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
DNMBP	23268	broad.mit.edu	36	10	101644784	101644784	+	Missense_Mutation	SNP	A	G	G			TCGA-27-2519-01	TCGA-27-2519-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr10:101644784A>G	uc001kqj.2	-	c.3065T>C	c.(3064-3066)GTA>GCA	p.V1022A	DNMBP_uc001kqg.2_Missense_Mutation_p.V310A|DNMBP_uc001kqh.2_Missense_Mutation_p.V654A	NM_015221	NP_056036	Q6XZF7	DNMBP_HUMAN	dynamin binding protein	1022	BAR.				intracellular signal transduction|regulation of Rho protein signal transduction	cell junction|cytoskeleton|Golgi stack|synapse	protein binding|Rho guanyl-nucleotide exchange factor activity			ovary(5)	5		Colorectal(252;0.234)												0.45	60.948809	61.035359	18	22	AA		KEEP	---	---	---	---	capture		Epithelial(162;2.94e-10)|all cancers(201;3.15e-08)	Missense_Mutation	SNP	101644784	101644784	4857	10	A	G	G	14	14	DNMBP	G	4	4
C10orf113	387638	broad.mit.edu	36	10	21475290	21475290	+	Missense_Mutation	SNP	G	A	A			TCGA-27-2519-01	TCGA-27-2519-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr10:21475290G>A	uc001iqm.1	-	c.124C>T	c.(124-126)CCA>TCA	p.P42S	NEBL_uc001iqk.1_Intron	NM_001010896	NP_001010896	Q5VZT2	CJ113_HUMAN	hypothetical protein LOC387638	42										ovary(3)|pancreas(1)	4														0.466216	211.268488	211.414669	69	79	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	21475290	21475290	1619	10	G	A	A	41	41	C10orf113	A	2	2
PTEN	5728	broad.mit.edu	36	10	89701879	89701879	+	Missense_Mutation	SNP	C	T	T			TCGA-27-2519-01	TCGA-27-2519-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr10:89701879C>T	uc001kfb.1	+	c.517C>T	c.(517-519)CGC>TGC	p.R173C		NM_000314	NP_000305	P60484	PTEN_HUMAN	phosphatase and tensin homolog	173	Phosphatase tensin-type.		R -> C (in endometrial hyperplasia; loss of phosphatase activity towards Ins(1,3,4,5)P4 and PtdIns(3,4,5)P3; retains ability to bind phospholipid membranes).|R -> P (loss of phosphatase activity towards Ins(1,3,4,5)P4).|R -> H (loss of phosphatase activity towards Ins(1,3,4,5)P4).		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.R173C(32)|p.V166fs*17(3)|p.G165fs*9(3)|p.R173fs*10(2)|p.Y27_N212>Y(2)|p.G165_K342del(1)|p.G165_*404del(1)|p.R172fs*5(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)					R173C(REH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)	31	p.R173C(REH-Tumor)|p.R173C(639V-Tumor)	264	TCGA GBM(2;<1E-8)|TSP Lung(26;0.18)			0.466667	268.050834	268.233623	91	104	CC		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(1;0.214)	UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218)	Missense_Mutation	SNP	89701879	89701879	13192	10	C	T	T	27	27	PTEN	T	1	1
GRM5	2915	broad.mit.edu	36	11	88420307	88420307	+	Missense_Mutation	SNP	G	A	A			TCGA-27-2519-01	TCGA-27-2519-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:88420307G>A	uc001pcq.1	-	c.382C>T	c.(382-384)CGC>TGC	p.R128C	GRM5_uc001pcp.1_Missense_Mutation_p.R128C|GRM5_uc009yvm.1_Missense_Mutation_p.R128C|GRM5_uc009yvn.1_Missense_Mutation_p.R128C	NM_000842	NP_000833	P41594	GRM5_HUMAN	glutamate receptor, metabotropic 5 isoform b	128	Extracellular (Potential).				activation of phospholipase C activity by metabotropic glutamate receptor signaling pathway|synaptic transmission	integral to plasma membrane	G-protein coupled receptor activity|glutamate receptor activity			central_nervous_system(4)|ovary(1)	5		Acute lymphoblastic leukemia(157;2.54e-05)|all_hematologic(158;0.00834)			Acamprosate(DB00659)									0.201835	48.791014	57.793328	22	87	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	88420307	88420307	7079	11	G	A	A	40	40	GRM5	A	1	1
ANO4	121601	broad.mit.edu	36	12	100004595	100004595	+	Silent	SNP	C	T	T			TCGA-27-2519-01	TCGA-27-2519-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:100004595C>T	uc001thx.1	+	c.1563C>T	c.(1561-1563)TTC>TTT	p.F521F	ANO4_uc001thw.1_Silent_p.F486F|ANO4_uc001thy.1_Silent_p.F41F	NM_178826	NP_849148	Q32M45	ANO4_HUMAN	anoctamin 4	521	Helical; (Potential).					chloride channel complex	chloride channel activity			ovary(4)	4														0.322148	540.333639	557.054164	192	404	CC		KEEP	---	---	---	---	capture			Silent	SNP	100004595	100004595	707	12	C	T	T	31	31	ANO4	T	1	1
EML1	2009	broad.mit.edu	36	14	99433261	99433261	+	Missense_Mutation	SNP	G	A	A			TCGA-27-2519-01	TCGA-27-2519-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr14:99433261G>A	uc001ygr.1	+	c.761G>A	c.(760-762)CGT>CAT	p.R254H	EML1_uc010avt.1_Missense_Mutation_p.R222H|EML1_uc001ygq.1_Missense_Mutation_p.R254H|EML1_uc001ygs.1_Missense_Mutation_p.R235H	NM_001008707	NP_001008707	O00423	EMAL1_HUMAN	echinoderm microtubule associated protein like 1	235						cytoplasm|microtubule|microtubule associated complex	calcium ion binding|protein binding			large_intestine(2)|ovary(1)|pancreas(1)	4		Melanoma(154;0.0879)|all_epithelial(191;0.216)												0.413793	105.185254	105.749433	36	51	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	99433261	99433261	5288	14	G	A	A	40	40	EML1	A	1	1
LTK	4058	broad.mit.edu	36	15	39586758	39586758	+	Silent	SNP	G	C	C			TCGA-27-2519-01	TCGA-27-2519-01	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)			0.277778	8.045479	8.863214	5	13	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
CIB2	10518	broad.mit.edu	36	15	76190664	76190664	+	Silent	SNP	C	T	T			TCGA-27-2519-01	TCGA-27-2519-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr15:76190664C>T	uc002bdb.1	-	c.96G>A	c.(94-96)TCG>TCA	p.S32S	CIB2_uc002bdc.1_5'UTR	NM_006383	NP_006374	O75838	CIB2_HUMAN	DNA-dependent protein kinase catalytic	32							calcium ion binding				0														0.534884	146.163596	146.255992	46	40	CC		KEEP	---	---	---	---	capture			Silent	SNP	76190664	76190664	3555	15	C	T	T	27	27	CIB2	T	1	1
MNT	4335	broad.mit.edu	36	17	2237386	2237386	+	Silent	SNP	A	C	C			TCGA-27-2519-01	TCGA-27-2519-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr17:2237386A>C	uc002fur.1	-	c.1308T>G	c.(1306-1308)GGT>GGG	p.G436G		NM_020310	NP_064706	Q99583	MNT_HUMAN	MAX binding protein	436					multicellular organismal development|negative regulation of cell proliferation|regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription corepressor activity|transcription regulator activity				0														0.5	7.271769	7.271769	4	4	AA		KEEP	---	---	---	---	capture		Colorectal(2;1.37e-05)|READ - Rectum adenocarcinoma(2;8.68e-05)	Silent	SNP	2237386	2237386	10069	17	A	C	C	6	6	MNT	C	4	4
SGCA	6442	broad.mit.edu	36	17	45600005	45600005	+	Missense_Mutation	SNP	G	A	A			TCGA-27-2519-01	TCGA-27-2519-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:45600005G>A	uc002iqi.1	+	c.221G>A	c.(220-222)CGG>CAG	p.R74Q	SGCA_uc002iqj.1_Missense_Mutation_p.R74Q	NM_000023	NP_000014	Q16586	SGCA_HUMAN	sarcoglycan, alpha isoform 1 precursor	74	Extracellular (Potential).		R -> W (in LGMD2D).		muscle contraction|muscle organ development	cytoplasm|cytoskeleton|integral to membrane|sarcoglycan complex|sarcolemma	calcium ion binding			ovary(2)	2														0.344444	88.896519	90.820434	31	59	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	45600005	45600005	14690	17	G	A	A	39	39	SGCA	A	1	1
ARHGAP28	79822	broad.mit.edu	36	18	6849897	6849897	+	Splice_Site_SNP	SNP	G	T	T			TCGA-27-2519-01	TCGA-27-2519-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr18:6849897G>T	uc002knc.1	+	c.570_splice	c.e5+1	p.V190_splice	ARHGAP28_uc002knd.1_Splice_Site_SNP_p.V83_splice|ARHGAP28_uc002kne.1_Splice_Site_SNP_p.V83_splice|ARHGAP28_uc002knf.1_Splice_Site_SNP_p.V74_splice	NM_030672	NP_109597			Rho GTPase activating protein 28 isoform b						signal transduction	intracellular				pancreas(1)	1		Colorectal(10;0.168)												0.342857	216.551283	221.125524	72	138	GG		KEEP	---	---	---	---	capture			Splice_Site_SNP	SNP	6849897	6849897	889	18	G	T	T	44	44	ARHGAP28	T	5	3
KLK15	55554	broad.mit.edu	36	19	56021719	56021719	+	Silent	SNP	G	A	A			TCGA-27-2519-01	TCGA-27-2519-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:56021719G>A	uc002ptl.1	-	c.588C>T	c.(586-588)GGC>GGT	p.G196G	KLK1_uc002ptk.1_5'Flank|KLK15_uc002ptn.1_Intron|KLK15_uc002ptm.1_Intron|KLK15_uc002pto.1_Silent_p.G195G|KLK15_uc010eod.1_Intron	NM_017509	NP_059979	Q9H2R5	KLK15_HUMAN	kallikrein-related peptidase 15 isoform 4	196	Peptidase S1.				proteolysis	extracellular region	serine-type endopeptidase activity			lung(1)|breast(1)	2		all_neural(266;0.057)				Pancreas(140;10 2513 7143 9246)								0.504425	172.173109	172.175045	57	56	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(262;0.00758)|GBM - Glioblastoma multiforme(134;0.0143)	Silent	SNP	56021719	56021719	8717	19	G	A	A	38	38	KLK15	A	1	1
BRSK1	84446	broad.mit.edu	36	19	60505999	60505999	+	Missense_Mutation	SNP	G	C	C			TCGA-27-2519-01	TCGA-27-2519-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:60505999G>C	uc002qkf.1	+	c.1028G>C	c.(1027-1029)GGC>GCC	p.G343A	BRSK1_uc002qkg.1_Missense_Mutation_p.G327A|BRSK1_uc002qkh.1_Missense_Mutation_p.G22A	NM_032430	NP_115806	Q8TDC3	BRSK1_HUMAN	BR serine/threonine kinase 1	343	UBA.				establishment of cell polarity|G2/M transition DNA damage checkpoint|neuron differentiation|protein phosphorylation|response to UV	cell junction|cytoplasm|nucleus	ATP binding|magnesium ion binding|protein serine/threonine kinase activity	p.G327D(1)		ovary(2)|stomach(1)|lung(1)|breast(1)|skin(1)	6		Renal(1328;0.245)								333				0.441176	93.887209	94.099624	30	38	GG		KEEP	---	---	---	---	capture	BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0474)	Missense_Mutation	SNP	60505999	60505999	1554	19	G	C	C	42	42	BRSK1	C	3	3
TCHH	7062	broad.mit.edu	36	1	150347196	150347196	+	Missense_Mutation	SNP	T	A	A			TCGA-27-2519-01	TCGA-27-2519-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr1:150347196T>A	uc001ezp.2	-	c.5121A>T	c.(5119-5121)AGA>AGT	p.R1707S	TCHH_uc009wne.1_Missense_Mutation_p.R1707S	NM_007113	NP_009044	Q07283	TRHY_HUMAN	trichohyalin	1707	23 X 26 AA approximate tandem repeats.				keratinization	cytoskeleton	calcium ion binding			ovary(3)|kidney(1)|central_nervous_system(1)	5	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)													0.313725	109.220942	113.960086	48	105	TT		KEEP	---	---	---	---	capture	LUSC - Lung squamous cell carcinoma(543;0.206)		Missense_Mutation	SNP	150347196	150347196	16226	1	T	A	A	62	62	TCHH	A	4	4
TCHH	7062	broad.mit.edu	36	1	150347671	150347671	+	Missense_Mutation	SNP	C	T	T			TCGA-27-2519-01	TCGA-27-2519-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:150347671C>T	uc001ezp.2	-	c.4646G>A	c.(4645-4647)CGG>CAG	p.R1549Q	TCHH_uc009wne.1_Missense_Mutation_p.R1549Q	NM_007113	NP_009044	Q07283	TRHY_HUMAN	trichohyalin	1549	23 X 26 AA approximate tandem repeats.				keratinization	cytoskeleton	calcium ion binding			ovary(3)|kidney(1)|central_nervous_system(1)	5	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)													0.263473	115.841566	124.279086	44	123	CC		KEEP	---	---	---	---	capture	LUSC - Lung squamous cell carcinoma(543;0.206)		Missense_Mutation	SNP	150347671	150347671	16226	1	C	T	T	23	23	TCHH	T	1	1
OR2M2	391194	broad.mit.edu	36	1	246410691	246410691	+	Missense_Mutation	SNP	C	T	T			TCGA-27-2519-01	TCGA-27-2519-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:246410691C>T	uc001iea.1	+	c.781C>T	c.(781-783)CGG>TGG	p.R261W		NM_001004688	NP_001004688	Q96R28	OR2M2_HUMAN	olfactory receptor, family 2, subfamily M,	261	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(3)	3	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)													0.295499	406.677372	425.764704	151	360	CC		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(106;0.0245)		Missense_Mutation	SNP	246410691	246410691	11416	1	C	T	T	19	19	OR2M2	T	1	1
AIM1L	55057	broad.mit.edu	36	1	26530639	26530639	+	Silent	SNP	G	A	A			TCGA-27-2519-01	TCGA-27-2519-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:26530639G>A	uc001bmd.2	-	c.1107C>T	c.(1105-1107)GGC>GGT	p.G369G		NM_001039775	NP_001034864	Q8N1P7	AIM1L_HUMAN	absent in melanoma 1-like	369	Beta/gamma crystallin 'Greek key' 8.						sugar binding			pancreas(1)	1		all_cancers(24;4.67e-25)|Colorectal(325;3.46e-05)|all_lung(284;5.94e-05)|Lung NSC(340;7.26e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.00637)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)												0.358974	112.113639	114.163985	42	75	GG		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;1.51e-27)|Colorectal(126;1.61e-08)|COAD - Colon adenocarcinoma(152;9.32e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.000792)|BRCA - Breast invasive adenocarcinoma(304;0.00104)|STAD - Stomach adenocarcinoma(196;0.00154)|GBM - Glioblastoma multiforme(114;0.00858)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.165)|LUSC - Lung squamous cell carcinoma(448;0.239)	Silent	SNP	26530639	26530639	434	1	G	A	A	38	38	AIM1L	A	1	1
TM9SF4	9777	broad.mit.edu	36	20	30209373	30209373	+	Missense_Mutation	SNP	G	A	A			TCGA-27-2519-01	TCGA-27-2519-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr20:30209373G>A	uc002wxj.2	+	c.1445G>A	c.(1444-1446)CGC>CAC	p.R482H	TM9SF4_uc002wxk.2_Missense_Mutation_p.R465H|TM9SF4_uc010gdz.1_Missense_Mutation_p.R361H	NM_014742	NP_055557	Q92544	TM9S4_HUMAN	transmembrane 9 superfamily protein member 4	482						integral to membrane				central_nervous_system(1)|pancreas(1)	2														0.237037	146.648958	163.730247	64	206	GG		KEEP	---	---	---	---	capture	UCEC - Uterine corpus endometrioid carcinoma (5;0.0241)		Missense_Mutation	SNP	30209373	30209373	16510	20	G	A	A	38	38	TM9SF4	A	1	1
MC3R	4159	broad.mit.edu	36	20	54257835	54257835	+	Missense_Mutation	SNP	G	A	A			TCGA-27-2519-01	TCGA-27-2519-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr20:54257835G>A	uc002xxb.2	+	c.640G>A	c.(640-642)GTG>ATG	p.V214M		NM_019888	NP_063941	P41968	MC3R_HUMAN	melanocortin 3 receptor	214	Helical; Name=4; (Potential).				activation of phospholipase C activity by G-protein coupled receptor protein signaling pathway coupled to IP3 second messenger|positive regulation of cAMP biosynthetic process	integral to plasma membrane	melanocyte-stimulating hormone receptor activity|neuropeptide binding|protein binding			ovary(2)	2														0.217082	133.842935	154.580918	61	220	GG		KEEP	---	---	---	---	capture	Colorectal(105;0.202)		Missense_Mutation	SNP	54257835	54257835	9754	20	G	A	A	40	40	MC3R	A	1	1
SCN9A	6335	broad.mit.edu	36	2	166763690	166763690	+	Missense_Mutation	SNP	C	T	T			TCGA-27-2519-01	TCGA-27-2519-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:166763690C>T	uc002udq.2	-	c.5672G>A	c.(5671-5673)CGT>CAT	p.R1891H		NM_002977	NP_002968	Q15858	SCN9A_HUMAN	sodium channel, voltage-gated, type IX, alpha	1902	IQ.					voltage-gated sodium channel complex	voltage-gated sodium channel activity			ovary(6)|central_nervous_system(5)	11					Lamotrigine(DB00555)|Lidocaine(DB00281)									0.340807	209.331072	214.326236	76	147	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	166763690	166763690	14407	2	C	T	T	19	19	SCN9A	T	1	1
C2orf89	129293	broad.mit.edu	36	2	84904649	84904649	+	Missense_Mutation	SNP	G	A	A			TCGA-27-2519-01	TCGA-27-2519-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:84904649G>A	uc002sou.2	-	c.1126C>T	c.(1126-1128)CGG>TGG	p.R376W		NM_001080824	NP_001074293	Q86V40	CB089_HUMAN	hypothetical protein LOC129293	425	Extracellular (Potential).					integral to membrane				ovary(1)	1														0.305556	25.656015	26.846695	11	25	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	84904649	84904649	2295	2	G	A	A	38	38	C2orf89	A	1	1
ANO10	55129	broad.mit.edu	36	3	43593741	43593741	+	Nonsense_Mutation	SNP	G	T	T			TCGA-27-2519-01	TCGA-27-2519-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:43593741G>T	uc003cmv.1	-	c.609C>A	c.(607-609)TAC>TAA	p.Y203*	ANO10_uc003cmw.1_Nonsense_Mutation_p.Y137*|ANO10_uc010hil.1_Intron	NM_018075	NP_060545	Q9NW15	ANO10_HUMAN	transmembrane protein 16K	203	Cytoplasmic (Potential).					chloride channel complex	chloride channel activity			ovary(2)	2														0.155556	8.283737	13.425779	7	38	GG		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	43593741	43593741	704	3	G	T	T	36	36	ANO10	T	5	3
OR5H6	79295	broad.mit.edu	36	3	99466318	99466318	+	Missense_Mutation	SNP	G	C	C			TCGA-27-2519-01	TCGA-27-2519-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:99466318G>C	uc003dsi.1	+	c.500G>C	c.(499-501)GGT>GCT	p.G167A		NM_001005479	NP_001005479	Q8NGV6	OR5H6_HUMAN	olfactory receptor, family 5, subfamily H,	167	Helical; Name=4; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			large_intestine(1)|skin(1)	2														0.27572	208.293401	219.320434	67	176	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	99466318	99466318	11573	3	G	C	C	44	44	OR5H6	C	3	3
NDST4	64579	broad.mit.edu	36	4	116217134	116217134	+	Missense_Mutation	SNP	T	A	A			TCGA-27-2519-01	TCGA-27-2519-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr4:116217134T>A	uc003ibu.1	-	c.508A>T	c.(508-510)AAC>TAC	p.N170Y	NDST4_uc010imw.1_Intron|NDST4_uc010imx.1_Intron	NM_022569	NP_072091	Q9H3R1	NDST4_HUMAN	N-deacetylase/N-sulfotransferase (heparan	170	Lumenal (Potential).|Heparan sulfate N-deacetylase 4.					Golgi membrane|integral to membrane	[heparan sulfate]-glucosamine N-sulfotransferase activity|hydrolase activity			ovary(1)	1		Ovarian(17;0.156)												0.292683	152.977384	160.833411	60	145	TT		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(123;0.000562)	Missense_Mutation	SNP	116217134	116217134	10657	4	T	A	A	62	62	NDST4	A	4	4
KLKB1	3818	broad.mit.edu	36	4	187410233	187410233	+	Missense_Mutation	SNP	C	A	A	rs61733605	unknown	TCGA-27-2519-01	TCGA-27-2519-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:187410233C>A	uc003iyy.1	+	c.1213C>A	c.(1213-1215)CAG>AAG	p.Q405K		NM_000892	NP_000883	P03952	KLKB1_HUMAN	plasma kallikrein B1 precursor	405	Peptidase S1.				blood coagulation, intrinsic pathway|Factor XII activation|fibrinolysis|plasminogen activation|positive regulation of fibrinolysis	cytoplasm|extracellular space|plasma membrane	serine-type endopeptidase activity			ovary(1)	1		all_cancers(14;1.55e-52)|all_epithelial(14;7.69e-39)|all_lung(41;1.34e-13)|Lung NSC(41;3.58e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.00664)|Hepatocellular(41;0.00886)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|all_neural(102;0.243)												0.325301	149.389238	153.886433	54	112	CC		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(60;1.29e-10)|BRCA - Breast invasive adenocarcinoma(30;3.8e-05)|GBM - Glioblastoma multiforme(59;0.000131)|STAD - Stomach adenocarcinoma(60;0.000292)|LUSC - Lung squamous cell carcinoma(40;0.00241)|READ - Rectum adenocarcinoma(43;0.168)	Missense_Mutation	SNP	187410233	187410233	8726	4	C	A	A	25	25	KLKB1	A	3	3
OTOP1	133060	broad.mit.edu	36	4	4279319	4279319	+	Silent	SNP	G	A	A			TCGA-27-2519-01	TCGA-27-2519-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr4:4279319G>A	uc003ghp.1	-	c.174C>T	c.(172-174)GCC>GCT	p.A58A		NM_177998	NP_819056	Q7RTM1	OTOP1_HUMAN	otopetrin 1	58					biomineral tissue development	extracellular space|integral to membrane				ovary(2)	2														0.3	8.521001	8.878423	3	7	GG		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (64;0.168)	Silent	SNP	4279319	4279319	11717	4	G	A	A	39	39	OTOP1	A	1	1
REST	5978	broad.mit.edu	36	4	57492564	57492564	+	Missense_Mutation	SNP	C	T	T			TCGA-27-2519-01	TCGA-27-2519-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:57492564C>T	uc003hch.1	+	c.2783C>T	c.(2782-2784)ACG>ATG	p.T928M	REST_uc003hci.1_Missense_Mutation_p.T928M|REST_uc010ihf.1_Missense_Mutation_p.T602M	NM_005612	NP_005603	Q13127	REST_HUMAN	RE1-silencing transcription factor	928					transcription, DNA-dependent	cytoplasm|nucleus	transcription repressor activity|zinc ion binding			skin(2)|ovary(1)|lung(1)	4	Glioma(25;0.08)|all_neural(26;0.181)													0.330189	98.791072	101.49909	35	71	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	57492564	57492564	13704	4	C	T	T	19	19	REST	T	1	1
PSD2	84249	broad.mit.edu	36	5	139197521	139197521	+	Missense_Mutation	SNP	C	G	G			TCGA-27-2519-01	TCGA-27-2519-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:139197521C>G	uc003leu.1	+	c.1793C>G	c.(1792-1794)GCC>GGC	p.A598G		NM_032289	NP_115665	Q9BQI7	PSD2_HUMAN	pleckstrin and Sec7 domain containing 2	598	PH.				regulation of ARF protein signal transduction	cytoplasm|integral to membrane	ARF guanyl-nucleotide exchange factor activity			ovary(1)	1														0.238095	40.192672	44.140318	15	48	CC		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		Missense_Mutation	SNP	139197521	139197521	13100	5	C	G	G	26	26	PSD2	G	3	3
GABRA1	2554	broad.mit.edu	36	5	161256786	161256786	+	Missense_Mutation	SNP	C	T	T			TCGA-27-2519-01	TCGA-27-2519-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:161256786C>T	uc010jiw.1	+	c.1151C>T	c.(1150-1152)CCG>CTG	p.P384L	GABRA1_uc010jix.1_Missense_Mutation_p.P384L|GABRA1_uc010jiy.1_Missense_Mutation_p.P384L|GABRA1_uc003lyx.2_Missense_Mutation_p.P384L|GABRA1_uc010jiz.1_Missense_Mutation_p.P384L|GABRA1_uc010jja.1_Missense_Mutation_p.P384L|GABRA1_uc010jjb.1_Missense_Mutation_p.P384L	NM_000806	NP_001121120	P14867	GBRA1_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha	384	Cytoplasmic (Probable).				gamma-aminobutyric acid signaling pathway|synaptic transmission	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity			ovary(2)|pancreas(1)	3	Renal(175;0.00259)	Medulloblastoma(196;0.0208)|all_neural(177;0.0672)			Alprazolam(DB00404)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Chlordiazepoxide(DB00475)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ethanol(DB00898)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Flumazenil(DB01205)|Flurazepam(DB00690)|Halazepam(DB00801)|Halothane(DB01159)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Metharbital(DB00463)|Methohexital(DB00474)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Picrotoxin(DB00466)|Prazepam(DB01588)|Primidone(DB00794)|Progabide(DB00837)|Propofol(DB00818)|Quazepam(DB01589)|Secobarbital(DB00418)|Sevoflurane(DB01236)|Talbutal(DB00306)|Thiamylal(DB01154)|Thiopental(DB00599)|Topiramate(DB00273)|Zaleplon(DB00962)|Zolpidem(DB00425)									0.252381	130.718552	142.385816	53	157	CC		KEEP	---	---	---	---	capture	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.228)	Missense_Mutation	SNP	161256786	161256786	6411	5	C	T	T	23	23	GABRA1	T	1	1
RAB3C	115827	broad.mit.edu	36	5	57949379	57949379	+	Silent	SNP	C	T	T			TCGA-27-2519-01	TCGA-27-2519-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:57949379C>T	uc003jrp.1	+	c.177C>T	c.(175-177)TTC>TTT	p.F59F		NM_138453	NP_612462	Q96E17	RAB3C_HUMAN	RAB3C, member RAS oncogene family	59	Effector region (By similarity).				protein transport|small GTPase mediated signal transduction	plasma membrane	GTP binding			ovary(1)|central_nervous_system(1)	2		all_cancers(5;9.93e-10)|all_epithelial(5;1.49e-10)|all_lung(5;8.97e-05)|Lung NSC(5;0.000139)|Prostate(74;0.0664)												0.295455	109.276536	114.214996	39	93	CC		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(10;1.8e-34)	Silent	SNP	57949379	57949379	13392	5	C	T	T	31	31	RAB3C	T	1	1
PKHD1	5314	broad.mit.edu	36	6	52018889	52018889	+	Missense_Mutation	SNP	C	T	T			TCGA-27-2519-01	TCGA-27-2519-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:52018889C>T	uc003pah.1	-	c.2464G>A	c.(2464-2466)GAT>AAT	p.D822N	PKHD1_uc003pai.1_Missense_Mutation_p.D822N	NM_138694	NP_619639	P08F94	PKHD1_HUMAN	fibrocystin isoform 1	822	Extracellular (Potential).				cell-cell adhesion|cilium assembly|homeostatic process|kidney development|negative regulation of cellular component movement	anchored to external side of plasma membrane|apical plasma membrane|integral to membrane|microtubule basal body	protein binding|receptor activity			ovary(12)|large_intestine(5)|central_nervous_system(3)	20	Lung NSC(77;0.0605)									1537				0.324324	239.915668	247.007011	84	175	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	52018889	52018889	12396	6	C	T	T	31	31	PKHD1	T	1	1
TRPV6	55503	broad.mit.edu	36	7	142282418	142282418	+	Missense_Mutation	SNP	T	A	A			TCGA-27-2519-01	TCGA-27-2519-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr7:142282418T>A	uc003wbx.1	-	c.1400A>T	c.(1399-1401)TAC>TTC	p.Y467F	TRPV6_uc003wbw.1_Missense_Mutation_p.Y253F|TRPV6_uc010lou.1_Missense_Mutation_p.Y338F	NM_018646	NP_061116	Q9H1D0	TRPV6_HUMAN	transient receptor potential cation channel,	467	Helical; (Potential).				regulation of calcium ion-dependent exocytosis	integral to plasma membrane	calcium channel activity|calmodulin binding			ovary(1)	1	Melanoma(164;0.059)													0.233463	138.238695	154.992104	60	197	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	142282418	142282418	17151	7	T	A	A	57	57	TRPV6	A	4	4
ARHGEF5	7984	broad.mit.edu	36	7	143693243	143693243	+	Missense_Mutation	SNP	G	A	A			TCGA-27-2519-01	TCGA-27-2519-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:143693243G>A	uc003wel.1	+	c.2548G>A	c.(2548-2550)GAA>AAA	p.E850K	ARHGEF5_uc003wek.2_Missense_Mutation_p.E850K|ARHGEF5_uc003wem.1_5'Flank	NM_005435	NP_005426	Q12774	ARHG5_HUMAN	rho guanine nucleotide exchange factor 5	850					intracellular signal transduction|regulation of Rho protein signal transduction	intracellular	GTP binding|protein binding|Rho guanyl-nucleotide exchange factor activity				0	Melanoma(164;0.14)													0.147059	25.730849	37.876966	15	87	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	143693243	143693243	924	7	G	A	A	37	37	ARHGEF5	A	1	1
ZNF786	136051	broad.mit.edu	36	7	148399095	148399095	+	Missense_Mutation	SNP	C	T	T			TCGA-27-2519-01	TCGA-27-2519-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:148399095C>T	uc003wfh.2	-	c.1702G>A	c.(1702-1704)GGG>AGG	p.G568R	ZNF786_uc003wfi.2_Missense_Mutation_p.G482R	NM_152411	NP_689624	Q8N393	ZN786_HUMAN	zinc finger protein 786	568	C2H2-type 10.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			breast(3)|skin(1)	4	Melanoma(164;0.15)													0.340909	42.012603	42.996334	15	29	CC		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(82;0.00463)		Missense_Mutation	SNP	148399095	148399095	18756	7	C	T	T	23	23	ZNF786	T	1	1
FAM126A	84668	broad.mit.edu	36	7	22952152	22952152	+	Missense_Mutation	SNP	G	A	A			TCGA-27-2519-01	TCGA-27-2519-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:22952152G>A	uc003svm.2	-	c.1147C>T	c.(1147-1149)CGG>TGG	p.R383W	FAM126A_uc003svn.2_3'UTR	NM_032581	NP_115970	Q9BYI3	HYCCI_HUMAN	family with sequence similarity 126, member A	383						cytoplasm|membrane	signal transducer activity			central_nervous_system(1)	1														0.221509	326.810746	371.285059	138	485	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	22952152	22952152	5626	7	G	A	A	40	40	FAM126A	A	1	1
AMPH	273	broad.mit.edu	36	7	38483091	38483091	+	Missense_Mutation	SNP	G	A	A			TCGA-27-2519-01	TCGA-27-2519-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:38483091G>A	uc003tgu.1	-	c.400C>T	c.(400-402)CGC>TGC	p.R134C	AMPH_uc003tgv.1_Missense_Mutation_p.R134C	NM_001635	NP_001626	P49418	AMPH_HUMAN	amphiphysin isoform 1	134	BAR.				endocytosis|synaptic transmission	actin cytoskeleton|cell junction|synaptic vesicle membrane				ovary(3)|liver(1)	4														0.207317	74.047609	87.08178	34	130	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	38483091	38483091	591	7	G	A	A	37	37	AMPH	A	1	1
GRM3	2913	broad.mit.edu	36	7	86253874	86253874	+	Missense_Mutation	SNP	G	A	A			TCGA-27-2519-01	TCGA-27-2519-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:86253874G>A	uc003uid.1	+	c.830G>A	c.(829-831)CGC>CAC	p.R277H	GRM3_uc010lef.1_Missense_Mutation_p.R275H|GRM3_uc010leg.1_Missense_Mutation_p.R149H|GRM3_uc010leh.1_Intron	NM_000840	NP_000831	Q14832	GRM3_HUMAN	glutamate receptor, metabotropic 3 precursor	277	Extracellular (Potential).				synaptic transmission	integral to plasma membrane				ovary(3)|central_nervous_system(2)	5	Esophageal squamous(14;0.0058)|all_lung(186;0.132)|Lung NSC(181;0.142)				Acamprosate(DB00659)|Nicotine(DB00184)	GBM(52;969 1098 3139 52280)								0.136364	19.454165	33.544271	15	95	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	86253874	86253874	7077	7	G	A	A	38	38	GRM3	A	1	1
ZHX2	22882	broad.mit.edu	36	8	124034435	124034435	+	Missense_Mutation	SNP	A	C	C			TCGA-27-2519-01	TCGA-27-2519-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr8:124034435A>C	uc003ypk.1	+	c.1504A>C	c.(1504-1506)ACC>CCC	p.T502P	ZHX2_uc010mdh.1_Missense_Mutation_p.T502P	NM_014943	NP_055758	Q9Y6X8	ZHX2_HUMAN	zinc fingers and homeoboxes 2	502						cytoplasm|nucleus|plasma membrane	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|skin(1)	2	Lung NSC(37;2e-09)|Ovarian(258;0.0205)|Hepatocellular(40;0.105)					Esophageal Squamous(94;1056 1388 11767 13799 49639)								0.291667	86.566862	90.295345	28	68	AA		KEEP	---	---	---	---	capture	STAD - Stomach adenocarcinoma(47;0.00527)		Missense_Mutation	SNP	124034435	124034435	18267	8	A	C	C	6	6	ZHX2	C	4	4
FER1L6	654463	broad.mit.edu	36	8	125179267	125179267	+	Silent	SNP	C	A	A			TCGA-27-2519-01	TCGA-27-2519-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr8:125179267C>A	uc003yqw.1	+	c.4845C>A	c.(4843-4845)ATC>ATA	p.I1615I		NM_001039112	NP_001034201	Q2WGJ9	FR1L6_HUMAN	fer-1-like 6	1615	C2 6.|Cytoplasmic (Potential).					integral to membrane				ovary(5)|central_nervous_system(1)|skin(1)	7	Lung NSC(37;4.1e-12)|Ovarian(258;0.00438)|all_neural(195;0.0741)													0.328467	121.921749	125.499186	45	92	CC		KEEP	---	---	---	---	capture	STAD - Stomach adenocarcinoma(47;0.00186)		Silent	SNP	125179267	125179267	6052	8	C	A	A	32	32	FER1L6	A	3	3
TEX15	56154	broad.mit.edu	36	8	30820714	30820714	+	Nonsense_Mutation	SNP	G	A	A			TCGA-27-2519-01	TCGA-27-2519-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr8:30820714G>A	uc003xil.1	-	c.5362C>T	c.(5362-5364)CGA>TGA	p.R1788*		NM_031271	NP_112561	Q9BXT5	TEX15_HUMAN	testis expressed 15	1788										ovary(3)	3														0.297872	72.066643	75.498249	28	66	GG		KEEP	---	---	---	---	capture		KIRC - Kidney renal clear cell carcinoma(542;0.0918)|Kidney(114;0.111)	Nonsense_Mutation	SNP	30820714	30820714	16306	8	G	A	A	40	40	TEX15	A	5	1
PTPN3	5774	broad.mit.edu	36	9	111193238	111193238	+	Splice_Site_SNP	SNP	C	T	T			TCGA-27-2519-01	TCGA-27-2519-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr9:111193238C>T	uc004bed.1	-	c.2106_splice	c.e20+1	p.N702_splice	PTPN3_uc004beb.1_Splice_Site_SNP_p.N571_splice|PTPN3_uc004bec.1_Splice_Site_SNP_p.N526_splice|PTPN3_uc010mtu.1_Splice_Site_SNP|PTPN3_uc010mtv.1_Splice_Site_SNP_p.N170_splice	NM_002829	NP_002820			protein tyrosine phosphatase, non-receptor type						negative regulation of membrane protein ectodomain proteolysis|negative regulation of mitotic cell cycle	cytoplasm|cytoskeleton|internal side of plasma membrane	ATPase binding|cytoskeletal protein binding|phosphotyrosine binding|protein tyrosine phosphatase activity			ovary(3)	3														0.372093	47.095443	47.710816	16	27	CC		KEEP	---	---	---	---	capture			Splice_Site_SNP	SNP	111193238	111193238	13246	9	C	T	T	19	19	PTPN3	T	5	1
ARSF	416	broad.mit.edu	36	X	3004636	3004636	+	Missense_Mutation	SNP	A	C	C			TCGA-27-2519-01	TCGA-27-2519-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chrX:3004636A>C	uc004cre.1	+	c.209A>C	c.(208-210)CAG>CCG	p.Q70P	ARSF_uc004crf.1_Missense_Mutation_p.Q70P	NM_004042	NP_004033	P54793	ARSF_HUMAN	arylsulfatase F precursor	70						extracellular region	arylsulfatase activity|metal ion binding			ovary(2)	2		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)												0.571429	56.104197	56.228791	16	12	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	3004636	3004636	1009	23	A	C	C	7	7	ARSF	C	4	4
CACNA1F	778	broad.mit.edu	36	X	48975174	48975174	+	Missense_Mutation	SNP	A	C	C			TCGA-27-2519-01	TCGA-27-2519-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chrX:48975174A>C	uc004dnb.1	-	c.185T>G	c.(184-186)GTG>GGG	p.V62G	CACNA1F_uc010nip.1_Missense_Mutation_p.V62G	NM_005183	NP_005174	O60840	CAC1F_HUMAN	calcium channel, voltage-dependent, L type,	62	Cytoplasmic (Potential).				axon guidance|detection of light stimulus involved in visual perception	voltage-gated calcium channel complex	protein binding|voltage-gated calcium channel activity			breast(3)|ovary(1)|kidney(1)|skin(1)	6					Verapamil(DB00661)					279				0.324324	7.699227	8.986459	12	25	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	48975174	48975174	2659	23	A	C	C	6	6	CACNA1F	C	4	4
ZMYM3	9203	broad.mit.edu	36	X	70386253	70386253	+	Missense_Mutation	SNP	A	C	C			TCGA-27-2519-01	TCGA-27-2519-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chrX:70386253A>C	uc004dzh.1	-	c.1253T>G	c.(1252-1254)GTC>GGC	p.V418G	ZMYM3_uc004dzi.1_Missense_Mutation_p.V418G|ZMYM3_uc004dzj.1_Missense_Mutation_p.V418G|ZMYM3_uc004dzk.2_Missense_Mutation_p.V418G|ZMYM3_uc004dzl.2_Missense_Mutation_p.V418G|ZMYM3_uc004dzm.2_Missense_Mutation_p.V418G	NM_201599	NP_963893	Q14202	ZMYM3_HUMAN	zinc finger protein 261	418	MYM-type 2.				multicellular organismal development	nucleus	DNA binding|zinc ion binding			ovary(1)	1	Renal(35;0.156)													0.416667	8.73203	8.834795	5	7	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	70386253	70386253	18292	23	A	C	C	10	10	ZMYM3	C	4	4
PHKA1	5255	broad.mit.edu	36	X	71738594	71738594	+	Missense_Mutation	SNP	C	T	T			TCGA-27-2519-01	TCGA-27-2519-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:71738594C>T	uc004eax.2	-	c.3044G>A	c.(3043-3045)CGT>CAT	p.R1015H	PHKA1_uc004eay.2_Intron	NM_002637	NP_002628	P46020	KPB1_HUMAN	phosphorylase kinase, alpha 1 (muscle) isoform	1015					glucose metabolic process|glycogen catabolic process	cytosol|plasma membrane	calmodulin binding|glucan 1,4-alpha-glucosidase activity|phosphorylase kinase activity			ovary(3)	3	Renal(35;0.156)													0.5	43.451022	43.451022	14	14	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	71738594	71738594	12267	23	C	T	T	19	19	PHKA1	T	1	1
TP53	7157	broad.mit.edu	36	17	7517819	7517819	+	Frame_Shift_Del	DEL	G	-	-	rs28934574	unknown	TCGA-27-2519-01	TCGA-27-2519-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:7517819_7517819delG	uc002gim.2	-	c.844_844delC	c.(844-846)CGGfs	p.R282fs	TP53_uc002gig.1_Intron|TP53_uc002gih.1_Frame_Shift_Del_p.R282fs|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Frame_Shift_Del_p.R150fs|TP53_uc010cng.1_Frame_Shift_Del_p.R150fs|TP53_uc002gii.1_Frame_Shift_Del_p.R150fs|TP53_uc010cnh.1_Frame_Shift_Del_p.R282fs|TP53_uc010cni.1_Frame_Shift_Del_p.R282fs|TP53_uc002gij.2_Frame_Shift_Del_p.R282fs	NM_001126112	NP_001119584	P04637	P53_HUMAN	tumor protein p53 isoform a	282	|Interaction with E4F1.|Interaction with HIPK1 (By similarity).|Interaction with AXIN1 (By similarity).		R -> G (in LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> L (in sporadic cancers; somatic mutation).|R -> P (in sporadic cancers; somatic mutation).|DR -> EW (in sporadic cancers; somatic mutation).|R -> Q (in a familial cancer not matching LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> H (in a sporadic cancer; somatic mutation).		activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of gene-specific transcription from RNA polymerase II promoter|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray	chromatin|cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork	ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|promoter binding|promoter binding|protease binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|sequence-specific DNA binding transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|ubiquitin protein ligase binding|zinc ion binding	p.R282W(358)|p.R282G(25)|p.0?(6)|p.R282R(3)|p.R282fs*24(2)|p.D281fs*63(2)|p.D281_R282>EW(2)|p.A276_R283delACPGRDRR(1)|p.D281_R282insXX(1)|p.C275fs*20(1)|p.?(1)|p.R282_E287delRRTEEE(1)|p.L265_K305del41(1)|p.D281_R282delDR(1)|p.G279fs*59(1)|p.R280fs*62(1)|p.R283_T284>T(1)|p.S269fs*21(1)|p.R282fs*63(1)|p.V272_K292del21(1)|p.C275_R283delCACPGRDRR(1)		large_intestine(4614)|breast(2344)|upper_aerodigestive_tract(2150)|lung(1958)|ovary(1559)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1212)|stomach(1127)|urinary_tract(1113)|central_nervous_system(1072)|liver(805)|skin(693)|pancreas(370)|biliary_tract(247)|soft_tissue(209)|prostate(192)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(41)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1)	21904		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)		Pancreas(47;798 1329 9957 10801)		111	p.R282G(NCIH510-Tumor)|p.R282W(HUPT3-Tumor)|p.V274fs(SCC9-Tumor)|p.R282W(CAL29-Tumor)|p.R282W(EFE184-Tumor)|p.R282W(OVKATE-Tumor)	690	TCGA GBM(1;<1E-8)|TSP Lung(2;<1E-8)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)			0.62			57	35				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	7517819	7517819	16923	17	G	-	-	39	39	TP53	-	5	5
PRR21	643905	broad.mit.edu	36	2	240630790	240630817	+	Frame_Shift_Del	DEL	GTGGGTGAAGAGGCATGGATGAAGGACT	-	-			TCGA-27-2519-01	TCGA-27-2519-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:240630790_240630817delGTGGGTGAAGAGGCATGGATGAAGGACT	uc002vys.1	-	c.256_283delAGTCCTTCATCCATGCCTCTTCACCCAC	c.(256-285)AGTCCTTCATCCATGCCTCTTCACCCACGGfs	p.S86fs		NM_001080835	NP_001074304	Q8WXC7	PRR21_HUMAN	hypothetical protein LOC643905	86_95	Pro-rich.									ovary(1)	1														0.57			27	20				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	240630790	240630817	13040	2	GTGGGTGAAGAGGCATGGATGAAGGACT	-	-	40	40	PRR21	-	5	5
MAP1B	4131	broad.mit.edu	36	5	71528792	71528792	+	Frame_Shift_Del	DEL	A	-	-			TCGA-27-2519-01	TCGA-27-2519-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:71528792_71528792delA	uc003kbw.2	+	c.3854_3854delA	c.(3853-3855)GAGfs	p.E1285fs	MAP1B_uc010iyw.1_Frame_Shift_Del_p.E1302fs|MAP1B_uc010iyx.1_Frame_Shift_Del_p.E1159fs|MAP1B_uc010iyy.1_Frame_Shift_Del_p.E1159fs	NM_005909	NP_005900	P46821	MAP1B_HUMAN	microtubule-associated protein 1B	1285						microtubule|microtubule associated complex	structural molecule activity			large_intestine(2)|ovary(1)|central_nervous_system(1)|pancreas(1)	5		Lung NSC(167;0.00202)|Ovarian(174;0.0175)|Prostate(461;0.142)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;7.99e-54)		Melanoma(17;367 822 11631 31730 47712)								0.33			41	85				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	71528792	71528792	9611	5	A	-	-	11	11	MAP1B	-	5	5
IRF5	3663	broad.mit.edu	36	7	128374603	128374617	+	Splice_Site_Del	DEL	ACTCTGCGGCCGCCT	-	-			TCGA-27-2519-01	TCGA-27-2519-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:128374603_128374617delACTCTGCGGCCGCCT	uc003vog.1	+	c.e7_splice_site			IRF5_uc010llr.1_In_Frame_Del_p.LCGRL162del|IRF5_uc010lls.1_In_Frame_Del_p.LCGRL162del|IRF5_uc003voh.1_Splice_Site_Del|IRF5_uc010llt.1_Intron|IRF5_uc003voi.1_Splice_Site_Del|IRF5_uc003vok.2_3'UTR|IRF5_uc010llu.1_In_Frame_Del_p.LCGRL162del|IRF5_uc003voj.2_Splice_Site_Del|IRF5_uc010llv.1_3'UTR|IRF5_uc010llw.1_In_Frame_Del_p.LCGRL162del	NM_002200	NP_002191			interferon regulatory factor 5 isoform a						interferon-gamma-mediated signaling pathway|regulation of transcription, DNA-dependent|type I interferon-mediated signaling pathway	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity				0														0.38			9	15				---	---	---	---	capture_indel			Splice_Site_Del	DEL	128374603	128374617	8136	7	ACTCTGCGGCCGCCT	-	-	6	6	IRF5	-	5	5
RAD23B	5887	broad.mit.edu	36	9	109124202	109124204	+	In_Frame_Del	DEL	ACA	-	-			TCGA-27-2519-01	TCGA-27-2519-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:109124202_109124204delACA	uc004bde.1	+	c.799_801delACA	c.(799-801)ACAdel	p.T269del		NM_002874	NP_002865	P54727	RD23B_HUMAN	UV excision repair protein RAD23 homolog B	269	Poly-Thr.				nucleotide-excision repair, DNA damage recognition|nucleotide-excision repair, DNA damage removal|proteasomal ubiquitin-dependent protein catabolic process|regulation of proteasomal ubiquitin-dependent protein catabolic process	cytoplasm|nucleoplasm|proteasome complex|XPC complex	damaged DNA binding|polyubiquitin binding|single-stranded DNA binding			ovary(1)	1														0.32			33	69				---	---	---	---	capture_indel			In_Frame_Del	DEL	109124202	109124204	13443	9	ACA	-	-	14	14	RAD23B	-	5	5
