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
MMP13	4322	broad.mit.edu	36	11	102330460	102330460	+	Missense_Mutation	SNP	G	A	A			TCGA-12-0688-01	TCGA-12-0688-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:102330460G>A	uc001phl.1	-	c.448C>T	c.(448-450)CCT>TCT	p.P150S		NM_002427	NP_002418	P45452	MMP13_HUMAN	matrix metalloproteinase 13 preproprotein	150					collagen catabolic process|proteolysis	extracellular space	metalloendopeptidase activity|zinc ion binding			ovary(2)	2		all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)												0.41	121.569997	122.273084	41	59	GG		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(274;0.0144)	Missense_Mutation	SNP	102330460	102330460	10042	11	G	A	A	41	41	MMP13	A	2	2
MUC2	4583	broad.mit.edu	36	11	1083324	1083324	+	Missense_Mutation	SNP	G	A	A			TCGA-12-0688-01	TCGA-12-0688-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:1083324G>A	uc001lsx.1	+	c.12229G>A	c.(12229-12231)GGC>AGC	p.G4077S		NM_002457	NP_002448	Q02817	MUC2_HUMAN	mucin 2 precursor	4077				TGTQTPTT -> NGLQAPTP (in Ref. 4).		inner mucus layer|outer mucus layer	protein binding			lung(1)|breast(1)	2		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)			Pranlukast(DB01411)									0.16	7.390076	10.137157	4	21	GG		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Missense_Mutation	SNP	1083324	1083324	10369	11	G	A	A	39	39	MUC2	A	1	1
BRSK2	9024	broad.mit.edu	36	11	1389377	1389377	+	Missense_Mutation	SNP	T	C	C			TCGA-12-0688-01	TCGA-12-0688-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr11:1389377T>C	uc001ltm.2	+	c.167T>C	c.(166-168)CTC>CCC	p.L56P	BRSK2_uc009ycv.1_Intron|BRSK2_uc001lth.1_Intron|BRSK2_uc001lti.2_Intron|BRSK2_uc001ltj.1_Intron|BRSK2_uc001ltk.1_Intron|BRSK2_uc001ltl.1_Intron	NM_003957	NP_003948	Q8IWQ3	BRSK2_HUMAN	BR serine/threonine kinase 2	21	Protein kinase.				establishment of cell polarity|neuron differentiation|protein phosphorylation		ATP binding|magnesium ion binding|protein serine/threonine kinase activity				0		all_epithelial(84;4.17e-05)|Breast(177;0.000307)|Ovarian(85;0.0014)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)								1394				0.545455	13.739771	13.758637	6	5	TT		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(625;0.00144)|Lung(200;0.0713)|LUSC - Lung squamous cell carcinoma(625;0.0842)	Missense_Mutation	SNP	1389377	1389377	1555	11	T	C	C	54	54	BRSK2	C	4	4
MS4A3	932	broad.mit.edu	36	11	59585312	59585312	+	Missense_Mutation	SNP	C	A	A			TCGA-12-0688-01	TCGA-12-0688-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:59585312C>A	uc001nom.1	+	c.103C>A	c.(103-105)CAG>AAG	p.Q35K	MS4A3_uc001non.1_Missense_Mutation_p.Q35K|MS4A3_uc001noo.1_Intron	NM_006138	NP_006129	Q96HJ5	MS4A3_HUMAN	membrane-spanning 4-domains, subfamily A, member	35	Cytoplasmic (Potential).			Q -> H (in Ref. 1; AAA62319).		endomembrane system|integral to membrane|perinuclear region of cytoplasm	protein binding|receptor activity			ovary(2)	2		all_epithelial(135;0.245)												0.398496	153.242788	154.44297	53	80	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	59585312	59585312	10254	11	C	A	A	21	21	MS4A3	A	3	3
GPRC5A	9052	broad.mit.edu	36	12	12952666	12952666	+	Silent	SNP	C	T	T			TCGA-12-0688-01	TCGA-12-0688-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:12952666C>T	uc001rba.1	+	c.216C>T	c.(214-216)CTC>CTT	p.L72L	GPRC5A_uc001raz.1_Silent_p.L72L	NM_003979	NP_003970	Q8NFJ5	RAI3_HUMAN	G protein-coupled receptor, family C, group 5,	72	Helical; Name=2; (Potential).					cytoplasmic vesicle membrane|Golgi apparatus|integral to plasma membrane	G-protein coupled receptor activity				0		Prostate(47;0.141)			Tretinoin(DB00755)									0.406667	353.069571	355.358711	122	178	CC		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(232;0.0708)	Silent	SNP	12952666	12952666	7000	12	C	T	T	30	30	GPRC5A	T	2	2
ATF7IP	55729	broad.mit.edu	36	12	14491234	14491234	+	Missense_Mutation	SNP	G	T	T			TCGA-12-0688-01	TCGA-12-0688-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:14491234G>T	uc001rbw.1	+	c.1975G>T	c.(1975-1977)GAT>TAT	p.D659Y	ATF7IP_uc001rbu.2_Missense_Mutation_p.D659Y|ATF7IP_uc001rbv.1_Missense_Mutation_p.D658Y|ATF7IP_uc001rbx.1_Missense_Mutation_p.D658Y|ATF7IP_uc001rby.2_Missense_Mutation_p.D659Y|ATF7IP_uc001rca.1_Missense_Mutation_p.D659Y	NM_018179	NP_060649	Q6VMQ6	MCAF1_HUMAN	activating transcription factor 7 interacting	659	Interaction with SETDB1.|Potential.				DNA methylation|interspecies interaction between organisms|positive regulation of transcription, DNA-dependent|regulation of RNA polymerase II transcriptional preinitiation complex assembly|transcription, DNA-dependent		protein binding			lung(3)|ovary(1)|skin(1)	5														0.370968	62.00883	62.915716	23	39	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	14491234	14491234	1106	12	G	T	T	33	33	ATF7IP	T	3	3
RDH5	5959	broad.mit.edu	36	12	54404057	54404057	+	Silent	SNP	T	C	C			TCGA-12-0688-01	TCGA-12-0688-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr12:54404057T>C	uc001shk.1	+	c.690T>C	c.(688-690)CCT>CCC	p.P230P	RDH5_uc001shj.2_3'UTR|RDH5_uc001shl.1_Silent_p.P230P	NM_002905	NP_002896	Q92781	RDH1_HUMAN	retinol dehydrogenase 5 (11-cis and 9-cis)	230					oxidation-reduction process|response to stimulus|visual perception	membrane	binding|retinol dehydrogenase activity			ovary(1)	1					NADH(DB00157)|Vitamin A(DB00162)									0.263158	7.118272	9.245148	10	28	TT		KEEP	---	---	---	---	capture			Silent	SNP	54404057	54404057	13664	12	T	C	C	54	54	RDH5	C	4	4
SYNE2	23224	broad.mit.edu	36	14	63703851	63703851	+	Missense_Mutation	SNP	C	T	T			TCGA-12-0688-01	TCGA-12-0688-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr14:63703851C>T	uc001xgl.1	+	c.16753C>T	c.(16753-16755)CGC>TGC	p.R5585C	SYNE2_uc001xgm.1_Missense_Mutation_p.R5585C|SYNE2_uc010apy.1_Missense_Mutation_p.R1970C|SYNE2_uc001xgn.1_Missense_Mutation_p.R547C|SYNE2_uc001xgo.1_Non-coding_Transcript|SYNE2_uc010aqa.1_5'UTR|SYNE2_uc001xgq.1_5'Flank	NM_182914	NP_878918	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	5585	Cytoplasmic (Potential).				centrosome localization|cytoskeletal anchoring at nuclear membrane|nuclear migration along microfilament|positive regulation of cell migration	cytoskeleton|filopodium membrane|focal adhesion|integral to membrane|lamellipodium membrane|mitochondrial part|nuclear outer membrane|nucleoplasm|sarcoplasmic reticulum membrane|SUN-KASH complex|Z disc	actin binding|protein binding			ovary(8)|breast(4)|central_nervous_system(1)|pancreas(1)	14														0.398305	126.209782	127.240625	47	71	CC		KEEP	---	---	---	---	capture		all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)	Missense_Mutation	SNP	63703851	63703851	15967	14	C	T	T	27	27	SYNE2	T	1	1
WDR72	256764	broad.mit.edu	36	15	51676731	51676731	+	Silent	SNP	C	T	T			TCGA-12-0688-01	TCGA-12-0688-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr15:51676731C>T	uc002acj.2	-	c.2985G>A	c.(2983-2985)GCG>GCA	p.A995A		NM_182758	NP_877435	Q3MJ13	WDR72_HUMAN	WD repeat domain 72	995										lung(1)	1														0.379433	315.270981	318.861957	107	175	CC		KEEP	---	---	---	---	capture		all cancers(107;0.0511)	Silent	SNP	51676731	51676731	17895	15	C	T	T	23	23	WDR72	T	1	1
HYDIN	54768	broad.mit.edu	36	16	69495193	69495193	+	Silent	SNP	G	A	A			TCGA-12-0688-01	TCGA-12-0688-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:69495193G>A	uc002ezr.1	-	c.8682C>T	c.(8680-8682)AAC>AAT	p.N2894N	HYDIN_uc002ezs.1_Silent_p.N426N	NM_032821	NP_116210	Q4G0P3	HYDIN_HUMAN	hydrocephalus inducing isoform a	2895										ovary(1)	1		Ovarian(137;0.0654)												0.178571	39.439591	50.325868	20	92	GG		KEEP	---	---	---	---	capture			Silent	SNP	69495193	69495193	7767	16	G	A	A	40	40	HYDIN	A	1	1
HYDIN	54768	broad.mit.edu	36	16	69579349	69579349	+	Silent	SNP	C	T	T			TCGA-12-0688-01	TCGA-12-0688-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:69579349C>T	uc002ezr.1	-	c.4170G>A	c.(4168-4170)AAG>AAA	p.K1390K		NM_032821	NP_116210	Q4G0P3	HYDIN_HUMAN	hydrocephalus inducing isoform a	1391										ovary(1)	1		Ovarian(137;0.0654)												0.219355	82.856874	94.112636	34	121	CC		KEEP	---	---	---	---	capture			Silent	SNP	69579349	69579349	7767	16	C	T	T	24	24	HYDIN	T	2	2
GATA6	2627	broad.mit.edu	36	18	18016969	18016969	+	Missense_Mutation	SNP	T	A	A			TCGA-12-0688-01	TCGA-12-0688-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr18:18016969T>A	uc002ktt.1	+	c.1587T>A	c.(1585-1587)AAT>AAA	p.N529K	GATA6_uc002ktu.1_Missense_Mutation_p.N529K	NM_005257	NP_005248	Q92908	GATA6_HUMAN	GATA binding protein 6	529					blood coagulation|cardiac vascular smooth muscle cell differentiation|cellular response to hypoxia|gene-specific transcription from RNA polymerase II promoter|intestinal epithelial cell differentiation|male gonad development|negative regulation of apoptosis|negative regulation of gene-specific transcription from RNA polymerase II promoter|negative regulation of transforming growth factor-beta1 production|negative regulation of transforming growth factor-beta2 production|outflow tract septum morphogenesis|positive regulation of angiogenesis|positive regulation of cell cycle arrest|positive regulation of gene-specific transcription from RNA polymerase II promoter|response to drug|response to growth factor stimulus		promoter binding|protein binding|protein kinase binding|sequence-specific DNA binding transcription factor activity|transcription factor binding|transcription repressor activity|zinc ion binding			central_nervous_system(3)	3	all_cancers(21;0.00271)|all_epithelial(16;7.31e-05)|Ovarian(2;0.116)|Lung NSC(20;0.123)|all_lung(20;0.246)					Colon(8;48 282 46199 46856)|Melanoma(177;170 2725 12489 26999)								0.38961	83.443271	84.260989	30	47	TT		KEEP	---	---	---	---	capture	STAD - Stomach adenocarcinoma(5;0.106)		Missense_Mutation	SNP	18016969	18016969	6522	18	T	A	A	49	49	GATA6	A	4	4
CDH2	1000	broad.mit.edu	36	18	23845940	23845940	+	Silent	SNP	A	C	C			TCGA-12-0688-01	TCGA-12-0688-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr18:23845940A>C	uc002kwg.1	-	c.414T>G	c.(412-414)GTT>GTG	p.V138V		NM_001792	NP_001783	P19022	CADH2_HUMAN	cadherin 2, type 1 preproprotein	138					adherens junction organization|cell junction assembly|positive regulation of muscle cell differentiation	catenin complex|integral to membrane	alpha-catenin binding|beta-catenin binding|calcium ion binding|gamma-catenin binding			ovary(3)	3										264				0.415205	238.507785	239.578052	71	100	AA		KEEP	---	---	---	---	capture			Silent	SNP	23845940	23845940	3234	18	A	C	C	5	5	CDH2	C	4	4
RALBP1	10928	broad.mit.edu	36	18	9506893	9506893	+	Missense_Mutation	SNP	A	G	G			TCGA-12-0688-01	TCGA-12-0688-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr18:9506893A>G	uc002kob.1	+	c.295A>G	c.(295-297)AGT>GGT	p.S99G	RALBP1_uc002koc.1_Missense_Mutation_p.S99G	NM_006788	NP_006779	Q15311	RBP1_HUMAN	ralA binding protein 1	99					chemotaxis|positive regulation of Cdc42 GTPase activity|small GTPase mediated signal transduction|transport	cytosol|membrane	ATPase activity, coupled to movement of substances|Rac GTPase activator activity|Rac GTPase binding|Ral GTPase binding			central_nervous_system(1)	1										246				0.406504	164.927396	165.866839	50	73	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	9506893	9506893	13472	18	A	G	G	3	3	RALBP1	G	4	4
SBNO2	22904	broad.mit.edu	36	19	1064547	1064547	+	Missense_Mutation	SNP	T	C	C			TCGA-12-0688-01	TCGA-12-0688-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr19:1064547T>C	uc002lrk.2	-	c.2234A>G	c.(2233-2235)CAG>CGG	p.Q745R	SBNO2_uc002lrj.2_Missense_Mutation_p.Q688R|SBNO2_uc010dse.1_Missense_Mutation_p.Q728R	NM_014963	NP_055778	Q9Y2G9	SBNO2_HUMAN	strawberry notch homolog 2 isoform 1	745					macrophage activation involved in immune response|negative regulation of transcription, DNA-dependent|regulation of inflammatory response|transcription, DNA-dependent		transcription repressor activity				0		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;7.93e-06)|all_lung(49;1.25e-05)|Breast(49;0.000172)|Hepatocellular(1079;0.137)												0.358974	39.134988	39.819625	14	25	TT		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)	Missense_Mutation	SNP	1064547	1064547	14344	19	T	C	C	55	55	SBNO2	C	4	4
CYP4F12	66002	broad.mit.edu	36	19	15656890	15656890	+	Missense_Mutation	SNP	C	T	T			TCGA-12-0688-01	TCGA-12-0688-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:15656890C>T	uc002nbl.2	+	c.998C>T	c.(997-999)ACG>ATG	p.T333M		NM_023944	NP_076433	Q9HCS2	CP4FC_HUMAN	cytochrome P450, family 4, subfamily F,	333					oxidation-reduction process|xenobiotic metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	aromatase activity|electron carrier activity|heme binding|oxygen binding			ovary(2)|central_nervous_system(2)	4	Acute lymphoblastic leukemia(2;0.0367)													0.263158	55.525421	60.350935	25	70	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	15656890	15656890	4352	19	C	T	T	19	19	CYP4F12	T	1	1
ZNF554	115196	broad.mit.edu	36	19	2784912	2784912	+	Missense_Mutation	SNP	A	T	T			TCGA-12-0688-01	TCGA-12-0688-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr19:2784912A>T	uc002lwm.2	+	c.679A>T	c.(679-681)AAT>TAT	p.N227Y	ZNF554_uc002lwl.2_Missense_Mutation_p.N176Y	NM_001102651	NP_001096121	Q86TJ5	ZN554_HUMAN	zinc finger protein 554	227					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1		Hepatocellular(1079;0.137)												0.301255	183.913969	192.342157	72	167	AA		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)	Missense_Mutation	SNP	2784912	2784912	18580	19	A	T	T	13	13	ZNF554	T	4	4
FCGBP	8857	broad.mit.edu	36	19	45072145	45072145	+	Silent	SNP	G	A	A			TCGA-12-0688-01	TCGA-12-0688-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:45072145G>A	uc002omp.2	-	c.11010C>T	c.(11008-11010)TTC>TTT	p.F3670F		NM_003890	NP_003881	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	3670	VWFD 9.					extracellular region	protein binding			ovary(4)|central_nervous_system(1)	5	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)													0.207207	99.032547	116.666153	46	176	GG		KEEP	---	---	---	---	capture	Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)		Silent	SNP	45072145	45072145	6015	19	G	A	A	37	37	FCGBP	A	1	1
TPRX1	284355	broad.mit.edu	36	19	52997366	52997366	+	Silent	SNP	C	T	T			TCGA-12-0688-01	TCGA-12-0688-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:52997366C>T	uc002php.1	-	c.714G>A	c.(712-714)CCG>CCA	p.P238P		NM_198479	NP_940881	Q8N7U7	TPRX1_HUMAN	tetra-peptide repeat homeobox	238	Gly-rich.				regulation of transcription, DNA-dependent	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0		all_cancers(25;3.02e-09)|all_epithelial(76;7e-07)|all_lung(116;2.48e-06)|Lung NSC(112;5.15e-06)|Ovarian(192;0.0139)|all_neural(266;0.0146)|Breast(70;0.133)				Esophageal Squamous(123;175 2281 3051 32395)								0.5	30.450697	30.450697	10	10	CC		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(262;0.000241)|all cancers(93;0.00036)|Epithelial(262;0.0127)|GBM - Glioblastoma multiforme(486;0.048)	Silent	SNP	52997366	52997366	16966	19	C	T	T	31	31	TPRX1	T	1	1
MCOLN1	57192	broad.mit.edu	36	19	7497685	7497685	+	Silent	SNP	G	A	A			TCGA-12-0688-01	TCGA-12-0688-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:7497685G>A	uc002mgo.1	+	c.444G>A	c.(442-444)GCG>GCA	p.A148A	MCOLN1_uc002mgp.1_Missense_Mutation_p.R35H	NM_020533	NP_065394	Q9GZU1	MCLN1_HUMAN	mucolipin 1	148					calcium ion transport|cellular iron ion homeostasis|transferrin transport	integral to plasma membrane|late endosome membrane|lysosomal membrane	cation channel activity|iron ion transmembrane transporter activity			breast(1)	1														0.248521	101.008666	110.703974	42	127	GG		KEEP	---	---	---	---	capture			Silent	SNP	7497685	7497685	9784	19	G	A	A	40	40	MCOLN1	A	1	1
KIAA1543	57662	broad.mit.edu	36	19	7583309	7583309	+	Missense_Mutation	SNP	G	A	A			TCGA-12-0688-01	TCGA-12-0688-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:7583309G>A	uc002mgu.2	+	c.2011G>A	c.(2011-2013)GAA>AAA	p.E671K	KIAA1543_uc002mgv.2_Missense_Mutation_p.E644K|KIAA1543_uc002mgw.1_5'Flank	NM_001080429	NP_001073898	Q9P1Y5	CAMP3_HUMAN	hypothetical protein LOC57662 isoform 1	644					epithelial cell-cell adhesion|microtubule anchoring|regulation of microtubule cytoskeleton organization|zonula adherens maintenance	cytoplasm|microtubule|zonula adherens	microtubule minus-end binding			pancreas(1)	1														0.363636	7.418591	7.62957	4	7	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	7583309	7583309	8552	19	G	A	A	41	41	KIAA1543	A	2	2
IVL	3713	broad.mit.edu	36	1	151150568	151150568	+	Silent	SNP	A	C	C			TCGA-12-0688-01	TCGA-12-0688-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr1:151150568A>C	uc001fau.1	+	c.1671A>C	c.(1669-1671)CCA>CCC	p.P557P	IVL_uc009wns.1_Silent_p.P557P	NM_005547	NP_005538	P07476	INVO_HUMAN	involucrin	557					isopeptide cross-linking via N6-(L-isoglutamyl)-L-lysine|keratinization|response to UV-B	cornified envelope|cytoplasm	protein binding, bridging|structural molecule activity			ovary(3)	3	Lung NSC(65;3.97e-29)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)													0.361111	120.297996	122.130655	39	69	AA		KEEP	---	---	---	---	capture	LUSC - Lung squamous cell carcinoma(543;0.171)		Silent	SNP	151150568	151150568	8233	1	A	C	C	7	7	IVL	C	4	4
C1orf9	51430	broad.mit.edu	36	1	170787279	170787279	+	Missense_Mutation	SNP	C	T	T			TCGA-12-0688-01	TCGA-12-0688-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:170787279C>T	uc001giq.2	+	c.67C>T	c.(67-69)CCC>TCC	p.P23S	C1orf9_uc009wwd.1_Missense_Mutation_p.P23S	NM_014283	NP_055098	Q9UBS9	OSPT_HUMAN	chromosome 1 open reading frame 9 protein	23					multicellular organismal development|ossification	integral to membrane|rough endoplasmic reticulum membrane				ovary(2)	2		Breast(1374;0.212)				Colon(43;174 953 11768 38880 47057)								0.266667	9.700712	11.257178	8	22	CC		KEEP	---	---	---	---	capture		Colorectal(1306;3.98e-05)|KIRC - Kidney renal clear cell carcinoma(1967;0.00544)	Missense_Mutation	SNP	170787279	170787279	2143	1	C	T	T	30	30	C1orf9	T	2	2
PADI6	353238	broad.mit.edu	36	1	17572288	17572288	+	Silent	SNP	G	A	A			TCGA-12-0688-01	TCGA-12-0688-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:17572288G>A	uc001bak.1	+	c.267G>A	c.(265-267)TCG>TCA	p.S89S		NM_207421	NP_997304	Q6TGC4	PADI6_HUMAN	peptidylarginine deiminase type 6	81					peptidyl-citrulline biosynthetic process from peptidyl-arginine	cytoplasm|nucleus	calcium ion binding|protein-arginine deiminase activity			breast(1)	1		Colorectal(325;3.46e-05)|Breast(348;0.000162)|all_lung(284;0.000337)|Lung NSC(340;0.000419)|Renal(390;0.000518)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)			L-Citrulline(DB00155)									0.397849	91.56081	92.405085	37	56	GG		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (279;0.00488)|BRCA - Breast invasive adenocarcinoma(304;7.59e-06)|COAD - Colon adenocarcinoma(227;1.18e-05)|Kidney(64;0.000186)|KIRC - Kidney renal clear cell carcinoma(64;0.00272)|STAD - Stomach adenocarcinoma(196;0.0134)|READ - Rectum adenocarcinoma(331;0.0655)|Lung(427;0.189)	Silent	SNP	17572288	17572288	11797	1	G	A	A	38	38	PADI6	A	1	1
OR14I1	401994	broad.mit.edu	36	1	246911807	246911807	+	Missense_Mutation	SNP	T	C	C			TCGA-12-0688-01	TCGA-12-0688-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr1:246911807T>C	uc001ieu.1	-	c.422A>G	c.(421-423)CAG>CGG	p.Q141R		NM_001004734	NP_001004734	A6ND48	O14I1_HUMAN	olfactory receptor, family 14, subfamily I,	141	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0														0.3875	90.812478	91.697085	31	49	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	246911807	246911807	11353	1	T	C	C	55	55	OR14I1	C	4	4
TASP1	55617	broad.mit.edu	36	20	13457135	13457135	+	Missense_Mutation	SNP	G	C	C			TCGA-12-0688-01	TCGA-12-0688-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr20:13457135G>C	uc002woi.1	-	c.819C>G	c.(817-819)TGC>TGG	p.C273W	TASP1_uc002woh.1_Missense_Mutation_p.C250W	NM_017714	NP_060184	Q9H6P5	TASP1_HUMAN	taspase 1 precursor	273					asparagine catabolic process via L-aspartate|positive regulation of transcription, DNA-dependent|protein maturation		threonine-type endopeptidase activity				0														0.416667	11.068855	11.142252	5	7	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	13457135	13457135	16111	20	G	C	C	34	34	TASP1	C	3	3
RPN2	6185	broad.mit.edu	36	20	35269224	35269224	+	Silent	SNP	T	C	C			TCGA-12-0688-01	TCGA-12-0688-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr20:35269224T>C	uc002xgp.1	+	c.825T>C	c.(823-825)CCT>CCC	p.P275P	RPN2_uc002xgo.2_Silent_p.P275P|RPN2_uc010gfw.1_Silent_p.P118P|RPN2_uc002xgq.1_Silent_p.P243P	NM_002951	NP_002942	P04844	RPN2_HUMAN	ribophorin II isoform 1 precursor	275	Lumenal (Potential).				post-translational protein modification|protein N-linked glycosylation via asparagine	integral to membrane|nucleus|oligosaccharyltransferase complex	dolichyl-diphosphooligosaccharide-protein glycotransferase activity|protein binding			ovary(2)	2		Myeloproliferative disorder(115;0.00878)												0.243626	198.630063	219.749938	86	267	TT		KEEP	---	---	---	---	capture			Silent	SNP	35269224	35269224	14087	20	T	C	C	55	55	RPN2	C	4	4
SLC13A3	64849	broad.mit.edu	36	20	44628344	44628344	+	Silent	SNP	G	A	A			TCGA-12-0688-01	TCGA-12-0688-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr20:44628344G>A	uc002xsf.1	-	c.1425C>T	c.(1423-1425)ATC>ATT	p.I475I	SLC13A3_uc002xsg.1_Silent_p.I428I|SLC13A3_uc010gho.1_Silent_p.I393I|SLC13A3_uc002xse.1_5'Flank|SLC13A3_uc010ghm.1_Silent_p.I62I|SLC13A3_uc010ghn.1_Silent_p.I444I	NM_022829	NP_073740	Q8WWT9	S13A3_HUMAN	solute carrier family 13 member 3 isoform a	475	Helical; (Potential).					integral to membrane|plasma membrane	high affinity sodium:dicarboxylate symporter activity			ovary(1)	1		Myeloproliferative disorder(115;0.0122)			Succinic acid(DB00139)									0.29052	242.4567	255.343845	95	232	GG		KEEP	---	---	---	---	capture			Silent	SNP	44628344	44628344	14888	20	G	A	A	37	37	SLC13A3	A	1	1
KCNG1	3755	broad.mit.edu	36	20	49059640	49059640	+	Missense_Mutation	SNP	C	G	G			TCGA-12-0688-01	TCGA-12-0688-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr20:49059640C>G	uc002xwa.2	-	c.643G>C	c.(643-645)GAC>CAC	p.D215H	KCNG1_uc002xwb.2_Missense_Mutation_p.D215H	NM_002237	NP_002228	Q9UIX4	KCNG1_HUMAN	potassium voltage-gated channel, subfamily G,	215	Cytoplasmic (Potential).					voltage-gated potassium channel complex	voltage-gated potassium channel activity			ovary(1)|central_nervous_system(1)	2														0.175439	23.321986	28.977864	10	47	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	49059640	49059640	8332	20	C	G	G	31	31	KCNG1	G	3	3
COL6A2	1292	broad.mit.edu	36	21	46356847	46356847	+	Silent	SNP	C	T	T			TCGA-12-0688-01	TCGA-12-0688-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr21:46356847C>T	uc002zia.1	+	c.642C>T	c.(640-642)AAC>AAT	p.N214N	COL6A2_uc002zhy.1_Silent_p.N214N|COL6A2_uc002zhz.1_Silent_p.N214N|COL6A2_uc002zib.1_Intron	NM_001849	NP_001840	P12110	CO6A2_HUMAN	alpha 2 type VI collagen isoform 2C2 precursor	214	VWFA 1.|Nonhelical region.				axon guidance|cell-cell adhesion|extracellular matrix organization|protein heterotrimerization	collagen|extracellular space|protein complex	extracellular matrix structural constituent|protein binding, bridging			central_nervous_system(7)|ovary(1)	8	Breast(49;0.245)													0.322034	50.405574	52.064373	19	40	CC		KEEP	---	---	---	---	capture		Colorectal(79;0.0303)|READ - Rectum adenocarcinoma(84;0.0649)	Silent	SNP	46356847	46356847	3838	21	C	T	T	19	19	COL6A2	T	1	1
CHCHD10	400916	broad.mit.edu	36	22	22439640	22439640	+	Missense_Mutation	SNP	A	C	C			TCGA-12-0688-01	TCGA-12-0688-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr22:22439640A>C	uc002zxw.1	-	c.182T>G	c.(181-183)GTG>GGG	p.V61G		NM_213720	NP_998885	Q8WYQ3	CHC10_HUMAN	coiled-coil-helix-coiled-coil-helix domain	61						mitochondrion					0														0.384615	6.381903	6.561601	5	8	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	22439640	22439640	3449	22	A	C	C	6	6	CHCHD10	C	4	4
VRK2	7444	broad.mit.edu	36	2	58227012	58227012	+	Missense_Mutation	SNP	G	A	A			TCGA-12-0688-01	TCGA-12-0688-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:58227012G>A	uc002rzo.1	+	c.1081G>A	c.(1081-1083)GAA>AAA	p.E361K	VRK2_uc010fcb.1_Missense_Mutation_p.E361K|VRK2_uc002rzp.1_Missense_Mutation_p.E361K|VRK2_uc002rzq.1_Missense_Mutation_p.E361K|VRK2_uc002rzr.1_Missense_Mutation_p.E361K|VRK2_uc010fcc.1_Missense_Mutation_p.E243K|VRK2_uc002rzv.1_Missense_Mutation_p.E361K|VRK2_uc010fcd.1_Missense_Mutation_p.E338K|VRK2_uc002rzs.1_Missense_Mutation_p.E361K|VRK2_uc002rzt.1_Missense_Mutation_p.E243K|VRK2_uc002rzu.1_Missense_Mutation_p.E361K	NM_006296	NP_006287	Q86Y07	VRK2_HUMAN	vaccinia related kinase 2 isoform 1	361					protein phosphorylation	integral to membrane	ATP binding|protein binding|protein serine/threonine kinase activity			ovary(1)	1										181				0.333333	59.157809	60.705745	21	42	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	58227012	58227012	17787	2	G	A	A	37	37	VRK2	A	1	1
WDR92	116143	broad.mit.edu	36	2	68215410	68215410	+	Missense_Mutation	SNP	A	C	C			TCGA-12-0688-01	TCGA-12-0688-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr2:68215410A>C	uc002see.1	-	c.794T>G	c.(793-795)GTC>GGC	p.V265G	WDR92_uc002sed.1_Non-coding_Transcript|WDR92_uc002sef.1_Missense_Mutation_p.V265G|WDR92_uc002seg.1_Missense_Mutation_p.V164G	NM_138458	NP_612467	Q96MX6	WDR92_HUMAN	monad	265	WD 5.				apoptosis|histone lysine methylation		methylated histone residue binding				0														0.454545	16.326495	16.389806	10	12	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	68215410	68215410	17913	2	A	C	C	10	10	WDR92	C	4	4
CBLB	868	broad.mit.edu	36	3	106883326	106883326	+	Missense_Mutation	SNP	A	G	G			TCGA-12-0688-01	TCGA-12-0688-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr3:106883326A>G	uc003dwc.1	-	c.2228T>C	c.(2227-2229)CTG>CCG	p.L743P	CBLB_uc003dwd.1_Missense_Mutation_p.L743P|CBLB_uc003dwe.1_Missense_Mutation_p.L743P|CBLB_uc003dwa.1_Missense_Mutation_p.L2P|CBLB_uc003dwb.1_Missense_Mutation_p.L208P	NM_170662	NP_733762	Q13191	CBLB_HUMAN	Cas-Br-M (murine) ecotropic retroviral	743	Pro-rich.				cell surface receptor linked signaling pathway|NLS-bearing substrate import into nucleus	cytoplasm|nucleus	calcium ion binding|ligase activity|signal transducer activity|zinc ion binding			ovary(3)|lung(2)|skin(1)	6						GBM(93;588 1337 9788 29341 43499)								0.323308	129.079243	132.765074	43	90	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	106883326	106883326	2820	3	A	G	G	7	7	CBLB	G	4	4
PHLDB2	90102	broad.mit.edu	36	3	113115171	113115171	+	Missense_Mutation	SNP	C	T	T			TCGA-12-0688-01	TCGA-12-0688-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr3:113115171C>T	uc010hqa.1	+	c.1651C>T	c.(1651-1653)CCT>TCT	p.P551S	PHLDB2_uc003dyc.1_Missense_Mutation_p.P578S|PHLDB2_uc003dyd.1_Missense_Mutation_p.P551S|PHLDB2_uc003dyf.2_Missense_Mutation_p.P551S|PHLDB2_uc003dyg.1_Missense_Mutation_p.P551S|PHLDB2_uc003dyh.1_Missense_Mutation_p.P551S|PHLDB2_uc003dyi.1_Missense_Mutation_p.P137S	NM_145753	NP_665696	Q86SQ0	PHLB2_HUMAN	pleckstrin homology-like domain, family B,	551						cytoplasm|intermediate filament cytoskeleton|plasma membrane				ovary(4)	4														0.361111	311.088127	316.62542	117	207	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	113115171	113115171	12276	3	C	T	T	30	30	PHLDB2	T	2	2
CCDC48	79825	broad.mit.edu	36	3	130240372	130240372	+	Silent	SNP	G	A	A			TCGA-12-0688-01	TCGA-12-0688-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:130240372G>A	uc003ell.1	+	c.288G>A	c.(286-288)TCG>TCA	p.S96S		NM_024768	NP_079044	Q9HA90	CCD48_HUMAN	coiled-coil domain containing 48	533	Potential.										0														0.336788	176.374465	180.942656	65	128	GG		KEEP	---	---	---	---	capture			Silent	SNP	130240372	130240372	2942	3	G	A	A	37	37	CCDC48	A	1	1
LRRC33	375387	broad.mit.edu	36	3	197872486	197872486	+	Silent	SNP	C	T	T			TCGA-12-0688-01	TCGA-12-0688-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr3:197872486C>T	uc003fwv.1	+	c.1575C>T	c.(1573-1575)TCC>TCT	p.S525S		NM_198565	NP_940967	Q86YC3	LRC33_HUMAN	leucine rich repeat containing 33	525	Extracellular (Potential).|LRR 18.					integral to membrane				ovary(2)|central_nervous_system(1)	3	all_cancers(143;8.88e-09)|Ovarian(172;0.0634)|Breast(254;0.135)													0.399381	380.924407	383.779362	129	194	CC		KEEP	---	---	---	---	capture	Epithelial(36;1.9e-23)|all cancers(36;1.76e-21)|OV - Ovarian serous cystadenocarcinoma(49;1.5e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00326)	Silent	SNP	197872486	197872486	9363	3	C	T	T	21	21	LRRC33	T	2	2
EGF	1950	broad.mit.edu	36	4	111128429	111128429	+	Silent	SNP	T	C	C			TCGA-12-0688-01	TCGA-12-0688-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr4:111128429T>C	uc003hzy.2	+	c.2572T>C	c.(2572-2574)TTG>CTG	p.L858L	EGF_uc010imk.1_Intron	NM_001963	NP_001954	P01133	EGF_HUMAN	epidermal growth factor (beta-urogastrone)	858	EGF-like 6.|Extracellular (Potential).				angiogenesis|DNA replication|epidermal growth factor receptor signaling pathway|negative regulation of epidermal growth factor receptor signaling pathway|negative regulation of secretion|platelet activation|platelet degranulation|positive regulation of catenin import into nucleus|positive regulation of epidermal growth factor receptor activity|positive regulation of MAP kinase activity|positive regulation of mitosis|regulation of calcium ion import|regulation of protein localization at cell surface	integral to membrane|plasma membrane|platelet alpha granule lumen	calcium ion binding|epidermal growth factor receptor binding|growth factor activity|transmembrane receptor protein tyrosine kinase activator activity			central_nervous_system(1)	1		Hepatocellular(203;0.0893)			Sulindac(DB00605)					724				0.393548	194.554179	196.087507	61	94	TT		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(123;9.87e-06)	Silent	SNP	111128429	111128429	5151	4	T	C	C	64	64	EGF	C	4	4
FGFBP2	83888	broad.mit.edu	36	4	15573413	15573413	+	Silent	SNP	C	T	T			TCGA-12-0688-01	TCGA-12-0688-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:15573413C>T	uc003gon.1	-	c.438G>A	c.(436-438)GGG>GGA	p.G146G	FGFBP2_uc010ieb.1_Silent_p.G146G	NM_031950	NP_114156	Q9BYJ0	FGFP2_HUMAN	killer-specific secretory protein of 37 kDa	146						extracellular space	growth factor binding				0														0.333333	183.579707	189.44373	79	158	CC		KEEP	---	---	---	---	capture			Silent	SNP	15573413	15573413	6098	4	C	T	T	30	30	FGFBP2	T	2	2
FRG1	2483	broad.mit.edu	36	4	191115556	191115556	+	Missense_Mutation	SNP	G	C	C			TCGA-12-0688-01	TCGA-12-0688-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr4:191115556G>C	uc003izs.1	+	c.442G>C	c.(442-444)GCT>CCT	p.A148P	FRG1_uc003izr.1_Non-coding_Transcript	NM_004477	NP_004468	Q14331	FRG1_HUMAN	FSHD region gene 1	148					nuclear mRNA splicing, via spliceosome|rRNA processing	Cajal body|catalytic step 2 spliceosome|nuclear speck|nucleolus					0		all_cancers(14;1.44e-58)|all_epithelial(14;6.32e-41)|all_lung(41;8.13e-17)|Lung NSC(41;2.13e-16)|Breast(6;2.54e-06)|Melanoma(20;0.000263)|Hepatocellular(41;0.00213)|Renal(120;0.0183)|all_hematologic(60;0.0358)|Prostate(90;0.0421)|all_neural(102;0.147)												0.116279	7.143974	13.374472	5	38	GG		KEEP	---	---	---	---	capture		all cancers(3;1.73e-30)|Epithelial(3;5.85e-30)|OV - Ovarian serous cystadenocarcinoma(60;5.56e-15)|BRCA - Breast invasive adenocarcinoma(30;9.14e-06)|Lung(3;3.54e-05)|STAD - Stomach adenocarcinoma(60;8.83e-05)|LUSC - Lung squamous cell carcinoma(40;0.000198)|GBM - Glioblastoma multiforme(59;0.00892)|READ - Rectum adenocarcinoma(43;0.161)	Missense_Mutation	SNP	191115556	191115556	6294	4	G	C	C	42	42	FRG1	C	3	3
STAP1	26228	broad.mit.edu	36	4	68132000	68132000	+	Missense_Mutation	SNP	T	C	C			TCGA-12-0688-01	TCGA-12-0688-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr4:68132000T>C	uc003hde.2	+	c.644T>C	c.(643-645)ATT>ACT	p.I215T	STAP1_uc003hdf.2_Missense_Mutation_p.I215T	NM_012108	NP_036240	Q9ULZ2	STAP1_HUMAN	signal transducing adaptor family member 1	215	SH2.				cellular membrane fusion|intracellular protein transport	cytoplasm					0														0.117647	11.852709	21.622561	8	60	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	68132000	68132000	15771	4	T	C	C	52	52	STAP1	C	4	4
PDHA2	5161	broad.mit.edu	36	4	96980349	96980349	+	Missense_Mutation	SNP	G	A	A			TCGA-12-0688-01	TCGA-12-0688-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr4:96980349G>A	uc003htr.2	+	c.25G>A	c.(25-27)GTG>ATG	p.V9M		NM_005390	NP_005381	P29803	ODPAT_HUMAN	pyruvate dehydrogenase (lipoamide) alpha 2	9					glycolysis|oxidation-reduction process	mitochondrial matrix	pyruvate dehydrogenase (acetyl-transferring) activity			central_nervous_system(1)	1		Hepatocellular(203;0.114)			NADH(DB00157)									0.451613	80.683898	80.810729	28	34	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(123;1.23e-06)	Missense_Mutation	SNP	96980349	96980349	12086	4	G	A	A	40	40	PDHA2	A	1	1
SLC6A19	340024	broad.mit.edu	36	5	1270004	1270004	+	Missense_Mutation	SNP	G	A	A			TCGA-12-0688-01	TCGA-12-0688-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:1270004G>A	uc003jbw.2	+	c.1117G>A	c.(1117-1119)GCG>ACG	p.A373T		NM_001003841	NP_001003841	Q695T7	S6A19_HUMAN	solute carrier family 6, member 19	373	Extracellular (Potential).				cellular nitrogen compound metabolic process	integral to plasma membrane	amino acid transmembrane transporter activity|neurotransmitter:sodium symporter activity				0	all_cancers(3;3.55e-15)|Lung NSC(6;2.89e-14)|all_lung(6;2.2e-13)|all_epithelial(6;3.75e-10)													0.379679	381.762718	386.508636	142	232	GG		KEEP	---	---	---	---	capture	Epithelial(17;0.000356)|all cancers(22;0.00137)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|Lung(60;0.185)		Missense_Mutation	SNP	1270004	1270004	15179	5	G	A	A	38	38	SLC6A19	A	1	1
GRIA1	2890	broad.mit.edu	36	5	153046070	153046070	+	Silent	SNP	C	T	T			TCGA-12-0688-01	TCGA-12-0688-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:153046070C>T	uc003luy.2	+	c.1122C>T	c.(1120-1122)GAC>GAT	p.D374D	GRIA1_uc003lva.2_Silent_p.D374D|GRIA1_uc003luz.2_Silent_p.D279D|GRIA1_uc010jia.1_Silent_p.D354D	NM_000827	NP_000818	P42261	GRIA1_HUMAN	glutamate receptor, ionotropic, AMPA 1 isoform	374	Extracellular (Potential).				synaptic transmission	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|dendritic spine|endocytic vesicle membrane|endoplasmic reticulum membrane|neuronal cell body|postsynaptic density|postsynaptic membrane	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity|kainate selective glutamate receptor activity|PDZ domain binding			ovary(4)|skin(1)	5		Medulloblastoma(196;0.0391)|all_neural(177;0.16)|all_hematologic(541;0.21)			Desflurane(DB01189)|Enflurane(DB00228)|Halothane(DB01159)|Isoflurane(DB00753)|L-Glutamic Acid(DB00142)|Methoxyflurane(DB01028)|Sevoflurane(DB01236)									0.317647	73.0014	75.51066	27	58	CC		KEEP	---	---	---	---	capture	Kidney(363;0.000173)|KIRC - Kidney renal clear cell carcinoma(527;0.000785)		Silent	SNP	153046070	153046070	7045	5	C	T	T	19	19	GRIA1	T	1	1
PIK3R1	5295	broad.mit.edu	36	5	67626842	67626842	+	Missense_Mutation	SNP	A	G	G			TCGA-12-0688-01	TCGA-12-0688-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr5:67626842A>G	uc003jva.1	+	c.1679A>G	c.(1678-1680)GAC>GGC	p.D560G	PIK3R1_uc003jvb.1_Missense_Mutation_p.D560G|PIK3R1_uc003jvc.1_Missense_Mutation_p.D260G|PIK3R1_uc003jvd.1_Missense_Mutation_p.D290G|PIK3R1_uc003jve.1_Missense_Mutation_p.D239G	NM_181523	NP_852664	P27986	P85A_HUMAN	phosphoinositide-3-kinase, regulatory subunit 1	560					epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|growth hormone receptor signaling pathway|insulin receptor signaling pathway|insulin-like growth factor receptor signaling pathway|interspecies interaction between organisms|leukocyte migration|nerve growth factor receptor signaling pathway|phosphatidylinositol 3-kinase cascade|phosphatidylinositol phosphorylation|phosphatidylinositol-mediated signaling|platelet activation|positive regulation of establishment of protein localization in plasma membrane|positive regulation of glucose import|T cell costimulation|T cell receptor signaling pathway	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex	1-phosphatidylinositol binding|ErbB-3 class receptor binding|insulin binding|insulin receptor binding|insulin receptor substrate binding|insulin-like growth factor receptor binding|phosphatidylinositol 3-kinase regulator activity|protein phosphatase binding	p.D560_S565del(1)|p.R557_K561>Q(1)|p.?(1)		endometrium(34)|central_nervous_system(27)|large_intestine(20)|breast(5)|ovary(5)|haematopoietic_and_lymphoid_tissue(3)|lung(2)|urinary_tract(1)|skin(1)|pancreas(1)	99		Lung NSC(167;1.99e-05)|Prostate(74;0.00308)|Ovarian(174;0.00473)|Colorectal(97;0.0176)			Isoproterenol(DB01064)				p.557_561REIDK>Q(AN3CA-Tumor)	370	TCGA GBM(4;<1E-8)			0.382353	161.365066	163.016226	52	84	AA		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(47;3.76e-51)|Lung(70;0.0211)	Missense_Mutation	SNP	67626842	67626842	12342	5	A	G	G	10	10	PIK3R1	G	4	4
C6orf186	728464	broad.mit.edu	36	6	110673900	110673900	+	Missense_Mutation	SNP	T	G	G			TCGA-12-0688-01	TCGA-12-0688-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr6:110673900T>G	uc010kdu.1	-	c.1043A>C	c.(1042-1044)GAC>GCC	p.D348A	C6orf186_uc003pub.2_Missense_Mutation_p.D151A	NM_001123364	NP_001116836	Q5JXM2	CF186_HUMAN	chromosome 6 open reading frame 186	348						extracellular region					0														0.39916	305.169481	307.287891	95	143	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	110673900	110673900	2452	6	T	G	G	58	58	C6orf186	G	4	4
LPA	4018	broad.mit.edu	36	6	160926167	160926167	+	Missense_Mutation	SNP	C	T	T			TCGA-12-0688-01	TCGA-12-0688-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:160926167C>T	uc003qtl.1	-	c.4190G>A	c.(4189-4191)CGA>CAA	p.R1397Q		NM_005577	NP_005568	P08519	APOA_HUMAN	lipoprotein Lp(a) precursor	3905	Kringle 35.				blood circulation|lipid metabolic process|lipid transport|lipoprotein metabolic process|proteolysis|receptor-mediated endocytosis	plasma lipoprotein particle	apolipoprotein binding|endopeptidase inhibitor activity|fibronectin binding|heparin binding|serine-type endopeptidase activity			ovary(3)|pancreas(1)	4		Breast(66;0.000496)|Ovarian(120;0.0303)|Prostate(117;0.0965)			Aminocaproic Acid(DB00513)									0.353135	301.841606	307.60088	107	196	CC		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(65;2.5e-17)|BRCA - Breast invasive adenocarcinoma(81;6.48e-06)	Missense_Mutation	SNP	160926167	160926167	9276	6	C	T	T	31	31	LPA	T	1	1
OR10C1	442194	broad.mit.edu	36	6	29515958	29515958	+	Missense_Mutation	SNP	C	T	T			TCGA-12-0688-01	TCGA-12-0688-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:29515958C>T	uc003nmh.1	+	c.187C>T	c.(187-189)CGC>TGC	p.R63C	OR11A1_uc010jrh.1_Intron	NM_013941	NP_039229	Q6IFQ5	Q6IFQ5_HUMAN	olfactory receptor, family 10, subfamily C,	63						integral to membrane	olfactory receptor activity				0														0.404145	215.984614	217.510931	78	115	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	29515958	29515958	11304	6	C	T	T	27	27	OR10C1	T	1	1
GRM4	2914	broad.mit.edu	36	6	34112334	34112334	+	Missense_Mutation	SNP	T	C	C			TCGA-12-0688-01	TCGA-12-0688-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr6:34112334T>C	uc003oir.2	-	c.1531A>G	c.(1531-1533)AGC>GGC	p.S511G	GRM4_uc010jvh.1_Missense_Mutation_p.S511G|GRM4_uc010jvi.1_Missense_Mutation_p.S203G|GRM4_uc010jvj.1_Missense_Mutation_p.S395G|GRM4_uc003oio.1_Missense_Mutation_p.S203G|GRM4_uc003oip.1_Non-coding_Transcript|GRM4_uc003oiq.1_Missense_Mutation_p.S378G	NM_000841	NP_000832	Q14833	GRM4_HUMAN	glutamate receptor, metabotropic 4	511	Extracellular (Potential).				activation of MAPK activity|inhibition of adenylate cyclase activity by metabotropic glutamate receptor signaling pathway|neuroprotection|neurotransmitter secretion|positive regulation of MAPKKK cascade	cytoplasmic vesicle|integral to plasma membrane	G-protein coupled receptor activity|glutamate receptor activity			ovary(1)	1					L-Glutamic Acid(DB00142)									0.205128	10.275582	13.459752	8	31	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	34112334	34112334	7078	6	T	C	C	54	54	GRM4	C	4	4
IRF4	3662	broad.mit.edu	36	6	342159	342159	+	Missense_Mutation	SNP	G	A	A			TCGA-12-0688-01	TCGA-12-0688-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:342159G>A	uc003msz.2	+	c.544G>A	c.(544-546)GTC>ATC	p.V182I	IRF4_uc010jne.1_Missense_Mutation_p.V182I|IRF4_uc003mta.2_Non-coding_Transcript|IRF4_uc003mtb.2_Missense_Mutation_p.V181I|IRF4_uc003mtc.1_Missense_Mutation_p.V12I	NM_002460	NP_002451	Q15306	IRF4_HUMAN	interferon regulatory factor 4	182					interferon-gamma-mediated signaling pathway|positive regulation of interleukin-10 biosynthetic process|positive regulation of interleukin-13 biosynthetic process|positive regulation of interleukin-2 biosynthetic process|positive regulation of interleukin-4 biosynthetic process|regulation of T-helper cell differentiation|T cell activation|type I interferon-mediated signaling pathway	cytoplasm	DNA binding|RNA polymerase II transcription factor activity|sequence-specific DNA binding transcription factor activity|transcription activator activity|transcription factor binding			ovary(1)	1		Breast(5;0.0155)|all_lung(73;0.0691)|all_hematologic(90;0.0895)								223				0.395939	217.211091	219.07531	78	119	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(45;0.03)|BRCA - Breast invasive adenocarcinoma(62;0.0702)	Missense_Mutation	SNP	342159	342159	8135	6	G	A	A	40	40	IRF4	A	1	1
C6orf126	389383	broad.mit.edu	36	6	35855166	35855166	+	Silent	SNP	C	A	A			TCGA-12-0688-01	TCGA-12-0688-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:35855166C>A	uc010jvz.1	+	c.264C>A	c.(262-264)TCC>TCA	p.S88S	C6orf126_uc003olc.1_Missense_Mutation_p.Q115K|C6orf127_uc003old.2_5'Flank	NM_207409	NP_997292	Q6UWE3	CF126_HUMAN	hypothetical protein LOC389383	88					digestion|lipid catabolic process	extracellular region	enzyme activator activity				0														0.444444	11.706633	11.729259	4	5	CC		KEEP	---	---	---	---	capture			Silent	SNP	35855166	35855166	2428	6	C	A	A	21	21	C6orf126	A	3	3
NFKBIE	4794	broad.mit.edu	36	6	44337467	44337467	+	Missense_Mutation	SNP	C	T	T			TCGA-12-0688-01	TCGA-12-0688-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:44337467C>T	uc003oxe.1	-	c.982G>A	c.(982-984)GAC>AAC	p.D328N		NM_004556	NP_004547	O00221	IKBE_HUMAN	nuclear factor of kappa light polypeptide gene	328	ANK 3.				cytoplasmic sequestering of transcription factor		protein binding			breast(2)	2	all_cancers(18;2e-05)|all_lung(25;0.00747)|Hepatocellular(11;0.00908)|Ovarian(13;0.0273)													0.397059	71.500066	72.133425	27	41	CC		KEEP	---	---	---	---	capture	Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)		Missense_Mutation	SNP	44337467	44337467	10780	6	C	T	T	29	29	NFKBIE	T	2	2
FAM83B	222584	broad.mit.edu	36	6	54914050	54914050	+	Silent	SNP	G	A	A			TCGA-12-0688-01	TCGA-12-0688-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:54914050G>A	uc003pck.1	+	c.2322G>A	c.(2320-2322)AAG>AAA	p.K774K		NM_001010872	NP_001010872	Q5T0W9	FA83B_HUMAN	hypothetical protein LOC222584	774										ovary(6)	6	Lung NSC(77;0.0178)|Renal(3;0.122)													0.431579	121.859269	122.24722	41	54	GG		KEEP	---	---	---	---	capture			Silent	SNP	54914050	54914050	5860	6	G	A	A	36	36	FAM83B	A	2	2
CNTNAP2	26047	broad.mit.edu	36	7	147743507	147743507	+	Missense_Mutation	SNP	C	T	T			TCGA-12-0688-01	TCGA-12-0688-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:147743507C>T	uc003weu.1	+	c.3862C>T	c.(3862-3864)CGC>TGC	p.R1288C	CNTNAP2_uc003wev.1_Missense_Mutation_p.R65C	NM_014141	NP_054860	Q9UHC6	CNTP2_HUMAN	cell recognition molecule Caspr2 precursor	1288	Cytoplasmic (Potential).				behavior|cell adhesion|clustering of voltage-gated potassium channels|limbic system development|neuron recognition|signal transduction|striatum development|superior temporal gyrus development|thalamus development|transmission of nerve impulse	axolemma|cell body fiber|dendrite|juxtaparanode region of axon|voltage-gated potassium channel complex	receptor binding	p.R1288C(1)		ovary(9)|central_nervous_system(1)|pancreas(1)	11	Melanoma(164;0.153)	all_cancers(3;3.51e-10)|all_epithelial(3;1.4e-05)|Myeloproliferative disorder(3;0.00452)|Lung NSC(3;0.0067)|all_lung(3;0.00794)												0.232558	73.306053	81.739442	30	99	CC		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(82;0.0319)		Missense_Mutation	SNP	147743507	147743507	3785	7	C	T	T	23	23	CNTNAP2	T	1	1
SSPO	23145	broad.mit.edu	36	7	149115567	149115567	+	Missense_Mutation	SNP	A	C	C			TCGA-12-0688-01	TCGA-12-0688-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr7:149115567A>C	uc010lpk.1	+	c.3557A>C	c.(3556-3558)GAC>GCC	p.D1186A		NM_198455	NP_940857	A2VEC9	SSPO_HUMAN	SCO-spondin	1186	VWFD 3.				cell adhesion	extracellular space	peptidase inhibitor activity				0	Melanoma(164;0.165)|Ovarian(565;0.177)													0.4375	20.024395	20.078432	7	9	AA		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(82;0.00625)		Missense_Mutation	SNP	149115567	149115567	15705	7	A	C	C	10	10	SSPO	C	4	4
SP4	6671	broad.mit.edu	36	7	21517396	21517396	+	Missense_Mutation	SNP	A	G	G			TCGA-12-0688-01	TCGA-12-0688-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr7:21517396A>G	uc003sva.1	+	c.2339A>G	c.(2338-2340)AAC>AGC	p.N780S	SP4_uc003svb.1_Missense_Mutation_p.N467S	NM_003112	NP_003103	Q02446	SP4_HUMAN	Sp4 transcription factor	780					regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|RNA polymerase II transcription factor activity|transcription coactivator activity|zinc ion binding			ovary(3)	3														0.267176	100.971294	107.380416	35	96	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	21517396	21517396	15466	7	A	G	G	2	2	SP4	G	4	4
C7orf27	221927	broad.mit.edu	36	7	2547509	2547509	+	Missense_Mutation	SNP	G	A	A			TCGA-12-0688-01	TCGA-12-0688-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:2547509G>A	uc003smi.1	-	c.1270C>T	c.(1270-1272)CGG>TGG	p.R424W	C7orf27_uc003smh.2_5'UTR	NM_152743	NP_689956	Q6PJG6	BRAT1_HUMAN	hypothetical protein LOC221927	424					response to ionizing radiation	nucleus	protein binding				0		Ovarian(82;0.0779)												0.234043	27.506254	30.544617	11	36	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(56;2.91e-14)	Missense_Mutation	SNP	2547509	2547509	2489	7	G	A	A	39	39	C7orf27	A	1	1
ASL	435	broad.mit.edu	36	7	65192084	65192084	+	Silent	SNP	C	G	G			TCGA-12-0688-01	TCGA-12-0688-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:65192084C>G	uc003tuo.1	+	c.1029C>G	c.(1027-1029)CTC>CTG	p.L343L	ASL_uc003tup.1_Silent_p.L343L|ASL_uc003tuq.1_Silent_p.L323L|ASL_uc003tur.1_Silent_p.L317L	NM_000048	NP_001020114	P04424	ARLY_HUMAN	argininosuccinate lyase isoform 1	343					arginine biosynthetic process via ornithine|arginine catabolic process|urea cycle	cytosol	argininosuccinate lyase activity			breast(2)	2					L-Arginine(DB00125)									0.298077	88.199642	91.981424	31	73	CC		KEEP	---	---	---	---	capture			Silent	SNP	65192084	65192084	1063	7	C	G	G	30	30	ASL	G	3	3
TM7SF4	81501	broad.mit.edu	36	8	105429947	105429947	+	De_novo_Start_OutOfFrame	SNP	C	T	T			TCGA-12-0688-01	TCGA-12-0688-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr8:105429947C>T	uc003ylx.1	+	c.-9C>T	c.(-11--7)GACGC>GATGC			NM_030788	NP_110415			dendritic cell-specific transmembrane protein						osteoclast differentiation	cell surface|integral to membrane|plasma membrane				pancreas(2)|large_intestine(1)|ovary(1)	4														0.355932	115.115379	117.273692	42	76	CC		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(57;1.61e-06)|STAD - Stomach adenocarcinoma(118;0.229)		De_novo_Start_OutOfFrame	SNP	105429947	105429947	16506	8	C	T	T	19	19	TM7SF4	T	5	1
FAM83H	286077	broad.mit.edu	36	8	144880793	144880793	+	Silent	SNP	G	A	A			TCGA-12-0688-01	TCGA-12-0688-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr8:144880793G>A	uc003yzk.1	-	c.2826C>T	c.(2824-2826)TCC>TCT	p.S942S	FAM83H_uc010mfk.1_Non-coding_Transcript	NM_198488	NP_940890	Q6ZRV2	FA83H_HUMAN	hypothetical protein LOC286077	942					biomineral tissue development					lung(1)|central_nervous_system(1)|pancreas(1)	3	all_cancers(97;3.74e-11)|all_epithelial(106;2.62e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)													0.324324	34.435391	35.424377	12	25	GG		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(54;3.38e-41)|Epithelial(56;6.8e-40)|all cancers(56;6.43e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.146)		Silent	SNP	144880793	144880793	5866	8	G	A	A	39	39	FAM83H	A	1	1
PXDNL	137902	broad.mit.edu	36	8	52484027	52484027	+	Nonsense_Mutation	SNP	C	A	A			TCGA-12-0688-01	TCGA-12-0688-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr8:52484027C>A	uc003xqu.2	-	c.2710G>T	c.(2710-2712)GAG>TAG	p.E904*	PXDNL_uc003xqt.2_Non-coding_Transcript	NM_144651	NP_653252	A1KZ92	PXDNL_HUMAN	peroxidasin homolog-like	904					hydrogen peroxide catabolic process|oxidation-reduction process	extracellular space	heme binding|peroxidase activity			ovary(1)|pancreas(1)	2		all_cancers(86;0.107)|Lung NSC(129;0.00641)|all_epithelial(80;0.00716)|all_lung(136;0.015)												0.295455	62.72651	66.014329	26	62	CC		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	52484027	52484027	13306	8	C	A	A	30	30	PXDNL	A	5	3
OR1L1	26737	broad.mit.edu	36	9	124464086	124464086	+	Missense_Mutation	SNP	A	G	G			TCGA-12-0688-01	TCGA-12-0688-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr9:124464086A>G	uc004bms.1	+	c.421A>G	c.(421-423)ACC>GCC	p.T141A		NM_001005236	NP_001005236	Q8NH94	OR1L1_HUMAN	olfactory receptor, family 1, subfamily L,	141	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1														0.432	526.40681	527.914963	162	213	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	124464086	124464086	11369	9	A	G	G	10	10	OR1L1	G	4	4
EXD3	54932	broad.mit.edu	36	9	139321241	139321241	+	Silent	SNP	C	T	T			TCGA-12-0688-01	TCGA-12-0688-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr9:139321241C>T	uc004cmp.2	-	c.2613G>A	c.(2611-2613)CCG>CCA	p.P871P	EXD3_uc010ncf.1_Silent_p.P509P	NM_017820	NP_060290	Q8N9H8	MUT7_HUMAN	hypothetical protein LOC54932	871					nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	intracellular	3'-5' exonuclease activity|nucleic acid binding				0														0.62069	56.344695	56.713097	18	11	CC		KEEP	---	---	---	---	capture			Silent	SNP	139321241	139321241	5492	9	C	T	T	23	23	EXD3	T	1	1
TRPM3	80036	broad.mit.edu	36	9	72588920	72588920	+	Missense_Mutation	SNP	C	T	T			TCGA-12-0688-01	TCGA-12-0688-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr9:72588920C>T	uc004aid.1	-	c.1069G>A	c.(1069-1071)GTG>ATG	p.V357M	TRPM3_uc004ahu.1_Missense_Mutation_p.V187M|TRPM3_uc004ahv.1_Missense_Mutation_p.V187M|TRPM3_uc004ahw.1_Missense_Mutation_p.V229M|TRPM3_uc004ahx.1_Missense_Mutation_p.V204M|TRPM3_uc004ahy.1_Missense_Mutation_p.V229M|TRPM3_uc004ahz.1_Missense_Mutation_p.V204M|TRPM3_uc004aia.1_Missense_Mutation_p.V204M|TRPM3_uc004aib.1_Missense_Mutation_p.V204M|TRPM3_uc004aic.2_Missense_Mutation_p.V357M|TRPM3_uc010mor.1_Missense_Mutation_p.V357M|TRPM3_uc004aie.2_Missense_Mutation_p.V204M|TRPM3_uc004aif.1_Missense_Mutation_p.V229M|TRPM3_uc004aig.1_Missense_Mutation_p.V204M	NM_001007471	NP_066003	Q9HCF6	TRPM3_HUMAN	transient receptor potential cation channel,	382	Cytoplasmic (Potential).					integral to membrane	calcium channel activity			ovary(3)|central_nervous_system(2)|pancreas(2)	7														0.25	59.189835	64.620187	24	72	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	72588920	72588920	17138	9	C	T	T	19	19	TRPM3	T	1	1
ROR2	4920	broad.mit.edu	36	9	93525903	93525903	+	Silent	SNP	C	T	T			TCGA-12-0688-01	TCGA-12-0688-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr9:93525903C>T	uc004arj.1	-	c.2694G>A	c.(2692-2694)CAG>CAA	p.Q898Q	ROR2_uc004ari.1_Intron	NM_004560	NP_004551	Q01974	ROR2_HUMAN	receptor tyrosine kinase-like orphan receptor 2	898	Cytoplasmic (Potential).				negative regulation of cell proliferation|positive regulation of cell migration|protein phosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|transmembrane receptor protein tyrosine kinase activity|Wnt-protein binding			lung(6)|central_nervous_system(5)|ovary(3)|large_intestine(2)	16										461				0.389105	294.041778	296.810475	100	157	CC		KEEP	---	---	---	---	capture			Silent	SNP	93525903	93525903	14006	9	C	T	T	32	32	ROR2	T	2	2
FGF13	2258	broad.mit.edu	36	X	137612886	137612886	+	Nonsense_Mutation	SNP	G	A	A			TCGA-12-0688-01	TCGA-12-0688-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:137612886G>A	uc004fam.1	-	c.328C>T	c.(328-330)CGA>TGA	p.R110*	FGF13_uc004fan.1_Nonsense_Mutation_p.R57*	NM_004114	NP_004105	Q92913	FGF13_HUMAN	fibroblast growth factor 13 isoform 1	110					cell-cell signaling|MAPKKK cascade|nervous system development	cytoplasm|nucleus	growth factor activity|protein kinase activator activity			large_intestine(1)|ovary(1)	2	Acute lymphoblastic leukemia(192;0.000127)													0.703704	179.202659	182.211197	57	24	GG		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	137612886	137612886	6079	23	G	A	A	38	38	FGF13	A	5	1
PTPN2	5771	broad.mit.edu	36	18	12784472	12784472	+	Frame_Shift_Del	DEL	T	-	-			TCGA-12-0688-01	TCGA-12-0688-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:12784472_12784472delT	uc002krp.1	-	c.1053_1053delA	c.(1051-1053)AAAfs	p.K351fs	PTPN2_uc002krl.1_Frame_Shift_Del_p.K351fs|PTPN2_uc002krm.1_Intron|PTPN2_uc002krn.1_Frame_Shift_Del_p.K374fs|PTPN2_uc002kro.1_Frame_Shift_Del_p.K351fs	NM_002828	NP_536347	P17706	PTN2_HUMAN	protein tyrosine phosphatase, non-receptor type	351					interferon-gamma-mediated signaling pathway|regulation of interferon-gamma-mediated signaling pathway	endoplasmic reticulum|nucleoplasm	protein binding				0		Lung NSC(161;8.94e-06)												0.40			49	74				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	12784472	12784472	13240	18	T	-	-	60	60	PTPN2	-	5	5
NFIC	4782	broad.mit.edu	36	19	3404868	3404869	+	Frame_Shift_Ins	INS	-	C	C			TCGA-12-0688-01	TCGA-12-0688-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:3404868_3404869insC	uc002lxo.1	+	c.1350_1351insC	c.(1348-1353)AAACCCfs	p.K450fs	NFIC_uc002lxp.1_Intron	NM_205843	NP_995315	P08651	NFIC_HUMAN	nuclear factor I/C isoform 2	459_460					DNA replication|negative regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of gene-specific transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity				0		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;7.8e-05)|Epithelial(107;2.94e-108)|BRCA - Breast invasive adenocarcinoma(158;0.00154)|STAD - Stomach adenocarcinoma(1328;0.191)										0.38			5	8				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	3404868	3404869	10772	19	-	C	C	2	2	NFIC	C	5	5
NOTCH2	4853	broad.mit.edu	36	1	120341427	120341427	+	Frame_Shift_Del	DEL	C	-	-			TCGA-12-0688-01	TCGA-12-0688-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:120341427_120341427delC	uc001eik.1	-	c.467_467delG	c.(466-468)GGAfs	p.G156fs	NOTCH2_uc001eil.2_Frame_Shift_Del_p.G156fs|NOTCH2_uc001eim.2_Frame_Shift_Del_p.G73fs|NOTCH2_uc009who.1_Frame_Shift_Del_p.G117fs	NM_024408	NP_077719	Q04721	NOTC2_HUMAN	notch 2 preproprotein	156	Extracellular (Potential).|EGF-like 4.				anti-apoptosis|bone remodeling|cell cycle arrest|cell fate determination|cell growth|hemopoiesis|induction of apoptosis|negative regulation of cell proliferation|nervous system development|Notch receptor processing|Notch signaling pathway|organ morphogenesis|positive regulation of Ras protein signal transduction|regulation of transcription, DNA-dependent|stem cell maintenance|transcription, DNA-dependent	cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm	calcium ion binding|ligand-regulated transcription factor activity|protein binding|receptor activity			haematopoietic_and_lymphoid_tissue(7)|ovary(4)|lung(3)|central_nervous_system(2)|kidney(2)|breast(1)	19	all_neural(166;0.153)	all_lung(203;1.96e-06)|Lung NSC(69;1.47e-05)|all_epithelial(167;0.000809)		Lung(183;0.0242)|LUSC - Lung squamous cell carcinoma(189;0.133)						581				0.36			81	144				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	120341427	120341427	10951	1	C	-	-	30	30	NOTCH2	-	5	5
