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
NNMT	4837	broad.mit.edu	36	11	113687984	113687984	+	Missense_Mutation	SNP	G	A	A			TCGA-14-1827-01	TCGA-14-1827-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:113687984G>A	uc001por.1	+	c.370G>A	c.(370-372)GGT>AGT	p.G124S	NNMT_uc001pos.1_Missense_Mutation_p.G124S	NM_006169	NP_006160	P40261	NNMT_HUMAN	nicotinamide N-methyltransferase	124					xenobiotic metabolic process	cytosol	nicotinamide N-methyltransferase activity|pyridine N-methyltransferase activity			ovary(1)	1		all_cancers(61;4.83e-16)|all_epithelial(67;7.28e-09)|all_hematologic(158;0.000135)|Melanoma(852;0.000902)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Prostate(24;0.0906)		BRCA - Breast invasive adenocarcinoma(274;2.79e-06)|Epithelial(105;1.32e-05)|all cancers(92;0.000144)|OV - Ovarian serous cystadenocarcinoma(223;0.128)	Niacin(DB00627)									0.226277	77.851057	87.27906	31	106	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	113687984	113687984	10912	11	G	A	A	43	43	NNMT	A	2	2
SRPR	6734	broad.mit.edu	36	11	125640443	125640443	+	Missense_Mutation	SNP	C	T	T			TCGA-14-1827-01	TCGA-14-1827-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:125640443C>T	uc001qdh.1	-	c.1241G>A	c.(1240-1242)CGT>CAT	p.R414H		NM_003139	NP_003130	P08240	SRPR_HUMAN	signal recognition particle receptor	414					SRP-dependent cotranslational protein targeting to membrane	integral to membrane|signal recognition particle receptor complex	GTP binding|GTPase activity|receptor activity|signal recognition particle binding				0	all_hematologic(175;0.145)			BRCA - Breast invasive adenocarcinoma(274;1.1e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0736)										0.331325	154.386646	158.562568	55	111	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	125640443	125640443	15676	11	C	T	T	19	19	SRPR	T	1	1
APBB1	322	broad.mit.edu	36	11	6379436	6379436	+	Missense_Mutation	SNP	G	A	A			TCGA-14-1827-01	TCGA-14-1827-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:6379436G>A	uc001mdb.1	-	c.1447C>T	c.(1447-1449)CGC>TGC	p.R483C	APBB1_uc001mcz.1_Missense_Mutation_p.R102C|APBB1_uc001mda.2_Missense_Mutation_p.R8C|APBB1_uc001mdc.1_Missense_Mutation_p.R481C	NM_001164	NP_001155	O00213	APBB1_HUMAN	amyloid beta A4 precursor protein-binding,	483	PID 1.				apoptosis|axonogenesis|cell cycle arrest|histone H4 acetylation|negative regulation of cell growth|negative regulation of S phase of mitotic cell cycle|negative regulation of thymidylate synthase biosynthetic process|positive regulation of apoptosis|regulation of transcription, DNA-dependent|response to DNA damage stimulus|signal transduction|transcription, DNA-dependent	cytoplasm|growth cone|lamellipodium|nucleus|plasma membrane|synapse	beta-amyloid binding|chromatin binding|histone binding|proline-rich region binding|transcription activator activity|transcription factor binding			breast(2)	2		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)		Epithelial(150;6.49e-08)|BRCA - Breast invasive adenocarcinoma(625;0.194)		GBM(147;1810 2556 5672 39622)								0.312775	191.852347	198.931224	71	156	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	6379436	6379436	769	11	G	A	A	37	37	APBB1	A	1	1
BBS1	582	broad.mit.edu	36	11	66038587	66038587	+	Missense_Mutation	SNP	G	T	T			TCGA-14-1827-01	TCGA-14-1827-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:66038587G>T	uc001oii.1	+	c.405G>T	c.(403-405)GAG>GAT	p.E135D	BBS1_uc001oij.1_Missense_Mutation_p.E98D|BBS1_uc001oik.1_Missense_Mutation_p.E22D|BBS1_uc001oil.1_Missense_Mutation_p.E98D	NM_024649	NP_078925	Q8NFJ9	BBS1_HUMAN	Bardet-Biedl syndrome 1	98					photoreceptor cell maintenance|response to stimulus|retina homeostasis|sensory cilium assembly	BBSome|cilium membrane|cytoplasm	protein binding			ovary(1)	1						GBM(152;173 2612 9770 10137)								0.110345	15.397877	37.181529	16	129	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	66038587	66038587	1356	11	G	T	T	34	34	BBS1	T	3	3
NCOR2	9612	broad.mit.edu	36	12	123390858	123390858	+	Missense_Mutation	SNP	C	A	A			TCGA-14-1827-01	TCGA-14-1827-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:123390858C>A	uc009zyd.1	-	c.5444G>T	c.(5443-5445)CGG>CTG	p.R1815L	NCOR2_uc009zye.1_Missense_Mutation_p.R1799L|NCOR2_uc001ugh.2_Missense_Mutation_p.R1808L|NCOR2_uc001ugi.2_Missense_Mutation_p.R1798L	NM_006312	NP_006303	Q9Y618	NCOR2_HUMAN	nuclear receptor co-repressor 2 isoform 1	1816					cellular lipid metabolic process|negative regulation of gene-specific transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|regulation of cellular ketone metabolic process by negative regulation of transcription from an RNA polymerase II promoter|transcription, DNA-dependent	nuclear body|nucleus|transcriptional repressor complex	DNA binding|histone deacetylase binding|Notch binding|protein N-terminus binding|transcription corepressor activity|transcription repressor activity			ovary(1)|skin(1)	2	all_neural(191;0.0804)|Medulloblastoma(191;0.163)			Epithelial(86;3.99e-05)|OV - Ovarian serous cystadenocarcinoma(86;9.14e-05)|all cancers(50;0.000402)|BRCA - Breast invasive adenocarcinoma(302;0.0764)										0.5	9.996551	9.996551	4	4	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	123390858	123390858	10635	12	C	A	A	23	23	NCOR2	A	3	3
TMEM132D	121256	broad.mit.edu	36	12	128125495	128125495	+	Silent	SNP	G	A	A			TCGA-14-1827-01	TCGA-14-1827-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:128125495G>A	uc009zyl.1	-	c.2178C>T	c.(2176-2178)TAC>TAT	p.Y726Y	TMEM132D_uc001uia.2_Silent_p.Y264Y	NM_133448	NP_597705	Q14C87	T132D_HUMAN	transmembrane protein 132D	726	Extracellular (Potential).					integral to membrane				ovary(10)|pancreas(2)	12	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0934)|Breast(359;0.133)		OV - Ovarian serous cystadenocarcinoma(86;0.000288)|Epithelial(86;0.0116)|all cancers(50;0.0246)										0.342697	179.644217	183.524345	61	117	GG		KEEP	---	---	---	---	capture			Silent	SNP	128125495	128125495	16579	12	G	A	A	40	40	TMEM132D	A	1	1
ABCC9	10060	broad.mit.edu	36	12	21862394	21862394	+	Missense_Mutation	SNP	G	A	A			TCGA-14-1827-01	TCGA-14-1827-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:21862394G>A	uc001rfh.1	-	c.3728C>T	c.(3727-3729)TCG>TTG	p.S1243L	ABCC9_uc001rfi.1_Missense_Mutation_p.S1243L|ABCC9_uc001rfj.1_Missense_Mutation_p.S1207L	NM_020297	NP_064693	O60706	ABCC9_HUMAN	ATP-binding cassette, sub-family C, member 9	1243	Extracellular (Potential).|ABC transmembrane type-1 2.				defense response to virus|potassium ion import	ATP-sensitive potassium channel complex	ATP binding|ATPase activity, coupled to transmembrane movement of substances|potassium channel regulator activity|sulfonylurea receptor activity			ovary(4)	4					Adenosine triphosphate(DB00171)|Glibenclamide(DB01016)									0.345324	152.260941	155.196183	48	91	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	21862394	21862394	60	12	G	A	A	37	37	ABCC9	A	1	1
LRRIQ1	84125	broad.mit.edu	36	12	84045740	84045740	+	Splice_Site_SNP	SNP	G	A	A			TCGA-14-1827-01	TCGA-14-1827-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:84045740G>A	uc001tac.1	+	c.e18_splice_site				NM_001079910	NP_001073379			leucine-rich repeats and IQ motif containing 1											ovary(4)|central_nervous_system(1)	5				GBM - Glioblastoma multiforme(134;0.212)										0.236842	22.855601	25.261156	9	29	GG		KEEP	---	---	---	---	capture			Splice_Site_SNP	SNP	84045740	84045740	9405	12	G	A	A	36	36	LRRIQ1	A	5	2
DIAPH3	81624	broad.mit.edu	36	13	59442991	59442991	+	Nonsense_Mutation	SNP	A	T	T			TCGA-14-1827-01	TCGA-14-1827-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr13:59442991A>T	uc001vht.1	-	c.1955T>A	c.(1954-1956)TTA>TAA	p.L652*	DIAPH3_uc001vhu.1_Nonsense_Mutation_p.L389*|DIAPH3_uc001vhv.2_Nonsense_Mutation_p.L230*	NM_001042517	NP_001035982	Q9NSV4	DIAP3_HUMAN	diaphanous homolog 3 isoform a	652	FH2.				actin cytoskeleton organization		actin binding|Rho GTPase binding			ovary(2)	2		Breast(118;0.052)|Prostate(109;0.103)|Hepatocellular(98;0.132)		GBM - Glioblastoma multiforme(99;2.77e-05)										0.205882	17.611908	20.334389	7	27	AA		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	59442991	59442991	4699	13	A	T	T	13	13	DIAPH3	T	5	4
SYNE2	23224	broad.mit.edu	36	14	63612490	63612490	+	Silent	SNP	C	T	T			TCGA-14-1827-01	TCGA-14-1827-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr14:63612490C>T	uc001xgl.1	+	c.10941C>T	c.(10939-10941)TCC>TCT	p.S3647S	SYNE2_uc001xgm.1_Silent_p.S3647S|SYNE2_uc010apy.1_Silent_p.S9S|SYNE2_uc010apw.1_Silent_p.S353S|SYNE2_uc010apx.1_Silent_p.S39S	NM_182914	NP_878918	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	3647	Cytoplasmic (Potential).				centrosome localization|cytoskeletal anchoring at nuclear membrane|nuclear migration along microfilament|positive regulation of cell migration	cytoskeleton|filopodium membrane|focal adhesion|integral to membrane|lamellipodium membrane|mitochondrial part|nuclear outer membrane|nucleoplasm|sarcoplasmic reticulum membrane|SUN-KASH complex|Z disc	actin binding|protein binding			ovary(8)|breast(4)|central_nervous_system(1)|pancreas(1)	14				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)										0.333333	53.833907	55.161388	18	36	CC		KEEP	---	---	---	---	capture			Silent	SNP	63612490	63612490	15967	14	C	T	T	23	23	SYNE2	T	1	1
C15orf53	400359	broad.mit.edu	36	15	36777822	36777822	+	Silent	SNP	C	T	T			TCGA-14-1827-01	TCGA-14-1827-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr15:36777822C>T	uc001zkf.1	+	c.324C>T	c.(322-324)TGC>TGT	p.C108C		NM_207444	NP_997327	Q8NAA6	CO053_HUMAN	hypothetical protein LOC400359	108											0		all_cancers(109;1.75e-13)|all_epithelial(112;1.02e-11)|Lung NSC(122;1.9e-09)|all_lung(180;4.04e-08)|Melanoma(134;0.091)|Colorectal(260;0.198)		GBM - Glioblastoma multiforme(113;8.39e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0321)										0.106509	9.338221	35.333509	18	151	CC		KEEP	---	---	---	---	capture			Silent	SNP	36777822	36777822	1851	15	C	T	T	25	25	C15orf53	T	2	2
FSIP1	161835	broad.mit.edu	36	15	37697390	37697390	+	Missense_Mutation	SNP	C	T	T			TCGA-14-1827-01	TCGA-14-1827-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr15:37697390C>T	uc001zki.1	-	c.1537G>A	c.(1537-1539)GTT>ATT	p.V513I		NM_152597	NP_689810	Q8NA03	FSIP1_HUMAN	fibrous sheath interacting protein 1	513										ovary(2)	2		all_cancers(109;2.66e-19)|all_epithelial(112;2.66e-16)|Lung NSC(122;1.5e-11)|all_lung(180;4.03e-10)|Melanoma(134;0.0575)|Ovarian(310;0.0827)|Colorectal(260;0.119)		GBM - Glioblastoma multiforme(113;8.22e-06)|BRCA - Breast invasive adenocarcinoma(123;0.142)										0.342246	194.183595	198.276244	64	123	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	37697390	37697390	6325	15	C	T	T	19	19	FSIP1	T	1	1
TP53BP1	7158	broad.mit.edu	36	15	41501444	41501444	+	Missense_Mutation	SNP	C	G	G			TCGA-14-1827-01	TCGA-14-1827-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr15:41501444C>G	uc001zrr.2	-	c.4001G>C	c.(4000-4002)AGC>ACC	p.S1334T	TP53BP1_uc001zrq.2_Missense_Mutation_p.S1334T|TP53BP1_uc001zrs.1_Missense_Mutation_p.S1329T	NM_005657	NP_005648	Q12888	TP53B_HUMAN	tumor protein p53 binding protein 1 isoform 3	1329					double-strand break repair via homologous recombination|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	condensed chromosome kinetochore|cytoplasm|nucleoplasm	protein binding|transcription activator activity			ovary(2)|large_intestine(1)|pancreas(1)|kidney(1)|skin(1)	6		all_cancers(109;6.94e-11)|all_epithelial(112;2.69e-09)|Lung NSC(122;7.86e-07)|all_lung(180;7.84e-06)|Melanoma(134;0.0728)		GBM - Glioblastoma multiforme(94;1.59e-06)						421				0.381443	110.652748	111.84806	37	60	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	41501444	41501444	16925	15	C	G	G	28	28	TP53BP1	G	3	3
PIGQ	9091	broad.mit.edu	36	16	564178	564178	+	Missense_Mutation	SNP	G	T	T			TCGA-14-1827-01	TCGA-14-1827-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:564178G>T	uc002cho.1	+	c.103G>T	c.(103-105)GTC>TTC	p.V35F	PIGQ_uc010bqw.1_Missense_Mutation_p.V35F|PIGQ_uc002chm.2_Missense_Mutation_p.V35F|PIGQ_uc002chn.1_Missense_Mutation_p.V35F	NM_148920	NP_683721	Q9BRB3	PIGQ_HUMAN	phosphatidylinositol glycan anchor biosynthesis,	35					C-terminal protein lipidation|carbohydrate metabolic process|preassembly of GPI anchor in ER membrane	endoplasmic reticulum membrane|integral to membrane	phosphatidylinositol N-acetylglucosaminyltransferase activity			central_nervous_system(1)	1		Hepatocellular(780;0.00335)												0.333333	7.134919	7.411033	4	8	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	564178	564178	12320	16	G	T	T	44	44	PIGQ	T	3	3
LRRC50	123872	broad.mit.edu	36	16	82761285	82761285	+	Silent	SNP	G	A	A			TCGA-14-1827-01	TCGA-14-1827-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:82761285G>A	uc002fhl.2	+	c.1350G>A	c.(1348-1350)CCG>CCA	p.P450P		NM_178452	NP_848547	Q8NEP3	LRC50_HUMAN	leucine rich repeat containing 50	450	Pro-rich.				axonemal dynein complex assembly|cilium morphogenesis	cilium axoneme|cytoplasm|spindle pole	dynein binding			ovary(4)|pancreas(1)	5														0.421053	24.398073	24.501057	8	11	GG		KEEP	---	---	---	---	capture			Silent	SNP	82761285	82761285	9384	16	G	A	A	38	38	LRRC50	A	1	1
FAM38B	63895	broad.mit.edu	36	18	10686408	10686408	+	Silent	SNP	G	A	A			TCGA-14-1827-01	TCGA-14-1827-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr18:10686408G>A	uc002koq.1	-	c.183C>T	c.(181-183)TTC>TTT	p.F61F		NM_022068	NP_071351	Q9H5I5	PIEZ2_HUMAN	hypothetical protein LOC63895	2206	Helical; (Potential).					integral to membrane	ion channel activity			ovary(1)	1														0.214286	28.59027	32.797146	12	44	GG		KEEP	---	---	---	---	capture			Silent	SNP	10686408	10686408	5776	18	G	A	A	37	37	FAM38B	A	1	1
KDM4B	23030	broad.mit.edu	36	19	5061737	5061737	+	Silent	SNP	G	C	C			TCGA-14-1827-01	TCGA-14-1827-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:5061737G>C	uc002mbq.2	+	c.1023G>C	c.(1021-1023)GTG>GTC	p.V341V	KDM4B_uc002mbr.2_Silent_p.V99V|KDM4B_uc002mbs.2_Silent_p.V73V	NM_015015	NP_055830	O94953	KDM4B_HUMAN	jumonji domain containing 2B	341					chromatin modification|oxidation-reduction process|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	nucleic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|zinc ion binding			lung(1)	1														0.24	14.236892	15.780143	6	19	GG		KEEP	---	---	---	---	capture			Silent	SNP	5061737	5061737	8435	19	G	C	C	46	46	KDM4B	C	3	3
UBE2M	9040	broad.mit.edu	36	19	63759545	63759545	+	Missense_Mutation	SNP	G	T	T			TCGA-14-1827-01	TCGA-14-1827-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:63759545G>T	uc002qtl.2	-	c.361C>A	c.(361-363)CCA>ACA	p.P121T	CHMP2A_uc002qti.1_5'Flank|CHMP2A_uc002qtj.1_5'Flank|CHMP2A_uc002qtk.1_5'Flank	NM_003969	NP_003960	P61081	UBC12_HUMAN	ubiquitin-conjugating enzyme E2M	121					post-translational protein modification|protein neddylation		ATP binding|NEDD8 ligase activity|protein binding|ribosomal S6-glutamic acid ligase activity|ubiquitin-protein ligase activity			ovary(1)|pancreas(1)	2		all_cancers(17;4.4e-22)|all_epithelial(17;2.15e-16)|Lung NSC(17;1.24e-06)|all_lung(17;5.41e-06)|Colorectal(82;3.46e-05)|Renal(17;0.00179)|all_neural(62;0.00607)|Ovarian(87;0.0443)|Breast(46;0.0928)|Medulloblastoma(540;0.184)		UCEC - Uterine corpus endometrioid carcinoma (67;0.0434)|all cancers(4;1.39e-13)|Epithelial(4;1.01e-10)|OV - Ovarian serous cystadenocarcinoma(4;2.34e-09)|GBM - Glioblastoma multiforme(193;0.0102)|Lung(386;0.179)										0.5	16.274857	16.274857	5	5	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	63759545	63759545	17422	19	G	T	T	42	42	UBE2M	T	3	3
SPTA1	6708	broad.mit.edu	36	1	156879749	156879749	+	Missense_Mutation	SNP	G	A	A			TCGA-14-1827-01	TCGA-14-1827-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:156879749G>A	uc001fst.1	-	c.4429C>T	c.(4429-4431)CGT>TGT	p.R1477C		NM_003126	NP_003117	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	1477	Spectrin 14.				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)													0.27957	74.812487	78.87473	26	67	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	156879749	156879749	15630	1	G	A	A	40	40	SPTA1	A	1	1
TNNI1	7135	broad.mit.edu	36	1	199647149	199647149	+	Missense_Mutation	SNP	G	A	A			TCGA-14-1827-01	TCGA-14-1827-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:199647149G>A	uc009wzw.1	-	c.415C>T	c.(415-417)CGG>TGG	p.R139W	TNNI1_uc009wzv.1_Missense_Mutation_p.R118W|TNNI1_uc001gwo.1_Non-coding_Transcript|TNNI1_uc001gwp.2_Missense_Mutation_p.R118W	NM_003281	NP_003272	P19237	TNNI1_HUMAN	troponin I, skeletal, slow	139					muscle filament sliding|regulation of striated muscle contraction	cytosol|troponin complex	actin binding|tropomyosin binding				0														0.6875	37.830368	38.331355	11	5	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	199647149	199647149	16867	1	G	A	A	38	38	TNNI1	A	1	1
FRRS1	391059	broad.mit.edu	36	1	99978957	99978957	+	Missense_Mutation	SNP	C	T	T			TCGA-14-1827-01	TCGA-14-1827-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:99978957C>T	uc001dsh.1	-	c.556G>A	c.(556-558)GTT>ATT	p.V186I		NM_001013660	NP_001013682	Q6ZNA5	FRRS1_HUMAN	stromal cell derived factor receptor 2 homolog	186					electron transport chain|transport	integral to membrane	ferric-chelate reductase activity|metal ion binding				0		all_epithelial(167;2.09e-06)|all_lung(203;0.000435)|Lung NSC(277;0.00201)		Epithelial(280;0.0718)|all cancers(265;0.126)|COAD - Colon adenocarcinoma(174;0.148)|Lung(183;0.206)										0.109402	71.497241	159.859117	64	521	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	99978957	99978957	6310	1	C	T	T	19	19	FRRS1	T	1	1
KCNB1	3745	broad.mit.edu	36	20	47423495	47423495	+	Missense_Mutation	SNP	C	T	T			TCGA-14-1827-01	TCGA-14-1827-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr20:47423495C>T	uc002xur.1	-	c.2009G>A	c.(2008-2010)CGA>CAA	p.R670Q	KCNB1_uc002xus.1_Missense_Mutation_p.R670Q	NM_004975	NP_004966	Q14721	KCNB1_HUMAN	potassium voltage-gated channel, Shab-related	670	Cytoplasmic (Potential).				energy reserve metabolic process|regulation of insulin secretion	voltage-gated potassium channel complex	protein binding|voltage-gated potassium channel activity			pancreas(1)	1			BRCA - Breast invasive adenocarcinoma(12;0.000405)|COAD - Colon adenocarcinoma(4;0.14)|Colorectal(8;0.166)											0.319149	88.221306	90.951079	30	64	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	47423495	47423495	8317	20	C	T	T	31	31	KCNB1	T	1	1
KCNJ15	3772	broad.mit.edu	36	21	38593518	38593518	+	Missense_Mutation	SNP	G	C	C			TCGA-14-1827-01	TCGA-14-1827-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr21:38593518G>C	uc002ywv.1	+	c.465G>C	c.(463-465)TTG>TTC	p.L155F	KCNJ15_uc002yww.1_Missense_Mutation_p.L155F|KCNJ15_uc002ywx.1_Missense_Mutation_p.L155F|KCNJ15_uc010gnu.1_Missense_Mutation_p.L155F	NM_002243	NP_733933	Q99712	IRK15_HUMAN	potassium inwardly-rectifying channel J15	155	Helical; Name=M2; (By similarity).				synaptic transmission	integral to plasma membrane	inward rectifier potassium channel activity			ovary(2)|breast(1)|central_nervous_system(1)	4														0.142132	13.992896	38.507808	28	169	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	38593518	38593518	8354	21	G	C	C	45	45	KCNJ15	C	3	3
PRR5-ARHGAP8	553158	broad.mit.edu	36	22	43634279	43634279	+	Silent	SNP	G	A	A			TCGA-14-1827-01	TCGA-14-1827-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr22:43634279G>A	uc003bfd.1	+	c.1512G>A	c.(1510-1512)GTG>GTA	p.V504V	PRR5-ARHGAP8_uc003bfc.1_Silent_p.V425V|PRR5-ARHGAP8_uc003bff.1_Silent_p.V330V|ARHGAP8_uc010gzv.1_Intron|ARHGAP8_uc003bfj.1_Silent_p.V325V|ARHGAP8_uc003bfk.1_Silent_p.V294V|PRR5-ARHGAP8_uc003bfl.1_Non-coding_Transcript	NM_181335	NP_851852			Rho GTPase activating protein 8 isoform 2												0														0.746914	775.311197	793.21258	242	82	GG		KEEP	---	---	---	---	capture			Silent	SNP	43634279	43634279	13050	22	G	A	A	47	47	PRR5-ARHGAP8	A	2	2
IL1F6	27179	broad.mit.edu	36	2	113481969	113481969	+	Silent	SNP	C	T	T			TCGA-14-1827-01	TCGA-14-1827-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:113481969C>T	uc002tip.1	+	c.354C>T	c.(352-354)TTC>TTT	p.F118F		NM_014440	NP_055255	Q9UHA7	IL1F6_HUMAN	interleukin 1 family, member 6 (epsilon)	118					immune response|inflammatory response	extracellular space	cytokine activity|interleukin-1 receptor binding			ovary(2)	2														0.375	161.778022	163.765237	54	90	CC		KEEP	---	---	---	---	capture			Silent	SNP	113481969	113481969	7955	2	C	T	T	31	31	IL1F6	T	1	1
STK36	27148	broad.mit.edu	36	2	219271858	219271858	+	Missense_Mutation	SNP	G	T	T			TCGA-14-1827-01	TCGA-14-1827-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:219271858G>T	uc002viu.1	+	c.3347G>T	c.(3346-3348)AGC>ATC	p.S1116I	STK36_uc002viv.1_Missense_Mutation_p.S1095I|STK36_uc002viw.1_Missense_Mutation_p.S294I|STK36_uc002vix.1_Missense_Mutation_p.S161I	NM_015690	NP_056505	Q9NRP7	STK36_HUMAN	serine/threonine kinase 36	1116					cilium assembly|positive regulation of hh target transcription factor activity|positive regulation of smoothened signaling pathway|post-embryonic development|protein phosphorylation	aggresome|cytoplasm|focal adhesion|intermediate filament cytoskeleton|nucleus	ATP binding|magnesium ion binding|protein serine/threonine kinase activity|transcription factor binding			ovary(4)|lung(2)|breast(1)|central_nervous_system(1)	8		Renal(207;0.0915)		Epithelial(149;9.65e-07)|all cancers(144;0.000174)|LUSC - Lung squamous cell carcinoma(224;0.00813)|Lung(261;0.00984)						551				0.38	50.504055	51.138185	19	31	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	219271858	219271858	15822	2	G	T	T	34	34	STK36	T	3	3
ANO7	50636	broad.mit.edu	36	2	241790365	241790365	+	Silent	SNP	C	T	T			TCGA-14-1827-01	TCGA-14-1827-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:241790365C>T	uc002wax.2	+	c.858C>T	c.(856-858)GTC>GTT	p.V286V		NM_001001891	NP_001001891	Q6IWH7	ANO7_HUMAN	transmembrane protein 16G isoform NGEP long	286	Extracellular (Potential).					cell junction|chloride channel complex|cytosol	chloride channel activity			pancreas(2)|central_nervous_system(1)	3														0.361111	36.965692	37.576587	13	23	CC		KEEP	---	---	---	---	capture			Silent	SNP	241790365	241790365	710	2	C	T	T	30	30	ANO7	T	2	2
CCDC88A	55704	broad.mit.edu	36	2	55376938	55376938	+	Missense_Mutation	SNP	T	A	A			TCGA-14-1827-01	TCGA-14-1827-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr2:55376938T>A	uc002ryv.1	-	c.5048A>T	c.(5047-5049)CAA>CTA	p.Q1683L	CCDC88A_uc002ryr.1_Missense_Mutation_p.Q1656L|CCDC88A_uc002rys.2_Missense_Mutation_p.Q641L|CCDC88A_uc002ryt.1_5'UTR|CCDC88A_uc010fbw.1_Missense_Mutation_p.Q185L|CCDC88A_uc010fbx.1_Non-coding_Transcript|CCDC88A_uc002ryu.1_Missense_Mutation_p.Q938L|CCDC88A_uc002ryw.2_Missense_Mutation_p.Q967L|CCDC88A_uc010fby.1_Missense_Mutation_p.Q535L	NM_018084	NP_060554	Q3V6T2	GRDN_HUMAN	coiled-coil domain containing 88A isoform 2	1684					activation of protein kinase B activity|cell migration|cellular membrane organization|DNA replication|lamellipodium assembly|microtubule cytoskeleton organization|regulation of actin cytoskeleton organization|regulation of cell proliferation|regulation of DNA replication|regulation of neuron projection development|TOR signaling cascade	cytoplasmic membrane-bounded vesicle|cytosol|endoplasmic reticulum|Golgi apparatus|lamellipodium|plasma membrane	actin binding|microtubule binding|phosphatidylinositol binding|protein homodimerization activity|protein kinase B binding			ovary(2)	2														0.157895	7.527588	13.915363	9	48	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	55376938	55376938	2988	2	T	A	A	63	63	CCDC88A	A	4	4
GAP43	2596	broad.mit.edu	36	3	116877794	116877794	+	Missense_Mutation	SNP	C	T	T			TCGA-14-1827-01	TCGA-14-1827-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr3:116877794C>T	uc003ebr.1	+	c.383C>T	c.(382-384)CCA>CTA	p.P128L	GAP43_uc003ebq.1_Missense_Mutation_p.P92L	NM_002045	NP_002036	P17677	NEUM_HUMAN	growth associated protein 43 isoform 2	92					activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|cell differentiation|nervous system development|regulation of growth|response to wounding	cell junction|growth cone membrane|synapse	calmodulin binding			ovary(1)	1				GBM - Glioblastoma multiforme(114;0.164)										0.4	62.233316	62.715468	22	33	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	116877794	116877794	6499	3	C	T	T	21	21	GAP43	T	2	2
FSTL1	11167	broad.mit.edu	36	3	121604355	121604355	+	Missense_Mutation	SNP	C	G	G			TCGA-14-1827-01	TCGA-14-1827-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr3:121604355C>G	uc003eds.1	-	c.795G>C	c.(793-795)ATG>ATC	p.M265I		NM_007085	NP_009016	Q12841	FSTL1_HUMAN	follistatin-like 1 precursor	265	VWFC.				BMP signaling pathway	extracellular space	calcium ion binding|heparin binding			central_nervous_system(1)	1				GBM - Glioblastoma multiforme(114;0.189)										0.172775	75.755632	95.074749	33	158	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	121604355	121604355	6328	3	C	G	G	29	29	FSTL1	G	3	3
OTOP1	133060	broad.mit.edu	36	4	4279144	4279144	+	Missense_Mutation	SNP	G	T	T			TCGA-14-1827-01	TCGA-14-1827-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr4:4279144G>T	uc003ghp.1	-	c.349C>A	c.(349-351)CAC>AAC	p.H117N		NM_177998	NP_819056	Q7RTM1	OTOP1_HUMAN	otopetrin 1	117					biomineral tissue development	extracellular space|integral to membrane				ovary(2)	2				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)										0.25	9.101183	10.00463	4	12	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	4279144	4279144	11717	4	G	T	T	46	46	OTOP1	T	3	3
PCDHGA10	56106	broad.mit.edu	36	5	140774919	140774919	+	Missense_Mutation	SNP	A	T	T			TCGA-14-1827-01	TCGA-14-1827-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr5:140774919A>T	uc003lkl.1	+	c.1993A>T	c.(1993-1995)ACC>TCC	p.T665S	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc010jfx.1_Intron|PCDHGA3_uc003ljm.1_Intron|PCDHGB1_uc003ljo.1_Intron|PCDHGA4_uc003ljq.1_Intron|PCDHGB2_uc003ljs.1_Intron|PCDHGA5_uc003lju.1_Intron|PCDHGB3_uc003ljw.1_Intron|PCDHGA6_uc003ljy.1_Intron|PCDHGA7_uc003lka.1_Intron|PCDHGB4_uc003lkc.1_Intron|PCDHGA8_uc003lkd.1_Intron|PCDHGB5_uc003lkf.1_Intron|PCDHGA9_uc003lkh.1_Intron|PCDHGB6_uc003lkj.1_Intron|PCDHGA10_uc003lkk.1_Missense_Mutation_p.T665S|PCDHGB7_uc003lkm.1_5'Flank|PCDHGB7_uc003lkn.1_5'Flank	NM_018913	NP_061736	Q9Y5H3	PCDGA_HUMAN	protocadherin gamma subfamily A, 10 isoform 1	665	Cadherin 6.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)											0.388889	13.813523	14.010121	7	11	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	140774919	140774919	11971	5	A	T	T	6	6	PCDHGA10	T	4	4
LMAN2	10960	broad.mit.edu	36	5	176710823	176710823	+	Missense_Mutation	SNP	G	A	A			TCGA-14-1827-01	TCGA-14-1827-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:176710823G>A	uc003mge.1	-	c.272C>T	c.(271-273)ACC>ATC	p.T91I	LMAN2_uc003mgd.1_Missense_Mutation_p.T91I	NM_006816	NP_006807	Q12907	LMAN2_HUMAN	lectin, mannose-binding 2 precursor	91	Lumenal (Potential).|L-type lectin-like.				protein transport	endoplasmic reticulum membrane|ER-Golgi intermediate compartment membrane|Golgi membrane|integral to membrane	sugar binding				0	all_cancers(89;2.04e-05)|Renal(175;0.000269)|Lung NSC(126;0.000832)|all_lung(126;0.00152)	all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)											0.330508	100.378842	103.386206	39	79	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	176710823	176710823	9167	5	G	A	A	44	44	LMAN2	A	2	2
C6	729	broad.mit.edu	36	5	41195102	41195102	+	Silent	SNP	G	A	A			TCGA-14-1827-01	TCGA-14-1827-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:41195102G>A	uc003jml.1	-	c.1722C>T	c.(1720-1722)GAC>GAT	p.D574D	C6_uc003jmk.2_Silent_p.D565D	NM_001115131	NP_001108603	P13671	CO6_HUMAN	complement component 6 precursor	565	TSP type-1 3.				complement activation, classical pathway|cytolysis|innate immune response	membrane attack complex	protein binding			ovary(3)|central_nervous_system(2)	5		Breast(839;1.07e-05)|Ovarian(839;0.0228)|Lung SC(612;0.0548)|Lung NSC(810;0.128)|all_neural(839;0.157)												0.40625	74.2325	74.72514	26	38	GG		KEEP	---	---	---	---	capture			Silent	SNP	41195102	41195102	2416	5	G	A	A	40	40	C6	A	1	1
TULP4	56995	broad.mit.edu	36	6	158790131	158790131	+	Missense_Mutation	SNP	C	T	T			TCGA-14-1827-01	TCGA-14-1827-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:158790131C>T	uc003qrf.1	+	c.659C>T	c.(658-660)CCG>CTG	p.P220L	TULP4_uc003qrg.1_Missense_Mutation_p.P220L	NM_020245	NP_064630	Q9NRJ4	TULP4_HUMAN	tubby like protein 4 isoform 1	220					intracellular signal transduction|regulation of transcription, DNA-dependent|response to nutrient	cytoplasm	protein binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1		Breast(66;0.000781)|Ovarian(120;0.0308)|Lung SC(201;0.164)|Prostate(117;0.171)		OV - Ovarian serous cystadenocarcinoma(65;1.64e-18)|BRCA - Breast invasive adenocarcinoma(81;2.67e-05)										0.411765	268.095704	269.472867	84	120	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	158790131	158790131	17331	6	C	T	T	23	23	TULP4	T	1	1
SLC22A3	6581	broad.mit.edu	36	6	160749887	160749887	+	Nonsense_Mutation	SNP	G	A	A			TCGA-14-1827-01	TCGA-14-1827-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:160749887G>A	uc003qti.1	+	c.801G>A	c.(799-801)TGG>TGA	p.W267*		NM_021977	NP_068812	O75751	S22A3_HUMAN	solute carrier family 22 member 3	267						integral to plasma membrane|membrane fraction	protein binding|quaternary ammonium group transmembrane transporter activity			ovary(1)|central_nervous_system(1)	2		Breast(66;0.00028)|Ovarian(120;0.0308)|Prostate(117;0.218)		OV - Ovarian serous cystadenocarcinoma(65;9.47e-17)|BRCA - Breast invasive adenocarcinoma(81;9.75e-06)						170				0.445833	323.610246	324.219863	107	133	GG		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	160749887	160749887	14952	6	G	A	A	42	42	SLC22A3	A	5	2
TSPAN12	23554	broad.mit.edu	36	7	120266184	120266184	+	Silent	SNP	A	T	T			TCGA-14-1827-01	TCGA-14-1827-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr7:120266184A>T	uc003vjk.1	-	c.168T>A	c.(166-168)ATT>ATA	p.I56I		NM_012338	NP_036470	O95859	TSN12_HUMAN	transmembrane 4 superfamily member 12	56	Extracellular (Potential).				angiogenesis|cell surface receptor linked signaling pathway|regulation of angiogenesis|retina layer formation	integral to plasma membrane|membrane fraction					0	all_neural(327;0.117)													0.143662	86.391053	129.804748	51	304	AA		KEEP	---	---	---	---	capture			Silent	SNP	120266184	120266184	17187	7	A	T	T	1	1	TSPAN12	T	4	4
EGFR	1956	broad.mit.edu	36	7	55178518	55178518	+	Silent	SNP	C	T	T			TCGA-14-1827-01	TCGA-14-1827-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:55178518C>T	uc003tqk.1	+	c.267C>T	c.(265-267)GTC>GTT	p.V89V	EGFR_uc003tqh.1_Silent_p.V89V|EGFR_uc003tqi.1_Silent_p.V89V|EGFR_uc003tqj.1_Silent_p.V89V|EGFR_uc010kzg.1_Silent_p.V89V	NM_005228	NP_005219	P00533	EGFR_HUMAN	epidermal growth factor receptor isoform a	89	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.V30_R297>G(5)		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)		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)		Cetuximab(DB00002)|Erlotinib(DB00530)|Gefitinib(DB00317)|Lapatinib(DB01259)|Lidocaine(DB00281)|Panitumumab(DB01269)|Trastuzumab(DB00072)			8		608	TCGA GBM(3;<1E-8)|TSP Lung(4;<1E-8)			0.984709	3230.838839	3248.62303	966	15	CC		KEEP	---	---	---	---	capture			Silent	SNP	55178518	55178518	5156	7	C	T	T	30	30	EGFR	T	2	2
EGFR	1956	broad.mit.edu	36	7	55178619	55178619	+	Missense_Mutation	SNP	C	T	T			TCGA-14-1827-01	TCGA-14-1827-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:55178619C>T	uc003tqk.1	+	c.368C>T	c.(367-369)TCT>TTT	p.S123F	EGFR_uc003tqh.1_Missense_Mutation_p.S123F|EGFR_uc003tqi.1_Missense_Mutation_p.S123F|EGFR_uc003tqj.1_Missense_Mutation_p.S123F|EGFR_uc010kzg.1_Missense_Mutation_p.S123F	NM_005228	NP_005219	P00533	EGFR_HUMAN	epidermal growth factor receptor isoform a	123	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.V30_R297>G(5)		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)		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)		Cetuximab(DB00002)|Erlotinib(DB00530)|Gefitinib(DB00317)|Lapatinib(DB01259)|Lidocaine(DB00281)|Panitumumab(DB01269)|Trastuzumab(DB00072)			8		608	TCGA GBM(3;<1E-8)|TSP Lung(4;<1E-8)			0.981595	3586.664404	3617.066981	960	18	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	55178619	55178619	5156	7	C	T	T	32	32	EGFR	T	2	2
SAMD9	54809	broad.mit.edu	36	7	92568761	92568761	+	Missense_Mutation	SNP	C	T	T			TCGA-14-1827-01	TCGA-14-1827-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:92568761C>T	uc003umf.1	-	c.4586G>A	c.(4585-4587)CGT>CAT	p.R1529H	SAMD9_uc003umg.1_Missense_Mutation_p.R1529H|SAMD9_uc010lfa.1_Missense_Mutation_p.R1529H	NM_017654	NP_060124	Q5K651	SAMD9_HUMAN	sterile alpha motif domain containing 9	1529						cytoplasm				ovary(3)|breast(1)|central_nervous_system(1)	5	all_cancers(62;5.71e-11)|all_epithelial(64;3.25e-10)|Breast(17;0.000675)|Lung NSC(181;0.0969)|all_lung(186;0.125)		STAD - Stomach adenocarcinoma(171;0.000302)											0.170455	28.069854	37.114429	15	73	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	92568761	92568761	14306	7	C	T	T	19	19	SAMD9	T	1	1
TRRAP	8295	broad.mit.edu	36	7	98414415	98414415	+	Silent	SNP	C	T	T			TCGA-14-1827-01	TCGA-14-1827-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:98414415C>T	uc003upp.1	+	c.8565C>T	c.(8563-8565)TGC>TGT	p.C2855C	TRRAP_uc003upq.1_Silent_p.C2837C|TRRAP_uc003upr.1_Silent_p.C2554C	NM_003496	NP_003487	Q9Y4A5	TRRAP_HUMAN	transformation/transcription domain-associated	2855	FAT.				histone deubiquitination|histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	NuA4 histone acetyltransferase complex|PCAF complex|STAGA complex|transcription factor TFTC complex	phosphotransferase activity, alcohol group as acceptor|protein binding|transcription cofactor activity			ovary(9)|large_intestine(8)|central_nervous_system(6)|stomach(2)|lung(1)|liver(1)	27	all_cancers(62;6.96e-09)|all_epithelial(64;4.86e-09)|Lung NSC(181;0.01)|all_lung(186;0.016)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)							1847				0.2	13.414946	16.339706	7	28	CC		KEEP	---	---	---	---	capture			Silent	SNP	98414415	98414415	17152	7	C	T	T	27	27	TRRAP	T	1	1
RSPO2	340419	broad.mit.edu	36	8	109039497	109039497	+	Silent	SNP	C	T	T			TCGA-14-1827-01	TCGA-14-1827-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr8:109039497C>T	uc003yms.1	-	c.603G>A	c.(601-603)AGG>AGA	p.R201R	RSPO2_uc003ymq.1_Silent_p.R134R|RSPO2_uc003ymr.1_Silent_p.R137R	NM_178565	NP_848660	Q6UXX9	RSPO2_HUMAN	R-spondin family, member 2	201	TSP type-1.				Wnt receptor signaling pathway	extracellular region	heparin binding			ovary(2)|skin(2)|pancreas(1)|lung(1)	6			OV - Ovarian serous cystadenocarcinoma(57;1.55e-09)											0.274119	483.552679	513.500271	179	474	CC		KEEP	---	---	---	---	capture			Silent	SNP	109039497	109039497	14190	8	C	T	T	26	26	RSPO2	T	2	2
KCTD9	54793	broad.mit.edu	36	8	25352775	25352775	+	Missense_Mutation	SNP	C	T	T			TCGA-14-1827-01	TCGA-14-1827-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr8:25352775C>T	uc003xeo.1	-	c.436G>A	c.(436-438)GAA>AAA	p.E146K	PPP2R2A_uc003xek.1_Intron	NM_017634	NP_060104	Q7L273	KCTD9_HUMAN	potassium channel tetramerisation domain	146	BTB.					voltage-gated potassium channel complex	voltage-gated potassium channel activity				0		all_cancers(63;0.0164)|Ovarian(32;0.000878)|all_epithelial(46;0.00542)|Breast(100;0.0164)|Hepatocellular(4;0.114)|Prostate(55;0.191)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0219)|Epithelial(17;2.39e-12)|Colorectal(74;0.0129)|COAD - Colon adenocarcinoma(73;0.0438)										0.483871	98.549967	98.563832	30	32	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	25352775	25352775	8422	8	C	T	T	31	31	KCTD9	T	1	1
FCN2	2220	broad.mit.edu	36	9	136916912	136916912	+	Missense_Mutation	SNP	G	A	A			TCGA-14-1827-01	TCGA-14-1827-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr9:136916912G>A	uc004cfg.1	+	c.308G>A	c.(307-309)CGT>CAT	p.R103H	FCN2_uc004cfh.1_Missense_Mutation_p.R65H	NM_004108	NP_004099	Q15485	FCN2_HUMAN	ficolin 2 isoform a precursor	103	Fibrinogen C-terminal.				complement activation, lectin pathway|opsonization|signal transduction	collagen|extracellular space	antigen binding|calcium ion binding|calcium-dependent protein binding|receptor binding|sugar binding			large_intestine(1)	1		Myeloproliferative disorder(178;0.0333)		OV - Ovarian serous cystadenocarcinoma(145;3.58e-08)|Epithelial(140;6.41e-08)|all cancers(34;3.96e-07)										0.484848	46.49464	46.501337	16	17	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	136916912	136916912	6029	9	G	A	A	40	40	FCN2	A	1	1
INPPL1	3636	broad.mit.edu	36	11	71626748	71626751	+	Frame_Shift_Del	DEL	GGGC	-	-			TCGA-14-1827-01	TCGA-14-1827-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:71626748_71626751delGGGC	uc001osf.1	+	c.3567_3570delGGGC	c.(3565-3570)CAGGGCfs	p.Q1189fs	INPPL1_uc001osg.1_Frame_Shift_Del_p.Q947fs	NM_001567	NP_001558	O15357	SHIP2_HUMAN	inositol polyphosphate phosphatase-like 1	1189_1190					actin filament organization|cell adhesion|endocytosis	actin cortical patch|cytosol	actin binding|SH2 domain binding|SH3 domain binding			skin(2)|ovary(1)	3												OREG0021191	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.57			4	3				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	71626748	71626751	8062	11	GGGC	-	-	35	35	INPPL1	-	5	5
STON2	85439	broad.mit.edu	36	14	80813338	80813339	+	Frame_Shift_Ins	INS	-	AA	AA			TCGA-14-1827-01	TCGA-14-1827-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:80813338_80813339insAA	uc001xvk.1	-	c.2069_2070insTT	c.(2068-2070)CTCfs	p.L690fs	STON2_uc001xvm.1_Frame_Shift_Ins_p.L690fs|STON2_uc001xvl.1_Frame_Shift_Ins_p.L487fs	NM_033104	NP_149095	Q8WXE9	STON2_HUMAN	stonin 2	690	MHD.				endocytosis|intracellular protein transport|regulation of endocytosis	clathrin adaptor complex|nucleolus	protein binding			pancreas(2)	2				BRCA - Breast invasive adenocarcinoma(234;0.0348)										0.39			63	100				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	80813338	80813339	15838	14	-	AA	AA	45	45	STON2	AA	5	5
ABAT	18	broad.mit.edu	36	16	8770198	8770199	+	Frame_Shift_Ins	INS	-	T	T			TCGA-14-1827-01	TCGA-14-1827-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:8770198_8770199insT	uc002czc.2	+	c.683_684insT	c.(682-684)ACGfs	p.T228fs	ABAT_uc002czd.2_Frame_Shift_Ins_p.T228fs|ABAT_uc010buh.1_Frame_Shift_Ins_p.T170fs|ABAT_uc010bui.1_Frame_Shift_Ins_p.T228fs	NM_020686	NP_065737	P80404	GABT_HUMAN	4-aminobutyrate aminotransferase precursor	228					behavioral response to cocaine|gamma-aminobutyric acid catabolic process|neurotransmitter catabolic process|neurotransmitter secretion	4-aminobutyrate transaminase complex|mitochondrial matrix	(S)-3-amino-2-methylpropionate transaminase activity|4-aminobutyrate transaminase activity|protein homodimerization activity|pyridoxal phosphate binding|succinate-semialdehyde dehydrogenase binding				0					Divalproex sodium(DB00510)|Isoniazid(DB00951)|L-Alanine(DB00160)|L-Glutamic Acid(DB00142)|Pyridoxal Phosphate(DB00114)|Pyruvic acid(DB00119)|Tiagabine(DB00906)|Valproic Acid(DB00313)|Vigabatrin(DB01080)									0.35			77	142				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	8770198	8770199	28	16	-	T	T	19	19	ABAT	T	5	5
SERPINB4	6318	broad.mit.edu	36	18	59476739	59476739	+	Frame_Shift_Del	DEL	T	-	-			TCGA-14-1827-01	TCGA-14-1827-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:59476739_59476739delT	uc002ljg.1	-	c.457_457delA	c.(457-459)AGTfs	p.S153fs	SERPINB4_uc002ljh.1_Intron|SERPINB3_uc002lji.1_Frame_Shift_Del_p.S153fs|SERPINB3_uc010dqa.1_Frame_Shift_Del_p.S153fs|SERPINB3_uc010dqb.1_3'UTR			P48594	SPB4_HUMAN	SCCA1/SCCA2 fusion protein.	153					immune response|regulation of proteolysis	cytoplasm|extracellular region	protein binding|serine-type endopeptidase inhibitor activity			ovary(1)|lung(1)	2										163				0.34			18	35				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	59476739	59476739	14591	18	T	-	-	56	56	SERPINB4	-	5	5
TSHZ3	57616	broad.mit.edu	36	19	36460754	36460762	+	In_Frame_Del	DEL	GGGTGGAGA	-	-			TCGA-14-1827-01	TCGA-14-1827-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:36460754_36460762delGGGTGGAGA	uc002nsy.2	-	c.1777_1785delTCTCCACCC	c.(1777-1785)TCTCCACCCdel	p.SPP593del		NM_020856	NP_065907	Q63HK5	TSH3_HUMAN	zinc finger protein 537	593_595					regulation of respiratory gaseous exchange by neurological system process|regulation of transcription, DNA-dependent	growth cone|nucleus	chromatin binding|protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription repressor activity|zinc ion binding			ovary(4)|pancreas(1)|lung(1)|skin(1)	7	Esophageal squamous(110;0.226)													0.58			323	235				---	---	---	---	capture_indel			In_Frame_Del	DEL	36460754	36460762	17176	19	GGGTGGAGA	-	-	47	47	TSHZ3	-	5	5
EFHD2	79180	broad.mit.edu	36	1	15609361	15609361	+	Frame_Shift_Del	DEL	C	-	-			TCGA-14-1827-01	TCGA-14-1827-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:15609361_15609361delC	uc001awh.1	+	c.307_307delC	c.(307-309)CAGfs	p.Q103fs		NM_024329	NP_077305	Q96C19	EFHD2_HUMAN	EF-hand domain family, member D2	103	EF-hand 1.					membrane raft					0		Renal(390;0.00145)|Breast(348;0.00173)|Colorectal(325;0.00215)|all_lung(284;0.00366)|Lung NSC(340;0.00395)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0798)|Hepatocellular(190;0.152)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.59e-07)|COAD - Colon adenocarcinoma(227;3.79e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000119)|KIRC - Kidney renal clear cell carcinoma(229;0.00251)|STAD - Stomach adenocarcinoma(313;0.00727)|READ - Rectum adenocarcinoma(331;0.0649)										0.46			18	21				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	15609361	15609361	5137	1	C	-	-	25	25	EFHD2	-	5	5
