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
GPAM	57678	broad.mit.edu	36	10	113911439	113911439	+	Silent	SNP	G	A	A			TCGA-76-6282-01	TCGA-76-6282-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr10:113911439G>A	uc009xxy.1	-	c.1470C>T	c.(1468-1470)TGC>TGT	p.C490C	GPAM_uc001kzp.2_Silent_p.C490C|GPAM_uc001kzq.1_Silent_p.C490C	NM_020918	NP_065969	Q9HCL2	GPAT1_HUMAN	mitochondrial glycerol 3-phosphate	490	Mitochondrial intermembrane (Potential).|Helical; (Potential).				phospholipid biosynthetic process|triglyceride biosynthetic process	integral to membrane|mitochondrial outer membrane	glycerol-3-phosphate O-acyltransferase activity			ovary(1)	1						Ovarian(161;1017 2606 18293 52943)								0.4	20.06472	20.247661	8	12	GG		KEEP	---	---	---	---	capture		Epithelial(162;0.0306)|all cancers(201;0.123)	Silent	SNP	113911439	113911439	6862	10	G	A	A	42	42	GPAM	A	2	2
UBE4A	9354	broad.mit.edu	36	11	117760823	117760823	+	Missense_Mutation	SNP	A	T	T			TCGA-76-6282-01	TCGA-76-6282-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr11:117760823A>T	uc001psv.1	+	c.2386A>T	c.(2386-2388)AAC>TAC	p.N796Y	UBE4A_uc001psw.1_Missense_Mutation_p.N789Y	NM_004788	NP_004779	Q14139	UBE4A_HUMAN	ubiquitination factor E4A	789					ubiquitin-dependent protein catabolic process	ubiquitin ligase complex	protein binding			ovary(2)|breast(1)|kidney(1)	4	all_hematologic(175;0.046)	Medulloblastoma(222;0.0425)|Breast(348;0.181)|all_hematologic(192;0.196)|all_neural(223;0.234)												0.2	39.653775	48.018872	20	80	AA		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(274;3.28e-05)	Missense_Mutation	SNP	117760823	117760823	17440	11	A	T	T	13	13	UBE4A	T	4	4
KRTAP5-5	439915	broad.mit.edu	36	11	1608029	1608029	+	Missense_Mutation	SNP	G	C	C			TCGA-76-6282-01	TCGA-76-6282-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:1608029G>C	uc001lty.1	+	c.383G>C	c.(382-384)GGC>GCC	p.G128A		NM_001001480	NP_001001480	Q701N2	KRA55_HUMAN	keratin associated protein 5-5	128	8 X 4 AA repeats of C-C-X-P.					keratin filament				lung(1)	1		all_epithelial(84;0.00018)|Ovarian(85;0.0014)|Breast(177;0.00147)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)												0.230769	8.120433	8.982343	3	10	GG		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(625;0.000614)|Lung(200;0.0681)|LUSC - Lung squamous cell carcinoma(625;0.082)	Missense_Mutation	SNP	1608029	1608029	8886	11	G	C	C	42	42	KRTAP5-5	C	3	3
ANO5	203859	broad.mit.edu	36	11	22252710	22252710	+	Missense_Mutation	SNP	C	T	T			TCGA-76-6282-01	TCGA-76-6282-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:22252710C>T	uc001mqi.1	+	c.2255C>T	c.(2254-2256)ACG>ATG	p.T752M	ANO5_uc001mqj.1_Missense_Mutation_p.T751M	NM_213599	NP_998764	Q75V66	ANO5_HUMAN	anoctamin 5 isoform a	752	Helical; (Potential).					chloride channel complex|endoplasmic reticulum membrane	chloride channel activity			central_nervous_system(3)|ovary(1)	4														0.164557	23.227214	31.666674	13	66	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	22252710	22252710	708	11	C	T	T	19	19	ANO5	T	1	1
OR52B4	143496	broad.mit.edu	36	11	4345828	4345828	+	Missense_Mutation	SNP	C	T	T			TCGA-76-6282-01	TCGA-76-6282-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:4345828C>T	uc001lyx.1	-	c.274G>A	c.(274-276)GGG>AGG	p.G92R		NM_001005161	NP_001005161	Q8NGK2	O52B4_HUMAN	olfactory receptor, family 52, subfamily B,	92	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0		Medulloblastoma(188;0.0075)|Breast(177;0.0249)|all_neural(188;0.0577)												0.205128	16.875512	20.023477	8	31	CC		KEEP	---	---	---	---	capture		Epithelial(150;1.57e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0826)|LUSC - Lung squamous cell carcinoma(625;0.19)	Missense_Mutation	SNP	4345828	4345828	11522	11	C	T	T	21	21	OR52B4	T	2	2
OR8K3	219473	broad.mit.edu	36	11	55842402	55842402	+	Missense_Mutation	SNP	C	T	T			TCGA-76-6282-01	TCGA-76-6282-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:55842402C>T	uc001niq.1	+	c.44C>T	c.(43-45)ACG>ATG	p.T15M		NM_001005202	NP_001005202	Q8NH51	OR8K3_HUMAN	olfactory receptor, family 8, subfamily K,	15	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|large_intestine(1)|central_nervous_system(1)	4	Esophageal squamous(21;0.00448)													0.202247	36.948897	44.350652	18	71	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	55842402	55842402	11655	11	C	T	T	19	19	OR8K3	T	1	1
MS4A12	54860	broad.mit.edu	36	11	60021370	60021370	+	Missense_Mutation	SNP	G	C	C			TCGA-76-6282-01	TCGA-76-6282-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:60021370G>C	uc001npr.1	+	c.3G>C	c.(1-3)ATG>ATC	p.M1I	MS4A12_uc009ynb.1_Missense_Mutation_p.M1I	NM_017716	NP_060186	Q9NXJ0	M4A12_HUMAN	membrane-spanning 4-domains, subfamily A, member	1	Cytoplasmic (Potential).					integral to membrane	receptor activity				0														0.304878	79.598045	82.353085	25	57	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	60021370	60021370	10249	11	G	C	C	45	45	MS4A12	C	3	3
KLC2	64837	broad.mit.edu	36	11	65789790	65789790	+	Missense_Mutation	SNP	G	C	C			TCGA-76-6282-01	TCGA-76-6282-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:65789790G>C	uc001ohb.1	+	c.1423G>C	c.(1423-1425)GCC>CCC	p.A475P	RAB1B_uc001ohf.1_5'Flank|KLC2_uc009yra.1_Intron|KLC2_uc001ohc.1_Missense_Mutation_p.A475P|KLC2_uc001ohd.1_Missense_Mutation_p.A398P|KLC2_uc001ohe.1_Missense_Mutation_p.A336P	NM_022822	NP_073733	Q9H0B6	KLC2_HUMAN	kinesin light chain 2 isoform 1	475	TPR 6.				blood coagulation	cytosol|kinesin complex|microtubule	microtubule motor activity|protein binding				0														0.210526	8.6888	10.16238	4	15	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	65789790	65789790	8646	11	G	C	C	46	46	KLC2	C	3	3
ITPR2	3709	broad.mit.edu	36	12	26759549	26759549	+	Missense_Mutation	SNP	G	A	A			TCGA-76-6282-01	TCGA-76-6282-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:26759549G>A	uc001rhg.1	-	c.805C>T	c.(805-807)CGC>TGC	p.R269C		NM_002223	NP_002214	Q14571	ITPR2_HUMAN	inositol 1,4,5-triphosphate receptor, type 2	269	Cytoplasmic (Potential).|MIR 3.|Inositol-1,4,5-triphosphate binding (By similarity).				activation of phospholipase C activity|energy reserve metabolic process|nerve growth factor receptor signaling pathway|platelet activation|regulation of insulin secretion|response to hypoxia	integral to membrane|plasma membrane enriched fraction|platelet dense tubular network membrane|sarcoplasmic reticulum membrane	calcium ion transmembrane transporter activity|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity			kidney(6)|ovary(4)|upper_aerodigestive_tract(1)|lung(1)|skin(1)	13	Colorectal(261;0.0847)									1600				0.311927	91.306999	94.741836	34	75	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	26759549	26759549	8225	12	G	A	A	38	38	ITPR2	A	1	1
OTX2	5015	broad.mit.edu	36	14	56338773	56338773	+	Missense_Mutation	SNP	C	A	A			TCGA-76-6282-01	TCGA-76-6282-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr14:56338773C>A	uc001xcq.1	-	c.327G>T	c.(325-327)CAG>CAT	p.Q109H	OTX2_uc001xcp.1_Missense_Mutation_p.Q101H|OTX2_uc010aou.1_Missense_Mutation_p.Q101H	NM_021728	NP_068374	P32243	OTX2_HUMAN	orthodenticle homeobox 2 isoform a	101	Poly-Gln.				axon guidance|forebrain development|midbrain development|regulation of fibroblast growth factor receptor signaling pathway|regulation of smoothened signaling pathway|regulation of transcription, DNA-dependent	growth cone|nucleus	eukaryotic initiation factor 4E binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulator activity			ovary(1)	1	Medulloblastoma(1;0.00184)|all_neural(1;0.00414)													0.373626	83.847337	85.187059	34	57	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	56338773	56338773	11734	14	C	A	A	32	32	OTX2	A	3	3
RYR3	6263	broad.mit.edu	36	15	31749915	31749915	+	Missense_Mutation	SNP	T	G	G			TCGA-76-6282-01	TCGA-76-6282-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr15:31749915T>G	uc001zhi.1	+	c.5726T>G	c.(5725-5727)GTT>GGT	p.V1909G	RYR3_uc010bar.1_Missense_Mutation_p.V1909G	NM_001036	NP_001027	Q15413	RYR3_HUMAN	ryanodine receptor 3	1909	4 X approximate repeats.|Cytoplasmic (By similarity).				cellular calcium ion homeostasis	integral to membrane	calcium ion binding|receptor activity|ryanodine-sensitive calcium-release channel activity			ovary(5)|central_nervous_system(4)|lung(1)	10		all_lung(180;7.18e-09)												0.375	7.943139	8.197504	6	10	TT		KEEP	---	---	---	---	capture		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)	Missense_Mutation	SNP	31749915	31749915	14250	15	T	G	G	60	60	RYR3	G	4	4
VPS18	57617	broad.mit.edu	36	15	38980336	38980336	+	Silent	SNP	G	A	A			TCGA-76-6282-01	TCGA-76-6282-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr15:38980336G>A	uc001zne.1	+	c.2028G>A	c.(2026-2028)CCG>CCA	p.P676P		NM_020857	NP_065908	Q9P253	VPS18_HUMAN	vacuolar protein sorting 18	676	Clathrin.				endosome organization|lysosome organization|protein transport	HOPS complex|late endosome membrane|lysosomal membrane	metal ion binding|protein binding			ovary(2)|large_intestine(1)	3		all_cancers(109;1.35e-17)|all_epithelial(112;3.78e-15)|Lung NSC(122;9.68e-11)|all_lung(180;2.25e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)												0.245283	32.150293	35.281341	13	40	GG		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(113;1.07e-05)|COAD - Colon adenocarcinoma(120;0.15)|BRCA - Breast invasive adenocarcinoma(123;0.164)	Silent	SNP	38980336	38980336	17761	15	G	A	A	39	39	VPS18	A	1	1
SLC27A2	11001	broad.mit.edu	36	15	48262389	48262389	+	Missense_Mutation	SNP	C	T	T			TCGA-76-6282-01	TCGA-76-6282-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr15:48262389C>T	uc001zxw.1	+	c.473C>T	c.(472-474)TCG>TTG	p.S158L	SLC27A2_uc010bes.1_Missense_Mutation_p.S158L	NM_003645	NP_003636	O14975	S27A2_HUMAN	solute carrier family 27 (fatty acid	158	Lumenal (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)												0.414894	109.008832	109.602564	39	55	CC		KEEP	---	---	---	---	capture		all cancers(107;1.16e-06)|GBM - Glioblastoma multiforme(94;0.000113)	Missense_Mutation	SNP	48262389	48262389	15023	15	C	T	T	31	31	SLC27A2	T	1	1
SRRM2	23524	broad.mit.edu	36	16	2752978	2752978	+	Silent	SNP	C	T	T			TCGA-76-6282-01	TCGA-76-6282-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:2752978C>T	uc002crk.1	+	c.2448C>T	c.(2446-2448)CGC>CGT	p.R816R	SRRM2_uc002crj.1_Silent_p.R720R|SRRM2_uc002crl.1_Silent_p.R816R|SRRM2_uc010bsu.1_Silent_p.R720R	NM_016333	NP_057417	Q9UQ35	SRRM2_HUMAN	splicing coactivator subunit SRm300	816	Arg-rich.|Ser-rich.				nuclear mRNA splicing, via spliceosome	Cajal body|catalytic step 2 spliceosome|nuclear speck	C2H2 zinc finger domain binding|protein N-terminus binding|RNA binding			ovary(1)|central_nervous_system(1)|pancreas(1)	3														0.282528	200.37945	211.813564	76	193	CC		KEEP	---	---	---	---	capture			Silent	SNP	2752978	2752978	15683	16	C	T	T	28	28	SRRM2	T	2	2
SRRM2	23524	broad.mit.edu	36	16	2753967	2753967	+	Missense_Mutation	SNP	C	G	G			TCGA-76-6282-01	TCGA-76-6282-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:2753967C>G	uc002crk.1	+	c.3437C>G	c.(3436-3438)CCT>CGT	p.P1146R	SRRM2_uc002crj.1_Missense_Mutation_p.P1050R|SRRM2_uc002crl.1_Missense_Mutation_p.P1146R|SRRM2_uc010bsu.1_Missense_Mutation_p.P1050R	NM_016333	NP_057417	Q9UQ35	SRRM2_HUMAN	splicing coactivator subunit SRm300	1146	Ser-rich.				nuclear mRNA splicing, via spliceosome	Cajal body|catalytic step 2 spliceosome|nuclear speck	C2H2 zinc finger domain binding|protein N-terminus binding|RNA binding			ovary(1)|central_nervous_system(1)|pancreas(1)	3														0.385714	79.56837	80.382201	27	43	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	2753967	2753967	15683	16	C	G	G	24	24	SRRM2	G	3	3
ZNF205	7755	broad.mit.edu	36	16	3105523	3105523	+	Missense_Mutation	SNP	C	A	A			TCGA-76-6282-01	TCGA-76-6282-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:3105523C>A	uc002cub.1	+	c.224C>A	c.(223-225)CCC>CAC	p.P75H	MGC3771_uc002ctz.2_Non-coding_Transcript|MGC3771_uc010bte.1_Non-coding_Transcript|ZNF205_uc002cua.1_Missense_Mutation_p.P75H	NM_001042428	NP_003447	O95201	ZN205_HUMAN	zinc finger protein 205	75					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding|zinc ion binding				0														0.173913	7.489263	9.795231	4	19	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	3105523	3105523	18355	16	C	A	A	22	22	ZNF205	A	3	3
MSLNL	401827	broad.mit.edu	36	16	770270	770270	+	Silent	SNP	G	A	A			TCGA-76-6282-01	TCGA-76-6282-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:770270G>A	uc002cjz.1	-	c.732C>T	c.(730-732)TCC>TCT	p.S244S		NM_001025190	NP_001020361	Q96KJ4	MSLNL_HUMAN	mesothelin-like	Error:Variant_position_missing_in_Q96KJ4_after_alignment					cell adhesion	integral to membrane				breast(3)|ovary(1)	4														0.25	7.718871	8.400847	3	9	GG		KEEP	---	---	---	---	capture			Silent	SNP	770270	770270	10275	16	G	A	A	35	35	MSLNL	A	2	2
GRIN2A	2903	broad.mit.edu	36	16	9765039	9765039	+	Missense_Mutation	SNP	C	T	T			TCGA-76-6282-01	TCGA-76-6282-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:9765039C>T	uc002czp.1	-	c.3863G>A	c.(3862-3864)CGT>CAT	p.R1288H	GRIN2A_uc002czq.1_Missense_Mutation_p.R1288H|GRIN2A_uc002czr.2_Intron|GRIN2A_uc002czo.2_5'Flank	NM_000833	NP_000824	Q12879	NMDE1_HUMAN	N-methyl-D-aspartate receptor subunit 2A isoform	1288	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				0.24359	45.937394	50.577635	19	59	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	9765039	9765039	7058	16	C	T	T	19	19	GRIN2A	T	1	1
CCL2	6347	broad.mit.edu	36	17	29607422	29607422	+	Missense_Mutation	SNP	G	A	A			TCGA-76-6282-01	TCGA-76-6282-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:29607422G>A	uc002hhy.1	+	c.145G>A	c.(145-147)GCG>ACG	p.A49T		NM_002982	NP_002973	P13500	CCL2_HUMAN	small inducible cytokine A2 precursor	49				Missing: 90% reduction in activity.|Missing: 83% reduction in activity.	angiogenesis|anti-apoptosis|apoptotic cell clearance|astrocyte cell migration|cell adhesion|cellular response to interferon-gamma|cellular response to interleukin-1|cellular response to lipopolysaccharide|cellular response to tumor necrosis factor|G-protein signaling, coupled to cyclic nucleotide second messenger|helper T cell extravasation|humoral immune response|inflammatory response|JAK-STAT cascade|macrophage chemotaxis|monocyte chemotaxis|positive regulation of nitric-oxide synthase biosynthetic process|positive regulation of T cell activation|protein phosphorylation|viral genome replication	extracellular space	CCR2 chemokine receptor binding|chemokine activity|protein kinase activity|signal transducer activity			pancreas(1)	1	Breast(3;0.00224)	Ovarian(249;0.0694)|Breast(31;0.151)|Lung NSC(157;0.153)			Atorvastatin(DB01076)|Danazol(DB01406)|Mimosine(DB01055)|Simvastatin(DB00641)									0.385965	62.679424	63.313428	22	35	GG		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (308;0.000241)|BRCA - Breast invasive adenocarcinoma(366;0.0103)	Missense_Mutation	SNP	29607422	29607422	3016	17	G	A	A	38	38	CCL2	A	1	1
KRT33A	3883	broad.mit.edu	36	17	36760284	36760284	+	Missense_Mutation	SNP	T	G	G			TCGA-76-6282-01	TCGA-76-6282-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr17:36760284T>G	uc002hwk.1	-	c.262A>C	c.(262-264)ATC>CTC	p.I88L		NM_004138	NP_004129	O76009	KT33A_HUMAN	keratin 33A	88	Coil 1A.|Rod.					intermediate filament	protein binding|structural molecule activity				0		Breast(137;0.000496)												0.227273	26.83036	29.831804	10	34	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	36760284	36760284	8784	17	T	G	G	51	51	KRT33A	G	4	4
COG1	9382	broad.mit.edu	36	17	68707653	68707653	+	Missense_Mutation	SNP	A	C	C			TCGA-76-6282-01	TCGA-76-6282-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr17:68707653A>C	uc002jjg.1	+	c.968A>C	c.(967-969)CAC>CCC	p.H323P	COG1_uc002jjf.1_Missense_Mutation_p.H323P|COG1_uc002jjh.1_Missense_Mutation_p.H323P	NM_018714	NP_061184	Q8WTW3	COG1_HUMAN	component of oligomeric golgi complex 1	323					Golgi organization|intra-Golgi vesicle-mediated transport|protein transport	Golgi membrane|Golgi transport complex	protein binding			ovary(1)	1														0.3	7.026869	7.82095	6	14	AA		KEEP	---	---	---	---	capture	LUSC - Lung squamous cell carcinoma(166;0.197)		Missense_Mutation	SNP	68707653	68707653	3795	17	A	C	C	6	6	COG1	C	4	4
DSC1	1823	broad.mit.edu	36	18	26977626	26977626	+	Missense_Mutation	SNP	C	T	T			TCGA-76-6282-01	TCGA-76-6282-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr18:26977626C>T	uc002kwn.1	-	c.1066G>A	c.(1066-1068)GAA>AAA	p.E356K	DSC1_uc002kwm.1_Missense_Mutation_p.E356K	NM_024421	NP_077739	Q08554	DSC1_HUMAN	desmocollin 1 isoform Dsc1a preproprotein	356	Extracellular (Potential).|Cadherin 3.				homophilic cell adhesion	desmosome|gap junction|integral to membrane|membrane fraction	calcium ion binding			ovary(3)	3														0.325	39.160603	40.247918	13	27	CC		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(10;0.00778)		Missense_Mutation	SNP	26977626	26977626	4949	18	C	T	T	32	32	DSC1	T	2	2
ZNF536	9745	broad.mit.edu	36	19	35731499	35731499	+	Missense_Mutation	SNP	G	T	T			TCGA-76-6282-01	TCGA-76-6282-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:35731499G>T	uc002nsu.1	+	c.3133G>T	c.(3133-3135)GCC>TCC	p.A1045S	ZNF536_uc010edd.1_Missense_Mutation_p.A1045S	NM_014717	NP_055532	O15090	ZN536_HUMAN	zinc finger protein 536	1045					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	zinc ion binding			ovary(7)|large_intestine(2)	9	Esophageal squamous(110;0.0834)													0.209677	29.338933	34.176833	13	49	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	35731499	35731499	18568	19	G	T	T	34	34	ZNF536	T	3	3
CD22	933	broad.mit.edu	36	19	40520729	40520729	+	Missense_Mutation	SNP	C	T	T			TCGA-76-6282-01	TCGA-76-6282-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:40520729C>T	uc010edt.1	+	c.950C>T	c.(949-951)CCG>CTG	p.P317L	CD22_uc010edu.1_Missense_Mutation_p.P317L|CD22_uc010edv.1_Missense_Mutation_p.P317L|CD22_uc002nzb.2_Intron|CD22_uc010edw.1_Missense_Mutation_p.P145L|CD22_uc010edx.1_Non-coding_Transcript	NM_001771	NP_001762	P20273	CD22_HUMAN	CD22 molecule	317	Extracellular (Potential).|Ig-like C2-type 2.				cell adhesion		protein binding|sugar binding			ovary(4)	4	all_lung(56;9.78e-09)|Lung NSC(56;1.46e-08)|Esophageal squamous(110;0.162)				OspA lipoprotein(DB00045)	Ovarian(42;1009 1133 23674 26041)								0.227273	12.564622	14.065615	5	17	CC		KEEP	---	---	---	---	capture	Epithelial(14;5.83e-19)|OV - Ovarian serous cystadenocarcinoma(14;3.19e-18)|all cancers(14;3.41e-16)|LUSC - Lung squamous cell carcinoma(66;0.0417)		Missense_Mutation	SNP	40520729	40520729	3112	19	C	T	T	23	23	CD22	T	1	1
SHKBP1	92799	broad.mit.edu	36	19	45788742	45788742	+	Missense_Mutation	SNP	A	G	G			TCGA-76-6282-01	TCGA-76-6282-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr19:45788742A>G	uc002oob.1	+	c.1913A>G	c.(1912-1914)AAC>AGC	p.N638S	SHKBP1_uc002ooc.1_Missense_Mutation_p.N613S|SHKBP1_uc002ood.1_Missense_Mutation_p.N546S|SHKBP1_uc002ooe.1_Missense_Mutation_p.N475S|SHKBP1_uc002oof.1_Missense_Mutation_p.N474S|LTBP4_uc002oog.1_5'Flank	NM_138392	NP_612401	Q8TBC3	SHKB1_HUMAN	SH3KBP1 binding protein 1	638						voltage-gated potassium channel complex	voltage-gated potassium channel activity			ovary(1)|pancreas(1)	2														0.304348	22.118216	22.902685	7	16	AA		KEEP	---	---	---	---	capture	Lung(22;0.000114)|LUSC - Lung squamous cell carcinoma(20;0.000384)		Missense_Mutation	SNP	45788742	45788742	14779	19	A	G	G	2	2	SHKBP1	G	4	4
TNFSF9	8744	broad.mit.edu	36	19	6486006	6486006	+	Missense_Mutation	SNP	G	A	A			TCGA-76-6282-01	TCGA-76-6282-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:6486006G>A	uc002mfh.1	+	c.694G>A	c.(694-696)GCC>ACC	p.A232T		NM_003811	NP_003802	P41273	TNFL9_HUMAN	tumor necrosis factor (ligand) superfamily,	232	Extracellular (Potential).				apoptosis|cell proliferation|cell-cell signaling|immune response|signal transduction	extracellular space|integral to membrane	cytokine activity|tumor necrosis factor receptor binding			central_nervous_system(1)	1														0.352941	16.45006	16.771917	6	11	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	6486006	6486006	16853	19	G	A	A	38	38	TNFSF9	A	1	1
MUC16	94025	broad.mit.edu	36	19	8910297	8910297	+	Silent	SNP	C	T	T			TCGA-76-6282-01	TCGA-76-6282-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:8910297C>T	uc002mkp.1	-	c.32334G>A	c.(32332-32334)TCG>TCA	p.S10778S		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	10780	Thr-rich.|Extracellular (Potential).				cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			ovary(15)|large_intestine(1)|pancreas(1)|breast(1)|skin(1)	19														0.32967	83.779416	86.090095	30	61	CC		KEEP	---	---	---	---	capture			Silent	SNP	8910297	8910297	10367	19	C	T	T	23	23	MUC16	T	1	1
AADACL3	126767	broad.mit.edu	36	1	12708270	12708270	+	Missense_Mutation	SNP	T	C	C			TCGA-76-6282-01	TCGA-76-6282-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr1:12708270T>C	uc009vnn.1	+	c.773T>C	c.(772-774)GTA>GCA	p.V258A	AADACL3_uc001aug.1_Missense_Mutation_p.V188A	NM_001103170	NP_001096640	Q5VUY0	ADCL3_HUMAN	arylacetamide deacetylase-like 3 isoform 1	258							hydrolase activity				0	Ovarian(185;0.249)	Lung NSC(185;8.27e-05)|all_lung(284;9.47e-05)|Renal(390;0.000147)|Colorectal(325;0.000583)|Breast(348;0.000596)|Ovarian(437;0.00965)|Hepatocellular(190;0.0245)|Myeloproliferative disorder(586;0.0255)												0.242857	51.049044	55.262117	17	53	TT		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.13e-06)|COAD - Colon adenocarcinoma(227;0.000274)|BRCA - Breast invasive adenocarcinoma(304;0.000311)|Kidney(185;0.00217)|KIRC - Kidney renal clear cell carcinoma(229;0.00579)|STAD - Stomach adenocarcinoma(313;0.00743)|READ - Rectum adenocarcinoma(331;0.0649)	Missense_Mutation	SNP	12708270	12708270	13	1	T	C	C	57	57	AADACL3	C	4	4
C1orf129	80133	broad.mit.edu	36	1	169231222	169231222	+	Silent	SNP	C	T	T			TCGA-76-6282-01	TCGA-76-6282-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:169231222C>T	uc001ghg.1	+	c.1263C>T	c.(1261-1263)CCC>CCT	p.P421P	C1orf129_uc009wvy.1_Silent_p.P228P	NM_025063	NP_079339	Q5TGP6	CA129_HUMAN	hypothetical protein LOC80133	421							binding			pancreas(1)	1	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)													0.338235	67.702478	69.276792	23	45	CC		KEEP	---	---	---	---	capture			Silent	SNP	169231222	169231222	2063	1	C	T	T	22	22	C1orf129	T	2	2
RRP1B	23076	broad.mit.edu	36	21	43932277	43932277	+	Missense_Mutation	SNP	G	A	A			TCGA-76-6282-01	TCGA-76-6282-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr21:43932277G>A	uc002zdk.1	+	c.1594G>A	c.(1594-1596)GTC>ATC	p.V532I	RRP1B_uc002zdl.1_Missense_Mutation_p.V65I	NM_015056	NP_055871	Q14684	RRP1B_HUMAN	ribosomal RNA processing 1 homolog B	532					rRNA processing	cytosol|nucleolus|preribosome, small subunit precursor	protein binding				0														0.272727	30.510081	32.540454	12	32	GG		KEEP	---	---	---	---	capture		STAD - Stomach adenocarcinoma(101;0.178)	Missense_Mutation	SNP	43932277	43932277	14168	21	G	A	A	40	40	RRP1B	A	1	1
TPTE	7179	broad.mit.edu	36	21	9955750	9955750	+	Missense_Mutation	SNP	C	T	T			TCGA-76-6282-01	TCGA-76-6282-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr21:9955750C>T	uc002yip.1	-	c.1000G>A	c.(1000-1002)GTA>ATA	p.V334I	TPTE_uc002yiq.1_Missense_Mutation_p.V316I|TPTE_uc002yir.1_Missense_Mutation_p.V296I|TPTE_uc010gkv.1_Missense_Mutation_p.V196I|TPTE_uc002yis.1_Non-coding_Transcript	NM_199261	NP_954870	P56180	TPTE_HUMAN	transmembrane phosphatase with tensin homology	334	Phosphatase tensin-type.				signal transduction	integral to membrane	ion channel activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			ovary(2)|lung(1)|breast(1)|skin(1)	5														0.116279	28.285512	59.386514	25	190	CC		KEEP	---	---	---	---	capture	Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)	Missense_Mutation	SNP	9955750	9955750	16974	21	C	T	T	19	19	TPTE	T	1	1
RGL4	266747	broad.mit.edu	36	22	22364585	22364585	+	Silent	SNP	G	A	A			TCGA-76-6282-01	TCGA-76-6282-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr22:22364585G>A	uc002zxn.1	+	c.243G>A	c.(241-243)CCG>CCA	p.P81P	LOC91316_uc002zxh.2_Non-coding_Transcript|LOC91316_uc002zxi.2_Non-coding_Transcript|LOC91316_uc002zxj.2_Intron|LOC91316_uc002zxk.2_Intron|LOC91316_uc010gua.1_Intron|LOC91316_uc002zxl.2_Intron|LOC91316_uc002zxm.2_Intron|RGL4_uc002zxo.1_Silent_p.P81P|RGL4_uc002zxp.1_5'UTR|RGL4_uc002zxq.1_5'UTR	NM_153615	NP_705843	Q8IZJ4	RGDSR_HUMAN	ral guanine nucleotide dissociation	81					small GTPase mediated signal transduction	cytoplasmic membrane-bounded vesicle	guanyl-nucleotide exchange factor activity			ovary(1)	1										238				0.314815	88.527533	91.813986	34	74	GG		KEEP	---	---	---	---	capture			Silent	SNP	22364585	22364585	13752	22	G	A	A	38	38	RGL4	A	1	1
MYO18B	84700	broad.mit.edu	36	22	24753542	24753542	+	Silent	SNP	G	A	A			TCGA-76-6282-01	TCGA-76-6282-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr22:24753542G>A	uc003abz.1	+	c.7602G>A	c.(7600-7602)GCG>GCA	p.A2534A	MYO18B_uc003aca.1_Silent_p.A2415A|MYO18B_uc010guy.1_Silent_p.A2416A|MYO18B_uc010guz.1_Silent_p.A2414A|MYO18B_uc010gva.1_Silent_p.A517A|MYO18B_uc010gvb.1_Non-coding_Transcript	NM_032608	NP_115997	Q8IUG5	MY18B_HUMAN	myosin XVIIIB	2534						nucleus|sarcomere|unconventional myosin complex	actin binding|ATP binding|motor activity			ovary(5)|central_nervous_system(3)|large_intestine(2)|breast(2)	12										968				0.214286	14.337176	16.446117	6	22	GG		KEEP	---	---	---	---	capture			Silent	SNP	24753542	24753542	10461	22	G	A	A	39	39	MYO18B	A	1	1
MFSD9	84804	broad.mit.edu	36	2	102701799	102701799	+	Missense_Mutation	SNP	G	A	A			TCGA-76-6282-01	TCGA-76-6282-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:102701799G>A	uc002tcb.1	-	c.937C>T	c.(937-939)CGC>TGC	p.R313C	MFSD9_uc010fja.1_Non-coding_Transcript	NM_032718	NP_116107	Q8NBP5	MFSD9_HUMAN	major facilitator superfamily domain containing	313					response to antibiotic	integral to membrane	tetracycline:hydrogen antiporter activity			ovary(2)|breast(2)	4														0.233333	15.213136	17.163969	7	23	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	102701799	102701799	9929	2	G	A	A	38	38	MFSD9	A	1	1
AGAP1	116987	broad.mit.edu	36	2	236323802	236323802	+	Silent	SNP	C	T	T			TCGA-76-6282-01	TCGA-76-6282-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:236323802C>T	uc002vvs.1	+	c.604C>T	c.(604-606)CTG>TTG	p.L202L	AGAP1_uc002vvt.1_Silent_p.L202L	NM_001037131	NP_001032208	Q9UPQ3	AGAP1_HUMAN	centaurin, gamma 2 isoform 1	202	Small GTPase-like.				protein transport|regulation of ARF GTPase activity|small GTPase mediated signal transduction	cytoplasm	ARF GTPase activator activity|GTP binding|zinc ion binding			ovary(2)	2														0.280992	99.098093	104.314356	34	87	CC		KEEP	---	---	---	---	capture			Silent	SNP	236323802	236323802	368	2	C	T	T	24	24	AGAP1	T	2	2
BOC	91653	broad.mit.edu	36	3	114479690	114479690	+	Missense_Mutation	SNP	G	A	A			TCGA-76-6282-01	TCGA-76-6282-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:114479690G>A	uc003dzz.1	+	c.1601G>A	c.(1600-1602)CGC>CAC	p.R534H	BOC_uc003dzx.1_Missense_Mutation_p.R533H|BOC_uc003dzy.1_Missense_Mutation_p.R533H|BOC_uc003eab.1_Missense_Mutation_p.R234H|BOC_uc003eac.2_5'Flank	NM_033254	NP_150279	Q9BWV1	BOC_HUMAN	brother of CDO	533	Fibronectin type-III 1.|Extracellular (Potential).				cell adhesion|muscle cell differentiation|positive regulation of myoblast differentiation	integral to membrane|plasma membrane	protein binding			ovary(3)|breast(1)|central_nervous_system(1)|pancreas(1)	6														0.241935	64.554004	72.046859	30	94	GG		KEEP	---	---	---	---	capture	Epithelial(53;0.227)		Missense_Mutation	SNP	114479690	114479690	1506	3	G	A	A	38	38	BOC	A	1	1
FGD5	152273	broad.mit.edu	36	3	14837058	14837058	+	Silent	SNP	T	C	C			TCGA-76-6282-01	TCGA-76-6282-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr3:14837058T>C	uc003bzc.1	+	c.753T>C	c.(751-753)TAT>TAC	p.Y251Y		NM_152536	NP_689749	Q6ZNL6	FGD5_HUMAN	FYVE, RhoGEF and PH domain containing 5	492					actin cytoskeleton organization|filopodium assembly|regulation of Cdc42 GTPase activity|regulation of cell shape	cytoskeleton|Golgi apparatus|lamellipodium|ruffle	metal ion binding|Rho guanyl-nucleotide exchange factor activity|small GTPase binding			ovary(3)|kidney(1)|pancreas(1)	5														0.428571	52.555132	52.738708	18	24	TT		KEEP	---	---	---	---	capture			Silent	SNP	14837058	14837058	6073	3	T	C	C	51	51	FGD5	C	4	4
EFHB	151651	broad.mit.edu	36	3	19949770	19949770	+	Missense_Mutation	SNP	T	A	A			TCGA-76-6282-01	TCGA-76-6282-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr3:19949770T>A	uc003cbl.2	-	c.745A>T	c.(745-747)ATA>TTA	p.I249L	EFHB_uc003cbm.1_Missense_Mutation_p.I119L	NM_144715	NP_653316	Q8N7U6	EFHB_HUMAN	EF hand domain family, member B	249					signal transduction	proteinaceous extracellular matrix	calcium ion binding				0														0.133333	6.779782	10.693531	4	26	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	19949770	19949770	5133	3	T	A	A	51	51	EFHB	A	4	4
KDR	3791	broad.mit.edu	36	4	55650978	55650978	+	Nonsense_Mutation	SNP	G	A	A			TCGA-76-6282-01	TCGA-76-6282-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr4:55650978G>A	uc003has.1	-	c.3094C>T	c.(3094-3096)CGA>TGA	p.R1032*	KDR_uc003hat.1_Nonsense_Mutation_p.R1032*	NM_002253	NP_002244	P35968	VGFR2_HUMAN	kinase insert domain receptor (a type III	1032	Protein kinase.|Cytoplasmic (Potential).				angiogenesis|cell differentiation|interspecies interaction between organisms|positive regulation of endothelial cell migration|positive regulation of endothelial cell proliferation|positive regulation of focal adhesion assembly|positive regulation of positive chemotaxis|protein phosphorylation|regulation of cell shape	integral to plasma membrane	ATP binding|growth factor binding|Hsp90 protein binding|integrin binding|receptor signaling protein tyrosine kinase activity|vascular endothelial growth factor receptor activity			lung(9)|soft_tissue(4)|central_nervous_system(4)|large_intestine(2)|ovary(2)|kidney(1)	22	all_cancers(7;0.0255)|all_lung(4;0.00175)|Lung NSC(11;0.00384)|all_epithelial(27;0.034)|Glioma(25;0.08)|all_neural(26;0.101)				Sorafenib(DB00398)|Sunitinib(DB01268)					1022	TSP Lung(20;0.16)			0.268657	44.02048	47.257335	18	49	GG		KEEP	---	---	---	---	capture	Epithelial(7;0.189)		Nonsense_Mutation	SNP	55650978	55650978	8445	4	G	A	A	40	40	KDR	A	5	1
PROL1	58503	broad.mit.edu	36	4	71309766	71309766	+	Missense_Mutation	SNP	G	T	T			TCGA-76-6282-01	TCGA-76-6282-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr4:71309766G>T	uc003hfi.1	+	c.132G>T	c.(130-132)TGG>TGT	p.W44C		NM_021225	NP_067048	Q99935	PROL1_HUMAN	proline rich, lacrimal 1	44	Pro-rich.				regulation of sensory perception of pain	extracellular region	endopeptidase inhibitor activity			large_intestine(1)	1		all_hematologic(202;0.196)												0.265306	64.307703	69.185024	26	72	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	71309766	71309766	12997	4	G	T	T	43	43	PROL1	T	3	3
HSD17B13	345275	broad.mit.edu	36	4	88458519	88458519	+	Missense_Mutation	SNP	G	A	A			TCGA-76-6282-01	TCGA-76-6282-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr4:88458519G>A	uc003hqo.1	-	c.304C>T	c.(304-306)CGC>TGC	p.R102C	HSD17B13_uc010ikk.1_Intron	NM_178135	NP_835236	Q7Z5P4	DHB13_HUMAN	hydroxysteroid (17-beta) dehydrogenase 13	102					oxidation-reduction process	extracellular region	binding|oxidoreductase activity				0		Acute lymphoblastic leukemia(40;0.244)|all_hematologic(202;0.248)												0.277778	39.204201	41.602151	15	39	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(123;0.000308)	Missense_Mutation	SNP	88458519	88458519	7677	4	G	A	A	37	37	HSD17B13	A	1	1
NAIP	4671	broad.mit.edu	36	5	70342924	70342924	+	Missense_Mutation	SNP	C	A	A			TCGA-76-6282-01	TCGA-76-6282-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:70342924C>A	uc003kar.1	-	c.602G>T	c.(601-603)GGT>GTT	p.G201V	NAIP_uc003kat.1_Intron|NAIP_uc003kas.1_Intron	NM_004536	NP_004527	Q13075	BIRC1_HUMAN	NLR family, apoptosis inhibitory protein isoform	201	BIR 2.				anti-apoptosis|apoptosis|negative regulation of caspase activity|nervous system development	basolateral plasma membrane|cytoplasm	caspase inhibitor activity|metal ion binding|nucleoside-triphosphatase activity|nucleotide binding			central_nervous_system(1)	1		Lung NSC(167;4.15e-05)|Prostate(74;0.00996)|Ovarian(174;0.0448)|Breast(144;0.198)												0.166667	10.755308	13.916146	5	25	CC		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(47;3.04e-60)|Epithelial(20;7.09e-58)|all cancers(19;1.13e-53)|Lung(70;0.0174)	Missense_Mutation	SNP	70342924	70342924	10543	5	C	A	A	18	18	NAIP	A	3	3
MAP1B	4131	broad.mit.edu	36	5	71526808	71526808	+	Missense_Mutation	SNP	C	A	A			TCGA-76-6282-01	TCGA-76-6282-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:71526808C>A	uc003kbw.2	+	c.1870C>A	c.(1870-1872)CAA>AAA	p.Q624K	MAP1B_uc010iyw.1_Missense_Mutation_p.Q641K|MAP1B_uc010iyx.1_Missense_Mutation_p.Q498K|MAP1B_uc010iyy.1_Missense_Mutation_p.Q498K	NM_005909	NP_005900	P46821	MAP1B_HUMAN	microtubule-associated protein 1B	624	Lys-rich (highly basic, contains many KKEE and KKEI/V repeats).					microtubule|microtubule associated complex	structural molecule activity			large_intestine(2)|ovary(1)|central_nervous_system(1)|pancreas(1)	5		Lung NSC(167;0.00202)|Ovarian(174;0.0175)|Prostate(461;0.142)|Breast(144;0.198)				Melanoma(17;367 822 11631 31730 47712)								0.421053	14.417702	14.535377	8	11	CC		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(47;7.99e-54)	Missense_Mutation	SNP	71526808	71526808	9611	5	C	A	A	25	25	MAP1B	A	3	3
MYLIP	29116	broad.mit.edu	36	6	16238787	16238787	+	Missense_Mutation	SNP	C	G	G			TCGA-76-6282-01	TCGA-76-6282-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:16238787C>G	uc003nbq.1	+	c.108C>G	c.(106-108)ATC>ATG	p.I36M	MYLIP_uc003nbr.1_Intron	NM_013262	NP_037394	Q8WY64	MYLIP_HUMAN	myosin regulatory light chain interacting	36	FERM.				cellular component movement|nervous system development	cytoplasm|cytoskeleton|extrinsic to membrane	cytoskeletal protein binding|ubiquitin-protein ligase activity|zinc ion binding			pancreas(1)	1	Breast(50;0.0799)|Ovarian(93;0.103)	all_hematologic(90;0.0895)												0.333333	68.753539	70.303609	21	42	CC		KEEP	---	---	---	---	capture	Epithelial(50;0.241)		Missense_Mutation	SNP	16238787	16238787	10450	6	C	G	G	29	29	MYLIP	G	3	3
MYLIP	29116	broad.mit.edu	36	6	16238865	16238865	+	Silent	SNP	C	T	T			TCGA-76-6282-01	TCGA-76-6282-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:16238865C>T	uc003nbq.1	+	c.186C>T	c.(184-186)ATC>ATT	p.I62I	MYLIP_uc003nbr.1_Intron	NM_013262	NP_037394	Q8WY64	MYLIP_HUMAN	myosin regulatory light chain interacting	62	FERM.				cellular component movement|nervous system development	cytoplasm|cytoskeleton|extrinsic to membrane	cytoskeletal protein binding|ubiquitin-protein ligase activity|zinc ion binding			pancreas(1)	1	Breast(50;0.0799)|Ovarian(93;0.103)	all_hematologic(90;0.0895)												0.408163	60.325942	60.676059	20	29	CC		KEEP	---	---	---	---	capture	Epithelial(50;0.241)		Silent	SNP	16238865	16238865	10450	6	C	T	T	32	32	MYLIP	T	2	2
MDGA1	266727	broad.mit.edu	36	6	37720398	37720398	+	Missense_Mutation	SNP	T	G	G			TCGA-76-6282-01	TCGA-76-6282-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr6:37720398T>G	uc003onu.1	-	c.2254A>C	c.(2254-2256)ACC>CCC	p.T752P	MDGA1_uc003onv.1_Missense_Mutation_p.T21P	NM_153487	NP_705691	Q8NFP4	MDGA1_HUMAN	MAM domain containing	752	MAM.				brain development|neuron migration|spinal cord association neuron differentiation	anchored to plasma membrane				central_nervous_system(2)	2														0.235294	6.586357	7.681724	4	13	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	37720398	37720398	9795	6	T	G	G	59	59	MDGA1	G	4	4
OR2A25	392138	broad.mit.edu	36	7	143402823	143402823	+	Missense_Mutation	SNP	T	C	C			TCGA-76-6282-01	TCGA-76-6282-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr7:143402823T>C	uc003wdv.1	+	c.578T>C	c.(577-579)ATT>ACT	p.I193T		NM_001004488	NP_001004488	A4D2G3	O2A25_HUMAN	olfactory receptor, family 2, subfamily A,	193	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0	Melanoma(164;0.0783)													0.172932	53.534958	66.988275	23	110	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	143402823	143402823	11384	7	T	C	C	52	52	OR2A25	C	4	4
CARD11	84433	broad.mit.edu	36	7	2932920	2932920	+	Missense_Mutation	SNP	A	C	C			TCGA-76-6282-01	TCGA-76-6282-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr7:2932920A>C	uc003smv.2	-	c.1786T>G	c.(1786-1788)TTT>GTT	p.F596V		NM_032415	NP_115791	Q9BXL7	CAR11_HUMAN	caspase recruitment domain family, member 11	596					positive regulation of cytokine production|positive regulation of NF-kappaB transcription factor activity|regulation of apoptosis|T cell costimulation|T cell receptor signaling pathway	cytosol|membrane raft|plasma membrane	CARD domain binding|guanylate kinase activity			haematopoietic_and_lymphoid_tissue(43)|ovary(2)|kidney(2)|central_nervous_system(1)	48		Ovarian(82;0.0115)								1492				0.222222	7.889251	9.168407	4	14	AA		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(56;8.44e-14)	Missense_Mutation	SNP	2932920	2932920	2764	7	A	C	C	2	2	CARD11	C	4	4
ZMIZ2	83637	broad.mit.edu	36	7	44763614	44763614	+	Missense_Mutation	SNP	A	C	C			TCGA-76-6282-01	TCGA-76-6282-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr7:44763614A>C	uc003tlr.1	+	c.481A>C	c.(481-483)ACC>CCC	p.T161P	ZMIZ2_uc003tlq.1_Missense_Mutation_p.T129P|ZMIZ2_uc003tls.1_Missense_Mutation_p.T161P|ZMIZ2_uc003tlt.1_5'Flank|ZMIZ2_uc010kyj.1_5'Flank	NM_031449	NP_113637	Q8NF64	ZMIZ2_HUMAN	zinc finger, MIZ-type containing 2 isoform 1	161	Ala-rich.				positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nuclear replication fork	ligand-dependent nuclear receptor transcription coactivator activity|protein binding|zinc ion binding			ovary(2)|large_intestine(2)|breast(1)	5						NSCLC(20;604 852 1948 16908 50522)								0.25	7.425891	8.602706	5	15	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	44763614	44763614	18288	7	A	C	C	6	6	ZMIZ2	C	4	4
COBL	23242	broad.mit.edu	36	7	51255118	51255118	+	Missense_Mutation	SNP	C	G	G			TCGA-76-6282-01	TCGA-76-6282-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:51255118C>G	uc003tpr.2	-	c.59G>C	c.(58-60)CGT>CCT	p.R20P	COBL_uc010kzc.1_Missense_Mutation_p.R20P|COBL_uc003tpt.2_Missense_Mutation_p.R20P	NM_015198	NP_056013	O75128	COBL_HUMAN	cordon-bleu homolog	20										ovary(2)|skin(1)	3	Glioma(55;0.08)					NSCLC(189;2119 2138 12223 30818 34679)								0.30303	8.503194	9.68703	10	23	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	51255118	51255118	3791	7	C	G	G	19	19	COBL	G	3	3
EGFR	1956	broad.mit.edu	36	7	55199000	55199000	+	Missense_Mutation	SNP	G	C	C			TCGA-76-6282-01	TCGA-76-6282-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:55199000G>C	uc003tqk.1	+	c.1712G>C	c.(1711-1713)TGC>TCC	p.C571S	EGFR_uc003tqi.1_Missense_Mutation_p.C571S|EGFR_uc003tqj.1_Missense_Mutation_p.C571S|EGFR_uc010kzg.1_Missense_Mutation_p.C526S|EGFR_uc003tqn.1_5'Flank	NM_005228	NP_005219	P00533	EGFR_HUMAN	epidermal growth factor receptor isoform a	571	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			lung(8200)|central_nervous_system(103)|upper_aerodigestive_tract(37)|prostate(32)|ovary(31)|thyroid(23)|breast(11)|peritoneum(9)|oesophagus(9)|salivary_gland(9)|large_intestine(8)|stomach(6)|urinary_tract(6)|skin(5)|adrenal_gland(5)|kidney(4)|soft_tissue(4)|bone(3)|NS(2)|haematopoietic_and_lymphoid_tissue(2)|thymus(2)|liver(2)|eye(1)|pancreas(1)	8515	all_cancers(1;1.57e-46)|all_epithelial(1;5.62e-37)|Lung NSC(1;9.29e-25)|all_lung(1;4.39e-23)|Esophageal squamous(2;7.55e-08)|Breast(14;0.0318)				Cetuximab(DB00002)|Erlotinib(DB00530)|Gefitinib(DB00317)|Lapatinib(DB01259)|Lidocaine(DB00281)|Panitumumab(DB01269)|Trastuzumab(DB00072)			8		608	TCGA GBM(3;<1E-8)|TSP Lung(4;<1E-8)			0.753731	2559.066183	2614.056569	707	231	GG		KEEP	---	---	---	---	capture	GBM - Glioblastoma multiforme(1;0)|all cancers(1;2.19e-314)|Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00164)|Epithelial(13;0.0607)		Missense_Mutation	SNP	55199000	55199000	5156	7	G	C	C	46	46	EGFR	C	3	3
RIMS2	9699	broad.mit.edu	36	8	105070773	105070773	+	Nonsense_Mutation	SNP	C	T	T			TCGA-76-6282-01	TCGA-76-6282-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr8:105070773C>T	uc003yls.2	+	c.2326C>T	c.(2326-2328)CGA>TGA	p.R776*	RIMS2_uc003ylp.2_Nonsense_Mutation_p.R998*|RIMS2_uc003ylw.2_Nonsense_Mutation_p.R790*|RIMS2_uc003ylq.2_Nonsense_Mutation_p.R790*|RIMS2_uc003ylr.2_Nonsense_Mutation_p.R837*	NM_014677	NP_055492	Q9UQ26	RIMS2_HUMAN	regulating synaptic membrane exocytosis 2	1060					intracellular protein transport	cell junction|presynaptic membrane	Rab GTPase binding|zinc ion binding			ovary(6)|lung(2)|breast(2)|large_intestine(1)|central_nervous_system(1)|skin(1)|pancreas(1)	14										728				0.256098	54.838832	59.260815	21	61	CC		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(57;7.7e-07)|STAD - Stomach adenocarcinoma(118;0.229)		Nonsense_Mutation	SNP	105070773	105070773	13845	8	C	T	T	23	23	RIMS2	T	5	1
PHKA2	5256	broad.mit.edu	36	X	18825279	18825279	+	Missense_Mutation	SNP	G	C	C			TCGA-76-6282-01	TCGA-76-6282-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:18825279G>C	uc004cyv.2	-	c.3205C>G	c.(3205-3207)CGC>GGC	p.R1069G	PHKA2_uc004cyu.2_Missense_Mutation_p.R375G|PHKA2_uc010nfe.1_Missense_Mutation_p.R101G|PHKA2_uc010nff.1_Non-coding_Transcript	NM_000292	NP_000283	P46019	KPB2_HUMAN	phosphorylase kinase, alpha 2 (liver)	1069	Calmodulin-binding (Potential).				glucose metabolic process|glycogen catabolic process|protein modification process	cytosol|phosphorylase kinase complex|plasma membrane	calmodulin binding|glucan 1,4-alpha-glucosidase activity|phosphorylase kinase activity			ovary(1)|central_nervous_system(1)	2	Hepatocellular(33;0.183)													0.384615	7.450841	7.607904	5	8	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	18825279	18825279	12268	23	G	C	C	38	38	PHKA2	C	3	3
NACA	4666	broad.mit.edu	36	12	55398199	55398206	+	Frame_Shift_Del	DEL	TTGTGGGT	-	-			TCGA-76-6282-01	TCGA-76-6282-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:55398199_55398206delTTGTGGGT	uc009zoy.1	-	c.3375_3382delACCCACAA	c.(3373-3384)GCACCCACAACCfs	p.A1125fs	NACA_uc001slz.2_Intron|NACA_uc001sly.2_Intron|NACA_uc001smc.2_Intron|NACA_uc001sma.2_Intron|NACA_uc001smb.2_Intron	NM_001113203	NP_001106674	Q13765	NACA_HUMAN	nascent polypeptide-associated complex alpha	Error:Variant_position_missing_in_Q13765_after_alignment					interspecies interaction between organisms|protein transport|transcription, DNA-dependent|translation	nascent polypeptide-associated complex|nucleus	DNA binding			ovary(1)	1									p.A1125fs(SW837-Tumor)|p.A1125fs(KYSE180-Tumor)|p.A1125fs(NCIH684-Tumor)|p.T1127I(BICR31-Tumor)|p.A1125fs(DMS273-Tumor)	449				0.92			11	1				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	55398199	55398206	10528	12	TTGTGGGT	-	-	60	60	NACA	-	5	5
OTOP2	92736	broad.mit.edu	36	17	70435427	70435427	+	Frame_Shift_Del	DEL	C	-	-			TCGA-76-6282-01	TCGA-76-6282-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:70435427_70435427delC	uc002jmg.1	+	c.582_582delC	c.(580-582)CACfs	p.H194fs	OTOP2_uc002jmf.1_3'UTR	NM_178160	NP_835454	Q7RTS6	OTOP2_HUMAN	otopetrin 2	194						integral to membrane				ovary(3)|large_intestine(1)	4	all_lung(278;0.172)|Lung NSC(278;0.207)													0.31			8	18				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	70435427	70435427	11718	17	C	-	-	18	18	OTOP2	-	5	5
POU4F2	5458	broad.mit.edu	36	4	147779908	147779916	+	In_Frame_Del	DEL	GGCGGCGGC	-	-			TCGA-76-6282-01	TCGA-76-6282-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:147779908_147779916delGGCGGCGGC	uc003ikv.1	+	c.166_174delGGCGGCGGC	c.(166-174)GGCGGCGGCdel	p.GGG65del		NM_004575	NP_004566	Q12837	PO4F2_HUMAN	Brn3b POU domain transcription factor	65_67	Poly-Gly.				negative regulation of transcription from RNA polymerase II promoter	nuclear speck	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulator activity			breast(1)	1	all_hematologic(180;0.151)													0.50			4	4				---	---	---	---	capture_indel			In_Frame_Del	DEL	147779908	147779916	12709	4	GGCGGCGGC	-	-	47	47	POU4F2	-	5	5
DND1	373863	broad.mit.edu	36	5	140032469	140032469	+	Frame_Shift_Del	DEL	T	-	-			TCGA-76-6282-01	TCGA-76-6282-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:140032469_140032469delT	uc003lgt.1	-	c.349_349delA	c.(349-351)ACGfs	p.T117fs		NM_194249	NP_919225	Q8IYX4	DND1_HUMAN	dead end homolog 1	117	RRM 1.				multicellular organismal development|negative regulation of gene silencing by miRNA	cytoplasm|nucleus	AU-rich element binding|nucleotide binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)											0.33			2	4				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	140032469	140032469	4849	5	T	-	-	59	59	DND1	-	5	5
