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
CABP2	51475	broad.mit.edu	36	11	67044203	67044203	+	Silent	SNP	G	A	A			TCGA-12-0822-01	TCGA-12-0822-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:67044203G>A	uc001omc.1	-	c.384C>T	c.(382-384)GGC>GGT	p.G128G	CABP2_uc001omd.1_Silent_p.G71G|CABP2_uc001ome.1_Silent_p.G134G	NM_016366	NP_057450	Q9NPB3	CABP2_HUMAN	calcium binding protein 2 isoform 1	128	EF-hand 2.				signal transduction	Golgi apparatus|perinuclear region of cytoplasm|plasma membrane	calcium ion binding				0														0.175	9.197534	13.203994	7	33	GG		KEEP	---	---	---	---	capture			Silent	SNP	67044203	67044203	2648	11	G	A	A	38	38	CABP2	A	1	1
TMTC1	83857	broad.mit.edu	36	12	29677450	29677450	+	Missense_Mutation	SNP	C	A	A			TCGA-12-0822-01	TCGA-12-0822-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:29677450C>A	uc001rjb.1	-	c.701G>T	c.(700-702)AGT>ATT	p.S234I	TMTC1_uc001riz.1_5'UTR|TMTC1_uc001rja.1_Missense_Mutation_p.S78I|TMTC1_uc001rjc.1_Missense_Mutation_p.S296I	NM_175861	NP_787057	Q8IUR5	TMTC1_HUMAN	transmembrane and tetratricopeptide repeat	234						integral to membrane	binding				0	Lung NSC(12;7.61e-10)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.032)													0.30303	24.641048	25.781942	10	23	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	29677450	29677450	16801	12	C	A	A	20	20	TMTC1	A	3	3
SCNN1A	6337	broad.mit.edu	36	12	6335237	6335237	+	Missense_Mutation	SNP	G	A	A			TCGA-12-0822-01	TCGA-12-0822-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:6335237G>A	uc001qnw.1	-	c.1123C>T	c.(1123-1125)CTC>TTC	p.L375F	SCNN1A_uc001qnv.1_Missense_Mutation_p.L16F|SCNN1A_uc001qnx.1_Missense_Mutation_p.L316F	NM_001038	NP_001029	P37088	SCNNA_HUMAN	sodium channel, nonvoltage-gated 1 alpha	316	Extracellular (By similarity).				excretion|response to stimulus|sensory perception of taste	apical plasma membrane	WW domain binding				0					Amiloride(DB00594)|Triamterene(DB00384)									0.340502	507.76091	520.316407	190	368	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	6335237	6335237	14409	12	G	A	A	35	35	SCNN1A	A	2	2
TAPBPL	55080	broad.mit.edu	36	12	6433131	6433131	+	Missense_Mutation	SNP	G	A	A			TCGA-12-0822-01	TCGA-12-0822-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:6433131G>A	uc001qog.2	+	c.553G>A	c.(553-555)GTG>ATG	p.V185M	LOC678655_uc001qob.2_5'Flank|LOC678655_uc001qoc.2_5'Flank|LOC678655_uc009zel.1_5'Flank|LOC678655_uc009zem.1_5'Flank|LOC678655_uc001qof.2_5'Flank|TAPBPL_uc001qoh.2_Missense_Mutation_p.V43M|TAPBPL_uc001qoi.1_Non-coding_Transcript	NM_018009	NP_060479	Q9BX59	TPSNR_HUMAN	TAP binding protein-like	185	Lumenal (Potential).|Ig-like V-type.				antigen processing and presentation of endogenous peptide antigen via MHC class I	endoplasmic reticulum membrane|integral to membrane|microsome|plasma membrane					0														0.540984	184.741017	184.918576	66	56	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	6433131	6433131	16074	12	G	A	A	48	48	TAPBPL	A	2	2
SLITRK5	26050	broad.mit.edu	36	13	87126111	87126111	+	Missense_Mutation	SNP	A	T	T			TCGA-12-0822-01	TCGA-12-0822-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr13:87126111A>T	uc001vln.1	+	c.467A>T	c.(466-468)GAG>GTG	p.E156V	SLITRK5_uc010afg.1_Missense_Mutation_p.E156V	NM_015567	NP_056382	O94991	SLIK5_HUMAN	SLIT and NTRK-like family, member 5	156	LRR 4.|Extracellular (Potential).					integral to membrane				ovary(2)|pancreas(2)|central_nervous_system(1)	5	all_neural(89;0.101)|Medulloblastoma(90;0.163)													0.206667	124.712059	148.628063	62	238	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	87126111	87126111	15244	13	A	T	T	11	11	SLITRK5	T	4	4
FRMD6	122786	broad.mit.edu	36	14	51256663	51256663	+	Missense_Mutation	SNP	C	T	T			TCGA-12-0822-01	TCGA-12-0822-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr14:51256663C>T	uc001wzd.1	+	c.1165C>T	c.(1165-1167)CAC>TAC	p.H389Y	FRMD6_uc001wzb.1_Missense_Mutation_p.H381Y|FRMD6_uc001wzc.1_Missense_Mutation_p.H381Y|FRMD6_uc001wze.1_Missense_Mutation_p.H312Y|FRMD6_uc001wzf.1_Missense_Mutation_p.H82Y|FRMD6_uc001wzg.1_Missense_Mutation_p.H31Y	NM_152330	NP_689543	Q96NE9	FRMD6_HUMAN	FERM domain containing 6	389						cytoskeleton|mitochondrion|plasma membrane	binding			ovary(1)|central_nervous_system(1)	2	all_epithelial(31;0.0163)|Breast(41;0.089)													0.131579	14.9507	29.99822	15	99	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	51256663	51256663	6304	14	C	T	T	21	21	FRMD6	T	2	2
ARNT2	9915	broad.mit.edu	36	15	78642607	78642607	+	Missense_Mutation	SNP	T	A	A			TCGA-12-0822-01	TCGA-12-0822-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr15:78642607T>A	uc002bfr.1	+	c.1288T>A	c.(1288-1290)TAC>AAC	p.Y430N	ARNT2_uc002bfs.1_Missense_Mutation_p.Y419N	NM_014862	NP_055677	Q9HBZ2	ARNT2_HUMAN	aryl hydrocarbon receptor nuclear translocator	430	PAC.				central nervous system development|in utero embryonic development|response to hypoxia		aryl hydrocarbon receptor binding|DNA binding|protein heterodimerization activity|sequence-specific DNA binding transcription factor activity|signal transducer activity|transcription regulator activity	p.Y430N(1)		central_nervous_system(3)|ovary(1)|pancreas(1)	5			BRCA - Breast invasive adenocarcinoma(143;0.134)											0.169789	238.908192	326.946051	145	709	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	78642607	78642607	984	15	T	A	A	57	57	ARNT2	A	4	4
GPR114	221188	broad.mit.edu	36	16	56158939	56158939	+	Silent	SNP	C	G	G			TCGA-12-0822-01	TCGA-12-0822-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:56158939C>G	uc002elx.2	+	c.756C>G	c.(754-756)TCC>TCG	p.S252S	GPR114_uc002ely.1_Silent_p.S252S	NM_153837	NP_722579	Q8IZF4	GP114_HUMAN	G protein-coupled receptor 114	252	Helical; Name=1; (Potential).				neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			central_nervous_system(1)	1														0.298701	44.476962	47.27808	23	54	CC		KEEP	---	---	---	---	capture			Silent	SNP	56158939	56158939	6905	16	C	G	G	22	22	GPR114	G	3	3
MYO19	80179	broad.mit.edu	36	17	31945933	31945933	+	Missense_Mutation	SNP	C	T	T			TCGA-12-0822-01	TCGA-12-0822-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:31945933C>T	uc002hmw.1	-	c.428G>A	c.(427-429)CGC>CAC	p.R143H	MYO19_uc010cuu.1_Non-coding_Transcript|MYO19_uc002hmx.1_Missense_Mutation_p.R143H	NM_025109	NP_079385	Q96H55	MYO19_HUMAN	myosin head domain containing 1 isoform 1	143	Myosin head-like.					mitochondrial outer membrane|myosin complex	actin binding|ATP binding|motor activity			ovary(1)	1		Breast(25;0.00957)|Ovarian(249;0.17)	Kidney(155;0.104)	UCEC - Uterine corpus endometrioid carcinoma (308;0.0185)										0.226316	90.639868	103.714827	43	147	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	31945933	31945933	10462	17	C	T	T	27	27	MYO19	T	1	1
GAA	2548	broad.mit.edu	36	17	75696099	75696099	+	Silent	SNP	C	A	A			TCGA-12-0822-01	TCGA-12-0822-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:75696099C>A	uc002jxo.1	+	c.841C>A	c.(841-843)CGG>AGG	p.R281R	GAA_uc002jxp.1_Silent_p.R281R|GAA_uc002jxq.1_Silent_p.R281R	NM_001079803	NP_001073272	P10253	LYAG_HUMAN	acid alpha-glucosidase preproprotein	281					cardiac muscle contraction|diaphragm contraction|glucose metabolic process|glycogen catabolic process|lysosome organization|maltose metabolic process|sucrose metabolic process|tongue morphogenesis|vacuolar sequestering|ventricular cardiac muscle tissue morphogenesis	lysosomal membrane	carbohydrate binding|maltose alpha-glucosidase activity			ovary(1)	1	all_neural(118;0.117)		OV - Ovarian serous cystadenocarcinoma(97;0.0292)|BRCA - Breast invasive adenocarcinoma(99;0.139)		Acarbose(DB00284)									0.215686	13.389385	17.212759	11	40	CC		KEEP	---	---	---	---	capture			Silent	SNP	75696099	75696099	6398	17	C	A	A	23	23	GAA	A	3	3
ALOXE3	59344	broad.mit.edu	36	17	7959008	7959008	+	Missense_Mutation	SNP	G	A	A			TCGA-12-0822-01	TCGA-12-0822-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:7959008G>A	uc002gka.1	-	c.995C>T	c.(994-996)ACG>ATG	p.T332M	ALOXE3_uc010cnr.1_Missense_Mutation_p.T176M	NM_021628	NP_067641	Q9BYJ1	LOXE3_HUMAN	arachidonate lipoxygenase 3	176	Lipoxygenase.				leukotriene biosynthetic process|oxidation-reduction process		iron ion binding|lipoxygenase activity			lung(1)|central_nervous_system(1)	2														0.216321	338.52314	395.856197	167	605	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	7959008	7959008	545	17	G	A	A	40	40	ALOXE3	A	1	1
LAMA1	284217	broad.mit.edu	36	18	6999320	6999320	+	Nonsense_Mutation	SNP	G	A	A			TCGA-12-0822-01	TCGA-12-0822-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr18:6999320G>A	uc002knm.1	-	c.3919C>T	c.(3919-3921)CGA>TGA	p.R1307*		NM_005559	NP_005550	P25391	LAMA1_HUMAN	laminin, alpha 1 precursor	1307	Laminin IV type A 2.				axon guidance|cell adhesion|cell surface receptor linked signaling pathway|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	extracellular space|laminin-1 complex|laminin-3 complex	extracellular matrix structural constituent|receptor binding			ovary(8)|large_intestine(4)|breast(2)|pancreas(2)|central_nervous_system(1)	17		Colorectal(10;0.172)			Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)					1597				0.22069	127.534439	148.388108	64	226	GG		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	6999320	6999320	8928	18	G	A	A	38	38	LAMA1	A	5	1
RALBP1	10928	broad.mit.edu	36	18	9514725	9514725	+	Missense_Mutation	SNP	C	T	T			TCGA-12-0822-01	TCGA-12-0822-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr18:9514725C>T	uc002kob.1	+	c.1187C>T	c.(1186-1188)GCG>GTG	p.A396V	RALBP1_uc002koc.1_Missense_Mutation_p.A396V	NM_006788	NP_006779	Q15311	RBP1_HUMAN	ralA binding protein 1	396					chemotaxis|positive regulation of Cdc42 GTPase activity|small GTPase mediated signal transduction|transport	cytosol|membrane	ATPase activity, coupled to movement of substances|Rac GTPase activator activity|Rac GTPase binding|Ral GTPase binding			central_nervous_system(1)	1									p.A396V(SNU1040-Tumor)	246				0.228188	67.439285	77.50296	34	115	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	9514725	9514725	13472	18	C	T	T	27	27	RALBP1	T	1	1
FBN3	84467	broad.mit.edu	36	19	8044001	8044001	+	Missense_Mutation	SNP	G	A	A			TCGA-12-0822-01	TCGA-12-0822-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:8044001G>A	uc002mjf.1	-	c.7883C>T	c.(7882-7884)ACG>ATG	p.T2628M	FBN3_uc002mje.1_Missense_Mutation_p.T424M	NM_032447	NP_115823	Q75N90	FBN3_HUMAN	fibrillin 3 precursor	2628	EGF-like 44; calcium-binding.					proteinaceous extracellular matrix	calcium ion binding|extracellular matrix structural constituent			ovary(6)|central_nervous_system(1)|pancreas(1)	8														0.380952	18.590125	18.852539	8	13	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	8044001	8044001	5940	19	G	A	A	40	40	FBN3	A	1	1
SPAG17	200162	broad.mit.edu	36	1	118425406	118425406	+	Missense_Mutation	SNP	C	G	G			TCGA-12-0822-01	TCGA-12-0822-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:118425406C>G	uc001ehk.1	-	c.2050G>C	c.(2050-2052)GAT>CAT	p.D684H		NM_206996	NP_996879	Q6Q759	SPG17_HUMAN	sperm associated antigen 17	684						cilium|flagellar axoneme|microtubule				ovary(2)|large_intestine(1)	3	Esophageal squamous(2;0.0106)	all_cancers(81;0.0204)|all_lung(203;9.46e-05)|Lung NSC(69;0.000675)|all_epithelial(167;0.01)		Lung(183;0.0858)										0.223684	42.239496	47.570494	17	59	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	118425406	118425406	15482	1	C	G	G	32	32	SPAG17	G	3	3
ATP1A2	477	broad.mit.edu	36	1	158365234	158365234	+	Missense_Mutation	SNP	C	G	G			TCGA-12-0822-01	TCGA-12-0822-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:158365234C>G	uc001fvc.1	+	c.1186C>G	c.(1186-1188)CAT>GAT	p.H396D	ATP1A2_uc001fvb.1_Missense_Mutation_p.H396D|ATP1A2_uc001fvd.1_Missense_Mutation_p.H132D|ATP1A2_uc009wtg.1_Missense_Mutation_p.H84D	NM_000702	NP_000693	P50993	AT1A2_HUMAN	Na+/K+ -ATPase alpha 2 subunit proprotein	396	Cytoplasmic (Potential).				ATP biosynthetic process	sodium:potassium-exchanging ATPase complex	ATP binding|metal ion binding|sodium:potassium-exchanging ATPase activity			ovary(2)|central_nervous_system(2)	4	all_cancers(52;1.11e-16)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)|LUSC - Lung squamous cell carcinoma(543;0.246)											0.181637	164.617862	212.371453	91	410	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	158365234	158365234	1148	1	C	G	G	21	21	ATP1A2	G	3	3
LMX1A	4009	broad.mit.edu	36	1	163589012	163589012	+	Missense_Mutation	SNP	G	A	A			TCGA-12-0822-01	TCGA-12-0822-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:163589012G>A	uc001gcy.1	-	c.188C>T	c.(187-189)GCC>GTC	p.A63V	LMX1A_uc001gcz.1_Missense_Mutation_p.A63V	NM_177398	NP_796372	Q8TE12	LMX1A_HUMAN	LIM homeobox transcription factor 1, alpha	63	LIM zinc-binding 1.				regulation of transcription, DNA-dependent	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulator activity|zinc ion binding			central_nervous_system(3)|pancreas(1)	4	all_hematologic(923;0.248)													0.148936	11.744363	22.83782	14	80	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	163589012	163589012	9190	1	G	A	A	42	42	LMX1A	A	2	2
FAM5C	339479	broad.mit.edu	36	1	188334885	188334885	+	Missense_Mutation	SNP	G	T	T			TCGA-12-0822-01	TCGA-12-0822-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:188334885G>T	uc001gse.1	-	c.1187C>A	c.(1186-1188)ACC>AAC	p.T396N		NM_199051	NP_950252	Q76B58	FAM5C_HUMAN	family with sequence similarity 5, member C	396						extracellular region				lung(2)|ovary(1)|kidney(1)	4	Prostate(682;0.198)													0.215686	19.508001	23.435195	11	40	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	188334885	188334885	5817	1	G	T	T	44	44	FAM5C	T	3	3
TFB2M	64216	broad.mit.edu	36	1	244771048	244771048	+	Missense_Mutation	SNP	G	A	A			TCGA-12-0822-01	TCGA-12-0822-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:244771048G>A	uc001ibn.1	-	c.1099C>T	c.(1099-1101)CCT>TCT	p.P367S		NM_022366	NP_071761	Q9H5Q4	TFB2M_HUMAN	transcription factor B2, mitochondrial	367					positive regulation of transcription, DNA-dependent|transcription initiation from mitochondrial promoter	mitochondrial nucleoid	protein binding|rRNA (adenine-N6,N6-)-dimethyltransferase activity|transcription cofactor activity			ovary(1)	1	all_cancers(71;4.25e-05)|all_epithelial(71;4.92e-06)|Ovarian(71;0.0254)|all_lung(81;0.0272)|Breast(184;0.0318)|Lung NSC(105;0.0376)		OV - Ovarian serous cystadenocarcinoma(106;0.00358)											0.162791	12.900215	17.546296	7	36	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	244771048	244771048	16322	1	G	A	A	43	43	TFB2M	A	2	2
RBM39	9584	broad.mit.edu	36	20	33776479	33776479	+	Missense_Mutation	SNP	A	T	T			TCGA-12-0822-01	TCGA-12-0822-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr20:33776479A>T	uc002xeb.1	-	c.429T>A	c.(427-429)GAT>GAA	p.D143E	RBM39_uc002xdz.1_Missense_Mutation_p.D119E|RBM39_uc002xea.1_5'UTR|RBM39_uc010gfn.1_5'UTR|RBM39_uc002xeg.1_Missense_Mutation_p.D121E|RBM39_uc002xec.1_Missense_Mutation_p.D143E|RBM39_uc002xed.1_5'UTR|RBM39_uc002xee.1_5'UTR|RBM39_uc002xef.1_5'UTR	NM_184234	NP_909122	Q14498	RBM39_HUMAN	RNA binding motif protein 39 isoform a	143					mRNA processing|regulation of transcription, DNA-dependent|RNA splicing|transcription, DNA-dependent	centrosome|nuclear speck	nucleotide binding|protein binding|RNA binding			ovary(1)|central_nervous_system(1)	2	all_epithelial(2;0.00295)|Lung NSC(9;0.00453)|Breast(12;0.00544)|all_lung(11;0.00676)													0.267094	297.600162	320.511004	125	343	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	33776479	33776479	13595	20	A	T	T	16	16	RBM39	T	4	4
NCOA3	8202	broad.mit.edu	36	20	45698306	45698306	+	Missense_Mutation	SNP	G	C	C			TCGA-12-0822-01	TCGA-12-0822-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr20:45698306G>C	uc002xtk.1	+	c.1769G>C	c.(1768-1770)AGA>ACA	p.R590T	NCOA3_uc010ght.1_Missense_Mutation_p.R600T|NCOA3_uc002xtl.1_Missense_Mutation_p.R590T|NCOA3_uc002xtm.1_Missense_Mutation_p.R590T|NCOA3_uc002xtn.1_Missense_Mutation_p.R590T	NM_181659	NP_858045	Q9Y6Q9	NCOA3_HUMAN	nuclear receptor coactivator 3 isoform a	590	Ser-rich.				androgen receptor signaling pathway|cellular lipid metabolic process|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nucleoplasm	androgen receptor binding|histone acetyltransferase activity|ligand-dependent nuclear receptor binding|protein N-terminus binding|signal transducer activity|thyroid hormone receptor binding|transcription regulator activity			ovary(3)|lung(1)|skin(1)	5										361				0.139303	85.147268	135.673123	56	346	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	45698306	45698306	10629	20	G	C	C	33	33	NCOA3	C	3	3
PKDREJ	10343	broad.mit.edu	36	22	45031187	45031187	+	Missense_Mutation	SNP	G	A	A			TCGA-12-0822-01	TCGA-12-0822-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr22:45031187G>A	uc003bhh.1	-	c.6697C>T	c.(6697-6699)CAC>TAC	p.H2233Y		NM_006071	NP_006062	Q9NTG1	PKDRE_HUMAN	receptor for egg jelly-like protein precursor	2233	Cytoplasmic (Potential).				acrosome reaction|neuropeptide signaling pathway	integral to membrane	calcium ion binding|ion channel activity			breast(3)|ovary(2)	5		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00459)										0.375	77.923147	79.022547	30	50	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	45031187	45031187	12395	22	G	A	A	47	47	PKDREJ	A	2	2
LONRF2	164832	broad.mit.edu	36	2	100269884	100269884	+	Missense_Mutation	SNP	G	A	A			TCGA-12-0822-01	TCGA-12-0822-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:100269884G>A	uc002tal.2	-	c.1994C>T	c.(1993-1995)GCG>GTG	p.A665V		NM_198461	NP_940863	Q1L5Z9	LONF2_HUMAN	LON peptidase N-terminal domain and ring finger	665	Lon.				proteolysis		ATP-dependent peptidase activity|zinc ion binding			large_intestine(1)	1														0.11194	10.836861	30.781644	15	119	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	100269884	100269884	9267	2	G	A	A	38	38	LONRF2	A	1	1
CDK15	65061	broad.mit.edu	36	2	202406915	202406915	+	Missense_Mutation	SNP	G	A	A			TCGA-12-0822-01	TCGA-12-0822-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:202406915G>A	uc002uyt.2	+	c.706G>A	c.(706-708)GGA>AGA	p.G236R	CDK15_uc010ftm.1_Missense_Mutation_p.G101R|CDK15_uc002uys.2_Missense_Mutation_p.G185R|CDK15_uc010ftn.1_Missense_Mutation_p.G185R|CDK15_uc010fto.1_Missense_Mutation_p.G215R	NM_139158	NP_631897	Q96Q40	CDK15_HUMAN	PFTAIRE protein kinase 2	236	Protein kinase.				protein phosphorylation		ATP binding|cyclin-dependent protein kinase activity|metal ion binding|protein binding			breast(2)|ovary(1)|lung(1)|kidney(1)	5					Adenosine triphosphate(DB00171)					431				0.25974	189.953037	206.06081	80	228	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	202406915	202406915	3260	2	G	A	A	43	43	CDK15	A	2	2
TTC27	55622	broad.mit.edu	36	2	32836960	32836960	+	Missense_Mutation	SNP	A	G	G			TCGA-12-0822-01	TCGA-12-0822-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr2:32836960A>G	uc002rom.1	+	c.1550A>G	c.(1549-1551)AAG>AGG	p.K517R	TTC27_uc002ron.1_Non-coding_Transcript	NM_017735	NP_060205	Q6P3X3	TTC27_HUMAN	tetratricopeptide repeat domain 27	517							protein binding			central_nervous_system(1)	1														0.177606	89.098492	114.457324	46	213	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	32836960	32836960	17249	2	A	G	G	3	3	TTC27	G	4	4
NRXN1	9378	broad.mit.edu	36	2	51108613	51108613	+	Silent	SNP	C	A	A			TCGA-12-0822-01	TCGA-12-0822-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:51108613C>A	uc002rxe.2	-	c.303G>T	c.(301-303)GCG>GCT	p.A101A	NRXN1_uc010fbr.1_Silent_p.A101A|NRXN1_uc002rxd.1_Silent_p.A101A	NM_004801	NP_004792	P58400	NRX1B_HUMAN	neurexin 1 isoform alpha1 precursor	164	Extracellular (Potential).|Laminin G-like.				neuron cell-cell adhesion|neuronal signal transduction	cell surface|endocytic vesicle|integral to membrane|presynaptic membrane	cell adhesion molecule binding|receptor binding			ovary(2)	2		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.192)	Lung(47;0.0813)|LUSC - Lung squamous cell carcinoma(58;0.116)											0.307692	6.594314	7.023879	4	9	CC		KEEP	---	---	---	---	capture			Silent	SNP	51108613	51108613	11070	2	C	A	A	31	31	NRXN1	A	3	3
FAM193A	8603	broad.mit.edu	36	4	2643864	2643864	+	Silent	SNP	C	T	T			TCGA-12-0822-01	TCGA-12-0822-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:2643864C>T	uc010icl.1	+	c.1425C>T	c.(1423-1425)ACC>ACT	p.T475T	FAM193A_uc010ick.1_Silent_p.T475T|FAM193A_uc003gfd.1_Silent_p.T475T|FAM193A_uc010icm.1_Non-coding_Transcript|FAM193A_uc003gfe.1_Silent_p.T329T	NM_003704	NP_003695	P78312	F193A_HUMAN	hypothetical protein LOC8603	475										ovary(3)	3														0.230769	6.517461	7.381899	3	10	CC		KEEP	---	---	---	---	capture			Silent	SNP	2643864	2643864	5735	4	C	T	T	24	24	FAM193A	T	2	2
CARD6	84674	broad.mit.edu	36	5	40888427	40888427	+	Silent	SNP	A	G	G			TCGA-12-0822-01	TCGA-12-0822-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr5:40888427A>G	uc003jmg.1	+	c.1236A>G	c.(1234-1236)GCA>GCG	p.A412A		NM_032587	NP_115976	Q9BX69	CARD6_HUMAN	caspase recruitment domain family, member 6	412					apoptosis|regulation of apoptosis	intracellular				ovary(2)|skin(2)|lung(1)	5														0.248421	537.539152	592.257859	236	714	AA		KEEP	---	---	---	---	capture			Silent	SNP	40888427	40888427	2769	5	A	G	G	7	7	CARD6	G	4	4
E2F3	1871	broad.mit.edu	36	6	20588112	20588112	+	Missense_Mutation	SNP	A	T	T			TCGA-12-0822-01	TCGA-12-0822-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr6:20588112A>T	uc003nda.2	+	c.450A>T	c.(448-450)TTA>TTT	p.L150F	E2F3_uc003ncz.2_Missense_Mutation_p.L150F	NM_001949	NP_001940	O00716	E2F3_HUMAN	E2F transcription factor 3	150	Cyclin A/CDK2 binding (Potential).				G1 phase of mitotic cell cycle|G2 phase of mitotic cell cycle|transcription initiation from RNA polymerase II promoter	transcription factor complex	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			lung(1)	1	all_cancers(95;0.154)|all_epithelial(95;0.0585)|Breast(50;0.146)|Ovarian(93;0.148)		OV - Ovarian serous cystadenocarcinoma(7;0.0068)|all cancers(50;0.0148)|Epithelial(50;0.0562)											0.214646	335.756331	395.304801	170	622	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	20588112	20588112	5054	6	A	T	T	13	13	E2F3	T	4	4
VARS	7407	broad.mit.edu	36	6	31855229	31855229	+	Missense_Mutation	SNP	C	T	T			TCGA-12-0822-01	TCGA-12-0822-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:31855229C>T	uc003nxe.1	-	c.3352G>A	c.(3352-3354)GTG>ATG	p.V1118M	C6orf27_uc003nxb.2_5'Flank|C6orf27_uc003nxd.2_5'Flank|VARS_uc003nxf.1_Missense_Mutation_p.V55M	NM_006295	NP_006286	P26640	SYVC_HUMAN	valyl-tRNA synthetase	1118					translational elongation|valyl-tRNA aminoacylation	cytosol	ATP binding|protein binding|valine-tRNA ligase activity			ovary(1)	1					L-Valine(DB00161)									0.155844	14.660062	23.427109	12	65	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	31855229	31855229	17688	6	C	T	T	19	19	VARS	T	1	1
CNTNAP2	26047	broad.mit.edu	36	7	146449105	146449105	+	Missense_Mutation	SNP	C	T	T			TCGA-12-0822-01	TCGA-12-0822-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:146449105C>T	uc003weu.1	+	c.856C>T	c.(856-858)CGG>TGG	p.R286W		NM_014141	NP_054860	Q9UHC6	CNTP2_HUMAN	cell recognition molecule Caspr2 precursor	286	Laminin G-like 1.|Extracellular (Potential).				behavior|cell adhesion|clustering of voltage-gated potassium channels|limbic system development|neuron recognition|signal transduction|striatum development|superior temporal gyrus development|thalamus development|transmission of nerve impulse	axolemma|cell body fiber|dendrite|juxtaparanode region of axon|voltage-gated potassium channel complex	receptor binding			ovary(9)|central_nervous_system(1)|pancreas(1)	11	Melanoma(164;0.153)	all_cancers(3;3.51e-10)|all_epithelial(3;1.4e-05)|Myeloproliferative disorder(3;0.00452)|Lung NSC(3;0.0067)|all_lung(3;0.00794)	OV - Ovarian serous cystadenocarcinoma(82;0.0319)											0.307506	305.844286	319.506808	127	286	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	146449105	146449105	3785	7	C	T	T	27	27	CNTNAP2	T	1	1
STAG3	10734	broad.mit.edu	36	7	99647383	99647383	+	Missense_Mutation	SNP	A	G	G			TCGA-12-0822-01	TCGA-12-0822-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr7:99647383A>G	uc003utx.1	+	c.3545A>G	c.(3544-3546)GAA>GGA	p.E1182G	GATS_uc003uty.2_Non-coding_Transcript|GATS_uc010lgt.1_Intron|GATS_uc003utz.2_Intron|GATS_uc003uua.2_Intron|STAG3_uc003uub.1_Missense_Mutation_p.E407G|GATS_uc003uuc.1_3'UTR|GATS_uc003uud.1_Non-coding_Transcript|GATS_uc010lgu.1_Non-coding_Transcript	NM_012447	NP_036579	Q9UJ98	STAG3_HUMAN	stromal antigen 3	1182	Poly-Glu.				chromosome segregation|synaptonemal complex assembly	chromosome, centromeric region|meiotic cohesin complex|synaptonemal complex	binding			ovary(3)|skin(2)|lung(1)|kidney(1)	7	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)									331				0.183603	313.26517	394.631235	159	707	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	99647383	99647383	15762	7	A	G	G	9	9	STAG3	G	4	4
UNC5D	137970	broad.mit.edu	36	8	35661775	35661775	+	Silent	SNP	A	C	C			TCGA-12-0822-01	TCGA-12-0822-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr8:35661775A>C	uc003xjr.1	+	c.885A>C	c.(883-885)TCA>TCC	p.S295S	UNC5D_uc003xjs.1_Silent_p.S290S|UNC5D_uc003xjt.1_Silent_p.S64S	NM_080872	NP_543148	Q6UXZ4	UNC5D_HUMAN	unc-5 homolog D	295	TSP type-1 1.|Extracellular (Potential).				apoptosis|axon guidance	integral to membrane	receptor activity			ovary(2)|pancreas(1)	3				READ - Rectum adenocarcinoma(1;1.31e-05)|Colorectal(1;0.000723)										0.176471	13.338218	18.381189	9	42	AA		KEEP	---	---	---	---	capture			Silent	SNP	35661775	35661775	17553	8	A	C	C	7	7	UNC5D	C	4	4
TRAF1	7185	broad.mit.edu	36	9	122715755	122715755	+	Missense_Mutation	SNP	C	G	G			TCGA-12-0822-01	TCGA-12-0822-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr9:122715755C>G	uc004bku.1	-	c.377G>C	c.(376-378)TGG>TCG	p.W126S	TRAF1_uc010mvl.1_Missense_Mutation_p.W126S	NM_005658	NP_005649	Q13077	TRAF1_HUMAN	TNF receptor-associated factor 1	126					apoptosis|positive regulation of NF-kappaB transcription factor activity|protein complex assembly|regulation of apoptosis|signal transduction	cytoplasm	protein binding|zinc ion binding			skin(2)|ovary(1)	3														0.104839	6.901704	26.158515	13	111	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	122715755	122715755	16981	9	C	G	G	21	21	TRAF1	G	3	3
NTRK2	4915	broad.mit.edu	36	9	86515499	86515499	+	Silent	SNP	C	T	T			TCGA-12-0822-01	TCGA-12-0822-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr9:86515499C>T	uc004anz.1	+	c.556C>T	c.(556-558)CTG>TTG	p.L186L	NTRK2_uc004anv.1_Silent_p.L186L|NTRK2_uc004anw.1_Silent_p.L186L|NTRK2_uc004anx.1_Silent_p.L186L|NTRK2_uc004any.1_Silent_p.L186L|NTRK2_uc004aoa.1_Silent_p.L186L|NTRK2_uc004aob.1_Silent_p.L186L	NM_006180	NP_006171	Q16620	NTRK2_HUMAN	neurotrophic tyrosine kinase, receptor, type 2	186	Extracellular (Potential).|LRRCT.				activation of adenylate cyclase activity|cell differentiation|nerve growth factor receptor signaling pathway|nervous system development|protein phosphorylation	integral to plasma membrane	ATP binding|neurotrophin receptor activity|transmembrane receptor protein tyrosine kinase activity			lung(8)|ovary(1)|liver(1)|central_nervous_system(1)|skin(1)	12										348	TSP Lung(25;0.17)			0.214683	399.2676	466.882942	193	706	CC		KEEP	---	---	---	---	capture			Silent	SNP	86515499	86515499	11112	9	C	T	T	24	24	NTRK2	T	2	2
ZCCHC12	170261	broad.mit.edu	36	X	117843653	117843653	+	Missense_Mutation	SNP	G	A	A			TCGA-12-0822-01	TCGA-12-0822-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:117843653G>A	uc004equ.1	+	c.418G>A	c.(418-420)GCT>ACT	p.A140T	ZCCHC12_uc010nqj.1_Missense_Mutation_p.A140T	NM_173798	NP_776159	Q6PEW1	ZCH12_HUMAN	zinc finger, CCHC domain containing 12	140					regulation of transcription, DNA-dependent|transcription, DNA-dependent		nucleic acid binding|zinc ion binding			ovary(1)	1														0.445946	83.948358	84.138496	33	41	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	117843653	117843653	18169	23	G	A	A	34	34	ZCCHC12	A	2	2
ZCCHC12	170261	broad.mit.edu	36	X	117843955	117843955	+	Missense_Mutation	SNP	G	C	C			TCGA-12-0822-01	TCGA-12-0822-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:117843955G>C	uc004equ.1	+	c.720G>C	c.(718-720)GAG>GAC	p.E240D	ZCCHC12_uc010nqj.1_Missense_Mutation_p.E240D	NM_173798	NP_776159	Q6PEW1	ZCH12_HUMAN	zinc finger, CCHC domain containing 12	240					regulation of transcription, DNA-dependent|transcription, DNA-dependent		nucleic acid binding|zinc ion binding			ovary(1)	1														0.367089	87.258631	88.483729	29	50	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	117843955	117843955	18169	23	G	C	C	33	33	ZCCHC12	C	3	3
LDOC1	23641	broad.mit.edu	36	X	140098801	140098801	+	Missense_Mutation	SNP	G	C	C			TCGA-12-0822-01	TCGA-12-0822-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:140098801G>C	uc004fbj.1	-	c.72C>G	c.(70-72)AGC>AGG	p.S24R		NM_012317	NP_036449	O95751	LDOC1_HUMAN	leucine zipper, down-regulated in cancer 1	24					negative regulation of cell proliferation	nucleus	protein binding				0	Acute lymphoblastic leukemia(192;7.65e-05)													0.25	6.789791	7.701815	4	12	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	140098801	140098801	9033	23	G	C	C	42	42	LDOC1	C	3	3
MAGEB6	158809	broad.mit.edu	36	X	26121970	26121970	+	Missense_Mutation	SNP	A	G	G			TCGA-12-0822-01	TCGA-12-0822-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chrX:26121970A>G	uc004dbr.1	+	c.86A>G	c.(85-87)CAG>CGG	p.Q29R	MAGEB6_uc010ngc.1_5'UTR|MAGEB6_uc010ngd.1_Missense_Mutation_p.Q29R	NM_173523	NP_775794	Q8N7X4	MAGB6_HUMAN	melanoma antigen family B, 6	29										ovary(3)	3														0.555556	82.539375	82.683177	30	24	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	26121970	26121970	9560	23	A	G	G	7	7	MAGEB6	G	4	4
KDM5D	8284	broad.mit.edu	36	Y	20329281	20329281	+	Missense_Mutation	SNP	G	A	A			TCGA-12-0822-01	TCGA-12-0822-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrY:20329281G>A	uc004fug.1	-	c.3326C>T	c.(3325-3327)GCG>GTG	p.A1109V	KDM5D_uc004fuf.1_Missense_Mutation_p.A284V|KDM5D_uc010nwy.1_Missense_Mutation_p.A1052V	NM_004653	NP_004644	Q9BY66	KDM5D_HUMAN	jumonji, AT rich interactive domain 1D	1109					chromatin modification|oxidation-reduction process|spermatogenesis	nucleus	DNA binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|protein binding|zinc ion binding			skin(1)	1					Vitamin C(DB00126)									0.464789	90.758743	90.835612	33	38	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	20329281	20329281	8442	24	G	A	A	38	38	KDM5D	A	1	1
IL17C	27189	broad.mit.edu	36	16	87233022	87233023	+	Frame_Shift_Ins	INS	-	C	C			TCGA-12-0822-01	TCGA-12-0822-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:87233022_87233023insC	uc002fla.1	+	c.139_140insC	c.(139-141)GCCfs	p.A47fs		NM_013278	NP_037410	Q9P0M4	IL17C_HUMAN	interleukin 17C	47					cell surface receptor linked signaling pathway|cell-cell signaling|inflammatory response	extracellular space|soluble fraction	cytokine activity				0				BRCA - Breast invasive adenocarcinoma(80;0.0477)										0.33			2	4				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	87233022	87233023	7937	16	-	C	C	42	42	IL17C	C	5	5
SNX27	81609	broad.mit.edu	36	1	149851559	149851560	+	Frame_Shift_Ins	INS	-	G	G			TCGA-12-0822-01	TCGA-12-0822-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:149851559_149851560insG	uc001eyn.1	+	c.258_259insG	c.(256-261)CCCGGGfs	p.P86fs		NM_030918	NP_112180	Q96L92	SNX27_HUMAN	sorting nexin family member 27	86_87	PDZ.				cell communication|protein transport|signal transduction	cytosol|early endosome	phosphatidylinositol binding|protein binding			ovary(2)|central_nervous_system(1)	3	Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		LUSC - Lung squamous cell carcinoma(543;0.181)			Colon(46;291 966 40145 41237 41888)								0.33			2	4				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	149851559	149851560	15397	1	-	G	G	23	23	SNX27	G	5	5
LARP1	23367	broad.mit.edu	36	5	154153582	154153583	+	Frame_Shift_Ins	INS	-	C	C			TCGA-12-0822-01	TCGA-12-0822-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:154153582_154153583insC	uc003lvp.1	+	c.898_899insC	c.(898-900)GCCfs	p.A300fs	LARP1_uc003lvo.1_Frame_Shift_Ins_p.A223fs|LARP1_uc010jie.1_Frame_Shift_Ins_p.A95fs	NM_033551	NP_291029	Q6PKG0	LARP1_HUMAN	la related protein isoform 2	300							protein binding|RNA binding			ovary(2)|pancreas(1)	3	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)											0.33			2	4				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	154153582	154153583	8951	5	-	C	C	42	42	LARP1	C	5	5
