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
KNDC1	85442	broad.mit.edu	36	10	134862304	134862304	+	Missense_Mutation	SNP	A	C	C			TCGA-06-0166-01	TCGA-06-0166-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr10:134862304A>C	uc001llz.1	+	c.2302A>C	c.(2302-2304)AAC>CAC	p.N768H	KNDC1_uc001lma.1_Missense_Mutation_p.N703H|KNDC1_uc001lmb.1_Missense_Mutation_p.N180H	NM_152643	NP_689856	Q76NI1	VKIND_HUMAN	kinase non-catalytic C-lobe domain (KIND)	768	Pro-rich.				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)												0.266667	12.094811	12.83139	4	11	AA		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(35;8.77e-06)|Epithelial(32;1.13e-05)|all cancers(32;1.51e-05)	Missense_Mutation	SNP	134862304	134862304	8740	10	A	C	C	1	1	KNDC1	C	4	4
C10orf71	118461	broad.mit.edu	36	10	50201491	50201491	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0166-01	TCGA-06-0166-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr10:50201491G>A	uc001jhp.1	+	c.895G>A	c.(895-897)GAA>AAA	p.E299K		NM_199459	NP_955629	Q711Q0	CJ071_HUMAN	hypothetical protein LOC118461 isoform 2	299											0														0.321429	52.4291	54.015743	18	38	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	50201491	50201491	1651	10	G	A	A	33	33	C10orf71	A	2	2
CHST3	9469	broad.mit.edu	36	10	73437281	73437281	+	Missense_Mutation	SNP	C	G	G			TCGA-06-0166-01	TCGA-06-0166-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr10:73437281C>G	uc001jsn.1	+	c.486C>G	c.(484-486)TTC>TTG	p.F162L		NM_004273	NP_004264	Q7LGC8	CHST3_HUMAN	carbohydrate (chondroitin 6) sulfotransferase 3	162	Lumenal (Potential).				chondroitin sulfate biosynthetic process	Golgi membrane|integral to membrane	chondroitin 6-sulfotransferase activity				0														0.214286	6.617084	7.67269	3	11	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	73437281	73437281	3539	10	C	G	G	31	31	CHST3	G	3	3
PTEN	5728	broad.mit.edu	36	10	89701862	89701862	+	Missense_Mutation	SNP	C	G	G			TCGA-06-0166-01	TCGA-06-0166-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr10:89701862C>G	uc001kfb.1	+	c.500C>G	c.(499-501)ACT>AGT	p.T167S		NM_000314	NP_000305	P60484	PTEN_HUMAN	phosphatase and tensin homolog	167	Phosphatase tensin-type.		T -> P (in breast cancer; severely reduced protein phosphatase activity).	T->A,D: 60% reduction in phosphatase activity towards PtdIns(3,4,5)P3.	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.V166fs*17(3)|p.G165fs*9(3)|p.Y27_N212>Y(2)|p.V166fs*10(1)|p.T167I(1)|p.G165_K342del(1)|p.G165_*404del(1)|p.T167S(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		264	TCGA GBM(2;<1E-8)|TSP Lung(26;0.18)			0.329412	179.9464	184.329536	56	114	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)	Missense_Mutation	SNP	89701862	89701862	13192	10	C	G	G	20	20	PTEN	G	3	3
KRTAP5-5	439915	broad.mit.edu	36	11	1607758	1607758	+	Missense_Mutation	SNP	T	C	C			TCGA-06-0166-01	TCGA-06-0166-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr11:1607758T>C	uc001lty.1	+	c.112T>C	c.(112-114)TGT>CGT	p.C38R		NM_001001480	NP_001001480	Q701N2	KRA55_HUMAN	keratin associated protein 5-5	38						keratin filament				lung(1)	1		all_epithelial(84;0.00018)|Ovarian(85;0.0014)|Breast(177;0.00147)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)												0.15625	7.455461	11.065996	5	27	TT		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(625;0.000614)|Lung(200;0.0681)|LUSC - Lung squamous cell carcinoma(625;0.082)	Missense_Mutation	SNP	1607758	1607758	8886	11	T	C	C	55	55	KRTAP5-5	C	4	4
MYOD1	4654	broad.mit.edu	36	11	17698428	17698428	+	Missense_Mutation	SNP	G	T	T			TCGA-06-0166-01	TCGA-06-0166-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:17698428G>T	uc001mni.1	+	c.523G>T	c.(523-525)GCA>TCA	p.A175S		NM_002478	NP_002469	P15172	MYOD1_HUMAN	myogenic differentiation 1	175					muscle cell fate commitment|positive regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of muscle cell differentiation|protein phosphorylation|skeletal muscle tissue development	nuclear chromatin|transcription factor complex	E-box binding|protein heterodimerization activity|sequence-specific enhancer binding RNA polymerase II transcription factor activity|transcription coactivator activity			breast(2)|ovary(1)	3														0.517241	45.541403	45.550166	15	14	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	17698428	17698428	10483	11	G	T	T	38	38	MYOD1	T	3	3
CDC42BPG	55561	broad.mit.edu	36	11	64355655	64355655	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0166-01	TCGA-06-0166-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:64355655G>C	uc001obs.2	-	c.3202C>G	c.(3202-3204)CTG>GTG	p.L1068V		NM_017525	NP_059995	Q6DT37	MRCKG_HUMAN	CDC42 binding protein kinase gamma (DMPK-like)	1068					actin cytoskeleton reorganization|intracellular signal transduction|protein phosphorylation	cell leading edge|centrosome	ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity|small GTPase regulator activity			lung(3)|central_nervous_system(1)	4										665		OREG0004016	type=REGULATORY REGION|Gene=CDC42BPG|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	0.190476	7.185169	9.06923	4	17	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	64355655	64355655	3202	11	G	C	C	34	34	CDC42BPG	C	3	3
TMEM132D	121256	broad.mit.edu	36	12	128124816	128124816	+	Nonsense_Mutation	SNP	C	A	A			TCGA-06-0166-01	TCGA-06-0166-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:128124816C>A	uc009zyl.1	-	c.2857G>T	c.(2857-2859)GAG>TAG	p.E953*	TMEM132D_uc001uia.2_Nonsense_Mutation_p.E491*	NM_133448	NP_597705	Q14C87	T132D_HUMAN	transmembrane protein 132D	953	Cytoplasmic (Potential).					integral to membrane		p.E953*(1)		ovary(10)|pancreas(2)	12	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0934)|Breast(359;0.133)												0.126984	37.514369	63.123887	24	165	CC		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(86;0.000288)|Epithelial(86;0.0116)|all cancers(50;0.0246)	Nonsense_Mutation	SNP	128124816	128124816	16579	12	C	A	A	31	31	TMEM132D	A	5	3
LRP1	4035	broad.mit.edu	36	12	55876248	55876248	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0166-01	TCGA-06-0166-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:55876248G>C	uc001snd.1	+	c.8813G>C	c.(8812-8814)GGC>GCC	p.G2938A		NM_002332	NP_002323	Q07954	LRP1_HUMAN	low density lipoprotein-related protein 1	2938	LDL-receptor class A 20.|Extracellular (Potential).				apoptotic cell clearance|multicellular organismal development|negative regulation of Wnt receptor signaling pathway|positive regulation of cholesterol efflux|regulation of phospholipase A2 activity	coated pit|integral to plasma membrane|nucleus	apolipoprotein E binding|calcium ion binding|lipoprotein particle receptor binding|lipoprotein transporter activity|protein complex binding|receptor activity			ovary(7)|large_intestine(2)|pancreas(2)|skin(1)|central_nervous_system(1)	13					Alteplase(DB00009)|Anistreplase(DB00029)|Antihemophilic Factor(DB00025)|Becaplermin(DB00102)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031)					1456				0.25	6.680848	8.413491	7	21	GG		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(357;0.0103)	Missense_Mutation	SNP	55876248	55876248	9324	12	G	C	C	42	42	LRP1	C	3	3
CDKL1	8814	broad.mit.edu	36	14	49932284	49932284	+	Missense_Mutation	SNP	A	G	G			TCGA-06-0166-01	TCGA-06-0166-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr14:49932284A>G	uc010anu.1	-	c.623T>C	c.(622-624)GTT>GCT	p.V208A	CDKL1_uc001wxz.1_Missense_Mutation_p.V19A	NM_004196	NP_004187	Q00532	CDKL1_HUMAN	cyclin-dependent kinase-like 1	18	ATP (By similarity).|Protein kinase.				protein phosphorylation	cytoplasm|nucleus	ATP binding|cyclin-dependent protein kinase activity			ovary(1)	1	all_epithelial(31;0.000746)|Breast(41;0.0102)									153				0.288462	93.413295	97.582009	30	74	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	49932284	49932284	3282	14	A	G	G	2	2	CDKL1	G	4	4
KCNH5	27133	broad.mit.edu	36	14	62517600	62517600	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0166-01	TCGA-06-0166-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr14:62517600C>T	uc001xfx.1	-	c.685G>A	c.(685-687)GCC>ACC	p.A229T	KCNH5_uc001xfy.1_Missense_Mutation_p.A229T|KCNH5_uc001xfz.1_Missense_Mutation_p.A171T|KCNH5_uc001xga.2_Missense_Mutation_p.A171T	NM_139318	NP_647479	Q8NCM2	KCNH5_HUMAN	potassium voltage-gated channel, subfamily H,	229	Helical; Name=Segment S1; (Potential).				regulation of transcription, DNA-dependent	integral to membrane	calmodulin binding|two-component sensor activity|voltage-gated potassium channel activity			ovary(4)|central_nervous_system(1)	5														0.253521	44.514686	48.431544	18	53	CC		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(108;0.00958)|BRCA - Breast invasive adenocarcinoma(234;0.168)	Missense_Mutation	SNP	62517600	62517600	8340	14	C	T	T	27	27	KCNH5	T	1	1
HERC2	8924	broad.mit.edu	36	15	26134388	26134388	+	Missense_Mutation	SNP	A	G	G			TCGA-06-0166-01	TCGA-06-0166-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr15:26134388A>G	uc001zbj.1	-	c.6184T>C	c.(6184-6186)TTC>CTC	p.F2062L		NM_004667	NP_004658	O95714	HERC2_HUMAN	hect domain and RLD 2	2062					DNA repair|intracellular protein transport|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|regulation of mitotic metaphase/anaphase transition	anaphase-promoting complex	guanyl-nucleotide exchange factor activity|heme binding|protein binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(4)|lung(4)|skin(2)|central_nervous_system(1)	11		all_lung(180;1.3e-11)|Breast(32;0.000194)|Colorectal(260;0.227)								1580				0.361702	56.563001	57.353861	17	30	AA		KEEP	---	---	---	---	capture		all cancers(64;3.93e-09)|Epithelial(43;9.99e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0271)|GBM - Glioblastoma multiforme(186;0.0497)|Lung(196;0.199)	Missense_Mutation	SNP	26134388	26134388	7341	15	A	G	G	3	3	HERC2	G	4	4
SLTM	79811	broad.mit.edu	36	15	56973671	56973671	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0166-01	TCGA-06-0166-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr15:56973671G>A	uc002afp.1	-	c.1391C>T	c.(1390-1392)CCC>CTC	p.P464L	SLTM_uc002afn.1_Missense_Mutation_p.P33L|SLTM_uc002afo.1_Missense_Mutation_p.P446L|SLTM_uc002afq.1_Missense_Mutation_p.P33L|SLTM_uc010bgd.1_Missense_Mutation_p.P33L	NM_024755	NP_079031	Q9NWH9	SLTM_HUMAN	modulator of estrogen induced transcription	464					apoptosis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	nucleotide binding|RNA binding			ovary(1)	1														0.23913	29.501951	32.359959	11	35	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	56973671	56973671	15252	15	G	A	A	43	43	SLTM	A	2	2
GCNT3	9245	broad.mit.edu	36	15	57698993	57698993	+	Nonsense_Mutation	SNP	C	T	T			TCGA-06-0166-01	TCGA-06-0166-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr15:57698993C>T	uc002agd.1	+	c.1264C>T	c.(1264-1266)CAG>TAG	p.Q422*	GCNT3_uc002age.1_Nonsense_Mutation_p.Q422*|GCNT3_uc002agf.1_Nonsense_Mutation_p.Q422*|GCNT3_uc010bgf.1_Nonsense_Mutation_p.Q422*	NM_004751	NP_004742	O95395	GCNT3_HUMAN	glucosaminyl (N-acetyl) transferase 3, mucin	422	Lumenal (Potential).				protein O-linked glycosylation	Golgi membrane|integral to membrane|membrane fraction	beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase activity|N-acetyllactosaminide beta-1,6-N-acetylglucosaminyltransferase activity			ovary(1)|central_nervous_system(1)	2														0.344262	346.815432	354.666796	126	240	CC		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	57698993	57698993	6568	15	C	T	T	29	29	GCNT3	T	5	2
RASGRF1	5923	broad.mit.edu	36	15	77107230	77107230	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0166-01	TCGA-06-0166-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr15:77107230G>A	uc002beq.1	-	c.1289C>T	c.(1288-1290)ACG>ATG	p.T430M	RASGRF1_uc002bep.1_Missense_Mutation_p.T291M|RASGRF1_uc010blm.1_Missense_Mutation_p.T352M|RASGRF1_uc002ber.2_Missense_Mutation_p.T430M	NM_002891	NP_002882	Q13972	RGRF1_HUMAN	Ras protein-specific guanine	430					activation of Rac GTPase activity|apoptosis|induction of apoptosis by extracellular signals|long-term memory|nerve growth factor receptor signaling pathway|neuron projection development|regulation of Rac protein signal transduction|small GTPase mediated signal transduction|synaptic transmission	cytosol|growth cone|plasma membrane|synaptosome	Rho guanyl-nucleotide exchange factor activity			skin(2)|ovary(1)|central_nervous_system(1)	4										694				0.167969	78.957705	105.709541	43	213	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	77107230	77107230	13533	15	G	A	A	40	40	RASGRF1	A	1	1
ATF7IP2	80063	broad.mit.edu	36	16	10432004	10432004	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0166-01	TCGA-06-0166-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:10432004G>A	uc002czu.1	+	c.26G>A	c.(25-27)CGG>CAG	p.R9Q	ATF7IP2_uc002czv.1_Missense_Mutation_p.R9Q|ATF7IP2_uc002czw.1_Missense_Mutation_p.R9Q|ATF7IP2_uc010bul.1_Non-coding_Transcript	NM_024997	NP_079273	Q5U623	MCAF2_HUMAN	activating transcription factor 7 interacting	9					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus					0														0.296875	50.099677	52.46129	19	45	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	10432004	10432004	1107	16	G	A	A	39	39	ATF7IP2	A	1	1
ABCC1	4363	broad.mit.edu	36	16	16126159	16126159	+	Silent	SNP	G	A	A			TCGA-06-0166-01	TCGA-06-0166-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:16126159G>A	uc010bvi.1	+	c.3603G>A	c.(3601-3603)GTG>GTA	p.V1201V	ABCC1_uc010bvj.1_Silent_p.V1142V|ABCC1_uc010bvk.1_Silent_p.V1145V|ABCC1_uc010bvl.1_Silent_p.V1201V|ABCC1_uc010bvm.1_Silent_p.V1086V|ABCC1_uc002del.2_Silent_p.V1095V	NM_004996	NP_004987	P33527	MRP1_HUMAN	ATP-binding cassette, sub-family C, member 1	1201	Cytoplasmic.|ABC transmembrane type-1 2.				hormone biosynthetic process|leukotriene biosynthetic process|prostanoid metabolic process|response to drug	Golgi apparatus|integral to plasma membrane|membrane fraction|nucleus	ATP binding|ATPase activity, coupled to transmembrane movement of substances			ovary(4)	4					Daunorubicin(DB00694)|Glibenclamide(DB01016)|Probenecid(DB01032)|Saquinavir(DB01232)|Sulfinpyrazone(DB01138)									0.264463	77.041315	83.112861	32	89	GG		KEEP	---	---	---	---	capture			Silent	SNP	16126159	16126159	50	16	G	A	A	46	46	ABCC1	A	2	2
DDX28	55794	broad.mit.edu	36	16	66614333	66614333	+	Silent	SNP	G	A	A			TCGA-06-0166-01	TCGA-06-0166-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:66614333G>A	uc002evh.1	-	c.274C>T	c.(274-276)CTA>TTA	p.L92L	DUS2L_uc002evi.1_5'Flank|DUS2L_uc002evj.1_5'Flank	NM_018380	NP_060850	Q9NUL7	DDX28_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 28	92						mitochondrial nucleoid|nucleus	ATP binding|ATP-dependent helicase activity|RNA binding			skin(1)	1		Ovarian(137;0.0563)												0.266667	7.474036	8.228553	4	11	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(108;0.0116)|Epithelial(162;0.0474)|all cancers(182;0.233)	Silent	SNP	66614333	66614333	4526	16	G	A	A	34	34	DDX28	A	2	2
CLEC3A	10143	broad.mit.edu	36	16	76622080	76622080	+	Silent	SNP	C	T	T			TCGA-06-0166-01	TCGA-06-0166-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:76622080C>T	uc002ffh.2	+	c.435C>T	c.(433-435)AAC>AAT	p.N145N		NM_005752	NP_005743	O75596	CLC3A_HUMAN	C-type lectin domain family 3 member A	145	C-type lectin.				skeletal system development	extracellular region	sugar binding				0														0.309645	161.251311	167.585441	61	136	CC		KEEP	---	---	---	---	capture			Silent	SNP	76622080	76622080	3648	16	C	T	T	19	19	CLEC3A	T	1	1
TBC1D29	26083	broad.mit.edu	36	17	25911274	25911274	+	Missense_Mutation	SNP	T	A	A			TCGA-06-0166-01	TCGA-06-0166-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr17:25911274T>A	uc002hfh.1	+	c.26T>A	c.(25-27)CTA>CAA	p.L9Q	TBC1D29_uc002hfi.1_Non-coding_Transcript	NM_015594	NP_056409	Q9UFV1	TBC29_HUMAN	TBC1 domain family, member 29	9	Rab-GAP TBC; truncated.					intracellular	Rab GTPase activator activity				0		Myeloproliferative disorder(56;0.0255)												0.2	11.261025	13.35342	5	20	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	25911274	25911274	16140	17	T	A	A	53	53	TBC1D29	A	4	4
MYO19	80179	broad.mit.edu	36	17	31939071	31939071	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0166-01	TCGA-06-0166-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:31939071C>T	uc002hmw.1	-	c.1174G>A	c.(1174-1176)GTA>ATA	p.V392I	MYO19_uc010cuu.1_Non-coding_Transcript	NM_025109	NP_079385	Q96H55	MYO19_HUMAN	myosin head domain containing 1 isoform 1	392	Myosin head-like.					mitochondrial outer membrane|myosin complex	actin binding|ATP binding|motor activity			ovary(1)	1		Breast(25;0.00957)|Ovarian(249;0.17)												0.357143	26.836404	27.341992	10	18	CC		KEEP	---	---	---	---	capture	Kidney(155;0.104)	UCEC - Uterine corpus endometrioid carcinoma (308;0.0185)	Missense_Mutation	SNP	31939071	31939071	10462	17	C	T	T	18	18	MYO19	T	2	2
MPP3	4356	broad.mit.edu	36	17	39253907	39253907	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0166-01	TCGA-06-0166-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:39253907C>T	uc002ieh.1	-	c.805G>A	c.(805-807)GCC>ACC	p.A269T	MPP3_uc002iei.2_Missense_Mutation_p.A244T|MPP3_uc002iej.1_Non-coding_Transcript|MPP3_uc010czi.1_Missense_Mutation_p.A244T	NM_001932	NP_001923	Q13368	MPP3_HUMAN	palmitoylated membrane protein 3	244	SH3.				signal transduction	cell surface|integral to plasma membrane	guanylate kinase activity			large_intestine(1)	1		Breast(137;0.00394)												0.296875	49.799426	52.161318	19	45	CC		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(366;0.119)	Missense_Mutation	SNP	39253907	39253907	10127	17	C	T	T	26	26	MPP3	T	2	2
SPIRE1	56907	broad.mit.edu	36	18	12486095	12486095	+	Missense_Mutation	SNP	C	A	A			TCGA-06-0166-01	TCGA-06-0166-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr18:12486095C>A	uc002kre.1	-	c.979G>T	c.(979-981)GGT>TGT	p.G327C	SPIRE1_uc002krc.1_Non-coding_Transcript|SPIRE1_uc010dle.1_Missense_Mutation_p.G168C|SPIRE1_uc002krd.1_Missense_Mutation_p.G168C	NM_001128626	NP_001122098	Q08AE8	SPIR1_HUMAN	spire homolog 1 isoform a	327						cytoskeleton|perinuclear region of cytoplasm	actin binding|zinc ion binding				0														0.252874	55.904652	60.731573	22	65	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	12486095	12486095	15584	18	C	A	A	21	21	SPIRE1	A	3	3
ILF3	3609	broad.mit.edu	36	19	10659360	10659360	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0166-01	TCGA-06-0166-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:10659360G>A	uc002mpo.1	+	c.2410G>A	c.(2410-2412)GAC>AAC	p.D804N	ILF3_uc002mpn.1_Missense_Mutation_p.D800N|ILF3_uc002mpq.1_Silent_p.P102P	NM_012218	NP_036350	Q12906	ILF3_HUMAN	interleukin enhancer binding factor 3 isoform a	800	Interaction with PRMT1.				M phase|negative regulation of transcription, DNA-dependent|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	mitochondrion|nucleolus|ribonucleoprotein complex	DNA binding|double-stranded RNA binding|protein binding|protein binding|transcription activator activity|transcription repressor activity			ovary(3)	3														0.232759	61.577714	69.155814	27	89	GG		KEEP	---	---	---	---	capture	Epithelial(33;6.86e-06)|all cancers(31;1.65e-05)		Missense_Mutation	SNP	10659360	10659360	8013	19	G	A	A	37	37	ILF3	A	1	1
LDLR	3949	broad.mit.edu	36	19	11094883	11094883	+	Missense_Mutation	SNP	C	A	A			TCGA-06-0166-01	TCGA-06-0166-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:11094883C>A	uc002mqk.2	+	c.2174C>A	c.(2173-2175)TCC>TAC	p.S725Y		NM_000527	NP_000518	P01130	LDLR_HUMAN	low density lipoprotein receptor precursor	725	Clustered O-linked oligosaccharides.|Extracellular (Potential).				cholesterol homeostasis|cholesterol metabolic process|interspecies interaction between organisms|intestinal cholesterol absorption|low-density lipoprotein particle clearance|receptor-mediated endocytosis	clathrin-coated endocytic vesicle membrane|coated pit|early endosome|endosome membrane|external side of plasma membrane|integral to plasma membrane|low-density lipoprotein particle|lysosome	calcium ion binding|low-density lipoprotein receptor activity|protein binding|very-low-density lipoprotein particle receptor activity			ovary(2)	2		Lung NSC(9;0.000245)|Renal(1328;0.0007)|Hepatocellular(1079;0.0524)			Methyl aminolevulinate(DB00992)|Porfimer(DB00707)	GBM(18;201 575 7820 21545)				1109				0.419118	147.807286	148.590009	57	79	CC		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(1328;1.36e-05)|STAD - Stomach adenocarcinoma(1328;0.000766)|Lung(535;0.197)	Missense_Mutation	SNP	11094883	11094883	9028	19	C	A	A	30	30	LDLR	A	3	3
ZNF180	7733	broad.mit.edu	36	19	49673514	49673514	+	Nonsense_Mutation	SNP	G	A	A			TCGA-06-0166-01	TCGA-06-0166-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:49673514G>A	uc002ozf.2	-	c.1024C>T	c.(1024-1026)CAA>TAA	p.Q342*	ZNF180_uc002ozh.2_5'UTR|ZNF180_uc002ozi.2_Nonsense_Mutation_p.Q315*|ZNF180_uc002ozg.2_Nonsense_Mutation_p.Q341*|ZNF180_uc010ejm.1_Nonsense_Mutation_p.Q317*	NM_013256	NP_037388	Q9UJW8	ZN180_HUMAN	zinc finger protein 180	342					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2		Prostate(69;0.0435)				Esophageal Squamous(180;1353 2003 32862 46574 49854)								0.338164	193.575002	198.374806	70	137	GG		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	49673514	49673514	18339	19	G	A	A	45	45	ZNF180	A	5	2
FPR3	2359	broad.mit.edu	36	19	57019733	57019733	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0166-01	TCGA-06-0166-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:57019733G>A	uc002pxt.1	+	c.920G>A	c.(919-921)CGT>CAT	p.R307H	FPR3_uc010eph.1_Missense_Mutation_p.R307H	NM_002030	NP_002021	P25089	FPR3_HUMAN	formyl peptide receptor-like 2	307	Cytoplasmic (Potential).				cellular component movement|chemotaxis	integral to membrane|plasma membrane	N-formyl peptide receptor activity				0														0.251799	172.815272	188.374528	70	208	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	57019733	57019733	6286	19	G	A	A	40	40	FPR3	A	1	1
PEX19	5824	broad.mit.edu	36	1	158521477	158521477	+	Missense_Mutation	SNP	A	G	G			TCGA-06-0166-01	TCGA-06-0166-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr1:158521477A>G	uc001fvs.1	-	c.62T>C	c.(61-63)CTT>CCT	p.L21P	PEX19_uc001fvt.1_5'UTR	NM_002857	NP_002848	P40855	PEX19_HUMAN	peroxisomal biogenesis factor 19 isoform a	21	Necessary for PEX19 function on peroxisome biogenesis.|Docking to the peroxisome membrane and binding to PEX3.				peroxisome membrane biogenesis|peroxisome organization|protein targeting to peroxisome|transmembrane transport	brush border membrane|cytosol|integral to membrane|nucleus|peroxisomal membrane	protein binding|protein N-terminus binding				0	all_cancers(52;1.27e-18)|all_hematologic(112;0.093)													0.176923	54.86046	67.632268	23	107	AA		KEEP	---	---	---	---	capture	BRCA - Breast invasive adenocarcinoma(70;0.111)		Missense_Mutation	SNP	158521477	158521477	12166	1	A	G	G	3	3	PEX19	G	4	4
LPHN2	23266	broad.mit.edu	36	1	82228751	82228751	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0166-01	TCGA-06-0166-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:82228751G>C	uc001dit.2	+	c.3546G>C	c.(3544-3546)AAG>AAC	p.K1182N	LPHN2_uc001dis.1_Missense_Mutation_p.K162N|LPHN2_uc001diu.1_Missense_Mutation_p.K1182N|LPHN2_uc001div.1_3'UTR|LPHN2_uc009wcd.1_3'UTR|LPHN2_uc001diw.1_Missense_Mutation_p.K809N	NM_012302	NP_036434	O95490	LPHN2_HUMAN	latrophilin 2 precursor	1238	Cytoplasmic (Potential).				neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity|latrotoxin receptor activity|sugar binding			ovary(2)|central_nervous_system(1)	3														0.176166	69.434472	88.510932	34	159	GG		KEEP	---	---	---	---	capture		all cancers(265;0.00142)|Epithelial(280;0.00829)|OV - Ovarian serous cystadenocarcinoma(397;0.077)|STAD - Stomach adenocarcinoma(256;0.248)	Missense_Mutation	SNP	82228751	82228751	9289	1	G	C	C	35	35	LPHN2	C	3	3
MMP24	10893	broad.mit.edu	36	20	33315014	33315014	+	Silent	SNP	C	T	T			TCGA-06-0166-01	TCGA-06-0166-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr20:33315014C>T	uc002xbu.1	+	c.663C>T	c.(661-663)AAC>AAT	p.N221N		NM_006690	NP_006681	Q9Y5R2	MMP24_HUMAN	matrix metalloproteinase 24 preproprotein	274	Extracellular (Potential).				proteolysis	integral to plasma membrane|proteinaceous extracellular matrix	calcium ion binding|enzyme activator activity|metalloendopeptidase activity|zinc ion binding				0														0.388889	17.311393	17.508848	7	11	CC		KEEP	---	---	---	---	capture	BRCA - Breast invasive adenocarcinoma(18;0.00252)		Silent	SNP	33315014	33315014	10052	20	C	T	T	19	19	MMP24	T	1	1
SYS1	90196	broad.mit.edu	36	20	43425672	43425672	+	Silent	SNP	G	C	C			TCGA-06-0166-01	TCGA-06-0166-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr20:43425672G>C	uc002xnv.1	+	c.87G>C	c.(85-87)TCG>TCC	p.S29S	SYS1_uc010gha.1_Non-coding_Transcript|SYS1_uc002xnw.1_Silent_p.S29S|SYS1-DBNDD2_uc002xnx.1_5'UTR	NM_033542	NP_291020	Q8N2H4	SYS1_HUMAN	SYS1 Golgi-localized integral membrane protein	29	Helical; (Potential).				protein transport	Golgi membrane|integral to membrane					0		Myeloproliferative disorder(115;0.0122)												0.190476	6.885252	8.769413	4	17	GG		KEEP	---	---	---	---	capture			Silent	SNP	43425672	43425672	15985	20	G	C	C	38	38	SYS1	C	3	3
PRR5-ARHGAP8	553158	broad.mit.edu	36	22	43561080	43561080	+	Silent	SNP	C	G	G			TCGA-06-0166-01	TCGA-06-0166-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr22:43561080C>G	uc003bfd.1	+	c.771C>G	c.(769-771)GGC>GGG	p.G257G	PRR5-ARHGAP8_uc003bfc.1_Silent_p.G134G|PRR5-ARHGAP8_uc003bff.1_Silent_p.G39G|PRR5-ARHGAP8_uc003bfg.1_Silent_p.G39G|ARHGAP8_uc003bfi.2_Silent_p.G3G|ARHGAP8_uc010gzv.1_Silent_p.G3G|ARHGAP8_uc003bfj.1_Silent_p.G3G|ARHGAP8_uc003bfk.1_Silent_p.G3G|PRR5-ARHGAP8_uc003bfl.1_Non-coding_Transcript	NM_181335	NP_851852			Rho GTPase activating protein 8 isoform 2												0														0.266667	9.490843	10.230599	4	11	CC		KEEP	---	---	---	---	capture			Silent	SNP	43561080	43561080	13050	22	C	G	G	26	26	PRR5-ARHGAP8	G	3	3
ZRANB3	84083	broad.mit.edu	36	2	135676894	135676894	+	Missense_Mutation	SNP	A	G	G			TCGA-06-0166-01	TCGA-06-0166-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr2:135676894A>G	uc002tum.1	-	c.3119T>C	c.(3118-3120)CTC>CCC	p.L1040P	ZRANB3_uc002tuk.1_Missense_Mutation_p.L583P|ZRANB3_uc002tul.1_Missense_Mutation_p.L1038P	NM_032143	NP_115519	Q5FWF4	ZRAB3_HUMAN	zinc finger, RAN-binding domain containing 3	1040						intracellular	ATP binding|DNA binding|endonuclease activity|helicase activity|zinc ion binding				0														0.217391	12.259982	13.956916	5	18	AA		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(221;0.135)	Missense_Mutation	SNP	135676894	135676894	18828	2	A	G	G	11	11	ZRANB3	G	4	4
ZNF385B	151126	broad.mit.edu	36	2	180016365	180016365	+	Missense_Mutation	SNP	C	G	G			TCGA-06-0166-01	TCGA-06-0166-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:180016365C>G	uc002unn.2	-	c.1273G>C	c.(1273-1275)GCA>CCA	p.A425P	ZNF385B_uc002unj.1_Missense_Mutation_p.A323P|ZNF385B_uc002unl.1_Missense_Mutation_p.A322P|ZNF385B_uc002unm.1_Missense_Mutation_p.A349P|ZNF385B_uc002unk.2_Non-coding_Transcript	NM_152520	NP_001106869	Q569K4	Z385B_HUMAN	zinc finger protein 385B isoform 1	425						nucleus	nucleic acid binding|zinc ion binding			ovary(1)	1						Colon(155;204 2491 32774 51842)								0.266667	6.867372	7.627722	4	11	CC		KEEP	---	---	---	---	capture	Epithelial(96;0.174)|OV - Ovarian serous cystadenocarcinoma(117;0.201)		Missense_Mutation	SNP	180016365	180016365	18469	2	C	G	G	26	26	ZNF385B	G	3	3
DYNC2LI1	51626	broad.mit.edu	36	2	43877412	43877412	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0166-01	TCGA-06-0166-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:43877412G>A	uc002rtl.1	+	c.631G>A	c.(631-633)GCA>ACA	p.A211T	DYNC2LI1_uc002rtj.1_Missense_Mutation_p.A210T|DYNC2LI1_uc002rtk.1_Missense_Mutation_p.A210T	NM_016008	NP_057092	Q8TCX1	DC2L1_HUMAN	dynein 2 light intermediate chain isoform 1	210						apical part of cell|axonemal dynein complex|cilium axoneme|cytoplasm|microtubule|motile primary cilium	motor activity			ovary(1)	1		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)												0.192982	42.584285	52.620275	22	92	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	43877412	43877412	5033	2	G	A	A	46	46	DYNC2LI1	A	2	2
XCR1	2829	broad.mit.edu	36	3	46038347	46038347	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0166-01	TCGA-06-0166-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr3:46038347C>T	uc003cpe.1	-	c.97G>A	c.(97-99)GCC>ACC	p.A33T	XCR1_uc003cpf.1_Missense_Mutation_p.A33T|XCR1_uc010hiz.1_Missense_Mutation_p.A33T	NM_005283	NP_005274	P46094	XCR1_HUMAN	XC chemokine receptor 1	33	Helical; Name=1; (Potential).				chemotaxis|G-protein signaling, coupled to cyclic nucleotide second messenger|inflammatory response	integral to plasma membrane	chemokine receptor activity			ovary(1)	1														0.230769	73.820121	84.199585	36	120	CC		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(193;0.00113)|KIRC - Kidney renal clear cell carcinoma(197;0.0172)|Kidney(197;0.0203)	Missense_Mutation	SNP	46038347	46038347	18006	3	C	T	T	27	27	XCR1	T	1	1
NBEAL2	23218	broad.mit.edu	36	3	47015842	47015842	+	Missense_Mutation	SNP	C	A	A			TCGA-06-0166-01	TCGA-06-0166-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr3:47015842C>A	uc003cqp.2	+	c.3577C>A	c.(3577-3579)CCT>ACT	p.P1193T	NBEAL2_uc010hjm.1_Missense_Mutation_p.P701T|NBEAL2_uc010hjn.1_5'Flank	NM_015175	NP_055990	Q6ZNJ1	NBEL2_HUMAN	neurobeachin-like 2	1193	Leu-rich.						binding			ovary(1)	1		Acute lymphoblastic leukemia(5;0.0534)												0.266667	6.478246	7.234431	4	11	CC		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(193;0.0012)|KIRC - Kidney renal clear cell carcinoma(197;0.00575)|Kidney(197;0.00656)	Missense_Mutation	SNP	47015842	47015842	10585	3	C	A	A	18	18	NBEAL2	A	3	3
LIMCH1	22998	broad.mit.edu	36	4	41347311	41347311	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0166-01	TCGA-06-0166-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr4:41347311G>A	uc003gvz.2	+	c.2965G>A	c.(2965-2967)GAG>AAG	p.E989K	LIMCH1_uc003gvu.2_Missense_Mutation_p.E604K|LIMCH1_uc003gvv.2_Missense_Mutation_p.E604K|LIMCH1_uc003gvw.2_Missense_Mutation_p.E604K|LIMCH1_uc003gvx.2_Missense_Mutation_p.E592K|LIMCH1_uc003gwe.2_Missense_Mutation_p.E604K|LIMCH1_uc003gvy.2_Missense_Mutation_p.E433K|LIMCH1_uc003gwa.2_Missense_Mutation_p.E445K|LIMCH1_uc003gwc.2_Missense_Mutation_p.E450K|LIMCH1_uc003gwd.2_Missense_Mutation_p.E438K	NM_014988	NP_055803	Q9UPQ0	LIMC1_HUMAN	LIM and calponin homology domains 1 isoform a	604					actomyosin structure organization		actin binding|zinc ion binding			ovary(2)|pancreas(1)	3														0.133333	13.996193	23.785857	10	65	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	41347311	41347311	9123	4	G	A	A	41	41	LIMCH1	A	2	2
FTMT	94033	broad.mit.edu	36	5	121215873	121215873	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0166-01	TCGA-06-0166-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:121215873G>A	uc003kss.1	+	c.316G>A	c.(316-318)GTG>ATG	p.V106M		NM_177478	NP_803431	Q8N4E7	FTMT_HUMAN	mitochondrial ferritin	106	Ferritin-like diiron.				cellular iron ion homeostasis|iron ion transport|oxidation-reduction process|positive regulation of cell proliferation|positive regulation of lyase activity|positive regulation of oxidoreductase activity|positive regulation of transferase activity	mitochondrion	ferric iron binding|ferroxidase activity			ovary(1)	1		all_cancers(142;0.0124)|Prostate(80;0.0322)												0.342593	99.342216	101.706192	37	71	GG		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(527;0.206)	Epithelial(69;0.000171)|OV - Ovarian serous cystadenocarcinoma(64;0.000188)|all cancers(49;0.0027)	Missense_Mutation	SNP	121215873	121215873	6336	5	G	A	A	40	40	FTMT	A	1	1
PCDHGA11	56105	broad.mit.edu	36	5	140780994	140780994	+	Missense_Mutation	SNP	C	A	A			TCGA-06-0166-01	TCGA-06-0166-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:140780994C>A	uc003lkq.1	+	c.16C>A	c.(16-18)CAG>AAG	p.Q6K	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_uc003lkd.1_Intron|PCDHGB5_uc003lkf.1_Intron|PCDHGA9_uc003lkh.1_Intron|PCDHGB6_uc003lkj.1_Intron|PCDHGA10_uc003lkl.1_Intron|PCDHGB7_uc003lkn.1_Intron|PCDHGA11_uc003lko.1_Missense_Mutation_p.Q6K|PCDHGA11_uc003lkp.1_Missense_Mutation_p.Q6K	NM_018914	NP_061737	Q9Y5H2	PCDGB_HUMAN	protocadherin gamma subfamily A, 11 isoform 1	6					homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding				0														0.307692	8.50278	8.928272	4	9	CC		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		Missense_Mutation	SNP	140780994	140780994	11972	5	C	A	A	17	17	PCDHGA11	A	3	3
FCHSD1	89848	broad.mit.edu	36	5	141006401	141006401	+	Missense_Mutation	SNP	T	G	G			TCGA-06-0166-01	TCGA-06-0166-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr5:141006401T>G	uc003llk.1	-	c.997A>C	c.(997-999)ACC>CCC	p.T333P	FCHSD1_uc010jgg.1_5'UTR|FCHSD1_uc003llj.1_Non-coding_Transcript	NM_033449	NP_258260	Q86WN1	FCSD1_HUMAN	FCH and double SH3 domains 1	333									FCHSD1/BRAF(2)	skin(2)|ovary(1)|central_nervous_system(1)	4														0.444444	9.395772	9.420314	4	5	TT		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		Missense_Mutation	SNP	141006401	141006401	6026	5	T	G	G	58	58	FCHSD1	G	4	4
FCHSD1	89848	broad.mit.edu	36	5	141009222	141009222	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0166-01	TCGA-06-0166-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:141009222C>T	uc003llk.1	-	c.299G>A	c.(298-300)CGA>CAA	p.R100Q	FCHSD1_uc010jgg.1_5'Flank|FCHSD1_uc003llj.1_Non-coding_Transcript	NM_033449	NP_258260	Q86WN1	FCSD1_HUMAN	FCH and double SH3 domains 1	100									FCHSD1/BRAF(2)	skin(2)|ovary(1)|central_nervous_system(1)	4														0.238889	94.870453	106.061667	43	137	CC		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		Missense_Mutation	SNP	141009222	141009222	6026	5	C	T	T	31	31	FCHSD1	T	1	1
AGXT2	64902	broad.mit.edu	36	5	35068650	35068650	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0166-01	TCGA-06-0166-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:35068650C>T	uc003jjf.1	-	c.713G>A	c.(712-714)GGA>GAA	p.G238E		NM_031900	NP_114106	Q9BYV1	AGT2_HUMAN	alanine-glyoxylate aminotransferase 2 precursor	238					glyoxylate metabolic process|pyrimidine base metabolic process|pyrimidine nucleoside catabolic process	mitochondrial matrix	(R)-3-amino-2-methylpropionate-pyruvate transaminase activity|alanine-glyoxylate transaminase activity|pyridoxal phosphate binding			ovary(3)	3	all_lung(31;4.52e-05)				Glycine(DB00145)|L-Alanine(DB00160)|Pyridoxal Phosphate(DB00114)|Pyruvic acid(DB00119)									0.2	6.708907	8.3698	4	16	CC		KEEP	---	---	---	---	capture	COAD - Colon adenocarcinoma(61;0.174)|Colorectal(62;0.229)	GBM - Glioblastoma multiforme(108;0.181)	Missense_Mutation	SNP	35068650	35068650	408	5	C	T	T	30	30	AGXT2	T	2	2
GMPR	2766	broad.mit.edu	36	6	16387011	16387011	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0166-01	TCGA-06-0166-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:16387011C>T	uc003nbs.1	+	c.565C>T	c.(565-567)CGC>TGC	p.R189C		NM_006877	NP_006868	P36959	GMPR1_HUMAN	guanosine monophosphate reductase	189					nucleotide metabolic process|oxidation-reduction process|purine base metabolic process|purine-containing compound salvage|response to cold	cytosol	GMP reductase activity|metal ion binding			ovary(1)	1	Breast(50;0.0427)|Ovarian(93;0.103)	all_hematologic(90;0.0895)												0.263158	69.268713	74.064524	25	70	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	16387011	16387011	6765	6	C	T	T	23	23	GMPR	T	1	1
DPP6	1804	broad.mit.edu	36	7	154308290	154308290	+	Nonsense_Mutation	SNP	C	A	A			TCGA-06-0166-01	TCGA-06-0166-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:154308290C>A	uc003wlk.1	+	c.2148C>A	c.(2146-2148)TAC>TAA	p.Y716*	DPP6_uc003wli.1_Nonsense_Mutation_p.Y652*|DPP6_uc003wlm.1_Nonsense_Mutation_p.Y654*	NM_130797	NP_570629	P42658	DPP6_HUMAN	dipeptidyl-peptidase 6 isoform 1	716	Extracellular (Potential).				cell death|proteolysis	integral to membrane	dipeptidyl-peptidase activity|serine-type peptidase activity			pancreas(3)|breast(1)	4	all_neural(206;0.181)	all_hematologic(28;0.0044)|all_lung(21;0.0176)|Lung NSC(21;0.0204)				NSCLC(125;1384 1783 2490 7422 34254)								0.363636	8.01527	8.187197	4	7	CC		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(82;0.0562)		Nonsense_Mutation	SNP	154308290	154308290	4914	7	C	A	A	18	18	DPP6	A	5	3
PCLO	27445	broad.mit.edu	36	7	82433026	82433026	+	Missense_Mutation	SNP	T	A	A			TCGA-06-0166-01	TCGA-06-0166-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr7:82433026T>A	uc003uhx.2	-	c.4014A>T	c.(4012-4014)AAA>AAT	p.K1338N	PCLO_uc003uhv.2_Missense_Mutation_p.K1338N	NM_033026	NP_149015	Q9Y6V0	PCLO_HUMAN	piccolo isoform 1	1270					cytoskeleton organization|synaptic vesicle exocytosis	cell junction|cytoskeleton|synaptic vesicle	calcium ion binding|calcium-dependent phospholipid binding|profilin binding|transporter activity|zinc ion binding			ovary(7)	7														0.294872	114.087407	119.962157	46	110	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	82433026	82433026	12003	7	T	A	A	64	64	PCLO	A	4	4
DYNC1I1	1780	broad.mit.edu	36	7	95295336	95295336	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0166-01	TCGA-06-0166-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:95295336C>T	uc003uoc.2	+	c.397C>T	c.(397-399)CTC>TTC	p.L133F	DYNC1I1_uc003uob.1_Intron|DYNC1I1_uc003uod.2_Missense_Mutation_p.L116F|DYNC1I1_uc003uoe.2_Intron|DYNC1I1_uc010lfl.1_Missense_Mutation_p.L122F	NM_004411	NP_004402	O14576	DC1I1_HUMAN	dynein, cytoplasmic 1, intermediate chain 1	133					vesicle transport along microtubule	condensed chromosome kinetochore|cytoplasmic dynein complex|microtubule|perinuclear region of cytoplasm|spindle pole	microtubule binding|microtubule motor activity			ovary(3)|kidney(1)	4	all_cancers(62;9.39e-10)|all_epithelial(64;2.28e-09)|Lung NSC(181;0.165)|all_lung(186;0.191)													0.242152	436.721018	477.277721	162	507	CC		KEEP	---	---	---	---	capture	STAD - Stomach adenocarcinoma(171;0.0957)		Missense_Mutation	SNP	95295336	95295336	5028	7	C	T	T	28	28	DYNC1I1	T	2	2
ZNF618	114991	broad.mit.edu	36	9	115790483	115790483	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0166-01	TCGA-06-0166-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr9:115790483G>A	uc004bid.1	+	c.139G>A	c.(139-141)GAG>AAG	p.E47K	ZNF618_uc004bib.1_Missense_Mutation_p.E47K|ZNF618_uc004bic.1_Missense_Mutation_p.E47K	NM_133374	NP_588615	Q5T7W0	ZN618_HUMAN	zinc finger protein 618	47					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0														0.210526	28.068857	32.487083	12	45	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	115790483	115790483	18637	9	G	A	A	37	37	ZNF618	A	1	1
PLXNB3	5365	broad.mit.edu	36	X	152695969	152695969	+	Silent	SNP	C	G	G			TCGA-06-0166-01	TCGA-06-0166-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:152695969C>G	uc004fii.1	+	c.5040C>G	c.(5038-5040)CGC>CGG	p.R1680R	SRPK3_uc004fik.1_5'UTR|PLXNB3_uc010nuk.1_Silent_p.R1703R	NM_005393	NP_005384	Q9ULL4	PLXB3_HUMAN	plexin B3	1680	Cytoplasmic (Potential).				axon guidance	integral to membrane|intracellular|plasma membrane	protein binding|receptor activity			lung(1)	1	all_hematologic(71;4.25e-06)|all_lung(58;3.83e-05)|Lung NSC(58;5.54e-05)|Acute lymphoblastic leukemia(192;6.56e-05)													0.25	6.620328	7.301611	3	9	CC		KEEP	---	---	---	---	capture			Silent	SNP	152695969	152695969	12551	23	C	G	G	27	27	PLXNB3	G	3	3
BCOR	54880	broad.mit.edu	36	X	39817115	39817115	+	Nonsense_Mutation	SNP	G	A	A			TCGA-06-0166-01	TCGA-06-0166-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:39817115G>A	uc004den.2	-	c.2428C>T	c.(2428-2430)CGA>TGA	p.R810*	BCOR_uc004dep.2_Nonsense_Mutation_p.R810*|BCOR_uc004deo.2_Nonsense_Mutation_p.R810*|BCOR_uc004dem.2_Nonsense_Mutation_p.R810*|BCOR_uc004deq.2_Nonsense_Mutation_p.R810*	NM_001123385	NP_001116857	Q6W2J9	BCOR_HUMAN	BCL-6 interacting corepressor isoform c	810					chromatin modification|heart development|negative regulation of bone mineralization|negative regulation of histone H3-K36 methylation|negative regulation of histone H3-K4 methylation|negative regulation of tooth mineralization|odontogenesis|palate development|protein ubiquitination|specification of axis polarity|transcription, DNA-dependent	nucleus	heat shock protein binding|histone deacetylase binding|promoter binding|transcription corepressor activity|transcription factor binding			ovary(2)|kidney(1)|central_nervous_system(1)	4														0.522059	217.825274	217.883311	71	65	GG		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	39817115	39817115	1407	23	G	A	A	39	39	BCOR	A	5	1
KRTAP5-5	439915	broad.mit.edu	36	11	1607767	1607775	+	In_Frame_Del	DEL	GGCTGTGGA	-	-			TCGA-06-0166-01	TCGA-06-0166-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:1607767_1607775delGGCTGTGGA	uc001lty.1	+	c.121_129delGGCTGTGGA	c.(121-129)GGCTGTGGAdel	p.GCG47del		NM_001001480	NP_001001480	Q701N2	KRA55_HUMAN	keratin associated protein 5-5	47_49						keratin filament				lung(1)	1		all_epithelial(84;0.00018)|Ovarian(85;0.0014)|Breast(177;0.00147)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.000614)|Lung(200;0.0681)|LUSC - Lung squamous cell carcinoma(625;0.082)										0.53			25	22				---	---	---	---	capture_indel			In_Frame_Del	DEL	1607767	1607775	8886	11	GGCTGTGGA	-	-	39	39	KRTAP5-5	-	5	5
