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
ZNF33A	7581	broad.mit.edu	36	10	38385081	38385081	+	Missense_Mutation	SNP	T	G	G			TCGA-14-0867-01	TCGA-14-0867-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr10:38385081T>G	uc001izg.1	+	c.2023T>G	c.(2023-2025)TGT>GGT	p.C675G	ZNF33A_uc001izh.1_Missense_Mutation_p.C674G|ZNF33A_uc001izi.1_Intron	NM_006954	NP_008885	Q06730	ZN33A_HUMAN	zinc finger protein 33A isoform a	674	C2H2-type 13.				regulation of transcription, DNA-dependent	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)|skin(1)	3														0.513944	422.18753	422.230653	129	122	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	38385081	38385081	18446	10	T	G	G	55	55	ZNF33A	G	4	4
TTC18	118491	broad.mit.edu	36	10	74705271	74705271	+	Missense_Mutation	SNP	A	C	C			TCGA-14-0867-01	TCGA-14-0867-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr10:74705271A>C	uc009xrc.1	-	c.2822T>G	c.(2821-2823)CTT>CGT	p.L941R	TTC18_uc001jtv.2_Missense_Mutation_p.L45R|TTC18_uc001jtw.2_Missense_Mutation_p.L45R|TTC18_uc001jtx.1_Missense_Mutation_p.L322R|TTC18_uc001jty.1_Missense_Mutation_p.L941R	NM_145170	NP_660153	Q5T0N1	TTC18_HUMAN	tetratricopeptide repeat domain 18	941	TPR 4.						binding			ovary(2)|central_nervous_system(1)	3	Prostate(51;0.0119)													0.175	8.095812	12.093336	7	33	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	74705271	74705271	17239	10	A	C	C	3	3	TTC18	C	4	4
PTEN	5728	broad.mit.edu	36	10	89682891	89682891	+	Missense_Mutation	SNP	G	A	A			TCGA-14-0867-01	TCGA-14-0867-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr10:89682891G>A	uc001kfb.1	+	c.395G>A	c.(394-396)GGT>GAT	p.G132D		NM_000314	NP_000305	P60484	PTEN_HUMAN	phosphatase and tensin homolog	132	Phosphatase tensin-type.		G -> V (in one patient with clinical findings suggesting hamartoma tumor syndrome).		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.G132D(5)|p.Y27_N212>Y(2)|p.G132V(1)|p.K128fs*47(1)|p.G132R(1)|p.T131fs*42(1)|p.R130fs*2(1)|p.A121_F145del(1)|p.F56fs*2(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)	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)				31		264	TCGA GBM(2;<1E-8)|TSP Lung(26;0.18)			0.754335	875.716132	896.089242	261	85	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	89682891	89682891	13192	10	G	A	A	44	44	PTEN	A	2	2
CYP2C9	1559	broad.mit.edu	36	10	96738739	96738739	+	Silent	SNP	G	T	T			TCGA-14-0867-01	TCGA-14-0867-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr10:96738739G>T	uc001kka.2	+	c.1437G>T	c.(1435-1437)GTG>GTT	p.V479V	CYP2C9_uc009xut.1_Silent_p.V477V	NM_000771	NP_000762	P11712	CP2C9_HUMAN	cytochrome P450, family 2, subfamily C,	479					exogenous drug catabolic process|monocarboxylic acid metabolic process|monoterpenoid metabolic process|oxidative demethylation|steroid metabolic process|urea metabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	(S)-limonene 6-monooxygenase activity|(S)-limonene 7-monooxygenase activity|4-hydroxyacetophenone monooxygenase activity|caffeine oxidase activity|drug binding|electron carrier activity|heme binding|oxygen binding|steroid hydroxylase activity			ovary(2)	2		Colorectal(252;0.0902)		all cancers(201;6.93e-05)	Acenocoumarol(DB01418)|Alosetron(DB00969)|Amiodarone(DB01118)|Antihemophilic Factor(DB00025)|Aprepitant(DB00673)|Bosentan(DB00559)|Carprofen(DB00821)|Carvedilol(DB01136)|Celecoxib(DB00482)|Clomipramine(DB01242)|Dapsone(DB00250)|Delavirdine(DB00705)|Desloratadine(DB00967)|Desogestrel(DB00304)|Diclofenac(DB00586)|Esomeprazole(DB00736)|Etodolac(DB00749)|Fluconazole(DB00196)|Fluoxetine(DB00472)|Flurbiprofen(DB00712)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Formoterol(DB00983)|Gemfibrozil(DB01241)|Ginkgo biloba(DB01381)|Glibenclamide(DB01016)|Glimepiride(DB00222)|Glipizide(DB01067)|Guanfacine(DB01018)|Hydromorphone(DB00327)|Ibuprofen(DB01050)|Imipramine(DB00458)|Irbesartan(DB01029)|Ketoconazole(DB01026)|Lansoprazole(DB00448)|Losartan(DB00678)|Lumiracoxib(DB01283)|Marinol(DB00470)|Mefenamic acid(DB00784)|Meloxicam(DB00814)|Mephenytoin(DB00532)|Metronidazole(DB00916)|Miconazole(DB01110)|Midazolam(DB00683)|Montelukast(DB00471)|Nateglinide(DB00731)|Nelfinavir(DB00220)|Nicardipine(DB00622)|Oxymorphone(DB01192)|Pantoprazole(DB00213)|Paramethadione(DB00617)|Phenprocoumon(DB00946)|Phenytoin(DB00252)|Pravastatin(DB00175)|Quinidine(DB00908)|Ritonavir(DB00503)|Rosiglitazone(DB00412)|Sertraline(DB01104)|Sildenafil(DB00203)|Sulfamethoxazole(DB01015)|Suprofen(DB00870)|Tamoxifen(DB00675)|Tenoxicam(DB00469)|Terfenadine(DB00342)|Tolbutamide(DB01124)|Torasemide(DB00214)|Troleandomycin(DB01361)|Valdecoxib(DB00580)|Valsartan(DB00177)|Voriconazole(DB00582)|Warfarin(DB00682)|Zafirlukast(DB00549)|Zileuton(DB00744)	Ovarian(54;1266 1406 16072 35076)								0.738202	2096.977228	2142.618041	657	233	GG		KEEP	---	---	---	---	capture			Silent	SNP	96738739	96738739	4333	10	G	T	T	46	46	CYP2C9	T	3	3
C11orf63	79864	broad.mit.edu	36	11	122280221	122280221	+	Silent	SNP	G	A	A			TCGA-14-0867-01	TCGA-14-0867-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:122280221G>A	uc001pym.1	+	c.723G>A	c.(721-723)CCG>CCA	p.P241P	C11orf63_uc001pyl.1_Silent_p.P241P	NM_024806	NP_079082	Q6NUN7	CK063_HUMAN	hypothetical protein LOC79864 isoform 1	241										ovary(3)	3		Breast(109;0.00249)|Lung NSC(97;0.0177)|all_lung(97;0.018)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;5.34e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0311)										0.555556	49.425945	49.498306	15	12	GG		KEEP	---	---	---	---	capture			Silent	SNP	122280221	122280221	1693	11	G	A	A	39	39	C11orf63	A	1	1
CCDC63	160762	broad.mit.edu	36	12	109806434	109806434	+	Silent	SNP	C	A	A			TCGA-14-0867-01	TCGA-14-0867-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:109806434C>A	uc001trv.1	+	c.1071C>A	c.(1069-1071)ATC>ATA	p.I357I	CCDC63_uc001trw.1_Silent_p.I272I	NM_152591	NP_689804	Q8NA47	CCD63_HUMAN	coiled-coil domain containing 63	357	Potential.									ovary(1)|pancreas(1)	2														0.363014	146.830916	149.242789	53	93	CC		KEEP	---	---	---	---	capture			Silent	SNP	109806434	109806434	2957	12	C	A	A	30	30	CCDC63	A	3	3
GPR109B	8843	broad.mit.edu	36	12	121766930	121766930	+	Missense_Mutation	SNP	A	C	C			TCGA-14-0867-01	TCGA-14-0867-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr12:121766930A>C	uc001ucy.2	-	c.308T>G	c.(307-309)GTG>GGG	p.V103G	GPR81_uc001ucw.1_Intron	NM_006018	NP_006009	P49019	G109B_HUMAN	G protein-coupled receptor 109B	103	Helical; Name=3; (Potential).					integral to plasma membrane	purinergic nucleotide receptor activity, G-protein coupled			ovary(1)	1	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;2.12e-05)|Epithelial(86;3.19e-05)|BRCA - Breast invasive adenocarcinoma(302;0.196)	Mepenzolate(DB04843)|Niacin(DB00627)									0.5	8.815324	8.815324	5	5	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	121766930	121766930	6900	12	A	C	C	6	6	GPR109B	C	4	4
KRT5	3852	broad.mit.edu	36	12	51196813	51196813	+	Silent	SNP	G	A	A			TCGA-14-0867-01	TCGA-14-0867-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:51196813G>A	uc001san.1	-	c.1314C>T	c.(1312-1314)GCC>GCT	p.A438A	KRT5_uc009zmh.1_Silent_p.A438A	NM_000424	NP_000415	P13647	K2C5_HUMAN	keratin 5	438	Rod.|Coil 2.		A -> D (in WC-EBS).		epidermis development|hemidesmosome assembly	cytosol|keratin filament	protein binding|structural constituent of cytoskeleton				0				BRCA - Breast invasive adenocarcinoma(357;0.189)										0.45092	439.683016	440.365591	147	179	GG		KEEP	---	---	---	---	capture			Silent	SNP	51196813	51196813	8794	12	G	A	A	43	43	KRT5	A	2	2
RB1	5925	broad.mit.edu	36	13	47835029	47835029	+	Nonsense_Mutation	SNP	C	T	T			TCGA-14-0867-01	TCGA-14-0867-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr13:47835029C>T	uc001vcb.1	+	c.796C>T	c.(796-798)CAA>TAA	p.Q266*	RB1_uc010act.1_Intron|RB1_uc010acs.1_Non-coding_Transcript	NM_000321	NP_000312	P06400	RB_HUMAN	retinoblastoma 1	266					androgen receptor signaling pathway|cell cycle arrest|chromatin remodeling|G1 phase of mitotic cell cycle|interspecies interaction between organisms|maintenance of mitotic sister chromatid cohesion|mitotic cell cycle G1/S transition checkpoint|myoblast differentiation|negative regulation of cell growth|negative regulation of protein kinase activity|negative regulation of S phase of mitotic cell cycle|negative regulation of sequence-specific DNA binding transcription factor activity|positive regulation of mitotic metaphase/anaphase transition|protein localization to chromosome, centromeric region|Ras protein signal transduction|regulation of centromere complex assembly|regulation of cohesin localization to chromatin|regulation of lipid kinase activity|regulation of transcription involved in G1/S phase of mitotic cell cycle|S phase of mitotic cell cycle|sister chromatid biorientation	chromatin|PML body|Rb-E2F complex|SWI/SNF complex	androgen receptor binding|DNA binding|kinase binding|phosphoprotein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription factor binding|transcription repressor activity|ubiquitin protein ligase binding	p.0?(13)		lung(93)|eye(89)|central_nervous_system(47)|bone(22)|breast(20)|urinary_tract(17)|haematopoietic_and_lymphoid_tissue(14)|ovary(10)|soft_tissue(8)|prostate(8)|skin(7)|endometrium(5)|cervix(3)|liver(3)|salivary_gland(2)|stomach(2)|oesophagus(1)|adrenal_gland(1)|kidney(1)|gastrointestinal_tract_(site_indeterminate)(1)|pituitary(1)	355		all_cancers(8;6.9e-71)|all_epithelial(8;4.61e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;1.51e-09)|Lung NSC(96;7.03e-07)|Breast(56;1.53e-05)|Prostate(109;0.000493)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301)		GBM - Glioblastoma multiforme(2;9.98e-18)|LUSC - Lung squamous cell carcinoma(3;0.013)	Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)			6		568	TCGA GBM(7;6.82e-08)|TSP Lung(12;0.097)|TCGA Ovarian(6;0.080)			0.740741	63.606696	65.022142	20	7	CC		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	47835029	47835029	13559	13	C	T	T	17	17	RB1	T	5	2
MDGA2	161357	broad.mit.edu	36	14	46635816	46635816	+	Missense_Mutation	SNP	T	C	C			TCGA-14-0867-01	TCGA-14-0867-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr14:46635816T>C	uc001wwj.2	-	c.979A>G	c.(979-981)ATT>GTT	p.I327V	MDGA2_uc001wwi.2_Missense_Mutation_p.I98V|MDGA2_uc010ani.1_5'UTR	NM_001113498	NP_001106970	Q7Z553	MDGA2_HUMAN	MAM domain containing 1 isoform 1	327	Ig-like 3.				spinal cord motor neuron differentiation	anchored to membrane|plasma membrane				ovary(3)|large_intestine(1)|pancreas(1)	5														0.383178	130.251465	131.531345	41	66	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	46635816	46635816	9796	14	T	C	C	51	51	MDGA2	C	4	4
C14orf149	112849	broad.mit.edu	36	14	59012441	59012441	+	Nonsense_Mutation	SNP	G	A	A			TCGA-14-0867-01	TCGA-14-0867-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr14:59012441G>A	uc001xee.1	-	c.838C>T	c.(838-840)CGA>TGA	p.R280*		NM_144581	NP_653182	Q96EM0	PRCM_HUMAN	proline racemase-like	280							proline racemase activity			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(108;0.14)	L-Proline(DB00172)									0.140741	31.645779	48.453595	19	116	GG		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	59012441	59012441	1800	14	G	A	A	39	39	C14orf149	A	5	1
SYNE2	23224	broad.mit.edu	36	14	63750794	63750794	+	Silent	SNP	C	T	T			TCGA-14-0867-01	TCGA-14-0867-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr14:63750794C>T	uc001xgl.1	+	c.19186C>T	c.(19186-19188)CTA>TTA	p.L6396L	SYNE2_uc001xgm.1_Silent_p.L6396L|SYNE2_uc010apy.1_Silent_p.L2781L|SYNE2_uc001xgn.1_Silent_p.L1358L|SYNE2_uc001xgo.1_Non-coding_Transcript|SYNE2_uc010aqa.1_Silent_p.L366L|SYNE2_uc001xgq.1_Silent_p.L761L|SYNE2_uc001xgr.1_Silent_p.L179L|SYNE2_uc001xgs.1_Silent_p.L30L|SYNE2_uc001xgt.1_5'Flank	NM_182914	NP_878918	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	6396	Cytoplasmic (Potential).				centrosome localization|cytoskeletal anchoring at nuclear membrane|nuclear migration along microfilament|positive regulation of cell migration	cytoskeleton|filopodium membrane|focal adhesion|integral to membrane|lamellipodium membrane|mitochondrial part|nuclear outer membrane|nucleoplasm|sarcoplasmic reticulum membrane|SUN-KASH complex|Z disc	actin binding|protein binding			ovary(8)|breast(4)|central_nervous_system(1)|pancreas(1)	14				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)										0.29902	149.477232	156.854669	61	143	CC		KEEP	---	---	---	---	capture			Silent	SNP	63750794	63750794	15967	14	C	T	T	32	32	SYNE2	T	2	2
PCSK6	5046	broad.mit.edu	36	15	99751044	99751044	+	Missense_Mutation	SNP	C	T	T			TCGA-14-0867-01	TCGA-14-0867-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr15:99751044C>T	uc002bxa.1	-	c.1105G>A	c.(1105-1107)GTC>ATC	p.V369I	PCSK6_uc010bpd.1_Missense_Mutation_p.V239I|PCSK6_uc002bwy.1_Missense_Mutation_p.V369I|PCSK6_uc010bpe.1_Missense_Mutation_p.V369I|PCSK6_uc002bxb.1_Missense_Mutation_p.V369I|PCSK6_uc002bxc.1_Missense_Mutation_p.V369I|PCSK6_uc002bxd.1_Missense_Mutation_p.V369I|PCSK6_uc002bxe.1_Missense_Mutation_p.V369I|PCSK6_uc002bxg.1_Missense_Mutation_p.V369I	NM_138320	NP_612193	P29122	PCSK6_HUMAN	paired basic amino acid cleaving system 4	369	Catalytic.				glycoprotein metabolic process|nerve growth factor processing|nerve growth factor production|nerve growth factor receptor signaling pathway|regulation of BMP signaling pathway|secretion by cell	cell surface|endomembrane system|endoplasmic reticulum|extracellular matrix|extracellular space|Golgi lumen|membrane|soluble fraction	eukaryotic cell surface binding|heparin binding|nerve growth factor binding|serine-type endopeptidase activity			pancreas(2)	2	Lung NSC(78;0.00102)|all_lung(78;0.00128)|Melanoma(26;0.00505)		OV - Ovarian serous cystadenocarcinoma(32;0.000803)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)											0.397351	335.684647	338.480736	120	182	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	99751044	99751044	12025	15	C	T	T	19	19	PCSK6	T	1	1
EMP2	2013	broad.mit.edu	36	16	10534406	10534406	+	Missense_Mutation	SNP	C	T	T			TCGA-14-0867-01	TCGA-14-0867-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:10534406C>T	uc002czy.1	-	c.361G>A	c.(361-363)GAA>AAA	p.E121K	EMP2_uc002czx.1_5'Flank	NM_001424	NP_001415	P54851	EMP2_HUMAN	epithelial membrane protein 2	121					cell proliferation	integral to membrane					0						GBM(158;2021 2691 14714 39478)								0.421053	92.280594	92.695068	32	44	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	10534406	10534406	5295	16	C	T	T	29	29	EMP2	T	2	2
INPP5K	51763	broad.mit.edu	36	17	1346415	1346415	+	Missense_Mutation	SNP	G	A	A			TCGA-14-0867-01	TCGA-14-0867-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:1346415G>A	uc002fsr.1	-	c.1133C>T	c.(1132-1134)TCC>TTC	p.S378F	INPP5K_uc002fsq.1_Missense_Mutation_p.S302F|INPP5K_uc002fss.1_Missense_Mutation_p.S302F|INPP5K_uc010cjr.1_Missense_Mutation_p.S302F	NM_016532	NP_570122	Q9BT40	INP5K_HUMAN	inositol polyphosphate-5-phosphatase K isoform	378	Required for ruffle localization.				actin cytoskeleton organization	cytosol|endoplasmic reticulum|membrane fraction|neuron projection|ruffle	inositol 1,3,4,5-tetrakisphosphate 5-phosphatase activity|inositol bisphosphate phosphatase activity|inositol bisphosphate phosphatase activity|inositol trisphosphate phosphatase activity|inositol-1,4,5-trisphosphate 5-phosphatase activity|inositol-polyphosphate 5-phosphatase activity|lipid phosphatase activity|protein binding				0														0.146667	9.368605	18.389173	11	64	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	1346415	1346415	8061	17	G	A	A	41	41	INPP5K	A	2	2
NF1	4763	broad.mit.edu	36	17	26703492	26703492	+	Nonsense_Mutation	SNP	C	T	T			TCGA-14-0867-01	TCGA-14-0867-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:26703492C>T	uc002hgg.1	+	c.7549C>T	c.(7549-7551)CGA>TGA	p.R2517*	NF1_uc002hgh.1_Nonsense_Mutation_p.R2496*|NF1_uc010cso.1_Nonsense_Mutation_p.R705*	NM_001042492	NP_001035957	P21359	NF1_HUMAN	neurofibromin isoform 1	2517					actin cytoskeleton organization|adrenal gland development|artery morphogenesis|camera-type eye morphogenesis|cerebral cortex development|collagen fibril organization|forebrain astrocyte development|forebrain morphogenesis|heart development|liver development|MAPKKK cascade|metanephros development|myelination in peripheral nervous system|negative regulation of cell migration|negative regulation of endothelial cell proliferation|negative regulation of MAP kinase activity|negative regulation of MAPKKK cascade|negative regulation of neuroblast proliferation|negative regulation of oligodendrocyte differentiation|negative regulation of transcription factor import into nucleus|osteoblast differentiation|phosphatidylinositol 3-kinase cascade|pigmentation|positive regulation of adenylate cyclase activity|positive regulation of neuron apoptosis|Ras protein signal transduction|regulation of blood vessel endothelial cell migration|regulation of bone resorption|response to hypoxia|smooth muscle tissue development|spinal cord development|sympathetic nervous system development|visual learning|wound healing	axon|cytoplasm|dendrite|intrinsic to internal side of plasma membrane|nucleus	protein binding|Ras GTPase activator activity	p.?(1)		soft_tissue(155)|central_nervous_system(56)|large_intestine(27)|lung(19)|haematopoietic_and_lymphoid_tissue(13)|ovary(12)|autonomic_ganglia(7)|skin(3)|stomach(2)|breast(2)|thyroid(1)|prostate(1)|kidney(1)|pancreas(1)	300		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)						847	TCGA GBM(6;<1E-8)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)			0.822785	649.337709	672.606739	195	42	CC		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	26703492	26703492	10756	17	C	T	T	23	23	NF1	T	5	1
SERPINB2	5055	broad.mit.edu	36	18	59721280	59721280	+	Missense_Mutation	SNP	C	T	T			TCGA-14-0867-01	TCGA-14-0867-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr18:59721280C>T	uc002ljo.1	+	c.1009C>T	c.(1009-1011)CGG>TGG	p.R337W	SERPINB2_uc010dqh.1_Missense_Mutation_p.R267W|SERPINB2_uc002ljp.1_Intron|SERPINB2_uc002ljq.1_Intron	NM_002575	NP_002566	P05120	PAI2_HUMAN	serine (or cysteine) proteinase inhibitor, clade	337					anti-apoptosis|blood coagulation|fibrinolysis|regulation of proteolysis	extracellular space|Golgi apparatus|plasma membrane	serine-type endopeptidase inhibitor activity			lung(1)|skin(1)	2		Esophageal squamous(42;0.131)			Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)|Urokinase(DB00013)									0.459459	52.570076	52.623086	17	20	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	59721280	59721280	14589	18	C	T	T	19	19	SERPINB2	T	1	1
ZNF99	7652	broad.mit.edu	36	19	22743928	22743928	+	Silent	SNP	A	T	T			TCGA-14-0867-01	TCGA-14-0867-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr19:22743928A>T	uc002nqx.1	-	c.105T>A	c.(103-105)GCT>GCA	p.A35A		NM_001080409	NP_001073878	A8MXY4	ZNF99_HUMAN	zinc finger protein 99	35	KRAB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.102)												0.321839	78.57112	81.022753	28	59	AA		KEEP	---	---	---	---	capture			Silent	SNP	22743928	22743928	18808	19	A	T	T	11	11	ZNF99	T	4	4
LRG1	116844	broad.mit.edu	36	19	4489792	4489792	+	Silent	SNP	G	A	A			TCGA-14-0867-01	TCGA-14-0867-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:4489792G>A	uc002mau.1	-	c.204C>T	c.(202-204)GCC>GCT	p.A68A	PLIN5_uc002mat.1_Intron	NM_052972	NP_443204	P02750	A2GL_HUMAN	leucine-rich alpha-2-glycoprotein 1	68						extracellular region|membrane				ovary(1)	1		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0148)|STAD - Stomach adenocarcinoma(1328;0.18)										0.517857	90.874994	90.890615	29	27	GG		KEEP	---	---	---	---	capture			Silent	SNP	4489792	4489792	9315	19	G	A	A	39	39	LRG1	A	1	1
FUT1	2523	broad.mit.edu	36	19	53945394	53945394	+	Silent	SNP	G	A	A			TCGA-14-0867-01	TCGA-14-0867-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:53945394G>A	uc002pkk.1	-	c.957C>T	c.(955-957)GGC>GGT	p.G319G	FUT1_uc010emg.1_Silent_p.G319G	NM_000148	NP_000139	P19526	FUT1_HUMAN	fucosyltransferase 1	319	Lumenal (Potential).				L-fucose catabolic process|protein glycosylation	Golgi cisterna membrane|integral to plasma membrane|membrane fraction	galactoside 2-alpha-L-fucosyltransferase activity			ovary(1)	1		all_lung(116;1.7e-06)|all_epithelial(76;3.52e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000135)|all cancers(93;0.000354)|Epithelial(262;0.0191)|GBM - Glioblastoma multiforme(486;0.0222)										0.336	213.827628	219.773843	84	166	GG		KEEP	---	---	---	---	capture			Silent	SNP	53945394	53945394	6352	19	G	A	A	38	38	FUT1	A	1	1
LILRA2	11027	broad.mit.edu	36	19	59778223	59778223	+	Missense_Mutation	SNP	G	A	A			TCGA-14-0867-01	TCGA-14-0867-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:59778223G>A	uc002qgg.2	+	c.566G>A	c.(565-567)CGC>CAC	p.R189H	LILRA2_uc010ern.1_Missense_Mutation_p.R189H|LILRA2_uc002qgf.1_Missense_Mutation_p.R189H|LILRA2_uc010ero.1_Missense_Mutation_p.R177H	NM_006866	NP_006857	Q8N149	LIRA2_HUMAN	leukocyte immunoglobulin-like receptor,	189	Extracellular (Potential).|Ig-like C2-type 2.				defense response	integral to membrane	antigen binding|receptor activity			ovary(1)	1				GBM - Glioblastoma multiforme(193;0.0963)										0.135593	34.588126	57.363765	24	153	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	59778223	59778223	9111	19	G	A	A	38	38	LILRA2	A	1	1
CASZ1	54897	broad.mit.edu	36	1	10631734	10631734	+	Silent	SNP	G	A	A			TCGA-14-0867-01	TCGA-14-0867-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:10631734G>A	uc001aro.1	-	c.3138C>T	c.(3136-3138)GAC>GAT	p.D1046D	CASZ1_uc001arp.1_Silent_p.D1046D	NM_001079843	NP_001073312	Q86V15	CASZ1_HUMAN	castor homolog 1, zinc finger isoform a	1046	C2H2-type 4.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|zinc ion binding				0	Ovarian(185;0.203)|all_lung(157;0.204)	Lung NSC(185;4.96e-06)|all_lung(284;1.22e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00212)|Hepatocellular(190;0.00913)|Ovarian(437;0.0229)|Myeloproliferative disorder(586;0.0255)	STAD - Stomach adenocarcinoma(5;0.0224)	UCEC - Uterine corpus endometrioid carcinoma (279;0.0265)|Colorectal(212;3.54e-08)|COAD - Colon adenocarcinoma(227;9.56e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000219)|Kidney(185;0.00142)|KIRC - Kidney renal clear cell carcinoma(229;0.00381)|READ - Rectum adenocarcinoma(331;0.0419)|STAD - Stomach adenocarcinoma(132;0.0623)										0.611111	34.725351	34.919272	11	7	GG		KEEP	---	---	---	---	capture			Silent	SNP	10631734	10631734	2804	1	G	A	A	40	40	CASZ1	A	1	1
ATXN7L2	127002	broad.mit.edu	36	1	109834468	109834468	+	Missense_Mutation	SNP	G	A	A			TCGA-14-0867-01	TCGA-14-0867-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:109834468G>A	uc001dxr.1	+	c.1289G>A	c.(1288-1290)CGC>CAC	p.R430H	ATXN7L2_uc001dxs.1_Missense_Mutation_p.R57H|ATXN7L2_uc001dxt.1_5'Flank	NM_153340	NP_699171	Q5T6C5	AT7L2_HUMAN	ataxin 7-like 2	430										ovary(2)	2		all_epithelial(167;0.00197)|all_lung(203;0.00291)|Lung NSC(277;0.00453)		Colorectal(144;0.0129)|Lung(183;0.0426)|Epithelial(280;0.0675)|READ - Rectum adenocarcinoma(129;0.0693)|all cancers(265;0.071)|LUSC - Lung squamous cell carcinoma(189;0.228)								OREG0013635	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.252955	243.011953	266.472667	107	316	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	109834468	109834468	1237	1	G	A	A	38	38	ATXN7L2	A	1	1
ACAP3	116983	broad.mit.edu	36	1	1225927	1225927	+	Missense_Mutation	SNP	C	T	T			TCGA-14-0867-01	TCGA-14-0867-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:1225927C>T	uc001aeb.1	-	c.347G>A	c.(346-348)CGG>CAG	p.R116Q	ACAP3_uc001ady.1_5'Flank|ACAP3_uc001adz.1_Missense_Mutation_p.R74Q|ACAP3_uc001aea.1_Missense_Mutation_p.R74Q|ACAP3_uc001aec.1_Missense_Mutation_p.R74Q	NM_030649	NP_085152	Q96P50	ACAP3_HUMAN	ArfGAP with coiled-coil, ankyrin repeat and PH	116					filopodium assembly|regulation of ARF GTPase activity|signal transduction		ARF GTPase activator activity|cytoskeletal adaptor activity|SH3 domain binding|zinc ion binding				0														0.186047	16.575085	20.548341	8	35	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	1225927	1225927	121	1	C	T	T	23	23	ACAP3	T	1	1
OR10X1	128367	broad.mit.edu	36	1	156816034	156816034	+	Missense_Mutation	SNP	C	T	T			TCGA-14-0867-01	TCGA-14-0867-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:156816034C>T	uc001fsr.1	-	c.280G>A	c.(280-282)GTC>ATC	p.V94I		NM_001004477	NP_001004477	Q8NGY0	O10X1_HUMAN	olfactory receptor, family 10, subfamily X,	94	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1	all_hematologic(112;0.0378)													0.445378	152.950396	153.260271	53	66	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	156816034	156816034	11328	1	C	T	T	19	19	OR10X1	T	1	1
COPA	1314	broad.mit.edu	36	1	158528563	158528563	+	Missense_Mutation	SNP	T	A	A			TCGA-14-0867-01	TCGA-14-0867-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr1:158528563T>A	uc001fvv.2	-	c.3037A>T	c.(3037-3039)AAT>TAT	p.N1013Y	COPA_uc009wti.1_Missense_Mutation_p.N1004Y	NM_001098398	NP_001091868	P53621	COPA_HUMAN	coatomer protein complex, subunit alpha isoform	1004					COPI coating of Golgi vesicle|intracellular protein transport|pancreatic juice secretion|retrograde vesicle-mediated transport, Golgi to ER	COPI vesicle coat|cytosol|extracellular space|microsome|soluble fraction	hormone activity|structural molecule activity			ovary(1)	1	all_cancers(52;8.15e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)											0.148148	6.569899	12.996619	8	46	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	158528563	158528563	3865	1	T	A	A	61	61	COPA	A	4	4
DPT	1805	broad.mit.edu	36	1	166936913	166936913	+	Nonsense_Mutation	SNP	G	A	A			TCGA-14-0867-01	TCGA-14-0867-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:166936913G>A	uc001gfp.1	-	c.505C>T	c.(505-507)CGA>TGA	p.R169*		NM_001937	NP_001928	Q07507	DERM_HUMAN	dermatopontin precursor	169	2 X 53-55 AA tandem repeats.|3 X 6 AA repeats of D-R-[EQ]-W-[NQK]- [FY].				cell adhesion	extracellular space|proteinaceous extracellular matrix				ovary(1)	1	all_hematologic(923;0.208)													0.248201	347.735856	379.773769	138	418	GG		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	166936913	166936913	4923	1	G	A	A	39	39	DPT	A	5	1
XPR1	9213	broad.mit.edu	36	1	179109564	179109564	+	Silent	SNP	C	T	T			TCGA-14-0867-01	TCGA-14-0867-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:179109564C>T	uc001goi.1	+	c.1671C>T	c.(1669-1671)GCC>GCT	p.A557A	XPR1_uc009wxn.1_Silent_p.A492A	NM_004736	NP_004727	Q9UBH6	XPR1_HUMAN	xenotropic and polytropic retrovirus receptor	557	EXS.|Cytoplasmic (Potential).					integral to plasma membrane	G-protein coupled receptor activity				0														0.3	62.949882	65.450166	21	49	CC		KEEP	---	---	---	---	capture			Silent	SNP	179109564	179109564	18034	1	C	T	T	24	24	XPR1	T	2	2
RYR2	6262	broad.mit.edu	36	1	235956206	235956206	+	Missense_Mutation	SNP	G	A	A			TCGA-14-0867-01	TCGA-14-0867-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:235956206G>A	uc001hyl.1	+	c.10700G>A	c.(10699-10701)CGT>CAT	p.R3567H		NM_001035	NP_001026	Q92736	RYR2_HUMAN	cardiac muscle ryanodine receptor	3567					cardiac muscle contraction|detection of calcium ion|induction of apoptosis by ionic changes|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum|response to caffeine|response to hypoxia|response to redox state	calcium channel complex|plasma membrane|plasma membrane enriched fraction|sarcoplasmic reticulum membrane	calcium ion binding|calmodulin binding|identical protein binding|protein kinase A catalytic subunit binding|protein kinase A regulatory subunit binding|receptor activity|ryanodine-sensitive calcium-release channel activity|suramin binding	p.R3565H(1)		ovary(17)|large_intestine(6)|central_nervous_system(6)|pancreas(3)|breast(1)	33	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)											0.412969	366.322997	368.259389	121	172	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	235956206	235956206	14249	1	G	A	A	40	40	RYR2	A	1	1
PAFAH2	5051	broad.mit.edu	36	1	26189880	26189880	+	Silent	SNP	C	T	T			TCGA-14-0867-01	TCGA-14-0867-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:26189880C>T	uc001bld.2	-	c.15G>A	c.(13-15)CAG>CAA	p.Q5Q	PAFAH2_uc001ble.2_Silent_p.Q5Q	NM_000437	NP_000428	Q99487	PAFA2_HUMAN	platelet-activating factor acetylhydrolase 2	5					lipid catabolic process	cytoplasm	1-alkyl-2-acetylglycerophosphocholine esterase activity|phospholipid binding			ovary(2)	2		Colorectal(325;3.47e-05)|Lung NSC(340;6.23e-05)|all_lung(284;9.48e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0155)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0298)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;3.84e-25)|Colorectal(126;3.57e-08)|COAD - Colon adenocarcinoma(152;1.84e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|BRCA - Breast invasive adenocarcinoma(304;0.00105)|STAD - Stomach adenocarcinoma(196;0.00155)|GBM - Glioblastoma multiforme(114;0.00717)|READ - Rectum adenocarcinoma(331;0.0649)										0.432802	556.218344	557.955406	190	249	CC		KEEP	---	---	---	---	capture			Silent	SNP	26189880	26189880	11803	1	C	T	T	20	20	PAFAH2	T	2	2
FAF1	11124	broad.mit.edu	36	1	50834418	50834418	+	Missense_Mutation	SNP	C	T	T			TCGA-14-0867-01	TCGA-14-0867-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:50834418C>T	uc009vyx.1	-	c.803G>A	c.(802-804)AGA>AAA	p.R268K	FAF1_uc009vyw.1_Intron|FAF1_uc001cse.1_Missense_Mutation_p.R268K	NM_007051	NP_008982	Q9UNN5	FAF1_HUMAN	FAS-associated factor 1	268					apoptosis|cytoplasmic sequestering of NF-kappaB|positive regulation of apoptosis|positive regulation of protein complex assembly|proteasomal ubiquitin-dependent protein catabolic process|regulation of protein catabolic process	CD95 death-inducing signaling complex|cytosol|perinuclear region of cytoplasm	heat shock protein binding|NF-kappaB binding|protein kinase binding|protein kinase regulator activity	p.0?(1)		ovary(1)|pancreas(1)	2				GBM - Glioblastoma multiforme(3;3.18e-11)|all cancers(3;0.00526)										0.479339	537.812855	537.948079	174	189	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	50834418	50834418	5566	1	C	T	T	32	32	FAF1	T	2	2
COL24A1	255631	broad.mit.edu	36	1	86024715	86024715	+	Silent	SNP	T	G	G			TCGA-14-0867-01	TCGA-14-0867-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr1:86024715T>G	uc001dlj.1	-	c.3969A>C	c.(3967-3969)CCA>CCC	p.P1323P	COL24A1_uc001dli.1_Silent_p.P459P|COL24A1_uc001dlk.1_Non-coding_Transcript	NM_152890	NP_690850	Q17RW2	COOA1_HUMAN	collagen, type XXIV, alpha 1	1323	Collagen-like 15.				cell adhesion	collagen	extracellular matrix structural constituent			ovary(3)|central_nervous_system(1)	4				all cancers(265;0.0627)|Epithelial(280;0.0689)										0.258065	8.005186	9.726866	8	23	TT		KEEP	---	---	---	---	capture			Silent	SNP	86024715	86024715	3821	1	T	G	G	55	55	COL24A1	G	4	4
ZFP64	55734	broad.mit.edu	36	20	50134673	50134673	+	Missense_Mutation	SNP	C	T	T			TCGA-14-0867-01	TCGA-14-0867-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr20:50134673C>T	uc002xwk.1	-	c.1768G>A	c.(1768-1770)GTC>ATC	p.V590I	ZFP64_uc002xwj.1_Missense_Mutation_p.V371I	NM_199427	NP_955459	Q9NPA5	ZF64A_HUMAN	zinc finger protein 64 isoform d	435	C2H2-type 9.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1														0.25	91.135262	100.433492	41	123	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	50134673	50134673	18241	20	C	T	T	19	19	ZFP64	T	1	1
PRPF6	24148	broad.mit.edu	36	20	62130317	62130317	+	Silent	SNP	C	T	T			TCGA-14-0867-01	TCGA-14-0867-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr20:62130317C>T	uc002yho.1	+	c.2382C>T	c.(2380-2382)AAC>AAT	p.N794N	PRPF6_uc002yhp.1_Silent_p.N754N	NM_012469	NP_036601	O94906	PRP6_HUMAN	PRP6 pre-mRNA processing factor 6 homolog	794					assembly of spliceosomal tri-snRNP|positive regulation of transcription from RNA polymerase II promoter|spliceosome assembly	catalytic step 2 spliceosome|nucleoplasm|U4/U6 snRNP|U4/U6 x U5 tri-snRNP complex|U5 snRNP	androgen receptor binding|ribonucleoprotein binding|transcription coactivator activity			ovary(2)	2	all_cancers(38;6.47e-12)|all_epithelial(29;1.26e-13)|Lung NSC(23;9.37e-10)|all_lung(23;3.23e-09)													0.5	6.549944	6.549944	2	2	CC		KEEP	---	---	---	---	capture			Silent	SNP	62130317	62130317	13017	20	C	T	T	17	17	PRPF6	T	2	2
SCN9A	6335	broad.mit.edu	36	2	166849542	166849542	+	Missense_Mutation	SNP	C	A	A			TCGA-14-0867-01	TCGA-14-0867-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:166849542C>A	uc002udq.2	-	c.1641G>T	c.(1639-1641)AGG>AGT	p.R547S	SCN9A_uc002udr.1_Missense_Mutation_p.R418S|SCN9A_uc002uds.1_Missense_Mutation_p.R418S|SCN9A_uc002udt.1_Missense_Mutation_p.R418S	NM_002977	NP_002968	Q15858	SCN9A_HUMAN	sodium channel, voltage-gated, type IX, alpha	547						voltage-gated sodium channel complex	voltage-gated sodium channel activity			ovary(6)|central_nervous_system(5)	11					Lamotrigine(DB00555)|Lidocaine(DB00281)									0.492063	81.7121	81.715657	31	32	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	166849542	166849542	14407	2	C	A	A	26	26	SCN9A	A	3	3
FASTKD2	22868	broad.mit.edu	36	2	207345268	207345268	+	Missense_Mutation	SNP	C	A	A			TCGA-14-0867-01	TCGA-14-0867-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:207345268C>A	uc002vbx.1	+	c.1233C>A	c.(1231-1233)TTC>TTA	p.F411L	FASTKD2_uc002vbu.1_Missense_Mutation_p.F395L|FASTKD2_uc002vbv.1_Missense_Mutation_p.F395L|FASTKD2_uc002vbw.1_Missense_Mutation_p.F395L	NM_014929	NP_055744	Q9NYY8	FAKD2_HUMAN	FAST kinase domains 2	411					apoptosis|cellular respiration	mitochondrion	ATP binding|protein kinase activity			ovary(2)	2				LUSC - Lung squamous cell carcinoma(261;0.0718)|Epithelial(149;0.119)|Lung(261;0.138)										0.238095	12.562238	13.880303	5	16	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	207345268	207345268	5922	2	C	A	A	31	31	FASTKD2	A	3	3
C2orf57	165100	broad.mit.edu	36	2	232166892	232166892	+	Missense_Mutation	SNP	G	A	A			TCGA-14-0867-01	TCGA-14-0867-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:232166892G>A	uc002vrz.1	+	c.986G>A	c.(985-987)CGC>CAC	p.R329H		NM_152614	NP_689827	Q53QW1	CB057_HUMAN	hypothetical protein LOC165100	329										ovary(1)	1		Renal(207;0.025)|all_hematologic(139;0.0735)|Acute lymphoblastic leukemia(138;0.164)		Epithelial(121;1.33e-11)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(119;0.014)										0.2	10.058105	12.1545	5	20	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	232166892	232166892	2266	2	G	A	A	38	38	C2orf57	A	1	1
CEBPZ	10153	broad.mit.edu	36	2	37282429	37282429	+	Silent	SNP	A	T	T			TCGA-14-0867-01	TCGA-14-0867-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr2:37282429A>T	uc002rpz.1	-	c.3147T>A	c.(3145-3147)ACT>ACA	p.T1049T		NM_005760	NP_005751	Q03701	CEBPZ_HUMAN	CCAAT/enhancer binding protein zeta	1049					regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	nucleus	DNA binding			pancreas(1)	1		all_hematologic(82;0.21)												0.384615	8.96618	9.119248	5	8	AA		KEEP	---	---	---	---	capture			Silent	SNP	37282429	37282429	3337	2	A	T	T	15	15	CEBPZ	T	4	4
ZNF2	7549	broad.mit.edu	36	2	95210917	95210917	+	Missense_Mutation	SNP	A	T	T			TCGA-14-0867-01	TCGA-14-0867-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr2:95210917A>T	uc002suf.1	+	c.614A>T	c.(613-615)GAG>GTG	p.E205V	ZNF2_uc002sug.1_Missense_Mutation_p.E163V|ZNF2_uc010fhs.1_Missense_Mutation_p.E126V	NM_021088	NP_066574	Q9BSG1	ZNF2_HUMAN	zinc finger protein 2 isoform a	205	C2H2-type 2.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Ovarian(717;0.00768)		READ - Rectum adenocarcinoma(193;0.0222)										0.176471	9.234099	14.287443	9	42	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	95210917	95210917	18351	2	A	T	T	11	11	ZNF2	T	4	4
FAHD2B	151313	broad.mit.edu	36	2	97115277	97115277	+	Missense_Mutation	SNP	C	T	T			TCGA-14-0867-01	TCGA-14-0867-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:97115277C>T	uc002sxm.1	-	c.571G>A	c.(571-573)GTG>ATG	p.V191M		NM_199336	NP_955368	Q6P2I3	FAH2B_HUMAN	fumarylacetoacetate hydrolase domain containing	191							hydrolase activity|metal ion binding				0														0.25	63.082066	68.307726	23	69	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	97115277	97115277	5571	2	C	T	T	19	19	FAHD2B	T	1	1
AGPAT9	84803	broad.mit.edu	36	4	84676815	84676815	+	Missense_Mutation	SNP	C	G	G			TCGA-14-0867-01	TCGA-14-0867-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:84676815C>G	uc003how.1	+	c.16C>G	c.(16-18)CTG>GTG	p.L6V	AGPAT9_uc003hox.1_Missense_Mutation_p.L6V|AGPAT9_uc003hoy.1_Missense_Mutation_p.L6V	NM_032717	NP_116106	Q53EU6	GPAT3_HUMAN	lysophosphatidic acid acyltransferase theta	6					phospholipid biosynthetic process|regulation of TOR signaling cascade|triglyceride biosynthetic process	endoplasmic reticulum membrane|integral to membrane	glycerol-3-phosphate O-acyltransferase activity				0		Hepatocellular(203;0.114)												0.705882	25.78108	26.41942	12	5	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	84676815	84676815	395	4	C	G	G	28	28	AGPAT9	G	3	3
SOX30	11063	broad.mit.edu	36	5	157010786	157010786	+	Silent	SNP	T	A	A			TCGA-14-0867-01	TCGA-14-0867-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr5:157010786T>A	uc003lxb.1	-	c.879A>T	c.(877-879)CCA>CCT	p.P293P	SOX30_uc003lxc.1_Silent_p.P293P	NM_178424	NP_848511	O94993	SOX30_HUMAN	SRY (sex determining region Y)-box 30 isoform a	293					regulation of transcription from RNA polymerase II promoter|regulation of transcription, DNA-dependent|response to corticosteroid stimulus|transcription, DNA-dependent	nucleus|nucleus	sequence-specific DNA binding|sequence-specific DNA binding RNA polymerase II transcription factor activity			ovary(1)|central_nervous_system(1)	2	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.138)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			Esophageal Squamous(31;525 799 19355 21125 41744)								0.612903	64.330049	64.675987	19	12	TT		KEEP	---	---	---	---	capture			Silent	SNP	157010786	157010786	15452	5	T	A	A	55	55	SOX30	A	4	4
C6orf174	387104	broad.mit.edu	36	6	127879352	127879352	+	Missense_Mutation	SNP	C	T	T			TCGA-14-0867-01	TCGA-14-0867-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:127879352C>T	uc003qbf.1	-	c.101G>A	c.(100-102)AGA>AAA	p.R34K	C6orf174_uc003qbg.2_Missense_Mutation_p.R34K	NM_001012279	NP_001012279	Q5TF21	CF174_HUMAN	hypothetical protein LOC387104	34						integral to membrane				breast(3)|ovary(2)	5				GBM - Glioblastoma multiforme(226;0.026)|all cancers(137;0.161)										0.222222	33.86046	38.975302	16	56	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	127879352	127879352	2450	6	C	T	T	32	32	C6orf174	T	2	2
MTHFD1L	25902	broad.mit.edu	36	6	151378393	151378393	+	Silent	SNP	G	A	A			TCGA-14-0867-01	TCGA-14-0867-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:151378393G>A	uc003qob.1	+	c.2457G>A	c.(2455-2457)CGG>CGA	p.R819R	MTHFD1L_uc003qoc.1_Silent_p.R767R	NM_015440	NP_056255	Q6UB35	C1TM_HUMAN	methylenetetrahydrofolate dehydrogenase (NADP+	819	Formyltetrahydrofolate synthetase.				folic acid-containing compound biosynthetic process|formate metabolic process|one-carbon metabolic process|tetrahydrofolate metabolic process	mitochondrion	ATP binding|formate-tetrahydrofolate ligase activity|protein homodimerization activity			ovary(3)|large_intestine(1)	4		Ovarian(120;0.128)		OV - Ovarian serous cystadenocarcinoma(155;8.7e-12)										0.386417	488.827362	493.636106	165	262	GG		KEEP	---	---	---	---	capture			Silent	SNP	151378393	151378393	10321	6	G	A	A	43	43	MTHFD1L	A	2	2
PIK3CG	5294	broad.mit.edu	36	7	106307345	106307345	+	Missense_Mutation	SNP	A	T	T			TCGA-14-0867-01	TCGA-14-0867-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr7:106307345A>T	uc003vdv.2	+	c.2537A>T	c.(2536-2538)CAG>CTG	p.Q846L	PIK3CG_uc003vdu.1_Missense_Mutation_p.Q846L|PIK3CG_uc003vdw.1_Missense_Mutation_p.Q846L	NM_002649	NP_002640	P48736	PK3CG_HUMAN	phosphoinositide-3-kinase, catalytic, gamma	846	PI3K/PI4K.				G-protein coupled receptor protein signaling pathway|phosphatidylinositol-mediated signaling|platelet activation	phosphatidylinositol 3-kinase complex	1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol-4,5-bisphosphate 3-kinase activity|protein binding			central_nervous_system(8)|lung(7)|pancreas(3)|ovary(2)|skin(1)	21										292				0.444961	874.012866	875.716629	287	358	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	106307345	106307345	12340	7	A	T	T	7	7	PIK3CG	T	4	4
FOXP2	93986	broad.mit.edu	36	7	114086964	114086964	+	Silent	SNP	G	A	A			TCGA-14-0867-01	TCGA-14-0867-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:114086964G>A	uc003vgz.2	+	c.1722G>A	c.(1720-1722)AAG>AAA	p.K574K	FOXP2_uc003vgu.2_Non-coding_Transcript|FOXP2_uc003vha.2_Silent_p.K457K|FOXP2_uc003vhb.2_Silent_p.K549K|FOXP2_uc010ljz.1_Silent_p.K364K|FOXP2_uc003vhe.1_Silent_p.K119K	NM_148898	NP_683697	O15409	FOXP2_HUMAN	forkhead box P2 isoform II	549	Fork-head.				camera-type eye development|caudate nucleus development|cerebellum development|cerebral cortex development|embryo development|growth|lung alveolus development|negative regulation of gene-specific transcription from RNA polymerase II promoter|pattern specification process|positive regulation of epithelial cell proliferation involved in lung morphogenesis|positive regulation of mesenchymal cell proliferation|post-embryonic development|putamen development|regulation of sequence-specific DNA binding transcription factor activity|righting reflex|skeletal muscle tissue development|smooth muscle tissue development|vocal learning	cytoplasm|transcription factor complex	chromatin binding|DNA bending activity|double-stranded DNA binding|promoter binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|zinc ion binding			ovary(4)|lung(1)|breast(1)|pancreas(1)	7														0.173516	83.340944	105.359659	38	181	GG		KEEP	---	---	---	---	capture			Silent	SNP	114086964	114086964	6273	7	G	A	A	35	35	FOXP2	A	2	2
GIMAP8	155038	broad.mit.edu	36	7	149805590	149805590	+	Missense_Mutation	SNP	G	A	A			TCGA-14-0867-01	TCGA-14-0867-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:149805590G>A	uc003whj.1	+	c.1787G>A	c.(1786-1788)CGG>CAG	p.R596Q		NM_175571	NP_783161	Q8ND71	GIMA8_HUMAN	GTPase, IMAP family member 8	596						endoplasmic reticulum|Golgi apparatus|mitochondrion	GTP binding			ovary(1)|breast(1)|central_nervous_system(1)	3			OV - Ovarian serous cystadenocarcinoma(82;0.0218)	UCEC - Uterine corpus endometrioid carcinoma (81;0.17)										0.188235	31.359412	39.089754	16	69	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	149805590	149805590	6653	7	G	A	A	39	39	GIMAP8	A	1	1
STEAP1	26872	broad.mit.edu	36	7	89631795	89631795	+	Missense_Mutation	SNP	G	C	C			TCGA-14-0867-01	TCGA-14-0867-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:89631795G>C	uc003ujx.1	+	c.831G>C	c.(829-831)TGG>TGC	p.W277C		NM_012449	NP_036581	Q9UHE8	STEA1_HUMAN	six transmembrane epithelial antigen of the	277	Helical; (Potential).				electron transport chain|ion transport|iron ion homeostasis	cell-cell junction|endosome membrane|integral to plasma membrane	channel activity|electron carrier activity|flavin adenine dinucleotide binding|iron ion binding|oxidoreductase activity				0	all_hematologic(106;0.112)													0.431579	403.979929	405.143491	123	162	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	89631795	89631795	15797	7	G	C	C	41	41	STEAP1	C	3	3
VPS13B	157680	broad.mit.edu	36	8	100916678	100916678	+	Missense_Mutation	SNP	T	C	C			TCGA-14-0867-01	TCGA-14-0867-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr8:100916678T>C	uc003yiv.1	+	c.9767T>C	c.(9766-9768)ATT>ACT	p.I3256T	VPS13B_uc003yiw.1_Missense_Mutation_p.I3231T	NM_017890	NP_060360	Q7Z7G8	VP13B_HUMAN	vacuolar protein sorting 13B isoform 5	3256					protein transport					ovary(7)|skin(4)|lung(3)|central_nervous_system(2)|pancreas(2)|breast(1)|kidney(1)	20	Breast(36;3.73e-07)		OV - Ovarian serous cystadenocarcinoma(57;0.00636)			Colon(161;2205 2542 7338 31318)				1116				0.325203	113.758534	117.092803	40	83	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	100916678	100916678	17757	8	T	C	C	52	52	VPS13B	C	4	4
MAK16	84549	broad.mit.edu	36	8	33475517	33475517	+	Missense_Mutation	SNP	G	C	C			TCGA-14-0867-01	TCGA-14-0867-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr8:33475517G>C	uc003xjj.1	+	c.731G>C	c.(730-732)AGT>ACT	p.S244T	C8orf41_uc010lvu.1_Intron	NM_032509	NP_115898	Q9BXY0	MAK16_HUMAN	MAK16 homolog	244	Asp-rich.					nucleolus				ovary(1)	1														0.2	10.860561	12.954185	5	20	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	33475517	33475517	9581	8	G	C	C	36	36	MAK16	C	3	3
PALM2-AKAP2	445815	broad.mit.edu	36	9	111744878	111744878	+	Silent	SNP	C	A	A			TCGA-14-0867-01	TCGA-14-0867-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr9:111744878C>A	uc004bei.2	+	c.588C>A	c.(586-588)GTC>GTA	p.V196V	PALM2_uc004bef.1_Silent_p.V198V|PALM2_uc004beg.1_Silent_p.V164V|PALM2_uc004beh.2_Silent_p.V196V|PALM2-AKAP2_uc004bek.2_Intron|PALM2-AKAP2_uc004bej.2_Intron|PALM2-AKAP2_uc004bel.1_Intron	NM_001004065	NP_001004065	Q9Y2D5	AKAP2_HUMAN	A kinase (PRKA) anchor protein 2 isoform 1	Error:Variant_position_missing_in_Q9Y2D5_after_alignment							enzyme binding			ovary(3)|central_nervous_system(2)	5														0.392562	514.132941	519.023366	190	294	CC		KEEP	---	---	---	---	capture			Silent	SNP	111744878	111744878	11826	9	C	A	A	30	30	PALM2-AKAP2	A	3	3
DFNB31	25861	broad.mit.edu	36	9	116208589	116208589	+	Silent	SNP	G	C	C			TCGA-14-0867-01	TCGA-14-0867-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr9:116208589G>C	uc004biz.2	-	c.2103C>G	c.(2101-2103)GGC>GGG	p.G701G	DFNB31_uc004biy.2_Silent_p.G318G|DFNB31_uc004bja.2_Silent_p.G701G|DFNB31_uc004bix.1_Silent_p.G350G	NM_015404	NP_001077354	Q9P202	WHRN_HUMAN	CASK-interacting protein CIP98 isoform 1	701	Pro-rich.				inner ear receptor stereocilium organization|response to stimulus|retina homeostasis|sensory perception of sound|visual perception	cytoplasm|growth cone|stereocilium				ovary(4)|central_nervous_system(1)|pancreas(1)	6														0.25	9.602063	10.504727	4	12	GG		KEEP	---	---	---	---	capture			Silent	SNP	116208589	116208589	4634	9	G	C	C	34	34	DFNB31	C	3	3
PLXNA3	55558	broad.mit.edu	36	X	153341751	153341751	+	Missense_Mutation	SNP	C	T	T			TCGA-14-0867-01	TCGA-14-0867-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:153341751C>T	uc004flm.1	+	c.34C>T	c.(34-36)CTT>TTT	p.L12F		NM_017514	NP_059984	P51805	PLXA3_HUMAN	plexin A3	12					axon guidance	integral to membrane|intracellular|plasma membrane	transmembrane receptor activity			ovary(1)|central_nervous_system(1)	2	all_cancers(53;5.05e-16)|all_epithelial(53;1.87e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)													0.583333	25.527833	25.600799	7	5	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	153341751	153341751	12547	23	C	T	T	24	24	PLXNA3	T	2	2
C11orf2	738	broad.mit.edu	36	11	64632886	64632902	+	Frame_Shift_Del	DEL	ACATTAAGGCCTCTCTG	-	-			TCGA-14-0867-01	TCGA-14-0867-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:64632886_64632902delACATTAAGGCCTCTCTG	uc001ocr.1	+	c.1367_1383delACATTAAGGCCTCTCTG	c.(1366-1383)CACATTAAGGCCTCTCTGfs	p.H456fs	C11orf2_uc001ocs.1_Frame_Shift_Del_p.H332fs	NM_013265	NP_037397	Q9UID3	FFR_HUMAN	chromosome 11 open reading frame2	456_461					lipid transport|protein transport	Golgi apparatus|integral to membrane					0														0.43			15	20				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	64632886	64632902	1670	11	ACATTAAGGCCTCTCTG	-	-	6	6	C11orf2	-	5	5
TP53	7157	broad.mit.edu	36	17	7520046	7520046	+	Frame_Shift_Del	DEL	C	-	-			TCGA-14-0867-01	TCGA-14-0867-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:7520046_7520046delC	uc002gim.2	-	c.366_366delG	c.(364-366)GTGfs	p.V122fs	TP53_uc002gig.1_Frame_Shift_Del_p.V122fs|TP53_uc002gih.1_Frame_Shift_Del_p.V122fs|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_5'Flank|TP53_uc010cng.1_5'Flank|TP53_uc002gii.1_5'Flank|TP53_uc010cnh.1_Frame_Shift_Del_p.V122fs|TP53_uc010cni.1_Frame_Shift_Del_p.V122fs|TP53_uc002gij.2_Frame_Shift_Del_p.V122fs|TP53_uc010cnj.1_5'Flank|TP53_uc002gin.2_Intron|TP53_uc002gio.2_Intron|TP53_uc010cnk.1_Frame_Shift_Del_p.V137fs	NM_001126112	NP_001119584	P04637	P53_HUMAN	tumor protein p53 isoform a	122	Required for interaction with FBXO42.||Interaction with HIPK1 (By similarity).|Interaction with AXIN1 (By similarity).		V -> L (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.0?(6)|p.G59fs*23(3)|p.V122fs*26(2)|p.V73fs*9(1)|p.G105_T125del21(1)|p.V122fs*46(1)|p.Y107fs*44(1)|p.P13fs*18(1)|p.S33fs*23(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)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)		Pancreas(47;798 1329 9957 10801)		111		690	TCGA GBM(1;<1E-8)|TSP Lung(2;<1E-8)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)			0.78			170	48				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	7520046	7520046	16923	17	C	-	-	29	29	TP53	-	5	5
SLC9A1	6548	broad.mit.edu	36	1	27313285	27313286	+	Frame_Shift_Ins	INS	-	C	C			TCGA-14-0867-01	TCGA-14-0867-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:27313285_27313286insC	uc001bnm.1	-	c.431_432insG	c.(430-432)GGCfs	p.G144fs	SLC9A1_uc001bnn.1_Frame_Shift_Ins_p.G144fs	NM_003047	NP_003038	P19634	SL9A1_HUMAN	solute carrier family 9, isoform A1	144	Helical; Name=M3; (Potential).				regulation of pH	integral to membrane	sodium:hydrogen antiporter activity			ovary(1)|central_nervous_system(1)	2				UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Epithelial(14;2.19e-50)|OV - Ovarian serous cystadenocarcinoma(117;1.8e-29)|Colorectal(126;7.61e-09)|COAD - Colon adenocarcinoma(152;9.32e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000521)|KIRC - Kidney renal clear cell carcinoma(1967;0.00079)|STAD - Stomach adenocarcinoma(196;0.00125)|READ - Rectum adenocarcinoma(331;0.046)	Amiloride(DB00594)									0.33			2	4				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	27313285	27313286	15206	1	-	C	C	42	42	SLC9A1	C	5	5
MYT1	4661	broad.mit.edu	36	20	62341567	62341567	+	Frame_Shift_Del	DEL	T	-	-			TCGA-14-0867-01	TCGA-14-0867-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:62341567_62341567delT	uc002yii.1	+	c.3104_3104delT	c.(3103-3105)ATGfs	p.M1035fs	MYT1_uc002yij.1_Frame_Shift_Del_p.M694fs|MYT1_uc002yik.1_Frame_Shift_Del_p.M1fs	NM_004535	NP_004526	Q01538	MYT1_HUMAN	myelin transcription factor 1	1035					cell differentiation|nervous system development|regulation of transcription, DNA-dependent	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)	2	all_cancers(38;1.82e-11)|all_epithelial(29;3.3e-13)|Lung NSC(23;5.21e-10)|all_lung(23;1.92e-09)					GBM(59;481 1041 20555 21139 33705)				1819				0.41			44	63				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	62341567	62341567	10501	20	T	-	-	51	51	MYT1	-	5	5
LDOC1L	84247	broad.mit.edu	36	22	43271945	43271950	+	In_Frame_Del	DEL	ATTGGC	-	-			TCGA-14-0867-01	TCGA-14-0867-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:43271945_43271950delATTGGC	uc003beu.1	-	c.151_156delGCCAAT	c.(151-156)GCCAATdel	p.AN51del	LDOC1L_uc010gzs.1_In_Frame_Del_p.AN51del	NM_032287	NP_115663	Q6ICC9	LDOCL_HUMAN	leucine zipper, down-regulated in cancer 1-like	51_52	Potential.									ovary(1)	1		Ovarian(80;0.024)|all_neural(38;0.0416)		LUAD - Lung adenocarcinoma(64;0.0161)										0.63			173	100				---	---	---	---	capture_indel			In_Frame_Del	DEL	43271945	43271950	9034	22	ATTGGC	-	-	12	12	LDOC1L	-	5	5
SATB2	23314	broad.mit.edu	36	2	199845297	199845298	+	Frame_Shift_Ins	INS	-	T	T			TCGA-14-0867-01	TCGA-14-0867-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:199845297_199845298insT	uc002uuy.1	-	c.2083_2084insA	c.(2083-2085)CTGfs	p.L695fs	SATB2_uc010fsq.1_Frame_Shift_Ins_p.L577fs|SATB2_uc002uuz.1_Frame_Shift_Ins_p.L695fs|SATB2_uc002uva.1_Frame_Shift_Ins_p.L695fs	NM_015265	NP_056080	Q9UPW6	SATB2_HUMAN	SATB homeobox 2	695						cytoplasm|nuclear matrix	sequence-specific DNA binding transcription factor activity			ovary(1)	1						Colon(30;262 767 11040 24421 36230)								0.75			522	175				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	199845297	199845298	14335	2	-	T	T	7	7	SATB2	T	5	5
CCDC108	255101	broad.mit.edu	36	2	219577024	219577025	+	Frame_Shift_Ins	INS	-	CA	CA			TCGA-14-0867-01	TCGA-14-0867-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:219577024_219577025insCA	uc002vjl.1	-	c.5448_5449insTG	c.(5446-5451)CCCACAfs	p.P1816fs	MIR375_hsa-mir-375|MI0000783_5'Flank	NM_194302	NP_919278	Q6ZU64	CC108_HUMAN	coiled-coil domain containing 108 isoform 1	1816_1817	Glu-rich.					integral to membrane	structural molecule activity			ovary(2)|pancreas(1)	3		Renal(207;0.0915)		Epithelial(149;1.12e-06)|all cancers(144;0.000196)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)										0.48			286	309				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	219577024	219577025	2863	2	-	CA	CA	59	59	CCDC108	CA	5	5
PCDHGA2	56113	broad.mit.edu	36	5	140699094	140699095	+	Frame_Shift_Del	DEL	AG	-	-			TCGA-14-0867-01	TCGA-14-0867-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:140699094_140699095delAG	uc003ljk.1	+	c.372_373delAG	c.(370-375)ACAGATfs	p.T124fs	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljj.1_Frame_Shift_Del_p.T124fs	NM_018915	NP_061738	Q9Y5H1	PCDG2_HUMAN	protocadherin gamma subfamily A, 2 isoform 1	124_125	Cadherin 1.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)											0.44			23	29				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	140699094	140699095	11974	5	AG	-	-	7	7	PCDHGA2	-	5	5
CDKN2A	1029	broad.mit.edu	36	9	21984441	21984442	+	Frame_Shift_Ins	INS	-	C	C			TCGA-14-0867-01	TCGA-14-0867-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:21984441_21984442insC	uc003zpl.1	-	c.12_13insG	c.(10-15)GGGCGGfs	p.G4fs	CDKN2B-AS_uc010miw.1_5'Flank|CDKN2B-AS_uc010mix.1_5'Flank|CDKN2B-AS_uc003zpm.1_5'Flank|MTAP_uc003zpi.1_Intron	NM_058195	NP_478102	P42771	CD2A1_HUMAN	cyclin-dependent kinase inhibitor 2A isoform 4	Error:Variant_position_missing_in_P42771_after_alignment					cell cycle arrest|cell cycle checkpoint|G1 phase of mitotic cell cycle|G1/S transition of mitotic cell cycle|induction of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of cell-matrix adhesion|negative regulation of cyclin-dependent protein kinase activity|negative regulation of NF-kappaB transcription factor activity|positive regulation of macrophage apoptosis|positive regulation of smooth muscle cell apoptosis|Ras protein signal transduction|replicative senescence	cytosol|nucleus	cyclin-dependent protein kinase inhibitor activity|NF-kappaB binding|protein binding|protein binding|protein kinase binding	p.0?(197)|p.A4_P11del(12)		haematopoietic_and_lymphoid_tissue(647)|skin(417)|upper_aerodigestive_tract(405)|central_nervous_system(380)|lung(319)|pancreas(237)|oesophagus(230)|urinary_tract(225)|pleura(94)|liver(91)|ovary(76)|soft_tissue(73)|biliary_tract(71)|bone(70)|breast(46)|stomach(44)|kidney(39)|NS(28)|thyroid(24)|cervix(23)|meninges(18)|genital_tract(15)|endometrium(13)|prostate(11)|autonomic_ganglia(10)|large_intestine(9)|salivary_gland(8)|adrenal_gland(6)|eye(4)|vulva(2)|small_intestine(1)	3636		all_cancers(5;0)|Acute lymphoblastic leukemia(3;0)|all_hematologic(3;0)|all_epithelial(2;2.37e-290)|Lung NSC(2;1.26e-139)|all_lung(2;4.48e-131)|Glioma(2;3.26e-60)|all_neural(2;2.1e-52)|Renal(3;1.07e-46)|Esophageal squamous(3;3.83e-46)|Melanoma(2;2.74e-34)|Breast(3;1.14e-11)|Ovarian(3;0.000128)|Hepatocellular(5;0.00162)|Colorectal(97;0.172)		all cancers(2;0)|GBM - Glioblastoma multiforme(3;0)|Lung(2;4.07e-74)|Epithelial(2;1.08e-61)|LUSC - Lung squamous cell carcinoma(2;3.82e-48)|LUAD - Lung adenocarcinoma(2;4.56e-26)|OV - Ovarian serous cystadenocarcinoma(39;7.64e-10)|BRCA - Breast invasive adenocarcinoma(2;5.01e-09)|STAD - Stomach adenocarcinoma(4;4.63e-07)|Kidney(2;5.79e-07)|KIRC - Kidney renal clear cell carcinoma(2;7.27e-07)|COAD - Colon adenocarcinoma(8;5.15e-05)				17		76	TSP Lung(5;3.83e-07)			0.33			2	4				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	21984441	21984442	3290	9	-	C	C	38	38	CDKN2A	C	5	5
WNK2	65268	broad.mit.edu	36	9	95064121	95064122	+	Frame_Shift_Ins	INS	-	T	T			TCGA-14-0867-01	TCGA-14-0867-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:95064121_95064122insT	uc004ati.1	+	c.3271_3272insT	c.(3271-3273)CTGfs	p.L1091fs	WNK2_uc004atj.1_Frame_Shift_Ins_p.L1091fs|WNK2_uc004atk.2_Frame_Shift_Ins_p.L728fs	NM_006648	NP_006639	Q9Y3S1	WNK2_HUMAN	WNK lysine deficient protein kinase 2	1091					intracellular protein kinase cascade|protein phosphorylation		ATP binding|protein binding|protein serine/threonine kinase activity			ovary(2)|lung(2)|stomach(1)|large_intestine(1)|central_nervous_system(1)	7										1420				0.39			7	11				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	95064121	95064122	17952	9	-	T	T	32	32	WNK2	T	5	5
