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	127575208	127575208	+	Missense_Mutation	SNP	C	A	A			TCGA-02-0047-01	TCGA-02-0047-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr10:127575208C>A	uc009yan.1	+	c.7C>A	c.(7-9)CCC>ACC	p.P3T	DHX32_uc001ljg.1_5'Flank|FANK1_uc001ljh.2_Missense_Mutation_p.P3T	NM_145235	NP_660278	Q8TC84	FANK1_HUMAN	fibronectin type III and ankyrin repeat domains	3						cytoplasm|nucleus				ovary(1)	1		all_lung(145;0.00752)|Lung NSC(174;0.0115)|Colorectal(57;0.0847)|all_neural(114;0.0936)												0.238095	10.508536	11.795213	5	16	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	127575208	127575208	5908	10	C	A	A	26	26	FANK1	A	3	3
MYO3A	53904	broad.mit.edu	36	10	26486429	26486429	+	Missense_Mutation	SNP	T	A	A			TCGA-02-0047-01	TCGA-02-0047-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr10:26486429T>A	uc001isn.2	+	c.2978T>A	c.(2977-2979)CTT>CAT	p.L993H	MYO3A_uc009xko.1_Missense_Mutation_p.L993H|MYO3A_uc009xkp.1_Non-coding_Transcript|MYO3A_uc009xkq.1_Intron	NM_017433	NP_059129	Q8NEV4	MYO3A_HUMAN	myosin IIIA	993	Myosin head-like.				protein autophosphorylation|response to stimulus|sensory perception of sound|visual perception	cytoplasm|filamentous actin|filopodium|myosin complex	actin binding|actin-dependent ATPase activity|ADP binding|ATP binding|calmodulin binding|plus-end directed microfilament motor activity|protein serine/threonine kinase activity			ovary(6)|lung(3)|central_nervous_system(2)|breast(1)|kidney(1)|pancreas(1)	14										781				0.164474	39.676225	55.941859	25	127	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	26486429	26486429	10471	10	T	A	A	56	56	MYO3A	A	4	4
MUC2	4583	broad.mit.edu	36	11	1083364	1083364	+	Missense_Mutation	SNP	C	G	G			TCGA-02-0047-01	TCGA-02-0047-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:1083364C>G	uc001lsx.1	+	c.12269C>G	c.(12268-12270)ACT>AGT	p.T4090S		NM_002457	NP_002448	Q02817	MUC2_HUMAN	mucin 2 precursor	4090						inner mucus layer|outer mucus layer	protein binding			lung(1)|breast(1)	2		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)			Pranlukast(DB01411)									0.214286	7.517087	8.572524	3	11	CC		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Missense_Mutation	SNP	1083364	1083364	10369	11	C	G	G	20	20	MUC2	G	3	3
DDX6	1656	broad.mit.edu	36	11	118131407	118131407	+	Missense_Mutation	SNP	C	T	T			TCGA-02-0047-01	TCGA-02-0047-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:118131407C>T	uc001pub.2	-	c.1190G>A	c.(1189-1191)GGT>GAT	p.G397D	DDX6_uc001pua.2_Missense_Mutation_p.G97D|DDX6_uc001puc.2_Missense_Mutation_p.G397D	NM_004397	NP_004388	P26196	DDX6_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 6	397	Helicase C-terminal.				exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay	cytoplasmic mRNA processing body|cytosol|RNA-induced silencing complex|stress granule	ATP binding|ATP-dependent helicase activity|protein binding|RNA binding|RNA helicase activity			ovary(1)	1	all_hematologic(175;0.0839)	Renal(330;0.0183)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)|Hepatocellular(160;0.0893)|Breast(348;0.0979)|all_hematologic(192;0.103)								317				0.309524	101.503747	105.564207	39	87	CC		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(223;3.39e-06)|BRCA - Breast invasive adenocarcinoma(274;3.4e-05)|Colorectal(284;0.0377)	Missense_Mutation	SNP	118131407	118131407	4548	11	C	T	T	18	18	DDX6	T	2	2
OR5M3	219482	broad.mit.edu	36	11	55994092	55994092	+	Missense_Mutation	SNP	G	A	A			TCGA-02-0047-01	TCGA-02-0047-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:55994092G>A	uc001niw.1	-	c.458C>T	c.(457-459)ACG>ATG	p.T153M		NM_001004742	NP_001004742	Q8NGP4	OR5M3_HUMAN	olfactory receptor, family 5, subfamily M,	153	Helical; Name=4; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)	2	Esophageal squamous(21;0.00448)													0.391129	273.218038	275.792509	97	151	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	55994092	55994092	11585	11	G	A	A	40	40	OR5M3	A	1	1
SCYL1	57410	broad.mit.edu	36	11	65060063	65060063	+	Missense_Mutation	SNP	C	T	T			TCGA-02-0047-01	TCGA-02-0047-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:65060063C>T	uc001oea.1	+	c.1450C>T	c.(1450-1452)CGG>TGG	p.R484W	SCYL1_uc009yqk.1_Missense_Mutation_p.R484W|SCYL1_uc001oeb.1_Missense_Mutation_p.R484W|SCYL1_uc001oec.1_Missense_Mutation_p.R484W|SCYL1_uc001oed.1_Missense_Mutation_p.R341W|SCYL1_uc001oee.1_Missense_Mutation_p.R128W	NM_020680	NP_065731	Q96KG9	NTKL_HUMAN	SCY1-like 1 isoform A	484					protein phosphorylation|regulation of transcription, DNA-dependent|retrograde vesicle-mediated transport, Golgi to ER|transcription, DNA-dependent	cis-Golgi network|COPI vesicle coat|ER-Golgi intermediate compartment|microtubule organizing center|nucleus	ATP binding|DNA binding|protein tyrosine kinase activity			skin(1)	1										387				0.393035	230.541912	232.53393	79	122	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	65060063	65060063	14432	11	C	T	T	23	23	SCYL1	T	1	1
FAT3	120114	broad.mit.edu	36	11	92173382	92173382	+	Missense_Mutation	SNP	C	G	G			TCGA-02-0047-01	TCGA-02-0047-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:92173382C>G	uc001pdj.2	+	c.7555C>G	c.(7555-7557)CGA>GGA	p.R2519G		NM_001008781	NP_001008781	Q8TDW7	FAT3_HUMAN	FAT tumor suppressor homolog 3	2519	Cadherin 23.|Extracellular (Potential).				homophilic cell adhesion|multicellular organismal development	integral to membrane|plasma membrane	calcium ion binding			ovary(4)|pancreas(1)	5		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)									TCGA Ovarian(4;0.039)			0.25	9.796529	10.702819	4	12	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	92173382	92173382	5927	11	C	G	G	31	31	FAT3	G	3	3
B4GALNT3	283358	broad.mit.edu	36	12	533240	533240	+	Silent	SNP	G	A	A			TCGA-02-0047-01	TCGA-02-0047-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:533240G>A	uc001qii.1	+	c.1890G>A	c.(1888-1890)CCG>CCA	p.P630P	B4GALNT3_uc001qij.1_Silent_p.P533P|B4GALNT3_uc001qik.1_Silent_p.P179P	NM_173593	NP_775864	Q6L9W6	B4GN3_HUMAN	beta	630	Lumenal (Potential).					Golgi cisterna membrane|integral to membrane	N-acetyl-beta-glucosaminyl-glycoprotein 4-beta-N-acetylgalactosaminyltransferase activity				0	all_cancers(10;0.0158)|all_epithelial(11;0.0274)|Ovarian(42;0.0512)|all_lung(10;0.154)|Lung NSC(10;0.215)													0.352	250.537628	255.361539	88	162	GG		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(31;0.00018)|BRCA - Breast invasive adenocarcinoma(9;0.0262)		Silent	SNP	533240	533240	1289	12	G	A	A	39	39	B4GALNT3	A	1	1
RBP5	83758	broad.mit.edu	36	12	7172615	7172615	+	Nonsense_Mutation	SNP	G	T	T			TCGA-02-0047-01	TCGA-02-0047-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:7172615G>T	uc001qsq.1	-	c.24C>A	c.(22-24)TAC>TAA	p.Y8*	CLSTN3_uc001qsr.1_5'Flank	NM_031491	NP_113679	P82980	RET5_HUMAN	retinol binding protein 5, cellular	8						cytoplasm	retinal binding|retinol binding|transporter activity			ovary(1)	1					Vitamin A(DB00162)									0.363636	8.992284	9.174025	4	7	GG		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	7172615	7172615	13628	12	G	T	T	36	36	RBP5	T	5	3
CLSTN3	9746	broad.mit.edu	36	12	7185950	7185950	+	Silent	SNP	G	A	A			TCGA-02-0047-01	TCGA-02-0047-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:7185950G>A	uc001qss.1	+	c.1524G>A	c.(1522-1524)GAG>GAA	p.E508E	CLSTN3_uc001qsr.1_Silent_p.E496E	NM_014718	NP_055533	Q9BQT9	CSTN3_HUMAN	calsyntenin 3	496	Extracellular (Potential).				homophilic cell adhesion	endoplasmic reticulum membrane|Golgi membrane|integral to membrane|plasma membrane	calcium ion binding			large_intestine(1)	1												OREG0021650	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.483871	46.520721	46.527821	15	16	GG		KEEP	---	---	---	---	capture			Silent	SNP	7185950	7185950	3701	12	G	A	A	35	35	CLSTN3	A	2	2
TPTE2	93492	broad.mit.edu	36	13	18939405	18939405	+	Missense_Mutation	SNP	A	C	C			TCGA-02-0047-01	TCGA-02-0047-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr13:18939405A>C	uc001umd.1	-	c.472T>G	c.(472-474)TAC>GAC	p.Y158D	TPTE2_uc001ume.1_Intron|TPTE2_uc009zzl.1_Intron|TPTE2_uc009zzm.1_Intron|TPTE2_uc009zzk.1_Intron	NM_199254	NP_954863	Q6XPS3	TPTE2_HUMAN	TPTE and PTEN homologous inositol lipid	158	Helical; (Potential).					endoplasmic reticulum membrane|integral to membrane	ion channel activity|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity				0		all_cancers(29;1.23e-20)|all_lung(29;1.97e-20)|all_epithelial(30;5.86e-20)|Lung NSC(5;3.36e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162)												0.319149	98.125052	100.852697	30	64	AA		KEEP	---	---	---	---	capture		all cancers(112;1.73e-05)|Epithelial(112;7.42e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000785)|Lung(94;0.0176)|LUSC - Lung squamous cell carcinoma(192;0.089)	Missense_Mutation	SNP	18939405	18939405	16975	13	A	C	C	13	13	TPTE2	C	4	4
PABPC3	5042	broad.mit.edu	36	13	24569552	24569552	+	Missense_Mutation	SNP	G	A	A			TCGA-02-0047-01	TCGA-02-0047-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr13:24569552G>A	uc001upy.1	+	c.1216G>A	c.(1216-1218)GCT>ACT	p.A406T		NM_030979	NP_112241	Q9H361	PABP3_HUMAN	poly(A) binding protein, cytoplasmic 3	406					mRNA metabolic process	cytoplasm	nucleotide binding|poly(A) RNA binding			ovary(3)|skin(1)	4		Lung SC(185;0.0225)|Breast(139;0.0602)												0.39759	287.795416	290.072034	99	150	GG		KEEP	---	---	---	---	capture		all cancers(112;0.0071)|Epithelial(112;0.0398)|OV - Ovarian serous cystadenocarcinoma(117;0.151)|GBM - Glioblastoma multiforme(144;0.222)|Lung(94;0.241)	Missense_Mutation	SNP	24569552	24569552	11780	13	G	A	A	34	34	PABPC3	A	2	2
DIS3	22894	broad.mit.edu	36	13	72234103	72234103	+	Missense_Mutation	SNP	T	A	A			TCGA-02-0047-01	TCGA-02-0047-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr13:72234103T>A	uc001vix.2	-	c.2301A>T	c.(2299-2301)TTA>TTT	p.L767F	DIS3_uc001viy.2_Missense_Mutation_p.L737F|DIS3_uc001viz.2_Non-coding_Transcript	NM_014953	NP_055768	Q9Y2L1	RRP44_HUMAN	DIS3 mitotic control isoform b	767					CUT catabolic process|exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay|rRNA catabolic process|rRNA processing	cytosol|exosome (RNase complex)|nucleolus|nucleoplasm	3'-5'-exoribonuclease activity|endonuclease activity|guanyl-nucleotide exchange factor activity|protein binding|RNA binding				0		Breast(118;0.0074)|Acute lymphoblastic leukemia(28;0.0195)									Multiple Myeloma(4;0.011)			0.408759	165.07468	166.070883	56	81	TT		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(99;0.000181)	Missense_Mutation	SNP	72234103	72234103	4714	13	T	A	A	53	53	DIS3	A	4	4
GPR132	29933	broad.mit.edu	36	14	104589271	104589271	+	Missense_Mutation	SNP	C	T	T			TCGA-02-0047-01	TCGA-02-0047-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr14:104589271C>T	uc001yqd.1	-	c.248G>A	c.(247-249)TGC>TAC	p.C83Y	GPR132_uc001yqe.1_Missense_Mutation_p.C74Y|GPR132_uc001yqc.1_5'UTR	NM_013345	NP_037477	Q9UNW8	GP132_HUMAN	G protein-coupled receptor 132	83	Helical; Name=2; (Potential).				response to stress	integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(2)|central_nervous_system(1)	3		all_cancers(154;0.0953)|Melanoma(154;0.155)|all_epithelial(191;0.219)												0.3125	115.057953	120.085826	50	110	CC		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(23;0.00778)|all cancers(16;0.00936)|Epithelial(46;0.0227)	Epithelial(152;0.02)|all cancers(159;0.0419)|OV - Ovarian serous cystadenocarcinoma(161;0.0521)	Missense_Mutation	SNP	104589271	104589271	6916	14	C	T	T	25	25	GPR132	T	2	2
PIGH	5283	broad.mit.edu	36	14	67136522	67136522	+	Missense_Mutation	SNP	G	C	C			TCGA-02-0047-01	TCGA-02-0047-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr14:67136522G>C	uc001xjr.1	-	c.152C>G	c.(151-153)GCG>GGG	p.A51G		NM_004569	NP_004560	Q14442	PIGH_HUMAN	phosphatidylinositol glycan anchor biosynthesis,	51					C-terminal protein lipidation|preassembly of GPI anchor in ER membrane	endoplasmic reticulum membrane|mitochondrion|nucleolus	phosphatidylinositol N-acetylglucosaminyltransferase activity			ovary(1)	1												OREG0022750	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.333333	6.320203	6.542508	3	6	GG		KEEP	---	---	---	---	capture		all cancers(60;0.000592)|OV - Ovarian serous cystadenocarcinoma(108;0.00395)|BRCA - Breast invasive adenocarcinoma(234;0.00933)	Missense_Mutation	SNP	67136522	67136522	12313	14	G	C	C	38	38	PIGH	C	3	3
ASB2	51676	broad.mit.edu	36	14	93475280	93475280	+	Missense_Mutation	SNP	T	G	G			TCGA-02-0047-01	TCGA-02-0047-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr14:93475280T>G	uc001ycd.1	-	c.1448A>C	c.(1447-1449)CAC>CCC	p.H483P	ASB2_uc001ycb.1_Missense_Mutation_p.H161P|ASB2_uc001ycc.1_Missense_Mutation_p.H467P|ASB2_uc001yce.1_Missense_Mutation_p.H413P	NM_016150	NP_057234	Q96Q27	ASB2_HUMAN	ankyrin repeat and SOCS box-containing protein	467					intracellular signal transduction					pancreas(1)	1		all_cancers(154;0.13)												0.545455	9.126156	9.135241	6	5	TT		KEEP	---	---	---	---	capture		COAD - Colon adenocarcinoma(157;0.217)|Epithelial(152;0.232)	Missense_Mutation	SNP	93475280	93475280	1041	14	T	G	G	59	59	ASB2	G	4	4
RYR3	6263	broad.mit.edu	36	15	31834573	31834573	+	Missense_Mutation	SNP	G	A	A			TCGA-02-0047-01	TCGA-02-0047-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr15:31834573G>A	uc001zhi.1	+	c.8415G>A	c.(8413-8415)ATG>ATA	p.M2805I	RYR3_uc010bar.1_Missense_Mutation_p.M2805I	NM_001036	NP_001027	Q15413	RYR3_HUMAN	ryanodine receptor 3	2805	4.|Cytoplasmic (By similarity).|4 X approximate repeats.				cellular calcium ion homeostasis	integral to membrane	calcium ion binding|receptor activity|ryanodine-sensitive calcium-release channel activity			ovary(5)|central_nervous_system(4)|lung(1)	10		all_lung(180;7.18e-09)												0.324324	33.385575	34.399872	12	25	GG		KEEP	---	---	---	---	capture		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)	Missense_Mutation	SNP	31834573	31834573	14250	15	G	A	A	47	47	RYR3	A	2	2
BUB1B	701	broad.mit.edu	36	15	38300234	38300234	+	Silent	SNP	G	A	A			TCGA-02-0047-01	TCGA-02-0047-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr15:38300234G>A	uc001zkx.2	+	c.3135G>A	c.(3133-3135)GGG>GGA	p.G1045G	PAK6_uc010bbl.1_Intron|PAK6_uc010bbm.1_Intron	NM_001211	NP_001202	O60566	BUB1B_HUMAN	budding uninhibited by benzimidazoles 1 beta	1045	Protein kinase.				anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|cell division|cell proliferation|mitotic cell cycle spindle assembly checkpoint|mitotic prometaphase|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|phosphatidylinositol-mediated signaling|protein localization to kinetochore|protein phosphorylation|spindle organization	anaphase-promoting complex|condensed chromosome outer kinetochore|cytosol|microtubule organizing center|perinuclear region of cytoplasm|spindle midzone	ATP binding|protein binding|protein serine/threonine kinase activity			ovary(1)|kidney(1)	2		all_cancers(109;1.12e-18)|all_epithelial(112;1.61e-15)|Lung NSC(122;5.63e-11)|all_lung(180;1.4e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)								298				0.361842	163.481203	166.035589	55	97	GG		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(113;1.83e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0556)	Silent	SNP	38300234	38300234	1605	15	G	A	A	43	43	BUB1B	A	2	2
MEGF11	84465	broad.mit.edu	36	15	63996265	63996265	+	Missense_Mutation	SNP	C	G	G			TCGA-02-0047-01	TCGA-02-0047-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr15:63996265C>G	uc002apm.2	-	c.2170G>C	c.(2170-2172)GCC>CCC	p.A724P	MEGF11_uc010bhn.1_Missense_Mutation_p.A649P|MEGF11_uc002apl.2_Missense_Mutation_p.A649P|MEGF11_uc002apn.1_Missense_Mutation_p.A724P	NM_032445	NP_115821	A6BM72	MEG11_HUMAN	multiple EGF-like-domains 11	724	EGF-like 12.					basolateral plasma membrane|integral to membrane				pancreas(1)	1												OREG0023198	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.3	7.722077	8.078918	3	7	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	63996265	63996265	9850	15	C	G	G	26	26	MEGF11	G	3	3
CSPG4	1464	broad.mit.edu	36	15	73756275	73756275	+	Silent	SNP	G	A	A			TCGA-02-0047-01	TCGA-02-0047-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr15:73756275G>A	uc002baw.1	-	c.5640C>T	c.(5638-5640)TTC>TTT	p.F1880F		NM_001897	NP_001888	Q6UVK1	CSPG4_HUMAN	chondroitin sulfate proteoglycan 4	1880	CSPG 13.|Extracellular (Potential).|Cysteine-containing.|Neurite growth inhibition (By similarity).				angiogenesis|cell differentiation|intracellular signal transduction|positive regulation of peptidyl-tyrosine phosphorylation|tissue remodeling	apical plasma membrane|cell surface|integral to plasma membrane|lamellipodium membrane	protein kinase binding|signal transducer activity			ovary(2)|pancreas(1)	3										549				0.388889	10.89268	11.124965	7	11	GG		KEEP	---	---	---	---	capture			Silent	SNP	73756275	73756275	4101	15	G	A	A	41	41	CSPG4	A	2	2
C16orf91	283951	broad.mit.edu	36	16	1418505	1418505	+	Silent	SNP	C	T	T			TCGA-02-0047-01	TCGA-02-0047-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:1418505C>T	uc002cls.1	-	c.147G>A	c.(145-147)GCG>GCA	p.A49A		NM_001010878	NP_001010878	Q4G0I0	CSMT1_HUMAN	hypothetical protein LOC283951	Error:Variant_position_missing_in_Q4G0I0_after_alignment						integral to membrane					0														0.392857	30.919923	31.200899	11	17	CC		KEEP	---	---	---	---	capture			Silent	SNP	1418505	1418505	1897	16	C	T	T	27	27	C16orf91	T	1	1
PIGS	94005	broad.mit.edu	36	17	23906109	23906109	+	Missense_Mutation	SNP	G	C	C			TCGA-02-0047-01	TCGA-02-0047-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:23906109G>C	uc002hbo.1	-	c.1279C>G	c.(1279-1281)CTC>GTC	p.L427V	UNC119_uc002hbk.1_5'Flank|UNC119_uc002hbm.1_5'Flank|PIGS_uc010crn.1_Missense_Mutation_p.L78V|PIGS_uc002hbn.1_Missense_Mutation_p.L419V	NM_033198	NP_149975	Q96S52	PIGS_HUMAN	phosphatidylinositol glycan anchor biosynthesis,	427	Lumenal (Potential).				attachment of GPI anchor to protein|C-terminal protein lipidation	GPI-anchor transamidase complex	protein binding			breast(2)|urinary_tract(1)|kidney(1)	4	Lung NSC(42;0.00431)													0.163265	7.005721	12.276263	8	41	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	23906109	23906109	12322	17	G	C	C	34	34	PIGS	C	3	3
AMAC1	146861	broad.mit.edu	36	17	30545364	30545364	+	Missense_Mutation	SNP	G	A	A			TCGA-02-0047-01	TCGA-02-0047-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:30545364G>A	uc002hjd.1	-	c.76C>T	c.(76-78)CGC>TGC	p.R26C		NM_152462	NP_689675	Q8N808	AMAC1_HUMAN	acyl-malonyl condensing enzyme 1	26						integral to membrane					0														0.418033	151.498038	152.21398	51	71	GG		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(366;0.0917)	Missense_Mutation	SNP	30545364	30545364	562	17	G	A	A	39	39	AMAC1	A	1	1
GSDMA	284110	broad.mit.edu	36	17	35376077	35376077	+	Silent	SNP	C	T	T			TCGA-02-0047-01	TCGA-02-0047-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:35376077C>T	uc002htl.1	+	c.253C>T	c.(253-255)CTG>TTG	p.L85L	GSDMA_uc002htm.1_Silent_p.L85L	NM_178171	NP_835465	Q96QA5	GSDMA_HUMAN	gasdermin 1	85					apoptosis|induction of apoptosis	perinuclear region of cytoplasm					0														0.3125	108.249908	112.257933	40	88	CC		KEEP	---	---	---	---	capture			Silent	SNP	35376077	35376077	7096	17	C	T	T	28	28	GSDMA	T	2	2
KRT15	3866	broad.mit.edu	36	17	36926711	36926711	+	Missense_Mutation	SNP	C	T	T			TCGA-02-0047-01	TCGA-02-0047-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:36926711C>T	uc002hwy.1	-	c.613G>A	c.(613-615)GTT>ATT	p.V205I	KRT15_uc002hwz.1_Missense_Mutation_p.V107I|KRT15_uc002hxa.1_Missense_Mutation_p.V40I|KRT15_uc002hxb.1_Missense_Mutation_p.V40I	NM_002275	NP_002266	P19012	K1C15_HUMAN	keratin 15	205	Rod.|Coil 1B.				epidermis development	intermediate filament	protein binding|structural constituent of cytoskeleton				0		Breast(137;0.000286)												0.35	169.27705	172.847282	63	117	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	36926711	36926711	8767	17	C	T	T	19	19	KRT15	T	1	1
ARSG	22901	broad.mit.edu	36	17	63902853	63902853	+	Missense_Mutation	SNP	G	A	A			TCGA-02-0047-01	TCGA-02-0047-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:63902853G>A	uc002jhc.2	+	c.1136G>A	c.(1135-1137)AGC>AAC	p.S379N	ARSG_uc002jhb.1_Missense_Mutation_p.S215N	NM_014960	NP_055775	Q96EG1	ARSG_HUMAN	Arylsulfatase G	379					sulfur compound metabolic process	endoplasmic reticulum|extracellular space|lysosome	arylsulfatase activity|metal ion binding			ovary(1)	1														0.259459	125.406614	135.106728	48	137	GG		KEEP	---	---	---	---	capture	BRCA - Breast invasive adenocarcinoma(8;5.34e-07)|LUSC - Lung squamous cell carcinoma(166;0.24)		Missense_Mutation	SNP	63902853	63902853	1010	17	G	A	A	34	34	ARSG	A	2	2
ABR	29	broad.mit.edu	36	17	900592	900592	+	Missense_Mutation	SNP	C	T	T			TCGA-02-0047-01	TCGA-02-0047-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:900592C>T	uc002fsd.1	-	c.1594G>A	c.(1594-1596)GGC>AGC	p.G532S	ABR_uc002fsg.1_Missense_Mutation_p.G495S|ABR_uc002fse.1_Missense_Mutation_p.G486S|ABR_uc002fsh.1_Intron	NM_021962	NP_068781	Q12979	ABR_HUMAN	active breakpoint cluster region-related	532	C2.				apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity|protein binding|Rho guanyl-nucleotide exchange factor activity				0						Esophageal Squamous(197;2016 2115 4129 29033 46447)								0.273504	82.557573	87.960718	32	85	CC		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (25;0.0228)	Missense_Mutation	SNP	900592	900592	100	17	C	T	T	23	23	ABR	T	1	1
HOOK2	29911	broad.mit.edu	36	19	12743209	12743209	+	Splice_Site_SNP	SNP	A	C	C			TCGA-02-0047-01	TCGA-02-0047-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr19:12743209A>C	uc002muy.2	-	c.600_splice	c.e8+1	p.Q200_splice	HOOK2_uc002muz.2_Splice_Site_SNP_p.Q200_splice	NM_013312	NP_037444			hook homolog 2 isoform 1						early endosome to late endosome transport|endocytosis|endosome organization|endosome to lysosome transport|lysosome organization|microtubule cytoskeleton organization|protein transport	centrosome|FHF complex|microtubule	identical protein binding|microtubule binding			ovary(1)|breast(1)	2														0.25	7.189385	8.101682	4	12	AA		KEEP	---	---	---	---	capture			Splice_Site_SNP	SNP	12743209	12743209	7575	19	A	C	C	14	14	HOOK2	C	5	4
HMG20B	10362	broad.mit.edu	36	19	3529077	3529077	+	Missense_Mutation	SNP	G	A	A			TCGA-02-0047-01	TCGA-02-0047-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:3529077G>A	uc002lya.1	+	c.907G>A	c.(907-909)GTC>ATC	p.V303I	HMG20B_uc002lyb.1_Missense_Mutation_p.V201I	NM_006339	NP_006330	Q9P0W2	HM20B_HUMAN	high-mobility group 20B	303					blood coagulation|cell cycle|chromatin modification|regulation of transcription, DNA-dependent	chromosome|nucleoplasm	DNA binding|sequence-specific DNA binding transcription factor activity				0		Hepatocellular(1079;0.137)												0.145833	11.032351	16.789673	7	41	GG		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0025)|STAD - Stomach adenocarcinoma(1328;0.18)	Missense_Mutation	SNP	3529077	3529077	7513	19	G	A	A	40	40	HMG20B	A	1	1
PLIN4	729359	broad.mit.edu	36	19	4467684	4467684	+	Missense_Mutation	SNP	G	C	C			TCGA-02-0047-01	TCGA-02-0047-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:4467684G>C	uc002mar.1	-	c.158C>G	c.(157-159)GCC>GGC	p.A53G		NM_001080400	NP_001073869	Q96Q06	PLIN4_HUMAN	plasma membrane associated protein, S3-12	53						lipid particle|plasma membrane					0														0.4	8.197774	8.284195	4	6	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	4467684	4467684	12518	19	G	C	C	42	42	PLIN4	C	3	3
LTBP4	8425	broad.mit.edu	36	19	45808366	45808366	+	Silent	SNP	C	G	G			TCGA-02-0047-01	TCGA-02-0047-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:45808366C>G	uc002ooh.1	+	c.1974C>G	c.(1972-1974)GCC>GCG	p.A658A	LTBP4_uc002oog.1_Silent_p.A621A|LTBP4_uc002ooi.1_Silent_p.A591A|LTBP4_uc002ooj.1_5'UTR|LTBP4_uc010ehb.1_5'Flank|LTBP4_uc002ook.1_5'Flank|LTBP4_uc002ool.1_5'Flank	NM_001042544	NP_001036009	Q8N2S1	LTBP4_HUMAN	latent transforming growth factor beta binding	658	Cys-rich.|EGF-like 5; calcium-binding (Potential).				growth hormone secretion|multicellular organismal development|protein folding|regulation of cell differentiation|regulation of cell growth|regulation of proteolysis|regulation of transforming growth factor beta receptor signaling pathway	extracellular space|proteinaceous extracellular matrix	calcium ion binding|glycosaminoglycan binding|integrin binding|transforming growth factor beta binding|transforming growth factor beta receptor activity			central_nervous_system(1)	1														0.272727	7.070382	7.551848	3	8	CC		KEEP	---	---	---	---	capture	Lung(22;0.000158)|LUSC - Lung squamous cell carcinoma(20;0.000384)		Silent	SNP	45808366	45808366	9452	19	C	G	G	23	23	LTBP4	G	3	3
CD101	9398	broad.mit.edu	36	1	117354340	117354340	+	Missense_Mutation	SNP	A	T	T			TCGA-02-0047-01	TCGA-02-0047-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr1:117354340A>T	uc009whd.1	+	c.389A>T	c.(388-390)TAC>TTC	p.Y130F		NM_004258	NP_004249	Q93033	IGSF2_HUMAN	immunoglobulin superfamily, member 2	130	Extracellular (Potential).|Ig-like C2-type 1.				cell surface receptor linked signaling pathway	integral to membrane|plasma membrane	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides			ovary(1)	1														0.243902	48.564678	53.462241	20	62	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	117354340	117354340	3089	1	A	T	T	14	14	CD101	T	4	4
VPS13D	55187	broad.mit.edu	36	1	12341146	12341146	+	Missense_Mutation	SNP	C	T	T			TCGA-02-0047-01	TCGA-02-0047-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:12341146C>T	uc001atv.1	+	c.10043C>T	c.(10042-10044)CCG>CTG	p.P3348L	VPS13D_uc001atw.1_Missense_Mutation_p.P3323L|VPS13D_uc001atx.1_Missense_Mutation_p.P2535L	NM_015378	NP_056193	Q5THJ4	VP13D_HUMAN	vacuolar protein sorting 13D isoform 1	3347					protein localization					ovary(4)|pancreas(1)	5	Ovarian(185;0.249)	Lung NSC(185;4.08e-05)|all_lung(284;4.55e-05)|Renal(390;0.000147)|Colorectal(325;0.00058)|Breast(348;0.00093)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)												0.148936	35.521375	52.16239	21	120	CC		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (279;0.0327)|Colorectal(212;4.63e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000289)|COAD - Colon adenocarcinoma(227;0.000801)|Kidney(185;0.00216)|KIRC - Kidney renal clear cell carcinoma(229;0.00544)|STAD - Stomach adenocarcinoma(313;0.012)|READ - Rectum adenocarcinoma(331;0.0476)|Lung(427;0.209)	Missense_Mutation	SNP	12341146	12341146	17759	1	C	T	T	23	23	VPS13D	T	1	1
PTPRC	5788	broad.mit.edu	36	1	196988006	196988006	+	Silent	SNP	C	T	T			TCGA-02-0047-01	TCGA-02-0047-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:196988006C>T	uc001gur.1	+	c.3207C>T	c.(3205-3207)ATC>ATT	p.I1069I	PTPRC_uc001gus.1_Silent_p.I1021I|PTPRC_uc001gut.1_Silent_p.I908I	NM_002838	NP_002829	P08575	PTPRC_HUMAN	protein tyrosine phosphatase, receptor type, C	1069	Tyrosine-protein phosphatase 2.|Cytoplasmic (Potential).				axon guidance|B cell proliferation|B cell receptor signaling pathway|defense response to virus|immunoglobulin biosynthetic process|negative regulation of cytokine-mediated signaling pathway|negative regulation of protein kinase activity|negative regulation of T cell mediated cytotoxicity|positive regulation of antigen receptor-mediated signaling pathway|positive regulation of B cell proliferation|positive regulation of protein kinase activity|positive regulation of T cell proliferation|regulation of S phase|release of sequestered calcium ion into cytosol|T cell differentiation|T cell receptor signaling pathway	focal adhesion|integral to plasma membrane|membrane raft	protein kinase binding|transmembrane receptor protein tyrosine phosphatase activity			breast(4)|skin(2)|ovary(2)|lung(1)|kidney(1)|pancreas(1)	11										815				0.208955	65.1207	75.633183	28	106	CC		KEEP	---	---	---	---	capture			Silent	SNP	196988006	196988006	13254	1	C	T	T	32	32	PTPRC	T	2	2
PCNXL2	80003	broad.mit.edu	36	1	231461634	231461634	+	Silent	SNP	C	T	T			TCGA-02-0047-01	TCGA-02-0047-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:231461634C>T	uc001hvl.2	-	c.597G>A	c.(595-597)GCG>GCA	p.A199A	PCNXL2_uc009xfu.1_Non-coding_Transcript|PCNXL2_uc009xfv.1_Non-coding_Transcript	NM_014801	NP_055616	A6NKB5	PCX2_HUMAN	pecanex-like 2	199						integral to membrane				central_nervous_system(1)|pancreas(1)	2		all_cancers(173;0.0347)|Prostate(94;0.137)												0.393333	167.895348	169.388214	59	91	CC		KEEP	---	---	---	---	capture			Silent	SNP	231461634	231461634	12012	1	C	T	T	19	19	PCNXL2	T	1	1
RYR2	6262	broad.mit.edu	36	1	235861459	235861459	+	Missense_Mutation	SNP	T	C	C			TCGA-02-0047-01	TCGA-02-0047-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr1:235861459T>C	uc001hyl.1	+	c.6550T>C	c.(6550-6552)TCC>CCC	p.S2184P		NM_001035	NP_001026	Q92736	RYR2_HUMAN	cardiac muscle ryanodine receptor	2184	Cytoplasmic (By similarity).|4 X approximate repeats.				cardiac muscle contraction|detection of calcium ion|induction of apoptosis by ionic changes|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum|response to caffeine|response to hypoxia|response to redox state	calcium channel complex|plasma membrane|plasma membrane enriched fraction|sarcoplasmic reticulum membrane	calcium ion binding|calmodulin binding|identical protein binding|protein kinase A catalytic subunit binding|protein kinase A regulatory subunit binding|receptor activity|ryanodine-sensitive calcium-release channel activity|suramin binding			ovary(17)|large_intestine(6)|central_nervous_system(6)|pancreas(3)|breast(1)	33	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)												0.215686	27.398197	31.202921	11	40	TT		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(106;0.00606)		Missense_Mutation	SNP	235861459	235861459	14249	1	T	C	C	58	58	RYR2	C	4	4
BTBD3	22903	broad.mit.edu	36	20	11847075	11847075	+	Missense_Mutation	SNP	A	G	G			TCGA-02-0047-01	TCGA-02-0047-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr20:11847075A>G	uc002wnz.1	+	c.152A>G	c.(151-153)GAA>GGA	p.E51G	BTBD3_uc002wny.1_5'UTR|BTBD3_uc002woa.1_5'UTR	NM_014962	NP_852108	Q9Y2F9	BTBD3_HUMAN	BTB/POZ domain containing protein 3 isoform a	51										ovary(2)|central_nervous_system(1)	3														0.390244	459.799044	463.697158	144	225	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	11847075	11847075	1578	20	A	G	G	9	9	BTBD3	G	4	4
RPRD1B	58490	broad.mit.edu	36	20	36110264	36110264	+	Missense_Mutation	SNP	T	C	C			TCGA-02-0047-01	TCGA-02-0047-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr20:36110264T>C	uc002xho.2	+	c.382T>C	c.(382-384)TCT>CCT	p.S128P		NM_021215	NP_067038	Q9NQG5	RPR1B_HUMAN	Regulation of nuclear pre-mRNA domain containing	128	CID.									pancreas(1)	1														0.24	59.547876	65.721454	24	76	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	36110264	36110264	14095	20	T	C	C	58	58	RPRD1B	C	4	4
DNAJC28	54943	broad.mit.edu	36	21	33782567	33782567	+	Missense_Mutation	SNP	A	G	G			TCGA-02-0047-01	TCGA-02-0047-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr21:33782567A>G	uc002yrv.1	-	c.1004T>C	c.(1003-1005)GTC>GCC	p.V335A	DNAJC28_uc002yrw.1_Missense_Mutation_p.V335A|DNAJC28_uc010gmc.1_Missense_Mutation_p.V335A	NM_017833	NP_060303	Q9NX36	DJC28_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 28	335	Potential.			LIVPILTRQKVHFDAQKEIVRAQKIYETLIKTKEVTDRNPN NLDQGEGEKTPEIKKGFLNWMNLWKFIKIRSF -> CSHPD QAKSPF (in Ref. 2; BAA91185).			heat shock protein binding				0														0.135135	56.404304	85.038853	30	192	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	33782567	33782567	4829	21	A	G	G	10	10	DNAJC28	G	4	4
SOX10	6663	broad.mit.edu	36	22	36699448	36699448	+	Nonstop_Mutation	SNP	T	G	G			TCGA-02-0047-01	TCGA-02-0047-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr22:36699448T>G	uc003aun.1	-	c.1401A>C	c.(1399-1401)TAA>TAC	p.*467Y	POLR2F_uc003aum.1_Intron|SOX10_uc003auo.1_Nonstop_Mutation_p.*467Y	NM_006941	NP_008872	P56693	SOX10_HUMAN	SRY (sex determining region Y)-box 10	467						cytoplasm|nucleus	identical protein binding|RNA polymerase II transcription factor activity|transcription coactivator activity				0	Melanoma(58;0.045)					Melanoma(39;342 1098 6220 32775 40068)|GBM(21;140 497 5227 16059 19275)				67				0.333333	17.944704	18.387164	6	12	TT		KEEP	---	---	---	---	capture			Nonstop_Mutation	SNP	36699448	36699448	15441	22	T	G	G	64	64	SOX10	G	5	4
CELSR1	9620	broad.mit.edu	36	22	45186172	45186172	+	Missense_Mutation	SNP	C	T	T			TCGA-02-0047-01	TCGA-02-0047-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr22:45186172C>T	uc003bhw.1	-	c.4760G>A	c.(4759-4761)GGC>GAC	p.G1587D		NM_014246	NP_055061	Q9NYQ6	CELR1_HUMAN	cadherin EGF LAG seven-pass G-type receptor 1	1587	Extracellular (Potential).|Laminin G-like 1.				central nervous system development|homophilic cell adhesion|neural tube closure|neuropeptide signaling pathway	integral to plasma membrane	calcium ion binding|G-protein coupled receptor activity|protein dimerization activity			pancreas(2)|skin(1)	3		Ovarian(80;0.00142)|Breast(42;0.00296)|all_neural(38;0.0416)|Colorectal(5;0.0766)												0.320388	83.439438	86.391229	33	70	CC		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (28;0.00643)|BRCA - Breast invasive adenocarcinoma(115;0.171)	Missense_Mutation	SNP	45186172	45186172	3354	22	C	T	T	26	26	CELSR1	T	2	2
PLXNB2	23654	broad.mit.edu	36	22	49061486	49061486	+	Silent	SNP	C	T	T			TCGA-02-0047-01	TCGA-02-0047-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr22:49061486C>T	uc003bkv.2	-	c.3807G>A	c.(3805-3807)GAG>GAA	p.E1269E	PLXNB2_uc003bkt.1_Silent_p.E61E|PLXNB2_uc003bku.1_Silent_p.E254E	NM_012401	NP_036533	O15031	PLXB2_HUMAN	plexin B2	1269	Cytoplasmic (Potential).				regulation of small GTPase mediated signal transduction	integral to membrane|intracellular	GTPase activator activity|protein binding|receptor activity			ovary(4)|central_nervous_system(1)	5		all_cancers(38;5.78e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)												0.25641	50.56152	54.759807	20	58	CC		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)	Silent	SNP	49061486	49061486	12550	22	C	T	T	24	24	PLXNB2	T	2	2
SLC9A4	389015	broad.mit.edu	36	2	102461919	102461919	+	Missense_Mutation	SNP	G	A	A			TCGA-02-0047-01	TCGA-02-0047-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:102461919G>A	uc002tbz.2	+	c.446G>A	c.(445-447)CGG>CAG	p.R149Q		NM_001011552	NP_001011552	Q6AI14	SL9A4_HUMAN	solute carrier family 9 (sodium/hydrogen	149	Cytoplasmic (Potential).				regulation of pH	apical plasma membrane|basolateral plasma membrane|integral to membrane	sodium:hydrogen antiporter activity			central_nervous_system(1)	1														0.330709	114.478938	117.668691	42	85	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	102461919	102461919	15213	2	G	A	A	39	39	SLC9A4	A	1	1
DES	1674	broad.mit.edu	36	2	219994348	219994348	+	Missense_Mutation	SNP	T	A	A			TCGA-02-0047-01	TCGA-02-0047-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr2:219994348T>A	uc002vll.1	+	c.1066T>A	c.(1066-1068)TTT>ATT	p.F356I		NM_001927	NP_001918	P17661	DESM_HUMAN	desmin	356	Rod.|Coil 2B.				cytoskeleton organization|muscle filament sliding|regulation of heart contraction	cytosol|Z disc	protein binding|structural constituent of cytoskeleton	p.F356I(1)		central_nervous_system(2)	2		Renal(207;0.0183)												0.337079	79.725393	81.813506	30	59	TT		KEEP	---	---	---	---	capture		Epithelial(149;5.25e-07)|all cancers(144;0.000103)|Lung(261;0.00533)|LUSC - Lung squamous cell carcinoma(224;0.008)	Missense_Mutation	SNP	219994348	219994348	4628	2	T	A	A	52	52	DES	A	4	4
GPC1	2817	broad.mit.edu	36	2	241054167	241054167	+	Silent	SNP	G	C	C			TCGA-02-0047-01	TCGA-02-0047-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:241054167G>C	uc002vyw.2	+	c.1464G>C	c.(1462-1464)TCG>TCC	p.S488S		NM_002081	NP_002072	P35052	GPC1_HUMAN	glypican 1 precursor	488					axon guidance	anchored to membrane|extracellular space|integral to plasma membrane|proteinaceous extracellular matrix	heparan sulfate proteoglycan binding			breast(1)	1		all_epithelial(40;2.79e-15)|Breast(86;2.41e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0335)|Lung NSC(271;0.106)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)												0.32	9.533327	10.410244	8	17	GG		KEEP	---	---	---	---	capture		Epithelial(32;4.51e-33)|all cancers(36;1.74e-30)|OV - Ovarian serous cystadenocarcinoma(60;4.73e-15)|Kidney(56;2.99e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;9.1e-06)|Colorectal(34;0.000487)|Lung(119;0.0013)|LUSC - Lung squamous cell carcinoma(224;0.0154)|COAD - Colon adenocarcinoma(134;0.0194)|READ - Rectum adenocarcinoma(96;0.0949)	Silent	SNP	241054167	241054167	6871	2	G	C	C	39	39	GPC1	C	3	3
SPTBN1	6711	broad.mit.edu	36	2	54705590	54705590	+	Missense_Mutation	SNP	G	A	A			TCGA-02-0047-01	TCGA-02-0047-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:54705590G>A	uc002rxu.1	+	c.1328G>A	c.(1327-1329)CGT>CAT	p.R443H	SPTBN1_uc002rxv.1_Missense_Mutation_p.R443H|SPTBN1_uc002rxx.1_Missense_Mutation_p.R430H	NM_003128	NP_003119	Q01082	SPTB2_HUMAN	spectrin, beta, non-erythrocytic 1 isoform 1	443	Spectrin 2.				actin filament capping|axon guidance	cytosol|nucleolus|plasma membrane|sarcomere|spectrin	actin binding|calmodulin binding|protein binding|structural constituent of cytoskeleton			ovary(2)|breast(2)|central_nervous_system(2)	6														0.252632	56.1561	61.434664	24	71	GG		KEEP	---	---	---	---	capture	Lung(47;0.24)		Missense_Mutation	SNP	54705590	54705590	15633	2	G	A	A	40	40	SPTBN1	A	1	1
BCL11A	53335	broad.mit.edu	36	2	60541883	60541883	+	Missense_Mutation	SNP	C	G	G			TCGA-02-0047-01	TCGA-02-0047-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:60541883C>G	uc002sae.1	-	c.1668G>C	c.(1666-1668)CAG>CAC	p.Q556H	BCL11A_uc002sab.1_Missense_Mutation_p.Q556H|BCL11A_uc002sac.1_Intron|BCL11A_uc002sad.1_Missense_Mutation_p.Q404H|BCL11A_uc002saf.1_Missense_Mutation_p.Q522H	NM_022893	NP_075044	Q9H165	BC11A_HUMAN	B-cell CLL/lymphoma 11A isoform 1	556					protein sumoylation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	nucleic acid binding|zinc ion binding			central_nervous_system(6)|breast(3)|ovary(1)|skin(1)	11										131				0.098592	6.686214	18.115955	7	64	CC		KEEP	---	---	---	---	capture	LUSC - Lung squamous cell carcinoma(5;9.29e-08)|Lung(5;1.34e-06)|Epithelial(17;0.0562)|all cancers(80;0.199)		Missense_Mutation	SNP	60541883	60541883	1384	2	C	G	G	28	28	BCL11A	G	3	3
PIK3CA	5290	broad.mit.edu	36	3	180404247	180404247	+	Missense_Mutation	SNP	T	A	A			TCGA-02-0047-01	TCGA-02-0047-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr3:180404247T>A	uc003fjk.1	+	c.1035T>A	c.(1033-1035)AAT>AAA	p.N345K		NM_006218	NP_006209	P42336	PK3CA_HUMAN	phosphoinositide-3-kinase, catalytic, alpha	345	C2.				epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|platelet activation|T cell costimulation|T cell receptor signaling pathway		1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol-4,5-bisphosphate 3-kinase activity	p.N345K(29)|p.N345I(1)		breast(1506)|large_intestine(749)|endometrium(244)|urinary_tract(195)|ovary(136)|skin(112)|stomach(89)|thyroid(77)|central_nervous_system(69)|lung(61)|upper_aerodigestive_tract(48)|haematopoietic_and_lymphoid_tissue(27)|cervix(25)|biliary_tract(22)|liver(20)|oesophagus(17)|pancreas(11)|penis(8)|pituitary(8)|autonomic_ganglia(4)|kidney(2)|prostate(2)|meninges(1)|eye(1)|NS(1)|soft_tissue(1)|bone(1)	3437	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)					Colon(199;1504 1750 3362 26421 31210 32040)		57		621	TCGA GBM(8;5.49e-07)			0.333333	161.503852	165.485227	54	108	TT		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Missense_Mutation	SNP	180404247	180404247	12337	3	T	A	A	51	51	PIK3CA	A	4	4
FBXO8	26269	broad.mit.edu	36	4	175417551	175417551	+	Silent	SNP	C	A	A			TCGA-02-0047-01	TCGA-02-0047-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:175417551C>A	uc003itp.1	-	c.330G>T	c.(328-330)GGG>GGT	p.G110G	FBXO8_uc003itq.1_Silent_p.G69G	NM_012180	NP_036312	Q9NRD0	FBX8_HUMAN	F-box only protein 8	110	F-box.				regulation of ARF protein signal transduction|ubiquitin-dependent protein catabolic process	cytoplasm|ubiquitin ligase complex	ARF guanyl-nucleotide exchange factor activity			breast(2)	2		Prostate(90;0.00201)|Melanoma(52;0.012)|Renal(120;0.0183)|all_neural(102;0.0887)|all_hematologic(60;0.107)												0.211679	66.895279	77.428468	29	108	CC		KEEP	---	---	---	---	capture		all cancers(43;7.29e-18)|Epithelial(43;1.85e-15)|OV - Ovarian serous cystadenocarcinoma(60;5.62e-09)|GBM - Glioblastoma multiforme(59;0.00115)|STAD - Stomach adenocarcinoma(60;0.00299)|LUSC - Lung squamous cell carcinoma(193;0.1)	Silent	SNP	175417551	175417551	5998	4	C	A	A	18	18	FBXO8	A	3	3
WWC2	80014	broad.mit.edu	36	4	184438974	184438974	+	Missense_Mutation	SNP	G	C	C			TCGA-02-0047-01	TCGA-02-0047-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr4:184438974G>C	uc010irx.1	+	c.2614G>C	c.(2614-2616)GAA>CAA	p.E872Q	WWC2_uc003ivk.2_Missense_Mutation_p.E667Q|WWC2_uc003ivl.2_Non-coding_Transcript|WWC2_uc010iry.1_Missense_Mutation_p.E554Q|WWC2_uc003ivn.2_Missense_Mutation_p.E387Q|WWC2_uc010irz.1_Missense_Mutation_p.E189Q|WWC2_uc003ivo.2_5'Flank	NM_024949	NP_079225	Q6AWC2	WWC2_HUMAN	WW and C2 domain containing 2	872	Potential.									ovary(2)|lung(1)	3		all_lung(41;5.28e-14)|Lung NSC(41;1.35e-13)|Colorectal(36;0.00681)|Hepatocellular(41;0.00886)|Renal(120;0.00992)|Prostate(90;0.0237)|all_hematologic(60;0.0592)|Esophageal squamous(56;0.179)|all_neural(102;0.202)												0.25	8.919457	9.600947	3	9	GG		KEEP	---	---	---	---	capture		all cancers(43;3.38e-24)|Epithelial(43;1.4e-20)|OV - Ovarian serous cystadenocarcinoma(60;1.09e-09)|GBM - Glioblastoma multiforme(59;3.33e-05)|Colorectal(24;3.58e-05)|STAD - Stomach adenocarcinoma(60;4.21e-05)|COAD - Colon adenocarcinoma(29;0.000171)|LUSC - Lung squamous cell carcinoma(40;0.0145)|READ - Rectum adenocarcinoma(43;0.242)	Missense_Mutation	SNP	184438974	184438974	17986	4	G	C	C	41	41	WWC2	C	3	3
PCDHGA8	9708	broad.mit.edu	36	5	140754287	140754287	+	Missense_Mutation	SNP	G	A	A			TCGA-02-0047-01	TCGA-02-0047-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:140754287G>A	uc003lkd.1	+	c.1723G>A	c.(1723-1725)GTG>ATG	p.V575M	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc010jfx.1_Intron|PCDHGA3_uc003ljm.1_Intron|PCDHGB1_uc003ljo.1_Intron|PCDHGA4_uc003ljq.1_Intron|PCDHGB2_uc003ljs.1_Intron|PCDHGA5_uc003lju.1_Intron|PCDHGB3_uc003ljw.1_Intron|PCDHGA6_uc003ljy.1_Intron|PCDHGA7_uc003lka.1_Intron|PCDHGB4_uc003lkc.1_Intron|PCDHGA8_uc003lkb.2_Missense_Mutation_p.V575M	NM_032088	NP_114477	Q9Y5G5	PCDG8_HUMAN	protocadherin gamma subfamily A, 8 isoform 1	575	Extracellular (Potential).|Cadherin 6.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding				0														0.255385	195.269223	212.914022	83	242	GG		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		Missense_Mutation	SNP	140754287	140754287	11980	5	G	A	A	40	40	PCDHGA8	A	1	1
ADAMTS2	9509	broad.mit.edu	36	5	178489582	178489582	+	Missense_Mutation	SNP	G	A	A			TCGA-02-0047-01	TCGA-02-0047-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:178489582G>A	uc003mjw.1	-	c.2414C>T	c.(2413-2415)ACG>ATG	p.T805M		NM_014244	NP_055059	O95450	ATS2_HUMAN	ADAM metallopeptidase with thrombospondin type 1	805	Spacer.				collagen catabolic process	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			large_intestine(1)|lung(1)|ovary(1)|pancreas(1)	4	all_cancers(89;0.000456)|all_epithelial(37;0.000138)|Renal(175;0.000159)|Lung NSC(126;0.00184)|all_lung(126;0.00326)	all_cancers(40;0.00604)|all_neural(177;0.00411)|Medulloblastoma(196;0.00508)|Lung NSC(249;0.0569)|all_lung(500;0.129)|all_hematologic(541;0.211)								1974				0.372727	107.749163	109.312725	41	69	GG		KEEP	---	---	---	---	capture	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	GBM - Glioblastoma multiforme(465;0.0473)	Missense_Mutation	SNP	178489582	178489582	266	5	G	A	A	40	40	ADAMTS2	A	1	1
ADAMTS2	9509	broad.mit.edu	36	5	178518381	178518381	+	Missense_Mutation	SNP	C	T	T			TCGA-02-0047-01	TCGA-02-0047-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:178518381C>T	uc003mjw.1	-	c.1081G>A	c.(1081-1083)GAT>AAT	p.D361N	ADAMTS2_uc003mjx.1_Missense_Mutation_p.D361N	NM_014244	NP_055059	O95450	ATS2_HUMAN	ADAM metallopeptidase with thrombospondin type 1	361	Peptidase M12B.				collagen catabolic process	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			large_intestine(1)|lung(1)|ovary(1)|pancreas(1)	4	all_cancers(89;0.000456)|all_epithelial(37;0.000138)|Renal(175;0.000159)|Lung NSC(126;0.00184)|all_lung(126;0.00326)	all_cancers(40;0.00604)|all_neural(177;0.00411)|Medulloblastoma(196;0.00508)|Lung NSC(249;0.0569)|all_lung(500;0.129)|all_hematologic(541;0.211)								1974				0.244681	110.318373	121.442762	46	142	CC		KEEP	---	---	---	---	capture	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	GBM - Glioblastoma multiforme(465;0.0473)	Missense_Mutation	SNP	178518381	178518381	266	5	C	T	T	31	31	ADAMTS2	T	1	1
GFM2	84340	broad.mit.edu	36	5	74064650	74064650	+	Missense_Mutation	SNP	G	A	A			TCGA-02-0047-01	TCGA-02-0047-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:74064650G>A	uc010izj.1	-	c.1636C>T	c.(1636-1638)CGT>TGT	p.R546C	GFM2_uc003kdh.1_Missense_Mutation_p.R514C|GFM2_uc003kdi.1_Missense_Mutation_p.R467C|GFM2_uc010izk.1_Non-coding_Transcript	NM_032380	NP_115756	Q969S9	RRF2M_HUMAN	mitochondrial elongation factor G2 isoform 1	514					mitochondrial translation|ribosome disassembly	mitochondrion	GTP binding|GTPase activity				0		all_lung(232;0.00101)|Lung NSC(167;0.00278)|Ovarian(174;0.0129)|Breast(144;0.231)												0.246377	78.57736	86.663309	34	104	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(47;1.86e-56)	Missense_Mutation	SNP	74064650	74064650	6610	5	G	A	A	38	38	GFM2	A	1	1
GFM2	84340	broad.mit.edu	36	5	74077346	74077346	+	Silent	SNP	T	C	C			TCGA-02-0047-01	TCGA-02-0047-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr5:74077346T>C	uc010izj.1	-	c.858A>G	c.(856-858)AAA>AAG	p.K286K	GFM2_uc003kdh.1_Silent_p.K254K|GFM2_uc003kdi.1_Silent_p.K254K|GFM2_uc010izk.1_Non-coding_Transcript|GFM2_uc003kdj.1_Silent_p.K254K|GFM2_uc010izl.1_Silent_p.K212K	NM_032380	NP_115756	Q969S9	RRF2M_HUMAN	mitochondrial elongation factor G2 isoform 1	254					mitochondrial translation|ribosome disassembly	mitochondrion	GTP binding|GTPase activity				0		all_lung(232;0.00101)|Lung NSC(167;0.00278)|Ovarian(174;0.0129)|Breast(144;0.231)												0.330827	140.158121	143.529598	44	89	TT		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(47;1.86e-56)	Silent	SNP	74077346	74077346	6610	5	T	C	C	56	56	GFM2	C	4	4
LAMA2	3908	broad.mit.edu	36	6	129412780	129412780	+	Missense_Mutation	SNP	T	A	A			TCGA-02-0047-01	TCGA-02-0047-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr6:129412780T>A	uc003qbn.1	+	c.137T>A	c.(136-138)CTT>CAT	p.L46H	LAMA2_uc003qbo.1_Missense_Mutation_p.L46H|LAMA2_uc010kfe.1_Missense_Mutation_p.L46H	NM_000426	NP_000417	P24043	LAMA2_HUMAN	laminin alpha 2 subunit isoform a precursor	46	Laminin N-terminal.				cell adhesion|muscle organ development|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	laminin-1 complex	receptor binding|structural molecule activity			ovary(8)|breast(1)	9														0.340136	138.200737	141.523611	50	97	TT		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(136;0.178)|all cancers(137;0.245)	Missense_Mutation	SNP	129412780	129412780	8929	6	T	A	A	56	56	LAMA2	A	4	4
SASH1	23328	broad.mit.edu	36	6	148907058	148907058	+	Missense_Mutation	SNP	G	A	A			TCGA-02-0047-01	TCGA-02-0047-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:148907058G>A	uc003qme.1	+	c.2759G>A	c.(2758-2760)CGC>CAC	p.R920H	SASH1_uc003qmf.1_Missense_Mutation_p.R330H	NM_015278	NP_056093	O94885	SASH1_HUMAN	SAM and SH3 domain containing 1	920							protein binding			central_nervous_system(1)	1		Ovarian(120;0.0169)												0.16055	54.032699	77.915528	35	183	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(155;5.63e-11)|GBM - Glioblastoma multiforme(68;0.0701)	Missense_Mutation	SNP	148907058	148907058	14329	6	G	A	A	38	38	SASH1	A	1	1
PLEKHG1	57480	broad.mit.edu	36	6	151193856	151193856	+	Missense_Mutation	SNP	G	A	A			TCGA-02-0047-01	TCGA-02-0047-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:151193856G>A	uc003qny.1	+	c.1916G>A	c.(1915-1917)GGG>GAG	p.G639E	PLEKHG1_uc003qnz.1_Missense_Mutation_p.G639E	NM_001029884	NP_001025055	Q9ULL1	PKHG1_HUMAN	pleckstrin homology domain containing, family G	639					regulation of Rho protein signal transduction	intracellular	Rho guanyl-nucleotide exchange factor activity			ovary(2)	2														0.228571	58.145557	65.241469	24	81	GG		KEEP	---	---	---	---	capture	BRCA - Breast invasive adenocarcinoma(37;0.0923)	OV - Ovarian serous cystadenocarcinoma(155;6.69e-13)	Missense_Mutation	SNP	151193856	151193856	12494	6	G	A	A	43	43	PLEKHG1	A	2	2
PLG	5340	broad.mit.edu	36	6	161093167	161093167	+	Missense_Mutation	SNP	C	T	T			TCGA-02-0047-01	TCGA-02-0047-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:161093167C>T	uc003qtm.2	+	c.2156C>T	c.(2155-2157)GCC>GTC	p.A719V		NM_000301	NP_000292	P00747	PLMN_HUMAN	plasminogen	719	Peptidase S1.				extracellular matrix disassembly|fibrinolysis|negative regulation of cell proliferation|negative regulation of cell-substrate adhesion|negative regulation of fibrinolysis|platelet activation|platelet degranulation|positive regulation of fibrinolysis|proteolysis|tissue remodeling	extracellular space|extrinsic to external side of plasma membrane|platelet alpha granule lumen	apolipoprotein binding|cell surface binding|serine-type endopeptidase activity			ovary(1)	1					Aminocaproic Acid(DB00513)|Streptokinase(DB00086)|Tranexamic Acid(DB00302)|Urokinase(DB00013)									0.277778	73.51355	78.307278	30	78	CC		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(65;5.24e-17)|BRCA - Breast invasive adenocarcinoma(81;7.08e-06)	Missense_Mutation	SNP	161093167	161093167	12512	6	C	T	T	26	26	PLG	T	2	2
TREML2	79865	broad.mit.edu	36	6	41270469	41270469	+	Missense_Mutation	SNP	G	A	A			TCGA-02-0047-01	TCGA-02-0047-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:41270469G>A	uc010jxm.1	-	c.634C>T	c.(634-636)CCT>TCT	p.P212S		NM_024807	NP_079083	Q5T2D2	TRML2_HUMAN	triggering receptor expressed on myeloid	153	Extracellular (Potential).				T cell activation	cell surface|integral to membrane|plasma membrane	protein binding|receptor activity			ovary(1)|central_nervous_system(1)	2	Ovarian(28;0.0418)|Colorectal(47;0.196)													0.363636	90.893275	92.325586	32	56	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	41270469	41270469	17017	6	G	A	A	43	43	TREML2	A	2	2
DEFB110	245913	broad.mit.edu	36	6	50084877	50084877	+	Missense_Mutation	SNP	G	T	T			TCGA-02-0047-01	TCGA-02-0047-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:50084877G>T	uc003pab.1	-	c.122C>A	c.(121-123)ACG>AAG	p.T41K		NM_001037728	NP_001032817	Q30KQ9	DB110_HUMAN	beta-defensin 110	44					defense response to bacterium	extracellular region				ovary(1)	1	Lung NSC(77;0.042)													0.091463	9.402938	36.97602	15	149	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	50084877	50084877	4577	6	G	T	T	40	40	DEFB110	T	3	3
GAL3ST4	79690	broad.mit.edu	36	7	99596199	99596199	+	Missense_Mutation	SNP	C	T	T			TCGA-02-0047-01	TCGA-02-0047-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:99596199C>T	uc003utt.1	-	c.749G>A	c.(748-750)CGA>CAA	p.R250Q	C7orf43_uc003utr.1_5'Flank|C7orf43_uc003uts.1_5'Flank|GAL3ST4_uc003utu.1_Missense_Mutation_p.R250Q|GAL3ST4_uc010lgq.1_Missense_Mutation_p.R188Q	NM_024637	NP_078913	Q96RP7	G3ST4_HUMAN	galactose-3-O-sulfotransferase 4	250	Lumenal (Potential).				cell-cell signaling|oligosaccharide metabolic process|proteoglycan biosynthetic process|sulfur compound metabolic process	Golgi cisterna membrane|integral to membrane|membrane fraction	3'-phosphoadenosine 5'-phosphosulfate binding|galactosylceramide sulfotransferase activity|proteoglycan sulfotransferase activity			ovary(3)	3	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)													0.326531	333.37435	343.835907	128	264	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	99596199	99596199	6464	7	C	T	T	31	31	GAL3ST4	T	1	1
ASAH1	427	broad.mit.edu	36	8	17961249	17961249	+	Missense_Mutation	SNP	C	T	T			TCGA-02-0047-01	TCGA-02-0047-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr8:17961249C>T	uc003wyn.2	-	c.970G>A	c.(970-972)GAT>AAT	p.D324N	ASAH1_uc003wyl.2_Missense_Mutation_p.D308N|ASAH1_uc010ltb.1_Non-coding_Transcript|ASAH1_uc003wym.2_Missense_Mutation_p.D283N|ASAH1_uc003wyo.2_Missense_Mutation_p.D302N	NM_004315	NP_004306	Q13510	ASAH1_HUMAN	N-acylsphingosine amidohydrolase 1 isoform b	308					ceramide metabolic process	lysosome	ceramidase activity				0														0.165877	64.991557	87.340153	35	176	CC		KEEP	---	---	---	---	capture		Colorectal(111;0.0646)|COAD - Colon adenocarcinoma(73;0.228)	Missense_Mutation	SNP	17961249	17961249	1024	8	C	T	T	31	31	ASAH1	T	1	1
DNAJC5B	85479	broad.mit.edu	36	8	67126399	67126399	+	Silent	SNP	C	T	T			TCGA-02-0047-01	TCGA-02-0047-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr8:67126399C>T	uc003xvs.1	+	c.63C>T	c.(61-63)TAC>TAT	p.Y21Y	DNAJC5B_uc003xvt.1_Non-coding_Transcript	NM_033105	NP_149096	Q9UF47	DNJ5B_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 5	21	J.				protein folding	membrane	heat shock protein binding|unfolded protein binding				0		Lung NSC(129;0.114)|all_lung(136;0.188)												0.338462	178.887294	183.388109	66	129	CC		KEEP	---	---	---	---	capture	Epithelial(68;0.0213)|all cancers(69;0.0839)|BRCA - Breast invasive adenocarcinoma(89;0.0886)|OV - Ovarian serous cystadenocarcinoma(28;0.112)		Silent	SNP	67126399	67126399	4834	8	C	T	T	19	19	DNAJC5B	T	1	1
SNAPC4	6621	broad.mit.edu	36	9	138392236	138392236	+	Silent	SNP	G	C	C			TCGA-02-0047-01	TCGA-02-0047-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr9:138392236G>C	uc004chh.1	-	c.3864C>G	c.(3862-3864)GGC>GGG	p.G1288G		NM_003086	NP_003077	Q5SXM2	SNPC4_HUMAN	small nuclear RNA activating complex,	1288	SNAPC2-binding.				regulation of transcription, DNA-dependent|snRNA transcription from RNA polymerase II promoter|snRNA transcription from RNA polymerase III promoter	snRNA-activating protein complex	DNA binding|sequence-specific DNA binding transcription factor activity				0		Myeloproliferative disorder(178;0.0511)												0.277778	7.152456	7.905815	5	13	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(145;5.31e-06)|Epithelial(140;7.13e-06)	Silent	SNP	138392236	138392236	15337	9	G	C	C	42	42	SNAPC4	C	3	3
USP9X	8239	broad.mit.edu	36	X	40960384	40960384	+	Nonsense_Mutation	SNP	C	T	T			TCGA-02-0047-01	TCGA-02-0047-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:40960384C>T	uc004dfb.1	+	c.5620C>T	c.(5620-5622)CAA>TAA	p.Q1874*	USP9X_uc004dfc.1_Nonsense_Mutation_p.Q1874*	NM_001039590	NP_001034679	Q93008	USP9X_HUMAN	ubiquitin specific protease 9, X-linked isoform	1874					BMP signaling pathway|cell division|chromosome segregation|female gamete generation|mitosis|protein deubiquitination|transforming growth factor beta receptor signaling pathway|ubiquitin-dependent protein catabolic process	cytoplasm	co-SMAD binding|cysteine-type endopeptidase activity|ubiquitin thiolesterase activity			ovary(1)	1						Ovarian(172;1807 2695 35459 49286)								0.647887	138.560121	139.926606	46	25	CC		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	40960384	40960384	17654	23	C	T	T	29	29	USP9X	T	5	2
GJB1	2705	broad.mit.edu	36	X	70360779	70360779	+	Missense_Mutation	SNP	T	G	G			TCGA-02-0047-01	TCGA-02-0047-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chrX:70360779T>G	uc004dzf.2	+	c.497T>G	c.(496-498)GTC>GGC	p.V166G	GJB1_uc004dzg.2_Missense_Mutation_p.V166G|GJB1_uc010nlc.1_Missense_Mutation_p.V166G	NM_001097642	NP_001091111	P08034	CXB1_HUMAN	gap junction protein, beta 1, 32kDa	166	Extracellular (Probable).				cell-cell signaling|cellular membrane organization|gap junction assembly|nervous system development	connexon complex|endoplasmic reticulum membrane|integral to membrane	gap junction channel activity			breast(1)	1	Renal(35;0.156)													0.375	7.017243	7.128886	3	5	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	70360779	70360779	6675	23	T	G	G	58	58	GJB1	G	4	4
MICALCL	84953	broad.mit.edu	36	11	12272963	12272965	+	In_Frame_Del	DEL	CTA	-	-			TCGA-02-0047-01	TCGA-02-0047-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:12272963_12272965delCTA	uc001mkg.1	+	c.1409_1411delCTA	c.(1408-1413)CCTACA>CCA	p.T471del		NM_032867	NP_116256	Q6ZW33	MICLK_HUMAN	MICAL C-terminal like	471					cell differentiation|multicellular organismal development|spermatogenesis	cytoplasm	mitogen-activated protein kinase binding				0				Epithelial(150;0.00177)										0.42			5	7				---	---	---	---	capture_indel			In_Frame_Del	DEL	12272963	12272965	9962	11	CTA	-	-	24	24	MICALCL	-	5	5
CORO1B	57175	broad.mit.edu	36	11	66962774	66962775	+	Frame_Shift_Ins	INS	-	G	G			TCGA-02-0047-01	TCGA-02-0047-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:66962774_66962775insG	uc001olj.1	-	c.1287_1288insC	c.(1285-1290)CCCGCCfs	p.P429fs	PTPRCAP_uc001oli.1_5'Flank|CORO1B_uc009yrs.1_Non-coding_Transcript|CORO1B_uc001olk.1_Frame_Shift_Ins_p.P429fs|CORO1B_uc009yrt.1_Non-coding_Transcript|CORO1B_uc009yru.1_Non-coding_Transcript|CORO1B_uc001oll.1_Frame_Shift_Ins_p.P429fs	NM_020441	NP_065174	Q9BR76	COR1B_HUMAN	coronin, actin binding protein, 1B	429_430					actin cytoskeleton organization	actin cytoskeleton|cytoplasm	actin filament binding			large_intestine(1)|ovary(1)	2			BRCA - Breast invasive adenocarcinoma(15;3.26e-06)											0.33			2	4				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	66962774	66962775	3892	11	-	G	G	27	27	CORO1B	G	5	5
SPACA3	124912	broad.mit.edu	36	17	28346756	28346756	+	Frame_Shift_Del	DEL	C	-	-			TCGA-02-0047-01	TCGA-02-0047-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:28346756_28346756delC	uc002hhs.1	+	c.251_251delC	c.(250-252)TCCfs	p.S84fs	SPACA3_uc010cte.1_Non-coding_Transcript	NM_173847	NP_776246	Q8IXA5	SACA3_HUMAN	sperm acrosome associated 3	84	Helical; Signal-anchor for type II membrane protein; (Potential).				cell wall macromolecule catabolic process|defense response to Gram-positive bacterium|monocyte activation|peptidoglycan catabolic process|positive regulation of macrophage activation|positive regulation of phagocytosis|response to virus	acrosomal membrane|extracellular region|integral to membrane|lysosome	bacterial cell surface binding|lysozyme activity|protein binding			ovary(1)	1			BRCA - Breast invasive adenocarcinoma(9;0.193)											0.38			53	88				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	28346756	28346756	15474	17	C	-	-	30	30	SPACA3	-	5	5
