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
PTEN	5728	broad.mit.edu	36	10	89707692	89707692	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0875-01	TCGA-06-0875-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr10:89707692C>T	uc001kfb.1	+	c.737C>T	c.(736-738)CCG>CTG	p.P246L		NM_000314	NP_000305	P60484	PTEN_HUMAN	phosphatase and tensin homolog	246	C2 tensin-type.		P -> L (in CD and BZS).		apoptosis|canonical Wnt receptor signaling pathway|cell proliferation|central nervous system development|induction of apoptosis|inositol phosphate dephosphorylation|negative regulation of cell migration|negative regulation of focal adhesion assembly|negative regulation of protein kinase B signaling cascade|negative regulation of protein phosphorylation|nerve growth factor receptor signaling pathway|phosphatidylinositol dephosphorylation|phosphatidylinositol-mediated signaling|positive regulation of sequence-specific DNA binding transcription factor activity|protein stabilization|regulation of cyclin-dependent protein kinase activity|regulation of neuron projection development|T cell receptor signaling pathway	cytosol|internal side of plasma membrane|PML body	enzyme binding|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity|lipid binding|magnesium ion binding|PDZ domain binding|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity|phosphatidylinositol-3-phosphatase activity|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity	p.P246L(6)|p.L247fs*10(2)|p.L247fs*11(1)|p.L247fs*12(1)|p.F243fs*9(1)|p.G165_*404del(1)|p.P246fs*11(1)|p.P246_L247insGP(1)|p.G165_K342del(1)		endometrium(831)|central_nervous_system(654)|skin(119)|haematopoietic_and_lymphoid_tissue(101)|prostate(97)|large_intestine(90)|breast(67)|lung(63)|ovary(58)|thyroid(29)|stomach(29)|upper_aerodigestive_tract(25)|cervix(21)|liver(20)|vulva(17)|kidney(15)|NS(14)|soft_tissue(12)|urinary_tract(12)|eye(8)|pancreas(6)|salivary_gland(5)|bone(5)|biliary_tract(4)|autonomic_ganglia(2)|meninges(2)|testis(1)|oesophagus(1)	2308		all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132)						31	p.Q245fs(NCIH1781-Tumor)	264	TCGA GBM(2;<1E-8)|TSP Lung(26;0.18)			0.674699	193.028818	195.276792	56	27	CC		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(1;0.214)	UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218)	Missense_Mutation	SNP	89707692	89707692	13192	10	C	T	T	23	23	PTEN	T	1	1
PTEN	5728	broad.mit.edu	36	10	89710639	89710639	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0875-01	TCGA-06-0875-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr10:89710639G>A	uc001kfb.1	+	c.810G>A	c.(808-810)ATG>ATA	p.M270I		NM_000314	NP_000305	P60484	PTEN_HUMAN	phosphatase and tensin homolog	270	C2 tensin-type.				apoptosis|canonical Wnt receptor signaling pathway|cell proliferation|central nervous system development|induction of apoptosis|inositol phosphate dephosphorylation|negative regulation of cell migration|negative regulation of focal adhesion assembly|negative regulation of protein kinase B signaling cascade|negative regulation of protein phosphorylation|nerve growth factor receptor signaling pathway|phosphatidylinositol dephosphorylation|phosphatidylinositol-mediated signaling|positive regulation of sequence-specific DNA binding transcription factor activity|protein stabilization|regulation of cyclin-dependent protein kinase activity|regulation of neuron projection development|T cell receptor signaling pathway	cytosol|internal side of plasma membrane|PML body	enzyme binding|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity|lipid binding|magnesium ion binding|PDZ domain binding|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity|phosphatidylinositol-3-phosphatase activity|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity	p.D268_F279>VGQNVSLLGKYI(2)|p.G165_K342del(1)|p.G165_*404del(1)		endometrium(831)|central_nervous_system(654)|skin(119)|haematopoietic_and_lymphoid_tissue(101)|prostate(97)|large_intestine(90)|breast(67)|lung(63)|ovary(58)|thyroid(29)|stomach(29)|upper_aerodigestive_tract(25)|cervix(21)|liver(20)|vulva(17)|kidney(15)|NS(14)|soft_tissue(12)|urinary_tract(12)|eye(8)|pancreas(6)|salivary_gland(5)|bone(5)|biliary_tract(4)|autonomic_ganglia(2)|meninges(2)|testis(1)|oesophagus(1)	2308		all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132)						31		264	TCGA GBM(2;<1E-8)|TSP Lung(26;0.18)			0.6	33.719713	33.878948	12	8	GG		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(1;0.214)	UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218)	Missense_Mutation	SNP	89710639	89710639	13192	10	G	A	A	48	48	PTEN	A	2	2
ZC3H12C	85463	broad.mit.edu	36	11	109540354	109540354	+	Missense_Mutation	SNP	A	G	G			TCGA-06-0875-01	TCGA-06-0875-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr11:109540354A>G	uc009yxw.1	+	c.1334A>G	c.(1333-1335)GAT>GGT	p.D445G	ZC3H12C_uc001pkr.2_Missense_Mutation_p.D414G	NM_033390	NP_203748	Q9C0D7	ZC12C_HUMAN	zinc finger CCCH-type containing 12C	445							endonuclease activity|nucleic acid binding|zinc ion binding				0		all_cancers(61;3.24e-13)|all_epithelial(67;1.27e-07)|Melanoma(852;1.46e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;3.95e-05)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Breast(348;0.0544)												0.193548	6.423687	9.159203	6	25	AA		KEEP	---	---	---	---	capture		Epithelial(105;1.72e-06)|BRCA - Breast invasive adenocarcinoma(274;1.17e-05)|all cancers(92;9e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0279)	Missense_Mutation	SNP	109540354	109540354	18151	11	A	G	G	12	12	ZC3H12C	G	4	4
MRGPRX2	117194	broad.mit.edu	36	11	19034114	19034114	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0875-01	TCGA-06-0875-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:19034114G>A	uc001mph.1	-	c.412C>T	c.(412-414)CGC>TGC	p.R138C	MRGPRX2_uc009yhu.1_Missense_Mutation_p.R138C	NM_054030	NP_473371	Q96LB1	MRGX2_HUMAN	MAS-related GPR, member X2	138	Cytoplasmic (Potential).				sensory perception of pain|sleep	integral to membrane|plasma membrane	G-protein coupled receptor activity|neuropeptide binding			ovary(1)	1						GBM(198;1966 2199 4849 37227 49954)								0.225	62.369966	70.70364	27	93	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	19034114	19034114	10160	11	G	A	A	37	37	MRGPRX2	A	1	1
MRGPRE	116534	broad.mit.edu	36	11	3206197	3206197	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0875-01	TCGA-06-0875-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:3206197G>A	uc001lxq.2	-	c.406C>T	c.(406-408)CGC>TGC	p.R136C	MRGPRE_uc009ydy.1_Missense_Mutation_p.R136C	NM_001039165	NP_001034254	Q86SM8	MRGRE_HUMAN	MAS-related GPR, member E	136	Cytoplasmic (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity			large_intestine(1)|ovary(1)	2		Medulloblastoma(188;0.00106)|all_epithelial(84;0.00111)|Breast(177;0.00328)|Ovarian(85;0.00556)|all_neural(188;0.00681)												0.5	20.424234	20.424234	7	7	GG		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(625;0.00529)|LUSC - Lung squamous cell carcinoma(625;0.19)	Missense_Mutation	SNP	3206197	3206197	10156	11	G	A	A	40	40	MRGPRE	A	1	1
MAPK8IP1	9479	broad.mit.edu	36	11	45882247	45882247	+	Missense_Mutation	SNP	A	G	G			TCGA-06-0875-01	TCGA-06-0875-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr11:45882247A>G	uc001nbr.1	+	c.1625A>G	c.(1624-1626)TAT>TGT	p.Y542C		NM_005456	NP_005447	Q9UQF2	JIP1_HUMAN	mitogen-activated protein kinase 8 interacting	542	SH3.				vesicle-mediated transport	nucleus|perinuclear region of cytoplasm	kinesin binding|MAP-kinase scaffold activity|protein kinase inhibitor activity	p.Y542C(1)		ovary(1)	1														0.36	137.854573	140.005416	45	80	AA		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(35;0.231)	Missense_Mutation	SNP	45882247	45882247	9667	11	A	G	G	16	16	MAPK8IP1	G	4	4
OR5R1	219479	broad.mit.edu	36	11	55941791	55941791	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0875-01	TCGA-06-0875-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:55941791C>T	uc001niu.1	-	c.494G>A	c.(493-495)CGT>CAT	p.R165H		NM_001004744	NP_001004744	Q8NH85	OR5R1_HUMAN	olfactory receptor, family 5, subfamily R,	165	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)	2	Esophageal squamous(21;0.00448)													0.347518	136.019214	138.918817	49	92	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	55941791	55941791	11590	11	C	T	T	19	19	OR5R1	T	1	1
LRRC55	219527	broad.mit.edu	36	11	56706722	56706722	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0875-01	TCGA-06-0875-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:56706722G>A	uc001njl.1	+	c.779G>A	c.(778-780)CGC>CAC	p.R260H		NM_001005210	NP_001005210	Q6ZSA7	LRC55_HUMAN	leucine rich repeat containing 55	230	LRRCT.					integral to membrane					0														0.381443	202.101915	204.493546	74	120	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	56706722	56706722	9386	11	G	A	A	38	38	LRRC55	A	1	1
NADSYN1	55191	broad.mit.edu	36	11	70870662	70870662	+	Missense_Mutation	SNP	A	C	C			TCGA-06-0875-01	TCGA-06-0875-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr11:70870662A>C	uc001oqn.1	+	c.1093A>C	c.(1093-1095)ACC>CCC	p.T365P	NADSYN1_uc001oqo.1_Missense_Mutation_p.T105P|NADSYN1_uc001oqp.1_5'UTR	NM_018161	NP_060631	Q6IA69	NADE_HUMAN	NAD synthetase 1	365	Ligase (By similarity).				NAD biosynthetic process	cytosol	ATP binding|hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds|NAD+ synthase (glutamine-hydrolyzing) activity|protein binding			ovary(2)	2					L-Glutamic Acid(DB00142)|L-Glutamine(DB00130)	Ovarian(79;763 1781 6490 50276)								0.5	6.407621	6.407621	4	4	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	70870662	70870662	10534	11	A	C	C	6	6	NADSYN1	C	4	4
RNF169	254225	broad.mit.edu	36	11	74224617	74224617	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0875-01	TCGA-06-0875-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:74224617C>T	uc001ovl.2	+	c.1321C>T	c.(1321-1323)CGG>TGG	p.R441W	XRRA1_uc001ovm.2_Intron	NM_001098638	NP_001092108	Q8NCN4	RN169_HUMAN	ring finger protein 169	441							zinc ion binding			ovary(1)	1														0.402542	268.371029	270.331339	95	141	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	74224617	74224617	13937	11	C	T	T	27	27	RNF169	T	1	1
PPP1CC	5501	broad.mit.edu	36	12	109652725	109652725	+	Missense_Mutation	SNP	T	A	A			TCGA-06-0875-01	TCGA-06-0875-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr12:109652725T>A	uc001tru.1	-	c.410A>T	c.(409-411)TAT>TTT	p.Y137F		NM_002710	NP_002701	P36873	PP1G_HUMAN	protein phosphatase 1, catalytic subunit, gamma	137					cell division|glycogen metabolic process|mitotic prometaphase|triglyceride catabolic process	cleavage furrow|condensed chromosome kinetochore|cytosol|midbody|MLL5-L complex|nuclear speck|nucleolus|PTW/PP1 phosphatase complex	metal ion binding|protein binding|protein kinase binding|protein serine/threonine phosphatase activity			central_nervous_system(1)	1														0.184397	60.768906	73.939377	26	115	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	109652725	109652725	12786	12	T	A	A	49	49	PPP1CC	A	4	4
DNAH10	196385	broad.mit.edu	36	12	122982530	122982530	+	Silent	SNP	G	A	A			TCGA-06-0875-01	TCGA-06-0875-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:122982530G>A	uc001uft.2	+	c.12864G>A	c.(12862-12864)AGG>AGA	p.R4288R	DNAH10_uc001ufu.2_Silent_p.R201R	NM_001083900	NP_001077369	Q8IVF4	DYH10_HUMAN	DNAH10 variant protein (Fragment).	4288					microtubule-based movement	cilium axoneme|cytoplasm|dynein complex|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(3)|central_nervous_system(1)|skin(1)	5	all_neural(191;0.101)|Medulloblastoma(191;0.163)													0.433824	175.693473	176.214096	59	77	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)	Silent	SNP	122982530	122982530	4780	12	G	A	A	42	42	DNAH10	A	2	2
C12orf4	57102	broad.mit.edu	36	12	4513624	4513624	+	Nonsense_Mutation	SNP	A	C	C			TCGA-06-0875-01	TCGA-06-0875-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr12:4513624A>C	uc001qms.1	-	c.284T>G	c.(283-285)TTA>TGA	p.L95*	C12orf4_uc001qmt.1_Nonsense_Mutation_p.L95*	NM_020374	NP_065107	Q9NQ89	CL004_HUMAN	hypothetical protein LOC57102	95											0														0.430556	215.836561	216.440439	62	82	AA		KEEP	---	---	---	---	capture	Colorectal(7;0.00165)|COAD - Colon adenocarcinoma(12;0.0229)	BRCA - Breast invasive adenocarcinoma(232;0.0281)	Nonsense_Mutation	SNP	4513624	4513624	1729	12	A	C	C	13	13	C12orf4	C	5	4
KRT2	3849	broad.mit.edu	36	12	51331909	51331909	+	Silent	SNP	A	G	G			TCGA-06-0875-01	TCGA-06-0875-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr12:51331909A>G	uc001sat.1	-	c.285T>C	c.(283-285)GGT>GGC	p.G95G		NM_000423	NP_000414	P35908	K22E_HUMAN	keratin 2	95	Head.				keratinization|keratinocyte activation|keratinocyte migration|keratinocyte proliferation	Golgi apparatus|keratin filament	protein binding|structural constituent of cytoskeleton			ovary(2)	2														0.272727	7.321445	7.83285	3	8	AA		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(357;0.19)	Silent	SNP	51331909	51331909	8772	12	A	G	G	2	2	KRT2	G	4	4
CLSTN3	9746	broad.mit.edu	36	12	7187031	7187031	+	Silent	SNP	C	T	T			TCGA-06-0875-01	TCGA-06-0875-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:7187031C>T	uc001qss.1	+	c.1740C>T	c.(1738-1740)CAC>CAT	p.H580H	CLSTN3_uc001qsr.1_Silent_p.H568H	NM_014718	NP_055533	Q9BQT9	CSTN3_HUMAN	calsyntenin 3	568	Extracellular (Potential).				homophilic cell adhesion	endoplasmic reticulum membrane|Golgi membrane|integral to membrane|plasma membrane	calcium ion binding			large_intestine(1)	1														0.333333	214.864478	220.869307	82	164	CC		KEEP	---	---	---	---	capture			Silent	SNP	7187031	7187031	3701	12	C	T	T	19	19	CLSTN3	T	1	1
PLD4	122618	broad.mit.edu	36	14	104465093	104465093	+	Silent	SNP	C	G	G			TCGA-06-0875-01	TCGA-06-0875-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr14:104465093C>G	uc001ypu.1	+	c.129C>G	c.(127-129)GGC>GGG	p.G43G		NM_138790	NP_620145	Q96BZ4	PLD4_HUMAN	phospholipase D family, member 4	43	Helical; (Potential).				lipid catabolic process	integral to membrane	NAPE-specific phospholipase D activity|phospholipase D activity			central_nervous_system(1)	1		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)			Choline(DB00122)									0.307692	10.294156	10.723316	4	9	CC		KEEP	---	---	---	---	capture	all cancers(16;0.00067)|OV - Ovarian serous cystadenocarcinoma(23;0.00976)|Epithelial(46;0.0201)|GBM - Glioblastoma multiforme(11;0.116)		Silent	SNP	104465093	104465093	12474	14	C	G	G	28	28	PLD4	G	3	3
MDGA2	161357	broad.mit.edu	36	14	46420998	46420998	+	Silent	SNP	A	G	G			TCGA-06-0875-01	TCGA-06-0875-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr14:46420998A>G	uc001wwj.2	-	c.2208T>C	c.(2206-2208)AGT>AGC	p.S736S	MDGA2_uc001wwh.2_5'UTR|MDGA2_uc001wwi.2_Silent_p.S507S|MDGA2_uc010ani.1_Silent_p.S296S	NM_001113498	NP_001106970	Q7Z553	MDGA2_HUMAN	MAM domain containing 1 isoform 1	736					spinal cord motor neuron differentiation	anchored to membrane|plasma membrane				ovary(3)|large_intestine(1)|pancreas(1)	5														0.266667	9.692843	10.43084	4	11	AA		KEEP	---	---	---	---	capture			Silent	SNP	46420998	46420998	9796	14	A	G	G	6	6	MDGA2	G	4	4
CDKL1	8814	broad.mit.edu	36	14	49878684	49878684	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0875-01	TCGA-06-0875-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr14:49878684G>A	uc010anu.1	-	c.2386C>T	c.(2386-2388)CAT>TAT	p.H796Y	CDKL1_uc001wxz.1_Missense_Mutation_p.H125Y	NM_004196	NP_004187	Q00532	CDKL1_HUMAN	cyclin-dependent kinase-like 1	124	Protein kinase.				protein phosphorylation	cytoplasm|nucleus	ATP binding|cyclin-dependent protein kinase activity			ovary(1)	1	all_epithelial(31;0.000746)|Breast(41;0.0102)									153				0.493671	118.41964	118.422457	39	40	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	49878684	49878684	3282	14	G	A	A	48	48	CDKL1	A	2	2
NIN	51199	broad.mit.edu	36	14	50266074	50266074	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0875-01	TCGA-06-0875-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr14:50266074G>A	uc001wyi.1	-	c.5995C>T	c.(5995-5997)CGC>TGC	p.R1999C	NIN_uc001wyj.1_Non-coding_Transcript|NIN_uc001wyk.1_Missense_Mutation_p.R1286C|NIN_uc010anx.1_Missense_Mutation_p.R2005C|NIN_uc001wym.1_Missense_Mutation_p.R1999C|NIN_uc001wyo.1_Missense_Mutation_p.R1999C|NIN_uc001wyn.1_Non-coding_Transcript	NM_020921	NP_065972	Q8N4C6	NIN_HUMAN	ninein isoform 2	1999	Potential.				centrosome localization	centrosome|microtubule	calcium ion binding|GTP binding|protein binding			ovary(1)|kidney(1)|central_nervous_system(1)|skin(1)	4	all_epithelial(31;0.00244)|Breast(41;0.127)									745				0.6	81.026063	81.418632	27	18	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	50266074	50266074	10818	14	G	A	A	40	40	NIN	A	1	1
AK7	122481	broad.mit.edu	36	14	96019180	96019180	+	Silent	SNP	C	T	T			TCGA-06-0875-01	TCGA-06-0875-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr14:96019180C>T	uc001yfn.2	+	c.1845C>T	c.(1843-1845)GAC>GAT	p.D615D		NM_152327	NP_689540	Q96M32	KAD7_HUMAN	adenylate kinase 7	615	Potential.				cell projection organization	cytosol	adenylate kinase activity|ATP binding|cytidylate kinase activity			ovary(1)	1		all_cancers(154;0.0482)|all_epithelial(191;0.128)|Melanoma(154;0.155)												0.174603	22.630168	28.88944	11	52	CC		KEEP	---	---	---	---	capture		Epithelial(152;0.134)|COAD - Colon adenocarcinoma(157;0.228)	Silent	SNP	96019180	96019180	447	14	C	T	T	19	19	AK7	T	1	1
NIPA1	123606	broad.mit.edu	36	15	20600273	20600273	+	Missense_Mutation	SNP	G	T	T			TCGA-06-0875-01	TCGA-06-0875-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr15:20600273G>T	uc001yvc.1	-	c.987C>A	c.(985-987)GAC>GAA	p.D329E	NIPA1_uc001yvd.1_Missense_Mutation_p.D159E|NIPA1_uc001yve.1_Missense_Mutation_p.D254E	NM_144599	NP_653200	Q7RTP0	NIPA1_HUMAN	non-imprinted in Prader-Willi/Angelman syndrome	329	Cytoplasmic (Potential).				cell death	early endosome|integral to membrane|plasma membrane					0		all_cancers(20;2.26e-25)|all_epithelial(15;2.1e-22)|Lung NSC(15;3.36e-17)|all_lung(15;1.04e-16)|Breast(32;0.000776)|Colorectal(260;0.0488)												0.268817	66.631793	71.119036	25	68	GG		KEEP	---	---	---	---	capture		all cancers(64;4.18e-06)|Epithelial(43;3.97e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00165)	Missense_Mutation	SNP	20600273	20600273	10823	15	G	T	T	36	36	NIPA1	T	3	3
AKAP13	11214	broad.mit.edu	36	15	84071686	84071686	+	Missense_Mutation	SNP	C	G	G			TCGA-06-0875-01	TCGA-06-0875-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr15:84071686C>G	uc002blu.1	+	c.7087C>G	c.(7087-7089)CGA>GGA	p.R2363G	AKAP13_uc002blv.1_Missense_Mutation_p.R2359G|AKAP13_uc010bnf.1_Missense_Mutation_p.R980G|AKAP13_uc002blw.1_Missense_Mutation_p.R824G|AKAP13_uc002blx.1_Missense_Mutation_p.R604G	NM_006738	NP_006729	Q12802	AKP13_HUMAN	A-kinase anchor protein 13 isoform 1	2359	Interaction with ESR1.|Potential.				apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|membrane|membrane fraction|nucleus	cAMP-dependent protein kinase activity|metal ion binding|protein binding|Rho guanyl-nucleotide exchange factor activity|signal transducer activity			central_nervous_system(3)|kidney(2)|urinary_tract(1)|ovary(1)|liver(1)	8						Melanoma(94;603 1453 3280 32295 32951)								0.333333	50.092301	51.268985	16	32	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	84071686	84071686	452	15	C	G	G	23	23	AKAP13	G	3	3
ACAN	176	broad.mit.edu	36	15	87218654	87218654	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0875-01	TCGA-06-0875-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr15:87218654C>T	uc002bmy.1	+	c.7189C>T	c.(7189-7191)CGC>TGC	p.R2397C	ACAN_uc002bmz.1_Missense_Mutation_p.R2298C|ACAN_uc002bna.1_Missense_Mutation_p.R603C	NM_013227	NP_037359			aggrecan isoform 2 precursor											ovary(2)|central_nervous_system(1)	3	Lung NSC(78;0.0392)|all_lung(78;0.077)													0.333333	8.421838	8.643325	3	6	CC		KEEP	---	---	---	---	capture	BRCA - Breast invasive adenocarcinoma(143;0.146)		Missense_Mutation	SNP	87218654	87218654	118	15	C	T	T	19	19	ACAN	T	1	1
CLCN7	1186	broad.mit.edu	36	16	1447257	1447257	+	Missense_Mutation	SNP	T	C	C	rs71726965	unknown	TCGA-06-0875-01	TCGA-06-0875-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr16:1447257T>C	uc002clv.2	-	c.821A>G	c.(820-822)AAG>AGG	p.K274R	CLCN7_uc002clw.2_Missense_Mutation_p.K250R	NM_001287	NP_001278	P51798	CLCN7_HUMAN	chloride channel 7 isoform a	274						integral to membrane|lysosomal membrane	antiporter activity|ATP binding|voltage-gated chloride channel activity			ovary(1)	1		Hepatocellular(780;0.0893)												0.241379	60.835264	66.140175	21	66	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	1447257	1447257	3604	16	T	C	C	56	56	CLCN7	C	4	4
IRX3	79191	broad.mit.edu	36	16	52876389	52876389	+	Missense_Mutation	SNP	T	G	G			TCGA-06-0875-01	TCGA-06-0875-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr16:52876389T>G	uc002eht.1	-	c.905A>C	c.(904-906)GAC>GCC	p.D302A		NM_024336	NP_077312	P78415	IRX3_HUMAN	iroquois homeobox 3	302					multicellular organismal development|regulation of transcription, DNA-dependent	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulator activity				0						GBM(143;1830 1866 4487 4646 37383)								0.428571	6.490075	6.598525	6	8	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	52876389	52876389	8149	16	T	G	G	58	58	IRX3	G	4	4
COG4	25839	broad.mit.edu	36	16	69109129	69109129	+	Silent	SNP	C	G	G			TCGA-06-0875-01	TCGA-06-0875-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:69109129C>G	uc002ezc.1	-	c.270G>C	c.(268-270)CTG>CTC	p.L90L	COG4_uc010cfu.1_Non-coding_Transcript|COG4_uc002ezd.1_Silent_p.L90L|COG4_uc002eze.1_5'UTR	NM_015386	NP_056201	Q9H9E3	COG4_HUMAN	component of oligomeric golgi complex 4	86	Interacts with STX5.				Golgi organization|Golgi vesicle prefusion complex stabilization|protein transport|retrograde vesicle-mediated transport, Golgi to ER	Golgi membrane|Golgi transport complex	protein binding				0		Ovarian(137;0.0694)												0.205607	59.187204	67.788136	22	85	CC		KEEP	---	---	---	---	capture			Silent	SNP	69109129	69109129	3798	16	C	G	G	29	29	COG4	G	3	3
TAT	6898	broad.mit.edu	36	16	70161283	70161283	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0875-01	TCGA-06-0875-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:70161283C>T	uc002fap.2	-	c.1100G>A	c.(1099-1101)CGC>CAC	p.R367H		NM_000353	NP_000344	P17735	ATTY_HUMAN	tyrosine aminotransferase	367					2-oxoglutarate metabolic process|glutamate metabolic process|L-phenylalanine catabolic process|tyrosine catabolic process	cytosol	1-aminocyclopropane-1-carboxylate synthase activity|L-tyrosine:2-oxoglutarate aminotransferase activity|pyridoxal phosphate binding			ovary(2)	2		Ovarian(137;0.125)			L-Glutamic Acid(DB00142)|L-Phenylalanine(DB00120)|L-Tyrosine(DB00135)|Pyridoxal Phosphate(DB00114)	Melanoma(198;542 2142 10292 21661 50033)|Esophageal Squamous(48;487 1013 5572 44395 52594)								0.4	54.785365	55.223763	20	30	CC		KEEP	---	---	---	---	capture		Kidney(780;0.0157)	Missense_Mutation	SNP	70161283	70161283	16112	16	C	T	T	27	27	TAT	T	1	1
USP10	9100	broad.mit.edu	36	16	83370054	83370054	+	Silent	SNP	C	A	A			TCGA-06-0875-01	TCGA-06-0875-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:83370054C>A	uc002fii.1	+	c.2262C>A	c.(2260-2262)GTC>GTA	p.V754V	USP10_uc002fij.1_Silent_p.V280V	NM_005153	NP_005144	Q14694	UBP10_HUMAN	ubiquitin specific protease 10	754					DNA damage response, signal transduction by p53 class mediator|DNA repair|protein deubiquitination|ubiquitin-dependent protein catabolic process	early endosome|intermediate filament cytoskeleton|nucleus	cystic fibrosis transmembrane conductance regulator binding|p53 binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity				0														0.343284	58.402747	59.8571	23	44	CC		KEEP	---	---	---	---	capture			Silent	SNP	83370054	83370054	17603	16	C	A	A	32	32	USP10	A	3	3
GPR179	440435	broad.mit.edu	36	17	33740490	33740490	+	Missense_Mutation	SNP	G	T	T			TCGA-06-0875-01	TCGA-06-0875-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:33740490G>T	uc002hpz.1	-	c.2488C>A	c.(2488-2490)CCC>ACC	p.P830T		NM_001004334	NP_001004334	Q6PRD1	GP179_HUMAN	GPR158-like 1	830	Cytoplasmic (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(3)	3	Breast(7;2.97e-12)	Breast(25;0.0101)|Ovarian(249;0.15)												0.333333	7.432929	7.820935	5	10	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	33740490	33740490	6949	17	G	T	T	44	44	GPR179	T	3	3
PCGF2	7703	broad.mit.edu	36	17	34145929	34145929	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0875-01	TCGA-06-0875-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:34145929G>C	uc002hqp.1	-	c.597C>G	c.(595-597)GAC>GAG	p.D199E	PCGF2_uc002hqn.1_Missense_Mutation_p.R201G|PCGF2_uc002hqo.1_Missense_Mutation_p.R201G|PCGF2_uc010cvo.1_Missense_Mutation_p.D74E|PCGF2_uc002hqq.1_Missense_Mutation_p.R201G	NM_007144	NP_009075	P35227	PCGF2_HUMAN	ring finger protein 110	199							DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			central_nervous_system(1)|skin(1)	2	Breast(7;9.07e-22)													0.375	8.62314	8.732827	3	5	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	34145929	34145929	11995	17	G	C	C	40	40	PCGF2	C	3	3
WSCD1	23302	broad.mit.edu	36	17	5932041	5932041	+	Silent	SNP	C	T	T			TCGA-06-0875-01	TCGA-06-0875-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:5932041C>T	uc010cli.1	+	c.435C>T	c.(433-435)TAC>TAT	p.Y145Y	WSCD1_uc002gcn.1_Silent_p.Y145Y|WSCD1_uc002gco.1_Silent_p.Y145Y|WSCD1_uc010clj.1_Intron	NM_015253	NP_056068	Q658N2	WSCD1_HUMAN	WSC domain containing 1	145	WSC 1.					integral to membrane	sulfotransferase activity				0														0.293333	56.316537	59.186529	22	53	CC		KEEP	---	---	---	---	capture			Silent	SNP	5932041	5932041	17980	17	C	T	T	17	17	WSCD1	T	2	2
SLC16A6	9120	broad.mit.edu	36	17	63778649	63778649	+	Missense_Mutation	SNP	T	G	G			TCGA-06-0875-01	TCGA-06-0875-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr17:63778649T>G	uc002jgz.1	-	c.1247A>C	c.(1246-1248)GAG>GCG	p.E416A	ARSG_uc002jhc.2_Intron|SLC16A6_uc002jha.1_Missense_Mutation_p.E416A	NM_004694	NP_004685	O15403	MOT7_HUMAN	solute carrier family 16, member 6	416	Cytoplasmic (Potential).					integral to plasma membrane|membrane fraction	monocarboxylic acid transmembrane transporter activity|symporter activity				0	all_cancers(12;1.24e-09)				Pyruvic acid(DB00119)									0.346154	128.530821	131.249635	45	85	TT		KEEP	---	---	---	---	capture	BRCA - Breast invasive adenocarcinoma(8;3.17e-08)|LUSC - Lung squamous cell carcinoma(166;0.24)		Missense_Mutation	SNP	63778649	63778649	14908	17	T	G	G	54	54	SLC16A6	G	4	4
TP53	7157	broad.mit.edu	36	17	7517819	7517819	+	Missense_Mutation	SNP	G	A	A	rs28934574	unknown	TCGA-06-0875-01	TCGA-06-0875-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:7517819G>A	uc002gim.2	-	c.844C>T	c.(844-846)CGG>TGG	p.R282W	TP53_uc002gig.1_Intron|TP53_uc002gih.1_Missense_Mutation_p.R282W|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Missense_Mutation_p.R150W|TP53_uc010cng.1_Missense_Mutation_p.R150W|TP53_uc002gii.1_Missense_Mutation_p.R150W|TP53_uc010cnh.1_Missense_Mutation_p.R282W|TP53_uc010cni.1_Missense_Mutation_p.R282W|TP53_uc002gij.2_Missense_Mutation_p.R282W	NM_001126112	NP_001119584	P04637	P53_HUMAN	tumor protein p53 isoform a	282	|Interaction with E4F1.|Interaction with HIPK1 (By similarity).|Interaction with AXIN1 (By similarity).		R -> G (in LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> L (in sporadic cancers; somatic mutation).|R -> P (in sporadic cancers; somatic mutation).|DR -> EW (in sporadic cancers; somatic mutation).|R -> Q (in a familial cancer not matching LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> H (in a sporadic cancer; somatic mutation).		activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of gene-specific transcription from RNA polymerase II promoter|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray	chromatin|cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork	ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|promoter binding|promoter binding|protease binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|sequence-specific DNA binding transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|ubiquitin protein ligase binding|zinc ion binding	p.R282W(358)|p.R282G(25)|p.0?(6)|p.R282R(3)|p.R282fs*24(2)|p.D281fs*63(2)|p.D281_R282>EW(2)|p.A276_R283delACPGRDRR(1)|p.D281_R282insXX(1)|p.C275fs*20(1)|p.?(1)|p.R282_E287delRRTEEE(1)|p.L265_K305del41(1)|p.D281_R282delDR(1)|p.G279fs*59(1)|p.R280fs*62(1)|p.R283_T284>T(1)|p.S269fs*21(1)|p.R282fs*63(1)|p.V272_K292del21(1)|p.C275_R283delCACPGRDRR(1)		large_intestine(4614)|breast(2344)|upper_aerodigestive_tract(2150)|lung(1958)|ovary(1559)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1212)|stomach(1127)|urinary_tract(1113)|central_nervous_system(1072)|liver(805)|skin(693)|pancreas(370)|biliary_tract(247)|soft_tissue(209)|prostate(192)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(41)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1)	21904		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)				Pancreas(47;798 1329 9957 10801)		111	p.R282G(NCIH510-Tumor)|p.R282W(HUPT3-Tumor)|p.V274fs(SCC9-Tumor)|p.R282W(CAL29-Tumor)|p.R282W(EFE184-Tumor)|p.R282W(OVKATE-Tumor)	690	TCGA GBM(1;<1E-8)|TSP Lung(2;<1E-8)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)			0.612903	130.264127	130.956707	38	24	GG		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Missense_Mutation	SNP	7517819	7517819	16923	17	G	A	A	39	39	TP53	A	1	1
GPS1	2873	broad.mit.edu	36	17	77608249	77608249	+	Missense_Mutation	SNP	T	C	C			TCGA-06-0875-01	TCGA-06-0875-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr17:77608249T>C	uc002kdk.1	+	c.1541T>C	c.(1540-1542)CTG>CCG	p.L514P	GPS1_uc002kdl.1_Missense_Mutation_p.L478P|GPS1_uc010dij.1_Missense_Mutation_p.L513P|GPS1_uc002kdm.1_Missense_Mutation_p.L458P|GPS1_uc002kdn.1_Missense_Mutation_p.L474P|GPS1_uc002kdo.1_Missense_Mutation_p.L477P	NM_212492	NP_997657	Q13098	CSN1_HUMAN	G protein pathway suppressor 1 isoform 1	478					cell cycle|inactivation of MAPK activity|JNK cascade	cytoplasm|signalosome	GTPase inhibitor activity|protein binding			central_nervous_system(1)	1	all_neural(118;0.0878)|Ovarian(332;0.227)|all_lung(278;0.246)													0.309524	72.609924	75.330846	26	58	TT		KEEP	---	---	---	---	capture	BRCA - Breast invasive adenocarcinoma(99;0.0114)|OV - Ovarian serous cystadenocarcinoma(97;0.0211)		Missense_Mutation	SNP	77608249	77608249	7008	17	T	C	C	55	55	GPS1	C	4	4
HOOK2	29911	broad.mit.edu	36	19	12737980	12737980	+	Missense_Mutation	SNP	T	C	C			TCGA-06-0875-01	TCGA-06-0875-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr19:12737980T>C	uc002muy.2	-	c.1448A>G	c.(1447-1449)GAG>GGG	p.E483G	HOOK2_uc002muz.2_Missense_Mutation_p.E483G	NM_013312	NP_037444	Q96ED9	HOOK2_HUMAN	hook homolog 2 isoform 1	483	Sufficient for interaction with microtubules.|Potential.				early endosome to late endosome transport|endocytosis|endosome organization|endosome to lysosome transport|lysosome organization|microtubule cytoskeleton organization|protein transport	centrosome|FHF complex|microtubule	identical protein binding|microtubule binding			ovary(1)|breast(1)	2												OREG0025273	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.333333	11.67658	12.214334	7	14	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	12737980	12737980	7575	19	T	C	C	54	54	HOOK2	C	4	4
ATP13A1	57130	broad.mit.edu	36	19	19617490	19617490	+	Missense_Mutation	SNP	T	G	G			TCGA-06-0875-01	TCGA-06-0875-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr19:19617490T>G	uc002nnh.2	-	c.3470A>C	c.(3469-3471)AAC>ACC	p.N1157T	GMIP_uc002nnd.1_5'Flank|ATP13A1_uc002nne.1_Missense_Mutation_p.N297T|ATP13A1_uc002nnf.2_Missense_Mutation_p.N525T|ATP13A1_uc002nng.1_Missense_Mutation_p.N1039T	NM_020410	NP_065143	Q9HD20	AT131_HUMAN	ATPase type 13A1	1157	Extracellular (Potential).				ATP biosynthetic process|cation transport	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|metal ion binding			ovary(3)|large_intestine(2)|central_nervous_system(1)	6						Esophageal Squamous(142;920 1789 9047 14684 24777)								0.4	6.662333	6.758817	4	6	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	19617490	19617490	1142	19	T	G	G	60	60	ATP13A1	G	4	4
HPN	3249	broad.mit.edu	36	19	40248658	40248658	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0875-01	TCGA-06-0875-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:40248658C>T	uc002nxq.1	+	c.1097C>T	c.(1096-1098)ACG>ATG	p.T366M	HPN_uc002nxr.1_Missense_Mutation_p.T366M|HPN_uc002nxs.1_Missense_Mutation_p.T208M|HPN_uc002nxt.1_Missense_Mutation_p.T250M	NM_002151	NP_892028	P05981	HEPS_HUMAN	hepsin	366	Extracellular (Potential).|Peptidase S1.				cell growth|proteolysis	cytoplasm|integral to plasma membrane	scavenger receptor activity|serine-type endopeptidase activity			ovary(1)|central_nervous_system(1)	2	all_lung(56;5.38e-08)|Lung NSC(56;8.61e-08)|Esophageal squamous(110;0.162)				Coagulation factor VIIa(DB00036)									0.46831	385.011198	385.261994	133	151	CC		KEEP	---	---	---	---	capture	LUSC - Lung squamous cell carcinoma(66;0.0849)		Missense_Mutation	SNP	40248658	40248658	7628	19	C	T	T	19	19	HPN	T	1	1
NUCB1	4924	broad.mit.edu	36	19	54106280	54106280	+	Missense_Mutation	SNP	C	G	G			TCGA-06-0875-01	TCGA-06-0875-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:54106280C>G	uc002plb.2	+	c.439C>G	c.(439-441)CAT>GAT	p.H147D	NUCB1_uc002pla.2_Missense_Mutation_p.H147D|NUCB1_uc002plc.1_Missense_Mutation_p.H147D	NM_006184	NP_006175	Q02818	NUCB1_HUMAN	nucleobindin 1	147						ER-Golgi intermediate compartment|extracellular space|Golgi apparatus|membrane|microtubule cytoskeleton	calcium ion binding|DNA binding				0		all_lung(116;4.89e-05)|Lung NSC(112;8.3e-05)|all_epithelial(76;8.64e-05)|all_neural(266;0.0506)|Ovarian(192;0.113)												0.173077	17.136693	22.39983	9	43	CC		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(262;0.000171)|all cancers(93;0.000333)|Epithelial(262;0.0174)|GBM - Glioblastoma multiforme(486;0.0244)	Missense_Mutation	SNP	54106280	54106280	11123	19	C	G	G	25	25	NUCB1	G	3	3
ZNF264	9422	broad.mit.edu	36	19	62414799	62414799	+	Silent	SNP	G	A	A			TCGA-06-0875-01	TCGA-06-0875-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:62414799G>A	uc002qob.1	+	c.522G>A	c.(520-522)GAG>GAA	p.E174E		NM_003417	NP_003408	O43296	ZN264_HUMAN	zinc finger protein 264	174					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0822)|Renal(1328;0.157)												0.184615	25.660692	31.72531	12	53	GG		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0135)	Silent	SNP	62414799	62414799	18396	19	G	A	A	34	34	ZNF264	A	2	2
MUC16	94025	broad.mit.edu	36	19	8907404	8907404	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0875-01	TCGA-06-0875-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:8907404C>T	uc002mkp.1	-	c.35227G>A	c.(35227-35229)GTG>ATG	p.V11743M		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	11745	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														0.518182	175.875066	175.906563	57	53	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	8907404	8907404	10367	19	C	T	T	18	18	MUC16	T	2	2
FLG	2312	broad.mit.edu	36	1	150549337	150549337	+	Nonsense_Mutation	SNP	G	C	C			TCGA-06-0875-01	TCGA-06-0875-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:150549337G>C	uc001ezu.1	-	c.4649C>G	c.(4648-4650)TCA>TGA	p.S1550*		NM_002016	NP_002007	P20930	FILA_HUMAN	filaggrin	1550	Ser-rich.				keratinocyte differentiation	cytoplasmic membrane-bounded vesicle|intermediate filament	calcium ion binding|structural molecule activity			ovary(9)	9	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)													0.388106	817.649467	824.661691	248	391	GG		KEEP	---	---	---	---	capture	LUSC - Lung squamous cell carcinoma(543;0.206)		Nonsense_Mutation	SNP	150549337	150549337	6160	1	G	C	C	45	45	FLG	C	5	3
FMO1	2326	broad.mit.edu	36	1	169503464	169503464	+	Missense_Mutation	SNP	C	A	A	rs56841822	unknown	TCGA-06-0875-01	TCGA-06-0875-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:169503464C>A	uc009wvz.1	+	c.291C>A	c.(289-291)CAC>CAA	p.H97Q	FMO1_uc001ghl.1_Missense_Mutation_p.H97Q|FMO1_uc001ghm.1_Missense_Mutation_p.H97Q|FMO1_uc001ghn.1_Missense_Mutation_p.H97Q	NM_002021	NP_002012	Q01740	FMO1_HUMAN	flavin containing monooxygenase 1	97					NADPH oxidation|organic acid metabolic process|toxin metabolic process|xenobiotic metabolic process	endoplasmic reticulum lumen|integral to membrane|intrinsic to endoplasmic reticulum membrane|microsome	flavin adenine dinucleotide binding|flavin-containing monooxygenase activity|NADP binding				0	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)													0.203704	75.28297	88.48562	33	129	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	169503464	169503464	6196	1	C	A	A	20	20	FMO1	A	3	3
ZNF362	149076	broad.mit.edu	36	1	33518468	33518468	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0875-01	TCGA-06-0875-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:33518468G>A	uc001bxc.1	+	c.506G>A	c.(505-507)AGC>AAC	p.S169N		NM_152493	NP_689706	Q5T0B9	ZN362_HUMAN	zinc finger protein 362	169					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.211)				Pancreas(162;1431 2676 35353 38425)								0.361446	146.546946	149.352722	60	106	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	33518468	33518468	18460	1	G	A	A	34	34	ZNF362	A	2	2
TM2D1	83941	broad.mit.edu	36	1	61963319	61963319	+	Missense_Mutation	SNP	C	A	A			TCGA-06-0875-01	TCGA-06-0875-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:61963319C>A	uc001czz.1	-	c.62G>T	c.(61-63)GGT>GTT	p.G21V		NM_032027	NP_114416	Q9BX74	TM2D1_HUMAN	beta-amyloid binding protein precursor	21					apoptosis					ovary(1)	1														0.409091	142.273857	143.062271	45	65	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	61963319	61963319	16493	1	C	A	A	18	18	TM2D1	A	3	3
AGRN	375790	broad.mit.edu	36	1	971470	971470	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0875-01	TCGA-06-0875-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:971470G>A	uc001ack.1	+	c.2873G>A	c.(2872-2874)GGC>GAC	p.G958D		NM_198576	NP_940978	O00468	AGRIN_HUMAN	agrin	958	Kazal-like 9.				axon guidance|clustering of voltage-gated sodium channels|muscarinic acetylcholine receptor signaling pathway|receptor clustering	basal lamina	laminin binding|structural constituent of cytoskeleton			central_nervous_system(2)|breast(1)	3	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)												0.406593	195.279917	196.6754	74	108	GG		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (11;0.00462)|Epithelial(90;5.98e-38)|OV - Ovarian serous cystadenocarcinoma(86;5.43e-23)|Colorectal(212;5.97e-05)|COAD - Colon adenocarcinoma(227;0.000201)|Kidney(185;0.0024)|BRCA - Breast invasive adenocarcinoma(365;0.00246)|STAD - Stomach adenocarcinoma(132;0.00645)|KIRC - Kidney renal clear cell carcinoma(229;0.0354)|Lung(427;0.201)	Missense_Mutation	SNP	971470	971470	400	1	G	A	A	42	42	AGRN	A	2	2
CHGB	1114	broad.mit.edu	36	20	5852212	5852212	+	Silent	SNP	C	T	T			TCGA-06-0875-01	TCGA-06-0875-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr20:5852212C>T	uc002wmg.1	+	c.1422C>T	c.(1420-1422)TAC>TAT	p.Y474Y		NM_001819	NP_001810	P05060	SCG1_HUMAN	chromogranin B precursor	474						extracellular space	hormone activity			breast(3)|ovary(1)	4														0.434343	252.792635	253.539504	86	112	CC		KEEP	---	---	---	---	capture			Silent	SNP	5852212	5852212	3473	20	C	T	T	19	19	CHGB	T	1	1
TRPM2	7226	broad.mit.edu	36	21	44650345	44650345	+	Silent	SNP	G	A	A			TCGA-06-0875-01	TCGA-06-0875-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr21:44650345G>A	uc010gpt.1	+	c.2787G>A	c.(2785-2787)CGG>CGA	p.R929R	TRPM2_uc002zet.1_Silent_p.R929R|TRPM2_uc002zeu.1_Silent_p.R929R|TRPM2_uc002zew.1_Silent_p.R929R|TRPM2_uc002zex.1_Silent_p.R715R|TRPM2_uc002zey.1_Silent_p.R442R	NM_003307	NP_003298	O94759	TRPM2_HUMAN	transient receptor potential cation channel,	929	Cytoplasmic (Potential).					integral to plasma membrane	ADP-ribose diphosphatase activity|calcium channel activity|sodium channel activity			ovary(1)|central_nervous_system(1)|pancreas(1)	3														0.44	325.334796	326.113217	110	140	GG		KEEP	---	---	---	---	capture			Silent	SNP	44650345	44650345	17137	21	G	A	A	41	41	TRPM2	A	2	2
PI4KA	5297	broad.mit.edu	36	22	19395645	19395645	+	Silent	SNP	A	G	G	rs1135934	by-frequency	TCGA-06-0875-01	TCGA-06-0875-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr22:19395645A>G	uc002zsz.2	-	c.5733T>C	c.(5731-5733)GGT>GGC	p.G1911G	PI4KA_uc010gsp.1_Silent_p.G302G|PI4KA_uc002zsy.2_Silent_p.G721G	NM_058004	NP_477352	P42356	PI4KA_HUMAN	phosphatidylinositol 4-kinase type 3 alpha	1911	PI3K/PI4K.				phosphatidylinositol biosynthetic process|phosphatidylinositol-mediated signaling|synaptic transmission	Golgi-associated vesicle	1-phosphatidylinositol 4-kinase activity|ATP binding|protein binding			lung(2)|salivary_gland(1)	3	all_cancers(11;7.59e-25)|all_epithelial(7;1.34e-22)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0332)|all_neural(72;0.142)	Lung SC(17;0.0262)				GBM(136;1332 1831 3115 23601 50806)				873				0.428571	8.324844	8.355671	3	4	AA		KEEP	---	---	---	---	capture	LUSC - Lung squamous cell carcinoma(15;0.000536)|Lung(15;0.0108)|Epithelial(17;0.196)		Silent	SNP	19395645	19395645	12297	22	A	G	G	10	10	PI4KA	G	4	4
UQCR10	29796	broad.mit.edu	36	22	28495665	28495665	+	Splice_Site_SNP	SNP	A	G	G			TCGA-06-0875-01	TCGA-06-0875-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr22:28495665A>G	uc003agq.1	+	c.151_splice	c.e2-2	p.K51_splice	ZMAT5_uc003agm.1_5'Flank|ZMAT5_uc003agn.1_5'Flank|ZMAT5_uc003ago.1_5'Flank|UQCR10_uc003agp.1_Splice_Site_SNP	NM_013387	NP_037519			ubiquinol-cytochrome c reductase complex 7.2kDa						mitochondrial electron transport, ubiquinol to cytochrome c	mitochondrial inner membrane|respiratory chain	ubiquinol-cytochrome-c reductase activity			ovary(1)	1														0.25	7.718947	8.400959	3	9	AA		KEEP	---	---	---	---	capture			Splice_Site_SNP	SNP	28495665	28495665	17577	22	A	G	G	7	7	UQCR10	G	5	4
SCN9A	6335	broad.mit.edu	36	2	166858071	166858071	+	Nonsense_Mutation	SNP	G	T	T			TCGA-06-0875-01	TCGA-06-0875-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:166858071G>T	uc002udq.2	-	c.1023C>A	c.(1021-1023)TAC>TAA	p.Y341*	SCN9A_uc002udr.1_Nonsense_Mutation_p.Y212*|SCN9A_uc002uds.1_Nonsense_Mutation_p.Y212*|SCN9A_uc002udt.1_Nonsense_Mutation_p.Y212*	NM_002977	NP_002968	Q15858	SCN9A_HUMAN	sodium channel, voltage-gated, type IX, alpha	341	I.					voltage-gated sodium channel complex	voltage-gated sodium channel activity			ovary(6)|central_nervous_system(5)	11					Lamotrigine(DB00555)|Lidocaine(DB00281)									0.235294	7.374331	8.483625	4	13	GG		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	166858071	166858071	14407	2	G	T	T	48	48	SCN9A	T	5	3
TMEM198	130612	broad.mit.edu	36	2	220122301	220122301	+	Missense_Mutation	SNP	A	G	G			TCGA-06-0875-01	TCGA-06-0875-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr2:220122301A>G	uc002vme.1	+	c.926A>G	c.(925-927)AAT>AGT	p.N309S	TMEM198_uc002vmf.1_Missense_Mutation_p.N309S	NM_001005209	NP_001005209	Q66K66	TM198_HUMAN	transmembrane protein 198	309						integral to membrane				ovary(1)	1		Renal(207;0.0376)												0.375	125.204461	126.629214	39	65	AA		KEEP	---	---	---	---	capture		Epithelial(149;6.49e-08)|all cancers(144;6.45e-06)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00802)	Missense_Mutation	SNP	220122301	220122301	16654	2	A	G	G	4	4	TMEM198	G	4	4
TMEM18	129787	broad.mit.edu	36	2	667305	667305	+	Missense_Mutation	SNP	A	G	G			TCGA-06-0875-01	TCGA-06-0875-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr2:667305A>G	uc002qwl.1	-	c.41T>C	c.(40-42)ATC>ACC	p.I14T	TMEM18_uc002qwk.1_5'Flank	NM_152834	NP_690047	Q96B42	TMM18_HUMAN	transmembrane protein 18	14					cell migration	integral to membrane|nuclear membrane				ovary(1)	1	all_hematologic(175;0.0429)|Acute lymphoblastic leukemia(172;0.0627)	all_cancers(51;5.27e-05)|all_epithelial(98;2.11e-06)|Ovarian(717;0.0253)												0.416667	7.310031	7.417691	5	7	AA		KEEP	---	---	---	---	capture		all cancers(51;1.95e-21)|Epithelial(75;9.47e-21)|OV - Ovarian serous cystadenocarcinoma(76;8.15e-18)|GBM - Glioblastoma multiforme(21;0.0285)	Missense_Mutation	SNP	667305	667305	16632	2	A	G	G	12	12	TMEM18	G	4	4
CLDN18	51208	broad.mit.edu	36	3	139200564	139200564	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0875-01	TCGA-06-0875-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:139200564G>A	uc003ero.1	+	c.164G>A	c.(163-165)CGA>CAA	p.R55Q		NM_001002026	NP_001002026	P56856	CLD18_HUMAN	claudin 18 isoform 2	55	Extracellular (Potential).				calcium-independent cell-cell adhesion|tight junction assembly	integral to membrane|tight junction	identical protein binding|structural molecule activity			ovary(1)	1														0.379447	270.833709	274.060507	96	157	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	139200564	139200564	3615	3	G	A	A	37	37	CLDN18	A	1	1
TGFBR2	7048	broad.mit.edu	36	3	30707976	30707976	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0875-01	TCGA-06-0875-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr3:30707976C>T	uc003cen.1	+	c.1660C>T	c.(1660-1662)CTC>TTC	p.L554F	TGFBR2_uc003ceo.1_Missense_Mutation_p.L529F	NM_001024847	NP_001020018	P37173	TGFR2_HUMAN	transforming growth factor, beta receptor II	529	Protein kinase.|Cytoplasmic (Potential).				activation of protein kinase activity|brain development|embryonic cranial skeleton morphogenesis|embryonic hemopoiesis|heart development|myeloid dendritic cell differentiation|palate development|pathway-restricted SMAD protein phosphorylation|patterning of blood vessels|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|positive regulation of B cell tolerance induction|positive regulation of mesenchymal cell proliferation|positive regulation of NK T cell differentiation|positive regulation of reactive oxygen species metabolic process|positive regulation of T cell tolerance induction|positive regulation of tolerance induction to self antigen|response to cholesterol|response to drug|transforming growth factor beta receptor signaling pathway|transforming growth factor beta receptor signaling pathway|vasculogenesis	caveola|external side of plasma membrane|transforming growth factor beta receptor complex	ATP binding|glycosaminoglycan binding|metal ion binding|protein binding|receptor signaling protein serine/threonine kinase activity|SMAD binding|transforming growth factor beta binding|transforming growth factor beta receptor activity, type II|type I transforming growth factor beta receptor binding|type I transforming growth factor beta receptor binding|type III transforming growth factor beta receptor binding			pancreas(9)|large_intestine(6)|stomach(3)|ovary(3)|lung(2)|central_nervous_system(1)	24										132				0.215686	97.558139	112.813449	44	160	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	30707976	30707976	16350	3	C	T	T	32	32	TGFBR2	T	2	2
CELSR3	1951	broad.mit.edu	36	3	48671786	48671786	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0875-01	TCGA-06-0875-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr3:48671786C>T	uc003cuf.1	-	c.3496G>A	c.(3496-3498)GAA>AAA	p.E1166K	CELSR3_uc003cul.1_Missense_Mutation_p.E1096K	NM_001407	NP_001398	Q9NYQ7	CELR3_HUMAN	cadherin EGF LAG seven-pass G-type receptor 3	1096	Extracellular (Potential).|Cadherin 8.				homophilic cell adhesion|multicellular organismal development|neuropeptide signaling pathway	integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity|protein binding			ovary(4)|central_nervous_system(2)|skin(1)	7														0.417391	286.465735	287.833869	96	134	CC		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00549)|Kidney(197;0.00619)	Missense_Mutation	SNP	48671786	48671786	3356	3	C	T	T	31	31	CELSR3	T	1	1
BSN	8927	broad.mit.edu	36	3	49674304	49674304	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0875-01	TCGA-06-0875-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr3:49674304C>T	uc003cxe.2	+	c.10022C>T	c.(10021-10023)CCC>CTC	p.P3341L		NM_003458	NP_003449	Q9UPA5	BSN_HUMAN	bassoon protein	3341					synaptic transmission	cell junction|cytoplasm|cytoskeleton|nucleus|synaptosome	zinc ion binding			ovary(5)|central_nervous_system(1)|pancreas(1)	7														0.175	43.956916	55.868984	21	99	CC		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(193;6.66e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.0032)|Kidney(197;0.00336)	Missense_Mutation	SNP	49674304	49674304	1561	3	C	T	T	22	22	BSN	T	2	2
RFT1	91869	broad.mit.edu	36	3	53114804	53114804	+	Missense_Mutation	SNP	C	A	A			TCGA-06-0875-01	TCGA-06-0875-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr3:53114804C>A	uc003dgj.1	-	c.882G>T	c.(880-882)CAG>CAT	p.Q294H	RFT1_uc003dgk.1_Missense_Mutation_p.Q255H	NM_052859	NP_443091	Q96AA3	RFT1_HUMAN	RFT1 homolog	294					carbohydrate transport|dolichol-linked oligosaccharide biosynthetic process|post-translational protein modification|protein N-linked glycosylation via asparagine	integral to membrane	lipid transporter activity				0														0.245098	56.12048	62.161434	25	77	CC		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(193;6.98e-05)|Kidney(197;0.0017)|KIRC - Kidney renal clear cell carcinoma(197;0.00192)|OV - Ovarian serous cystadenocarcinoma(275;0.104)	Missense_Mutation	SNP	53114804	53114804	13729	3	C	A	A	28	28	RFT1	A	3	3
TMEM155	132332	broad.mit.edu	36	4	122900921	122900921	+	Missense_Mutation	SNP	G	T	T			TCGA-06-0875-01	TCGA-06-0875-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr4:122900921G>T	uc003idx.1	-	c.371C>A	c.(370-372)ACT>AAT	p.T124N	TMEM155_uc003idy.1_Missense_Mutation_p.T124N	NM_152399	NP_689612	Q4W5P6	TM155_HUMAN	transmembrane protein 155	124						extracellular region					0														0.166667	7.253907	11.038926	6	30	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	122900921	122900921	16605	4	G	T	T	36	36	TMEM155	T	3	3
TLR2	7097	broad.mit.edu	36	4	154845538	154845538	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0875-01	TCGA-06-0875-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:154845538C>T	uc003inq.1	+	c.2029C>T	c.(2029-2031)CGG>TGG	p.R677W	TLR2_uc003inr.1_Missense_Mutation_p.R677W|TLR2_uc003ins.1_Missense_Mutation_p.R677W|TLR2_uc010ipt.1_Missense_Mutation_p.R677W	NM_003264	NP_003255	O60603	TLR2_HUMAN	toll-like receptor 2	677	TIR.|Cytoplasmic (Potential).		R -> W.		cellular response to diacyl bacterial lipopeptide|cellular response to lipoteichoic acid|cellular response to triacyl bacterial lipopeptide|detection of diacyl bacterial lipopeptide|detection of triacyl bacterial lipopeptide|I-kappaB phosphorylation|induction of apoptosis|inflammatory response|innate immune response|MyD88-dependent toll-like receptor signaling pathway|positive regulation of chemokine production|positive regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of inflammatory response|positive regulation of interferon-beta production|positive regulation of interleukin-12 production|positive regulation of interleukin-18 production|positive regulation of interleukin-6 production|positive regulation of interleukin-8 production|positive regulation of NF-kappaB import into nucleus|positive regulation of NF-kappaB transcription factor activity|positive regulation of nitric-oxide synthase biosynthetic process|positive regulation of toll-like receptor signaling pathway|positive regulation of tumor necrosis factor production|positive regulation of Wnt receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway	cytoplasm|integral to plasma membrane|Toll-like receptor 1-Toll-like receptor 2 protein complex	Gram-positive bacterial cell surface binding|lipopolysaccharide receptor activity|peptidoglycan binding|protein heterodimerization activity|transmembrane receptor activity|triacyl lipopeptide binding				0	all_hematologic(180;0.093)	Renal(120;0.117)												0.401869	247.870017	249.651448	86	128	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	154845538	154845538	16481	4	C	T	T	27	27	TLR2	T	1	1
DNAH5	1767	broad.mit.edu	36	5	13788337	13788337	+	Silent	SNP	G	A	A			TCGA-06-0875-01	TCGA-06-0875-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:13788337G>A	uc003jfd.2	-	c.11664C>T	c.(11662-11664)TAC>TAT	p.Y3888Y	DNAH5_uc003jfc.2_Silent_p.Y56Y	NM_001369	NP_001360	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	3888					microtubule-based movement	cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(14)|breast(1)|central_nervous_system(1)|pancreas(1)	17	Lung NSC(4;0.00476)													0.420635	157.714856	158.391459	53	73	GG		KEEP	---	---	---	---	capture			Silent	SNP	13788337	13788337	4787	5	G	A	A	40	40	DNAH5	A	1	1
PCDHA12	56137	broad.mit.edu	36	5	140237164	140237164	+	Silent	SNP	C	T	T			TCGA-06-0875-01	TCGA-06-0875-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:140237164C>T	uc003lic.1	+	c.1923C>T	c.(1921-1923)GAC>GAT	p.D641D	PCDHA1_uc003lha.1_Intron|PCDHA1_uc003lhb.1_Intron|PCDHA2_uc003lhd.1_Intron|PCDHA3_uc003lhf.1_Intron|PCDHA4_uc003lhh.1_Intron|PCDHA4_uc003lhi.1_Intron|PCDHA5_uc003lhk.1_Intron|PCDHA5_uc003lhl.1_Intron|PCDHA6_uc003lho.1_Intron|PCDHA6_uc003lhn.1_Intron|PCDHA7_uc003lhq.1_Intron|PCDHA8_uc003lhs.1_Intron|PCDHA9_uc003lhu.1_Intron|PCDHA10_uc003lhx.1_Intron|PCDHA10_uc003lhw.1_Intron|PCDHA11_uc003lia.1_Intron|PCDHA12_uc003lib.1_Silent_p.D641D	NM_018903	NP_061726	Q9UN75	PCDAC_HUMAN	protocadherin alpha 12 isoform 1 precursor	641	Cadherin 6.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding|protein binding				0						Pancreas(113;759 1672 13322 24104 50104)								0.339806	94.497914	96.832322	35	68	CC		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		Silent	SNP	140237164	140237164	11942	5	C	T	T	19	19	PCDHA12	T	1	1
IL12B	3593	broad.mit.edu	36	5	158676333	158676333	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0875-01	TCGA-06-0875-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:158676333G>A	uc003lxr.1	-	c.925C>T	c.(925-927)CGG>TGG	p.R309W		NM_002187	NP_002178	P29460	IL12B_HUMAN	interleukin 12B precursor	309	Fibronectin type-III.				cell cycle arrest|cell migration|defense response to Gram-negative bacterium|interferon-gamma biosynthetic process|natural killer cell activation|negative regulation of interleukin-10 production|negative regulation of interleukin-17 production|negative regulation of smooth muscle cell proliferation|positive regulation of activated T cell proliferation|positive regulation of activation of JAK2 kinase activity|positive regulation of cell adhesion|positive regulation of defense response to virus by host|positive regulation of granulocyte macrophage colony-stimulating factor production|positive regulation of inflammatory response|positive regulation of interferon-gamma biosynthetic process|positive regulation of interferon-gamma production|positive regulation of interleukin-10 production|positive regulation of interleukin-12 production|positive regulation of interleukin-17 production|positive regulation of memory T cell differentiation|positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target|positive regulation of natural killer cell proliferation|positive regulation of NF-kappaB import into nucleus|positive regulation of NK T cell activation|positive regulation of NK T cell proliferation|positive regulation of osteoclast differentiation|positive regulation of smooth muscle cell apoptosis|positive regulation of T cell mediated cytotoxicity|positive regulation of T-helper 1 type immune response|positive regulation of T-helper 17 cell lineage commitment|positive regulation of T-helper 17 type immune response|positive regulation of tissue remodeling|positive regulation of tumor necrosis factor production|positive regulation of tyrosine phosphorylation of Stat3 protein|positive regulation of tyrosine phosphorylation of Stat4 protein|positive regulation of tyrosine phosphorylation of Stat5 protein|regulation of tyrosine phosphorylation of Stat1 protein|response to UV-B|sexual reproduction|T-helper 1 type immune response|T-helper cell differentiation	interleukin-12 complex|interleukin-23 complex|membrane	cytokine activity|cytokine receptor activity|interleukin-12 receptor binding|protein heterodimerization activity				0	Renal(175;0.00196)	Medulloblastoma(196;0.0354)|all_neural(177;0.138)										OREG0016989	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.366412	137.373986	139.42582	48	83	GG		KEEP	---	---	---	---	capture	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)		Missense_Mutation	SNP	158676333	158676333	7926	5	G	A	A	38	38	IL12B	A	1	1
WISP3	8838	broad.mit.edu	36	6	112492672	112492672	+	Missense_Mutation	SNP	A	G	G			TCGA-06-0875-01	TCGA-06-0875-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr6:112492672A>G	uc003pvo.1	+	c.422A>G	c.(421-423)GAG>GGG	p.E141G	WISP3_uc003pvm.1_Missense_Mutation_p.E123G|WISP3_uc003pvn.1_Non-coding_Transcript|WISP3_uc003pvp.1_Missense_Mutation_p.E100G	NM_198239	NP_003871	O95389	WISP3_HUMAN	WNT1 inducible signaling pathway protein 3	123					cell-cell signaling|regulation of cell growth|signal transduction	extracellular region|soluble fraction	growth factor activity|insulin-like growth factor binding				0		all_cancers(87;0.000196)|Acute lymphoblastic leukemia(125;1.18e-05)|all_hematologic(75;0.000114)|all_epithelial(87;0.00542)|Colorectal(196;0.0209)												0.311594	261.650908	270.373884	86	190	AA		KEEP	---	---	---	---	capture		all cancers(137;0.0283)|OV - Ovarian serous cystadenocarcinoma(136;0.0613)|Epithelial(106;0.0827)|GBM - Glioblastoma multiforme(226;0.0972)|BRCA - Breast invasive adenocarcinoma(108;0.246)	Missense_Mutation	SNP	112492672	112492672	17948	6	A	G	G	11	11	WISP3	G	4	4
KDM1B	221656	broad.mit.edu	36	6	18315645	18315645	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0875-01	TCGA-06-0875-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:18315645C>T	uc003nco.1	+	c.1088C>T	c.(1087-1089)GCC>GTC	p.A363V	KDM1B_uc003ncn.1_Missense_Mutation_p.A334V	NM_153042	NP_694587	Q8NB78	KDM1B_HUMAN	amine oxidase (flavin containing) domain 1	566					multicellular organismal development|oxidation-reduction process|regulation of DNA methylation|regulation of gene expression by genetic imprinting|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	histone demethylase activity (H3-dimethyl-K4 specific)|histone demethylase activity (H3-monomethyl-K4 specific)|oxidoreductase activity|zinc ion binding				0														0.405594	172.741583	173.84928	58	85	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	18315645	18315645	8429	6	C	T	T	26	26	KDM1B	T	2	2
SCGN	10590	broad.mit.edu	36	6	25761657	25761657	+	Missense_Mutation	SNP	G	T	T			TCGA-06-0875-01	TCGA-06-0875-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:25761657G>T	uc003nfb.1	+	c.151G>T	c.(151-153)GAT>TAT	p.D51Y	SCGN_uc010jpz.1_Intron	NM_006998	NP_008929	O76038	SEGN_HUMAN	secretagogin precursor	51						extracellular region|transport vesicle membrane	calcium ion binding			ovary(2)|pancreas(1)	3														0.231884	38.261203	42.80685	16	53	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	25761657	25761657	14385	6	G	T	T	45	45	SCGN	T	3	3
PRSS35	167681	broad.mit.edu	36	6	84290672	84290672	+	Nonsense_Mutation	SNP	C	T	T			TCGA-06-0875-01	TCGA-06-0875-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:84290672C>T	uc003pjz.1	+	c.793C>T	c.(793-795)CGA>TGA	p.R265*	PRSS35_uc010kbm.1_Nonsense_Mutation_p.R265*|PRSS35_uc010kbn.1_Nonsense_Mutation_p.R265*	NM_153362	NP_699193	Q8N3Z0	PRS35_HUMAN	protease, serine, 35	265	Peptidase S1.				proteolysis	extracellular region	serine-type endopeptidase activity			ovary(1)	1		all_cancers(76;0.000113)|Acute lymphoblastic leukemia(125;1.09e-08)|all_hematologic(105;3.12e-05)|all_epithelial(107;0.0575)												0.468085	200.839168	200.963977	66	75	CC		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(397;0.0768)	Nonsense_Mutation	SNP	84290672	84290672	13074	6	C	T	T	19	19	PRSS35	T	5	1
C7orf52	375607	broad.mit.edu	36	7	100603513	100603513	+	Silent	SNP	C	T	T			TCGA-06-0875-01	TCGA-06-0875-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:100603513C>T	uc003uxy.1	-	c.321G>A	c.(319-321)CTG>CTA	p.L107L	C7orf52_uc003uxz.1_Silent_p.L107L	NM_198571	NP_940973	Q8N8M0	CG052_HUMAN	hypothetical protein LOC375607	107	N-acetyltransferase.						N-acetyltransferase activity			ovary(1)	1	Lung NSC(181;0.168)|all_lung(186;0.215)													0.236111	37.032426	41.622295	17	55	CC		KEEP	---	---	---	---	capture			Silent	SNP	100603513	100603513	2508	7	C	T	T	21	21	C7orf52	T	2	2
GPR141	353345	broad.mit.edu	36	7	37746594	37746594	+	Missense_Mutation	SNP	T	A	A			TCGA-06-0875-01	TCGA-06-0875-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr7:37746594T>A	uc003tfm.1	+	c.74T>A	c.(73-75)TTC>TAC	p.F25Y		NM_181791	NP_861456	Q7Z602	GP141_HUMAN	G protein-coupled receptor 141	25	Helical; Name=1; (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(3)	3										74				0.105079	43.474948	132.027358	60	511	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	37746594	37746594	6923	7	T	A	A	62	62	GPR141	A	4	4
TXNDC3	51314	broad.mit.edu	36	7	37890496	37890496	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0875-01	TCGA-06-0875-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:37890496C>T	uc003tfn.1	+	c.1061C>T	c.(1060-1062)TCG>TTG	p.S354L		NM_016616	NP_057700	Q8N427	TXND3_HUMAN	thioredoxin domain containing 3	354	NDK 2.				cell differentiation|cell redox homeostasis|CTP biosynthetic process|GTP biosynthetic process|multicellular organismal development|spermatogenesis|UTP biosynthetic process	cytoplasm|microtubule cytoskeleton	ATP binding|nucleoside diphosphate kinase activity			ovary(1)|breast(1)|central_nervous_system(1)	3						Ovarian(108;903 1537 27096 29907 47400)								0.190476	104.152351	126.722512	48	204	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	37890496	37890496	17354	7	C	T	T	31	31	TXNDC3	T	1	1
AMPH	273	broad.mit.edu	36	7	38497231	38497231	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0875-01	TCGA-06-0875-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:38497231C>T	uc003tgu.1	-	c.340G>A	c.(340-342)GTG>ATG	p.V114M	AMPH_uc003tgv.1_Missense_Mutation_p.V114M	NM_001635	NP_001626	P49418	AMPH_HUMAN	amphiphysin isoform 1	114	BAR.				endocytosis|synaptic transmission	actin cytoskeleton|cell junction|synaptic vesicle membrane				ovary(3)|liver(1)	4														0.227723	277.784293	312.130894	115	390	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	38497231	38497231	591	7	C	T	T	19	19	AMPH	T	1	1
ABCB4	5244	broad.mit.edu	36	7	86873539	86873539	+	Splice_Site_SNP	SNP	C	T	T			TCGA-06-0875-01	TCGA-06-0875-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:86873539C>T	uc003uiv.1	-	c.3507_splice	c.e26+1	p.H1169_splice	ABCB4_uc003uiw.1_Splice_Site_SNP_p.H1162_splice|ABCB4_uc003uix.1_Splice_Site_SNP_p.H1115_splice	NM_018849	NP_061337			ATP-binding cassette, subfamily B, member 4						cellular lipid metabolic process	apical plasma membrane|Golgi membrane|integral to plasma membrane|intercellular canaliculus|membrane fraction	ATP binding|xenobiotic-transporting ATPase activity			ovary(4)|pancreas(1)	5	Esophageal squamous(14;0.0058)|all_lung(186;0.201)|Lung NSC(181;0.203)													0.125908	66.504351	122.939913	52	361	CC		KEEP	---	---	---	---	capture			Splice_Site_SNP	SNP	86873539	86873539	44	7	C	T	T	19	19	ABCB4	T	5	1
SAMD9L	219285	broad.mit.edu	36	7	92601887	92601887	+	Missense_Mutation	SNP	T	C	C			TCGA-06-0875-01	TCGA-06-0875-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr7:92601887T>C	uc003umh.1	-	c.1334A>G	c.(1333-1335)GAG>GGG	p.E445G	SAMD9L_uc003umj.1_Missense_Mutation_p.E445G|SAMD9L_uc003umi.1_Missense_Mutation_p.E445G|SAMD9L_uc010lfb.1_Missense_Mutation_p.E445G|SAMD9L_uc003umk.1_Missense_Mutation_p.E445G|SAMD9L_uc010lfc.1_Missense_Mutation_p.E445G|SAMD9L_uc010lfd.1_Missense_Mutation_p.E445G|SAMD9L_uc010lfe.1_Missense_Mutation_p.E445G	NM_152703	NP_689916	Q8IVG5	SAM9L_HUMAN	sterile alpha motif domain containing 9-like	445										ovary(4)	4	all_cancers(62;4.15e-11)|all_epithelial(64;2.29e-10)|Breast(17;0.000675)|Lung NSC(181;0.0755)|all_lung(186;0.0989)													0.107246	44.11382	96.920335	37	308	TT		KEEP	---	---	---	---	capture	STAD - Stomach adenocarcinoma(171;0.000302)		Missense_Mutation	SNP	92601887	92601887	14307	7	T	C	C	54	54	SAMD9L	C	4	4
TFPI2	7980	broad.mit.edu	36	7	93356455	93356455	+	Silent	SNP	G	A	A			TCGA-06-0875-01	TCGA-06-0875-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:93356455G>A	uc003unb.1	-	c.288C>T	c.(286-288)TGC>TGT	p.C96C	GNGT1_uc003umx.1_Intron|TFPI2_uc003umy.1_Silent_p.C96C|TFPI2_uc003umz.1_Silent_p.C96C|TFPI2_uc003una.1_Silent_p.C85C|TFPI2_uc010lfg.1_Intron	NM_006528	NP_006519	P48307	TFPI2_HUMAN	tissue factor pathway inhibitor 2	96	BPTI/Kunitz inhibitor 2.				blood coagulation	proteinaceous extracellular matrix	extracellular matrix structural constituent|serine-type endopeptidase inhibitor activity			pancreas(1)	1	all_cancers(62;4.45e-10)|all_epithelial(64;2.92e-09)|Lung NSC(181;0.218)													0.115016	37.67668	83.385505	36	277	GG		KEEP	---	---	---	---	capture	STAD - Stomach adenocarcinoma(171;0.000967)		Silent	SNP	93356455	93356455	16337	7	G	A	A	42	42	TFPI2	A	2	2
CYP3A43	64816	broad.mit.edu	36	7	99285242	99285242	+	Missense_Mutation	SNP	T	C	C			TCGA-06-0875-01	TCGA-06-0875-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr7:99285242T>C	uc003ury.1	+	c.659T>C	c.(658-660)TTA>TCA	p.L220S	CYP3A43_uc003urx.1_Missense_Mutation_p.L220S|CYP3A43_uc003urz.1_Missense_Mutation_p.L220S|CYP3A43_uc003usa.1_Non-coding_Transcript|CYP3A43_uc010lgi.1_Intron|CYP3A43_uc003usb.1_Silent_p.F82F	NM_022820	NP_073731	Q9HB55	CP343_HUMAN	cytochrome P450, family 3, subfamily A,	220			Missing (in allele CYP3A43*2).		oxidation-reduction process|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	aromatase activity|electron carrier activity|heme binding			ovary(1)	1	Esophageal squamous(72;0.0166)|Lung NSC(181;0.0211)|all_lung(186;0.0323)				Cetirizine(DB00341)|Doxycycline(DB00254)									0.22695	91.332686	100.976293	32	109	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	99285242	99285242	4344	7	T	C	C	61	61	CYP3A43	C	4	4
ADAM32	203102	broad.mit.edu	36	8	39199891	39199891	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0875-01	TCGA-06-0875-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr8:39199891G>A	uc003xmt.2	+	c.1502G>A	c.(1501-1503)CGT>CAT	p.R501H	ADAM32_uc003xmu.2_Missense_Mutation_p.R395H|ADAM32_uc003xmv.1_Missense_Mutation_p.V23I	NM_145004	NP_659441	Q8TC27	ADA32_HUMAN	a disintegrin and metalloprotease domain 32	501	Extracellular (Potential).|Cys-rich.				proteolysis	integral to membrane	metalloendopeptidase activity|zinc ion binding			ovary(1)|lung(1)|kidney(1)	3		all_cancers(7;3e-05)|all_lung(54;0.00187)|Hepatocellular(245;0.00745)|Lung NSC(58;0.00771)|Breast(189;0.0503)							p.R501Q(NCIH2106-Tumor)	1163				0.423077	33.120407	33.254717	11	15	GG		KEEP	---	---	---	---	capture	LUSC - Lung squamous cell carcinoma(45;6.2e-07)|Colorectal(1;0.00699)|READ - Rectum adenocarcinoma(1;0.146)		Missense_Mutation	SNP	39199891	39199891	250	8	G	A	A	40	40	ADAM32	A	1	1
IDO1	3620	broad.mit.edu	36	8	39904667	39904667	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0875-01	TCGA-06-0875-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr8:39904667G>C	uc003xnm.1	+	c.1018G>C	c.(1018-1020)GTC>CTC	p.V340L	IDO1_uc003xnn.1_Non-coding_Transcript	NM_002164	NP_002155	P14902	I23O1_HUMAN	indoleamine-pyrrole 2,3 dioxygenase	340					female pregnancy|oxidation-reduction process|tryptophan catabolic process	cytosol	electron carrier activity|heme binding|indoleamine 2,3-dioxygenase activity|tryptophan 2,3-dioxygenase activity			central_nervous_system(2)	2					L-Tryptophan(DB00150)									0.166667	8.884584	11.412907	4	20	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	39904667	39904667	7801	8	G	C	C	44	44	IDO1	C	3	3
NIPAL2	79815	broad.mit.edu	36	8	99284568	99284568	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0875-01	TCGA-06-0875-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr8:99284568G>A	uc003yil.1	-	c.824C>T	c.(823-825)ACG>ATG	p.T275M	NIPAL2_uc003yim.1_Missense_Mutation_p.T275M	NM_024759	NP_079035	Q9H841	NPAL2_HUMAN	NIPA-like domain containing 2	275						integral to membrane					0														0.396694	141.27449	142.404408	48	73	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	99284568	99284568	10826	8	G	A	A	40	40	NIPAL2	A	1	1
AGPAT2	10555	broad.mit.edu	36	9	138688104	138688104	+	Missense_Mutation	SNP	C	A	A			TCGA-06-0875-01	TCGA-06-0875-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr9:138688104C>A	uc004cii.1	-	c.758G>T	c.(757-759)AGG>ATG	p.R253M	AGPAT2_uc004cij.1_Missense_Mutation_p.R221M	NM_006412	NP_006403	O15120	PLCB_HUMAN	1-acylglycerol-3-phosphate O-acyltransferase 2	253					phosphatidic acid biosynthetic process|positive regulation of cytokine production|positive regulation of cytokine-mediated signaling pathway|triglyceride biosynthetic process	endoplasmic reticulum membrane|integral to membrane	1-acylglycerol-3-phosphate O-acyltransferase activity				0	all_cancers(76;0.0893)|all_epithelial(76;0.231)	Myeloproliferative disorder(178;0.0511)												0.185185	8.65537	11.170193	5	22	CC		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(145;9.87e-06)|Epithelial(140;0.000123)	Missense_Mutation	SNP	138688104	138688104	390	9	C	A	A	24	24	AGPAT2	A	3	3
LCN12	286256	broad.mit.edu	36	9	138966628	138966628	+	Missense_Mutation	SNP	T	G	G			TCGA-06-0875-01	TCGA-06-0875-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr9:138966628T>G	uc004ckb.1	+	c.28T>G	c.(28-30)TGG>GGG	p.W10G	LCN12_uc004ckc.2_Missense_Mutation_p.W10G	NM_178536	NP_848631	Q6JVE5	LCN12_HUMAN	lipocalcin 12	10					lipid metabolic process	extracellular region	binding|transporter activity				0	all_cancers(76;0.11)	Myeloproliferative disorder(178;0.0511)												0.5	11.411475	11.411475	7	7	TT		KEEP	---	---	---	---	capture	STAD - Stomach adenocarcinoma(284;0.19)	OV - Ovarian serous cystadenocarcinoma(145;7.8e-06)|Epithelial(140;0.000106)	Missense_Mutation	SNP	138966628	138966628	9006	9	T	G	G	59	59	LCN12	G	4	4
RUSC2	9853	broad.mit.edu	36	9	35550384	35550384	+	Missense_Mutation	SNP	G	T	T			TCGA-06-0875-01	TCGA-06-0875-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr9:35550384G>T	uc003zww.1	+	c.3747G>T	c.(3745-3747)GAG>GAT	p.E1249D	RUSC2_uc010mkq.1_Non-coding_Transcript|RUSC2_uc003zwx.2_Missense_Mutation_p.E1249D	NM_014806	NP_055621	Q8N2Y8	RUSC2_HUMAN	RUN and SH3 domain containing 2	1249	Poly-Glu.					cytosol				ovary(1)	1														0.483516	127.270255	127.292681	44	47	GG		KEEP	---	---	---	---	capture	Lung(28;0.000837)|LUSC - Lung squamous cell carcinoma(32;0.00109)|STAD - Stomach adenocarcinoma(86;0.194)		Missense_Mutation	SNP	35550384	35550384	14231	9	G	T	T	35	35	RUSC2	T	3	3
KANK1	23189	broad.mit.edu	36	9	720069	720069	+	Missense_Mutation	SNP	C	G	G			TCGA-06-0875-01	TCGA-06-0875-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr9:720069C>G	uc003zgl.1	+	c.2717C>G	c.(2716-2718)ACC>AGC	p.T906S	KANK1_uc003zgm.2_Missense_Mutation_p.T906S|KANK1_uc003zgn.1_Missense_Mutation_p.T906S|KANK1_uc003zgs.1_Missense_Mutation_p.T748S|KANK1_uc010mgx.1_5'Flank|KANK1_uc010mgy.1_5'Flank	NM_015158	NP_055973	Q14678	KANK1_HUMAN	KN motif and ankyrin repeat domains 1 isoform a	906					negative regulation of actin filament polymerization	cytoplasm				ovary(2)|central_nervous_system(1)|pancreas(1)	4		Lung NSC(10;9.84e-12)|all_lung(10;1.02e-11)|Breast(48;0.128)												0.285714	31.63672	33.078036	10	25	CC		KEEP	---	---	---	---	capture		Epithelial(6;0.000153)|OV - Ovarian serous cystadenocarcinoma(1;0.000358)|Lung(218;0.0222)	Missense_Mutation	SNP	720069	720069	8280	9	C	G	G	18	18	KANK1	G	3	3
TMEM2	23670	broad.mit.edu	36	9	73494946	73494946	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0875-01	TCGA-06-0875-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr9:73494946C>T	uc004aij.1	-	c.3733G>A	c.(3733-3735)GTC>ATC	p.V1245I	TMEM2_uc010mos.1_Missense_Mutation_p.V1182I|TMEM2_uc004aik.1_Missense_Mutation_p.V79I	NM_013390	NP_037522	Q9UHN6	TMEM2_HUMAN	transmembrane protein 2 isoform a	1245						integral to membrane				ovary(2)	2		all_epithelial(88;4.56e-14)|Myeloproliferative disorder(762;0.0255)												0.350515	99.52891	101.437429	34	63	CC		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(74;7.45e-21)|OV - Ovarian serous cystadenocarcinoma(323;1.02e-16)	Missense_Mutation	SNP	73494946	73494946	16656	9	C	T	T	19	19	TMEM2	T	1	1
TMC1	117531	broad.mit.edu	36	9	74577221	74577221	+	Missense_Mutation	SNP	A	T	T			TCGA-06-0875-01	TCGA-06-0875-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr9:74577221A>T	uc004aiz.1	+	c.814A>T	c.(814-816)AGG>TGG	p.R272W	TMC1_uc010moz.1_Missense_Mutation_p.R230W|TMC1_uc004aja.1_Non-coding_Transcript|TMC1_uc004ajb.1_Non-coding_Transcript|TMC1_uc004ajc.1_Missense_Mutation_p.R126W|TMC1_uc010mpa.1_Missense_Mutation_p.R126W	NM_138691	NP_619636	Q8TDI8	TMC1_HUMAN	transmembrane channel-like 1	272	Extracellular (Potential).				sensory perception of sound	integral to membrane				ovary(1)	1						Pancreas(75;173 1345 14232 34245 43413)								0.726872	563.273217	573.808305	165	62	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	74577221	74577221	16514	9	A	T	T	7	7	TMC1	T	4	4
ASB11	140456	broad.mit.edu	36	X	15217578	15217578	+	Missense_Mutation	SNP	C	A	A			TCGA-06-0875-01	TCGA-06-0875-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:15217578C>A	uc004cwp.1	-	c.624G>T	c.(622-624)AGG>AGT	p.R208S	ASB11_uc004cwo.1_Missense_Mutation_p.R187S|ASB11_uc010nes.1_Non-coding_Transcript|ASB11_uc010net.1_Missense_Mutation_p.R191S	NM_080873	NP_543149	Q8WXH4	ASB11_HUMAN	ankyrin repeat and SOCS box-containing protein	208	ANK 5.				intracellular signal transduction					breast(2)|skin(1)	3	Hepatocellular(33;0.183)													0.208122	183.170853	214.23538	82	312	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	15217578	15217578	1033	23	C	A	A	22	22	ASB11	A	3	3
GRPR	2925	broad.mit.edu	36	X	16080354	16080354	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0875-01	TCGA-06-0875-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:16080354G>A	uc004cxj.1	+	c.820G>A	c.(820-822)GCC>ACC	p.A274T		NM_005314	NP_005305	P30550	GRPR_HUMAN	gastrin-releasing peptide receptor	274	Helical; Name=6; (Potential).				cell proliferation	integral to plasma membrane	bombesin receptor activity			ovary(3)	3	Hepatocellular(33;0.183)													0.234694	161.251321	180.098475	69	225	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	16080354	16080354	7087	23	G	A	A	38	38	GRPR	A	1	1
FTHL17	53940	broad.mit.edu	36	X	30999809	30999809	+	Silent	SNP	G	A	A			TCGA-06-0875-01	TCGA-06-0875-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:30999809G>A	uc004dcl.1	-	c.183C>T	c.(181-183)GAC>GAT	p.D61D		NM_031894	NP_114100	Q9BXU8	FHL17_HUMAN	ferritin, heavy polypeptide-like 17	61	Ferritin-like diiron.				cellular iron ion homeostasis|iron ion transport|oxidation-reduction process		ferric iron binding|oxidoreductase activity				0														0.565	355.284116	356.019059	113	87	GG		KEEP	---	---	---	---	capture			Silent	SNP	30999809	30999809	6334	23	G	A	A	40	40	FTHL17	A	1	1
SPIN4	139886	broad.mit.edu	36	X	62487265	62487265	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0875-01	TCGA-06-0875-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:62487265G>C	uc004dvf.1	-	c.159C>G	c.(157-159)AAC>AAG	p.N53K		NM_001012968	NP_001012986	Q56A73	SPIN4_HUMAN	spindlin family, member 4	53					gamete generation					ovary(1)|lung(1)	2														0.206897	12.36479	14.579302	6	23	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	62487265	62487265	15568	23	G	C	C	40	40	SPIN4	C	3	3
GJB1	2705	broad.mit.edu	36	X	70360779	70360779	+	Missense_Mutation	SNP	T	G	G			TCGA-06-0875-01	TCGA-06-0875-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chrX:70360779T>G	uc004dzf.2	+	c.497T>G	c.(496-498)GTC>GGC	p.V166G	GJB1_uc004dzg.2_Missense_Mutation_p.V166G|GJB1_uc010nlc.1_Missense_Mutation_p.V166G	NM_001097642	NP_001091111	P08034	CXB1_HUMAN	gap junction protein, beta 1, 32kDa	166	Extracellular (Probable).				cell-cell signaling|cellular membrane organization|gap junction assembly|nervous system development	connexon complex|endoplasmic reticulum membrane|integral to membrane	gap junction channel activity			breast(1)	1	Renal(35;0.156)													0.263158	8.716506	9.725594	5	14	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	70360779	70360779	6675	23	T	G	G	58	58	GJB1	G	4	4
ZADH2	284273	broad.mit.edu	36	18	71049981	71049988	+	Frame_Shift_Del	DEL	GGTGGGCA	-	-			TCGA-06-0875-01	TCGA-06-0875-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:71049981_71049988delGGTGGGCA	uc002llx.1	-	c.14_21delTGCCCACC	c.(13-21)GTGCCCACCfs	p.V5fs	TSHZ1_uc002lly.1_5'Flank	NM_175907	NP_787103	Q8N4Q0	ZADH2_HUMAN	zinc binding alcohol dehydrogenase domain	5_7					oxidation-reduction process	peroxisome	oxidoreductase activity|zinc ion binding				0		Esophageal squamous(42;0.131)|Prostate(75;0.155)		READ - Rectum adenocarcinoma(2;0.0276)|BRCA - Breast invasive adenocarcinoma(31;0.216)										0.36			10	18				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	71049981	71049988	18094	18	GGTGGGCA	-	-	39	39	ZADH2	-	5	5
KIAA1211	57482	broad.mit.edu	36	4	56884461	56884461	+	Frame_Shift_Del	DEL	A	-	-			TCGA-06-0875-01	TCGA-06-0875-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:56884461_56884461delA	uc003hbk.2	+	c.3349_3349delA	c.(3349-3351)AAAfs	p.K1117fs		NM_020722	NP_065773	Q6ZU35	K1211_HUMAN	hypothetical protein LOC57482	1117										ovary(1)|skin(1)	2	Glioma(25;0.08)|all_neural(26;0.101)													0.51			28	27				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	56884461	56884461	8523	4	A	-	-	5	5	KIAA1211	-	5	5
