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	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	i_TCGAscape_Amplification_Peaks	i_TCGAscape_Deletion_Peaks	DrugBank	i_ACHILLES_Top_Genes	i_CCLE_ONCOMAP_overlapping_mutations	i_CCLE_ONCOMAP_total_mutations_in_gene	i_CCLE_SEQ_overlapping_mutations	i_CCLE_SEQ_total_mutations_in_gene	MUTSIG_Significant_Genes	OREGANNO_ID	OREGANNO_Values	i_tumor_f	i_init_t_lod	i_t_lod_fstar	i_t_alt_count	i_t_ref_count	i_normal_best_gt	i_failure_reasons	i_judgement	validation_status	validation_method	validation_tumor_sample	validation_alt_allele	dataset	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	type	classification	start	end	gene	chr	ref_allele	tum_allele1	tum_allele2	context_orig	context65	gene_name	newbase	categ	categ_ignoring_null_categ
POLL	27343	broad.mit.edu	36	10	103333257	103333258	+	Missense_Mutation	DNP	GT	TC	TC			TCGA-28-1746-01	TCGA-28-1746-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:103333257_103333258GT>TC	uc001ktg.1	-	c.1062_1063AC>GA	c.(1060-1065)CAACAG>CAGAAG	p.Q355K	POLL_uc001ktd.1_5'Flank|POLL_uc001kte.1_Missense_Mutation_p.Q47K|POLL_uc001kth.1_Missense_Mutation_p.Q80K|POLL_uc001kti.1_Missense_Mutation_p.Q355K|POLL_uc001ktj.1_Missense_Mutation_p.Q355K|POLL_uc001ktf.2_Missense_Mutation_p.Q263K|POLL_uc001ktk.1_Missense_Mutation_p.Q94K|POLL_uc001ktl.1_Missense_Mutation_p.Q267K|POLL_uc001ktm.1_Missense_Mutation_p.Q355K	NM_013274	NP_037406	Q9UGP5	DPOLL_HUMAN	polymerase (DNA directed), lambda	355					DNA replication|nucleotide-excision repair|somatic hypermutation of immunoglobulin genes	nucleus	DNA binding|DNA-directed DNA polymerase activity|lyase activity|metal ion binding				0		Colorectal(252;0.234)		Epithelial(162;1.55e-08)|all cancers(201;6.64e-07)										0.352941	13.841786	14.167291	6	11	GG		KEEP	---	---	---	---	capture			Missense_Mutation	DNP	103333257	103333258	12633	10	GT	TC	TC	48	48	POLL	TC	3	3
ITIH5	80760	broad.mit.edu	36	10	7667962	7667962	+	Missense_Mutation	SNP	C	T	T			TCGA-28-1746-01	TCGA-28-1746-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr10:7667962C>T	uc001ijq.1	-	c.1016G>A	c.(1015-1017)CGG>CAG	p.R339Q	ITIH5_uc001ijr.1_Missense_Mutation_p.R339Q|ITIH5_uc001ijp.1_Missense_Mutation_p.R125Q	NM_030569	NP_085046	Q86UX2	ITIH5_HUMAN	inter-alpha trypsin inhibitor heavy chain	339	VWFA.				hyaluronan metabolic process	extracellular region	serine-type endopeptidase inhibitor activity			ovary(2)|central_nervous_system(2)	4														0.096774	6.824267	27.043035	12	112	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	7667962	7667962	8211	10	C	T	T	23	23	ITIH5	T	1	1
PTEN	5728	broad.mit.edu	36	10	89680785	89680785	+	Missense_Mutation	SNP	G	A	A			TCGA-28-1746-01	TCGA-28-1746-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr10:89680785G>A	uc001kfb.1	+	c.212G>A	c.(211-213)TGT>TAT	p.C71Y		NM_000314	NP_000305	P60484	PTEN_HUMAN	phosphatase and tensin homolog	71	Phosphatase tensin-type.		C -> Y (in CD; loss of phosphatase activity towards Ins(1,3,4,5)P4).		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 focal adhesion assembly|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 sequence-specific DNA binding transcription factor activity|protein stabilization|regulation of cyclin-dependent protein kinase activity|regulation of neuron projection development|T cell receptor signaling pathway	cytosol|internal side of plasma membrane|PML body	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.L70fs*7(4)|p.C71Y(2)|p.Y27_N212>Y(2)|p.C71fs*6(1)|p.F56fs*2(1)|p.C71W(1)		endometrium(831)|central_nervous_system(654)|skin(119)|haematopoietic_and_lymphoid_tissue(101)|prostate(97)|large_intestine(90)|breast(67)|lung(63)|ovary(58)|thyroid(29)|stomach(29)|upper_aerodigestive_tract(25)|cervix(21)|liver(20)|vulva(17)|kidney(15)|NS(14)|soft_tissue(12)|urinary_tract(12)|eye(8)|pancreas(6)|salivary_gland(5)|bone(5)|biliary_tract(4)|autonomic_ganglia(2)|meninges(2)|testis(1)|oesophagus(1)	2308		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)				31		264	TCGA GBM(2;<1E-8)|TSP Lung(26;0.18)			0.666667	80.65656	81.618396	26	13	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	89680785	89680785	13192	10	G	A	A	48	48	PTEN	A	2	2
RRP12	23223	broad.mit.edu	36	10	99150902	99150903	+	Missense_Mutation	DNP	CT	AA	AA			TCGA-28-1746-01	TCGA-28-1746-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:99150902_99150903CT>AA	uc001knf.1	-	c.76_77AG>TT	c.(76-78)AGC>TTC	p.S26F	RRP12_uc009xvn.1_Missense_Mutation_p.S26F	NM_015179	NP_055994	Q5JTH9	RRP12_HUMAN	ribosomal RNA processing 12 homolog	26						integral to membrane|nuclear membrane|nucleolus	protein binding			ovary(2)|central_nervous_system(1)	3		Colorectal(252;0.162)		Epithelial(162;2.72e-09)|all cancers(201;1.76e-07)										0.6	6.721783	6.764889	3	2	CC		KEEP	---	---	---	---	capture			Missense_Mutation	DNP	99150902	99150903	14166	10	CT	AA	AA	28	28	RRP12	AA	3	3
CHRNA10	57053	broad.mit.edu	36	11	3647603	3647603	+	Missense_Mutation	SNP	A	G	G			TCGA-28-1746-01	TCGA-28-1746-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr11:3647603A>G	uc001lyf.1	-	c.206T>C	c.(205-207)ATG>ACG	p.M69T		NM_020402	NP_065135	Q9GZZ6	ACH10_HUMAN	cholinergic receptor, nicotinic, alpha 10	69	Extracellular (Potential).				regulation of cell proliferation|synaptic transmission, cholinergic	cell junction|postsynaptic membrane	calcium channel activity|receptor activity|receptor binding			ovary(1)	1		Medulloblastoma(188;0.0075)|Breast(177;0.0164)|all_neural(188;0.0577)		BRCA - Breast invasive adenocarcinoma(625;0.0344)|LUSC - Lung squamous cell carcinoma(625;0.192)	Chloroprocaine(DB01161)|Methadone(DB00333)|Nicotine(DB00184)|Pentolinium(DB01090)|Procaine(DB00721)|Trimethaphan(DB01116)	Melanoma(153;17 1869 2949 7120 36888)								0.363934	318.889051	323.87709	111	194	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	3647603	3647603	3516	11	A	G	G	8	8	CHRNA10	G	4	4
OR51B6	390058	broad.mit.edu	36	11	5329792	5329792	+	Missense_Mutation	SNP	G	A	A			TCGA-28-1746-01	TCGA-28-1746-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:5329792G>A	uc001mar.1	+	c.479G>A	c.(478-480)CGC>CAC	p.R160H	HBG2_uc001mak.1_Intron|HBE1_uc001mam.1_Intron|OR51B5_uc001maq.1_Intron	NM_001004750	NP_001004750	Q9H340	O51B6_HUMAN	olfactory receptor, family 51, subfamily B,	160	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;2.9e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)										0.287234	137.164654	144.808843	54	134	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	5329792	5329792	11502	11	G	A	A	38	38	OR51B6	A	1	1
MS4A6E	245802	broad.mit.edu	36	11	59861828	59861828	+	Silent	SNP	G	C	C			TCGA-28-1746-01	TCGA-28-1746-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:59861828G>C	uc001npd.1	+	c.186G>C	c.(184-186)CTG>CTC	p.L62L		NM_139249	NP_640342	Q96DS6	M4A6E_HUMAN	membrane-spanning 4-domains, subfamily A, member	62	Helical; (Potential).					integral to membrane	receptor activity				0														0.441718	229.582881	230.064085	72	91	GG		KEEP	---	---	---	---	capture			Silent	SNP	59861828	59861828	10258	11	G	C	C	48	48	MS4A6E	C	3	3
GPHA2	170589	broad.mit.edu	36	11	64459108	64459108	+	Silent	SNP	C	T	T			TCGA-28-1746-01	TCGA-28-1746-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:64459108C>T	uc001oca.1	-	c.219G>A	c.(217-219)CTG>CTA	p.L73L		NM_130769	NP_570125	Q96T91	GPHA2_HUMAN	glycoprotein hormone alpha 2	73						extracellular region	hormone activity				0														0.636364	44.25432	44.614006	14	8	CC		KEEP	---	---	---	---	capture			Silent	SNP	64459108	64459108	6882	11	C	T	T	21	21	GPHA2	T	2	2
NAA25	80018	broad.mit.edu	36	12	110976663	110976663	+	Nonsense_Mutation	SNP	G	A	A			TCGA-28-1746-01	TCGA-28-1746-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:110976663G>A	uc001ttm.1	-	c.1540C>T	c.(1540-1542)CGA>TGA	p.R514*	NAA25_uc001ttn.2_Non-coding_Transcript|NAA25_uc009zvz.1_Nonsense_Mutation_p.R486*|NAA25_uc009zwa.1_Nonsense_Mutation_p.R514*	NM_024953	NP_079229	Q14CX7	NAA25_HUMAN	mitochondrial distribution and morphology 20	514						cytoplasm	protein binding			ovary(1)|breast(1)|pancreas(1)	3														0.510204	157.181513	157.19173	50	48	GG		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	110976663	110976663	10516	12	G	A	A	37	37	NAA25	A	5	1
GPR109B	8843	broad.mit.edu	36	12	121766250	121766250	+	Missense_Mutation	SNP	C	T	T			TCGA-28-1746-01	TCGA-28-1746-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:121766250C>T	uc001ucy.2	-	c.988G>A	c.(988-990)GAG>AAG	p.E330K	GPR81_uc001ucw.1_Intron	NM_006018	NP_006009	P49019	G109B_HUMAN	G protein-coupled receptor 109B	330	Cytoplasmic (Potential).					integral to plasma membrane	purinergic nucleotide receptor activity, G-protein coupled			ovary(1)	1	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;2.12e-05)|Epithelial(86;3.19e-05)|BRCA - Breast invasive adenocarcinoma(302;0.196)	Mepenzolate(DB04843)|Niacin(DB00627)									0.16	8.687635	11.436171	4	21	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	121766250	121766250	6900	12	C	T	T	31	31	GPR109B	T	1	1
POLE	5426	broad.mit.edu	36	12	131719342	131719342	+	Silent	SNP	C	T	T			TCGA-28-1746-01	TCGA-28-1746-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:131719342C>T	uc001uks.1	-	c.6117G>A	c.(6115-6117)GGG>GGA	p.G2039G	POLE_uc001ukq.1_Silent_p.G249G|POLE_uc001ukr.1_Silent_p.G843G	NM_006231	NP_006222	Q07864	DPOE1_HUMAN	DNA polymerase epsilon catalytic subunit	2039					base-excision repair, gap-filling|DNA synthesis involved in DNA repair|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|nucleotide-excision repair, DNA gap filling|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|transcription-coupled nucleotide-excision repair	nucleoplasm	chromatin binding|DNA binding|DNA-directed DNA polymerase activity|nucleotide binding|protein binding|zinc ion binding			ovary(3)|lung(1)|central_nervous_system(1)	5	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0416)		OV - Ovarian serous cystadenocarcinoma(86;5.22e-08)|Epithelial(86;4.03e-07)|all cancers(50;1.18e-05)										0.314286	29.510828	30.585878	11	24	CC		KEEP	---	---	---	---	capture			Silent	SNP	131719342	131719342	12624	12	C	T	T	22	22	POLE	T	2	2
STAT2	6773	broad.mit.edu	36	12	55029676	55029676	+	Silent	SNP	C	T	T			TCGA-28-1746-01	TCGA-28-1746-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:55029676C>T	uc001slc.1	-	c.1221G>A	c.(1219-1221)GAG>GAA	p.E407E	STAT2_uc001slb.1_5'UTR|STAT2_uc001sld.1_Silent_p.E403E	NM_005419	NP_005410	P52630	STAT2_HUMAN	signal transducer and activator of transcription	407					interspecies interaction between organisms|JAK-STAT cascade|regulation of transcription from RNA polymerase II promoter|regulation of type I interferon-mediated signaling pathway|response to virus|type I interferon-mediated signaling pathway	cytosol|nucleoplasm|plasma membrane	calcium ion binding|DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|signal transducer activity			ovary(1)|lung(1)|kidney(1)	3														0.468293	295.011918	295.187534	96	109	CC		KEEP	---	---	---	---	capture			Silent	SNP	55029676	55029676	15785	12	C	T	T	28	28	STAT2	T	2	2
GRIP1	23426	broad.mit.edu	36	12	65125420	65125420	+	Missense_Mutation	SNP	A	T	T			TCGA-28-1746-01	TCGA-28-1746-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr12:65125420A>T	uc001stk.1	-	c.1334T>A	c.(1333-1335)CTC>CAC	p.L445H	GRIP1_uc001stj.1_Missense_Mutation_p.L227H|GRIP1_uc001stl.1_Missense_Mutation_p.L337H|GRIP1_uc001stm.1_Missense_Mutation_p.L445H	NM_021150	NP_066973	Q9Y3R0	GRIP1_HUMAN	glutamate receptor interacting protein 1	497	PDZ 4.				androgen receptor signaling pathway|intracellular signal transduction|positive regulation of transcription, DNA-dependent|synaptic transmission	cell junction|cytoplasmic membrane-bounded vesicle|cytosol|endoplasmic reticulum|postsynaptic membrane	androgen receptor binding|beta-catenin binding|protein C-terminus binding|receptor signaling complex scaffold activity|transcription coactivator activity			ovary(2)	2			GBM - Glioblastoma multiforme(2;0.00069)	GBM - Glioblastoma multiforme(28;0.0933)										0.45082	161.29442	161.552957	55	67	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	65125420	65125420	7066	12	A	T	T	11	11	GRIP1	T	4	4
KCNC2	3747	broad.mit.edu	36	12	73728243	73728243	+	Silent	SNP	C	T	T			TCGA-28-1746-01	TCGA-28-1746-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:73728243C>T	uc001sxg.1	-	c.1737G>A	c.(1735-1737)ACG>ACA	p.T579T	KCNC2_uc009zry.1_Silent_p.T579T|KCNC2_uc001sxe.1_Silent_p.T579T|KCNC2_uc001sxf.1_Intron	NM_139137	NP_631875	Q96PR1	KCNC2_HUMAN	Shaw-related voltage-gated potassium channel	579	Cytoplasmic (Potential).				energy reserve metabolic process|regulation of insulin secretion	voltage-gated potassium channel complex	voltage-gated potassium channel activity			breast(2)|pancreas(2)|skin(1)|lung(1)	6														0.516381	1095.352819	1095.500079	331	310	CC		KEEP	---	---	---	---	capture			Silent	SNP	73728243	73728243	8320	12	C	T	T	31	31	KCNC2	T	1	1
DGKH	160851	broad.mit.edu	36	13	41691421	41691421	+	Missense_Mutation	SNP	T	G	G			TCGA-28-1746-01	TCGA-28-1746-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr13:41691421T>G	uc001uyl.1	+	c.3269T>G	c.(3268-3270)GTG>GGG	p.V1090G	DGKH_uc001uym.1_Missense_Mutation_p.V1090G|DGKH_uc001uyn.1_Non-coding_Transcript|DGKH_uc001uyo.1_Missense_Mutation_p.V945G|DGKH_uc001uyp.2_Non-coding_Transcript	NM_178009	NP_821077	Q86XP1	DGKH_HUMAN	diacylglycerol kinase, eta isoform 2	1090					activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|intracellular signal transduction|platelet activation|protein oligomerization	endosome|plasma membrane	ATP binding|diacylglycerol kinase activity|metal ion binding			ovary(2)	2		Lung NSC(96;1.02e-05)|Prostate(109;0.0168)|Lung SC(185;0.0262)|Breast(139;0.0709)|Hepatocellular(98;0.114)		OV - Ovarian serous cystadenocarcinoma(117;5.88e-05)|GBM - Glioblastoma multiforme(144;0.000935)|BRCA - Breast invasive adenocarcinoma(63;0.109)										0.166667	6.672094	11.761538	8	40	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	41691421	41691421	4649	13	T	G	G	59	59	DGKH	G	4	4
OR4M1	441670	broad.mit.edu	36	14	19318975	19318975	+	Silent	SNP	T	C	C			TCGA-28-1746-01	TCGA-28-1746-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr14:19318975T>C	uc001vwf.1	+	c.654T>C	c.(652-654)TAT>TAC	p.Y218Y		NM_001005500	NP_001005500	Q8NGD0	OR4M1_HUMAN	olfactory receptor, family 4, subfamily M,	218	Helical; Name=5; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)										0.195652	323.980281	395.558706	162	666	TT		KEEP	---	---	---	---	capture			Silent	SNP	19318975	19318975	11485	14	T	C	C	51	51	OR4M1	C	4	4
CATSPERB	79820	broad.mit.edu	36	14	91175204	91175204	+	Missense_Mutation	SNP	G	A	A			TCGA-28-1746-01	TCGA-28-1746-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr14:91175204G>A	uc001xzs.1	-	c.1576C>T	c.(1576-1578)CTT>TTT	p.L526F	CATSPERB_uc010aub.1_Missense_Mutation_p.L48F	NM_024764	NP_079040	Q9H7T0	CTSRB_HUMAN	cation channel, sperm-associated, beta	526					cell differentiation|multicellular organismal development|spermatogenesis	integral to membrane				breast(2)|ovary(1)	3		all_cancers(154;0.0663)|all_epithelial(191;0.236)								637				0.402174	107.240413	108.014274	37	55	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	91175204	91175204	2810	14	G	A	A	33	33	CATSPERB	A	2	2
FBLN5	10516	broad.mit.edu	36	14	91473232	91473232	+	Missense_Mutation	SNP	C	T	T			TCGA-28-1746-01	TCGA-28-1746-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr14:91473232C>T	uc010aue.1	-	c.314G>A	c.(313-315)GGC>GAC	p.G105D	FBLN5_uc010aud.1_Missense_Mutation_p.G69D|FBLN5_uc001xzx.2_Missense_Mutation_p.G64D	NM_006329	NP_006320	Q9UBX5	FBLN5_HUMAN	fibulin 5 precursor	64	EGF-like 1; calcium-binding (Potential).				cell-matrix adhesion|elastic fiber assembly|protein localization at cell surface|regulation of removal of superoxide radicals	extracellular space|proteinaceous extracellular matrix|soluble fraction	calcium ion binding|integrin binding|protein C-terminus binding			ovary(3)|lung(1)|skin(1)	5		all_cancers(154;0.0722)								478				0.494253	125.690918	125.691835	43	44	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	91473232	91473232	5936	14	C	T	T	26	26	FBLN5	T	2	2
CAPN3	825	broad.mit.edu	36	15	40476331	40476331	+	Missense_Mutation	SNP	G	A	A			TCGA-28-1746-01	TCGA-28-1746-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr15:40476331G>A	uc001zpn.1	+	c.1157G>A	c.(1156-1158)CGT>CAT	p.R386H	CAPN3_uc001zpk.1_3'UTR|CAPN3_uc001zpl.1_Missense_Mutation_p.R299H|CAPN3_uc001zpm.1_Missense_Mutation_p.R299H|CAPN3_uc001zpo.1_Missense_Mutation_p.R386H|CAPN3_uc001zpp.1_Missense_Mutation_p.R338H	NM_000070	NP_000061	P20807	CAN3_HUMAN	calpain 3 isoform a	386	Calpain catalytic.				muscle organ development|proteolysis	cytoplasm	calcium ion binding|calcium-dependent cysteine-type endopeptidase activity|signal transducer activity			central_nervous_system(1)	1		all_cancers(109;1.65e-16)|all_epithelial(112;8.34e-15)|Lung NSC(122;3.56e-09)|all_lung(180;1.68e-08)|Melanoma(134;0.0574)|Colorectal(260;0.152)		GBM - Glioblastoma multiforme(94;7.36e-07)										0.831461	242.551015	251.74561	74	15	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	40476331	40476331	2746	15	G	A	A	40	40	CAPN3	A	1	1
PRKCB	5579	broad.mit.edu	36	16	24138809	24138809	+	Silent	SNP	C	T	T			TCGA-28-1746-01	TCGA-28-1746-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:24138809C>T	uc002dmd.1	+	c.1890C>T	c.(1888-1890)TTC>TTT	p.F630F	PRKCB_uc002dme.1_Non-coding_Transcript	NM_212535	NP_997700	P05771	KPCB_HUMAN	protein kinase C, beta isoform 1	630	AGC-kinase C-terminal.				apoptosis|B cell activation|B cell receptor signaling pathway|intracellular signal transduction|lipoprotein transport|platelet activation|positive regulation of I-kappaB kinase/NF-kappaB cascade|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|synaptic transmission|transcription, DNA-dependent	cytosol|nucleus|plasma membrane	androgen receptor binding|ATP binding|chromatin binding|histone binding|histone kinase activity (H3-T6 specific)|ligand-dependent nuclear receptor transcription coactivator activity|protein kinase C activity|protein kinase C binding|zinc ion binding			ovary(3)|central_nervous_system(3)|lung(2)|large_intestine(1)	9					Vitamin E(DB00163)					395				0.367647	68.37756	69.415205	25	43	CC		KEEP	---	---	---	---	capture			Silent	SNP	24138809	24138809	12951	16	C	T	T	31	31	PRKCB	T	1	1
ZNF689	115509	broad.mit.edu	36	16	30523240	30523240	+	Missense_Mutation	SNP	A	G	G			TCGA-28-1746-01	TCGA-28-1746-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr16:30523240A>G	uc002dyx.1	-	c.1349T>C	c.(1348-1350)CTG>CCG	p.L450P	ZNF689_uc010bzy.1_Missense_Mutation_p.C106R	NM_138447	NP_612456	Q96CS4	ZN689_HUMAN	zinc finger protein HIT-39	450	C2H2-type 11.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0			Colorectal(24;0.198)											0.176471	6.919477	8.592387	3	14	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	30523240	30523240	18689	16	A	G	G	7	7	ZNF689	G	4	4
ALG1	56052	broad.mit.edu	36	16	5070950	5070950	+	Missense_Mutation	SNP	A	C	C			TCGA-28-1746-01	TCGA-28-1746-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr16:5070950A>C	uc002cyn.1	+	c.964A>C	c.(964-966)AAA>CAA	p.K322Q	ALG1_uc002cyj.1_Missense_Mutation_p.K211Q|ALG1_uc002cym.1_Missense_Mutation_p.K322Q|ALG1_uc010bue.1_Missense_Mutation_p.K211Q	NM_019109	NP_061982	Q9BT22	ALG1_HUMAN	beta-1,4-mannosyltransferase	322	Lumenal (Potential).				dolichol-linked oligosaccharide biosynthetic process|lipopolysaccharide biosynthetic process|post-translational protein modification|protein N-linked glycosylation via asparagine	endoplasmic reticulum membrane|integral to membrane	chitobiosyldiphosphodolichol beta-mannosyltransferase activity			ovary(1)	1		Ovarian(90;0.0164)												0.227273	7.057386	8.568546	5	17	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	5070950	5070950	513	16	A	C	C	5	5	ALG1	C	4	4
RRAD	6236	broad.mit.edu	36	16	65513624	65513624	+	Silent	SNP	G	A	A			TCGA-28-1746-01	TCGA-28-1746-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:65513624G>A	uc002eqn.2	-	c.783C>T	c.(781-783)AAC>AAT	p.N261N	RRAD_uc002eqo.2_Silent_p.N261N	NM_001128850	NP_001122322	P55042	RAD_HUMAN	Ras-related associated with diabetes	261					small GTPase mediated signal transduction	plasma membrane	calmodulin binding|GTP binding|GTPase activity				0		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0862)|Epithelial(162;0.198)										0.3	35.508134	37.295651	15	35	GG		KEEP	---	---	---	---	capture			Silent	SNP	65513624	65513624	14151	16	G	A	A	40	40	RRAD	A	1	1
DNAH9	1770	broad.mit.edu	36	17	11767899	11767899	+	Silent	SNP	C	T	T			TCGA-28-1746-01	TCGA-28-1746-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:11767899C>T	uc002gne.1	+	c.11793C>T	c.(11791-11793)AAC>AAT	p.N3931N	DNAH9_uc010coo.1_Silent_p.N3225N|DNAH9_uc002gnf.1_Silent_p.N243N	NM_001372	NP_001363	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9 isoform 2	3931	AAA 6 (By similarity).				cell projection organization|cellular component movement|microtubule-based movement|spermatogenesis	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(4)|breast(3)|central_nervous_system(2)|pancreas(1)	10		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)										0.291317	284.129295	298.014875	104	253	CC		KEEP	---	---	---	---	capture			Silent	SNP	11767899	11767899	4791	17	C	T	T	19	19	DNAH9	T	1	1
MYOCD	93649	broad.mit.edu	36	17	12596514	12596514	+	Missense_Mutation	SNP	C	T	T			TCGA-28-1746-01	TCGA-28-1746-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:12596514C>T	uc002gno.1	+	c.1184C>T	c.(1183-1185)ACG>ATG	p.T395M	MYOCD_uc002gnn.1_Missense_Mutation_p.T395M|MYOCD_uc002gnp.1_Missense_Mutation_p.T299M|MYOCD_uc002gnq.1_Missense_Mutation_p.T114M	NM_153604	NP_705832	Q8IZQ8	MYCD_HUMAN	myocardin	395	SAP.				cardiac cell differentiation|positive regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of smooth muscle contraction|regulation of smooth muscle cell differentiation|transcription, DNA-dependent	nucleus	nucleic acid binding|transcription factor binding			central_nervous_system(2)|ovary(1)	3				UCEC - Uterine corpus endometrioid carcinoma (92;0.0969)										0.288136	40.056321	42.430964	17	42	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	12596514	12596514	10482	17	C	T	T	19	19	MYOCD	T	1	1
MYO15A	51168	broad.mit.edu	36	17	17995209	17995209	+	Missense_Mutation	SNP	G	A	A			TCGA-28-1746-01	TCGA-28-1746-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:17995209G>A	uc010cpt.1	+	c.7534G>A	c.(7534-7536)GTG>ATG	p.V2512M	MYO15A_uc010cpu.1_Missense_Mutation_p.V2512M	NM_016239	NP_057323	Q9UKN7	MYO15_HUMAN	myosin XV	2512	Tail.				sensory perception of sound	cytoplasm|myosin complex|stereocilium	actin binding|ATP binding|calmodulin binding|motor activity			ovary(2)|pancreas(1)|breast(1)|central_nervous_system(1)|skin(1)	6	all_neural(463;0.228)													0.666667	58.891055	59.629879	20	10	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	17995209	17995209	10458	17	G	A	A	40	40	MYO15A	A	1	1
FAM83G	644815	broad.mit.edu	36	17	18822632	18822632	+	Missense_Mutation	SNP	C	T	T			TCGA-28-1746-01	TCGA-28-1746-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:18822632C>T	uc002guw.1	-	c.1072G>A	c.(1072-1074)GAC>AAC	p.D358N	SLC5A10_uc002gur.1_Intron|SLC5A10_uc002gut.1_Intron|SLC5A10_uc002guu.1_Intron|SLC5A10_uc002guv.1_Intron	NM_001039999	NP_001035088	A6ND36	FA83G_HUMAN	hypothetical protein LOC644815	358										ovary(1)	1														0.636364	23.12772	23.307805	7	4	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	18822632	18822632	5865	17	C	T	T	31	31	FAM83G	T	1	1
TNFAIP1	7126	broad.mit.edu	36	17	23692404	23692404	+	Silent	SNP	C	T	T			TCGA-28-1746-01	TCGA-28-1746-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:23692404C>T	uc002hax.1	+	c.390C>T	c.(388-390)TCC>TCT	p.S130S	TNFAIP1_uc002hay.1_Silent_p.S130S	NM_021137	NP_066960	Q13829	BACD2_HUMAN	tumor necrosis factor, alpha-induced protein 1	130					apoptosis|cell migration|DNA replication|embryo development|immune response|negative regulation of Rho protein signal transduction|proteasomal ubiquitin-dependent protein catabolic process|protein ubiquitination|stress fiber assembly	Cul3-RING ubiquitin ligase complex|endosome|nucleus|voltage-gated potassium channel complex	GTP-Rho binding|voltage-gated potassium channel activity				0	all_lung(13;0.000294)|Lung NSC(42;0.000964)			UCEC - Uterine corpus endometrioid carcinoma (53;0.153)										0.333333	15.608387	16.190815	8	16	CC		KEEP	---	---	---	---	capture			Silent	SNP	23692404	23692404	16813	17	C	T	T	24	24	TNFAIP1	T	2	2
KIF2B	84643	broad.mit.edu	36	17	49256051	49256051	+	Missense_Mutation	SNP	A	G	G			TCGA-28-1746-01	TCGA-28-1746-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr17:49256051A>G	uc002iua.2	+	c.658A>G	c.(658-660)AAG>GAG	p.K220E		NM_032559	NP_115948	Q8N4N8	KIF2B_HUMAN	kinesin family member 2B	220	Kinesin-motor.				blood coagulation|cell division|microtubule depolymerization|microtubule-based movement|mitotic prometaphase|regulation of chromosome segregation	condensed chromosome kinetochore|cytosol|microtubule|microtubule organizing center|nucleolus|spindle	ATP binding|microtubule motor activity			ovary(5)	5														0.389831	70.354425	70.966579	23	36	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	49256051	49256051	8609	17	A	G	G	9	9	KIF2B	G	4	4
TP53	7157	broad.mit.edu	36	17	7517839	7517839	+	Missense_Mutation	SNP	C	T	T			TCGA-28-1746-01	TCGA-28-1746-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:7517839C>T	uc002gim.2	-	c.824G>A	c.(823-825)TGT>TAT	p.C275Y	TP53_uc002gig.1_Intron|TP53_uc002gih.1_Missense_Mutation_p.C275Y|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Missense_Mutation_p.C143Y|TP53_uc010cng.1_Missense_Mutation_p.C143Y|TP53_uc002gii.1_Missense_Mutation_p.C143Y|TP53_uc010cnh.1_Missense_Mutation_p.C275Y|TP53_uc010cni.1_Missense_Mutation_p.C275Y|TP53_uc002gij.2_Missense_Mutation_p.C275Y	NM_001126112	NP_001119584	P04637	P53_HUMAN	tumor protein p53 isoform a	275	Interaction with DNA.||Interaction with E4F1.|Interaction with HIPK1 (By similarity).|Interaction with AXIN1 (By similarity).		C -> S (in sporadic cancers; somatic mutation).|C -> G (in sporadic cancers; somatic mutation).|C -> F (in sporadic cancers; somatic mutation).|C -> W (in sporadic cancers; somatic mutation).|C -> Y (in LFS; germline mutation and in sporadic cancers; somatic mutation).|C -> R (in sporadic cancers; somatic mutation).		activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of gene-specific transcription from RNA polymerase II promoter|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray	chromatin|cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork	ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|promoter binding|promoter binding|protease binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|sequence-specific DNA binding transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|ubiquitin protein ligase binding|zinc ion binding	p.C275Y(44)|p.C275F(31)|p.0?(6)|p.C275S(2)|p.C275fs*20(1)|p.?(1)|p.L265_K305del41(1)|p.R273_C275delRVC(1)|p.F270_D281del12(1)|p.A276fs*29(1)|p.S269fs*21(1)|p.C275fs*67(1)|p.C275fs*70(1)|p.V272_K292del21(1)|p.C275_R283delCACPGRDRR(1)		large_intestine(4614)|breast(2344)|upper_aerodigestive_tract(2150)|lung(1958)|ovary(1559)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1212)|stomach(1127)|urinary_tract(1113)|central_nervous_system(1072)|liver(805)|skin(693)|pancreas(370)|biliary_tract(247)|soft_tissue(209)|prostate(192)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(41)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1)	21904		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)		Pancreas(47;798 1329 9957 10801)		111	p.C275Y(GI1-Tumor)|p.C275F(CHAGOK1-Tumor)|p.V274fs(SCC9-Tumor)|p.C275F(JHOM2B-Tumor)	690	TCGA GBM(1;<1E-8)|TSP Lung(2;<1E-8)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)			0.483871	85.033421	85.047842	30	32	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	7517839	7517839	16923	17	C	T	T	17	17	TP53	T	2	2
OR7C1	26664	broad.mit.edu	36	19	14771439	14771439	+	Silent	SNP	G	A	A			TCGA-28-1746-01	TCGA-28-1746-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:14771439G>A	uc002mzv.1	-	c.510C>T	c.(508-510)ACC>ACT	p.T170T		NM_198944	NP_945182	O76099	OR7C1_HUMAN	olfactory receptor, family 7, subfamily C,	170	Extracellular (Potential).				sensory perception of smell|spermatogenesis	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)	2														0.469136	349.734305	349.941797	114	129	GG		KEEP	---	---	---	---	capture			Silent	SNP	14771439	14771439	11628	19	G	A	A	39	39	OR7C1	A	1	1
SPINT2	10653	broad.mit.edu	36	19	43470363	43470363	+	Silent	SNP	C	T	T			TCGA-28-1746-01	TCGA-28-1746-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:43470363C>T	uc002ohr.1	+	c.285C>T	c.(283-285)GCC>GCT	p.A95A	SPINT2_uc002ohs.1_Silent_p.A38A	NM_021102	NP_066925	O43291	SPIT2_HUMAN	serine protease inhibitor, Kunitz type, 2	95	Extracellular (Potential).				cellular component movement	cytoplasm|extracellular region|integral to membrane|soluble fraction	serine-type endopeptidase inhibitor activity				0	all_cancers(60;6.83e-07)		Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292)											0.277778	14.167441	14.967076	5	13	CC		KEEP	---	---	---	---	capture			Silent	SNP	43470363	43470363	15581	19	C	T	T	21	21	SPINT2	T	2	2
EGLN2	112398	broad.mit.edu	36	19	45998956	45998956	+	Silent	SNP	C	T	T			TCGA-28-1746-01	TCGA-28-1746-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:45998956C>T	uc010ehd.1	+	c.639C>T	c.(637-639)CTC>CTT	p.L213L	EGLN2_uc002opg.2_Silent_p.L213L|EGLN2_uc002oph.1_Silent_p.L213L|EGLN2_uc002opi.1_Silent_p.L213L	NM_080732	NP_542770	Q96KS0	EGLN2_HUMAN	EGL nine (C.elegans) homolog 2	213					cell redox homeostasis|estrogen receptor signaling pathway|oxidation-reduction process|positive regulation of protein catabolic process|regulation of cell growth|response to hypoxia	cytoplasm|nucleus	ferrous iron binding|L-ascorbic acid binding|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|oxygen sensor activity			ovary(2)	2			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)		Vitamin C(DB00126)									0.461538	15.040761	15.058128	6	7	CC		KEEP	---	---	---	---	capture			Silent	SNP	45998956	45998956	5158	19	C	T	T	29	29	EGLN2	T	2	2
PSG9	5678	broad.mit.edu	36	19	48463963	48463963	+	Silent	SNP	C	T	T			TCGA-28-1746-01	TCGA-28-1746-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:48463963C>T	uc002owd.2	-	c.243G>A	c.(241-243)TCG>TCA	p.S81S	PSG9_uc002owc.2_Silent_p.S10S|PSG9_uc002owe.2_Silent_p.S81S|PSG9_uc002owf.2_Silent_p.S81S|PSG9_uc002owg.2_Silent_p.S81S|PSG9_uc002owh.2_Silent_p.S81S	NM_002784	NP_002775	Q00887	PSG9_HUMAN	pregnancy specific beta-1-glycoprotein 9	81	Ig-like V-type.				female pregnancy	extracellular region				ovary(1)	1		Prostate(69;0.00682)												0.38474	700.657758	707.783277	237	379	CC		KEEP	---	---	---	---	capture			Silent	SNP	48463963	48463963	13115	19	C	T	T	19	19	PSG9	T	1	1
C3	718	broad.mit.edu	36	19	6647606	6647606	+	Missense_Mutation	SNP	C	T	T			TCGA-28-1746-01	TCGA-28-1746-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:6647606C>T	uc002mfm.1	-	c.2861G>A	c.(2860-2862)CGT>CAT	p.R954H		NM_000064	NP_000055	P01024	CO3_HUMAN	complement component 3 precursor	954		Cleavage; by factor I (Potential).			complement activation, alternative pathway|complement activation, classical pathway|G-protein coupled receptor protein signaling pathway|inflammatory response|positive regulation vascular endothelial growth factor production	extracellular space	endopeptidase inhibitor activity|receptor binding			ovary(1)|pancreas(1)	2				GBM - Glioblastoma multiforme(1328;1.36e-05)|Lung(535;0.00661)										0.263158	21.07263	23.055852	10	28	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	6647606	6647606	2296	19	C	T	T	19	19	C3	T	1	1
PIAS3	10401	broad.mit.edu	36	1	144289492	144289492	+	Missense_Mutation	SNP	G	A	A			TCGA-28-1746-01	TCGA-28-1746-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:144289492G>A	uc001eoc.1	+	c.98G>A	c.(97-99)CGG>CAG	p.R33Q	PIAS3_uc001eod.1_5'Flank	NM_006099	NP_006090	Q9Y6X2	PIAS3_HUMAN	protein inhibitor of activated STAT, 3	33	SAP.				positive regulation of protein sumoylation|protein sumoylation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear speck	enzyme binding|nucleic acid binding|protein C-terminus binding|zinc ion binding				0	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)													0.446029	665.245645	666.490957	219	272	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	144289492	144289492	12301	1	G	A	A	39	39	PIAS3	A	1	1
ITLN2	142683	broad.mit.edu	36	1	159187570	159187570	+	Missense_Mutation	SNP	C	A	A			TCGA-28-1746-01	TCGA-28-1746-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:159187570C>A	uc001fxd.1	-	c.328G>T	c.(328-330)GAT>TAT	p.D110Y	ITLN2_uc009wts.1_Missense_Mutation_p.D109Y	NM_080878	NP_543154	Q8WWU7	ITLN2_HUMAN	intelectin 2	110	Fibrinogen C-terminal.				signal transduction	extracellular region	receptor binding|sugar binding			ovary(1)	1	all_cancers(52;2.99e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00275)											0.225	11.565969	14.451612	9	31	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	159187570	159187570	8215	1	C	A	A	29	29	ITLN2	A	3	3
SELP	6403	broad.mit.edu	36	1	167838918	167838918	+	Missense_Mutation	SNP	G	A	A			TCGA-28-1746-01	TCGA-28-1746-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:167838918G>A	uc001ggi.2	-	c.1675C>T	c.(1675-1677)CGC>TGC	p.R559C	SELP_uc009wvr.1_Missense_Mutation_p.R559C|SELP_uc001ggh.2_Missense_Mutation_p.R394C	NM_003005	NP_002996	P16109	LYAM3_HUMAN	selectin P precursor	559	Extracellular (Potential).|Sushi 6.				defense response to Gram-negative bacterium|platelet activation|platelet degranulation|positive regulation of platelet activation|response to lipopolysaccharide	external side of plasma membrane|extracellular space|integral to plasma membrane|membrane fraction|platelet alpha granule membrane|platelet dense granule membrane|soluble fraction	fucose binding|glycosphingolipid binding|heparin binding|lipopolysaccharide binding|oligosaccharide binding|sialic acid binding			ovary(2)	2	all_hematologic(923;0.208)				Clopidogrel(DB00758)|Heparin(DB01109)|Tirofiban(DB00775)									0.456522	129.14522	129.295406	42	50	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	167838918	167838918	14505	1	G	A	A	40	40	SELP	A	1	1
TMCC2	9911	broad.mit.edu	36	1	203504889	203504889	+	Silent	SNP	C	T	T			TCGA-28-1746-01	TCGA-28-1746-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:203504889C>T	uc001hbz.1	+	c.936C>T	c.(934-936)GAC>GAT	p.D312D	TMCC2_uc001hca.2_Silent_p.D87D|TMCC2_uc001hcb.1_Silent_p.D72D|TMCC2_uc001hcc.1_5'UTR|TMCC2_uc001hcd.2_Silent_p.D79D	NM_014858	NP_055673	O75069	TMCC2_HUMAN	transmembrane and coiled-coil domain family 2	312						integral to membrane				pancreas(1)	1	Breast(84;0.0871)		BRCA - Breast invasive adenocarcinoma(75;0.117)											0.333333	24.46639	25.130412	9	18	CC		KEEP	---	---	---	---	capture			Silent	SNP	203504889	203504889	16523	1	C	T	T	17	17	TMCC2	T	2	2
PLXNA2	5362	broad.mit.edu	36	1	206300661	206300661	+	Missense_Mutation	SNP	C	T	T			TCGA-28-1746-01	TCGA-28-1746-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:206300661C>T	uc001hgz.1	-	c.2731G>A	c.(2731-2733)GCT>ACT	p.A911T		NM_025179	NP_079455	O75051	PLXA2_HUMAN	plexin A2	911	Extracellular (Potential).|IPT/TIG 1.				axon guidance	integral to membrane|intracellular|plasma membrane				ovary(2)	2				OV - Ovarian serous cystadenocarcinoma(81;0.199)										0.452055	93.290477	93.431864	33	40	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	206300661	206300661	12546	1	C	T	T	27	27	PLXNA2	T	1	1
B3GALNT2	148789	broad.mit.edu	36	1	233724691	233724691	+	Silent	SNP	G	A	A			TCGA-28-1746-01	TCGA-28-1746-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:233724691G>A	uc001hxc.1	-	c.183C>T	c.(181-183)CGC>CGT	p.R61R	B3GALNT2_uc001hxd.1_Silent_p.R102R	NM_152490	NP_689703	Q8NCR0	B3GL2_HUMAN	beta-1,3-N-acetylgalactosaminyltransferase 2	61	Lumenal (Potential).				protein glycosylation	Golgi membrane|integral to membrane	galactosyltransferase activity			breast(1)	1	Ovarian(103;0.0634)|Breast(184;0.23)	all_cancers(173;0.0539)|Prostate(94;0.0353)	OV - Ovarian serous cystadenocarcinoma(106;0.000117)											0.405286	231.53093	233.31117	92	135	GG		KEEP	---	---	---	---	capture			Silent	SNP	233724691	233724691	1267	1	G	A	A	46	46	B3GALNT2	A	2	2
OR2T6	254879	broad.mit.edu	36	1	246617616	246617616	+	Silent	SNP	C	T	T	rs61736237	unknown	TCGA-28-1746-01	TCGA-28-1746-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:246617616C>T	uc001iei.1	+	c.84C>T	c.(82-84)TTC>TTT	p.F28F		NM_001005471	NP_001005471	Q8NHC8	OR2T6_HUMAN	olfactory receptor, family 2, subfamily T,	28	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)	2	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)											0.233871	73.018907	81.051538	29	95	CC		KEEP	---	---	---	---	capture			Silent	SNP	246617616	246617616	11435	1	C	T	T	31	31	OR2T6	T	1	1
OSCP1	127700	broad.mit.edu	36	1	36661614	36661614	+	Missense_Mutation	SNP	C	T	T			TCGA-28-1746-01	TCGA-28-1746-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:36661614C>T	uc001cap.1	-	c.587G>A	c.(586-588)GGT>GAT	p.G196D	OSCP1_uc001caq.1_Missense_Mutation_p.G186D	NM_145047	NP_659484	Q8WVF1	OSCP1_HUMAN	oxidored-nitro domain-containing protein isoform	196					transport	basal plasma membrane				ovary(2)|central_nervous_system(1)|pancreas(1)	4														0.433962	212.156722	212.759649	69	90	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	36661614	36661614	11697	1	C	T	T	18	18	OSCP1	T	2	2
C8B	732	broad.mit.edu	36	1	57167791	57167791	+	Missense_Mutation	SNP	G	C	C			TCGA-28-1746-01	TCGA-28-1746-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:57167791G>C	uc001cyp.1	-	c.1650C>G	c.(1648-1650)TGC>TGG	p.C550W		NM_000066	NP_000057	P07358	CO8B_HUMAN	complement component 8, beta polypeptide	550	TSP type-1 2.				complement activation, alternative pathway|complement activation, classical pathway|cytolysis	membrane attack complex				central_nervous_system(2)|large_intestine(1)|ovary(1)	4														0.290323	46.312126	48.763772	18	44	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	57167791	57167791	2526	1	G	C	C	34	34	C8B	C	3	3
TTL	150465	broad.mit.edu	36	2	112977223	112977223	+	Missense_Mutation	SNP	T	A	A			TCGA-28-1746-01	TCGA-28-1746-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr2:112977223T>A	uc002thu.1	+	c.869T>A	c.(868-870)ATA>AAA	p.I290K	TTL_uc010fkm.1_Non-coding_Transcript	NM_153712	NP_714923	Q8NG68	TTL_HUMAN	tubulin tyrosine ligase	290	TTL.				protein modification process		ATP binding|tubulin-tyrosine ligase activity				0		Ovarian(717;0.024)		BRCA - Breast invasive adenocarcinoma(221;6.17e-07)|STAD - Stomach adenocarcinoma(1183;0.00644)						130				0.425926	141.930198	142.447306	46	62	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	112977223	112977223	17276	2	T	A	A	49	49	TTL	A	4	4
C1QL2	165257	broad.mit.edu	36	2	119631654	119631654	+	Missense_Mutation	SNP	G	A	A			TCGA-28-1746-01	TCGA-28-1746-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:119631654G>A	uc002tlo.2	-	c.662C>T	c.(661-663)GCG>GTG	p.A221V		NM_182528	NP_872334	Q7Z5L3	C1QL2_HUMAN	complement component 1, q subcomponent-like 2	221	C1q.					collagen				pancreas(1)	1														0.25	16.877235	18.215035	6	18	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	119631654	119631654	2026	2	G	A	A	38	38	C1QL2	A	1	1
TMEM177	80775	broad.mit.edu	36	2	120155045	120155045	+	Nonsense_Mutation	SNP	G	A	A			TCGA-28-1746-01	TCGA-28-1746-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:120155045G>A	uc010flg.1	+	c.146G>A	c.(145-147)TGG>TAG	p.W49*	TMEM177_uc002tme.2_Intron|TMEM177_uc002tmc.1_Nonsense_Mutation_p.W49*|TMEM177_uc002tmd.2_Nonsense_Mutation_p.W49*|TMEM177_uc010flh.1_Nonsense_Mutation_p.W49*|TMEM177_uc010fli.1_Nonsense_Mutation_p.W49*	NM_001105198	NP_085054	Q53S58	TM177_HUMAN	transmembrane protein 177	49						integral to membrane				ovary(1)	1	Colorectal(110;0.196)													0.35	36.140501	36.933299	14	26	GG		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	120155045	120155045	16628	2	G	A	A	47	47	TMEM177	A	5	2
XIRP2	129446	broad.mit.edu	36	2	167468332	167468332	+	Missense_Mutation	SNP	C	G	G			TCGA-28-1746-01	TCGA-28-1746-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:167468332C>G	uc002udx.1	+	c.94C>G	c.(94-96)CAT>GAT	p.H32D	XIRP2_uc010fpn.1_Missense_Mutation_p.H32D|XIRP2_uc010fpo.1_Missense_Mutation_p.H32D|XIRP2_uc010fpp.1_Missense_Mutation_p.H32D	NM_152381	NP_689594	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2 isoform 1	Error:Variant_position_missing_in_A4UGR9_after_alignment					actin cytoskeleton organization	cell junction	actin binding			ovary(6)|pancreas(1)|skin(1)	8														0.4	138.072043	139.121614	48	72	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	167468332	167468332	18011	2	C	G	G	21	21	XIRP2	G	3	3
PPIG	9360	broad.mit.edu	36	2	170196683	170196683	+	Missense_Mutation	SNP	G	C	C			TCGA-28-1746-01	TCGA-28-1746-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:170196683G>C	uc002uez.1	+	c.923G>C	c.(922-924)AGA>ACA	p.R308T	PPIG_uc010fpx.1_Missense_Mutation_p.R293T|PPIG_uc010fpy.1_Missense_Mutation_p.R301T|PPIG_uc002ufa.2_Missense_Mutation_p.R308T|PPIG_uc002ufb.1_Missense_Mutation_p.R308T|PPIG_uc002ufd.1_Missense_Mutation_p.R305T	NM_004792	NP_004783	Q13427	PPIG_HUMAN	peptidylprolyl isomerase G	308					protein folding|RNA splicing	nuclear matrix|nuclear speck	cyclosporin A binding|peptidyl-prolyl cis-trans isomerase activity			ovary(2)|central_nervous_system(1)	3					L-Proline(DB00172)									0.465753	114.246354	114.320533	34	39	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	170196683	170196683	12759	2	G	C	C	33	33	PPIG	C	3	3
TTN	7273	broad.mit.edu	36	2	179341871	179341871	+	Silent	SNP	G	A	A			TCGA-28-1746-01	TCGA-28-1746-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:179341871G>A	uc002umr.1	-	c.8937C>T	c.(8935-8937)AAC>AAT	p.N2979N	TTN_uc002ums.1_Silent_p.N2933N|TTN_uc010frc.1_Silent_p.N2933N|TTN_uc010frd.1_Silent_p.N2933N|TTN_uc002unb.1_Silent_p.N2979N	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	2979										ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)							8722				0.493976	126.767901	126.770559	41	42	GG		KEEP	---	---	---	---	capture			Silent	SNP	179341871	179341871	17290	2	G	A	A	40	40	TTN	A	1	1
NRP2	8828	broad.mit.edu	36	2	206318816	206318816	+	Silent	SNP	G	A	A			TCGA-28-1746-01	TCGA-28-1746-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:206318816G>A	uc002vaw.1	+	c.1743G>A	c.(1741-1743)GCG>GCA	p.A581A	NRP2_uc002vau.1_Silent_p.A581A|NRP2_uc002vav.1_Silent_p.A581A|NRP2_uc002vax.1_Silent_p.A581A|NRP2_uc002vay.1_Silent_p.A581A	NM_201266	NP_957718	O60462	NRP2_HUMAN	neuropilin 2 isoform 1 precursor	581	Extracellular (Potential).|F5/8 type C 2.				axon guidance|cell adhesion	integral to membrane|membrane fraction|plasma membrane	heparin binding|metal ion binding|vascular endothelial growth factor receptor activity			ovary(1)|central_nervous_system(1)	2														0.363636	43.42667	44.130108	16	28	GG		KEEP	---	---	---	---	capture			Silent	SNP	206318816	206318816	11066	2	G	A	A	39	39	NRP2	A	1	1
AGFG1	3267	broad.mit.edu	36	2	228109612	228109612	+	Silent	SNP	T	C	C			TCGA-28-1746-01	TCGA-28-1746-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr2:228109612T>C	uc002vpd.1	+	c.1305T>C	c.(1303-1305)GTT>GTC	p.V435V	AGFG1_uc002vpc.1_Silent_p.V411V|AGFG1_uc002vpe.1_Silent_p.V411V|AGFG1_uc002vpf.1_Silent_p.V371V	NM_004504	NP_004495	P52594	AGFG1_HUMAN	HIV-1 Rev binding protein isoform 2	411					cell differentiation|mRNA export from nucleus|multicellular organismal development|regulation of ARF GTPase activity|spermatogenesis	cytoplasmic membrane-bounded vesicle|Golgi apparatus|nuclear pore	ARF GTPase activator activity|DNA binding|protein binding|RNA binding|zinc ion binding			skin(2)|ovary(1)|central_nervous_system(1)	4														0.5	205.24713	205.24713	62	62	TT		KEEP	---	---	---	---	capture			Silent	SNP	228109612	228109612	383	2	T	C	C	63	63	AGFG1	C	4	4
ITSN2	50618	broad.mit.edu	36	2	24322585	24322585	+	Nonsense_Mutation	SNP	C	T	T			TCGA-28-1746-01	TCGA-28-1746-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:24322585C>T	uc002rfe.1	-	c.3491G>A	c.(3490-3492)TGG>TAG	p.W1164*	ITSN2_uc002rff.1_Nonsense_Mutation_p.W1137*|ITSN2_uc002rfg.1_Nonsense_Mutation_p.W1164*|ITSN2_uc002rfh.1_Non-coding_Transcript	NM_006277	NP_006268	Q9NZM3	ITSN2_HUMAN	intersectin 2 isoform 1	1165	SH3 5.				endocytosis|regulation of Rho protein signal transduction	cytoplasm	calcium ion binding|Rho guanyl-nucleotide exchange factor activity|SH3/SH2 adaptor activity			kidney(2)|ovary(1)|central_nervous_system(1)	4	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)													0.492308	304.985566	304.995728	96	99	CC		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	24322585	24322585	8231	2	C	T	T	21	21	ITSN2	T	5	2
OTOF	9381	broad.mit.edu	36	2	26541310	26541310	+	Missense_Mutation	SNP	C	T	T			TCGA-28-1746-01	TCGA-28-1746-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:26541310C>T	uc002rhk.1	-	c.4891G>A	c.(4891-4893)GGG>AGG	p.G1631R	OTOF_uc002rhh.1_Missense_Mutation_p.G864R|OTOF_uc002rhi.1_Missense_Mutation_p.G941R|OTOF_uc002rhj.1_Missense_Mutation_p.G864R	NM_194248	NP_919224	Q9HC10	OTOF_HUMAN	otoferlin isoform a	1631	Cytoplasmic (Potential).				cellular membrane fusion|sensory perception of sound|synaptic vesicle exocytosis	basolateral plasma membrane|cell junction|cytosol|endoplasmic reticulum membrane|integral to membrane|membrane fraction|synaptic vesicle membrane	calcium ion binding			ovary(3)|breast(2)|central_nervous_system(1)|pancreas(1)	7	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GBM(102;732 1451 20652 24062 31372)								0.636364	19.120983	19.299496	7	4	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	26541310	26541310	11715	2	C	T	T	21	21	OTOF	T	2	2
FAM161A	84140	broad.mit.edu	36	2	61920455	61920455	+	Silent	SNP	A	G	G			TCGA-28-1746-01	TCGA-28-1746-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr2:61920455A>G	uc002sbm.2	-	c.1188T>C	c.(1186-1188)TCT>TCC	p.S396S	FAM161A_uc002sbl.2_Silent_p.S287S|FAM161A_uc002sbn.2_Silent_p.S206S|FAM161A_uc010fcm.1_Non-coding_Transcript|FAM161A_uc010fcn.1_Silent_p.S287S	NM_032180	NP_115556	Q3B820	F161A_HUMAN	hypothetical protein LOC84140	396					response to stimulus|visual perception					large_intestine(2)|ovary(1)	3														0.284091	65.939062	69.623354	25	63	AA		KEEP	---	---	---	---	capture			Silent	SNP	61920455	61920455	5676	2	A	G	G	11	11	FAM161A	G	4	4
DOK1	1796	broad.mit.edu	36	2	74637261	74637261	+	Missense_Mutation	SNP	G	A	A			TCGA-28-1746-01	TCGA-28-1746-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:74637261G>A	uc002sms.1	+	c.958G>A	c.(958-960)GAC>AAC	p.D320N	LOXL3_uc002smp.1_5'Flank|LOXL3_uc002smq.1_5'Flank|LOXL3_uc010ffn.1_5'Flank|DOK1_uc002smr.1_Missense_Mutation_p.D181N|DOK1_uc010ffo.1_Missense_Mutation_p.D181N|DOK1_uc002smt.1_Missense_Mutation_p.D106N|DOK1_uc002smu.1_Missense_Mutation_p.D106N|DOK1_uc002smv.1_Missense_Mutation_p.D181N|DOK1_uc002smw.1_Missense_Mutation_p.D106N	NM_001381	NP_001372	Q99704	DOK1_HUMAN	docking protein 1	320					fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway	cytosol|perinuclear region of cytoplasm	insulin receptor binding				0						Esophageal Squamous(36;520 860 12502 33616 51270)								0.420635	160.058892	160.749745	53	73	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	74637261	74637261	4880	2	G	A	A	41	41	DOK1	A	2	2
GGCX	2677	broad.mit.edu	36	2	85634919	85634919	+	Silent	SNP	C	T	T			TCGA-28-1746-01	TCGA-28-1746-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:85634919C>T	uc002sps.1	-	c.747G>A	c.(745-747)CTG>CTA	p.L249L		NM_000821	NP_000812	P38435	VKGC_HUMAN	gamma-glutamyl carboxylase isoform 1	249	Lumenal (Potential).				blood coagulation|peptidyl-glutamic acid carboxylation|post-translational protein modification	endoplasmic reticulum membrane|integral to membrane|membrane fraction	gamma-glutamyl carboxylase activity			ovary(1)	1					Anisindione(DB01125)|Coagulation Factor IX(DB00100)|Coagulation factor VIIa(DB00036)|Drotrecogin alfa(DB00055)|L-Glutamic Acid(DB00142)|Menadione(DB00170)|Phytonadione(DB01022)									0.428571	84.119286	84.434002	30	40	CC		KEEP	---	---	---	---	capture			Silent	SNP	85634919	85634919	6624	2	C	T	T	29	29	GGCX	T	2	2
ETV5	2119	broad.mit.edu	36	3	187306118	187306118	+	Silent	SNP	G	A	A			TCGA-28-1746-01	TCGA-28-1746-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:187306118G>A	uc003fpy.1	-	c.249C>T	c.(247-249)CAC>CAT	p.H83H	ETV5_uc003fpz.1_Silent_p.H41H	NM_004454	NP_004445	P41161	ETV5_HUMAN	ets variant gene 5 (ets-related molecule)	41					cellular response to oxidative stress|regulation of transcription, DNA-dependent	nucleus	promoter binding|sequence-specific DNA binding transcription factor activity			ovary(2)|skin(2)|breast(1)	5	all_cancers(143;4.06e-12)|Ovarian(172;0.0386)|Breast(254;0.247)		OV - Ovarian serous cystadenocarcinoma(80;1.62e-24)							170				0.330645	112.687953	115.917763	41	83	GG		KEEP	---	---	---	---	capture			Silent	SNP	187306118	187306118	5475	3	G	A	A	40	40	ETV5	A	1	1
TRIM71	131405	broad.mit.edu	36	3	32907952	32907952	+	Missense_Mutation	SNP	G	A	A			TCGA-28-1746-01	TCGA-28-1746-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:32907952G>A	uc003cff.1	+	c.2252G>A	c.(2251-2253)CGG>CAG	p.R751Q		NM_001039111	NP_001034200	Q2Q1W2	LIN41_HUMAN	tripartite motif-containing 71	751	NHL 4.				multicellular organismal development	cytoplasm	zinc ion binding			ovary(2)|large_intestine(1)	3														0.315789	14.940002	15.515415	6	13	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	32907952	32907952	17093	3	G	A	A	39	39	TRIM71	A	1	1
TDGF1	6997	broad.mit.edu	36	3	46595603	46595603	+	Missense_Mutation	SNP	T	C	C			TCGA-28-1746-01	TCGA-28-1746-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr3:46595603T>C	uc003cpv.1	+	c.50T>C	c.(49-51)ATG>ACG	p.M17T	LRRC2_uc003cpu.2_Intron	NM_003212	NP_003203	P13385	TDGF1_HUMAN	teratocarcinoma-derived growth factor 1	17					activation of MAPK activity|anterior/posterior axis specification, embryo|mammary gland development|morphogenesis of a branching structure|negative regulation of apoptosis|peptidyl-serine phosphorylation|positive regulation of cell migration|positive regulation of peptidyl-tyrosine phosphorylation	anchored to membrane|cell surface|extrinsic to plasma membrane	growth factor activity				0				BRCA - Breast invasive adenocarcinoma(193;0.00114)|KIRC - Kidney renal clear cell carcinoma(197;0.0173)|Kidney(197;0.0204)										0.473118	269.469897	269.587805	88	98	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	46595603	46595603	16252	3	T	C	C	51	51	TDGF1	C	4	4
INTS12	57117	broad.mit.edu	36	4	106823676	106823676	+	Missense_Mutation	SNP	T	C	C			TCGA-28-1746-01	TCGA-28-1746-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr4:106823676T>C	uc003hxw.1	-	c.1052A>G	c.(1051-1053)AAT>AGT	p.N351S	INTS12_uc010ilr.1_Missense_Mutation_p.N351S	NM_020395	NP_065128	Q96CB8	INT12_HUMAN	integrator complex subunit 12	351	Ser-rich.				snRNA processing	integrator complex	protein binding|zinc ion binding				0				OV - Ovarian serous cystadenocarcinoma(123;5.12e-07)										0.494595	566.397432	566.407715	183	187	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	106823676	106823676	8078	4	T	C	C	52	52	INTS12	C	4	4
SLCO6A1	133482	broad.mit.edu	36	5	101843943	101843943	+	Silent	SNP	G	A	A			TCGA-28-1746-01	TCGA-28-1746-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:101843943G>A	uc003knn.2	-	c.453C>T	c.(451-453)TAC>TAT	p.Y151Y	SLCO6A1_uc003kno.2_Silent_p.Y151Y|SLCO6A1_uc003knp.1_Silent_p.Y151Y|SLCO6A1_uc003knq.1_Silent_p.Y151Y	NM_173488	NP_775759	Q86UG4	SO6A1_HUMAN	solute carrier organic anion transporter family,	151	Helical; Name=2; (Potential).					integral to membrane|plasma membrane	transporter activity			ovary(3)|central_nervous_system(1)	4		all_cancers(142;8e-09)|all_epithelial(76;2.83e-12)|Prostate(80;0.00125)|Colorectal(57;0.00342)|Ovarian(225;0.024)|Lung NSC(167;0.0259)|all_lung(232;0.0323)		Epithelial(69;1.47e-15)|COAD - Colon adenocarcinoma(37;0.0113)										0.391813	203.788784	205.540703	67	104	GG		KEEP	---	---	---	---	capture			Silent	SNP	101843943	101843943	15229	5	G	A	A	40	40	SLCO6A1	A	1	1
GABRG2	2566	broad.mit.edu	36	5	161501840	161501840	+	Missense_Mutation	SNP	G	A	A			TCGA-28-1746-01	TCGA-28-1746-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:161501840G>A	uc010jjc.1	+	c.982G>A	c.(982-984)GTC>ATC	p.V328I	GABRG2_uc003lyy.2_Missense_Mutation_p.V288I|GABRG2_uc003lyz.2_Missense_Mutation_p.V288I	NM_198903	NP_944493	P18507	GBRG2_HUMAN	gamma-aminobutyric acid A receptor, gamma 2	288	Helical; (Probable).				gamma-aminobutyric acid signaling pathway	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	benzodiazepine receptor activity|chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity|protein binding			ovary(4)	4	Renal(175;0.000319)	Medulloblastoma(196;0.0208)|all_neural(177;0.0672)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0734)|OV - Ovarian serous cystadenocarcinoma(192;0.135)|Epithelial(171;0.136)										0.373288	309.754257	313.849521	109	183	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	161501840	161501840	6423	5	G	A	A	40	40	GABRG2	A	1	1
NSD1	64324	broad.mit.edu	36	5	176569316	176569316	+	Missense_Mutation	SNP	C	T	T			TCGA-28-1746-01	TCGA-28-1746-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:176569316C>T	uc003mfr.2	+	c.1310C>T	c.(1309-1311)TCA>TTA	p.S437L	NSD1_uc003mft.2_Missense_Mutation_p.S168L|NSD1_uc003mfs.1_Missense_Mutation_p.S334L	NM_022455	NP_071900	Q96L73	NSD1_HUMAN	nuclear receptor binding SET domain protein 1	437					negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|nucleus	androgen receptor binding|chromatin binding|estrogen receptor binding|histone methyltransferase activity (H3-K36 specific)|histone methyltransferase activity (H4-K20 specific)|ligand-dependent nuclear receptor binding|retinoid X receptor binding|thyroid hormone receptor binding|transcription corepressor activity|zinc ion binding			ovary(2)|kidney(1)	3	all_cancers(89;1.57e-05)|Renal(175;0.000269)|Lung NSC(126;0.00111)|all_lung(126;0.002)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)|Epithelial(233;0.198)	Kidney(146;0.235)						492				0.443182	108.08959	108.339638	39	49	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	176569316	176569316	11074	5	C	T	T	29	29	NSD1	T	2	2
MAN1A1	4121	broad.mit.edu	36	6	119551336	119551336	+	Missense_Mutation	SNP	G	T	T			TCGA-28-1746-01	TCGA-28-1746-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:119551336G>T	uc003pym.1	-	c.1652C>A	c.(1651-1653)ACT>AAT	p.T551N		NM_005907	NP_005898	P33908	MA1A1_HUMAN	mannosidase, alpha, class 1A, member 1	551	Lumenal (Potential).				post-translational protein modification|protein N-linked glycosylation via asparagine	endoplasmic reticulum|ER-Golgi intermediate compartment|Golgi membrane|integral to membrane|membrane fraction	calcium ion binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity			ovary(2)|central_nervous_system(1)	3		all_epithelial(87;0.173)		OV - Ovarian serous cystadenocarcinoma(136;0.0612)|GBM - Glioblastoma multiforme(226;0.0702)|all cancers(137;0.115)		Ovarian(136;8 1825 12608 33541 47587)								0.352713	270.585829	275.504141	91	167	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	119551336	119551336	9593	6	G	T	T	36	36	MAN1A1	T	3	3
TIAM2	26230	broad.mit.edu	36	6	155500341	155500341	+	Silent	SNP	G	A	A			TCGA-28-1746-01	TCGA-28-1746-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:155500341G>A	uc003qqb.1	+	c.1533G>A	c.(1531-1533)GGG>GGA	p.G511G	TIAM2_uc003qqd.1_Silent_p.G511G|TIAM2_uc003qqe.1_Silent_p.G511G|TIAM2_uc010kjj.1_Silent_p.G44G	NM_012454	NP_036586	Q8IVF5	TIAM2_HUMAN	T-cell lymphoma invasion and metastasis 2	511	PH 1.				apoptosis|cellular lipid metabolic process|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|filopodium|growth cone|lamellipodium	receptor signaling protein activity|Rho guanyl-nucleotide exchange factor activity			ovary(3)|breast(1)	4		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;8.1e-13)|BRCA - Breast invasive adenocarcinoma(81;0.0053)										0.368421	37.536886	38.116272	14	24	GG		KEEP	---	---	---	---	capture			Silent	SNP	155500341	155500341	16419	6	G	A	A	44	44	TIAM2	A	2	2
KIF25	3834	broad.mit.edu	36	6	168182230	168182230	+	Missense_Mutation	SNP	C	T	T			TCGA-28-1746-01	TCGA-28-1746-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:168182230C>T	uc003qwk.1	+	c.466C>T	c.(466-468)CGG>TGG	p.R156W	KIF25_uc003qwl.1_Missense_Mutation_p.R156W	NM_030615	NP_085118	Q9UIL4	KIF25_HUMAN	kinesin family member 25 isoform 1	156	Kinesin-motor.				microtubule-based movement|mitotic sister chromatid segregation	cytoplasm|kinesin complex|microtubule	ATP binding|microtubule motor activity			ovary(1)|pancreas(1)	2		Breast(66;1.07e-05)|Ovarian(120;0.0728)		Epithelial(4;7.7e-30)|OV - Ovarian serous cystadenocarcinoma(33;5.82e-22)|BRCA - Breast invasive adenocarcinoma(4;1.38e-10)|GBM - Glioblastoma multiforme(31;0.000756)										0.206897	13.236607	15.544019	6	23	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	168182230	168182230	8604	6	C	T	T	19	19	KIF25	T	1	1
RPS10	6204	broad.mit.edu	36	6	34500879	34500879	+	Missense_Mutation	SNP	G	A	A			TCGA-28-1746-01	TCGA-28-1746-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:34500879G>A	uc003ojm.1	-	c.98C>T	c.(97-99)CCG>CTG	p.P33L	RPS10_uc003ojn.1_Missense_Mutation_p.P33L	NM_001014	NP_001005	P46783	RS10_HUMAN	ribosomal protein S10	33					endocrine pancreas development|translational elongation|translational termination|viral transcription	cytosolic small ribosomal subunit|nucleolus	protein binding				0						Colon(121;749 1624 4895 8687 22360)								0.39759	104.761574	105.521836	33	50	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	34500879	34500879	14099	6	G	A	A	39	39	RPS10	A	1	1
ENPP5	59084	broad.mit.edu	36	6	46237424	46237424	+	Silent	SNP	C	T	T			TCGA-28-1746-01	TCGA-28-1746-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:46237424C>T	uc003oxz.1	-	c.1032G>A	c.(1030-1032)GCG>GCA	p.A344A	ENPP5_uc003oya.1_Silent_p.A344A|ENPP5_uc010jzc.1_3'UTR	NM_021572	NP_067547	Q9UJA9	ENPP5_HUMAN	ectonucleotide pyrophosphatase/phosphodiesterase	344						extracellular region|integral to membrane	hydrolase activity				0														0.277778	14.769983	15.568014	5	13	CC		KEEP	---	---	---	---	capture			Silent	SNP	46237424	46237424	5326	6	C	T	T	19	19	ENPP5	T	1	1
AGAP3	116988	broad.mit.edu	36	7	150471817	150471817	+	Missense_Mutation	SNP	C	T	T			TCGA-28-1746-01	TCGA-28-1746-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:150471817C>T	uc003wjg.1	+	c.2590C>T	c.(2590-2592)CGG>TGG	p.R864W	AGAP3_uc003wje.1_Missense_Mutation_p.R533W|AGAP3_uc003wjj.1_Missense_Mutation_p.R363W|AGAP3_uc003wjk.1_Missense_Mutation_p.R282W	NM_031946	NP_114152	Q96P47	AGAP3_HUMAN	centaurin, gamma 3 isoform a	828	ANK 3.				regulation of ARF GTPase activity|small GTPase mediated signal transduction	cytoplasm|membrane	ARF GTPase activator activity|GTP binding|GTPase activity|zinc ion binding			central_nervous_system(2)|ovary(1)	3														0.294118	28.687345	29.948108	10	24	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	150471817	150471817	371	7	C	T	T	23	23	AGAP3	T	1	1
UBE3C	9690	broad.mit.edu	36	7	156733954	156733954	+	Silent	SNP	C	G	G			TCGA-28-1746-01	TCGA-28-1746-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:156733954C>G	uc010lqs.1	+	c.2613C>G	c.(2611-2613)CTC>CTG	p.L871L	UBE3C_uc003wni.2_Silent_p.L234L	NM_014671	NP_055486	Q15386	UBE3C_HUMAN	ubiquitin protein ligase E3C	871	HECT.				protein polyubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	nucleus|proteasome complex	protein binding|ubiquitin-protein ligase activity			large_intestine(1)|ovary(1)	2		all_hematologic(28;0.0185)|all_epithelial(9;0.0664)	OV - Ovarian serous cystadenocarcinoma(82;0.00448)	UCEC - Uterine corpus endometrioid carcinoma (81;0.19)										0.352941	114.275254	116.21792	36	66	CC		KEEP	---	---	---	---	capture			Silent	SNP	156733954	156733954	17439	7	C	G	G	32	32	UBE3C	G	3	3
USP17L2	377630	broad.mit.edu	36	8	12032181	12032181	+	Missense_Mutation	SNP	C	T	T			TCGA-28-1746-01	TCGA-28-1746-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr8:12032181C>T	uc003wvc.1	-	c.1498G>A	c.(1498-1500)GTG>ATG	p.V500M		NM_201402	NP_958804	Q6R6M4	U17L2_HUMAN	deubiquitinating enzyme 3	500				V -> M (in Ref. 1; AAR91701).	apoptosis|cell cycle|G2/M transition checkpoint|mitotic cell cycle G1/S transition checkpoint|protein deubiquitination|ubiquitin-dependent protein catabolic process	nucleus	ubiquitin thiolesterase activity|ubiquitin-specific protease activity				0														0.555556	32.552854	32.601606	10	8	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	12032181	12032181	17611	8	C	T	T	19	19	USP17L2	T	1	1
MAGEC3	139081	broad.mit.edu	36	X	140812380	140812380	+	Silent	SNP	T	C	C			TCGA-28-1746-01	TCGA-28-1746-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chrX:140812380T>C	uc004fbr.1	+	c.1170T>C	c.(1168-1170)AGT>AGC	p.S390S	MAGEC3_uc004fbs.1_Silent_p.S92S|MAGEC3_uc010nsj.1_Silent_p.S92S|MAGEC3_uc010nsk.1_Silent_p.S92S	NM_138702	NP_619647	Q8TD91	MAGC3_HUMAN	melanoma antigen family C, 3 isoform 1	390	Pro-rich.									skin(2)|central_nervous_system(1)	3	Acute lymphoblastic leukemia(192;6.56e-05)													0.8	12.71545	13.120683	4	1	TT		KEEP	---	---	---	---	capture			Silent	SNP	140812380	140812380	9563	23	T	C	C	58	58	MAGEC3	C	4	4
MAGEA10	4109	broad.mit.edu	36	X	151054260	151054260	+	Missense_Mutation	SNP	A	T	T			TCGA-28-1746-01	TCGA-28-1746-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chrX:151054260A>T	uc004ffk.1	-	c.489T>A	c.(487-489)AGT>AGA	p.S163R	MAGEA10_uc004ffl.1_Missense_Mutation_p.S163R|MAGEA10_uc010ntj.1_Missense_Mutation_p.S163R	NM_001011543	NP_066386	P43363	MAGAA_HUMAN	melanoma antigen family A, 10	163	MAGE.										0	Acute lymphoblastic leukemia(192;6.56e-05)													0.27027	52.872523	56.392638	20	54	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	151054260	151054260	9541	23	A	T	T	6	6	MAGEA10	T	4	4
HAUS7	55559	broad.mit.edu	36	X	152374931	152374931	+	Missense_Mutation	SNP	C	T	T			TCGA-28-1746-01	TCGA-28-1746-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:152374931C>T	uc004fhn.1	-	c.721G>A	c.(721-723)GCG>ACG	p.A241T	HAUS7_uc004fhl.2_Non-coding_Transcript|HAUS7_uc004fhm.2_Non-coding_Transcript|HAUS7_uc004fho.1_Missense_Mutation_p.A241T|HAUS7_uc004fhp.1_Non-coding_Transcript	NM_207107	NP_996990	Q99871	HAUS7_HUMAN	UCH interacting protein 1 isoform b	241	Potential.				cell division|centrosome organization|mitosis|spindle assembly	centrosome|HAUS complex|microtubule|nucleolus|plasma membrane|spindle	thioesterase binding				0														0.383333	63.261299	63.95826	23	37	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	152374931	152374931	7253	23	C	T	T	27	27	HAUS7	T	1	1
G6PD	2539	broad.mit.edu	36	X	153413865	153413865	+	Missense_Mutation	SNP	T	G	G			TCGA-28-1746-01	TCGA-28-1746-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chrX:153413865T>G	uc004flx.1	-	c.1384A>C	c.(1384-1386)AAG>CAG	p.K462Q	G6PD_uc004fly.1_Missense_Mutation_p.K432Q	NM_000402	NP_001035810	P11413	G6PD_HUMAN	glucose-6-phosphate dehydrogenase isoform a	432					cellular response to oxidative stress|cholesterol biosynthetic process|cytokine production|erythrocyte maturation|glucose 6-phosphate metabolic process|glutathione metabolic process|negative regulation of protein glutathionylation|pentose-phosphate shunt, oxidative branch|ribose phosphate biosynthetic process	centrosome|cytosol|internal side of plasma membrane|intracellular membrane-bounded organelle	glucose binding|glucose-6-phosphate dehydrogenase activity|NADP binding|protein homodimerization activity			ovary(4)	4	all_cancers(53;5.05e-16)|all_epithelial(53;1.87e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)													0.181818	8.487409	10.579374	4	18	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	153413865	153413865	6397	23	T	G	G	62	62	G6PD	G	4	4
TMEM27	57393	broad.mit.edu	36	X	15573066	15573066	+	Missense_Mutation	SNP	G	A	A			TCGA-28-1746-01	TCGA-28-1746-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:15573066G>A	uc004cxc.1	-	c.211C>T	c.(211-213)CAT>TAT	p.H71Y		NM_020665	NP_065716	Q9HBJ8	TMM27_HUMAN	transmembrane protein 27	71	Extracellular (Potential).				proteolysis	integral to membrane	metallopeptidase activity|peptidyl-dipeptidase activity			ovary(1)	1	Hepatocellular(33;0.183)													0.403315	224.367347	225.836375	73	108	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	15573066	15573066	16691	23	G	A	A	47	47	TMEM27	A	2	2
RPS6KA3	6197	broad.mit.edu	36	X	20092996	20092996	+	Missense_Mutation	SNP	C	A	A			TCGA-28-1746-01	TCGA-28-1746-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:20092996C>A	uc004czu.1	-	c.1706G>T	c.(1705-1707)AGA>ATA	p.R569I	RPS6KA3_uc004czv.1_Missense_Mutation_p.R556I	NM_004586	NP_004577	P51812	KS6A3_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide	569	Protein kinase 2.				axon guidance|central nervous system development|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of caspase activity|nerve growth factor receptor signaling pathway|protein phosphorylation|skeletal system development|stress-activated MAPK cascade|synaptic transmission|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|caspase inhibitor activity|magnesium ion binding|protein serine/threonine kinase activity			central_nervous_system(4)|ovary(1)|stomach(1)|breast(1)	7										144				0.444444	121.287524	121.529427	40	50	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	20092996	20092996	14132	23	C	A	A	32	32	RPS6KA3	A	3	3
POLA1	5422	broad.mit.edu	36	X	24632426	24632426	+	Splice_Site_SNP	SNP	G	A	A			TCGA-28-1746-01	TCGA-28-1746-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:24632426G>A	uc004dbl.1	+	c.e4_splice_site			POLA1_uc004dbm.2_Splice_Site_SNP|POLA1_uc004dbn.1_Splice_Site_SNP	NM_016937	NP_058633			polymerase (DNA-directed), alpha						cell proliferation|DNA replication checkpoint|DNA replication, synthesis of RNA primer|DNA-dependent DNA replication initiation|double-strand break repair via nonhomologous end joining|interspecies interaction between organisms|lagging strand elongation|leading strand elongation|M/G1 transition of mitotic cell cycle|regulation of transcription involved in G1/S phase of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|cytoplasm|nuclear envelope|nuclear matrix|nucleolus|nucleoplasm	chromatin binding|DNA-directed DNA polymerase activity|metal ion binding|nucleoside binding			ovary(2)|skin(1)	3					Clofarabine(DB00631)|Fludarabine(DB01073)									0.456818	609.054172	609.775032	201	239	GG		KEEP	---	---	---	---	capture			Splice_Site_SNP	SNP	24632426	24632426	12615	23	G	A	A	33	33	POLA1	A	5	2
ZNF157	7712	broad.mit.edu	36	X	47157740	47157740	+	Missense_Mutation	SNP	T	A	A			TCGA-28-1746-01	TCGA-28-1746-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chrX:47157740T>A	uc004dhr.1	+	c.1324T>A	c.(1324-1326)TAT>AAT	p.Y442N		NM_003446	NP_003437	P51786	ZN157_HUMAN	zinc finger protein 157	442	C2H2-type 11.				negative regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0														0.578947	308.833839	309.76262	99	72	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	47157740	47157740	18328	23	T	A	A	61	61	ZNF157	A	4	4
MAGEH1	28986	broad.mit.edu	36	X	55495665	55495665	+	Missense_Mutation	SNP	G	A	A			TCGA-28-1746-01	TCGA-28-1746-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:55495665G>A	uc004dum.1	+	c.133G>A	c.(133-135)GAA>AAA	p.E45K		NM_014061	NP_054780	Q9H213	MAGH1_HUMAN	melanoma antigen, family H, 1 protein	45	MAGE.				apoptosis					ovary(1)|lung(1)|central_nervous_system(1)	3														0.5	13.873661	13.873661	5	5	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	55495665	55495665	9571	23	G	A	A	37	37	MAGEH1	A	1	1
SLC17A6	57084	broad.mit.edu	36	11	22343755	22343756	+	Frame_Shift_Ins	INS	-	GTAG	GTAG			TCGA-28-1746-01	TCGA-28-1746-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:22343755_22343756insGTAG	uc001mqk.1	+	c.835_836insGTAG	c.(835-837)CGTfs	p.R279fs		NM_020346	NP_065079	Q9P2U8	VGLU2_HUMAN	solute carrier family 17 (sodium-dependent	279	Cytoplasmic (Potential).				sodium ion transport	cell junction|integral to membrane|synaptic vesicle membrane|synaptosome	L-glutamate transmembrane transporter activity|symporter activity			ovary(3)|breast(1)	4														0.33			99	204				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	22343755	22343756	14917	11	-	GTAG	GTAG	19	19	SLC17A6	GTAG	5	5
VDAC1	7416	broad.mit.edu	36	5	133344366	133344374	+	In_Frame_Del	DEL	GTTGCTCTG	-	-			TCGA-28-1746-01	TCGA-28-1746-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:133344366_133344374delGTTGCTCTG	uc003kyp.1	-	c.496_504delCAGAGCAAC	c.(496-504)CAGAGCAACdel	p.QSN166del	VDAC1_uc003kyq.1_In_Frame_Del_p.QSN166del|VDAC1_uc003kyr.1_In_Frame_Del_p.QSN166del	NM_003374	NP_003365	P21796	VDAC1_HUMAN	voltage-dependent anion channel 1	166_168	Beta stranded.				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)	NSCLC(127;1776 1806 35523 41489 48154)				247				0.39			27	43				---	---	---	---	capture_indel			In_Frame_Del	DEL	133344366	133344374	17713	5	GTTGCTCTG	-	-	36	36	VDAC1	-	5	5
