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
CHUK	1147	broad.mit.edu	36	10	101971858	101971858	+	Splice_Site_SNP	SNP	C	T	T			TCGA-14-0790-01	TCGA-14-0790-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr10:101971858C>T	uc001kqp.1	-	c.385_splice	c.e4+1	p.G129_splice		NM_001278	NP_001269			conserved helix-loop-helix ubiquitous kinase						I-kappaB phosphorylation|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|T cell receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	CD40 receptor complex|cytosol|internal side of plasma membrane|nucleus	ATP binding|identical protein binding|IkappaB kinase activity			ovary(2)|central_nervous_system(2)|large_intestine(1)|lung(1)|breast(1)	7		Colorectal(252;0.117)				Ovarian(159;52 1904 10536 35305 37148)				415				0.73913	55.584306	56.774056	17	6	CC		KEEP	---	---	---	---	capture		Epithelial(162;2.05e-10)|all cancers(201;1.91e-08)	Splice_Site_SNP	SNP	101971858	101971858	3550	10	C	T	T	18	18	CHUK	T	5	2
TRUB1	142940	broad.mit.edu	36	10	116688102	116688102	+	Missense_Mutation	SNP	A	C	C			TCGA-14-0790-01	TCGA-14-0790-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr10:116688102A>C	uc001lcd.1	+	c.100A>C	c.(100-102)ACC>CCC	p.T34P		NM_139169	NP_631908	Q8WWH5	TRUB1_HUMAN	TruB pseudouridine (psi) synthase homolog 1	34					pseudouridine synthesis|tRNA processing		pseudouridine synthase activity|RNA binding				0		Colorectal(252;0.09)|Breast(234;0.174)|Lung NSC(174;0.245)												0.571429	8.177078	8.205497	4	3	AA		KEEP	---	---	---	---	capture		Epithelial(162;0.00879)|all cancers(201;0.0243)	Missense_Mutation	SNP	116688102	116688102	17153	10	A	C	C	10	10	TRUB1	C	4	4
RTKN2	219790	broad.mit.edu	36	10	63627763	63627763	+	Silent	SNP	G	T	T			TCGA-14-0790-01	TCGA-14-0790-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr10:63627763G>T	uc001jlw.1	-	c.1740C>A	c.(1738-1740)ACC>ACA	p.T580T	RTKN2_uc009xpf.1_Intron|RTKN2_uc001jlv.1_Silent_p.T234T	NM_145307	NP_660350	Q8IZC4	RTKN2_HUMAN	rhotekin 2	580					signal transduction	intracellular					0	Prostate(12;0.0297)|all_hematologic(501;0.215)													0.828571	194.090784	201.232831	58	12	GG		KEEP	---	---	---	---	capture			Silent	SNP	63627763	63627763	14203	10	G	T	T	47	47	RTKN2	T	3	3
LGR4	55366	broad.mit.edu	36	11	27347114	27347114	+	Missense_Mutation	SNP	C	T	T			TCGA-14-0790-01	TCGA-14-0790-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:27347114C>T	uc001mrj.2	-	c.1732G>A	c.(1732-1734)GGC>AGC	p.G578S	LGR4_uc001mrk.2_Missense_Mutation_p.G554S	NM_018490	NP_060960	Q9BXB1	LGR4_HUMAN	leucine-rich repeat-containing G protein-coupled	578	Helical; Name=2; (Potential).					integral to membrane|plasma membrane	protein-hormone receptor activity			ovary(1)	1														0.379845	154.139399	155.774955	49	80	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	27347114	27347114	9082	11	C	T	T	24	24	LGR4	T	2	2
HARBI1	283254	broad.mit.edu	36	11	46594056	46594056	+	Missense_Mutation	SNP	C	T	T			TCGA-14-0790-01	TCGA-14-0790-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:46594056C>T	uc001ncy.1	-	c.308G>A	c.(307-309)TGT>TAT	p.C103Y	ATG13_uc001ncz.1_5'Flank|ATG13_uc009yld.1_5'Flank|ATG13_uc001nda.1_5'Flank|ATG13_uc001ndb.1_5'Flank|ATG13_uc001ndc.1_5'Flank	NM_173811	NP_776172	Q96MB7	HARB1_HUMAN	harbinger transposase derived 1	103						cytoplasm|nucleus	metal ion binding|nuclease activity				0														0.444015	321.708891	322.426847	115	144	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	46594056	46594056	7240	11	C	T	T	17	17	HARBI1	T	2	2
SBNO1	55206	broad.mit.edu	36	12	122360292	122360292	+	Silent	SNP	C	T	T			TCGA-14-0790-01	TCGA-14-0790-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:122360292C>T	uc009zxw.1	-	c.3360G>A	c.(3358-3360)GCG>GCA	p.A1120A	SBNO1_uc009zxv.1_Non-coding_Transcript|SBNO1_uc001uer.1_Silent_p.A1119A|SBNO1_uc009zxx.1_Silent_p.A71A|SBNO1_uc001ues.1_Silent_p.A71A	NM_018183	NP_060653	A3KN83	SBNO1_HUMAN	sno, strawberry notch homolog 1	1120							ATP binding|DNA binding|hydrolase activity			breast(5)|ovary(1)|kidney(1)	7	all_neural(191;0.101)|Medulloblastoma(191;0.163)													0.407303	431.028753	433.69484	145	211	CC		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(86;0.000701)|Epithelial(86;0.00197)	Silent	SNP	122360292	122360292	14343	12	C	T	T	19	19	SBNO1	T	1	1
KRT3	3850	broad.mit.edu	36	12	51471847	51471847	+	Silent	SNP	C	T	T			TCGA-14-0790-01	TCGA-14-0790-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:51471847C>T	uc001say.1	-	c.1209G>A	c.(1207-1209)ACG>ACA	p.T403T		NM_057088	NP_476429	P12035	K2C3_HUMAN	keratin 3	403	Rod.|Coil 2.				epithelial cell differentiation|intermediate filament cytoskeleton organization	keratin filament	structural molecule activity				0														0.367347	105.67989	107.19357	36	62	CC		KEEP	---	---	---	---	capture			Silent	SNP	51471847	51471847	8781	12	C	T	T	23	23	KRT3	T	1	1
OR6C4	341418	broad.mit.edu	36	12	54231881	54231881	+	Missense_Mutation	SNP	G	A	A			TCGA-14-0790-01	TCGA-14-0790-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:54231881G>A	uc001shc.1	+	c.604G>A	c.(604-606)GTT>ATT	p.V202I		NM_001005494	NP_001005494	Q8NGE1	OR6C4_HUMAN	olfactory receptor, family 6, subfamily C,	202	Helical; Name=5; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0														0.269388	166.92242	178.696332	66	179	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	54231881	54231881	11603	12	G	A	A	40	40	OR6C4	A	1	1
VWF	7450	broad.mit.edu	36	12	5961364	5961364	+	Missense_Mutation	SNP	C	T	T			TCGA-14-0790-01	TCGA-14-0790-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:5961364C>T	uc001qnn.1	-	c.7136G>A	c.(7135-7137)CGT>CAT	p.R2379H		NM_000552	NP_000543	P04275	VWF_HUMAN	von Willebrand factor preproprotein	2379					blood coagulation, intrinsic pathway|cell-substrate adhesion|platelet activation|platelet degranulation|protein homooligomerization	endoplasmic reticulum|platelet alpha granule lumen|proteinaceous extracellular matrix|Weibel-Palade body	chaperone binding|collagen binding|glycoprotein binding|immunoglobulin binding|integrin binding|protease binding|protein homodimerization activity|protein N-terminus binding			ovary(3)|pancreas(2)|breast(1)|central_nervous_system(1)	7					Antihemophilic Factor(DB00025)									0.325967	161.557001	166.423694	59	122	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	5961364	5961364	17818	12	C	T	T	19	19	VWF	T	1	1
GLIPR1	11010	broad.mit.edu	36	12	74161049	74161049	+	Missense_Mutation	SNP	A	G	G			TCGA-14-0790-01	TCGA-14-0790-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr12:74161049A>G	uc001sxs.1	+	c.122A>G	c.(121-123)CAT>CGT	p.H41R	GLIPR1_uc009zsb.1_Missense_Mutation_p.H41R	NM_006851	NP_006842	P48060	GLIP1_HUMAN	GLI pathogenesis-related 1 precursor	41					cellular lipid metabolic process	extracellular region|integral to membrane				large_intestine(1)|ovary(1)	2														0.327273	144.268965	148.647962	54	111	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	74161049	74161049	6709	12	A	G	G	8	8	GLIPR1	G	4	4
UHRF1BP1L	23074	broad.mit.edu	36	12	98977294	98977294	+	Missense_Mutation	SNP	T	C	C			TCGA-14-0790-01	TCGA-14-0790-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr12:98977294T>C	uc001tgq.1	-	c.1892A>G	c.(1891-1893)AAA>AGA	p.K631R	UHRF1BP1L_uc001tgp.1_Missense_Mutation_p.K281R	NM_015054	NP_055869	A0JNW5	UH1BL_HUMAN	UHRF1 (ICBP90) binding protein 1-like isoform a	631										ovary(1)	1														0.10177	30.260702	65.993233	23	203	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	98977294	98977294	17527	12	T	C	C	64	64	UHRF1BP1L	C	4	4
C13orf39	196541	broad.mit.edu	36	13	102141257	102141257	+	Silent	SNP	G	A	A			TCGA-14-0790-01	TCGA-14-0790-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr13:102141257G>A	uc001vpj.1	-	c.189C>T	c.(187-189)TAC>TAT	p.Y63Y	C13orf39_uc001vpk.1_Silent_p.Y63Y	NM_001010977	NP_001010977	Q5VZV1	MT21C_HUMAN	hypothetical protein LOC196541	63							methyltransferase activity				0														0.46696	322.813824	323.029926	106	121	GG		KEEP	---	---	---	---	capture			Silent	SNP	102141257	102141257	1780	13	G	A	A	40	40	C13orf39	A	1	1
CDADC1	81602	broad.mit.edu	36	13	48763832	48763832	+	Silent	SNP	A	C	C			TCGA-14-0790-01	TCGA-14-0790-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr13:48763832A>C	uc001vcu.1	+	c.1483A>C	c.(1483-1485)AGA>CGA	p.R495R	CDADC1_uc001vcv.1_Non-coding_Transcript	NM_030911	NP_112173	Q9BWV3	CDAC1_HUMAN	cytidine and dCMP deaminase domain containing 1	495							hydrolase activity|zinc ion binding				0		Lung NSC(96;0.000705)|Breast(56;0.0011)|Prostate(109;0.00446)|Hepatocellular(98;0.0556)|Glioma(44;0.236)												0.401015	240.081575	241.770415	79	118	AA		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(9;0.206)	GBM - Glioblastoma multiforme(99;1.06e-08)|COAD - Colon adenocarcinoma(199;0.216)	Silent	SNP	48763832	48763832	3181	13	A	C	C	11	11	CDADC1	C	4	4
AHNAK2	113146	broad.mit.edu	36	14	104479502	104479502	+	Missense_Mutation	SNP	C	T	T			TCGA-14-0790-01	TCGA-14-0790-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr14:104479502C>T	uc010axc.1	-	c.13331G>A	c.(13330-13332)CGG>CAG	p.R4444Q	AHNAK2_uc001ypx.2_Missense_Mutation_p.R4344Q	NM_138420	NP_612429	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	4444						nucleus				ovary(1)	1		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)												0.501742	452.792643	452.79341	144	143	CC		KEEP	---	---	---	---	capture	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)		Missense_Mutation	SNP	104479502	104479502	418	14	C	T	T	23	23	AHNAK2	T	1	1
RNASE11	122651	broad.mit.edu	36	14	20122335	20122335	+	Missense_Mutation	SNP	G	T	T			TCGA-14-0790-01	TCGA-14-0790-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr14:20122335G>T	uc010ahv.1	-	c.139C>A	c.(139-141)CAG>AAG	p.Q47K	RNASE11_uc010ahw.1_Missense_Mutation_p.Q47K|RNASE11_uc001vxs.1_Missense_Mutation_p.Q47K|RNASE11_uc010ahx.1_Missense_Mutation_p.Q47K	NM_145250	NP_660293	Q8TAA1	RNS11_HUMAN	ribonuclease, RNase A family, 11 (non-active)	47						extracellular region	nucleic acid binding|pancreatic ribonuclease activity			ovary(3)	3	all_cancers(95;0.00238)	all_lung(585;0.235)												0.416667	643.386984	646.37061	205	287	GG		KEEP	---	---	---	---	capture	Epithelial(56;1.85e-06)|all cancers(55;1.46e-05)	GBM - Glioblastoma multiforme(265;0.0139)	Missense_Mutation	SNP	20122335	20122335	13878	14	G	T	T	48	48	RNASE11	T	3	3
JUB	84962	broad.mit.edu	36	14	22520565	22520565	+	Missense_Mutation	SNP	G	C	C			TCGA-14-0790-01	TCGA-14-0790-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr14:22520565G>C	uc001whz.1	-	c.751C>G	c.(751-753)CCC>GCC	p.P251A		NM_032876	NP_116265	Q96IF1	JUB_HUMAN	ajuba isoform 1	251	PreLIM.				cell cycle|gene silencing by miRNA|positive regulation of protein complex assembly	cell-cell junction|cytoplasmic mRNA processing body|microtubule organizing center	alpha-catenin binding|zinc ion binding				0	all_cancers(95;4.6e-05)					Esophageal Squamous(134;328 1721 9795 37986 41605)								0.5	6.31714	6.31714	4	4	GG		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(265;0.0122)	Missense_Mutation	SNP	22520565	22520565	8272	14	G	C	C	42	42	JUB	C	3	3
ARID4A	5926	broad.mit.edu	36	14	57901601	57901601	+	Missense_Mutation	SNP	A	G	G			TCGA-14-0790-01	TCGA-14-0790-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr14:57901601A>G	uc001xdp.1	+	c.3041A>G	c.(3040-3042)GAT>GGT	p.D1014G	ARID4A_uc001xdo.1_Missense_Mutation_p.D1014G|ARID4A_uc001xdq.1_Missense_Mutation_p.D1014G|ARID4A_uc010apg.1_Missense_Mutation_p.D692G	NM_002892	NP_002883	P29374	ARI4A_HUMAN	retinoblastoma-binding protein 1 isoform I	1014					chromatin assembly or disassembly|negative regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	chromatin|transcriptional repressor complex	chromatin binding|DNA binding|sequence-specific DNA binding transcription factor activity|transcription repressor activity			ovary(3)|lung(1)	4														0.396947	337.345945	339.780062	104	158	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	57901601	57901601	934	14	A	G	G	12	12	ARID4A	G	4	4
PLCB2	5330	broad.mit.edu	36	15	38370294	38370294	+	Missense_Mutation	SNP	G	C	C			TCGA-14-0790-01	TCGA-14-0790-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr15:38370294G>C	uc001zld.1	-	c.3073C>G	c.(3073-3075)CAG>GAG	p.Q1025E	PLCB2_uc001zlc.1_Missense_Mutation_p.Q9E|PLCB2_uc010bbo.1_Missense_Mutation_p.Q1021E	NM_004573	NP_004564	Q00722	PLCB2_HUMAN	phospholipase C, beta 2	1025	Potential.				activation of phospholipase C activity|intracellular signal transduction|lipid catabolic process|phospholipid metabolic process|synaptic transmission	cytosol	calcium ion binding|phosphatidylinositol phospholipase C activity|signal transducer activity			ovary(3)|breast(3)|kidney(1)|pancreas(1)	8		all_cancers(109;9.35e-19)|all_epithelial(112;1.18e-15)|Lung NSC(122;2.45e-11)|all_lung(180;6.47e-10)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)								1073				0.478261	79.749171	79.768018	22	24	GG		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(113;9.38e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0508)	Missense_Mutation	SNP	38370294	38370294	12454	15	G	C	C	48	48	PLCB2	C	3	3
VPS39	23339	broad.mit.edu	36	15	40245221	40245221	+	Missense_Mutation	SNP	G	A	A			TCGA-14-0790-01	TCGA-14-0790-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr15:40245221G>A	uc001zpd.1	-	c.1799C>T	c.(1798-1800)GCT>GTT	p.A600V	VPS39_uc001zpb.1_5'UTR|VPS39_uc001zpc.1_Missense_Mutation_p.A589V	NM_015289	NP_056104	Q96JC1	VPS39_HUMAN	vacuolar protein sorting 39	600					protein transport	HOPS complex|late endosome membrane|lysosomal membrane	small GTPase regulator activity			ovary(1)|pancreas(1)	2		all_cancers(109;6.78e-16)|all_epithelial(112;1.81e-14)|Lung NSC(122;5.01e-09)|all_lung(180;2.24e-08)|Melanoma(134;0.0574)|Colorectal(260;0.152)												0.464968	235.757481	235.925574	73	84	GG		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(94;3.05e-06)	Missense_Mutation	SNP	40245221	40245221	17776	15	G	A	A	34	34	VPS39	A	2	2
SLC27A2	11001	broad.mit.edu	36	15	48305552	48305552	+	Missense_Mutation	SNP	G	A	A			TCGA-14-0790-01	TCGA-14-0790-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr15:48305552G>A	uc001zxw.1	+	c.1243G>A	c.(1243-1245)GTC>ATC	p.V415I	SLC27A2_uc010bes.1_Missense_Mutation_p.V362I|SLC27A2_uc001zxx.1_Missense_Mutation_p.V180I	NM_003645	NP_003636	O14975	S27A2_HUMAN	solute carrier family 27 (fatty acid	415	Cytoplasmic (Potential).				bile acid biosynthetic process|fatty acid alpha-oxidation	endoplasmic reticulum membrane|integral to membrane|peroxisomal matrix|peroxisomal membrane	ATP binding|long-chain fatty acid-CoA ligase activity|phytanate-CoA ligase activity|pristanate-CoA ligase activity			ovary(1)	1		all_lung(180;0.00177)												0.443662	190.553806	190.937036	63	79	GG		KEEP	---	---	---	---	capture		all cancers(107;1.16e-06)|GBM - Glioblastoma multiforme(94;0.000113)	Missense_Mutation	SNP	48305552	48305552	15023	15	G	A	A	40	40	SLC27A2	A	1	1
ACAN	176	broad.mit.edu	36	15	87196106	87196106	+	Missense_Mutation	SNP	G	A	A			TCGA-14-0790-01	TCGA-14-0790-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr15:87196106G>A	uc002bmy.1	+	c.2104G>A	c.(2104-2106)GTG>ATG	p.V702M	ACAN_uc002bmz.1_Missense_Mutation_p.V702M	NM_013227	NP_037359			aggrecan isoform 2 precursor											ovary(2)|central_nervous_system(1)	3	Lung NSC(78;0.0392)|all_lung(78;0.077)													0.413793	35.195259	35.383269	12	17	GG		KEEP	---	---	---	---	capture	BRCA - Breast invasive adenocarcinoma(143;0.146)		Missense_Mutation	SNP	87196106	87196106	118	15	G	A	A	40	40	ACAN	A	1	1
IL4R	3566	broad.mit.edu	36	16	27281246	27281246	+	Missense_Mutation	SNP	G	A	A			TCGA-14-0790-01	TCGA-14-0790-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:27281246G>A	uc002don.1	+	c.1072G>A	c.(1072-1074)GTG>ATG	p.V358M	IL4R_uc010bxy.1_Missense_Mutation_p.V358M|IL4R_uc002doo.1_Missense_Mutation_p.V198M	NM_000418	NP_000409	P24394	IL4RA_HUMAN	interleukin 4 receptor alpha chain isoform a	358	Cytoplasmic (Potential).				immune response|production of molecular mediator involved in inflammatory response	integral to plasma membrane	identical protein binding|interleukin-4 receptor activity|receptor signaling protein activity			ovary(1)|skin(1)	2														0.52381	166.721025	166.772395	55	50	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	27281246	27281246	7999	16	G	A	A	40	40	IL4R	A	1	1
C16orf7	9605	broad.mit.edu	36	16	88310436	88310436	+	Silent	SNP	G	C	C			TCGA-14-0790-01	TCGA-14-0790-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:88310436G>C	uc002fom.1	-	c.366C>G	c.(364-366)CTC>CTG	p.L122L	C16orf7_uc002fol.1_Silent_p.L52L	NM_004913	NP_004904	Q9Y2B5	CP007_HUMAN	chromosome 16 open reading frame 7	122					ATP synthesis coupled proton transport		GTPase activator activity|transporter activity				0		Lung NSC(15;2.19e-05)|all_lung(18;3.07e-05)|all_hematologic(23;0.0256)												0.445255	850.371397	851.795342	244	304	GG		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(80;0.0273)	Silent	SNP	88310436	88310436	1881	16	G	C	C	33	33	C16orf7	C	3	3
GRIN2A	2903	broad.mit.edu	36	16	9765696	9765696	+	Missense_Mutation	SNP	G	A	A			TCGA-14-0790-01	TCGA-14-0790-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:9765696G>A	uc002czp.1	-	c.3206C>T	c.(3205-3207)ACG>ATG	p.T1069M	GRIN2A_uc002czq.1_Missense_Mutation_p.T1069M|GRIN2A_uc002czr.2_Missense_Mutation_p.T1069M	NM_000833	NP_000824	Q12879	NMDE1_HUMAN	N-methyl-D-aspartate receptor subunit 2A isoform	1069	Cytoplasmic (Potential).				response to ethanol	cell junction|N-methyl-D-aspartate selective glutamate receptor complex|outer membrane-bounded periplasmic space|postsynaptic membrane	N-methyl-D-aspartate selective glutamate receptor activity|zinc ion binding			ovary(4)|lung(1)|breast(1)|kidney(1)|skin(1)	8					Felbamate(DB00949)|Glycine(DB00145)|L-Glutamic Acid(DB00142)|Loperamide(DB00836)|Memantine(DB01043)					324				0.451713	437.571374	438.216878	145	176	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	9765696	9765696	7058	16	G	A	A	40	40	GRIN2A	A	1	1
MYH4	4622	broad.mit.edu	36	17	10310315	10310315	+	Silent	SNP	G	A	A			TCGA-14-0790-01	TCGA-14-0790-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:10310315G>A	uc002gmn.1	-	c.348C>T	c.(346-348)TAC>TAT	p.Y116Y		NM_017533	NP_060003	Q9Y623	MYH4_HUMAN	myosin, heavy polypeptide 4, skeletal muscle	116	Myosin head-like.				muscle filament sliding	muscle myosin complex|myosin filament|sarcomere	actin binding|ATP binding|calmodulin binding|microfilament motor activity|structural constituent of muscle			ovary(10)|central_nervous_system(1)	11														0.438849	182.35706	182.809644	61	78	GG		KEEP	---	---	---	---	capture			Silent	SNP	10310315	10310315	10432	17	G	A	A	40	40	MYH4	A	1	1
PRPF8	10594	broad.mit.edu	36	17	1523796	1523796	+	Missense_Mutation	SNP	A	G	G			TCGA-14-0790-01	TCGA-14-0790-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr17:1523796A>G	uc002fte.1	-	c.3440T>C	c.(3439-3441)GTT>GCT	p.V1147A		NM_006445	NP_006436	Q6P2Q9	PRP8_HUMAN	U5 snRNP-specific protein	1147					nuclear mRNA splicing, via spliceosome|response to stimulus|visual perception	catalytic step 2 spliceosome|nuclear speck|U5 snRNP	protein binding|RNA binding			ovary(2)|lung(1)	3														0.401274	216.298856	217.635612	63	94	AA		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (25;0.0855)	Missense_Mutation	SNP	1523796	1523796	13018	17	A	G	G	2	2	PRPF8	G	4	4
ACCN1	40	broad.mit.edu	36	17	28375135	28375135	+	Silent	SNP	C	T	T			TCGA-14-0790-01	TCGA-14-0790-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:28375135C>T	uc002hht.1	-	c.1206G>A	c.(1204-1206)GCG>GCA	p.A402A	ACCN1_uc002hhu.1_Silent_p.A351A	NM_183377	NP_899233	Q16515	ACCN1_HUMAN	amiloride-sensitive cation channel 1, neuronal	351	Extracellular (By similarity).				central nervous system development|peripheral nervous system development|synaptic transmission	integral to plasma membrane	ligand-gated sodium channel activity|protein binding			ovary(2)|large_intestine(1)|central_nervous_system(1)	4		Breast(31;0.042)|Ovarian(249;0.202)			Amiloride(DB00594)									0.420168	310.866313	312.188372	100	138	CC		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (308;0.13)|BRCA - Breast invasive adenocarcinoma(366;0.215)	Silent	SNP	28375135	28375135	129	17	C	T	T	23	23	ACCN1	T	1	1
C17orf53	78995	broad.mit.edu	36	17	39581004	39581004	+	Missense_Mutation	SNP	C	T	T			TCGA-14-0790-01	TCGA-14-0790-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:39581004C>T	uc002ifi.1	+	c.307C>T	c.(307-309)CCT>TCT	p.P103S	C17orf53_uc010czq.1_Missense_Mutation_p.P103S|C17orf53_uc002ifj.1_Missense_Mutation_p.P103S|C17orf53_uc002ifk.1_Non-coding_Transcript	NM_024032	NP_076937	Q8N3J3	CQ053_HUMAN	hypothetical protein LOC78995	103											0		Breast(137;0.0364)|Prostate(33;0.0376)												0.391061	198.13186	199.984255	70	109	CC		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(366;0.114)	Missense_Mutation	SNP	39581004	39581004	1919	17	C	T	T	26	26	C17orf53	T	2	2
CTDP1	9150	broad.mit.edu	36	18	75614680	75614680	+	Missense_Mutation	SNP	G	A	A			TCGA-14-0790-01	TCGA-14-0790-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr18:75614680G>A	uc002lnh.1	+	c.2788G>A	c.(2788-2790)GAG>AAG	p.E930K	CTDP1_uc002lni.1_3'UTR|CTDP1_uc010drd.1_3'UTR	NM_004715	NP_004706	Q9Y5B0	CTDP1_HUMAN	CTD (carboxy-terminal domain, RNA polymerase II,	930					positive regulation of viral transcription|protein dephosphorylation|transcription elongation from RNA polymerase II promoter|viral reproduction	nucleoplasm	CTD phosphatase activity|DNA-directed RNA polymerase activity				0		Esophageal squamous(42;0.0157)|Melanoma(33;0.144)												0.44	66.64373	66.800441	22	28	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(15;5.2e-06)|BRCA - Breast invasive adenocarcinoma(31;0.0277)	Missense_Mutation	SNP	75614680	75614680	4161	18	G	A	A	37	37	CTDP1	A	1	1
CPAMD8	27151	broad.mit.edu	36	19	16868126	16868126	+	Missense_Mutation	SNP	G	C	C			TCGA-14-0790-01	TCGA-14-0790-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:16868126G>C	uc002nfb.1	-	c.5428C>G	c.(5428-5430)CCG>GCG	p.P1810A	CPAMD8_uc002nfd.1_Missense_Mutation_p.P275A	NM_015692	NP_056507	Q8IZJ3	CPMD8_HUMAN	C3 and PZP-like, alpha-2-macroglobulin domain	1763						extracellular space|plasma membrane	serine-type endopeptidase inhibitor activity			ovary(4)|breast(4)|large_intestine(3)|pancreas(1)	12										1067				0.266667	6.436562	7.225895	4	11	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	16868126	16868126	3933	19	G	C	C	42	42	CPAMD8	C	3	3
MATK	4145	broad.mit.edu	36	19	3734948	3734948	+	Missense_Mutation	SNP	G	T	T			TCGA-14-0790-01	TCGA-14-0790-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:3734948G>T	uc002lyv.1	-	c.449C>A	c.(448-450)TCC>TAC	p.S150Y	MATK_uc002lyt.1_Missense_Mutation_p.S149Y|MATK_uc002lyu.1_Missense_Mutation_p.S108Y|MATK_uc010dtq.1_Missense_Mutation_p.S149Y	NM_002378	NP_647611	P42679	MATK_HUMAN	megakaryocyte-associated tyrosine kinase isoform	149	SH2.				cell proliferation|mesoderm development|positive regulation of cell proliferation|protein phosphorylation	cytoplasm|nucleus	ATP binding|non-membrane spanning protein tyrosine kinase activity			ovary(1)|lung(1)|large_intestine(1)	3		Hepatocellular(1079;0.137)								245				0.205128	13.977994	17.126843	8	31	GG		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00461)|STAD - Stomach adenocarcinoma(1328;0.18)	Missense_Mutation	SNP	3734948	3734948	9716	19	G	T	T	41	41	MATK	T	3	3
KIR2DL1	3802	broad.mit.edu	36	19	59976727	59976727	+	Silent	SNP	C	T	T			TCGA-14-0790-01	TCGA-14-0790-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:59976727C>T	uc010erz.1	+	c.201C>T	c.(199-201)AAC>AAT	p.N67N	KIR2DS4_uc010erv.1_Intron|KIR2DS4_uc010erx.1_Intron|KIR2DS4_uc010esa.1_Intron|KIR3DP1_uc002qgw.1_Intron|KIR2DL3_uc010erw.1_Intron|KIR2DL1_uc002qgz.1_Intron|KIR2DL1_uc010ery.1_Intron|KIR2DL3_uc002qha.1_Intron|KIR2DL1_uc002qhb.1_Silent_p.N67N	NM_014218	NP_055033	P43626	KI2L1_HUMAN	killer cell immunoglobulin-like receptor, two	67	Extracellular (Potential).|Ig-like C2-type 1.				immune response|natural killer cell inhibitory signaling pathway	integral to plasma membrane	protein binding|receptor activity				0						GBM(72;624 1217 3963 34152 38303)								0.353933	353.759532	360.449063	126	230	CC		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(193;0.0192)	Silent	SNP	59976727	59976727	8628	19	C	T	T	19	19	KIR2DL1	T	1	1
ZSCAN1	284312	broad.mit.edu	36	19	63257084	63257084	+	Silent	SNP	C	T	T			TCGA-14-0790-01	TCGA-14-0790-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:63257084C>T	uc002qrc.1	+	c.1080C>T	c.(1078-1080)TCC>TCT	p.S360S		NM_182572	NP_872378	Q8NBB4	ZSCA1_HUMAN	zinc finger and SCAN domain containing 1	360					regulation of transcription, DNA-dependent|viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1		Colorectal(82;5.46e-05)|all_neural(62;0.0182)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)												0.373134	69.571751	70.512953	25	42	CC		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0152)	Silent	SNP	63257084	63257084	18830	19	C	T	T	23	23	ZSCAN1	T	1	1
CD58	965	broad.mit.edu	36	1	116880236	116880236	+	Missense_Mutation	SNP	G	A	A			TCGA-14-0790-01	TCGA-14-0790-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:116880236G>A	uc001egm.1	-	c.502C>T	c.(502-504)CGT>TGT	p.R168C	CD58_uc001egn.1_Non-coding_Transcript|CD58_uc001ego.1_Intron|CD58_uc001egp.2_Missense_Mutation_p.R168C	NM_001779	NP_001770	P19256	LFA3_HUMAN	CD58 molecule isoform 1	168	Extracellular (Potential).|Ig-like C2-type.				blood coagulation|cell-cell adhesion|leukocyte migration	anchored to membrane|integral to plasma membrane	protein binding				0	Lung SC(450;0.225)	all_cancers(81;0.000363)|all_lung(203;0.000118)|all_epithelial(167;0.000149)|Lung NSC(69;0.000577)												0.439306	229.975683	230.530912	76	97	GG		KEEP	---	---	---	---	capture		Lung(183;0.0086)|LUSC - Lung squamous cell carcinoma(189;0.0528)|Colorectal(144;0.0775)|all cancers(265;0.109)|Epithelial(280;0.118)|COAD - Colon adenocarcinoma(174;0.121)	Missense_Mutation	SNP	116880236	116880236	3153	1	G	A	A	40	40	CD58	A	1	1
SPAG17	200162	broad.mit.edu	36	1	118425297	118425297	+	Missense_Mutation	SNP	A	T	T			TCGA-14-0790-01	TCGA-14-0790-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr1:118425297A>T	uc001ehk.1	-	c.2159T>A	c.(2158-2160)CTG>CAG	p.L720Q		NM_206996	NP_996879	Q6Q759	SPG17_HUMAN	sperm associated antigen 17	720						cilium|flagellar axoneme|microtubule				ovary(2)|large_intestine(1)	3	Esophageal squamous(2;0.0106)	all_cancers(81;0.0204)|all_lung(203;9.46e-05)|Lung NSC(69;0.000675)|all_epithelial(167;0.01)												0.448161	428.198239	428.899874	134	165	AA		KEEP	---	---	---	---	capture		Lung(183;0.0858)	Missense_Mutation	SNP	118425297	118425297	15482	1	A	T	T	7	7	SPAG17	T	4	4
SPAG17	200162	broad.mit.edu	36	1	118430114	118430114	+	Silent	SNP	A	C	C			TCGA-14-0790-01	TCGA-14-0790-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr1:118430114A>C	uc001ehk.1	-	c.1716T>G	c.(1714-1716)ACT>ACG	p.T572T		NM_206996	NP_996879	Q6Q759	SPG17_HUMAN	sperm associated antigen 17	572						cilium|flagellar axoneme|microtubule				ovary(2)|large_intestine(1)	3	Esophageal squamous(2;0.0106)	all_cancers(81;0.0204)|all_lung(203;9.46e-05)|Lung NSC(69;0.000675)|all_epithelial(167;0.01)												0.46114	286.33798	286.593109	89	104	AA		KEEP	---	---	---	---	capture		Lung(183;0.0858)	Silent	SNP	118430114	118430114	15482	1	A	C	C	15	15	SPAG17	C	4	4
SPTA1	6708	broad.mit.edu	36	1	156921703	156921703	+	Missense_Mutation	SNP	C	T	T	rs28934004	unknown	TCGA-14-0790-01	TCGA-14-0790-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:156921703C>T	uc001fst.1	-	c.83G>A	c.(82-84)CGT>CAT	p.R28H		NM_003126	NP_003117	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	28	Spectrin 1.		R -> C (in EL2).|R -> L (in EL2).		actin filament capping|actin filament organization|axon guidance|regulation of cell shape	cytosol|intrinsic to internal side of plasma membrane|spectrin|spectrin-associated cytoskeleton	actin filament binding|calcium ion binding|structural constituent of cytoskeleton			ovary(4)|breast(1)	5	all_hematologic(112;0.0378)													0.392045	201.529284	203.327096	69	107	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	156921703	156921703	15630	1	C	T	T	19	19	SPTA1	T	1	1
SPEN	23013	broad.mit.edu	36	1	16075659	16075659	+	Missense_Mutation	SNP	C	A	A			TCGA-14-0790-01	TCGA-14-0790-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:16075659C>A	uc001axk.1	+	c.780C>A	c.(778-780)AGC>AGA	p.S260R		NM_015001	NP_055816	Q96T58	MINT_HUMAN	spen homolog, transcriptional regulator	260	Ser-rich.|Arg-rich.|By similarity.				interspecies interaction between organisms|negative regulation of transcription, DNA-dependent|Notch signaling pathway	nucleus	nucleotide binding|protein binding|RNA binding			ovary(6)|breast(3)|lung(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	14		Colorectal(325;0.000258)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)								551				0.128713	11.94121	25.697345	13	88	CC		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(313;0.013)|READ - Rectum adenocarcinoma(331;0.0681)	Missense_Mutation	SNP	16075659	16075659	15550	1	C	A	A	26	26	SPEN	A	3	3
LEFTY2	7044	broad.mit.edu	36	1	224193744	224193744	+	Missense_Mutation	SNP	G	A	A			TCGA-14-0790-01	TCGA-14-0790-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:224193744G>A	uc001hpt.1	-	c.677C>T	c.(676-678)GCG>GTG	p.A226V	LEFTY2_uc009xek.1_Intron	NM_003240	NP_003231	O00292	LFTY2_HUMAN	endometrial bleeding associated factor	226					cell growth|multicellular organismal development|platelet activation|platelet degranulation|transforming growth factor beta receptor signaling pathway	extracellular space|platelet alpha granule lumen	cytokine activity|growth factor activity|transforming growth factor beta receptor binding				0	Breast(184;0.197)					Colon(172;116 2643 9098 43333)								0.592593	43.62647	43.841928	16	11	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	224193744	224193744	9040	1	G	A	A	38	38	LEFTY2	A	1	1
RPL5	6125	broad.mit.edu	36	1	93072946	93072946	+	Missense_Mutation	SNP	G	A	A			TCGA-14-0790-01	TCGA-14-0790-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:93072946G>A	uc001doz.1	+	c.212G>A	c.(211-213)GGG>GAG	p.G71E	FAM69A_uc001dpc.2_Intron|RPL5_uc001dpa.1_Non-coding_Transcript|RPL5_uc001dpb.1_Missense_Mutation_p.G21E|RPL5_uc001dpd.1_5'Flank|SNORD21_uc001dpe.2_5'Flank	NM_000969	NP_000960	P46777	RL5_HUMAN	ribosomal protein L5	71					endocrine pancreas development|ribosomal large subunit biogenesis|rRNA processing|translational elongation|translational termination|viral transcription	cytosolic large ribosomal subunit|nucleolus	5S rRNA binding|protein binding|structural constituent of ribosome				0		all_lung(203;0.00265)|Lung NSC(277;0.0056)|all_neural(321;0.185)|Melanoma(281;0.192)|Glioma(108;0.203)												0.140541	41.844762	64.914322	26	159	GG		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(16;0.000305)|all cancers(265;0.000343)|Epithelial(280;0.0927)	Missense_Mutation	SNP	93072946	93072946	14076	1	G	A	A	43	43	RPL5	A	2	2
BCAR3	8412	broad.mit.edu	36	1	93805541	93805541	+	Missense_Mutation	SNP	C	T	T			TCGA-14-0790-01	TCGA-14-0790-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:93805541C>T	uc001dpz.1	-	c.2182G>A	c.(2182-2184)GAC>AAC	p.D728N	BCAR3_uc001dpy.1_Missense_Mutation_p.D637N|BCAR3_uc001dqa.1_Missense_Mutation_p.D728N|BCAR3_uc001dqb.1_Missense_Mutation_p.D728N|BCAR3_uc001dpx.2_Missense_Mutation_p.D404N	NM_003567	NP_003558	O75815	BCAR3_HUMAN	breast cancer antiestrogen resistance 3	728	Ras-GEF.				response to drug|small GTPase mediated signal transduction	intracellular	guanyl-nucleotide exchange factor activity|protein binding			ovary(1)|lung(1)|central_nervous_system(1)	3		all_lung(203;0.00145)|Lung NSC(277;0.00662)												0.453846	181.513553	181.75414	59	71	CC		KEEP	---	---	---	---	capture		all cancers(265;0.0126)|GBM - Glioblastoma multiforme(16;0.0467)|Epithelial(280;0.166)	Missense_Mutation	SNP	93805541	93805541	1370	1	C	T	T	31	31	BCAR3	T	1	1
CRYBB2	1415	broad.mit.edu	36	22	23957599	23957599	+	Missense_Mutation	SNP	C	T	T			TCGA-14-0790-01	TCGA-14-0790-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr22:23957599C>T	uc003abp.1	+	c.478C>T	c.(478-480)CGT>TGT	p.R160C		NM_000496	NP_000487	P43320	CRBB2_HUMAN	crystallin, beta B2	160	Beta/gamma crystallin 'Greek key' 4.				response to stimulus|visual perception		structural constituent of eye lens				0														0.360976	207.09707	210.582481	74	131	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	23957599	23957599	4050	22	C	T	T	23	23	CRYBB2	T	1	1
IL18RAP	8807	broad.mit.edu	36	2	102434843	102434843	+	Missense_Mutation	SNP	C	T	T			TCGA-14-0790-01	TCGA-14-0790-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:102434843C>T	uc002tbx.1	+	c.1570C>T	c.(1570-1572)CCT>TCT	p.P524S	IL18RAP_uc010fiz.1_Missense_Mutation_p.P382S	NM_003853	NP_003844	O95256	I18RA_HUMAN	interleukin 18 receptor accessory protein	524	TIR.|Cytoplasmic (Potential).				cell surface receptor linked signaling pathway|inflammatory response|innate immune response	integral to membrane	transmembrane receptor activity			ovary(2)	2														0.138298	59.066057	94.712556	39	243	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	102434843	102434843	7949	2	C	T	T	18	18	IL18RAP	T	2	2
LIMS1	3987	broad.mit.edu	36	2	108658880	108658880	+	Silent	SNP	C	T	T			TCGA-14-0790-01	TCGA-14-0790-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:108658880C>T	uc002tek.2	+	c.795C>T	c.(793-795)CGC>CGT	p.R265R	LIMS1_uc002tef.1_Silent_p.R215R|LIMS1_uc002teg.1_Silent_p.R203R|LIMS1_uc002teh.1_Silent_p.R203R|LIMS1_uc002tei.1_Silent_p.R203R|LIMS1_uc002tej.1_Silent_p.R240R	NM_004987	NP_004978	P48059	LIMS1_HUMAN	LIM and senescent cell antigen-like domains 1	203	LIM zinc-binding 4.				cell aging|cell junction assembly|cellular response to transforming growth factor beta stimulus|negative regulation of transcription, DNA-dependent	cytosol|focal adhesion|perinuclear region of cytoplasm	protein binding|transcription repressor activity|zinc ion binding				0														0.586207	105.753306	106.129119	34	24	CC		KEEP	---	---	---	---	capture			Silent	SNP	108658880	108658880	9129	2	C	T	T	27	27	LIMS1	T	1	1
DPP10	57628	broad.mit.edu	36	2	116163926	116163926	+	Missense_Mutation	SNP	G	A	A			TCGA-14-0790-01	TCGA-14-0790-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:116163926G>A	uc002tla.1	+	c.535G>A	c.(535-537)GTC>ATC	p.V179I	DPP10_uc002tlb.1_Missense_Mutation_p.V129I|DPP10_uc002tlc.1_Missense_Mutation_p.V175I|DPP10_uc002tle.1_Missense_Mutation_p.V129I|DPP10_uc002tlf.1_Missense_Mutation_p.V172I	NM_020868	NP_065919	Q8N608	DPP10_HUMAN	dipeptidyl peptidase 10 isoform long	179	Extracellular (Potential).				proteolysis	integral to membrane|membrane fraction	serine-type peptidase activity			ovary(5)|large_intestine(2)|breast(1)|skin(1)	9														0.46729	153.449715	153.548217	50	57	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	116163926	116163926	4911	2	G	A	A	40	40	DPP10	A	1	1
ACVR2A	92	broad.mit.edu	36	2	148392613	148392613	+	Missense_Mutation	SNP	A	C	C			TCGA-14-0790-01	TCGA-14-0790-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr2:148392613A>C	uc002twg.1	+	c.944A>C	c.(943-945)AAA>ACA	p.K315T	ACVR2A_uc002twh.1_Missense_Mutation_p.K315T	NM_001616	NP_001607	P27037	AVR2A_HUMAN	activin A receptor, type IIA precursor	315	Cytoplasmic (Potential).|Protein kinase.				activin receptor signaling pathway|BMP signaling pathway|positive regulation of activin receptor signaling pathway|positive regulation of bone mineralization|positive regulation of erythrocyte differentiation|positive regulation of osteoblast differentiation|positive regulation of protein phosphorylation|protein phosphorylation	cytoplasm|inhibin-betaglycan-ActRII complex|integral to plasma membrane	ATP binding|coreceptor activity|inhibin beta-A binding|metal ion binding|receptor signaling protein serine/threonine kinase activity|transforming growth factor beta receptor activity			stomach(8)|large_intestine(2)|kidney(1)	11										196				0.157895	8.823494	13.069155	6	32	AA		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(221;0.0969)	Missense_Mutation	SNP	148392613	148392613	224	2	A	C	C	1	1	ACVR2A	C	4	4
OBSL1	23363	broad.mit.edu	36	2	220141162	220141162	+	Missense_Mutation	SNP	G	C	C			TCGA-14-0790-01	TCGA-14-0790-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:220141162G>C	uc010fwk.1	-	c.1141C>G	c.(1141-1143)CTG>GTG	p.L381V	OBSL1_uc010fwl.1_5'Flank|OBSL1_uc002vmi.2_Missense_Mutation_p.L381V|OBSL1_uc002vmj.2_5'UTR	NM_015311	NP_056126	O75147	OBSL1_HUMAN	obscurin-like 1	381	Ig-like 4.				cardiac myofibril assembly	intercalated disc|M band|perinuclear region of cytoplasm|Z disc	cytoskeletal adaptor activity				0		Renal(207;0.0376)										OREG0003988	type=REGULATORY REGION|Gene=OBSL1|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	0.315789	7.358316	7.988853	6	13	GG		KEEP	---	---	---	---	capture		Epithelial(149;2.02e-07)|all cancers(144;1.68e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00834)	Missense_Mutation	SNP	220141162	220141162	11218	2	G	C	C	34	34	OBSL1	C	3	3
RAB11FIP5	26056	broad.mit.edu	36	2	73193000	73193000	+	Silent	SNP	G	C	C	rs34138742	unknown	TCGA-14-0790-01	TCGA-14-0790-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:73193000G>C	uc002siu.2	-	c.414C>G	c.(412-414)GGC>GGG	p.G138G		NM_015470	NP_056285	Q9BXF6	RFIP5_HUMAN	RAB11 family interacting protein 5 (class I)	138					protein transport	mitochondrial outer membrane|recycling endosome membrane	gamma-tubulin binding				0														0.2	7.287569	8.963234	4	16	GG		KEEP	---	---	---	---	capture			Silent	SNP	73193000	73193000	13356	2	G	C	C	42	42	RAB11FIP5	C	3	3
KIDINS220	57498	broad.mit.edu	36	2	8860706	8860706	+	Silent	SNP	A	G	G			TCGA-14-0790-01	TCGA-14-0790-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr2:8860706A>G	uc002qzc.1	-	c.606T>C	c.(604-606)AAT>AAC	p.N202N	KIDINS220_uc002qzd.1_Silent_p.N160N|KIDINS220_uc002qzf.2_Silent_p.N203N	NM_020738	NP_065789	Q9ULH0	KDIS_HUMAN	kinase D-interacting substrate of 220 kDa	202	ANK 7.|Cytoplasmic (Potential).				activation of MAPKK activity|nerve growth factor receptor signaling pathway	cytosol|integral to membrane				ovary(3)|central_nervous_system(1)	4	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)													0.509091	96.999961	97.003914	28	27	AA		KEEP	---	---	---	---	capture			Silent	SNP	8860706	8860706	8582	2	A	G	G	4	4	KIDINS220	G	4	4
MYLK	4638	broad.mit.edu	36	3	124858820	124858820	+	Silent	SNP	C	T	T			TCGA-14-0790-01	TCGA-14-0790-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr3:124858820C>T	uc003ego.1	-	c.4131G>A	c.(4129-4131)ACG>ACA	p.T1377T	MYLK_uc003egp.1_Silent_p.T1308T|MYLK_uc003egq.1_Silent_p.T1377T|MYLK_uc003egr.1_Silent_p.T1308T|MYLK_uc003egs.1_Silent_p.T1201T|MYLK_uc010hrr.1_De_novo_Start_InFrame|MYLK_uc003egn.1_Silent_p.T568T	NM_053025	NP_444253	Q15746	MYLK_HUMAN	myosin light chain kinase isoform 1	1377	Actin-binding (calcium/calmodulin- insensitive) (By similarity).|Fibronectin type-III.				aorta smooth muscle tissue morphogenesis|muscle contraction|protein phosphorylation	cytosol	actin binding|ATP binding|calmodulin binding|metal ion binding|myosin light chain kinase activity			ovary(6)	6		Lung NSC(201;0.0496)							(MFE319-Tumor)	766				0.477477	162.671896	162.720484	53	58	CC		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(114;0.0736)	Silent	SNP	124858820	124858820	10451	3	C	T	T	19	19	MYLK	T	1	1
RTP1	132112	broad.mit.edu	36	3	188400298	188400298	+	Missense_Mutation	SNP	C	T	T			TCGA-14-0790-01	TCGA-14-0790-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr3:188400298C>T	uc003frg.1	+	c.538C>T	c.(538-540)CGC>TGC	p.R180C		NM_153708	NP_714919	P59025	RTP1_HUMAN	receptor transporting protein 1	180	Cytoplasmic (Potential).				protein insertion into membrane	cell surface|integral to membrane|plasma membrane	olfactory receptor binding			ovary(2)|breast(1)	3	all_cancers(143;5.33e-12)|Ovarian(172;0.0339)													0.432432	48.425023	48.565152	16	21	CC		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(80;5.56e-18)	GBM - Glioblastoma multiforme(93;0.0269)	Missense_Mutation	SNP	188400298	188400298	14213	3	C	T	T	23	23	RTP1	T	1	1
CYP8B1	1582	broad.mit.edu	36	3	42891854	42891854	+	Silent	SNP	C	T	T			TCGA-14-0790-01	TCGA-14-0790-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr3:42891854C>T	uc003cmh.1	-	c.459G>A	c.(457-459)ACG>ACA	p.T153T	CCBP2_uc003cmd.1_Intron|CCBP2_uc003cmg.2_Intron|CCBP2_uc010hie.1_Intron|CYP8B1_uc010hif.1_Silent_p.T153T	NM_004391	NP_004382	Q9UNU6	CP8B1_HUMAN	cytochrome P450, family 8, subfamily B,	153					bile acid biosynthetic process|oxidation-reduction process|xenobiotic metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	7alpha-hydroxycholest-4-en-3-one 12alpha-hydroxylase activity|electron carrier activity|heme binding|oxygen binding|sterol 12-alpha-hydroxylase activity			ovary(2)	2														0.413534	158.909803	159.775252	55	78	CC		KEEP	---	---	---	---	capture		KIRC - Kidney renal clear cell carcinoma(284;0.213)|Kidney(284;0.249)	Silent	SNP	42891854	42891854	4363	3	C	T	T	19	19	CYP8B1	T	1	1
ZFP42	132625	broad.mit.edu	36	4	189161746	189161746	+	Missense_Mutation	SNP	C	T	T			TCGA-14-0790-01	TCGA-14-0790-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:189161746C>T	uc003izg.1	+	c.791C>T	c.(790-792)ACG>ATG	p.T264M	ZFP42_uc003izh.1_Missense_Mutation_p.T264M|ZFP42_uc003izi.1_Missense_Mutation_p.T264M|ZFP42_uc010isp.1_Missense_Mutation_p.T264M	NM_174900	NP_777560	Q96MM3	ZFP42_HUMAN	zinc finger protein 42	264	C2H2-type 3.				female gonad development|male gonad development|meiosis|regulation of transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1		all_cancers(14;6.2e-52)|all_epithelial(14;7.36e-37)|all_lung(41;2.29e-15)|Lung NSC(41;6.7e-15)|Breast(6;1.53e-05)|Melanoma(20;3.01e-05)|Hepatocellular(41;0.00335)|all_hematologic(60;0.014)|Renal(120;0.0183)|Prostate(90;0.0421)|Colorectal(36;0.227)												0.43956	119.386859	119.676563	40	51	CC		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(60;1.54e-11)|BRCA - Breast invasive adenocarcinoma(30;4.21e-06)|GBM - Glioblastoma multiforme(59;8.93e-05)|STAD - Stomach adenocarcinoma(60;0.000279)|LUSC - Lung squamous cell carcinoma(40;0.00902)|READ - Rectum adenocarcinoma(43;0.157)	Missense_Mutation	SNP	189161746	189161746	18238	4	C	T	T	19	19	ZFP42	T	1	1
RUFY3	22902	broad.mit.edu	36	4	71891182	71891182	+	Missense_Mutation	SNP	G	A	A			TCGA-14-0790-01	TCGA-14-0790-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr4:71891182G>A	uc003hfr.1	+	c.1805G>A	c.(1804-1806)CGA>CAA	p.R602Q		NM_001037442	NP_001032519	Q7L099	RUFY3_HUMAN	RUN and FYVE domain containing 3 isoform 1	Error:Variant_position_missing_in_Q7L099_after_alignment					negative regulation of axonogenesis	filopodium|growth cone					0		all_hematologic(202;0.248)												0.51875	516.984041	517.084653	166	154	GG		KEEP	---	---	---	---	capture	Lung(101;0.235)		Missense_Mutation	SNP	71891182	71891182	14220	4	G	A	A	37	37	RUFY3	A	1	1
HPSE	10855	broad.mit.edu	36	4	84442408	84442408	+	Missense_Mutation	SNP	C	T	T			TCGA-14-0790-01	TCGA-14-0790-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:84442408C>T	uc003hoj.2	-	c.1244G>A	c.(1243-1245)GGC>GAC	p.G415D	HPSE_uc010ika.1_Missense_Mutation_p.G357D|HPSE_uc003hok.2_Missense_Mutation_p.G415D	NM_001098540	NP_006656	Q9Y251	HPSE_HUMAN	heparanase	415					carbohydrate metabolic process|proteoglycan metabolic process	extracellular region|lysosomal membrane	beta-glucuronidase activity|cation binding			ovary(1)	1		Hepatocellular(203;0.114)			Heparin(DB01109)									0.52	276.912654	276.972677	91	84	CC		KEEP	---	---	---	---	capture		COAD - Colon adenocarcinoma(81;0.141)	Missense_Mutation	SNP	84442408	84442408	7636	4	C	T	T	26	26	HPSE	T	2	2
ZNF608	57507	broad.mit.edu	36	5	124012703	124012703	+	Missense_Mutation	SNP	C	A	A			TCGA-14-0790-01	TCGA-14-0790-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:124012703C>A	uc003ktq.1	-	c.1273G>T	c.(1273-1275)GAC>TAC	p.D425Y	ZNF608_uc003ktr.1_Intron|ZNF608_uc003kts.1_Missense_Mutation_p.D425Y|ZNF608_uc003ktt.1_Missense_Mutation_p.D425Y	NM_020747	NP_065798	Q9ULD9	ZN608_HUMAN	zinc finger protein 608	425						intracellular	zinc ion binding			skin(3)|ovary(2)|lung(1)	6		all_cancers(142;0.186)|Prostate(80;0.081)								447				0.493151	108.293756	108.296818	36	37	CC		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(527;0.159)|Kidney(363;0.221)	OV - Ovarian serous cystadenocarcinoma(64;0.00126)|Epithelial(69;0.00238)|all cancers(49;0.00783)	Missense_Mutation	SNP	124012703	124012703	18629	5	C	A	A	29	29	ZNF608	A	3	3
FBXO38	81545	broad.mit.edu	36	5	147761847	147761847	+	Silent	SNP	G	A	A			TCGA-14-0790-01	TCGA-14-0790-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:147761847G>A	uc003lpf.1	+	c.372G>A	c.(370-372)GAG>GAA	p.E124E	FBXO38_uc003lpg.1_Silent_p.E124E|FBXO38_uc003lph.2_Silent_p.E124E	NM_205836	NP_995308	Q6PIJ6	FBX38_HUMAN	F-box protein 38 isoform b	124						cytoplasm|nucleus				ovary(4)|skin(1)	5														0.464455	325.935785	326.167395	98	113	GG		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		Silent	SNP	147761847	147761847	5983	5	G	A	A	35	35	FBXO38	A	2	2
AHRR	57491	broad.mit.edu	36	5	475883	475883	+	Missense_Mutation	SNP	G	A	A			TCGA-14-0790-01	TCGA-14-0790-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:475883G>A	uc003jav.1	+	c.493G>A	c.(493-495)GTG>ATG	p.V165M	AHRR_uc003jaw.1_Missense_Mutation_p.V161M|AHRR_uc010isy.1_Missense_Mutation_p.V11M|AHRR_uc010isz.1_Missense_Mutation_p.V161M|AHRR_uc003jax.1_De_novo_Start_OutOfFrame|AHRR_uc003jay.1_Missense_Mutation_p.V21M	NM_020731	NP_065782	A9YTQ3	AHRR_HUMAN	arylhydrocarbon receptor repressor	165	PAS.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|signal transducer activity|transcription regulator activity			breast(2)	2														0.558442	127.62477	127.853424	43	34	GG		KEEP	---	---	---	---	capture	Epithelial(17;0.0011)|OV - Ovarian serous cystadenocarcinoma(19;0.00353)|all cancers(22;0.00354)|Lung(60;0.0863)		Missense_Mutation	SNP	475883	475883	420	5	G	A	A	40	40	AHRR	A	1	1
GRM1	2911	broad.mit.edu	36	6	146797169	146797169	+	Silent	SNP	C	A	A			TCGA-14-0790-01	TCGA-14-0790-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:146797169C>A	uc010khw.1	+	c.3129C>A	c.(3127-3129)ACC>ACA	p.T1043T	GRM1_uc010khv.1_3'UTR|GRM1_uc003qll.2_3'UTR	NM_000838	NP_000829	Q13255	GRM1_HUMAN	glutamate receptor, metabotropic 1 isoform alpha	1043	Cytoplasmic (Potential).				synaptic transmission	integral to plasma membrane	G-protein coupled receptor activity|glutamate receptor activity			ovary(4)|central_nervous_system(3)|large_intestine(2)	9		Ovarian(120;0.0387)			Acamprosate(DB00659)|L-Glutamic Acid(DB00142)									0.417391	148.990329	149.672453	48	67	CC		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(155;5.35e-08)|GBM - Glioblastoma multiforme(68;0.00762)	Silent	SNP	146797169	146797169	7075	6	C	A	A	23	23	GRM1	A	3	3
TIAM2	26230	broad.mit.edu	36	6	155608489	155608489	+	Missense_Mutation	SNP	C	T	T			TCGA-14-0790-01	TCGA-14-0790-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:155608489C>T	uc003qqb.1	+	c.3584C>T	c.(3583-3585)GCG>GTG	p.A1195V	TIAM2_uc003qqd.1_Missense_Mutation_p.A1195V|TIAM2_uc003qqe.1_Missense_Mutation_p.A1195V|TIAM2_uc010kjj.1_Missense_Mutation_p.A728V|TIAM2_uc003qqf.1_Missense_Mutation_p.A571V|TIAM2_uc003qqg.1_Missense_Mutation_p.A507V|TIAM2_uc003qqh.1_Missense_Mutation_p.A120V	NM_012454	NP_036586	Q8IVF5	TIAM2_HUMAN	T-cell lymphoma invasion and metastasis 2	1195	DH.				apoptosis|cellular lipid metabolic process|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|filopodium|growth cone|lamellipodium	receptor signaling protein activity|Rho guanyl-nucleotide exchange factor activity			ovary(3)|breast(1)	4		Ovarian(120;0.196)												0.350305	477.06072	486.76316	172	319	CC		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(155;8.1e-13)|BRCA - Breast invasive adenocarcinoma(81;0.0053)	Missense_Mutation	SNP	155608489	155608489	16419	6	C	T	T	27	27	TIAM2	T	1	1
EPO	2056	broad.mit.edu	36	7	100157522	100157522	+	Missense_Mutation	SNP	C	T	T			TCGA-14-0790-01	TCGA-14-0790-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:100157522C>T	uc003uwi.1	+	c.161C>T	c.(160-162)ACG>ATG	p.T54M		NM_000799	NP_000790	P01588	EPO_HUMAN	erythropoietin precursor	54					blood circulation|erythrocyte maturation|positive regulation of cell proliferation|positive regulation of DNA replication|positive regulation of gene-specific transcription|positive regulation of Ras protein signal transduction|positive regulation of tyrosine phosphorylation of Stat5 protein|signal transduction	extracellular space	erythropoietin receptor binding|hormone activity			central_nervous_system(2)	2	Lung NSC(181;0.041)|all_lung(186;0.0581)				Darbepoetin alfa(DB00012)|Epoetin alfa(DB00016)					64				0.236842	107.874904	119.904117	45	145	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	100157522	100157522	5381	7	C	T	T	19	19	EPO	T	1	1
ASZ1	136991	broad.mit.edu	36	7	116812111	116812111	+	Missense_Mutation	SNP	C	G	G			TCGA-14-0790-01	TCGA-14-0790-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:116812111C>G	uc003vjb.2	-	c.592G>C	c.(592-594)GTT>CTT	p.V198L		NM_130768	NP_570124	Q8WWH4	ASZ1_HUMAN	ankyrin repeat, SAM and basic leucine zipper	198	ANK 5.				cell differentiation|DNA methylation involved in gamete generation|gene silencing by RNA|male meiosis|multicellular organismal development|piRNA metabolic process|spermatogenesis	pi-body	signal transducer activity			central_nervous_system(2)|ovary(1)	3	Lung NSC(10;0.00156)|all_lung(10;0.00175)													0.461538	330.784332	331.05208	96	112	CC		KEEP	---	---	---	---	capture	STAD - Stomach adenocarcinoma(10;0.000512)		Missense_Mutation	SNP	116812111	116812111	1088	7	C	G	G	20	20	ASZ1	G	3	3
VIPR2	7434	broad.mit.edu	36	7	158595344	158595344	+	Missense_Mutation	SNP	G	A	A			TCGA-14-0790-01	TCGA-14-0790-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:158595344G>A	uc003woh.1	-	c.179C>T	c.(178-180)ACG>ATG	p.T60M	VIPR2_uc010lqx.1_Non-coding_Transcript|VIPR2_uc010lqy.1_Non-coding_Transcript	NM_003382	NP_003373	P41587	VIPR2_HUMAN	vasoactive intestinal peptide receptor 2	60	Extracellular (Potential).				cell-cell signaling	integral to plasma membrane				lung(1)|central_nervous_system(1)	2	Ovarian(565;0.152)	all_cancers(7;1.13e-11)|all_epithelial(9;0.000545)|all_hematologic(28;0.00603)				Pancreas(154;1876 1931 2329 17914 20079)								0.337931	132.457214	135.812372	49	96	GG		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(82;0.00231)	UCEC - Uterine corpus endometrioid carcinoma (81;0.2)|STAD - Stomach adenocarcinoma(7;0.18)	Missense_Mutation	SNP	158595344	158595344	17737	7	G	A	A	40	40	VIPR2	A	1	1
ZPBP	11055	broad.mit.edu	36	7	50068191	50068191	+	Missense_Mutation	SNP	C	T	T			TCGA-14-0790-01	TCGA-14-0790-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:50068191C>T	uc003tou.1	-	c.427G>A	c.(427-429)GAA>AAA	p.E143K	ZPBP_uc010kyw.1_Missense_Mutation_p.E142K	NM_007009	NP_008940	Q9BS86	ZPBP1_HUMAN	zona pellucida binding protein	143					binding of sperm to zona pellucida	extracellular region					0	Glioma(55;0.08)|all_neural(89;0.245)													0.29918	200.977907	209.772575	73	171	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	50068191	50068191	18823	7	C	T	T	31	31	ZPBP	T	1	1
EGFR	1956	broad.mit.edu	36	7	55189316	55189316	+	Missense_Mutation	SNP	C	T	T			TCGA-14-0790-01	TCGA-14-0790-01	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)			0.928497	2965.78079	3139.745827	896	69	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
ZNF618	114991	broad.mit.edu	36	9	115790545	115790545	+	Silent	SNP	C	T	T			TCGA-14-0790-01	TCGA-14-0790-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr9:115790545C>T	uc004bid.1	+	c.201C>T	c.(199-201)CCC>CCT	p.P67P	ZNF618_uc004bib.1_Silent_p.P67P|ZNF618_uc004bic.1_Silent_p.P67P	NM_133374	NP_588615	Q5T7W0	ZN618_HUMAN	zinc finger protein 618	67					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0														0.630435	94.677793	95.365346	29	17	CC		KEEP	---	---	---	---	capture			Silent	SNP	115790545	115790545	18637	9	C	T	T	23	23	ZNF618	T	1	1
ARHGAP6	395	broad.mit.edu	36	X	11070335	11070335	+	Silent	SNP	G	A	A			TCGA-14-0790-01	TCGA-14-0790-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:11070335G>A	uc004cup.1	-	c.2196C>T	c.(2194-2196)TTC>TTT	p.F732F	ARHGAP6_uc004cuo.1_Non-coding_Transcript|ARHGAP6_uc004cum.1_Silent_p.F529F|ARHGAP6_uc004cun.1_Silent_p.F552F	NM_013427	NP_038286	O43182	RHG06_HUMAN	Rho GTPase activating protein 6 isoform 1	732					actin filament polymerization|activation of phospholipase C activity|negative regulation of focal adhesion assembly|negative regulation of stress fiber assembly|Rho protein signal transduction	actin filament|cytosol	phospholipase activator activity|phospholipase binding|Rho GTPase activator activity|SH3 domain binding|SH3/SH2 adaptor activity			urinary_tract(1)|lung(1)	2														0.483986	430.586539	430.649191	136	145	GG		KEEP	---	---	---	---	capture			Silent	SNP	11070335	11070335	901	23	G	A	A	37	37	ARHGAP6	A	1	1
BCORL1	63035	broad.mit.edu	36	X	128976946	128976946	+	Silent	SNP	G	A	A			TCGA-14-0790-01	TCGA-14-0790-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:128976946G>A	uc004evb.1	+	c.2517G>A	c.(2515-2517)GCG>GCA	p.A839A	BCORL1_uc010nrc.1_Silent_p.A741A|BCORL1_uc010nrd.1_Silent_p.A741A	NM_021946	NP_068765	Q5H9F3	BCORL_HUMAN	BCL6 co-repressor-like 1	839					chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus				ovary(4)|breast(2)|lung(1)	7														0.427273	257.000848	258.014796	94	126	GG		KEEP	---	---	---	---	capture			Silent	SNP	128976946	128976946	1408	23	G	A	A	40	40	BCORL1	A	1	1
GPR112	139378	broad.mit.edu	36	X	135313141	135313141	+	Missense_Mutation	SNP	C	A	A			TCGA-14-0790-01	TCGA-14-0790-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:135313141C>A	uc004ezu.1	+	c.8648C>A	c.(8647-8649)ACT>AAT	p.T2883N	GPR112_uc010nsb.1_Missense_Mutation_p.T2678N	NM_153834	NP_722576	Q8IZF6	GP112_HUMAN	G-protein coupled receptor 112	2883	Extracellular (Potential).				neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(5)|large_intestine(2)|lung(1)|breast(1)|skin(1)|pancreas(1)	11	Acute lymphoblastic leukemia(192;0.000127)									487				0.473684	135.662683	135.720334	45	50	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	135313141	135313141	6903	23	C	A	A	20	20	GPR112	A	3	3
CDR1	1038	broad.mit.edu	36	X	139694125	139694125	+	Missense_Mutation	SNP	C	T	T			TCGA-14-0790-01	TCGA-14-0790-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:139694125C>T	uc004fbg.1	-	c.73G>A	c.(73-75)GTA>ATA	p.V25I		NM_004065	NP_004056	P51861	CDR1_HUMAN	cerebellar degeneration-related protein 1,	25	23 X 6 AA approximate repeats.|4.										0	Acute lymphoblastic leukemia(192;7.65e-05)	Lung SC(4;0.051)												0.505587	555.521563	555.532386	181	177	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	139694125	139694125	3300	23	C	T	T	19	19	CDR1	T	1	1
DNASE1L1	1774	broad.mit.edu	36	X	153286608	153286608	+	Missense_Mutation	SNP	C	G	G			TCGA-14-0790-01	TCGA-14-0790-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:153286608C>G	uc004fks.1	-	c.146G>C	c.(145-147)CGC>CCC	p.R49P	DNASE1L1_uc004fkt.1_Missense_Mutation_p.R49P|DNASE1L1_uc004fku.1_Missense_Mutation_p.R49P|DNASE1L1_uc004fkv.1_Missense_Mutation_p.R49P|DNASE1L1_uc004fkw.1_Missense_Mutation_p.R49P	NM_006730	NP_006721	P49184	DNSL1_HUMAN	deoxyribonuclease I-like 1 precursor	49					DNA catabolic process	endoplasmic reticulum	DNA binding|endodeoxyribonuclease activity, producing 5'-phosphomonoesters				0	all_cancers(53;3.7e-16)|all_epithelial(53;2.97e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)													0.25	6.340204	8.286153	8	24	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	153286608	153286608	4844	23	C	G	G	27	27	DNASE1L1	G	3	3
SCML2	10389	broad.mit.edu	36	X	18258629	18258629	+	Silent	SNP	C	T	T			TCGA-14-0790-01	TCGA-14-0790-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:18258629C>T	uc004cyl.2	-	c.90G>A	c.(88-90)AGG>AGA	p.R30R	SCML2_uc004cyk.2_Non-coding_Transcript|SCML2_uc010nfd.1_Silent_p.R30R	NM_006089	NP_006080	Q9UQR0	SCML2_HUMAN	sex comb on midleg-like 2	30					anatomical structure morphogenesis|regulation of transcription, DNA-dependent	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity				0	Hepatocellular(33;0.183)					Esophageal Squamous(100;1252 1965 19021 35517)								0.352941	93.426813	95.046898	30	55	CC		KEEP	---	---	---	---	capture			Silent	SNP	18258629	18258629	14392	23	C	T	T	22	22	SCML2	T	2	2
FAM47C	442444	broad.mit.edu	36	X	36938463	36938463	+	Missense_Mutation	SNP	G	A	A			TCGA-14-0790-01	TCGA-14-0790-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:36938463G>A	uc004ddl.1	+	c.2059G>A	c.(2059-2061)GTA>ATA	p.V687I		NM_001013736	NP_001013758	Q5HY64	FA47C_HUMAN	hypothetical protein LOC442444	687										ovary(3)	3														0.451327	145.713334	145.928085	51	62	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	36938463	36938463	5792	23	G	A	A	40	40	FAM47C	A	1	1
FLT3LG	2323	broad.mit.edu	36	19	54673977	54673978	+	Splice_Site_Ins	INS	-	C	C			TCGA-14-0790-01	TCGA-14-0790-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:54673977_54673978insC	uc002pnu.1	+	c.e6_splice_site			FLT3LG_uc002pnv.1_Splice_Site_Ins|FLT3LG_uc002pnw.1_Splice_Site_Ins|FLT3LG_uc002pnx.2_Splice_Site_Ins	NM_001459	NP_001450			fms-related tyrosine kinase 3 ligand						positive regulation of cell proliferation|signal transduction	extracellular space|integral to membrane|plasma membrane|soluble fraction	cytokine activity				0		all_lung(116;1.62e-07)|Lung NSC(112;8.47e-07)|all_neural(266;0.0381)|Ovarian(192;0.0392)		OV - Ovarian serous cystadenocarcinoma(262;0.00154)|GBM - Glioblastoma multiforme(486;0.0246)										0.33			2	4				---	---	---	---	capture_indel			Splice_Site_Ins	INS	54673977	54673978	6185	19	-	C	C	34	34	FLT3LG	C	5	5
S1PR1	1901	broad.mit.edu	36	1	101477903	101477905	+	In_Frame_Del	DEL	ATT	-	-			TCGA-14-0790-01	TCGA-14-0790-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:101477903_101477905delATT	uc001dud.2	+	c.775_777delATT	c.(775-777)ATTdel	p.I260del	S1PR1_uc009weg.1_In_Frame_Del_p.I260del	NM_001400	NP_001391	P21453	S1PR1_HUMAN	sphingosine-1-phosphate receptor 1	260	Helical; Name=6; (By similarity).				cell adhesion	integral to membrane	lysosphingolipid and lysophosphatidic acid receptor activity			ovary(2)	2														0.42			118	164				---	---	---	---	capture_indel			In_Frame_Del	DEL	101477903	101477905	14273	1	ATT	-	-	4	4	S1PR1	-	5	5
SNAPC4	6621	broad.mit.edu	36	9	138402012	138402013	+	Splice_Site_Ins	INS	-	A	A			TCGA-14-0790-01	TCGA-14-0790-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:138402012_138402013insA	uc004chh.1	-	c.e11_splice_site				NM_003086	NP_003077			small nuclear RNA activating complex,						regulation of transcription, DNA-dependent|snRNA transcription from RNA polymerase II promoter|snRNA transcription from RNA polymerase III promoter	snRNA-activating protein complex	DNA binding|sequence-specific DNA binding transcription factor activity				0		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;5.31e-06)|Epithelial(140;7.13e-06)										0.48			63	67				---	---	---	---	capture_indel			Splice_Site_Ins	INS	138402012	138402013	15337	9	-	A	A	61	61	SNAPC4	A	5	5
