Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Genome_Change	Annotation_Transcript	Transcript_Strand	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	i_TCGAscape_Amplification_Peaks	i_TCGAscape_Deletion_Peaks	DrugBank	i_ACHILLES_Top_Genes	i_CCLE_ONCOMAP_overlapping_mutations	i_CCLE_ONCOMAP_total_mutations_in_gene	i_CCLE_SEQ_overlapping_mutations	i_CCLE_SEQ_total_mutations_in_gene	MUTSIG_Significant_Genes	OREGANNO_ID	OREGANNO_Values	i_tumor_f	i_init_t_lod	i_t_lod_fstar	i_t_alt_count	i_t_ref_count	i_normal_best_gt	i_failure_reasons	i_judgement	validation_status	validation_method	validation_tumor_sample	validation_alt_allele	dataset	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	type	classification	start	end	gene	chr	ref_allele	tum_allele1	tum_allele2	context_orig	context65	gene_name	newbase	categ	categ_ignoring_null_categ
INA	9118	broad.mit.edu	36	10	105027037	105027037	+	Missense_Mutation	SNP	G	C	C			TCGA-27-2527-01	TCGA-27-2527-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr10:105027037G>C	uc001kws.1	+	c.79G>C	c.(79-81)GCC>CCC	p.A27P	INA_uc009xxj.1_Missense_Mutation_p.A27P	NM_032727	NP_116116	Q16352	AINX_HUMAN	internexin neuronal intermediate filament	27	Head.				cell differentiation|nervous system development	neurofilament	structural constituent of cytoskeleton			ovary(1)|breast(1)	2														0.235294	7.191007	8.28191	4	13	GG		KEEP	---	---	---	---	capture		Epithelial(162;3.45e-09)|all cancers(201;9.17e-08)|BRCA - Breast invasive adenocarcinoma(275;0.198)	Missense_Mutation	SNP	105027037	105027037	8031	10	G	C	C	38	38	INA	C	3	3
PDCD11	22984	broad.mit.edu	36	10	105166326	105166326	+	Missense_Mutation	SNP	A	G	G			TCGA-27-2527-01	TCGA-27-2527-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr10:105166326A>G	uc001kwy.1	+	c.1607A>G	c.(1606-1608)TAT>TGT	p.Y536C		NM_014976	NP_055791	Q14690	RRP5_HUMAN	programmed cell death 11	536					mRNA processing|rRNA processing	nucleolus	RNA binding|transcription factor binding			ovary(2)|breast(2)|skin(2)|central_nervous_system(1)	7		Colorectal(252;0.0747)|Breast(234;0.128)								545		OREG0020494	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.106061	25.741922	56.247774	21	177	AA		KEEP	---	---	---	---	capture		Epithelial(162;7.21e-09)|all cancers(201;1.17e-08)|BRCA - Breast invasive adenocarcinoma(275;0.208)	Missense_Mutation	SNP	105166326	105166326	12038	10	A	G	G	16	16	PDCD11	G	4	4
KIAA1598	57698	broad.mit.edu	36	10	118661322	118661322	+	Missense_Mutation	SNP	T	G	G			TCGA-27-2527-01	TCGA-27-2527-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr10:118661322T>G	uc001lcx.2	-	c.1328A>C	c.(1327-1329)GAA>GCA	p.E443A	KIAA1598_uc009xyw.1_Missense_Mutation_p.E443A|KIAA1598_uc001lcz.2_Missense_Mutation_p.E443A|KIAA1598_uc001lcy.2_Missense_Mutation_p.E413A	NM_018330	NP_060800	A0MZ66	SHOT1_HUMAN	shootin1 isoform b	443					axon guidance	axon					0														0.150327	50.423317	68.353297	23	130	TT		KEEP	---	---	---	---	capture		all cancers(201;0.00494)	Missense_Mutation	SNP	118661322	118661322	8555	10	T	G	G	62	62	KIAA1598	G	4	4
CPXM2	119587	broad.mit.edu	36	10	125496502	125496502	+	Missense_Mutation	SNP	C	T	T			TCGA-27-2527-01	TCGA-27-2527-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr10:125496502C>T	uc001lhk.1	-	c.2039G>A	c.(2038-2040)CGC>CAC	p.R680H	CPXM2_uc001lhj.2_Intron	NM_198148	NP_937791	Q8N436	CPXM2_HUMAN	carboxypeptidase X (M14 family), member 2	680					cell adhesion|proteolysis	extracellular space	metallocarboxypeptidase activity|zinc ion binding			ovary(2)	2		all_lung(145;0.174)|Colorectal(57;0.178)|Glioma(114;0.222)|all_neural(114;0.226)|Lung NSC(174;0.233)												0.190939	125.172875	152.737954	59	250	CC		KEEP	---	---	---	---	capture		COAD - Colon adenocarcinoma(40;0.212)|Colorectal(40;0.237)	Missense_Mutation	SNP	125496502	125496502	3977	10	C	T	T	27	27	CPXM2	T	1	1
GDF2	2658	broad.mit.edu	36	10	48036634	48036634	+	Silent	SNP	C	T	T			TCGA-27-2527-01	TCGA-27-2527-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr10:48036634C>T	uc001jfa.1	-	c.66G>A	c.(64-66)GGG>GGA	p.G22G		NM_016204	NP_057288	Q9UK05	GDF2_HUMAN	growth differentiation factor 2	22					activin receptor signaling pathway|BMP signaling pathway|cartilage development|cellular iron ion homeostasis|growth|negative regulation of angiogenesis|negative regulation of blood vessel endothelial cell migration|negative regulation of cell growth|negative regulation of DNA replication|negative regulation of endothelial cell proliferation|ossification|pathway-restricted SMAD protein phosphorylation|patterning of blood vessels|positive regulation of angiogenesis|positive regulation of endothelial cell proliferation|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of transcription, DNA-dependent	extracellular space	cytokine activity|growth factor activity			ovary(2)	2														0.210526	7.797763	9.265303	4	15	CC		KEEP	---	---	---	---	capture			Silent	SNP	48036634	48036634	6582	10	C	T	T	30	30	GDF2	T	2	2
NCOA4	8031	broad.mit.edu	36	10	51249178	51249178	+	Missense_Mutation	SNP	T	G	G			TCGA-27-2527-01	TCGA-27-2527-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr10:51249178T>G	uc009xon.1	+	c.79T>G	c.(79-81)TCC>GCC	p.S27A	PARG_uc001jih.1_Intron|NCOA4_uc001jis.2_Missense_Mutation_p.S11A|NCOA4_uc001jit.1_Missense_Mutation_p.S11A|NCOA4_uc009xoo.1_Missense_Mutation_p.S11A	NM_005437	NP_005428	Q13772	NCOA4_HUMAN	nuclear receptor coactivator 4 isoform 3	11					androgen receptor signaling pathway|male gonad development|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	androgen receptor binding|transcription coactivator activity			central_nervous_system(1)|kidney(1)	2										48				0.166667	11.436574	17.136226	9	45	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	51249178	51249178	10630	10	T	G	G	54	54	NCOA4	G	4	4
MMP13	4322	broad.mit.edu	36	11	102321606	102321606	+	Missense_Mutation	SNP	C	A	A			TCGA-27-2527-01	TCGA-27-2527-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:102321606C>A	uc001phl.1	-	c.1294G>T	c.(1294-1296)GAT>TAT	p.D432Y		NM_002427	NP_002418	P45452	MMP13_HUMAN	matrix metalloproteinase 13 preproprotein	432	Hemopexin-like 4.	Calcium 3; via carbonyl oxygen (By similarity).			collagen catabolic process|proteolysis	extracellular space	metalloendopeptidase activity|zinc ion binding			ovary(2)	2		all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)												0.154762	39.929604	59.079106	26	142	CC		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(274;0.0144)	Missense_Mutation	SNP	102321606	102321606	10042	11	C	A	A	32	32	MMP13	A	3	3
HPS5	11234	broad.mit.edu	36	11	18265744	18265744	+	Silent	SNP	C	T	T			TCGA-27-2527-01	TCGA-27-2527-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:18265744C>T	uc001mod.1	-	c.2631G>A	c.(2629-2631)TCG>TCA	p.S877S	HPS5_uc001moe.1_Silent_p.S763S|HPS5_uc001mof.1_Silent_p.S763S	NM_181507	NP_852609	Q9UPZ3	HPS5_HUMAN	Hermansky-Pudlak syndrome 5 isoform a	877						cytosol				ovary(1)|pancreas(1)	2														0.161538	43.195125	57.357853	21	109	CC		KEEP	---	---	---	---	capture			Silent	SNP	18265744	18265744	7634	11	C	T	T	23	23	HPS5	T	1	1
EXT2	2132	broad.mit.edu	36	11	44086121	44086121	+	Missense_Mutation	SNP	C	T	T			TCGA-27-2527-01	TCGA-27-2527-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:44086121C>T	uc001mya.1	+	c.382C>T	c.(382-384)CGC>TGC	p.R128C	EXT2_uc001mxy.1_Missense_Mutation_p.R108C|EXT2_uc001mxz.1_Missense_Mutation_p.R95C|EXT2_uc009ykt.1_Missense_Mutation_p.R95C	NM_207122	NP_997005	Q93063	EXT2_HUMAN	exostosin 2 isoform 2	95	Lumenal (Potential).				glycosaminoglycan biosynthetic process|heparan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process|ossification|signal transduction	Golgi membrane|integral to membrane|intrinsic to endoplasmic reticulum membrane	glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity|heparan sulfate N-acetylglucosaminyltransferase activity|N-acetylglucosaminyl-proteoglycan 4-beta-glucuronosyltransferase activity|protein heterodimerization activity				0										271				0.179104	24.058662	30.551614	12	55	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	44086121	44086121	5518	11	C	T	T	31	31	EXT2	T	1	1
OR4A5	81318	broad.mit.edu	36	11	51268653	51268653	+	Missense_Mutation	SNP	C	T	T	rs5002407	by-hapmap	TCGA-27-2527-01	TCGA-27-2527-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:51268653C>T	uc001nhi.1	-	c.319G>A	c.(319-321)GGG>AGG	p.G107R		NM_001005272	NP_001005272	Q8NH83	OR4A5_HUMAN	olfactory receptor, family 4, subfamily A,	107	Helical; Name=3; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|central_nervous_system(1)	2		all_lung(304;0.236)												0.161905	31.911334	43.32604	17	88	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	51268653	51268653	11449	11	C	T	T	21	21	OR4A5	T	2	2
GPR109A	338442	broad.mit.edu	36	12	121753033	121753033	+	Missense_Mutation	SNP	G	A	A			TCGA-27-2527-01	TCGA-27-2527-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:121753033G>A	uc001ucx.1	-	c.751C>T	c.(751-753)CGG>TGG	p.R251W	GPR81_uc001ucw.1_Intron	NM_177551	NP_808219	Q8TDS4	G109A_HUMAN	G protein-coupled receptor 109A	251	Extracellular (Potential).				negative regulation of lipid catabolic process|neutrophil apoptosis|positive regulation of adiponectin secretion|positive regulation of neutrophil apoptosis	integral to membrane|plasma membrane	nicotinic acid receptor activity|purinergic nucleotide receptor activity, G-protein coupled			ovary(1)	1	all_neural(191;0.0837)|Medulloblastoma(191;0.163)				Mepenzolate(DB04843)|Niacin(DB00627)									0.15	30.78704	44.867411	18	102	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(86;2.12e-05)|Epithelial(86;3.19e-05)|BRCA - Breast invasive adenocarcinoma(302;0.196)	Missense_Mutation	SNP	121753033	121753033	6899	12	G	A	A	38	38	GPR109A	A	1	1
CACNA1C	775	broad.mit.edu	36	12	2586425	2586425	+	Missense_Mutation	SNP	C	T	T			TCGA-27-2527-01	TCGA-27-2527-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:2586425C>T	uc009zdu.1	+	c.3284C>T	c.(3283-3285)ACG>ATG	p.T1095M	CACNA1C_uc009zdv.1_Missense_Mutation_p.T1072M|CACNA1C_uc001qkb.2_Missense_Mutation_p.T1075M|CACNA1C_uc001qkc.2_Missense_Mutation_p.T1075M|CACNA1C_uc001qke.2_Missense_Mutation_p.T1075M|CACNA1C_uc001qkf.2_Missense_Mutation_p.T1075M|CACNA1C_uc001qjz.2_Missense_Mutation_p.T1075M|CACNA1C_uc001qkd.2_Missense_Mutation_p.T1075M|CACNA1C_uc001qkg.2_Missense_Mutation_p.T1075M|CACNA1C_uc009zdw.1_Missense_Mutation_p.T1075M|CACNA1C_uc001qkh.2_Missense_Mutation_p.T1075M|CACNA1C_uc001qkl.2_Missense_Mutation_p.T1095M|CACNA1C_uc001qkn.2_Missense_Mutation_p.T1075M|CACNA1C_uc001qko.2_Missense_Mutation_p.T1095M|CACNA1C_uc001qkp.2_Missense_Mutation_p.T1075M|CACNA1C_uc001qkr.2_Missense_Mutation_p.T1075M|CACNA1C_uc001qku.2_Missense_Mutation_p.T1075M|CACNA1C_uc001qkq.2_Missense_Mutation_p.T1075M|CACNA1C_uc001qks.2_Missense_Mutation_p.T1075M|CACNA1C_uc001qkt.2_Missense_Mutation_p.T1075M|CACNA1C_uc001qka.1_Missense_Mutation_p.T610M|CACNA1C_uc001qki.1_Missense_Mutation_p.T811M|CACNA1C_uc001qkj.1_Missense_Mutation_p.T811M|CACNA1C_uc001qkk.1_Missense_Mutation_p.T811M|CACNA1C_uc001qkm.1_Missense_Mutation_p.T811M	NM_199460	NP_955630	Q13936	CAC1C_HUMAN	calcium channel, voltage-dependent, L type,	1095	Extracellular (Potential).|III.				axon guidance|calcium ion transport into cytosol|energy reserve metabolic process|regulation of insulin secretion	cytoplasm|postsynaptic density|voltage-gated calcium channel complex	calmodulin binding|voltage-gated calcium channel activity			ovary(10)|central_nervous_system(1)	11					Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Mibefradil(DB01388)|Nicardipine(DB00622)|Verapamil(DB00661)									0.171053	25.429277	33.204224	13	63	CC		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(31;0.00256)	LUAD - Lung adenocarcinoma(1;0.134)	Missense_Mutation	SNP	2586425	2586425	2656	12	C	T	T	19	19	CACNA1C	T	1	1
SYT10	341359	broad.mit.edu	36	12	33429447	33429447	+	Missense_Mutation	SNP	G	A	A			TCGA-27-2527-01	TCGA-27-2527-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:33429447G>A	uc001rll.1	-	c.1124C>T	c.(1123-1125)CCG>CTG	p.P375L	SYT10_uc009zju.1_Missense_Mutation_p.P185L	NM_198992	NP_945343	Q6XYQ8	SYT10_HUMAN	synaptotagmin X	375	C2 2.|Cytoplasmic (Potential).					cell junction|integral to membrane|synaptic vesicle membrane	metal ion binding|transporter activity			ovary(1)	1	Lung NSC(5;8.37e-07)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0334)													0.188406	60.178497	72.709768	26	112	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	33429447	33429447	15987	12	G	A	A	39	39	SYT10	A	1	1
C12orf68	387856	broad.mit.edu	36	12	46864689	46864689	+	Missense_Mutation	SNP	C	T	T			TCGA-27-2527-01	TCGA-27-2527-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:46864689C>T	uc001rrj.1	+	c.517C>T	c.(517-519)CCA>TCA	p.P173S		NM_001013635	NP_001013657	Q52MB2	CL068_HUMAN	hypothetical protein LOC387856	173						cytoplasm				central_nervous_system(1)	1														0.25	8.491186	9.401301	4	12	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	46864689	46864689	1754	12	C	T	T	26	26	C12orf68	T	2	2
KIAA0748	9840	broad.mit.edu	36	12	53642820	53642820	+	Missense_Mutation	SNP	C	T	T			TCGA-27-2527-01	TCGA-27-2527-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:53642820C>T	uc001sgn.2	-	c.1129G>A	c.(1129-1131)GCA>ACA	p.A377T	KIAA0748_uc001sgl.2_Missense_Mutation_p.A239T|KIAA0748_uc001sgm.2_Missense_Mutation_p.A124T|KIAA0748_uc001sgo.2_Non-coding_Transcript	NM_001098815	NP_001092285	A2RU30	K0748_HUMAN	hypothetical protein LOC9840	377										ovary(1)|central_nervous_system(1)	2														0.145299	30.893799	45.055149	17	100	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	53642820	53642820	8497	12	C	T	T	28	28	KIAA0748	T	2	2
C1S	716	broad.mit.edu	36	12	7044660	7044660	+	Missense_Mutation	SNP	T	A	A			TCGA-27-2527-01	TCGA-27-2527-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr12:7044660T>A	uc001qsj.1	+	c.1044T>A	c.(1042-1044)AGT>AGA	p.S348R	C1S_uc001qsl.1_Missense_Mutation_p.S348R|C1S_uc009zfr.1_Missense_Mutation_p.S181R|C1S_uc001qsk.1_Missense_Mutation_p.S348R|C1S_uc009zfs.1_Non-coding_Transcript	NM_201442	NP_958850	P09871	C1S_HUMAN	complement component 1, s subcomponent	348	Sushi 1.				complement activation, classical pathway|innate immune response|proteolysis	extracellular region	calcium ion binding|serine-type endopeptidase activity				0					Abciximab(DB00054)|Adalimumab(DB00051)|Basiliximab(DB00074)|Cetuximab(DB00002)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Immune globulin(DB00028)|Muromonab(DB00075)|Rituximab(DB00073)|Trastuzumab(DB00072)	GBM(156;750 1943 12971 24779 31015)								0.118343	22.785729	46.976564	20	149	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	7044660	7044660	2041	12	T	A	A	57	57	C1S	A	4	4
KLHL1	57626	broad.mit.edu	36	13	69433515	69433515	+	Missense_Mutation	SNP	G	A	A			TCGA-27-2527-01	TCGA-27-2527-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr13:69433515G>A	uc001vip.1	-	c.743C>T	c.(742-744)GCC>GTC	p.A248V		NM_020866	NP_065917	Q9NR64	KLHL1_HUMAN	kelch-like 1 protein	248	BTB.				actin cytoskeleton organization	cytoplasm|cytoskeleton	actin binding				0		Breast(118;0.000162)												0.162338	44.723311	61.381829	25	129	GG		KEEP	---	---	---	---	capture		COAD - Colon adenocarcinoma(199;0.000193)|GBM - Glioblastoma multiforme(99;0.000211)	Missense_Mutation	SNP	69433515	69433515	8677	13	G	A	A	42	42	KLHL1	A	2	2
SPTBN5	51332	broad.mit.edu	36	15	39955646	39955646	+	Silent	SNP	G	A	A			TCGA-27-2527-01	TCGA-27-2527-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr15:39955646G>A	uc001zos.1	-	c.3975C>T	c.(3973-3975)AGC>AGT	p.S1325S		NM_016642	NP_057726	Q9NRC6	SPTN5_HUMAN	spectrin, beta, non-erythrocytic 5	1360	Spectrin 10.				actin cytoskeleton organization|actin filament capping|axon guidance	cytosol|membrane|spectrin				ovary(1)|central_nervous_system(1)	2		all_cancers(109;1.84e-17)|all_epithelial(112;1.12e-15)|Lung NSC(122;7.6e-10)|all_lung(180;4.15e-09)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.173)												0.16	19.67351	27.924392	12	63	GG		KEEP	---	---	---	---	capture		all cancers(2;4.33e-34)|Epithelial(2;1.72e-25)|OV - Ovarian serous cystadenocarcinoma(18;8.32e-20)|GBM - Glioblastoma multiforme(94;4.69e-07)|Colorectal(2;0.00104)|COAD - Colon adenocarcinoma(120;0.0405)|READ - Rectum adenocarcinoma(92;0.0908)	Silent	SNP	39955646	39955646	15636	15	G	A	A	38	38	SPTBN5	A	1	1
HERC1	8925	broad.mit.edu	36	15	61735542	61735542	+	Missense_Mutation	SNP	C	T	T			TCGA-27-2527-01	TCGA-27-2527-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr15:61735542C>T	uc002amp.1	-	c.9668G>A	c.(9667-9669)CGA>CAA	p.R3223Q		NM_003922	NP_003913	Q15751	HERC1_HUMAN	guanine nucleotide exchange factor p532	3223					protein modification process|transport	cytosol|Golgi apparatus|membrane	acid-amino acid ligase activity|ARF guanyl-nucleotide exchange factor activity			ovary(5)|central_nervous_system(2)|lung(1)|breast(1)	9														0.186441	22.4102	27.83052	11	48	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	61735542	61735542	7340	15	C	T	T	31	31	HERC1	T	1	1
TMC3	342125	broad.mit.edu	36	15	79416003	79416003	+	Splice_Site_SNP	SNP	A	G	G			TCGA-27-2527-01	TCGA-27-2527-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr15:79416003A>G	uc002bgo.1	-	c.2203_splice	c.e20+1	p.A735_splice	TMC3_uc010blr.1_Splice_Site_SNP	NM_001080532	NP_001074001			transmembrane channel-like 3							integral to membrane				ovary(1)|liver(1)	2														0.140078	79.443333	111.569371	36	221	AA		KEEP	---	---	---	---	capture			Splice_Site_SNP	SNP	79416003	79416003	16516	15	A	G	G	14	14	TMC3	G	5	4
CNGB1	1258	broad.mit.edu	36	16	56552291	56552291	+	Missense_Mutation	SNP	T	C	C			TCGA-27-2527-01	TCGA-27-2527-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr16:56552291T>C	uc002emt.1	-	c.488A>G	c.(487-489)GAG>GGG	p.E163G	CNGB1_uc010cdh.1_Missense_Mutation_p.E163G|CNGB1_uc002emu.1_Missense_Mutation_p.E163G	NM_001297	NP_001288	Q14028	CNGB1_HUMAN	cyclic nucleotide gated channel beta 1 isoform	163					sensory perception of smell	intracellular cyclic nucleotide activated cation channel complex	cAMP binding|intracellular cAMP activated cation channel activity			breast(3)|pancreas(1)	4						Colon(156;1293 1853 16336 28962 38659)								0.210526	6.52733	8.083404	4	15	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	56552291	56552291	3738	16	T	C	C	54	54	CNGB1	C	4	4
MNT	4335	broad.mit.edu	36	17	2237386	2237386	+	Silent	SNP	A	C	C			TCGA-27-2527-01	TCGA-27-2527-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr17:2237386A>C	uc002fur.1	-	c.1308T>G	c.(1306-1308)GGT>GGG	p.G436G		NM_020310	NP_064706	Q99583	MNT_HUMAN	MAX binding protein	436					multicellular organismal development|negative regulation of cell proliferation|regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription corepressor activity|transcription regulator activity				0														0.384615	6.42975	6.626754	5	8	AA		KEEP	---	---	---	---	capture		Colorectal(2;1.37e-05)|READ - Rectum adenocarcinoma(2;8.68e-05)	Silent	SNP	2237386	2237386	10069	17	A	C	C	6	6	MNT	C	4	4
TTC25	83538	broad.mit.edu	36	17	37346283	37346283	+	Silent	SNP	G	A	A			TCGA-27-2527-01	TCGA-27-2527-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:37346283G>A	uc002hyj.2	+	c.429G>A	c.(427-429)GGG>GGA	p.G143G	TTC25_uc010cxt.1_Non-coding_Transcript|TTC25_uc010cxs.1_Silent_p.G143G	NM_031421	NP_113609	Q96NG3	TTC25_HUMAN	tetratricopeptide repeat domain 25	143						cytoplasm	protein binding			ovary(1)	1		all_cancers(22;8.16e-06)|Breast(137;0.000143)|all_epithelial(22;0.000236)												0.219178	39.922525	45.181856	16	57	GG		KEEP	---	---	---	---	capture			Silent	SNP	37346283	37346283	17247	17	G	A	A	43	43	TTC25	A	2	2
BZRAP1	9256	broad.mit.edu	36	17	53744929	53744929	+	Missense_Mutation	SNP	C	G	G			TCGA-27-2527-01	TCGA-27-2527-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:53744929C>G	uc002ivx.2	-	c.2252G>C	c.(2251-2253)GGC>GCC	p.G751A	BZRAP1_uc010dcs.1_Missense_Mutation_p.G691A	NM_004758	NP_004749	O95153	RIMB1_HUMAN	peripheral benzodiazepine receptor-associated	751						mitochondrion	benzodiazepine receptor binding				0	Medulloblastoma(34;0.127)|all_neural(34;0.237)													0.137097	32.609537	48.395386	17	107	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	53744929	53744929	1611	17	C	G	G	26	26	BZRAP1	G	3	3
KDSR	2531	broad.mit.edu	36	18	59185315	59185315	+	Missense_Mutation	SNP	G	C	C			TCGA-27-2527-01	TCGA-27-2527-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr18:59185315G>C	uc010dpw.1	-	c.17C>G	c.(16-18)GCC>GGC	p.A6G		NM_002035	NP_002026	Q06136	KDSR_HUMAN	3-ketodihydrosphingosine reductase precursor	6					3-keto-sphinganine metabolic process|oxidation-reduction process	endoplasmic reticulum membrane|extracellular space|integral to membrane	3-dehydrosphinganine reductase activity|binding				0									p.A6G(SNU719-Tumor)	107				0.444444	9.191875	9.216256	4	5	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	59185315	59185315	8446	18	G	C	C	42	42	KDSR	C	3	3
ZNF497	162968	broad.mit.edu	36	19	63560642	63560642	+	Missense_Mutation	SNP	G	T	T			TCGA-27-2527-01	TCGA-27-2527-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:63560642G>T	uc002qsh.1	-	c.172C>A	c.(172-174)CAA>AAA	p.Q58K	A1BG_uc002qsf.1_Intron|ZNF497_uc002qsi.1_Missense_Mutation_p.Q58K|ZNF497_uc010eup.1_Missense_Mutation_p.Q58K	NM_198458	NP_940860	Q6ZNH5	ZN497_HUMAN	zinc finger protein 497	58					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			central_nervous_system(2)	2		all_cancers(17;3.11e-12)|all_epithelial(17;9.43e-09)|Colorectal(82;0.000256)|Lung NSC(17;0.000607)|all_lung(17;0.0024)|all_neural(62;0.0412)|Ovarian(87;0.156)								25				0.6	7.02026	7.063118	3	2	GG		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0278)	Missense_Mutation	SNP	63560642	63560642	18540	19	G	T	T	46	46	ZNF497	T	3	3
ZNF324B	388569	broad.mit.edu	36	19	63659050	63659050	+	Silent	SNP	C	T	T			TCGA-27-2527-01	TCGA-27-2527-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:63659050C>T	uc002qsv.1	+	c.927C>T	c.(925-927)GGC>GGT	p.G309G	ZNF324B_uc002qsu.1_Silent_p.G299G|ZNF324B_uc010euq.1_Silent_p.G309G	NM_207395	NP_997278	Q6AW86	Z324B_HUMAN	zinc finger protein 324B	309					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1		all_cancers(17;1.81e-17)|all_epithelial(17;1.21e-12)|Lung NSC(17;2.8e-05)|all_lung(17;0.000139)|Colorectal(82;0.000147)|Renal(17;0.00528)|all_neural(62;0.0133)|Ovarian(87;0.156)|Medulloblastoma(540;0.232)												0.188679	20.067016	24.838446	10	43	CC		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0164)|Lung(386;0.179)	Silent	SNP	63659050	63659050	18437	19	C	T	T	27	27	ZNF324B	T	1	1
PHGDH	26227	broad.mit.edu	36	1	120087058	120087058	+	Missense_Mutation	SNP	C	G	G			TCGA-27-2527-01	TCGA-27-2527-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:120087058C>G	uc001ehz.1	+	c.1315C>G	c.(1315-1317)CAA>GAA	p.Q439E	PHGDH_uc009whm.1_Missense_Mutation_p.Q337E|PHGDH_uc001eia.1_Missense_Mutation_p.Q438E|PHGDH_uc009whn.1_Intron|PHGDH_uc001eib.1_Missense_Mutation_p.Q405E|PHGDH_uc001eic.1_Non-coding_Transcript	NM_006623	NP_006614	O43175	SERA_HUMAN	phosphoglycerate dehydrogenase	439					brain development|L-serine biosynthetic process|oxidation-reduction process		electron carrier activity|NAD binding|phosphoglycerate dehydrogenase activity			ovary(1)	1	all_cancers(5;1.18e-09)|all_epithelial(5;2.16e-10)|Melanoma(3;1.93e-05)|all_neural(166;0.219)	all_lung(203;3.66e-05)|Lung NSC(69;0.000202)|all_epithelial(167;0.0347)			NADH(DB00157)									0.129032	13.036977	25.511462	12	81	CC		KEEP	---	---	---	---	capture		Lung(183;0.0111)|LUSC - Lung squamous cell carcinoma(189;0.0593)	Missense_Mutation	SNP	120087058	120087058	12264	1	C	G	G	21	21	PHGDH	G	3	3
HSPA6	3310	broad.mit.edu	36	1	159761230	159761230	+	Missense_Mutation	SNP	T	G	G			TCGA-27-2527-01	TCGA-27-2527-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr1:159761230T>G	uc001gap.1	+	c.158T>G	c.(157-159)GTC>GGC	p.V53G	HSPA6_uc001gaq.1_Missense_Mutation_p.V53G	NM_002155	NP_002146	P17066	HSP76_HUMAN	heat shock 70kDa protein 6 (HSP70B')	53					response to unfolded protein		ATP binding			skin(1)	1	all_cancers(52;4.89e-16)|all_hematologic(112;0.0207)													0.5	8.222413	8.222413	5	5	TT		KEEP	---	---	---	---	capture	BRCA - Breast invasive adenocarcinoma(70;0.00376)		Missense_Mutation	SNP	159761230	159761230	7714	1	T	G	G	58	58	HSPA6	G	4	4
TAS1R2	80834	broad.mit.edu	36	1	19054008	19054008	+	Silent	SNP	C	T	T			TCGA-27-2527-01	TCGA-27-2527-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:19054008C>T	uc001bba.1	-	c.543G>A	c.(541-543)CTG>CTA	p.L181L		NM_152232	NP_689418	Q8TE23	TS1R2_HUMAN	taste receptor, type 1, member 2	181	Extracellular (Potential).				detection of chemical stimulus involved in sensory perception of sweet taste	integral to membrane|plasma membrane	protein heterodimerization activity|taste receptor activity			ovary(1)|central_nervous_system(1)	2		Colorectal(325;3.46e-05)|all_lung(284;0.000321)|Lung NSC(340;0.000398)|Renal(390;0.000518)|Breast(348;0.000812)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)			Aspartame(DB00168)									0.121212	6.852631	16.138858	8	58	CC		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (279;0.00466)|BRCA - Breast invasive adenocarcinoma(304;3.56e-05)|Kidney(64;0.000177)|KIRC - Kidney renal clear cell carcinoma(64;0.00262)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)	Silent	SNP	19054008	19054008	16085	1	C	T	T	25	25	TAS1R2	T	2	2
FMN2	56776	broad.mit.edu	36	1	238437996	238437996	+	Silent	SNP	A	T	T			TCGA-27-2527-01	TCGA-27-2527-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr1:238437996A>T	uc009xgl.1	+	c.3702A>T	c.(3700-3702)CCA>CCT	p.P1234P		NM_020066	NP_064450	Q9NZ56	FMN2_HUMAN	formin 2	1087	Pro-rich.|FH1.				actin cytoskeleton organization|establishment of meiotic spindle localization|intracellular signal transduction|meiotic chromosome movement towards spindle pole|meiotic metaphase I|multicellular organismal development|oogenesis|polar body extrusion after meiotic divisions		actin binding			ovary(4)|pancreas(3)|large_intestine(1)|central_nervous_system(1)	9	Ovarian(103;0.127)	all_cancers(173;0.013)								1289				0.7	22.128093	22.485898	7	3	AA		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(106;0.0106)		Silent	SNP	238437996	238437996	6192	1	A	T	T	6	6	FMN2	T	4	4
COL16A1	1307	broad.mit.edu	36	1	31898803	31898803	+	Silent	SNP	G	T	T			TCGA-27-2527-01	TCGA-27-2527-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:31898803G>T	uc001btk.1	-	c.3849C>A	c.(3847-3849)CCC>CCA	p.P1283P	COL16A1_uc001bti.1_5'UTR|COL16A1_uc001btj.1_Silent_p.P1081P	NM_001856	NP_001847	Q07092	COGA1_HUMAN	alpha 1 type XVI collagen precursor	1283	Triple-helical region 2 (COL2) with 2 imperfections.				cell adhesion|female pregnancy|integrin-mediated signaling pathway	collagen type XVI	integrin binding|structural molecule activity			ovary(8)	8		Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0423)|all_neural(195;0.0837)|Breast(348;0.116)				Colon(143;498 1786 21362 25193 36625)								0.133758	31.683805	52.101457	21	136	GG		KEEP	---	---	---	---	capture		STAD - Stomach adenocarcinoma(196;0.059)	Silent	SNP	31898803	31898803	3811	1	G	T	T	43	43	COL16A1	T	3	3
DAB1	1600	broad.mit.edu	36	1	57264244	57264244	+	Missense_Mutation	SNP	G	A	A			TCGA-27-2527-01	TCGA-27-2527-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:57264244G>A	uc001cys.1	-	c.784C>T	c.(784-786)CCC>TCC	p.P262S	DAB1_uc001cyt.1_Missense_Mutation_p.P260S|DAB1_uc001cyq.1_Missense_Mutation_p.P260S|DAB1_uc001cyr.1_Missense_Mutation_p.P176S|DAB1_uc009vzw.1_Missense_Mutation_p.P244S|DAB1_uc009vzx.1_Missense_Mutation_p.P262S	NM_021080	NP_066566	O75553	DAB1_HUMAN	disabled homolog 1	295				P -> S (in Ref. 6; AAH67447).	cell differentiation|nervous system development					ovary(1)	1										395				0.165289	81.155811	106.876022	40	202	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	57264244	57264244	4383	1	G	A	A	43	43	DAB1	A	2	2
TRPM2	7226	broad.mit.edu	36	21	44650974	44650974	+	Missense_Mutation	SNP	G	C	C			TCGA-27-2527-01	TCGA-27-2527-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr21:44650974G>C	uc010gpt.1	+	c.2860G>C	c.(2860-2862)GCC>CCC	p.A954P	TRPM2_uc002zet.1_Missense_Mutation_p.A954P|TRPM2_uc002zeu.1_Missense_Mutation_p.A954P|TRPM2_uc002zew.1_Missense_Mutation_p.A954P|TRPM2_uc002zex.1_Missense_Mutation_p.A740P|TRPM2_uc002zey.1_Missense_Mutation_p.A467P	NM_003307	NP_003298	O94759	TRPM2_HUMAN	transient receptor potential cation channel,	954	Helical; (Potential).					integral to plasma membrane	ADP-ribose diphosphatase activity|calcium channel activity|sodium channel activity			ovary(1)|central_nervous_system(1)|pancreas(1)	3														0.2	6.952168	8.581419	4	16	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	44650974	44650974	17137	21	G	C	C	42	42	TRPM2	C	3	3
ZDHHC8	29801	broad.mit.edu	36	22	18508769	18508769	+	Silent	SNP	G	A	A			TCGA-27-2527-01	TCGA-27-2527-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr22:18508769G>A	uc002zrr.1	+	c.924G>A	c.(922-924)GAG>GAA	p.E308E	ZDHHC8_uc002zrq.1_Silent_p.E308E|ZDHHC8_uc010gsa.1_Silent_p.E114E	NM_013373	NP_037505	Q9ULC8	ZDHC8_HUMAN	zinc finger, DHHC domain containing 8	308	Cytoplasmic (Potential).					cytoplasmic vesicle membrane|integral to membrane	acyltransferase activity|zinc ion binding			ovary(1)	1	Colorectal(54;0.0993)													0.32	11.978793	12.765778	8	17	GG		KEEP	---	---	---	---	capture			Silent	SNP	18508769	18508769	18209	22	G	A	A	33	33	ZDHHC8	A	2	2
PRAME	23532	broad.mit.edu	36	22	21223261	21223261	+	Missense_Mutation	SNP	T	C	C			TCGA-27-2527-01	TCGA-27-2527-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr22:21223261T>C	uc002zwf.1	-	c.272A>G	c.(271-273)CAT>CGT	p.H91R	PRAME_uc010gtr.1_Missense_Mutation_p.H91R|PRAME_uc002zwg.1_Missense_Mutation_p.H91R|PRAME_uc002zwh.1_Missense_Mutation_p.H91R|PRAME_uc002zwi.1_Missense_Mutation_p.H91R|PRAME_uc002zwj.1_Missense_Mutation_p.H91R|PRAME_uc002zwk.1_Missense_Mutation_p.H91R	NM_206956	NP_996839	P78395	PRAME_HUMAN	preferentially expressed antigen in melanoma	91					apoptosis|cell differentiation|negative regulation of apoptosis|negative regulation of cell differentiation|negative regulation of retinoic acid receptor signaling pathway|positive regulation of cell proliferation|regulation of growth|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus|plasma membrane	retinoic acid receptor binding|transcription repressor activity			central_nervous_system(2)	2	all_hematologic(9;0.0135)|Acute lymphoblastic leukemia(84;0.17)	all_hematologic(6;1.74e-30)|Acute lymphoblastic leukemia(6;7.75e-22)|all_lung(157;4.03e-05)				Melanoma(73;1707 1838 15168 27201)				1184				0.218009	107.34327	122.806872	46	165	TT		KEEP	---	---	---	---	capture		READ - Rectum adenocarcinoma(21;0.0649)	Missense_Mutation	SNP	21223261	21223261	12860	22	T	C	C	51	51	PRAME	C	4	4
CELSR1	9620	broad.mit.edu	36	22	45238408	45238408	+	Missense_Mutation	SNP	C	G	G			TCGA-27-2527-01	TCGA-27-2527-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr22:45238408C>G	uc003bhw.1	-	c.4043G>C	c.(4042-4044)CGC>CCC	p.R1348P		NM_014246	NP_055061	Q9NYQ6	CELR1_HUMAN	cadherin EGF LAG seven-pass G-type receptor 1	1348	Extracellular (Potential).|EGF-like 1; calcium-binding.				central nervous system development|homophilic cell adhesion|neural tube closure|neuropeptide signaling pathway	integral to plasma membrane	calcium ion binding|G-protein coupled receptor activity|protein dimerization activity			pancreas(2)|skin(1)	3		Ovarian(80;0.00142)|Breast(42;0.00296)|all_neural(38;0.0416)|Colorectal(5;0.0766)												0.285714	6.569368	7.166102	4	10	CC		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (28;0.00643)|BRCA - Breast invasive adenocarcinoma(115;0.171)	Missense_Mutation	SNP	45238408	45238408	3354	22	C	G	G	27	27	CELSR1	G	3	3
TTC30A	92104	broad.mit.edu	36	2	178191667	178191667	+	Silent	SNP	A	C	C			TCGA-27-2527-01	TCGA-27-2527-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr2:178191667A>C	uc002ulo.1	-	c.9T>G	c.(7-9)GGT>GGG	p.G3G		NM_152275	NP_689488	Q86WT1	TT30A_HUMAN	tetratricopeptide repeat domain 30A	3					cell projection organization	cilium	binding				0														0.235294	8.694192	9.781955	4	13	AA		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(117;0.000423)|Epithelial(96;0.00373)|all cancers(119;0.0169)		Silent	SNP	178191667	178191667	17253	2	A	C	C	10	10	TTC30A	C	4	4
TTN	7273	broad.mit.edu	36	2	179166985	179166985	+	Missense_Mutation	SNP	C	T	T			TCGA-27-2527-01	TCGA-27-2527-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:179166985C>T	uc002umr.1	-	c.50677G>A	c.(50677-50679)GTG>ATG	p.V16893M	TTN_uc002ums.1_Missense_Mutation_p.V10588M|TTN_uc010frc.1_Missense_Mutation_p.V10521M|TTN_uc010frd.1_Missense_Mutation_p.V10396M	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	17820										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										8722				0.175182	87.710948	115.000983	48	226	CC		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)		Missense_Mutation	SNP	179166985	179166985	17290	2	C	T	T	17	17	TTN	T	2	2
ALS2CR12	130540	broad.mit.edu	36	2	201924285	201924285	+	Missense_Mutation	SNP	G	A	A			TCGA-27-2527-01	TCGA-27-2527-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:201924285G>A	uc010ftg.1	-	c.88C>T	c.(88-90)CGC>TGC	p.R30C	ALS2CR12_uc002uya.2_Missense_Mutation_p.R30C|ALS2CR12_uc010fth.1_Non-coding_Transcript	NM_139163	NP_631902	Q96Q35	AL2SB_HUMAN	amyotrophic lateral sclerosis 2 (juvenile)	30					regulation of GTPase activity		protein binding			ovary(1)|breast(1)|central_nervous_system(1)	3														0.138298	20.513119	32.402496	13	81	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	201924285	201924285	556	2	G	A	A	40	40	ALS2CR12	A	1	1
NRXN1	9378	broad.mit.edu	36	2	50704012	50704012	+	Missense_Mutation	SNP	C	T	T	rs34326676	unknown	TCGA-27-2527-01	TCGA-27-2527-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:50704012C>T	uc002rxe.2	-	c.1078G>A	c.(1078-1080)GGA>AGA	p.G360R	NRXN1_uc010fbq.1_Missense_Mutation_p.G40R|NRXN1_uc002rxb.2_Missense_Mutation_p.G40R|NRXN1_uc002rxc.1_Non-coding_Transcript	NM_004801	NP_004792	P58400	NRX1B_HUMAN	neurexin 1 isoform alpha1 precursor	170	Extracellular (Potential).|Laminin G-like.				neuron cell-cell adhesion|neuronal signal transduction	cell surface|endocytic vesicle|integral to membrane|presynaptic membrane	cell adhesion molecule binding|receptor binding			ovary(2)	2		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.192)												0.118182	17.291248	33.052347	13	97	CC		KEEP	---	---	---	---	capture	Lung(47;0.0813)|LUSC - Lung squamous cell carcinoma(58;0.116)		Missense_Mutation	SNP	50704012	50704012	11070	2	C	T	T	21	21	NRXN1	T	2	2
FANCD2	2177	broad.mit.edu	36	3	10083908	10083908	+	Missense_Mutation	SNP	T	C	C			TCGA-27-2527-01	TCGA-27-2527-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr3:10083908T>C	uc003buw.1	+	c.2401T>C	c.(2401-2403)TGC>CGC	p.C801R	FANCD2_uc003bux.1_Missense_Mutation_p.C801R|FANCD2_uc003buy.1_Missense_Mutation_p.C801R|FANCD2_uc010hcw.1_Non-coding_Transcript	NM_033084	NP_149075	Q9BXW9	FACD2_HUMAN	Fanconi anemia complementation group D2 isoform	801					DNA repair|response to gamma radiation	nucleoplasm	protein binding|protein binding			central_nervous_system(2)|ovary(1)|skin(1)	4										587				0.171875	23.983339	30.496988	11	53	TT		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(96;0.148)	Missense_Mutation	SNP	10083908	10083908	5901	3	T	C	C	55	55	FANCD2	C	4	4
IRAK2	3656	broad.mit.edu	36	3	10229939	10229939	+	Missense_Mutation	SNP	G	A	A			TCGA-27-2527-01	TCGA-27-2527-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:10229939G>A	uc003bve.1	+	c.577G>A	c.(577-579)GGA>AGA	p.G193R		NM_001570	NP_001561	O43187	IRAK2_HUMAN	interleukin-1 receptor-associated kinase 2	193					activation of MAPK activity|I-kappaB kinase/NF-kappaB cascade|inflammatory response|innate immune response|interleukin-1-mediated signaling pathway|JNK cascade|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of NF-kappaB transcription factor activity|positive regulation of NF-kappaB transcription factor activity|regulation of cytokine-mediated signaling pathway|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cell surface|cytosol|endosome membrane|plasma membrane	ATP binding|NF-kappaB-inducing kinase activity|protein heterodimerization activity|protein homodimerization activity			lung(5)|breast(3)	8										288				0.194444	59.908263	72.457293	28	116	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	10229939	10229939	8126	3	G	A	A	47	47	IRAK2	A	2	2
FGD5	152273	broad.mit.edu	36	3	14837955	14837955	+	Silent	SNP	C	A	A			TCGA-27-2527-01	TCGA-27-2527-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr3:14837955C>A	uc003bzc.1	+	c.1650C>A	c.(1648-1650)CCC>CCA	p.P550P		NM_152536	NP_689749	Q6ZNL6	FGD5_HUMAN	FYVE, RhoGEF and PH domain containing 5	791					actin cytoskeleton organization|filopodium assembly|regulation of Cdc42 GTPase activity|regulation of cell shape	cytoskeleton|Golgi apparatus|lamellipodium|ruffle	metal ion binding|Rho guanyl-nucleotide exchange factor activity|small GTPase binding			ovary(3)|kidney(1)|pancreas(1)	5														0.110368	25.198527	70.097319	33	266	CC		KEEP	---	---	---	---	capture			Silent	SNP	14837955	14837955	6073	3	C	A	A	22	22	FGD5	A	3	3
PIK3CA	5290	broad.mit.edu	36	3	180434779	180434779	+	Missense_Mutation	SNP	A	G	G			TCGA-27-2527-01	TCGA-27-2527-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr3:180434779A>G	uc003fjk.1	+	c.3140A>G	c.(3139-3141)CAT>CGT	p.H1047R		NM_006218	NP_006209	P42336	PK3CA_HUMAN	phosphoinositide-3-kinase, catalytic, alpha	1047	PI3K/PI4K.		H -> L (in cancer).|H -> R (in KERSEB; shows an increase in lipid kinase activity; oncogenic in vivo).|H -> Y (in cancer).		epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|platelet activation|T cell costimulation|T cell receptor signaling pathway		1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol-4,5-bisphosphate 3-kinase activity	p.H1047R(1204)|p.H1047L(134)|p.H1047Y(4)|p.H1047T(1)		breast(1506)|large_intestine(749)|endometrium(244)|urinary_tract(195)|ovary(136)|skin(112)|stomach(89)|thyroid(77)|central_nervous_system(69)|lung(61)|upper_aerodigestive_tract(48)|haematopoietic_and_lymphoid_tissue(27)|cervix(25)|biliary_tract(22)|liver(20)|oesophagus(17)|pancreas(11)|penis(8)|pituitary(8)|autonomic_ganglia(4)|kidney(2)|prostate(2)|meninges(1)|eye(1)|NS(1)|soft_tissue(1)|bone(1)	3437	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)					Colon(199;1504 1750 3362 26421 31210 32040)	H1047R(BT20_BREAST)|H1047R(NCIH1048_LUNG)|H1047R(MCAS_OVARY)|H1047R(HCC1954_BREAST)|H1047R(RKO_LARGE_INTESTINE)|H1047L(EFM19_BREAST)|H1047R(CAL33_UPPER_AERODIGESTIVE_TRACT)|H1047R(CAL29_URINARY_TRACT)|H1047R(DETROIT562_UPPER_AERODIGESTIVE_TRACT)|H1047R(LS180_LARGE_INTESTINE)|H1047R(T47D_BREAST)|H1047R(HCT116_LARGE_INTESTINE)|H1047R(HSC2_UPPER_AERODIGESTIVE_TRACT)|H1047R(SKOV3_OVARY)|H1047R(MDAMB453_BREAST)	57	p.H1047R(LS180-Tumor)|p.H1047R(UACC893-Tumor)|p.H1047R(HSC2-Tumor)|p.H1047R(BT20-Tumor)|p.H1047R(SKOV3-Tumor)|p.H1047L(GP2D-Tumor)|p.H1047R(T47D-Tumor)|p.H1047R(SNU840-Tumor)|p.H1047R(CAL148-Tumor)|p.H1047R(HCT116-Tumor)|p.H1047R(SNUC5-Tumor)|p.H1047R(MCAS-Tumor)|p.H1047R(SNU1076-Tumor)|p.H1047R(HCC1954-Tumor)|p.H1047L(OAW42-Tumor)|p.H1047L(EFM19-Tumor)|p.H1047R(RKO-Tumor)|p.H1047R(CAL29-Tumor)|p.H1047R(CAL33-Tumor)|p.H1047R(MDAMB453-Tumor)|p.H1047R(NCIH1048-Tumor)|p.H1047R(SNU407-Tumor)	621	TCGA GBM(8;5.49e-07)			0.093458	6.869052	24.649718	10	97	AA		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Missense_Mutation	SNP	180434779	180434779	12337	3	A	G	G	8	8	PIK3CA	G	4	4
IL1RAP	3556	broad.mit.edu	36	3	191827860	191827860	+	Missense_Mutation	SNP	G	A	A			TCGA-27-2527-01	TCGA-27-2527-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:191827860G>A	uc003fsq.2	+	c.830G>A	c.(829-831)CGC>CAC	p.R277H	IL1RAP_uc003fsk.1_Missense_Mutation_p.R277H|IL1RAP_uc003fsl.1_Missense_Mutation_p.R277H|IL1RAP_uc010hzf.1_Missense_Mutation_p.R136H|IL1RAP_uc003fsm.1_Missense_Mutation_p.R277H|IL1RAP_uc010hzg.1_Missense_Mutation_p.R277H|IL1RAP_uc003fsn.1_Non-coding_Transcript|IL1RAP_uc003fso.1_Missense_Mutation_p.R277H|IL1RAP_uc003fsp.1_Non-coding_Transcript	NM_134470	NP_608273	Q9NPH3	IL1AP_HUMAN	interleukin 1 receptor accessory protein isoform	277	Extracellular (Potential).|Ig-like C2-type 3.				inflammatory response|innate immune response|protein complex assembly	extracellular region|integral to plasma membrane					0	all_cancers(143;3.61e-10)|Ovarian(172;0.0733)|Breast(254;0.21)								p.R277H(SNUC2A-Tumor)	227				0.156425	49.68406	69.853466	28	151	GG		KEEP	---	---	---	---	capture	Lung(62;1.95e-06)|LUSC - Lung squamous cell carcinoma(58;2.05e-06)	GBM - Glioblastoma multiforme(93;0.00851)	Missense_Mutation	SNP	191827860	191827860	7961	3	G	A	A	38	38	IL1RAP	A	1	1
XIRP1	165904	broad.mit.edu	36	3	39204288	39204288	+	Silent	SNP	C	T	T			TCGA-27-2527-01	TCGA-27-2527-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr3:39204288C>T	uc003cjk.1	-	c.1653G>A	c.(1651-1653)CGG>CGA	p.R551R	XIRP1_uc003cji.2_Silent_p.R551R|XIRP1_uc003cjj.2_Intron|XIRP1_uc010hhp.1_Silent_p.R551R	NM_194293	NP_919269	Q702N8	XIRP1_HUMAN	xin actin-binding repeat containing 1	551	Interaction with CTNNB1 (By similarity).|Xin 12.						actin binding			ovary(4)|breast(2)|central_nervous_system(1)|pancreas(1)	8														0.175439	36.297031	47.572418	20	94	CC		KEEP	---	---	---	---	capture		KIRC - Kidney renal clear cell carcinoma(284;0.0517)|Kidney(284;0.065)	Silent	SNP	39204288	39204288	18010	3	C	T	T	18	18	XIRP1	T	2	2
PBRM1	55193	broad.mit.edu	36	3	52570880	52570880	+	Missense_Mutation	SNP	G	A	A			TCGA-27-2527-01	TCGA-27-2527-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:52570880G>A	uc003des.2	-	c.4231C>T	c.(4231-4233)CGC>TGC	p.R1411C	PBRM1_uc003dex.2_Non-coding_Transcript|PBRM1_uc003deq.2_Missense_Mutation_p.R1411C|PBRM1_uc003der.2_Missense_Mutation_p.R1379C|PBRM1_uc003det.2_Missense_Mutation_p.R1426C|PBRM1_uc003deu.2_Missense_Mutation_p.R1426C|PBRM1_uc003dev.2_Non-coding_Transcript|PBRM1_uc003dew.2_Missense_Mutation_p.R1411C|PBRM1_uc010hmk.1_Missense_Mutation_p.R1386C|PBRM1_uc003dey.2_Missense_Mutation_p.R1359C|PBRM1_uc003dez.1_Missense_Mutation_p.R1410C	NM_181042	NP_060635	Q86U86	PB1_HUMAN	polybromo 1 isoform 4	1411	HMG box.				chromatin remodeling|mitosis|negative regulation of cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear chromosome	chromatin binding|DNA binding|protein binding			kidney(136)|breast(4)	140														0.157197	158.482714	217.682832	83	445	GG		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)	Missense_Mutation	SNP	52570880	52570880	11911	3	G	A	A	39	39	PBRM1	A	1	1
ADAM29	11086	broad.mit.edu	36	4	176133864	176133864	+	Missense_Mutation	SNP	G	A	A			TCGA-27-2527-01	TCGA-27-2527-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr4:176133864G>A	uc003iuc.1	+	c.613G>A	c.(613-615)GTC>ATC	p.V205I	ADAM29_uc003iud.1_Missense_Mutation_p.V205I|ADAM29_uc003iue.1_Missense_Mutation_p.V205I|ADAM29_uc010irr.1_Missense_Mutation_p.V205I	NM_014269	NP_055084	Q9UKF5	ADA29_HUMAN	ADAM metallopeptidase domain 29 preproprotein	205	Peptidase M12B.|Extracellular (Potential).		V -> I (in a colorectal cancer sample; somatic mutation).		proteolysis|spermatogenesis	integral to plasma membrane	metalloendopeptidase activity|zinc ion binding	p.V205I(1)		ovary(3)|large_intestine(2)|central_nervous_system(2)|skin(2)|pancreas(1)	10		Breast(14;0.00908)|Melanoma(52;0.00951)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)				Ovarian(140;1727 1835 21805 25838 41440)			p.V205I(SNUC5-Tumor)|p.V205I(HCC2279-Tumor)	106				0.147239	38.188004	57.687492	24	139	GG		KEEP	---	---	---	---	capture		all cancers(43;3.08e-19)|Epithelial(43;6.24e-18)|OV - Ovarian serous cystadenocarcinoma(60;1.78e-09)|STAD - Stomach adenocarcinoma(60;0.00303)|GBM - Glioblastoma multiforme(59;0.0106)|LUSC - Lung squamous cell carcinoma(193;0.0286)	Missense_Mutation	SNP	176133864	176133864	248	4	G	A	A	40	40	ADAM29	A	1	1
UGT2B11	10720	broad.mit.edu	36	4	70114545	70114545	+	Missense_Mutation	SNP	G	A	A			TCGA-27-2527-01	TCGA-27-2527-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr4:70114545G>A	uc003heh.1	-	c.485C>T	c.(484-486)GCG>GTG	p.A162V		NM_001073	NP_001064	O75310	UDB11_HUMAN	UDP glucuronosyltransferase 2 family,	162					estrogen metabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	glucuronosyltransferase activity			ovary(1)	1														0.223529	82.687077	94.618577	38	132	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	70114545	70114545	17515	4	G	A	A	38	38	UGT2B11	A	1	1
TCF7	6932	broad.mit.edu	36	5	133479601	133479601	+	Missense_Mutation	SNP	A	C	C			TCGA-27-2527-01	TCGA-27-2527-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr5:133479601A>C	uc003kyt.1	+	c.419A>C	c.(418-420)CAC>CCC	p.H140P	CDKN2AIPNL_uc003kys.1_Intron|TCF7_uc003kyu.1_Missense_Mutation_p.H25P|TCF7_uc003kyv.1_Missense_Mutation_p.H25P|TCF7_uc003kyw.1_Missense_Mutation_p.H25P|TCF7_uc003kyx.1_5'UTR|TCF7_uc003kyy.1_Missense_Mutation_p.H25P|TCF7_uc003kyz.1_Missense_Mutation_p.H25P|TCF7_uc003kza.1_Missense_Mutation_p.H25P	NM_003202	NP_998813	P36402	TCF7_HUMAN	transcription factor 7 (T-cell specific,	140					cellular response to interleukin-4|immune response|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent|Wnt receptor signaling pathway	nucleus	promoter binding|protein binding|RNA polymerase II transcription factor activity				0		Breast(839;0.058)												0.222222	8.311597	10.961021	8	28	AA		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)		Missense_Mutation	SNP	133479601	133479601	16222	5	A	C	C	6	6	TCF7	C	4	4
EGR1	1958	broad.mit.edu	36	5	137830918	137830918	+	Missense_Mutation	SNP	C	A	A			TCGA-27-2527-01	TCGA-27-2527-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:137830918C>A	uc003ldb.1	+	c.881C>A	c.(880-882)GCC>GAC	p.A294D		NM_001964	NP_001955	P18146	EGR1_HUMAN	early growth response 1	294					cellular response to heparin|cellular response to mycophenolic acid|glomerular mesangial cell proliferation|positive regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of glomerular metanephric mesangial cell proliferation|regulation of protein sumoylation|type I interferon-mediated signaling pathway	cytoplasm|nucleus	protein binding|sequence-specific DNA binding transcription factor activity|specific RNA polymerase II transcription factor activity|zinc ion binding			ovary(1)	1														0.169173	77.989234	105.636014	45	221	CC		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(527;0.004)|Kidney(363;0.00592)		Missense_Mutation	SNP	137830918	137830918	5160	5	C	A	A	26	26	EGR1	A	3	3
GABRB2	2561	broad.mit.edu	36	5	160685954	160685954	+	Missense_Mutation	SNP	G	A	A			TCGA-27-2527-01	TCGA-27-2527-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:160685954G>A	uc003lys.1	-	c.1190C>T	c.(1189-1191)ACG>ATG	p.T397M	GABRB2_uc003lyr.1_Intron|GABRB2_uc003lyt.1_Intron|GABRB2_uc010jiu.1_Intron	NM_021911	NP_068711	P47870	GBRB2_HUMAN	gamma-aminobutyric acid (GABA) A receptor, beta	397	Cytoplasmic (Probable).				gamma-aminobutyric acid signaling pathway|synaptic transmission	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	chloride channel activity|GABA-A receptor activity				0	Renal(175;0.00259)	Medulloblastoma(196;0.021)|all_neural(177;0.0463)			Ethchlorvynol(DB00189)|Flurazepam(DB00690)|Lorazepam(DB00186)|Midazolam(DB00683)									0.134228	30.027245	49.337147	20	129	GG		KEEP	---	---	---	---	capture	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)		Missense_Mutation	SNP	160685954	160685954	6418	5	G	A	A	40	40	GABRB2	A	1	1
TMEM174	134288	broad.mit.edu	36	5	72505152	72505152	+	Missense_Mutation	SNP	C	T	T	rs34059261	unknown	TCGA-27-2527-01	TCGA-27-2527-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:72505152C>T	uc003kco.1	+	c.326C>T	c.(325-327)CCG>CTG	p.P109L	TMEM174_uc010izc.1_Missense_Mutation_p.P109L	NM_153217	NP_694949	Q8WUU8	TM174_HUMAN	transmembrane protein 174	109						integral to membrane				ovary(1)	1		Lung NSC(167;0.0378)|Ovarian(174;0.0908)|Prostate(461;0.165)												0.155	55.427411	78.160023	31	169	CC		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(47;1.46e-54)	Missense_Mutation	SNP	72505152	72505152	16624	5	C	T	T	23	23	TMEM174	T	1	1
NEU1	4758	broad.mit.edu	36	6	31938485	31938485	+	Silent	SNP	C	T	T			TCGA-27-2527-01	TCGA-27-2527-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:31938485C>T	uc003nxq.2	-	c.48G>A	c.(46-48)GGG>GGA	p.G16G	NEU1_uc010jtg.1_Non-coding_Transcript|NEU1_uc003nxr.2_Non-coding_Transcript|NEU1_uc010jth.1_5'UTR|NEU1_uc003nxs.2_Silent_p.G16G	NM_000434	NP_000425	Q99519	NEUR1_HUMAN	neuraminidase precursor	16						cytoplasmic membrane-bounded vesicle|lysosomal lumen|lysosomal membrane|plasma membrane	exo-alpha-sialidase activity|protein binding			ovary(1)	1					Oseltamivir(DB00198)|Zanamivir(DB00558)									0.177215	25.233629	32.968093	14	65	CC		KEEP	---	---	---	---	capture			Silent	SNP	31938485	31938485	10740	6	C	T	T	26	26	NEU1	T	2	2
PKHD1	5314	broad.mit.edu	36	6	51859931	51859931	+	Silent	SNP	C	T	T			TCGA-27-2527-01	TCGA-27-2527-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:51859931C>T	uc003pah.1	-	c.7068G>A	c.(7066-7068)CCG>CCA	p.P2356P	PKHD1_uc010jzn.1_Silent_p.P339P|PKHD1_uc003pai.1_Silent_p.P2356P	NM_138694	NP_619639	P08F94	PKHD1_HUMAN	fibrocystin isoform 1	2356	Extracellular (Potential).				cell-cell adhesion|cilium assembly|homeostatic process|kidney development|negative regulation of cellular component movement	anchored to external side of plasma membrane|apical plasma membrane|integral to membrane|microtubule basal body	protein binding|receptor activity			ovary(12)|large_intestine(5)|central_nervous_system(3)	20	Lung NSC(77;0.0605)								p.P2356P(JHUEM1-Tumor)	1537				0.189024	62.348897	77.173857	31	133	CC		KEEP	---	---	---	---	capture			Silent	SNP	51859931	51859931	12396	6	C	T	T	27	27	PKHD1	T	1	1
DSP	1832	broad.mit.edu	36	6	7528936	7528936	+	Missense_Mutation	SNP	G	A	A			TCGA-27-2527-01	TCGA-27-2527-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:7528936G>A	uc003mxp.1	+	c.6442G>A	c.(6442-6444)GCC>ACC	p.A2148T	DSP_uc003mxq.1_Missense_Mutation_p.A1549T	NM_004415	NP_004406	P15924	DESP_HUMAN	desmoplakin isoform I	2148	Plectin 4.|Globular 2.				cellular component disassembly involved in apoptosis|keratinocyte differentiation|peptide cross-linking	cornified envelope|cytoplasm|desmosome	protein binding, bridging|structural constituent of cytoskeleton			central_nervous_system(6)|ovary(2)	8	Ovarian(93;0.0584)	all_hematologic(90;0.236)												0.22973	77.795783	87.692852	34	114	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(45;0.000508)	Missense_Mutation	SNP	7528936	7528936	4965	6	G	A	A	38	38	DSP	A	1	1
C6orf165	154313	broad.mit.edu	36	6	88227545	88227545	+	Silent	SNP	G	A	A			TCGA-27-2527-01	TCGA-27-2527-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:88227545G>A	uc003plv.1	+	c.1581G>A	c.(1579-1581)ACG>ACA	p.T527T	C6orf165_uc003plw.1_Silent_p.T339T|C6orf165_uc010kbv.1_Non-coding_Transcript|SLC35A1_uc003plx.1_Non-coding_Transcript	NM_001031743	NP_001026913	Q8IYR0	CF165_HUMAN	hypothetical protein LOC154313 isoform 1	527										central_nervous_system(1)	1		all_cancers(76;3.93e-06)|Acute lymphoblastic leukemia(125;3.55e-10)|Prostate(29;3.51e-09)|all_hematologic(105;3.29e-06)|all_epithelial(107;0.00575)												0.2	40.998999	48.532231	18	72	GG		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(108;0.0419)	Silent	SNP	88227545	88227545	2446	6	G	A	A	37	37	C6orf165	A	1	1
SDK1	221935	broad.mit.edu	36	7	4181978	4181978	+	Missense_Mutation	SNP	T	C	C			TCGA-27-2527-01	TCGA-27-2527-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr7:4181978T>C	uc003smx.1	+	c.4982T>C	c.(4981-4983)ATG>ACG	p.M1661T	SDK1_uc010kso.1_Intron|SDK1_uc003smy.1_Missense_Mutation_p.M148T	NM_152744	NP_689957	Q7Z5N4	SDK1_HUMAN	sidekick 1 isoform 1	1661	Fibronectin type-III 10.				cell adhesion	integral to membrane				large_intestine(3)|ovary(2)	5		all_cancers(1;0.127)|Ovarian(82;0.0177)|Myeloproliferative disorder(862;0.194)												0.097561	8.77562	35.378622	16	148	TT		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (126;0.121)|OV - Ovarian serous cystadenocarcinoma(56;9.65e-15)	Missense_Mutation	SNP	4181978	4181978	14454	7	T	C	C	51	51	SDK1	C	4	4
GLI3	2737	broad.mit.edu	36	7	41970678	41970678	+	Silent	SNP	G	A	A			TCGA-27-2527-01	TCGA-27-2527-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:41970678G>A	uc003thu.2	-	c.4518C>T	c.(4516-4518)TTC>TTT	p.F1506F		NM_000168	NP_000159	P10071	GLI3_HUMAN	GLI-Kruppel family member GLI3	1506	Asp/Glu-rich (acidic).				negative regulation of alpha-beta T cell differentiation|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of smoothened signaling pathway|negative regulation of transcription from RNA polymerase II promoter|negative thymic T cell selection|positive regulation of alpha-beta T cell differentiation|positive regulation of gene-specific transcription from RNA polymerase II promoter|thymocyte apoptosis	cilium|cytosol|nucleolus	beta-catenin binding|histone acetyltransferase binding|histone deacetylase binding|sequence-specific DNA binding transcription factor activity|transcription activator activity|transcription repressor activity|zinc ion binding			large_intestine(2)|ovary(2)|central_nervous_system(1)|lung(1)|kidney(1)|pancreas(1)	8									p.F1506F(HT115-Tumor)|p.F1506F(SNU81-Tumor)	806				0.172414	37.2312	48.99278	20	96	GG		KEEP	---	---	---	---	capture			Silent	SNP	41970678	41970678	6707	7	G	A	A	37	37	GLI3	A	1	1
TRRAP	8295	broad.mit.edu	36	7	98419786	98419786	+	Missense_Mutation	SNP	G	A	A			TCGA-27-2527-01	TCGA-27-2527-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:98419786G>A	uc003upp.1	+	c.9169G>A	c.(9169-9171)GCT>ACT	p.A3057T	TRRAP_uc003upq.1_Missense_Mutation_p.A3028T|TRRAP_uc003upr.1_Missense_Mutation_p.A2745T	NM_003496	NP_003487	Q9Y4A5	TRRAP_HUMAN	transformation/transcription domain-associated	3057	FAT.				histone deubiquitination|histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	NuA4 histone acetyltransferase complex|PCAF complex|STAGA complex|transcription factor TFTC complex	phosphotransferase activity, alcohol group as acceptor|protein binding|transcription cofactor activity			ovary(9)|large_intestine(8)|central_nervous_system(6)|stomach(2)|lung(1)|liver(1)	27	all_cancers(62;6.96e-09)|all_epithelial(64;4.86e-09)|Lung NSC(181;0.01)|all_lung(186;0.016)|Esophageal squamous(72;0.0274)									1847				0.141994	77.492993	118.408798	47	284	GG		KEEP	---	---	---	---	capture	STAD - Stomach adenocarcinoma(171;0.215)		Missense_Mutation	SNP	98419786	98419786	17152	7	G	A	A	34	34	TRRAP	A	2	2
ANK1	286	broad.mit.edu	36	8	41873092	41873092	+	Missense_Mutation	SNP	G	C	C			TCGA-27-2527-01	TCGA-27-2527-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr8:41873092G>C	uc003xom.1	-	c.64C>G	c.(64-66)CAG>GAG	p.Q22E		NM_020475	NP_065208	P16157	ANK1_HUMAN	ankyrin 1 isoform 4	Error:Variant_position_missing_in_P16157_after_alignment					axon guidance|cytoskeleton organization|exocytosis|maintenance of epithelial cell apical/basal polarity|signal transduction	basolateral plasma membrane|cytosol|sarcomere|sarcoplasmic reticulum|spectrin-associated cytoskeleton	cytoskeletal adaptor activity|enzyme binding|protein binding|spectrin binding|structural constituent of cytoskeleton			ovary(3)|lung(2)|central_nervous_system(2)|breast(1)	8	Ovarian(28;0.00541)|Colorectal(14;0.0398)|Lung SC(25;0.211)	all_lung(54;0.000626)|Lung NSC(58;0.00245)|Esophageal squamous(32;0.0559)|Hepatocellular(245;0.0663)|Renal(179;0.188)												0.172414	6.550133	9.513356	5	24	GG		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(14;0.000984)|Lung(22;0.00108)|Colorectal(10;0.00245)|LUSC - Lung squamous cell carcinoma(45;0.00392)|COAD - Colon adenocarcinoma(11;0.0264)		Missense_Mutation	SNP	41873092	41873092	623	8	G	C	C	46	46	ANK1	C	3	3
ZNF704	619279	broad.mit.edu	36	8	81762184	81762184	+	Nonsense_Mutation	SNP	G	T	T			TCGA-27-2527-01	TCGA-27-2527-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr8:81762184G>T	uc003yby.1	-	c.390C>A	c.(388-390)TAC>TAA	p.Y130*		NM_001033723	NP_001028895	Q6ZNC4	ZN704_HUMAN	zinc finger protein 704	130						intracellular	zinc ion binding				0	all_cancers(3;8.53e-08)|all_epithelial(4;4.59e-10)|Breast(3;2.56e-06)|Lung NSC(7;2.58e-06)|all_lung(9;9.4e-06)											OREG0018841	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.6	6.913894	6.955658	3	2	GG		KEEP	---	---	---	---	capture	BRCA - Breast invasive adenocarcinoma(6;0.00401)|Epithelial(68;0.00448)|all cancers(69;0.0277)		Nonsense_Mutation	SNP	81762184	81762184	18702	8	G	T	T	36	36	ZNF704	T	5	3
RALYL	138046	broad.mit.edu	36	8	85937124	85937124	+	Missense_Mutation	SNP	G	A	A			TCGA-27-2527-01	TCGA-27-2527-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr8:85937124G>A	uc003yct.2	+	c.491G>A	c.(490-492)CGT>CAT	p.R164H	RALYL_uc003ycq.2_Missense_Mutation_p.R151H|RALYL_uc003ycr.2_Missense_Mutation_p.R151H|RALYL_uc003ycs.2_Missense_Mutation_p.R151H|RALYL_uc010lzy.1_Missense_Mutation_p.R140H|RALYL_uc003ycu.2_Missense_Mutation_p.R78H|RALYL_uc003ycv.2_Missense_Mutation_p.R63H	NM_001100391	NP_001093861	Q86SE5	RALYL_HUMAN	RALY RNA binding protein-like isoform 1	151							identical protein binding|nucleotide binding|RNA binding			ovary(1)	1														0.139535	6.405769	11.856921	6	37	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	85937124	85937124	13480	8	G	A	A	40	40	RALYL	A	1	1
KCNS2	3788	broad.mit.edu	36	8	99509811	99509811	+	Missense_Mutation	SNP	G	A	A			TCGA-27-2527-01	TCGA-27-2527-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr8:99509811G>A	uc003yin.1	+	c.428G>A	c.(427-429)AGC>AAC	p.S143N	KCNS2_uc010mbl.1_Missense_Mutation_p.S143N	NM_020697	NP_065748	Q9ULS6	KCNS2_HUMAN	potassium voltage-gated channel,	143	Cytoplasmic (Potential).					voltage-gated potassium channel complex	voltage-gated potassium channel activity			ovary(1)	1	Breast(36;2.4e-06)					Pancreas(138;844 2489 9202 24627)								0.114286	10.115847	25.540819	12	93	GG		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(57;0.0448)		Missense_Mutation	SNP	99509811	99509811	8394	8	G	A	A	34	34	KCNS2	A	2	2
FRMD7	90167	broad.mit.edu	36	X	131039960	131039960	+	Missense_Mutation	SNP	C	A	A			TCGA-27-2527-01	TCGA-27-2527-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:131039960C>A	uc004ewn.1	-	c.1766G>T	c.(1765-1767)AGG>ATG	p.R589M		NM_194277	NP_919253	Q6ZUT3	FRMD7_HUMAN	nystagmus 1 protein	589					regulation of neuron projection development	cytoskeleton|growth cone|neuronal cell body	binding				0	Acute lymphoblastic leukemia(192;0.000127)													0.306569	110.891625	115.46652	42	95	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	131039960	131039960	6305	23	C	A	A	24	24	FRMD7	A	3	3
GPR50	9248	broad.mit.edu	36	X	150100417	150100417	+	Silent	SNP	C	T	T			TCGA-27-2527-01	TCGA-27-2527-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:150100417C>T	uc010ntg.1	+	c.1704C>T	c.(1702-1704)GCC>GCT	p.A568A		NM_004224	NP_004215	Q13585	MTR1L_HUMAN	G protein-coupled receptor 50	568	Cytoplasmic (Potential).|Pro-rich.				cell-cell signaling	integral to plasma membrane	melatonin receptor activity			large_intestine(1)|lung(1)|ovary(1)|pancreas(1)	4	Acute lymphoblastic leukemia(192;6.56e-05)													0.336364	107.243092	109.847749	37	73	CC		KEEP	---	---	---	---	capture			Silent	SNP	150100417	150100417	6972	23	C	T	T	23	23	GPR50	T	1	1
MICALCL	84953	broad.mit.edu	36	11	12272963	12272965	+	In_Frame_Del	DEL	CTA	-	-			TCGA-27-2527-01	TCGA-27-2527-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:12272963_12272965delCTA	uc001mkg.1	+	c.1409_1411delCTA	c.(1408-1413)CCTACA>CCA	p.T471del		NM_032867	NP_116256	Q6ZW33	MICLK_HUMAN	MICAL C-terminal like	471					cell differentiation|multicellular organismal development|spermatogenesis	cytoplasm	mitogen-activated protein kinase binding				0				Epithelial(150;0.00177)										0.40			8	12				---	---	---	---	capture_indel			In_Frame_Del	DEL	12272963	12272965	9962	11	CTA	-	-	24	24	MICALCL	-	5	5
