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
KIF1B	23095	broad.mit.edu	37	1	10394612	10394612	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4187-01A-01D-1126-08	TCGA-BR-4187-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	0b45eb56-8286-4094-8bff-d0cf5c05cda9	30a6f1ff-df78-470a-b645-0e46c00252d8	g.chr1:10394612G>A	uc001aqx.3	+	28	3161	c.2959G>A	c.(2959-2961)GTG>ATG	p.V987M	KIF1B_uc001aqw.3_Missense_Mutation_p.V941M|KIF1B_uc001aqy.2_Missense_Mutation_p.V961M|KIF1B_uc001aqz.2_Missense_Mutation_p.V987M|KIF1B_uc001ara.2_Missense_Mutation_p.V947M|KIF1B_uc001arb.2_Missense_Mutation_p.V973M	NM_015074	NP_055889	O60333	KIF1B_HUMAN	kinesin family member 1B isoform b	987					anterograde axon cargo transport|apoptosis|neuromuscular synaptic transmission|neuron-neuron synaptic transmission	cytoplasmic vesicle membrane|microtubule|microtubule associated complex|mitochondrion	ATP binding|ATPase activity|kinesin binding|microtubule motor activity|protein binding			ovary(2)|upper_aerodigestive_tract(1)	3	Ovarian(185;0.203)	all_lung(284;1.31e-05)|Lung NSC(185;2.2e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0259)|Colorectal(212;9.79e-07)|COAD - Colon adenocarcinoma(227;0.000143)|BRCA - Breast invasive adenocarcinoma(304;0.000413)|Kidney(185;0.00134)|KIRC - Kidney renal clear cell carcinoma(229;0.0037)|STAD - Stomach adenocarcinoma(132;0.0113)|READ - Rectum adenocarcinoma(331;0.0642)		GCTGTATCCCGTGCCCCTGAT	0.512													11	144					0	0	0.013537	0	0	
EFCAB7	84455	broad.mit.edu	37	1	64021086	64021086	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4187-01A-01D-1126-08	TCGA-BR-4187-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	0b45eb56-8286-4094-8bff-d0cf5c05cda9	30a6f1ff-df78-470a-b645-0e46c00252d8	g.chr1:64021086A>G	uc001dbf.2	+	9	1408	c.1114A>G	c.(1114-1116)ACT>GCT	p.T372A		NM_032437	NP_115813	A8K855	EFCB7_HUMAN	EF-hand calcium binding domain 7	372							calcium ion binding				0						TCCTTCCACAACTGGCTGTAG	0.358													6	104					0	0	0.003080	0	0	
COL11A1	1301	broad.mit.edu	37	1	103352525	103352525	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4187-01A-01D-1126-08	TCGA-BR-4187-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	0b45eb56-8286-4094-8bff-d0cf5c05cda9	30a6f1ff-df78-470a-b645-0e46c00252d8	g.chr1:103352525C>A	uc001dul.2	-	63	5014	c.4696G>T	c.(4696-4698)GAT>TAT	p.D1566Y	COL11A1_uc001duk.2_Missense_Mutation_p.D762Y|COL11A1_uc001dum.2_Missense_Mutation_p.D1578Y|COL11A1_uc001dun.2_Missense_Mutation_p.D1527Y|COL11A1_uc009weh.2_Missense_Mutation_p.D1450Y	NM_001854	NP_001845	P12107	COBA1_HUMAN	alpha 1 type XI collagen isoform A	1566					collagen fibril organization|detection of mechanical stimulus involved in sensory perception of sound|visual perception	collagen type XI	extracellular matrix binding|extracellular matrix structural constituent|protein binding, bridging			ovary(6)|breast(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)|pancreas(1)	12		all_epithelial(167;2.52e-07)|all_lung(203;3.11e-05)|Lung NSC(277;6.61e-05)|Breast(1374;0.181)		Lung(183;0.186)|all cancers(265;0.242)|Epithelial(280;0.248)		ATATTATCATCTGCATCTGCT	0.398													11	129					0.00010058	0.000167117	0.013537	1	0	
AMY2B	280	broad.mit.edu	37	1	104120221	104120221	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4187-01A-01D-1126-08	TCGA-BR-4187-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	0b45eb56-8286-4094-8bff-d0cf5c05cda9	30a6f1ff-df78-470a-b645-0e46c00252d8	g.chr1:104120221G>A	uc001duq.2	+	10	1827	c.1211G>A	c.(1210-1212)CGC>CAC	p.R404H	AMY2B_uc010ouo.1_RNA|LOC648740_uc001dur.2_Missense_Mutation_p.R404H|AMY2B_uc001dus.1_RNA	NM_020978	NP_066188	P19961	AMY2B_HUMAN	amylase, pancreatic, alpha-2B precursor	404					carbohydrate metabolic process|digestion	extracellular region	alpha-amylase activity|metal ion binding				0		all_epithelial(167;3.05e-05)|all_lung(203;0.000199)|Lung NSC(277;0.000451)		Colorectal(144;0.0669)|all cancers(265;0.083)|Epithelial(280;0.094)|Lung(183;0.112)		CATCGATGGCGCCAAATAAGG	0.343													18	243					0	0	0.008871	0	0	
NBPF10	100132406	broad.mit.edu	37	1	145302714	145302714	+	Silent	SNP	A	G	G	rs9424867		TCGA-BR-4187-01A-01D-1126-08	TCGA-BR-4187-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	0b45eb56-8286-4094-8bff-d0cf5c05cda9	30a6f1ff-df78-470a-b645-0e46c00252d8	g.chr1:145302714A>G	uc001end.3	+	8	1187	c.1152A>G	c.(1150-1152)TTA>TTG	p.L384L	NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|NBPF10_uc001emp.3_Intron|NBPF10_uc010oyi.1_5'UTR|NBPF10_uc001emq.1_Silent_p.L113L	NM_001039703	NP_001034792	A6NDV3	A6NDV3_HUMAN	hypothetical protein LOC100132406	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment											0	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		AGGAGAAGTTACGGGAAGGGA	0.527													7	181					0	0	0.001984	0	0	
TNN	63923	broad.mit.edu	37	1	175046731	175046731	+	Silent	SNP	C	T	T			TCGA-BR-4187-01A-01D-1126-08	TCGA-BR-4187-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	0b45eb56-8286-4094-8bff-d0cf5c05cda9	30a6f1ff-df78-470a-b645-0e46c00252d8	g.chr1:175046731C>T	uc001gkl.1	+	2	290	c.177C>T	c.(175-177)GAC>GAT	p.D59D	TNN_uc010pmx.1_Silent_p.D59D	NM_022093	NP_071376	Q9UQP3	TENN_HUMAN	tenascin N precursor	59					cell growth|cell migration|signal transduction	extracellular space|proteinaceous extracellular matrix				large_intestine(5)|ovary(3)|central_nervous_system(1)	9		Breast(1374;0.000962)		KIRC - Kidney renal clear cell carcinoma(1967;0.00198)		TTCAGGTTGACGCTGACCCTC	0.597													7	40					0	0	0.003080	0	0	
ASTN1	460	broad.mit.edu	37	1	176999973	176999973	+	Silent	SNP	G	A	A			TCGA-BR-4187-01A-01D-1126-08	TCGA-BR-4187-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	0b45eb56-8286-4094-8bff-d0cf5c05cda9	30a6f1ff-df78-470a-b645-0e46c00252d8	g.chr1:176999973G>A	uc001glc.2	-	4	1193	c.981C>T	c.(979-981)AGC>AGT	p.S327S	ASTN1_uc001glb.1_Silent_p.S327S|ASTN1_uc001gld.1_Silent_p.S327S|ASTN1_uc009wwx.1_Silent_p.S327S|ASTN1_uc001gle.3_RNA|MIR488_hsa-mir-488|MI0003123_5'Flank	NM_004319	NP_004310	O14525	ASTN1_HUMAN	astrotactin isoform 1	327					cell migration|neuron cell-cell adhesion	integral to membrane				ovary(6)|skin(5)|central_nervous_system(2)|large_intestine(1)|lung(1)	15						GCTTTCTCTGGCTGCTGGAGG	0.473													9	42					0	0	0.010729	0	0	
USH2A	7399	broad.mit.edu	37	1	216073486	216073486	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4187-01A-01D-1126-08	TCGA-BR-4187-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	0b45eb56-8286-4094-8bff-d0cf5c05cda9	30a6f1ff-df78-470a-b645-0e46c00252d8	g.chr1:216073486G>A	uc001hku.1	-	40	7912	c.7525C>T	c.(7525-7527)CGG>TGG	p.R2509W		NM_206933	NP_996816	O75445	USH2A_HUMAN	usherin isoform B	2509	Extracellular (Potential).|Fibronectin type-III 11.				maintenance of organ identity|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	basement membrane|cytoplasm|integral to membrane|stereocilium membrane	collagen binding			ovary(20)|upper_aerodigestive_tract(2)|skin(2)|kidney(1)|central_nervous_system(1)	26				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		GCAACCAACCGAAACATATAC	0.423										HNSCC(13;0.011)			9	75					0	0	0.008291	0	0	
MUC2	4583	broad.mit.edu	37	11	1093349	1093349	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4187-01A-01D-1126-08	TCGA-BR-4187-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	0b45eb56-8286-4094-8bff-d0cf5c05cda9	30a6f1ff-df78-470a-b645-0e46c00252d8	g.chr11:1093349C>T	uc001lsx.1	+	31	12281	c.12254C>T	c.(12253-12255)CCC>CTC	p.P4085L		NM_002457	NP_002448	Q02817	MUC2_HUMAN	mucin 2 precursor	4085						inner mucus layer|outer mucus layer	protein binding			lung(1)|breast(1)	2		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	accccgacacccatctccacc	0													3	24					0	0	0.004672	0	0	
SOX6	55553	broad.mit.edu	37	11	15994601	15994601	+	Silent	SNP	G	A	A			TCGA-BR-4187-01A-01D-1126-08	TCGA-BR-4187-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	0b45eb56-8286-4094-8bff-d0cf5c05cda9	30a6f1ff-df78-470a-b645-0e46c00252d8	g.chr11:15994601G>A	uc001mme.2	-	16	2313	c.2280C>T	c.(2278-2280)ATC>ATT	p.I760I	SOX6_uc001mmd.2_Silent_p.I723I|SOX6_uc001mmf.2_Silent_p.I720I|SOX6_uc001mmg.2_Silent_p.I727I	NM_001145819	NP_001139291	P35712	SOX6_HUMAN	SRY (sex determining region Y)-box 6 isoform 4	747					muscle organ development	nucleus	sequence-specific DNA binding transcription factor activity			ovary(3)	3						TTGCCATAGTGATAGCACCAG	0.502													7	36					0	0	0.004482	0	0	
RARG	5916	broad.mit.edu	37	12	53607425	53607425	+	Silent	SNP	C	T	T			TCGA-BR-4187-01A-01D-1126-08	TCGA-BR-4187-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	0b45eb56-8286-4094-8bff-d0cf5c05cda9	30a6f1ff-df78-470a-b645-0e46c00252d8	g.chr12:53607425C>T	uc001sce.2	-	8	1358	c.873G>A	c.(871-873)GGG>GGA	p.G291G	RARG_uc001scd.2_Silent_p.G280G|RARG_uc010sob.1_Silent_p.G269G|RARG_uc001scf.2_Silent_p.G291G|RARG_uc001scg.2_Silent_p.G219G|RARG_uc010soc.1_Silent_p.G170G|RARG_uc010sod.1_Silent_p.G328G	NM_000966	NP_000957	P13631	RARG_HUMAN	retinoic acid receptor, gamma isoform 1	291	Ligand-binding.				canonical Wnt receptor signaling pathway|embryonic eye morphogenesis|embryonic hindlimb morphogenesis|negative regulation of cell proliferation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of apoptosis|positive regulation of transcription from RNA polymerase II promoter|regulation of cell size|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|response to retinoic acid	integral to membrane|transcription factor complex	retinoic acid receptor activity|retinoid X receptor binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			breast(2)|ovary(1)|lung(1)	4					Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Etretinate(DB00926)|Tazarotene(DB00799)|Tretinoin(DB00755)	TCAGGGTCAGCCCGTCGGAGA	0.612											OREG0021862	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	48					0	0	0.014758	0	0	
ZFC3H1	196441	broad.mit.edu	37	12	72023392	72023392	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4187-01A-01D-1126-08	TCGA-BR-4187-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	0b45eb56-8286-4094-8bff-d0cf5c05cda9	30a6f1ff-df78-470a-b645-0e46c00252d8	g.chr12:72023392G>T	uc001swo.2	-	19	4182	c.3823C>A	c.(3823-3825)CAT>AAT	p.H1275N		NM_144982	NP_659419	O60293	ZC3H1_HUMAN	proline/serine-rich coiled-coil 2	1275					RNA processing	intracellular	metal ion binding			ovary(2)|breast(1)|central_nervous_system(1)|skin(1)	5						TACTTACTATGACCTTTACTT	0.264													5	39					0.000602214	0.000985442	0.014758	1	0	
WSCD2	9671	broad.mit.edu	37	12	108589947	108589947	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4187-01A-01D-1126-08	TCGA-BR-4187-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	0b45eb56-8286-4094-8bff-d0cf5c05cda9	30a6f1ff-df78-470a-b645-0e46c00252d8	g.chr12:108589947G>A	uc001tms.2	+	2	1082	c.338G>A	c.(337-339)CGA>CAA	p.R113Q	WSCD2_uc001tmt.2_Missense_Mutation_p.R113Q	NM_014653	NP_055468	Q2TBF2	WSCD2_HUMAN	WSC domain containing 2	113						integral to membrane				ovary(1)|large_intestine(1)|breast(1)	3						GCCTGGAGCCGAGCCCTCAAG	0.597													4	39					0	0	0.009096	0	0	
CUL4A	8451	broad.mit.edu	37	13	113893752	113893752	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4187-01A-01D-1126-08	TCGA-BR-4187-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	0b45eb56-8286-4094-8bff-d0cf5c05cda9	30a6f1ff-df78-470a-b645-0e46c00252d8	g.chr13:113893752G>A	uc010tjy.1	+	11	933	c.922G>A	c.(922-924)GAC>AAC	p.D308N	CUL4A_uc010tjx.1_Missense_Mutation_p.D208N|CUL4A_uc010agu.2_Missense_Mutation_p.D169N|CUL4A_uc010tjz.1_5'UTR	NM_001008895	NP_001008895	Q13619	CUL4A_HUMAN	cullin 4A isoform 1	308					cell cycle arrest|DNA repair|G1/S transition of mitotic cell cycle|induction of apoptosis by intracellular signals|interspecies interaction between organisms|negative regulation of cell proliferation|ubiquitin-dependent protein catabolic process	Cul4A-RING ubiquitin ligase complex	ubiquitin protein ligase binding			central_nervous_system(2)|skin(1)	3	Lung NSC(43;0.0161)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0482)|all_epithelial(44;0.0148)|all_lung(25;0.0271)|Lung NSC(25;0.0977)|Breast(118;0.188)	all cancers(43;0.112)			CTCAGGGCTCGACCACTTACT	0.557													4	66					0	0	0.009096	0	0	
BCL8	606	broad.mit.edu	37	15	20872194	20872194	+	RNA	SNP	C	G	G			TCGA-BR-4187-01A-01D-1126-08	TCGA-BR-4187-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	0b45eb56-8286-4094-8bff-d0cf5c05cda9	30a6f1ff-df78-470a-b645-0e46c00252d8	g.chr15:20872194C>G	uc010tzd.1	-	4		c.893G>C								Homo sapiens mRNA; cDNA DKFZp686P1536 (from clone DKFZp686P1536).												0						aaaacaagttcttccttacag	0.085													3	7					0	0	0.004672	0	0	
HDC	3067	broad.mit.edu	37	15	50540522	50540522	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4187-01A-01D-1126-08	TCGA-BR-4187-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	0b45eb56-8286-4094-8bff-d0cf5c05cda9	30a6f1ff-df78-470a-b645-0e46c00252d8	g.chr15:50540522T>C	uc001zxz.2	-	10	1166	c.1060A>G	c.(1060-1062)AGC>GGC	p.S354G	HDC_uc001zxy.2_Missense_Mutation_p.S97G|HDC_uc010uff.1_Intron	NM_002112	NP_002103	P19113	DCHS_HUMAN	histidine decarboxylase	354					catecholamine biosynthetic process|histidine metabolic process		histidine decarboxylase activity			large_intestine(2)|skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)	6		all_lung(180;0.0138)		all cancers(107;1.12e-06)|GBM - Glioblastoma multiforme(94;9.95e-05)	L-Histidine(DB00117)|Pyridoxal Phosphate(DB00114)	AACCGTCGGCTCAGGGGGATC	0.522													8	53					0	0	0.003080	0	0	
WASH3P	374666	broad.mit.edu	37	15	102515299	102515299	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4187-01A-01D-1126-08	TCGA-BR-4187-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	0b45eb56-8286-4094-8bff-d0cf5c05cda9	30a6f1ff-df78-470a-b645-0e46c00252d8	g.chr15:102515299G>A	uc002cdi.2	+	9	1943	c.523G>A	c.(523-525)GGC>AGC	p.G175S	WASH3P_uc002cdl.2_Missense_Mutation_p.G175S|WASH3P_uc002cdk.2_RNA|WASH3P_uc002cdp.2_Missense_Mutation_p.G175S|WASH3P_uc010bpo.2_RNA|WASH3P_uc002cdq.2_RNA|WASH3P_uc002cdr.2_RNA	NR_003659				RecName: Full=WAS protein family homolog 2; AltName: Full=Protein FAM39B; AltName: Full=CXYorf1-like protein on chromosome 2;												0						TGGGGGCATCGGCAAGGCCAA	0.652													3	15					0	0	0.004672	0	0	
RGS11	8786	broad.mit.edu	37	16	321028	321028	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4187-01A-01D-1126-08	TCGA-BR-4187-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	0b45eb56-8286-4094-8bff-d0cf5c05cda9	30a6f1ff-df78-470a-b645-0e46c00252d8	g.chr16:321028C>T	uc002cgj.1	-	13	937	c.934G>A	c.(934-936)GTG>ATG	p.V312M	RGS11_uc002cgi.1_Missense_Mutation_p.V291M|RGS11_uc010bqs.1_Missense_Mutation_p.V301M|RGS11_uc002cgk.1_Missense_Mutation_p.V128M	NM_183337	NP_899180	O94810	RGS11_HUMAN	regulator of G-protein signalling 11 isoform 1	312	RGS.				G-protein coupled receptor protein signaling pathway|intracellular signal transduction|negative regulation of signal transduction|regulation of G-protein coupled receptor protein signaling pathway	cytoplasm|heterotrimeric G-protein complex	GTPase activator activity|signal transducer activity			lung(1)|pancreas(1)	2		all_cancers(16;6.71e-07)|all_epithelial(16;1.59e-06)|Hepatocellular(16;0.000105)|Lung NSC(18;0.00769)|all_lung(18;0.0186)				GCCCGCCCCACGGGGTCCTCC	0.682													4	19					0	0	0.014758	0	0	
GRIN2A	2903	broad.mit.edu	37	16	9862888	9862888	+	Silent	SNP	G	A	A			TCGA-BR-4187-01A-01D-1126-08	TCGA-BR-4187-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	0b45eb56-8286-4094-8bff-d0cf5c05cda9	30a6f1ff-df78-470a-b645-0e46c00252d8	g.chr16:9862888G>A	uc002czo.3	-	12	2963	c.2415C>T	c.(2413-2415)AAC>AAT	p.N805N	GRIN2A_uc010uym.1_Silent_p.N805N|GRIN2A_uc010uyn.1_Silent_p.N648N|GRIN2A_uc002czr.3_Silent_p.N805N	NM_001134407	NP_001127879	Q12879	NMDE1_HUMAN	N-methyl-D-aspartate receptor subunit 2A isoform	805	Extracellular (Potential).				response to ethanol	cell junction|N-methyl-D-aspartate selective glutamate receptor complex|outer membrane-bounded periplasmic space|postsynaptic membrane	N-methyl-D-aspartate selective glutamate receptor activity|zinc ion binding			skin(32)|NS(5)|ovary(4)|large_intestine(1)|lung(1)|breast(1)|kidney(1)	45					Felbamate(DB00949)|Glycine(DB00145)|L-Glutamic Acid(DB00142)|Loperamide(DB00836)|Memantine(DB01043)	TCATCACCTCGTTCTTCTCGT	0.552													6	77					0	0	0.006214	0	0	
OTOA	146183	broad.mit.edu	37	16	21726384	21726384	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4187-01A-01D-1126-08	TCGA-BR-4187-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	0b45eb56-8286-4094-8bff-d0cf5c05cda9	30a6f1ff-df78-470a-b645-0e46c00252d8	g.chr16:21726384C>T	uc002djh.2	+	13	1400	c.1399C>T	c.(1399-1401)CGC>TGC	p.R467C	uc002diq.3_Intron|OTOA_uc010vbj.1_Missense_Mutation_p.R388C|OTOA_uc002dji.2_Missense_Mutation_p.R143C|OTOA_uc010vbk.1_Missense_Mutation_p.R115C	NM_144672	NP_653273	Q7RTW8	OTOAN_HUMAN	otoancorin isoform 1	481					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)		CAGCATGAAACGCAAGGACAT	0.582													11	279					0	0	0.010729	0	0	
SPNS1	83985	broad.mit.edu	37	16	28993708	28993708	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4187-01A-01D-1126-08	TCGA-BR-4187-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	0b45eb56-8286-4094-8bff-d0cf5c05cda9	30a6f1ff-df78-470a-b645-0e46c00252d8	g.chr16:28993708G>A	uc010vdi.1	+	9	1137	c.997G>A	c.(997-999)GGA>AGA	p.G333R	uc010vct.1_Intron|SPNS1_uc002drx.2_Missense_Mutation_p.G260R|SPNS1_uc002dsa.2_Missense_Mutation_p.G333R|SPNS1_uc002drz.2_Missense_Mutation_p.G281R|SPNS1_uc010byp.2_Missense_Mutation_p.G259R|SPNS1_uc010byq.1_Missense_Mutation_p.G265R|LAT_uc010vdj.1_5'Flank|LAT_uc002dsb.2_5'Flank|LAT_uc002dsd.2_5'Flank|LAT_uc002dsc.2_5'Flank|LAT_uc010vdk.1_5'Flank|LAT_uc010vdl.1_5'Flank	NM_001142448	NP_001135920	Q9H2V7	SPNS1_HUMAN	spinster homolog 1 isoform 1	333	Helical; (Potential).				lipid transport|transmembrane transport	integral to membrane|mitochondrial inner membrane	protein binding				0						CTGCCTGACCGGAGTCCTGGG	0.652													5	78					0	0	0.001984	0	0	
BCKDK	10295	broad.mit.edu	37	16	31122413	31122413	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4187-01A-01D-1126-08	TCGA-BR-4187-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	0b45eb56-8286-4094-8bff-d0cf5c05cda9	30a6f1ff-df78-470a-b645-0e46c00252d8	g.chr16:31122413C>T	uc002eaw.3	+	9	1034	c.718C>T	c.(718-720)CGC>TGC	p.R240C	BCKDK_uc002eav.3_Missense_Mutation_p.R240C|BCKDK_uc010cah.2_RNA|BCKDK_uc010cai.2_Missense_Mutation_p.R240C	NM_005881	NP_005872	O14874	BCKD_HUMAN	branched chain ketoacid dehydrogenase kinase	240	Histidine kinase.				branched chain family amino acid catabolic process|peptidyl-histidine phosphorylation	mitochondrial alpha-ketoglutarate dehydrogenase complex	[3-methyl-2-oxobutanoate dehydrogenase (acetyl-transferring)] kinase activity|ATP binding|protein binding|protein serine/threonine kinase activity|two-component sensor activity			stomach(1)|breast(1)	2						TATCCGCAGACGCCTGTGTGA	0.433													8	37					0	0	0.008291	0	0	
KRT37	8688	broad.mit.edu	37	17	39580071	39580071	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4187-01A-01D-1126-08	TCGA-BR-4187-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	0b45eb56-8286-4094-8bff-d0cf5c05cda9	30a6f1ff-df78-470a-b645-0e46c00252d8	g.chr17:39580071G>A	uc002hwp.1	-	2	565	c.518C>T	c.(517-519)GCC>GTC	p.A173V	uc002hwo.1_RNA	NM_003770	NP_003761	O76014	KRT37_HUMAN	keratin 37	173	Rod.|Coil 1B.					intermediate filament	structural molecule activity			skin(1)	1		Breast(137;0.000496)				AATCAGCCTGGCATTCTCAGC	0.403													4	88					0	0	0.014758	0	0	
POTEC	388468	broad.mit.edu	37	18	14513764	14513764	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4187-01A-01D-1126-08	TCGA-BR-4187-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	0b45eb56-8286-4094-8bff-d0cf5c05cda9	30a6f1ff-df78-470a-b645-0e46c00252d8	g.chr18:14513764C>T	uc010dln.2	-	10	1884	c.1430G>A	c.(1429-1431)CGG>CAG	p.R477Q	POTEC_uc010xaj.1_RNA	NM_001137671	NP_001131143	B2RU33	POTEC_HUMAN	ANKRD26-like family B, member 2	477										skin(3)	3						AAGTTGTTTCCGGGTATCATT	0.358													4	70					0	0	0.009096	0	0	
NLRP5	126206	broad.mit.edu	37	19	56539525	56539525	+	Silent	SNP	C	T	T			TCGA-BR-4187-01A-01D-1126-08	TCGA-BR-4187-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	0b45eb56-8286-4094-8bff-d0cf5c05cda9	30a6f1ff-df78-470a-b645-0e46c00252d8	g.chr19:56539525C>T	uc002qmj.2	+	7	1926	c.1926C>T	c.(1924-1926)AGC>AGT	p.S642S	NLRP5_uc002qmi.2_Silent_p.S623S	NM_153447	NP_703148	P59047	NALP5_HUMAN	NACHT, LRR and PYD containing protein 5	642						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)		GCCTCGTGAGCGAAGACGTAA	0.557													4	61					0	0	0.009096	0	0	
PLB1	151056	broad.mit.edu	37	2	28785965	28785965	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4187-01A-01D-1126-08	TCGA-BR-4187-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	0b45eb56-8286-4094-8bff-d0cf5c05cda9	30a6f1ff-df78-470a-b645-0e46c00252d8	g.chr2:28785965C>T	uc002rmb.1	+	18	1205	c.1205C>T	c.(1204-1206)ACG>ATG	p.T402M	PLB1_uc010ezj.1_Missense_Mutation_p.T413M|PLB1_uc002rmc.2_Missense_Mutation_p.T90M	NM_153021	NP_694566	Q6P1J6	PLB1_HUMAN	phospholipase B1 precursor	402	4 X 308-326 AA approximate repeats.|2.|Extracellular (Potential).				lipid catabolic process|retinoid metabolic process|steroid metabolic process	apical plasma membrane|integral to membrane	lysophospholipase activity|phospholipase A2 activity|retinyl-palmitate esterase activity			ovary(4)|large_intestine(2)|skin(2)|breast(1)	9	Acute lymphoblastic leukemia(172;0.155)					GACTCTCTCACGGTAAGTGAC	0.502													6	50					0	0	0.001168	0	0	
Unknown	0	broad.mit.edu	37	2	96619736	96619736	+	RNA	SNP	T	C	C			TCGA-BR-4187-01A-01D-1126-08	TCGA-BR-4187-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	0b45eb56-8286-4094-8bff-d0cf5c05cda9	30a6f1ff-df78-470a-b645-0e46c00252d8	g.chr2:96619736T>C	uc010yug.1	-	14		c.1239A>G								Homo sapiens cDNA FLJ54441 complete cds, highly similar to Homo sapiens ankyrin repeat domain 36 (ANKRD36), mRNA.																		TGCAACAGCATCCGGTCTGTA	0.383													3	6					0	0	0.009096	0	0	
NMI	9111	broad.mit.edu	37	2	152128240	152128240	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4187-01A-01D-1126-08	TCGA-BR-4187-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	0b45eb56-8286-4094-8bff-d0cf5c05cda9	30a6f1ff-df78-470a-b645-0e46c00252d8	g.chr2:152128240T>C	uc002txi.2	-	7	971	c.641A>G	c.(640-642)GAC>GGC	p.D214G		NM_004688	NP_004679	Q13287	NMI_HUMAN	N-myc and STAT interactor	214					inflammatory response|JAK-STAT cascade|transcription from RNA polymerase II promoter	cytoplasm|nucleus	nucleotide binding|protein binding|transcription cofactor activity				0				BRCA - Breast invasive adenocarcinoma(221;0.0571)		CAAAATCTTGTCAGCCACTAA	0.294													8	41					0	0	0.003163	0	0	
KRTAP10-10	353333	broad.mit.edu	37	21	46057679	46057679	+	Silent	SNP	C	T	T			TCGA-BR-4187-01A-01D-1126-08	TCGA-BR-4187-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	0b45eb56-8286-4094-8bff-d0cf5c05cda9	30a6f1ff-df78-470a-b645-0e46c00252d8	g.chr21:46057679C>T	uc002zfq.2	+	1	407	c.345C>T	c.(343-345)TTC>TTT	p.F115F	C21orf29_uc002zfe.1_Intron|C21orf29_uc010gpv.1_Intron	NM_181688	NP_859016	P60014	KR10A_HUMAN	keratin associated protein 10-10	115	15 X 5 AA repeats of C-C-X(3).					keratin filament					0						ctgtgtgcttcgtgcctacct	0.343													9	148					0	0	0.004482	0	0	
GGT3P	2679	broad.mit.edu	37	22	18778612	18778612	+	RNA	SNP	C	T	T	rs1055042	by1000genomes	TCGA-BR-4187-01A-01D-1126-08	TCGA-BR-4187-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	0b45eb56-8286-4094-8bff-d0cf5c05cda9	30a6f1ff-df78-470a-b645-0e46c00252d8	g.chr22:18778612C>T	uc011ago.1	-	2		c.208G>A			GGT3P_uc011agp.1_RNA|GGT3P_uc002zob.1_RNA					Homo sapiens cDNA clone IMAGE:5761295, **** WARNING: chimeric clone ****.												0						GCGGCCACGGCAGCCCTGGTG	0.597													5	11					0	0	0.001984	0	0	
LOC96610	96610	broad.mit.edu	37	22	22664698	22664698	+	RNA	SNP	C	T	T			TCGA-BR-4187-01A-01D-1126-08	TCGA-BR-4187-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	0b45eb56-8286-4094-8bff-d0cf5c05cda9	30a6f1ff-df78-470a-b645-0e46c00252d8	g.chr22:22664698C>T	uc011aim.1	+	31		c.2213C>T			LOC96610_uc011aiq.1_RNA					Parts of antibodies, mostly variable regions.												0						GTCAGGAACGCGGACCACGGG	0.493													4	37					0	0	0.001168	0	0	
MCM2	4171	broad.mit.edu	37	3	127340016	127340016	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4187-01A-01D-1126-08	TCGA-BR-4187-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	0b45eb56-8286-4094-8bff-d0cf5c05cda9	30a6f1ff-df78-470a-b645-0e46c00252d8	g.chr3:127340016G>A	uc003ejp.2	+	15	2606	c.2549G>A	c.(2548-2550)CGC>CAC	p.R850H	MCM2_uc011bkm.1_Missense_Mutation_p.R720H|MCM2_uc010hsl.2_RNA|MCM2_uc011bkn.1_Missense_Mutation_p.R803H	NM_004526	NP_004517	P49736	MCM2_HUMAN	minichromosome maintenance complex component 2	850					cell cycle checkpoint|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle	chromatin|MCM complex	ATP binding|helicase activity|metal ion binding			ovary(3)|skin(1)	4						CAGCGCAACCGCTTTGGGGCC	0.542													7	58					0	0	0.003080	0	0	
MUC4	4585	broad.mit.edu	37	3	195507385	195507385	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4187-01A-01D-1126-08	TCGA-BR-4187-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	0b45eb56-8286-4094-8bff-d0cf5c05cda9	30a6f1ff-df78-470a-b645-0e46c00252d8	g.chr3:195507385G>A	uc011bto.1	-	3	11142	c.10682C>T	c.(10681-10683)GCA>GTA	p.A3561V	MUC4_uc003fva.2_5'Flank|MUC4_uc003fvb.2_5'Flank|MUC4_uc003fvc.2_5'Flank|MUC4_uc003fvd.2_5'Flank|MUC4_uc003fve.2_5'Flank|MUC4_uc010hzr.2_5'Flank|MUC4_uc011btf.1_5'Flank|MUC4_uc011btg.1_5'Flank|MUC4_uc011bth.1_5'Flank|MUC4_uc011bti.1_5'Flank|MUC4_uc011btj.1_5'Flank|MUC4_uc011btk.1_5'Flank|MUC4_uc011btl.1_5'Flank|MUC4_uc011btm.1_5'Flank|MUC4_uc011btn.1_5'Flank|MUC4_uc003fvo.2_Intron|MUC4_uc003fvp.2_Intron|MUC4_uc010hzu.1_Intron	NM_018406	NP_060876	Q99102	MUC4_HUMAN	mucin 4 isoform a	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment					cell-matrix adhesion	integral to plasma membrane|proteinaceous extracellular matrix	ErbB-2 class receptor binding|extracellular matrix constituent, lubricant activity				0	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		ACCTGTGGATGCTGAGGAAGT	0.572													3	6					0	0	0.003080	0	0	
MUC4	4585	broad.mit.edu	37	3	195513420	195513420	+	Silent	SNP	G	A	A	rs71321842	by1000genomes	TCGA-BR-4187-01A-01D-1126-08	TCGA-BR-4187-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	0b45eb56-8286-4094-8bff-d0cf5c05cda9	30a6f1ff-df78-470a-b645-0e46c00252d8	g.chr3:195513420G>A	uc011bto.1	-	2	5491	c.5031C>T	c.(5029-5031)CAC>CAT	p.H1677H	MUC4_uc003fvo.2_Intron|MUC4_uc003fvp.2_Intron|MUC4_uc010hzu.1_Intron	NM_018406	NP_060876	Q99102	MUC4_HUMAN	mucin 4 isoform a	471					cell-matrix adhesion	integral to plasma membrane|proteinaceous extracellular matrix	ErbB-2 class receptor binding|extracellular matrix constituent, lubricant activity				0	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GAGGGGTGGCGTGACCGGTGG	0.612													4	26					0	0	0.001168	0	0	
SH3TC1	54436	broad.mit.edu	37	4	8235216	8235216	+	Silent	SNP	C	T	T			TCGA-BR-4187-01A-01D-1126-08	TCGA-BR-4187-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	0b45eb56-8286-4094-8bff-d0cf5c05cda9	30a6f1ff-df78-470a-b645-0e46c00252d8	g.chr4:8235216C>T	uc003gkv.3	+	14	3359	c.3258C>T	c.(3256-3258)AGC>AGT	p.S1086S	SH3TC1_uc003gkw.3_Silent_p.S1010S|SH3TC1_uc003gkx.3_RNA|SH3TC1_uc003gky.2_RNA	NM_018986	NP_061859	Q8TE82	S3TC1_HUMAN	SH3 domain and tetratricopeptide repeats 1	1086							binding			large_intestine(2)|pancreas(1)	3						TGCGGCAGAGCGAGCTGGTGG	0.527													4	32					0	0	0.014758	0	0	
PCDHA13	56136	broad.mit.edu	37	5	140263466	140263466	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4187-01A-01D-1126-08	TCGA-BR-4187-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	0b45eb56-8286-4094-8bff-d0cf5c05cda9	30a6f1ff-df78-470a-b645-0e46c00252d8	g.chr5:140263466G>A	uc003lif.2	+	1	1613	c.1613G>A	c.(1612-1614)CGC>CAC	p.R538H	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhi.2_Intron|PCDHA4_uc003lhh.1_Intron|PCDHA5_uc003lhk.1_Intron|PCDHA5_uc003lhl.2_Intron|PCDHA6_uc003lhn.2_Intron|PCDHA6_uc003lho.2_Intron|PCDHA7_uc003lhq.2_Intron|PCDHA8_uc003lhs.2_Intron|PCDHA9_uc003lhu.2_Intron|PCDHA10_uc003lhw.2_Intron|PCDHA10_uc003lhx.2_Intron|PCDHA11_uc003lia.2_Intron|PCDHA12_uc003lic.2_Intron|PCDHA13_uc003lie.1_Missense_Mutation_p.R538H|PCDHA13_uc003lid.2_Missense_Mutation_p.R538H	NM_018904	NP_061727	Q9Y5I0	PCDAD_HUMAN	protocadherin alpha 13 isoform 1 precursor	538	Cadherin 5.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(3)|skin(2)|central_nervous_system(1)	6			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GTGAGCGCGCGCGACTCTGGC	0.682													10	59					0	0	0.008291	0	0	
OR2J3	442186	broad.mit.edu	37	6	29079853	29079853	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4187-01A-01D-1126-08	TCGA-BR-4187-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	0b45eb56-8286-4094-8bff-d0cf5c05cda9	30a6f1ff-df78-470a-b645-0e46c00252d8	g.chr6:29079853G>A	uc011dll.1	+	1	186	c.186G>A	c.(184-186)ATG>ATA	p.M62I		NM_001005216	NP_001005216	O76001	OR2J3_HUMAN	olfactory receptor, family 2, subfamily J,	62	Helical; Name=2; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0						ACACACCAATGTACTTCTTCC	0.458													17	194					0	0	0.007413	0	0	
HLA-J	3137	broad.mit.edu	37	6	29977377	29977377	+	Missense_Mutation	SNP	C	G	G			TCGA-BR-4187-01A-01D-1126-08	TCGA-BR-4187-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	0b45eb56-8286-4094-8bff-d0cf5c05cda9	30a6f1ff-df78-470a-b645-0e46c00252d8	g.chr6:29977377C>G	uc003rtl.3	+	5	758	c.396C>G	c.(394-396)TTC>TTG	p.F132L	HLA-G_uc011dmb.1_3'UTR|NCRNA00171_uc011dme.1_Intron|HLA-J_uc003nou.3_RNA|HLA-J_uc003nov.3_RNA					Homo sapiens major histocompatibility complex, class I, J (pseudogene), mRNA (cDNA clone IMAGE:4694038).												0						TTTGTGACTTCAAGAACCCTG	0.458													4	46					0	0	0.009096	0	0	
HLA-J	3137	broad.mit.edu	37	6	29977409	29977409	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4187-01A-01D-1126-08	TCGA-BR-4187-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	0b45eb56-8286-4094-8bff-d0cf5c05cda9	30a6f1ff-df78-470a-b645-0e46c00252d8	g.chr6:29977409T>C	uc003rtl.3	+	5	790	c.428T>C	c.(427-429)ATC>ACC	p.I143T	HLA-G_uc011dmb.1_3'UTR|NCRNA00171_uc011dme.1_Intron|HLA-J_uc003nou.3_RNA|HLA-J_uc003nov.3_RNA					Homo sapiens major histocompatibility complex, class I, J (pseudogene), mRNA (cDNA clone IMAGE:4694038).												0						TGCAAAGGCATCTGAATGTGT	0.512													3	29					0	0	0.001168	0	0	
PPT2	9374	broad.mit.edu	37	6	32123534	32123534	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4187-01A-01D-1126-08	TCGA-BR-4187-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	0b45eb56-8286-4094-8bff-d0cf5c05cda9	30a6f1ff-df78-470a-b645-0e46c00252d8	g.chr6:32123534C>T	uc003nzx.2	+	4	975	c.407C>T	c.(406-408)TCC>TTC	p.S136F	PRRT1_uc003nzu.2_5'Flank|uc003nzv.3_5'Flank|PPT2_uc003nzw.2_Missense_Mutation_p.S142F|PPT2_uc011dpi.1_RNA|PPT2_uc003nzy.1_RNA|PPT2_uc003nzz.2_Missense_Mutation_p.S136F|PPT2_uc003oaa.2_Missense_Mutation_p.S136F|PPT2_uc010jtu.1_Missense_Mutation_p.S136F	NM_005155	NP_005146	Q9UMR5	PPT2_HUMAN	palmitoyl-protein thioesterase 2 isoform a	136					protein modification process	lysosome	palmitoyl-(protein) hydrolase activity				0						ATCTCCCTCTCCTCTCCACAG	0.527													11	81					0	0	0.013537	0	0	
RPS6KA2	6196	broad.mit.edu	37	6	166844008	166844008	+	Missense_Mutation	SNP	G	A	A	rs145694057		TCGA-BR-4187-01A-01D-1126-08	TCGA-BR-4187-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	0b45eb56-8286-4094-8bff-d0cf5c05cda9	30a6f1ff-df78-470a-b645-0e46c00252d8	g.chr6:166844008G>A	uc003qvb.1	-	16	1733	c.1514C>T	c.(1513-1515)TCG>TTG	p.S505L	RPS6KA2_uc011ego.1_Missense_Mutation_p.S416L|RPS6KA2_uc010kkl.1_Missense_Mutation_p.S416L|RPS6KA2_uc003qvc.1_Missense_Mutation_p.S513L|RPS6KA2_uc003qvd.1_Missense_Mutation_p.S530L	NM_021135	NP_066958	Q15349	KS6A2_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide	505	Protein kinase 2.				axon guidance|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|stress-activated MAPK cascade|synaptic transmission|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|nucleoplasm	ATP binding|magnesium ion binding|protein serine/threonine kinase activity			ovary(2)|lung(2)|skin(2)|large_intestine(1)|central_nervous_system(1)	8		Breast(66;2.04e-05)|Ovarian(120;0.0652)|Prostate(117;0.105)		OV - Ovarian serous cystadenocarcinoma(33;2.76e-18)|GBM - Glioblastoma multiforme(31;9.94e-06)|BRCA - Breast invasive adenocarcinoma(81;1.36e-05)		TTCGCGCTCCGAGAAGTATCT	0.597													7	67					0	0	0.003080	0	0	
LMTK2	22853	broad.mit.edu	37	7	97766742	97766742	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4187-01A-01D-1126-08	TCGA-BR-4187-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	0b45eb56-8286-4094-8bff-d0cf5c05cda9	30a6f1ff-df78-470a-b645-0e46c00252d8	g.chr7:97766742A>C	uc003upd.1	+	2	512	c.219A>C	c.(217-219)GAA>GAC	p.E73D		NM_014916	NP_055731	Q8IWU2	LMTK2_HUMAN	lemur tyrosine kinase 2 precursor	73					early endosome to late endosome transport|endocytic recycling|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|protein autophosphorylation|receptor recycling|transferrin transport	early endosome|Golgi apparatus|integral to membrane|perinuclear region of cytoplasm|recycling endosome	ATP binding|myosin VI binding|protein phosphatase inhibitor activity|protein serine/threonine kinase activity|protein tyrosine kinase activity			lung(9)|stomach(3)|pancreas(2)|large_intestine(1)|breast(1)	16	all_cancers(62;3.23e-09)|all_epithelial(64;7.65e-10)|Lung NSC(181;0.00902)|all_lung(186;0.0104)|Esophageal squamous(72;0.0125)					AGGACCCAGAAATAGACTTTA	0.368													4	67					0	0	0.009096	0	0	
NUP205	23165	broad.mit.edu	37	7	135307616	135307616	+	Silent	SNP	C	T	T	rs144174512		TCGA-BR-4187-01A-01D-1126-08	TCGA-BR-4187-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	0b45eb56-8286-4094-8bff-d0cf5c05cda9	30a6f1ff-df78-470a-b645-0e46c00252d8	g.chr7:135307616C>T	uc003vsw.2	+	31	4453	c.4422C>T	c.(4420-4422)GGC>GGT	p.G1474G	NUP205_uc003vsx.2_RNA	NM_015135	NP_055950	Q92621	NU205_HUMAN	nucleoporin 205kDa	1474					carbohydrate metabolic process|glucose transport|mRNA transport|protein import into nucleus, docking|regulation of glucose transport|transmembrane transport|viral reproduction	nuclear pore	protein binding			ovary(3)|breast(1)|central_nervous_system(1)|skin(1)	6						AAAGTTATGGCGCCGCCCTCA	0.398													6	66					0	0	0.004482	0	0	
AMAC1L2	83650	broad.mit.edu	37	8	11189042	11189042	+	Missense_Mutation	SNP	G	A	A	rs142654795	byFrequency	TCGA-BR-4187-01A-01D-1126-08	TCGA-BR-4187-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	0b45eb56-8286-4094-8bff-d0cf5c05cda9	30a6f1ff-df78-470a-b645-0e46c00252d8	g.chr8:11189042G>A	uc003wtp.1	+	1	548	c.427G>A	c.(427-429)GCT>ACT	p.A143T		NM_054028	NP_473369	Q96KT7	AMCL2_HUMAN	acyl-malonyl condensing enzyme	143	DUF6 1.					integral to membrane					0			STAD - Stomach adenocarcinoma(15;0.00676)	COAD - Colon adenocarcinoma(149;0.0563)		CGTATGCTCCGCTGTCCTCAC	0.582													14	152					0	0	0.003163	0	0	
ZFPM2	23414	broad.mit.edu	37	8	106813401	106813401	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4187-01A-01D-1126-08	TCGA-BR-4187-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	0b45eb56-8286-4094-8bff-d0cf5c05cda9	30a6f1ff-df78-470a-b645-0e46c00252d8	g.chr8:106813401G>A	uc003ymd.2	+	8	1114	c.1091G>A	c.(1090-1092)CGA>CAA	p.R364Q	ZFPM2_uc011lhs.1_Missense_Mutation_p.R95Q|uc003yme.1_5'Flank	NM_012082	NP_036214	Q8WW38	FOG2_HUMAN	zinc finger protein, multitype 2	364	C2H2-type 3.				blood coagulation|negative regulation of fat cell differentiation|outflow tract septum morphogenesis|right ventricular cardiac muscle tissue morphogenesis|ventricular septum morphogenesis	nucleoplasm	DNA binding|RNA polymerase II transcription coactivator activity|transcription corepressor activity|transcription factor binding|zinc ion binding			ovary(4)|large_intestine(1)	5			OV - Ovarian serous cystadenocarcinoma(57;8.28e-08)			GCTGCCTTCCGATGTAATCAC	0.507													13	139					0	0	0.020292	0	0	
TAF1L	138474	broad.mit.edu	37	9	32630718	32630718	+	Silent	SNP	G	A	A			TCGA-BR-4187-01A-01D-1126-08	TCGA-BR-4187-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	0b45eb56-8286-4094-8bff-d0cf5c05cda9	30a6f1ff-df78-470a-b645-0e46c00252d8	g.chr9:32630718G>A	uc003zrg.1	-	1	4950	c.4860C>T	c.(4858-4860)TAC>TAT	p.Y1620Y	uc003zrh.1_5'Flank	NM_153809	NP_722516	Q8IZX4	TAF1L_HUMAN	TBP-associated factor RNA polymerase 1-like	1620					male meiosis|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter|transcription initiation, DNA-dependent	transcription factor TFIID complex	DNA binding|histone acetyltransferase activity|protein serine/threonine kinase activity|TBP-class protein binding			lung(8)|skin(6)|central_nervous_system(4)|large_intestine(3)|ovary(2)|stomach(1)|breast(1)|pancreas(1)	26			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.00301)		TAATTGTCTGGTAACAGATGT	0.393													10	114					0	0	0.006214	0	0	
FRMPD1	22844	broad.mit.edu	37	9	37711391	37711391	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4187-01A-01D-1126-08	TCGA-BR-4187-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	0b45eb56-8286-4094-8bff-d0cf5c05cda9	30a6f1ff-df78-470a-b645-0e46c00252d8	g.chr9:37711391C>T	uc004aag.1	+	5	451	c.407C>T	c.(406-408)TCG>TTG	p.S136L	FRMPD1_uc004aah.1_Missense_Mutation_p.S136L	NM_014907	NP_055722	Q5SYB0	FRPD1_HUMAN	FERM and PDZ domain containing 1	136						cytoskeleton|cytosol|plasma membrane				ovary(4)|central_nervous_system(2)|skin(2)|breast(1)	9				GBM - Glioblastoma multiforme(29;0.00655)		CGCTGCACGTCGGTAAATCTC	0.438													10	174					0	0	0.010729	0	0	
Unknown	0	broad.mit.edu	37	9	66454789	66454789	+	RNA	SNP	T	C	C			TCGA-BR-4187-01A-01D-1126-08	TCGA-BR-4187-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	0b45eb56-8286-4094-8bff-d0cf5c05cda9	30a6f1ff-df78-470a-b645-0e46c00252d8	g.chr9:66454789T>C	uc010mng.1	-	2		c.508A>G			uc004aec.2_5'Flank					Homo sapiens cDNA, FLJ98602.																		CACACAGGAGTCACACTCAGG	0.522													3	23					0	0	0.009096	0	0	
Unknown	0	broad.mit.edu	37	9	66454904	66454904	+	RNA	SNP	C	T	T			TCGA-BR-4187-01A-01D-1126-08	TCGA-BR-4187-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	0b45eb56-8286-4094-8bff-d0cf5c05cda9	30a6f1ff-df78-470a-b645-0e46c00252d8	g.chr9:66454904C>T	uc010mng.1	-	2		c.393G>A			uc004aec.2_5'Flank					Homo sapiens cDNA, FLJ98602.																		GACTGTTTCGCGAGCTCTGTG	0.522													3	15					0	0	0.009096	0	0	
Unknown	0	broad.mit.edu	37	9	66455009	66455009	+	RNA	SNP	T	C	C			TCGA-BR-4187-01A-01D-1126-08	TCGA-BR-4187-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	0b45eb56-8286-4094-8bff-d0cf5c05cda9	30a6f1ff-df78-470a-b645-0e46c00252d8	g.chr9:66455009T>C	uc010mng.1	-	2		c.288A>G			uc004aec.2_5'Flank					Homo sapiens cDNA, FLJ98602.																		AGACTCCCCATTTTGCAGGAA	0.498													4	54					0	0	0.014758	0	0	
Unknown	0	broad.mit.edu	37	9	66465815	66465815	+	RNA	SNP	C	T	T	rs113425371	by1000genomes	TCGA-BR-4187-01A-01D-1126-08	TCGA-BR-4187-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	0b45eb56-8286-4094-8bff-d0cf5c05cda9	30a6f1ff-df78-470a-b645-0e46c00252d8	g.chr9:66465815C>T	uc004aec.2	+	3		c.448C>T								Homo sapiens, clone IMAGE:5213378, mRNA.																		CTCTTTTTACCACACTGTCTA	0.328													3	26					0	0	0.009096	0	0	
Unknown	0	broad.mit.edu	37	9	66465820	66465820	+	RNA	SNP	T	A	A	rs112593313	by1000genomes	TCGA-BR-4187-01A-01D-1126-08	TCGA-BR-4187-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	0b45eb56-8286-4094-8bff-d0cf5c05cda9	30a6f1ff-df78-470a-b645-0e46c00252d8	g.chr9:66465820T>A	uc004aec.2	+	3		c.453T>A								Homo sapiens, clone IMAGE:5213378, mRNA.																		TTTACCACACTGTCTATATAC	0.323													3	25					0	0	0.009096	0	0	
Unknown	0	broad.mit.edu	37	9	66466237	66466237	+	RNA	SNP	C	G	G			TCGA-BR-4187-01A-01D-1126-08	TCGA-BR-4187-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	0b45eb56-8286-4094-8bff-d0cf5c05cda9	30a6f1ff-df78-470a-b645-0e46c00252d8	g.chr9:66466237C>G	uc004aec.2	+	3		c.870C>G								Homo sapiens, clone IMAGE:5213378, mRNA.																		gagagccggacagactccatt	0.085													3	28					0	0	0.003080	0	0	
Unknown	0	broad.mit.edu	37	9	90745740	90745740	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4187-01A-01D-1126-08	TCGA-BR-4187-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	0b45eb56-8286-4094-8bff-d0cf5c05cda9	30a6f1ff-df78-470a-b645-0e46c00252d8	g.chr9:90745740A>G	uc011lti.1	-	4	2241	c.2212T>C	c.(2212-2214)TGT>CGT	p.C738R	uc004apx.1_5'Flank					SubName: Full=cDNA FLJ59639;																		AACTGCTTACATGCAGGTGAG	0.562													6	41					0	0	0.001168	0	0	
TNC	3371	broad.mit.edu	37	9	117808747	117808747	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4187-01A-01D-1126-08	TCGA-BR-4187-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	0b45eb56-8286-4094-8bff-d0cf5c05cda9	30a6f1ff-df78-470a-b645-0e46c00252d8	g.chr9:117808747T>G	uc004bjj.3	-	17	5429	c.5067A>C	c.(5065-5067)GAA>GAC	p.E1689D	TNC_uc010mvf.2_Intron	NM_002160	NP_002151	P24821	TENA_HUMAN	tenascin C precursor	1689	Fibronectin type-III 12.				cell adhesion|response to wounding|signal transduction	extracellular space	receptor binding|syndecan binding			central_nervous_system(4)|upper_aerodigestive_tract(1)|ovary(1)|skin(1)	7						TTCCATAGAGTTCAATTTCGT	0.443													5	141					0	0	0.001984	0	0	
Unknown	0	broad.mit.edu	37	MT	13350	13350	+	RNA	SNP	A	G	G			TCGA-BR-4187-01A-01D-1126-08	TCGA-BR-4187-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	0b45eb56-8286-4094-8bff-d0cf5c05cda9	30a6f1ff-df78-470a-b645-0e46c00252d8	g.chrM:13350A>G	uc004cox.3	+	1		c.1014A>G			uc004coy.2_5'Flank|uc004coz.1_5'Flank					Homo sapiens NADH dehydrogenase subunit 5 (MTND5) mRNA, RNA 5, complete cds; mitochondrial gene for mitochondrial product.																		TTCAAAGCCATACTATTTATG	0.428													262	600					0	0	0.014410	0	0	
SLC9A6	10479	broad.mit.edu	37	X	135084305	135084305	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4187-01A-01D-1126-08	TCGA-BR-4187-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	0b45eb56-8286-4094-8bff-d0cf5c05cda9	30a6f1ff-df78-470a-b645-0e46c00252d8	g.chrX:135084305G>T	uc004ezj.2	+	6	812	c.736G>T	c.(736-738)GTT>TTT	p.V246F	SLC9A6_uc004ezk.2_Missense_Mutation_p.V278F|SLC9A6_uc011mvx.1_Missense_Mutation_p.V226F	NM_006359	NP_006350	Q92581	SL9A6_HUMAN	solute carrier family 9 (sodium/hydrogen	246	Helical; (Potential).				regulation of pH	early endosome membrane|endoplasmic reticulum membrane|integral to membrane|microsome|plasma membrane|recycling endosome membrane	sodium:hydrogen antiporter activity			ovary(1)	1	Acute lymphoblastic leukemia(192;0.000127)					TCAAGTTGATGTTGAACTCTA	0.353													16	72					6.49762e-13	1.09647e-12	0.006122	1	0	
CHRM3	1131	broad.mit.edu	37	1	239549887	239549887	+	RNA	DEL	G	-	-			TCGA-BR-4187-01A-01D-1126-08	TCGA-BR-4187-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	0b45eb56-8286-4094-8bff-d0cf5c05cda9	30a6f1ff-df78-470a-b645-0e46c00252d8	g.chr1:239549887delG	uc001hyo.1	+	1		c.23delG						P20309	ACM3_HUMAN	Homo sapiens clone N10 NTera2D1 teratocarcinoma, m3 muscarinic acetylcholine receptor mRNA, partial cds.						cell proliferation|energy reserve metabolic process|nervous system development|protein modification process|regulation of insulin secretion	basolateral plasma membrane|cell junction|integral to plasma membrane|postsynaptic membrane	muscarinic acetylcholine receptor activity|phosphatidylinositol phospholipase C activity			ovary(4)|skin(1)	5	Ovarian(103;0.127)	all_cancers(173;0.00567)|all_neural(198;0.203)	OV - Ovarian serous cystadenocarcinoma(106;0.00989)		Anisotropine Methylbromide(DB00517)|Atropine(DB00572)|Benzquinamide(DB00767)|Cevimeline(DB00185)|Cryptenamine(DB00785)|Cyclizine(DB01176)|Darifenacin(DB00496)|Diphemanil Methylsulfate(DB00729)|Diphenidol(DB01231)|Homatropine Methylbromide(DB00725)|Methotrimeprazine(DB01403)|Metixene(DB00340)|Olanzapine(DB00334)|Oxybutynin(DB01062)|Oxyphencyclimine(DB00383)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Solifenacin(DB01591)|Thiethylperazine(DB00372)|Tiotropium(DB01409)|Tolterodine(DB01036)|Tridihexethyl(DB00505)	CTCTCAGTCCGGggaggagga	0.493													2	4	---	---	---	---						.
RPGR	6103	broad.mit.edu	37	X	38145532	38145534	+	In_Frame_Del	DEL	TCC	-	-			TCGA-BR-4187-01A-01D-1126-08	TCGA-BR-4187-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	0b45eb56-8286-4094-8bff-d0cf5c05cda9	30a6f1ff-df78-470a-b645-0e46c00252d8	g.chrX:38145532_38145534delTCC	uc004ded.1	-	15	2886_2888	c.2718_2720delGGA	c.(2716-2721)GAGGAA>GAA	p.906_907EE>E	RPGR_uc004deb.2_Intron|RPGR_uc004dea.2_Intron|RPGR_uc004dec.2_Intron	NM_001034853	NP_001030025	Q92834	RPGR_HUMAN	retinitis pigmentosa GTPase regulator isoform C	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment					intracellular protein transport|response to stimulus|visual perception	Golgi apparatus|photoreceptor outer segment	guanyl-nucleotide exchange factor activity|protein binding			ovary(1)	1						cccttctccttcctcttctccct	0.000													3	6	---	---	---	---						.
