Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	t_alt_count	t_ref_count	validation_status	validation_method	validation_tumor_sample	validation_alt_allele	filter
CLSTN1	22883	broad.mit.edu	37	1	9801267	9801267	+	Silent	SNP	C	T	T	rs149205224		TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:9801267C>T	uc001aqh.2	-	10	2163	c.1404G>A	c.(1402-1404)CCG>CCA	p.P468P	CLSTN1_uc001aqi.2_Silent_p.P458P|CLSTN1_uc010oag.1_Silent_p.P468P	NM_001009566	NP_001009566	O94985	CSTN1_HUMAN	calsyntenin 1 isoform 1	468	Extracellular (Potential).				homophilic cell adhesion	cell junction|cell projection|endoplasmic reticulum membrane|Golgi membrane|integral to membrane|nucleus|postsynaptic membrane	calcium ion binding			skin(1)	1	all_lung(157;0.222)	all_lung(284;4.03e-05)|Lung NSC(185;6.93e-05)|Renal(390;0.000147)|Colorectal(325;0.00205)|Breast(348;0.00314)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0234)|Colorectal(212;8.36e-08)|COAD - Colon adenocarcinoma(227;1.93e-05)|Kidney(185;0.000342)|BRCA - Breast invasive adenocarcinoma(304;0.000949)|KIRC - Kidney renal clear cell carcinoma(229;0.00122)|STAD - Stomach adenocarcinoma(132;0.00644)|READ - Rectum adenocarcinoma(331;0.0419)		GAGTCACACTCGGGAATTCTA	0.527													14	80	---	---	---	---	PASS
MST1P9	11223	broad.mit.edu	37	1	17085908	17085908	+	Intron	SNP	C	G	G	rs1805293	by1000genomes	TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17085908C>G	uc010ock.1	-						CROCC_uc009voy.1_Intron|MST1P9_uc001azp.3_5'UTR	NR_002729				SubName: Full=Hepatocyte growth factor-like protein homolog;												0						AGCAGGCGCTCCACTCAGCCC	0.701													7	24	---	---	---	---	PASS
EIF4G3	8672	broad.mit.edu	37	1	21221941	21221941	+	Silent	SNP	G	A	A			TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:21221941G>A	uc001bec.2	-	12	2141	c.1885C>T	c.(1885-1887)CTG>TTG	p.L629L	EIF4G3_uc010odi.1_Silent_p.L233L|EIF4G3_uc010odj.1_Silent_p.L628L|EIF4G3_uc009vpz.2_Silent_p.L349L|EIF4G3_uc001bed.2_Silent_p.L629L|EIF4G3_uc001bef.2_Silent_p.L628L|EIF4G3_uc001bee.2_Silent_p.L635L	NM_003760	NP_003751	O43432	IF4G3_HUMAN	eukaryotic translation initiation factor 4	629	EIF4E-binding (By similarity).				interspecies interaction between organisms|regulation of translational initiation|RNA metabolic process	eukaryotic translation initiation factor 4F complex	protein binding|RNA cap binding|translation initiation factor activity			skin(1)	1		all_lung(284;2.61e-06)|Lung NSC(340;2.81e-06)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00149)|Ovarian(437;0.00338)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.023)|COAD - Colon adenocarcinoma(152;5.42e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000327)|GBM - Glioblastoma multiforme(114;0.000696)|Kidney(64;0.0018)|STAD - Stomach adenocarcinoma(196;0.00644)|KIRC - Kidney renal clear cell carcinoma(64;0.0185)|READ - Rectum adenocarcinoma(331;0.124)|Lung(427;0.191)		AAGTCCAGCAGAAACTCCCTG	0.453													16	131	---	---	---	---	PASS
ZSCAN20	7579	broad.mit.edu	37	1	33956856	33956856	+	Missense_Mutation	SNP	C	A	A			TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:33956856C>A	uc001bxj.3	+	6	1165	c.998C>A	c.(997-999)ACT>AAT	p.T333N	ZSCAN20_uc001bxk.2_Missense_Mutation_p.T279N|ZSCAN20_uc009vui.2_Missense_Mutation_p.T333N	NM_145238	NP_660281	P17040	ZSC20_HUMAN	zinc finger protein 31	333					viral reproduction	mitochondrion|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)|central_nervous_system(1)|pancreas(1)	4		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.211)				GAGACCAAGACTTTCCTGGCA	0.517													11	75	---	---	---	---	PASS
DENND2C	163259	broad.mit.edu	37	1	115144173	115144173	+	Missense_Mutation	SNP	A	C	C			TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:115144173A>C	uc001efd.1	-	13	2473	c.1771T>G	c.(1771-1773)TAC>GAC	p.Y591D	DENND2C_uc001eez.2_RNA|DENND2C_uc001efc.1_Missense_Mutation_p.Y534D	NM_198459	NP_940861	Q68D51	DEN2C_HUMAN	DENN/MADD domain containing 2C	591	DENN.									skin(3)	3	all_epithelial(7;9.54e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;4.64e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)		ACCATGCAGTATACCTCAGGG	0.363													70	329	---	---	---	---	PASS
PDE4DIP	9659	broad.mit.edu	37	1	144912241	144912241	+	Missense_Mutation	SNP	C	A	A			TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144912241C>A	uc001elw.3	-	15	2325	c.2034G>T	c.(2032-2034)CAG>CAT	p.Q678H	NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Missense_Mutation_p.Q744H|PDE4DIP_uc001emc.1_Missense_Mutation_p.Q678H|PDE4DIP_uc001emd.1_Missense_Mutation_p.Q678H|PDE4DIP_uc001emb.1_Missense_Mutation_p.Q841H|PDE4DIP_uc001eme.1_Missense_Mutation_p.Q207H|PDE4DIP_uc001emf.1_Missense_Mutation_p.Q463H	NM_014644	NP_055459	Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein isoform	678	Potential.				cellular protein complex assembly	centrosome|Golgi apparatus|myofibril|nucleus	enzyme binding			ovary(4)|haematopoietic_and_lymphoid_tissue(1)	5				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		GGCGCAGGGCCTGTAATTCTG	0.433			T	PDGFRB	MPD								12	97	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	1	151740624	151740624	+	IGR	SNP	T	G	G			TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151740624T>G								OAZ3 (-3181 upstream) : OAZ3 (-5179 downstream)																							CTCCCAGACCTCTGCCCATTG	0.567													13	58	---	---	---	---	PASS
MEF2D	4209	broad.mit.edu	37	1	156446973	156446973	+	Missense_Mutation	SNP	C	T	T			TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156446973C>T	uc001fpc.2	-	7	1076	c.686G>A	c.(685-687)CGG>CAG	p.R229Q	MEF2D_uc001fpb.2_Missense_Mutation_p.R229Q|MEF2D_uc001fpd.2_Missense_Mutation_p.R229Q|MEF2D_uc001fpe.1_Missense_Mutation_p.R229Q|MEF2D_uc009wsa.2_RNA	NM_005920	NP_005911	Q14814	MEF2D_HUMAN	myocyte enhancer factor 2D	229					apoptosis|muscle organ development|nervous system development|positive regulation of transcription from RNA polymerase II promoter	nucleus	activating transcription factor binding|histone deacetylase binding|RNA polymerase II regulatory region sequence-specific DNA binding|sequence-specific DNA binding RNA polymerase II transcription factor activity			ovary(1)	1	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					AGGGGAAGCCCGAGCACTGAC	0.552													4	30	---	---	---	---	PASS
C1orf157	284573	broad.mit.edu	37	1	204006475	204006475	+	Intron	SNP	A	C	C			TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:204006475A>C	uc001haj.2	-						C1orf157_uc001hak.2_RNA|C1orf157_uc010pqo.1_RNA	NR_027902				Homo sapiens cDNA FLJ40343 fis, clone TESTI2032774.												0	all_cancers(21;0.083)|Breast(84;0.193)|all_epithelial(62;0.21)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|BRCA - Breast invasive adenocarcinoma(75;0.0754)|Kidney(21;0.0934)|Epithelial(59;0.233)			TCAGCTGCCAATCACTGGAAG	0.547													3	23	---	---	---	---	PASS
SIPA1L2	57568	broad.mit.edu	37	1	232651061	232651061	+	Nonsense_Mutation	SNP	C	A	A			TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:232651061C>A	uc001hvg.2	-	1	183	c.25G>T	c.(25-27)GAA>TAA	p.E9*		NM_020808	NP_065859	Q9P2F8	SI1L2_HUMAN	signal-induced proliferation-associated 1 like	9					regulation of small GTPase mediated signal transduction	intracellular	GTPase activator activity			ovary(2)|central_nervous_system(2)|pancreas(1)|skin(1)	6		all_cancers(173;0.00605)|Prostate(94;0.128)|all_epithelial(177;0.186)				TGCTTCTCTTCTTGTGACTGC	0.453													5	60	---	---	---	---	PASS
PFN4	375189	broad.mit.edu	37	2	24338472	24338472	+	Missense_Mutation	SNP	A	T	T			TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:24338472A>T	uc002rfa.1	-	5	547	c.371T>A	c.(370-372)CTA>CAA	p.L124Q	LOC375190_uc002rew.2_Intron	NM_199346	NP_955378	Q8NHR9	PROF4_HUMAN	profilin family, member 4	124					actin cytoskeleton organization	actin cytoskeleton|cytoplasm	actin binding			ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TTTTTTTCTTAGGTAGTCTCC	0.274													20	86	---	---	---	---	PASS
XPO1	7514	broad.mit.edu	37	2	61706022	61706022	+	Missense_Mutation	SNP	T	C	C			TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61706022T>C	uc002sbj.2	-	25	3877	c.3149A>G	c.(3148-3150)CAT>CGT	p.H1050R	XPO1_uc010fcl.2_Missense_Mutation_p.H1046R|XPO1_uc010ypn.1_Missense_Mutation_p.H1046R|XPO1_uc002sbk.2_Missense_Mutation_p.H611R|XPO1_uc002sbg.2_Missense_Mutation_p.H247R|XPO1_uc002sbh.2_Missense_Mutation_p.H697R	NM_003400	NP_003391	O14980	XPO1_HUMAN	exportin 1	1050					intracellular protein transport|mitotic prometaphase|mRNA metabolic process|mRNA transport|viral genome transport in host cell|viral infectious cycle	annulate lamellae|Cajal body|cytosol|kinetochore|nuclear envelope|nucleolus|ribonucleoprotein complex	protein binding|protein transporter activity|RNA binding			ovary(1)|haematopoietic_and_lymphoid_tissue(1)|central_nervous_system(1)|skin(1)	4			LUSC - Lung squamous cell carcinoma(7;5.71e-05)|Epithelial(17;0.0662)|all cancers(80;0.226)			TTGACGTTTATGTTTCTCTTC	0.378													26	84	---	---	---	---	PASS
NCRNA00164	554226	broad.mit.edu	37	2	132912316	132912316	+	RNA	SNP	G	A	A			TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:132912316G>A	uc002tti.3	-	4		c.780C>T			NCRNA00164_uc002ttj.3_RNA	NR_027019				Homo sapiens non-protein coding RNA 164, mRNA (cDNA clone IMAGE:5169389), with apparent retained intron.												0						TTTCCTTATGGCCAGTAAAAG	0.294													3	6	---	---	---	---	PASS
DYNC1I2	1781	broad.mit.edu	37	2	172604426	172604426	+	3'UTR	SNP	G	C	C			TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:172604426G>C	uc002uha.1	+	18					DYNC1I2_uc002uhc.2_3'UTR|DYNC1I2_uc002uhb.1_3'UTR|DYNC1I2_uc010zds.1_3'UTR|DYNC1I2_uc002uhe.1_3'UTR|DYNC1I2_uc002uhf.1_3'UTR|DYNC1I2_uc010zdt.1_3'UTR|DYNC1I2_uc002uhg.1_3'UTR|DYNC1I2_uc010zdu.1_3'UTR	NM_001378	NP_001369	Q13409	DC1I2_HUMAN	dynein, cytoplasmic 1, intermediate chain 2						G2/M transition of mitotic cell cycle|interspecies interaction between organisms|microtubule-based movement|transport	centrosome|cytosol|dynein complex|microtubule|vesicle	microtubule motor activity			ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(117;0.198)			TGTAACTAGTGGATTTGGGAA	0.403													4	23	---	---	---	---	PASS
GLS	2744	broad.mit.edu	37	2	191797463	191797463	+	Intron	SNP	T	A	A			TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:191797463T>A	uc002usf.2	+						GLS_uc002use.2_Missense_Mutation_p.Y558N|GLS_uc002usg.1_Missense_Mutation_p.Y219N|GLS_uc002ush.2_Intron|GLS_uc010zgi.1_Intron|GLS_uc010zgj.1_Intron	NM_014905	NP_055720	O94925	GLSK_HUMAN	glutaminase precursor						cellular amino acid biosynthetic process|glutamate secretion|glutamine catabolic process|neurotransmitter secretion	mitochondrial matrix	glutaminase activity			ovary(1)|skin(1)	2			OV - Ovarian serous cystadenocarcinoma(117;0.00625)|Epithelial(96;0.0744)|all cancers(119;0.181)		L-Glutamic Acid(DB00142)|L-Glutamine(DB00130)	ACCATTGGACTATGAAAGTCT	0.348													7	30	---	---	---	---	PASS
CNOT10	25904	broad.mit.edu	37	3	32750281	32750281	+	Silent	SNP	T	A	A			TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:32750281T>A	uc003cfc.1	+	4	654	c.399T>A	c.(397-399)GGT>GGA	p.G133G	CNOT10_uc011axi.1_5'UTR|CNOT10_uc003cfd.1_Silent_p.G133G|CNOT10_uc003cfe.1_Silent_p.G133G|CNOT10_uc010hfv.1_RNA|CNOT10_uc011axj.1_Silent_p.G193G|CNOT10_uc010hfw.1_5'UTR	NM_015442	NP_056257	Q9H9A5	CNOTA_HUMAN	CCR4-NOT transcription complex, subunit 10	133					nuclear-transcribed mRNA poly(A) tail shortening	cytosol	protein binding			central_nervous_system(1)|skin(1)	2						TATCAGTTGGTGAAAAACTTT	0.353													19	69	---	---	---	---	PASS
SCN10A	6336	broad.mit.edu	37	3	38798548	38798548	+	Silent	SNP	G	T	T			TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:38798548G>T	uc003ciq.2	-	8	1053	c.1053C>A	c.(1051-1053)CGC>CGA	p.R351R		NM_006514	NP_006505	Q9Y5Y9	SCNAA_HUMAN	sodium channel, voltage-gated, type X, alpha	351	I.				sensory perception	voltage-gated sodium channel complex				ovary(5)|skin(3)|large_intestine(1)|kidney(1)	10				KIRC - Kidney renal clear cell carcinoma(284;0.0769)|Kidney(284;0.0945)	Benzocaine(DB01086)|Bupivacaine(DB00297)|Chloroprocaine(DB01161)|Cocaine(DB00907)|Dibucaine(DB00527)|Dyclonine(DB00645)|Hexylcaine(DB00473)|Levobupivacaine(DB01002)|Lidocaine(DB00281)|Mepivacaine(DB00961)|Oxybuprocaine(DB00892)|Procaine(DB00721)|Proparacaine(DB00807)|Ropivacaine(DB00296)	GTGTCATGAGGCGGAACAGTG	0.522													19	47	---	---	---	---	PASS
TWF2	11344	broad.mit.edu	37	3	52273016	52273016	+	Missense_Mutation	SNP	C	T	T			TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52273016C>T	uc003ddd.2	-	1	168	c.17G>A	c.(16-18)GGC>GAC	p.G6D	TWF2_uc010hmc.2_Missense_Mutation_p.G6D|uc003dde.2_5'Flank	NM_007284	NP_009215	Q6IBS0	TWF2_HUMAN	twinfilin-like protein	6	ADF-H 1.					cytoskeleton|perinuclear region of cytoplasm	actin binding|ATP binding			stomach(1)|ovary(1)|lung(1)	3				BRCA - Breast invasive adenocarcinoma(193;2.43e-05)|Kidney(197;0.000539)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)		ACCGTGGATGCCCGTTTGGTG	0.751													3	13	---	---	---	---	PASS
KLF3	51274	broad.mit.edu	37	4	38698861	38698861	+	Missense_Mutation	SNP	A	G	G			TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:38698861A>G	uc003gth.3	+	6	1347	c.1015A>G	c.(1015-1017)AGG>GGG	p.R339G		NM_016531	NP_057615	P57682	KLF3_HUMAN	Kruppel-like factor 3 (basic)	339	C2H2-type 3.				multicellular organismal development	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|lung(1)	2						TGCCCTCCATAGGAAACGCCA	0.522													63	177	---	---	---	---	PASS
KDR	3791	broad.mit.edu	37	4	55955623	55955623	+	Missense_Mutation	SNP	C	A	A			TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:55955623C>A	uc003has.2	-	25	3624	c.3322G>T	c.(3322-3324)GGG>TGG	p.G1108W	KDR_uc003hat.1_Missense_Mutation_p.G1108W	NM_002253	NP_002244	P35968	VGFR2_HUMAN	kinase insert domain receptor precursor	1108	Protein kinase.|Cytoplasmic (Potential).				angiogenesis|cell differentiation|interspecies interaction between organisms|positive regulation of endothelial cell migration|positive regulation of endothelial cell proliferation|positive regulation of focal adhesion assembly|positive regulation of positive chemotaxis|regulation of cell shape	integral to plasma membrane	ATP binding|growth factor binding|Hsp90 protein binding|integrin binding|receptor signaling protein tyrosine kinase activity|vascular endothelial growth factor receptor activity			lung(16)|soft_tissue(4)|central_nervous_system(4)|large_intestine(2)|stomach(2)|skin(2)|ovary(2)|kidney(1)	33	all_cancers(7;0.0255)|all_lung(4;0.00175)|Lung NSC(11;0.00384)|all_epithelial(27;0.034)|Glioma(25;0.08)|all_neural(26;0.101)		Epithelial(7;0.189)		Sorafenib(DB00398)|Sunitinib(DB01268)	ATCTTTACCCCAGGATATGGA	0.383			Mis		NSCLC|angiosarcoma				Familial_Infantile_Hemangioma	TSP Lung(20;0.16)			10	55	---	---	---	---	PASS
SMARCA5	8467	broad.mit.edu	37	4	144471156	144471156	+	Missense_Mutation	SNP	C	A	A			TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:144471156C>A	uc003ijg.2	+	23	3454	c.2992C>A	c.(2992-2994)CAG>AAG	p.Q998K		NM_003601	NP_003592	O60264	SMCA5_HUMAN	SWI/SNF-related matrix-associated	998	SANT 2.				CenH3-containing nucleosome assembly at centromere|nucleosome positioning|regulation of transcription from RNA polymerase II promoter|transcription initiation, DNA-dependent	condensed chromosome|nucleolus|nucleoplasm|NURF complex|RSF complex	ATP binding|ATPase activity|DNA binding|helicase activity|nucleosome binding|protein binding			skin(1)	1	all_hematologic(180;0.158)					TTAGGAGCTCCAGAGGAGATG	0.333													3	43	---	---	---	---	PASS
FSTL5	56884	broad.mit.edu	37	4	162306769	162306769	+	3'UTR	SNP	T	A	A			TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:162306769T>A	uc003iqh.2	-	16					FSTL5_uc003iqi.2_3'UTR|FSTL5_uc010iqv.2_3'UTR|uc010iqu.1_Intron	NM_020116	NP_064501	Q8N475	FSTL5_HUMAN	follistatin-like 5 isoform a							extracellular region	calcium ion binding			ovary(2)|pancreas(2)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)|skin(1)	8	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.179)		CAATTTATTTTATTTGGACCA	0.259													3	6	---	---	---	---	PASS
DDX60L	91351	broad.mit.edu	37	4	169294885	169294885	+	Missense_Mutation	SNP	T	C	C			TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:169294885T>C	uc003irq.3	-	35	4929	c.4708A>G	c.(4708-4710)ATT>GTT	p.I1570V		NM_001012967	NP_001012985	Q5H9U9	DDX6L_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60-like	1570							ATP binding|ATP-dependent helicase activity|RNA binding			ovary(1)	1		Prostate(90;0.00876)|Renal(120;0.0183)|all_neural(102;0.0837)|Melanoma(52;0.132)		GBM - Glioblastoma multiforme(119;0.175)		AATGGTGAAATGGCTACTCTT	0.413													11	343	---	---	---	---	PASS
CD180	4064	broad.mit.edu	37	5	66481767	66481767	+	Missense_Mutation	SNP	A	C	C			TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:66481767A>C	uc003juy.2	-	2	317	c.169T>G	c.(169-171)TTT>GTT	p.F57V		NM_005582	NP_005573	Q99467	CD180_HUMAN	CD180 molecule precursor	57	LRR 1.|Extracellular (Potential).				inflammatory response|innate immune response	integral to membrane|plasma membrane	receptor activity			ovary(1)	1		Lung NSC(167;4.94e-05)|Prostate(74;0.00601)|Ovarian(174;0.0654)|Breast(144;0.198)|Colorectal(97;0.234)		Lung(70;0.0046)		AATTCCAAAAATTCTGTTGTG	0.299													26	109	---	---	---	---	PASS
RASGRF2	5924	broad.mit.edu	37	5	80511696	80511696	+	Missense_Mutation	SNP	C	A	A			TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:80511696C>A	uc003kha.1	+	24	3356	c.3356C>A	c.(3355-3357)ACA>AAA	p.T1119K	RNU5E_uc011cto.1_Intron|RASGRF2_uc011ctn.1_RNA	NM_006909	NP_008840	O14827	RGRF2_HUMAN	Ras protein-specific guanine	1119	Ras-GEF.|Responsible of the affinity for farnesylated versus geranylgeranylated Ras (By similarity).				apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|synaptic transmission	cytosol|endoplasmic reticulum membrane|plasma membrane	protein binding|Rho guanyl-nucleotide exchange factor activity			breast(5)|ovary(3)|large_intestine(2)|central_nervous_system(1)|skin(1)	12		Lung NSC(167;0.00498)|all_lung(232;0.00531)|Ovarian(174;0.0357)		OV - Ovarian serous cystadenocarcinoma(54;4.22e-42)|Epithelial(54;4.04e-35)|all cancers(79;2.52e-29)		TCTTTTTAGACAAAAGCTCTA	0.299													11	55	---	---	---	---	PASS
FAM114A2	10827	broad.mit.edu	37	5	153413855	153413855	+	Missense_Mutation	SNP	G	C	C			TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:153413855G>C	uc003lvb.2	-	3	881	c.293C>G	c.(292-294)GCT>GGT	p.A98G	FAM114A2_uc003lvc.2_Missense_Mutation_p.A98G|FAM114A2_uc003lvd.2_Missense_Mutation_p.A98G|FAM114A2_uc003lve.2_Intron|FAM114A2_uc011dda.1_Intron	NM_018691	NP_061161	Q9NRY5	F1142_HUMAN	hypothetical protein LOC10827	98							purine nucleotide binding				0						AGCTACTGTAGCCGAGGCTGA	0.413													4	154	---	---	---	---	PASS
CAGE1	285782	broad.mit.edu	37	6	7373333	7373333	+	Silent	SNP	C	T	T			TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:7373333C>T	uc003mxi.2	-	4	2032	c.1311G>A	c.(1309-1311)GAG>GAA	p.E437E	CAGE1_uc003mxh.2_RNA|CAGE1_uc003mxj.2_Silent_p.E328E|CAGE1_uc003mxk.1_Silent_p.E328E	NM_205864	NP_995586	Q8TC20	CAGE1_HUMAN	cancer antigen 1	573											0	Ovarian(93;0.0418)					TCAAGACTTCCTCTAATTGAT	0.348													8	52	---	---	---	---	PASS
NOL7	51406	broad.mit.edu	37	6	13621067	13621067	+	3'UTR	SNP	C	G	G			TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:13621067C>G	uc003naz.2	+	8						NM_016167	NP_057251	Q9UMY1	NOL7_HUMAN	nucleolar protein 7, 27kDa							mitochondrion|nucleolus					0	Breast(50;0.00669)|Ovarian(93;0.0634)	all_hematologic(90;0.135)	Epithelial(50;0.176)			TAAATCAATGCTAAATGAAGA	0.269													9	25	---	---	---	---	PASS
TTBK1	84630	broad.mit.edu	37	6	43252048	43252048	+	Missense_Mutation	SNP	C	A	A			TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43252048C>A	uc003ouq.1	+	14	3849	c.3570C>A	c.(3568-3570)AGC>AGA	p.S1190R		NM_032538	NP_115927	Q5TCY1	TTBK1_HUMAN	tau tubulin kinase 1	1190				S -> SS (in Ref. 5; AAH36764).		cell junction|cytoplasm|nucleus	ATP binding|protein binding|protein serine/threonine kinase activity			lung(4)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	9			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0125)|OV - Ovarian serous cystadenocarcinoma(102;0.0399)			CCATCACCAGCAGGTGAGAAA	0.667													4	5	---	---	---	---	PASS
CYP39A1	51302	broad.mit.edu	37	6	46563727	46563727	+	Silent	SNP	A	T	T			TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:46563727A>T	uc003oyf.1	-	8	1266	c.1062T>A	c.(1060-1062)ATT>ATA	p.I354I	CYP39A1_uc011dwa.1_Silent_p.I334I|CYP39A1_uc010jzd.1_Silent_p.I182I	NM_016593	NP_057677	Q9NYL5	CP39A_HUMAN	cytochrome P450, family 39, subfamily A,	354					bile acid biosynthetic process|bile acid catabolic process|digestion|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	24-hydroxycholesterol 7alpha-hydroxylase activity|electron carrier activity|heme binding|oxysterol 7-alpha-hydroxylase activity			ovary(1)	1						AGCTTACCAAAATTTCCACAG	0.338													39	151	---	---	---	---	PASS
C6orf138	442213	broad.mit.edu	37	6	48035980	48035980	+	Missense_Mutation	SNP	C	A	A			TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:48035980C>A	uc011dwm.1	-	1	446	c.361G>T	c.(361-363)GTG>TTG	p.V121L	C6orf138_uc011dwn.1_Intron|C6orf138_uc003ozf.2_Missense_Mutation_p.V138L	NM_001013732	NP_001013754	Q6ZW05	CF138_HUMAN	hypothetical protein LOC442213	138						integral to membrane	hedgehog receptor activity			central_nervous_system(1)	1						ATTTCCAGCACGGCTCGGTGG	0.498													26	138	---	---	---	---	PASS
KLHL31	401265	broad.mit.edu	37	6	53520057	53520057	+	Missense_Mutation	SNP	T	A	A			TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:53520057T>A	uc003pcb.3	-	2	155	c.14A>T	c.(13-15)AAG>ATG	p.K5M		NM_001003760	NP_001003760	Q9H511	KLH31_HUMAN	kelch repeat and BTB (POZ) domain containing 1	5					regulation of transcription, DNA-dependent|transcription, DNA-dependent					ovary(1)	1	Lung NSC(77;0.0158)					GACAATCTTCTTTTTGGGTGC	0.358													6	54	---	---	---	---	PASS
KLHL31	401265	broad.mit.edu	37	6	53520093	53520093	+	5'UTR	SNP	G	A	A			TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:53520093G>A	uc003pcb.3	-	2						NM_001003760	NP_001003760	Q9H511	KLH31_HUMAN	kelch repeat and BTB (POZ) domain containing 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent					ovary(1)	1	Lung NSC(77;0.0158)					ACTGTTACAGGCAAGAGCTTG	0.318													5	34	---	---	---	---	PASS
COX7A2	1347	broad.mit.edu	37	6	75947673	75947673	+	Silent	SNP	C	T	T			TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:75947673C>T	uc003phv.1	-	4	300	c.225G>A	c.(223-225)GTG>GTA	p.V75V		NM_001865	NP_001856	P14406	CX7A2_HUMAN	cytochrome c oxidase subunit VIIa polypeptide 2	75						mitochondrial respiratory chain	cytochrome-c oxidase activity|electron carrier activity				0						GAAATGAAGCCACAGCCAGCT	0.358													10	39	---	---	---	---	PASS
MICAL1	64780	broad.mit.edu	37	6	109774523	109774523	+	Missense_Mutation	SNP	C	G	G			TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:109774523C>G	uc003ptj.2	-	3	768	c.514G>C	c.(514-516)GGG>CGG	p.G172R	MICAL1_uc003ptk.2_Missense_Mutation_p.G172R|MICAL1_uc010kdr.2_Missense_Mutation_p.G172R|MICAL1_uc011eaq.1_Missense_Mutation_p.G191R	NM_022765	NP_073602	Q8TDZ2	MICA1_HUMAN	microtubule associated monoxygenase, calponin	172					cytoskeleton organization|signal transduction	cytoplasm|intermediate filament	SH3 domain binding|zinc ion binding			breast(2)|ovary(1)	3		all_cancers(87;0.000189)|Acute lymphoblastic leukemia(125;3.07e-08)|all_hematologic(75;3.33e-06)|all_epithelial(87;0.00686)|Lung SC(18;0.0743)|Colorectal(196;0.101)|all_lung(197;0.149)		Epithelial(106;0.0142)|all cancers(137;0.0197)|OV - Ovarian serous cystadenocarcinoma(136;0.0233)|BRCA - Breast invasive adenocarcinoma(108;0.0574)		ATTTCCACCCCCAGCAGCAAT	0.577													22	71	---	---	---	---	PASS
SLC16A10	117247	broad.mit.edu	37	6	111499630	111499630	+	Intron	SNP	A	C	C			TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:111499630A>C	uc003pus.2	+						SLC16A10_uc003put.2_Intron	NM_018593	NP_061063	Q8TF71	MOT10_HUMAN	solute carrier family 16, member 10						aromatic amino acid transport|cellular nitrogen compound metabolic process|ion transport	basolateral plasma membrane|integral to membrane	amino acid transmembrane transporter activity				0		all_cancers(87;0.00172)|Acute lymphoblastic leukemia(125;2.27e-07)|all_hematologic(75;1.38e-05)|all_epithelial(87;0.0313)|Colorectal(196;0.0466)		OV - Ovarian serous cystadenocarcinoma(136;0.0703)|Epithelial(106;0.12)|all cancers(137;0.132)		GTTATACTGAAATACGAATAA	0.159													11	37	---	---	---	---	PASS
RFX6	222546	broad.mit.edu	37	6	117241586	117241586	+	Silent	SNP	C	T	T			TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:117241586C>T	uc003pxm.2	+	12	1359	c.1296C>T	c.(1294-1296)AGC>AGT	p.S432S		NM_173560	NP_775831	Q8HWS3	RFX6_HUMAN	regulatory factor X, 6	432					glucose homeostasis|pancreatic A cell differentiation|pancreatic D cell differentiation|pancreatic E cell differentiation|positive regulation of transcription, DNA-dependent|regulation of insulin secretion|transcription, DNA-dependent|type B pancreatic cell differentiation	nucleus	protein binding|transcription regulatory region DNA binding			ovary(1)|pancreas(1)|skin(1)	3						TTTCAGGCAGCACAGACACTG	0.323													52	187	---	---	---	---	PASS
MAS1	4142	broad.mit.edu	37	6	160328147	160328147	+	Missense_Mutation	SNP	C	A	A			TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:160328147C>A	uc003qsz.2	+	1	174	c.160C>A	c.(160-162)CTC>ATC	p.L54I		NM_002377	NP_002368	P04201	MAS_HUMAN	MAS1 oncogene	54	Helical; Name=1; (Potential).				anatomical structure morphogenesis|cell proliferation|protein kinase C signaling cascade	integral to plasma membrane	angiotensin type II receptor activity			ovary(2)|lung(2)	4		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;2.44e-18)|BRCA - Breast invasive adenocarcinoma(81;5.6e-06)		TGGGATTCTCCTCTGGTTCCT	0.502													55	215	---	---	---	---	PASS
ABCA13	154664	broad.mit.edu	37	7	48634311	48634311	+	Silent	SNP	G	A	A			TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:48634311G>A	uc003toq.2	+	58	14671	c.14646G>A	c.(14644-14646)GAG>GAA	p.E4882E	ABCA13_uc010kys.1_Silent_p.E1957E|ABCA13_uc010kyt.1_RNA|ABCA13_uc010kyu.1_Silent_p.E612E	NM_152701	NP_689914	Q86UQ4	ABCAD_HUMAN	ATP binding cassette, sub-family A (ABC1),	4882	ABC transporter 2.				transport	integral to membrane	ATP binding|ATPase activity			ovary(5)|central_nervous_system(4)|skin(1)	10						TTCAGGATGAGCCCAGCTCTG	0.493													22	96	---	---	---	---	PASS
GRM3	2913	broad.mit.edu	37	7	86394381	86394381	+	5'UTR	SNP	T	A	A			TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:86394381T>A	uc003uid.2	+	2					GRM3_uc010lef.2_5'UTR|GRM3_uc010leg.2_Intron|GRM3_uc010leh.2_Intron	NM_000840	NP_000831	Q14832	GRM3_HUMAN	glutamate receptor, metabotropic 3 precursor						synaptic transmission	integral to plasma membrane				lung(4)|ovary(3)|central_nervous_system(2)|skin(2)|haematopoietic_and_lymphoid_tissue(1)|prostate(1)	13	Esophageal squamous(14;0.0058)|all_lung(186;0.132)|Lung NSC(181;0.142)				Acamprosate(DB00659)|Nicotine(DB00184)	AGGCCAAAGATCCAGTTTGGA	0.388													18	99	---	---	---	---	PASS
NUP205	23165	broad.mit.edu	37	7	135298932	135298932	+	Missense_Mutation	SNP	C	T	T			TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:135298932C>T	uc003vsw.2	+	23	3252	c.3221C>T	c.(3220-3222)TCT>TTT	p.S1074F		NM_015135	NP_055950	Q92621	NU205_HUMAN	nucleoporin 205kDa	1074					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						TGTGCATGCTCTGATACATCT	0.358													28	116	---	---	---	---	PASS
CDCA2	157313	broad.mit.edu	37	8	25327412	25327412	+	Missense_Mutation	SNP	A	G	G			TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:25327412A>G	uc003xep.1	+	7	1215	c.736A>G	c.(736-738)ATA>GTA	p.I246V	PPP2R2A_uc003xek.2_Intron|CDCA2_uc011lae.1_Missense_Mutation_p.I246V|CDCA2_uc003xeq.1_Missense_Mutation_p.I231V|CDCA2_uc003xer.1_5'UTR	NM_152562	NP_689775	Q69YH5	CDCA2_HUMAN	cell division cycle associated 2	246					cell division|mitosis	cytoplasm|nucleus					0		all_cancers(63;0.0378)|Ovarian(32;0.000878)|all_epithelial(46;0.0162)|Breast(100;0.0164)|Prostate(55;0.191)		UCEC - Uterine corpus endometrioid carcinoma (27;0.022)|Epithelial(17;1.37e-11)|Colorectal(74;0.0129)|COAD - Colon adenocarcinoma(73;0.0443)		TTTCCCCAAGATATCATCTAA	0.333													37	138	---	---	---	---	PASS
PCMTD1	115294	broad.mit.edu	37	8	52746175	52746175	+	Missense_Mutation	SNP	C	T	T			TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:52746175C>T	uc003xqx.3	-	4	826	c.485G>A	c.(484-486)CGA>CAA	p.R162Q	PCMTD1_uc011ldm.1_Missense_Mutation_p.R32Q|PCMTD1_uc003xqw.3_Missense_Mutation_p.R162Q|PCMTD1_uc011ldn.1_5'UTR|PCMTD1_uc010lya.2_Missense_Mutation_p.R86Q|PCMTD1_uc011ldo.1_Missense_Mutation_p.R162Q	NM_052937	NP_443169	Q96MG8	PCMD1_HUMAN	protein-L-isoaspartate (D-aspartate)	162						cytoplasm	protein-L-isoaspartate (D-aspartate) O-methyltransferase activity				0		Lung NSC(129;0.0795)|all_lung(136;0.144)				ACAATAAATTCGATCATACTG	0.363													46	135	---	---	---	---	PASS
CREB3	10488	broad.mit.edu	37	9	35736114	35736114	+	Silent	SNP	C	T	T			TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35736114C>T	uc003zxv.2	+	7	1134	c.681C>T	c.(679-681)AGC>AGT	p.S227S	CREB3_uc010mla.2_Silent_p.S146S	NM_006368	NP_006359	O43889	CREB3_HUMAN	cAMP responsive element binding protein 3	251	Cytoplasmic (Potential).				chemotaxis|induction of positive chemotaxis|interspecies interaction between organisms|negative regulation of cell cycle|positive regulation of calcium ion transport|positive regulation of cell migration|positive regulation of transcription, DNA-dependent|reactivation of latent virus|regulation of cell proliferation	cytosol|endoplasmic reticulum|endoplasmic reticulum membrane|Golgi apparatus|integral to membrane|integral to membrane|nucleus|nucleus	cAMP response element binding protein binding|CCR1 chemokine receptor binding|DNA binding|protein dimerization activity|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|sequence-specific DNA binding transcription factor activity				0	all_epithelial(49;0.167)		Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)	GBM - Glioblastoma multiforme(74;0.0285)		CCAGCAGCAGCAGCACCTGCA	0.498											OREG0019176	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	48	123	---	---	---	---	PASS
INVS	27130	broad.mit.edu	37	9	103002449	103002449	+	Silent	SNP	C	T	T			TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:103002449C>T	uc004bap.1	+	6	935	c.723C>T	c.(721-723)ACC>ACT	p.T241T	INVS_uc010mta.1_Silent_p.T145T|INVS_uc011lve.1_Silent_p.T145T|INVS_uc004bao.1_Silent_p.T241T|INVS_uc004baq.1_Silent_p.T145T|INVS_uc004bar.1_Silent_p.T145T|INVS_uc010mtb.1_5'UTR	NM_014425	NP_055240	Q9Y283	INVS_HUMAN	inversin isoform a	241	ANK 7.				negative regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway	cytoplasm|membrane|microtubule|nucleus|spindle	calmodulin binding			ovary(2)	2		Acute lymphoblastic leukemia(62;0.056)				ATGTCTTGACCTCATATGAAA	0.443													24	86	---	---	---	---	PASS
FAM107B	83641	broad.mit.edu	37	10	14816481	14816481	+	Missense_Mutation	SNP	C	T	T			TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:14816481C>T	uc001ina.1	-	1	416	c.182G>A	c.(181-183)GGC>GAC	p.G61D	FAM107B_uc010qbu.1_RNA	NM_031453	NP_113641	Q9H098	F107B_HUMAN	hypothetical protein LOC83641	Error:Variant_position_missing_in_Q9H098_after_alignment										breast(4)	4						TGGCTGTCTGCCTGCTTTGGC	0.547													33	97	---	---	---	---	PASS
MYPN	84665	broad.mit.edu	37	10	69881727	69881727	+	Missense_Mutation	SNP	T	A	A			TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:69881727T>A	uc001jnm.3	+	3	717	c.532T>A	c.(532-534)TGC>AGC	p.C178S	MYPN_uc001jnl.1_Missense_Mutation_p.C178S|MYPN_uc001jnn.3_Intron|MYPN_uc001jno.3_Missense_Mutation_p.C178S|MYPN_uc001jnp.1_Missense_Mutation_p.C178S|MYPN_uc009xps.2_Missense_Mutation_p.C178S|MYPN_uc009xpt.2_Missense_Mutation_p.C178S|MYPN_uc010qit.1_5'UTR|MYPN_uc010qiu.1_RNA	NM_032578	NP_115967	Q86TC9	MYPN_HUMAN	myopalladin	178	Interaction with CARP.					nucleus|sarcomere	actin binding			ovary(3)|skin(2)	5						ACCTCGTGCCTGCAAAAACCA	0.408													3	68	---	---	---	---	PASS
BBS1	582	broad.mit.edu	37	11	66291217	66291217	+	Missense_Mutation	SNP	A	C	C			TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66291217A>C	uc001oij.1	+	11	986	c.974A>C	c.(973-975)CAG>CCG	p.Q325P	BBS1_uc001oii.1_Missense_Mutation_p.Q362P|BBS1_uc010rpg.1_Missense_Mutation_p.Q228P|BBS1_uc001oik.1_Missense_Mutation_p.Q249P|BBS1_uc001oil.1_Intron|ZDHHC24_uc001oim.1_Intron|ZDHHC24_uc009yrg.1_Intron|BBS1_uc010rph.1_5'UTR	NM_024649	NP_078925	Q8NFJ9	BBS1_HUMAN	Bardet-Biedl syndrome 1	325					nonmotile primary cilium assembly|photoreceptor cell maintenance|response to stimulus|retina homeostasis	BBSome|cilium membrane|cytoplasm	protein binding			ovary(1)	1						TGGACAGTGCAGATGCCCGCA	0.617									Bardet-Biedl_syndrome				6	14	---	---	---	---	PASS
C11orf59	55004	broad.mit.edu	37	11	71809264	71809264	+	Intron	SNP	G	T	T			TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:71809264G>T	uc001ort.2	-						LRTOMT_uc010rqv.1_Intron|LRTOMT_uc010rqw.1_Intron|LRTOMT_uc001ors.3_Intron|C11orf59_uc009ytb.2_Intron|C11orf59_uc001oru.1_Missense_Mutation_p.T80N	NM_017907	NP_060377	Q6IAA8	LTOR1_HUMAN	hypothetical protein LOC55004						cell growth|cellular protein localization|cellular response to amino acid stimulus|cholesterol homeostasis|endosome localization|endosome organization|lysosome localization|lysosome organization|positive regulation of MAPKKK cascade|positive regulation of TOR signaling cascade|regulation of cholesterol efflux|regulation of cholesterol esterification|regulation of cholesterol import|regulation of receptor recycling	Golgi apparatus|lysosomal membrane|plasma membrane|Ragulator complex	protein binding				0						CTGAGGCAGAGTGGGTGAACC	0.542													3	9	---	---	---	---	PASS
PAH	5053	broad.mit.edu	37	12	103306603	103306603	+	Missense_Mutation	SNP	A	T	T			TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:103306603A>T	uc001tjq.1	-	3	606	c.134T>A	c.(133-135)GTT>GAT	p.V45D	PAH_uc010swc.1_Missense_Mutation_p.V45D	NM_000277	NP_000268	P00439	PH4H_HUMAN	phenylalanine hydroxylase	45	ACT.				catecholamine biosynthetic process|L-phenylalanine catabolic process|neurotransmitter biosynthetic process	cytosol	phenylalanine 4-monooxygenase activity			ovary(4)	4					Epinephrine(DB00668)|L-Phenylalanine(DB00120)|Levodopa(DB01235)|Norepinephrine(DB00368)|Tetrahydrobiopterin(DB00360)	CAATGCACCAACTTCTTCTTT	0.368													22	160	---	---	---	---	PASS
TMEM132D	121256	broad.mit.edu	37	12	130184668	130184668	+	Missense_Mutation	SNP	G	T	T			TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:130184668G>T	uc009zyl.1	-	2	983	c.655C>A	c.(655-657)CCG>ACG	p.P219T		NM_133448	NP_597705	Q14C87	T132D_HUMAN	transmembrane protein 132D precursor	219	Extracellular (Potential).					integral to membrane		p.P219L(1)		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)		GTCCCCTCCGGCTGGTCCACG	0.687													14	61	---	---	---	---	PASS
FREM2	341640	broad.mit.edu	37	13	39433593	39433593	+	Missense_Mutation	SNP	C	G	G			TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:39433593C>G	uc001uwv.2	+	14	7694	c.7385C>G	c.(7384-7386)TCC>TGC	p.S2462C	FREM2_uc001uww.2_Missense_Mutation_p.S548C	NM_207361	NP_997244	Q5SZK8	FREM2_HUMAN	FRAS1-related extracellular matrix protein 2	2462	Extracellular (Potential).				cell communication|homophilic cell adhesion|multicellular organismal development	integral to membrane|plasma membrane	calcium ion binding			ovary(7)|pancreas(1)|haematopoietic_and_lymphoid_tissue(1)|central_nervous_system(1)|skin(1)	11		Lung NSC(96;1.04e-07)|Prostate(109;0.00384)|Breast(139;0.00396)|Lung SC(185;0.0565)|Hepatocellular(188;0.114)		all cancers(112;3.32e-07)|Epithelial(112;1.66e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00154)|BRCA - Breast invasive adenocarcinoma(63;0.00631)|GBM - Glioblastoma multiforme(144;0.0312)		TTTACGTCATCCAAGATGGTC	0.562													3	114	---	---	---	---	PASS
RBM26	64062	broad.mit.edu	37	13	79911406	79911406	+	Missense_Mutation	SNP	C	G	G	rs140188767		TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:79911406C>G	uc001vkz.2	-	19	2584	c.2570G>C	c.(2569-2571)CGG>CCG	p.R857P	RBM26_uc001vky.2_Missense_Mutation_p.R828P|RBM26_uc001vla.2_Missense_Mutation_p.R831P|RBM26_uc010tia.1_Missense_Mutation_p.R212P|RBM26_uc001vkx.2_Missense_Mutation_p.R567P	NM_022118	NP_071401	Q5T8P6	RBM26_HUMAN	RNA binding motif protein 26	855					mRNA processing		nucleotide binding|protein binding|RNA binding|zinc ion binding			ovary(1)	1		Acute lymphoblastic leukemia(28;0.0279)		GBM - Glioblastoma multiforme(99;0.0188)		TCCTCTGCCCCGACCAGATGA	0.532													15	60	---	---	---	---	PASS
STRN3	29966	broad.mit.edu	37	14	31404443	31404443	+	Missense_Mutation	SNP	A	T	T			TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:31404443A>T	uc001wqu.2	-	7	1130	c.914T>A	c.(913-915)TTT>TAT	p.F305Y	STRN3_uc001wqv.2_Missense_Mutation_p.F305Y|STRN3_uc010tpj.1_RNA	NM_001083893	NP_001077362	Q13033	STRN3_HUMAN	nuclear autoantigen isoform 1	305					negative regulation of estrogen receptor signaling pathway|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|response to estradiol stimulus	cytoplasm|dendrite|Golgi apparatus|neuronal cell body|nucleoplasm|nucleus|plasma membrane|protein complex	armadillo repeat domain binding|calmodulin binding|protein complex binding|protein phosphatase 2A binding|sequence-specific DNA binding transcription factor activity				0	Hepatocellular(127;0.0877)|Breast(36;0.148)		LUAD - Lung adenocarcinoma(48;0.00192)|Lung(238;0.0119)|BRCA - Breast invasive adenocarcinoma(188;0.0805)	GBM - Glioblastoma multiforme(265;0.0124)		TAAAAAATCAAATTCTTTCAG	0.418													35	139	---	---	---	---	PASS
KCNH5	27133	broad.mit.edu	37	14	63453891	63453891	+	Missense_Mutation	SNP	C	T	T			TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:63453891C>T	uc001xfx.2	-	5	499	c.448G>A	c.(448-450)GCC>ACC	p.A150T	KCNH5_uc001xfy.2_Missense_Mutation_p.A150T|KCNH5_uc001xfz.1_Missense_Mutation_p.A92T|KCNH5_uc001xga.2_Missense_Mutation_p.A92T	NM_139318	NP_647479	Q8NCM2	KCNH5_HUMAN	potassium voltage-gated channel, subfamily H,	150	Cytoplasmic (Potential).				regulation of transcription, DNA-dependent	integral to membrane	calmodulin binding|two-component sensor activity|voltage-gated potassium channel activity			ovary(4)|skin(4)|central_nervous_system(1)	9				OV - Ovarian serous cystadenocarcinoma(108;0.00958)|BRCA - Breast invasive adenocarcinoma(234;0.168)		GTCAATCGGGCAAATTTCGTC	0.388													7	101	---	---	---	---	PASS
TCL6	27004	broad.mit.edu	37	14	96129988	96129988	+	Intron	SNP	T	C	C			TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:96129988T>C	uc001yeq.2	+						TCL6_uc001yep.1_Intron|TCL6_uc001yes.2_5'UTR|TCL6_uc001yet.1_5'UTR|TCL6_uc001yeu.2_5'UTR|TCL6_uc001yev.2_5'UTR|TCL1B_uc001yew.2_RNA|TCL1B_uc001yex.2_RNA|TCL1B_uc010avj.2_RNA	NM_020554	NP_065579			SubName: Full=T-cell leukemia/lymphoma 6 ORF163;												0		all_cancers(154;0.103)		Epithelial(152;0.0655)|all cancers(159;0.149)|BRCA - Breast invasive adenocarcinoma(234;0.206)|COAD - Colon adenocarcinoma(157;0.207)		GCCAGTTTCATGTCTTGTGAT	0.448			T	TRA@	T-ALL								16	44	---	---	---	---	PASS
AQR	9716	broad.mit.edu	37	15	35196663	35196663	+	Missense_Mutation	SNP	A	T	T			TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:35196663A>T	uc001ziv.2	-	19	2056	c.1875T>A	c.(1873-1875)TTT>TTA	p.F625L		NM_014691	NP_055506	O60306	AQR_HUMAN	aquarius	625						catalytic step 2 spliceosome	RNA binding			large_intestine(1)	1		Lung NSC(122;8.7e-10)|all_lung(180;1.47e-08)		all cancers(64;4.34e-18)|GBM - Glioblastoma multiforme(113;4.59e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0283)		AAAACACTCTAAATGTCCTTG	0.308													30	119	---	---	---	---	PASS
SPG11	80208	broad.mit.edu	37	15	44877930	44877930	+	Silent	SNP	A	T	T			TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:44877930A>T	uc001ztx.2	-	29	5056	c.5025T>A	c.(5023-5025)TCT>TCA	p.S1675S	SPG11_uc010bdw.2_5'Flank|SPG11_uc010ueh.1_Silent_p.S1675S|SPG11_uc010uei.1_Silent_p.S1675S|SPG11_uc001zty.1_Silent_p.S404S	NM_025137	NP_079413	Q96JI7	SPTCS_HUMAN	spatacsin isoform 1	1675	Extracellular (Potential).				cell death	cytosol|integral to membrane|nucleus	protein binding			ovary(4)|skin(1)	5		all_cancers(109;1.29e-14)|all_epithelial(112;1.26e-12)|Lung NSC(122;1.34e-07)|all_lung(180;1.21e-06)|Melanoma(134;0.0122)		all cancers(107;2.93e-22)|GBM - Glioblastoma multiforme(94;1.55e-06)|COAD - Colon adenocarcinoma(120;0.0432)|Colorectal(105;0.0484)|Lung(196;0.104)|LUSC - Lung squamous cell carcinoma(244;0.214)		TTTCCAAAATAGATCTACATT	0.393													36	180	---	---	---	---	PASS
CYP1A2	1544	broad.mit.edu	37	15	75042328	75042328	+	Silent	SNP	G	A	A	rs17861153	byFrequency	TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:75042328G>A	uc002ayr.1	+	2	313	c.249G>A	c.(247-249)ACG>ACA	p.T83T		NM_000761	NP_000752	P05177	CP1A2_HUMAN	cytochrome P450, family 1, subfamily A,	83			T -> M (in allele CYP1A2*9).		alkaloid metabolic process|exogenous drug catabolic process|methylation|monocarboxylic acid metabolic process|monoterpenoid metabolic process|oxidative deethylation|oxidative demethylation|steroid catabolic process|toxin biosynthetic process|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	aromatase activity|caffeine oxidase activity|demethylase activity|electron carrier activity|enzyme binding|heme binding|oxygen binding			ovary(3)|breast(1)	4					Acenocoumarol(DB01418)|Acetaminophen(DB00316)|Aciclovir(DB00787)|Alosetron(DB00969)|Aminophenazone(DB01424)|Amitriptyline(DB00321)|Anagrelide(DB00261)|Azelastine(DB00972)|Bortezomib(DB00188)|Caffeine(DB00201)|Carmustine(DB00262)|Chlordiazepoxide(DB00475)|Chlorpromazine(DB00477)|Chlorzoxazone(DB00356)|Cimetidine(DB00501)|Cinacalcet(DB01012)|Ciprofloxacin(DB00537)|Clomipramine(DB01242)|Clotrimazole(DB00257)|Clozapine(DB00363)|Conjugated Estrogens(DB00286)|Cyclobenzaprine(DB00924)|Dacarbazine(DB00851)|Desloratadine(DB00967)|Diazepam(DB00829)|Dibucaine(DB00527)|Diclofenac(DB00586)|Duloxetine(DB00476)|Enoxacin(DB00467)|Esomeprazole(DB00736)|Estradiol(DB00783)|Estrone(DB00655)|Fluorouracil(DB00544)|Flutamide(DB00499)|Fluvoxamine(DB00176)|Frovatriptan(DB00998)|Grepafloxacin(DB00365)|Haloperidol(DB00502)|Hesperetin(DB01094)|Imipramine(DB00458)|Ketoconazole(DB01026)|Leflunomide(DB01097)|Levobupivacaine(DB01002)|Levofloxacin(DB01137)|Lidocaine(DB00281)|Lomefloxacin(DB00978)|Melatonin(DB01065)|Mephenytoin(DB00532)|Mexiletine(DB00379)|Mirtazapine(DB00370)|Norfloxacin(DB01059)|Nortriptyline(DB00540)|Ofloxacin(DB01165)|Olanzapine(DB00334)|Ondansetron(DB00904)|Palonosetron(DB00377)|Pantoprazole(DB00213)|Pefloxacin(DB00487)|Pimozide(DB01100)|Propafenone(DB01182)|Propranolol(DB00571)|Quinidine(DB00908)|Ramelteon(DB00980)|Ranitidine(DB00863)|Rasagiline(DB01367)|Rifampin(DB01045)|Riluzole(DB00740)|Rofecoxib(DB00533)|Ropinirole(DB00268)|Ropivacaine(DB00296)|Tacrine(DB00382)|Telithromycin(DB00976)|Terfenadine(DB00342)|Theophylline(DB00277)|Thiabendazole(DB00730)|Tizanidine(DB00697)|Tolbutamide(DB01124)|Verapamil(DB00661)|Warfarin(DB00682)|Zileuton(DB00744)|Zolmitriptan(DB00315)	TTGGCTCCACGCCCGTGCTGG	0.667													12	41	---	---	---	---	PASS
SNX33	257364	broad.mit.edu	37	15	75942230	75942230	+	Missense_Mutation	SNP	G	A	A			TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:75942230G>A	uc002bau.2	+	1	883	c.787G>A	c.(787-789)GTC>ATC	p.V263I	IMP3_uc002bat.2_5'Flank|SNX33_uc002bav.2_5'UTR	NM_153271	NP_695003	Q8WV41	SNX33_HUMAN	sorting nexin 33	263	PX.				cell communication		phosphatidylinositol binding|protein binding			ovary(1)	1						TGCCTCACCCGTCTACCGGCG	0.542													39	136	---	---	---	---	PASS
TARSL2	123283	broad.mit.edu	37	15	102261432	102261432	+	Nonsense_Mutation	SNP	T	A	A			TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:102261432T>A	uc002bxm.2	-	3	518	c.463A>T	c.(463-465)AAG>TAG	p.K155*	TARSL2_uc010usi.1_RNA	NM_152334	NP_689547	A2RTX5	SYTC2_HUMAN	threonyl-tRNA synthetase-like 2	155					threonyl-tRNA aminoacylation	cytoplasm	ATP binding|threonine-tRNA ligase activity			ovary(2)	2	Lung NSC(78;0.000991)|all_lung(78;0.00128)|Melanoma(26;0.00505)		OV - Ovarian serous cystadenocarcinoma(32;0.000268)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)			GTATCCCCCTTTTTTCCATAA	0.408													45	203	---	---	---	---	PASS
CACNA1H	8912	broad.mit.edu	37	16	1257814	1257814	+	Silent	SNP	C	T	T			TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1257814C>T	uc002cks.2	+	15	3356	c.3108C>T	c.(3106-3108)GTC>GTT	p.V1036V	CACNA1H_uc002ckt.2_Silent_p.V1036V|CACNA1H_uc002cku.2_5'Flank|CACNA1H_uc010brj.2_5'Flank|CACNA1H_uc002ckv.2_5'Flank	NM_021098	NP_066921	O95180	CAC1H_HUMAN	calcium channel, voltage-dependent, T type,	1036	Cytoplasmic (Potential).				aldosterone biosynthetic process|axon guidance|cellular response to hormone stimulus|cellular response to potassium ion|cortisol biosynthetic process|muscle contraction|myoblast fusion|positive regulation of acrosome reaction|regulation of heart contraction	voltage-gated calcium channel complex	low voltage-gated calcium channel activity			breast(2)	2		Hepatocellular(780;0.00369)			Flunarizine(DB04841)|Mibefradil(DB01388)	AGACGTCGGTCCACTTCGAGG	0.622													3	7	---	---	---	---	PASS
TRAP1	10131	broad.mit.edu	37	16	3727664	3727664	+	Intron	SNP	G	C	C			TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3727664G>C	uc002cvt.3	-						TRAP1_uc002cvs.2_5'UTR|TRAP1_uc010uxf.1_Intron	NM_016292	NP_057376	Q12931	TRAP1_HUMAN	TNF receptor-associated protein 1 precursor						cellular response to oxidative stress|protein folding	mitochondrion	ATP binding|tumor necrosis factor receptor binding|unfolded protein binding			central_nervous_system(1)	1		Ovarian(90;0.0261)				GAAGGCCTGTGGGGCAGAGGC	0.567													6	37	---	---	---	---	PASS
BFAR	51283	broad.mit.edu	37	16	14761821	14761821	+	3'UTR	SNP	C	T	T			TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:14761821C>T	uc002dco.2	+	8					BFAR_uc002dcp.2_3'UTR|BFAR_uc010uzh.1_3'UTR	NM_016561	NP_057645	Q9NZS9	BFAR_HUMAN	bifunctional apoptosis regulator						anti-apoptosis|apoptosis	endoplasmic reticulum membrane|integral to plasma membrane|membrane fraction	structural molecule activity|zinc ion binding			ovary(1)|skin(1)	2						ATCAAAAGCTCCAACCATGTC	0.532													4	3	---	---	---	---	PASS
PDILT	204474	broad.mit.edu	37	16	20380853	20380853	+	Silent	SNP	G	T	T			TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:20380853G>T	uc002dhc.1	-	8	1300	c.1077C>A	c.(1075-1077)CTC>CTA	p.L359L		NM_174924	NP_777584	Q8N807	PDILT_HUMAN	protein disulfide isomerase-like, testis	359					cell differentiation|cell redox homeostasis|multicellular organismal development|spermatogenesis	endoplasmic reticulum	isomerase activity			large_intestine(1)	1						CAAATTTCTTGAGGCTTTCGT	0.443													48	214	---	---	---	---	PASS
SCNN1G	6340	broad.mit.edu	37	16	23203706	23203706	+	Missense_Mutation	SNP	A	G	G			TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:23203706A>G	uc002dlm.1	+	4	791	c.652A>G	c.(652-654)ACC>GCC	p.T218A		NM_001039	NP_001030	P51170	SCNNG_HUMAN	sodium channel, nonvoltage-gated 1, gamma	218	Extracellular (By similarity).				excretion|sensory perception of taste	apical plasma membrane|integral to plasma membrane	ligand-gated sodium channel activity|WW domain binding			ovary(2)|skin(2)|large_intestine(1)|pancreas(1)	6				GBM - Glioblastoma multiforme(48;0.0366)	Amiloride(DB00594)|Triamterene(DB00384)	TGCCACCTACACCTTCAGCTC	0.483													16	85	---	---	---	---	PASS
PDXDC2	283970	broad.mit.edu	37	16	70058574	70058574	+	Splice_Site	SNP	C	G	G			TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70058574C>G	uc002eyb.2	-	8		c.822_splice	c.e8-1		CLEC18C_uc002exy.2_Intron|PDXDC2_uc002eyc.2_Splice_Site					Homo sapiens cDNA: FLJ23482 fis, clone KAIA03142.												0						GCTGCCGTTCCTAGGATAAAA	0.438													9	26	---	---	---	---	PASS
CPNE7	27132	broad.mit.edu	37	16	89657544	89657544	+	Missense_Mutation	SNP	G	A	A			TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89657544G>A	uc002fnp.2	+	15	1533	c.1403G>A	c.(1402-1404)GGC>GAC	p.G468D	CPNE7_uc002fnq.2_Missense_Mutation_p.G393D	NM_014427	NP_055242	Q9UBL6	CPNE7_HUMAN	copine 7 isoform b	468	VWFA.				lipid metabolic process		transporter activity				0		all_hematologic(23;0.0748)		all cancers(4;3.63e-08)|OV - Ovarian serous cystadenocarcinoma(4;1.7e-06)|BRCA - Breast invasive adenocarcinoma(80;0.0147)		GGCATCCAGGGCGTGGTGGAG	0.706													4	17	---	---	---	---	PASS
CD300LG	146894	broad.mit.edu	37	17	41926061	41926061	+	Missense_Mutation	SNP	G	A	A			TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:41926061G>A	uc002iem.2	+	2	220	c.179G>A	c.(178-180)CGC>CAC	p.R60H	CD300LG_uc002iek.1_Missense_Mutation_p.R60H|CD300LG_uc002iel.1_Missense_Mutation_p.R60H|CD300LG_uc010czk.2_Missense_Mutation_p.R60H|CD300LG_uc010wil.1_Missense_Mutation_p.R60H|CD300LG_uc010czl.2_Missense_Mutation_p.R60H	NM_145273	NP_660316	Q6UXG3	CLM9_HUMAN	CD300 molecule-like family member g precursor	60	Extracellular (Potential).|Ig-like V-type.					apical plasma membrane|basolateral plasma membrane|integral to membrane|multivesicular body membrane	receptor activity				0		Breast(137;0.0199)		BRCA - Breast invasive adenocarcinoma(366;0.115)		CTCTTCTCTCGCTGCTCTGGC	0.592													18	53	---	---	---	---	PASS
CDH7	1005	broad.mit.edu	37	18	63430077	63430077	+	Translation_Start_Site	SNP	A	T	T			TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:63430077A>T	uc002ljz.2	+	2	324	c.-1A>T	c.(-3-1)AAAGA>AATGA		CDH7_uc002lka.2_Translation_Start_Site|CDH7_uc002lkb.2_Translation_Start_Site	NM_033646	NP_387450	Q9ULB5	CADH7_HUMAN	cadherin 7, type 2 preproprotein						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)				GAAAAAAAAAAGATGAAGTTG	0.428													8	43	---	---	---	---	PASS
HNRNPM	4670	broad.mit.edu	37	19	8528506	8528506	+	Missense_Mutation	SNP	T	A	A			TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8528506T>A	uc010dwe.2	+	5	454	c.374T>A	c.(373-375)ATG>AAG	p.M125K	HNRNPM_uc010dwc.1_Missense_Mutation_p.M125K|HNRNPM_uc010xke.1_Missense_Mutation_p.M125K|HNRNPM_uc010dwd.2_Missense_Mutation_p.M125K|HNRNPM_uc002mka.2_Missense_Mutation_p.M5K	NM_005968	NP_005959	P52272	HNRPM_HUMAN	heterogeneous nuclear ribonucleoprotein M	125	RRM 1.				alternative nuclear mRNA splicing, via spliceosome	catalytic step 2 spliceosome|integral to plasma membrane|nuclear matrix|nucleolus|paraspeckles	nucleotide binding|protein domain specific binding|RNA binding				0						GAAGAGAGCATGAAAAAAGCT	0.413													27	88	---	---	---	---	PASS
TSHZ3	57616	broad.mit.edu	37	19	31768802	31768802	+	Missense_Mutation	SNP	C	A	A			TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:31768802C>A	uc002nsy.3	-	2	1962	c.1897G>T	c.(1897-1899)GGG>TGG	p.G633W		NM_020856	NP_065907	Q63HK5	TSH3_HUMAN	zinc finger protein 537	633					negative regulation of transcription, DNA-dependent|regulation of respiratory gaseous exchange by neurological system process	growth cone|nucleus	chromatin binding|protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(4)|skin(2)|pancreas(1)|lung(1)	8	Esophageal squamous(110;0.226)					GAAAGCTTCCCATCCGGCTCC	0.582													13	66	---	---	---	---	PASS
RUVBL2	10856	broad.mit.edu	37	19	49517740	49517740	+	Splice_Site	SNP	G	A	A			TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49517740G>A	uc002plr.1	+	12	1015	c.1002_splice	c.e12-1	p.R334_splice	RUVBL2_uc002plq.1_Splice_Site_p.R289_splice|RUVBL2_uc002pls.1_Splice_Site|RUVBL2_uc010emn.1_Splice_Site_p.R289_splice|RUVBL2_uc010yac.1_Splice_Site_p.R289_splice	NM_006666	NP_006657	Q9Y230	RUVB2_HUMAN	RuvB-like 2						cellular response to UV|DNA recombination|DNA repair|histone H2A acetylation|histone H4 acetylation|protein folding|regulation of growth|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|Ino80 complex|membrane|MLL1 complex|NuA4 histone acetyltransferase complex|nuclear matrix	ATP binding|ATP-dependent DNA helicase activity|damaged DNA binding|identical protein binding|unfolded protein binding				0		all_epithelial(76;5.29e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		all cancers(93;0.000449)|OV - Ovarian serous cystadenocarcinoma(262;0.000555)|GBM - Glioblastoma multiforme(486;0.00585)|Epithelial(262;0.047)		CTCTTCCTCAGAATCCGGGGC	0.453													9	41	---	---	---	---	PASS
ZNF415	55786	broad.mit.edu	37	19	53612726	53612726	+	Missense_Mutation	SNP	T	C	C			TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53612726T>C	uc002qax.2	-	7	1065	c.716A>G	c.(715-717)AAT>AGT	p.N239S	ZNF415_uc002qat.2_Missense_Mutation_p.N203S|ZNF415_uc002qaw.2_Missense_Mutation_p.N191S|ZNF415_uc010yds.1_Missense_Mutation_p.N191S|ZNF415_uc010ydt.1_Missense_Mutation_p.N191S|ZNF415_uc002qau.2_Missense_Mutation_p.N178S|ZNF415_uc002qav.2_Missense_Mutation_p.N203S|ZNF415_uc002qba.2_5'UTR|ZNF415_uc002qay.2_Missense_Mutation_p.N178S|ZNF415_uc002qaz.2_Missense_Mutation_p.N239S	NR_028343		Q09FC8	ZN415_HUMAN	RecName: Full=Zinc finger protein 415;	239					regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|microtubule cytoskeleton|nucleolus	DNA binding|zinc ion binding			ovary(1)	1				GBM - Glioblastoma multiforme(134;0.0191)		CCCATATTTATTAGAAACATG	0.358													35	152	---	---	---	---	PASS
C20orf79	140856	broad.mit.edu	37	20	18794452	18794452	+	5'UTR	SNP	A	G	G			TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:18794452A>G	uc002wrk.2	+	1					uc002wrj.1_Intron	NM_178483	NP_848578	Q9UJQ7	CT079_HUMAN	hypothetical protein LOC140856								sterol binding			skin(3)	3						GGGGACTAGCACAGGAAGATG	0.517													9	45	---	---	---	---	PASS
FRG1B	284802	broad.mit.edu	37	20	29633992	29633992	+	Intron	SNP	A	G	G			TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29633992A>G	uc010ztl.1	+						FRG1B_uc002wvm.1_RNA|FRG1B_uc010ztj.1_Intron|FRG1B_uc010ztk.1_Intron					Homo sapiens cDNA FLJ32537 fis, clone SMINT2000400, highly similar to Homo sapiens FRG1 mRNA.												0						TAAAATATTCAGAGGAAATGC	0.308													5	44	---	---	---	---	PASS
SALL4	57167	broad.mit.edu	37	20	50406800	50406800	+	Missense_Mutation	SNP	A	G	G			TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:50406800A>G	uc002xwh.3	-	2	2323	c.2222T>C	c.(2221-2223)TTT>TCT	p.F741S	SALL4_uc010gii.2_Intron|SALL4_uc002xwi.3_Intron	NM_020436	NP_065169	Q9UJQ4	SALL4_HUMAN	sal-like 4	741					transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2						CTGCAGGTTAAAAGGGGCAGG	0.592													8	35	---	---	---	---	PASS
CASS4	57091	broad.mit.edu	37	20	55027845	55027845	+	Missense_Mutation	SNP	A	G	G			TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:55027845A>G	uc002xxp.2	+	6	1838	c.1613A>G	c.(1612-1614)GAT>GGT	p.D538G	CASS4_uc002xxq.3_Missense_Mutation_p.D538G|CASS4_uc002xxr.2_Missense_Mutation_p.D538G|CASS4_uc010zze.1_Missense_Mutation_p.D484G|CASS4_uc010gio.2_Intron	NM_001164116	NP_001157588	Q9NQ75	CASS4_HUMAN	HEF-like protein isoform a	538					cell adhesion	cytoplasm|cytoskeleton|focal adhesion	two-component sensor activity			ovary(2)|skin(1)	3						GAAAGCTTGGATAATCGCAAT	0.488													3	91	---	---	---	---	PASS
N6AMT1	29104	broad.mit.edu	37	21	30255320	30255320	+	Missense_Mutation	SNP	G	T	T			TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:30255320G>T	uc002ymo.1	-	2	234	c.208C>A	c.(208-210)CAG>AAG	p.Q70K	N6AMT1_uc002ymp.1_Missense_Mutation_p.Q70K|N6AMT1_uc002ymq.1_RNA	NM_013240	NP_037372	Q9Y5N5	HEMK2_HUMAN	N-6 adenine-specific DNA methyltransferase 1	70					positive regulation of cell growth	protein complex	nucleic acid binding|protein binding|protein methyltransferase activity				0						TACAAAGCCTGAGGGCCTATC	0.343													19	69	---	---	---	---	PASS
DSCAM	1826	broad.mit.edu	37	21	41450747	41450747	+	Missense_Mutation	SNP	C	A	A			TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:41450747C>A	uc002yyq.1	-	26	5030	c.4578G>T	c.(4576-4578)AGG>AGT	p.R1526S	DSCAM_uc002yyr.1_RNA	NM_001389	NP_001380	O60469	DSCAM_HUMAN	Down syndrome cell adhesion molecule isoform	1526	Extracellular (Potential).|Fibronectin type-III 6.				cell adhesion|dendrite self-avoidance|negative regulation of cell adhesion|positive regulation of axon extension involved in axon guidance|positive regulation of phosphorylation	axon|extracellular region|growth cone|integral to plasma membrane|membrane fraction	protein binding			ovary(6)|skin(4)|upper_aerodigestive_tract(1)	11		all_cancers(19;0.186)|Prostate(19;1.15e-05)|all_epithelial(19;0.0103)				AGAGAGAGGTCCTCTGAGCTG	0.582													6	41	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	22	18844763	18844763	+	RNA	SNP	T	C	C			TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:18844763T>C	uc002zoe.2	+	4		c.2017T>C			uc002zof.2_5'Flank					Homo sapiens cDNA FLJ76361 complete cds.																		TCACAGCCTCTGAGGGCAGCA	0.562													3	17	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	22	18844888	18844888	+	RNA	SNP	A	G	G			TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:18844888A>G	uc002zoe.2	+	4		c.2142A>G			uc002zof.2_5'Flank					Homo sapiens cDNA FLJ76361 complete cds.																		GCTCACGGAAATACAGCTTCA	0.587													6	36	---	---	---	---	PASS
MYO18B	84700	broad.mit.edu	37	22	26422488	26422488	+	Missense_Mutation	SNP	A	G	G			TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:26422488A>G	uc003abz.1	+	43	6798	c.6548A>G	c.(6547-6549)CAC>CGC	p.H2183R	MYO18B_uc003aca.1_Missense_Mutation_p.H2064R|MYO18B_uc010guy.1_Missense_Mutation_p.H2065R|MYO18B_uc010guz.1_Missense_Mutation_p.H2063R|MYO18B_uc011aka.1_Missense_Mutation_p.H1337R|MYO18B_uc011akb.1_Missense_Mutation_p.H1696R|MYO18B_uc010gva.1_Missense_Mutation_p.H166R|MYO18B_uc010gvb.1_RNA	NM_032608	NP_115997	Q8IUG5	MY18B_HUMAN	myosin XVIIIB	2183						nucleus|sarcomere|unconventional myosin complex	actin binding|ATP binding|motor activity			ovary(5)|central_nervous_system(3)|large_intestine(2)|breast(2)	12						ACCAATGTCCACAGCAAGACC	0.552													19	90	---	---	---	---	PASS
C22orf9	23313	broad.mit.edu	37	22	45607978	45607978	+	Missense_Mutation	SNP	C	G	G			TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:45607978C>G	uc003bfx.1	-	2	141	c.75G>C	c.(73-75)AAG>AAC	p.K25N	C22orf9_uc003bfv.1_Missense_Mutation_p.K34N|C22orf9_uc003bfw.1_Missense_Mutation_p.K30N|C22orf9_uc010gzx.2_Missense_Mutation_p.K7N	NM_001009880	NP_001009880	Q6ICG6	K0930_HUMAN	hypothetical protein LOC23313 isoform b	25							protein binding				0		Ovarian(80;0.00965)|all_neural(38;0.0244)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0178)|READ - Rectum adenocarcinoma(1;0.000617)|Colorectal(1;0.0024)		TGCGGTCATCCTTGAAGCACC	0.602													6	33	---	---	---	---	PASS
ZFX	7543	broad.mit.edu	37	X	24197791	24197791	+	Missense_Mutation	SNP	G	A	A			TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:24197791G>A	uc004dbf.2	+	4	808	c.550G>A	c.(550-552)GAC>AAC	p.D184N	ZFX_uc004dbd.1_Missense_Mutation_p.D184N|ZFX_uc010nfx.1_Intron|ZFX_uc004dbe.2_Missense_Mutation_p.D184N|ZFX_uc011mjv.1_Missense_Mutation_p.D223N|ZFX_uc010nfy.1_Missense_Mutation_p.D184N	NM_003410	NP_003401	P17010	ZFX_HUMAN	zinc finger protein, X-linked	184					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|transcription coactivator activity|zinc ion binding			ovary(2)	2						ATTGGTAGCAGACTGTGCCTC	0.418													41	72	---	---	---	---	PASS
SSX8	280659	broad.mit.edu	37	X	52655349	52655349	+	RNA	SNP	T	A	A	rs34990448	by1000genomes	TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:52655349T>A	uc011moa.1	+	4		c.476T>A			SSX8_uc011mob.1_RNA					Homo sapiens cDNA FLJ56587 complete cds, highly similar to Protein SSX8.												0						TAGGTTTCAATGTCACCCTCC	0.308													5	82	---	---	---	---	PASS
STAG2	10735	broad.mit.edu	37	X	123179198	123179198	+	Missense_Mutation	SNP	G	A	A			TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:123179198G>A	uc004etz.3	+	7	986	c.647G>A	c.(646-648)CGA>CAA	p.R216Q	STAG2_uc004eua.2_Missense_Mutation_p.R216Q|STAG2_uc004eub.2_Missense_Mutation_p.R216Q|STAG2_uc004euc.2_Missense_Mutation_p.R216Q|STAG2_uc004eud.2_Missense_Mutation_p.R216Q|STAG2_uc004eue.2_Missense_Mutation_p.R216Q	NM_006603	NP_006594	Q8N3U4	STAG2_HUMAN	stromal antigen 2 isoform b	216					cell division|meiosis|mitotic metaphase/anaphase transition|mitotic prometaphase|negative regulation of DNA endoreduplication|sister chromatid cohesion	chromatin|chromosome, centromeric region|nucleoplasm	protein binding			ovary(4)|skin(1)	5						AGAGCATTTCGACATACAAGC	0.343													71	125	---	---	---	---	PASS
MAGEC3	139081	broad.mit.edu	37	X	140985251	140985251	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:140985251G>A	uc011mwp.1	+	7	1707	c.1707G>A	c.(1705-1707)TGG>TGA	p.W569*	MAGEC3_uc004fbs.2_Nonsense_Mutation_p.W271*|MAGEC3_uc010nsj.2_Nonsense_Mutation_p.W271*	NM_138702	NP_619647	Q8TD91	MAGC3_HUMAN	melanoma antigen family C, 3 isoform 1	569	MAGE 2.									skin(2)|central_nervous_system(1)	3	Acute lymphoblastic leukemia(192;6.56e-05)					AGGTCATCTGGGAAGTGTTGA	0.498													4	98	---	---	---	---	PASS
GABRA3	2556	broad.mit.edu	37	X	151336625	151336625	+	3'UTR	SNP	G	T	T			TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:151336625G>T	uc010ntk.1	-	10						NM_000808	NP_000799	P34903	GBRA3_HUMAN	gamma-aminobutyric acid A receptor, alpha 3						gamma-aminobutyric acid signaling pathway	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	benzodiazepine receptor activity|chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity|protein binding			ovary(1)	1	Acute lymphoblastic leukemia(192;6.56e-05)				Alprazolam(DB00404)|Diazepam(DB00829)|Ethchlorvynol(DB00189)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Lorazepam(DB00186)|Meprobamate(DB00371)|Midazolam(DB00683)	ATACGCGAAGGGGAGCCCCGG	0.473													3	27	---	---	---	---	PASS
RBMS1	5937	broad.mit.edu	37	2	161282846	161282847	+	Intron	INS	-	AAGG	AAGG	rs138498508	by1000genomes	TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:161282846_161282847insAAGG	uc002ubo.2	-						RBMS1_uc002ubn.2_Intron|RBMS1_uc002ubi.3_Intron|RBMS1_uc002ubm.2_Intron|RBMS1_uc002ubp.2_Intron|RBMS1_uc010fox.2_Intron	NM_016836	NP_058520	P29558	RBMS1_HUMAN	RNA binding motif, single stranded interacting						DNA replication|RNA processing	nucleus	double-stranded DNA binding|nucleotide binding|protein binding|RNA binding|single-stranded DNA binding				0						ggaaggaaggaaaggaaggaag	0.099													2	4	---	---	---	---	
YIPF7	285525	broad.mit.edu	37	4	44651969	44651969	+	Intron	DEL	A	-	-	rs35447406		TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:44651969delA	uc010ifx.1	-						YIPF7_uc010ify.1_Intron	NM_182592	NP_872398	Q8N8F6	YIPF7_HUMAN	Yip1 domain family, member 7							endoplasmic reticulum membrane|integral to membrane					0						agactctgtcaaaaaaaaaaa	0.179													4	2	---	---	---	---	
FRAS1	80144	broad.mit.edu	37	4	79371639	79371640	+	Intron	INS	-	T	T	rs138438777	by1000genomes	TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:79371639_79371640insT	uc003hlb.2	+							NM_025074	NP_079350	Q86XX4	FRAS1_HUMAN	Fraser syndrome 1						cell communication	integral to membrane|plasma membrane	metal ion binding			large_intestine(5)	5						ttgttttcttattttttttttc	0.277													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190514054	190514055	+	IGR	DEL	GT	-	-	rs79143395		TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190514054_190514055delGT								None (None upstream) : FRG1 (347919 downstream)																							GTtgtgtgtggtgtgtgtgtgt	0.193													4	2	---	---	---	---	
FAM153B	202134	broad.mit.edu	37	5	175530031	175530031	+	Intron	DEL	G	-	-			TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:175530031delG	uc003mdk.2	+							NM_001079529	NP_001072997	P0C7A2	F153B_HUMAN	hypothetical protein LOC202134											ovary(1)	1	all_cancers(89;0.00406)|Renal(175;0.000269)|Lung NSC(126;0.0103)|all_lung(126;0.0164)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)|all_hematologic(541;0.214)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)	Kidney(146;0.0965)		CCTGCACTGCGTGGTGTGCAC	0.507													3	3	---	---	---	---	
SYCP2L	221711	broad.mit.edu	37	6	10908125	10908126	+	Intron	INS	-	T	T	rs145403835		TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:10908125_10908126insT	uc003mzo.2	+						SYCP2L_uc011din.1_Intron|SYCP2L_uc010jow.2_Intron	NM_001040274	NP_001035364	Q5T4T6	SYC2L_HUMAN	synaptonemal complex protein 2-like							nucleus				ovary(1)|skin(1)	2	Breast(50;0.0838)|Ovarian(93;0.107)	all_hematologic(90;0.135)	Epithelial(50;0.239)			ATACAGATAGGttttttttttt	0.178													4	3	---	---	---	---	
MAPK13	5603	broad.mit.edu	37	6	36098497	36098498	+	Intron	INS	-	GGGGGGC	GGGGGGC	rs146539855	by1000genomes	TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:36098497_36098498insGGGGGGC	uc003ols.2	+						MAPK13_uc003olt.2_Intron	NM_002754	NP_002745	O15264	MK13_HUMAN	mitogen-activated protein kinase 13						cell cycle|intracellular protein kinase cascade|nerve growth factor receptor signaling pathway|positive regulation of interleukin-6 production|Ras protein signal transduction|response to stress		ATP binding|MAP kinase activity|protein binding			breast(2)|central_nervous_system(1)	3						CCTgggccgctggggggcgggg	0.599													3	3	---	---	---	---	
FAM83B	222584	broad.mit.edu	37	6	54792182	54792182	+	Intron	DEL	T	-	-			TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:54792182delT	uc003pck.2	+							NM_001010872	NP_001010872	Q5T0W9	FA83B_HUMAN	hypothetical protein LOC222584											ovary(6)	6	Lung NSC(77;0.0178)|Renal(3;0.122)					TATTTGGGAGTTTTTTTTTTA	0.224													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	71063447	71063448	+	IGR	DEL	CA	-	-	rs74931118		TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:71063447_71063448delCA								COL9A1 (50661 upstream) : FAM135A (59659 downstream)																							tacacacacccacacacacaca	0.257													4	2	---	---	---	---	
AIM1	202	broad.mit.edu	37	6	106966842	106966843	+	Intron	DEL	AT	-	-	rs9486376	byFrequency	TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:106966842_106966843delAT	uc003prh.2	+							NM_001624	NP_001615	Q9Y4K1	AIM1_HUMAN	absent in melanoma 1								sugar binding			breast(4)|ovary(2)|upper_aerodigestive_tract(1)|large_intestine(1)|skin(1)	9	Breast(9;0.0138)|all_epithelial(6;0.169)	all_cancers(87;4.67e-25)|all_epithelial(87;5.46e-21)|Acute lymphoblastic leukemia(125;2.15e-07)|all_hematologic(75;5.28e-06)|Colorectal(196;3.46e-05)|all_lung(197;5.94e-05)|Lung NSC(302;7.26e-05)|Ovarian(999;0.00473)	Epithelial(6;0.00114)|all cancers(7;0.00726)|BRCA - Breast invasive adenocarcinoma(8;0.0114)|OV - Ovarian serous cystadenocarcinoma(5;0.0305)	all cancers(137;1.73e-50)|Epithelial(106;2.42e-48)|OV - Ovarian serous cystadenocarcinoma(136;1.51e-27)|BRCA - Breast invasive adenocarcinoma(108;0.00104)|GBM - Glioblastoma multiforme(226;0.00858)		ttaaaaaCACATGTGTGCGcac	0.109													4	2	---	---	---	---	
TRDN	10345	broad.mit.edu	37	6	123812278	123812281	+	Intron	DEL	GAAG	-	-			TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:123812278_123812281delGAAG	uc003pzj.1	-						TRDN_uc003pzk.1_Intron|TRDN_uc003pzl.1_Intron|TRDN_uc010ken.2_Intron	NM_006073	NP_006064	Q13061	TRDN_HUMAN	triadin						muscle contraction	integral to membrane|plasma membrane|sarcoplasmic reticulum membrane	receptor binding			ovary(1)	1				GBM - Glioblastoma multiforme(226;0.184)		aggaacgaaagaaggaaggaagga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	4589342	4589343	+	IGR	INS	-	A	A			TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:4589342_4589343insA								SDK1 (280713 upstream) : FOXK1 (94045 downstream)																							aggaaagaaggaaaaaaaaaaa	0.282													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	37860763	37860764	+	Intron	DEL	TA	-	-	rs71554525		TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:37860763_37860764delTA	uc003tfl.2	+											Homo sapiens, clone IMAGE:3881224, mRNA.																		AAGTTGTGGTTATATATATATA	0.228													4	2	---	---	---	---	
XKR6	286046	broad.mit.edu	37	8	11058891	11058892	+	5'Flank	DEL	GC	-	-			TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:11058891_11058892delGC	uc003wtk.1	-							NM_173683	NP_775954	Q5GH73	XKR6_HUMAN	XK, Kell blood group complex subunit-related							integral to membrane				ovary(1)|skin(1)	2				Lung(29;0.0407)|COAD - Colon adenocarcinoma(149;0.0555)		gggagggacggcgggggggggg	0.252													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	55243464	55243464	+	IGR	DEL	A	-	-	rs35886430		TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:55243464delA								MRPL15 (182390 upstream) : SOX17 (127031 downstream)																							GTTTAGTTTGAAAAAAAAAAA	0.139													4	2	---	---	---	---	
AQP7P1	375719	broad.mit.edu	37	9	67272723	67272724	+	Intron	DEL	GC	-	-			TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:67272723_67272724delGC	uc004aem.1	-						AQP7P1_uc004aen.1_Intron|AQP7P1_uc004aeo.1_RNA|AQP7P1_uc004aep.1_RNA					Homo sapiens aquaporin 7 pseudogene 1, mRNA (cDNA clone IMAGE:6191443).												0						AGGTGAAGATGCGGGGGGGGGG	0.579													4	2	---	---	---	---	
YME1L1	10730	broad.mit.edu	37	10	27434231	27434231	+	Intron	DEL	A	-	-			TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:27434231delA	uc001iti.2	-						YME1L1_uc001itj.2_Intron|YME1L1_uc010qdl.1_Intron|YME1L1_uc009xkv.2_Intron	NM_139312	NP_647473	Q96TA2	YMEL1_HUMAN	YME1-like 1 isoform 1						protein catabolic process|proteolysis	membrane|mitochondrion	ATP binding|metal ion binding|metalloendopeptidase activity|nucleoside-triphosphatase activity			ovary(1)	1						AAAAAAAAACAAAAAAAAAAC	0.159													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	99553709	99553711	+	IGR	DEL	TCT	-	-			TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:99553709_99553711delTCT								SFRP5 (21953 upstream) : GOLGA7B (56285 downstream)																							ttcttcttcctCTTCTtcttctt	0.034													4	2	---	---	---	---	
CACNA2D4	93589	broad.mit.edu	37	12	2016939	2016951	+	Intron	DEL	GCCTGGTGAGTAT	-	-	rs113797488		TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:2016939_2016951delGCCTGGTGAGTAT	uc001qjp.2	-						CACNA2D4_uc009zds.1_Intron|CACNA2D4_uc009zdt.1_Intron	NM_172364	NP_758952	Q7Z3S7	CA2D4_HUMAN	voltage-gated calcium channel alpha(2)delta-4							integral to membrane	calcium channel activity|metal ion binding|voltage-gated ion channel activity			ovary(1)	1	Ovarian(42;0.107)	Myeloproliferative disorder(1001;0.206)	OV - Ovarian serous cystadenocarcinoma(31;0.00113)	Kidney(2;0.0205)|KIRC - Kidney renal clear cell carcinoma(2;0.0451)		TGGTGGGCCAGCCTGGTGAGTATGCCTGGTGGG	0.662													5	6	---	---	---	---	
PUS7L	83448	broad.mit.edu	37	12	44130669	44130669	+	Intron	DEL	A	-	-			TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:44130669delA	uc001rnq.3	-						PUS7L_uc001rnr.3_Intron|PUS7L_uc001rns.3_Intron|PUS7L_uc009zkb.2_Intron	NM_001098615	NP_001092085	Q9H0K6	PUS7L_HUMAN	pseudouridylate synthase 7 homolog (S.						pseudouridine synthesis|tRNA processing		pseudouridine synthase activity|RNA binding			pancreas(1)	1	all_cancers(12;0.00027)	Lung NSC(34;0.114)|all_lung(34;0.24)		GBM - Glioblastoma multiforme(48;0.0402)		CCCTGCTATTAAAAAAAAAAA	0.308													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	77054710	77054711	+	IGR	DEL	AA	-	-	rs35714759		TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:77054710_77054711delAA								OSBPL8 (101121 upstream) : ZDHHC17 (103143 downstream)																							TCTGGGCTATaaaaaaaaaaaa	0.297													5	3	---	---	---	---	
PLEKHG7	440107	broad.mit.edu	37	12	93155415	93155415	+	Intron	DEL	A	-	-			TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:93155415delA	uc001tcj.2	+							NM_001004330	NP_001004330	Q6ZR37	PKHG7_HUMAN	pleckstrin homology domain containing, family G						regulation of Rho protein signal transduction	intracellular	Rho guanyl-nucleotide exchange factor activity			ovary(1)	1						agaaagaaagaaagaaagaaa	0.090													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	106675569	106675570	+	IGR	DEL	AC	-	-	rs35465446		TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:106675569_106675570delAC								CKAP4 (33856 upstream) : TCP11L2 (21011 downstream)																							acaaaattCAacacacacacac	0.005													4	2	---	---	---	---	
STARD13	90627	broad.mit.edu	37	13	33752053	33752054	+	Intron	INS	-	A	A			TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:33752053_33752054insA	uc001uuw.2	-						STARD13_uc001uuu.2_Intron|STARD13_uc001uuv.2_Intron|STARD13_uc001uux.2_Intron|STARD13_uc010tec.1_Intron|STARD13_uc010abh.1_Intron	NM_178006	NP_821074	Q9Y3M8	STA13_HUMAN	StAR-related lipid transfer (START) domain						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|lipid particle|mitochondrial membrane	GTPase activator activity|protein binding			ovary(2)|pancreas(1)|skin(1)	4	all_epithelial(80;0.155)	Lung SC(185;0.0367)		all cancers(112;1.31e-05)|Epithelial(112;0.000142)|BRCA - Breast invasive adenocarcinoma(63;0.00936)|OV - Ovarian serous cystadenocarcinoma(117;0.0533)|Lung(94;0.143)|GBM - Glioblastoma multiforme(144;0.143)		ggaaaggaaggaaggaaggaag	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	68871267	68871268	+	IGR	DEL	GT	-	-	rs72434019		TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:68871267_68871268delGT								None (None upstream) : None (None downstream)																							gtgggtgtgcgtgtgtgtgtgt	0.252													4	3	---	---	---	---	
GPC5	2262	broad.mit.edu	37	13	93377129	93377130	+	Intron	DEL	AC	-	-	rs71878491		TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:93377129_93377130delAC	uc010tif.1	+							NM_004466	NP_004457	P78333	GPC5_HUMAN	glypican 5 precursor							anchored to membrane|extracellular space|integral to plasma membrane|proteinaceous extracellular matrix	heparan sulfate proteoglycan binding			ovary(2)|skin(2)|upper_aerodigestive_tract(1)	5	all_cancers(3;1.43e-07)|all_neural(89;0.0804)|Medulloblastoma(90;0.163)	Lung NSC(4;0.00454)				tcctacacatacacacacacac	0.134													4	2	---	---	---	---	
KLHL28	54813	broad.mit.edu	37	14	45400413	45400413	+	Intron	DEL	T	-	-			TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:45400413delT	uc001wvq.2	-						KLHL28_uc001wvr.2_Intron	NM_017658	NP_060128	Q9NXS3	KLH28_HUMAN	BTB (POZ) domain containing 5											ovary(1)	1						CATACAAGTCTTTTTTTTTTT	0.284													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	59435674	59435675	+	IGR	DEL	TT	-	-	rs72239757		TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:59435674_59435675delTT								DACT1 (320638 upstream) : DAAM1 (219724 downstream)																							tctctctctctttctttctttc	0.020													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	82284362	82284363	+	IGR	INS	-	CTTC	CTTC	rs150527150	by1000genomes	TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:82284362_82284363insCTTC								SEL1L (284157 upstream) : None (None downstream)																							cttccttccttcttcctttctt	0.129													4	3	---	---	---	---	
SLC28A1	9154	broad.mit.edu	37	15	85443186	85443187	+	Intron	INS	-	GAAGGAAGGAAG	GAAGGAAGGAAG			TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:85443186_85443187insGAAGGAAGGAAG	uc002blg.2	+						SLC28A1_uc010upd.1_Intron|SLC28A1_uc010bnb.2_Intron|SLC28A1_uc010upe.1_Intron|SLC28A1_uc010upf.1_Intron|SLC28A1_uc010upg.1_Intron	NM_004213	NP_004204	O00337	S28A1_HUMAN	solute carrier family 28, member 1 isoform 1						nucleobase, nucleoside and nucleotide metabolic process	integral to plasma membrane|membrane fraction	nucleoside binding			skin(2)|ovary(1)	3			BRCA - Breast invasive adenocarcinoma(143;0.0587)			aaggaaggaaggaaggaaggaa	0.025													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	17841472	17841473	+	IGR	INS	-	GGAA	GGAA	rs149621876	by1000genomes	TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:17841472_17841473insGGAA								XYLT1 (276734 upstream) : NOMO2 (669710 downstream)																							gaaggaaggatggaaggaagga	0.005													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	87302142	87302142	+	Intron	DEL	A	-	-	rs144361402		TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:87302142delA	uc002fjt.1	-											Homo sapiens cDNA FLJ43761 fis, clone TESTI2048109.																		CCTTTGATTTAAAAAAAAAAT	0.343													2	4	---	---	---	---	
TNFSF12-TNFSF13	407977	broad.mit.edu	37	17	7451454	7451455	+	5'Flank	INS	-	TCCTTCCTTCCT	TCCTTCCTTCCT			TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7451454_7451455insTCCTTCCTTCCT	uc002ghi.1	+						TNFSF12_uc002ghg.2_5'Flank|TNFSF12_uc002ghh.2_5'Flank	NM_172089	NP_742086	Q8IZK7	Q8IZK7_HUMAN	TNFSF12-TNFSF13 protein						immune response	extracellular space|membrane	cytokine activity|tumor necrosis factor receptor binding				0		Prostate(122;0.157)				gccAATTTTGGtccttccttcc	0.010													5	3	---	---	---	---	
SOCS7	30837	broad.mit.edu	37	17	36546898	36546901	+	Intron	DEL	TTCC	-	-	rs34208536		TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:36546898_36546901delTTCC	uc002hqa.2	+						SOCS7_uc010cvl.2_Intron|SOCS7_uc002hqb.2_Intron	NM_014598	NP_055413	O14512	SOCS7_HUMAN	suppressor of cytokine signaling 7						intracellular signal transduction|negative regulation of signal transduction|regulation of growth	cytoplasm|nucleus|plasma membrane	protein binding|SH3 domain binding			skin(1)	1	Breast(7;3.47e-17)					tttgttcgttttccttccttcctt	0.000													5	3	---	---	---	---	
SLC35B1	10237	broad.mit.edu	37	17	47783728	47783728	+	Intron	DEL	G	-	-	rs138147992		TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:47783728delG	uc002iph.1	-						SLC35B1_uc002ipi.1_Intron|SLC35B1_uc002ipj.1_Intron|SLC35B1_uc010wly.1_Intron	NM_005827	NP_005818	P78383	S35B1_HUMAN	solute carrier family 35, member B1							endoplasmic reticulum membrane|integral to membrane|microsome	UDP-galactose transmembrane transporter activity				0						aaaaaaaaaagaaaagaaaag	0.378													6	3	---	---	---	---	
MYCBPAP	84073	broad.mit.edu	37	17	48603775	48603776	+	Intron	INS	-	TATT	TATT	rs149225883	by1000genomes	TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48603775_48603776insTATT	uc010wmr.1	+						MYCBPAP_uc002iqz.2_Intron	NM_032133	NP_115509	Q8TBZ2	MYBPP_HUMAN	Myc-binding protein-associated protein						cell differentiation|multicellular organismal development|spermatogenesis|synaptic transmission	cytoplasm|membrane	protein binding			urinary_tract(2)|skin(2)|ovary(1)|pancreas(1)	6	Breast(11;1.23e-18)		BRCA - Breast invasive adenocarcinoma(22;1.23e-09)			atctatctatctatttatttat	0.233													4	2	---	---	---	---	
HEATR6	63897	broad.mit.edu	37	17	58156289	58156289	+	5'UTR	DEL	G	-	-			TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:58156289delG	uc002iyk.1	-	1						NM_022070	NP_071353	Q6AI08	HEAT6_HUMAN	HEAT repeat containing 6								binding			ovary(1)|skin(1)	2	all_cancers(5;2.25e-13)|Breast(5;4.84e-25)|all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		BRCA - Breast invasive adenocarcinoma(1;5.93e-19)|Epithelial(12;7.59e-12)|all cancers(12;1.26e-10)			TTCTACGGGCGGGGGGGGTGG	0.627													4	2	---	---	---	---	
BRIP1	83990	broad.mit.edu	37	17	59882316	59882321	+	Intron	DEL	TGTGTG	-	-	rs72225869		TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:59882316_59882321delTGTGTG	uc002izk.1	-							NM_032043	NP_114432	Q9BX63	FANCJ_HUMAN	BRCA1 interacting protein C-terminal helicase 1						DNA damage checkpoint|double-strand break repair|regulation of transcription from RNA polymerase II promoter	cytoplasm|nucleus	ATP binding|ATP-dependent DNA helicase activity|DNA binding|protein binding			ovary(1)	1						TCTCTCTTTCtgtgtgtgtgtgtgtg	0.097			F|N|Mis			AML|leukemia|breast		Direct_reversal_of_damage|Involved_in_tolerance_or_repair_of_DNA_crosslinks	Fanconi_Anemia				4	2	---	---	---	---	
SETBP1	26040	broad.mit.edu	37	18	42448678	42448685	+	Intron	DEL	AGGAAGGA	-	-	rs67399583		TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:42448678_42448685delAGGAAGGA	uc010dni.2	+						SETBP1_uc002lay.2_Intron	NM_015559	NP_056374	Q9Y6X0	SETBP_HUMAN	SET binding protein 1 isoform a							nucleus	DNA binding			upper_aerodigestive_tract(2)|large_intestine(1)	3				Colorectal(1;0.0622)|COAD - Colon adenocarcinoma(74;0.201)		gaaggaagggaggaaggaaggaaggaag	0.101									Schinzel-Giedion_syndrome				4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	45293739	45293740	+	IGR	INS	-	A	A	rs2852944		TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:45293739_45293740insA								IER3IP1 (590994 upstream) : SMAD2 (65727 downstream)																							aggaaggaaggagaaagaaaga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	3332891	3332891	+	IGR	DEL	T	-	-	rs142857348	by1000genomes	TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3332891delT								CELF5 (35820 upstream) : NFIC (26725 downstream)																							tcttccttcctttccttcctt	0.000													3	4	---	---	---	---	
PNPLA6	10908	broad.mit.edu	37	19	7623628	7623629	+	Intron	INS	-	CTC	CTC	rs149281719		TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7623628_7623629insCTC	uc010xjq.1	+						PNPLA6_uc002mgq.1_Intron|PNPLA6_uc010xjp.1_Intron|PNPLA6_uc002mgr.1_Intron|PNPLA6_uc002mgs.2_Intron|PNPLA6_uc002mgt.1_Intron	NM_006702	NP_006693	Q8IY17	PLPL6_HUMAN	neuropathy target esterase isoform b						cell death|lipid catabolic process|phosphatidylcholine metabolic process	endoplasmic reticulum membrane|integral to membrane	lysophospholipase activity			ovary(3)	3						GTATTCTCTCTTTTTTTTTTGC	0.545													2	4	---	---	---	---	
RINL	126432	broad.mit.edu	37	19	39359605	39359606	+	3'UTR	INS	-	G	G	rs144552100	by1000genomes	TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39359605_39359606insG	uc002ojq.2	-	12					RINL_uc002ojr.1_3'UTR|RINL_uc010xuo.1_3'UTR	NM_198445	NP_940847	Q6ZS11	RINL_HUMAN	Ras and Rab interactor-like								GTPase activator activity			pancreas(1)	1						ggctaatttttgtttttttttt	0.000													9	4	---	---	---	---	
PRKD2	25865	broad.mit.edu	37	19	47185097	47185097	+	Intron	DEL	T	-	-			TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47185097delT	uc002pfh.2	-						PRKD2_uc002pfd.2_Intron|PRKD2_uc010eks.2_Intron|PRKD2_uc010ekt.2_Intron|PRKD2_uc002pfe.2_Intron|PRKD2_uc002pff.2_Intron|PRKD2_uc002pfg.2_Intron|PRKD2_uc002pfi.2_Intron|PRKD2_uc002pfj.2_Intron|PRKD2_uc010xye.1_Intron|PRKD2_uc002pfk.2_Intron	NM_001079881	NP_001073350	Q9BZL6	KPCD2_HUMAN	protein kinase D2 isoform A						cell death|intracellular signal transduction|positive regulation of transcription from RNA polymerase II promoter|protein autophosphorylation|T cell receptor signaling pathway	cytoplasm|membrane|nucleus	ATP binding|metal ion binding|protein kinase C activity			ovary(2)|central_nervous_system(2)|stomach(1)|large_intestine(1)|lung(1)	7		Ovarian(192;0.0129)|all_neural(266;0.0459)|Breast(70;0.212)		OV - Ovarian serous cystadenocarcinoma(262;0.000189)|all cancers(93;0.000545)|Epithelial(262;0.0219)|GBM - Glioblastoma multiforme(486;0.0353)		CCATCCATACttttttttttt	0.274													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	20151841	20151842	+	IGR	INS	-	CAC	CAC	rs10627070		TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:20151841_20151842insCAC								ZDHHC8 (16312 upstream) : LOC150197 (42013 downstream)																							accaccaccatcaccaccacca	0.025													5	3	---	---	---	---	
ASCC2	84164	broad.mit.edu	37	22	30203916	30203917	+	Intron	INS	-	A	A	rs78855417		TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:30203916_30203917insA	uc003agr.2	-						ASCC2_uc003ags.2_Intron|ASCC2_uc003agt.2_Intron|ASCC2_uc011akr.1_Intron	NM_032204	NP_115580	Q9H1I8	ASCC2_HUMAN	activating signal cointegrator 1 complex subunit						regulation of transcription, DNA-dependent|transcription, DNA-dependent						0			OV - Ovarian serous cystadenocarcinoma(5;0.000103)|Epithelial(10;0.0169)|all cancers(5;0.0259)			acaacaacaacaaaaaaaaaaa	0.149													4	2	---	---	---	---	
MAP3K15	389840	broad.mit.edu	37	X	19431232	19431233	+	Intron	DEL	AC	-	-			TCGA-BP-5010-01A-02D-1421-08	TCGA-BP-5010-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:19431232_19431233delAC	uc004czk.1	-						MAP3K15_uc004czj.1_Intron	NM_001001671	NP_001001671	Q6ZN16	M3K15_HUMAN	mitogen-activated protein kinase kinase kinase								ATP binding|MAP kinase kinase kinase activity|metal ion binding			ovary(3)|lung(2)|stomach(1)|skin(1)	7	Hepatocellular(33;0.183)					ATGTTTTTATacacacacacac	0.144													4	3	---	---	---	---	
