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
CUL2	8453	broad.mit.edu	36	10	35339309	35339309	+	Missense_Mutation	SNP	A	T	T			TCGA-32-1982-01	TCGA-32-1982-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr10:35339309A>T	uc001ixv.1	-	c.2174T>A	c.(2173-2175)CTG>CAG	p.L725Q	CUL2_uc009xma.1_Missense_Mutation_p.L594Q|CUL2_uc001ixw.1_Missense_Mutation_p.L725Q	NM_003591	NP_003582	Q13617	CUL2_HUMAN	cullin 2	725					cell cycle arrest|G1/S transition of mitotic cell cycle|induction of apoptosis by intracellular signals|interspecies interaction between organisms|negative regulation of cell proliferation|ubiquitin-dependent protein catabolic process	cullin-RING ubiquitin ligase complex	ubiquitin protein ligase binding			ovary(3)	3														0.523077	111.756162	111.786578	34	31	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	35339309	35339309	4215	10	A	T	T	7	7	CUL2	T	4	4
ZNF37A	7587	broad.mit.edu	36	10	38444223	38444223	+	Silent	SNP	G	T	T			TCGA-32-1982-01	TCGA-32-1982-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr10:38444223G>T	uc001izk.1	+	c.237G>T	c.(235-237)CTG>CTT	p.L79L	ZNF37A_uc001izl.1_Silent_p.L79L|ZNF37A_uc001izm.1_Silent_p.L79L	NM_001007094	NP_003412	P17032	ZN37A_HUMAN	zinc finger protein 37a	79	KRAB.				regulation of transcription, DNA-dependent	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			breast(1)	1														0.451613	43.946774	44.009957	14	17	GG		KEEP	---	---	---	---	capture			Silent	SNP	38444223	38444223	18464	10	G	T	T	47	47	ZNF37A	T	3	3
LRRC18	474354	broad.mit.edu	36	10	49791801	49791801	+	Missense_Mutation	SNP	C	T	T			TCGA-32-1982-01	TCGA-32-1982-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr10:49791801C>T	uc001jhd.1	-	c.406G>A	c.(406-408)GTG>ATG	p.V136M	WDFY4_uc001jha.2_Intron|LRRC18_uc001jhe.1_Missense_Mutation_p.V136M	NM_001006939	NP_001006940	Q8N456	LRC18_HUMAN	leucine rich repeat containing 18	136	LRR 5.					cytoplasm				ovary(1)|pancreas(1)	2														0.342857	33.496728	34.256766	12	23	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	49791801	49791801	9348	10	C	T	T	19	19	LRRC18	T	1	1
CHAT	1103	broad.mit.edu	36	10	50540739	50540739	+	Missense_Mutation	SNP	C	T	T			TCGA-32-1982-01	TCGA-32-1982-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr10:50540739C>T	uc001jhz.2	+	c.1882C>T	c.(1882-1884)CGG>TGG	p.R628W	CHAT_uc001jhv.1_Missense_Mutation_p.R510W|CHAT_uc001jhx.1_Missense_Mutation_p.R510W|CHAT_uc001jhy.1_Missense_Mutation_p.R510W|CHAT_uc001jia.2_Missense_Mutation_p.R546W	NM_020549	NP_066266	P28329	CLAT_HUMAN	choline acetyltransferase isoform 2	628					neurotransmitter biosynthetic process|neurotransmitter secretion	cytosol|nucleus	choline O-acetyltransferase activity			central_nervous_system(3)	3		all_neural(218;0.107)			Choline(DB00122)									0.41	113.605425	114.297836	41	59	CC		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(2;0.000585)	Missense_Mutation	SNP	50540739	50540739	3447	10	C	T	T	27	27	CHAT	T	1	1
OR5T3	390154	broad.mit.edu	36	11	55777165	55777165	+	Missense_Mutation	SNP	C	T	T			TCGA-32-1982-01	TCGA-32-1982-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:55777165C>T	uc001nin.1	+	c.914C>T	c.(913-915)TCA>TTA	p.S305L		NM_001004747	NP_001004747	Q8NGG3	OR5T3_HUMAN	olfactory receptor, family 5, subfamily T,	305	Helical; Name=7; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0	Esophageal squamous(21;0.00448)													0.193333	58.780275	71.954791	29	121	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	55777165	55777165	11593	11	C	T	T	29	29	OR5T3	T	2	2
LRRK2	120892	broad.mit.edu	36	12	38975548	38975548	+	Silent	SNP	G	A	A			TCGA-32-1982-01	TCGA-32-1982-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:38975548G>A	uc001rmg.2	+	c.2931G>A	c.(2929-2931)CTG>CTA	p.L977L	LRRK2_uc001rmh.1_Silent_p.L599L|LRRK2_uc009zjw.1_5'UTR	NM_198578	NP_940980	Q5S007	LRRK2_HUMAN	leucine-rich repeat kinase 2	977					activation of MAPKK activity|determination of adult lifespan|intracellular distribution of mitochondria|negative regulation of branching morphogenesis of a nerve|negative regulation of dendritic spine morphogenesis|negative regulation of neuroblast proliferation|negative regulation of neuron maturation|neuromuscular junction development|neuron death|peptidyl-serine phosphorylation|positive regulation of autophagy|positive regulation of programmed cell death|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of protein ubiquitination|protein autophosphorylation|regulation of kidney size|regulation of locomotion|regulation of membrane potential|response to oxidative stress|small GTPase mediated signal transduction|tangential migration from the subventricular zone to the olfactory bulb	external side of mitochondrial outer membrane	ATP binding|GTP binding|GTP-dependent protein kinase activity|GTPase activator activity|MAP kinase kinase activity|protein homodimerization activity|tubulin binding			ovary(11)|lung(2)|upper_aerodigestive_tract(1)|large_intestine(1)|stomach(1)|urinary_tract(1)|pancreas(1)	18	all_cancers(12;0.00108)|Breast(8;0.218)	Lung NSC(34;0.0942)|all_lung(34;0.11)								1771				0.226804	52.895551	59.544444	22	75	GG		KEEP	---	---	---	---	capture			Silent	SNP	38975548	38975548	9409	12	G	A	A	47	47	LRRK2	A	2	2
ANO2	57101	broad.mit.edu	36	12	5594692	5594692	+	Missense_Mutation	SNP	G	A	A			TCGA-32-1982-01	TCGA-32-1982-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:5594692G>A	uc001qnm.1	-	c.1852C>T	c.(1852-1854)CGC>TGC	p.R618C		NM_020373	NP_065106	Q9NQ90	ANO2_HUMAN	anoctamin 2	622	Cytoplasmic (Potential).					chloride channel complex|plasma membrane	intracellular calcium activated chloride channel activity			ovary(4)|large_intestine(2)|central_nervous_system(1)	7														0.294118	25.739112	27.027492	10	24	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	5594692	5594692	705	12	G	A	A	38	38	ANO2	A	1	1
LRRIQ1	84125	broad.mit.edu	36	12	83984807	83984807	+	Nonsense_Mutation	SNP	G	T	T			TCGA-32-1982-01	TCGA-32-1982-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:83984807G>T	uc001tac.1	+	c.2695G>T	c.(2695-2697)GGA>TGA	p.G899*	LRRIQ1_uc001tab.1_Nonsense_Mutation_p.G899*	NM_001079910	NP_001073379	Q96JM4	LRIQ1_HUMAN	leucine-rich repeats and IQ motif containing 1	899	LRR 4.									ovary(4)|central_nervous_system(1)	5														0.156863	14.666334	20.396839	8	43	GG		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(134;0.212)	Nonsense_Mutation	SNP	83984807	83984807	9405	12	G	T	T	47	47	LRRIQ1	T	5	3
MYH6	4624	broad.mit.edu	36	14	22939770	22939770	+	Silent	SNP	G	A	A			TCGA-32-1982-01	TCGA-32-1982-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr14:22939770G>A	uc001wjv.2	-	c.1398C>T	c.(1396-1398)TTC>TTT	p.F466F	MYH6_uc010akp.1_Silent_p.F466F	NM_002471	NP_002462	P13533	MYH6_HUMAN	myosin heavy chain 6	466	Myosin head-like.				adult heart development|atrial cardiac muscle tissue morphogenesis|cardiac muscle fiber development|in utero embryonic development|muscle filament sliding|regulation of ATPase activity|regulation of blood pressure|regulation of heart rate|regulation of the force of heart contraction|sarcomere organization|striated muscle contraction|ventricular cardiac muscle tissue morphogenesis|visceral muscle development	cytosol|focal adhesion|muscle myosin complex|myosin filament|nucleus|sarcomere	actin binding|actin-dependent ATPase activity|ATP binding|calmodulin binding|microfilament motor activity|protein kinase binding|structural constituent of muscle			pancreas(2)|ovary(1)	3	all_cancers(95;2.54e-05)													0.205882	30.62143	36.069274	14	54	GG		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(265;0.00764)|READ - Rectum adenocarcinoma(4;0.0289)|Colorectal(4;0.0441)	Silent	SNP	22939770	22939770	10433	14	G	A	A	37	37	MYH6	A	1	1
RYR3	6263	broad.mit.edu	36	15	31682644	31682644	+	Missense_Mutation	SNP	G	A	A			TCGA-32-1982-01	TCGA-32-1982-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr15:31682644G>A	uc001zhi.1	+	c.1951G>A	c.(1951-1953)GCG>ACG	p.A651T	RYR3_uc010bar.1_Missense_Mutation_p.A651T	NM_001036	NP_001027	Q15413	RYR3_HUMAN	ryanodine receptor 3	651	Cytoplasmic (By similarity).|B30.2/SPRY 1.				cellular calcium ion homeostasis	integral to membrane	calcium ion binding|receptor activity|ryanodine-sensitive calcium-release channel activity			ovary(5)|central_nervous_system(4)|lung(1)	10		all_lung(180;7.18e-09)												0.310881	159.732409	165.878802	60	133	GG		KEEP	---	---	---	---	capture		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)	Missense_Mutation	SNP	31682644	31682644	14250	15	G	A	A	38	38	RYR3	A	1	1
MFAP1	4236	broad.mit.edu	36	15	41892789	41892789	+	Missense_Mutation	SNP	C	G	G			TCGA-32-1982-01	TCGA-32-1982-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr15:41892789C>G	uc001zth.1	-	c.676G>C	c.(676-678)GAG>CAG	p.E226Q		NM_005926	NP_005917	P55081	MFAP1_HUMAN	microfibrillar-associated protein 1	226						microfibril				skin(1)	1		all_cancers(109;7.57e-15)|all_epithelial(112;3.51e-12)|Lung NSC(122;4.72e-08)|all_lung(180;4.9e-07)|Melanoma(134;0.027)|Colorectal(260;0.215)												0.247956	260.720075	281.959023	91	276	CC		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(94;4.33e-07)	Missense_Mutation	SNP	41892789	41892789	9903	15	C	G	G	30	30	MFAP1	G	3	3
PKD1	5310	broad.mit.edu	36	16	2092427	2092427	+	Missense_Mutation	SNP	C	G	G			TCGA-32-1982-01	TCGA-32-1982-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:2092427C>G	uc002cos.1	-	c.9157G>C	c.(9157-9159)GCC>CCC	p.A3053P	PKD1_uc002cot.1_Missense_Mutation_p.A3053P|PKD1_uc010bse.1_Non-coding_Transcript	NM_001009944	NP_001009944	P98161	PKD1_HUMAN	polycystin 1 isoform 1 precursor	3053	GPS.|Extracellular (Potential).				calcium-independent cell-matrix adhesion|homophilic cell adhesion|neuropeptide signaling pathway	basolateral plasma membrane|integral to plasma membrane	protein domain specific binding|sugar binding			central_nervous_system(1)	1														0.6	8.024117	8.067544	3	2	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	2092427	2092427	12387	16	C	G	G	27	27	PKD1	G	3	3
IL4R	3566	broad.mit.edu	36	16	27271407	27271407	+	Missense_Mutation	SNP	G	A	A			TCGA-32-1982-01	TCGA-32-1982-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:27271407G>A	uc002don.1	+	c.559G>A	c.(559-561)GCA>ACA	p.A187T	IL4R_uc002dom.1_Missense_Mutation_p.A187T|IL4R_uc010bxy.1_Missense_Mutation_p.A187T|IL4R_uc002doo.1_Missense_Mutation_p.A27T	NM_000418	NP_000409	P24394	IL4RA_HUMAN	interleukin 4 receptor alpha chain isoform a	187	Extracellular (Potential).|Fibronectin type-III.				immune response|production of molecular mediator involved in inflammatory response	integral to plasma membrane	identical protein binding|interleukin-4 receptor activity|receptor signaling protein activity			ovary(1)|skin(1)	2														0.277487	136.611745	145.110528	53	138	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	27271407	27271407	7999	16	G	A	A	38	38	IL4R	A	1	1
NLRC3	197358	broad.mit.edu	36	16	3554695	3554695	+	Missense_Mutation	SNP	C	T	T	rs61732418	unknown	TCGA-32-1982-01	TCGA-32-1982-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:3554695C>T	uc010btn.1	-	c.244G>A	c.(244-246)GGA>AGA	p.G82R		NM_178844	NP_849172	Q7RTR2	NLRC3_HUMAN	NOD3 protein	82					I-kappaB kinase/NF-kappaB cascade|negative regulation of NF-kappaB transcription factor activity|T cell activation	cytoplasm	ATP binding			ovary(2)|pancreas(2)|central_nervous_system(1)|skin(1)	6														0.2	10.664673	12.754574	5	20	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	3554695	3554695	10871	16	C	T	T	23	23	NLRC3	T	1	1
SETD6	79918	broad.mit.edu	36	16	57109550	57109550	+	Missense_Mutation	SNP	T	C	C			TCGA-32-1982-01	TCGA-32-1982-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr16:57109550T>C	uc002ens.1	+	c.887T>C	c.(886-888)ATG>ACG	p.M296T	SETD6_uc002enr.1_Missense_Mutation_p.M272T|SETD6_uc010cdm.1_Non-coding_Transcript	NM_024860	NP_079136	Q8TBK2	SETD6_HUMAN	SET domain containing 6	296					negative regulation of NF-kappaB transcription factor activity|peptidyl-lysine monomethylation|regulation of inflammatory response	nucleus	NF-kappaB binding|protein-lysine N-methyltransferase activity			ovary(1)	1														0.29927	116.32313	121.255044	41	96	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	57109550	57109550	14624	16	T	C	C	51	51	SETD6	C	4	4
ATP6V0D1	9114	broad.mit.edu	36	16	66034550	66034550	+	Missense_Mutation	SNP	C	T	T			TCGA-32-1982-01	TCGA-32-1982-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:66034550C>T	uc002ete.1	-	c.514G>A	c.(514-516)GAC>AAC	p.D172N		NM_004691	NP_004682	P61421	VA0D1_HUMAN	ATPase, H+ transporting, lysosomal, V0 subunit	172					ATP hydrolysis coupled proton transport|cellular iron ion homeostasis|insulin receptor signaling pathway|transferrin transport	endosome membrane|proton-transporting V-type ATPase, V0 domain|vacuolar proton-transporting V-type ATPase complex					0		Ovarian(137;0.0563)												0.323699	152.025986	156.808013	56	117	CC		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(108;0.0439)|Epithelial(162;0.101)	Missense_Mutation	SNP	66034550	66034550	1192	16	C	T	T	30	30	ATP6V0D1	T	2	2
STUB1	10273	broad.mit.edu	36	16	671824	671824	+	Missense_Mutation	SNP	G	T	T			TCGA-32-1982-01	TCGA-32-1982-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:671824G>T	uc002cit.1	+	c.555G>T	c.(553-555)GAG>GAT	p.E185D	STUB1_uc002ciu.1_Missense_Mutation_p.E113D|STUB1_uc010bqz.1_Non-coding_Transcript|STUB1_uc002civ.1_Non-coding_Transcript|JMJD8_uc002ciw.1_3'UTR|JMJD8_uc002cix.1_3'UTR|JMJD8_uc002ciy.1_3'UTR	NM_005861	NP_005852	Q9UNE7	CHIP_HUMAN	STIP1 homology and U-box containing protein 1	185					cellular response to misfolded protein|DNA repair|misfolded or incompletely synthesized protein catabolic process|positive regulation of cellular chaperone-mediated protein complex assembly|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of protein ubiquitination|proteasomal ubiquitin-dependent protein catabolic process|protein autoubiquitination|protein maturation|protein polyubiquitination|regulation of glucocorticoid metabolic process|ubiquitin-dependent SMAD protein catabolic process	cytoplasm|nuclear inclusion body|ubiquitin conjugating enzyme complex|ubiquitin ligase complex	Hsp70 protein binding|Hsp90 protein binding|kinase binding|misfolded protein binding|protein binding, bridging|protein homodimerization activity|SMAD binding|TPR domain binding|ubiquitin-ubiquitin ligase activity				0		Hepatocellular(780;0.00335)												0.253333	43.47922	47.631344	19	56	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	671824	671824	15855	16	G	T	T	35	35	STUB1	T	3	3
CDH1	999	broad.mit.edu	36	16	67413466	67413466	+	Silent	SNP	C	T	T			TCGA-32-1982-01	TCGA-32-1982-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:67413466C>T	uc002ewg.1	+	c.1773C>T	c.(1771-1773)AAC>AAT	p.N591N	CDH1_uc010cfg.1_Silent_p.N530N	NM_004360	NP_004351	P12830	CADH1_HUMAN	cadherin 1, type 1 preproprotein	591	Extracellular (Potential).|Cadherin 4.				adherens junction organization|cellular component disassembly involved in apoptosis|cellular response to indole-3-methanol|cellular response to lithium ion|homophilic cell adhesion|negative regulation of cell-cell adhesion|positive regulation of transcription factor import into nucleus|regulation of immune response	actin cytoskeleton|aggresome|apical junction complex|catenin complex|cell-cell adherens junction|focal adhesion|integral to membrane|lateral plasma membrane|perinuclear region of cytoplasm	cell adhesion molecule binding|gamma-catenin binding|transcription activator activity			breast(136)|stomach(71)|biliary_tract(8)|endometrium(3)|soft_tissue(2)|large_intestine(2)|urinary_tract(2)|oesophagus(2)|ovary(2)|thyroid(1)|central_nervous_system(1)|lung(1)	231		all_neural(199;0.0189)|Ovarian(137;0.0563)								231				0.254237	111.004592	120.700615	45	132	CC		KEEP	---	---	---	---	capture		Epithelial(162;8.44e-05)|all cancers(182;0.000404)|OV - Ovarian serous cystadenocarcinoma(108;0.000426)|BRCA - Breast invasive adenocarcinoma(181;0.0261)	Silent	SNP	67413466	67413466	3224	16	C	T	T	19	19	CDH1	T	1	1
HYDIN	54768	broad.mit.edu	36	16	69564833	69564833	+	Missense_Mutation	SNP	G	A	A			TCGA-32-1982-01	TCGA-32-1982-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:69564833G>A	uc002ezr.1	-	c.5290C>T	c.(5290-5292)CGG>TGG	p.R1764W	HYDIN_uc002ezt.1_Non-coding_Transcript|HYDIN_uc002ezu.1_Missense_Mutation_p.R67W	NM_032821	NP_116210	Q4G0P3	HYDIN_HUMAN	hydrocephalus inducing isoform a	1765										ovary(1)	1		Ovarian(137;0.0654)												0.100503	13.383327	45.069738	20	179	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	69564833	69564833	7767	16	G	A	A	40	40	HYDIN	A	1	1
ZNF624	57547	broad.mit.edu	36	17	16467225	16467225	+	Missense_Mutation	SNP	C	T	T			TCGA-32-1982-01	TCGA-32-1982-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:16467225C>T	uc010cpi.1	-	c.1700G>A	c.(1699-1701)CGT>CAT	p.R567H		NM_020787	NP_065838	Q9P2J8	ZN624_HUMAN	zinc finger protein 624	567	C2H2-type 11.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			large_intestine(1)|ovary(1)	2						NSCLC(186;1023 2134 13330 38202 39800)								0.098131	11.331219	45.913604	21	193	CC		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (92;0.0837)	Missense_Mutation	SNP	16467225	16467225	18643	17	C	T	T	19	19	ZNF624	T	1	1
RAD51C	5889	broad.mit.edu	36	17	54127379	54127379	+	Silent	SNP	A	G	G			TCGA-32-1982-01	TCGA-32-1982-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr17:54127379A>G	uc002iwu.1	+	c.234A>G	c.(232-234)ACA>ACG	p.T78T	TEX14_uc002iwr.1_5'Flank|TEX14_uc002iws.1_5'Flank|TEX14_uc010dcz.1_5'Flank|TEX14_uc010dda.1_5'Flank|RAD51C_uc010ddc.1_Non-coding_Transcript|RAD51C_uc002iwv.1_Non-coding_Transcript|RAD51C_uc002iww.1_Non-coding_Transcript|RAD51C_uc002iwt.1_Silent_p.T78T	NM_058216	NP_478123	O43502	RA51C_HUMAN	RAD51 homolog C isoform 1	78					blood coagulation|DNA repair	mitochondrion|nucleoplasm|perinuclear region of cytoplasm	ATP binding|DNA binding|DNA-dependent ATPase activity				0	Medulloblastoma(34;0.127)|all_neural(34;0.237)													0.271429	102.488786	109.084213	38	102	AA		KEEP	---	---	---	---	capture			Silent	SNP	54127379	54127379	13448	17	A	G	G	8	8	RAD51C	G	4	4
GALK1	2584	broad.mit.edu	36	17	71265764	71265764	+	Missense_Mutation	SNP	C	G	G			TCGA-32-1982-01	TCGA-32-1982-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:71265764C>G	uc002jpk.1	-	c.1147G>C	c.(1147-1149)GCA>CCA	p.A383P		NM_000154	NP_000145	P51570	GALK1_HUMAN	galactokinase 1	383					galactose catabolic process	cytosol	ATP binding|galactokinase activity|galactose binding				0	all_cancers(13;1.5e-07)													0.363636	6.494473	6.714748	4	7	CC		KEEP	---	---	---	---	capture	all cancers(21;1.03e-06)|Epithelial(20;1.92e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00194)|Lung(188;0.132)|LUSC - Lung squamous cell carcinoma(166;0.154)		Missense_Mutation	SNP	71265764	71265764	6467	17	C	G	G	28	28	GALK1	G	3	3
DNAH2	146754	broad.mit.edu	36	17	7603864	7603864	+	Missense_Mutation	SNP	G	A	A			TCGA-32-1982-01	TCGA-32-1982-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:7603864G>A	uc002giu.1	+	c.2668G>A	c.(2668-2670)GCA>ACA	p.A890T		NM_020877	NP_065928	Q9P225	DYH2_HUMAN	dynein heavy chain domain 3	890	Stem (By similarity).				ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(6)|central_nervous_system(1)	7		all_cancers(10;4.66e-07)|Prostate(122;0.081)												0.295699	289.598823	303.493517	110	262	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	7603864	7603864	4785	17	G	A	A	42	42	DNAH2	A	2	2
KIAA0427	9811	broad.mit.edu	36	18	44399978	44399978	+	Missense_Mutation	SNP	G	C	C			TCGA-32-1982-01	TCGA-32-1982-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr18:44399978G>C	uc002ldd.1	+	c.44G>C	c.(43-45)AGC>ACC	p.S15T	KIAA0427_uc002ldc.1_Missense_Mutation_p.S15T	NM_014772	NP_055587	O43310	CTIF_HUMAN	hypothetical protein LOC9811 isoform 1	15	Interaction with NCBP1/CBP80.				nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|regulation of translational initiation	perinuclear region of cytoplasm	protein binding				0														0.444444	9.291911	9.31697	4	5	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	44399978	44399978	8483	18	G	C	C	34	34	KIAA0427	C	3	3
CTDP1	9150	broad.mit.edu	36	18	75558965	75558965	+	Missense_Mutation	SNP	A	G	G			TCGA-32-1982-01	TCGA-32-1982-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr18:75558965A>G	uc002lnh.1	+	c.610A>G	c.(610-612)ATG>GTG	p.M204V	CTDP1_uc002lni.1_Missense_Mutation_p.M204V|CTDP1_uc010drd.1_Missense_Mutation_p.M204V	NM_004715	NP_004706	Q9Y5B0	CTDP1_HUMAN	CTD (carboxy-terminal domain, RNA polymerase II,	204	FCP1 homology.				positive regulation of viral transcription|protein dephosphorylation|transcription elongation from RNA polymerase II promoter|viral reproduction	nucleoplasm	CTD phosphatase activity|DNA-directed RNA polymerase activity				0		Esophageal squamous(42;0.0157)|Melanoma(33;0.144)												0.339286	55.998046	57.281497	19	37	AA		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(15;5.2e-06)|BRCA - Breast invasive adenocarcinoma(31;0.0277)	Missense_Mutation	SNP	75558965	75558965	4161	18	A	G	G	12	12	CTDP1	G	4	4
RFX1	5989	broad.mit.edu	36	19	13935506	13935506	+	Missense_Mutation	SNP	T	C	C			TCGA-32-1982-01	TCGA-32-1982-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr19:13935506T>C	uc002mxv.1	-	c.2414A>G	c.(2413-2415)GAG>GGG	p.E805G		NM_002918	NP_002909	P22670	RFX1_HUMAN	regulatory factor X1	805	Necessary for dimerization.				immune response|regulation of transcription, DNA-dependent	nucleus	DNA binding|protein binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|transcription regulator activity			lung(1)|pancreas(1)	2														0.3125	8.658441	9.165697	5	11	TT		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(19;6.67e-23)		Missense_Mutation	SNP	13935506	13935506	13734	19	T	C	C	54	54	RFX1	C	4	4
WIZ	58525	broad.mit.edu	36	19	15397302	15397302	+	Silent	SNP	T	G	G			TCGA-32-1982-01	TCGA-32-1982-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr19:15397302T>G	uc002nba.2	-	c.1482A>C	c.(1480-1482)CCA>CCC	p.P494P	WIZ_uc002nbb.2_Silent_p.P453P	NM_021241	NP_067064	O95785	WIZ_HUMAN	widely-interspaced zinc finger motifs	1310						nucleus	zinc ion binding				0														0.32	8.507451	9.334229	8	17	TT		KEEP	---	---	---	---	capture			Silent	SNP	15397302	15397302	17949	19	T	G	G	59	59	WIZ	G	4	4
ATP8B3	148229	broad.mit.edu	36	19	1743112	1743112	+	Missense_Mutation	SNP	C	T	T			TCGA-32-1982-01	TCGA-32-1982-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:1743112C>T	uc002ltw.1	-	c.2078G>A	c.(2077-2079)CGG>CAG	p.R693Q	ATP8B3_uc002ltv.1_Missense_Mutation_p.R646Q|ATP8B3_uc002ltx.1_Non-coding_Transcript	NM_138813	NP_620168	O60423	AT8B3_HUMAN	ATPase, class I, type 8B, member 3	693	Cytoplasmic (Potential).				ATP biosynthetic process		ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity				0		Hepatocellular(1079;0.137)												0.214286	6.762872	7.785708	3	11	CC		KEEP	---	---	---	---	capture		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)	Missense_Mutation	SNP	1743112	1743112	1215	19	C	T	T	23	23	ATP8B3	T	1	1
IL12RB1	3594	broad.mit.edu	36	19	18045347	18045347	+	Missense_Mutation	SNP	G	A	A			TCGA-32-1982-01	TCGA-32-1982-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:18045347G>A	uc002nhx.1	-	c.883C>T	c.(883-885)CGG>TGG	p.R295W	IL12RB1_uc002nhw.1_Missense_Mutation_p.R255W|IL12RB1_uc002nhy.1_Missense_Mutation_p.R255W	NM_005535	NP_005526	P42701	I12R1_HUMAN	interleukin 12 receptor, beta 1 isoform 1	255	Extracellular (Potential).|Fibronectin type-III 3.				cellular response to interferon-gamma|interleukin-12-mediated signaling pathway|positive regulation of activated T cell proliferation|positive regulation of defense response to virus by host|positive regulation of interferon-gamma production|positive regulation of memory T cell differentiation|positive regulation of T cell mediated cytotoxicity|positive regulation of T-helper 1 type immune response|positive regulation of T-helper 17 cell lineage commitment|positive regulation of T-helper 17 type immune response	interleukin-12 receptor complex|interleukin-23 receptor complex	cytokine receptor activity			pancreas(1)	1														0.202899	26.309796	31.973399	14	55	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	18045347	18045347	7927	19	G	A	A	38	38	IL12RB1	A	1	1
ZNF257	113835	broad.mit.edu	36	19	22063152	22063152	+	Missense_Mutation	SNP	G	A	A			TCGA-32-1982-01	TCGA-32-1982-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:22063152G>A	uc010ecx.1	+	c.760G>A	c.(760-762)GAG>AAG	p.E254K	ZNF257_uc010ecy.1_Missense_Mutation_p.E222K	NM_033468	NP_258429	Q9Y2Q1	ZN257_HUMAN	zinc finger protein 257	254					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		all_lung(12;0.0961)|Lung NSC(12;0.103)												0.216867	41.290133	47.443775	18	65	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	22063152	22063152	18391	19	G	A	A	33	33	ZNF257	A	2	2
KLK6	5653	broad.mit.edu	36	19	56154280	56154280	+	Silent	SNP	G	A	A			TCGA-32-1982-01	TCGA-32-1982-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:56154280G>A	uc002puh.1	-	c.714C>T	c.(712-714)AAC>AAT	p.N238N	KLK6_uc010eoj.1_Missense_Mutation_p.T101M|KLK6_uc002puj.1_Silent_p.N122N|KLK6_uc002puk.1_Missense_Mutation_p.T132M|KLK6_uc002pul.1_Silent_p.N229N|KLK6_uc002pum.1_Silent_p.N122N|KLK6_uc002pui.1_Silent_p.N229N	NM_001012965	NP_001012983	Q92876	KLK6_HUMAN	kallikrein-related peptidase 6 isoform B	229	Peptidase S1.				amyloid precursor protein metabolic process|central nervous system development|collagen catabolic process|hormone metabolic process|myelination|positive regulation of G-protein coupled receptor protein signaling pathway|protein autoprocessing|proteolysis|regulation of cell differentiation|tissue regeneration	endoplasmic reticulum|extracellular region|microsome|mitochondrion|nucleolus	protein binding|serine-type endopeptidase activity				0		all_neural(266;0.026)												0.220339	148.228527	169.469905	65	230	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(262;0.00372)|GBM - Glioblastoma multiforme(134;0.00871)	Silent	SNP	56154280	56154280	8722	19	G	A	A	40	40	KLK6	A	1	1
NLRP13	126204	broad.mit.edu	36	19	61114991	61114991	+	Silent	SNP	G	A	A			TCGA-32-1982-01	TCGA-32-1982-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:61114991G>A	uc002qmg.1	-	c.2004C>T	c.(2002-2004)GAC>GAT	p.D668D		NM_176810	NP_789780	Q86W25	NAL13_HUMAN	NACHT, leucine rich repeat and PYD containing	668							ATP binding			ovary(3)|skin(2)|pancreas(1)|lung(1)	7		Colorectal(82;3.48e-05)|Ovarian(87;0.0481)|Renal(1328;0.218)												0.193651	131.231121	158.791194	61	254	GG		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(193;0.0642)	Silent	SNP	61114991	61114991	10878	19	G	A	A	40	40	NLRP13	A	1	1
ADAMTS10	81794	broad.mit.edu	36	19	8574748	8574748	+	Silent	SNP	G	A	A			TCGA-32-1982-01	TCGA-32-1982-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:8574748G>A	uc002mkj.1	-	c.456C>T	c.(454-456)GAC>GAT	p.D152D	ADAMTS10_uc002mkk.1_De_novo_Start_OutOfFrame	NM_030957	NP_112219	Q9H324	ATS10_HUMAN	ADAM metallopeptidase with thrombospondin type 1	152					proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			pancreas(2)|skin(1)	3														0.242105	51.575769	57.341468	23	72	GG		KEEP	---	---	---	---	capture			Silent	SNP	8574748	8574748	257	19	G	A	A	40	40	ADAMTS10	A	1	1
MUC16	94025	broad.mit.edu	36	19	8919871	8919871	+	Silent	SNP	G	T	T			TCGA-32-1982-01	TCGA-32-1982-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:8919871G>T	uc002mkp.1	-	c.28575C>A	c.(28573-28575)ACC>ACA	p.T9525T		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	9527	Ser-rich.|Thr-rich.|Extracellular (Potential).				cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			ovary(15)|large_intestine(1)|pancreas(1)|breast(1)|skin(1)	19														0.236948	140.598699	156.347137	59	190	GG		KEEP	---	---	---	---	capture			Silent	SNP	8919871	8919871	10367	19	G	T	T	47	47	MUC16	T	3	3
MTMR11	10903	broad.mit.edu	36	1	148168291	148168291	+	Missense_Mutation	SNP	T	C	C			TCGA-32-1982-01	TCGA-32-1982-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr1:148168291T>C	uc001etm.1	-	c.1573A>G	c.(1573-1575)ATC>GTC	p.I525V	SF3B4_uc001etj.1_5'Flank|SF3B4_uc001etk.1_5'Flank|SF3B4_uc009wll.1_5'Flank|MTMR11_uc001etl.2_Missense_Mutation_p.I569V	NM_181873	NP_870988	A4FU01	MTMRB_HUMAN	myotubularin related protein 11	597	Myotubularin phosphatase.						phosphatase activity			central_nervous_system(1)	1	Breast(34;0.0009)|Ovarian(49;0.0377)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)									238				0.269939	128.653294	136.419991	44	119	TT		KEEP	---	---	---	---	capture	LUSC - Lung squamous cell carcinoma(543;0.221)|STAD - Stomach adenocarcinoma(528;0.247)		Missense_Mutation	SNP	148168291	148168291	10333	1	T	C	C	49	49	MTMR11	C	4	4
LYST	1130	broad.mit.edu	36	1	234060299	234060299	+	Silent	SNP	G	A	A			TCGA-32-1982-01	TCGA-32-1982-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:234060299G>A	uc001hxj.1	-	c.42C>T	c.(40-42)ACC>ACT	p.T14T	LYST_uc009xgb.1_Non-coding_Transcript|LYST_uc001hxl.1_Silent_p.T14T|LYST_uc001hxm.2_Non-coding_Transcript|LYST_uc001hxn.1_Silent_p.T14T	NM_000081	NP_000072	Q99698	LYST_HUMAN	lysosomal trafficking regulator	14					defense response to bacterium|defense response to protozoan|defense response to virus|endosome to lysosome transport via multivesicular body sorting pathway|leukocyte chemotaxis|mast cell secretory granule organization|melanosome organization|natural killer cell mediated cytotoxicity|protein transport	cytoplasm|microtubule cytoskeleton	protein binding			ovary(6)|breast(4)|central_nervous_system(2)	12	Ovarian(103;0.0634)|Breast(184;0.23)	all_cancers(173;0.00246)|Prostate(94;0.0771)|Acute lymphoblastic leukemia(190;0.228)												0.333333	75.582405	77.411601	25	50	GG		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(106;0.000674)		Silent	SNP	234060299	234060299	9505	1	G	A	A	39	39	LYST	A	1	1
OR2T33	391195	broad.mit.edu	36	1	246503343	246503343	+	Missense_Mutation	SNP	G	A	A			TCGA-32-1982-01	TCGA-32-1982-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:246503343G>A	uc001ied.1	-	c.397C>T	c.(397-399)CTC>TTC	p.L133F		NM_001004695	NP_001004695	Q8NG76	O2T33_HUMAN	olfactory receptor, family 2, subfamily T,	133	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			large_intestine(1)|ovary(1)	2	all_cancers(71;0.000124)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)													0.144444	42.527786	64.434627	26	154	GG		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(106;0.0245)		Missense_Mutation	SNP	246503343	246503343	11430	1	G	A	A	33	33	OR2T33	A	2	2
OR2T27	403239	broad.mit.edu	36	1	246880424	246880424	+	Missense_Mutation	SNP	G	T	T			TCGA-32-1982-01	TCGA-32-1982-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:246880424G>T	uc001iet.1	-	c.385C>A	c.(385-387)CCT>ACT	p.P129T		NM_001001824	NP_001001824	Q8NH04	O2T27_HUMAN	olfactory receptor, family 2, subfamily T,	129	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0	all_cancers(71;1.15e-05)|all_epithelial(71;5.29e-06)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.089)|Lung NSC(105;0.0969)|Melanoma(84;0.199)	all_cancers(173;0.237)												0.109756	7.117044	19.506669	9	73	GG		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(106;0.0265)		Missense_Mutation	SNP	246880424	246880424	11427	1	G	T	T	43	43	OR2T27	T	3	3
BACH1	571	broad.mit.edu	36	21	29623832	29623832	+	Missense_Mutation	SNP	C	T	T			TCGA-32-1982-01	TCGA-32-1982-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr21:29623832C>T	uc002ynj.1	+	c.1723C>T	c.(1723-1725)CGC>TGC	p.R575C	BACH1_uc002ynk.1_Missense_Mutation_p.R575C|BACH1_uc002ynl.1_Missense_Mutation_p.R575C	NM_001186	NP_996749	O14867	BACH1_HUMAN	BTB and CNC homology 1 isoform a	575	Basic motif.				regulation of transcription, DNA-dependent	nucleus	protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)|liver(1)	2														0.25	22.958325	25.003126	9	27	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	29623832	29623832	1304	21	C	T	T	31	31	BACH1	T	1	1
CABIN1	23523	broad.mit.edu	36	22	22891503	22891503	+	Missense_Mutation	SNP	A	G	G			TCGA-32-1982-01	TCGA-32-1982-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr22:22891503A>G	uc002zzi.1	+	c.4916A>G	c.(4915-4917)TAT>TGT	p.Y1639C	CABIN1_uc002zzj.1_Missense_Mutation_p.Y1560C|CABIN1_uc002zzl.1_Missense_Mutation_p.Y1639C|CABIN1_uc002zzm.1_Missense_Mutation_p.Y64C	NM_012295	NP_036427	Q9Y6J0	CABIN_HUMAN	calcineurin binding protein 1	1639					cell surface receptor linked signaling pathway|chromatin modification	nucleus	protein phosphatase inhibitor activity			ovary(2)|central_nervous_system(1)|pancreas(1)	4														0.222222	16.337652	18.252459	6	21	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	22891503	22891503	2644	22	A	G	G	16	16	CABIN1	G	4	4
MYO7B	4648	broad.mit.edu	36	2	128099464	128099464	+	Missense_Mutation	SNP	G	A	A			TCGA-32-1982-01	TCGA-32-1982-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:128099464G>A	uc002top.1	+	c.4021G>A	c.(4021-4023)GCC>ACC	p.A1341T	MYO7B_uc002toq.1_Missense_Mutation_p.A194T|MYO7B_uc002tor.1_Missense_Mutation_p.A194T	NM_001080527	NP_001073996	Q6PIF6	MYO7B_HUMAN	myosin VIIB	1341	FERM 1.					apical plasma membrane|myosin complex	actin binding|ATP binding|motor activity			ovary(1)|pancreas(1)	2	Colorectal(110;0.1)													0.333333	13.06917	13.438596	5	10	GG		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(221;0.0753)	Missense_Mutation	SNP	128099464	128099464	10478	2	G	A	A	38	38	MYO7B	A	1	1
AMMECR1L	83607	broad.mit.edu	36	2	128348008	128348008	+	Missense_Mutation	SNP	G	A	A			TCGA-32-1982-01	TCGA-32-1982-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:128348008G>A	uc002tpl.1	-	c.271C>T	c.(271-273)CGG>TGG	p.R91W	AMMECR1L_uc002tpm.1_Missense_Mutation_p.R91W	NM_031445	NP_113633	Q6DCA0	AMERL_HUMAN	AMME chromosomal region gene 1-like	91										central_nervous_system(1)	1	Colorectal(110;0.1)													0.336493	204.776552	209.758519	71	140	GG		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(221;0.07)	Missense_Mutation	SNP	128348008	128348008	582	2	G	A	A	39	39	AMMECR1L	A	1	1
TPO	7173	broad.mit.edu	36	2	1523418	1523418	+	Silent	SNP	C	T	T			TCGA-32-1982-01	TCGA-32-1982-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:1523418C>T	uc002qwr.1	+	c.2664C>T	c.(2662-2664)GGC>GGT	p.G888G	TPO_uc010ewj.1_Intron|TPO_uc002qwt.1_Silent_p.G715G|TPO_uc002qwu.1_Silent_p.G831G|TPO_uc002qwv.1_Silent_p.G844G|TPO_uc002qww.1_Silent_p.G888G|TPO_uc002qwx.1_Silent_p.G831G|TPO_uc002qwy.1_Silent_p.G184G|TPO_uc002qwz.1_Intron	NM_000547	NP_000538	P07202	PERT_HUMAN	thyroid peroxidase isoform a	888	Cytoplasmic (Potential).				cellular nitrogen compound metabolic process|hormone biosynthetic process|hydrogen peroxide catabolic process|oxidation-reduction process	cell surface|cytoplasm|integral to plasma membrane	calcium ion binding|heme binding|iodide peroxidase activity			ovary(6)|pancreas(6)|skin(3)|lung(1)|kidney(1)	17	all_hematologic(175;0.0487)|Acute lymphoblastic leukemia(172;0.0627)	all_cancers(51;0.0338)			Carbimazole(DB00389)|Methimazole(DB00763)|Propylthiouracil(DB00550)					723				0.190476	31.605825	39.091399	16	68	CC		KEEP	---	---	---	---	capture		all cancers(51;0.0356)|OV - Ovarian serous cystadenocarcinoma(76;0.0748)|Epithelial(75;0.12)	Silent	SNP	1523418	1523418	16954	2	C	T	T	27	27	TPO	T	1	1
TTN	7273	broad.mit.edu	36	2	179165441	179165441	+	Missense_Mutation	SNP	T	G	G			TCGA-32-1982-01	TCGA-32-1982-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr2:179165441T>G	uc002umr.1	-	c.51833A>C	c.(51832-51834)AAT>ACT	p.N17278T	TTN_uc002ums.1_Missense_Mutation_p.N10973T|TTN_uc010frc.1_Missense_Mutation_p.N10906T|TTN_uc010frd.1_Missense_Mutation_p.N10781T	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	18205										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				0.295082	389.696279	405.728753	126	301	TT		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)		Missense_Mutation	SNP	179165441	179165441	17290	2	T	G	G	52	52	TTN	G	4	4
TTN	7273	broad.mit.edu	36	2	179185126	179185126	+	Missense_Mutation	SNP	C	T	T			TCGA-32-1982-01	TCGA-32-1982-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:179185126C>T	uc002umr.1	-	c.42553G>A	c.(42553-42555)GGA>AGA	p.G14185R	TTN_uc002ums.1_Missense_Mutation_p.G7880R|TTN_uc010frc.1_Missense_Mutation_p.G7813R|TTN_uc010frd.1_Missense_Mutation_p.G7688R	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	15112										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				0.306122	39.204018	40.848157	15	34	CC		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)		Missense_Mutation	SNP	179185126	179185126	17290	2	C	T	T	21	21	TTN	T	2	2
DNAH7	56171	broad.mit.edu	36	2	196389884	196389884	+	Silent	SNP	C	T	T			TCGA-32-1982-01	TCGA-32-1982-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:196389884C>T	uc002utj.2	-	c.9474G>A	c.(9472-9474)TCG>TCA	p.S3158S		NM_018897	NP_061720	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7	3158	AAA 5 (By similarity).				ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|microtubule motor activity			ovary(2)	2														0.253333	50.395131	54.533741	19	56	CC		KEEP	---	---	---	---	capture			Silent	SNP	196389884	196389884	4789	2	C	T	T	23	23	DNAH7	T	1	1
APOB	338	broad.mit.edu	36	2	21109785	21109785	+	Nonsense_Mutation	SNP	C	A	A			TCGA-32-1982-01	TCGA-32-1982-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:21109785C>A	uc002red.1	-	c.1015G>T	c.(1015-1017)GAG>TAG	p.E339*		NM_000384	NP_000375	P04114	APOB_HUMAN	apolipoprotein B precursor	339	Vitellogenin.				cholesterol homeostasis|cholesterol metabolic process|leukocyte migration|low-density lipoprotein particle clearance|low-density lipoprotein particle remodeling|platelet activation|positive regulation of cholesterol storage|positive regulation of macrophage derived foam cell differentiation|receptor-mediated endocytosis|response to virus|very-low-density lipoprotein particle assembly	chylomicron remnant|clathrin-coated endocytic vesicle membrane|endoplasmic reticulum lumen|endoplasmic reticulum membrane|endosome lumen|endosome membrane|intermediate-density lipoprotein particle|low-density lipoprotein particle|mature chylomicron|microsome|plasma membrane|very-low-density lipoprotein particle	cholesterol transporter activity|enzyme binding|heparin binding|low-density lipoprotein particle receptor binding|phospholipid binding|protein heterodimerization activity			ovary(11)|central_nervous_system(3)|large_intestine(2)|pancreas(1)|skin(1)	18	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)				Atorvastatin(DB01076)									0.27459	166.803526	177.981508	67	177	CC		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	21109785	21109785	796	2	C	A	A	29	29	APOB	A	5	3
C2orf71	388939	broad.mit.edu	36	2	29147982	29147982	+	Missense_Mutation	SNP	C	T	T			TCGA-32-1982-01	TCGA-32-1982-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:29147982C>T	uc002rmt.1	-	c.2650G>A	c.(2650-2652)GCC>ACC	p.A884T		NM_001029883	NP_001025054	A6NGG8	CB071_HUMAN	hypothetical protein LOC388939	884					response to stimulus|visual perception	photoreceptor outer segment					0														0.352381	93.806971	95.752428	37	68	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	29147982	29147982	2279	2	C	T	T	26	26	C2orf71	T	2	2
CHDH	55349	broad.mit.edu	36	3	53831639	53831639	+	Silent	SNP	G	A	A			TCGA-32-1982-01	TCGA-32-1982-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:53831639G>A	uc003dgz.1	-	c.774C>T	c.(772-774)GCC>GCT	p.A258A		NM_018397	NP_060867	Q8NE62	CHDH_HUMAN	choline dehydrogenase	258					alcohol metabolic process|oxidation-reduction process		choline dehydrogenase activity|flavin adenine dinucleotide binding			ovary(1)|central_nervous_system(1)	2		Hepatocellular(537;0.152)			Choline(DB00122)									0.179487	29.304968	36.841472	14	64	GG		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(193;0.000158)|KIRC - Kidney renal clear cell carcinoma(284;0.00588)|Kidney(284;0.00673)|OV - Ovarian serous cystadenocarcinoma(275;0.118)	Silent	SNP	53831639	53831639	3467	3	G	A	A	39	39	CHDH	A	1	1
ZFP42	132625	broad.mit.edu	36	4	189161068	189161068	+	Missense_Mutation	SNP	C	T	T			TCGA-32-1982-01	TCGA-32-1982-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:189161068C>T	uc003izg.1	+	c.113C>T	c.(112-114)GCG>GTG	p.A38V	ZFP42_uc003izh.1_Missense_Mutation_p.A38V|ZFP42_uc003izi.1_Missense_Mutation_p.A38V|ZFP42_uc010isp.1_Missense_Mutation_p.A38V	NM_174900	NP_777560	Q96MM3	ZFP42_HUMAN	zinc finger protein 42	38					female gonad development|male gonad development|meiosis|regulation of transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1		all_cancers(14;6.2e-52)|all_epithelial(14;7.36e-37)|all_lung(41;2.29e-15)|Lung NSC(41;6.7e-15)|Breast(6;1.53e-05)|Melanoma(20;3.01e-05)|Hepatocellular(41;0.00335)|all_hematologic(60;0.014)|Renal(120;0.0183)|Prostate(90;0.0421)|Colorectal(36;0.227)												0.268657	89.158419	95.620845	36	98	CC		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(60;1.54e-11)|BRCA - Breast invasive adenocarcinoma(30;4.21e-06)|GBM - Glioblastoma multiforme(59;8.93e-05)|STAD - Stomach adenocarcinoma(60;0.000279)|LUSC - Lung squamous cell carcinoma(40;0.00902)|READ - Rectum adenocarcinoma(43;0.157)	Missense_Mutation	SNP	189161068	189161068	18238	4	C	T	T	27	27	ZFP42	T	1	1
ZFP42	132625	broad.mit.edu	36	4	189161634	189161634	+	Missense_Mutation	SNP	G	A	A			TCGA-32-1982-01	TCGA-32-1982-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr4:189161634G>A	uc003izg.1	+	c.679G>A	c.(679-681)GTT>ATT	p.V227I	ZFP42_uc003izh.1_Missense_Mutation_p.V227I|ZFP42_uc003izi.1_Missense_Mutation_p.V227I|ZFP42_uc010isp.1_Missense_Mutation_p.V227I	NM_174900	NP_777560	Q96MM3	ZFP42_HUMAN	zinc finger protein 42	227	C2H2-type 2.				female gonad development|male gonad development|meiosis|regulation of transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1		all_cancers(14;6.2e-52)|all_epithelial(14;7.36e-37)|all_lung(41;2.29e-15)|Lung NSC(41;6.7e-15)|Breast(6;1.53e-05)|Melanoma(20;3.01e-05)|Hepatocellular(41;0.00335)|all_hematologic(60;0.014)|Renal(120;0.0183)|Prostate(90;0.0421)|Colorectal(36;0.227)												0.237762	79.177447	88.163432	34	109	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(60;1.54e-11)|BRCA - Breast invasive adenocarcinoma(30;4.21e-06)|GBM - Glioblastoma multiforme(59;8.93e-05)|STAD - Stomach adenocarcinoma(60;0.000279)|LUSC - Lung squamous cell carcinoma(40;0.00902)|READ - Rectum adenocarcinoma(43;0.157)	Missense_Mutation	SNP	189161634	189161634	18238	4	G	A	A	40	40	ZFP42	A	1	1
SULT1B1	27284	broad.mit.edu	36	4	70650109	70650109	+	Missense_Mutation	SNP	C	G	G			TCGA-32-1982-01	TCGA-32-1982-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:70650109C>G	uc003hen.1	-	c.294G>C	c.(292-294)GAG>GAC	p.E98D		NM_014465	NP_055280	O43704	ST1B1_HUMAN	sulfotransferase family, cytosolic, 1B, member	98					3'-phosphoadenosine 5'-phosphosulfate metabolic process|cellular biogenic amine metabolic process|flavonoid metabolic process|steroid metabolic process|sulfation|thyroid hormone metabolic process|xenobiotic metabolic process	cytosol					0														0.25	83.089278	89.908369	30	90	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	70650109	70650109	15896	4	C	G	G	32	32	SULT1B1	G	3	3
PRKG2	5593	broad.mit.edu	36	4	82293823	82293823	+	Missense_Mutation	SNP	T	C	C			TCGA-32-1982-01	TCGA-32-1982-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr4:82293823T>C	uc003hmh.1	-	c.989A>G	c.(988-990)AAG>AGG	p.K330R		NM_006259	NP_006250	Q13237	KGP2_HUMAN	protein kinase, cGMP-dependent, type II	330	cGMP 2.				platelet activation|protein phosphorylation|signal transduction	cytosol	ATP binding|cGMP binding|cGMP-dependent protein kinase activity			breast(3)|central_nervous_system(2)|ovary(1)|large_intestine(1)	7										728				0.336364	117.741784	120.347112	37	73	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	82293823	82293823	12966	4	T	C	C	56	56	PRKG2	C	4	4
PCDHA1	56147	broad.mit.edu	36	5	140147731	140147731	+	Missense_Mutation	SNP	G	A	A			TCGA-32-1982-01	TCGA-32-1982-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:140147731G>A	uc003lhb.1	+	c.1672G>A	c.(1672-1674)GAG>AAG	p.E558K	PCDHA1_uc003lha.1_Intron|PCDHA1_uc003lgz.1_Missense_Mutation_p.E558K	NM_018900	NP_061723	Q9Y5I3	PCDA1_HUMAN	protocadherin alpha 1 isoform 1 precursor	558	Cadherin 5.|Extracellular (Potential).				homophilic cell adhesion|nervous system development	extracellular region|integral to plasma membrane	calcium ion binding|protein binding				0														0.207101	75.331707	88.771489	35	134	GG		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		Missense_Mutation	SNP	140147731	140147731	11939	5	G	A	A	37	37	PCDHA1	A	1	1
PCDHA8	56140	broad.mit.edu	36	5	140201565	140201565	+	Missense_Mutation	SNP	G	A	A			TCGA-32-1982-01	TCGA-32-1982-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:140201565G>A	uc003lhs.1	+	c.475G>A	c.(475-477)GAT>AAT	p.D159N	PCDHA1_uc003lha.1_Intron|PCDHA1_uc003lhb.1_Intron|PCDHA2_uc003lhd.1_Intron|PCDHA3_uc003lhf.1_Intron|PCDHA4_uc003lhh.1_Intron|PCDHA4_uc003lhi.1_Intron|PCDHA5_uc003lhk.1_Intron|PCDHA5_uc003lhl.1_Intron|PCDHA6_uc003lho.1_Intron|PCDHA6_uc003lhn.1_Intron|PCDHA7_uc003lhq.1_Intron|PCDHA8_uc003lhr.1_Missense_Mutation_p.D159N	NM_018911	NP_061734	Q9Y5H6	PCDA8_HUMAN	protocadherin alpha 8 isoform 1 precursor	159	Cadherin 2.|Extracellular (Potential).				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding|protein binding				0														0.292135	138.536057	145.41957	52	126	GG		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		Missense_Mutation	SNP	140201565	140201565	11950	5	G	A	A	37	37	PCDHA8	A	1	1
PCDHGB4	8641	broad.mit.edu	36	5	140749310	140749310	+	Missense_Mutation	SNP	C	T	T			TCGA-32-1982-01	TCGA-32-1982-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:140749310C>T	uc003lkc.1	+	c.1675C>T	c.(1675-1677)CGG>TGG	p.R559W	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc010jfx.1_Intron|PCDHGA3_uc003ljm.1_Intron|PCDHGB1_uc003ljo.1_Intron|PCDHGA4_uc003ljq.1_Intron|PCDHGB2_uc003ljs.1_Intron|PCDHGA5_uc003lju.1_Intron|PCDHGB3_uc003ljw.1_Intron|PCDHGA6_uc003ljy.1_Intron|PCDHGA7_uc003lka.1_Intron|PCDHGA8_uc003lkd.1_5'Flank|PCDHGB4_uc010jfy.1_Missense_Mutation_p.R559W|PCDHGA8_uc003lkb.2_5'Flank	NM_003736	NP_003727	Q9UN71	PCDGG_HUMAN	protocadherin gamma subfamily B, 4 isoform 1	559	Cadherin 5.|Extracellular (Potential).				calcium-dependent cell-cell adhesion|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding				0														0.272727	30.096747	32.135406	12	32	CC		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		Missense_Mutation	SNP	140749310	140749310	11985	5	C	T	T	19	19	PCDHGB4	T	1	1
SLC36A3	285641	broad.mit.edu	36	5	150653171	150653171	+	Silent	SNP	G	A	A			TCGA-32-1982-01	TCGA-32-1982-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:150653171G>A	uc003ltx.1	-	c.351C>T	c.(349-351)TAC>TAT	p.Y117Y	SLC36A3_uc003ltv.1_Silent_p.Y61Y|SLC36A3_uc003ltw.1_Silent_p.Y117Y	NM_181774	NP_861439	Q495N2	S36A3_HUMAN	solute carrier family 36, member 3 isoform 2	117	Cytoplasmic (Potential).					integral to membrane				ovary(2)	2		Medulloblastoma(196;0.109)|all_hematologic(541;0.243)												0.304348	54.84784	57.205426	21	48	GG		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		Silent	SNP	150653171	150653171	15092	5	G	A	A	40	40	SLC36A3	A	1	1
ANKRA2	57763	broad.mit.edu	36	5	72892806	72892806	+	Missense_Mutation	SNP	G	A	A			TCGA-32-1982-01	TCGA-32-1982-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:72892806G>A	uc003kcu.1	-	c.353C>T	c.(352-354)TCT>TTT	p.S118F	ANKRA2_uc003kcv.1_Missense_Mutation_p.S118F	NM_023039	NP_075526	Q9H9E1	ANRA2_HUMAN	ankyrin repeat, family A (RFXANK-like), 2	118						cytoskeleton|cytosol|membrane	low-density lipoprotein particle binding				0		Lung NSC(167;0.0378)|Ovarian(174;0.0908)												0.24026	92.894445	102.378854	37	117	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(47;3.71e-54)	Missense_Mutation	SNP	72892806	72892806	639	5	G	A	A	33	33	ANKRA2	A	2	2
MICAL1	64780	broad.mit.edu	36	6	109874055	109874055	+	Missense_Mutation	SNP	C	G	G			TCGA-32-1982-01	TCGA-32-1982-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:109874055C>G	uc003ptj.1	-	c.2558G>C	c.(2557-2559)GGC>GCC	p.G853A	MICAL1_uc003ptk.1_Missense_Mutation_p.G853A|MICAL1_uc010kdr.1_Missense_Mutation_p.G767A	NM_022765	NP_073602	Q8TDZ2	MICA1_HUMAN	microtubule associated monoxygenase, calponin	853					cytoskeleton organization|oxidation-reduction process|signal transduction	cytoplasm|intermediate filament	SH3 domain binding|zinc ion binding			breast(2)|ovary(1)	3		all_cancers(87;0.000189)|Acute lymphoblastic leukemia(125;3.07e-08)|all_hematologic(75;3.33e-06)|all_epithelial(87;0.00686)|Lung SC(18;0.0743)|Colorectal(196;0.101)|all_lung(197;0.149)												0.304348	11.900328	12.697715	7	16	CC		KEEP	---	---	---	---	capture		Epithelial(106;0.0142)|all cancers(137;0.0197)|OV - Ovarian serous cystadenocarcinoma(136;0.0233)|BRCA - Breast invasive adenocarcinoma(108;0.0574)	Missense_Mutation	SNP	109874055	109874055	9959	6	C	G	G	26	26	MICAL1	G	3	3
HBS1L	10767	broad.mit.edu	36	6	135360413	135360413	+	Missense_Mutation	SNP	G	C	C			TCGA-32-1982-01	TCGA-32-1982-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:135360413G>C	uc003qez.1	-	c.614C>G	c.(613-615)TCT>TGT	p.S205C	HBS1L_uc003qey.1_Missense_Mutation_p.S41C	NM_006620	NP_006611	Q9Y450	HBS1L_HUMAN	HBS1-like isoform 1	205					signal transduction		GTP binding|GTPase activity|translation elongation factor activity				0	Colorectal(23;0.221)													0.259804	153.971327	164.635982	53	151	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(155;0.0046)|GBM - Glioblastoma multiforme(68;0.00702)	Missense_Mutation	SNP	135360413	135360413	7269	6	G	C	C	33	33	HBS1L	C	3	3
BCLAF1	9774	broad.mit.edu	36	6	136624213	136624213	+	Silent	SNP	T	C	C			TCGA-32-1982-01	TCGA-32-1982-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr6:136624213T>C	uc003qgx.1	-	c.2640A>G	c.(2638-2640)AAA>AAG	p.K880K	BCLAF1_uc003qgw.1_Silent_p.K707K|BCLAF1_uc003qgy.1_Silent_p.K829K	NM_014739	NP_055554	Q9NYF8	BCLF1_HUMAN	BCL2-associated transcription factor 1 isoform	880					induction of apoptosis|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleolus	DNA binding|protein binding|transcription repressor activity			ovary(1)	1	Colorectal(23;0.24)					Colon(142;1534 1789 5427 7063 28491)								0.133829	127.346699	197.309049	72	466	TT		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(68;0.00226)|OV - Ovarian serous cystadenocarcinoma(155;0.00331)	Silent	SNP	136624213	136624213	1404	6	T	C	C	52	52	BCLAF1	C	4	4
SYNE1	23345	broad.mit.edu	36	6	152873073	152873073	+	Nonsense_Mutation	SNP	G	A	A			TCGA-32-1982-01	TCGA-32-1982-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:152873073G>A	uc010kiw.1	-	c.529C>T	c.(529-531)CAA>TAA	p.Q177*	SYNE1_uc003qot.2_Nonsense_Mutation_p.Q184*|SYNE1_uc003qou.2_Nonsense_Mutation_p.Q177*|SYNE1_uc010kjb.1_Nonsense_Mutation_p.Q177*|SYNE1_uc003qpa.1_Nonsense_Mutation_p.Q177*	NM_182961	NP_892006	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	177	Actin-binding.|Cytoplasmic (Potential).				cell death|cytoskeletal anchoring at nuclear membrane|Golgi organization|muscle cell differentiation|nuclear matrix anchoring at nuclear membrane	cytoskeleton|Golgi apparatus|integral to membrane|nuclear outer membrane|postsynaptic membrane|sarcomere|SUN-KASH complex	actin binding|lamin binding			central_nervous_system(15)|ovary(8)|large_intestine(5)|pancreas(2)	30		Ovarian(120;0.0955)												0.207171	123.455956	143.40341	52	199	GG		KEEP	---	---	---	---	capture	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)	Nonsense_Mutation	SNP	152873073	152873073	15966	6	G	A	A	47	47	SYNE1	A	5	2
EEF1A1	1915	broad.mit.edu	36	6	74285025	74285025	+	Missense_Mutation	SNP	C	T	T			TCGA-32-1982-01	TCGA-32-1982-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:74285025C>T	uc003phi.1	-	c.802G>A	c.(802-804)GAG>AAG	p.E268K	EEF1A1_uc003phd.1_5'UTR|EEF1A1_uc003phe.1_Missense_Mutation_p.E258K|EEF1A1_uc003phf.1_Missense_Mutation_p.E268K|EEF1A1_uc003phg.1_Missense_Mutation_p.E268K|EEF1A1_uc003phh.1_Missense_Mutation_p.E114K|EEF1A1_uc003phj.1_Missense_Mutation_p.E268K|EEF1A1_uc003phk.1_Missense_Mutation_p.E268K|EEF1A1_uc003phl.2_Intron|EEF1A1_uc003phm.1_Intron	NM_001402	NP_001393	P68104	EF1A1_HUMAN	eukaryotic translation elongation factor 1 alpha	268						cytosol|eukaryotic translation elongation factor 1 complex	GTP binding|GTPase activity|protein binding|translation elongation factor activity				0												OREG0003895	type=REGULATORY REGION|Gene=D16891|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	0.263158	75.362238	81.179079	30	84	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	74285025	74285025	5110	6	C	T	T	30	30	EEF1A1	T	2	2
RABL5	64792	broad.mit.edu	36	7	100746431	100746431	+	Missense_Mutation	SNP	C	A	A			TCGA-32-1982-01	TCGA-32-1982-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:100746431C>A	uc003uyl.1	-	c.319G>T	c.(319-321)GTC>TTC	p.V107F	RABL5_uc010lhw.1_Non-coding_Transcript|RABL5_uc003uym.1_Missense_Mutation_p.V77F|RABL5_uc010lhx.1_5'UTR	NM_022777	NP_073614	Q9H7X7	RABL5_HUMAN	RAB, member RAS oncogene family-like 5 isoform	107							GTP binding				0	Lung NSC(181;0.215)													0.21466	98.971261	113.327462	41	150	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	100746431	100746431	13432	7	C	A	A	17	17	RABL5	A	3	3
NUP205	23165	broad.mit.edu	36	7	134954960	134954960	+	Missense_Mutation	SNP	G	T	T			TCGA-32-1982-01	TCGA-32-1982-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:134954960G>T	uc003vsw.1	+	c.4213G>T	c.(4213-4215)GAC>TAC	p.D1405Y	NUP205_uc003vsx.1_5'Flank	NM_015135	NP_055950	Q92621	NU205_HUMAN	nucleoporin 205kDa	1405					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														0.176471	63.451586	81.906971	33	154	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	134954960	134954960	11164	7	G	T	T	33	33	NUP205	T	3	3
KEL	3792	broad.mit.edu	36	7	142361073	142361073	+	Silent	SNP	G	A	A			TCGA-32-1982-01	TCGA-32-1982-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:142361073G>A	uc003wcb.1	-	c.1017C>T	c.(1015-1017)GAC>GAT	p.D339D		NM_000420	NP_000411	P23276	KELL_HUMAN	Kell blood group, metallo-endopeptidase	339	Extracellular (Potential).				proteolysis|vasoconstriction	integral to membrane|plasma membrane	metal ion binding|metalloendopeptidase activity|protein binding			ovary(3)|central_nervous_system(1)	4	Melanoma(164;0.059)													0.219643	270.863223	311.383555	123	437	GG		KEEP	---	---	---	---	capture			Silent	SNP	142361073	142361073	8448	7	G	A	A	40	40	KEL	A	1	1
ELMO1	9844	broad.mit.edu	36	7	37321008	37321008	+	Missense_Mutation	SNP	C	T	T			TCGA-32-1982-01	TCGA-32-1982-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:37321008C>T	uc003tfk.1	-	c.163G>A	c.(163-165)GAT>AAT	p.D55N	ELMO1_uc010kxg.1_Missense_Mutation_p.D55N	NM_014800	NP_055615	Q92556	ELMO1_HUMAN	engulfment and cell motility 1 isoform 1	55					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														0.129032	15.84919	28.302881	12	81	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	37321008	37321008	5257	7	C	T	T	31	31	ELMO1	T	1	1
PKD1L1	168507	broad.mit.edu	36	7	47833581	47833581	+	Missense_Mutation	SNP	G	C	C			TCGA-32-1982-01	TCGA-32-1982-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:47833581G>C	uc003tny.1	-	c.6746C>G	c.(6745-6747)GCC>GGC	p.A2249G	C7orf69_uc003toa.1_Intron|PKD1L1_uc003tob.2_5'UTR	NM_138295	NP_612152	Q8TDX9	PK1L1_HUMAN	polycystin-1L1	2249	Cytoplasmic (Potential).				cell-cell adhesion	integral to membrane				ovary(7)|breast(1)	8														0.153846	6.710722	9.66795	4	22	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	47833581	47833581	12388	7	G	C	C	42	42	PKD1L1	C	3	3
EGFR	1956	broad.mit.edu	36	7	55200537	55200537	+	Missense_Mutation	SNP	G	T	T			TCGA-32-1982-01	TCGA-32-1982-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:55200537G>T	uc003tqk.1	+	c.1793G>T	c.(1792-1794)GGA>GTA	p.G598V	EGFR_uc003tqi.1_Missense_Mutation_p.G598V|EGFR_uc003tqj.1_Missense_Mutation_p.G598V|EGFR_uc010kzg.1_Missense_Mutation_p.G553V|EGFR_uc003tqn.1_Non-coding_Transcript	NM_005228	NP_005219	P00533	EGFR_HUMAN	epidermal growth factor receptor isoform a	598	Approximate.|Extracellular (Potential).				activation of phospholipase A2 activity by calcium-mediated signaling|activation of phospholipase C activity|axon guidance|cell proliferation|cell-cell adhesion|negative regulation of apoptosis|negative regulation of epidermal growth factor receptor signaling pathway|ossification|positive regulation of catenin import into nucleus|positive regulation of cell migration|positive regulation of cyclin-dependent protein kinase activity involved in G1/S|positive regulation of epithelial cell proliferation|positive regulation of MAP kinase activity|positive regulation of nitric oxide biosynthetic process|positive regulation of phosphorylation|positive regulation of protein kinase B signaling cascade|protein autophosphorylation|protein insertion into membrane|regulation of nitric-oxide synthase activity|regulation of peptidyl-tyrosine phosphorylation|response to stress|response to UV-A	basolateral plasma membrane|endoplasmic reticulum membrane|endosome|extracellular space|Golgi membrane|integral to membrane|nuclear membrane|Shc-EGFR complex	actin filament binding|ATP binding|double-stranded DNA binding|epidermal growth factor receptor activity|identical protein binding|MAP/ERK kinase kinase activity|protein heterodimerization activity|protein phosphatase binding|receptor signaling protein tyrosine kinase activity	p.G598V(16)		lung(8200)|central_nervous_system(103)|upper_aerodigestive_tract(37)|prostate(32)|ovary(31)|thyroid(23)|breast(11)|peritoneum(9)|oesophagus(9)|salivary_gland(9)|large_intestine(8)|stomach(6)|urinary_tract(6)|skin(5)|adrenal_gland(5)|kidney(4)|soft_tissue(4)|bone(3)|NS(2)|haematopoietic_and_lymphoid_tissue(2)|thymus(2)|liver(2)|eye(1)|pancreas(1)	8515	all_cancers(1;1.57e-46)|all_epithelial(1;5.62e-37)|Lung NSC(1;9.29e-25)|all_lung(1;4.39e-23)|Esophageal squamous(2;7.55e-08)|Breast(14;0.0318)				Cetuximab(DB00002)|Erlotinib(DB00530)|Gefitinib(DB00317)|Lapatinib(DB01259)|Lidocaine(DB00281)|Panitumumab(DB01269)|Trastuzumab(DB00072)			8		608	TCGA GBM(3;<1E-8)|TSP Lung(4;<1E-8)			0.825381	2480.94952	2579.290528	813	172	GG		KEEP	---	---	---	---	capture	GBM - Glioblastoma multiforme(1;0)|all cancers(1;2.19e-314)|Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00164)|Epithelial(13;0.0607)		Missense_Mutation	SNP	55200537	55200537	5156	7	G	T	T	41	41	EGFR	T	3	3
ENPP2	5168	broad.mit.edu	36	8	120682165	120682165	+	Silent	SNP	C	T	T			TCGA-32-1982-01	TCGA-32-1982-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr8:120682165C>T	uc003yos.1	-	c.906G>A	c.(904-906)TCG>TCA	p.S302S	ENPP2_uc003yot.1_Silent_p.S302S|ENPP2_uc010mdd.1_Silent_p.S302S	NM_006209	NP_006200	Q13822	ENPP2_HUMAN	autotaxin isoform 1 preproprotein	302					cellular component movement|chemotaxis|G-protein coupled receptor protein signaling pathway|immune response|phosphate metabolic process|phosphatidylcholine catabolic process|regulation of cell migration	extracellular space|integral to plasma membrane	alkylglycerophosphoethanolamine phosphodiesterase activity|calcium ion binding|lysophospholipase activity|nucleic acid binding|nucleotide diphosphatase activity|phosphodiesterase I activity|polysaccharide binding|scavenger receptor activity|transcription factor binding|zinc ion binding			ovary(2)|central_nervous_system(2)|large_intestine(1)|kidney(1)	6	Lung NSC(37;5.03e-06)|Ovarian(258;0.0249)|Hepatocellular(40;0.161)					Melanoma(20;305 879 2501 4818 31020)								0.294737	76.56224	80.14437	28	67	CC		KEEP	---	---	---	---	capture	STAD - Stomach adenocarcinoma(47;0.00185)		Silent	SNP	120682165	120682165	5323	8	C	T	T	23	23	ENPP2	T	1	1
ENPP2	5168	broad.mit.edu	36	8	120698977	120698977	+	Missense_Mutation	SNP	G	A	A			TCGA-32-1982-01	TCGA-32-1982-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr8:120698977G>A	uc003yos.1	-	c.487C>T	c.(487-489)CGC>TGC	p.R163C	ENPP2_uc003yot.1_Missense_Mutation_p.R163C|ENPP2_uc010mdd.1_Missense_Mutation_p.R163C	NM_006209	NP_006200	Q13822	ENPP2_HUMAN	autotaxin isoform 1 preproprotein	163					cellular component movement|chemotaxis|G-protein coupled receptor protein signaling pathway|immune response|phosphate metabolic process|phosphatidylcholine catabolic process|regulation of cell migration	extracellular space|integral to plasma membrane	alkylglycerophosphoethanolamine phosphodiesterase activity|calcium ion binding|lysophospholipase activity|nucleic acid binding|nucleotide diphosphatase activity|phosphodiesterase I activity|polysaccharide binding|scavenger receptor activity|transcription factor binding|zinc ion binding			ovary(2)|central_nervous_system(2)|large_intestine(1)|kidney(1)	6	Lung NSC(37;5.03e-06)|Ovarian(258;0.0249)|Hepatocellular(40;0.161)					Melanoma(20;305 879 2501 4818 31020)								0.243243	22.560716	24.781312	9	28	GG		KEEP	---	---	---	---	capture	STAD - Stomach adenocarcinoma(47;0.00185)		Missense_Mutation	SNP	120698977	120698977	5323	8	G	A	A	37	37	ENPP2	A	1	1
TSNARE1	203062	broad.mit.edu	36	8	143308778	143308778	+	Missense_Mutation	SNP	T	C	C			TCGA-32-1982-01	TCGA-32-1982-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr8:143308778T>C	uc003ywj.1	-	c.1519A>G	c.(1519-1521)ATC>GTC	p.I507V	TSNARE1_uc003ywk.1_Missense_Mutation_p.I506V	NM_145003	NP_659440	Q96NA8	TSNA1_HUMAN	t-SNARE domain containing 1	506	Poly-Ile.|Helical; (Potential).				vesicle-mediated transport	integral to membrane					0	all_cancers(97;7.39e-11)|all_epithelial(106;8.98e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000332)|Ovarian(258;0.0315)|Acute lymphoblastic leukemia(118;0.155)													0.33871	54.549792	55.978848	21	41	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	143308778	143308778	17181	8	T	C	C	51	51	TSNARE1	C	4	4
ADAM28	10863	broad.mit.edu	36	8	24237363	24237363	+	Silent	SNP	G	A	A			TCGA-32-1982-01	TCGA-32-1982-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr8:24237363G>A	uc003xdy.1	+	c.792G>A	c.(790-792)AAG>AAA	p.K264K	ADAM28_uc003xdx.1_Silent_p.K264K|ADAM28_uc010lua.1_5'Flank	NM_014265	NP_055080	Q9UKQ2	ADA28_HUMAN	ADAM metallopeptidase domain 28 isoform 1	264	Peptidase M12B.|Extracellular (Potential).				proteolysis|spermatogenesis	extracellular region|integral to membrane|plasma membrane	metalloendopeptidase activity|zinc ion binding			skin(2)|lung(1)|central_nervous_system(1)	4		Prostate(55;0.0959)				NSCLC(193;488 2149 22258 34798 40734)				410				0.313043	101.707591	105.316055	36	79	GG		KEEP	---	---	---	---	capture		Colorectal(74;0.0129)|COAD - Colon adenocarcinoma(73;0.0434)|BRCA - Breast invasive adenocarcinoma(99;0.175)	Silent	SNP	24237363	24237363	247	8	G	A	A	33	33	ADAM28	A	2	2
JPH1	56704	broad.mit.edu	36	8	75334249	75334249	+	Missense_Mutation	SNP	C	T	T			TCGA-32-1982-01	TCGA-32-1982-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr8:75334249C>T	uc003yae.1	-	c.1183G>A	c.(1183-1185)GCG>ACG	p.A395T	JPH1_uc003yaf.2_Missense_Mutation_p.A395T|JPH1_uc003yag.1_Missense_Mutation_p.A259T	NM_020647	NP_065698	Q9HDC5	JPH1_HUMAN	junctophilin 1	395	Ala-rich.|Cytoplasmic (Potential).				calcium ion transport into cytosol|regulation of ryanodine-sensitive calcium-release channel activity	integral to membrane|junctional membrane complex|junctional sarcoplasmic reticulum membrane|plasma membrane				ovary(1)	1	Breast(64;0.00576)													0.303571	44.353441	46.282227	17	39	CC		KEEP	---	---	---	---	capture	BRCA - Breast invasive adenocarcinoma(89;0.0499)|Epithelial(68;0.0728)|all cancers(69;0.176)		Missense_Mutation	SNP	75334249	75334249	8264	8	C	T	T	27	27	JPH1	T	1	1
EPB41L4B	54566	broad.mit.edu	36	9	111057674	111057674	+	Silent	SNP	C	T	T			TCGA-32-1982-01	TCGA-32-1982-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr9:111057674C>T	uc004bdz.1	-	c.1107G>A	c.(1105-1107)ACG>ACA	p.T369T	EPB41L4B_uc004bea.1_Silent_p.T369T	NM_019114	NP_061987	Q9H329	E41LB_HUMAN	erythrocyte membrane protein band 4.1 like 4B	369	FERM.					cytoplasm|cytoskeleton|extrinsic to membrane	cytoskeletal protein binding|structural constituent of cytoskeleton			ovary(1)|central_nervous_system(1)	2														0.230769	77.428194	87.789896	36	120	CC		KEEP	---	---	---	---	capture			Silent	SNP	111057674	111057674	5349	9	C	T	T	27	27	EPB41L4B	T	1	1
MID2	11043	broad.mit.edu	36	X	106971058	106971058	+	Silent	SNP	G	A	A			TCGA-32-1982-01	TCGA-32-1982-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:106971058G>A	uc004enl.1	+	c.447G>A	c.(445-447)ACG>ACA	p.T149T	MID2_uc004enk.1_Silent_p.T149T	NM_012216	NP_036348	Q9UJV3	TRIM1_HUMAN	midline 2 isoform 1	169	B box-type 1; degenerate.					centrosome|microtubule	ligase activity|zinc ion binding			ovary(1)	1														0.31	81.896398	85.054454	31	69	GG		KEEP	---	---	---	---	capture			Silent	SNP	106971058	106971058	9968	23	G	A	A	38	38	MID2	A	1	1
MAGEA6	4105	broad.mit.edu	36	X	151620278	151620278	+	Missense_Mutation	SNP	G	T	T			TCGA-32-1982-01	TCGA-32-1982-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:151620278G>T	uc004ffq.1	+	c.312G>T	c.(310-312)GAG>GAT	p.E104D	MAGEA6_uc004ffr.1_Missense_Mutation_p.E104D|MAGEA6_uc010ntl.1_Missense_Mutation_p.E104D	NM_005363	NP_787064	P43360	MAGA6_HUMAN	melanoma antigen family A, 6	104							protein binding				0	Acute lymphoblastic leukemia(192;6.56e-05)													0.241379	135.276334	149.439288	56	176	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	151620278	151620278	9549	23	G	T	T	36	36	MAGEA6	T	3	3
DKC1	1736	broad.mit.edu	36	X	153657779	153657779	+	Missense_Mutation	SNP	G	A	A			TCGA-32-1982-01	TCGA-32-1982-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:153657779G>A	uc004fmm.1	+	c.1462G>A	c.(1462-1464)GAG>AAG	p.E488K	DKC1_uc010nvf.1_Missense_Mutation_p.E483K	NM_001363	NP_001354	O60832	DKC1_HUMAN	dyskerin isoform 1	488	Nuclear and nucleolar localization.				cell proliferation|pseudouridine synthesis|rRNA processing	Cajal body|nucleolus|telomerase holoenzyme complex	protein binding|pseudouridine synthase activity|RNA binding|telomerase activity				0	all_cancers(53;8.15e-17)|all_epithelial(53;1.1e-10)|all_lung(58;6.63e-07)|Lung NSC(58;2.08e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)													0.410256	46.591777	46.866404	16	23	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	153657779	153657779	4721	23	G	A	A	37	37	DKC1	A	1	1
CXorf59	286464	broad.mit.edu	36	X	36013457	36013457	+	Silent	SNP	C	T	T			TCGA-32-1982-01	TCGA-32-1982-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:36013457C>T	uc004ddk.1	+	c.522C>T	c.(520-522)CTC>CTT	p.L174L		NM_173695	NP_775966	Q8N9S7	CX059_HUMAN	hypothetical protein LOC286464	174						integral to membrane				central_nervous_system(1)	1														0.289474	91.529044	96.057311	33	81	CC		KEEP	---	---	---	---	capture			Silent	SNP	36013457	36013457	4279	23	C	T	T	30	30	CXorf59	T	2	2
HDAC6	10013	broad.mit.edu	36	X	48546306	48546306	+	Missense_Mutation	SNP	G	A	A			TCGA-32-1982-01	TCGA-32-1982-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:48546306G>A	uc004dks.1	+	c.178G>A	c.(178-180)GGC>AGC	p.G60S	HDAC6_uc004dkr.1_Missense_Mutation_p.G60S|HDAC6_uc010nig.1_5'UTR|HDAC6_uc004dkt.1_Missense_Mutation_p.G60S|HDAC6_uc004dku.2_Missense_Mutation_p.G60S	NM_006044	NP_006035	Q9UBN7	HDAC6_HUMAN	histone deacetylase 6	60					aggresome assembly|cellular response to hydrogen peroxide|Hsp90 deacetylation|lysosome localization|macroautophagy|misfolded or incompletely synthesized protein catabolic process|negative regulation of hydrogen peroxide metabolic process|negative regulation of oxidoreductase activity|negative regulation of proteolysis|peptidyl-lysine deacetylation|polyubiquitinated misfolded protein transport|positive regulation of apoptosis|positive regulation of cellular chaperone-mediated protein complex assembly|positive regulation of epithelial cell migration|positive regulation of receptor biosynthetic process|positive regulation of signal transduction|regulation of androgen receptor signaling pathway|regulation of microtubule-based movement|regulation of receptor activity|regulation of transcription, DNA-dependent|response to growth factor stimulus|response to toxin|transcription, DNA-dependent|tubulin deacetylation	aggresome|caveola|cell leading edge|cytosol|histone deacetylase complex|microtubule associated complex|perinuclear region of cytoplasm	actin binding|alpha-tubulin binding|beta-catenin binding|dynein complex binding|histone deacetylase activity (H3-K16 specific)|histone deacetylase binding|Hsp90 protein binding|microtubule binding|NAD-dependent histone deacetylase activity (H3-K14 specific)|NAD-dependent histone deacetylase activity (H3-K9 specific)|NAD-dependent histone deacetylase activity (H4-K16 specific)|polyubiquitin binding|specific transcriptional repressor activity|tau protein binding|tubulin deacetylase activity|zinc ion binding			ovary(3)	3					Vorinostat(DB02546)	Pancreas(112;205 1675 2305 8976 15959)				170				0.235294	20.283238	22.461606	8	26	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	48546306	48546306	7294	23	G	A	A	39	39	HDAC6	A	1	1
SMC1A	8243	broad.mit.edu	36	X	53455869	53455869	+	Missense_Mutation	SNP	G	T	T			TCGA-32-1982-01	TCGA-32-1982-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:53455869G>T	uc004dsg.1	-	c.914C>A	c.(913-915)ACC>AAC	p.T305N	SMC1A_uc004dsh.1_Missense_Mutation_p.T283N	NM_006306	NP_006297	Q14683	SMC1A_HUMAN	structural maintenance of chromosomes 1A	305	Potential.				cell cycle checkpoint|cell division|DNA repair|meiosis|mitotic metaphase/anaphase transition|mitotic prometaphase|mitotic sister chromatid cohesion|mitotic spindle organization|negative regulation of DNA endoreduplication|nuclear mRNA splicing, via spliceosome|response to radiation|signal transduction in response to DNA damage	cohesin core heterodimer|condensed chromosome kinetochore|condensed nuclear chromosome|cytoplasm|meiotic cohesin complex|nucleoplasm	ATP binding|chromatin binding|microtubule motor activity|protein heterodimerization activity			ovary(5)	5														0.268293	50.276828	54.216499	22	60	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	53455869	53455869	15279	23	G	T	T	44	44	SMC1A	T	3	3
LAS1L	81887	broad.mit.edu	36	X	64651476	64651476	+	Missense_Mutation	SNP	T	G	G			TCGA-32-1982-01	TCGA-32-1982-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chrX:64651476T>G	uc004dwa.1	-	c.2030A>C	c.(2029-2031)GAC>GCC	p.D677A	LAS1L_uc004dvy.1_Missense_Mutation_p.D190A|LAS1L_uc004dvz.1_Missense_Mutation_p.D190A|LAS1L_uc004dwc.1_Missense_Mutation_p.D660A|LAS1L_uc004dwd.1_Missense_Mutation_p.D618A	NM_031206	NP_112483	Q9Y4W2	LAS1L_HUMAN	LAS1-like	677						MLL1 complex|nucleolus	protein binding			ovary(3)|large_intestine(1)	4														0.3	6.471983	7.303786	6	14	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	64651476	64651476	8959	23	T	G	G	58	58	LAS1L	G	4	4
TAF1	6872	broad.mit.edu	36	X	70544638	70544638	+	Silent	SNP	C	T	T			TCGA-32-1982-01	TCGA-32-1982-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:70544638C>T	uc004dzt.2	+	c.4356C>T	c.(4354-4356)CGC>CGT	p.R1452R	TAF1_uc004dzu.2_Silent_p.R1431R|TAF1_uc010nle.1_5'UTR|TAF1_uc010nlf.1_5'UTR|TAF1_uc004dzx.2_Non-coding_Transcript|TAF1_uc004dzy.2_Non-coding_Transcript|TAF1_uc004dzv.2_Silent_p.R605R|TAF1_uc010nld.1_Non-coding_Transcript	NM_004606	NP_004597	P21675	TAF1_HUMAN	TBP-associated factor 1 isoform 1	1431	Bromo 1.|Interaction with ASF1A and ASF1B.|Protein kinase 2.				G1 phase of mitotic cell cycle|interspecies interaction between organisms|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|positive regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of transcription initiation from RNA polymerase II promoter|protein autophosphorylation|regulation of transcription involved in G2/M-phase of mitotic cell cycle|response to DNA damage stimulus|RNA polymerase II transcriptional preinitiation complex assembly|transcription elongation from RNA polymerase II promoter|viral reproduction	MLL1 complex|transcription factor TFIID complex	ATP binding|histone acetyl-lysine binding|histone acetyltransferase activity|p53 binding|protein binding|protein serine/threonine kinase activity|sequence-specific DNA binding|TBP-class protein binding|transcription coactivator activity			ovary(5)|breast(4)|large_intestine(2)|central_nervous_system(2)|lung(1)|skin(1)	15	Renal(35;0.156)	all_lung(315;0.000321)								472				0.260116	112.707593	121.713798	45	128	CC		KEEP	---	---	---	---	capture			Silent	SNP	70544638	70544638	16034	23	C	T	T	27	27	TAF1	T	1	1
RPA4	29935	broad.mit.edu	36	X	96026447	96026447	+	Missense_Mutation	SNP	C	T	T			TCGA-32-1982-01	TCGA-32-1982-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:96026447C>T	uc004efv.2	+	c.482C>T	c.(481-483)ACG>ATG	p.T161M	DIAPH2_uc004eft.2_Intron|DIAPH2_uc004efu.2_Intron|DIAPH2_uc004efs.2_Intron	NM_013347	NP_037479	Q13156	RFA4_HUMAN	replication protein A4, 34kDa	161					DNA damage checkpoint|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|nucleotide-excision repair	DNA replication factor A complex|nucleoplasm	single-stranded DNA binding				0														0.273743	122.795912	131.055201	49	130	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	96026447	96026447	14018	23	C	T	T	19	19	RPA4	T	1	1
PCDH19	57526	broad.mit.edu	36	X	99549514	99549514	+	Silent	SNP	G	A	A			TCGA-32-1982-01	TCGA-32-1982-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:99549514G>A	uc010nmz.1	-	c.738C>T	c.(736-738)AGC>AGT	p.S246S	PCDH19_uc004efw.2_Silent_p.S246S|PCDH19_uc004efx.2_Silent_p.S246S	NM_020766	NP_001098713	Q8TAB3	PCD19_HUMAN	protocadherin 19 isoform b	246	Cadherin 3.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(2)|breast(2)|upper_aerodigestive_tract(1)|urinary_tract(1)|skin(1)	7														0.324201	182.955626	188.959764	71	148	GG		KEEP	---	---	---	---	capture			Silent	SNP	99549514	99549514	11934	23	G	A	A	38	38	PCDH19	A	1	1
ACE	1636	broad.mit.edu	36	17	58908386	58908386	+	Frame_Shift_Del	DEL	G	-	-			TCGA-32-1982-01	TCGA-32-1982-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:58908386_58908386delG	uc002jau.1	+	c.199_199delG	c.(199-201)GCCfs	p.A67fs	ACE_uc010ddu.1_5'UTR	NM_000789	NP_000780	P12821	ACE_HUMAN	angiotensin I converting enzyme isoform 1	67	Extracellular (Potential).|Peptidase M2 1.				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)									0.33			2	4				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	58908386	58908386	137	17	G	-	-	38	38	ACE	-	5	5
DND1	373863	broad.mit.edu	36	5	140032469	140032469	+	Frame_Shift_Del	DEL	T	-	-			TCGA-32-1982-01	TCGA-32-1982-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:140032469_140032469delT	uc003lgt.1	-	c.349_349delA	c.(349-351)ACGfs	p.T117fs		NM_194249	NP_919225	Q8IYX4	DND1_HUMAN	dead end homolog 1	117	RRM 1.				multicellular organismal development|negative regulation of gene silencing by miRNA	cytoplasm|nucleus	AU-rich element binding|nucleotide binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)											0.43			6	8				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	140032469	140032469	4849	5	T	-	-	59	59	DND1	-	5	5
