ - Rectum adenocarcinoma(331;0.0649)		GCCATTGGAGTCTGCACTGGC	0.537													10	23	---	---	---	---	PASS
HSPG2	3339	broad.mit.edu	37	1	22204732	22204732	+	Missense_Mutation	SNP	G	A	A	rs142904402		TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22204732G>A	uc001bfj.2	-	21	2672	c.2632C>T	c.(2632-2634)CGC>TGC	p.R878C	HSPG2_uc009vqd.2_Missense_Mutation_p.R879C	NM_005529	NP_005520	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2 precursor	878					angiogenesis|cell adhesion|lipid metabolic process|lipoprotein metabolic process	basement membrane|extracellular space|plasma membrane	protein C-terminus binding			ovary(5)|large_intestine(2)|central_nervous_system(1)|skin(1)	9		Colorectal(325;3.46e-05)|all_lung(284;7.93e-05)|Lung NSC(340;8.71e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0498)|OV - Ovarian serous cystadenocarcinoma(117;1.14e-26)|Colorectal(126;4.18e-07)|COAD - Colon adenocarcinoma(152;1.82e-05)|GBM - Glioblastoma multiforme(114;3.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000756)|STAD - Stomach adenocarcinoma(196;0.00656)|KIRC - Kidney renal clear cell carcinoma(1967;0.00942)|READ - Rectum adenocarcinoma(331;0.0721)|Lung(427;0.223)	Becaplermin(DB00102)|Palifermin(DB00039)	TCGTCACAGCGCACAATCTCC	0.642													3	44	---	---	---	---	PASS
MAP3K6	9064	broad.mit.edu	37	1	27690800	27690800	+	Missense_Mutation	SNP	C	A	A			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:27690800C>A	uc001bny.1	-	4	839	c.590G>T	c.(589-591)GGC>GTC	p.G197V	MAP3K6_uc009vsw.1_Missense_Mutation_p.G189V|MAP3K6_uc001bnz.1_5'Flank	NM_004672	NP_004663	O95382	M3K6_HUMAN	mitogen-activated protein kinase kinase kinase	197					activation of JUN kinase activity		ATP binding|magnesium ion binding|MAP kinase kinase kinase activity			breast(4)|lung(3)|ovary(1)|central_nervous_system(1)	9		all_lung(284;1.6e-05)|Lung NSC(340;2.92e-05)|Colorectal(325;3.46e-05)|Renal(390;0.0007)|Breast(348;0.0021)|Ovarian(437;0.0175)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0416)|OV - Ovarian serous cystadenocarcinoma(117;1.69e-27)|Colorectal(126;1.24e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00132)|KIRC - Kidney renal clear cell carcinoma(1967;0.00163)|STAD - Stomach adenocarcinoma(196;0.00303)|READ - Rectum adenocarcinoma(331;0.0419)		ATCAGCCAGGCCCCGCAGAAG	0.672													46	111	---	---	---	---	PASS
INADL	10207	broad.mit.edu	37	1	62594542	62594542	+	Silent	SNP	G	A	A			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:62594542G>A	uc001dab.2	+	41	5310	c.5196G>A	c.(5194-5196)GGG>GGA	p.G1732G	INADL_uc001dac.2_RNA|INADL_uc009wag.2_Silent_p.G516G	NM_176877	NP_795352	Q8NI35	INADL_HUMAN	InaD-like	1732	PDZ 10.				intracellular signal transduction|tight junction assembly	apical plasma membrane|perinuclear region of cytoplasm|tight junction	protein binding			ovary(3)|skin(1)	4						GCATTAACGGGCAACCTTTGG	0.433													4	209	---	---	---	---	PASS
DNAJB4	11080	broad.mit.edu	37	1	78481811	78481811	+	Silent	SNP	G	A	A			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:78481811G>A	uc001dij.2	+	3	1053	c.894G>A	c.(892-894)CTG>CTA	p.L298L	DNAJB4_uc010orn.1_Silent_p.L183L	NM_007034	NP_008965	Q9UDY4	DNJB4_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 4	298					protein folding|response to heat|response to unfolded protein	cytoplasm|plasma membrane	heat shock protein binding|unfolded protein binding				0						GATATGGGCTGCCATTTCCAA	0.388													54	104	---	---	---	---	PASS
ZNF687	57592	broad.mit.edu	37	1	151263418	151263418	+	Silent	SNP	C	A	A			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151263418C>A	uc001exq.2	+	9	3545	c.3447C>A	c.(3445-3447)TCC>TCA	p.S1149S	ZNF687_uc009wmo.2_Silent_p.S1149S|ZNF687_uc009wmp.2_3'UTR	NM_020832	NP_065883	Q8N1G0	ZN687_HUMAN	zinc finger protein 687	1149	C2H2-type 9.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleolus	DNA binding|zinc ion binding			central_nervous_system(3)|ovary(1)	4	Lung SC(34;0.00471)|Ovarian(49;0.0147)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.112)|LUSC - Lung squamous cell carcinoma(543;0.181)			CCCCTGGCTCCCTGAGCCGAC	0.622													28	46	---	---	---	---	PASS
CADM3	57863	broad.mit.edu	37	1	159162491	159162491	+	Missense_Mutation	SNP	G	A	A			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:159162491G>A	uc001ftl.2	+	3	495	c.353G>A	c.(352-354)CGA>CAA	p.R118Q	CADM3_uc009wsx.1_Missense_Mutation_p.R152Q|CADM3_uc009wsy.1_Missense_Mutation_p.R118Q|CADM3_uc001ftk.2_Missense_Mutation_p.R152Q	NM_001127173	NP_001120645	Q8N126	CADM3_HUMAN	cell adhesion molecule 3 isoform 2	118	Ig-like V-type.|Extracellular (Potential).				adherens junction organization|cell junction assembly|heterophilic cell-cell adhesion|homophilic cell adhesion	cell-cell junction|integral to membrane	protein homodimerization activity			ovary(2)	2	all_hematologic(112;0.0429)					ATGCCTGTGCGAACTGCCAAG	0.562													4	201	---	---	---	---	PASS
KLHL20	27252	broad.mit.edu	37	1	173703125	173703125	+	Silent	SNP	A	T	T			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:173703125A>T	uc001gjc.2	+	3	476	c.297A>T	c.(295-297)GGA>GGT	p.G99G	KLHL20_uc010pmr.1_Intron|KLHL20_uc009wwf.2_Silent_p.G81G|KLHL20_uc001gjd.2_Silent_p.G99G	NM_014458	NP_055273	Q9Y2M5	KLH20_HUMAN	kelch-like 20	99	BTB.				cytoskeleton organization|negative regulation of apoptosis|proteasomal ubiquitin-dependent protein catabolic process|response to interferon-alpha	actin cytoskeleton|cell surface|Cul3-RING ubiquitin ligase complex|Golgi apparatus|perinuclear region of cytoplasm|PML body	actin binding|interferon-gamma binding|ubiquitin-protein ligase activity			ovary(1)	1						TGTTTACAGGAGAATTGGCAG	0.473													35	92	---	---	---	---	PASS
HMCN1	83872	broad.mit.edu	37	1	186113746	186113746	+	Missense_Mutation	SNP	G	T	T	rs149329415		TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:186113746G>T	uc001grq.1	+	91	14406	c.14177G>T	c.(14176-14178)GGC>GTC	p.G4726V	HMCN1_uc001grs.1_Missense_Mutation_p.G295V	NM_031935	NP_114141	Q96RW7	HMCN1_HUMAN	hemicentin 1 precursor	4726	TSP type-1 4.				response to stimulus|visual perception	basement membrane	calcium ion binding			ovary(22)|skin(1)	23						AGAACAAGGGGCTGCTCCGAC	0.542													72	151	---	---	---	---	PASS
CFHR4	10877	broad.mit.edu	37	1	196876024	196876024	+	Intron	SNP	G	C	C			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:196876024G>C	uc001gto.2	+						CFHR4_uc009wyy.2_Missense_Mutation_p.R157T|CFHR4_uc001gtp.2_Missense_Mutation_p.R158T	NM_006684	NP_006675	Q92496	FHR4_HUMAN	complement factor H-related 4 precursor							extracellular region	lipid transporter activity			ovary(1)|pancreas(1)|skin(1)	3						GAGAATTCCAGAGCCAAGAGT	0.363													33	78	---	---	---	---	PASS
ASPM	259266	broad.mit.edu	37	1	197091068	197091068	+	Missense_Mutation	SNP	T	C	C			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:197091068T>C	uc001gtu.2	-	16	4104	c.3847A>G	c.(3847-3849)AAA>GAA	p.K1283E	ASPM_uc001gtv.2_Missense_Mutation_p.K1283E|ASPM_uc001gtw.3_Intron	NM_018136	NP_060606	Q8IZT6	ASPM_HUMAN	asp (abnormal spindle)-like, microcephaly	1283					mitosis	cytoplasm|nucleus	calmodulin binding			ovary(4)|central_nervous_system(2)	6						AGATCTGTTTTTAGTTTATAT	0.313													52	156	---	---	---	---	PASS
ASPM	259266	broad.mit.edu	37	1	197091070	197091070	+	Missense_Mutation	SNP	A	G	G			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:197091070A>G	uc001gtu.2	-	16	4102	c.3845T>C	c.(3844-3846)CTA>CCA	p.L1282P	ASPM_uc001gtv.2_Missense_Mutation_p.L1282P|ASPM_uc001gtw.3_Intron	NM_018136	NP_060606	Q8IZT6	ASPM_HUMAN	asp (abnormal spindle)-like, microcephaly	1282					mitosis	cytoplasm|nucleus	calmodulin binding			ovary(4)|central_nervous_system(2)	6						ATCTGTTTTTAGTTTATATTT	0.318													52	154	---	---	---	---	PASS
CACNA1S	779	broad.mit.edu	37	1	201029896	201029896	+	Missense_Mutation	SNP	T	G	G			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:201029896T>G	uc001gvv.2	-	26	3531	c.3304A>C	c.(3304-3306)ATT>CTT	p.I1102L		NM_000069	NP_000060	Q13698	CAC1S_HUMAN	calcium channel, voltage-dependent, L type,	1102	Cytoplasmic (Potential).				axon guidance	I band|T-tubule|voltage-gated calcium channel complex	high voltage-gated calcium channel activity			ovary(3)|central_nervous_system(1)|skin(1)	5					Magnesium Sulfate(DB00653)|Verapamil(DB00661)	TTTTTGGGAATGTAGCACCTC	0.532													138	332	---	---	---	---	PASS
PQLC3	130814	broad.mit.edu	37	2	11312070	11312070	+	Missense_Mutation	SNP	G	A	A			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:11312070G>A	uc002rbc.2	+	5	507	c.374G>A	c.(373-375)AGC>AAC	p.S125N	PQLC3_uc010yjk.1_Missense_Mutation_p.S125N	NM_152391	NP_689604	Q8N755	PQLC3_HUMAN	PQ loop repeat containing 3 precursor	125						integral to membrane					0	all_hematologic(175;0.0797)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.0978)|OV - Ovarian serous cystadenocarcinoma(76;0.132)		ACTTTCATCAGCGCGGCCAGT	0.398													79	154	---	---	---	---	PASS
ZNF513	130557	broad.mit.edu	37	2	27601531	27601531	+	Missense_Mutation	SNP	G	A	A			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27601531G>A	uc002rkk.2	-	3	802	c.602C>T	c.(601-603)ACT>ATT	p.T201I	ZNF513_uc002rkj.2_Missense_Mutation_p.T139I	NM_144631	NP_653232	Q8N8E2	ZN513_HUMAN	zinc finger protein 513	201					regulation of transcription, DNA-dependent|response to stimulus|retina development in camera-type eye|transcription, DNA-dependent|visual perception	nucleus	transcription regulatory region DNA binding|zinc ion binding			ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CTTCTCGCCAGTGTGGGTGCG	0.667													12	74	---	---	---	---	PASS
VWA3B	200403	broad.mit.edu	37	2	98914472	98914472	+	Missense_Mutation	SNP	C	A	A			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:98914472C>A	uc002syo.2	+	24	3524	c.3260C>A	c.(3259-3261)GCC>GAC	p.A1087D	VWA3B_uc002syn.1_RNA|VWA3B_uc010yvi.1_Missense_Mutation_p.A744D|VWA3B_uc002syp.1_Missense_Mutation_p.A479D|VWA3B_uc002syq.1_Missense_Mutation_p.A363D|VWA3B_uc002syr.1_Missense_Mutation_p.A404D|VWA3B_uc002sys.2_RNA	NM_144992	NP_659429	Q502W6	VWA3B_HUMAN	von Willebrand factor A domain containing 3B	1087										ovary(3)|large_intestine(2)|skin(1)	6						GTGGGGGGCGCCATGCCCTGC	0.587													36	137	---	---	---	---	PASS
MGAT5	4249	broad.mit.edu	37	2	135076310	135076310	+	Missense_Mutation	SNP	G	C	C			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:135076310G>C	uc002ttv.1	+	4	718	c.573G>C	c.(571-573)GAG>GAC	p.E191D		NM_002410	NP_002401	Q09328	MGT5A_HUMAN	N-acetylglucosaminyltransferase V	191	Lumenal (Potential).				post-translational protein modification|protein N-linked glycosylation via asparagine	Golgi membrane|integral to membrane	alpha-1,6-mannosyl-glycoprotein 6-beta-N-acetylglucosaminyltransferase activity			ovary(2)|skin(1)	3				BRCA - Breast invasive adenocarcinoma(221;0.0964)		ACCTCAGTGAGGTGAGTAGCT	0.448													77	114	---	---	---	---	PASS
WHSC1	7468	broad.mit.edu	37	4	1941230	1941230	+	Intron	SNP	G	C	C			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:1941230G>C	uc003gdz.3	+						WHSC1_uc003geb.3_Intron|WHSC1_uc003gec.3_Intron|WHSC1_uc003ged.3_Intron|WHSC1_uc003gee.3_Intron|WHSC1_uc003gef.3_Intron|WHSC1_uc003gei.3_5'UTR|WHSC1_uc003gdy.1_Intron|WHSC1_uc010icd.1_Intron|WHSC1_uc003gea.1_Intron|WHSC1_uc010ice.1_Intron|WHSC1_uc003geh.1_Intron	NM_001042424	NP_001035889	O96028	NSD2_HUMAN	Wolf-Hirschhorn syndrome candidate 1 protein						anatomical structure morphogenesis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|cytoplasm|nuclear membrane|nucleolus	DNA binding|histone-lysine N-methyltransferase activity|zinc ion binding			ovary(3)|lung(3)|skin(2)|pancreas(1)	9		all_epithelial(65;1.34e-05)	OV - Ovarian serous cystadenocarcinoma(23;0.00606)	STAD - Stomach adenocarcinoma(129;0.232)		tttatgttcagatttttccaT	0.144			T	IGH@	MM								3	8	---	---	---	---	PASS
C4orf21	55345	broad.mit.edu	37	4	113510905	113510905	+	Silent	SNP	A	G	G			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:113510905A>G	uc003iau.2	-	11	3313	c.3102T>C	c.(3100-3102)GAT>GAC	p.D1034D	C4orf21_uc003iav.2_5'Flank|C4orf21_uc003iaw.2_Silent_p.D1034D	NM_018392	NP_060862	Q6ZU11	YD002_HUMAN	prematurely terminated mRNA decay factor-like	Error:Variant_position_missing_in_Q6ZU11_after_alignment						integral to membrane	zinc ion binding				0		Ovarian(17;0.156)		OV - Ovarian serous cystadenocarcinoma(123;0.000676)		AATGAAGATCATCAGGTAAAG	0.363													67	139	---	---	---	---	PASS
TRIP13	9319	broad.mit.edu	37	5	916051	916051	+	Missense_Mutation	SNP	G	C	C			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:916051G>C	uc003jbr.2	+	12	1276	c.1166G>C	c.(1165-1167)AGA>ACA	p.R389T		NM_004237	NP_004228	Q15645	PCH2_HUMAN	thyroid hormone receptor interactor 13	389					double-strand break repair|reciprocal meiotic recombination|synaptonemal complex assembly|transcription from RNA polymerase II promoter		ATP binding|identical protein binding|nucleoside-triphosphatase activity|transcription cofactor activity				0			Epithelial(17;0.00147)|OV - Ovarian serous cystadenocarcinoma(19;0.00271)|all cancers(22;0.00622)|Lung(60;0.165)			CGGGTCCTGAGAAAACTCCCC	0.542													130	213	---	---	---	---	PASS
PCDHA9	9752	broad.mit.edu	37	5	140229361	140229361	+	Silent	SNP	G	A	A			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140229361G>A	uc003lhu.2	+	1	2005	c.1281G>A	c.(1279-1281)GCG>GCA	p.A427A	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhi.2_Intron|PCDHA4_uc003lhh.1_Intron|PCDHA5_uc003lhk.1_Intron|PCDHA5_uc003lhl.2_Intron|PCDHA6_uc003lhn.2_Intron|PCDHA6_uc003lho.2_Intron|PCDHA7_uc003lhq.2_Intron|PCDHA8_uc003lhs.2_Intron|PCDHA9_uc003lht.1_Silent_p.A427A	NM_031857	NP_114063	Q9Y5H5	PCDA9_HUMAN	protocadherin alpha 9 isoform 1 precursor	427	Cadherin 4.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding|protein binding			large_intestine(2)|ovary(2)|skin(1)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGGTTACCGCGCGGGACGGGG	0.627													78	137	---	---	---	---	PASS
FAT2	2196	broad.mit.edu	37	5	150905349	150905349	+	Missense_Mutation	SNP	A	G	G			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:150905349A>G	uc003lue.3	-	17	10499	c.10486T>C	c.(10486-10488)TGG>CGG	p.W3496R	GM2A_uc011dcs.1_Intron|FAT2_uc003lud.3_Missense_Mutation_p.W189R	NM_001447	NP_001438	Q9NYQ8	FAT2_HUMAN	FAT tumor suppressor 2 precursor	3496	Extracellular (Potential).|Cadherin 31.				epithelial cell migration|homophilic cell adhesion	cell-cell adherens junction|integral to membrane|nucleus	calcium ion binding			ovary(4)|upper_aerodigestive_tract(1)|skin(1)	6		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			AGCTGATACCATTCCTGAGCC	0.567													44	92	---	---	---	---	PASS
MAK	4117	broad.mit.edu	37	6	10802230	10802230	+	Silent	SNP	A	T	T			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:10802230A>T	uc003mzl.2	-	7	955	c.726T>A	c.(724-726)GTT>GTA	p.V242V	SYCP2L_uc011dim.1_Intron|TMEM14B_uc010jos.1_Intron|MAK_uc010jot.2_RNA|MAK_uc010jou.2_RNA|MAK_uc003mzm.2_Silent_p.V242V|MAK_uc010jov.1_RNA	NM_005906	NP_005897	P20794	MAK_HUMAN	male germ cell-associated kinase	242	Protein kinase.				cell differentiation|multicellular organismal development|spermatogenesis		ATP binding|cyclin-dependent protein kinase activity			breast(2)|skin(1)	3	Breast(50;0.107)|Ovarian(93;0.107)	all_hematologic(90;0.117)				AGTTTATAGGAACACACTGGG	0.443													20	134	---	---	---	---	PASS
HIST1H2AM	8336	broad.mit.edu	37	6	27860669	27860669	+	Missense_Mutation	SNP	C	T	T			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:27860669C>T	uc003nkb.1	-	1	295	c.259G>A	c.(259-261)GCC>ACC	p.A87T	HIST1H3J_uc003nka.2_5'Flank|HIST1H2BO_uc003nkc.1_5'Flank	NM_003514	NP_003505	P0C0S8	H2A1_HUMAN	histone cluster 1, H2am	87					nucleosome assembly	nucleosome|nucleus	DNA binding|enzyme binding			ovary(2)	2						TTGCGGATGGCCAGCTGCAAG	0.602													6	291	---	---	---	---	PASS
ZNF318	24149	broad.mit.edu	37	6	43305844	43305844	+	Silent	SNP	C	T	T			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43305844C>T	uc003oux.2	-	10	5970	c.5892G>A	c.(5890-5892)AAG>AAA	p.K1964K	ZNF318_uc003ouw.2_Intron	NM_014345	NP_055160	Q5VUA4	ZN318_HUMAN	zinc finger protein 318	1964					meiosis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	nucleic acid binding|zinc ion binding			ovary(3)|breast(2)|central_nervous_system(1)|skin(1)	7			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0171)|OV - Ovarian serous cystadenocarcinoma(102;0.0579)			TCTCTGGCCTCTTCTTGTTTT	0.428													108	208	---	---	---	---	PASS
SDK1	221935	broad.mit.edu	37	7	4014046	4014046	+	Silent	SNP	G	A	A			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:4014046G>A	uc003smx.2	+	13	2002	c.1863G>A	c.(1861-1863)ACG>ACA	p.T621T		NM_152744	NP_689957	Q7Z5N4	SDK1_HUMAN	sidekick 1 precursor	621	Ig-like C2-type 6.				cell adhesion	integral to membrane				large_intestine(3)|ovary(2)|skin(1)	6		all_cancers(1;0.127)|Ovarian(82;0.0177)|Myeloproliferative disorder(862;0.194)		UCEC - Uterine corpus endometrioid carcinoma (126;0.121)|OV - Ovarian serous cystadenocarcinoma(56;9.65e-15)		CATCGAGCACGTCTAGGATCG	0.547													21	65	---	---	---	---	PASS
WBSCR17	64409	broad.mit.edu	37	7	70886059	70886059	+	Missense_Mutation	SNP	G	T	T			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:70886059G>T	uc003tvy.2	+	5	930	c.930G>T	c.(928-930)TGG>TGT	p.W310C	WBSCR17_uc003tvz.2_Missense_Mutation_p.W9C	NM_022479	NP_071924	Q6IS24	GLTL3_HUMAN	UDP-GalNAc:polypeptide	310	Lumenal (Potential).					Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			skin(3)|upper_aerodigestive_tract(1)|ovary(1)|pancreas(1)|central_nervous_system(1)	7		all_cancers(73;0.2)|Lung NSC(55;0.094)|all_lung(88;0.125)				CAAAAGACTGGTGGGACGCCG	0.582													36	72	---	---	---	---	PASS
ZNF3	7551	broad.mit.edu	37	7	99669413	99669413	+	Missense_Mutation	SNP	C	T	T			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99669413C>T	uc003usq.2	-	6	1001	c.694G>A	c.(694-696)GAG>AAG	p.E232K	ZNF3_uc003usp.2_Intron|ZNF3_uc003usr.2_Missense_Mutation_p.E232K|ZNF3_uc010lgj.2_Missense_Mutation_p.E196K|ZNF3_uc003uss.2_Missense_Mutation_p.E239K|ZNF3_uc003ust.3_Missense_Mutation_p.E232K	NM_032924	NP_116313	P17036	ZNF3_HUMAN	zinc finger protein 3 isoform 2	232	C2H2-type 2.				cell differentiation|leukocyte activation|multicellular organismal development	nucleus	DNA binding|identical protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)	Ovarian(593;2.06e-05)|Myeloproliferative disorder(862;0.0122)|Breast(660;0.029)	STAD - Stomach adenocarcinoma(171;0.129)			TTCCCACACTCATTACATTCA	0.433													48	114	---	---	---	---	PASS
TBXAS1	6916	broad.mit.edu	37	7	139529248	139529248	+	Missense_Mutation	SNP	T	C	C			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:139529248T>C	uc011kqv.1	+	1	226	c.62T>C	c.(61-63)CTG>CCG	p.L21P	TBXAS1_uc003vvh.2_Missense_Mutation_p.L21P|TBXAS1_uc010lne.2_Intron|TBXAS1_uc011kqu.1_Missense_Mutation_p.L21P|TBXAS1_uc003vvi.2_Missense_Mutation_p.L21P|TBXAS1_uc003vvj.2_Missense_Mutation_p.L21P|TBXAS1_uc011kqw.1_5'UTR|TBXAS1_uc011kqx.1_Missense_Mutation_p.L21P	NM_001130966	NP_001124438	P24557	THAS_HUMAN	thromboxane A synthase 1, platelet isoform	20	Helical; (Potential).				hormone biosynthetic process|prostaglandin biosynthetic process|xenobiotic metabolic process	endoplasmic reticulum lumen|endoplasmic reticulum membrane|integral to membrane	electron carrier activity|heme binding|monooxygenase activity|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen|thromboxane-A synthase activity			ovary(2)|breast(1)	3	Melanoma(164;0.0142)					ACGGTGGCCCTGTCAGTGGCT	0.572													9	42	---	---	---	---	PASS
GIMAP6	474344	broad.mit.edu	37	7	150325294	150325294	+	Missense_Mutation	SNP	T	C	C			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150325294T>C	uc003whn.2	-	3	816	c.392A>G	c.(391-393)CAA>CGA	p.Q131R	GIMAP6_uc003whm.2_Missense_Mutation_p.Q51R	NM_024711	NP_078987	Q6P9H5	GIMA6_HUMAN	GTPase, IMAP family member 6	131							GTP binding			upper_aerodigestive_tract(1)|ovary(1)|skin(1)	3			OV - Ovarian serous cystadenocarcinoma(82;0.0145)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		CCGGCCCAGTTGTGTCACCAG	0.632													53	134	---	---	---	---	PASS
SHH	6469	broad.mit.edu	37	7	155596300	155596300	+	Missense_Mutation	SNP	T	C	C			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:155596300T>C	uc003wmk.1	-	3	834	c.683A>G	c.(682-684)GAC>GGC	p.D228G	SHH_uc003wmh.1_Intron|SHH_uc003wmi.1_Intron|SHH_uc003wmj.1_Missense_Mutation_p.D141G	NM_000193	NP_000184	Q15465	SHH_HUMAN	sonic hedgehog preproprotein	228					androgen metabolic process|axon guidance|branching involved in ureteric bud morphogenesis|CD4-positive or CD8-positive, alpha-beta T cell lineage commitment|embryonic digit morphogenesis|hindbrain development|intein-mediated protein splicing|lymphoid progenitor cell differentiation|metanephric mesenchymal cell proliferation involved in metanephros development|midbrain development|negative regulation of cell migration|negative regulation of kidney smooth muscle cell differentiation|negative regulation of ureter smooth muscle cell differentiation|negative thymic T cell selection|neural crest cell migration|neuroblast proliferation|patterning of blood vessels|positive regulation of alpha-beta T cell differentiation|positive regulation of immature T cell proliferation in thymus|positive regulation of kidney smooth muscle cell differentiation|positive regulation of mesenchymal cell proliferation involved in ureter development|positive regulation of T cell differentiation in thymus|positive regulation of ureter smooth muscle cell differentiation|positive thymic T cell selection|proteolysis|sclerotome development|stem cell development|thymus development|vasculogenesis|ventral midline development	cell surface|extracellular space|membrane raft|plasma membrane	calcium ion binding|laminin-1 binding|peptidase activity|signal transducer activity|zinc ion binding			central_nervous_system(3)|lung(1)	4	all_neural(206;0.101)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.00882)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		GCCCTGGTCGTCCGCCGCCAG	0.701													3	12	---	---	---	---	PASS
SDC2	6383	broad.mit.edu	37	8	97621837	97621837	+	3'UTR	SNP	A	C	C			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:97621837A>C	uc003yhv.1	+	5					SDC2_uc011lgu.1_3'UTR	NM_002998	NP_002989	P34741	SDC2_HUMAN	syndecan 2 precursor							integral to plasma membrane	cytoskeletal protein binding|PDZ domain binding			ovary(2)	2	Breast(36;3.41e-05)				Sargramostim(DB00020)	AAGCTTTTGCATAGAATAATG	0.299													10	23	---	---	---	---	PASS
RPL30	6156	broad.mit.edu	37	8	99054891	99054891	+	Missense_Mutation	SNP	G	C	C	rs9879		TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:99054891G>C	uc003yif.2	-	4	350	c.280C>G	c.(280-282)CTG>GTG	p.L94V	RPL30_uc010mbk.1_Intron|SNORA72_uc003yig.1_5'Flank	NM_000989	NP_000980	P62888	RL30_HUMAN	ribosomal protein L30	94					endocrine pancreas development|translational elongation|translational termination|viral transcription	cytosolic large ribosomal subunit	RNA binding|structural constituent of ribosome				0	Breast(36;1.43e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.192)			ATGATAGCCAGTGTGCACACT	0.368													45	114	---	---	---	---	PASS
TAF1L	138474	broad.mit.edu	37	9	32634993	32634993	+	Missense_Mutation	SNP	C	G	G			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:32634993C>G	uc003zrg.1	-	1	675	c.585G>C	c.(583-585)TTG>TTC	p.L195F	uc003zrh.1_RNA	NM_153809	NP_722516	Q8IZX4	TAF1L_HUMAN	TBP-associated factor RNA polymerase 1-like	195					male meiosis|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter|transcription initiation, DNA-dependent	transcription factor TFIID complex	DNA binding|histone acetyltransferase activity|protein serine/threonine kinase activity|TBP-class protein binding			lung(8)|skin(6)|central_nervous_system(4)|large_intestine(3)|ovary(2)|stomach(1)|breast(1)|pancreas(1)	26			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.00301)		TCTCTGAGGCCAAAAAGGAAG	0.473													5	116	---	---	---	---	PASS
TMEM2	23670	broad.mit.edu	37	9	74305109	74305109	+	Silent	SNP	C	T	T			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:74305109C>T	uc011lsa.1	-	22	4290	c.3750G>A	c.(3748-3750)GTG>GTA	p.V1250V	TMEM2_uc011lrz.1_Silent_p.V243V|TMEM2_uc010mos.2_Silent_p.V1187V|TMEM2_uc011lsb.1_RNA|TMEM2_uc004aik.2_Silent_p.V84V	NM_013390	NP_037522	Q9UHN6	TMEM2_HUMAN	transmembrane protein 2 isoform a	1250						integral to membrane				ovary(2)	2		all_epithelial(88;4.56e-14)|Myeloproliferative disorder(762;0.0255)		GBM - Glioblastoma multiforme(74;7.45e-21)|OV - Ovarian serous cystadenocarcinoma(323;1.02e-16)		TGCACGGATCCACAACAAGGA	0.458													41	124	---	---	---	---	PASS
SVEP1	79987	broad.mit.edu	37	9	113238449	113238449	+	Intron	SNP	T	G	G			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:113238449T>G	uc010mtz.2	-						SVEP1_uc010mua.1_Intron|SVEP1_uc004beu.2_3'UTR	NM_153366	NP_699197	Q4LDE5	SVEP1_HUMAN	polydom						cell adhesion	cytoplasm|extracellular region|membrane	calcium ion binding			ovary(7)	7						TGCAGATTAGTCTTGCCAACT	0.303													36	65	---	---	---	---	PASS
SLC34A3	142680	broad.mit.edu	37	9	140126522	140126522	+	Splice_Site	SNP	A	T	T			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140126522A>T	uc004cmf.1	+	3	272	c.86_splice	c.e3-2	p.G29_splice	SLC34A3_uc004cmc.1_Splice_Site|SLC34A3_uc004cmd.1_Splice_Site_p.G29_splice|SLC34A3_uc011met.1_Splice_Site_p.G29_splice	NM_080877	NP_543153	Q8N130	NPT2C_HUMAN	solute carrier family 34 (sodium phosphate),						cellular phosphate ion homeostasis	apical plasma membrane|integral to membrane	sodium-dependent phosphate transmembrane transporter activity|sodium:phosphate symporter activity				0	all_cancers(76;0.0926)		STAD - Stomach adenocarcinoma(284;0.0698)	OV - Ovarian serous cystadenocarcinoma(145;6.37e-05)|Epithelial(140;0.00057)		CTACCTCCACAGGGACCTCCA	0.622													73	254	---	---	---	---	PASS
FBXO18	84893	broad.mit.edu	37	10	5937075	5937075	+	Intron	SNP	G	T	T			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:5937075G>T	uc001iis.2	+						FBXO18_uc001iir.2_Intron|FBXO18_uc009xig.2_Intron|FBXO18_uc001iit.2_Missense_Mutation_p.G27W	NM_178150	NP_835363	Q8NFZ0	FBX18_HUMAN	F-box only protein, helicase, 18 isoform 2						DNA repair	nucleus	ATP binding|ATP-dependent DNA helicase activity|DNA binding			ovary(2)|skin(1)	3						ACATTGCGCAGGGCCCCTGGG	0.532													41	82	---	---	---	---	PASS
ST8SIA6	338596	broad.mit.edu	37	10	17432536	17432536	+	Missense_Mutation	SNP	G	A	A			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:17432536G>A	uc001ipd.2	-	3	284	c.284C>T	c.(283-285)ACG>ATG	p.T95M	ST8SIA6_uc010qce.1_RNA|uc001ipe.2_Intron|uc001ipf.1_Intron	NM_001004470	NP_001004470	P61647	SIA8F_HUMAN	ST8 alpha-N-acetyl-neuraminide	95	Lumenal (Potential).				post-translational protein modification|protein N-linked glycosylation via asparagine	integral to Golgi membrane	alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity			ovary(1)	1						TTACCCTTTCGTTTTGTTAGA	0.363													11	344	---	---	---	---	PASS
ZEB1	6935	broad.mit.edu	37	10	31810616	31810616	+	Missense_Mutation	SNP	G	A	A			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:31810616G>A	uc001ivs.3	+	7	2416	c.2353G>A	c.(2353-2355)GAC>AAC	p.D785N	ZEB1_uc001ivr.3_Missense_Mutation_p.D567N|ZEB1_uc010qee.1_Missense_Mutation_p.D567N|ZEB1_uc010qef.1_Missense_Mutation_p.D567N|ZEB1_uc009xlj.1_Missense_Mutation_p.D711N|ZEB1_uc010qeg.1_Missense_Mutation_p.D644N|ZEB1_uc009xlk.1_Missense_Mutation_p.D567N|ZEB1_uc001ivt.3_Missense_Mutation_p.D567N|ZEB1_uc001ivu.3_Missense_Mutation_p.D786N|ZEB1_uc001ivv.3_Missense_Mutation_p.D765N|ZEB1_uc010qeh.1_Missense_Mutation_p.D718N|ZEB1_uc009xlo.1_Missense_Mutation_p.D768N|ZEB1_uc009xlp.2_Missense_Mutation_p.D769N	NM_030751	NP_110378	P37275	ZEB1_HUMAN	zinc finger E-box binding homeobox 1 isoform b	785					cell proliferation|immune response|negative regulation of transcription from RNA polymerase II promoter|positive regulation of neuron differentiation	cytoplasm	E-box binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription corepressor activity|zinc ion binding			ovary(3)|central_nervous_system(2)	5		Prostate(175;0.0156)				TTGTGTTACAGACTCAGAACC	0.443													63	112	---	---	---	---	PASS
CBARA1	10367	broad.mit.edu	37	10	74326491	74326491	+	Missense_Mutation	SNP	G	T	T			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:74326491G>T	uc001jtb.1	-	2	194	c.61C>A	c.(61-63)CAT>AAT	p.H21N		NM_006077	NP_006068	Q9BPX6	MICU1_HUMAN	calcium binding atopy-related autoantigen 1	21					calcium ion import|defense response|elevation of mitochondrial calcium ion concentration	integral to membrane|mitochondrial inner membrane	calcium ion binding|protein binding			ovary(1)	1						GATCCTCCATGGTACCATCGA	0.488													16	23	---	---	---	---	PASS
PTEN	5728	broad.mit.edu	37	10	89720677	89720677	+	Missense_Mutation	SNP	T	G	G			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:89720677T>G	uc001kfb.2	+	9	1859	c.828T>G	c.(826-828)AAT>AAG	p.N276K		NM_000314	NP_000305	P60484	PTEN_HUMAN	phosphatase and tensin homolog	276	C2 tensin-type.				activation of mitotic anaphase-promoting complex activity|apoptosis|canonical Wnt receptor signaling pathway|cell proliferation|central nervous system development|induction of apoptosis|inositol phosphate dephosphorylation|negative regulation of cell migration|negative regulation of cyclin-dependent protein kinase activity involved in G1/S|negative regulation of focal adhesion assembly|negative regulation of G1/S transition of mitotic cell cycle|negative regulation of protein kinase B signaling cascade|negative regulation of protein phosphorylation|nerve growth factor receptor signaling pathway|phosphatidylinositol dephosphorylation|phosphatidylinositol-mediated signaling|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|positive regulation of sequence-specific DNA binding transcription factor activity|protein stabilization|regulation of neuron projection development|T cell receptor signaling pathway	cytosol|internal side of plasma membrane|PML body	anaphase-promoting complex binding|enzyme binding|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity|lipid binding|magnesium ion binding|PDZ domain binding|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity|phosphatidylinositol-3-phosphatase activity|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity	p.R55fs*1(4)|p.?(2)|p.N212fs*1(2)|p.Y27fs*1(2)|p.D268_F279>VGQNVSLLGKYI(2)|p.N276fs*15(2)|p.G165_*404del(1)|p.G165_K342del(1)|p.W274_F341del(1)		endometrium(831)|central_nervous_system(657)|skin(121)|haematopoietic_and_lymphoid_tissue(101)|large_intestine(99)|prostate(97)|breast(73)|lung(65)|ovary(58)|thyroid(29)|stomach(29)|upper_aerodigestive_tract(25)|cervix(24)|liver(20)|vulva(17)|kidney(15)|NS(14)|soft_tissue(13)|urinary_tract(12)|eye(8)|pancreas(6)|salivary_gland(5)|bone(5)|biliary_tract(4)|autonomic_ganglia(2)|meninges(2)|testis(1)|oesophagus(1)	2334		all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132)	KIRC - Kidney renal clear cell carcinoma(1;0.214)	UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218)		TTTGGGTAAATACATTCTTCA	0.259		31	D|Mis|N|F|S		glioma| prostate|endometrial	harmartoma|glioma| prostate|endometrial			Proteus_syndrome|Cowden_syndrome|Juvenile_Polyposis|Hereditary_Mixed_Polyposis_Syndrome_type_1|Bannayan-Riley-Ruvalcaba_syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)			46	40	---	---	---	---	PASS
PTEN	5728	broad.mit.edu	37	10	89720741	89720741	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:89720741C>T	uc001kfb.2	+	9	1923	c.892C>T	c.(892-894)CAA>TAA	p.Q298*		NM_000314	NP_000305	P60484	PTEN_HUMAN	phosphatase and tensin homolog	298	C2 tensin-type.				activation of mitotic anaphase-promoting complex activity|apoptosis|canonical Wnt receptor signaling pathway|cell proliferation|central nervous system development|induction of apoptosis|inositol phosphate dephosphorylation|negative regulation of cell migration|negative regulation of cyclin-dependent protein kinase activity involved in G1/S|negative regulation of focal adhesion assembly|negative regulation of G1/S transition of mitotic cell cycle|negative regulation of protein kinase B signaling cascade|negative regulation of protein phosphorylation|nerve growth factor receptor signaling pathway|phosphatidylinositol dephosphorylation|phosphatidylinositol-mediated signaling|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|positive regulation of sequence-specific DNA binding transcription factor activity|protein stabilization|regulation of neuron projection development|T cell receptor signaling pathway	cytosol|internal side of plasma membrane|PML body	anaphase-promoting complex binding|enzyme binding|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity|lipid binding|magnesium ion binding|PDZ domain binding|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity|phosphatidylinositol-3-phosphatase activity|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity	p.R55fs*1(4)|p.Q298*(2)|p.?(2)|p.N212fs*1(2)|p.Y27fs*1(2)|p.G165_*404del(1)|p.G165_K342del(1)|p.W274_F341del(1)		endometrium(831)|central_nervous_system(657)|skin(121)|haematopoietic_and_lymphoid_tissue(101)|large_intestine(99)|prostate(97)|breast(73)|lung(65)|ovary(58)|thyroid(29)|stomach(29)|upper_aerodigestive_tract(25)|cervix(24)|liver(20)|vulva(17)|kidney(15)|NS(14)|soft_tissue(13)|urinary_tract(12)|eye(8)|pancreas(6)|salivary_gland(5)|bone(5)|biliary_tract(4)|autonomic_ganglia(2)|meninges(2)|testis(1)|oesophagus(1)	2334		all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132)	KIRC - Kidney renal clear cell carcinoma(1;0.214)	UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218)		TCTATGTGATCAAGAAATCGA	0.323		31	D|Mis|N|F|S		glioma| prostate|endometrial	harmartoma|glioma| prostate|endometrial			Proteus_syndrome|Cowden_syndrome|Juvenile_Polyposis|Hereditary_Mixed_Polyposis_Syndrome_type_1|Bannayan-Riley-Ruvalcaba_syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)			9	186	---	---	---	---	PASS
GBF1	8729	broad.mit.edu	37	10	104121490	104121490	+	Missense_Mutation	SNP	C	G	G			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:104121490C>G	uc001kux.1	+	14	1744	c.1504C>G	c.(1504-1506)CTT>GTT	p.L502V	GBF1_uc001kuy.1_Missense_Mutation_p.L502V|GBF1_uc001kuz.1_Missense_Mutation_p.L503V	NM_004193	NP_004184	Q92538	GBF1_HUMAN	golgi-specific brefeldin A resistant guanine	502					COPI coating of Golgi vesicle|post-Golgi vesicle-mediated transport|regulation of ARF protein signal transduction|retrograde vesicle-mediated transport, Golgi to ER	Golgi membrane	ARF guanyl-nucleotide exchange factor activity|protein binding			ovary(1)|central_nervous_system(1)	2		Colorectal(252;0.0236)		Epithelial(162;5.16e-08)|all cancers(201;1.19e-06)		CATCAAAAAGCTTATGGAGAT	0.443													83	116	---	---	---	---	PASS
C10orf79	80217	broad.mit.edu	37	10	105963446	105963446	+	Missense_Mutation	SNP	A	G	G			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:105963446A>G	uc001kxw.2	-	8	1195	c.1079T>C	c.(1078-1080)CTG>CCG	p.L360P	C10orf79_uc001kxx.3_Missense_Mutation_p.L361P|C10orf79_uc001kxy.1_Missense_Mutation_p.L361P|C10orf79_uc001kxz.2_Missense_Mutation_p.L361P	NM_025145	NP_079421	Q8NDM7	WDR96_HUMAN	hypothetical protein LOC80217	360	WD 5.										0		Colorectal(252;0.178)		Epithelial(162;4.83e-10)|all cancers(201;2.26e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0194)		TGTTTGAATCAGCAACACTGT	0.318													4	199	---	---	---	---	PASS
SHOC2	8036	broad.mit.edu	37	10	112764372	112764372	+	Silent	SNP	A	G	G			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:112764372A>G	uc001kzl.3	+	5	1330	c.981A>G	c.(979-981)TTA>TTG	p.L327L	SHOC2_uc009xxx.2_Silent_p.L327L|SHOC2_uc010qrg.1_5'UTR|SHOC2_uc001kzn.2_Silent_p.L281L	NM_007373	NP_031399	Q9UQ13	SHOC2_HUMAN	soc-2 suppressor of clear homolog	327	LRR 10.				fibroblast growth factor receptor signaling pathway|positive regulation of Ras protein signal transduction|Ras protein signal transduction	nucleus|protein phosphatase type 1 complex	protein phosphatase binding|protein phosphatase regulator activity			ovary(1)|skin(1)	2				Epithelial(162;0.000796)|all cancers(201;0.011)|BRCA - Breast invasive adenocarcinoma(275;0.126)		AGAGTCTTTTATCAAGTCTTG	0.363													83	96	---	---	---	---	PASS
CRY2	1408	broad.mit.edu	37	11	45891723	45891723	+	Silent	SNP	C	T	T			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:45891723C>T	uc010rgn.1	+	8	1399	c.1377C>T	c.(1375-1377)GGC>GGT	p.G459G	CRY2_uc009ykw.2_Silent_p.G377G|CRY2_uc010rgo.1_Silent_p.G181G	NM_021117	NP_066940	Q49AN0	CRY2_HUMAN	cryptochrome 2 (photolyase-like) isoform 1	438	FAD-binding.|Required for inhibition of CLOCK-ARNTL- mediated transcription (By similarity).				DNA repair|protein-chromophore linkage|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	blue light photoreceptor activity|damaged DNA binding|DNA photolyase activity|nucleotide binding|protein binding|single-stranded DNA binding			central_nervous_system(1)	1						TGGGCTTTGGCCGTCGCACGG	0.587													5	149	---	---	---	---	PASS
ZFP91	80829	broad.mit.edu	37	11	58377371	58377371	+	Missense_Mutation	SNP	A	G	G			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:58377371A>G	uc001nmx.3	+	3	607	c.439A>G	c.(439-441)AGA>GGA	p.R147G	ZFP91_uc001nmy.3_Missense_Mutation_p.R147G|ZFP91-CNTF_uc010rkm.1_RNA	NM_053023	NP_444251	Q96JP5	ZFP91_HUMAN	zinc finger protein 91	147					activation of NF-kappaB-inducing kinase activity|protein K63-linked ubiquitination	nucleus	nucleic acid binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)	1		Breast(21;0.00725)|all_epithelial(135;0.0101)|all_lung(304;0.24)				TGCTGCATCTAGACCTAGCCG	0.478													60	122	---	---	---	---	PASS
SLC22A12	116085	broad.mit.edu	37	11	64368297	64368297	+	Missense_Mutation	SNP	G	T	T			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64368297G>T	uc001oam.1	+	9	2232	c.1485G>T	c.(1483-1485)TGG>TGT	p.W495C	SLC22A12_uc001oal.1_Missense_Mutation_p.W274C|SLC22A12_uc009yps.1_Missense_Mutation_p.W461C|SLC22A12_uc001oan.1_Missense_Mutation_p.W387C|SLC22A12_uc009ypt.2_Missense_Mutation_p.W313C	NM_144585	NP_653186	Q96S37	S22AC_HUMAN	urate anion exchanger 1 isoform a	495	Helical; (Potential).				cellular homeostasis|response to drug|urate metabolic process	apical plasma membrane|brush border membrane|integral to membrane	PDZ domain binding|urate transmembrane transporter activity			ovary(1)	1						ATGGCCCCTGGCTGCCCTTGC	0.677													45	107	---	---	---	---	PASS
FOXRED1	55572	broad.mit.edu	37	11	126142904	126142904	+	Missense_Mutation	SNP	G	T	T			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:126142904G>T	uc001qdi.2	+	3	394	c.347G>T	c.(346-348)TGT>TTT	p.C116F	FOXRED1_uc010sbn.1_5'UTR|FOXRED1_uc010sbo.1_RNA|FOXRED1_uc010sbp.1_5'UTR|FOXRED1_uc010sbq.1_5'UTR|FOXRED1_uc001qdj.2_5'UTR|FOXRED1_uc010sbr.1_Missense_Mutation_p.C102F|FOXRED1_uc001qdk.2_5'UTR	NM_017547	NP_060017	Q96CU9	FXRD1_HUMAN	FAD-dependent oxidoreductase domain containing	116						integral to membrane|mitochondrion	oxidoreductase activity|protein binding				0	all_hematologic(175;0.145)	Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.0739)|all_lung(97;0.0798)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.1e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0729)		GGTGGGATTTGTCAGCAGTTC	0.478													48	112	---	---	---	---	PASS
FOXRED1	55572	broad.mit.edu	37	11	126142905	126142905	+	Nonsense_Mutation	SNP	T	A	A			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:126142905T>A	uc001qdi.2	+	3	395	c.348T>A	c.(346-348)TGT>TGA	p.C116*	FOXRED1_uc010sbn.1_5'UTR|FOXRED1_uc010sbo.1_RNA|FOXRED1_uc010sbp.1_5'UTR|FOXRED1_uc010sbq.1_5'UTR|FOXRED1_uc001qdj.2_5'UTR|FOXRED1_uc010sbr.1_Nonsense_Mutation_p.C102*|FOXRED1_uc001qdk.2_5'UTR	NM_017547	NP_060017	Q96CU9	FXRD1_HUMAN	FAD-dependent oxidoreductase domain containing	116						integral to membrane|mitochondrion	oxidoreductase activity|protein binding				0	all_hematologic(175;0.145)	Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.0739)|all_lung(97;0.0798)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.1e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0729)		GTGGGATTTGTCAGCAGTTCT	0.473													47	112	---	---	---	---	PASS
WNK1	65125	broad.mit.edu	37	12	993869	993869	+	Missense_Mutation	SNP	C	G	G	rs143361850		TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:993869C>G	uc001qio.3	+	19	4406	c.3899C>G	c.(3898-3900)TCC>TGC	p.S1300C	WNK1_uc001qip.3_Missense_Mutation_p.S1053C|WNK1_uc001qir.3_Missense_Mutation_p.S473C	NM_018979	NP_061852	Q9H4A3	WNK1_HUMAN	WNK lysine deficient protein kinase 1	1300					intracellular protein kinase cascade|ion transport|neuron development	cytoplasm	ATP binding|protein binding|protein kinase inhibitor activity|protein serine/threonine kinase activity			stomach(6)|breast(6)|ovary(5)|lung(4)|large_intestine(1)|central_nervous_system(1)	23	all_cancers(10;0.00611)|all_epithelial(11;0.00825)|all_lung(10;0.0331)|Ovarian(42;0.0512)|Lung NSC(10;0.0632)		Epithelial(1;1.74e-08)|all cancers(1;7.04e-08)|OV - Ovarian serous cystadenocarcinoma(31;0.000423)|BRCA - Breast invasive adenocarcinoma(9;0.0149)|Colorectal(1;0.0197)			TCTGCATCATCCCTTAGTCTA	0.433													58	157	---	---	---	---	PASS
ACVRL1	94	broad.mit.edu	37	12	52312803	52312803	+	Silent	SNP	T	C	C			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52312803T>C	uc001rzj.2	+	9	1564	c.1281T>C	c.(1279-1281)GAT>GAC	p.D427D	ACVRL1_uc001rzk.2_Silent_p.D427D|ACVRL1_uc010snm.1_Silent_p.D253D	NM_000020	NP_000011	P37023	ACVL1_HUMAN	activin A receptor type II-like 1 precursor	427	Cytoplasmic (Potential).|Protein kinase.				blood vessel endothelial cell proliferation involved in sprouting angiogenesis|blood vessel maturation|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of endothelial cell migration|negative regulation of focal adhesion assembly|positive regulation of BMP signaling pathway|positive regulation of transcription, DNA-dependent|regulation of blood pressure|regulation of blood vessel endothelial cell migration|regulation of DNA replication|regulation of endothelial cell proliferation|transforming growth factor beta receptor signaling pathway|wound healing, spreading of epidermal cells	cell surface|integral to plasma membrane	activin binding|activin receptor activity, type I|ATP binding|metal ion binding|receptor signaling protein serine/threonine kinase activity|SMAD binding|transforming growth factor beta binding|transforming growth factor beta receptor activity			lung(2)	2				BRCA - Breast invasive adenocarcinoma(357;0.0991)	Adenosine triphosphate(DB00171)	CCTTCTATGATGTGGTGCCCA	0.552									Hereditary_Hemorrhagic_Telangiectasia				55	105	---	---	---	---	PASS
KRT75	9119	broad.mit.edu	37	12	52827998	52827998	+	Missense_Mutation	SNP	G	A	A	rs148964521		TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52827998G>A	uc001saj.2	-	1	113	c.91C>T	c.(91-93)CGC>TGC	p.R31C		NM_004693	NP_004684	O95678	K2C75_HUMAN	keratin 75	31	Head.					keratin filament	structural molecule activity				0				BRCA - Breast invasive adenocarcinoma(357;0.192)		GAGCTGAAGCGGGAGCGGCCA	0.662													27	36	---	---	---	---	PASS
COQ10A	93058	broad.mit.edu	37	12	56663289	56663289	+	Missense_Mutation	SNP	T	C	C			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56663289T>C	uc001sko.3	+	4	781	c.520T>C	c.(520-522)TGG>CGG	p.W174R	COQ10A_uc001skp.3_Missense_Mutation_p.W142R|COQ10A_uc001skq.3_Missense_Mutation_p.W157R	NM_144576	NP_653177	Q96MF6	CQ10A_HUMAN	coenzyme Q10 homolog A isoform a	174						mitochondrial inner membrane				ovary(1)	1						AGAGACTATTTGGCGATTCAG	0.443													111	202	---	---	---	---	PASS
NUP107	57122	broad.mit.edu	37	12	69126417	69126417	+	Nonsense_Mutation	SNP	G	T	T			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:69126417G>T	uc001suf.2	+	23	2114	c.1999G>T	c.(1999-2001)GAG>TAG	p.E667*	NUP107_uc001sug.2_Nonsense_Mutation_p.E426*|NUP107_uc010stj.1_Nonsense_Mutation_p.E638*	NM_020401	NP_065134	P57740	NU107_HUMAN	nucleoporin 107kDa	667					carbohydrate metabolic process|glucose transport|mitotic prometaphase|mRNA export from nucleus|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	condensed chromosome kinetochore|cytosol|Nup107-160 complex	nucleocytoplasmic transporter activity|protein binding			skin(1)	1	Breast(13;6.25e-06)		Lung(24;0.000131)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.00694)			TAATAAATAGGAGGATCGTTT	0.323													4	92	---	---	---	---	PASS
STAB2	55576	broad.mit.edu	37	12	104126850	104126850	+	Missense_Mutation	SNP	G	A	A	rs147807697	by1000genomes	TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:104126850G>A	uc001tjw.2	+	51	5536	c.5350G>A	c.(5350-5352)GAC>AAC	p.D1784N	STAB2_uc009zug.2_RNA	NM_017564	NP_060034	Q8WWQ8	STAB2_HUMAN	stabilin 2 precursor	1784	Extracellular (Potential).|FAS1 6.				angiogenesis|cell adhesion|defense response to bacterium|receptor-mediated endocytosis	cytoplasm|external side of plasma membrane|integral to plasma membrane	Gram-negative bacterial cell surface binding|hyaluronic acid binding|low-density lipoprotein receptor activity|protein disulfide oxidoreductase activity|scavenger receptor activity			ovary(9)|skin(5)	14						CTGGCCCACCGACCAAGCCCT	0.522													71	175	---	---	---	---	PASS
SKA3	221150	broad.mit.edu	37	13	21742170	21742170	+	Missense_Mutation	SNP	C	T	T			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:21742170C>T	uc001unt.2	-	4	794	c.700G>A	c.(700-702)GAA>AAA	p.E234K	SKA3_uc001unv.2_Missense_Mutation_p.E152K|SKA3_uc001unu.2_Missense_Mutation_p.E234K	NM_145061	NP_659498	Q8IX90	SKA3_HUMAN	SKA3	234					cell division|chromosome segregation|mitosis|regulation of microtubule polymerization or depolymerization	condensed chromosome outer kinetochore|cytoplasm|spindle microtubule	protein binding				0						GTGTAATCTTCATTTAAACAC	0.299													61	121	---	---	---	---	PASS
GPR12	2835	broad.mit.edu	37	13	27333002	27333002	+	Silent	SNP	C	T	T			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:27333002C>T	uc010aal.2	-	2	1185	c.963G>A	c.(961-963)CCG>CCA	p.P321P	GPR12_uc010tdl.1_Silent_p.P162P	NM_005288	NP_005279	P47775	GPR12_HUMAN	G protein-coupled receptor 12	321	Cytoplasmic (Potential).					integral to plasma membrane					0	Colorectal(5;5.77e-05)	Breast(139;0.198)		Epithelial(112;9.37e-07)|OV - Ovarian serous cystadenocarcinoma(117;1.16e-06)|all cancers(112;8.31e-06)|GBM - Glioblastoma multiforme(144;0.00121)|Lung(94;0.111)|LUSC - Lung squamous cell carcinoma(192;0.184)		CGAGACTGGACGGGATGCAGC	0.557													11	73	---	---	---	---	PASS
AKAP11	11215	broad.mit.edu	37	13	42874542	42874542	+	Missense_Mutation	SNP	G	T	T			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:42874542G>T	uc001uys.1	+	8	1835	c.1660G>T	c.(1660-1662)GCA>TCA	p.A554S		NM_016248	NP_057332	Q9UKA4	AKA11_HUMAN	A-kinase anchor protein 11	554					intracellular protein kinase cascade	microtubule organizing center	protein kinase A binding|protein phosphatase 1 binding			ovary(1)|central_nervous_system(1)	2		Lung NSC(96;1.86e-05)|Prostate(109;0.0165)|Lung SC(185;0.0262)|Breast(139;0.0707)|Hepatocellular(98;0.114)		OV - Ovarian serous cystadenocarcinoma(117;0.000365)|GBM - Glioblastoma multiforme(144;0.00116)|BRCA - Breast invasive adenocarcinoma(63;0.19)		TCAAAAATTTGCAGCAGATCT	0.303													4	169	---	---	---	---	PASS
GPR183	1880	broad.mit.edu	37	13	99948279	99948279	+	Missense_Mutation	SNP	C	G	G	rs141594545		TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:99948279C>G	uc001vog.2	-	2	295	c.121G>C	c.(121-123)GTC>CTC	p.V41L	UBAC2_uc001voa.3_Intron|UBAC2_uc010tiu.1_Intron|UBAC2_uc001vob.3_Intron|UBAC2_uc010tiv.1_Intron|UBAC2_uc001vod.2_Intron|UBAC2_uc001voc.2_Intron|UBAC2_uc010tiw.1_Intron	NM_004951	NP_004942	P32249	GP183_HUMAN	EBV-induced G protein-coupled receptor 2	41	Helical; Name=1; (Potential).				humoral immune response|mature B cell differentiation involved in immune response	integral to plasma membrane	purinergic nucleotide receptor activity, G-protein coupled				0						ATGATGAAGACGAGGCTGTAA	0.458													10	145	---	---	---	---	PASS
MOAP1	64112	broad.mit.edu	37	14	93649475	93649475	+	3'UTR	SNP	G	T	T			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:93649475G>T	uc001ybj.2	-	3					C14orf109_uc001ybk.3_5'Flank|C14orf109_uc010auo.2_5'Flank	NM_022151	NP_071434	Q96BY2	MOAP1_HUMAN	modulator of apoptosis 1						activation of caspase activity|apoptotic nuclear change	cytoplasm	protein homodimerization activity			skin(2)|ovary(1)	3		all_cancers(154;0.00528)|Acute lymphoblastic leukemia(33;0.0497)|all_epithelial(191;0.125)|all_neural(303;0.13)		Epithelial(152;0.178)|all cancers(159;0.2)|COAD - Colon adenocarcinoma(157;0.204)		AGAGTATATAGACTGTTCTAC	0.428													3	28	---	---	---	---	PASS
EIF2AK4	440275	broad.mit.edu	37	15	40268968	40268968	+	Silent	SNP	C	A	A			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:40268968C>A	uc001zkm.1	+	12	2222	c.2172C>A	c.(2170-2172)CCC>CCA	p.P724P	EIF2AK4_uc010bbj.1_Silent_p.P453P	NM_001013703	NP_001013725	Q9P2K8	E2AK4_HUMAN	eukaryotic translation initiation factor 2 alpha	724	Protein kinase 2.				translation	cytosolic ribosome	aminoacyl-tRNA ligase activity|ATP binding|eukaryotic translation initiation factor 2alpha kinase activity|protein homodimerization activity			lung(2)|stomach(1)|skin(1)	4		all_cancers(109;1.05e-19)|all_epithelial(112;4.38e-17)|Lung NSC(122;1.09e-12)|all_lung(180;3.56e-11)|Melanoma(134;0.0575)|Ovarian(310;0.0826)|Colorectal(260;0.119)		GBM - Glioblastoma multiforme(113;5.31e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0616)		CCCGTTTCCCCGCCACCGGCC	0.711													35	98	---	---	---	---	PASS
SQRDL	58472	broad.mit.edu	37	15	45962137	45962137	+	Silent	SNP	A	G	G			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:45962137A>G	uc001zvt.2	+	5	606	c.417A>G	c.(415-417)CGA>CGG	p.R139R	SQRDL_uc001zvu.2_Silent_p.R139R|SQRDL_uc001zvv.2_Silent_p.R139R	NM_021199	NP_067022	Q9Y6N5	SQRD_HUMAN	sulfide dehydrogenase like precursor	139							oxidoreductase activity			ovary(1)	1		Lung NSC(122;0.000117)|all_lung(180;0.000737)|Melanoma(134;0.0417)		all cancers(107;5.89e-18)|GBM - Glioblastoma multiforme(94;1.21e-06)|COAD - Colon adenocarcinoma(120;0.17)|Colorectal(133;0.188)		TCTCCTACCGATATCTTATTA	0.448													100	272	---	---	---	---	PASS
ADAM10	102	broad.mit.edu	37	15	58904077	58904077	+	Missense_Mutation	SNP	A	G	G			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:58904077A>G	uc002afd.1	-	12	2069	c.1625T>C	c.(1624-1626)CTC>CCC	p.L542P	ADAM10_uc010bgc.1_RNA|ADAM10_uc010ugz.1_Missense_Mutation_p.L241P|ADAM10_uc002afe.1_Intron|ADAM10_uc002aff.1_Missense_Mutation_p.L79P	NM_001110	NP_001101	O14672	ADA10_HUMAN	ADAM metallopeptidase domain 10 precursor	542	Extracellular (Potential).|Disintegrin.				cell-cell signaling|constitutive protein ectodomain proteolysis|epidermal growth factor receptor signaling pathway|in utero embryonic development|integrin-mediated signaling pathway|monocyte activation|negative regulation of cell adhesion|Notch receptor processing|Notch signaling pathway|PMA-inducible membrane protein ectodomain proteolysis|positive regulation of cell growth|positive regulation of cell proliferation|positive regulation of T cell chemotaxis|protein phosphorylation|response to tumor necrosis factor	cell surface|endomembrane system|Golgi-associated vesicle|integral to membrane|nucleus|plasma membrane	integrin binding|metalloendopeptidase activity|protein homodimerization activity|protein kinase binding|SH3 domain binding|zinc ion binding			skin(2)	2				GBM - Glioblastoma multiforme(80;0.202)		TGCTGGGCAGAGAGCTGTGAA	0.413													42	115	---	---	---	---	PASS
RNF111	54778	broad.mit.edu	37	15	59323305	59323305	+	Missense_Mutation	SNP	G	A	A			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:59323305G>A	uc002afv.2	+	2	563	c.284G>A	c.(283-285)CGC>CAC	p.R95H	RNF111_uc002afs.2_Missense_Mutation_p.R95H|RNF111_uc002aft.2_Missense_Mutation_p.R95H|RNF111_uc002afu.2_Missense_Mutation_p.R95H|RNF111_uc002afw.2_Missense_Mutation_p.R95H	NM_017610	NP_060080	Q6ZNA4	RN111_HUMAN	ring finger protein 111	95					multicellular organismal development|positive regulation of transcription, DNA-dependent	cytoplasm|nucleus	protein binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(2)	2				all cancers(107;0.194)		AGGAAAAAACGCAAAAGCCAG	0.423													4	134	---	---	---	---	PASS
ALPK3	57538	broad.mit.edu	37	15	85405941	85405941	+	Missense_Mutation	SNP	T	C	C			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:85405941T>C	uc002ble.2	+	10	4978	c.4811T>C	c.(4810-4812)CTC>CCC	p.L1604P	ALPK3_uc010upc.1_5'Flank	NM_020778	NP_065829	Q96L96	ALPK3_HUMAN	alpha-kinase 3	1604	Alpha-type protein kinase.				heart development	nucleus	ATP binding|protein serine/threonine kinase activity			stomach(3)|ovary(3)|lung(2)|skin(2)|central_nervous_system(1)|breast(1)	12			BRCA - Breast invasive adenocarcinoma(143;0.0587)			GGGGACAAGCTCTTTGGGCGA	0.582													56	116	---	---	---	---	PASS
SRRM2	23524	broad.mit.edu	37	16	2809634	2809634	+	Missense_Mutation	SNP	G	T	T			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2809634G>T	uc002crk.2	+	9	1354	c.805G>T	c.(805-807)GCT>TCT	p.A269S	SRRM2_uc002crj.1_Missense_Mutation_p.A173S|SRRM2_uc002crl.1_Missense_Mutation_p.A269S|SRRM2_uc010bsu.1_Missense_Mutation_p.A173S	NM_016333	NP_057417	Q9UQ35	SRRM2_HUMAN	splicing coactivator subunit SRm300	269	Ser-rich.					Cajal body|catalytic step 2 spliceosome|nuclear speck	C2H2 zinc finger domain binding|protein N-terminus binding|RNA binding			ovary(1)|pancreas(1)|central_nervous_system(1)|skin(1)	4						TGCTGACTCTGCTTCCTCCTC	0.517													57	94	---	---	---	---	PASS
UBN1	29855	broad.mit.edu	37	16	4920562	4920562	+	Missense_Mutation	SNP	G	T	T			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:4920562G>T	uc002cyb.2	+	10	1696	c.1357G>T	c.(1357-1359)GGC>TGC	p.G453C	UBN1_uc010uxw.1_Missense_Mutation_p.G453C|UBN1_uc002cyc.2_Missense_Mutation_p.G453C	NM_001079514	NP_001072982	Q9NPG3	UBN1_HUMAN	ubinuclein 1	453					chromatin modification|interspecies interaction between organisms|regulation of transcription from RNA polymerase II promoter	PML body|tight junction	DNA binding|sequence-specific DNA binding transcription factor activity			skin(2)	2						GGAAGCCATTGGCAGGGCGAT	0.577													32	42	---	---	---	---	PASS
PYCARD	29108	broad.mit.edu	37	16	31213020	31213020	+	Missense_Mutation	SNP	C	G	G			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31213020C>G	uc010cak.2	-	3	714	c.474G>C	c.(472-474)AAG>AAC	p.K158N	PYCARD_uc002ebm.2_Missense_Mutation_p.K139N	NM_013258	NP_037390	Q9ULZ3	ASC_HUMAN	PYD and CARD domain containing isoform a	158	CARD.				induction of apoptosis|positive regulation of interleukin-1 beta secretion|positive regulation of NF-kappaB transcription factor activity|proteolysis|tumor necrosis factor-mediated signaling pathway	IkappaB kinase complex	caspase activator activity|cysteine-type endopeptidase activity|protein homodimerization activity|Pyrin domain binding				0						GCTTCCGCATCTTGCTTGGGT	0.602													53	103	---	---	---	---	PASS
FTO	79068	broad.mit.edu	37	16	53878083	53878083	+	Missense_Mutation	SNP	T	G	G			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:53878083T>G	uc002ehr.2	+	4	990	c.768T>G	c.(766-768)AGT>AGG	p.S256R	FTO_uc010vha.1_5'UTR	NM_001080432	NP_001073901	Q9C0B1	FTO_HUMAN	fat mass and obesity associated	256	Fe2OG dioxygenase domain.				DNA dealkylation involved in DNA repair|oxidative single-stranded DNA demethylation|oxidative single-stranded RNA demethylation|RNA repair	nucleus	DNA-N1-methyladenine dioxygenase activity|ferrous iron binding|oxidative DNA demethylase activity|oxidative RNA demethylase activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen				0						AAGAGGAAAGTGAGGATGACT	0.373													46	108	---	---	---	---	PASS
PLEKHG4	25894	broad.mit.edu	37	16	67318935	67318935	+	Missense_Mutation	SNP	C	T	T			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67318935C>T	uc002eso.3	+	12	4547	c.2012C>T	c.(2011-2013)CCC>CTC	p.P671L	PLEKHG4_uc002esp.3_Missense_Mutation_p.P478L|PLEKHG4_uc002esq.3_Missense_Mutation_p.P671L|PLEKHG4_uc010cef.2_Missense_Mutation_p.P671L|PLEKHG4_uc002ess.3_Missense_Mutation_p.P671L|PLEKHG4_uc010ceg.2_Missense_Mutation_p.P590L	NM_015432	NP_056247	Q58EX7	PKHG4_HUMAN	pleckstrin homology domain containing, family G	671					regulation of Rho protein signal transduction	intracellular	Rho guanyl-nucleotide exchange factor activity			skin(1)|pancreas(1)	2				OV - Ovarian serous cystadenocarcinoma(108;0.00376)|Epithelial(162;0.0173)|all cancers(182;0.116)|Kidney(780;0.119)		GCCCACCCTCCCCTGAGGAAG	0.627													22	56	---	---	---	---	PASS
ZNF276	92822	broad.mit.edu	37	16	89789584	89789584	+	Silent	SNP	G	A	A			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89789584G>A	uc002fos.3	+	3	646	c.549G>A	c.(547-549)GCG>GCA	p.A183A	C16orf7_uc002fom.1_5'Flank|ZNF276_uc010ciq.2_Translation_Start_Site|ZNF276_uc002fop.2_Silent_p.A108A|ZNF276_uc002foq.3_Silent_p.A108A|ZNF276_uc010cir.2_RNA|ZNF276_uc002for.3_Translation_Start_Site|ZNF276_uc010cis.2_Translation_Start_Site|ZNF276_uc002fot.3_RNA|ZNF276_uc010vpm.1_Silent_p.A21A|ZNF276_uc010cit.1_Translation_Start_Site	NM_001113525	NP_001106997	Q8N554	ZN276_HUMAN	zinc finger protein 276 isoform a	183					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Lung NSC(15;2.19e-05)|all_lung(18;3.07e-05)|all_hematologic(23;0.0256)		BRCA - Breast invasive adenocarcinoma(80;0.0278)		AGGAGGGAGCGTGTCTGGGTG	0.637													33	67	---	---	---	---	PASS
RILP	83547	broad.mit.edu	37	17	1549792	1549792	+	Missense_Mutation	SNP	A	T	T			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1549792A>T	uc002ftd.2	-	8	1444	c.1150T>A	c.(1150-1152)TGT>AGT	p.C384S	SCARF1_uc002fsy.1_5'Flank|SCARF1_uc002fsz.1_5'Flank|SCARF1_uc002fta.1_5'Flank|SCARF1_uc010cjv.1_5'Flank	NM_031430	NP_113618	Q96NA2	RILP_HUMAN	Rab interacting lysosomal protein	384					endosome to lysosome transport|protein transport	late endosome membrane|lysosomal membrane|phagocytic vesicle membrane	Rab GTPase binding			ovary(1)	1				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)		AGGGCAGAACAGGGCGGATCA	0.602													77	170	---	---	---	---	PASS
KDM6B	23135	broad.mit.edu	37	17	7756374	7756374	+	Missense_Mutation	SNP	G	A	A			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7756374G>A	uc002giw.1	+	21	5043	c.4667G>A	c.(4666-4668)CGG>CAG	p.R1556Q	KDM6B_uc002gix.2_Missense_Mutation_p.R858Q|TMEM88_uc002giy.2_5'Flank	NM_001080424	NP_001073893	O15054	KDM6B_HUMAN	lysine (K)-specific demethylase 6B	1556					inflammatory response	nucleus	metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen			central_nervous_system(1)|pancreas(1)	2						AGCCTGGTGCGGGCAGGGAAG	0.622													3	79	---	---	---	---	PASS
MYH4	4622	broad.mit.edu	37	17	10369589	10369589	+	Splice_Site	SNP	C	T	T			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10369589C>T	uc002gmn.2	-	4	459	c.348_splice	c.e4+1	p.Y116_splice	uc002gml.1_Intron	NM_017533	NP_060003	Q9Y623	MYH4_HUMAN	myosin, heavy polypeptide 4, skeletal muscle						muscle filament sliding	muscle myosin complex|myosin filament|sarcomere	actin binding|ATP binding|calmodulin binding|microfilament motor activity|structural constituent of muscle			ovary(10)|skin(2)|central_nervous_system(1)	13						AGGGTGCTCACGTAGATCATC	0.433													30	144	---	---	---	---	PASS
MYOCD	93649	broad.mit.edu	37	17	12569403	12569403	+	5'UTR	SNP	A	C	C			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:12569403A>C	uc002gnn.2	+	1					MYOCD_uc002gno.2_5'UTR	NM_153604	NP_705832	Q8IZQ8	MYCD_HUMAN	myocardin isoform 2						cardiac muscle cell differentiation|negative regulation of cell proliferation|negative regulation of cyclin-dependent protein kinase activity|positive regulation of smooth muscle cell differentiation|positive regulation of smooth muscle contraction|positive regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation|regulation of histone acetylation|smooth muscle cell differentiation	nucleus	nucleic acid binding|RNA polymerase II transcription factor binding transcription factor activity|transcription factor binding			central_nervous_system(2)|skin(2)|ovary(1)	5				UCEC - Uterine corpus endometrioid carcinoma (92;0.0969)		AGTTGGATGAATTCTGGGTTG	0.632													3	5	---	---	---	---	PASS
EPN2	22905	broad.mit.edu	37	17	19186450	19186450	+	Silent	SNP	C	A	A			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:19186450C>A	uc002gvd.3	+	3	466	c.18C>A	c.(16-18)ATC>ATA	p.I6I	EPN2_uc002gvc.2_Silent_p.I6I|EPN2_uc010vyn.1_Silent_p.I6I|EPN2_uc010cql.1_Intron|EPN2_uc002gve.3_Silent_p.I6I|EPN2_uc002gvf.3_Intron|EPN2_uc010vyo.1_Intron|EPN2_uc002gvg.1_Silent_p.I6I|EPN2_uc010vyp.1_Silent_p.I6I|EPN2_uc010vyq.1_Silent_p.I6I|EPN2_uc002gvh.1_Silent_p.I6I	NM_014964	NP_055779	O95208	EPN2_HUMAN	epsin 2 isoform b	6					endocytosis		lipid binding			skin(1)	1	all_cancers(12;3.11e-05)|all_epithelial(12;0.00121)|Hepatocellular(7;0.00345)|Breast(13;0.143)					CTTCGTCTATCAGACGGCAGA	0.453													4	103	---	---	---	---	PASS
HAP1	9001	broad.mit.edu	37	17	39884564	39884564	+	Missense_Mutation	SNP	C	A	A			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39884564C>A	uc002hxm.1	-	7	1101	c.1089G>T	c.(1087-1089)ATG>ATT	p.M363I	JUP_uc010wfs.1_Intron|HAP1_uc002hxn.1_Missense_Mutation_p.M363I|HAP1_uc002hxo.1_Missense_Mutation_p.M371I|HAP1_uc002hxp.1_Missense_Mutation_p.M363I	NM_177977	NP_817084	P54257	HAP1_HUMAN	huntingtin-associated protein 1 isoform 2	363	Glu-rich.|HAP1 N-terminal.				brain development|protein localization|synaptic transmission	actin cytoskeleton	protein binding			ovary(2)	2		Breast(137;0.000162)	BRCA - Breast invasive adenocarcinoma(4;0.0677)			ACAGCTCAGCCATCTGTTGGC	0.657													9	75	---	---	---	---	PASS
C17orf65	339201	broad.mit.edu	37	17	42255170	42255170	+	5'UTR	SNP	G	A	A			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42255170G>A	uc002ifn.2	-	4					ASB16_uc002ifl.1_Intron|ASB16_uc002ifm.1_Intron	NM_178542	NP_848637	Q495Z4	CQ065_HUMAN	hypothetical protein LOC339201												0		Breast(137;0.00765)|Prostate(33;0.0313)		BRCA - Breast invasive adenocarcinoma(366;0.114)		CATGGAGGGAGCAGCAGGAGG	0.637													4	10	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	17	44910750	44910750	+	IGR	SNP	C	A	A			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:44910750C>A								WNT3 (14668 upstream) : WNT9B (18218 downstream)																							CTCTGGCATGCCAAGGCCTGA	0.512													3	45	---	---	---	---	PASS
TOM1L1	10040	broad.mit.edu	37	17	53027421	53027421	+	Missense_Mutation	SNP	A	G	G			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:53027421A>G	uc002iud.2	+	14	1479	c.1304A>G	c.(1303-1305)GAT>GGT	p.D435G	TOM1L1_uc010dca.1_Missense_Mutation_p.D424G|TOM1L1_uc010wnb.1_Missense_Mutation_p.D428G|TOM1L1_uc010wnc.1_Missense_Mutation_p.D358G|TOM1L1_uc010dbz.2_Missense_Mutation_p.D358G|TOM1L1_uc010wnd.1_Missense_Mutation_p.D323G	NM_005486	NP_005477	O75674	TM1L1_HUMAN	target of myb1-like 1	435					intracellular protein transport|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway	cytosol|endosome membrane|Golgi stack|lysosome	SH3 domain binding|ubiquitin binding			ovary(1)	1						ACAAAAAGTGATCTCCAGCCA	0.343													50	102	---	---	---	---	PASS
PSMC5	5705	broad.mit.edu	37	17	61908394	61908394	+	Splice_Site	SNP	A	G	G			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:61908394A>G	uc002jcb.2	+	8	721	c.680_splice	c.e8-2	p.G227_splice	PSMC5_uc010ddy.2_Splice_Site_p.G204_splice|PSMC5_uc010ddz.2_Splice_Site_p.G148_splice|PSMC5_uc002jcc.2_Splice_Site_p.G219_splice|PSMC5_uc002jcd.2_Splice_Site_p.G219_splice	NM_002805	NP_002796	P62195	PRS8_HUMAN	proteasome 26S ATPase subunit 5						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of programmed cell death|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of transcription, DNA-dependent|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|transcription from RNA polymerase II promoter|viral reproduction	cytoplasm|nucleus|proteasome complex	ATP binding|ATPase activity|thyrotropin-releasing hormone receptor binding|transcription cofactor activity|transcription factor binding			large_intestine(1)	1						GCCTCCACACAGGGGCAAGAA	0.532													37	85	---	---	---	---	PASS
SLC39A6	25800	broad.mit.edu	37	18	33706569	33706569	+	Missense_Mutation	SNP	A	C	C			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:33706569A>C	uc010dmy.2	-	2	692	c.402T>G	c.(400-402)CAT>CAG	p.H134Q	SLC39A6_uc002kzj.2_Intron	NM_012319	NP_036451	Q13433	S39A6_HUMAN	solute carrier family 39 (zinc transporter),	134	His-rich.|Extracellular (Potential).					integral to membrane|lamellipodium membrane	zinc ion transmembrane transporter activity			ovary(1)|pancreas(1)	2						CAGAAGCAGCatgattatggt	0.234													13	85	---	---	---	---	PASS
GADD45B	4616	broad.mit.edu	37	19	2476511	2476511	+	Intron	SNP	T	A	A			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2476511T>A	uc002lwb.1	+						GADD45B_uc010dtd.1_Intron|GADD45B_uc002lwc.1_5'UTR	NM_015675	NP_056490	O75293	GA45B_HUMAN	growth arrest and DNA-damage-inducible, beta						activation of MAPKKK activity|apoptosis|cell differentiation|multicellular organismal development|response to stress						0		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)		CACTGATCCCTCTTTCCTGGT	0.552													14	39	---	---	---	---	PASS
ZNF653	115950	broad.mit.edu	37	19	11597661	11597661	+	Missense_Mutation	SNP	C	A	A			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11597661C>A	uc002mrz.1	-	6	1431	c.1378G>T	c.(1378-1380)GCT>TCT	p.A460S		NM_138783	NP_620138	Q96CK0	ZN653_HUMAN	zinc finger protein 653	460					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						AGGCCGTCAGCATCCATCACC	0.701													5	17	---	---	---	---	PASS
SSBP4	170463	broad.mit.edu	37	19	18543023	18543023	+	Missense_Mutation	SNP	A	G	G			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:18543023A>G	uc002niy.2	+	10	941	c.703A>G	c.(703-705)ATG>GTG	p.M235V	SSBP4_uc002niz.2_Missense_Mutation_p.M213V	NM_032627	NP_116016	Q9BWG4	SSBP4_HUMAN	single stranded DNA binding protein 4 isoform a	235	Pro-rich.					nucleus	single-stranded DNA binding				0						TGCCATGAACATGTAAGACCC	0.642													14	40	---	---	---	---	PASS
ZNF780A	284323	broad.mit.edu	37	19	40582092	40582092	+	Missense_Mutation	SNP	T	C	C			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:40582092T>C	uc002omy.2	-	6	482	c.257A>G	c.(256-258)GAG>GGG	p.E86G	ZNF780A_uc002omw.3_Missense_Mutation_p.E102G|ZNF780A_uc002omz.2_Missense_Mutation_p.E86G|ZNF780A_uc010xvh.1_Missense_Mutation_p.E87G	NM_001010880	NP_001010880	O75290	Z780A_HUMAN	zinc finger protein 780A isoform b	86					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	all_cancers(60;9.55e-06)|all_lung(34;1.17e-07)|Lung NSC(34;1.41e-07)|Ovarian(47;0.0925)					AGATACTTTCTCAGGTCCATA	0.323													42	78	---	---	---	---	PASS
PSG1	5669	broad.mit.edu	37	19	43348720	43348720	+	Missense_Mutation	SNP	C	T	T			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:43348720C>T	uc002oux.1	-	5	1225	c.1076G>A	c.(1075-1077)CGT>CAT	p.R359H	PSG3_uc002ouf.2_Intron|PSG1_uc002oug.1_Intron|PSG11_uc002ouw.2_Intron|PSG7_uc002ous.1_Intron|PSG7_uc002out.1_Intron|PSG10_uc002ouv.1_Intron|PSG8_uc002ouj.3_Intron|PSG8_uc002ouk.3_Intron|PSG8_uc002oul.3_Intron|PSG8_uc002oum.3_Intron|PSG1_uc002oun.2_RNA|PSG8_uc002oup.3_Intron|PSG10_uc010eip.2_RNA|PSG1_uc002our.1_Intron|PSG1_uc010eio.1_Intron|PSG1_uc002ouy.1_Missense_Mutation_p.R337H	NM_006905	NP_008836	P11464	PSG1_HUMAN	pregnancy specific beta-1-glycoprotein 1	345	Ig-like C2-type 3.				female pregnancy	extracellular region				ovary(2)	2		Prostate(69;0.00682)				TTGTCCTGAACGGTAATAGGT	0.468													86	219	---	---	---	---	PASS
GLTSCR1	29998	broad.mit.edu	37	19	48198183	48198183	+	Missense_Mutation	SNP	C	A	A			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:48198183C>A	uc002phh.3	+	9	3116	c.2922C>A	c.(2920-2922)AAC>AAA	p.N974K	GLTSCR1_uc002phi.3_Missense_Mutation_p.N732K	NM_015711	NP_056526	Q9NZM4	GSCR1_HUMAN	glioma tumor suppressor candidate region gene 1	974							protein binding			pancreas(3)	3		all_cancers(25;1.8e-07)|all_lung(116;5.73e-06)|Lung NSC(112;9.69e-06)|all_epithelial(76;2.42e-05)|all_neural(266;0.0332)|Ovarian(192;0.086)		all cancers(93;0.000358)|OV - Ovarian serous cystadenocarcinoma(262;0.000576)|Epithelial(262;0.0212)|GBM - Glioblastoma multiforme(486;0.0355)		TCCTCCAGAACAAGGCTGGGG	0.687													6	18	---	---	---	---	PASS
CLEC11A	6320	broad.mit.edu	37	19	51228703	51228703	+	Silent	SNP	C	T	T			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51228703C>T	uc002psy.2	+	4	1129	c.951C>T	c.(949-951)TAC>TAT	p.Y317Y		NM_002975	NP_002966	Q9Y240	CLC11_HUMAN	stem cell growth factor precursor	317	C-type lectin.				positive regulation of cell proliferation	cytoplasm|extracellular region	growth factor activity|sugar binding			ovary(1)	1		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00641)|GBM - Glioblastoma multiforme(134;0.028)		GTCTCTACTACGTCTGCGAGT	0.701													10	9	---	---	---	---	PASS
ZNF525	170958	broad.mit.edu	37	19	53889703	53889703	+	3'UTR	SNP	T	A	A			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53889703T>A	uc010eqn.2	+	4					ZNF525_uc002qbl.2_RNA|ZNF765_uc010ydx.1_Intron	NR_003699				Homo sapiens cDNA FLJ39718 fis, clone SMINT2013695.												0						CACGTTACCATATCAAGCTGA	0.383													45	111	---	---	---	---	PASS
ZNF525	170958	broad.mit.edu	37	19	53889727	53889727	+	3'UTR	SNP	A	G	G			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53889727A>G	uc010eqn.2	+	4					ZNF525_uc002qbl.2_RNA|ZNF765_uc010ydx.1_Intron	NR_003699				Homo sapiens cDNA FLJ39718 fis, clone SMINT2013695.												0						TGTCACCACTATCTGGACAGT	0.373													36	82	---	---	---	---	PASS
ZNF587	84914	broad.mit.edu	37	19	58370327	58370327	+	Missense_Mutation	SNP	T	C	C			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58370327T>C	uc002qql.2	+	3	685	c.547T>C	c.(547-549)TCA>CCA	p.S183P	ZNF587_uc002qqb.2_Missense_Mutation_p.S140P|ZNF587_uc010yhh.1_Missense_Mutation_p.S140P|ZNF587_uc002qqi.1_Missense_Mutation_p.S140P|ZNF587_uc002qqj.1_RNA|ZNF814_uc002qqk.2_Intron|ZNF587_uc010yhk.1_Missense_Mutation_p.S182P	NM_032828	NP_116217	Q96SQ5	ZN587_HUMAN	zinc finger protein 587	183					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Colorectal(82;0.000256)|all_neural(62;0.0577)|Breast(46;0.147)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0264)		TCTGCCCAGTTCAGGATTGTG	0.468													7	296	---	---	---	---	PASS
TSHZ2	128553	broad.mit.edu	37	20	51871758	51871758	+	Silent	SNP	G	T	T			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:51871758G>T	uc002xwo.2	+	2	2717	c.1761G>T	c.(1759-1761)CTG>CTT	p.L587L		NM_173485	NP_775756	Q9NRE2	TSH2_HUMAN	teashirt zinc finger homeobox 2	587					multicellular organismal development	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(5)|haematopoietic_and_lymphoid_tissue(1)	6			STAD - Stomach adenocarcinoma(23;0.1)			TGATGCCACTGGTTTCTATGC	0.527													12	229	---	---	---	---	PASS
L3MBTL2	83746	broad.mit.edu	37	22	41605813	41605813	+	Silent	SNP	C	A	A			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41605813C>A	uc003azo.2	+	2	192	c.138C>A	c.(136-138)TCC>TCA	p.S46S	L3MBTL2_uc010gyi.1_5'UTR|L3MBTL2_uc003azn.2_RNA|uc003azp.1_RNA	NM_031488	NP_113676	Q969R5	LMBL2_HUMAN	l(3)mbt-like 2	46					chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	methylated histone residue binding|transcription corepressor activity|zinc ion binding			ovary(2)|central_nervous_system(1)	3						AGAGCAGCTCCTATCTGGAGG	0.542													5	208	---	---	---	---	PASS
CYB5R3	1727	broad.mit.edu	37	22	43024287	43024287	+	Missense_Mutation	SNP	C	A	A			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:43024287C>A	uc003bcz.2	-	5	418	c.334G>T	c.(334-336)GTT>TTT	p.V112F	CYB5R3_uc010gzc.1_5'UTR|CYB5R3_uc003bcw.2_Missense_Mutation_p.V102F|CYB5R3_uc011aps.1_Missense_Mutation_p.V145F|CYB5R3_uc003bcy.2_Missense_Mutation_p.V89F|CYB5R3_uc003bcx.2_Missense_Mutation_p.V89F	NM_000398	NP_000389	P00387	NB5R3_HUMAN	cytochrome b5 reductase 3 isoform m	112	FAD-binding FR-type.				blood circulation|cholesterol biosynthetic process|water-soluble vitamin metabolic process	endoplasmic reticulum membrane|hemoglobin complex|mitochondrial outer membrane	cytochrome-b5 reductase activity			skin(1)	1					NADH(DB00157)	TTGAAGTAAACCTGCAAGACA	0.587													81	155	---	---	---	---	PASS
SMS	6611	broad.mit.edu	37	X	22002497	22002497	+	Missense_Mutation	SNP	G	T	T			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:22002497G>T	uc004dag.2	+	8	927	c.826G>T	c.(826-828)GAT>TAT	p.D276Y	SMS_uc010nfs.2_Intron|SMS_uc010nft.2_Missense_Mutation_p.D53Y	NM_004595	NP_004586	P52788	SPSY_HUMAN	spermine synthase	276		Proton acceptor (Probable).		D->N: 200,000-fold decrease in catalytic efficiency.	methionine metabolic process|spermine biosynthetic process	cytosol	spermidine synthase activity|spermine synthase activity			ovary(1)	1					Spermine(DB00127)	TGTGATTAATGATTTGACAGC	0.393													20	94	---	---	---	---	PASS
KLHL4	56062	broad.mit.edu	37	X	86890699	86890699	+	Missense_Mutation	SNP	G	A	A			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:86890699G>A	uc004efb.2	+	9	2031	c.1849G>A	c.(1849-1851)GGA>AGA	p.G617R	KLHL4_uc004efa.2_Missense_Mutation_p.G617R	NM_019117	NP_061990	Q9C0H6	KLHL4_HUMAN	kelch-like 4 isoform 1	617	Kelch 4.					cytoplasm|microtubule cytoskeleton|nucleolus	actin binding			ovary(2)|lung(1)|breast(1)|central_nervous_system(1)	5						CACATACAATGGATTCTTATA	0.458													38	23	---	---	---	---	PASS
TCEAL4	79921	broad.mit.edu	37	X	102841696	102841696	+	Missense_Mutation	SNP	A	T	T			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:102841696A>T	uc004ekl.2	+	3	386	c.93A>T	c.(91-93)GAA>GAT	p.E31D	TCEAL4_uc004ekn.2_Missense_Mutation_p.E31D|TCEAL4_uc004ekm.2_Missense_Mutation_p.E31D|TCEAL4_uc004eko.2_Missense_Mutation_p.E31D	NM_024863	NP_079139	Q96EI5	TCAL4_HUMAN	transcription elongation factor A (SII)-like 4	31	Glu-rich.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus					0						GAAAGCCAGAAGTAACTTGTA	0.259													12	6	---	---	---	---	PASS
COL4A6	1288	broad.mit.edu	37	X	107681171	107681171	+	Splice_Site	SNP	C	A	A			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:107681171C>A	uc004enw.3	-	2	169	c.66_splice	c.e2+1	p.A22_splice	COL4A6_uc004env.3_Splice_Site_p.A21_splice|COL4A6_uc011msn.1_Splice_Site_p.A21_splice|COL4A6_uc010npk.2_Splice_Site_p.A21_splice|COL4A6_uc004enx.2_Splice_Site|COL4A6_uc004eny.2_Splice_Site|COL4A5_uc004enz.1_5'Flank|COL4A5_uc011mso.1_5'Flank	NM_001847	NP_001838	Q14031	CO4A6_HUMAN	type IV alpha 6 collagen isoform A precursor						cell adhesion|extracellular matrix organization	collagen type IV	extracellular matrix structural constituent|protein binding			ovary(6)|urinary_tract(1)|large_intestine(1)	8						AAGAGACTCACCGCTGCTGCC	0.552									Alport_syndrome_with_Diffuse_Leiomyomatosis				11	10	---	---	---	---	PASS
SLC35E2B	728661	broad.mit.edu	37	1	1669647	1669648	+	Intron	DEL	CT	-	-			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1669647_1669648delCT	uc001ahh.3	-						SLC35E2_uc009vkm.1_Intron|SLC35E2_uc001ahy.2_Intron|SLC35E2_uc001ahz.2_Intron|SLC35E2_uc001aib.1_Intron	NM_001110781	NP_001104251	P0CK96	S352B_HUMAN	similar to solute carrier family 35, member E2							integral to membrane					0						GTGGGCACCACTCTGAGTGGTC	0.673													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	11691955	11691966	+	IGR	DEL	AAGAAAGAAAGA	-	-	rs11804766	by1000genomes	TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11691955_11691966delAAGAAAGAAAGA								PTCHD2 (94316 upstream) : FBXO2 (16484 downstream)																							ggaaggaaggaagaaagaaagaaagaaagaaa	0.132													5	3	---	---	---	---	
FBLIM1	54751	broad.mit.edu	37	1	16103361	16103362	+	Intron	INS	-	A	A	rs36071270		TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16103361_16103362insA	uc001axd.1	+						FBLIM1_uc001axe.1_Intron|FBLIM1_uc001axf.2_Intron|FBLIM1_uc001axh.1_Intron|FBLIM1_uc001axi.1_Intron	NM_017556	NP_060026	Q8WUP2	FBLI1_HUMAN	filamin-binding LIM protein-1 isoform a						cell adhesion|cell junction assembly|regulation of cell shape	cell cortex|cytoskeleton|cytosol|focal adhesion|intracellular membrane-bounded organelle	zinc ion binding			skin(1)	1		Colorectal(325;0.000257)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.56e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|KIRC - Kidney renal clear cell carcinoma(229;0.00244)|READ - Rectum adenocarcinoma(331;0.0649)|STAD - Stomach adenocarcinoma(313;0.138)		aactccatctcaaaaaaaaaaa	0.149													4	2	---	---	---	---	
BAT2L2	23215	broad.mit.edu	37	1	171519129	171519129	+	Intron	DEL	T	-	-	rs67131565		TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:171519129delT	uc010pmg.1	+						BAT2L2_uc010pmh.1_Intron	NM_015172	NP_055987	Q9Y520	PRC2C_HUMAN	HBxAg transactivated protein 2								protein C-terminus binding				0						CTTTGGCTAGTTTTTTTTTTT	0.299													4	5	---	---	---	---	
HEATR1	55127	broad.mit.edu	37	1	236760425	236760426	+	Intron	INS	-	AA	AA	rs66463182		TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:236760425_236760426insAA	uc001hyd.1	-							NM_018072	NP_060542	Q9H583	HEAT1_HUMAN	protein BAP28						rRNA processing	nucleolus|ribonucleoprotein complex	protein binding			ovary(2)|skin(1)	3	Ovarian(103;0.0634)|Breast(184;0.133)	all_cancers(173;0.0255)|Prostate(94;0.175)	OV - Ovarian serous cystadenocarcinoma(106;0.00117)			tccatgtctccaaaaaaaaaaa	0.149													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	121352655	121352655	+	IGR	DEL	G	-	-			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:121352655delG								LOC84931 (128730 upstream) : GLI2 (140544 downstream)																							TTCTTgccccgccccgccccg	0.368													4	2	---	---	---	---	
SNED1	25992	broad.mit.edu	37	2	242007468	242007468	+	Intron	DEL	A	-	-			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:242007468delA	uc002wah.1	+						SNED1_uc002wai.1_Intron|SNED1_uc002waj.1_Intron|SNED1_uc002wak.2_Intron	NM_001080437	NP_001073906	Q8TER0	SNED1_HUMAN	6720455I24Rik homolog precursor						cell-matrix adhesion	extracellular region	calcium ion binding			breast(1)|central_nervous_system(1)	2		all_cancers(19;7.48e-31)|all_epithelial(40;1.35e-12)|Breast(86;0.000148)|Renal(207;0.00528)|Ovarian(221;0.104)|Esophageal squamous(248;0.131)|all_lung(227;0.17)|all_hematologic(139;0.182)|Melanoma(123;0.238)		Epithelial(32;6.46e-32)|all cancers(36;6.23e-29)|OV - Ovarian serous cystadenocarcinoma(60;2.1e-14)|Kidney(56;6.35e-09)|KIRC - Kidney renal clear cell carcinoma(57;5.98e-08)|BRCA - Breast invasive adenocarcinoma(100;3.66e-06)|Lung(119;0.00072)|LUSC - Lung squamous cell carcinoma(224;0.00553)|Colorectal(34;0.0162)|COAD - Colon adenocarcinoma(134;0.109)		GGACTGTACCACCTGCCGCTC	0.657													5	6	---	---	---	---	
FANCD2	2177	broad.mit.edu	37	3	10143086	10143087	+	3'UTR	INS	-	A	A	rs138111025	by1000genomes	TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10143086_10143087insA	uc003bux.1	+	44					FANCD2_uc003buy.1_3'UTR|FANCD2_uc010hcw.1_RNA|C3orf24_uc003buz.2_Intron	NM_001018115	NP_001018125	Q9BXW9	FACD2_HUMAN	Fanconi anemia complementation group D2 isoform						DNA repair|response to gamma radiation	nucleoplasm	protein binding|protein binding			central_nervous_system(2)|ovary(1)|skin(1)	4				OV - Ovarian serous cystadenocarcinoma(96;0.148)		tttttttttttaaagacgggga	0.153			D|Mis|N|F			AML|leukemia		Involved_in_tolerance_or_repair_of_DNA_crosslinks	Fanconi_Anemia				3	4	---	---	---	---	
TMF1	7110	broad.mit.edu	37	3	69082571	69082571	+	Intron	DEL	A	-	-			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:69082571delA	uc003dnn.2	-						TMF1_uc011bfx.1_Intron	NM_007114	NP_009045	P82094	TMF1_HUMAN	TATA element modulatory factor 1						regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	Golgi membrane|nucleus	DNA binding|protein binding|transcription cofactor activity				0		Lung NSC(201;0.0193)|Prostate(884;0.174)		BRCA - Breast invasive adenocarcinoma(55;4.48e-05)|Epithelial(33;0.000274)|LUSC - Lung squamous cell carcinoma(21;0.0123)|KIRC - Kidney renal clear cell carcinoma(39;0.211)|Kidney(39;0.247)		GAGAAAATGTAAAAATCTACA	0.274													5	4	---	---	---	---	
GSK3B	2932	broad.mit.edu	37	3	119582462	119582462	+	Intron	DEL	A	-	-			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:119582462delA	uc003edo.2	-						GSK3B_uc003edn.2_Intron|GSK3B_uc003edm.2_5'Flank	NM_001146156	NP_001139628	P49841	GSK3B_HUMAN	glycogen synthase kinase 3 beta isoform 2						axon guidance|epithelial to mesenchymal transition|ER overload response|glycogen metabolic process|hippocampus development|negative regulation of apoptosis|negative regulation of protein binding|negative regulation of protein complex assembly|nerve growth factor receptor signaling pathway|peptidyl-serine phosphorylation|phosphatidylinositol-mediated signaling|positive regulation of cell-matrix adhesion|positive regulation of protein complex assembly|positive regulation of protein export from nucleus|positive regulation of Rac GTPase activity|regulation of microtubule-based process|superior temporal gyrus development	Axin-APC-beta-catenin-GSK3B complex|beta-catenin destruction complex|centrosome|cytosol|nucleus|plasma membrane	ATP binding|beta-catenin binding|NF-kappaB binding|p53 binding|protein kinase A catalytic subunit binding|protein serine/threonine kinase activity|RNA polymerase II transcription factor binding|tau-protein kinase activity|ubiquitin protein ligase binding			lung(2)	2				GBM - Glioblastoma multiforme(114;0.24)	Lithium(DB01356)	CCTGCAGTACAAAAAAAGGGA	0.433													16	13	---	---	---	---	
RUFY3	22902	broad.mit.edu	37	4	71588132	71588132	+	5'UTR	DEL	T	-	-			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:71588132delT	uc003hfq.2	+	1					RUFY3_uc003hfp.3_Intron|RUFY3_uc011cax.1_5'UTR|RUFY3_uc003hfr.2_5'UTR	NM_014961	NP_055776	Q7L099	RUFY3_HUMAN	RUN and FYVE domain containing 3 isoform 2						negative regulation of axonogenesis	filopodium|growth cone					0		all_hematologic(202;0.248)	Lung(101;0.235)			GTATTTTTCCTTTTTTTTTTT	0.323													2	4	---	---	---	---	
PDZD2	23037	broad.mit.edu	37	5	32010190	32010191	+	Intron	INS	-	AAAAAAAAAA	AAAAAAAAAA	rs66669782		TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32010190_32010191insAAAAAAAAAA	uc003jhl.2	+						PDZD2_uc003jhm.2_Intron|PDZD2_uc011cnx.1_Intron	NM_178140	NP_835260	O15018	PDZD2_HUMAN	PDZ domain containing 2						cell adhesion	cell-cell junction|endoplasmic reticulum|extracellular region|nucleus				central_nervous_system(4)|ovary(2)|skin(2)|large_intestine(1)	9						aagactgtctcaaaaaaaagaa	0.158													5	4	---	---	---	---	
VDAC1	7416	broad.mit.edu	37	5	133316325	133316326	+	Intron	INS	-	A	A	rs55708320		TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:133316325_133316326insA	uc003kyp.1	-						VDAC1_uc003kyq.1_Intron|VDAC1_uc003kyr.1_Intron	NM_003374	NP_003365	P21796	VDAC1_HUMAN	voltage-dependent anion channel 1						apoptosis|interspecies interaction between organisms	mitochondrial nucleoid|mitochondrial outer membrane|plasma membrane|pore complex	porin activity|protein binding|voltage-gated anion channel activity				0			KIRC - Kidney renal clear cell carcinoma(527;0.00806)|Kidney(363;0.02)		Dihydroxyaluminium(DB01375)	TGGGCTTTCttaaaaaaaaaaa	0.446													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	12514213	12514236	+	IGR	DEL	CACACACACACACACACACACGCG	-	-	rs145031469	by1000genomes	TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:12514213_12514236delCACACACACACACACACACACGCG								EDN1 (216787 upstream) : PHACTR1 (202652 downstream)																							cacacacacacacacacacacacacacacacgcgcacacacaca	0.308													5	3	---	---	---	---	
SUPT3H	8464	broad.mit.edu	37	6	44900656	44900656	+	Intron	DEL	T	-	-			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:44900656delT	uc003oxo.2	-						SUPT3H_uc003oxn.1_Intron|SUPT3H_uc011dvv.1_Intron|SUPT3H_uc003oxp.2_Intron|SUPT3H_uc011dvw.1_Intron	NM_181356	NP_852001	O75486	SUPT3_HUMAN	suppressor of Ty 3 homolog isoform 2						histone deubiquitination|histone H3 acetylation|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter|transcription initiation, DNA-dependent	STAGA complex|transcription factor TFTC complex	DNA binding|transcription coactivator activity			ovary(2)|breast(1)	3						AAGAATTCCATTAACAAATCA	0.358													4	2	---	---	---	---	
INTS1	26173	broad.mit.edu	37	7	1546840	1546840	+	5'Flank	DEL	T	-	-	rs111819550		TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:1546840delT	uc003skn.2	-						INTS1_uc003skq.2_5'Flank	NM_001080453	NP_001073922	Q8N201	INT1_HUMAN	integrator complex subunit 1						snRNA processing	integral to membrane|integrator complex|nuclear membrane					0		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0181)|OV - Ovarian serous cystadenocarcinoma(56;6.99e-15)		GTCAttattcttttttttttt	0.269													3	4	---	---	---	---	
TNRC18	84629	broad.mit.edu	37	7	5352561	5352563	+	In_Frame_Del	DEL	GAG	-	-			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:5352561_5352563delGAG	uc003soi.3	-	27	8308_8310	c.7959_7961delCTC	c.(7957-7962)TCCTCT>TCT	p.2653_2654SS>S		NM_001080495	NP_001073964	O15417	TNC18_HUMAN	trinucleotide repeat containing 18	2653_2654	Ser-rich.						DNA binding				0		Ovarian(82;0.142)		UCEC - Uterine corpus endometrioid carcinoma (126;0.195)|OV - Ovarian serous cystadenocarcinoma(56;5.32e-15)		ggacgaggaagaggaggaggagg	0.153													4	2	---	---	---	---	
OSBPL3	26031	broad.mit.edu	37	7	24854483	24854483	+	Intron	DEL	G	-	-	rs4490736		TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:24854483delG	uc003sxf.2	-						OSBPL3_uc003sxd.2_Intron|OSBPL3_uc003sxe.2_Intron|OSBPL3_uc003sxg.2_Intron|OSBPL3_uc003sxh.2_Intron|OSBPL3_uc003sxi.2_Intron	NM_015550	NP_056365	Q9H4L5	OSBL3_HUMAN	oxysterol-binding protein-like protein 3 isoform						lipid transport		lipid binding|protein binding			skin(1)	1						acagaccttaggggagtaaga	0.090													8	4	---	---	---	---	
ABCA13	154664	broad.mit.edu	37	7	48266654	48266654	+	Intron	DEL	A	-	-			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:48266654delA	uc003toq.2	+						ABCA13_uc003top.2_Intron|ABCA13_uc010kyr.2_Intron	NM_152701	NP_689914	Q86UQ4	ABCAD_HUMAN	ATP binding cassette, sub-family A (ABC1),						transport	integral to membrane	ATP binding|ATPase activity			ovary(5)|central_nervous_system(4)|skin(1)	10						TTAAGCCATTAAAAAAAAATC	0.338													3	3	---	---	---	---	
GDAP1	54332	broad.mit.edu	37	8	75275019	75275020	+	Intron	INS	-	TTTTTTT	TTTTTTT	rs6150661		TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:75275019_75275020insTTTTTTT	uc003yah.2	+						GDAP1_uc011lfj.1_Intron|GDAP1_uc003yai.2_Intron	NM_018972	NP_061845	Q8TB36	GDAP1_HUMAN	ganglioside-induced differentiation-associated							cytoplasm					0	Breast(64;0.00769)	Myeloproliferative disorder(644;0.0122)	BRCA - Breast invasive adenocarcinoma(89;0.0499)|Epithelial(68;0.104)|all cancers(69;0.234)			CTCTCTCTCTCttttttttttt	0.396													6	5	---	---	---	---	
RGS22	26166	broad.mit.edu	37	8	101011387	101011387	+	Intron	DEL	A	-	-	rs35746502		TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:101011387delA	uc003yjb.1	-						RGS22_uc003yja.1_Intron|RGS22_uc003yjc.1_Intron	NM_015668	NP_056483	Q8NE09	RGS22_HUMAN	regulator of G-protein signaling 22						negative regulation of signal transduction	cytoplasm|plasma membrane	GTPase activator activity|signal transducer activity			ovary(3)|skin(2)|breast(1)|central_nervous_system(1)	7			Epithelial(11;6.71e-08)|all cancers(13;4.19e-06)|OV - Ovarian serous cystadenocarcinoma(57;0.000469)|STAD - Stomach adenocarcinoma(118;0.169)			cccattccttaaaaaaaaaaa	0.015													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	68430364	68430365	+	IGR	INS	-	A	A	rs140332329		TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68430364_68430365insA								FAM27B (636175 upstream) : MIR1299 (571874 downstream)																							TTATGCAGAAGAAAAAATTAAC	0.322													5	3	---	---	---	---	
COL27A1	85301	broad.mit.edu	37	9	117040764	117040765	+	Intron	DEL	AA	-	-			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:117040764_117040765delAA	uc011lxl.1	+						COL27A1_uc004bii.2_Intron	NM_032888	NP_116277	Q8IZC6	CORA1_HUMAN	collagen, type XXVII, alpha 1 precursor						cell adhesion		extracellular matrix structural constituent			ovary(3)|skin(1)	4						tggtggtgataatggtggtggt	0.050													5	3	---	---	---	---	
EXOSC2	23404	broad.mit.edu	37	9	133573185	133573186	+	Intron	INS	-	T	T			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:133573185_133573186insT	uc004bzu.2	+						EXOSC2_uc011mbz.1_Intron|EXOSC2_uc011mca.1_Intron	NM_014285	NP_055100	Q13868	EXOS2_HUMAN	exosome component 2						exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay|positive regulation of cell growth|rRNA processing	cytosol|exosome (RNase complex)|nucleolus	3'-5'-exoribonuclease activity|7S RNA binding|protein binding			ovary(1)	1		Acute lymphoblastic leukemia(5;0.0508)|all_hematologic(13;0.0588)		OV - Ovarian serous cystadenocarcinoma(145;0.000324)		ACTGGTTCATGttttttttttt	0.198													9	6	---	---	---	---	
CCAR1	55749	broad.mit.edu	37	10	70550932	70550933	+	Intron	INS	-	AT	AT			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70550932_70550933insAT	uc001joo.2	+						CCAR1_uc010qjb.1_Intron	NM_018237	NP_060707	Q8IX12	CCAR1_HUMAN	cell-cycle and apoptosis regulatory protein 1						apoptosis|cell cycle|nuclear mRNA splicing, via spliceosome|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleoplasm|perinuclear region of cytoplasm	calcium ion binding|nucleic acid binding|protein binding			ovary(6)|large_intestine(1)	7						AATCTAATAAAATGTATTTTTT	0.257													57	28	---	---	---	---	
SGPL1	8879	broad.mit.edu	37	10	72611185	72611186	+	Intron	INS	-	TA	TA	rs144998273	by1000genomes	TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:72611185_72611186insTA	uc001jrm.2	+							NM_003901	NP_003892	O95470	SGPL1_HUMAN	sphingosine-1-phosphate lyase 1						apoptosis|carboxylic acid metabolic process|ceramide metabolic process|sphingolipid catabolic process	integral to endoplasmic reticulum membrane	carboxy-lyase activity|pyridoxal phosphate binding|sphinganine-1-phosphate aldolase activity				0					Pyridoxal Phosphate(DB00114)	ctgctaaacactaaacatccta	0.005													4	2	---	---	---	---	
GLUD1	2746	broad.mit.edu	37	10	88819234	88819234	+	Intron	DEL	A	-	-	rs35013042		TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:88819234delA	uc001keh.2	-						GLUD1_uc001keg.2_Intron|GLUD1_uc010qmp.1_Intron	NM_005271	NP_005262	P00367	DHE3_HUMAN	glutamate dehydrogenase 1 precursor						glutamate biosynthetic process|glutamate catabolic process|positive regulation of insulin secretion	mitochondrial matrix	ADP binding|ATP binding|glutamate dehydrogenase|glutamate dehydrogenase activity|GTP binding|identical protein binding|leucine binding|NAD+ binding				0					L-Glutamic Acid(DB00142)|NADH(DB00157)	TCTATTTAGGAAAAAAAAAAA	0.328													4	2	---	---	---	---	
C11orf85	283129	broad.mit.edu	37	11	64708307	64708308	+	Intron	INS	-	TTT	TTT	rs56019033		TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64708307_64708308insTTT	uc001ocb.1	-						C11orf85_uc001occ.1_Intron|C11orf85_uc001ocd.1_Intron	NM_001037225	NP_001032302	Q3KP22	CK085_HUMAN	hypothetical protein LOC283129												0						ttttttctttcttttttttttt	0.173													3	3	---	---	---	---	
NCAPD3	23310	broad.mit.edu	37	11	134037497	134037499	+	Intron	DEL	ACT	-	-	rs10569176		TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:134037497_134037499delACT	uc001qhd.1	-						NCAPD3_uc010scm.1_Intron|NCAPD3_uc009zda.1_Intron|NCAPD3_uc001qhc.1_Intron	NM_015261	NP_056076	P42695	CNDD3_HUMAN	non-SMC condensin II complex, subunit D3						cell division|mitotic chromosome condensation	nuclear centromeric heterochromatin|nuclear condensin complex	methylated histone residue binding			ovary(2)|upper_aerodigestive_tract(1)|lung(1)|kidney(1)	5	all_hematologic(175;0.127)	all_cancers(12;1.68e-21)|all_epithelial(12;5.86e-16)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000182)|Medulloblastoma(222;0.0245)|all_neural(223;0.0505)|Esophageal squamous(93;0.0559)		Epithelial(10;8.74e-10)|BRCA - Breast invasive adenocarcinoma(10;1e-08)|all cancers(11;1.46e-08)|OV - Ovarian serous cystadenocarcinoma(99;0.00345)|Lung(977;0.227)		GGGCACACTCACTAGTGAGATGA	0.581													4	3	---	---	---	---	
KIAA0528	9847	broad.mit.edu	37	12	22625451	22625451	+	Intron	DEL	T	-	-			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:22625451delT	uc001rfq.2	-						KIAA0528_uc010sir.1_Intron|KIAA0528_uc010sis.1_Intron|KIAA0528_uc010sit.1_Intron|KIAA0528_uc010siu.1_Intron|KIAA0528_uc001rfr.2_Intron	NM_014802	NP_055617	Q86YS7	K0528_HUMAN	hypothetical protein LOC9847								protein binding			ovary(1)|large_intestine(1)|breast(1)|central_nervous_system(1)	4						TTATCACAGGTTTTTTTTTCC	0.284													4	2	---	---	---	---	
VDR	7421	broad.mit.edu	37	12	48240278	48240278	+	Intron	DEL	C	-	-			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:48240278delC	uc001rqm.2	-						VDR_uc001rql.2_Intron|VDR_uc001rqn.2_Intron|VDR_uc010slq.1_Intron	NM_001017535	NP_001017535	P11473	VDR_HUMAN	vitamin D (1,25-dihydroxyvitamin D3) receptor						decidualization|negative regulation of cell proliferation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of vitamin D 24-hydroxylase activity|regulation of calcidiol 1-monooxygenase activity|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	retinoid X receptor binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|vitamin D3 receptor activity|zinc ion binding			ovary(1)|central_nervous_system(1)|skin(1)	3		Acute lymphoblastic leukemia(13;0.109)|all_hematologic(14;0.214)		GBM - Glioblastoma multiforme(48;0.17)	Calcidiol(DB00146)|Calcipotriol(DB02300)|Calcitriol(DB00136)|Dihydrotachysterol(DB01070)|Ergocalciferol(DB00153)|Paricalcitol(DB00910)	AGCTGAGGAGCCGCCCACCCA	0.602													4	2	---	---	---	---	
BAZ2A	11176	broad.mit.edu	37	12	56999550	56999550	+	Intron	DEL	T	-	-			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56999550delT	uc001slq.1	-						BAZ2A_uc001slp.1_Intron|BAZ2A_uc009zov.1_5'Flank|BAZ2A_uc009zow.1_Intron	NM_013449	NP_038477	Q9UIF9	BAZ2A_HUMAN	bromodomain adjacent to zinc finger domain, 2A						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						GCAGAAGTCCTTTTTTTTTTT	0.308													16	8	---	---	---	---	
NAV3	89795	broad.mit.edu	37	12	78224970	78224975	+	5'Flank	DEL	AGAGAC	-	-	rs72186592	by1000genomes	TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:78224970_78224975delAGAGAC	uc001syp.2	+						NAV3_uc001syo.2_5'Flank	NM_014903	NP_055718	Q8IVL0	NAV3_HUMAN	neuron navigator 3							nuclear outer membrane	ATP binding|nucleoside-triphosphatase activity			large_intestine(6)|ovary(5)|lung(2)|breast(1)|skin(1)|kidney(1)|pancreas(1)	17						agagagagagagagacagagagagag	0.204										HNSCC(70;0.22)			2	5	---	---	---	---	
USP44	84101	broad.mit.edu	37	12	95911790	95911790	+	3'UTR	DEL	A	-	-			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:95911790delA	uc001teg.2	-	6					USP44_uc001teh.2_3'UTR|USP44_uc009zte.2_3'UTR	NM_001042403	NP_001035862	Q9H0E7	UBP44_HUMAN	ubiquitin thiolesterase 44						anaphase|cell division|mitosis|negative regulation of mitotic anaphase-promoting complex activity|protein deubiquitination|regulation of spindle checkpoint|ubiquitin-dependent protein catabolic process	nucleus	protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity|zinc ion binding			lung(1)|breast(1)|central_nervous_system(1)	3						TATACTTTGTAAAAAAAAAAA	0.239													4	2	---	---	---	---	
CCDC53	51019	broad.mit.edu	37	12	102433477	102433477	+	Intron	DEL	T	-	-			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:102433477delT	uc010svw.1	-						CCDC53_uc010svx.1_Intron|CCDC53_uc010svy.1_Intron|CCDC53_uc010svz.1_Intron	NM_016053	NP_057137	Q9Y3C0	CCD53_HUMAN	coiled-coil domain containing 53							WASH complex	protein binding				0						TTTGACTTCCTTTTTTTTTTT	0.249													4	3	---	---	---	---	
STAB2	55576	broad.mit.edu	37	12	104086413	104086416	+	Intron	DEL	GAGA	-	-	rs71809816		TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:104086413_104086416delGAGA	uc001tjw.2	+							NM_017564	NP_060034	Q8WWQ8	STAB2_HUMAN	stabilin 2 precursor						angiogenesis|cell adhesion|defense response to bacterium|receptor-mediated endocytosis	cytoplasm|external side of plasma membrane|integral to plasma membrane	Gram-negative bacterial cell surface binding|hyaluronic acid binding|low-density lipoprotein receptor activity|protein disulfide oxidoreductase activity|scavenger receptor activity			ovary(9)|skin(5)	14						gcacgtgtgtgaGAGAGAGAGAGA	0.118													3	3	---	---	---	---	
C12orf51	283450	broad.mit.edu	37	12	112655141	112655142	+	Intron	DEL	AC	-	-	rs4767497		TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112655141_112655142delAC	uc009zwc.2	-						C12orf51_uc001ttr.1_Intron	NM_001109662	NP_001103132			chromosome 12 open reading frame 51											ovary(1)|lung(1)	2						acacacacatacacacacacac	0.084													4	2	---	---	---	---	
IRF9	10379	broad.mit.edu	37	14	24635590	24635590	+	3'UTR	DEL	T	-	-			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24635590delT	uc001wmq.2	+	9					RNF31_uc001wmp.2_RNA|IRF9_uc010alj.2_3'UTR	NM_006084	NP_006075	Q00978	IRF9_HUMAN	interferon-stimulated transcription factor 3,						interferon-gamma-mediated signaling pathway|response to virus|transcription from RNA polymerase II promoter|type I interferon-mediated signaling pathway	cytosol|nucleoplasm	DNA binding|identical protein binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1				GBM - Glioblastoma multiforme(265;0.00853)		TTTTTTATCCTTTTTTTTTTT	0.423													4	2	---	---	---	---	
STXBP6	29091	broad.mit.edu	37	14	25282149	25282149	+	Intron	DEL	C	-	-			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:25282149delC	uc001wpu.2	-						STXBP6_uc001wpv.2_Intron|STXBP6_uc001wpw.2_Intron|STXBP6_uc001wpt.2_Intron	NM_014178	NP_054897	Q8NFX7	STXB6_HUMAN	amisyn						vesicle-mediated transport	cytoplasm|integral to membrane					0				GBM - Glioblastoma multiforme(265;0.0296)		TGTTACTTTTCCTTATGATAG	0.418													4	2	---	---	---	---	
ABCD4	5826	broad.mit.edu	37	14	74757386	74757387	+	Intron	INS	-	T	T	rs35064021		TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:74757386_74757387insT	uc001xpr.2	-						ABCD4_uc001xps.2_Intron|ABCD4_uc001xpt.2_Intron|ABCD4_uc010tur.1_Intron|ABCD4_uc001xpu.2_Intron	NM_005050	NP_005041	O14678	ABCD4_HUMAN	ATP-binding cassette, sub-family D, member 4							ATP-binding cassette (ABC) transporter complex|integral to membrane|peroxisomal membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances			upper_aerodigestive_tract(2)|large_intestine(1)|ovary(1)	4				BRCA - Breast invasive adenocarcinoma(234;0.00153)		gaggcagggtcttttttttttt	0.025													4	2	---	---	---	---	
FOXN3	1112	broad.mit.edu	37	14	89647259	89647260	+	Intron	INS	-	GCAGAGAACATGCATGGA	GCAGAGAACATGCATGGA	rs140257053	by1000genomes	TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:89647259_89647260insGCAGAGAACATGCATGGA	uc001xxo.3	-						FOXN3_uc001xxn.3_Intron|FOXN3_uc010atk.2_Intron	NM_001085471	NP_001078940	O00409	FOXN3_HUMAN	checkpoint suppressor 1 isoform 1						DNA damage checkpoint|embryo development|G2 phase of mitotic cell cycle|negative regulation of transcription, DNA-dependent|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|protein C-terminus 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			skin(2)|ovary(1)	3						agagacagagggcagagacaga	0.173													4	2	---	---	---	---	
TGM5	9333	broad.mit.edu	37	15	43526902	43526902	+	Intron	DEL	G	-	-			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43526902delG	uc001zrd.1	-						TGM5_uc001zrc.1_Intron|TGM5_uc001zre.1_Intron	NM_201631	NP_963925	O43548	TGM5_HUMAN	transglutaminase 5 isoform 1						epidermis development|peptide cross-linking	cytoplasm	acyltransferase activity|metal ion binding|protein-glutamine gamma-glutamyltransferase activity			central_nervous_system(1)	1		all_cancers(109;1.37e-14)|all_epithelial(112;1.26e-12)|Lung NSC(122;2.46e-08)|all_lung(180;2.75e-07)|Melanoma(134;0.0476)|Colorectal(260;0.216)		GBM - Glioblastoma multiforme(94;4e-07)	L-Glutamine(DB00130)	CCCTCTCACAGGGCTTCACCC	0.547													37	17	---	---	---	---	
PGPEP1L	145814	broad.mit.edu	37	15	99514424	99514430	+	Intron	DEL	GGGGGGG	-	-	rs74852431		TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:99514424_99514430delGGGGGGG	uc002bum.2	-						PGPEP1L_uc010bop.2_Intron|PGPEP1L_uc002bun.2_Intron	NM_001102612	NP_001096082	A6NFU8	PGPIL_HUMAN	pyroglutamyl-peptidase 1-like protein						proteolysis		cysteine-type peptidase activity				0						CTCAGTTGATGGGGGGGGGGGGGGGGT	0.614													8	4	---	---	---	---	
PDXDC1	23042	broad.mit.edu	37	16	15081850	15081851	+	Intron	DEL	TT	-	-	rs112580671		TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:15081850_15081851delTT	uc002dda.3	+						PDXDC1_uc010uzl.1_Intron|PDXDC1_uc010uzm.1_Intron|PDXDC1_uc010bvc.1_Intron|PDXDC1_uc002dcz.2_Intron|PDXDC1_uc002ddb.3_Intron|PDXDC1_uc010uzn.1_Intron|PDXDC1_uc002ddc.2_Intron	NM_015027	NP_055842	Q6P996	PDXD1_HUMAN	pyridoxal-dependent decarboxylase domain						carboxylic acid metabolic process		carboxy-lyase activity|protein binding|pyridoxal phosphate binding			skin(1)	1					Pyridoxal Phosphate(DB00114)	TATACAATTCTTTTTTTTTTTT	0.302													2	4	---	---	---	---	
NKD1	85407	broad.mit.edu	37	16	50667707	50667708	+	3'UTR	INS	-	C	C			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:50667707_50667708insC	uc002egg.1	+	10						NM_033119	NP_149110	Q969G9	NKD1_HUMAN	naked cuticle homolog 1						Wnt receptor signaling pathway	cytoplasm|plasma membrane	calcium ion binding|protein binding				0		all_cancers(37;0.229)		GBM - Glioblastoma multiforme(240;0.243)		CCTCCCCAGGGCCCCACCCTGC	0.351													4	3	---	---	---	---	
HSBP1	3281	broad.mit.edu	37	16	83843057	83843057	+	Intron	DEL	C	-	-			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:83843057delC	uc002fgy.1	+							NM_001537	NP_001528	O75506	HSBP1_HUMAN	heat shock factor binding protein 1						negative regulation of transcription from RNA polymerase II promoter	nucleus	transcription corepressor activity				0		all_cancers(2;0.00573)|all_epithelial(2;0.0309)		BRCA - Breast invasive adenocarcinoma(80;0.0404)		ttttttttttcttttcttttc	0.229													3	5	---	---	---	---	
ZFPM1	161882	broad.mit.edu	37	16	88593211	88593211	+	Intron	DEL	T	-	-	rs35678431		TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:88593211delT	uc002fkv.2	+							NM_153813	NP_722520	Q8IX07	FOG1_HUMAN	zinc finger protein, multitype 1						blood coagulation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleoplasm	DNA binding|transcription factor binding|zinc ion binding			central_nervous_system(1)	1				BRCA - Breast invasive adenocarcinoma(80;0.0478)		GTTCCTACCCTCCCCCCCCAG	0.687													5	3	---	---	---	---	
RAP1GAP2	23108	broad.mit.edu	37	17	2703722	2703743	+	Intron	DEL	GGCTGTCCCGGGGACTCCTCCA	-	-	rs72122107		TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:2703722_2703743delGGCTGTCCCGGGGACTCCTCCA	uc010ckd.2	+						RAP1GAP2_uc010cke.2_Intron	NM_015085	NP_055900	Q684P5	RPGP2_HUMAN	RAP1 GTPase activating protein 2 isoform 1						regulation of small GTPase mediated signal transduction	centrosome|cytosol|perinuclear region of cytoplasm	GTPase activator activity			ovary(1)	1						TGGTGGTTTGGGCTGTCCCGGGGACTCCTCCATACAGATGCT	0.595													11	5	---	---	---	---	
MAP2K3	5606	broad.mit.edu	37	17	21217018	21217020	+	Intron	DEL	CCT	-	-	rs72412380		TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21217018_21217020delCCT	uc002gys.2	+						MAP2K3_uc002gyt.2_Intron|MAP2K3_uc002gyu.2_Intron	NM_145109	NP_659731	P46734	MP2K3_HUMAN	mitogen-activated protein kinase kinase 3						activation of MAPK activity|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|positive regulation of transcription, DNA-dependent|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|nucleoplasm	ATP binding|MAP kinase kinase activity|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity				0				COAD - Colon adenocarcinoma(3;0.0131)|Colorectal(15;0.0553)		TACCTGGCTCCCTCCTCCCTCCT	0.389													3	3	---	---	---	---	
TNS4	84951	broad.mit.edu	37	17	38638838	38638841	+	Intron	DEL	ACAC	-	-			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:38638838_38638841delACAC	uc010cxb.2	-						TNS4_uc002huu.3_5'Flank	NM_032865	NP_116254	Q8IZW8	TENS4_HUMAN	tensin 4 precursor						apoptosis|protein localization	cytoplasm|cytoskeleton|focal adhesion	actin binding			large_intestine(1)|ovary(1)|central_nervous_system(1)|skin(1)	4		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(5;5.91e-05)			tctactaaagacacacacacacac	0.000													6	3	---	---	---	---	
IGF2BP1	10642	broad.mit.edu	37	17	47076718	47076719	+	Intron	INS	-	A	A	rs141190373	by1000genomes	TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:47076718_47076719insA	uc002iom.2	+						IGF2BP1_uc010dbj.2_Intron	NM_006546	NP_006537	Q9NZI8	IF2B1_HUMAN	insulin-like growth factor 2 mRNA binding						CRD-mediated mRNA stabilization|negative regulation of translation|regulation of mRNA stability involved in response to stress	CRD-mediated mRNA stability complex|cytosol|dendritic spine|lamellipodium|nucleus|plasma membrane|stress granule	mRNA 3'-UTR binding|mRNA 5'-UTR binding|nucleotide binding|protein binding|translation regulator activity			kidney(1)	1						TTACAGCTTGTAAAAAAAAAAT	0.441													2	4	---	---	---	---	
BCAS3	54828	broad.mit.edu	37	17	59465992	59465992	+	Intron	DEL	A	-	-			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:59465992delA	uc002iyv.3	+						BCAS3_uc002iyu.3_Intron|BCAS3_uc002iyw.3_Frame_Shift_Del_p.G887fs|BCAS3_uc002iyy.3_Intron|BCAS3_uc002iyz.3_Intron|BCAS3_uc002iza.3_Intron|BCAS3_uc002izb.3_Intron|BCAS3_uc002izc.3_Intron|BCAS3_uc002izd.3_Intron	NM_001099432	NP_001092902	Q9H6U6	BCAS3_HUMAN	breast carcinoma amplified sequence 3 isoform 1							nucleus				ovary(2)|central_nervous_system(2)|skin(1)	5			BRCA - Breast invasive adenocarcinoma(1;3.11e-12)|Epithelial(12;8.2e-07)|all cancers(12;5.33e-06)			AAAAAAAAGGAAAAAAAAAAC	0.428													4	2	---	---	---	---	
NPLOC4	55666	broad.mit.edu	37	17	79580154	79580154	+	Intron	DEL	A	-	-	rs151110419		TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79580154delA	uc002kat.3	-						NPLOC4_uc002kau.3_Intron|NPLOC4_uc010wur.1_Intron	NM_017921	NP_060391	Q8TAT6	NPL4_HUMAN	nuclear protein localization 4						cellular membrane fusion|ER-associated protein catabolic process|Golgi organization	cytosol|endoplasmic reticulum|nuclear outer membrane-endoplasmic reticulum membrane network|nucleus	zinc ion binding			ovary(1)|central_nervous_system(1)	2	all_neural(118;0.0878)|Melanoma(429;0.242)|all_lung(278;0.246)		BRCA - Breast invasive adenocarcinoma(99;0.0282)|OV - Ovarian serous cystadenocarcinoma(97;0.0739)			ATAAAAAGCTAAAAAAAAAAA	0.318													4	2	---	---	---	---	
ARHGAP28	79822	broad.mit.edu	37	18	6887430	6887430	+	Intron	DEL	T	-	-	rs71769082		TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:6887430delT	uc010wzi.1	+						ARHGAP28_uc002knc.2_Intron|ARHGAP28_uc002knd.2_Intron|ARHGAP28_uc002kne.2_Intron|ARHGAP28_uc002knf.2_Intron			B4DXL2	B4DXL2_HUMAN	SubName: Full=Putative uncharacterized protein ARHGAP28;						signal transduction	intracellular				pancreas(1)	1		Colorectal(10;0.168)				TGGTATCTTGttttttttttt	0.264													4	2	---	---	---	---	
KIAA1328	57536	broad.mit.edu	37	18	34465687	34465687	+	Intron	DEL	T	-	-			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:34465687delT	uc002kzz.2	+							NM_020776	NP_065827	Q86T90	K1328_HUMAN	hypothetical protein LOC57536											central_nervous_system(1)	1				COAD - Colon adenocarcinoma(74;0.195)		TGACTAtttcttttttttttt	0.164													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	26113543	26113543	+	IGR	DEL	A	-	-			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:26113543delA								C20orf191 (18866 upstream) : MIR663 (75279 downstream)																							TCTTTGCCTTAACAACATTAT	0.363													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	44756553	44756588	+	IGR	DEL	CACCACCACCATCACCACCACCACCACCACCACCAT	-	-	rs138063878	by1000genomes	TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:44756553_44756588delCACCACCACCATCACCACCACCACCACCACCACCAT								CRYAA (163640 upstream) : SIK1 (77810 downstream)																							ccaccatcaccaccaccaccatcaccaccaccaccaccaccaccatcaccaccacc	0.000													4	2	---	---	---	---	
MSL3	10943	broad.mit.edu	37	X	11781972	11781973	+	Frame_Shift_Ins	INS	-	ATCC	ATCC			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:11781972_11781973insATCC	uc004cuw.2	+	8	928_929	c.823_824insATCC	c.(823-825)TATfs	p.Y275fs	MSL3_uc004cuv.1_Frame_Shift_Ins_p.Y275fs|MSL3_uc004cux.2_Frame_Shift_Ins_p.Y216fs|MSL3_uc011mig.1_Frame_Shift_Ins_p.Y126fs|MSL3_uc011mih.1_Frame_Shift_Ins_p.Y263fs|MSL3_uc004cuy.2_Frame_Shift_Ins_p.Y109fs|MSL3_uc011mii.1_Frame_Shift_Ins_p.Y109fs	NM_078629	NP_523353	Q8N5Y2	MS3L1_HUMAN	male-specific lethal 3-like 1 isoform a	275					histone H4-K16 acetylation|multicellular organismal development|transcription from RNA polymerase II promoter	MSL complex	DNA binding|methylated histone residue binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1						GGTTTTACTCTATCCATATGAA	0.366													106	97	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	24447607	24447607	+	IGR	DEL	T	-	-			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:24447607delT								FAM48B1 (64067 upstream) : PDK3 (35737 downstream)																							attaaacctcttttttttTTT	0.164													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	48634368	48634372	+	IGR	DEL	AGTAG	-	-			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:48634368_48634372delAGTAG								GLOD5 (2306 upstream) : GATA1 (10610 downstream)																							GGCCTGGCCAAGTAGAATAAGAGTG	0.502													6	6	---	---	---	---	
WNK3	65267	broad.mit.edu	37	X	54265637	54265637	+	Intron	DEL	A	-	-			TCGA-BP-5199-01A-01D-1429-08	TCGA-BP-5199-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:54265637delA	uc004dtd.1	-						WNK3_uc004dtc.1_Intron	NM_001002838	NP_001002838	Q9BYP7	WNK3_HUMAN	WNK lysine deficient protein kinase 3 isoform 2						intracellular protein kinase cascade|positive regulation of establishment of protein localization in plasma membrane|positive regulation of peptidyl-threonine phosphorylation|positive regulation of rubidium ion transmembrane transporter activity|positive regulation of rubidium ion transport|positive regulation of sodium ion transmembrane transporter activity|positive regulation of sodium ion transport|protein autophosphorylation	adherens junction|tight junction	ATP binding|protein binding|protein serine/threonine kinase activity|rubidium ion transmembrane transporter activity|sodium ion transmembrane transporter activity			lung(4)|ovary(3)|kidney(2)|central_nervous_system(2)	11						TGAAGCTTTTAAAAAAAAAAA	0.229													4	2	---	---	---	---	
