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
PWWP2B	170394	broad.mit.edu	36	10	134068297	134068297	+	Silent	SNP	A	C	C			TCGA-26-5132-01	TCGA-26-5132-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr10:134068297A>C	uc001lll.2	+	c.303A>C	c.(301-303)CCA>CCC	p.P101P	PWWP2B_uc009ybe.1_Silent_p.P101P	NM_138499	NP_612508	Q6NUJ5	PWP2B_HUMAN	PWWP domain containing 2 isoform 1	101	Pro-rich.										0		all_cancers(35;6.69e-12)|all_epithelial(44;1.55e-08)|Lung NSC(174;0.000845)|all_lung(145;0.00144)|all_neural(114;0.0299)|Breast(234;0.106)|Colorectal(31;0.109)|Melanoma(40;0.123)|Glioma(114;0.203)|all_hematologic(284;0.224)												0.3	7.125255	7.480399	3	7	AA		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(35;7.49e-05)|Epithelial(32;0.00016)|all cancers(32;0.000186)	Silent	SNP	134068297	134068297	13304	10	A	C	C	6	6	PWWP2B	C	4	4
MUC2	4583	broad.mit.edu	36	11	1074747	1074747	+	Missense_Mutation	SNP	C	T	T			TCGA-26-5132-01	TCGA-26-5132-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:1074747C>T	uc001lsx.1	+	c.2542C>T	c.(2542-2544)CGC>TGC	p.R848C		NM_002457	NP_002448	Q02817	MUC2_HUMAN	mucin 2 precursor	848						inner mucus layer|outer mucus layer	protein binding			lung(1)|breast(1)	2		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)			Pranlukast(DB01411)									0.454545	13.172015	13.191985	5	6	CC		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Missense_Mutation	SNP	1074747	1074747	10369	11	C	T	T	19	19	MUC2	T	1	1
PANX3	116337	broad.mit.edu	36	11	123994596	123994596	+	Missense_Mutation	SNP	A	G	G			TCGA-26-5132-01	TCGA-26-5132-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr11:123994596A>G	uc001qah.1	+	c.734A>G	c.(733-735)AAG>AGG	p.K245R		NM_052959	NP_443191	Q96QZ0	PANX3_HUMAN	pannexin 3	245	Extracellular (Potential).				protein hexamerization	gap junction|integral to membrane	gap junction hemi-channel activity|ion channel activity				0	all_hematologic(175;0.215)	Breast(109;0.00109)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)												0.387387	145.202268	146.43506	43	68	AA		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0219)	Missense_Mutation	SNP	123994596	123994596	11839	11	A	G	G	3	3	PANX3	G	4	4
NELL1	4745	broad.mit.edu	36	11	21553108	21553108	+	Silent	SNP	T	C	C			TCGA-26-5132-01	TCGA-26-5132-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr11:21553108T>C	uc009yid.1	+	c.2481T>C	c.(2479-2481)TGT>TGC	p.C827C	NELL1_uc001mqe.1_Silent_p.C799C|NELL1_uc001mqf.1_Silent_p.C752C|NELL1_uc001mqh.1_Silent_p.C344C	NM_006157	NP_006148	Q92832	NELL1_HUMAN	nel-like 1 isoform 1 precursor	799	VWFC 5.				cell adhesion|nervous system development	extracellular region	calcium ion binding|structural molecule activity			ovary(2)|large_intestine(1)	3														0.375	180.521071	182.493877	54	90	TT		KEEP	---	---	---	---	capture			Silent	SNP	21553108	21553108	10732	11	T	C	C	60	60	NELL1	C	4	4
OR5D18	219438	broad.mit.edu	36	11	55344052	55344052	+	Missense_Mutation	SNP	T	C	C			TCGA-26-5132-01	TCGA-26-5132-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr11:55344052T>C	uc001nhx.1	+	c.371T>C	c.(370-372)TTC>TCC	p.F124S		NM_001001952	NP_001001952	Q8NGL1	OR5DI_HUMAN	olfactory receptor, family 5, subfamily D,	124	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1		all_epithelial(135;0.208)												0.413302	593.379892	596.141415	174	247	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	55344052	55344052	11567	11	T	C	C	62	62	OR5D18	C	4	4
SUDS3	64426	broad.mit.edu	36	12	117325693	117325693	+	Missense_Mutation	SNP	A	G	G			TCGA-26-5132-01	TCGA-26-5132-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr12:117325693A>G	uc001twz.1	+	c.791A>G	c.(790-792)TAT>TGT	p.Y264C		NM_022491	NP_071936	Q9H7L9	SDS3_HUMAN	suppressor of defective silencing 3	264					chromatin modification|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	Sin3 complex	histone deacetylase binding				0	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)													0.444444	55.296634	55.393219	16	20	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	117325693	117325693	15887	12	A	G	G	16	16	SUDS3	G	4	4
ABCC9	10060	broad.mit.edu	36	12	21886552	21886552	+	Missense_Mutation	SNP	A	T	T			TCGA-26-5132-01	TCGA-26-5132-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr12:21886552A>T	uc001rfh.1	-	c.3436T>A	c.(3436-3438)TTT>ATT	p.F1146I	ABCC9_uc001rfi.1_Missense_Mutation_p.F1146I|ABCC9_uc001rfj.1_Missense_Mutation_p.F1110I	NM_020297	NP_064693	O60706	ABCC9_HUMAN	ATP-binding cassette, sub-family C, member 9	1146	Helical; Name=14; (Potential).|ABC transmembrane type-1 2.				defense response to virus|potassium ion import	ATP-sensitive potassium channel complex	ATP binding|ATPase activity, coupled to transmembrane movement of substances|potassium channel regulator activity|sulfonylurea receptor activity			ovary(4)	4					Adenosine triphosphate(DB00171)|Glibenclamide(DB01016)									0.634921	125.311642	126.319106	40	23	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	21886552	21886552	60	12	A	T	T	3	3	ABCC9	T	4	4
ITPR2	3709	broad.mit.edu	36	12	26700011	26700011	+	Missense_Mutation	SNP	C	T	T			TCGA-26-5132-01	TCGA-26-5132-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:26700011C>T	uc001rhg.1	-	c.2486G>A	c.(2485-2487)AGG>AAG	p.R829K		NM_002223	NP_002214	Q14571	ITPR2_HUMAN	inositol 1,4,5-triphosphate receptor, type 2	829	Cytoplasmic (Potential).				activation of phospholipase C activity|energy reserve metabolic process|nerve growth factor receptor signaling pathway|platelet activation|regulation of insulin secretion|response to hypoxia	integral to membrane|plasma membrane enriched fraction|platelet dense tubular network membrane|sarcoplasmic reticulum membrane	calcium ion transmembrane transporter activity|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity			kidney(6)|ovary(4)|upper_aerodigestive_tract(1)|lung(1)|skin(1)	13	Colorectal(261;0.0847)									1600				0.088608	6.308969	33.396728	14	144	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	26700011	26700011	8225	12	C	T	T	24	24	ITPR2	T	2	2
ADAMTS20	80070	broad.mit.edu	36	12	42057462	42057462	+	Silent	SNP	G	C	C			TCGA-26-5132-01	TCGA-26-5132-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:42057462G>C	uc001rnn.1	-	c.4968C>G	c.(4966-4968)GCC>GCG	p.A1656A		NM_025003	NP_079279	P59510	ATS20_HUMAN	a disintegrin-like and metalloprotease with	1656	TSP type-1 15.					proteinaceous extracellular matrix	zinc ion binding			central_nervous_system(5)|ovary(4)|lung(3)|large_intestine(2)|skin(2)|urinary_tract(1)|kidney(1)|pancreas(1)	19	all_cancers(12;2.6e-05)|Lung SC(27;0.184)	Lung NSC(34;0.0569)|all_lung(34;0.129)								2149				0.774194	89.316874	91.457031	24	7	GG		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(48;0.0473)	Silent	SNP	42057462	42057462	267	12	G	C	C	47	47	ADAMTS20	C	3	3
RB1	5925	broad.mit.edu	36	13	47851731	47851731	+	Nonsense_Mutation	SNP	C	T	T	rs3092891	by-frequency,by-hapmap	TCGA-26-5132-01	TCGA-26-5132-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr13:47851731C>T	uc001vcb.1	+	c.1333C>T	c.(1333-1335)CGA>TGA	p.R445*		NM_000321	NP_000312	P06400	RB_HUMAN	retinoblastoma 1	445	Domain A.|Pocket; binds T and E1A.				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.R445*(2)		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)			Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)			6	p.R445*(639V-Tumor)	568	TCGA GBM(7;6.82e-08)|TSP Lung(12;0.097)|TCGA Ovarian(6;0.080)			0.742857	84.36336	86.233198	26	9	CC		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(2;9.98e-18)|LUSC - Lung squamous cell carcinoma(3;0.013)	Nonsense_Mutation	SNP	47851731	47851731	13559	13	C	T	T	27	27	RB1	T	5	1
THBS1	7057	broad.mit.edu	36	15	37661808	37661808	+	Missense_Mutation	SNP	G	A	A			TCGA-26-5132-01	TCGA-26-5132-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr15:37661808G>A	uc001zkh.1	+	c.190G>A	c.(190-192)GCC>ACC	p.A64T		NM_003246	NP_003237	P07996	TSP1_HUMAN	thrombospondin 1 precursor	64	TSP N-terminal.|Heparin-binding.				activation of MAPK activity|anti-apoptosis|apoptosis|cell adhesion|cell cycle arrest|cell migration|cellular response to heat|chronic inflammatory response|engulfment of apoptotic cell|immune response|induction of apoptosis|negative regulation of angiogenesis|negative regulation of antigen processing and presentation of peptide or polysaccharide antigen via MHC class II|negative regulation of blood vessel endothelial cell migration|negative regulation of caspase activity|negative regulation of cGMP-mediated signaling|negative regulation of dendritic cell antigen processing and presentation|negative regulation of endothelial cell proliferation|negative regulation of fibrinolysis|negative regulation of fibroblast growth factor receptor signaling pathway|negative regulation of focal adhesion assembly|negative regulation of interleukin-12 production|negative regulation of nitric oxide mediated signal transduction|negative regulation of plasma membrane long-chain fatty acid transport|negative regulation of plasminogen activation|peptide cross-linking|platelet activation|platelet degranulation|positive regulation of angiogenesis|positive regulation of blood vessel endothelial cell migration|positive regulation of fibroblast migration|positive regulation of macrophage activation|positive regulation of macrophage chemotaxis|positive regulation of oxygen and reactive oxygen species metabolic process|positive regulation of phosphorylation|positive regulation of protein kinase B signaling cascade|positive regulation of transforming growth factor beta receptor signaling pathway|positive regulation of transforming growth factor-beta1 production|positive regulation of translation|positive regulation of tumor necrosis factor biosynthetic process|response to calcium ion|response to drug|response to glucose stimulus|response to hypoxia|response to magnesium ion|response to progesterone stimulus|sprouting angiogenesis	external side of plasma membrane|extracellular matrix|fibrinogen complex|platelet alpha granule lumen	calcium ion binding|collagen V binding|eukaryotic cell surface binding|fibrinogen binding|fibroblast growth factor 2 binding|fibronectin binding|heparin binding|identical protein binding|integrin binding|laminin binding|low-density lipoprotein particle binding|phosphatidylserine binding|proteoglycan binding|structural molecule activity|transforming growth factor beta binding			central_nervous_system(3)|ovary(2)	5		all_cancers(109;1.35e-17)|all_epithelial(112;2.07e-15)|Lung NSC(122;4.44e-11)|all_lung(180;1.11e-09)|Melanoma(134;0.0574)|Colorectal(260;0.117)|Ovarian(310;0.223)			Becaplermin(DB00102)									0.330579	101.34688	104.431039	40	81	GG		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(113;2.77e-06)|BRCA - Breast invasive adenocarcinoma(123;0.105)	Missense_Mutation	SNP	37661808	37661808	16381	15	G	A	A	46	46	THBS1	A	2	2
LTK	4058	broad.mit.edu	36	15	39586758	39586758	+	Silent	SNP	G	C	C			TCGA-26-5132-01	TCGA-26-5132-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr15:39586758G>C	uc001zoa.2	-	c.1368C>G	c.(1366-1368)GGC>GGG	p.G456G	LTK_uc010bcg.1_Silent_p.G67G|LTK_uc001zob.2_Silent_p.G395G	NM_002344	NP_002335	P29376	LTK_HUMAN	leukocyte receptor tyrosine kinase isoform 1	456	Cytoplasmic (Potential).				protein phosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane|soluble fraction	ATP binding|transmembrane receptor protein tyrosine kinase activity			lung(6)|central_nervous_system(1)	7		all_cancers(109;1.89e-19)|all_epithelial(112;2.28e-16)|Lung NSC(122;5.34e-11)|all_lung(180;1.33e-09)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.172)								314	TSP Lung(18;0.14)			0.342857	16.207438	17.057566	12	23	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(18;2.1e-17)|GBM - Glioblastoma multiforme(113;1.34e-06)|Colorectal(105;0.0148)|BRCA - Breast invasive adenocarcinoma(123;0.113)	Silent	SNP	39586758	39586758	9456	15	G	C	C	42	42	LTK	C	3	3
CDAN1	146059	broad.mit.edu	36	15	40810232	40810232	+	Missense_Mutation	SNP	C	T	T			TCGA-26-5132-01	TCGA-26-5132-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr15:40810232C>T	uc001zql.1	-	c.2030G>A	c.(2029-2031)CGG>CAG	p.R677Q	CDAN1_uc001zqj.1_Non-coding_Transcript|CDAN1_uc001zqk.1_Missense_Mutation_p.G3R	NM_138477	NP_612486	Q8IWY9	CDAN1_HUMAN	codanin 1	677						integral to membrane	protein binding			ovary(2)	2		all_cancers(109;5.4e-16)|all_epithelial(112;2.97e-14)|Lung NSC(122;1.75e-08)|all_lung(180;5.99e-08)|Melanoma(134;0.0179)|Colorectal(260;0.215)												0.52381	105.27966	105.310939	33	30	CC		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(94;2.49e-07)	Missense_Mutation	SNP	40810232	40810232	3182	15	C	T	T	23	23	CDAN1	T	1	1
PKD1	5310	broad.mit.edu	36	16	2105396	2105396	+	Missense_Mutation	SNP	G	A	A			TCGA-26-5132-01	TCGA-26-5132-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:2105396G>A	uc002cos.1	-	c.2081C>T	c.(2080-2082)CCC>CTC	p.P694L	PKD1_uc002cot.1_Missense_Mutation_p.P694L	NM_001009944	NP_001009944	P98161	PKD1_HUMAN	polycystin 1 isoform 1 precursor	694	Extracellular (Potential).				calcium-independent cell-matrix adhesion|homophilic cell adhesion|neuropeptide signaling pathway	basolateral plasma membrane|integral to plasma membrane	protein domain specific binding|sugar binding			central_nervous_system(1)	1														0.444444	11.799212	11.823325	4	5	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	2105396	2105396	12387	16	G	A	A	43	43	PKD1	A	2	2
ZCCHC14	23174	broad.mit.edu	36	16	86006390	86006390	+	Missense_Mutation	SNP	G	T	T			TCGA-26-5132-01	TCGA-26-5132-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:86006390G>T	uc002fjz.1	-	c.1057C>A	c.(1057-1059)CTG>ATG	p.L353M	ZCCHC14_uc002fka.1_Non-coding_Transcript|ZCCHC14_uc002fkb.2_Missense_Mutation_p.L129M	NM_015144	NP_055959	Q8WYQ9	ZCH14_HUMAN	zinc finger, CCHC domain containing 14	353					cell communication		nucleic acid binding|phosphatidylinositol binding|zinc ion binding			breast(1)	1														0.432161	254.212078	255.012214	86	113	GG		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(80;0.0285)	Missense_Mutation	SNP	86006390	86006390	18171	16	G	T	T	34	34	ZCCHC14	T	3	3
PRPF8	10594	broad.mit.edu	36	17	1524579	1524579	+	Missense_Mutation	SNP	T	C	C			TCGA-26-5132-01	TCGA-26-5132-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr17:1524579T>C	uc002fte.1	-	c.3206A>G	c.(3205-3207)AAT>AGT	p.N1069S		NM_006445	NP_006436	Q6P2Q9	PRP8_HUMAN	U5 snRNP-specific protein	1069					nuclear mRNA splicing, via spliceosome|response to stimulus|visual perception	catalytic step 2 spliceosome|nuclear speck|U5 snRNP	protein binding|RNA binding			ovary(2)|lung(1)	3														0.420245	456.034747	457.839795	137	189	TT		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (25;0.0855)	Missense_Mutation	SNP	1524579	1524579	13018	17	T	C	C	52	52	PRPF8	C	4	4
ALDH3A1	218	broad.mit.edu	36	17	19585108	19585108	+	Missense_Mutation	SNP	C	T	T			TCGA-26-5132-01	TCGA-26-5132-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:19585108C>T	uc010cqu.1	-	c.697G>A	c.(697-699)GCC>ACC	p.A233T	ALDH3A1_uc002gwj.1_Missense_Mutation_p.A233T|ALDH3A1_uc010cqv.1_Missense_Mutation_p.A233T|ALDH3A1_uc002gwk.1_Missense_Mutation_p.A350T|ALDH3A1_uc002gwl.1_Missense_Mutation_p.A160T	NM_000691	NP_000682	P30838	AL3A1_HUMAN	aldehyde dehydrogenase 3A1	233					cellular aldehyde metabolic process|oxidation-reduction process	cytosol|endoplasmic reticulum	alcohol dehydrogenase (NADP+) activity|aldehyde dehydrogenase (NAD) activity			ovary(1)|pancreas(1)	2	all_cancers(12;4.01e-05)|all_epithelial(12;0.00301)|Breast(13;0.186)				NADH(DB00157)									0.494118	128.447333	128.449876	42	43	CC		KEEP	---	---	---	---	capture		Colorectal(15;0.0829)	Missense_Mutation	SNP	19585108	19585108	500	17	C	T	T	27	27	ALDH3A1	T	1	1
KRT9	3857	broad.mit.edu	36	17	36978154	36978154	+	Silent	SNP	G	A	A			TCGA-26-5132-01	TCGA-26-5132-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:36978154G>A	uc002hxe.2	-	c.1180C>T	c.(1180-1182)CTG>TTG	p.L394L		NM_000226	NP_000217	P35527	K1C9_HUMAN	keratin 9	394	Rod.|Coil 2.				intermediate filament organization|skin development		protein binding|structural constituent of cytoskeleton			ovary(1)|central_nervous_system(1)|pancreas(1)	3		Breast(137;0.000307)												0.434263	334.837309	335.782581	109	142	GG		KEEP	---	---	---	---	capture			Silent	SNP	36978154	36978154	8816	17	G	A	A	33	33	KRT9	A	2	2
C19orf40	91442	broad.mit.edu	36	19	38156833	38156833	+	Missense_Mutation	SNP	G	A	A			TCGA-26-5132-01	TCGA-26-5132-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:38156833G>A	uc002nud.2	+	c.271G>A	c.(271-273)GTT>ATT	p.V91I	CCDC123_uc002nty.1_5'Flank|CCDC123_uc010edg.1_5'Flank|CCDC123_uc002ntz.1_5'Flank|CCDC123_uc002nua.2_5'Flank|CCDC123_uc002nuc.1_5'Flank	NM_152266	NP_689479	Q9BTP7	FAP24_HUMAN	Fanconi anemia-associated protein, 24 kDa	91					DNA repair	Fanconi anaemia nuclear complex	chromatin binding|DNA binding|protein binding				0	Esophageal squamous(110;0.137)													0.503546	221.925963	221.92753	71	70	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	38156833	38156833	1987	19	G	A	A	40	40	C19orf40	A	1	1
PALM	5064	broad.mit.edu	36	19	682135	682135	+	Missense_Mutation	SNP	G	C	C			TCGA-26-5132-01	TCGA-26-5132-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:682135G>C	uc002lpm.1	+	c.310G>C	c.(310-312)GCC>CCC	p.A104P	PALM_uc002lpn.1_Missense_Mutation_p.A104P	NM_002579	NP_002570	O75781	PALM_HUMAN	paralemmin isoform 1	104					cellular component movement|regulation of cell shape	cytoplasmic membrane-bounded vesicle|integral to plasma membrane					0		all_epithelial(18;2.19e-21)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;3.55e-06)|all_lung(49;5.41e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)												0.2	9.191947	10.863605	4	16	GG		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)|Lung(535;0.201)	Missense_Mutation	SNP	682135	682135	11824	19	G	C	C	38	38	PALM	C	3	3
GJA5	2702	broad.mit.edu	36	1	145697176	145697176	+	Silent	SNP	G	A	A			TCGA-26-5132-01	TCGA-26-5132-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:145697176G>A	uc001eps.1	-	c.795C>T	c.(793-795)CCC>CCT	p.P265P	NBPF11_uc009wjd.1_Intron|NBPF11_uc009wje.1_Intron|GJA5_uc001ept.1_Silent_p.P265P|GJA5_uc009wjk.1_Silent_p.P265P	NM_181703	NP_859054	P36382	CXA5_HUMAN	connexin 40	265	Cytoplasmic (Potential).				angiogenesis|cell-cell junction assembly|muscle contraction	integral to membrane				ovary(1)	1	all_hematologic(923;0.0276)													0.369159	242.990532	246.201842	79	135	GG		KEEP	---	---	---	---	capture	LUSC - Lung squamous cell carcinoma(543;0.202)		Silent	SNP	145697176	145697176	6672	1	G	A	A	39	39	GJA5	A	1	1
PRPF3	9129	broad.mit.edu	36	1	148585235	148585235	+	Silent	SNP	G	A	A			TCGA-26-5132-01	TCGA-26-5132-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:148585235G>A	uc001eum.2	+	c.1758G>A	c.(1756-1758)GGG>GGA	p.G586G	PRPF3_uc009wlq.1_Non-coding_Transcript	NM_004698	NP_004689	O43395	PRPF3_HUMAN	PRP3 pre-mRNA processing factor 3 homolog	586					nuclear mRNA splicing, via spliceosome|response to stimulus|visual perception	Cajal body|cytoplasm|nuclear speck|spliceosomal complex	protein binding			ovary(1)	1	Lung NSC(24;5.57e-29)|Breast(34;0.000844)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Colorectal(459;0.171)					Ovarian(168;1070 2670 5178 20729)								0.336364	432.499624	442.95395	148	292	GG		KEEP	---	---	---	---	capture	LUSC - Lung squamous cell carcinoma(543;0.171)	Colorectal(1306;0.0149)	Silent	SNP	148585235	148585235	13008	1	G	A	A	43	43	PRPF3	A	2	2
FAM5C	339479	broad.mit.edu	36	1	188500775	188500775	+	Missense_Mutation	SNP	C	T	T			TCGA-26-5132-01	TCGA-26-5132-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:188500775C>T	uc001gse.1	-	c.461G>A	c.(460-462)CGG>CAG	p.R154Q		NM_199051	NP_950252	Q76B58	FAM5C_HUMAN	family with sequence similarity 5, member C	154						extracellular region				lung(2)|ovary(1)|kidney(1)	4	Prostate(682;0.198)													0.38961	179.866793	181.510179	60	94	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	188500775	188500775	5817	1	C	T	T	23	23	FAM5C	T	1	1
OR2G6	391211	broad.mit.edu	36	1	246751771	246751771	+	Silent	SNP	G	A	A			TCGA-26-5132-01	TCGA-26-5132-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:246751771G>A	uc001ien.1	+	c.201G>A	c.(199-201)TCG>TCA	p.S67S		NM_001013355	NP_001013373	Q5TZ20	OR2G6_HUMAN	olfactory receptor, family 2, subfamily G,	67	Helical; Name=2; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)	2	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)	all_cancers(173;0.0156)												0.422886	249.540909	250.583511	85	116	GG		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(106;0.0265)		Silent	SNP	246751771	246751771	11406	1	G	A	A	40	40	OR2G6	A	1	1
MACF1	23499	broad.mit.edu	36	1	39680574	39680574	+	Nonsense_Mutation	SNP	C	T	T			TCGA-26-5132-01	TCGA-26-5132-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:39680574C>T	uc009vvr.1	+	c.14272C>T	c.(14272-14274)CGA>TGA	p.R4758*	MACF1_uc009vvo.1_Nonsense_Mutation_p.R4256*|MACF1_uc009vvp.1_Nonsense_Mutation_p.R4256*|MACF1_uc009vvs.1_Nonsense_Mutation_p.R4758*	NM_033044	NP_149033	Q9UPN3	MACF1_HUMAN	microfilament and actin filament cross-linker	4256	Spectrin 29.				cell cycle arrest	cytoplasm|cytoskeleton	actin filament binding|calcium ion binding|microtubule binding			ovary(8)|breast(3)|central_nervous_system(3)	14	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)												0.39823	134.750873	135.774908	45	68	CC		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)		Nonsense_Mutation	SNP	39680574	39680574	9521	1	C	T	T	23	23	MACF1	T	5	1
KCNQ4	9132	broad.mit.edu	36	1	41056764	41056764	+	Missense_Mutation	SNP	A	G	G			TCGA-26-5132-01	TCGA-26-5132-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr1:41056764A>G	uc001cgh.1	+	c.533A>G	c.(532-534)GAC>GGC	p.D178G	KCNQ4_uc001cgi.1_Missense_Mutation_p.D178G	NM_004700	NP_004691	P56696	KCNQ4_HUMAN	potassium voltage-gated channel KQT-like protein	178	Helical; Name=Segment S3; (Potential).				sensory perception of sound	basal plasma membrane|voltage-gated potassium channel complex				central_nervous_system(1)	1	Ovarian(52;0.00769)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0255)												0.369231	71.291315	72.264343	24	41	AA		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(33;1.38e-17)		Missense_Mutation	SNP	41056764	41056764	8390	1	A	G	G	10	10	KCNQ4	G	4	4
MYSM1	114803	broad.mit.edu	36	1	58913790	58913790	+	Missense_Mutation	SNP	C	T	T			TCGA-26-5132-01	TCGA-26-5132-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:58913790C>T	uc009wab.1	-	c.1441G>A	c.(1441-1443)GAC>AAC	p.D481N	MYSM1_uc001czc.2_Non-coding_Transcript	NM_001085487	NP_001078956	Q5VVJ2	MYSM1_HUMAN	Myb-like, SWIRM and MPN domains 1	481					histone deubiquitination|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromatin remodeling complex	DNA binding|histone binding|metal ion binding|metallopeptidase activity|transcription coactivator activity|ubiquitin thiolesterase activity|ubiquitin-specific protease activity				0	all_cancers(7;9.36e-06)													0.333333	60.652102	62.20289	21	42	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	58913790	58913790	10496	1	C	T	T	32	32	MYSM1	T	2	2
CD93	22918	broad.mit.edu	36	20	23013459	23013459	+	Silent	SNP	G	A	A			TCGA-26-5132-01	TCGA-26-5132-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr20:23013459G>A	uc002wsv.1	-	c.1371C>T	c.(1369-1371)GGC>GGT	p.G457G		NM_012072	NP_036204	Q9NPY3	C1QR1_HUMAN	CD93 antigen precursor	457	Extracellular (Potential).|EGF-like 5; calcium-binding (Potential).				cell-cell adhesion|interspecies interaction between organisms|macrophage activation|phagocytosis	integral to membrane|plasma membrane	calcium ion binding|complement component C1q binding|receptor activity|sugar binding			large_intestine(2)	2	Colorectal(13;0.0352)|Lung NSC(19;0.0542)|all_lung(19;0.118)													0.360656	189.599596	192.726782	66	117	GG		KEEP	---	---	---	---	capture			Silent	SNP	23013459	23013459	3175	20	G	A	A	34	34	CD93	A	2	2
DNMT3L	29947	broad.mit.edu	36	21	44493352	44493352	+	Missense_Mutation	SNP	A	G	G			TCGA-26-5132-01	TCGA-26-5132-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr21:44493352A>G	uc002zeh.1	-	c.980T>C	c.(979-981)ATC>ACC	p.I327T	DNMT3L_uc002zeg.1_Missense_Mutation_p.I327T	NM_013369	NP_037501	Q9UJW3	DNM3L_HUMAN	cytosine-5-methyltransferase 3-like protein	327					DNA methylation|regulation of gene expression by genetic imprinting|spermatogenesis	cytosol	enzyme activator activity|enzyme binding|transcription repressor activity|zinc ion binding				0														0.25	7.919334	8.81119	4	12	AA		KEEP	---	---	---	---	capture		Colorectal(79;0.0165)|READ - Rectum adenocarcinoma(84;0.0781)	Missense_Mutation	SNP	44493352	44493352	4861	21	A	G	G	12	12	DNMT3L	G	4	4
CLTCL1	8218	broad.mit.edu	36	22	17568877	17568877	+	Missense_Mutation	SNP	T	G	G			TCGA-26-5132-01	TCGA-26-5132-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr22:17568877T>G	uc002zpb.1	-	c.3728A>C	c.(3727-3729)AAC>ACC	p.N1243T	CLTCL1_uc002zpc.1_Non-coding_Transcript|CLTCL1_uc010grm.1_Intron|CLTCL1_uc002zpd.1_Missense_Mutation_p.N150T|CLTCL1_uc002zpe.1_Missense_Mutation_p.T203P	NM_007098	NP_009029	P53675	CLH2_HUMAN	clathrin, heavy polypeptide-like 1	1243	Involved in binding clathrin light chain (By similarity).|Proximal segment.|Heavy chain arm.				anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis	clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network	protein binding|signal transducer activity|structural molecule activity			ovary(4)|central_nervous_system(1)	5	Colorectal(54;0.0993)								p.N1243S(HEC108-Tumor)	1206				0.375	6.885013	7.160818	6	10	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	17568877	17568877	3705	22	T	G	G	60	60	CLTCL1	G	4	4
SCN7A	6332	broad.mit.edu	36	2	167037086	167037086	+	Missense_Mutation	SNP	C	T	T			TCGA-26-5132-01	TCGA-26-5132-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:167037086C>T	uc002udu.1	-	c.559G>A	c.(559-561)GTA>ATA	p.V187I	SCN7A_uc010fpm.1_Non-coding_Transcript	NM_002976	NP_002967	Q01118	SCN7A_HUMAN	sodium channel, voltage-gated, type VII, alpha	187	Helical; Name=S3 of repeat I; (By similarity).				muscle contraction	voltage-gated sodium channel complex	voltage-gated sodium channel activity			large_intestine(1)	1														0.5	54.053418	54.053418	18	18	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	167037086	167037086	14405	2	C	T	T	19	19	SCN7A	T	1	1
FBXO41	150726	broad.mit.edu	36	2	73347166	73347166	+	Missense_Mutation	SNP	G	A	A			TCGA-26-5132-01	TCGA-26-5132-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:73347166G>A	uc002sjb.1	-	c.1241C>T	c.(1240-1242)ACG>ATG	p.T414M		NM_001080410	NP_001073879	Q8TF61	FBX41_HUMAN	F-box protein 41	353						intracellular	protein binding|zinc ion binding			pancreas(1)	1														0.291667	17.617321	18.549226	7	17	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	73347166	73347166	5987	2	G	A	A	40	40	FBXO41	A	1	1
DNAJC19	131118	broad.mit.edu	36	3	182188555	182188555	+	Missense_Mutation	SNP	T	C	C			TCGA-26-5132-01	TCGA-26-5132-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr3:182188555T>C	uc003fkt.1	-	c.79A>G	c.(79-81)AAG>GAG	p.K27E	DNAJC19_uc003fku.1_Non-coding_Transcript	NM_145261	NP_660304	Q96DA6	TIM14_HUMAN	translocase of the inner mitochondrial membrane	27	Mitochondrial matrix (Potential).				genitalia development|protein folding|protein targeting to mitochondrion|transmembrane transport|visual perception	integral to membrane|mitochondrial inner membrane	heat shock protein binding				0	all_cancers(143;3.12e-14)|Ovarian(172;0.0212)													0.443243	291.936655	292.454239	82	103	TT		KEEP	---	---	---	---	capture	Epithelial(37;3.05e-36)|OV - Ovarian serous cystadenocarcinoma(80;1.55e-22)		Missense_Mutation	SNP	182188555	182188555	4821	3	T	C	C	62	62	DNAJC19	C	4	4
DCHS2	54798	broad.mit.edu	36	4	155439079	155439079	+	Missense_Mutation	SNP	G	T	T			TCGA-26-5132-01	TCGA-26-5132-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr4:155439079G>T	uc003inw.1	-	c.4472C>A	c.(4471-4473)GCT>GAT	p.A1491D		NM_017639	NP_060109	Q6V1P9	PCD23_HUMAN	dachsous 2 isoform 1	1491	Cadherin 13.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(3)|pancreas(1)	4	all_hematologic(180;0.208)	Renal(120;0.0854)												0.386885	345.374248	348.796128	118	187	GG		KEEP	---	---	---	---	capture		LUSC - Lung squamous cell carcinoma(193;0.107)	Missense_Mutation	SNP	155439079	155439079	4459	4	G	T	T	34	34	DCHS2	T	3	3
LGI2	55203	broad.mit.edu	36	4	24623178	24623178	+	Missense_Mutation	SNP	C	T	T			TCGA-26-5132-01	TCGA-26-5132-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:24623178C>T	uc003grf.1	-	c.697G>A	c.(697-699)GTG>ATG	p.V233M		NM_018176	NP_060646	Q8N0V4	LGI2_HUMAN	leucine-rich repeat LGI family, member 2	233	EAR 1.					extracellular region					0		Breast(46;0.173)												0.382353	234.801947	237.277896	78	126	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	24623178	24623178	9078	4	C	T	T	20	20	LGI2	T	2	2
SLC6A19	340024	broad.mit.edu	36	5	1267110	1267110	+	Missense_Mutation	SNP	G	A	A			TCGA-26-5132-01	TCGA-26-5132-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:1267110G>A	uc003jbw.2	+	c.817G>A	c.(817-819)GCA>ACA	p.A273T		NM_001003841	NP_001003841	Q695T7	S6A19_HUMAN	solute carrier family 6, member 19	273	Helical; Name=6; (Potential).				cellular nitrogen compound metabolic process	integral to plasma membrane	amino acid transmembrane transporter activity|neurotransmitter:sodium symporter activity				0	all_cancers(3;3.55e-15)|Lung NSC(6;2.89e-14)|all_lung(6;2.2e-13)|all_epithelial(6;3.75e-10)													0.497487	295.778641	295.77915	99	100	GG		KEEP	---	---	---	---	capture	Epithelial(17;0.000356)|all cancers(22;0.00137)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|Lung(60;0.185)		Missense_Mutation	SNP	1267110	1267110	15179	5	G	A	A	38	38	SLC6A19	A	1	1
SLC6A3	6531	broad.mit.edu	36	5	1456128	1456128	+	Missense_Mutation	SNP	G	A	A	rs28364997	unknown	TCGA-26-5132-01	TCGA-26-5132-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:1456128G>A	uc003jck.2	-	c.1676C>T	c.(1675-1677)GCG>GTG	p.A559V		NM_001044	NP_001035	Q01959	SC6A3_HUMAN	solute carrier family 6 (neurotransmitter	559					cell death|neurotransmitter biosynthetic process	axon|cytoplasm|integral to plasma membrane|neuronal cell body				ovary(3)|breast(2)|pancreas(1)	6					Amphetamine(DB00182)|Benztropine(DB00245)|Bupropion(DB01156)|Chloroprocaine(DB01161)|Cocaine(DB00907)|Dextroamphetamine(DB01576)|Diethylpropion(DB00937)|Duloxetine(DB00476)|Fencamfamine(DB01463)|Mazindol(DB00579)|Methylphenidate(DB00422)|Modafinil(DB00745)|Phenmetrazine(DB00830)|Phentermine(DB00191)|Procaine(DB00721)									0.421687	99.608589	100.053053	35	48	GG		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(19;0.00928)|all cancers(22;0.0262)		Missense_Mutation	SNP	1456128	1456128	15182	5	G	A	A	38	38	SLC6A3	A	1	1
ADAMTS12	81792	broad.mit.edu	36	5	33612330	33612330	+	Silent	SNP	G	A	A			TCGA-26-5132-01	TCGA-26-5132-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:33612330G>A	uc003jia.1	-	c.3558C>T	c.(3556-3558)GAC>GAT	p.D1186D	ADAMTS12_uc010iuq.1_Silent_p.D1101D	NM_030955	NP_112217	P58397	ATS12_HUMAN	ADAM metallopeptidase with thrombospondin type 1	1186	Spacer 2.				proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(4)|lung(1)|kidney(1)|skin(1)	7														0.39322	339.135896	342.080233	116	179	GG		KEEP	---	---	---	---	capture			Silent	SNP	33612330	33612330	258	5	G	A	A	40	40	ADAMTS12	A	1	1
HEY2	23493	broad.mit.edu	36	6	126122486	126122486	+	Missense_Mutation	SNP	C	T	T			TCGA-26-5132-01	TCGA-26-5132-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:126122486C>T	uc003qad.1	+	c.859C>T	c.(859-861)CCC>TCC	p.P287S		NM_012259	NP_036391	Q9UBP5	HEY2_HUMAN	hairy/enhancer-of-split related with YRPW motif	287	Ala-rich.				negative regulation of gene-specific transcription from RNA polymerase II promoter|nervous system development|Notch signaling pathway|organ morphogenesis	nucleus	DNA binding|histone deacetylase binding|sequence-specific DNA binding transcription factor activity|transcription repressor activity				0														0.359331	363.035478	369.306013	129	230	CC		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (4;0.0608)|GBM - Glioblastoma multiforme(226;0.0361)|all cancers(137;0.193)	Missense_Mutation	SNP	126122486	126122486	7362	6	C	T	T	22	22	HEY2	T	2	2
HIST1H4G	8369	broad.mit.edu	36	6	26355167	26355167	+	Silent	SNP	C	T	T			TCGA-26-5132-01	TCGA-26-5132-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:26355167C>T	uc003nhf.1	-	c.18G>A	c.(16-18)AAG>AAA	p.K6K		NM_003547	NP_003538	Q99525	H4G_HUMAN	histone cluster 1, H4g	6					nucleosome assembly	nucleosome|nucleus	DNA binding				0		all_hematologic(11;0.0945)|Acute lymphoblastic leukemia(11;0.167)												0.351648	96.371877	98.138734	32	59	CC		KEEP	---	---	---	---	capture			Silent	SNP	26355167	26355167	7456	6	C	T	T	24	24	HIST1H4G	T	2	2
KRBA1	84626	broad.mit.edu	36	7	149062000	149062000	+	Silent	SNP	A	T	T			TCGA-26-5132-01	TCGA-26-5132-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr7:149062000A>T	uc003wfz.1	+	c.3024A>T	c.(3022-3024)GGA>GGT	p.G1008G	KRBA1_uc010lpj.1_Non-coding_Transcript|KRBA1_uc003wga.1_Non-coding_Transcript|KRBA1_uc003wgb.1_Silent_p.G615G	NM_032534	NP_115923	A5PL33	KRBA1_HUMAN	KRAB A domain containing 1	1008										ovary(1)|central_nervous_system(1)	2	Melanoma(164;0.165)|Ovarian(565;0.177)													0.285714	21.029693	22.476599	10	25	AA		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(82;0.00625)		Silent	SNP	149062000	149062000	8754	7	A	T	T	11	11	KRBA1	T	4	4
HOXA6	3203	broad.mit.edu	36	7	27151960	27151960	+	Missense_Mutation	SNP	G	A	A			TCGA-26-5132-01	TCGA-26-5132-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:27151960G>A	uc003syo.1	-	c.544C>T	c.(544-546)CGG>TGG	p.R182W	HOXA5_uc003syn.1_5'Flank	NM_024014	NP_076919	P31267	HXA6_HUMAN	homeobox A6	182	Homeobox.				regulation of transcription, DNA-dependent	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulator activity			ovary(1)|central_nervous_system(1)	2														0.320542	356.405423	369.076791	142	301	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	27151960	27151960	7588	7	G	A	A	40	40	HOXA6	A	1	1
CCDC132	55610	broad.mit.edu	36	7	92823207	92823207	+	Missense_Mutation	SNP	T	C	C			TCGA-26-5132-01	TCGA-26-5132-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr7:92823207T>C	uc003umo.1	+	c.2654T>C	c.(2653-2655)TTA>TCA	p.L885S	CCDC132_uc003ump.1_Missense_Mutation_p.L855S|CCDC132_uc003umq.1_Non-coding_Transcript|CCDC132_uc003umr.1_Non-coding_Transcript	NM_017667	NP_060137	Q96JG6	CC132_HUMAN	coiled-coil domain containing 132 isoform a	885											0	all_cancers(62;2.64e-11)|all_epithelial(64;1.4e-10)|Breast(17;0.000675)|Lung NSC(181;0.0618)|all_lung(186;0.0837)													0.284722	130.093258	136.101235	41	103	TT		KEEP	---	---	---	---	capture	STAD - Stomach adenocarcinoma(171;0.000302)		Missense_Mutation	SNP	92823207	92823207	2887	7	T	C	C	61	61	CCDC132	C	4	4
OR2AE1	81392	broad.mit.edu	36	7	99312342	99312342	+	Missense_Mutation	SNP	T	C	C			TCGA-26-5132-01	TCGA-26-5132-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr7:99312342T>C	uc003usc.1	-	c.251A>G	c.(250-252)AAC>AGC	p.N84S		NM_001005276	NP_001005276	Q8NHA4	O2AE1_HUMAN	olfactory receptor, family 2, subfamily AE,	84	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0	Esophageal squamous(72;0.0166)|Lung NSC(181;0.0211)|all_lung(186;0.0323)													0.289216	180.311073	188.458266	59	145	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	99312342	99312342	11389	7	T	C	C	60	60	OR2AE1	C	4	4
ANK1	286	broad.mit.edu	36	8	41638609	41638609	+	Missense_Mutation	SNP	C	T	T			TCGA-26-5132-01	TCGA-26-5132-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr8:41638609C>T	uc003xom.1	-	c.5609G>A	c.(5608-5610)CGC>CAC	p.R1870H	NKX6-3_uc010lxa.1_Intron|ANK1_uc003xoh.1_Missense_Mutation_p.R983H|ANK1_uc003xoi.1_Missense_Mutation_p.R1829H|ANK1_uc003xoj.1_Missense_Mutation_p.R1829H|ANK1_uc003xok.1_Missense_Mutation_p.R1829H|ANK1_uc003xol.1_Missense_Mutation_p.R1667H|ANK1_uc003xob.1_Non-coding_Transcript|ANK1_uc003xoc.1_Missense_Mutation_p.R104H|ANK1_uc003xod.1_Missense_Mutation_p.R104H|ANK1_uc003xof.1_Intron	NM_020475	NP_065208	P16157	ANK1_HUMAN	ankyrin 1 isoform 4	1829	55 kDa regulatory domain.			R->G: Abolishes interaction with OBSCN (in isoform Mu17).	axon guidance|cytoskeleton organization|exocytosis|maintenance of epithelial cell apical/basal polarity|signal transduction	basolateral plasma membrane|cytosol|sarcomere|sarcoplasmic reticulum|spectrin-associated cytoskeleton	cytoskeletal adaptor activity|enzyme binding|protein binding|spectrin binding|structural constituent of cytoskeleton			ovary(3)|lung(2)|central_nervous_system(2)|breast(1)	8	Ovarian(28;0.00541)|Colorectal(14;0.0398)|Lung SC(25;0.211)	all_lung(54;0.000626)|Lung NSC(58;0.00245)|Esophageal squamous(32;0.0559)|Hepatocellular(245;0.0663)|Renal(179;0.188)												0.352459	123.002754	125.338356	43	79	CC		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(14;0.000984)|Lung(22;0.00108)|Colorectal(10;0.00245)|LUSC - Lung squamous cell carcinoma(45;0.00392)|COAD - Colon adenocarcinoma(11;0.0264)		Missense_Mutation	SNP	41638609	41638609	623	8	C	T	T	27	27	ANK1	T	1	1
SLC28A3	64078	broad.mit.edu	36	9	86106962	86106962	+	Missense_Mutation	SNP	A	G	G			TCGA-26-5132-01	TCGA-26-5132-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr9:86106962A>G	uc010mpz.1	-	c.497T>C	c.(496-498)CTA>CCA	p.L166P	SLC28A3_uc004anu.1_Missense_Mutation_p.L166P|SLC28A3_uc010mqb.1_Missense_Mutation_p.L97P	NM_022127	NP_071410	Q9HAS3	S28A3_HUMAN	concentrative Na+-nucleoside cotransporter	166	Cytoplasmic (Potential).				nucleobase, nucleoside and nucleotide metabolic process	integral to membrane|plasma membrane	nucleoside binding			ovary(1)|pancreas(1)	2						Ovarian(106;425 1539 34835 42413 43572)								0.42487	278.4934	279.447107	82	111	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	86106962	86106962	15030	9	A	G	G	15	15	SLC28A3	G	4	4
NAA35	60560	broad.mit.edu	36	9	87817815	87817815	+	Missense_Mutation	SNP	A	T	T			TCGA-26-5132-01	TCGA-26-5132-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr9:87817815A>T	uc004aoi.2	+	c.1325A>T	c.(1324-1326)AAC>ATC	p.N442I	NAA35_uc004aoj.2_Missense_Mutation_p.N442I	NM_024635	NP_078911	Q5VZE5	NAA35_HUMAN	corneal wound healing-related protein	442					smooth muscle cell proliferation	cytoplasm|nucleus|plasma membrane				central_nervous_system(1)	1														0.290323	72.089838	75.752107	27	66	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	87817815	87817815	10518	9	A	T	T	2	2	NAA35	T	4	4
SUSD3	203328	broad.mit.edu	36	9	94881667	94881667	+	Silent	SNP	C	T	T			TCGA-26-5132-01	TCGA-26-5132-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr9:94881667C>T	uc004atb.1	+	c.519C>T	c.(517-519)AGC>AGT	p.S173S	SUSD3_uc004atc.1_Silent_p.S160S	NM_145006	NP_659443	Q96L08	SUSD3_HUMAN	sushi domain containing 3	173	Cytoplasmic (Potential).					integral to membrane				breast(2)|skin(2)|ovary(1)|lung(1)	6														0.41573	101.341385	101.896355	37	52	CC		KEEP	---	---	---	---	capture			Silent	SNP	94881667	94881667	15929	9	C	T	T	27	27	SUSD3	T	1	1
MAGEA6	4105	broad.mit.edu	36	X	151620778	151620778	+	Missense_Mutation	SNP	T	A	A			TCGA-26-5132-01	TCGA-26-5132-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chrX:151620778T>A	uc004ffq.1	+	c.812T>A	c.(811-813)TTC>TAC	p.F271Y	MAGEA6_uc004ffr.1_Missense_Mutation_p.F271Y|MAGEA6_uc010ntl.1_Missense_Mutation_p.F271Y	NM_005363	NP_787064	P43360	MAGA6_HUMAN	melanoma antigen family A, 6	271	MAGE.						protein binding				0	Acute lymphoblastic leukemia(192;6.56e-05)													0.142857	47.563428	77.683693	35	210	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	151620778	151620778	9549	23	T	A	A	62	62	MAGEA6	A	4	4
DCAF8L1	139425	broad.mit.edu	36	X	27908706	27908706	+	Missense_Mutation	SNP	A	G	G			TCGA-26-5132-01	TCGA-26-5132-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chrX:27908706A>G	uc004dbx.1	-	c.667T>C	c.(667-669)TGG>CGG	p.W223R		NM_001017930	NP_001017930	A6NGE4	DC8L1_HUMAN	WD repeat domain 42B	223	WD 1.									ovary(3)	3														0.848485	97.620701	101.461603	28	5	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	27908706	27908706	4448	23	A	G	G	6	6	DCAF8L1	G	4	4
MED12	9968	broad.mit.edu	36	X	70258155	70258155	+	Nonsense_Mutation	SNP	C	T	T			TCGA-26-5132-01	TCGA-26-5132-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:70258155C>T	uc004dyy.1	+	c.865C>T	c.(865-867)CAG>TAG	p.Q289*	MED12_uc004dyz.1_Nonsense_Mutation_p.Q289*|MED12_uc004dza.1_Nonsense_Mutation_p.Q136*	NM_005120	NP_005111	Q93074	MED12_HUMAN	mediator complex subunit 12	289					androgen receptor signaling pathway|negative regulation of Wnt receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	mediator complex	ligand-dependent nuclear receptor transcription coactivator activity|protein C-terminus binding|protein domain specific binding|receptor activity|RNA polymerase II transcription mediator activity|thyroid hormone receptor binding|transcription activator activity|vitamin D receptor binding			ovary(1)|breast(1)|central_nervous_system(1)|skin(1)	4	Renal(35;0.156)													0.25	31.546451	34.503673	13	39	CC		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	70258155	70258155	9817	23	C	T	T	29	29	MED12	T	5	2
TOP1	7150	broad.mit.edu	36	20	39138260	39138262	+	In_Frame_Del	DEL	AGG	-	-			TCGA-26-5132-01	TCGA-26-5132-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:39138260_39138262delAGG	uc002xjl.1	+	c.191_193delAGG	c.(190-195)AAGGAG>AAG	p.E65del	TOP1_uc010gge.1_Non-coding_Transcript	NM_003286	NP_003277	P11387	TOP1_HUMAN	DNA topoisomerase I	65	Lys-rich.				DNA topological change|DNA unwinding involved in replication|interspecies interaction between organisms|phosphorylation|programmed cell death|response to drug	chromosome|nucleolus|nucleoplasm	ATP binding|chromatin DNA binding|DNA topoisomerase (ATP-hydrolyzing) activity|DNA topoisomerase type I activity|protein binding			breast(2)|ovary(1)|central_nervous_system(1)|kidney(1)	5		Myeloproliferative disorder(115;0.00878)			Irinotecan(DB00762)|Lucanthone(DB04967)|Topotecan(DB01030)					252				0.39			56	88				---	---	---	---	capture_indel			In_Frame_Del	DEL	39138260	39138262	16905	20	AGG	-	-	3	3	TOP1	-	5	5
HDAC2	3066	broad.mit.edu	36	6	114371253	114371256	+	Frame_Shift_Del	DEL	CTTT	-	-			TCGA-26-5132-01	TCGA-26-5132-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:114371253_114371256delCTTT	uc003pwd.1	-	c.1612_1615delAAAG	c.(1612-1617)AAAGCTfs	p.K538fs	HDAC2_uc003pwc.1_Frame_Shift_Del_p.K414fs|HDAC2_uc003pwe.1_Frame_Shift_Del_p.K414fs	NM_001527	NP_001518	Q92769	HDAC2_HUMAN	histone deacetylase 2	444_445					blood coagulation|chromatin remodeling|dendrite development|embryonic digit morphogenesis|epidermal cell differentiation|eyelid development in camera-type eye|fungiform papilla formation|hair follicle placode formation|maintenance of chromatin silencing|negative regulation of apoptosis|negative regulation of cell cycle|negative regulation of gene-specific transcription from RNA polymerase II promoter|negative regulation of MHC class II biosynthetic process|negative regulation of neuron projection development|negative regulation of sequence-specific DNA binding transcription factor activity|nerve growth factor receptor signaling pathway|odontogenesis of dentine-containing tooth|positive regulation of cell proliferation|positive regulation of collagen biosynthetic process|positive regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of proteolysis|positive regulation of receptor biosynthetic process	cytoplasm|ESC/E(Z) complex|NuRD complex|Sin3 complex	chromatin binding|enzyme binding|histone deacetylase activity (H3-K16 specific)|NAD-dependent histone deacetylase activity (H3-K14 specific)|NAD-dependent histone deacetylase activity (H3-K9 specific)|NAD-dependent histone deacetylase activity (H4-K16 specific)|sequence-specific DNA binding|specific transcriptional repressor activity|transcription activator activity|transcription factor binding			skin(2)|central_nervous_system(1)	3		all_cancers(87;0.000629)|all_epithelial(87;0.00274)|Colorectal(196;0.0317)|all_lung(197;0.24)		all cancers(137;0.00318)|OV - Ovarian serous cystadenocarcinoma(136;0.00569)|Epithelial(106;0.0112)|GBM - Glioblastoma multiforme(226;0.0832)	Vorinostat(DB02546)					302				0.41			74	106				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	114371253	114371256	7290	6	CTTT	-	-	28	28	HDAC2	-	5	5
DDX31	64794	broad.mit.edu	36	9	134460320	134460321	+	Splice_Site_Del	DEL	CC	-	-			TCGA-26-5132-01	TCGA-26-5132-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:134460320_134460321delCC	uc004cbq.1	-	c.e20_splice_site			DDX31_uc010mzu.1_Splice_Site_Del	NM_022779	NP_073616			DEAD (Asp-Glu-Ala-Asp) box polypeptide 31							nucleolus	ATP binding|ATP-dependent helicase activity|RNA binding			central_nervous_system(1)	1				OV - Ovarian serous cystadenocarcinoma(145;2.67e-06)|Epithelial(140;7.61e-05)										0.39			100	155				---	---	---	---	capture_indel			Splice_Site_Del	DEL	134460320	134460321	4527	9	CC	-	-	26	26	DDX31	-	5	5
