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
TIAL1	7073	broad.mit.edu	36	10	121325291	121325291	+	Missense_Mutation	SNP	T	G	G			TCGA-28-1750-01	TCGA-28-1750-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr10:121325291T>G	uc001lej.1	-	c.1055A>C	c.(1054-1056)CAA>CCA	p.Q352P	TIAL1_uc001leh.1_Missense_Mutation_p.Q313P|TIAL1_uc001lei.1_Missense_Mutation_p.Q335P|TIAL1_uc001lek.1_Missense_Mutation_p.Q212P|TIAL1_uc009xzi.1_Missense_Mutation_p.Q204P	NM_001033925	NP_001029097	Q01085	TIAR_HUMAN	TIA-1 related protein isoform 2	335					apoptosis|defense response|induction of apoptosis|regulation of transcription from RNA polymerase II promoter	lysosome|nucleus|stress granule	nucleotide binding|RNA binding|RNA polymerase II transcription factor activity			ovary(1)	1		Lung NSC(174;0.094)|all_lung(145;0.123)		all cancers(201;0.00239)|BRCA - Breast invasive adenocarcinoma(275;0.0932)										0.325	24.949919	26.043099	13	27	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	121325291	121325291	16417	10	T	G	G	63	63	TIAL1	G	4	4
ARHGAP22	58504	broad.mit.edu	36	10	49331456	49331456	+	Missense_Mutation	SNP	C	G	G			TCGA-28-1750-01	TCGA-28-1750-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr10:49331456C>G	uc001jgu.1	-	c.933G>C	c.(931-933)CAG>CAC	p.Q311H	ARHGAP22_uc001jgt.1_Missense_Mutation_p.Q295H|ARHGAP22_uc001jgv.1_5'UTR|ARHGAP22_uc001jgr.1_5'Flank|ARHGAP22_uc001jgs.1_Missense_Mutation_p.Q205H	NM_021226	NP_067049	Q7Z5H3	RHG22_HUMAN	Rho GTPase activating protein 2	295	Rho-GAP.				angiogenesis|cell differentiation|regulation of small GTPase mediated signal transduction|regulation of transcription, DNA-dependent|small GTPase mediated signal transduction|transcription, DNA-dependent	cytosol|nucleus	GTPase activator activity			ovary(1)	1														0.263158	8.559978	9.529734	5	14	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	49331456	49331456	883	10	C	G	G	24	24	ARHGAP22	G	3	3
PTEN	5728	broad.mit.edu	36	10	89682885	89682885	+	Missense_Mutation	SNP	G	A	A			TCGA-28-1750-01	TCGA-28-1750-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr10:89682885G>A	uc001kfb.1	+	c.389G>A	c.(388-390)CGA>CAA	p.R130Q		NM_000314	NP_000305	P60484	PTEN_HUMAN	phosphatase and tensin homolog	130	Phosphatase tensin-type.		R -> L (in CD and endometrial hyperplasia; loss of phosphatase activity towards Ins(1,3,4,5)P4; retains ability to bind phospholipid membranes).|R -> Q (in CD; loss of phosphatase activity towards Ins(1,3,4,5)P4; retains ability to bind phospholipid membranes).|R -> G (loss of phosphatase activity towards Ins(1,3,4,5)P4 and PtdIns(3,4,5)P3).	R->M: Does not affect the ability to inhibit AKT/PKB activation.	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.R130Q(43)|p.R130fs*4(12)|p.R130L(7)|p.R130*(7)|p.R130P(4)|p.R130G(3)|p.K128_R130del(3)|p.Y27_N212>Y(2)|p.K128fs*47(1)|p.R130fs*2(1)|p.T131fs*50(1)|p.A121_F145del(1)|p.F56fs*2(1)		endometrium(831)|central_nervous_system(654)|skin(119)|haematopoietic_and_lymphoid_tissue(101)|prostate(97)|large_intestine(90)|breast(67)|lung(63)|ovary(58)|thyroid(29)|stomach(29)|upper_aerodigestive_tract(25)|cervix(21)|liver(20)|vulva(17)|kidney(15)|NS(14)|soft_tissue(12)|urinary_tract(12)|eye(8)|pancreas(6)|salivary_gland(5)|bone(5)|biliary_tract(4)|autonomic_ganglia(2)|meninges(2)|testis(1)|oesophagus(1)	2308		all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132)	KIRC - Kidney renal clear cell carcinoma(1;0.214)	UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218)			R130Q(MDAPCA2B_PROSTATE)|R130Q(MFE296_ENDOMETRIUM)|R130fs*4(AN3CA_ENDOMETRIUM)|R130Q(JHUEM1_ENDOMETRIUM)	31	p.R130Q(MFE296-Tumor)|p.R130Q(JHUEM1-Tumor)|p.R130Q(SNU81-Tumor)|p.R130Q(639V-Tumor)|p.R130fs(AN3CA-Tumor)	264	TCGA GBM(2;<1E-8)|TSP Lung(26;0.18)			0.606838	240.191276	241.383697	71	46	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	89682885	89682885	13192	10	G	A	A	37	37	PTEN	A	1	1
OR4C15	81309	broad.mit.edu	36	11	55079170	55079170	+	Missense_Mutation	SNP	A	G	G			TCGA-28-1750-01	TCGA-28-1750-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr11:55079170A>G	uc001nho.1	+	c.812A>G	c.(811-813)TAT>TGT	p.Y271C		NM_001001920	NP_001001920	Q8NGM1	OR4CF_HUMAN	olfactory receptor, family 4, subfamily C,	217	Helical; Name=5; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1														0.191111	97.051081	117.07724	43	182	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	55079170	55079170	11454	11	A	G	G	16	16	OR4C15	G	4	4
SLC15A3	51296	broad.mit.edu	36	11	60470730	60470730	+	Missense_Mutation	SNP	G	A	A			TCGA-28-1750-01	TCGA-28-1750-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:60470730G>A	uc001nqn.1	-	c.698C>T	c.(697-699)CCT>CTT	p.P233L	SLC15A3_uc001nqo.1_Missense_Mutation_p.P233L	NM_016582	NP_057666	Q8IY34	S15A3_HUMAN	solute carrier family 15, member 3	233	Helical; (Potential).				oligopeptide transport|protein transport	integral to membrane|lysosomal membrane	peptide:hydrogen symporter activity				0														0.157895	6.313106	8.432979	3	16	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	60470730	60470730	14895	11	G	A	A	35	35	SLC15A3	A	2	2
LTBR	4055	broad.mit.edu	36	12	6364667	6364667	+	Missense_Mutation	SNP	G	C	C			TCGA-28-1750-01	TCGA-28-1750-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:6364667G>C	uc001qny.1	+	c.333G>C	c.(331-333)GAG>GAC	p.E111D	LTBR_uc001qnz.1_Missense_Mutation_p.E106D	NM_002342	NP_002333	P36941	TNR3_HUMAN	lymphotoxin beta receptor	111	Extracellular (Potential).|TNFR-Cys 2.				apoptosis|cellular response to mechanical stimulus|interspecies interaction between organisms|positive regulation of I-kappaB kinase/NF-kappaB cascade	integral to membrane	protein binding|receptor activity				0										109				0.183333	12.981522	18.647895	11	49	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	6364667	6364667	9453	12	G	C	C	35	35	LTBR	C	3	3
MGAT4C	25834	broad.mit.edu	36	12	84897860	84897860	+	Missense_Mutation	SNP	A	G	G			TCGA-28-1750-01	TCGA-28-1750-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr12:84897860A>G	uc001tai.2	-	c.775T>C	c.(775-777)TAC>CAC	p.Y259H	MGAT4C_uc001tah.2_Missense_Mutation_p.Y259H|MGAT4C_uc001tal.2_Missense_Mutation_p.Y259H|MGAT4C_uc001taj.2_Missense_Mutation_p.Y259H|MGAT4C_uc001tak.2_Missense_Mutation_p.Y259H	NM_013244	NP_037376	Q9UBM8	MGT4C_HUMAN	UDP-N-acetylglucosamine: alpha-1,3-D-mannoside	259	Lumenal (Potential).				post-translational protein modification|protein N-linked glycosylation via asparagine	Golgi membrane|integral to membrane	alpha-1,3-mannosylglycoprotein 4-beta-N-acetylglucosaminyltransferase activity|metal ion binding			ovary(3)	3														0.220339	29.937279	34.194248	13	46	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	84897860	84897860	9937	12	A	G	G	15	15	MGAT4C	G	4	4
FAM179B	23116	broad.mit.edu	36	14	44501760	44501760	+	Missense_Mutation	SNP	T	G	G			TCGA-28-1750-01	TCGA-28-1750-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr14:44501760T>G	uc001wvw.1	+	c.386T>G	c.(385-387)TTC>TGC	p.F129C	FAM179B_uc001wvv.1_Missense_Mutation_p.F129C|FAM179B_uc010anc.1_Non-coding_Transcript|KLHL28_uc001wvq.1_5'Flank|KLHL28_uc001wvr.1_5'Flank|FAM179B_uc010anb.1_Missense_Mutation_p.F129C|FAM179B_uc001wvu.2_Missense_Mutation_p.F129C	NM_015091	NP_055906	Q9Y4F4	F179B_HUMAN	hypothetical protein LOC23116	129							binding				0														0.444444	8.895281	8.919874	4	5	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	44501760	44501760	5712	14	T	G	G	62	62	FAM179B	G	4	4
ESRRB	2103	broad.mit.edu	36	14	75998744	75998744	+	Silent	SNP	G	A	A			TCGA-28-1750-01	TCGA-28-1750-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr14:75998744G>A	uc001xso.1	+	c.501G>A	c.(499-501)GGG>GGA	p.G167G	ESRRB_uc001xsp.1_Silent_p.G167G|ESRRB_uc001xsq.1_Silent_p.G167G|ESRRB_uc001xsr.1_Silent_p.G167G	NM_004452	NP_004443	A2VDJ2	A2VDJ2_HUMAN	estrogen-related receptor beta	167					regulation of transcription, DNA-dependent	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(234;0.0213)										0.204918	156.465872	186.019741	75	291	GG		KEEP	---	---	---	---	capture			Silent	SNP	75998744	75998744	5454	14	G	A	A	41	41	ESRRB	A	2	2
EPB42	2038	broad.mit.edu	36	15	41286044	41286044	+	Missense_Mutation	SNP	C	T	T			TCGA-28-1750-01	TCGA-28-1750-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr15:41286044C>T	uc001zrb.2	-	c.1484G>A	c.(1483-1485)CGT>CAT	p.R495H	EPB42_uc001zqz.2_Missense_Mutation_p.R132H|EPB42_uc010bde.1_Missense_Mutation_p.R310H|EPB42_uc001zra.2_Missense_Mutation_p.R465H	NM_000119	NP_000110	P16452	EPB42_HUMAN	erythrocyte membrane protein band 4.2 isoform 1	465					erythrocyte maturation|peptide cross-linking|regulation of cell shape	cytoplasm|cytoskeleton|plasma membrane	ATP binding|protein binding|protein-glutamine gamma-glutamyltransferase activity|structural constituent of cytoskeleton			ovary(2)	2		all_cancers(109;1.37e-14)|all_epithelial(112;1.26e-12)|Lung NSC(122;2.46e-08)|all_lung(180;2.75e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;8.7e-07)										0.375	45.490812	46.164735	18	30	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	41286044	41286044	5351	15	C	T	T	19	19	EPB42	T	1	1
ZNF263	10127	broad.mit.edu	36	16	3275075	3275075	+	Missense_Mutation	SNP	C	T	T			TCGA-28-1750-01	TCGA-28-1750-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:3275075C>T	uc002cuq.1	+	c.403C>T	c.(403-405)CGG>TGG	p.R135W	ZNF263_uc002cup.1_Intron	NM_005741	NP_005732	O14978	ZN263_HUMAN	zinc finger protein 263	135					regulation of transcription, DNA-dependent|viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1														0.196078	17.514394	21.920129	10	41	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	3275075	3275075	18395	16	C	T	T	27	27	ZNF263	T	1	1
KIF2B	84643	broad.mit.edu	36	17	49257281	49257281	+	Missense_Mutation	SNP	G	A	A			TCGA-28-1750-01	TCGA-28-1750-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:49257281G>A	uc002iua.2	+	c.1888G>A	c.(1888-1890)GTA>ATA	p.V630I		NM_032559	NP_115948	Q8N4N8	KIF2B_HUMAN	kinesin family member 2B	630					blood coagulation|cell division|microtubule depolymerization|microtubule-based movement|mitotic prometaphase|regulation of chromosome segregation	condensed chromosome kinetochore|cytosol|microtubule|microtubule organizing center|nucleolus|spindle	ATP binding|microtubule motor activity			ovary(5)	5														0.307692	9.486254	9.920414	4	9	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	49257281	49257281	8609	17	G	A	A	36	36	KIF2B	A	2	2
CABYR	26256	broad.mit.edu	36	18	19989666	19989666	+	Missense_Mutation	SNP	A	T	T			TCGA-28-1750-01	TCGA-28-1750-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr18:19989666A>T	uc002kux.1	+	c.203A>T	c.(202-204)GAG>GTG	p.E68V	CABYR_uc002kuy.1_Missense_Mutation_p.E68V|CABYR_uc002kuz.1_Missense_Mutation_p.E68V|CABYR_uc002kva.1_Missense_Mutation_p.E50V|CABYR_uc002kvb.1_5'UTR|CABYR_uc002kvc.1_Missense_Mutation_p.E68V|CABYR_uc010dlw.1_Non-coding_Transcript	NM_012189	NP_036321	O75952	CABYR_HUMAN	calcium-binding tyrosine	68					ciliary or flagellar motility|signal transduction|sperm capacitation	cytoplasm|cytoskeleton|flagellum|motile cilium|nucleus	calcium ion binding|cAMP-dependent protein kinase regulator activity|enzyme binding|protein heterodimerization activity|SH3 domain binding				0	all_cancers(21;9.13e-05)|all_epithelial(16;5.49e-07)|Lung NSC(20;0.00171)|all_lung(20;0.0055)|Colorectal(14;0.0305)|Ovarian(20;0.17)													0.189189	8.601021	11.95371	7	30	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	19989666	19989666	2652	18	A	T	T	11	11	CABYR	T	4	4
CCDC105	126402	broad.mit.edu	36	19	14982853	14982853	+	Silent	SNP	C	A	A			TCGA-28-1750-01	TCGA-28-1750-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:14982853C>A	uc002nae.1	+	c.216C>A	c.(214-216)CGC>CGA	p.R72R		NM_173482	NP_775753	Q8IYK2	CC105_HUMAN	coiled-coil domain containing 105	72					microtubule cytoskeleton organization	microtubule				ovary(1)	1														0.4	10.196182	10.284057	4	6	CC		KEEP	---	---	---	---	capture			Silent	SNP	14982853	14982853	2860	19	C	A	A	28	28	CCDC105	A	3	3
GDF15	9518	broad.mit.edu	36	19	18360629	18360630	+	Missense_Mutation	DNP	GC	AG	AG			TCGA-28-1750-01	TCGA-28-1750-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:18360629_18360630GC>AG	uc002niv.2	+	c.811_812GC>AG	c.(811-813)GCG>AGG	p.A271R		NM_004864	NP_004855	Q99988	GDF15_HUMAN	growth differentiation factor 15	271					cell-cell signaling|transforming growth factor beta receptor signaling pathway	extracellular space	cytokine activity|growth factor activity			central_nervous_system(1)	1												OREG0025363	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.241379	9.998651	11.780909	7	22	GG		KEEP	---	---	---	---	capture			Missense_Mutation	DNP	18360629	18360630	6581	19	GC	AG	AG	34	34	GDF15	AG	2	2
TMPRSS9	360200	broad.mit.edu	36	19	2361371	2361371	+	Silent	SNP	C	T	T			TCGA-28-1750-01	TCGA-28-1750-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:2361371C>T	uc002lvw.1	+	c.1131C>T	c.(1129-1131)GAC>GAT	p.D377D	TMPRSS9_uc002lvv.1_Silent_p.D411D	NM_182973	NP_892018	Q7Z410	TMPS9_HUMAN	transmembrane protease, serine 9	377	Extracellular (Potential).|Peptidase S1 1.				proteolysis	integral to plasma membrane	serine-type endopeptidase activity			ovary(1)	1				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)										0.3125	11.690131	12.179736	5	11	CC		KEEP	---	---	---	---	capture			Silent	SNP	2361371	2361371	16794	19	C	T	T	19	19	TMPRSS9	T	1	1
NLRP8	126205	broad.mit.edu	36	19	61151449	61151449	+	Splice_Site_SNP	SNP	T	C	C			TCGA-28-1750-01	TCGA-28-1750-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr19:61151449T>C	uc002qmh.1	+	c.e1_splice_site			NLRP8_uc010etg.1_Splice_Site_SNP	NM_176811	NP_789781			NLR family, pyrin domain containing 8							cytoplasm	ATP binding			ovary(4)|breast(3)|large_intestine(1)|kidney(1)|skin(1)	10		Colorectal(82;0.000147)|Ovarian(87;0.17)		GBM - Glioblastoma multiforme(193;0.0695)										0.348101	153.505059	156.709438	55	103	TT		KEEP	---	---	---	---	capture			Splice_Site_SNP	SNP	61151449	61151449	10886	19	T	C	C	59	59	NLRP8	C	5	4
C4BPA	722	broad.mit.edu	36	1	205384652	205384652	+	Silent	SNP	C	T	T			TCGA-28-1750-01	TCGA-28-1750-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:205384652C>T	uc001hfo.1	+	c.1761C>T	c.(1759-1761)AGC>AGT	p.S587S		NM_000715	NP_000706	P04003	C4BPA_HUMAN	complement component 4 binding protein, alpha	587					complement activation, classical pathway|innate immune response	extracellular region	protein binding			large_intestine(1)|ovary(1)	2														0.323077	56.564448	58.364634	21	44	CC		KEEP	---	---	---	---	capture			Silent	SNP	205384652	205384652	2344	1	C	T	T	27	27	C4BPA	T	1	1
OR13G1	441933	broad.mit.edu	36	1	245902739	245902739	+	Silent	SNP	C	T	T			TCGA-28-1750-01	TCGA-28-1750-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:245902739C>T	uc001idi.1	-	c.228G>A	c.(226-228)CCG>CCA	p.P76P		NM_001005487	NP_001005487	Q8NGZ3	O13G1_HUMAN	olfactory receptor, family 13, subfamily G,	76	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0	all_cancers(71;3.24e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)		OV - Ovarian serous cystadenocarcinoma(106;0.017)											0.270833	33.263768	35.531726	13	35	CC		KEEP	---	---	---	---	capture			Silent	SNP	245902739	245902739	11348	1	C	T	T	31	31	OR13G1	T	1	1
OR2T27	403239	broad.mit.edu	36	1	246879973	246879973	+	Missense_Mutation	SNP	G	A	A			TCGA-28-1750-01	TCGA-28-1750-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:246879973G>A	uc001iet.1	-	c.836C>T	c.(835-837)ACC>ATC	p.T279I		NM_001001824	NP_001001824	Q8NH04	O2T27_HUMAN	olfactory receptor, family 2, subfamily T,	279	Helical; Name=7; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0	all_cancers(71;1.15e-05)|all_epithelial(71;5.29e-06)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.089)|Lung NSC(105;0.0969)|Melanoma(84;0.199)	all_cancers(173;0.237)	OV - Ovarian serous cystadenocarcinoma(106;0.0265)											0.39726	85.464796	86.137101	29	44	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	246879973	246879973	11427	1	G	A	A	44	44	OR2T27	A	2	2
TACSTD2	4070	broad.mit.edu	36	1	58814754	58814754	+	Silent	SNP	A	G	G			TCGA-28-1750-01	TCGA-28-1750-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr1:58814754A>G	uc001cyz.2	-	c.663T>C	c.(661-663)GAT>GAC	p.D221D		NM_002353	NP_002344	P09758	TACD2_HUMAN	tumor-associated calcium signal transducer 2	221	Extracellular (Potential).				cell proliferation|cell surface receptor linked signaling pathway|visual perception	cytosol|integral to plasma membrane	receptor activity				0	all_cancers(7;6.54e-05)													0.193548	6.525659	9.257267	6	25	AA		KEEP	---	---	---	---	capture			Silent	SNP	58814754	58814754	16029	1	A	G	G	8	8	TACSTD2	G	4	4
TCP10L	140290	broad.mit.edu	36	21	32872923	32872923	+	Silent	SNP	G	A	A			TCGA-28-1750-01	TCGA-28-1750-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr21:32872923G>A	uc002ypw.2	-	c.450C>T	c.(448-450)GCC>GCT	p.A150A		NM_144659	NP_653260	Q9NV44	CU077_HUMAN	T-complex 10A-2	Error:Variant_position_missing_in_Q9NV44_after_alignment											0														0.22467	125.150132	140.934156	51	176	GG		KEEP	---	---	---	---	capture			Silent	SNP	32872923	32872923	16237	21	G	A	A	47	47	TCP10L	A	2	2
ZNF295	49854	broad.mit.edu	36	21	42285335	42285335	+	Missense_Mutation	SNP	G	C	C			TCGA-28-1750-01	TCGA-28-1750-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr21:42285335G>C	uc002zab.2	-	c.1939C>G	c.(1939-1941)CAG>GAG	p.Q647E	ZNF295_uc002yzz.2_Intron|ZNF295_uc002yzy.2_Missense_Mutation_p.Q647E|ZNF295_uc002zaa.2_Missense_Mutation_p.Q647E|ZNF295_uc010gou.1_Missense_Mutation_p.Q647E	NM_001098402	NP_065778	Q9ULJ3	ZN295_HUMAN	zinc finger protein 295 isoform L	647					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	methyl-CpG binding|zinc ion binding			ovary(1)|central_nervous_system(1)	2														0.214286	8.82731	10.947516	6	22	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	42285335	42285335	18419	21	G	C	C	45	45	ZNF295	C	3	3
UFD1L	7353	broad.mit.edu	36	22	17835427	17835428	+	Missense_Mutation	DNP	CA	AT	AT			TCGA-28-1750-01	TCGA-28-1750-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:17835427_17835428CA>AT	uc002zpm.1	-	c.390_391TG>AT	c.(388-393)CCTGAC>CCATAC	p.D131Y	UFD1L_uc002zpn.1_Missense_Mutation_p.D120Y|UFD1L_uc002zpo.1_Missense_Mutation_p.D131Y|UFD1L_uc002zpp.1_Missense_Mutation_p.D84Y|UFD1L_uc010grq.1_Missense_Mutation_p.D84Y	NM_005659	NP_005650	Q92890	UFD1_HUMAN	ubiquitin fusion degradation 1-like isoform A	131					skeletal system development|ubiquitin-dependent protein catabolic process	cytosol|nucleus	protein binding|ubiquitin-specific protease activity				0	Colorectal(54;0.0993)													0.140845	7.894373	16.755684	10	61	CC		KEEP	---	---	---	---	capture			Missense_Mutation	DNP	17835427	17835428	17493	22	CA	AT	AT	29	29	UFD1L	AT	3	3
PLXNB2	23654	broad.mit.edu	36	22	49070538	49070538	+	Silent	SNP	C	T	T			TCGA-28-1750-01	TCGA-28-1750-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr22:49070538C>T	uc003bkv.2	-	c.603G>A	c.(601-603)ACG>ACA	p.T201T		NM_012401	NP_036533	O15031	PLXB2_HUMAN	plexin B2	201	Extracellular (Potential).|Sema.				regulation of small GTPase mediated signal transduction	integral to membrane|intracellular	GTPase activator activity|protein binding|receptor activity			ovary(4)|central_nervous_system(1)	5		all_cancers(38;5.78e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)										0.625	31.053448	31.274918	10	6	CC		KEEP	---	---	---	---	capture			Silent	SNP	49070538	49070538	12550	22	C	T	T	23	23	PLXNB2	T	1	1
CNTN4	152330	broad.mit.edu	36	3	2883578	2883578	+	Silent	SNP	C	T	T			TCGA-28-1750-01	TCGA-28-1750-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr3:2883578C>T	uc003bpc.1	+	c.597C>T	c.(595-597)ACC>ACT	p.T199T	CNTN4_uc003bpb.1_5'UTR|CNTN4_uc003bpd.1_Silent_p.T199T	NM_175607	NP_783302	Q8IWV2	CNTN4_HUMAN	contactin 4 isoform a precursor	199	Ig-like C2-type 2.				axon guidance|axonal fasciculation|brain development|negative regulation of neuron differentiation|neuron cell-cell adhesion|regulation of synaptic plasticity	anchored to membrane|axon|extracellular region|plasma membrane	protein binding			large_intestine(2)|ovary(2)|lung(1)|central_nervous_system(1)|pancreas(1)	7		Ovarian(110;0.156)		Epithelial(13;0.000695)|all cancers(10;0.0047)|OV - Ovarian serous cystadenocarcinoma(96;0.01)										0.643275	364.628886	367.758556	110	61	CC		KEEP	---	---	---	---	capture			Silent	SNP	2883578	2883578	3781	3	C	T	T	23	23	CNTN4	T	1	1
SLC6A19	340024	broad.mit.edu	36	5	1272631	1272632	+	Missense_Mutation	DNP	CT	AG	AG			TCGA-28-1750-01	TCGA-28-1750-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:1272631_1272632CT>AG	uc003jbw.2	+	c.1390_1391CT>AG	c.(1390-1392)CTG>AGG	p.L464R		NM_001003841	NP_001003841	Q695T7	S6A19_HUMAN	solute carrier family 6, member 19	464	Helical; Name=9; (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)		Epithelial(17;0.000356)|all cancers(22;0.00137)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|Lung(60;0.185)											0.307692	7.236021	7.642892	4	9	CC		KEEP	---	---	---	---	capture			Missense_Mutation	DNP	1272631	1272632	15179	5	CT	AG	AG	24	24	SLC6A19	AG	3	3
FBN2	2201	broad.mit.edu	36	5	127652116	127652116	+	Missense_Mutation	SNP	C	T	T			TCGA-28-1750-01	TCGA-28-1750-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:127652116C>T	uc003kuu.1	-	c.6670G>A	c.(6670-6672)GGA>AGA	p.G2224R		NM_001999	NP_001990	P35556	FBN2_HUMAN	fibrillin 2 precursor	2224	EGF-like 37; calcium-binding.				bone trabecula formation|negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta|positive regulation of bone mineralization|positive regulation of osteoblast differentiation	microfibril	calcium ion binding|extracellular matrix structural constituent			ovary(8)|large_intestine(4)|kidney(1)|pancreas(1)	14		all_cancers(142;0.0216)|Prostate(80;0.0551)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0821)|Epithelial(69;0.146)						1552				0.108434	17.577692	42.774078	18	148	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	127652116	127652116	5939	5	C	T	T	21	21	FBN2	T	2	2
FAT2	2196	broad.mit.edu	36	5	150903797	150903797	+	Missense_Mutation	SNP	C	T	T			TCGA-28-1750-01	TCGA-28-1750-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:150903797C>T	uc003lue.2	-	c.7084G>A	c.(7084-7086)GAA>AAA	p.E2362K		NM_001447	NP_001438	Q9NYQ8	FAT2_HUMAN	FAT tumor suppressor 2 precursor	2362	Extracellular (Potential).|Cadherin 20.				epithelial cell migration|homophilic cell adhesion	cell-cell adherens junction|integral to membrane|nucleus	calcium ion binding			ovary(4)	4		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)											0.169014	87.796041	117.316215	48	236	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	150903797	150903797	5926	5	C	T	T	29	29	FAT2	T	2	2
AHRR	57491	broad.mit.edu	36	5	486034	486034	+	Missense_Mutation	SNP	C	A	A			TCGA-28-1750-01	TCGA-28-1750-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:486034C>A	uc003jav.1	+	c.1150C>A	c.(1150-1152)CTT>ATT	p.L384I	AHRR_uc003jaw.1_Missense_Mutation_p.L362I|AHRR_uc010isy.1_Missense_Mutation_p.L212I|AHRR_uc010isz.1_Missense_Mutation_p.L362I|AHRR_uc003jax.1_Missense_Mutation_p.L125I|AHRR_uc003jay.1_Missense_Mutation_p.L222I|AHRR_uc003jaz.1_5'UTR	NM_020731	NP_065782	A9YTQ3	AHRR_HUMAN	arylhydrocarbon receptor repressor	366					regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|signal transducer activity|transcription regulator activity			breast(2)	2			Epithelial(17;0.0011)|OV - Ovarian serous cystadenocarcinoma(19;0.00353)|all cancers(22;0.00354)|Lung(60;0.0863)											0.444444	8.493712	8.518529	4	5	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	486034	486034	420	5	C	A	A	24	24	AHRR	A	3	3
KIAA1919	91749	broad.mit.edu	36	6	111694142	111694142	+	Silent	SNP	C	T	T			TCGA-28-1750-01	TCGA-28-1750-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:111694142C>T	uc003puv.2	+	c.684C>T	c.(682-684)AAC>AAT	p.N228N		NM_153369	NP_699200	Q5TF39	NAGT1_HUMAN	sodium-dependent glucose transporter 1	228	Cytoplasmic (Potential).				carbohydrate transport|sodium ion transport	apical plasma membrane|integral to membrane	symporter activity	p.N228N(1)		ovary(3)	3		all_cancers(87;2.35e-05)|Acute lymphoblastic leukemia(125;2.13e-07)|all_hematologic(75;5.28e-06)|all_epithelial(87;0.00138)|Colorectal(196;0.0209)		OV - Ovarian serous cystadenocarcinoma(136;0.055)|all cancers(137;0.0871)|Epithelial(106;0.0884)										0.16	8.085466	10.836117	4	21	CC		KEEP	---	---	---	---	capture			Silent	SNP	111694142	111694142	8573	6	C	T	T	19	19	KIAA1919	T	1	1
C4B	721	broad.mit.edu	36	6	32072296	32072296	+	Missense_Mutation	SNP	C	T	T			TCGA-28-1750-01	TCGA-28-1750-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:32072296C>T	uc003nyy.2	+	c.3616C>T	c.(3616-3618)CCT>TCT	p.P1206S	C4B_uc010jto.1_Missense_Mutation_p.P1206S	NM_001002029	NP_001002029	P0C0L5	CO4B_HUMAN	complement component 4B preproprotein	1206					complement activation, classical pathway|inflammatory response|innate immune response	extracellular space	endopeptidase inhibitor activity				0										129				0.238095	9.664189	10.981196	5	16	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	32072296	32072296	2343	6	C	T	T	22	22	C4B	T	2	2
GNB2	2783	broad.mit.edu	36	7	100112939	100112939	+	Nonsense_Mutation	SNP	A	T	T			TCGA-28-1750-01	TCGA-28-1750-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr7:100112939A>T	uc003uwb.1	+	c.232A>T	c.(232-234)AAG>TAG	p.K78*	GNB2_uc003uwc.1_Nonsense_Mutation_p.K34*|GNB2_uc010lhd.1_Nonsense_Mutation_p.K34*|GNB2_uc010lhe.1_Nonsense_Mutation_p.K34*|GNB2_uc003uwd.1_5'UTR|GNB2_uc010lhf.1_Intron|GNB2_uc003uwe.1_Nonsense_Mutation_p.K78*|GNB2_uc003uwf.1_5'UTR	NM_005273	NP_005264	P62879	GBB2_HUMAN	guanine nucleotide-binding protein, beta-2	78	WD 1.				cellular response to glucagon stimulus|energy reserve metabolic process|G-protein coupled receptor protein signaling pathway|synaptic transmission	perinuclear region of cytoplasm|plasma membrane	GTPase activity|protein binding|signal transducer activity			ovary(2)	2	Lung NSC(181;0.035)|all_lung(186;0.0509)|Esophageal squamous(72;0.0817)	Ovarian(593;0.238)												0.277778	7.044959	7.863158	5	13	AA		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	100112939	100112939	6786	7	A	T	T	9	9	GNB2	T	5	4
PPP1R9A	55607	broad.mit.edu	36	7	94578600	94578600	+	Missense_Mutation	SNP	G	A	A			TCGA-28-1750-01	TCGA-28-1750-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:94578600G>A	uc010lfj.1	+	c.1489G>A	c.(1489-1491)GTA>ATA	p.V497I	PPP1R9A_uc003unp.1_Missense_Mutation_p.V497I|PPP1R9A_uc003unq.1_Missense_Mutation_p.V497I	NM_017650	NP_060120	Q9ULJ8	NEB1_HUMAN	protein phosphatase 1, regulatory (inhibitor)	497	Interacts with protein phosphatase 1 (By similarity).					cell junction|synapse|synaptosome	actin binding			ovary(2)|skin(1)	3	all_cancers(62;9.12e-11)|all_epithelial(64;4.34e-09)		STAD - Stomach adenocarcinoma(171;0.0031)											0.147368	20.84108	32.151047	14	81	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	94578600	94578600	12814	7	G	A	A	48	48	PPP1R9A	A	2	2
POLE3	54107	broad.mit.edu	36	9	115211050	115211050	+	Silent	SNP	G	A	A			TCGA-28-1750-01	TCGA-28-1750-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr9:115211050G>A	uc004bhn.1	-	c.306C>T	c.(304-306)GCC>GCT	p.A102A		NM_017443	NP_059139	Q9NRF9	DPOE3_HUMAN	DNA polymerase epsilon subunit 3	102	Potential.				DNA replication|histone H3 acetylation	Ada2/Gcn5/Ada3 transcription activator complex	DNA-directed DNA polymerase activity|protein binding|sequence-specific DNA binding				0														0.644068	343.854263	347.105464	114	63	GG		KEEP	---	---	---	---	capture			Silent	SNP	115211050	115211050	12626	9	G	A	A	35	35	POLE3	A	2	2
PTCH1	5727	broad.mit.edu	36	9	97251983	97251983	+	Silent	SNP	C	T	T			TCGA-28-1750-01	TCGA-28-1750-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr9:97251983C>T	uc004avk.2	-	c.3510G>A	c.(3508-3510)TTG>TTA	p.L1170L	PTCH1_uc010mro.1_Silent_p.L1019L|PTCH1_uc010mrp.1_Silent_p.L1019L|PTCH1_uc010mrq.1_Silent_p.L1019L|PTCH1_uc004avl.2_Silent_p.L1019L|PTCH1_uc010mrr.1_Silent_p.L1104L|PTCH1_uc004avm.2_Silent_p.L1169L|PTCH1_uc010mrn.1_5'UTR	NM_000264	NP_001077076	Q13635	PTC1_HUMAN	patched isoform L	1170	Helical; (Potential).				embryonic limb morphogenesis|negative regulation of multicellular organism growth|protein processing|regulation of smoothened signaling pathway|smoothened signaling pathway	integral to plasma membrane	hedgehog receptor activity	p.L1170_P1180>WT(1)		skin(229)|central_nervous_system(43)|bone(33)|upper_aerodigestive_tract(10)|lung(5)|large_intestine(4)|oesophagus(3)|ovary(3)|breast(2)|vulva(1)	333		Medulloblastoma(1;7.87e-06)|all_neural(1;0.000555)|Acute lymphoblastic leukemia(62;0.136)								509				0.159341	44.174063	64.305643	29	153	CC		KEEP	---	---	---	---	capture			Silent	SNP	97251983	97251983	13184	9	C	T	T	25	25	PTCH1	T	2	2
MAP7D2	256714	broad.mit.edu	36	X	19940471	19940471	+	Silent	SNP	C	A	A			TCGA-28-1750-01	TCGA-28-1750-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:19940471C>A	uc010nfo.1	-	c.1989G>T	c.(1987-1989)GGG>GGT	p.G663G	MAP7D2_uc004czq.1_Silent_p.G507G|MAP7D2_uc004czr.1_Silent_p.G622G	NM_152780	NP_689993	Q96T17	MA7D2_HUMAN	MAP7 domain containing 2	622										ovary(2)|breast(1)	3														0.124183	56.762294	120.555885	57	402	CC		KEEP	---	---	---	---	capture			Silent	SNP	19940471	19940471	9651	23	C	A	A	22	22	MAP7D2	A	3	3
MAGEB10	139422	broad.mit.edu	36	X	27749814	27749814	+	Missense_Mutation	SNP	C	T	T			TCGA-28-1750-01	TCGA-28-1750-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:27749814C>T	uc004dbw.1	+	c.470C>T	c.(469-471)TCT>TTT	p.S157F	MAGEB10_uc010nge.1_Missense_Mutation_p.S157F	NM_182506	NP_872312	Q96LZ2	MAGBA_HUMAN	melanoma antigen family B, 10	157	MAGE.									lung(1)|breast(1)|central_nervous_system(1)	3														0.247423	60.259165	65.887059	24	73	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	27749814	27749814	9554	23	C	T	T	32	32	MAGEB10	T	2	2
MXRA5	25878	broad.mit.edu	36	X	3271801	3271801	+	Missense_Mutation	SNP	A	G	G			TCGA-28-1750-01	TCGA-28-1750-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chrX:3271801A>G	uc004crg.2	-	c.74T>C	c.(73-75)CTG>CCG	p.L25P		NM_015419	NP_056234	Q9NR99	MXRA5_HUMAN	adlican	25						extracellular region				ovary(5)|lung(1)|central_nervous_system(1)	7		all_lung(23;0.00031)|Lung NSC(23;0.000946)												0.807692	65.980322	68.275107	21	5	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	3271801	3271801	10397	23	A	G	G	7	7	MXRA5	G	4	4
FOXP3	50943	broad.mit.edu	36	X	48997349	48997349	+	Missense_Mutation	SNP	C	A	A			TCGA-28-1750-01	TCGA-28-1750-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:48997349C>A	uc010niq.1	-	c.835G>T	c.(835-837)GGT>TGT	p.G279C	FOXP3_uc004dnf.2_Missense_Mutation_p.G314C|FOXP3_uc004dne.2_Missense_Mutation_p.G279C	NM_001114377	NP_001107849	Q9BZS1	FOXP3_HUMAN	forkhead box P3 isoform b	314					B cell homeostasis|cerebellum development|chromatin remodeling|embryo development|myeloid cell homeostasis|negative regulation of activated T cell proliferation|negative regulation of chronic inflammatory response|negative regulation of CREB transcription factor activity|negative regulation of cytokine secretion|negative regulation of gene-specific transcription from RNA polymerase II promoter|negative regulation of histone acetylation|negative regulation of histone deacetylation|negative regulation of interferon-gamma biosynthetic process|negative regulation of interferon-gamma production|negative regulation of interleukin-10 production|negative regulation of interleukin-2 biosynthetic process|negative regulation of interleukin-2 production|negative regulation of interleukin-4 production|negative regulation of interleukin-5 production|negative regulation of interleukin-6 production|negative regulation of isotype switching to IgE isotypes|negative regulation of NF-kappaB transcription factor activity|negative regulation of T cell cytokine production|negative regulation of tumor necrosis factor production|pattern specification process|positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation|positive regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of histone acetylation|positive regulation of immature T cell proliferation in thymus|positive regulation of peripheral T cell tolerance induction|positive regulation of T cell anergy|positive regulation of transforming growth factor-beta1 production|post-embryonic development|regulation of isotype switching to IgG isotypes|T cell homeostasis|T cell receptor signaling pathway|tolerance induction to self antigen	cytoplasm|cytoplasm|nucleus|transcription factor complex	chromatin binding|DNA bending activity|double-stranded DNA binding|histone acetyltransferase binding|histone deacetylase binding|NF-kappaB binding|NFAT protein binding|promoter binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription corepressor activity|zinc ion binding				0	Ovarian(276;0.236)					GBM(182;1432 2112 16160 23073 31774)								0.147541	8.436752	15.725718	9	52	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	48997349	48997349	6274	23	C	A	A	22	22	FOXP3	A	3	3
IQSEC2	23096	broad.mit.edu	36	X	53296514	53296514	+	Missense_Mutation	SNP	C	A	A			TCGA-28-1750-01	TCGA-28-1750-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:53296514C>A	uc004dsd.1	-	c.1969G>T	c.(1969-1971)GCC>TCC	p.A657S	IQSEC2_uc004dsc.1_Missense_Mutation_p.A452S	NM_001111125	NP_001104595	Q5JU85	IQEC2_HUMAN	IQ motif and Sec7 domain 2 isoform1	647	Pro-rich.				regulation of ARF protein signal transduction	cytoplasm	ARF guanyl-nucleotide exchange factor activity			ovary(3)	3														0.37037	22.20161	22.576818	10	17	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	53296514	53296514	8121	23	C	A	A	28	28	IQSEC2	A	3	3
VCX	26609	broad.mit.edu	36	X	7771992	7771992	+	Missense_Mutation	SNP	C	G	G			TCGA-28-1750-01	TCGA-28-1750-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:7771992C>G	uc004crz.1	+	c.556C>G	c.(556-558)CAG>GAG	p.Q186E	VCX_uc010ndn.1_Intron	NM_013452	NP_038480	Q9H320	VCX1_HUMAN	variable charge, X chromosome	186	9.|10 X 10 AA tandem repeats of L-S-Q-E-S- [EQ]-V-E-E-P.|Glu-rich.				chromatin organization|ribosome assembly|spermatogenesis	nucleolus	chromatin binding				0		Colorectal(8;0.0136)|Medulloblastoma(8;0.184)												0.307692	6.588722	7.02142	4	9	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	7771992	7771992	17707	23	C	G	G	29	29	VCX	G	3	3
MGAT2	4247	broad.mit.edu	36	14	49159054	49159055	+	Frame_Shift_Del	DEL	TG	-	-			TCGA-28-1750-01	TCGA-28-1750-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:49159054_49159055delTG	uc001wwr.1	+	c.1318_1319delTG	c.(1318-1320)TGTfs	p.C440fs	SDCCAG1_uc010anj.1_Intron|RPL36AL_uc001wwq.1_5'Flank	NM_002408	NP_002399	Q10469	MGAT2_HUMAN	mannosyl (alpha-1,6-)-glycoprotein	440	Lumenal (Potential).				oligosaccharide biosynthetic process|post-translational protein modification|protein N-linked glycosylation via asparagine	Golgi membrane|Golgi stack|integral to membrane|membrane fraction	alpha-1,6-mannosylglycoprotein 2-beta-N-acetylglucosaminyltransferase activity				0	all_epithelial(31;0.0021)|Breast(41;0.0124)													0.69			9	4				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	49159054	49159055	9933	14	TG	-	-	55	55	MGAT2	-	5	5
CNOT1	23019	broad.mit.edu	36	16	57133738	57133738	+	Frame_Shift_Del	DEL	T	-	-			TCGA-28-1750-01	TCGA-28-1750-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:57133738_57133738delT	uc002env.1	-	c.4578_4578delA	c.(4576-4578)GAAfs	p.E1526fs	CNOT1_uc002enw.1_Non-coding_Transcript|CNOT1_uc002enu.2_Frame_Shift_Del_p.E1521fs	NM_016284	NP_057368	A5YKK6	CNOT1_HUMAN	CCR4-NOT transcription complex, subunit 1	1526					nuclear-transcribed mRNA poly(A) tail shortening|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasmic mRNA processing body|cytosol				ovary(4)|central_nervous_system(2)	6				Kidney(780;0.0722)|OV - Ovarian serous cystadenocarcinoma(108;0.173)|Epithelial(162;0.239)										0.32			56	119				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	57133738	57133738	3755	16	T	-	-	52	52	CNOT1	-	5	5
ABR	29	broad.mit.edu	36	17	856123	856124	+	Frame_Shift_Ins	INS	-	G	G			TCGA-28-1750-01	TCGA-28-1750-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:856123_856124insG	uc002fsd.1	-	c.2526_2527insC	c.(2524-2529)CCCATTfs	p.P842fs	ABR_uc002fsg.1_Frame_Shift_Ins_p.P805fs|ABR_uc002fse.1_Frame_Shift_Ins_p.P796fs|ABR_uc002fsf.1_Frame_Shift_Ins_p.P379fs	NM_021962	NP_068781	Q12979	ABR_HUMAN	active breakpoint cluster region-related	842_843	Rho-GAP.				apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity|protein binding|Rho guanyl-nucleotide exchange factor activity				0				UCEC - Uterine corpus endometrioid carcinoma (25;0.0228)		Esophageal Squamous(197;2016 2115 4129 29033 46447)								0.33			2	4				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	856123	856124	100	17	-	G	G	51	51	ABR	G	5	5
NPC1	4864	broad.mit.edu	36	18	19372595	19372596	+	Frame_Shift_Del	DEL	GA	-	-			TCGA-28-1750-01	TCGA-28-1750-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:19372595_19372596delGA	uc002kum.2	-	c.2949_2950delTC	c.(2947-2952)ACTCCGfs	p.T983fs		NM_000271	NP_000262	O15118	NPC1_HUMAN	Niemann-Pick disease, type C1 precursor	983_984					autophagy|bile acid metabolic process|cholesterol efflux|cholesterol homeostasis|lysosomal transport	endoplasmic reticulum|integral to plasma membrane|late endosome membrane|lysosomal membrane|nuclear envelope|perinuclear region of cytoplasm	hedgehog receptor activity|protein binding|sterol transporter activity			ovary(2)	2	all_cancers(21;0.000106)|all_epithelial(16;6.57e-07)|Lung NSC(20;0.00166)|all_lung(20;0.00536)|Colorectal(14;0.0202)|Ovarian(20;0.127)													0.47			27	30				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	19372595	19372596	10974	18	GA	-	-	41	41	NPC1	-	5	5
FAT2	2196	broad.mit.edu	36	5	150905194	150905202	+	In_Frame_Del	DEL	GCCCGCACC	-	-			TCGA-28-1750-01	TCGA-28-1750-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:150905194_150905202delGCCCGCACC	uc003lue.2	-	c.5679_5687delGGTGCGGGC	c.(5677-5688)ATGGTGCGGGCC>ATC	p.1893_1896MVRA>I		NM_001447	NP_001438	Q9NYQ8	FAT2_HUMAN	FAT tumor suppressor 2 precursor	1893_1896	Extracellular (Potential).				epithelial cell migration|homophilic cell adhesion	cell-cell adherens junction|integral to membrane|nucleus	calcium ion binding			ovary(4)	4		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)											0.32			49	104				---	---	---	---	capture_indel			In_Frame_Del	DEL	150905194	150905202	5926	5	GCCCGCACC	-	-	42	42	FAT2	-	5	5
GRINA	2907	broad.mit.edu	36	8	145137444	145137445	+	Frame_Shift_Ins	INS	-	G	G			TCGA-28-1750-01	TCGA-28-1750-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:145137444_145137445insG	uc003zan.1	+	c.65_66insG	c.(64-66)CCGfs	p.P22fs	GRINA_uc003zao.1_Frame_Shift_Ins_p.P22fs|GRINA_uc003zap.1_Frame_Shift_Ins_p.P22fs	NM_001009184	NP_001009184	Q7Z429	GRINA_HUMAN	glutamate receptor, ionotropic, N-methyl	22	Pro-rich.					integral to membrane				central_nervous_system(1)	1	all_cancers(97;8.2e-11)|all_epithelial(106;1.1e-09)|Lung NSC(106;5.89e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.31e-40)|Epithelial(56;1.16e-39)|all cancers(56;6.43e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)											0.33			2	4				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	145137444	145137445	7064	8	-	G	G	23	23	GRINA	G	5	5
FOXH1	8928	broad.mit.edu	36	8	145670589	145670590	+	Frame_Shift_Ins	INS	-	C	C			TCGA-28-1750-01	TCGA-28-1750-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:145670589_145670590insC	uc003zdc.1	-	c.937_938insG	c.(937-939)GTGfs	p.V313fs	FOXH1_uc010mga.1_Non-coding_Transcript	NM_003923	NP_003914	O75593	FOXH1_HUMAN	forkhead box H1	313	SMAD-interaction domain (SID).				axial mesoderm development|blood vessel development|cell migration involved in gastrulation|embryonic heart tube anterior/posterior pattern formation|floor plate formation|heart looping|negative regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|regulation of sequence-specific DNA binding transcription factor activity|specification of organ position|transforming growth factor beta receptor signaling pathway	activin responsive factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|protein domain specific binding|R-SMAD binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding				0	all_cancers(97;4.61e-11)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.08e-41)|Epithelial(56;8.67e-41)|all cancers(56;1.76e-35)|BRCA - Breast invasive adenocarcinoma(115;0.035)|Colorectal(110;0.055)											0.33			2	4				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	145670589	145670590	6253	8	-	C	C	6	6	FOXH1	C	5	5
FAM102A	399665	broad.mit.edu	36	9	129782169	129782170	+	Frame_Shift_Ins	INS	-	A	A			TCGA-28-1750-01	TCGA-28-1750-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:129782169_129782170insA	uc004bsx.1	-	c.68_69insT	c.(67-69)GCGfs	p.A23fs		NM_001035254	NP_976050	Q5T9C2	F102A_HUMAN	early estrogen-induced gene 1 protein isoform a	23										ovary(1)	1														0.82			27	6				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	129782169	129782170	5579	9	-	A	A	23	23	FAM102A	A	5	5
