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	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	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	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values
C1orf177	163747	broad.mit.edu	37	1	55280638	55280638	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0882-01A-01W-0424-08	TCGA-06-0882-10A-01W-0424-08									Somatic	Phase_I	Capture				Illumina GAIIx	385a3692-3208-479f-9f39-37fb65501b80	4ed08351-1e32-42e5-b009-e2f723cedfc5	g.chr1:55280638G>A	uc001cyb.3	+	8	1030	c.976G>A	c.(976-978)GTC>ATC	p.V326I	C1orf177_uc001cya.3_Missense_Mutation_p.V326I	NM_001110533	NP_001104003	Q3ZCV2	CA177_HUMAN	hypothetical protein LOC163747 isoform 2	326											0						ATGCAAACCCGTCAACCAGCC	0.552												
FCRL4	83417	broad.mit.edu	37	1	157551332	157551332	+	Missense_Mutation	SNP	C	T	T	rs150354637		TCGA-06-0882-01A-01W-0424-08	TCGA-06-0882-10A-01W-0424-08									Somatic	Phase_I	Capture				Illumina GAIIx	385a3692-3208-479f-9f39-37fb65501b80	4ed08351-1e32-42e5-b009-e2f723cedfc5	g.chr1:157551332C>T	uc001fqw.2	-	7	1374	c.1238G>A	c.(1237-1239)CGG>CAG	p.R413Q	FCRL4_uc010phy.1_RNA	NM_031282	NP_112572	Q96PJ5	FCRL4_HUMAN	Fc receptor-like 4 precursor	413	Cytoplasmic (Potential).					integral to membrane|plasma membrane	receptor activity			ovary(2)|kidney(1)|skin(1)	4	all_hematologic(112;0.0378)|Hepatocellular(266;0.178)	Prostate(1639;0.245)				TGACTTCCTCCGACGCCAGCA	0.602												
PAPPA2	60676	broad.mit.edu	37	1	176661413	176661413	+	Silent	SNP	T	C	C			TCGA-06-0882-01A-01W-0424-08	TCGA-06-0882-10A-01W-0424-08									Somatic	Phase_I	Capture				Illumina GAIIx	385a3692-3208-479f-9f39-37fb65501b80	4ed08351-1e32-42e5-b009-e2f723cedfc5	g.chr1:176661413T>C	uc001gkz.2	+	6	3747	c.2583T>C	c.(2581-2583)ACT>ACC	p.T861T	PAPPA2_uc009www.2_RNA	NM_020318	NP_064714	Q9BXP8	PAPP2_HUMAN	pappalysin 2 isoform 1	861					cell differentiation|proteolysis|regulation of cell growth	extracellular region|intracellular|membrane	metalloendopeptidase activity|zinc ion binding			ovary(7)|central_nervous_system(5)|skin(2)|lung(1)|breast(1)	16						AGTCCCTCACTATCCACTGGC	0.502												
RAB3GAP2	25782	broad.mit.edu	37	1	220335581	220335581	+	Missense_Mutation	SNP	A	C	C			TCGA-06-0882-01A-01W-0424-08	TCGA-06-0882-10A-01W-0424-08									Somatic	Phase_I	Capture				Illumina GAIIx	385a3692-3208-479f-9f39-37fb65501b80	4ed08351-1e32-42e5-b009-e2f723cedfc5	g.chr1:220335581A>C	uc010puk.1	-	28	3348	c.3184T>G	c.(3184-3186)TTA>GTA	p.L1062V	RAB3GAP2_uc001hmf.2_RNA|RAB3GAP2_uc001hmg.2_Missense_Mutation_p.L642V|RAB3GAP2_uc001hmh.2_Missense_Mutation_p.L6V	NM_012414	NP_036546	Q9H2M9	RBGPR_HUMAN	rab3 GTPase-activating protein, non-catalytic	1062					intracellular protein transport	cytoplasm|soluble fraction	GTPase activator activity|protein heterodimerization activity			central_nervous_system(1)	1				GBM - Glioblastoma multiforme(131;0.0443)		CTTTTAACTAAGAACGTATTC	0.284												
ARMC3	219681	broad.mit.edu	37	10	23297794	23297794	+	Missense_Mutation	SNP	A	G	G			TCGA-06-0882-01A-01W-0424-08	TCGA-06-0882-10A-01W-0424-08									Somatic	Phase_I	Capture				Illumina GAIIx	385a3692-3208-479f-9f39-37fb65501b80	4ed08351-1e32-42e5-b009-e2f723cedfc5	g.chr10:23297794A>G	uc001irm.3	+	16	2062	c.1979A>G	c.(1978-1980)AAA>AGA	p.K660R	ARMC3_uc010qcv.1_Missense_Mutation_p.K653R|ARMC3_uc010qcw.1_Missense_Mutation_p.K397R	NM_173081	NP_775104	Q5W041	ARMC3_HUMAN	armadillo repeat containing 3	660							binding				0						ATAGAAGACAAATCAGAGCCA	0.378												
PTEN	5728	broad.mit.edu	37	10	89711900	89711900	+	Missense_Mutation	SNP	G	A	A	rs121913294		TCGA-06-0882-01A-01W-0424-08	TCGA-06-0882-10A-01W-0424-08									Somatic	Phase_I	Capture				Illumina GAIIx	385a3692-3208-479f-9f39-37fb65501b80	4ed08351-1e32-42e5-b009-e2f723cedfc5	g.chr10:89711900G>A	uc001kfb.2	+	7	1549	c.518G>A	c.(517-519)CGC>CAC	p.R173H		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).		activation of mitotic anaphase-promoting complex activity|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 cyclin-dependent protein kinase activity involved in G1/S|negative regulation of focal adhesion assembly|negative regulation of G1/S transition of mitotic cell cycle|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 protein ubiquitination involved in ubiquitin-dependent protein catabolic process|positive regulation of sequence-specific DNA binding transcription factor activity|protein stabilization|regulation of neuron projection development|T cell receptor signaling pathway	cytosol|internal side of plasma membrane|PML body	anaphase-promoting complex binding|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.R173H(22)|p.R55fs*1(4)|p.V166fs*17(3)|p.?(3)|p.G165fs*9(3)|p.R173fs*10(2)|p.Y27fs*1(2)|p.Y27_N212>Y(2)|p.G165_K342del(1)|p.G165_*404del(1)|p.R173R(1)|p.R173P(1)|p.R172fs*5(1)		endometrium(831)|central_nervous_system(657)|skin(121)|haematopoietic_and_lymphoid_tissue(101)|large_intestine(99)|prostate(97)|breast(73)|lung(65)|ovary(58)|thyroid(29)|stomach(29)|upper_aerodigestive_tract(25)|cervix(24)|liver(20)|vulva(17)|kidney(15)|NS(14)|soft_tissue(13)|urinary_tract(12)|eye(8)|pancreas(6)|salivary_gland(5)|bone(5)|biliary_tract(4)|autonomic_ganglia(2)|meninges(2)|testis(1)|oesophagus(1)	2334		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)		AGTCAGAGGCGCTATGTGTAT	0.348	R173H(RL952_ENDOMETRIUM)	31	D|Mis|N|F|S		glioma| prostate|endometrial	harmartoma|glioma| prostate|endometrial			Proteus_syndrome|Cowden_syndrome|Juvenile_Polyposis|Hereditary_Mixed_Polyposis_Syndrome_type_1|Bannayan-Riley-Ruvalcaba_syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)		
ST5	6764	broad.mit.edu	37	11	8752166	8752166	+	Frame_Shift_Del	DEL	C	-	-			TCGA-06-0882-01A-01W-0424-08	TCGA-06-0882-10A-01W-0424-08									Somatic	Phase_I	Capture				Illumina GAIIx	385a3692-3208-479f-9f39-37fb65501b80	4ed08351-1e32-42e5-b009-e2f723cedfc5	g.chr11:8752166delC	uc001mgt.2	-	3	857	c.671delG	c.(670-672)GGCfs	p.G224fs	ST5_uc009yfr.2_Intron|ST5_uc001mgu.2_Intron|ST5_uc001mgv.2_Frame_Shift_Del_p.G224fs|ST5_uc010rbq.1_Intron|ST5_uc001mgw.1_Frame_Shift_Del_p.G224fs	NM_213618	NP_998783	P78524	ST5_HUMAN	suppression of tumorigenicity 5 isoform 1	224					positive regulation of ERK1 and ERK2 cascade		protein binding			upper_aerodigestive_tract(1)	1				Epithelial(150;2.63e-07)|BRCA - Breast invasive adenocarcinoma(625;0.0352)		CCTCCGGAGGCCCTTGAAATC	0.642												
OR8J3	81168	broad.mit.edu	37	11	55904404	55904404	+	Missense_Mutation	SNP	G	C	C	rs143365733	byFrequency	TCGA-06-0882-01A-01W-0424-08	TCGA-06-0882-10A-01W-0424-08									Somatic	Phase_I	Capture				Illumina GAIIx	385a3692-3208-479f-9f39-37fb65501b80	4ed08351-1e32-42e5-b009-e2f723cedfc5	g.chr11:55904404G>C	uc010riz.1	-	1	791	c.791C>G	c.(790-792)ACC>AGC	p.T264S		NM_001004064	NP_001004064	Q8NGG0	OR8J3_HUMAN	olfactory receptor, family 8, subfamily J,	264	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(2)	2	Esophageal squamous(21;0.00693)					TGAGTGGTTGGTTTGGGGCTG	0.428												
SLC22A20	440044	broad.mit.edu	37	11	64981482	64981482	+	Missense_Mutation	SNP	C	A	A			TCGA-06-0882-01A-01W-0424-08	TCGA-06-0882-10A-01W-0424-08									Somatic	Phase_I	Capture				Illumina GAIIx	385a3692-3208-479f-9f39-37fb65501b80	4ed08351-1e32-42e5-b009-e2f723cedfc5	g.chr11:64981482C>A	uc010roc.1	+	1	136	c.133C>A	c.(133-135)CCC>ACC	p.P45T	SLC22A20_uc010rob.1_Missense_Mutation_p.P45T	NM_001004326	NP_001004326	A6NK97	S22AK_HUMAN	solute carrier family 22, member 20	45	Extracellular (Potential).				ion transport	integral to membrane	transmembrane transporter activity			central_nervous_system(1)	1						GGCCGCTGTCCCCCCCCACCA	0.692												
TIGD3	220359	broad.mit.edu	37	11	65124539	65124539	+	Missense_Mutation	SNP	C	G	G			TCGA-06-0882-01A-01W-0424-08	TCGA-06-0882-10A-01W-0424-08									Somatic	Phase_I	Capture				Illumina GAIIx	385a3692-3208-479f-9f39-37fb65501b80	4ed08351-1e32-42e5-b009-e2f723cedfc5	g.chr11:65124539C>G	uc001odo.3	+	2	1423	c.1260C>G	c.(1258-1260)GAC>GAG	p.D420E		NM_145719	NP_663771	Q6B0B8	TIGD3_HUMAN	tigger transposable element derived 3	420					regulation of transcription, DNA-dependent	chromosome, centromeric region|nucleus	DNA binding				0						AGAAGGGGGACAGAGAGGGTG	0.587												
ITGB7	3695	broad.mit.edu	37	12	53590514	53590514	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0882-01A-01W-0424-08	TCGA-06-0882-10A-01W-0424-08									Somatic	Phase_I	Capture				Illumina GAIIx	385a3692-3208-479f-9f39-37fb65501b80	4ed08351-1e32-42e5-b009-e2f723cedfc5	g.chr12:53590514C>T	uc009zmv.2	-	5	736	c.665G>A	c.(664-666)CGC>CAC	p.R222H	ITGB7_uc001scc.2_Missense_Mutation_p.R222H|ITGB7_uc010snz.1_RNA|ITGB7_uc010soa.1_3'UTR	NM_000889	NP_000880	P26010	ITB7_HUMAN	integrin, beta 7 precursor	222	VWFA.|Extracellular (Potential).				cell-matrix adhesion|integrin-mediated signaling pathway|multicellular organismal development|regulation of immune response	integrin complex	identical protein binding|metal ion binding|receptor activity			ovary(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)|breast(1)	8						TGACTGGCAGCGCTCCAGCCG	0.622												
LHFP	10186	broad.mit.edu	37	13	40175282	40175282	+	Silent	SNP	G	A	A			TCGA-06-0882-01A-01W-0424-08	TCGA-06-0882-10A-01W-0424-08									Somatic	Phase_I	Capture				Illumina GAIIx	385a3692-3208-479f-9f39-37fb65501b80	4ed08351-1e32-42e5-b009-e2f723cedfc5	g.chr13:40175282G>A	uc001uxf.2	-	2	583	c.72C>T	c.(70-72)TGC>TGT	p.C24C		NM_005780	NP_005771	Q9Y693	LHFP_HUMAN	lipoma HMGIC fusion partner precursor	24						integral to membrane	DNA binding		HMGA2/LHFP(2)	soft_tissue(2)|lung(1)|breast(1)	4		Lung NSC(96;3.55e-06)|Breast(139;0.00408)|Ovarian(182;0.0107)|Prostate(109;0.0118)|Lung SC(185;0.0719)|Hepatocellular(188;0.114)		OV - Ovarian serous cystadenocarcinoma(117;6.48e-46)|Epithelial(112;8.43e-42)|all cancers(112;1.42e-36)|GBM - Glioblastoma multiforme(144;0.00187)|BRCA - Breast invasive adenocarcinoma(63;0.00886)|KIRC - Kidney renal clear cell carcinoma(186;0.048)|Kidney(163;0.0601)|LUSC - Lung squamous cell carcinoma(192;0.105)		AGAACCCCACGCAGGAGGTGG	0.537			T	HMGA2	lipoma							
C14orf182	283551	broad.mit.edu	37	14	50472507	50472507	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0882-01A-01W-0424-08	TCGA-06-0882-10A-01W-0424-08									Somatic	Phase_I	Capture				Illumina GAIIx	385a3692-3208-479f-9f39-37fb65501b80	4ed08351-1e32-42e5-b009-e2f723cedfc5	g.chr14:50472507C>T	uc001wxi.1	-	1	1732	c.11G>A	c.(10-12)CGG>CAG	p.R4Q		NM_001012706	NP_001012724	A1A4T8	CN182_HUMAN	hypothetical protein LOC283551	4											0						GGTTGCCATCCGACCTGTCAT	0.507												
TDRD9	122402	broad.mit.edu	37	14	104493271	104493271	+	Missense_Mutation	SNP	T	C	C			TCGA-06-0882-01A-01W-0424-08	TCGA-06-0882-10A-01W-0424-08									Somatic	Phase_I	Capture				Illumina GAIIx	385a3692-3208-479f-9f39-37fb65501b80	4ed08351-1e32-42e5-b009-e2f723cedfc5	g.chr14:104493271T>C	uc001yom.3	+	28	3307	c.3277T>C	c.(3277-3279)TCC>CCC	p.S1093P	TDRD9_uc001yon.3_Missense_Mutation_p.S831P	NM_153046	NP_694591	Q8NDG6	TDRD9_HUMAN	tudor domain containing 9	1093					cell differentiation|DNA methylation involved in gamete generation|fertilization|gene silencing by RNA|male meiosis|multicellular organismal development|piRNA metabolic process|spermatogenesis	nucleus|piP-body	ATP binding|ATP-dependent helicase activity|nucleic acid binding			ovary(2)|central_nervous_system(1)	3		all_cancers(154;0.109)|Melanoma(154;0.0525)|all_epithelial(191;0.0768)				GTCCTACGAGTCCAAGGTGTG	0.582												
PLCB2	5330	broad.mit.edu	37	15	40596215	40596215	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0882-01A-01W-0424-08	TCGA-06-0882-10A-01W-0424-08									Somatic	Phase_I	Capture				Illumina GAIIx	385a3692-3208-479f-9f39-37fb65501b80	4ed08351-1e32-42e5-b009-e2f723cedfc5	g.chr15:40596215G>A	uc001zld.2	-	2	450	c.149C>T	c.(148-150)ACG>ATG	p.T50M	PLCB2_uc010bbo.2_Missense_Mutation_p.T50M|PLCB2_uc010ucm.1_Missense_Mutation_p.T50M|PLCB2_uc001zle.3_Missense_Mutation_p.T50M	NM_004573	NP_004564	Q00722	PLCB2_HUMAN	phospholipase C, beta 2	50					activation of phospholipase C activity|intracellular signal transduction|lipid catabolic process|phospholipid metabolic process|synaptic transmission	cytosol	calcium ion binding|phosphatidylinositol phospholipase C activity|signal transducer activity			ovary(3)|breast(3)|kidney(1)|pancreas(1)	8		all_cancers(109;9.35e-19)|all_epithelial(112;1.18e-15)|Lung NSC(122;2.45e-11)|all_lung(180;6.47e-10)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;9.38e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0508)		ACTTTGATACGTCCAGTATAA	0.527												
RPAP1	26015	broad.mit.edu	37	15	41810014	41810014	+	Silent	SNP	T	C	C			TCGA-06-0882-01A-01W-0424-08	TCGA-06-0882-10A-01W-0424-08									Somatic	Phase_I	Capture				Illumina GAIIx	385a3692-3208-479f-9f39-37fb65501b80	4ed08351-1e32-42e5-b009-e2f723cedfc5	g.chr15:41810014T>C	uc001zod.2	-	24	4138	c.4014A>G	c.(4012-4014)ACA>ACG	p.T1338T	RPAP1_uc001zoc.2_Silent_p.T357T	NM_015540	NP_056355	Q9BWH6	RPAP1_HUMAN	RNA polymerase II associated protein 1	1338						nucleus	DNA binding|DNA-directed RNA polymerase activity			large_intestine(1)	1		all_cancers(109;6.59e-20)|all_epithelial(112;7.67e-17)|Lung NSC(122;5.34e-11)|all_lung(180;4.17e-10)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.173)		OV - Ovarian serous cystadenocarcinoma(18;2.84e-17)|GBM - Glioblastoma multiforme(113;1.68e-06)|Colorectal(105;0.0163)|BRCA - Breast invasive adenocarcinoma(123;0.117)		CCAGCAGCCATGTTTTCTGCA	0.562												
ABCC1	4363	broad.mit.edu	37	16	16225756	16225756	+	Silent	SNP	C	T	T			TCGA-06-0882-01A-01W-0424-08	TCGA-06-0882-10A-01W-0424-08									Somatic	Phase_I	Capture				Illumina GAIIx	385a3692-3208-479f-9f39-37fb65501b80	4ed08351-1e32-42e5-b009-e2f723cedfc5	g.chr16:16225756C>T	uc010bvi.2	+	27	4105	c.3930C>T	c.(3928-3930)CTC>CTT	p.L1310L	ABCC1_uc010bvj.2_Silent_p.L1251L|ABCC1_uc010bvk.2_Silent_p.L1254L|ABCC1_uc010bvl.2_Silent_p.L1310L|ABCC1_uc010bvm.2_Silent_p.L1195L|ABCC1_uc002del.3_Silent_p.L1204L	NM_004996	NP_004987	P33527	MRP1_HUMAN	ATP-binding cassette, sub-family C, member 1	1310	ABC transporter 2.|Cytoplasmic.				hormone biosynthetic process|leukotriene biosynthetic process|prostanoid metabolic process|response to drug	Golgi apparatus|integral to plasma membrane|membrane fraction|nucleus	ATP binding|ATPase activity, coupled to transmembrane movement of substances			ovary(4)	4					Daunorubicin(DB00694)|Glibenclamide(DB01016)|Probenecid(DB01032)|Saquinavir(DB01232)|Sulfinpyrazone(DB01138)	ACTTCGTTCTCAGGCACATCA	0.607												
RLTPR	146206	broad.mit.edu	37	16	67683169	67683169	+	Silent	SNP	C	T	T			TCGA-06-0882-01A-01W-0424-08	TCGA-06-0882-10A-01W-0424-08									Somatic	Phase_I	Capture				Illumina GAIIx	385a3692-3208-479f-9f39-37fb65501b80	4ed08351-1e32-42e5-b009-e2f723cedfc5	g.chr16:67683169C>T	uc002etn.2	+	19	1821	c.1701C>T	c.(1699-1701)GAC>GAT	p.D567D	RLTPR_uc010cel.1_Silent_p.D560D|RLTPR_uc010vjr.1_Silent_p.D531D	NM_001013838	NP_001013860	Q6F5E8	LR16C_HUMAN	RGD motif, leucine rich repeats, tropomodulin	567	LRR 12.									breast(1)	1		Acute lymphoblastic leukemia(13;3.23e-05)|all_hematologic(13;0.00251)|Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0146)|Epithelial(162;0.0481)|all cancers(182;0.232)		AGACCCTGGACGACGTCCTGC	0.637												
DRG2	1819	broad.mit.edu	37	17	18007951	18007951	+	Missense_Mutation	SNP	A	T	T			TCGA-06-0882-01A-01W-0424-08	TCGA-06-0882-10A-01W-0424-08									Somatic	Phase_I	Capture				Illumina GAIIx	385a3692-3208-479f-9f39-37fb65501b80	4ed08351-1e32-42e5-b009-e2f723cedfc5	g.chr17:18007951A>T	uc002gsh.1	+	11	965	c.910A>T	c.(910-912)ACA>TCA	p.T304S	DRG2_uc002gsi.1_RNA|DRG2_uc002gsj.1_Missense_Mutation_p.T304S	NM_001388	NP_001379	P55039	DRG2_HUMAN	developmentally regulated GTP binding protein 2	304					signal transduction		GTP binding			ovary(1)	1	all_neural(463;0.228)					GCCAGACTTCACAGACGCCAT	0.607												
FAM18B	51030	broad.mit.edu	37	17	18708852	18708852	+	Splice_Site	SNP	A	G	G	rs2589696		TCGA-06-0882-01A-01W-0424-08	TCGA-06-0882-10A-01W-0424-08									Somatic	Phase_I	Capture				Illumina GAIIx	385a3692-3208-479f-9f39-37fb65501b80	4ed08351-1e32-42e5-b009-e2f723cedfc5	g.chr17:18708852A>G	uc002gum.2	+	7	617	c.592_splice	c.e7-2	p.N198_splice	FAM18B_uc002gun.2_Splice_Site_p.N134_splice	NM_016078	NP_057162	Q9NYZ1	F18B1_HUMAN	hypothetical protein LOC51030							integral to membrane					0				UCEC - Uterine corpus endometrioid carcinoma (53;0.0872)|READ - Rectum adenocarcinoma(1115;0.0967)		TGTCTTTTGCAGAACACTGGA	0.368												
SLFN12	55106	broad.mit.edu	37	17	33749828	33749828	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0882-01A-01W-0424-08	TCGA-06-0882-10A-01W-0424-08									Somatic	Phase_I	Capture				Illumina GAIIx	385a3692-3208-479f-9f39-37fb65501b80	4ed08351-1e32-42e5-b009-e2f723cedfc5	g.chr17:33749828C>T	uc002hji.3	-	2	597	c.220G>A	c.(220-222)GGA>AGA	p.G74R	SLFN12_uc002hjj.3_Missense_Mutation_p.G74R|SLFN12_uc010cts.2_Missense_Mutation_p.G74R	NM_018042	NP_060512	Q8IYM2	SLN12_HUMAN	schlafen family member 12	74							ATP binding			skin(1)	1		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		AGTCCTATTCCATCTTTTGTA	0.363												
SLFN12	55106	broad.mit.edu	37	17	33749831	33749831	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0882-01A-01W-0424-08	TCGA-06-0882-10A-01W-0424-08									Somatic	Phase_I	Capture				Illumina GAIIx	385a3692-3208-479f-9f39-37fb65501b80	4ed08351-1e32-42e5-b009-e2f723cedfc5	g.chr17:33749831C>T	uc002hji.3	-	2	594	c.217G>A	c.(217-219)GAT>AAT	p.D73N	SLFN12_uc002hjj.3_Missense_Mutation_p.D73N|SLFN12_uc010cts.2_Missense_Mutation_p.D73N	NM_018042	NP_060512	Q8IYM2	SLN12_HUMAN	schlafen family member 12	73							ATP binding			skin(1)	1		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		CCTATTCCATCTTTTGTATAA	0.368												
LYZL6	57151	broad.mit.edu	37	17	34261842	34261842	+	Silent	SNP	G	T	T			TCGA-06-0882-01A-01W-0424-08	TCGA-06-0882-10A-01W-0424-08									Somatic	Phase_I	Capture				Illumina GAIIx	385a3692-3208-479f-9f39-37fb65501b80	4ed08351-1e32-42e5-b009-e2f723cedfc5	g.chr17:34261842G>T	uc002hkj.1	-	4	555	c.405C>A	c.(403-405)GGC>GGA	p.G135G	LYZL6_uc002hkk.1_Silent_p.G135G	NM_020426	NP_065159	O75951	LYZL6_HUMAN	lysozyme-like 6 precursor	135					cell wall macromolecule catabolic process	extracellular region	lysozyme activity				0				UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		AGAGTGGCCGGCCTGAACAGT	0.537												
HOXB9	3219	broad.mit.edu	37	17	46703491	46703491	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0882-01A-01W-0424-08	TCGA-06-0882-10A-01W-0424-08									Somatic	Phase_I	Capture				Illumina GAIIx	385a3692-3208-479f-9f39-37fb65501b80	4ed08351-1e32-42e5-b009-e2f723cedfc5	g.chr17:46703491G>C	uc002inx.2	-	1	345	c.141C>G	c.(139-141)TTC>TTG	p.F47L		NM_024017	NP_076922	P17482	HXB9_HUMAN	homeobox B9	47					canonical Wnt receptor signaling pathway|cell chemotaxis	mitochondrion|nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0						TGCACGAGGGGAACTCCAGGT	0.687												
HOXB9	3219	broad.mit.edu	37	17	46703538	46703538	+	Nonsense_Mutation	SNP	G	A	A			TCGA-06-0882-01A-01W-0424-08	TCGA-06-0882-10A-01W-0424-08									Somatic	Phase_I	Capture				Illumina GAIIx	385a3692-3208-479f-9f39-37fb65501b80	4ed08351-1e32-42e5-b009-e2f723cedfc5	g.chr17:46703538G>A	uc002inx.2	-	1	298	c.94C>T	c.(94-96)CAG>TAG	p.Q32*		NM_024017	NP_076922	P17482	HXB9_HUMAN	homeobox B9	32					canonical Wnt receptor signaling pathway|cell chemotaxis	mitochondrion|nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0						CTCGCGTACTGGCCAGAAGGA	0.622												
CACNG1	786	broad.mit.edu	37	17	65041001	65041001	+	Silent	SNP	C	T	T			TCGA-06-0882-01A-01W-0424-08	TCGA-06-0882-10A-01W-0424-08									Somatic	Phase_I	Capture				Illumina GAIIx	385a3692-3208-479f-9f39-37fb65501b80	4ed08351-1e32-42e5-b009-e2f723cedfc5	g.chr17:65041001C>T	uc002jfu.2	+	1	296	c.225C>T	c.(223-225)CCC>CCT	p.P75P		NM_000727	NP_000718	Q06432	CCG1_HUMAN	voltage-dependent calcium channel gamma-1	75					muscle contraction	voltage-gated calcium channel complex	voltage-gated calcium channel activity				0	all_cancers(12;1.04e-10)|Breast(2;1.45e-16)|all_epithelial(3;4.81e-12)				Amlodipine(DB00381)|Diltiazem(DB00343)|Ibutilide(DB00308)|Lercanidipine(DB00528)|Magnesium Sulfate(DB00653)|Nimodipine(DB00393)|Nitrendipine(DB01054)|Verapamil(DB00661)	TCACCCTGCCCGGGGGTAACG	0.637												
KIF19	124602	broad.mit.edu	37	17	72345359	72345359	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0882-01A-01W-0424-08	TCGA-06-0882-10A-01W-0424-08									Somatic	Phase_I	Capture				Illumina GAIIx	385a3692-3208-479f-9f39-37fb65501b80	4ed08351-1e32-42e5-b009-e2f723cedfc5	g.chr17:72345359G>A	uc002jkm.3	+	10	1222	c.1084G>A	c.(1084-1086)GCC>ACC	p.A362T	KIF19_uc002jkj.2_Missense_Mutation_p.A362T|KIF19_uc002jkk.2_Missense_Mutation_p.A320T|KIF19_uc002jkl.2_Missense_Mutation_p.A320T	NM_153209	NP_694941	Q2TAC6	KIF19_HUMAN	kinesin family member 19	362	Potential.				microtubule-based movement	cytoplasm|microtubule	ATP binding|microtubule motor activity				0						CTACCACATCGCCCAGTACAC	0.642												
LAMA1	284217	broad.mit.edu	37	18	6978310	6978310	+	Silent	SNP	C	T	T			TCGA-06-0882-01A-01W-0424-08	TCGA-06-0882-10A-01W-0424-08									Somatic	Phase_I	Capture				Illumina GAIIx	385a3692-3208-479f-9f39-37fb65501b80	4ed08351-1e32-42e5-b009-e2f723cedfc5	g.chr18:6978310C>T	uc002knm.2	-	43	6169	c.6075G>A	c.(6073-6075)ACG>ACA	p.T2025T	LAMA1_uc010wzj.1_Silent_p.T1501T	NM_005559	NP_005550	P25391	LAMA1_HUMAN	laminin, alpha 1 precursor	2025	Domain II and I.				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)|upper_aerodigestive_tract(2)|breast(2)|skin(2)|pancreas(2)|central_nervous_system(1)	21		Colorectal(10;0.172)			Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)	CGTCCCTCAGCGTGCTCACCG	0.537												
SETBP1	26040	broad.mit.edu	37	18	42530386	42530386	+	Missense_Mutation	SNP	G	T	T	rs146321232		TCGA-06-0882-01A-01W-0424-08	TCGA-06-0882-10A-01W-0424-08									Somatic	Phase_I	Capture				Illumina GAIIx	385a3692-3208-479f-9f39-37fb65501b80	4ed08351-1e32-42e5-b009-e2f723cedfc5	g.chr18:42530386G>T	uc010dni.2	+	4	1377	c.1081G>T	c.(1081-1083)GCA>TCA	p.A361S		NM_015559	NP_056374	Q9Y6X0	SETBP_HUMAN	SET binding protein 1 isoform a	361						nucleus	DNA binding			upper_aerodigestive_tract(2)|large_intestine(1)	3				Colorectal(1;0.0622)|COAD - Colon adenocarcinoma(74;0.201)		TGCCCAGAAAGCATTTGACAA	0.478									Schinzel-Giedion_syndrome			
ZNF254	9534	broad.mit.edu	37	19	24309636	24309636	+	Silent	SNP	C	T	T			TCGA-06-0882-01A-01W-0424-08	TCGA-06-0882-10A-01W-0424-08									Somatic	Phase_I	Capture				Illumina GAIIx	385a3692-3208-479f-9f39-37fb65501b80	4ed08351-1e32-42e5-b009-e2f723cedfc5	g.chr19:24309636C>T	uc002nru.2	+	4	968	c.834C>T	c.(832-834)TCC>TCT	p.S278S	ZNF254_uc010xrk.1_Silent_p.S193S	NM_203282	NP_975011	O75437	ZN254_HUMAN	zinc finger protein 254	278	C2H2-type 3.				negative regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		all_cancers(12;0.086)|all_lung(12;0.00528)|Lung NSC(12;0.00731)|all_epithelial(12;0.0186)				TTAATCGATCCTCAAATCTTA	0.378												
MEGF8	1954	broad.mit.edu	37	19	42861568	42861568	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0882-01A-01W-0424-08	TCGA-06-0882-10A-01W-0424-08									Somatic	Phase_I	Capture				Illumina GAIIx	385a3692-3208-479f-9f39-37fb65501b80	4ed08351-1e32-42e5-b009-e2f723cedfc5	g.chr19:42861568G>A	uc002otl.3	+	27	5277	c.4642G>A	c.(4642-4644)GTG>ATG	p.V1548M	MEGF8_uc002otm.3_Missense_Mutation_p.V1156M	NM_001410	NP_001401	Q7Z7M0	MEGF8_HUMAN	multiple EGF-like-domains 8	1615	Extracellular (Potential).|Kelch 8.					integral to membrane	calcium ion binding|structural molecule activity			ovary(1)	1		Prostate(69;0.00682)				CCCCCAGACCGTGGAGCTGCC	0.652												
DUXA	503835	broad.mit.edu	37	19	57669795	57669795	+	Silent	SNP	T	C	C			TCGA-06-0882-01A-01W-0424-08	TCGA-06-0882-10A-01W-0424-08									Somatic	Phase_I	Capture				Illumina GAIIx	385a3692-3208-479f-9f39-37fb65501b80	4ed08351-1e32-42e5-b009-e2f723cedfc5	g.chr19:57669795T>C	uc002qoa.1	-	4	384	c.339A>G	c.(337-339)TTA>TTG	p.L113L		NM_001012729	NP_001012747	A6NLW8	DUXA_HUMAN	double homeobox A	113	Homeobox 2.					nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0822)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0123)		TGAGAGTGTGTAACTGAGAGG	0.488												
OTOF	9381	broad.mit.edu	37	2	26686908	26686908	+	Missense_Mutation	SNP	C	T	T	rs143889717		TCGA-06-0882-01A-01W-0424-08	TCGA-06-0882-10A-01W-0424-08									Somatic	Phase_I	Capture				Illumina GAIIx	385a3692-3208-479f-9f39-37fb65501b80	4ed08351-1e32-42e5-b009-e2f723cedfc5	g.chr2:26686908C>T	uc002rhk.2	-	40	5154	c.5027G>A	c.(5026-5028)CGC>CAC	p.R1676H	OTOF_uc010yla.1_Missense_Mutation_p.R406H|OTOF_uc002rhh.2_Missense_Mutation_p.R909H|OTOF_uc002rhi.2_Missense_Mutation_p.R986H|OTOF_uc002rhj.2_Missense_Mutation_p.R909H	NM_194248	NP_919224	Q9HC10	OTOF_HUMAN	otoferlin isoform a	1676	Cytoplasmic (Potential).				cellular membrane fusion|sensory perception of sound|synaptic vesicle exocytosis	basolateral plasma membrane|cell junction|cytosol|endoplasmic reticulum membrane|integral to membrane|membrane fraction|synaptic vesicle membrane	calcium ion binding			ovary(3)|breast(2)|central_nervous_system(1)|pancreas(1)	7	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GCAGCCTGCGCGGGGGATGTC	0.667												
TTN	7273	broad.mit.edu	37	2	179463526	179463526	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0882-01A-01W-0424-08	TCGA-06-0882-10A-01W-0424-08									Somatic	Phase_I	Capture				Illumina GAIIx	385a3692-3208-479f-9f39-37fb65501b80	4ed08351-1e32-42e5-b009-e2f723cedfc5	g.chr2:179463526C>T	uc010zfg.1	-	240	49431	c.49207G>A	c.(49207-49209)GTG>ATG	p.V16403M	uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Missense_Mutation_p.V10098M|TTN_uc010zfi.1_Missense_Mutation_p.V10031M|TTN_uc010zfj.1_Missense_Mutation_p.V9906M	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	17330							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GCTGGACCCACGCCAGCAGCA	0.428												
CPS1	1373	broad.mit.edu	37	2	211469880	211469880	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0882-01A-01W-0424-08	TCGA-06-0882-10A-01W-0424-08									Somatic	Phase_I	Capture				Illumina GAIIx	385a3692-3208-479f-9f39-37fb65501b80	4ed08351-1e32-42e5-b009-e2f723cedfc5	g.chr2:211469880G>C	uc002vee.3	+	17	2023	c.1891G>C	c.(1891-1893)GAA>CAA	p.E631Q	CPS1_uc010fur.2_Missense_Mutation_p.E637Q|CPS1_uc010fus.2_Missense_Mutation_p.E180Q	NM_001875	NP_001866	P31327	CPSM_HUMAN	carbamoyl-phosphate synthetase 1 isoform b	631	ATP-grasp 1.				carbamoyl phosphate biosynthetic process|citrulline biosynthetic process|glutamine metabolic process|glycogen catabolic process|nitric oxide metabolic process|positive regulation of vasodilation|response to lipopolysaccharide|triglyceride catabolic process|urea cycle	mitochondrial nucleoid	ATP binding|carbamoyl-phosphate synthase (ammonia) activity			ovary(8)|central_nervous_system(3)|breast(1)|skin(1)	13				Epithelial(149;0.00697)|Lung(261;0.0521)|LUSC - Lung squamous cell carcinoma(261;0.0544)|all cancers(144;0.0843)		AGGTTGGAAAGAAATAGAATA	0.408												
COL4A4	1286	broad.mit.edu	37	2	227917071	227917071	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0882-01A-01W-0424-08	TCGA-06-0882-10A-01W-0424-08									Somatic	Phase_I	Capture				Illumina GAIIx	385a3692-3208-479f-9f39-37fb65501b80	4ed08351-1e32-42e5-b009-e2f723cedfc5	g.chr2:227917071G>A	uc010zlt.1	-	32	3572	c.2918C>T	c.(2917-2919)ACA>ATA	p.T973I		NM_000092	NP_000083	P53420	CO4A4_HUMAN	alpha 4 type IV collagen precursor	973	Triple-helical region.				axon guidance|glomerular basement membrane development	basal lamina|collagen type IV	extracellular matrix structural constituent|protein binding			ovary(5)|central_nervous_system(3)|pancreas(1)|breast(1)|skin(1)	11		Renal(207;0.00844)|all_lung(227;0.0187)|Lung NSC(271;0.0879)|all_hematologic(139;0.21)|Esophageal squamous(248;0.242)		Epithelial(121;6.7e-11)|all cancers(144;5.39e-08)|Lung(261;0.0132)|LUSC - Lung squamous cell carcinoma(224;0.0181)		TTCCCCAGGTGTTCCCTTTTG	0.403												
TASP1	55617	broad.mit.edu	37	20	13514755	13514755	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0882-01A-01W-0424-08	TCGA-06-0882-10A-01W-0424-08									Somatic	Phase_I	Capture				Illumina GAIIx	385a3692-3208-479f-9f39-37fb65501b80	4ed08351-1e32-42e5-b009-e2f723cedfc5	g.chr20:13514755C>T	uc002woi.2	-	9	826	c.709G>A	c.(709-711)GCT>ACT	p.A237T	TASP1_uc010zri.1_Intron|TASP1_uc002woh.2_Missense_Mutation_p.A214T|TASP1_uc010zrj.1_RNA	NM_017714	NP_060184	Q9H6P5	TASP1_HUMAN	taspase 1 precursor	237					asparagine catabolic process via L-aspartate|positive regulation of transcription, DNA-dependent|protein maturation		threonine-type endopeptidase activity				0						ACAACCACAGCGCCTACCGTG	0.507												
REM1	28954	broad.mit.edu	37	20	30070268	30070268	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0882-01A-01W-0424-08	TCGA-06-0882-10A-01W-0424-08									Somatic	Phase_I	Capture				Illumina GAIIx	385a3692-3208-479f-9f39-37fb65501b80	4ed08351-1e32-42e5-b009-e2f723cedfc5	g.chr20:30070268G>A	uc002wwa.2	+	4	886	c.602G>A	c.(601-603)CGC>CAC	p.R201H		NM_014012	NP_054731	O75628	REM1_HUMAN	RAS-like GTP-binding protein REM	201					small GTPase mediated signal transduction	membrane	calmodulin binding|GTP binding|GTPase activity			lung(2)|pancreas(2)	4	all_cancers(5;0.000119)|Lung NSC(7;1.32e-05)|all_lung(7;2.14e-05)|all_hematologic(12;0.158)|Ovarian(7;0.198)		Colorectal(19;0.00254)|COAD - Colon adenocarcinoma(19;0.0347)			GACTTGGCCCGCTGCCGAGAA	0.612												
TRPM2	7226	broad.mit.edu	37	21	45826547	45826547	+	Missense_Mutation	SNP	C	A	A			TCGA-06-0882-01A-01W-0424-08	TCGA-06-0882-10A-01W-0424-08									Somatic	Phase_I	Capture				Illumina GAIIx	385a3692-3208-479f-9f39-37fb65501b80	4ed08351-1e32-42e5-b009-e2f723cedfc5	g.chr21:45826547C>A	uc002zet.1	+	20	3074	c.2861C>A	c.(2860-2862)GCC>GAC	p.A954D	TRPM2_uc002zeu.1_Missense_Mutation_p.A954D|TRPM2_uc002zew.1_Missense_Mutation_p.A954D|TRPM2_uc010gpt.1_Missense_Mutation_p.A954D|TRPM2_uc002zex.1_Missense_Mutation_p.A740D|TRPM2_uc002zey.1_Missense_Mutation_p.A467D	NM_003307	NP_003298	O94759	TRPM2_HUMAN	transient receptor potential cation channel,	954	Helical; (Potential).					integral to plasma membrane	ADP-ribose diphosphatase activity|calcium channel activity|sodium channel activity			ovary(1)|central_nervous_system(1)|pancreas(1)	3						GCCAAGCAGGCCATCCTCATC	0.607												
CNTN6	27255	broad.mit.edu	37	3	1427473	1427473	+	Missense_Mutation	SNP	A	G	G	rs143460057		TCGA-06-0882-01A-01W-0424-08	TCGA-06-0882-10A-01W-0424-08									Somatic	Phase_I	Capture				Illumina GAIIx	385a3692-3208-479f-9f39-37fb65501b80	4ed08351-1e32-42e5-b009-e2f723cedfc5	g.chr3:1427473A>G	uc003boz.2	+	20	2963	c.2696A>G	c.(2695-2697)AAA>AGA	p.K899R	CNTN6_uc011asj.1_Missense_Mutation_p.K827R|CNTN6_uc003bpa.2_Missense_Mutation_p.K899R	NM_014461	NP_055276	Q9UQ52	CNTN6_HUMAN	contactin 6 precursor	899					axon guidance|cell adhesion|central nervous system development|Notch signaling pathway	anchored to membrane|plasma membrane				skin(3)|lung(2)|breast(2)|pancreas(1)	8		all_cancers(2;0.000164)|all_epithelial(2;0.107)		Epithelial(13;0.000233)|all cancers(10;0.0013)|OV - Ovarian serous cystadenocarcinoma(96;0.0139)		GTTACCACCAAAAAGTCTCGT	0.453												
CCR5	1234	broad.mit.edu	37	3	46414783	46414783	+	Silent	SNP	C	T	T			TCGA-06-0882-01A-01W-0424-08	TCGA-06-0882-10A-01W-0424-08									Somatic	Phase_I	Capture				Illumina GAIIx	385a3692-3208-479f-9f39-37fb65501b80	4ed08351-1e32-42e5-b009-e2f723cedfc5	g.chr3:46414783C>T	uc003cpo.3	+	3	512	c.390C>T	c.(388-390)GTC>GTT	p.V130V	CCR5_uc010hjd.2_Silent_p.V130V	NM_001100168	NP_001093638	P51681	CCR5_HUMAN	chemokine (C-C motif) receptor 5	130	Cytoplasmic (Potential).				cell-cell signaling|cellular defense response|dendritic cell chemotaxis|elevation of cytosolic calcium ion concentration|entry into host cell|immune response|inflammatory response|initiation of viral infection	endosome|external side of plasma membrane|integral to plasma membrane	actin binding|C-C chemokine receptor activity|coreceptor activity|phosphatidylinositol phospholipase C activity			lung(4)|upper_aerodigestive_tract(1)|central_nervous_system(1)	6				BRCA - Breast invasive adenocarcinoma(193;0.00112)|KIRC - Kidney renal clear cell carcinoma(197;0.017)|Kidney(197;0.02)	Maraviroc(DB04835)	ACCTGGCTGTCGTCCATGCTG	0.478												
STAB1	23166	broad.mit.edu	37	3	52543899	52543899	+	Silent	SNP	C	T	T			TCGA-06-0882-01A-01W-0424-08	TCGA-06-0882-10A-01W-0424-08									Somatic	Phase_I	Capture				Illumina GAIIx	385a3692-3208-479f-9f39-37fb65501b80	4ed08351-1e32-42e5-b009-e2f723cedfc5	g.chr3:52543899C>T	uc003dej.2	+	23	2435	c.2361C>T	c.(2359-2361)GTC>GTT	p.V787V		NM_015136	NP_055951	Q9NY15	STAB1_HUMAN	stabilin 1 precursor	787	Extracellular (Potential).				cell adhesion|cell-cell signaling|defense response to bacterium|inflammatory response|negative regulation of angiogenesis|receptor-mediated endocytosis	integral to plasma membrane	bacterial cell surface binding|hyaluronic acid binding|low-density lipoprotein receptor activity|protein disulfide oxidoreductase activity|scavenger receptor activity			large_intestine(3)|upper_aerodigestive_tract(2)|central_nervous_system(1)|breast(1)|skin(1)|pancreas(1)	9				BRCA - Breast invasive adenocarcinoma(193;1.73e-05)|Kidney(197;0.00182)|KIRC - Kidney renal clear cell carcinoma(197;0.00205)|OV - Ovarian serous cystadenocarcinoma(275;0.0482)		GCGGCTGTGTCCATGGTCTCT	0.632												
KDR	3791	broad.mit.edu	37	4	55984940	55984940	+	Nonsense_Mutation	SNP	C	T	T			TCGA-06-0882-01A-01W-0424-08	TCGA-06-0882-10A-01W-0424-08									Somatic	Phase_I	Capture				Illumina GAIIx	385a3692-3208-479f-9f39-37fb65501b80	4ed08351-1e32-42e5-b009-e2f723cedfc5	g.chr4:55984940C>T	uc003has.2	-	3	491	c.189G>A	c.(187-189)TGG>TGA	p.W63*	KDR_uc003hat.1_Nonsense_Mutation_p.W63*|KDR_uc011bzx.1_Nonsense_Mutation_p.W63*	NM_002253	NP_002244	P35968	VGFR2_HUMAN	kinase insert domain receptor precursor	63	Ig-like C2-type 1.|Extracellular (Potential).				angiogenesis|cell differentiation|interspecies interaction between organisms|positive regulation of endothelial cell migration|positive regulation of endothelial cell proliferation|positive regulation of focal adhesion assembly|positive regulation of positive chemotaxis|regulation of cell shape	integral to plasma membrane	ATP binding|growth factor binding|Hsp90 protein binding|integrin binding|receptor signaling protein tyrosine kinase activity|vascular endothelial growth factor receptor activity			lung(16)|soft_tissue(4)|central_nervous_system(4)|large_intestine(2)|stomach(2)|skin(2)|ovary(2)|kidney(1)	33	all_cancers(7;0.0255)|all_lung(4;0.00175)|Lung NSC(11;0.00384)|all_epithelial(27;0.034)|Glioma(25;0.08)|all_neural(26;0.101)		Epithelial(7;0.189)		Sorafenib(DB00398)|Sunitinib(DB01268)	GATTATTGGGCCAAAGCCAGT	0.448			Mis		NSCLC|angiosarcoma				Familial_Infantile_Hemangioma	TSP Lung(20;0.16)		
HELT	391723	broad.mit.edu	37	4	185941817	185941817	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0882-01A-01W-0424-08	TCGA-06-0882-10A-01W-0424-08									Somatic	Phase_I	Capture				Illumina GAIIx	385a3692-3208-479f-9f39-37fb65501b80	4ed08351-1e32-42e5-b009-e2f723cedfc5	g.chr4:185941817C>T	uc011ckq.1	+	4	875	c.875C>T	c.(874-876)CCC>CTC	p.P292L	HELT_uc011cko.1_Missense_Mutation_p.P207L|HELT_uc003ixa.3_Missense_Mutation_p.P206L|HELT_uc011ckp.1_Missense_Mutation_p.P150L	NM_001029887	NP_001025058	A6NFD8	HELT_HUMAN	HES/HEY-like transcription factor	292	Pro-rich.						DNA binding				0		all_lung(41;9.65e-12)|Lung NSC(41;1.64e-11)|Colorectal(36;0.0215)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|Prostate(90;0.0283)|all_hematologic(60;0.0749)		all cancers(43;8.92e-26)|Epithelial(43;3.02e-23)|OV - Ovarian serous cystadenocarcinoma(60;2.59e-11)|Colorectal(24;4.79e-05)|BRCA - Breast invasive adenocarcinoma(30;7.72e-05)|GBM - Glioblastoma multiforme(59;0.000274)|COAD - Colon adenocarcinoma(29;0.000362)|STAD - Stomach adenocarcinoma(60;0.000756)|LUSC - Lung squamous cell carcinoma(40;0.00902)|READ - Rectum adenocarcinoma(43;0.155)		CAGCACAGCCCCTTCCTGACA	0.736												
KDM1B	221656	broad.mit.edu	37	6	18213891	18213891	+	Missense_Mutation	SNP	C	A	A			TCGA-06-0882-01A-01W-0424-08	TCGA-06-0882-10A-01W-0424-08									Somatic	Phase_I	Capture				Illumina GAIIx	385a3692-3208-479f-9f39-37fb65501b80	4ed08351-1e32-42e5-b009-e2f723cedfc5	g.chr6:18213891C>A	uc003nco.1	+	12	1454	c.1379C>A	c.(1378-1380)GCC>GAC	p.A460D	KDM1B_uc003ncn.1_Missense_Mutation_p.A431D|KDM1B_uc003ncp.1_Missense_Mutation_p.A16D|KDM1B_uc003ncq.1_Missense_Mutation_p.A16D	NM_153042	NP_694587	Q8NB78	KDM1B_HUMAN	amine oxidase (flavin containing) domain 1	663					multicellular organismal development|regulation of DNA methylation|regulation of gene expression by genetic imprinting|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	histone demethylase activity (H3-dimethyl-K4 specific)|histone demethylase activity (H3-monomethyl-K4 specific)|oxidoreductase activity|zinc ion binding			skin(1)	1						TTGCAGATTGCCTTGCAATTT	0.463												
VPS52	6293	broad.mit.edu	37	6	33232605	33232605	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0882-01A-01W-0424-08	TCGA-06-0882-10A-01W-0424-08									Somatic	Phase_I	Capture				Illumina GAIIx	385a3692-3208-479f-9f39-37fb65501b80	4ed08351-1e32-42e5-b009-e2f723cedfc5	g.chr6:33232605G>A	uc003odm.1	-	13	1564	c.1354C>T	c.(1354-1356)CGG>TGG	p.R452W	VPS52_uc003odn.1_Missense_Mutation_p.R263W	NM_022553	NP_072047	Q8N1B4	VPS52_HUMAN	vacuolar protein sorting 52	452					protein transport	endosome membrane|Golgi apparatus				ovary(4)|skin(1)	5						TTACGGAACCGGAGAACAATG	0.483												
TFAP2B	7021	broad.mit.edu	37	6	50810943	50810943	+	Silent	SNP	C	A	A			TCGA-06-0882-01A-01W-0424-08	TCGA-06-0882-10A-01W-0424-08									Somatic	Phase_I	Capture				Illumina GAIIx	385a3692-3208-479f-9f39-37fb65501b80	4ed08351-1e32-42e5-b009-e2f723cedfc5	g.chr6:50810943C>A	uc003pag.2	+	7	1387	c.1221C>A	c.(1219-1221)GCC>GCA	p.A407A		NM_003221	NP_003212	Q92481	AP2B_HUMAN	transcription factor AP-2 beta	407				QLCKEFTDLLAQDRTPIGNSRPSPILEPGIQSCLTHFSLIT HGFGAPAICAALTALQNYLTEALKGMDKMFLNNTTTNRHTS GEGPGSKTGDKEEKHRK -> GNFVKNLRIYWRRTGHR (in Ref. 1; CAA71047).	nervous system development|positive regulation of transcription from RNA polymerase II promoter		protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity				0	Lung NSC(77;0.156)					GCTTCGGCGCCCCGGCCATTT	0.627												
TRIP6	7205	broad.mit.edu	37	7	100466151	100466151	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0882-01A-01W-0424-08	TCGA-06-0882-10A-01W-0424-08									Somatic	Phase_I	Capture				Illumina GAIIx	385a3692-3208-479f-9f39-37fb65501b80	4ed08351-1e32-42e5-b009-e2f723cedfc5	g.chr7:100466151C>T	uc003uww.2	+	4	568	c.398C>T	c.(397-399)ACG>ATG	p.T133M	TRIP6_uc010lhk.1_RNA	NM_003302	NP_003293	Q15654	TRIP6_HUMAN	thyroid receptor-interacting protein 6	133					focal adhesion assembly|positive regulation of cell migration|regulation of transcription, DNA-dependent|release of cytoplasmic sequestered NF-kappaB|transcription, DNA-dependent	cytoplasm|cytoskeleton|focal adhesion|nucleus	identical protein binding|interleukin-1 receptor binding|kinase binding|thyroid hormone receptor binding|zinc ion binding			central_nervous_system(2)	2	Lung NSC(181;0.041)|all_lung(186;0.0581)					GCCTACCGCACGGGCTCCCTG	0.637												
GRM8	2918	broad.mit.edu	37	7	126086220	126086220	+	Silent	SNP	G	A	A			TCGA-06-0882-01A-01W-0424-08	TCGA-06-0882-10A-01W-0424-08									Somatic	Phase_I	Capture				Illumina GAIIx	385a3692-3208-479f-9f39-37fb65501b80	4ed08351-1e32-42e5-b009-e2f723cedfc5	g.chr7:126086220G>A	uc003vlr.2	-	9	2948	c.2637C>T	c.(2635-2637)GGC>GGT	p.G879G	GRM8_uc003vls.2_RNA|GRM8_uc011kof.1_RNA|GRM8_uc003vlt.2_Silent_p.G879G|GRM8_uc010lkz.1_RNA	NM_000845	NP_000836	O00222	GRM8_HUMAN	glutamate receptor, metabotropic 8 isoform a	879	Cytoplasmic (Potential).				negative regulation of cAMP biosynthetic process|sensory perception of smell|visual perception	integral to plasma membrane				lung(15)|ovary(5)|pancreas(1)|breast(1)|skin(1)	23		Prostate(267;0.186)			L-Glutamic Acid(DB00142)	TTTTCACCTCGCCATTTGGTC	0.453										HNSCC(24;0.065)		
RAB11FIP1	80223	broad.mit.edu	37	8	37732071	37732071	+	Silent	SNP	G	A	A			TCGA-06-0882-01A-01W-0424-08	TCGA-06-0882-10A-01W-0424-08									Somatic	Phase_I	Capture				Illumina GAIIx	385a3692-3208-479f-9f39-37fb65501b80	4ed08351-1e32-42e5-b009-e2f723cedfc5	g.chr8:37732071G>A	uc003xkm.1	-	3	1628	c.1584C>T	c.(1582-1584)TCC>TCT	p.S528S	RAB11FIP1_uc010lvz.1_Silent_p.S376S|RAB11FIP1_uc003xkn.1_Silent_p.S528S|RAB11FIP1_uc003xkl.1_5'Flank|RAB11FIP1_uc003xko.1_5'Flank|RAB11FIP1_uc003xkp.1_Silent_p.S376S	NM_001002814	NP_001002814	Q6WKZ4	RFIP1_HUMAN	RAB11 family interacting protein 1 isoform 3	528					protein transport	centrosome|phagocytic vesicle membrane|recycling endosome	protein binding			ovary(1)|central_nervous_system(1)|skin(1)	3		Lung NSC(58;0.118)|all_lung(54;0.195)	LUSC - Lung squamous cell carcinoma(8;3.62e-11)			CCCTCGGAGAGGAAATTGGAG	0.547												
MID2	11043	broad.mit.edu	37	X	107160914	107160914	+	Missense_Mutation	SNP	G	T	T			TCGA-06-0882-01A-01W-0424-08	TCGA-06-0882-10A-01W-0424-08									Somatic	Phase_I	Capture				Illumina GAIIx	385a3692-3208-479f-9f39-37fb65501b80	4ed08351-1e32-42e5-b009-e2f723cedfc5	g.chrX:107160914G>T	uc004enl.2	+	7	1953	c.1380G>T	c.(1378-1380)GAG>GAT	p.E460D	MID2_uc004enk.2_Intron	NM_012216	NP_036348	Q9UJV3	TRIM1_HUMAN	midline 2 isoform 1	460	Fibronectin type-III.					centrosome|microtubule	ligase activity|zinc ion binding			ovary(1)	1						TGTGGCCAGAGATAAGGAAAT	0.468