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
LOC440563	440563	broad.mit.edu	37	1	13183615	13183615	+	Silent	SNP	T	C	C			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:13183615T>C	uc010obg.1	-	1	353	c.258A>G	c.(256-258)GCA>GCG	p.A86A		NM_001136561	NP_001130033	B2RXH8	B2RXH8_HUMAN	heterogeneous nuclear ribonucleoprotein C-like	86						ribonucleoprotein complex	nucleic acid binding|nucleotide binding				0						CTTTTGGCTCTGCAGCCAGGT	0.493													8	61	---	---	---	---	PASS
MST1P2	11209	broad.mit.edu	37	1	16975093	16975093	+	RNA	SNP	C	T	T	rs2095111	by1000genomes	TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16975093C>T	uc010och.1	+	7		c.1553C>T			MST1P2_uc001azk.2_RNA|MST1P2_uc001azl.3_RNA|MST1P2_uc009vox.2_RNA|MST1P2_uc001azm.3_RNA	NR_027504				Homo sapiens cDNA FLJ43241 fis, clone HEART1000010, weakly  similar to Hepatocyte growth factor-like protein precursor.												0						TGGGGATAGCCATGGGCCCTG	0.622													15	51	---	---	---	---	PASS
TMEM222	84065	broad.mit.edu	37	1	27648817	27648817	+	Silent	SNP	C	T	T			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:27648817C>T	uc001bnr.3	+	1	182	c.129C>T	c.(127-129)GTC>GTT	p.V43V	TMEM222_uc001bns.3_RNA|TMEM222_uc001bnt.3_RNA|TMEM222_uc001bnu.3_RNA	NM_032125	NP_115501	Q9H0R3	TM222_HUMAN	transmembrane protein 222	43	Extracellular (Potential).					integral to membrane	protein binding				0						CCGGCGGCGTCGCCATGGATG	0.677													4	14	---	---	---	---	PASS
NBPF14	25832	broad.mit.edu	37	1	148004487	148004487	+	3'UTR	SNP	T	A	A	rs138320683	by1000genomes	TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:148004487T>A	uc001eqq.2	-	22					LOC200030_uc010ozz.1_Intron|LOC200030_uc001eqe.2_Intron|LOC200030_uc001eqf.2_Intron|LOC200030_uc001eqg.2_Intron|FLJ39739_uc001eqo.1_Intron|NBPF14_uc010pab.1_3'UTR|NBPF14_uc010pac.1_3'UTR	NM_015383	NP_056198	Q5TI25	NBPFE_HUMAN	hypothetical protein LOC25832							cytoplasm				ovary(1)	1	all_hematologic(923;0.032)					TTCATTCAAATCTTCACGTGC	0.498													4	56	---	---	---	---	PASS
LASS2	29956	broad.mit.edu	37	1	150939613	150939613	+	Silent	SNP	G	T	T			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150939613G>T	uc001evy.2	-	8	1065	c.678C>A	c.(676-678)GCC>GCA	p.A226A	LASS2_uc001evz.2_Silent_p.A226A|LASS2_uc009wmh.2_Silent_p.A76A	NM_181746	NP_859530	Q96G23	CERS2_HUMAN	LAG1 longevity assurance 2	226	Helical; (Potential).|TLC.					endoplasmic reticulum membrane|integral to membrane|nuclear membrane	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|sphingosine N-acyltransferase activity				0	all_lung(15;8.07e-35)|Lung NSC(24;7.93e-31)|Lung SC(34;0.00202)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211)			GGATGTAATTGGCAAACCAGG	0.502													11	62	---	---	---	---	PASS
RPL31P11	641311	broad.mit.edu	37	1	161654816	161654816	+	RNA	SNP	G	T	T			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161654816G>T	uc001gbc.2	-	1		c.227C>A				NR_002595				Homo sapiens cDNA clone IMAGE:6574909, containing frame-shift errors.												0						ATCAATGCGCGCATCTGGAGT	0.507													2	1	---	---	---	---	PASS
GPR52	9293	broad.mit.edu	37	1	174418158	174418158	+	Silent	SNP	C	A	A			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:174418158C>A	uc001gka.1	+	1	947	c.909C>A	c.(907-909)ACC>ACA	p.T303T	RABGAP1L_uc001gjw.2_Intron|RABGAP1L_uc001gjx.2_Intron|RABGAP1L_uc001gjy.2_Intron|RABGAP1L_uc001gjz.2_Intron|uc010pmu.1_RNA	NM_005684	NP_005675	Q9Y2T5	GPR52_HUMAN	G protein-coupled receptor 52	303	Helical; Name=7; (Potential).					integral to plasma membrane	G-protein coupled receptor activity			skin(1)	1						TCTTAACAACCTGGCTTGCAA	0.423													15	84	---	---	---	---	PASS
DNAH14	127602	broad.mit.edu	37	1	225273305	225273305	+	Silent	SNP	T	C	C			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:225273305T>C	uc001how.2	+	21	3602	c.3387T>C	c.(3385-3387)GCT>GCC	p.A1129A		NM_001373	NP_001364	Q0VDD8	DYH14_HUMAN	dynein, axonemal, heavy polypeptide 14 isoform	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment					microtubule-based movement	cilium axoneme|cytoplasm|dynein complex|microtubule	ATP binding|microtubule motor activity			central_nervous_system(1)	1						ATGAAGCTGCTCTTGAAAAAA	0.299													59	89	---	---	---	---	PASS
B3GALNT2	148789	broad.mit.edu	37	1	235618936	235618936	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:235618936G>T	uc001hxc.2	-	9	1315	c.1086C>A	c.(1084-1086)GAC>GAA	p.D362E		NM_152490	NP_689703	Q8NCR0	B3GL2_HUMAN	beta-1,3-N-acetylgalactosaminyltransferase 2	362	Lumenal (Potential).				protein glycosylation	Golgi membrane|integral to membrane	galactosyltransferase activity			breast(1)	1	Ovarian(103;0.0634)|Breast(184;0.23)	all_cancers(173;0.0539)|Prostate(94;0.0353)	OV - Ovarian serous cystadenocarcinoma(106;0.000117)			CAGCTTCGAGGTCTATGTAAC	0.413													21	113	---	---	---	---	PASS
CCDC75	253635	broad.mit.edu	37	2	37321281	37321281	+	Silent	SNP	A	G	G			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:37321281A>G	uc010ezz.2	+	7	730	c.585A>G	c.(583-585)GAA>GAG	p.E195E	CCDC75_uc002rpr.3_Silent_p.E92E	NM_174931	NP_777591	Q8N954	CCD75_HUMAN	coiled-coil domain containing 75	195						intracellular	nucleic acid binding				0		all_hematologic(82;0.21)				aggagactgaagaagatgaag	0.244													25	88	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	2	38709825	38709825	+	3'UTR	SNP	C	G	G			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:38709825C>G	uc002rqu.1	+	2										SubName: Full=RPLP0 protein;																		tttgtggctgctgcccctgtg	0.353													3	5	---	---	---	---	PASS
PSME4	23198	broad.mit.edu	37	2	54150203	54150203	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:54150203A>G	uc002rxp.2	-	16	2017	c.1961T>C	c.(1960-1962)ATA>ACA	p.I654T	PSME4_uc010yop.1_Missense_Mutation_p.I540T|PSME4_uc010yoq.1_RNA|PSME4_uc010fbu.1_Missense_Mutation_p.I29T|PSME4_uc010fbv.1_Intron	NM_014614	NP_055429	Q14997	PSME4_HUMAN	proteasome (prosome, macropain) activator	654					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|cell differentiation|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|M/G1 transition of mitotic cell cycle|mRNA metabolic process|multicellular organismal development|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|spermatogenesis|viral reproduction	nuclear speck|proteasome complex	binding			ovary(2)|breast(2)|pancreas(1)	5			Lung(47;0.125)|LUSC - Lung squamous cell carcinoma(58;0.181)			AAGCTGAGTTATAACACTGCA	0.333													4	120	---	---	---	---	PASS
DNAH6	1768	broad.mit.edu	37	2	84945368	84945368	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:84945368A>G	uc010fgb.2	+	59	9789	c.9652A>G	c.(9652-9654)AGA>GGA	p.R3218G	DNAH6_uc002sot.2_5'UTR	NM_001370	NP_001361	Q9C0G6	DYH6_HUMAN	dynein, axonemal, heavy polypeptide 6	3218	AAA 5 (By similarity).				microtubule-based movement	cilium axoneme|cytoplasm|dynein complex|microtubule	ATP binding|ATPase activity|microtubule motor activity			central_nervous_system(1)	1						GGAAGAACAAAGAATTAAGCT	0.378													32	133	---	---	---	---	PASS
C2orf55	343990	broad.mit.edu	37	2	99413819	99413819	+	Silent	SNP	T	C	C			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:99413819T>C	uc002szf.1	-	8	2892	c.2598A>G	c.(2596-2598)AGA>AGG	p.R866R		NM_207362	NP_997245	Q6NV74	CB055_HUMAN	hypothetical protein LOC343990	866											0						GCACCTGGCCTCTCTCGGGCA	0.607													4	72	---	---	---	---	PASS
DPP10	57628	broad.mit.edu	37	2	116594279	116594279	+	Silent	SNP	C	A	A	rs138029087		TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:116594279C>A	uc002tla.1	+	24	2596	c.2139C>A	c.(2137-2139)GGC>GGA	p.G713G	DPP10_uc002tlb.1_Silent_p.G663G|DPP10_uc002tlc.1_Silent_p.G709G|DPP10_uc002tle.2_Silent_p.G717G|DPP10_uc002tlf.1_Silent_p.G706G	NM_020868	NP_065919	Q8N608	DPP10_HUMAN	dipeptidyl peptidase 10 isoform long	713	Extracellular (Potential).				proteolysis	integral to membrane|membrane fraction	serine-type peptidase activity			ovary(5)|large_intestine(2)|skin(2)|breast(1)	10						ATGTTCATGGCTTGAAAGAAG	0.313													24	48	---	---	---	---	PASS
PABPC1P2	728773	broad.mit.edu	37	2	147346243	147346243	+	Nonsense_Mutation	SNP	C	T	T			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:147346243C>T	uc002twf.3	+	1	1619	c.703C>T	c.(703-705)CAG>TAG	p.Q235*		NR_026904				RecName: Full=Putative protein PABPC1-like; AltName: Full=Polyadenylate-binding protein pseudogene 2;												0						AGCTATCCCACAGACCCAGAA	0.512													6	61	---	---	---	---	PASS
LRP2	4036	broad.mit.edu	37	2	170027130	170027130	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:170027130A>G	uc002ues.2	-	59	11524	c.11311T>C	c.(11311-11313)TGC>CGC	p.C3771R		NM_004525	NP_004516	P98164	LRP2_HUMAN	low density lipoprotein-related protein 2	3771	LDL-receptor class A 32.|Extracellular (Potential).				hormone biosynthetic process|protein glycosylation|receptor-mediated endocytosis|vitamin D metabolic process	coated pit|integral to membrane|lysosome	calcium ion binding|receptor activity|SH3 domain binding			ovary(13)|skin(6)|central_nervous_system(4)|large_intestine(3)|kidney(2)|pancreas(1)	29				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	Gentamicin(DB00798)|Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)|Urokinase(DB00013)	GAGGGAATGCACTGCTGATTG	0.512													20	42	---	---	---	---	PASS
ZSWIM2	151112	broad.mit.edu	37	2	187702081	187702081	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:187702081A>G	uc002upu.1	-	5	735	c.695T>C	c.(694-696)ATT>ACT	p.I232T		NM_182521	NP_872327	Q8NEG5	ZSWM2_HUMAN	zinc finger, SWIM domain containing 2	232	ZZ-type.				apoptosis		zinc ion binding			ovary(2)|skin(1)	3			OV - Ovarian serous cystadenocarcinoma(117;0.0274)|Epithelial(96;0.164)			ATTACAGGGAATCCCAAGGTG	0.343													6	215	---	---	---	---	PASS
MYO1B	4430	broad.mit.edu	37	2	192246126	192246126	+	Intron	SNP	T	C	C			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:192246126T>C	uc010fsg.2	+						MYO1B_uc002usq.2_Intron|MYO1B_uc002usr.2_Intron|MYO1B_uc002ust.1_Missense_Mutation_p.V13A	NM_001130158	NP_001123630	O43795	MYO1B_HUMAN	myosin IB isoform 1							myosin complex	actin binding|ATP binding|calmodulin binding|motor activity			central_nervous_system(5)|large_intestine(2)|ovary(1)	8			OV - Ovarian serous cystadenocarcinoma(117;0.0112)|Epithelial(96;0.104)|all cancers(119;0.236)			TGTCTGAGTGTCATTGTTTTG	0.423													4	68	---	---	---	---	PASS
DNAH7	56171	broad.mit.edu	37	2	196737119	196737119	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:196737119G>T	uc002utj.3	-	40	6589	c.6488C>A	c.(6487-6489)GCA>GAA	p.A2163E		NM_018897	NP_061720	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7	2163	AAA 3 (By similarity).				ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|microtubule motor activity			skin(10)|ovary(2)	12						ATTCTTCATTGCTTCTTTATA	0.333													22	134	---	---	---	---	PASS
DNAH7	56171	broad.mit.edu	37	2	196737120	196737120	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:196737120C>T	uc002utj.3	-	40	6588	c.6487G>A	c.(6487-6489)GCA>ACA	p.A2163T		NM_018897	NP_061720	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7	2163	AAA 3 (By similarity).				ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|microtubule motor activity			skin(10)|ovary(2)	12						TTCTTCATTGCTTCTTTATAC	0.333													22	133	---	---	---	---	PASS
NIF3L1	60491	broad.mit.edu	37	2	201768224	201768224	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:201768224G>T	uc002uwm.2	+	7	1048	c.957G>T	c.(955-957)ATG>ATT	p.M319I	NIF3L1_uc002uwl.2_Missense_Mutation_p.M292I|NIF3L1_uc002uwn.2_Missense_Mutation_p.M292I|NIF3L1_uc002uwo.2_Missense_Mutation_p.M319I|NIF3L1_uc002uwp.2_Missense_Mutation_p.M319I|NIF3L1_uc002uwq.2_Missense_Mutation_p.C273F	NM_001136039	NP_001129511	Q9GZT8	NIF3L_HUMAN	NIF3 NGG1 interacting factor 3-like 1 isoform 1	319					positive regulation of transcription, DNA-dependent		transcription factor binding			skin(1)	1						TAGGTGAGATGTCCCATCATG	0.398													14	74	---	---	---	---	PASS
DCBLD2	131566	broad.mit.edu	37	3	98531249	98531249	+	Silent	SNP	T	C	C			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:98531249T>C	uc003dtd.2	-	10	1653	c.1290A>G	c.(1288-1290)AGA>AGG	p.R430R	DCBLD2_uc003dte.2_Silent_p.R430R	NM_080927	NP_563615	Q96PD2	DCBD2_HUMAN	discoidin, CUB and LCCL domain containing 2	430	Extracellular (Potential).|F5/8 type C.				cell adhesion|intracellular receptor mediated signaling pathway|negative regulation of cell growth|wound healing	cell surface|integral to plasma membrane				ovary(2)|central_nervous_system(1)	3						TAGGATTCACTCTAATAAAAC	0.343													6	146	---	---	---	---	PASS
CBLB	868	broad.mit.edu	37	3	105389115	105389115	+	Missense_Mutation	SNP	C	A	A	rs66833786		TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:105389115C>A	uc003dwc.2	-	18	2973	c.2651G>T	c.(2650-2652)AGA>ATA	p.R884I	CBLB_uc003dwa.2_Missense_Mutation_p.R99I|CBLB_uc011bhi.1_Missense_Mutation_p.R862I	NM_170662	NP_733762	Q13191	CBLB_HUMAN	Cas-Br-M (murine) ecotropic retroviral	884	Pro-rich.				cell surface receptor linked signaling pathway|NLS-bearing substrate import into nucleus	cytoplasm|nucleus	calcium ion binding|ligase activity|signal transducer activity|zinc ion binding			lung(4)|ovary(3)|breast(1)|skin(1)	9						CTGTGATGTTCTGTTAGTTTT	0.368			Mis S		AML								78	128	---	---	---	---	PASS
MUC4	4585	broad.mit.edu	37	3	195505960	195505960	+	Missense_Mutation	SNP	G	C	C	rs112020305	by1000genomes	TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195505960G>C	uc011bto.1	-	3	12567	c.12107C>G	c.(12106-12108)ACC>AGC	p.T4036S	MUC4_uc003fva.2_5'Flank|MUC4_uc003fvb.2_5'Flank|MUC4_uc003fvc.2_5'Flank|MUC4_uc003fvd.2_5'Flank|MUC4_uc003fve.2_5'Flank|MUC4_uc010hzr.2_5'Flank|MUC4_uc011btf.1_5'Flank|MUC4_uc011btg.1_5'Flank|MUC4_uc011bth.1_5'Flank|MUC4_uc011bti.1_5'Flank|MUC4_uc011btj.1_5'Flank|MUC4_uc011btk.1_5'Flank|MUC4_uc011btl.1_5'Flank|MUC4_uc011btm.1_5'Flank|MUC4_uc011btn.1_5'Flank|MUC4_uc003fvo.2_Intron|MUC4_uc003fvp.2_Intron|MUC4_uc010hzu.1_Intron	NM_018406	NP_060876	Q99102	MUC4_HUMAN	mucin 4 isoform a	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment					cell-matrix adhesion	integral to plasma membrane|proteinaceous extracellular matrix	ErbB-2 class receptor binding|extracellular matrix constituent, lubricant activity				0	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GGAAGCGTCGGTGACAGGAAG	0.587													5	41	---	---	---	---	PASS
MUC4	4585	broad.mit.edu	37	3	195513758	195513758	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195513758G>C	uc011bto.1	-	2	5153	c.4693C>G	c.(4693-4695)CAC>GAC	p.H1565D	MUC4_uc003fvo.2_Intron|MUC4_uc003fvp.2_Intron|MUC4_uc010hzu.1_Intron	NM_018406	NP_060876	Q99102	MUC4_HUMAN	mucin 4 isoform a	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment					cell-matrix adhesion	integral to plasma membrane|proteinaceous extracellular matrix	ErbB-2 class receptor binding|extracellular matrix constituent, lubricant activity				0	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GGGGTGGTGTGACCTGTGGAT	0.572													3	50	---	---	---	---	PASS
HTT	3064	broad.mit.edu	37	4	3210609	3210609	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3210609G>A	uc011bvq.1	+	47	6413	c.6268G>A	c.(6268-6270)GTG>ATG	p.V2090M		NM_002111	NP_002102	P42858	HD_HUMAN	huntingtin	2088					establishment of mitotic spindle orientation|Golgi organization|retrograde vesicle-mediated transport, Golgi to ER|vesicle transport along microtubule	autophagic vacuole|axon|cytoplasmic vesicle membrane|cytosol|dendrite|endoplasmic reticulum|Golgi apparatus|late endosome|membrane fraction|nucleus|protein complex	beta-tubulin binding|dynactin binding|dynein intermediate chain binding|p53 binding|transcription factor binding			skin(2)|ovary(1)|lung(1)	4		all_epithelial(65;0.18)		UCEC - Uterine corpus endometrioid carcinoma (64;0.187)		GGATGGGCACGTGTCACTGGA	0.577													5	69	---	---	---	---	PASS
ANK2	287	broad.mit.edu	37	4	114286249	114286249	+	Missense_Mutation	SNP	T	A	A			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:114286249T>A	uc003ibe.3	+	41	11043	c.10943T>A	c.(10942-10944)CTC>CAC	p.L3648H	ANK2_uc003ibd.3_Missense_Mutation_p.L1554H|ANK2_uc003ibf.3_Missense_Mutation_p.L1563H|ANK2_uc011cgc.1_Missense_Mutation_p.L739H|ANK2_uc003ibg.3_Missense_Mutation_p.L547H|ANK2_uc003ibh.3_Missense_Mutation_p.L237H|ANK2_uc011cgd.1_Missense_Mutation_p.L950H	NM_001148	NP_001139	Q01484	ANK2_HUMAN	ankyrin 2 isoform 1	3615	Death.				axon guidance|signal transduction	apical plasma membrane|basolateral plasma membrane|cytoskeleton|cytosol|sarcomere	protein binding|protein binding			central_nervous_system(7)|ovary(3)|large_intestine(2)|breast(1)|skin(1)	14		Ovarian(17;0.0448)|Hepatocellular(203;0.218)		OV - Ovarian serous cystadenocarcinoma(123;4.92e-05)		ATTGTTCATCTCATGGAGACC	0.408													14	60	---	---	---	---	PASS
RAI14	26064	broad.mit.edu	37	5	34830951	34830951	+	3'UTR	SNP	T	C	C			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:34830951T>C	uc003jir.2	+	18					RAI14_uc010iur.2_3'UTR|RAI14_uc011coj.1_3'UTR|RAI14_uc003jis.2_3'UTR|RAI14_uc003jit.2_3'UTR|RAI14_uc011cok.1_3'UTR	NM_015577	NP_056392	Q9P0K7	RAI14_HUMAN	retinoic acid induced 14 isoform a							cell cortex|cytoskeleton	protein binding			ovary(1)	1	all_lung(31;0.000191)					GCTGCCATTGTTCTCATTCGT	0.512													5	26	---	---	---	---	PASS
ERBB2IP	55914	broad.mit.edu	37	5	65317151	65317151	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:65317151A>G	uc003juk.1	+	8	843	c.535A>G	c.(535-537)ACT>GCT	p.T179A	ERBB2IP_uc003juh.1_Missense_Mutation_p.T179A|ERBB2IP_uc003jui.1_Missense_Mutation_p.T179A|ERBB2IP_uc003juj.1_Missense_Mutation_p.T179A|ERBB2IP_uc011cqx.1_Missense_Mutation_p.T179A|ERBB2IP_uc011cqy.1_Missense_Mutation_p.T179A|ERBB2IP_uc011cqz.1_Missense_Mutation_p.T179A|ERBB2IP_uc010iwx.1_Missense_Mutation_p.T179A|ERBB2IP_uc003jul.1_Missense_Mutation_p.T179A	NM_018695	NP_061165	Q96RT1	LAP2_HUMAN	ERBB2 interacting protein isoform 2	179	LRR 7.				basal protein localization|cell adhesion|cell cycle|cell growth|epidermal growth factor receptor signaling pathway|establishment or maintenance of epithelial cell apical/basal polarity|integrin-mediated signaling pathway|intermediate filament cytoskeleton organization	basement membrane|cytoplasm|hemidesmosome|nucleus	ErbB-2 class receptor binding|integrin binding|structural constituent of cytoskeleton			ovary(3)|lung(2)|central_nervous_system(2)	7		Lung NSC(167;9.45e-06)|Prostate(74;0.0139)|Ovarian(174;0.0547)|Breast(144;0.093)|Colorectal(97;0.234)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0767)|Lung(70;0.00191)		TATGAACAGAACTATGAATAG	0.333													4	80	---	---	---	---	PASS
IQGAP2	10788	broad.mit.edu	37	5	75896708	75896708	+	Silent	SNP	C	G	G			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:75896708C>G	uc003kek.2	+	11	1365	c.1143C>G	c.(1141-1143)GCC>GCG	p.A381A		NM_006633	NP_006624	Q13576	IQGA2_HUMAN	IQ motif containing GTPase activating protein 2	381					small GTPase mediated signal transduction	actin cytoskeleton	actin binding|calmodulin binding|GTPase inhibitor activity|Ras GTPase activator activity			ovary(6)|central_nervous_system(1)	7		all_lung(232;0.000514)|Lung NSC(167;0.00135)|Prostate(461;0.00838)|Ovarian(174;0.0149)		all cancers(79;1.38e-36)		TAAACCAGGCCTTGGAAAGCA	0.448													18	108	---	---	---	---	PASS
MAN2A1	4124	broad.mit.edu	37	5	109183362	109183362	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:109183362G>C	uc003kou.1	+	19	3810	c.2847G>C	c.(2845-2847)CAG>CAC	p.Q949H		NM_002372	NP_002363	Q16706	MA2A1_HUMAN	mannosidase, alpha, class 2A, member 1	949	Lumenal (Potential).				mannose metabolic process|post-translational protein modification|protein N-linked glycosylation via asparagine	Golgi membrane|integral to membrane	alpha-mannosidase activity|carbohydrate binding|mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase activity|zinc ion binding			ovary(1)|central_nervous_system(1)|pancreas(1)	3		all_cancers(142;8.66e-07)|all_epithelial(76;7.73e-09)|Prostate(80;0.000303)|Lung NSC(167;0.0186)|all_lung(232;0.0241)|Ovarian(225;0.0444)|Colorectal(57;0.0959)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;2.17e-10)|Epithelial(69;1.37e-09)|COAD - Colon adenocarcinoma(37;0.141)		tgttAGGTCAGATTGAAGTTA	0.323													4	92	---	---	---	---	PASS
HLA-A	3105	broad.mit.edu	37	6	29910607	29910607	+	Silent	SNP	G	C	C	rs72555397		TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:29910607G>C	uc003nol.2	+	2	147	c.147G>C	c.(145-147)GTG>GTC	p.V49V	HLA-G_uc011dmb.1_Intron|HCG4P6_uc003nog.1_Intron|HLA-A_uc010jrq.2_5'UTR|HLA-A_uc003nok.2_5'UTR|HLA-A_uc003non.2_Silent_p.V49V|HLA-A_uc003noo.2_Silent_p.V49V|HLA-A_uc010jrr.2_Silent_p.V49V|HLA-A_uc003nom.2_5'UTR|HLA-A_uc010klp.2_Silent_p.V21V|HLA-A_uc011dmc.1_5'UTR|HLA-A_uc011dmd.1_5'Flank	NM_002116	NP_002107	P30443	1A01_HUMAN	major histocompatibility complex, class I, A	49	Extracellular (Potential).|Alpha-1.				antigen processing and presentation of peptide antigen via MHC class I|interferon-gamma-mediated signaling pathway|interspecies interaction between organisms|regulation of immune response|type I interferon-mediated signaling pathway	integral to plasma membrane|MHC class I protein complex	MHC class I receptor activity			upper_aerodigestive_tract(1)|ovary(1)	2						TCATCGCCGTGGGCTACGTGG	0.692									Melanoma_Familial_Clustering_of|Lichen_Sclerosis_et_Atrophicus_Familial_Clustering_of|Osteosarcoma_Familial_Clustering_of|Naso-/Oropharyngeal/Laryngeal_Cancer_Familial_Clustering_of	Multiple Myeloma(9;0.094)			3	11	---	---	---	---	PASS
LRFN2	57497	broad.mit.edu	37	6	40400231	40400231	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:40400231G>A	uc003oph.1	-	2	1087	c.622C>T	c.(622-624)CGG>TGG	p.R208W		NM_020737	NP_065788	Q9ULH4	LRFN2_HUMAN	leucine rich repeat and fibronectin type III	208	LRR 7.|Extracellular (Potential).					cell junction|integral to membrane|postsynaptic membrane				ovary(2)|skin(1)	3	Ovarian(28;0.0418)|Colorectal(47;0.196)					TTCTGCAGCCGATTGGAGGTG	0.612													9	29	---	---	---	---	PASS
HGC6.3	100128124	broad.mit.edu	37	6	168377135	168377135	+	Silent	SNP	T	C	C	rs75642682		TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:168377135T>C	uc010kks.1	-	1	485	c.198A>G	c.(196-198)CAA>CAG	p.Q66Q		NM_001129895	NP_001123367	Q9UM08	Q9UM08_HUMAN	hypothetical protein LOC100128124	66											0						CTGCAGTGTGTTGGGAGGAGG	0.622													4	19	---	---	---	---	PASS
HGC6.3	100128124	broad.mit.edu	37	6	168377136	168377136	+	Missense_Mutation	SNP	T	G	G	rs77639335		TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:168377136T>G	uc010kks.1	-	1	484	c.197A>C	c.(196-198)CAA>CCA	p.Q66P		NM_001129895	NP_001123367	Q9UM08	Q9UM08_HUMAN	hypothetical protein LOC100128124	66											0						TGCAGTGTGTTGGGAGGAGGA	0.622													5	18	---	---	---	---	PASS
POLD2	5425	broad.mit.edu	37	7	44155783	44155783	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:44155783G>A	uc010kxz.2	-	9	1600	c.950C>T	c.(949-951)CCG>CTG	p.P317L	POLD2_uc003tke.3_Missense_Mutation_p.P317L|POLD2_uc010kya.2_Missense_Mutation_p.P317L|POLD2_uc003tkf.3_Missense_Mutation_p.P317L	NM_006230	NP_006221	P49005	DPOD2_HUMAN	DNA-directed DNA polymerase delta 2	317					base-excision repair|DNA strand elongation involved in DNA replication|nucleotide-excision repair, DNA gap filling|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|transcription-coupled nucleotide-excision repair	nucleoplasm	DNA binding|DNA-directed DNA polymerase activity|protein binding			ovary(2)	2						AGTGGCCAGCGGGAACATGCA	0.622													4	51	---	---	---	---	PASS
ZNF727	442319	broad.mit.edu	37	7	63529902	63529902	+	Silent	SNP	C	T	T			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:63529902C>T	uc011kdm.1	+	3	320	c.141C>T	c.(139-141)ATC>ATT	p.I47I		NM_001159522	NP_001152994	A8MUV8	ZN727_HUMAN	zinc finger protein 727	47	KRAB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						GTCTTGCTATCTTTAAGCCAG	0.403													5	117	---	---	---	---	PASS
MAGI2	9863	broad.mit.edu	37	7	77814874	77814874	+	Intron	SNP	C	T	T			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:77814874C>T	uc003ugx.2	-						MAGI2_uc003ugy.2_Intron|MAGI2_uc010ldx.1_Intron|MAGI2_uc010ldy.1_3'UTR	NM_012301	NP_036433	Q86UL8	MAGI2_HUMAN	membrane associated guanylate kinase, WW and PDZ							cell junction|synapse|synaptosome	phosphatase binding			ovary(5)|lung(4)|breast(1)|skin(1)	11		all_cancers(73;0.0064)|all_epithelial(88;0.087)|all_neural(109;0.0936)|Medulloblastoma(109;0.166)|Melanoma(862;0.236)				CTGATACTATCAGAAGAATGA	0.383													14	50	---	---	---	---	PASS
SRRT	51593	broad.mit.edu	37	7	100483954	100483954	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100483954G>C	uc003uwy.2	+	14	1813	c.1545G>C	c.(1543-1545)CAG>CAC	p.Q515H	SRRT_uc010lhl.1_Missense_Mutation_p.Q514H|SRRT_uc003uxa.2_Missense_Mutation_p.Q514H|SRRT_uc003uwz.2_Missense_Mutation_p.Q515H	NM_015908	NP_056992	Q9BXP5	SRRT_HUMAN	arsenate resistance protein 2 isoform a	515					cell proliferation|primary miRNA processing|response to arsenic-containing substance	cytoplasm|nucleoplasm	protein binding			ovary(2)	2						AGCACAAGCAGATTGTGCGCA	0.622													5	15	---	---	---	---	PASS
LAMB4	22798	broad.mit.edu	37	7	107689798	107689798	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:107689798T>C	uc010ljo.1	-	27	4179	c.4095A>G	c.(4093-4095)ATA>ATG	p.I1365M	LAMB4_uc003vey.2_Missense_Mutation_p.I1365M|LAMB4_uc010ljp.1_Missense_Mutation_p.I334M	NM_007356	NP_031382	A4D0S4	LAMB4_HUMAN	laminin, beta 4 precursor	1365	Domain II.				cell adhesion	basement membrane				ovary(4)|breast(2)|large_intestine(1)|skin(1)	8						GGATATCTGGTATCTTAATCT	0.308													5	224	---	---	---	---	PASS
C7orf66	154907	broad.mit.edu	37	7	108524161	108524161	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:108524161T>C	uc003vfo.2	-	2	299	c.251A>G	c.(250-252)GAG>GGG	p.E84G		NM_001024607	NP_001019778	A4D0T2	CG066_HUMAN	hypothetical protein LOC154907	84						integral to membrane				ovary(2)	2						TATGTATCCCTCATGAATTCT	0.393													6	184	---	---	---	---	PASS
DLC1	10395	broad.mit.edu	37	8	12947921	12947921	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:12947921A>G	uc003wwm.2	-	15	4358	c.3914T>C	c.(3913-3915)CTC>CCC	p.L1305P	DLC1_uc003wwk.1_Missense_Mutation_p.L868P|DLC1_uc003wwl.1_Missense_Mutation_p.L902P|DLC1_uc011kxx.1_Missense_Mutation_p.L794P	NM_182643	NP_872584	Q96QB1	RHG07_HUMAN	deleted in liver cancer 1 isoform 1	1305					actin cytoskeleton organization|activation of caspase activity|focal adhesion assembly|forebrain development|heart morphogenesis|hindbrain morphogenesis|induction of apoptosis|negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of Rho protein signal transduction|negative regulation of stress fiber assembly|neural tube closure|positive regulation of protein dephosphorylation|regulation of cell shape|small GTPase mediated signal transduction	caveola|cytosol|focal adhesion|nucleus	Rho GTPase activator activity|SH2 domain binding			ovary(3)|pancreas(2)|lung(1)|kidney(1)	7						TTCCAGAGTGAGGGGCTTCAG	0.517													4	58	---	---	---	---	PASS
KIAA1967	57805	broad.mit.edu	37	8	22464177	22464177	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:22464177G>C	uc003xch.2	+	4	345	c.208G>C	c.(208-210)GGG>CGG	p.G70R	KIAA1967_uc003xci.2_Missense_Mutation_p.G70R|KIAA1967_uc003xcj.1_5'UTR	NM_199205	NP_954675	Q8N163	K1967_HUMAN	p30 DBC protein	70					apoptosis|positive regulation of apoptosis	mitochondrial matrix|nucleus	enzyme binding|enzyme inhibitor activity			ovary(1)|central_nervous_system(1)|skin(1)	3		Prostate(55;0.0421)|Breast(100;0.102)|all_epithelial(46;0.142)		BRCA - Breast invasive adenocarcinoma(99;0.00593)|Colorectal(74;0.0157)|COAD - Colon adenocarcinoma(73;0.064)		TGACTACTTTGGGGTTGTGGA	0.463													9	234	---	---	---	---	PASS
ADAM28	10863	broad.mit.edu	37	8	24170950	24170950	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:24170950C>T	uc003xdy.2	+	6	516	c.433C>T	c.(433-435)CCC>TCC	p.P145S	ADAM28_uc003xdx.2_Missense_Mutation_p.P145S|ADAM28_uc011kzz.1_Intron|ADAM28_uc011laa.1_RNA	NM_014265	NP_055080	Q9UKQ2	ADA28_HUMAN	ADAM metallopeptidase domain 28 isoform 1	145					proteolysis|spermatogenesis	extracellular region|integral to membrane|plasma membrane	metalloendopeptidase activity|zinc ion binding			skin(3)|lung(1)|central_nervous_system(1)	5		Prostate(55;0.0959)		Colorectal(74;0.0129)|COAD - Colon adenocarcinoma(73;0.0434)|BRCA - Breast invasive adenocarcinoma(99;0.175)		ACCTTTAAGCCCCATACATCG	0.438													36	83	---	---	---	---	PASS
MCM4	4173	broad.mit.edu	37	8	48875365	48875365	+	Silent	SNP	A	G	G			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:48875365A>G	uc003xqk.1	+	6	638	c.543A>G	c.(541-543)GAA>GAG	p.E181E	PRKDC_uc003xqi.2_5'Flank|PRKDC_uc003xqj.2_5'Flank|PRKDC_uc011ldh.1_5'Flank|MCM4_uc003xql.1_Silent_p.E181E|MCM4_uc011ldi.1_Silent_p.E168E|MCM4_uc010lxw.1_RNA	NM_182746	NP_877423	P33991	MCM4_HUMAN	minichromosome maintenance complex component 4	181					cell cycle checkpoint|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle	MCM complex	ATP binding|DNA binding|helicase activity|protein binding			ovary(2)|skin(2)	4		all_cancers(86;0.026)|all_epithelial(80;0.000748)|Lung NSC(129;0.00327)|all_lung(136;0.00354)				CTAAAGAAGAAGAAAATGTTG	0.348													5	180	---	---	---	---	PASS
DENND3	22898	broad.mit.edu	37	8	142185510	142185510	+	Silent	SNP	C	T	T			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:142185510C>T	uc003yvy.2	+	14	2525	c.2247C>T	c.(2245-2247)ACC>ACT	p.T749T	DENND3_uc010mep.2_Silent_p.T710T|DENND3_uc003yvz.1_Silent_p.T433T	NM_014957	NP_055772	A2RUS2	DEND3_HUMAN	DENN/MADD domain containing 3	749										ovary(1)	1	all_cancers(97;7.36e-15)|all_epithelial(106;2.33e-13)|Lung NSC(106;1.23e-05)|all_lung(105;1.75e-05)|Ovarian(258;0.01)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.105)			TCCTCCTAACCGAAGGAAGGC	0.493											OREG0019025	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	3	37	---	---	---	---	PASS
CNTNAP3	79937	broad.mit.edu	37	9	39171364	39171364	+	Splice_Site	SNP	A	G	G			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:39171364A>G	uc004abi.2	-	8	1572	c.1333_splice	c.e8+1	p.G445_splice	CNTNAP3_uc004abj.2_Splice_Site_p.G445_splice|CNTNAP3_uc011lqr.1_Splice_Site|CNTNAP3_uc004abk.1_Splice_Site_p.G445_splice|CNTNAP3_uc011lqs.1_Splice_Site_p.G445_splice|CNTNAP3_uc004abl.1_Splice_Site_p.G357_splice	NM_033655	NP_387504	Q9BZ76	CNTP3_HUMAN	cell recognition molecule CASPR3 precursor						cell adhesion|cell recognition|signal transduction	extracellular region|integral to membrane|plasma membrane	receptor binding			ovary(1)	1				GBM - Glioblastoma multiforme(29;0.02)|Lung(182;0.0681)		TACAACTGTTACCTGCTGTGA	0.483													3	44	---	---	---	---	PASS
MIR204	406987	broad.mit.edu	37	9	73424944	73424944	+	RNA	SNP	C	A	A			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:73424944C>A	hsa-mir-204|MI0000284	-			c.57C>A			TRPM3_uc004ahu.2_Intron|TRPM3_uc004ahv.2_Intron|TRPM3_uc004ahw.2_Intron|TRPM3_uc004ahx.2_Intron|TRPM3_uc004ahy.2_Intron|TRPM3_uc004ahz.2_Intron|TRPM3_uc004aia.2_Intron|TRPM3_uc004aib.2_Intron|TRPM3_uc004aid.2_Intron|TRPM3_uc004aic.2_Intron|TRPM3_uc010mor.2_Intron|TRPM3_uc004aie.2_Intron|TRPM3_uc004aif.2_Intron|TRPM3_uc004aig.2_Intron|uc004aih.1_RNA																	0						TTCATATATTCTCAGGCATAG	0.478													17	76	---	---	---	---	PASS
NEBL	10529	broad.mit.edu	37	10	21074611	21074611	+	3'UTR	SNP	C	T	T			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:21074611C>T	uc001iqi.2	-	28					NEBL_uc001iqj.2_RNA|NEBL_uc001iqk.2_3'UTR	NM_006393	NP_006384	O76041	NEBL_HUMAN	nebulette sarcomeric isoform						regulation of actin filament length		actin binding|structural constituent of muscle			ovary(2)	2						AAAGTATCTTCTATCTTTTAA	0.358													4	17	---	---	---	---	PASS
TTC18	118491	broad.mit.edu	37	10	75095189	75095189	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:75095189T>C	uc009xrc.2	-	8	1007	c.886A>G	c.(886-888)AGT>GGT	p.S296G	TTC18_uc001jty.2_Missense_Mutation_p.S296G|TTC18_uc009xrd.1_Missense_Mutation_p.S104G	NM_145170	NP_660153	Q5T0N1	TTC18_HUMAN	tetratricopeptide repeat domain 18	296							binding			ovary(2)|central_nervous_system(1)	3	Prostate(51;0.0119)					TCTTCTTACCTGACCACTGCA	0.383													24	114	---	---	---	---	PASS
HHEX	3087	broad.mit.edu	37	10	94454434	94454434	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:94454434C>A	uc001kid.2	+	4	785	c.722C>A	c.(721-723)GCC>GAC	p.A241D		NM_002729	NP_002720	Q03014	HHEX_HUMAN	hematopoietically expressed homeobox	241					anterior/posterior pattern formation|B cell differentiation|cell cycle|DNA conformation change|negative regulation of angiogenesis|negative regulation of transcription by competitive promoter binding|negative regulation of transcription from RNA polymerase II promoter|negative regulation of vascular endothelial growth factor receptor signaling pathway|poly(A)+ mRNA export from nucleus|positive regulation of transcription from RNA polymerase II promoter|positive regulation of Wnt receptor signaling pathway|protein localization to nucleus|Wnt receptor signaling pathway	cytoplasm|nucleus|protein-DNA complex	DNA bending activity|eukaryotic initiation factor 4E binding|protein homodimerization activity|repressing transcription factor binding|sequence-specific DNA binding|TBP-class protein binding|transcription regulatory region DNA binding			ovary(1)	1						CCCTCCCCTGCCTCCCAGGAA	0.463													4	62	---	---	---	---	PASS
RRP12	23223	broad.mit.edu	37	10	99125881	99125881	+	Silent	SNP	T	C	C			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:99125881T>C	uc001knf.2	-	29	3640	c.3501A>G	c.(3499-3501)GAA>GAG	p.E1167E	RRP12_uc001kne.2_Silent_p.E182E|RRP12_uc009xvl.2_Silent_p.E284E|RRP12_uc009xvm.2_Silent_p.E885E|RRP12_uc010qou.1_Silent_p.E1106E|RRP12_uc009xvn.2_Silent_p.E1067E	NM_015179	NP_055994	Q5JTH9	RRP12_HUMAN	ribosomal RNA processing 12 homolog isoform 1	1167						integral to membrane|nuclear membrane|nucleolus	protein binding			ovary(2)|central_nervous_system(1)	3		Colorectal(252;0.162)		Epithelial(162;2.72e-09)|all cancers(201;1.76e-07)		CACCTTCCTCTTCCTCCATCT	0.577													18	49	---	---	---	---	PASS
CRTAC1	55118	broad.mit.edu	37	10	99664546	99664546	+	Silent	SNP	C	T	T			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:99664546C>T	uc001kou.1	-	7	1232	c.876G>A	c.(874-876)GGG>GGA	p.G292G	CRTAC1_uc001kov.2_Silent_p.G281G|CRTAC1_uc001kot.1_Silent_p.G82G	NM_018058	NP_060528	Q9NQ79	CRAC1_HUMAN	cartilage acidic protein 1 precursor	292	FG-GAP 3; atypical.					proteinaceous extracellular matrix	calcium ion binding			ovary(4)|pancreas(1)	5		Colorectal(252;0.24)		Epithelial(162;2.18e-10)|all cancers(201;3.27e-09)		CGACACCTCGCCCATGCTGGT	0.607													3	24	---	---	---	---	PASS
NAP1L4	4676	broad.mit.edu	37	11	2992733	2992733	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:2992733G>A	uc001lxc.2	-	6	488	c.347C>T	c.(346-348)CCA>CTA	p.P116L	NAP1L4_uc010qxm.1_Missense_Mutation_p.P116L|NAP1L4_uc010qxn.1_Missense_Mutation_p.P116L	NM_005969	NP_005960	Q99733	NP1L4_HUMAN	nucleosome assembly protein 1-like 4	116					nucleosome assembly	chromatin assembly complex|cytoplasm	unfolded protein binding			ovary(1)	1		all_epithelial(84;0.000236)|Medulloblastoma(188;0.00106)|Breast(177;0.00328)|Ovarian(85;0.00556)|all_neural(188;0.00681)		BRCA - Breast invasive adenocarcinoma(625;0.00301)|LUSC - Lung squamous cell carcinoma(625;0.211)		CGCATCTGTTGGTTCAACATC	0.343													22	161	---	---	---	---	PASS
DNHD1	144132	broad.mit.edu	37	11	6566997	6566997	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6566997G>C	uc001mdw.3	+	21	5392	c.4828G>C	c.(4828-4830)GGT>CGT	p.G1610R	DNHD1_uc001mds.1_Missense_Mutation_p.G320R	NM_144666	NP_653267	Q96M86	DNHD1_HUMAN	dynein heavy chain domain 1 isoform 1	1610					microtubule-based movement	dynein complex	microtubule motor activity			ovary(2)	2		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.171)		Epithelial(150;3.93e-08)|BRCA - Breast invasive adenocarcinoma(625;0.13)		GTATCACTTGGGTTCACCTCA	0.512													18	47	---	---	---	---	PASS
MUC15	143662	broad.mit.edu	37	11	26582715	26582715	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:26582715T>C	uc001mqx.2	-	4	1168	c.902A>G	c.(901-903)TAC>TGC	p.Y301C	ANO3_uc010rdr.1_Intron|ANO3_uc001mqt.3_Intron|ANO3_uc010rds.1_Intron|ANO3_uc010rdt.1_Intron|MUC15_uc001mqw.2_Missense_Mutation_p.Y328C|MUC15_uc001mqy.2_Missense_Mutation_p.Y278C	NM_145650	NP_663625	Q8N387	MUC15_HUMAN	mucin 15 isoform b	301	Cytoplasmic (Potential).					extracellular region|integral to membrane|plasma membrane				ovary(1)|central_nervous_system(1)|pancreas(1)	3						TGGATTGTAGTAGCTAGAATT	0.388													4	187	---	---	---	---	PASS
LRP4	4038	broad.mit.edu	37	11	46894661	46894661	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:46894661C>G	uc001ndn.3	-	30	4719	c.4573G>C	c.(4573-4575)GAT>CAT	p.D1525H	uc001ndl.2_RNA	NM_002334	NP_002325	O75096	LRP4_HUMAN	low density lipoprotein receptor-related protein	1525	Extracellular (Potential).|LDL-receptor class B 18.				endocytosis|negative regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway	integral to membrane	calcium ion binding|receptor activity			skin(2)|upper_aerodigestive_tract(1)|ovary(1)	4				Lung(87;0.159)		CTGCGGGTATCATAGTCCAGG	0.502													9	48	---	---	---	---	PASS
NPAS4	266743	broad.mit.edu	37	11	66192144	66192144	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66192144C>T	uc001ohx.1	+	7	1959	c.1783C>T	c.(1783-1785)CGG>TGG	p.R595W	NPAS4_uc010rpc.1_Missense_Mutation_p.R385W	NM_178864	NP_849195	Q8IUM7	NPAS4_HUMAN	neuronal PAS domain protein 4	595					transcription, DNA-dependent		DNA binding|signal transducer activity				0						AGCCCAGCTCCGGGGCCCCCT	0.592													3	21	---	---	---	---	PASS
DIXDC1	85458	broad.mit.edu	37	11	111857650	111857650	+	Splice_Site	SNP	T	C	C			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:111857650T>C	uc001pml.2	+	10	1359	c.1062_splice	c.e10+2	p.K354_splice	DIXDC1_uc001pmm.2_Splice_Site_p.K143_splice|DIXDC1_uc001pmn.2_Splice_Site_p.K60_splice|DIXDC1_uc010rwq.1_5'Flank	NM_001037954	NP_001033043	Q155Q3	DIXC1_HUMAN	DIX domain containing 1 isoform a						multicellular organismal development|positive regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway	cytosol|focal adhesion	actin binding|gamma-tubulin binding|signal transducer activity			ovary(1)	1		all_cancers(61;7.58e-15)|all_epithelial(67;5.42e-09)|Melanoma(852;1.91e-06)|all_hematologic(158;0.000405)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0112)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		Epithelial(105;2.99e-07)|BRCA - Breast invasive adenocarcinoma(274;6.72e-07)|all cancers(92;6.25e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.0548)		GACTTAAAGGTATGTCAAGAC	0.269													4	177	---	---	---	---	PASS
LOC100288778	100288778	broad.mit.edu	37	12	88906	88906	+	Silent	SNP	A	T	T			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:88906A>T	uc010scy.1	+	7	882	c.327A>T	c.(325-327)CCA>CCT	p.P109P	LOC100288778_uc010scz.1_RNA|LOC100288778_uc010sdc.1_RNA|LOC100288778_uc010sdd.1_Silent_p.P109P|LOC100288778_uc010sde.1_Silent_p.P109P|LOC100288778_uc010sdf.1_Silent_p.P109P|LOC100288778_uc010sdg.1_Silent_p.P109P|LOC100288778_uc010sdh.1_RNA					SubName: Full=Actin nucleation promoting factor; Flags: Fragment;												0						ccccaccaccacccccaGCTC	0.512													5	24	---	---	---	---	PASS
NOP2	4839	broad.mit.edu	37	12	6672820	6672820	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6672820C>A	uc001qpk.1	-	6	692	c.648G>T	c.(646-648)GAG>GAT	p.E216D	NOP2_uc009zeq.1_5'Flank|NOP2_uc001qph.1_Missense_Mutation_p.E212D|NOP2_uc001qpi.1_Missense_Mutation_p.E212D|NOP2_uc001qpj.1_Intron|NOP2_uc001qpl.1_Missense_Mutation_p.E249D|NOP2_uc001qpm.1_Missense_Mutation_p.E216D			P46087	NOP2_HUMAN	Homo sapiens cDNA FLJ31646 fis, clone NT2RI2003921, highly similar to PROLIFERATING-CELL NUCLEOLAR ANTIGEN P120.	216					positive regulation of cell proliferation|rRNA processing	nucleolus	protein binding|RNA binding|S-adenosylmethionine-dependent methyltransferase activity			ovary(2)	2						CAAATGGTTCCTCATCCACAT	0.572											OREG0021630	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	11	37	---	---	---	---	PASS
FAM186A	121006	broad.mit.edu	37	12	50744578	50744578	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:50744578T>C	uc001rwl.2	-	4	6175	c.6037A>G	c.(6037-6039)AGA>GGA	p.R2013G	FAM186A_uc010smt.1_Missense_Mutation_p.R1791G	NM_001145475	NP_001138947	A6NE01	F186A_HUMAN	family with sequence similarity 186, member A	2013											0						TGAAATGTTCTAAATGATTCT	0.423													4	166	---	---	---	---	PASS
ZFC3H1	196441	broad.mit.edu	37	12	72004144	72004144	+	3'UTR	SNP	T	C	C			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:72004144T>C	uc001swo.2	-	35						NM_144982	NP_659419	O60293	ZC3H1_HUMAN	proline/serine-rich coiled-coil 2						RNA processing	intracellular	metal ion binding			ovary(2)|breast(1)|central_nervous_system(1)|skin(1)	5						AGCCTAATCTTGAAGAATCAT	0.378													4	89	---	---	---	---	PASS
ZCCHC8	55596	broad.mit.edu	37	12	122967187	122967187	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:122967187G>A	uc001ucn.2	-	8	858	c.727C>T	c.(727-729)CCA>TCA	p.P243S	ZCCHC8_uc001ucm.2_Missense_Mutation_p.P5S|ZCCHC8_uc009zxp.2_Missense_Mutation_p.P5S|ZCCHC8_uc009zxq.2_Missense_Mutation_p.P5S	NM_017612	NP_060082	Q6NZY4	ZCHC8_HUMAN	zinc finger, CCHC domain containing 8	243	CCHC-type.					catalytic step 2 spliceosome	nucleic acid binding|protein binding|zinc ion binding				0	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;5.25e-05)|Epithelial(86;0.000113)|BRCA - Breast invasive adenocarcinoma(302;0.202)		TTTACCATTGGGCAATCTTTC	0.303													19	34	---	---	---	---	PASS
C13orf15	28984	broad.mit.edu	37	13	42042974	42042974	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:42042974A>G	uc001uyi.2	+	4	708	c.406A>G	c.(406-408)AGT>GGT	p.S136G		NM_014059	NP_054778	Q9H4X1	RGC32_HUMAN	response gene to complement 32	136					cell cycle|regulation of cyclin-dependent protein kinase activity	microtubule organizing center|nucleus					0		Lung NSC(96;7.5e-06)|Prostate(109;0.0181)|Breast(139;0.0204)|Lung SC(185;0.0262)|Hepatocellular(98;0.114)		all cancers(112;8.62e-09)|Epithelial(112;8.99e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000504)|GBM - Glioblastoma multiforme(144;0.000909)|BRCA - Breast invasive adenocarcinoma(63;0.0679)		AACTTTAGCAAGTAAGTACAT	0.308													18	46	---	---	---	---	PASS
CARS2	79587	broad.mit.edu	37	13	111353886	111353886	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:111353886C>T	uc001vrd.2	-	3	332	c.292G>A	c.(292-294)GAT>AAT	p.D98N	CARS2_uc010tjm.1_RNA	NM_024537	NP_078813	Q9HA77	SYCM_HUMAN	cysteinyl-tRNA synthetase 2, mitochondrial	98					cysteinyl-tRNA aminoacylation	cytosol|mitochondrial matrix	ATP binding|cysteine-tRNA ligase activity|metal ion binding				0	all_lung(23;3.61e-05)|Lung NSC(43;0.00144)|Lung SC(71;0.0753)|all_neural(89;0.077)|Medulloblastoma(90;0.148)		BRCA - Breast invasive adenocarcinoma(86;0.163)		L-Cysteine(DB00151)	CGAATGATATCAAATCTAACA	0.328													4	107	---	---	---	---	PASS
PELI2	57161	broad.mit.edu	37	14	56757030	56757030	+	Silent	SNP	G	T	T			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:56757030G>T	uc001xch.2	+	5	838	c.552G>T	c.(550-552)GGG>GGT	p.G184G		NM_021255	NP_067078	Q9HAT8	PELI2_HUMAN	pellino 2	184					innate immune response|MyD88-dependent toll-like receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of MAPKKK cascade|positive regulation of protein phosphorylation|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway	cytosol	protein binding			ovary(1)	1						ACATGGATGGGCTCACTACTA	0.532													11	26	---	---	---	---	PASS
DAAM1	23002	broad.mit.edu	37	14	59834241	59834241	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:59834241C>T	uc001xdz.1	+	25	3076	c.2951C>T	c.(2950-2952)TCA>TTA	p.S984L	DAAM1_uc001xea.1_Missense_Mutation_p.S974L|DAAM1_uc001xec.1_RNA	NM_014992	NP_055807	Q9Y4D1	DAAM1_HUMAN	dishevelled-associated activator of	984	FH2.				actin cytoskeleton organization	cytoplasm|plasma membrane	actin binding|Rho GTPase binding			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(108;0.165)		CAAGCTGTGTCAGAAGCCAAA	0.408													29	82	---	---	---	---	PASS
PAPLN	89932	broad.mit.edu	37	14	73721593	73721593	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:73721593G>C	uc010ttx.1	+	13	1657	c.1494G>C	c.(1492-1494)AAG>AAC	p.K498N	PAPLN_uc001xnw.3_Missense_Mutation_p.K471N|PAPLN_uc010arl.2_RNA|PAPLN_uc010ttw.1_RNA|PAPLN_uc010tty.1_Missense_Mutation_p.K498N	NM_173462	NP_775733	O95428	PPN_HUMAN	papilin	498	TSP type-1 5.					proteinaceous extracellular matrix	metalloendopeptidase activity|serine-type endopeptidase inhibitor activity|zinc ion binding			ovary(1)|central_nervous_system(1)|skin(1)	3				BRCA - Breast invasive adenocarcinoma(234;0.00394)|OV - Ovarian serous cystadenocarcinoma(108;0.0468)		AGTGCTCCAAGAGCTGCAGCT	0.672													2	0	---	---	---	---	PASS
DICER1	23405	broad.mit.edu	37	14	95566195	95566195	+	Silent	SNP	G	T	T			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:95566195G>T	uc001ydw.2	-	23	4310	c.4128C>A	c.(4126-4128)CCC>CCA	p.P1376P	DICER1_uc010avh.1_Silent_p.P274P|DICER1_uc001ydv.2_Silent_p.P1366P|DICER1_uc001ydx.2_Silent_p.P1376P|DICER1_uc001ydy.1_Silent_p.P228P	NM_030621	NP_085124	Q9UPY3	DICER_HUMAN	dicer1	1376	RNase III 1.				negative regulation of Schwann cell proliferation|negative regulation of transcription from RNA polymerase II promoter|nerve development|neuron projection morphogenesis|peripheral nervous system myelin formation|positive regulation of myelination|positive regulation of Schwann cell differentiation|pre-miRNA processing|production of siRNA involved in RNA interference|targeting of mRNA for destruction involved in RNA interference	cytosol|RNA-induced silencing complex	ATP binding|ATP-dependent helicase activity|double-stranded RNA binding|metal ion binding|protein binding|ribonuclease III activity			skin(2)|ovary(1)|pancreas(1)|lung(1)	5		all_cancers(154;0.0621)|all_epithelial(191;0.223)		Epithelial(152;0.211)|COAD - Colon adenocarcinoma(157;0.215)		AATTCACAGGGGGATCAAATA	0.368			Mis F|N			pleuropulmonary blastoma			DICER_1_syndrome_|Familial_Multinodular_Goiter_				7	147	---	---	---	---	PASS
C14orf177	283598	broad.mit.edu	37	14	99183555	99183555	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:99183555A>G	uc001yfz.1	+	4	741	c.322A>G	c.(322-324)ACA>GCA	p.T108A		NM_182560	NP_872366	Q52M58	CN177_HUMAN	hypothetical protein LOC283598	108											0		Melanoma(154;0.128)				ATTTTGTGCTACACCAAGATT	0.398													3	47	---	---	---	---	PASS
SNX33	257364	broad.mit.edu	37	15	75942381	75942381	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:75942381G>T	uc002bau.2	+	1	1034	c.938G>T	c.(937-939)TGG>TTG	p.W313L	IMP3_uc002bat.2_5'Flank|SNX33_uc002bav.2_5'UTR	NM_153271	NP_695003	Q8WV41	SNX33_HUMAN	sorting nexin 33	313	PX.				cell communication		phosphatidylinositol binding|protein binding			ovary(1)	1						CTCATCCTCTGGATGGACCAC	0.577													4	29	---	---	---	---	PASS
GOLGA6L10	647042	broad.mit.edu	37	15	83014132	83014132	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:83014132C>G	uc010uny.1	-	6	513	c.415G>C	c.(415-417)GAG>CAG	p.E139Q	GOLGA6L10_uc010unt.1_RNA|uc002bhl.2_Intron|uc002bhm.2_Intron|GOLGA6L10_uc002bia.1_5'Flank	NM_198181	NP_937824	A6NI86	GG6LA_HUMAN	golgi autoantigen, golgin subfamily a, 6D-like	151											0						GCTGGGGGCTCTGGGGCCAGG	0.522													4	9	---	---	---	---	PASS
GRIN2A	2903	broad.mit.edu	37	16	9858733	9858733	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:9858733A>G	uc002czo.3	-	13	3216	c.2668T>C	c.(2668-2670)TCC>CCC	p.S890P	GRIN2A_uc010uym.1_Missense_Mutation_p.S890P|GRIN2A_uc010uyn.1_Missense_Mutation_p.S733P|GRIN2A_uc002czr.3_Missense_Mutation_p.S890P	NM_001134407	NP_001127879	Q12879	NMDE1_HUMAN	N-methyl-D-aspartate receptor subunit 2A isoform	890	Cytoplasmic (Potential).				response to ethanol	cell junction|N-methyl-D-aspartate selective glutamate receptor complex|outer membrane-bounded periplasmic space|postsynaptic membrane	N-methyl-D-aspartate selective glutamate receptor activity|zinc ion binding			skin(32)|NS(5)|ovary(4)|large_intestine(1)|lung(1)|breast(1)|kidney(1)	45					Felbamate(DB00949)|Glycine(DB00145)|L-Glutamic Acid(DB00142)|Loperamide(DB00836)|Memantine(DB01043)	TTGCTCTGGGATCCCGTCAGA	0.468													5	184	---	---	---	---	PASS
CPPED1	55313	broad.mit.edu	37	16	12758923	12758923	+	Silent	SNP	G	T	T			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:12758923G>T	uc002dca.3	-	4	876	c.765C>A	c.(763-765)ACC>ACA	p.T255T	CPPED1_uc002dcb.3_Silent_p.T113T|CPPED1_uc002dbz.3_RNA	NM_018340	NP_060810	Q9BRF8	CPPED_HUMAN	calcineurin-like phosphoesterase domain	255							hydrolase activity|metal ion binding				0						GGTTCTGGTAGGTACCCCCGG	0.567													3	44	---	---	---	---	PASS
ARL6IP1	23204	broad.mit.edu	37	16	18804527	18804527	+	3'UTR	SNP	C	A	A			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:18804527C>A	uc002dfl.1	-	6					RPS15A_uc002dfh.1_5'Flank|RPS15A_uc002dfi.1_5'Flank|RPS15A_uc002dfj.1_5'Flank|RPS15A_uc002dfk.1_5'Flank|ARL6IP1_uc010van.1_3'UTR|ARL6IP1_uc010bvz.1_RNA	NM_015161	NP_055976	Q15041	AR6P1_HUMAN	ADP-ribosylation factor-like 6 interacting							integral to membrane	protein binding				0						GAAACGGTTCCCGGGGCAATG	0.408													7	30	---	---	---	---	PASS
UMOD	7369	broad.mit.edu	37	16	20355352	20355352	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:20355352A>G	uc002dgz.2	-	6	1454	c.1325T>C	c.(1324-1326)ATG>ACG	p.M442T	UMOD_uc002dha.2_Missense_Mutation_p.M442T|UMOD_uc002dhb.2_Missense_Mutation_p.M475T	NM_003361	NP_003352	P07911	UROM_HUMAN	uromodulin precursor	442	ZP.				cellular defense response|negative regulation of cell proliferation	anchored to membrane|apical plasma membrane|basolateral plasma membrane|cilium membrane|extrinsic to membrane|primary cilium|spindle pole	calcium ion binding			ovary(1)|skin(1)	2						ACACCTGACCATTGGCTGTAG	0.547													20	92	---	---	---	---	PASS
RNF40	9810	broad.mit.edu	37	16	30776560	30776560	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30776560C>T	uc002dzq.2	+	7	953	c.830C>T	c.(829-831)ACA>ATA	p.T277I	RNF40_uc010caa.2_Missense_Mutation_p.T277I|RNF40_uc010cab.2_Missense_Mutation_p.T277I|RNF40_uc010vfa.1_Intron|RNF40_uc002dzr.2_Missense_Mutation_p.T277I|RNF40_uc010vfb.1_Intron	NM_014771	NP_055586	O75150	BRE1B_HUMAN	ring finger protein 40	277	Potential.				histone H2B ubiquitination|histone monoubiquitination|ubiquitin-dependent protein catabolic process	nucleus|synaptosome|ubiquitin ligase complex	protein homodimerization activity|ubiquitin protein ligase binding|zinc ion binding			central_nervous_system(1)	1			Colorectal(24;0.198)			GAGATGGAGACAACAGTGGAG	0.567													22	83	---	---	---	---	PASS
ANKRD11	29123	broad.mit.edu	37	16	89354863	89354863	+	Intron	SNP	C	T	T			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89354863C>T	uc002fmx.1	-						ANKRD11_uc002fmy.1_Intron|ANKRD11_uc002fnc.1_Intron|ANKRD11_uc002fnd.2_3'UTR|ANKRD11_uc002fne.2_Intron|ANKRD11_uc002fnb.1_Intron	NM_013275	NP_037407	Q6UB99	ANR11_HUMAN	ankyrin repeat domain 11							nucleus				ovary(4)|large_intestine(1)|central_nervous_system(1)	6		all_hematologic(23;0.00824)|Colorectal(91;0.0475)		Epithelial(1;5.33e-11)|all cancers(4;2.6e-09)|OV - Ovarian serous cystadenocarcinoma(4;2.29e-07)|BRCA - Breast invasive adenocarcinoma(80;0.0142)		CGGCTAGCTACGGGGAAACAA	0.607													10	7	---	---	---	---	PASS
SHMT1	6470	broad.mit.edu	37	17	18243556	18243556	+	Nonsense_Mutation	SNP	G	T	T			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:18243556G>T	uc002gta.2	-	7	805	c.615C>A	c.(613-615)TAC>TAA	p.Y205*	SHMT1_uc002gsz.2_5'UTR|SHMT1_uc002gtb.2_Nonsense_Mutation_p.Y205*|SHMT1_uc010cqb.2_Nonsense_Mutation_p.Y205*|SHMT1_uc010vxt.1_Nonsense_Mutation_p.Y67*|SHMT1_uc002gtd.1_Nonsense_Mutation_p.Y205*	NM_004169	NP_004160	P34896	GLYC_HUMAN	serine hydroxymethyltransferase 1 (soluble)	205					carnitine biosynthetic process|folic acid metabolic process|L-serine catabolic process|one-carbon metabolic process|purine base biosynthetic process	cytosol|nucleus	glycine hydroxymethyltransferase activity|protein homodimerization activity|pyridoxal phosphate binding			ovary(1)	1					Glycine(DB00145)|Mimosine(DB01055)|Pyridoxal Phosphate(DB00114)|Tetrahydrofolic acid(DB00116)	GGTTTCGGGAGTAGCAGCTGG	0.577													10	36	---	---	---	---	PASS
RPL19	6143	broad.mit.edu	37	17	37357533	37357533	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:37357533G>C	uc002hrq.1	+	2	135	c.73G>C	c.(73-75)GAC>CAC	p.D25H	RPL19_uc002hrr.1_Missense_Mutation_p.D23H	NM_000981	NP_000972	P84098	RL19_HUMAN	ribosomal protein L19	25					endocrine pancreas development|translational elongation|translational termination|viral transcription	cytosolic large ribosomal subunit	RNA binding|structural constituent of ribosome				0						GGTCTGGTTAGACCCCAATGA	0.483													17	41	---	---	---	---	PASS
TRIM25	7706	broad.mit.edu	37	17	54981679	54981679	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:54981679G>C	uc002iut.2	-	3	924	c.864C>G	c.(862-864)ATC>ATG	p.I288M	TRIM25_uc010dcj.2_Missense_Mutation_p.I80M	NM_005082	NP_005073	Q14258	TRI25_HUMAN	tripartite motif-containing 25	288	Interaction with influenza A virus NS1.|Potential.				innate immune response|interspecies interaction between organisms|negative regulation of type I interferon production|response to virus	cell junction|cytosol|nucleus	sequence-specific DNA binding transcription factor activity|ubiquitin-protein ligase activity|zinc ion binding			lung(1)|breast(1)|skin(1)	3	Breast(9;6.15e-08)					TCAAGGTCTGGATCTCACTCT	0.453													23	168	---	---	---	---	PASS
ACOX1	51	broad.mit.edu	37	17	73941664	73941664	+	3'UTR	SNP	T	C	C			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73941664T>C	uc002jqf.2	-	14					ACOX1_uc010wsq.1_3'UTR|ACOX1_uc002jqe.2_3'UTR|ACOX1_uc010wsr.1_3'UTR	NM_007292	NP_009223	Q15067	ACOX1_HUMAN	acyl-Coenzyme A oxidase 1 isoform b						fatty acid beta-oxidation using acyl-CoA oxidase|generation of precursor metabolites and energy|prostaglandin metabolic process|very long-chain fatty acid metabolic process	peroxisomal matrix	acyl-CoA dehydrogenase activity|acyl-CoA oxidase activity|flavin adenine dinucleotide binding|protein N-terminus binding			ovary(1)	1						ACATTGACTTTAAGAAAAAAT	0.299													5	24	---	---	---	---	PASS
DSC2	1824	broad.mit.edu	37	18	28651750	28651750	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:28651750G>A	uc002kwl.3	-	13	2400	c.1946C>T	c.(1945-1947)CCT>CTT	p.P649L	DSC2_uc002kwk.3_Missense_Mutation_p.P649L	NM_024422	NP_077740	Q02487	DSC2_HUMAN	desmocollin 2 isoform Dsc2a preproprotein	649	Extracellular (Potential).|Cadherin 5.				homophilic cell adhesion	desmosome|integral to membrane	calcium ion binding			ovary(2)|skin(1)	3			OV - Ovarian serous cystadenocarcinoma(10;0.0241)			CACTGTTATAGGTACTACATA	0.373													10	71	---	---	---	---	PASS
DSG1	1828	broad.mit.edu	37	18	28908167	28908167	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:28908167G>T	uc002kwp.2	+	4	444	c.232G>T	c.(232-234)GCT>TCT	p.A78S		NM_001942	NP_001933	Q02413	DSG1_HUMAN	desmoglein 1 preproprotein	78	Extracellular (Potential).|Cadherin 1.				calcium-dependent cell-cell adhesion|cell-cell junction assembly|cellular component disassembly involved in apoptosis|homophilic cell adhesion|protein stabilization	cytosol|desmosome|integral to membrane|internal side of plasma membrane	calcium ion binding|gamma-catenin binding|toxin binding			skin(3)|ovary(2)|central_nervous_system(2)	7			OV - Ovarian serous cystadenocarcinoma(10;0.00559)			CTCAGATTGTGCTGCAAACCA	0.373													18	52	---	---	---	---	PASS
CPLX4	339302	broad.mit.edu	37	18	56964114	56964114	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:56964114A>G	uc002lhy.2	-	3	486	c.299T>C	c.(298-300)GTG>GCG	p.V100A		NM_181654	NP_857637	Q7Z7G2	CPLX4_HUMAN	complexin 4 precursor	100					exocytosis|neurotransmitter transport	cell junction|synapse	syntaxin binding			ovary(1)	1		Colorectal(73;0.175)				AGGTAAATCCACATCATCTCC	0.353													5	100	---	---	---	---	PASS
ELAVL1	1994	broad.mit.edu	37	19	8038737	8038737	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8038737T>C	uc002mjb.2	-	4	469	c.302A>G	c.(301-303)GAG>GGG	p.E101G		NM_001419	NP_001410	Q15717	ELAV1_HUMAN	ELAV-like 1	101					3'-UTR-mediated mRNA stabilization|multicellular organismal development	cytoplasm|nucleoplasm	identical protein binding|mRNA binding|nucleotide binding				0						TTTGATCACCTCTGAGCTCGG	0.547													5	91	---	---	---	---	PASS
CALR	811	broad.mit.edu	37	19	13051666	13051666	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13051666G>T	uc002mvu.2	+	7	1005	c.925G>T	c.(925-927)GAT>TAT	p.D309Y	CALR_uc002mvv.2_5'Flank	NM_004343	NP_004334	P27797	CALR_HUMAN	calreticulin precursor	309	C-domain.				cell cycle arrest|cellular senescence|glucocorticoid receptor signaling pathway|negative regulation of neuron differentiation|negative regulation of retinoic acid receptor signaling pathway|negative regulation of steroid hormone receptor signaling pathway|negative regulation of transcription from RNA polymerase II promoter|negative regulation of translation|peptide antigen assembly with MHC class I protein complex|positive regulation of cell cycle|positive regulation of cell proliferation|positive regulation of DNA replication|positive regulation of phagocytosis|post-translational protein modification|protein export from nucleus|protein maturation by protein folding|protein N-linked glycosylation via asparagine|protein stabilization|regulation of apoptosis|sequestering of calcium ion	cytosol|endoplasmic reticulum lumen|extracellular space|MHC class I peptide loading complex|nucleus|perinuclear region of cytoplasm|polysome|proteinaceous extracellular matrix	androgen receptor binding|calcium ion binding|chaperone binding|complement component C1q binding|DNA binding|integrin binding|mRNA binding|protein binding involved in protein folding|sugar binding|ubiquitin protein ligase binding|unfolded protein binding|zinc ion binding			ovary(1)	1					Alteplase(DB00009)|Anistreplase(DB00029)|Antihemophilic Factor(DB00025)|Reteplase(DB00015)|Tenecteplase(DB00031)	CTATGCCTATGATAACTTTGG	0.532													19	67	---	---	---	---	PASS
JAK3	3718	broad.mit.edu	37	19	17954627	17954627	+	Silent	SNP	G	T	T			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17954627G>T	uc002nhn.3	-	3	367	c.267C>A	c.(265-267)TCC>TCA	p.S89S	JAK3_uc010ebh.2_RNA|JAK3_uc002nho.2_Silent_p.S89S|JAK3_uc010xpx.1_Silent_p.S89S|JAK3_uc010xpy.1_Intron	NM_000215	NP_000206	P52333	JAK3_HUMAN	Janus kinase 3	89	FERM.|Interaction with cytokine/interferon/growth hormone receptors (By similarity).				B cell differentiation|cytokine-mediated signaling pathway|enzyme linked receptor protein signaling pathway|intracellular protein kinase cascade|negative regulation of dendritic cell cytokine production|negative regulation of FasL biosynthetic process|negative regulation of interleukin-10 production|negative regulation of interleukin-12 production|negative regulation of T-helper 1 cell differentiation|negative regulation of thymocyte apoptosis|peptidyl-tyrosine phosphorylation|positive regulation of anti-apoptosis|response to interleukin-15|response to interleukin-2|response to interleukin-4|response to interleukin-9|T cell homeostasis	cytoskeleton|cytosol|endomembrane system|membrane	ATP binding|non-membrane spanning protein tyrosine kinase activity|protein binding			haematopoietic_and_lymphoid_tissue(40)|lung(5)|breast(5)|ovary(3)|stomach(2)|upper_aerodigestive_tract(1)	56						CATCCTCCACGGAGAAGATGT	0.582		2	Mis		acute megakaryocytic leukemia|								3	10	---	---	---	---	PASS
ZNF714	148206	broad.mit.edu	37	19	21299645	21299645	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:21299645C>A	uc002npo.3	+	5	535	c.175C>A	c.(175-177)CCA>ACA	p.P59T	ZNF714_uc002npl.2_5'UTR|ZNF714_uc010ecp.1_Missense_Mutation_p.P11T|ZNF714_uc002npn.2_RNA	NM_182515	NP_872321	Q96N38	ZN714_HUMAN	zinc finger protein 714	59					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						AGACCTTTGGCCAGAGCAAGA	0.333													31	106	---	---	---	---	PASS
CD22	933	broad.mit.edu	37	19	35829090	35829090	+	Silent	SNP	G	A	A			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:35829090G>A	uc010edt.2	+	6	1082	c.1005G>A	c.(1003-1005)ACG>ACA	p.T335T	CD22_uc010xst.1_Silent_p.T163T|CD22_uc010edu.2_Intron|CD22_uc010edv.2_Silent_p.T335T|CD22_uc002nzb.3_Intron|CD22_uc010edx.2_RNA	NM_001771	NP_001762	P20273	CD22_HUMAN	CD22 molecule precursor	335	Extracellular (Potential).|Ig-like C2-type 3.				cell adhesion		protein binding|sugar binding			ovary(5)|lung(3)|breast(1)	9	all_lung(56;9.78e-09)|Lung NSC(56;1.46e-08)|Esophageal squamous(110;0.162)		Epithelial(14;5.83e-19)|OV - Ovarian serous cystadenocarcinoma(14;3.19e-18)|all cancers(14;3.41e-16)|LUSC - Lung squamous cell carcinoma(66;0.0417)		OspA lipoprotein(DB00045)	AACCTTCCACGGTTCAGATCC	0.602													5	67	---	---	---	---	PASS
IL28A	282616	broad.mit.edu	37	19	39759493	39759493	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39759493G>T	uc002oku.1	+	2	239	c.187G>T	c.(187-189)GCC>TCC	p.A63S		NM_172138	NP_742150	Q8IZJ0	IL28A_HUMAN	interleukin 28A precursor	63					response to virus	extracellular space	cytokine activity			ovary(1)|skin(1)	2	all_cancers(60;1.85e-07)|all_lung(34;4.03e-08)|Lung NSC(34;4.66e-08)|all_epithelial(25;6.4e-07)|Ovarian(47;0.0512)		Epithelial(26;5.39e-26)|all cancers(26;4.1e-23)|Lung(45;0.000278)|LUSC - Lung squamous cell carcinoma(53;0.000335)			GGCCAAAGATGCCTTAGTGAG	0.612													4	9	---	---	---	---	PASS
ITPKC	80271	broad.mit.edu	37	19	41243640	41243640	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41243640C>G	uc002oot.2	+	6	1847	c.1814C>G	c.(1813-1815)GCT>GGT	p.A605G		NM_025194	NP_079470	Q96DU7	IP3KC_HUMAN	inositol 1,4,5-trisphosphate 3-kinase C	605						cytoplasm|nucleus	ATP binding|calmodulin binding|inositol trisphosphate 3-kinase activity				0			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)			CTTCGTGAAGCTCTGGAGATC	0.572													6	118	---	---	---	---	PASS
NAPSA	9476	broad.mit.edu	37	19	50862276	50862276	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50862276C>T	uc002prx.2	-	8	1080	c.1027G>A	c.(1027-1029)GTC>ATC	p.V343I	NR1H2_uc002prv.3_Intron	NM_004851	NP_004842	O96009	NAPSA_HUMAN	napsin A preproprotein	343					proteolysis	extracellular region	aspartic-type endopeptidase activity				0		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00743)|GBM - Glioblastoma multiforme(134;0.0183)		ACCTGGATGACGTAATCATGG	0.557													12	50	---	---	---	---	PASS
SIGLEC8	27181	broad.mit.edu	37	19	51961425	51961425	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51961425G>T	uc002pwt.2	-	1	284	c.217C>A	c.(217-219)CCA>ACA	p.P73T	SIGLEC8_uc010yda.1_Missense_Mutation_p.P73T|SIGLEC8_uc002pwu.2_RNA|SIGLEC8_uc010eox.2_Missense_Mutation_p.P73T	NM_014442	NP_055257	Q9NYZ4	SIGL8_HUMAN	sialic acid binding Ig-like lectin 8 precursor	73	Ig-like V-type.|Extracellular (Potential).				cell adhesion	integral to membrane	sugar binding|transmembrane receptor activity			ovary(2)|kidney(1)|central_nervous_system(1)|skin(1)	5		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000627)|OV - Ovarian serous cystadenocarcinoma(262;0.00979)		TCTTGGTATGGTCTGTCTCCT	0.587													28	112	---	---	---	---	PASS
ZNF132	7691	broad.mit.edu	37	19	58945135	58945135	+	Missense_Mutation	SNP	A	T	T			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58945135A>T	uc002qst.3	-	3	2077	c.1676T>A	c.(1675-1677)ATT>AAT	p.I559N		NM_003433	NP_003424	P52740	ZN132_HUMAN	zinc finger protein 132	559	C2H2-type 13.					nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			upper_aerodigestive_tract(1)|ovary(1)	2		all_cancers(17;4.4e-22)|all_epithelial(17;2.15e-16)|Lung NSC(17;1.24e-06)|all_lung(17;5.41e-06)|Colorectal(82;3.46e-05)|Renal(17;0.00179)|all_neural(62;0.00607)|Ovarian(87;0.0443)|Breast(46;0.0928)|Medulloblastoma(540;0.184)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0171)|Lung(386;0.182)		CCAGTGTTCAATGAGAGTGGA	0.448													11	58	---	---	---	---	PASS
DDX17	10521	broad.mit.edu	37	22	38890893	38890893	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38890893T>C	uc003avy.3	-	7	1142	c.1039A>G	c.(1039-1041)AGG>GGG	p.R347G	DDX17_uc003avx.3_Missense_Mutation_p.R347G|DDX17_uc011anu.1_Missense_Mutation_p.R260G	NM_001098504	NP_001091974	Q92841	DDX17_HUMAN	DEAD box polypeptide 17 isoform 3	268	Helicase ATP-binding.				RNA processing	nucleus	ATP binding|ATP-dependent helicase activity|RNA binding|RNA helicase activity|RNA-dependent ATPase activity			skin(3)|upper_aerodigestive_tract(1)	4	Melanoma(58;0.0286)					TTACACACCCTGATTTGGTCA	0.413													4	72	---	---	---	---	PASS
ENTHD1	150350	broad.mit.edu	37	22	40231926	40231926	+	Silent	SNP	G	A	A			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:40231926G>A	uc003ayg.2	-	4	881	c.630C>T	c.(628-630)TGC>TGT	p.C210C		NM_152512	NP_689725	Q8IYW4	ENTD1_HUMAN	ENTH domain containing 1	210										ovary(2)|skin(1)	3	Melanoma(58;0.0749)					GAACATCTTGGCAATGCTCTT	0.343													22	147	---	---	---	---	PASS
GLUD2	2747	broad.mit.edu	37	X	120182654	120182654	+	Silent	SNP	G	A	A			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:120182654G>A	uc004eto.2	+	1	1193	c.1116G>A	c.(1114-1116)TTG>TTA	p.L372L		NM_012084	NP_036216	P49448	DHE4_HUMAN	glutamate dehydrogenase 2 precursor	372					glutamate biosynthetic process|glutamate catabolic process	mitochondrial matrix	ADP binding|glutamate dehydrogenase|glutamate dehydrogenase activity|GTP binding|leucine binding			pancreas(1)	1					L-Glutamic Acid(DB00142)|NADH(DB00157)	GAAGCATCTTGGAGGTCGACT	0.498													4	88	---	---	---	---	PASS
PLEKHM2	23207	broad.mit.edu	37	1	16056542	16056556	+	Intron	DEL	GGGCGGGGCGGGGCG	-	-	rs12729712		TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16056542_16056556delGGGCGGGGCGGGGCG	uc010obo.1	+							NM_015164	NP_055979	Q8IWE5	PKHM2_HUMAN	pleckstrin homology domain containing, family M						Golgi organization	cytoplasm	kinesin binding			ovary(1)	1		Colorectal(325;0.000259)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.00057)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;9.18e-07)|COAD - Colon adenocarcinoma(227;4.5e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000133)|KIRC - Kidney renal clear cell carcinoma(229;0.00262)|STAD - Stomach adenocarcinoma(313;0.00774)|READ - Rectum adenocarcinoma(331;0.0657)		TCGCCTACCTgggcggggcggggcggggcggggcg	0.465													4	2	---	---	---	---	
CROCCL2	114819	broad.mit.edu	37	1	16802965	16802965	+	Frame_Shift_Del	DEL	G	-	-			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16802965delG	uc001ayr.3	-	2	180	c.80delC	c.(79-81)CCTfs	p.P27fs	CROCCL2_uc001ayt.2_RNA					Homo sapiens mRNA for KIAA1922 protein, partial cds.												0						AGCTTGGACAGGGAGTCCTGC	0.627													4	2	---	---	---	---	
CROCC	9696	broad.mit.edu	37	1	17299014	17299014	+	3'UTR	DEL	A	-	-	rs6661019	by1000genomes	TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17299014delA	uc001azt.2	+	37					CROCC_uc001azu.2_3'UTR|CROCC_uc001azv.2_3'UTR	NM_014675	NP_055490	Q5TZA2	CROCC_HUMAN	ciliary rootlet coiled-coil						cell cycle|cell projection organization|centrosome organization|protein localization	actin cytoskeleton|centriole|ciliary rootlet|plasma membrane	kinesin binding|structural molecule activity			ovary(2)|breast(2)|central_nervous_system(1)	5		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000174)|all_lung(284;0.000234)|Renal(390;0.000518)|Ovarian(437;0.00669)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.63e-06)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.181)		CAGCCCCCCCACCCAGAGCCC	0.672													4	2	---	---	---	---	
UCK2	7371	broad.mit.edu	37	1	165877195	165877195	+	3'UTR	DEL	T	-	-			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:165877195delT	uc001gdp.2	+	7					UCK2_uc010plb.1_3'UTR	NM_012474	NP_036606	Q9BZX2	UCK2_HUMAN	uridine-cytidine kinase 2						pyrimidine base metabolic process|pyrimidine nucleoside salvage	cytosol	ATP binding|phosphotransferase activity, alcohol group as acceptor|uridine kinase activity			ovary(1)	1	all_hematologic(923;0.048)|Acute lymphoblastic leukemia(8;0.155)					ATGCCTTTGATTTTTTTTTTC	0.383													4	2	---	---	---	---	
ATP1B1	481	broad.mit.edu	37	1	169101269	169101270	+	RNA	INS	-	G	G			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:169101269_169101270insG	uc001gfs.1	+	6		c.1513_1514insG						P05026	AT1B1_HUMAN	Synthetic construct DNA, clone: pF1KB8186, Homo sapiens ATP1B1 gene for ATPase, Na+/K+ transporting, beta 1 polypeptide, without stop codon, in Flexi system.						ATP biosynthetic process|blood coagulation|leukocyte migration	sodium:potassium-exchanging ATPase complex	protein binding|sodium:potassium-exchanging ATPase activity			ovary(1)	1	all_hematologic(923;0.208)					tttttttttttttttttttttg	0.312													4	2	---	---	---	---	
PLEKHA6	22874	broad.mit.edu	37	1	204243074	204243074	+	Intron	DEL	T	-	-			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:204243074delT	uc001hau.2	-							NM_014935	NP_055750	Q9Y2H5	PKHA6_HUMAN	phosphoinositol 3-phosphate-binding protein-3											ovary(3)|pancreas(1)	4	all_cancers(21;0.0222)|Breast(84;0.179)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|BRCA - Breast invasive adenocarcinoma(75;0.0833)|Kidney(21;0.0934)|Epithelial(59;0.229)			attttatttattttttgagac	0.189													4	2	---	---	---	---	
MIA3	375056	broad.mit.edu	37	1	222827876	222827876	+	Intron	DEL	T	-	-			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:222827876delT	uc001hnl.2	+						MIA3_uc001hnm.2_Intron	NM_198551	NP_940953	Q5JRA6	MIA3_HUMAN	melanoma inhibitory activity family, member 3						exocytosis|negative regulation of cell adhesion|negative regulation of cell migration|positive regulation of leukocyte migration|protein transport|wound healing	endoplasmic reticulum membrane|integral to membrane	protein binding			ovary(4)|central_nervous_system(1)	5				GBM - Glioblastoma multiforme(131;0.0199)		CAAAATTGCATTAGAAAGATA	0.418													39	19	---	---	---	---	
SIPA1L2	57568	broad.mit.edu	37	1	232563343	232563344	+	Intron	DEL	AA	-	-			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:232563343_232563344delAA	uc001hvg.2	-						SIPA1L2_uc001hvf.2_Intron	NM_020808	NP_065859	Q9P2F8	SI1L2_HUMAN	signal-induced proliferation-associated 1 like						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)				gttacttgctaaatggggtgat	0.084													4	2	---	---	---	---	
LYST	1130	broad.mit.edu	37	1	235918888	235918889	+	Frame_Shift_Ins	INS	-	T	T			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:235918888_235918889insT	uc001hxj.2	-	25	7293_7294	c.7118_7119insA	c.(7117-7119)AATfs	p.N2373fs	LYST_uc009xga.1_5'Flank	NM_000081	NP_000072	Q99698	LYST_HUMAN	lysosomal trafficking regulator	2373					defense response to bacterium|defense response to protozoan|defense response to virus|endosome to lysosome transport via multivesicular body sorting pathway|leukocyte chemotaxis|mast cell secretory granule organization|melanosome organization|natural killer cell mediated cytotoxicity|protein transport	cytoplasm|microtubule cytoskeleton	protein binding			ovary(6)|breast(4)|central_nervous_system(2)	12	Ovarian(103;0.0634)|Breast(184;0.23)	all_cancers(173;0.00246)|Prostate(94;0.0771)|Acute lymphoblastic leukemia(190;0.228)	OV - Ovarian serous cystadenocarcinoma(106;0.000674)			AAAATCCACGATTCTTCAGAAA	0.327									Chediak-Higashi_syndrome				90	46	---	---	---	---	
C2orf39	92749	broad.mit.edu	37	2	26646948	26646948	+	Intron	DEL	G	-	-			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:26646948delG	uc002rhg.2	+						C2orf39_uc010eym.1_Intron	NM_145038	NP_659475	Q96MC2	CC164_HUMAN	hypothetical protein LOC92749												0	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TTCTTTACTTGGCCTAAGTTA	0.318													4	2	---	---	---	---	
GGCX	2677	broad.mit.edu	37	2	85788402	85788402	+	Intron	DEL	A	-	-	rs11350741		TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:85788402delA	uc002sps.2	-						GGCX_uc010yss.1_5'Flank|GGCX_uc010yst.1_Intron	NM_000821	NP_000812	P38435	VKGC_HUMAN	gamma-glutamyl carboxylase isoform 1						blood coagulation|peptidyl-glutamic acid carboxylation|post-translational protein modification	endoplasmic reticulum membrane|integral to membrane|membrane fraction	gamma-glutamyl carboxylase activity			ovary(1)	1					Anisindione(DB01125)|Coagulation Factor IX(DB00100)|Coagulation factor VIIa(DB00036)|Drotrecogin alfa(DB00055)|L-Glutamic Acid(DB00142)|Menadione(DB00170)|Phytonadione(DB01022)	CCCACAGAGGACCCCCCCCCC	0.652													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	96593512	96593513	+	Intron	INS	-	AGT	AGT	rs138688034	by1000genomes	TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:96593512_96593513insAGT	uc002sva.1	-						uc010yug.1_Intron|uc002svc.1_5'Flank					Homo sapiens cDNA FLJ41632 fis, clone FCBBF1000297, highly  similar to Human protein immuno-reactive with anti-PTH polyclonal antibodies mRNA.																		CATTATCCCACATGTCTTTCTT	0.386													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	102515376	102515377	+	IGR	INS	-	AGTT	AGTT	rs140237191	by1000genomes	TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:102515376_102515377insAGTT								MAP4K4 (4225 upstream) : IL1R2 (92929 downstream)																							CTCATTGGCTCAGCGCACTCTC	0.510													4	4	---	---	---	---	
SLC35F5	80255	broad.mit.edu	37	2	114483287	114483287	+	Intron	DEL	G	-	-	rs67850681	by1000genomes	TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:114483287delG	uc002tku.1	-						SLC35F5_uc002tkt.2_Intron	NM_025181	NP_079457	Q8WV83	S35F5_HUMAN	solute carrier family 35, member F5						transport	integral to membrane					0						CAACGCCATAGAAAAAAAAAC	0.388													4	2	---	---	---	---	
RALB	5899	broad.mit.edu	37	2	121015943	121015944	+	Intron	DEL	GT	-	-			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:121015943_121015944delGT	uc002tmk.2	+						RALB_uc010yys.1_Intron|RALB_uc002tml.2_Intron|RALB_uc002tmm.2_Intron|RALB_uc010yyt.1_Intron	NM_002881	NP_002872	P11234	RALB_HUMAN	v-ral simian leukemia viral oncogene homolog B						apoptosis|cell cycle|cytokinesis|nerve growth factor receptor signaling pathway|Ras protein signal transduction|regulation of exocyst assembly|regulation of exocyst localization	cytosol|midbody|plasma membrane	GTP binding|GTPase activity|protein binding			lung(3)	3		Prostate(154;0.122)				CCTGAATGCAGTGTGTGTGTGT	0.327													4	2	---	---	---	---	
STK39	27347	broad.mit.edu	37	2	168996615	168996615	+	Intron	DEL	G	-	-			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:168996615delG	uc002uea.2	-							NM_013233	NP_037365	Q9UEW8	STK39_HUMAN	serine threonine kinase 39 (STE20/SPS1 homolog,						response to stress	cytoplasm|nucleus	ATP binding|protein binding|receptor signaling protein serine/threonine kinase activity			central_nervous_system(1)|skin(1)	2						CTTCAAAGCTGGGAATTATGC	0.393													4	2	---	---	---	---	
TMPPE	643853	broad.mit.edu	37	3	33135687	33135687	+	Frame_Shift_Del	DEL	T	-	-			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:33135687delT	uc003cfk.2	-	2	192	c.1delA	c.(1-3)ATGfs	p.M1fs	GLB1_uc003cfh.1_Intron|GLB1_uc003cfi.1_Intron|GLB1_uc003cfj.1_Intron|GLB1_uc011axk.1_Intron|TMPPE_uc011axl.1_Intron	NM_001039770	NP_001034859	Q6ZT21	TMPPE_HUMAN	transmembrane protein with	1						integral to membrane	metal ion binding				0						AAGATGGCCATTTTCTCTGCT	0.572													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	48162288	48162288	+	IGR	DEL	G	-	-			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:48162288delG								MAP4 (31519 upstream) : CDC25A (36380 downstream)																							GAGAGCTCATGTATAGGTTAA	0.448													4	2	---	---	---	---	
SIDT1	54847	broad.mit.edu	37	3	113325706	113325707	+	Intron	INS	-	A	A			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113325706_113325707insA	uc003eak.2	+						SIDT1_uc011bif.1_Intron|SIDT1_uc003eaj.1_Intron|SIDT1_uc011big.1_Intron|SIDT1_uc011bih.1_Intron|SIDT1_uc011bii.1_Intron	NM_017699	NP_060169	Q9NXL6	SIDT1_HUMAN	SID1 transmembrane family, member 1 precursor							integral to membrane				ovary(3)|pancreas(1)|skin(1)	5						AACTTTTTTGTAAAAAAAGTGC	0.431													3	6	---	---	---	---	
KALRN	8997	broad.mit.edu	37	3	123762180	123762180	+	Intron	DEL	T	-	-			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:123762180delT	uc003ehd.2	+									O60229	KALRN_HUMAN	Homo sapiens cDNA FLJ41073 fis, clone 3NB692008178.						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|nervous system development|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|vesicle-mediated transport	actin cytoskeleton|cytosol	ATP binding|GTPase activator activity|metal ion binding|protein binding|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity			large_intestine(2)|ovary(2)|central_nervous_system(1)|skin(1)	6						tgaggggaggttttttttagg	0.000													4	2	---	---	---	---	
STAG1	10274	broad.mit.edu	37	3	136078254	136078255	+	Intron	DEL	GC	-	-			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:136078254_136078255delGC	uc003era.1	-						STAG1_uc003erb.1_Intron	NM_005862	NP_005853	Q8WVM7	STAG1_HUMAN	stromal antigen 1						cell division|chromosome segregation|mitotic metaphase/anaphase transition|mitotic prometaphase	cell junction|chromatin|chromosome, centromeric region|nucleoplasm	protein binding			ovary(2)	2						TTCTCTTCTTGCATTGAATTTT	0.277													4	2	---	---	---	---	
KCNMB3	27094	broad.mit.edu	37	3	178984772	178984773	+	5'UTR	INS	-	TC	TC	rs138080982	by1000genomes	TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:178984772_178984773insTC	uc003fjp.1	-	1					KCNMB3_uc011bqc.1_5'UTR	NM_171828	NP_741979	Q9NPA1	KCMB3_HUMAN	calcium-activated potassium channel beta 3						detection of calcium ion|platelet activation|regulation of action potential in neuron	voltage-gated potassium channel complex	calcium-activated potassium channel activity|potassium channel regulator activity				0	all_cancers(143;5.6e-17)|Ovarian(172;0.0172)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;2.41e-27)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.03)			CCGAAGCTGCTTCTCTCTCTTT	0.584													4	3	---	---	---	---	
BDH1	622	broad.mit.edu	37	3	197274733	197274733	+	Intron	DEL	C	-	-	rs68027877		TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:197274733delC	uc003fxr.2	-						BDH1_uc003fxs.2_Intron|BDH1_uc003fxt.2_Intron|BDH1_uc003fxu.2_Intron	NM_203314	NP_976059	Q02338	BDH_HUMAN	3-hydroxybutyrate dehydrogenase, type 1						cellular lipid metabolic process|ketone body biosynthetic process|ketone body catabolic process	mitochondrial matrix	3-hydroxybutyrate dehydrogenase activity			ovary(1)	1	all_cancers(143;3.35e-10)|Ovarian(172;0.0418)|Breast(254;0.0437)	Lung NSC(153;0.118)	Epithelial(36;3.52e-24)|all cancers(36;1.79e-22)|OV - Ovarian serous cystadenocarcinoma(49;2.32e-19)|LUSC - Lung squamous cell carcinoma(58;1.02e-06)|Lung(62;1.34e-06)	GBM - Glioblastoma multiforme(93;0.0977)	NADH(DB00157)	ctgccctcatcctggatgctg	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	6903325	6903328	+	IGR	DEL	TCTG	-	-	rs34392397		TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:6903325_6903328delTCTG								KIAA0232 (17428 upstream) : TBC1D14 (7843 downstream)																							TGGATGTGTTTCTGTCTACTGTGT	0.593													4	2	---	---	---	---	
KLB	152831	broad.mit.edu	37	4	39449786	39449786	+	Intron	DEL	A	-	-			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:39449786delA	uc003gua.2	+						KLB_uc011byj.1_Intron	NM_175737	NP_783864	Q86Z14	KLOTB_HUMAN	klotho beta						carbohydrate metabolic process	integral to membrane|plasma membrane	cation binding|fibroblast growth factor binding|hydrolase activity, hydrolyzing O-glycosyl compounds			skin(1)	1						AATAAATGTCAAAAAAAACCC	0.264													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	41844010	41844010	+	IGR	DEL	T	-	-			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:41844010delT								PHOX2B (93023 upstream) : TMEM33 (93127 downstream)																							TACTTTTCTATTTTTTTTTTC	0.318													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	52844273	52844273	+	IGR	DEL	C	-	-			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:52844273delC								DCUN1D4 (61272 upstream) : LRRC66 (15594 downstream)																							CTTCAGTCTTCTGATGGCAAC	0.428													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	52844275	52844276	+	IGR	DEL	GA	-	-			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:52844275_52844276delGA								DCUN1D4 (61274 upstream) : LRRC66 (15591 downstream)																							TCAGTCTTCTGATGGCAACTTT	0.436													4	2	---	---	---	---	
LRIT3	345193	broad.mit.edu	37	4	110792127	110792127	+	3'UTR	DEL	T	-	-			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:110792127delT	uc003hzx.3	+	3					LRIT3_uc003hzw.3_3'UTR	NM_198506	NP_940908	Q3SXY7	LRIT3_HUMAN	leucine-rich repeat, immunoglobulin-like and							integral to membrane					0				OV - Ovarian serous cystadenocarcinoma(123;0.0011)		ATAATGTTGATTTTTTTTCTT	0.264													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	132664184	132664185	+	IGR	DEL	TC	-	-			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:132664184_132664185delTC								None (None upstream) : None (None downstream)																							atctcttacgtctctctctctc	0.158													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	28679027	28679028	+	IGR	DEL	AC	-	-			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:28679027_28679028delAC								None (None upstream) : None (None downstream)																							AAACATGCATACACACACACAC	0.401													4	2	---	---	---	---	
SPEF2	79925	broad.mit.edu	37	5	35644819	35644820	+	Intron	DEL	CT	-	-	rs140309566		TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:35644819_35644820delCT	uc003jjo.2	+						SPEF2_uc003jjn.1_Intron|SPEF2_uc003jjq.3_Intron	NM_024867	NP_079143	Q9C093	SPEF2_HUMAN	KPL2 protein isoform 1						nucleobase, nucleoside, nucleotide and nucleic acid metabolic process		ATP binding|nucleobase, nucleoside, nucleotide kinase activity|protein dimerization activity			skin(2)|ovary(1)|central_nervous_system(1)	4	all_lung(31;7.56e-05)		Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			CTCTTGCTGACTCTCACCTCTA	0.485													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	68294819	68294820	+	Intron	DEL	CT	-	-			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:68294819_68294820delCT	uc003jvf.1	-											Homo sapiens cDNA FLJ46633 fis, clone TRACH2025705.																		TTTGTGTGCCCTCTCTTGGTTC	0.480													4	2	---	---	---	---	
ACAT2	39	broad.mit.edu	37	6	160182976	160182990	+	5'UTR	DEL	TGCGCGGGGAGGTGG	-	-	rs149786744	by1000genomes	TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:160182976_160182990delTGCGCGGGGAGGTGG	uc010kjy.2	+	1					uc003qsp.2_Intron|ACAT2_uc011efw.1_5'Flank	NM_005891	NP_005882	Q9BWD1	THIC_HUMAN	acetyl-Coenzyme A acetyltransferase 2							mitochondrion|nucleolus	acetyl-CoA C-acetyltransferase activity|protein binding			ovary(1)|central_nervous_system(1)	2		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;1.51e-18)|BRCA - Breast invasive adenocarcinoma(81;5.87e-06)		CACAGTGGGATGCGCGGGGAGGTGGTGCGCGGGGA	0.465													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	57696574	57696579	+	5'Flank	DEL	GGGGGT	-	-	rs150717737	by1000genomes	TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57696574_57696579delGGGGGT	uc003tso.1	+											Homo sapiens macronuclear mRNA.																		tgagaatggcgggggtgagaatggcg	0.029													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	90956470	90956470	+	IGR	DEL	G	-	-			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:90956470delG								FZD1 (58339 upstream) : MTERF (474990 downstream)																							TTCTTGCACTGGCCATCTTGT	0.423													4	2	---	---	---	---	
STAG3	10734	broad.mit.edu	37	7	99780151	99780152	+	Intron	INS	-	T	T			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99780151_99780152insT	uc003utx.1	+						STAG3_uc010lgs.1_Intron|STAG3_uc011kjk.1_Intron	NM_012447	NP_036579	Q9UJ98	STAG3_HUMAN	stromal antigen 3						chromosome segregation|synaptonemal complex assembly	chromosome, centromeric region|meiotic cohesin complex|synaptonemal complex	binding			ovary(4)|skin(2)|lung(1)|kidney(1)	8	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					GACTCAAGGACTTTTTTTTTAA	0.342													4	2	---	---	---	---	
AGFG2	3268	broad.mit.edu	37	7	100137226	100137226	+	Intron	DEL	G	-	-			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100137226delG	uc003uvf.2	+						AGFG2_uc003uvg.1_Intron	NM_006076	NP_006067	O95081	AGFG2_HUMAN	ArfGAP with FG repeats 2						regulation of ARF GTPase activity		ARF GTPase activator activity|zinc ion binding			central_nervous_system(1)	1						AGGTCggcgtggggggacccg	0.318													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	123841817	123841817	+	Intron	DEL	A	-	-			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:123841817delA	uc011koc.1	+											Homo sapiens disrupted in Rett 1 mRNA sequence.																		TTCCCCAGGTAACACACCCTG	0.428													4	2	---	---	---	---	
GRM8	2918	broad.mit.edu	37	7	126174072	126174072	+	Intron	DEL	T	-	-			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:126174072delT	uc003vlr.2	-						GRM8_uc003vls.2_Intron|GRM8_uc011kof.1_Intron|GRM8_uc003vlt.2_Intron|GRM8_uc010lkz.1_Intron	NM_000845	NP_000836	O00222	GRM8_HUMAN	glutamate receptor, metabotropic 8 isoform a						negative regulation of cAMP biosynthetic process|sensory perception of smell|visual perception	integral to plasma membrane				lung(15)|ovary(5)|pancreas(1)|breast(1)|skin(1)	23		Prostate(267;0.186)			L-Glutamic Acid(DB00142)	AAGAGTCTCGTTTTTTTTCCC	0.343										HNSCC(24;0.065)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	58846428	58846429	+	IGR	DEL	TT	-	-			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:58846428_58846429delTT								C8orf71 (649140 upstream) : FAM110B (60684 downstream)																							GACTCCTTCCTTTTAAAACACC	0.371													4	2	---	---	---	---	
TCEB1	6921	broad.mit.edu	37	8	74858870	74858870	+	Frame_Shift_Del	DEL	A	-	-			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:74858870delA	uc003xzx.1	-	4	419	c.334delT	c.(334-336)TGTfs	p.C112fs	TCEB1_uc003xzy.1_Frame_Shift_Del_p.C112fs|TCEB1_uc003xzz.1_Frame_Shift_Del_p.C96fs|TCEB1_uc003yaa.1_Frame_Shift_Del_p.C112fs	NM_005648	NP_005639	Q15369	ELOC_HUMAN	elongin C	112					interspecies interaction between organisms|positive regulation of viral transcription|regulation of transcription from RNA polymerase II promoter|transcription elongation from RNA polymerase II promoter|ubiquitin-dependent protein catabolic process|viral reproduction	cytosol|nucleoplasm	protein binding				0	Breast(64;0.0311)		Epithelial(68;0.0136)|all cancers(69;0.0431)|BRCA - Breast invasive adenocarcinoma(89;0.0499)			tttatttaaCAATCTAAGAAG	0.353													27	14	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	87247548	87247548	+	IGR	DEL	A	-	-	rs35314286		TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:87247548delA								SLC7A13 (4939 upstream) : WWP1 (107446 downstream)																							ctttattgctaaaaaaatatg	0.000													4	2	---	---	---	---	
KDM4C	23081	broad.mit.edu	37	9	6930235	6930235	+	Intron	DEL	T	-	-			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:6930235delT	uc003zkh.2	+						KDM4C_uc010mhu.2_Intron|KDM4C_uc011lmi.1_Intron|KDM4C_uc011lmj.1_Intron|KDM4C_uc003zkg.2_Intron|KDM4C_uc011lmk.1_Intron|KDM4C_uc011lml.1_Intron	NM_015061	NP_055876	Q9H3R0	KDM4C_HUMAN	jumonji domain containing 2C isoform 1						positive regulation of cell proliferation|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|transcription, DNA-dependent	nuclear chromatin	androgen receptor binding|enzyme binding|histone demethylase activity (H3-K9 specific)|nucleic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|zinc ion binding			ovary(1)	1						CACAGGTAGGTTTTTTGGATA	0.408													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	31816015	31816015	+	IGR	DEL	A	-	-			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:31816015delA								None (None upstream) : ACO1 (568586 downstream)																							CTCTGACATCAAAAAAAAATT	0.383													4	2	---	---	---	---	
VPS13A	23230	broad.mit.edu	37	9	79891299	79891300	+	Intron	INS	-	G	G			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:79891299_79891300insG	uc004akr.2	+						VPS13A_uc004akp.3_Intron|VPS13A_uc004akq.3_Intron|VPS13A_uc004aks.2_Intron	NM_033305	NP_150648	Q96RL7	VP13A_HUMAN	vacuolar protein sorting 13A isoform A						Golgi to endosome transport|protein transport	intracellular	protein binding			pancreas(3)|skin(3)|ovary(2)|large_intestine(1)|central_nervous_system(1)	10						GTTGGTAATGTGGGGGGCACAC	0.312													4	2	---	---	---	---	
TLE1	7088	broad.mit.edu	37	9	84302820	84302820	+	Intron	DEL	G	-	-			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:84302820delG	uc004aly.2	-						TLE1_uc004alz.2_Intron|TLE1_uc011lsr.1_Intron|TLE1_uc004ama.1_Intron|TLE1_uc011lss.1_Intron|TLE1_uc004amb.2_Intron|uc004amc.2_5'Flank|uc004amd.2_5'Flank	NM_005077	NP_005068	Q04724	TLE1_HUMAN	transducin-like enhancer protein 1						negative regulation of Wnt receptor signaling pathway|organ morphogenesis|transcription, DNA-dependent|Wnt receptor signaling pathway		transcription factor binding			ovary(1)|skin(1)	2						GAGAAACAAAGGGGGGGGCGC	0.642													4	2	---	---	---	---	
ECM2	1842	broad.mit.edu	37	9	95262904	95262904	+	Intron	DEL	T	-	-			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:95262904delT	uc004ash.2	-						CENPP_uc004arz.2_Intron|CENPP_uc010mqx.2_Intron|ECM2_uc004asf.3_Intron|ECM2_uc011lty.1_Intron|ECM2_uc004asg.2_Intron|ECM2_uc010mqz.1_Intron	NM_001393	NP_001384	O94769	ECM2_HUMAN	extracellular matrix protein 2 precursor						cell-matrix adhesion		integrin binding			ovary(1)|skin(1)	2						cttagcaccatttttttttcc	0.080													4	2	---	---	---	---	
RAD23B	5887	broad.mit.edu	37	9	110078222	110078222	+	Intron	DEL	A	-	-			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:110078222delA	uc004bde.2	+						RAD23B_uc011lwa.1_Intron|RAD23B_uc011lwb.1_Intron	NM_002874	NP_002865	P54727	RD23B_HUMAN	UV excision repair protein RAD23 homolog B						nucleotide-excision repair, DNA damage recognition|nucleotide-excision repair, DNA damage removal|proteasomal ubiquitin-dependent protein catabolic process|regulation of proteasomal ubiquitin-dependent protein catabolic process	cytoplasm|nucleoplasm|proteasome complex|XPC complex	damaged DNA binding|polyubiquitin binding|single-stranded DNA binding			ovary(1)	1						GTCatagtgtaatgattaggt	0.129								Direct_reversal_of_damage|NER					4	2	---	---	---	---	
HDHD3	81932	broad.mit.edu	37	9	116135769	116135769	+	3'UTR	DEL	G	-	-			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:116135769delG	uc004bhi.1	-	2					HDHD3_uc004bhj.2_3'UTR|HDHD3_uc004bhk.2_3'UTR	NM_031219	NP_112496	Q9BSH5	HDHD3_HUMAN	haloacid dehalogenase-like hydrolase domain								phosphoglycolate phosphatase activity|protein binding				0						AAAGGCCGCAGGGAGAGGGGG	0.562													7	5	---	---	---	---	
SPTAN1	6709	broad.mit.edu	37	9	131347294	131347294	+	Intron	DEL	C	-	-	rs11382658		TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131347294delC	uc004bvl.3	+						SPTAN1_uc011mbg.1_Intron|SPTAN1_uc011mbh.1_Intron|SPTAN1_uc004bvm.3_Intron|SPTAN1_uc004bvn.3_Intron	NM_003127	NP_003118	Q13813	SPTA2_HUMAN	spectrin, alpha, non-erythrocytic 1						actin filament capping|axon guidance|cellular component disassembly involved in apoptosis	cytosol|intracellular membrane-bounded organelle|membrane fraction|microtubule cytoskeleton|spectrin	actin binding|calcium ion binding|calmodulin binding|structural constituent of cytoskeleton			breast(5)|ovary(4)|pancreas(1)	10						gcctgaatttctttttttttt	0.045													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	30180219	30180219	+	IGR	DEL	C	-	-			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:30180219delC								SVIL (154355 upstream) : KIAA1462 (121510 downstream)																							CCCCTGATCACCATATCTGGC	0.448													4	2	---	---	---	---	
PCDH15	65217	broad.mit.edu	37	10	56230163	56230163	+	Intron	DEL	G	-	-	rs144562628	by1000genomes	TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:56230163delG	uc001jju.1	-						PCDH15_uc010qhq.1_Intron|PCDH15_uc010qhr.1_Intron|PCDH15_uc010qhs.1_Intron|PCDH15_uc010qht.1_Intron|PCDH15_uc010qhu.1_Intron|PCDH15_uc001jjv.1_Intron|PCDH15_uc010qhv.1_Intron|PCDH15_uc010qhw.1_Intron|PCDH15_uc010qhx.1_Intron|PCDH15_uc010qhy.1_Intron|PCDH15_uc010qhz.1_Intron|PCDH15_uc010qia.1_Intron|PCDH15_uc010qib.1_Intron|PCDH15_uc001jjw.2_Intron	NM_033056	NP_149045	Q96QU1	PCD15_HUMAN	protocadherin 15 isoform CD1-4 precursor						equilibrioception|homophilic cell adhesion|photoreceptor cell maintenance|sensory perception of sound	extracellular region|extracellular space|integral to membrane|photoreceptor outer segment|plasma membrane|stereocilium|synapse	calcium ion binding			pancreas(5)|ovary(4)|upper_aerodigestive_tract(2)|skin(2)	13		Melanoma(3;0.117)|Lung SC(717;0.238)				ggctgcaggtgggggaggtca	0.000										HNSCC(58;0.16)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	82768370	82768371	+	IGR	DEL	AG	-	-			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:82768370_82768371delAG								SH2D4B (362054 upstream) : NRG3 (866699 downstream)																							agagagagaaagagagagagag	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	91761899	91761904	+	IGR	DEL	GAGAGA	-	-	rs145577326		TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:91761899_91761904delGAGAGA								KIF20B (227199 upstream) : HTR7 (738674 downstream)																							AAAAAagagcgagagagagagagaga	0.316													3	4	---	---	---	---	
CPEB3	22849	broad.mit.edu	37	10	93902982	93902982	+	Intron	DEL	T	-	-			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:93902982delT	uc001khw.1	-						CPEB3_uc001khu.1_Intron|CPEB3_uc001khv.1_Intron|CPEB3_uc010qnn.1_Intron	NM_014912	NP_055727	Q8NE35	CPEB3_HUMAN	cytoplasmic polyadenylation element binding								nucleotide binding|RNA binding				0		Colorectal(252;0.0869)				GTTTTGAGGGTTGTTTTCTAT	0.308													4	2	---	---	---	---	
CRTAC1	55118	broad.mit.edu	37	10	99642362	99642362	+	Intron	DEL	C	-	-	rs684225	by1000genomes	TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:99642362delC	uc001kou.1	-						CRTAC1_uc001kov.2_Intron|CRTAC1_uc001kot.1_Intron	NM_018058	NP_060528	Q9NQ79	CRAC1_HUMAN	cartilage acidic protein 1 precursor							proteinaceous extracellular matrix	calcium ion binding			ovary(4)|pancreas(1)	5		Colorectal(252;0.24)		Epithelial(162;2.18e-10)|all cancers(201;3.27e-09)		TAATATCACTCCCACCCTGGT	0.547													4	2	---	---	---	---	
HPSE2	60495	broad.mit.edu	37	10	100991967	100991968	+	Intron	INS	-	AT	AT			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:100991967_100991968insAT	uc001kpn.1	-						HPSE2_uc009xwc.1_Intron|HPSE2_uc001kpo.1_Intron|HPSE2_uc009xwd.1_Intron	NM_021828	NP_068600	Q8WWQ2	HPSE2_HUMAN	heparanase 2						carbohydrate metabolic process	intracellular|membrane	cation binding|heparanase activity			ovary(1)	1				Epithelial(162;1.8e-09)|all cancers(201;4.72e-07)		CGCGCGCGCGCGcatacacaca	0.342													4	3	---	---	---	---	
TRIM8	81603	broad.mit.edu	37	10	104414727	104414727	+	Intron	DEL	G	-	-			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:104414727delG	uc001kvz.2	+							NM_030912	NP_112174	Q9BZR9	TRIM8_HUMAN	tripartite motif-containing 8							cytoplasm|PML body	ligase activity|protein homodimerization activity|zinc ion binding			ovary(1)	1		Colorectal(252;0.122)		Epithelial(162;3.93e-09)|all cancers(201;1.02e-07)|BRCA - Breast invasive adenocarcinoma(275;0.215)		TTGGGAGCCTGGGGCAGCCTG	0.617													4	2	---	---	---	---	
CNNM2	54805	broad.mit.edu	37	10	104678907	104678909	+	In_Frame_Del	DEL	CCG	-	-			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:104678907_104678909delCCG	uc001kwm.2	+	1	794_796	c.670_672delCCG	c.(670-672)CCGdel	p.P227del	CNNM2_uc001kwn.2_In_Frame_Del_p.P227del|CNNM2_uc001kwl.2_In_Frame_Del_p.P227del	NM_017649	NP_060119	Q9H8M5	CNNM2_HUMAN	cyclin M2 isoform 1	227					ion transport	integral to membrane				ovary(1)|central_nervous_system(1)	2		Colorectal(252;0.103)|all_hematologic(284;0.152)|Breast(234;0.198)		Epithelial(162;7.89e-09)|all cancers(201;1.82e-07)|BRCA - Breast invasive adenocarcinoma(275;0.215)		GGCCGGGCTCCCGCCGCCCCCGT	0.719													4	2	---	---	---	---	
SIPA1	6494	broad.mit.edu	37	11	65406494	65406495	+	Intron	DEL	CA	-	-			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65406494_65406495delCA	uc001ofb.2	+						SIPA1_uc010rom.1_5'Flank|SIPA1_uc001ofd.2_5'Flank	NM_006747	NP_006738	Q96FS4	SIPA1_HUMAN	signal-induced proliferation-associated protein						cell proliferation|cytoskeleton organization|intracellular signal transduction|negative regulation of cell adhesion|negative regulation of cell cycle|negative regulation of cell growth	cytosol|endomembrane system|membrane|perinuclear region of cytoplasm	Rap GTPase activator activity				0						CTACACCCGTCACACACACACA	0.366													5	3	---	---	---	---	
CNTN5	53942	broad.mit.edu	37	11	99145929	99145929	+	Intron	DEL	A	-	-			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:99145929delA	uc001pga.2	+						CNTN5_uc009ywv.1_Intron|CNTN5_uc001pfz.2_Intron|CNTN5_uc001pgb.2_Intron	NM_014361	NP_055176	O94779	CNTN5_HUMAN	contactin 5 isoform long						cell adhesion	anchored to membrane|plasma membrane	protein binding			skin(3)|ovary(2)|pancreas(2)|breast(1)	8		all_hematologic(158;1.22e-05)|Acute lymphoblastic leukemia(157;3.81e-05)|Melanoma(852;0.219)		BRCA - Breast invasive adenocarcinoma(274;0.00146)|KIRC - Kidney renal clear cell carcinoma(183;0.156)|Kidney(183;0.196)		ATTGATATATAAAAAAAAACT	0.299													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	134380688	134380689	+	IGR	INS	-	A	A			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:134380688_134380689insA								B3GAT1 (98876 upstream) : None (None downstream)																							CTGCCTGCCCCTGCTCACCCAG	0.649													4	2	---	---	---	---	
SLCO1A2	6579	broad.mit.edu	37	12	21459632	21459632	+	Intron	DEL	A	-	-			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:21459632delA	uc001rer.2	-						SLCO1A2_uc001res.2_Intron|SLCO1A2_uc010siq.1_Intron|SLCO1A2_uc010sio.1_Intron|SLCO1A2_uc010sip.1_Intron|SLCO1A2_uc001ret.2_Intron|SLCO1A2_uc001reu.2_Intron	NM_021094	NP_066580	P46721	SO1A2_HUMAN	organic anion transporting polypeptide A						bile acid metabolic process|sodium-independent organic anion transport	integral to membrane|plasma membrane	bile acid transmembrane transporter activity|organic anion transmembrane transporter activity			large_intestine(1)|pancreas(1)|ovary(1)|skin(1)	4						CAAATATAAGAAAAATAACAT	0.224													4	2	---	---	---	---	
CRYL1	51084	broad.mit.edu	37	13	20979096	20979096	+	Intron	DEL	G	-	-			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:20979096delG	uc001une.2	-						CRYL1_uc001unf.2_Intron|CRYL1_uc001ung.2_Intron	NM_015974	NP_057058	Q9Y2S2	CRYL1_HUMAN	lambda-crystallin						fatty acid metabolic process	cytosol	3-hydroxyacyl-CoA dehydrogenase activity|L-gulonate 3-dehydrogenase activity|NAD+ binding|protein homodimerization activity				0		all_cancers(29;2.27e-23)|all_epithelial(30;1.69e-19)|all_lung(29;8.29e-18)|Lung SC(185;0.0262)|Ovarian(182;0.0827)|Hepatocellular(188;0.244)		all cancers(112;6.6e-05)|Epithelial(112;0.00178)|OV - Ovarian serous cystadenocarcinoma(117;0.0169)|Lung(94;0.0215)|GBM - Glioblastoma multiforme(144;0.0402)|LUSC - Lung squamous cell carcinoma(192;0.061)		GCTGGCTCCTGGGGGTTCGAA	0.388													4	2	---	---	---	---	
EVL	51466	broad.mit.edu	37	14	100599303	100599303	+	Intron	DEL	C	-	-			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:100599303delC	uc001ygt.2	+						EVL_uc001ygv.2_Intron|EVL_uc001ygu.2_Intron|EVL_uc010avu.2_Intron	NM_016337	NP_057421	Q9UI08	EVL_HUMAN	Enah/Vasp-like						actin polymerization or depolymerization|axon guidance|cell surface receptor linked signaling pathway|organ morphogenesis	cytoskeleton|cytosol|focal adhesion|lamellipodium	actin binding|profilin binding|SH3 domain binding			large_intestine(2)|ovary(1)	3		Melanoma(154;0.152)				CAGCAGCAGGCCTGCCCTCAC	0.682													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20476715	20476715	+	IGR	DEL	T	-	-			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20476715delT								None (None upstream) : GOLGA6L6 (260379 downstream)																							Atttttttgcttttttttttg	0.209													4	5	---	---	---	---	
GOLGA8G	283768	broad.mit.edu	37	15	28771696	28771696	+	Intron	DEL	A	-	-			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:28771696delA	uc001zbu.2	-						GOLGA8G_uc001zbt.3_Intron|GOLGA8G_uc001zbv.2_Intron|GOLGA8F_uc010uah.1_Intron|uc002cdz.2_5'Flank	NM_001012420	NP_001012420			golgi autoantigen, golgin subfamily a, 8G												0		all_lung(180;1.98e-11)|Breast(32;0.000194)|Colorectal(260;0.227)		all cancers(64;4.69e-10)|Epithelial(43;5.34e-09)|BRCA - Breast invasive adenocarcinoma(123;0.0201)|GBM - Glioblastoma multiforme(186;0.0503)|Lung(196;0.171)		TCTGGATTCCaaaaaaaaaaa	0.493													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	30369053	30369053	+	IGR	DEL	T	-	-			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:30369053delT								TJP1 (254347 upstream) : FAM7A3 (26882 downstream)																							ACTAGGATGATTTTTTTTTGT	0.234													4	2	---	---	---	---	
HEXA	3073	broad.mit.edu	37	15	72671505	72671505	+	5'Flank	DEL	T	-	-			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:72671505delT	uc002aun.3	-						CELF6_uc002auk.3_5'Flank|HEXA_uc010ukn.1_5'Flank|HEXA_uc002auo.3_5'Flank|HEXA_uc010bix.2_5'Flank|HEXA_uc010biy.2_5'Flank|HEXA_uc010uko.1_5'Flank|HEXA_uc010biz.1_5'Flank	NM_000520	NP_000511	P06865	HEXA_HUMAN	hexosaminidase A preproprotein						cell death	lysosome	beta-N-acetylhexosaminidase activity|cation binding|protein heterodimerization activity			ovary(3)|upper_aerodigestive_tract(1)	4						ATGGTTTTTCTTTTTTTTCTA	0.269													4	2	---	---	---	---	
FAM108C1	58489	broad.mit.edu	37	15	80992739	80992739	+	Intron	DEL	G	-	-			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:80992739delG	uc002bfu.2	+						FAM108C1_uc002bft.2_Intron	NM_021214	NP_067037	Q6PCB6	F108C_HUMAN	hypothetical protein LOC58489								hydrolase activity				0						ATCCACAGAAGTCGTCTTTGA	0.438													4	2	---	---	---	---	
MAN2A2	4122	broad.mit.edu	37	15	91455121	91455121	+	Intron	DEL	A	-	-			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:91455121delA	uc010bnz.2	+						MAN2A2_uc002bqc.2_Intron|MAN2A2_uc010uql.1_Intron|MAN2A2_uc010uqm.1_Intron|MAN2A2_uc010uqn.1_5'Flank	NM_006122	NP_006113	P49641	MA2A2_HUMAN	mannosidase, alpha, class 2A, member 2						mannose metabolic process|post-translational protein modification|protein N-linked glycosylation via asparagine	Golgi membrane|integral to membrane	alpha-mannosidase activity|carbohydrate binding|mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase activity|zinc ion binding			large_intestine(2)|ovary(1)	3	Lung NSC(78;0.0771)|all_lung(78;0.137)		Lung(145;0.229)			gatgaggaagaaagggcaaat	0.060													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	29308897	29308897	+	Intron	DEL	G	-	-			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:29308897delG	uc010vct.1	-											RecName: Full=Nuclear pore complex-interacting protein-like 2; Flags: Precursor;																		AGAGCATCCAGGGGGCCAGGC	0.602													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33974702	33974703	+	IGR	INS	-	A	A	rs138374783		TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33974702_33974703insA								MIR1826 (9110 upstream) : UBE2MP1 (429099 downstream)																							ggtctatggtgaaaaagaaata	0.000													4	2	---	---	---	---	
ITGAE	3682	broad.mit.edu	37	17	3654762	3654763	+	Intron	INS	-	G	G			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:3654762_3654763insG	uc002fwo.3	-							NM_002208	NP_002199	P38570	ITAE_HUMAN	integrin, alpha E precursor						cell adhesion|integrin-mediated signaling pathway	integrin complex	receptor activity			large_intestine(2)|breast(1)|pancreas(1)	4				UCEC - Uterine corpus endometrioid carcinoma (3;0.0813)		CTGAAGGGGCTGAGGTGAGGCC	0.619													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	12553231	12553231	+	IGR	DEL	G	-	-			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:12553231delG								MAP2K4 (506181 upstream) : MYOCD (15976 downstream)																							AAGGGGCAGAGGGCATGTAAA	0.308													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	25269114	25269114	+	IGR	DEL	A	-	-			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:25269114delA								None (None upstream) : WSB1 (351992 downstream)																							TAGGTCTGTGAAAAAAATGAG	0.264													4	2	---	---	---	---	
C17orf67	339210	broad.mit.edu	37	17	54887268	54887268	+	Intron	DEL	T	-	-			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:54887268delT	uc010dci.2	-						C17orf67_uc002iuq.2_Intron	NM_001085430	NP_001078899	Q0P5P2	CQ067_HUMAN	hypothetical protein LOC339210 precursor							extracellular region					0	Breast(9;2.49e-06)					acacacacccttacacacacc	0.000													4	2	---	---	---	---	
PRR11	55771	broad.mit.edu	37	17	57278797	57278797	+	Intron	DEL	A	-	-			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:57278797delA	uc002ixf.1	+						PRR11_uc002ixg.1_Intron	NM_018304	NP_060774	Q96HE9	PRR11_HUMAN	proline rich 11											ovary(2)	2	Medulloblastoma(34;0.0922)|all_neural(34;0.101)					GGAAACTGGGAAAAGTGGTTT	0.229													4	2	---	---	---	---	
NFATC1	4772	broad.mit.edu	37	18	77249693	77249693	+	Intron	DEL	C	-	-	rs445630	by1000genomes	TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:77249693delC	uc010xfg.1	+						NFATC1_uc002lnd.2_Intron|NFATC1_uc002lne.2_Intron|NFATC1_uc010xfh.1_Intron|NFATC1_uc010xfj.1_Intron|NFATC1_uc002lnf.2_Intron|NFATC1_uc002lng.2_Intron|NFATC1_uc010xfk.1_Intron	NM_006162	NP_006153	O95644	NFAC1_HUMAN	nuclear factor of activated T-cells, cytosolic						intracellular signal transduction|positive regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	cytoplasm|nucleus	FK506 binding|protein binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding			large_intestine(1)|ovary(1)	2		Esophageal squamous(42;0.0157)|Melanoma(33;0.144)		OV - Ovarian serous cystadenocarcinoma(15;3.73e-07)|BRCA - Breast invasive adenocarcinoma(31;0.0257)		gcagaCCACACCCCAGCCCAC	0.358													4	2	---	---	---	---	
RNF126	55658	broad.mit.edu	37	19	662218	662218	+	Intron	DEL	A	-	-			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:662218delA	uc010drs.2	-							NM_194460	NP_919442	Q9BV68	RN126_HUMAN	ring finger protein 126								protein binding|zinc ion binding				0		all_epithelial(18;2.78e-22)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;3.55e-06)|all_lung(49;5.41e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		gaaaccctggaaaaggggcct	0.254													4	2	---	---	---	---	
C20orf132	140699	broad.mit.edu	37	20	35748029	35748030	+	Intron	INS	-	A	A			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:35748029_35748030insA	uc010zvu.1	-						C20orf132_uc002xgk.2_Intron	NM_152503	NP_689716	Q9H579	CT132_HUMAN	hypothetical protein LOC140699 isoform 1												0		Myeloproliferative disorder(115;0.00878)				gagagggacagaaagaaagaga	0.153													16	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	59560485	59560485	+	IGR	DEL	C	-	-			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:59560485delC								MIR646 (676860 upstream) : CDH4 (267074 downstream)																							TGGAATGACTCCCCCACTGAC	0.433													4	2	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11071749	11071750	+	Intron	INS	-	ACTT	ACTT	rs148241564		TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11071749_11071750insACTT	uc002yit.1	-						BAGE_uc002yix.2_Intron	NM_182482	NP_872288			B melanoma antigen family, member 2 precursor												0			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		gctcagtgataacttaaccacc	0.000													4	2	---	---	---	---	
KLHL34	257240	broad.mit.edu	37	X	21674384	21674384	+	Frame_Shift_Del	DEL	T	-	-			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:21674384delT	uc004czz.1	-	1	2065	c.1523delA	c.(1522-1524)AAGfs	p.K508fs		NM_153270	NP_695002	Q8N239	KLH34_HUMAN	kelch-like 34	508	Kelch 4.									ovary(1)	1						GGGTGCCTTCTTGCTCCAAAC	0.632													4	2	---	---	---	---	
POLA1	5422	broad.mit.edu	37	X	24753780	24753780	+	Intron	DEL	T	-	-			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:24753780delT	uc004dbl.2	+							NM_016937	NP_058633	P09884	DPOLA_HUMAN	DNA-directed DNA polymerase alpha 1						cell proliferation|DNA replication checkpoint|DNA replication, synthesis of RNA primer|DNA-dependent DNA replication initiation|double-strand break repair via nonhomologous end joining|interspecies interaction between organisms|lagging strand elongation|leading strand elongation|M/G1 transition of mitotic cell cycle|regulation of transcription involved in G1/S phase of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|cytoplasm|nuclear envelope|nuclear matrix|nucleolus|nucleoplasm	chromatin binding|DNA-directed DNA polymerase activity|metal ion binding|nucleoside binding			ovary(2)|skin(1)	3					Clofarabine(DB00631)|Fludarabine(DB01073)	TGCAAGATAGTTTTTTTTTTT	0.348													4	4	---	---	---	---	
PHF8	23133	broad.mit.edu	37	X	54022352	54022353	+	Intron	INS	-	A	A			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:54022352_54022353insA	uc004dsu.2	-						PHF8_uc004dst.2_Intron|PHF8_uc004dsv.2_Intron|PHF8_uc004dsw.2_Intron|PHF8_uc004dsx.2_Intron|PHF8_uc004dsy.2_Intron	NM_015107	NP_055922	Q9UPP1	PHF8_HUMAN	PHD finger protein 8						brain development|G1/S transition of mitotic cell cycle|negative regulation of chromatin silencing at rDNA|positive regulation of transcription from RNA polymerase I promoter|transcription, DNA-dependent	nucleolus	chromatin binding|histone demethylase activity (H3-K27 specific)|histone demethylase activity (H3-K36 specific)|histone demethylase activity (H3-K9 specific)|histone demethylase activity (H4-K20 specific)|iron ion binding|methylated histone residue binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|zinc ion binding			ovary(3)	3						tatccacatgcaaaaaaaaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	70183287	70183287	+	IGR	DEL	A	-	-			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:70183287delA								SLC7A3 (32328 upstream) : SNX12 (26077 downstream)																							TCTCCTAGCCaaaaaaaaagg	0.214													4	2	---	---	---	---	
CT45A5	441521	broad.mit.edu	37	X	134967138	134967140	+	Intron	DEL	AAA	-	-			TCGA-CJ-4640-01A-02D-1386-10	TCGA-CJ-4640-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:134967138_134967140delAAA	uc011mvu.1	-						CT45A6_uc004ezf.2_Intron	NM_001007551	NP_001007552	Q6NSH3	CT455_HUMAN	cancer/testis antigen family 45, member A5												0						ACAAGAAATTAAAAAAAAAAAAA	0.128													6	3	---	---	---	---	
