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
FANK1	92565	broad.mit.edu	36	10	127575202	127575202	+	Missense_Mutation	SNP	A	T	T			TCGA-06-0213-01	TCGA-06-0213-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr10:127575202A>T	uc009yan.1	+	c.1A>T	c.(1-3)ATG>TTG	p.M1L	DHX32_uc001ljg.1_5'Flank|FANK1_uc001ljh.2_Missense_Mutation_p.M1L	NM_145235	NP_660278	Q8TC84	FANK1_HUMAN	fibronectin type III and ankyrin repeat domains	1						cytoplasm|nucleus				ovary(1)	1		all_lung(145;0.00752)|Lung NSC(174;0.0115)|Colorectal(57;0.0847)|all_neural(114;0.0936)												0.137931	6.781856	10.45706	4	25	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	127575202	127575202	5908	10	A	T	T	8	8	FANK1	T	4	4
KNDC1	85442	broad.mit.edu	36	10	134888279	134888279	+	Silent	SNP	C	G	G			TCGA-06-0213-01	TCGA-06-0213-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr10:134888279C>G	uc001llz.1	+	c.5145C>G	c.(5143-5145)TCC>TCG	p.S1715S		NM_152643	NP_689856	Q76NI1	VKIND_HUMAN	kinase non-catalytic C-lobe domain (KIND)	1715	Ras-GEF.				regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction					ovary(1)	1		all_cancers(35;4.16e-10)|all_epithelial(44;2.07e-08)|Lung NSC(174;0.000845)|all_lung(145;0.00145)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.173)|Glioma(114;0.203)												0.397059	78.207484	78.838863	27	41	CC		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(35;8.77e-06)|Epithelial(32;1.13e-05)|all cancers(32;1.51e-05)	Silent	SNP	134888279	134888279	8740	10	C	G	G	21	21	KNDC1	G	3	3
MPP7	143098	broad.mit.edu	36	10	28460520	28460520	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0213-01	TCGA-06-0213-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr10:28460520C>T	uc001iua.1	-	c.422G>A	c.(421-423)CGT>CAT	p.R141H	MPP7_uc009xkz.1_Non-coding_Transcript|MPP7_uc001iub.1_Missense_Mutation_p.R141H|MPP7_uc009xla.1_Missense_Mutation_p.R141H	NM_173496	NP_775767	Q5T2T1	MPP7_HUMAN	palmitoylated membrane protein 7	141	PDZ.				establishment of cell polarity|positive regulation of protein complex assembly|protein localization to adherens junction|tight junction assembly	MPP7-DLG1-LIN7 complex|tight junction	protein complex scaffold|protein domain specific binding|protein heterodimerization activity|signaling adaptor activity			ovary(1)	1														0.260664	133.22585	144.169669	55	156	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	28460520	28460520	10131	10	C	T	T	19	19	MPP7	T	1	1
PTEN	5728	broad.mit.edu	36	10	89710832	89710832	+	Nonsense_Mutation	SNP	C	T	T			TCGA-06-0213-01	TCGA-06-0213-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr10:89710832C>T	uc001kfb.1	+	c.1003C>T	c.(1003-1005)CGA>TGA	p.R335*		NM_000314	NP_000305	P60484	PTEN_HUMAN	phosphatase and tensin homolog	335	C2 tensin-type.			KANKDKANR->AAGADAANA: Reduces growth suppression activity and promotes anchorage-independent growth. Reduces binding to phospholipid membranes in vitro; phosphatase activity towards PtdIns(3,4,5)P3 is not affected.	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.R335*(21)|p.G165_*404del(1)|p.W274_F341del(1)|p.D326_K342del(1)|p.G165_K342del(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)						31	p.R335*(SNU1040-Tumor)	264	TCGA GBM(2;<1E-8)|TSP Lung(26;0.18)			0.368421	98.635406	100.066626	35	60	CC		KEEP	---	---	---	---	capture	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)	Nonsense_Mutation	SNP	89710832	89710832	13192	10	C	T	T	23	23	PTEN	T	5	1
TTC12	54970	broad.mit.edu	36	11	112738381	112738381	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0213-01	TCGA-06-0213-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:112738381G>A	uc001pnv.1	+	c.1681G>A	c.(1681-1683)GTT>ATT	p.V561I	TTC12_uc001pnu.1_Missense_Mutation_p.V555I|TTC12_uc001pnw.2_Non-coding_Transcript|TTC12_uc001pnx.1_Missense_Mutation_p.V405I	NM_017868	NP_060338	Q9H892	TTC12_HUMAN	tetratricopeptide repeat domain 12	555							binding			pancreas(2)|central_nervous_system(1)	3		all_cancers(61;2.73e-16)|all_epithelial(67;8.64e-10)|Melanoma(852;1.46e-05)|all_hematologic(158;0.00014)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Prostate(24;0.183)|Renal(330;0.187)												0.227273	54.673239	62.145627	25	85	GG		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(274;5.3e-06)|Epithelial(105;8.37e-05)|all cancers(92;0.000694)	Missense_Mutation	SNP	112738381	112738381	17233	11	G	A	A	48	48	TTC12	A	2	2
SRPR	6734	broad.mit.edu	36	11	125642295	125642295	+	Missense_Mutation	SNP	C	G	G			TCGA-06-0213-01	TCGA-06-0213-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:125642295C>G	uc001qdh.1	-	c.511G>C	c.(511-513)GGG>CGG	p.G171R	FOXRED1_uc001qdi.1_5'Flank|FOXRED1_uc001qdj.1_5'Flank	NM_003139	NP_003130	P08240	SRPR_HUMAN	signal recognition particle receptor	171					SRP-dependent cotranslational protein targeting to membrane	integral to membrane|signal recognition particle receptor complex	GTP binding|GTPase activity|receptor activity|signal recognition particle binding				0	all_hematologic(175;0.145)													0.274939	309.927034	328.657705	113	298	CC		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(274;1.1e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0736)	Missense_Mutation	SNP	125642295	125642295	15676	11	C	G	G	22	22	SRPR	G	3	3
OR5L2	26338	broad.mit.edu	36	11	55351570	55351570	+	Silent	SNP	A	G	G			TCGA-06-0213-01	TCGA-06-0213-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr11:55351570A>G	uc001nhy.1	+	c.300A>G	c.(298-300)CAA>CAG	p.Q100Q		NM_001004739	NP_001004739	Q8NGL0	OR5L2_HUMAN	olfactory receptor, family 5, subfamily L,	100	Helical; Name=3; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1		all_epithelial(135;0.208)												0.296296	279.901838	290.912741	88	209	AA		KEEP	---	---	---	---	capture			Silent	SNP	55351570	55351570	11581	11	A	G	G	4	4	OR5L2	G	4	4
GLYATL1	92292	broad.mit.edu	36	11	58480068	58480068	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0213-01	TCGA-06-0213-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:58480068C>T	uc001nnh.1	+	c.994C>T	c.(994-996)CCA>TCA	p.P332S	GLYATL1_uc001nnf.1_Missense_Mutation_p.P301S|GLYATL1_uc001nni.1_Missense_Mutation_p.P301S|GLYATL1_uc001nnj.1_Missense_Mutation_p.P301S	NM_080661	NP_542392	Q969I3	GLYL1_HUMAN	glycine-N-acyltransferase-like 1	301						mitochondrion	glycine N-acyltransferase activity			ovary(1)	1					Glycine(DB00145)									0.252174	73.519	79.934659	29	86	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	58480068	58480068	6748	11	C	T	T	30	30	GLYATL1	T	2	2
POLR3B	55703	broad.mit.edu	36	12	105348364	105348364	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0213-01	TCGA-06-0213-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:105348364G>A	uc001tlp.1	+	c.1447G>A	c.(1447-1449)GAC>AAC	p.D483N	POLR3B_uc001tlq.1_Missense_Mutation_p.D425N	NM_018082	NP_060552	Q9NW08	RPC2_HUMAN	polymerase (RNA) III (DNA directed) polypeptide	483					innate immune response|positive regulation of innate immune response|positive regulation of interferon-beta production|response to virus|termination of RNA polymerase III transcription|transcription elongation from RNA polymerase III promoter	nucleoplasm	DNA binding|DNA-directed RNA polymerase activity|metal ion binding|ribonucleoside binding			ovary(1)|central_nervous_system(1)	2														0.279503	115.900669	122.943247	45	116	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	105348364	105348364	12657	12	G	A	A	41	41	POLR3B	A	2	2
RIMBP2	23504	broad.mit.edu	36	12	129487473	129487473	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0213-01	TCGA-06-0213-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:129487473G>A	uc001uil.2	-	c.1922C>T	c.(1921-1923)CCG>CTG	p.P641L	RIMBP2_uc001uim.2_Missense_Mutation_p.P549L|RIMBP2_uc001uin.1_Missense_Mutation_p.P300L	NM_015347	NP_056162	O15034	RIMB2_HUMAN	RIM-binding protein 2	641	Pro-rich.					cell junction|synapse				ovary(3)|large_intestine(2)|central_nervous_system(2)|pancreas(1)	8	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.213)												0.166667	6.98483	9.513744	4	20	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(86;4.29e-06)|all cancers(50;4.56e-05)|Epithelial(86;5.41e-05)	Missense_Mutation	SNP	129487473	129487473	13838	12	G	A	A	39	39	RIMBP2	A	1	1
PIK3C2G	5288	broad.mit.edu	36	12	18326302	18326302	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0213-01	TCGA-06-0213-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:18326302C>T	uc001rds.1	+	c.20C>T	c.(19-21)ACG>ATG	p.T7M	PIK3C2G_uc001rdt.1_Missense_Mutation_p.T7M	NM_004570	NP_004561	O75747	P3C2G_HUMAN	phosphoinositide-3-kinase, class 2, gamma	7					cell communication|phosphatidylinositol-mediated signaling	membrane|phosphatidylinositol 3-kinase complex	1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol binding|phosphatidylinositol-4-phosphate 3-kinase activity	p.T7M(1)		central_nervous_system(6)|lung(4)|ovary(2)|breast(1)	13		Hepatocellular(102;0.194)								655				0.363636	21.292587	21.653065	8	14	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	18326302	18326302	12335	12	C	T	T	19	19	PIK3C2G	T	1	1
KRT7	3855	broad.mit.edu	36	12	50928772	50928772	+	Silent	SNP	C	A	A			TCGA-06-0213-01	TCGA-06-0213-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:50928772C>A	uc001saa.1	+	c.1371C>A	c.(1369-1371)ATC>ATA	p.I457I		NM_005556	NP_005547	P08729	K2C7_HUMAN	keratin 7	457	Tail.				cytoskeleton organization|DNA replication|interphase|interspecies interaction between organisms|regulation of translation	Golgi apparatus|keratin filament|nucleus	protein binding|structural molecule activity				0														0.336957	78.290566	80.456766	31	61	CC		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(357;0.105)	Silent	SNP	50928772	50928772	8798	12	C	A	A	30	30	KRT7	A	3	3
KRT2	3849	broad.mit.edu	36	12	51325359	51325359	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0213-01	TCGA-06-0213-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:51325359C>T	uc001sat.1	-	c.1631G>A	c.(1630-1632)CGA>CAA	p.R544Q		NM_000423	NP_000414	P35908	K22E_HUMAN	keratin 2	544	Tail.				keratinization|keratinocyte activation|keratinocyte migration|keratinocyte proliferation	Golgi apparatus|keratin filament	protein binding|structural constituent of cytoskeleton			ovary(2)	2														0.318339	234.708726	243.181169	92	197	CC		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(357;0.19)	Missense_Mutation	SNP	51325359	51325359	8772	12	C	T	T	31	31	KRT2	T	1	1
HOXC9	3225	broad.mit.edu	36	12	52680674	52680674	+	Silent	SNP	G	C	C			TCGA-06-0213-01	TCGA-06-0213-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:52680674G>C	uc001sep.1	+	c.435G>C	c.(433-435)TCG>TCC	p.S145S	HOXC9_uc001seq.1_Silent_p.S145S	NM_006897	NP_008828	P31274	HXC9_HUMAN	homeobox C9	145					multicellular organismal development|regulation of transcription, DNA-dependent	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription activator activity			large_intestine(1)|pancreas(1)	2														0.75	6.318298	6.535765	3	1	GG		KEEP	---	---	---	---	capture			Silent	SNP	52680674	52680674	7609	12	G	C	C	38	38	HOXC9	C	3	3
CD163L1	283316	broad.mit.edu	36	12	7477532	7477532	+	Silent	SNP	C	T	T			TCGA-06-0213-01	TCGA-06-0213-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:7477532C>T	uc001qsy.1	-	c.150G>A	c.(148-150)CTG>CTA	p.L50L		NM_174941	NP_777601	Q9NR16	C163B_HUMAN	scavenger receptor cysteine-rich type 1	50	SRCR 1.|Extracellular (Potential).					extracellular region|integral to membrane|plasma membrane	scavenger receptor activity			ovary(8)|central_nervous_system(1)	9														0.297753	131.397784	137.912099	53	125	CC		KEEP	---	---	---	---	capture			Silent	SNP	7477532	7477532	3095	12	C	T	T	21	21	CD163L1	T	2	2
DCN	1634	broad.mit.edu	36	12	90076345	90076345	+	Nonsense_Mutation	SNP	G	A	A			TCGA-06-0213-01	TCGA-06-0213-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:90076345G>A	uc001tbs.1	-	c.397C>T	c.(397-399)CGA>TGA	p.R133*	DCN_uc001tbo.1_Intron|DCN_uc001tbp.1_Intron|DCN_uc001tbq.1_Intron|DCN_uc001tbr.1_Intron|DCN_uc001tbt.1_Nonsense_Mutation_p.R133*|DCN_uc001tbu.1_Nonsense_Mutation_p.R133*	NM_133503	NP_598010	P07585	PGS2_HUMAN	decorin isoform a preproprotein	133	LRR 3.				organ morphogenesis	extracellular space		p.R133*(1)		central_nervous_system(2)|ovary(1)|lung(1)	4														0.305936	170.939261	178.297624	67	152	GG		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	90076345	90076345	4468	12	G	A	A	40	40	DCN	A	5	1
RB1	5925	broad.mit.edu	36	13	47928486	47928486	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0213-01	TCGA-06-0213-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr13:47928486G>C	uc001vcb.1	+	c.1960G>C	c.(1960-1962)GTG>CTG	p.V654L		NM_000321	NP_000312	P06400	RB_HUMAN	retinoblastoma 1	654	Pocket; binds T and E1A.|Domain B.		V -> E (in RB).		androgen receptor signaling pathway|cell cycle arrest|chromatin remodeling|G1 phase of mitotic cell cycle|interspecies interaction between organisms|maintenance of mitotic sister chromatid cohesion|mitotic cell cycle G1/S transition checkpoint|myoblast differentiation|negative regulation of cell growth|negative regulation of protein kinase activity|negative regulation of S phase of mitotic cell cycle|negative regulation of sequence-specific DNA binding transcription factor activity|positive regulation of mitotic metaphase/anaphase transition|protein localization to chromosome, centromeric region|Ras protein signal transduction|regulation of centromere complex assembly|regulation of cohesin localization to chromatin|regulation of lipid kinase activity|regulation of transcription involved in G1/S phase of mitotic cell cycle|S phase of mitotic cell cycle|sister chromatid biorientation	chromatin|PML body|Rb-E2F complex|SWI/SNF complex	androgen receptor binding|DNA binding|kinase binding|phosphoprotein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription factor binding|transcription repressor activity|ubiquitin protein ligase binding	p.V654fs*6(1)|p.V654L(1)		lung(93)|eye(89)|central_nervous_system(47)|bone(22)|breast(20)|urinary_tract(17)|haematopoietic_and_lymphoid_tissue(14)|ovary(10)|soft_tissue(8)|prostate(8)|skin(7)|endometrium(5)|cervix(3)|liver(3)|salivary_gland(2)|stomach(2)|oesophagus(1)|adrenal_gland(1)|kidney(1)|gastrointestinal_tract_(site_indeterminate)(1)|pituitary(1)	355		all_cancers(8;6.9e-71)|all_epithelial(8;4.61e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;1.51e-09)|Lung NSC(96;7.03e-07)|Breast(56;1.53e-05)|Prostate(109;0.000493)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301)			Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)			6	p.V654M(MPP89-Tumor)	568	TCGA GBM(7;6.82e-08)|TSP Lung(12;0.097)|TCGA Ovarian(6;0.080)			0.393939	37.366213	37.691701	13	20	GG		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(2;9.98e-18)|LUSC - Lung squamous cell carcinoma(3;0.013)	Missense_Mutation	SNP	47928486	47928486	13559	13	G	C	C	35	35	RB1	C	3	3
JAG2	3714	broad.mit.edu	36	14	104689012	104689012	+	Silent	SNP	G	A	A			TCGA-06-0213-01	TCGA-06-0213-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr14:104689012G>A	uc001yqg.1	-	c.1149C>T	c.(1147-1149)GCC>GCT	p.A383A	JAG2_uc001yqf.1_5'Flank|JAG2_uc001yqh.1_Silent_p.A383A	NM_002226	NP_002217	Q9Y219	JAG2_HUMAN	jagged 2 isoform a precursor	383	EGF-like 4.|Extracellular (Potential).				auditory receptor cell fate commitment|cell communication|cell cycle|Notch receptor processing|Notch signaling pathway|regulation of cell migration|regulation of cell proliferation|spermatogenesis|thymic T cell selection	integral to plasma membrane	calcium ion binding|growth factor activity|Notch binding			lung(3)	3		all_cancers(154;0.0336)|all_epithelial(191;0.0729)|Melanoma(154;0.155)								501				0.4	17.646644	17.777926	6	9	GG		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(23;0.00989)|all cancers(16;0.0114)|Epithelial(46;0.0272)	Epithelial(152;0.047)|OV - Ovarian serous cystadenocarcinoma(161;0.148)|all cancers(159;0.208)	Silent	SNP	104689012	104689012	8239	14	G	A	A	43	43	JAG2	A	2	2
RIN3	79890	broad.mit.edu	36	14	92188318	92188318	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0213-01	TCGA-06-0213-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr14:92188318G>A	uc001yap.1	+	c.1171G>A	c.(1171-1173)GTT>ATT	p.V391I	RIN3_uc010auk.1_Missense_Mutation_p.V53I|RIN3_uc001yaq.1_Missense_Mutation_p.V316I|RIN3_uc001yar.1_Missense_Mutation_p.V53I|RIN3_uc001yas.1_Missense_Mutation_p.V53I	NM_024832	NP_079108	Q8TB24	RIN3_HUMAN	Ras and Rab interactor 3	391	Pro-rich.				endocytosis|signal transduction	cytoplasmic membrane-bounded vesicle|early endosome	GTPase activator activity|Ras GTPase binding				0		all_cancers(154;0.0701)												0.271845	66.350633	71.188049	28	75	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	92188318	92188318	13850	14	G	A	A	40	40	RIN3	A	1	1
C15orf39	56905	broad.mit.edu	36	15	73286285	73286285	+	Silent	SNP	G	A	A			TCGA-06-0213-01	TCGA-06-0213-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr15:73286285G>A	uc002azp.2	+	c.843G>A	c.(841-843)CAG>CAA	p.Q281Q	C15orf39_uc002azq.2_Silent_p.Q281Q|C15orf39_uc002azr.2_5'Flank	NM_015492	NP_056307	Q6ZRI6	CO039_HUMAN	hypothetical protein LOC56905	281											0														0.375	9.122931	9.232716	3	5	GG		KEEP	---	---	---	---	capture			Silent	SNP	73286285	73286285	1843	15	G	A	A	35	35	C15orf39	A	2	2
TMC3	342125	broad.mit.edu	36	15	79411907	79411907	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0213-01	TCGA-06-0213-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr15:79411907G>A	uc002bgo.1	-	c.3211C>T	c.(3211-3213)CCG>TCG	p.P1071S	TMC3_uc010blr.1_Non-coding_Transcript	NM_001080532	NP_001074001	Q7Z5M5	TMC3_HUMAN	transmembrane channel-like 3	1071	Cytoplasmic (Potential).					integral to membrane				ovary(1)|liver(1)	2														0.25	19.692212	21.505245	8	24	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	79411907	79411907	16516	15	G	A	A	43	43	TMC3	A	2	2
NPRL3	8131	broad.mit.edu	36	16	107362	107362	+	Missense_Mutation	SNP	C	G	G			TCGA-06-0213-01	TCGA-06-0213-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:107362C>G	uc002cfr.1	-	c.331G>C	c.(331-333)GAT>CAT	p.D111H	NPRL3_uc002cfp.1_Non-coding_Transcript|NPRL3_uc002cfq.1_Intron|NPRL3_uc002cfs.1_Intron	NM_001077350	NP_001070818	Q12980	NPRL3_HUMAN	conserved gene telomeric to alpha globin cluster	111							protein binding			ovary(1)	1														0.2	13.360122	15.452846	5	20	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	107362	107362	11003	16	C	G	G	32	32	NPRL3	G	3	3
RABEP2	79874	broad.mit.edu	36	16	28829999	28829999	+	Silent	SNP	G	C	C			TCGA-06-0213-01	TCGA-06-0213-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:28829999G>C	uc002drq.1	-	c.897C>G	c.(895-897)GGC>GGG	p.G299G	RABEP2_uc010byn.1_Intron|RABEP2_uc002drr.2_Silent_p.G299G	NM_024816	NP_079092	Q9H5N1	RABE2_HUMAN	rabaptin, RAB GTPase binding effector protein 2	299	Potential.				endocytosis|protein transport	early endosome	growth factor activity|GTPase activator activity			ovary(1)|breast(1)	2						Pancreas(66;639 1284 10093 31061 49099)								0.230769	6.398113	8.180036	6	20	GG		KEEP	---	---	---	---	capture			Silent	SNP	28829999	28829999	13421	16	G	C	C	42	42	RABEP2	C	3	3
PRSS53	339105	broad.mit.edu	36	16	31003000	31003000	+	Missense_Mutation	SNP	A	C	C			TCGA-06-0213-01	TCGA-06-0213-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr16:31003000A>C	uc002eaq.1	-	c.1583T>G	c.(1582-1584)GTC>GGC	p.V528G	PRSS53_uc002ear.1_Missense_Mutation_p.V322G	NM_001039503	NP_001034592	Q2L4Q9	PRS53_HUMAN	polyserase 3	528					proteolysis	extracellular region	serine-type endopeptidase activity				0														0.222222	8.689488	9.968497	4	14	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	31003000	31003000	13083	16	A	C	C	10	10	PRSS53	C	4	4
CX3CL1	6376	broad.mit.edu	36	16	55974002	55974002	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0213-01	TCGA-06-0213-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:55974002G>A	uc002eli.1	+	c.751G>A	c.(751-753)GGA>AGA	p.G251R		NM_002996	NP_002987	P78423	X3CL1_HUMAN	chemokine (C-X3-C motif) ligand 1	251	Mucin-like stalk.|Extracellular (Potential).				cell adhesion|cytokine-mediated signaling pathway|defense response|immune response|leukocyte adhesive activation|positive regulation of calcium-independent cell-cell adhesion|positive regulation of inflammatory response	cell surface|extracellular space|integral to membrane|plasma membrane	chemokine activity				0														0.130952	17.168628	28.290572	11	73	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	55974002	55974002	4234	16	G	A	A	43	43	CX3CL1	A	2	2
RAB40C	57799	broad.mit.edu	36	16	615964	615964	+	Missense_Mutation	SNP	T	G	G			TCGA-06-0213-01	TCGA-06-0213-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr16:615964T>G	uc002chr.1	+	c.407T>G	c.(406-408)GTC>GGC	p.V136G	RAB40C_uc002chq.1_Missense_Mutation_p.V117G	NM_021168	NP_066991	Q96S21	RB40C_HUMAN	RAB40C, member RAS oncogene family	136					protein transport|small GTPase mediated signal transduction	plasma membrane	GTP binding				0		Hepatocellular(780;0.0218)				Melanoma(123;1631 1690 28262 44104 44957)								0.26087	9.840076	11.124345	6	17	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	615964	615964	13401	16	T	G	G	58	58	RAB40C	G	4	4
SCN4A	6329	broad.mit.edu	36	17	59372298	59372298	+	Silent	SNP	C	T	T			TCGA-06-0213-01	TCGA-06-0213-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:59372298C>T	uc002jds.1	-	c.5076G>A	c.(5074-5076)GGG>GGA	p.G1692G		NM_000334	NP_000325	P35499	SCN4A_HUMAN	voltage-gated sodium channel type 4 alpha	1692					muscle contraction	voltage-gated sodium channel complex	voltage-gated sodium channel activity			ovary(1)|pancreas(1)|skin(1)	3					Lamotrigine(DB00555)									0.294118	109.80104	114.93036	40	96	CC		KEEP	---	---	---	---	capture			Silent	SNP	59372298	59372298	14402	17	C	T	T	22	22	SCN4A	T	2	2
ITGB4	3691	broad.mit.edu	36	17	71256715	71256715	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0213-01	TCGA-06-0213-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:71256715G>A	uc002jpg.1	+	c.3310G>A	c.(3310-3312)GAC>AAC	p.D1104N	ITGB4_uc002jph.1_Missense_Mutation_p.D1104N|ITGB4_uc002jpi.2_Missense_Mutation_p.D1104N|ITGB4_uc002jpj.1_Missense_Mutation_p.D1104N	NM_000213	NP_000204	P16144	ITB4_HUMAN	integrin beta 4 isoform 1 precursor	1104	Cytoplasmic (Potential).				cell communication|cell-matrix adhesion|hemidesmosome assembly|integrin-mediated signaling pathway|multicellular organismal development	integrin complex	protein binding|receptor activity			lung(4)	4	all_cancers(13;1.5e-07)									754				0.219512	20.858632	23.825811	9	32	GG		KEEP	---	---	---	---	capture	all cancers(21;8.32e-07)|Epithelial(20;1.92e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00194)|Lung(188;0.132)|LUSC - Lung squamous cell carcinoma(166;0.154)		Missense_Mutation	SNP	71256715	71256715	8201	17	G	A	A	41	41	ITGB4	A	2	2
B3GNT8	374907	broad.mit.edu	36	19	46624386	46624386	+	Silent	SNP	C	T	T			TCGA-06-0213-01	TCGA-06-0213-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:46624386C>T	uc002oqs.1	-	c.138G>A	c.(136-138)ACG>ACA	p.T46T	B3GNT8_uc002oqt.1_Intron|B3GNT8_uc010ehu.1_Silent_p.T46T	NM_198540	NP_940942	Q7Z7M8	B3GN8_HUMAN	UDP-GlcNAc:betaGal	46	Lumenal (Potential).				poly-N-acetyllactosamine biosynthetic process|protein glycosylation	Golgi membrane|integral to membrane	galactosyltransferase activity|protein N-acetylglucosaminyltransferase activity				0														0.27027	21.36554	23.108045	10	27	CC		KEEP	---	---	---	---	capture			Silent	SNP	46624386	46624386	1284	19	C	T	T	27	27	B3GNT8	T	1	1
ACP6	51205	broad.mit.edu	36	1	145598208	145598208	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0213-01	TCGA-06-0213-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:145598208C>T	uc001epr.2	-	c.406G>A	c.(406-408)GGA>AGA	p.G136R	NBPF11_uc009wjd.1_Intron|NBPF11_uc009wje.1_Intron|ACP6_uc009wjj.1_Missense_Mutation_p.G93R	NM_016361	NP_057445	Q9NPH0	PPA6_HUMAN	acid phosphatase 6, lysophosphatidic	136					lipid metabolic process	extracellular region|mitochondrion	acid phosphatase activity|protein binding			ovary(4)	4	all_hematologic(923;0.0276)													0.210526	36.755231	42.649749	16	60	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	145598208	145598208	166	1	C	T	T	22	22	ACP6	T	2	2
FLG	2312	broad.mit.edu	36	1	150542144	150542144	+	Missense_Mutation	SNP	C	A	A			TCGA-06-0213-01	TCGA-06-0213-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:150542144C>A	uc001ezu.1	-	c.11842G>T	c.(11842-11844)GGC>TGC	p.G3948C		NM_002016	NP_002007	P20930	FILA_HUMAN	filaggrin	3948	Ser-rich.				keratinocyte differentiation	cytoplasmic membrane-bounded vesicle|intermediate filament	calcium ion binding|structural molecule activity			ovary(9)	9	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)													0.312139	145.079945	150.51965	54	119	CC		KEEP	---	---	---	---	capture	LUSC - Lung squamous cell carcinoma(543;0.206)		Missense_Mutation	SNP	150542144	150542144	6160	1	C	A	A	21	21	FLG	A	3	3
USF1	7391	broad.mit.edu	36	1	159279072	159279072	+	Missense_Mutation	SNP	G	T	T			TCGA-06-0213-01	TCGA-06-0213-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:159279072G>T	uc001fxi.1	-	c.71C>A	c.(70-72)ACT>AAT	p.T24N	USF1_uc001fxj.1_De_novo_Start_OutOfFrame	NM_007122	NP_996888	P22415	USF1_HUMAN	upstream stimulatory factor 1 isoform 1	24					cellular response to insulin stimulus|glucose homeostasis|late viral mRNA transcription|lipid homeostasis|negative regulation of fibrinolysis|positive regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter by glucose|response to hypoxia|response to UV	transcription factor complex	bHLH transcription factor binding|histone deacetylase binding|protein heterodimerization activity|protein homodimerization activity|protein kinase binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity			ovary(1)|central_nervous_system(1)	2	all_cancers(52;6.73e-18)|Breast(13;0.012)|all_hematologic(112;0.093)													0.175	8.368544	12.415264	7	33	GG		KEEP	---	---	---	---	capture	BRCA - Breast invasive adenocarcinoma(70;0.00122)		Missense_Mutation	SNP	159279072	159279072	17594	1	G	T	T	36	36	USF1	T	3	3
SH2D1B	117157	broad.mit.edu	36	1	160635344	160635344	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0213-01	TCGA-06-0213-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:160635344G>A	uc001gbz.1	-	c.356C>T	c.(355-357)ACA>ATA	p.T119I	SH2D1B_uc001gca.1_Intron	NM_053282	NP_444512	O14796	SH21B_HUMAN	SH2 domain containing 1B	119										pancreas(1)	1	all_hematologic(112;0.115)													0.260504	72.364865	78.548678	31	88	GG		KEEP	---	---	---	---	capture	BRCA - Breast invasive adenocarcinoma(70;0.126)		Missense_Mutation	SNP	160635344	160635344	14722	1	G	A	A	48	48	SH2D1B	A	2	2
MYOC	4653	broad.mit.edu	36	1	169887940	169887940	+	Silent	SNP	G	T	T			TCGA-06-0213-01	TCGA-06-0213-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:169887940G>T	uc001ghu.1	-	c.435C>A	c.(433-435)CTC>CTA	p.L145L		NM_000261	NP_000252	Q99972	MYOC_HUMAN	myocilin	145	Potential.				anatomical structure morphogenesis	cilium|extracellular space|rough endoplasmic reticulum	structural molecule activity			lung(1)	1	all_cancers(6;5.47e-10)|all_hematologic(923;0.088)|Acute lymphoblastic leukemia(37;0.181)													0.175926	93.653433	125.776558	57	267	GG		KEEP	---	---	---	---	capture			Silent	SNP	169887940	169887940	10481	1	G	T	T	41	41	MYOC	T	3	3
RBBP5	5929	broad.mit.edu	36	1	203332571	203332571	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0213-01	TCGA-06-0213-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:203332571G>A	uc001hbu.1	-	c.1258C>T	c.(1258-1260)CCG>TCG	p.P420S	RBBP5_uc001hbv.1_Missense_Mutation_p.P420S	NM_005057	NP_005048	Q15291	RBBP5_HUMAN	retinoblastoma binding protein 5	420					histone H3-K4 methylation|regulation of transcription, DNA-dependent|response to estrogen stimulus|transcription, DNA-dependent	MLL1 complex|Set1C/COMPASS complex	promoter binding|protein binding			lung(1)	1	Breast(84;0.0505)													0.281853	184.296038	195.353572	73	186	GG		KEEP	---	---	---	---	capture	BRCA - Breast invasive adenocarcinoma(75;0.0923)		Missense_Mutation	SNP	203332571	203332571	13563	1	G	A	A	44	44	RBBP5	A	2	2
SYT14	255928	broad.mit.edu	36	1	208334323	208334323	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0213-01	TCGA-06-0213-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:208334323C>T	uc001hht.2	+	c.476C>T	c.(475-477)CCG>CTG	p.P159L	SYT14_uc009xcv.1_Missense_Mutation_p.P159L|SYT14_uc001hhs.2_Missense_Mutation_p.P204L|SYT14_uc001hhu.2_Non-coding_Transcript|SYT14_uc001hhw.2_Missense_Mutation_p.P121L	NM_153262	NP_694994	Q8NB59	SYT14_HUMAN	synaptotagmin XIV	159	Cytoplasmic (Potential).					integral to membrane				ovary(1)|skin(1)	2														0.350877	58.785366	59.902381	20	37	CC		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(81;0.085)	Missense_Mutation	SNP	208334323	208334323	15991	1	C	T	T	23	23	SYT14	T	1	1
OBSCN	84033	broad.mit.edu	36	1	226535072	226535072	+	Missense_Mutation	SNP	A	C	C			TCGA-06-0213-01	TCGA-06-0213-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr1:226535072A>C	uc009xez.1	+	c.8149A>C	c.(8149-8151)ACC>CCC	p.T2717P	OBSCN_uc001hsn.1_Missense_Mutation_p.T2717P|OBSCN_uc001hsp.1_Missense_Mutation_p.T416P|OBSCN_uc001hsq.1_5'UTR	NM_001098623	NP_001092093	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and	2717	Ig-like 26.				apoptosis|cell differentiation|induction of apoptosis by extracellular signals|multicellular organismal development|nerve growth factor receptor signaling pathway|protein phosphorylation|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|M band|Z disc	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity|Rho guanyl-nucleotide exchange factor activity|structural constituent of muscle|titin binding			large_intestine(7)|breast(5)|ovary(4)|skin(2)|stomach(1)|central_nervous_system(1)|pancreas(1)	21		Prostate(94;0.0405)								4006				0.175	6.548875	10.648474	7	33	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	226535072	226535072	11217	1	A	C	C	6	6	OBSCN	C	4	4
COL8A2	1296	broad.mit.edu	36	1	36338259	36338259	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0213-01	TCGA-06-0213-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:36338259C>T	uc001bzv.1	-	c.172G>A	c.(172-174)GAG>AAG	p.E58K	COL8A2_uc001bzw.1_Intron	NM_005202	NP_005193	P25067	CO8A2_HUMAN	collagen, type VIII, alpha 2	58	Nonhelical region (NC2).				angiogenesis|cell-cell adhesion|extracellular matrix organization	basement membrane|collagen	extracellular matrix structural constituent|protein binding, bridging			central_nervous_system(1)	1		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)										OREG0013361	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.247619	59.791801	65.883093	26	79	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	36338259	36338259	3844	1	C	T	T	29	29	COL8A2	T	2	2
CYP4A11	1579	broad.mit.edu	36	1	47179528	47179528	+	Silent	SNP	G	A	A			TCGA-06-0213-01	TCGA-06-0213-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:47179528G>A	uc001cqp.2	-	c.165C>T	c.(163-165)CCC>CCT	p.P55P	CYP4A11_uc001cqq.2_Silent_p.P55P	NM_000778	NP_000769	Q02928	CP4AB_HUMAN	cytochrome P450, family 4, subfamily A,	55					long-chain fatty acid metabolic process|oxidation-reduction process|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	alkane 1-monooxygenase activity|electron carrier activity|heme binding|oxygen binding			ovary(2)	2					NADH(DB00157)									0.376471	192.15712	194.434498	64	106	GG		KEEP	---	---	---	---	capture			Silent	SNP	47179528	47179528	4348	1	G	A	A	35	35	CYP4A11	A	2	2
LHX8	431707	broad.mit.edu	36	1	75386945	75386945	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0213-01	TCGA-06-0213-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:75386945G>A	uc001dgo.1	+	c.800G>A	c.(799-801)CGT>CAT	p.R267H	LHX8_uc001dgq.1_Missense_Mutation_p.R206H	NM_001001933	NP_001001933	Q68G74	LHX8_HUMAN	LIM homeobox 8	267	Homeobox.				regulation of transcription, DNA-dependent	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulator activity|zinc ion binding			ovary(3)	3														0.35443	75.175267	76.651537	28	51	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	75386945	75386945	9102	1	G	A	A	40	40	LHX8	A	1	1
MCOLN2	255231	broad.mit.edu	36	1	85194788	85194788	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0213-01	TCGA-06-0213-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:85194788C>T	uc001dkm.1	-	c.479G>A	c.(478-480)GGC>GAC	p.G160D	MCOLN2_uc001dkn.1_Non-coding_Transcript	NM_153259	NP_694991	Q8IZK6	MCLN2_HUMAN	mucolipin 2	160						integral to membrane	ion channel activity			ovary(3)	3														0.348548	233.125305	238.004703	84	157	CC		KEEP	---	---	---	---	capture		all cancers(265;0.0111)|Epithelial(280;0.0263)|OV - Ovarian serous cystadenocarcinoma(397;0.217)	Missense_Mutation	SNP	85194788	85194788	9785	1	C	T	T	26	26	MCOLN2	T	2	2
TRPM2	7226	broad.mit.edu	36	21	44635801	44635801	+	Silent	SNP	G	C	C			TCGA-06-0213-01	TCGA-06-0213-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr21:44635801G>C	uc010gpt.1	+	c.1659G>C	c.(1657-1659)GCG>GCC	p.A553A	TRPM2_uc002zet.1_Silent_p.A553A|TRPM2_uc002zeu.1_Silent_p.A553A|TRPM2_uc002zew.1_Silent_p.A553A|TRPM2_uc002zex.1_Silent_p.A339A|TRPM2_uc002zey.1_Silent_p.A66A	NM_003307	NP_003298	O94759	TRPM2_HUMAN	transient receptor potential cation channel,	553	Cytoplasmic (Potential).					integral to plasma membrane	ADP-ribose diphosphatase activity|calcium channel activity|sodium channel activity			ovary(1)|central_nervous_system(1)|pancreas(1)	3														0.380952	6.95824	7.331017	8	13	GG		KEEP	---	---	---	---	capture			Silent	SNP	44635801	44635801	17137	21	G	C	C	38	38	TRPM2	C	3	3
PLA2G6	8398	broad.mit.edu	36	22	36871406	36871406	+	Missense_Mutation	SNP	T	G	G			TCGA-06-0213-01	TCGA-06-0213-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr22:36871406T>G	uc003auy.1	-	c.410A>C	c.(409-411)CAC>CCC	p.H137P	PLA2G6_uc003auz.1_Missense_Mutation_p.H137P|PLA2G6_uc003ava.1_Missense_Mutation_p.H137P|PLA2G6_uc003avb.2_Missense_Mutation_p.H137P|PLA2G6_uc010gxk.1_Intron	NM_003560	NP_003551	O60733	PA2G6_HUMAN	phospholipase A2, group VI isoform a	137					cardiolipin biosynthetic process|cell death|lipid catabolic process	centrosome|membrane				ovary(1)	1	Melanoma(58;0.045)				Quinacrine(DB01103)									0.466667	7.606812	7.637742	7	8	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	36871406	36871406	12434	22	T	G	G	59	59	PLA2G6	G	4	4
BUB1	699	broad.mit.edu	36	2	111124705	111124705	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0213-01	TCGA-06-0213-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:111124705C>T	uc002tgc.1	-	c.2093G>A	c.(2092-2094)TGC>TAC	p.C698Y	BUB1_uc010fkb.1_Missense_Mutation_p.C698Y	NM_004336	NP_004327	O43683	BUB1_HUMAN	budding uninhibited by benzimidazoles 1	698					apoptosis|cell division|chromosome segregation|interspecies interaction between organisms|mitotic cell cycle spindle assembly checkpoint|mitotic prometaphase|protein phosphorylation|regulation of sister chromatid cohesion	condensed chromosome kinetochore|cytosol	ATP binding|protein binding|protein serine/threonine kinase activity			ovary(1)|lung(1)|kidney(1)	3		Ovarian(717;0.0822)								375				0.333333	34.55155	35.57704	14	28	CC		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(221;0.0556)	Missense_Mutation	SNP	111124705	111124705	1604	2	C	T	T	25	25	BUB1	T	2	2
COL3A1	1281	broad.mit.edu	36	2	189577093	189577093	+	Silent	SNP	G	A	A			TCGA-06-0213-01	TCGA-06-0213-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:189577093G>A	uc002uqj.1	+	c.2802G>A	c.(2800-2802)TCG>TCA	p.S934S		NM_000090	NP_000081	P02461	CO3A1_HUMAN	collagen type III alpha 1 preproprotein	934	Triple-helical region.				axon guidance|cell-matrix adhesion|collagen biosynthetic process|collagen fibril organization|fibril organization|heart development|integrin-mediated signaling pathway|negative regulation of immune response|peptide cross-linking|platelet activation|response to cytokine stimulus|response to radiation|skin development|transforming growth factor beta receptor signaling pathway	collagen type III|extracellular space	extracellular matrix structural constituent|integrin binding|platelet-derived growth factor binding	p.S934S(1)		central_nervous_system(7)|ovary(4)|large_intestine(2)	13					Collagenase(DB00048)|Palifermin(DB00039)					1079				0.263158	33.796843	36.690774	15	42	GG		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(117;0.0106)|Epithelial(96;0.141)		Silent	SNP	189577093	189577093	3826	2	G	A	A	38	38	COL3A1	A	1	1
NBEAL1	65065	broad.mit.edu	36	2	203745773	203745773	+	Missense_Mutation	SNP	A	G	G			TCGA-06-0213-01	TCGA-06-0213-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr2:203745773A>G	uc002uzt.2	+	c.2318A>G	c.(2317-2319)AAA>AGA	p.K773R	NBEAL1_uc002uzs.2_Missense_Mutation_p.K773R	NM_001099273	NP_001092743	Q6ZS30	NBEL1_HUMAN	neurobeachin-like 1 isoform 1	2063	BEACH.						binding			ovary(1)	1														0.358852	250.574302	254.237919	75	134	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	203745773	203745773	10584	2	A	G	G	1	1	NBEAL1	G	4	4
DTX3L	151636	broad.mit.edu	36	3	123772179	123772179	+	Missense_Mutation	SNP	A	G	G			TCGA-06-0213-01	TCGA-06-0213-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr3:123772179A>G	uc003efk.1	+	c.2123A>G	c.(2122-2124)CAC>CGC	p.H708R	DTX3L_uc010hrj.1_Missense_Mutation_p.H196R	NM_138287	NP_612144	Q8TDB6	DTX3L_HUMAN	deltex 3-like	708					histone monoubiquitination|response to DNA damage stimulus	cytoplasm|nucleus	histone binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(2)|breast(1)	3														0.252336	76.981418	82.936344	27	80	AA		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(114;0.0459)	Missense_Mutation	SNP	123772179	123772179	4981	3	A	G	G	6	6	DTX3L	G	4	4
ALG1L	200810	broad.mit.edu	36	3	127132089	127132089	+	Splice_Site_SNP	SNP	C	A	A			TCGA-06-0213-01	TCGA-06-0213-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr3:127132089C>A	uc003eig.1	-	c.348_splice	c.e5+1	p.Q116_splice		NM_001015050	NP_001015050			hypothetical protein LOC200810								transferase activity, transferring glycosyl groups				0														0.241379	8.790356	10.58886	7	22	CC		KEEP	---	---	---	---	capture			Splice_Site_SNP	SNP	127132089	127132089	520	3	C	A	A	18	18	ALG1L	A	5	3
KBTBD12	166348	broad.mit.edu	36	3	129164735	129164735	+	Missense_Mutation	SNP	T	G	G			TCGA-06-0213-01	TCGA-06-0213-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr3:129164735T>G	uc010hsr.1	+	c.1506T>G	c.(1504-1506)TGT>TGG	p.C502W	KBTBD12_uc003ejy.2_Missense_Mutation_p.C109W|KBTBD12_uc010hsq.1_Non-coding_Transcript|KBTBD12_uc003eka.2_Missense_Mutation_p.C77W	NM_207335	NP_997218	Q3ZCT8	KBTBC_HUMAN	kelch domain containing 6	502	Kelch 3.									ovary(1)	1														0.321429	6.365262	7.389499	9	19	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	129164735	129164735	8296	3	T	G	G	59	59	KBTBD12	G	4	4
FGD5	152273	broad.mit.edu	36	3	14935272	14935272	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0213-01	TCGA-06-0213-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:14935272G>A	uc003bzc.1	+	c.2774G>A	c.(2773-2775)CGC>CAC	p.R925H	FGD5_uc003bzd.1_Missense_Mutation_p.R244H	NM_152536	NP_689749	Q6ZNL6	FGD5_HUMAN	FYVE, RhoGEF and PH domain containing 5	1166	PH 1.				actin cytoskeleton organization|filopodium assembly|regulation of Cdc42 GTPase activity|regulation of cell shape	cytoskeleton|Golgi apparatus|lamellipodium|ruffle	metal ion binding|Rho guanyl-nucleotide exchange factor activity|small GTPase binding			ovary(3)|kidney(1)|pancreas(1)	5														0.383562	76.383677	77.250865	28	45	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	14935272	14935272	6073	3	G	A	A	38	38	FGD5	A	1	1
OR5AC2	81050	broad.mit.edu	36	3	99289371	99289371	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0213-01	TCGA-06-0213-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:99289371G>A	uc003dse.1	+	c.665G>A	c.(664-666)CGT>CAT	p.R222H		NM_054106	NP_473447	Q9NZP5	O5AC2_HUMAN	olfactory receptor, family 5, subfamily AC,	222	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0														0.396226	59.662386	60.162252	21	32	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	99289371	99289371	11551	3	G	A	A	40	40	OR5AC2	A	1	1
CHSY3	337876	broad.mit.edu	36	5	129271755	129271755	+	Missense_Mutation	SNP	C	G	G			TCGA-06-0213-01	TCGA-06-0213-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:129271755C>G	uc003kvd.1	+	c.889C>G	c.(889-891)CTT>GTT	p.L297V		NM_175856	NP_787052	Q70JA7	CHSS3_HUMAN	chondroitin sulfate synthase 3	297	Lumenal (Potential).					Golgi cisterna membrane|integral to membrane	glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity|metal ion binding|N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase activity			ovary(2)|pancreas(1)	3		all_cancers(142;0.0227)|Breast(839;0.198)|Prostate(80;0.215)|Lung NSC(810;0.239)												0.275229	88.600842	93.5609	30	79	CC		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	OV - Ovarian serous cystadenocarcinoma(64;0.136)	Missense_Mutation	SNP	129271755	129271755	3547	5	C	G	G	28	28	CHSY3	G	3	3
SLIT3	6586	broad.mit.edu	36	5	168107925	168107925	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0213-01	TCGA-06-0213-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:168107925G>A	uc010jjg.1	-	c.2230C>T	c.(2230-2232)CGC>TGC	p.R744C	SLIT3_uc003mab.1_Missense_Mutation_p.R744C	NM_003062	NP_003053	O75094	SLIT3_HUMAN	slit homolog 3	744	LRRNT 4.				apoptosis involved in luteolysis|axon extension involved in axon guidance|cellular response to hormone stimulus|negative chemotaxis|negative regulation of cell growth|negative regulation of chemokine-mediated signaling pathway|response to cortisol stimulus|Roundabout signaling pathway	extracellular space|mitochondrion	calcium ion binding|Roundabout binding			ovary(3)	3	Renal(175;0.000159)|Lung NSC(126;0.0174)|all_lung(126;0.0392)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)				Ovarian(29;311 847 10864 17279 24903)								0.339367	216.564862	221.602675	75	146	GG		KEEP	---	---	---	---	capture	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)		Missense_Mutation	SNP	168107925	168107925	15239	5	G	A	A	39	39	SLIT3	A	1	1
ULBP1	80329	broad.mit.edu	36	6	150332861	150332861	+	Silent	SNP	C	T	T			TCGA-06-0213-01	TCGA-06-0213-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:150332861C>T	uc003qnp.1	+	c.642C>T	c.(640-642)GCC>GCT	p.A214A		NM_025218	NP_079494	Q9BZM6	N2DL1_HUMAN	UL16 binding protein 1	214					antigen processing and presentation|immune response|natural killer cell activation|regulation of immune response	anchored to membrane|endoplasmic reticulum|MHC class I protein complex	MHC class I receptor activity			pancreas(1)	1		Ovarian(120;0.0907)												0.212121	16.70973	19.235539	7	26	CC		KEEP	---	---	---	---	capture	BRCA - Breast invasive adenocarcinoma(37;0.193)	OV - Ovarian serous cystadenocarcinoma(155;2.14e-11)	Silent	SNP	150332861	150332861	17530	6	C	T	T	22	22	ULBP1	T	2	2
PACRG	135138	broad.mit.edu	36	6	163155279	163155279	+	Silent	SNP	G	A	A			TCGA-06-0213-01	TCGA-06-0213-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:163155279G>A	uc003qua.1	+	c.267G>A	c.(265-267)TCG>TCA	p.S89S	PACRG_uc003qub.1_Silent_p.S89S|PACRG_uc003quc.1_Silent_p.S89S	NM_152410	NP_689623	Q96M98	PACRG_HUMAN	parkin co-regulated gene protein isoform 1	89											0		Breast(66;2.41e-05)|Ovarian(120;0.0245)|Prostate(117;0.0273)|all_neural(5;0.0416)|Glioma(2;0.203)												0.35206	260.078717	265.228508	94	173	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(33;4.31e-19)|GBM - Glioblastoma multiforme(2;7.42e-11)|BRCA - Breast invasive adenocarcinoma(81;3.19e-05)|KIRC - Kidney renal clear cell carcinoma(3;0.205)|Kidney(3;0.242)	Silent	SNP	163155279	163155279	11786	6	G	A	A	37	37	PACRG	A	1	1
PSORS1C1	170679	broad.mit.edu	36	6	31214507	31214507	+	Missense_Mutation	SNP	T	C	C			TCGA-06-0213-01	TCGA-06-0213-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr6:31214507T>C	uc003nsl.1	+	c.139T>C	c.(139-141)TGC>CGC	p.C47R	PSORS1C1_uc010jsj.1_Intron|PSORS1C1_uc003nsn.1_Intron|PSORS1C2_uc003nso.2_Intron	NM_014068	NP_054787	Q9UIG5	PS1C1_HUMAN	SEEK1 protein	47										ovary(1)	1														0.315353	214.016562	221.324527	76	165	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	31214507	31214507	13168	6	T	C	C	63	63	PSORS1C1	C	4	4
MRAP2	112609	broad.mit.edu	36	6	84855805	84855805	+	Missense_Mutation	SNP	C	A	A			TCGA-06-0213-01	TCGA-06-0213-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:84855805C>A	uc003pkg.2	+	c.504C>A	c.(502-504)AAC>AAA	p.N168K	MRAP2_uc010kbo.1_Missense_Mutation_p.N82K	NM_138409	NP_612418	Q96G30	MRAP2_HUMAN	melanocortin 2 receptor accessory protein 2	168					positive regulation of cAMP biosynthetic process|protein localization at cell surface	endoplasmic reticulum|plasma membrane	adrenocorticotropin hormone receptor binding|type 1 melanocortin receptor binding|type 3 melanocortin receptor binding|type 4 melanocortin receptor binding|type 5 melanocortin receptor binding				0														0.253521	88.420476	96.261546	36	106	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	84855805	84855805	10146	6	C	A	A	20	20	MRAP2	A	3	3
RELN	5649	broad.mit.edu	36	7	103204258	103204258	+	Nonsense_Mutation	SNP	G	A	A			TCGA-06-0213-01	TCGA-06-0213-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:103204258G>A	uc003vca.1	-	c.526C>T	c.(526-528)CAG>TAG	p.Q176*	RELN_uc010liz.1_Nonsense_Mutation_p.Q176*	NM_005045	NP_005036	P78509	RELN_HUMAN	reelin isoform a	176	Reelin.				axon guidance|cell adhesion|cerebral cortex tangential migration|glial cell differentiation|neuron migration|peptidyl-tyrosine phosphorylation|positive regulation of protein kinase activity|positive regulation of small GTPase mediated signal transduction|response to pain|spinal cord patterning	cytoplasm|dendrite|extracellular space|proteinaceous extracellular matrix	metal ion binding|protein serine/threonine/tyrosine kinase activity|serine-type peptidase activity			ovary(8)|large_intestine(2)|central_nervous_system(2)|pancreas(1)|skin(1)	14						NSCLC(146;835 1944 15585 22231 52158)								0.214286	94.545005	110.389509	45	165	GG		KEEP	---	---	---	---	capture		COAD - Colon adenocarcinoma(1;8.98e-05)|Colorectal(1;0.00184)	Nonsense_Mutation	SNP	103204258	103204258	13689	7	G	A	A	46	46	RELN	A	5	2
CTTNBP2	83992	broad.mit.edu	36	7	117219255	117219255	+	Missense_Mutation	SNP	G	T	T			TCGA-06-0213-01	TCGA-06-0213-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:117219255G>T	uc003vjf.1	-	c.1231C>A	c.(1231-1233)CAA>AAA	p.Q411K		NM_033427	NP_219499	Q8WZ74	CTTB2_HUMAN	cortactin binding protein 2	411	Pro-rich.									ovary(4)	4	Lung NSC(10;0.0018)|all_lung(10;0.002)													0.201245	188.35277	228.395645	97	385	GG		KEEP	---	---	---	---	capture		LUSC - Lung squamous cell carcinoma(290;0.133)	Missense_Mutation	SNP	117219255	117219255	4204	7	G	T	T	45	45	CTTNBP2	T	3	3
NPSR1	387129	broad.mit.edu	36	7	34664576	34664576	+	Missense_Mutation	SNP	C	A	A			TCGA-06-0213-01	TCGA-06-0213-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:34664576C>A	uc003teh.1	+	c.27C>A	c.(25-27)AGC>AGA	p.S9R	AAA1_uc010kwo.1_Intron|AAA1_uc010kwp.1_Intron|AAA1_uc003tdz.2_Intron|AAA1_uc010kwq.1_Intron|AAA1_uc003teb.1_Intron|AAA1_uc010kwr.1_Intron|AAA1_uc010kws.1_Intron|NPSR1_uc003teg.1_Missense_Mutation_p.S9R|NPSR1_uc010kwt.1_5'UTR|NPSR1_uc010kwu.1_5'UTR|NPSR1_uc010kwv.1_Missense_Mutation_p.S9R|NPSR1_uc003tei.1_Missense_Mutation_p.S9R|NPSR1_uc010kww.1_Missense_Mutation_p.S9R	NM_207173	NP_997056	Q6W5P4	NPSR1_HUMAN	G protein-coupled receptor for asthma	9	Extracellular (Potential).					cytoplasm|integral to membrane|plasma membrane	vasopressin receptor activity			pancreas(1)|skin(1)	2					Halothane(DB01159)									0.184971	62.838853	78.911452	32	141	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	34664576	34664576	11005	7	C	A	A	28	28	NPSR1	A	3	3
WBSCR17	64409	broad.mit.edu	36	7	70235860	70235860	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0213-01	TCGA-06-0213-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:70235860G>A	uc003tvy.1	+	c.136G>A	c.(136-138)GCC>ACC	p.A46T		NM_022479	NP_071924	Q6IS24	GLTL3_HUMAN	UDP-GalNAc:polypeptide	46	Lumenal (Potential).					Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			ovary(1)|central_nervous_system(1)|pancreas(1)	3		all_cancers(73;0.2)|Lung NSC(55;0.094)|all_lung(88;0.125)												0.219512	35.013932	40.955108	18	64	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	70235860	70235860	17836	7	G	A	A	38	38	WBSCR17	A	1	1
SRCRB4D	136853	broad.mit.edu	36	7	75871638	75871638	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0213-01	TCGA-06-0213-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:75871638C>T	uc003ufb.1	-	c.55G>A	c.(55-57)GGG>AGG	p.G19R	ZP3_uc003ufc.2_Intron	NM_080744	NP_542782	Q8WTU2	SRB4D_HUMAN	scavenger receptor cysteine rich domain	19						extracellular region|membrane	scavenger receptor activity			pancreas(1)	1														0.25	106.680629	116.220425	42	126	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	75871638	75871638	15651	7	C	T	T	22	22	SRCRB4D	T	2	2
TNFSF15	9966	broad.mit.edu	36	9	116592802	116592802	+	Silent	SNP	G	A	A			TCGA-06-0213-01	TCGA-06-0213-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr9:116592802G>A	uc004bjh.1	-	c.507C>T	c.(505-507)GGC>GGT	p.G169G	TNFSF15_uc004bjg.1_Silent_p.G110G	NM_005118	NP_005109	O95150	TNF15_HUMAN	tumor necrosis factor (ligand) superfamily,	169	Extracellular (Potential).				activation of caspase activity|activation of NF-kappaB-inducing kinase activity|cytokine metabolic process|immune response	extracellular space|integral to plasma membrane	cytokine activity|tumor necrosis factor receptor binding				0														0.291667	34.737431	36.599735	14	34	GG		KEEP	---	---	---	---	capture			Silent	SNP	116592802	116592802	16849	9	G	A	A	42	42	TNFSF15	A	2	2
TDRD7	23424	broad.mit.edu	36	9	99285262	99285262	+	Nonsense_Mutation	SNP	C	G	G			TCGA-06-0213-01	TCGA-06-0213-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr9:99285262C>G	uc004axj.1	+	c.2723C>G	c.(2722-2724)TCA>TGA	p.S908*	TDRD7_uc010msp.1_Nonsense_Mutation_p.S160*	NM_014290	NP_055105	Q8NHU6	TDRD7_HUMAN	tudor domain containing 7	908	Interacts with CDK17 (By similarity).|Interacts with CABLES1 (By similarity).				lens fiber cell differentiation|lens morphogenesis in camera-type eye|posttranscriptional regulation of gene expression|spermatogenesis	chromatoid body	mRNA binding			ovary(2)|pancreas(1)	3		Acute lymphoblastic leukemia(62;0.158)												0.275	103.717302	109.192148	33	87	CC		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	99285262	99285262	16262	9	C	G	G	29	29	TDRD7	G	5	3
ARMCX2	9823	broad.mit.edu	36	X	100797438	100797438	+	Missense_Mutation	SNP	T	G	G			TCGA-06-0213-01	TCGA-06-0213-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chrX:100797438T>G	uc004eid.1	-	c.1793A>C	c.(1792-1794)TAC>TCC	p.Y598S	ARMCX2_uc004eie.2_Missense_Mutation_p.Y598S|ARMCX2_uc004eif.2_Missense_Mutation_p.Y598S|ARMCX2_uc004eig.2_Missense_Mutation_p.Y598S|ARMCX2_uc010nnt.1_Missense_Mutation_p.Y598S|ARMCX2_uc010nnu.1_Missense_Mutation_p.Y598S	NM_177949	NP_808818	Q7L311	ARMX2_HUMAN	ALEX2 protein	598						integral to membrane	binding			ovary(6)	6														0.293878	233.419392	242.725439	72	173	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	100797438	100797438	978	23	T	G	G	57	57	ARMCX2	G	4	4
RNF128	79589	broad.mit.edu	36	X	105925514	105925514	+	Missense_Mutation	SNP	A	G	G			TCGA-06-0213-01	TCGA-06-0213-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chrX:105925514A>G	uc004eml.1	+	c.1202A>G	c.(1201-1203)GAT>GGT	p.D401G	RNF128_uc004emk.1_Missense_Mutation_p.D375G	NM_194463	NP_919445	Q8TEB7	RN128_HUMAN	ring finger protein 128 isoform 1	401						endomembrane system|integral to membrane|perinuclear region of cytoplasm	zinc ion binding			ovary(1)|central_nervous_system(1)	2														0.328025	317.147415	325.36726	103	211	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	105925514	105925514	13913	23	A	G	G	12	12	RNF128	G	4	4
LAMP2	3920	broad.mit.edu	36	X	119464269	119464269	+	Silent	SNP	G	T	T			TCGA-06-0213-01	TCGA-06-0213-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:119464269G>T	uc004ess.2	-	c.783C>A	c.(781-783)TCC>TCA	p.S261S	LAMP2_uc004est.2_Silent_p.S261S|LAMP2_uc010nqp.1_Silent_p.S261S	NM_001122606	NP_001116078	P13473	LAMP2_HUMAN	lysosomal-associated membrane protein 2 isoform	261	Lumenal (Potential).|Second lumenal domain.				platelet activation|platelet degranulation	endosome membrane|integral to membrane|late endosome|lysosomal membrane|membrane fraction|plasma membrane|platelet dense granule membrane				ovary(1)	1														0.29661	90.380507	94.745119	35	83	GG		KEEP	---	---	---	---	capture			Silent	SNP	119464269	119464269	8941	23	G	T	T	47	47	LAMP2	T	3	3
GRIA3	2892	broad.mit.edu	36	X	122356566	122356566	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0213-01	TCGA-06-0213-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:122356566G>A	uc004etq.2	+	c.817G>A	c.(817-819)GTC>ATC	p.V273I	GRIA3_uc004etr.2_Missense_Mutation_p.V273I|GRIA3_uc004ets.2_Non-coding_Transcript	NM_007325	NP_015564	P42263	GRIA3_HUMAN	glutamate receptor, ionotrophic, AMPA 3 isoform	273	Extracellular (Potential).				glutamate signaling pathway|synaptic transmission	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity			ovary(3)|pancreas(1)	4					L-Glutamic Acid(DB00142)					217				0.299107	166.521016	174.610298	67	157	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	122356566	122356566	7047	23	G	A	A	48	48	GRIA3	A	2	2
THOC2	57187	broad.mit.edu	36	X	122589288	122589288	+	Silent	SNP	G	A	A			TCGA-06-0213-01	TCGA-06-0213-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:122589288G>A	uc004etu.1	-	c.2694C>T	c.(2692-2694)AGC>AGT	p.S898S	THOC2_uc004ett.1_Silent_p.S783S	NM_001081550	NP_001075019	Q8NI27	THOC2_HUMAN	THO complex 2 isoform 1	898	Potential.				intronless viral mRNA export from host nucleus|mRNA processing|RNA splicing	THO complex part of transcription export complex	protein binding|RNA binding			ovary(3)	3														0.321918	131.868272	135.983043	47	99	GG		KEEP	---	---	---	---	capture			Silent	SNP	122589288	122589288	16393	23	G	A	A	34	34	THOC2	A	2	2
TAF1	6872	broad.mit.edu	36	X	70504111	70504111	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0213-01	TCGA-06-0213-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:70504111G>A	uc004dzt.2	+	c.218G>A	c.(217-219)GGG>GAG	p.G73E	TAF1_uc004dzu.2_Missense_Mutation_p.G73E	NM_004606	NP_004597	P21675	TAF1_HUMAN	TBP-associated factor 1 isoform 1	73	Protein kinase 1.				G1 phase of mitotic cell cycle|interspecies interaction between organisms|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|positive regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of transcription initiation from RNA polymerase II promoter|protein autophosphorylation|regulation of transcription involved in G2/M-phase of mitotic cell cycle|response to DNA damage stimulus|RNA polymerase II transcriptional preinitiation complex assembly|transcription elongation from RNA polymerase II promoter|viral reproduction	MLL1 complex|transcription factor TFIID complex	ATP binding|histone acetyl-lysine binding|histone acetyltransferase activity|p53 binding|protein binding|protein serine/threonine kinase activity|sequence-specific DNA binding|TBP-class protein binding|transcription coactivator activity	p.G73E(1)		ovary(5)|breast(4)|large_intestine(2)|central_nervous_system(2)|lung(1)|skin(1)	15	Renal(35;0.156)	all_lung(315;0.000321)								472				0.225352	39.067151	43.983716	16	55	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	70504111	70504111	16034	23	G	A	A	43	43	TAF1	A	2	2
COL24A1	255631	broad.mit.edu	36	1	86061965	86061967	+	In_Frame_Del	DEL	TTG	-	-			TCGA-06-0213-01	TCGA-06-0213-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:86061965_86061967delTTG	uc001dlj.1	-	c.3724_3726delCAA	c.(3724-3726)CAAdel	p.Q1242del	COL24A1_uc001dli.1_In_Frame_Del_p.Q378del|COL24A1_uc001dlk.1_Non-coding_Transcript	NM_152890	NP_690850	Q17RW2	COOA1_HUMAN	collagen, type XXIV, alpha 1	1242	Collagen-like 13.				cell adhesion	collagen	extracellular matrix structural constituent			ovary(3)|central_nervous_system(1)	4				all cancers(265;0.0627)|Epithelial(280;0.0689)										0.33			120	245				---	---	---	---	capture_indel			In_Frame_Del	DEL	86061965	86061967	3821	1	TTG	-	-	56	56	COL24A1	-	5	5
PRIM2	5558	broad.mit.edu	36	6	57620875	57620876	+	Splice_Site_Ins	INS	-	T	T			TCGA-06-0213-01	TCGA-06-0213-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:57620875_57620876insT	uc003pdx.1	+	c.e16_splice_site				NM_000947	NP_000938			DNA primase polypeptide 2						DNA replication, synthesis of RNA primer|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition 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|nucleoplasm	4 iron, 4 sulfur cluster binding|DNA binding|DNA primase activity|metal ion binding				0				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)										0.50			3	3				---	---	---	---	capture_indel			Splice_Site_Ins	INS	57620875	57620876	12934	6	-	T	T	4	4	PRIM2	T	5	5
