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
ITIH5	80760	broad.mit.edu	36	10	7699115	7699115	+	Missense_Mutation	SNP	G	T	T			TCGA-32-1970-01	TCGA-32-1970-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr10:7699115G>T	uc001ijq.1	-	c.789C>A	c.(787-789)GAC>GAA	p.D263E	ITIH5_uc001ijr.1_Missense_Mutation_p.D263E|ITIH5_uc001ijp.1_Missense_Mutation_p.D49E	NM_030569	NP_085046	Q86UX2	ITIH5_HUMAN	inter-alpha trypsin inhibitor heavy chain	263					hyaluronan metabolic process	extracellular region	serine-type endopeptidase inhibitor activity			ovary(2)|central_nervous_system(2)	4														0.772414	400.879744	410.756594	112	33	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	7699115	7699115	8211	10	G	T	T	40	40	ITIH5	T	3	3
CYP2C18	1562	broad.mit.edu	36	10	96437607	96437607	+	Silent	SNP	C	T	T			TCGA-32-1970-01	TCGA-32-1970-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr10:96437607C>T	uc001kjv.2	+	c.259C>T	c.(259-261)CTG>TTG	p.L87L	CYP2C18_uc001kjw.2_Silent_p.L87L|CYP2C19_uc009xus.1_5'Flank|CYP2C19_uc001kjx.1_5'Flank	NM_000772	NP_000763	P33260	CP2CI_HUMAN	cytochrome P450 family 2 subfamily C polypeptide	87					oxidation-reduction process|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	aromatase activity|electron carrier activity|heme binding|oxygen binding			ovary(3)|lung(1)	4		Colorectal(252;0.09)												0.745665	454.754169	464.225283	129	44	CC		KEEP	---	---	---	---	capture		all cancers(201;2.8e-06)|KIRC - Kidney renal clear cell carcinoma(50;0.0646)|Kidney(138;0.0805)	Silent	SNP	96437607	96437607	4330	10	C	T	T	24	24	CYP2C18	T	2	2
CWF19L2	143884	broad.mit.edu	36	11	106705901	106705901	+	Missense_Mutation	SNP	C	T	T			TCGA-32-1970-01	TCGA-32-1970-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:106705901C>T	uc001pjj.2	-	c.2032G>A	c.(2032-2034)GCC>ACC	p.A678T	CWF19L2_uc001pjh.2_Non-coding_Transcript|CWF19L2_uc009yxo.1_Non-coding_Transcript	NM_152434	NP_689647	Q2TBE0	C19L2_HUMAN	CWF19-like 2, cell cycle control	832							catalytic activity				0		Melanoma(852;1.75e-05)|all_epithelial(67;6.27e-05)|Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Breast(348;0.0258)												0.388889	18.819605	19.014684	7	11	CC		KEEP	---	---	---	---	capture		Epithelial(105;7.18e-06)|BRCA - Breast invasive adenocarcinoma(274;1.65e-05)|all cancers(92;1.76e-05)	Missense_Mutation	SNP	106705901	106705901	4232	11	C	T	T	25	25	CWF19L2	T	2	2
SOX6	55553	broad.mit.edu	36	11	15964422	15964422	+	Missense_Mutation	SNP	C	T	T			TCGA-32-1970-01	TCGA-32-1970-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:15964422C>T	uc001mme.1	-	c.2126G>A	c.(2125-2127)CGC>CAC	p.R709H	SOX6_uc001mmd.1_Missense_Mutation_p.R672H|SOX6_uc001mmf.1_Missense_Mutation_p.R669H|SOX6_uc001mmg.1_Missense_Mutation_p.R676H	NM_033326	NP_201583	P35712	SOX6_HUMAN	SRY (sex determining region Y)-box 6 isoform 2	696					muscle organ development	nucleus	sequence-specific DNA binding transcription factor activity			ovary(3)	3														0.198992	168.827752	202.28305	79	318	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	15964422	15964422	15455	11	C	T	T	27	27	SOX6	T	1	1
MRGPRX3	117195	broad.mit.edu	36	11	18115418	18115418	+	Silent	SNP	G	A	A			TCGA-32-1970-01	TCGA-32-1970-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:18115418G>A	uc001mnu.1	+	c.93G>A	c.(91-93)ACG>ACA	p.T31T	MRGPRX3_uc009yhg.1_Silent_p.T31T	NM_054031	NP_473372	Q96LB0	MRGX3_HUMAN	MAS-related GPR, member X3	31	Extracellular (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(1)|pancreas(1)	2														0.419672	393.256199	394.971459	128	177	GG		KEEP	---	---	---	---	capture			Silent	SNP	18115418	18115418	10161	11	G	A	A	39	39	MRGPRX3	A	1	1
MYBPC3	4607	broad.mit.edu	36	11	47316757	47316757	+	Missense_Mutation	SNP	C	T	T			TCGA-32-1970-01	TCGA-32-1970-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:47316757C>T	uc001nfa.2	-	c.2198G>A	c.(2197-2199)CGC>CAC	p.R733H		NM_000256	NP_000247	Q14896	MYPC3_HUMAN	myosin binding protein C, cardiac	732	Ig-like C2-type 5.		R -> C (in CMH4).		cardiac muscle contraction|cell adhesion|muscle filament sliding|regulation of muscle filament sliding|regulation of striated muscle contraction|ventricular cardiac muscle tissue morphogenesis	C zone|cytosol|striated muscle myosin thick filament	actin binding|ATPase activator activity|metal ion binding|myosin heavy chain binding|structural constituent of muscle|titin binding			ovary(2)|central_nervous_system(1)	3														0.442308	67.519754	67.67009	23	29	CC		KEEP	---	---	---	---	capture		Lung(87;0.176)	Missense_Mutation	SNP	47316757	47316757	10408	11	C	T	T	27	27	MYBPC3	T	1	1
OR4B1	119765	broad.mit.edu	36	11	48195541	48195541	+	Missense_Mutation	SNP	G	A	A			TCGA-32-1970-01	TCGA-32-1970-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:48195541G>A	uc001ngr.1	+	c.604G>A	c.(604-606)GGA>AGA	p.G202R		NM_001005470	NP_001005470	Q8NGF8	OR4B1_HUMAN	olfactory receptor, family 4, subfamily B,	202	Helical; Name=5; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|pancreas(1)	2														0.439759	227.641638	228.168141	73	93	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	48195541	48195541	11450	11	G	A	A	47	47	OR4B1	A	2	2
OR1S1	219959	broad.mit.edu	36	11	57738957	57738957	+	Silent	SNP	C	T	T			TCGA-32-1970-01	TCGA-32-1970-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:57738957C>T	uc001nmo.1	+	c.165C>T	c.(163-165)AAC>AAT	p.N55N		NM_001004458	NP_001004458	Q8NH92	OR1S1_HUMAN	olfactory receptor, family 1, subfamily S,	55	Helical; Name=1; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			breast(1)	1		Breast(21;0.0589)												0.35443	395.083393	402.461951	140	255	CC		KEEP	---	---	---	---	capture			Silent	SNP	57738957	57738957	11378	11	C	T	T	19	19	OR1S1	T	1	1
MS4A3	932	broad.mit.edu	36	11	59593667	59593667	+	Silent	SNP	C	T	T			TCGA-32-1970-01	TCGA-32-1970-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:59593667C>T	uc001nom.1	+	c.558C>T	c.(556-558)TGC>TGT	p.C186C	MS4A3_uc001non.1_Silent_p.C140C|MS4A3_uc001noo.1_Silent_p.C63C	NM_006138	NP_006129	Q96HJ5	MS4A3_HUMAN	membrane-spanning 4-domains, subfamily A, member	186	Helical; (Potential).					endomembrane system|integral to membrane|perinuclear region of cytoplasm	protein binding|receptor activity			ovary(2)	2		all_epithelial(135;0.245)												0.361757	395.625707	402.121017	140	247	CC		KEEP	---	---	---	---	capture			Silent	SNP	59593667	59593667	10254	11	C	T	T	27	27	MS4A3	T	1	1
POLD4	57804	broad.mit.edu	36	11	66876841	66876841	+	Missense_Mutation	SNP	G	A	A			TCGA-32-1970-01	TCGA-32-1970-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:66876841G>A	uc001okm.1	-	c.196C>T	c.(196-198)CGG>TGG	p.R66W	POLD4_uc001okn.1_Non-coding_Transcript|POLD4_uc001oko.1_Non-coding_Transcript|POLD4_uc001okp.1_3'UTR	NM_021173	NP_066996	Q9HCU8	DPOD4_HUMAN	polymerase (DNA-directed), delta 4	66					base-excision repair|DNA strand elongation involved in DNA replication|nucleotide-excision repair, DNA gap filling|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|transcription-coupled nucleotide-excision repair	nucleoplasm	DNA-directed DNA polymerase activity|protein binding				0														0.179487	24.204876	31.746289	14	64	GG		KEEP	---	---	---	---	capture	BRCA - Breast invasive adenocarcinoma(15;3.08e-06)		Missense_Mutation	SNP	66876841	66876841	12621	11	G	A	A	40	40	POLD4	A	1	1
MTNR1B	4544	broad.mit.edu	36	11	92354508	92354508	+	Silent	SNP	C	A	A			TCGA-32-1970-01	TCGA-32-1970-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:92354508C>A	uc001pdk.1	+	c.471C>A	c.(469-471)ACC>ACA	p.T157T		NM_005959	NP_005950	P49286	MTR1B_HUMAN	melatonin receptor 1B	157	Helical; Name=4; (Potential).				G-protein signaling, coupled to cyclic nucleotide second messenger|glucose homeostasis|regulation of insulin secretion|synaptic transmission	integral to plasma membrane	melatonin receptor activity			central_nervous_system(1)	1		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)			Ramelteon(DB00980)									0.337349	72.864476	74.811375	28	55	CC		KEEP	---	---	---	---	capture			Silent	SNP	92354508	92354508	10345	11	C	A	A	22	22	MTNR1B	A	3	3
TMEM132B	114795	broad.mit.edu	36	12	124400472	124400472	+	Missense_Mutation	SNP	G	A	A			TCGA-32-1970-01	TCGA-32-1970-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:124400472G>A	uc001uhe.1	+	c.574G>A	c.(574-576)GAG>AAG	p.E192K		NM_052907	NP_443139	Q14DG7	T132B_HUMAN	transmembrane protein 132B	192	Extracellular (Potential).					integral to membrane				ovary(5)|large_intestine(1)|breast(1)|pancreas(1)	8	all_neural(191;0.101)|Medulloblastoma(191;0.163)													0.327103	95.087599	97.92492	35	72	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(86;0.000423)|Epithelial(86;0.00394)|all cancers(50;0.0362)	Missense_Mutation	SNP	124400472	124400472	16577	12	G	A	A	37	37	TMEM132B	A	1	1
PRPF40B	25766	broad.mit.edu	36	12	48316867	48316867	+	Missense_Mutation	SNP	C	T	T			TCGA-32-1970-01	TCGA-32-1970-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:48316867C>T	uc001rur.1	+	c.1462C>T	c.(1462-1464)CGC>TGC	p.R488C	PRPF40B_uc001rup.1_Missense_Mutation_p.R510C|PRPF40B_uc001ruq.1_Missense_Mutation_p.R482C|PRPF40B_uc001rus.1_Missense_Mutation_p.R431C	NM_001031698	NP_001026868	Q6NWY9	PR40B_HUMAN	Huntingtin interacting protein C isoform 1	488					mRNA processing|RNA splicing	nuclear speck				ovary(1)|kidney(1)|pancreas(1)	3												OREG0021797	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.353383	132.298833	134.813615	47	86	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	48316867	48316867	13015	12	C	T	T	19	19	PRPF40B	T	1	1
SMARCC2	6601	broad.mit.edu	36	12	54845541	54845541	+	Silent	SNP	A	G	G			TCGA-32-1970-01	TCGA-32-1970-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr12:54845541A>G	uc001skb.1	-	c.2967T>C	c.(2965-2967)GCT>GCC	p.A989A	SMARCC2_uc001ska.1_Silent_p.A1020A|SMARCC2_uc001skc.1_Silent_p.A1019A|SMARCC2_uc001skd.1_Silent_p.A1020A	NM_003075	NP_003066	Q8TAQ2	SMRC2_HUMAN	SWI/SNF-related matrix-associated	989	Pro-rich.				chromatin assembly or disassembly|chromatin remodeling|negative regulation of transcription, DNA-dependent|nervous system development|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	chromatin|nBAF complex|npBAF complex|nucleoplasm|SWI/SNF complex	chromatin binding|DNA binding|protein binding|transcription coactivator activity			lung(2)|central_nervous_system(2)|ovary(1)|skin(1)	6														0.24	6.999908	8.58584	6	19	AA		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(18;0.123)		Silent	SNP	54845541	54845541	15274	12	A	G	G	11	11	SMARCC2	G	4	4
RB1	5925	broad.mit.edu	36	13	47937352	47937352	+	Nonsense_Mutation	SNP	T	A	A			TCGA-32-1970-01	TCGA-32-1970-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr13:47937352T>A	uc001vcb.1	+	c.2336T>A	c.(2335-2337)TTG>TAG	p.L779*		NM_000321	NP_000312	P06400	RB_HUMAN	retinoblastoma 1	779	Interaction with LIMD1.|Domain C; mediates interaction with E4F1.				androgen receptor signaling pathway|cell cycle arrest|chromatin remodeling|G1 phase of mitotic cell cycle|interspecies interaction between organisms|maintenance of mitotic sister chromatid cohesion|mitotic cell cycle G1/S transition checkpoint|myoblast differentiation|negative regulation of cell growth|negative regulation of protein kinase activity|negative regulation of S phase of mitotic cell cycle|negative regulation of sequence-specific DNA binding transcription factor activity|positive regulation of mitotic metaphase/anaphase transition|protein localization to chromosome, centromeric region|Ras protein signal transduction|regulation of centromere complex assembly|regulation of cohesin localization to chromatin|regulation of lipid kinase activity|regulation of transcription involved in G1/S phase of mitotic cell cycle|S phase of mitotic cell cycle|sister chromatid biorientation	chromatin|PML body|Rb-E2F complex|SWI/SNF complex	androgen receptor binding|DNA binding|kinase binding|phosphoprotein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription factor binding|transcription repressor activity|ubiquitin protein ligase binding			lung(93)|eye(89)|central_nervous_system(47)|bone(22)|breast(20)|urinary_tract(17)|haematopoietic_and_lymphoid_tissue(14)|ovary(10)|soft_tissue(8)|prostate(8)|skin(7)|endometrium(5)|cervix(3)|liver(3)|salivary_gland(2)|stomach(2)|oesophagus(1)|adrenal_gland(1)|kidney(1)|gastrointestinal_tract_(site_indeterminate)(1)|pituitary(1)	355		all_cancers(8;6.9e-71)|all_epithelial(8;4.61e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;1.51e-09)|Lung NSC(96;7.03e-07)|Breast(56;1.53e-05)|Prostate(109;0.000493)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301)			Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)			6		568	TCGA GBM(7;6.82e-08)|TSP Lung(12;0.097)|TCGA Ovarian(6;0.080)			0.737374	477.722288	487.809899	146	52	TT		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(2;9.98e-18)|LUSC - Lung squamous cell carcinoma(3;0.013)	Nonsense_Mutation	SNP	47937352	47937352	13559	13	T	A	A	63	63	RB1	A	5	4
TRAF3	7187	broad.mit.edu	36	14	102441306	102441306	+	Missense_Mutation	SNP	T	C	C			TCGA-32-1970-01	TCGA-32-1970-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr14:102441306T>C	uc001ymc.1	+	c.1139T>C	c.(1138-1140)CTG>CCG	p.L380P	TRAF3_uc001ymd.1_Missense_Mutation_p.L380P|TRAF3_uc001yme.1_Missense_Mutation_p.L355P	NM_145725	NP_663777	Q13114	TRAF3_HUMAN	TNF receptor-associated factor 3 isoform 1	380					apoptosis|induction of apoptosis|negative regulation of NF-kappaB transcription factor activity|negative regulation of type I interferon production|regulation of defense response to virus|regulation of interferon-beta production|regulation of proteolysis|toll-like receptor signaling pathway|tumor necrosis factor-mediated signaling pathway	CD40 receptor complex|cytosol|endosome|internal side of plasma membrane|mitochondrion	signal transducer activity|ubiquitin-protein ligase activity|zinc ion binding				0		all_cancers(154;7.87e-06)|all_epithelial(191;0.0024)												0.322581	23.845945	24.709055	10	21	TT		KEEP	---	---	---	---	capture		Epithelial(152;9.92e-24)|all cancers(159;2.23e-21)|OV - Ovarian serous cystadenocarcinoma(161;7.85e-12)|Colorectal(3;0.0971)	Missense_Mutation	SNP	102441306	102441306	16983	14	T	C	C	55	55	TRAF3	C	4	4
C14orf145	145508	broad.mit.edu	36	14	80398895	80398895	+	Missense_Mutation	SNP	G	A	A			TCGA-32-1970-01	TCGA-32-1970-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr14:80398895G>A	uc001xux.1	-	c.721C>T	c.(721-723)CGC>TGC	p.R241C	C14orf145_uc001xuy.1_Missense_Mutation_p.R99C|C14orf145_uc001xuz.2_Missense_Mutation_p.R241C	NM_152446	NP_689659	Q6ZU80	CN145_HUMAN	hypothetical protein LOC145508	241	Potential.							p.R241C(1)		central_nervous_system(1)	1										1				0.368421	171.486869	174.085882	63	108	GG		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(234;0.0586)	Missense_Mutation	SNP	80398895	80398895	1797	14	G	A	A	40	40	C14orf145	A	1	1
FLRT2	23768	broad.mit.edu	36	14	85158219	85158219	+	Missense_Mutation	SNP	T	C	C			TCGA-32-1970-01	TCGA-32-1970-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr14:85158219T>C	uc001xvr.1	+	c.608T>C	c.(607-609)CTC>CCC	p.L203P	FLRT2_uc010atd.1_Missense_Mutation_p.L203P	NM_013231	NP_037363	O43155	FLRT2_HUMAN	fibronectin leucine rich transmembrane protein	203	Extracellular (Potential).				cell adhesion	integral to plasma membrane|proteinaceous extracellular matrix	protein binding, bridging|receptor signaling protein activity			ovary(3)	3														0.336207	125.894079	128.644842	39	77	TT		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(234;0.0319)	Missense_Mutation	SNP	85158219	85158219	6181	14	T	C	C	54	54	FLRT2	C	4	4
POTEB	339010	broad.mit.edu	36	15	19305441	19305441	+	Missense_Mutation	SNP	T	C	C			TCGA-32-1970-01	TCGA-32-1970-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr15:19305441T>C	uc001ytu.1	-	c.1577A>G	c.(1576-1578)AAC>AGC	p.N526S	POTEB_uc010axv.1_Non-coding_Transcript	NM_207355	NP_997238	Q6S5H4	POTEB_HUMAN	protein expressed in prostate, ovary, testis,	526	Potential.										0														0.094923	41.088289	115.706916	43	410	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	19305441	19305441	12691	15	T	C	C	60	60	POTEB	C	4	4
LTK	4058	broad.mit.edu	36	15	39586758	39586758	+	Silent	SNP	G	C	C			TCGA-32-1970-01	TCGA-32-1970-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr15:39586758G>C	uc001zoa.2	-	c.1368C>G	c.(1366-1368)GGC>GGG	p.G456G	LTK_uc010bcg.1_Silent_p.G67G|LTK_uc001zob.2_Silent_p.G395G	NM_002344	NP_002335	P29376	LTK_HUMAN	leukocyte receptor tyrosine kinase isoform 1	456	Cytoplasmic (Potential).				protein phosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane|soluble fraction	ATP binding|transmembrane receptor protein tyrosine kinase activity			lung(6)|central_nervous_system(1)	7		all_cancers(109;1.89e-19)|all_epithelial(112;2.28e-16)|Lung NSC(122;5.34e-11)|all_lung(180;1.33e-09)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.172)								314	TSP Lung(18;0.14)			0.26087	12.130342	13.26376	6	17	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(18;2.1e-17)|GBM - Glioblastoma multiforme(113;1.34e-06)|Colorectal(105;0.0148)|BRCA - Breast invasive adenocarcinoma(123;0.113)	Silent	SNP	39586758	39586758	9456	15	G	C	C	42	42	LTK	C	3	3
GATM	2628	broad.mit.edu	36	15	43456271	43456271	+	Missense_Mutation	SNP	G	T	T			TCGA-32-1970-01	TCGA-32-1970-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr15:43456271G>T	uc001zvc.1	-	c.108C>A	c.(106-108)TTC>TTA	p.F36L	GATM_uc001zvb.1_5'UTR	NM_001482	NP_001473	P50440	GATM_HUMAN	L-arginine:glycine amidinotransferase precursor	36					creatine biosynthetic process	mitochondrial inner membrane|mitochondrial intermembrane space	glycine amidinotransferase activity|protein binding				0		all_cancers(109;1.25e-09)|all_epithelial(112;5.56e-08)|Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)			Creatine(DB00148)|Glycine(DB00145)|L-Ornithine(DB00129)									0.5	109.741189	109.741189	38	38	GG		KEEP	---	---	---	---	capture		all cancers(107;4.87e-16)|GBM - Glioblastoma multiforme(94;1.97e-06)	Missense_Mutation	SNP	43456271	43456271	6527	15	G	T	T	41	41	GATM	T	3	3
MEGF11	84465	broad.mit.edu	36	15	63978257	63978257	+	Missense_Mutation	SNP	G	T	T			TCGA-32-1970-01	TCGA-32-1970-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr15:63978257G>T	uc002apm.2	-	c.2837C>A	c.(2836-2838)ACA>AAA	p.T946K	MEGF11_uc010bhn.1_Missense_Mutation_p.T871K|MEGF11_uc002apl.2_Missense_Mutation_p.T871K|MEGF11_uc002apn.1_Missense_Mutation_p.T946K	NM_032445	NP_115821	A6BM72	MEG11_HUMAN	multiple EGF-like-domains 11	946						basolateral plasma membrane|integral to membrane				pancreas(1)	1														0.469231	194.665491	194.772594	61	69	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	63978257	63978257	9850	15	G	T	T	48	48	MEGF11	T	3	3
PGPEP1L	145814	broad.mit.edu	36	15	97330202	97330202	+	Missense_Mutation	SNP	C	T	T			TCGA-32-1970-01	TCGA-32-1970-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr15:97330202C>T	uc002bum.1	-	c.346G>A	c.(346-348)GTG>ATG	p.V116M	PGPEP1L_uc010bop.1_Missense_Mutation_p.V62M|PGPEP1L_uc002bun.1_Non-coding_Transcript	NM_001102612	NP_001096082	A6NFU8	PGPIL_HUMAN	hypothetical protein LOC145814	116					proteolysis		cysteine-type peptidase activity				0														0.439759	209.148469	209.673635	73	93	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	97330202	97330202	12227	15	C	T	T	19	19	PGPEP1L	T	1	1
TMEM219	124446	broad.mit.edu	36	16	29886891	29886891	+	Missense_Mutation	SNP	A	G	G			TCGA-32-1970-01	TCGA-32-1970-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr16:29886891A>G	uc002duw.2	+	c.400A>G	c.(400-402)ACA>GCA	p.T134A	BOLA2_uc010bzb.1_Intron|BOLA2_uc010bzc.1_Intron|TMEM219_uc002duy.2_Missense_Mutation_p.T134A|TMEM219_uc010bzk.1_Missense_Mutation_p.T134A|TMEM219_uc002duz.2_Missense_Mutation_p.T134A|TMEM219_uc010bzl.1_Non-coding_Transcript	NM_194280	NP_919256	Q86XT9	TM219_HUMAN	transmembrane protein 219	134						integral to membrane					0														0.178947	89.178849	116.957709	51	234	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	29886891	29886891	16678	16	A	G	G	6	6	TMEM219	G	4	4
SNX20	124460	broad.mit.edu	36	16	49265002	49265002	+	Missense_Mutation	SNP	C	T	T			TCGA-32-1970-01	TCGA-32-1970-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:49265002C>T	uc002egk.1	-	c.767G>A	c.(766-768)CGC>CAC	p.R256H	SNX20_uc002egh.2_Intron|SNX20_uc002egi.2_Intron	NM_182854	NP_878274	Q7Z614	SNX20_HUMAN	sorting nexin 20 isoform 1	256					cell communication|protein transport	endosome membrane|nucleus|plasma membrane	phosphatidylinositol binding|protein binding			ovary(1)	1														0.473684	53.135517	53.158954	18	20	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	49265002	49265002	15392	16	C	T	T	27	27	SNX20	T	1	1
CPNE2	221184	broad.mit.edu	36	16	55711021	55711021	+	Silent	SNP	C	T	T			TCGA-32-1970-01	TCGA-32-1970-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:55711021C>T	uc010cct.1	+	c.717C>T	c.(715-717)CCC>CCT	p.P239P	CPNE2_uc002eks.1_Silent_p.P213P|CPNE2_uc010ccu.1_Silent_p.P213P	NM_152727	NP_689940	Q96FN4	CPNE2_HUMAN	copine II	213	C2 2.									central_nervous_system(1)	1		all_neural(199;0.224)												0.458333	35.522581	35.558884	11	13	CC		KEEP	---	---	---	---	capture			Silent	SNP	55711021	55711021	3950	16	C	T	T	24	24	CPNE2	T	2	2
PKD1L2	114780	broad.mit.edu	36	16	79738566	79738566	+	Missense_Mutation	SNP	C	T	T			TCGA-32-1970-01	TCGA-32-1970-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:79738566C>T	uc002fgh.1	-	c.5026G>A	c.(5026-5028)GCC>ACC	p.A1676T	PKD1L2_uc002fgg.1_Non-coding_Transcript	NM_052892	NP_443124	Q7Z442	PK1L2_HUMAN	polycystin 1-like 2 isoform a	1676	Cytoplasmic (Potential).				neuropeptide signaling pathway	integral to membrane	calcium ion binding|ion channel activity|sugar binding			ovary(1)|central_nervous_system(1)|pancreas(1)	3														0.473054	237.500203	237.605852	79	88	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	79738566	79738566	12389	16	C	T	T	27	27	PKD1L2	T	1	1
SLC47A2	146802	broad.mit.edu	36	17	19558679	19558679	+	Missense_Mutation	SNP	C	T	T			TCGA-32-1970-01	TCGA-32-1970-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:19558679C>T	uc002gwe.2	-	c.241G>A	c.(241-243)GGA>AGA	p.G81R	SLC47A2_uc002gwg.2_Missense_Mutation_p.G81R|SLC47A2_uc002gwf.2_Missense_Mutation_p.G81R|SLC47A2_uc002gwh.2_Non-coding_Transcript|SLC47A2_uc002gwi.1_Non-coding_Transcript|SLC47A2_uc010cqs.1_Non-coding_Transcript|SLC47A2_uc010cqt.1_Non-coding_Transcript	NM_152908	NP_690872	Q86VL8	S47A2_HUMAN	solute carrier family 47, member 2 isoform 1	81	Helical; (Potential).					integral to membrane|plasma membrane	drug:hydrogen antiporter activity				0	all_cancers(12;2.3e-05)|all_epithelial(12;0.0024)|Breast(13;0.245)													0.416	304.06212	305.59924	104	146	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	19558679	19558679	15145	17	C	T	T	23	23	SLC47A2	T	1	1
DHRS13	147015	broad.mit.edu	36	17	24252414	24252414	+	Silent	SNP	C	T	T			TCGA-32-1970-01	TCGA-32-1970-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:24252414C>T	uc002hde.2	-	c.402G>A	c.(400-402)GCG>GCA	p.A134A	DHRS13_uc002hdd.2_Silent_p.A84A	NM_144683	NP_653284	Q6UX07	DHR13_HUMAN	dehydrogenase/reductase (SDR family) member 13	134					oxidation-reduction process	extracellular region	binding|oxidoreductase activity				0	all_cancers(5;2.12e-15)|all_epithelial(6;3.44e-19)|Lung NSC(42;0.01)													0.369565	87.904388	89.286086	34	58	CC		KEEP	---	---	---	---	capture	Epithelial(11;1.59e-06)|all cancers(11;9.27e-06)|BRCA - Breast invasive adenocarcinoma(11;5.78e-05)|OV - Ovarian serous cystadenocarcinoma(11;0.0602)		Silent	SNP	24252414	24252414	4668	17	C	T	T	19	19	DHRS13	T	1	1
AXIN2	8313	broad.mit.edu	36	17	60984410	60984410	+	Missense_Mutation	SNP	G	A	A			TCGA-32-1970-01	TCGA-32-1970-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:60984410G>A	uc002jfi.1	-	c.791C>T	c.(790-792)ACG>ATG	p.T264M	AXIN2_uc002jfh.1_Missense_Mutation_p.T264M|AXIN2_uc010den.1_Missense_Mutation_p.T264M|AXIN2_uc002jfj.1_Missense_Mutation_p.T264M	NM_004655	NP_004646	Q9Y2T1	AXIN2_HUMAN	axin 2	264					cellular protein localization|cellular response to organic cyclic compound|dorsal/ventral axis specification|intramembranous ossification|maintenance of DNA repeat elements|mRNA stabilization|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of catenin import into nucleus|negative regulation of cell proliferation|negative regulation of osteoblast differentiation|odontogenesis|positive regulation of cell death|positive regulation of epithelial to mesenchymal transition|positive regulation of protein phosphorylation|regulation of centromeric sister chromatid cohesion|regulation of mismatch repair|Wnt receptor signaling pathway involved in somitogenesis	Axin-APC-beta-catenin-GSK3B complex|cell cortex|centrosome|cytoplasmic membrane-bounded vesicle|cytoplasmic microtubule|nucleus|plasma membrane|postsynaptic density	armadillo repeat domain binding|beta-catenin binding|GTPase activator activity|protein kinase binding|signal transducer activity			central_nervous_system(1)|skin(1)	2										240				0.462963	152.77576	152.899883	50	58	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	60984410	60984410	1258	17	G	A	A	40	40	AXIN2	A	1	1
NEURL4	84461	broad.mit.edu	36	17	7161358	7161358	+	Silent	SNP	G	A	A			TCGA-32-1970-01	TCGA-32-1970-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:7161358G>A	uc002gga.1	-	c.4374C>T	c.(4372-4374)TTC>TTT	p.F1458F	GPS2_uc010cme.1_5'Flank|GPS2_uc002gfv.1_5'Flank|GPS2_uc002gfw.1_5'Flank|GPS2_uc002gfx.1_5'Flank|NEURL4_uc002gfy.1_Non-coding_Transcript|GPS2_uc002gfz.1_5'UTR|NEURL4_uc002ggb.1_Silent_p.F1456F	NM_032442	NP_115818	Q96JN8	NEUL4_HUMAN	neuralized homolog 4 isoform 1	1458							protein binding			ovary(1)	1														0.88172	274.115069	287.449622	82	11	GG		KEEP	---	---	---	---	capture			Silent	SNP	7161358	7161358	10747	17	G	A	A	37	37	NEURL4	A	1	1
TP53	7157	broad.mit.edu	36	17	7517863	7517863	+	Missense_Mutation	SNP	C	G	G			TCGA-32-1970-01	TCGA-32-1970-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:7517863C>G	uc002gim.2	-	c.800G>C	c.(799-801)CGG>CCG	p.R267P	TP53_uc002gig.1_Intron|TP53_uc002gih.1_Missense_Mutation_p.R267P|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Missense_Mutation_p.R135P|TP53_uc010cng.1_Missense_Mutation_p.R135P|TP53_uc002gii.1_Missense_Mutation_p.R135P|TP53_uc010cnh.1_Missense_Mutation_p.R267P|TP53_uc010cni.1_Missense_Mutation_p.R267P|TP53_uc002gij.2_Missense_Mutation_p.R267P	NM_001126112	NP_001119584	P04637	P53_HUMAN	tumor protein p53 isoform a	267	|Interaction with E4F1.|Interaction with HIPK1 (By similarity).|Interaction with AXIN1 (By similarity).		R -> H (in a sporadic cancer; somatic mutation).|R -> G (in sporadic cancers; somatic mutation).|R -> P (in sporadic cancers; somatic mutation).|R -> Q (in LFS; germline mutation and in sporadic cancers; somatic mutation).		activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of gene-specific transcription from RNA polymerase II promoter|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray	chromatin|cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork	ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|promoter binding|promoter binding|protease binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|sequence-specific DNA binding transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|ubiquitin protein ligase binding|zinc ion binding	p.R267P(13)|p.R267Q(7)|p.0?(6)|p.G262_F270delGNLLGRNSF(2)|p.G266_E271delGRNSFE(2)|p.?(2)|p.G262_S269delGNLLGRNS(2)|p.G266fs*4(1)|p.N268fs*77(1)|p.L265_K305del41(1)|p.E258fs*71(1)|p.L265_R267delLGR(1)|p.R267L(1)|p.G266_N268delGRN(1)|p.G262fs*2(1)		large_intestine(4614)|breast(2344)|upper_aerodigestive_tract(2150)|lung(1958)|ovary(1559)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1212)|stomach(1127)|urinary_tract(1113)|central_nervous_system(1072)|liver(805)|skin(693)|pancreas(370)|biliary_tract(247)|soft_tissue(209)|prostate(192)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(41)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1)	21904		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)				Pancreas(47;798 1329 9957 10801)		111	p.R267P(NCIH1437-Tumor)|p.R267P(JHH7-Tumor)	690	TCGA GBM(1;<1E-8)|TSP Lung(2;<1E-8)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)			0.862069	93.196445	96.875304	25	4	CC		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Missense_Mutation	SNP	7517863	7517863	16923	17	C	G	G	23	23	TP53	G	3	3
NOTCH3	4854	broad.mit.edu	36	19	15152617	15152617	+	Missense_Mutation	SNP	C	T	T			TCGA-32-1970-01	TCGA-32-1970-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:15152617C>T	uc002nan.1	-	c.3017G>A	c.(3016-3018)CGC>CAC	p.R1006H	NOTCH3_uc002nao.1_Missense_Mutation_p.R954H	NM_000435	NP_000426	Q9UM47	NOTC3_HUMAN	Notch homolog 3	1006	Extracellular (Potential).|EGF-like 26.		R -> C (in CADASIL).		Notch receptor processing|Notch signaling pathway|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to membrane|nucleoplasm|plasma membrane	calcium ion binding|protein binding|receptor activity			ovary(5)|lung(2)|central_nervous_system(1)	8										417				0.233333	11.676996	13.667854	7	23	CC		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(3;2.6e-20)|Epithelial(3;1.34e-16)|all cancers(3;5.13e-15)		Missense_Mutation	SNP	15152617	15152617	10953	19	C	T	T	27	27	NOTCH3	T	1	1
F2RL3	9002	broad.mit.edu	36	19	16861950	16861950	+	Missense_Mutation	SNP	G	A	A			TCGA-32-1970-01	TCGA-32-1970-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:16861950G>A	uc002nfa.1	+	c.676G>A	c.(676-678)GTG>ATG	p.V226M		NM_003950	NP_003941	Q96RI0	PAR4_HUMAN	coagulation factor II (thrombin) receptor-like 3	226	Extracellular (Potential).				activation of phospholipase C activity by G-protein coupled receptor protein signaling pathway coupled to IP3 second messenger|platelet activation|platelet dense granule organization|positive regulation of release of sequestered calcium ion into cytosol	extracellular region|integral to plasma membrane	thrombin receptor activity				0														0.222222	7.805894	9.073864	4	14	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	16861950	16861950	5540	19	G	A	A	40	40	F2RL3	A	1	1
FFAR3	2865	broad.mit.edu	36	19	40541768	40541768	+	Missense_Mutation	SNP	C	T	T			TCGA-32-1970-01	TCGA-32-1970-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:40541768C>T	uc002nzd.1	+	c.136C>T	c.(136-138)CGC>TGC	p.R46C	FFAR3_uc010edy.1_Missense_Mutation_p.R46C	NM_005304	NP_005295	O14843	FFAR3_HUMAN	free fatty acid receptor 3	46	Cytoplasmic.					integral to plasma membrane	G-protein coupled receptor activity|lipid binding				0	all_lung(56;9.78e-09)|Lung NSC(56;1.46e-08)|Esophageal squamous(110;0.162)					Esophageal Squamous(185;1742 2042 21963 24215 27871)								0.135189	95.78964	160.684591	68	435	CC		KEEP	---	---	---	---	capture	Epithelial(14;1.29e-19)|OV - Ovarian serous cystadenocarcinoma(14;4.63e-18)|all cancers(14;5.19e-17)|LUSC - Lung squamous cell carcinoma(66;0.0221)		Missense_Mutation	SNP	40541768	40541768	6066	19	C	T	T	23	23	FFAR3	T	1	1
FCGBP	8857	broad.mit.edu	36	19	45084187	45084187	+	Missense_Mutation	SNP	C	G	G	rs2542318	by-2hit-2allele	TCGA-32-1970-01	TCGA-32-1970-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:45084187C>G	uc002omp.2	-	c.8157G>C	c.(8155-8157)CAG>CAC	p.Q2719H		NM_003890	NP_003881	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	2719				Q -> H (in Ref. 1; BAA19526).		extracellular region	protein binding			ovary(4)|central_nervous_system(1)	5	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)													0.219178	32.954135	38.264852	16	57	CC		KEEP	---	---	---	---	capture	Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)		Missense_Mutation	SNP	45084187	45084187	6015	19	C	G	G	24	24	FCGBP	G	3	3
ZNF229	7772	broad.mit.edu	36	19	49624760	49624760	+	Missense_Mutation	SNP	G	A	A			TCGA-32-1970-01	TCGA-32-1970-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:49624760G>A	uc002oze.1	-	c.2036C>T	c.(2035-2037)ACG>ATG	p.T679M	ZNF229_uc010ejk.1_Missense_Mutation_p.T333M|ZNF229_uc010ejl.1_Missense_Mutation_p.T673M	NM_014518	NP_055333	Q9UJW7	ZN229_HUMAN	zinc finger protein 229	679					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)|pancreas(1)	2		Prostate(69;0.0352)												0.443038	309.244604	309.913744	105	132	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	49624760	49624760	18373	19	G	A	A	40	40	ZNF229	A	1	1
AP2A1	160	broad.mit.edu	36	19	54977621	54977621	+	Missense_Mutation	SNP	C	G	G			TCGA-32-1970-01	TCGA-32-1970-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:54977621C>G	uc002ppn.1	+	c.301C>G	c.(301-303)CTG>GTG	p.L101V	AP2A1_uc010enj.1_Intron|AP2A1_uc002ppo.1_Missense_Mutation_p.L101V	NM_014203	NP_055018	O95782	AP2A1_HUMAN	adaptor-related protein complex 2, alpha 1	101					axon guidance|endocytosis|epidermal growth factor receptor signaling pathway|Golgi to endosome transport|intracellular protein transport|negative regulation of epidermal growth factor receptor signaling pathway|nerve growth factor receptor signaling pathway|regulation of defense response to virus by virus|synaptic transmission|viral reproduction	AP-2 adaptor complex|clathrin coat of trans-Golgi network vesicle|cytosol	protein binding|protein transporter activity			ovary(2)	2		all_lung(116;3.24e-07)|Lung NSC(112;1.6e-06)|all_neural(266;0.0459)|Ovarian(192;0.0728)												0.354839	32.191565	32.777491	11	20	CC		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(262;0.0023)|GBM - Glioblastoma multiforme(134;0.0157)	Missense_Mutation	SNP	54977621	54977621	749	19	C	G	G	28	28	AP2A1	G	3	3
TNFRSF8	943	broad.mit.edu	36	1	12087079	12087079	+	Nonsense_Mutation	SNP	C	T	T			TCGA-32-1970-01	TCGA-32-1970-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:12087079C>T	uc001atq.1	+	c.325C>T	c.(325-327)CGA>TGA	p.R109*		NM_001243	NP_001234	P28908	TNR8_HUMAN	tumor necrosis factor receptor superfamily,	109	TNFR-Cys 3.|Extracellular (Potential).				cellular response to mechanical stimulus|negative regulation of cell proliferation|positive regulation of apoptosis|positive regulation of TRAIL biosynthetic process|positive regulation of tumor necrosis factor biosynthetic process	cytoplasm|integral to membrane|plasma membrane				skin(2)|ovary(1)|pancreas(1)|central_nervous_system(1)	5	Ovarian(185;0.249)	Lung NSC(185;8.71e-05)|all_lung(284;9.89e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)								756				0.477273	124.360846	124.398814	42	46	CC		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.66e-06)|COAD - Colon adenocarcinoma(227;0.000261)|BRCA - Breast invasive adenocarcinoma(304;0.000304)|Kidney(185;0.000777)|KIRC - Kidney renal clear cell carcinoma(229;0.00261)|STAD - Stomach adenocarcinoma(313;0.0073)|READ - Rectum adenocarcinoma(331;0.0649)	Nonsense_Mutation	SNP	12087079	12087079	16840	1	C	T	T	31	31	TNFRSF8	T	5	1
HRNR	388697	broad.mit.edu	36	1	150459884	150459884	+	Missense_Mutation	SNP	C	G	G			TCGA-32-1970-01	TCGA-32-1970-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:150459884C>G	uc001ezt.1	-	c.845G>C	c.(844-846)AGC>ACC	p.S282T		NM_001009931	NP_001009931	Q86YZ3	HORN_HUMAN	hornerin	282	3.				keratinization		calcium ion binding|protein binding			ovary(1)	1	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)													0.297297	240.86739	251.753453	88	208	CC		KEEP	---	---	---	---	capture	LUSC - Lung squamous cell carcinoma(543;0.206)		Missense_Mutation	SNP	150459884	150459884	7653	1	C	G	G	28	28	HRNR	G	3	3
ASPM	259266	broad.mit.edu	36	1	195327694	195327694	+	Missense_Mutation	SNP	G	T	T			TCGA-32-1970-01	TCGA-32-1970-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:195327694G>T	uc001gtu.1	-	c.9410C>A	c.(9409-9411)GCT>GAT	p.A3137D	ASPM_uc001gtv.1_Missense_Mutation_p.A1552D|ASPM_uc001gtw.2_Missense_Mutation_p.A985D	NM_018136	NP_060606	Q8IZT6	ASPM_HUMAN	asp (abnormal spindle)-like, microcephaly	3137					mitosis	cytoplasm|nucleus	calmodulin binding			ovary(4)|central_nervous_system(2)	6														0.40411	171.894721	173.067988	59	87	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	195327694	195327694	1075	1	G	T	T	34	34	ASPM	T	3	3
TRIM58	25893	broad.mit.edu	36	1	246105858	246105858	+	Missense_Mutation	SNP	C	T	T			TCGA-32-1970-01	TCGA-32-1970-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:246105858C>T	uc001ido.1	+	c.905C>T	c.(904-906)CCG>CTG	p.P302L	OR2W3_uc001idp.1_5'UTR	NM_015431	NP_056246	Q8NG06	TRI58_HUMAN	tripartite motif-containing 58	302	B30.2/SPRY.					intracellular	zinc ion binding			ovary(1)|lung(1)|central_nervous_system(1)|pancreas(1)	4	all_cancers(71;0.000139)|all_epithelial(71;1.58e-05)|Breast(184;0.0117)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)	all_cancers(173;0.0286)												0.336842	93.977991	96.21141	32	63	CC		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(106;0.0319)		Missense_Mutation	SNP	246105858	246105858	17077	1	C	T	T	23	23	TRIM58	T	1	1
OR2L3	391192	broad.mit.edu	36	1	246291263	246291263	+	Silent	SNP	G	T	T			TCGA-32-1970-01	TCGA-32-1970-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:246291263G>T	uc001idx.1	+	c.657G>T	c.(655-657)CGG>CGT	p.R219R	OR2L13_uc001ids.1_Intron	NM_001004687	NP_001004687	Q8NG85	OR2L3_HUMAN	olfactory receptor, family 2, subfamily L,	219	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)													0.267943	132.502313	142.669308	56	153	GG		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(106;0.0278)		Silent	SNP	246291263	246291263	11414	1	G	T	T	43	43	OR2L3	T	3	3
OR2G6	391211	broad.mit.edu	36	1	246752023	246752023	+	Silent	SNP	C	T	T			TCGA-32-1970-01	TCGA-32-1970-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:246752023C>T	uc001ien.1	+	c.453C>T	c.(451-453)AGC>AGT	p.S151S		NM_001013355	NP_001013373	Q5TZ20	OR2G6_HUMAN	olfactory receptor, family 2, subfamily G,	151	Helical; Name=4; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)	2	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)	all_cancers(173;0.0156)												0.5125	119.67021	119.680937	41	39	CC		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(106;0.0265)		Silent	SNP	246752023	246752023	11406	1	C	T	T	27	27	OR2G6	T	1	1
GJB4	127534	broad.mit.edu	36	1	35000234	35000234	+	Silent	SNP	G	T	T			TCGA-32-1970-01	TCGA-32-1970-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:35000234G>T	uc001bxv.1	+	c.792G>T	c.(790-792)GGG>GGT	p.G264G	GJB4_uc001bxw.2_Silent_p.G264G	NM_153212	NP_694944	Q9NTQ9	CXB4_HUMAN	gap junction protein, beta 4	264	Cytoplasmic (Potential).				cell communication	connexon complex|integral to membrane	gap junction channel activity			ovary(2)|central_nervous_system(1)	3		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.234)												0.259259	9.251704	10.664452	7	20	GG		KEEP	---	---	---	---	capture			Silent	SNP	35000234	35000234	6678	1	G	T	T	44	44	GJB4	T	3	3
KIAA0562	9731	broad.mit.edu	36	1	3721889	3721889	+	Missense_Mutation	SNP	G	C	C			TCGA-32-1970-01	TCGA-32-1970-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:3721889G>C	uc001aky.1	-	c.2715C>G	c.(2713-2715)AGC>AGG	p.S905R		NM_014704	NP_055519	O60308	K0562_HUMAN	glycine-, glutamate-,	905							binding				0	all_cancers(77;0.0395)|Ovarian(185;0.0634)|all_lung(157;0.222)|Lung NSC(156;0.227)	all_epithelial(116;3.96e-21)|all_lung(118;2.74e-08)|Lung NSC(185;6.4e-06)|Breast(487;0.00066)|Renal(390;0.00121)|Hepatocellular(190;0.00335)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.031)|Lung SC(97;0.0548)|Medulloblastoma(700;0.212)												0.339286	61.319673	62.592752	19	37	GG		KEEP	---	---	---	---	capture		Epithelial(90;6.85e-39)|OV - Ovarian serous cystadenocarcinoma(86;1.59e-22)|GBM - Glioblastoma multiforme(42;3.16e-16)|Colorectal(212;2.01e-05)|COAD - Colon adenocarcinoma(227;7.99e-05)|BRCA - Breast invasive adenocarcinoma(365;0.000389)|Kidney(185;0.000513)|STAD - Stomach adenocarcinoma(132;0.00709)|KIRC - Kidney renal clear cell carcinoma(229;0.00714)|Lung(427;0.137)	Missense_Mutation	SNP	3721889	3721889	8491	1	G	C	C	46	46	KIAA0562	C	3	3
DPH2	1802	broad.mit.edu	36	1	44210124	44210124	+	Silent	SNP	G	T	T			TCGA-32-1970-01	TCGA-32-1970-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:44210124G>T	uc001ckz.1	+	c.963G>T	c.(961-963)CGG>CGT	p.R321R	DPH2_uc001cla.1_Intron|DPH2_uc001clb.1_Silent_p.R245R	NM_001384	NP_001375	Q9BQC3	DPH2_HUMAN	diphthamide biosynthesis protein 2 isoform a	321					peptidyl-diphthamide biosynthetic process from peptidyl-histidine	cytoplasm				ovary(1)	1	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0511)												0.266667	95.84208	103.889689	44	121	GG		KEEP	---	---	---	---	capture			Silent	SNP	44210124	44210124	4904	1	G	T	T	42	42	DPH2	T	3	3
PTGFR	5737	broad.mit.edu	36	1	78774751	78774751	+	Nonsense_Mutation	SNP	C	T	T			TCGA-32-1970-01	TCGA-32-1970-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:78774751C>T	uc001din.1	+	c.871C>T	c.(871-873)CGA>TGA	p.R291*	PTGFR_uc001dim.1_3'UTR	NM_000959	NP_000950	P43088	PF2R_HUMAN	prostaglandin F receptor isoform a precursor	291	Helical; Name=7; (Potential).				parturition	extracellular region|integral to plasma membrane	prostaglandin F receptor activity			ovary(3)	3					Bimatoprost(DB00905)|Latanoprost(DB00654)|Travoprost(DB00287)									0.498039	414.728517	414.729327	127	128	CC		KEEP	---	---	---	---	capture		Colorectal(170;0.248)	Nonsense_Mutation	SNP	78774751	78774751	13204	1	C	T	T	23	23	PTGFR	T	5	1
TGM6	343641	broad.mit.edu	36	20	2332044	2332044	+	Missense_Mutation	SNP	A	G	G			TCGA-32-1970-01	TCGA-32-1970-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr20:2332044A>G	uc002wfy.1	+	c.991A>G	c.(991-993)AAT>GAT	p.N331D	TGM6_uc010gal.1_Missense_Mutation_p.N331D	NM_198994	NP_945345	O95932	TGM3L_HUMAN	transglutaminase 6	331					peptide cross-linking		acyltransferase activity|metal ion binding|protein-glutamine gamma-glutamyltransferase activity			ovary(3)	3					L-Glutamine(DB00130)									0.25	7.049819	9.318221	9	27	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	2332044	2332044	16362	20	A	G	G	9	9	TGM6	G	4	4
ZNFX1	57169	broad.mit.edu	36	20	47320417	47320417	+	Nonsense_Mutation	SNP	G	A	A			TCGA-32-1970-01	TCGA-32-1970-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr20:47320417G>A	uc002xui.1	-	c.1339C>T	c.(1339-1341)CGA>TGA	p.R447*		NM_021035	NP_066363	Q9P2E3	ZNFX1_HUMAN	zinc finger, NFX1-type containing 1	447							metal ion binding			ovary(2)	2														0.200637	137.367677	163.516679	63	251	GG		KEEP	---	---	---	---	capture	BRCA - Breast invasive adenocarcinoma(12;0.00173)|COAD - Colon adenocarcinoma(4;0.14)|Colorectal(8;0.166)		Nonsense_Mutation	SNP	47320417	47320417	18809	20	G	A	A	40	40	ZNFX1	A	5	1
PRIC285	85441	broad.mit.edu	36	20	61670728	61670728	+	Missense_Mutation	SNP	G	A	A			TCGA-32-1970-01	TCGA-32-1970-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr20:61670728G>A	uc002yfm.2	-	c.1157C>T	c.(1156-1158)GCG>GTG	p.A386V	PRIC285_uc002yfl.1_5'Flank	NM_001037335	NP_001032412	Q9BYK8	PR285_HUMAN	PPAR-alpha interacting complex protein 285	386					cellular lipid metabolic process|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleoplasm	ATP binding|DNA binding|helicase activity|ribonuclease activity|RNA binding|transcription coactivator activity|zinc ion binding			central_nervous_system(2)	2	all_cancers(38;2.51e-11)|all_epithelial(29;8.27e-13)													0.353659	76.654321	78.200752	29	53	GG		KEEP	---	---	---	---	capture	Epithelial(9;1.27e-08)|all cancers(9;7.32e-08)|BRCA - Breast invasive adenocarcinoma(10;5.15e-06)		Missense_Mutation	SNP	61670728	61670728	12928	20	G	A	A	38	38	PRIC285	A	1	1
CECR2	27443	broad.mit.edu	36	22	16362144	16362144	+	Silent	SNP	C	G	G			TCGA-32-1970-01	TCGA-32-1970-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr22:16362144C>G	uc010gqw.1	+	c.555C>G	c.(553-555)TCC>TCG	p.S185S	CECR2_uc010gqv.1_Silent_p.S64S|CECR2_uc002zml.2_Silent_p.S64S|CECR2_uc002zmm.1_Silent_p.S64S	NM_031413	NP_113601	Q9BXF3	CECR2_HUMAN	cat eye syndrome chromosome region, candidate 2	227					chromatin modification|cytokinesis|cytoskeleton organization|DNA fragmentation involved in apoptotic nuclear change|vesicle-mediated transport		protein binding			ovary(1)|skin(1)	2		all_epithelial(15;0.139)												0.230769	7.117775	7.981716	3	10	CC		KEEP	---	---	---	---	capture		Lung(27;0.146)	Silent	SNP	16362144	16362144	3339	22	C	G	G	23	23	CECR2	G	3	3
ZNRF3	84133	broad.mit.edu	36	22	27775795	27775795	+	Nonsense_Mutation	SNP	C	A	A			TCGA-32-1970-01	TCGA-32-1970-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr22:27775795C>A	uc003aeg.2	+	c.1326C>A	c.(1324-1326)TAC>TAA	p.Y442*	ZNRF3_uc003aeh.1_Nonsense_Mutation_p.Y442*	NM_032173	NP_115549	Q9ULT6	ZNRF3_HUMAN	zinc and ring finger 3	542	Cytoplasmic (Potential).					integral to membrane	zinc ion binding			ovary(1)	1														0.363636	7.362776	7.555805	4	7	CC		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	27775795	27775795	18817	22	C	A	A	18	18	ZNRF3	A	5	3
DPP10	57628	broad.mit.edu	36	2	116213930	116213930	+	Silent	SNP	G	A	A			TCGA-32-1970-01	TCGA-32-1970-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:116213930G>A	uc002tla.1	+	c.843G>A	c.(841-843)CCG>CCA	p.P281P	DPP10_uc002tlb.1_Silent_p.P231P|DPP10_uc002tlc.1_Silent_p.P277P|DPP10_uc002tle.1_Silent_p.P231P|DPP10_uc002tlf.1_Silent_p.P274P	NM_020868	NP_065919	Q8N608	DPP10_HUMAN	dipeptidyl peptidase 10 isoform long	281	Extracellular (Potential).				proteolysis	integral to membrane|membrane fraction	serine-type peptidase activity			ovary(5)|large_intestine(2)|breast(1)|skin(1)	9														0.387352	282.587291	285.402121	98	155	GG		KEEP	---	---	---	---	capture			Silent	SNP	116213930	116213930	4911	2	G	A	A	40	40	DPP10	A	1	1
UGGT1	56886	broad.mit.edu	36	2	128656247	128656247	+	Missense_Mutation	SNP	G	T	T			TCGA-32-1970-01	TCGA-32-1970-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:128656247G>T	uc002tps.1	+	c.4157G>T	c.(4156-4158)TGT>TTT	p.C1386F	UGGT1_uc002tpr.1_Missense_Mutation_p.C1362F	NM_020120	NP_064505	Q9NYU2	UGGG1_HUMAN	UDP-glucose ceramide glucosyltransferase-like 1	1386	Glucosyltransferase (By similarity).				'de novo' posttranslational protein folding|post-translational protein modification|protein N-linked glycosylation via asparagine	endoplasmic reticulum lumen|ER-Golgi intermediate compartment	UDP-glucose:glycoprotein glucosyltransferase activity|unfolded protein binding			ovary(1)	1														0.420792	257.753855	258.855547	85	117	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	128656247	128656247	17499	2	G	T	T	48	48	UGGT1	T	3	3
GCA	25801	broad.mit.edu	36	2	162912416	162912416	+	Missense_Mutation	SNP	G	C	C			TCGA-32-1970-01	TCGA-32-1970-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:162912416G>C	uc002ucg.1	+	c.110G>C	c.(109-111)GGA>GCA	p.G37A		NM_012198	NP_036330	P28676	GRAN_HUMAN	grancalcin, EF-hand calcium binding protein	37					cellular membrane fusion	cytoplasm|plasma membrane	calcium ion binding|protein homodimerization activity				0														0.45082	189.916358	190.172597	55	67	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	162912416	162912416	6549	2	G	C	C	41	41	GCA	C	3	3
GLS	2744	broad.mit.edu	36	2	191473664	191473664	+	Silent	SNP	G	A	A			TCGA-32-1970-01	TCGA-32-1970-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:191473664G>A	uc002usf.2	+	c.735G>A	c.(733-735)AAG>AAA	p.K245K	GLS_uc002use.2_Silent_p.K245K	NM_014905	NP_055720	O94925	GLSK_HUMAN	glutaminase	245					cellular amino acid biosynthetic process|glutamate secretion|glutamine catabolic process|neurotransmitter secretion	mitochondrial matrix	glutaminase activity			ovary(1)	1					L-Glutamic Acid(DB00142)|L-Glutamine(DB00130)									0.179775	37.969916	46.534184	16	73	GG		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(117;0.00625)|Epithelial(96;0.0744)|all cancers(119;0.181)		Silent	SNP	191473664	191473664	6731	2	G	A	A	35	35	GLS	A	2	2
ALK	238	broad.mit.edu	36	2	29327626	29327626	+	Missense_Mutation	SNP	A	C	C			TCGA-32-1970-01	TCGA-32-1970-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr2:29327626A>C	uc002rmy.1	-	c.2053T>G	c.(2053-2055)TTC>GTC	p.F685V		NM_004304	NP_004295	Q9UM73	ALK_HUMAN	anaplastic lymphoma kinase	685	Extracellular (Potential).				protein autophosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|protein binding|transmembrane receptor protein tyrosine kinase activity		NPM1/ALK(632)|EML4/ALK(191)|CLTC/ALK(44)|TPM3/ALK(33)|ATIC/ALK(24)|RANBP2/ALK(14)|TPM4/ALK(12)|TFG/ALK(7)|MSN/ALK(6)|CARS/ALK(5)|VCL/ALK(4)|KIF5B/ALK(4)|PPFIBP1/ALK(3)|SEC31A/ALK(3)|SQSTM1/ALK(2)	haematopoietic_and_lymphoid_tissue(726)|lung(200)|autonomic_ganglia(95)|soft_tissue(59)|kidney(4)|large_intestine(3)|ovary(3)|central_nervous_system(1)|breast(1)|pancreas(1)	1093	Acute lymphoblastic leukemia(172;0.155)				Adenosine triphosphate(DB00171)					777				0.259259	7.517009	9.024696	7	20	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	29327626	29327626	528	2	A	C	C	2	2	ALK	C	4	4
STXBP5L	9515	broad.mit.edu	36	3	122247066	122247066	+	Missense_Mutation	SNP	G	A	A			TCGA-32-1970-01	TCGA-32-1970-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:122247066G>A	uc003eec.2	+	c.464G>A	c.(463-465)CGG>CAG	p.R155Q		NM_014980	NP_055795	Q9Y2K9	STB5L_HUMAN	syntaxin binding protein 5-like	155					exocytosis|protein transport	cytoplasm|integral to membrane|plasma membrane				ovary(7)	7														0.402439	314.481641	316.527507	99	147	GG		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(114;0.0694)	Missense_Mutation	SNP	122247066	122247066	15877	3	G	A	A	39	39	STXBP5L	A	1	1
MECOM	2122	broad.mit.edu	36	3	170316563	170316563	+	Silent	SNP	C	T	T			TCGA-32-1970-01	TCGA-32-1970-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr3:170316563C>T	uc003ffl.2	-	c.1707G>A	c.(1705-1707)TCG>TCA	p.S569S	MECOM_uc010hwn.1_Silent_p.S597S|MECOM_uc010hwk.1_Silent_p.S432S|MECOM_uc010hwl.1_Silent_p.S473S|MECOM_uc003ffi.2_Silent_p.S409S|MECOM_uc003ffj.2_Silent_p.S474S|MECOM_uc003ffn.2_Silent_p.S399S|MECOM_uc010hwm.1_Silent_p.S409S|MECOM_uc003ffk.2_Silent_p.S399S	NM_005241	NP_005232	Q13465	MDS1_HUMAN	ecotropic viral integration site 1 isoform b	Error:Variant_position_missing_in_Q13465_after_alignment							sequence-specific DNA binding transcription factor activity			lung(3)|skin(2)|ovary(1)|pancreas(1)|central_nervous_system(1)	8									p.S409S(ZR7530-Tumor)	646				0.518293	277.573841	277.621434	85	79	CC		KEEP	---	---	---	---	capture			Silent	SNP	170316563	170316563	9811	3	C	T	T	23	23	MECOM	T	1	1
RBMS3	27303	broad.mit.edu	36	3	30007605	30007605	+	Missense_Mutation	SNP	C	G	G			TCGA-32-1970-01	TCGA-32-1970-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr3:30007605C>G	uc003cel.1	+	c.1208C>G	c.(1207-1209)ACA>AGA	p.T403R	RBMS3_uc003cek.1_Missense_Mutation_p.T387R|RBMS3_uc010hfq.1_Missense_Mutation_p.T400R|RBMS3_uc003cem.1_Missense_Mutation_p.T385R|RBMS3_uc010hfr.1_Missense_Mutation_p.T387R	NM_001003793	NP_001003793	Q6XE24	RBMS3_HUMAN	RNA binding motif, single stranded interacting	403						cytoplasm	nucleotide binding|RNA binding			central_nervous_system(1)	1		Ovarian(412;0.0956)												0.424779	168.685208	169.242492	48	65	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	30007605	30007605	13612	3	C	G	G	17	17	RBMS3	G	3	3
CCR9	10803	broad.mit.edu	36	3	45917425	45917425	+	Silent	SNP	G	A	A			TCGA-32-1970-01	TCGA-32-1970-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:45917425G>A	uc003coz.1	+	c.141G>A	c.(139-141)GCG>GCA	p.A47A	LZTFL1_uc003coy.1_Intron|CCR9_uc010hiv.1_Silent_p.A35A|CCR9_uc003cpa.1_Silent_p.A35A|CCR9_uc010hiw.1_Silent_p.A35A	NM_031200	NP_006632	P51686	CCR9_HUMAN	chemokine (C-C motif) receptor 9 isoform A	47	Extracellular (Potential).				cellular defense response|chemotaxis|elevation of cytosolic calcium ion concentration|immune response	integral to plasma membrane				ovary(2)	2														0.429658	337.976647	339.101034	113	150	GG		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(193;0.00118)|KIRC - Kidney renal clear cell carcinoma(197;0.0182)|Kidney(197;0.0214)	Silent	SNP	45917425	45917425	3075	3	G	A	A	37	37	CCR9	A	1	1
STAB1	23166	broad.mit.edu	36	3	52515273	52515273	+	Silent	SNP	G	A	A			TCGA-32-1970-01	TCGA-32-1970-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:52515273G>A	uc003dej.1	+	c.1797G>A	c.(1795-1797)GCG>GCA	p.A599A	STAB1_uc003dei.1_Silent_p.A599A	NM_015136	NP_055951	Q9NY15	STAB1_HUMAN	stabilin 1 precursor	599	Extracellular (Potential).|FAS1 2.				cell adhesion|cell-cell signaling|defense response to bacterium|inflammatory response|negative regulation of angiogenesis|receptor-mediated endocytosis	integral to plasma membrane	bacterial cell surface binding|hyaluronic acid binding|low-density lipoprotein receptor activity|protein disulfide oxidoreductase activity|scavenger receptor activity			large_intestine(3)|pancreas(1)|breast(1)|central_nervous_system(1)|skin(1)	7														0.307692	21.690307	22.547451	8	18	GG		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(193;1.73e-05)|Kidney(197;0.00182)|KIRC - Kidney renal clear cell carcinoma(197;0.00205)|OV - Ovarian serous cystadenocarcinoma(275;0.0482)	Silent	SNP	52515273	52515273	15755	3	G	A	A	37	37	STAB1	A	1	1
FRG2	448831	broad.mit.edu	36	4	191184163	191184163	+	Silent	SNP	G	C	C			TCGA-32-1970-01	TCGA-32-1970-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr4:191184163G>C	uc003izv.1	-	c.384C>G	c.(382-384)TCC>TCG	p.S128S		NM_001005217	NP_001005217	Q64ET8	FRG2_HUMAN	FSHD region gene 2	128						nucleus				ovary(1)	1		all_cancers(14;1.01e-50)|all_epithelial(14;6.7e-35)|all_lung(41;2.17e-14)|Lung NSC(41;4.95e-14)|Breast(6;3.4e-05)|Melanoma(20;0.000539)|Hepatocellular(41;0.0218)|Renal(120;0.0376)|all_hematologic(60;0.0489)|Prostate(90;0.0513)												0.448052	197.813899	198.180945	69	85	GG		KEEP	---	---	---	---	capture		all cancers(3;3.83e-31)|Epithelial(3;1.36e-30)|OV - Ovarian serous cystadenocarcinoma(60;1.99e-15)|BRCA - Breast invasive adenocarcinoma(30;8.54e-06)|Lung(3;3.23e-05)|STAD - Stomach adenocarcinoma(60;8.24e-05)|LUSC - Lung squamous cell carcinoma(40;0.000184)|GBM - Glioblastoma multiforme(59;0.00831)|READ - Rectum adenocarcinoma(43;0.155)	Silent	SNP	191184163	191184163	6295	4	G	C	C	35	35	FRG2	C	3	3
GPR78	27201	broad.mit.edu	36	4	8634261	8634261	+	Missense_Mutation	SNP	G	A	A			TCGA-32-1970-01	TCGA-32-1970-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr4:8634261G>A	uc003glk.1	+	c.652G>A	c.(652-654)GCC>ACC	p.A218T	CPZ_uc003gll.1_Non-coding_Transcript	NM_080819	NP_543009	Q96P69	GPR78_HUMAN	G protein-coupled receptor 78	218	Cytoplasmic (Potential).				activation of adenylate cyclase activity by G-protein signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			central_nervous_system(4)|ovary(2)	6														0.5	11.39859	11.39859	4	4	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	8634261	8634261	6985	4	G	A	A	38	38	GPR78	A	1	1
PCDHA2	56146	broad.mit.edu	36	5	140156931	140156931	+	Missense_Mutation	SNP	C	T	T			TCGA-32-1970-01	TCGA-32-1970-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:140156931C>T	uc003lhd.1	+	c.2198C>T	c.(2197-2199)GCG>GTG	p.A733V	PCDHA1_uc003lha.1_Intron|PCDHA1_uc003lhb.1_Intron|PCDHA2_uc003lhc.1_Missense_Mutation_p.A733V	NM_018905	NP_061728	Q9Y5H9	PCDA2_HUMAN	protocadherin alpha 2 isoform 1 precursor	733	Cytoplasmic (Potential).				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding|protein binding			ovary(4)	4														0.412371	113.781075	114.431423	40	57	CC		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		Missense_Mutation	SNP	140156931	140156931	11944	5	C	T	T	27	27	PCDHA2	T	1	1
PCDHGB1	56104	broad.mit.edu	36	5	140710263	140710263	+	Silent	SNP	C	T	T			TCGA-32-1970-01	TCGA-32-1970-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:140710263C>T	uc003ljo.1	+	c.252C>T	c.(250-252)AAC>AAT	p.N84N	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc010jfx.1_Intron|PCDHGA3_uc003ljm.1_Intron|PCDHGB1_uc003ljn.1_Silent_p.N84N	NM_018922	NP_061745	Q9Y5G3	PCDGD_HUMAN	protocadherin gamma subfamily B, 1 isoform 1	84	Cadherin 1.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding				0												OREG0016856	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.304348	77.265896	80.407776	28	64	CC		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		Silent	SNP	140710263	140710263	11982	5	C	T	T	19	19	PCDHGB1	T	1	1
FAM71B	153745	broad.mit.edu	36	5	156525447	156525447	+	Missense_Mutation	SNP	C	T	T			TCGA-32-1970-01	TCGA-32-1970-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:156525447C>T	uc003lwn.1	-	c.311G>A	c.(310-312)CGG>CAG	p.R104Q		NM_130899	NP_570969	Q8TC56	FA71B_HUMAN	family with sequence similarity 71, member B	104						nucleus				ovary(3)|pancreas(1)	4	Renal(175;0.00212)	Medulloblastoma(196;0.0523)|all_neural(177;0.21)												0.311111	77.16853	80.027443	28	62	CC		KEEP	---	---	---	---	capture	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)		Missense_Mutation	SNP	156525447	156525447	5831	5	C	T	T	23	23	FAM71B	T	1	1
RANBP17	64901	broad.mit.edu	36	5	170658420	170658420	+	Missense_Mutation	SNP	C	T	T			TCGA-32-1970-01	TCGA-32-1970-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:170658420C>T	uc003mba.1	+	c.3220C>T	c.(3220-3222)CGC>TGC	p.R1074C	RANBP17_uc003mbb.1_Missense_Mutation_p.R399C|RANBP17_uc010jjs.1_Non-coding_Transcript	NM_022897	NP_075048	Q9H2T7	RBP17_HUMAN	RAN binding protein 17	1074					mRNA transport|protein import into nucleus|transmembrane transport	cytoplasm|nuclear pore	GTP binding|protein transporter activity			ovary(2)|central_nervous_system(1)	3	Renal(175;0.000159)|Lung NSC(126;0.00751)|all_lung(126;0.0123)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)								661				0.393939	74.035194	74.685075	26	40	CC		KEEP	---	---	---	---	capture	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)		Missense_Mutation	SNP	170658420	170658420	13487	5	C	T	T	27	27	RANBP17	T	1	1
FBXW11	23291	broad.mit.edu	36	5	171232548	171232548	+	Missense_Mutation	SNP	G	A	A			TCGA-32-1970-01	TCGA-32-1970-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:171232548G>A	uc003mbm.1	-	c.1210C>T	c.(1210-1212)CGG>TGG	p.R404W	FBXW11_uc003mbl.1_Missense_Mutation_p.R391W|FBXW11_uc003mbn.1_Missense_Mutation_p.R370W	NM_012300	NP_036432	Q9UKB1	FBW1B_HUMAN	F-box and WD repeat domain containing 11 isoform	404	WD 5.				cell cycle|negative regulation of gene-specific transcription|positive regulation of circadian rhythm|positive regulation of gene-specific transcription|positive regulation of proteolysis|protein dephosphorylation|protein destabilization|protein polyubiquitination|rhythmic process|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process|Wnt receptor signaling pathway	cytosol|nucleus|SCF ubiquitin ligase complex	protein binding|specific transcriptional repressor activity|transcription activator activity|ubiquitin-protein ligase activity			ovary(1)|breast(1)	2	Renal(175;0.000159)|Lung NSC(126;0.00384)|all_lung(126;0.00659)	Medulloblastoma(196;0.00853)|all_neural(177;0.026)												0.322581	105.359222	108.823726	40	84	GG		KEEP	---	---	---	---	capture	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)		Missense_Mutation	SNP	171232548	171232548	6001	5	G	A	A	38	38	FBXW11	A	1	1
C7	730	broad.mit.edu	36	5	41012616	41012616	+	Silent	SNP	G	A	A			TCGA-32-1970-01	TCGA-32-1970-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:41012616G>A	uc003jmh.1	+	c.2082G>A	c.(2080-2082)CCG>CCA	p.P694P		NM_000587	NP_000578	P10643	CO7_HUMAN	complement component 7 precursor	694					complement activation, alternative pathway|complement activation, classical pathway|cytolysis	extracellular region|membrane attack complex					0		Ovarian(839;0.0112)												0.5	25.199939	25.199939	8	8	GG		KEEP	---	---	---	---	capture			Silent	SNP	41012616	41012616	2482	5	G	A	A	40	40	C7	A	1	1
ACTBL2	345651	broad.mit.edu	36	5	56814075	56814075	+	Missense_Mutation	SNP	C	T	T			TCGA-32-1970-01	TCGA-32-1970-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:56814075C>T	uc003jrm.1	-	c.217G>A	c.(217-219)GAG>AAG	p.E73K		NM_001017992	NP_001017992	Q562R1	ACTBL_HUMAN	actin, beta-like 2	73						cytoplasm|cytoskeleton	ATP binding			ovary(3)	3		Lung NSC(810;0.000135)|Prostate(74;0.055)|Breast(144;0.0707)|Ovarian(174;0.182)												0.372881	63.547666	64.379903	22	37	CC		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(10;4.24e-37)	Missense_Mutation	SNP	56814075	56814075	195	5	C	T	T	31	31	ACTBL2	T	1	1
BCLAF1	9774	broad.mit.edu	36	6	136639099	136639099	+	Missense_Mutation	SNP	C	A	A			TCGA-32-1970-01	TCGA-32-1970-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:136639099C>A	uc003qgx.1	-	c.1257G>T	c.(1255-1257)CAG>CAT	p.Q419H	BCLAF1_uc003qgw.1_Intron|BCLAF1_uc003qgy.1_Missense_Mutation_p.Q417H	NM_014739	NP_055554	Q9NYF8	BCLF1_HUMAN	BCL2-associated transcription factor 1 isoform	419					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)								0.14966	187.390815	273.882154	110	625	CC		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(68;0.00226)|OV - Ovarian serous cystadenocarcinoma(155;0.00331)	Missense_Mutation	SNP	136639099	136639099	1404	6	C	A	A	24	24	BCLAF1	A	3	3
CDK13	8621	broad.mit.edu	36	7	40094308	40094308	+	Nonsense_Mutation	SNP	C	T	T			TCGA-32-1970-01	TCGA-32-1970-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:40094308C>T	uc003thh.2	+	c.3088C>T	c.(3088-3090)CAG>TAG	p.Q1030*	CDK13_uc003thi.2_Nonsense_Mutation_p.Q1030*|CDK13_uc003thj.1_Nonsense_Mutation_p.Q81*	NM_003718	NP_003709	Q14004	CDK13_HUMAN	cell division cycle 2-like 5 isoform 1	1030					alternative nuclear mRNA splicing, via spliceosome|hemopoiesis|interspecies interaction between organisms|phosphorylation of RNA polymerase II C-terminal domain|positive regulation of cell proliferation|regulation of mitosis	nuclear cyclin-dependent protein kinase holoenzyme complex|nuclear speck	ATP binding|cyclin-dependent protein kinase activity|protein binding|RNA polymerase II carboxy-terminal domain kinase activity			lung(2)|ovary(1)|skin(1)	4										238				0.239521	90.305518	100.659277	40	127	CC		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	40094308	40094308	3258	7	C	T	T	25	25	CDK13	T	5	2
EGFR	1956	broad.mit.edu	36	7	55189316	55189316	+	Missense_Mutation	SNP	C	T	T			TCGA-32-1970-01	TCGA-32-1970-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:55189316C>T	uc003tqk.1	+	c.866C>T	c.(865-867)GCC>GTC	p.A289V	EGFR_uc003tqh.1_Missense_Mutation_p.A289V|EGFR_uc003tqi.1_Missense_Mutation_p.A289V|EGFR_uc003tqj.1_Missense_Mutation_p.A289V|EGFR_uc010kzg.1_Missense_Mutation_p.A244V	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.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)			0.550209	1603.82492	1605.938839	526	430	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	55189316	55189316	5156	7	C	T	T	26	26	EGFR	T	2	2
ZNF107	51427	broad.mit.edu	36	7	63804716	63804716	+	Missense_Mutation	SNP	C	A	A			TCGA-32-1970-01	TCGA-32-1970-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:63804716C>A	uc003ttd.1	+	c.599C>A	c.(598-600)GCC>GAC	p.A200D	ZNF107_uc003tte.1_Missense_Mutation_p.A200D	NM_016220	NP_057304	Q9UII5	ZN107_HUMAN	zinc finger protein 107	200	C2H2-type 5.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1		Lung NSC(55;0.00948)|all_lung(88;0.0249)												0.262911	138.11953	148.939307	56	157	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	63804716	63804716	18306	7	C	A	A	26	26	ZNF107	A	3	3
MAGI2	9863	broad.mit.edu	36	7	77645335	77645335	+	Missense_Mutation	SNP	C	T	T			TCGA-32-1970-01	TCGA-32-1970-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:77645335C>T	uc003ugx.1	-	c.2332G>A	c.(2332-2334)GAT>AAT	p.D778N	MAGI2_uc003ugy.1_Missense_Mutation_p.D764N|MAGI2_uc010ldx.1_Missense_Mutation_p.D371N	NM_012301	NP_036433	Q86UL8	MAGI2_HUMAN	membrane associated guanylate kinase, WW and PDZ	778	PDZ 4.					cell junction|synapse|synaptosome	phosphatase binding			ovary(5)	5		all_cancers(73;0.0064)|all_epithelial(88;0.087)|all_neural(109;0.0936)|Medulloblastoma(109;0.166)|Melanoma(862;0.236)												0.220513	99.420942	113.445378	43	152	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	77645335	77645335	9574	7	C	T	T	30	30	MAGI2	T	2	2
PCLO	27445	broad.mit.edu	36	7	82420496	82420496	+	Missense_Mutation	SNP	G	A	A			TCGA-32-1970-01	TCGA-32-1970-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:82420496G>A	uc003uhx.2	-	c.7709C>T	c.(7708-7710)CCA>CTA	p.P2570L	PCLO_uc003uhv.2_Missense_Mutation_p.P2570L|PCLO_uc010lec.1_5'Flank	NM_033026	NP_149015	Q9Y6V0	PCLO_HUMAN	piccolo isoform 1	2501					cytoskeleton organization|synaptic vesicle exocytosis	cell junction|cytoskeleton|synaptic vesicle	calcium ion binding|calcium-dependent phospholipid binding|profilin binding|transporter activity|zinc ion binding			ovary(7)	7														0.224537	235.658867	265.788099	97	335	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	82420496	82420496	12003	7	G	A	A	47	47	PCLO	A	2	2
GRM3	2913	broad.mit.edu	36	7	86254156	86254156	+	Missense_Mutation	SNP	G	A	A			TCGA-32-1970-01	TCGA-32-1970-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:86254156G>A	uc003uid.1	+	c.1112G>A	c.(1111-1113)CGC>CAC	p.R371H	GRM3_uc010lef.1_Missense_Mutation_p.R369H|GRM3_uc010leg.1_Missense_Mutation_p.R243H|GRM3_uc010leh.1_Intron	NM_000840	NP_000831	Q14832	GRM3_HUMAN	glutamate receptor, metabotropic 3 precursor	371	Extracellular (Potential).				synaptic transmission	integral to plasma membrane				ovary(3)|central_nervous_system(2)	5	Esophageal squamous(14;0.0058)|all_lung(186;0.132)|Lung NSC(181;0.142)				Acamprosate(DB00659)|Nicotine(DB00184)	GBM(52;969 1098 3139 52280)								0.213235	63.405048	73.736076	29	107	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	86254156	86254156	7077	7	G	A	A	38	38	GRM3	A	1	1
GRM3	2913	broad.mit.edu	36	7	86254270	86254270	+	Missense_Mutation	SNP	G	A	A			TCGA-32-1970-01	TCGA-32-1970-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:86254270G>A	uc003uid.1	+	c.1226G>A	c.(1225-1227)CGC>CAC	p.R409H	GRM3_uc010lef.1_Missense_Mutation_p.R407H|GRM3_uc010leg.1_Missense_Mutation_p.R281H|GRM3_uc010leh.1_Intron	NM_000840	NP_000831	Q14832	GRM3_HUMAN	glutamate receptor, metabotropic 3 precursor	409	Extracellular (Potential).				synaptic transmission	integral to plasma membrane				ovary(3)|central_nervous_system(2)	5	Esophageal squamous(14;0.0058)|all_lung(186;0.132)|Lung NSC(181;0.142)				Acamprosate(DB00659)|Nicotine(DB00184)	GBM(52;969 1098 3139 52280)								0.257471	279.738802	302.907846	112	323	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	86254270	86254270	7077	7	G	A	A	38	38	GRM3	A	1	1
STEAP1	26872	broad.mit.edu	36	7	89629261	89629261	+	Missense_Mutation	SNP	T	C	C			TCGA-32-1970-01	TCGA-32-1970-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr7:89629261T>C	uc003ujx.1	+	c.695T>C	c.(694-696)CTG>CCG	p.L232P	STEAP1_uc010lem.1_Missense_Mutation_p.L232P	NM_012449	NP_036581	Q9UHE8	STEA1_HUMAN	six transmembrane epithelial antigen of the	232	Ferric oxidoreductase.|Helical; (Potential).				electron transport chain|ion transport|iron ion homeostasis	cell-cell junction|endosome membrane|integral to plasma membrane	channel activity|electron carrier activity|flavin adenine dinucleotide binding|iron ion binding|oxidoreductase activity				0	all_hematologic(106;0.112)													0.235925	208.706028	232.496046	88	285	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	89629261	89629261	15797	7	T	C	C	55	55	STEAP1	C	4	4
ENPP2	5168	broad.mit.edu	36	8	120698940	120698940	+	Missense_Mutation	SNP	C	T	T			TCGA-32-1970-01	TCGA-32-1970-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr8:120698940C>T	uc003yos.1	-	c.524G>A	c.(523-525)CGT>CAT	p.R175H	ENPP2_uc003yot.1_Missense_Mutation_p.R175H|ENPP2_uc010mdd.1_Missense_Mutation_p.R175H	NM_006209	NP_006200	Q13822	ENPP2_HUMAN	autotaxin isoform 1 preproprotein	175					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)								0.444444	71.298575	71.442593	24	30	CC		KEEP	---	---	---	---	capture	STAD - Stomach adenocarcinoma(47;0.00185)		Missense_Mutation	SNP	120698940	120698940	5323	8	C	T	T	19	19	ENPP2	T	1	1
BAI1	575	broad.mit.edu	36	8	143622029	143622029	+	Silent	SNP	C	T	T			TCGA-32-1970-01	TCGA-32-1970-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr8:143622029C>T	uc003ywm.1	+	c.4515C>T	c.(4513-4515)CAC>CAT	p.H1505H		NM_001702	NP_001693	O14514	BAI1_HUMAN	brain-specific angiogenesis inhibitor 1	1505	Cytoplasmic (Potential).|Necessary for interaction with MAGI1.				axonogenesis|cell adhesion|negative regulation of cell proliferation|neuropeptide signaling pathway|peripheral nervous system development	cell-cell junction|integral to plasma membrane	G-protein coupled receptor activity|protein binding			ovary(1)|breast(1)|central_nervous_system(1)|pancreas(1)	4	all_cancers(97;2.84e-12)|all_epithelial(106;5.91e-09)|Lung NSC(106;0.000322)|all_lung(105;0.000616)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0315)|Acute lymphoblastic leukemia(118;0.155)									829				0.666667	19.152839	19.37456	6	3	CC		KEEP	---	---	---	---	capture			Silent	SNP	143622029	143622029	1319	8	C	T	T	19	19	BAI1	T	1	1
ZNF704	619279	broad.mit.edu	36	8	81762184	81762184	+	Nonsense_Mutation	SNP	G	T	T			TCGA-32-1970-01	TCGA-32-1970-01	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)	0.333333	8.091222	8.388823	4	8	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
TMEM67	91147	broad.mit.edu	36	8	94837180	94837180	+	Splice_Site_SNP	SNP	A	T	T			TCGA-32-1970-01	TCGA-32-1970-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr8:94837180A>T	uc003ygd.2	+	c.194_splice	c.e2-2	p.G65_splice	TMEM67_uc003yga.2_Intron|TMEM67_uc010mat.1_Splice_Site_SNP|TMEM67_uc010mau.1_Splice_Site_SNP_p.G75_splice|TMEM67_uc010mav.1_Splice_Site_SNP_p.G75_splice|TMEM67_uc010maw.1_Splice_Site_SNP_p.G75_splice	NM_153704	NP_714915			meckelin isoform 1						cilium assembly|ER-associated protein catabolic process|negative regulation of centrosome duplication	centrosome|cilium membrane|cytoplasmic vesicle membrane|endoplasmic reticulum membrane|integral to membrane|microtubule basal body	unfolded protein binding			ovary(2)	2	Breast(36;4.14e-07)													0.134615	9.192558	15.922381	7	45	AA		KEEP	---	---	---	---	capture	BRCA - Breast invasive adenocarcinoma(8;0.00896)		Splice_Site_SNP	SNP	94837180	94837180	16735	8	A	T	T	15	15	TMEM67	T	5	4
OR13C9	286362	broad.mit.edu	36	9	106419374	106419374	+	Silent	SNP	C	T	T			TCGA-32-1970-01	TCGA-32-1970-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr9:106419374C>T	uc004bcf.1	-	c.933G>A	c.(931-933)CCG>CCA	p.P311P		NM_001001956	NP_001001956	Q8NGT0	O13C9_HUMAN	olfactory receptor, family 13, subfamily C,	311	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0														0.324873	356.757198	367.48413	128	266	CC		KEEP	---	---	---	---	capture			Silent	SNP	106419374	106419374	11345	9	C	T	T	31	31	OR13C9	T	1	1
BAT2L1	84726	broad.mit.edu	36	9	133340543	133340543	+	Missense_Mutation	SNP	G	A	A			TCGA-32-1970-01	TCGA-32-1970-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr9:133340543G>A	uc004can.2	+	c.3206G>A	c.(3205-3207)CGT>CAT	p.R1069H	BAT2L1_uc010mzj.1_Missense_Mutation_p.R652H|BAT2L1_uc004cao.2_Missense_Mutation_p.R427H	NM_013318	NP_037450	Q5JSZ5	PRC2B_HUMAN	HLA-B associated transcript 2-like	1069							protein binding				0														0.253731	40.543175	44.231903	17	50	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	133340543	133340543	1341	9	G	A	A	40	40	BAT2L1	A	1	1
CEL	1056	broad.mit.edu	36	9	134935784	134935784	+	Missense_Mutation	SNP	G	A	A			TCGA-32-1970-01	TCGA-32-1970-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr9:134935784G>A	uc010naa.1	+	c.1411G>A	c.(1411-1413)GCC>ACC	p.A471T		NM_001807	NP_001798	P19835	CEL_HUMAN	carboxyl ester lipase precursor	468					cholesterol catabolic process|fatty acid catabolic process|intestinal cholesterol absorption|intestinal lipid catabolic process|pancreatic juice secretion|protein esterification|regulation of synaptic transmission|triglyceride metabolic process		acylglycerol lipase activity|heparin binding|sterol esterase activity|triglyceride lipase activity			pancreas(1)	1														0.099125	14.425305	69.40753	34	309	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(145;1.03e-40)|Epithelial(140;3.58e-37)|GBM - Glioblastoma multiforme(294;0.00164)|READ - Rectum adenocarcinoma(205;0.196)	Missense_Mutation	SNP	134935784	134935784	3342	9	G	A	A	38	38	CEL	A	1	1
EGFL6	25975	broad.mit.edu	36	X	13534464	13534464	+	Missense_Mutation	SNP	G	A	A			TCGA-32-1970-01	TCGA-32-1970-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:13534464G>A	uc004cvj.1	+	c.566G>A	c.(565-567)CGA>CAA	p.R189Q	EGFL6_uc004cvi.1_Missense_Mutation_p.R189Q	NM_015507	NP_056322	Q8IUX8	EGFL6_HUMAN	epidermal growth factor-like protein 6	189	EGF-like 4; calcium-binding (Potential).				cell adhesion|cell cycle|cell differentiation|multicellular organismal development	basement membrane|extracellular space|membrane	calcium ion binding|integrin binding			breast(2)	2														0.889571	488.473922	512.93884	145	18	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	13534464	13534464	5152	23	G	A	A	37	37	EGFL6	A	1	1
AWAT1	158833	broad.mit.edu	36	X	69376477	69376477	+	Missense_Mutation	SNP	T	C	C			TCGA-32-1970-01	TCGA-32-1970-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chrX:69376477T>C	uc004dxy.1	+	c.800T>C	c.(799-801)CTC>CCC	p.L267P		NM_001013579	NP_001013597	Q58HT5	AWAT1_HUMAN	acyl-CoA wax alcohol acyltransferase 1	267					lipid biosynthetic process	endoplasmic reticulum membrane|integral to membrane	long-chain-alcohol O-fatty-acyltransferase activity			ovary(3)	3														0.291667	8.913515	9.997076	7	17	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	69376477	69376477	1255	23	T	C	C	54	54	AWAT1	C	4	4
NACA	4666	broad.mit.edu	36	12	55395936	55395937	+	Frame_Shift_Ins	INS	-	T	T			TCGA-32-1970-01	TCGA-32-1970-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:55395936_55395937insT	uc009zoy.1	-	c.5644_5645insA	c.(5644-5646)ACGfs	p.T1882fs	NACA_uc001slz.2_Intron|NACA_uc001sly.2_Intron|NACA_uc001smc.2_Intron|NACA_uc001sma.2_Frame_Shift_Ins_p.T729fs|NACA_uc001smb.2_Intron	NM_001113203	NP_001106674	Q13765	NACA_HUMAN	nascent polypeptide-associated complex alpha	19					interspecies interaction between organisms|protein transport|transcription, DNA-dependent|translation	nascent polypeptide-associated complex|nucleus	DNA binding			ovary(1)	1									p.T1882R(MHHES1-Tumor)	449				0.38			70	113				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	55395936	55395937	10528	12	-	T	T	40	40	NACA	T	5	5
TNK2	10188	broad.mit.edu	36	3	197081402	197081403	+	Frame_Shift_Ins	INS	-	G	G			TCGA-32-1970-01	TCGA-32-1970-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:197081402_197081403insG	uc003fvt.1	-	c.1711_1712insC	c.(1711-1713)CAGfs	p.Q571fs	TNK2_uc003fvq.1_5'Flank|TNK2_uc003fvr.1_Frame_Shift_Ins_p.Q18fs|TNK2_uc003fvs.1_Frame_Shift_Ins_p.Q540fs|TNK2_uc003fvu.1_Frame_Shift_Ins_p.Q508fs|TNK2_uc010hzw.1_Non-coding_Transcript|TNK2_uc003fvv.1_Frame_Shift_Ins_p.Q338fs	NM_001010938	NP_001010938	Q07912	ACK1_HUMAN	tyrosine kinase, non-receptor, 2 isoform 2	508				Missing (in Ref. 4; AAH08884).	positive regulation of peptidyl-tyrosine phosphorylation|protein phosphorylation|protein ubiquitination|small GTPase mediated signal transduction	adherens junction|cytoplasmic vesicle membrane|endosome|nucleus	ATP binding|GTPase inhibitor activity|metal ion binding|non-membrane spanning protein tyrosine kinase activity|protein binding			ovary(3)|central_nervous_system(3)|lung(2)|stomach(1)|skin(1)	10	all_cancers(143;6.48e-09)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;1.46e-22)|OV - Ovarian serous cystadenocarcinoma(49;8.3e-19)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;0.000757)	Adenosine triphosphate(DB00171)					288				0.47			7	8				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	197081402	197081403	16859	3	-	G	G	55	55	TNK2	G	5	5
