Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	t_alt_count	t_ref_count	validation_status	validation_method	validation_tumor_sample	validation_alt_allele	pox	qox	pox_cutoff	isArtifactMode	oxoGCut	init_n_lod
KIAA1751	85452	broad.mit.edu	37	1	1896465	1896465	+	Silent	SNP	G	A	A			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr1:1896465G>A	uc001aim.1	-	13	1593	c.1437C>T	c.(1435-1437)GGC>GGT	p.G479G	KIAA1751_uc009vkz.1_Silent_p.G479G	NM_001080484	NP_001073953	Q9C0B2	K1751_HUMAN	hypothetical protein LOC85452	479										pancreas(1)	1	all_cancers(77;0.000708)|all_epithelial(69;0.000943)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;6.04e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Medulloblastoma(700;0.151)|Lung SC(97;0.217)		Epithelial(90;8.79e-39)|OV - Ovarian serous cystadenocarcinoma(86;9.61e-25)|GBM - Glioblastoma multiforme(42;1.2e-07)|Colorectal(212;4.84e-05)|COAD - Colon adenocarcinoma(227;0.000214)|Kidney(185;0.00254)|BRCA - Breast invasive adenocarcinoma(365;0.00461)|STAD - Stomach adenocarcinoma(132;0.00645)|KIRC - Kidney renal clear cell carcinoma(229;0.037)|Lung(427;0.205)		TCTTTGTCCCGCCCACGGGCT	0.677000													8	24					0	0	0.003080	0	0	
GPR153	387509	broad.mit.edu	37	1	6311551	6311551	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr1:6311551G>A	uc001amp.1	-	4	1086	c.826C>T	c.(826-828)CCC>TCC	p.P276S	GPR153_uc001amo.1_5'Flank	NM_207370	NP_997253	Q6NV75	GP153_HUMAN	G protein-coupled receptor 153	276	Extracellular (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity				0	Ovarian(185;0.0634)	all_cancers(23;8.07e-33)|all_epithelial(116;4.45e-18)|all_lung(118;1.09e-06)|all_neural(13;3.68e-06)|Lung NSC(185;1.52e-05)|all_hematologic(16;2.39e-05)|Acute lymphoblastic leukemia(12;0.000372)|Glioma(11;0.00127)|Renal(390;0.00188)|Colorectal(325;0.00342)|Breast(487;0.00475)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.15)		Epithelial(90;1.91e-37)|GBM - Glioblastoma multiforme(13;4.87e-29)|OV - Ovarian serous cystadenocarcinoma(86;3.03e-19)|Colorectal(212;1.33e-07)|COAD - Colon adenocarcinoma(227;1.36e-05)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000911)|BRCA - Breast invasive adenocarcinoma(365;0.00109)|STAD - Stomach adenocarcinoma(132;0.00313)|READ - Rectum adenocarcinoma(331;0.0642)|Lung(427;0.246)		GCCATCCAGGGCGCTGAGGCG	0.697000													8	23					0	0	0.003080	0	0	
MIIP	60672	broad.mit.edu	37	1	12081808	12081808	+	Missense_Mutation	SNP	C	G	G			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr1:12081808C>G	uc001ato.1	+	2	205	c.25C>G	c.(25-27)CAG>GAG	p.Q9E		NM_021933	NP_068752	Q5JXC2	MIIP_HUMAN	invasion inhibitory protein 45	9										ovary(1)	1						GGAACTGGCACAGCTGCGGCT	0.682000													8	35					0	0	0.004482	0	0	
VAV3	10451	broad.mit.edu	37	1	108307785	108307785	+	Silent	SNP	G	A	A			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr1:108307785G>A	uc001dvk.1	-	9	888	c.834C>T	c.(832-834)TAC>TAT	p.Y278Y	VAV3_uc010ouw.1_Silent_p.Y278Y|VAV3_uc001dvl.1_Silent_p.Y102Y|VAV3_uc010oux.1_Silent_p.Y278Y	NM_006113	NP_006104	Q9UKW4	VAV3_HUMAN	vav 3 guanine nucleotide exchange factor isoform	278	DH.				angiogenesis|apoptosis|B cell receptor signaling pathway|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|platelet activation|positive regulation of B cell proliferation|regulation of Rho protein signal transduction|response to DNA damage stimulus|response to drug|small GTPase mediated signal transduction	cytosol	GTPase activator activity|metal ion binding|SH3/SH2 adaptor activity			ovary(5)|lung(2)|breast(2)	9		all_epithelial(167;5.38e-05)|all_lung(203;0.000314)|Lung NSC(277;0.000594)		Colorectal(144;0.0331)|Lung(183;0.128)|Epithelial(280;0.204)		AGTACTGCCCGTAAATAACCA	0.373000													10	46					0	0	0.010729	0	0	
KCNA3	3738	broad.mit.edu	37	1	111215835	111215835	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr1:111215835C>T	uc001dzv.1	-	1	1821	c.1597G>A	c.(1597-1599)GAA>AAA	p.E533K		NM_002232	NP_002223	P22001	KCNA3_HUMAN	potassium voltage-gated channel, shaker-related	533						voltage-gated potassium channel complex	delayed rectifier potassium channel activity			ovary(4)|pancreas(1)	5		all_cancers(81;3.92e-06)|all_epithelial(167;1.28e-05)|all_lung(203;0.000199)|Lung NSC(277;0.000398)		Lung(183;0.0235)|Colorectal(144;0.0306)|all cancers(265;0.0752)|Epithelial(280;0.0821)|COAD - Colon adenocarcinoma(174;0.132)|LUSC - Lung squamous cell carcinoma(189;0.133)		CCCCCCTCTTCGATCACCATA	0.527000													18	65					0	0	0.010504	0	0	
LINGO4	339398	broad.mit.edu	37	1	151774430	151774430	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr1:151774430C>T	uc001ezf.1	-	2	941	c.751G>A	c.(751-753)GGG>AGG	p.G251R		NM_001004432	NP_001004432	Q6UY18	LIGO4_HUMAN	leucine rich repeat and Ig domain containing 4	251	Extracellular (Potential).					integral to membrane				large_intestine(1)	1	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.14)		LUSC - Lung squamous cell carcinoma(543;0.181)			AGATTGAGCCCAACCAGGCTC	0.642000													13	86					0	0	0.016723	0	0	
TCHH	7062	broad.mit.edu	37	1	152080772	152080772	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr1:152080772G>A	uc001ezp.2	-	2	4921	c.4921C>T	c.(4921-4923)CGT>TGT	p.R1641C	TCHH_uc009wne.1_Missense_Mutation_p.R1641C	NM_007113	NP_009044	Q07283	TRHY_HUMAN	trichohyalin	1641	23 X 26 AA approximate tandem repeats.				keratinization	cytoskeleton	calcium ion binding			ovary(3)|kidney(1)|central_nervous_system(1)	5	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			TTTCTGTCACGCTCTTGGCGG	0.592000													23	131					0	0	0.012319	0	0	
HRNR	388697	broad.mit.edu	37	1	152185612	152185612	+	Silent	SNP	A	G	G			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr1:152185612A>G	uc001ezt.1	-	3	8569	c.8493T>C	c.(8491-8493)TTT>TTC	p.F2831F		NM_001009931	NP_001009931	Q86YZ3	HORN_HUMAN	hornerin	2831					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)			TGCTACTAGGAAAACTGAGAA	0.388000													40	78					0	0	0.021022	0	0	
HRNR	388697	broad.mit.edu	37	1	152193511	152193511	+	Silent	SNP	C	G	G			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr1:152193511C>G	uc001ezt.1	-	3	670	c.594G>C	c.(592-594)GGG>GGC	p.G198G		NM_001009931	NP_001009931	Q86YZ3	HORN_HUMAN	hornerin	198	2.				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)			ACTGCCCTGACCCAGACCCAC	0.557000													13	98					0	0	0.013537	0	0	
NUP210L	91181	broad.mit.edu	37	1	154033097	154033097	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr1:154033097T>G	uc001fdw.2	-	20	2841	c.2769A>C	c.(2767-2769)GAA>GAC	p.E923D	NUP210L_uc009woq.2_Intron|NUP210L_uc010peh.1_Missense_Mutation_p.E923D	NM_207308	NP_997191	Q5VU65	P210L_HUMAN	nucleoporin 210kDa-like isoform 1	923						integral to membrane				skin(5)|ovary(4)|large_intestine(1)|central_nervous_system(1)	11	all_lung(78;9.35e-31)|Lung NSC(65;1.33e-28)|Hepatocellular(266;0.0877)|Melanoma(130;0.128)		LUSC - Lung squamous cell carcinoma(543;0.151)|Colorectal(543;0.198)			AACCAGATCCTTCCACAAGGC	0.383000													11	125					0	0	0.013537	0	0	
OR10X1	128367	broad.mit.edu	37	1	158549454	158549454	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr1:158549454A>C	uc010pin.1	-	1	236	c.236T>G	c.(235-237)CTT>CGT	p.L79R		NM_001004477	NP_001004477	Q8NGY0	O10X1_HUMAN	olfactory receptor, family 10, subfamily X,	79	Helical; Name=2; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1	all_hematologic(112;0.0378)					GAGTGCACTAAGGAAGAGATA	0.498000													16	89					0	0	0.004990	0	0	
ILDR2	387597	broad.mit.edu	37	1	166927077	166927077	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr1:166927077A>G	uc001gdx.1	-	2	364	c.308T>C	c.(307-309)GTA>GCA	p.V103A		NM_199351	NP_955383	Q71H61	ILDR2_HUMAN	immunoglobulin-like domain containing receptor	103	Ig-like V-type.|Extracellular (Potential).					integral to membrane				ovary(1)	1						TTTTGAAGCTACTACTCGAAC	0.498000													17	118					0	0	0.007413	0	0	
SELP	6403	broad.mit.edu	37	1	169572294	169572294	+	Missense_Mutation	SNP	G	A	A	rs144811959	byFrequency	TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr1:169572294G>A	uc001ggi.3	-	10	1740	c.1675C>T	c.(1675-1677)CGC>TGC	p.R559C	SELP_uc001ggh.2_Missense_Mutation_p.R394C|SELP_uc009wvr.2_Missense_Mutation_p.R559C	NM_003005	NP_002996	P16109	LYAM3_HUMAN	selectin P precursor	559	Extracellular (Potential).|Sushi 6.				platelet activation|platelet degranulation|positive regulation of platelet activation	external side of plasma membrane|extracellular space|integral to plasma membrane|membrane fraction|platelet alpha granule membrane|platelet dense granule membrane|soluble fraction	fucose binding|glycosphingolipid binding|heparin binding|lipopolysaccharide binding|oligosaccharide binding|sialic acid binding			ovary(2)|skin(2)	4	all_hematologic(923;0.208)				Clopidogrel(DB00758)|Heparin(DB01109)|Tirofiban(DB00775)	TCTGTCCAGCGTCCCGATCGA	0.448000													17	85					0	0	0.004990	0	0	
RASAL2	9462	broad.mit.edu	37	1	178414760	178414760	+	Silent	SNP	C	T	T			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr1:178414760C>T	uc001glr.2	+	7	1271	c.1146C>T	c.(1144-1146)CTC>CTT	p.L382L	RASAL2_uc001glq.2_Silent_p.L530L	NM_004841	NP_004832	Q9UJF2	NGAP_HUMAN	RAS protein activator like 2 isoform 1	382	Ras-GAP.				negative regulation of Ras protein signal transduction|signal transduction	cytoplasm|intrinsic to internal side of plasma membrane	Ras GTPase activator activity			ovary(2)|breast(2)|large_intestine(1)	5						AGGAATACCTCAAGTTGGTGG	0.403000													15	92					0	0	0.004007	0	0	
F13B	2165	broad.mit.edu	37	1	197026201	197026201	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr1:197026201A>T	uc001gtt.1	-	7	1157	c.1113T>A	c.(1111-1113)CAT>CAA	p.H371Q		NM_001994	NP_001985	P05160	F13B_HUMAN	coagulation factor XIII B subunit precursor	371	Sushi 6.				blood coagulation	extracellular region				upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	3						CATTCGATCCATGGAGAAGGT	0.388000													13	68					0	0	0.020292	0	0	
MDM4	4194	broad.mit.edu	37	1	204511962	204511962	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr1:204511962C>T	uc001hba.2	+	8	724	c.562C>T	c.(562-564)CTT>TTT	p.L188F	MDM4_uc001hbd.1_RNA|MDM4_uc010pqw.1_RNA|MDM4_uc010pqx.1_Missense_Mutation_p.L61F|MDM4_uc001hay.1_Missense_Mutation_p.L188F|MDM4_uc001hbb.2_Missense_Mutation_p.L61F|MDM4_uc010pqy.1_Intron|MDM4_uc001hbc.2_RNA|MDM4_uc009xbe.1_RNA	NM_002393	NP_002384	O15151	MDM4_HUMAN	mouse double minute 4 homolog	188					apoptosis|cell proliferation|cellular response to hypoxia|G0 to G1 transition|negative regulation of apoptosis|negative regulation of cell cycle arrest|negative regulation of cell proliferation|negative regulation of protein catabolic process|negative regulation of transcription from RNA polymerase II promoter|protein complex assembly|protein stabilization	nucleus	enzyme binding|zinc ion binding			upper_aerodigestive_tract(1)|ovary(1)|central_nervous_system(1)	3	all_cancers(21;0.00146)|all_neural(3;0.0218)|Glioma(3;0.0382)|Breast(84;0.112)|all_epithelial(62;0.118)|Prostate(682;0.227)		GBM - Glioblastoma multiforme(2;3.15e-47)|all cancers(3;3.56e-32)|KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|Epithelial(59;0.143)|BRCA - Breast invasive adenocarcinoma(75;0.143)			TAGGCTGGACCTTGGATTTGA	0.378000			A		GBM|bladder|retinoblastoma								15	89					0	0	0.020292	0	0	
IL20	50604	broad.mit.edu	37	1	207039928	207039928	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr1:207039928A>T	uc001her.2	+	3	369	c.325A>T	c.(325-327)ATC>TTC	p.I109F	IL20_uc010pry.1_Missense_Mutation_p.I180F|IL20_uc009xby.2_Missense_Mutation_p.I109F	NM_018724	NP_061194	Q9NYY1	IL20_HUMAN	interleukin 20 precursor	109					positive regulation of keratinocyte differentiation|positive regulation of tyrosine phosphorylation of Stat3 protein|regulation of inflammatory response	extracellular space	cytokine activity|interleukin-20 receptor binding				0	Breast(84;0.201)			OV - Ovarian serous cystadenocarcinoma(81;0.00459)		TCTCCGGAAGATCAGCAGCCT	0.517000													66	378					0	0	0.014410	0	0	
LOC642826	642826	broad.mit.edu	37	10	47207813	47207813	+	RNA	SNP	T	C	C			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr10:47207813T>C	uc001jei.2	-	12		c.1586A>G			uc009xnf.2_Missense_Mutation_p.H132R					Homo sapiens cDNA, FLJ99065.												0						TTTACTTACATGGTTTGTACA	0.294000													3	22					0	0	0.009096	0	0	
CYP2C9	1559	broad.mit.edu	37	10	96707655	96707655	+	Silent	SNP	T	C	C			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr10:96707655T>C	uc001kka.3	+	4	626	c.601T>C	c.(601-603)TTG>CTG	p.L201L	CYP2C9_uc009xut.2_Silent_p.L201L	NM_000771	NP_000762	P11712	CP2C9_HUMAN	cytochrome P450, family 2, subfamily C,	201					exogenous drug catabolic process|monocarboxylic acid metabolic process|monoterpenoid metabolic process|oxidative demethylation|steroid metabolic process|urea metabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	(S)-limonene 6-monooxygenase activity|(S)-limonene 7-monooxygenase activity|4-hydroxyacetophenone monooxygenase activity|caffeine oxidase activity|drug binding|electron carrier activity|heme binding|oxygen binding|steroid hydroxylase activity			skin(4)|ovary(2)	6		Colorectal(252;0.0902)		all cancers(201;6.93e-05)	Acenocoumarol(DB01418)|Alosetron(DB00969)|Amiodarone(DB01118)|Antihemophilic Factor(DB00025)|Aprepitant(DB00673)|Bosentan(DB00559)|Carprofen(DB00821)|Carvedilol(DB01136)|Celecoxib(DB00482)|Clomipramine(DB01242)|Dapsone(DB00250)|Delavirdine(DB00705)|Desloratadine(DB00967)|Desogestrel(DB00304)|Diclofenac(DB00586)|Esomeprazole(DB00736)|Etodolac(DB00749)|Fluconazole(DB00196)|Fluoxetine(DB00472)|Flurbiprofen(DB00712)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Formoterol(DB00983)|Gemfibrozil(DB01241)|Ginkgo biloba(DB01381)|Glibenclamide(DB01016)|Glimepiride(DB00222)|Glipizide(DB01067)|Guanfacine(DB01018)|Hydromorphone(DB00327)|Ibuprofen(DB01050)|Imipramine(DB00458)|Irbesartan(DB01029)|Ketoconazole(DB01026)|Lansoprazole(DB00448)|Losartan(DB00678)|Lumiracoxib(DB01283)|Marinol(DB00470)|Mefenamic acid(DB00784)|Meloxicam(DB00814)|Mephenytoin(DB00532)|Metronidazole(DB00916)|Miconazole(DB01110)|Midazolam(DB00683)|Montelukast(DB00471)|Nateglinide(DB00731)|Nelfinavir(DB00220)|Nicardipine(DB00622)|Oxymorphone(DB01192)|Pantoprazole(DB00213)|Paramethadione(DB00617)|Phenprocoumon(DB00946)|Phenytoin(DB00252)|Pravastatin(DB00175)|Quinidine(DB00908)|Ritonavir(DB00503)|Rosiglitazone(DB00412)|Sertraline(DB01104)|Sildenafil(DB00203)|Sulfamethoxazole(DB01015)|Suprofen(DB00870)|Tamoxifen(DB00675)|Tenoxicam(DB00469)|Terfenadine(DB00342)|Tolbutamide(DB01124)|Torasemide(DB00214)|Troleandomycin(DB01361)|Valdecoxib(DB00580)|Valsartan(DB00177)|Voriconazole(DB00582)|Warfarin(DB00682)|Zafirlukast(DB00549)|Zileuton(DB00744)	AATGGAAAAGTTGAATGAAAA	0.368000													51	76					0	0	0.014410	0	0	
COL17A1	1308	broad.mit.edu	37	10	105798252	105798252	+	Silent	SNP	C	T	T			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr10:105798252C>T	uc001kxr.2	-	45	3151	c.2982G>A	c.(2980-2982)CCG>CCA	p.P994P		NM_000494	NP_000485	Q9UMD9	COHA1_HUMAN	alpha 1 type XVII collagen	994	Extracellular (Potential).|Triple-helical region.				cell-matrix adhesion|epidermis development|hemidesmosome assembly	basement membrane|cell-cell junction|collagen|hemidesmosome|integral to plasma membrane	protein binding			ovary(4)|pancreas(1)	5		Colorectal(252;0.103)|Breast(234;0.122)		Epithelial(162;2.5e-09)|all cancers(201;7.94e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0165)		GGGGCCCTGGCGGGCCTGACA	0.602000													72	84					0	0	0.014410	0	0	
ADRB1	153	broad.mit.edu	37	10	115804689	115804689	+	Silent	SNP	C	T	T			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr10:115804689C>T	uc001lba.2	+	1	884	c.798C>T	c.(796-798)CTC>CTT	p.L266L		NM_000684	NP_000675	P08588	ADRB1_HUMAN	beta-1-adrenergic receptor	266	Cytoplasmic (By similarity).				positive regulation of cAMP biosynthetic process	integral to plasma membrane	alpha-2A adrenergic receptor binding|beta1-adrenergic receptor activity|protein heterodimerization activity				0		Colorectal(252;0.172)|Breast(234;0.188)		Epithelial(162;0.0124)|all cancers(201;0.0298)	Acebutolol(DB01193)|Alprenolol(DB00866)|Amiodarone(DB01118)|Arbutamine(DB01102)|Atenolol(DB00335)|Betaxolol(DB00195)|Bevantolol(DB01295)|Bisoprolol(DB00612)|Bretylium(DB01158)|Carteolol(DB00521)|Carvedilol(DB01136)|Desipramine(DB01151)|Dobutamine(DB00841)|Dopamine(DB00988)|Epinephrine(DB00668)|Esmolol(DB00187)|Isoetharine(DB00221)|Isoproterenol(DB01064)|Labetalol(DB00598)|Levobunolol(DB01210)|Metipranolol(DB01214)|Metoprolol(DB00264)|Nadolol(DB01203)|Norepinephrine(DB00368)|Oxprenolol(DB01580)|Penbutolol(DB01359)|Pindolol(DB00960)|Practolol(DB01297)|Propranolol(DB00571)|Risperidone(DB00734)|Timolol(DB00373)|Ziprasidone(DB00246)	GCCGTTTCCTCGGCGGCCCAG	0.398000													6	4					0	0	0.001984	0	0	
PNLIPRP3	119548	broad.mit.edu	37	10	118215240	118215240	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr10:118215240T>A	uc001lcl.3	+	5	564	c.463T>A	c.(463-465)TTT>ATT	p.F155I		NM_001011709	NP_001011709	Q17RR3	LIPR3_HUMAN	pancreatic lipase-related protein 3 precursor	155					lipid catabolic process	extracellular region	triglyceride lipase activity			ovary(1)	1				all cancers(201;0.0131)		TCAGAAAAAATTTGAATATTC	0.373000													19	38					0	0	0.006122	0	0	
C11orf41	25758	broad.mit.edu	37	11	33589770	33589770	+	Silent	SNP	G	A	A			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr11:33589770G>A	uc001mup.3	+	8	3478	c.3354G>A	c.(3352-3354)GTG>GTA	p.V1118V	C11orf41_uc001mun.1_Silent_p.V1118V	NM_012194	NP_036326	Q6ZVL6	CK041_HUMAN	hypothetical protein LOC25758	1112						integral to membrane				ovary(2)	2						GCTACACTGTGCAGGTAGGTG	0.562000													9	21					0	0	0.006214	0	0	
OR5T3	390154	broad.mit.edu	37	11	56019933	56019933	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr11:56019933C>A	uc010rjd.1	+	1	258	c.258C>A	c.(256-258)CAC>CAA	p.H86Q		NM_001004747	NP_001004747	Q8NGG3	OR5T3_HUMAN	olfactory receptor, family 5, subfamily T,	86	Helical; Name=2; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0	Esophageal squamous(21;0.00448)					CCTGGCTCCACAACCCCATGT	0.363000													19	54					2.4624e-09	2.85325e-09	0.008871	1	0	
INCENP	3619	broad.mit.edu	37	11	61898025	61898025	+	Missense_Mutation	SNP	G	C	C			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr11:61898025G>C	uc001nsw.1	+	4	1228	c.1026G>C	c.(1024-1026)AAG>AAC	p.K342N	INCENP_uc009ynv.2_Missense_Mutation_p.K342N|INCENP_uc009ynw.1_Missense_Mutation_p.K342N|INCENP_uc001nsx.1_Missense_Mutation_p.K342N	NM_001040694	NP_001035784	Q9NQS7	INCE_HUMAN	inner centromere protein antigens 135/155kDa	342					chromosome segregation|cytokinesis|mitotic prometaphase	centromeric heterochromatin|condensed chromosome kinetochore|cytosol|microtubule|spindle	protein binding			lung(1)	1						TTGCCAAGAAGACTGCCGAAG	0.607000													12	54					0	0	0.013537	0	0	
SLC3A2	6520	broad.mit.edu	37	11	62648671	62648671	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr11:62648671A>C	uc001nwd.2	+	4	703	c.479A>C	c.(478-480)AAG>ACG	p.K160T	SLC3A2_uc001nwb.2_Missense_Mutation_p.K191T|SLC3A2_uc001nwc.2_Missense_Mutation_p.K161T|SLC3A2_uc001nwe.2_Missense_Mutation_p.K129T|SLC3A2_uc001nwf.2_Missense_Mutation_p.K98T|SLC3A2_uc001nwg.2_Missense_Mutation_p.K59T|SLC3A2_uc010rml.1_5'Flank	NM_002394	NP_002385	P08195	4F2_HUMAN	solute carrier family 3, member 2 isoform c	160	Cytoplasmic (Potential).				blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport	apical plasma membrane|cell surface|integral to membrane|melanosome	calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding				0						GCCGCGGCTAAGTTCACGGGC	0.687000											OREG0021031	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	7	14					0	0	0.001984	0	0	
RBM4	5936	broad.mit.edu	37	11	66410965	66410965	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr11:66410965G>A	uc009yrj.2	+	3	945	c.457G>A	c.(457-459)GCG>ACG	p.A153T	RBM4_uc009yrk.2_Missense_Mutation_p.A128T|RBM4_uc001oiw.1_Missense_Mutation_p.A153T|RBM4_uc001oix.1_Intron|RBM4_uc010rpj.1_Intron|RBM4_uc001oiy.1_Missense_Mutation_p.A153T|RBM4_uc001oiz.1_Missense_Mutation_p.A153T	NM_002896	NP_002887	Q9BWF3	RBM4_HUMAN	RNA binding motif protein 4	153					circadian regulation of gene expression|entrainment of circadian clock by photoperiod|mRNA processing|negative regulation of translation in response to stress|negative regulation of translation involved in gene silencing by miRNA|negative regulation of translational initiation|positive regulation of muscle cell differentiation|regulation of alternative nuclear mRNA splicing, via spliceosome|regulation of nucleocytoplasmic transport|RNA splicing|stress-activated MAPK cascade	nuclear speck|nucleolus|stress granule	miRNA binding|mRNA 3'-UTR binding|nucleotide binding|protein binding|zinc ion binding			ovary(1)	1				Lung(977;0.0112)|LUSC - Lung squamous cell carcinoma(976;0.0266)		GCTTAGGACTGCGCCCGGGAT	0.582000													24	100					0	0	0.021523	0	0	
IGHMBP2	3508	broad.mit.edu	37	11	68703977	68703977	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr11:68703977A>G	uc001ook.1	+	13	2131	c.2029A>G	c.(2029-2031)AGC>GGC	p.S677G	IGHMBP2_uc001ool.1_Missense_Mutation_p.S301G|IGHMBP2_uc001oom.1_Missense_Mutation_p.S255G	NM_002180	NP_002171	P38935	SMBP2_HUMAN	immunoglobulin mu binding protein 2	677	SS DNA-binding (By similarity).				cell death|DNA recombination|DNA repair|DNA replication|protein homooligomerization|transcription, DNA-dependent|translation	axon|growth cone|nucleus|ribonucleoprotein complex	ATP binding|ATP-dependent 5'-3' DNA helicase activity|ATP-dependent 5'-3' RNA helicase activity|ribosome binding|single-stranded DNA binding|transcription factor binding|tRNA binding|zinc ion binding				0			STAD - Stomach adenocarcinoma(18;0.0208)|LUAD - Lung adenocarcinoma(13;0.0713)			CAGGACCGGAAGCCAGCGGCA	0.627000													8	87					0	0	0.003080	0	0	
FAT3	120114	broad.mit.edu	37	11	92534124	92534124	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr11:92534124G>A	uc001pdj.3	+	9	7962	c.7945G>A	c.(7945-7947)GAC>AAC	p.D2649N		NM_001008781	NP_001008781	Q8TDW7	FAT3_HUMAN	FAT tumor suppressor homolog 3	2649	Cadherin 24.|Extracellular (Potential).				homophilic cell adhesion|multicellular organismal development	integral to membrane|plasma membrane	calcium ion binding			ovary(4)|pancreas(1)	5		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)				TTCAGTGGCCGACCTCCTGGA	0.458000										TCGA Ovarian(4;0.039)			7	28					0	0	0.003080	0	0	
ATM	472	broad.mit.edu	37	11	108163407	108163407	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr11:108163407C>T	uc001pkb.1	+	30	4883	c.4498C>T	c.(4498-4500)CAG>TAG	p.Q1500*	ATM_uc009yxr.1_Nonsense_Mutation_p.Q1500*|ATM_uc001pke.1_Nonsense_Mutation_p.Q152*|ATM_uc001pkf.2_Intron	NM_000051	NP_000042	Q13315	ATM_HUMAN	ataxia telangiectasia mutated isoform 1	1500					cell cycle arrest|cellular response to gamma radiation|DNA damage induced protein phosphorylation|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|double-strand break repair via homologous recombination|G2/M transition DNA damage checkpoint|histone mRNA catabolic process|mitotic cell cycle spindle assembly checkpoint|negative regulation of B cell proliferation|peptidyl-serine phosphorylation|positive regulation of DNA damage response, signal transduction by p53 class mediator|pre-B cell allelic exclusion|protein autophosphorylation|reciprocal meiotic recombination|replicative senescence	cytoplasmic membrane-bounded vesicle|nucleoplasm	1-phosphatidylinositol-3-kinase activity|ATP binding|DNA binding|DNA-dependent protein kinase activity|identical protein binding|protein complex binding|protein dimerization activity|protein N-terminus binding			haematopoietic_and_lymphoid_tissue(174)|lung(25)|breast(15)|large_intestine(9)|ovary(5)|kidney(5)|central_nervous_system(4)|upper_aerodigestive_tract(1)|stomach(1)|NS(1)	240		all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147)		CTTATTAAGTCAGGTTTGCCA	0.403000			D|Mis|N|F|S		T-PLL	leukemia|lymphoma|medulloblastoma|glioma		Genes_defective_in_diseases_associated_with_sensitivity_to_DNA_damaging_agents	Ataxia_Telangiectasia	TSP Lung(14;0.12)			97	140					0	0	0.014410	0	0	
SLC37A2	219855	broad.mit.edu	37	11	124949017	124949017	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr11:124949017T>G	uc001qbn.2	+	5	575	c.324T>G	c.(322-324)TTT>TTG	p.F108L	SLC37A2_uc010sau.1_Missense_Mutation_p.F108L	NM_001145290	NP_001138762	Q8TED4	SPX2_HUMAN	solute carrier family 37 (glycerol-3-phosphate	108	Helical; (Potential).				carbohydrate transport|transmembrane transport	integral to membrane				ovary(2)	2	all_hematologic(175;0.215)	Breast(109;0.012)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.152)|all_lung(97;0.159)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.61e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0384)		GTGGGGTTTTTGGGGAGCGGC	0.438000													35	163					0	0	0.021022	0	0	
NCAPD2	9918	broad.mit.edu	37	12	6623969	6623969	+	Silent	SNP	G	A	A			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr12:6623969G>A	uc001qoo.2	+	9	916	c.870G>A	c.(868-870)CTG>CTA	p.L290L	NCAPD2_uc009zen.1_Silent_p.L162L|NCAPD2_uc010sfd.1_Silent_p.L245L	NM_014865	NP_055680	Q15021	CND1_HUMAN	non-SMC condensin I complex, subunit D2	290	Interactions with SMC2 and SMC4.				cell division|mitotic chromosome condensation	condensin core heterodimer|cytoplasm	histone binding			ovary(2)|lung(1)|breast(1)|kidney(1)	5						CCCAAGAGCTGAGTCGAGACC	0.473000													21	118					0	0	0.010504	0	0	
SOX5	6660	broad.mit.edu	37	12	23757383	23757383	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr12:23757383C>A	uc001rfw.2	-	9	1204	c.1102G>T	c.(1102-1104)GCT>TCT	p.A368S	SOX5_uc001rfx.2_Missense_Mutation_p.A355S|SOX5_uc001rfy.2_Missense_Mutation_p.A355S|SOX5_uc010siv.1_Missense_Mutation_p.A355S|SOX5_uc010siw.1_RNA|SOX5_uc001rfz.1_Missense_Mutation_p.A320S	NM_006940	NP_008871	P35711	SOX5_HUMAN	SRY (sex determining region Y)-box 5 isoform a	368					transcription from RNA polymerase II promoter	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			ovary(5)|lung(1)	6						GGAGATACAGCAGCACCAAGG	0.507000													17	103					6.94344e-10	8.13163e-10	0.006122	1	0	
NELL2	4753	broad.mit.edu	37	12	44926420	44926420	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr12:44926420C>A	uc001rog.2	-	16	2343	c.1748G>T	c.(1747-1749)TGC>TTC	p.C583F	NELL2_uc001rof.3_Missense_Mutation_p.C582F|NELL2_uc001roh.2_Missense_Mutation_p.C583F|NELL2_uc009zkd.2_Intron|NELL2_uc010skz.1_Missense_Mutation_p.C633F|NELL2_uc010sla.1_Missense_Mutation_p.C606F|NELL2_uc001roi.1_Missense_Mutation_p.C583F|NELL2_uc010slb.1_Missense_Mutation_p.C582F	NM_001145108	NP_001138580	Q99435	NELL2_HUMAN	NEL-like protein 2 isoform b precursor	583	EGF-like 5; calcium-binding (Potential).				cell adhesion	extracellular region	calcium ion binding|protein binding|structural molecule activity			skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)	4	Lung SC(27;0.192)	Lung NSC(34;0.144)		GBM - Glioblastoma multiforme(48;0.092)		GCCATCTCTGCACTCACAGTG	0.428000													48	70					6.42738e-09	7.4084e-09	0.014410	1	0	
ARID2	196528	broad.mit.edu	37	12	46244555	46244555	+	Silent	SNP	C	G	G			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr12:46244555C>G	uc001ros.1	+	15	2649	c.2649C>G	c.(2647-2649)GTC>GTG	p.V883V	ARID2_uc001ror.2_Silent_p.V883V|ARID2_uc009zkg.1_Silent_p.V339V|ARID2_uc009zkh.1_Silent_p.V510V|ARID2_uc001rou.1_Silent_p.V217V	NM_152641	NP_689854	Q68CP9	ARID2_HUMAN	AT rich interactive domain 2 (ARID, RFX-like)	883	Gln-rich.				chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding|zinc ion binding			ovary(6)|skin(3)|upper_aerodigestive_tract(1)	10	Lung SC(27;0.192)|Renal(347;0.236)	Lung NSC(34;0.106)|all_lung(34;0.22)	OV - Ovarian serous cystadenocarcinoma(5;0.00691)	GBM - Glioblastoma multiforme(48;0.0153)		TTGCTGGTGTCCCAAGTCCAC	0.448000													9	92					0	0	0.006214	0	0	
KRT73	319101	broad.mit.edu	37	12	53004496	53004496	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr12:53004496G>A	uc001sas.2	-	7	1269	c.1234C>T	c.(1234-1236)CGG>TGG	p.R412W		NM_175068	NP_778238	Q86Y46	K2C73_HUMAN	keratin 73	412	Rod.|Coil 2.					keratin filament	structural molecule activity			large_intestine(2)|ovary(2)|skin(2)	6				BRCA - Breast invasive adenocarcinoma(357;0.189)		CGCAGCATCCGTGCCAGCTCC	0.647000													9	103					0	0	0.008291	0	0	
ERBB3	2065	broad.mit.edu	37	12	56489534	56489534	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr12:56489534C>A	uc001sjh.2	+	17	2192	c.1999C>A	c.(1999-2001)CGT>AGT	p.R667S	ERBB3_uc009zoj.2_Intron|ERBB3_uc010sqb.1_Missense_Mutation_p.R24S|ERBB3_uc010sqc.1_Missense_Mutation_p.R608S|ERBB3_uc009zok.2_Missense_Mutation_p.R109S|ERBB3_uc001sjk.2_5'Flank	NM_001982	NP_001973	P21860	ERBB3_HUMAN	erbB-3 isoform 1 precursor	667	Cytoplasmic (Potential).				cranial nerve development|heart development|negative regulation of cell adhesion|negative regulation of neuron apoptosis|negative regulation of secretion|negative regulation of signal transduction|neuron apoptosis|phosphatidylinositol 3-kinase cascade|positive regulation of phosphatidylinositol 3-kinase cascade|regulation of cell proliferation|Schwann cell differentiation|transmembrane receptor protein tyrosine kinase signaling pathway|wound healing	basolateral plasma membrane|extracellular space|integral to plasma membrane|receptor complex	ATP binding|growth factor binding|protein heterodimerization activity|protein homodimerization activity|protein tyrosine kinase activator activity|receptor signaling protein tyrosine kinase activity|transmembrane receptor protein tyrosine kinase activity			lung(3)|central_nervous_system(2)|stomach(1)|ovary(1)|skin(1)	8			OV - Ovarian serous cystadenocarcinoma(18;0.112)			TCTCTACTGGCGTGGGCGCCG	0.438000													62	83					8.77104e-35	1.07913e-34	0.014410	1	0	
GLT8D2	83468	broad.mit.edu	37	12	104393227	104393227	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr12:104393227A>G	uc001tkh.1	-	6	756	c.350T>C	c.(349-351)GTC>GCC	p.V117A	GLT8D2_uc001tki.1_Missense_Mutation_p.V117A	NM_031302	NP_112592	Q9H1C3	GL8D2_HUMAN	glycosyltransferase 8 domain containing 2	117	Lumenal (Potential).					integral to membrane	transferase activity, transferring glycosyl groups			ovary(1)|skin(1)	2						CCCTTTGAGGACCATCGGGTT	0.443000													23	100					0	0	0.012319	0	0	
POP5	51367	broad.mit.edu	37	12	121018991	121018991	+	Silent	SNP	G	A	A			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr12:121018991G>A	uc001tys.2	-	2	122	c.90C>T	c.(88-90)AGC>AGT	p.S30S	POP5_uc001tyt.2_Silent_p.S30S	NM_015918	NP_057002	Q969H6	POP5_HUMAN	processing of precursor 5 isoform a	30					tRNA processing		protein binding|ribonuclease P activity				0	all_neural(191;0.077)|Medulloblastoma(191;0.0922)					GTACGAGGCTGCTCAGAACTC	0.662000													11	59					0	0	0.013537	0	0	
TMEM132D	121256	broad.mit.edu	37	12	129566418	129566418	+	Silent	SNP	T	C	C			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr12:129566418T>C	uc009zyl.1	-	7	2137	c.1809A>G	c.(1807-1809)CAA>CAG	p.Q603Q	TMEM132D_uc001uia.2_Silent_p.Q141Q	NM_133448	NP_597705	Q14C87	T132D_HUMAN	transmembrane protein 132D precursor	603	Extracellular (Potential).					integral to membrane				ovary(10)|pancreas(2)|upper_aerodigestive_tract(1)|skin(1)	14	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0934)|Breast(359;0.133)		OV - Ovarian serous cystadenocarcinoma(86;0.000288)|Epithelial(86;0.0116)|all cancers(50;0.0246)		TGATGTCCACTTGCCAGTCTG	0.632000													9	69					0	0	0.006214	0	0	
EP400	57634	broad.mit.edu	37	12	132547087	132547087	+	Silent	SNP	G	A	A	rs12366766		TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr12:132547087G>A	uc001ujn.2	+	46	8210	c.8175G>A	c.(8173-8175)CAG>CAA	p.Q2725Q	EP400_uc001ujl.2_Silent_p.Q2724Q|EP400_uc001ujm.2_Silent_p.Q2644Q|EP400_uc001ujp.2_5'UTR	NM_015409	NP_056224	Q96L91	EP400_HUMAN	E1A binding protein p400	2761	Poly-Gln.|Interaction with ZNF42 (By similarity).				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)		agcagcagcagcaacaacagc	0.289000													4	41					0	0	0.009096	0	0	
POLE	5426	broad.mit.edu	37	12	133233758	133233758	+	Silent	SNP	C	T	T			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr12:133233758C>T	uc001uks.1	-	29	3590	c.3546G>A	c.(3544-3546)AAG>AAA	p.K1182K	POLE_uc001ukr.1_5'UTR|POLE_uc010tbq.1_RNA|POLE_uc009zyu.1_Silent_p.K1155K	NM_006231	NP_006222	Q07864	DPOE1_HUMAN	DNA-directed DNA polymerase epsilon	1182					base-excision repair, gap-filling|DNA synthesis involved in DNA repair|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|nucleotide-excision repair, DNA gap filling|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|transcription-coupled nucleotide-excision repair	nucleoplasm	chromatin binding|DNA binding|DNA-directed DNA polymerase activity|nucleotide binding|protein binding|zinc ion binding			ovary(3)|skin(3)|lung(1)|central_nervous_system(1)	8	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0416)		OV - Ovarian serous cystadenocarcinoma(86;5.22e-08)|Epithelial(86;4.03e-07)|all cancers(50;1.18e-05)		GCTCACTGATCTTCTTCTGCT	0.567000								DNA_polymerases_(catalytic_subunits)|Direct_reversal_of_damage					14	64					0	0	0.003163	0	0	
FLT1	2321	broad.mit.edu	37	13	29001983	29001983	+	Silent	SNP	G	A	A			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr13:29001983G>A	uc001usb.3	-	9	1467	c.1182C>T	c.(1180-1182)GAC>GAT	p.D394D	FLT1_uc010aar.1_Silent_p.D394D|FLT1_uc001usc.3_Silent_p.D394D|FLT1_uc010tdp.1_Silent_p.D394D	NM_002019	NP_002010	P17948	VGFR1_HUMAN	fms-related tyrosine kinase 1 isoform 1	394	Ig-like C2-type 4.|Extracellular (Potential).				cell differentiation|female pregnancy|positive regulation of vascular endothelial growth factor receptor signaling pathway	extracellular space|Golgi apparatus|integral to plasma membrane|nucleus	ATP binding|growth factor binding|vascular endothelial growth factor receptor activity			lung(10)|central_nervous_system(5)|ovary(3)|stomach(2)|skin(2)|urinary_tract(1)|breast(1)	24	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0262)|Breast(139;0.188)	Colorectal(13;0.000674)	all cancers(112;0.0301)|Epithelial(112;0.155)|GBM - Glioblastoma multiforme(144;0.184)|OV - Ovarian serous cystadenocarcinoma(117;0.205)|Lung(94;0.207)	Sunitinib(DB01268)	CTTCAGTTACGTCCTTGATAA	0.388000													19	72					0	0	0.012319	0	0	
SLC46A3	283537	broad.mit.edu	37	13	29292018	29292018	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr13:29292018T>A	uc001usi.2	-	1	1088	c.118A>T	c.(118-120)ACT>TCT	p.T40S	SLC46A3_uc001usg.2_5'Flank|SLC46A3_uc001usj.2_Missense_Mutation_p.T40S|SLC46A3_uc001ush.2_Missense_Mutation_p.T40S|SLC46A3_uc001usk.2_5'Flank	NM_181785	NP_861450	Q7Z3Q1	S46A3_HUMAN	solute carrier family 46, member 3 isoform a	40	Extracellular (Potential).				transmembrane transport	integral to membrane				central_nervous_system(1)|skin(1)	2		Lung SC(185;0.0367)		all cancers(112;0.159)		GATGAAAAAGTGTAGTTGCCA	0.368000													14	105					0	0	0.020292	0	0	
DGKH	160851	broad.mit.edu	37	13	42740687	42740687	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr13:42740687C>T	uc001uyl.1	+	9	1016	c.995C>T	c.(994-996)CCT>CTT	p.P332L	DGKH_uc010tfh.1_Missense_Mutation_p.P332L|DGKH_uc001uym.1_Missense_Mutation_p.P332L|DGKH_uc010tfi.1_Missense_Mutation_p.P87L|DGKH_uc010tfj.1_Missense_Mutation_p.P187L|DGKH_uc001uyn.1_RNA|DGKH_uc001uyo.1_Missense_Mutation_p.P187L|DGKH_uc001uyp.2_RNA	NM_178009	NP_821077	Q86XP1	DGKH_HUMAN	diacylglycerol kinase, eta isoform 2	332	DAGKc.				activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|intracellular signal transduction|platelet activation|protein oligomerization	endosome|plasma membrane	ATP binding|diacylglycerol kinase activity|metal ion binding			ovary(2)	2		Lung NSC(96;1.02e-05)|Prostate(109;0.0168)|Lung SC(185;0.0262)|Breast(139;0.0709)|Hepatocellular(98;0.114)		OV - Ovarian serous cystadenocarcinoma(117;5.88e-05)|GBM - Glioblastoma multiforme(144;0.000935)|BRCA - Breast invasive adenocarcinoma(63;0.109)		TGTGTTAGTCCTCTATTGGTT	0.358000													17	111					0	0	0.004990	0	0	
KPNA3	3839	broad.mit.edu	37	13	50279853	50279853	+	Missense_Mutation	SNP	G	C	C			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr13:50279853G>C	uc001vdj.2	-	15	1691	c.1276C>G	c.(1276-1278)CAA>GAA	p.Q426E		NM_002267	NP_002258	O00505	IMA3_HUMAN	karyopherin alpha 3	426	ARM 9.				interspecies interaction between organisms|NLS-bearing substrate import into nucleus|protein complex assembly	cytoplasm|nuclear pore	nuclear localization sequence binding|protein transporter activity				0		Lung NSC(96;2.46e-05)|Breast(56;9.7e-05)|Prostate(109;0.00174)|Hepatocellular(98;0.0207)|Myeloproliferative disorder(33;0.163)|Lung SC(185;0.187)|all_neural(104;0.19)		GBM - Glioblastoma multiforme(99;1.42e-09)		TGAACCACTTGAGAATCTTTC	0.363000													15	97					0	0	0.020292	0	0	
TGM1	7051	broad.mit.edu	37	14	24724611	24724611	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr14:24724611T>A	uc001wod.2	-	11	1728	c.1604A>T	c.(1603-1605)AAC>ATC	p.N535I	TGM1_uc010tog.1_Missense_Mutation_p.N93I	NM_000359	NP_000350	P22735	TGM1_HUMAN	transglutaminase 1	535					cell envelope organization|keratinization|peptide cross-linking	cornified envelope|intrinsic to membrane	acyltransferase activity|metal ion binding|protein binding|protein-glutamine gamma-glutamyltransferase activity			central_nervous_system(2)|ovary(1)	3				GBM - Glioblastoma multiforme(265;0.0186)	L-Glutamine(DB00130)	CTCCCGCATGTTGGAGCTGAT	0.547000													10	37					0	0	0.006214	0	0	
HECTD1	25831	broad.mit.edu	37	14	31585523	31585523	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr14:31585523T>C	uc001wrc.1	-	30	6026	c.5537A>G	c.(5536-5538)TAT>TGT	p.Y1846C	HECTD1_uc001wra.1_5'UTR|HECTD1_uc001wrb.1_5'UTR|HECTD1_uc001wrd.1_Missense_Mutation_p.Y1314C	NM_015382	NP_056197	Q9ULT8	HECD1_HUMAN	HECT domain containing 1	1846					protein ubiquitination involved in ubiquitin-dependent protein catabolic process	intracellular	metal ion binding|protein binding|ubiquitin-protein ligase activity			ovary(3)|large_intestine(1)|lung(1)	5	Hepatocellular(127;0.0877)|Breast(36;0.176)		LUAD - Lung adenocarcinoma(48;0.00292)|Lung(238;0.0164)|BRCA - Breast invasive adenocarcinoma(188;0.111)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.00617)		TTTTTGTACATAGTAAAAGAT	0.378000													35	56					0	0	0.015359	0	0	
SPTB	6710	broad.mit.edu	37	14	65252605	65252605	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr14:65252605T>A	uc001xht.2	-	16	3680	c.3626A>T	c.(3625-3627)AAG>ATG	p.K1209M	SPTB_uc001xhr.2_Missense_Mutation_p.K1209M|SPTB_uc001xhs.2_Missense_Mutation_p.K1209M|SPTB_uc001xhu.2_Missense_Mutation_p.K1209M	NM_000347	NP_000338	P11277	SPTB1_HUMAN	spectrin beta isoform b	1209	Spectrin 9.				actin filament capping|axon guidance	cell surface|cytosol|intrinsic to internal side of plasma membrane|protein complex|spectrin|spectrin-associated cytoskeleton	actin filament binding|structural constituent of cytoskeleton			ovary(7)|skin(2)|lung(1)|central_nervous_system(1)	11		all_lung(585;4.15e-09)		all cancers(60;4.33e-34)|OV - Ovarian serous cystadenocarcinoma(108;8.32e-20)|BRCA - Breast invasive adenocarcinoma(234;0.0628)		ATCCTCAAACTTCCGGATCCC	0.512000													53	171					0	0	0.014410	0	0	
KIAA1409	57578	broad.mit.edu	37	14	94088124	94088124	+	Silent	SNP	C	T	T			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr14:94088124C>T	uc001ybv.1	+	28	4163	c.4080C>T	c.(4078-4080)GAC>GAT	p.D1360D	KIAA1409_uc001ybs.1_Silent_p.D1338D	NM_020818	NP_065869	Q9P2D8	UNC79_HUMAN	hypothetical protein LOC57578	1515						integral to membrane				ovary(10)|skin(4)|large_intestine(3)	17		all_cancers(154;0.0354)|all_epithelial(191;0.216)		Epithelial(152;0.188)		TTACATTAGACGAACATCGTA	0.438000													13	73					0	0	0.013537	0	0	
ADAM6	8755	broad.mit.edu	37	14	107218824	107218824	+	RNA	SNP	G	A	A			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr14:107218824G>A	uc010tyt.1	-	12		c.890C>T								Parts of antibodies, mostly variable regions.												0						ATTAATACGTGAGACCCACAC	0.562000													5	171					0	0	0.014758	0	0	
HERC2	8924	broad.mit.edu	37	15	28412927	28412927	+	Missense_Mutation	SNP	G	A	A	rs146303265	byFrequency	TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr15:28412927G>A	uc001zbj.2	-	68	10566	c.10460C>T	c.(10459-10461)TCG>TTG	p.S3487L		NM_004667	NP_004658	O95714	HERC2_HUMAN	hect domain and RLD 2	3487					DNA repair|intracellular protein transport|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	nucleus	guanyl-nucleotide exchange factor activity|heme binding|protein binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(4)|lung(4)|skin(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)	13		all_lung(180;1.3e-11)|Breast(32;0.000194)|Colorectal(260;0.227)		all cancers(64;3.93e-09)|Epithelial(43;9.99e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0271)|GBM - Glioblastoma multiforme(186;0.0497)|Lung(196;0.199)		TGAGGGGGCCGACGGAGTCAC	0.532000													24	118					0	0	0.018920	0	0	
KIAA1370	56204	broad.mit.edu	37	15	52970229	52970229	+	Translation_Start_Site	SNP	A	C	C			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr15:52970229A>C	uc002acg.3	-	2	143	c.-10T>G	c.(-12--8)ATTGG>ATGGG		KIAA1370_uc002ach.3_RNA|KIAA1370_uc010bfg.1_Translation_Start_Site	NM_019600	NP_062546	Q32MH5	K1370_HUMAN	hypothetical protein LOC56204												0				all cancers(107;0.0803)		TTTCACATCCAATTTTCGCCC	0.458000													20	68					0	0	0.008871	0	0	
TEX9	374618	broad.mit.edu	37	15	56704540	56704540	+	Missense_Mutation	SNP	G	C	C			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr15:56704540G>C	uc002adp.2	+	10	874	c.869G>C	c.(868-870)AGT>ACT	p.S290T	TEX9_uc010ugl.1_Missense_Mutation_p.S215T	NM_198524	NP_940926	Q8N6V9	TEX9_HUMAN	testis expressed 9	290	Potential.										0				all cancers(107;0.0394)|GBM - Glioblastoma multiforme(80;0.056)		CAGGCTGCAAGTAGTCAAAGT	0.328000													15	74					0	0	0.020292	0	0	
MNS1	55329	broad.mit.edu	37	15	56748664	56748664	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr15:56748664G>A	uc002adr.2	-	3	446	c.281C>T	c.(280-282)GCT>GTT	p.A94V	MNS1_uc010bfo.2_5'UTR	NM_018365	NP_060835	Q8NEH6	MNS1_HUMAN	meiosis-specific nuclear structural 1	94	Potential.|Glu-rich.				meiosis					ovary(1)	1				all cancers(107;0.0196)|GBM - Glioblastoma multiforme(80;0.101)		CAATTCCATAGCCAGTTTTTC	0.348000													8	59					0	0	0.003080	0	0	
EDC3	80153	broad.mit.edu	37	15	74948184	74948184	+	Missense_Mutation	SNP	G	C	C			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr15:74948184G>C	uc002ayn.2	-	7	1198	c.710C>G	c.(709-711)CCA>CGA	p.P237R	EDC3_uc002ayo.2_Missense_Mutation_p.P237R|EDC3_uc002aym.2_Missense_Mutation_p.P237R	NM_001142443	NP_001135915	Q96F86	EDC3_HUMAN	enhancer of mRNA decapping 3	237	Required for interaction with DDX6 (By similarity).				exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay	cytoplasmic mRNA processing body|cytosol	protein binding|RNA binding			ovary(1)	1						CCTTTCATTTGGGATGCCCCG	0.507000													37	126					0	0	0.006999	0	0	
LOC645752	645752	broad.mit.edu	37	15	78212095	78212095	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr15:78212095C>A	uc010bky.2	-	10	844	c.80G>T	c.(79-81)AGG>ATG	p.R27M		NR_027024				SubName: Full=GOLGA6 protein; Flags: Fragment;												0						GGACAAGCTCCTCTTCAGCTC	0.557000													73	351					6.64032e-35	8.21599e-35	0.014410	1	0	
KIAA1199	57214	broad.mit.edu	37	15	81187373	81187373	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr15:81187373T>C	uc002bfw.1	+	10	1389	c.1129T>C	c.(1129-1131)TAC>CAC	p.Y377H	KIAA1199_uc010unn.1_Missense_Mutation_p.Y377H	NM_018689	NP_061159	Q8WUJ3	K1199_HUMAN	KIAA1199 precursor	377										upper_aerodigestive_tract(1)|ovary(1)|skin(1)	3						CGAGGTTGTCTACAAAAAAGG	0.498000													13	125					0	0	0.003163	0	0	
ADAMTSL3	57188	broad.mit.edu	37	15	84506901	84506901	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr15:84506901G>T	uc002bjz.3	+	7	885	c.661G>T	c.(661-663)GCC>TCC	p.A221S	ADAMTSL3_uc002bjy.1_Missense_Mutation_p.A221S|ADAMTSL3_uc010bmt.1_Missense_Mutation_p.A221S|ADAMTSL3_uc010bmu.1_Missense_Mutation_p.A221S	NM_207517	NP_997400	P82987	ATL3_HUMAN	ADAMTS-like 3 precursor	221						proteinaceous extracellular matrix	metallopeptidase activity|zinc ion binding			ovary(6)|central_nervous_system(5)|lung(5)|large_intestine(4)|breast(3)|skin(2)|kidney(1)|pancreas(1)	27			BRCA - Breast invasive adenocarcinoma(143;0.211)			TGGAGTCTGTGCCGGCGATGG	0.522000													15	113					0.000308642	0.000341377	0.003163	1	0	
KLHL25	64410	broad.mit.edu	37	15	86311859	86311859	+	Nonsense_Mutation	SNP	C	A	A			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr15:86311859C>A	uc002bly.2	-	2	1386	c.1183G>T	c.(1183-1185)GGA>TGA	p.G395*		NM_022480	NP_071925	Q9H0H3	ENC2_HUMAN	BTB/POZ KELCH domain protein	395	Kelch 3.					cytoplasm				ovary(2)	2						GATGTGTGTCCCCCCACCACA	0.602000													15	60					4.14922e-12	4.93847e-12	0.004007	1	0	
AGBL1	123624	broad.mit.edu	37	15	87089267	87089267	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr15:87089267A>C	uc002blz.1	+	19	2662	c.2582A>C	c.(2581-2583)AAG>ACG	p.K861T		NM_152336	NP_689549	Q96MI9	CBPC4_HUMAN	ATP/GTP binding protein-like 1	861					C-terminal protein deglutamylation|protein side chain deglutamylation|proteolysis	cytosol	metallocarboxypeptidase activity|tubulin binding|zinc ion binding				0						TCCCAAAAGAAGAATGTGTTC	0.438000													6	84					0	0	0.001168	0	0	
BLM	641	broad.mit.edu	37	15	91304081	91304081	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr15:91304081A>G	uc002bpr.2	+	7	1575	c.1478A>G	c.(1477-1479)AAT>AGT	p.N493S	BLM_uc010uqh.1_Missense_Mutation_p.N493S|BLM_uc010uqi.1_Missense_Mutation_p.N118S|BLM_uc010bnx.2_Missense_Mutation_p.N493S|BLM_uc002bps.1_Missense_Mutation_p.N55S	NM_000057	NP_000048	P54132	BLM_HUMAN	Bloom syndrome protein	493					double-strand break repair via homologous recombination|G2 phase of mitotic cell cycle|G2/M transition DNA damage checkpoint|negative regulation of cell division|positive regulation of transcription, DNA-dependent|protein oligomerization|regulation of cyclin-dependent protein kinase activity|replication fork processing|replication fork protection|response to X-ray	cytoplasm|lateral element|nuclear matrix|nucleolus|PML body	ATP binding|bubble DNA binding|DNA strand annealing activity|four-way junction helicase activity|G-quadruplex DNA binding|p53 binding			ovary(3)|skin(2)|breast(1)	6	Lung NSC(78;0.0875)|all_lung(78;0.109)		Lung(145;0.189)			CCTTTATTCAATACCCATTTA	0.403000			Mis|N|F			leukemia|lymphoma|skin squamous cell |other cancers		Genes_defective_in_diseases_associated_with_sensitivity_to_DNA_damaging_agents	Bloom_syndrome				15	188					0	0	0.003163	0	0	
PGPEP1L	145814	broad.mit.edu	37	15	99511811	99511811	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr15:99511811A>C	uc002bum.2	-	5	693	c.487T>G	c.(487-489)TTG>GTG	p.L163V	PGPEP1L_uc010bop.2_Silent_p.P107P|PGPEP1L_uc002bun.2_RNA	NM_001102612	NP_001096082	A6NFU8	PGPIL_HUMAN	pyroglutamyl-peptidase 1-like protein	163					proteolysis		cysteine-type peptidase activity				0						ATGACTCTCAAGGCTCTTCCC	0.562000													5	27					0	0	0.014758	0	0	
LYSMD4	145748	broad.mit.edu	37	15	100272076	100272076	+	Silent	SNP	A	G	G			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr15:100272076A>G	uc002bvk.2	-	2	192	c.129T>C	c.(127-129)TCT>TCC	p.S43S	LYSMD4_uc002bvj.1_Intron|LYSMD4_uc010bou.1_Intron|LYSMD4_uc002bvl.2_Missense_Mutation_p.L14P|LYSMD4_uc002bvm.2_Silent_p.S43S|LYSMD4_uc010bov.2_Silent_p.S43S			Q5XG99	LYSM4_HUMAN	SubName: Full=cDNA FLJ77040, highly similar to Homo sapiens LysM, putative peptidoglycan-binding, domain containing 4, mRNA; SubName: Full=LysM, putative peptidoglycan-binding, domain containing 4, isoform CRA_c;	43	Extracellular (Potential).				cell wall macromolecule catabolic process	integral to membrane					0	Lung NSC(78;0.00335)|all_lung(78;0.00659)|Melanoma(26;0.00778)|Medulloblastoma(229;0.163)		OV - Ovarian serous cystadenocarcinoma(32;0.00162)|LUSC - Lung squamous cell carcinoma(107;0.17)|Lung(145;0.208)			CCACACGGTGAGACTCTTCTT	0.627000													7	67					0	0	0.003080	0	0	
TSC2	7249	broad.mit.edu	37	16	2134593	2134593	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr16:2134593G>A	uc002con.2	+	34	4476	c.4370G>A	c.(4369-4371)CGG>CAG	p.R1457Q	TSC2_uc010bsd.2_Missense_Mutation_p.R1434Q|TSC2_uc002coo.2_Missense_Mutation_p.R1390Q|TSC2_uc010uvv.1_Missense_Mutation_p.R1354Q|TSC2_uc010uvw.1_Missense_Mutation_p.R1342Q|TSC2_uc002cop.2_Missense_Mutation_p.R1213Q|TSC2_uc002coq.2_Missense_Mutation_p.R232Q|TSC2_uc002cor.2_Missense_Mutation_p.R158Q	NM_000548	NP_000539	P49815	TSC2_HUMAN	tuberous sclerosis 2 isoform 1	1457					cell cycle arrest|endocytosis|heart development|insulin receptor signaling pathway|insulin-like growth factor receptor signaling pathway|negative regulation of cell size|negative regulation of phosphatidylinositol 3-kinase cascade|negative regulation of protein kinase B signaling cascade|negative regulation of TOR signaling cascade|negative regulation of Wnt receptor signaling pathway|nerve growth factor receptor signaling pathway|neural tube closure|phosphatidylinositol-mediated signaling|positive chemotaxis|protein import into nucleus|protein kinase B signaling cascade|regulation of endocytosis|regulation of insulin receptor signaling pathway|regulation of small GTPase mediated signal transduction	Golgi apparatus|nucleus|perinuclear region of cytoplasm|TSC1-TSC2 complex	GTPase activator activity|protein homodimerization activity			central_nervous_system(4)|lung(3)|ovary(2)|pancreas(1)	10		Hepatocellular(780;0.0202)				AGTGGCCTCCGGCCCCGAGGT	0.672000			D|Mis|N|F|S			hamartoma|renal cell			Tuberous_Sclerosis				8	23					0	0	0.004482	0	0	
OTOA	146183	broad.mit.edu	37	16	21698841	21698841	+	Silent	SNP	G	A	A			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr16:21698841G>A	uc002djh.2	+	7	508	c.507G>A	c.(505-507)CAG>CAA	p.Q169Q	uc002diq.3_Intron|OTOA_uc010vbj.1_Silent_p.Q90Q	NM_144672	NP_653273	Q7RTW8	OTOAN_HUMAN	otoancorin isoform 1	169					sensory perception of sound	anchored to membrane|apical plasma membrane|proteinaceous extracellular matrix				ovary(1)|central_nervous_system(1)|skin(1)	3				GBM - Glioblastoma multiforme(48;0.0414)		GGTGTTTCCAGATGCTGAACT	0.572000													34	80					0	0	0.010818	0	0	
TMEM219	124446	broad.mit.edu	37	16	29979459	29979459	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr16:29979459C>A	uc002duw.2	+	4	636	c.469C>A	c.(469-471)CCC>ACC	p.P157T	uc002dtf.2_Intron|BOLA2_uc010bzb.1_Intron|TMEM219_uc002duy.2_Missense_Mutation_p.P157T|TMEM219_uc010bzk.1_Missense_Mutation_p.P157T|TMEM219_uc002duz.2_Missense_Mutation_p.P157T|TMEM219_uc010bzl.1_RNA	NM_194280	NP_919256	Q86XT9	TM219_HUMAN	transmembrane protein 219	157						integral to membrane					0						CAGCCAGCCACCCATATCCTG	0.542000													19	141					7.41877e-09	8.50634e-09	0.012319	1	0	
MAF	4094	broad.mit.edu	37	16	79633675	79633675	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr16:79633675A>T	uc002ffn.2	-	1	948	c.125T>A	c.(124-126)ATC>AAC	p.I42N	MAF_uc002ffm.2_Missense_Mutation_p.I42N	NM_001031804	NP_001026974	O75444	MAF_HUMAN	v-maf musculoaponeurotic fibrosarcoma oncogene	42					transcription from RNA polymerase II promoter	chromatin|nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			lung(1)	1		all_epithelial(2;0.139)|Lung NSC(2;0.186)|Melanoma(2;0.211)		UCEC - Uterine corpus endometrioid carcinoma (2;0.0178)		CTGGCTGATGATGCGGTCGGT	0.612000			T	IGH@	MM								10	44					0	0	0.006214	0	0	
MYH3	4621	broad.mit.edu	37	17	10544483	10544483	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr17:10544483C>T	uc002gmq.1	-	18	2161	c.2084G>A	c.(2083-2085)CGG>CAG	p.R695Q		NM_002470	NP_002461	P11055	MYH3_HUMAN	myosin, heavy chain 3, skeletal muscle,	695	Myosin head-like.				muscle filament sliding|muscle organ development	cytosol|myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|microfilament motor activity			ovary(4)|central_nervous_system(2)|pancreas(1)	7						ACCGTTACACCGCAGCTGGTG	0.483000													13	56					0	0	0.013537	0	0	
RNF112	7732	broad.mit.edu	37	17	19318451	19318451	+	Silent	SNP	C	T	T			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr17:19318451C>T	uc010vyw.1	+	11	1426	c.1227C>T	c.(1225-1227)AAC>AAT	p.N409N	RNF112_uc010vyv.1_Silent_p.N410N|RNF112_uc010vyx.1_Silent_p.N292N	NM_007148	NP_009079	Q7Z5V9	Q7Z5V9_HUMAN	ring finger protein 112	409							GTP binding|GTPase activity|zinc ion binding			ovary(2)	2						GGTACTGGAACGAGGGGCGCG	0.637000													31	58					0	0	0.012213	0	0	
SSH2	85464	broad.mit.edu	37	17	28004742	28004742	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr17:28004742C>T	uc002heo.1	-	6	416	c.416G>A	c.(415-417)GGC>GAC	p.G139D	SSH2_uc010wbh.1_Missense_Mutation_p.G166D|SSH2_uc002hep.1_Missense_Mutation_p.G139D|SSH2_uc002heq.2_Missense_Mutation_p.G146D|SSH2_uc002her.2_Missense_Mutation_p.G139D|SSH2_uc010csc.1_Missense_Mutation_p.G139D	NM_033389	NP_203747	Q76I76	SSH2_HUMAN	slingshot 2	139					actin cytoskeleton organization|regulation of actin polymerization or depolymerization|regulation of axonogenesis|regulation of lamellipodium assembly	cytoplasm|cytoskeleton	actin binding|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			skin(2)	2						CAAAACTAAGCCCATGGTACA	0.443000													11	112					0	0	0.013537	0	0	
EVI2A	2123	broad.mit.edu	37	17	29645449	29645449	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr17:29645449T>G	uc002hgm.2	-	2	798	c.583A>C	c.(583-585)ACT>CCT	p.T195P	NF1_uc002hgg.2_Intron|NF1_uc002hgh.2_Intron|NF1_uc002hgi.1_Intron|NF1_uc010cso.2_Intron|EVI2A_uc002hgl.2_Missense_Mutation_p.T218P	NM_014210	NP_055025	P22794	EVI2A_HUMAN	ecotropic viral integration site 2A isoform 2	195	Cytoplasmic (Potential).					integral to membrane	transmembrane receptor activity			ovary(1)|breast(1)	2		all_cancers(10;6.97e-11)|all_epithelial(10;0.0051)|all_hematologic(16;0.0149)|Breast(31;0.0155)|Myeloproliferative disorder(56;0.0255)|Acute lymphoblastic leukemia(14;0.0257)|all_lung(9;0.0468)|Lung NSC(157;0.094)		UCEC - Uterine corpus endometrioid carcinoma (4;6.64e-05)|all cancers(4;5.94e-13)|Epithelial(4;7.98e-12)|OV - Ovarian serous cystadenocarcinoma(4;9.4e-12)|GBM - Glioblastoma multiforme(4;0.18)		CTTTTCCAAGTGTCTGATTCA	0.468000													11	48					0	0	0.010729	0	0	
NLE1	54475	broad.mit.edu	37	17	33464132	33464132	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr17:33464132T>A	uc002hiy.1	-	7	744	c.716A>T	c.(715-717)GAG>GTG	p.E239V	NLE1_uc010ctn.1_5'UTR|NLE1_uc002hiz.1_5'UTR	NM_018096	NP_060566	Q9NVX2	NLE1_HUMAN	Notchless gene homolog isoform a	239	WD 3.					nucleolus				breast(3)|ovary(1)	4		Ovarian(249;0.17)				GAGGATGCGCTCACAGCGGCC	0.632000													10	69					0	0	0.006214	0	0	
PSME3	10197	broad.mit.edu	37	17	40986840	40986840	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr17:40986840C>A	uc002ibr.2	+	4	416	c.190C>A	c.(190-192)CTC>ATC	p.L64I	PSME3_uc002ibp.2_Missense_Mutation_p.L3I|PSME3_uc002ibq.2_Missense_Mutation_p.L64I|PSME3_uc002ibs.2_Missense_Mutation_p.L75I|PSME3_uc010whd.1_5'UTR	NM_005789	NP_005780	P61289	PSME3_HUMAN	proteasome activator subunit 3 isoform 1	64					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|regulation of proteasomal protein catabolic process|S phase of mitotic cell cycle|viral reproduction	cytoplasm|nucleus|proteasome activator complex	endopeptidase activator activity|identical protein binding|MDM2 binding|p53 binding				0		Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.156)		TGACATGAATCTCCCAGTCCC	0.428000													55	72					1.46168e-27	1.78831e-27	0.014410	1	0	
KIF2B	84643	broad.mit.edu	37	17	51901650	51901650	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr17:51901650A>C	uc002iua.2	+	1	1412	c.1256A>C	c.(1255-1257)AAC>ACC	p.N419T	uc010wna.1_RNA	NM_032559	NP_115948	Q8N4N8	KIF2B_HUMAN	kinesin family member 2B	419	Kinesin-motor.				blood coagulation|cell division|microtubule depolymerization|microtubule-based movement|mitotic prometaphase|regulation of chromosome segregation	condensed chromosome kinetochore|cytosol|microtubule|microtubule organizing center|nucleolus|spindle	ATP binding|microtubule motor activity			ovary(5)|skin(3)	8						ACACCTGTCAACGCTCACTCA	0.512000													11	68					0	0	0.010729	0	0	
ST8SIA5	29906	broad.mit.edu	37	18	44260170	44260170	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr18:44260170C>T	uc002lcj.1	-	7	1534	c.966G>A	c.(964-966)TGG>TGA	p.W322*	ST8SIA5_uc002lci.1_Nonsense_Mutation_p.W169*|ST8SIA5_uc010xcy.1_Nonsense_Mutation_p.W358*|ST8SIA5_uc010xcz.1_Nonsense_Mutation_p.W291*	NM_013305	NP_037437	O15466	SIA8E_HUMAN	ST8 alpha-N-acetyl-neuraminide	322	Lumenal (Potential).				glycosphingolipid biosynthetic process|protein glycosylation	integral to Golgi membrane				upper_aerodigestive_tract(1)|ovary(1)|pancreas(1)	3						TGGGGAAGGCCCAGAAGCCAA	0.627000													26	73					0	0	0.004656	0	0	
CDH7	1005	broad.mit.edu	37	18	63511056	63511056	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr18:63511056T>G	uc002ljz.2	+	7	1315	c.990T>G	c.(988-990)GAT>GAG	p.D330E	CDH7_uc002lka.2_Missense_Mutation_p.D330E|CDH7_uc002lkb.2_Missense_Mutation_p.D330E	NM_033646	NP_387450	Q9ULB5	CADH7_HUMAN	cadherin 7, type 2 preproprotein	330	Extracellular (Potential).|Cadherin 3.				adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(2)|pancreas(1)|skin(1)	4		Esophageal squamous(42;0.129)				AGGAGCTGGATTTTGAAGCCA	0.418000													19	42					0	0	0.007413	0	0	
SALL3	27164	broad.mit.edu	37	18	76753964	76753964	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr18:76753964C>T	uc002lmt.2	+	2	1973	c.1973C>T	c.(1972-1974)ACG>ATG	p.T658M	SALL3_uc010dra.2_Missense_Mutation_p.T265M	NM_171999	NP_741996	Q9BXA9	SALL3_HUMAN	sal-like 3	658					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)|large_intestine(1)|central_nervous_system(1)	4		Esophageal squamous(42;0.129)|Melanoma(33;0.16)|Prostate(75;0.167)		OV - Ovarian serous cystadenocarcinoma(15;4.69e-06)|BRCA - Breast invasive adenocarcinoma(31;0.0256)		TCGATGCAAACGTCGGAAACC	0.647000													10	12					0	0	0.006214	0	0	
MUC16	94025	broad.mit.edu	37	19	9071727	9071727	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr19:9071727T>G	uc002mkp.2	-	3	15923	c.15719A>C	c.(15718-15720)AAG>ACG	p.K5240T		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	5242	Thr-rich.|Extracellular (Potential).				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						CACTGTGGACTTATCATGGTC	0.473000													24	118					0	0	0.018920	0	0	
ZNF793	390927	broad.mit.edu	37	19	38028045	38028045	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr19:38028045A>G	uc010efm.2	+	8	927	c.485A>G	c.(484-486)AAG>AGG	p.K162R	ZNF793_uc010xts.1_Missense_Mutation_p.K162R|ZNF793_uc010efo.2_Intron	NM_001013659	NP_001013681	Q6ZN11	ZN793_HUMAN	zinc finger protein 793	162					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			TGTGCAAAAAAGCAAGATGAG	0.398000													6	63					0	0	0.001984	0	0	
CYP2A7	1549	broad.mit.edu	37	19	41383171	41383171	+	Missense_Mutation	SNP	A	T	T	rs150178247		TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr19:41383171A>T	uc002opm.2	-	7	1627	c.1085T>A	c.(1084-1086)TTT>TAT	p.F362Y	CYP2A7_uc002opo.2_Missense_Mutation_p.F362Y|CYP2A7_uc002opn.2_Missense_Mutation_p.F311Y	NM_000764	NP_000755	P20853	CP2A7_HUMAN	cytochrome P450, family 2, subfamily A,	362						endoplasmic reticulum membrane|microsome	aromatase activity|electron carrier activity|heme binding|oxygen binding			ovary(1)|haematopoietic_and_lymphoid_tissue(1)|skin(1)	3			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)			CACGTCTCCAAATCTTTGGAT	0.532000													35	186					0	0	0.005524	0	0	
PSG8	440533	broad.mit.edu	37	19	43258561	43258561	+	Silent	SNP	G	A	A			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr19:43258561G>A	uc002ouo.2	-	5	1265	c.1167C>T	c.(1165-1167)AGC>AGT	p.S389S	PSG3_uc002ouf.2_Intron|PSG1_uc002oug.1_Intron|PSG8_uc010eim.2_RNA|PSG8_uc002oui.2_Silent_p.S228S|PSG8_uc002ouh.2_Silent_p.S389S|PSG8_uc010ein.2_Silent_p.S267S|PSG8_uc002ouj.3_Silent_p.S171S|PSG8_uc002ouk.3_Silent_p.S228S|PSG8_uc002oul.3_Silent_p.S389S|PSG8_uc002oum.3_Silent_p.S296S|PSG1_uc002oun.2_Intron|PSG8_uc002oup.3_Silent_p.S296S	NM_182707	NP_874366	Q9UQ74	PSG8_HUMAN	pregnancy specific beta-1-glycoprotein 8 isoform	389	Ig-like C2-type 3.					extracellular region					0		Prostate(69;0.00899)				CATAGAGCCCGCTATGCTTTG	0.468000													113	210					0	0	0.014410	0	0	
ZNF227	7770	broad.mit.edu	37	19	44740983	44740983	+	Nonstop_Mutation	SNP	G	T	T			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr19:44740983G>T	uc002oyu.2	+	6	2605	c.2400G>T	c.(2398-2400)TAG>TAT	p.*800Y	ZNF227_uc010xwu.1_Nonstop_Mutation_p.*749Y|ZNF227_uc002oyv.2_Nonstop_Mutation_p.*800Y|ZNF227_uc010xwv.1_Nonstop_Mutation_p.*749Y|ZNF227_uc010xww.1_Nonstop_Mutation_p.*721Y|ZNF227_uc002oyw.2_Nonstop_Mutation_p.*772Y|ZNF227_uc010ejh.2_Nonstop_Mutation_p.*793Y|ZNF235_uc002oyx.1_Intron|ZNF235_uc010eji.2_Intron	NM_182490	NP_872296	Q86WZ6	ZN227_HUMAN	zinc finger protein 227	800					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1		Prostate(69;0.0435)				AAAAGCTTTAGAAATGAGAAA	0.388000													9	24					2.27111e-07	2.56378e-07	0.013537	1	0	
SLC6A16	28968	broad.mit.edu	37	19	49814483	49814483	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr19:49814483G>T	uc002pmz.2	-	2	356	c.122C>A	c.(121-123)TCT>TAT	p.S41Y	SLC6A16_uc002pna.2_Missense_Mutation_p.S41Y|hsa-mir-4324|MI0015854_5'Flank	NM_014037	NP_054756	Q9GZN6	S6A16_HUMAN	solute carrier family 6, member 16	41	Cytoplasmic (Potential).					integral to membrane|intracellular	neurotransmitter:sodium symporter activity			skin(2)|ovary(1)|kidney(1)	4		all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392)		OV - Ovarian serous cystadenocarcinoma(262;0.00099)|GBM - Glioblastoma multiforme(486;0.0336)		AGATGTTGCAGACCGGGTCAA	0.547000													12	41					6.40141e-05	7.18928e-05	0.010729	1	0	
TEAD2	8463	broad.mit.edu	37	19	49862699	49862699	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr19:49862699C>T	uc002pnj.2	-	3	381	c.290G>A	c.(289-291)CGA>CAA	p.R97Q	TEAD2_uc002png.2_Missense_Mutation_p.R97Q|TEAD2_uc002pnh.2_Missense_Mutation_p.R97Q|TEAD2_uc002pni.2_Missense_Mutation_p.R97Q|TEAD2_uc010yao.1_5'UTR|TEAD2_uc010emw.2_Missense_Mutation_p.R97Q	NM_003598	NP_003589	Q15562	TEAD2_HUMAN	TEA domain family member 2	97	TEA.				hippo signaling cascade		DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(2)|ovary(1)	3		all_lung(116;7.65e-05)|Lung NSC(112;0.000132)|all_neural(266;0.0506)|Ovarian(192;0.15)		OV - Ovarian serous cystadenocarcinoma(262;0.00093)|GBM - Glioblastoma multiforme(486;0.0467)		GACCTGTTTTCGAGTTCGGGT	0.512000													73	100					0	0	0.014410	0	0	
CNOT3	4849	broad.mit.edu	37	19	54656052	54656052	+	Silent	SNP	G	C	C			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr19:54656052G>C	uc002qdj.1	+	14	2006	c.1695G>C	c.(1693-1695)CTG>CTC	p.L565L	CNOT3_uc010yel.1_Silent_p.L565L|CNOT3_uc002qdi.2_Silent_p.L478L|CNOT3_uc002qdk.1_Silent_p.L565L|CNOT3_uc010ere.1_RNA|CNOT3_uc002qdl.2_Silent_p.L20L	NM_014516	NP_055331	O75175	CNOT3_HUMAN	CCR4-NOT transcription complex, subunit 3	565	Pro-rich.				nuclear-transcribed mRNA poly(A) tail shortening|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasmic mRNA processing body|cytosol|nucleus	protein binding			ovary(2)|haematopoietic_and_lymphoid_tissue(1)	3	all_cancers(19;0.0065)|all_epithelial(19;0.00348)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)					CGCTGCACCTGACCGAGCGAG	0.667000													12	78					0	0	0.010729	0	0	
LILRA2	11027	broad.mit.edu	37	19	55087526	55087526	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr19:55087526A>G	uc002qgg.3	+	6	1294	c.1205A>G	c.(1204-1206)AAC>AGC	p.N402S	LILRA2_uc010ern.2_Missense_Mutation_p.N402S|LILRA2_uc002qgf.2_Missense_Mutation_p.N402S|LILRA2_uc010yfe.1_Missense_Mutation_p.N402S|LILRA2_uc010yff.1_Missense_Mutation_p.N390S|LILRA2_uc010ero.2_Missense_Mutation_p.N390S|LILRA2_uc010yfg.1_Intron	NM_001130917	NP_001124389	Q8N149	LIRA2_HUMAN	leukocyte immunoglobulin-like receptor,	402	Ig-like C2-type 4.|Extracellular (Potential).				defense response	integral to membrane	antigen binding|receptor activity			ovary(1)	1				GBM - Glioblastoma multiforme(193;0.0963)		CTCAGCTCCAACCCCTACCTG	0.607000													24	63					0	0	0.016522	0	0	
NLRP5	126206	broad.mit.edu	37	19	56569735	56569735	+	Nonsense_Mutation	SNP	T	A	A			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr19:56569735T>A	uc002qmj.2	+	14	3429	c.3429T>A	c.(3427-3429)TGT>TGA	p.C1143*	NLRP5_uc002qmi.2_Nonsense_Mutation_p.C1124*	NM_153447	NP_703148	P59047	NALP5_HUMAN	NACHT, LRR and PYD containing protein 5	1143						mitochondrion|nucleolus	ATP binding			ovary(3)|skin(2)|kidney(1)|central_nervous_system(1)	7		Colorectal(82;3.46e-05)|Ovarian(87;0.0481)|Renal(1328;0.157)		GBM - Glioblastoma multiforme(193;0.0326)		TGAAGCTGTGTTCGGCCTTTG	0.498000													8	39					0	0	0.003080	0	0	
ZNF584	201514	broad.mit.edu	37	19	58929139	58929139	+	Silent	SNP	C	T	T			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr19:58929139C>T	uc002qsp.2	+	4	1706	c.1254C>T	c.(1252-1254)GTC>GTT	p.V418V	ZNF584_uc010yia.1_RNA|ZNF584_uc002qsr.2_Silent_p.V373V|ZNF584_uc010yib.1_3'UTR	NM_173548	NP_775819	Q8IVC4	ZN584_HUMAN	zinc finger protein 584	418					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		all_cancers(17;5.3e-17)|all_epithelial(17;3.71e-12)|Lung NSC(17;8.3e-05)|Colorectal(82;0.000147)|all_lung(17;0.000386)|Renal(17;0.00528)|all_neural(62;0.0133)|Ovarian(87;0.156)|Medulloblastoma(540;0.232)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0271)		ATGGGAAGGTCGTTAGCTGCT	0.512000													13	69					0	0	0.003163	0	0	
GDF7	151449	broad.mit.edu	37	2	20870362	20870362	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr2:20870362C>T	uc002rdz.1	+	2	1106	c.530C>T	c.(529-531)CCG>CTG	p.P177L		NM_182828	NP_878248	Q7Z4P5	GDF7_HUMAN	growth differentiation factor 7 preproprotein	177					activin receptor signaling pathway|BMP signaling pathway|growth|pathway-restricted SMAD protein phosphorylation|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of transcription, DNA-dependent	extracellular space	cytokine activity|growth factor activity				0	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TGGACTTCTCCGCCGTTGCTG	0.716000													3	10					0	0	0.004672	0	0	
GPN1	11321	broad.mit.edu	37	2	27861084	27861084	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr2:27861084T>A	uc010ymc.1	+	8	595	c.574T>A	c.(574-576)TAC>AAC	p.Y192N	GPN1_uc010ezf.2_Missense_Mutation_p.Y166N|GPN1_uc010yma.1_Missense_Mutation_p.Y99N|GPN1_uc010ymb.1_Missense_Mutation_p.Y83N|GPN1_uc010ymd.1_Missense_Mutation_p.Y73N|GPN1_uc010yme.1_Missense_Mutation_p.Y192N|GPN1_uc010ezg.1_Missense_Mutation_p.Y73N	NM_007266	NP_009197	Q9HCN4	GPN1_HUMAN	GPN-loop GTPase 1 isoform a	178						cytoplasm	GTP binding|nucleoside-triphosphatase activity|protein binding				0						CAGCATCTTATACAAAACCAA	0.373000													10	39					0	0	0.008291	0	0	
NRXN1	9378	broad.mit.edu	37	2	50724814	50724814	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr2:50724814T>A	uc010fbq.2	-	14	4133	c.2656A>T	c.(2656-2658)AAC>TAC	p.N886Y	NRXN1_uc002rxb.3_Missense_Mutation_p.N518Y|NRXN1_uc002rxe.3_Missense_Mutation_p.N846Y|NRXN1_uc002rxc.1_RNA	NM_001135659	NP_001129131	P58400	NRX1B_HUMAN	neurexin 1 isoform alpha2 precursor	212	Extracellular (Potential).|Laminin G-like.				angiogenesis|neuron cell-cell adhesion|neuronal signal transduction	cell surface|endocytic vesicle|integral to membrane|presynaptic membrane	cell adhesion molecule binding|receptor binding			ovary(2)	2		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.192)	Lung(47;0.0813)|LUSC - Lung squamous cell carcinoma(58;0.116)			GTCTCTATGTTATGGAACTCC	0.403000													23	64					0	0	0.021523	0	0	
CCDC85A	114800	broad.mit.edu	37	2	56420020	56420020	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr2:56420020G>A	uc002rzn.2	+	2	1187	c.685G>A	c.(685-687)GCG>ACG	p.A229T		NM_001080433	NP_001073902	Q96PX6	CC85A_HUMAN	coiled-coil domain containing 85A	229	His-rich.									breast(3)|ovary(2)	5			LUSC - Lung squamous cell carcinoma(58;0.127)|Lung(47;0.132)			CAAGCACCACGCGAGCAGTGG	0.682000													6	29					0	0	0.001168	0	0	
ANXA4	307	broad.mit.edu	37	2	70033572	70033572	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr2:70033572T>A	uc002sfr.3	+	5	475	c.248T>A	c.(247-249)GTG>GAG	p.V83E	ANXA4_uc010yqn.1_Intron|ANXA4_uc002sfs.3_Intron|ANXA4_uc010yqo.1_5'UTR	NM_001153	NP_001144	P09525	ANXA4_HUMAN	annexin IV	81	Annexin 1.				anti-apoptosis|signal transduction	cytoplasm	calcium ion binding|calcium-dependent phospholipid binding|phospholipase inhibitor activity				0						CAGGTGATTGTGGGGATGATG	0.512000													18	84					0	0	0.007413	0	0	
RAB11FIP5	26056	broad.mit.edu	37	2	73316049	73316049	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr2:73316049T>G	uc002siu.3	-	2	1067	c.826A>C	c.(826-828)ACC>CCC	p.T276P	RAB11FIP5_uc002sit.3_Missense_Mutation_p.T198P	NM_015470	NP_056285	Q9BXF6	RFIP5_HUMAN	RAB11 family interacting protein 5 (class I)	276					protein transport	mitochondrial outer membrane|recycling endosome membrane	gamma-tubulin binding				0						GGTGAGCGGGTGAGGAGTTCG	0.692000													5	16					0	0	0.003080	0	0	
KDM3A	55818	broad.mit.edu	37	2	86716717	86716717	+	Missense_Mutation	SNP	C	G	G			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr2:86716717C>G	uc002sri.3	+	23	3835	c.3508C>G	c.(3508-3510)CCA>GCA	p.P1170A	KDM3A_uc010ytj.1_Missense_Mutation_p.P1170A|KDM3A_uc010ytk.1_Missense_Mutation_p.P1118A	NM_018433	NP_060903	Q9Y4C1	KDM3A_HUMAN	jumonji domain containing 1A	1170	JmjC.				androgen receptor signaling pathway|cell differentiation|formaldehyde biosynthetic process|histone H3-K9 demethylation|hormone-mediated signaling pathway|positive regulation of transcription, DNA-dependent|spermatogenesis|transcription, DNA-dependent	cytoplasm|nucleus	androgen receptor binding|iron ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen			breast(2)|ovary(1)|central_nervous_system(1)|skin(1)	5						AAAAGAGAAGCCAGGAGCACT	0.418000													10	62					0	0	0.006214	0	0	
MARCO	8685	broad.mit.edu	37	2	119751970	119751970	+	Silent	SNP	G	A	A			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr2:119751970G>A	uc002tln.1	+	17	1569	c.1437G>A	c.(1435-1437)GGG>GGA	p.G479G	MARCO_uc010yyf.1_Silent_p.G401G	NM_006770	NP_006761	Q9UEW3	MARCO_HUMAN	macrophage receptor with collagenous structure	479	SRCR.|Extracellular (Potential).				cell surface receptor linked signaling pathway|innate immune response	collagen|integral to plasma membrane	pattern recognition receptor activity|scavenger receptor activity			ovary(3)|skin(2)|central_nervous_system(1)	6						AAGGCACTGGGCAGATCTGGC	0.547000													13	67					0	0	0.004990	0	0	
GLI2	2736	broad.mit.edu	37	2	121746631	121746631	+	Silent	SNP	G	A	A			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr2:121746631G>A	uc010flp.2	+	13	3171	c.3141G>A	c.(3139-3141)GCG>GCA	p.A1047A	GLI2_uc002tmq.1_Silent_p.A719A|GLI2_uc002tmr.1_Silent_p.A702A|GLI2_uc002tmt.3_Silent_p.A719A|GLI2_uc002tmu.3_Silent_p.A702A	NM_005270	NP_005261	P10070	GLI2_HUMAN	GLI-Kruppel family member GLI2	1047					axon guidance|branching morphogenesis of a tube|cell proliferation|cerebellar cortex morphogenesis|developmental growth|embryonic digestive tract development|epidermal cell differentiation|floor plate formation|heart development|hindgut morphogenesis|kidney development|lung development|negative regulation of transcription from RNA polymerase II promoter|odontogenesis of dentine-containing tooth|osteoblast development|osteoblast differentiation|pituitary gland development|positive regulation of DNA replication|positive regulation of T cell differentiation in thymus|positive regulation of transcription from RNA polymerase II promoter|proximal/distal pattern formation|skeletal system development|smoothened signaling pathway involved in ventral spinal cord interneuron specification|spinal cord ventral commissure morphogenesis	nucleus|nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(8)|lung(2)|breast(1)|central_nervous_system(1)|pancreas(1)	13	Renal(3;0.0496)	Prostate(154;0.0623)				TGGACGGCGCGGGGCCCGAGG	0.736000													8	21					0	0	0.006214	0	0	
XIRP2	129446	broad.mit.edu	37	2	168103997	168103997	+	Missense_Mutation	SNP	G	A	A	rs111389244		TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr2:168103997G>A	uc002udx.2	+	8	6113	c.6095G>A	c.(6094-6096)CGT>CAT	p.R2032H	XIRP2_uc010fpn.2_Intron|XIRP2_uc010fpo.2_Intron|XIRP2_uc010fpp.2_Intron|XIRP2_uc002udy.2_Missense_Mutation_p.R1857H|XIRP2_uc010fpq.2_Missense_Mutation_p.R1810H|XIRP2_uc010fpr.2_Intron|XIRP2_uc010fps.1_5'Flank	NM_152381	NP_689594	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2 isoform 1	1857					actin cytoskeleton organization	cell junction	actin binding			skin(7)|ovary(6)|pancreas(1)	14						GTCATAGATCGTGAACAAAAC	0.393000													9	42					0	0	0.008291	0	0	
HECW2	57520	broad.mit.edu	37	2	197183523	197183523	+	Silent	SNP	C	T	T			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr2:197183523C>T	uc002utm.1	-	9	2274	c.2091G>A	c.(2089-2091)TCG>TCA	p.S697S	HECW2_uc002utl.1_Silent_p.S341S	NM_020760	NP_065811	Q9P2P5	HECW2_HUMAN	HECT, C2 and WW domain containing E3 ubiquitin	697					protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm	ubiquitin-protein ligase activity			skin(5)|ovary(5)|lung(4)|pancreas(2)|central_nervous_system(1)|kidney(1)	18						CGGATTCCTGCGACCCTTCGG	0.612000													5	43					0	0	0.014758	0	0	
PARD3B	117583	broad.mit.edu	37	2	205989155	205989155	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr2:205989155G>T	uc002var.1	+	9	1477	c.1270G>T	c.(1270-1272)GAT>TAT	p.D424Y	PARD3B_uc010fub.1_Missense_Mutation_p.D424Y|PARD3B_uc002vao.1_Missense_Mutation_p.D424Y|PARD3B_uc002vap.1_Missense_Mutation_p.D424Y|PARD3B_uc002vaq.1_Missense_Mutation_p.D424Y	NM_152526	NP_689739	Q8TEW8	PAR3L_HUMAN	par-3 partitioning defective 3 homolog B isoform	424	PDZ 2.				cell cycle|cell division	endomembrane system|tight junction				skin(2)|ovary(1)|breast(1)	4		all_cancers(1;2.88e-06)|all_epithelial(1;3.23e-06)		Epithelial(149;0.0739)		AGCAATAAAAGATGGCCGCCT	0.373000													16	82					1.5739e-10	1.85314e-10	0.004007	1	0	
NMUR1	10316	broad.mit.edu	37	2	232392858	232392858	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr2:232392858G>A	uc002vry.3	-	2	984	c.874C>T	c.(874-876)CGG>TGG	p.R292W		NM_006056	NP_006047	Q9HB89	NMUR1_HUMAN	neuromedin U receptor 1	292	Cytoplasmic (Potential).				activation of phospholipase C activity by G-protein coupled receptor protein signaling pathway coupled to IP3 second messenger|calcium ion transport|calcium-mediated signaling|chloride transport|smooth muscle contraction	integral to plasma membrane|membrane fraction	neuromedin U receptor activity			lung(3)|central_nervous_system(1)|pancreas(1)	5		Renal(207;0.025)|all_hematologic(139;0.094)|Acute lymphoblastic leukemia(138;0.164)		Epithelial(121;8.37e-11)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(119;0.0142)		ACTTGTCTCCGGCCCCGATCG	0.647000													9	74					0	0	0.006214	0	0	
KIF16B	55614	broad.mit.edu	37	20	16486769	16486769	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr20:16486769T>G	uc002wpg.1	-	8	924	c.766A>C	c.(766-768)AGT>CGT	p.S256R	KIF16B_uc010gch.1_Missense_Mutation_p.S256R|KIF16B_uc010gci.1_Missense_Mutation_p.S256R|KIF16B_uc010gcj.1_Missense_Mutation_p.S256R	NM_024704	NP_078980	Q96L93	KI16B_HUMAN	kinesin-like motor protein C20orf23	256	Kinesin-motor.				cell communication|early endosome to late endosome transport|endoderm development|epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|formation of primary germ layer|Golgi to endosome transport|microtubule-based movement|receptor catabolic process|regulation of receptor recycling	early endosome membrane|microtubule	ATP binding|phosphatidylinositol-3,4,5-trisphosphate binding|phosphatidylinositol-3,4-bisphosphate binding|phosphatidylinositol-3,5-bisphosphate binding|phosphatidylinositol-3-phosphate binding|plus-end-directed microtubule motor activity			skin(2)|large_intestine(1)|central_nervous_system(1)|lung(1)|breast(1)|ovary(1)|kidney(1)	8						GCACGCTCACTTCCGGCAAGA	0.458000													27	142					0	0	0.012213	0	0	
C20orf12	55184	broad.mit.edu	37	20	18429663	18429663	+	Missense_Mutation	SNP	C	G	G			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr20:18429663C>G	uc010zsa.1	-	7	860	c.651G>C	c.(649-651)GAG>GAC	p.E217D	C20orf12_uc002wqr.3_RNA|C20orf12_uc002wqs.3_Missense_Mutation_p.E84D|C20orf12_uc002wqq.3_Missense_Mutation_p.E198D|C20orf12_uc002wqu.1_RNA|C20orf12_uc010gct.1_RNA	NM_001099407	NP_001092877	Q9NVP4	CT012_HUMAN	hypothetical protein LOC55184	25						intracellular	zinc ion binding			ovary(1)	1		Myeloproliferative disorder(85;0.0122)				TTCTCATTATCTCCGTGCTTG	0.368000													17	116					0	0	0.007413	0	0	
PHF20	51230	broad.mit.edu	37	20	34526800	34526800	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr20:34526800C>T	uc002xek.1	+	16	2593	c.2482C>T	c.(2482-2484)CGT>TGT	p.R828C		NM_016436	NP_057520	Q9BVI0	PHF20_HUMAN	PHD finger protein 20	828					regulation of transcription, DNA-dependent|transcription, DNA-dependent	MLL1 complex	DNA binding|zinc ion binding			ovary(1)	1	Breast(12;0.00631)|all_lung(11;0.0145)					GCCCCTGCCGCGTTCTGTGGA	0.602000													17	82					0	0	0.004007	0	0	
EPB41L1	2036	broad.mit.edu	37	20	34778617	34778617	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr20:34778617C>T	uc002xfb.2	+	11	1369	c.1198C>T	c.(1198-1200)CAG>TAG	p.Q400*	EPB41L1_uc002xeu.2_Nonsense_Mutation_p.Q338*|EPB41L1_uc010zvo.1_Nonsense_Mutation_p.Q400*|EPB41L1_uc002xev.2_Nonsense_Mutation_p.Q400*|EPB41L1_uc002xew.2_Nonsense_Mutation_p.Q303*|EPB41L1_uc002xex.2_Nonsense_Mutation_p.Q369*|EPB41L1_uc002xey.2_Nonsense_Mutation_p.Q327*|EPB41L1_uc002xez.2_Nonsense_Mutation_p.Q338*	NM_012156	NP_036288	Q9H4G0	E41L1_HUMAN	erythrocyte membrane protein band 4.1-like 1	400					cortical actin cytoskeleton organization|synaptic transmission	cytoskeleton|cytosol|extrinsic to membrane|plasma membrane	actin binding|structural molecule activity			ovary(2)|pancreas(1)	3	Breast(12;0.0239)					TGGGAGGACCCAGGCACAGAC	0.637000													9	90					0	0	0.004482	0	0	
CHD6	84181	broad.mit.edu	37	20	40049424	40049424	+	Missense_Mutation	SNP	C	T	T	rs61752058	byFrequency	TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr20:40049424C>T	uc002xka.1	-	31	6029	c.5851G>A	c.(5851-5853)GAG>AAG	p.E1951K		NM_032221	NP_115597	Q8TD26	CHD6_HUMAN	chromodomain helicase DNA binding protein 6	1951					chromatin remodeling|nervous system development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	ATP binding|ATP-dependent helicase activity|chromatin binding|DNA binding			ovary(6)|skin(5)|lung(2)|central_nervous_system(1)	14		Myeloproliferative disorder(115;0.00425)				TCATCATTCTCGAGGCCATGC	0.502000													51	269					0	0	0.014410	0	0	
IFT52	51098	broad.mit.edu	37	20	42252656	42252656	+	Silent	SNP	G	A	A			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr20:42252656G>A	uc002xkw.2	+	10	1016	c.894G>A	c.(892-894)CTG>CTA	p.L298L	IFT52_uc002xky.2_Silent_p.L298L|IFT52_uc002xkx.2_RNA|IFT52_uc010ggn.2_Silent_p.L274L|IFT52_uc002xkz.2_Silent_p.L298L	NM_016004	NP_057088	Q9Y366	IFT52_HUMAN	intraflagellar transport 52 homolog	298						intraflagellar transport particle B|microtubule-based flagellum	protein C-terminus binding			ovary(2)	2		Myeloproliferative disorder(115;0.00452)	COAD - Colon adenocarcinoma(18;0.0031)			TCTTCCAGCTGGATACCACCT	0.532000													44	556					0	0	0.014410	0	0	
TOX2	84969	broad.mit.edu	37	20	42574562	42574562	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr20:42574562A>G	uc002xlf.3	+	1	27	c.10A>G	c.(10-12)ACT>GCT	p.T4A	TOX2_uc010ggo.2_Intron|TOX2_uc002xle.3_Intron|TOX2_uc010ggp.2_Intron	NM_001098798	NP_001092268	Q96NM4	TOX2_HUMAN	TOX high mobility group box family member 2	4					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			ovary(1)	1		Myeloproliferative disorder(115;0.00452)	COAD - Colon adenocarcinoma(18;0.00189)			TATGCAGCAGACTCGCACAGA	0.537000													5	122					0	0	0.014758	0	0	
SLC12A5	57468	broad.mit.edu	37	20	44674590	44674590	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr20:44674590G>A	uc010zxl.1	+	13	1788	c.1712G>A	c.(1711-1713)GGC>GAC	p.G571D	SLC12A5_uc010zxm.1_RNA|SLC12A5_uc002xrb.2_Missense_Mutation_p.G548D	NM_001134771	NP_001128243	Q9H2X9	S12A5_HUMAN	solute carrier family 12 (potassium-chloride	571	Helical; (Potential).				potassium ion transport|sodium ion transport	integral to membrane	potassium:chloride symporter activity			ovary(2)|large_intestine(1)|central_nervous_system(1)|skin(1)	5		Myeloproliferative disorder(115;0.0122)			Bumetanide(DB00887)|Potassium Chloride(DB00761)	TGCGAGATTGGCATCCTCATT	0.582000													34	321					0	0	0.019004	0	0	
ADNP	23394	broad.mit.edu	37	20	49509123	49509123	+	Missense_Mutation	SNP	G	C	C			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr20:49509123G>C	uc002xvt.1	-	5	2473	c.2128C>G	c.(2128-2130)CCA>GCA	p.P710A	ADNP_uc002xvu.1_Missense_Mutation_p.P710A	NM_015339	NP_056154	Q9H2P0	ADNP_HUMAN	activity-dependent neuroprotector	710						nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)	2						GCCAGACTTGGAGACTGATTA	0.463000													10	214					0	0	0.010729	0	0	
C20orf106	200232	broad.mit.edu	37	20	55100041	55100041	+	Silent	SNP	A	G	G			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr20:55100041A>G	uc002xxx.2	+	1	257	c.177A>G	c.(175-177)AAA>AAG	p.K59K	GCNT7_uc010zzg.1_Intron|C20orf107_uc010zzh.1_Silent_p.K59K	NM_001012971	NP_001012989	Q5JX71	CT106_HUMAN	hypothetical protein LOC200232 precursor	59	Helical; (Potential).					integral to membrane					0			Colorectal(105;0.202)			TTGGGAGCAAATGGCTCTGGC	0.483000													16	198					0	0	0.006122	0	0	
SLC17A9	63910	broad.mit.edu	37	20	61588204	61588204	+	Silent	SNP	C	G	G			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr20:61588204C>G	uc002yea.3	+	2	331	c.147C>G	c.(145-147)GTC>GTG	p.V49V	SLC17A9_uc002ydz.3_Silent_p.V43V|SLC17A9_uc011aap.1_Silent_p.V69V	NM_022082	NP_071365	Q9BYT1	S17A9_HUMAN	vesicular nucleotide transporter SLC17A9	49					exocytosis|transmembrane transport	integral to membrane	transporter activity			ovary(1)|skin(1)	2						TCTGCACCGTCTCCATGAGCC	0.647000													9	86					0	0	0.004482	0	0	
KRTAP13-2	337959	broad.mit.edu	37	21	31744376	31744376	+	Silent	SNP	G	A	A			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr21:31744376G>A	uc002ynz.3	-	1	182	c.156C>T	c.(154-156)CTC>CTT	p.L52L		NM_181621	NP_853652	Q52LG2	KR132_HUMAN	keratin associated protein 13-2	52	1.|5 X 10 AA approximate repeats.					intermediate filament					0						AGCCCCTATAGAGAGAGGAAC	0.612000													8	95					0	0	0.006214	0	0	
KRTAP19-7	337974	broad.mit.edu	37	21	31933515	31933515	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr21:31933515A>C	uc011adb.1	-	1	94	c.94T>G	c.(94-96)TTC>GTC	p.F32V		NM_181614	NP_853645	Q3SYF9	KR197_HUMAN	keratin associated protein 19-7	32						intermediate filament					0						AGTCTGCGGAAGCTGCCACAT	0.547000													18	133					0	0	0.004990	0	0	
DYRK1A	1859	broad.mit.edu	37	21	38845158	38845158	+	Missense_Mutation	SNP	G	C	C			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr21:38845158G>C	uc002ywk.2	+	2	258	c.183G>C	c.(181-183)CAG>CAC	p.Q61H	DYRK1A_uc002ywg.1_RNA|DYRK1A_uc010gno.1_RNA|DYRK1A_uc002ywh.1_Missense_Mutation_p.Q32H|DYRK1A_uc002ywi.2_Missense_Mutation_p.Q61H|DYRK1A_uc002ywj.2_Missense_Mutation_p.Q61H|DYRK1A_uc002ywl.2_Missense_Mutation_p.Q61H|DYRK1A_uc002ywm.2_Missense_Mutation_p.Q61H	NM_001396	NP_001387	Q13627	DYR1A_HUMAN	dual-specificity tyrosine-(Y)-phosphorylation	61					nervous system development|peptidyl-tyrosine phosphorylation|protein autophosphorylation	nuclear speck	ATP binding|non-membrane spanning protein tyrosine kinase activity|protein binding|protein self-association|protein serine/threonine kinase activity			ovary(2)|lung(1)|breast(1)	4						ATTCTGACCAGATTCAGCAAC	0.423000													18	67					0	0	0.007413	0	0	
MX1	4599	broad.mit.edu	37	21	42821220	42821220	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr21:42821220C>T	uc002yzh.2	+	16	2377	c.1430C>T	c.(1429-1431)ACG>ATG	p.T477M	MX1_uc002yzi.2_Missense_Mutation_p.T477M|MX1_uc010goq.2_Missense_Mutation_p.T477M	NM_001144925	NP_001138397	P20591	MX1_HUMAN	myxovirus resistance protein 1	477					induction of apoptosis|response to virus|type I interferon-mediated signaling pathway	cytosol	GTP binding|GTPase activity|protein binding			ovary(1)	1		Prostate(19;3.18e-07)|all_epithelial(19;0.0277)				CACACCGTGACGGGTGAGTGC	0.463000													15	68					0	0	0.006122	0	0	
MYH9	4627	broad.mit.edu	37	22	36681783	36681783	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr22:36681783G>A	uc003apg.2	-	37	5426	c.5195C>T	c.(5194-5196)GCC>GTC	p.A1732V		NM_002473	NP_002464	P35579	MYH9_HUMAN	myosin, heavy polypeptide 9, non-muscle	1732	Potential.				actin cytoskeleton reorganization|actin filament-based movement|angiogenesis|axon guidance|blood vessel endothelial cell migration|cytokinesis|integrin-mediated signaling pathway|leukocyte migration|membrane protein ectodomain proteolysis|monocyte differentiation|platelet formation|protein transport|regulation of cell shape	actomyosin contractile ring|cleavage furrow|cytosol|myosin complex|nucleus|ruffle|stress fiber|uropod	actin filament binding|actin-dependent ATPase activity|ADP binding|ATP binding|calmodulin binding|microfilament motor activity|protein anchor|protein homodimerization activity			breast(3)|ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|lung(1)|skin(1)|kidney(1)|pancreas(1)	11						ctccagctGGGCGATGCGGGC	0.587000			T	ALK	ALCL		Deafness|autosomal dominant 17|Epstein syndrome|Fechtner syndrome|May-Hegglin anomaly|Sebastian syndrome		Hereditary_Macrothrombocytopenia_MYH9-associated				8	19					0	0	0.003080	0	0	
BAIAP2L2	80115	broad.mit.edu	37	22	38482283	38482283	+	Missense_Mutation	SNP	C	G	G			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr22:38482283C>G	uc003auw.2	-	12	1577	c.1433G>C	c.(1432-1434)AGC>ACC	p.S478T	BAIAP2L2_uc003auv.2_RNA	NM_025045	NP_079321	Q6UXY1	BI2L2_HUMAN	BAI1-associated protein 2-like 2	478					filopodium assembly|signal transduction		cytoskeletal adaptor activity|SH3 domain binding			pancreas(1)	1	Melanoma(58;0.045)					GCTGCCCATGCTGCTGCGGCG	0.706000													13	22					0	0	0.016723	0	0	
FAM83F	113828	broad.mit.edu	37	22	40417550	40417550	+	Missense_Mutation	SNP	C	T	T	rs145428025		TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr22:40417550C>T	uc003ayk.1	+	4	1130	c.1036C>T	c.(1036-1038)CGG>TGG	p.R346W		NM_138435	NP_612444	Q8NEG4	FA83F_HUMAN	hypothetical protein LOC113828	346										breast(1)	1						CTGGGCTGCCCGGCAACAGCG	0.677000													7	36					0	0	0.003080	0	0	
MST1R	4486	broad.mit.edu	37	3	49928023	49928023	+	Missense_Mutation	SNP	G	C	C			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr3:49928023G>C	uc003cxy.3	-	18	3969	c.3705C>G	c.(3703-3705)GAC>GAG	p.D1235E	MST1R_uc011bdc.1_Missense_Mutation_p.D114E	NM_002447	NP_002438	Q04912	RON_HUMAN	macrophage stimulating 1 receptor precursor	1235	Cytoplasmic (Potential).|Protein kinase.				cellular component movement|defense response|multicellular organismal development|positive regulation of cell proliferation|single fertilization|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|macrophage colony-stimulating factor receptor activity|protein binding			ovary(5)|lung(1)	6				BRCA - Breast invasive adenocarcinoma(193;4.65e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.00553)|Kidney(197;0.00625)		AGTACTCCCTGTCCAGGATGT	0.547000													7	33					0	0	0.004482	0	0	
PARP14	54625	broad.mit.edu	37	3	122414498	122414498	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr3:122414498T>C	uc003efq.3	+	5	883	c.824T>C	c.(823-825)TTT>TCT	p.F275S	PARP14_uc010hrk.2_RNA	NM_017554	NP_060024	Q460N5	PAR14_HUMAN	poly (ADP-ribose) polymerase family, member 14	275					regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus|plasma membrane	NAD+ ADP-ribosyltransferase activity			ovary(2)|breast(2)|lung(1)|pancreas(1)	6				GBM - Glioblastoma multiforme(114;0.0531)		ATTGAATTTTTTGACAGAAAA	0.214000													3	25					0	0	0.004672	0	0	
ITGB5	3693	broad.mit.edu	37	3	124515266	124515266	+	Silent	SNP	G	A	A			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr3:124515266G>A	uc003eho.2	-	10	1959	c.1662C>T	c.(1660-1662)TCC>TCT	p.S554S	ITGB5_uc010hrx.2_RNA	NM_002213	NP_002204	P18084	ITB5_HUMAN	integrin, beta 5 precursor	554	Extracellular (Potential).|II.|Cysteine-rich tandem repeats.				cell-matrix adhesion|integrin-mediated signaling pathway|multicellular organismal development|muscle contraction	integrin complex	receptor activity			skin(2)	2				GBM - Glioblastoma multiforme(114;0.163)		TCCTGGCACAGGAGAAGTTGT	0.577000													18	130					0	0	0.008871	0	0	
CLSTN2	64084	broad.mit.edu	37	3	140122503	140122503	+	Nonsense_Mutation	SNP	G	T	T			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr3:140122503G>T	uc003etn.2	+	3	455	c.265G>T	c.(265-267)GAG>TAG	p.E89*	CLSTN2_uc003etm.2_Nonsense_Mutation_p.E89*	NM_022131	NP_071414	Q9H4D0	CSTN2_HUMAN	calsyntenin 2 precursor	89	Extracellular (Potential).|Cadherin 1.				homophilic cell adhesion	endoplasmic reticulum membrane|Golgi membrane|integral to membrane|plasma membrane	calcium ion binding			skin(3)|large_intestine(2)|pancreas(1)|central_nervous_system(1)	7						CCATGGCCAGGAGCTGCCCTT	0.527000										HNSCC(16;0.037)			33	181					1.06801e-11	1.2643e-11	0.009535	1	0	
MME	4311	broad.mit.edu	37	3	154856014	154856014	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr3:154856014G>A	uc010hvr.1	+	9	1055	c.844G>A	c.(844-846)GAA>AAA	p.E282K	MME_uc003fab.1_Missense_Mutation_p.E282K|MME_uc003fac.1_Missense_Mutation_p.E282K|MME_uc003fad.1_Missense_Mutation_p.E282K|MME_uc003fae.1_Missense_Mutation_p.E282K	NM_007289	NP_009220	P08473	NEP_HUMAN	membrane metallo-endopeptidase	282	Extracellular (Potential).				cell-cell signaling|proteolysis	integral to plasma membrane	metal ion binding|metalloendopeptidase activity|protein binding			ovary(2)|central_nervous_system(1)	3		all_neural(597;0.00391)|Myeloproliferative disorder(1037;0.0122)	LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.135)		Candoxatril(DB00616)	ATTGGAAAAAGAAATTGCCAA	0.338000													19	72					0	0	0.008871	0	0	
PIK3CA	5290	broad.mit.edu	37	3	178952007	178952007	+	Missense_Mutation	SNP	A	G	G	rs121913288		TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr3:178952007A>G	uc003fjk.2	+	21	3219	c.3062A>G	c.(3061-3063)TAC>TGC	p.Y1021C		NM_006218	NP_006209	P42336	PK3CA_HUMAN	phosphoinositide-3-kinase, catalytic, alpha	1021	PI3K/PI4K.		Y -> C (in cancer).|Y -> H (in cancer).|Y -> N (in cancer).		epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|platelet activation|T cell costimulation|T cell receptor signaling pathway		1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol-4,5-bisphosphate 3-kinase activity	p.Y1021C(17)|p.Y1021H(2)|p.Y1021N(1)		breast(1564)|large_intestine(776)|endometrium(246)|urinary_tract(195)|ovary(141)|skin(112)|stomach(98)|thyroid(77)|central_nervous_system(69)|lung(65)|upper_aerodigestive_tract(58)|haematopoietic_and_lymphoid_tissue(27)|cervix(25)|biliary_tract(22)|liver(20)|oesophagus(17)|pancreas(11)|penis(8)|pituitary(8)|autonomic_ganglia(4)|prostate(3)|kidney(2)|meninges(1)|eye(1)|NS(1)|soft_tissue(1)|bone(1)	3553	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)			GACATTGCATACATTCGAAAG	0.388000		57	Mis		colorectal|gastric|gliobastoma|breast					HNSCC(19;0.045)|TSP Lung(28;0.18)			15	50					0	0	0.020292	0	0	
C4orf37	285555	broad.mit.edu	37	4	98633959	98633959	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr4:98633959G>A	uc003htt.1	-	10	1301	c.1211C>T	c.(1210-1212)GCA>GTA	p.A404V		NM_174952	NP_777612	Q8N412	CD037_HUMAN	hypothetical protein LOC285555	404											0				OV - Ovarian serous cystadenocarcinoma(123;2.27e-08)		ATTGTATGCTGCAGGACCTGA	0.343000													5	93					0	0	0.014758	0	0	
FAT4	79633	broad.mit.edu	37	4	126370611	126370611	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr4:126370611G>T	uc003ifj.3	+	9	8440	c.8440G>T	c.(8440-8442)GCA>TCA	p.A2814S	FAT4_uc011cgp.1_Missense_Mutation_p.A1112S|FAT4_uc003ifi.1_Missense_Mutation_p.A292S	NM_024582	NP_078858	Q6V0I7	FAT4_HUMAN	FAT tumor suppressor homolog 4 precursor	2814	Cadherin 27.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(9)|skin(5)|upper_aerodigestive_tract(2)|pancreas(2)	18						TATAATGGATGCAAGTCTTCC	0.398000													16	66					4.14922e-12	4.93847e-12	0.004007	1	0	
ODZ3	55714	broad.mit.edu	37	4	183713739	183713739	+	Nonsense_Mutation	SNP	G	T	T			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr4:183713739G>T	uc003ivd.1	+	25	5951	c.5914G>T	c.(5914-5916)GAA>TAA	p.E1972*		NM_001080477	NP_001073946	Q9P273	TEN3_HUMAN	odz, odd Oz/ten-m homolog 3	1972	Extracellular (Potential).|YD 11.				signal transduction	integral to membrane					0		all_lung(41;2.69e-14)|Lung NSC(41;1.92e-11)|Melanoma(52;1.74e-05)|Colorectal(36;0.0062)|Breast(14;0.00748)|all_hematologic(60;0.0162)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|Prostate(90;0.0283)|all_neural(102;0.155)|Medulloblastoma(177;0.184)		all cancers(43;1.42e-24)|Epithelial(43;6.86e-23)|OV - Ovarian serous cystadenocarcinoma(60;2.16e-11)|Colorectal(24;9.75e-06)|STAD - Stomach adenocarcinoma(60;2.96e-05)|COAD - Colon adenocarcinoma(29;0.00103)|GBM - Glioblastoma multiforme(59;0.00462)|LUSC - Lung squamous cell carcinoma(40;0.0391)|READ - Rectum adenocarcinoma(43;0.0487)		TACCTATGATGAAACAGCAGG	0.403000													42	174					2.40579e-17	2.92705e-17	0.006230	1	0	
SLC6A3	6531	broad.mit.edu	37	5	1409887	1409887	+	Silent	SNP	C	T	T			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr5:1409887C>T	uc003jck.2	-	10	1468	c.1347G>A	c.(1345-1347)ACG>ACA	p.T449T		NM_001044	NP_001035	Q01959	SC6A3_HUMAN	solute carrier family 6 (neurotransmitter	449	Helical; Name=9; (Potential).				cell death|neurotransmitter biosynthetic process	axon|cytoplasm|integral to plasma membrane|neuronal cell body				ovary(3)|breast(2)|pancreas(1)	6			OV - Ovarian serous cystadenocarcinoma(19;0.00928)|all cancers(22;0.0262)		Amphetamine(DB00182)|Benztropine(DB00245)|Bupropion(DB01156)|Chloroprocaine(DB01161)|Cocaine(DB00907)|Dextroamphetamine(DB01576)|Diethylpropion(DB00937)|Duloxetine(DB00476)|Fencamfamine(DB01463)|Mazindol(DB00579)|Methylphenidate(DB00422)|Modafinil(DB00745)|Phenmetrazine(DB00830)|Phentermine(DB00191)|Procaine(DB00721)	CGATGAAGAGCGTGAAGAGCT	0.582000													8	75					0	0	0.003080	0	0	
ADCY2	108	broad.mit.edu	37	5	7396565	7396565	+	Silent	SNP	C	G	G			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr5:7396565C>G	uc003jdz.1	+	1	223	c.156C>G	c.(154-156)CTC>CTG	p.L52L		NM_020546	NP_065433	Q08462	ADCY2_HUMAN	adenylate cyclase 2	52	Helical; (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	cytoplasm|dendrite|integral to membrane|plasma membrane	ATP binding|metal ion binding			ovary(5)|pancreas(1)|skin(1)	7						TCCTGCTGCTCATCGTCATGG	0.716000													11	57					0	0	0.013537	0	0	
C5orf49	134121	broad.mit.edu	37	5	7832018	7832018	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr5:7832018T>G	uc003jea.3	-	3	519	c.389A>C	c.(388-390)AAG>ACG	p.K130T		NM_001089584	NP_001083053	A4QMS7	CE049_HUMAN	hypothetical protein LOC134121	130											0						GATGTCGTTCTTCCTGTAGAA	0.582000													39	109					0	0	0.006999	0	0	
DNAH5	1767	broad.mit.edu	37	5	13922344	13922344	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr5:13922344C>T	uc003jfd.2	-	5	574	c.532G>A	c.(532-534)GCC>ACC	p.A178T	DNAH5_uc003jfe.1_RNA	NM_001369	NP_001360	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	178	Stem (By similarity).				microtubule-based movement	cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(14)|skin(13)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1)|pancreas(1)	31	Lung NSC(4;0.00476)					TGGCTCGTGGCTCTGAGAGCA	0.552000									Kartagener_syndrome				16	39					0	0	0.004007	0	0	
MARCH11	441061	broad.mit.edu	37	5	16067798	16067798	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr5:16067798C>T	uc003jfo.2	-	4	1204	c.991G>A	c.(991-993)GAA>AAA	p.E331K	MARCH11_uc010itw.1_Missense_Mutation_p.E87K	NM_001102562	NP_001096032	A6NNE9	MARHB_HUMAN	membrane-associated ring finger (C3HC4) 11	331						cytoplasmic vesicle membrane|integral to membrane	ligase activity|zinc ion binding				0						CTGCTTTCTTCGATGTCTGTG	0.478000													40	51					0	0	0.021022	0	0	
PDZD2	23037	broad.mit.edu	37	5	32089722	32089722	+	Silent	SNP	C	T	T			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr5:32089722C>T	uc003jhl.2	+	20	6556	c.6168C>T	c.(6166-6168)CGC>CGT	p.R2056R	PDZD2_uc003jhm.2_Silent_p.R2056R	NM_178140	NP_835260	O15018	PDZD2_HUMAN	PDZ domain containing 2	2056					cell adhesion	cell-cell junction|endoplasmic reticulum|extracellular region|nucleus				central_nervous_system(4)|ovary(2)|skin(2)|large_intestine(1)	9						GTGAGCCGCGCCTGGCCAGCC	0.647000													25	134					0	0	0.004656	0	0	
ARAP3	64411	broad.mit.edu	37	5	141033762	141033762	+	Nonsense_Mutation	SNP	C	A	A			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr5:141033762C>A	uc003llm.2	-	33	4468	c.4390G>T	c.(4390-4392)GAG>TAG	p.E1464*	ARAP3_uc003lll.2_Nonsense_Mutation_p.E415*|ARAP3_uc011dbe.1_Nonsense_Mutation_p.E1113*|ARAP3_uc003lln.2_Nonsense_Mutation_p.E1295*	NM_022481	NP_071926	Q8WWN8	ARAP3_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH	1464	Pro-rich.				cytoskeleton organization|negative regulation of cell migration|negative regulation of Rho protein signal transduction|regulation of ARF GTPase activity|regulation of cell shape|small GTPase mediated signal transduction|vesicle-mediated transport	cytoskeleton|cytosol|lamellipodium|plasma membrane|ruffle	ARF GTPase activator activity|phosphatidylinositol-3,4,5-trisphosphate binding|phosphatidylinositol-3,4-bisphosphate binding|Rho GTPase activator activity|zinc ion binding			breast(5)|ovary(1)|large_intestine(1)	7						GGAGGGGGCTCAGGTGGCCTC	0.612000													20	69					2.37509e-13	2.85794e-13	0.010504	1	0	
PPP1R2P3	153743	broad.mit.edu	37	5	156277985	156277985	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr5:156277985C>T	uc003lwf.1	+	1	437	c.412C>T	c.(412-414)CGA>TGA	p.R138*		NR_002168				RecName: Full=Putative protein phosphatase inhibitor 2-like protein 3; AltName: Full=Protein phosphatase 1, regulatory subunit 2 pseudogene 3;												0						AGAAAAAAAGCGACAATTTGA	0.418000													16	52					0	0	0.004007	0	0	
ERVFRDE1	405754	broad.mit.edu	37	6	11105535	11105535	+	Silent	SNP	C	T	T			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr6:11105535C>T	uc003mzt.2	-	2	379	c.9G>A	c.(7-9)CTG>CTA	p.L3L	LOC221710_uc003mzr.2_Intron|LOC221710_uc011dio.1_Intron	NM_207582	NP_997465	P60508	EFRD1_HUMAN	syncytin 2	3						integral to membrane|plasma membrane|virion					0						CCAGCAGGAGCAGGCCCATGG	0.478000													7	37					0	0	0.006214	0	0	
HIST1H1C	3006	broad.mit.edu	37	6	26056139	26056139	+	Missense_Mutation	SNP	C	G	G	rs145521943		TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr6:26056139C>G	uc003nfw.2	-	1	561	c.518G>C	c.(517-519)AGC>ACC	p.S173T		NM_005319	NP_005310	P16403	H12_HUMAN	histone cluster 1, H1c	173					nucleosome assembly	nucleosome|nucleus	DNA binding			ovary(3)|skin(2)	5						CTTCTTTGGGCTCTTAGCCAC	0.562000													107	119					0	0	0.014410	0	0	
HIST1H4E	8367	broad.mit.edu	37	6	26204985	26204985	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr6:26204985T>A	uc003ngy.2	+	1	113	c.113T>A	c.(112-114)CTT>CAT	p.L38H		NM_003545	NP_003536	P62805	H4_HUMAN	histone cluster 1, H4e	38					CenH3-containing nucleosome assembly at centromere|negative regulation of megakaryocyte differentiation|phosphatidylinositol-mediated signaling|telomere maintenance	nucleoplasm|nucleosome	DNA binding|protein binding			ovary(1)	1		all_hematologic(11;0.196)				ATCCGGCGCCTTGCTCGTCGC	0.572000													42	70					0	0	0.011902	0	0	
PBX2	5089	broad.mit.edu	37	6	32155509	32155509	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr6:32155509T>A	uc003oav.1	-	5	1056	c.785A>T	c.(784-786)TAT>TTT	p.Y262F	PBX2_uc003oaw.2_Missense_Mutation_p.Y262F	NM_002586	NP_002577	P40425	PBX2_HUMAN	pre-B-cell leukemia homeobox 2	262	Homeobox; TALE-type.						transcription factor binding			ovary(1)	1						GGAGTAGAAATACTCATTTAG	0.517000													3	33					0	0	0.004672	0	0	
C6orf125	84300	broad.mit.edu	37	6	33679443	33679443	+	Silent	SNP	C	T	T			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr6:33679443C>T	uc003ofa.1	-	1	62	c.21G>A	c.(19-21)CGG>CGA	p.R7R	C6orf125_uc010jve.1_RNA	NM_032340	NP_115716	Q9BRT2	CF125_HUMAN	hypothetical protein LOC84300	7											0						TAAGAAAACGCCGGTACCGGC	0.667000													3	30					0	0	0.004672	0	0	
RIPPLY2	134701	broad.mit.edu	37	6	84563444	84563444	+	Silent	SNP	C	T	T			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr6:84563444C>T	uc003pke.2	+	2	277	c.126C>T	c.(124-126)GAC>GAT	p.D42D		NM_001009994	NP_001009994	Q5TAB7	RIPP2_HUMAN	ripply2 protein	42					somite rostral/caudal axis specification	nucleus					0						CCTGGGTGGACGCCGGAGGCA	0.667000													5	42					0	0	0.001168	0	0	
NCOA7	135112	broad.mit.edu	37	6	126248844	126248844	+	Missense_Mutation	SNP	C	G	G			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr6:126248844C>G	uc010kes.2	+	16	3008	c.2559C>G	c.(2557-2559)TTC>TTG	p.F853L	NCOA7_uc003qae.3_Missense_Mutation_p.F853L|NCOA7_uc003qah.2_Missense_Mutation_p.F842L|NCOA7_uc003qai.2_Missense_Mutation_p.F853L|NCOA7_uc010ket.2_Missense_Mutation_p.F738L|NCOA7_uc003qak.2_Missense_Mutation_p.F130L	NM_181782	NP_861447	Q8NI08	NCOA7_HUMAN	nuclear receptor coactivator 7 isoform 1	853	TLD.				cell wall macromolecule catabolic process|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	protein binding			lung(2)|ovary(1)	3				UCEC - Uterine corpus endometrioid carcinoma (4;0.0803)|GBM - Glioblastoma multiforme(226;0.0193)|all cancers(137;0.237)		CTTTCAAGTTCAGTGACCACT	0.393000													7	105					0	0	0.003080	0	0	
RSPO3	84870	broad.mit.edu	37	6	127471646	127471646	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr6:127471646T>A	uc003qar.2	+	3	655	c.365T>A	c.(364-366)CTT>CAT	p.L122H	RSPO3_uc003qas.1_Missense_Mutation_p.L122H	NM_032784	NP_116173	Q9BXY4	RSPO3_HUMAN	R-spondin 3 precursor	122	FU 2.					extracellular region	heparin binding				0				GBM - Glioblastoma multiforme(226;0.0555)		TACTTACACCTTGGAAAGTGC	0.363000													26	42					0	0	0.021523	0	0	
SLC22A1	6580	broad.mit.edu	37	6	160560841	160560841	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr6:160560841G>A	uc003qtc.2	+	7	1323	c.1218G>A	c.(1216-1218)ATG>ATA	p.M406I	SLC22A1_uc003qtd.2_Missense_Mutation_p.M406I	NM_003057	NP_003048	O15245	S22A1_HUMAN	solute carrier family 22 member 1 isoform a	406	Helical; (Potential).					basolateral plasma membrane|integral to plasma membrane|membrane fraction	organic cation transmembrane transporter activity|protein binding				0		Breast(66;0.000776)|Ovarian(120;0.00556)		OV - Ovarian serous cystadenocarcinoma(65;2.73e-17)|BRCA - Breast invasive adenocarcinoma(81;1.1e-06)		TCTACCCCATGGCCATGTCAA	0.527000													15	61					0	0	0.003163	0	0	
NCF1B	654816	broad.mit.edu	37	7	72639986	72639986	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr7:72639986G>A	uc011kes.1	+	3	221	c.217G>A	c.(217-219)GGC>AGC	p.G73S	FKBP6_uc003twz.2_Intron|NCF1B_uc011ker.1_Missense_Mutation_p.G75S	NM_000265	NP_000256			neutrophil cytosolic factor 1												0						CGAGTACTGCGGCACGCTCAT	0.622000													4	73					0	0	0.014758	0	0	
NCF1B	654816	broad.mit.edu	37	7	72640036	72640036	+	Silent	SNP	T	C	C			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr7:72640036T>C	uc011kes.1	+	3	271	c.267T>C	c.(265-267)CTT>CTC	p.L89L	FKBP6_uc003twz.2_Intron|NCF1B_uc011ker.1_Silent_p.L91L	NM_000265	NP_000256			neutrophil cytosolic factor 1												0						CCCACCTCCTTGACTTCTTCA	0.507000													4	40					0	0	0.009096	0	0	
MAGI2	9863	broad.mit.edu	37	7	77885499	77885499	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr7:77885499A>C	uc003ugx.2	-	10	2062	c.1808T>G	c.(1807-1809)CTT>CGT	p.L603R	MAGI2_uc003ugy.2_Missense_Mutation_p.L603R|MAGI2_uc010ldx.1_Missense_Mutation_p.L212R|MAGI2_uc010ldy.1_Missense_Mutation_p.L212R|MAGI2_uc011kgr.1_Missense_Mutation_p.L435R|MAGI2_uc011kgs.1_Missense_Mutation_p.L440R	NM_012301	NP_036433	Q86UL8	MAGI2_HUMAN	membrane associated guanylate kinase, WW and PDZ	603						cell junction|synapse|synaptosome	phosphatase binding			ovary(5)|lung(4)|breast(1)|skin(1)	11		all_cancers(73;0.0064)|all_epithelial(88;0.087)|all_neural(109;0.0936)|Medulloblastoma(109;0.166)|Melanoma(862;0.236)				TAAGGTCATAAGTTCAGCTTG	0.522000													5	44					0	0	0.001984	0	0	
ZNF804B	219578	broad.mit.edu	37	7	88963320	88963320	+	Nonsense_Mutation	SNP	G	T	T			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr7:88963320G>T	uc011khi.1	+	4	1562	c.1024G>T	c.(1024-1026)GAA>TAA	p.E342*		NM_181646	NP_857597	A4D1E1	Z804B_HUMAN	zinc finger protein 804B	342						intracellular	zinc ion binding			ovary(5)|skin(3)|pancreas(2)|upper_aerodigestive_tract(1)	11	all_hematologic(106;0.125)|Lung NSC(181;0.15)|all_lung(186;0.151)		STAD - Stomach adenocarcinoma(171;0.0513)			TACCAGCAGAGAAAAAGAAAC	0.353000										HNSCC(36;0.09)			7	54					8.12818e-05	9.082e-05	0.001984	1	0	
AKAP9	10142	broad.mit.edu	37	7	91632525	91632525	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr7:91632525A>C	uc003ulg.2	+	8	3519	c.3294A>C	c.(3292-3294)GAA>GAC	p.E1098D	AKAP9_uc003ule.2_Missense_Mutation_p.E1110D|AKAP9_uc003ulf.2_Missense_Mutation_p.E1098D|AKAP9_uc003uli.2_Missense_Mutation_p.E723D	NM_005751	NP_005742	Q99996	AKAP9_HUMAN	A-kinase anchor protein 9 isoform 2	1110	Potential.				G2/M transition of mitotic cell cycle|signal transduction|synaptic transmission|transport	centrosome|cytosol|Golgi apparatus	receptor binding			breast(7)|ovary(6)|lung(5)|skin(3)|large_intestine(2)|prostate(2)|central_nervous_system(1)	26	all_cancers(62;2.46e-09)|all_epithelial(64;4.42e-08)|Breast(17;0.00206)|all_lung(186;0.185)|all_hematologic(106;0.215)|Lung NSC(181;0.249)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			TTCAGAAAGAACTCAATGTAC	0.328000			T	BRAF	papillary thyroid								29	282					0	0	0.007291	0	0	
TRRAP	8295	broad.mit.edu	37	7	98503872	98503872	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr7:98503872C>T	uc003upp.2	+	13	1318	c.1109C>T	c.(1108-1110)ACT>ATT	p.T370I	TRRAP_uc011kis.1_Missense_Mutation_p.T370I|TRRAP_uc003upr.2_Missense_Mutation_p.T62I	NM_003496	NP_003487	Q9Y4A5	TRRAP_HUMAN	transformation/transcription domain-associated	370					histone deubiquitination|histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	NuA4 histone acetyltransferase complex|PCAF complex|STAGA complex|transcription factor TFTC complex	phosphotransferase activity, alcohol group as acceptor|protein binding|transcription cofactor activity			ovary(9)|large_intestine(8)|central_nervous_system(6)|skin(6)|stomach(5)|upper_aerodigestive_tract(1)|lung(1)|liver(1)	37	all_cancers(62;6.96e-09)|all_epithelial(64;4.86e-09)|Lung NSC(181;0.01)|all_lung(186;0.016)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)			GCCAGAGAGACTCTAAGGTAT	0.413000													7	113					0	0	0.003080	0	0	
TRRAP	8295	broad.mit.edu	37	7	98581821	98581821	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr7:98581821T>A	uc003upp.2	+	60	9349	c.9140T>A	c.(9139-9141)ATC>AAC	p.I3047N	TRRAP_uc011kis.1_Missense_Mutation_p.I3018N|TRRAP_uc003upr.2_Missense_Mutation_p.I2735N	NM_003496	NP_003487	Q9Y4A5	TRRAP_HUMAN	transformation/transcription domain-associated	3047	FAT.				histone deubiquitination|histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	NuA4 histone acetyltransferase complex|PCAF complex|STAGA complex|transcription factor TFTC complex	phosphotransferase activity, alcohol group as acceptor|protein binding|transcription cofactor activity			ovary(9)|large_intestine(8)|central_nervous_system(6)|skin(6)|stomach(5)|upper_aerodigestive_tract(1)|lung(1)|liver(1)	37	all_cancers(62;6.96e-09)|all_epithelial(64;4.86e-09)|Lung NSC(181;0.01)|all_lung(186;0.016)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)			TATGGAAAAATCGCCCGGAAA	0.438000													28	320					0	0	0.010818	0	0	
Unknown	0	broad.mit.edu	37	7	124116920	124116920	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr7:124116920G>A	uc011kod.1	+	1	496	c.496G>A	c.(496-498)GAC>AAC	p.D166N		NM_001085395	NP_001078864			RecName: Full=Putative RNA polymerase II subunit A C-terminal domain phosphatase SSU72-like protein 2;          Short=CTD phosphatase SSU72-like protein 2;          EC=3.1.3.16;																		GCAGCAGTCCGACGACATGGA	0.522000													15	36					0	0	0.003163	0	0	
ADRA1A	148	broad.mit.edu	37	8	26722075	26722075	+	Missense_Mutation	SNP	C	T	T	rs140950299		TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr8:26722075C>T	uc003xfh.1	-	1	848	c.412G>A	c.(412-414)GTC>ATC	p.V138I	ADRA1A_uc003xfc.1_Missense_Mutation_p.V138I|ADRA1A_uc010lul.1_Missense_Mutation_p.V138I|ADRA1A_uc003xfd.1_RNA|ADRA1A_uc003xfe.1_Missense_Mutation_p.V138I|ADRA1A_uc010lum.1_Missense_Mutation_p.V138I|ADRA1A_uc003xff.1_RNA|ADRA1A_uc003xfg.1_Missense_Mutation_p.V138I	NM_000680	NP_000671	P35348	ADA1A_HUMAN	alpha-1A-adrenergic receptor isoform 1	138	Cytoplasmic (By similarity).				activation of phospholipase C activity|aging|apoptosis|calcium ion transport into cytosol|cell-cell signaling|intracellular protein kinase cascade|negative regulation of cell proliferation|negative regulation of Rho protein signal transduction|negative regulation of synaptic transmission, GABAergic|positive regulation of action potential|positive regulation of cardiac muscle contraction|positive regulation of ERK1 and ERK2 cascade|positive regulation of protein kinase C signaling cascade|positive regulation of vasoconstriction|response to drug|response to hormone stimulus|response to stress|smooth muscle contraction	integral to plasma membrane	alpha1-adrenergic receptor activity			breast(2)|ovary(1)|lung(1)|skin(1)	5		all_cancers(63;0.122)|Ovarian(32;2.61e-05)|all_epithelial(46;0.118)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0228)|Epithelial(17;4.92e-10)|Colorectal(74;0.0132)|READ - Rectum adenocarcinoma(644;0.115)	Alfuzosin(DB00346)|Amiodarone(DB01118)|Amphetamine(DB00182)|Benzphetamine(DB00865)|Bethanidine(DB00217)|Carvedilol(DB01136)|Dapiprazole(DB00298)|Debrisoquin(DB04840)|Dextroamphetamine(DB01576)|Doxazosin(DB00590)|Epinastine(DB00751)|Epinephrine(DB00668)|Ergotamine(DB00696)|Flupenthixol(DB00875)|Guanadrel Sulfate(DB00226)|Guanethidine(DB01170)|Labetalol(DB00598)|Lisdexamfetamine(DB01255)|Maprotiline(DB00934)|Mephentermine(DB01365)|Metaraminol(DB00610)|Methamphetamine(DB01577)|Methotrimeprazine(DB01403)|Methoxamine(DB00723)|Midodrine(DB00211)|Nefazodone(DB01149)|Nicergoline(DB00699)|Nilutamide(DB00665)|Norepinephrine(DB00368)|Norgestrel(DB00506)|Oxymetazoline(DB00935)|Perphenazine(DB00850)|Phendimetrazine(DB01579)|Phenoxybenzamine(DB00925)|Phenylephrine(DB00388)|Phenylpropanolamine(DB00397)|Prazosin(DB00457)|Promazine(DB00420)|Promethazine(DB01069)|Propericiazine(DB01608)|Propiomazine(DB00777)|Pseudoephedrine(DB00852)|Risperidone(DB00734)|Sertindole(DB06144)|Tamsulosin(DB00706)|Terazosin(DB01162)|Thioridazine(DB00679)|Tolazoline(DB00797)|Trazodone(DB00656)|Trifluoperazine(DB00831)|Ziprasidone(DB00246)	CTCTGGGTGACGATGGTTGGG	0.632000													10	50					0	0	0.006214	0	0	
TEX15	56154	broad.mit.edu	37	8	30701489	30701489	+	Nonsense_Mutation	SNP	A	C	C			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr8:30701489A>C	uc003xil.2	-	1	5045	c.5045T>G	c.(5044-5046)TTA>TGA	p.L1682*		NM_031271	NP_112561	Q9BXT5	TEX15_HUMAN	testis expressed 15	1682										ovary(3)|upper_aerodigestive_tract(2)|skin(2)	7				KIRC - Kidney renal clear cell carcinoma(542;0.0918)|Kidney(114;0.111)		ACATGGTTTTAATGTGTGTTT	0.348000													16	81					0	0	0.010504	0	0	
GDAP1	54332	broad.mit.edu	37	8	75262744	75262744	+	Silent	SNP	G	A	A			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr8:75262744G>A	uc003yah.2	+	1	127	c.48G>A	c.(46-48)GCG>GCA	p.A16A	GDAP1_uc011lfj.1_5'UTR|GDAP1_uc003yai.2_Intron	NM_018972	NP_061845	Q8TB36	GDAP1_HUMAN	ganglioside-induced differentiation-associated	16				AE -> GK (in Ref. 1; CAA76892).		cytoplasm					0	Breast(64;0.00769)	Myeloproliferative disorder(644;0.0122)	BRCA - Breast invasive adenocarcinoma(89;0.0499)|Epithelial(68;0.104)|all cancers(69;0.234)			CCTTGAGGGCGGAAGGCAAGG	0.642000													8	29					0	0	0.003080	0	0	
RGS22	26166	broad.mit.edu	37	8	101075729	101075729	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr8:101075729T>C	uc003yjb.1	-	8	1462	c.1267A>G	c.(1267-1269)AAA>GAA	p.K423E	RGS22_uc003yja.1_Missense_Mutation_p.K242E|RGS22_uc003yjc.1_Missense_Mutation_p.K411E|RGS22_uc011lgz.1_RNA|RGS22_uc010mbo.1_RNA	NM_015668	NP_056483	Q8NE09	RGS22_HUMAN	regulator of G-protein signaling 22	423					negative regulation of signal transduction	cytoplasm|plasma membrane	GTPase activator activity|signal transducer activity			ovary(3)|skin(2)|breast(1)|central_nervous_system(1)	7			Epithelial(11;6.71e-08)|all cancers(13;4.19e-06)|OV - Ovarian serous cystadenocarcinoma(57;0.000469)|STAD - Stomach adenocarcinoma(118;0.169)			AATGTACCTTTTATAAATTTC	0.383000													14	82					0	0	0.016723	0	0	
DCAF13	25879	broad.mit.edu	37	8	104427550	104427550	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr8:104427550G>A	uc003yln.2	+	1	609	c.332G>A	c.(331-333)CGC>CAC	p.R111H	SLC25A32_uc003yll.2_5'Flank|SLC25A32_uc011lhr.1_5'Flank|DCAF13_uc003ylm.1_5'UTR|DCAF13_uc003ylo.2_5'UTR	NM_015420	NP_056235	Q9NV06	DCA13_HUMAN	WD repeats and SOF1 domain containing	Error:Variant_position_missing_in_Q9NV06_after_alignment					rRNA processing	CUL4 RING ubiquitin ligase complex|nucleolus|ribonucleoprotein complex				breast(1)	1						CCAGCAGGCCGCCGCTCCGCG	0.637000													12	53					0	0	0.010729	0	0	
RIMS2	9699	broad.mit.edu	37	8	104709365	104709365	+	Silent	SNP	A	G	G			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr8:104709365A>G	uc003ylp.2	+	2	367	c.228A>G	c.(226-228)GGA>GGG	p.G76G		NM_001100117	NP_001093587	Q9UQ26	RIMS2_HUMAN	regulating synaptic membrane exocytosis 2	107	RabBD.				intracellular protein transport	cell junction|presynaptic membrane	metal ion binding|Rab GTPase binding			ovary(6)|lung(2)|breast(2)|skin(2)|large_intestine(1)|central_nervous_system(1)|pancreas(1)	15			OV - Ovarian serous cystadenocarcinoma(57;7.7e-07)|STAD - Stomach adenocarcinoma(118;0.229)			AGAAGATGGGAGAAGAATCAC	0.403000										HNSCC(12;0.0054)			15	69					0	0	0.004007	0	0	
TG	7038	broad.mit.edu	37	8	133898821	133898821	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr8:133898821G>T	uc003ytw.2	+	9	1245	c.1204G>T	c.(1204-1206)GCC>TCC	p.A402S		NM_003235	NP_003226	P01266	THYG_HUMAN	thyroglobulin precursor	402					hormone biosynthetic process|signal transduction|thyroid gland development|thyroid hormone generation	extracellular space	hormone activity			ovary(8)|breast(4)|pancreas(1)|central_nervous_system(1)|skin(1)	15	Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)	Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0559)|Breast(495;0.0735)	BRCA - Breast invasive adenocarcinoma(115;0.000701)	KIRC - Kidney renal clear cell carcinoma(542;0.0546)		TCCAAGAGTAGCCAGATTTGC	0.557000													10	214					1.08611e-07	1.23242e-07	0.010729	1	0	
ZNF623	9831	broad.mit.edu	37	8	144732869	144732869	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr8:144732869C>T	uc003yzd.2	+	1	916	c.827C>T	c.(826-828)TCG>TTG	p.S276L	ZNF623_uc011lkp.1_Missense_Mutation_p.S236L|ZNF623_uc003yzc.2_Missense_Mutation_p.S236L	NM_014789	NP_055604	O75123	ZN623_HUMAN	zinc finger protein 623 isoform 1	276	C2H2-type 6.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	all_cancers(97;3.74e-11)|all_epithelial(106;2.62e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;5.28e-40)|all cancers(56;5.23e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.146)			ATAAGGAGCTCGAGCCTCATT	0.468000													4	68					0	0	0.009096	0	0	
PTPRD	5789	broad.mit.edu	37	9	8331655	8331655	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr9:8331655T>C	uc003zkk.2	-	43	6172	c.5461A>G	c.(5461-5463)ATT>GTT	p.I1821V	PTPRD_uc003zkp.2_Missense_Mutation_p.I1415V|PTPRD_uc003zkq.2_Missense_Mutation_p.I1414V|PTPRD_uc003zkr.2_Missense_Mutation_p.I1405V|PTPRD_uc003zks.2_Missense_Mutation_p.I1414V|PTPRD_uc003zkl.2_Missense_Mutation_p.I1812V|PTPRD_uc003zkm.2_Missense_Mutation_p.I1808V|PTPRD_uc003zkn.2_Missense_Mutation_p.I1410V|PTPRD_uc003zko.2_Missense_Mutation_p.I1411V	NM_002839	NP_002830	P23468	PTPRD_HUMAN	protein tyrosine phosphatase, receptor type, D	1821	Cytoplasmic (Potential).|Tyrosine-protein phosphatase 2.				transmembrane receptor protein tyrosine phosphatase signaling pathway	integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			lung(14)|large_intestine(3)|ovary(2)|breast(2)|urinary_tract(1)	22		all_cancers(3;3.38e-95)|all_epithelial(3;2.84e-91)|all_lung(3;7.3e-56)|Lung NSC(3;1.82e-52)|Renal(3;3.42e-19)|all_hematologic(3;0.000134)|all_neural(3;0.00409)|Acute lymphoblastic leukemia(23;0.0069)|Melanoma(3;0.0121)|Myeloproliferative disorder(4;0.0122)|Medulloblastoma(3;0.0144)|Lung SC(3;0.0301)|Ovarian(56;0.0694)|Hepatocellular(3;0.0824)		all cancers(1;3.38e-12)|Epithelial(1;2.12e-09)|STAD - Stomach adenocarcinoma(1;1.29e-07)|KIRC - Kidney renal clear cell carcinoma(3;5.49e-07)|Kidney(3;6.36e-07)|GBM - Glioblastoma multiforme(50;9.05e-05)|Lung(1;0.000189)|BRCA - Breast invasive adenocarcinoma(1;0.00178)|LUSC - Lung squamous cell carcinoma(1;0.0115)|LUAD - Lung adenocarcinoma(58;0.119)		ATGAAGTCAATAAATCCTTCT	0.468000										TSP Lung(15;0.13)			31	71					0	0	0.009535	0	0	
FOXB2	442425	broad.mit.edu	37	9	79634960	79634960	+	Silent	SNP	C	T	T			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr9:79634960C>T	uc004ako.1	+	1	390	c.390C>T	c.(388-390)GCC>GCT	p.A130A		NM_001013735	NP_001013757	Q5VYV0	FOXB2_HUMAN	forkhead box B2	130					brain development|embryo development|pattern specification process|regulation of sequence-specific DNA binding transcription factor activity|tissue development	transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding				0						CGCCGGGCGCCGGTCCGGGAG	0.433000													4	12					0	0	0.009096	0	0	
EPB41L4B	54566	broad.mit.edu	37	9	111947780	111947780	+	Nonsense_Mutation	SNP	T	A	A			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr9:111947780T>A	uc004bdz.1	-	23	2702	c.2407A>T	c.(2407-2409)AAA>TAA	p.K803*		NM_019114	NP_061987	Q9H329	E41LB_HUMAN	erythrocyte membrane protein band 4.1 like 4B	803						cytoplasm|cytoskeleton|extrinsic to membrane	cytoskeletal protein binding|structural constituent of cytoskeleton			ovary(1)|central_nervous_system(1)|skin(1)	3						AGCCTCGTTTTGATTGGAGGG	0.637000													8	43					0	0	0.004482	0	0	
PAPPA	5069	broad.mit.edu	37	9	118974066	118974066	+	Silent	SNP	G	A	A			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr9:118974066G>A	uc004bjn.2	+	4	2154	c.1773G>A	c.(1771-1773)GAG>GAA	p.E591E	PAPPA_uc011lxp.1_Intron|PAPPA_uc011lxq.1_Intron	NM_002581	NP_002572	Q13219	PAPP1_HUMAN	pregnancy-associated plasma protein A	591					cell differentiation|female pregnancy	cytoplasm|extracellular region|membrane	metalloendopeptidase activity|zinc ion binding			ovary(4)|skin(4)|pancreas(1)	9						TGGAGACAGAGCCCTCCTTCG	0.552000													24	126					0	0	0.016522	0	0	
RAPGEF1	2889	broad.mit.edu	37	9	134497285	134497285	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr9:134497285C>A	uc004cbc.2	-	11	1882	c.1752G>T	c.(1750-1752)AAG>AAT	p.K584N	RAPGEF1_uc004cbb.2_Missense_Mutation_p.K602N|RAPGEF1_uc010mzm.2_RNA|RAPGEF1_uc010mzn.2_Missense_Mutation_p.K589N|RAPGEF1_uc004cbd.2_Missense_Mutation_p.K589N|RAPGEF1_uc010mzs.1_Missense_Mutation_p.K30N|RAPGEF1_uc010mzl.1_Missense_Mutation_p.K30N|RAPGEF1_uc010mzo.1_Missense_Mutation_p.K30N|RAPGEF1_uc010mzp.1_Missense_Mutation_p.K30N|RAPGEF1_uc010mzq.1_Missense_Mutation_p.K30N|RAPGEF1_uc010mzr.1_Missense_Mutation_p.K30N	NM_005312	NP_005303	Q13905	RPGF1_HUMAN	guanine nucleotide-releasing factor 2 isoform a	584					activation of MAPKK activity|nerve growth factor receptor signaling pathway|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|endosome	guanyl-nucleotide exchange factor activity|SH3 domain binding			lung(3)|ovary(2)|breast(1)|skin(1)	7		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;2.19e-05)|Epithelial(140;0.000364)		CCATGAGGAGCTTGTTCTTCT	0.622000													6	24					0.000157383	0.000174959	0.003080	1	0	
C9orf96	169436	broad.mit.edu	37	9	136253262	136253262	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr9:136253262A>C	uc004cdk.2	+	5	387	c.326A>C	c.(325-327)GAG>GCG	p.E109A	C9orf96_uc004cdl.2_RNA	NM_153710	NP_714921	Q8NE28	SGK71_HUMAN	hypothetical protein LOC169436	109	Protein kinase.						ATP binding|protein kinase activity			stomach(2)|central_nervous_system(2)	4				OV - Ovarian serous cystadenocarcinoma(145;1.06e-07)|Epithelial(140;1.28e-06)|all cancers(34;1.46e-05)		CTGGTGATGGAGTTCAATGAG	0.572000													22	64					0	0	0.018920	0	0	
MXRA5	25878	broad.mit.edu	37	X	3227890	3227890	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chrX:3227890C>A	uc004crg.3	-	7	8511	c.8354G>T	c.(8353-8355)GGA>GTA	p.G2785V		NM_015419	NP_056234	Q9NR99	MXRA5_HUMAN	adlican precursor	2785	Ig-like C2-type 12.					extracellular region				ovary(5)|lung(1)|central_nervous_system(1)|skin(1)	8		all_lung(23;0.00031)|Lung NSC(23;0.000946)				AAATCTGTTTCCATACAGACG	0.512000													15	33					0.000422831	0.000465327	0.004007	1	0	
ARAF	369	broad.mit.edu	37	X	47422726	47422726	+	Missense_Mutation	SNP	G	C	C			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chrX:47422726G>C	uc011mlq.1	+	3	331	c.198G>C	c.(196-198)AAG>AAC	p.K66N	ARAF_uc011mln.1_RNA|ARAF_uc011mlo.1_5'UTR|ARAF_uc011mlp.1_Missense_Mutation_p.K66N|ARAF_uc004dic.1_5'Flank	NM_001654	NP_001645	P10398	ARAF_HUMAN	v-raf murine sarcoma 3611 viral oncogene	66	RBD.				intracellular signal transduction|negative regulation of apoptosis|positive regulation of peptidyl-serine phosphorylation		ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|receptor signaling protein activity			large_intestine(3)|lung(2)|ovary(1)|skin(1)	7					Adenosine triphosphate(DB00171)	GACTCATCAAGGGGTGAGTGT	0.557000													4	18					0	0	0.009096	0	0	
PHF8	23133	broad.mit.edu	37	X	54014281	54014281	+	Silent	SNP	G	A	A			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chrX:54014281G>A	uc004dsu.2	-	15	2008	c.1935C>T	c.(1933-1935)GAC>GAT	p.D645D	PHF8_uc004dst.2_Silent_p.D609D|PHF8_uc004dsv.2_Silent_p.D475D|PHF8_uc004dsw.2_Silent_p.D508D|PHF8_uc004dsx.2_Silent_p.D373D|PHF8_uc004dsy.2_Silent_p.D609D	NM_015107	NP_055922	Q9UPP1	PHF8_HUMAN	PHD finger protein 8	645					brain development|G1/S transition of mitotic cell cycle|negative regulation of chromatin silencing at rDNA|positive regulation of transcription from RNA polymerase I promoter|transcription, DNA-dependent	nucleolus	chromatin binding|histone demethylase activity (H3-K27 specific)|histone demethylase activity (H3-K36 specific)|histone demethylase activity (H3-K9 specific)|histone demethylase activity (H4-K20 specific)|iron ion binding|methylated histone residue binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|zinc ion binding			ovary(3)	3						AGTCAAATTCGTCTTCCATCA	0.453000													6	25					0	0	0.001168	0	0	
AR	367	broad.mit.edu	37	X	66765698	66765698	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chrX:66765698A>G	uc004dwu.1	+	1	1825	c.710A>G	c.(709-711)AAG>AGG	p.K237R	AR_uc011mpd.1_Missense_Mutation_p.K237R|AR_uc011mpe.1_RNA|AR_uc011mpf.1_Missense_Mutation_p.K237R	NM_000044	NP_000035	P10275	ANDR_HUMAN	androgen receptor isoform 1	235	Modulating.				cell death|cell growth|cell proliferation|cell-cell signaling|negative regulation of apoptosis|negative regulation of integrin biosynthetic process|positive regulation of cell proliferation|positive regulation of integrin biosynthetic process|positive regulation of NF-kappaB transcription factor activity|positive regulation of phosphorylation|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase III promoter|regulation of establishment of protein localization in plasma membrane|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|transport	cytoplasm|nuclear chromatin|nucleoplasm	androgen binding|androgen receptor activity|beta-catenin binding|enzyme binding|ligand-regulated transcription factor activity|protein dimerization activity|sequence-specific DNA binding transcription factor activity|transcription factor binding|transcription regulatory region DNA binding|zinc ion binding			ovary(3)|lung(2)|breast(2)|central_nervous_system(1)	8	all_cancers(1;0.173)|Prostate(1;2.27e-16)|all_epithelial(1;0.102)	all_lung(315;1.3e-11)			Bicalutamide(DB01128)|Cyproterone(DB04839)|Dromostanolone(DB00858)|Finasteride(DB01216)|Fluoxymesterone(DB01185)|Flutamide(DB00499)|Nandrolone(DB00984)|Nilutamide(DB00665)|Oxandrolone(DB00621)|Testosterone(DB00624)	GACAACGCCAAGGAGTTGTGT	0.607000									Androgen_Insensitivity_Syndrome				15	13					0	0	0.020292	0	0	
P2RY10	27334	broad.mit.edu	37	X	78216896	78216896	+	Silent	SNP	T	A	A			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chrX:78216896T>A	uc004ede.2	+	4	1248	c.879T>A	c.(877-879)CTT>CTA	p.L293L	P2RY10_uc004edf.2_Silent_p.L293L	NM_014499	NP_055314	O00398	P2Y10_HUMAN	G-protein coupled purinergic receptor P2Y10	293	Helical; Name=7; (Potential).					integral to membrane|plasma membrane	purinergic nucleotide receptor activity, G-protein coupled			ovary(2)|lung(2)|breast(1)	5						GCCTGTGCCTTGCAAGTCTCT	0.443000													55	164					0	0	0.014410	0	0	
LOC442459	442459	broad.mit.edu	37	X	98974959	98974959	+	RNA	SNP	C	T	T			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chrX:98974959C>T	uc011mrd.1	-	8		c.1384G>A				NR_024608				Homo sapiens DNA repair protein mRNA, complete cds.												0						GATGTTCCTGCGGGGTGTGTA	0.512000													4	60					0	0	0.009096	0	0	
MCART6	401612	broad.mit.edu	37	X	103349893	103349893	+	Silent	SNP	C	T	T			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chrX:103349893C>T	uc004elu.2	-	2	229	c.48G>A	c.(46-48)ACG>ACA	p.T16T		NM_001012755	NP_001012773	Q5H9E4	MCAR6_HUMAN	mitochondrial carrier triple repeat 6	16					transport	integral to membrane|mitochondrial inner membrane					0						CCTCTGCTCGCGTCCTGTGCT	0.517000													15	17					0	0	0.003163	0	0	
ACTRT1	139741	broad.mit.edu	37	X	127185859	127185859	+	Silent	SNP	G	A	A			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chrX:127185859G>A	uc004eum.2	-	1	524	c.327C>T	c.(325-327)ACC>ACT	p.T109T		NM_138289	NP_612146	Q8TDG2	ACTT1_HUMAN	actin-related protein T1	109						cytoplasm|cytoskeleton				ovary(2)|central_nervous_system(2)|skin(1)	5						AAGAGGGCTCGGTCATAAGTA	0.478000													83	165					0	0	0.014410	0	0	
GPR50	9248	broad.mit.edu	37	X	150349052	150349052	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chrX:150349052C>T	uc010ntg.1	+	2	1132	c.997C>T	c.(997-999)CGT>TGT	p.R333C	uc004fes.1_5'Flank|GPR50_uc011myc.1_3'UTR	NM_004224	NP_004215	Q13585	MTR1L_HUMAN	G protein-coupled receptor 50	333	Cytoplasmic (Potential).|Pro-rich.				cell-cell signaling	integral to plasma membrane	melatonin receptor activity			large_intestine(1)|lung(1)|ovary(1)|pancreas(1)	4	Acute lymphoblastic leukemia(192;6.56e-05)					GCAGGAGGCCCGTACCCTGGC	0.567000													36	79					0	0	0.019004	0	0	
F8	2157	broad.mit.edu	37	X	154176146	154176146	+	Nonsense_Mutation	SNP	G	T	T			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chrX:154176146G>T	uc004fmt.2	-	13	2111	c.1940C>A	c.(1939-1941)TCA>TAA	p.S647*		NM_000132	NP_000123	P00451	FA8_HUMAN	coagulation factor VIII isoform a precursor	647	F5/8 type A 2.|Plastocyanin-like 4.				acute-phase response|blood coagulation, intrinsic pathway|cell adhesion|platelet activation|platelet degranulation	extracellular space|plasma membrane|platelet alpha granule lumen	copper ion binding|oxidoreductase activity|protein binding			ovary(5)|large_intestine(2)|pancreas(2)|upper_aerodigestive_tract(1)|skin(1)	11	all_cancers(53;7.19e-17)|all_epithelial(53;9.83e-11)|all_lung(58;6.63e-07)|Lung NSC(58;2.08e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)				Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Drotrecogin alfa(DB00055)	CAAACAAACTGACAACTGCAA	0.378000													14	19					1.05317e-09	1.22683e-09	0.020292	1	0	
ATM	472	broad.mit.edu	37	11	108121510	108121511	+	Frame_Shift_Del	DEL	TC	-	-			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr11:108121510_108121511delTC	uc001pkb.1	+	10	1703_1704	c.1318_1319delTC	c.(1318-1320)TCTfs	p.S440fs	ATM_uc009yxr.1_Frame_Shift_Del_p.S440fs	NM_000051	NP_000042	Q13315	ATM_HUMAN	ataxia telangiectasia mutated isoform 1	440					cell cycle arrest|cellular response to gamma radiation|DNA damage induced protein phosphorylation|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|double-strand break repair via homologous recombination|G2/M transition DNA damage checkpoint|histone mRNA catabolic process|mitotic cell cycle spindle assembly checkpoint|negative regulation of B cell proliferation|peptidyl-serine phosphorylation|positive regulation of DNA damage response, signal transduction by p53 class mediator|pre-B cell allelic exclusion|protein autophosphorylation|reciprocal meiotic recombination|replicative senescence	cytoplasmic membrane-bounded vesicle|nucleoplasm	1-phosphatidylinositol-3-kinase activity|ATP binding|DNA binding|DNA-dependent protein kinase activity|identical protein binding|protein complex binding|protein dimerization activity|protein N-terminus binding			haematopoietic_and_lymphoid_tissue(174)|lung(25)|breast(15)|large_intestine(9)|ovary(5)|kidney(5)|central_nervous_system(4)|upper_aerodigestive_tract(1)|stomach(1)|NS(1)	240		all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147)		GATGATACTATCTCAGCTTCTA	0.401			D|Mis|N|F|S		T-PLL	leukemia|lymphoma|medulloblastoma|glioma		Genes_defective_in_diseases_associated_with_sensitivity_to_DNA_damaging_agents	Ataxia_Telangiectasia	TSP Lung(14;0.12)			42	90	---	---	---	---						.
SSH2	85464	broad.mit.edu	37	17	27963708	27963709	+	Frame_Shift_Ins	INS	-	G	G			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr17:27963708_27963709insG	uc002heo.1	-	14	1458_1459	c.1458_1459insC	c.(1456-1461)ACCTCAfs	p.T486fs	SSH2_uc010wbh.1_Frame_Shift_Ins_p.T513fs	NM_033389	NP_203747	Q76I76	SSH2_HUMAN	slingshot 2	486_487					actin cytoskeleton organization|regulation of actin polymerization or depolymerization|regulation of axonogenesis|regulation of lamellipodium assembly	cytoplasm|cytoskeleton	actin binding|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			skin(2)	2						TGGTCTGCTGAGGTGGTGATAT	0.475													99	170	---	---	---	---						.
BAHCC1	57597	broad.mit.edu	37	17	79423467	79423467	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-6454-01A-11D-1800-08	TCGA-BR-6454-11A-01D-1800-08									Somatic	Phase_I	Capture				Illumina GAIIx	e716ee38-12c6-4cf9-aee2-1ca60ed8f8b5	02a6d96b-8aee-4512-8454-f01a984641b0	g.chr17:79423467delG	uc002kaf.2	+	14	4714	c.4714delG	c.(4714-4716)GGGfs	p.G1572fs	BAHCC1_uc002kae.2_Frame_Shift_Del_p.G802fs	NM_001080519	NP_001073988	Q9P281	BAHC1_HUMAN	BAH domain and coiled-coil containing 1	1572							DNA binding			ovary(1)	1	all_neural(118;0.0804)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0224)|OV - Ovarian serous cystadenocarcinoma(97;0.116)			GGCTACCCCCGGGGGGCGCAT	0.682													2	4	---	---	---	---						.
