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
SRPR	6734	broad.mit.edu	36	11	125639519	125639519	+	Nonsense_Mutation	SNP	C	A	A			TCGA-06-0750-01	TCGA-06-0750-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:125639519C>A	uc001qdh.1	-	c.1651G>T	c.(1651-1653)GGA>TGA	p.G551*		NM_003139	NP_003130	P08240	SRPR_HUMAN	signal recognition particle receptor	551					SRP-dependent cotranslational protein targeting to membrane	integral to membrane|signal recognition particle receptor complex	GTP binding|GTPase activity|receptor activity|signal recognition particle binding				0	all_hematologic(175;0.145)													0.345455	99.411178	101.733479	38	72	CC		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(274;1.1e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0736)	Nonsense_Mutation	SNP	125639519	125639519	15676	11	C	A	A	24	24	SRPR	A	5	3
IFITM5	387733	broad.mit.edu	36	11	289395	289395	+	Silent	SNP	C	G	G			TCGA-06-0750-01	TCGA-06-0750-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:289395C>G	uc001low.1	-	c.96G>C	c.(94-96)CCG>CCC	p.P32P		NM_001025295	NP_001020466	A6NNB3	IFM5_HUMAN	interferon induced transmembrane protein 5	32	Extracellular (Potential).				multicellular organismal development|regulation of bone mineralization|response to biotic stimulus	integral to membrane|plasma membrane					0		all_cancers(49;1.12e-06)|all_epithelial(84;0.000375)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)												0.4	7.433575	7.537887	4	6	CC		KEEP	---	---	---	---	capture		all cancers(45;5.73e-28)|Epithelial(43;3.42e-27)|OV - Ovarian serous cystadenocarcinoma(40;1.14e-20)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0328)|LUSC - Lung squamous cell carcinoma(625;0.122)	Silent	SNP	289395	289395	7830	11	C	G	G	27	27	IFITM5	G	3	3
PHLDA2	7262	broad.mit.edu	36	11	2907067	2907067	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0750-01	TCGA-06-0750-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:2907067C>T	uc001lxa.1	-	c.104G>A	c.(103-105)CGC>CAC	p.R35H	PHLDA2_uc009yds.1_Missense_Mutation_p.R35H	NM_003311	NP_003302	Q53GA4	PHLA2_HUMAN	pleckstrin homology-like domain family A member	35	PH.				apoptosis	cytoplasm|membrane					0		all_epithelial(84;0.000124)|Medulloblastoma(188;0.00106)|Breast(177;0.00328)|Ovarian(85;0.00556)|all_neural(188;0.00681)|all_lung(207;0.198)												0.358491	50.614469	51.547081	19	34	CC		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(625;0.0025)|LUSC - Lung squamous cell carcinoma(625;0.19)	Missense_Mutation	SNP	2907067	2907067	12273	11	C	T	T	27	27	PHLDA2	T	1	1
OR52J3	119679	broad.mit.edu	36	11	5024985	5024985	+	Silent	SNP	G	A	A			TCGA-06-0750-01	TCGA-06-0750-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:5024985G>A	uc001lzx.1	+	c.654G>A	c.(652-654)TCG>TCA	p.S218S		NM_001001916	NP_001001916	Q8NH60	O52J3_HUMAN	olfactory receptor, family 52, subfamily J,	218	Helical; Name=5; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			lung(1)	1		Medulloblastoma(188;0.00131)|all_neural(188;0.0189)|Breast(177;0.0204)												0.337662	283.402401	290.582258	104	204	GG		KEEP	---	---	---	---	capture		Epithelial(150;9.29e-10)|BRCA - Breast invasive adenocarcinoma(625;0.135)|LUSC - Lung squamous cell carcinoma(625;0.19)	Silent	SNP	5024985	5024985	11532	11	G	A	A	40	40	OR52J3	A	1	1
OR5W2	390148	broad.mit.edu	36	11	55437894	55437894	+	Silent	SNP	C	T	T			TCGA-06-0750-01	TCGA-06-0750-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:55437894C>T	uc001nib.1	-	c.741G>A	c.(739-741)GCG>GCA	p.A247A		NM_001001960	NP_001001960	Q8NH69	OR5W2_HUMAN	olfactory receptor, family 5, subfamily W,	247	Helical; Name=6; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1						Melanoma(48;171 1190 15239 43886 49348)								0.238636	51.532338	57.021522	21	67	CC		KEEP	---	---	---	---	capture			Silent	SNP	55437894	55437894	11595	11	C	T	T	23	23	OR5W2	T	1	1
HRASLS2	54979	broad.mit.edu	36	11	63077079	63077079	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0750-01	TCGA-06-0750-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:63077079G>C	uc001nxg.1	-	c.422C>G	c.(421-423)GCA>GGA	p.A141G		NM_017878	NP_060348	Q9NWW9	HRSL2_HUMAN	HRAS-like suppressor 2	141											0														0.230769	6.620259	9.373238	9	30	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	63077079	63077079	7642	11	G	C	C	46	46	HRASLS2	C	3	3
PDE2A	5138	broad.mit.edu	36	11	71971180	71971180	+	Missense_Mutation	SNP	A	G	G			TCGA-06-0750-01	TCGA-06-0750-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr11:71971180A>G	uc001osm.1	-	c.1807T>C	c.(1807-1809)TTC>CTC	p.F603L	PDE2A_uc001osn.1_Missense_Mutation_p.F347L|PDE2A_uc001oso.1_Missense_Mutation_p.F582L	NM_002599	NP_002590	O00408	PDE2A_HUMAN	phosphodiesterase 2A, cGMP-stimulated isoform 1	603					platelet activation|signal transduction	cytosol	3',5'-cyclic-AMP phosphodiesterase activity|3',5'-cyclic-GMP phosphodiesterase activity|cGMP binding|cGMP-stimulated cyclic-nucleotide phosphodiesterase activity|metal ion binding			ovary(2)|breast(1)	3					Sildenafil(DB00203)|Sulindac(DB00605)									0.361702	103.689764	105.285597	34	60	AA		KEEP	---	---	---	---	capture	BRCA - Breast invasive adenocarcinoma(5;3.55e-05)		Missense_Mutation	SNP	71971180	71971180	12057	11	A	G	G	1	1	PDE2A	G	4	4
OR5P2	120065	broad.mit.edu	36	11	7774767	7774767	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0750-01	TCGA-06-0750-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:7774767G>A	uc001mfp.1	-	c.299C>T	c.(298-300)GCG>GTG	p.A100V		NM_153444	NP_703145	Q8WZ92	OR5P2_HUMAN	olfactory receptor, family 5, subfamily P,	100	Helical; Name=3; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|central_nervous_system(1)	3														0.355769	204.496149	208.306174	74	134	GG		KEEP	---	---	---	---	capture		Epithelial(150;8.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)	Missense_Mutation	SNP	7774767	7774767	11588	11	G	A	A	38	38	OR5P2	A	1	1
ZFC3H1	196441	broad.mit.edu	36	12	70343396	70343396	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0750-01	TCGA-06-0750-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:70343396G>A	uc001swo.1	-	c.262C>T	c.(262-264)CGC>TGC	p.R88C	ZFC3H1_uc001swp.2_Missense_Mutation_p.R88C|THAP2_uc001swq.1_5'Flank	NM_144982	NP_659419	O60293	ZC3H1_HUMAN	proline/serine-rich coiled-coil 2	88	Ser-rich.				RNA processing	intracellular	metal ion binding			ovary(2)|breast(1)|central_nervous_system(1)	4												OREG0021993	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.383929	231.816096	234.452456	86	138	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	70343396	70343396	18221	12	G	A	A	40	40	ZFC3H1	A	1	1
NR1H4	9971	broad.mit.edu	36	12	99428876	99428876	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0750-01	TCGA-06-0750-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:99428876G>A	uc001tht.1	+	c.299G>A	c.(298-300)CGT>CAT	p.R100H	NR1H4_uc001thp.1_Missense_Mutation_p.R90H|NR1H4_uc001thq.1_Missense_Mutation_p.R90H|NR1H4_uc001thr.1_Missense_Mutation_p.R90H|NR1H4_uc001ths.1_Missense_Mutation_p.R100H	NM_005123	NP_005114	Q96RI1	NR1H4_HUMAN	nuclear receptor subfamily 1, group H, member 4	100					bile acid metabolic process|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|thyroid hormone receptor activity|transcription coactivator activity|transcription corepressor activity|zinc ion binding			ovary(1)|lung(1)|skin(1)	3														0.369128	149.87575	152.121788	55	94	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	99428876	99428876	11024	12	G	A	A	40	40	NR1H4	A	1	1
GABRA5	2558	broad.mit.edu	36	15	24665553	24665553	+	Missense_Mutation	SNP	T	C	C			TCGA-06-0750-01	TCGA-06-0750-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr15:24665553T>C	uc001zbd.1	+	c.65T>C	c.(64-66)ATG>ACG	p.M22T	GABRB3_uc001zbb.1_Intron	NM_000810	NP_000801	P31644	GBRA5_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha	22					gamma-aminobutyric acid signaling pathway|synaptic transmission	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity			ovary(1)	1		all_lung(180;4.59e-13)|Breast(32;0.000563)|Colorectal(260;0.227)			Alprazolam(DB00404)|Ethchlorvynol(DB00189)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Lorazepam(DB00186)|Meprobamate(DB00371)|Midazolam(DB00683)									0.373626	176.423804	178.986427	68	114	TT		KEEP	---	---	---	---	capture		all cancers(64;1.45e-08)|Epithelial(43;4.96e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0232)|Lung(196;0.182)	Missense_Mutation	SNP	24665553	24665553	6415	15	T	C	C	51	51	GABRA5	C	4	4
CHSY1	22856	broad.mit.edu	36	15	99535541	99535541	+	Nonsense_Mutation	SNP	G	A	A			TCGA-06-0750-01	TCGA-06-0750-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr15:99535541G>A	uc002bwt.1	-	c.1984C>T	c.(1984-1986)CAG>TAG	p.Q662*		NM_014918	NP_055733	Q86X52	CHSS1_HUMAN	carbohydrate (chondroitin) synthase 1	662	Lumenal (Potential).				chondroitin sulfate biosynthetic process	Golgi cisterna membrane|integral to membrane	glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity|metal ion binding|N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase activity				0	Lung NSC(78;0.00217)|all_lung(78;0.00271)|Melanoma(26;0.00505)													0.126904	35.233463	61.987223	25	172	GG		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(32;0.000932)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)		Nonsense_Mutation	SNP	99535541	99535541	3546	15	G	A	A	47	47	CHSY1	A	5	2
DPEP1	1800	broad.mit.edu	36	16	88231807	88231807	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0750-01	TCGA-06-0750-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:88231807G>A	uc010cin.1	+	c.992G>A	c.(991-993)AGG>AAG	p.R331K	DPEP1_uc002fnr.2_Missense_Mutation_p.R331K|DPEP1_uc002fns.2_Missense_Mutation_p.R331K	NM_001128141	NP_001121613	P16444	DPEP1_HUMAN	dipeptidase 1	331					proteolysis	anchored to membrane|apical plasma membrane|microvillus membrane	dipeptidase activity|dipeptidyl-peptidase activity|metal ion binding|metalloexopeptidase activity|protein binding			large_intestine(1)	1		all_lung(18;0.0054)|all_hematologic(23;0.094)			Cilastatin(DB01597)									0.298701	63.19331	65.982925	23	54	GG		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(80;0.0258)	Missense_Mutation	SNP	88231807	88231807	4897	16	G	A	A	35	35	DPEP1	A	2	2
FKBP10	60681	broad.mit.edu	36	17	37228998	37228998	+	Silent	SNP	C	T	T			TCGA-06-0750-01	TCGA-06-0750-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:37228998C>T	uc002hxv.2	+	c.738C>T	c.(736-738)ATC>ATT	p.I246I	FKBP10_uc002hxw.1_5'UTR	NM_021939	NP_068758	Q96AY3	FKB10_HUMAN	FK506 binding protein 10, 65 kDa	246	PPIase FKBP-type 2.				protein folding	endoplasmic reticulum lumen|membrane	calcium ion binding|FK506 binding|peptidyl-prolyl cis-trans isomerase activity			ovary(1)	1		Breast(137;0.00122)												0.320574	170.221074	176.216766	67	142	CC		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(366;0.148)	Silent	SNP	37228998	37228998	6140	17	C	T	T	30	30	FKBP10	T	2	2
FXR2	9513	broad.mit.edu	36	17	7436335	7436335	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0750-01	TCGA-06-0750-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:7436335G>A	uc002gia.1	-	c.1888C>T	c.(1888-1890)CGC>TGC	p.R630C	SOX15_uc002ghy.1_5'Flank|SOX15_uc002ghz.1_5'Flank	NM_004860	NP_004851	P51116	FXR2_HUMAN	fragile X mental retardation syndrome related	630						cytosolic large ribosomal subunit	protein binding|RNA binding	p.0?(1)			0														0.319048	176.663523	182.767759	67	143	GG		KEEP	---	---	---	---	capture		READ - Rectum adenocarcinoma(115;0.17)	Missense_Mutation	SNP	7436335	7436335	6367	17	G	A	A	40	40	FXR2	A	1	1
DSG1	1828	broad.mit.edu	36	18	27188662	27188662	+	Silent	SNP	C	T	T			TCGA-06-0750-01	TCGA-06-0750-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr18:27188662C>T	uc002kwp.1	+	c.2505C>T	c.(2503-2505)GTC>GTT	p.V835V		NM_001942	NP_001933	Q02413	DSG1_HUMAN	desmoglein 1 preproprotein	835	Desmoglein repeat 1.|Cytoplasmic (Potential).				calcium-dependent cell-cell adhesion|cell-cell junction assembly|cellular component disassembly involved in apoptosis|homophilic cell adhesion|protein stabilization	cytosol|desmosome|integral to membrane|internal side of plasma membrane	calcium ion binding|gamma-catenin binding|toxin binding			ovary(2)|central_nervous_system(2)	4														0.146893	76.30154	118.691523	52	302	CC		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(10;0.00559)		Silent	SNP	27188662	27188662	4960	18	C	T	T	29	29	DSG1	T	2	2
SLC14A2	8170	broad.mit.edu	36	18	41466313	41466313	+	Missense_Mutation	SNP	G	T	T			TCGA-06-0750-01	TCGA-06-0750-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr18:41466313G>T	uc010dnj.1	+	c.522G>T	c.(520-522)AGG>AGT	p.R174S	SLC14A2_uc002lbb.2_Missense_Mutation_p.R174S|SLC14A2_uc002lbe.1_Missense_Mutation_p.R174S	NM_007163	NP_009094	Q15849	UT2_HUMAN	solute carrier family 14 (urea transporter),	174						apical plasma membrane|integral to membrane|membrane fraction	protein binding|urea transmembrane transporter activity			ovary(1)|central_nervous_system(1)	2														0.389831	192.88858	194.751301	69	108	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	41466313	41466313	14892	18	G	T	T	44	44	SLC14A2	T	3	3
MC4R	4160	broad.mit.edu	36	18	56189953	56189953	+	Missense_Mutation	SNP	T	A	A			TCGA-06-0750-01	TCGA-06-0750-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr18:56189953T>A	uc002lie.1	-	c.610A>T	c.(610-612)ATG>TTG	p.M204L		NM_005912	NP_005903	P32245	MC4R_HUMAN	melanocortin 4 receptor	204	Helical; Name=5; (Potential).				feeding behavior|G-protein signaling, coupled to cAMP nucleotide second messenger|positive regulation of bone resorption|positive regulation of cAMP biosynthetic process	integral to membrane|plasma membrane	melanocyte-stimulating hormone receptor activity|neuropeptide binding|ubiquitin protein ligase binding				0		Colorectal(73;0.0946)												0.162921	56.064167	75.284583	29	149	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	56189953	56189953	9755	18	T	A	A	51	51	MC4R	A	4	4
MAP1S	55201	broad.mit.edu	36	19	17705106	17705106	+	Nonsense_Mutation	SNP	G	T	T			TCGA-06-0750-01	TCGA-06-0750-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:17705106G>T	uc002nhe.1	+	c.2893G>T	c.(2893-2895)GAG>TAG	p.E965*	MAP1S_uc010eba.1_Intron|MAP1S_uc002nhf.1_Nonsense_Mutation_p.E213*	NM_018174	NP_060644	Q66K74	MAP1S_HUMAN	BPY2 interacting protein 1	965	Necessary for association with actin (By similarity).|Necessary for interaction with RASSF1 isoform A and isoform C.|Necessary for association with microtubules.				apoptosis|brain development|microtubule bundle formation|mitochondrion transport along microtubule|neuron projection morphogenesis	cytosol|dendrite|microtubule|neuronal cell body|nucleus|perinuclear region of cytoplasm|spindle|synapse	actin filament binding|beta-tubulin binding|DNA binding|microtubule binding			central_nervous_system(1)	1														0.4	16.24678	16.377955	6	9	GG		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	17705106	17705106	9617	19	G	T	T	45	45	MAP1S	T	5	3
ZNF98	148198	broad.mit.edu	36	19	22366302	22366302	+	Missense_Mutation	SNP	T	A	A			TCGA-06-0750-01	TCGA-06-0750-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr19:22366302T>A	uc002nqt.2	-	c.1575A>T	c.(1573-1575)AAA>AAT	p.K525N		NM_001098626	NP_001092096	A6NK75	ZNF98_HUMAN	zinc finger protein 98	525	C2H2-type 13.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1		all_cancers(12;0.0536)|all_lung(12;0.00187)|Lung NSC(12;0.0019)|all_epithelial(12;0.00542)|Hepatocellular(1079;0.244)												0.275862	40.681111	43.300821	16	42	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	22366302	22366302	18807	19	T	A	A	56	56	ZNF98	A	4	4
C1orf187	374946	broad.mit.edu	36	1	11688912	11688912	+	Missense_Mutation	SNP	C	G	G			TCGA-06-0750-01	TCGA-06-0750-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:11688912C>G	uc001asr.1	+	c.10C>G	c.(10-12)CCT>GCT	p.P4A		NM_198545	NP_940947	Q8NBI3	DRAXI_HUMAN	chromosome 1 open reading frame 187	4					axon guidance|commissural neuron differentiation in spinal cord|dorsal spinal cord development|forebrain development|negative regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway	extracellular region					0	Ovarian(185;0.249)	Lung NSC(185;4.15e-05)|all_lung(284;4.76e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00826)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)												0.291667	9.293427	10.248392	7	17	CC		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.48e-06)|COAD - Colon adenocarcinoma(227;0.000283)|BRCA - Breast invasive adenocarcinoma(304;0.000316)|Kidney(185;0.000841)|KIRC - Kidney renal clear cell carcinoma(229;0.00269)|STAD - Stomach adenocarcinoma(313;0.00754)|READ - Rectum adenocarcinoma(331;0.0651)	Missense_Mutation	SNP	11688912	11688912	2089	1	C	G	G	26	26	C1orf187	G	3	3
SCNN1D	6339	broad.mit.edu	36	1	1212194	1212194	+	Silent	SNP	C	T	T			TCGA-06-0750-01	TCGA-06-0750-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:1212194C>T	uc001adu.1	+	c.603C>T	c.(601-603)AGC>AGT	p.S201S	SCNN1D_uc001adt.1_Silent_p.S365S|SCNN1D_uc001adx.2_5'UTR|SCNN1D_uc001adv.1_Silent_p.S201S|SCNN1D_uc001adw.1_Silent_p.S267S	NM_002978	NP_002969	P51172	SCNND_HUMAN	sodium channel, nonvoltage-gated 1, delta	201	Extracellular (By similarity).				response to stimulus|sensory perception of taste	integral to membrane	ligand-gated sodium channel activity|protein binding				0	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)			Amiloride(DB00594)|Triamterene(DB00384)									0.468354	109.7162	109.779494	37	42	CC		KEEP	---	---	---	---	capture		Epithelial(90;3.01e-35)|OV - Ovarian serous cystadenocarcinoma(86;2.46e-21)|Colorectal(212;0.000157)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00229)|BRCA - Breast invasive adenocarcinoma(365;0.00251)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.034)|Lung(427;0.199)	Silent	SNP	1212194	1212194	14411	1	C	T	T	26	26	SCNN1D	T	2	2
FLG	2312	broad.mit.edu	36	1	150548013	150548013	+	Silent	SNP	C	T	T			TCGA-06-0750-01	TCGA-06-0750-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:150548013C>T	uc001ezu.1	-	c.5973G>A	c.(5971-5973)GCG>GCA	p.A1991A		NM_002016	NP_002007	P20930	FILA_HUMAN	filaggrin	1991	Ser-rich.				keratinocyte differentiation	cytoplasmic membrane-bounded vesicle|intermediate filament	calcium ion binding|structural molecule activity			ovary(9)	9	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)													0.24866	518.093405	571.705306	232	701	CC		KEEP	---	---	---	---	capture	LUSC - Lung squamous cell carcinoma(543;0.206)		Silent	SNP	150548013	150548013	6160	1	C	T	T	19	19	FLG	T	1	1
ARHGEF2	9181	broad.mit.edu	36	1	154194296	154194296	+	Missense_Mutation	SNP	T	C	C			TCGA-06-0750-01	TCGA-06-0750-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr1:154194296T>C	uc001fmu.1	-	c.1679A>G	c.(1678-1680)GAC>GGC	p.D560G	ARHGEF2_uc001fmr.1_Missense_Mutation_p.D488G|ARHGEF2_uc001fms.1_Missense_Mutation_p.D515G|ARHGEF2_uc001fmt.1_Missense_Mutation_p.D516G	NM_004723	NP_004714	Q92974	ARHG2_HUMAN	rho/rac guanine nucleotide exchange factor 2	516	PH.				actin filament organization|apoptosis|cell division|cell morphogenesis|induction of apoptosis by extracellular signals|intracellular protein transport|mitosis|negative regulation of microtubule depolymerization|nerve growth factor receptor signaling pathway|positive regulation of NF-kappaB transcription factor activity|regulation of cell proliferation|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|Golgi apparatus|microtubule|ruffle membrane|spindle|tight junction	microtubule binding|Rac GTPase binding|Rac guanyl-nucleotide exchange factor activity|zinc ion binding			ovary(1)	1	Hepatocellular(266;0.133)|all_hematologic(923;0.145)|all_neural(408;0.195)					Melanoma(178;35 2768 6610 28839)								0.315789	9.374317	9.989034	6	13	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	154194296	154194296	917	1	T	C	C	58	58	ARHGEF2	C	4	4
KLHL20	27252	broad.mit.edu	36	1	172011567	172011567	+	Missense_Mutation	SNP	G	T	T			TCGA-06-0750-01	TCGA-06-0750-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:172011567G>T	uc001gjc.1	+	c.1601G>T	c.(1600-1602)TGG>TTG	p.W534L	KLHL20_uc009wwf.1_Missense_Mutation_p.W516L	NM_014458	NP_055273	Q9Y2M5	KLH20_HUMAN	kelch-like 20	534	Kelch 5.				cytoskeleton organization|negative regulation of apoptosis|proteasomal ubiquitin-dependent protein catabolic process|response to interferon-alpha	actin cytoskeleton|cell surface|Cul3-RING ubiquitin ligase complex|Golgi apparatus|perinuclear region of cytoplasm|PML body	actin binding|interferon-gamma binding|ubiquitin-protein ligase activity			ovary(1)	1						GBM(159;862 2695 6559 23041)								0.306122	119.314192	124.245187	45	102	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	172011567	172011567	8687	1	G	T	T	47	47	KLHL20	T	3	3
KIF21B	23046	broad.mit.edu	36	1	199224285	199224285	+	Nonsense_Mutation	SNP	G	T	T			TCGA-06-0750-01	TCGA-06-0750-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:199224285G>T	uc001gvs.1	-	c.3309C>A	c.(3307-3309)TAC>TAA	p.Y1103*	KIF21B_uc001gvr.1_Nonsense_Mutation_p.Y1103*|KIF21B_uc009wzl.1_Nonsense_Mutation_p.Y1103*	NM_017596	NP_060066	O75037	KI21B_HUMAN	kinesin family member 21B	1103					microtubule-based movement	cytoplasm|microtubule	ATP binding|microtubule motor activity			ovary(3)	3														0.25	7.643198	8.804182	5	15	GG		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	199224285	199224285	8600	1	G	T	T	40	40	KIF21B	T	5	3
IRF6	3664	broad.mit.edu	36	1	208028592	208028592	+	Silent	SNP	C	G	G			TCGA-06-0750-01	TCGA-06-0750-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:208028592C>G	uc001hhq.1	-	c.1200G>C	c.(1198-1200)CGG>CGC	p.R400R	IRF6_uc009xct.1_Silent_p.R400R	NM_006147	NP_006138	O14896	IRF6_HUMAN	interferon regulatory factor 6	400					cell cycle arrest|interferon-gamma-mediated signaling pathway|mammary gland epithelial cell differentiation|negative regulation of cell proliferation|positive regulation of transcription, DNA-dependent|type I interferon-mediated signaling pathway	cytoplasm|nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			ovary(2)	2														0.235294	8.592063	9.681299	4	13	CC		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(81;0.0351)	Silent	SNP	208028592	208028592	8137	1	C	G	G	30	30	IRF6	G	3	3
SYDE2	84144	broad.mit.edu	36	1	85428608	85428608	+	Missense_Mutation	SNP	C	A	A			TCGA-06-0750-01	TCGA-06-0750-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:85428608C>A	uc009wcm.1	-	c.1161G>T	c.(1159-1161)TTG>TTT	p.L387F	SYDE2_uc001dku.2_Missense_Mutation_p.L387F	NM_032184	NP_115560	Q5VT97	SYDE2_HUMAN	synapse defective 1, Rho GTPase, homolog 2	387					activation of Rho GTPase activity|small GTPase mediated signal transduction	cytosol	Rho GTPase activator activity			ovary(1)|central_nervous_system(1)	2														0.107143	6.909214	19.779128	9	75	CC		KEEP	---	---	---	---	capture		all cancers(265;0.0126)|Epithelial(280;0.0336)	Missense_Mutation	SNP	85428608	85428608	15957	1	C	A	A	29	29	SYDE2	A	3	3
C20orf185	359710	broad.mit.edu	36	20	31120315	31120315	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0750-01	TCGA-06-0750-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr20:31120315C>T	uc002wym.1	+	c.1024C>T	c.(1024-1026)CGG>TGG	p.R342W		NM_182658	NP_872599	P59826	LPLC3_HUMAN	antimicrobial peptide RYA3	342					innate immune response	cytoplasm|extracellular region	lipid binding|protein binding			ovary(4)	4														0.306306	84.099623	87.818945	34	77	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	31120315	31120315	2175	20	C	T	T	27	27	C20orf185	T	1	1
PHF20	51230	broad.mit.edu	36	20	33950768	33950768	+	Missense_Mutation	SNP	G	T	T			TCGA-06-0750-01	TCGA-06-0750-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr20:33950768G>T	uc002xek.1	+	c.1345G>T	c.(1345-1347)GAC>TAC	p.D449Y	PHF20_uc002xei.1_Missense_Mutation_p.D449Y|PHF20_uc010gfo.1_Missense_Mutation_p.D449Y|PHF20_uc002xej.1_Missense_Mutation_p.D333Y	NM_016436	NP_057520	Q9BVI0	PHF20_HUMAN	PHD finger protein 20	449					regulation of transcription, DNA-dependent|transcription, DNA-dependent	MLL1 complex	DNA binding|zinc ion binding			ovary(1)	1	Breast(12;0.00631)|all_lung(11;0.0145)													0.258824	52.406818	56.888582	22	63	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	33950768	33950768	12254	20	G	T	T	33	33	PHF20	T	3	3
TMPRSS3	64699	broad.mit.edu	36	21	42676249	42676249	+	Silent	SNP	C	T	T			TCGA-06-0750-01	TCGA-06-0750-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr21:42676249C>T	uc002zbb.1	-	c.744G>A	c.(742-744)ACG>ACA	p.T248T	TMPRSS3_uc002zay.1_5'UTR|TMPRSS3_uc002zaz.1_Silent_p.T121T|TMPRSS3_uc002zba.1_Silent_p.T121T|TMPRSS3_uc002zbc.1_Silent_p.T248T|TMPRSS3_uc002zbd.1_Silent_p.T248T	NM_024022	NP_115780	P57727	TMPS3_HUMAN	transmembrane protease, serine 3 isoform 1	248	Peptidase S1.|Extracellular (Potential).				cellular sodium ion homeostasis|proteolysis	endoplasmic reticulum membrane|integral to membrane	scavenger receptor activity|serine-type endopeptidase activity|sodium channel regulator activity			ovary(2)|breast(1)	3														0.316456	60.043132	62.41231	25	54	CC		KEEP	---	---	---	---	capture			Silent	SNP	42676249	42676249	16789	21	C	T	T	27	27	TMPRSS3	T	1	1
GGT5	2687	broad.mit.edu	36	22	22952188	22952188	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0750-01	TCGA-06-0750-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr22:22952188C>T	uc002zzp.2	-	c.1085G>A	c.(1084-1086)CGC>CAC	p.R362H	GGT5_uc002zzo.2_Missense_Mutation_p.R362H|GGT5_uc002zzr.2_Missense_Mutation_p.R330H|GGT5_uc002zzq.2_Missense_Mutation_p.R330H	NM_001099781	NP_001093251	P36269	GGT5_HUMAN	gamma-glutamyltransferase 5 isoform a	362	Extracellular (Potential).				glutathione biosynthetic process|hormone biosynthetic process|leukotriene biosynthetic process|prostanoid metabolic process	integral to membrane|plasma membrane	acyltransferase activity|gamma-glutamyltransferase activity			ovary(2)	2														0.356164	69.12633	70.457937	26	47	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	22952188	22952188	6630	22	C	T	T	27	27	GGT5	T	1	1
SMCR7L	54471	broad.mit.edu	36	22	38239698	38239698	+	Silent	SNP	C	G	G			TCGA-06-0750-01	TCGA-06-0750-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr22:38239698C>G	uc003axw.2	+	c.816C>G	c.(814-816)GGC>GGG	p.G272G	SMCR7L_uc010gxz.1_Silent_p.G94G|SMCR7L_uc003axx.1_Silent_p.G272G|SMCR7L_uc003axy.1_Silent_p.G94G	NM_019008	NP_061881	Q9NQG6	SMC7L_HUMAN	hypothetical protein LOC54471	272						integral to membrane|mitochondrion				central_nervous_system(1)	1	Melanoma(58;0.04)											OREG0026577	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.222222	9.656898	12.375537	8	28	CC		KEEP	---	---	---	---	capture			Silent	SNP	38239698	38239698	15289	22	C	G	G	28	28	SMCR7L	G	3	3
GPR17	2840	broad.mit.edu	36	2	128124850	128124850	+	Missense_Mutation	SNP	G	T	T			TCGA-06-0750-01	TCGA-06-0750-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:128124850G>T	uc002tpc.1	+	c.155G>T	c.(154-156)GGC>GTC	p.G52V	LIMS2_uc002tow.1_5'Flank|LIMS2_uc002tox.1_Intron|LIMS2_uc010fmb.1_Intron|LIMS2_uc002toy.1_Intron|LIMS2_uc002toz.1_Intron|LIMS2_uc002tpa.1_Intron|LIMS2_uc002tpb.1_Intron|GPR17_uc002tpd.1_Missense_Mutation_p.G24V	NM_005291	NP_005282	Q13304	GPR17_HUMAN	G protein-coupled receptor 17	52	Extracellular (Potential).					integral to plasma membrane	chemokine receptor activity|purinergic nucleotide receptor activity, G-protein coupled				0	Colorectal(110;0.1)	Ovarian(717;0.15)										OREG0014966	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.368932	205.656341	208.761682	76	130	GG		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(221;0.0677)	Missense_Mutation	SNP	128124850	128124850	6942	2	G	T	T	42	42	GPR17	T	3	3
FAM123C	205147	broad.mit.edu	36	2	131238179	131238179	+	Silent	SNP	C	T	T			TCGA-06-0750-01	TCGA-06-0750-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:131238179C>T	uc002trw.2	+	c.2064C>T	c.(2062-2064)AAC>AAT	p.N688N	FAM123C_uc010fms.1_Silent_p.N688N|FAM123C_uc010fmt.1_Silent_p.N688N|FAM123C_uc010fmu.1_Silent_p.N688N|FAM123C_uc010fmv.1_Silent_p.N688N	NM_152698	NP_689911	Q8N944	F123C_HUMAN	hypothetical protein LOC205147	688										pancreas(2)|ovary(1)	3	Colorectal(110;0.1)													0.386364	46.598535	47.08406	17	27	CC		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(221;0.13)	Silent	SNP	131238179	131238179	5621	2	C	T	T	19	19	FAM123C	T	1	1
ANKRD36B	57730	broad.mit.edu	36	2	97515216	97515216	+	Missense_Mutation	SNP	T	G	G			TCGA-06-0750-01	TCGA-06-0750-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr2:97515216T>G	uc002sxy.1	-	c.1559A>C	c.(1558-1560)AAC>ACC	p.N520T	ANKRD36B_uc010fie.1_Missense_Mutation_p.N164T	NM_025190	NP_079466	Q8N2N9	AN36B_HUMAN	ankyrin repeat domain 36B	752	Potential.										0														0.555556	6.888463	6.892119	5	4	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	97515216	97515216	674	2	T	G	G	60	60	ANKRD36B	G	4	4
IL1RAP	3556	broad.mit.edu	36	3	191844764	191844764	+	Missense_Mutation	SNP	G	T	T			TCGA-06-0750-01	TCGA-06-0750-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:191844764G>T	uc003fsq.2	+	c.1085G>T	c.(1084-1086)TGT>TTT	p.C362F	IL1RAP_uc003fsm.1_Missense_Mutation_p.C362F|IL1RAP_uc010hzg.1_Missense_Mutation_p.C362F|IL1RAP_uc003fsn.1_Non-coding_Transcript|IL1RAP_uc003fso.1_Missense_Mutation_p.C362F|IL1RAP_uc003fsp.1_Non-coding_Transcript	NM_134470	NP_608273	Q9NPH3	IL1AP_HUMAN	interleukin 1 receptor accessory protein isoform	362	Extracellular (Potential).				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.C362F(HS737.T-Tumor)|p.C362F(8305C-Tumor)|p.C362F(CADOES1-Tumor)	227				0.166667	7.818842	14.340481	10	50	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	191844764	191844764	7961	3	G	T	T	48	48	IL1RAP	T	3	3
LRBA	987	broad.mit.edu	36	4	152155236	152155236	+	Missense_Mutation	SNP	G	T	T			TCGA-06-0750-01	TCGA-06-0750-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr4:152155236G>T	uc010ipj.1	-	c.9C>A	c.(7-9)AGC>AGA	p.S3R	LRBA_uc003ilu.2_Missense_Mutation_p.S3R|LRBA_uc003ilx.1_Missense_Mutation_p.S3R|LRBA_uc003ily.2_3'UTR	NM_006726	NP_006717	P50851	LRBA_HUMAN	LPS-responsive vesicle trafficking, beach and	3						endoplasmic reticulum|Golgi apparatus|integral to membrane|lysosome|plasma membrane	protein binding			ovary(3)|breast(3)	6	all_hematologic(180;0.151)													0.5	10.498782	10.498782	4	4	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	152155236	152155236	9304	4	G	T	T	38	38	LRBA	T	3	3
TMEM144	55314	broad.mit.edu	36	4	159355839	159355839	+	Silent	SNP	C	G	G			TCGA-06-0750-01	TCGA-06-0750-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:159355839C>G	uc003ipx.1	+	c.156C>G	c.(154-156)GCC>GCG	p.A52A	TMEM144_uc010iqi.1_Non-coding_Transcript	NM_018342	NP_060812	Q7Z5S9	TM144_HUMAN	transmembrane protein 144	52	Helical; (Potential).					integral to membrane					0	all_hematologic(180;0.24)	Renal(120;0.0854)												0.34375	152.869535	156.323151	55	105	CC		KEEP	---	---	---	---	capture		COAD - Colon adenocarcinoma(41;0.0539)	Silent	SNP	159355839	159355839	16590	4	C	G	G	24	24	TMEM144	G	3	3
NPFFR2	10886	broad.mit.edu	36	4	73232141	73232141	+	Silent	SNP	C	T	T			TCGA-06-0750-01	TCGA-06-0750-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:73232141C>T	uc003hgg.1	+	c.1317C>T	c.(1315-1317)AAC>AAT	p.N439N	NPFFR2_uc010iig.1_Silent_p.N221N|NPFFR2_uc003hgh.1_Silent_p.N337N|NPFFR2_uc003hgi.1_Silent_p.N340N|NPFFR2_uc003hgj.1_Non-coding_Transcript	NM_004885	NP_444264	Q9Y5X5	NPFF2_HUMAN	neuropeptide FF receptor 2 isoform 1	439	Cytoplasmic (Potential).				detection of abiotic stimulus	actin cytoskeleton|integral to plasma membrane	neuropeptide receptor activity			ovary(2)|central_nervous_system(1)	3														0.303191	150.213414	156.707617	57	131	CC		KEEP	---	---	---	---	capture	Lung(101;0.0935)|LUSC - Lung squamous cell carcinoma(112;0.138)		Silent	SNP	73232141	73232141	10982	4	C	T	T	19	19	NPFFR2	T	1	1
FSTL4	23105	broad.mit.edu	36	5	132562935	132562935	+	Missense_Mutation	SNP	G	T	T			TCGA-06-0750-01	TCGA-06-0750-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:132562935G>T	uc003kyn.1	-	c.2280C>A	c.(2278-2280)GAC>GAA	p.D760E	FSTL4_uc003kym.1_Missense_Mutation_p.D409E	NM_015082	NP_055897	Q6MZW2	FSTL4_HUMAN	follistatin-like 4	760						extracellular region	calcium ion binding			central_nervous_system(1)	1		all_cancers(142;0.244)												0.356436	98.081961	99.911084	36	65	GG		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)		Missense_Mutation	SNP	132562935	132562935	6330	5	G	T	T	44	44	FSTL4	T	3	3
ARHGAP26	23092	broad.mit.edu	36	5	142261750	142261750	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0750-01	TCGA-06-0750-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:142261750G>A	uc003lmu.1	+	c.664G>A	c.(664-666)GGG>AGG	p.G222R	ARHGAP26_uc003lmt.1_Missense_Mutation_p.G222R	NM_015071	NP_055886	Q9UNA1	RHG26_HUMAN	GTPase regulator associated with the focal	222					actin cytoskeleton organization|filopodium assembly|nervous system development|small GTPase mediated signal transduction	cytoskeleton|cytosol|focal adhesion	cytoskeletal adaptor activity|Rho GTPase activator activity|SH3 domain binding			ovary(1)	1		all_hematologic(541;0.0416)								831				0.163636	52.433156	70.156969	27	138	GG		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		Missense_Mutation	SNP	142261750	142261750	887	5	G	A	A	39	39	ARHGAP26	A	1	1
PIK3R1	5295	broad.mit.edu	36	5	67627002	67627002	+	Splice_Site_SNP	SNP	A	G	G			TCGA-06-0750-01	TCGA-06-0750-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr5:67627002A>G	uc003jva.1	+	c.1746_splice	c.e14-2	p.M582_splice	PIK3R1_uc003jvb.1_Splice_Site_SNP_p.M582_splice|PIK3R1_uc003jvc.1_Splice_Site_SNP_p.M282_splice|PIK3R1_uc003jvd.1_Splice_Site_SNP_p.M312_splice|PIK3R1_uc003jve.1_Splice_Site_SNP_p.M261_splice	NM_181523	NP_852664			phosphoinositide-3-kinase, regulatory subunit 1						epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|growth hormone receptor signaling pathway|insulin receptor signaling pathway|insulin-like growth factor receptor signaling pathway|interspecies interaction between organisms|leukocyte migration|nerve growth factor receptor signaling pathway|phosphatidylinositol 3-kinase cascade|phosphatidylinositol phosphorylation|phosphatidylinositol-mediated signaling|platelet activation|positive regulation of establishment of protein localization in plasma membrane|positive regulation of glucose import|T cell costimulation|T cell receptor signaling pathway	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex	1-phosphatidylinositol binding|ErbB-3 class receptor binding|insulin binding|insulin receptor binding|insulin receptor substrate binding|insulin-like growth factor receptor binding|phosphatidylinositol 3-kinase regulator activity|protein phosphatase binding	p.?(2)|p.Y580fs*1(1)		endometrium(34)|central_nervous_system(27)|large_intestine(20)|breast(5)|ovary(5)|haematopoietic_and_lymphoid_tissue(3)|lung(2)|urinary_tract(1)|skin(1)|pancreas(1)	99		Lung NSC(167;1.99e-05)|Prostate(74;0.00308)|Ovarian(174;0.00473)|Colorectal(97;0.0176)			Isoproterenol(DB01064)				(ONCODG1-Tumor)|(NIHOVCAR3-Tumor)|(OV56-Tumor)|(PF382-Tumor)	370	TCGA GBM(4;<1E-8)			0.346154	75.576897	77.217934	27	51	AA		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(47;3.76e-51)|Lung(70;0.0211)	Splice_Site_SNP	SNP	67627002	67627002	12342	5	A	G	G	7	7	PIK3R1	G	5	4
SNX14	57231	broad.mit.edu	36	6	86310195	86310195	+	Nonsense_Mutation	SNP	C	A	A			TCGA-06-0750-01	TCGA-06-0750-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:86310195C>A	uc003pkr.1	-	c.1111G>T	c.(1111-1113)GAA>TAA	p.E371*	SNX14_uc003pkp.1_Nonsense_Mutation_p.E234*|SNX14_uc003pkq.1_5'UTR|SNX14_uc003pks.1_Nonsense_Mutation_p.E327*|SNX14_uc003pkt.1_Nonsense_Mutation_p.E371*	NM_153816	NP_722523	Q9Y5W7	SNX14_HUMAN	sorting nexin 14 isoform a	371	RGS.				cell communication|protein transport	integral to membrane	phosphatidylinositol binding|signal transducer activity				0		all_cancers(76;4.83e-07)|Acute lymphoblastic leukemia(125;3.3e-08)|Prostate(29;2.55e-07)|all_hematologic(105;3.66e-05)|all_epithelial(107;0.000695)|Lung NSC(302;0.197)|all_lung(197;0.24)												0.342857	30.487534	31.251923	12	23	CC		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(108;0.0423)	Nonsense_Mutation	SNP	86310195	86310195	15385	6	C	A	A	30	30	SNX14	A	5	3
BPGM	669	broad.mit.edu	36	7	133997263	133997263	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0750-01	TCGA-06-0750-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:133997263C>T	uc003vrv.1	+	c.464C>T	c.(463-465)TCG>TTG	p.S155L	BPGM_uc003vrw.1_Missense_Mutation_p.S155L|BPGM_uc003vrx.1_Missense_Mutation_p.S155L	NM_199186	NP_954655	P07738	PMGE_HUMAN	2,3-bisphosphoglycerate mutase	155					glycolysis|respiratory gaseous exchange		2,3-bisphospho-D-glycerate 2-phosphohydrolase activity|bisphosphoglycerate mutase activity|phosphoglycerate mutase activity				0														0.171233	48.889403	63.80536	25	121	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	133997263	133997263	1516	7	C	T	T	31	31	BPGM	T	1	1
MICALL2	79778	broad.mit.edu	36	7	1451075	1451075	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0750-01	TCGA-06-0750-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:1451075G>C	uc003skj.2	-	c.1157C>G	c.(1156-1158)GCT>GGT	p.A386G	MICALL2_uc003ski.2_5'Flank	NM_182924	NP_891554	Q8IY33	MILK2_HUMAN	MICAL-like 2 isoform 1	386						cytoplasm|cytoskeleton	zinc ion binding			central_nervous_system(1)	1		Ovarian(82;0.0253)												0.375	6.444187	6.545323	3	5	GG		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (27;0.0178)|OV - Ovarian serous cystadenocarcinoma(56;6.01e-15)	Missense_Mutation	SNP	1451075	1451075	9964	7	G	C	C	34	34	MICALL2	C	3	3
EGFR	1956	broad.mit.edu	36	7	55189315	55189316	+	Missense_Mutation	DNP	GC	AA	AA			TCGA-06-0750-01	TCGA-06-0750-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:55189315_55189316GC>AA	uc003tqk.1	+	c.865_866GC>AA	c.(865-867)GCC>AAC	p.A289N	EGFR_uc003tqh.1_Missense_Mutation_p.A289N|EGFR_uc003tqi.1_Missense_Mutation_p.A289N|EGFR_uc003tqj.1_Missense_Mutation_p.A289N|EGFR_uc010kzg.1_Missense_Mutation_p.A244N	NM_005228	NP_005219	P00533	EGFR_HUMAN	epidermal growth factor receptor isoform a	289	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.A289V(20)|p.V30_R297>G(10)|p.A289T(3)|p.A289D(3)		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	p.A289V(HEC6-Tumor)|p.A289D(HS683-Tumor)|p.A289V(RL952-Tumor)	608	TCGA GBM(3;<1E-8)|TSP Lung(4;<1E-8)			0.132845	123.628917	248.850256	127	829	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	DNP	55189315	55189316	5156	7	GC	AA	AA	46	46	EGFR	AA	2	2
EGFR	1956	broad.mit.edu	36	7	55200531	55200531	+	Missense_Mutation	SNP	C	G	G			TCGA-06-0750-01	TCGA-06-0750-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:55200531C>G	uc003tqk.1	+	c.1787C>G	c.(1786-1788)CCG>CGG	p.P596R	EGFR_uc003tqi.1_Missense_Mutation_p.P596R|EGFR_uc003tqj.1_Missense_Mutation_p.P596R|EGFR_uc010kzg.1_Missense_Mutation_p.P551R|EGFR_uc003tqn.1_Non-coding_Transcript	NM_005228	NP_005219	P00533	EGFR_HUMAN	epidermal growth factor receptor isoform a	596	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.P596L(2)		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)			0.252298	619.854195	674.384988	247	732	CC		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	55200531	55200531	5156	7	C	G	G	23	23	EGFR	G	3	3
PUF60	22827	broad.mit.edu	36	8	144971776	144971776	+	Missense_Mutation	SNP	C	G	G			TCGA-06-0750-01	TCGA-06-0750-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr8:144971776C>G	uc003yzs.1	-	c.982G>C	c.(982-984)GCA>CCA	p.A328P	SCRIB_uc003yzo.1_5'Flank|SCRIB_uc003yzp.1_5'Flank|PUF60_uc003yzq.1_Missense_Mutation_p.A285P|PUF60_uc003yzr.1_Missense_Mutation_p.A268P|PUF60_uc003yzt.1_Missense_Mutation_p.A311P|PUF60_uc003yzu.1_Missense_Mutation_p.A317P	NM_078480	NP_510965	Q9UHX1	PUF60_HUMAN	poly-U binding splicing factor 60KDa isoform a	328	Ala-rich.|Inhibits homodimerization.|Inhibits transcriptional repression, interaction with ERCC3 and apoptosis induction.				apoptosis|mRNA processing|regulation of transcription, DNA-dependent|RNA splicing|transcription, DNA-dependent	nucleus|ribonucleoprotein complex	DNA binding|nucleotide binding|protein binding|RNA binding				0	all_cancers(97;2.31e-11)|all_epithelial(106;1.58e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)													0.384615	8.277528	8.458691	5	8	CC		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;1.23e-39)|all cancers(56;6.82e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.18)		Missense_Mutation	SNP	144971776	144971776	13282	8	C	G	G	25	25	PUF60	G	3	3
ZNF704	619279	broad.mit.edu	36	8	81762184	81762184	+	Nonsense_Mutation	SNP	G	T	T			TCGA-06-0750-01	TCGA-06-0750-01	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)	0.291667	16.561096	17.467934	7	17	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
SLC34A3	142680	broad.mit.edu	36	9	139248782	139248782	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0750-01	TCGA-06-0750-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr9:139248782C>T	uc004cme.1	+	c.1187C>T	c.(1186-1188)ACG>ATG	p.T396M	SLC34A3_uc004cmf.1_Missense_Mutation_p.T396M	NM_080877	NP_543153	Q8N130	NPT2C_HUMAN	solute carrier family 34 (sodium phosphate),	396	Extracellular (Potential).				cellular phosphate ion homeostasis	apical plasma membrane|integral to membrane	sodium-dependent phosphate transmembrane transporter activity|sodium:phosphate symporter activity				0	all_cancers(76;0.0926)													0.425532	56.091739	56.319076	20	27	CC		KEEP	---	---	---	---	capture	STAD - Stomach adenocarcinoma(284;0.0698)	OV - Ovarian serous cystadenocarcinoma(145;6.37e-05)|Epithelial(140;0.00057)	Missense_Mutation	SNP	139248782	139248782	15066	9	C	T	T	19	19	SLC34A3	T	1	1
DMD	1756	broad.mit.edu	36	X	32573009	32573009	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0750-01	TCGA-06-0750-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:32573009G>C	uc004dda.1	-	c.1142C>G	c.(1141-1143)ACT>AGT	p.T381S	DMD_uc004dcz.2_Missense_Mutation_p.T258S|DMD_uc004dcy.1_Missense_Mutation_p.T377S|DMD_uc004ddb.1_Missense_Mutation_p.T373S|DMD_uc010ngo.1_Intron|DMD_uc004ddf.2_Missense_Mutation_p.T373S|DMD_uc010ngp.1_Intron|DMD_uc010ngq.1_Intron|DMD_uc010ngr.1_Missense_Mutation_p.T92S	NM_004006	NP_004001	P11532	DMD_HUMAN	dystrophin Dp427m isoform	381	Spectrin 1.				muscle filament sliding|peptide biosynthetic process	cell surface|costamere|cytoskeleton|cytosol|dystrophin-associated glycoprotein complex|sarcolemma	actin binding|dystroglycan binding|nitric-oxide synthase binding|protein binding|structural constituent of cytoskeleton|structural constituent of muscle|zinc ion binding			ovary(3)|pancreas(2)|large_intestine(1)	6		all_cancers(2;1.22e-16)|Acute lymphoblastic leukemia(2;4.65e-06)|all_hematologic(2;0.00108)|all_epithelial(3;0.00626)|all_neural(2;0.0189)|all_lung(315;0.182)|Glioma(3;0.203)												0.125	13.521691	23.415174	9	63	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	32573009	32573009	4760	23	G	C	C	36	36	DMD	C	3	3
PCDH11Y	83259	broad.mit.edu	36	Y	5028500	5028500	+	Missense_Mutation	SNP	A	G	G			TCGA-06-0750-01	TCGA-06-0750-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chrY:5028500A>G	uc004fqo.1	+	c.2881A>G	c.(2881-2883)AAG>GAG	p.K961E	PCDH11Y_uc010nwg.1_Missense_Mutation_p.K950E|PCDH11Y_uc004fql.1_Missense_Mutation_p.K950E|PCDH11Y_uc004fqm.1_Missense_Mutation_p.K950E|PCDH11Y_uc004fqn.1_Missense_Mutation_p.K961E|PCDH11Y_uc004fqp.1_Missense_Mutation_p.K732E	NM_032973	NP_116755	Q9BZA8	PC11Y_HUMAN	protocadherin 11 Y-linked isoform c	961	Cytoplasmic (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding				0														0.15748	30.814217	45.03384	20	107	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	5028500	5028500	11929	24	A	G	G	5	5	PCDH11Y	G	4	4
C21orf58	54058	broad.mit.edu	36	21	46546413	46546414	+	In_Frame_Ins	INS	-	TGG	TGG			TCGA-06-0750-01	TCGA-06-0750-01										Phase_I	Unspecified				Illumina GAIIx	g.chr21:46546413_46546414insTGG	uc002zjf.1	-	c.896_897insCCA	c.(895-897)CAT>CACCAT	p.299_299H>HH	C21orf58_uc002ziz.2_Intron|C21orf58_uc002zja.2_In_Frame_Ins_p.193_193H>HH|C21orf58_uc002zjc.1_In_Frame_Ins_p.193_193H>HH|C21orf58_uc010gqj.1_Non-coding_Transcript	NM_058180	NP_478060	P58505	CU058_HUMAN	hypothetical protein LOC54058	299	Poly-His.									pancreas(1)	1	Breast(49;0.112)			Colorectal(79;0.239)										0.33			2	4				---	---	---	---	capture_indel			In_Frame_Ins	INS	46546413	46546414	2209	21	-	TGG	TGG	8	8	C21orf58	TGG	5	5
