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	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	t_alt_count	t_ref_count	validation_status	validation_method	validation_tumor_sample	validation_alt_allele	filter
PODN	127435	broad.mit.edu	37	1	53544621	53544621	+	Missense_Mutation	SNP	T	A	A			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:53544621T>A	uc001cuv.2	+	8	1590	c.1583T>A	c.(1582-1584)CTG>CAG	p.L528Q	PODN_uc001cuw.2_Missense_Mutation_p.L509Q|PODN_uc010onr.1_Missense_Mutation_p.L509Q|PODN_uc010ons.1_Missense_Mutation_p.L386Q	NM_153703	NP_714914	Q7Z5L7	PODN_HUMAN	podocan	480	LRR 16.				negative regulation of cell migration|negative regulation of cell proliferation	cytoplasm|extracellular space|proteinaceous extracellular matrix	collagen binding			ovary(1)|pancreas(1)	2						CTGCGTGAGCTGTACCTCACC	0.667													6	5	---	---	---	---	PASS
LRRC42	115353	broad.mit.edu	37	1	54428065	54428065	+	Missense_Mutation	SNP	G	C	C			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:54428065G>C	uc001cwj.1	+	6	1110	c.910G>C	c.(910-912)GAG>CAG	p.E304Q	LRRC42_uc001cwl.1_Missense_Mutation_p.E304Q|LRRC42_uc001cwk.1_Missense_Mutation_p.E304Q|LRRC42_uc009vzm.1_Missense_Mutation_p.E304Q	NM_052940	NP_443172	Q9Y546	LRC42_HUMAN	leucine rich repeat containing 42	304											0						CTGCAAGACAGAGGGCTGGGC	0.443													11	37	---	---	---	---	PASS
DAB1	1600	broad.mit.edu	37	1	57610988	57610988	+	Missense_Mutation	SNP	C	A	A			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:57610988C>A	uc001cys.1	-	5	856	c.182G>T	c.(181-183)TGT>TTT	p.C61F	DAB1_uc001cyt.1_Missense_Mutation_p.C61F|DAB1_uc001cyq.1_Missense_Mutation_p.C61F|DAB1_uc001cyr.1_Missense_Mutation_p.C61F|DAB1_uc009vzw.1_Missense_Mutation_p.C61F|DAB1_uc009vzx.1_Missense_Mutation_p.C61F	NM_021080	NP_066566	O75553	DAB1_HUMAN	disabled homolog 1	61	PID.				cell differentiation|nervous system development					skin(2)|ovary(1)	3						GGAATCTTGACATAACTTGTC	0.393													84	50	---	---	---	---	PASS
LRRC7	57554	broad.mit.edu	37	1	70257828	70257828	+	Missense_Mutation	SNP	G	C	C			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:70257828G>C	uc001dep.2	+	2	322	c.292G>C	c.(292-294)GAC>CAC	p.D98H	LRRC7_uc001deo.1_Missense_Mutation_p.D136H|LRRC7_uc009wbg.2_5'UTR	NM_020794	NP_065845	Q96NW7	LRRC7_HUMAN	leucine rich repeat containing 7	98	LRR 4.					centrosome|focal adhesion|nucleolus	protein binding			ovary(9)|breast(2)|central_nervous_system(2)|liver(1)	14						TAAAGAACTCGACATCAGTAA	0.299													78	70	---	---	---	---	PASS
HHLA3	11147	broad.mit.edu	37	1	70820859	70820859	+	Missense_Mutation	SNP	G	A	A			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:70820859G>A	uc001dfa.2	+	1	367	c.225G>A	c.(223-225)ATG>ATA	p.M75I	ANKRD13C_uc001dex.3_5'Flank|ANKRD13C_uc009wbk.2_5'Flank|ANKRD13C_uc001dey.3_5'Flank|HHLA3_uc010oqp.1_Intron|HHLA3_uc001dfb.2_Intron|HHLA3_uc001dfc.2_Intron	NM_001036645	NP_001031722	Q9XRX5	HHLA3_HUMAN	HERV-H LTR-associating 3 isoform 2	75							protein binding				0						gaagaggaatgaaggccaaac	0.204													9	15	---	---	---	---	PASS
CTH	1491	broad.mit.edu	37	1	70895467	70895467	+	Intron	SNP	G	T	T			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:70895467G>T	uc001dfd.2	+						CTH_uc009wbl.1_Intron|CTH_uc001dfe.2_Intron|CTH_uc010oqq.1_Intron	NM_001902	NP_001893	P32929	CGL_HUMAN	cystathionase isoform 1						cysteine biosynthetic process|hydrogen sulfide biosynthetic process|protein homotetramerization|protein-pyridoxal-5-phosphate linkage via peptidyl-N6-pyridoxal phosphate-L-lysine	cytoplasm|nucleus	cystathionine gamma-lyase activity|L-cysteine desulfhydrase activity|pyridoxal phosphate binding			lung(1)	1					L-Cysteine(DB00151)|Pyridoxal Phosphate(DB00114)	TAAAAAACTTGTTCTTTCAGC	0.303													47	40	---	---	---	---	PASS
LRRIQ3	127255	broad.mit.edu	37	1	74649223	74649223	+	Missense_Mutation	SNP	C	A	A			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:74649223C>A	uc001dfy.3	-	2	338	c.146G>T	c.(145-147)TGC>TTC	p.C49F	LRRIQ3_uc001dfz.3_RNA	NM_001105659	NP_001099129	A6PVS8	LRIQ3_HUMAN	leucine-rich repeats and IQ motif containing 3	49										ovary(2)	2						aagagagatgcaagactgcaa	0.149													57	40	---	---	---	---	PASS
PDE4DIP	9659	broad.mit.edu	37	1	144863397	144863397	+	Silent	SNP	T	C	C			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144863397T>C	uc001elw.3	-	37	6297	c.6006A>G	c.(6004-6006)AAA>AAG	p.K2002K	NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Silent_p.K1896K|PDE4DIP_uc001elv.3_Silent_p.K1009K|PDE4DIP_uc001ema.2_3'UTR	NM_014644	NP_055459	Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein isoform	2002	Potential.				cellular protein complex assembly	centrosome|Golgi apparatus|myofibril|nucleus	enzyme binding			ovary(4)|haematopoietic_and_lymphoid_tissue(1)	5				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		AGAGCTGCTGTTTCTCTTCAC	0.527			T	PDGFRB	MPD								81	288	---	---	---	---	PASS
ANP32E	81611	broad.mit.edu	37	1	150193072	150193072	+	Intron	SNP	G	T	T			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150193072G>T	uc001etw.2	-						ANP32E_uc010pbt.1_Intron|ANP32E_uc010pbu.1_Intron|ANP32E_uc010pbv.1_Intron|ANP32E_uc001etv.3_Intron	NM_030920	NP_112182	Q9BTT0	AN32E_HUMAN	acidic (leucine-rich) nuclear phosphoprotein 32							cytoplasmic membrane-bounded vesicle|nucleus	phosphatase inhibitor activity				0	Lung NSC(24;7.29e-29)|Breast(34;0.00211)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.171)			TTCTTAAAGAGTGGAAAGAAA	0.338													77	302	---	---	---	---	PASS
HRNR	388697	broad.mit.edu	37	1	152191550	152191550	+	Missense_Mutation	SNP	G	A	A			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152191550G>A	uc001ezt.1	-	3	2631	c.2555C>T	c.(2554-2556)TCA>TTA	p.S852L		NM_001009931	NP_001009931	Q86YZ3	HORN_HUMAN	hornerin	852	9.				keratinization		calcium ion binding|protein binding			skin(2)|ovary(1)	3	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			GCCGGAGCTTGATGACTGCCC	0.572													21	71	---	---	---	---	PASS
BCAN	63827	broad.mit.edu	37	1	156618424	156618424	+	Silent	SNP	G	A	A			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156618424G>A	uc001fpp.2	+	6	1170	c.834G>A	c.(832-834)CAG>CAA	p.Q278Q	BCAN_uc001fpo.2_Silent_p.Q278Q	NM_021948	NP_068767	Q96GW7	PGCB_HUMAN	brevican isoform 1	278	Link 2.				cell adhesion	anchored to membrane|proteinaceous extracellular matrix	hyaluronic acid binding|sugar binding			ovary(1)|pancreas(1)	2	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					CGTACTGCCAGGAGCGGGGTG	0.527													46	173	---	---	---	---	PASS
VANGL2	57216	broad.mit.edu	37	1	160389286	160389286	+	Silent	SNP	G	A	A			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160389286G>A	uc001fwb.1	+	5	986	c.687G>A	c.(685-687)GTG>GTA	p.V229V	VANGL2_uc001fwc.1_Silent_p.V229V	NM_020335	NP_065068	Q9ULK5	VANG2_HUMAN	vang-like 2	229	Helical; Name=4; (Potential).				apical protein localization|heart looping|nonmotile primary cilium assembly	apical plasma membrane|integral to membrane				ovary(1)	1	all_cancers(52;1.08e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			TTCTTTTCGTGCACTACCTGG	0.647													24	97	---	---	---	---	PASS
HSPA6	3310	broad.mit.edu	37	1	161495444	161495444	+	Missense_Mutation	SNP	G	C	C			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161495444G>C	uc001gap.2	+	2	1656	c.996G>C	c.(994-996)CAG>CAC	p.Q332H	HSPA6_uc001gaq.2_Missense_Mutation_p.Q332H	NM_002155	NP_002146	P17066	HSP76_HUMAN	heat shock 70kDa protein 6 (HSP70B')	332					response to unfolded protein		ATP binding			skin(1)	1	all_cancers(52;4.89e-16)|all_hematologic(112;0.0207)		BRCA - Breast invasive adenocarcinoma(70;0.00376)			ACAAGGCCCAGATTCATGACG	0.602													6	50	---	---	---	---	PASS
FAM5C	339479	broad.mit.edu	37	1	190067570	190067570	+	Missense_Mutation	SNP	T	A	A			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:190067570T>A	uc001gse.1	-	8	2111	c.1879A>T	c.(1879-1881)ATC>TTC	p.I627F	FAM5C_uc010pot.1_Missense_Mutation_p.I525F	NM_199051	NP_950252	Q76B58	FAM5C_HUMAN	family with sequence similarity 5, member C	627						extracellular region				lung(2)|ovary(1)|kidney(1)|skin(1)	5	Prostate(682;0.198)					CTCAGGTAGATGTGTACTGTC	0.463													125	414	---	---	---	---	PASS
CACNA1S	779	broad.mit.edu	37	1	201030449	201030449	+	Silent	SNP	G	C	C			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:201030449G>C	uc001gvv.2	-	25	3428	c.3201C>G	c.(3199-3201)ACC>ACG	p.T1067T		NM_000069	NP_000060	Q13698	CAC1S_HUMAN	calcium channel, voltage-dependent, L type,	1067	Cytoplasmic (Potential).|Dihydropyridine binding (By similarity).|III.				axon guidance	I band|T-tubule|voltage-gated calcium channel complex	high voltage-gated calcium channel activity			ovary(3)|central_nervous_system(1)|skin(1)	5					Magnesium Sulfate(DB00653)|Verapamil(DB00661)	GCTCCTGGAAGGTGACAATGA	0.527													22	81	---	---	---	---	PASS
ZC3H11A	9877	broad.mit.edu	37	1	203816789	203816789	+	Missense_Mutation	SNP	G	C	C	rs142558234		TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:203816789G>C	uc001hac.2	+	15	2136	c.1520G>C	c.(1519-1521)CGG>CCG	p.R507P	ZC3H11A_uc001had.2_Missense_Mutation_p.R507P|ZC3H11A_uc001hae.2_Missense_Mutation_p.R507P|ZC3H11A_uc001haf.2_Missense_Mutation_p.R507P|ZC3H11A_uc010pqm.1_Missense_Mutation_p.R453P|ZC3H11A_uc001hag.1_Missense_Mutation_p.R507P	NM_014827	NP_055642	O75152	ZC11A_HUMAN	zinc finger CCCH-type containing 11A	507							nucleic acid binding|protein binding|zinc ion binding			lung(1)|central_nervous_system(1)	2	all_cancers(21;0.0904)|all_epithelial(62;0.234)		BRCA - Breast invasive adenocarcinoma(75;0.109)			GGGGCAAGGCGGCTGCTGCGA	0.537													24	137	---	---	---	---	PASS
PIK3C2B	5287	broad.mit.edu	37	1	204438582	204438582	+	Missense_Mutation	SNP	G	C	C			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:204438582G>C	uc001haw.2	-	3	828	c.349C>G	c.(349-351)CCC>GCC	p.P117A	PIK3C2B_uc010pqv.1_Missense_Mutation_p.P117A|PIK3C2B_uc001hax.1_Missense_Mutation_p.P117A|PIK3C2B_uc009xbd.1_RNA	NM_002646	NP_002637	O00750	P3C2B_HUMAN	phosphoinositide-3-kinase, class 2 beta	117	Interaction with GRB2.				cell communication|phosphatidylinositol-mediated signaling	endoplasmic reticulum|microsome|nucleus|phosphatidylinositol 3-kinase complex|plasma membrane	1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol binding|phosphatidylinositol-4-phosphate 3-kinase activity|protein binding			lung(2)|breast(2)|stomach(1)|prostate(1)|central_nervous_system(1)	7	all_cancers(21;0.00347)|all_neural(3;0.0218)|Glioma(3;0.0382)|all_epithelial(62;0.171)|Breast(84;0.179)|Prostate(682;0.227)		GBM - Glioblastoma multiforme(2;2.69e-45)|all cancers(3;1.66e-30)|KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.143)|Epithelial(59;0.193)			TTGGGCCAGGGATCTGAGCCA	0.572													48	58	---	---	---	---	PASS
NUCKS1	64710	broad.mit.edu	37	1	205687487	205687487	+	Missense_Mutation	SNP	T	C	C			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:205687487T>C	uc001hdb.2	-	7	913	c.653A>G	c.(652-654)AAG>AGG	p.K218R		NM_022731	NP_073568	Q9H1E3	NUCKS_HUMAN	nuclear casein kinase and cyclin-dependent	218						nucleus					0	Breast(84;0.07)		BRCA - Breast invasive adenocarcinoma(75;0.0194)			AGATGTTTTCTTTTCTGGCGG	0.517													236	316	---	---	---	---	PASS
CENPF	1063	broad.mit.edu	37	1	214826228	214826228	+	Missense_Mutation	SNP	A	T	T			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:214826228A>T	uc001hkm.2	+	16	8392	c.8218A>T	c.(8218-8220)AGT>TGT	p.S2740C		NM_016343	NP_057427	P49454	CENPF_HUMAN	centromere protein F	2836	Potential.|Sufficient for self-association.|Sufficient for centromere localization.				cell differentiation|cell division|cell proliferation|DNA replication|G2 phase of mitotic cell cycle|kinetochore assembly|metaphase plate congression|mitotic cell cycle spindle assembly checkpoint|mitotic prometaphase|muscle organ development|negative regulation of transcription, DNA-dependent|protein transport|regulation of G2/M transition of mitotic cell cycle|regulation of striated muscle tissue development|response to drug	condensed chromosome outer kinetochore|cytosol|midbody|nuclear envelope|nuclear matrix|perinuclear region of cytoplasm|spindle pole	chromatin binding|dynein binding|protein C-terminus binding|protein homodimerization activity|transcription factor binding			ovary(6)|central_nervous_system(4)|large_intestine(2)|skin(1)	13				all cancers(67;0.00836)|OV - Ovarian serous cystadenocarcinoma(81;0.00855)|GBM - Glioblastoma multiforme(131;0.0694)|Epithelial(68;0.0833)		AGAATGTCTCAGTTCACAGAA	0.333													133	148	---	---	---	---	PASS
ITPKB	3707	broad.mit.edu	37	1	226829751	226829751	+	Missense_Mutation	SNP	G	C	C			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:226829751G>C	uc010pvo.1	-	5	2662	c.2322C>G	c.(2320-2322)ATC>ATG	p.I774M		NM_002221	NP_002212	P27987	IP3KB_HUMAN	1D-myo-inositol-trisphosphate 3-kinase B	774	Calmodulin-binding (By similarity).						ATP binding|calmodulin binding|inositol trisphosphate 3-kinase activity			ovary(4)|central_nervous_system(1)	5		Prostate(94;0.0773)				GGTCCACCTCGATCATCTTCT	0.627													136	163	---	---	---	---	PASS
RYR2	6262	broad.mit.edu	37	1	237604779	237604779	+	Missense_Mutation	SNP	G	A	A			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:237604779G>A	uc001hyl.1	+	13	1286	c.1166G>A	c.(1165-1167)CGT>CAT	p.R389H		NM_001035	NP_001026	Q92736	RYR2_HUMAN	cardiac muscle ryanodine receptor	389	Cytoplasmic (By similarity).|MIR 5.				cardiac muscle contraction|detection of calcium ion|induction of apoptosis by ionic changes|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum|response to caffeine|response to hypoxia|response to redox state	calcium channel complex|cytosol|plasma membrane|plasma membrane enriched fraction|sarcoplasmic reticulum membrane	calcium ion binding|calmodulin binding|identical protein binding|protein kinase A catalytic subunit binding|protein kinase A regulatory subunit binding|receptor activity|ryanodine-sensitive calcium-release channel activity|suramin binding			ovary(17)|large_intestine(6)|central_nervous_system(6)|pancreas(3)|breast(1)	33	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			TCTATACAACGTAAGGTAAGG	0.358													38	103	---	---	---	---	PASS
SDCCAG8	10806	broad.mit.edu	37	1	243493836	243493836	+	Intron	SNP	T	C	C			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:243493836T>C	uc001hzw.2	+						SDCCAG8_uc010pyk.1_Intron|SDCCAG8_uc010pyl.1_Intron|SDCCAG8_uc001hzx.2_Intron	NM_006642	NP_006633	Q86SQ7	SDCG8_HUMAN	serologically defined colon cancer antigen 8						establishment of cell polarity|G2/M transition of mitotic cell cycle|tube formation	cell-cell junction|centriole|cytosol	protein binding				0	all_cancers(71;0.000545)|all_epithelial(71;0.000509)|all_lung(81;0.0821)|Ovarian(71;0.0919)|all_neural(11;0.101)|Breast(184;0.218)	all_cancers(173;0.00395)	all cancers(7;1.58e-07)|GBM - Glioblastoma multiforme(7;5.12e-06)|OV - Ovarian serous cystadenocarcinoma(106;0.00392)	COAD - Colon adenocarcinoma(196;0.145)		TGTTCTATCCTGGCAGGCTTT	0.388													18	104	---	---	---	---	PASS
VN1R5	317705	broad.mit.edu	37	1	247419831	247419831	+	Nonsense_Mutation	SNP	T	A	A			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247419831T>A	uc010pyu.1	+	2	458	c.458T>A	c.(457-459)TTG>TAG	p.L153*		NM_173858	NP_776257	Q7Z5H4	VN1R5_HUMAN	vomeronasal 1 receptor 5	153	Extracellular (Potential).				response to pheromone	integral to membrane|plasma membrane	pheromone receptor activity				0	all_cancers(71;5.7e-05)|all_epithelial(71;1.03e-05)|Breast(184;0.0226)|Ovarian(71;0.0377)|all_lung(81;0.0607)|Lung NSC(105;0.0661)	all_cancers(173;0.0314)	OV - Ovarian serous cystadenocarcinoma(106;0.00854)			ATCTTCTCCTTGGCAAAGCTC	0.488													79	239	---	---	---	---	PASS
OR2G3	81469	broad.mit.edu	37	1	247769642	247769642	+	Missense_Mutation	SNP	A	T	T			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247769642A>T	uc010pyz.1	+	1	755	c.755A>T	c.(754-756)TAT>TTT	p.Y252F		NM_001001914	NP_001001914	Q8NGZ4	OR2G3_HUMAN	olfactory receptor, family 2, subfamily G,	252	Helical; Name=6; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			central_nervous_system(1)	1	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)			ATTATATTCTATGGCACCATA	0.488													68	78	---	---	---	---	PASS
TRIM58	25893	broad.mit.edu	37	1	248039548	248039548	+	Missense_Mutation	SNP	A	C	C			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248039548A>C	uc001ido.2	+	6	1266	c.1218A>C	c.(1216-1218)GAA>GAC	p.E406D	OR2W3_uc001idp.1_Intron	NM_015431	NP_056246	Q8NG06	TRI58_HUMAN	tripartite motif-containing 58	406	B30.2/SPRY.					intracellular	zinc ion binding	p.E406*(1)		skin(3)|ovary(1)|pancreas(1)|lung(1)|central_nervous_system(1)	7	all_cancers(71;0.000139)|all_epithelial(71;1.58e-05)|Breast(184;0.0117)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)	all_cancers(173;0.0286)	OV - Ovarian serous cystadenocarcinoma(106;0.0319)			TCCAACTGGAAAGTCCTCGCT	0.488													103	362	---	---	---	---	PASS
OR2T1	26696	broad.mit.edu	37	1	248570350	248570350	+	Missense_Mutation	SNP	A	G	G			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248570350A>G	uc010pzm.1	+	1	1055	c.1055A>G	c.(1054-1056)AAG>AGG	p.K352R		NM_030904	NP_112166	O43869	OR2T1_HUMAN	olfactory receptor, family 2, subfamily T,	352	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			pancreas(1)	1	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			GGAGCTCTGAAGAGGGCCTTG	0.522													69	375	---	---	---	---	PASS
DYNC2LI1	51626	broad.mit.edu	37	2	44032358	44032358	+	Silent	SNP	C	T	T			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:44032358C>T	uc002rtk.2	+	12	1062	c.966C>T	c.(964-966)GTC>GTT	p.V322V	DYNC2LI1_uc002rtj.2_Silent_p.V322V|DYNC2LI1_uc002rtl.2_Silent_p.V323V|DYNC2LI1_uc010ynz.1_Silent_p.V196V	NM_016008	NP_057092	Q8TCX1	DC2L1_HUMAN	dynein 2 light intermediate chain isoform 1	322						apical part of cell|axonemal dynein complex|cilium axoneme|cytoplasm|microtubule|motile primary cilium	motor activity			ovary(1)	1		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)				AAAATGAAGTCGATGAGATGA	0.378													64	79	---	---	---	---	PASS
ETAA1	54465	broad.mit.edu	37	2	67630366	67630366	+	Silent	SNP	A	T	T			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:67630366A>T	uc002sdz.1	+	5	691	c.552A>T	c.(550-552)ACA>ACT	p.T184T		NM_019002	NP_061875	Q9NY74	ETAA1_HUMAN	ETAA16 protein	184	Potential.					cytoplasm|nucleus				ovary(3)|large_intestine(1)	4						GGTTAAAAACACAAAGTCAAG	0.259													29	51	---	---	---	---	PASS
DUSP11	8446	broad.mit.edu	37	2	73993667	73993667	+	Silent	SNP	G	A	A			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:73993667G>A	uc002sjp.2	-	8	855	c.813C>T	c.(811-813)CTC>CTT	p.L271L		NM_003584	NP_003575	O75319	DUS11_HUMAN	dual specificity phosphatase 11	224					RNA processing	nucleus	protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity|RNA binding			skin(1)	1						CTGGTTGCATGAGATGTGCTG	0.418													76	215	---	---	---	---	PASS
VPS24	51652	broad.mit.edu	37	2	86769390	86769390	+	Missense_Mutation	SNP	C	G	G			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:86769390C>G	uc002srj.2	-	2	220	c.91G>C	c.(91-93)GAC>CAC	p.D31H	VPS24_uc002srk.2_Intron|VPS24_uc002srl.2_Missense_Mutation_p.D31H|VPS24_uc010ytl.1_Missense_Mutation_p.D60H	NM_016079	NP_057163	Q9Y3E7	CHMP3_HUMAN	vacuolar protein sorting 24 isoform 1	31	Potential.|Intramolecular interaction with C- terminus.				cell cycle|cell division|cellular membrane organization|endosome transport|protein transport	cytosol|late endosome membrane	protein binding			central_nervous_system(1)	1						ATTTGCCTGTCAACAACTCTC	0.328													21	137	---	---	---	---	PASS
CNGA3	1261	broad.mit.edu	37	2	99013489	99013489	+	Missense_Mutation	SNP	C	T	T			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:99013489C>T	uc002syt.2	+	8	2273	c.1856C>T	c.(1855-1857)GCG>GTG	p.A619V	CNGA3_uc002syu.2_Missense_Mutation_p.A601V|CNGA3_uc010fij.2_Missense_Mutation_p.A623V	NM_001298	NP_001289	Q16281	CNGA3_HUMAN	cyclic nucleotide gated channel alpha 3 isoform	619					signal transduction|visual perception	integral to membrane	cGMP binding			ovary(5)|upper_aerodigestive_tract(1)	6						CTGGCCAGGGCGGGCGCGGAC	0.622													9	31	---	---	---	---	PASS
MYO7B	4648	broad.mit.edu	37	2	128370181	128370181	+	Intron	SNP	C	G	G			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:128370181C>G	uc002top.2	+							NM_001080527	NP_001073996	Q6PIF6	MYO7B_HUMAN	myosin VIIB							apical plasma membrane|myosin complex	actin binding|ATP binding|motor activity			ovary(1)|pancreas(1)	2	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0753)		AGCCTCAGGTCAGTTCCCACT	0.632													9	15	---	---	---	---	PASS
SPOPL	339745	broad.mit.edu	37	2	139326626	139326626	+	Silent	SNP	A	T	T			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:139326626A>T	uc002tvh.2	+	11	1555	c.1155A>T	c.(1153-1155)CCA>CCT	p.P385P		NM_001001664	NP_001001664	Q6IQ16	SPOPL_HUMAN	speckle-type POZ protein-like	385						nucleus				skin(2)|breast(1)	3				BRCA - Breast invasive adenocarcinoma(221;0.0296)		TTGGCATTCCACGCAAACGGC	0.443													288	301	---	---	---	---	PASS
STK39	27347	broad.mit.edu	37	2	169023809	169023809	+	Missense_Mutation	SNP	C	A	A			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:169023809C>A	uc002uea.2	-	3	590	c.430G>T	c.(430-432)GGT>TGT	p.G144C		NM_013233	NP_037365	Q9UEW8	STK39_HUMAN	serine threonine kinase 39 (STE20/SPS1 homolog,	144	Protein kinase.				response to stress	cytoplasm|nucleus	ATP binding|protein binding|receptor signaling protein serine/threonine kinase activity			central_nervous_system(1)|skin(1)	2						ATCCACTTACCTCCACTTAGT	0.398													50	41	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179399114	179399114	+	Silent	SNP	C	T	T			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179399114C>T	uc010zfg.1	-	307	94748	c.94524G>A	c.(94522-94524)AAG>AAA	p.K31508K	uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Silent_p.K25203K|TTN_uc010zfi.1_Silent_p.K25136K|TTN_uc010zfj.1_Silent_p.K25011K	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	32435							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)			CTCTTTCTATCTTCTGCTTCA	0.458													35	145	---	---	---	---	PASS
STAT1	6772	broad.mit.edu	37	2	191845378	191845378	+	Missense_Mutation	SNP	C	T	T			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:191845378C>T	uc002usj.2	-	19	1988	c.1600G>A	c.(1600-1602)GAT>AAT	p.D534N	STAT1_uc010fse.1_Missense_Mutation_p.D534N|STAT1_uc002usk.2_Missense_Mutation_p.D534N|STAT1_uc002usl.2_Missense_Mutation_p.D536N|STAT1_uc010fsf.1_Missense_Mutation_p.D346N	NM_007315	NP_009330	P42224	STAT1_HUMAN	signal transducer and activator of transcription	534					activation of caspase activity|I-kappaB kinase/NF-kappaB cascade|interferon-gamma-mediated signaling pathway|interspecies interaction between organisms|regulation of interferon-gamma-mediated signaling pathway|regulation of type I interferon-mediated signaling pathway|response to virus|type I interferon-mediated signaling pathway|tyrosine phosphorylation of STAT protein	cytosol|nucleolus|nucleoplasm	calcium ion binding|protein binding|RNA polymerase II core promoter sequence-specific DNA binding|RNA polymerase II core promoter sequence-specific DNA binding transcription factor activity|signal transducer activity			lung(3)|breast(3)|central_nervous_system(2)|upper_aerodigestive_tract(1)|ovary(1)	10			OV - Ovarian serous cystadenocarcinoma(117;0.00434)|Epithelial(96;0.0555)|all cancers(119;0.141)		Fludarabine(DB01073)	ATGAGACCATCGGGGCTGGCG	0.433													16	64	---	---	---	---	PASS
PLCL1	5334	broad.mit.edu	37	2	198950527	198950527	+	Silent	SNP	G	A	A	rs144546582		TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:198950527G>A	uc010fsp.2	+	2	2577	c.2286G>A	c.(2284-2286)TCG>TCA	p.S762S	PLCL1_uc002uuv.3_Silent_p.S683S	NM_001114661	NP_001108133	Q15111	PLCL1_HUMAN	RecName: Full=Inactive phospholipase C-like protein 1;          Short=PLC-L1; AltName: Full=Phospholipase C-deleted in lung carcinoma; AltName: Full=Phospholipase C-related but catalytically inactive protein;          Short=PRIP;	762	C2.				intracellular signal transduction|lipid metabolic process	cytoplasm	calcium ion binding|phosphatidylinositol phospholipase C activity|signal transducer activity			ovary(1)|skin(1)	2					Quinacrine(DB01103)	CGGATTGTTCGGAACAAAGAA	0.423													56	173	---	---	---	---	PASS
AOX1	316	broad.mit.edu	37	2	201515770	201515770	+	Missense_Mutation	SNP	T	A	A			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:201515770T>A	uc002uvx.2	+	26	3022	c.2921T>A	c.(2920-2922)ATC>AAC	p.I974N	AOX1_uc010zhf.1_Missense_Mutation_p.I530N|AOX1_uc010fsu.2_Missense_Mutation_p.I340N	NM_001159	NP_001150	Q06278	ADO_HUMAN	aldehyde oxidase 1	974					inflammatory response|reactive oxygen species metabolic process	cytoplasm	2 iron, 2 sulfur cluster binding|aldehyde oxidase activity|flavin adenine dinucleotide binding|iron ion binding|NAD binding|xanthine dehydrogenase activity			ovary(4)|pancreas(1)|skin(1)	6					Brimonidine(DB00484)|Chlorpromazine(DB00477)|Famciclovir(DB00426)|Menadione(DB00170)|Methotrexate(DB00563)|NADH(DB00157)|Palonosetron(DB00377)|Penciclovir(DB00299)|Raloxifene(DB00481)|Zaleplon(DB00962)|Zonisamide(DB00909)	AAGAACCTAATCCAGTGTTGG	0.393													89	98	---	---	---	---	PASS
ERBB4	2066	broad.mit.edu	37	2	212543914	212543914	+	Intron	SNP	G	A	A			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:212543914G>A	uc002veg.1	-						ERBB4_uc002veh.1_Intron|ERBB4_uc010zji.1_Intron|ERBB4_uc010zjj.1_Intron|ERBB4_uc010fut.1_Intron	NM_005235	NP_005226	Q15303	ERBB4_HUMAN	v-erb-a erythroblastic leukemia viral oncogene						cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent|transmembrane receptor protein tyrosine kinase signaling pathway	basolateral plasma membrane|cytoplasm|integral to membrane|nucleus	ATP binding|protein binding|receptor signaling protein tyrosine kinase activity|transmembrane receptor protein tyrosine kinase activity			lung(21)|skin(5)|stomach(2)|breast(2)|upper_aerodigestive_tract(1)|large_intestine(1)|pancreas(1)	33		Renal(323;0.06)|Lung NSC(271;0.197)		UCEC - Uterine corpus endometrioid carcinoma (47;0.214)|Epithelial(149;5.86e-06)|all cancers(144;2.95e-05)|Lung(261;0.00244)|LUSC - Lung squamous cell carcinoma(224;0.00266)		CAGCAGCTGTGAAACACCAAA	0.438										TSP Lung(8;0.080)			11	37	---	---	---	---	PASS
COL4A4	1286	broad.mit.edu	37	2	227973933	227973933	+	Intron	SNP	T	A	A			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:227973933T>A	uc010zlt.1	-							NM_000092	NP_000083	P53420	CO4A4_HUMAN	alpha 4 type IV collagen precursor						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)		AGCAGTGCTGTACTTACCACT	0.468													135	182	---	---	---	---	PASS
B3GNT7	93010	broad.mit.edu	37	2	232263482	232263482	+	Missense_Mutation	SNP	G	A	A			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:232263482G>A	uc002vrs.2	+	2	1232	c.1052G>A	c.(1051-1053)GGC>GAC	p.G351D		NM_145236	NP_660279	Q8NFL0	B3GN7_HUMAN	UDP-GlcNAc:betaGal	351	Lumenal (Potential).				protein glycosylation	Golgi membrane|integral to membrane	galactosyltransferase activity				0		Renal(207;0.025)|all_hematologic(139;0.094)|Acute lymphoblastic leukemia(138;0.164)|Medulloblastoma(418;0.232)		Epithelial(121;3.22e-11)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(119;0.0139)		AAGACTTTCGGCATCTCCCGG	0.637													8	44	---	---	---	---	PASS
CNTN4	152330	broad.mit.edu	37	3	3081782	3081782	+	Missense_Mutation	SNP	A	G	G			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:3081782A>G	uc003bpc.2	+	19	2446	c.2225A>G	c.(2224-2226)TAC>TGC	p.Y742C	CNTN4_uc003bpb.1_Missense_Mutation_p.Y413C|CNTN4_uc003bpe.2_Missense_Mutation_p.Y414C|CNTN4_uc003bpf.2_Missense_Mutation_p.Y413C|CNTN4_uc003bpg.2_5'UTR	NM_175607	NP_783200	Q8IWV2	CNTN4_HUMAN	contactin 4 isoform a precursor	742	Fibronectin type-III 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)		TTCCGGCCCTACGGTAAAATG	0.517													44	49	---	---	---	---	PASS
VHL	7428	broad.mit.edu	37	3	10183766	10183766	+	Missense_Mutation	SNP	C	G	G			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10183766C>G	uc003bvc.2	+	1	448	c.235C>G	c.(235-237)CGC>GGC	p.R79G	VHL_uc003bvd.2_Missense_Mutation_p.R79G	NM_000551	NP_000542	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor isoform 1	79			R -> P (in VHLD).		anti-apoptosis|cell morphogenesis|negative regulation of cell proliferation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of cell differentiation|positive regulation of transcription, DNA-dependent|protein stabilization|protein ubiquitination|proteolysis	cytosol|endoplasmic reticulum|membrane|mitochondrion|nucleus	protein binding|transcription factor binding	p.F76fs*80(2)|p.R79fs*80(2)|p.S72_V87>L(1)|p.R79R(1)|p.R60fs*35(1)|p.R79P(1)|p.R79_P81>P(1)|p.C77_R79del(1)|p.N78_R79insN(1)|p.R79H(1)|p.N78fs*80(1)|p.V74fs*77(1)|p.F76fs*81(1)|p.R79fs*52(1)|p.R79fs*88(1)		kidney(1273)|soft_tissue(24)|adrenal_gland(15)|large_intestine(13)|pancreas(5)|endometrium(4)|thyroid(3)|upper_aerodigestive_tract(3)|central_nervous_system(2)|lung(2)|pleura(1)|paratesticular_tissues(1)	1346				Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569)		CTTCTGCAATCGCAGTCCGCG	0.711		1	D|Mis|N|F|S		renal|hemangioma|pheochromocytoma	renal|hemangioma|pheochromocytoma			von_Hippel-Lindau_disease|Chuvash_Polycythemia_|Pheochromocytoma_(Adrenal)_Familial				5	9	---	---	---	---	PASS
EPM2AIP1	9852	broad.mit.edu	37	3	37032748	37032748	+	Silent	SNP	T	C	C			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:37032748T>C	uc003cgk.2	-	1	2048	c.1821A>G	c.(1819-1821)CCA>CCG	p.P607P	MLH1_uc011aye.1_5'Flank|MLH1_uc003cgl.2_5'Flank|MLH1_uc011ayb.1_5'Flank|MLH1_uc010hge.2_5'Flank|MLH1_uc003cgn.3_5'Flank|MLH1_uc011ayc.1_5'Flank|MLH1_uc011ayd.1_5'Flank|MLH1_uc003cgo.2_5'Flank	NM_014805	NP_055620	Q7L775	EPMIP_HUMAN	EPM2A interacting protein 1	607						endoplasmic reticulum					0						CAAAGCCTTATGGATTAGATT	0.368													44	65	---	---	---	---	PASS
CSRNP1	64651	broad.mit.edu	37	3	39185792	39185792	+	Nonsense_Mutation	SNP	G	A	A			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:39185792G>A	uc003cjg.2	-	4	830	c.616C>T	c.(616-618)CGA>TGA	p.R206*	CSRNP1_uc003cjh.2_Nonsense_Mutation_p.R206*	NM_033027	NP_149016	Q96S65	CSRN1_HUMAN	AXIN1 up-regulated 1	206					apoptosis|positive regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(4)|skin(1)	5						GCTCGACGTCGCCGGGCTGGG	0.632													58	54	---	---	---	---	PASS
KBTBD5	131377	broad.mit.edu	37	3	42729785	42729785	+	Missense_Mutation	SNP	A	G	G			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:42729785A>G	uc003clv.1	+	2	1404	c.1304A>G	c.(1303-1305)TAC>TGC	p.Y435C		NM_152393	NP_689606	Q2TBA0	KBTB5_HUMAN	kelch repeat and BTB (POZ) domain containing 5	435	Kelch 2.									ovary(1)	1				KIRC - Kidney renal clear cell carcinoma(284;0.214)		GTCATGTGCTACGACAGGCTG	0.647													15	13	---	---	---	---	PASS
KIF15	56992	broad.mit.edu	37	3	44882596	44882596	+	Missense_Mutation	SNP	C	A	A			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:44882596C>A	uc003cnx.3	+	29	3600	c.3451C>A	c.(3451-3453)CAT>AAT	p.H1151N	KIF15_uc010hiq.2_Missense_Mutation_p.H1054N|KIF15_uc010hir.2_Missense_Mutation_p.H199N	NM_020242	NP_064627	Q9NS87	KIF15_HUMAN	kinesin family member 15	1151	Potential.				blood coagulation|cell proliferation|microtubule-based movement|mitosis	centrosome|cytosol|microtubule|plus-end kinesin complex|spindle	ATP binding|DNA binding|microtubule motor activity			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;0.0099)|KIRC - Kidney renal clear cell carcinoma(197;0.0564)|Kidney(197;0.0707)		CTTTCAAACACATTTGGCAAA	0.338													20	41	---	---	---	---	PASS
BAP1	8314	broad.mit.edu	37	3	52443746	52443746	+	Silent	SNP	C	A	A			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52443746C>A	uc003ddx.2	-	2	166	c.51G>T	c.(49-51)CTG>CTT	p.L17L	PHF7_uc003ddy.2_5'Flank|PHF7_uc003ddz.2_5'Flank	NM_004656	NP_004647	Q92560	BAP1_HUMAN	BRCA1 associated protein-1	17					monoubiquitinated histone H2A deubiquitination|negative regulation of cell proliferation|protein K48-linked deubiquitination|regulation of cell cycle|regulation of cell growth|ubiquitin-dependent protein catabolic process	cytoplasm|nucleolus|PR-DUB complex	chromatin binding|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity	p.?(1)		pleura(32)|eye(28)|lung(2)|ovary(2)|breast(1)	65				BRCA - Breast invasive adenocarcinoma(193;1.72e-05)|Kidney(197;0.0018)|KIRC - Kidney renal clear cell carcinoma(197;0.00203)|OV - Ovarian serous cystadenocarcinoma(275;0.0277)		CTTCCACGAGCAGGGTGAAGA	0.692			N|Mis|F|S|O		uveal melanoma|breast|NSCLC								3	38	---	---	---	---	PASS
CRYBG3	131544	broad.mit.edu	37	3	97660112	97660112	+	Missense_Mutation	SNP	C	G	G			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:97660112C>G	uc003drx.2	+	17	2846	c.2782C>G	c.(2782-2784)CAG>GAG	p.Q928E	CRYBG3_uc010hoz.1_RNA	NM_153605	NP_705833			beta-gamma crystallin domain containing 3												0						AAAGAATACTCAGATCTGGTA	0.433													52	218	---	---	---	---	PASS
MORC1	27136	broad.mit.edu	37	3	108773739	108773739	+	Intron	SNP	T	C	C			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:108773739T>C	uc003dxl.2	-						MORC1_uc011bhn.1_Intron	NM_014429	NP_055244	Q86VD1	MORC1_HUMAN	MORC family CW-type zinc finger 1						cell differentiation|multicellular organismal development|spermatogenesis	nucleus	ATP binding|zinc ion binding			ovary(3)|skin(3)|breast(2)	8						TCTGAGAAAATATATGCATAT	0.303													39	100	---	---	---	---	PASS
KALRN	8997	broad.mit.edu	37	3	124351436	124351436	+	Missense_Mutation	SNP	G	T	T			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:124351436G>T	uc003ehg.2	+	35	5473	c.5346G>T	c.(5344-5346)AAG>AAT	p.K1782N	KALRN_uc003ehi.2_Missense_Mutation_p.K155N|KALRN_uc003ehk.2_Missense_Mutation_p.K85N|KALRN_uc003ehj.2_Missense_Mutation_p.K85N	NM_001024660	NP_001019831	O60229	KALRN_HUMAN	kalirin, RhoGEF kinase isoform 1	1782					apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|nervous system development|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|vesicle-mediated transport	actin cytoskeleton|cytosol	ATP binding|GTPase activator activity|metal ion binding|protein binding|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity			large_intestine(2)|ovary(2)|central_nervous_system(1)|skin(1)	6						ACAGCGGGAAGGCAGATGGAA	0.557													62	123	---	---	---	---	PASS
TRIM42	287015	broad.mit.edu	37	3	140407277	140407277	+	Missense_Mutation	SNP	C	A	A			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:140407277C>A	uc003eto.1	+	3	1944	c.1753C>A	c.(1753-1755)CAG>AAG	p.Q585K		NM_152616	NP_689829	Q8IWZ5	TRI42_HUMAN	tripartite motif-containing 42	585						intracellular	zinc ion binding			lung(2)|skin(2)|upper_aerodigestive_tract(1)|breast(1)|central_nervous_system(1)	7						CCAGTCTGTACAGAACAGCAG	0.577													71	123	---	---	---	---	PASS
PEX5L	51555	broad.mit.edu	37	3	179616027	179616027	+	Missense_Mutation	SNP	C	T	T			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:179616027C>T	uc003fki.1	-	3	231	c.101G>A	c.(100-102)GGC>GAC	p.G34D	PEX5L_uc011bqd.1_5'UTR|PEX5L_uc011bqe.1_Intron|PEX5L_uc011bqf.1_5'UTR|PEX5L_uc003fkj.1_Intron|PEX5L_uc010hxd.1_Missense_Mutation_p.G32D|PEX5L_uc011bqg.1_Missense_Mutation_p.G10D|PEX5L_uc011bqh.1_Intron	NM_016559	NP_057643	Q8IYB4	PEX5R_HUMAN	peroxisomal biogenesis factor 5-like	34					protein import into peroxisome matrix|regulation of cAMP-mediated signaling	cytosol|peroxisomal membrane	peroxisome matrix targeting signal-1 binding			ovary(3)|large_intestine(1)	4	all_cancers(143;3.94e-14)|Ovarian(172;0.0338)|Breast(254;0.183)		OV - Ovarian serous cystadenocarcinoma(80;1.75e-26)|GBM - Glioblastoma multiforme(14;0.000518)			CGCCCTAGAGCCTTTTCCCTA	0.418													80	160	---	---	---	---	PASS
IDUA	3425	broad.mit.edu	37	4	995294	995294	+	Missense_Mutation	SNP	G	A	A			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:995294G>A	uc003gby.2	+	5	620	c.532G>A	c.(532-534)GAG>AAG	p.E178K	IDUA_uc003gbz.2_RNA|IDUA_uc003gca.2_Missense_Mutation_p.E131K	NM_000203	NP_000194	P35475	IDUA_HUMAN	alpha-L-iduronidase precursor	178					disaccharide metabolic process	lysosome	cation binding|L-iduronidase activity				0			OV - Ovarian serous cystadenocarcinoma(23;0.0158)		Laronidase(DB00090)	GTGGAACTTCGAGACGTGGAA	0.597													40	135	---	---	---	---	PASS
IDUA	3425	broad.mit.edu	37	4	995327	995327	+	Missense_Mutation	SNP	G	C	C			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:995327G>C	uc003gby.2	+	5	653	c.565G>C	c.(565-567)GAC>CAC	p.D189H	IDUA_uc003gbz.2_RNA|IDUA_uc003gca.2_Missense_Mutation_p.D142H	NM_000203	NP_000194	P35475	IDUA_HUMAN	alpha-L-iduronidase precursor	189					disaccharide metabolic process	lysosome	cation binding|L-iduronidase activity				0			OV - Ovarian serous cystadenocarcinoma(23;0.0158)		Laronidase(DB00090)	CCACGACTTTGACAACGTCTC	0.602													39	107	---	---	---	---	PASS
DRD5	1816	broad.mit.edu	37	4	9784478	9784478	+	Missense_Mutation	SNP	C	A	A			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:9784478C>A	uc003gmb.3	+	1	1221	c.825C>A	c.(823-825)AGC>AGA	p.S275R		NM_000798	NP_000789	P21918	DRD5_HUMAN	dopamine receptor D5	275	Cytoplasmic (Potential).				activation of adenylate cyclase activity by dopamine receptor signaling pathway|activation of phospholipase C activity by dopamine receptor signaling pathway|cellular calcium ion homeostasis|negative regulation of NAD(P)H oxidase activity|reactive oxygen species metabolic process|synaptic transmission, dopaminergic	integral to plasma membrane				skin(1)	1					Apomorphine(DB00714)|Carphenazine(DB01038)|Fenoldopam(DB00800)|Zuclopenthixol(DB01624)	GCCGGAGCAGCGCAGCCTGCG	0.637													8	65	---	---	---	---	PASS
TECRL	253017	broad.mit.edu	37	4	65275039	65275039	+	Missense_Mutation	SNP	C	T	T			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:65275039C>T	uc003hcv.2	-	1	140	c.31G>A	c.(31-33)GAA>AAA	p.E11K	TECRL_uc003hcw.2_Missense_Mutation_p.E11K	NM_001010874	NP_001010874	Q5HYJ1	TECRL_HUMAN	steroid 5 alpha-reductase 2-like 2	11					lipid metabolic process	cytoplasm|integral to membrane	oxidoreductase activity, acting on the CH-CH group of donors				0						CTCTTGCGTTCCGAAGCGAGG	0.418													101	86	---	---	---	---	PASS
PDE5A	8654	broad.mit.edu	37	4	120419875	120419875	+	Missense_Mutation	SNP	C	T	T			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:120419875C>T	uc003idh.2	-	21	2664	c.2509G>A	c.(2509-2511)GAG>AAG	p.E837K	uc003ide.3_Intron|PDE5A_uc003idf.2_Missense_Mutation_p.E795K|PDE5A_uc003idg.2_Missense_Mutation_p.E785K	NM_001083	NP_001074	O76074	PDE5A_HUMAN	phosphodiesterase 5A isoform 1	837	Catalytic (By similarity).				platelet activation|signal transduction	cytosol	3',5'-cyclic-GMP phosphodiesterase activity|cGMP binding|zinc ion binding				0					Dipyridamole(DB00975)|Pentoxifylline(DB00806)|Sildenafil(DB00203)|Tadalafil(DB00820)|Theophylline(DB00277)|Vardenafil(DB00862)	AAACAGTCCTCTGACACGTGG	0.502													4	155	---	---	---	---	PASS
RXFP1	59350	broad.mit.edu	37	4	159559192	159559192	+	Missense_Mutation	SNP	A	G	G			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:159559192A>G	uc003ipz.2	+	13	1086	c.1004A>G	c.(1003-1005)CAA>CGA	p.Q335R	RXFP1_uc010iqj.1_Missense_Mutation_p.Q164R|RXFP1_uc011cja.1_Missense_Mutation_p.Q230R|RXFP1_uc010iqo.2_Intron|RXFP1_uc011cjb.1_Intron|RXFP1_uc010iqk.2_Missense_Mutation_p.Q203R|RXFP1_uc011cjc.1_Missense_Mutation_p.Q254R|RXFP1_uc011cjd.1_Missense_Mutation_p.Q254R|RXFP1_uc010iql.2_Missense_Mutation_p.Q179R|RXFP1_uc011cje.1_Missense_Mutation_p.Q362R|RXFP1_uc010iqm.2_Missense_Mutation_p.Q302R|RXFP1_uc011cjf.1_Missense_Mutation_p.Q205R|RXFP1_uc010iqn.2_Missense_Mutation_p.Q281R	NM_021634	NP_067647	Q9HBX9	RXFP1_HUMAN	relaxin/insulin-like family peptide receptor 1	335	Extracellular (Potential).|LRR 8.					integral to membrane|plasma membrane	G-protein coupled receptor activity|metal ion binding				0	all_hematologic(180;0.24)	Renal(120;0.0854)		COAD - Colon adenocarcinoma(41;0.0219)		CAGAAAATTCAAGCAAACCAA	0.289													18	62	---	---	---	---	PASS
ZFP42	132625	broad.mit.edu	37	4	188924632	188924632	+	Missense_Mutation	SNP	A	G	G			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:188924632A>G	uc003izg.1	+	3	916	c.671A>G	c.(670-672)AAA>AGA	p.K224R	ZFP42_uc003izh.1_Missense_Mutation_p.K224R|ZFP42_uc003izi.1_Missense_Mutation_p.K224R	NM_174900	NP_777560	Q96MM3	ZFP42_HUMAN	zinc finger protein 42	224	C2H2-type 2.				female gonad development|male gonad development|meiosis	cytoplasm|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|skin(1)	2		all_cancers(14;6.2e-52)|all_epithelial(14;7.36e-37)|all_lung(41;2.29e-15)|Lung NSC(41;6.7e-15)|Breast(6;1.53e-05)|Melanoma(20;3.01e-05)|Hepatocellular(41;0.00335)|all_hematologic(60;0.014)|Renal(120;0.0183)|Prostate(90;0.0421)|Colorectal(36;0.227)		OV - Ovarian serous cystadenocarcinoma(60;1.54e-11)|BRCA - Breast invasive adenocarcinoma(30;4.21e-06)|GBM - Glioblastoma multiforme(59;8.93e-05)|STAD - Stomach adenocarcinoma(60;0.000279)|LUSC - Lung squamous cell carcinoma(40;0.00902)|READ - Rectum adenocarcinoma(43;0.157)		GAATGTGGGAAAGCGTTCGTT	0.507													28	104	---	---	---	---	PASS
SLC6A19	340024	broad.mit.edu	37	5	1201974	1201974	+	Intron	SNP	T	A	A			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:1201974T>A	uc003jbw.3	+							NM_001003841	NP_001003841	Q695T7	S6A19_HUMAN	solute carrier family 6, member 19						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)			GGAGGTAGGCTGGCCGGGCGG	0.692													13	6	---	---	---	---	PASS
CDH9	1007	broad.mit.edu	37	5	26915732	26915732	+	Intron	SNP	A	T	T			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:26915732A>T	uc003jgs.1	-						CDH9_uc010iug.2_Intron	NM_016279	NP_057363	Q9ULB4	CADH9_HUMAN	cadherin 9, type 2 preproprotein						adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(5)|skin(2)|upper_aerodigestive_tract(1)|haematopoietic_and_lymphoid_tissue(1)	9						ATTAGAATATACCTACCGACT	0.318													6	165	---	---	---	---	PASS
PLCXD3	345557	broad.mit.edu	37	5	41313840	41313840	+	Missense_Mutation	SNP	G	T	T	rs144321987	byFrequency	TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:41313840G>T	uc003jmm.1	-	3	947	c.845C>A	c.(844-846)ACG>AAG	p.T282K		NM_001005473	NP_001005473	Q63HM9	PLCX3_HUMAN	phosphatidylinositol-specific phospholipase C, X	282					intracellular signal transduction|lipid catabolic process		phospholipase C activity|signal transducer activity			skin(2)|urinary_tract(1)|ovary(1)|lung(1)|central_nervous_system(1)	6						TGGCTTCTGCGTGCGGACCCA	0.423													33	25	---	---	---	---	PASS
FNIP1	96459	broad.mit.edu	37	5	131008213	131008213	+	Nonsense_Mutation	SNP	C	A	A			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:131008213C>A	uc003kvs.1	-	14	2066	c.1924G>T	c.(1924-1926)GGA>TGA	p.G642*	RAPGEF6_uc003kvp.1_Intron|FNIP1_uc003kvt.1_Nonsense_Mutation_p.G614*|FNIP1_uc010jdm.1_Nonsense_Mutation_p.G597*	NM_133372	NP_588613	Q8TF40	FNIP1_HUMAN	folliculin interacting protein 1 isoform 1	642					regulation of protein phosphorylation	cytoplasm	protein binding			pancreas(1)|skin(1)	2		all_cancers(142;0.00347)|Lung NSC(810;0.106)|all_lung(232;0.123)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Lung(113;0.0665)		TCTGAAATTCCTAGCAGCTCC	0.373													173	159	---	---	---	---	PASS
UQCRQ	27089	broad.mit.edu	37	5	132202732	132202732	+	Intron	SNP	G	A	A			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:132202732G>A	uc003kya.1	+						GDF9_uc003kxz.1_5'Flank|GDF9_uc011cxj.1_5'Flank	NM_014402	NP_055217	O14949	QCR8_HUMAN	ubiquinol-cytochrome c reductase, complex III						respiratory electron transport chain	mitochondrial inner membrane|respiratory chain	ubiquinol-cytochrome-c reductase activity				0		all_cancers(142;0.105)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			TGCCGCGTGAGTGCCTTGGGC	0.542													30	21	---	---	---	---	PASS
AFF4	27125	broad.mit.edu	37	5	132232283	132232283	+	Nonsense_Mutation	SNP	G	T	T			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:132232283G>T	uc003kyd.2	-	11	2447	c.2039C>A	c.(2038-2040)TCA>TAA	p.S680*	AFF4_uc011cxk.1_Nonsense_Mutation_p.S358*|AFF4_uc003kye.1_Nonsense_Mutation_p.S680*	NM_014423	NP_055238	Q9UHB7	AFF4_HUMAN	ALL1 fused gene from 5q31	680					transcription from RNA polymerase II promoter	mitochondrion|nucleolus	protein binding|sequence-specific DNA binding transcription factor activity			ovary(2)|kidney(2)|skin(1)	5		all_cancers(142;0.145)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			TTCCTCCACTGAGGAGGGTTT	0.478													90	67	---	---	---	---	PASS
PCDHB3	56132	broad.mit.edu	37	5	140481455	140481455	+	Missense_Mutation	SNP	G	A	A			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140481455G>A	uc003lio.2	+	1	1222	c.1222G>A	c.(1222-1224)GCG>ACG	p.A408T	uc003lin.2_Intron	NM_018937	NP_061760	Q9Y5E6	PCDB3_HUMAN	protocadherin beta 3 precursor	408	Extracellular (Potential).|Cadherin 4.				calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission	integral to plasma membrane	calcium ion binding			ovary(1)|pancreas(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			GTCAGAAGGCGCGCTGGACAG	0.483													37	74	---	---	---	---	PASS
PCDHB10	56126	broad.mit.edu	37	5	140573030	140573030	+	Missense_Mutation	SNP	T	G	G			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140573030T>G	uc003lix.2	+	1	1079	c.905T>G	c.(904-906)TTT>TGT	p.F302C		NM_018930	NP_061753	Q9UN67	PCDBA_HUMAN	protocadherin beta 10 precursor	302	Extracellular (Potential).|Cadherin 3.				calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission	integral to membrane|plasma membrane	calcium ion binding			ovary(1)|skin(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			GGGGAAATCTTTCTCAGAGAA	0.373													43	97	---	---	---	---	PASS
PCDHGB2	56103	broad.mit.edu	37	5	140740522	140740522	+	Missense_Mutation	SNP	A	C	C			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140740522A>C	uc003ljs.1	+	1	820	c.820A>C	c.(820-822)AAC>CAC	p.N274H	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc003ljm.1_Intron|PCDHGA3_uc010jfx.1_Intron|PCDHGB1_uc003ljo.1_Intron|PCDHGA4_uc003ljq.1_Intron|PCDHGB2_uc011dar.1_Missense_Mutation_p.N274H	NM_018923	NP_061746	Q9Y5G2	PCDGE_HUMAN	protocadherin gamma subfamily B, 2 isoform 1	274	Extracellular (Potential).|Cadherin 3.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGAAGGCATAAACGCAGAGAT	0.478													14	47	---	---	---	---	PASS
PPARGC1B	133522	broad.mit.edu	37	5	149213089	149213089	+	Nonsense_Mutation	SNP	G	T	T			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:149213089G>T	uc003lrc.2	+	5	1495	c.1453G>T	c.(1453-1455)GAG>TAG	p.E485*	PPARGC1B_uc003lrb.1_Nonsense_Mutation_p.E485*|PPARGC1B_uc003lrd.2_Nonsense_Mutation_p.E446*|PPARGC1B_uc003lrf.2_Nonsense_Mutation_p.E464*|PPARGC1B_uc003lre.1_Nonsense_Mutation_p.E464*	NM_133263	NP_573570	Q86YN6	PRGC2_HUMAN	peroxisome proliferator-activated receptor	485					estrogen receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter	mediator complex	AF-2 domain binding|estrogen receptor binding|ligand-dependent nuclear receptor transcription coactivator activity|nucleotide binding|receptor activator activity|RNA binding|RNA polymerase II transcription cofactor activity				0			KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)			ACTGAACCCTGAGCTGGGCCC	0.662													7	1	---	---	---	---	PASS
PRPF4B	8899	broad.mit.edu	37	6	4032628	4032628	+	Missense_Mutation	SNP	A	G	G			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:4032628A>G	uc003mvv.2	+	2	968	c.877A>G	c.(877-879)AGA>GGA	p.R293G	PRPF4B_uc011dhv.1_RNA	NM_003913	NP_003904	Q13523	PRP4B_HUMAN	serine/threonine-protein kinase PRP4K	293	Arg/Lys-rich (basic).					catalytic step 2 spliceosome	ATP binding|protein binding|protein serine/threonine kinase activity			breast(5)	5	Ovarian(93;0.0925)	all_hematologic(90;0.0895)				TAAAAAATCCAGATCCCCAGT	0.338													54	103	---	---	---	---	PASS
LRRC16A	55604	broad.mit.edu	37	6	25488700	25488700	+	Intron	SNP	G	T	T			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:25488700G>T	uc011djw.1	+						LRRC16A_uc010jpx.2_Intron|LRRC16A_uc010jpy.2_Intron	NM_017640	NP_060110	Q5VZK9	LR16A_HUMAN	leucine rich repeat containing 16A						actin filament organization|blood coagulation|cell migration|lamellipodium assembly|ruffle organization|urate metabolic process	cytosol|lamellipodium|nucleus				ovary(1)|breast(1)|central_nervous_system(1)|pancreas(1)	4						GGATTTTCTTGATGTTGCAGG	0.488													51	148	---	---	---	---	PASS
SLC17A2	10246	broad.mit.edu	37	6	25917239	25917239	+	Missense_Mutation	SNP	A	T	T			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:25917239A>T	uc011dkb.1	-	6	809	c.726T>A	c.(724-726)AGT>AGA	p.S242R	SLC17A2_uc011dkc.1_Missense_Mutation_p.S242R|SLC17A2_uc003nfl.2_Missense_Mutation_p.S242R			O00624	NPT3_HUMAN	SubName: Full=Solute carrier family 17 (Sodium phosphate), member 2, isoform CRA_b; SubName: Full=Putative uncharacterized protein SLC17A2;	242					phosphate metabolic process	integral to plasma membrane|membrane fraction	sodium:phosphate symporter activity			ovary(1)	1						TTTCCCTAACACTTATGCACG	0.512													29	67	---	---	---	---	PASS
SYNGAP1	8831	broad.mit.edu	37	6	33408702	33408702	+	Missense_Mutation	SNP	C	T	T			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33408702C>T	uc011dri.1	+	11	2068	c.1873C>T	c.(1873-1875)CTC>TTC	p.L625F	SYNGAP1_uc010juy.2_Missense_Mutation_p.L610F|SYNGAP1_uc010juz.2_Missense_Mutation_p.L337F	NM_006772	NP_006763	Q96PV0	SYGP1_HUMAN	synaptic Ras GTPase activating protein 1	625	Ras-GAP.				negative regulation of Ras protein signal transduction|signal transduction	cytoplasm|intrinsic to internal side of plasma membrane	Ras GTPase activator activity|SH3 domain binding			ovary(4)	4						AACCCTCACCCTCATTGCCAA	0.438													6	61	---	---	---	---	PASS
MAPK13	5603	broad.mit.edu	37	6	36100432	36100432	+	Missense_Mutation	SNP	C	T	T			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:36100432C>T	uc003ols.2	+	3	382	c.284C>T	c.(283-285)TCC>TTC	p.S95F	MAPK13_uc003olt.2_RNA	NM_002754	NP_002745	O15264	MK13_HUMAN	mitogen-activated protein kinase 13	95	Protein kinase.				cell cycle|intracellular protein kinase cascade|nerve growth factor receptor signaling pathway|positive regulation of interleukin-6 production|Ras protein signal transduction|response to stress		ATP binding|MAP kinase activity|protein binding			breast(2)|central_nervous_system(1)	3						ACCCCAGCCTCCTCCCTGCGC	0.607													21	214	---	---	---	---	PASS
ZNF292	23036	broad.mit.edu	37	6	87969104	87969104	+	Silent	SNP	A	G	G			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:87969104A>G	uc003plm.3	+	8	5798	c.5757A>G	c.(5755-5757)CTA>CTG	p.L1919L		NM_015021	NP_055836	O60281	ZN292_HUMAN	zinc finger protein 292	1919	C2H2-type 9.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(4)	4		all_cancers(76;3.82e-09)|Prostate(29;1.34e-10)|Acute lymphoblastic leukemia(125;2.17e-10)|all_hematologic(105;1.08e-06)|all_epithelial(107;5.31e-05)		BRCA - Breast invasive adenocarcinoma(108;0.0199)		AGGATGCACTATTTAAGCACT	0.308													18	28	---	---	---	---	PASS
FHL5	9457	broad.mit.edu	37	6	97053783	97053783	+	Missense_Mutation	SNP	C	G	G			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:97053783C>G	uc003pos.1	+	5	745	c.340C>G	c.(340-342)CGC>GGC	p.R114G	FHL5_uc003pot.1_Missense_Mutation_p.R114G	NM_020482	NP_065228	Q5TD97	FHL5_HUMAN	activator of cAMP-responsive element modulator	114	LIM zinc-binding 2.					nucleus	zinc ion binding			ovary(2)	2		all_cancers(76;1.57e-07)|Acute lymphoblastic leukemia(125;4.93e-10)|all_hematologic(75;3.55e-07)|all_epithelial(107;0.00266)|Colorectal(196;0.0341)|Lung NSC(302;0.204)		BRCA - Breast invasive adenocarcinoma(108;0.0948)		TACAGGTTCCCGCAAAATGGA	0.353													27	72	---	---	---	---	PASS
EPB41L2	2037	broad.mit.edu	37	6	131276358	131276358	+	Nonsense_Mutation	SNP	G	A	A			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:131276358G>A	uc003qch.2	-	3	774	c.592C>T	c.(592-594)CAG>TAG	p.Q198*	EPB41L2_uc003qcg.1_Nonsense_Mutation_p.Q198*|EPB41L2_uc011eby.1_Nonsense_Mutation_p.Q198*|EPB41L2_uc003qci.2_Nonsense_Mutation_p.Q198*|EPB41L2_uc010kfk.2_Nonsense_Mutation_p.Q198*|EPB41L2_uc010kfl.1_Nonsense_Mutation_p.Q198*	NM_001431	NP_001422	O43491	E41L2_HUMAN	erythrocyte membrane protein band 4.1-like 2	198					cortical actin cytoskeleton organization	extrinsic to membrane|plasma membrane|spectrin	actin binding|structural molecule activity			central_nervous_system(1)|skin(1)	2	Breast(56;0.0639)			OV - Ovarian serous cystadenocarcinoma(155;0.0271)|GBM - Glioblastoma multiforme(226;0.0355)		TCATTGGTCTGCACTTCCTTG	0.438													45	323	---	---	---	---	PASS
ENPP3	5169	broad.mit.edu	37	6	131995401	131995401	+	Missense_Mutation	SNP	G	T	T			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:131995401G>T	uc003qcu.3	+	9	1089	c.742G>T	c.(742-744)GCC>TCC	p.A248S	ENPP3_uc010kfn.1_RNA|ENPP3_uc011ecc.1_Missense_Mutation_p.A214S|ENPP3_uc010kfo.1_RNA|ENPP3_uc010kfp.1_RNA|ENPP3_uc010kfq.2_RNA|ENPP3_uc003qcv.2_Missense_Mutation_p.A248S	NM_005021	NP_005012	O14638	ENPP3_HUMAN	ectonucleotide pyrophosphatase/phosphodiesterase	248	Extracellular (Potential).|Phosphodiesterase.				immune response|nucleoside triphosphate catabolic process|phosphate metabolic process	extracellular region|integral to plasma membrane|perinuclear region of cytoplasm	metal ion binding|nucleic acid binding|nucleoside-triphosphate diphosphatase activity|nucleotide diphosphatase activity|phosphodiesterase I activity|polysaccharide binding|scavenger receptor activity			ovary(3)|skin(1)	4	Breast(56;0.0753)			GBM - Glioblastoma multiforme(226;0.0252)|OV - Ovarian serous cystadenocarcinoma(155;0.0511)		AAATAATCCAGCCTGGTGGCA	0.423													16	77	---	---	---	---	PASS
KIAA1244	57221	broad.mit.edu	37	6	138531058	138531058	+	Silent	SNP	G	A	A	rs138636575		TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:138531058G>A	uc003qhu.2	+	4	231	c.231G>A	c.(229-231)TCG>TCA	p.S77S		NM_020340	NP_065073	Q5TH69	BIG3_HUMAN	brefeldin A-inhibited guanine	77					regulation of ARF protein signal transduction	cytoplasm|integral to membrane	ARF guanyl-nucleotide exchange factor activity			ovary(1)|skin(1)	2	Breast(32;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.00102)|GBM - Glioblastoma multiforme(68;0.00259)		AGCTTCTGTCGGAAGAGAGGT	0.458													52	139	---	---	---	---	PASS
SHPRH	257218	broad.mit.edu	37	6	146244844	146244844	+	Silent	SNP	C	T	T			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:146244844C>T	uc003qlf.2	-	18	3879	c.3480G>A	c.(3478-3480)CAG>CAA	p.Q1160Q	SHPRH_uc003qld.2_Silent_p.Q1169Q|SHPRH_uc003qle.2_Silent_p.Q1169Q|SHPRH_uc003qlg.1_Silent_p.Q716Q|SHPRH_uc003qlh.2_Silent_p.Q85Q|SHPRH_uc003qli.1_Silent_p.Q85Q	NM_001042683	NP_001036148	Q149N8	SHPRH_HUMAN	SNF2 histone linker PHD RING helicase isoform a	1160					DNA repair|nucleosome assembly	nucleosome|nucleus	ATP binding|DNA binding|helicase activity|ligase activity|zinc ion binding			ovary(1)|kidney(1)|central_nervous_system(1)	3		Ovarian(120;0.0365)		OV - Ovarian serous cystadenocarcinoma(155;1.47e-07)|GBM - Glioblastoma multiforme(68;0.0124)		TTCGCACTCGCTGAACTAGCT	0.363													73	99	---	---	---	---	PASS
ARID1B	57492	broad.mit.edu	37	6	157522135	157522135	+	Silent	SNP	T	C	C			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:157522135T>C	uc003qqn.2	+	18	4505	c.4353T>C	c.(4351-4353)AAT>AAC	p.N1451N	ARID1B_uc003qqo.2_Silent_p.N1411N|ARID1B_uc003qqp.2_Silent_p.N1398N	NM_017519	NP_059989	Q8NFD5	ARI1B_HUMAN	AT rich interactive domain 1B (SWI1-like)	1456					chromatin-mediated maintenance of transcription|nervous system development|transcription, DNA-dependent	SWI/SNF complex	DNA binding|protein binding|transcription coactivator activity			ovary(1)|breast(1)	2		Breast(66;0.000162)|Ovarian(120;0.0265)		OV - Ovarian serous cystadenocarcinoma(65;3.19e-17)|BRCA - Breast invasive adenocarcinoma(81;1.01e-05)		CAGCACGCAATGATATGCCTT	0.617													23	37	---	---	---	---	PASS
LPA	4018	broad.mit.edu	37	6	161020694	161020694	+	Intron	SNP	G	A	A			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:161020694G>A	uc003qtl.2	-							NM_005577	NP_005568	P08519	APOA_HUMAN	lipoprotein Lp(a) precursor						blood circulation|lipid metabolic process|lipid transport|lipoprotein metabolic process|proteolysis|receptor-mediated endocytosis	plasma lipoprotein particle	apolipoprotein binding|endopeptidase inhibitor activity|fibronectin binding|heparin binding|serine-type endopeptidase activity			ovary(3)|skin(2)|pancreas(1)	6		Breast(66;0.000496)|Ovarian(120;0.0303)|Prostate(117;0.0965)		OV - Ovarian serous cystadenocarcinoma(65;2.5e-17)|BRCA - Breast invasive adenocarcinoma(81;6.48e-06)	Aminocaproic Acid(DB00513)	AGTCAGTGCTGAAATTAAAAC	0.413													57	161	---	---	---	---	PASS
SMOC2	64094	broad.mit.edu	37	6	169053815	169053815	+	Missense_Mutation	SNP	G	A	A			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:169053815G>A	uc003qws.1	+	11	1212	c.1192G>A	c.(1192-1194)GTG>ATG	p.V398M	SMOC2_uc003qwr.1_Missense_Mutation_p.V409M|SMOC2_uc011egu.1_Missense_Mutation_p.V75M	NM_022138	NP_071421	Q9H3U7	SMOC2_HUMAN	SPARC related modular calcium binding 2	398	2 (Potential).|EF-hand 2.				signal transduction	basement membrane	calcium ion binding			ovary(1)	1		Breast(66;0.000141)|Esophageal squamous(34;0.222)|Ovarian(120;0.231)		OV - Ovarian serous cystadenocarcinoma(33;1.31e-19)|BRCA - Breast invasive adenocarcinoma(81;3.06e-06)|GBM - Glioblastoma multiforme(31;0.00109)		ATACTGTGACGTGAATAATGA	0.458													18	76	---	---	---	---	PASS
RBAK	57786	broad.mit.edu	37	7	5105028	5105028	+	Silent	SNP	A	G	G			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:5105028A>G	uc010kss.1	+	6	2265	c.1941A>G	c.(1939-1941)GGA>GGG	p.G647G	LOC389458_uc003snr.2_Intron|RBAK_uc003sns.1_Silent_p.G647G	NM_021163	NP_066986	Q9NYW8	RBAK_HUMAN	RB-associated KRAB repressor	647	Interaction with AR.				negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	nucleic acid binding|zinc ion binding			ovary(3)|kidney(1)|skin(1)	5		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0916)|OV - Ovarian serous cystadenocarcinoma(56;2.44e-14)		GCCATTCAGGAGAGAAACCCT	0.398													14	285	---	---	---	---	PASS
PLEKHA8	84725	broad.mit.edu	37	7	30092432	30092432	+	Missense_Mutation	SNP	A	G	G			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:30092432A>G	uc003tam.1	+	7	837	c.746A>G	c.(745-747)GAG>GGG	p.E249G	PLEKHA8_uc003tao.2_Missense_Mutation_p.E133G|PLEKHA8_uc003tap.1_Missense_Mutation_p.E249G|PLEKHA8_uc003tan.2_Missense_Mutation_p.E249G	NM_032639	NP_116028	Q96JA3	PKHA8_HUMAN	pleckstrin homology domain containing, family A	249					protein transport	cytoplasm	glycolipid binding|glycolipid transporter activity			breast(3)|ovary(1)	4						AAATCTGCAGAGATAGACTGC	0.294													29	58	---	---	---	---	PASS
VPS41	27072	broad.mit.edu	37	7	38768321	38768321	+	Missense_Mutation	SNP	C	T	T			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:38768321C>T	uc003tgy.2	-	26	2356	c.2330G>A	c.(2329-2331)CGA>CAA	p.R777Q	VPS41_uc003tgz.2_Missense_Mutation_p.R752Q|VPS41_uc010kxn.2_Missense_Mutation_p.R688Q|VPS41_uc003tgx.2_RNA	NM_014396	NP_055211	P49754	VPS41_HUMAN	vacuolar protein sorting 41 isoform 1	777					Golgi vesicle transport|intracellular protein transport|vesicle-mediated transport	cytosol|Golgi-associated vesicle|HOPS complex|membrane fraction	zinc ion binding			skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)	4						CATTTGAGTTCGGTGCATTTT	0.393													42	183	---	---	---	---	PASS
HECW1	23072	broad.mit.edu	37	7	43484216	43484216	+	Missense_Mutation	SNP	C	A	A			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:43484216C>A	uc003tid.1	+	11	2050	c.1445C>A	c.(1444-1446)ACC>AAC	p.T482N	HECW1_uc011kbi.1_Missense_Mutation_p.T482N	NM_015052	NP_055867	Q76N89	HECW1_HUMAN	NEDD4-like ubiquitin-protein ligase 1	482	Glu-rich.				protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm|nucleus	ubiquitin-protein ligase activity			ovary(8)|lung(6)|breast(4)|skin(4)|pancreas(1)	23						CCAGCCAGCACCAAGGAGGAG	0.537													11	15	---	---	---	---	PASS
HECW1	23072	broad.mit.edu	37	7	43546832	43546832	+	Missense_Mutation	SNP	T	A	A			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:43546832T>A	uc003tid.1	+	22	4333	c.3728T>A	c.(3727-3729)TTT>TAT	p.F1243Y	HECW1_uc011kbi.1_Missense_Mutation_p.F1209Y	NM_015052	NP_055867	Q76N89	HECW1_HUMAN	NEDD4-like ubiquitin-protein ligase 1	1243					protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm|nucleus	ubiquitin-protein ligase activity			ovary(8)|lung(6)|breast(4)|skin(4)|pancreas(1)	23						GCCAAAGGATTTGGTCAGGGT	0.488													93	116	---	---	---	---	PASS
ABCA13	154664	broad.mit.edu	37	7	48318575	48318575	+	Missense_Mutation	SNP	T	C	C			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:48318575T>C	uc003toq.2	+	18	7809	c.7784T>C	c.(7783-7785)CTT>CCT	p.L2595P	ABCA13_uc010kys.1_5'Flank	NM_152701	NP_689914	Q86UQ4	ABCAD_HUMAN	ATP binding cassette, sub-family A (ABC1),	2595					transport	integral to membrane	ATP binding|ATPase activity			ovary(5)|central_nervous_system(4)|skin(1)	10						GTGCCATTTCTTGACTTGGCC	0.308													95	137	---	---	---	---	PASS
EGFR	1956	broad.mit.edu	37	7	55241711	55241711	+	Missense_Mutation	SNP	C	G	G			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:55241711C>G	uc003tqk.2	+	18	2405	c.2159C>G	c.(2158-2160)TCC>TGC	p.S720C	EGFR_uc010kzg.1_Missense_Mutation_p.S675C|EGFR_uc011kco.1_Missense_Mutation_p.S667C	NM_005228	NP_005219	P00533	EGFR_HUMAN	epidermal growth factor receptor isoform a	720	Cytoplasmic (Potential).|Protein kinase.|ATP.				activation of phospholipase A2 activity by calcium-mediated signaling|activation of phospholipase C activity|axon guidance|cell proliferation|cell-cell adhesion|negative regulation of apoptosis|negative regulation of epidermal growth factor receptor signaling pathway|ossification|positive regulation of catenin import into nucleus|positive regulation of cell migration|positive regulation of cyclin-dependent protein kinase activity involved in G1/S|positive regulation of epithelial cell proliferation|positive regulation of MAP kinase activity|positive regulation of nitric oxide biosynthetic process|positive regulation of phosphorylation|positive regulation of protein kinase B signaling cascade|protein autophosphorylation|protein insertion into membrane|regulation of nitric-oxide synthase activity|regulation of peptidyl-tyrosine phosphorylation|response to stress|response to UV-A	basolateral plasma membrane|endoplasmic reticulum membrane|endosome|extracellular space|Golgi membrane|integral to membrane|nuclear membrane|Shc-EGFR complex	actin filament binding|ATP binding|double-stranded DNA binding|epidermal growth factor receptor activity|identical protein binding|MAP/ERK kinase kinase activity|protein heterodimerization activity|protein phosphatase binding|receptor signaling protein tyrosine kinase activity	p.S720F(5)|p.S720P(2)|p.S720S(1)|p.S720T(1)		lung(9213)|central_nervous_system(103)|stomach(41)|upper_aerodigestive_tract(39)|prostate(32)|ovary(31)|thyroid(24)|breast(11)|peritoneum(9)|oesophagus(9)|salivary_gland(9)|large_intestine(8)|kidney(8)|urinary_tract(6)|skin(5)|adrenal_gland(5)|soft_tissue(4)|bone(3)|NS(2)|pancreas(2)|haematopoietic_and_lymphoid_tissue(2)|thymus(2)|liver(2)|eye(1)	9571	all_cancers(1;1.57e-46)|all_epithelial(1;5.62e-37)|Lung NSC(1;9.29e-25)|all_lung(1;4.39e-23)|Esophageal squamous(2;7.55e-08)|Breast(14;0.0318)		GBM - Glioblastoma multiforme(1;0)|all cancers(1;2.19e-314)|Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00164)|Epithelial(13;0.0607)		Cetuximab(DB00002)|Erlotinib(DB00530)|Gefitinib(DB00317)|Lapatinib(DB01259)|Lidocaine(DB00281)|Panitumumab(DB01269)|Trastuzumab(DB00072)	GTGCTGGGCTCCGGTGCGTTC	0.572		8	A|O|Mis		glioma|NSCLC	NSCLC			Lung_Cancer_Familial_Clustering_of	TCGA GBM(3;<1E-08)|TSP Lung(4;<1E-08)			7	176	---	---	---	---	PASS
CRCP	27297	broad.mit.edu	37	7	65617210	65617210	+	Nonsense_Mutation	SNP	G	T	T			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:65617210G>T	uc003tus.2	+	6	458	c.313G>T	c.(313-315)GAA>TAA	p.E105*	CRCP_uc003tuv.2_RNA|CRCP_uc011kdw.1_Nonsense_Mutation_p.E98*|CRCP_uc003tut.2_Nonsense_Mutation_p.E72*|CRCP_uc003tuu.2_Nonsense_Mutation_p.E28*	NM_014478	NP_055293	O75575	RPC9_HUMAN	calcitonin gene-related peptide-receptor	105					acrosome reaction|innate immune response|response to virus|transcription from RNA polymerase III promoter	DNA polymerase III complex|nucleus|plasma membrane	calcitonin receptor activity|DNA-directed RNA polymerase activity|nucleotide binding				0						GGAAGAGAGTGAAGAGCGGCT	0.527													20	81	---	---	---	---	PASS
CROT	54677	broad.mit.edu	37	7	87011274	87011274	+	Missense_Mutation	SNP	G	C	C			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:87011274G>C	uc003uit.2	+	11	1272	c.1027G>C	c.(1027-1029)GAT>CAT	p.D343H	CROT_uc003uiu.2_Missense_Mutation_p.D371H	NM_021151	NP_066974	Q9UKG9	OCTC_HUMAN	peroxisomal carnitine O-octanoyltransferase	343					fatty acid beta-oxidation using acyl-CoA oxidase|generation of precursor metabolites and energy|transport	peroxisomal matrix	carnitine O-octanoyltransferase activity			ovary(2)|lung(1)	3	Esophageal squamous(14;0.0058)|all_lung(186;0.201)|Lung NSC(181;0.203)				L-Carnitine(DB00583)	TTATTATGTGGATGAGAAAAT	0.274													15	127	---	---	---	---	PASS
ADAM22	53616	broad.mit.edu	37	7	87792411	87792411	+	Silent	SNP	A	G	G			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:87792411A>G	uc003ujn.2	+	23	2071	c.1992A>G	c.(1990-1992)TTA>TTG	p.L664L	ADAM22_uc003ujk.1_Silent_p.L664L|ADAM22_uc003ujl.1_Silent_p.L664L|ADAM22_uc003ujm.2_Silent_p.L664L|ADAM22_uc003ujo.2_Silent_p.L664L|ADAM22_uc003ujp.1_Silent_p.L716L	NM_021723	NP_068369	Q9P0K1	ADA22_HUMAN	ADAM metallopeptidase domain 22 isoform 1	664	Cys-rich.|Extracellular (Potential).				cell adhesion|central nervous system development|negative regulation of cell adhesion|proteolysis	integral to membrane	integrin binding|metalloendopeptidase activity|protein binding|receptor activity|zinc ion binding			ovary(4)|skin(2)|lung(1)|kidney(1)	8	Esophageal squamous(14;0.00202)		STAD - Stomach adenocarcinoma(171;0.215)			TGATGTGCTTAGAACACAGGT	0.428													121	257	---	---	---	---	PASS
LRCH4	4034	broad.mit.edu	37	7	100179992	100179992	+	Missense_Mutation	SNP	C	G	G			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100179992C>G	uc003uvj.2	-	2	364	c.311G>C	c.(310-312)AGA>ACA	p.R104T	LRCH4_uc010lgz.2_RNA|LRCH4_uc003uvi.2_RNA|LRCH4_uc011kjx.1_RNA	NM_002319	NP_002310	O75427	LRCH4_HUMAN	leucine-rich repeats and calponin homology (CH)	104	LRR 3.				nervous system development	PML body	protein binding			large_intestine(1)|ovary(1)	2	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					GTTCAGGCATCTCAGGCAATT	0.637													17	114	---	---	---	---	PASS
LAMB1	3912	broad.mit.edu	37	7	107621203	107621203	+	Nonsense_Mutation	SNP	C	A	A			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:107621203C>A	uc003vew.2	-	8	1065	c.730G>T	c.(730-732)GGA>TGA	p.G244*	LAMB1_uc003vev.2_Nonsense_Mutation_p.G268*|LAMB1_uc003vex.2_Nonsense_Mutation_p.G244*|LAMB1_uc010ljn.1_Nonsense_Mutation_p.G330*	NM_002291	NP_002282	P07942	LAMB1_HUMAN	laminin, beta 1 precursor	244	Laminin N-terminal.				axon guidance|odontogenesis|positive regulation of cell migration|positive regulation of epithelial cell proliferation|substrate adhesion-dependent cell spreading	extracellular space|laminin-1 complex|laminin-10 complex|laminin-2 complex|laminin-8 complex|perinuclear region of cytoplasm	extracellular matrix structural constituent			ovary(4)|skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)	8					Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)	AGGTTATCTCCCAAAGTATGC	0.363													70	123	---	---	---	---	PASS
LUZP6	767558	broad.mit.edu	37	7	135661836	135661836	+	Missense_Mutation	SNP	C	G	G			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:135661836C>G	uc003vte.3	-	1	369	c.13G>C	c.(13-15)GAG>CAG	p.E5Q	LUZP6_uc010lmv.2_RNA	NM_145808	NP_665807	Q538Z0	LUZP6_HUMAN	myotrophin	Error:Variant_position_missing_in_Q538Z0_after_alignment											0						CACATGAACTCCTTGTCGCAC	0.617													55	146	---	---	---	---	PASS
CLEC2L	154790	broad.mit.edu	37	7	139225243	139225243	+	Intron	SNP	C	G	G			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:139225243C>G	uc010lnd.2	+							NM_001080511	NP_001073980	P0C7M8	CLC2L_HUMAN	C-type lectin domain family 2, member L							integral to membrane	sugar binding				0	Melanoma(164;0.233)					GGTGAGTGTGCCAAGGTGAAG	0.602													7	9	---	---	---	---	PASS
OR2F1	26211	broad.mit.edu	37	7	143657910	143657910	+	Missense_Mutation	SNP	C	A	A			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:143657910C>A	uc003wds.1	+	1	891	c.847C>A	c.(847-849)CCA>ACA	p.P283T		NM_012369	NP_036501	Q13607	OR2F1_HUMAN	olfactory receptor, family 2, subfamily F,	283	Helical; Name=7; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(2)|ovary(1)	3	Melanoma(164;0.0903)					CATTTTAACACCAATGCTGAA	0.463													84	125	---	---	---	---	PASS
SSPO	23145	broad.mit.edu	37	7	149510823	149510823	+	Missense_Mutation	SNP	C	A	A			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:149510823C>A	uc010lpk.2	+	72	10108	c.10108C>A	c.(10108-10110)CTG>ATG	p.L3370M		NM_198455	NP_940857	A2VEC9	SSPO_HUMAN	SCO-spondin precursor	3370					cell adhesion	extracellular space	peptidase inhibitor activity				0	Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			CTGCCTGGACCTGCTGACCGG	0.697													16	36	---	---	---	---	PASS
CDK5	1020	broad.mit.edu	37	7	150754047	150754047	+	Missense_Mutation	SNP	C	T	T			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150754047C>T	uc003wir.1	-	3	203	c.142G>A	c.(142-144)GCC>ACC	p.A48T	CDK5_uc003wis.1_Missense_Mutation_p.A48T|SLC4A2_uc003wit.3_5'Flank	NM_004935	NP_004926	Q00535	CDK5_HUMAN	cyclin-dependent kinase 5 isoform 1	48	Protein kinase.				activation of pro-apoptotic gene products|blood coagulation|cell division|cell proliferation|embryo development|negative regulation of transcription, DNA-dependent|positive regulation of neuron apoptosis	axon|cytosol|dendrite|growth cone|lamellipodium|membrane|neuromuscular junction|neuronal cell body	acetylcholine receptor activator activity|ATP binding|cyclin-dependent protein kinase activity|ErbB-2 class receptor binding|ErbB-3 class receptor binding|tau-protein kinase activity			lung(1)|central_nervous_system(1)	2		Breast(660;0.159)|Ovarian(593;0.182)	OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)|LUSC - Lung squamous cell carcinoma(290;0.008)|Lung(243;0.00942)|BRCA - Breast invasive adenocarcinoma(188;0.242)		TCCCGGAGGGCGGAACTCGGC	0.662													26	40	---	---	---	---	PASS
BAG4	9530	broad.mit.edu	37	8	38066523	38066523	+	Intron	SNP	C	T	T			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38066523C>T	uc003xky.1	+						BAG4_uc003xkz.1_Intron	NM_004874	NP_004865	O95429	BAG4_HUMAN	BCL2-associated athanogene 4						anti-apoptosis|apoptosis|protein folding	cytoplasm|nucleus	receptor signaling protein activity			ovary(1)	1	Colorectal(12;0.000442)	all_lung(54;0.00787)|Lung NSC(58;0.0295)|Hepatocellular(245;0.121)				TTCTTCTTCTCAATCTAGAAC	0.403													26	115	---	---	---	---	PASS
ANK1	286	broad.mit.edu	37	8	41522505	41522505	+	Intron	SNP	C	T	T			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:41522505C>T	uc003xok.2	-						NKX6-3_uc010lxa.1_Intron|ANK1_uc003xoh.2_Intron|ANK1_uc003xoi.2_Intron|ANK1_uc003xoj.2_Intron|ANK1_uc003xol.2_Intron|ANK1_uc003xom.2_Intron|ANK1_uc011lcl.1_Missense_Mutation_p.V13M|ANK1_uc003xod.2_Missense_Mutation_p.V13M|ANK1_uc003xoc.2_Missense_Mutation_p.V13M|ANK1_uc003xof.2_Missense_Mutation_p.V13M	NM_020476	NP_065209	P16157	ANK1_HUMAN	ankyrin 1 isoform 1						axon guidance|cytoskeleton organization|exocytosis|maintenance of epithelial cell apical/basal polarity|signal transduction	basolateral plasma membrane|cytosol|sarcomere|sarcoplasmic reticulum|spectrin-associated cytoskeleton	cytoskeletal adaptor activity|enzyme binding|protein binding|spectrin binding|structural constituent of cytoskeleton			ovary(3)|central_nervous_system(3)|lung(2)|breast(1)	9	Ovarian(28;0.00541)|Colorectal(14;0.0398)|Lung SC(25;0.211)	all_lung(54;0.000626)|Lung NSC(58;0.00245)|Esophageal squamous(32;0.0559)|Hepatocellular(245;0.0663)|Renal(179;0.188)	OV - Ovarian serous cystadenocarcinoma(14;0.000984)|Lung(22;0.00108)|Colorectal(10;0.00245)|LUSC - Lung squamous cell carcinoma(45;0.00392)|COAD - Colon adenocarcinoma(11;0.0264)			CTCAGCAGCACCAGCGTGACC	0.627													19	19	---	---	---	---	PASS
RB1CC1	9821	broad.mit.edu	37	8	53596442	53596442	+	Intron	SNP	C	G	G			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:53596442C>G	uc003xre.3	-						RB1CC1_uc003xrf.3_Intron	NM_014781	NP_055596	Q8TDY2	RBCC1_HUMAN	Rb1-inducible coiled coil protein 1 isoform 1						autophagy|cell cycle|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytosol|nucleus|pre-autophagosomal structure|ULK1-ATG13-FIP200 complex	protein binding			ovary(8)|upper_aerodigestive_tract(1)|large_intestine(1)|skin(1)	11		all_cancers(86;0.137)|all_epithelial(80;0.00494)|Lung NSC(129;0.011)|all_lung(136;0.023)				CTCTTGAATACCTACCGTCCC	0.418													5	153	---	---	---	---	PASS
CYP7B1	9420	broad.mit.edu	37	8	65527680	65527680	+	Silent	SNP	G	A	A			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:65527680G>A	uc003xvj.2	-	4	1164	c.960C>T	c.(958-960)GAC>GAT	p.D320D		NM_004820	NP_004811	O75881	CP7B1_HUMAN	cytochrome P450, family 7, subfamily B,	320					bile acid biosynthetic process|cell death|cholesterol metabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	25-hydroxycholesterol 7alpha-hydroxylase activity|electron carrier activity|heme binding|oxysterol 7-alpha-hydroxylase activity			ovary(3)	3		all_cancers(86;0.217)|Lung NSC(129;0.0521)|all_lung(136;0.0906)|all_epithelial(80;0.215)				GGTCAATTTCGTCACGCACTG	0.488													19	103	---	---	---	---	PASS
ZFHX4	79776	broad.mit.edu	37	8	77617343	77617343	+	Missense_Mutation	SNP	A	T	T			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:77617343A>T	uc003yav.2	+	2	1407	c.1020A>T	c.(1018-1020)AAA>AAT	p.K340N	ZFHX4_uc003yat.1_Missense_Mutation_p.K340N|ZFHX4_uc003yau.1_Missense_Mutation_p.K340N|ZFHX4_uc003yaw.1_Missense_Mutation_p.K340N	NM_024721	NP_078997	Q86UP3	ZFHX4_HUMAN	zinc finger homeodomain 4	340						nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(8)|large_intestine(4)|breast(2)|lung(1)	15			BRCA - Breast invasive adenocarcinoma(89;0.0895)			AACCAAAAAAATCCACTTCTG	0.433										HNSCC(33;0.089)			100	132	---	---	---	---	PASS
LRRCC1	85444	broad.mit.edu	37	8	86037118	86037118	+	Missense_Mutation	SNP	C	T	T			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:86037118C>T	uc003ycw.2	+	8	1370	c.1216C>T	c.(1216-1218)CCA>TCA	p.P406S	LRRCC1_uc010lzz.1_RNA|LRRCC1_uc010maa.1_Missense_Mutation_p.P107S|LRRCC1_uc003ycx.2_Missense_Mutation_p.P313S|LRRCC1_uc003ycy.2_Missense_Mutation_p.P386S	NM_033402	NP_208325	Q9C099	LRCC1_HUMAN	sodium channel associated protein 2 isoform a	406					cell division|mitosis	centriole|nucleus					0						ATCAGAAAAGCCAAAGACTGA	0.299													54	159	---	---	---	---	PASS
CNGB3	54714	broad.mit.edu	37	8	87683247	87683247	+	Missense_Mutation	SNP	G	A	A	rs146488853		TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:87683247G>A	uc003ydx.2	-	4	464	c.418C>T	c.(418-420)CGT>TGT	p.R140C	CNGB3_uc010maj.2_Missense_Mutation_p.R2C	NM_019098	NP_061971	Q9NQW8	CNGB3_HUMAN	cyclic nucleotide gated channel beta 3	140	Cytoplasmic (Potential).				signal transduction|visual perception	integral to membrane	cGMP binding			ovary(2)|pancreas(1)	3						GTTCTTTGACGCATTCTTTTC	0.473													214	540	---	---	---	---	PASS
TM7SF4	81501	broad.mit.edu	37	8	105361153	105361153	+	Missense_Mutation	SNP	A	T	T			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:105361153A>T	uc003ylx.1	+	2	422	c.373A>T	c.(373-375)ATG>TTG	p.M125L		NM_030788	NP_110415	Q9H295	TM7S4_HUMAN	dendritic cell-specific transmembrane protein	125					osteoclast differentiation	cell surface|integral to membrane|plasma membrane				pancreas(2)|large_intestine(1)|ovary(1)	4			OV - Ovarian serous cystadenocarcinoma(57;1.61e-06)|STAD - Stomach adenocarcinoma(118;0.229)			CCTAGATGGTATGACTTGCAA	0.418													77	157	---	---	---	---	PASS
ADCY8	114	broad.mit.edu	37	8	132052079	132052079	+	Silent	SNP	T	C	C			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:132052079T>C	uc003ytd.3	-	1	757	c.501A>G	c.(499-501)GAA>GAG	p.E167E	ADCY8_uc010mds.2_Silent_p.E167E	NM_001115	NP_001106	P40145	ADCY8_HUMAN	adenylate cyclase 8	167	Cytoplasmic (Potential).				activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|inhibition of adenylate cyclase activity by G-protein signaling pathway|nerve growth factor receptor signaling pathway|synaptic transmission|transmembrane transport|water transport	integral to membrane|membrane fraction|plasma membrane	ATP binding|calcium- and calmodulin-responsive adenylate cyclase activity|metal ion binding			skin(4)|large_intestine(1)|central_nervous_system(1)	6	Esophageal squamous(12;0.00693)|Ovarian(258;0.00707)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000538)			GGTAGAGGCGTTCCAAATCCC	0.527										HNSCC(32;0.087)			23	140	---	---	---	---	PASS
DENND3	22898	broad.mit.edu	37	8	142154342	142154342	+	Missense_Mutation	SNP	C	G	G			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:142154342C>G	uc003yvy.2	+	5	757	c.479C>G	c.(478-480)CCT>CGT	p.P160R	DENND3_uc010mep.2_Missense_Mutation_p.P173R	NM_014957	NP_055772	A2RUS2	DEND3_HUMAN	DENN/MADD domain containing 3	160	DENN.									ovary(1)	1	all_cancers(97;7.36e-15)|all_epithelial(106;2.33e-13)|Lung NSC(106;1.23e-05)|all_lung(105;1.75e-05)|Ovarian(258;0.01)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.105)			AGCCCGCCACCTGGACCGCTC	0.363													114	105	---	---	---	---	PASS
SMARCA2	6595	broad.mit.edu	37	9	2081948	2081948	+	Missense_Mutation	SNP	G	A	A			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:2081948G>A	uc003zhc.2	+	15	2400	c.2301G>A	c.(2299-2301)ATG>ATA	p.M767I	SMARCA2_uc003zhd.2_Missense_Mutation_p.M767I|SMARCA2_uc010mha.2_Missense_Mutation_p.M758I	NM_003070	NP_003061	P51531	SMCA2_HUMAN	SWI/SNF-related matrix-associated	767	Helicase ATP-binding.				chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development	intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex	ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding			ovary(2)|central_nervous_system(1)	3		all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09)		GBM - Glioblastoma multiforme(50;0.0475)		CTTATCTGATGGAGCACAAAA	0.428													199	120	---	---	---	---	PASS
RFX3	5991	broad.mit.edu	37	9	3225139	3225139	+	Missense_Mutation	SNP	G	C	C			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:3225139G>C	uc003zhr.2	-	18	2465	c.2153C>G	c.(2152-2154)CCA>CGA	p.P718R	RFX3_uc010mhd.2_Missense_Mutation_p.P718R	NM_134428	NP_602304	P48380	RFX3_HUMAN	regulatory factor X3 isoform b	718					cell maturation|ciliary cell motility|cilium assembly|cilium movement involved in determination of left/right asymmetry|endocrine pancreas development|negative regulation of transcription, DNA-dependent|positive regulation of transcription from RNA polymerase II promoter|positive regulation of type B pancreatic cell development|regulation of insulin secretion	nuclear chromatin	protein binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|transcription regulatory region DNA binding			ovary(2)|central_nervous_system(1)|pancreas(1)	4				GBM - Glioblastoma multiforme(50;0.00124)|Lung(2;0.0337)		CAGGAGGCTTGGTTGCACGCC	0.502													22	57	---	---	---	---	PASS
MAMDC2	256691	broad.mit.edu	37	9	72741227	72741227	+	Silent	SNP	C	A	A			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:72741227C>A	uc004ahm.2	+	6	1413	c.796C>A	c.(796-798)CGG>AGG	p.R266R	MAMDC2_uc004ahn.2_RNA	NM_153267	NP_694999	Q7Z304	MAMC2_HUMAN	MAM domain containing 2 precursor	266	MAM 2.					endoplasmic reticulum|membrane				central_nervous_system(1)|pancreas(1)	2						CCTTTACACTCGGGATGTGGC	0.547													7	21	---	---	---	---	PASS
MAMDC2	256691	broad.mit.edu	37	9	72741230	72741230	+	Missense_Mutation	SNP	G	A	A			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:72741230G>A	uc004ahm.2	+	6	1416	c.799G>A	c.(799-801)GAT>AAT	p.D267N	MAMDC2_uc004ahn.2_RNA	NM_153267	NP_694999	Q7Z304	MAMC2_HUMAN	MAM domain containing 2 precursor	267	MAM 2.					endoplasmic reticulum|membrane				central_nervous_system(1)|pancreas(1)	2						TTACACTCGGGATGTGGCTGG	0.552													10	22	---	---	---	---	PASS
TLE1	7088	broad.mit.edu	37	9	84202721	84202721	+	Missense_Mutation	SNP	C	G	G			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:84202721C>G	uc004aly.2	-	17	2293	c.1852G>C	c.(1852-1854)GGA>CGA	p.G618R	TLE1_uc004alz.2_Missense_Mutation_p.G628R|TLE1_uc011lsr.1_Missense_Mutation_p.G603R	NM_005077	NP_005068	Q04724	TLE1_HUMAN	transducin-like enhancer protein 1	618	WD 4.				negative regulation of Wnt receptor signaling pathway|organ morphogenesis|transcription, DNA-dependent|Wnt receptor signaling pathway		transcription factor binding			ovary(1)|skin(1)	2						CAGCTGGCTCCGTCTGTGTGG	0.502													44	23	---	---	---	---	PASS
FRMD3	257019	broad.mit.edu	37	9	85863243	85863243	+	Missense_Mutation	SNP	C	G	G			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:85863243C>G	uc004ams.1	-	14	1586	c.1384G>C	c.(1384-1386)GAG>CAG	p.E462Q	FRMD3_uc004amr.1_Missense_Mutation_p.E448Q|FRMD3_uc004amq.1_Missense_Mutation_p.E119Q	NM_174938	NP_777598	A2A2Y4	FRMD3_HUMAN	FERM domain containing 3	462						cytoplasm|cytoskeleton|extrinsic to membrane|integral to membrane	cytoskeletal protein binding			ovary(1)|central_nervous_system(1)	2						ATGTCAATCTCATCGTCATCC	0.433													58	179	---	---	---	---	PASS
ZNF883	169834	broad.mit.edu	37	9	115760453	115760453	+	Silent	SNP	G	T	T			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:115760453G>T	uc011lwy.1	-	5	1326	c.87C>A	c.(85-87)ACC>ACA	p.T29T		NM_001101338	NP_001094808	P0CG24	ZN883_HUMAN	hypothetical protein LOC169834	29	C2H2-type 1.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						TCTGATGCTGGGTCAGGGATG	0.383													124	59	---	---	---	---	PASS
FAM102A	399665	broad.mit.edu	37	9	130710472	130710472	+	Missense_Mutation	SNP	G	A	A			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130710472G>A	uc004bsx.1	-	6	573	c.494C>T	c.(493-495)CCA>CTA	p.P165L	FAM102A_uc004bsw.1_Missense_Mutation_p.P23L|FAM102A_uc004bsy.1_5'UTR	NM_001035254	NP_001030331	Q5T9C2	F102A_HUMAN	early estrogen-induced gene 1 protein isoform a	165	Ser-rich.									ovary(1)	1						ATCCTGGCCTGGGATGGAGAT	0.617													39	34	---	---	---	---	PASS
SETX	23064	broad.mit.edu	37	9	135203765	135203765	+	Missense_Mutation	SNP	C	T	T			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:135203765C>T	uc004cbk.2	-	10	3403	c.3220G>A	c.(3220-3222)GAG>AAG	p.E1074K	SETX_uc004cbj.2_Missense_Mutation_p.E693K|SETX_uc010mzt.2_Missense_Mutation_p.E693K	NM_015046	NP_055861	Q7Z333	SETX_HUMAN	senataxin	1074					cell death|double-strand break repair|RNA processing	cytoplasm|nucleolus|nucleoplasm	ATP binding|DNA helicase activity			ovary(2)|skin(1)	3		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;6.82e-06)|Epithelial(140;0.000171)		TCAGATTCCTCAAACTGAAAA	0.383													128	92	---	---	---	---	PASS
KIAA0649	9858	broad.mit.edu	37	9	138378032	138378032	+	Missense_Mutation	SNP	C	T	T			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:138378032C>T	uc004cfr.1	+	4	2225	c.1676C>T	c.(1675-1677)CCG>CTG	p.P559L		NM_014811	NP_055626	Q5T8A7	K0649_HUMAN	1A6/DRIM (down-regulated in metastasis)	559						nucleolus	protein binding			ovary(2)|central_nervous_system(1)	3				OV - Ovarian serous cystadenocarcinoma(145;6.91e-08)|Epithelial(140;4.69e-07)|all cancers(34;9.33e-06)		GAGAGCTGCCCGCAGGCTGCC	0.617													105	95	---	---	---	---	PASS
FAM107B	83641	broad.mit.edu	37	10	14816587	14816587	+	Missense_Mutation	SNP	C	G	G			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:14816587C>G	uc001ina.1	-	1	310	c.76G>C	c.(76-78)GCT>CCT	p.A26P	FAM107B_uc010qbu.1_RNA	NM_031453	NP_113641	Q9H098	F107B_HUMAN	hypothetical protein LOC83641	Error:Variant_position_missing_in_Q9H098_after_alignment										breast(4)	4						GCGAGCAGAGCTGAGCACGGA	0.517													24	64	---	---	---	---	PASS
PTER	9317	broad.mit.edu	37	10	16526710	16526710	+	Silent	SNP	G	T	T	rs147446984	byFrequency	TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:16526710G>T	uc001iog.1	+	3	534	c.327G>T	c.(325-327)ACG>ACT	p.T109T	PTER_uc001ioh.1_Silent_p.T109T|PTER_uc001ioi.1_Silent_p.T109T|PTER_uc009xjp.1_Silent_p.T109T	NM_030664	NP_109589	Q96BW5	PTER_HUMAN	phosphotriesterase related	109					catabolic process		hydrolase activity, acting on ester bonds|zinc ion binding			ovary(2)	2						ACACACAGACGTTGAAGAGGC	0.488													48	31	---	---	---	---	PASS
APBB1IP	54518	broad.mit.edu	37	10	26855898	26855898	+	Missense_Mutation	SNP	G	C	C			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:26855898G>C	uc001iss.2	+	15	1803	c.1482G>C	c.(1480-1482)AAG>AAC	p.K494N		NM_019043	NP_061916	Q7Z5R6	AB1IP_HUMAN	amyloid beta (A4) precursor protein-binding,	494					blood coagulation|signal transduction	cytoskeleton|cytosol|focal adhesion|lamellipodium				lung(4)|skin(2)|central_nervous_system(1)	7						AGGATAAGAAGCCAGCCCTCG	0.478													18	14	---	---	---	---	PASS
SVIL	6840	broad.mit.edu	37	10	29770543	29770543	+	Missense_Mutation	SNP	C	G	G			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:29770543C>G	uc001iut.1	-	28	5823	c.5070G>C	c.(5068-5070)GAG>GAC	p.E1690D	LOC387647_uc001iup.2_Intron|LOC387647_uc001iuq.1_Intron|SVIL_uc010qdw.1_Missense_Mutation_p.E604D|SVIL_uc001iuu.1_Missense_Mutation_p.E1264D|SVIL_uc009xlc.2_Missense_Mutation_p.E482D	NM_021738	NP_068506	O95425	SVIL_HUMAN	supervillin isoform 2	1690					cytoskeleton organization|skeletal muscle tissue development	cell junction|costamere|invadopodium|nucleus|podosome	actin filament binding			ovary(5)|upper_aerodigestive_tract(1)	6		Breast(68;0.103)				CGGGGTTCTTCTCATTCGATC	0.493													14	621	---	---	---	---	PASS
ZNF33B	7582	broad.mit.edu	37	10	43127419	43127419	+	Missense_Mutation	SNP	G	C	C			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:43127419G>C	uc001jaf.1	-	4	323	c.208C>G	c.(208-210)CCA>GCA	p.P70A	ZNF33B_uc009xmg.1_Missense_Mutation_p.P70A|ZNF33B_uc001jae.1_RNA|ZNF33B_uc001jag.1_5'UTR	NM_006955	NP_008886	Q06732	ZN33B_HUMAN	zinc finger protein 33B	70	KRAB.					nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0						AGTCTCCATGGTTCTTCTCCT	0.443													15	515	---	---	---	---	PASS
GDF10	2662	broad.mit.edu	37	10	48429014	48429014	+	Missense_Mutation	SNP	G	T	T			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:48429014G>T	uc001jfb.2	-	2	1328	c.872C>A	c.(871-873)GCC>GAC	p.A291D	GDF10_uc009xnp.2_Missense_Mutation_p.A290D|GDF10_uc009xnq.1_Missense_Mutation_p.A291D	NM_004962	NP_004953	P55107	BMP3B_HUMAN	growth differentiation factor 10 precursor	291					growth|skeletal system development|transforming growth factor beta receptor signaling pathway	extracellular space	cytokine activity|growth factor activity			lung(1)|central_nervous_system(1)	2						GGCCTGCGCGGCTCGGCGCAC	0.721													7	3	---	---	---	---	PASS
NLRP6	171389	broad.mit.edu	37	11	281741	281741	+	Silent	SNP	A	C	C			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:281741A>C	uc010qvs.1	+	4	2007	c.2007A>C	c.(2005-2007)GGA>GGC	p.G669G	NLRP6_uc010qvt.1_Silent_p.G669G	NM_138329	NP_612202	P59044	NALP6_HUMAN	NLR family, pyrin domain containing 6	669						cytoplasm	ATP binding			upper_aerodigestive_tract(1)|skin(1)	2		all_cancers(49;1.12e-06)|all_epithelial(84;0.000375)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;4.28e-28)|Epithelial(43;2.47e-27)|OV - Ovarian serous cystadenocarcinoma(40;4.66e-21)|BRCA - Breast invasive adenocarcinoma(625;3.57e-05)|Lung(200;0.0485)|LUSC - Lung squamous cell carcinoma(625;0.122)		GCCCTGCTGGACAGGCACTGC	0.652													28	79	---	---	---	---	PASS
MUC2	4583	broad.mit.edu	37	11	1093584	1093584	+	Silent	SNP	A	T	T			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1093584A>T	uc001lsx.1	+	31	12516	c.12489A>T	c.(12487-12489)CCA>CCT	p.P4163P		NM_002457	NP_002448	Q02817	MUC2_HUMAN	mucin 2 precursor	4163				P -> A (in Ref. 4).		inner mucus layer|outer mucus layer	protein binding			lung(1)|breast(1)	2		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	cGGTGACCGCAACCCCAACAC	0.348													15	28	---	---	---	---	PASS
OR51I1	390063	broad.mit.edu	37	11	5462167	5462167	+	Missense_Mutation	SNP	T	C	C			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5462167T>C	uc010qze.1	-	1	578	c.578A>G	c.(577-579)GAC>GGC	p.D193G	HBG2_uc001mak.1_Intron|HBE1_uc001mam.1_Intron|OR51B5_uc001maq.1_Intron	NM_001005288	NP_001005288	Q9H343	O51I1_HUMAN	olfactory receptor, family 51, subfamily I,	193	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;1.92e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		AACATGGATGTCTCCACATGC	0.443													16	48	---	---	---	---	PASS
OR51I2	390064	broad.mit.edu	37	11	5474866	5474866	+	Silent	SNP	C	A	A	rs145725236		TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5474866C>A	uc010qzf.1	+	1	148	c.148C>A	c.(148-150)CGA>AGA	p.R50R	HBG2_uc001mak.1_Intron|HBE1_uc001mam.1_Intron|OR51B5_uc001maq.1_Intron	NM_001004754	NP_001004754	Q9H344	O51I2_HUMAN	olfactory receptor, family 51, subfamily I,	50	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|skin(2)	4		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;1.09e-10)|BRCA - Breast invasive adenocarcinoma(625;0.135)		GCAGGCTGTGCGAGTGGAGCC	0.577													25	62	---	---	---	---	PASS
EIF4G2	1982	broad.mit.edu	37	11	10825569	10825569	+	Silent	SNP	G	A	A			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:10825569G>A	uc001mjc.2	-	8	996	c.579C>T	c.(577-579)CTC>CTT	p.L193L	EIF4G2_uc001mjb.2_5'UTR|EIF4G2_uc009ygf.2_5'UTR|EIF4G2_uc001mjd.2_Silent_p.L193L|EIF4G2_uc001mjf.1_5'UTR|SNORD97_uc009yge.2_5'Flank	NM_001418	NP_001409	P78344	IF4G2_HUMAN	eukaryotic translation initiation factor 4	193	MIF4G.				cell cycle arrest|cell death|regulation of translational initiation|RNA metabolic process	eukaryotic translation initiation factor 4F complex	protein binding|translation initiation factor activity			ovary(1)|central_nervous_system(1)	2				all cancers(16;2.8e-07)|Epithelial(150;4.18e-07)|BRCA - Breast invasive adenocarcinoma(625;0.111)		CCTCCTCGGGGAGGAGGGGAT	0.388													35	104	---	---	---	---	PASS
DGKZ	8525	broad.mit.edu	37	11	46397475	46397475	+	Missense_Mutation	SNP	A	G	G			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:46397475A>G	uc001ncn.1	+	22	2674	c.2549A>G	c.(2548-2550)TAC>TGC	p.Y850C	DGKZ_uc001nch.1_Missense_Mutation_p.Y678C|DGKZ_uc010rgq.1_Missense_Mutation_p.Y605C|DGKZ_uc001ncj.1_Missense_Mutation_p.Y628C|DGKZ_uc010rgr.1_Missense_Mutation_p.Y627C|DGKZ_uc001nck.1_Missense_Mutation_p.Y440C|DGKZ_uc001ncl.2_Missense_Mutation_p.Y662C|DGKZ_uc001ncm.2_Missense_Mutation_p.Y661C|DGKZ_uc009yky.1_Missense_Mutation_p.Y662C|DGKZ_uc010rgs.1_Missense_Mutation_p.Y639C	NM_001105540	NP_001099010	Q13574	DGKZ_HUMAN	diacylglycerol kinase zeta isoform 4	850					activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|cell migration|intracellular signal transduction|mitotic cell cycle G1/S transition DNA damage checkpoint|negative regulation of mitotic cell cycle|platelet activation	cytoplasm|lamellipodium|nucleus|plasma membrane	ATP binding|diacylglycerol kinase activity|diacylglycerol kinase activity|lipid kinase activity|metal ion binding|protein binding|protein C-terminus binding			pancreas(1)|central_nervous_system(1)|skin(1)	3				GBM - Glioblastoma multiforme(35;0.0259)|Lung(87;0.141)		GCCCTGCACTACGACAAGGAG	0.701													11	9	---	---	---	---	PASS
OR5W2	390148	broad.mit.edu	37	11	55681828	55681828	+	Silent	SNP	A	T	T			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55681828A>T	uc010rir.1	-	1	231	c.231T>A	c.(229-231)ACT>ACA	p.T77T		NM_001001960	NP_001001960	Q8NH69	OR5W2_HUMAN	olfactory receptor, family 5, subfamily W,	77	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|skin(1)	2						TCTTGGGCCCAGTTGCAGTAG	0.413													44	86	---	---	---	---	PASS
OR8H1	219469	broad.mit.edu	37	11	56057972	56057972	+	Missense_Mutation	SNP	C	A	A			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:56057972C>A	uc010rje.1	-	1	567	c.567G>T	c.(565-567)ATG>ATT	p.M189I		NM_001005199	NP_001005199	Q8NGG4	OR8H1_HUMAN	olfactory receptor, family 8, subfamily H,	189	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|pancreas(1)|skin(1)	3	Esophageal squamous(21;0.00448)					CGTATGTGTCCATGCAGGACA	0.428													60	131	---	---	---	---	PASS
OR5M11	219487	broad.mit.edu	37	11	56309961	56309961	+	Missense_Mutation	SNP	T	C	C			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:56309961T>C	uc010rjl.1	-	1	773	c.773A>G	c.(772-774)TAT>TGT	p.Y258C		NM_001005245	NP_001005245	Q96RB7	OR5MB_HUMAN	olfactory receptor, family 5, subfamily M,	258	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0						TGGTCTTATATACATGCAAAA	0.433													52	88	---	---	---	---	PASS
OR4D11	219986	broad.mit.edu	37	11	59271632	59271632	+	Missense_Mutation	SNP	T	A	A			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:59271632T>A	uc001noa.1	+	1	584	c.584T>A	c.(583-585)CTT>CAT	p.L195H		NM_001004706	NP_001004706	Q8NGI4	OR4DB_HUMAN	olfactory receptor, family 4, subfamily D,	195	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|skin(1)	2						ACTTTTGCTCTTGAGTTCTTG	0.488													79	212	---	---	---	---	PASS
SPTBN2	6712	broad.mit.edu	37	11	66468296	66468296	+	Missense_Mutation	SNP	C	T	T			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66468296C>T	uc001ojd.2	-	16	3346	c.3274G>A	c.(3274-3276)GAA>AAA	p.E1092K		NM_006946	NP_008877	O15020	SPTN2_HUMAN	spectrin, beta, non-erythrocytic 2	1092	Spectrin 8.				actin filament capping|axon guidance|cell death|vesicle-mediated transport	cytosol|spectrin	actin binding|structural constituent of cytoskeleton			large_intestine(1)|pancreas(1)|central_nervous_system(1)|skin(1)	4						GCCGGCCCTTCTTCAGAGGCC	0.687													11	28	---	---	---	---	PASS
PCF11	51585	broad.mit.edu	37	11	82880157	82880157	+	Missense_Mutation	SNP	C	T	T			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:82880157C>T	uc001ozx.3	+	8	3125	c.2780C>T	c.(2779-2781)GCG>GTG	p.A927V	PCF11_uc010rsu.1_Missense_Mutation_p.A1058V	NM_015885	NP_056969	O94913	PCF11_HUMAN	pre-mRNA cleavage complex II protein Pcf11	927	Gly-rich.				mRNA 3'-end processing|mRNA cleavage|nuclear mRNA splicing, via spliceosome|termination of RNA polymerase II transcription	mRNA cleavage factor complex				ovary(1)	1						TCAGGGGCTGCGATTAGGTTT	0.542													24	43	---	---	---	---	PASS
GRIA4	2893	broad.mit.edu	37	11	105789538	105789538	+	Missense_Mutation	SNP	A	G	G			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:105789538A>G	uc001pix.2	+	11	1816	c.1370A>G	c.(1369-1371)CAT>CGT	p.H457R	GRIA4_uc001piw.2_Missense_Mutation_p.H457R	NM_000829	NP_000820	P48058	GRIA4_HUMAN	glutamate receptor, ionotrophic, AMPA 4 isoform	457	Extracellular (Potential).				glutamate signaling pathway|synaptic transmission	cell junction|endocytic vesicle membrane|integral to membrane|postsynaptic membrane	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity			ovary(3)|skin(3)|lung(1)|central_nervous_system(1)	8		Melanoma(852;0.000902)|Acute lymphoblastic leukemia(157;0.000994)|all_hematologic(158;0.0017)|Breast(348;0.0323)		BRCA - Breast invasive adenocarcinoma(274;0.000147)|Epithelial(105;0.0291)|all cancers(92;0.0899)	L-Glutamic Acid(DB00142)	ATTGCAAAACATATTGGTATC	0.358													26	63	---	---	---	---	PASS
EXPH5	23086	broad.mit.edu	37	11	108398896	108398896	+	Silent	SNP	T	G	G			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:108398896T>G	uc001pkk.2	-	4	570	c.459A>C	c.(457-459)GCA>GCC	p.A153A	EXPH5_uc010rvy.1_Intron|EXPH5_uc010rvz.1_5'UTR|EXPH5_uc010rwa.1_Silent_p.A77A	NM_015065	NP_055880	Q8NEV8	EXPH5_HUMAN	exophilin 5 isoform a	153					intracellular protein transport		Rab GTPase binding			skin(3)|ovary(2)	5		all_cancers(61;3.99e-08)|Acute lymphoblastic leukemia(157;3.97e-05)|Melanoma(852;4.04e-05)|all_epithelial(67;0.000116)|all_hematologic(158;0.000315)|Breast(348;0.104)|all_neural(303;0.16)		Epithelial(105;8.1e-06)|BRCA - Breast invasive adenocarcinoma(274;1.22e-05)|all cancers(92;0.000129)|OV - Ovarian serous cystadenocarcinoma(223;0.11)|Colorectal(284;0.184)		TAGGAGGTCCTGCATGGCCAT	0.418													46	82	---	---	---	---	PASS
OR10S1	219873	broad.mit.edu	37	11	123847651	123847651	+	Silent	SNP	G	T	T			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:123847651G>T	uc001pzm.1	-	1	748	c.748C>A	c.(748-750)CGG>AGG	p.R250R		NM_001004474	NP_001004474	Q8NGN2	O10S1_HUMAN	olfactory receptor, family 10, subfamily S,	250	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|skin(1)	2		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0399)		GAGAAGGCCCGCTGCCGGCCC	0.617													45	69	---	---	---	---	PASS
OR10G8	219869	broad.mit.edu	37	11	123900704	123900704	+	Missense_Mutation	SNP	C	G	G			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:123900704C>G	uc001pzp.1	+	1	375	c.375C>G	c.(373-375)ATC>ATG	p.I125M		NM_001004464	NP_001004464	Q8NGN5	O10G8_HUMAN	olfactory receptor, family 10, subfamily G,	125	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|skin(1)	2		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0521)		ACCTGGCCATCAGTTACCCGC	0.567													67	131	---	---	---	---	PASS
C1R	715	broad.mit.edu	37	12	7241522	7241522	+	Missense_Mutation	SNP	C	T	T			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:7241522C>T	uc010sfy.1	-	6	888	c.829G>A	c.(829-831)GAC>AAC	p.D277N	C1R_uc010sfz.1_Missense_Mutation_p.D291N|C1R_uc010sga.1_Missense_Mutation_p.D243N	NM_001733	NP_001724	P00736	C1R_HUMAN	complement component 1, r subcomponent	277	CUB 2.				complement activation, classical pathway|innate immune response|proteolysis	extracellular region	calcium ion binding|serine-type endopeptidase activity				0					Abciximab(DB00054)|Adalimumab(DB00051)|Alefacept(DB00092)|Alemtuzumab(DB00087)|Basiliximab(DB00074)|Bevacizumab(DB00112)|Cetuximab(DB00002)|Daclizumab(DB00111)|Efalizumab(DB00095)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Immune globulin(DB00028)|Muromonab(DB00075)|Natalizumab(DB00108)|Palivizumab(DB00110)|Rituximab(DB00073)|Tositumomab(DB00081)|Trastuzumab(DB00072)	CTGCTGGTGTCGAGGTCGGGG	0.562													15	22	---	---	---	---	PASS
LMO3	55885	broad.mit.edu	37	12	16704154	16704154	+	3'UTR	SNP	G	C	C			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:16704154G>C	uc001rdk.1	-	4					LMO3_uc001rdj.1_3'UTR|LMO3_uc010shy.1_3'UTR|LMO3_uc001rdl.1_3'UTR|LMO3_uc009zii.1_RNA|LMO3_uc010shz.1_3'UTR|LMO3_uc001rdm.1_3'UTR|LMO3_uc001rdo.1_RNA|LMO3_uc001rdp.1_RNA|LMO3_uc001rdn.1_3'UTR|LMO3_uc009zij.1_RNA|LMO3_uc009zik.1_RNA	NM_018640	NP_061110	Q8TAP4	LMO3_HUMAN	LIM domain only 3						regulation of transcription, DNA-dependent|transcription, DNA-dependent		zinc ion binding				0		Hepatocellular(102;0.244)				GATGTTGATAGATCAGCGAAC	0.388													77	151	---	---	---	---	PASS
ITPR2	3709	broad.mit.edu	37	12	26709222	26709222	+	Silent	SNP	T	C	C			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:26709222T>C	uc001rhg.2	-	36	5325	c.4908A>G	c.(4906-4908)GAA>GAG	p.E1636E		NM_002223	NP_002214	Q14571	ITPR2_HUMAN	inositol 1,4,5-triphosphate receptor, type 2	1636	Cytoplasmic (Potential).				activation of phospholipase C activity|energy reserve metabolic process|nerve growth factor receptor signaling pathway|platelet activation|regulation of insulin secretion|response to hypoxia	integral to membrane|plasma membrane enriched fraction|platelet dense tubular network membrane|sarcoplasmic reticulum membrane	calcium ion transmembrane transporter activity|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity			kidney(6)|ovary(4)|skin(2)|upper_aerodigestive_tract(1)|lung(1)	14	Colorectal(261;0.0847)					GGAACAGCAGTTCTGGACTGT	0.473													90	159	---	---	---	---	PASS
SYT10	341359	broad.mit.edu	37	12	33579079	33579079	+	Nonsense_Mutation	SNP	G	T	T			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:33579079G>T	uc001rll.1	-	2	800	c.503C>A	c.(502-504)TCA>TAA	p.S168*	SYT10_uc009zju.1_5'UTR	NM_198992	NP_945343	Q6XYQ8	SYT10_HUMAN	synaptotagmin X	168	Cytoplasmic (Potential).					cell junction|integral to membrane|synaptic vesicle membrane	metal ion binding|transporter activity			ovary(1)|skin(1)	2	Lung NSC(5;8.37e-07)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0334)					TTACCGGGTTGATGACGTAGG	0.279													149	333	---	---	---	---	PASS
ADAMTS20	80070	broad.mit.edu	37	12	43925955	43925955	+	Missense_Mutation	SNP	G	C	C			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:43925955G>C	uc010skx.1	-	3	497	c.497C>G	c.(496-498)CCT>CGT	p.P166R		NM_025003	NP_079279	P59510	ATS20_HUMAN	a disintegrin-like and metalloprotease with	166						proteinaceous extracellular matrix	zinc ion binding			central_nervous_system(5)|ovary(4)|lung(3)|large_intestine(2)|skin(2)|urinary_tract(1)|kidney(1)|pancreas(1)	19	all_cancers(12;2.6e-05)|Lung SC(27;0.184)	Lung NSC(34;0.0569)|all_lung(34;0.129)		GBM - Glioblastoma multiforme(48;0.0473)		CTTCATTATAGGTTCTAAGAA	0.348													21	151	---	---	---	---	PASS
TROAP	10024	broad.mit.edu	37	12	49719645	49719645	+	Missense_Mutation	SNP	G	T	T			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49719645G>T	uc001rtx.3	+	5	778	c.611G>T	c.(610-612)TGC>TTC	p.C204F	TROAP_uc009zlh.2_Missense_Mutation_p.C204F|TROAP_uc001rty.2_5'Flank	NM_005480	NP_005471	Q12815	TROAP_HUMAN	tastin isoform 1	204					cell adhesion	cytoplasm				ovary(1)	1						CGGACATTGTGCCCCCAGAGG	0.632													24	60	---	---	---	---	PASS
FAIM2	23017	broad.mit.edu	37	12	50264382	50264382	+	Missense_Mutation	SNP	G	T	T			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:50264382G>T	uc001rvj.1	-	12	1001	c.856C>A	c.(856-858)CCT>ACT	p.P286T	FAIM2_uc001rvi.1_Missense_Mutation_p.P240T|FAIM2_uc001rvk.1_RNA	NM_012306	NP_036438	Q9BWQ8	FAIM2_HUMAN	Fas apoptotic inhibitory molecule 2	286					anti-apoptosis|apoptosis	cell junction|integral to membrane|postsynaptic membrane				large_intestine(1)|ovary(1)|skin(1)	3						TACTCCTCAGGGCTCAGCGAG	0.517													54	84	---	---	---	---	PASS
KRT6A	3853	broad.mit.edu	37	12	52884946	52884946	+	Missense_Mutation	SNP	C	T	T			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52884946C>T	uc001sam.2	-	3	975	c.766G>A	c.(766-768)GAA>AAA	p.E256K		NM_005554	NP_005545	P02538	K2C6A_HUMAN	keratin 6A	256	Coil 1B.|Rod.				cell differentiation|ectoderm development|positive regulation of cell proliferation	keratin filament	protein binding|structural constituent of cytoskeleton			ovary(4)|skin(1)	5				BRCA - Breast invasive adenocarcinoma(357;0.189)		TTGTTGATTTCATCCTCATAT	0.453													88	170	---	---	---	---	PASS
HOXC12	3228	broad.mit.edu	37	12	54350155	54350155	+	Silent	SNP	C	T	T			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54350155C>T	uc010soq.1	+	2	654	c.654C>T	c.(652-654)CGC>CGT	p.R218R		NM_173860	NP_776272	P31275	HXC12_HUMAN	homeobox C12	218	Homeobox.				multicellular organismal development	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			upper_aerodigestive_tract(1)	1						GGAAGAAGCGCAAGCCCTATT	0.592													88	149	---	---	---	---	PASS
HOXC11	3227	broad.mit.edu	37	12	54367289	54367289	+	Missense_Mutation	SNP	C	G	G			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54367289C>G	uc001sem.2	+	1	380	c.264C>G	c.(262-264)AGC>AGG	p.S88R		NM_014212	NP_055027	O43248	HXC11_HUMAN	homeobox C11	88					endoderm development	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1						ATCGGAACAGCTACTCCTCCT	0.627			T	NUP98	AML								82	145	---	---	---	---	PASS
DNAJC14	85406	broad.mit.edu	37	12	56221155	56221155	+	Nonsense_Mutation	SNP	G	A	A			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56221155G>A	uc001shx.1	-	2	1492	c.1288C>T	c.(1288-1290)CGA>TGA	p.R430*	DNAJC14_uc001shu.1_Nonsense_Mutation_p.R430*|DNAJC14_uc009zob.1_Nonsense_Mutation_p.R430*|DNAJC14_uc001shy.1_Nonsense_Mutation_p.R430*	NM_032364	NP_115740	Q6Y2X3	DJC14_HUMAN	dopamine receptor interacting protein	430					protein folding|protein transport	endoplasmic reticulum membrane|integral to membrane	heat shock protein binding|unfolded protein binding			ovary(3)|large_intestine(1)	4						GTCAAGAGTCGAGCCACTTCC	0.542													82	153	---	---	---	---	PASS
GAS2L3	283431	broad.mit.edu	37	12	101012343	101012343	+	Missense_Mutation	SNP	G	A	A	rs147048300	by1000genomes	TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:101012343G>A	uc001thu.2	+	8	852	c.626G>A	c.(625-627)CGG>CAG	p.R209Q	GAS2L3_uc009zty.2_Missense_Mutation_p.R209Q|GAS2L3_uc001thv.2_Missense_Mutation_p.R105Q	NM_174942	NP_777602	Q86XJ1	GA2L3_HUMAN	growth arrest-specific 2 like 3	209	GAR.				cell cycle arrest					skin(1)	1						TCATGCTGTCGGCATGAAGAG	0.398													8	232	---	---	---	---	PASS
SRRM4	84530	broad.mit.edu	37	12	119583288	119583288	+	Missense_Mutation	SNP	T	G	G			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:119583288T>G	uc001txa.1	+	9	1166	c.874T>G	c.(874-876)TCC>GCC	p.S292A		NM_194286	NP_919262	A7MD48	SRRM4_HUMAN	KIAA1853 protein	292	Ser-rich.				cell differentiation|mRNA processing|nervous system development|regulation of RNA splicing|RNA splicing	nucleus	mRNA binding			ovary(2)	2						AAATGACACGTCCTCGCCACC	0.637													6	17	---	---	---	---	PASS
EP400	57634	broad.mit.edu	37	12	132508341	132508341	+	Silent	SNP	A	T	T			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:132508341A>T	uc001ujn.2	+	23	4745	c.4710A>T	c.(4708-4710)ATA>ATT	p.I1570I	EP400_uc001ujl.2_Silent_p.I1569I|EP400_uc001ujm.2_Silent_p.I1489I	NM_015409	NP_056224	Q96L91	EP400_HUMAN	E1A binding protein p400	1606					histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent	NuA4 histone acetyltransferase complex|nuclear speck	ATP binding|DNA binding|helicase activity			central_nervous_system(4)|ovary(3)|breast(3)|skin(2)	12	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.198)		OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06)		TAGTGAAAATAGCTCAGCTGG	0.493													53	82	---	---	---	---	PASS
GOLGA3	2802	broad.mit.edu	37	12	133350809	133350809	+	Missense_Mutation	SNP	A	T	T			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:133350809A>T	uc001ukz.1	-	23	4800	c.4241T>A	c.(4240-4242)CTG>CAG	p.L1414Q		NM_005895	NP_005886	Q08378	GOGA3_HUMAN	Golgi autoantigen, golgin subfamily a, 3	1414	Potential.				intra-Golgi vesicle-mediated transport	Golgi cisterna membrane|Golgi transport complex	protein binding|transporter activity			ovary(3)|central_nervous_system(2)|pancreas(1)	6	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0176)|Lung NSC(355;0.204)		OV - Ovarian serous cystadenocarcinoma(86;2.27e-08)|Epithelial(86;3.34e-07)|all cancers(50;9.4e-06)		CGGTGGTCTCAGCAGCTCCTC	0.622													20	44	---	---	---	---	PASS
HTR2A	3356	broad.mit.edu	37	13	47409668	47409668	+	Missense_Mutation	SNP	A	T	T			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:47409668A>T	uc001vbq.2	-	3	854	c.720T>A	c.(718-720)TTT>TTA	p.F240L	HTR2A_uc001vbr.2_Missense_Mutation_p.F140L|HTR2A_uc010acr.2_Missense_Mutation_p.F240L	NM_000621	NP_000612	P28223	5HT2A_HUMAN	5-hydroxytryptamine receptor 2A isoform 1	240	Helical; Name=5; (By similarity).				ERK1 and ERK2 cascade|phosphatidylinositol 3-kinase cascade|phosphatidylinositol biosynthetic process|release of sequestered calcium ion into cytosol|response to drug|synaptic transmission	integral to plasma membrane	1-(4-iodo-2,5-dimethoxyphenyl)propan-2-amine binding|drug binding|phosphatidylinositol phospholipase C activity|serotonin binding|serotonin receptor activity			ovary(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	6		all_lung(13;7.2e-10)|Lung NSC(96;3.77e-07)|Breast(56;2.06e-05)|Prostate(109;0.00116)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)|Myeloproliferative disorder(33;0.0333)		GBM - Glioblastoma multiforme(144;4.67e-05)|COAD - Colon adenocarcinoma(199;0.224)	Aripiprazole(DB01238)|Chlorpromazine(DB00477)|Chlorprothixene(DB01239)|Cisapride(DB00604)|Clomipramine(DB01242)|Clozapine(DB00363)|Cyclobenzaprine(DB00924)|Cyproheptadine(DB00434)|Dihydroergotamine(DB00320)|Donepezil(DB00843)|Epinastine(DB00751)|Ergotamine(DB00696)|Fluvoxamine(DB00176)|Mesoridazine(DB00933)|Methysergide(DB00247)|Mianserin(DB06148)|Minaprine(DB00805)|Mirtazapine(DB00370)|Nefazodone(DB01149)|Olanzapine(DB00334)|Paliperidone(DB01267)|Paroxetine(DB00715)|Prochlorperazine(DB00433)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Quetiapine(DB01224)|Risperidone(DB00734)|Sertindole(DB06144)|Thiethylperazine(DB00372)|Thioridazine(DB00679)|Tranylcypromine(DB00752)|Trazodone(DB00656)|Venlafaxine(DB00285)|Ziprasidone(DB00246)	AAAATGACACAAAAGAGCCGA	0.438													34	33	---	---	---	---	PASS
ATP7B	540	broad.mit.edu	37	13	52520501	52520501	+	Silent	SNP	C	T	T			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:52520501C>T	uc001vfw.2	-	13	3136	c.2979G>A	c.(2977-2979)ACG>ACA	p.T993T	ATP7B_uc010adv.2_Silent_p.T563T|ATP7B_uc001vfx.2_Silent_p.T786T|ATP7B_uc001vfy.2_Silent_p.T882T|ATP7B_uc010tgt.1_Intron|ATP7B_uc010tgu.1_Silent_p.T945T|ATP7B_uc010tgv.1_Silent_p.T915T|ATP7B_uc001vfv.2_Silent_p.T265T|ATP7B_uc010tgs.1_Silent_p.T265T	NM_000053	NP_000044	P35670	ATP7B_HUMAN	ATPase, Cu++ transporting, beta polypeptide	993	Helical; (Potential).				ATP biosynthetic process|cellular copper ion homeostasis|copper ion import|response to copper ion|sequestering of calcium ion	Golgi membrane|integral to plasma membrane|late endosome|mitochondrion	ATP binding|copper ion binding|copper-exporting ATPase activity|protein binding			ovary(1)|central_nervous_system(1)|skin(1)	3		Breast(56;0.000207)|Lung NSC(96;0.000845)|Prostate(109;0.0235)|Hepatocellular(98;0.065)|all_neural(104;0.19)		GBM - Glioblastoma multiforme(99;5.25e-08)		CCATGACAGCCGTGGGCGTGG	0.642									Wilson_disease				16	5	---	---	---	---	PASS
SALL2	6297	broad.mit.edu	37	14	21991560	21991560	+	Missense_Mutation	SNP	C	G	G			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:21991560C>G	uc001wbe.2	-	2	2584	c.2302G>C	c.(2302-2304)GAG>CAG	p.E768Q	SALL2_uc010tly.1_Missense_Mutation_p.E766Q|SALL2_uc010tlz.1_Missense_Mutation_p.E631Q|SALL2_uc001wbf.3_Intron|SALL2_uc010tma.1_Missense_Mutation_p.E633Q|SALL2_uc001wbg.1_Intron	NM_005407	NP_005398	Q9Y467	SALL2_HUMAN	sal-like 2	768	Poly-Glu.						DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)|large_intestine(1)	3	all_cancers(95;0.000662)			GBM - Glioblastoma multiforme(265;0.0151)		tcatcctcctcttcctcctcc	0.458													40	107	---	---	---	---	PASS
JUB	84962	broad.mit.edu	37	14	23444075	23444075	+	Silent	SNP	G	A	A			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23444075G>A	uc001whz.2	-	6	1771	c.1395C>T	c.(1393-1395)GCC>GCT	p.A465A	JUB_uc001why.2_Silent_p.A48A	NM_032876	NP_116265	Q96IF1	JUB_HUMAN	ajuba isoform 1	465	LIM zinc-binding 3.				cell cycle|gene silencing by miRNA|positive regulation of protein complex assembly	cell-cell junction|cytoplasmic mRNA processing body|microtubule organizing center	alpha-catenin binding|zinc ion binding				0	all_cancers(95;4.6e-05)			GBM - Glioblastoma multiforme(265;0.0122)		GTTGGCCACAGGCTGCACACT	0.577													177	47	---	---	---	---	PASS
NID2	22795	broad.mit.edu	37	14	52534597	52534597	+	Silent	SNP	G	A	A			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:52534597G>A	uc001wzo.2	-	2	747	c.513C>T	c.(511-513)CGC>CGT	p.R171R	NID2_uc010tqs.1_Silent_p.R171R|NID2_uc010tqt.1_Silent_p.R171R|NID2_uc001wzp.2_Silent_p.R171R	NM_007361	NP_031387	Q14112	NID2_HUMAN	nidogen 2 precursor	171	NIDO.					basement membrane	calcium ion binding|collagen binding			pancreas(2)|breast(2)|ovary(1)|liver(1)|skin(1)	7	Breast(41;0.0639)|all_epithelial(31;0.123)					GCAGCGCCCCGCGCTTGACCT	0.632													24	432	---	---	---	---	PASS
TXNDC16	57544	broad.mit.edu	37	14	52955213	52955213	+	Intron	SNP	A	G	G			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:52955213A>G	uc001wzs.2	-						TXNDC16_uc010tqu.1_Intron|TXNDC16_uc010aoe.2_Intron	NM_020784	NP_065835	Q9P2K2	TXD16_HUMAN	thioredoxin domain containing 16 isoform 1						cell redox homeostasis	extracellular region					0	Breast(41;0.0716)					CCCTAGAAATACATTAATTTT	0.199													22	45	---	---	---	---	PASS
C14orf135	64430	broad.mit.edu	37	14	60574806	60574806	+	Intron	SNP	G	T	T			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:60574806G>T	uc001xer.3	+						C14orf135_uc001xeq.2_Intron	NM_022495	NP_071940	Q63HM2	CN135_HUMAN	hepatitis C virus F protein-binding protein 2							integral to membrane				ovary(2)	2		Myeloproliferative disorder(585;0.163)		OV - Ovarian serous cystadenocarcinoma(108;0.127)		CTGGATTAGCGTGTGGTCTTG	0.413													46	91	---	---	---	---	PASS
ADAM21	8747	broad.mit.edu	37	14	70925402	70925402	+	Missense_Mutation	SNP	A	T	T			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:70925402A>T	uc001xmd.2	+	1	1186	c.1186A>T	c.(1186-1188)AAT>TAT	p.N396Y		NM_003813	NP_003804	Q9UKJ8	ADA21_HUMAN	ADAM metallopeptidase domain 21 preproprotein	396	Peptidase M12B.|Extracellular (Potential).				proteolysis|single fertilization	integral to membrane	metalloendopeptidase activity|zinc ion binding			pancreas(1)|skin(1)	2				all cancers(60;0.00326)|BRCA - Breast invasive adenocarcinoma(234;0.00646)|OV - Ovarian serous cystadenocarcinoma(108;0.0401)		ATGTCTGCATAATCCTCCAAG	0.438													185	79	---	---	---	---	PASS
SIPA1L1	26037	broad.mit.edu	37	14	72200451	72200451	+	Missense_Mutation	SNP	C	T	T			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:72200451C>T	uc001xms.2	+	19	5341	c.4993C>T	c.(4993-4995)CCT>TCT	p.P1665S	SIPA1L1_uc001xmt.2_Missense_Mutation_p.P1644S|SIPA1L1_uc001xmu.2_Missense_Mutation_p.P1644S|SIPA1L1_uc001xmv.2_Missense_Mutation_p.P1665S|SIPA1L1_uc010ttm.1_Missense_Mutation_p.P1119S|SIPA1L1_uc001xmw.2_Missense_Mutation_p.P430S	NM_015556	NP_056371	O43166	SI1L1_HUMAN	signal-induced proliferation-associated 1 like	1665					actin cytoskeleton reorganization|activation of Rap GTPase activity|regulation of dendritic spine morphogenesis	cell junction|cytoplasm|dendritic spine|postsynaptic density|postsynaptic membrane|synaptosome	GTPase activator activity			ovary(3)|breast(1)	4				all cancers(60;0.00169)|BRCA - Breast invasive adenocarcinoma(234;0.00912)|OV - Ovarian serous cystadenocarcinoma(108;0.0109)		TATGCCCGACCCTGGCCTGAT	0.587													36	52	---	---	---	---	PASS
ABCD4	5826	broad.mit.edu	37	14	74753465	74753465	+	Missense_Mutation	SNP	C	T	T			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:74753465C>T	uc001xpr.2	-	18	1843	c.1691G>A	c.(1690-1692)CGC>CAC	p.R564H	ABCD4_uc001xps.2_Missense_Mutation_p.R405H|ABCD4_uc001xpt.2_Missense_Mutation_p.R405H|ABCD4_uc010tur.1_Missense_Mutation_p.R460H	NM_005050	NP_005041	O14678	ABCD4_HUMAN	ATP-binding cassette, sub-family D, member 4	564	ABC transporter.					ATP-binding cassette (ABC) transporter complex|integral to membrane|peroxisomal membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances			upper_aerodigestive_tract(2)|large_intestine(1)|ovary(1)	4				BRCA - Breast invasive adenocarcinoma(234;0.00153)		CTGGCCGATGCGATAGAGCTC	0.582													11	102	---	---	---	---	PASS
FLRT2	23768	broad.mit.edu	37	14	86088921	86088921	+	Missense_Mutation	SNP	A	G	G			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:86088921A>G	uc001xvr.2	+	2	1830	c.1063A>G	c.(1063-1065)ATG>GTG	p.M355V	FLRT2_uc010atd.2_Missense_Mutation_p.M355V	NM_013231	NP_037363	O43155	FLRT2_HUMAN	fibronectin leucine rich transmembrane protein 2	355	Extracellular (Potential).|LRRCT.				cell adhesion	integral to plasma membrane|proteinaceous extracellular matrix	protein binding, bridging|receptor signaling protein activity			ovary(3)|haematopoietic_and_lymphoid_tissue(1)	4				BRCA - Breast invasive adenocarcinoma(234;0.0319)		GGAATTAAATATGAATCTTTT	0.547													269	94	---	---	---	---	PASS
HSP90AA1	3320	broad.mit.edu	37	14	102605647	102605647	+	Missense_Mutation	SNP	T	C	C			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:102605647T>C	uc001ykv.3	-	1	440	c.95A>G	c.(94-96)GAC>GGC	p.D32G	WDR20_uc001yky.1_5'Flank|WDR20_uc001yla.2_5'Flank|WDR20_uc001ykz.2_5'Flank|WDR20_uc001ylb.2_5'Flank|WDR20_uc010txu.1_5'Flank|WDR20_uc001ylc.2_5'Flank|WDR20_uc001yld.2_5'Flank|WDR20_uc001yle.2_5'Flank|WDR20_uc001ylf.2_5'Flank	NM_001017963	NP_001017963	P07900	HS90A_HUMAN	heat shock 90kDa protein 1, alpha isoform 1	Error:Variant_position_missing_in_P07900_after_alignment					axon guidance|cellular chaperone-mediated protein complex assembly|G2/M transition of mitotic cell cycle|nitric oxide metabolic process|positive regulation of nitric oxide biosynthetic process|protein import into mitochondrial outer membrane|protein refolding|regulation of nitric-oxide synthase activity|response to unfolded protein|signal transduction	cytosol|melanosome|plasma membrane	ATP binding|ATPase activity|nitric-oxide synthase regulator activity|protein homodimerization activity|TPR domain binding|unfolded protein binding			ovary(2)|central_nervous_system(2)|prostate(1)|lung(1)|breast(1)	7					Rifabutin(DB00615)	ATCCAGACGGTCGCGCGGGTA	0.642													21	34	---	---	---	---	PASS
CYFIP1	23191	broad.mit.edu	37	15	22962496	22962496	+	Missense_Mutation	SNP	A	T	T			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:22962496A>T	uc001yus.2	+	20	2320	c.2216A>T	c.(2215-2217)CAC>CTC	p.H739L	CYFIP1_uc001yut.2_Missense_Mutation_p.H739L|CYFIP1_uc010aya.1_Missense_Mutation_p.H767L|CYFIP1_uc001yuu.2_Missense_Mutation_p.H308L	NM_014608	NP_055423	Q7L576	CYFP1_HUMAN	cytoplasmic FMR1 interacting protein 1 isoform	739					axon extension|lamellipodium assembly|regulation of cell shape|ruffle organization	cell junction|lamellipodium|mRNA cap binding complex|perinuclear region of cytoplasm|ruffle|synapse|synaptosome	actin filament binding|Rac GTPase binding			ovary(4)|pancreas(3)|liver(1)|skin(1)	9		all_cancers(20;2.26e-25)|all_epithelial(15;2.1e-22)|Lung NSC(15;3.36e-17)|all_lung(15;1.04e-16)|Breast(32;0.000776)|Colorectal(260;0.0488)		all cancers(64;2.22e-06)|Epithelial(43;1.49e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00101)		GCCACGATCCACCTCCCGCCG	0.507													21	23	---	---	---	---	PASS
SHF	90525	broad.mit.edu	37	15	45491044	45491044	+	Nonsense_Mutation	SNP	T	A	A			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:45491044T>A	uc001zuy.2	-	2	724	c.229A>T	c.(229-231)AAG>TAG	p.K77*		NM_138356	NP_612365	Q7M4L6	SHF_HUMAN	Src homology 2 domain containing F	77										ovary(1)	1		all_cancers(109;8.13e-11)|all_epithelial(112;6.29e-09)|Lung NSC(122;3.57e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;4.1e-16)|GBM - Glioblastoma multiforme(94;5.98e-06)		CTTTTCTTCTTCTGTTTTGGC	0.572											OREG0023105	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	123	84	---	---	---	---	PASS
MYO5A	4644	broad.mit.edu	37	15	52641006	52641006	+	Intron	SNP	T	A	A			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:52641006T>A	uc002aby.2	-						MYO5A_uc002abx.3_Intron|MYO5A_uc010ugd.1_Intron|MYO5A_uc002aca.1_Intron|MYO5A_uc002acb.1_Intron|MYO5A_uc002acc.1_Intron	NM_000259	NP_000250	Q9Y4I1	MYO5A_HUMAN	myosin VA isoform 1						actin filament-based movement|transport	cytoplasm|growth cone|myosin complex|ruffle	actin binding|ATP binding|calmodulin binding|microfilament motor activity			ovary(3)|central_nervous_system(1)	4				all cancers(107;0.0085)|Colorectal(133;0.077)|READ - Rectum adenocarcinoma(133;0.196)		AAAAAAAAGGTATAATTACCT	0.299													6	10	---	---	---	---	PASS
SGK269	79834	broad.mit.edu	37	15	77471208	77471208	+	Missense_Mutation	SNP	C	G	G			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:77471208C>G	uc002bcm.2	-	3	3369	c.3061G>C	c.(3061-3063)GAG>CAG	p.E1021Q	SGK269_uc002bcn.2_Missense_Mutation_p.E1021Q	NM_024776	NP_079052	Q9H792	PEAK1_HUMAN	NKF3 kinase family member	1021					cell migration|protein autophosphorylation|substrate adhesion-dependent cell spreading	actin cytoskeleton|cytoplasm|focal adhesion	ATP binding|non-membrane spanning protein tyrosine kinase activity|protein binding				0				STAD - Stomach adenocarcinoma(199;0.124)		AATGCATTCTCTGCTCTACCC	0.468													36	110	---	---	---	---	PASS
EFTUD1	79631	broad.mit.edu	37	15	82523274	82523274	+	Missense_Mutation	SNP	C	G	G			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:82523274C>G	uc002bgt.1	-	8	939	c.770G>C	c.(769-771)GGC>GCC	p.G257A	EFTUD1_uc002bgu.1_Missense_Mutation_p.G206A	NM_024580	NP_078856	Q7Z2Z2	ETUD1_HUMAN	elongation factor Tu GTP binding domain	257					mature ribosome assembly		GTP binding|GTPase activity|ribosome binding|translation elongation factor activity			ovary(1)	1						CTTTTTGATGCCAATTTTTTG	0.289													17	140	---	---	---	---	PASS
TARSL2	123283	broad.mit.edu	37	15	102244059	102244059	+	Intron	SNP	T	C	C			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:102244059T>C	uc002bxm.2	-						TARSL2_uc002bxl.2_5'Flank|TARSL2_uc010usi.1_Intron	NM_152334	NP_689547	A2RTX5	SYTC2_HUMAN	threonyl-tRNA synthetase-like 2						threonyl-tRNA aminoacylation	cytoplasm	ATP binding|threonine-tRNA ligase activity			ovary(2)	2	Lung NSC(78;0.000991)|all_lung(78;0.00128)|Melanoma(26;0.00505)		OV - Ovarian serous cystadenocarcinoma(32;0.000268)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)			AATCAATCCTTACCTTAAAAA	0.294													56	47	---	---	---	---	PASS
PARN	5073	broad.mit.edu	37	16	14720998	14720998	+	Missense_Mutation	SNP	T	C	C			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:14720998T>C	uc010uzd.1	-	5	434	c.292A>G	c.(292-294)AAT>GAT	p.N98D	PARN_uc010uzc.1_Missense_Mutation_p.N37D|PARN_uc010uze.1_Intron|PARN_uc010uzf.1_Intron|PARN_uc010uzg.1_Intron	NM_002582	NP_002573	O95453	PARN_HUMAN	poly(A)-specific ribonuclease (deadenylation	98					female gamete generation|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|nuclear-transcribed mRNA poly(A) tail shortening|RNA modification	cytosol|nucleolus	metal ion binding|mRNA 3'-UTR binding|nucleotide binding|poly(A)-specific ribonuclease activity|protein binding			ovary(2)	2						GAGGATCTATTGAAGGGTTTC	0.368													16	11	---	---	---	---	PASS
TRADD	8717	broad.mit.edu	37	16	67189189	67189189	+	Silent	SNP	C	T	T			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67189189C>T	uc002eri.1	-	4	518	c.438G>A	c.(436-438)CGG>CGA	p.R146R	TRADD_uc002erh.1_Silent_p.R86R	NM_003789	NP_003780	Q15628	TRADD_HUMAN	TNFRSF1A-associated via death domain	146					activation of caspase activity|activation of pro-apoptotic gene products|induction of apoptosis by extracellular signals|positive regulation of I-kappaB kinase/NF-kappaB cascade|tumor necrosis factor-mediated signaling pathway	cytoskeleton|cytosol|receptor complex	binding, bridging|death domain binding|identical protein binding|kinase binding|signal transducer activity			lung(1)	1		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0143)|Epithelial(162;0.0335)|all cancers(182;0.184)		CATCCCGGAGCCGGTCGGGCT	0.697													5	20	---	---	---	---	PASS
CENPT	80152	broad.mit.edu	37	16	67866358	67866358	+	Missense_Mutation	SNP	C	A	A			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67866358C>A	uc002eun.3	-	5	750	c.201G>T	c.(199-201)AGG>AGT	p.R67S	CENPT_uc002eum.3_Missense_Mutation_p.R67S|CENPT_uc010vkc.1_5'UTR|CENPT_uc010vkd.1_5'UTR|CENPT_uc010vke.1_5'UTR	NM_025082	NP_079358	Q96BT3	CENPT_HUMAN	centromere protein T	67					mitotic prometaphase	condensed chromosome kinetochore|cytosol|nucleus	DNA binding				0		Acute lymphoblastic leukemia(13;0.000299)|all_hematologic(13;0.0184)|Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.00429)|Epithelial(162;0.019)|all cancers(182;0.124)		GGGTACTTACCCTGGCTCCAT	0.607													31	63	---	---	---	---	PASS
COX10	1352	broad.mit.edu	37	17	13980210	13980210	+	Silent	SNP	G	A	A			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:13980210G>A	uc002gof.3	+	3	540	c.336G>A	c.(334-336)AAG>AAA	p.K112K	COX10_uc010vvs.1_Intron|COX10_uc010vvt.1_5'UTR	NM_001303	NP_001294	Q12887	COX10_HUMAN	heme A:farnesyltransferase precursor	112					heme a biosynthetic process|heme O biosynthetic process|respiratory chain complex IV assembly	integral to membrane|mitochondrial membrane	protoheme IX farnesyltransferase activity				0		all_lung(20;0.06)|Lung SC(565;0.168)		UCEC - Uterine corpus endometrioid carcinoma (92;0.106)		TGTCCAGAAAGCCAAATGAAA	0.413													53	42	---	---	---	---	PASS
FAM27L	284123	broad.mit.edu	37	17	21825572	21825572	+	RNA	SNP	C	T	T			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21825572C>T	uc002gyz.2	+	1		c.203C>T				NR_028336				Homo sapiens family with sequence similarity 27-like, mRNA (cDNA clone MGC:35151 IMAGE:5169482), complete cds.												0				UCEC - Uterine corpus endometrioid carcinoma (53;0.11)|BRCA - Breast invasive adenocarcinoma(1;0.00463)		ggagggtgttcgggtgagtct	0.000													29	104	---	---	---	---	PASS
MYO18A	399687	broad.mit.edu	37	17	27437117	27437117	+	Silent	SNP	G	A	A			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:27437117G>A	uc002hdt.1	-	19	3248	c.3090C>T	c.(3088-3090)GAC>GAT	p.D1030D	MYO18A_uc010wbc.1_Silent_p.D572D|MYO18A_uc002hds.2_Silent_p.D572D|MYO18A_uc010csa.1_Silent_p.D1030D|MYO18A_uc002hdu.1_Silent_p.D1030D|MYO18A_uc010wbd.1_Silent_p.D699D	NM_078471	NP_510880	Q92614	MY18A_HUMAN	myosin 18A isoform a	1030	Myosin head-like.				anti-apoptosis|DNA metabolic process	ER-Golgi intermediate compartment|myosin complex	ATP binding|DNA binding|DNA-dependent ATPase activity|identical protein binding|motor activity				0			Epithelial(11;4.97e-05)|BRCA - Breast invasive adenocarcinoma(11;0.000221)|all cancers(11;0.000234)|Colorectal(6;0.0102)|COAD - Colon adenocarcinoma(6;0.031)			CGATGAGGGCGTCCTGCCGAG	0.622													10	30	---	---	---	---	PASS
NF1	4763	broad.mit.edu	37	17	29701119	29701119	+	Missense_Mutation	SNP	G	C	C			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:29701119G>C	uc002hgg.2	+	58	8799	c.8466G>C	c.(8464-8466)CAG>CAC	p.Q2822H	NF1_uc002hgh.2_Missense_Mutation_p.Q2801H|NF1_uc010cso.2_Missense_Mutation_p.Q1028H|NF1_uc010wbu.1_RNA	NM_001042492	NP_001035957	P21359	NF1_HUMAN	neurofibromin isoform 1	2822					actin cytoskeleton organization|adrenal gland development|artery morphogenesis|camera-type eye morphogenesis|cerebral cortex development|collagen fibril organization|forebrain astrocyte development|forebrain morphogenesis|heart development|liver development|MAPKKK cascade|metanephros development|myelination in peripheral nervous system|negative regulation of cell migration|negative regulation of endothelial cell proliferation|negative regulation of MAP kinase activity|negative regulation of MAPKKK cascade|negative regulation of neuroblast proliferation|negative regulation of oligodendrocyte differentiation|negative regulation of transcription factor import into nucleus|osteoblast differentiation|phosphatidylinositol 3-kinase cascade|pigmentation|positive regulation of adenylate cyclase activity|positive regulation of neuron apoptosis|Ras protein signal transduction|regulation of blood vessel endothelial cell migration|regulation of bone resorption|response to hypoxia|smooth muscle tissue development|spinal cord development|sympathetic nervous system development|visual learning|wound healing	axon|cytoplasm|dendrite|intrinsic to internal side of plasma membrane|nucleus	protein binding|Ras GTPase activator activity			soft_tissue(159)|central_nervous_system(56)|lung(28)|large_intestine(27)|haematopoietic_and_lymphoid_tissue(18)|ovary(18)|autonomic_ganglia(12)|breast(3)|skin(3)|stomach(2)|thyroid(1)|prostate(1)|kidney(1)|pancreas(1)	330		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)		GCCAAGTGCAGAAGCAAAGAA	0.463			D|Mis|N|F|S|O		neurofibroma|glioma	neurofibroma|glioma			Neurofibromatosis_type_1	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)			15	75	---	---	---	---	PASS
KRT37	8688	broad.mit.edu	37	17	39580033	39580033	+	Missense_Mutation	SNP	C	A	A			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39580033C>A	uc002hwp.1	-	2	603	c.556G>T	c.(556-558)GCT>TCT	p.A186S	uc002hwo.1_RNA	NM_003770	NP_003761	O76014	KRT37_HUMAN	keratin 37	186	Rod.|Coil 1B.					intermediate filament	structural molecule activity			skin(1)	1		Breast(137;0.000496)				AAGTCATCAGCAGCCAGCTTC	0.313													13	68	---	---	---	---	PASS
SKAP1	8631	broad.mit.edu	37	17	46257527	46257527	+	Missense_Mutation	SNP	C	T	T			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:46257527C>T	uc002ini.1	-	9	827	c.715G>A	c.(715-717)GAC>AAC	p.D239N	SKAP1_uc002inj.1_Missense_Mutation_p.D239N|SKAP1_uc010dbd.1_Missense_Mutation_p.D145N|SKAP1_uc010dbe.1_Missense_Mutation_p.D239N	NM_003726	NP_003717	Q86WV1	SKAP1_HUMAN	src kinase associated phosphoprotein 1 isoform	239					positive regulation of transcription from RNA polymerase II promoter|T cell receptor signaling pathway	cytoplasm|nucleus|plasma membrane	antigen binding|protein kinase binding|SH2 domain binding				0						CTTGGGGAGTCAAAACCATCA	0.358													34	86	---	---	---	---	PASS
APPBP2	10513	broad.mit.edu	37	17	58543698	58543698	+	Missense_Mutation	SNP	T	C	C	rs140223877		TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:58543698T>C	uc002iys.1	-	5	914	c.626A>G	c.(625-627)TAT>TGT	p.Y209C	APPBP2_uc010ddl.1_Missense_Mutation_p.Y138C	NM_006380	NP_006371	Q92624	APBP2_HUMAN	amyloid beta precursor protein-binding protein	209	TPR 3.				intracellular protein transport	cytoplasmic vesicle membrane|microtubule|microtubule associated complex|nucleus	microtubule motor activity|protein binding				0	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;3.67e-13)|all cancers(12;1.44e-11)|Colorectal(3;0.01)			CAGTTCTCCATAGAGTGCAGC	0.348													102	124	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	17	62385903	62385903	+	IGR	SNP	G	A	A			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:62385903G>A								TEX2 (45250 upstream) : PECAM1 (13961 downstream)																							GCAAGTTTCCGGAGCTCTTTG	0.498													12	56	---	---	---	---	PASS
KIAA1632	57724	broad.mit.edu	37	18	43531083	43531083	+	Silent	SNP	G	C	C			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:43531083G>C	uc002lbm.2	-	4	1474	c.1374C>G	c.(1372-1374)CTC>CTG	p.L458L	KIAA1632_uc002lbo.1_Silent_p.L458L	NM_020964	NP_066015	Q9HCE0	EPG5_HUMAN	hypothetical protein LOC57724	458					autophagy						0						TCTGCAGCCAGAGAAGAATAT	0.348													20	71	---	---	---	---	PASS
SMAD7	4092	broad.mit.edu	37	18	46474754	46474754	+	Missense_Mutation	SNP	C	A	A	rs34000389		TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:46474754C>A	uc002ldg.2	-	2	954	c.667G>T	c.(667-669)GCA>TCA	p.A223S	SMAD7_uc010xde.1_Missense_Mutation_p.A8S	NM_005904	NP_005895	O15105	SMAD7_HUMAN	SMAD family member 7	223					adherens junction assembly|artery morphogenesis|BMP signaling pathway|cellular protein complex localization|negative regulation of BMP signaling pathway|negative regulation of cell migration|negative regulation of epithelial to mesenchymal transition|negative regulation of pathway-restricted SMAD protein phosphorylation|negative regulation of peptidyl-serine phosphorylation|negative regulation of peptidyl-threonine phosphorylation|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription by competitive promoter binding|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transforming growth factor beta receptor signaling pathway|negative regulation of ubiquitin-protein ligase activity|pathway-restricted SMAD protein phosphorylation|positive regulation of anti-apoptosis|positive regulation of cell-cell adhesion|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of protein ubiquitination|protein stabilization|regulation of activin receptor signaling pathway|response to laminar fluid shear stress|transforming growth factor beta receptor signaling pathway|ventricular cardiac muscle tissue morphogenesis|ventricular septum morphogenesis	centrosome|cytosol|nucleolus|plasma membrane|transcription factor complex	activin binding|beta-catenin binding|I-SMAD binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transforming growth factor beta receptor, inhibitory cytoplasmic mediator activity|type I transforming growth factor beta receptor binding|ubiquitin protein ligase binding				0	Colorectal(1;0.0518)					ATCTACTCACCAGTTGGTTTG	0.423													3	59	---	---	---	---	PASS
MUC16	94025	broad.mit.edu	37	19	9038137	9038137	+	Splice_Site	SNP	C	A	A			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9038137C>A	uc002mkp.2	-	8	36344	c.36140_splice	c.e8-1	p.T12047_splice		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16						cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			lung(30)|ovary(15)|breast(8)|large_intestine(1)|skin(1)|prostate(1)|pancreas(1)	57						GTCACTGGAGCTGAGAAAAAA	0.453													3	7	---	---	---	---	PASS
ZGLP1	100125288	broad.mit.edu	37	19	10419279	10419279	+	Missense_Mutation	SNP	C	T	T			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10419279C>T	uc002mnw.3	-	1	955	c.79G>A	c.(79-81)GCT>ACT	p.A27T	FDX1L_uc002mnx.1_Intron	NM_001103167	NP_001096637	P0C6A0	ZGLP1_HUMAN	GATA like protein-1	27					multicellular organismal development	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1						CTGGGTTTAGCCGGCCAGGGG	0.597													3	44	---	---	---	---	PASS
CACNA1A	773	broad.mit.edu	37	19	13356036	13356036	+	Missense_Mutation	SNP	A	C	C			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13356036A>C	uc010dze.2	-	31	5149	c.4913T>G	c.(4912-4914)GTT>GGT	p.V1638G	CACNA1A_uc010xnd.1_Missense_Mutation_p.V343G|CACNA1A_uc002mwx.3_Missense_Mutation_p.V343G|CACNA1A_uc010dzc.2_Missense_Mutation_p.V1163G|CACNA1A_uc002mwy.3_Missense_Mutation_p.V1637G|CACNA1A_uc010xne.1_Missense_Mutation_p.V1166G|CACNA1A_uc002mwv.3_Missense_Mutation_p.V154G	NM_001127221	NP_001120693	O00555	CAC1A_HUMAN	calcium channel, alpha 1A subunit isoform 3	1638	Helical; Name=S3 of repeat IV; (Potential).|IV.				cell death|elevation of cytosolic calcium ion concentration|energy reserve metabolic process|membrane depolarization|regulation of insulin secretion	cytoplasm|nucleus	syntaxin binding			large_intestine(2)	2			OV - Ovarian serous cystadenocarcinoma(19;5.07e-21)		Bepridil(DB01244)|Cinnarizine(DB00568)|Loperamide(DB00836)|Nisoldipine(DB00401)|Pregabalin(DB00230)	GCTGCCCAGAACAGTCACAAA	0.572													29	53	---	---	---	---	PASS
AKAP8	10270	broad.mit.edu	37	19	15465755	15465755	+	Missense_Mutation	SNP	C	G	G			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15465755C>G	uc002nav.2	-	14	2111	c.2050G>C	c.(2050-2052)GAG>CAG	p.E684Q	AKAP8_uc010dzy.2_Missense_Mutation_p.E233Q	NM_005858	NP_005849	O43823	AKAP8_HUMAN	A-kinase anchor protein 8	684					signal transduction	nuclear matrix				ovary(1)|breast(1)	2						TCTTTAGACTCTGCATCAGTT	0.532													5	161	---	---	---	---	PASS
FAM125A	93343	broad.mit.edu	37	19	17533273	17533273	+	Intron	SNP	G	T	T			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17533273G>T	uc002ngo.1	+						FAM125A_uc002ngp.1_Intron|FAM125A_uc002ngq.1_Intron	NM_138401	NP_612410	Q96EY5	F125A_HUMAN	family with sequence similarity 125, member A						protein transport	late endosome membrane|microtubule organizing center|nucleus	SH3 domain binding				0						ATAGGGTAGGGCCACCCCCCA	0.577													26	55	---	---	---	---	PASS
NCAN	1463	broad.mit.edu	37	19	19344641	19344641	+	Silent	SNP	G	C	C			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:19344641G>C	uc002nlz.2	+	9	3162	c.3063G>C	c.(3061-3063)GGG>GGC	p.G1021G	NCAN_uc010ecc.1_Silent_p.G585G	NM_004386	NP_004377	O14594	NCAN_HUMAN	chondroitin sulfate proteoglycan 3 precursor	1021	EGF-like 1.				axon guidance|cell adhesion	extracellular region	calcium ion binding|hyaluronic acid binding|sugar binding			ovary(4)	4			Epithelial(12;0.00544)			TTCATGGAGGGACATGTAATG	0.488													37	193	---	---	---	---	PASS
CYP2A13	1553	broad.mit.edu	37	19	41594403	41594403	+	Silent	SNP	G	A	A			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41594403G>A	uc002opt.2	+	1	36	c.27G>A	c.(25-27)GTG>GTA	p.V9V		NM_000766	NP_000757	Q16696	CP2AD_HUMAN	cytochrome P450, family 2, subfamily A,	9					xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	aromatase activity|coumarin 7-hydroxylase activity|electron carrier activity|heme binding			ovary(2)|skin(1)	3					Clomipramine(DB01242)|Nicotine(DB00184)	TGCTTCTGGTGACCTTGCTGG	0.582													13	63	---	---	---	---	PASS
ZNF225	7768	broad.mit.edu	37	19	44622331	44622331	+	Intron	SNP	G	T	T			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44622331G>T	uc002oyj.1	+						ZNF225_uc010eje.1_Intron|ZNF225_uc010ejf.1_Intron	NM_013362	NP_037494	Q9UK10	ZN225_HUMAN	zinc finger protein 225						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Prostate(69;0.0352)|all_neural(266;0.202)				GCATATGTTCGATGCTGTAGG	0.527													59	134	---	---	---	---	PASS
MYH14	79784	broad.mit.edu	37	19	50796886	50796886	+	Missense_Mutation	SNP	A	T	T			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50796886A>T	uc002prr.1	+	37	5335	c.5288A>T	c.(5287-5289)GAG>GTG	p.E1763V	MYH14_uc010enu.1_Missense_Mutation_p.E1804V|MYH14_uc002prq.1_Missense_Mutation_p.E1771V|MYH14_uc010ycb.1_Missense_Mutation_p.E114V|MYH14_uc002prs.1_Missense_Mutation_p.E114V	NM_024729	NP_079005	Q7Z406	MYH14_HUMAN	myosin, heavy chain 14 isoform 2	1763	Potential.				axon guidance|regulation of cell shape	myosin complex	actin binding|ATP binding|calmodulin binding|motor activity			central_nervous_system(1)	1		all_neural(266;0.0571)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.00389)|GBM - Glioblastoma multiforme(134;0.0195)		GAAGAGCTGGAGGAGGAGCAG	0.627													13	31	---	---	---	---	PASS
ZNF600	162966	broad.mit.edu	37	19	53269323	53269323	+	Silent	SNP	G	A	A			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53269323G>A	uc002qab.3	-	3	1972	c.1686C>T	c.(1684-1686)ACC>ACT	p.T562T		NM_198457	NP_940859	Q6ZNG1	ZN600_HUMAN	zinc finger protein 600	562	C2H2-type 15.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0				OV - Ovarian serous cystadenocarcinoma(262;0.0241)|GBM - Glioblastoma multiforme(134;0.0404)		TGTGACTGAAGGTCTTGCCAC	0.438													75	420	---	---	---	---	PASS
NLRP8	126205	broad.mit.edu	37	19	56466391	56466391	+	Missense_Mutation	SNP	A	C	C			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56466391A>C	uc002qmh.2	+	3	1038	c.967A>C	c.(967-969)ACG>CCG	p.T323P	NLRP8_uc010etg.2_Missense_Mutation_p.T323P	NM_176811	NP_789781	Q86W28	NALP8_HUMAN	NLR family, pyrin domain containing 8	323	NACHT.					cytoplasm	ATP binding			ovary(4)|breast(3)|central_nervous_system(2)|skin(2)|large_intestine(1)|kidney(1)	13		Colorectal(82;0.000147)|Ovarian(87;0.17)		GBM - Glioblastoma multiforme(193;0.0695)		GCTGAGCAAAACGATGCTTCC	0.517													102	153	---	---	---	---	PASS
USP29	57663	broad.mit.edu	37	19	57641900	57641900	+	Missense_Mutation	SNP	G	C	C			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57641900G>C	uc002qny.2	+	4	2213	c.1857G>C	c.(1855-1857)CAG>CAC	p.Q619H		NM_020903	NP_065954	Q9HBJ7	UBP29_HUMAN	ubiquitin specific peptidase 29	619					protein modification process|ubiquitin-dependent protein catabolic process		cysteine-type peptidase activity|protein binding|ubiquitin thiolesterase activity			lung(6)|ovary(2)|breast(2)|pancreas(1)	11		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;0.026)		AGCAGCATCAGAGAGACCTGG	0.493													21	91	---	---	---	---	PASS
TMC2	117532	broad.mit.edu	37	20	2577827	2577827	+	Silent	SNP	C	T	T			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:2577827C>T	uc002wgf.1	+	10	1122	c.1107C>T	c.(1105-1107)GGC>GGT	p.G369G	TMC2_uc002wgg.1_Silent_p.G353G|TMC2_uc010zpw.1_Silent_p.G201G|TMC2_uc010zpx.1_Silent_p.G200G	NM_080751	NP_542789	Q8TDI7	TMC2_HUMAN	transmembrane cochlear-expressed protein 2	369	Cytoplasmic (Potential).					integral to membrane				ovary(3)	3						GAAGCACAGGCGAAGGGGAGA	0.527													29	63	---	---	---	---	PASS
ADAM33	80332	broad.mit.edu	37	20	3660177	3660177	+	Missense_Mutation	SNP	C	A	A			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3660177C>A	uc002wit.2	-	2	226	c.139G>T	c.(139-141)GAT>TAT	p.D47Y	ADAM33_uc002wir.1_Missense_Mutation_p.D47Y|ADAM33_uc002wiu.2_Missense_Mutation_p.D47Y|ADAM33_uc002wiw.1_RNA|ADAM33_uc010gba.1_Missense_Mutation_p.D47Y|ADAM33_uc010gbb.1_Missense_Mutation_p.D47Y|ADAM33_uc002wix.1_Missense_Mutation_p.D47Y|ADAM33_uc010zqg.1_Missense_Mutation_p.D47Y|ADAM33_uc010zqh.1_Missense_Mutation_p.D47Y|ADAM33_uc002wiy.2_Missense_Mutation_p.D47Y	NM_025220	NP_079496	Q9BZ11	ADA33_HUMAN	ADAM metallopeptidase domain 33 isoform alpha	47	Extracellular (Potential).				proteolysis	integral to membrane	metalloendopeptidase activity|zinc ion binding			large_intestine(2)|ovary(1)|skin(1)	4						GGTTGTCCATCCAGGACCCAG	0.642													6	25	---	---	---	---	PASS
RBBP9	10741	broad.mit.edu	37	20	18470558	18470558	+	Silent	SNP	G	A	A			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:18470558G>A	uc002wqy.2	-	5	487	c.411C>T	c.(409-411)GAC>GAT	p.D137D		NM_006606	NP_006597	O75884	RBBP9_HUMAN	retinoblastoma binding protein 9	137						cytoplasm|nucleus	hydrolase activity			haematopoietic_and_lymphoid_tissue(1)	1						GGAACGGGTCGTCAGTAGAGC	0.483													92	80	---	---	---	---	PASS
REM1	28954	broad.mit.edu	37	20	30071999	30071999	+	Silent	SNP	C	T	T			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30071999C>T	uc002wwa.2	+	5	947	c.663C>T	c.(661-663)TTC>TTT	p.F221F	NCRNA00028_uc010ztn.1_5'Flank	NM_014012	NP_054731	O75628	REM1_HUMAN	RAS-like GTP-binding protein REM	221					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)			ACTGTAAATTCATCGAGACAT	0.657													5	43	---	---	---	---	PASS
HCK	3055	broad.mit.edu	37	20	30689285	30689285	+	Missense_Mutation	SNP	A	G	G			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30689285A>G	uc002wxh.2	+	13	1715	c.1544A>G	c.(1543-1545)TAC>TGC	p.Y515C	HCK_uc010gdy.2_Missense_Mutation_p.Y494C|HCK_uc002wxi.2_Missense_Mutation_p.Y493C	NM_002110	NP_002101	P08631	HCK_HUMAN	hemopoietic cell kinase isoform p61HCK	515	Protein kinase.				interspecies interaction between organisms|mesoderm development|regulation of defense response to virus by virus|viral reproduction	caveola|cytosol	ATP binding|non-membrane spanning protein tyrosine kinase activity|protein binding			lung(4)|ovary(2)|central_nervous_system(2)|pancreas(1)	9			UCEC - Uterine corpus endometrioid carcinoma (5;0.0241)			GATGACTTCTACACGGCCACA	0.607													14	40	---	---	---	---	PASS
CHMP4B	128866	broad.mit.edu	37	20	32438759	32438759	+	Missense_Mutation	SNP	G	C	C			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:32438759G>C	uc002xaa.2	+	3	526	c.370G>C	c.(370-372)GAC>CAC	p.D124H		NM_176812	NP_789782	Q9H444	CHM4B_HUMAN	chromatin modifying protein 4B	124	Potential.				cellular membrane organization|endosome transport|protein transport	cytosol|late endosome membrane	protein binding			ovary(1)|central_nervous_system(1)	2						CATTTGAAGGGACATCGATAA	0.473													12	164	---	---	---	---	PASS
CHMP4B	128866	broad.mit.edu	37	20	32438855	32438855	+	Missense_Mutation	SNP	G	C	C			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:32438855G>C	uc002xaa.2	+	3	622	c.466G>C	c.(466-468)GGA>CGA	p.G156R		NM_176812	NP_789782	Q9H444	CHM4B_HUMAN	chromatin modifying protein 4B	156	Potential.				cellular membrane organization|endosome transport|protein transport	cytosol|late endosome membrane	protein binding			ovary(1)|central_nervous_system(1)	2						TGTAGGGTTTGGAGAAGAGTT	0.448													11	197	---	---	---	---	PASS
DDX27	55661	broad.mit.edu	37	20	47835940	47835940	+	Silent	SNP	C	T	T	rs150992243	by1000genomes	TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:47835940C>T	uc002xuh.2	+	1	109	c.48C>T	c.(46-48)GCC>GCT	p.A16A		NM_017895	NP_060365	Q96GQ7	DDX27_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 27	16						nucleus	ATP binding|ATP-dependent helicase activity|nucleic acid binding|protein binding			kidney(2)	2			BRCA - Breast invasive adenocarcinoma(12;0.000899)|COAD - Colon adenocarcinoma(4;0.14)|Colorectal(8;0.166)			AGTTAAGGGCCGGACCGCAGG	0.607													14	24	---	---	---	---	PASS
KCNB1	3745	broad.mit.edu	37	20	48098748	48098748	+	Silent	SNP	G	T	T			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:48098748G>T	uc002xur.1	-	1	434	c.270C>A	c.(268-270)GGC>GGA	p.G90G	KCNB1_uc002xus.1_Silent_p.G90G	NM_004975	NP_004966	Q14721	KCNB1_HUMAN	potassium voltage-gated channel, Shab-related	90	Cytoplasmic (Potential).				energy reserve metabolic process|regulation of insulin secretion	voltage-gated potassium channel complex	protein binding|voltage-gated potassium channel activity			pancreas(1)|skin(1)	2			BRCA - Breast invasive adenocarcinoma(12;0.000405)|COAD - Colon adenocarcinoma(4;0.14)|Colorectal(8;0.166)			AGGTGAAGGCGCCCGGGTGGC	0.607													8	60	---	---	---	---	PASS
SPATA2	9825	broad.mit.edu	37	20	48523016	48523016	+	Missense_Mutation	SNP	T	A	A			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:48523016T>A	uc010gie.2	-	3	1053	c.703A>T	c.(703-705)AGC>TGC	p.S235C	SPATA2_uc002xuw.2_Missense_Mutation_p.S235C|SPATA2_uc010zyn.1_Missense_Mutation_p.S98C	NM_001135773	NP_001129245	Q9UM82	SPAT2_HUMAN	spermatogenesis associated 2	235					cell differentiation|multicellular organismal development|spermatogenesis	cytoplasm|nucleus				central_nervous_system(1)|skin(1)	2	Hepatocellular(150;0.133)		BRCA - Breast invasive adenocarcinoma(9;4.03e-06)			GCCCGCTCGCTGGCCGACTTC	0.682													16	77	---	---	---	---	PASS
CASS4	57091	broad.mit.edu	37	20	55027781	55027781	+	Missense_Mutation	SNP	C	T	T			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:55027781C>T	uc002xxp.2	+	6	1774	c.1549C>T	c.(1549-1551)CGG>TGG	p.R517W	CASS4_uc002xxq.3_Missense_Mutation_p.R517W|CASS4_uc002xxr.2_Missense_Mutation_p.R517W|CASS4_uc010zze.1_Missense_Mutation_p.R463W|CASS4_uc010gio.2_Intron	NM_001164116	NP_001157588	Q9NQ75	CASS4_HUMAN	HEF-like protein isoform a	517					cell adhesion	cytoplasm|cytoskeleton|focal adhesion	two-component sensor activity			ovary(2)|skin(1)	3						GAACAGAATTCGGGACCAGAT	0.463													36	80	---	---	---	---	PASS
NPEPL1	79716	broad.mit.edu	37	20	57289620	57289620	+	Missense_Mutation	SNP	G	A	A			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:57289620G>A	uc010zzs.1	+	11	1402	c.1307G>A	c.(1306-1308)CGA>CAA	p.R436Q	NPEPL1_uc010zzr.1_Missense_Mutation_p.R388Q|NPEPL1_uc002xzn.2_RNA|NPEPL1_uc010gjo.1_Missense_Mutation_p.R408Q|NPEPL1_uc002xzp.2_3'UTR	NM_024663	NP_078939	Q8NDH3	PEPL1_HUMAN	aminopeptidase-like 1	436					proteolysis	cytoplasm	aminopeptidase activity|manganese ion binding|metalloexopeptidase activity				0	all_lung(29;0.0175)		BRCA - Breast invasive adenocarcinoma(13;2.88e-09)|Colorectal(105;0.109)			CCCTAGGACCGAGACAACAGC	0.647													3	6	---	---	---	---	PASS
CHRNA4	1137	broad.mit.edu	37	20	61982049	61982049	+	Silent	SNP	G	A	A			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:61982049G>A	uc002yes.2	-	5	892	c.714C>T	c.(712-714)GTC>GTT	p.V238V	CHRNA4_uc002yet.1_Silent_p.V62V|CHRNA4_uc011aaw.1_RNA|CHRNA4_uc010gke.1_Silent_p.V167V|CHRNA4_uc002yev.1_Silent_p.V62V|CHRNA4_uc010gkf.1_Silent_p.V62V	NM_000744	NP_000735	P43681	ACHA4_HUMAN	cholinergic receptor, nicotinic, alpha 4 subunit	238	Extracellular (Potential).				B cell activation|behavioral response to nicotine|calcium ion transport|cognition|DNA repair|membrane depolarization|regulation of action potential|regulation of dopamine secretion|regulation of inhibitory postsynaptic membrane potential|response to hypoxia|response to oxidative stress|sensory perception of pain|synaptic transmission, cholinergic	cell junction|dendrite|external side of plasma membrane|membrane fraction|neuronal cell body|nicotinic acetylcholine-gated receptor-channel complex|postsynaptic membrane	acetylcholine receptor activity|nicotinic acetylcholine-activated cation-selective channel activity			central_nervous_system(1)|skin(1)	2	all_cancers(38;1.71e-10)				Nicotine(DB00184)|Varenicline(DB01273)	GCCGCCGGATGACGAAGGCAT	0.597													29	49	---	---	---	---	PASS
GRIK1	2897	broad.mit.edu	37	21	31062214	31062214	+	Silent	SNP	G	C	C			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:31062214G>C	uc002yno.1	-	3	842	c.378C>G	c.(376-378)CTC>CTG	p.L126L	GRIK1_uc002ynn.2_Silent_p.L126L|GRIK1_uc011acs.1_Silent_p.L126L|GRIK1_uc011act.1_Silent_p.L70L|GRIK1_uc010glq.1_Intron|GRIK1_uc002ynr.2_Silent_p.L126L	NM_000830	NP_000821	P39086	GRIK1_HUMAN	glutamate receptor, ionotropic, kainate 1	126	Extracellular (Potential).				central nervous system development|synaptic transmission	cell junction|postsynaptic membrane	kainate selective glutamate receptor activity			large_intestine(1)|ovary(1)|skin(1)	3					L-Glutamic Acid(DB00142)|Topiramate(DB00273)	GTGGAACTTCGAGAGCATTGC	0.517													11	296	---	---	---	---	PASS
SUSD2	56241	broad.mit.edu	37	22	24584086	24584086	+	Missense_Mutation	SNP	C	T	T			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24584086C>T	uc002zzn.1	+	13	2368	c.2324C>T	c.(2323-2325)ACC>ATC	p.T775I		NM_019601	NP_062547	Q9UGT4	SUSD2_HUMAN	sushi domain containing 2 precursor	775	Sushi.|Extracellular (Potential).				immune response	integral to membrane	polysaccharide binding|protein binding|scavenger receptor activity			skin(1)	1						TCCTCACCCACCCCGAAGTGC	0.647													15	203	---	---	---	---	PASS
CACNG2	10369	broad.mit.edu	37	22	36960438	36960438	+	Missense_Mutation	SNP	A	T	T			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:36960438A>T	uc003aps.1	-	4	1214	c.932T>A	c.(931-933)CTC>CAC	p.L311H		NM_006078	NP_006069	Q9Y698	CCG2_HUMAN	voltage-dependent calcium channel gamma-2	311					membrane depolarization|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|synaptic transmission	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|endocytic vesicle membrane|voltage-gated calcium channel complex	protein binding|voltage-gated calcium channel activity				0						GTTGGAGTGGAGAGAGTCCTT	0.532													29	73	---	---	---	---	PASS
IL17REL	400935	broad.mit.edu	37	22	50439241	50439241	+	Missense_Mutation	SNP	G	A	A			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50439241G>A	uc003bje.1	-	5	393	c.161C>T	c.(160-162)ACG>ATG	p.T54M		NM_001001694	NP_001001694	Q6ZVW7	I17EL_HUMAN	interleukin 17 receptor E-like	54										pancreas(1)	1		all_cancers(38;5.53e-07)|all_epithelial(38;3.84e-06)|all_lung(38;0.00208)|Breast(42;0.0104)|Lung NSC(38;0.0199)|Ovarian(80;0.0907)|Lung SC(80;0.236)		BRCA - Breast invasive adenocarcinoma(115;0.2)|LUAD - Lung adenocarcinoma(64;0.247)		CTGACACTGCGTCTCCTGGGT	0.706													17	35	---	---	---	---	PASS
CLCN4	1183	broad.mit.edu	37	X	10176330	10176330	+	Silent	SNP	C	A	A			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:10176330C>A	uc004csy.3	+	9	1519	c.1089C>A	c.(1087-1089)ACC>ACA	p.T363T	CLCN4_uc011mid.1_Silent_p.T269T	NM_001830	NP_001821	P51793	CLCN4_HUMAN	chloride channel 4	363						early endosome membrane|integral to membrane|late endosome membrane	antiporter activity|ATP binding|voltage-gated chloride channel activity			ovary(2)|lung(2)|upper_aerodigestive_tract(1)	5						GCAAGACCACCAGGCTGGGGA	0.607													56	260	---	---	---	---	PASS
ARHGAP6	395	broad.mit.edu	37	X	11682535	11682535	+	Silent	SNP	G	A	A			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:11682535G>A	uc004cup.1	-	1	1287	c.414C>T	c.(412-414)GAC>GAT	p.D138D	ARHGAP6_uc004cuo.1_RNA|ARHGAP6_uc004cur.1_Silent_p.D138D	NM_013427	NP_038286	O43182	RHG06_HUMAN	Rho GTPase activating protein 6 isoform 1	138					actin filament polymerization|activation of phospholipase C activity|negative regulation of focal adhesion assembly|negative regulation of stress fiber assembly|Rho protein signal transduction	actin filament|cytosol	phospholipase activator activity|phospholipase binding|Rho GTPase activator activity|SH3 domain binding|SH3/SH2 adaptor activity			urinary_tract(1)|lung(1)	2						CAGAAGGCAGGTCCCAGGCCA	0.627													19	38	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	X	26178760	26178760	+	IGR	SNP	C	T	T			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:26178760C>T								MAGEB18 (19908 upstream) : MAGEB6 (31797 downstream)																							CCGTGGGAAACGCCGAGAGAC	0.577													31	115	---	---	---	---	PASS
TAB3	257397	broad.mit.edu	37	X	30873081	30873081	+	Missense_Mutation	SNP	T	C	C			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:30873081T>C	uc004dcj.2	-	6	1364	c.701A>G	c.(700-702)CAG>CGG	p.Q234R	TAB3_uc004dck.2_Missense_Mutation_p.Q234R|TAB3_uc010ngl.2_Missense_Mutation_p.Q234R	NM_152787	NP_690000	Q8N5C8	TAB3_HUMAN	mitogen-activated protein kinase kinase kinase 7	234	Pro-rich.				activation of MAPK activity|I-kappaB kinase/NF-kappaB cascade|innate immune response|JNK cascade|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|positive regulation of NF-kappaB transcription factor activity|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|endosome membrane|plasma membrane	protein binding|zinc ion binding			ovary(1)	1						CTGAGATGTCTGTCTAATATA	0.478													32	27	---	---	---	---	PASS
FAM47A	158724	broad.mit.edu	37	X	34150182	34150182	+	Missense_Mutation	SNP	G	A	A			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:34150182G>A	uc004ddg.2	-	1	247	c.214C>T	c.(214-216)CGC>TGC	p.R72C		NM_203408	NP_981953	Q5JRC9	FA47A_HUMAN	hypothetical protein LOC158724	72								p.R72H(1)		ovary(4)|central_nervous_system(1)	5						TCGTCACGGCGACAAACGAGA	0.537													40	141	---	---	---	---	PASS
PHF16	9767	broad.mit.edu	37	X	46893118	46893118	+	Missense_Mutation	SNP	A	T	T			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:46893118A>T	uc004dgx.2	+	7	834	c.783A>T	c.(781-783)AAA>AAT	p.K261N	PHF16_uc004dgy.2_Missense_Mutation_p.K261N	NM_001077445	NP_001070913	Q92613	JADE3_HUMAN	PHD finger protein 16	261					histone H3 acetylation|histone H4-K12 acetylation|histone H4-K5 acetylation|histone H4-K8 acetylation	histone acetyltransferase complex	zinc ion binding				0						GTCCAAAGAAAGGTGGAGCCC	0.552													10	29	---	---	---	---	PASS
PHF16	9767	broad.mit.edu	37	X	46917581	46917581	+	Missense_Mutation	SNP	C	A	A			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:46917581C>A	uc004dgx.2	+	11	1625	c.1574C>A	c.(1573-1575)ACA>AAA	p.T525K	PHF16_uc004dgy.2_Missense_Mutation_p.T525K	NM_001077445	NP_001070913	Q92613	JADE3_HUMAN	PHD finger protein 16	525					histone H3 acetylation|histone H4-K12 acetylation|histone H4-K5 acetylation|histone H4-K8 acetylation	histone acetyltransferase complex	zinc ion binding				0						CTTCCTTTGACAAATGCACTT	0.388													25	160	---	---	---	---	PASS
ZNF41	7592	broad.mit.edu	37	X	47308234	47308234	+	Missense_Mutation	SNP	G	A	A			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:47308234G>A	uc004dhs.3	-	4	1128	c.1061C>T	c.(1060-1062)CCC>CTC	p.P354L	ZNF41_uc004dhu.3_Missense_Mutation_p.P346L|ZNF41_uc004dht.3_Missense_Mutation_p.P226L|ZNF41_uc004dhv.3_Missense_Mutation_p.P322L|ZNF41_uc004dhw.3_Missense_Mutation_p.P314L|ZNF41_uc004dhy.3_Missense_Mutation_p.P312L|ZNF41_uc004dhx.3_Missense_Mutation_p.P312L|ZNF41_uc011mlm.1_Missense_Mutation_p.P226L	NM_153380	NP_700359	P51814	ZNF41_HUMAN	zinc finger protein 41	354	C2H2-type 2; degenerate.					nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(3)	3		all_lung(315;0.000129)				ATCAACCTGGGGTTTCTGGGG	0.423													68	239	---	---	---	---	PASS
SLC35A2	7355	broad.mit.edu	37	X	48767184	48767184	+	Missense_Mutation	SNP	G	T	T			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:48767184G>T	uc004dlo.1	-	2	185	c.181C>A	c.(181-183)CCA>ACA	p.P61T	SLC35A2_uc011mml.1_Missense_Mutation_p.P74T|SLC35A2_uc004dlp.1_Missense_Mutation_p.P61T|SLC35A2_uc011mmm.1_Missense_Mutation_p.P89T|SLC35A2_uc011mmn.1_Intron|SLC35A2_uc004dlr.1_5'UTR|SLC35A2_uc004dlq.2_Missense_Mutation_p.P61T|SLC35A2_uc011mmo.1_Missense_Mutation_p.P74T	NM_005660	NP_005651	P78381	S35A2_HUMAN	solute carrier family 35, member A2 isoform a	61					galactose metabolic process	Golgi membrane|integral to membrane|nucleus	sugar:hydrogen symporter activity|UDP-galactose transmembrane transporter activity			breast(1)	1						CGGTCCCCTGGCAACGTGCGG	0.597													5	19	---	---	---	---	PASS
WDR45	11152	broad.mit.edu	37	X	48933067	48933067	+	Silent	SNP	G	T	T			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:48933067G>T	uc004dmk.1	-	9	955	c.783C>A	c.(781-783)GTC>GTA	p.V261V	PRAF2_uc004dmh.2_5'Flank|PRAF2_uc004dmi.2_5'Flank|PRAF2_uc011mmt.1_Silent_p.V159V|WDR45_uc004dmj.1_Silent_p.V222V|WDR45_uc004dml.1_Silent_p.V262V|WDR45_uc004dmm.1_Silent_p.V226V|WDR45_uc010nim.1_Intron|WDR45_uc004dmn.1_Silent_p.V152V|WDR45_uc004dmo.1_Silent_p.V284V|WDR45_uc004dmp.1_Silent_p.V262V	NM_001029896	NP_001025067	Q9Y484	WIPI4_HUMAN	WD repeat domain 45 isoform 2	261	WD 3.				autophagy|response to starvation	organelle membrane	phosphatidylinositol-3,5-bisphosphate binding			ovary(1)	1						CAAAGATATGGACAGTACCCT	0.552													6	19	---	---	---	---	PASS
IQSEC2	23096	broad.mit.edu	37	X	53284070	53284070	+	Missense_Mutation	SNP	C	T	T			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:53284070C>T	uc004dsd.2	-	4	1244	c.1043G>A	c.(1042-1044)CGC>CAC	p.R348H	IQSEC2_uc004dsc.2_Missense_Mutation_p.R143H	NM_001111125	NP_001104595	Q5JU85	IQEC2_HUMAN	IQ motif and Sec7 domain 2 isoform1	338	IQ.				regulation of ARF protein signal transduction	cytoplasm	ARF guanyl-nucleotide exchange factor activity			ovary(3)	3						GGCAGCCCTGCGGCTCAGGAA	0.602													5	22	---	---	---	---	PASS
ZXDA	7789	broad.mit.edu	37	X	57936554	57936554	+	Nonsense_Mutation	SNP	C	A	A			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:57936554C>A	uc004dve.2	-	1	514	c.301G>T	c.(301-303)GAG>TAG	p.E101*		NM_007156	NP_009087	P98168	ZXDA_HUMAN	zinc finger, X-linked, duplicated A	101					positive regulation of transcription, DNA-dependent	nucleus	C2H2 zinc finger domain binding|identical protein binding|nucleic acid binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1						CCCGCGGTCTCCACGTCGCCA	0.746													4	21	---	---	---	---	PASS
VSIG4	11326	broad.mit.edu	37	X	65242194	65242194	+	Missense_Mutation	SNP	C	T	T			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:65242194C>T	uc004dwh.2	-	8	1238	c.1111G>A	c.(1111-1113)GCC>ACC	p.A371T	VSIG4_uc004dwi.2_Missense_Mutation_p.A277T|VSIG4_uc010nkq.1_3'UTR|VSIG4_uc004dwj.2_3'UTR|VSIG4_uc011moy.1_3'UTR|VSIG4_uc004dwk.2_3'UTR|VSIG4_uc004dwl.2_Intron	NM_007268	NP_009199	Q9Y279	VSIG4_HUMAN	V-set and immunoglobulin domain containing 4	371	Cytoplasmic (Potential).				complement activation, alternative pathway	integral to membrane	protein binding				0						TTGATCTGGGCGATGATCTGG	0.517													25	83	---	---	---	---	PASS
OPHN1	4983	broad.mit.edu	37	X	67454367	67454367	+	Missense_Mutation	SNP	G	T	T			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:67454367G>T	uc004dww.3	-	6	742	c.448C>A	c.(448-450)CAC>AAC	p.H150N	OPHN1_uc011mpg.1_Missense_Mutation_p.H150N|OPHN1_uc004dwx.2_Missense_Mutation_p.H150N	NM_002547	NP_002538	O60890	OPHN1_HUMAN	oligophrenin 1	150					axon guidance|endocytosis|filopodium assembly|small GTPase mediated signal transduction|substrate-dependent cell migration, cell extension	axon|cell junction|cytosol|dendritic spine|synapse	cytoskeletal adaptor activity|Rho GTPase activator activity|SH3 domain binding			ovary(2)	2						GAAGACAGGTGTAAGTGCCGA	0.408													34	129	---	---	---	---	PASS
IGBP1	3476	broad.mit.edu	37	X	69354654	69354654	+	Missense_Mutation	SNP	C	A	A			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:69354654C>A	uc004dxv.2	+	2	969	c.470C>A	c.(469-471)GCT>GAT	p.A157D	IGBP1_uc004dxw.2_Missense_Mutation_p.A157D	NM_001551	NP_001542	P78318	IGBP1_HUMAN	immunoglobulin binding protein 1	157					B cell activation|negative regulation of caspase activity|negative regulation of stress-activated MAPK cascade|negative regulation of transcription from RNA polymerase II promoter|regulation of microtubule-based movement|response to interleukin-1|response to tumor necrosis factor|signal transduction	cytoplasm	protein phosphatase type 2A regulator activity			kidney(1)|pancreas(1)	2						CAAAGACAGGCTAAAATACAG	0.498													11	105	---	---	---	---	PASS
NLGN3	54413	broad.mit.edu	37	X	70389551	70389551	+	Silent	SNP	C	T	T			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:70389551C>T	uc004dzb.2	+	7	2395	c.2091C>T	c.(2089-2091)TCC>TCT	p.S697S	NLGN3_uc004dzc.2_Silent_p.S580S|NLGN3_uc011mps.1_Silent_p.S677S|NLGN3_uc004dze.2_Silent_p.S515S	NM_018977	NP_061850	Q9NZ94	NLGN3_HUMAN	neuroligin 3	717	Helical; (Potential).				neuron cell-cell adhesion|positive regulation of synaptogenesis|receptor-mediated endocytosis|social behavior|synapse assembly	cell surface|endocytic vesicle|integral to plasma membrane|synapse	neurexin binding|receptor activity			ovary(1)	1	Renal(35;0.156)					TGGGGGCCTCCCTCCTGTTCC	0.637													29	34	---	---	---	---	PASS
PHKA1	5255	broad.mit.edu	37	X	71872438	71872438	+	Missense_Mutation	SNP	T	A	A			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:71872438T>A	uc004eax.3	-	12	1502	c.1201A>T	c.(1201-1203)ATG>TTG	p.M401L	PHKA1_uc004eay.3_Missense_Mutation_p.M401L|PHKA1_uc011mqi.1_Missense_Mutation_p.M401L	NM_002637	NP_002628	P46020	KPB1_HUMAN	phosphorylase kinase, alpha 1 (muscle) isoform	401					glucose metabolic process|glycogen catabolic process	cytosol|plasma membrane	calmodulin binding|glucan 1,4-alpha-glucosidase activity|phosphorylase kinase activity			ovary(3)|skin(1)	4	Renal(35;0.156)					TGACCCCACATGTGAGGCAAT	0.433													28	42	---	---	---	---	PASS
CDX4	1046	broad.mit.edu	37	X	72674404	72674404	+	Missense_Mutation	SNP	G	A	A			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:72674404G>A	uc011mqk.1	+	3	838	c.838G>A	c.(838-840)GTT>ATT	p.V280I		NM_005193	NP_005184	O14627	CDX4_HUMAN	caudal type homeobox 4	280						nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0	Renal(35;0.156)					GATACAGCAGGTTATAGTCTC	0.428													16	55	---	---	---	---	PASS
CYLC1	1538	broad.mit.edu	37	X	83128919	83128919	+	Missense_Mutation	SNP	G	C	C			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:83128919G>C	uc004eei.1	+	4	1224	c.1203G>C	c.(1201-1203)AAG>AAC	p.K401N	CYLC1_uc004eeh.1_Missense_Mutation_p.K400N	NM_021118	NP_066941	P35663	CYLC1_HUMAN	cylicin, basic protein of sperm head	401	4.				cell differentiation|multicellular organismal development|spermatogenesis	acrosomal matrix|cytoskeletal calyx	structural molecule activity			ovary(4)|skin(1)	5						AGGATGCAAAGAAAATTACAT	0.318													6	31	---	---	---	---	PASS
RPS6KA6	27330	broad.mit.edu	37	X	83401975	83401975	+	Intron	SNP	A	C	C			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:83401975A>C	uc004eej.1	-						RPS6KA6_uc011mqt.1_Intron|RPS6KA6_uc011mqu.1_Intron|RPS6KA6_uc010nmo.1_Intron	NM_014496	NP_055311	Q9UK32	KS6A6_HUMAN	ribosomal protein S6 kinase polypeptide 6						axon guidance|central nervous system development|intracellular protein kinase cascade|synaptic transmission	cytosol|nucleoplasm	ATP binding|magnesium ion binding|protein serine/threonine kinase activity			lung(5)|stomach(1)|central_nervous_system(1)|skin(1)	8						gaataaaaaaaGATTACATAC	0.254													18	64	---	---	---	---	PASS
HDX	139324	broad.mit.edu	37	X	83724375	83724375	+	Missense_Mutation	SNP	C	T	T	rs141784700	byFrequency	TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:83724375C>T	uc004eek.1	-	3	465	c.356G>A	c.(355-357)AGG>AAG	p.R119K	HDX_uc011mqv.1_Missense_Mutation_p.R119K|HDX_uc004eel.1_Missense_Mutation_p.R61K	NM_144657	NP_653258	Q7Z353	HDX_HUMAN	highly divergent homeobox	119						nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			upper_aerodigestive_tract(1)|ovary(1)	2						TGTTCCTTGCCTACTTGATGA	0.388													118	192	---	---	---	---	PASS
PCDH19	57526	broad.mit.edu	37	X	99551818	99551818	+	Missense_Mutation	SNP	G	T	T			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:99551818G>T	uc010nmz.2	-	6	4580	c.2904C>A	c.(2902-2904)GAC>GAA	p.D968E	PCDH19_uc004efw.3_Missense_Mutation_p.D920E|PCDH19_uc004efx.3_Missense_Mutation_p.D921E	NM_020766	NP_001098713	Q8TAB3	PCD19_HUMAN	protocadherin 19 isoform b	968	Cytoplasmic (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(2)|breast(2)|upper_aerodigestive_tract(1)|urinary_tract(1)|skin(1)	7						TCCAGCACCTGTCAGAGTGGC	0.493													43	144	---	---	---	---	PASS
HNRNPH2	3188	broad.mit.edu	37	X	100668298	100668298	+	Missense_Mutation	SNP	C	A	A			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:100668298C>A	uc004ehm.2	+	2	1492	c.1322C>A	c.(1321-1323)TCC>TAC	p.S441Y	HNRNPH2_uc004ehn.2_Missense_Mutation_p.S441Y	NM_019597	NP_062543	P55795	HNRH2_HUMAN	heterogeneous nuclear ribonucleoprotein H2	441					nuclear mRNA splicing, via spliceosome	actin cytoskeleton|cytoplasm|heterogeneous nuclear ribonucleoprotein complex|nucleoplasm	nucleotide binding|protein binding|RNA binding				0						CAGGAAAACTCCAGTGACTAT	0.453													93	374	---	---	---	---	PASS
ARMCX2	9823	broad.mit.edu	37	X	100911569	100911569	+	Missense_Mutation	SNP	G	T	T			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:100911569G>T	uc004eid.2	-	3	1361	c.1006C>A	c.(1006-1008)CCT>ACT	p.P336T	ARMCX2_uc004eie.3_Missense_Mutation_p.P336T|ARMCX2_uc004eif.3_Missense_Mutation_p.P336T|ARMCX2_uc004eig.3_Missense_Mutation_p.P336T|ARMCX2_uc010nnt.2_Missense_Mutation_p.P336T	NM_177949	NP_808818	Q7L311	ARMX2_HUMAN	ALEX2 protein	336						integral to membrane	binding			ovary(6)	6						TCAGAATCAGGGACCTCTGCC	0.607													23	111	---	---	---	---	PASS
NRK	203447	broad.mit.edu	37	X	105152981	105152981	+	Missense_Mutation	SNP	C	A	A			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:105152981C>A	uc004emd.2	+	13	1651	c.1348C>A	c.(1348-1350)CAG>AAG	p.Q450K	NRK_uc010npc.1_Missense_Mutation_p.Q118K	NM_198465	NP_940867	Q7Z2Y5	NRK_HUMAN	Nik related kinase	450	Gln-rich.						ATP binding|protein serine/threonine kinase activity|small GTPase regulator activity			breast(7)|ovary(3)|lung(2)|large_intestine(1)|central_nervous_system(1)	14						CATGCCACTACAGGCTCAGGT	0.572										HNSCC(51;0.14)			11	44	---	---	---	---	PASS
UTP14A	10813	broad.mit.edu	37	X	129059031	129059031	+	Missense_Mutation	SNP	C	A	A			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:129059031C>A	uc004euz.2	+	12	1637	c.1609C>A	c.(1609-1611)CAG>AAG	p.Q537K	UTP14A_uc011mup.1_Missense_Mutation_p.Q485K|UTP14A_uc011muq.1_Missense_Mutation_p.Q483K	NM_006649	NP_006640	Q9BVJ6	UT14A_HUMAN	UTP14, U3 small nucleolar ribonucleoprotein,	537					rRNA processing	nucleolus|small-subunit processome	protein binding			ovary(2)	2						AGAAGGGCAGCAGTCAGAGAG	0.478													44	208	---	---	---	---	PASS
TFDP3	51270	broad.mit.edu	37	X	132351916	132351916	+	Missense_Mutation	SNP	C	A	A			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:132351916C>A	uc004exb.1	-	1	461	c.372G>T	c.(370-372)AGG>AGT	p.R124S		NM_016521	NP_057605	Q5H9I0	TFDP3_HUMAN	transcription factor Dp family, member 3	124	Potential.					transcription factor complex	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1	Acute lymphoblastic leukemia(192;0.000127)					TGGTCCCTTTCCTCTGCACCG	0.587													35	124	---	---	---	---	PASS
GPR112	139378	broad.mit.edu	37	X	135405392	135405392	+	Missense_Mutation	SNP	C	A	A			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:135405392C>A	uc004ezu.1	+	5	817	c.526C>A	c.(526-528)CGT>AGT	p.R176S	GPR112_uc010nsb.1_Intron	NM_153834	NP_722576	Q8IZF6	GP112_HUMAN	G-protein coupled receptor 112	176	Extracellular (Potential).				neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(5)|large_intestine(2)|skin(2)|lung(1)|breast(1)|pancreas(1)	12	Acute lymphoblastic leukemia(192;0.000127)					AAGCATGATGCGTAGCTTTCC	0.448													118	185	---	---	---	---	PASS
LDOC1	23641	broad.mit.edu	37	X	140271150	140271150	+	Silent	SNP	C	G	G			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:140271150C>G	uc004fbj.2	-	1	161	c.57G>C	c.(55-57)CTG>CTC	p.L19L		NM_012317	NP_036449	O95751	LDOC1_HUMAN	leucine zipper, down-regulated in cancer 1	19					negative regulation of cell proliferation	nucleus	protein binding				0	Acute lymphoblastic leukemia(192;7.65e-05)					TCTCGATGCTCAGGGCGCGGT	0.677													4	35	---	---	---	---	PASS
MAGEA11	4110	broad.mit.edu	37	X	148797511	148797511	+	Missense_Mutation	SNP	C	T	T	rs141055931		TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:148797511C>T	uc004fdq.2	+	5	467	c.365C>T	c.(364-366)CCT>CTT	p.P122L	HSFX2_uc004fdl.2_Intron|HSFX1_uc004fdm.2_Intron|MAGEA11_uc004fdr.2_Missense_Mutation_p.P93L	NM_005366	NP_005357	P43364	MAGAB_HUMAN	melanoma antigen family A, 11 isoform a	122						cytoplasm|nucleus	protein binding			ovary(2)	2	Acute lymphoblastic leukemia(192;6.56e-05)|Colorectal(9;0.0662)					CACTGCAAGCCTGAGGAAGGC	0.577													13	125	---	---	---	---	PASS
MAGEA3	4102	broad.mit.edu	37	X	151935780	151935780	+	Silent	SNP	C	T	T	rs150153047		TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:151935780C>T	uc004fgp.2	-	3	596	c.387G>A	c.(385-387)CCG>CCA	p.P129P		NM_005362	NP_005353	P43357	MAGA3_HUMAN	melanoma antigen family A, 3	129	MAGE.										0	Acute lymphoblastic leukemia(192;6.56e-05)					CCTTTGTGACCGGCTCCCTGG	0.527													96	167	---	---	---	---	PASS
FLNA	2316	broad.mit.edu	37	X	153594739	153594739	+	Missense_Mutation	SNP	G	T	T			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:153594739G>T	uc004fkk.2	-	8	1414	c.1165C>A	c.(1165-1167)CCC>ACC	p.P389T	FLNA_uc010nuu.1_Missense_Mutation_p.P389T	NM_001110556	NP_001104026	P21333	FLNA_HUMAN	filamin A, alpha isoform 2	389	Filamin 2.				actin crosslink formation|actin cytoskeleton reorganization|cell junction assembly|cytoplasmic sequestering of protein|establishment of protein localization|inhibition of adenylate cyclase activity by dopamine receptor signaling pathway|negative regulation of protein catabolic process|negative regulation of sequence-specific DNA binding transcription factor activity|platelet activation|platelet degranulation|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of transcription factor import into nucleus|protein localization at cell surface|protein stabilization|receptor clustering	cell cortex|cytosol|extracellular region|nucleus|plasma membrane	actin filament binding|Fc-gamma receptor I complex binding|glycoprotein binding|GTP-Ral binding|protein homodimerization activity|Rac GTPase binding|signal transducer activity|transcription factor binding			breast(6)	6	all_cancers(53;3.7e-16)|all_epithelial(53;2.97e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					TCCAGGCCGGGACCTTGGGCT	0.597													18	98	---	---	---	---	PASS
PLXNA3	55558	broad.mit.edu	37	X	153692007	153692007	+	Missense_Mutation	SNP	C	G	G			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:153692007C>G	uc004flm.2	+	6	1694	c.1521C>G	c.(1519-1521)CAC>CAG	p.H507Q		NM_017514	NP_059984	P51805	PLXA3_HUMAN	plexin A3 precursor	507	Extracellular (Potential).				axon guidance	integral to membrane|intracellular|plasma membrane	transmembrane receptor activity			upper_aerodigestive_tract(1)|ovary(1)|central_nervous_system(1)	3	all_cancers(53;5.05e-16)|all_epithelial(53;1.87e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					GGGACCCGCACTGTGGTTGGT	0.706													6	15	---	---	---	---	PASS
CTAG2	30848	broad.mit.edu	37	X	153880851	153880851	+	Silent	SNP	G	A	A			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:153880851G>A	uc004fmi.1	-	2	377	c.324C>T	c.(322-324)ATC>ATT	p.I108I	CTAG2_uc004fmh.1_Silent_p.I108I	NM_020994	NP_066274	O75638	CTAG2_HUMAN	cancer/testis antigen 2 isoform LAGE-1b	108						centrosome				pancreas(1)	1	all_cancers(53;5.05e-16)|all_epithelial(53;1.87e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					CCCGGGACAGGATCCTGCGGA	0.612													25	104	---	---	---	---	PASS
RBM15	64783	broad.mit.edu	37	1	110882542	110882543	+	Frame_Shift_Del	DEL	TG	-	-			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:110882542_110882543delTG	uc001dzl.1	+	1	598_599	c.515_516delTG	c.(514-516)CTGfs	p.L172fs	RBM15_uc001dzm.1_Frame_Shift_Del_p.L172fs|uc001dzj.2_5'Flank	NM_022768	NP_073605	Q96T37	RBM15_HUMAN	RNA binding motif protein 15	172	RRM 1.				interspecies interaction between organisms	nucleus	nucleotide binding|protein binding|RNA binding			ovary(3)	3		all_cancers(81;2.89e-06)|all_epithelial(167;2.96e-06)|all_lung(203;0.000116)|Lung NSC(277;0.000233)|Breast(1374;0.0634)		BRCA - Breast invasive adenocarcinoma(282;0.000224)|Epithelial(280;0.000476)|Kidney(133;0.000539)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|all cancers(265;0.00144)|Lung(183;0.0238)|Colorectal(144;0.103)|LUSC - Lung squamous cell carcinoma(189;0.135)		TACAAGACTCTGAAGATAAGCG	0.609			T	MKL1	acute megakaryocytic leukemia						OREG0013656	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	67	31	---	---	---	---	
ASH1L	55870	broad.mit.edu	37	1	155347813	155347814	+	Intron	INS	-	A	A			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155347813_155347814insA	uc009wqq.2	-						RAG1AP1_uc010pey.1_Intron|ASH1L_uc001fkt.2_Intron	NM_018489	NP_060959	Q9NR48	ASH1L_HUMAN	absent, small, or homeotic 1-like						cell-cell signaling|DNA packaging|regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	chromosome|Golgi apparatus|nucleus|tight junction	DNA binding|histone-lysine N-methyltransferase activity|zinc ion binding			skin(5)|ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|kidney(1)|pancreas(1)	11	Hepatocellular(266;0.0997)|all_neural(408;0.129)|all_hematologic(923;0.145)		Epithelial(20;1.74e-08)|all cancers(21;3.29e-08)|BRCA - Breast invasive adenocarcinoma(34;0.021)			gactccgtctcaaaaaaaaaac	0.094													4	2	---	---	---	---	
TTN	7273	broad.mit.edu	37	2	179393337	179393343	+	Frame_Shift_Del	DEL	TTAATAT	-	-			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179393337_179393343delTTAATAT	uc010zfg.1	-	309	99655_99661	c.99431_99437delATATTAA	c.(99430-99438)AATATTAATfs	p.N33144fs	uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Frame_Shift_Del_p.N26839fs|TTN_uc010zfi.1_Frame_Shift_Del_p.N26772fs|TTN_uc010zfj.1_Frame_Shift_Del_p.N26647fs|TTN_uc002umq.2_Frame_Shift_Del_p.N161fs	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	34071_34073							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)			TTGTCCTTCATTAATATTTTGAGATCT	0.391													29	27	---	---	---	---	
ANKAR	150709	broad.mit.edu	37	2	190541861	190541861	+	Intron	DEL	G	-	-	rs56090484		TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:190541861delG	uc002uqw.1	+						ANKAR_uc002uqu.2_Intron|ANKAR_uc002uqv.1_Intron	NM_144708	NP_653309	Q7Z5J8	ANKAR_HUMAN	ankyrin and armadillo repeat containing							integral to membrane	binding			ovary(2)|pancreas(1)|skin(1)	4			OV - Ovarian serous cystadenocarcinoma(117;0.00156)|Epithelial(96;0.0256)|all cancers(119;0.0744)			ttttttttttggaacagagtc	0.124													9	4	---	---	---	---	
MOGAT1	116255	broad.mit.edu	37	2	223562830	223562831	+	Intron	INS	-	T	T	rs148576038	by1000genomes	TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:223562830_223562831insT	uc010fws.1	+						MOGAT1_uc010fwt.1_Intron	NM_058165	NP_477513	Q96PD6	MOGT1_HUMAN	monoacylglycerol O-acyltransferase 1						glycerol metabolic process	endoplasmic reticulum membrane|integral to membrane	2-acylglycerol O-acyltransferase activity			breast(1)	1		Renal(207;0.0183)		Epithelial(121;4.13e-10)|all cancers(144;2.06e-07)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.0105)		AGCAGATGGGGTTTTAGTGAGA	0.381													1	6	---	---	---	---	
C3orf18	51161	broad.mit.edu	37	3	50599335	50599336	+	Intron	INS	-	T	T	rs35405680		TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:50599335_50599336insT	uc003das.2	-						C3orf18_uc003dar.2_Intron|C3orf18_uc011bdr.1_Intron|C3orf18_uc010hlo.2_Intron|C3orf18_uc010hlp.2_Intron|C3orf18_uc003dat.2_Intron	NM_016210	NP_057294	Q9UK00	CC018_HUMAN	hypothetical protein LOC51161							integral to membrane				pancreas(1)	1				BRCA - Breast invasive adenocarcinoma(193;0.000278)|KIRC - Kidney renal clear cell carcinoma(197;0.0175)|Kidney(197;0.0207)		CTTCATGCCtcttttttttttt	0.282													4	2	---	---	---	---	
NMD3	51068	broad.mit.edu	37	3	160953120	160953121	+	Intron	INS	-	A	A			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:160953120_160953121insA	uc003feb.1	+						NMD3_uc003fec.2_Intron|NMD3_uc003fed.1_Intron|NMD3_uc010hwh.2_Intron	NM_015938	NP_057022	Q96D46	NMD3_HUMAN	NMD3 homolog						protein transport	cytoplasm|nucleolus|nucleoplasm				ovary(1)	1			Lung(72;0.00111)|LUSC - Lung squamous cell carcinoma(72;0.00156)			tttctgttaggaaaaaaaaaaa	0.079													8	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	193701166	193701167	+	IGR	DEL	AC	-	-	rs113253998		TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:193701166_193701167delAC								OPA1 (285567 upstream) : LOC100128023 (9717 downstream)																							AGAAAACGAAacacacacacac	0.228													4	2	---	---	---	---	
PCDH7	5099	broad.mit.edu	37	4	30723874	30723874	+	Frame_Shift_Del	DEL	C	-	-			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:30723874delC	uc003gsk.1	+	1	1838	c.830delC	c.(829-831)ACCfs	p.T277fs	PCDH7_uc011bxw.1_Intron|PCDH7_uc011bxx.1_Frame_Shift_Del_p.T277fs	NM_002589	NP_002580	O60245	PCDH7_HUMAN	protocadherin 7 isoform a precursor	277	Cadherin 2.|Extracellular (Potential).				homophilic cell adhesion	integral to plasma membrane	calcium ion binding			upper_aerodigestive_tract(1)|ovary(1)|liver(1)|skin(1)	4						TACGAGCTGACCCTGCGAGTG	0.692													2	6	---	---	---	---	
DMP1	1758	broad.mit.edu	37	4	88580361	88580362	+	Intron	INS	-	T	T			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:88580361_88580362insT	uc003hqv.2	+						DMP1_uc003hqw.2_Intron	NM_004407	NP_004398	Q13316	DMP1_HUMAN	dentin matrix acidic phosphoprotein 1 isoform 1						biomineral tissue development|ossification	cytoplasm|nucleus|proteinaceous extracellular matrix	calcium ion binding|integrin binding			pancreas(1)|skin(1)	2		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.227)		OV - Ovarian serous cystadenocarcinoma(123;0.000516)		CCTTCCTTTCCTTTTTTGCAGG	0.332													70	91	---	---	---	---	
RXFP1	59350	broad.mit.edu	37	4	159549906	159549906	+	Intron	DEL	G	-	-			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:159549906delG	uc003ipz.2	+						RXFP1_uc010iqj.1_Intron|RXFP1_uc011cja.1_Intron|RXFP1_uc010iqo.2_Intron|RXFP1_uc011cjb.1_Intron|RXFP1_uc010iqk.2_Intron|RXFP1_uc011cjc.1_Intron|RXFP1_uc011cjd.1_Intron|RXFP1_uc010iql.2_Intron|RXFP1_uc011cje.1_Intron|RXFP1_uc010iqm.2_Intron|RXFP1_uc011cjf.1_Intron|RXFP1_uc010iqn.2_Intron	NM_021634	NP_067647	Q9HBX9	RXFP1_HUMAN	relaxin/insulin-like family peptide receptor 1							integral to membrane|plasma membrane	G-protein coupled receptor activity|metal ion binding				0	all_hematologic(180;0.24)	Renal(120;0.0854)		COAD - Colon adenocarcinoma(41;0.0219)		TCTTTCTACTGTTTTTTCACA	0.279													20	19	---	---	---	---	
GEMIN5	25929	broad.mit.edu	37	5	154292267	154292267	+	Intron	DEL	A	-	-			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:154292267delA	uc003lvx.3	-						GEMIN5_uc011ddk.1_Intron	NM_015465	NP_056280	Q8TEQ6	GEMI5_HUMAN	gemin 5						ncRNA metabolic process|protein complex assembly|spliceosomal snRNP assembly	Cajal body|cytosol|spliceosomal complex	protein binding|snRNA binding			skin(2)|ovary(1)	3	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)			TCTAAGTAACAAAAAAAAAAA	0.383													6	4	---	---	---	---	
BTN2A1	11120	broad.mit.edu	37	6	26460170	26460171	+	Intron	INS	-	CACAGGGAGATTCCACAGGGA	CACAGGGAGATTCCACAGGGA	rs142117310	by1000genomes	TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26460170_26460171insCACAGGGAGATTCCACAGGGA	uc003nib.1	+						BTN2A1_uc003nic.1_Intron|BTN2A1_uc003nid.1_Intron|BTN2A1_uc011dko.1_Intron	NM_007049	NP_008980	Q7KYR7	BT2A1_HUMAN	butyrophilin, subfamily 2, member A1 isoform 1						lipid metabolic process	integral to plasma membrane				ovary(1)|skin(1)	2						ACTCCCTTTTCCACTCTCCCTG	0.480													4	2	---	---	---	---	
HLA-DRB5	3127	broad.mit.edu	37	6	32521545	32521546	+	Intron	INS	-	AAGG	AAGG	rs70993877		TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32521545_32521546insAAGG	uc003obk.3	-						HLA-DRB1_uc011dqa.1_Intron|HLA-DRB6_uc003obm.1_Intron|HLA-DRB6_uc003obn.1_Intron	NM_002125	NP_002116	Q30154	DRB5_HUMAN	major histocompatibility complex, class II, DR						antigen processing and presentation of peptide or polysaccharide antigen via MHC class II|immune response	endoplasmic reticulum membrane|Golgi apparatus|integral to membrane|late endosome membrane|lysosomal membrane|MHC class II protein complex					0						TTGGGGAAAGACTTTATCCAGG	0.436													5	3	---	---	---	---	
GCM1	8521	broad.mit.edu	37	6	52992826	52992827	+	3'UTR	INS	-	AAAAAAAA	AAAAAAAA	rs71726666		TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:52992826_52992827insAAAAAAAA	uc003pbp.2	-	6						NM_003643	NP_003634	Q9NP62	GCM1_HUMAN	glial cells missing homolog a							transcription factor complex	DNA binding|sequence-specific DNA binding transcription factor activity|transcription factor binding			central_nervous_system(1)	1	Lung NSC(77;0.0755)					gactctgtctcaaaaaaaaaaa	0.084													5	3	---	---	---	---	
SNAP91	9892	broad.mit.edu	37	6	84371392	84371393	+	Intron	INS	-	T	T			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:84371392_84371393insT	uc011dze.1	-						SNAP91_uc003pkb.2_Intron|SNAP91_uc003pkc.2_Intron|SNAP91_uc003pkd.2_Intron|SNAP91_uc003pka.2_Intron|SNAP91_uc011dzf.1_Intron	NM_014841	NP_055656	O60641	AP180_HUMAN	synaptosomal-associated protein, 91kDa homolog						clathrin coat assembly	clathrin coat|coated pit|plasma membrane	1-phosphatidylinositol binding|clathrin binding			ovary(1)	1		all_cancers(76;0.000243)|Acute lymphoblastic leukemia(125;2.91e-07)|all_hematologic(105;0.000337)|all_epithelial(107;0.0575)		BRCA - Breast invasive adenocarcinoma(397;0.0967)		GCATAGTACTATTTTTTTTTAA	0.322													11	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	108326821	108326821	+	IGR	DEL	T	-	-	rs112205315		TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:108326821delT								SEC63 (47339 upstream) : OSTM1 (35794 downstream)																							TCATCAATGAttttttttttt	0.264													4	3	---	---	---	---	
TMEM181	57583	broad.mit.edu	37	6	159049261	159049262	+	Intron	DEL	TG	-	-			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:159049261_159049262delTG	uc003qrm.3	+						TMEM181_uc010kjr.1_Intron	NM_020823	NP_065874	Q9P2C4	TM181_HUMAN	G protein-coupled receptor 178						pathogenesis	integral to membrane	toxin binding			ovary(2)|central_nervous_system(1)	3		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;8.15e-18)|BRCA - Breast invasive adenocarcinoma(81;1.38e-05)		AAGCAGGGGCtgtgtgtgtgtg	0.426													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	65226569	65226569	+	Intron	DEL	T	-	-			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:65226569delT	uc003tud.1	-						CCT6P1_uc003tug.2_Intron|CCT6P1_uc003tuh.2_Intron|CCT6P1_uc003tui.2_Intron					Homo sapiens hypothetical LOC441242, mRNA (cDNA clone MGC:87648 IMAGE:5267764), complete cds.																		gcccggccCCttttttttttt	0.149													9	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	101977570	101977571	+	IGR	INS	-	T	T			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:101977570_101977571insT								SH2B2 (15393 upstream) : SPDYE6 (8622 downstream)																							GCATGGGTCCAttttttttttt	0.139													4	2	---	---	---	---	
NAMPT	10135	broad.mit.edu	37	7	105917289	105917290	+	Intron	INS	-	A	A			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:105917289_105917290insA	uc003vdq.2	-						NAMPT_uc003vdr.1_Intron|NAMPT_uc011klu.1_Intron	NM_005746	NP_005737	P43490	NAMPT_HUMAN	nicotinamide phosphoribosyltransferase						cell-cell signaling|NAD biosynthetic process|nicotinamide metabolic process|positive regulation of cell proliferation|positive regulation of nitric-oxide synthase biosynthetic process|signal transduction|water-soluble vitamin metabolic process	cytosol	cytokine activity|nicotinamide phosphoribosyltransferase activity|nicotinate phosphoribosyltransferase activity|nicotinate-nucleotide diphosphorylase (carboxylating) activity			large_intestine(1)	1						actcggtttccaaaaaaaaaaa	0.114													5	3	---	---	---	---	
CNOT4	4850	broad.mit.edu	37	7	135048672	135048674	+	In_Frame_Del	DEL	TGT	-	-			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:135048672_135048674delTGT	uc011kpy.1	-	10	1864_1866	c.1772_1774delACA	c.(1771-1776)AACACT>ACT	p.N591del	CNOT4_uc003vss.2_Intron|CNOT4_uc011kpz.1_In_Frame_Del_p.N588del|CNOT4_uc003vst.2_Intron	NM_001008225	NP_001008226	O95628	CNOT4_HUMAN	CCR4-NOT transcription complex, subunit 4	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment					nuclear-transcribed mRNA poly(A) tail shortening|protein autoubiquitination|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytosol|nucleus	nucleotide binding|protein binding|RNA binding|ubiquitin-protein ligase activity|zinc ion binding				0						GTGGTGGCAGTGTTGGACGTTGG	0.552													225	118	---	---	---	---	
EPHX2	2053	broad.mit.edu	37	8	27369617	27369617	+	Intron	DEL	G	-	-	rs78320281		TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:27369617delG	uc003xfu.2	+						EPHX2_uc010lut.1_Intron|EPHX2_uc010luu.2_Intron|EPHX2_uc010luv.2_Intron|EPHX2_uc003xfv.2_Intron|EPHX2_uc010luw.2_Intron|EPHX2_uc011lam.1_Intron	NM_001979	NP_001970	P34913	HYES_HUMAN	epoxide hydrolase 2, cytoplasmic						aromatic compound catabolic process|cellular calcium ion homeostasis|drug metabolic process|inflammatory response|positive regulation of vasodilation|reactive oxygen species metabolic process|regulation of blood pressure|response to toxin|xenobiotic metabolic process	cytosol|focal adhesion|Golgi apparatus|nucleolus|peroxisome|soluble fraction	epoxide hydrolase activity|metal ion binding|protein homodimerization activity			ovary(1)	1		Ovarian(32;2.61e-05)|all_epithelial(46;0.207)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0226)|Epithelial(17;1.12e-09)|Colorectal(74;0.157)	Tamoxifen(DB00675)	cctgtctcaagaaaaaaaaaa	0.154													4	2	---	---	---	---	
MTERFD1	51001	broad.mit.edu	37	8	97256341	97256342	+	Intron	DEL	TG	-	-	rs6993518	by1000genomes	TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:97256341_97256342delTG	uc003yhs.1	-						MTERFD1_uc003yhr.1_Intron|MTERFD1_uc010mbd.1_Intron	NM_015942	NP_057026	Q96E29	MTER1_HUMAN	MTERF domain containing 1 precursor						negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	mitochondrion	transcription regulatory region DNA binding			ovary(1)	1	Breast(36;5.16e-05)					TGAATCGTTATGTAGAAATAGT	0.233													51	33	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	142723793	142723795	+	IGR	DEL	TGG	-	-			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:142723793_142723795delTGG								FLJ43860 (206463 upstream) : MIR1302-7 (143808 downstream)																							atggtgatgatggtggtggtggt	0.020													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	66545695	66545695	+	Intron	DEL	A	-	-			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66545695delA	uc010mnh.1	-						uc004aef.2_Intron					Homo sapiens cDNA FLJ20444 fis, clone KAT05128.																		CTGTAAGAGGAAAAAAAAACA	0.373													4	2	---	---	---	---	
KIAA0368	23392	broad.mit.edu	37	9	114206518	114206519	+	Intron	INS	-	A	A			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:114206518_114206519insA	uc004bfe.1	-						KIAA0368_uc010muc.1_Intron	NM_001080398	NP_001073867			KIAA0368 protein												0						GTGTGTCATTTAAAAAAAAAAA	0.332													4	2	---	---	---	---	
CACNB2	783	broad.mit.edu	37	10	18825203	18825204	+	Intron	DEL	GG	-	-	rs7098625		TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:18825203_18825204delGG	uc001ipr.2	+						CACNB2_uc009xjz.1_Intron|CACNB2_uc001ips.2_Intron|CACNB2_uc001ipt.2_Intron|CACNB2_uc001ipu.2_Intron|CACNB2_uc001ipv.2_Intron|CACNB2_uc009xka.1_Intron|CACNB2_uc001ipw.2_Intron|CACNB2_uc001ipx.2_Intron|CACNB2_uc001ipz.2_Intron|CACNB2_uc001ipy.2_Intron|CACNB2_uc010qco.1_Intron|CACNB2_uc001iqa.2_Intron|NSUN6_uc001iqb.2_Intron	NM_201596	NP_963890	Q08289	CACB2_HUMAN	calcium channel, voltage-dependent, beta 2						axon guidance|neuromuscular junction development	integral to plasma membrane|sarcolemma|voltage-gated calcium channel complex	protein binding|voltage-gated calcium channel activity			large_intestine(1)|central_nervous_system(1)|skin(1)	3					Magnesium Sulfate(DB00653)|Verapamil(DB00661)	ttttttttttgggggacaaggt	0.139													10	7	---	---	---	---	
MS4A6E	245802	broad.mit.edu	37	11	60107623	60107624	+	Intron	DEL	GA	-	-			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:60107623_60107624delGA	uc001npd.2	+							NM_139249	NP_640342	Q96DS6	M4A6E_HUMAN	membrane-spanning 4-domains, subfamily A, member							integral to membrane	receptor activity				0						CTGACAAGCTGAGAGTTCACTG	0.257													6	4	---	---	---	---	
CACNA1C	775	broad.mit.edu	37	12	2789725	2789726	+	Intron	INS	-	C	C			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:2789725_2789726insC	uc009zdu.1	+						CACNA1C_uc009zdv.1_Intron|CACNA1C_uc001qkb.2_Intron|CACNA1C_uc001qkc.2_Intron|CACNA1C_uc001qke.2_Intron|CACNA1C_uc001qkf.2_Intron|CACNA1C_uc001qjz.2_Intron|CACNA1C_uc001qkd.2_Intron|CACNA1C_uc001qkg.2_Intron|CACNA1C_uc009zdw.1_Intron|CACNA1C_uc001qkh.2_Intron|CACNA1C_uc001qkl.2_Intron|CACNA1C_uc001qkn.2_Intron|CACNA1C_uc001qko.2_Intron|CACNA1C_uc001qkp.2_Intron|CACNA1C_uc001qkr.2_Intron|CACNA1C_uc001qku.2_Intron|CACNA1C_uc001qkq.2_Intron|CACNA1C_uc001qks.2_Intron|CACNA1C_uc001qkt.2_Intron|CACNA1C_uc001qki.1_Frame_Shift_Ins_p.A1617fs|CACNA1C_uc001qkj.1_Intron|CACNA1C_uc001qkk.1_Intron|CACNA1C_uc001qkm.1_Frame_Shift_Ins_p.A1606fs|CACNA1C_uc010sea.1_Intron|uc001qkx.1_Intron|CACNA1C_uc001qky.1_Intron	NM_199460	NP_955630	Q13936	CAC1C_HUMAN	calcium channel, voltage-dependent, L type,						axon guidance|calcium ion transport into cytosol|energy reserve metabolic process|regulation of insulin secretion	cytoplasm|postsynaptic density|voltage-gated calcium channel complex	calmodulin binding|voltage-gated calcium channel activity			ovary(10)|central_nervous_system(1)	11			OV - Ovarian serous cystadenocarcinoma(31;0.00256)	LUAD - Lung adenocarcinoma(1;0.134)	Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Mibefradil(DB01388)|Nicardipine(DB00622)|Verapamil(DB00661)	AGGCTGCACAGCCCCCCAGCAT	0.579													10	5	---	---	---	---	
TROAP	10024	broad.mit.edu	37	12	49719150	49719151	+	Intron	DEL	AA	-	-	rs111795391		TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49719150_49719151delAA	uc001rtx.3	+						TROAP_uc009zlh.2_Intron|TROAP_uc001rty.2_5'Flank	NM_005480	NP_005471	Q12815	TROAP_HUMAN	tastin isoform 1						cell adhesion	cytoplasm				ovary(1)	1						tctatttcttaaaaaaaaaaaa	0.203													6	3	---	---	---	---	
CORO1C	23603	broad.mit.edu	37	12	109056093	109056094	+	Intron	INS	-	T	T	rs149021672	by1000genomes	TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:109056093_109056094insT	uc001tnj.2	-						CORO1C_uc009zva.2_Intron|CORO1C_uc010sxf.1_Intron	NM_014325	NP_055140	Q9ULV4	COR1C_HUMAN	coronin, actin binding protein, 1C isoform 1						actin cytoskeleton organization|phagocytosis|signal transduction	actin cytoskeleton	actin filament binding			skin(3)	3						GTGTTAGGCGgttttttttttg	0.193													4	2	---	---	---	---	
HNF1A	6927	broad.mit.edu	37	12	121435128	121435129	+	Intron	INS	-	G	G			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:121435128_121435129insG	uc001tzg.2	+						HNF1A_uc001tzf.2_Intron|HNF1A_uc010szn.1_Intron	NM_000545	NP_000536	P20823	HNF1A_HUMAN	hepatic nuclear factor-1-alpha						glucose homeostasis|glucose import|insulin secretion|positive regulation of transcription initiation from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|renal glucose absorption	cytoplasm|nucleus|protein complex	DNA binding|protein dimerization activity|protein heterodimerization activity|protein homodimerization activity|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding			liver(92)|large_intestine(15)|endometrium(6)|breast(2)|lung(1)	116	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					aattagtggcaggtcccagtgg	0.267									Hepatic_Adenoma_Familial_Clustering_of				4	2	---	---	---	---	
NPAS3	64067	broad.mit.edu	37	14	34029215	34029216	+	Intron	INS	-	A	A			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:34029215_34029216insA	uc001wru.2	+						NPAS3_uc001wrs.2_Intron|NPAS3_uc001wrt.2_Intron|NPAS3_uc001wrv.2_Intron|NPAS3_uc001wrw.2_Intron	NM_173159	NP_071406	Q8IXF0	NPAS3_HUMAN	neuronal PAS domain protein 3 isoform 3						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|signal transducer activity			ovary(1)|skin(1)	2	Breast(36;0.0102)|Hepatocellular(127;0.133)		LUAD - Lung adenocarcinoma(48;0.00169)|Lung(238;0.00968)	GBM - Glioblastoma multiforme(1;1.31e-09)|all cancers(1;0.000112)|OV - Ovarian serous cystadenocarcinoma(311;0.115)		gactctgtctcaaaaaaaaaaa	0.089													8	4	---	---	---	---	
TRAPPC6B	122553	broad.mit.edu	37	14	39626311	39626311	+	Intron	DEL	A	-	-	rs138686072		TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:39626311delA	uc001wut.1	-						TRAPPC6B_uc001wuu.1_Intron|TRAPPC6B_uc001wuv.1_Intron|TRAPPC6B_uc010tqd.1_Intron	NM_001079537	NP_001073005	Q86SZ2	TPC6B_HUMAN	trafficking protein particle complex 6B isoform						vesicle-mediated transport	endoplasmic reticulum|Golgi apparatus	guanylate cyclase activity|heme binding				0	Hepatocellular(127;0.213)		LUAD - Lung adenocarcinoma(48;0.000565)|Lung(238;0.000711)	GBM - Glioblastoma multiforme(112;0.0128)		actccatctcaaaaaaaaaaa	0.169													12	7	---	---	---	---	
ERO1L	30001	broad.mit.edu	37	14	53150867	53150870	+	Intron	DEL	ACAG	-	-	rs144715857		TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:53150867_53150870delACAG	uc001wzv.2	-						ERO1L_uc001wzw.2_Intron|ERO1L_uc010aof.2_Intron	NM_014584	NP_055399	Q96HE7	ERO1A_HUMAN	ERO1-like precursor						chaperone mediated protein folding requiring cofactor|electron transport chain|protein thiol-disulfide exchange|response to temperature stimulus|transport	endoplasmic reticulum lumen|endoplasmic reticulum membrane|microsome	disulfide oxidoreductase activity|flavin adenine dinucleotide binding|oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor				0	Breast(41;0.226)					acacacacacacaGAGAGAGTTGG	0.221													4	2	---	---	---	---	
SYNE2	23224	broad.mit.edu	37	14	64625797	64625797	+	Intron	DEL	T	-	-	rs113291922		TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:64625797delT	uc001xgm.2	+						SYNE2_uc001xgl.2_Intron|SYNE2_uc010apy.2_Intron|SYNE2_uc001xgn.2_Intron|SYNE2_uc001xgo.2_Intron|SYNE2_uc001xgp.2_Intron|SYNE2_uc010aqa.2_5'Flank	NM_015180	NP_055995	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2						centrosome localization|cytoskeletal anchoring at nuclear membrane|nuclear migration along microfilament|positive regulation of cell migration	cytoskeleton|filopodium membrane|focal adhesion|integral to membrane|lamellipodium membrane|mitochondrial part|nuclear outer membrane|nucleoplasm|sarcoplasmic reticulum membrane|SUN-KASH complex|Z disc	actin binding|protein binding			ovary(8)|breast(4)|central_nervous_system(1)|pancreas(1)	14				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)		TTGAGTGGCCTTTTTTTTTTC	0.289													4	2	---	---	---	---	
GPHN	10243	broad.mit.edu	37	14	67525732	67525732	+	Intron	DEL	A	-	-			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:67525732delA	uc001xiy.2	+						GPHN_uc001xix.2_Intron|GPHN_uc010tss.1_Intron|GPHN_uc010tst.1_Intron|GPHN_uc010tsu.1_Intron	NM_001024218	NP_001019389	Q9NQX3	GEPH_HUMAN	gephyrin isoform 2						Mo-molybdopterin cofactor biosynthetic process|water-soluble vitamin metabolic process	cell junction|cytoplasm|cytoskeleton|postsynaptic membrane	ATP binding|metal ion binding|nucleotidyltransferase activity			ovary(2)	2		all_cancers(7;0.0476)|all_hematologic(31;0.0116)		Epithelial(1;1.73e-08)|all cancers(60;3.15e-07)|OV - Ovarian serous cystadenocarcinoma(108;0.000275)|BRCA - Breast invasive adenocarcinoma(234;0.00323)|Colorectal(3;0.0938)|KIRC - Kidney renal clear cell carcinoma(182;0.184)		Taaaaaaaggaaaaaaaaaaa	0.299			T	MLL	AL								4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	97235205	97235205	+	IGR	DEL	T	-	-			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:97235205delT								PAPOLA (201759 upstream) : VRK1 (28479 downstream)																							tctccctcccttccttcctat	0.000													10	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	25826462	25826462	+	IGR	DEL	T	-	-			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:25826462delT								UBE3A (142334 upstream) : ATP10A (97400 downstream)																							AGACCTTTCGTTTTTTTTTTT	0.249													4	2	---	---	---	---	
PARN	5073	broad.mit.edu	37	16	14700252	14700252	+	Intron	DEL	G	-	-	rs62037478		TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:14700252delG	uc010uzd.1	-						PARN_uc010uzc.1_Intron|PARN_uc010uze.1_Intron|PARN_uc010uzf.1_Intron|PARN_uc010uzg.1_Intron	NM_002582	NP_002573	O95453	PARN_HUMAN	poly(A)-specific ribonuclease (deadenylation						female gamete generation|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|nuclear-transcribed mRNA poly(A) tail shortening|RNA modification	cytosol|nucleolus	metal ion binding|mRNA 3'-UTR binding|nucleotide binding|poly(A)-specific ribonuclease activity|protein binding			ovary(2)	2						aagaccctgagggaaaaaaaa	0.139													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	28596109	28596110	+	Intron	INS	-	A	A			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:28596109_28596110insA	uc010vct.1	-						CCDC101_uc002dqf.2_Intron					RecName: Full=Nuclear pore complex-interacting protein-like 2; Flags: Precursor;																		gactccatctcaaaaaaaaaaa	0.238													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	55005968	55005968	+	IGR	DEL	T	-	-			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:55005968delT								IRX5 (37575 upstream) : IRX6 (352503 downstream)																							tttcctttcctttccttcctt	0.000													4	2	---	---	---	---	
TP53	7157	broad.mit.edu	37	17	7578469	7578469	+	Frame_Shift_Del	DEL	C	-	-			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7578469delC	uc002gim.2	-	5	655	c.461delG	c.(460-462)GGCfs	p.G154fs	TP53_uc002gig.1_Frame_Shift_Del_p.G154fs|TP53_uc002gih.2_Frame_Shift_Del_p.G154fs|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Frame_Shift_Del_p.G22fs|TP53_uc010cng.1_Frame_Shift_Del_p.G22fs|TP53_uc002gii.1_Frame_Shift_Del_p.G22fs|TP53_uc010cnh.1_Frame_Shift_Del_p.G154fs|TP53_uc010cni.1_Frame_Shift_Del_p.G154fs|TP53_uc002gij.2_Frame_Shift_Del_p.G154fs|TP53_uc010cnj.1_RNA|TP53_uc002gin.2_Frame_Shift_Del_p.G61fs|TP53_uc002gio.2_Frame_Shift_Del_p.G22fs|TP53_uc010vug.1_Frame_Shift_Del_p.G115fs	NM_001126112	NP_001119584	P04637	P53_HUMAN	tumor protein p53 isoform a	154	Required for interaction with FBXO42.||Interaction with HIPK1 (By similarity).|Interaction with AXIN1 (By similarity).		G -> D (in sporadic cancers; somatic mutation).|G -> S (in sporadic cancers; somatic mutation).|G -> A (in sporadic cancers; somatic mutation).|G -> V (in a brain tumor with no family history; germline mutation and in sporadic cancers; somatic mutation).|G -> I (in sporadic cancers; somatic mutation; requires 2 nucleotide substitutions).|G -> C (in a sporadic cancer; somatic mutation).		activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray	cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork	ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding	p.G154V(36)|p.G154G(12)|p.G154S(9)|p.0?(7)|p.G154D(6)|p.P152fs*14(4)|p.G154I(3)|p.G154fs*27(3)|p.G154fs*16(2)|p.G154fs*14(2)|p.P153fs*26(2)|p.P153fs*22(2)|p.P151_V173del23(1)|p.G154_R156delGTR(1)|p.G154C(1)|p.Q144_G154del11(1)|p.D148_T155delDSTPPPGT(1)|p.G154A(1)|p.S149fs*72(1)|p.G154fs*22(1)|p.D148fs*23(1)|p.P153_G154insX(1)		large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1)	22245		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)		GACGCGGGTGCCGGGCGGGGG	0.607		111	Mis|N|F		breast|colorectal|lung|sarcoma|adrenocortical|glioma|multiple other tumour types	breast|sarcoma|adrenocortical carcinoma|glioma|multiple other tumour types		Other_conserved_DNA_damage_response_genes	Hereditary_Adrenocortical_Cancer|Endometrial_Cancer_Familial_Clustering_of|Hereditary_Breast-Ovarian_Cancer_non-BRCA1/2|Li-Fraumeni_syndrome|Osteosarcoma_Familial_Clustering_of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)			42	48	---	---	---	---	
TRIM37	4591	broad.mit.edu	37	17	57094987	57094987	+	Intron	DEL	T	-	-			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:57094987delT	uc002iwy.3	-						TRIM37_uc002iwz.3_Intron|TRIM37_uc002ixa.3_Intron|TRIM37_uc010woc.1_Intron	NM_001005207	NP_001005207	O94972	TRI37_HUMAN	tripartite motif-containing 37 protein							perinuclear region of cytoplasm|peroxisome	ligase activity|protein binding|zinc ion binding			lung(2)|pancreas(2)|ovary(1)|skin(1)|breast(1)	7	Medulloblastoma(34;0.0922)|all_neural(34;0.101)					GAGCAGAATCttttttttttt	0.179									Mulibrey_Nanism				4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	60330427	60330430	+	IGR	DEL	CTCA	-	-	rs10541847		TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:60330427_60330430delCTCA								MED13 (187784 upstream) : TBC1D3P2 (11639 downstream)																							GGACAAACACCTCACTCATTCCAG	0.333													1	5	---	---	---	---	
ABCA6	23460	broad.mit.edu	37	17	67109140	67109140	+	Intron	DEL	A	-	-	rs34141662		TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:67109140delA	uc002jhw.1	-						ABCA6_uc002jhx.1_Intron	NM_080284	NP_525023	Q8N139	ABCA6_HUMAN	ATP-binding cassette, sub-family A, member 6						transport	integral to membrane	ATP binding|ATPase activity			upper_aerodigestive_tract(2)|large_intestine(2)|ovary(2)|skin(1)	7	Breast(10;5.65e-12)					CAGCTGATCTAAAAAAAAAAG	0.284													4	2	---	---	---	---	
KIAA0802	23255	broad.mit.edu	37	18	8785010	8785011	+	Intron	INS	-	T	T	rs142102394	by1000genomes	TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:8785010_8785011insT	uc002knr.2	+						KIAA0802_uc002knq.2_Intron|KIAA0802_uc010dkw.1_Intron	NM_015210	NP_056025	Q9Y4B5	CC165_HUMAN	hypothetical protein LOC23255												0						GTTGGGCTCCGttttttttgtt	0.361													7	4	---	---	---	---	
ABCA7	10347	broad.mit.edu	37	19	1046580	1046580	+	Intron	DEL	G	-	-			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1046580delG	uc002lqw.3	+						ABCA7_uc010dsb.1_Intron	NM_019112	NP_061985	Q8IZY2	ABCA7_HUMAN	ATP-binding cassette, sub-family A, member 7						phagocytosis|transmembrane transport	ATP-binding cassette (ABC) transporter complex|endosome membrane|Golgi membrane|integral to membrane|plasma membrane	ATP binding|ATPase activity|transporter activity			pancreas(7)|ovary(1)|central_nervous_system(1)	9		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		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)		AGGGTCTGGTGGGGGGGGGGA	0.652													3	7	---	---	---	---	
ZNF557	79230	broad.mit.edu	37	19	7082210	7082214	+	Intron	DEL	AGGTC	-	-	rs140739902		TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7082210_7082214delAGGTC	uc002mgb.2	+						ZNF557_uc002mga.2_Intron|ZNF557_uc002mgc.2_Intron	NM_001044388	NP_001037853	Q8N988	ZN557_HUMAN	zinc finger protein 557 isoform b						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)|pancreas(1)	2				Lung(535;0.179)		ttggatcatgaggtcaggtcaggag	0.083													4	4	---	---	---	---	
MUC16	94025	broad.mit.edu	37	19	9080282	9080283	+	Intron	DEL	AG	-	-			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9080282_9080283delAG	uc002mkp.2	-							NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16						cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			lung(30)|ovary(15)|breast(8)|large_intestine(1)|skin(1)|prostate(1)|pancreas(1)	57						aaagaaagaaagagaaagaaag	0.015													5	3	---	---	---	---	
KIAA1683	80726	broad.mit.edu	37	19	18380444	18380444	+	Intron	DEL	A	-	-			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:18380444delA	uc002nin.2	-						KIAA1683_uc010ebn.2_Intron|KIAA1683_uc010xqe.1_Intron	NM_025249	NP_079525	Q9H0B3	K1683_HUMAN	KIAA1683 isoform b							mitochondrion				ovary(2)	2						CAAAAATGCTAAATTCTAAAA	0.333													7	4	---	---	---	---	
WDR88	126248	broad.mit.edu	37	19	33637339	33637342	+	Intron	DEL	TTCC	-	-			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:33637339_33637342delTTCC	uc002nui.2	+							NM_173479	NP_775750	Q6ZMY6	WDR88_HUMAN	PQQ repeat and WD repeat domain containing											ovary(1)|breast(1)|central_nervous_system(1)	3	Esophageal squamous(110;0.137)					TAGGTCCTATttccttccttcctt	0.221													8	5	---	---	---	---	
MEGF8	1954	broad.mit.edu	37	19	42858270	42858271	+	Intron	INS	-	T	T	rs36065839		TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42858270_42858271insT	uc002otl.3	+						MEGF8_uc002otm.3_Intron	NM_001410	NP_001401	Q7Z7M0	MEGF8_HUMAN	multiple EGF-like-domains 8							integral to membrane	calcium ion binding|structural molecule activity			ovary(1)	1		Prostate(69;0.00682)				TAGTATTGCTGTTTTTTTTTTT	0.520													4	3	---	---	---	---	
CALM3	808	broad.mit.edu	37	19	47112265	47112265	+	Intron	DEL	G	-	-			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47112265delG	uc002pew.2	+						CALM3_uc010ekp.2_Intron|CALM3_uc010xyc.1_Intron	NM_005184	NP_005175	P62158	CALM_HUMAN	calmodulin 3						activation of phospholipase C activity|G-protein coupled receptor protein signaling pathway|glucose metabolic process|glycogen catabolic process|muscle contraction|negative regulation of ryanodine-sensitive calcium-release channel activity|nerve growth factor receptor signaling pathway|nitric oxide metabolic process|platelet activation|platelet degranulation|positive regulation of ryanodine-sensitive calcium-release channel activity|regulation of cytokinesis|regulation of nitric-oxide synthase activity|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum|response to calcium ion|synaptic transmission	centrosome|cytosol|extracellular region|nucleoplasm|plasma membrane|spindle microtubule|spindle pole	calcium ion binding|N-terminal myristoylation domain binding|phospholipase binding|protein domain specific binding|thioesterase binding|titin binding			ovary(1)	1		Ovarian(192;0.0129)|all_neural(266;0.0459)|Breast(70;0.212)		OV - Ovarian serous cystadenocarcinoma(262;0.000338)|all cancers(93;0.000683)|Epithelial(262;0.0181)|GBM - Glioblastoma multiforme(486;0.0341)	Aprindine(DB01429)|Bepridil(DB01244)|Dibucaine(DB00527)|Felodipine(DB01023)|Flunarizine(DB04841)|Fluphenazine(DB00623)|Isoflurane(DB00753)|Loperamide(DB00836)|Miconazole(DB01110)|Perphenazine(DB00850)|Phenoxybenzamine(DB00925)|Pimozide(DB01100)|Promethazine(DB01069)	CTTGATCTCTGGAACAAGAAG	0.567													51	30	---	---	---	---	
SIGLEC10	89790	broad.mit.edu	37	19	51919482	51919482	+	Intron	DEL	G	-	-			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51919482delG	uc002pwo.2	-						SIGLEC10_uc002pwp.2_Intron|SIGLEC10_uc002pwq.2_Intron|SIGLEC10_uc002pwr.2_Intron|SIGLEC10_uc010ycy.1_Intron|SIGLEC10_uc010ycz.1_Intron|SIGLEC10_uc010eow.2_Frame_Shift_Del_p.L44fs|SIGLEC10_uc002pws.1_Intron	NM_033130	NP_149121	Q96LC7	SIG10_HUMAN	sialic acid binding Ig-like lectin 10 precursor						cell adhesion	extracellular region|integral to membrane|plasma membrane	sugar binding			skin(1)	1		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000668)|OV - Ovarian serous cystadenocarcinoma(262;0.0101)		aaggggtacagggaggagCAC	0.408													119	89	---	---	---	---	
ZNF880	400713	broad.mit.edu	37	19	52877717	52877717	+	Intron	DEL	T	-	-	rs77187934		TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:52877717delT	uc002pzc.2	+						ZNF880_uc002pzb.3_Intron	NM_001145434	NP_001138906	Q6PDB4	ZN880_HUMAN	zinc finger protein LOC400713						regulation of transcription, DNA-dependent	intracellular	nucleic acid binding|zinc ion binding				0						GGCCCCATAAttttttttttt	0.254													6	3	---	---	---	---	
NOP56	10528	broad.mit.edu	37	20	2633326	2633331	+	Intron	DEL	GGGCGC	-	-	rs28970277	byFrequency	TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:2633326_2633331delGGGCGC	uc002wgh.2	+						NOP56_uc010zpy.1_Intron|MIR1292_hsa-mir-1292|MI0006433_5'Flank|NOP56_uc002wgi.2_5'Flank|SNORD110_uc002wgj.2_5'Flank|SNORA51_uc002wgk.1_5'Flank|NOP56_uc002wgm.1_5'Flank	NM_006392	NP_006383	O00567	NOP56_HUMAN	nucleolar protein 5A						rRNA processing	box C/D snoRNP complex|pre-snoRNP complex	protein binding|snoRNA binding			ovary(1)|pancreas(1)	2						AGTGGTTGCGGGGCGCGGGCGACGCG	0.573													10	7	---	---	---	---	
ZNFX1	57169	broad.mit.edu	37	20	47870567	47870567	+	Intron	DEL	T	-	-	rs11353174		TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:47870567delT	uc002xui.2	-							NM_021035	NP_066363	Q9P2E3	ZNFX1_HUMAN	zinc finger, NFX1-type containing 1								metal ion binding			ovary(2)	2			BRCA - Breast invasive adenocarcinoma(12;0.00173)|COAD - Colon adenocarcinoma(4;0.14)|Colorectal(8;0.166)			ttcttttttcttttttttttt	0.194													5	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	15200018	15200018	+	IGR	DEL	T	-	-			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:15200018delT								POTED (186112 upstream) : C21orf15 (15437 downstream)																							TGTTTTCATCTTTTTTTTTTT	0.507													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	18511131	18511132	+	IGR	INS	-	GAAGGAAG	GAAGGAAG	rs140421958	by1000genomes	TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:18511131_18511132insGAAGGAAG								C21orf34 (529037 upstream) : CXADR (374198 downstream)																							AGTTGTGTGCAgaaggaaggaa	0.099													6	4	---	---	---	---	
TCN2	6948	broad.mit.edu	37	22	31019234	31019235	+	Intron	INS	-	C	C	rs141234711	by1000genomes	TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:31019234_31019235insC	uc003aip.1	+						TCN2_uc003aiq.1_Intron|TCN2_uc003air.1_Intron	NM_000355	NP_000346	P20062	TCO2_HUMAN	transcobalamin II precursor						cobalamin metabolic process|cobalamin transport|cobalt ion transport	extracellular space	cobalamin binding			central_nervous_system(1)	1					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	TGAAGCCTTAGAATTTTTATGC	0.366													4	4	---	---	---	---	
CBY1	25776	broad.mit.edu	37	22	39067413	39067423	+	Intron	DEL	TCTGCACAGGA	-	-			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:39067413_39067423delTCTGCACAGGA	uc003awb.2	+						CBY1_uc011any.1_3'UTR|CBY1_uc003awc.2_Intron|uc003awd.2_RNA	NM_001002880	NP_001002880	Q9Y3M2	CBY1_HUMAN	PKD2 interactor, golgi and endoplasmic reticulum						cardiac muscle cell differentiation|fat cell differentiation|negative regulation of transcription, DNA-dependent|protein localization	nuclear speck|trans-Golgi network	beta-catenin binding|identical protein binding			ovary(1)	1	Melanoma(58;0.04)					ccagttggagtctgcacaggatctgcacagc	0.000													7	4	---	---	---	---	
BRD1	23774	broad.mit.edu	37	22	50192941	50192967	+	Intron	DEL	GAGGGGACAGAGGAGACAGAGGGGATG	-	-			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50192941_50192967delGAGGGGACAGAGGAGACAGAGGGGATG	uc003biv.2	-						BRD1_uc011arf.1_Intron|BRD1_uc011arg.1_Intron|BRD1_uc011arh.1_Intron|BRD1_uc003biu.3_Intron	NM_014577	NP_055392	O95696	BRD1_HUMAN	bromodomain containing protein 1						histone H3 acetylation	MOZ/MORF histone acetyltransferase complex	zinc ion binding			pancreas(1)	1		all_cancers(38;6.11e-10)|all_epithelial(38;8.06e-09)|all_lung(38;6.64e-05)|Lung NSC(38;0.0011)|Breast(42;0.00235)|Ovarian(80;0.0139)|Lung SC(80;0.164)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0369)|BRCA - Breast invasive adenocarcinoma(115;0.21)		CACCgggacagaggggacagaggagacagaggggatggaggggacag	0.524													10	10	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	3442597	3442597	+	IGR	DEL	A	-	-			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:3442597delA								MXRA5 (177913 upstream) : PRKX (79816 downstream)																							caccaccatcaccaccatcac	0.000													4	2	---	---	---	---	
MAGEB2	4113	broad.mit.edu	37	X	30237824	30237825	+	3'UTR	INS	-	T	T			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:30237824_30237825insT	uc004dbz.2	+	2						NM_002364	NP_002355	O15479	MAGB2_HUMAN	melanoma antigen family B, 2								protein binding			ovary(1)	1						AACTTGTTGACTTTTTTTTTTT	0.322													4	2	---	---	---	---	
ABCB7	22	broad.mit.edu	37	X	74295152	74295153	+	Intron	INS	-	A	A			TCGA-60-2708-01	TCGA-60-2708-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:74295152_74295153insA	uc004eca.2	-						ABCB7_uc004ebz.2_Intron|ABCB7_uc011mqn.1_Intron|ABCB7_uc010nls.2_Intron|ABCB7_uc010nlt.2_Intron	NM_004299	NP_004290	O75027	ABCB7_HUMAN	ATP-binding cassette, sub-family B, member 7						cellular iron ion homeostasis	integral to membrane|mitochondrial inner membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances|heme transporter activity			ovary(1)	1						TTGCTACTAATGAGAATTTAAG	0.322													22	15	---	---	---	---	
