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
EGR2	1959	broad.mit.edu	36	10	64244072	64244072	+	Missense_Mutation	SNP	C	G	G			TCGA-06-0745-01	TCGA-06-0745-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr10:64244072C>G	uc001jmi.1	-	c.332G>C	c.(331-333)GGC>GCC	p.G111A	EGR2_uc001jmh.1_Missense_Mutation_p.G53A|EGR2_uc009xph.1_Missense_Mutation_p.G111A	NM_000399	NP_000390	P11161	EGR2_HUMAN	early growth response 2 protein isoform a	111					fat cell differentiation|gene-specific transcription from RNA polymerase II promoter	nucleus	DNA binding|RNA polymerase II activating transcription factor binding|sequence-specific DNA binding transcription factor activity|ubiquitin protein ligase binding|zinc ion binding			ovary(2)	2	Prostate(12;0.0297)|all_hematologic(501;0.228)													0.652174	160.293821	161.703153	45	24	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	64244072	64244072	5161	10	C	G	G	26	26	EGR2	G	3	3
PPP2R1B	5519	broad.mit.edu	36	11	111142287	111142287	+	Silent	SNP	G	C	C			TCGA-06-0745-01	TCGA-06-0745-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:111142287G>C	uc001plw.1	-	c.9C>G	c.(7-9)GGC>GGG	p.G3G	PPP2R1B_uc001plx.1_Silent_p.G3G	NM_181699	NP_859050	P30154	2AAB_HUMAN	beta isoform of regulatory subunit A, protein	3							protein binding				0		all_cancers(61;2.34e-15)|all_epithelial(67;1.72e-09)|Melanoma(852;1.91e-06)|all_hematologic(158;0.000405)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0112)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)												0.421053	15.99911	16.121623	8	11	GG		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(274;1.13e-06)|Epithelial(105;2.36e-06)|all cancers(92;3.78e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0761)	Silent	SNP	111142287	111142287	12819	11	G	C	C	38	38	PPP2R1B	C	3	3
OR4D5	219875	broad.mit.edu	36	11	123316344	123316344	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0745-01	TCGA-06-0745-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:123316344G>A	uc001pzk.1	+	c.811G>A	c.(811-813)GTC>ATC	p.V271I		NM_001001965	NP_001001965	Q8NGN0	OR4D5_HUMAN	olfactory receptor, family 4, subfamily D,	271	Helical; Name=7; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)												0.438424	251.007805	251.683056	89	114	GG		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0399)	Missense_Mutation	SNP	123316344	123316344	11464	11	G	A	A	40	40	OR4D5	A	1	1
KIF18A	81930	broad.mit.edu	36	11	28014585	28014585	+	Silent	SNP	C	T	T			TCGA-06-0745-01	TCGA-06-0745-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:28014585C>T	uc001msc.2	-	c.2151G>A	c.(2149-2151)CCG>CCA	p.P717P		NM_031217	NP_112494	Q8NI77	KI18A_HUMAN	kinesin family member 18A	717					blood coagulation|microtubule depolymerization|microtubule-based movement|mitotic metaphase plate congression|mitotic prometaphase|protein transport	caveola|cytosol|kinetochore microtubule|microtubule organizing center|nucleus|ruffle	actin binding|ATP binding|microtubule plus-end binding|plus-end-directed microtubule motor activity|tubulin-dependent ATPase activity|ubiquitin binding			ovary(2)	2														0.34375	60.330411	61.710637	22	42	CC		KEEP	---	---	---	---	capture			Silent	SNP	28014585	28014585	8591	11	C	T	T	19	19	KIF18A	T	1	1
ART1	417	broad.mit.edu	36	11	3638052	3638052	+	Missense_Mutation	SNP	A	T	T			TCGA-06-0745-01	TCGA-06-0745-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr11:3638052A>T	uc001lye.1	+	c.727A>T	c.(727-729)ATC>TTC	p.I243F	ART1_uc009yeb.1_Missense_Mutation_p.I243F	NM_004314	NP_004305	P52961	NAR1_HUMAN	ADP-ribosyltransferase 1	243					protein ADP-ribosylation	anchored to membrane|integral to plasma membrane|sarcoplasmic reticulum membrane	NAD(P)+-protein-arginine ADP-ribosyltransferase activity|NAD+ ADP-ribosyltransferase activity				0		Medulloblastoma(188;0.0025)|Breast(177;0.00328)|all_neural(188;0.0227)			Becaplermin(DB00102)									0.348485	127.315404	129.987251	46	86	AA		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(625;0.0351)|LUSC - Lung squamous cell carcinoma(625;0.195)	Missense_Mutation	SNP	3638052	3638052	1015	11	A	T	T	12	12	ART1	T	4	4
STIM1	6786	broad.mit.edu	36	11	4033370	4033370	+	Missense_Mutation	SNP	A	G	G			TCGA-06-0745-01	TCGA-06-0745-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr11:4033370A>G	uc001lyv.1	+	c.424A>G	c.(424-426)ATC>GTC	p.I142V	STIM1_uc009yef.1_Missense_Mutation_p.I142V	NM_003156	NP_003147	Q13586	STIM1_HUMAN	stromal interaction molecule 1 precursor	142	SAM.|Extracellular (Potential).				activation of store-operated calcium channel activity|calcium ion transport|detection of calcium ion|platelet activation	integral to endoplasmic reticulum membrane|integral to plasma membrane|microtubule	calcium ion binding|microtubule plus-end binding			pancreas(1)	1		Breast(177;0.00159)|Medulloblastoma(188;0.00258)|all_neural(188;0.0233)												0.6	6.524711	6.569317	3	2	AA		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(625;0.114)|LUSC - Lung squamous cell carcinoma(625;0.141)	Missense_Mutation	SNP	4033370	4033370	15803	11	A	G	G	12	12	STIM1	G	4	4
MYBPC3	4607	broad.mit.edu	36	11	47313218	47313218	+	Silent	SNP	A	C	C			TCGA-06-0745-01	TCGA-06-0745-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr11:47313218A>C	uc001nfa.2	-	c.2856T>G	c.(2854-2856)CCT>CCG	p.P952P		NM_000256	NP_000247	Q14896	MYPC3_HUMAN	myosin binding protein C, cardiac	951	Fibronectin type-III 2.				cardiac muscle contraction|cell adhesion|muscle filament sliding|regulation of muscle filament sliding|regulation of striated muscle contraction|ventricular cardiac muscle tissue morphogenesis	C zone|cytosol|striated muscle myosin thick filament	actin binding|ATPase activator activity|metal ion binding|myosin heavy chain binding|structural constituent of muscle|titin binding			ovary(2)|central_nervous_system(1)	3														0.25	7.324905	8.003029	3	9	AA		KEEP	---	---	---	---	capture		Lung(87;0.176)	Silent	SNP	47313218	47313218	10408	11	A	C	C	7	7	MYBPC3	C	4	4
AHNAK	79026	broad.mit.edu	36	11	62055309	62055309	+	Silent	SNP	G	A	A			TCGA-06-0745-01	TCGA-06-0745-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:62055309G>A	uc001ntl.1	-	c.3156C>T	c.(3154-3156)GGC>GGT	p.G1052G	AHNAK_uc001ntk.1_Intron	NM_001620	NP_001611	Q09666	AHNK_HUMAN	AHNAK nucleoprotein isoform 1	1052					nervous system development	nucleus	protein binding			ovary(10)|pancreas(4)	14		Melanoma(852;0.155)												0.457143	235.277118	235.557322	80	95	GG		KEEP	---	---	---	---	capture			Silent	SNP	62055309	62055309	417	11	G	A	A	42	42	AHNAK	A	2	2
KCNC2	3747	broad.mit.edu	36	12	73887831	73887831	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0745-01	TCGA-06-0745-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:73887831G>A	uc001sxg.1	-	c.200C>T	c.(199-201)GCG>GTG	p.A67V	KCNC2_uc009zry.1_Missense_Mutation_p.A67V|KCNC2_uc001sxe.1_Missense_Mutation_p.A67V|KCNC2_uc001sxf.1_Missense_Mutation_p.A67V	NM_139137	NP_631875	Q96PR1	KCNC2_HUMAN	Shaw-related voltage-gated potassium channel	67	Gly/Pro-rich (insert).|Cytoplasmic (Potential).				energy reserve metabolic process|regulation of insulin secretion	voltage-gated potassium channel complex	voltage-gated potassium channel activity			breast(2)|pancreas(2)|skin(1)|lung(1)	6														0.3125	25.876817	26.857745	10	22	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	73887831	73887831	8320	12	G	A	A	38	38	KCNC2	A	1	1
MYCBP2	23077	broad.mit.edu	36	13	76733448	76733448	+	Missense_Mutation	SNP	A	G	G			TCGA-06-0745-01	TCGA-06-0745-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr13:76733448A>G	uc001vkf.1	-	c.1597T>C	c.(1597-1599)TGG>CGG	p.W533R	MYCBP2_uc010aev.1_5'UTR	NM_015057	NP_055872	O75592	MYCB2_HUMAN	MYC binding protein 2	533					regulation of mitotic metaphase/anaphase transition|regulation of transcription, DNA-dependent|transcription, DNA-dependent	anaphase-promoting complex	ligase activity|protein binding|zinc ion binding			ovary(4)|breast(4)|lung(2)|pancreas(1)	11		Breast(118;0.212)|Acute lymphoblastic leukemia(28;0.22)												0.347222	74.458666	75.939637	25	47	AA		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(99;0.109)	Missense_Mutation	SNP	76733448	76733448	10413	13	A	G	G	8	8	MYCBP2	G	4	4
JPH4	84502	broad.mit.edu	36	14	23114823	23114823	+	Silent	SNP	G	C	C			TCGA-06-0745-01	TCGA-06-0745-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr14:23114823G>C	uc001wkr.1	-	c.1062C>G	c.(1060-1062)GGC>GGG	p.G354G	JPH4_uc001wkq.1_Silent_p.G354G|JPH4_uc001wks.1_Silent_p.G354G	NM_032452	NP_115828	Q96JJ6	JPH4_HUMAN	junctophilin 4	354	Cytoplasmic (Potential).|MORN 8.				calcium ion transport into cytosol|regulation of ryanodine-sensitive calcium-release channel activity	integral to membrane|junctional sarcoplasmic reticulum membrane				ovary(1)|pancreas(1)	2	all_cancers(95;0.000251)													0.5	7.621769	7.621769	3	3	GG		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(265;0.00654)	Silent	SNP	23114823	23114823	8267	14	G	C	C	46	46	JPH4	C	3	3
AKAP6	9472	broad.mit.edu	36	14	32360422	32360422	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0745-01	TCGA-06-0745-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr14:32360422G>C	uc001wrq.1	+	c.3652G>C	c.(3652-3654)GAA>CAA	p.E1218Q		NM_004274	NP_004265	Q13023	AKAP6_HUMAN	A-kinase anchor protein 6	1218					protein targeting	calcium channel complex|nuclear membrane|sarcoplasmic reticulum	protein kinase A binding|receptor binding			breast(6)|ovary(5)|large_intestine(2)|lung(2)|pancreas(1)	16	Breast(36;0.0388)|Prostate(35;0.15)					Melanoma(49;821 1200 7288 13647 42351)				483				0.694444	182.978443	185.406758	50	22	GG		KEEP	---	---	---	---	capture	LUAD - Lung adenocarcinoma(48;0.00107)|Lung(238;0.00677)|STAD - Stomach adenocarcinoma(7;0.116)	GBM - Glioblastoma multiforme(265;0.019)	Missense_Mutation	SNP	32360422	32360422	458	14	G	C	C	41	41	AKAP6	C	3	3
SMEK1	55671	broad.mit.edu	36	14	91006967	91006967	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0745-01	TCGA-06-0745-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr14:91006967G>C	uc001xzn.1	-	c.1627C>G	c.(1627-1629)CTT>GTT	p.L543V	SMEK1_uc001xzm.1_Missense_Mutation_p.L530V|SMEK1_uc001xzo.1_Missense_Mutation_p.L530V|SMEK1_uc010atz.1_Missense_Mutation_p.L304V|SMEK1_uc001xzp.1_Non-coding_Transcript	NM_032560	NP_115949	Q6IN85	P4R3A_HUMAN	SMEK homolog 1, suppressor of mek1	543						microtubule organizing center|nucleus	protein binding				0		all_cancers(154;0.0691)|all_epithelial(191;0.219)												0.301075	86.363262	89.650332	28	65	GG		KEEP	---	---	---	---	capture		COAD - Colon adenocarcinoma(157;0.221)	Missense_Mutation	SNP	91006967	91006967	15291	14	G	C	C	33	33	SMEK1	C	3	3
TRPM1	4308	broad.mit.edu	36	15	29081480	29081480	+	Nonsense_Mutation	SNP	G	T	T			TCGA-06-0745-01	TCGA-06-0745-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr15:29081480G>T	uc001zfm.1	-	c.4649C>A	c.(4648-4650)TCA>TAA	p.S1550*	TRPM1_uc010azy.1_Nonsense_Mutation_p.S1457*|TRPM1_uc001zfl.1_Non-coding_Transcript	NM_002420	NP_002411	Q7Z4N2	TRPM1_HUMAN	transient receptor potential cation channel,	1550	Cytoplasmic (Potential).				cellular response to light stimulus|visual perception	integral to plasma membrane	calcium channel activity|receptor activity			ovary(2)|pancreas(1)|skin(1)	4		all_lung(180;1.92e-11)												0.704698	334.718326	340.298001	105	44	GG		KEEP	---	---	---	---	capture		all cancers(64;3.52e-16)|Epithelial(43;1.65e-11)|GBM - Glioblastoma multiforme(186;3.57e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00533)|COAD - Colon adenocarcinoma(236;0.0609)|Lung(196;0.199)	Nonsense_Mutation	SNP	29081480	29081480	17136	15	G	T	T	45	45	TRPM1	T	5	3
SPTBN5	51332	broad.mit.edu	36	15	39965452	39965452	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0745-01	TCGA-06-0745-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr15:39965452G>C	uc001zos.1	-	c.1188C>G	c.(1186-1188)TTC>TTG	p.F396L		NM_016642	NP_057726	Q9NRC6	SPTN5_HUMAN	spectrin, beta, non-erythrocytic 5	431	Spectrin 2.				actin cytoskeleton organization|actin filament capping|axon guidance	cytosol|membrane|spectrin				ovary(1)|central_nervous_system(1)	2		all_cancers(109;1.84e-17)|all_epithelial(112;1.12e-15)|Lung NSC(122;7.6e-10)|all_lung(180;4.15e-09)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.173)												0.384615	16.67427	16.825172	5	8	GG		KEEP	---	---	---	---	capture		all cancers(2;4.33e-34)|Epithelial(2;1.72e-25)|OV - Ovarian serous cystadenocarcinoma(18;8.32e-20)|GBM - Glioblastoma multiforme(94;4.69e-07)|Colorectal(2;0.00104)|COAD - Colon adenocarcinoma(120;0.0405)|READ - Rectum adenocarcinoma(92;0.0908)	Missense_Mutation	SNP	39965452	39965452	15636	15	G	C	C	41	41	SPTBN5	C	3	3
HCN4	10021	broad.mit.edu	36	15	71447078	71447078	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0745-01	TCGA-06-0745-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr15:71447078G>C	uc002avp.1	-	c.587C>G	c.(586-588)GCC>GGC	p.A196G		NM_005477	NP_005468	Q9Y3Q4	HCN4_HUMAN	hyperpolarization activated cyclic	196	Cytoplasmic (Potential).				blood circulation|muscle contraction	integral to membrane	cAMP binding|protein binding|sodium channel activity|voltage-gated potassium channel activity			ovary(5)|liver(1)	6														0.375	11.33439	11.557195	6	10	GG		KEEP	---	---	---	---	capture		COAD - Colon adenocarcinoma(1;0.142)	Missense_Mutation	SNP	71447078	71447078	7281	15	G	C	C	42	42	HCN4	C	3	3
CIITA	4261	broad.mit.edu	36	16	10900360	10900360	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0745-01	TCGA-06-0745-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:10900360C>T	uc002daj.2	+	c.439C>T	c.(439-441)CCC>TCC	p.P147S	CIITA_uc002dag.2_Missense_Mutation_p.P146S|CIITA_uc002dah.2_Missense_Mutation_p.P147S|CIITA_uc010bup.1_Missense_Mutation_p.P146S|CIITA_uc002dai.2_Missense_Mutation_p.P146S|CIITA_uc002dak.2_Missense_Mutation_p.P146S	NM_000246	NP_000237	P33076	C2TA_HUMAN	class II transactivator	146					interferon-gamma-mediated signaling pathway|negative regulation of collagen biosynthetic process|negative regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of MHC class I biosynthetic process|positive regulation of MHC class II biosynthetic process|response to antibiotic|transcription, DNA-dependent	nucleus	activating transcription factor binding|ATP binding|promoter binding|protein C-terminus binding|protein complex binding|RNA polymerase II transcription factor activity|transcription activator activity|transcription coactivator activity|transcription repressor activity			central_nervous_system(1)	1										532				0.305882	68.406646	71.271578	26	59	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	10900360	10900360	3562	16	C	T	T	19	19	CIITA	T	1	1
GTF3C1	2975	broad.mit.edu	36	16	27390688	27390688	+	Missense_Mutation	SNP	C	G	G			TCGA-06-0745-01	TCGA-06-0745-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:27390688C>G	uc002dov.1	-	c.4408G>C	c.(4408-4410)GAG>CAG	p.E1470Q	GTF3C1_uc002dou.2_Missense_Mutation_p.E1470Q	NM_001520	NP_001511	Q12789	TF3C1_HUMAN	general transcription factor IIIC, polypeptide	1470					5S class rRNA transcription from RNA polymerase III type 1 promoter|tRNA transcription from RNA polymerase III promoter	transcription factor TFIIIC complex	DNA binding|protein binding			ovary(2)|breast(1)|pancreas(1)	4														0.323232	100.470761	103.214189	32	67	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	27390688	27390688	7152	16	C	G	G	30	30	GTF3C1	G	3	3
OR1F1	4992	broad.mit.edu	36	16	3194557	3194557	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0745-01	TCGA-06-0745-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:3194557G>A	uc002cug.1	+	c.310G>A	c.(310-312)GTT>ATT	p.V104I		NM_012360	NP_036492	O43749	OR1F1_HUMAN	olfactory receptor, family 1, subfamily F,	104	Helical; Name=3; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0														0.353211	208.859024	212.97793	77	141	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	3194557	3194557	11362	16	G	A	A	40	40	OR1F1	A	1	1
CHD9	80205	broad.mit.edu	36	16	51747982	51747982	+	Missense_Mutation	SNP	T	A	A			TCGA-06-0745-01	TCGA-06-0745-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr16:51747982T>A	uc002ehb.1	+	c.480T>A	c.(478-480)CAT>CAA	p.H160Q	CHD9_uc002egy.1_Missense_Mutation_p.H160Q|CHD9_uc002egz.1_Missense_Mutation_p.H160Q|CHD9_uc002eha.1_Missense_Mutation_p.H160Q|CHD9_uc002ehc.1_Missense_Mutation_p.H160Q	NM_025134	NP_079410	Q3L8U1	CHD9_HUMAN	chromodomain helicase DNA binding protein 9	160					cellular lipid metabolic process|chromatin assembly or disassembly|chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromatin|cytoplasm|nucleoplasm	ATP binding|chromatin binding|DNA binding|helicase activity|protein binding			lung(2)|central_nervous_system(1)|breast(1)|skin(1)|ovary(1)|kidney(1)	7		all_cancers(37;0.0212)								1157				0.481752	214.84553	214.885087	66	71	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	51747982	51747982	3466	16	T	A	A	51	51	CHD9	A	4	4
CTU2	348180	broad.mit.edu	36	16	87306759	87306759	+	Missense_Mutation	SNP	C	A	A			TCGA-06-0745-01	TCGA-06-0745-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:87306759C>A	uc010chz.1	+	c.895C>A	c.(895-897)CTG>ATG	p.L299M	CTU2_uc002flm.1_Missense_Mutation_p.L228M|CTU2_uc002fln.1_Missense_Mutation_p.L228M|CTU2_uc010cia.1_Missense_Mutation_p.L141M	NM_001012759	NP_001012777	Q2VPK5	CTU2_HUMAN	hypothetical protein LOC348180 isoform 1	228					tRNA thio-modification|tRNA wobble uridine modification	cytoplasm|protein complex|soluble fraction	protein binding			skin(1)	1														0.327273	49.332928	50.787338	18	37	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	87306759	87306759	4207	16	C	A	A	20	20	CTU2	A	3	3
CNTNAP1	8506	broad.mit.edu	36	17	38095108	38095108	+	Missense_Mutation	SNP	T	G	G			TCGA-06-0745-01	TCGA-06-0745-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr17:38095108T>G	uc002iay.1	+	c.1672T>G	c.(1672-1674)TCT>GCT	p.S558A		NM_003632	NP_003623	P78357	CNTP1_HUMAN	contactin associated protein 1 precursor	558	EGF-like 1.|Extracellular (Potential).				axon guidance|cell adhesion	paranode region of axon	receptor activity|receptor binding|SH3 domain binding|SH3/SH2 adaptor activity			ovary(2)	2		Breast(137;0.000143)												0.108696	6.544704	13.51971	5	41	TT		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(366;0.143)	Missense_Mutation	SNP	38095108	38095108	3784	17	T	G	G	58	58	CNTNAP1	G	4	4
TBX2	6909	broad.mit.edu	36	17	56837750	56837750	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0745-01	TCGA-06-0745-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:56837750G>C	uc002izf.1	+	c.1427G>C	c.(1426-1428)GGC>GCC	p.G476A	TBX2_uc002ize.2_3'UTR|TBX2_uc002izg.1_Missense_Mutation_p.G332A	NM_005994	NP_005985	Q13207	TBX2_HUMAN	T-box 2	486	Gly-rich.				cell aging|positive regulation of cell proliferation		sequence-specific DNA binding|transcription repressor activity				0						GBM(3;187 253 11467 14965 23079)								0.235294	6.990355	8.081627	4	13	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	56837750	56837750	16181	17	G	C	C	42	42	TBX2	C	3	3
ITGB4	3691	broad.mit.edu	36	17	71245027	71245027	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0745-01	TCGA-06-0745-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:71245027C>T	uc002jpg.1	+	c.2020C>T	c.(2020-2022)CGG>TGG	p.R674W	ITGB4_uc002jph.1_Missense_Mutation_p.R674W|ITGB4_uc010dgo.1_Missense_Mutation_p.R674W|ITGB4_uc002jpi.2_Missense_Mutation_p.R674W|ITGB4_uc010dgp.1_Missense_Mutation_p.R674W|ITGB4_uc002jpj.1_Missense_Mutation_p.R674W	NM_000213	NP_000204	P16144	ITB4_HUMAN	integrin beta 4 isoform 1 precursor	674	Extracellular (Potential).			IHPGLCEDLRSCVQCQAWGTGEKKGRTCEECNFKVKMVDEL KRAEEVVVRCSFRDEDDDCTYSYTMEGDGAPGPNSTVLVHK KK -> STRASARTYAPACSARRGAPARRRGARVRNATSRS RWWTSLREARRWWCAAPSGTRMTTAPTATPWKVTAPLGPTA LSWCTRRR (in Ref. 5; CAB61345).	cell communication|cell-matrix adhesion|hemidesmosome assembly|integrin-mediated signaling pathway|multicellular organismal development	integrin complex	protein binding|receptor activity			lung(4)	4	all_cancers(13;1.5e-07)									754				0.388889	20.856316	21.038454	7	11	CC		KEEP	---	---	---	---	capture	all cancers(21;8.32e-07)|Epithelial(20;1.92e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00194)|Lung(188;0.132)|LUSC - Lung squamous cell carcinoma(166;0.154)		Missense_Mutation	SNP	71245027	71245027	8201	17	C	T	T	23	23	ITGB4	T	1	1
LAMA1	284217	broad.mit.edu	36	18	7001325	7001325	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0745-01	TCGA-06-0745-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr18:7001325G>C	uc002knm.1	-	c.3661C>G	c.(3661-3663)CTG>GTG	p.L1221V		NM_005559	NP_005550	P25391	LAMA1_HUMAN	laminin, alpha 1 precursor	1221	Laminin IV type A 2.				axon guidance|cell adhesion|cell surface receptor linked signaling pathway|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	extracellular space|laminin-1 complex|laminin-3 complex	extracellular matrix structural constituent|receptor binding			ovary(8)|large_intestine(4)|breast(2)|pancreas(2)|central_nervous_system(1)	17		Colorectal(10;0.172)			Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)					1597				0.333333	7.020662	7.242737	3	6	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	7001325	7001325	8928	18	G	C	C	34	34	LAMA1	C	3	3
ATG4D	84971	broad.mit.edu	36	19	10518573	10518573	+	Silent	SNP	T	C	C			TCGA-06-0745-01	TCGA-06-0745-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr19:10518573T>C	uc002mov.1	+	c.552T>C	c.(550-552)TCT>TCC	p.S184S	ATG4D_uc010dxh.1_Non-coding_Transcript|ATG4D_uc010dxi.1_Intron|ATG4D_uc010dxj.1_Intron	NM_032885	NP_116274	Q86TL0	ATG4D_HUMAN	APG4 autophagy 4 homolog D	184					autophagy|protein transport	cytoplasm	cysteine-type endopeptidase activity				0														0.186047	9.431786	13.528464	8	35	TT		KEEP	---	---	---	---	capture	Epithelial(33;9.2e-06)|all cancers(31;3.9e-05)		Silent	SNP	10518573	10518573	1118	19	T	C	C	54	54	ATG4D	C	4	4
JAK3	3718	broad.mit.edu	36	19	17814249	17814249	+	Missense_Mutation	SNP	T	C	C			TCGA-06-0745-01	TCGA-06-0745-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr19:17814249T>C	uc002nhn.2	-	c.737A>G	c.(736-738)GAT>GGT	p.D246G	JAK3_uc010ebh.1_Non-coding_Transcript|JAK3_uc002nho.2_Missense_Mutation_p.D246G	NM_000215	NP_000206	P52333	JAK3_HUMAN	Janus kinase 3	246	FERM.				B cell differentiation|cytokine-mediated signaling pathway|enzyme linked receptor protein signaling pathway|intracellular protein kinase cascade|negative regulation of dendritic cell cytokine production|negative regulation of FasL biosynthetic process|negative regulation of interleukin-10 production|negative regulation of interleukin-12 production|negative regulation of T-helper 1 cell differentiation|negative regulation of thymocyte apoptosis|peptidyl-tyrosine phosphorylation|positive regulation of anti-apoptosis|response to interleukin-15|response to interleukin-2|response to interleukin-4|response to interleukin-9|T cell homeostasis	cytoskeleton|cytosol|endomembrane system|membrane	ATP binding|non-membrane spanning protein tyrosine kinase activity|protein binding			haematopoietic_and_lymphoid_tissue(36)|lung(3)|ovary(3)|stomach(2)|breast(2)	46								2		364				0.5	9.794705	9.794705	4	4	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	17814249	17814249	8243	19	T	C	C	50	50	JAK3	C	4	4
ZNF813	126017	broad.mit.edu	36	19	58686973	58686973	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0745-01	TCGA-06-0745-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:58686973G>A	uc002qbu.2	+	c.1675G>A	c.(1675-1677)GTT>ATT	p.V559I	ZNF813_uc010eqq.1_Intron	NM_001004301	NP_001004301	Q6ZN06	ZN813_HUMAN	zinc finger protein 813	559	C2H2-type 13.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			large_intestine(1)	1														0.725	95.491274	97.315122	29	11	GG		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(134;0.00619)	Missense_Mutation	SNP	58686973	58686973	18773	19	G	A	A	44	44	ZNF813	A	2	2
C3	718	broad.mit.edu	36	19	6665208	6665208	+	Silent	SNP	G	C	C			TCGA-06-0745-01	TCGA-06-0745-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:6665208G>C	uc002mfm.1	-	c.651C>G	c.(649-651)GTC>GTG	p.V217V		NM_000064	NP_000055	P01024	CO3_HUMAN	complement component 3 precursor	217					complement activation, alternative pathway|complement activation, classical pathway|G-protein coupled receptor protein signaling pathway|inflammatory response|positive regulation vascular endothelial growth factor production	extracellular space	endopeptidase inhibitor activity|receptor binding			ovary(1)|pancreas(1)	2														0.337209	93.748687	95.764423	29	57	GG		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(1328;1.36e-05)|Lung(535;0.00661)	Silent	SNP	6665208	6665208	2296	19	G	C	C	33	33	C3	C	3	3
MUC16	94025	broad.mit.edu	36	19	8933189	8933189	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0745-01	TCGA-06-0745-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:8933189C>T	uc002mkp.1	-	c.15257G>A	c.(15256-15258)CGC>CAC	p.R5086H		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	5088	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														0.302857	141.109202	147.180143	53	122	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	8933189	8933189	10367	19	C	T	T	27	27	MUC16	T	1	1
PTCHD2	57540	broad.mit.edu	36	1	11519313	11519313	+	Missense_Mutation	SNP	G	T	T			TCGA-06-0745-01	TCGA-06-0745-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:11519313G>T	uc001ash.2	+	c.4162G>T	c.(4162-4164)GCA>TCA	p.A1388S		NM_020780	NP_065831	Q9P2K9	PTHD2_HUMAN	patched domain containing 2	1388	Cytoplasmic (Potential).				cholesterol homeostasis|regulation of lipid transport|smoothened signaling pathway	endoplasmic reticulum|integral to membrane|nuclear membrane	hedgehog receptor activity			ovary(2)|pancreas(1)|breast(1)|skin(1)	5	Ovarian(185;0.249)	Lung NSC(185;4.16e-05)|all_lung(284;4.76e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)												0.8125	42.184966	43.6532	13	3	GG		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.13e-07)|COAD - Colon adenocarcinoma(227;4.83e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000325)|Kidney(185;0.000877)|KIRC - Kidney renal clear cell carcinoma(229;0.00273)|STAD - Stomach adenocarcinoma(313;0.00766)|READ - Rectum adenocarcinoma(331;0.0549)	Missense_Mutation	SNP	11519313	11519313	13187	1	G	T	T	38	38	PTCHD2	T	3	3
LGR6	59352	broad.mit.edu	36	1	200554149	200554149	+	Missense_Mutation	SNP	C	G	G			TCGA-06-0745-01	TCGA-06-0745-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:200554149C>G	uc001gxu.1	+	c.2095C>G	c.(2095-2097)CTG>GTG	p.L699V	LGR6_uc001gxv.1_Missense_Mutation_p.L647V|LGR6_uc009xab.1_Non-coding_Transcript|LGR6_uc001gxw.1_Missense_Mutation_p.L560V	NM_001017403	NP_001017403	Q9HBX8	LGR6_HUMAN	leucine-rich repeat-containing G protein-coupled	699	Helical; Name=4; (Potential).					integral to membrane|plasma membrane	protein-hormone receptor activity			large_intestine(4)|ovary(3)|pancreas(1)	8														0.333333	7.922361	8.143586	3	6	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	200554149	200554149	9084	1	C	G	G	28	28	LGR6	G	3	3
RYR2	6262	broad.mit.edu	36	1	236014631	236014631	+	Silent	SNP	C	G	G			TCGA-06-0745-01	TCGA-06-0745-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:236014631C>G	uc001hyl.1	+	c.12996C>G	c.(12994-12996)GCC>GCG	p.A4332A		NM_001035	NP_001026	Q92736	RYR2_HUMAN	cardiac muscle ryanodine receptor	4332					cardiac muscle contraction|detection of calcium ion|induction of apoptosis by ionic changes|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum|response to caffeine|response to hypoxia|response to redox state	calcium channel complex|plasma membrane|plasma membrane enriched fraction|sarcoplasmic reticulum membrane	calcium ion binding|calmodulin binding|identical protein binding|protein kinase A catalytic subunit binding|protein kinase A regulatory subunit binding|receptor activity|ryanodine-sensitive calcium-release channel activity|suramin binding			ovary(17)|large_intestine(6)|central_nervous_system(6)|pancreas(3)|breast(1)	33	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)												0.351648	85.943857	87.722691	32	59	CC		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(106;0.00606)		Silent	SNP	236014631	236014631	14249	1	C	G	G	21	21	RYR2	G	3	3
SMYD3	64754	broad.mit.edu	36	1	244093749	244093749	+	Missense_Mutation	SNP	T	G	G			TCGA-06-0745-01	TCGA-06-0745-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr1:244093749T>G	uc001ibl.1	-	c.876A>C	c.(874-876)AAA>AAC	p.K292N	SMYD3_uc001ibk.1_Missense_Mutation_p.K233N|SMYD3_uc001ibi.1_Missense_Mutation_p.K103N|SMYD3_uc001ibj.1_Missense_Mutation_p.K103N	NM_022743	NP_073580	Q9H7B4	SMYD3_HUMAN	SET and MYND domain containing 3	292						cytoplasm|nucleus	histone-lysine N-methyltransferase activity|protein binding|zinc ion binding				0	all_cancers(71;0.000291)|all_epithelial(71;0.000174)|Ovarian(71;0.0377)|all_lung(81;0.0568)|Lung NSC(105;0.0804)|Breast(184;0.173)|Melanoma(84;0.242)	all_cancers(173;0.0496)|Acute lymphoblastic leukemia(190;0.164)												0.423077	111.770428	112.171107	33	45	TT		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(106;0.0129)	all cancers(4;0.028)|GBM - Glioblastoma multiforme(49;0.0537)	Missense_Mutation	SNP	244093749	244093749	15323	1	T	G	G	64	64	SMYD3	G	4	4
PRDM16	63976	broad.mit.edu	36	1	3319021	3319021	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0745-01	TCGA-06-0745-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:3319021G>C	uc001akf.1	+	c.2400G>C	c.(2398-2400)GAG>GAC	p.E800D	PRDM16_uc001akc.1_Missense_Mutation_p.E800D|PRDM16_uc001akd.1_Missense_Mutation_p.E800D|PRDM16_uc001ake.1_Missense_Mutation_p.E800D|PRDM16_uc009vlh.1_Missense_Mutation_p.E501D	NM_022114	NP_071397	Q9HAZ2	PRD16_HUMAN	PR domain containing 16 isoform 1	800	Mediates interaction with SKI and regulation of TGF-beta signaling.|Interaction with CTBP1 and CTBP2 (By similarity).				brown fat cell differentiation|negative regulation of granulocyte differentiation|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transforming growth factor beta receptor signaling pathway|negative regulation of transforming growth factor beta receptor signaling pathway|positive regulation of transcription, DNA-dependent|regulation of cellular respiration|transcription, DNA-dependent	transcriptional repressor complex	protein binding|sequence-specific DNA binding|transcription activator activity|transcription coactivator activity|transcription repressor activity|zinc ion binding			ovary(1)|lung(1)|central_nervous_system(1)	3	all_cancers(77;0.00208)|all_epithelial(69;0.000732)|Ovarian(185;0.0634)|Lung NSC(156;0.109)|all_lung(157;0.111)	all_epithelial(116;2.03e-21)|all_lung(118;7.55e-09)|Lung NSC(185;1.28e-06)|Breast(487;0.000792)|Renal(390;0.00137)|Hepatocellular(190;0.00515)|Myeloproliferative disorder(586;0.0267)|Ovarian(437;0.0365)|Lung SC(97;0.114)|Medulloblastoma(700;0.134)								1161				0.333333	8.737288	9.122913	5	10	GG		KEEP	---	---	---	---	capture		Epithelial(90;5.59e-35)|OV - Ovarian serous cystadenocarcinoma(86;1.99e-20)|GBM - Glioblastoma multiforme(42;3.72e-11)|Colorectal(212;0.000425)|BRCA - Breast invasive adenocarcinoma(365;0.000946)|COAD - Colon adenocarcinoma(227;0.000968)|Kidney(185;0.00155)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0175)|Lung(427;0.137)	Missense_Mutation	SNP	3319021	3319021	12899	1	G	C	C	34	34	PRDM16	C	3	3
SLC17A9	63910	broad.mit.edu	36	20	61067431	61067431	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0745-01	TCGA-06-0745-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr20:61067431G>A	uc002yea.2	+	c.970G>A	c.(970-972)GTC>ATC	p.V324I	SLC17A9_uc002ydz.2_Missense_Mutation_p.V318I	NM_022082	NP_071365	Q9BYT1	S17A9_HUMAN	vesicular nucleotide transporter SLC17A9	324	Helical; (Potential).				exocytosis|transmembrane transport	integral to membrane	transporter activity	p.V324I(1)		ovary(1)	1														0.247059	339.714722	374.321677	147	448	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	61067431	61067431	14920	20	G	A	A	40	40	SLC17A9	A	1	1
CBR1	873	broad.mit.edu	36	21	36364340	36364340	+	Missense_Mutation	SNP	G	T	T			TCGA-06-0745-01	TCGA-06-0745-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr21:36364340G>T	uc002yvb.1	+	c.57G>T	c.(55-57)TTG>TTT	p.L19F	SETD4_uc002yva.1_Intron|CBR1_uc010gmx.1_Missense_Mutation_p.L19F|CBR1_uc010gmy.1_Missense_Mutation_p.L19F	NM_001757	NP_001748	P16152	CBR1_HUMAN	carbonyl reductase 1	19	NADP.				drug metabolic process|oxidation-reduction process|vitamin K metabolic process	cytoplasm	15-hydroxyprostaglandin dehydrogenase (NADP+) activity|carbonyl reductase (NADPH) activity|prostaglandin-E2 9-reductase activity|protein binding				0					Acetohexamide(DB00414)|Lubiprostone(DB01046)									0.277778	9.663669	10.466684	5	13	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	36364340	36364340	2827	21	G	T	T	47	47	CBR1	T	3	3
RGL4	266747	broad.mit.edu	36	22	22370417	22370417	+	Nonsense_Mutation	SNP	G	T	T			TCGA-06-0745-01	TCGA-06-0745-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr22:22370417G>T	uc002zxn.1	+	c.1279G>T	c.(1279-1281)GAA>TAA	p.E427*	LOC91316_uc002zxj.2_Intron|LOC91316_uc002zxk.2_Intron|LOC91316_uc010gua.1_Intron|LOC91316_uc002zxl.2_Intron|LOC91316_uc002zxm.2_Intron|RGL4_uc002zxo.1_Nonsense_Mutation_p.E427*|RGL4_uc002zxp.1_Nonsense_Mutation_p.E291*|RGL4_uc002zxq.1_Nonsense_Mutation_p.E291*	NM_153615	NP_705843	Q8IZJ4	RGDSR_HUMAN	ral guanine nucleotide dissociation	427	Ras-GEF.				small GTPase mediated signal transduction	cytoplasmic membrane-bounded vesicle	guanyl-nucleotide exchange factor activity			ovary(1)	1										238				0.333333	28.617302	29.427478	11	22	GG		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	22370417	22370417	13752	22	G	T	T	41	41	RGL4	T	5	3
CHEK2	11200	broad.mit.edu	36	22	27460518	27460518	+	Silent	SNP	C	T	T			TCGA-06-0745-01	TCGA-06-0745-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr22:27460518C>T	uc003adt.1	-	c.192G>A	c.(190-192)GAG>GAA	p.E64E	CHEK2_uc003ads.1_5'UTR|CHEK2_uc010gvh.1_Silent_p.E64E|CHEK2_uc010gvi.1_Silent_p.E64E|CHEK2_uc010gvj.1_Non-coding_Transcript|CHEK2_uc003adr.1_Non-coding_Transcript|CHEK2_uc010gvk.1_Non-coding_Transcript|CHEK2_uc003adu.1_Silent_p.E64E|CHEK2_uc003adv.1_Silent_p.E64E|CHEK2_uc003adw.1_Silent_p.E64E|CHEK2_uc003adx.1_5'UTR|CHEK2_uc003ady.1_Silent_p.E64E|CHEK2_uc003adz.1_5'UTR	NM_001005735	NP_001005735	O96017	CHK2_HUMAN	protein kinase CHK2 isoform c	64			E -> K (in prostate cancer; somatic mutation).		cell cycle|DNA damage checkpoint|DNA damage response, signal transduction resulting in induction of apoptosis|protein phosphorylation|replicative senescence	PML body	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity			central_nervous_system(17)|ovary(1)	18										268				0.416667	174.907238	175.794606	60	84	CC		KEEP	---	---	---	---	capture			Silent	SNP	27460518	27460518	3469	22	C	T	T	32	32	CHEK2	T	2	2
SBF1	6305	broad.mit.edu	36	22	49248613	49248613	+	Missense_Mutation	SNP	C	G	G			TCGA-06-0745-01	TCGA-06-0745-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr22:49248613C>G	uc003blh.1	-	c.1864G>C	c.(1864-1866)GAC>CAC	p.D622H	SBF1_uc003blg.1_Missense_Mutation_p.D622H|SBF1_uc003bli.1_Missense_Mutation_p.D623H	NM_002972	NP_002963	O95248	MTMR5_HUMAN	SET binding factor 1 isoform a	622					protein dephosphorylation	integral to membrane|nucleus	protein tyrosine/serine/threonine phosphatase activity				0		all_cancers(38;5.78e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)												0.480769	83.072529	83.089276	25	27	CC		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(115;0.206)|LUAD - Lung adenocarcinoma(64;0.247)	Missense_Mutation	SNP	49248613	49248613	14339	22	C	G	G	29	29	SBF1	G	3	3
LCT	3938	broad.mit.edu	36	2	136286625	136286625	+	Silent	SNP	G	A	A			TCGA-06-0745-01	TCGA-06-0745-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:136286625G>A	uc002tuu.1	-	c.2079C>T	c.(2077-2079)AAC>AAT	p.N693N		NM_002299	NP_002290	P09848	LPH_HUMAN	lactase-phlorizin hydrolase preproprotein	693	Extracellular (Potential).|4 X approximate repeats.|2.				carbohydrate metabolic process|polysaccharide digestion	apical plasma membrane|integral to plasma membrane|membrane fraction	cation binding|glycosylceramidase activity|lactase activity			ovary(7)|central_nervous_system(2)|lung(1)|pancreas(1)	11														0.358621	146.653735	149.208271	52	93	GG		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(221;0.169)	Silent	SNP	136286625	136286625	9017	2	G	A	A	40	40	LCT	A	1	1
MYT1L	23040	broad.mit.edu	36	2	1791894	1791894	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0745-01	TCGA-06-0745-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:1791894C>T	uc002qxe.1	-	c.3133G>A	c.(3133-3135)GGA>AGA	p.G1045R	MYT1L_uc002qxd.1_Missense_Mutation_p.G1043R|MYT1L_uc010ewk.1_Missense_Mutation_p.G41R	NM_015025	NP_055840	Q9UL68	MYT1L_HUMAN	myelin transcription factor 1-like	1045					cell differentiation|nervous system development|regulation of transcription, DNA-dependent	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(5)|central_nervous_system(1)	6	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.037)|all_epithelial(98;0.241)												0.447154	167.003792	167.303805	55	68	CC		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(76;0.169)|all cancers(51;0.244)	Missense_Mutation	SNP	1791894	1791894	10502	2	C	T	T	21	21	MYT1L	T	2	2
FAM82A1	151393	broad.mit.edu	36	2	38032690	38032690	+	Silent	SNP	A	T	T			TCGA-06-0745-01	TCGA-06-0745-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr2:38032690A>T	uc002rqn.1	+	c.828A>T	c.(826-828)CCA>CCT	p.P276P	FAM82A1_uc002rqk.1_Intron|FAM82A1_uc002rql.1_Intron|FAM82A1_uc002rqm.1_Intron	NM_144713	NP_653314	Q96LZ7	RMD2_HUMAN	family with sequence similarity 82, member A1	Error:Variant_position_missing_in_Q96LZ7_after_alignment						cytoplasm|integral to membrane|microtubule|spindle pole	binding			ovary(1)	1														0.410714	146.633044	147.412006	46	66	AA		KEEP	---	---	---	---	capture			Silent	SNP	38032690	38032690	5856	2	A	T	T	8	8	FAM82A1	T	4	4
FSTL1	11167	broad.mit.edu	36	3	121604778	121604778	+	Splice_Site_SNP	SNP	C	T	T			TCGA-06-0745-01	TCGA-06-0745-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr3:121604778C>T	uc003eds.1	-	c.694_splice	c.e8+1	p.K232_splice		NM_007085	NP_009016			follistatin-like 1 precursor						BMP signaling pathway	extracellular space	calcium ion binding|heparin binding			central_nervous_system(1)	1														0.381579	84.554504	85.490086	29	47	CC		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(114;0.189)	Splice_Site_SNP	SNP	121604778	121604778	6328	3	C	T	T	20	20	FSTL1	T	5	2
GRIP2	80852	broad.mit.edu	36	3	14512988	14512988	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0745-01	TCGA-06-0745-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:14512988G>C	uc003byt.1	-	c.3058C>G	c.(3058-3060)CGA>GGA	p.R1020G	GRIP2_uc003bys.1_Missense_Mutation_p.R551G|GRIP2_uc010heh.1_Non-coding_Transcript	NM_001080423	NP_001073892	Q9C0E4	GRIP2_HUMAN	glutamate receptor interacting protein 2	922					synaptic transmission	cytosol|plasma membrane	protein binding			pancreas(1)	1														0.190476	6.987683	8.869431	4	17	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	14512988	14512988	7067	3	G	C	C	40	40	GRIP2	C	3	3
OR5K4	403278	broad.mit.edu	36	3	99555548	99555548	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0745-01	TCGA-06-0745-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:99555548G>A	uc003dsk.1	+	c.161G>A	c.(160-162)CGT>CAT	p.R54H		NM_001005517	NP_001005517	A6NMS3	OR5K4_HUMAN	olfactory receptor, family 5, subfamily K,	54	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			central_nervous_system(1)	1														0.644195	553.262433	558.153945	172	95	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	99555548	99555548	11579	3	G	A	A	40	40	OR5K4	A	1	1
SOD3	6649	broad.mit.edu	36	4	24410702	24410702	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0745-01	TCGA-06-0745-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr4:24410702G>C	uc003gqz.1	+	c.461G>C	c.(460-462)GGC>GCC	p.G154A	SOD3_uc003gqy.1_Non-coding_Transcript|SOD3_uc010ies.1_Missense_Mutation_p.G154A	NM_003102	NP_003093	P08294	SODE_HUMAN	superoxide dismutase 3, extracellular precursor	154					oxidation-reduction process|removal of superoxide radicals	extracellular space|mitochondrion|soluble fraction	copper ion binding|heparin binding|protein binding|superoxide dismutase activity|zinc ion binding				0		Breast(46;0.0503)												0.444444	8.793308	8.818078	4	5	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	24410702	24410702	15422	4	G	C	C	42	42	SOD3	C	3	3
CSN1S1	1446	broad.mit.edu	36	4	70845234	70845234	+	Silent	SNP	T	C	C			TCGA-06-0745-01	TCGA-06-0745-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr4:70845234T>C	uc003hep.1	+	c.480T>C	c.(478-480)CCT>CCC	p.P160P	CSN1S1_uc003heq.1_Silent_p.P151P|CSN1S1_uc003her.1_Silent_p.P152P	NM_001890	NP_001881	P47710	CASA1_HUMAN	casein alpha s1 isoform 1	160						extracellular region	protein binding|transporter activity				0														0.446494	408.336613	409.012655	121	150	TT		KEEP	---	---	---	---	capture			Silent	SNP	70845234	70845234	4088	4	T	C	C	56	56	CSN1S1	C	4	4
SEC31A	22872	broad.mit.edu	36	4	84004682	84004682	+	Nonsense_Mutation	SNP	G	A	A			TCGA-06-0745-01	TCGA-06-0745-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr4:84004682G>A	uc003hnf.1	-	c.1291C>T	c.(1291-1293)CAG>TAG	p.Q431*	SEC31A_uc003hng.1_Nonsense_Mutation_p.Q431*|SEC31A_uc003hnh.1_Nonsense_Mutation_p.Q431*|SEC31A_uc003hni.1_Nonsense_Mutation_p.Q431*|SEC31A_uc003hnj.1_Nonsense_Mutation_p.Q431*|SEC31A_uc003hnk.1_Nonsense_Mutation_p.Q431*|SEC31A_uc003hnl.1_Nonsense_Mutation_p.Q431*|SEC31A_uc003hnm.1_Nonsense_Mutation_p.Q431*|SEC31A_uc003hnn.1_Nonsense_Mutation_p.Q431*|SEC31A_uc003hno.2_Nonsense_Mutation_p.Q431*|SEC31A_uc003hne.1_Nonsense_Mutation_p.Q203*	NM_001077207	NP_055748	O94979	SC31A_HUMAN	SEC31 homolog A isoform 1	431	Interaction with SEC13.				COPII vesicle coating|post-translational protein modification|protein N-linked glycosylation via asparagine|protein transport|response to calcium ion	COPII vesicle coat|cytosol|endoplasmic reticulum membrane|perinuclear region of cytoplasm	calcium-dependent protein binding		SEC31A/JAK2(4)|SEC31A/ALK(3)	haematopoietic_and_lymphoid_tissue(4)|soft_tissue(3)|breast(1)	8		Hepatocellular(203;0.114)												0.356164	69.92584	71.257898	26	47	GG		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	84004682	84004682	14484	4	G	A	A	45	45	SEC31A	A	5	2
PCDHB3	56132	broad.mit.edu	36	5	140461816	140461816	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0745-01	TCGA-06-0745-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:140461816G>A	uc003lio.1	+	c.1399G>A	c.(1399-1401)GCC>ACC	p.A467T		NM_018937	NP_061760	Q9Y5E6	PCDB3_HUMAN	protocadherin beta 3 precursor	467	Extracellular (Potential).|Cadherin 5.				calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission	integral to plasma membrane	calcium ion binding			ovary(1)|pancreas(1)	2														0.436364	268.245185	269.024289	96	124	GG		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)		Missense_Mutation	SNP	140461816	140461816	11963	5	G	A	A	38	38	PCDHB3	A	1	1
PCDHB13	56123	broad.mit.edu	36	5	140575783	140575783	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0745-01	TCGA-06-0745-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:140575783C>T	uc003lja.1	+	c.1904C>T	c.(1903-1905)GCG>GTG	p.A635V		NM_018933	NP_061756	Q9Y5F0	PCDBD_HUMAN	protocadherin beta 13 precursor	635	Cadherin 6.|Extracellular (Potential).				calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission	integral to membrane|plasma membrane	calcium ion binding			ovary(1)	1														0.349206	112.784738	115.302316	44	82	CC		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)		Missense_Mutation	SNP	140575783	140575783	11958	5	C	T	T	27	27	PCDHB13	T	1	1
MAST4	375449	broad.mit.edu	36	5	66452656	66452656	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0745-01	TCGA-06-0745-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:66452656C>T	uc003jut.1	+	c.1148C>T	c.(1147-1149)ACG>ATG	p.T383M	MAST4_uc003juu.1_Missense_Mutation_p.T393M|MAST4_uc003juv.1_Missense_Mutation_p.T378M	NM_015183	NP_055998	O15021	MAST4_HUMAN	microtubule associated serine/threonine kinase	575	Protein kinase.				protein phosphorylation	cytoplasm	ATP binding|magnesium ion binding|protein serine/threonine kinase activity			lung(6)|ovary(2)|kidney(2)|breast(2)|central_nervous_system(1)	13		Lung NSC(167;8.56e-06)|Prostate(74;0.00637)|Ovarian(174;0.0563)|Breast(144;0.0586)|Colorectal(97;0.245)								805				0.4375	20.622935	20.677345	7	9	CC		KEEP	---	---	---	---	capture		Lung(70;0.011)	Missense_Mutation	SNP	66452656	66452656	9711	5	C	T	T	19	19	MAST4	T	1	1
GPR98	84059	broad.mit.edu	36	5	90017406	90017406	+	Missense_Mutation	SNP	A	G	G			TCGA-06-0745-01	TCGA-06-0745-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr5:90017406A>G	uc003kju.1	+	c.6328A>G	c.(6328-6330)ATC>GTC	p.I2110V	GPR98_uc003kjt.1_5'UTR	NM_032119	NP_115495	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98 precursor	2110	Extracellular (Potential).				cell communication|cell-cell adhesion|maintenance of organ identity|neuropeptide signaling pathway|photoreceptor cell maintenance	cell surface|cytoplasm|integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity			ovary(11)|central_nervous_system(3)|pancreas(2)	16		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)												0.426471	96.145957	96.469563	29	39	AA		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)	Missense_Mutation	SNP	90017406	90017406	6997	5	A	G	G	16	16	GPR98	G	4	4
SNX9	51429	broad.mit.edu	36	6	158262561	158262561	+	Missense_Mutation	SNP	A	T	T			TCGA-06-0745-01	TCGA-06-0745-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr6:158262561A>T	uc003qqv.1	+	c.960A>T	c.(958-960)GAA>GAT	p.E320D		NM_016224	NP_057308	Q9Y5X1	SNX9_HUMAN	sorting nexin 9	320	PX.				cell communication|intracellular protein transport|lipid tube assembly|positive regulation of GTPase activity|positive regulation of protein oligomerization|receptor-mediated endocytosis	clathrin-coated vesicle|cytoplasmic vesicle membrane|extrinsic to internal side of plasma membrane|ruffle|trans-Golgi network	1-phosphatidylinositol binding|protein homodimerization activity|ubiquitin protein ligase binding				0		Breast(66;0.000776)|Ovarian(120;0.0303)|Prostate(117;0.167)												0.422222	113.53413	114.009365	38	52	AA		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(65;8.06e-18)|BRCA - Breast invasive adenocarcinoma(81;4.48e-05)	Missense_Mutation	SNP	158262561	158262561	15409	6	A	T	T	3	3	SNX9	T	4	4
DLD	1738	broad.mit.edu	36	7	107344997	107344997	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0745-01	TCGA-06-0745-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:107344997C>T	uc003vet.1	+	c.1090C>T	c.(1090-1092)CAC>TAC	p.H364Y		NM_000108	NP_000099	P09622	DLDH_HUMAN	dihydrolipoamide dehydrogenase precursor	364	FAD.				branched chain family amino acid catabolic process|cell redox homeostasis|lysine catabolic process|regulation of acetyl-CoA biosynthetic process from pyruvate|tricarboxylic acid cycle	mitochondrial matrix	dihydrolipoyl dehydrogenase activity			central_nervous_system(1)	1					NADH(DB00157)									0.235294	82.729027	92.530257	36	117	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	107344997	107344997	4731	7	C	T	T	29	29	DLD	T	2	2
TFEC	22797	broad.mit.edu	36	7	115369261	115369261	+	Silent	SNP	T	C	C			TCGA-06-0745-01	TCGA-06-0745-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr7:115369261T>C	uc003vhj.1	-	c.585A>G	c.(583-585)GAA>GAG	p.E195E	TFEC_uc003vhk.1_Silent_p.E166E|TFEC_uc003vhl.2_Silent_p.E166E	NM_012252	NP_036384	O14948	TFEC_HUMAN	transcription factor EC isoform a	195					regulation of transcription, DNA-dependent	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription corepressor activity|transcription regulator activity			large_intestine(1)	1														0.118557	23.852613	51.698963	23	171	TT		KEEP	---	---	---	---	capture	STAD - Stomach adenocarcinoma(10;0.00878)		Silent	SNP	115369261	115369261	16330	7	T	C	C	60	60	TFEC	C	4	4
FTSJ2	29960	broad.mit.edu	36	7	2248324	2248324	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0745-01	TCGA-06-0745-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:2248324C>T	uc003slm.1	-	c.7G>A	c.(7-9)GGG>AGG	p.G3R	FTSJ2_uc003slk.1_5'UTR|FTSJ2_uc003sll.1_5'UTR|FTSJ2_uc003sln.1_Non-coding_Transcript|FTSJ2_uc003slo.1_5'UTR|NUDT1_uc003slp.1_5'Flank|NUDT1_uc003slq.1_5'Flank|NUDT1_uc003slr.1_5'Flank|NUDT1_uc003sls.1_5'Flank|NUDT1_uc003slt.1_5'Flank|NUDT1_uc003slu.1_5'Flank|NUDT1_uc003slv.1_5'Flank	NM_013393	NP_037525	Q9UI43	RRMJ2_HUMAN	FtsJ homolog 2	3					cell proliferation	mitochondrion|nucleolus	nucleic acid binding|rRNA (uridine-2'-O-)-methyltransferase activity			ovary(1)	1		Ovarian(82;0.0253)												0.285714	20.485917	21.641583	8	20	CC		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (27;0.0822)|OV - Ovarian serous cystadenocarcinoma(56;2.7e-14)	Missense_Mutation	SNP	2248324	2248324	6339	7	C	T	T	22	22	FTSJ2	T	2	2
PKD1L1	168507	broad.mit.edu	36	7	47904153	47904153	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0745-01	TCGA-06-0745-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:47904153G>C	uc003tny.1	-	c.2228C>G	c.(2227-2229)CCG>CGG	p.P743R		NM_138295	NP_612152	Q8TDX9	PK1L1_HUMAN	polycystin-1L1	743	Extracellular (Potential).|REJ.				cell-cell adhesion	integral to membrane				ovary(7)|breast(1)	8														0.2	7.062886	10.634347	8	32	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	47904153	47904153	12388	7	G	C	C	39	39	PKD1L1	C	3	3
COL28A1	340267	broad.mit.edu	36	7	7379407	7379407	+	Silent	SNP	G	A	A			TCGA-06-0745-01	TCGA-06-0745-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:7379407G>A	uc003src.1	-	c.2655C>T	c.(2653-2655)AAC>AAT	p.N885N		NM_001037763	NP_001032852	Q2UY09	COSA1_HUMAN	collagen, type XXVIII precursor	885	VWFA 2.				cell adhesion	basement membrane|collagen	serine-type endopeptidase inhibitor activity				0		Ovarian(82;0.0789)												0.248447	98.427041	107.690744	40	121	GG		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (126;0.228)	Silent	SNP	7379407	7379407	3824	7	G	A	A	40	40	COL28A1	A	1	1
FAM135B	51059	broad.mit.edu	36	8	139233393	139233393	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0745-01	TCGA-06-0745-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr8:139233393G>C	uc003yuy.1	-	c.2507C>G	c.(2506-2508)GCT>GGT	p.A836G	FAM135B_uc003yux.1_Missense_Mutation_p.A737G|FAM135B_uc003yuz.1_Non-coding_Transcript|FAM135B_uc003yva.2_Missense_Mutation_p.A398G|FAM135B_uc003yvb.2_Missense_Mutation_p.A398G	NM_015912	NP_056996	Q49AJ0	F135B_HUMAN	hypothetical protein LOC51059	836										ovary(7)	7	all_epithelial(106;8.29e-14)|Lung NSC(106;6.88e-06)|all_lung(105;1.44e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)													0.413462	140.412747	141.091077	43	61	GG		KEEP	---	---	---	---	capture	BRCA - Breast invasive adenocarcinoma(115;0.0805)		Missense_Mutation	SNP	139233393	139233393	5646	8	G	C	C	34	34	FAM135B	C	3	3
MYOM2	9172	broad.mit.edu	36	8	2080287	2080287	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0745-01	TCGA-06-0745-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr8:2080287C>T	uc003wpx.2	+	c.4373C>T	c.(4372-4374)GCG>GTG	p.A1458V		NM_003970	NP_003961	P54296	MYOM2_HUMAN	myomesin 2	1458					muscle contraction	myosin filament	structural constituent of muscle			ovary(4)|central_nervous_system(1)	5		Ovarian(12;0.0572)|Colorectal(14;0.0844)|Hepatocellular(245;0.217)												0.182927	29.497002	37.221218	15	67	CC		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(11;1.85e-05)|Colorectal(4;0.0101)|READ - Rectum adenocarcinoma(4;0.148)|COAD - Colon adenocarcinoma(4;0.179)	Missense_Mutation	SNP	2080287	2080287	10487	8	C	T	T	27	27	MYOM2	T	1	1
NEFL	4747	broad.mit.edu	36	8	24867160	24867160	+	Nonsense_Mutation	SNP	G	T	T			TCGA-06-0745-01	TCGA-06-0745-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr8:24867160G>T	uc003xee.1	-	c.1236C>A	c.(1234-1236)TAC>TAA	p.Y412*		NM_006158	NP_006149	P07196	NFL_HUMAN	neurofilament, light polypeptide 68kDa	412	Tail.|Tail, subdomain A.				anterograde axon cargo transport|axon transport of mitochondrion|neurofilament bundle assembly|retrograde axon cargo transport|synaptic transmission	cytosol|neurofilament	identical protein binding|protein C-terminus binding|structural constituent of cytoskeleton			ovary(1)|central_nervous_system(1)	2		Ovarian(32;0.00965)|Prostate(55;0.157)												0.15	6.820022	11.451345	6	34	GG		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (27;0.0197)|Epithelial(17;2.44e-10)|Colorectal(74;0.0108)|COAD - Colon adenocarcinoma(73;0.0375)	Nonsense_Mutation	SNP	24867160	24867160	10714	8	G	T	T	36	36	NEFL	T	5	3
DOCK5	80005	broad.mit.edu	36	8	25255176	25255176	+	Missense_Mutation	SNP	C	A	A			TCGA-06-0745-01	TCGA-06-0745-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr8:25255176C>A	uc003xeg.1	+	c.2444C>A	c.(2443-2445)GCA>GAA	p.A815E	DOCK5_uc010luf.1_Non-coding_Transcript|DOCK5_uc003xei.1_Missense_Mutation_p.A385E|DOCK5_uc003xej.1_Non-coding_Transcript|DOCK5_uc003xeh.1_Missense_Mutation_p.A529E	NM_024940	NP_079216	Q9H7D0	DOCK5_HUMAN	dedicator of cytokinesis 5	815						cytoplasm	GTP binding|GTPase binding|guanyl-nucleotide exchange factor activity			ovary(3)	3		all_cancers(63;0.0361)|Ovarian(32;0.000711)|all_epithelial(46;0.0153)|Hepatocellular(4;0.115)|Prostate(55;0.13)|Breast(100;0.143)				Pancreas(145;34 1887 3271 10937 30165)								0.555556	15.575446	15.59955	5	4	CC		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (27;0.0267)|Epithelial(17;1.07e-11)|Colorectal(74;0.0276)|COAD - Colon adenocarcinoma(73;0.0828)	Missense_Mutation	SNP	25255176	25255176	4874	8	C	A	A	25	25	DOCK5	A	3	3
DUSP4	1846	broad.mit.edu	36	8	29263424	29263424	+	Missense_Mutation	SNP	C	A	A			TCGA-06-0745-01	TCGA-06-0745-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr8:29263424C>A	uc003xhm.1	-	c.291G>T	c.(289-291)TTG>TTT	p.L97F	DUSP4_uc003xhl.1_5'Flank	NM_001394	NP_001385	Q13115	DUS4_HUMAN	dual specificity phosphatase 4 isoform 1	97	Rhodanese.				endoderm formation|inactivation of MAPK activity|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	nucleoplasm	MAP kinase tyrosine/serine/threonine phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/threonine phosphatase activity				0														0.272727	6.719921	7.232425	3	8	CC		KEEP	---	---	---	---	capture		KIRC - Kidney renal clear cell carcinoma(542;0.094)|Kidney(114;0.113)	Missense_Mutation	SNP	29263424	29263424	5012	8	C	A	A	25	25	DUSP4	A	3	3
RB1CC1	9821	broad.mit.edu	36	8	53736101	53736101	+	Missense_Mutation	SNP	T	C	C			TCGA-06-0745-01	TCGA-06-0745-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr8:53736101T>C	uc003xre.2	-	c.1565A>G	c.(1564-1566)AAA>AGA	p.K522R	RB1CC1_uc003xrf.2_Missense_Mutation_p.K522R	NM_014781	NP_055596	Q8TDY2	RBCC1_HUMAN	Rb1-inducible coiled coil protein 1 isoform 1	522					autophagy|cell cycle|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytosol|nucleus|pre-autophagosomal structure|ULK1-ATG13-FIP200 complex	protein binding			ovary(8)|large_intestine(1)	9		all_cancers(86;0.137)|all_epithelial(80;0.00494)|Lung NSC(129;0.011)|all_lung(136;0.023)				GBM(180;1701 2102 13475 42023 52570)								0.22	30.999426	34.60776	11	39	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	53736101	53736101	13560	8	T	C	C	64	64	RB1CC1	C	4	4
C8orf34	116328	broad.mit.edu	36	8	69543606	69543606	+	Nonsense_Mutation	SNP	C	T	T			TCGA-06-0745-01	TCGA-06-0745-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr8:69543606C>T	uc010lyz.1	+	c.475C>T	c.(475-477)CGA>TGA	p.R159*	C8orf34_uc010lyy.1_Nonsense_Mutation_p.R159*|C8orf34_uc003xyb.1_Nonsense_Mutation_p.R134*	NM_052958	NP_443190	Q49A92	CH034_HUMAN	hypothetical protein LOC116328	159					signal transduction		cAMP-dependent protein kinase regulator activity			large_intestine(1)	1														0.466667	64.070672	64.11409	21	24	CC		KEEP	---	---	---	---	capture	Epithelial(68;0.0117)|OV - Ovarian serous cystadenocarcinoma(28;0.0227)|all cancers(69;0.0502)		Nonsense_Mutation	SNP	69543606	69543606	2532	8	C	T	T	31	31	C8orf34	T	5	1
QRFP	347148	broad.mit.edu	36	9	132758700	132758700	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0745-01	TCGA-06-0745-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr9:132758700G>A	uc004bzy.1	-	c.347C>T	c.(346-348)GCT>GTT	p.A116V		NM_198180	NP_937823	P83859	OX26_HUMAN	RF(Arg-Phe)amide family 26 amino acid peptide	116					locomotory behavior|neuropeptide signaling pathway|positive regulation of blood pressure|regulation of feeding behavior	extracellular region	neuropeptide hormone activity|orexigenic neuropeptide QRFP receptor binding				0	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)												0.447059	221.338549	221.758627	76	94	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(145;6.17e-05)|Epithelial(140;0.000267)	Missense_Mutation	SNP	132758700	132758700	13335	9	G	A	A	34	34	QRFP	A	2	2
FAM120A	23196	broad.mit.edu	36	9	95334266	95334266	+	Silent	SNP	C	A	A			TCGA-06-0745-01	TCGA-06-0745-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr9:95334266C>A	uc004atw.1	+	c.1743C>A	c.(1741-1743)ATC>ATA	p.I581I	FAM120A_uc004atx.2_Silent_p.I363I|FAM120A_uc004aty.1_Silent_p.I362I|FAM120A_uc004atz.1_Silent_p.I230I|FAM120A_uc010mrg.1_5'UTR	NM_014612	NP_055427	Q9NZB2	F120A_HUMAN	hypothetical protein LOC23196	581						cytoplasm|plasma membrane	RNA binding				0														0.252174	66.310813	72.734274	29	86	CC		KEEP	---	---	---	---	capture			Silent	SNP	95334266	95334266	5612	9	C	A	A	29	29	FAM120A	A	3	3
CTAG2	30848	broad.mit.edu	36	X	153534870	153534870	+	Silent	SNP	A	C	C			TCGA-06-0745-01	TCGA-06-0745-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chrX:153534870A>C	uc004fmi.1	-	c.114T>G	c.(112-114)GGT>GGG	p.G38G	CTAG2_uc004fmh.1_Silent_p.G38G	NM_020994	NP_066274	O75638	CTAG2_HUMAN	cancer/testis antigen 2 isoform LAGE-1b	38	Gly-rich.					centrosome				pancreas(1)	1	all_cancers(53;5.05e-16)|all_epithelial(53;1.87e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)													0.4	7.592831	7.681392	4	6	AA		KEEP	---	---	---	---	capture			Silent	SNP	153534870	153534870	4150	23	A	C	C	6	6	CTAG2	C	4	4
MXRA5	25878	broad.mit.edu	36	X	3249887	3249887	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0745-01	TCGA-06-0745-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:3249887C>T	uc004crg.2	-	c.3839G>A	c.(3838-3840)AGA>AAA	p.R1280K		NM_015419	NP_056234	Q9NR99	MXRA5_HUMAN	adlican	1280						extracellular region				ovary(5)|lung(1)|central_nervous_system(1)	7		all_lung(23;0.00031)|Lung NSC(23;0.000946)												0.769231	275.151729	282.057239	80	24	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	3249887	3249887	10397	23	C	T	T	32	32	MXRA5	T	2	2
CHM	1121	broad.mit.edu	36	X	85105395	85105395	+	Missense_Mutation	SNP	C	A	A			TCGA-06-0745-01	TCGA-06-0745-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:85105395C>A	uc004eet.1	-	c.633G>T	c.(631-633)AAG>AAT	p.K211N		NM_000390	NP_000381	P24386	RAE1_HUMAN	choroideremia isoform a	211					intracellular protein transport|protein geranylgeranylation|response to stimulus|visual perception	Rab-protein geranylgeranyltransferase complex	GTPase activator activity|Rab geranylgeranyltransferase activity			ovary(1)	1		all_lung(315;5.41e-06)												0.840426	244.021784	254.368676	79	15	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	85105395	85105395	3484	23	C	A	A	32	32	CHM	A	3	3
PCDH11X	27328	broad.mit.edu	36	X	90977387	90977387	+	Silent	SNP	A	T	T			TCGA-06-0745-01	TCGA-06-0745-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chrX:90977387A>T	uc004efk.1	+	c.228A>T	c.(226-228)CGA>CGT	p.R76R	PCDH11X_uc004efl.1_Silent_p.R76R|PCDH11X_uc004efn.1_Silent_p.R76R|PCDH11X_uc004efo.1_Silent_p.R76R|PCDH11X_uc010nmv.1_Silent_p.R76R|PCDH11X_uc004efm.1_Silent_p.R76R|PCDH11X_uc004efi.2_Silent_p.R105R|PCDH11X_uc004efh.1_Silent_p.R76R|PCDH11X_uc004efj.1_Silent_p.R76R	NM_032968	NP_116750	Q9BZA7	PC11X_HUMAN	protocadherin 11 X-linked isoform c	76	Extracellular (Potential).|Cadherin 1.				homophilic cell adhesion	integral to plasma membrane	calcium ion binding			large_intestine(2)	2						NSCLC(38;925 1092 2571 38200 45895)								0.786885	305.355041	314.629163	96	26	AA		KEEP	---	---	---	---	capture			Silent	SNP	90977387	90977387	11928	23	A	T	T	9	9	PCDH11X	T	4	4
ATE1	11101	broad.mit.edu	36	10	123673769	123673769	+	Splice_Site_Del	DEL	A	-	-			TCGA-06-0745-01	TCGA-06-0745-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:123673769_123673769delA	uc001lfp.1	-	c.e2_splice_site			ATE1_uc001lfq.1_Splice_Site_Del|ATE1_uc001lfr.1_Splice_Site_Del|ATE1_uc009xzu.1_Intron	NM_007041	NP_008972			arginyltransferase 1 isoform 2						protein arginylation	cytoplasm|nucleus	acyltransferase activity|arginyltransferase activity				0		all_neural(114;0.061)|Lung NSC(174;0.095)|all_lung(145;0.124)|Breast(234;0.212)												0.69			51	23				---	---	---	---	capture_indel			Splice_Site_Del	DEL	123673769	123673769	1097	10	A	-	-	14	14	ATE1	-	5	5
MICALCL	84953	broad.mit.edu	36	11	12272960	12272965	+	In_Frame_Del	DEL	CTCCTA	-	-			TCGA-06-0745-01	TCGA-06-0745-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:12272960_12272965delCTCCTA	uc001mkg.1	+	c.1406_1411delCTCCTA	c.(1405-1413)CCTCCTACA>CCA	p.PT470del		NM_032867	NP_116256	Q6ZW33	MICLK_HUMAN	MICAL C-terminal like	470_471					cell differentiation|multicellular organismal development|spermatogenesis	cytoplasm	mitogen-activated protein kinase binding				0				Epithelial(150;0.00177)										0.32			7	15				---	---	---	---	capture_indel			In_Frame_Del	DEL	12272960	12272965	9962	11	CTCCTA	-	-	24	24	MICALCL	-	5	5
ZNF598	90850	broad.mit.edu	36	16	1989883	1989884	+	In_Frame_Ins	INS	-	TCC	TCC			TCGA-06-0745-01	TCGA-06-0745-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:1989883_1989884insTCC	uc002cof.1	-	c.1667_1668insGGA	c.(1666-1668)GAC>GAGGAC	p.555_556insE	ZNF598_uc002coe.1_5'UTR	NM_178167	NP_835461	Q86UK7	ZN598_HUMAN	zinc finger protein 598	555_556						intracellular	zinc ion binding				0														0.43			6	8				---	---	---	---	capture_indel			In_Frame_Ins	INS	1989883	1989884	18623	16	-	TCC	TCC	40	40	ZNF598	TCC	5	5
BCL2	596	broad.mit.edu	36	18	59136774	59136776	+	In_Frame_Del	DEL	CCA	-	-			TCGA-06-0745-01	TCGA-06-0745-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:59136774_59136776delCCA	uc002lit.1	-	c.104_106delTGG	c.(103-108)GTGGGC>GGC	p.V35del	BCL2_uc002liu.1_In_Frame_Del_p.V35del|BCL2_uc002liv.1_In_Frame_Del_p.V35del	NM_000633	NP_000624	P10415	BCL2_HUMAN	B-cell lymphoma protein 2 alpha isoform	35		Cleavage; by caspase-3.			activation of pro-apoptotic gene products|anti-apoptosis|apoptosis in response to endoplasmic reticulum stress|B cell proliferation|B cell receptor signaling pathway|defense response to virus|female pregnancy|humoral immune response|induction of apoptosis by intracellular signals|negative regulation of cellular pH reduction|negative regulation of mitochondrial depolarization|negative regulation of neuron apoptosis|neuron apoptosis|positive regulation of B cell proliferation|positive regulation of cell growth|protein polyubiquitination|regulation of mitochondrial membrane permeability|regulation of mitochondrial membrane potential|regulation of protein heterodimerization activity|regulation of protein homodimerization activity|regulation of transmembrane transporter activity|release of cytochrome c from mitochondria|response to cytokine stimulus|response to DNA damage stimulus|response to drug|response to iron ion|response to nicotine|response to toxin	endoplasmic reticulum membrane|mitochondrial outer membrane|nuclear membrane|pore complex	BH3 domain binding|channel activity|protease binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding|transcription activator activity			central_nervous_system(1)	1		all_hematologic(56;1.18e-20)|Prostate(75;0.0872)		Lung(128;0.0234)|READ - Rectum adenocarcinoma(59;0.0935)	Docetaxel(DB01248)|Fludarabine(DB01073)|Melatonin(DB01065)|Paclitaxel(DB01229)|Rasagiline(DB01367)					37				0.32			35	75				---	---	---	---	capture_indel			In_Frame_Del	DEL	59136774	59136776	1386	18	CCA	-	-	22	22	BCL2	-	5	5
NUMBL	9253	broad.mit.edu	36	19	45865706	45865708	+	In_Frame_Del	DEL	TGC	-	-			TCGA-06-0745-01	TCGA-06-0745-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:45865706_45865708delTGC	uc002oon.1	-	c.1335_1337delGCA	c.(1333-1338)CAGCAA>CAA	p.445_446QQ>Q	NUMBL_uc002ooo.1_In_Frame_Del_p.444_445QQ>Q	NM_004756	NP_004747	Q9Y6R0	NUMBL_HUMAN	numb homolog (Drosophila)-like	445_446	Poly-Gln.				cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process	cytoplasm	protein binding			ovary(1)	1			Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105)											0.40			4	6				---	---	---	---	capture_indel			In_Frame_Del	DEL	45865706	45865708	11157	19	TGC	-	-	63	63	NUMBL	-	5	5
