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	TCGAscape_Amplification_Peaks	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_judgement	validation_status	validation_method	validation_tumor_sample	validation_alt_allele	dataset	Oncotatorv0393GAF20hg19Feb2011dbSNPbuild132UniProtRelease2011_6	type	classification	start	end	gene	chr	ref_allele	tum_allele1	tum_allele2	newbase	context_orig	context65	gene_name	categ	categ_ignoring_null_categ
SFXN3	81855	broad.mit.edu	37	10	102799248	102799248	+	Missense_Mutation	SNP	C	G	G			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:102799248C>G	uc010qpx.1	+	c.896C>G	c.(895-897)TCC>TGC	p.S299C	SFXN3_uc001ksp.2_Missense_Mutation_p.S295C|SFXN3_uc001ksq.2_Missense_Mutation_p.S295C	NM_030971	NP_112233	Q9BWM7	SFXN3_HUMAN	sideroflexin 3	295					iron ion homeostasis	integral to membrane|mitochondrial membrane	cation transmembrane transporter activity			ovary(1)	1		Colorectal(252;0.234)		Epithelial(162;6.98e-09)|all cancers(201;3.55e-07)										0.03629	-34.820025	23.000592	9	239	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	102799248	102799248	14687	10	C	G	G	G	390	30	SFXN3	3	3
RAB11FIP2	22841	broad.mit.edu	37	10	119798615	119798615	+	Missense_Mutation	SNP	C	A	A			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:119798615C>A	uc009xyz.1	-	c.1133G>T	c.(1132-1134)GGG>GTG	p.G378V	RAB11FIP2_uc001ldj.1_Missense_Mutation_p.G378V	NM_014904	NP_055719	Q7L804	RFIP2_HUMAN	RAB11 family interacting protein 2	378					protein transport	plasma membrane|recycling endosome membrane	protein homodimerization activity				0		Colorectal(252;0.235)		all cancers(201;0.0238)										0.356688	135.733527	138.583253	56	101	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	119798615	119798615	13353	10	C	A	A	A	286	22	RAB11FIP2	2	2
KNDC1	85442	broad.mit.edu	37	10	134999869	134999869	+	Silent	SNP	G	T	T	rs35998551	by1000genomes	TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:134999869G>T	uc001llz.1	+	c.1017G>T	c.(1015-1017)CCG>CCT	p.P339P	KNDC1_uc001lma.1_Silent_p.P274P	NM_152643	NP_689856	Q76NI1	VKIND_HUMAN	kinase non-catalytic C-lobe domain (KIND)	339					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)		OV - Ovarian serous cystadenocarcinoma(35;8.77e-06)|Epithelial(32;1.13e-05)|all cancers(32;1.51e-05)										0.078947	0.300151	7.175584	3	35	KEEP	---	---	---	---	capture		Silent	SNP	134999869	134999869	8740	10	G	T	T	T	496	39	KNDC1	1	1
MRPS16	51021	broad.mit.edu	37	10	75010727	75010727	+	Silent	SNP	C	A	A			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:75010727C>A	uc001jts.1	-	c.297G>T	c.(295-297)CTG>CTT	p.L99L	DNAJC9_uc010qkg.1_5'Flank|MRPS16_uc010qkh.1_Intron|MRPS16_uc001jtt.1_Non-coding_Transcript	NM_016065	NP_057149	Q9Y3D3	RT16_HUMAN	mitochondrial ribosomal protein S16 precursor	99					translation	mitochondrial small ribosomal subunit	protein binding|structural constituent of ribosome				0	Prostate(51;0.0119)													0.343023	156.358875	160.109644	59	113	KEEP	---	---	---	---	capture		Silent	SNP	75010727	75010727	10219	10	C	A	A	A	314	25	MRPS16	2	2
MRPS16	51021	broad.mit.edu	37	10	75011685	75011685	+	Missense_Mutation	SNP	G	C	C			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:75011685G>C	uc001jts.1	-	c.110C>G	c.(109-111)GCT>GGT	p.A37G	MRPS16_uc010qkh.1_Non-coding_Transcript|MRPS16_uc001jtt.1_Non-coding_Transcript	NM_016065	NP_057149	Q9Y3D3	RT16_HUMAN	mitochondrial ribosomal protein S16 precursor	37					translation	mitochondrial small ribosomal subunit	protein binding|structural constituent of ribosome				0	Prostate(51;0.0119)													0.125	1.964466	6.435114	4	28	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	75011685	75011685	10219	10	G	C	C	C	442	34	MRPS16	3	3
CYP2C8	1558	broad.mit.edu	37	10	96818250	96818250	+	Missense_Mutation	SNP	G	C	C			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:96818250G>C	uc001kkb.2	-	c.661C>G	c.(661-663)CTA>GTA	p.L221V	CYP2C8_uc001kkc.2_Non-coding_Transcript|CYP2C8_uc010qoa.1_Missense_Mutation_p.L151V|CYP2C8_uc010qob.1_Missense_Mutation_p.L135V|CYP2C8_uc010qoc.1_Missense_Mutation_p.L119V|CYP2C8_uc010qod.1_Missense_Mutation_p.L135V	NM_000770	NP_000761	P10632	CP2C8_HUMAN	cytochrome P450, family 2, subfamily C,	221					exogenous drug catabolic process|organic acid metabolic process|oxidative demethylation|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	aromatase activity|caffeine oxidase activity|electron carrier activity|heme binding|oxygen binding				0		Colorectal(252;0.0397)		all cancers(201;6.21e-05)	Aminophenazone(DB01424)|Amiodarone(DB01118)|Amodiaquine(DB00613)|Benzphetamine(DB00865)|Carbamazepine(DB00564)|Cerivastatin(DB00439)|Diclofenac(DB00586)|Fluvastatin(DB01095)|Fosphenytoin(DB01320)|Gemfibrozil(DB01241)|Ketoconazole(DB01026)|Lapatinib(DB01259)|Lovastatin(DB00227)|Midazolam(DB00683)|Montelukast(DB00471)|Nicardipine(DB00622)|Paclitaxel(DB01229)|Phenytoin(DB00252)|Pioglitazone(DB01132)|Repaglinide(DB00912)|Rifampin(DB01045)|Rosiglitazone(DB00412)|Simvastatin(DB00641)|Sitagliptin(DB01261)|Tolbutamide(DB01124)|Torasemide(DB00214)|Tretinoin(DB00755)|Trimethoprim(DB00440)|Warfarin(DB00682)|Zafirlukast(DB00549)|Zopiclone(DB01198)									0.303571	58.953635	60.881846	17	39	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	96818250	96818250	4332	10	G	C	C	C	425	33	CYP2C8	3	3
TMEM123	114908	broad.mit.edu	37	11	102272716	102272716	+	Missense_Mutation	SNP	G	C	C			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:102272716G>C	uc001pha.2	-	c.379C>G	c.(379-381)CAG>GAG	p.Q127E	TMEM123_uc009yxc.2_Missense_Mutation_p.Q108E	NM_052932	NP_443164	Q8N131	PORIM_HUMAN	transmembrane protein 123 precursor	127	Thr-rich.|Extracellular (Potential).				oncosis	external side of plasma membrane|integral to membrane	receptor activity			breast(2)	2	all_cancers(8;0.00027)|all_epithelial(12;0.0021)|Lung NSC(15;0.227)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0033)	Epithelial(9;0.0314)|Lung(13;0.109)|all cancers(10;0.12)|LUSC - Lung squamous cell carcinoma(19;0.151)	BRCA - Breast invasive adenocarcinoma(274;0.0149)						67				0.050167	-25.014549	39.122257	15	284	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	102272716	102272716	16567	11	G	C	C	C	585	45	TMEM123	3	3
VPS11	55823	broad.mit.edu	37	11	118948942	118948942	+	Silent	SNP	C	T	T			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:118948942C>T	uc010ryx.1	+	c.1821C>T	c.(1819-1821)TTC>TTT	p.F607F	VPS11_uc010ryy.1_Silent_p.F453F	NM_021729	NP_068375	Q9H270	VPS11_HUMAN	vacuolar protein sorting 11	607					protein transport	cytoplasmic membrane-bounded vesicle|HOPS complex|late endosome membrane|lysosomal membrane	nucleotide binding|protein binding|zinc ion binding			ovary(2)|central_nervous_system(1)	3	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.88e-05)										0.032609	-51.752816	14.136124	9	267	KEEP	---	---	---	---	capture		Silent	SNP	118948942	118948942	17755	11	C	T	T	T	389	30	VPS11	2	2
SORL1	6653	broad.mit.edu	37	11	121420743	121420743	+	Missense_Mutation	SNP	C	T	T			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:121420743C>T	uc001pxx.2	+	c.2126C>T	c.(2125-2127)TCA>TTA	p.S709L		NM_003105	NP_003096	Q92673	SORL_HUMAN	sortilin-related receptor containing LDLR class	709	Extracellular (Potential).				cholesterol metabolic process|lipid transport|receptor-mediated endocytosis	integral to plasma membrane|low-density lipoprotein particle	low-density lipoprotein particle binding|transmembrane receptor activity			ovary(5)|breast(4)|large_intestine(2)|central_nervous_system(1)|pancreas(1)	13		Breast(109;0.00119)|Medulloblastoma(222;0.0429)|all_neural(223;0.113)		BRCA - Breast invasive adenocarcinoma(274;3.34e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.108)						937				0.066667	-9.404904	13.970802	8	112	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	121420743	121420743	15434	11	C	T	T	T	377	29	SORL1	2	2
MUC5B	727897	broad.mit.edu	37	11	1275485	1275485	+	Silent	SNP	C	A	A			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:1275485C>A	uc009ycr.1	+	c.16386C>A	c.(16384-16386)GCC>GCA	p.A5462A	MUC5B_uc001ltb.2_Silent_p.A5130A	NM_017511	NP_059981	Q9HC84	MUC5B_HUMAN	SubName: Full=Mucin 5AC, oligomeric mucus/gel-forming;	5126	VWFD 4.				cell adhesion	extracellular region	extracellular matrix structural constituent|protein binding				0		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)										0.482759	36.943173	36.950864	14	15	KEEP	---	---	---	---	capture		Silent	SNP	1275485	1275485	10373	11	C	A	A	A	288	23	MUC5B	1	1
KCNJ5	3762	broad.mit.edu	37	11	128781480	128781480	+	Silent	SNP	C	T	T			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:128781480C>T	uc001qet.2	+	c.312C>T	c.(310-312)TTC>TTT	p.F104F	KCNJ5_uc009zck.2_Silent_p.F104F|KCNJ5_uc001qew.2_Silent_p.F104F	NM_000890	NP_000881	P48544	IRK5_HUMAN	potassium inwardly-rectifying channel J5	104	Helical; Name=M1; (By similarity).				synaptic transmission	voltage-gated potassium channel complex	G-protein activated inward rectifier potassium channel activity|protein binding				0	all_hematologic(175;0.0641)	Lung NSC(97;0.00038)|all_lung(97;0.000817)|Breast(109;0.00123)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)		OV - Ovarian serous cystadenocarcinoma(99;0.0059)|LUSC - Lung squamous cell carcinoma(976;0.021)|Lung(977;0.0215)	Glibenclamide(DB01016)	Pancreas(108;2548 5082)|Esophageal Squamous(165;4544 6231)								0.090909	0.598912	22.880335	12	120	KEEP	---	---	---	---	capture		Silent	SNP	128781480	128781480	8359	11	C	T	T	T	402	31	KCNJ5	1	1
SLC6A5	9152	broad.mit.edu	37	11	20622793	20622793	+	Missense_Mutation	SNP	C	T	T			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:20622793C>T	uc001mqd.2	+	c.122C>T	c.(121-123)CCC>CTC	p.P41L	SLC6A5_uc009yic.2_5'UTR	NM_004211	NP_004202	Q9Y345	SC6A5_HUMAN	solute carrier family 6 (neurotransmitter	41	Cytoplasmic (Potential).				synaptic transmission	integral to plasma membrane	glycine:sodium symporter activity|neurotransmitter:sodium symporter activity			ovary(2)|breast(1)	3					Glycine(DB00145)									0.75	10.053933	10.256016	3	1	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	20622793	20622793	15184	11	C	T	T	T	286	22	SLC6A5	2	2
ZNF195	7748	broad.mit.edu	37	11	3380816	3380816	+	Silent	SNP	G	A	A			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:3380816G>A	uc001lxt.2	-	c.1422C>T	c.(1420-1422)GTC>GTT	p.V474V	ZNF195_uc001lxv.2_Silent_p.V451V|ZNF195_uc001lxs.2_Silent_p.V402V|ZNF195_uc010qxr.1_Silent_p.V455V|ZNF195_uc009ydz.2_Silent_p.V429V|ZNF195_uc001lxu.2_Silent_p.V406V	NM_001130520	NP_001123992	O14628	ZN195_HUMAN	zinc finger protein 195 isoform 1	474	C2H2-type 5.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Medulloblastoma(188;0.00106)|Breast(177;0.00328)|all_neural(188;0.00681)|Ovarian(85;0.00965)		BRCA - Breast invasive adenocarcinoma(625;0.0361)|LUSC - Lung squamous cell carcinoma(625;0.2)										0.412088	212.594994	213.821719	75	107	KEEP	---	---	---	---	capture		Silent	SNP	3380816	3380816	18349	11	G	A	A	A	418	33	ZNF195	2	2
OR5AS1	219447	broad.mit.edu	37	11	55798482	55798482	+	Missense_Mutation	SNP	G	T	T			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:55798482G>T	uc010riw.1	+	c.588G>T	c.(586-588)CAG>CAT	p.Q196H		NM_001001921	NP_001001921	Q8N127	O5AS1_HUMAN	olfactory receptor, family 5, subfamily AS,	196	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(3)|liver(1)	4	Esophageal squamous(21;0.00693)													0.336735	436.986936	448.558596	165	325	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	55798482	55798482	11556	11	G	T	T	T	438	34	OR5AS1	2	2
OR8H2	390151	broad.mit.edu	37	11	55873052	55873052	+	Silent	SNP	C	T	T			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:55873052C>T	uc010riy.1	+	c.534C>T	c.(532-534)TTC>TTT	p.F178F		NM_001005200	NP_001005200	Q8N162	OR8H2_HUMAN	olfactory receptor, family 8, subfamily H,	178	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1	Esophageal squamous(21;0.00693)													0.111782	33.711544	83.038158	37	294	KEEP	---	---	---	---	capture		Silent	SNP	55873052	55873052	11649	11	C	T	T	T	415	32	OR8H2	2	2
OR4D9	390199	broad.mit.edu	37	11	59282631	59282631	+	Silent	SNP	G	A	A			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:59282631G>A	uc010rkv.1	+	c.246G>A	c.(244-246)CTG>CTA	p.L82L		NM_001004711	NP_001004711	Q8NGE8	OR4D9_HUMAN	olfactory receptor, family 4, subfamily D,	82	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0														0.034314	-37.261558	10.929807	7	197	KEEP	---	---	---	---	capture		Silent	SNP	59282631	59282631	11466	11	G	A	A	A	574	45	OR4D9	2	2
PHRF1	57661	broad.mit.edu	37	11	609537	609537	+	Missense_Mutation	SNP	C	A	A			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:609537C>A	uc001lqe.2	+	c.4081C>A	c.(4081-4083)CCG>ACG	p.P1361T	PHRF1_uc010qwc.1_Missense_Mutation_p.P1360T|PHRF1_uc010qwd.1_Missense_Mutation_p.P1359T|PHRF1_uc010qwe.1_Missense_Mutation_p.P1357T|PHRF1_uc009ybz.1_Missense_Mutation_p.P1151T|PHRF1_uc009yca.1_Non-coding_Transcript	NM_020901	NP_065952	Q9P1Y6	PHRF1_HUMAN	PHD and ring finger domains 1	1361							RNA polymerase binding|zinc ion binding				0														0.272727	5.917969	6.431873	3	8	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	609537	609537	12285	11	C	A	A	A	286	22	PHRF1	2	2
OR52B2	255725	broad.mit.edu	37	11	6191554	6191554	+	Missense_Mutation	SNP	C	T	T			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:6191554C>T	uc010qzy.1	-	c.3G>A	c.(1-3)ATG>ATA	p.M1I		NM_001004052	NP_001004052	Q96RD2	O52B2_HUMAN	olfactory receptor, family 52, subfamily B,	1	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;3.69e-08)|BRCA - Breast invasive adenocarcinoma(625;0.135)		NSCLC(5;186 261 1778 7098 14207)								0.354839	55.32475	56.47929	22	40	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	6191554	6191554	11521	11	C	T	T	T	377	29	OR52B2	2	2
SLC3A2	6520	broad.mit.edu	37	11	62656063	62656063	+	Silent	SNP	C	T	T			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:62656063C>T	uc001nwb.2	+	c.1884C>T	c.(1882-1884)CTC>CTT	p.L628L	SLC3A2_uc001nwc.2_Silent_p.L598L|SLC3A2_uc001nwd.2_Silent_p.L597L|SLC3A2_uc001nwe.2_Silent_p.L566L|SLC3A2_uc001nwf.2_Silent_p.L535L|SLC3A2_uc001nwg.2_Silent_p.L496L	NM_001012661	NP_001012679	P08195	4F2_HUMAN	solute carrier family 3, member 2 isoform a	597	Extracellular (Potential).				blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport	apical plasma membrane|cell surface|integral to membrane|melanosome	calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding				0														0.225	33.211219	38.77195	18	62	KEEP	---	---	---	---	capture		Silent	SNP	62656063	62656063	15124	11	C	T	T	T	366	29	SLC3A2	2	2
RPS6KA4	8986	broad.mit.edu	37	11	64128005	64128005	+	Missense_Mutation	SNP	G	A	A			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:64128005G>A	uc001oae.2	+	c.403G>A	c.(403-405)GAG>AAG	p.E135K	RPS6KA4_uc001oad.2_Missense_Mutation_p.E135K|RPS6KA4_uc010rnl.1_Missense_Mutation_p.E72K|RPS6KA4_uc001oaf.2_Missense_Mutation_p.E135K|RPS6KA4_uc009ypp.2_Missense_Mutation_p.E135K	NM_003942	NP_003933	O75676	KS6A4_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide	135	Protein kinase 1.				axon guidance|intracellular protein kinase cascade|protein phosphorylation|regulation of transcription, DNA-dependent	cytoplasm|nucleus	ATP binding|magnesium ion binding|mitogen-activated protein kinase p38 binding|ribosomal protein S6 kinase activity			lung(3)|ovary(1)|breast(1)	5										85				0.235294	8.993094	10.081467	4	13	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	64128005	64128005	14133	11	G	A	A	A	533	41	RPS6KA4	2	2
NAALADL1	10004	broad.mit.edu	37	11	64813372	64813372	+	Missense_Mutation	SNP	C	A	A			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:64813372C>A	uc001ocn.2	-	c.1958G>T	c.(1957-1959)CGG>CTG	p.R653L	NAALADL1_uc010rnw.1_Missense_Mutation_p.R129L|NAALADL1_uc009ypz.2_Non-coding_Transcript	NM_005468	NP_005459	Q9UQQ1	NALDL_HUMAN	N-acetylated alpha-linked acidic	653	Extracellular (Potential).				proteolysis	apical plasma membrane|integral to membrane	carboxypeptidase activity|dipeptidase activity|metal ion binding|metallopeptidase activity				0														0.12	3.013576	6.550777	3	22	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	64813372	64813372	10524	11	C	A	A	A	299	23	NAALADL1	1	1
ACER3	55331	broad.mit.edu	37	11	76637694	76637694	+	Missense_Mutation	SNP	C	T	T			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:76637694C>T	uc009yum.1	+	c.197C>T	c.(196-198)TCT>TTT	p.S66F	ACER3_uc010rsg.1_Missense_Mutation_p.S24F|ACER3_uc009yul.1_Non-coding_Transcript|ACER3_uc001oxu.2_Non-coding_Transcript|ACER3_uc009yun.1_Missense_Mutation_p.S24F|ACER3_uc009yuo.1_5'UTR|ACER3_uc010rsh.1_Intron|ACER3_uc010rsi.1_5'UTR|ACER3_uc010rsj.1_5'UTR	NM_018367	NP_060837	Q9NUN7	ACER3_HUMAN	phytoceramidase, alkaline	66	Helical; (Potential).				ceramide metabolic process|phytosphingosine biosynthetic process|positive regulation of cell proliferation|sphingosine biosynthetic process	integral to endoplasmic reticulum membrane|integral to Golgi membrane	phytoceramidase activity				0														0.155844	21.642295	30.361671	12	65	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	76637694	76637694	141	11	C	T	T	T	416	32	ACER3	2	2
DEPDC4	120863	broad.mit.edu	37	12	100649949	100649949	+	Missense_Mutation	SNP	G	C	C			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:100649949G>C	uc009ztv.1	-	c.756C>G	c.(754-756)TTC>TTG	p.F252L	DEPDC4_uc001thh.1_Non-coding_Transcript|DEPDC4_uc001thi.2_Missense_Mutation_p.F252L|DEPDC4_uc001thj.1_Missense_Mutation_p.F198L|DEPDC4_uc001thk.1_Missense_Mutation_p.F63L|DEPDC4_uc001thl.1_Non-coding_Transcript	NM_152317	NP_689530	Q8N2C3	DEPD4_HUMAN	DEP domain containing 4	252					intracellular signal transduction						0														0.045977	-9.279399	9.864079	4	83	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	100649949	100649949	4620	12	G	C	C	C	425	33	DEPDC4	3	3
TAS2R31	259290	broad.mit.edu	37	12	11183031	11183031	+	Missense_Mutation	SNP	T	C	C			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:11183031T>C	uc001qzo.1	-	c.904A>G	c.(904-906)AAA>GAA	p.K302E	PRR4_uc009zhp.2_Intron|PRH1_uc001qzb.3_Intron|PRH1_uc001qzc.2_Intron|PRB4_uc001qzf.1_Intron|PRH1_uc001qzj.2_Intron	NM_176885	NP_795366	P59538	T2R31_HUMAN	taste receptor, type 2, member 31	302	Cytoplasmic (Potential).				sensory perception of taste	integral to membrane	G-protein coupled receptor activity				0														0.030172	-39.153697	17.008872	7	225	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	11183031	11183031	16096	12	T	C	C	C	806	62	TAS2R31	4	4
GALNT8	26290	broad.mit.edu	37	12	4870202	4870202	+	Missense_Mutation	SNP	G	T	T			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:4870202G>T	uc001qne.1	+	c.1252G>T	c.(1252-1254)GCC>TCC	p.A418S		NM_017417	NP_059113	Q9NY28	GALT8_HUMAN	polypeptide N-acetylgalactosaminyltransferase 8	418	Lumenal (Potential).					Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			ovary(1)|pancreas(1)	2						Colon(108;631 1558 7270 20097 39846)								0.429825	143.055278	143.544828	49	65	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	4870202	4870202	6483	12	G	T	T	T	494	38	GALNT8	1	1
KCNA1	3736	broad.mit.edu	37	12	5020578	5020578	+	Missense_Mutation	SNP	G	A	A			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:5020578G>A	uc001qnh.2	+	c.34G>A	c.(34-36)GCT>ACT	p.A12T		NM_000217	NP_000208	Q09470	KCNA1_HUMAN	potassium voltage-gated channel subfamily A	12					synaptic transmission	juxtaparanode region of axon|voltage-gated potassium channel complex	delayed rectifier potassium channel activity|potassium ion transmembrane transporter activity			ovary(1)	1					Desflurane(DB01189)|Enflurane(DB00228)|Isoflurane(DB00753)|Methoxyflurane(DB01028)|Sevoflurane(DB01236)									0.361111	33.291682	33.89137	13	23	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	5020578	5020578	8306	12	G	A	A	A	546	42	KCNA1	2	2
PDE1B	5153	broad.mit.edu	37	12	54968907	54968907	+	Missense_Mutation	SNP	C	G	G			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:54968907C>G	uc001sgd.1	+	c.1090C>G	c.(1090-1092)CTA>GTA	p.L364V	PDE1B_uc010soz.1_Missense_Mutation_p.L227V|PDE1B_uc010spa.1_Missense_Mutation_p.L323V|PDE1B_uc001sgf.2_Missense_Mutation_p.L227V|PDE1B_uc001sge.2_Missense_Mutation_p.L344V|PDE1B_uc009znq.2_Missense_Mutation_p.L160V	NM_000924	NP_000915	Q01064	PDE1B_HUMAN	phosphodiesterase 1B isoform 1	364	Catalytic (By similarity).				activation of phospholipase C activity|apoptosis|nerve growth factor receptor signaling pathway|platelet activation	cytosol|nucleus	3',5'-cyclic-AMP phosphodiesterase activity|calmodulin binding|calmodulin-dependent cyclic-nucleotide phosphodiesterase activity|metal ion binding			ovary(1)	1														0.035714	-20.253706	12.519987	5	135	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	54968907	54968907	12055	12	C	G	G	G	415	32	PDE1B	3	3
BAZ2A	11176	broad.mit.edu	37	12	57009066	57009066	+	Missense_Mutation	SNP	A	T	T			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:57009066A>T	uc001slq.1	-	c.468T>A	c.(466-468)AGT>AGA	p.S156R	BAZ2A_uc001slp.1_Missense_Mutation_p.S154R|BAZ2A_uc010sqr.1_Missense_Mutation_p.S156R|BAZ2A_uc009zow.1_Missense_Mutation_p.S154R	NM_013449	NP_038477	Q9UIF9	BAZ2A_HUMAN	bromodomain adjacent to zinc finger domain, 2A	156					chromatin silencing at rDNA|DNA methylation|transcription, DNA-dependent	chromatin silencing complex|nucleolus|rDNA heterochromatin	DNA binding|histone acetyl-lysine binding|ligand-dependent nuclear receptor binding|RNA binding|transcription regulator activity|zinc ion binding				0														0.369231	56.570743	57.551783	24	41	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	57009066	57009066	1352	12	A	T	T	T	128	10	BAZ2A	3	3
INHBE	83729	broad.mit.edu	37	12	57850041	57850041	+	Missense_Mutation	SNP	C	T	T			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:57850041C>T	uc001snw.2	+	c.463C>T	c.(463-465)CGC>TGC	p.R155C		NM_031479	NP_113667	P58166	INHBE_HUMAN	activin beta E precursor	155					growth	extracellular region	growth factor activity|hormone activity			breast(2)|central_nervous_system(1)	3						GBM(191;1808 2166 15720 36624 50371)						OREG0021944	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.389744	428.591141	432.715388	152	238	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	57850041	57850041	8045	12	C	T	T	T	299	23	INHBE	1	1
CCT2	10576	broad.mit.edu	37	12	69993722	69993722	+	Silent	SNP	G	C	C			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:69993722G>C	uc001svb.1	+	c.1515G>C	c.(1513-1515)CTG>CTC	p.L505L	CCT2_uc009zrm.1_Non-coding_Transcript|CCT2_uc009zrn.1_Intron|CCT2_uc010stl.1_Silent_p.L458L	NM_006431	NP_006422	P78371	TCPB_HUMAN	chaperonin containing TCP1, subunit 2	505					'de novo' posttranslational protein folding	nucleus	ATP binding|unfolded protein binding			central_nervous_system(1)|skin(1)	2	all_cancers(2;7.7e-106)|Breast(13;2.15e-06)|Esophageal squamous(21;0.187)		Epithelial(6;2.72e-18)|GBM - Glioblastoma multiforme(2;2.58e-10)|Lung(24;0.000185)|OV - Ovarian serous cystadenocarcinoma(12;0.00126)|STAD - Stomach adenocarcinoma(21;0.00501)|Kidney(9;0.143)|LUSC - Lung squamous cell carcinoma(43;0.24)											0.05618	-5.103874	13.325883	5	84	KEEP	---	---	---	---	capture		Silent	SNP	69993722	69993722	3080	12	G	C	C	C	574	45	CCT2	3	3
RCBTB1	55213	broad.mit.edu	37	13	50123709	50123709	+	Missense_Mutation	SNP	C	G	G			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:50123709C>G	uc001vde.1	-	c.930G>C	c.(928-930)TGG>TGC	p.W310C		NM_018191	NP_060661	Q8NDN9	RCBT1_HUMAN	regulator of chromosome condensation (RCC1) and	310	RCC1 6.				cell cycle|chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus					0		Lung NSC(96;2.1e-05)|Breast(56;0.00015)|Prostate(109;0.00314)|Hepatocellular(98;0.0207)|Myeloproliferative disorder(33;0.163)|Lung SC(185;0.187)|all_neural(104;0.19)	KIRC - Kidney renal clear cell carcinoma(9;0.206)	GBM - Glioblastoma multiforme(99;4.7e-09)										0.177419	20.070231	26.190306	11	51	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	50123709	50123709	13640	13	C	G	G	G	286	22	RCBTB1	3	3
FBXL3	26224	broad.mit.edu	37	13	77589622	77589622	+	Missense_Mutation	SNP	G	C	C			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:77589622G>C	uc001vkd.2	-	c.565C>G	c.(565-567)CTC>GTC	p.L189V		NM_012158	NP_036290	Q9UKT7	FBXL3_HUMAN	F-box and leucine-rich repeat protein 3	189	LRR 2.				regulation of circadian rhythm|rhythmic process|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process	cytoplasm|nucleus|SCF ubiquitin ligase complex	protein binding|ubiquitin-protein ligase activity				0		Breast(118;0.212)|Acute lymphoblastic leukemia(28;0.218)		GBM - Glioblastoma multiforme(99;0.0521)										0.153285	49.08196	64.834794	21	116	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	77589622	77589622	5957	13	G	C	C	C	429	33	FBXL3	3	3
AHNAK2	113146	broad.mit.edu	37	14	105413013	105413013	+	Silent	SNP	C	T	T			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:105413013C>T	uc010axc.1	-	c.8775G>A	c.(8773-8775)CTG>CTA	p.L2925L	AHNAK2_uc001ypx.2_Silent_p.L2825L	NM_138420	NP_612429	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	2925						nucleus				ovary(1)	1		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)											0.039604	-67.069745	25.35107	16	388	KEEP	---	---	---	---	capture		Silent	SNP	105413013	105413013	418	14	C	T	T	T	366	29	AHNAK2	2	2
AHNAK2	113146	broad.mit.edu	37	14	105413043	105413043	+	Missense_Mutation	SNP	C	G	G			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:105413043C>G	uc010axc.1	-	c.8745G>C	c.(8743-8745)CAG>CAC	p.Q2915H	AHNAK2_uc001ypx.2_Missense_Mutation_p.Q2815H	NM_138420	NP_612429	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	2915						nucleus				ovary(1)	1		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)											0.038902	-62.227218	38.180623	17	420	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	105413043	105413043	418	14	C	G	G	G	415	32	AHNAK2	3	3
SIPA1L1	26037	broad.mit.edu	37	14	72152196	72152196	+	Missense_Mutation	SNP	G	T	T			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:72152196G>T	uc001xms.2	+	c.3222G>T	c.(3220-3222)AAG>AAT	p.K1074N	SIPA1L1_uc001xmt.2_Missense_Mutation_p.K1074N|SIPA1L1_uc001xmu.2_Missense_Mutation_p.K1074N|SIPA1L1_uc001xmv.2_Missense_Mutation_p.K1074N|SIPA1L1_uc010ttm.1_Missense_Mutation_p.K549N	NM_015556	NP_056371	O43166	SI1L1_HUMAN	signal-induced proliferation-associated 1 like	1074					actin cytoskeleton reorganization|activation of Rap GTPase activity|regulation of dendritic spine morphogenesis	cell junction|cytoplasm|dendritic spine|postsynaptic density|postsynaptic membrane|synaptosome	GTPase activator activity			ovary(3)|breast(1)	4				all cancers(60;0.00169)|BRCA - Breast invasive adenocarcinoma(234;0.00912)|OV - Ovarian serous cystadenocarcinoma(108;0.0109)										0.605634	233.232301	234.610162	86	56	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	72152196	72152196	14824	14	G	T	T	T	451	35	SIPA1L1	2	2
GABRB3	2562	broad.mit.edu	37	15	26793029	26793029	+	Missense_Mutation	SNP	C	T	T			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:26793029C>T	uc001zbb.2	-	c.1501G>A	c.(1501-1503)GTG>ATG	p.V501M	GABRB3_uc010uae.1_Missense_Mutation_p.V360M|GABRB3_uc001zaz.2_Missense_Mutation_p.V445M|GABRB3_uc001zba.2_Missense_Mutation_p.V445M	NM_021912	NP_068712	P28472	GBRB3_HUMAN	gamma-aminobutyric acid (GABA) A receptor, beta	445	Cytoplasmic (Probable).				synaptic transmission	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity			ovary(1)|lung(1)|liver(1)|central_nervous_system(1)	4		all_cancers(20;1.89e-22)|all_lung(180;6.35e-15)|Breast(32;0.000279)|Colorectal(260;0.232)		all cancers(64;1.46e-07)|Epithelial(43;2.89e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0251)|COAD - Colon adenocarcinoma(236;0.235)|Lung(196;0.243)	Ethchlorvynol(DB00189)|Flurazepam(DB00690)|Lorazepam(DB00186)|Midazolam(DB00683)									0.335878	106.246621	109.37483	44	87	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	26793029	26793029	6419	15	C	T	T	T	221	17	GABRB3	2	2
BUB1B	701	broad.mit.edu	37	15	40505533	40505533	+	Missense_Mutation	SNP	G	A	A			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:40505533G>A	uc001zkx.3	+	c.2536G>A	c.(2536-2538)GAT>AAT	p.D846N		NM_001211	NP_001202	O60566	BUB1B_HUMAN	budding uninhibited by benzimidazoles 1 beta	846	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)		GBM - Glioblastoma multiforme(113;1.83e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0556)						298				0.351648	87.569351	89.337312	32	59	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	40505533	40505533	1605	15	G	A	A	A	533	41	BUB1B	2	2
OIP5	11339	broad.mit.edu	37	15	41624440	41624440	+	Missense_Mutation	SNP	G	A	A			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:41624440G>A	uc001znp.2	-	c.320C>T	c.(319-321)TCC>TTC	p.S107F	NUSAP1_uc001znq.3_5'Flank|NUSAP1_uc001znr.3_5'Flank|NUSAP1_uc001zns.3_5'Flank|NUSAP1_uc010bce.2_5'Flank|NUSAP1_uc001znt.3_5'Flank|NUSAP1_uc001znv.3_5'Flank|NUSAP1_uc001znu.3_5'Flank|NUSAP1_uc010ucw.1_5'Flank	NM_007280	NP_009211	O43482	MS18B_HUMAN	Opa interacting protein 5	107					cell communication|cell division|CenH3-containing nucleosome assembly at centromere|mitosis	Cajal body|chromatin|chromosome, centromeric region	protein binding				0		all_cancers(109;4.16e-14)|all_epithelial(112;7.09e-12)|Lung NSC(122;1.14e-09)|all_lung(180;2.56e-08)|Melanoma(134;0.091)|Colorectal(260;0.175)		OV - Ovarian serous cystadenocarcinoma(18;1.49e-16)|GBM - Glioblastoma multiforme(113;1.29e-06)|BRCA - Breast invasive adenocarcinoma(123;0.163)								OREG0023073	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.129032	7.444607	15.788853	8	54	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	41624440	41624440	11253	15	G	A	A	A	533	41	OIP5	2	2
JMJD7-PLA2G4B	8681	broad.mit.edu	37	15	42139578	42139578	+	Missense_Mutation	SNP	C	T	T			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:42139578C>T	uc001zoo.3	+	c.2684C>T	c.(2683-2685)CCG>CTG	p.P895L	JMJD7-PLA2G4B_uc010bcn.2_Intron|JMJD7-PLA2G4B_uc001zoq.3_Missense_Mutation_p.P365L|JMJD7-PLA2G4B_uc010bco.2_Missense_Mutation_p.P664L	NM_005090	NP_005081	P0C869	PA24B_HUMAN	JMJD7-PLA2G4B protein	664	PLA2c.				arachidonic acid metabolic process|calcium-mediated signaling|glycerophospholipid catabolic process|inflammatory response|parturition	cytosol|early endosome membrane|extracellular region|mitochondrial membrane	calcium ion binding|calcium-dependent phospholipase A2 activity|calcium-dependent phospholipid binding|lysophospholipase activity			large_intestine(1)	1														0.27933	124.075801	131.914248	50	129	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	42139578	42139578	8259	15	C	T	T	T	299	23	JMJD7-PLA2G4B	1	1
LCMT2	9836	broad.mit.edu	37	15	43620678	43620678	+	Missense_Mutation	SNP	G	C	C			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:43620678G>C	uc001zrg.2	-	c.2010C>G	c.(2008-2010)TTC>TTG	p.F670L	LCMT2_uc010udn.1_Missense_Mutation_p.F249L|ADAL_uc001zrh.2_5'Flank|ADAL_uc010udo.1_5'Flank	NM_014793	NP_055608	O60294	LCMT2_HUMAN	leucine carboxyl methyltransferase 2	670					tRNA processing		methyltransferase activity|protein binding				0		all_cancers(109;2.12e-14)|all_epithelial(112;1.99e-12)|Lung NSC(122;2.46e-08)|all_lung(180;2.75e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;8.1e-07)	L-Leucine(DB00149)									0.108108	24.184662	46.720295	16	132	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	43620678	43620678	9003	15	G	C	C	C	581	45	LCMT2	3	3
LCMT2	9836	broad.mit.edu	37	15	43622436	43622436	+	Missense_Mutation	SNP	C	G	G			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:43622436C>G	uc001zrg.2	-	c.252G>C	c.(250-252)CAG>CAC	p.Q84H	LCMT2_uc010udn.1_Intron|ADAL_uc001zrh.2_5'Flank|ADAL_uc010udo.1_5'Flank	NM_014793	NP_055608	O60294	LCMT2_HUMAN	leucine carboxyl methyltransferase 2	84					tRNA processing		methyltransferase activity|protein binding				0		all_cancers(109;2.12e-14)|all_epithelial(112;1.99e-12)|Lung NSC(122;2.46e-08)|all_lung(180;2.75e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;8.1e-07)	L-Leucine(DB00149)									0.074074	0.754746	10.817083	4	50	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	43622436	43622436	9003	15	C	G	G	G	415	32	LCMT2	3	3
GCNT3	9245	broad.mit.edu	37	15	59910672	59910672	+	Missense_Mutation	SNP	G	C	C			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:59910672G>C	uc002age.2	+	c.235G>C	c.(235-237)GAG>CAG	p.E79Q	GCNT3_uc002agd.2_Missense_Mutation_p.E79Q	NM_004751	NP_004742	O95395	GCNT3_HUMAN	glucosaminyl (N-acetyl) transferase 3, mucin	79	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														0.028112	-44.710308	16.390831	7	242	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	59910672	59910672	6568	15	G	C	C	C	429	33	GCNT3	3	3
THSD4	79875	broad.mit.edu	37	15	72020963	72020963	+	Missense_Mutation	SNP	G	T	T			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:72020963G>T	uc002atb.1	+	c.1433G>T	c.(1432-1434)GGA>GTA	p.G478V	THSD4_uc002atd.1_Missense_Mutation_p.G152V|THSD4_uc010ukg.1_Missense_Mutation_p.G118V|THSD4_uc002ate.2_Missense_Mutation_p.G118V	NM_024817	NP_079093	Q6ZMP0	THSD4_HUMAN	thrombospondin, type I, domain containing 4	478						proteinaceous extracellular matrix	metalloendopeptidase activity			ovary(2)	2														0.041667	-33.419681	10.098571	8	184	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	72020963	72020963	16406	15	G	T	T	T	533	41	THSD4	2	2
MAN2C1	4123	broad.mit.edu	37	15	75654689	75654689	+	Missense_Mutation	SNP	C	G	G			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:75654689C>G	uc002baf.2	-	c.1003G>C	c.(1003-1005)GAG>CAG	p.E335Q	MAN2C1_uc002bag.2_Missense_Mutation_p.E335Q|MAN2C1_uc002bah.2_Missense_Mutation_p.E335Q|MAN2C1_uc010bkk.2_Missense_Mutation_p.E236Q|MAN2C1_uc010umi.1_Missense_Mutation_p.E117Q|MAN2C1_uc010umj.1_Non-coding_Transcript	NM_006715	NP_006706	Q9NTJ4	MA2C1_HUMAN	mannosidase, alpha, class 2C, member 1	335					mannose metabolic process		alpha-mannosidase activity|carbohydrate binding|protein binding|zinc ion binding				0														0.155556	17.306556	22.395533	7	38	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	75654689	75654689	9601	15	C	G	G	G	390	30	MAN2C1	3	3
IL16	3603	broad.mit.edu	37	15	81592196	81592196	+	Silent	SNP	C	T	T			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:81592196C>T	uc010unp.1	+	c.2655C>T	c.(2653-2655)ATC>ATT	p.I885I	IL16_uc010blq.1_Silent_p.I797I|IL16_uc002bge.3_Non-coding_Transcript|IL16_uc002bgh.3_Silent_p.I843I|IL16_uc002bgg.2_Silent_p.I843I|IL16_uc002bgi.1_Silent_p.I233I|IL16_uc002bgj.2_Silent_p.I337I|IL16_uc002bgk.2_Silent_p.I142I|IL16_uc002bgl.1_Silent_p.I142I|IL16_uc010unq.1_Silent_p.I142I	NM_172217	NP_757366	Q14005	IL16_HUMAN	interleukin 16 isoform 2	843					immune response|interspecies interaction between organisms|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|extracellular space|nucleus|plasma membrane	cytokine activity			ovary(2)|lung(1)|skin(1)	4														0.081967	-2.778391	8.091694	5	56	KEEP	---	---	---	---	capture		Silent	SNP	81592196	81592196	7934	15	C	T	T	T	369	29	IL16	2	2
RBBP6	5930	broad.mit.edu	37	16	24581790	24581790	+	Missense_Mutation	SNP	G	T	T			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:24581790G>T	uc002dmh.2	+	c.3779G>T	c.(3778-3780)GGA>GTA	p.G1260V	RBBP6_uc010vcb.1_Missense_Mutation_p.G1127V|RBBP6_uc002dmi.2_Missense_Mutation_p.G1226V|RBBP6_uc010bxr.2_Intron|RBBP6_uc002dmk.2_Missense_Mutation_p.G1093V	NM_006910	NP_008841	Q7Z6E9	RBBP6_HUMAN	retinoblastoma-binding protein 6 isoform 1	1260					protein ubiquitination involved in ubiquitin-dependent protein catabolic process	chromosome|nucleolus|ubiquitin ligase complex	nucleic acid binding|protein binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(3)|pancreas(1)	4				GBM - Glioblastoma multiforme(48;0.0518)										0.380952	58.673741	59.460432	24	39	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	24581790	24581790	13564	16	G	T	T	T	533	41	RBBP6	2	2
CDH11	1009	broad.mit.edu	37	16	65038648	65038649	+	Missense_Mutation	DNP	CC	AA	AA			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:65038648_65038649CC>AA	uc002eoi.2	-	c.124_125GG>TT	c.(124-126)GGC>TTC	p.G42F	CDH11_uc010cdn.2_Non-coding_Transcript|CDH11_uc002eoj.2_Missense_Mutation_p.G42F|CDH11_uc010vin.1_Intron|CDH11_uc010vio.1_Missense_Mutation_p.G42F	NM_001797	NP_001788	P55287	CAD11_HUMAN	cadherin 11, type 2 preproprotein	42					adherens junction organization|cell junction assembly|homophilic cell adhesion|ossification|skeletal system development	integral to membrane|plasma membrane	calcium ion binding|protein binding			lung(7)|ovary(2)	9		Ovarian(137;0.0973)		OV - Ovarian serous cystadenocarcinoma(108;0.205)						239	TSP Lung(24;0.17)			0.307692	20.300585	21.152111	8	18	KEEP	---	---	---	---	capture		Missense_Mutation	DNP	65038648	65038649	3226	16	CC	AA	AA	AA	338	26	CDH11	2	2
IRF8	3394	broad.mit.edu	37	16	85942710	85942710	+	Missense_Mutation	SNP	G	A	A	rs34712374		TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:85942710G>A	uc002fjh.2	+	c.289G>A	c.(289-291)GAC>AAC	p.D97N	IRF8_uc002fji.2_Missense_Mutation_p.D97N|IRF8_uc010chp.2_Non-coding_Transcript	NM_002163	NP_002154	Q02556	IRF8_HUMAN	interferon regulatory factor 8	97	IRF tryptophan pentad repeat.				interferon-gamma-mediated signaling pathway|negative regulation of transcription from RNA polymerase II promoter|type I interferon-mediated signaling pathway	nucleus	DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity			breast(2)|ovary(1)	3		Prostate(104;0.0771)												0.362319	67.25095	68.403964	25	44	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	85942710	85942710	8139	16	G	A	A	A	533	41	IRF8	2	2
CENPBD1	92806	broad.mit.edu	37	16	90038109	90038109	+	Silent	SNP	C	G	G			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:90038109C>G	uc002fpr.2	-	c.222G>C	c.(220-222)CTG>CTC	p.L74L	AFG3L1_uc002fps.1_5'Flank|AFG3L1_uc002fpt.1_5'Flank|AFG3L1_uc002fpu.1_5'Flank|AFG3L1_uc002fpv.1_5'Flank|AFG3L1_uc002fpw.1_5'Flank|AFG3L1_uc002fpx.1_5'Flank	NM_145039	NP_659476	B2RD01	CENP1_HUMAN	CENPB DNA-binding domains containing 1	74						chromosome, centromeric region|nucleus	DNA binding				0														0.173913	10.885278	13.19354	4	19	KEEP	---	---	---	---	capture		Silent	SNP	90038109	90038109	3361	16	C	G	G	G	366	29	CENPBD1	3	3
MYH1	4619	broad.mit.edu	37	17	10399410	10399410	+	Missense_Mutation	SNP	C	A	A			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:10399410C>A	uc002gmo.2	-	c.5026G>T	c.(5026-5028)GCT>TCT	p.A1676S		NM_005963	NP_005954	P12882	MYH1_HUMAN	myosin, heavy chain 1, skeletal muscle, adult	1676	Potential.					muscle myosin complex|myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|motor activity			ovary(10)|breast(3)|kidney(1)|skin(1)	15										585				0.294737	65.15286	68.740896	28	67	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	10399410	10399410	10424	17	C	A	A	A	338	26	MYH1	2	2
MYOCD	93649	broad.mit.edu	37	17	12655756	12655756	+	Missense_Mutation	SNP	G	A	A			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:12655756G>A	uc002gno.2	+	c.1151G>A	c.(1150-1152)CGA>CAA	p.R384Q	MYOCD_uc002gnn.2_Missense_Mutation_p.R384Q|MYOCD_uc002gnp.1_Missense_Mutation_p.R288Q|MYOCD_uc002gnq.2_Missense_Mutation_p.R103Q	NM_001146312	NP_001139784	Q8IZQ8	MYCD_HUMAN	myocardin isoform 1	384	SAP.				cardiac cell differentiation|positive regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of smooth muscle contraction|regulation of smooth muscle cell differentiation|transcription, DNA-dependent	nucleus	nucleic acid binding|transcription factor binding			central_nervous_system(2)|ovary(1)	3				UCEC - Uterine corpus endometrioid carcinoma (92;0.0969)										0.157895	17.448311	25.936084	12	64	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	12655756	12655756	10482	17	G	A	A	A	481	37	MYOCD	1	1
VTN	7448	broad.mit.edu	37	17	26696372	26696372	+	Missense_Mutation	SNP	C	T	T			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:26696372C>T	uc002hbc.2	-	c.607G>A	c.(607-609)GAG>AAG	p.E203K	SARM1_uc010wah.1_Intron|SEBOX_uc010crk.1_5'Flank|SARM1_uc010waj.1_Intron|SARM1_uc010crl.1_5'Flank	NM_000638	NP_000629	P04004	VTNC_HUMAN	vitronectin precursor	203	Hemopexin-like 1.				cell adhesion mediated by integrin|immune response|negative regulation of blood coagulation|negative regulation of endopeptidase activity|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of protein binding|positive regulation of receptor-mediated endocytosis|positive regulation of smooth muscle cell migration|positive regulation of vascular endothelial growth factor receptor signaling pathway|positive regulation of wound healing|smooth muscle cell-matrix adhesion	alphav-beta3 integrin-vitronectin complex|extracellular space	heparin binding|integrin binding|scavenger receptor activity			ovary(1)|kidney(1)	2	all_lung(13;0.000533)|Lung NSC(42;0.00171)			UCEC - Uterine corpus endometrioid carcinoma (53;0.153)	Urokinase(DB00013)									0.062992	-11.897129	13.375149	8	119	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	26696372	26696372	17806	17	C	T	T	T	403	31	VTN	1	1
FOXN1	8456	broad.mit.edu	37	17	26851622	26851622	+	Silent	SNP	C	G	G			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:26851622C>G	uc010crm.2	+	c.225C>G	c.(223-225)CCC>CCG	p.P75P	FOXN1_uc002hbj.2_Silent_p.P75P	NM_003593	NP_003584	O15353	FOXN1_HUMAN	forkhead box N1	75					defense response|embryo development|epithelial cell proliferation|keratinocyte differentiation|negative regulation of gene-specific transcription from RNA polymerase II promoter|organ morphogenesis|pattern specification process|regulation of sequence-specific DNA binding transcription factor activity|thymus development	transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding			skin(1)	1	Lung NSC(42;0.00431)													0.138889	17.716436	26.693759	10	62	KEEP	---	---	---	---	capture		Silent	SNP	26851622	26851622	6265	17	C	G	G	G	288	23	FOXN1	3	3
RAB11FIP4	84440	broad.mit.edu	37	17	29758831	29758831	+	Missense_Mutation	SNP	G	T	T			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:29758831G>T	uc002hgn.1	+	c.160G>T	c.(160-162)GTG>TTG	p.V54L		NM_032932	NP_116321	Q86YS3	RFIP4_HUMAN	RAB11 family interacting protein 4 (class II)	54	EF-hand.				cytokinesis|interspecies interaction between organisms|protein transport	cleavage furrow|cytoplasmic membrane-bounded vesicle|midbody|recycling endosome membrane	ADP-ribosylation factor binding|calcium ion binding|protein homodimerization activity|Rab GTPase binding				0		all_cancers(10;3.62e-13)|all_epithelial(10;0.000387)|all_lung(9;0.0132)|Breast(31;0.014)|all_hematologic(16;0.015)|Myeloproliferative disorder(56;0.0255)|Acute lymphoblastic leukemia(14;0.0259)|Ovarian(249;0.0423)|Lung NSC(157;0.066)												0.291667	48.430623	51.240318	21	51	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	29758831	29758831	13355	17	G	T	T	T	572	44	RAB11FIP4	2	2
ANKFN1	162282	broad.mit.edu	37	17	54450167	54450167	+	Silent	SNP	C	T	T			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:54450167C>T	uc002iun.1	+	c.771C>T	c.(769-771)CTC>CTT	p.L257L		NM_153228	NP_694960	Q8N957	ANKF1_HUMAN	ankyrin-repeat and fibronectin type III domain	257										large_intestine(1)|ovary(1)	2														0.132867	28.934898	47.641782	19	124	KEEP	---	---	---	---	capture		Silent	SNP	54450167	54450167	628	17	C	T	T	T	405	32	ANKFN1	2	2
ACE	1636	broad.mit.edu	37	17	61574336	61574336	+	Silent	SNP	G	T	T			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:61574336G>T	uc002jau.1	+	c.3681G>T	c.(3679-3681)ACG>ACT	p.T1227T	ACE_uc002jav.1_Silent_p.T653T|ACE_uc010ddv.1_Silent_p.T454T|ACE_uc010wpj.1_Silent_p.T612T|ACE_uc002jaw.1_Non-coding_Transcript|ACE_uc010wpk.1_Silent_p.T432T	NM_000789	NP_000780	P12821	ACE_HUMAN	angiotensin I converting enzyme 1 isoform 1	1227	Extracellular (Potential).|Peptidase M2 2.				angiotensin catabolic process in blood|arachidonic acid secretion|blood vessel remodeling|hemopoietic stem cell differentiation|hormone catabolic process|kidney development|mononuclear cell proliferation|peptide catabolic process|regulation of renal output by angiotensin|regulation of smooth muscle cell migration|regulation of vasoconstriction|regulation of vasodilation	endosome|external side of plasma membrane|extracellular space|integral to membrane|membrane fraction|plasma membrane	actin binding|bradykinin receptor binding|carboxypeptidase activity|chloride ion binding|drug binding|metallopeptidase activity|peptidyl-dipeptidase activity|zinc ion binding			ovary(2)|pancreas(1)	3					Benazepril(DB00542)|Captopril(DB01197)|Deserpidine(DB01089)|Enalapril(DB00584)|Fosinopril(DB00492)|Lisinopril(DB00722)|Moexipril(DB00691)|Perindopril(DB00790)|Quinapril(DB00881)|Ramipril(DB00178)|Rescinnamine(DB01180)|Spirapril(DB01348)|Trandolapril(DB00519)									0.454545	13.569962	13.590149	5	6	KEEP	---	---	---	---	capture		Silent	SNP	61574336	61574336	137	17	G	T	T	T	483	38	ACE	1	1
CCDC45	90799	broad.mit.edu	37	17	62533820	62533820	+	Silent	SNP	C	A	A			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:62533820C>A	uc002jem.2	+	c.2389C>A	c.(2389-2391)CGG>AGG	p.R797R	CCDC45_uc002jen.2_Non-coding_Transcript|CCDC45_uc010wqb.1_Silent_p.R633R	NM_138363	NP_612372	Q96GE4	CCD45_HUMAN	coiled-coil domain containing 45	797							protein binding			ovary(1)	1	Breast(5;1.32e-14)		BRCA - Breast invasive adenocarcinoma(8;8.6e-12)											0.073171	-1.106684	6.573103	3	38	KEEP	---	---	---	---	capture		Silent	SNP	62533820	62533820	2939	17	C	A	A	A	295	23	CCDC45	1	1
SMURF2	64750	broad.mit.edu	37	17	62568061	62568061	+	Missense_Mutation	SNP	T	C	C			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:62568061T>C	uc002jep.1	-	c.871A>G	c.(871-873)ATC>GTC	p.I291V	SMURF2_uc002jeq.1_Missense_Mutation_p.I50V|SMURF2_uc002jer.1_Missense_Mutation_p.I50V	NM_022739	NP_073576	Q9HAU4	SMUF2_HUMAN	SMAD specific E3 ubiquitin protein ligase 2	291					BMP signaling pathway|negative regulation of transcription, DNA-dependent|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|regulation of transforming growth factor beta receptor signaling pathway|transforming growth factor beta receptor signaling pathway|ubiquitin-dependent SMAD protein catabolic process	cytosol|membrane raft|nucleus|plasma membrane|ubiquitin ligase complex	identical protein binding|SMAD binding|ubiquitin-protein ligase activity			lung(1)	1	Breast(5;1.32e-14)		BRCA - Breast invasive adenocarcinoma(8;9.88e-12)							363				0.277778	54.570669	57.76985	20	52	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	62568061	62568061	15320	17	T	C	C	C	663	51	SMURF2	4	4
KIAA0753	9851	broad.mit.edu	37	17	6493842	6493842	+	Missense_Mutation	SNP	G	A	A			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:6493842G>A	uc002gde.3	-	c.2549C>T	c.(2548-2550)CCC>CTC	p.P850L	KIAA0753_uc010vtd.1_Missense_Mutation_p.P306L|KIAA0753_uc010clo.2_Missense_Mutation_p.P551L|KIAA0753_uc010vte.1_Missense_Mutation_p.P551L	NM_014804	NP_055619	Q2KHM9	K0753_HUMAN	hypothetical protein LOC9851	850											0				COAD - Colon adenocarcinoma(228;0.157)										0.252525	62.236611	67.736907	25	74	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	6493842	6493842	8498	17	G	A	A	A	559	43	KIAA0753	2	2
HELZ	9931	broad.mit.edu	37	17	65083055	65083055	+	Missense_Mutation	SNP	G	C	C			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:65083055G>C	uc010wqk.1	-	c.5387C>G	c.(5386-5388)TCT>TGT	p.S1796C	HELZ_uc002jfv.3_Non-coding_Transcript|HELZ_uc002jfx.3_Missense_Mutation_p.S1795C	NM_014877	NP_055692			helicase with zinc finger domain											ovary(1)|pancreas(1)	2	all_cancers(12;1.24e-11)|Breast(2;1.05e-17)|all_epithelial(3;3.87e-13)													0.060241	-6.476488	27.065054	10	156	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	65083055	65083055	7332	17	G	C	C	C	429	33	HELZ	3	3
GPS1	2873	broad.mit.edu	37	17	80014187	80014187	+	Missense_Mutation	SNP	G	A	A			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:80014187G>A	uc002kdk.1	+	c.1075G>A	c.(1075-1077)GAG>AAG	p.E359K	GPS1_uc002kdl.1_Missense_Mutation_p.E323K|GPS1_uc010dij.1_Missense_Mutation_p.E358K|GPS1_uc002kdm.1_Missense_Mutation_p.E303K|GPS1_uc002kdn.1_Missense_Mutation_p.E319K|GPS1_uc002kdo.1_Missense_Mutation_p.E322K|GPS1_uc010wvh.1_Missense_Mutation_p.E315K	NM_212492	NP_997657	Q13098	CSN1_HUMAN	G protein pathway suppressor 1 isoform 1	323					cell cycle|inactivation of MAPK activity|JNK cascade	cytoplasm|signalosome	GTPase inhibitor activity|protein binding			central_nervous_system(1)	1	all_neural(118;0.0878)|Ovarian(332;0.227)|all_lung(278;0.246)		BRCA - Breast invasive adenocarcinoma(99;0.0114)|OV - Ovarian serous cystadenocarcinoma(97;0.0211)											0.15625	57.006931	82.257972	35	189	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	80014187	80014187	7008	17	G	A	A	A	533	41	GPS1	2	2
FOXK2	3607	broad.mit.edu	37	17	80542037	80542037	+	Missense_Mutation	SNP	G	A	A			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:80542037G>A	uc002kfn.2	+	c.1252G>A	c.(1252-1254)GAA>AAA	p.E418K	FOXK2_uc002kfm.1_Missense_Mutation_p.E418K|FOXK2_uc010diu.2_Intron	NM_004514	NP_004505	Q01167	FOXK2_HUMAN	forkhead box K2	418					embryo development|negative regulation of gene-specific transcription from RNA polymerase II promoter|pattern specification process|regulation of sequence-specific DNA binding transcription factor activity|tissue development	transcription factor complex	DNA bending activity|double-stranded DNA binding|magnesium ion binding|promoter binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding				0	Breast(20;0.00106)|all_neural(118;0.0952)		OV - Ovarian serous cystadenocarcinoma(97;0.0371)|BRCA - Breast invasive adenocarcinoma(99;0.0415)											0.12	3.21186	6.750153	3	22	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	80542037	80542037	6261	17	G	A	A	A	533	41	FOXK2	2	2
DLGAP1	9229	broad.mit.edu	37	18	3729134	3729134	+	Splice_Site_SNP	SNP	C	A	A			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:3729134C>A	uc002kmf.2	-	c.1591_splice	c.e4+1	p.V531_splice	DLGAP1_uc010wyz.1_Splice_Site_SNP_p.V531_splice|DLGAP1_uc002kme.1_Splice_Site_SNP_p.V229_splice|DLGAP1_uc010dkn.2_Splice_Site_SNP_p.G229_splice|DLGAP1_uc010wyw.1_Splice_Site_SNP_p.V237_splice|DLGAP1_uc010wyx.1_Splice_Site_SNP_p.G243_splice|DLGAP1_uc010wyy.1_Splice_Site_SNP_p.A243_splice|DLGAP1_uc002kmg.2_Splice_Site_SNP_p.V229_splice|DLGAP1_uc002kmk.2_Splice_Site_SNP_p.G531_splice	NM_004746	NP_004737			discs large homolog-associated protein 1 isoform						synaptic transmission	cell junction|postsynaptic density|postsynaptic membrane				ovary(2)|pancreas(1)|skin(1)	4		Colorectal(8;0.0257)												0.53125	47.176332	47.203881	17	15	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	3729134	3729134	4739	18	C	A	A	A	234	18	DLGAP1	5	2
ARHGAP28	79822	broad.mit.edu	37	18	6889985	6889985	+	Silent	SNP	C	T	T			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:6889985C>T	uc002knc.2	+	c.1479C>T	c.(1477-1479)TTC>TTT	p.F493F	ARHGAP28_uc002knd.2_Silent_p.F386F|ARHGAP28_uc002kne.2_Silent_p.F386F|ARHGAP28_uc010wzi.1_Silent_p.F368F|ARHGAP28_uc002knf.2_Silent_p.F377F	NM_030672	NP_109597	B4DXL2	B4DXL2_HUMAN	Rho GTPase activating protein 28 isoform b	368					signal transduction	intracellular				pancreas(1)	1		Colorectal(10;0.168)												0.042683	-25.726468	11.108221	7	157	KEEP	---	---	---	---	capture		Silent	SNP	6889985	6889985	889	18	C	T	T	T	376	29	ARHGAP28	2	2
RDH8	50700	broad.mit.edu	37	19	10132255	10132255	+	Nonsense_Mutation	SNP	C	T	T			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:10132255C>T	uc002mmr.2	+	c.766C>T	c.(766-768)CAG>TAG	p.Q256*		NM_015725	NP_056540	Q9NYR8	RDH8_HUMAN	retinol dehydrogenase 8 (all-trans)	256					estrogen biosynthetic process|oxidation-reduction process|response to stimulus|visual perception	cytoplasm|integral to plasma membrane	binding|estradiol 17-beta-dehydrogenase activity|NADP-retinol dehydrogenase activity|retinol dehydrogenase activity			ovary(3)|pancreas(1)	4			Epithelial(33;4.24e-05)		Vitamin A(DB00162)									0.461538	29.389355	29.42349	12	14	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	10132255	10132255	13665	19	C	T	T	T	221	17	RDH8	5	2
KEAP1	9817	broad.mit.edu	37	19	10602581	10602581	+	Missense_Mutation	SNP	C	T	T			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:10602581C>T	uc002moq.1	-	c.997G>A	c.(997-999)GGC>AGC	p.G333S	KEAP1_uc002mop.1_Missense_Mutation_p.G51S|KEAP1_uc002mor.1_Missense_Mutation_p.G333S	NM_012289	NP_036421	Q14145	KEAP1_HUMAN	kelch-like ECH-associated protein 1	333	Kelch 1.		G -> C (in a NSCLC cell line; strongly reduces interaction with NFE2L2 and reduces repression of NFE2L2-dependent gene expression).		regulation of transcription, DNA-dependent|transcription, DNA-dependent	centrosome|midbody|nucleus	protein binding			breast(2)|ovary(1)|pancreas(1)	4			OV - Ovarian serous cystadenocarcinoma(20;2.71e-09)|Epithelial(33;2.32e-06)|all cancers(31;1.42e-05)											0.576923	43.924742	44.058296	15	11	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	10602581	10602581	8447	19	C	T	T	T	299	23	KEAP1	1	1
PRKCSH	5589	broad.mit.edu	37	19	11560101	11560101	+	Silent	SNP	A	G	G			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:11560101A>G	uc010xlz.1	+	c.1482A>G	c.(1480-1482)AAA>AAG	p.K494K	PRKCSH_uc002mrt.2_Silent_p.K487K|PRKCSH_uc002mru.2_Silent_p.K484K|PRKCSH_uc010dya.2_Silent_p.K269K|PRKCSH_uc010dyb.2_Silent_p.K484K	NM_002743	NP_002734	P14314	GLU2B_HUMAN	protein kinase C substrate 80K-H isoform 1	487					innate immune response|intracellular protein kinase cascade|post-translational protein modification|protein folding|protein N-linked glycosylation via asparagine	endoplasmic reticulum lumen	calcium ion binding|protein kinase C binding				0														0.174757	44.292183	54.57276	18	85	KEEP	---	---	---	---	capture		Silent	SNP	11560101	11560101	12959	19	A	G	G	G	37	3	PRKCSH	4	4
ZNF878	729747	broad.mit.edu	37	19	12157506	12157506	+	Nonsense_Mutation	SNP	G	A	A			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:12157506G>A	uc002mta.1	-	c.214C>T	c.(214-216)CAG>TAG	p.Q72*		NM_001080404	NP_001073873			zinc finger protein 878												0														0.156977	46.302359	65.628137	27	145	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	12157506	12157506	18799	19	G	A	A	A	611	47	ZNF878	5	2
STK11	6794	broad.mit.edu	37	19	1220449	1220449	+	Missense_Mutation	SNP	A	T	T			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:1220449A>T	uc002lrl.1	+	c.542A>T	c.(541-543)AAC>ATC	p.N181I		NM_000455	NP_000446	Q15831	STK11_HUMAN	serine/threonine protein kinase 11	181	Protein kinase.				anoikis|cell cycle arrest|energy reserve metabolic process|insulin receptor signaling pathway|positive regulation of transforming growth factor beta receptor signaling pathway|protein phosphorylation|regulation of fatty acid biosynthetic process|regulation of fatty acid oxidation	cytosol|nucleus	ATP binding|magnesium ion binding|protein serine/threonine kinase activity	p.0?(19)|p.Y156fs*87(4)		lung(162)|cervix(35)|skin(15)|large_intestine(12)|pancreas(6)|gastrointestinal_tract_(site_indeterminate)(5)|ovary(4)|stomach(3)|upper_aerodigestive_tract(1)|testis(1)|liver(1)|biliary_tract(1)|small_intestine(1)|urinary_tract(1)|breast(1)|oesophagus(1)|prostate(1)|kidney(1)	252		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;7.93e-06)|all_lung(49;1.25e-05)|Breast(49;0.000172)|Renal(1328;0.0183)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|Lung(535;0.00942)|STAD - Stomach adenocarcinoma(1328;0.18)				14		1341	TSP Lung(3;<1E-8)			0.428571	8.624325	8.655348	3	4	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	1220449	1220449	15807	19	A	T	T	T	26	2	STK11	3	3
TCF3	6929	broad.mit.edu	37	19	1619133	1619133	+	Missense_Mutation	SNP	G	C	C			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:1619133G>C	uc002ltq.2	-	c.1274C>G	c.(1273-1275)TCT>TGT	p.S425C	TCF3_uc002lto.2_Missense_Mutation_p.S237C|TCF3_uc002ltt.3_Missense_Mutation_p.S476C|TCF3_uc002ltr.2_Missense_Mutation_p.S476C|TCF3_uc002lts.1_Missense_Mutation_p.S392C|TCF3_uc010dso.1_Non-coding_Transcript	NM_003200	NP_003191	P15923	TFE2_HUMAN	transcription factor 3 isoform E12	476					B cell lineage commitment|B cell lineage commitment|G1 phase of mitotic cell cycle|immunoglobulin V(D)J recombination|muscle cell differentiation|positive regulation of B cell proliferation|positive regulation of cell cycle|positive regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of muscle cell differentiation	cytoplasm|nucleus|protein complex|transcription factor complex	bHLH transcription factor binding|DNA binding|E-box binding|identical protein binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|sequence-specific DNA binding transcription factor activity|transcription activator activity|transcription factor binding|vitamin D response element binding			large_intestine(1)|skin(1)	2		Acute lymphoblastic leukemia(61;5.94e-12)|all_hematologic(61;1.27e-07)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)						128				0.085714	4.692492	16.872186	6	64	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	1619133	1619133	16220	19	G	C	C	C	429	33	TCF3	3	3
ZNF91	7644	broad.mit.edu	37	19	23542873	23542873	+	Missense_Mutation	SNP	C	G	G	rs1816638		TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:23542873C>G	uc002nre.2	-	c.2908G>C	c.(2908-2910)GAA>CAA	p.E970Q	ZNF91_uc002nrd.2_5'Flank|ZNF91_uc010xrj.1_Missense_Mutation_p.E938Q	NM_003430	NP_003421	Q05481	ZNF91_HUMAN	zinc finger protein 91	970	C2H2-type 30.				regulation of transcription, DNA-dependent	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0		all_lung(12;0.0349)|Lung NSC(12;0.0538)|all_epithelial(12;0.0611)												0.034965	-21.358522	12.273476	5	138	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	23542873	23542873	18804	19	C	G	G	G	416	32	ZNF91	3	3
MIER2	54531	broad.mit.edu	37	19	326574	326574	+	Missense_Mutation	SNP	C	G	G			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:326574C>G	uc002lok.1	-	c.518G>C	c.(517-519)AGA>ACA	p.R173T		NM_017550	NP_060020	Q8N344	MIER2_HUMAN	mesoderm induction early response 1, family	173					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding				0		all_cancers(10;1.05e-30)|all_epithelial(18;3.04e-19)|Acute lymphoblastic leukemia(61;4.36e-14)|all_hematologic(61;4.84e-09)|Lung NSC(49;2.49e-05)|all_lung(49;4.36e-05)|Breast(49;0.000304)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)										0.059406	-5.737576	14.782065	6	95	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	326574	326574	9971	19	C	G	G	G	416	32	MIER2	3	3
ZNF781	163115	broad.mit.edu	37	19	38160502	38160502	+	Missense_Mutation	SNP	A	C	C			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:38160502A>C	uc002ogy.2	-	c.548T>G	c.(547-549)ATA>AGA	p.I183R	ZNF781_uc002ogz.2_Missense_Mutation_p.I178R	NM_152605	NP_689818	Q8N8C0	ZN781_HUMAN	zinc finger protein 781	183					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0														0.176	55.689869	68.045492	22	103	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	38160502	38160502	18752	19	A	C	C	C	208	16	ZNF781	4	4
CREB3L3	84699	broad.mit.edu	37	19	4171672	4171672	+	Silent	SNP	C	T	T			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:4171672C>T	uc002lzl.2	+	c.1092C>T	c.(1090-1092)CAC>CAT	p.H364H	CREB3L3_uc002lzm.2_Silent_p.H354H|CREB3L3_uc010xib.1_Silent_p.H353H|CREB3L3_uc010xic.1_Nonsense_Mutation_p.Q320*	NM_032607	NP_115996	Q68CJ9	CR3L3_HUMAN	cAMP responsive element binding protein 3-like	364	Lumenal (Potential).	Cleavage; by PS1 (By similarity).			regulation of transcription, DNA-dependent|response to unfolded protein	endoplasmic reticulum membrane|integral to membrane|nucleus	protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0232)|STAD - Stomach adenocarcinoma(1328;0.18)										0.131868	25.977044	49.951851	24	158	KEEP	---	---	---	---	capture		Silent	SNP	4171672	4171672	3997	19	C	T	T	T	220	17	CREB3L3	2	2
PSG5	5673	broad.mit.edu	37	19	43680050	43680050	+	Silent	SNP	G	C	C			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:43680050G>C	uc002ovv.2	-	c.960C>G	c.(958-960)CGC>CGG	p.R320R	PSG6_uc010xwk.1_Intron|PSG5_uc010eir.2_Intron|PSG5_uc002ovu.2_Silent_p.R227R|PSG5_uc002ovx.2_Silent_p.R227R|PSG5_uc002ovw.2_Intron	NM_002781	NP_002772	Q15238	PSG5_HUMAN	pregnancy specific beta-1-glycoprotein 5	227	Ig-like C2-type 1.				female pregnancy	extracellular region					0		Prostate(69;0.00899)												0.348018	261.147563	265.779484	79	148	KEEP	---	---	---	---	capture		Silent	SNP	43680050	43680050	13111	19	G	C	C	C	587	46	PSG5	3	3
EML2	24139	broad.mit.edu	37	19	46124837	46124837	+	Silent	SNP	G	A	A			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:46124837G>A	uc010xxm.1	-	c.1503C>T	c.(1501-1503)CTC>CTT	p.L501L	EML2_uc002pcn.2_Silent_p.L300L|EML2_uc002pco.2_Non-coding_Transcript|EML2_uc002pcp.2_Silent_p.L184L|EML2_uc010xxl.1_Silent_p.L447L|EML2_uc010xxn.1_Non-coding_Transcript|EML2_uc010xxo.1_Silent_p.L300L|EML2_uc010ekj.2_Missense_Mutation_p.S267F	NM_012155	NP_036287	O95834	EMAL2_HUMAN	echinoderm microtubule associated protein like	300	WD 5.				sensory perception of sound|visual perception	cytoplasm|intracellular membrane-bounded organelle|microtubule|microtubule associated complex	catalytic activity|protein binding			large_intestine(1)|ovary(1)	2		Ovarian(192;0.179)|all_neural(266;0.224)		OV - Ovarian serous cystadenocarcinoma(262;0.00553)|GBM - Glioblastoma multiforme(486;0.131)|Epithelial(262;0.197)										0.44898	61.237588	61.349463	22	27	KEEP	---	---	---	---	capture		Silent	SNP	46124837	46124837	5289	19	G	A	A	A	418	33	EML2	2	2
IGFL2	147920	broad.mit.edu	37	19	46652280	46652280	+	Missense_Mutation	SNP	C	A	A			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:46652280C>A	uc002peb.2	+	c.38C>A	c.(37-39)CCC>CAC	p.P13H	IGFL2_uc010xxv.1_Intron	NM_001002915	NP_001002915	Q6UWQ7	IGFL2_HUMAN	IGF-like family member 2 isoform a	Error:Variant_position_missing_in_Q6UWQ7_after_alignment						extracellular region					0		Ovarian(192;0.0908)|all_neural(266;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.00493)|GBM - Glioblastoma multiforme(486;0.031)|Epithelial(262;0.247)										0.3125	11.768683	12.269773	5	11	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	46652280	46652280	7888	19	C	A	A	A	286	22	IGFL2	2	2
GRIN2D	2906	broad.mit.edu	37	19	48908350	48908350	+	Silent	SNP	G	A	A			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:48908350G>A	uc002pjc.3	+	c.825G>A	c.(823-825)GTG>GTA	p.V275V		NM_000836	NP_000827	O15399	NMDE4_HUMAN	N-methyl-D-aspartate receptor subunit 2D	275	Extracellular (Potential).					cell junction|outer membrane-bounded periplasmic space|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|protein binding			ovary(3)|breast(3)	6		all_epithelial(76;1.11e-06)|all_lung(116;5.79e-06)|Lung NSC(112;1.18e-05)|all_neural(266;0.0189)|Ovarian(192;0.0261)|Breast(70;0.203)		all cancers(93;0.00014)|OV - Ovarian serous cystadenocarcinoma(262;0.000233)|Epithelial(262;0.0112)|GBM - Glioblastoma multiforme(486;0.0161)	L-Glutamic Acid(DB00142)|Loperamide(DB00836)|Orphenadrine(DB01173)									0.210526	8.988277	10.46231	4	15	KEEP	---	---	---	---	capture		Silent	SNP	48908350	48908350	7061	19	G	A	A	A	600	47	GRIN2D	2	2
SIGLEC9	27180	broad.mit.edu	37	19	51629008	51629008	+	Silent	SNP	C	T	T			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:51629008C>T	uc010yct.1	+	c.576C>T	c.(574-576)ACC>ACT	p.T192T	SIGLEC9_uc002pvu.2_Silent_p.T192T	NM_014441	NP_055256	Q9Y336	SIGL9_HUMAN	sialic acid binding Ig-like lectin 9 precursor	192	Extracellular (Potential).|Ig-like C2-type 1.				cell adhesion|cell surface receptor linked signaling pathway	integral to plasma membrane	sugar binding				0		all_neural(266;0.0529)		GBM - Glioblastoma multiforme(134;0.000826)|OV - Ovarian serous cystadenocarcinoma(262;0.00295)										0.460784	132.707687	132.844715	47	55	KEEP	---	---	---	---	capture		Silent	SNP	51629008	51629008	14810	19	C	T	T	T	262	21	SIGLEC9	2	2
BIRC8	112401	broad.mit.edu	37	19	53793072	53793072	+	Missense_Mutation	SNP	C	T	T			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:53793072C>T	uc002qbk.2	-	c.556G>A	c.(556-558)GAG>AAG	p.E186K		NM_033341	NP_203127	Q96P09	BIRC8_HUMAN	baculoviral IAP repeat-containing 8	186					apoptosis		zinc ion binding			lung(1)	1				GBM - Glioblastoma multiforme(134;0.00304)										0.082645	-0.948084	20.495941	10	111	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	53793072	53793072	1465	19	C	T	T	T	390	30	BIRC8	2	2
INSR	3643	broad.mit.edu	37	19	7125477	7125477	+	Silent	SNP	G	T	T			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:7125477G>T	uc002mgd.1	-	c.3075C>A	c.(3073-3075)CTC>CTA	p.L1025L	INSR_uc002mge.1_Silent_p.L1013L	NM_000208	NP_000199	P06213	INSR_HUMAN	insulin receptor isoform Long precursor	1025	Protein kinase.|Cytoplasmic (Potential).				activation of MAPK activity|activation of protein kinase B activity|carbohydrate metabolic process|fibroblast growth factor receptor signaling pathway|G-protein coupled receptor protein signaling pathway|glucose homeostasis|heart morphogenesis|peptidyl-tyrosine phosphorylation|positive regulation of cell migration|positive regulation of cell proliferation|positive regulation of developmental growth|positive regulation of DNA replication|positive regulation of glucose import|positive regulation of glycogen biosynthetic process|positive regulation of glycolysis|positive regulation of MAPKKK cascade|positive regulation of mitosis|positive regulation of nitric oxide biosynthetic process|positive regulation of protein kinase B signaling cascade|positive regulation of protein phosphorylation|positive regulation of respiratory burst|protein autophosphorylation|protein heterotetramerization|regulation of embryonic development|regulation of gene-specific transcription|transformation of host cell by virus	caveola|endosome membrane|insulin receptor complex|microsome	ATP binding|GTP binding|insulin binding|insulin receptor activity|insulin receptor substrate binding|insulin-like growth factor I binding|insulin-like growth factor II binding|insulin-like growth factor receptor binding|metal ion binding|phosphatidylinositol 3-kinase binding|PTB domain binding|receptor signaling protein tyrosine kinase activity|SH2 domain binding			ovary(4)|lung(3)|central_nervous_system(2)|large_intestine(1)|stomach(1)|skin(1)	12					Insulin Glargine recombinant(DB00047)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)					649				0.103896	2.94378	14.975261	8	69	KEEP	---	---	---	---	capture		Silent	SNP	7125477	7125477	8074	19	G	T	T	T	522	41	INSR	2	2
PTBP1	5725	broad.mit.edu	37	19	808703	808703	+	Silent	SNP	C	T	T			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:808703C>T	uc002lpp.2	+	c.1404C>T	c.(1402-1404)GGC>GGT	p.G468G	PTBP1_uc002lpq.2_Silent_p.G461G|PTBP1_uc002lpr.2_Silent_p.G442G|PTBP1_uc002lps.2_Silent_p.G108G|PTBP1_uc002lpt.2_Non-coding_Transcript|PTBP1_uc002lpu.1_Silent_p.G438G	NM_002819	NP_002810	P26599	PTBP1_HUMAN	polypyrimidine tract-binding protein 1 isoform	442					nuclear mRNA splicing, via spliceosome	heterogeneous nuclear ribonucleoprotein complex|nucleolus|nucleoplasm	nucleotide binding|poly-pyrimidine tract binding|protein binding			kidney(1)	1		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;6.59e-06)|all_lung(49;9.97e-06)|Breast(49;0.000172)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)										0.291667	19.715226	20.648258	7	17	KEEP	---	---	---	---	capture		Silent	SNP	808703	808703	13179	19	C	T	T	T	353	28	PTBP1	2	2
MTOR	2475	broad.mit.edu	37	1	11297992	11297992	+	Missense_Mutation	SNP	C	G	G			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:11297992C>G	uc001asd.2	-	c.2116G>C	c.(2116-2118)GAG>CAG	p.E706Q		NM_004958	NP_004949	P42345	MTOR_HUMAN	FK506 binding protein 12-rapamycin associated	706					cell growth|cellular response to hypoxia|insulin receptor signaling pathway|nerve growth factor receptor signaling pathway|peptidyl-serine phosphorylation|phosphatidylinositol-mediated signaling|protein autophosphorylation|protein catabolic process|response to amino acid stimulus|response to nutrient|T cell costimulation|TOR signaling cascade	endoplasmic reticulum membrane|Golgi membrane|lysosome|mitochondrial outer membrane|phosphatidylinositol 3-kinase complex|PML body|TORC1 complex|TORC2 complex	ATP binding|phosphoprotein binding|protein serine/threonine kinase activity			central_nervous_system(7)|ovary(4)|kidney(3)|large_intestine(2)|skin(2)|lung(1)	19										1389				0.08046	3.06113	18.669109	7	80	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	11297992	11297992	10347	1	C	G	G	G	377	29	MTOR	3	3
ANKRD34A	284615	broad.mit.edu	37	1	145473380	145473380	+	Missense_Mutation	SNP	C	A	A			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:145473380C>A	uc001enq.1	+	c.52C>A	c.(52-54)CTA>ATA	p.L18I	NBPF10_uc001emp.3_Intron|POLR3GL_uc001enp.1_5'Flank	NM_001039888	NP_001034977	Q69YU3	AN34A_HUMAN	ankyrin repeat domain 34	18	ANK 1.										0	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)													0.513889	107.16832	107.180146	37	35	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	145473380	145473380	669	1	C	A	A	A	363	28	ANKRD34A	2	2
DENND4B	9909	broad.mit.edu	37	1	153911514	153911514	+	Silent	SNP	G	C	C			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:153911514G>C	uc001fdd.1	-	c.1827C>G	c.(1825-1827)CTC>CTG	p.L609L		NM_014856	NP_055671	O75064	DEN4B_HUMAN	DENN/MADD domain containing 4B	609	dDENN.									ovary(1)	1	all_lung(78;2.89e-32)|Lung NSC(65;2.27e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)											0.071429	0.789464	8.738348	3	39	KEEP	---	---	---	---	capture		Silent	SNP	153911514	153911514	4613	1	G	C	C	C	574	45	DENND4B	3	3
ZBTB7B	51043	broad.mit.edu	37	1	154987712	154987712	+	Silent	SNP	G	T	T			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:154987712G>T	uc001fgj.3	+	c.678G>T	c.(676-678)CCG>CCT	p.P226P	ZBTB7B_uc001fgk.3_Silent_p.P192P|ZBTB7B_uc009wpa.2_Silent_p.P192P|ZBTB7B_uc010peq.1_Silent_p.P226P|ZBTB7B_uc001fgl.3_Silent_p.P192P	NM_015872	NP_056956	O15156	ZBT7B_HUMAN	zinc finger and BTB domain containing 7B	192	Pro-rich.				cell differentiation|ectoderm development|multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|specific RNA polymerase II transcription factor activity|zinc ion binding				0	all_epithelial(22;2.77e-30)|all_lung(78;4.1e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		BRCA - Breast invasive adenocarcinoma(34;0.00034)											0.240506	44.797371	49.644738	19	60	KEEP	---	---	---	---	capture		Silent	SNP	154987712	154987712	18141	1	G	T	T	T	483	38	ZBTB7B	1	1
FCRL1	115350	broad.mit.edu	37	1	157765949	157765949	+	Missense_Mutation	SNP	G	T	T			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:157765949G>T	uc001frg.2	-	c.1230C>A	c.(1228-1230)GAC>GAA	p.D410E	FCRL1_uc001frf.2_Non-coding_Transcript|FCRL1_uc001frh.2_Missense_Mutation_p.D409E|FCRL1_uc001fri.2_3'UTR|FCRL1_uc001frj.2_Non-coding_Transcript	NM_052938	NP_443170	Q96LA6	FCRL1_HUMAN	Fc receptor-like 1 isoform 1 precursor	410	ITIM motif 4.|Cytoplasmic (Potential).					integral to membrane|plasma membrane	receptor activity			ovary(3)	3	all_hematologic(112;0.0378)		LUSC - Lung squamous cell carcinoma(543;0.24)			GBM(54;482 1003 11223 30131 35730)								0.28972	86.382782	90.622381	31	76	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	157765949	157765949	6031	1	G	T	T	T	620	48	FCRL1	2	2
CASP9	842	broad.mit.edu	37	1	15819510	15819510	+	Silent	SNP	C	T	T			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:15819510C>T	uc001awn.2	-	c.1179G>A	c.(1177-1179)GTG>GTA	p.V393V	CASP9_uc001awm.1_3'UTR|CASP9_uc001awo.2_Silent_p.V243V|CASP9_uc001awp.2_Silent_p.V237V|CASP9_uc009voi.2_Silent_p.V237V|CASP9_uc010obm.1_Silent_p.V310V|CASP9_uc001awq.2_Silent_p.V310V	NM_001229	NP_001220	P55211	CASP9_HUMAN	caspase 9 isoform alpha preproprotein	393					activation of caspase activity by cytochrome c|induction of apoptosis by intracellular signals|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling	cytosol	cysteine-type endopeptidase activity|enzyme activator activity|protein binding			central_nervous_system(1)|kidney(1)	2		Breast(348;0.000207)|all_lung(284;0.000211)|Colorectal(325;0.000259)|Lung NSC(340;0.000269)|Renal(390;0.000518)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;8.49e-07)|COAD - Colon adenocarcinoma(227;4.36e-05)|BRCA - Breast invasive adenocarcinoma(304;0.00013)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.00763)|READ - Rectum adenocarcinoma(331;0.0655)						893				0.333333	150.767757	155.586048	65	130	KEEP	---	---	---	---	capture		Silent	SNP	15819510	15819510	2798	1	C	T	T	T	366	29	CASP9	2	2
OR6Y1	391112	broad.mit.edu	37	1	158517081	158517081	+	Missense_Mutation	SNP	G	T	T			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:158517081G>T	uc010pil.1	-	c.815C>A	c.(814-816)GCC>GAC	p.A272D		NM_001005189	NP_001005189	Q8NGX8	OR6Y1_HUMAN	olfactory receptor, family 6, subfamily Y,	272	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1	all_hematologic(112;0.0378)													0.496269	391.151935	391.15533	133	135	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	158517081	158517081	11624	1	G	T	T	T	546	42	OR6Y1	2	2
PPOX	5498	broad.mit.edu	37	1	161137915	161137915	+	Missense_Mutation	SNP	G	C	C			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:161137915G>C	uc001fyj.2	+	c.469G>C	c.(469-471)GAG>CAG	p.E157Q	PPOX_uc001fyn.2_Intron|PPOX_uc001fyg.2_Missense_Mutation_p.E157Q|PPOX_uc001fyl.2_Missense_Mutation_p.E123Q|PPOX_uc001fym.2_Non-coding_Transcript|PPOX_uc001fyk.2_5'UTR|PPOX_uc001fyh.2_5'UTR|PPOX_uc010pkg.1_Intron|PPOX_uc009wuc.1_5'UTR|PPOX_uc010pkh.1_Intron|PPOX_uc001fyi.2_Intron	NM_001122764	NP_001116236	P50336	PPOX_HUMAN	protoporphyrinogen oxidase	157					heme biosynthetic process|oxidation-reduction process	intrinsic to mitochondrial inner membrane|mitochondrial intermembrane space	flavin adenine dinucleotide binding|oxygen-dependent protoporphyrinogen oxidase activity			ovary(1)	1	all_cancers(52;3.73e-19)|Breast(13;0.000577)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00275)											0.041667	-11.486614	10.188909	4	92	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	161137915	161137915	12783	1	G	C	C	C	585	45	PPOX	3	3
ATF6	22926	broad.mit.edu	37	1	161736217	161736217	+	Missense_Mutation	SNP	C	G	G			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:161736217C>G	uc001gbr.2	+	c.67C>G	c.(67-69)CTG>GTG	p.L23V	ATF6_uc001gbq.1_Missense_Mutation_p.L23V	NM_007348	NP_031374	P18850	ATF6A_HUMAN	activating transcription factor 6	23	Cytoplasmic (Potential).|Transcription activation.				positive regulation of gene-specific transcription involved in unfolded protein response|protein folding	endoplasmic reticulum membrane|Golgi membrane|integral to membrane|nuclear envelope|nucleoplasm	protein dimerization activity|RNA polymerase II transcription factor activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity			ovary(2)	2	all_hematologic(112;0.156)		BRCA - Breast invasive adenocarcinoma(70;0.00953)											0.097561	12.002565	31.952612	12	111	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	161736217	161736217	1103	1	C	G	G	G	363	28	ATF6	3	3
KCNK2	3776	broad.mit.edu	37	1	215259970	215259970	+	Missense_Mutation	SNP	C	G	G			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:215259970C>G	uc001hkq.2	+	c.306C>G	c.(304-306)TTC>TTG	p.F102L	KCNK2_uc001hko.2_Missense_Mutation_p.F98L|KCNK2_uc009xdm.2_Non-coding_Transcript|KCNK2_uc001hkp.2_Non-coding_Transcript|KCNK2_uc010pua.1_Non-coding_Transcript|KCNK2_uc001hkr.3_Missense_Mutation_p.F87L	NM_001017425	NP_001017425	O95069	KCNK2_HUMAN	potassium channel, subfamily K, member 2 isoform	102							outward rectifier potassium channel activity				0				OV - Ovarian serous cystadenocarcinoma(81;0.0399)|all cancers(67;0.0556)|GBM - Glioblastoma multiforme(131;0.068)	Dofetilide(DB00204)									0.054152	-19.223676	38.846938	15	262	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	215259970	215259970	8371	1	C	G	G	G	376	29	KCNK2	3	3
USH2A	7399	broad.mit.edu	37	1	215848324	215848324	+	Missense_Mutation	SNP	C	A	A			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:215848324C>A	uc001hku.1	-	c.12929G>T	c.(12928-12930)AGC>ATC	p.S4310I		NM_206933	NP_996816	O75445	USH2A_HUMAN	usherin isoform B	4310	Fibronectin type-III 28.|Extracellular (Potential).				maintenance of organ identity|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	basement membrane|cytoplasm|integral to membrane|stereocilium membrane	collagen binding			ovary(20)|kidney(1)|central_nervous_system(1)	22				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)										0.524862	273.015968	273.112742	95	86	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	215848324	215848324	17598	1	C	A	A	A	364	28	USH2A	2	2
USH2A	7399	broad.mit.edu	37	1	215914740	215914740	+	Missense_Mutation	SNP	G	C	C			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:215914740G>C	uc001hku.1	-	c.11688C>G	c.(11686-11688)ATC>ATG	p.I3896M		NM_206933	NP_996816	O75445	USH2A_HUMAN	usherin isoform B	3896	Fibronectin type-III 24.|Extracellular (Potential).				maintenance of organ identity|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	basement membrane|cytoplasm|integral to membrane|stereocilium membrane	collagen binding			ovary(20)|kidney(1)|central_nervous_system(1)	22				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)										0.161905	81.9106	104.739984	34	176	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	215914740	215914740	17598	1	G	C	C	C	577	45	USH2A	3	3
RAB3GAP2	25782	broad.mit.edu	37	1	220386243	220386243	+	Missense_Mutation	SNP	T	A	A			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:220386243T>A	uc010puk.1	-	c.372A>T	c.(370-372)TTA>TTT	p.L124F	RAB3GAP2_uc001hmf.2_Non-coding_Transcript|RAB3GAP2_uc001hmg.2_5'UTR|RAB3GAP2_uc010pum.1_Missense_Mutation_p.L124F	NM_012414	NP_036546	Q9H2M9	RBGPR_HUMAN	rab3 GTPase-activating protein, non-catalytic	124					intracellular protein transport	cytoplasm|soluble fraction	GTPase activator activity|protein heterodimerization activity			central_nervous_system(1)	1				GBM - Glioblastoma multiforme(131;0.0443)										0.523256	123.685547	123.727313	45	41	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	220386243	220386243	13395	1	T	A	A	A	790	61	RAB3GAP2	3	3
PGBD5	79605	broad.mit.edu	37	1	230486821	230486821	+	Silent	SNP	C	G	G			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:230486821C>G	uc001htv.2	-	c.867G>C	c.(865-867)CTG>CTC	p.L289L	PGBD5_uc010pwb.1_Silent_p.L190L	NM_024554	NP_078830	Q8N414	PGBD5_HUMAN	piggyBac transposable element derived 5	190						integral to membrane				ovary(2)|central_nervous_system(1)	3	Breast(184;0.0397)	Prostate(94;0.167)		GBM - Glioblastoma multiforme(131;0.201)										0.082353	0.148409	15.271364	7	78	KEEP	---	---	---	---	capture		Silent	SNP	230486821	230486821	12207	1	C	G	G	G	366	29	PGBD5	3	3
MTR	4548	broad.mit.edu	37	1	237049656	237049656	+	Missense_Mutation	SNP	A	C	C			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:237049656A>C	uc001hyi.3	+	c.2840A>C	c.(2839-2841)GAA>GCA	p.E947A	MTR_uc010pxw.1_Missense_Mutation_p.E540A|MTR_uc010pxx.1_Missense_Mutation_p.E896A|MTR_uc010pxy.1_Missense_Mutation_p.E801A	NM_000254	NP_000245	Q99707	METH_HUMAN	5-methyltetrahydrofolate-homocysteine	947	AdoMet activation.				nervous system development|xenobiotic metabolic process	cytosol	cobalamin binding|homocysteine S-methyltransferase activity|methionine synthase activity|protein binding|zinc ion binding			ovary(1)|central_nervous_system(1)|pancreas(1)	3	Ovarian(103;0.0634)|Breast(184;0.221)	all_cancers(173;2.79e-22)|all_epithelial(177;4.84e-14)|Breast(1374;0.00123)|Prostate(94;0.0181)|Lung SC(1967;0.0262)|Acute lymphoblastic leukemia(190;0.117)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)	KIRC - Kidney renal clear cell carcinoma(1967;0.248)	Hydroxocobalamin(DB00200)|L-Methionine(DB00134)|Tetrahydrofolic acid(DB00116)									0.206186	55.410554	63.229927	20	77	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	237049656	237049656	10351	1	A	C	C	C	117	9	MTR	4	4
OR2M7	391196	broad.mit.edu	37	1	248487240	248487240	+	Missense_Mutation	SNP	C	G	G			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:248487240C>G	uc010pzk.1	-	c.631G>C	c.(631-633)GTT>CTT	p.V211L		NM_001004691	NP_001004691	Q8NG81	OR2M7_HUMAN	olfactory receptor, family 2, subfamily M,	211	Helical; Name=5; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)											0.482394	1019.732946	1019.886175	274	294	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	248487240	248487240	11420	1	C	G	G	G	221	17	OR2M7	3	3
SEPN1	57190	broad.mit.edu	37	1	26139275	26139275	+	Missense_Mutation	SNP	C	T	T			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:26139275C>T	uc010oer.1	+	c.1379C>T	c.(1378-1380)TCC>TTC	p.S460F	SEPN1_uc010oes.1_Missense_Mutation_p.S426F	NM_020451	NP_065184	Q9NZV5	SELN_HUMAN	selenoprotein N, 1 isoform 1 precursor	460						endoplasmic reticulum membrane|extracellular region	protein binding			ovary(2)	2		Colorectal(325;3.46e-05)|Lung NSC(340;0.00038)|all_lung(284;0.00051)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0155)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0505)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0421)|OV - Ovarian serous cystadenocarcinoma(117;1.26e-25)|Colorectal(126;3.01e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.000751)|BRCA - Breast invasive adenocarcinoma(304;0.00099)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.0143)|READ - Rectum adenocarcinoma(331;0.0649)										0.354839	27.71319	28.289851	11	20	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	26139275	26139275	14542	1	C	T	T	T	390	30	SEPN1	2	2
TMEM39B	55116	broad.mit.edu	37	1	32568034	32568034	+	Silent	SNP	C	T	T			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:32568034C>T	uc001bue.3	+	c.1242C>T	c.(1240-1242)TTC>TTT	p.F414F	TMEM39B_uc010ogv.1_Silent_p.F413F|TMEM39B_uc001buf.3_Silent_p.F214F|TMEM39B_uc010ogw.1_Silent_p.F214F	NM_018056	NP_060526	Q9GZU3	TM39B_HUMAN	transmembrane protein 39B	413						integral to membrane					0		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Ovarian(437;0.101)|Breast(348;0.174)												0.084746	-0.347481	20.313512	10	108	KEEP	---	---	---	---	capture		Silent	SNP	32568034	32568034	16701	1	C	T	T	T	415	32	TMEM39B	2	2
TSPAN1	10103	broad.mit.edu	37	1	46649908	46649908	+	Missense_Mutation	SNP	G	A	A			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:46649908G>A	uc001cpd.2	+	c.103G>A	c.(103-105)GAT>AAT	p.D35N	TSPAN1_uc009vyd.1_Missense_Mutation_p.D35N	NM_005727	NP_005718	O60635	TSN1_HUMAN	tetraspan 1	35	Extracellular (Potential).					integral to membrane|lysosomal membrane				ovary(1)	1	Acute lymphoblastic leukemia(166;0.155)	Medulloblastoma(700;0.00498)|all_neural(321;0.0212)												0.096591	3.439973	32.167991	17	159	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	46649908	46649908	17184	1	G	A	A	A	481	37	TSPAN1	1	1
NSUN4	387338	broad.mit.edu	37	1	46827467	46827467	+	Silent	SNP	C	G	G			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:46827467C>G	uc001cpr.1	+	c.1104C>G	c.(1102-1104)CTC>CTG	p.L368L	NSUN4_uc010omc.1_Silent_p.L319L|NSUN4_uc009vyf.1_Silent_p.L217L|NSUN4_uc009vyg.1_Silent_p.L319L|NSUN4_uc001cpt.1_Non-coding_Transcript|NSUN4_uc001cps.1_Non-coding_Transcript	NM_199044	NP_950245	Q96CB9	NSUN4_HUMAN	NOL1/NOP2/Sun domain family 4 protein	368							methyltransferase activity				0	Acute lymphoblastic leukemia(166;0.155)													0.191919	49.460531	58.244877	19	80	KEEP	---	---	---	---	capture		Silent	SNP	46827467	46827467	11085	1	C	G	G	G	366	29	NSUN4	3	3
CHD6	84181	broad.mit.edu	37	20	40122243	40122243	+	Missense_Mutation	SNP	C	T	T			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:40122243C>T	uc002xka.1	-	c.1249G>A	c.(1249-1251)GAT>AAT	p.D417N	CHD6_uc002xkd.2_Missense_Mutation_p.D395N	NM_032221	NP_115597	Q8TD26	CHD6_HUMAN	chromodomain helicase DNA binding protein 6	417	Chromo 2.				chromatin assembly or disassembly|chromatin remodeling|nervous system development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromatin|nucleus	ATP binding|ATP-dependent helicase activity|chromatin binding|DNA binding			ovary(6)|lung(2)|central_nervous_system(1)|skin(1)	10		Myeloproliferative disorder(115;0.00425)												0.045113	-17.673314	11.754998	6	127	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	40122243	40122243	3463	20	C	T	T	T	416	32	CHD6	2	2
FAM65C	140876	broad.mit.edu	37	20	49209728	49209728	+	Missense_Mutation	SNP	G	C	C			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:49209728G>C	uc010zyt.1	-	c.2218C>G	c.(2218-2220)CGC>GGC	p.R740G	FAM65C_uc010zyu.1_Non-coding_Transcript|FAM65C_uc002xvm.2_Missense_Mutation_p.R736G	NM_080829	NP_543019	Q96MK2	FA65C_HUMAN	hypothetical protein LOC140876	736										ovary(2)	2														0.327273	48.225766	49.683918	18	37	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	49209728	49209728	5824	20	G	C	C	C	507	39	FAM65C	3	3
LRRN4	164312	broad.mit.edu	37	20	6022399	6022399	+	Missense_Mutation	SNP	G	C	C			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:6022399G>C	uc002wmo.2	-	c.1492C>G	c.(1492-1494)CAG>GAG	p.Q498E		NM_152611	NP_689824	Q8WUT4	LRRN4_HUMAN	leucine rich repeat neuronal 4 precursor	498	Extracellular (Potential).					integral to membrane					0														0.036866	-32.188512	18.248706	8	209	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	6022399	6022399	9413	20	G	C	C	C	585	45	LRRN4	3	3
SETD4	54093	broad.mit.edu	37	21	37420692	37420692	+	Missense_Mutation	SNP	C	G	G			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr21:37420692C>G	uc002yuw.1	-	c.210G>C	c.(208-210)GAG>GAC	p.E70D	SETD4_uc002yux.1_Missense_Mutation_p.E46D|SETD4_uc002yuu.2_Intron|SETD4_uc002yuv.2_Missense_Mutation_p.E70D|SETD4_uc002yuy.2_Missense_Mutation_p.E70D|SETD4_uc002yuz.2_Missense_Mutation_p.E46D|SETD4_uc002yva.2_Missense_Mutation_p.E46D	NM_017438	NP_059134	Q9NVD3	SETD4_HUMAN	SET domain containing 4 isoform a	70	SET.									large_intestine(1)|ovary(1)	2														0.377717	466.935963	471.765534	139	229	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	37420692	37420692	14622	21	C	G	G	G	311	24	SETD4	3	3
COL18A1	80781	broad.mit.edu	37	21	46908346	46908346	+	Silent	SNP	G	T	T			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr21:46908346G>T	uc011afs.1	+	c.3156G>T	c.(3154-3156)CTG>CTT	p.L1052L	COL18A1_uc002zhg.2_Silent_p.L637L|COL18A1_uc002zhi.2_Silent_p.L817L	NM_130444	NP_569711	P39060	COIA1_HUMAN	alpha 1 type XVIII collagen isoform 3 precursor	1052	Triple-helical region 4 (COL4).				cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception	collagen|extracellular space	extracellular matrix structural constituent|metal ion binding|protein binding			central_nervous_system(1)	1				Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929)					p.L817L(HEC59-Tumor)	1836				0.058394	-13.316654	14.697843	8	129	KEEP	---	---	---	---	capture		Silent	SNP	46908346	46908346	3813	21	G	T	T	T	587	46	COL18A1	2	2
CRKL	1399	broad.mit.edu	37	22	21288146	21288146	+	Missense_Mutation	SNP	C	G	G			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:21288146C>G	uc002ztf.2	+	c.391C>G	c.(391-393)CTG>GTG	p.L131V	CRKL_uc002ztg.1_Non-coding_Transcript	NM_005207	NP_005198	P46109	CRKL_HUMAN	v-crk sarcoma virus CT10 oncogene homolog	131	SH3 1.				JNK cascade|Ras protein signal transduction	cytosol	protein tyrosine kinase activity|SH3/SH2 adaptor activity|signal transducer activity				0	all_cancers(11;1.16e-25)|all_epithelial(7;3.37e-24)|Lung NSC(8;7.25e-16)|all_lung(8;1.37e-14)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0332)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.000204)|Lung(15;0.00494)|Epithelial(17;0.176)			Pancreas(85;3 1441 23889 42519 42763)				67				0.125	41.488483	66.771457	23	161	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	21288146	21288146	4024	22	C	G	G	G	415	32	CRKL	3	3
MYO18B	84700	broad.mit.edu	37	22	26317265	26317265	+	Silent	SNP	A	G	G			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:26317265A>G	uc003abz.1	+	c.5406A>G	c.(5404-5406)AGA>AGG	p.R1802R	MYO18B_uc003aca.1_Silent_p.R1683R|MYO18B_uc010guy.1_Silent_p.R1684R|MYO18B_uc010guz.1_Silent_p.R1682R|MYO18B_uc011aka.1_Silent_p.R956R|MYO18B_uc011akb.1_Silent_p.R1315R	NM_032608	NP_115997	Q8IUG5	MY18B_HUMAN	myosin XVIIIB	1802	Tail.					nucleus|sarcomere|unconventional myosin complex	actin binding|ATP binding|motor activity			ovary(5)|central_nervous_system(3)|large_intestine(2)|breast(2)	12										968				0.2	5.944769	6.781273	2	8	KEEP	---	---	---	---	capture		Silent	SNP	26317265	26317265	10461	22	A	G	G	G	141	11	MYO18B	4	4
NF2	4771	broad.mit.edu	37	22	30077432	30077432	+	Missense_Mutation	SNP	G	C	C	rs74315505		TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:30077432G>C	uc003age.3	+	c.1579G>C	c.(1579-1581)GAA>CAA	p.E527Q	NF2_uc003afy.3_Missense_Mutation_p.E527Q|NF2_uc003afz.3_Missense_Mutation_p.E444Q|NF2_uc003agf.3_Missense_Mutation_p.E527Q|NF2_uc003agb.3_Missense_Mutation_p.E450Q|NF2_uc003agc.3_Missense_Mutation_p.E489Q|NF2_uc003agd.3_Intron|NF2_uc003agg.3_Missense_Mutation_p.E527Q|NF2_uc003aga.3_Missense_Mutation_p.E485Q|NF2_uc003agh.3_Missense_Mutation_p.E486Q|NF2_uc003agi.3_Missense_Mutation_p.E444Q|NF2_uc003agj.3_Intron|NF2_uc003agk.3_Missense_Mutation_p.E489Q|NF2_uc010gvp.2_Missense_Mutation_p.E191Q|NF2_uc011akq.1_Missense_Mutation_p.E153Q	NM_000268	NP_000259	P35240	MERL_HUMAN	neurofibromin 2 isoform 1	527					actin cytoskeleton organization|negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of cell-cell adhesion|negative regulation of cell-matrix adhesion|negative regulation of DNA replication|negative regulation of tyrosine phosphorylation of Stat3 protein|negative regulation of tyrosine phosphorylation of Stat5 protein|positive regulation of stress fiber assembly|regulation of hippo signaling cascade|Schwann cell proliferation	cytoskeleton|early endosome|extrinsic to membrane|filopodium membrane|nucleolus|perinuclear region of cytoplasm|ruffle membrane	cytoskeletal protein binding|protein binding	p.Y153*(2)|p.?(2)|p.L127_D382del(2)|p.L140_P252del(2)|p.G502_I577del(1)|p.K525fs*18(1)|p.E527fs*22(1)|p.A145_L163del(1)		meninges(371)|soft_tissue(271)|central_nervous_system(20)|kidney(10)|pleura(9)|skin(7)|large_intestine(5)|breast(5)|urinary_tract(3)|thyroid(2)|endometrium(2)|ovary(2)|lung(2)|stomach(2)|bone(2)|pituitary(1)	714										350				0.035971	-20.942797	11.53783	5	134	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	30077432	30077432	10757	22	G	C	C	C	533	41	NF2	3	3
TBC1D8	11138	broad.mit.edu	37	2	101646204	101646205	+	Missense_Mutation	DNP	GA	AG	AG			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:101646204_101646205GA>AG	uc010fiv.2	-	c.1925_1926TC>CT	c.(1924-1926)CTC>CCT	p.L642P	TBC1D8_uc002tau.3_Missense_Mutation_p.L399P	NM_001102426	NP_001095896	O95759	TBCD8_HUMAN	TBC1 domain family, member 8	642	Rab-GAP TBC.				blood circulation|positive regulation of cell proliferation	intracellular|membrane	calcium ion binding|Rab GTPase activator activity			ovary(3)	3														0.275862	60.956227	64.895555	24	63	KEEP	---	---	---	---	capture		Missense_Mutation	DNP	101646204	101646205	16151	2	GA	AG	AG	AG	574	45	TBC1D8	2	2
POTEE	445582	broad.mit.edu	37	2	131976380	131976380	+	Silent	SNP	C	T	T			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:131976380C>T	uc002tsn.2	+	c.405C>T	c.(403-405)GTC>GTT	p.V135V	PLEKHB2_uc002tsh.2_Intron|POTEE_uc002tsk.2_5'UTR|POTEE_uc002tsl.2_5'UTR	NM_001083538	NP_001077007	Q6S8J3	POTEE_HUMAN	protein expressed in prostate, ovary, testis,	135							ATP binding				0														0.231343	64.491812	73.33956	31	103	KEEP	---	---	---	---	capture		Silent	SNP	131976380	131976380	12694	2	C	T	T	T	379	30	POTEE	2	2
ACVR1	90	broad.mit.edu	37	2	158626930	158626930	+	Missense_Mutation	SNP	C	T	T			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:158626930C>T	uc002tzm.3	-	c.740G>A	c.(739-741)AGG>AAG	p.R247K	ACVR1_uc002tzn.3_Missense_Mutation_p.R247K|ACVR1_uc010fog.2_Missense_Mutation_p.R247K	NM_001111067	NP_001104537	Q04771	ACVR1_HUMAN	activin A receptor, type I precursor	247	Cytoplasmic (Potential).|Protein kinase.				BMP signaling pathway|G1/S transition of mitotic cell cycle|negative regulation of activin receptor signaling pathway|negative regulation of apoptosis|positive regulation of bone mineralization|positive regulation of osteoblast differentiation|positive regulation of transcription, DNA-dependent|protein phosphorylation|transforming growth factor beta receptor signaling pathway	activin receptor complex	activin binding|ATP binding|follistatin binding|metal ion binding|protein homodimerization activity|SMAD binding|transforming growth factor beta binding			ovary(2)|skin(1)	3				BRCA - Breast invasive adenocarcinoma(221;0.104)	Adenosine triphosphate(DB00171)					185				0.297468	133.458211	139.255523	47	111	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	158626930	158626930	221	2	C	T	T	T	312	24	ACVR1	2	2
SCN9A	6335	broad.mit.edu	37	2	167168258	167168258	+	Missense_Mutation	SNP	C	T	T			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:167168258C>T	uc010fpl.2	-	c.9G>A	c.(7-9)ATG>ATA	p.M3I		NM_002977	NP_002968	Q15858	SCN9A_HUMAN	sodium channel, voltage-gated, type IX, alpha	3						voltage-gated sodium channel complex	voltage-gated sodium channel activity			ovary(6)|central_nervous_system(5)	11					Lamotrigine(DB00555)|Lidocaine(DB00281)									0.393258	88.592579	89.484124	35	54	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	167168258	167168258	14407	2	C	T	T	T	221	17	SCN9A	2	2
TTN	7273	broad.mit.edu	37	2	179650595	179650595	+	Missense_Mutation	SNP	C	T	T			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:179650595C>T	uc010zfg.1	-	c.2350G>A	c.(2350-2352)GGA>AGA	p.G784R	TTN_uc010zfh.1_Missense_Mutation_p.G738R|TTN_uc010zfi.1_Missense_Mutation_p.G738R|TTN_uc010zfj.1_Missense_Mutation_p.G738R|TTN_uc002unb.2_Missense_Mutation_p.G784R|TTN_uc010frg.1_Missense_Mutation_p.G366R	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	784										ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)							8722				0.266667	64.484196	68.894508	24	66	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	179650595	179650595	17290	2	C	T	T	T	286	22	TTN	2	2
CRYGB	1419	broad.mit.edu	37	2	209007437	209007437	+	Silent	SNP	C	T	T			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:209007437C>T	uc002vcp.3	-	c.453G>A	c.(451-453)GAG>GAA	p.E151E		NM_005210	NP_005201	P07316	CRGB_HUMAN	crystallin, gamma B	151	Beta/gamma crystallin 'Greek key' 4.				visual perception		structural constituent of eye lens				0				Epithelial(149;0.0641)|LUSC - Lung squamous cell carcinoma(261;0.0703)|Lung(261;0.132)										0.14433	42.753402	66.417629	28	166	KEEP	---	---	---	---	capture		Silent	SNP	209007437	209007437	4054	2	C	T	T	T	259	20	CRYGB	2	2
SPAG16	79582	broad.mit.edu	37	2	214354705	214354705	+	Missense_Mutation	SNP	G	C	C			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:214354705G>C	uc002veq.2	+	c.961G>C	c.(961-963)GAT>CAT	p.D321H	SPAG16_uc010fuz.1_Missense_Mutation_p.D172H|SPAG16_uc002ver.2_Missense_Mutation_p.D267H|SPAG16_uc010zjk.1_Missense_Mutation_p.D227H	NM_024532	NP_078808	Q8N0X2	SPG16_HUMAN	sperm associated antigen 16 isoform 1	321					cilium assembly	cilium axoneme|flagellar axoneme				ovary(1)	1		Renal(323;0.00461)		UCEC - Uterine corpus endometrioid carcinoma (47;0.0525)|Epithelial(149;7.07e-07)|all cancers(144;7.96e-05)|Lung(261;0.00255)|LUSC - Lung squamous cell carcinoma(224;0.00599)										0.113636	18.381575	31.341034	10	78	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	214354705	214354705	15481	2	G	C	C	C	429	33	SPAG16	3	3
SPEG	10290	broad.mit.edu	37	2	220344819	220344819	+	Missense_Mutation	SNP	G	C	C			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:220344819G>C	uc010fwg.2	+	c.5299G>C	c.(5299-5301)GAG>CAG	p.E1767Q		NM_005876	NP_005867	Q15772	SPEG_HUMAN	SPEG complex locus	1767	Protein kinase 1.				muscle organ development|negative regulation of cell proliferation|protein phosphorylation	nucleus	ATP binding|protein serine/threonine kinase activity			ovary(4)|stomach(2)|central_nervous_system(1)	7		Renal(207;0.0183)		Epithelial(149;4.5e-10)|all cancers(144;7.93e-08)|Lung(261;0.00639)|LUSC - Lung squamous cell carcinoma(224;0.00829)|READ - Rectum adenocarcinoma(5;0.163)						482				0.054054	-6.696899	16.530312	6	105	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	220344819	220344819	15548	2	G	C	C	C	481	37	SPEG	3	3
CYP1B1	1545	broad.mit.edu	37	2	38301556	38301556	+	Missense_Mutation	SNP	C	T	T			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:38301556C>T	uc002rqo.2	-	c.976G>A	c.(976-978)GAC>AAC	p.D326N		NM_000104	NP_000095	Q16678	CP1B1_HUMAN	cytochrome P450, family 1, subfamily B,	326					oxidation-reduction process|visual perception|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	aromatase activity|electron carrier activity|heme binding|oxygen binding|protein binding			ovary(1)|central_nervous_system(1)	2		all_hematologic(82;0.21)			Estrone(DB00655)					68				0.294118	8.517304	9.198395	5	12	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	38301556	38301556	4316	2	C	T	T	T	377	29	CYP1B1	2	2
SLC8A1	6546	broad.mit.edu	37	2	40656137	40656137	+	Silent	SNP	G	T	T			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:40656137G>T	uc002rrx.2	-	c.1284C>A	c.(1282-1284)ACC>ACA	p.T428T	SLC8A1_uc002rry.2_Silent_p.T428T|SLC8A1_uc002rrz.2_Silent_p.T428T|SLC8A1_uc002rsa.2_Silent_p.T428T|SLC8A1_uc002rsd.3_Silent_p.T428T|SLC8A1_uc002rsb.1_Silent_p.T428T|SLC8A1_uc010fan.1_Silent_p.T428T|SLC8A1_uc002rsc.1_Silent_p.T428T	NM_021097	NP_066920	P32418	NAC1_HUMAN	solute carrier family 8 (sodium/calcium	428	Calx-beta 1.|Cytoplasmic (Potential).				cell communication|muscle contraction|platelet activation	integral to plasma membrane	calcium:sodium antiporter activity|calmodulin binding|heat shock protein binding			ovary(1)|kidney(1)|central_nervous_system(1)	3					Alpha-Linolenic Acid(DB00132)|Icosapent(DB00159)									0.052083	-11.612571	8.767228	5	91	KEEP	---	---	---	---	capture		Silent	SNP	40656137	40656137	15203	2	G	T	T	T	600	47	SLC8A1	2	2
EXOC6B	23233	broad.mit.edu	37	2	72945355	72945355	+	Silent	SNP	C	T	T			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:72945355C>T	uc010fep.2	-	c.546G>A	c.(544-546)GTG>GTA	p.V182V	EXOC6B_uc002sij.2_Silent_p.V182V	NM_015189	NP_056004	Q9Y2D4	EXC6B_HUMAN	SEC15-like 2	182					protein transport|vesicle docking involved in exocytosis	exocyst				central_nervous_system(2)	2														0.152	27.233715	41.740588	19	106	KEEP	---	---	---	---	capture		Silent	SNP	72945355	72945355	5502	2	C	T	T	T	366	29	EXOC6B	2	2
ZNF514	84874	broad.mit.edu	37	2	95815686	95815686	+	Missense_Mutation	SNP	C	T	T			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:95815686C>T	uc002sud.1	-	c.763G>A	c.(763-765)GAT>AAT	p.D255N	ZNF514_uc002sue.1_Missense_Mutation_p.D182N	NM_032788	NP_116177	Q96K75	ZN514_HUMAN	zinc finger protein 514	182					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0														0.110345	21.764751	65.366987	32	258	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	95815686	95815686	18553	2	C	T	T	T	377	29	ZNF514	2	2
EIF5B	9669	broad.mit.edu	37	2	99980189	99980189	+	Missense_Mutation	SNP	A	C	C			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:99980189A>C	uc002tab.2	+	c.1001A>C	c.(1000-1002)AAA>ACA	p.K334T		NM_015904	NP_056988	O60841	IF2P_HUMAN	eukaryotic translation initiation factor 5B	334					regulation of translational initiation	cytosol	GTP binding|GTPase activity|protein binding|translation initiation factor activity			ovary(1)|pancreas(1)	2						Colon(162;2388 2567 2705 3444)								0.45283	85.596959	85.699244	24	29	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	99980189	99980189	5235	2	A	C	C	C	13	1	EIF5B	4	4
EIF5B	9669	broad.mit.edu	37	2	99998629	99998629	+	Missense_Mutation	SNP	G	C	C			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:99998629G>C	uc002tab.2	+	c.2069G>C	c.(2068-2070)AGA>ACA	p.R690T		NM_015904	NP_056988	O60841	IF2P_HUMAN	eukaryotic translation initiation factor 5B	690					regulation of translational initiation	cytosol	GTP binding|GTPase activity|protein binding|translation initiation factor activity			ovary(1)|pancreas(1)	2						Colon(162;2388 2567 2705 3444)								0.076923	2.01943	13.931338	5	60	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	99998629	99998629	5235	2	G	C	C	C	429	33	EIF5B	3	3
CCDC52	152185	broad.mit.edu	37	3	113225439	113225439	+	Missense_Mutation	SNP	C	T	T			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:113225439C>T	uc003eag.3	-	c.14G>A	c.(13-15)AGA>AAA	p.R5K	CCDC52_uc003eaf.3_Non-coding_Transcript|CCDC52_uc011bie.1_Missense_Mutation_p.R17K|CCDC52_uc003eai.1_Missense_Mutation_p.R5K	NM_144718	NP_653319	Q8N0Z3	SPICE_HUMAN	coiled-coil domain containing 52	5					cell division|mitosis	centriole|spindle	protein binding				0														0.097561	2.867796	9.518098	4	37	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	113225439	113225439	2945	3	C	T	T	T	416	32	CCDC52	2	2
ATP6V1A	523	broad.mit.edu	37	3	113528247	113528247	+	Missense_Mutation	SNP	G	C	C			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:113528247G>C	uc003eao.2	+	c.1827G>C	c.(1825-1827)CAG>CAC	p.Q609H	ATP6V1A_uc011bik.1_Missense_Mutation_p.Q576H	NM_001690	NP_001681	P38606	VATA_HUMAN	ATPase, H+ transporting, lysosomal V1 subunit A	609					ATP hydrolysis coupled proton transport|cellular iron ion homeostasis|insulin receptor signaling pathway|transferrin transport	cytosol|integral to plasma membrane|proton-transporting V-type ATPase, V1 domain	ATP binding|hydrogen ion transporting ATP synthase activity, rotational mechanism|proton-transporting ATPase activity, rotational mechanism			ovary(2)	2														0.088235	8.994911	26.475778	9	93	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	113528247	113528247	1196	3	G	C	C	C	425	33	ATP6V1A	3	3
IQSEC1	9922	broad.mit.edu	37	3	12961967	12961967	+	Silent	SNP	C	G	G			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:12961967C>G	uc011auw.1	-	c.1983G>C	c.(1981-1983)CGG>CGC	p.R661R	IQSEC1_uc003bxt.2_Silent_p.R675R|IQSEC1_uc003bxu.3_Silent_p.R553R	NM_001134382	NP_001127854	Q6DN90	IQEC1_HUMAN	IQ motif and Sec7 domain 1 isoform a	675	SEC7.				regulation of ARF protein signal transduction	cytoplasm|nucleus	ARF guanyl-nucleotide exchange factor activity			ovary(1)	1														0.032258	-30.642921	13.760549	6	180	KEEP	---	---	---	---	capture		Silent	SNP	12961967	12961967	8120	3	C	G	G	G	379	30	IQSEC1	3	3
AADACL2	344752	broad.mit.edu	37	3	151475041	151475041	+	Missense_Mutation	SNP	G	C	C			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:151475041G>C	uc003ezc.2	+	c.865G>C	c.(865-867)GAG>CAG	p.E289Q	AADACL2_uc010hvn.2_Missense_Mutation_p.E76Q	NM_207365	NP_997248	Q6P093	ADCL2_HUMAN	arylacetamide deacetylase-like 2 precursor	289						extracellular region|integral to membrane	carboxylesterase activity				0			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0813)											0.051724	-8.754267	15.909791	6	110	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	151475041	151475041	12	3	G	C	C	C	585	45	AADACL2	3	3
GNB4	59345	broad.mit.edu	37	3	179132738	179132738	+	Missense_Mutation	SNP	G	C	C			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:179132738G>C	uc003fjv.3	-	c.365C>G	c.(364-366)TCT>TGT	p.S122C	GNB4_uc003fju.3_Missense_Mutation_p.S33C	NM_021629	NP_067642	Q9HAV0	GBB4_HUMAN	guanine nucleotide-binding protein, beta-4	122	WD 2.				cellular response to glucagon stimulus|energy reserve metabolic process	plasma membrane	signal transducer activity			skin(2)	2	all_cancers(143;2.01e-16)|Ovarian(172;0.0172)|Breast(254;0.191)		OV - Ovarian serous cystadenocarcinoma(80;5.78e-26)|GBM - Glioblastoma multiforme(14;0.0169)|BRCA - Breast invasive adenocarcinoma(182;0.237)			Melanoma(105;1405 1491 7265 20440 33721)								0.121076	43.399781	74.759668	27	196	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	179132738	179132738	6789	3	G	C	C	C	429	33	GNB4	3	3
YEATS2	55689	broad.mit.edu	37	3	183508768	183508768	+	Missense_Mutation	SNP	G	A	A			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:183508768G>A	uc003fly.2	+	c.3097G>A	c.(3097-3099)GGA>AGA	p.G1033R	YEATS2_uc003flz.2_Missense_Mutation_p.D112N	NM_018023	NP_060493	Q9ULM3	YETS2_HUMAN	YEATS domain containing 2	1033					histone H3 acetylation|negative regulation of gene-specific transcription from RNA polymerase II promoter	Ada2/Gcn5/Ada3 transcription activator complex	specific transcriptional repressor activity|TBP-class protein binding			ovary(2)|large_intestine(1)	3	all_cancers(143;6.55e-10)|Ovarian(172;0.0303)		all cancers(12;2.38e-42)|Epithelial(37;1.9e-36)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)											0.285714	78.704217	83.032407	30	75	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	183508768	183508768	18055	3	G	A	A	A	507	39	YEATS2	1	1
FETUB	26998	broad.mit.edu	37	3	186370114	186370114	+	Silent	SNP	G	T	T			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:186370114G>T	uc010hyq.2	+	c.843G>T	c.(841-843)GTG>GTT	p.V281V	FETUB_uc011brz.1_Silent_p.V133V|FETUB_uc003fqn.2_Silent_p.V281V|FETUB_uc003fqo.2_Silent_p.V176V|FETUB_uc010hyr.2_Silent_p.V244V|FETUB_uc010hys.2_Silent_p.V133V|FETUB_uc003fqp.3_Silent_p.V216V	NM_014375	NP_055190	Q9UGM5	FETUB_HUMAN	fetuin B precursor	281						extracellular space	cysteine-type endopeptidase inhibitor activity			ovary(1)|lung(1)	2	all_cancers(143;6.64e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;5.73e-20)	GBM - Glioblastoma multiforme(93;0.0479)										0.333333	182.920657	188.470482	75	150	KEEP	---	---	---	---	capture		Silent	SNP	186370114	186370114	6058	3	G	T	T	T	600	47	FETUB	2	2
OXSM	54995	broad.mit.edu	37	3	25833286	25833286	+	Missense_Mutation	SNP	G	C	C			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:25833286G>C	uc003cdn.2	+	c.775G>C	c.(775-777)GAT>CAT	p.D259H	NGLY1_uc011awo.1_5'Flank|OXSM_uc011awp.1_5'UTR|OXSM_uc010hfh.2_Intron	NM_017897	NP_060367	Q9NWU1	OXSM_HUMAN	3-oxoacyl-ACP synthase, mitochondrial isoform 1	259					acyl-CoA metabolic process|medium-chain fatty acid biosynthetic process|short-chain fatty acid biosynthetic process	mitochondrion	3-oxoacyl-[acyl-carrier-protein] synthase activity			ovary(1)|breast(1)	2														0.068702	0.462675	25.657596	9	122	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	25833286	25833286	11748	3	G	C	C	C	429	33	OXSM	3	3
COL7A1	1294	broad.mit.edu	37	3	48605555	48605555	+	Missense_Mutation	SNP	C	G	G			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:48605555C>G	uc003ctz.2	-	c.7843G>C	c.(7843-7845)GAT>CAT	p.D2615H		NM_000094	NP_000085	Q02388	CO7A1_HUMAN	alpha 1 type VII collagen precursor	2615	Triple-helical region.				cell adhesion|epidermis development	basement membrane|collagen type VII	protein binding|serine-type endopeptidase inhibitor activity			ovary(4)|breast(3)|skin(2)	9				BRCA - Breast invasive adenocarcinoma(193;0.000293)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)										0.120968	28.632306	46.095466	15	109	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	48605555	48605555	3842	3	C	G	G	G	416	32	COL7A1	3	3
PRICKLE2	166336	broad.mit.edu	37	3	64148775	64148775	+	Missense_Mutation	SNP	C	T	T			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:64148775C>T	uc003dmf.2	-	c.175G>A	c.(175-177)GAG>AAG	p.E59K		NM_198859	NP_942559	Q7Z3G6	PRIC2_HUMAN	prickle-like 2	59	PET.					cytoplasm|nuclear membrane	zinc ion binding			ovary(4)	4		Lung NSC(201;0.136)		BRCA - Breast invasive adenocarcinoma(55;0.000971)|KIRC - Kidney renal clear cell carcinoma(15;0.00443)|Kidney(15;0.00497)										0.041812	-41.466332	23.300775	12	275	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	64148775	64148775	12930	3	C	T	T	T	416	32	PRICKLE2	2	2
SRGAP3	9901	broad.mit.edu	37	3	9101977	9101977	+	Missense_Mutation	SNP	G	C	C			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:9101977G>C	uc003brf.1	-	c.739C>G	c.(739-741)CTG>GTG	p.L247V	SRGAP3_uc003brg.1_Missense_Mutation_p.L247V|SRGAP3_uc003bri.1_Non-coding_Transcript|SRGAP3_uc003brk.2_Missense_Mutation_p.L247V|SRGAP3_uc003brj.1_Missense_Mutation_p.L107V	NM_014850	NP_055665	O43295	SRGP2_HUMAN	SLIT-ROBO Rho GTPase activating protein 3	247					regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity|protein binding		SRGAP3/RAF1(4)	central_nervous_system(4)|urinary_tract(1)|breast(1)	6				OV - Ovarian serous cystadenocarcinoma(96;0.0563)										0.034965	-21.542909	12.074446	5	138	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	9101977	9101977	15661	3	G	C	C	C	425	33	SRGAP3	3	3
BOD1L	259282	broad.mit.edu	37	4	13605037	13605037	+	Missense_Mutation	SNP	G	C	C			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:13605037G>C	uc003gmz.1	-	c.3487C>G	c.(3487-3489)CAA>GAA	p.Q1163E	BOD1L_uc010idr.1_Missense_Mutation_p.Q500E	NM_148894	NP_683692	Q8NFC6	BOD1L_HUMAN	biorientation of chromosomes in cell division	1163							DNA binding			ovary(5)|breast(1)	6														0.096386	18.368	45.483641	16	150	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	13605037	13605037	1508	4	G	C	C	C	585	45	BOD1L	3	3
TIGD4	201798	broad.mit.edu	37	4	153691681	153691681	+	Missense_Mutation	SNP	G	A	A			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:153691681G>A	uc003imy.2	-	c.476C>T	c.(475-477)TCG>TTG	p.S159L		NM_145720	NP_663772	Q8IY51	TIGD4_HUMAN	tigger transposable element derived 4	159						chromosome, centromeric region|nucleus	chromatin binding|DNA binding			ovary(1)	1	all_hematologic(180;0.093)													0.082192	-2.010183	10.96698	6	67	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	153691681	153691681	16427	4	G	A	A	A	481	37	TIGD4	1	1
TRIM2	23321	broad.mit.edu	37	4	154215474	154215474	+	Missense_Mutation	SNP	C	G	G			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:154215474C>G	uc003inh.2	+	c.623C>G	c.(622-624)TCT>TGT	p.S208C	TRIM2_uc003ing.2_Missense_Mutation_p.S181C	NM_015271	NP_056086	Q9C040	TRIM2_HUMAN	tripartite motif-containing 2 isoform 1	181						cytoplasm	zinc ion binding			central_nervous_system(1)	1	all_hematologic(180;0.093)	Medulloblastoma(177;0.00225)		GBM - Glioblastoma multiforme(119;0.0102)|LUSC - Lung squamous cell carcinoma(193;0.0703)										0.048077	-11.319571	11.281452	5	99	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	154215474	154215474	17038	4	C	G	G	G	416	32	TRIM2	3	3
GUCY1A3	2982	broad.mit.edu	37	4	156634681	156634681	+	Silent	SNP	C	G	G			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:156634681C>G	uc003iov.2	+	c.1518C>G	c.(1516-1518)CTC>CTG	p.L506L	GUCY1A3_uc010iqc.2_Silent_p.L506L|GUCY1A3_uc003iow.2_Silent_p.L506L|GUCY1A3_uc010iqd.2_Silent_p.L505L|GUCY1A3_uc003iox.2_Silent_p.L506L|GUCY1A3_uc003ioz.2_Silent_p.L271L|GUCY1A3_uc003ioy.2_Silent_p.L506L|GUCY1A3_uc010iqe.2_Silent_p.L271L|GUCY1A3_uc003ipa.2_Intron|GUCY1A3_uc003ipb.2_Silent_p.L506L	NM_000856	NP_000847	Q02108	GCYA3_HUMAN	guanylate cyclase 1, soluble, alpha 3 isoform A	506	Guanylate cyclase.				blood circulation|intracellular signal transduction|nitric oxide mediated signal transduction|platelet activation	guanylate cyclase complex, soluble	GTP binding|guanylate cyclase activity|heme binding|receptor activity			central_nervous_system(2)|ovary(1)	3	all_hematologic(180;0.24)	Renal(120;0.0854)		COAD - Colon adenocarcinoma(41;0.17)										0.071429	1.352161	11.950991	4	52	KEEP	---	---	---	---	capture		Silent	SNP	156634681	156634681	7174	4	C	G	G	G	366	29	GUCY1A3	3	3
TMEM144	55314	broad.mit.edu	37	4	159161476	159161476	+	Silent	SNP	C	T	T			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:159161476C>T	uc003ipx.2	+	c.708C>T	c.(706-708)TTC>TTT	p.F236F	TMEM144_uc010iqi.2_Non-coding_Transcript	NM_018342	NP_060812	Q7Z5S9	TM144_HUMAN	transmembrane protein 144	236	Helical; (Potential).					integral to membrane					0	all_hematologic(180;0.24)	Renal(120;0.0854)		COAD - Colon adenocarcinoma(41;0.0539)										0.052632	-11.602838	8.493631	5	90	KEEP	---	---	---	---	capture		Silent	SNP	159161476	159161476	16590	4	C	T	T	T	376	29	TMEM144	2	2
NCAPG	64151	broad.mit.edu	37	4	17818967	17818967	+	Missense_Mutation	SNP	C	T	T			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:17818967C>T	uc003gpp.2	+	c.859C>T	c.(859-861)CGG>TGG	p.R287W	NCAPG_uc011bxj.1_5'UTR	NM_022346	NP_071741	Q9BPX3	CND3_HUMAN	chromosome condensation protein G	287	HEAT 5.				cell division|mitotic chromosome condensation	condensin complex|cytoplasm|nucleus	protein binding			large_intestine(1)	1				STAD - Stomach adenocarcinoma(129;0.18)										0.056497	-19.393178	17.20031	10	167	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	17818967	17818967	10606	4	C	T	T	T	399	31	NCAPG	1	1
ACSL1	2180	broad.mit.edu	37	4	185697770	185697770	+	Silent	SNP	G	C	C			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:185697770G>C	uc003iww.2	-	c.624C>G	c.(622-624)CTC>CTG	p.L208L	ACSL1_uc011ckm.1_Silent_p.L37L|ACSL1_uc003iwt.1_Silent_p.L208L|ACSL1_uc003iwu.1_Silent_p.L208L|ACSL1_uc011ckn.1_Silent_p.L174L|ACSL1_uc003iwv.1_Silent_p.L208L|ACSL1_uc010ise.1_5'Flank	NM_001995	NP_001986	P33121	ACSL1_HUMAN	acyl-CoA synthetase long-chain family member 1	208	Cytoplasmic (Potential).				digestion|fatty acid metabolic process|long-chain fatty-acyl-CoA biosynthetic process|regulation of fatty acid oxidation|triglyceride biosynthetic process	endoplasmic reticulum membrane|integral to membrane|microsome|mitochondrial outer membrane|peroxisomal membrane	ATP binding|long-chain fatty acid-CoA ligase activity			ovary(2)	2		all_lung(41;7.57e-14)|Lung NSC(41;1.81e-13)|Colorectal(36;0.00172)|Hepatocellular(41;0.00826)|Renal(120;0.00988)|Prostate(90;0.0235)|all_hematologic(60;0.0315)|all_neural(102;0.107)|Medulloblastoma(177;0.146)		all cancers(43;1.33e-28)|Epithelial(43;5.3e-25)|OV - Ovarian serous cystadenocarcinoma(60;4.88e-11)|Colorectal(24;3.59e-06)|STAD - Stomach adenocarcinoma(60;2.72e-05)|GBM - Glioblastoma multiforme(59;2.83e-05)|BRCA - Breast invasive adenocarcinoma(30;7.66e-05)|COAD - Colon adenocarcinoma(29;0.000538)|LUSC - Lung squamous cell carcinoma(40;0.008)|READ - Rectum adenocarcinoma(43;0.0419)	Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)									0.041667	-11.375866	10.289289	4	92	KEEP	---	---	---	---	capture		Silent	SNP	185697770	185697770	178	4	G	C	C	C	418	33	ACSL1	3	3
KLHL5	51088	broad.mit.edu	37	4	39082722	39082722	+	Splice_Site_SNP	SNP	G	C	C			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:39082722G>C	uc003gtr.1	+	c.705_splice	c.e3-1	p.R235_splice	KLHL5_uc003gtp.2_Splice_Site_SNP_p.R189_splice|KLHL5_uc003gtq.2_Splice_Site_SNP_p.R48_splice|KLHL5_uc003gts.2_Splice_Site_SNP_p.R235_splice|KLHL5_uc003gtt.2_Splice_Site_SNP_p.R174_splice	NM_015990	NP_057074			kelch-like 5 isoform 1							cytoplasm|cytoskeleton	actin binding			ovary(1)	1														0.034247	-23.758402	10.730796	5	141	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	39082722	39082722	8706	4	G	C	C	C	429	33	KLHL5	5	3
GABRA2	2555	broad.mit.edu	37	4	46307713	46307713	+	Nonsense_Mutation	SNP	G	T	T			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:46307713G>T	uc003gxc.3	-	c.575C>A	c.(574-576)TCA>TAA	p.S192*	GABRA2_uc010igc.2_Nonsense_Mutation_p.S192*|GABRA2_uc011bzc.1_Nonsense_Mutation_p.S137*|GABRA2_uc003gxe.2_Nonsense_Mutation_p.S192*	NM_001114175	NP_001107647	P47869	GBRA2_HUMAN	gamma-aminobutyric acid A receptor, alpha 2	192	Extracellular (Probable).				gamma-aminobutyric acid signaling pathway|neurotransmitter transport|regulation of neurotransmitter levels	cell junction|chloride channel complex|integral to synaptic vesicle membrane|postsynaptic membrane	benzodiazepine receptor activity|chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity			ovary(2)	2					Alprazolam(DB00404)|Bromazepam(DB01558)|Diazepam(DB00829)|Ethchlorvynol(DB00189)|Fludiazepam(DB01567)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Lorazepam(DB00186)|Meprobamate(DB00371)|Midazolam(DB00683)									0.445946	84.835522	85.027705	33	41	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	46307713	46307713	6412	4	G	T	T	T	585	45	GABRA2	5	2
REST	5978	broad.mit.edu	37	4	57777211	57777211	+	Missense_Mutation	SNP	C	T	T			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:57777211C>T	uc003hch.2	+	c.407C>T	c.(406-408)TCA>TTA	p.S136L	REST_uc003hci.2_Missense_Mutation_p.S136L|REST_uc003hcj.1_Missense_Mutation_p.S136L|REST_uc010ihf.2_5'UTR	NM_005612	NP_005603	Q13127	REST_HUMAN	RE1-silencing transcription factor	136					transcription, DNA-dependent	cytoplasm|nucleus	transcription repressor activity|zinc ion binding			skin(2)|ovary(1)|lung(1)	4	Glioma(25;0.08)|all_neural(26;0.181)													0.05036	-17.999894	11.816058	7	132	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	57777211	57777211	13704	4	C	T	T	T	377	29	REST	2	2
MOBKL1A	92597	broad.mit.edu	37	4	71844961	71844961	+	Nonsense_Mutation	SNP	G	T	T			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:71844961G>T	uc011cba.1	+	c.541G>T	c.(541-543)GAA>TAA	p.E181*	MOBKL1A_uc003hfw.2_Nonsense_Mutation_p.E176*	NM_173468	NP_775739	Q7L9L4	MOL1A_HUMAN	MOB1, Mps One Binder kinase activator-like 1A	176					hippo signaling cascade|protein autophosphorylation	cytoplasm|nucleus	kinase activator activity|kinase binding|metal ion binding				0		all_hematologic(202;0.21)	Lung(101;0.235)											0.131429	21.955249	45.03687	23	152	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	71844961	71844961	10073	4	G	T	T	T	533	41	MOBKL1A	5	2
NKD2	85409	broad.mit.edu	37	5	1038130	1038130	+	Missense_Mutation	SNP	C	T	T			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:1038130C>T	uc003jbt.1	+	c.998C>T	c.(997-999)TCC>TTC	p.S333F	NKD2_uc010itf.1_3'UTR	NM_033120	NP_149111	Q969F2	NKD2_HUMAN	naked cuticle homolog 2	333	Interaction with TGFA.				exocytosis|Wnt receptor signaling pathway	cytoplasmic membrane-bounded vesicle|plasma membrane	calcium ion binding|ubiquitin protein ligase binding				0	Lung NSC(6;2.47e-13)|all_lung(6;1.67e-12)|all_epithelial(6;3.28e-09)		Epithelial(17;0.00093)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|all cancers(22;0.00417)|Lung(60;0.165)							126				0.3125	11.667387	12.169199	5	11	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	1038130	1038130	10843	5	C	T	T	T	390	30	NKD2	2	2
SRFBP1	153443	broad.mit.edu	37	5	121355964	121355964	+	Silent	SNP	G	A	A			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:121355964G>A	uc003kst.1	+	c.534G>A	c.(532-534)AAG>AAA	p.K178K		NM_152546	NP_689759	Q8NEF9	SRFB1_HUMAN	serum response factor binding protein 1	178					regulation of transcription, DNA-dependent|transcription, DNA-dependent	perinuclear region of cytoplasm					0		all_cancers(142;0.0124)|Prostate(80;0.0322)	KIRC - Kidney renal clear cell carcinoma(527;0.206)	OV - Ovarian serous cystadenocarcinoma(64;0.000227)|Epithelial(69;0.000365)|all cancers(49;0.00517)										0.36	104.269849	105.996466	36	64	KEEP	---	---	---	---	capture		Silent	SNP	121355964	121355964	15658	5	G	A	A	A	425	33	SRFBP1	2	2
SMAD5	4090	broad.mit.edu	37	5	135496714	135496714	+	Silent	SNP	C	T	T			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:135496714C>T	uc003lbj.1	+	c.573C>T	c.(571-573)AGC>AGT	p.S191S	SMAD5_uc003lbk.1_Silent_p.S191S|SMAD5_uc003lbl.1_Silent_p.S191S	NM_001001419	NP_001001419	Q99717	SMAD5_HUMAN	SMAD family member 5	191					BMP signaling pathway|embryonic pattern specification|regulation of transcription, DNA-dependent|transforming growth factor beta receptor signaling pathway	cytosol|integral to membrane|transcription factor complex	sequence-specific DNA binding transcription factor activity|transcription activator activity|transforming growth factor beta receptor, pathway-specific cytoplasmic mediator activity|ubiquitin protein ligase binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)											0.319672	198.384597	205.425022	78	166	KEEP	---	---	---	---	capture		Silent	SNP	135496714	135496714	15259	5	C	T	T	T	337	26	SMAD5	2	2
MATR3	9782	broad.mit.edu	37	5	138661216	138661216	+	Missense_Mutation	SNP	G	C	C			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:138661216G>C	uc003ldw.2	+	c.2380G>C	c.(2380-2382)GAA>CAA	p.E794Q	MATR3_uc003ldt.2_Missense_Mutation_p.E408Q|MATR3_uc003ldu.2_Missense_Mutation_p.E746Q|MATR3_uc003ldx.2_Missense_Mutation_p.E746Q|MATR3_uc010jfc.2_Missense_Mutation_p.E746Q|MATR3_uc011czb.1_Missense_Mutation_p.E458Q|MATR3_uc003ldz.2_Missense_Mutation_p.E746Q|MATR3_uc003lea.2_Missense_Mutation_p.E746Q|MATR3_uc003leb.2_Missense_Mutation_p.E408Q|MATR3_uc003lec.2_Missense_Mutation_p.E423Q	NM_199189	NP_954659	P43243	MATR3_HUMAN	matrin 3	746						nuclear inner membrane|nuclear matrix	nucleotide binding|protein binding|RNA binding|structural molecule activity|zinc ion binding			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)											0.039062	-16.443207	12.917882	5	123	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	138661216	138661216	9721	5	G	C	C	C	585	45	MATR3	3	3
PCDHA8	56140	broad.mit.edu	37	5	140222271	140222271	+	Silent	SNP	C	T	T			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:140222271C>T	uc003lhs.2	+	c.1365C>T	c.(1363-1365)TTC>TTT	p.F455F	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhi.2_Intron|PCDHA4_uc003lhh.1_Intron|PCDHA5_uc003lhk.1_Intron|PCDHA5_uc003lhl.2_Intron|PCDHA6_uc003lhn.2_Intron|PCDHA6_uc003lho.2_Intron|PCDHA7_uc003lhq.2_Intron|PCDHA8_uc003lhr.1_Silent_p.F455F	NM_018911	NP_061734	Q9Y5H6	PCDA8_HUMAN	protocadherin alpha 8 isoform 1 precursor	455	Cadherin 4.|Extracellular (Potential).				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding|protein binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)											0.149123	21.302046	34.773552	17	97	KEEP	---	---	---	---	capture		Silent	SNP	140222271	140222271	11950	5	C	T	T	T	402	31	PCDHA8	1	1
PCDHB3	56132	broad.mit.edu	37	5	140482231	140482231	+	Missense_Mutation	SNP	C	G	G			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:140482231C>G	uc003lio.2	+	c.1998C>G	c.(1996-1998)TTC>TTG	p.F666L		NM_018937	NP_061760	Q9Y5E6	PCDB3_HUMAN	protocadherin beta 3 precursor	666	Extracellular (Potential).|Cadherin 6.				calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission	integral to plasma membrane	calcium ion binding			ovary(1)|pancreas(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)											0.055556	-7.23522	15.202695	6	102	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	140482231	140482231	11963	5	C	G	G	G	415	32	PCDHB3	3	3
PCDHB10	56126	broad.mit.edu	37	5	140574422	140574422	+	Missense_Mutation	SNP	T	C	C			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:140574422T>C	uc003lix.2	+	c.2297T>C	c.(2296-2298)TTC>TCC	p.F766S		NM_018930	NP_061753	Q9UN67	PCDBA_HUMAN	protocadherin beta 10 precursor	766	Cytoplasmic (Potential).				calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission	integral to membrane|plasma membrane	calcium ion binding			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)											0.375887	178.146556	180.050605	53	88	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	140574422	140574422	11955	5	T	C	C	C	806	62	PCDHB10	4	4
PCDHB14	56122	broad.mit.edu	37	5	140603931	140603931	+	Missense_Mutation	SNP	C	T	T			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:140603931C>T	uc003ljb.2	+	c.854C>T	c.(853-855)TCA>TTA	p.S285L	PCDHB14_uc011dal.1_Missense_Mutation_p.S132L	NM_018934	NP_061757	Q9Y5E9	PCDBE_HUMAN	protocadherin beta 14 precursor	285	Extracellular (Potential).|Cadherin 3.				calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission	integral to membrane|plasma membrane	calcium ion binding			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			Ovarian(141;50 1831 27899 33809 37648)								0.346939	86.508368	88.540573	34	64	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	140603931	140603931	11959	5	C	T	T	T	377	29	PCDHB14	2	2
G3BP1	10146	broad.mit.edu	37	5	151173756	151173756	+	Missense_Mutation	SNP	A	G	G			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:151173756A>G	uc003lun.2	+	c.388A>G	c.(388-390)ATC>GTC	p.I130V	G3BP1_uc003lum.2_Missense_Mutation_p.I130V|G3BP1_uc011dcu.1_Intron|G3BP1_uc010jhz.2_Intron|G3BP1_uc003luq.2_5'Flank	NM_005754	NP_005745	Q13283	G3BP1_HUMAN	Ras-GTPase-activating protein SH3-domain-binding	130	NTF2.				Ras protein signal transduction|transport	cytosol|nucleus|plasma membrane	ATP binding|ATP-dependent DNA helicase activity|ATP-dependent RNA helicase activity|DNA binding|endonuclease activity|protein binding|RNA binding			ovary(1)	1		all_hematologic(541;0.0338)|Medulloblastoma(196;0.091)	Kidney(363;0.000171)|KIRC - Kidney renal clear cell carcinoma(527;0.000785)											0.204082	86.393606	98.318582	30	117	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	151173756	151173756	6392	5	A	G	G	G	208	16	G3BP1	4	4
GPRIN1	114787	broad.mit.edu	37	5	176025029	176025029	+	Missense_Mutation	SNP	C	T	T			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:176025029C>T	uc003meo.1	-	c.1807G>A	c.(1807-1809)GAG>AAG	p.E603K		NM_052899	NP_443131	Q7Z2K8	GRIN1_HUMAN	G protein-regulated inducer of neurite outgrowth	603						growth cone|plasma membrane				ovary(2)	2	all_cancers(89;0.00263)|Renal(175;0.000269)|Lung NSC(126;0.00902)|all_lung(126;0.0142)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)											0.166667	27.535573	37.655683	16	80	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	176025029	176025029	7005	5	C	T	T	T	416	32	GPRIN1	2	2
GOLPH3	64083	broad.mit.edu	37	5	32135777	32135777	+	Missense_Mutation	SNP	C	A	A			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:32135777C>A	uc003jhp.1	-	c.373G>T	c.(373-375)GAT>TAT	p.D125Y		NM_022130	NP_071413	Q9H4A6	GOLP3_HUMAN	golgi phosphoprotein 3	125					cell proliferation|positive regulation of TOR signaling cascade|regulation of mitochondrion organization	cytosol|endosome|Golgi cisterna membrane|mitochondrial intermembrane space|plasma membrane|trans-Golgi network	protein binding			ovary(1)	1										66				0.36	114.722185	116.886439	45	80	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	32135777	32135777	6841	5	C	A	A	A	416	32	GOLPH3	2	2
ADAMTS12	81792	broad.mit.edu	37	5	33684050	33684050	+	Missense_Mutation	SNP	C	T	T			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:33684050C>T	uc003jia.1	-	c.745G>A	c.(745-747)GAG>AAG	p.E249K	ADAMTS12_uc010iuq.1_Missense_Mutation_p.E249K	NM_030955	NP_112217	P58397	ATS12_HUMAN	ADAM metallopeptidase with thrombospondin type 1	249	Peptidase M12B.				proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(4)|lung(1)|kidney(1)|skin(1)	7														0.136364	15.936945	27.2094	12	76	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	33684050	33684050	258	5	C	T	T	T	390	30	ADAMTS12	2	2
ADAMTS12	81792	broad.mit.edu	37	5	33881537	33881537	+	Missense_Mutation	SNP	C	T	T			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:33881537C>T	uc003jia.1	-	c.176G>A	c.(175-177)CGA>CAA	p.R59Q	ADAMTS12_uc010iuq.1_Missense_Mutation_p.R59Q|ADAMTS12_uc003jib.1_Missense_Mutation_p.R59Q	NM_030955	NP_112217	P58397	ATS12_HUMAN	ADAM metallopeptidase with thrombospondin type 1	59					proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(4)|lung(1)|kidney(1)|skin(1)	7														0.120833	21.589625	55.464157	29	211	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	33881537	33881537	258	5	C	T	T	T	403	31	ADAMTS12	1	1
TRIP13	9319	broad.mit.edu	37	5	895027	895027	+	Missense_Mutation	SNP	T	C	C			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:895027T>C	uc003jbr.2	+	c.218T>C	c.(217-219)GTG>GCG	p.V73A	BRD9_uc003jbn.2_5'Flank|BRD9_uc011cmb.1_5'Flank|BRD9_uc003jbo.2_5'Flank|BRD9_uc003jbq.2_5'Flank|BRD9_uc011cmc.1_5'Flank|TRIP13_uc010ite.1_Missense_Mutation_p.V73A	NM_004237	NP_004228	Q15645	TRP13_HUMAN	thyroid hormone receptor interactor 13	73					transcription from RNA polymerase II promoter		ATP binding|identical protein binding|nucleoside-triphosphatase activity|transcription cofactor activity				0			Epithelial(17;0.00147)|OV - Ovarian serous cystadenocarcinoma(19;0.00271)|all cancers(22;0.00622)|Lung(60;0.165)							458				0.272727	91.198023	96.854181	33	88	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	895027	895027	17107	5	T	C	C	C	767	59	TRIP13	4	4
AIM1	202	broad.mit.edu	37	6	106968226	106968226	+	Missense_Mutation	SNP	G	A	A			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:106968226G>A	uc003prh.2	+	c.1919G>A	c.(1918-1920)AGA>AAA	p.R640K		NM_001624	NP_001615	Q9Y4K1	AIM1_HUMAN	absent in melanoma 1	640							sugar binding			breast(4)|ovary(2)|large_intestine(1)	7	Breast(9;0.0138)|all_epithelial(6;0.169)	all_cancers(87;4.67e-25)|all_epithelial(87;5.46e-21)|Acute lymphoblastic leukemia(125;2.15e-07)|all_hematologic(75;5.28e-06)|Colorectal(196;3.46e-05)|all_lung(197;5.94e-05)|Lung NSC(302;7.26e-05)|Ovarian(999;0.00473)	Epithelial(6;0.00114)|all cancers(7;0.00726)|BRCA - Breast invasive adenocarcinoma(8;0.0114)|OV - Ovarian serous cystadenocarcinoma(5;0.0305)	all cancers(137;1.73e-50)|Epithelial(106;2.42e-48)|OV - Ovarian serous cystadenocarcinoma(136;1.51e-27)|BRCA - Breast invasive adenocarcinoma(108;0.00104)|GBM - Glioblastoma multiforme(226;0.00858)						659				0.081633	-0.280528	17.192069	8	90	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	106968226	106968226	433	6	G	A	A	A	429	33	AIM1	2	2
REV3L	5980	broad.mit.edu	37	6	111695225	111695225	+	Nonsense_Mutation	SNP	C	A	A			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:111695225C>A	uc003puy.3	-	c.4333G>T	c.(4333-4335)GGA>TGA	p.G1445*	REV3L_uc003pux.3_Nonsense_Mutation_p.G1367*|REV3L_uc003puz.3_Nonsense_Mutation_p.G1367*	NM_002912	NP_002903	O60673	DPOLZ_HUMAN	DNA polymerase zeta	1445					DNA-dependent DNA replication|translesion synthesis	nucleus|zeta DNA polymerase complex	DNA binding|DNA-directed DNA polymerase activity|metal ion binding|nucleotide binding			large_intestine(2)|ovary(1)|skin(1)	4		all_cancers(87;7.57e-06)|Acute lymphoblastic leukemia(125;2.46e-08)|all_hematologic(75;1.08e-06)|all_epithelial(87;0.00138)|Colorectal(196;0.021)		OV - Ovarian serous cystadenocarcinoma(136;0.0314)|Epithelial(106;0.057)|all cancers(137;0.0663)										0.296296	126.614741	133.637427	56	133	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	111695225	111695225	13710	6	C	A	A	A	286	22	REV3L	5	2
VGLL2	245806	broad.mit.edu	37	6	117589584	117589584	+	Silent	SNP	G	A	A			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:117589584G>A	uc003pxn.2	+	c.321G>A	c.(319-321)CTG>CTA	p.L107L	VGLL2_uc003pxo.2_Silent_p.L107L	NM_182645	NP_872586	Q8N8G2	VGLL2_HUMAN	vestigial-like 2 isoform 1	107					transcription, DNA-dependent	nucleus	transcription regulator activity			central_nervous_system(1)	1				GBM - Glioblastoma multiforme(226;0.0254)|all cancers(137;0.0676)|OV - Ovarian serous cystadenocarcinoma(136;0.0757)										0.113208	3.829386	11.643289	6	47	KEEP	---	---	---	---	capture		Silent	SNP	117589584	117589584	17726	6	G	A	A	A	574	45	VGLL2	2	2
VIP	7432	broad.mit.edu	37	6	153076459	153076459	+	Nonsense_Mutation	SNP	C	T	T			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:153076459C>T	uc003qpe.2	+	c.286C>T	c.(286-288)CAA>TAA	p.Q96*	VIP_uc003qpf.2_Nonsense_Mutation_p.Q96*|VIP_uc010kjd.2_Nonsense_Mutation_p.Q96*	NM_003381	NP_003372	P01282	VIP_HUMAN	vasoactive intestinal peptide isoform 1	96				QL -> PP (in Ref. 8; AAA61286).	body fluid secretion|G-protein coupled receptor protein signaling pathway|positive regulation of cell proliferation	extracellular region	neuropeptide hormone activity				0		Ovarian(120;0.0654)		OV - Ovarian serous cystadenocarcinoma(155;4.5e-11)|BRCA - Breast invasive adenocarcinoma(81;0.144)										0.101695	1.900183	11.246396	6	53	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	153076459	153076459	17734	6	C	T	T	T	377	29	VIP	5	2
FBXO5	26271	broad.mit.edu	37	6	153296529	153296529	+	Missense_Mutation	SNP	C	T	T			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:153296529C>T	uc003qpg.2	-	c.331G>A	c.(331-333)GAA>AAA	p.E111K	FBXO5_uc003qph.2_Missense_Mutation_p.E65K	NM_012177	NP_036309	Q9UKT4	FBX5_HUMAN	F-box only protein 5 isoform a	111					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell division|mitotic metaphase/anaphase transition|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of mitotic cell cycle|regulation of transcription involved in G1/S phase of mitotic cell cycle	cytosol|nucleoplasm|spindle	metal ion binding|protein binding				0		Ovarian(120;0.125)		OV - Ovarian serous cystadenocarcinoma(155;4.38e-10)|BRCA - Breast invasive adenocarcinoma(81;0.0893)		NSCLC(121;372 1757 17721 17977 29669)								0.12605	15.032213	31.291399	15	104	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	153296529	153296529	5995	6	C	T	T	T	377	29	FBXO5	2	2
SYNJ2	8871	broad.mit.edu	37	6	158487540	158487540	+	Silent	SNP	C	A	A			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:158487540C>A	uc003qqx.1	+	c.1590C>A	c.(1588-1590)ATC>ATA	p.I530I	SYNJ2_uc011efm.1_Non-coding_Transcript|SYNJ2_uc003qqw.1_Silent_p.I530I|SYNJ2_uc003qqy.1_Silent_p.I243I|SYNJ2_uc011efn.1_Silent_p.I458I|SYNJ2_uc010kjo.1_Silent_p.I479I|SYNJ2_uc003qqz.1_Silent_p.I147I	NM_003898	NP_003889	O15056	SYNJ2_HUMAN	synaptojanin 2	530	Catalytic (By similarity).						nucleotide binding|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity|RNA binding			skin(1)	1				OV - Ovarian serous cystadenocarcinoma(65;4.42e-18)|BRCA - Breast invasive adenocarcinoma(81;4.23e-05)										0.078313	-8.133354	22.039236	13	153	KEEP	---	---	---	---	capture		Silent	SNP	158487540	158487540	15974	6	C	A	A	A	382	30	SYNJ2	2	2
MAP3K4	4216	broad.mit.edu	37	6	161470151	161470151	+	Missense_Mutation	SNP	T	G	G			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:161470151T>G	uc003qtn.2	+	c.847T>G	c.(847-849)TTT>GTT	p.F283V	MAP3K4_uc010kkc.1_Missense_Mutation_p.F283V|MAP3K4_uc003qto.2_Missense_Mutation_p.F283V|MAP3K4_uc011efz.1_Non-coding_Transcript|MAP3K4_uc011ega.1_5'UTR	NM_005922	NP_005913	Q9Y6R4	M3K4_HUMAN	mitogen-activated protein kinase kinase kinase 4	283					activation of MAPKK activity|JNK cascade|positive regulation of JUN kinase activity	perinuclear region of cytoplasm	ATP binding|MAP kinase kinase kinase activity|metal ion binding|protein binding			ovary(3)|lung(3)|skin(2)|stomach(1)	9		Breast(66;0.000776)|Ovarian(120;0.0367)|Prostate(117;0.0771)		OV - Ovarian serous cystadenocarcinoma(65;1.85e-18)|BRCA - Breast invasive adenocarcinoma(81;3.04e-05)						511				0.084337	1.858242	16.421019	7	76	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	161470151	161470151	9635	6	T	G	G	G	728	56	MAP3K4	4	4
MYLK4	340156	broad.mit.edu	37	6	2685595	2685595	+	Silent	SNP	G	A	A			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:2685595G>A	uc003mty.3	-	c.480C>T	c.(478-480)CAC>CAT	p.H160H		NM_001012418	NP_001012418	Q86YV6	MYLK4_HUMAN	myosin light chain kinase family, member 4	160	Protein kinase.				protein phosphorylation		ATP binding|protein serine/threonine kinase activity			breast(3)|ovary(1)	4	Ovarian(93;0.0412)	all_hematologic(90;0.0897)								535				0.377224	261.41677	265.117302	106	175	KEEP	---	---	---	---	capture		Silent	SNP	2685595	2685595	10454	6	G	A	A	A	516	40	MYLK4	1	1
OR2H1	26716	broad.mit.edu	37	6	29430097	29430097	+	Missense_Mutation	SNP	G	C	C			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:29430097G>C	uc003nmi.2	+	c.551G>C	c.(550-552)CGA>CCA	p.R184P	OR2H1_uc003nmj.1_Missense_Mutation_p.R184P|OR2H1_uc010jri.1_Missense_Mutation_p.R106P	NM_030883	NP_112145	Q9GZK4	OR2H1_HUMAN	olfactory receptor, family 2, subfamily H,	184	Extracellular (Potential).			R -> G (in Ref. 6; AAC00188).	sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0														0.02623	-56.269815	19.444287	8	297	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	29430097	29430097	11407	6	G	C	C	C	481	37	OR2H1	3	3
FLOT1	10211	broad.mit.edu	37	6	30708997	30708997	+	Silent	SNP	C	T	T			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:30708997C>T	uc003nrm.2	-	c.324G>A	c.(322-324)CAG>CAA	p.Q108Q	FLOT1_uc011dmr.1_Intron	NM_005803	NP_005794	O75955	FLOT1_HUMAN	flotillin 1	108						centriolar satellite|endosome|integral to membrane|melanosome|membrane fraction					0														0.067227	-6.692037	16.393029	8	111	KEEP	---	---	---	---	capture		Silent	SNP	30708997	30708997	6178	6	C	T	T	T	415	32	FLOT1	2	2
AGER	177	broad.mit.edu	37	6	32150773	32150773	+	Missense_Mutation	SNP	C	G	G			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:32150773C>G	uc003oap.1	-	c.584G>C	c.(583-585)AGA>ACA	p.R195T	AGER_uc003oak.1_5'Flank|AGER_uc003oar.2_Missense_Mutation_p.R78T|AGER_uc011dpm.1_Missense_Mutation_p.R78T|AGER_uc011dpn.1_Missense_Mutation_p.R78T|AGER_uc003oal.1_Missense_Mutation_p.R179T|AGER_uc010jtv.1_Missense_Mutation_p.R179T|AGER_uc011dpo.1_Missense_Mutation_p.R92T|AGER_uc003oam.1_Intron|AGER_uc003oan.1_Missense_Mutation_p.R165T|AGER_uc003oat.1_Missense_Mutation_p.R195T|AGER_uc003oao.1_Non-coding_Transcript|AGER_uc003oaq.1_Missense_Mutation_p.R165T|AGER_uc010jtw.1_Non-coding_Transcript|AGER_uc003oas.1_Missense_Mutation_p.R179T|AGER_uc003oau.1_Missense_Mutation_p.R179T|AGER_uc011dpp.1_Missense_Mutation_p.R179T|AGER_uc011dpq.1_Missense_Mutation_p.R195T	NM_001136	NP_001127	Q15109	RAGE_HUMAN	advanced glycosylation end product-specific	179	Extracellular (Potential).|Ig-like C2-type 1.				cell surface receptor linked signaling pathway|inflammatory response|innate immune response|neuron projection development|positive regulation of NF-kappaB transcription factor activity	integral to plasma membrane	S100 alpha binding|transmembrane receptor activity			breast(1)	1														0.17757	48.357858	58.833705	19	88	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	32150773	32150773	382	6	C	G	G	G	416	32	AGER	3	3
AGER	177	broad.mit.edu	37	6	32150922	32150922	+	Silent	SNP	C	T	T			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:32150922C>T	uc003oap.1	-	c.525G>A	c.(523-525)TTG>TTA	p.L175L	AGER_uc003oak.1_5'Flank|AGER_uc003oar.2_Silent_p.L58L|AGER_uc011dpm.1_Silent_p.L58L|AGER_uc011dpn.1_Silent_p.L58L|AGER_uc003oal.1_Silent_p.L159L|AGER_uc010jtv.1_Silent_p.L159L|AGER_uc011dpo.1_Silent_p.L72L|AGER_uc003oam.1_Intron|AGER_uc003oan.1_Silent_p.L145L|AGER_uc003oat.1_Silent_p.L175L|AGER_uc003oao.1_Non-coding_Transcript|AGER_uc003oaq.1_Silent_p.L145L|AGER_uc010jtw.1_Non-coding_Transcript|AGER_uc003oas.1_Silent_p.L159L|AGER_uc003oau.1_Silent_p.L159L|AGER_uc011dpp.1_Silent_p.L159L|AGER_uc011dpq.1_Silent_p.L175L|AGER_uc011dpr.1_Silent_p.L159L	NM_001136	NP_001127	Q15109	RAGE_HUMAN	advanced glycosylation end product-specific	159	Extracellular (Potential).|Ig-like C2-type 1.				cell surface receptor linked signaling pathway|inflammatory response|innate immune response|neuron projection development|positive regulation of NF-kappaB transcription factor activity	integral to plasma membrane	S100 alpha binding|transmembrane receptor activity			breast(1)	1														0.051282	-14.355844	10.600854	6	111	KEEP	---	---	---	---	capture		Silent	SNP	32150922	32150922	382	6	C	T	T	T	272	21	AGER	2	2
RGL2	5863	broad.mit.edu	37	6	33263957	33263957	+	Missense_Mutation	SNP	C	T	T			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:33263957C>T	uc003odv.2	-	c.616G>A	c.(616-618)GAC>AAC	p.D206N	RGL2_uc003odu.2_5'UTR|RGL2_uc010jur.2_Intron|RGL2_uc003odw.2_Missense_Mutation_p.D124N|RGL2_uc011drb.1_Missense_Mutation_p.D124N	NM_004761	NP_004752	O15211	RGL2_HUMAN	ral guanine nucleotide dissociation	206	N-terminal Ras-GEF.				Ras protein signal transduction|regulation of small GTPase mediated signal transduction	intracellular	Ras guanyl-nucleotide exchange factor activity			skin(2)|pancreas(1)	3										150				0.037543	-51.855466	15.950628	11	282	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	33263957	33263957	13750	6	C	T	T	T	377	29	RGL2	2	2
FGD2	221472	broad.mit.edu	37	6	36993601	36993601	+	Missense_Mutation	SNP	G	A	A			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:36993601G>A	uc010jwp.1	+	c.1492G>A	c.(1492-1494)GAA>AAA	p.E498K	FGD2_uc003ong.2_Missense_Mutation_p.E220K|FGD2_uc011dtv.1_Missense_Mutation_p.E126K|FGD2_uc003onj.1_Missense_Mutation_p.E75K	NM_173558	NP_775829	Q7Z6J4	FGD2_HUMAN	FYVE, RhoGEF and PH domain containing 2	498	FYVE-type.				actin cytoskeleton organization|apoptosis|filopodium assembly|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Cdc42 GTPase activity|regulation of cell shape|small GTPase mediated signal transduction	cytoskeleton|cytosol|early endosome membrane|Golgi apparatus|lamellipodium|nucleus|ruffle membrane	Rho guanyl-nucleotide exchange factor activity|small GTPase binding|zinc ion binding			lung(1)|pancreas(1)	2														0.064103	-8.192721	7.270874	5	73	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	36993601	36993601	6070	6	G	A	A	A	481	37	FGD2	1	1
TTBK1	84630	broad.mit.edu	37	6	43251404	43251404	+	Nonsense_Mutation	SNP	C	T	T			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:43251404C>T	uc003ouq.1	+	c.2926C>T	c.(2926-2928)CGA>TGA	p.R976*		NM_032538	NP_115927	Q5TCY1	TTBK1_HUMAN	tau tubulin kinase 1	976					protein phosphorylation	cell junction|cytoplasm|nucleus	ATP binding|protein binding|protein serine/threonine kinase activity			lung(4)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	9			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0125)|OV - Ovarian serous cystadenocarcinoma(102;0.0399)							85				0.451613	74.597504	74.722425	28	34	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	43251404	43251404	17230	6	C	T	T	T	295	23	TTBK1	5	1
MYO6	4646	broad.mit.edu	37	6	76551060	76551060	+	Missense_Mutation	SNP	G	A	A			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:76551060G>A	uc003pih.1	+	c.781G>A	c.(781-783)GAA>AAA	p.E261K	MYO6_uc003pig.1_Missense_Mutation_p.E261K|MYO6_uc003pii.1_Missense_Mutation_p.E261K	NM_004999	NP_004990	Q9UM54	MYO6_HUMAN	myosin VI	261	Myosin head-like.				actin filament-based movement|DNA damage response, signal transduction by p53 class mediator|endocytosis|intracellular protein transport|positive regulation of transcription from RNA polymerase II promoter|regulation of secretion|sensory perception of sound|synaptic transmission	cell cortex|clathrin coated vesicle membrane|coated pit|cytosol|DNA-directed RNA polymerase II, holoenzyme|filamentous actin|Golgi apparatus|nuclear membrane|perinuclear region of cytoplasm|ruffle membrane|unconventional myosin complex	actin filament binding|ADP binding|ATP binding|calmodulin binding|minus-end directed microfilament motor activity|protein binding			kidney(1)|pancreas(1)	2		all_hematologic(105;0.189)		BRCA - Breast invasive adenocarcinoma(397;0.223)										0.076923	-1.681007	10.235981	5	60	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	76551060	76551060	10476	6	G	A	A	A	429	33	MYO6	2	2
MUC17	140453	broad.mit.edu	37	7	100683576	100683576	+	Missense_Mutation	SNP	C	A	A			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:100683576C>A	uc003uxp.1	+	c.8879C>A	c.(8878-8880)ACC>AAC	p.T2960N	MUC17_uc010lho.1_Non-coding_Transcript	NM_001040105	NP_001035194	Q685J3	MUC17_HUMAN	mucin 17 precursor	2960	Extracellular (Potential).|Ser-rich.|48.|59 X approximate tandem repeats.					extracellular region|integral to membrane|plasma membrane	extracellular matrix constituent, lubricant activity			ovary(14)|breast(3)|lung(2)	19	Lung NSC(181;0.136)|all_lung(186;0.182)													0.356948	341.402242	348.024514	131	236	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	100683576	100683576	10368	7	C	A	A	A	234	18	MUC17	2	2
IQUB	154865	broad.mit.edu	37	7	123101650	123101650	+	Missense_Mutation	SNP	C	A	A			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:123101650C>A	uc003vkn.2	-	c.1768G>T	c.(1768-1770)GAC>TAC	p.D590Y	IQUB_uc011kny.1_5'UTR|IQUB_uc003vko.2_Missense_Mutation_p.D590Y|IQUB_uc010lkt.2_Non-coding_Transcript	NM_178827	NP_849149	Q8NA54	IQUB_HUMAN	IQ motif and ubiquitin domain containing	590										ovary(3)|large_intestine(1)	4														0.461538	16.147023	16.16393	6	7	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	123101650	123101650	8123	7	C	A	A	A	416	32	IQUB	2	2
NUP205	23165	broad.mit.edu	37	7	135310104	135310104	+	Splice_Site_SNP	SNP	G	T	T			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:135310104G>T	uc003vsw.2	+	c.4671_splice	c.e32+1	p.M1557_splice	NUP205_uc003vsx.2_Splice_Site_SNP	NM_015135	NP_055950			nucleoporin 205kDa						carbohydrate metabolic process|glucose transport|mRNA transport|protein import into nucleus, docking|regulation of glucose transport|transmembrane transport|viral reproduction	nuclear pore	protein binding			ovary(3)|breast(1)|central_nervous_system(1)|skin(1)	6														0.386555	138.19087	139.542783	46	73	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	135310104	135310104	11164	7	G	T	T	T	572	44	NUP205	5	2
GSTK1	373156	broad.mit.edu	37	7	142960620	142960620	+	Missense_Mutation	SNP	C	A	A			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:142960620C>A	uc003wcj.2	+	c.14C>A	c.(13-15)CCG>CAG	p.P5Q	GSTK1_uc003wci.2_Missense_Mutation_p.P5Q|GSTK1_uc011ksy.1_Missense_Mutation_p.P5Q|GSTK1_uc011ksz.1_Missense_Mutation_p.P5Q	NM_001143679	NP_001137151	Q9Y2Q3	GSTK1_HUMAN	glutathione S-transferase kappa 1 isoform b	5						outer membrane-bounded periplasmic space|peroxisome	glutathione transferase activity|identical protein binding|protein disulfide oxidoreductase activity				0	Melanoma(164;0.059)				Glutathione(DB00143)									0.043165	-21.274781	9.858499	6	133	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	142960620	142960620	7116	7	C	A	A	A	299	23	GSTK1	1	1
PTPRN2	5799	broad.mit.edu	37	7	157387990	157387990	+	Silent	SNP	C	T	T			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:157387990C>T	uc011kwa.1	-	c.2505G>A	c.(2503-2505)AGG>AGA	p.R835R	PTPRN2_uc003wno.2_Silent_p.R812R|PTPRN2_uc003wnp.2_Silent_p.R795R|PTPRN2_uc003wnq.2_Silent_p.R783R|PTPRN2_uc003wnr.2_Silent_p.R774R	NM_002847	NP_002838	Q92932	PTPR2_HUMAN	protein tyrosine phosphatase, receptor type, N	812	Cytoplasmic (Potential).|Tyrosine-protein phosphatase.					integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			ovary(4)|large_intestine(1)|pleura(1)	6	all_neural(206;0.181)	all_cancers(7;8.99e-13)|all_epithelial(9;2.4e-06)|all_hematologic(28;0.0155)|Breast(660;0.132)	OV - Ovarian serous cystadenocarcinoma(82;0.00463)	STAD - Stomach adenocarcinoma(7;0.0875)										0.061856	-8.526826	10.900403	6	91	KEEP	---	---	---	---	capture		Silent	SNP	157387990	157387990	13265	7	C	T	T	T	389	30	PTPRN2	2	2
DNAH11	8701	broad.mit.edu	37	7	21923947	21923947	+	Silent	SNP	C	T	T			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:21923947C>T	uc003svc.2	+	c.12447C>T	c.(12445-12447)ATC>ATT	p.I4149I		NM_003777	NP_003768	Q96DT5	DYH11_HUMAN	dynein, axonemal, heavy chain 11	4149					microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(8)|large_intestine(3)|pancreas(3)|central_nervous_system(1)	15														0.129412	12.358957	23.732895	11	74	KEEP	---	---	---	---	capture		Silent	SNP	21923947	21923947	4781	7	C	T	T	T	369	29	DNAH11	2	2
AOAH	313	broad.mit.edu	37	7	36656065	36656065	+	Missense_Mutation	SNP	C	T	T			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:36656065C>T	uc003tfh.3	-	c.767G>A	c.(766-768)GGA>GAA	p.G256E	AOAH_uc010kxf.2_Missense_Mutation_p.G256E|AOAH_uc011kba.1_Missense_Mutation_p.G224E	NM_001637	NP_001628	P28039	AOAH_HUMAN	acyloxyacyl hydrolase precursor	256					inflammatory response|lipid metabolic process	extracellular region	acyloxyacyl hydrolase activity|lipoprotein lipase activity				0														0.108108	3.770585	9.406094	4	33	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	36656065	36656065	736	7	C	T	T	T	390	30	AOAH	2	2
ELMO1	9844	broad.mit.edu	37	7	37136224	37136224	+	Missense_Mutation	SNP	G	A	A			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:37136224G>A	uc003tfk.1	-	c.1300C>T	c.(1300-1302)CCT>TCT	p.P434S	ELMO1_uc011kbc.1_Missense_Mutation_p.P338S|ELMO1_uc010kxg.1_Missense_Mutation_p.P434S	NM_014800	NP_055615	Q92556	ELMO1_HUMAN	engulfment and cell motility 1 isoform 1	434	ELMO.				actin cytoskeleton organization|apoptosis|cellular component movement|phagocytosis, engulfment|Rac protein signal transduction|regulation of defense response to virus by virus|viral reproduction	cytoskeleton|cytosol|plasma membrane	SH3 domain binding			ovary(3)	3														0.050505	-12.887757	8.303	5	94	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	37136224	37136224	5257	7	G	A	A	A	494	38	ELMO1	1	1
AKAP9	10142	broad.mit.edu	37	7	91712592	91712592	+	Nonsense_Mutation	SNP	G	T	T			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:91712592G>T	uc003ulg.2	+	c.8269G>T	c.(8269-8271)GAG>TAG	p.E2757*	AKAP9_uc003ulf.2_Nonsense_Mutation_p.E2749*|AKAP9_uc003uli.2_Nonsense_Mutation_p.E2380*|AKAP9_uc003ulj.2_Nonsense_Mutation_p.E527*|AKAP9_uc003ulk.2_Nonsense_Mutation_p.E32*	NM_005751	NP_005742	Q99996	AKAP9_HUMAN	A-kinase anchor protein 9 isoform 2	2769	Potential.|Glu-rich.				G2/M transition of mitotic cell cycle|signal transduction|synaptic transmission|transport	centrosome|cytosol|Golgi apparatus	receptor binding			ovary(5)|breast(4)|large_intestine(2)|skin(2)|central_nervous_system(1)	14	all_cancers(62;2.46e-09)|all_epithelial(64;4.42e-08)|Breast(17;0.00206)|all_lung(186;0.185)|all_hematologic(106;0.215)|Lung NSC(181;0.249)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)							807				0.053097	-13.252658	10.591627	6	107	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	91712592	91712592	462	7	G	T	T	T	585	45	AKAP9	5	2
DYNC1I1	1780	broad.mit.edu	37	7	95614143	95614143	+	Missense_Mutation	SNP	G	C	C			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:95614143G>C	uc003uoc.3	+	c.648G>C	c.(646-648)TTG>TTC	p.L216F	DYNC1I1_uc003uod.3_Missense_Mutation_p.L199F|DYNC1I1_uc003uob.2_Missense_Mutation_p.L179F|DYNC1I1_uc003uoe.3_Missense_Mutation_p.L196F|DYNC1I1_uc010lfl.2_Missense_Mutation_p.L205F	NM_004411	NP_004402	O14576	DC1I1_HUMAN	dynein, cytoplasmic 1, intermediate chain 1	216					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)		STAD - Stomach adenocarcinoma(171;0.0957)											0.373832	140.174317	141.669884	40	67	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	95614143	95614143	5028	7	G	C	C	C	581	45	DYNC1I1	3	3
FAM83H	286077	broad.mit.edu	37	8	144812586	144812586	+	Missense_Mutation	SNP	A	C	C			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:144812586A>C	uc003yzk.2	-	c.167T>G	c.(166-168)CTG>CGG	p.L56R	FAM83H_uc010mfk.1_5'Flank	NM_198488	NP_940890	Q6ZRV2	FA83H_HUMAN	FAM83H	56					biomineral tissue development					lung(1)|central_nervous_system(1)|pancreas(1)	3	all_cancers(97;3.74e-11)|all_epithelial(106;2.62e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;3.38e-41)|Epithelial(56;6.8e-40)|all cancers(56;6.43e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.146)											0.184397	57.382168	70.545576	26	115	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	144812586	144812586	5866	8	A	C	C	C	91	7	FAM83H	4	4
FBXL6	26233	broad.mit.edu	37	8	145581359	145581359	+	Silent	SNP	G	A	A			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:145581359G>A	uc003zcb.2	-	c.504C>T	c.(502-504)GGC>GGT	p.G168G	C8ORFK29_uc011llb.1_5'Flank|C8ORFK29_uc010mfw.2_5'Flank|C8ORFK29_uc003zby.3_5'Flank|FBXL6_uc003zbz.2_5'UTR|FBXL6_uc003zca.2_Silent_p.G168G|FBXL6_uc010mfx.2_5'UTR|GPR172A_uc003zcc.1_5'Flank|GPR172A_uc003zcd.1_5'Flank|GPR172A_uc003zce.1_5'Flank|GPR172A_uc010mfy.1_5'Flank|GPR172A_uc003zcf.1_5'Flank|GPR172A_uc011llc.1_5'Flank	NM_012162	NP_036294	Q8N531	FBXL6_HUMAN	F-box and leucine-rich repeat protein 6 isoform	168					proteolysis		ubiquitin-protein ligase activity				0	all_cancers(97;6.64e-12)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;4.43e-40)|Epithelial(56;1.48e-39)|all cancers(56;1.49e-34)|BRCA - Breast invasive adenocarcinoma(115;0.0441)|Colorectal(110;0.055)											0.166667	12.403639	18.741843	10	50	KEEP	---	---	---	---	capture		Silent	SNP	145581359	145581359	5960	8	G	A	A	A	535	42	FBXL6	2	2
CLU	1191	broad.mit.edu	37	8	27462598	27462598	+	Silent	SNP	G	A	A			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:27462598G>A	uc003xfz.1	-	c.828C>T	c.(826-828)CGC>CGT	p.R276R	CLU_uc010lux.1_Silent_p.R89R|CLU_uc003xfw.1_Silent_p.R224R|CLU_uc003xfx.1_Silent_p.R224R|CLU_uc003xfy.1_Silent_p.R235R	NM_001831	NP_001822	P10909	CLUS_HUMAN	clusterin isoform 1	224				R -> L (in Ref. 18; BAG36598).	complement activation, classical pathway|innate immune response|lipid metabolic process|negative regulation of apoptosis|negative regulation of protein homooligomerization|platelet activation|platelet degranulation|release of cytochrome c from mitochondria|response to misfolded protein|response to virus|reverse cholesterol transport	mitochondrion|platelet alpha granule lumen|spherical high-density lipoprotein particle	misfolded protein binding			ovary(2)	2		Ovarian(32;2.61e-05)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0204)|Colorectal(74;0.132)										0.226415	45.832423	53.130395	24	82	KEEP	---	---	---	---	capture		Silent	SNP	27462598	27462598	3706	8	G	A	A	A	587	46	CLU	2	2
GPR124	25960	broad.mit.edu	37	8	37689071	37689071	+	Missense_Mutation	SNP	G	A	A			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:37689071G>A	uc003xkj.2	+	c.1063G>A	c.(1063-1065)GCC>ACC	p.A355T	GPR124_uc010lvy.2_Missense_Mutation_p.A355T	NM_032777	NP_116166	Q96PE1	GP124_HUMAN	G protein-coupled receptor 124 precursor	355	Extracellular (Potential).				central nervous system development|endothelial cell migration|neuropeptide signaling pathway|regulation of angiogenesis|regulation of chemotaxis|sprouting angiogenesis	integral to membrane|plasma membrane	G-protein coupled receptor activity			large_intestine(2)|ovary(2)|skin(1)	5			BRCA - Breast invasive adenocarcinoma(5;2.75e-24)|LUSC - Lung squamous cell carcinoma(8;3.5e-10)											0.459459	43.363809	43.417373	17	20	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	37689071	37689071	6912	8	G	A	A	A	494	38	GPR124	1	1
SLCO5A1	81796	broad.mit.edu	37	8	70617448	70617448	+	Silent	SNP	G	A	A			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:70617448G>A	uc003xyl.2	-	c.1440C>T	c.(1438-1440)CCC>CCT	p.P480P	SLCO5A1_uc010lzb.2_Silent_p.P425P|SLCO5A1_uc011lfa.1_Intron|SLCO5A1_uc003xyk.2_Silent_p.P480P|SLCO5A1_uc010lzc.2_Silent_p.P425P	NM_030958	NP_112220	Q9H2Y9	SO5A1_HUMAN	solute carrier organic anion transporter family,	480	Helical; Name=8; (Potential).					integral to membrane|plasma membrane	transporter activity			ovary(3)	3	Breast(64;0.0654)		Epithelial(68;0.0141)|OV - Ovarian serous cystadenocarcinoma(28;0.0315)|all cancers(69;0.0594)											0.044944	-11.87102	7.829555	4	85	KEEP	---	---	---	---	capture		Silent	SNP	70617448	70617448	15228	8	G	A	A	A	600	47	SLCO5A1	2	2
ZFHX4	79776	broad.mit.edu	37	8	77764427	77764427	+	Missense_Mutation	SNP	C	A	A			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:77764427C>A	uc003yav.2	+	c.5135C>A	c.(5134-5136)CCA>CAA	p.P1712Q	ZFHX4_uc003yau.1_Missense_Mutation_p.P1757Q|ZFHX4_uc003yaw.1_Missense_Mutation_p.P1712Q	NM_024721	NP_078997	Q86UP3	ZFHX4_HUMAN	zinc finger homeodomain 4	1712	Gln-rich.				regulation of transcription, DNA-dependent	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulator activity|zinc ion binding			ovary(8)|large_intestine(4)|breast(2)|lung(1)	15			BRCA - Breast invasive adenocarcinoma(89;0.0895)											0.35	53.95213	55.145335	21	39	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	77764427	77764427	18223	8	C	A	A	A	273	21	ZFHX4	2	2
TGFBR1	7046	broad.mit.edu	37	9	101908883	101908883	+	Missense_Mutation	SNP	C	T	T			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:101908883C>T	uc004azc.2	+	c.1247C>T	c.(1246-1248)TCC>TTC	p.S416F	TGFBR1_uc004azd.2_Missense_Mutation_p.S339F|TGFBR1_uc011lvc.1_Missense_Mutation_p.S347F	NM_004612	NP_004603	P36897	TGFR1_HUMAN	transforming growth factor, beta receptor I	416	Protein kinase.|Cytoplasmic (Potential).				activation of MAPKK activity|anterior/posterior pattern formation|artery morphogenesis|collagen fibril organization|embryonic cranial skeleton morphogenesis|germ cell migration|heart development|kidney development|neuron fate commitment|palate development|parathyroid gland development|pathway-restricted SMAD protein phosphorylation|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|pharyngeal system development|positive regulation of cell growth|positive regulation of cell proliferation|positive regulation of cellular component movement|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of protein kinase B signaling cascade|positive regulation of SMAD protein import into nucleus|positive regulation of survival gene product expression|positive regulation of transcription, DNA-dependent|response to cholesterol|thymus development|transforming growth factor beta receptor signaling pathway	transforming growth factor beta receptor complex	ATP binding|I-SMAD binding|metal ion binding|transforming growth factor beta binding|transforming growth factor beta receptor activity, type I|type II transforming growth factor beta receptor binding			lung(2)|ovary(1)	3		Acute lymphoblastic leukemia(62;0.0559)							p.S416F(EVSAT-Tumor)	168				0.030928	-73.542545	20.018777	12	376	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	101908883	101908883	16349	9	C	T	T	T	390	30	TGFBR1	2	2
PPP3R2	5535	broad.mit.edu	37	9	104357089	104357090	+	Missense_Mutation	DNP	TC	AT	AT			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:104357089_104357090TC>AT	uc004bbr.2	-	c.123_124GA>AT	c.(121-126)CTGAGC>CTATGC	p.S42C	GRIN3A_uc004bbp.1_Intron|GRIN3A_uc004bbq.1_Intron|PPP3R2_uc010mtf.1_Intron	NM_147180	NP_671709	Q96LZ3	CANB2_HUMAN	protein phosphatase 3 regulatory subunit B, beta	39	EF-hand 1.|1.						calcium ion binding			ovary(1)|skin(1)	2		Acute lymphoblastic leukemia(62;0.0527)			Cyclosporine(DB00091)					16				0.391304	149.817197	151.501252	63	98	KEEP	---	---	---	---	capture		Missense_Mutation	DNP	104357089	104357090	12837	9	TC	AT	AT	AT	702	54	PPP3R2	3	3
OR13C8	138802	broad.mit.edu	37	9	107332126	107332126	+	Silent	SNP	G	A	A			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:107332126G>A	uc011lvo.1	+	c.678G>A	c.(676-678)CTG>CTA	p.L226L		NM_001004483	NP_001004483	Q8NGS7	O13C8_HUMAN	olfactory receptor, family 13, subfamily C,	226	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1														0.04698	-21.211516	11.399067	7	142	KEEP	---	---	---	---	capture		Silent	SNP	107332126	107332126	11344	9	G	A	A	A	574	45	OR13C8	2	2
OR13C8	138802	broad.mit.edu	37	9	107332309	107332309	+	Missense_Mutation	SNP	G	A	A			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:107332309G>A	uc011lvo.1	+	c.861G>A	c.(859-861)ATG>ATA	p.M287I		NM_001004483	NP_001004483	Q8NGS7	O13C8_HUMAN	olfactory receptor, family 13, subfamily C,	287	Helical; Name=7; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1														0.065421	-8.169064	12.825128	7	100	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	107332309	107332309	11344	9	G	A	A	A	585	45	OR13C8	2	2
EPB41L4B	54566	broad.mit.edu	37	9	112015721	112015721	+	Missense_Mutation	SNP	C	G	G			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:112015721C>G	uc004bdz.1	-	c.1279G>C	c.(1279-1281)GCA>CCA	p.A427P	EPB41L4B_uc004bea.2_Missense_Mutation_p.A427P	NM_019114	NP_061987	Q9H329	E41LB_HUMAN	erythrocyte membrane protein band 4.1 like 4B	427						cytoplasm|cytoskeleton|extrinsic to membrane	cytoskeletal protein binding|structural constituent of cytoskeleton			ovary(1)|central_nervous_system(1)	2														0.139535	28.053705	44.255098	18	111	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	112015721	112015721	5349	9	C	G	G	G	312	24	EPB41L4B	3	3
LMX1B	4010	broad.mit.edu	37	9	129453345	129453345	+	Missense_Mutation	SNP	C	G	G			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:129453345C>G	uc011maa.1	+	c.488C>G	c.(487-489)TCC>TGC	p.S163C	LMX1B_uc004bqi.2_Missense_Mutation_p.S163C|LMX1B_uc004bqj.2_Missense_Mutation_p.S163C	NM_002316	NP_002307	O60663	LMX1B_HUMAN	LIM homeobox transcription factor 1, beta	163					dorsal/ventral pattern formation|in utero embryonic development	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulator activity|zinc ion binding				0						Pancreas(110;1796 2278 18357 20466)								0.148148	6.280443	9.495299	4	23	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	129453345	129453345	9191	9	C	G	G	G	390	30	LMX1B	3	3
NOTCH1	4851	broad.mit.edu	37	9	139400074	139400074	+	Missense_Mutation	SNP	C	A	A			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:139400074C>A	uc004chz.2	-	c.4274G>T	c.(4273-4275)TGC>TTC	p.C1425F	NOTCH1_uc004cia.1_Missense_Mutation_p.C655F	NM_017617	NP_060087	P46531	NOTC1_HUMAN	notch1 preproprotein	1425	Extracellular (Potential).|EGF-like 36.				aortic valve morphogenesis|immune response|negative regulation of BMP signaling pathway|negative regulation of cell-substrate adhesion|negative regulation of gene-specific transcription|negative regulation of myoblast differentiation|negative regulation of osteoblast differentiation|Notch receptor processing	cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to membrane|nucleoplasm|plasma membrane	calcium ion binding|protein binding|receptor activity			haematopoietic_and_lymphoid_tissue(781)|lung(11)|central_nervous_system(10)|breast(4)|upper_aerodigestive_tract(1)|large_intestine(1)|oesophagus(1)|pancreas(1)	810	all_cancers(76;0.223)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;5.34e-06)|Epithelial(140;7.77e-06)						1552				0.3	21.694897	22.749521	9	21	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	139400074	139400074	10950	9	C	A	A	A	325	25	NOTCH1	2	2
PSIP1	11168	broad.mit.edu	37	9	15486913	15486913	+	Nonsense_Mutation	SNP	G	C	C			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:15486913G>C	uc003zlv.3	-	c.305C>G	c.(304-306)TCA>TGA	p.S102*	PSIP1_uc003zlw.3_Nonsense_Mutation_p.S102*|PSIP1_uc003zlz.3_Nonsense_Mutation_p.S102*|PSIP1_uc003zma.3_Nonsense_Mutation_p.S102*|PSIP1_uc003zly.2_Nonsense_Mutation_p.S102*	NM_033222	NP_150091	O75475	PSIP1_HUMAN	PC4 and SFRS1 interacting protein 1 isoform 2	102					initiation of viral infection|interspecies interaction between organisms|provirus integration|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytosol|nucleoplasm	DNA binding				0				GBM - Glioblastoma multiforme(50;2.38e-06)						239				0.18	47.694023	57.31873	18	82	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	15486913	15486913	13116	9	G	C	C	C	585	45	PSIP1	5	3
BNC2	54796	broad.mit.edu	37	9	16437286	16437286	+	Silent	SNP	C	T	T			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:16437286C>T	uc003zml.2	-	c.906G>A	c.(904-906)GAG>GAA	p.E302E	BNC2_uc011lmw.1_Silent_p.E207E|BNC2_uc003zmm.2_Silent_p.E260E|BNC2_uc003zmq.1_Silent_p.E316E|BNC2_uc003zmr.1_Silent_p.E339E|BNC2_uc003zmp.1_Silent_p.E330E|BNC2_uc010mij.1_Silent_p.E224E|BNC2_uc011lmv.1_Silent_p.E128E|BNC2_uc003zmo.1_Silent_p.E224E|BNC2_uc003zmj.2_Silent_p.E67E|BNC2_uc003zmk.2_Non-coding_Transcript|BNC2_uc003zmi.2_Silent_p.E67E|BNC2_uc003zmn.1_Silent_p.E67E	NM_017637	NP_060107	Q6ZN30	BNC2_HUMAN	basonuclin 2	302					regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus|plasma membrane	zinc ion binding			ovary(2)|central_nervous_system(1)	3				GBM - Glioblastoma multiforme(50;9.01e-08)										0.057971	-16.969903	25.443254	12	195	KEEP	---	---	---	---	capture		Silent	SNP	16437286	16437286	1500	9	C	T	T	T	415	32	BNC2	2	2
TOPORS	10210	broad.mit.edu	37	9	32543115	32543115	+	Missense_Mutation	SNP	C	G	G			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:32543115C>G	uc003zrb.2	-	c.1408G>C	c.(1408-1410)GAC>CAC	p.D470H	TOPORS_uc003zrc.2_Missense_Mutation_p.D403H	NM_005802	NP_005793	Q9NS56	TOPRS_HUMAN	topoisomerase I binding, arginine/serine-rich	470	Interaction with p53/TP53.|Required for sumoylation and localization to discrete nuclear foci.|Interaction with SUMO1.|Interaction with TOP1.				DNA damage response, signal transduction resulting in induction of apoptosis|maintenance of protein location in nucleus|proteasomal ubiquitin-dependent protein catabolic process|protein sumoylation|transcription, DNA-dependent|visual perception	nuclear speck|PML body	antigen binding|DNA binding|DNA topoisomerase I binding|SUMO ligase activity|ubiquitin-protein ligase activity|zinc ion binding			ovary(3)|skin(1)	4			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.0018)										0.078261	4.285235	25.187957	9	106	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	32543115	32543115	16912	9	C	G	G	G	377	29	TOPORS	3	3
RUSC2	9853	broad.mit.edu	37	9	35561270	35561270	+	Missense_Mutation	SNP	G	C	C			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:35561270G>C	uc003zww.2	+	c.4442G>C	c.(4441-4443)GGA>GCA	p.G1481A	RUSC2_uc010mkq.2_Non-coding_Transcript|RUSC2_uc003zwx.3_Missense_Mutation_p.G1481A	NM_014806	NP_055621	Q8N2Y8	RUSC2_HUMAN	RUN and SH3 domain containing 2	1481	SH3.					cytosol				ovary(1)	1			Lung(28;0.000837)|LUSC - Lung squamous cell carcinoma(32;0.00109)|STAD - Stomach adenocarcinoma(86;0.194)											0.057692	-2.292692	8.352624	3	49	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	35561270	35561270	14231	9	G	C	C	C	533	41	RUSC2	3	3
TLN1	7094	broad.mit.edu	37	9	35707217	35707217	+	Missense_Mutation	SNP	C	T	T			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:35707217C>T	uc003zxt.2	-	c.4807G>A	c.(4807-4809)GCC>ACC	p.A1603T		NM_006289	NP_006280	Q9Y490	TLN1_HUMAN	talin 1	1603	Interaction with SYNM.				axon guidance|cell adhesion|cell-cell junction assembly|cellular component movement|cytoskeletal anchoring at plasma membrane|muscle contraction|platelet activation|platelet degranulation	actin cytoskeleton|cell-cell junction|centrosome|cytosol|extracellular region|focal adhesion|intracellular membrane-bounded organelle|ruffle membrane	actin binding|insulin receptor binding|LIM domain binding|structural constituent of cytoskeleton|vinculin binding			breast(2)|ovary(1)|central_nervous_system(1)	4	all_epithelial(49;0.167)		Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)							587				0.566667	88.941038	89.15787	34	26	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	35707217	35707217	16477	9	C	T	T	T	325	25	TLN1	2	2
NPR2	4882	broad.mit.edu	37	9	35794089	35794089	+	Missense_Mutation	SNP	G	C	C			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:35794089G>C	uc003zyd.2	+	c.862G>C	c.(862-864)GAG>CAG	p.E288Q	NPR2_uc010mlb.2_Missense_Mutation_p.E288Q	NM_003995	NP_003986	P20594	ANPRB_HUMAN	natriuretic peptide receptor B precursor	288	Extracellular (Potential).				intracellular signal transduction|ossification|protein phosphorylation|receptor guanylyl cyclase signaling pathway|regulation of blood pressure	integral to membrane|plasma membrane	GTP binding|guanylate cyclase activity|natriuretic peptide receptor activity|peptide receptor activity, G-protein coupled|protein kinase activity			ovary(2)	2	all_epithelial(49;0.161)		LUSC - Lung squamous cell carcinoma(32;0.00521)|Lung(28;0.00697)|STAD - Stomach adenocarcinoma(86;0.194)		Erythrityl Tetranitrate(DB01613)|Nesiritide(DB04899)					170				0.069767	-0.011317	8.206799	3	40	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	35794089	35794089	11000	9	G	C	C	C	429	33	NPR2	3	3
GNAQ	2776	broad.mit.edu	37	9	80430572	80430572	+	Missense_Mutation	SNP	C	G	G			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:80430572C>G	uc004akw.2	-	c.436G>C	c.(436-438)GAT>CAT	p.D146H	GNAQ_uc011lso.1_5'UTR	NM_002072	NP_002063	P50148	GNAQ_HUMAN	guanine nucleotide binding protein (G protein),	146					activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity by dopamine receptor signaling pathway|glutamate signaling pathway|negative regulation of protein kinase activity|platelet activation|protein ADP-ribosylation|protein stabilization|regulation of action potential|regulation of catenin import into nucleus	cytoplasm|heterotrimeric G-protein complex	G-protein beta/gamma-subunit complex binding|G-protein-coupled receptor binding|GTP binding|GTPase activator activity|GTPase activity|signal transducer activity			eye(128)|skin(44)|meninges(11)|ovary(1)|kidney(1)	185										84				0.057692	-2.320579	8.350906	3	49	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	80430572	80430572	6778	9	C	G	G	G	377	29	GNAQ	3	3
HCFC1	3054	broad.mit.edu	37	X	153223608	153223608	+	Silent	SNP	G	A	A			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:153223608G>A	uc004fjp.2	-	c.1896C>T	c.(1894-1896)ATC>ATT	p.I632I		NM_005334	NP_005325	P51610	HCFC1_HUMAN	host cell factor 1	632	Interaction with SIN3A.				cell cycle|interspecies interaction between organisms|positive regulation of cell cycle|positive regulation of gene expression|protein stabilization|reactivation of latent virus|regulation of protein complex assembly|regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	mitochondrion|MLL1 complex|MLL5-L complex|Set1C/COMPASS complex	chromatin binding|identical protein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity			ovary(2)	2	all_cancers(53;6.23e-16)|all_epithelial(53;5.61e-10)|all_lung(58;3.99e-07)|Lung NSC(58;5.02e-07)|all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)													0.189189	11.798323	15.149262	7	30	KEEP	---	---	---	---	capture		Silent	SNP	153223608	153223608	7273	23	G	A	A	A	577	45	HCFC1	2	2
CXorf22	170063	broad.mit.edu	37	X	35988982	35988982	+	Missense_Mutation	SNP	T	C	C			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:35988982T>C	uc004ddj.2	+	c.1912T>C	c.(1912-1914)TAT>CAT	p.Y638H	CXorf22_uc010ngv.2_Non-coding_Transcript	NM_152632	NP_689845	Q6ZTR5	CX022_HUMAN	hypothetical protein LOC170063	638										large_intestine(1)|lung(1)|ovary(1)	3														0.818182	34.281538	35.327996	9	2	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	35988982	35988982	4262	23	T	C	C	C	793	61	CXorf22	4	4
KDM5C	8242	broad.mit.edu	37	X	53254005	53254005	+	Missense_Mutation	SNP	C	T	T			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:53254005C>T	uc004drz.2	-	c.67G>A	c.(67-69)GAG>AAG	p.E23K	KDM5C_uc011moc.1_Non-coding_Transcript|KDM5C_uc011mod.1_Missense_Mutation_p.E23K|KDM5C_uc004dsa.2_Missense_Mutation_p.E23K	NM_004187	NP_004178	P41229	KDM5C_HUMAN	jumonji, AT rich interactive domain 1C isoform	23	JmjN.				chromatin modification|oxidation-reduction process|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|protein binding|zinc ion binding			kidney(9)|ovary(5)|salivary_gland(1)|autonomic_ganglia(1)|haematopoietic_and_lymphoid_tissue(1)|oesophagus(1)	18														0.36	20.16417	20.597011	9	16	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	53254005	53254005	8441	23	C	T	T	T	403	31	KDM5C	1	1
UTY	7404	broad.mit.edu	37	Y	15372253	15372253	+	Nonsense_Mutation	SNP	G	A	A			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chrY:15372253G>A	uc004fsx.1	-	c.3751C>T	c.(3751-3753)CAG>TAG	p.Q1251*	UTY_uc004fsw.1_Nonsense_Mutation_p.Q914*|UTY_uc010nwx.1_Nonsense_Mutation_p.Q308*	NM_007125	NP_009056	O14607	UTY_HUMAN	tetratricopeptide repeat protein isoform 3	1251					chromatin modification|oxidation-reduction process	nucleus	metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen				0						Colon(103;1740 2135 40732 45171)								0.169231	19.180391	25.916888	11	54	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	15372253	15372253	17672	24	G	A	A	A	585	45	UTY	5	2
CEACAM16	388551	broad.mit.edu	37	19	45202701	45202702	+	Frame_Shift_Ins	INS	-	T	T	rs72168176		TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:45202701_45202702insT	uc002ozq.2	+	c.152_153insT	c.(151-153)ACTfs	p.T51fs	CEACAM16_uc010xxd.1_Intron	NM_001039213	NP_001034302	A7LI12	A7LI12_HUMAN	carcinoembryonic antigen-related cell adhesion	Error:Variant_position_missing_in_A7LI12_after_alignment										ovary(1)	1	Lung NSC(12;0.000698)|all_lung(12;0.002)	Prostate(69;0.0376)|Ovarian(192;0.231)												0.33			2	4		---	---	---	---	capture_indel		Frame_Shift_Ins	INS	45202701	45202702	3321	19	-	T	T	T	248	20	CEACAM16	5	5
SIGLEC5	8778	broad.mit.edu	37	19	52130914	52130914	+	Frame_Shift_Del	DEL	G	-	-			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:52130914_52130914delG	uc002pxe.2	-	c.1083_1083delC	c.(1081-1083)CCCfs	p.P361fs		NM_003830	NP_003821	O15389	SIGL5_HUMAN	sialic acid binding Ig-like lectin 5 precursor	361	Extracellular (Potential).				cell adhesion	integral to membrane	sugar binding			breast(1)|central_nervous_system(1)	2		all_neural(266;0.0726)		GBM - Glioblastoma multiforme(134;0.00124)|OV - Ovarian serous cystadenocarcinoma(262;0.0218)										0.40			10	15		---	---	---	---	capture_indel		Frame_Shift_Del	DEL	52130914	52130914	14806	19	G	-	-	-	444	35	SIGLEC5	5	5
NES	10763	broad.mit.edu	37	1	156646400	156646403	+	Frame_Shift_Del	DEL	GCGG	-	-			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:156646400_156646403delGCGG	uc001fpq.2	-	c.654_657delCCGC	c.(652-657)GCCCGCfs	p.A218fs		NM_006617	NP_006608	P48681	NEST_HUMAN	nestin	218_219	Coil 2B.|Rod.				brain development|embryonic camera-type eye development|negative regulation of apoptosis|positive regulation of intermediate filament depolymerization|positive regulation of neural precursor cell proliferation	cytoplasm|intermediate filament	intermediate filament binding|structural molecule activity			ovary(6)	6	all_hematologic(923;0.088)|Hepatocellular(266;0.158)													0.33			6	12		---	---	---	---	capture_indel		Frame_Shift_Del	DEL	156646400	156646403	10736	1	GCGG	-	-	-	483	38	NES	5	5
SH3D19	152503	broad.mit.edu	37	4	152096011	152096011	+	Frame_Shift_Del	DEL	G	-	-			TCGA-49-4486-01	TCGA-49-4486-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:152096011_152096011delG	uc010ipl.1	-	c.505_505delC	c.(505-507)CGAfs	p.R169fs	SH3D19_uc003imc.2_Frame_Shift_Del_p.R169fs|SH3D19_uc003ime.2_Frame_Shift_Del_p.R169fs|SH3D19_uc010ipm.2_Frame_Shift_Del_p.R169fs	NM_001009555	NP_001009555	Q5HYK7	SH319_HUMAN	SH3 domain containing 19 isoform a	169	Pro-rich.				cellular membrane organization|positive regulation of membrane protein ectodomain proteolysis|post-Golgi vesicle-mediated transport	cytosol|Golgi apparatus|nucleus|plasma membrane	proline-rich region binding			ovary(1)	1	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.138)												0.36			179	321		---	---	---	---	capture_indel		Frame_Shift_Del	DEL	152096011	152096011	14740	4	G	-	-	-	506	39	SH3D19	5	5
